diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000011.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000011.fa new file mode 100644 index 0000000000000000000000000000000000000000..fd5cbbef8a8b54fd5216e93380864b2ad719e2ac --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000011.fa @@ -0,0 +1,53 @@ +>GCF_002008305_PROKKA_00609 +-----------------------MLTIATRLDVMNRLGRAMADPTRSRILLNLLEGPGYP +AELAQALGLTRSNVSNHLACLRDCGIVAAEHQGRRTRYAIVDAHLARALSALLEVTLAVD +ASAPCLDPGCPVPGCCDTGQVAS +>GCF_002008305_PROKKA_00616 +-----------------------MMTIASRLDVMNRLGRALADPTRSRIILTLLDHPAYP +AELARDLDLTRPNVSNHLACLRDCGIVVSEPEGRRTRYEIADSHLAQALTALVDATLAVD +EDAPCIDPACSLPGCDAAGEGA- +>GCF_002008305_PROKKA_02074 +----------------------------------------MADPTRSRILMTLLERPAYP +AELARDLGLTRSNVSNHLACLRDCGIAVAVAEGRQTRYEIADAHLARALTALVEVTLAVD +ESAPCIDPACSLPGCDAAGEGA- +>GCF_003691675_PROKKA_00339 +-----------------------MMTIASRLDVMNRLGRALADPTRSRIILTLLDHPAYP +AELARDLDLTRPNVSNHLACLRDCGIVVSEPEGRRTRYEIADSHLAQALTALVDATLAVD +EDAPCIDPACSLPGCDAAGEGA- +>GCF_003691675_PROKKA_00350 +MQMCRYQQREPHTRGQQVLYAQRMLTIASRLDVMNRLGRAMADPTRSRILMTLLEGPSYP +AVLARDLGRV-------------------------------------------------- +----------------------- +>GCF_003691675_PROKKA_00789 +MQMCRYQQREPHTRGQQVLYAQRMLTIASRLDVMNRLGRAMADPTRSRILMTLLEGPSYP +AVLARDLGHV-------------------------------------------------- +----------------------- +>GCF_003691675_PROKKA_01769 +-----------------------MLTIATRLDVMNRLGRAMADPTRSRILLSLLEGPGYP +AELAQALGLSRSNVSNHLACLRDCGIVAVEHQGRRTRYAIVDAHLARALSSLLEVTLAVD +ASAPCLDPGCPVPRCCDTAEVAS +>GCF_003691675_PROKKA_01779 +-----------------------MMTIASRLDVMNRLGRALADPTRSRIILTLLDHPAYP +AELARDLDLTRPNVSNHLACLRDCGIVVSEPEGRRTRYEIADSHLAQALTALVDATLAVD +EDAPCIDPACSLPGCDAAGEGA- +>GCF_005280335_PROKKA_00719 +-----------------------MLTITSRLEVMNRLGRAMADPTRSRIILTLLDHPAYP +AELARDLDLTRPNVSNHLACLRDCGIVVSEPEGRRTRYEIADSHLAQALTALVDATLAVD +EDAPCIDPACSLPGCDAAGEGA- +>GCF_005280335_PROKKA_00727 +-----------------------MLTIASRLDVMNRLGRAMADPTRSRILMTLLEGPSYP +AVLARDLGLTRSNVSNHLTCLRDCGIVVAEPEGRQTRYEIADPHLGAAMTALVEVTLAVD +ENAPCVDATCTVPGCCPSGTVA- +>GCF_005280335_PROKKA_02366 +-----------------------MLTVASRLDVMNRLGRAMADPTRSRILMTLLDGPSYP +AVLSRELELTRSNVSNHLTCLRDCGIVVAEPEGRQTRYEIADPHLAAALTALVDVTLAVD +EHAPCVDSSCTVPGCCGTGAGE- +>GCF_023573625_PROKKA_02002 +----------------------------------------MADPTRSRILMTLLERPAYP +AELARDLGLTRSNVSNHLACLRDCGIAVAVAEGRQTRYEIADAHLARALTALVEVTLAVD +ESAPCLDPACSVPGCCEKGVGA- +>GCF_023573625_PROKKA_02005 +M----------------------STTTLTHVSALSRLGHALSDDTRTRILLALRDGPARP +SALAGELGVSKQVMSNQLACLRGCGLVTTTAEGRNVWYALADPRLGQTLGELLELTLTID +PD------CCSAAGCTCA----- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000018.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000018.fa new file mode 100644 index 0000000000000000000000000000000000000000..2f223aa90f2010c83cb3fd989cd1df330a41d0b1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000018.fa @@ -0,0 +1,73 @@ +>GCF_002008305_PROKKA_01559 +MPRVVTPLPPDQPAVLLAT--D-LARLGLPPDRARRSDLERVGQGFHRQRARPGTGWADL +GLPEPGHGFSPDHLAALLRRRPDAVLSHETAAHLHALPMPTRAWRRRDPATGELEADPPV +HLTVARGTRRVRRAGLMDHRRPLAPEFVTLVHGLRVTTVDRTWLDLCSLTPPWTFEDLVA +AGDHAVRHPWTPAGRTDPATTIAALRSALHASGRFHGRPAAREALDSVRVGADSPPETRL +RLALVAGGLPEPELQAALEPGDPVSPVADLAYRHVRLALQYDGAGHRTREQQARDARRDR +YGQARGWTTLRVTWADGREDFRGVVAVVRRRLGPSAST---------------------- +---- +>GCF_002008305_PROKKA_01658 +M-----PFAPDLPLVPVFTTRDVLER-GLPPSRVRRSDVLRLARGIHRRRDMPLRTWESA +GLPPPHHGVGLDLLTALLRSRPDAVLSHETAAHLHGLPLPPGGATRR----------AAV +EITLHRGTARARIPGVMEHRRPLPAGHVTSVLGLRVTTPERTWLDLCSIGHPWDEASLVS +AGDHLVRHPWSPRGRRPPITTVTALHEAMRPLGRFVGRPRATAALERVRVGADSPQETRL +RLALVEAGLGEPALQHVFDPGRRDAPEADLWFEDCRLVLQYDGEVHRSAEQHARDARRDQ +YYAERGQMTLHVTGRDVGEGYARVIEAVLRRRAQVSNGWD-------------------- +---A +>GCF_002008305_PROKKA_01845 +MPRRPAPLPPALAGR-VFTRREALDRLSLSSDRLRSLDLRQVTHGAHRAVVDVPGSWAAL +GYPRPVAALPPEE-AAVVVALTRGVASHLTAARLHGLVLPWWA-----------EEDMRV +HVSRPHRTGRTGRAGVACHGRTVPAEDRVEVHGVPVTSLERTWVDLCSLLRPDQVADAVV +AGDALVNRPWVDGSRLPPRTTASRLSAALERAGRFKGVRVARAALALIRVGADSPPETRL +RLALLDAGLPEPRLQAQLVSPAGERTDADMVVERSRVALHYDGGHHRTPEQQRRDARRDR +LWQEAGHLSITVMGADLAEDFRTVVAAVVRHDRAARATSTISAPAPAAGLSNVKSGEWAL +SNVG +>GCF_003691675_PROKKA_01269 +MPRVVTPLPPDQPAVLLAT--D-LARLGLPPDRARRSDLERVGQGFHRQRAHPGTGWADL +GLPEPGHGFSPDHLAALLRRRPDAVLSHETAAHLHGLPMPARAWRRRDPATGELDVDPPV +HLTVARGTRRVRRAGLMDHRRPLAPEFVTHVHGLRVTTVDRTWLDLCSLTPPWTFEDLVA +AGDHAVRHPWTPAGRTDPATTIAALRSALHASGRFHGRPAAREALDSVRVGADSPPETRL +RLALVAGGLPEPGLQAALEPEDPFSPVADVAYRHVRLALQYDGAGHRTREQQARDARRDR +YGQARGWTTLRVTWADGREDFRGVVAVVRRRLGHSAST---------------------- +---- +>GCF_003691675_PROKKA_01363 +M-----SFAPDLPLVPVFTTRDVLER-GLPPSRVRRSDVLRLARGIHRRRDMPLRTWESA +GLPPPHHGVGLDLLTALLRSRPDAVLSHETAAHLHGLPLPPGGATRR----------AAV +EITLHRGTARARIPGVMEHRRPLPAGHVTSVLGLRVTTPERTWLDLCSIGHPWDEASLVS +AGDHLVRHPWSPRGRRPPITTVTALHEAMRPLGRFVGRPRATAALERVRVGADSPQETRL +RLALVEAGLGEPTLQHVFDPGRRDAPEADLWFEDCRLVLQYDGEVHRSAEQHARDARRDQ +YYAERGQMTLHVTSRDVGEGYARVIEAVLRRRAQVSNGWD-------------------- +---A +>GCF_005280335_PROKKA_01236 +M----------------------------------------------------------- +------------------------------------------------------------ +----------------RVHRRTVPVEHRSVVHGLTVTSPERTWADLCAVRPRWDEADLVA +AGDHLVRHPWAGGGRLPPRTTVERLAEVLEALAPFHGVGRARAALGRVRVGADSAMETHA +RLALIDAGLGEPLLQHKVAPDDPALAESDLYFADLRVALEYDGEHHLGRQQQARDARRDR +RLLSYGVTPMRITAADHAEGYRSVIAQLQQRRRAHDSPSEETA-----------RGE--- +---S +>GCF_020097155_PROKKA_01147 +M----------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------------LERVRVGADSAVVSLA +RLALVDAGLGEPLLQHRLDPWDPDCPETHMFSPELAVALEYDGGGHLTPAQQARDARRDR +RLPARGVTPLRNTAEDHAEGYRRLIAQLQDRRRGR------------------------- +---- +>GCF_023573625_PROKKA_01486 +MPRVVTPLPPDQPAVLLAT--D-LARLGLPPDRARRSDLERVGQGFHRQRAHPGTGWADL +GLPEPGHGFSPDHLAALLRRRPDAVLSHETAAHLHGLPMPARAWRRRDPATGELDVDPPV +HLTVARGTRRVRRAGLMDHRRPLAPEFVTHVHGLRITTVDRTWLDLCSLTPPWTFEDLVA +AGDHAVRHPWTPAGRTDPATTIAALRWALHASGRFHGRPAAREALDSVRVGADSPPETRL +RLALVAGGLPEPELQAALEPGDPFSPVADLAYRHVRLALQYDGAGHRTREQQARDARRDR +YGQARGWTTLRVTWADGREDFRGVVAVVRRRLSPSAST---------------------- +---- +>GCF_023573625_PROKKA_01588 +M-----SFAPDLPLVPVFTTRDVLER-GLPPSRVRRSDVLRLARGIHRRRDMPLRTWESA +ELPPPHHGVGLDLLTALLRSRPDAVLSHETAAHLHGLPLPPGGATRR----------AAV +EITLHRGTARARIPGVMEHRRPLPAGHVTSVLGLRVTTPERTWLDLCSIGHPWDEASLVS +AGDHLVRHPWSPRGRRPPITTVTALHEAMRPLGRFVGRPRATAALERVRVGADSPQETRL +RLALVEAGLGEPTLQHVFDPGRRDAPEADLWFEDCRLVLQYDGEVHRSAEQHARDARRDQ +YYAERGQMTLHVTSRDVGEGYARVIEAVLRRRAQVSNGWD-------------------- +---A + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000030.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000030.fa new file mode 100644 index 0000000000000000000000000000000000000000..431f89d5e6f52ce910315d8bc381cd7a3404e8be --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000030.fa @@ -0,0 +1,56 @@ +>GCF_002008305_PROKKA_00169 +M-------TVGAG----------------LLLITLDNSILYTALPTLTADLGASGSSTLWIINAYPLVMAGLLLGAGTLG +DRIGHRRMFVVGLWIFGAASLAAALSPNPAFLIGARALLAVGAAAMMPATLALIRLAFNDPRERNIAIAIWGSLSIAGAA +LGPILGGALLERFWWGSVFLINVPVVVIALVATAIIAPHN-DPDPSK--KWDLVSSLYAMVGLVGTVLVIKELAHIPQ-- +----NWVLIAG-ALASAVIGFVLFVRRQGRLE-EPLIEFSIFRNRAFAGGSLAAFFAMFTIAGAQLATTQRFQLVEGFTP +LQAGLLVAASALGALPSGVLGAAILHIVGLRIIISGSLAIAALGLALAVLASANGS-----LPLLVVSFIVTGFGLGGTF +AVASAAIMGNAPPRKAGMAASIEEVSYEMGSLSAVALLGSLLTFVYATVVRLPDGTPA-------AAGESIADALGIADG +DLDVIAAATSAYDTAYLVTMIVLAVMLASGAALTNRLLRAYGRGSEA-MEYAENH +>GCF_003691675_PROKKA_00360 +M-------TVGAG----------------LLLITLDNSILYTALPTLTADLGASGSSTLWIINAYPLVMAGLLLGAGTLG +DRIGHRRMFVVGLWIFGAASLAAAFSPNPAFLIGARALLAVGAAAMMPATLALIRLAFDDPRERNIAIAIWGSLSIAGAA +LGPILGGALLERFWWGSVFLINVPVVAIALVATAIIAPHN-HPDPSK--KWDLVSSLYAMVGLVGTVLVIKELAHIPQ-- +----NWVLIAG-ALASAVIGFVLFVRRQGRLE-EPLIEFSIFRNRAFAGGSLAAFFAMFTIAGAQLATTQRFQLVEGFTP +LQAGLLVAAIALGALPSGVLGAAILHIVGLRIIISGSLAIAALGLALAVLASANGS-----LPLLVVSFIVTGFGLGGTF +AVASAAIMGNAPPRKAGMAASIEEVSYEMGSLSAVALLGSLLTFVYATVVRLPDGTPA-------AAGESIADALGIADG +DLDVIAAATSAYDTAYLVTMIVLAVMLASGAALTNRLLRAYGRGSEA-MEYAENH +>GCF_005280335_PROKKA_00171 +M-------------SALRRWSALAVLVLPVLLISIDMSVLGIAVPALSADLDPTSGQLLWIIDLYSFLLAGLLIFMGSLG +DRIGRRRILLIGAPLFGAASLAAAFASSAEMLIAARALLGVGGATLMPSTLGLIRTIFPDRAERRTAIAVWAMAFSGGAA +LGPVVGGILLERFWWGSVFLMNVPVMAVFLLVAPFLLPESRDPSPG---PFDPLSSVLSIAGIVGLVYALKTAAKSP--- +----DWTALAG--LVVGATALAWFIARQRRLA-HPMIDVALFRNVAFTSAVSVNVISVFAFMGLMFFLPQFLMLVQGMGP +AEAGLWMLPLAAAAVVGTLLAPLLARVVAVRTVILTGLALVIAGFAVGTRLDGAAP-----LVAFVLLSCLFGVGVGLAE +TLTNDVILTAAPPERAGAAAAISETGYEFGGAMGTAVLGTVGMAVYAARVQEAAGLPGLGPADAEAAAQTLAAAHRIGEG +LPDGGARLVEVANGAFTAGMDLVA-GIGIGVAAVTLLLAWRGLRSEARVERPVED +>GCF_005280335_PROKKA_00191 +M-------------------------------VILNETIMSVALPRLMAEFTVTAATAQWLTTGFMLTMAVVIPFTGWLL +NRMSLRAVFILAMGTFTAGTAIAGLAPTFGLLLTGRVVQAVGTAIMMPLLMTTVLNVVPLS-RRGRVMGLISIVISVAPA +SGPAVGGVILEHLSWRWLFFTVLPIAAIALAAGAAWVRNVTEPRPV---RLDVLSGVLSAVGFASLIFGLSSIGEAAAGN +AAMPPWI-----PVAVGVLALALFAVRQLRLKDDALLDLRTLSRPTFTVALAVMLTSMLALFGTIVLLPIYLQEVLGWTT +QQSGLALLPGGMVMALLGYVVGHLYDRVGAPPLIVPGAVLGAAGLWGYTFLSEDSS-----AFMVVGLHVLISTGLSMLF +SPLMTTALSALPRSLYAHGSALVSTLQQVAGAAGTALFITLLTV----------GTAS-------SVAGGLGEVASLMDG +------VHLAFLSGALVFTVNVVAVWFVKRPA-------------------PNPL +>GCF_005280335_PROKKA_02217 +MLSGTSTTSRGTGPAPVRAWLVLCAMSMLQFFIAVDVTVVNIALPSIGADLGVAGHSLTWVVVGYTITGGGLLMLGGRIG +DLLGRRRTLLVGTSVFGAASLLAGLAPSFPVLVAARLLQGAGEAVALPAAMATIVLLFPEGPRRSRALSVWAAVASCGLV +LGFALSGIITAHLGWRWVFLVSVPFILVVIVTALLLVPAD-RPASGGRVRLDLPGSLLLTACPLLFVYAAVEAGEPATG- +----LWV--SGVALLCAVLAAAGFVRVESRSP-NPLVPLTFFADRARLRANLTTMLLSGALSTSFLLFTFYLQDRLGIGP +LGAGLTMLPLAVALIVASVLVPRLLGRWGARACVLVGLGAAAGAMGVVALVAVLGSGATWLLPAML----LIAAGMGFGL +VGLQYIAVSGTTEEDAGIASGVQRASDQLGGAAGVAVYVGL----------------------------GFAPALHADAG +DPFVVAAVLA------VVGLVVGAVVISRSPSTAA--------------GQPQAG +>GCF_005280335_PROKKA_02334 +M-------TVGAG----------------LLLITLDNSILYTALPTLTADLGASGSSTLWIINAYPLVMAGLLLGAGTLG +DRIGHRRMFVVGLWIFGAASLAAAFSPSPAFLIGARALLAVGAAAMMPATLALIRLAFDDPRERNIAIAIWGSLSIAGAA +LGPILGGALLERFWWGSVFLINVPVVVIALVATAVIAPHN-DPDPSK--KWDLVSSLYAMVGLVGTVLVIKELAHIPQ-- +----NWVLIAG-ALASAVIGFVLFVRRQGRLE-EPLIEFSIFRNRAFAGGSLAAFFAMFTIAGAQLATTQRFQLVEGFTP +LQAGLLVAAIALGALPSGVLGAAILHIVGLRIIISGSLAIAALGLALAVLASANGS-----LPLLVVSFIVTGFGLGGTF +AVASAAIMGNAPPRKAGMAASIEEVSYEMGSLSAVALLGSLLTFVYATVVRLPDGTPA-------AAGESIADALGIADG +DLDVIAAATSAYDTAYLVTMIVLAVMLASGAALTNRLLRAYGRGSEA-MEYAENH +>GCF_023573625_PROKKA_02010 +M-------TVGAG----------------LLLITLDNSILYTALPTLTADLGASGSSTLWIINAYPLVMAGLLLGAGTLG +DRIGHRRMFVVGLWIFGAASLAAAFSPNPAFLIGARALLAVGAAAMMPATLALIRLAFDDPRERNIAIAIWGSLSIAGAA +LGPILGGALLERFWWGSVFLINVPVVAIALVATAIIAPHN-HPDPSK--KWDLVSSLYAMVGLVGTVLVIKELAHIPQ-- +----NWVLIAG-ALASAVIGFVLFVRRQGRLE-EPLIEFSIFRNRAFAGGSLAAFFAMFTIAGAQLATTQRFQLVEGFTP +LQAGLLVAATALGALPSGVLGAAILHIVGLRIIISGSLAIAALGLALAVLASANGS-----LPLLVVSFIVTGFGLGGTF +AVASAAIMGNAPPRKAGMAASIEEVSYEMGSLSAVALLGSLLTFVYATVVRLPDGTPA-------AAGESIADALGIADG +DLDVIAAATSAYDTAYLVTMIVLAVMLASGAALTNRLLRAYGRGSEA-MEYAENH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000033.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000033.fa new file mode 100644 index 0000000000000000000000000000000000000000..030e8e1e6637ff679ef00017d8760af4cfe6201e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000033.fa @@ -0,0 +1,56 @@ +>GCF_002008305_PROKKA_00260 +MPDSSPSTPSVRSGAPSRARRSSAWRQAR------SLRWRAFWAAAPLSRVYLAFGSAFLLASTASDIGLFGPGHGAIPV +LD-----GIAIASATSAFLAQWWR----STVGFALLLPGAVATVVGGSEVLFAVVAPVVLGAVAATA---------RSWG +FVVTAAVLALTWGVAQPF--------AVGQSN-ATWFILLLMSMGLGGGLFIRESLARRERDRRRVFEA------EERAR +LAAEA---ERRSLARDLHDVVAHNLTIISMQARTARYL--GAPEAAQGVLDVVGDSAKDALRDLRRMLSILQEDGIVDPS +GEPGAAGGADGATSADPVLSVAQLAEELRSLGMTVETDVR-CDQNAMPISVRSTLHRVLQEATTNVAKHAGEGARVCIEL +RDAGPDVVLEVEN--------TVTER-----SGPPQWNSSGVGLNSMRDRVATFGGTIEAGP-GGWGWRVRAVLPRSV-- +---------------------------------- +>GCF_003691675_PROKKA_02273 +MPDSSPSTPSVRSGAPSRARRSSAWRQAR------SLRWRAFWAAAPLSRVYLAFGSAFLLASTASDLGLIGPGLGAIPV +LD-----GIAIASATSAFLAQWWR----STVGFALLLPGAVATAAGGSEVLFAVVAPVVLGAVAATA---------RSWW +FVVTAAVLALTWGVAQPF--------AVGQSN-ATWFILLLMSMGLGGGLFIRESLARRERDRRRVFEA------EERAR +LAAEA---ERRSLARDLHDVVAHNLTIISMQARTARYL--GAPEAAQGVLDVVGDSAKDALRDLRRMLSILQEDGIVDPS +GEPGAAGGADGATSADPVLSVAQLAEELRSLGMTVETDVR-CDQNAMPISVRSTLHRVLQEATTNVAKHAGEGARVCIEL +RDAGPDVVLEVEN--------TVTER-----SGPPQWNSSGVGLNSMRDRVATFGGTIEAGP-GGWGWRVRAVLPRSV-- +---------------------------------- +>GCF_005280335_PROKKA_00109 +MPESTAVRSRLLSGAPRRARRSSSPDEES---LGPAGRWRAFWAAGPLSRVYLVAGSVLLLVSAASDLGLIGGGAFATAP +LD-----VAVIVSTTAAFLAQWWR----STVGFALLVPAGAATIAGGTEALVTLVTAAMLAAVTVTA---------RSWA +FVVAAATLALAWGVVRPV--------ASGRPS-EAWFVLALMTAALGVGLFIRESVARRERDRRRILEA------EERAR +LAAER---ERRSLARDLHDVVAHNLTIISMQARTAQYL--GTPEAAQSVLAVVGDSAKDALVDLRRMLAILQEDGIVDPA +GEPGAAGGADGATSADLALTAGRMAAELRSLGMSVEQDLR-FDPEAVPMSVRSALHRVLQEATTNAAKHAGTGAEVRIMV +AEQGRDVVLEVEN--------SVAAP-----QRSMRWNSSGVGLQSMRDRVATFGGTLEAGP-GGRGWLVRAAIPRAPEG +A--------------------------------- +>GCF_005280335_PROKKA_00590 +M--------------------------------------------AGVELAYL------------SDFISEMPWRHGVGW +-------VALGAAV-LALPLAWRRRFPVTVMLTISVLYIALASWVG--IELYASQVVLFLGFYSVGAWCPDRRRALWSRT +AVAAAMAVWLGWVTVDGFTDPEVGERGVNAYA-AVAAIQFLVNLAYFSGAWIFGDRAWREAIRRQRLEAAHAEIRAQQAR +IAAQEVSLERLRIARELHDVVAHHVTAMGVQAGAARLTLDRDPEAAAGHLRGIESSAREAVAELKTMVHTLR-DADAAPD +SLPRLADLED------LVAQAVRLGTDARLTRVGPEPRLG--------APAELALYRVAQEGLTNARRHAGPRAAVEVRL +RTEPERVELEVSDDGRARPDAEAGSERSPGGAGGAVPAGTGLGLVGMAERMASVGGTVRCGPKPGGGWLVRASVPTLPEP +GEDAAWDAPDEPAPAPDETVQPETMPDPTTEATR +>GCF_020097155_PROKKA_00077 +M---------------SRARLGSTLRSLLDPVSPPAGGRVRFWDAAPANRVYLVVGSVFSVASTTSDVMIELGRGGGDTR +AD-----IAFMVLACLAFLAQWWR----TTVAYAVVLLLMAASLVGGDAVSVVLVLPFVLGTVVATA---------QSGR +YLLAAGATALAWVVAVSLV-------GSGKVDGVAWLTLLLVVVGLGVGASIRAAKLQRVQDGRRIAEA------ERLAR +EAAER---ERRILARDLHDIVAHNLTIIAMQANAAQYL--GTPEAAQQVVRVVGESARDALTDLRRMLSILQEDGVVEPA +PTPGTPETDDAATVAQLGPGAERLAEELRLAGVDAAVRVE-LGEVGLNLGVRAALYRVMQESVTNVAKHAGPGQACEISI +EARGGEVVLEVVN--------TLPED----GPRSVVGNSSRVGLTSMRDRIEAFGGRLEVGPCGGDRWRVRAAVPR-PEA +---------------------------------- +>GCF_020097155_PROKKA_00524 +M-----------------------------------------------------VGG-LLLVWETADLALGAAGRPGGGL +LDSADALFSLGTGVTLVLALAGAR----ALMGCYTLL--VLSALASGFYALPVVTVGLAMGFAAL-Y---------LSRT +PLVVFSCTLLATTVLTAAL-------RPDHLD-VLPLMLVPALAGTAVGLLLRRESVSLERARRRNLEL------VEARD +RATAD---IRRSLARDLHDVVAQDLAVLAMQTQAIRVA--PDRAAQQRMADAVADVARQAHANLRGLLQVLYAGTDVDAR +RGTGTPDALDTALVTSSAQAARDAAARLRAHGFDVDLQVQEQDGVRAPRHVDATVHRIAHEAVTNVVKHAPAGGACQVLF +TLSPGQVRLRVLS--------ELSPAQHPGRPRDAPQPDGSFGVLNIRERAGLLGGRADVGPREG-RWHVDVRIPFGVPA +---------------------------------- +>GCF_023573625_PROKKA_00258 +MPDSSPSTPSVRSGAPSRARRSSAWRQAR------SLRWRAFWAAAPLSRVYLAFGSAFLLASTASDIGLFGPGHGVIPV +LD-----GIAIASVTSAFLAQWWR----STVGFALLLPGAVATVVGGSEVLFAVVAPVVLGAVAATA---------RSWG +FVVTAAVLALTWGVAQPF--------AVGQSN-ATWFILLLMSMGLGGGLFIRESLARRERDRRRVFEA------EERAR +LAAEA---ERRSLARDLHDVVAHNLTIISMQARTARYL--GAPEAAQGVLDVVGDSAKDALRDLRRMLSILQEDGIVDPS +GEPGAAGGADGATSADPVLSVAQLAEELRSLGMTVETDVR-CDQNAMPISVRSTLHRVLQEATTNVAKHAGEGARVCIEL +RDAGPDVVLEVEN--------TVTER-----SGPPQWNSSGVGLNSMRDRVATFGGTIEAGP-GGWGWRVRAVLPRSV-- +---------------------------------- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000037.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000037.fa new file mode 100644 index 0000000000000000000000000000000000000000..8ad39a0db79d584615b41b7030e14b828c0db28b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000037.fa @@ -0,0 +1,43 @@ +>GCF_002008305_PROKKA_00749 +MAARGET---------------TADRRGGRGTDRRPGTAGA--------VALGGAAGVLC +--GAGVMNAVT-----ALAGAPNFRGTFGAAFGAVDVLV-QALPLFVVNVLGSFLLGLLW +AASRRRGPD--WRPRLVAGLGTGFLGAFTTISSAVAL-VLWPVRLG----AAVSGAGG-- +---VLAAAVAVLL----VLALMAALSTAAAMLGLRAGGA-PGSRV--------VGTDRSE +ED---A +>GCF_003691675_PROKKA_00479 +MAARGEP---------------TADRRGGRGTDRRPGTAGA--------VALGGAAGVLC +--GAGVMNAVT-----ALAGAPNFRGTFGAAFGAVDVLV-QALPLFVVNVLGSFLLGLLW +AASRRRGPD--WRPRLVAGLGTGFLGAFTTISSAVAL-VLWPVRLG----AAVSGAGG-- +---VLTAAASVLL----VLALMAALSTAAAVLGLRAGGA-PGSRV--------VGADRSA +ED---A +>GCF_005280335_PROKKA_02181 +M--------------------------------RAPGVRGA--------VALGGAAGVVA +--GSTAMELVGVGGLLALAGRDG-----GVGLGPVAALAFAALPLAVVNVLGSFLLGLLL +ARSRHAGLD--RRPALVAGLGTGFLGSFTTIATAAAVFLLTPLEAGWSAIAASSGVGG-- +---FLSATAGLLLPPLALLALLAALSTAAAVLGLRLGGA-PARGADAEARVDGVASDGTA +ADGAPA +>GCF_020097155_PROKKA_00685 +MNA---------------------------------ALIVV--------VALGGGAG--- +--AAGRFLLDG-----LINTGREFRLPVGT---------------LTINITGSLLLGIIV +GAATHLGA------VPVAVLGTGVMGGYTTFSTASFE-TVRLARSGRITAAAINGLG--- +---------------------MLVVSVAAATAGILLGGT--------------------- +-----L +>GCF_020097155_PROKKA_00686 +MTTRTDTPMPDDQLPPDPDVDVSDPATTMRPVHLRWRYVGL--------VAVGGAGG--- +--TALRDVISS-----VLPADGGVS-----------------WSIFWINITGALALGVLL +EALAHRGPDAGRRRVLRLLLGTGVLGGFTTYSTLAES-TAALFLDG----HGLAGTG--- +----------YAL----LTVLSGAIATAC---GLVVAG---------------WFRPRTE +E----A +>GCF_020097155_PROKKA_02076 +M------------------------------ADARPAAGGAAARRTLPWVALGGAAGALA +SLGAGALIAQA-----MGPGDPSISGPLGTASATLA-------SVAAVNVLGSFLLGLLR +GASGRPGAR--WDPRLVAALGTGFLGAFTTFGTVAAT-LALPVMMT----AGLAATGDTW +WILLAVVVVGLLI----AVAVLAALSTAAAALGLHLGGRGAGSGS--------AGRPDGA +A----A +>GCF_023573625_PROKKA_00713 +MAARGET---------------TADRRGGRGTDRRPGTAGA--------VALGGAAGVLC +--GAGVMNAVT-----ALAGAPNFRGTFGAAFGAVDVLV-QALPLFVVNVLGSFLLGLLW +AASRCRGPD--WRPRLVAGLGTGFLGAFTTISSAVAL-VLWPVRLG----AAASGAGG-- +---VLAAAVAVLL----VLALMAALSTAAAVLGLRAGGA-PGSRA--------VGTDRSA +ED---A + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000038.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000038.fa new file mode 100644 index 0000000000000000000000000000000000000000..b8b87c1272aab50f2bab82db3eea899bbcdcd1d3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000038.fa @@ -0,0 +1,77 @@ +>GCF_002008305_PROKKA_00836 +M------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-----------------------------------------------------------------GWEHEDPRFDARATG +FANEPHRFGYIVEIDP---------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +--- +>GCF_002008305_PROKKA_00837 +M------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-----------------------------GRFKHEGANVIVADDGHVVAYMGDDERFDYLYKFVSKDIYRKNDRRHNMTL +LNEGDLYVARFSGTSDG-EIDGSGRVPADGTFDGSGRWIPLVQGGRSTVEGMAVDQVLVFTRLAADRVGATKMDRCEDVE +PSPGSGKIYVACTNNSQRGVDGQATADEANPRTENRDGHIVEITEHRGDHTSTRFTWDLLMLCGDPSQGDATYFGGFPVD +QVSPISCPDNLAFDTDGNLWISTDGAPDGIGYNDGLFKVAVEGRNRGQVAQFLSVPRDAETCGPVIHDDEAMVFVAVQHP +GEEGSYTDIRSAFPDYV-PSEARPGDGEVRGPRPSIVQVYRT-------------------------------------- +--- +>GCF_002008305_PROKKA_01778 +MLKRLLPMAGHTRGNRSAVTCELKCGNACAHPVPNTSANPTFQQIAETAISRRSALVGGTGLAAAVVIGSQVAQAPEALA +DNGRRPTGGGKLPFEPIAPVTRTVDTMTVPEGYDWGTVIRWGDPLFADSPEFDIEHQTGASQAAQFGYNNDYLNIITDGG +NDRSGYLVSNHEYTNENIMFSPEYIASNFEDVVNVGLQAHGLSIVELKCAKRGAQWEYVRGGRRNRRITGTTEFEVRGPA +AGHALLTTVEDPTGTRVLGTLNNCAGGTTPWGTVLSGEENFNQYFKGRGTAEEKRYGISTSATRRGWEKVHDRFDLTKPG +YENEANRFGWVVEIDPEDPTSTPVKHTLLGRFKHEAGTAVISPSGHAVVYSGDDERHDYLYKFVSAEKVREGDKKHNMRL +MDKGTLYVAKFSGDSPAAQIDGRGTLPSDGAFDGSGEWIALADEKTSFVPGMSLAEVLVYTRLAADKMGATKMDRPEDVE +TNPVTGKVYAALTNNTKR-----TAVDEANPVIGNRDGHVIEITERGGDHTSTTFTWVILLLAGDPAVSSSAYFAGYPKE +KVSPISCPDNLAFDSEGNLWISTDGQPGTIGYADALHKVTLDGAERGRVQQFLAVPRDAETCGPVIHDRDNSVFVNVQHP +GEDGTWGAHTSYFPDFLSPTGPVQVGDKVAAPRPSVVQVFNATGNNGVGKGAGKEKGNKGKGNGN----GNGKGNGNGKG +PKG +>GCF_003691675_PROKKA_01485 +MLKRLLPMAGHTRGNRSAVTCELKCGNACAHPVPNTSANPTFQQIAETAISRRSALVGGTGLAAAVVIGSQVAQAPEALA +DNGRRPTGGGKLPFEPIAPVSRTVDTMTVPEGYDWGTVIRWGDPLFADSPEFDIEHQTGASQAAQFGYNNDYLNIITDGG +NDRSGYLVSNHEYTNENIMFSPEYIASNFEDVVNVGLQAHGLSIVDLKRAKRGAPWEYVRGGRRNRRITGTTEFEVRGPA +AGHALLKTVEDPTGTRVLGTLNNCAGGTTPWGTVLSGEENFNQYFKGRGTAEEKRYGISAAATSRGWEKVHDRFDLTKPG +YENEANRFGWVVEIDPEDPTSTPVKHTLLGRFKHEAGTAVISPSGHAVVYSGDDERHDYLYKFVSAEKVREGDKKHNMRL +MDKGTLYVAKFSGDSPAAQIDGRGTLPSDGAFDGSGEWIALADEKTSFVPGMSLAEVLVYTRLAADKMGATKMDRPEDVE +TNPVTGKVYAALTNNTKR-----TAVDEANPVIGNRDGHVIEITERGGDHTSTTFTWVILLLAGDPAVSSSAYFAGYPKE +KVSPISCPDNLAFDSEGNLWISTDGQPGTIGYADALHKVTLDGAERGRVQQFLAVPRDAETCGPVIHDRDNSVFVNVQHP +GEDGTWGAHTSSFPDFLSPTGPVQVGDKVAAPRPCVVQVFNATGNNGIGKGAGKEKGNKGKGNGNGNGKGNGKGNGNGKG +PKG +>GCF_005280335_PROKKA_01099 +MLKRLLPMAGHTRGNRSAVTCALKCGNACSHPMPNTSANTTFQEIAETAISRRAALGVGGGLAAAVVIGAQVAQAPEALA +DNGAAPRGGGKLDYRAIAPVPRTVDTVTVPEGYDWGTVIRWGDPLFADSEEFDILHQTGASQAGQFGYNNDYLNIISDGG +NDRSGYLVSNHEYTNEYIMFPPAYIASNFTDVVDAAIEAHGLSIVDLKRAKQGAKWEYVRGGRRNRRITGTTPFTVTGPA +AGHALLKTVEDPTGTRVLGTLNNCAGGTTPWGTVLSGEENFNQYFKGRGTAEEKRYGIGTGTTERRWEEVHDRFDLTAPG +YENEANRFGWIVEIDPEDPASTPVKRTLLGRFKHEAGTAVVAPSGQAVVYSGDDERHDYLYKFVSAEKVVEGDKKHNMTL +LDEGTLYVARFTGDSPASEIDGRGTLPSDGEFDGSGEWIALTTDKKSFVPGMSVAEVLVYTRLAADKMGATKMDRPEDVE +TNPVNGKVYMALTNNTRR-----TAVDEANPVVGNRDGHVIELTERGGDHASTRFDWVILLLAGDPAVSSSVYFSGFPQE +KVSPISCPDNVAFDSAGNLWISTDGQPGAIGFGDALHKVTLDGPERGRVEQFLSVPRDAETCGPVVHDRDNSVFVNVQHP +GENGMWGAQTSYFPDYLDPAGPVQVGDKVAAPRPSVVQVFDVTGNNGVGKGSGKDKGGKGKGNKG----------GKGKG +PKA +>GCF_020097155_PROKKA_01023 +MLKRLLPMAGHTRGNRSAVTCELKCGNACSHPIPNTSANETFHSVAERAISRRAALGVGGGLAAAVVIGANVAHAPEALA +DNGLRPAGGGKLDFTAIQPVQRTVDTMTVPEGYDWGTIIRWGDPLFADSEEFDIEHQTGASAAGQFGYNNDYLNIISDGG +NHRRGYLVSNHEYTNENIMFSPEYIASNPEDVVNAGIESHGLSVVELERRKAGAKWEYVRGGRRNRRITGTTPFRVTGPA +AGHDLLKTVEDPTGTRVLGTLNNCSGGTTPWGTVLSGEENFNQYFKGRGTAEEKRYGISTSATQRGWERFHDRFDLTKAG +YENEAHRFGWVVEIDPEDPTSTPVKHTLLGRFKHEAGTAIISESGHAVVYSGDDERHDYLYKFVSSKKVIEGNKKHNMTL +MDEGTLYVAKFTGDSPASEIDGKGTLPSDGAFDGSGEWIALASHKKSYVPGMSLAEVLVFTRIAADKMGATKMDRPEDVE +TNPVNGKVYAALTNNTKR-----TAVDETNPVIGNRDGHVLEITEKCGDHTSTSFNWVILLLAGDPKVSSSAYFAGYPKE +LVSPISCPDNVAFDSEGNLWISTDGQPGTIGYADALHKVTLDGPERGRVQQFLAVPRDAETCGPVIHDRDNSVFVNVQHP +GEDGNWGAHTSYFPDFLSPNGPVQVGDKVAAPRPSVVQVFNATGNNGIGKGSGNKKGNHGKGRGN-----SAFGHAQGHG +PKK +>GCF_023573625_PROKKA_01707 +MLKRLLPMAGHTRGNRSAVTCELKCGNACAHPVPNTSANPTFQQIAETAISRRSALVGGTGLAAAVVIGSQVAQAPEALA +DNGRRPTGGGKLPFEPIAPVTRTVDTMTVPEGYDWGTVIRWGDPLFADSPEFDIEHQTGASQAAQFGYNNDYLNIITDGG +NDRSGYLVSNHEYTNENIMFSPEYIASNFEDVVNVGLQAHGLSIVELKRAKRGAPWEYVRGGRRNRRITGTTEFEVRGPA +AGHALLTTVEDPTGTRVLGTLNNCAGGTTPWGTVLSGEENFNQYFKGRGTAEEKRYGISTSATRRGWEKVHDRFDLTKPG +YENEANRFGWVVEIDPEDPTSTPVKHTLLGRFKHEAGTAVISPSGHAVVYSGDDERHDYLYKFVSAEKVRDGDKKHNMRL +MDKGTLYVARFSGDSPAAQIDGKGTLPSDGAFDGSGEWIALADEKTSFVPGMSLAEVLVYTRLAADKMGATKMDRPEDVE +TNPVTGKVYAALTNNTKR-----TAVDEANPVIGNRDGHVIEITERGGDHTSTTFTWVILLLAGDPAVSSSAYFAGYPKE +KVSPISCPDNLAFDSEGNLWISTDGQPGTIGYADALHKVTLDGAERGRVQQFLAVPRDAETCGPVIHDRDNSVFVNVQHP +GEDGTWGAHTSYFPDFLSPTGPVQVGDKVAAPRPCVVQVFNATGNNGIGKGAGKEKGNKGKGNGNGNGKGNGKGNGNGKG +PKG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000041.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000041.fa new file mode 100644 index 0000000000000000000000000000000000000000..50b5c13ef8c6b430667ada65bd8611e9e2b125b9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000041.fa @@ -0,0 +1,57 @@ +>GCF_002008305_PROKKA_01181 +MSSFETPQPPTARRRRRLLPLLSLGAAGLMLA---TACATGD--DGADQPHSDTASAST- +-SAAPERAAVGEGQGEPDALTGVTFTEGDGGAPTVEIDGEIDTDQPTTRVLTAGEGEQVQ +EGDVLKMSIAVVDPASGEVVAENFSGEP-EAVPVDDQLKSMNPEIHEMLVGSGAGTIVAA +YSPEYDVSVPQTESASPSASPSTQTQPAQLFVYKIDAILPKQAEGEEVTERDERLPDVTV +DEQSGRPSIAKPDGEAPQELVVQPLIEGEGHEVGADDTVTVQYEGVTWSDGEVFDSSWET +GQAITFSLNRVIEGWKEGLAGQKVGSRVLLSIPAEKAYGEQGSPP-DIGENEP-----LL +FVVDILDAQASA--TP----------------SAN +>GCF_003691675_PROKKA_00900 +MSSFETPQPPTARRRRRLLPLLSLGAAGLMLA---TACATGD--DGADQPHSDTASAST- +-SAAPERAAVGEGQGEPDALTGVTFTEGDGGAPTVEIDGEIDTDQPTTRVLTAGEGEQVQ +EGDVLKMSIAVVDPASGEVVAENFSGEP-EAVPVDDQLKSMNPEIHEMLVGSGAGTIVAA +YSPEYDVPVPQTESASPSASPSTQTQPAQLFVYKIDAILPKQAEGEEVTERDERLPDVTV +DEQSGRPSIAKPDGEAPQELVVQSLIEGEGREVGADDTVTVQYEGVTWSDGEVFDSSWET +GQAITFSLNQVIEGWKEGLAGQKVGSRVLLSIPAEKAYGEQGSPP-AIGENEP-----LL +FVVDILDAQAPA--TE----------------SAN +>GCF_005280335_PROKKA_01707 +MT---------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---DGTPEIGDAEGEAPSEMVVQPLIRGEGPEVGPDDSVTVNYVGETWSEGTRFDSSWER +GAPISFSLNQVIPGWKEGLAGQPVGSRVLLSIPAEKAYGEQGSPP-DIGPNEP-----LL +FVVDILDAQAPS--TP----------------PTN +>GCF_005280335_PROKKA_01708 +MSSFQTPETTTPRRRRRLLPLVSLGVAGLFLA---TACASGQ--DDTPEPQEDAASASQ- +-SAAPERAAVGEGQGEPDALEGLSFSEGEDGAPSVEVDGELATDQPTTRVLTAGEGDQVK +EGDVLKMSIAVVDPASGDVLAENFTGDP-ESVPVDQQLKSMNPEMHDLLVRNGVGSVVAA +YSPEREVPAPPADGASPSASPPPRPSPPSSSCTRSSRSCPRRP-------RARRSPSAT- +---SGCPR---------------------------------------------------- +------------------------------------------------------------ +--------------SP------------------- +>GCF_020097155_PROKKA_00314 +M-----------------RPLLPLALTVLMLSAGLTGCA---------------PSSPL- +-DSVQVEEVTGQAQGR-----------------SVKFQTPVAVEEVSIRQLRAGTGAELD +AGDAIVLKMDLFKGSDGTPIEAPFAGGPGQVIALDDQFKAQVPELHEALLQAQEGTMLAY +SS-------PQTAGAAGDESTAVE-------IYEVAQKIPTTIEGKTSPVPDG-LPPITE +DE-TGAPVVGPPQGQVPDELVAEYLIQGGGEPVQAGDTVIVHHLGMRWADAQVFDSSYQR +GAPARFVLDNVIKGWQKGLIGKRTGSRVVLSVPVDQAYGTEA----ELGDNAPFPAGDLL +FVIDILTTQP----TPPV--------------PTP +>GCF_020097155_PROKKA_01606 +MN--RAPSSAAAPRRRRPRTALSLSLAGLLLA---TACGAGESSDGSSSPASASSSAAAQ +GSEATSSSAAPVEYGDPAALDGLTFTVGADGTPSATVGKAIESDKAVVKTLTKGTGATPK +AGDVLRLSTALLDPATGKVLNENFTTQP-EMVAVGSDPASMNPYVHKAVYGAPVGSDVAV +Y-----LPAPSSSASAPSG---TEAAPAQLAVFRV------QGVAEQLPQADERLPKVSV +DPATGRPSIEKPTGSAPEELVVEPLIQGEGPEVEDTDTVAVQYQGVTWSDGSTFDSSYER +GTPATFSLDQVIAGWKEGLAGQKVGSRVLISVPSEKAYGAEGTPDGSIGKDED-----LL +FVVDILAAQPAAASSPAAPSGSTAPSGSSSASPSN +>GCF_023573625_PROKKA_01131 +MSSFETPQPPTARRRRRLLPLLSLGAAGLMLA---TACATGD--DGADQPHSDTASAST- +-SAAPERAAVGEGQGEPDALTGVTFTEGDGGAPTVEIDGEIDTDQPTTRVLTAGEGEQVQ +EGDVLKMSIAVVDPASGEVVAENFSGEP-EAVPVDDQLKSMNPEIHEMLVGNGAGTIVAA +YSPEYDVSVPQTESASPSASPSTQTQPAQLFVYKIDAILPKQAEGEEVTERDERLPDVTV +DEESGRPSIAKPDGEAPQELVVQPLIEGEGREVGADDTVTVQYEGVTWSDGEVFDSSWET +GQAITFSLNQVIEGWKEGLAGQKVGSRVLLSIPAEKAYGEQGSPP-DIGENEP-----LL +FVVDILDAQASA--TP----------------SAN + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000054.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000054.fa new file mode 100644 index 0000000000000000000000000000000000000000..40939862c3888bcc8e9172abff66092183c7a807 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000054.fa @@ -0,0 +1,56 @@ +>GCF_002008305_PROKKA_02253 +M-TLTLSARLERTAAEHPHSTALILGENRMTYAELQDQSQRLAGLMRQEGIGPGDRVALMVPNIPAFPVVFFAALQLGAV +VVPMNPLFKRREIECYLEDSGASMLWSVPSEEAVEGARERGVPLRTLGEDGLAPHLAESPGPVTETVERDLEDDAVILYT +SGTTGRPKGAQLTHRNMGTNADTVAETLIQLQHGETVLGCLPLFHVFGLTCALMAPVTIGASLALIPRFDPAVAAQTVRE +HAVDVFIGVPTMYGAVLAAAKDHPEDLASLRLGVSGGSAMPVELLRRFEATFDCEILEGYGLSETSPVACFNHPGEEHHP +GSIGRAVRGCEMQLVTPDGAVVPEGDEETLGEVWIRGENVMKGYWGKPEATAQAITEDGWFRSGDLARRDAAGNYYIVDR +TKDMILRGGLNVYPREIEEVLYEHPAVAEAAVVGVPHPELGQEVAAHVVLAPGAHATEEELIQHVKSQVAPYKYPRTVTV +RDGLPKTATGKILKRELTPAE +>GCF_002008305_PROKKA_02275 +M------------------------------------------GWRFLRG------------------------------ +--PLN--------------------------------------------------------------------------- +--------------------------------------------------------------------LDP--------- +-------------------------------------------------------------------------------- +---------------------------------------------------------------GD------------VEN +LDEVRLRGGMNVYPQEIEEVLYEHPALAEAAVVGVPHPELGEEVAAYVTLAPGATATEEELVAHVKSQVAPYKYPRSVVA +MDGLPKTATGKILKRELKAAR +>GCF_003691675_PROKKA_01952 +M-TLTLPARLERTAAEHPNSTALILGENRMTYAELHDQSQRLAGLMRQEGIGPGDRVALMVPNIPAFPVVFFAALQLGAV +VVPMNPLFKRREIEYYLEDSGASMLWSVPSEEAVEGARERGVPLRTLGEDGLAPHLAESPGPVTETVERDLEDDAVILYT +SGTTGRPKGAQLTHRNMGTNADTVAETLIQLQHGETVLGCLPLFHVFGLTCALMAPVTMGASLALIPRFDPAVAAQTVRE +HAVDVFIGVPTMYGAVLAAAKDHPEDLASLRLGVSGGSAMPVELLRRFEATFDCEILEGYGLSETSPVACFNHPGEEHHP +GSIGRAVRGCEMQLVTPDGAVVPEGDEETLGEVWIRGENVMKGYWGKPEATAQAITEDGWFRSGDLARRDAAGNYYIVDR +TKDMILRGGLNVYPREIEEVLYEHPAVAEAAVVGVPHPELGQEVAAHVVLAPGAHATEEELIQHVKSQVAPYKYPRTVTV +RDGLPKTATGKILKRELTPAE +>GCF_005280335_PROKKA_00488 +M-TLTLPARLERTAAEHPNSTALILGENRMTYAELQDQSQRLAGLMRQEGIGPGDRVALMVPNIPAFPVVFFAALQLGAV +VVPMNPLFKRRQIEYYPEDSGASMLWSVPSEDAVEGARERGVPLRTLGEDGLAPHLAESPGPVTETVERDLEDDAVILYT +SGTTGRPKGAQLTHRNMGTNADTAAETLIQLQHGETVLGCLPLFHVFGLTCALMAPVTTGASLALIPRFDPAVAAQTVRG +CAVDVFIGVPTMYGAVLAAAKDHPEDLASLRLGVSGGSAMPVELLRRFEATFHCEILEGYGLSETSPVACFNHPGEEHQP +GSIGRAVRGCELQLVTPDGAVVPEGDEETLGEVWIRGENVMKGYWGKPEATAQAITEDGWFRSGDLARRDAAGNYSIVDR +TKDMILRGGLNVYPREIEEVLYEHPAVAEAAVVGVPHPELGQEVAAHVVLAPGAHATEEELIQHVKSQVAPYKYPRTVSV +RDGLPKTATGKILKRELTPAE +>GCF_005280335_PROKKA_00493 +MPDVVVPILLERTAAAEPDRTALILGEERLTYAELQDQVHRIAGLLRSQGLGPGDRMAIMLPNVLAFPVLFFGALQVGAV +VVPMNPLFKTREIQYYLEDSGAVMLWGVPSEEAEAATQAVGVPFHALGADGLAPHLTASPGPVTEAAERDPQDDAVILYT +SGTTGRPKGAQLTHRNLTSNANTVVETLIHLKAGETILGCLPLFHVFGLTCSMLTCVSVGATLSLIPRFDPTQAIETIRR +DAVDVFIGVPTMYGAILTVGAEDPSALASLRVAVSGGSSMPVEVLRRFESTFGCQILEGYGLSETSPAACFNHPDTDRQP +GSIGTPIRGVELRLVTPGGEEVPEGDAETIGEVCIRGENIMKGYWGRPDATAEAIDDDGWFHSGDLGRRDAAGNYYIVDR +TKDMILRGGLNVYPREIEEVLYEHPAVAEAAVVGVPHPELGEDVAAYVVLAPGAEATEAELIAHVKDRVAPYKYPRTVHL +MDGLPKTATGKILKRELGTAG +>GCF_020097155_PROKKA_00434 +M-TLTLPARLERTAAEHPNSTALILGENRMTYAELQDQSQRLAGLMRQEGIGPGDRVALMVPNIPAFPVVFFAALQLGAV +VVPMNPLFKRREIEYYLEDSGASMLWSVPSEEAVEGARERGVPLRTLGEDGLAPHLAESPGPVTETVERDLEDDAVILYT +SGTTGRPKGAQLTHRNMGTNADTAAETLIQLQHGETVLGCLPLFHVFGLTCALMAPVTTGASLALIPRFDPAVAAQTVRE +CAVDVFIGVPTMYGAVLAAAKDHPEDLASLRLGVSGGSALPVELLRRFEATFDCEILEGYGLSETSPVACFNHPGEEHQP +GSIGRAVRGCEMQLVTPDGAVVPEDDEETLGEVWIRGENVMKGYWGKPEATAQAITEDGWFRSGDIARRDAAGNYYIVDR +TKDMILRGGLNVYPREIEEVLYEHPAVAEAAVVGVPHPELGQEVAAHVVLAPGAHATEEELIQHVKSQVAPYKYPRTVRV +RDGLPKTATGKILKRELTPAE +>GCF_023573625_PROKKA_02184 +M-TLTLPARLERTAAEHPNSTALILGENRMTYAELQDQSQRLAGLMRQEGIGPGDRVALMVPNIPAFPVVFFAALQLGAV +VVPMNPLFKRREIEYYLEDSGASMLWSVPSEEAVEGAREHGVPLRTLGEDGLAPHLAASPGPVTETVERDLEDDAVILYT +SGTTGRPKGAQLTHRNMGTNADTAAETLIQLQHGETVLGCLPLFHVFGLTCALMAPVTTGASLALIPRFDPAVAAQTVRE +CAVDVFIGVPTMYGAVLAAAKDHPEDLASLRLGVSGGSALPVELLRRFEATFDCEILEGYGLSETSPVACFNHPGEEHQP +GSIGRAVRGCEMQLVTPDGAVVPEGDEETLGEVWIRGENVMKGYWGKPEATAQAITEDGWFRSGDLARRDAAGNYYIVDR +TKDMILRGGLNVYPREIEEVLYEHPAVAEAAVVGVPHPELGQEVAAHVVLAPGAHATEEELIQHVKSQVAPYKYPRTVTV +RDGLPKTATGKILKRELTPAE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000059.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000059.fa new file mode 100644 index 0000000000000000000000000000000000000000..bc4194cb1fa6b0ead60c0f5808a46687bd2005c9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000059.fa @@ -0,0 +1,43 @@ +>GCF_002008305_PROKKA_00053 +MRADLTLIPTSRVPGCGSGHPTARPRYGDPVRPTSPRPAPAYLTDSVPARRGHPLGFAHR +GAAVDRENSLAAFVDAHAAGFTYLELDVRTTADGELLVFHDDTLDRVSTGRGRLRDHTWE +RLADVTVGGEPLLRFTELLTALPEARLNVDLKDRASAPALARILAEHGAWDRVLVASFHD +SRRRLFRRALARLGHPERAYGPERVATSGGAAAIAALVTLGPLGLTRWLRRCALDVDCVQ +VPVRHGRVPVATADFVRRCHAAGLPVHVWVVDEPAEIERLLDLGVDGVMTDRADVLAEVY +ARRGFWPQR +>GCF_003691675_PROKKA_02066 +------------------------------MRPTSPRPAPAYLTDSVPARRGHPLGFAHR +GAAVDRENSLAAFADAHAAGFTYLELDVRTTADGELVVFHDETLDRVSTGRGRLRDHTWE +RLADVTVGGEPLLRFTELLTALPEARLNVDLKDRASAPALARILAEHGAWDRVLVASFHD +SRRRLFRRALARLGHPERAYGPERVATSGGAAAIAALVTLGPLGLTRWLRRCALDVDCVQ +VPVRHGRVPVATADFVRRCHAAGLPVHVWVVDEPAEIERLLDLGVDGVMTDRADVLAEVY +DRRGFWPQR +>GCF_005280335_PROKKA_00346 +MT---------R----------RPPSS-------RHRPAPAYLADSAPGREGWPLGFAHR +GADVGRENSLAAFQAAHDAGFAYLELDVRTTSDGELVVFHDETLERVTTGRGRLQEHTWH +GLTEVHVGGEPLLRFADLLAALPEARLNVDLKDRAAAPAMARLLAEHEAWERVLVASFHD +SRRRAFRRALAALGHEDRAFGPGRVATSGGVAAIAALVALGPVGLTRWLARHALDIDCVQ +VPVRHGRVRVVTADFVRRCHAAGLPVHVWVIDEPDEMHRLLDLGVDGIMTDRADVLADVF +TTRGIWPQR +>GCF_020097155_PROKKA_00284 +ME---------DSSGSLAASSIRPPSSGPSSTPPPARPAPAYLADSAPGREGWPLGFAHR +GADVGRENSLAAFQAAHDAGFAYLELDVRTTSDGELVVFHDETLERVTTGRGRLQEHTWH +GLTEVHVGGEPLLRFADLLAALPEARLNVDLKDRAAAPAMARLLAEHEAWERVLVASFHD +SRRRAFRRAPAALGHEDRAFGPGRVATPGGAAAIAALVALGPVGLTRWLARHALDVDCVQ +VPVRHGRVRVVTADFVRRCHAAGLPVHVWVIDEPDEMHRLLALGVDGIMTDRADVLADVF +TTRGIWPQH +>GCF_020097155_PROKKA_00293 +MRI--------RA----------------ATTSPALRPAPAYLAASAPARRGWAVGFAHR +GAGNERENTLAAFTAAWEAGFRYLELDVRTTSDGVLVVFHDATLDRVSTAAGDFSALAWA +DFAAHTVGGEPFLRFADLLAALPEARFNVDLKDADAAPAMAALLAEHDAWDRVLVASFHD +SRRRAFRRAVAALGHPERAHGPERVATSGGAAAIAALVLLGPLGLTGWLRRHALDIDCVQ +VPLHQGRVPVVTADFVRRCHAAGLPVHVWVVDDPAEMERLLDLGVDGIMTDRADVLAEVF +TRRGIWPQR +>GCF_023573625_PROKKA_00048 +MRADLTLIPTSRVPGCGSGHSAVRPRYGDPVRPTSPRPAPAYLTDSVPARRGHPLGFAHR +GAAVDRENSLAAFVDAHAAGFTYLELDVRTTADGELVVFHDETLDRVSTGRGRLRDHTWE +RLADVTVGGEPLLRFTELLTALPEARLNVDLKDRASAPALARILAEHGAWDRVLVASFHD +SQRRLFRRALARLGHPERAYGPERVATSGGAAAIAALVTLGPLGLTRWLRRYALDVDCVQ +VPVRHGRVPVATADFVRRCHAAGLPVHVWVVDEPAEIERLLDLGVDGIMTDRADVLAEVY +ARRGLWPQR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000064.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000064.fa new file mode 100644 index 0000000000000000000000000000000000000000..363ac43be2984db1c1094e74872dcbff8b9efbd9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000064.fa @@ -0,0 +1,54 @@ +>GCF_002008305_PROKKA_00119 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +----------------------------------------------------------------------------MLLK +LIEPTSGEISFEGRDVLALKGEGLKDFRQRVQAVFQDPFSSLNPSFTVGRIIEEPL---------QTYRRGNATQRRARV +LELMDQVALPSHFHRRYPAELSGGQRQRVAIARALALNPELIVCDEPVSALDVLVQDQILTLLRRLQDELGLRSYLFISH +DLAVVRLISDYVCVMKDGRVVEAASSEEVFTNPRHPYTRRLLASIPGNELGIAVEADGTHV----------------- +>GCF_003691675_PROKKA_02135 +MD-PKHDDGAPG-------PGAAPA-------------VPAAGA--PLLEIRDLDVEFT-TQQGTVQAVEGASLTLPAGG +TLAIVGESGSGKSTTAMAAIGLLPGNGRVTAGSVRFAGEELVGLPESRMRRIRGRRIGLVPQDPMSNLNPVTRVGQQIGE +TLLTHGMATKKDVGAAVVEVMERAGIPEPARRAKQYPHELSGGLRQRVLIAIGLACRPQLLIADEPTSALDVTVQQVILD +QIGEMTRELGSSVLLITHDLGLAAERAQQLVVMHRGRVVESGDARAILEDPQHAYTRSLVAAAPS--VAAARLLPEAFDP +APVALAEDDTAALTTVALAKQDLTPLVEIRDLTKVYP-VRGHEDFIAVKDVSLKIPRGKTVSIVGESGSGKTTTARMLLK +LIEPTSGEITFEGRDVLALKGEGLKDFRQRVQAVFQDPFSSLNPSFTVGRIIEEPL---------QTYRRGNATQRRARV +LELMDQVALPSHFHRRYPAELSGGQRQRVAIARALALNPELIVCDEPVSALDVLVQDQILTLLRRLQDELGL-SYLFISH +DLAVVRLISDYVCVMKDGEVVEAASSEEVFTNPRHPYTRRLLASIPGNELGIAVEADGTHV----------------- +>GCF_005280335_PROKKA_00088 +M-----------------------TA-ALTTRENTAPAAEPAGARIPVAELRNLRVGFDDGAGGTRAVVHGVDLRIEPGQ +CVAIVGESGSGKSVTARTLVGLTGAGSRVSADLARLGEDDVLALDERAWRRRRGVRVGYILQDALVSLDPLRTVGAEIGD +VLRLHGVSDRGERRRRAADLLAEVGVPEPQVRLDQRPGELSGGLRQRALIASAVALQPELVIADEPTTALDVSVQVQVLE +LLSRL-KSSGTAVLLISHDFAVVSRLADHVLVMEGGRIVESGPVRRILDAPEHPYTRRLLAAIPSGDTRGQRLSPE---- +-PRAVV---THAPLV-AAPTAQGGPTLAARGLTKRYRGPDGR-DRTVVDDVSFDVFAGQTLGIVGESGSGKSTTAAMALG +LVQPDAGTVELDGRPWSGVSARARRARRRQVAVVYQDPLSSFDPRWNGERILADAAGAGVPPWASPARRRAARDDARARA +VDLARLVGLDPRHLTRSPARLSGGQRQRLAITRALAVQPRVLVLDEAVSALDVSVQAQVLDLLGDLKEGLGL-TSLFISH +DLGVIHHVSDRILVMKDGRAVEQGDADQVFHAPRHEYTRGLLASL--EQLSIR------------------------- +>GCF_005280335_PROKKA_00265 +MD-PKHDDGALGAGSHAAAPEAAPTAGTDPAGVGSAE-MPAPGA--PLLEIRDLDVEFR-TQQGTVKAVEGASLTLPAGG +TLAIVGESGSGKSTTAMAAIGLLPGNGRVTGGSVKFAGEELVGLSDAKMRRIRGRRIGLVPQDPMSNLNPVTRVGQQIGE +TLLTHGLATKKDVGAKVVEVMERAGIPEPARRAKQYPHELSGGLRQRVLIAIGLACRPQLLIADEPTSALDVTVQQVILD +QIDEMTRELGSSVLLITHDLGLAADRAQQLVVMHRGRVVESGDARAILEDPQHAYTRSLVAAAPS--VAAARLLPEAFDP +APSALKEDDTAALSTVALAKKDLTPLVEIRDLTKVYP-VRGHDDFTAAKDVSLKIPRGKTVSIVGESGSGKTTTARMLLK +LIEPTSGEITFEGKDVLGMKGEDLKDFRQRVQAVFQDPFSSLNPSFTVGRIIEEPL---------QTYKRGNAKERRARV +LELMEQVALPSHFHRRYPAELSGGQRQRVAIARALALNPELIVCDEPVSALDVLVQDQILTLLRRLQDELGL-SYLFISH +DLAVVRLISDYVCVMKDGEVVEAASSEEVFTNPRHPYTRRLLASIPGNELGIAVEADGEHV----------------- +>GCF_020097155_PROKKA_00137 +MSIPK-----------------SPTS-TLPSAVAPA----------PALSVHGLDVDYA-GRHGQAPALRDVRLEVPAGG +TLAVVGESGSGKSTLARVLLGLSAANARIRSGRIHVAGQTVDAADTDALARLRGRCIGFVPQDPVTGLNPVRTIGEQVVA +AVRTHTRLRVDDAYGRAEALLAEAGVDRPGHRLGQFPHELSGGLRQRVLIALALAGDPEVIVADEPTSALDATVQQQVLD +RLGLLQERTGAALVLITHDLAVAAGRAERIVVMRQGRIVEAGPAEQIAQSPQDSFTRRLVAASPG-----RR-------- +-PTARV---LAAPDVEAGPGADPAPVVRVRGLRHEYPGVHGSAPHVAVDGVDLDIRAGETLALIGESGSGKTTTGRLVLG +LETVREGSVQIRGVETAGVGGRAWRRARRHLQTVHQNPFASLDPRQTVERIVAEPL---------RAFSVGSRTERRDRV +TELLERVSLPAATASRRPGELSGGQRQRVAIARALALDPDVLVCDEPTSALDVSVQAQVLELLARLQDEQGL-ACLFITH +DLRVVWDIAHRVAVMRDGRILETAATERLFRAPEHPYTAELLAAA-----GVTAPLTGTQTSAGTMTPAGARALVGRP +>GCF_023573625_PROKKA_00127 +MD-PKHDDGAPG-------PGAAPA-------------VPAAGA--PLLEIRDLDVEFT-TQQGTVQAVEGASLTLPAGG +TLAIVGESGSGKSTTAMAAIGLLPGNGRVTAGSVRFAGEELVGLPESRMRRIRGRRIGLVPQDPMSNLNPVTRVGQQIGE +TLLTHGMATKKDVGAAVVEVMERAGIPEPARRAKQYPHELSGGLRQRVLIAIGLACRPQLLIADEPTSALDVTVQQVILD +QIGEMTRELGSSVLLITHDLGLAAERAQQLVVMHRGRVVESGDARAILEDPQHAYTRSLVAAAPS--VAAARLLPEAFDP +APVALAEDDTAALTTVALAKQDLTPLVEIRDLTKVYP-VRGHEDFIAVKDVSLKIPRGKTVSIVGESGSGKTTTARMLLK +LIEPTSGEITFEGRDVLALKGEGLKDFRQRVQAVFQDPFSSLNPSFTVGRIIEEPL---------QTYRRGNATQRRARV +LELMDQVALPSHFHRRYPAELSGGQRQRVAIARALALNPELIVCDEPVSALDVLVQDQILTLLRRLQDELGL-SYLFISH +DLAVVRLISDYVCVMKDGEVVEAASSEEVFTNPRHPYTRRLLASIPGNELGIAVEADGTHV----------------- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000065.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000065.fa new file mode 100644 index 0000000000000000000000000000000000000000..f9e971ae8e94a489633e2facfbf0405899ed2850 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000065.fa @@ -0,0 +1,37 @@ +>GCF_002008305_PROKKA_00175 +-----------------------MTPPA--ALLLDLDGTLLDHGRAARIALGQAM--QEA +GLTDADH---SSALLLWGELERIHFQEYLDGQTTFEEQRVRRVRAFLAHYGRTR-LDRTS +ALAWFDTYRTAYERAWS------------------------------------------- +------------------------------------------------------------ +-------------------------------------------- +>GCF_002008305_PROKKA_00854 +-----MSRDASTTPAGG--SAGAPAPPAWDAVLFDLDDTLLDLRSAQHAAFDATVRRQWA +GAADVDPAVLAEATDAFASDAGGHYGRYVAGELTFEEQRLARVADALRALGVPEDAATPL +DGLWTTDYEEVVRGHWALFPATADVLAEVRGTGRGVGIVTNNVEAYQRGKADALGLEWVE +VLIGSDTAGAPKPDPAPFLAGCSRLGTDPGRTLMVGDSLRHDVEGARSAGLVPVWMSPDA +PAHGGAEEPLWDEEHACWRMRAIGGLRTWLAA------------ +>GCF_003691675_PROKKA_00576 +-----MSRGASTTPADG--SAGAPAPPAWDAVLFDLDDTLLDLRSAQHAAFDATVRRQWA +GAADVDPAVLAEATEAFASDAGGHFGRYVAGELTFEEQRLARVADALRALGVPEDAATPL +DGLWTTDYEEVVRGHWALFPATADVLAEVRGTGRGVGIVTNNVEAYQRGKADALGLEWVE +VLIGSDTAGAPKPDPAPFLAGCSRLGTDPGRTLMVGDSLRHDVEGARSAGLVPVWMSPDA +PAHGGAEEPLWDEEHACWRMRAIGGLQTWLAA------------ +>GCF_005280335_PROKKA_02080 +MSGAPATGQATTTAAGGSPSSPAPAPPEWDAVLFDLDDTLLDLRAAQHAAFDATVRRQWA +GAADVDPARMAEATEAFASDAAGHYERYVAGELTFEQQRLARAADALRALGAPEESATPL +EALWTADYEDVVRGHWALFPATAEVLAQVRSSGRGVGIVTNNVEAYQRAKADALGLEWVD +VLIGSDTAGAPKPDPAPFLAGCARLGAEPGRTLMVGDSLTHDVAGARAAGLVPVWMSPAA +PARGAAEDPVWDPERGCWRLRAIGGLRAWLRR------------ +>GCF_020097155_PROKKA_01975 +-----MIR-----------TPGTPSAPVVDGVLFDLDDTLLDLRGAQLPAFAETVRAQWP +DAPPAEAGVFVRAADHFAADRSGHYQRYIAGELDFAGQRLARARDALAVLGAPGAVAEPD +PALWTDEYEVRVRAHWALFDDVVPTLATLRSSGVALGIVTNNVEAYQRAKADALGLEAIT +VLVGSDSAGAPKPDPAPFLEACRRMGTTPGRTACVGDSLSHDVRGARAAGLVPVWLRRGA +GAADGGGEGRWDAAEGAWTIGGLGALAAWFPGSGADLASGREVL +>GCF_023573625_PROKKA_00813 +-----MSRGASTTPADG--SAGAPAPPAWDAVLFDLDDTLLDLRSAQHAAFDATVRRQWA +GAADVDPAVLAEATEAFASDAGGHFGRYVAGELTFEEQRLARVADALRALGVPEDAATPL +DGLWTTDYEEVVRGHWALFPATADVLAEVRGTGRGVGIVTNNVEAYQRGKADALGLEWVE +VLIGSDTAGAPKPDPAPFLAGCSRLGTDPGRTLMVGDSLRHDVEGARSAGLVPVWMSPDA +PAHGGAEEPLWDEEHACWRMRAIGGLQTWLAA------------ + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000071.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000071.fa new file mode 100644 index 0000000000000000000000000000000000000000..b55e7cf4ce7d2ada11f0e4a1783aeefa6f85e985 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000071.fa @@ -0,0 +1,61 @@ +>GCF_002008305_PROKKA_00236 +MALSVLDLFSIGIGPSSSHTVGPMRAARRFTDSMGQHGVLERTARVHAELFGSLAATGVG +HGSDTAVLLGLAGQDPETIDPDACTGLVAEIVTGGRLPL-----DGRHEIAFDRQADLTL +HMRESLPGHPNGMRLTAYDDAGEQLHTRDYYSVGGGFVVTSDELEAELDATKDVNRTDDG +DTGEPYPFSTGAELAARCREAGLSIAELMLANEATRHDLDELRTQLLAIWAVMEECVHNG +VTRTEPILPGGLQVRRRAPALREHLLQT-T--------D--RTDPMWAMEWVNLFALAVN +EENASGGRIVTAPTNGAAGIIPAVMLYYMRFVLPEGATQQERDDKVVEFLLTAAAIGILY +KRNASISGAEVGCQGEVGSACSMAAGALCAVLGGTVDQVENAAEIGIEHNLGLTCDPVGG +LVQVPCIERNAIASVKAINAARLALLGDGSHRVTLDQAITTMRDTGADMKSKYKETSRGG +LAVNVIEC +>GCF_003691675_PROKKA_00102 +MALSVVDLFSVGIGPSSSHTVGPMRAGRRFALGLVERGLVDATERIHVQLFGSLSATGHG +HGSDRAVLLGLEGEDPETVDTDRANARVESMKAERRLALAAGAEQGGKDLDFDPDADLVM +HRRRSLPYHPNGMSFTAYDGSGEVVVERVYYSVGGGFVVD--------DEAAGADRVVED +ATEPPLPFSSGRELLNHCDREGISIPELMRRNEEAFRPWEAARAALLNTWRVMQECVEAG +CEATG-TLPGGLKVPRRAALLKEQLEVSAPRDGSAPPRDGGAPDALGAMEWVNLYALAVN +EQNASGGRIVTAPTNGAAGIIPAVLHYWRDFLARE-MTAEHIEDGVVDFLLTAAAIGILI +KENASISGAEMGCQGEVGSACSMAAAGLCQLLGGTPQQVENAAEVGIEHNLGLTCDPVGG +LVQIPCIERNAIASVKAINAARLCRRGDGRHTVSLDQAIKTMRETGQDMKVKYKETSRGG +LAVNVIEC +>GCF_003691675_PROKKA_02249 +MALSVLDLFSIGIGPSSSHTVGPMRAARRFTDSMGQHGVLERTARVHAELFGSLAATGVG +HGSDTAVLLGLAGQDPETIDPDACTGLVEEIVTGGRLPL-----DGRHEIAFDRQGDLTL +HMRESLPGHPNGMRLTAYDDAGEQLHTRDYYSVGGGFVVTSDELEAELDATKDVNRTDDG +DTGEPYPFSTGAELAARCHEAGLSIAELMLANEATRHDLDELRTRLLAIWAVMEECVHNG +VSRTEPILPGGLQVRRRAPALREHLLQT-T--------D--RTDPMWAMEWVNLFALAVN +EENASGGRIVTAPTNGAAGIIPAVMLYYMRFVLPEGATQQERDDKVVEFLLTAAAIGILY +KRNASISGAEVGCQGEVGSACSMAAGALCAVLGGTVDQVENAAEIGIEHNLGLTCDPVGG +LVQVPCIERNAIASVKAINAARLALLGDGSHRVTLDQAIKTMRDTGADMKSKYKETSRGG +LAVNVIEC +>GCF_005280335_PROKKA_00135 +MALSVLDLFSIGIGPSSSHTVGPMRAARRFTQSMDQHGVLERTARVEAELFGSLAATGIG +HGSDTAVLLGLAGQDPETIDPDACVGLVDEILQGGRMPL-----DGRHEIAFDRQKDMTL +HMRRTLPGHPNGMRLTAFDADGEQLHTRDYYSVGGGFVVTSDELEAELDESRDVSRHDDG +EGGEPYPFATGAELAGRCRTNGLSIAELMLANEATRHDLGELRTQLLAIWDVMQECVHNG +VTRTEPILPGGLKVRRRAPALRAHLLET-T--------D--RTDPMWAMEWVNLFALAVN +EENASGGRIVTAPTNGAAGIIPAVLHYYMRFVLPQDATQQERDDKVVEFLLTAAAIGILY +KRNASISGAEVGCQGEVGSACSMAAGALCAVLGGTVDQVENAAEIGIEHNLGLTCDPVGG +LVQVPCIERNAIASVKAINAARLALLGDGSHRVTLDQAIKTMRDTGADMKSKYKETSRGG +LAVNVIEC +>GCF_020097155_PROKKA_00100 +MALSILDLFSIGIGPSSSHTVGPMRAARRFTYALERDGLVERTARVKGELFGSLSATGVG +HGSDMAVILGLCGNDPETIDPEAAAPQVQACVEGGTLPL-----DGTHEIPFDRPKDLVL +HMRRSLPGHPNGMRLTAFDADGAELLTRDYYSVGGGFVVTGEELEAELDETRDVSRH--G +EEPEPHPFSTGADLIAQCEIHGLSIADVVRANEAARGDLADVEAKVLEIWDVMQECVAHG +IHRTEPILPGGLKVKRRAPGLHAQLLEKGT--------DGAEKDPMWAMEWVNLFALAVN +EENASFGRIVTAPTNGAAGIIPAVLHYYDRFVLPPGTPAEERRAKILDFLFTAAAIGILF +KRNASISGAEVGCQGEVGSACSMAAGALCAVLGGTPLQVENAAEIGIEHNLGLTCDPVGG +LVQVPCIERNAIASVKAINAARLALVGDGDHRVTLDQAIQTMRETGADMKSKYKETSRGG +LAVNVIEC +>GCF_023573625_PROKKA_00237 +MALSVLDLFSIGIGPSSSHTVGPMRAARRFTDSMGQHGVLERTARVHAELFGSLAATGVG +HGSDTAVLLGLAGQDPETIDPDACTGLVEEIVTGGRLPL-----DGRHEIAFDRQGDLTL +HMRESLPGHPNGMRLTAYDDAGEQLHTRDYYSVGGGFVVTSDELEAELDATKDVNRTDDG +DTGEPYPFSTGAELAARCHEAGLSIAELMLANEATRHDLDELRTRLLAIWAVMEECVHNG +VTRTEPILPGGLQVRRRAPALREHLLQT-T--------D--RTDPMWAMEWVNLFALAVN +EENASGGRIVTAPTNGAAGIIPAVMLYYMRFVLPKGATQQERDDKVVEFLLTAAAIGILY +KRNASISGAEVGCQGEVGSACSMAAGALCAVLGGTVDQVENAAEIGIEHNLGLTCDPVGG +LVQVPCIERNAIASVKAINAARLALLGDGSHRVTLDQAIKTMRDTGADMKSKYKETSRGG +LAVNVIEC + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000083.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000083.fa new file mode 100644 index 0000000000000000000000000000000000000000..e98b94f1d862965ba6fb793c6488fb84f356b1e6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000083.fa @@ -0,0 +1,43 @@ +>GCF_002008305_PROKKA_00412 +M--------------------SHVDTAPAASTPRAAEGRRPRRVKSQR-AKSEARLGWLL +AGPAFFVMLFVVLYPILQALYDSLFKYRLTAPGDREFVGLGNYGVILTDPVFWKGLGVTL +LITVVTVVVELILGFLLALAMHHAIKQTRGLIRTIILVPYGIITVVSAFAWFYMFSIDSG +YINAWFEWLPGVDADLNWFAQGSTALFVIMLSEIWKTTPFISLLLLAGLAQVPGDLTEAA +SVDGASWWQRMKLVILPNMKASI----MVAVLFRAMDAFRIFDSIYIMTNGAYGTEVLSL +LAYRTSIGRLEIGMGSAVSVILFLCVALMAVIAVKGF-KVDLADRGGSK +>GCF_003691675_PROKKA_00132 +M--------------------SHVDTAPAASTPRAAEGRRPRRVKSQR-AKSEARLGWLL +AGPAFFVMLFVVLYPILQALYDSLFTYRLTAPGDREFVGLGNYGVILTDPVFWKGLGVTL +LITVVTVVVELILGFLLALAMHHAIKQTRGLIRTIILVPYGIITVVSAFAWFYMFSIDSG +YINAWFEWLPGVDADLNWFAQGSTALFVIMLSEIWKTTPFISLLLLAGLAQVPGDLTEAA +SVDGASWWQRMKLVILPNMKASI----MVAVLFRAMDAFRIFDSIYIMTNGAYGTEVLSL +LAYRTSIGRLEIGMGSAVSVILFLCVALMAVIAVKGF-KVDLADRGGSK +>GCF_005280335_PROKKA_02547 +M--------------------SHVDTAPAASTPRTAEGRRPRRVKSQR-AKSEARLGWLL +AGPAFFVMLFVVMYPILQALYDSLFKYRLTAPDDREFVGLGNYGVILSDPVFWKDLGVTL +LITVVTVVVELILGFLLALAMHHAIKQTRGLIRTIILVPYGIITVVSAFAWFYMFSIDSG +YINAWFEWLPGVDADLNWFAQSNTALSVIMLSEIWKTTPFISLLLLAGLAQVPGDLTEAA +AVDGASWWQRMKLVILPNMKASI----MVAVLFRAMDAFRIFDSIYIMTNGAYGTEVLSL +LAYRTSIGRLEIGMGSAVSVILFLCVALMAVIAVKGF-KVDLADRGGSK +>GCF_005280335_PROKKA_02646 +MFTEVLPQQQVAPRPEAATAEPGIAESGIAESRTATDAPRPAKQKSRRTGRSFSIVPYLY +VLPAVALLLLWTYLPLAQTFELSFYDWNLLPTKAKEPVGLENYATVLTLPEMQQALGNTV +LYIGAFFLLSVALPVIFALLSKRVSGRAKTIYQALIFVPYLVTPVATSAIWRWLFAEEGG +TIPAVAHFF-GIDMG-NVFREPGASMIAVMVIVGWQLLGFGVLVVSAGLSGISPDYEHAA +GVDGARRWQITSRITLPLLSPSLVFLSLMTILLSAQWTFPMIDIITQGGPSGSSTNIYYL +L-YEFGFKNFDAGISAAAGVLFFIGFGLIALVFVELSEKLSFHD----N +>GCF_020097155_PROKKA_02415 +M--------------------SHVDTAPAASTPRAAEGRRPRRVKSAR-AKSEARLGWLL +AGPAFFIMLFVVLYPTVQAFYDSLFKYRLTAPQDREFVGLGNYGVILSDPVFWKDLGVTV +LITLVTVLVELVLGFLLALAMHHAIKQTRGLIRTIILVPYGIITVVSAFAWFYMFSIDSG +FVNNWFDWVPGITSDLNWFAQSGTALSVIMLSEIWKTTPFISLLLLAGLAQVPGDLTEAA +AVDGASWWQRMKLVILPNMKASI----MVAVLFRAMDAFRIFDSIYIMTNGAYGTEVLSL +LAYRTSIGRLEIGMGSAISVILFLCVALMAFTAVKVF-KVDLADRGGSK +>GCF_023573625_PROKKA_00415 +M--------------------SHVDTAPAASTPRAAEGRRPRRVKSQR-AKSEARLGWLL +AGPAFFVMLFVVLYPILQALYDSLFKYRLTAPGDREFVGLGNYGVILTDPVFWKGLGVTL +LITVVTVVVELILGFLLALAMHHAIKQTRGLIRTIILVPYGIITVVSAFAWFYMFSIDSG +YINAWFEWLPGVDADLNWFAQGSTALFVIMLSEIWKTTPFISLLLLAGLAQVPGDLTEAA +SVDGASWWQRMKLVILPNMKASI----MVAVLFRAMDAFRIFDSIYIMTNGAYGTEVLSL +LAYRTSIGRLEIGMGSAVSVILFLCVALMAVIAVKGF-KVDLADRGGSK + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000087.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000087.fa new file mode 100644 index 0000000000000000000000000000000000000000..0a0ace9efa38a6e3fd6ec986263cf8172e280ac8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000087.fa @@ -0,0 +1,48 @@ +>GCF_002008305_PROKKA_00489 +MTVTAEREKALLESVPTGL-LIDGEWRDASSGKTFDVKDPATGKVIASLQDANSDDAMAAFDAACAA--QADWARTPAKE +RADILRRAYDLINERAEDFALLMTLEMGKPLAEARGEVTYGNGFLRWFSEEAGRHYGRTLTVPEGTLRMQVHHRPVGPCL +LITPWNFPLAMATRKVGPAVAAGCTMVLKAAKLTPLTTQLFAQVMQEAGLPKGVLNVVAGSSASSISSPILQDRRLRKVS +FTGSTPVGVRLMKDAADNVLRTSMELGGNAPLIVFEDADLDAAVEGAFAAKMRNMGEACTAANRFLVHEDVAEEFTQKFV +AKLEALKPLRGTDPESTLGPIVDEGARDDIDQLVQDAVAAGGEVLTGGH---KIEGDGYFYAPTAI-KVEKGNPILQQEI +FGPVAPIVTFSSEEEAIEMANDTEYGLASYVFTKDQARMYRVAESIEFGLMGYNVGVISNPAAPFGGVKQSGLGREGGAE +GIEEYTSVQYI------GIADPWAATKA +>GCF_003691675_PROKKA_00210 +MTVTAEREKALLESVPTGL-LIDGEWRDASSGKTFDVKDPATGKVIASLQDANSDDAMAAFDAACAA--QADWARTPAKE +RADILRRAYDLINERAEDFALLMTLEMGKPLAEARGEVTYGNGFLRWFSEEAGRHYGRTLTVPEGTLRMQVHHRPVGPCL +LITPWNFPLAMATRKVGPAVAAGCTMVLKAAKLTPLTTQLFAQVMQEAGLPKGVLNVVAGSSASSISSPILQDRRLRKVS +FTGSTPVGVRLMKDAADNVLRTSMELGGNAPLIVFEDADLDAAVEGAFAAKMRNMGEACTAANRFLVHEDVAEEFTQKFV +AKLEALKPLRGTDPESTLGPIVDEGARDDIDQLVQDAVAAGGEVLTGGH---KIEGDGYFYAPTAI-KVEKGNPILQQEI +FGPVAPIVTFSSEEEAIEMANDTEYGLASYVFTKDQARMYRVAESIEFGLMGYNVGVISNPAAPFGGVKQSGLGREGGAE +GIEEYTSVQYI------GIADPWAATKA +>GCF_005280335_PROKKA_02458 +MTVTAEREKALLESVPTGL-LIDGEWRDASSGKTFDVKDPATGKVIASLQDANSDDAMAAFDAACAA--QADWARTPAKE +RADILRRAYDLINERAEDFALLMTLEMGKPLAEARGEVTYGNGFLRWFSEEAGRHYGRTLTVPEGTLRMQVHHRPVGPCL +LITPWNFPLAMATRKVGPAVAAGCTMVIKAAKLTPLTTQLFAQVMQEAGLPKGVLNVVAGSSASSISSPILQDRRLRKVS +FTGSTPVGVRLMKDAADNVLRTSMELGGNAPLIVFEDADLDAAVEGAFAAKMRNMGEACTAANRFLVHEDVAEEFTQKFV +AKLEALKPLRGTDPESTLGPIVDEGARDDIDQLVQDAVAAGGEVLTGGH---KIEGDGYFYAPTAI-KVEKGNPILQQEI +FGPVAPIVTFSSEEEAIEMANDTEYGLASYVFTKDQARMYRVAESIEFGLMGYNVGVISNPAAPFGGVKQSGLGREGGAE +GIEEYTTVQYI------GIADPWAAVKA +>GCF_020097155_PROKKA_02342 +MTVTAEREKALLESVPTGL-LIDGEWRDASSGKTFDVKDPATGKVIASLQDANSDDAMAAFEAAVAA--QADWARTPAQE +RADILRRAYDLINERAEDFALLMTLEMGKPLAEARGEVVYGNGFLRWFSEEATRHYGRTMIMPDGKLRMQVHHKPVGPSL +LITPWNFPLAMATRKVGPAVAAGCTMVLKAAKLTPLTTQLFAQVMLEAGLPKGVLNVVSGSSASAISGPILEDPRLRKVS +FTGSTPVGVRLMQDAAKNVLRSSMELGGNAPLIVFEDADMDKAVDGAFAAKLRNMGEACTAANRFLVHESVAEEFTRRFV +ERLEALKPLRGTDPESTLGPIVDEGARDDIHALIEEAVAAGGEILTGGH---KIEGDGYFYAPTAL-KVGKDNPILKKEI +FGPVAPIVTFSTEEEAIQMANDTEYGLASYVFTEDNARMHRVTEQIDFGIVGYNVGVVSNPAAPFGGVKQSGLGREGGAE +GIAEYTTVQYI------GIEDPFAGR-- +>GCF_023573625_PROKKA_00488 +MTVTAEREKALLESVPTGL-LIDGEWRDASSGKTFDVKDPATGKVIASLQDANSDDAMAAFDAACAA--QADWARTPAKE +RADILRRAYDLINERAEDFALLMTLEMGKPLAEARGEVTYGNGFLRWFSEEAGRHYGRTLTVPEGTLRMQVHHRPVGPCL +LITPWNFPLAMATRKVGPAVAAGCTMVLKAAKLTPLTTQLFAQVMQEAGLPKGVLNVVAGSSASSISSPILQDRRLRKVS +FTGSTPVGVRLMKDAADNVLRTSMELGGNAPLIVFEDADLDAAVEGAFAAKMRNMGEACTAANRFLVHEDVAEEFTQKFV +AKLEALKPLRGTDPESTLGPIVDEGARDDIDQLVQDAVAAGGEVLTGGH---KIEGDGYFYAPTAI-KVEKGNPILQQEI +FGPVAPIVTFSSEEEAIEMANDTEYGLASYVFTKDQARMYRVAESIEFGLMGYNVGVISNPAAPFGGVKQSGLGREGGAE +GIEEYTSVQYI------GIADPWAAAKA +>GCF_023573625_PROKKA_01553 +MTPTPD---------PTATQYIDGAWVPSSDGGTRTIHCPADGSEVGVVAEGTREDALAAIAAARRAFDSGEWSSTPAAE +RGDLLIRLADHILEHRDEFARAEALDTGKRLVEAEGDMADIAACFRYFGKIADQNPGRLVDAGDPTVLSRVVTEPVGVCG +MITPWNFPLLQAAWKIAPALAAGCTFVLKPAEQTPHTAILTMRALESLGLPAGVANLVLGPGAT-VGEPLSSHPDVDLVS +FTGGLATGKTIAQAAAGTVKKVALELGGKNPNVIFPDAHYEAALDNALNAAFTDSGLVCSAGTRLIVHESIAERFVDDLV +ERAGHIVMGGPFDEHAETGPLISAAHRDKVTDYVRRGVEAGARLRVGGHWGGEEHKDGFFYAPTVLDRCDRDNPAVIEEG +FGPVITVETFSTEAEAIEIANHTEYGLAGAVWSSDAGTCQRVSRALRHGTVWINDYHPYLPQAEWGGFKASGIGRELGPT +GLGEYVEHKHIYQNTEPAVTGWFADRR- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000102.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000102.fa new file mode 100644 index 0000000000000000000000000000000000000000..efb39595433ec0af2b477f7e4b83beb50787f4bc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000102.fa @@ -0,0 +1,43 @@ +>GCF_002008305_PROKKA_00656 +MT------------------SAVSTSPAPPRGGRDLKSAVLVGVGLLATALVGLFWLDWL +LVLLVVALLVGAVSEIAT----------------AVRGIGLDVPRPPLWVAAAVLPLTAW +R-----WGVPALFIALVACL------ALVAVWTALTRRRPAGQF-MLAGVFIVLWAPFLL +SFAAAL-------------LDEPLGHRMVAVLLLMVVSNDTFGYIVGYRFGRTPIAPRIS +PKKSWEGLAGSLAGSVLVGVVAVPLLVGQPWWVGAVLGVTTVAAATSGDFSESMVKRELG +IKDMSSALPGHGGVMDRLDSLVFAAPVAYTVLALPLT +>GCF_003691675_PROKKA_00393 +MT------------------SAVSTSPAPPRGGRDLKSAVLVGVGLLATALVGLFWLDWL +LVLLVVALLVGAVSEIAT----------------AVRGIGLDVPRPPLWVAAAVLPLTAW +R-----WGVPALFIALVACL------ALVAVWTALTRRRPAGQF-MLAGVFIVLWAPFLL +SFAAAL-------------LDEPLGHRMVAILLLMVVSNDTFGYIVGYRFGRTPIAPRIS +PKKSWEGLAGSLAGSVLVGVVAVPLLVGQPWWVGAVLGVTTVAAATSGDFSESMVKRELG +IKDMSSALPGHGGVMDRLDSLVFAAPVAYTVLALPLT +>GCF_005280335_PROKKA_00162 +MVGLLGPTAGGLLLGVVGVLAAASVIAAVLRARMGARNPELIG------NLVQRIGAWWA +MVAVLAAVL--ALGETATLLLFLVLTWLSLREFLTISPTGRADHRTLVWLFFVVTPLHYW +FVWEHWYGMFSVFIPVYAFLFLPVRAALAGRTEGFLRRAAAVQWAAMVCVYAVSHIPAVL +QLPVAMEHGRHMAEGSAPGSGDEAGALLLLFLLLVVQGSDVFQYVWGKTLGRRPIAPSVS +PNKTWEGFVGGVLTATALG-AALSFLTPFPWWVAALFAFVSCLLGFGGGLVMSAIKRDRG +IKDFGSLIPGHGGIMDRIDSLVFAAPVFFHLVRFFYA +>GCF_005280335_PROKKA_02307 +MT------------------TAVST-PAPPRGGRDLKSAVLVGVGLLVLALVGLVWLDWL +LVLLVVALLVGAVTEVAT----------------AVRGIGLQVPRPPLWAAAVALPVSAW +L-----WGVPALFVALAACL------ALLAVWTALTRHRPTGQF-MLAGVFIVLWAPFLL +SFAVAM-------------LDQPRGNLLVAITLLMVVSNDTFGYIVGYRFGRTPIAPRIS +PKKSWEGLAGSLAGSALVGVVTVPLFVGQPWWVGAILAVTTVAAATSGDFSESMVKRELG +IKDMSSALPGHGGVMDRLDSLVFAAPVAYTVLALPLT +>GCF_020097155_PROKKA_02164 +MT------------------PDATA-PSPPRGGRDLRSAVLVGVGLLGTALVGLVWLPWL +LVLLVVSLLVGAVNEVAV----------------AIRQIGLDVPRPPLWVGATVMPLAAW +T-----GGIPALFLALMASL------VLMFAWTAVTRRRPTGQF-MLAGTFVLLWAPFLL +SFAAAL-------------LDQPAGHMMVVCLVLMVVSNDTFGYMVGYRWGRTPIAPRIS +PKKSWEGALGSLAGSVAVGSVLVPVLVGHPWWAGALLGALTVGAATAGDFSESMVKRELG +IKDMSSALPGHGGIMDRLDSLVFAAPVAYAVLALPLS +>GCF_023573625_PROKKA_00626 +MT------------------SAVSTSPAPPRGGRDLKSAVLVGVGLLATALVGLFWLDWL +LVLLVVALLVGAVSEIAT----------------VVRGIGLDVPRPPLWVAAAVLPLTAW +R-----WGVPALFIALVACL------ALVAVWTALTRRRPAGQF-MLAGVFIVLWAPFLL +SFAAAL-------------LDEPLGHRMVAVLLLMVVSNDTFGYIVGYRFGRTPIAPRIS +PKKSWEGLAGSLAGSVLVGVVAVPLLVGQPWWVGAVLGVTTVAAATSGDFSESMVKRELG +IKDMSSALPGHGGVMDRLDSLVFAAPVAYTVLALPLT + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000123.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000123.fa new file mode 100644 index 0000000000000000000000000000000000000000..8f1469300d85f5c0375d8baaa154b1c74d9f9cda --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000123.fa @@ -0,0 +1,96 @@ +>GCF_002008305_PROKKA_01272 +MSA-----------------------------------ESSPL------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------------------------------------SAAAVDPEERRLEAA----- +----------------LRP------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------------------------------------KHLDEFVGQMRVREQLDLML +ASARLRD----------RAADHVLLSGPPGLGKTTLAMIVAAEMNAPLRLSSGPAI---------QHAGDLAAILSSLTE +---GEVLFLDEIHRMS--------RPAEEMLYMAMEDFRVDIVVGKGAGATSIPLELPPFTLVGATTRAGLLPGPLRDRF +GFTGHLDFYTEVELERVLRRSALLLDMRLATEGYRQI---ARRSRGTPRIANRLLRRVRDWALVKGLAEVGAHDAAAALD +MYEVDGRGLDRLDRSVLTALCTTFGGGPVGLSTLATAVGEEA--ETVETVAEPFLIREGMVARTPRGRVALPGAWEHLGL +A------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------APEATPGP------------------------------------------------- +>GCF_003691675_PROKKA_00991 +MSA-----------------------------------ESSPL------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------------------------------------SAAAVDPEERRLEAA----- +----------------LRP------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------------------------------------KHLDEFVGQMRVREQLDLML +ASARLRD----------RAADHVLLSGPPGLGKTTLAMIVAAEMNAPLRLSSGPAI---------QHAGDLAAILSSLTE +---GEVLFLDEIHRMS--------RPAEEMLYMAMEDFRVDIVVGKGAGATSIPLELPPFTLVGATTRAGLLPGPLRDRF +GFTGHLDFYTEVELERVLRRSALLLDMRLATEGYRQI---ARRSRGTPRIANRLLRRVRDWALVKGLAEVGAHDAAAALD +MYEVDGRGLDRLDRSVLTALCTTFGGGPVGLSTLATAVGEEA--ETVETVAEPFLIREGMVARTPRGRVALPGAWEHLGL +A------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------APEATPGP------------------------------------------------- +>GCF_005280335_PROKKA_01615 +MSA-----------------------------------EPSPL------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------------------------------------SGLAADPEERRLEAA----- +----------------LRP------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------------------------------------KHLDEFVGQRRVREQLDLML +ASARLRD----------RAADHVLLSGPPGLGKTTLAMIVAAEMNAPLRLSSGPAI---------QHAGDLAAILSSLTE +---GEVLFLDEIHRMS--------RPAEEMLYMAMEDFRVDIVVGKGAGATSIPLELPPFTLVGATTRAGLLPGPLRDRF +GFTGHLDFYAEAELERVLRRSALLLDVRLASDGYRQI---ATRSRGTPRIANRLLRRVRDWALVKGVEQVEADHAAAALD +MYDVDARGLDRLDRSVLTALCTTFGGGPVGLTTLATAVGEEA--ETVETVAEPFLIREGMVARTPRGRIALPGAWDHLGL +A------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------SPEAGSGA------------------------------------------------- +>GCF_020097155_PROKKA_01510 +MS-------------------------------------ERPV------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------------------------------------TAFEADAEERRLEAA----- +----------------LRP------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------------------------------------KHLDEFVGQARVREQLDLML +ASARLRD----------RAADHVLLSGPPGLGKTTLAMIVAQEMNAPLRLSSGPAI---------QNAGDLAAILSSLTE +---GEVLFLDEIHRMS--------RPAEEMLYMAMEDFRVDIVVGKGAGATSIPLELPPFTLVGATTRAGLLPGPLRDRF +GFTGHLEFYAIEELERVLRRSSALLDMRVETDGYRQI---ASRSRGTPRIANRLLRRVRDWALVKGLDTVDAEAASAALT +MYEVDARGLDRLDRSVLTALCTTFGGGPVGLTTLATAVGEEA--ETVETVAEPFLIREGMMARTPRGRVALPGAWDHLGM +T------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------PPEAPLG-------------------------------------------------- +>GCF_023573625_PROKKA_01230 +MSA-----------------------------------ESSPL------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------------------------------------SAAAVDPEERRLEAA----- +----------------LRP------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------------------------------------KHLDEFVGQMRVREQLDLML +ASARLRD----------RAADHVLLSGPPGLGKTTLAMIVAAEMNAPLRLSSGPAI---------QHAGDLAAILSSLTE +---GEVLFLDEIHRMS--------RPAEEMLYMAMEDFRVDIVVGKGAGATSIPLELPPFTLVGATTRAGLLPGPLRDRF +GFTGHLDFYTEVELERVLRRSALLLDMRLATEGYRQI---ARRSRGTPRIANRLLRRVRDWALVKGLAEVGAHDAAAALD +MYEVDGRGLDRLDRSVLTALCTTFGGGPVGLSTLATAVGEEA--ETVETVAEPFLIREGMVARTPRGRVALPGAWEHLGL +A------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------APEATPGP------------------------------------------------- +>GCF_023573625_PROKKA_01882 +MSILRVHDGLFGLTFQQALDKASPGATIALTPGTYAEFESIPVGNLRIIGAGSRPEDVILVTQLDVHGQISVENLTLQAP +HFHNAVRLHGPTASAVFLYTAIQPEPTGQFPAVYSEGGAVTVRRSTLDQGPGGCALYVEGQGTATFEDSTTGTVNAVAST +VTTVDSTHGAFHLSAASKVHARGTLCLAPAEGMRGLVLTAFSVLKAERLTTDITYLELSLEDSALDVAEVSTSSDVDVHV +MTSGGSHVQIPPDTVRVTDIDRQKAEQEVAERRQREEAAARRRAEEAAAEAAATGEAARQAAAEAQAEARRQEEAKPRAV +MWTAAQGADFTTVQDQLRPGDTLVLEEGDFHLPDPAIMLNCHIRGTGRADRIRLHGAVGIPNGATVRLENMLLVTPSTGN +AVNVHAGGNATLTGVLVDPTKAEVFSPLCSSGGRLTLNEVRVVSEPTSYLADVLGTQGGVIVAEDSTFGIVRLESSARAT +LTDCTANQLYVLGSGEALSLGTLRIPPTTPHLRALAVEEGGRGTIADLCVEEPCEVFVAGSLQIAHVSSAPHALHLITTD +TALHSIPEDAIATAEEPSQTATADATLVEHPGENSTGDREPSAGRGHDGADLADTNCDPMAQLSALTGLADVKNQVQTFI +AEVRFAEARRQRGFAVRRQTLHSQFLGNPGTGKTTVARLLGRALHQAGVLSSDVFVEVTREDLVSEHIGGTGPKTRRILE +SALGGILFIDEAYTLAEGGPQDFGREAIATLLAFMENHRDEFMV----ILAGYPEQMHAFFKAN--------PG-LRSRV +PLRFDFEDYSTAELVQMGLAALADDGFTVDPDAYRRTVAEAHRSSGD-RSNGRWVRNLND-RLVRHMAHRVMAESGAAED +MVGVEDERLTQVDPADLHALLGRSTEDDTGVDHLLVELDEMVGLETVKAWVRGLVAQAEADERLRDAGVDLPRPTYHMVF +AGSPGTGKTTVARLVGKLFHRLGILSTPQVVEASRERMVGRYIGHTEERTGLLLDEARGGVLFVDEAYQLDMPDSSNDFG +KVAVETLITRLEDDRHSFIAIFAGYTDRMAQFLSLNPGLASRVPHNIEFPDYSPDDIAEIVVRTLRRTWSFDETVLRSAV +AQGYAALPPESRANARQARNYADAISQAHKTWITESSTDGDDIRHIRDATIIGVLAAEPTGQDQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000128.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000128.fa new file mode 100644 index 0000000000000000000000000000000000000000..0bf4652897cce386e94e6f75e4ab3e14a3499235 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000128.fa @@ -0,0 +1,114 @@ +>GCF_002008305_PROKKA_01440 +MSLSSAAPTPPSVPLDP---AGAPHRPQLPGSERTPPARTLVELFDATAREHPDATALD----DGVEPLTYAELRERVDE +TARHLWAAGVRAGDRVGVRIASGTAALYVSILGVLAAGAAYVPVDADDPEERARLVFGEAKVAGVLTDERVYAPHPEHTA +DPAAEARAPGLEDDAWIIFTSGSTGTPKGVAVSHRSAAAFVDAEARIFLADDPLAPGDRVLAGLSVAFDASCEEMWLAWR +HGACLVPAPRSLVRSGMDLGPWLAERRITAVSTVPTLAAMWPTEAMDNVRLLIFGGEACPPELAARLAEDGREVWNTYGP +TEATVVACAAPLTGLGPVRIGLPLDGWDLAVVDPQTTLPVAEGETGELIIGGVGLARYLDPAKDAEKYAPMPSLGWERAY +RSGDLVVFEPEGLLFVGRADDQVKLGGRRIELGEVDAALQALPGVHGGAAAVQTTPAGHQILVGYLVPADPEAELDLHMA +REHLAAELPAALVPRLAVVDSLPTKTSGKVDRHALPWPLPGAEVDEDAPPPDEDTADGWVLRQWADVLGAPPKDADTDFF +EAGGGSLAAAQLVARLRLRHPAVTVQDVYRNPTAGALVAAVVGDD-GPRGIEVHDRHVDRTRHRT-----QWVQTLVGLP +VF-VLPALRLGVWTGLALNLLTLSGLAPGLPTVPWWVLIVAGLLVVTVPGRMLLTAATARLLLRGVSPGSYPRGGRVHLR +LWLAQQISDLVDPYSLAGATWVPAYARLLGNRIGKDVDMHTVPPVTGMLTVEEGAAIEPEVDLSGYWVDGDVVRLGEVRI +GADAVVGARSTLLPGAQVGAGAHVEAGSTVAGRVRGGQRHAGSPAVKVGKVK-SRGPAEAPRETPGWRLMATVLSTLISL +LPLVSAAAAA--AVAAWSLTWWPPAP------EAGPLAAVGTTAARLLAASPLVAGVWFLTQMLLVLVTVRLLALGITEG +HHPVRSRVGWQVWATERVLDAARDQLFPIYASRFTPTWLRLLGAEVGRGVEASTVVLLPCMTRVGDGAFLADDTMVSSYS +LDGGWMHVAPAKVGKRSFVGNSGMVPGGRTLRRDSLVAVLSTTPAKTKAGTSWMGSPPVRLRRNEVTADAALTYDPPARL +KAARTAWELLRAIPVWLHVALSLAVGATLAALIAVGTWALAFVLGGVVL---------LAAGAVAASLTVLAKRVFVGRI +RAGEHPLWSSFIWRNEVADTFTEFLAAPWFSRAAAGTPALVWFLRAMGARIGHGAWVESYWLPEADLVELGDGATVNRGC +VVQTHLFHDRVMSLDAVVLEDGATLGPHSVVLPAARLGRGTTVGAGSLVMRGEELPAGTWWLGNPV-----SPWRRPDGD +PAAAATPSREEA-------------------------------- +>GCF_003691675_PROKKA_01172 +MSLSSAAPTPPSVPLDP---AGAPHRPQLPGSERTPPARTLVELFDATAREHPDATALD----DGVEPLTYAELRERVDE +TARHLWAAGVRAGDRVGVRIASGTAALYVSILGVLAAGAAYVPVDADDPEERARLVFGEAKVAGVLTDERVYAPHPEHTA +DPAAEARAPGLEDDAWIIFTSGSTGTPKGVAVSHRSAAAFVDAEARIFLADDPLAPGDRVLAGLSVAFDASCEEMWLAWR +HGACLVPAPRSLVRSGMDLGPWLAERRITAVSTVPTLAAMWPTEAMDNVRLLIFGGEACPPELAARLAEDGREVWNTYGP +TEATVVACAAPLTGLGPVRIGLPLDGWDLAVVDPQTTLPVAEGETGELIIGGVGLARYLDPAKDAEKYAPMPSLGWERAY +RSGDLVVFEPEGLLFVGRADDQVKLGGRRIELGEVDAALQALPGVHGGAAAVQTTPAGHQILVGYLVPADPEAELDLHMA +REHLAAELPAALVPRLAVVDSLPTKTSGKVDRHALPWPLPGAEVDEDAPQPNEDTADGWVLRQWADVLGAPPKDADTDFF +EAGGGSLAAAQLVARLRLRHPAVTVQDVYRNPTAGALVAAVVGDD-GPRGIEVHDRHVDRTRHRT-----QWVQTLVGLP +VF-VLPALRLGVWTGLALNLLTLSGLAPGLPTVPWWVLIVAGLLVVTVPGRMLLTAATARLLLRGVSPGSYPRGGRVHLR +LWLAQQISDLVDPYSLAGATWVPAYARLLGNRIGKDVDMHTVPPVTGMLTVEEGAAIEPEVDLSGYWVDGDVVRLGEVRI +GADAVVGARSTLLPGAQVGAGAHVEAGSTVAGRVRGGQRHAGSPAVKVGKVK-SRGPAEAPRETPGWRLMATVLSTLISL +LPLVSAAAAA--AVAAWSLTWWPPAP------EAGPLAAVGTTAARLLAASPLVAGVWFLTQMLLVLVTVRLLALGITEG +HHPVRSRVGWQVWATERVLDAARDQLFPIYASRFTPTWLRLLGAEVGRGVEASTVVLLPCMTRVGDGAFLADDTMVSSYS +LDGGWMHVAPAKVGKRSFVGNSGMVPGGRTLRRDSLVAVLSTTPAKTKAGTSWMGSPPVRLRRNEVTADAALTYDPPARL +KAARTAWELLRAIPVWLHVALSLAVGATLAALIAVGTWALAFVLGGVVL---------LAAGAVAASLTVLAKRVFVGRI +RAGEHPLWSSFIWRNEVADTFTEFLAAPWFSRAAAGTPALVWFLRAMGARIGHGAWVESYWLPEADLVELGDGATVNRGC +VVQTHLFHDRVMSLDAVVLEDGATLGPHSVVLPAARLGRGTTVGAGSLVMRGEELPAGTWWLGNPV-----SPWRRPDGD +PAAAATPSREEA-------------------------------- +>GCF_005280335_PROKKA_01458 +MSHPSVAPVPPPDPVDPADDAAAVHPPQLPGALRTPPARTLVELFDATAREHPDAPALD----DGVEPLTYAELQARVDE +TARHLWAAGVRTGDRVGVRIASGTAALYVSILGVLAAGAAYVPVDADDPEERARLVFGEARVAGVLTDERVYAPAAVHAP +RPDAEDRAPGLEDDAWIIFTSGSTGTPKGVAVSHRSAAAFVDAEARIFLSEDPLAPGDRVLAGLSVAFDASCEEMWLAWR +HGACLVPAPRSLVRSGMDLGPWLAERRITAVSTVPTLAAMWPTEALDNVRLLIFGGEACPPELAARLAEDGREVWNTYGP +TEATVVACAAPLTGVGPVRIGLPLDGWDLAVVDPATGVPVAEGATGELIIGGVGLARYLDPVKDAEKYAPMPTLGWERAY +RSGDLVVFEPEGLLFVGRADDQVKLGGRRIELGEVDAALQALPGVHGGAAAVQTTPAGHQILVGYLVSADPEADLDLHLA +RERLAEELPAALVPRLALMDALPTKTSGKVDRHALPWPLPGAEPDDEAPQPDEASPHGWVLRQWADVLGAPPSGPDADFF +EAGGGSLAAAQLVARLRLRHPAVTVQDVYRSPTASALAAAVVGEDGGAGGIEVHDRHVASTRHRT-----QWAQTLVGLP +VF-VLPALRLGVWTGLALNLLALTGLAPGLPTVPWWVLAVAGLLVVTVPGRMLVTALAARLLLRGVEPGSHPRGGRVHLR +LWLAQQITDVVDPYSLAGAMWVPAYARLLGNRIGADVDLHSVPPVTGLLTVGEGASIEPEVDLSGYWVDGDVVRIGEVRI +GAGAVVGARSTLLPGARVGAGAHVEAGSTVAGRLRGGQRHAGSPAAKVGKVR-ADGPNVAPPRATGWRAVSTVLSTLVAL +LGLVAAGAAA--AVGAWSLTWWPPAD------PTGPAAAVGVTALRLLAASPLIAAVWFGAQMLLVLGAVRLLSVGITEG +HHPVRSRVGWQIWATERILDAARDHLFPLYASRFTPVWLRLLGAEVGRGVEASTVVLLPGMTRVGDGAFLADDTMVSSYS +LEGGWMHVAPAKVGKRAFVGNSGMVPAGRTLRRDSLVAVLSTTPAKTKAGTSWMGSPPVRLRRTEVAADASVTYAPTARL +KAARTGWELLRAIPVWLHVALTIATGAALAALTAVGTWALAAVLGGAVL---------LAAGAAAASLTVLAKKAFVGRV +RPGEHPLWSSFIWRNEVADTFTEFLAAPWFARAAAGTPALVWFLRAMGARIGRGAWVESYWLPEADLVTLGDGATVNRGC +VVQTHLFHDRVMSLDEVVLADGATLGPNSVVLPAARLGRGTTVGAGSLVMRGEELPAGTWWLGNPV-----SPWRRPDGV +PDPSPAPSREAA-------------------------------- +>GCF_020097155_PROKKA_01366 +M--TAPHPSTPRSAPHD---AGTPHAPQLPGTDRTPPPRTLIDILDATAREHPEAPALD----DSTAQLGYAELLDRVLE +SARFLQAHGIGAGDRVGVRIPSGTAALYVSILAVMAVGAAYVPVDADDPEERARLVFGEARVAGVLTGERALDDRAAAER +AEAPEARAPRLEDDAWIIFTSGSTGTPKGVAVSHRSAAAFVDAEARIFLTADPLGPGDRVLAGLSVAFDASCEEMWLAWR +HGACLVPAPRALVRSGMDLGPWLAERRITAVSTVPTLAAMWPTAALANVRLLIFGGEACPPDLAARLAVPGREVWNTYGP +TEATVVACAAPLAGEGPVRIGLPLDGWDLAVVDPASGVPVAEGETGELIIGGVGLARYLDPAKDAEKYAPMETLGWDRAY +RSGDLVLYDPAGLLFLGRADDQVKVGGRRIELGEVDAALQNLPGVQGGAAAVRTTPAGNQLLVGYLKPTGPLEGFDLDAA +HARLAEELPAAIVPRLALVDSLPTKTSGKVDRNALPWPLPGTAATDDADTPDESTPDGWVLAQWAAVLGAAPADGSTDFF +SAGGGSLAAAQLVARLRERHPGVTVQDVYRHPTADELVSAVLGE--GAEGIEVHERNVDTTRRRT-----QWAQTLVGLP +AF-ILPALRLGTWTGVAVNLLAATGLVPGLPTVPWWILALVGLFVVTAPGRMLVAGLTARALLHGVGPGAHPRGGRVHLR +LWLAQQVTDLVDPYSLAGAGWIPAYGRLLGNRIARDADLHALPPVTGLLTVGEGASIEPEVDLSGYWVDGDVLRVGTVEV +GAGAVVGSRSTLLPGAKVGAGAHVEAGSTVAGRLRGHQRHGGSPAVKLGKVKRGSAPAETAPDAAGWRVLSTLSSTAVAL +LPLAAVAAAA--AVGAWSLTWWPPAAA-----DASPLQAVGTAAARLLAASPLIAAVWFGVQMLLVLVAVRVLAIGITPG +HHPVRSRVGWQIWATERLLDAARDQLFPIYASRFTPTWLRWLGARVGKDVEASTVVLLPTMTQVGDGAFLADDTMVSSYT +LEDGWMHVAPAKVGKRSFVGNSGMVPGGRTLRRDSLVAVLSTTPAKTKAGTSWMGSPPVRLRRTEVEADASLTYAPPARL +KAARTGWELLRAIPVWLHVALTIAVGAALAALAAVGTWWLAALLGGAVL---------LAAGAVAAVVTVLAKRAFVGRV +RAGEHPLWSSFIWRNEVADTFTEFLAAPWFSRAAAGTPAMVWFLRGMGARIGRGAWVESYWLPEADLVTLGDGATVNRGC +VVQTHLFHDRVMALDEVVLADGATLGPNSVVLPAARLGEGTTVGAGSLVMRGEELPGGTWWLGNPV-----APWRRPGKT +PT---AHQRAAA---------ATGALPVIPDPTSAGGIR----- +>GCF_020097155_PROKKA_02442 +MTTQQFHPARAPAAATS---AVESEDRALYPVEPPPAPRTLVDILKATAAAHPDAVALEGHGPGGSAALNYMQLLARAEQ +VAARLREAGIGPGDRVGLRVPSGTTDLYVALVAILLSGAAYVPVDWDDPASRAETVFGEAAVACVIGEGMAITP--VDGV +APLRRTGAPGLEDDAWIIFTSGTTGLPKGVAITHRNAAALVDAEARMYLQDDPLGPGDRVMAGLAVSFDASCEEMWLAWR +HGAALIAAPREVVRSGPDLGAWIAQKRLTAISTVPTLAALWPDDSLVGIRLLIFGGEACPPELVARLATQDRELWNTYGP +TEATVIASGAILRPGQEVRIGLPVPGWKLAVVDP-EGRPVRWGEAGELVIGGVGLGRYLDPEKDAEKYAPLAALGWDRCY +RTGDMVVAEPEGLVFAGRIDDQVKISGKRIELGEVDAHLTAMPGVRAGAAAVQLTDSGTAVLVGYLMP-EKGVELDLPRI +RELMGERLPGGVVPTLAVVDELPMKSSGKVDRTALPWPLP-FDAGEAPPLPEDLR---WLAERWTAVLGPAPLTPESDFF +ALGGSSVAVAHLVTALREHHPQLEFPQVYANPTLAGMADLLAGM--ADSGPRVERRQPAAMPRFTGPAQIAWVTALTGVA +GLRYVAGATVAIW---ALGQFFGAGWVVTPPVLP---TLIAWAVLFSVPGRLYGTALVVRVLNAGLRPGRYRRGGLTHLR +VWAADRAIATARLEYLLGGPAASHVHRVFGTRVGSGAHLDHMPSATGLVRIGHGVSVGAEADLHGHWVEAGTFVLGEIVV +GDHARIGARSIVLPGVRVGSWAEIQAGSRVASSVPAHEYWGGSPLRRLGEAG-VTWPSEDPRAARGVRAWPVALAAAGQM +FTLAVLALLPMVALLPWVVLVLSPLRGATDFRDVLPVMALWVPVVVVLAVP-----TWF----LLVSAFVRLLAPLVKPG +FYPVHSLQAWAAWSIQNVMRRTLIGTYPVYASSATPWLMRLMGARIGRNVEISTVEAIPHLTVVEDGAFLADHSMAAVPR +VGRGWVHIGSTVIGRGSFVGNSAIVGPDRDLPDDALVAVLGVSPHRPAPGTSWLGRSPTAIPRVKVAADAAATFAPPRRL +KAARWAVELCRFVPAFIVGWLDIAVVYFLATVYMGASGQGSDPLRGVVVATVASLPAAVAAALIASAMPVLFKWALVGEF +VPQDRPLFSSFVWRNELMDAFVEVLAVPSLIRIGLGSPVLTMWARWMGVEIGRNAWVESWWLPETDLVSIADNATVNRGT +VLQTHLFHDRVMTMQPVRLDEGATLGPNSFMLPGSSLGPCATVRPGSLVLREDAVPGHSDWSGNPIRAVQDAPAAAATGD +TA---TRARARADHLDADERPQTGPIPVVATSTPA---REEPTS +>GCF_023573625_PROKKA_01390 +MSLSSAAPTPPSVPLDP---AGAPHRPQLPGSERTPPARTLVELFDATAREHPDATALD----DGVEPLTYAELRERVDE +TARHLWAAGVRAGDRVGVRIASGTAALYVSILGVLAAGAAYVPVDADDPEERARLVFGEAKVAGVLTDERVYAPHPEHTA +DPAAEARAPGLEDDAWIIFTSGSTGTPKGVAVSHRSAAAFVDAEARIFLADDPLAPGDRVLAGLSVAFDASCEEMWLAWR +HGACLVPAPRSLVRSGMDLGPWLAERRITAVSTVPTLAAMWPTEAMDNVRLLIFGGEACPPELAARLAEDGREVWNTYGP +TEATVVACAAPLTGLGPVRIGLPLDGWDLAVVDPQTTLPVAEGETGELIIGGVGLARYLDPAKDAEKYAPMPSLGWERAY +RSGDLVVFEPEGLLFVGRADDQVKLGGRRIELGEVDAALQALPGVHGGAAAVQTTPAGHQILVGYLVPADPEAELDLHMA +REHLAAELPAALVPRLAVVDSLPTKTSGKVDRHALPWPLPGAEVDEDAPQPNEDTADGWVLRQWADVLGAPPKDADTDFF +EAGGGSLAAAQLVARLRLRHPAVTVQDVYRNPTAGALVAAVVGDD-GPRGIEVHDRHVDRTRHRT-----QWVQTLVGLP +VF-VLPALRLGVWTGLALNLLTLSGLAPGLPTVPWWVLIVAGLLVVTVPGRMLLTAATARLLLRGVSPGSYPRGGRVHLR +LWLAQQISDLVDPYSLAGATWVPAYARLLGNRIGKDVDMHTVPPVTGMLTVEEGAAIEPEVDLSGYWVDGDVVRLGEVRI +GADAVVGARSTLLPGAQVGAGAHVEAGSTVAGRVRGGQRHAGSPAVKVGKVK-SRGPAEAPRETPGWRLMATVLSTLISL +LPLVSAAAAA--AVAAWSLTWWPPAP------EAGPLAAVGTTAARLLAASPLVAGVWFLTQMLLVLVTVRLLALGITEG +HHPVRSRVGWQVWATERVLDAARDQLFPIYASRFTPTWLRLLGAEVGRGVEASTVVLLPCMTRVGDGAFLADDTMVSSYS +LDGGWMHVAPAKVGKRSFVGNSGMVPGGRTLRRDSLVAVLSTTPAKTKAGTSWMGSPPVRLRRNEVTADAALTYDPPARL +KAARTAWELLRAIPVWLHVALSLAVGATLAALIAVGTWALAFVLGGVVL---------LAAGAVAASLTVLAKRVFVGRI +RAGEHPLWSSFIWRNEVADTFTEFLAAPWFSRAAAGTPALVWFLRAMGARIGHGAWVESYWLPEADLVELGDGATVNRGC +VVQTHLFHDRVMSLDAVVLEDGATLGPHSVVLPAARLGRGTTVGAGSLVMRGEELPAGTWWLGNPV-----SPWRRPDGD +PAAAATPSREEA-------------------------------- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000142.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000142.fa new file mode 100644 index 0000000000000000000000000000000000000000..049fb325be3f64c5e4d5839286fbb81a93b2565c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000142.fa @@ -0,0 +1,43 @@ +>GCF_002008305_PROKKA_01681 +--MRVLVTGGAGYLGSHTVLTLLEAGHDVLVLDSLVTATTTSLERVAELAETRLGGSRLR +LHVADIRRPEDYRGALADFGPAALVHFAGLKSPTESMTRPAAYYDVNVGGTAAVAEAALA +AGARTVLFSSSATVYGDRAPVPVAEDAATDPVSPYGHSKLMAEQVLRDVCATVDGGGLAM +LRYFNPVGAHPSGRLGEDPSGVPANLMPFVARVASGAYPELRVFGADFDTRDGSAVRDFI +HVMDLAEAHVAGLEWLAARVAAGGGTTTRVWNIGRGEGVTVFEMVRAFEAVTGGRIPYRV +VERRPGDIAESCAAVDAIGAEVGWHARRDVTAMVRDLWAWQEANPAGFSPRTE +>GCF_003691675_PROKKA_01385 +--MRVLVTGGAGYLGSHTVLTLLEAGHDVLVLDSLVTATTTSLERVAELAGTRLGGSRLR +LHVADIRRPEDYRGALADFGPAALVHFAGLKSPTESMTRPAAYYDVNVGGTAAVAEAALA +AGVRTVLFSSSATVYGDRAPVPVAEDAATDPVSPYGHSKLMAEQVLRDVCATVDGGGLAM +LRYFNPVGAHPSGRLGEDPSGVPANLMPFVARVASGAYPELRVFGADFDTRDGSAVRDFI +HVMDLAEAHVAGLEWLAARVATGGGTTTRVWNIGRGEGVTVFEMVRAFEAVTGGRIPYRV +VERRPGDIAESCAAVDAIGAEVGWHARRDVTAMVRDLWAWQEANPAGFSSRAE +>GCF_005280335_PROKKA_01197 +MPMRVLVTGGAGYLGSHTVVVLLEAGHDVLVLDSLVAGSTAPLERAAELAGVALGGRRLD +LVVADIRCPADYRAALEAFAPEAMVHFAGLKSPAESLSRPADYYDVNVGGTAAVAAAALA +AGARTVLFSSSATVYGDRAPVPVDETAPTDPVSPYGRSKLMAEQVLRDVCATTDGVGLAM +LRYFNPVGAHPSGRLGEDPRGVPANLMPFVARVATGAYPELQVFGADFPTRDGSAVRDFI +HVMDLAEAHLAALAWLAARRGDGAEPTTRVWNIGRGEGVTVFEMVRAFEEVTGARIPCRV +TARRAGDIAESCAAVDAVGAEVGWRARRDVTAMVRDLWAWQRAHPHGFGTGAA +>GCF_005280335_PROKKA_01209 +--MRVLVTGGAGFLGSHTVSVLLDAGHDVLVLDSLVSSTTVPLERIADLAGVTFGGSRLR +FHRADVREPTSYREAVVAFGPDAVVHFAGLKSPTESLADPASYYTVNVAGTAAVAEVAGG +AGVRAFLFSSSATVYGDEAPVPVGEDAAVAPVTPYGHSKLMAEQVLRHMHEAGRHMGVAV +LRYFNPVGAHPSGRLGEDPQGVPANLMPFVARVAGGRYEQLNVFGADFATRDGSAVRDFI +HVMDLAEAHVATLEWMVAQPGD--EVGVRVWNIGRGEGVTVFEMIQAFERVTGRPVPFQV +VGRRPGDIAASCASVDAIAATVGWRASRDTDAMVRDLWAWQQANPSGYAGDAP +>GCF_020097155_PROKKA_01126 +--MRALVTGGAGYLGSHTVTTLLDAGHDVLVLDSLAGAGRAGLERAAEVCGVGLGGARLR +LVVADIRRPEDWADEVVAWAPDTVVHFAGLKSPTESMASPAEYYSVNVGGTAHVAEAAVR +AGARTLLFSSSATVYGDRAPVPVAESAPIDPVSPYGRSKAMAEQVLTDVHAASPGLSVAS +LRYFNPVGAHPSGRMGEDPQGTPANLMPFVSRVASGAYPELTVFGADFATRDGSAVRDFI +HVMDLAEAHVAALEWMAARPSE--EAGVRVWNIGRGEGVTVFEMVRAFEEVTGRPVPFTV +GGRRAGDIAESCADVGAVARDVGWRARRDVREMVRDLWAWQQAEQEGDGG--P +>GCF_023573625_PROKKA_01610 +--MRVLVTGGAGYLGSHTVLTLLEAGHDVLVLDSLVTATTTSLERVAELAGTRLGGSRLR +LHVADIRRPEDYRGALADFGPAALVHFAGLKSPTESMTRPAAYYDVNVGGTAAVAEAALA +AGARTVLFSSSATVYGDRAPVPVAEDAATDPVSPYGHSKLMAEQVLRDVCATVDGGGLAM +LRYFNPVGAHPSGRLGEDPSGVPANLMPFVARVASGVYPELRVFGADFDTRDGSAVRDFI +HVMDLAEAHVAGLEWLAARVATGGGTTTRVWNIGRGEGVTVFEMVRAFEAVTGGRIPYRV +VERRPGDIAESCAAVDAIGAEVGWHARRDVTAMVRDLWAWQEANPAGFSSRTE + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000150.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000150.fa new file mode 100644 index 0000000000000000000000000000000000000000..2cb2ceb4253b341dfdee6f845dc678d0668b2301 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000150.fa @@ -0,0 +1,37 @@ +>GCF_002008305_PROKKA_01852 +MTTLTAPQADLDALRTPAAAAAHRVA-GERPAAAADATPALSVRDLVLEYPDGERGVLRA +LDEVSLDLLPGTFTAMVGPSGSGKSSLLAVAAGLVTPTSGSVSVAGREMAGLSRKERTAL +RGQEIGVIFQQPNLIPSLTAAEQLELTVHLDRDATRADRRAAKARAMELLERVDLADQAG +KRPHQLSGGQRQRVNIVRALMAS----PTLLLVDEPTSALDRERSAAVVDLLGTLTREEQ +VATLMVTHDHEFLSVTDRTLTMVDGRLSAE------ +>GCF_003691675_PROKKA_01548 +MTALTAPQADLDALRTPAAAAAHRVA-AERPATAADATPALSVRDLVLEYPDGERGVLRA +LDEVSLDLLPGTFTAMVGPSGSGKSSLLAVAAGLVTPTSGSVSVAGREMAGLSRKERTAL +RGQEIGMIFQQPNLIPSLTAAEQLELTVHLDRDATRADRKAARARALELLERVDLADQAR +KRPHQLSGGQRQRVNIVRALMAS----PTLLLVDEPTSALDRERSAAVVDLLGTLTREEQ +VATLMVTHDHEFLSATDRTLTMVDGRLHAE------ +>GCF_005280335_PROKKA_01016 +MTTTLASQTDLDPMRTPAAAAAHRIAPGTAAPDGSGGTPALSVRDLVLEYPDGERGVLRA +LDEVSLDLHAGTFTALVGPSGSGKSSLLAVAAGLVPPTSGTVTVAGRELTGLSRTERTGL +RGREIGVIFQQPNLIPSLTAAEQLELSVHLDRDATRTDRKAARDRAMALLERVDLADQAG +KRPHQLSGGQRQRVNIVRALMAS----PALLLVDEPTSALDRERSAAVVDLLGALTRDEG +TATLMVTHDHEFLAATDRTLTMVDGRLTD------- +>GCF_005280335_PROKKA_01058 +M---------------------------------STTTPVIQLSSVTKTYQRRD-----L +YTDASVTVIPGRAHAIVGPNGSGKSVMMRLMCGFLLPSSGSVTIDPRYLDG----RRT-- +FPDKFGVVIDKPGMLPHLTGLENL-------RRLAEIQKKIGDERIREVMQSFGLDPDAR +QRVHQYSLGMKQKLNLCQAVMED----PEVLVLDEPFNALDADSADALRGRLASFVADGG +TLVFTSHDSRDVEQLADSVIRLENGRVTQEDASPRT +>GCF_020097155_PROKKA_00958 +M-TISTHTPDLSAYRSPAAA---RVTAHDAAPAAPDAAPVLSVRDLVLEYPDGEGRTLRA +LDGVSLDLTPGTFTAMIGPSGSGKSSLLAVAAGLIAPTSGSVTVAGTELTGLSRAARTRL +RGDRIGVVFQQPNLLPSLTAREQLELVVRLDPKSTRADRTAAAARAQELLERVDLGRRAD +QRPHQLSGGQRQRVNIVRALMGTGSGAPALLLVDEPTSALDRERSAAVVELLGELTRQEG +VATLMVTHDHEFLGATDRVLTMVDGRLAA------- +>GCF_023573625_PROKKA_01772 +MTTLTAPQADLDALRTPAAAAAHRVA-GERPAAAADATPALSVRDLVLEYPDGERGVLRA +LDEVSLDLLPGTFTAMVGPSGSGKSSLLAVAAGLVTPTSGCVSVAGREMAGLSRKERTAL +RGQEIGMIFQQPNLIPSLTAAEQLELTVHLDRDATRADRRAAKARALELLERVDLADQAG +KRPHQLSGGQRQRVNIVRALMAS----PTLLLVDEPTSALDRERSAAVVDLLGTLTREEQ +VATLMVTHDHEFLSATDRTLTMVDGRLSAE------ + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000153.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000153.fa new file mode 100644 index 0000000000000000000000000000000000000000..ea775a02d62050d1322de76fd875209313d6610a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000153.fa @@ -0,0 +1,54 @@ +>GCF_002008305_PROKKA_01975 +MPPSQDAASLTQLGVIGVILLVVLFYGGTMIMSVAISKKKENADAYMTAGNQIGFGVSAASMTATWIWAASMYASVTAGY +TYGVSGPLHYGL-------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------- +>GCF_002008305_PROKKA_01976 +-------------------------------------------------------------------------------- +----------------MILFIYPFGRRIRAVAPRAHTLAEVMYARHGRSSQLMLAGSNVLGSVISLTSNFIAGGALISLL +SPLSFGAGILIVAAGVLLYTLWSGFRASVLTDFAQVMAMLGATVIIIPAVFFAAGGPDMFQAGVEAGHVTAQQQSFFSSD +AFMNQGAPYIAAVLAYAIGNQTIAQRLFAVREDLIKPTFITATLGYGGTVIGVGMLGVMALYLGVEPLDGDVNNLLPQMV +ADHLPLALVALAFLMIIGSLSSTADSDLSALSSIVMTDVYGQSVGRKNADPKTMLLIGRITMIVATAAALYFATAKFDIL +DLLVFVGALWGCLVFPVIASFYWGRITNVAFTVSVLAALTVFLPVRFEWIPIEGAWAFVVETLAILGVGVVLCIMCFGFF +GLRPAVVVGAIASVVMLFLGYGFLRDYATLTGSLVAYAVSFLVCWGLSVRSGQDFDFDRIARVTGDFDPATEDL---PQV +ERASAPVS +>GCF_003691675_PROKKA_01669 +MPPSQDAASLTQLGVIGVILLVALFYGGTMIMSVAISKKKENADAYMTAGNQIGFGVSAASMTATWIWAASMYASVTAGY +TYGVSGPLHYGLWGALMILFIYPFGRRIRAVAPRAHTLAEVMYARHGRSSQLMLAGSNVLGSVISLTSNFIAGGALISLL +SPLSFGAGILIVAAGVLLYTLWSGFRASVLTDFAQVMAMLGATVIIIPAVFFAAGGPGMFQAGVEAGHVTAQQQSFFSSE +AFMNQGAPYIAAVLAYAIGNQTIAQRLFAVREDLIKPTFITATLGYGGTVIGVGMLGVMALYLGVEPLDGDVNNLLPQMV +ADHLPLALVALAFLMIIGSLSSTADSDLSALSSIVMTDVYGQSVGRQNADPKTMLLIGRITMIVATAAALYFATAKFDIL +DLLVFVGALWGCLVFPVIASFYWGRITNVAFTASVLAALAVFLPVRFEWIPLEGAWAFVVETLAILGVGVVLGIMCFGFF +GLRPAVVVGAIASVVMLFLGYGFLRDYATLTGSLVAYAVSFLVCWGLSVRSGQDFDFDRIARVTGDFDPATEDL---PQV +ERASASVS +>GCF_005280335_PROKKA_00882 +MPPSQDGAELVQLGVIGVIVLVVFFYGGTMLMSLAISRRKENADAYMTAGNKIGFGVSAASMTATWIWASSMYASVTAGY +TYGVSGPIHYGLWGALMILFIYPFGRRIRKVAPRAHTLAEVMYARHGRSSQLMLAGSNVLGSVISLTSNFIAGGALIAIL +SPLSFGAGILIVAAGVLLYTLWSGFRASVLTDFAQVMAMLGATVVIIPAVFFAAGGPGMFEAGVQAGNVTAQQQDFFSSE +AFMNQGAPYIAAVLAYAIGNQTIAQRLFAVREDLIKPTFITATVGYGGTVIGVGMIGVMALYLGVQPLDGDVNNLLPQMV +SSYLPLLVVALAFLMIIGSLSSTADSDLSALSSIVMTDVYGQSVGRENANPKTMLLIGRVTMIVATAAALYFATARFNIL +DLLVFVGALWGCLVFPVIASFYWRKVTNAAFTVGVLAALAVFLPVRFEWIPLTGAWALVVEALAILGVGVVLGIMAFGFF +GLRAAVVVGALATAATAFVGFGFLRDYATLSGSLVAYAVSFLVCWGMSVRSGQDFDFDRIARVTGDFDPATDDAADRPVA +QPAGARAS +>GCF_020097155_PROKKA_00817 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +--------------------------------MSVLAALAVFLPVRFEWFPLEGAWAFVVETLAILGVGVALGIMCFGFF +GLRPAVVVGAIASVVMLFLGYGFLRDYATLTGSLVDYAVSFLVCWGLPVRSGQDFDFDQIARVTGDFDPATEDL---PQV +ERVAASVS +>GCF_023573625_PROKKA_01901 +MPPSQDAASLTQLGVIGVILLVALFYGGTMIMSVAISKKKENADAYMTAGNRIGFGVSAASMTATWIWAASMYASVTAGY +TYGVSGPLHYGLWGALMILFIYPFGRRIRAVAPRAHTLAEVMYARHGRSSQLMLAGSNVLGSVISLTSNFIAGGALISLL +SPLSFGAGILIVAAGVLLYTLWSGFRASVLTDFAQVMAMLGATVIIIPAVFFAAGGPDMFQTGVEAGHVTAQQQSFFSSD +AFMNQGAPYIAAVLAYAIGNQTIAQRLFAVREDLIKPTFITATLGYGGTVIGVGMLGVMALYLGVEPLDGDVNNLLPQMV +ADHLPLALVALAFLMIIGSLSSTADSDLSALSSIVMTDVYGQSVGRQNADPKTMLLIGRITMIVATAAALYFATAKFDIL +DLLVFVGALWGCLVFPVIASFYWGRITNVAFTASVLAALAVFLPVRFEWIPIEGAWAFVVETLAILGVGVVLGIMCFGFF +GLRPAVVVGAIASVVMLFLGYGFLRDYATLTGSLVAYAVSFLVCWGLSVRSGQDFDFDRIARVTGDFDPATEDL---PQV +ERASAPAS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000167.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000167.fa new file mode 100644 index 0000000000000000000000000000000000000000..650659c5696187001eb5b82633737b958b6076f4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000167.fa @@ -0,0 +1,84 @@ +>GCF_002008305_PROKKA_02184 +MDFSAPLDP-TPAAP-PAADAPPADVVARLQAELPGRVDVSAAALEAARADRSGHRSPAAPLAVVRARTVEDVQAACRIA +HGTRTPLVTRGAGTGLAGGAVAGAGEIVLDMTAMDRILEVSPADRVAVVEPGILNGALNAALAEHGLWWAPDPASKDIST +VGGNIAMNAGGLLCAKYGVTREAVLGLDVVLADGT-----------------------LLRLGHR--------------- +TVKGVTGYDLVALM-------------IGSEGTLGVIVGATLA--LRPAVRGVPVTLGGFFPDVVAGAAAAEAITGAGHV +PALMELMDEATLAAVRAHAG--PERGAALPESGAFLLVQADGAGAEADGEAMAALMRTHGGDVT----------VTVDPA +EGEALMALRRTAFPALE----RLGTPLVEDVAVPRSRMAEMFARIREIEARTGVAIPTT-AHAGDGNLHPILLFGAAAQV +GGAAEDAASIPADVWEAAG---ELFRAGLELGGTLTGEHGVGLLKRAFLRDELGDAQHDLQQRIKAVFDPHGILNPGKVF +-----------------------------------------TP------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------ +>GCF_003691675_PROKKA_01898 +MDFSAPLAPAAPLAPAPAADAPPADVVARLQAELPGRVDVSAAALQAARADRSGHRSPAAPRAVVRARTVEDVQAACRIA +HGTRTPLVTRGAGTGLAGGAVAGAGEIVLDMTAMDRILEVSPADRVAVVEPGILNGALNAALAEHGLWWAPDPASKDIST +VGGNIAMNAGGLLCAKYGVTREAVLGLDVVLADGT-----------------------LLRLGHR--------------- +TVKGVTGYDLVALM-------------IGSEGTLGVIVGATLA--LRPAVRGVPVTLGGFFPDVVAGAAAAEAITGAGHV +PALMELMDEATLAAVRAHAG--PERGAALPESGAFLLVQADGAGAEADGEAMAALMRAHGGDVT----------VTVDPA +EGEALMALRRTAFPALE----RLGTPLVEDVAVPRSRMAEMFARIREIEARTGVAIPTT-AHAGDGNLHPILLFGAAAQV +GGAAEDAASIPADVWEAAG---ELFRAGLELGGTLTGEHGVGLLKRAFLRDELGDAQHDLQQRIKAVFDPHGILNPGKVF +-----------------------------------------TP------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------ +>GCF_005280335_PROKKA_00566 +MD-----SPASPGAP-HPETTRPADVVARLQAALPGRVDVSPPPSRPPARDRSGHRSPAVPLAVVHAASVADVQAVCRLA +HETRTPLVTRGAGTGLAGGAVAGAGEVVLDVMGMDRILEVSPADRVAVVEPGILNGALNAALAEHGLWWAPDPASKDIST +VGGNIAMNAGGLLCAKYGVTREAVLGLDVVLADGT-----------------------LMRLGHR--------------- +TVKGVTGYDLTALM-------------IGSEGTLGVIVGATLS--LRPAVRGTQVTLGGFFPDVVAGAAAAEAVTGAGHV +PALMELMDEVTLAAVRADAG--PERGAALPESGAFLLVQADGAGAEEDGAAMADLMRAHGGDVT----------VTADHA +EGEALMALRRTAFPALE----RLGTPLVEDVAVPRSRMAEMFARIRDIEARTGIPIPTT-AHAGDGNLHPILLFGAAAQV +GGAAEDATSIPADVWEAAG---ELFRAGLELGGTLTGEHGVGLLKRAFLRDELGDAQHALQAKIKAVFDPHGILNPGKVF +-----------------------------------------TP------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------ +>GCF_020097155_PROKKA_00491 +MT--------------CIISVSPDDVLHRLRAALGDAVVTDPAALEPLRADRSGHRSPGAPLAAVRARTVEDVQAACRIA +HATGTPLVTRGAGTGLAGGAVAGPGQVVLDLSGMDRILEVAPEDRVAVVEPGVLNGALNRALEPHGLWWAPDPASKEIST +VGGNIAMNAGGLLCAKYGVTREAVLGLAVVLADGT-----------------------LMRLGHR--------------- +TVKGVTGYDLTALM-------------IGSEGTLGVIVEATLA--LRPLPEGAVHTLGAFFPDVAVGARAAAAITGAGHV +PAIMELMDEATLAAVRAHVS--ADDAARLPETGAFLLVQADGPGADEQAAAMAELIRSAGGEVT----------VTADPA +EADRLVSLRRTAFPALE----ALGTPLVEDVAVPRSRMPEMFARIREIEAETGLRIPTS-AHAGDGNLHPVVLFGEPSRV +GGEDGAQEAIPAEVWAAAG---MLFRAGLELGGTLTGEHGVGLLKRAFLKEELGEAQHGLQERIKAVFDPRGILNPGIVF +-----------------------------------------TP------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------ +>GCF_023573625_PROKKA_00166 +MLRSL------------------EDVLTK-----PGQVSGRALDRHAAAADASHFL--LVPEAVVTPTDAAEVGALMRAS +AAQGVSLTFRSGGTSLSGQAVTDS--VLVDVRKNFRDIEVLDEGARVRVRPGATVRQVNARLARHGRRLGPDPASEAACT +IGGVVANNSSGMNCGITENTYQTLESMTLVLPSGTVIDTAAPDADGILRHHEPHLYRGLAQLADRVRSDSASVATVRRQF +SMKNTMGYGLNALLDFDTPAQILAHLAIGSEGTLGFVAEAVFRTVVRPTHSATALLV---FEELQAANEALPALVDSR-- +AATVELLDATSLRVGQRLTGTPPIVRDLRVQDHAALLVEYSATTAEQ-----LEELRQHGEALTGRIGLSQPAGFTTDAD +ARAALWHLRKGLYASVAGARPQGTTALLEDIVVPVLALGRTCTALTQLFDRYDYRDSVIFGHAKDGNVHFML-------- +----TDDFADPARLQRYSDFTEDMVDLVLGEGGSLKAEHGTGRVMAPYVRRQYGDELYGVMREIKQLCDPGGVLNPGVLL +NDDPQAHLRHIKAEPSVAEEVDRCVSCGYCEPVCPSRDLTLTPRQRIVTLRAIRSARLAGDEALAQSLEEDYDYAAVQTC +AVDGMCQTACPVEINTGDLVKRLRRQETGAVAQAGWNLAAQHWGTASIVAGRALDLAAKLPAAATITANQLVRRIAGADS +VPLYSPELPRGGGRRRRPAPVGEPVAVYFPACVSAMFGPAQPGTGAPGAAGVQDSVLALAQRAGVELLVPSDIDALCCGT +PWSSKGKHTGQETITGRTIAALRRDSDHGRLPIVCDASSCTEGLRHALEVEVPPAGQQPLRILDAVEFTAEHLLPRLPEP +RRIPSLTLHPTCSSTRMGLNPALARVAEAIAEDVQIPDDWGCCAFAGDRGLLHPELTASATARQAEQVQAIDASAHASCN +RTCELGMSRATGYPYSHVLELLNQSTIAGG +>GCF_023573625_PROKKA_02129 +MDSSAPLDP-TRAAP-PAADAPPADVVARLQAELPGRVDVSAAALEAARADRSGHRSPAAPLAVVRARTVEDVQAACRIA +HGTRTPLVTRGAGTGLAGGAVAGAGEIVLDMTAMDRILEVSPADRVAVVEPGILNGALNAALAEHGLWWAPDPASKDIST +VGGNIAMNAGGLLCAKYGVTREAVLGLDVVLADGT-----------------------LLRLGHR--------------- +TVKGVTGYDLVALM-------------IGSEGTLGVIVGATLA--LRPAVRGVPVTLGGFFPDVVAGAAAAEAITGAGHV +PALMELMDEATLAAVRAHAG--PERGAALPESGAFLLVQADGAGAEADGEAMAALMRTHGGDVT----------VTVDPA +EGEALMALRRTAFPALE----RLGTPLVEDVAVPRSRMAEMFARIREIEARTGVAIPTT-AHAGDGNLHPILLFGAAAQV +GGAAEDAASIPADVWEAAG---ELFRAGLELGGTLTGEHGVGLLKRAFLRDELGDAQHDLQQRIKAVFDPHGILNPGKVF +-----------------------------------------TP------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +------------------------------ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000170.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000170.fa new file mode 100644 index 0000000000000000000000000000000000000000..ca025d5eeda08baebe218fd0fedf06f9928707aa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000170.fa @@ -0,0 +1,43 @@ +>GCF_002008305_PROKKA_02303 +MA-----PTAQDQSVHNVVIVGSGPAGYTAAIYTARAELSPVLVAGAVTAGGELMNTTEV +ENFPGFPEGVQGPELMANLEAQARRFNTEVVYDDVVQADLTSNPKVLTLGDGTQLRTHAV +ILTTGSAYRKLGVPGEERLSGHGVSWCATCDGFFFREQEIAVVGGGDSAMEEALFLTKFA +SKVTVLVRKDELRASKVMAHRAMENEKIEFRWNTEVTEVTGDDKVNTLRLRDTRTGEAST +LDVTGLFVAIGQDPRTDLVQGQVELTEHGTIRIDHPSSRTSQPGVFAAGDVTDHTYRQAV +TAAGSGCVAAQDVEHYLATVADVEEAAPAGPESDANPA +>GCF_003691675_PROKKA_01996 +MA-----PTAQDPSVHNVVIVGSGPAGYTAAIYTARADLSPVLVAGAVTAGGELMNTTEV +ENFPGFPEGVQGPELMANLEAQARRFDTEVVYDDVVQADLTSNPKVLTLGDGTQLRTHAV +ILTTGSAYRKLGVPGEERLSGHGVSWCATCDGFFFREQEIAVVGGGDSAMEEALFLTKFA +SKVTVLVRKDELRASKVMAHRAMENEKIEFRWNTEVTEVTGDDKVNTLRLRDTRTGEAST +LDVTGLFVAIGQDPRTDLVQGQVELTEHGTIRIDHPSSRTSQPGVFAAGDVTDHTYRQAV +TAAGSGCVAAQDVEHYLATVADVEEAAPAGPESDANPA +>GCF_005280335_PROKKA_00434 +MA-----PTAQDQSVHNVVIVGSGPAGYTAAIYTARAHLQPVLVAGSVTAGGELMNTTEV +ENFPGFPEGIQGPELMANLEAQARRFDTEVLYEDVVKADLTASPKVLTLGDGTELRAHAV +ILTTGSAYRKLGVEGEERLSGHGVSWCATCDGFFFREQEIAVVGGGDSAMEEALFLTKFA +SKVTVLVRKDELRASKVMARRALENEKIEFRWNTEVAEVIGGEKVQTLRLRDTQTGEEST +LDVTGLFVAIGQDPRTDLVQGQLELTEHGTIRIEHPSSRTSLPGVFAAGDVTDHTYRQAI +TAAGSGCVAAQDVEHYLATVADVEEAAPAGPDSDANPA +>GCF_005280335_PROKKA_00739 +MSTTSTDTTSTEQATDQLIIIGSGPAGYTAAIYAARAGLAPRVIAGSVTHGGALMNTTEV +ENFPGFPGGIQGPELMAGLAEQAARFGAVIEYDDADTVQLKQHLKEVTTLAGKTYRAPAV +IVATGSAYRELGLPEEKKLSGHGVSWCATCDGFFFREQDIIVVGGGDSAMEEALFLTRFA +KSVTVVVRRDALRASKIMAARAKDNEKIRFAYNSAVTAIHGTDKVTGVTLADTITGDTRE +VAATGVFVAIGHLPRTELVAGQLDLDDEGYIVVDARTTHTNLSGVFACGDAVDHRYRQAI +TAAGTGCAAALDAERYLAALHDAYSIATALVEEPTH-G +>GCF_020097155_PROKKA_00386 +MT-----TAEQDQQVRNVAIIGSGPAGYTAAIYTARANLSPVLLAGSVTAGGELMNTTEV +ENFPGFPEGIQGPELMANLEAQARRFDTEVVYDDVVQADLTSDPKVLTLGDGSQIRAHAV +IMTTGSAYRELGVEGEKRLSGHGVSWCATCDGFFFREQEIAVAGGGDSAMEEALFLTKFA +SKVHVLVRRGELRASKIMAQRALEEPKIEFHWNTEVAEVQGDDKLSTLTLRDTVTGEESS +LEVTGLFVAIGHDPRTDLVKGQLELTEHGTIRIDHPSSRTSVPGVFAAGDVTDHTYRQAI +TAAGSGCVAAQDVEHYLATVADVAEAAPAAPDSDSV-A +>GCF_023573625_PROKKA_02244 +MA-----PTAQDQSVHNVVIVGSGPAGYTAAIYTARADLSPVLVAGAVTAGGELMNTTEV +ENFPGFPEGVQGPELMANLEAQARRFNTEVVYDDVVQADLTSNPKVLTLGDGTQLRTHAV +ILTTGSAYRKLGVPGEERLSGHGVSWCATCDGFFFREQEIAVVGGGDSAMEEALFLTKFA +SKVTVLVRKDELRASKVMAHRAMENEKIEFRWNTEVTEVTGDDKVNTLRLRDTRTGEAST +LDVTGLFVAIGQDPRTDLVQGQVELTEHGTIRIDHPSSRTSQPGVFAAGDVTDHTYRQAI +TAAGSGCVAAQDVEHYLATVADVEEAAPAGPESDAVPA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000180.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000180.fa new file mode 100644 index 0000000000000000000000000000000000000000..5fac87d82275b1f177d788ccf2164660344fd405 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000180.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00007 +MSTSASSRPGQGRSTGKAAEPRSGRPVRKASG-SSQEDLVRAVPKAKVRRARLVLTRVDP +WSVLKLAFLLSVALGILTVVAAVALYSLSDVLGIFDRVNDVIGTVLGSEAGRYTVASLAP +LSTVTSLATVLAVVNVILLTALATVAALLYNLCASLVGGIGVTLTDD +>GCF_003691675_PROKKA_02012 +MSTSASSRPGQGRSTGKAAEPRSGRPVRKASG-SSQEDLVRAVPKAKVRRARLVLTRVDP +WSVLKLAFLLSVALGILTVVAAVALYSLSDVLGIFDRVNDVIGTVLGSEAGRYTVASLAP +LSTVTSLATVLAVVNVILLTALATVAALLYNLCASLVGGLGVTLTDD +>GCF_005280335_PROKKA_00417 +MSTSASSRPGKAAGAGRTAE-RSGRPVRKASG-SSQENLVRAVPKAKVRRARLMLNRVDP +WSVLKLAFLLSVALGILTVVAAVALYSLSDALGLFQRINDALGTVLGAESGRYTVQSLAP +LSTVVSLATVLAVLNVILLTALATVAALLYNVCAALVGGVGVTLTDD +>GCF_020097155_PROKKA_00369 +MSTSASSRPAGAKGAS------ASRPARRSSSRDSQEDLVRAVPKAKVRRARLQLTKVDP +WSVLKLAFLLSVALGIILVVATVGFYTLAELTGVFGKINDVLGTVLGTESGTYTVENLAP +LSTVVSLATVVAVLNVILLTALGVVGALLYNVCASLVGGVGVTLADD +>GCF_023573625_PROKKA_00007 +MSTSASSRPGQGRSTGKAAEPRSGRPVRKASG-SSQEDLVRAVPKAKVRRARLVLTRVDP +WSVLKLAFLLSVALGILTVVAAVALYSLSDVLGIFDRVNDVIGTVLGSEAGRYTVASLAP +LSTVTSLATVLAVVNVILLTALATVAALLYNLCASLVGGLGVTLTDD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000191.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000191.fa new file mode 100644 index 0000000000000000000000000000000000000000..4d8b3d0cee576b3f2bac69fafcbe246e84ce4554 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000191.fa @@ -0,0 +1,51 @@ +>GCF_002008305_PROKKA_00022 +MTEVISPARPRRNIELVLLLAALTIALGADLLGMIGTDAPLDSTAWVPLGIFGAATLVLH +VVLRLRAPYADPFMLPITALLNGLGLAMIHRLSQDAAMANPTSQLVWSVLAVLVASALVF +LVRDHRVLRRWPYLFLAASGVLLLLPLVPGLGLSMYGARIWIDVGFGTFQPGEIAKITLA +IFFAGYLSANRDLILLAGRRVGPVTFPRARDLGPLLAGWLLALGVLVFQRDLGSALLFFG +MFMAMLYIATSRASWILLGLGLIAFGAALAFLFMPHVTARFEIWLRAFDPEIYHRDFGGS +YQVVQGLFAMASGGLMGTGLGAGNPTQVPLSFSDMILTAIGEELGFVGLAAVLVLYLLLV +TRMMRAALGVRDAFGKVLASGLAFTMAWQVFVVMGGVTLVLPLTGLTTPFLAAGGSSLLA +NWIIVGLVLRISNAARRPVVVDGMVNASGPGAGHLDPGTALPAAAVPPG--------GGE +ER +>GCF_003691675_PROKKA_02040 +MTEVISPARPRRNIELVLLLAALAIALGADLLGMIGTDAPLDSTAWVPLGVFGAATLVLH +VVLRLRAPYADPFMLPITALLNGLGLAMIHRLSQDAAMANPTSQLVWSVLAVLVASALVF +LVRDHRVLRRWPYLFLAASGVLLLLPLVPGLGLSMYGARIWIDVGFGTFQPGEIAKITLA +IFFAGYLSANRDLILLAGRRVGPVTFPRARDLGPLLAGWLLALGVLVFQRDLGSALLFFG +MFMAMLYIATSRASWILLGLGLIAFGAALAFLFMPHVTARFEIWLRAFDPEIYHRDFGGS +YQVVQGLFAMASGGLMGTGLGAGNPTQVPLSFSDMILTAIGEELGFVGLAAVLVLYLLLV +TRMMRAALGVRDAFGKVLASGLAFTMAWQVFVVMGGVTLVLPLTGLTTPFLAAGGSSLLA +NWIIVGLVLRISNAARRPVVVDGMVNASGPGAGHLDPGTALPAAAVPPG--------GGE +ER +>GCF_005280335_PROKKA_00374 +MTEVISPARPRRNIELVLLLAALAIALGADLLGTIGTDAALDSTAWVPLGIFGAATLVLH +VVLRLRAPYADPFMLPITALLNGLGLAMIHRLSQDAAMANPTSQLVWSVLAIVVASALLF +LVRDHRVLRRWPYLFLAASGVLLLLPLVPGLGLSMYGARIWIDVGFGTFQPGEIAKITLA +IFFAGYLSANRDLILLAGRRVGPVTFPRARDLGPLLAGWLLALGVLVFQRDLGSALLFFG +MFMAMLYIATSRASWILLGLGLIAFGAALAFLFMPHVTARFEIWLRAFDPEIYHRNFGGS +YQVVQGLFAMASGGLMGTGLGAGNPTQVPLSFSDMILTAIGEELGFVGLAAVLVLYFLLV +TRMMRAALGVRDGFGKVLASGLAFTMAWQVFVVMGGVTLVLPLTGLTTPFLAAGGSSLLA +NWIIVGLVLRISNAARRPVVVDGMVNASGPGAGHLDPGTALPAAAVPMR--------GGE +AR +>GCF_020097155_PROKKA_00356 +MTEVISPPRPRRATELMLLLGAVALTLGADLLGTYTTTGALESTAWVPLTVFGCASLVLH +AVLRLRARYADPFILPIATLLNGLGIAMIHRLSADTAAARPTSQLAWSVLAVLVAAALVF +LVRDHRMLRRWPYVFLAVSGVLLLLPLVPGLGLSANGARIWINVGVGTFQPGEIAKITLA +IFFAGYLSTNRDLILLAGRRVGPMTFPRMRDLGPLLVAWAVAMGVLVFQRDLGSALLFFG +MFMAMLYIATSRASWVLLGLSLVAVGAAVAFLFLPHVTARFEIWLNAFDPEIYRRDFGGS +YQVVQGLFAMASGGLLGTGLGGGNPTQVPLSFSDMILAAIGEELGLVGLSAVLVLYLLLV +TRMARAALGVRDAFGKVLAAGLAFTMAWQVFVVMGGVTLVLPLTGLTTPFLAAGGSSLLA +NWIILGLVLRISHAARRPAVVDGMVNASGPGAGHLDPGAALPEPAQRPGPWRAAAPAGGE +AR +>GCF_023573625_PROKKA_00022 +MTEVISPARPRRNIELVLLLAALAIALGADLLGMIGTDAPLDSTAWVPLGIFGAATLVLH +VVLRLRAPYADPFMLPITALLNGLGLAMIHRLSQDAAMANPTSQLAWSVLAIVVASALVF +LVRDHRVLRRWPYLFLAASGVLLLLPLVPGLGLSMYGARIWIDVGFGTFQPGEIAKITLA +IFFAGYLSANRDLILLAGRRVGPVTFPRARDLGPLLAGWLLALGVLVFQRDLGSALLFFG +MFMAMLYIATSRASWILLGLGLIAFGAALAFLFMPHVTARFEIWLRAFDPEIYHRDFGGS +YQVVQGLFAMASGGLMGTGLGAGNPTQVPLSFSDMILTAIGEELGFVGLAAVLVLYLLLV +TRMMRAALGVRDAFGKVLASGLAFTMAWQVFVVMGGVTLVLPLTGLTTPFLAAGGSSLLA +NWIIVGLVLRISNAARRPVVVDGMVNASGPGAGHLDPGTALPAAAVPPG--------GGE +ER + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000192.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000192.fa new file mode 100644 index 0000000000000000000000000000000000000000..b40647cbb9589804db1a47803a9fdcbfd010bbcb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000192.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_00023 +MTLVLRYAARSDVGRVRAKNDDSAYVGRHLVVLADGMGGHVGGDVASASTVLDLAPLDAVGYEDPATVLPDEIQNANLIL +NELVHANPKLAGMGTTCTAALLAGTTLHIAHIGDSRAYRLANGEFSQVTTDHTFVQKLVDEGRLEAGEAPFHPNKNVLMR +VLGDVDASPELDVFEVPVAPGERWLFCSDGLTDVVSPEKIHEVLRDSEALNQAVDTLVDLTLKGGAPDNVTVVAFEIAEG +TAEELAPVPDVHLSEQALAAAHPPEVGPVSGLLLREDLDARPHLLVGAASNAVRTDRIPVVTRSSTRRRAAALLGETPVP +ENRPRRTAAVLT-----DGPDP--DVAARPDPSAPPAAPRGTAAAVGSSSAATPAATAADQPSDEAAEASATAPTPAPAT +SGPAGGPEDGAARRRRGKDDRPVQYRRGWFIPVFTTLLALTLAAVAVWGYLWTQTQYYVGANDGRIAVFKGVSQRLGPLE +LSHVDRQTDLPVDALPAYARDRVNAGMPARDVDHAEQIVAELRDSLHPNAPAPAGEPSERARPSTTPSSSSARPSDASGS +TAPTSPASSPSATGGEAP +>GCF_003691675_PROKKA_02041 +MTLVLRYAARSDVGRVRAKNDDSAYVGRHLVVLADGMGGHVGGDVASASTVLDLAPLDAVGYEDPATVLPDEIQNANLIL +NELVHANPKLAGMGTTCTAGLLAGTTLHIAHIGDSRAYRLADGEFSQVTTDHTFVQKLVDEGRLEAGEAPFHPNKNVLMR +VLGDVDASPELDVFEVPVAPGERWLFCSDGLTDVVPPEKIHEVLRDSEALNQAVDTLVDLTLKGGAPDNVTVVAFEIAEG +TAEELAPVPDVHLSEQALAAAHPPEVGPVSGLLLREDLDARPHLLVGAASNAVKTDRIPVVTRSSTRRRAAALLGETPVP +ENRPRRTAAVLT-----DGPDP--AAAPRPDASVPPAAPSGTAAAAGSSSAATPAATAADHPSDEAAEPMTTAPTPAPAT +AGPAGGPEDGAARRRRGKDDRPVQYRRGWFIPVFTTLLALTLAAVAVWGYLWTQTQYYVGANDGRIAVFKGVSQRLGPLE +LSHVDRQTDLPVDALPAYARDRVNAGMPARDVDHAEQIVAELRDSLHPNAPAPAGEPSERARPSTTPSSSSARPSDASGS +TAPTSPASSPSATGGEAP +>GCF_005280335_PROKKA_00373 +MTLVLRYAARSDVGRVRAKNDDSAYVGRHLVVLADGMGGHVGGDVASASTVLDLAPLDAVGYEDPATVLPDEIQNANLIL +NELVHANPKLAGMGTTCTAGLLAGTTLHMAHIGDSRAYRLADGEFSQVTTDHTFVQKLVDEGRLEAGEAPFHPNKNVLMR +VLGDVDASPELDVFEVPVAPGERWLFCSDGLTDVVSSEKIHEVLRDSEALNQAVDTLVDLTLKGGAPDNVTVVAFEIAEG +TAEEMAPVPDVHLTEQALAAAHPPEVGPVSGLLLREDLDARPHLLVGAASNAVKTDRIPVVTRSSTRRRAAALLGETPVP +ENRPRRTAAVLT-----DGPDR--DAAPRPDASAPPAAPSGTAAAAGSSSAAAPTATVADHPSDEAAEVSTRAATPAPAT +AGPAGGSQDGAARRRRGKDDRPVQYRRGWFIPVFTTLLALTLAAVAVWGYLWTQTQYYVGANDGRIAVFKGVSQRLGPLE +LSHVDRQTDLPVDALPVYARDRVNAGMAARDVDHAEQIVAELRDSLHPDAPAPAGEPSERAQPSTTPSSSSARPSDASGS +AAPTSPTASPSATGGEAP +>GCF_020097155_PROKKA_00355 +MTLVLHHAARTDVGRVRSKNDDSAYAGRHLAVLADGMGGHVGGDVASASTVLDLAHLDDVGYEDPATVLPDEIQNANLVL +TSLVHANPKLAGMGTTCTAGLLAGEVLHMAHIGDSRAYRLKDGEFTQVTRDHTFVQKLVDEGRLEAAEAQFHPNKNVLMR +VLGDVDASPELDVFEVPVAPGERWLLCSDGLTDVLSVERIRELIEPPATLAEAADALVAHTLRGGAPDNVTVVVFDVAEG +SPEELEPAGEVHLSDEALAAAHPADRGPVSGRLLAEELDARPHELVGAADAAVHSDRIPVVTRSATRRRAGVLLGESPVP +ENRPRRTAAHLTAPNASDVDDA--PAAPLTAAASPIETPAPADAATETPAVDAP----APAPGPEVDPADADAAPAPAAD +PAPAHAVETGRTSRRR-RRDRPVEYRRGWFIPVFTALLALILVVVAVWSYLWTQTQYYVGEDAGSVAVFQGVPQQLGPLE +LSHLDHTTDIPLDRLPAYAQERVGRGMAATDRAHADQIVEELR-TVSDTAAKGGGTP----------------------- +------------------ +>GCF_023573625_PROKKA_00023 +MTLVLRYAARSDVGRVRAKNDDSAYVGRHLAVLADGMGGHVGGDVASASTVLDLAPLDAVGYEDPATVLPDEIQNANLIL +NELVHANPKLAGMGTTCTAGLLAGTTLYMAHIGDSRAYRLVDGEFCQVTTDHTFVQKLVDEGRLEAGEAPFHPNKNVLMR +VLGDVDASPELDVFEVPVAPGERWLFCSDGLTDVVSPEKIHEVLRDSEALNQAVDTLVDLTLKGGAPDNVTVVAFEIAEG +SAEELAPVPDVHLSEQALAAAHPPEVGPVSGLLLREDLDARPHLLVGAASNAVKTDRIPVVTRSSTRRRAAALLGETPVP +ENRPRRTAAVLT-----DGPGPAADAAPRPDASAPPAAPSGTAAAAGSSAAATPAATAADRPSDEAAEASTTAATPSPVT +SGPAGGSEDGAARRRRGKDDRPVQYRRGWFIPVFTTLLALTLAAVAVWGYLWTQTQYYVGANDGRIAVFKGVSQRLGPLE +LSHVDRQTDLPVDALPAYARDRVNAGMAARDVDHAEQIVGELRDSLHPDAPAPAGEPSERARPSTTPSSSSARPSDASGS +AAPTSPASSPSATGGEAP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000198.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000198.fa new file mode 100644 index 0000000000000000000000000000000000000000..9876bab4b1b64f3083f9a502d19e3cebdc444190 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000198.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00039 +MMASKTPHQNVTFDLPTKDAGQDGDRTGHGYLALPASGKGPGVIVIQEWWGLVDHIKDVC +DRLADLGFVALAPDLYGGWIAHDGDEAGEMMQNLPAEEGARQLAGAVDWLLARDEVTSQT +VGAIGFCMGGGFVLALAAQQGDKVSAAVPFYGVGQGVPGDFSGVTAAVQGHYAEQDDSFP +VEDARRQEQQIREESGADVEYFYYDAPHAFHNDENPQGNYRPEAAALAWDRAVSFLKEKV +R +>GCF_003691675_PROKKA_02052 +MMASKTPHQNVTFDLPTKDAGQDGDRTGHGYLALPASGKGPGVIVIQEWWGLVDHIKDVC +DRLADLGFVALAPDLYGGWIAHDGDEAGEMMQNLPAEEGARQLAGAVDWLLARDEVTSQT +VGAIGFCMGGGFVLALAAQQGDKVSAAVPFYGVGQGVTGDFSGVTAAVQGHYAEQDDSFP +VEDARRQEQQIREESGADVEYFYYDAPHAFHNDENPQGNYRPEAAALAWDRAVSFLKEKV +R +>GCF_005280335_PROKKA_00361 +MMASKTPHQNTTFDLPSKDASHDGDQVGHGYLALPESGSGPAVIVIQEWWGLVDHIKDVC +DRLAAEGFVALAPDLYGGWIAHDGDEAGEMMQKLPAEEGARQLAGAVDWLLAREEVTSTT +VGAIGFCMGGGFVLALAAQQGEKVSAAVPFYGVGQGVPGDFAGVKAAIQGHYGEQDSMFS +VEDAKKQEQQIRDESGAEVEYFYYDAPHAFHNDDDPQGNYRPEAAALAWGRAVAFLKEKV +R +>GCF_020097155_PROKKA_00302 +MMASKTPHQNVSFPLPTKDAAH-GDQTGHGYLALPAAGKGPAVIVIQEWWGLVDHIKDVC +DRLAEEGFVALAPDLFGGWIAHDGDEAGEMMQNLPAEEGARQLAGAVDWLLARDEVTSSR +VEAIGFCMGGGFVLALAAQQGDKVSAAVPFYGVGQGVPGSFEGVTAAIQGHYAEQDDFFP +VEDAKKQERQIREESGAEVEYFYYDAPHAFHNDENPQGNYRPEAAQLAWDRAVSFLKEKV +R +>GCF_023573625_PROKKA_00034 +MMASKTPHQNVTFDLPTKDAGQDGDRTGHGYLALPASGKGPGVIVIQEWWGLVDHIKDVC +DRLADLGFVALAPDLYGGWIAHDGDEAGEMMQNLPAEEGARQLAGAVDWLLARDEVTSQT +VGAIGFCMGGGFVLALAAQQGDKVSAAVPFYGVGQGVPGDFSGVTAAVQGHYAEQDDSFP +VEDAREQAQQIREESGADVEYFYYDAPHAFHNDENPQGNYRPEAAALAWDRAVSFLKEKV +R + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000207.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000207.fa new file mode 100644 index 0000000000000000000000000000000000000000..aa78f956de1f4196011f19e918ca036de842d54b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000207.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_00054 +MSTQPPGLTTDAPDTPD-------------------DDPVREPLPTEALPIAPAGPRPEEPRAAVERLRAAARSRAAHPR +AVRVRQLKGLKRMLTEHADRFVAALGTDLGKPATEALITEIVSVRSEVDHALLHLTDWMEPRPVKLPLALRPASAEVRPR +PKGLVLVIGAWNYPVQLALAPVVGALAAGNTVVLSPSEKAPATAAALRELVPQYLDSALVSVVAGGKECNTALLAEPWDH +ILYTGGERVGRIVYEAAAKTLSPVTLELGGKSPAVVTPSRNTGAMARRIAWAKFTNAGQTCVAPDYVLAVGEAALRQVTA +ELPAALREFYGDDPRASKDYGRLISAEHAERLREMLQADLDAGAELLVGGDVDVAGRYMAPTVVTGVKPDGALMQEELFG +PILPVLTVDTFQDALDFIAERPHPLAAYLFTDRPSYHRAFDDQVQAGGLGYDVGLLHAGIATLPFGGIGASGMGAYHGIH +GFETFSHLRPSITKSDQVDTLKTAYPPYGRMKRALLPKML +>GCF_003691675_PROKKA_02067 +MSTQPPGLTTDSSDTPD-------------------DDPVREPLPTEALPIAPAGPRPEEPRAAVERLRAAARSRAAHPR +AVRVRQLKGLKRMLTEHADRFVAALGTDLGKPATEALITEIVSVRSEVDHALLHLTDWMEPRPVKLPLALRPASAEVRPR +PKGLVLVIGAWNYPVQLALAPVVGALAAGNTVVLSPSEKAPATAAALRELVPQYLDSALVSVVAGGKECNTELLAEPWDH +ILYTGGERVGRIVYEAAAKTLSPVTLELGGKSPAVVTPSRNTGAMARRIAWAKFTNAGQTCVAPDYVLAVGEAALRQVTA +ELPAALREFYGDDPRASRDYGRLISAEHAERLREMLQADLDAGAELLVGGDVDVAGRYMAPTVVTGVTPDGALMQEELFG +PILPVLTVDTFQDALDFIAERPHPLAAYLFTDRPSYHRAFDDQVQAGGLGYDVGLLHAGIATLPFGGIGASGMGAYHGIH +GFETFSHLRPSITKSDQVDTLKTAYPPYGRMKRALLPKML +>GCF_005280335_PROKKA_00344 +MSTQHPGIATDSPVSSDDDLRPGLDAAPVGPAGEDGDDPVREPLPTEALPLAPAGPRPEDPRAAVVRLRAAARSRAAHPR +AVRVRQLKGLKRLLTEGQDRLVAALGQDLGKPATEALMTEVVSVRSEVDHALLHLTDWMEPRPAKLPLALRPASAEVRPR +PKGLVLIIGAWNYPVQLTLAPLVGALAAGNAVVVSPSEKAPATAAALRELVAEHLDSALVSVVEGGKDCNTALLAEPWDH +ILYTGGERVGRIVYEAAAKTLSPVTLELGGKSPAVVTPSRNTGAMARRIAWAKFTNAGQTCVAPDYVLAVGDVAHRQVVE +ELPGALREFYGADPRASKDYGRLVSAEHAERLRDLLREDLDAGAVVLVGGDVDVAGRYMAPTVVTGVRPDGALMREEIFG +PILPVLRVDTFQEALDFIAERPHPLAAYLFTDRPSYHRAFDDQVQAGGLGYDVGLLHAGIATLPFGGVGASGIGAYHGVH +GFETFSHLRASITKSDQVDTLKTAYPPYGWVKRTMIPKML +>GCF_020097155_PROKKA_00282 +MSTQPPGLTTDSPDSPA-------------------DDPVREPLPTEALPIAPAGPRPEEPRAAVERLRAAARSRAAHPR +AVRVRQLKGLKRMLTEHADRFVAALGTDLGKPSTEALITEIVSVRSEVDHALLHLTDWMEPRPVKLPLALRPASAEVRPR +PKGLVLVIGAWNYPVQLALAPVVGALAAGNTVVLSPSEKAPATAAALRELVPQYLDSALVSVVAGGKDCNTELLAEPWDH +ILYTGGERVGRIVYEAAAKTLSPVTLELGGKSPAVVTPSRNTGAMARRITWAKFTNAGQTCVAPDYVLAVGEAALRQMTA +ELPAALREFYGDDPRASRDYGRLISAEHAERLREMLQADLDAGAELFVGGDVDVAGRYMAPTVVTGVKPDGALMQEELFG +PILPVLTVDTFQDALDFIAERPHPLAAYLFTDRPSYHRAFDDQVQAGGLGYDVGLLHAGIATLPFGGIGASGMGAYHGIH +GFETFSHLRPSIAKSDQVDTLKTAYPPYGRMKRALLPKML +>GCF_023573625_PROKKA_00049 +MSTQPPGLTTDSPDSPA-------------------DDPVREPLPTEALPIAPAGPRPEEPRAAVERLRAAARSRAAHPR +AVRVRQLKGLKRMLTEHADRFVAALGTDLGKPATEALITEIVSVRSEVDHALLHLTDWMEPRPVKLPLALRPASAEVRPR +PKGLVLVIGAWNYPVQLALAPVVGALAAGNTVVLSPSEKAPATAAALRELVPQYLDSALVSVVAGGKECNTALLAEPWDH +ILYTGGERVGRIVYEAAAKTLSPVTLELGGKSPAVVTPSRNTGAMARRIAWAKFTNAGQTCVAPDYVLAVGEAALRQVTA +EIPAALREFYGDDPRASKDYGRLISAEHAERLREMLQTDLDAGAELLVGGDVDVAGRYMAPTVVTGVRPDGALMQEELFG +PILPVLTVDTFQDALDFIAERPHPLAAYLFTDRPSYHRAFDDQVQAGGLGYDVGLLHAGIATLPFGGIGASGMGVYHGIH +GFETFSHLRPSITKSDQVDTLKTAYPPYGRMKRALLPKML diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000210.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000210.fa new file mode 100644 index 0000000000000000000000000000000000000000..ff6e3380cc1b761558897334963aa2873b0290c1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000210.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00057 +MAQPEPVRLVPGGAV------DRPAEQALLAAAAACDG-DVDAMVELL---RAASGAPSG +ED-AAPLDLPLTGAGRTREQWELLASVAAQDLSAARVLEPHLDALSILSQAGVPAPAGLL +GVYASESGGRTPALRPAPD--------------GPDTAWLLDGEKPWCSLADRCAAAVVT +GREADGTRRAVLVDLSHPGVAETDSAWPALGLAPIRTVGLAFDAVPGSAVGGAEWYLRRP +GFAWGGIGVAAVWFGGAVGIARTLRNATAARAAAEAEGRGPGPDQIGQAALGRVDRLLHA +MAALLARAADDVDAGRLDHGRGMVEADRIRGTVAQLCTEVMDVVGQATGPGPLTGSAAHA +RAVADLQVYLRQHHGHRDDARLGAALLTGETDGG---WTW +>GCF_003691675_PROKKA_02070 +MAQPEPVRLVPGGAV------DRPAEQALLAAAAACDG-DVDAMVELL---RAASGAASG +ED-AAPLDLPLTGAGRTREQWELLASVAAQDLSAARVLEPHLDALSILSQAGVPAPAGLL +GVYASESGGRTPALRPAPD--------------GPDTAWLLDGEKPWCSLAGRCAAAVVT +GREADGTRRAVLVDLSHPGVAETDSAWPALGLAPIRTVGLAFDAVPGIAVGGAEWYLRRP +GFAWGGIGVAAVWFGGAVGIARTLRNATAARAAAEAEGRGPGPDQIGQAALGRVDRLLHA +MAALLARAADDVDAGRLDHGRGMVEADRIRGTVAQLCTEVMDVVGQATGPGPLTGSAAHA +RAVADLQVYLRQHHGHRDDARLGAALLTGETDGG---WTW +>GCF_005280335_PROKKA_00338 +MAQPEPVRLAPPGRT-AEPDAARPAERALLAAASACDG-DVAPMLALLGAGRAPDTEASA +PDAAAPLELPLTGEGRTRQQWELLASVAAQDLSAARVLEPHLDALSILSQASVPAPAGLL +GVYASESGGRTPRLTPAPHDDDAGSASDGRPDAGPD-AWLLDGEKPWCSLADECAAAVIT +GREADGTRRAVLVDLDHPGVAETSSAWPALGLAPIRTVGLGFDAVPGTAVGGPEWYLRRP +GFAWGGIGVAAVWFGGAVGIARTLRDATRSRAAAEAEGRGPGPDQVAQAALGRVDRLLHA +MAALLARAAEDVDAGRLDHGRGMVEADRIRGTVAQLCTEVVDVVGQATGPGPLTGSAAHA +RAVADLQVYLRQHHAHRDDARLGRALLDGDADGG---WTW +>GCF_020097155_PROKKA_00278 +MSET-PWVHLPGAEGDGRPAAPTEAEAALLAAAR--DGEDGEAGIEPI---LA---LLSG +DDAAASLDLPLTGAGRTRRQWELLASVGAVSLPAARVLEPHLDALSILDQAGVPAPRGVL +GVYASESGGVSPSARPAPG------AAVGDE----DAVWRLDGDKPWCSLADRCTAAVVT +ARQEDGLRRAFLVDLGEPGMEVADPRWPSLGLAPITTVGLRFADVPAVPVGGPEWYLRRP +GFAWGGIGVAAVWFGGAVHVARTLRTSLERRTAAASDGSGPGPDQVGLAALGRVDRHLHA +MASLLGRAADDVDAGRLDHAHGLVEADRIRGTVAQLCTEVLDVVGQATGPGPLTGDAAHA +RAVADLQVYLRQHHGPRDDARLAESLLAADPAERAELQPW +>GCF_023573625_PROKKA_00052 +MAQPEPVRLVPGGAV------DRPAEQALLAAAAACDG-DVDAMVELL---RAASGAASG +ED-AAPLDLPLTGAGRTREQWELLASVAAQDLSAARVLEPHLDALSILSQAGVPAPAGLL +GVYASESGGRTPALRPVPD--------------GPDTAWLLDGEKPWCSLADRCAAAVVT +GREADGTRRAVLVDLSHPGVAETDSAWPALGLAPIRTVGLAFDAVPGSAVGGAEWYLRRP +GFAWGGIGVAAVWFGGAVGIARTLRNATAARAAAEAEGRGPGPDQIGQAALGRVDRLLHA +MAALLARAADDVDAGRLDHGRGMVEADRIRGTVAQLCTEVMDVVGQATGPGPLTGSAAHA +RAVADLQVYLRQHHGHRDDARLGAALLTGETDGG---WTW + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000212.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000212.fa new file mode 100644 index 0000000000000000000000000000000000000000..4434035ff82dc4ff37dc73de877974011fb2a35b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000212.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_00060 +MTLPTPVRLGRMQTSDA-APAA-DDDRTPSAPGPARLLDRSAVRLREDLAAGELSAREVTEAALAAAQTHADLGAFALLD +AEGARARAAELDAAHPRVAPRAVPGPRTSPAPDDDGAPASLHGLPLAYKDLIDVRGMPTRFGSALLADAPPAAQDDPLAL +RLRAAGTVTLGKTTVPEFGLDSYSENLVTAPARNPLDPTRTAGGSSGGAAAAVAAGILPFAPGSDGGGSIRIPAAACGLV +GLKPGRGELPMDEHADTVRNLTVSGPLAHTVEDAALLYDVLLSPEGLPGRVLPDLRRTVETARAGGAVDARRIGVTTASP +FASDLEISLARPAVTALTKAAAALDAGGHAVEDLSPYYGEDYHRDFRTVWTAGLLRAPLPEDAEAHVGAVAAHFLRTARA +AGRAELDDAAHRLEEWARGVRAQFAAVDVVMTPVLATAPPPVGHFLAMEPEANYEAQCAFTPYTSMVNVLGLPAVAVPVL +RDERGLNWSVQLIGRPGTSAPLLALAAHLELLLAG +>GCF_003691675_PROKKA_02073 +MTRATPVRLGRMQTSDA-APAADDDDRTPSAPGPARLLDRSAVRLREDLAAGELSAREVTEAALAAAQAHADLGAFALLD +AEGARTRAAELDAAHPRVAPRAVPGPHTSPAPDDDGAPASLHGLPLAYKDLIDVRGMPTRFGSALLADAPPAAQDDPLAL +RLRGAGTVTLGKTTVPEFGLDSYSENLVTAPARNPLDPTRTAGGSSGGAAAAVAAGILPFAPGSDGGGSIRIPAAACGLV +GLKPGRGELPMDEHADTVRNLTVSGPLAHTVEDAALLYDVMLTPEGLPGRVLSDLRRTVETARAGDAVDVRRIGVTTASP +FASDLEISLARPAVTALTKAAAALDAGGHAVEDLSPYYGEDYHRDFRTVWTAGLLRAPLPEDAEAHVGAVAAHFLRTARA +AGRAELDDAAHRLEEWAHGVRAQFAAVDVVMTPVLATAPPPVGHFLAMEPEANYEAQCAFTPYTSMVNVLGLPAVAVPVL +RDERGLNWSVQLIGRPGTSAPLLALAAHLELLLAG +>GCF_005280335_PROKKA_00335 +------------------------------------------MQLRDALAAGELSAREVTQAALDAAERHAGLGAFTLLD +PEGALARADEL---------------------DDDGARASLHGLPLAYKDLTDVRGLPTRHGSALLAGAPAAEEDAPLVR +RLVGAGTVTLGKTTVPEFGLDSYSENLVSAPARNPLDPARTPGGSSGGSAAAVAAGILPFAPGSDGGGSIRIPAAACGLV +GFKPGRGELPVDEPADTVRNLTVSGPLAHTVEDAALLYDELLTPEGLPGRVLADLRRTVETARAGGAVEGRRIGVTTASP +FAPDVPITLARPAVTALTKAAAALSAGGHAVQDLHPAYGEEYHRDFRTVWTSGLLRAPLPEDAEERVGAIAAHFLRTARS +AGRQEIDDAVRRLEAWARGVRGQFAAVDVVMTPVLAAAPPPVGHFLAMEPEDNYAAQCAFTPYTSMVNVLGLPAASVPVL +RDERGLSWSVQLIGRPGTSGALLALAAHLELLLAG +>GCF_020097155_PROKKA_00276 +-----------MAVSEPLSPSDQPTSPTPAPDAPARLLGRTALALRDALAAGELSAAEVTEASLAAAHAHAGLGAFVLLD +EDGARVRAAALDAR------------------PDDAAGASLRGLPLAFKDLTDVAGLPTRMGSAVLAQAPAAAEDDPLTT +RLRAAGTVLLGKTTVPEFGLDAYSENPVDPPARNPLDPSRTPGGSSGGSAAAVAAGILPFAPGSDGGGSVRIPAAACGLV +GLKPGRGTVPTDPGEDAVTNLTVSGPLAHTVEDAALLFDVMTSPEGLEGRTGPDLRRFLDARAAGEPVAPVRIGVSTASP +FSPDLEITLARPALSALARSGAALAAGGHAVDEFVPHYGERYHRDFRTAWTSGLLKAPLPDGAEALVGPVAASFLASARA +AGPEQIATAIGRLEAWAADVRGQFAAVDVVMTPVLAFAPPAIGHFLALDPEENYAEQCRFTPYTSMVNVLGLPAVAVPVL +RDEAGLSWSVQLVGRPGAEGRLLELAGHLRLLLAG +>GCF_023573625_PROKKA_00055 +MTLPTPVRLGRMQTSDA-APAA-DDDRTPSAPGPARLLDRSAVRLREDLAAGELSAREVTEAALAAAQTHADLGAFALLD +AEGARTRAAELDAAHPRVAPRAAPGPHTSPAPDDDGAPASLHGLPLAYKDLIDVRGMPTRFGSALLADAPPAAQDDPLAL +RLRAAGTVTLGKTTVPEFGLDSYSENLVTAPARNPLDPARTAGGSSGGAAAAVAAGILPFAPGSDGGGSIRIPAAACGLV +GLKPGRGELPMDEHADTVRNLTVSGPLAHTVEDAALLYDVLLSPEGLPGRVLPDLRRTVETARAGGAVDARRIGVTTASP +FASDLEISLARPAVTALTKAAAALDAGGHAVEDLSPYYGEDYHRDFRTVWTAGLLRAPLPEDAEAHVGAVAAHFLRTARA +AGRAELDDAAHRLEEWARGVRAQFAAVDVVMTPVLATAPPPVGHFLAMEPEANYEAQCAFTPYTSMVNVLGLPAVAVPVL +RDERGLNWSVQLIGRPGTSAPLLALAAHLELLLAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000219.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000219.fa new file mode 100644 index 0000000000000000000000000000000000000000..8a942ad604eed3d860076eca6a7c2e740af5b997 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000219.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00070 +MSDDHATDRPRTAADAEPGAPAEPGPAVAHPVDWAFAARTARSLAAAGPRFTPREATREA +EGLRAAAEAAVPHVHRLTGLEAARDLRDSQVLVVDRPTWSRAATQSFATLLDPTFAHLRD +TRPREH-AATTRVTRHATALEMGGILAWMSGKILGQYDPFIALPGPGGTAAGPAGGRLLL +VAPNVAQVRAEINVDPADFRLWVCLHEQTHRVQFAAAPWLREHLRGEITALTVGLFDKAE +SLPERLRTALAAANPLGREADAG--RTGTRDGHD---------AQDAVAARPAPGLLGAI +QDEEDRERLSRLTAVMSLLEGHANVVMDGVDSSVVSSVKTIRRRFDERGDRRSPLDRMLR +RLLGMDAKMAQYRDGQRFVAAAVAELGMAGFNVVWDAPELLPSEAELHAPETWVARIRAQ +A +>GCF_003691675_PROKKA_02083 +MSDDHATDRPRAAADAEPGAPAEPGPAVAHPVDWAFAARTARSLAAAGPRFTPREATREA +EGLRAAAEAAVPHVHRLTGLEAARDLRDSQVLVVDRPTWSRAATQSFATLLDPTFAHLRD +TRPREHAAATTRVTRHATALEMGGILAWMSGRILGQYDPFIALPGPGGTAGGPAGGRLLL +VAPNVAQVRAEINVDPADFRLWVCLHEQTHRVQFAAAPWLREHLRAEITALTVGLFDKAE +SLPERLRTALAAANPLGREADAG--RTGARDGHD---------AQDAAPARPTPGLLGAI +QDEEDRERLSRLTAVMSLLEGHANVVMDGVDSSVVSSVKTIRRRFDERGDRRSPLDRMLR +RVLGMDAKMAQYRDGQRFVAAAVAQLGMAGFNVVWDAPELLPSEAELHAPETWVARIRAQ +A +>GCF_005280335_PROKKA_00322 +MDT-------------------APADRVPQPVDWAFAARTAAALAPAGPRFTAREAAREA +AGLRAAAEASVPHVHRLTGLAAAEDLRDSQVLVVDRPTWSASATQSFATMLEPTFAHLQA +TRPQEYQAALTPVARHATALEMGGILAWLSGKVLGQYDPF----------AGPSGGRLLL +NAPSVAQVRTEINVDPEDFRLWVCLHEQTHRVQFAAAPWLRGHLQEQITALASGLFDKAE +SLPERLRSALAAANPLGRGSGAGAASTGPASGPDDGRPGPAQAGGDVVPARGA-GLLGAL +QDEEDRARLSHVTAVMSLLEGHANVVMDGVDADVVSSVKTIRRRFEDRADRRSPLDRMLR +RLLGMDAKMAQYRDGQRFVSAAVAELGMDGFNVVWDAPELLPTEDELHRPERWTARVRAQ +A +>GCF_020097155_PROKKA_00264 +MTAD------------------QPVPSPAHPVDWDAAARAAGSLAAAGPRIGTREARREA +EGLRAAAAASVAHVHRLTGLAAAEDLRDSQVLVVDRPTWSLANTQSFAGLLEPSFAHLRA +TRPQEYALTTAPLTRRAAALEMGGILAWLSSKVLGQYDPFSALPGPDGVPAGPAGGRLLL +VAPNVAQVRREIHVDPADFRLWVCLHEQTHRVQFAAAPWLRGHLQGEITALTGGLFDKAE +SLPERLRSALAAANPLGASTSPGAGR----AGQDDGAAGP--------GGRPALGLLGAI +QDEEDRARLSRLTAVMSLLEGHANVVMDAVDSSVVSSVKTIRRRFDARGDRRSGLDRLLR +RLLGMDAKMAQYRDGQRFVDAAVAELGRDGFNVVWDAPELLPSEEEIHAPDRWVARIRAQ +A +>GCF_023573625_PROKKA_00064 +MSDDHATDRPRTAADAEPGAPAEPGPAVAHPVDWAFAARTARSLAAAGPRFTPREATREA +EGLRAAAEAAVPHVHRLTGLEAARDLRDSQVLVVDRPTWSRAATQSFATLLDPTFAHLRD +TRPREHAAATTRVTRHATALEMGGILAWMSGRILGQYDPFIALPGPGGTAAGPAGGRLLL +VAPNVAQVRAEINVEPADFRLWVCLHEQTHRVQFAAAPWLREHLRAEITALTVGLFDKAE +SLPERLRTALAAANPLGREADAG--RIGTRDGHD---------AQDAAAARPAPGLLGAI +QDEEDRERLSRLTAVMSLLEGHANVVMDGVDSSVVSSVKTIRRRFDERGDRRSPLDRMLR +RLLGMDAKMAQYRDGQRFVAAAVAELGMAGFNVVWDAPELLPSEAELHAPETWGARIRAQ +A + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000230.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000230.fa new file mode 100644 index 0000000000000000000000000000000000000000..1240c2ffaedbec73e19d59d94e1d4cb104878d89 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000230.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00084 +MTDQPEMSPLTEPEREWVRVRRDFAAQEGVDHLDLDAVAAYYDAVLARSQAEADELDPEE +LAVLLDVVAVLLGEHLGARHGMQWVTVADEEGPALALRDTLSDAVVFPQPVVGQSWNDQA +TGEWMGGYVDWLGEQLQQIRADAGTLP------GA +>GCF_003691675_PROKKA_02097 +MTDQPEMSPLTEPEREWVRVRRDFAAQEGVDHLDLDAVAAYYDAVLARSQAEAEELDPEE +LAVLLDVVAVLLGEHLGARHGMQWVTVADEEGPALALRDTLSDAVVFPQPVVGQSWNHQA +TGEWMGEYVDWLGEQLQQIRADAGTRP------GA +>GCF_005280335_PROKKA_00307 +MTEQPEMHPLSEPEQEWVRVRREFAAQEGVDHLDLDAVAAYYDGVLARSVSEAEALDPDE +LAVLLDVVAVLLGEHLGARHGMQWVTVSDDEGPALALRDTLSDAVVFPQPAVGQAWNEQV +TGAWLGEYVDWLGEQLQGIRA--GDRPDGVAQQG- +>GCF_020097155_PROKKA_00251 +MSEQ-QIRPLTAAEQEWVAVRRDFAAQEGTGHLDLDAVDAYHGRLLARSRS--EDVDPDE +LGVLLDVVAVLLGEHLGARHGLAWVAVTEGDATDLGLRDPLSDAVVFPQSVVAQHWND-G +DAHWIPGYVDWLGAQLAPLREERRAAE------G- +>GCF_023573625_PROKKA_00079 +MTDQPEMSPLTEPEREWVRVRRDFAAQEGVDHLDLDAVAAYYDAVLARSQAEAEELDPEE +LAVLLDVVAVLLGEHLGARHGMQWVTVADEEGPALALRDTLSDAVVFPQPVVGQSWNHQA +TGEWMGEYVDWLGEQLQQIRADAGTRP------GA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000234.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000234.fa new file mode 100644 index 0000000000000000000000000000000000000000..493007cfdc62d92cc193131bbaa6c93603ecde1c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000234.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00089 +MTTSNNPDEIRADIERTRRELGQDVDALAEKVSPTKAVSRQTNRIKDGFIHAKENIMGSP +EQHRHEPSLGDRAHAVVDDA----RASAYDAAGQAQDRLGDAGDRVSEWADDAQHALHQA +PAQLRGRTAGNPLAAGLIAFGAGLLLSSLIPASRAEQRAAEGLKDQAAPLVDEAK----Q +AAQQLREDLEPAAREAAGSVKESAAEAASHLKEQGTDTAQGLKAESQDAARQVKDTAKDA +>GCF_003691675_PROKKA_02102 +MTTSNNPDEIRADIERTRRELGQDVDALAEKVSPTKAVSRQTNRIKDGFIHAKENIMGSP +EQHRHEPSLGDRAHGVIDDA----RASAYDAAGQAQDRLGDAGDRVSEWADDAQHALHQA +PAQLRGRTAGNPLAAGLIAFGAGLLLSSLIPASRAEQRAAEGLKDQAAPLVDEAK----Q +AAQQLREDLEPAAREAAGSVKESAAEAASHLKEQGTDTAQGLKAESQDAARQVKDTAKDA +>GCF_005280335_PROKKA_00302 +MTTSNNPDEIRAEIERTRHQLGQDVDALAEKVSPTKAVSRQTNRMKDGLLSVKENIMGSP +EDHGRQPSMGDRAHAAADDA----RASMHGAADQARDAMGHASDRVSGWADDAQHAVQQA +PAQLRGRTAGNPLAAGLIAFGAGLLVSSLIPASRVEQRAAEGLKEQAAPLVDEAK----Q +VAQQLREDLEPVARDAAQSVKESATEAVDHVKADGADKAQDLKAESQDAARQVKGAAQDG +>GCF_020097155_PROKKA_00247 +MTTSSNPDEIRAEIERTRHALGQDVDALAEKVSPTKAVSRQTNRVKDGFITVKENIMGTP +EHHEG-PGAVDRARFAAQDAAGQVQGTAHDVADQARGYAQQAGEAASQWVDDAQHAVQQA +PAQVRGRTAGNPLAAGLIALGAGWLIGSLIPASPVEKRAAERVKDQAAPLLESAKQEAAQ +VAQDVREQVEPEVRDAAASLKDSAAESVQSLKSEGAEKAQDLKGSSQDAAQQVKHAAKHA +>GCF_023573625_PROKKA_00084 +MTTSNNPDEIRADIERTRRELGQDVDALAEKVSPTKAVSRQTNRIKDGFIHAKENIMGSP +EQHRHEPSLGDRAHGVIDDA----RASAYDAAGQAQDRLGDAGDRVSEWADDAQLALQQA +PAQLRGRTAGNPLAAGLIAFGAGLLLSSLIPASRVEQRAAEGLKEQAAPLVDEAK----Q +AAQQLREDLEPAAREAAGSVKESAAEAASHLKEQGTDTAQDLKAESQDAARQVKDTAKDA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000236.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000236.fa new file mode 100644 index 0000000000000000000000000000000000000000..c780a995053aff7246923bcfeba09e81bf292d2e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000236.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00091 +MTPERLAAAFDGPSPALAATLLGCRLTVVAPDGAVTVRLTETEAYGNAGADPGAHSFRGR +TERNAALFGPPRRTYVYLNYGIHRCLNLVGHPEGEAGGVLLRAAEVLAGGDLAVARRGRD +TGPKLLSGPGNLGQGLGITLEMGHAPVEIVAAPPEVADDGGTSARLAAPAAPARFLLAPP +APRDPAEPPIEVVTGPRVGVSGEGGSVRFPWRFSVAGHRSVSAFRRGRNVPD +>GCF_003691675_PROKKA_02104 +MTPERLAAAFDGPSPALAATLLGCRLTVVAPDGAVTVRLTETEAYGNAGADPGAHSFRGR +TERNAALFGPPRRTYVYLNYGIHRCLNLVGHPEGEAGGVLLRAAEVLAGGDLAVARRGRD +TGPKLLSGPGNLGQGLGITLEMGHAPVEIVAAPPEVADDGGTPARLAAPAAPARFLLAPP +APRDPAAPPIEVVTGPRVGVSGEGGSVRFPWRFSVAGHRSVSAFRRGRNVPD +>GCF_005280335_PROKKA_00300 +MTPERLAAAFDGPSPALAATLLGCRLTVVAPDGAVTVRLTETEAYGDAGADPGAHSFRGR +TERNAALFGPPRRTYVYLNYGIHRCLNLVGHPEGEAGGVLLRAAEVLAGGDLAVARRGRD +TGLKLLSGPGNLGQGLGITLEMGHAPVEIVAAPPEVADDGGTPARL---AAPARFLLAPP +ASRDPAEPPIEVVTGPRVGVSGEGGSVRFPWRFNVAGHRSVSAFRRGRNVPD +>GCF_020097155_PROKKA_00245 +MTPERLAAAFDGPTPALAATLLGCRLTVVAPDGAVTVRLTETEAYGNAGADPGAHSFRGR +TERNAALFGPPRRTYVYLNYGIHRCLNLVGHPEGEAGGVLLRAAEVLAGGDLAVARRGRD +TGLKLLSGPGNLGQGLGITLQMGHVPVEIVAAPPEVADDGGTPARL---AAPARFLLAPP +ASRDPAEPPIEVVTGPRVGVSGEGGSVRFPWRFSVAGHRSVSAFRRGRNVPD +>GCF_023573625_PROKKA_00086 +MTPERLAAAFDGPSPALAATLLGCRLTVVAPDGAVTVRLTETEAYGNAGADPGAHSFRGR +TERNAALFGPPRRTYVYLNYGIHRCLNLVGHPEGEAGGVLLRAAEVLAGGDLAVARRGRD +TGPKLLSGPGNLGQGLGITLEMGHAPVEIVAAPPEVADDGGTSARLAAPAAPARFLLAPP +APRDPAEPPIEVVTGPRVGVSGEGGSVRFPWRFSVAGHRSVSAFRRGRNVPD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000246.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000246.fa new file mode 100644 index 0000000000000000000000000000000000000000..5bbbb7f7835f6ae5d48927cb2427bc9ac07e1333 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000246.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00102 +MSVPRLDPMPADRPLTLRSARTQDVPVIQALVEPLARERVLLQKEAVAYYEAIQEFVVAE +EADGTLAGFGALHVMWQDIAEVRTLAVSEAHRGTGVGHLIIEELLDRARAVGVERVFCLT +FEVEFFRRHGFEVMADQSAVDPEVYAELLRSTDEGVAEFLDLARVKPNTLGNTRMIRRL +>GCF_003691675_PROKKA_02115 +MSVPRLDPMPADRPLTLRSARTQDVPVIQALVEPLARERVLLQKEAVAYYEAIQEFVVAE +EADGTLAGFGALHVMWQDIAEVRTLAVSEAHRGAGVGHLIIEELLDRARAVGVERVFCLT +FEVEFFRRHGFEVMADQSAVDPEVYAELLRSTDEGVAEFLDLARVKPNTLGNTRMIRRL +>GCF_005280335_PROKKA_00288 +--------MPADRQITLRSARTGDVPAIRALVEPLAQERVLLQKEAVAFYEAIQEFVVAE +DADGSLAGFGALHVMWQDIAEVRTLAVSRDHRGAGVGHLILEELLRRARVVGVERVFCLT +FEVEFFRRHGFAVMADQSAVDPEVYAELLRSTDEGVAEFLDLARVKPNTLGNTRMIRTL +>GCF_020097155_PROKKA_00234 +--------MPAAPVVTVRPARTQDVPAIRALVSPLAERRLLLQKEAVAFYESIQEFMVAE +AEDGSLAGFGALHVMWQDIAEVRTLAVADAWLGAGVGHRILTALLERAREVGVARVFCLT +FEVEFFRRHGFEVMADQSAVDPEVYAELLRSTDEGVAEFLDLARVKPNTLGNTRMIRSL +>GCF_023573625_PROKKA_00097 +MSVPRLDPMPADRPLTLRSARTQDVPVIQALVEPLARERVLLQKEAVAYYEAIQEFVVAE +EPDGTLAGFGALHVMWQDIAEVRTLAVSEAHRGAGVGHLVIEELLDRARAVGVERVFCLT +FEVEFFRRHGFEVMADQSAVDPEVYAELLRSTDEGVAEFLDLARVKPNTLGNTRMIRRL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000254.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000254.fa new file mode 100644 index 0000000000000000000000000000000000000000..16ae09090b2ca62a3a2948970bc6fd899d551b91 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000254.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00111 +MTAGLAV-VLVLLCAVGALMGFRDAPNAAALPVRYRALTPRGALLLTGAVNTVGALLGIG +LITLSVHYFTSPAV-RSEIGPLAVGVSCAVTLVWGLLLWWRRLPGSSTHALISALAGSHL +AVRLSLHIDVAHTIFDLVRAEVLLSLLLSPLIAWALARLLTAPAMRLATRGTTVNVQHRA +RVALGISASAMAMGHGLQAGQR---MGVLWAAVLVGSGSVLAPDALTAEFVGGAFLFALA +VGLGTLGGAWRIAWTLTERLVRLDPLRASVAAVIPAGLLFVGSLVFHLPLSSTHTATAAI +VGAGQTQTYASVRWPTVLRVVGWWLLTPVACALLGLLGTLALLPL-A +>GCF_003691675_PROKKA_02124 +MTAGLAV-VLVLLCAVGALMGFRDAPNAAALPVRYRALTPRGALLLTGAVNTVGALLGIG +LITLSVHYFTSPAV-RSEIGPLAVGVSCAVTLVWGLLLWWRRLPGSSTHALISALAGSHL +AVRLRLHIDVAHTIFDLVRAEVLLSLLLSPLIAWALARLLTAPAMRLATRGTTVNVQHRA +RVALGISASAMAMGHGLQAGQR---MGVLWAAVLVGSGSVLAPDALTAEFVGGAFLFALA +VGLGTLGGAWRIAWTLTERLVRLDPLRASVAAVIPAGLLFVGSLVFHLPLSSTHTATAAI +VGAGQTQTYASVRWPTVLRVVGWWLLTPVACALLGLLGTLALLPL-A +>GCF_005280335_PROKKA_00279 +MTPGLAV-VALLLCALAAMMGFRDAPNAVALPVRFRALTPRLALVMTALINAVGALLGIG +LITLSVHYFTSPAV-RGDVGPLAVGVTAVVAVLWGLLLWWRRLPGSTTHAVLSALAGAHL +AVQLSLHDDLAGSILESVRVEVVLSLLLSPVIAWGLARLLTGPVVQVATTGTTVNVQRRA +RIALAVSAGAMAMGHGLQAGQR---VGVLWAAVLVGSGAALSPDALTAEFVVGSVLFALA +IALGTLGGAWRIAWTLTERLVRLDPLRASVAAVVPAGLLFVGSLVLHLPLSSTHTATAAI +VGAGQTQTYASVRWPTVLRVGGWWLLTPVVCAALGLLGTLALLPL-A +>GCF_020097155_PROKKA_00220 +MTAPLLVPVLVLLLAVGGLMGFRDAPNAVALAVRFRALTPRVALILSALLNAVGVLLGAL +MLTLGLPLMVAGGTARPEVLAL-VGVAAAVTLGWGVLAWRFRAPTSTTHALLASLAAAHV +ASVSALGSGLDPAFENGARWEVAASLLLSPVLAWGLARLTARPVLRLATTGTTVNVQHRA +RIALAVSTGLIALGHGVQAALRLLPLAVLVATAAVGTG--LPP----GTELSAAFVAAAA +VGIGTLGGAWGIAWTLTERLVILDPLRAAVAAVVPAVLLFAGTMLLHLPLSSTHTGVAGI +VGAGQTQSYASVRWGAVARVAVWWVATPLVCGSLAFAAGAVLLPLLG +>GCF_023573625_PROKKA_00106 +MTAGLAV-VLVLLCAVGALMGFRDAPNAAALPVRYRALTPRGALLLTGAVNTVGALLGIG +LITLSVHYFTSPAV-RSEIGPLAVGVSCAVTLVWGLLLWWRRLPGSSTHALISALAGSHL +AVRLSLHIDVAHTIFDLVRAEVLLSLLLSPLIAWALARLLTAPATRLATRGTTVNVQHRA +RVALGISASAMAMGHGLQAGQR---MGVLWAAVLVGSGSVLAPDALTAEFVGGAFLFALA +VGLGTLGGAWRIAWTLTERLVRLDPLRASVAAVIPAGLLFVGSLVFHLPLSSTHTATAAI +VGAGQTQTYASVRWPTVLRVVGWWLLTPVACALLGLLGTLALLPL-A + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000264.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000264.fa new file mode 100644 index 0000000000000000000000000000000000000000..634a6813bf3c97bdf2c2b0519e47d3ee36381876 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000264.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00126 +MSAQTQPAATRREDAPLGVLVGVDGSDQSVSAARWAQREAGLRGEPLTLVTAYSIPAYWG +YGADASGAVLDDSRLREGVQALLEEVAGKLDADGVRPELRVEIGDAAGVLVELSAEASLL +VSGARGRGGFMGRLLGSVAAALPGHAHCPVAIIPAGVEASRAGDRTAVVVGVDGSEQGRA +AALEAAEEARLRQAPLKLVCAVPPLGANAAWLAVSLDEEARERELRERLEAGAAWISSEF +PGLEVLTELVDGTPVDVLVDQTATARLTVVGTRGLGGFAGAIVGSTSRGVADHAKGPVLV +VPFREDVRLGRRASFGPVQDQSGS-- +>GCF_003691675_PROKKA_02140 +MSAQTQPAATRREDAPLGVLVGVDGSDQSVSAARWAQREAGLRGEPLTLVTAYSIPAYWG +YGADAGGAVLDDSRLREGVQALLEEVAGKLDADGVRPELRVEIGDAAGVLVELSAEASLL +VSGARGRGGFMGRLLGSVAAALPGHAHCPVAIIPAGVEASRAGDRTAVVVGVDGSEQGRA +AALEAAEEARLRQAPLKLVCAVPPLGANAAWLAVSLDEEARERELRERLDAGAAWISSEF +PGLEVLTELVDGTPVDVLVDQSATACLTVVGTRGLGGFAGAIVGSTSRGVADHAKGPVLV +VPFREDVRLSRRASFGPVQDQPES-- +>GCF_005280335_PROKKA_00259 +MSAQTQPAAP-REDAPLGVLVGVDGSEQSVSAARWAQREAGLRGEPLTLVTAYSIPAYWG +YGADAGGTVLDDSRLREGVQVLLDEVAAKLDADGVRPELRVEVGDAAGVLVDLSKAASLL +VSGGRGRGGFIGRLLGSVASALPGHAHCPVAIIPAGVEASRAADGAAVVAGVDGSEQGRA +AALVAAEEARIRQAPLKLVCALPPVGGNAAWLGVTLDEAAREQELRERLDAGAAWIASEF +PGLEVVTELVDGTPVDVMREQTATARLTVVGTRGLGGFTGALVGSTSRGVTDHAKGPVMV +VPFRKDARLGTRTKFGPVADQD---- +>GCF_020097155_PROKKA_00193 +MSAETTPSTL-PAEAPLGVLVGVDGSDQSISAARWAQREAGLRNLPLTLATAYTVPAFWG +YAADGAGLLTDDGRLHAGVEALLREVAGKLDPAGVAPELRVEVGDAAGVLIDLSAQAELL +VSGSRGRGGFIGRLLGSVSSALPGHAHCPVAIIPAGVEASRADSGAPVVVGVDGSEQGRA +AALVAAEEAQARKAPLHLISALPPISPNAAWLAVSLDEEAREQELRERLEDGARWLASEF +PGLEVTSELASGVPVDVMVEQTATARLTVLGTRGLGGFSGALMGSTSAGVANHAKGPVMV +VPFREDVRLGRRAEFGAVVDQDDPRV +>GCF_023573625_PROKKA_00134 +MSAQTQPAATRREDAPLGVLVGVDGSDQSVSAARWAQREAGLRGEPLTLVTAYSIPAYWG +YGADAGGAVLDDSRLREGVQALLEEVAGKLDADGVRPELRVEIGDAAGVLVELSAEASLL +VSGARGRGGFMGRLLGSVAAALPGHAHCPVAIIPAGVEASRAGDRTAVVVGVDGSEQGRA +AALEAAEEARLRQAPLKLVCAVPPLGANAAWLAVSLDEEARERELRERLDAGAAWISSEF +PGLEVLTELVDGTPVDVLVDQSATACLTVVGTRGLGGFAGAIVGSTSRGVADHAKGPVLV +VPFREDVRLGRRASFGPVQDQPES-- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000271.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000271.fa new file mode 100644 index 0000000000000000000000000000000000000000..60bba2a742987e20b1796c22c282c43c5a3244dc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000271.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00138 +--------MRELQQRIIAQQGVLPEIDPAAEVERRVAFLADYLAATGASGFVLGISGGVD +STVGGRLAQLAVERRRAQLGVTDAVALGGPDTTPPGEAGVGADVVPSRENPRFTAVRLPY +KVQHDEADARAAMDFVGADQDVTLNIAEAVQGLAAAFAEAVGEPISDYNQGNVKARIRMT +AQYAVAGAHGQLVIGTDHAAEAVTGFYTKFGDGGADVLPLAGLNKRQVRALGRELGAPEP +LWNKVPTADLLDGTPGQTDEAELGMTYEDIDDYLEGKDVPTEVAEKLEGIWLRSRHKRTT +PVTIHDDWWR +>GCF_003691675_PROKKA_02152 +--------MRELQQRIIAQQGVLPEIDPAAEVERRVAFLADYLAATGASGFVLGISGGVD +STVGGRLAQLAVERRRAQLGVPDAVALGGPGTTPPGEAGVGADVVPSRENPRFTAVRLPY +KVQHDEADARAAMDFVGADQDVTLNIAEAVQGLAAAFAEAVGEPISDYNQGNVKARIRMT +AQYAVAGAHGQLVIGTDQAAEAITGFYTKFGDGGADVLPLAGLNKRQVRALGRELGAPEP +LWNKVPTADLLDGTPGQTDEAELGMTYEDIDDYLEGKDVPTEVAEKLEGIWLRSRHKRTT +PVTIHDDWWR +>GCF_005280335_PROKKA_00246 +--------MRELQQQIIAEQGVRPQIDPAQEIERRVEFLVDYLEATGAAGFVLGISGGVD +STVGGRLAQLAVERRRARLGAPDAVALGGP-EAPRGA--PAADEAPSPQRPQFTAVRLPY +RQQKDEADARAAMDFVDADREITLDIAAGVEGIASAFVEATGDEIADFDKGNVKARMRMV +AQYALAGAHRQLVIGTDHAAEAVTGFYTKFGDGGADVLPLSGLNKRQVRALGRELGAPEH +LWNKVPTADLLDGNPGRTDEDELGMTYEHIDDYLEGGDIPEEAAEKLEGIWLRSRHKRTM +PVTVHDDWWR +>GCF_020097155_PROKKA_00180 +MPEPYAGAMRELQQQIIAEMGVRPEVDPAAEVEARVRFLVDYLEATGASGFVLGISGGVD +STTAGRLAQLAVERRRAELGTE-----------------AGDDAAPSRENPRFTAVRLPY +RVQADEADATAAMDFVGADGRVTLNIAEAVAGMASAFQEATGEPISDYNQGNVKARMRMV +AQYAIAGAHGQLVIGTDHAAESITGFFTKFGDGGADVLPLAGLDKRQVRAVAKELGAPEH +LWAKVPTADLLDGSPGRADEDELGLSYEHIDDYLEGREIPEEAAEKLEGVWRRSRHKRTT +PVTIHDDWWR +>GCF_023573625_PROKKA_00146 +--------MRELQQRIIAQQGVLPEIDPAAEVERRVAFLVDYLAATGASGFVLGISGGVD +STVGGRLAQLAVERRRAQLGVTDAVALGGPGTTPPGEAGVGADVVPSRENPRFTAVRLPY +KVQHDEADARAALDFVGADQDVTLNIAEAVQGLAAAFAEAVGEPISDYNQGNVKARIRMT +AQYAVAGAHGQLVIGTDQAAEAITGFYTKFGDGGADVLPLAGLNKRQVRALGRELGAPEP +LWNKVPTADLLDGTPGQTDEAELGMTYEDIDDYLEGKDVPTEVAEKLEGIWLRSRHKRTT +PVTIHDDWWR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000304.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000304.fa new file mode 100644 index 0000000000000000000000000000000000000000..932c1264390f1c05c85f35bf77580d2133107c92 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000304.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00203 +MTTYATLAARYADAFDSVAHGERAREAGRHLPFAALGELQAAGFGKVGVPEDAGGEGGGS +ETVLRLLMDLAARDVNTAHVWRSHLVFIATAMDQAPARRERWLRHIVDGDWAGSALAERA +GGAAPGRAATLASRDEGGTWVVRGQKYYATGSAFATWTAATVGIEGADLVSRRNSKRAGG +AVREPDRAVAVVRVRQPRVGIKDDWDGFGQRLTATGSVVLDDAAAEELLEVPRQDGPVPV +LMEATLLALQAGIGRAALTEGTQLLRQRRRTFNTGTAALPKDDPQLLEIMGQLAGRQAAA +ELMVREIGRLLDEGQDGADGAGPAEADVVAAS--AEAMAAAYRAQAVVPEAVLEVCTRIF +DTLGASATSATLRLDRHWRNARTLATHDPAAFKVRMAGDWLVNGTPPTAYTSAGEVPEGD +>GCF_003691675_PROKKA_02198 +MTTYATLAARYADAFDSVAHGERAREAGRHLPFAALAELQAAGFGKVGVPEDAGGEGGGS +ETVLRLLMDLAARDVNTAHVWRSHLVFIATAMDQAPARRERWLRHIVDGDWAGSALAERA +GGAAPGRAATLASRDEGGTWVVRGQKYYATGSAFATWTAATVGIEGADLVSRRNSKRAGG +AVREPDRAVAVVRVRQPRVGIKDDWDGFGQRLTATGSVVLDDAAAEELLEVPRQDGPVPV +LMEATLLALQAGIGRAALTEGTQLLRQRRRTFNTGTAALPKDDPQLLEIMGQLAGRQAAA +ELMVREIGRLLDEGQDGADGAGPAEADVVAAS--AEAMAAAYRAQAVVPEAVLEVCTRIF +DTLGASATSATLRLDRHWRNARTLATHDPAAFKVRMAGDWLVNGTPPTAYTSAGEVPEGD +>GCF_005280335_PROKKA_00188 +MTSYADLAARFADAFDAVGHGERAREAGRHLPFAVQRGLQEAGFGRVSVPEVAGGDGASH +ETALRLLMDLAARDVNTAHLWRSHLVFVATVLDQVPAAAEPWLERVVAGDWAGSALAER- +GTAAPGRAATMAERDEGGTWVVTGEKYYATGSAFATWTIATVGVDGDGLVSRRNSKRAGG +VVREPGRAVAVVRVRQPRVRVKDDWDGFGQRLTATGSVVLDGAAAEALLEVPRREGPVPV +LQEASLLALQVGVGRAALAEGVELLRARRRTFNTGTEALPAQDPQLLEIMGRLAGQLAAA +EALVRQVGGLMDEAEE----RGTAGDDDGAARLMEEAMVAAYRAQAVVPDAVLGVCTGIF +DTLGASATSAALQLDRHWRNARTLATHDPAAFKVRMAGDHLVNGTPPTAYTSAGVVDD-D +>GCF_020097155_PROKKA_00143 +MTTYATLAARYADAFDSVAHGERAREAGRHLPFAALGELQAAGFGKVGVPVDAGGEGGGS +ETVLRLLMDLAARDVNTAHVWRSHLVFIATAMDQAPARRDRWLRHIVAGDWAGSALAERA +GGAAPGRAATLASRDEGGTWVVRGQKYYATGSAFATWTAATVGIEGADLVSRRNSKRAGG +AVREPDRAVAVVRVRQPRVGIKDDWDGFGQRLTATGSVVLDDAAAEELLEVPRQDGPVPV +LMEATLLALQAGIGRAALTEGTQLLRKRRRTFNTGTAALPKDDPQLLEIMGQLAGRQAAA +ELMVREIGRLLDEGEDGADGAGLAEADVVAAS--AEAMAAAYRAQAVVPEAVLEVCTRIF +DTLGASATSATLRLDRHWRNARTLATHDPAAFKVRMAGDWLVNGTPPTAYTSAGDAQD-- +>GCF_023573625_PROKKA_00205 +MTTYATLAARYADAFDSVAHGERAREAGRHLPFAALGELQAAGFGKVGVPVDAGGEGGGS +ETVLRLLMDLAARDVNTAHVWRSHLVFIATAMDQAPARRERWLRHIVDGDWAGSALAERA +GGAAPGRAATLASRDEGGTWVVRGQKYYATGSAFATWTAATVGIEGADLVSRRNSKRAGG +AVREPDRAVAVVRVRQPRVGIKDDWDGFGQRLTATGSVVLDDAAAEELLEVPRQDGPVPV +LMEATLLALQAGIGRAALTEGTQLLRQRRRTFNTGTAALPKDDPQLLEIMGQLAGRQAAA +ELMVREIGRLLDEGEDGADGAGPAEADVVAAS--AEAMAAAYRAQAVVPEAVLEVCTRIF +DTLGASATSATLRLDRHWRNARTLATHDPAAYKVRMAGDWLVNGTPPTAYTSAGEVPEGD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000313.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000313.fa new file mode 100644 index 0000000000000000000000000000000000000000..b7075eefa35727797a4803ca21bf60a119b538d3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000313.fa @@ -0,0 +1,11 @@ +>GCF_002008305_PROKKA_00215 +MDRELRTPPELEGVDW-HDDAPRRPRPIVTLVAWIAILGLVLSVGAGIFSAF +>GCF_003691675_PROKKA_02208 +MDRELRTPPELEGVDW-HDDAPRRPRPIVTLVAWIAILGLVLSVGAGIFSAF +>GCF_005280335_PROKKA_00166 +MDRSNEIPPELQGLDWGEDDAPRRRRPLITLVAWLCIIGLVLGVAAGLFSIL +>GCF_020097155_PROKKA_00119 +M---ADLPPELEFAEFDDDPRPSAPSPWVRVLAVVVLLGLVGSLAAGLFGGI +>GCF_023573625_PROKKA_00215 +MDRELRTPPELEGVDW-HDGAPRRPRPIVTLVAWIAILGLVLSVGAGIFSAF + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000326.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000326.fa new file mode 100644 index 0000000000000000000000000000000000000000..5bae5677665d947bd8203b642d46ee3ce988dbb0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000326.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00235 +MAIHPVDATLEAAKIDPDQRAERLKGVKLDGAGWKYALTRALKEFGNDGGTDLAAKLTYY +LVLSLAPSLLAVFSILSLVLASNRGAIDDLLGELTGLVPSDYQPLVTNLVTTMSDSAGSG +GGIIALIIGIATALWSASAYVKAFNRSANTVYGYEEGRGLVKLTLTNLLTTLILIVGIVV +VLLSLALNRSLVDGFLQPIAGPLGMTGVVNFLSDTFLPVWAWAKWPVVVVILLVLIATLY +YTTPNVQKPRFHLFGPGNIVALVGMVLAAVALSVYFTQFAGYSAYGAIGTVMALLFALWI +FNIVLLLGLEVDAEVERARQLEAGLPAEARVQLPPKDVAGVEKRAEKQTAVEERGYELRA +VHEG------------------------R +>GCF_003691675_PROKKA_02248 +MAIHPVDATLEAAKIDPDQRAERLKGVKLDGAGWKYALTRALKEFGNDGGTDLAAKLTYY +LVLSLAPSLLAVFSILSLVLASNRGAIDDLLGQLTGLVPSDYQALVTNLVTTMSDSAASG +GGIIALVIGIATALWSASAYVKAFNRSANTVYGYEEGRGLVKLTLTNLLTTLILIVGIVV +VLISLALNRSLVDGFLQPIAGPLGMTGVVNFLSDTFLPVWAWVKWPVVVLILLLLIATLY +YTTPNVQKPRFHLFGPGNIVALVGMVLAAVALSVYFTQFAGYSAYGAIGTIMALLFALWI +FNIVLLLGLEVDAEVERARQLEAGLPAEARVQLPPKDVAGVEKRAEKQTAVEERGYELRA +VHEG------------------------R +>GCF_005280335_PROKKA_00136 +MAIHPVDATLQAAKIDPEERTERLQGVKLDGAGWKYALGRAFKEFGKDGGTDLAAKLTYF +MVLSLAPSLLAVFSILSLVLASNRGAIDDLMAQMTGLVPGEYQPLVTDLVTTMSESASGG +GGIVALVVGILTALWSASAYVKAFNRSVNTVYGYEEGRGFVKLTLSNLLTTLIMIVGIVV +VLISLALNRSLVDGFLAPIAGPLGMTGAVNFLSDTFLPIWAWVKWPVVVVILLLLIATLY +YTTPNVRKPSFNLFGPGNVFALVGMVLAAVGLSVYFTQFAGYSAYGAIGTIMALLFALWI +FNIVLLLGVEIDAEVERAKQLVAGLPAEEAVRLPPKDASALEKRVEKQTALQERGYELRA +THED------------------------R +>GCF_020097155_PROKKA_00101 +MAIHPVDATLEAARIDPEERTRRLKGVKLDGAGWKYAFTRALKEFGNDGGTDLAAKLTYF +MVLSLAPALLAVFSILTLVLSSNRSAVDDVVRQLTELVPADYQGVVGDVVDNLLGQA--G +GGVLALIIGILTALWSASAYVKAFSRASNQVYNYSEGRGFVKLTLTNLVTTVVMLVGIVL +VLISLALNRSLVDGFLAPIAGPLGMTDAVNFLSDTFLPIWAWLKWPVVVALLLVLIATLY +YFAPNVKKPSFHMFGPGNIFALVGMALAAVALYFYFTTLAGYSAYGAIGGVMALLFALWI +FNIVLLLGLEIDTEVERAKQLTAGMPAEDAVKLPPKDVSALEKKVEKQEELEEKGYELRA +LHDDGSDSDSDEGKGVSRAPRHAAGSHGA +>GCF_023573625_PROKKA_00236 +MAIHPVDATLEAAKIDPDQRAERLKGVKLDGAGWKYALTRALKEFGNDGGTDLAAKLTYY +LVLSLAPSLLAVFSILSLVLASNRGAIDDLLGQLTGLVPSDYQALVTNLVTTMSDSAASG +GGIIALVIGIATALWSASAYVKAFNRSANTVYGYEEGRGLVKLTLTNLLTTLILIVGIVV +VLISLALNRSLVDGFLQPIAGPLGMTGVVNFLSDTFLPVWAWVKWPVVVLILLVLIATLY +YTTPNVQKPRFHLFGPGNIVALVGMVLAAVALSVYFTQFAGYSAYGAIGTIMALLFALWI +FNIVLLLGLEVDAEVERARQLEAGLPAEARVQLPPKDVAGVEKRVEKQTTLEERGYELRA +VHEG------------------------R + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000334.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000334.fa new file mode 100644 index 0000000000000000000000000000000000000000..f6ec7d9aadc92b2a7500ec6ce51de293e73831de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000334.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00248 +------MDLSNQSAIVTGGASGLGHATARRLADAGAAVVVVDLPDRERETVRADAVAALG +PRARFVTGDVTAEDTAREAVAAALEAGPLRVLVNCAGVATPGKLVGRDGPLSAEVLSRVL +AINTVGTVAMMAQAAAAMKAQEPLGEDRGVIVNTASVAAYDGQIGQIAYSASKGAVVALT +LPAARELASSQIRVVTIAPGLMETPMMAGLPEAAREALSTKTPHPARLGRPEDHALLVEQ +IVSNPFLNGEVIRLDGAVRLEPR +>GCF_003691675_PROKKA_02260 +------MDLSNQSAIVTGGASGLGHATARRLADAGAAVVVVDLPDREGETVRADAVAALG +PRARFVTGDVTAEDTAREAVAAALEAGPLRVLVNCAGVATPGKLVGRDGPLSAEVLSRVL +AINTVGTVSMMAQAAAAMKAQEPLGEDRGVIVNTASVAAYDGQIGQIAYSASKGAVVSLT +LPAARELASSQIRVVTIAPGLMETPMMAGLPEAAREALSTKTPHPARLGRPEDYALLVEQ +IVSNPFLNGEVIRLDGAVRLEPR +>GCF_005280335_PROKKA_00122 +------MDLSNQSAIVTGGASGLGHATARRLAEAGAAVVVVDLPDREGETLRADAVAALG +PRARLVTGDVTAEATAEEAVAAALEAGPLRVLVNCAGVATPGKLVGRGGPLSAEVLTRVL +AINTVGTVNFMSRAAAAMQGQEPQGEDRGVIVNTASVAAYDGQIGQIAYAASKGAVVSLT +LPAARELAASQIRVVTIAPGLMETPMMAGLPEAAREALATKTPHPARLGRPEDYALLVEQ +IVANPFLNGEVIRLDGAVRLEPK +>GCF_020097155_PROKKA_00090 +MARRESLDLQGASAIVTGGASGLGHATARRLAAAGAAVVVVDLPDREGESLRADAVASLG +ERARFITGDVTAEATAEQAVAAALEAGPLRVLVNCAGVATPGKLVGRDGPLAAEALSRVL +AINVVGTVTMMARAAAVMKDQELWGEDRGVIVNTASVAAFDGQIGQIAYSASKGAVAALT +LPAARELAASQVRVVTIAPGLMETPMMAGLPEAAREALSTKTPHPARLGAPDDYALLVEQ +IVSNPFLNGETIRLDGAVRLEPR +>GCF_023573625_PROKKA_00248 +------MDLSNQSAIVTGGASGLGHATARRLADAGAAVVVVDLPDREGETVRADAVAALG +PRARFVTGDVTAEDTAREAVAAALEAGPLRVLVNCAGVATPGKLVGRDGPLSAEVLSRVL +AINTVGTVSMMAQAAAAMKAQEPLGEDRGVIVNTASVAAYDGQIGQIAYSASKGAVVALT +LPAARELASSQIRVVTIAPGLMETPMMAGLPEAAREALSTKTPHPARLGRPEDYALLVEQ +IVSNPFLNGEVIRLDGAVRLEPR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000335.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000335.fa new file mode 100644 index 0000000000000000000000000000000000000000..123a63f8d99b67a8b04dd28612ab2cf5cd47d5c8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000335.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00249 +MK-KPPLAQDPIREAARNWERHGWGDVARPMAAITSIMRAQQILLGRAQAALKPYGLTFA +RYELLALLNFSRENRMRMSKASALLQVHPTSVTNAVDRLEAAGLVERTPHESDRRALVLA +LTDEGRRVAVAATETLNAEVFGRSGFGPADVDTLIDVLGRFRAEAGDFQVDGPDAGAPAT +AEHTSS +>GCF_003691675_PROKKA_02261 +MK-KPPLAQDPIREAARNWERHGWGDVARPMAAITSIMRAQQILLGRAQAALKPYGLTFA +RYELLALLNFSREKRMRMSKASALLQVHPTSVTNAVDRLEAAGLVERTPHESDRRALVLA +LTDEGRRVAVAATETLNAEVFGRSGFDPADVDTLIDVLGRFRAEAGDFEADGPDAGAPAT +AEHTSS +>GCF_005280335_PROKKA_00121 +MK-NAPLPQDPIREAARNWERHGWGDVARPMAAVTSIMRAQQILLGRTQAALKPFGLTFA +RYELLALLNFSREKRMRMSKASALLQVHPTSVTNAVDRLESAGLVERTPHESDRRALVLA +LTDEGRRVAVAATETLNEEVFGRTGFDEADVDALIDVFGRFRAGAGDFEADGAD----TT +TERPSA +>GCF_020097155_PROKKA_00089 +MSTRDPLPQDPIREAARNWEHHGWGEVAAPMAAVTAIMRTQAILLARTQAVLKPFGLTFA +RYELLALLNFSRERRQLMSKAGALLQVHPTSVTNAVDRLEAAGLVERQPHETDRRALLLA +LTDEGRRVADAATEALNAEVFGATGFTDDDVAALNEILGRFRAGSGDFEA---------- +------ +>GCF_023573625_PROKKA_00249 +MK-KPPLAQDPIREAARNWERHGWGDVARPMAAITSIMRAQQILLGRAQAALKPYGLTFA +RYELLALLNFSREKRMRMSKASALLQVHPTSVTNAVDRLEAAGLVERTPHESDRRALVLA +LTDEGRRVAVAATETLNAEVFGRSGFDPADVDTLIDVLGRFRAEAGDFEADGPDAGAPAT +AEHTSS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000337.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000337.fa new file mode 100644 index 0000000000000000000000000000000000000000..7f9080e2dc8ab1ed812749dde0554d9692f82989 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000337.fa @@ -0,0 +1,70 @@ +>GCF_002008305_PROKKA_00255 +MTSPQTTESTTALPHERVEPKDTASAPFVARHIGPRPADVEHMLQTLGYDSLEALVDTAVPAGIRQPKPLELPAPLTESA +VLEQLREIAGRNVMKTQMIGQGFSDTVTPGVILRKVLENPAWYTAYTPYQPEISQGRLEALLNYQTMVQDLTGLDIANAS +LLDEASAAAEAVLLMHRANRRRTDGVTLLDADLFPQTLSVVRLRAEAVGIDVRVADLSAGIPEDVRAEVEEKGLCGVVLQ +QPGDSGRIHDHAAVIAQAKEAGALVTVAADILSLALITPPGEQGADIAVGSTQRFGVPLFFGGPHAAYMAVKEGLQRSMP +GRLVGVSHDDAGKPAYRLALQTREQHIRREKATSNICTAQALLAIVASMYAVYHGPQGIARIARHAHAQAVRLAEALRAG +GVEVAEEHFFDTITVRVPGRAEQVLQAAEENGVNLRLVDADTLRIAADETTVDADLVAVLTAFGLDAGSLPASAHEGAVA +TPAVPESLRRSSAFMMHPVFNTHHSETKMLRYLRRLSGYDLALDRTMIPLGSCTMKLNATAEMEAISWPEFCSIHPFAPD +HQTEGWRFLIADLEAKLAEITGYAGVSVAPNAGSQGEFAGLWAIRQYHLARGEGERDICLIPASAHGTNAASAVLAGLKV +VVVATADDGTIDAADLDAKIAANEGRIAAIMITYPSTHGVYDADVKEVCATVHAAGGQVYIDGANLNALVGLAQPGEFGG +DVSHLNLHKTFCIPHGGGGPGVGPVAVGEHLVPYLPSREALMTAAPHGSAGVLPISWAYIHLMGAEGLRSATAHALLGAN +YISRRLAPLYPTLYTGNDGLVAHECILDLRELTARTGVTAEDVCKRLIDYGFHAPTLAFPVAGTLMVEPTESEDLEEIER +FIEAMEAIHAEITAVTPETVADSVLRRAPHTLNVLMADEWDRPYSRAQAGTPVPSLRLDKYLPPVGRIDGAYGDRNLVCS +CPPPEAFEGAVADTADED------------ +>GCF_003691675_PROKKA_02269 +MTSPQTTESTTALPHERVEPKDTASAPFVARHIGPRPADVEHMLQTLGYDSLEALVDTAVPAGIRQPKPLELPAPLTESA +VLEQLREIAGRNVMKTQMIGQGFSDTVTPGVILRKVLENPAWYTAYTPYQPEISQGRLEALLNYQTMVQDLTGLDIANAS +LLDEASAAAEAVLLMHRANRRRTDGVTLLDADLFPQTLSVVRLRAEAVGIDVRVADLSAGIPEDVRAEVEEKGLCGVVLQ +QPGDSGRIHDHAAVIAQAKEAGALVTVAADILSLALITPPGEQGADIAVGSTQRFGVPLFFGGPHAAYMAVKEGLQRSMP +GRLVGVSHDDAGKPAYRLALQTREQHIRREKATSNICTAQALLAIVASMYAVYHGPQGIARIARHAHAQAVRLAEALRAG +GVEVAEEHFFDTITVRVPGRAEQVLQAAEENGVNLRLVDADTLRIAADETTVDADLVAVLTAFGLDAGSLPASAHEGAVA +TPAVPESLRRSSAFMTHPVFNTHHSETKMLRYLRRLSGYDLALDRTMIPLGSCTMKLNATAEMEAISWPEFCSIHPFAPD +HQTEGWRFLIADLEAKLAEITGYAGVSVAPNAGSQGEFAGLWAIRQYHLARGEGERDICLIPASAHGTNAASAVLAGLKV +VVVATADDGTIDAADLDAKIAANEGRIAAIMITYPSTHGVYDADVKEVCATVHAAGGQVYIDGANLNALVGLAQPGEFGG +DVSHLNLHKTFCIPHGGGGPGVGPVAVGEHLVPYLPSREALMTAAPHGSAGVLPISWAYIHLMGAEGLRSATAHALLGAN +YISRRLAPLYPTLYTGNDGLVAHECILDLRELTARTGVTAEDVCKRLIDYGFHAPTLAFPVAGTLMVEPTESEDLEEIER +FIEAMEAIHAEITAVTPETVADSVLRRAPHTLNVLMADEWDRPYSRAQAGTPVPSLRLDKYLPPVGRIDGAYGDRNLVCS +CPPPEAFEDAVADTADED------------ +>GCF_005280335_PROKKA_00114 +MTSPQTTESTTALPHERVEPKDTASAPFVARHIGPRPADVEHMLQTLGYDSLEALVDTAVPAGIRQPKPLELPAPLTESA +VLEQLREIAGRNVMKTQMIGQGFSDTVTPGVILRKVLENPAWYTAYTPYQPEISQGRLEALLNYQTMVQDLTGLDIANAS +LLDEASAAAEAVLLMHRANRRRTDGVTLLDADLFPQTLSVVRLRAEAVGIDVRVADLSAGIPEDVRAEVEEKGLCGVVLQ +QPGDSGRIHDHAAVIAQAKEAGALVTVAADILSLALITPPGEQGADIAVGSTQRFGVPLFFGGPHAAYMAVKEGLQRSMP +GRLVGVSHDDAGKPAYRLALQTREQHIRREKATSNICTAQALLAIVASMYAVYHGPQGIARIARHAHAQAVRLAEALRAG +GVEVAEEHFFDTLTVRVPGRAEQVLQAAEENGVNLRLVDADTLRIAADETTVDADLVAVLTAFGLDAGALPASAHEGAVA +TPAVPEALRRSSAFMTHPVFNTHHSETQMLRYLRRLSGYDLALDRTMIPLGSCTMKLNATAEMEAISWPEFCSIHPFAPD +HQTEGWRFLIADLEAKLAEITGYAGVSVAPNAGSQGEFAGLWAIRQYHLARGEGERDICLIPASAHGTNAASAVLAGLKV +VVVATADDGTIDAADLDAKIAANEGRIAAIMITYPSTHGVYDADVKEVCATVHAAGGQVYIDGANLNALVGLAQPGGFGG +DVSHLNLHKTFCIPHGGGGPGVGPVAVGEHLVPYLPSREALMTAAPHGSAGVLPISWAYIHLMGAEGLRSATEHALLGAN +YISRRLAPLYPTLYTGNDGLVAHECILDLRELTARTGVTAEDVCKRLIDYGFHAPTLAFPVAGTLMVEPTESEDLQEIER +FIEAMEAIHAEITAVTPETVADSVLRRAPHTLNVLMADEWDRPYSRAQAGTPVPSLRLDKYLPPVGRIDGAYGDRNLVCS +CPPPEAFEDAVADTADED------------ +>GCF_020097155_PROKKA_00082 +MTSPLTP----------TEPRDTASAPFVARHIGPRGEDVRHMLQTLGLGSVDELVDTAVPSVIRQSAPLDLPAPLTEAA +ALEQLREIAGRNVVKTQMIGQGFYDTVTPGVILRKVLENPAWYTAYTPYQPEISQGRLEALLNYQQMVEDLTALPIANAS +LLDEASAAAEAVLLMHRANRKKADGITLLDADLFPQTLTVAQMRAEAVGLEVRVADLSAGIPEDVRAEVEEKGLCGVVLQ +QPGDSGRLHDHSAVIAQAKEAGALITVAADILSLALITPPGEQGADIAIGSTQRFGVPLFFGGPHAAYLAVREGLQRSMP +GRLVGVSHDDAGKPAYRLALQTREQHIRREKATSNICTAQALLAITASMYAVYHGPAGITAIARHAHAQAHRLAIALAGA +GVEVAHAEYFDTLTLNVPGRAEEVVRAAEEAGVNLRLVDADIVRVACDETTVDEDLAAVLTAFGADPASLPAAPHEGAVQ +TPAVPEAQRRTSAFMTHPVFNTHRSETQMLRYITRLANRDLALDRTMIPLGSCTMKLNATTEMEAISWPEFCAIHPFAPD +HQTEGWRFLISDLEERLAEITGYAGVSVAPNAGSQGEFAGLWAIRQYHLAHGDGERDVCLIPASAHGTNAASAVLAGLRV +VVVATADDGTIDSADLDAKIAAHEGRVAAIMITYPSTHGVFDGDVTEVCDKVHAAGGQVYIDGANLNALVGLARPGAFGG +DVSHLNLHKTFCIPHGGGGPGVGPVAVGEHLVPFLPSAERLVTAAPHGSAGVLPISWAYIAMMGGEGLKDATEQALLNAN +YISRRLADHYPTLYTGEGGLVAHECILDLRELTAQTGVTAEDVCKRLIDYGFHAPTLAFPVAGTLMVEPTESEDLAELDR +FIDAMISIHAEITATTPETVEQSVLRRAPHTLGATTGEDWDRPYTRAQALYPLPSLVDDKYLPPVGRIDGAYGDRNLVCS +CPPPEAFEEAAASPESTEPVSAADTASTSH +>GCF_023573625_PROKKA_00254 +MTSPQTTESTTALPHERVEPKDTASAPFVARHIGPRPADVEHMLQTLGYDSLEALVDTAVPAGIRQPKPLELPAPLTESA +VLEQLREIAGRNVMKTQMIGQGFSDTVTPGVILRKVLENPAWYTAYTPYQPEISQGRLEALLNYQTMVQDLTGLDIANAS +LLDEASAAAEAVLLMHRANRRRTDGVTLLDADLFPQTLSVVRLRAEAVGIDVRVADLSAGIPQDVRAEVEEKGLCGVVLQ +QPGDSGRIHDHAAVIAQAKEAGALVTVAADILSLALITPPGEQGADIAVGSTQRFGVPLFFGGPHAAYMAVKEGLQRSMP +GRLVGVSHDDAGKPAYRLALQTREQHIRREKATSNICTAQALLAIVASMYAVYHGPQGIARIARHAHAQAVRLAEALRAG +GVEVAEEHFFDTITVRVPGRAEQVLKAAEENGVNLRLVDADTLRIAADETTVDADLVAVLTAFGLDAGSLPASAHEGAVA +TPAVPEALRRSSAFMTHPVFNTHHSETKMLRYLRRLSGYDLALDRTMIPLGSCTMKLNATAEMEAISWPEFCSIHPFAPD +HQTEGWRFLIEDLEAKLAEITGYAGVSVAPNAGSQGEFAGLWAIRQYHLARGEGERDICLIPASAHGTNAASAVLAGLKV +VVVATADDGTIDAADLDAKIAANEGRIAAIMITYPSTHGVYDADVKEVCATVHAAGGQVYIDGANLNALVGLAQPGEFGG +DVSHLNLHKTFCIPHGGGGPGVGPVAVGEHLVPYLPSREALMTAAPHGSAGVLPISWAYIHLMGAEGLRSATAHALLGAN +YISRRLAPLYPTLYTGNDGLVAHECILDLRELTARTGVTAEDVCKRLIDYGFHAPTLAFPVAGTLMVEPTESEDLEEIER +FIEAMEAIHAEITAVTPETVADSVLRRAPHTLNVLMADEWDRPYSRAQAGTPVPSLRLDKYLPPVGRIDGAYGDRNLVCS +CPPPEAFEGAVADTADED------------ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000352.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000352.fa new file mode 100644 index 0000000000000000000000000000000000000000..baebfffb3df98ea3c470042fbff4cc1f5bf18062 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000352.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00278 +MSVRTPDPNPGWLSDEDLYEARRRLPMVYVEAIPVRLDSLGYVTEIGLLYVADETGTFQR +TFVSGRVQYRETIRAALMRHLEKDLGPLAFPQLPPSVVPCTVAEYFPAPSETGLTDDRQH +AVALVYVVPVTGECQPRQNALELTWLTPEEALGEDIQAEFIGGRGDLVRQALAHVGWGR +>GCF_003691675_PROKKA_02293 +MSVRTPDPNPGWLSDEDLYEARRRLPMVYVEAIPVRLDSLGYVTEIGLLYVADETGTFQR +TFVSGRVQYRETIRAALMRHLEKDLGPLAFPQLPPSVVPCTVAEYFPAPSETGLTDDRQH +AVALVYVVPVTGECQPRQNALELTWLTPEEALGEDIQAEFIGGRGDLVRQALAHVGWGR +>GCF_005280335_PROKKA_00075 +MSVRTPDPNPGWLSDEDLYEARRRLPMVYVEAIPVRLDSLGYVTEIGLLYVADETGTFQR +TFVSGRVQYRETIRAALMRHLEKDLGPLAFPQLPPSVVPCTVAEYFPAPSETGLTDDRQH +AVALVYVVPVTGECQPRQNALELTWLTPEEALGQDIQAEFIGGRGDLVRQALAHVGWGR +>GCF_020097155_PROKKA_00060 +MSVRTPDPNPGWLNEEDLYEARRRLPMVYVEAIPVRVDALGYVSEIGLLYVADEEGQFQR +TFVSGRVMYRETIRGALMRHLEKDLGPLAFPQLPPSLVPCAVAEYFPAPSETGLTDDRQH +AVSLVYVVPVSGECSPRQDALELTWLTPQEALGEDVQAEFIGGRGNLVRQALAHVGWGR +>GCF_023573625_PROKKA_00277 +MSVRTPDPNPGWLSDEDLYEARRRLPMVYVEAIPVRLDSLGYVTEIGLLYVADETGTFQR +TFVSGRVQYRETIRAALMRHLEKDLGPLAFPQLPPSVVPCTVAEYFPAPSETGLTDDRQH +AVALVYVVPVTGECQPRQNALELTWLTPEEALGEDIQAEFIGGRGDLVRQALAHVGWGR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000358.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000358.fa new file mode 100644 index 0000000000000000000000000000000000000000..4f75c1e7400cd3b21fa1eb78e1083ae86ecc81ff --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000358.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00289 +M---TSTARSPRVSRRAALGLGVGALAVGGVAVVTDLAGAPAGP-LGANATALYGMRSST +GHTYATLPGRAGRIDVYRPPGQGPFPVLVWNAGSGWRSDRGYSDGVDVARGLVPHGYAVA +AFSVRSSKQGTFPAQVEDATAAVRWVRRNAPGLQLDAGRVAVAGSSSGGWNALMAGLTGG +QDLDREQVPLPGREVPDGGHAIPEEDRVQAIVDFFGPTDFLTMNRQMLPGACADYNRANR +LKHCHLDDRSTKSDMLGVPVLASGGLTRLASPIAHVRPDSPPLLVVHGRKDVTVPWGQSL +ELYRAAETAGLRTAFYSVAEGSHDLGMMTAKTRSAEVLRNGVPASAVHATISWSAVASFL +DAVLPR--- +>GCF_003691675_PROKKA_02311 +M---TSTARSPRVSRRAALGLGVGALAVGGVAVVTDLAGAPAGP-LGANATALYGMRSST +GHTYAALPGRAGRIDVYRPPGQGPFPVLVWNAGSGWRSDRGYSDGVDVARGLVPHGYAVA +AFSVRSSKQGTFPAQVEDATAAVRWVRRNAPGLQLDAGRVAVAGSSSGGWNALMAGLTGG +QDLDREQVPLPGREVPDGGHAIPEEDRVHAIVDFFGPTDFLRMNRQMLPGACADYNRANR +LEHCHLDDHSTKADMLGVPVLASGGLTRLASPIAHVRPDSPPLLVVHGRKDVTVPWGQSL +ELYRAAEAAGLRTAFYSVAEGGHDLGMMTAKTRSAEVLRTGVPASAVHASISWSAVASFL +DAVLPR--- +>GCF_005280335_PROKKA_00065 +M---ATSGRRGRLTRRAVLGLGAGALALGGGAAVANLAGVPPAP-VGPDVNALFGMRSST +GHRYADLPGRAGRVDVYRPQGPGPFPVVVWNAGSGWRDDRGYHDGQTVARGLVPHGYAVA +AFSVRSSKQGRFPAQVEDATAAVRWVRAHAVELDLDASRLTVAGTSSGGWNALMAGLTGG +RDLDRAHVPPPGREVPPGGHAIPEEDRVQAILDFFAPTDFLAMNAQMPPGACADYNRQRR +LEHCHLDDHSTKSAMLGVPVLASYGLTRLASPIAHVRPDSPPMMIVHGLKDPTVPWRQSL +ELYEAAEAAGVRAAFYSVADAGHDLGMMGGGWGSAEVLRSGVPLSAVHATISWAAVAAFL +DTVLPG--- +>GCF_020097155_PROKKA_00044 +MGGDTSTARAPRVRRRTLLGLGLGALAVGGTATALGHGSPVDSPALRQTMGALFGTTVIS +GIVYADLPGAAGRMDLYLPEGEGPFPVLAWNAGSGWRSDRGFQGGDAVARGLVPAGHAVA +AFSVRSAREDAFPAQVLDATAAVRHLRENAGELRVDPGRIAVGGNSSGGWNALMAGLTGG +RDLDRSAVPAPGDEVPEGGHAIPEEDRVQAIVDCFAPVDFLQMNVQMPRGACEEYDRRNH +TRHCHLDDASTKSRMLGAPVMARPELARLANPAVHVTPAAPPTLIVHGRADREVPYVQSR +GLYQAYVGAGVPVAMYSVEGAGHDLQMMARRVGRTDVVRSGLPRQAVHGSISWSAVAAFL +DVAMPRPRR +>GCF_023573625_PROKKA_00295 +M---TSTARSPRVSRRAALGLGVGALAVGGVAVVTDLAGAPAGP-LGANATALYGMRSST +GHTYAALPGRAGRIDVYRPPGQGPFPVLVWNAGSGWRSDRGYSDGVDVARGLVPHGYAVA +AFSVRSSKQGTFPAQVEDATAAVRWVRRNAPGLQLDAGRVAVAGSSSGGWNALMAGLTGG +QDLDREQVPLPGREVPDGGHAIPEEDRVHAIVDFFGPTDFLRMNRQMLPGACADYNRANR +LEHCHLDDHSTKADMLGVPVLASGGLTRLASPIAHVRPDSPPLLVVHGRKDVTVPWGQSL +ELYRAAEAAGLRTAFYSVAEGGHDLGMMTAKTRSAEVLRTGVPASAVHASISWSAVASFL +DAVLPR--- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000363.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000363.fa new file mode 100644 index 0000000000000000000000000000000000000000..72cf46212d22e3dac963f8b0305c0f8463d65a19 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000363.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_00296 +MADNATTSFADRALADAPTDYAQLREWVAQIAELTQPDSVQWVDGSEEERDRLADELVAAGTLTRLAEDKFPNSFAAFSD +PADVARVEDRTFICSEKEEDAGFTNNWMDPAKMHGILDDAFTGAMRGRTMYVIPFVMGHLDAEDPKYGVEITDSAYVVLS +MRIMARIGQDVLDKMSREQAFYVPAVHSVGAPLEPGEQDVPWPCNETKWIVHFPEERSIWSFGSGYGGNALLGKKCYALR +IASVMARDEAWLAEHMLILKLTNPEGRSYHITGAFPSACGKTNLALIDPTIEGWKAETLGDDITWIRAGKDGEFRVINPE +TGYFGVAPGTGWSTNPNAMRAISKGNSIFTNVALTDDGGVWWEGMTDEVPEHLTDWRGNDWTPEFGTPAAHPNSRFCTPI +EQTDMLADEYRDPRGVKLDAILFGGRRKTTVPLVTEAFDWEDGILKGATLSSETTAAAAGAVGVVRRDPMAMLPFLGYDA +GDYLAHWVRESGKADPEKLPRIYLVNWFRRNRDGGFAWPGFGENSRVLKWVVERLEGKAEAEETPIGLVPAAGSLDLSGI +EVSAEDLEDALKVDAAEWAEENELIEQWLGRFGESLPAVVRERFEAQKARFAQA +>GCF_003691675_PROKKA_00004 +MADNATTSFADRALADAPTDYAQLREWVAQIAELTQPDSVQWVDGSEEERDRLADELVAAGTLTRLAEDKFPHSFAAFSD +PADVARVEDRTFICSEKEEDAGFTNNWMDPAKMHGILDDAFTGAMRGRTMYVIPFVMGHLDAEDPKYGVEITDSAYVVLS +MRIMARIGQDVLDKMSREQAFYVPAVHSVGAPLEPGEQDVPWPCNETKWIVHFPEERSIWSFGSGYGGNALLGKKCYALR +IASVMARDEAWLAEHMLILKLTNPEGRSYHITGAFPSACGKTNLALIDPTIEGWKAETLGDDITWIRAGKDGEFRVINPE +TGYFGVAPGTGWSTNPNAMRAISKGNSIFTNVALTDDGGVWWEGMTDEVPEHLTDWRGNDWTPESGTPAAHPNSRFCTPI +EQTDMLADEYRDPRGVKLDAILFGGRRKTTVPLVTEAFDWEDGILKGATLSSETTAAAAGAVGVVRRDPMAMLPFLGYDA +GDYLAHWVRESGKADPEKLPRIYLVNWFRRNRDGGFAWPGFGENSRVLKWVVERLEGKAEAEETPIGLVPAAGSLDLSGL +EVSAEDLEDALKVDAAEWAEENELIEEWLGRFGESLPQAIRDRFEAQKQRFAQA +>GCF_005280335_PROKKA_00058 +MADNATTSFADRALQDAPTDYAQLREWVAQVAELTQPDAVQWVDGSEEEYARLADELVAAGTLTRLAEDKFPNSFAAFSD +PADVARVEDRTFICSEKEEDAGFTNNWMDPEKMHGILDDVFAGSMRGRTMYVIPFVMGHLDAEDPKYGVELTDSAYVVLS +MRIMARIGQDVLDKMSREQAFYVPAVHSVGAPLEPGQEDVPWPCNSTKWIVHFPEERSIWSFGSGYGGNALLGKKCYALR +IASVMARDEAWLAEHMLILKLTSPEGRSYHITGAFPSACGKTNLALIDPTIEGWKAETLGDDITWIRAGKDGEFRVINPE +TGYFGVAPGTGWSTNPNAMRAIAKGNSIFTNVALTDDGGVWWEGMTDEVPEHLTDWRGNDWTPASETPAAHPNSRFCTPI +EQTDMLADEYRDPKGVKLDAILFGGRRKTTVPLVTESFDWEDGILKAATLSSETTAAAAGAVGVVRRDPMAMLPFLGYDA +GDYLAHWVEESGKADPEKLPRIYLVNWFRRNRDGGFAWPGFGENSRVLKWVVERLEGRADAVETPIGHVPSPEALDLTGI +DVSAEDLEDALKVDAEEWAKENELIEEWLGRFGESLPAMVRERFEAQKERFARA +>GCF_020097155_PROKKA_00036 +MADNATTSFTELATKDAPTDYAQLREWVAGIAELTQPDAVHWVDGSQEEYDRLAAELVAAGTLTKLNEKKLPNSYAAFSD +PADVARVEDRTFICSEKEEDAGFTNNWMDPKEMHGILDDAFAGSMRGRTMYVIPFVMGHLDAEDPKYGVEITDSAYVVLS +MRIMARIGQDVLDKMSREQAFYVPAVHSVGAPLEPGEQDVPWPCNETKWIVHFPEERSIWSFGSGYGGNALLGKKCYALR +IASVMARDEAWLAEHMLILKLTNPEGRSYHITGAFPSACGKTNLALIDPTIEGWKAETLGDDITWIRAGKDGEFRVINPE +TGYFGVAPGTGWSTNPNAMRAISKGNSIFTNVALTDDGGVWWEGMTDEVPEHLTDWRGNDWTPESGTPAAHPNSRFCTPI +EQTDMLADEYRDPRGVKLDAILFGGRRKTTVPLVTEAFDWEDGILKGATLSSETTAAAAGAVGVVRRDPMAMLPFLGYDA +GDYLAHWVKESGKADPEKLPRIYLVNWFRRNRDGGFAWPGFGENSRVLKWVVERLEGKAGAEETPIGLVPAAGSLDLSGI +EVSAEDLEDALKVDAAEWAEENELIEEWLGRFGESLPQAIRDRFEAQKARFAQA +>GCF_023573625_PROKKA_00303 +MADNATTSFADRALADAPTDYAQLREWVAQIAELTQPDSVQWVDGSEEERDRLADELVAAGTLTRLAEDKFPNSFAAFSD +PADVARVEDRTFICSEKEEDAGFTNNWMDPAKMHGILDDAFTGAMRGRTMYVIPFVMGHLDAEDPKYGVEITDSAYVVLS +MRIMARIGQDVLDKMSREQAFYVPAVHSVGAPLEPGEQDVPWPCNETKWIVHFPEERSIWSFGSGYGGNALLGKKCYALR +IASVMARDEAWLAEHMLILKLTNPEGRSYHITGAFPSACGKTNLALIDPTIEGWKAETLGDDITWIRAGKDGEFRVINPE +TGYFGVAPGTGWSTNPNAMRAISKGNSIFTNVALTDDGGVWWEGMTDEVPEHLTDWRGNDWTPESGTPAAHPNSRFCTPI +EQTDMLADEYRDPRGVKLDAILFGGRRKTTVPLVTEAFDWEDGILKGATLSSETTAAAAGAVGVVRRDPMAMLPFLGYDA +GDYLAHWVRESGKADPEKLPRIYLVNWFRRNRDGGFAWPGFGENSRVLKWVVERLEGKAEAEETPIGLVPAAGSLDLSGL +EVSAEDLEDALKVDAAEWAEENELIEEWLGRFGESLPQAIRDRFEAQKQRFAQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000380.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000380.fa new file mode 100644 index 0000000000000000000000000000000000000000..fda4a680f1d5364930ecd27cd58d98f00c1f1e56 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000380.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00320 +MDPVIIGLLCGAVGLFTGVASMLAFRASERSRTVDLTVGEPTLAPGAAEVLSVVGRAYAV +VDDVDGVVRANPAAYALGLVRGHSLVQDQLRELTRTVRADGVIVERRMELPRGPLGQSSL +VVELRVAPLDEEYILILADDRTDVTRTEAMRHDFVVNVSHELKTPVGAISLLSEAIGDAA +EDEEAVRRFAARLGVESRRLSALVQDIIEFSRLQAKDVVQDGGPVDLNAVVADAVDRLRL +TAEDRGIALRVGGRVDAVVHGDQDQLMTAVRNLVDNAVRYSPEGTTVGIGLSSVDGLAQV +TVTDQGIGISPEEQERVFERFYRVDAARSRQTGGTGLGLSIVKHVVINHGGEVTLWSQPG +RGSTFTIRLPEW-GDGVAVD-GAPGA-AHVTERRGHRVTASAAPPTRKETSA +>GCF_003691675_PROKKA_00035 +MDPVIIGLLCGAVGLFTGVASMLAFRASERSRTVDLTVGEPTLAPGAAEVLSVVGRAYAV +VDDVDGVVRANPAAYALGLVRGHSLVQDQLRELTRTVRADGVIVERRMELPRGPLGQSSL +VVELRVAPLDEEYILILADDRTDVTRTEAMRHDFVVNVSHELKTPVGAISLLSEAIGDAA +EDEEAVRRFAARLGVESRRLSALVQDIIEFSRLQAKDVVQDGGPVDLNAVVADAVDRLRL +TAEDRGIALRVGGRVDAVVHGDQDQLMTAVRNLVDNAVRYSPEGTTVGIGLSSVDGLAQV +TVTDQGIGISPEEQERVFERFYRVDAARSRQTGGTGLGLSIVKHVVINHGGEVTLWSQPG +RGSTFTIRLPEW-GDGVAVD-GAPGA-AHVTERRGHRVTASAAPPTRKETSA +>GCF_005280335_PROKKA_00017 +MDPVIIGLLCGAVGLFIGVASMLAFRASERSRTVDLAVGEPTLAPGAAEVLAVVGRAYAV +VDDVDGVVRANPSAYALGLVRGHSLVQQQVKDLTRSVRAEGVIVERRLELPRGPLGQSSL +VVELRVAPLDEEYILILADDRTDVTRTEAMRHDFVVNVSHELKTPVGAISLLAEAIGDAA +EDEEAVRRFASRLGIESRRLTALVQDIIEFSRLQAKDVVQDGRAVDLNAVVADAVDRLRL +TAEDRGITLRVGGRVDAVVHGDADQLMTAVRNLVDNAVRYSPEGTTVGIGLSSADGLAQV +TVTDQGIGISPEEQERVFERFYRVDSARSRQTGGTGLGLSIVKHVVINHGGEVSLWSQPG +RGSTFTIRLPEWEDDGAAVD-GPPAA-SHVTERRGHRVTASAASPPRKESSA +>GCF_020097155_PROKKA_00013 +MDPVIIGLLCGAVGLLIGVASMLAFRASERSRTVDLSVEEPTLSPGAAEVLSVIGRSYIV +VDAVDGVVRANPSAYAMGLVRGHTLVPDALRELTGAVRADGVVRERQVDLPRDPRHQSSL +VVELRVAPLDDEYILVLAEDRTGAMRTEAMRHDFVVNVSHELKTPVGAISLLSEAIADAA +DDDDAVRRFARRLGVESTRLTALVQDIIEFSRLQAKDVVREGRSVDLNLVVAEAVDRVRL +TAEARGISIRAGGHVDTVVHGDPDQLMTAVRNLVDNAVRYSPDGTTVGVGLTSKDGLAQI +TVTDQGIGISPEEQERVFERFYRVDAARSRQTGGTGLGLSIVKHVVINHGGEVTLWSQPG +RGSTFTIRLPEWAQAPQTPDAGAPATVATLPERRGHRVAAAAA-PARKEHSA +>GCF_023573625_PROKKA_00327 +MDPVIIGLLCGAVGLFTGVASMLAFRASERSRTVDLTVGEPTLAPGAAEVLSVVGRAYAV +VDDVDGVVRANPAAYALGLVRGHSLVQDQLRELTRTVRADGVIVERRMELPRGPLGQSSL +VVELRVAPLDEEYILILADDRTDVTRTEAMRHDFVVNVSHELKTPVGAISLLSEAIGDAA +EDEEAVRRFAARLGVESRRLSALVQDIIEFSRLQAKDVVQDGGPVDLNAVVADAVDRLRL +TAEDRGIALRVGGRVDAVVHGDQDQLMTAVRNLVDNAVRYSPEGTTVGIGLSSVDGLAQV +TVTDQGIGISPEEQERVFERFYRVDAARSRQTGGTGLGLSIVKHVVINHGGEVTLWSQPG +RGSTFTIRLPEW-GDSVAVD-GAPGA-AHVTERRGHRVTASAAPPTRKETSA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000383.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000383.fa new file mode 100644 index 0000000000000000000000000000000000000000..69a4ae723adaf86590f3fca229baa6fd57ef0d53 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000383.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00323 +-----------------------MVFEVGETVVYPHHGAARIEEIKMRTIKGEEKMYLKL +KVAQGDLTIEVPAENVDLVGVRDVVDAEGLEHVMEVLRAEHVEEPTNWSRRYKANLEKLA +SGDVNKVAEVVRDLWRRDQDRGLSAGEKRMLAKARQVLVSELALAKKVTEEEAEGRLDKV +LEG +>GCF_003691675_PROKKA_00038 +-----------------------MVFEVGETVVYPHHGAARIEEIKMRTIKGEEKMYLKL +KVAQGDLTIEVPAENVDLVGVRDVVDAEGLEHVMEVLRAEHVEEPTNWSRRYKANLEKLA +SGDVNKVAEVVRDLWRRDQDRGLSAGEKRMLAKARQVLVSELALAKKVTEEEAEGRLDKV +LEG +>GCF_005280335_PROKKA_00014 +-----------------------MVFEVGETVVYPHHGAARIEEIKMRTIKGEEKMYLKL +KVAQGDLTIEVPAENVDLVGVRDVVDSEGLEEVVEVLQAEQVEEPTNWSRRYKANLEKLA +SGDVKKVAEVVRDLWRRDQDRGLSAGEKRMLSKARQVLVSELALAKKVTEEEAEGMLDQV +LEG +>GCF_020097155_PROKKA_00010 +MPDTRGVFRVSVVESTDRKGAFHMVFEVGETVVYPHHGAARIEEIKTRTIKGEEKMYLKL +KVAQGDLTIEVPAENVDLVGVRDVVDDKGLEHVVEVLQAEHVEEPTNWSRRYKANLEKLA +SGDVNKVSEVVRDLWRRDHDRGLSAGEKRMLSKARQVLVSELALAKKVSEEEAEGMLDKV +LEG +>GCF_023573625_PROKKA_00330 +-----------------------MVFEVGETVVYPHHGAARIEEIKMRTIKGEEKMYLKL +KVAQGDLTIEVPAENVDLVGVRDVVDAEGLEHVMEVLRAEHVEEPTNWSRRYKANLEKLA +SGDVNKVAEVVRDLWRRDQDRGLSAGEKRMLSKARQVLVSELALAKKVTEEEAEGRLDKV +LEG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000409.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000409.fa new file mode 100644 index 0000000000000000000000000000000000000000..566dfb29536f09f611412f5a72310618513e0a11 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000409.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00361 +---------------------------------------MPTGRIKFYDSTKGFGFAQTD +EGEEVHVPASALPAGVTELRGGTRVEFGVAEGRRGKQALSLRVLDAAPSVVRNHRPGATE +MAVLMEDLITWLDQASNGLRRGRYPQRAQAQKMAQVLRRVADDLEA +>GCF_003691675_PROKKA_00077 +---------------------------------------MPTGRIKFYDSTKGFGFAQTD +EGEEVHVPASALPAGVTELRGGTRVEFGVAEGRRGKQALSLRVLDAAPSVVRNHRPGATE +MAVLMEDLITWLDQTSNGLRRGRYPQRAQAQKMAQVLRRVADDLEA +>GCF_005280335_PROKKA_02600 +MPRRTAAPAPDPADPRRAHGSPGRRRDAGDTDDEEQVPHMPTGRIKFYDSAKGFGFAQTD +EGEEVHVPSSALPAGVTELRGGARVEFGVAEGRRGKQALSLRVLDAAPSSVRNHRPRPAE +MAVLMEDLIRWLDETSNGLRRGQYPQSGQAKKMAQVLRRVADDLEA +>GCF_020097155_PROKKA_02459 +---------------------------------------MPTGRIKFYDSAKGFGFAQTD +DGEEVHVPAAALPAGVSDLRSGTRVELGVAEGRRGKQALTVEVLDDAPSVVRNHRPSPEK +MAVLMEDLIKVLDQTSNGLRRGRYPQRAQAQKIAAVLRRVADDLEA +>GCF_023573625_PROKKA_00368 +---------------------------------------MPTGRIKFYDSTKGFGFAQTD +EGEEVHVPASALPAGVTELRGGTRVEFGVAEGRRGKQALSLRVLDAAPSVVRNHRPGATE +MAVLMEDLITWLDQTSNGLRRGRYPQRAQAQKMAQVLRRVADDLEA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000427.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000427.fa new file mode 100644 index 0000000000000000000000000000000000000000..1174f3f382d8f1d2dcc1676980db49ac399f5d72 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000427.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00385 +MLEIPRVEDNGRLGPVNSALVPRYGGTPTYALLPRLDEAAAAGVAPEIKVVGVPFDAGVS +YRPGARFGSGHVRQSSRLLRPYNPATDTSPFAQAQVVDAGDMAVNPFDIGEAIEAIQQDA +MDLTEDGSSLMTIGGDHTIALPLLRAASARAGEPVALLHFDAHLDTWDTYFGAEYTHGTP +FRRAVEEGILDTEAISHVGTRGPLYGKKDLDDDHRMGFGIVTSSDVFRQGVDEIVDQLRQ +RIGGRPLYISVDIDVLDPAHAPGTGTPEAGGITSRELLEILRGLRGLDIVGADLVEVAPA +YDHAELTGVAASHVAYDLISLMADRRATRAAAGEESAR +>GCF_003691675_PROKKA_00109 +MLEIPRVEDNGRLGPVNSALVPRYGGTPTYALLPRLDEAAAAGVAPEIKVVGVPFDAGVS +YRPGARFGSGHVRQSSRLLRPYNPATDTSPFAQAQVVDAGDMAVNPFDIGEAIEAIQQDA +MDLTEDGSSLMTIGGDHTIALPLLRAASARAGEPVALLHFDAHLDTWDTYFGAEYTHGTP +FRRAVEEGILDTEAISHVGTRGPLYGKKDLDDDHRMGFGIVTSSDVFRQGVDEIVDQLRQ +RIGGRPLYISVDIDVLDPAHAPGTGTPEAGGITSRELLEILRGLRGLDIVGADLVEVAPA +YDHAELTGVAASHVAYDLISLMADRRATRAAAGEESAR +>GCF_005280335_PROKKA_02570 +MLEIPRVEDNGRLGPVNSALVPRYGGAPTYALLPRLDEAAAAGVAPEIKVVGVPFDAGVS +YRPGARFGSGHVRQSSRLLRPYNPATDTSPFAQSQVVDAGDMAVNPFNIGEAIEAIQQDA +MDLTEDGASLMTIGGDHTIALPLLRAASARAGEPVALLHFDAHLDTWDTYFAAEYTHGTP +FRRAVEEGILDTEAISHVGTRGPLYGKKDLDDDHRMGFGIVTSSDVFRKGVDEIVDQLRQ +RIGDRPLYISVDIDVLDPAHAPGTGTPEAGGITSRELLEILRGLRGLDIVGADLVEVAPA +YDHAELTGVAASHVAYDLITLMADRRASRAAAGEEQGR +>GCF_020097155_PROKKA_01755 +MLEIPRVEDNGRLGPVNSALVPRYGGAPTYALLPRLDEAAAAGVAPEIKVVGVPFDAGVS +YRPGARFGSGHVRQSSRLLRPYNPATETSPFAQAQVVDTGDMAVNPFHIGEALESIQQDA +MDLTEDGASLMTIGGDHTIALPLLRAASARAGEPVALLHFDAHLDTWDTYFGAAYTHGTP +FRRAVEEGILDTEAISHVGTRGPLYGKKDLDDDHRMGFGIVTSSDVFRKGVDEIVDQLRQ +RIGGRPLYISVDIDVLDPAHAPGTGTPEAGGLTSRELLEILRGLRGLDIVGADLVEVAPA +YDHAELTGVAASHVAYDLISLMADRRATRAAAEGGVDA +>GCF_023573625_PROKKA_00391 +MLEIPRVEDNGRLGPVNSALVPRYGGAPTYALLPRLDEAAAAGVAPEIKVVGVPFDAGVS +YRPGARFGSGHVRQSSRLLRPYNPATDTSPFAQAQVVDAGDMAVNPFDIGEAIEAIQQDA +MDLTEDGSSLMTIGGDHTIALPLLRAASARAGEPVALLHFDAHLDTWDTYFGAEYTHGTP +FRRAVEEGILDTEAISHVGTRGPLYGKKDLDDDHRMGFGIVTSSDVFRQGVDEIVDQLRQ +RIGGRPLYISVDIDVLDPAHAPGTGTPEAGGITSRELLEILRGLRGLDIVGADLVEVAPA +YDQAELTGVAASHVAYDLISLMADRRATRAAAGEEPGR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000440.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000440.fa new file mode 100644 index 0000000000000000000000000000000000000000..1703b69b03a6adfd2190b38936776f5b7e2a01fe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000440.fa @@ -0,0 +1,55 @@ +>GCF_002008305_PROKKA_00403 +MSKIIYTLTDEAPMLATASLLPIVRAYAGTAGVELETRDISLAGRILAAFKDVLPEDQRTADALAELGELVKSPEANVIK +LPNISASVPQLRAAIKELQADGYALPEYPDEPKTDEEKDAKARYDSVKGSAVNPVLREGNSDRRAPKAVKAYAKRFPHSM +GEWTPDSKTAVATMGADDFRANEQSVTLPAADVLTIEFTGEDGKTTVLKEGLKVLKGEVVDGTFMSAKALDAFLAEQVKR +AKEEGILFSAHLKATMMKVSDPVIFGHVVKAYFSELFEKYGEQLAAAGLSANNGLAAIEGGLDKLDAETAEGVRAAIAAA +YENGPDVAMVNSAKGITNLHVPSDVIVDASMPAMIRTSGRMWNKDDQTQDTLAVIPDSSYAGVYQAVIDDCKANGAYDPT +TMGTVPNVGLMAQKAEEYGSHDKTFIMDAAGTVAVKNSAGETLLSHDVEAGDIWRACQTKDVPVRDWVKLAVTRARASQT +PAVFWLDETRAHDRELIKKVEEYLKEHDTEDLDIRILSPVEAAKLSVERIRRGEDTISVTGNVLRDYNTDLFPILELGTS +AKMLSVVPLLNGGGLFETGAGGSAPKHVQQLVEENHLRWDSLGEFLALAVSFEHEAVANENHRARVLADTLDAATGTLLI +EGKSPKRKVGELDNRGSHFYLALYWARELAKQTEDAELAAAAKPVAEELEAQEETILGELNGVQGSPVDLGGYYWPELEK +VTSVMRPSATLNAIVDKLSV +>GCF_003691675_PROKKA_00126 +MSKIIYTLTDEAPMLATASLLPIVRAYAGTAGVELETRDISLAGRILAAFKDVLPEEQRTADALAELGELVKTPEANVIK +LPNISASVPQLRAAIKELQAHGYALPEYPDEPKTDAEKDAKARYDSVKGSAVNPVLREGNSDRRAPKAVKAYAKRFPHSM +GEWTPDSKTAVATMGADDFRANEQSVTLPAADVLTIEFTGEDGKTTVLKEGLKVLKGEVVDGTFMSAKALDAFLAEQVKR +AKEEGILFSAHLKATMMKVSDPVIFGHVVKAYFSELFEKYGEQLAAAGLSANNGLAAIEGGLDKLDAETAEGVRAAIAAA +YENGPDVAMVNSAKGITNLHVPSDVIVDASMPAMIRTSGRMWNKDDQTQDTLAVIPDSSYAGVYQAVIDDCKANGAYDPT +TMGTVPNVGLMAQKAEEYGSHDKTFIMDAAGTVAVKNSAGETLLSHEVEAGDIWRACQTKDVPVRDWVKLAVTRARASQT +PAVFWLDETRAHDRELIKKVEEYLKEHDTEGLDLRILSPVEATKLSVERIRRGEDTISVTGNVLRDYNTDLFPILELGTS +AKMLSIVPLLNGGGLFETGAGGSAPKHVQQLLEENHLRWDSLGEFLALAVSFEHEAVANENHRAQVLADTLDAATGTLLI +EGKSPKRKVGELDNRGSHFYLALYWARELAKQTEDAELAAAAKPIAEELEAQEETILAELNGVQGSPVDLGGYYAPEMEK +VTSVMRPSATLNAIVDKLSV +>GCF_005280335_PROKKA_02553 +MSKIIYTLTDEAPMLATASLLPIVRAYAGTAGVELETRDISLAGRILAAFRDVLPEDQRTADALAELGELVKSPEANVIK +LPNISASVPQLRAAIKELQEDGYALPEYPDEPKTDEEKDAKARYDSVKGSAVNPVLREGNSDRRAPKAVKNYAKMFPHSM +GEWTPDSKTAVATMGADDFRSNEKSVTMPADDTLTIEFTGEDGKTTVLKEGLKVLAGEVVDGTFMSAKALDAFLAEQVKR +AKEEGILFSAHLKATMMKVSDPVIFGHVVKAYFSELFEKYGEQLEAAGLNPNNGLAAIEGGLDKLDAETAEGVKKAIAAA +YEEGPDVAMVNSAKGITNLHVPSDVIVDASMPAMIRTSGRMWNKDDQTQDTLAVIPDSSYAGIYQAVIEDCKKHGAYDPT +TMGTVPNVGLMAQKAEEYGSHDKTFILESAGTVAVKNAAGETLISHDVEAGDIWRACQTKDVPVRDWVKLAVTRARASQT +PAVFWLDETRAHDRELIAKVEEYLKEHDTEGLDLRILSPVEAAKLSVERIRRGEDTISVTGNVLRDYNTDLFPILELGTS +AKMLSVVPLLNGGGLFETGAGGSAPKHVQQLVEENHLRWDSLGEFLALAVSFEHEAVANENHRAQVLADTLDAATGTLLI +EGKSPQRKVGELDNRGSHFYLALYWARELAKQTEDAELVAAAKPVAEELEAQEETILAELNGVQGSPVDLGGYYWPELEK +VTSVMRPSATLNAIVDKLSV +>GCF_020097155_PROKKA_02422 +MSKIIYTLTDEAPMLATASLLPIVRAYAGTAGVELETRDISLAGRILAAFNDLLPEEQRVNDALAELGELVKTPEANVIK +LPNISASVPQLRAAIKELQADGYALPEYVDDPQTDKEKDARKRYDSVKGSAVNPVLREGNSDRRAPKAVKNYAKKFPHSM +GAWTADSKTAVATMGQDDFRSNEKSVTMPKDDVLSIEFTGQDGTTKILKEGLKVLEGEVVDGTFMSAKALDAFLAEQVTR +AKEEGVLFSAHLKATMMKVSDPVIFGHVVKAYFADLFAQYGEQLAAAGLDPNNGLAAIEAGLDKLDAETAEGVRKAIADA +YQNGPDVAMVNSDKGITNLHVPSDVIVDASMPAMIRTSGHMWDKDGAERDTLAVIPDSSYAGIYQVVIDDCKANGAYDPT +TMGTVPNVGLMAQKAEEYGSHDKTFVMEADGTVEVKDSAGEVLFSHEVEAEDIWRACQTKDVPVQDWVKLAVTRARASQT +PAVFWLDETRAHDRELIKKVEQYLQGHDTEGLDLRIMSPVEATKFTVERMRRGEDTITVTGNVLRDYNTDLFPILELGTS +AKMLSIVPLINGGGLFETGAGGSAPKHVQQLVGENHLRWDSLGEFLALAVSFEHEAAHNGNHRAQVLADTLDAATGILLI +EGKSPERKAGQLDNRGSHFYLALYWAQELAKQTADAELAAAAKPVAEELEAQEETILAELNGVQGSPVDLGGYYAPSMDK +VSEVMRPSATLNGIIATLGA +>GCF_023573625_PROKKA_00409 +MSKIIYTLTDEAPMLATASLLPIVRAYAGTAGVELETRDISLAGRILAAFKDVLPEEQRTADALAELGELVKSPEANVIK +LPNISASVPQLRAAIKELQADGYALPEYPDEPKTDEEKDAKARYDSVKGSAVNPVLREGNSDRRAPKAVKAYAKRFPHSM +GEWTPDSKTAVATMGADDFRANEQSVTLPAADVLTIEFTDEDGETTVLKEGLKVLKGEVVDGTFMSAKALDAFLAEQVKR +AKEEGILFSAHLKATMMKVSDPVIFGHVVKAYFSELFEKYGEQLAAAGLSANNGLAAIEGGLDKLDAETAEGVRAAIAAA +YENGPDVAMVNSAKGITNLHVPSDVIVDASMPAMIRNSGRMWNKHDQTQDTLAVIPDSSYAGVFQAVIDDCKANGAYDPT +TMGTVPNVGLMAQKAEEYGSHDKTFIMDAAGTVAVKNSAGETLLSHDVEAGDIWRACQTKDVPVRDWVKLAVTRARASQT +PAVFWLDETRAHDRELIKKVEEYLKEHDTEDLDIRILSPVEAAKLSVERIRRGEDTISVTGNVLRDYNTDLFPILELGTS +AKMLSVVPLLNGGGLFETGAGGSAPKHVQQLVEENHLRWDSLGEFLALAVSFEHEAVANENHRARVLADTLDAATGTLLI +EGKSPKRKVGELDNRGSHFYLALYWARELAKQTEDAELAAAAKPIAEELGAQEETILAELNGVQGSPVDLGGYYWPELEK +VTSVMRPSATLNAIVDKLSV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000449.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000449.fa new file mode 100644 index 0000000000000000000000000000000000000000..0338598dd282c7d949969cdcc106e3386d4956a4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000449.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00417 +MDTAALSPSPSPASGAEHAHVLTLACTNRKGIVHAVTGALLGVEADITESQQYGSPDTGD +FFMRVEFMTPAVREDIEQALAPVREEFGMRMGLWDAAHRMRTLVMCSKDGHTLNDLLFQQ +RAGTLPIEIPVVVSNHLDLQPLASFYGVPFIHVPVSKDPSSRDSKEAAEDRLRDLIAQFD +IELVVLARYMQILSDELCRDLAGMAINIHHSFLPSFKGARPYHQAHERGVKLIGATAHYV +TADLDEGPIIAQSVQPVTHAQTAADFVARGRDVEGSTLAQAVRWHAQHRVLTDGRRTVVF +S +>GCF_003691675_PROKKA_00138 +MDTAALSPSPSPASGAEHARVLTLACTNRKGIVHAVTGALLGVEADITESQQYDSPDTGD +FFMRVEFVTPATREDIEQALAPVREEFGMRMGLWDAAQRMRTLVMCSKDGHTLNDLLFQQ +RAGTLPIEIPVVVSNHLDLQPLASFYGVPFIHVPVSKDPSSRDSKEAAEDRLRDLIAQFD +IELVVLARYMQILSDELCRDLAGMAINIHHSFLPSFKGARPYHQAHERGVKLIGATAHYV +TADLDEGPIIAQSVQPVTHAQTAADFVARGRDVEGSTLAQAVRWHAQHRVLADGRRTVVF +S +>GCF_005280335_PROKKA_02543 +MDTATLSPSPTPASGAEHAHVLTLACTNRMGIVHAVSGALLQVGADITESQQYDSPESGD +FFMRVEFVTPARREEVAAALEPVREEFGMRMGLWDAGHRMRTLVMCSKDGHTLNDLLFQQ +RAGTLPIEIPVVVSNHLELQSLASFYGVPFIHVPVSADPESRDSKAAAEDRLRGLIAEYD +IELVVLARYMQILSDELCRDLAGMAINIHHSFLPSFKGARPYHQAHERGVKLIGATAHYV +TADLDEGPIIAQSVQPVTHAQTAADFVARGRDVEGSTLVQAVRWHAQHRVLADGRRTVVF +S +>GCF_020097155_PROKKA_02411 +MDSTPAAPS---EASARHRIVLTLSCPDRPGIVHAVTGALLEADANITESQQYDSPDTGT +FFMRVAVDAAATREEVEAAVRPVADRFGMHLQVWDADTPLRALVMCSKDGRTLNDLLFQQ +RTGSLPVQIPVVVSNHLDLQPLASFYGVPFIHVPLSTDPASRNSKAAAEDRLRELIREYE +IDVVVLARYMQILSDELCRDLEGMAINIHHSFLPSFKGARPYHQAHERGVKIIGATAHYV +TADLDEGPIIAQSVHPVTHAQTAEDFVERGRDVEGATLVQAVRWHAEHRVLLDGHRTVVF +S +>GCF_023573625_PROKKA_00420 +MDTAALSLSPSPASGAEHAHVLTLACTNRKGIVHAVTGALLGVEADITESQQYGSPDTGD +FFMRVEFMTPAVREDIEQALAPVREEFGMRMGLWDAAHRMRTLVMCSKDGHTLNDLLFQQ +RAGTLPIEIPVVVSNHLDLQPLASFYGVPFIHVPVSKDPSSRDSKEAAEDRLRDLIAQFD +IELVVLARYMQILSDELCRDLAGMAINIHHSFLPSFKGARPYHQAHERGVKLIGATAHYV +TADLDEGPIIAQSVQPVTHAQTAADFVARGRDVEGSTLAQAVRWHAQHRVLTDGRRTVVF +S + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000464.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000464.fa new file mode 100644 index 0000000000000000000000000000000000000000..4b9b5750d995f0cfe758a11e74a4681ea02a4043 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000464.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00435 +MSTTAETTIAAPRSRRLDPKYTRDGGGRGNFEMLAWLFMRISGVFLVVLIAVHLTTNLLV +GDGIHAIDFGFVAGKWAHPLWQFWDLALLWLAMLHGANGVRTIINDYTRRGSARFWLTMI +LYIATAVIIILGTLVIFTFDPCMVDASGALLEGSPAFCG +>GCF_003691675_PROKKA_00156 +MSTTAETTIAAPRSRRLDPKYTRDGGGRGNFEMLAWLFMRISGVFLVVLIAVHLTTNLLV +GDGIHAIDFGFVAGKWAHPLWQFWDLALLWLAMLHGANGVRTIINDYTRRGSARFWLTMI +LYIATAVIIILGTLVIFTFDPCMVDASGALLEGSPAFCG +>GCF_005280335_PROKKA_02522 +MSTTAETTIAAPRTGRIDPKYTRDKGGRGNFEMLAWLFMRVSGVILVLLIAVHLTSNLLM +GDGIQGIDFGFVAGKWAHPLWQFWDLALLWLAMLHGANGVRTIINDYTERGTARFWLTMI +LYIATAVIITLGTLVIFTFDPCMVDASGALLEGSPAFCG +>GCF_020097155_PROKKA_02393 +MSTTAETPLAAPRTGRLDSKYVRGESGKGNFEMLAWLFMRVSGVFLVVLVFAHIFANLMV +GDGISGLDFGFVAGKWANPLWQLWDLALLWLAMLHGANGVRTIINDYAERDGVRFWLSMI +LYVATAVIIVLGSLVIFTFDPCMVDASGALLEGSPAICR +>GCF_023573625_PROKKA_00438 +MSTTAETTIAAPRSRRLDPKYTRDGGGRGNFEMLAWLFMRISGVFLVVLIAVHLTTNLLV +GDGIHAIDFGFVAGKWAHPLWQFWDLALLWLAMLHGANGVRTIINDYTRRGSARFWLTMI +LYIATAVIIILGTLVIFTFDPCMVDASGALLEGSPAFCG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000473.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000473.fa new file mode 100644 index 0000000000000000000000000000000000000000..fbabd0a1177042589e977eee6b1a842427533b7c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000473.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00444 +-----MTAQPQA-EPFDAVEVIRTKRDRGTLSPEQIDWVVDAYTRGVVADEQMSALAMAI +LLNGMDRAEIARWTDAMIASGERMDFGGLTTPDGRPLATADKHSTGGVGDKITLPLAPLV +ASFGVAVPQLSGRGLGHTGGTLDKLEAIPGWRADLSNEAMLRQLSEVGAVICAAGSGLAP +ADKRLYALRDVTGTVEAIPLIASSIMSKKIAEGTGALVLDVKCGSGAFMKDEASARELAR +TMVDLGRDAGVDTSALLTDMSVPLGRTAGNALEVRESVEVLAGGGPADVVELTVALAAAM +LAGAGVTDVDPAEHLANGRAMDVWNRMIEAQGGDPRAALPTAAHTEDVVAETDGVLTELD +AMAVGLAAWRLGAGRERQGQAVQAAAGVEVHVRPGERVARGQKVLTLHTDTPERFERAKA +ALAGGWAVGELDDAAARTLRERSVILDRIG +>GCF_003691675_PROKKA_00165 +-----MTAQPQA-EPFDAVEVIRTKRDRGTLSPEQIDWVVDAYTRGVVADEQMSALAMAI +LLNGMDRAEIARWTDAMIASGERMDFGGLTTPDGRPLATADKHSTGGVGDKITLPLAPLV +ASFGVAVPQLSGRGLGHTGGTLDKLEAIPGWRADLSNEAMLRQLSEVGAVICAAGSGLAP +ADKRLYALRDVTGTVEAIPLIASSIMSKKIAEGTGALVLDVKCGSGAFMKDEASARELAR +TMVDLGRDAGVDTSALLTDMSVPLGRTAGNALEVRESVEVLAGGGPADVVELTVALAAAM +LAGAGVTDVDPAEHLANGRAMDVWNRMIEAQGGDPRAALPTAAHTEDVVAETDGVLTELD +AMAVGLTAWRLGAGRERQGQAVQAAAGVEVHVRPGERVARGQKVLTLHTDTPERFERARA +ALAGGWSVGELDDDAARALRERSVILDRIG +>GCF_005280335_PROKKA_02513 +-----MTAQQQA-EPFDAVEVIRAKRDRQTLSPEQIDWVVDAYTRGVVADEQMSALAMAI +LLNGMDRAEISRWTDAMIASGERMDFSGLTAPDGRVLPTADKHSTGGVGDKITLPLAPLV +ASYGVAVPQLSGRGLGHTGGTLDKLEAIPGWRADLTNEQMMRQLSEVGAVICAAGSGLAP +ADKRLYALRDVTGTVEAIPLIASSIMSKKIAEGTGALVLDVKCGSGAFMKDEASARELAR +TMVDLGRDAGVDTVALLTDMSVPLGLTAGNALEVRESVEVLAGGGPADVVELTVELARAM +LAGAGVTDVDPAQNLANGKAMDVWHRMIEAQGGDPRADLPTAAHTEDVVAEADGVLAELD +AMAVGLAAWRLGAGRERQGQPVQAGAGVELHVRPGERVARGQKVMTLHTDTPERFARAKA +ALEGGWAVAEKGEAEAAALRDRSVILDRIG +>GCF_020097155_PROKKA_02384 +MTTTSMPAQPAAPEAFDAIEVIRLKRDGHRLDPERIDWVVDAYTRGVVAPEQMSALAMAI +LLNGMDREEIARWTAAMIASGERMDFSGLSAPDGRRLATADKHSTGGVGDKITLPLAPLV +ASYGVAVPQLSGRGLGHTGGTLDKLESIPGWRADLTNDQMMRQLGEVGAVVCAAGAGLAP +ADKKLYALRDVTGTVEAIPLIASSIMSKKIAEGTGALVLDVKCGSGAFMKDEASARELAR +TMVDLGRDAGVDTSALLTDMSVPLGLTAGNALEVRESVEVLAGGGPADVVELTVELARAM +LAGAGVTDVDPAENLANGKAMDVWHRMIQAQGGDSHAELPAARHQETVTADADGVLTELD +AMAVGLAAWRLGAGRERQGEPVQAGAGVELHARPGDAVRAGQPLMTLHTDTPERFDRARA +ALAGGWAVTAADEAEAAALRSRSVILDRIG +>GCF_023573625_PROKKA_00447 +-----MTAQPQA-EPFDAVEVIRTKRDRGTLSPEQIDWVVDAYTRGVVADEQMSALAMAI +LLNGMDRAEIARWTDAMIASGERMDFGGLTTPDGRPLATADKHSTGGVGDKITLPLAPLV +ASFGVAVPQLSGRGLGHTGGTLDKLEAIPGWRADLSNEAMLRQLSEVGAVICAAGSGLAP +ADKRLYALRDVTGTVEAIPLIASSIMSKKIAEGTGALVLDVKCGSGAFMKDEASARELAR +TMVDLGRDAGVDTSALLTDMSVPLGRTAGNALEVRESVEVLAGGGPADVVELTVALAAAM +LAGAGVTDVDPAEHLANGRAMDVWNRMIEAQGGDPRAALPTAAHTEDVVAETDGVLTELD +AMAVGLAAWRLGAGRERQGQAVQAAAGVEVHVRPGERVAQGQKVLTLHTDTPERFERARA +ALAGGWAVGELDDVDARTLRERSVILDRIG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000474.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000474.fa new file mode 100644 index 0000000000000000000000000000000000000000..05ccc892028819dd2431b543141562e5ac58d378 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000474.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00445 +MLAWLEGAILHASAQWWVLPLTLLLCLLDGIVPIFPSESVLVALGAIVRDGHPFSLWALW +GVGFAGAFLGDVAAYAIGRAVGVERFRWMRLRRVRATVEVARHHLHSHGALLLFTARFIP +GGRVALNFTAGATRYPPVRFVALDLLSTASWAAYSIMIARLTAGWLENPVLQIAVSVTGA +ALVGLLLDRLLKALLRRRLGAGVKGLTLAEQEALR +>GCF_003691675_PROKKA_00166 +MLAWLEGAILHASAQWWVLPLTLLLCLLDGIVPIFPSESVLVALGAIVRDGHPFSLWALW +GVGFAGAFLGDVAAYAIGRAVGVERFRWMRLRRVRATVEVARHHLHSHGALLLFTARFIP +GGRVALNLTAGATRYPPVRFVALDLLSTASWAAYSIMIARLTAGWLENPVLQIAVSVTGA +ALVGLLLDRLLKALLRRRLGAGVKGLTLAEQEALR +>GCF_005280335_PROKKA_02512 +MLEWIEETVLHAAAQWWMLPLTLALCLLDGIVPVFPSESVIVALAAIVRDGQPFSLWALW +AVGFAGAFLGDILAYAIGRAVGVDRFRWMRTPRVRASVAVARHHLNGHGALLLFTGRFIP +GGRVAINLTAGAIRYPLHRFVVLDLLSTAAWSAYSIMIARLTTGWLDNALLQIAVSVTGA +ALVGVLLDRALKAVLRRRLGTGVKGLRQAEDEALR +>GCF_020097155_PROKKA_02383 +MVQALEQAILAGASHPWALPLAALLCLLDGLVPVFPSESVLVALASIVEDGRPFPLAALW +AAGFVGAFLGDVAAYGAGRGVGVTRFRWMRHGRVRRTIVMARRNLDSHGALLLFTARFIP +GGRVAVNLAAGAMHYSPWRFVGLDLVSTALWSVYSIAIARLTVGWLDSTVLRMAVAVLGA +ALVGLLLDRAVKALLRRRLARDGHRLGADEQAALR +>GCF_023573625_PROKKA_00448 +MLAWLEEAILHASAQWWVLPLTLLLCLLDGIVPIFPSESVLVALGAIVRDGHPFSLWALW +GVGFAGAFLGDVAAYAIGRAVGVERFRWMRLRRVRATVEVARHHLHSHGALLLFTARFIP +GGRVALNLTAGATRYPPVRFVALDLLSTASWAAYSIMIARLTAGWLENPVLQIAVSVTGA +ALVGLLLDRLLKALLRRRLGSGVKGLTLAEQEALR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000480.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000480.fa new file mode 100644 index 0000000000000000000000000000000000000000..bd40a08d70d6350cc7c94396d5dd29e5c3f57917 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000480.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00456 +MANPVMNSQNFQQQMQGGGQAQPGWYQGGQQSAQSPYGQQQSPYGQAQAFGAGQAAQQYA +HQQSMEDAFRAPSAGPEQTGRMTYNDVVGKTGLMLVLVVVAGAVGWFSPGLMIIGAIAGL +VLGLVNSFKREPSPVLIMLYALAEGLFLGGISAVFEAAYPGIVVQAVLGTFSVFAVMLAL +YTSGKFRPTPRMTKIVMTAMLGYLVFMLINLVLTWTGIANLRTGGLGLIIGAIAVLLAAY +SLTMDFEMAAVGVKNGAPQKYSWSVAFGLTVTLIWLYVEILRIVAILRGND +>GCF_003691675_PROKKA_00174 +MANPVMNSQNFQQQMQGGGQAQPGWYQGGQQSAQSPYGQQQSPYGQAQAFGAGQAAQQYA +HQQSMEDAFRAPSAGPEQTGRMTFNDVVGKTGLMLVLVVVAGAVGWFSPGLMIIGAIAGL +VLGLVNAFKREPSPVLIMAYAVAQGLFLGGISAFFEGAYPGIVVQAVLGTFSVFAVMLAL +YTSGKFRPTPRMTKIVMGAMIGYLVFMLVNLVLTWTGIGNMREGGLGLIIGAIAVLLAAY +SLTMDFEMAAVGVKNGAPQKYSWSVAFGLTVTLIWLYIEILRIVAILRGND +>GCF_005280335_PROKKA_02491 +MANPVMNSQNFQQQMQGGGQAQPGWYQGGTQSAQSPYGQQQSPYGQAQAFGAGQAAQQYA +HQQSMEDAFRAPSAGPEQTGRMTFNDVVGKTGLMLVLVVVAGAVGWFSPGLMIIGAIAGL +VLGLVNAFKREPSPVLIMAYAVAQGLFLGGISAFFEGAYPGIVVQAVLGTFSVFAVMLAL +YTSGKFRPTPRMTKIVMGAMIGYLVFMLVNMVLTWTGIGNMREGGLGLIIGAIAVLLAAY +SLTMDFEMAAVGVKNGAPQKYSWSVAFGLTVTLIWLYIEILRIVAILRGND +>GCF_020097155_PROKKA_02375 +MANPVMNSNNFQQQMH-AGQQQPGWYQNA--APQAPSGQQQSPYGQSQAYGAQQAAQQAA +FQQNMEQAFRAPAAGAAETGRMTYNDIVGKTALMLTLVVIGGAIGWTMPALMLIGAIVGL +VLGLVNSFKREPSPVLIMGYALAEGLFLGGISASFEAAYGGIVLQAVLGTVSVFAVMLAL +YTSGKFRPTPRMTKIVMAAMIGYMLFMLLNLVLTFTGIANLRLGAMGLIVGAVAVLLAAY +SLTMDFEMGAQGVKNGVPQKYSWTVAFGLTVTLIWLYVEILRILSILRSDD +>GCF_023573625_PROKKA_00456 +MANPVMNSQNFQQQMQGGGQAQPGWYQGGQQSAQSPYGQQQSPYGQAQAFGAGQAAQQYA +HQQSMEDAFRAPSAGPEQTGRMTFNDVVGKTGLMLVLVVVAGAVGWFSPGLMIIGAIAGL +VLGLVNAFKREPSPVLIMAYAVAQGLFLGGISAFFEGAYPGIVVQAVLGTFSVFAVMLAL +YTSGKFRPTPRMTKIVMGAMIGYLVFMLVNLVLTWTGIGNMREGGLGLIIGAIAVLLAAY +SLTMDFEMAAVGVKNGAPQKYSWSVAFGLTVTLIWLYIEILRIVAILRGND + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000491.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000491.fa new file mode 100644 index 0000000000000000000000000000000000000000..d55e6f028e6089949ff1217348690d017580a0ed --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000491.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_00468 +MVAELVEHA-------QTRQEPSSRPGQ-ARAEAGA--------AEATGLRTYVVDTSVLLSDPRALLHFAEHEVVLPLV +VVSELEAKRADPDLGYDARTALRLLDDLRGRHGALDQPVPITPEGGTLRIELNHVSVDVLPLGIRGTDNDSRILAVAKAL +ADEGAMVTVVSKDLPMRVKAAAMGLAADEYRHELVRDSGWRGTVSLSVAQERLDALYDDGEVDLAGVPLGTLT------- +-------GTGVETGPEEAPAEADRLPVNTGLVLTAPRGSALARVGEGGRACLVRGDRDVFGLHGRSAEQRLAIELLTDPS +VGIVSLGGRAGTGKSALALCAGLDAVMERREHRRVVVFRPLYAVGGQDLGYLPGSEGDKMGPWAQAVFDTLGALVSPSVV +DEVVDRGMLEILPLTHIRGRSLHDAWVIVDEAQSLERNVLLTVLSRMGRNSKVVLTHDVAQRDNLRVGRHDGIAAVVERL +KGHPLFGHVTLTRSERSPIAALVTDLLEEGRA +>GCF_003691675_PROKKA_00186 +MVAELVEHA-------QTRQEPSSRPGQ-ARAEAGA--------AEATGLRTYVVDTSVLLSDPRALLHFAEHEVVLPLV +VVSELEAKRADPDLGYYARTALRLLDDLRGRHGALDQPVPITPEGGTLRIELNHVSVDVLPLGIRGTDNDSRILAVAKAL +ADEGATVTVVSKDLPMRVKAAAMGLAADEYRHELVRDSGWRGTVSLSVAQERLDALYDDGEVDLAGVPLGTLT------- +-------GTGVETGPGEAPAEADRLPVNTGLVLTAPRGSALARVGEGGRACLVRGDRDVFGLHGRSAEQRLAIELLTDPS +VGIVSLGGRAGTGKSALALCAGLDAVMERREHRRVVVFRPLYAVGGQDLGYLPGSEGDKMGPWAQAVFDTLGALVSPSVV +DEVVDRGMLEILPLTHIRGRSLHDAWVIVDEAQSLERNVLLTVLSRMGRNSKVVLTHDVAQRDNLRVGRHDGIAAVVERL +KGHPLFGHVTLTRSERSPIAALVTDLLEEGRA +>GCF_005280335_PROKKA_02479 +MVAERVEHGRALTGTTEARPDAAGAAGHAAAARTGAADAVVAPDARETGLRTYVVDTSVLLSDPRAVLRFAEHEVILPLV +VVSELEAKRADPDLGYFARTALRLLDDLRGRHGALDRAVPISPEGGTLRVELNHVSTDVLPLGIRGTDNDSRILAVAKAF +ADEGRDVTVVSKDLPMRVKAAAMGLSADEYRHELVRDSGWRGTVTLTVEQELLDALYDDGEASLAGVPVDGTDGVGAGVE +ADGTGAGGSGVDRTGAEGPGAA-VLPVNTGLVLLAPRGSALARVAEGGRALLVRGDQDVFGLHGRSAEQRLAIDLLTDPA +VGIVSLGGRAGTGKSALALCAGLDAVMERREHRKVVVFRPLYAVGGQELGYLPGSEGEKMGPWAQAVFDTLGALVSPSVI +DEVVDRGMLEVLPLTHIRGRSLHDAWVIVDEAQSLERNVLLTVLSRMGRNSKVVLTHDVAQRDNLRVGRHDGIAAVVERL +KGHPLFGHVTLTRSERSPIAALVTEMLEDGRG +>GCF_020097155_PROKKA_02363 +M---------------TLQADGTGRHGR-GTGETGA---EVREGAASDGRRSYVVDTSVLLSDPRALVRFAEHEVVLPLV +VVSELEGKRQDPDLGHAARHALRLLEDLRVRHGSLEDAVPFTAQGGTLRVELNHVSTDVLPFGIRGTDNDSRILAVAKAL +ADEGRDVTLVSKDLPMRVKAAAMGLAADEYRHELVRDSGWRGAVSLRVDEDRLDSLYDDGRMGLHGIPLDEVA------- +-------GSGVDAVPGEPAPTAVDLPVNTGLSLTSPRAAGLARVREGGVATLVRGDADVFGLHGRSAAQRLAIDLLTDPS +VGIVSLGGRAGTGKSALALCAGLEAVMERREHRRVVVFRPLYAVGGQDLGYLPGTEGEKMGPWAQAVFDTLSAIVSPSVI +DEVVDRGMLEVLPLTHIRGRSLHDSWVIVDEAQSLERNVLLTVLSRMGRDSKVVLTHDVAQRDNLRVGRHDGIAAVVETL +KGHPLFGHVTLTRSERSPIAALVTELLEEGED +>GCF_023573625_PROKKA_00468 +MVAELVEHA-------QTRQEPSSRPGQ-ARAEAGP--------AEATGLRTYVVDTSVLLSDPRALLHFAEHEVVLPLV +VVSELEAKRADPDLGYYARTALRLLDDLRGRHGALDQPVPITPEGGTLRIELNHVSVDVLPLGIRGTDNDSRILAVAKAL +ADEGATVTVVSKDLPMRVKAAAMGLAADEYRHELVRDSGWRGTVSLSVAQERLDALYDDGEVDLAGVPLGTLT------- +-------GTGVETGPEEAPAEADRLPVNTGLVLTAPRGSALARVGEGGRACLVRGDRDVFGLHGRSAEQRLAIELLTDPS +VGIVSLGGRAGTGKSALALCAGLDAVMERREHRRVVVFRPLYAVGGQDLGYLPGSEGDKMGPWAQAVFDTLGALVSPSVV +DEVVDRGMLEILPLTHIRGRSLHDAWVIVDEAQSLERNVLLTVLSRMGRNSKVVLTHDVAQRDNLRVGRHDGIAAVVERL +KGHPLFGHVTLTRSERSPIAALVTDLLEEGRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000511.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000511.fa new file mode 100644 index 0000000000000000000000000000000000000000..8c7e1241ba0bbb23844f76e4575bb35625181033 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000511.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_00491 +MLTRLLKARLPEGTQYLVDRPMRIRLVFVVLGSVLVAGLEMVALASILPLVSLLTSGELGSPALEGLLARFGAVTVPEQT +VAFAVVIVLAFLLKAILVLAFRWWTMGFTNQNLIRTSATLLRYYLRADYGLHLTRTVGTLVNNVTGTSSMAYTGVVNASV +TFLTEAVTLVAVTVVVGVAMPLTGLGMALYFLAVAWVIKTVIRRPASRLGWTLVTAGERANTAALQGLENYKDVKIRGND +SAFMEEYRAARMESAEATRLKMILTMMPRYVLEVAFVAAIAALVAVAFIQGRGGEAFGSLALLAMAGFRVLPSMAALMAT +TNEIRTSWPAFERTTAELAAAQPVLHAADRPYERITFEESIEVRDASFTYPGKAEPVLRDIDLRIPFGSSYAFVGGSGAG +KTTLVDLVIGFHHAQRGGVYVDGVELEANPRGWWDNVAFVPQSVTVVNGTVLHNVLLDVEAAQTADRAEVERVLREAQLG +QWLDELPDGLDTVIGEGAVGVSGGQRQRLGIARALFRRPRLLVLDEATSALDNLTERRVTEVIESLRGRITVIVVAHRLS +TVKRCDQIVLMDQGRIIGQGTFAGLQETSPEFRELVRLGDLST +>GCF_003691675_PROKKA_00212 +MLTRLLKARLPEGTQYLVDRPMRIRLVFVVLGSVLVAGLEMVALASIIPLVSLLTSGELGSPALEGLLARFGAVTVPEQT +VAFAVVIVVAFLLKAILVLAFRWWTMGFTNQNLIRTSATLLRYYLRADYGLHLTRTVGTLVNNVTGTSSMAYTGVVNASV +TFLTEAVTLVAVAVVVGVAMPLTGLGMALYFLAVAWVIKTVIRRPASRLGWTLVTTGERANTAALQGLENYKDVKIRGND +SAFMEEYRAARMESAEAMRLKMILTMMPRYVLEVAFVAAIAALVAVAFIQGRGGEAFGSLALLAMAGFRVLPSMAALMAT +TNEIRTSWPAFERTTAELAAAQPVLHAADRPYERITFEEAIEVRDASFTYPGKAEPVLRDIDLRIPFGSSYAFVGGSGAG +KTTLVDLVIGFHHAQRGGVYVDGVELEANPRGWWDNVAFVPQSVTVVNGTVLHNVLLDVEAAQTADRAEVERVLREAQLG +QWLDELPDGLDTVIGEGAVGVSGGQRQRLGIARALFRRPRLLVLDEATSALDNLTERRVTEVIESLRGRITVIVVAHRLS +TVKRCDQIVLMDHGRIIGQGTFAGLQETSPEFRELVRLGDLST +>GCF_005280335_PROKKA_02456 +MLTRLLKARLPEGTQYLVDRPMRIRLVFVVLGSVLVAGLEMVALASILPLVSLLTSGELGSPALEGLLARFGAVTVPEQT +VAFAVVIVLAFLLKAILVLAFRWWTMGFTNQNLIRTSATLLRYYLRADYGLHLTRTVGTLVNNVTGTSSMAYTGVVNASV +TFLTEAVTLVAVAVVVGVSMPLTGLGMALYFLAVAWVIKAVIRRPASRLGWTLVTTGERANTAALQGLENYKDVKIRGND +SAFMEEYRAARAESAEATRLKMILTMMPRYVLEVAFVAAIAALVAVAFVQGRGGEAFGSLALLAMAGFRVLPSMAALMAT +TNEIRASWPAFERTTAELADAQPVLDAADRPYERLEFAREIEVRGASYTYPGSDEPVLRDIDLTIPFGTSYAFVGGSGAG +KTTLIDLLIGFHHAQDGAVLVDGVELEANPRGWWDNVAFVPQSVTVVNGSVLHNVVLDLEAAETADRAAVEQVLRDAQLG +EWLDALPEGLDTVIGEGAVGVSGGQRQRLGIARALFRRPRLLVLDEATSALDNLTERRVTEVIESLKGRITVLVVAHRLS +TVKHCDQIVLMDQGRIIGQGTFRGLQETSPEFQELVRLGDLSA +>GCF_020097155_PROKKA_02340 +MVTRLLKSRLPEGTQYLVDRPMRIRLGFVVLGSILVALLEMAALASILPLVNLLTTGSPGAPVITELLASVGAVSVAEQT +VAFAGVIVVAYLLKAVLVLSFRWWTMGFTNKNLIQTSAKLLRYYLRADYGLHLTRTVGTLVNNVTGTSSMAYTGVVNASV +TLLTEAVTLLAVGIVVGVTMPLTALGMGAYFLVVTLIIRHVIRKPASQLGWTLVVTGERANTAALQGLENYKDVKVRGND +SAFMDEYVDARRENAEAIRLKMILTMMPRYVLEVAFVAAIAGLVAVAFASGRGDQAFGSLALLAMAGFRLLPSIASVMAT +SNEIRASWPAFERTVAELKDAQPVLDAADRPYDRLPFERSLEARNASFTYPGKDEPVLKGIDLSIPFGASYAFVGGSGAG +KTTLVDLLIGFHHAQQGGVYVDGVELQADPRGWWDNVAFVPQSVTVVNGSVLHNVVLDIEAARTADRTEVERVLRDAQMG +DWLDALPDGLDTVVGEGAVGVSGGQRQRLGIARALYRRPRLLVLDEATSALDNVTERKVTDVIESLKGRITVIVVAHRLS +TVKHCDQVVLMDEGRILDQGTFAGLQETSPEFQELVRLGDLSS +>GCF_023573625_PROKKA_00490 +MLTRLLKARLPEGTQYLVDRPMRIRLVFVVLGSVLVAGLEMVALASILPLVSLLTSGELDSPALEGLLARFGAVTVPEQT +VAFAVVIVLAFLLKAILVLAFRWWTMGFTNQNLIRTSATLLRYYLRADYGLHLTRTVGTLVNNVTGTSSMAYTGVVNASV +TFLTEAVTLVAVAVVVGVAMPLTGLGMALYFLAVAWVIKTVIRRPASRLGWTLVTAGERANTAALQGLENYKDVKIRGND +SAFMEEYRAARMESAEATRLKMILTMMPRYVLEVAFVAAIAALVAVAFIQGRGGEAFGSLALLAMAGFRVLPSMAALMAT +TNEIRTSWPAFERTTAELAAAQPVLHAADRPYERVTFEEAIEVRDASFTYPGKAEPVLRDIDLRIPFGSSYAFVGGSGAG +KTTLVDLVIGFHHAQRGGVYVDGVELEANPRGWWDNVAFVPQSVTVVNGTVLHNVLLDVEAAQTADRAEVERVLREAQLG +QWLDELPDGLDTVIGEGAVGVSGGQRQRLGIARALFRRPRLLVLDEATSALDNLTERRVTEVIESLRGRITVIVVAHRLS +TVKRCDQIVLMDQGRIIGQGTFAGLQETSPEFRELVRLGDLST diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000513.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000513.fa new file mode 100644 index 0000000000000000000000000000000000000000..a7ba42d4f0f50adf0d56182b30a2b3a14d000ae7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000513.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00493 +MTTEDLGLD-PTARHVTVSAPGKVNLSLRVGPPGADGYHPVATVYLAVSLRETVTAIART +DG--RITVGPSGRHISLVDTQDVPWDERNLAHRAAAHLRHTLGLDPDSHGVHLEVAKQVP +VAGGMGGGSADAAAALLACSALWETGHTRAELAELAAPLGADVPFSVLGGAAVGLGTGVE +LTPVAARTPVHLVLVPADAGLSTPVVFQTLDELRREGHLPDGPPRPEVNEAVLRALTAAD +PLELATAMDNDLQTPAVVLFPELSDVLDLGLDEGALRGMVSGSGPTLLFVAQDEASALRL +ASAIEERTGVRALPVHGPVPGAHVL +>GCF_003691675_PROKKA_00214 +MTTEDLGLD-PTARHVTVSAPGKVNLSLRVGPPGADGYHPVATVYLAVSLRETVTAIART +DG--RITVGPSGRHISLVDTQDVPWDERNLAHRAAAHLRRTLGLDPDTHGVHLEVAKQVP +VAGGMGGGSADAAAALLACSALWETGHTRAELAELAAPLGADVPFSVLGGAAVGLGTGAE +LTPVAARTPVHLVLVPADAGLSTPVVFQTLDELRREGHLPDGPTRPEVNEAVLRALTAAD +PLELATAMDNDLQTPAVVLFPELSDVLDLGMDEGALRGMVSGSGPTLLFVAQDEASALRL +ASAIEERTGVRALPVHGPVPGAHVL +>GCF_005280335_PROKKA_02454 +MSEARAGLS-GTARHVTVSAPGKVNLSLRVGPPGADGYHPVATVYLAVSLRETVTAIART +DG--RVTVGPCPRQVSLVDSHDVPWDERNLAHRAAVHLRTALGLDEATHGVHLDVAKQVP +VAGGMGGGSADAAAALLACSVLWETGHTRSELAELAAPLGADVPFAVLGGAAVGLGTGAE +LTPVAARTPVHLVLVPADAGLSTPVVFGTLDELRRDGHVPEGAAHPEVNQEVVRALTAAD +PLALATVMDNDLQTPAVALFPDLGDVLDLGLDEGALRGMVSGSGPTLLFVVPDEHSALSL +ATAVEERTGVRALPVHGPVAGAHVL +>GCF_020097155_PROKKA_02338 +MS----GLPGPSARHVTVRAPGKVNLSLRVGPPRPDGYHPVASVYLAVSLAETVTAVARP +DGDARITLAESTRQPSSVDTRDVPWDERNLAHRAALHLRQSLGLAPETHGVHLEVSKQVP +VAGGMGGGSADAAAALLACSVLWDTGLTRSELAELAAPLGADVPFAVTGGAAVGRGTGSE +LTPVAARRPVHLVLVPADAGLSTPIVFRTLDELRSLGRAPEGQGEPAVDADVVRALAQAD +PLALALAMENDLQTPAVTLFPELSDVMDVGLDEGALRAMVSGSGPTLLLLAHSEQDAARL +ATAVQERTGVAALAVHGPVPGAHVL +>GCF_023573625_PROKKA_00492 +MTTEDLGLD-PTARHVTVSAPGKVNLSLRVGPPGADGYHPVATVYLAVSLRETVTAIART +DG--RITVGPSGRHISLVDTQDVPWDERNLAHRAAAHLRRTLGLDPDTHGVHLEVAKQVP +VAGGMGGGSADAAAALLACSALWETGHTRAELAELAAPLGADVPFSVLGGAAVGLGTGAE +LTPVAARTPVHLVLVPADAGLSTPVVFQTLDELRREGHLPDGPTRPEVNEAVLRALTAAD +PLELATAMDNDLQTPAVVLFPELSDVLDLGMDEGALRGMVSGSGPTLLFVAQDEASALRL +ASAIEERTGVRALPVHGPVPGAHVL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000518.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000518.fa new file mode 100644 index 0000000000000000000000000000000000000000..4e7549909ac0b22124bd27f96861ec0421e35c7a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000518.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00503 +M--PGAQGEDEAMSETTALRIRTGLDAVTVSGLTGDERAEVIASWARCGVEAVEPPARAD +AHRDADTARPWLQWHEDLVFLATSRTIESARGTHLLFHAACLAAPDTGAAMVLVAASGTG +KTTATRRLGPHFAYLTDETAIIAPDGLTVTPYPKPLSLLGSRGVRPKTQRGPDDLGLGPT +LPDARLARIAVLDRVRDPAGPVTPRAEAIELVAALEALVPQTSSLSLLPRGLVTLCRVLD +TVGGAQRLVYAEAEDLRDVVDGLLAAPPTSVTPAWEALTEEELRAS--VGAAAPGAVSRC +AVDDGILTDSGRLVLLASDRLVVLEGLGPSVWLLLDESRTAADVVACLRAEGPVPEDAEA +RVRKAMDALVSAGLATA-------------G +>GCF_003691675_PROKKA_00223 +M--PGAQGEDEAMSETTALRIGTGLDAVTVSGLTGDERAEVIASWARCGVEAVEPPARAD +AHRDADTARPWLQWHEDLVFLATSRTIESARGTHLMFHAACLAAPDTGAAIVLVAASGTG +KTTATRRLGPHFAYLTDETAIIAPDGLTVTPYPKPLSLLGSRGVRPKTQRGPDDLGLGPT +LPDARLARIAVLDRVRDPAGPVTPRAEAIELVAALAALVPQTSSLSLLPRGLVTLCRVLD +AVGGAQRLVYAEAEDLRGVVDGLLAAPPTPVTPAWEALTEEELSAS--VGVATPGAVSRC +AVDDGILTDSGRLVLLASDRLVVLEGLGPSVWLLLDEPRTAADVVARLRAEGPVPEDAEA +RVREAMDALVTAQLATT-------------G +>GCF_005280335_PROKKA_02447 +M--PAAPPDPSAAPVREALRIGAGLDAVTVSGLTGAERDELLRSWARCGVETVELTEDAD +AHRGPEHPRSWLDWHENLVFLATSRAIESARGTHLMFHAACLAAPDTGAAIVLAAASGTG +KTTATRRLGPHYAYLTDETAMVDPADLSVTPYPKPLSLLEPGGSRPKTQRGPDELGLGLT +RADAVLARIAVLDRVREAAAPVPARAEPMDVVTALQHLVPQTSSLSLLPRGLVALCTLLD +ALGGVQRLVYAEADDLRPVIDGLLAAAPQPVDPAWEPLDAAELAAS--EGAAEPGAVRRA +AAADGILTADGRLVLLAGTTLTVLDGIGPAVWFALESPLTPERIVARLAEDGPVPADAAE +RVAEAVAALESAGLLVTTPQGAGPEADALRS +>GCF_020097155_PROKKA_02331 +MTDPRRGG--------RAVRIPAGDGSTTAAGLDETGVRTLLDAWRRCGAEEVAAPAEGA +A--AYWEATGWDWFHENLVHSATTAAITAGVGRRLLFHGACLADPGTGSAVALVAASGTG +KTTATRRLGPHYAYLTDETVIVAPDTLEVTPFPKPLSLLGPSGVRPKTQVSPDELGLGDA +VP-ARLARLAVLDRVRDVDGPVTARAETMGLGDALIAVVPQTSSLARLPRGLRELCRVID +RLGGVQRLVYAEADGLRPVVDELLAAAPEPLEPAWEPLTPAELAASRETGDAAAGAARRE +AVDDGIVTDDGRLILLAGPQLAALEGLGPVVWLMLEEPLTNAQIVERLAAEGPVPDDAAD +RVADAVTALAESGLVRI-------------- +>GCF_023573625_PROKKA_00502 +M--PGAQGEDEAMSETTALRIGTGLDAVTVSGLTGDERAEVIASWARCGVEVVQPPTHTD +AHRGAHTASPWLQWHEDLVFLATSRAIESARGTHLLFHAACLAAPDTGAAMVLVAASGTG +KTTATRRLGPHFAYLTDETAIIAPDGLTVTPYPKPLSLLGSRGVRPKTQRGPDDLGLGPT +LPDARLARIAVLDRVRDPAGPVTPRAEAIELVAALEALVPQTSSLSLLPRGLVTLCRVLD +TVGGAQRLVYAEAEDLRDVVDGLLAAPPTPVTPAWEALTEEELRAS--VGAAVPGAVSRC +AVDDGILTDSGRLVLLASDRLVVLEGLGPSVWLLLDESRTAADVVARLRAEGPVPEDAEA +RVHEAMDALVTAELART-------------G + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000525.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000525.fa new file mode 100644 index 0000000000000000000000000000000000000000..f92d91b23dd007892c0d30d507310465d448f5c1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000525.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00512 +MTETPLAPEASVIVPSRGGAQRLPRLIGALAAQEDAPPFEAHVVVDGDVDGSEGMLAQLA +AEHPGLDLSWTVFGENRGRVAALNAGADATSGRILIRADDDLEPGPHYIRDHVAAHAGGS +GGVIGLTANVLPDSAYQRVYGDAQDEAHRRHAYALPAEQQWRHWAGNVSVPRTLHEELGG +YDPDYRRYGWEDVDFGYRLHAAGYPVEIRPELETRHHAAAVTTYTKARRALHSGSARQIF +IAKHGADALGGDRAPGGPWGAAVRAVAALSTERTIQYSSAVVERAAAVLPAPIARKLIAL +QVEAAAETGRTRPGRARRQF +>GCF_003691675_PROKKA_00232 +MTETPLTPEASVIVPSRGGAQRLPRLIGALAAQEDAPPFEVHVVVDGDVDGSEAVLGQLA +AERPGLDLSWTVFPENRGRVGALNAGADATSGRILIRADDDLEPGPHYIRDHVAAHSGEP +GGAIGLYLNVLEPTPYQRAYGDTQDVLHREHAYALQADQQWRHWAGNVSVPRALHQQIGG +YDPDYRQYGWEDIDYGYRLHAAGYPVVIRPELETRHHAAAVTTHSKAVRALHGTAARNLF +VGKHGAAPLGTIGAPRGVWGAAVRLVAWGTTEATLTRSSALIDAVADHLPRGLARRLIAL +QVEGAAEAGRAHPHRAQRSI +>GCF_005280335_PROKKA_02439 +MTETPLTPEASVIVPSRGGAQRLPRLIGALAAQEDAPPFEVHVVVDGDVDGSEAVLAQLA +AEYPGLDLSWTVFGENRGRVAALDAGADATSGRILIRADDDLEPGPHYIRDHVAAHDDVQ +RGVIGLTANVLPDSAYQRVYGDAQDEAHRRHAYALPAEQQWRHWAGNVSVPRVLHEELGG +YDPDYRRYGWEDVDFGYRLHAAGYPVEIRPELETRHHAAAVTTSTKARRALHSGSARQIF +IAKHGADALGGDRAPGGLWGAAVRAVATLSTERTIQYSSAVIERAAAVLPAPIARKLIAL +QVEAAAETGRTRPGRARRQF +>GCF_020097155_PROKKA_02322 +MSDQT-AYEASVIVPSRGGAGRLPRLIGALAAQEEAPPFDVHVVVDGDVDDSASALERLA +AAHPDLPLTWTVFEENRGRVAALNAGADATTGRILIRADDDLEPGVHYIRDHVAAHAEGP +GGAIGLYLNILESTPYQRVYGDAQDVLHREHAYALPADQQWRHWAGNVSVPRAVHEELGG +YDPDYRQYGWEDIDFGYRLHAAGYPVRIRPELATSHHAAAVTTYSKAVRALHGTAARNLF +IQKHGAEVLGGVDAPRGLWGAAVRLVALGATEGSLTRSSALIDAIADRVPITVARKLIAL +QVEGASEAGRAYPERAQRPI +>GCF_023573625_PROKKA_00511 +MTETPLTPEASVIVPSRGGAQRLPRLIGALAAQEDAPPFEVHVVVDGDVDGSEGMLAPLA +AEHPGLDLSWTVFGENRGRVAALNAGADATSGRILIRADDDLEPGPHYIRDHVAAHDDVQ +RGVIGLTANVLPDSAYQRVYGGAQDEAHRRHAYALPAEQQWRHWAGNVSVPRALHEELGG +YDPDYRRYGWEDVDFGYRLHAAGYPVEIRPELETRHHAAAVTTYTKARRALHSGSARQIF +IAKHGADALGGDRAPGGPWGAAVRAVAALSTERTIQYSSAVVERAAAVLPAPVARKLIAL +QVEAAAETGRTRPGRARRQF + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000528.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000528.fa new file mode 100644 index 0000000000000000000000000000000000000000..811110d41b02ff971c843c6fefc150e3af48302a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000528.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00522 +MRITETAIPGLLVLDLDVHGDNRGWFKENWQREKIRALAAEHPRLAALAPVQNNISFNDA +VGTTRGIHAEPWDKYVAVAHGRIFGAWVDLREGPSFGAVATVELGPEKAVFVPRGVGNSY +QTLEPDTAYTYLVNDHWSADAQGRYTFLNLADPTAAIAWPIPLEDAELSDKDRAHPMLAD +VTPMPSAPILVLGAGGQLGRALVARAEAAGIPVEAHGRDTWDMTDPASWPREHFRGLRAV +VNASAMTAVDAAETPEGRAQAWAVNAAAVAELARRCTKAGVPLAHVSTDYVFDGALPVGQ +EHPVDHPLAPLGVYGQSKAAGEAAVRTVPRHWIVRTSWVIGEGKNFVATMASLAERGIDP +AVVADQHGRLTFADDLADALLHLVTTDAPTGTFHMTNSGDVVTWHDVARWVFEDTGHDAA +RVSATTTAAYLAGKEGVAPRPTNSALDLGPLAAVGYTAPDQRERLRDHLTEFKAGTC +>GCF_003691675_PROKKA_00244 +MRITETAIPGLLVLDLDVHGDNRGWFKENWQREKIRALAAGHPRLASLAPVQNNISFNDA +VGTTRGIHAEPWDKYVAVAHGRIFGAWVDLREGPSFGAVATVELGPEKAVFVPRGVGNSY +QTLEPDTAYTYLVNDHWSADAQGQYTFLNLADPTAAIAWPIPLEDAELSDKDRAHPMLAD +VTPMPPAPILVLGAGGQLGRALVVRAEAAGIPVEAHGRDTWDMTDPASWPREHFRGLRAV +VNASAMTAVDAAETPEGRAQAWAVNATAVAELARRCTEAGVPLAHVSTDYVFDGTLPVGQ +EHPVDHPLAPLGVYGQSKAAGEAAVRTVPRHWIVRTSWVIGEGKNFVATMASLAERGIDP +AVVADQHGRLTFADDLADALLHLVTTDAPTGTFHMTNSGDVVTWHDVARWVFEDTGHDAG +HVSATTTAAYLAGKEGVAPRPTNSALDLGPLAAVGYTAPDQRERLRTYLR------R +>GCF_005280335_PROKKA_02427 +MKITETAIPGLLVIDLDVHGDNRGWFKENWQREKIRALAAEHPRLATLAPVQNNISFNDA +VGTTRGIHAEPWDKYVAVAHGRIFGAWVDLREGPSFGAVATVELGPEKAVFVPRGVGNSY +QTLEPDTAYTYLVNDHWSADAQSQYTFLNLADPTAAIAWPIPLEEAELSDKDRAHPMLAD +VTPMPPAPILVLGAGGQLGRALVARAEAAGIPVEAHDRTTWDLEDPDSWPREHFRGLRAV +VNASAMTAVDAAETPEGRAQAWAVNATAVAELARRCAEAGVPLAHVSTDYVFDGTLPVGQ +EHPVDHPLAPLGVYGQSKAAGEAAVRTVPRHWIVRTSWVIGEGRNFVATMASLAERGIDP +AVVDDQHGRLTFADDLADALLHLVTTDAPTGTFHMTNSGDVVTWHDVARWVFEDTGHDAA +RVSATTTAAYTAGKEGVAPRPTNSALDLGPLAVVGYTAPDQRGRLRDHLSELTGDAR +>GCF_020097155_PROKKA_02310 +MKITETAIPGLLVLDLDVHGDNRGWFKENWQREKIRALAAEHPRLASLAPVQNNISFNDA +VGTTRGIHAEPWDKYVAVAHGRIFGAWVDLREGPSFGAVATVELGPEKAVFVPRGVGNSY +QTLEPDTAYTYLVNDHWSADAQGQYTFLNLADPTAAIAWPIPLEDAELSDKDRAHPMLAD +VTPMPPAPILVLGAGGQLGRALVARAEAAGIPVEAHGRDTWDMTDPASWPREHFRGLRAV +VNASAMTAVDAAETPEGRAQAWAVNATAVAELARRCTEAGVPLAQVSTDYVFDGTLPVGQ +EHPVDHPLAPLGVYGQSKAAGEAAVRTVPRHWIVRTSWVIGEGKNFVATMASLAERGIDP +AVVADQHGRLTFADDLADALLHLVTTDAPTGTFHMTNSGDVVTWHDVARWVFEDTGHDAA +RVSAATTAEYMAGKEGAAPRPTNSALDLGPLAAVGYTAPDQRERLRDHLSEAAGGTR +>GCF_023573625_PROKKA_00522 +MRITETAIPGLLVLDLDVHGDNRGWFKENWQREKIRALAAEHPRLASLAPVQNNISFNDA +VGTTRGIHAEPWDKYVAVAHGRIFGAWVDLREGPSFGAVATVELGPEKAVFVPRGVGNSY +QTLEPDTAYTYLVNDHWSADAQGQYTFLNLADPTAAIAWPIALEDAELSDKDRAHPMLDD +VVPMPPAPILVLGAGGQLGRALVARAEAAGIPVEAHGRDTWDMADPASWPREHFRGLRAV +VNASAMTAVDTAETTEGRAQAWAVNATAVAELARRCTEAGVPLAHVSTDYVFDGALPVGQ +EHPVDHPLAPLGVYGQSKAAGEAAVRTVPRHWIVRTSWVIGEGKNFVATMASLAERGIDP +AVVADQHGRLTFADDLADALLHLVTTDAPTGTFHMTNSGDVVTWHDVARWVFEDTGHDAA +RVSATTTAAYLAGKEGVAPRPTNSALDLGPLAAVGYTAPDQRERLRDHLTEFKAGTC + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000536.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000536.fa new file mode 100644 index 0000000000000000000000000000000000000000..2cf73634aef1d947dac2387abf9a31f63c814dd2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000536.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00534 +MSRDHRPPIRNPFLPPTPEEPEVPARDGGHPAGDGGDADAPAASTAREDRLAEFRLGPAF +RPH--------------------------------------------------------- +--------PADRVPGPVPSARVLVVCTGNICRSAYVEYALQAQLNALLGDRGRAEVTSAG +TEPNQALTVPGPLLDRAPSRRVRAALTQHRPQQLTGRSLAGQDLVLTATDDHLDEVLRED +PAAVRRTFTILGMGTLLRDHGEELAAAVPPGAGVTALVTALAALR---------SRLIAH +GERPDADLPDPFRGPAEGYAAMAQTAQPIVELLAWEIARALDGDLVE-EEPTGA +>GCF_003691675_PROKKA_00258 +MSRDHRPPIRNPFLPPTPEEPEVPARDGGHPAGDGGDADAPAASTAREDRLAEFRLGPAF +RPHPADPATPRQRA--------------------------------TPTERTVAPAPVRA +AEPASPASPAGRVPGPLPSARVLVVCTGNICRSAYVEYALQAQLNALLGDRGRAVVTSAG +TEPNQALTVPGPLLDLAPSRRVRAALTQHRPQQLTGRSLADQDLVLTATDDHLDEVLRED +PAAVRRTFTILGMGTLLRDHGEELAAAVPPGAGVTALVTALAELR---------SRLIAQ +GERPDADLPDPFRGPAEGYAAMAQTAQPIVELLAWEIARALDGDLVE-EEPTGA +>GCF_005280335_PROKKA_02415 +MSQDRRAPIRNPFLEPGASVPGAPPRR--------ADADP-------EDRLAEFRLGPAF +GGRPAQPRRPQGFGGRTAPGEGTTTTPRPDGTAAAEPADTAAEPVDTAAEPAANPKTARP +AESAEAADAPAPAPAPLPTVRVLAVCTGNICRSAYVQHTLQAQLNALLGDRGRAEVTSAG +TEPNQALTVPEPLRELSPSRRVRAALTEHRPQQLTAASLWGQDLVITAADDHLEEVLRED +PGAVRRTFTVRGIGTLLGEHGEEIAAAVPPGAGLAALVDAMADLR---------VRLIGR +GEEPDADLPDPFRGPAEGYAQMVETARPIVELLAWEIARALDGDLVEDDEPTRV +>GCF_020097155_PROKKA_02297 +MSWFERPALRSPF----------------------------------------------- +-----------------------------------------------------------A +AAPGMDAPADDGAGGPL---RILTVCTGNICRSAWAHHVLQARLDAALG-ADVVEVSSAG +TGPNQALAVPEELLTLAPDAGVRAALAAHRPRRLTARVLAGQDLVLTATEAHRDAVVREA +PAALRRSATLLDAGALLAD-----PDAVAPGGGGRALVAALEAARREGRGLDAGRRGLFP +AGRRAADLADPFRGPAEGYTEMTRALEPALAAVEAAVVRAV--------EPAR- +>GCF_023573625_PROKKA_00537 +MSRDHRPPIRNPFLPPTPEEPEVPTRDGGHPAGDGGDAGAPAAATAREDRLAEFRLGPAF +LPHPADPAAPRQHA--------------------------------TPAERAVAPATAAA +AEPASPAAPADRVPGPLPSARVLVVCTGNICRSAYVEYALQAQLNALLGDRGRAVVTSAG +TEPNQALTVPGPLLDLAPSRRVRAALTQHRPQQLTGRSLADQDLVLTATDDHLDEVLRED +PAAVRRTFTILGMGTLLRDHGEELAAAVPPGAGVTALVTALAELR---------SRLIAQ +GERPDADLPDPFRGPAEGYAAMAQTAQPIVELLAWEIARALDGDLVE-EEPTGA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000539.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000539.fa new file mode 100644 index 0000000000000000000000000000000000000000..781f613f8debd9bd656a92a0c7c600db8f25cc53 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000539.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_00538 +M--PAH-PPHDDVAALPE---DVLARAERWAAEDPDPAHRDTLRAELDAAAGVGPEAAAARAALAARFAGPLVFGTAGLR +AEEGPGESRMNRLVVRRTAAGLAAHLWDGVGRDAAPPLAVVGYDARRGSAAFAADTAAVLTAAGVQTVLLPDPLPTPVLA +FAVRHLSADAGVMVTASHNPPADNGYKVYLGGRLTDEAGRGAQIVSPADAEIAARIDHAAWAADIPLADDGWTVAGPDLL +EAYRAAALGVLDDDRHGHRDLRVVYTPLHGVGGAVVPGLLEDAGFGPVHVVAEQAAPDPAFPTVAFPNPEEPGAMDLALA +LAAEVDADLVIANDPDADRLALAAPVTDADGARTWRMLSGDAVGTLLGAHAMPALHAAGRSAANSVVSSPQLAALAEANG +VRHHVTLTGFKWISRAPDLGFGYEEALGYCVDPDMVRDKDGITAALMAAELAAALTAQGRGLMDALADVDAVTGAMPSAQ +VSVRVADLSLIARTMTALRQQAPATLAGEPVTVRRDLAAGGDGLPPTDALLFATDSGTRVLVRPSGTEPKLKCYLGTRDA +DPAAAAERLEALRAEVTALVGG +>GCF_003691675_PROKKA_00262 +M--PAH-PPHDDVAALPE---DVLARAERWAAEDPDPAHRDTLRAELDAAAGVGPEAAAARAVLAARFAGPLAFGTAGLR +AEEGPGESRMNRLVVRRTAAGLAAHLWDGVGRDAAPPLAVVGYDARRGSAAFAADTAAVLTAAGVQTVLLPDPLPTPVLA +FAVRHLSADAGVMVTASHNPPADNGYKVYLGGRLTDEAGRGAQIVSPADAQIAARIDHAAWAADIPLADDGWTVAGPDLL +EAYRAAALGVLDDDRHGHRDLRVVYTPLHGVGGAVVPGLLEDAGFGPVHVVAEQAAPDPAFPTVAFPNPEEPGAMDLALA +LAAEVDADLVIANDPDADRLALAAPVTDAHGVRTWRMLSGDAVGTLLGAHAMPALHAAGRSAANSVVSSPQLAALAEANG +VRHHVTLTGFKWISRAPDLGFGYEEALGYCVDPDMVRDKDGITAALMAAELAAALTAQGRGLMDALADVDAVTGAMPSAQ +VSVRVADLSLIARTMTALRQQAPATLAGEPVTVRRDLAAGGDGLPPTDALLFATDSGTRVLVRPSGTEPKLKCYLGTRDA +DPAAAAERLEALRAEVTALVGG +>GCF_005280335_PROKKA_02411 +MSGPEHLPPTADDDAVPASEARALALAERWSVEDPDPMHREALRAELDAAAGSGPEAEAARASLASRFSGPLAFGTAGLR +AEEGPGESRMNRLVVRRTAAGLARHLWEDVGEDAAAPLAVVGYDARRGSLGFAQDTAAVLTAAGVQVVLLPDALPTPVLA +FAVRHLSADAGVMVTASHNPPADNGYKVYLGGRMTDEAGRGAQIVSPADVAIAELIDHEAWTADIPLAEDGWTVAGDELL +EAYREAALAVLDEDRHPDRALRIVYTPLHGVGGAVLPGLLDEAGFGPVHVVPEQAEPDPAFPTVAFPNPEEPGAMDLALA +LAAEVDADLVIANDPDADRLALAAPFPGPDGTRVWRMLSGDAVGTLLGAHLLPALAAAERSVANSVVSSPQLAALAEAQS +VAHHVTLTGFKWISRAPRLGFGYEEALGYCVDPDMVRDKDGITAALVAAELVAGLAARGCTVADALADVDAVTGSMPSGQ +VSVRVADLSVIPRTMAALRAQGPATLAGEPVTVRRDLAEGGAGLPSTDALLFATASGTRVLVRPSGTEPKLKCYLGARDA +DPAVAAERLEALRAEVAALVGG +>GCF_020097155_PROKKA_02293 +M------------RALDP---RVRELAERWSVEDPEPMHRAVLMDELAAADGDDPAAEAARASLASRFSGPLAFGTAGLR +AEEGPGESRMNRLVVRRTAAGLGRHLWNELGPDQPAPLVAVGYDARRGSADFAADTAAVLTAAGAQVVLLPRALPTPVLA +FAVRHLHADAGVMVTASHNPPADNGYKVYLGGRMTDEAGRGAQIVSPADVQIAAQIDHDAWTADIPLAAEGWEVAGEDLL +EAYRAAALGVLDPGGHPGRDLRIVYTPLHGVGGAVLPDLLAEAGFADVHVVPEQAAPDPAFPTVAFPNPEEPGAMDLALA +LAAEVGADLVIANDPDADRLALAVPAGDG-AAPSWRMLSGDAVGTLLGAHLLPRLAAQGRSAANSVVSAPQLAALAAAAG +VEHHVTLTGFKWISRAPRLGYGYEEALGYCVAPDMVRDKDGMTAALVAAELAASLKAAGRTLDDARADADAVTGSMPSGQ +VSVRVQDLRIIADTMAALRARPPAALAGDPVTVERDLAAGSADLPATDALLFATDAGTRVLVRPSGTEPKLKCYLGTQDA +DPTAAAARLDRLREEVAALVAG +>GCF_023573625_PROKKA_00541 +M--PAH-PPHDDVAALPE---DVLARAERWAAEDPDPAHRDTLRAELDAAAGVGPEAAAARAVLAARFAGPLAFGTAGLR +AEEGPGESRMNRLVVRRTAAGLAAHLWDGVGRDAAPPLAVVGYDARRGSAAFAADTAAVLTAAGVQTVLLPDPLPTPVLA +FAVRHLSADAGVMVTASHNPPADNGYKVYLGGRLTDEAGRGAQIVSPADAEIAARIDHAAWAADIPLADDGWTVAGPDLL +EAYRAAALGVLDDDRHGHRDLRVVYTPLHGVGGAVVPGLLEDAGFGPVHVVAEQAAPDPAFPTVAFPNPEEPGAMDLALA +LAAEVDADLVIANDPDADRLALAAPVTDADGVRTWRMLSGDAVGTLLGAHAMPALHAAGRSAANSVVSSPQLAALAEANG +VRHHVTLTGFKWISRAPDLGFGYEEALGYCVDPDMVRDKDGITAALMAAELAAALTAQGRGLMDALADVDAVTGAMPSAQ +VSVRVADLSLIARTMTALRQQAPATLAGEPVTVRRDLAAGGDGLPPTDALLFATDSGTRVLVRPSGTEPKLKCYLGTRDA +DPAAAAERLEALRAEVTALVGG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000548.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000548.fa new file mode 100644 index 0000000000000000000000000000000000000000..5dff397ec034f83a3ee7ecb6c334cc47bb28d24b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000548.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00549 +MSRP----ETPDTAPLPIVPPA-------------EDETARD-------------VEERS +AEP--AGWTSAMRTLDAGLVVGPRAYTSREVAQRLGVSMASARKIWRALGYPTSPEGHKA +FTEADIEAFESVLTLVRSGTLNEDTAISLARSIGQMTDRMVVWQIEALVEDKIASEGLTD +PEARRAVVDMLPDMVGPLEKSMRIVYRRQLNRAVQRLTVRVEAGLAASAEGRDGSESDAP +LPLARAVGFADMVSYTTLSRTMDDRTLARMVLRFESLAAETISAGGGWLVKTIGDEVMFN +AETPEAGAAIALSLAETIAADEELPSARVALTWGRVLSRMGDIYGPTVNLAARLTSLADP +GTVLVDAMTAAALSRDERFVLVPQPPRIVRGFGEVRPSLLLDGSAQTLLAD +>GCF_003691675_PROKKA_00274 +MSRP----ETPDTAPLPIVPPA-------------EDETARD-------------VEERS +AQP--AGWTSAMRTLDAGLVVGPRAYTSREVAQRLGVSMASARKIWRALGYPTSPEGHKA +FTEADIEAFESVLTLVRSGTLNEDTAISLARSIGQMTDRMVVWQIEALVEDKIASEDLTD +PEARRAVVDMLPDMVGPLEKAMRIVYRRQLNRAVQRLTVRVEAGLAASAQGRDGSESDAP +LPLARAVGFADMVSYTTLSRTMDDRTLARMVLRFESLAAETISAGGGWLVKTIGDEVMFN +AETPEAGAAIALSLAETIAADEELPSARVALTWGRVLSRMGDIYGPTVNLAARLTSLADP +GTVLVDAMTAAALSRDERFVLVPQPPRIVRGFGEVRPSLLLDGSAQTLLAD +>GCF_005280335_PROKKA_02397 +MSRA----ETPETAPLPIIAPDGSGPAEAPRRKDPHDERRADRHEDRRGEAAADRLEEVD +APPPGAGWTTAMRTLDAGLVVGPRAYTAREVAQRMGVSTASARKIWRALGYPTSPEGHKA +FTEADVEAFESVLELVRSGALNEDAAISLARSIGQMTDRMVVWQIEALVEDKIVSEGLTD +PEARRAAVDLLPEIVTPLERAMQIVYRRQLNRAVKRLTVRVEAGLAASEEGRDGSESDSP +LPLARAVGFADMVSYTTLSRTMDDRTLARMVQRFETLSAEIISAGGGWLVKTIGDEVMFN +AETPETGAAIALALAEAIAADDELPSARVALTWGRVLSRMGDIYGPTVNLAARLTSLADP +GTVLVDAMTAAALSRDERFVLVPQPPRIVRGVGEVRPSLLLNGSAQTLLAD +>GCF_020097155_PROKKA_02281 +MTRDTHHDAVPETAPLPVQAPAG------------AADPAVG-------------RRESD +ALH--HGWTSAIRTLDAGLLDRPRSYSRREAAQRLGISSVSARKIWRALGYPTVKDEEKV +FSAEDIDAFEQVLSLVRDGMLNEDTAISLARSVGQMTDRMVVWQIEALVEDQIAAEGKTD +PEARRAAVEMLPGLVEPLEKVMRIVYRRQLTNAVQRLTVRVEAGLAASERGRDGSEDDAP +LPLARAVGFADMVSYTTLSRTMGERTLARTVQRFESKAAEIIAAGGGWLVKTIGDEVLFN +AETPEAGATIALALAEAMADDDQLPAARVSLAWGRVLSRLGDIYGPTVNLASRLTSLADP +GTVLVDAMTAAALSRDERFVLVPQPPRIVRGFGEVRPSLLMNGAAQPLIAD +>GCF_023573625_PROKKA_00552 +MSRP----ETPDTAPLPIVPSA-------------EDETARD-------------VEERS +AQP--AGWTSAMRTLDAGLVVGPRAYTSREVARRLGVSMGSARKIWRALGYPTSPEGHKA +FTEADIEAFESVLTLVRSGTLNEDTAISLARSIGQMTDRMVVWQIEALVEDKIASEDLTD +PEARRAVVDMLPDMVGPLEKAMRIVYRRQLNRAVQRLTVRVEAGLAASAQGRDGSESDAP +LPLARAVGFADMVSYTTLSRTMDDRTLARMVLRFESLAAETISAGGGWLVKTIGDEVMFN +AETPEAGAAIALSLAETIAADEELPSARVALTWGRVLSRMGDIYGPTVNLAARLTSLADP +GTVLVDAMTAAALSRDERFVLVPQPPRIVRGFGEVRPSLLLDGSAQTLLAD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000556.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000556.fa new file mode 100644 index 0000000000000000000000000000000000000000..2101af411bda9b046bf105ee4138b3e5c0432d8a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000556.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00559 +MPATPRTSRT---PAVRPAP-ALPAPSARTVRWEIAIVLGLSLGKSAVYAIVQLIDKATQ +APLGEQTTVLNPALADRWAFDLTYQLLGIGFALVPVALVLHLMHLRGRNPFRVLGLDLRR +PGRDLAWGLGLFAAIGLGTLGVYAAGRALGITTAIVGSALGESWYQVPVLLLSALRHGLL +EEVIVGAWLVDRLGYLQRLRAAGLARDPAPAVP-----------SSWVSAEGLYLPTRAA +VVVLALALLRGAYHLYQGIGPGVGNALMGVVFALVFLRVRRVMPLVIAHTLLDAVGFVGY +PLLARAGLLG +>GCF_003691675_PROKKA_00284 +MPATPRTSRTPAGPAVRPAP-ALPAPSARTVRWEIAIVLGLSLGKSAVYAIVQLIDKATQ +APLGEQTTVLNPALADRWAFDLTYQLLGIGFALVPVALVLHLMHLRGRNPFRVLGLDLRR +PGRDLAWGLGLFAAIGLGTLGVYAAGRALGITTAIVGSALGESWYQVPVLLLSALRHGLL +EEVIVGAWLVDRLGYLQRLRAAGLAHDPAPAVP-----------SSWVSAEGLYLPTRAA +VVVFALALLRGAYHLYQGIGPGVGNALMGVVFALVFLRVRRVMPLVIAHTLLDAVGFVGY +PLLARAGLLG +>GCF_005280335_PROKKA_02384 +MSLPVPPALA------SPVPTALPAPSARTVRWEIAIVLGLSLGRSAVYAVVQLIDKATQ +APLGDQTTVLNPTVDDRWAFDLTYQLLGIAFALVPVLLVLHLMHLRGRNPFRTLGLDLRR +PGRDLAWGVGLFAVIGLGTLGVYAAGRALGLTTAIVANAMDESWYQIPVLLLSALRHSLL +EEVIVGAWLVDRIGYLQRLKAAGLDRDPVPAVPAAPARRTGAPSSSWTTPEGLFLPTCVA +TALLALALLRGAYHLYQGVGPGIGNALMGVVFVLVFLRVRRVMPLVVAHFLLNAVGFVGY +PLLARAGLLG +>GCF_020097155_PROKKA_02268 +MTATARPEHA-AGRRGPGAP-ALPAPSARTVRWEIAIVLGLSLGRSAVYAVVQLIDQATR +APLGDQTTVLNPTVADRWAFDLTYQLLGIAFSLVPVLLVLHLLWLRGRHPFRVLGLDLRR +PGRDLAWGLGLFTVIGVGTLGVYAAGRALGITTAIVANAMDESWYQVPVLLLSAARHALL +EEVIVGAWLIDRLGYLQRLREAGL-----------------GASSSWAGTEGLFLPLRTW +PVVLSLALLRGAYHLYQGVGPGIGNALMGAVFVLVFLRVRRVMPLVLAHFLLDAVGFVGY +PLLARAGLLG +>GCF_023573625_PROKKA_00562 +MPATPRTSRT---PAVRPAP-ALPAPSARTVRWEIAIVLGLSLGKSAVYAIVQLIDKATQ +APLGEQTTVLNPALADRWAFDLTYQLLGIGFSLVPVALVLHLMHLRGRDPFRVLGLDLRR +PGRDVAWGLGLFAAIGLGTLGVYAAGRALGITTAIVGSALGESWYQVPVLLLSALRHGLL +EEVIVGAWLVDRLGYLQRLRAAGLARDPAPAVP-----------SSWVSAEGLYLPTRVA +VVVLALALLRGAYHLYQGIGPGVGNALMGVVFALVFLRVRRVMPLVIAHALLDAVGFVGY +PLLARAGLLG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000560.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000560.fa new file mode 100644 index 0000000000000000000000000000000000000000..e843edce68b946c982ef6a731abdafe7e6748674 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000560.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00563 +--------------------------------------MGN--PSSSQPPHASDATPVDD +------PAAHPWRRYVAIGDSFSEGIGDPDPDRPGYHRGWADRLAEELSRLTPPGEDLAY +ANLAVRGKLLDQIAEDQVEPAIALRPDLISVCAGGNDILRGADPDEIAARLDAVVERLAS +AGATVLLFNATDVKGTPVIGRIRGTVAIYNENVRTIALRHDALVPDMWSLKDLARREMWA +EDRLHFSALGHHTIAAMVLDTLGVEHGLEHLRLSPPAPRTWRAARASDAAWVRTHLAPWV +VRRLRGVSSGDGVTAKRPVPEPLFGAPMPQGSDHTEPLDIVEP +>GCF_003691675_PROKKA_00288 +--------------------------------------MGN--PSSSQPPHASDATPVDD +------PAAHPWRRYVAIGDSFSEGIGDPDPDRPGYHRGWADRLAEELSRLTPPGEDLAY +ANLAVRGKLLDQIAEDQVEPALALRPDLISVCAGGNDILRGADPDEIAVRLDAVVERLAS +DGATVLLFNATDVKGTPVIGRIRGTVAIYNENVRTIALRHDALVPDMWSLKDLARREMWA +EDRLHFSALGHHTIAAMVLDTLGVEHGLEHLRLSPPAPRTWREARASDAAWVRTHLAPWV +ARRIRGVSSGDGVTAKRPVPEPLFGAPMPQGSDHTESLNVVEP +>GCF_005280335_PROKKA_02380 +MRAESPDGDDFPSESTGGGGRGRRGRLTDDGGASRLLLVSNQQESAPQHPAAAEAEPPAD +VVTRAETAAHPWRRYVAIGDSFTEGIGDPDPDRPGYHRGWADRAAEELARRTPDGEDLAY +ANLAVRGKLLDQIAADQVEPALALRPDLISVCAGGNDILRRADPDDVAVRLDAVVERLSA +NGATVLLFNATDTKDTPVLGRIRGTVAIYNENVRTVALRHDALVADMWSLKELARREMWA +EDRLHFSATGHHTIAAMVLDTLAVPHGLEPLRPEPAAPRTWRQARASDAAWARTHLAPWV +VRRIRGVSSGDGVSAKRPVPAPLFGAEMPHGSDPTEPLDVVAR +>GCF_020097155_PROKKA_02264 +METMSP--------------------------------LTN--TADSEPPHAEGHASA-- +------EPAHPWRRYVAVGDSFTEGIGDPDPERPGYHRGWADHLAEELARLTPAGEEFSY +ASLAVRGKLMDQIRADQIDPAVELAPDLVSICAGGNDILRRADPDETALHLDDAVGRLAE +TGATVLLFNVPDIKETPVLARIRGRVAIYNENIRTVAARHHAVVADMWSLKDLARPEMWA +PDRLHFSPVGHHTIAAMALDTLGVEHELEPLSPKRAAPRTWREARVDDARWARTHLVPWV +GRRLRGVSSGDGMQPKRPLPAPLFGADMPHGSDYTEH---AAD +>GCF_023573625_PROKKA_00566 +--------------------------------------MGN--PSSSQPPHASDATPVDD +------PAAHPWRRYVAIGDSFSEGIGDPDPERPGYHRGWADRLAEELSRLTPPGEDLAY +ANLAVRGKLLDQIAEDQVEPALALRPDLISVCAGGNDILRGADPDEIAVRLDAVVERLAS +DGATVLLFNATDVKGTPVIGRIRGTVAIYNENVRTIALRHDALVPDMWSLKDLARREMWA +EDRLHFSALGHHTIAAMVLDTLGVEHGLEHLRLSPPAPRTWREARASDAAWVRTHLAPWV +VRRLRGVSSGDGVTAKRPVPEPLFGAPMPQGSDHTEPLDVVEP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000564.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000564.fa new file mode 100644 index 0000000000000000000000000000000000000000..1dd63d1cd0b3bc3ee57aba39cf21e4781f014fc2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000564.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00567 +M----------DLPAG----------VTLRPWAEGDDLRLLEVWGDPADVQQHQDRAMLA +PDADTPWRHTLVAEDDGVPVGAGTVVAQALHPRRLWLYLEVAPTARRRGIGSALLGALRD +AVEQAHAAGQVTTTHLKTRFAVASRVAVATG----RSADAAEATAPAAGEEAGEAHAAQV +AGTEAFLVAAAFSPVQRSRRVAVAPGSIALPPLRDEDHPEGAVLEDAATGSVELTRAVAA +FYDAVHGWDPAQMSVGAAQQLILGPATGASGAVVLRDAPREEGGAVQAFAVSYTAERQDA +PADVFLGWDPELPLDQAQLAAGQLLAMLVAQHPVQVEVDEAMTALEPILDGLIAQRAAAT +LVDTRIWATDPA-- +>GCF_003691675_PROKKA_00292 +MTGAAGAAGHDDGGALFDSAAVAGGEIVLRPWRPGDDLALLEVWGDPANAQQHQDRAMLA +EDAERPWRRALVAEAAGVPVAAGVVYASSVHPRRLWLYVETAAAERRRGIGRALVAALRG +LAAEAHAAGAIPTTALKARFAKDALVPGVSGADPQTDAEGPAGQPPVDTEAVRSQTAALA +AGTEAFLVAEGFTPVQRSRRVAIAPGAIGLPDVRGEEHPDGVVLEEASTGSVELTQAVTA +FYDAVHAWDPSTLSVGAAQQLLLGPATGAAGAVVLRDAPKAEGGRIRAFAVSYTPERQDA +PADVLVGWDPELGEEDALQAVADLLALLVAQYPVQIEVDEAMAPLERIVDGLIGGNAART +LVDTYVFVDDAPGA +>GCF_005280335_PROKKA_02376 +MSGAY----DDDAGALFDSAAVSGGEVVLRPWRAGDDLALLQVWGDPANVQQHQDRAMLA +EDAERPWRRALVAEDAGVPVAAGVVYASSLHPQRLWLYVETAAPERRRGIGRALVAALRG +LAAEAHAAGTVPTAALKARFAKDALVPGT------------AVEEGVDTEAVRAQTAALA +AGTEAFLAAEGFTPVQRSRRVAVAPGAIGLPDVRDEDRPDGVVLEEASTGSVELTQAVAA +FYDAVHAWDPSTMSVGAAQQLLLGPATGASGAVVLRDAPKAEGGRIRAFAVSYTPERQEA +PADVLVGWDPELSEEDALQSVADLLALLVAQHPVQVEVDEAMAPLERIVDGLIGGNAART +LVDTYVFVDDAA-- +>GCF_020097155_PROKKA_02260 +MSPRH----DDDAPAL--TAAVSGGEVVLRPWAEGDDLRLLEVWGDPADVQQHQDRAMLA +ADADSPWRRTLVAEEDGVPVGAAVAFAQPLHPGRLWVYGEVARTVRGRGVGRALLEALRG +LVAAAHEAGAVPTTELKARFAVASRVPVGGG----EVVEAAPGEAPEAGAAGAEAHAAQV +AATERFLVAAGFTPVQRSRRIAVAPGVIALPALRDEEHPEGRVLEEISTGSVELTRAVAA +FYDAAHAWDPSQMSVGAAQQLILGPQTGAAGAVVLRDAPREEGGTIQAFAVSYTAERQDA +PADVLLGWDPSLGLEEAQLAVGDLLALLVAQHPVQVEADEAMTALEPILDALLAKRAAGT +LVDTRVWATDPS-- +>GCF_023573625_PROKKA_00570 +MTGAAGAAGHDDGGALFDSAAVGGGEIVLRPWRPGDDLALLEVWGDPANAQQHQDRAMLA +EDAERPWRRALVAEAAGVPVAAGVVYASSVHPRRLWLYVETAAAERRRGIGRALVAALRG +LAAEAHAAGAIPTTALKARFAKDALVPGVTGADPQTEADGATGRPPVDTDAVRSQTAALA +AGTEAFLVAEGFTPVQRSRRVAIAPGAIGLPDVRGEEHPDGVVLEEASTGSVELTQAVTA +FYDAVHAWDPSTLSVGAAQQLLLGPATGAAGAVVLRDAPKAEGGRIRAFAVSYTPERQDA +PADVLVGWDPELGEKDALQAVADLLALLVAQYPVQIEVDEAMAPLERIVDGLIGGNAART +LVDTYVFVDDATGA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000565.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000565.fa new file mode 100644 index 0000000000000000000000000000000000000000..09a617e84d039fce0e80966f3d0613a19ae65c2c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000565.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00572 +MTRKHLGFLNFGHWIHRP-----GAEPDARQALDDVVAMAVAAEDAGLDGAWLRVHHFQR +MFSSPFPILAAMAARTERISLGTGVIDLRYENPLYMAEAAATTDLISGGRLELGVSRGSP +EAALDGQAQFGYALDEGQTWADVTRERGRRFLSAVRGEGIATPDLTSGWAHSSQPLRIEP +HSPGLADRIWWGSGSVGSVAGAATDGYNMLSSTLLLQDDGRPFHVQQADQIARYREAFAA +AGHAGPGRTAVTRSAFVIQDREDELYFGRERASRDSSGMLEGGAARSGPTYAGSAEEVAE +KLAADDAVAAADWVLFANPNQLGVEYNAKIFAGWAEVWRLLGWDA +>GCF_003691675_PROKKA_00296 +------------------------------------------------------------ +---------------------------MRYENPLYMAEAAATTDLISGGRLELGVSRGSP +EAALDGQAQFGYALDEGQTWADVTRERGRRFLSAVRGEGIATPDLTSGWAHSSQPLRIGP +HSPGLADRIWWGSGSTPSAVEAGRDGYNMLSSTLLLQDDGRPFHVQQADQIARYREAFAA +AGHTGPGRTAVTRSAFVIQDREDELYFGRERASRDSSGMLEGGAARSGPTYAGSAEEVAE +KLAADDAVAAADWVLFANPNQLGVEYNAKIFAGWAEVWRLLGWDA +>GCF_005280335_PROKKA_02373 +MN----------ECCNR------------------------------------------- +--------------------------DIRYENPLYMAEAAATADLLAGGRLELGVSRGSP +EAAKDGQAQFGYELADGQTWAGVTRKRGRRFLAAVRGEGIATPDLASGWAHSSAPLRIEP +HSPGLADRIWWGSGSAGSAVEAAKDGYDMLSSTLLLQDDGRPFHVQQADQIAGYLEAYEA +AGHAGTGRTAVTRSAFVIQDHEDELYFGRDRNSRESAGMLDGGRARSGPTYAGSAEEVAE +KLAADDAVQAADWVLFANPNQLGPEYNAKIFAGWAEVWRLLGWDR +>GCF_020097155_PROKKA_02253 +MTTKNLGFLNFGHWIHRPRVGRRPVEPDAKQAIDDVVQMAVDAEAAGLDGAWIRIHHFQR +MFSSPFPILTAMAAHTERIHLGTGVIDLRYENPLYMAEAAATTDLLAGGRLELGVSRGSP +EAARDGQAQFGYELADGQTWSDVARERGRRLLAGVRGEGIATPDLSSGWAHSSAPLRIEP +HSPGLADRIWWGSGTVGSAVEAAKDGYGMLSSTLLLQDDGRPFHVQQADQIARYLEAYEA +GGHTTPARTAVTRSAFVIQDHEDELYFGRDRHSRDSSGHLDGGAARSGPTYAGSAEEVAE +LLAADDAVQAADWVLFANPNQLGAEYNAKLFAGWAEVWRLLGWDS +>GCF_023573625_PROKKA_00573 +MTRKHLGFLNFGHWIHRP-----GTAPDARQALDDVVAMAVAAEDAGLDGAWLRVHHFQR +MFSSPFPILAAMAARTERISLGTGVIDLRYENPLYMAEAAATTDLLSGGRLELGVSRGSP +EAALDGQAQFGYALAEGQTWADVTRERGRRFLSAVRGEGIATPDLTSGWAHSSQPLRIEP +HSPGLADRIWWGSGSVGSVAGAAADGYNMLSSTLLLQDDGRPFHVQQADQIARYREAFAA +AGHAGPGRTAVTRSAFVIQDREDELYFGRERASRDSSGMLEGGAARSGPTYAGSAEEVAE +KLAADDAVAAADWVLFANPNQLGVEYNAKIFAGWAEVWRLLGWDA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000589.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000589.fa new file mode 100644 index 0000000000000000000000000000000000000000..2c930c4ab9213cad685e312b20b137d20a656d4a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000589.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00657 +MTPRTTPDAEPVFELVEQDEIGYETTHVDAFMARAREARDGGAPLTAEEVRQARFATVNG +GYATDEVDDELDRLEEELAAAERQAFVAERGDEDWAADLEERVAELVARADRAPAERFRR +PSRADAVSYDVDQVDALVDRLRVTLAGAEDSTDPGAEGGLTADDVRRASFGEAEGAAGYE +EGQVDAYLDAAVDVLLRRA +>GCF_003691675_PROKKA_00394 +MTPRTTPDAEPVFELVEQDEIGYETTHVDAFMARAREARDGGAPLTAEEVRQARFATVNG +GYATDEVDDELDRLEEELAAAERQAFVAERGDEDWAADLEERVAELVARADRAPAERFRR +PSRADAVSYDVDQVDALVDRLRVTLAGAEDSTDPGAEGGLTADDVRRASFGEAEGAAGYE +EGQVDAYLDAAVDVLLRRA +>GCF_005280335_PROKKA_02306 +MTTRRPQDAEPPFELVEQDEIGYETSHVDAFLARAREAREGGAPLTADEVRQARFATVNG +GYATDEVDDELDRLEGELAAAEREAFVSERGDEDWSADLEERVAELVARADRAPAERFRR +PSREDATSYDVDAVDALVDRLRVTLAGAEGAAAPDARGGLTADDVRRASFGEAEGDRGYE +EGQVDAYLDAAVDVLLRRA +>GCF_020097155_PROKKA_02163 +MTP-TSPEARADFEHVGPDEIGYEPAHVDAFLERARRAEAGEGDLTAEDVRQARFATVNG +GYAADQVDDELDRLEEVLMGREREDAV---GDGAWDRELAERSQELLGRADRAPAERFRR +PSADDAQSYDVDDVDALVDRLRATLT--------DGSDELTADDVRRAGFASAQGGDGYD +EAQVDAYLDAAVDVLLRRG +>GCF_023573625_PROKKA_00627 +MTPRTTPDTEPVFELVEQDEIGYETTHVDAFMARAREARDGGAPLTAEEVRQARFATVNG +GYATDEVDDELDRLEEELAAAERQAFVAERGDEDWAADLEERVAELVARADRAPAERFRR +PSRADAVSYDVDQVDALVDRLRVTLAGAEGSTDPDAEGGLTADDVRRASFGEAEGAAGYE +EGQVDAYLDAAVDVLLRRA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000596.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000596.fa new file mode 100644 index 0000000000000000000000000000000000000000..1da022db9f4c2295fd1d1fb8654a46e5e4d3887a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000596.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00668 +MSSSEPTAPVPTAAQFRAAQQSEEFTELRRTHRSFAFPMTVAFFVWYLVFVIVGAFFPEF +MAIRLGGNITLGLILGLLQFVTTFLITFAYVRFSNRTLDPRATALRERLEREAA-GAHEN +PEATR +>GCF_003691675_PROKKA_00405 +MSSSEPTAPVPTAAQFRAAQQSEEFIELRRTHRSFAFPMTVAFFVWYLVFVIVGAFFPEF +MAIRLGGNITLGLILGLLQFVTTFLITFAYVRFSNRTLDPRATALRERLEREAA-GAHEN +PEATR +>GCF_005280335_PROKKA_02294 +MSSSEPTAPAPTAAQFRAAQQSEEFTELRSTYRSFAFPMTVAFFVWYLVFVIAGAFFPEF +MSIRLGGNITLGLVLGLLQFVTTFLITFAYVRFSNRTLDPRATALRERLEREAAGGAPET +PEATR +>GCF_020097155_PROKKA_02156 +MSTGPHTPPAPTPAQFRAAQDSPEFRELRRTQRSFAFPMTVTFFVWYLLFVILGAFFPQV +MAVRLGGNITLGLVLGLLQFVTTFAITFAYVRFSNRVLDPRAAALRERLEREAAGAAPET +PEVAL +>GCF_023573625_PROKKA_00638 +MSSSEPTAPVPTAAQFRAAQQSEEFIELRRTHRSFAFPMTVAFFVWYLVFVIVGAFFPEF +MAIRLGGNITLGLILGLLQFVTTFLITFAYVRFSNRTLDPRATALRERLEREAA-GAPEN +PEATR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000599.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000599.fa new file mode 100644 index 0000000000000000000000000000000000000000..73b78b84031a76593f73ddb809de78b06dfa2e8f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000599.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00671 +MTVVEILWYVAGVLAVALGLAVSIALHEIGHLVPAKLFGVRVTQYMIGFGPTLVSWRRGE +TEYGFKAVPLGGYVAMIGMLPPPRPGQTPRAASTGFVQQLGRMADDARAQAAEEVRPGDE +HRRFLALPVWKRVVIMLGGPFMNLLIALGATALLVTTVGTSQPSTTVAEVYRCVVTMQEQ +QARAASGG-TEDCRPGDPAAPAHEAGLRPGDTVLAFDGRPVSDWDALSAAIRDRAGQPTR +IEWERDGERMSATLTPRLTERPVTDALGRPERAPDGTVATHEVGFIGMGAQLETVRGTPL +DAGPLVAQQVRGVVDVVLVLPQRLWDTAVAVVTPAERDPDGPMSVVGVGRIAGEAAALEE +ATLTDKAALLLSLLAGVNVALMVFNLIPLLPLDGGHVAGALWEAVRRGWARITGRPDPGP +FDLARMLPLTYAVGAAMLLMGVILIVADIVEPVRLF +>GCF_003691675_PROKKA_00408 +MTVVEILWYVAGVLAVALGLAVSIALHEIGHLVPAKLFGVRVTQYMIGFGPTLVSWRRGE +TEYGFKAVPLGGYVAMIGMLPPPRPGQTPRAASTGFVQQLGRMADDARAQAAEEVRPGDE +HRRFLALPVWKRVVIMLGGPFMNLLIALGATALLVTTVGTSQPSTTVAEVYRCVVTMQEQ +QARAASGG-TEDCRPGDPAAPAHEAGLRPGDTVLAFDGRPVSDWDALSAAIRDRAGQPTR +IEWERDGERMSATLTPRLTERPVTDALGRPERAPDGTVATHEVGFIGMGAQLETVRGTPL +DAGPLVAQQVRGVVDVVLVLPQRLWDTAVAVVTPAERDPDGPMSVVGVGRIAGEAAALEE +ATLTDKAALLLSLLAGVNVALMVFNLIPLLPLDGGHVAGALWEAVRRGWARITGRPDPGP +FDLARMLPLTYAVGAAMLLMGVILIVADIVEPVRLF +>GCF_005280335_PROKKA_02291 +MSAVEVLWYVLGVVAVALGLAVSIALHEVGHLMPAKLFGVRVTQYMIGFGPTIASWRRGE +TEYGFKAVPLGGYVAMVGMLPPPRPGQEPRTASTGFVQQLGRMADDARTQAAAELTAADE +GRQFIQLPVWKRVVIMLGGPFMNLLIALGVTALLVTTVGTSQPSTTAAEVYRCVVTTDEQ +QARAAEGG-GQDCRPGDPVAPAHEAGLRPGDTVTSFDGRPVDDWDALSGLIRERAGQPTA +IEWERDGEPHSATITPRLTQRPVTDAVGRPERAPDGTALTEEVGFIGMGSQIETVQQSPL +AAGPVVAQQVRGVVDVVLVLPQRLWDTAVAVVTPAERDPDGPMSVVGVGRIAGEAAALQE +AELADKAALLLSLVAGVNVALMVFNLIPLLPLDGGHVAGALWEALRRGWARLRGRPDPGP +FDLARMLPLTYAVAGLMLVMGVVLIVADIVEPIRLF +>GCF_020097155_PROKKA_02153 +MSAVEALWFVGGVVVVALGLALSIALHEVGHLVPAKLFGVRVTQYMVGFGPTVASWRRGE +TEYGIKAFPLGGYVAMVGMLPPPKGGTVARTGSTGFRARAGRMADDARAQAAEEITAADE +GRQFIQLPVWKRVVIMLGGPFVNLLIALALTAVLVSTLGVARPSTTADEVFQCVVSQSEQ +QSRAADGGAAQDCRPGDPAAPAYEAGLRPGDRVVSFDGRDVGSWAELSTAIRARAGQATA +IAWERDGTRTESTLTPLLTERPVTDALGVPERGADGGVKTEPVGFIGLASRQETVTLAPW +EAVPLVGRQAQGVVGVILALPQRLWDTAVAVVTPAPRDPNGPMSVVGVGRIAGEAAALDT +ASPADKAALLLSLVAGVNVALLVFNLIPLLPLDGGHVAGALWEGLRRGWARLRGRPDPGP +FDLAVMMPLTYVVGAAMLAMGVLLIVADIVKPVQLF +>GCF_023573625_PROKKA_00641 +MTVVEILWYVAGVLAVALGLAVSIALHEIGHLVPAKLFGVRVTQYMIGFGPTLVSWRRGE +TEYGFKAVPLGGYVAMIGMLPPPRPGQTPRAASTGFVQQLGRMADDARAQAAEEVRPGDE +HRRFLALPVWKRVVIMLGGPFMNLLIALGATALLVTTVGTSQPSTTVAEVYRCVVTMQEQ +QARAASGG-TEDCRPGDPAAPAHEAGLRPGDTVLAFDGRPVSDWDALSAAIRDRAGQPTR +IEWERDGERMSATLTPRLTERPVTDALGRPERAPDGTVATHEVGFIGMGAQLETVRGTPL +DAGPLVAQQVRGVVDVVLVLPQRLWDTAVAVVTPAERDPDGPMSVVGVGRIAGEAAALEE +ATLTDKAALLLSLLAGVNVALMVFNLIPLLPLDGGHVAGALWEAVRRGWARITGRPDPGP +FDLARMLPLTYAVGAAMLLMGVILIVADIVEPVRLF + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000605.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000605.fa new file mode 100644 index 0000000000000000000000000000000000000000..6cc2104a1e73464775cc5772d9db7165ba6a499f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000605.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00677 +MSALRMLEAEREIPMDRLIPTIEQALLMAYHRTPGALKRARVEIDRATGHVTVWATELDE +DDTPIGEFDDTPNGFGRVAASTARQVMIQRMREEDDDKVLGEFKDKEGELVSGVIQQGLN +RHMVQVNLGTLEAVLPPPEQVPGEDYAHGRRIRAYVVSATRGAKGPSVTVSRSHPGLVRK +LFELEVPEIADGSVEITALAREAGHRTKMAVRATRPGVNAKGASIGEMGSRVRAVMTELN +DEKIDIVDHVDDPAAMIANALSPATTVSVEILDADQHSARAVVPEYQLSLAIGKEGQNAR +LAAKLTGWRIDIVGDGVTTSAPGR------------------------ +>GCF_003691675_PROKKA_00414 +MSALRMLEAEREIPMDRLIPTIEQALLMAYHRTPGALKRARVEIDRATGHVTVWATELDE +DDTPIGEFDDTPNGFGRVAASTARQVMIQRMREEDDDKVLGEFKDKEGELVSGVIQQGLN +RHMVQVNLGTLEAVLPPPEQVPGEDYAHGRRIRAYVVSATRGAKGPSVTVSRSHPGLVRK +LFELEVPEIADGSVEITALAREAGHRTKMAVRATRPGVNAKGASIGEMGSRVRAVMTELN +DEKIDIVDHVDDPAAMIANALSPATTVSVEILDADQHSARAVVPEYQLSLAIGKEGQNAR +LAAKLTGWRIDIVGDGVTTSAPGR------------------------ +>GCF_005280335_PROKKA_02285 +MSALRMLEAEREIPMDRLIPTIEQALLMAYHRTPGALKRARVEIDRVSGHVTVWATELDE +DGTPIGEFDDTPNGFGRVAASTARQVMIQRMREEDDDKVLGEFKDKEGELVSGLIQQGVN +RHMIQVNLGTLEAVLPPPEQVPGEDYSHGRRLRAYVVSATRGNKGPSVTVSRSHPGLVRK +LFELEVPEIADGSVEITALAREAGHRTKMAVRATRPGVNAKGASIGEMGSRVRAVMTELN +DEKIDIVEHAEDPAQMIANALSPAKTVSVEVLDADQHSARAVVPEHQLSLAIGKEGQNAR +LAAKLTGWRIDIVGDGSDASAPAR------------------------ +>GCF_020097155_PROKKA_02147 +MSALRMLVAERDIPLDRLVPAIEQALLIAYHRTPGAIKGSRVELDRSTGHVTVWAPEVED +DGTCVGEFDDTPNGFGRIAASTARQVIFQRLRDADDAKVLGEFKDREGELVSGVIQQGSH +RHMVQVDLGSLEAVLPPPEQVPGEDYRHGRRIRAVIVSATRGPKGPSVTLSRSHPNLVRR +LFALEVPEIADGTVEITALAREAGHRTKMAVKATRPGVNPKGAAIGEMGSRVRAVMTELG +GEKIDIVEHADDPAEMIKHALSPAQALSVEILDADQHSARAVVPQHQLSLAIGKEGQNAR +LAARLTGWRIDIVGDA--AQQPGADAAQQPGADAASEMAPATEAGAEA +>GCF_023573625_PROKKA_00647 +MSALRMLEAEREIPMDRLIPTIEQALLMAYHRTPGALKRARVEIDRATGHVTVWATELDE +DDTPIGEFDDTPNGFGRVAASTARQVMIQRMREEDDDKVLGEFKDKEGELVSGVIQQGLN +RHMVQVNLGTLEAVLPPPEQVPGEDYAHGRRIRAYVVSATRGAKGPSVTVSRSHPGLVRK +LFELEVPEIADGSVEITALAREAGHRTKMAVRATRPGVNAKGASIGEMGSRVRAVMTELN +DEKIDIVDHVDDPAAMIANALSPATTVSVEILDADQHSARAVVPEYQLSLAIGKEGQNAR +LAAKLTGWRIDIVGDGVTTSAPGR------------------------ + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000619.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000619.fa new file mode 100644 index 0000000000000000000000000000000000000000..81c7d7e6ec0a8e902814bdcc8a2821873f27c4ed --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000619.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00693 +MSAVRSAVIPSELLFGTVVPAMVTPMTDEGAVDLEAAAALAEHLVDRGADGLVVTGTTGE +TSTLTDDENVAMFRTVVEAVGDRARVVAGTGTNDTAHTLELSRRAAETGVDGLLLVTPYY +NKPNQAGIRAHFETVADGVDLPIMLYDIPGRSVMPIEPETLIALAQHPNIRALKDAKGDL +QSTTTVLAHTDLDLYSGDDGATLPLMALGAVGVVSVAAHAAPELYRQLVDAVHAGDLAGA +RDHHFALDPVQRGIMTHVQGAVAAKAVLAAQGVIPSAAVRLPLVQATRDELSVIRADLAE +AGITF +>GCF_003691675_PROKKA_00430 +MSAVRSAVIPSELLFGTVVPAMVTPMTDEGAVDLEAAAALAEHLVDRGADGLVVTGTTGE +TSTLTDDENVAMFRTVVEAVGDRARVVAGTGTNDTAHTLELSRRAAETGVDGLLLVTPYY +NKPNQAGIRAHFETVADGVDLPIMLYDIPGRSVMPIEPETLIALAQHPNIRALKDAKGDL +QSTTTVLAHTDLDLYSGDDGATLPLMALGAVGVVSVAAHAAPELYRQLVDAVHAGDLAGS +RDHHFALDPVQRGIMTHVQGAVAAKAVLAAQGVIPSAAVRLPLVQATPDELSVIRADLAE +AGITF +>GCF_005280335_PROKKA_02261 +MSAVRSASAPSELLFGTVVPAMVTPMTDEGAVDLEAAAALAEHLVDGGADGLVVTGTTGE +TSTLTDEENLAMFRTVVEAVGDRAKVVAGTGTNDTAHTLELSRRAKETGVDGLLLVTPYY +NKPNQAGIRAHFEAVADGVDLPIMLYDIPGRSVMPIEPETLIALAQHPNIRALKDAKGDL +QSTTTVLAHSDLDLYSGDDGATLPLMALGAVGVVSVAAHVAPGLYRKLVDAVHAGDLAAA +REHHFALDPVQRGIMTHVQGAVAAKAVLAAQGVIPSAAVRLPLVQASADELSDIRADLAE +AGITF +>GCF_020097155_PROKKA_02131 +MTDARRTVNPSELPFGTVVPAMVTPMDQDGAVDLQAAAVLATHLVDQGADALVITGTTGE +TSTLTDEENLAMFRTVVEAVGERARVIAGTGTNDTHHSLELSRRAAEIGVHGLLLVTPYY +NKPNQAGIRRHFETIADGVDLPIMLYDIPGRSVMPIQPETLVALAAHPNITALKDAKGDL +QSTTTVLAHTDLHVYSGDDGATLPLMAMGAVGVVSVAAHVAVPGYRALVDAVHAGDLRAA +RDAHFALDPVQRGIMSHVQGAVAAKTVLAGQGIIPTAAVRLPLVAADDAELAAIRADLAE +AGISF +>GCF_023573625_PROKKA_00663 +MSAVRSAVIPSELLFGTVVPAMVTPMTDEGAVDLEAAAVLAEHLVDRGADGLVVTGTTGE +TSTLTDDENVAMFRTVVEAVGDRARVVAGTGTNDTAHTLELSRRAAETGVDGLLLVTPYY +NKPNQAGIRAHFEAVADGVDLPIMLYDIPGRSVMPIEPETIIALAQHPNIRALKDAKGDL +QSTTTVLAHTDLDLYSGDDGATLPLMALGAVGVVSVAAHAAPELYRQLVDAVHAGDLAGA +RDHHFALDPVQRGIMTHVQGAVAAKAVLAAQGVIPSAAVRLPLVQATPDELSVIRADLAE +AGITF + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000621.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000621.fa new file mode 100644 index 0000000000000000000000000000000000000000..0921ecc73aef9f51bb75b831284b1390279cc42a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000621.fa @@ -0,0 +1,75 @@ +>GCF_002008305_PROKKA_00695 +MPAVSAVRGSLVGMATRTSPTR-SSSSSATSRSGSA-GRRGSGRKGSTATVPEADRPAAPLRALHTLWMGLATPVGAGFR +KLGPDVRIDREERRDGTGLVLLLLAALIAAVEWWGLRGTAVGRVVHGVVGGTVGWFALLVPIALLVVAVRCFRHATDHRA +NGRIIIGLLMATVAGSGIAHLVGGVPSAADAFEDMLGAGGMVGYLATAPLASLLTPVPVWVLMILLAFFSVLVLTATPVG +SIPQRIAGGYDWLTGQDPEGASEQRAARRAER--RRAREERREAEDLAAPLSVDAETGRTHPDHDQSYLDGPAAGAHAAG +ASRPGLFARLFGGRRAREEQAADAAPEHTASTAYDSPVIHEAEV------GSHAAPEAETTQVLP-RP------APRRAA +RGEQGVFDSEQA--AADARDAGRDASDDFDPWVDED-----DAPEDADA---EPQPPAGVRRPTAADRALEQVREHARAQ +REAAAPAAAAPEEDAGEDTPFALD-DA-----PRQGSGAAAPSS-SSAVPA-STPAPVPPVTAEPARGTQSELGGDVSYT +LPQSALLPAGPQPKERSEANDRVVAALTTTFTEFKVDAQVTGFSRGPTVTRYEVEVAPGTKVEKVTALEKNIAYAVASSD +VRILSPIPGKRAIGIEIPNTDKEVVALGDVLRSQAAQRTDHPMVMGVGKDVEGGYVVANLAKMPHMLVAGATGAGKSSFV +NSMITSILMRSTPDEVRMVMVDPKRVELTAYEGVPHLVTPIITSPKKAAEALQWVVKEMDTRYDDLAAFGYKHVDDFNKA +VRAGQVKLPPDSKRVLRPYPYLLVIVDELADLMMVAPRDVEDAIVRITQLARAAGIHLVLATQRPSVDVVTGLIKANVPS +RMAFATSSVTDSRVVLDQPGAEKLLGQGDALFLPMGKSKPMRVQGAWVNESEIHAVVEHVKSQMQVQYRADVIPEKTEKV +IDEDIGDDLDLLLQAVELVVTTQFGSTSMLQRKLRVGFAKAGRLMDLMESRGVVGPSEGSKARDVLVKPDDLADVLATIS +GDTPPSATS--GDGDASAGTGDGDASASAAP-----RDLVQEDLDSRPAAVDWNDEDDDEGSEDAWQLTGR +>GCF_003691675_PROKKA_00432 +-------------MATRTSPTR-SSSSSATSRSGSA-GRRGSGRKGSTATVPEADLPAAPLRALHTLWMGLATPVGAGFR +KLGPDVRIDREERRDGTGLLLLLLAALIAAVEWWGLRGTAIGRVVHGVVGGTVGWFALLVPIALLVVAVRCFRHATDHRA +NGRIIIGLLMATVAGSGIAHLVGGVPSAAEAFEDMLGAGGMVGYLATAPLASLLTPVPVWVLMILLAFFSVLVLTATPVG +SIPQRLAGGYDWLTGQDPEGASERRAARRDER--RRAREVRREAEDLATPLSVDAETGRTHPDHDQSYLDGPAAGAHAAG +ASRPGLLARLFGGRRAREDQAADAAPEHTAGTAYDSPVIHEAEA------GSHAAPEAETTQVLP-RP------APRRAA +RGEQDVFDAERA--AANARDADQDASDDFDPWVDED-----DAPEDADA---EPQPPAGVRRPTAADRALEQVREHARAQ +REAAAPAAASLEEDAGEDTPFALD-DA-----PGQGSGTAA--S-SSAVPA-STPAPVPPVTAEPARGTQSPLGGDVSYT +LPQSALLPAGPQPKERSEANDRVVAALTTTFTEFKVDAQVTGFSRGPTVTRYEVEVAPGTKVEKVTALEKNIAYAVASSD +VRILSPIPGKRAIGIEIPNTDKEVVALGDVLRSQAAQRTDHPMVMGVGKDVEGGYVVANLAKMPHMLVAGATGAGKSSFV +NSMITSILMRSTPDEVRMVMVDPKRVELTAYEGVPHLVTPIITSPKKAAEALQWVVKEMDTRYDDLAAFGYKHVDDFNKA +VRAGQVKLPPDSKRVLRPYPYLLVIVDELADLMMVAPRDVEDAIVRITQLARAAGIHLVLATQRPSVDVVTGLIKANVPS +RMAFATSSVTDSRVVLDQPGAEKLLGQGDALFLPMGKSKPMRVQGAWVNESEIHAVVEHVKSQMQVQYRADVIPEKTEKV +IDEDIGDDLDLLLQAVELVVTTQFGSTSMLQRKLRVGFAKAGRLMDLMESRGVVGPSEGSKARDVLVKPDDLADVLATIS +GDTPPSATS-----------GDGDASASAGP-----RDLVQEDLDSRPAAVDWNDEDDDEGSEDAWQLTGR +>GCF_005280335_PROKKA_02259 +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------MVLP-RP------TRRRPA +RGAQGVFDAERADDPAGSRDADRDASDDFDPWVDEE-----DAPEDADA---EPTPPAGVRRPTAADRALEQVREHARAQ +REAAAAA-----EEPAEDADVDLEVEE-----PGRAAGPAAPSSPAAAVPS-STPEPVPPVTAEPARGTQSELGGDVSYT +LPQSALLPAGPQPKERSEANDRVVAALTTTFTEFKVDAQVTGFSRGPTVTRYEVEVAPGTKVEKVTALEKNIAYAVASSD +VRILSPIPGKRAIGIEIPNTDKEVVALGDVLRSQAAQRTDHPMVMGVGKDVEGGYVVANLAKMPHMLVAGATGAGKSSFV +NSMITSILMRSTPDEVRMVMVDPKRVELTAYEGVPHLVTPIITSPKKAAEALQWVVKEMDTRYDDLAAFGYKHVDDFNKA +VRAGQVKLPPDSKRVLRPYPYLLVIVDELADLMMVAPRDVEDAIVRITQLARAAGIHLVLATQRPSVDVVTGLIKANVPS +RMAFATSSVTDSRVVLDQPGAEKLLGQGDALFLPMGKSKPMRVQGAWVNESEIHAVVEHVKSQMQVQYREDVVPEKTEKV +IDEDIGEDLDLLLQAVELVVTTQFGSTSMLQRKLRVGFAKAGRLMDLMESRGVVGPSEGSKARDVLVKPDDLADVLATIS +GDAPPSGGS--GEGGAPA--AAPAAPASAGP-----RDLVQEDLDARPAAQSWDDEDDDEGSEDAWQLTGR +>GCF_020097155_PROKKA_02130 +-------------MATRTSPAR-SSSSSAKSRSGSSRPAKGSSGKGASAASPDLDRQPAFARAVRTGWMALATPVGAAVR +KAGPDVRIARDDRRDGTGLLLVLVALLVAAVEWWGLRETAVGGVVHDVVGGTVGWFAFLLPVVLGVVAVRCFRHPLDHRA +NGRIVIGLLLATVAGSGIAHLVGGLPSAAESFADVLHAGGIVGYLATVPLASLLTAVPVWALMVALAVFSLLVITATPLG +SIGSRLRGAYAWLTGQDAEDAEARREQRRAERADRREAGEHRGEQTTADLFGDDRPGGRTHPDHDQSYLDAHGSSAAPAP +ARRPGLLARLFG--RGHEEPA--PAGRVSAPRAYESAVVEEAPAASRAASGSHAADEAPAAAVEPARPARRRNAAPRRAA +ATE--VFDAE----APRGRRSAPPADDDFDPWVDEDSADDLDRADDADTGALEVVPPAGVKRPTAADRALEQVREHARSQ +REATVEEAEKAEEHDDE----AWD-EHETLVLPTAAASAPAPAP-AAVVPSVSRPEPVPEVTPEPARPSRPPQDGGHPYE +LPQSALLPAGPQPKERTESNDRVVQALTTTFTEFKVDAQVTGFSRGPTVTRYEVEVAPGTKVEKVTALEKNIAYAVASSE +VRILSPIPGKRAIGIEIPNTDKEVVALGDVLRSQAAQRNDHPMIMGVGKDVEGGYVVANLAKMPHMLVAGATGAGKSSFV +NSMIVSILMRSTPDEVRMVMVDPKRVELTAYEGVPHLVTPIITSPKKAAEALQWVVKEMDTRYDDLAAFGFKHVDDFNRA +VRAGEVKLPPDSKRVLRPYPYLLVIVDELADLMMVAPRDVEDAIVRITQLARAAGIHLVLATQRPSVDVVTGLIKANVPS +RMAFATSSVTDSRVVLDQPGAEKLLGQGDALFLPMGKSKPMRVQGAWVNESEIHAVVEHVKAQMQVQYREDVVPEKSEKV +IDEDIGDDLDLLLQAVELVVTTQFGSTSMLQRKLRVGFAKAGRLMDLMESRGVVGPSEGSKARDVLVKPDDLADVLATIN +GDTPPSRPAAPASAAAPA--PAPAAATEAAPDRWASADLVGDDLDSRPAATSWDGEDDDEGSEDAWQLTGR +>GCF_023573625_PROKKA_00665 +-------------MATRTSPTRSSSSSSATSRSGSA-GRRGSGRKGSTATVPEADRPAAPLRALHTLWMGLATPVGAGFR +KLGPDVRIDREERRDGTGLVLLLLAALIAAVEWWGLRGTAVGRVVHGVVGGTVGWFALLVPIALLVVAVRCFRHATDHRA +NGRIIIGLLMATVAGSGIAHLVGGVPSAADAFEDMLSAGGMVGYLATAPLASLLTPVPVWVLMILLAFFSVLVLTATPVG +SIPQRIAGGYDWLTGQDPEGASEQRAARRAER--RRAREERREAEDLATPLSVDAETGRTHPDHDQSYLDGPAAGAHAAG +ASRPGLFARLFGGRRAREEQAADAAPEHTASTAYDSPVIHEAEA------GSHAAPEAETTQVLP-RP------APRRAA +RGEQGVFDAEQA--AADARDAGRDASDDFDPWVDED-----DAPEDADA---EPQPPAGVRRPTAADRALEQVREHARAQ +RESAAPAAARQEGDAGEDTPFALD-DA-----PGQGSGAAAPSS-SSAVPA-STPAPVPPVTAEPARGTQSELGGDVSYT +LPQSALLPAGPQPKERSEANDRVVAALTTTFTEFKVDAQVTGFSRGPTVTRYEVEVAPGTKVEKVTALEKNIAYAVASSD +VRILSPIPGKRAIGIEIPNTDKEVVALGDVLRSQAAQRTDHPMVMGVGKDVEGGYVVANLAKMPHMLVAGATGAGKSSFV +NSMITSILMRSTPDEVRMVMVDPKRVELTAYEGVPHLVTPIITSPKKAAEALQWVVKEMDTRYDDLAAFGYKHVDDFNKA +VRAGQVKLPPDSKRVLRPYPYLLVIVDELADLMMVAPRDVEDAIVRITQLARAAGIHLVLATQRPSVDVVTGLIKANVPS +RMAFATSSVTDSRVVLDQPGAEKLLGQGDALFLPMGKSKPMRVQGAWVNESEIHAVVEHVKSQMQVQYREDVIPEKTEKV +IDEDIGDDLDLLLQAVELVVTTQFGSTSMLQRKLRVGFAKAGRLMDLMESRGVVGPSEGSKARDVLVKPDDLADVLATIS +GDTPPSAAS-----------GDGDASASAAP-----RDLVQEDLDSCPAAVDWNDEDDDEGSEDAWQLTGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000643.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000643.fa new file mode 100644 index 0000000000000000000000000000000000000000..d3832fe5732a9016dad1a3968493c37e08aa6d5d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000643.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00724 +MRTRTLTGVATAALGAVVVAGAGPALAQTTLTQGSAITAPAGACSLTIVDDATAYTAAHC +GAGQWQIGSTVRDVDGTAIGTVSALPGDSGVDAVRVALADDVDVVGDWSTRPASSIGVGE +TVYTHGSSVPLGAPNTVSHTQTFEAATVCDDAYADQVALDTASTYAGDSGGAVYDAQQRV +VGVISGIAPVTFDAEGNVVGCDAQAMSSIMVPVESLDAL-DASAAPAAETAAAAETAPAA +ET--APAIADVAGPVADEDLPTGGEPAVDESELTEFTPAEEEAIAAELKA-RAEAAAEEE +AAEAAP--AAEAPVAEAAAPGVTDVVAAPAEGVAYGTQVVAQTDQGGFASVTVTAYDADG +TVLGQDGLDLTGEYRAWLPVPAEVPAGGSVVVTVVDAAGAATDATVTLGGQLVG +>GCF_003691675_PROKKA_00455 +MRTRTLTGVATAALGAVVVAGAGPALAQTTLTQGSAITAPAGACSLTIVDDATAYTAAHC +GAGQWQIGSTVRDVDGTAIGTVSALPGDSGVDAVRVALADDVDVVGDWSTRPASSIGVGE +TVYTHGSSVPLGAPNTVSHTQTFEAATVCDDAYADQVALDTASTYAGDSGGAVYDAQQRV +VGVISGIAPVTFDAEGNVVGCDAQAMSSIMVPVESLDAL-DASAAPAAETAAAAETAPAA +ET--APAIADVAGPVADEDLPTGGEPAVDESELTEFTPAEEEAIAAELKA-RAEAAAEEE +AAEAAP--AAEAPVAEAAAPGVTDVVAAPAEGVAYGTQVVAQTDQGGFASVTVTAYDADG +TVLGQDGLDLTGEYRAWLPVPAEVPAGGSVVVTVVDAAGAATDATVTLGGQLVG +>GCF_005280335_PROKKA_02234 +MRTRTLTGVATAALGAVVVAGAGPALAQTVITQGSALSAPAGACSLTIVDDATAYTAAHC +GAGQWEVGSPVLDAEGVQIGTVSGLPGTSGVDVVRVALAEDVEVVGEWSTRPAASVEVGE +TVFTHGSSVPLGAPNSLSHTQTFDAATVCDDAYSDQMALDVASTYPGDSGGAVYDAQQRV +VGVISGVAPVTFDEEGNVVGCDAQSLSSIMVPVESLDAVGQETAAPAAVEPAAAE-APAT +EVTETPAIADVAGPVADEDLPTGGEPAVDESELTEFTPAEEEAIRAELIE-RAEAEAAAE +APAEQP--AAEAPVAEAVVAGTEDVVAAPAEGVAYGTQVMAETSQGGFASVTVTAYDADG +TVLGVDGLDLTGEYRAWMPVPAEVPAGGSVVVTVVDAAGDATDTQVTLGGQLIG +>GCF_020097155_PROKKA_02106 +MKKTTLTGATTAALGAVVVAGAGSALAATPLTQGAALSVPAGECSITLVSDTTAFTAAHC +GAGQWTVGSAVHAADGARIGSVSALPGSTGVDVVKIALDEDVDVVGDWSTRPAASVKPGE +TVYTQGSSVPLGSPNSISDPETYDIAETCGDVYTDQVSLDAATTRPGDSGGAVYDAKQRV +VGVVSGLAPVSFDEEGRAVGCDAASLSTIMVPAESLKAV-AA--------------APAK +AT--APA-------------PTVGKHGVI---LKAPTAPAAKAPAAEKKAPAAKAPAAEK +KAAPAPTLGKHGVSAETATAGTTTLKVAPEDGIDFRTRVQATTKTGGFSYMAVTAYDAAG +KQIGHLHLHSDGQPMTWINTPAQVPAGGHIEVQLKDAAGQPTDATVTLGGVPVN +>GCF_023573625_PROKKA_00688 +MRTRTLTGVATAALGAVVVAGAGPALAQTTLTQGSAITAPAGACSLTIVDDATAYTAAHC +GAGQWQIGSTVRDVDGTAIGTVSALPGDSGVDAVRVALADDVDVVGDWSTRPASSIGVGE +TVYTHGSSVPLGAPNTVSHTQTFEAATVCDDAYADQVALDTASTYAGDSGGAVYDAQQRV +VGVISGIAPVTFDAEGNVVGCDAQAMSSIMVPVESLDAL-DASAAPAAETAAAAETAPAA +ET--APAIADVAGPVADEDLPTGGEPAVDESELTEFTPAEEEAIAAELKA-RAEAAAEEE +AAEAAP--AAEAPVAEAAAPGVTDVVAAPAEGVAYGTQVVAQTDQGGFASVTVTAYDADG +TVLGQDGLDLTGEYRAWLPVPAEVPAGGSVVVTVVDAAGAATDATVTLGGQLVG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000645.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000645.fa new file mode 100644 index 0000000000000000000000000000000000000000..bdd47e4c674a0c7d5fa38e0efdaf7bf8887386cd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000645.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00726 +MTTPGAPDASAPFTPQARHLAVVSGGSGDPSQTRMLAERMAESASAALSEHGVVPQIHLI +TLRELAVDIAQALVTFAISPALRAALDEVAQADAVIAVSPTYKASYSGLFKSFWDLAEPT +SVVGVPVLLGATGGTARHSLMIDTAMRPLFAYLKARIVPTAVFAASDDWGEAAGVQASMR +TDPLQSRIRAAGRDLAEITLSRPPRARAAAPA-DIDLEVTPFEQLLNPGP +>GCF_003691675_PROKKA_00457 +MTTPGAPDASAPFTPQARHLAVVSGGSGDPSQTRMLAERMAESASAALSEHGVVPQIHLI +TLRELAVDIAQALVTFAISPALRAALDEVAQADAVIAVSPTYKASYSGLFKSFWDLAEPT +SVVGVPVLLGATGGTARHSLMIDTAMRPLFAYLKARIVPTAVFAASDDWGEAAGVQASMR +TDPLQSRIRAAGRDLAEITLSRPPRARAAAPA-DIDLEVTPFEQLLNPGP +>GCF_005280335_PROKKA_02232 +MIGQGAFEATDPLMPQARHVAVVSGGSGDPSQTRMLAERMAEAASAALSEHGVVPEIHLI +TLRELATDIAQAMVTFAVSPALRAALDEVQQADAVIAVSPTFKASYSGLFKSFWDLVDDE +SLIGVPVLLGATGGTVRHSLMIDTALRPLFAYLKSRIVPTAVFAASDDWGEADGAQASTR +TDPLRSRIRSAGRDLAEILLNRPPRARAAAPE-TLDLEVTPFEQLLNPDA +>GCF_020097155_PROKKA_02104 +-MSTSAFESTDPFTPGARHIAVVSGGIGDPSQTRKLADRLARASADALSAAGVVPEIHVV +SLRELATDLGAGMVTTARSPALLDAVAQVEHADAVIAVSPTFKASYSGLFKSFVDLIDDE +ALVGVPVLLGATGGTARHSLMIDQAMRPLFAYLKARIVPTAVFAASDDWGRADGQNDSTR +TTPLDARIRAAGEDLAEVLRHRPARVRPAADATDDDLEVIPFDQLLHPGR +>GCF_023573625_PROKKA_00690 +MTTPGAPDASAPFTPQARHLAVVSGGSGDPSQTRMLAERMAESASAALSEHGVVPQIHLI +TLRELAVDIAQALVTFAISPALRAALDEVAQADAVIAVSPTYKASYSGLFKSFWDLAEPT +SVVGVPVLLGATGGTARHSLMIDTAMRPLFAYLKARIVPTAVFAASDDWGEAAGVQASMR +TDPLQSRIRAAGRDLAEITLSRPPRARAAAPA-DIDLEVTPFEQLLNPGP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000646.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000646.fa new file mode 100644 index 0000000000000000000000000000000000000000..0aa158b0694561c43d41790982dcc659289b4ccc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000646.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00727 +MQFGVFTIGDITADPTNGTAPTEHQRIKDTVKIARHAEQAGFEVFATGQHHNPPFVAPGN +PPTLLAYLAAQTETLQLSTATTLITTMDPVRLAEDYAYLQHLADGRVDLTMGRGNTGPVY +PWFGKDIRQGIQLAVENYNLLYRLWHEETVDWSGNHRTPLQDFTLTPQPLDGVAPFVWHG +SIRSPEIAEQAAYYGDGYFHNNIFWNKEHVIQMVRLYRQRYEYYGHGKAHQAYVALGGQA +YMAKNSQDAVAEFRPYFDNAPVYGHGPSLEDFSRMTPLTVGSPQQVIERTLTFRDWVGDY +QRQMFLIDHAGLPTDTVLRQIDLFGEEVLPVLRKEFDALKPDDVPAAPTHEFLVARARRG +EAPVPGGKEGSQAQLDRAAAAEQRATADAAKGGAAQ +>GCF_003691675_PROKKA_00458 +MQFGVFTIGDITADPTNGTAPTEHQRIKDTVKIARHAEQAGFEVFATGQHHNPPFVAPGN +PPTLLAYLAAQTETLQLSTATTLITTMDPVRLAEDYAYLQHLADGRVDLTMGRGNTGPVY +PWFGKDIRQGIQLAVENYNLLYRLWHEETVDWSGNHRTPLQDFTLTPQPLDGVAPFVWHG +SIRSPEIAEQAAYYGDGYFHNNIFWNKEHVIQMVRLYRQRYEYYGHGKAHQAYVALGGQA +YMAKNSQDAVAEFRPYFDNAPVYGHGPSLEDFSRMTPLTVGSPQQVIERTLTFRDWVGDY +QRQMFLIDHAGLPTDTVLRQIDLFGEEVLPVLRKEFDALKPDDVPAAPTHEFLVARARRG +EAPVPGGKEGSQAQLDRAAAAEQRATADAAKGGAAQ +>GCF_005280335_PROKKA_02231 +MQFGVFTIGDVTQDPTTGTTPTEHQRIKDTVRIAQHAAQAGFEVFATGQHHNPPFVAPGN +PPTLLAYLAAMTTDLQLSTATTLITTMDPVRLAEDYSYLQHLADGRVDLTMGRGNTGPVY +PWFGKDIRQGIPLAVENYNLLYRLWHEETVDWSGKFRSPLQNFTLTPQPLDGVAPFVWHG +SIRSAEIAEQAAYYGDGFFYNNIFWNKEHVIQMVRLYRQRYEYYGHGKAHQAYVALGGQA +YMAKNSQDAVKEFRPYFDNAPVYGHGPSLEQFSSMTPLTVGSPQQVIERTLGFRDWVGDY +QRQMFLIDHAGLPTDTVLKQIDIFGEEVLPVLRKEFAALKPDDVPEAPTHEFLVERARRG +EAPVPGGKEGSQAQIDRAAAAEKRAAAKAGEGA--- +>GCF_020097155_PROKKA_02103 +MQLGIFTIGDITADPTTGTTPTEHQRIKDTVTIARHAEQAGFDVFATGQHHNPPFVAPGN +PPTLLSHLAAVTETMTLSTATTLITTMDPVRLAEDYSYLQHLADGRVDLTLGRGNTGPVY +PWFGKDIRQGVNLAVENYNLLYRLWHEETVDWSGQFRTPLQDFTLTPQPLDGVAPFVWHG +SIRSPEIAEQAAYYGDGFFHNNIFWNKEHIIRMVRLYRQRFEHYGHGKAHQAYVGLGGQA +YMAKNSQDAVKEFRPYFDNAPVYGHGPSLEDFTSMTPLTVGSPQQVIERTLSFRDWVGDY +QRQMFLIDHAGLPTDTVLKQIDLFGEEVLPVLREEFAALKPDDVPEAPTHEFLVERARRG +EAPVPGGREGSPAHAAREAARAKQAEQQKKKEDA-R +>GCF_023573625_PROKKA_00691 +MQFGVFTIGDITADPTNGTAPTEHQRIKDTVKIARHAEQAGFEVFATGQHHNPPFVAPGN +PPTLLAYLAAQTETLQLSTATTLITTMDPVRLAEDYAYLQHLADGRVDLTMGRGNTGPVY +PWFGKDIRQGIQLAVENYNLLYRLWHEETVDWSGNHRTPLQDFTLTPQPLDGVAPFVWHG +SIRSPEIAEQAAYYGDGYFHNNIFWNKEHVIQMVRLYRQRYEYYGHGKAHQAYVALGGQA +YMAKNSQDAVAEFRPYFDNAPVYGHGPSLEDFSRMTPLTVGSPQQVIERTLTFRDWVGDY +QRQMFLIDHAGLPTDTVLRQIDLFGEEVLPVLRKEFDALKPDDVPAAPTHEFLVARARRG +EAPVPGGKEGSQAQLDRAAAAEQRATADAAKGGAAQ + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000652.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000652.fa new file mode 100644 index 0000000000000000000000000000000000000000..ec49045d9f2130d6dc5a3a7870ce90f161e4d943 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000652.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00734 +MTSALIWAALLGLTLGAGLLLILVTQPVGWRPSLEQRVEPQLRHHIPASRLLEEERAGAS +PWGTWGRILDPVVQAGVGWVQRISPGGAALDRKLAAAGLAVTSTDFRAQQVLSGAAGAAV +AAVLALSLTVTGRVPVITGVALVIAGGMAGFLLREQLLSLRVRRRREAILSEFPSVAELF +ALSVGAGESAAGALERIAGTARGELAGEFRTTLADMRAGASLSAALKAMGRRVQLAPVER +FIGGVLIALDRGTPLADVLRAQAQDVREMGRRELMEAAGRKEIQMMVPLVFGILPLTVIF +AVFPGISLMRLGF +>GCF_003691675_PROKKA_00465 +MTSALIWAALLGLTLGAGLLLILVTQPVGWRPSLEQRVEPQLRHHIPASRLLEEERAGAS +PWGTWGRILDPVVQAGVGWVQRISPGGAALDRKLAAAGLAVTSTDFRAQQVLSAAAGAAV +AAVLALSLTVTGRVPVITGVALVIAGGMAGFLLREQLLSLRVRRRREAILSEFPSVAELF +ALSVGAGESAAGALERIAGTARGELAGEFRTTLADMRAGASLSAALKAMGRRVQLAPVER +FIGGVLIALDRGTPLADVLRAQAQDVREMGRRELMEAAGRKEIQMMVPLVFGILPLTVIF +AVFPGISLMRLGF +>GCF_005280335_PROKKA_02219 +MSASLLWAALLGLTLGAGLLLIAVAQPLGWRPTLEQRVEPQLRHHTPASRLLEDEEAGAS +PWGAWGRILDPVLRAGVGWLHRLSPAGETLERKLAAAGMTVSAADFRAQQVLSAAAGAGI +ATAFSVALALAGRIPVVTGVGFVIVGGMAGYLLRDQLLSLRVQRRRAAILTEFPSVAELF +ALSVGAGESAAGALERIATTARGELAGEFRATLAEMRAGSSLSAALKSMGRRVQLAPVER +FIGGILIALDRGTPLADVLRAQAQDVREMGRRELMEAAGRKEIQMMVPIV---------- +-----------TR +>GCF_020097155_PROKKA_02095 +MSGGLLWGIALGLVMAAGVWLIVTAQPWGWRPSLEERIEPQLRHHVPASRLLADGRATST +PWGTWGRLLGPSLAGATRGLQRLSPAGESLTLKLQAAGSELSVMDFRAQQVLCAVIATAA +GTVLSVLLTLAGAVPVVSGVALVVAAGLSGYVLRDQMLTWAVARRRTAILTEFPSVAELF +ALSVGAGESATGAMERIVRSARGEMAGEFDRTLADVRAGASLSSALKAMGRRVQLEPVER +FIGGILIALDRGTPLADVLRAQAQDVRELGRRELMESAGRKEIQMMVPLVFGILPLTVVF +AIFPGLALLRLSF +>GCF_023573625_PROKKA_00698 +MTSALIWAALLGLTLGAGLLLILVTQPVGWRPSLEQRVEPQLRHHIPASRLLEEERAGAS +PWGAWGRILDPVVQAGVGWVQRISPGGVALDRKLAAAGLAVTSADFRAQQVLSAAAGAAV +AAVLALSLTVTGRVPVITGVALVIAGGMAGFLLRDQLLSLRARRRREAILSEFPSVAELF +ALSVGAGESAAGALERIAGTARGELAGEFRVTLADMRAGASLSAALKAMGRRVQLAPVER +FIGGVLIALDRGTPLADVLRAQAQDVREMGRRELMEAAGRKEIQMMVPLVFGILPLTVIF +AVFPGISLMRLGF + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000655.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000655.fa new file mode 100644 index 0000000000000000000000000000000000000000..5b88088449f2bbc54ab646d697fc2a5479f3a9a0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000655.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_00737 +MRSVNDVR--------------DERGAATVEFLGLTLVLLIPVVYLMIYVSQVQAAAFAS +VAAADQAVKAVVAEADHPSAGAAHATVELTLADYGVGAGQYDLTVGCDQGGCGTLEPGEV +VAVRVDVGVPVPLTPAAW-SLTPVTVGSDARQTVPRF +>GCF_003691675_PROKKA_00468 +MRSVNDVR--------------DERGAATVEFLGLTLVLLIPVVYLMIYVSQVQAAAFAS +VAAADQAVKAVVAEADHPSAGAAHATVELTLADYGVGAGQYDLTVGCDQGGCGTLEPGEV +VAVRVDVGVPVPLTPAAW-SLTPVTVGSDARQTVPRF +>GCF_005280335_PROKKA_02193 +MPIASDVR--------------DERGSATVEFLGLTLVLLIPVVYLMIYVSQVQAAAFAS +VAAADQAAKVVVSGTEGRSAAQAHAAVRLTLADFGIDYGAYELDLGCSAGDCVSLDPGEV +VQARVDVEVPIPLTPADW-SLAPVTVGSDARQAVPRF +>GCF_020097155_PROKKA_02092 +MPSATDARHGPTHAPWRGTDLADDVGSATVEFLGLSLILLIPLAYLMLFVSQVQAAAFGA +LASADQAARVMVSG-EGGNPGQAEGTIPLTLADYGFDAADAEWSVACDVGGCGTLEPGEV +VDVTVAISLDPPLLPDGWVSVDIATVDSHSRARMPRF +>GCF_023573625_PROKKA_00701 +MRSVNDVR--------------DERGAATVEFLGLTLVLLIPVVYLMIYVSQVQAAAFAS +VAAADQAVKAVVAEADHPSAGAAHATLELTLADYGVGAGQYDLTVGCDQGGCGTLEPGEV +VAVRVDVAVPVPLTPAAW-SMTPVTVGSDARQTVPRF + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000659.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000659.fa new file mode 100644 index 0000000000000000000000000000000000000000..f6f84f7c9a4772d1674c5663cba0bb6eceee2c2e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000659.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_00742 +MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALERAGVAPEDVDMV +YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLIRLGEADVVV +AGGQESMTNAPHLLPGARKGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA +RAEQDEVAAASHQRAARAQSEGVFEGEIAPVEVPQRKGDPLVVSQDEGVRPDTTAESLGA +LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAFAEEKGLTILATVGAPGQTAGPDSSQLH +SQPSDAINAAVRKQGWDVADLDFIEINEAFGAVAVQSLRDLDYPHEKTNIHGGAIALGHP +IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR +>GCF_003691675_PROKKA_00473 +MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALERAGVAPEDVDMV +YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLIRLGEADVVV +AGGQESMTNAPHLLPGARKGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA +RAEQDEVAAASHQRAARAQSEGVFEGEIAPVEVPQRKGDPLVVSQDEGVRPDTTAESLGA +LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAFAEEKGLTILATVGAPGQTAGPDSSQLH +SQPSDAINAAMRKQGWDVADLDFIEINEAFGAVAVQSLRDLDYPHEKTNIHGGAIALGHP +IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR +>GCF_005280335_PROKKA_02187 +MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALECAGVAPEDVDMV +YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLVRLGEADVVV +AGGQESMTNAPHLLPGARKGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA +RAEQDEVAAASHQRAARAQSEGVFEGEIAPVEVPQRKGDPLVVSQDEGVRPDTTAESLGA +LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAYAEEKGLTILATVGALGQTAGPDSSQLH +SQPSDAINAAMRKQGWDVADLDFIEINEAFGAVAVQSLRDLDYPHEKTNIHGGAIALGHP +IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR +>GCF_020097155_PROKKA_02085 +MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALERAGVAPEDVDMV +YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLIRLGEADVVV +AGGQESMTNAPHLLPGARKGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA +RAEQDEVAAASHQRAARAQSQGVFEGEIAPVEVPQRKGDPLVVSQDEGVRPDTTAESLGS +LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAFAEEKGLTVLATVGAPGQTAGPDSSQLH +SQPSDAINAAVRKQGWDVADLDFIEINEAFGAVAVQSLRDLGYPHEKTNIHGGAIALGHP +IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR +>GCF_023573625_PROKKA_00707 +MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALERAGVAPEDVDMV +YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLIRLGEADVVV +AGGQESMTNAPHLLPGARTGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA +RAEQDEVAAASHQRAARAQSEGVFEGEIAPVEIPQRKGDPLVVSQDEGVRPDTTAESLGA +LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAFAEEKGLTILATVGAPGQTAGPDSSQLH +SQPSDAINAAVRKQGWDVADLDFIEINEAFGAVAVQSLRDLGYPHEKTNIHGGAIALGHP +IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000666.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000666.fa new file mode 100644 index 0000000000000000000000000000000000000000..aec3e0ea674aecf25da0be93e4c40ebd15a07b5c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000666.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00753 +MSAALLTHPSRT------VDWPAMSTDNSRPEFARPEDAPEHDRADIDVAAESEQQRRAR +FERDALEFVDQLYSAALRMTRNPQDAEDLVQEAYTKAYSSFHQYRPGTNLKAWLYRILTN +TYINLYRKRQRQPLEADNPEVEDWQMARAAEHTSGGLRSAETEALDRLPDSQVKDALQAI +PEEFRLAVYFADVEGFAYKEIAEILDVPIGTVMSRLHRGRKQLRERLADYAAARGIKAQP +KKKTGRGGTKQTETSTKEATR +>GCF_003691675_PROKKA_00483 +MSAALLTHASRT------VDWPAMSTDNSRPEFARPEDAPEHDRADIDVAAESEQQRRAR +FERDALEFVDQLYSAALRMTRNPQDAEDLVQEAYTKAYSSFHQYRPGTNLKAWLYRILTN +TYINLYRKRQRQPLEADNPEVEDWQMARAAEHTSGGLRSAETEALDRLPDSQVKDALQAI +PEEFRLAVYFADVEGFAYKEIAEILDVPIGTVMSRLHRGRKQLRERLADYAAARGIKAQP +KKKTGRGGTKQTETSTKEATR +>GCF_005280335_PROKKA_02177 +MTTALMARPDRD------VDWRVMSTDNNLPEIARPADAPEHDRADIDVAAEDEQQRRAR +FERDALEFVDQLYSAAMRMTRNPQDAEDLVQEAYTKAYSSFHQYRPGTNLKAWLYRILTN +TYINLYRKRQRQPLEADSPEVEDWQMARAAEHTSSGLRSAETEALDHLPDSEVKDALQAI +PEEFRLAVYFADVEGFAYKEIAEILDVPIGTVMSRLHRGRKQLRERLADYAAERGIKAQP +-KKTGRGAAKKTETSTKEATR +>GCF_020097155_PROKKA_02072 +MAATLLERPVLTGSRGAAVDWPAMSTQNSTPEIARPADAPALDLPGIDVDAESEAQRRAR +FERDALEFVDQLYSAAMRMTRNPQDAEDLVQEAYTKAYSSFHQYRPGTNLKAWLYRILTN +TYINLYRKKQRQPLEADTDTVEDWQMARAAEHTSSGLRSAETEALDHLPDSEVKDALQAI +PEEFRLAVYFADVEGYAYKEIAEILDIPIGTVMSRLHRGRKQLRERLTDYAGERGMG--P +KGRTAQ------ETSTQEEKR +>GCF_023573625_PROKKA_00717 +MSAALLTHPSRT------VDWPAMSTDNSRPEFARPEDAPEHDRADIDVAAESEQQRRAR +FERDALEFVDQLYSAALRMTRNPQDAEDLVQEAYTKAYSSFHQYRPGTNLKAWLYRILTN +TYINLYRKRQRQPLEADNPEVEDWQMARAAEHTSGGLRSAETEALDRLPDSQVKDALQAI +PEEFRLAVYFADVEGFAYKEIAEILDVPIGTVMSRLHRGRKQLRERLADYAAARGIKAQP +KKKTGRGGTKQTETSTKEATR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000679.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000679.fa new file mode 100644 index 0000000000000000000000000000000000000000..62042f1fd348ba5a5e61bb0fdfc9c9857b6b112d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000679.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_00767 +MDTNTVFLLAAIGLYFLAMIAIGLYASRKNTDLDDYMLAGRDMKPSVAALSAGASDMSGWLLMGLPGAIYAAGLVEGWMA +VGLTVGAWVNWRVVAPRLRSYTEVAGNSITIPSFLENRFKDRTHILRIVAGLIILVFFTFYVSSGMVAGGKFVESTFGPE +SFYAQGISINYLTGMLVVAGITVLYTLFGGFLGASLTDVAQGVLMFLSLLAVPIVVILTMGGWDAVVEGIRAAD----AA +GGGVNHFSMFENATLIGVLSSLAWGLGYFGQPHIIVRFMALRTPHDAAVARRVGIGWMALSVFGAVMVALVGIAYFQANP +GTTLEDPETVFLVLASIMFHPFVAGLVLAAVLAAIMSTLSSQLIVCSSALVEDLYMLRGRTGSPTFTLWLGRIGVLVVAL +VAGLLALDPDSSVLELVSFAWAGFGAAFGPVILLALYWPRFTSWGAMAAMVTGAAVAWVWSEASAETWEWFGLYELLPGF +VAAFVVGVVVSLVTQRSRRVQRRIDAEFTGAIDIVAGREPDPDVAPAAMTRDAAGGSTAAAADPRAQA +>GCF_003691675_PROKKA_00497 +MDTNTVFLLAAIGLYFLAMIAIGLYASRKNTDLDDYMLAGRDMKPSVAALSAGASDMSGWLLMGLPGAIYAAGLVEGWMA +VGLTVGAWVNWRVVAPRLRSYTEVAGNSITIPSFLENRFKDRTHILRIVAGLIILVFFTFYVSSGMVAGGKFVESTFGPD +SFYAQGISINYLTGMLVVAGITVLYTLFGGFLGASLTDVAQGILMFLSLLAVPIVVILTMGGWDAVVEGIRAAD----AA +GGGVNHFSMFENATLIGVLSSLAWGLGYFGQPHIIVRFMALRTPHDAAVARRVGIGWMALSVFGAVMVALVGIAYFQANP +GTTLEDPETVFLVLASIMFHPFVAGLVLAAVLAAIMSTLSSQLIVCSSALVEDLYMLRGRTGSSTFTLWLGRIGVLVVAL +VAGLLALNPDSSVLELVSFAWAGFGAAFGPVILLALYWPRFTSWGAMAAMVTGAAVAWAWSEASAETWEWFGLYELLPGF +VAALVVGVVVSLVTQRSRRVQRRIDAEFTGAIDIVAGREPHPDVAPAAMTRDAAGGSTAAAADPRAQA +>GCF_005280335_PROKKA_02162 +MDQNTFFLILAIGLYFAAMIAIGLWASRKNTDLDDYMLAGRDMKPGVAALSAGASDMSGWLLMGLPGAVYAAGLVEAWMA +IGLTVGAWINWKVVAPRLRAYTQVAGNSITIPSFLENRFQDRTHILRIVSGLIILVFFTFYVSSGMVAGGKFVESTFGPE +SLYAQGVSVNYLTGMLVVAGITVLYTLFGGFLGASLTDVAQGTIMFLALIAVPIATIVAMGGWGAMVEGLRAADAASAAA +GEAVDHLSLFHNATLIGVLSSLAWGLGYFGQPHIIVRFMALRTVQDASTARRIGIGWMALSVFGAVMVALVGIAYFQANP +GTTLADPETVFLVLASILFHPFIAGLVLAAVLAAIMSTLSSQLIVCSSALVEDLYKLTGRQGSPRAMVWLGRIGVLVVAV +VAGLLALDPESSVLELVSFAWAGFGAAFGPVILLALYWQRFTSWGAMAAVVTGALVAWLWSEASAETWEWFGLYELLPGF +IAALVVGVVVSLLTQRSRPVQTRIEREFTGAVDVVAGR-----AAPTA-------------------- +>GCF_020097155_PROKKA_02058 +MDSNTAFLLAAIGLYFVAMIAIGLYAARRNNDLDDYMLAGRDMKPGVAALSAGASDMSGWLLMGLPGAVYASGLIEGWMA +IGLIVGAWVNWKVVAPRLRSYTEVAGDSITIPTFLENRFKDHTHILRIVAGLIILVFFTFYVSSGMVAGGKFVESTFGPD +SIYAQGVSVNYLTGMVVVAGITVLYTLFGGFLGASLTDVAQGVLMFLALLVVPVAVIATMGGWDQVLEGIRAAD---AAV +GPEADRFSLFQNATRIGVLSSLAWGLGYFGQPHIIVRFMALRTPQDAAAARRIGIGWMVLSVFGAVMVGLVGLAYFQANP +GTELNDPETVFLVLASILFHPFVAGLVLAAVLAAIMSTLSSQLIVCSSALVEDLYMLRGRRGSPRTMVWLGRIGVLVVAL +IAGLLALNPDASVLELVSFAWAGFGAAFGPVILLALYWERFTSWGAMAAMVVGAAVAWFWSTASADTWDWFGLYELLPGF +VAALAAGVVVSRLTRRPDHVQEHISGEFTGAADIVAGREPTALTGSTG----AVGGSTAA---PRA-- +>GCF_023573625_PROKKA_00731 +MDTNTVFLLAAIGLYFLAMIAIGLYASRKNTDLDDYMLAGRDMKPSVAALSAGASDMSGWLLMGLPGAIYAAGLVEGWMA +VGLTVGAWVNWRVVAPRLRSYTEVAGNSITIPSFLENRFKDRTHILRIVAGLIILVFFTFYVSSGMVAGGKFVESTFGPD +SFYAQGISINYLTGMLVVAGITVLYTLFGGFLGASLTDVAQGILMFLSLLAVPIVVILTMGGWDAVVEGIRAAD----AA +GGGVNHFSMFENATLIGVLSSLAWGLGYFGQPHIIVRFMALRTPHDAAVARRVGIGWMALSVFGAVMVALVGIAYFQANP +GTTLEDPETVFLVLASIMFHPFVAGLVLAAVLAAIMSTLSSQLIVCSSALVEDLYMLRGRTGSPTFTLWLGRIGVLVVAL +VAGLLALNPDSSVLELVSFAWAGFGAAFGPVILLALYWPRFTSWGAMAAMVTGAAVAWVWSEASAETWEWFGLYELLPGF +VAAFVVGVVVSLVTQRSRRVQRRIDAEFTGAIDIVAGREPDPDVAPAAMTRDAAGGSTASAADPRAQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000704.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000704.fa new file mode 100644 index 0000000000000000000000000000000000000000..eb389c72701b18441825afd20a21c3e95e588824 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000704.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00796 +MGAQIRVYRQKIASTSSMKKIFKAMELIATSRITKARERVSASLPYANAITRAVSAVSSQ +HDIDHVLTTEPENPTRAAVLIMSSDRGLAGAYSANVLRKAEQLLTRLGEEGKDVDVYVVG +RKAQTYFDFRGRGYKQLWTGQTDAPVAERAAEIGEVLVDAFLTDTADGGVDEIHVVFTEF +VSLVKQNPHVVRLLPLEVVEEEAATAEDVLPLYEYEPDAEEVLDALLPKYIESRIFNAML +QSAASELANRQRAMKSAGDNATSLIKDYTLLMNNARQAEITQELTELIAGADALNNS +>GCF_003691675_PROKKA_00527 +MGAQIRVYRQKIASTSSMKKIFKAMELIATSRITKARERVSASLPYANAITRAVSAVSSQ +HDIDHVLTTEPENPTRAAVLIMSSDRGLAGAYSANVLRKAEQLLTRLGEEGKDVDVYVVG +RKAQTYFDFRGRGYKQLWTGQTDAPVAERAAEIGEVLVDAFLTDTADGGVDEIHVVFTEF +VSLVKQNPHVVRLLPLEVVEEEAATAEDVLPLYEYEPDAEEVLDALLPKYIESRIFNAML +QSAASELANRQRAMKSAGDNATSLIKDYTLLMNNARQAEITQELTELIAGADALNNS +>GCF_005280335_PROKKA_02135 +MGAQIRVYRQKIASTSSMKKIFKAMELIATSRITKARERVNASLPYANAITRAVSAVSSQ +HDIDHVLTTEPENPTRAAVLILSSDRGLAGAYSANVLRKAEQLLTRLGEEGKDVDVYVVG +RKAQTYFDFRGREYKQLWTGQTDAPAAERASEIGETLVDAFLTDTAAGGVDEIHIVFTEF +VSLVKQNPHVVRLLPLEVVEEEVAAPEDVLPLYEYEPDAEEVLDALLPKYIESRIFNAML +QSAASELANRQRAMKSAGDNASGLIKDYTLLMNNARQAEITQELTELIAGADALNNS +>GCF_020097155_PROKKA_02028 +MGAQIRVYRQKIASTTSMKKIFKAMELIATSRITKARERVNQSLPYANAITRAVTAVSSQ +HDIDHVLTTEPENPTRAAVLIMSSDRGLAGAYSANVLRKAEQLLTALHEEGKDVDVYVVG +RKAQTYFDFRGREYKQLWTGQTDAPKAERAQEIGTILVESFLTDTAAGGVDEIHVVFTEF +VSLVKQNPHVIRLLPLEVVEQDVVSPEEVLPLYEFEPDADEVLDALLPKYIESRIFNAML +QSAASELANRQRAMKSAGDNASSLIKEFTLRMNNARQAEITQELTELIAGADALNNS +>GCF_023573625_PROKKA_00763 +MGAQIRVYRQKIASTSSMKKIFKAMELIATSRITKARERVSASLPYANAITRAVSAVSSQ +HDIDHVLTTEPENPTRAAVLIMSSDRGLAGAYSANVLRKAEQLLTRLGEEGKDVDVYVVG +RKAQTYFDFRGRGYKKLWTGQTDAPVAERAAEIGEVLVDAFLTDTADGGVDEIHVVFTEF +VSLVKQNPHVVRLLPLEVVEEEAATAEDVLPLYEYEPDAEEVLDALLPKYIESRIFNAML +QSAASELANRQRAMKSAGDNATSLIKDYTLLMNNARQAEITQELTELIAGADALNNS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000713.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000713.fa new file mode 100644 index 0000000000000000000000000000000000000000..057c6bd750e47bde79dafdc46168e0ef85d33510 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000713.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_00805 +MALTLVRLRWTLTLNQWRRSPFTLVVSVLGALYVLGMAAVAVTLLVTGLPALPDEARGATTVLVAAVVVLAWLVIPPFVT +GVDATLDPHSFVLFPVPARTLIAGLVLSAFTTPAGLATLAVLVGLGASWWDRPAALAAGLAGGALTAVTAVAIGSGLAGL +LAAYASRRRVRDVVSVLLFIPLMLGGVALSRAVASFEDFLAIAPQVARGAAWTPFGAGPAAAWAAAEGRGAAAALHLAVA +AAWCLAALALWHLAVRRTVEPVAVGGGGSRRVGAGADPTPLRWLGRPATGPRTAIAARAQRYWLADPRYAAGLIIIPLMA +VVLWFTGGLASGGGLGPGLLLILGPMTAWSLAYSISADIAYDHTAFHLHVVSGVRGVDDRWGRVLGLAGWGVPMILLVTT +ATVAAAGDWSLLAPMLGLALGLFGTTAGLSAFLSARFVYPVPKPGDSPFKTPQGAAMRTMLVQGASMLVSLALAVPFLVP +FIVRLATGAAVWGWVTVALGFAWGAVALWLGVRLGARWYDRAQAETYQAVAAF +>GCF_003691675_PROKKA_00536 +MALTLVRLRWTLTLNQWRRSPFTLVMSVLGALYVLGMAAVAVTLLVTGLPALPDEARGATTVLAAAVVVLAWLVIPPFVT +GVDATLDPHSFVLFPVPARTLIAGLVLSAFTTPVGLATLAVLVGLGASWWDRPAALAAGLAGGALTAVTAVAIGSGLAGL +LAAYASRRRVRDVVSVLLFIPLMLGGVALSQAIASFEDFLAIAPQVARGAAWTPFGAGPAAAWAAAEGRGAAVALHLAVA +AAWCLAALALWHLAVRRTVEPVAVGGGRSRRVAAGADPMPLRWLGRRATGPRTAIAARAQRYWLADPRYAAGLIIIPLMA +VLLWFTGGMAAEGGPGLGLLLILGPITAWSLAYSISADIAYDHTAFHLQVVSGVRGVDDRWGRVLGLAGWGVPMILLVTT +ATVAAAGDWSLLAPMLGLALGLFGTTAGLSAFVSARFVYPVPKPGDSPFATPQGAAMRTMLVQGAAMLVSLALAVPFLVP +FVVRLVTGAAVWGWVTVALGLAWGAVALWLGVRLGARWYDRAQAETYQAVAAF +>GCF_005280335_PROKKA_02125 +MALTLVRLRWALTLNQWRRSTFTLVLAVLGALYVLGLAVFVVVMLVTFLPDAWVVDRGTVTVIVASALALGWLLIPPFIT +GVDATLDPHSFVLFPVRARTLIAGLTLSAFTTPSGLATLIVMLGTGLSWWDIPAALAAALVGGALTAVTAVASGYGLAGL +MAAYAGRRRVREVLSIALLIPVMLSGVIVAQTLDSLGDLFDVAPRVAAVAAWTPFGAGPAAAWAVAEGQGLRAAAHLLVA +AAWCLAALALWHLAVRRTVEPVAVGGGSARE-AGRADGAPLRWLGRPATGPRTAIAARAQRYWLRDPRYAAGLVMIPVLA +AVLWFASTAGGDAGPGLGMLTMLGPVSAWALAYSISADIAYDHTAFHLHVVSGVRGADDRWGRVMGLAGWGVPALVVLTV +ATTAAADRWDLLPALLGLTLGLFGVTAAMSAFVSARFVYPVPKPGESPFKTPQGATMRIMLVQGAAMLVVVPLAVPVVVP +FVVALVTQSAVWGWATLAVGLAWGAVALWLGVRMGAAWYDRAQAETYQAVAAF +>GCF_020097155_PROKKA_02018 +MALTLTRLRWALTLNGWRRSTLTLVLSVLGALYFFGMAAMAVAALVVGLPEAELPVRGAVTVLVAAVVVLLWTILPPLVT +GVDATLDPSSFVLFPVPARTLVAGLLLSTFTTPIGALTLLGLLGVAASWWDTPAALAAAAVGAVLSAVTAVCLGYGVTGL +MSSFTGRRRVREAISLLVLIPLMLGGVALSRVMQSIDDLLWLGPVLANAAVWTPFGAGLGAGWAAAEGRWGLAGLRLLVA +LAWAVAAAALWMLAIRRTVEPAAVGSTDSAA-PRGDRATDLRWLGRPATSARTAIAARAQLYWFKDPRYMASLVTVPLMF +VLLWFMGTSGPEGAT--AILLAAGPVTAWALGYSLSADIAYDHTAFHLHVLAGVKGIDDRLGRVMGLLGWALPVVAGVTL +ATVAMHGDWSVLPAILGVSLGVLGACLGLSALVSARWVYPVPKPGDSPLKTPQGAAMRIMLVQGTSLLVTLVLLVPMAVP +FVVLLVTGAAVWSWVTLAVGLAWGALALWLGVRAGAAWYDRAQAETLQAVQSW +>GCF_023573625_PROKKA_00772 +MALTLVRLRWTLTLNQWRRSPFTLVMSVLGALYVLGMAAVAVTLLVTGLPALPDEARGATTVLAAAVVVLAWLVIPPFVT +GVDATLDPHSFVLFPVPARTLIAGLVLSAFTTPVGLATLAVLVGLGASWWDRPAALAVGLVGGALTAVTAVAIGSGLAGL +LAAYASRRRVRDVVSVLLFIPLMLGGLALSRAIASFEDFLAIAPQIARGAAWTPFGAGPAAAWAVAEGRGAAVALHLAVA +AAWCLAALALWHLAVRRTVEPVAVGGGRSRRVAAGADPTPLRWLGRPATGPRTAIAARAQRYWLADPRYAAGLIIIPLMA +VLLWFTGGMAGEGGPGLGLLLVLGPITAWSLAYSISADIAYDHTAFHLHVVSGVRGVDDRWGRVLGLAGWGVPMILLVTT +ATVAAAGDWSLLAPMLGLALGLFGTTAGLSAFVSARFVYPVPKPGDSPFATPQGAAMRTMLVQGAAMLVSLALAVPFLVP +FVVRLVTGAAVWGWITVALGLAWGAVALWLGVRLGARWYDRAQAETYQAVAAF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000723.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000723.fa new file mode 100644 index 0000000000000000000000000000000000000000..b0243d9fb2c0a45178bde2dbfef79f2ad448d388 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000723.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_00816 +MSAPASSSAGLPEGARVVLATHNAGKVRELRQLLAGAVPGLEVETAVVDAGAVGAPDVVE +DGVTFAQNALKKARAVAAHTGLIAVADDSGLAVDVLHGAPGIFSARWAGRHGDDRANLEL +LLAQLADVPDEHRGAQFVCAAALAVPSGPDAAGARAIHVEHVEHGRLPGTLLREPVGDGG +FGYDPILRPEGRDVSTAQLSPEDKNAISHRGHAFRALLPYLVDALDARP +>GCF_003691675_PROKKA_00548 +MSAPASSSAGLPEGARVVLATHNAGKVRELRQLLAGAVPGLDVEAAVVDAGAVGAPDVVE +DGVTFAQNALKKARAVAAHTGLIAVADDSGLAVDVLHGAPGIFSARWAGRHGDDRANLEL +LLAQLADVPDEHRGAQFVCAAALAVPSGPDAAGARAIHVEHVEHGRLPGTLLREPVGDGG +FGYDPILRPEGRDVSTAQLSPEDKNAISHRGHAFRALLPYLVDALDARP +>GCF_005280335_PROKKA_02114 +M---SGAATGVPEGARVVLATHNAGKVRELRQLLEGAVPGLDASVAVVDAGAVGAPDIVE +DGVTFAQNALKKARAVAAHTGLIAVADDSGLAVDVLHGAPGIFSARWAGRHGDDRANLEL +LLAQLADVPDAHRGAEFVCAAALAVPSSADARGTHAIHVEHVEHGRLRGTLLRAPVGDGG +FGYDPILRPDGRDESTAQLSAADKNAISHRGHAFRALLPYLVDALDARA +>GCF_020097155_PROKKA_02005 +MSTPTAPVA--PAGARVVLATHNAGKVRELRSLLAEALPALDVETAVVDAGAVGAPDVVE +DGVTFEQNALKKARAVAAHTGLIAVADDSGLAVDVLGGAPGIFSARWAGRHGDDKANLEL +LLAQLGDVPDEHRGAAFVCAAALATPRGGD----------HVELGRMPGMLLREPVGDGG +FGYDPILRPAGEDRSTAQLSSAEKNAISHRGQAFRALLPHLVAALSADS +>GCF_023573625_PROKKA_00785 +MSAPASSSAGLPEGARIVLATHNAGKVRELRQLLAGAVPGLDVEAAVVDAGAVGAPDVVE +DGVTFAQNALKKARAVAAHTGLIAVADDSGLAVDVLHGAPGIFSARWAGRHGDDRANLEL +LLAQLADVPDEHRGAQFVCAAALAVPSGPDAAGARAIHVEHVEHGRLPGTLLREPVGDGG +FGYDPILRPEGRDVSTAQLSPEDKNAISHRGHAFRALLPYLVDALDARP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000730.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000730.fa new file mode 100644 index 0000000000000000000000000000000000000000..e27e59a8e6a67c0f54fc0c69ee26735ab4d199cf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000730.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_00823 +MQPTRRAFLGGGLGLLGLGVAGC----TTSPAAP-SSAAPSSSGPG-RLLVVGAPARALTRDPARALDVESFRLIRQVFE +TLLGVDADTGAPTPRLAERHEESDGGRLHTFHLVSGVVFDDGEPCDAAAVVANIERWAAAPAPVDGTVSPPSSFVSAFGG +YAGDADSAFAGVEAHGELEVRLRLHSPRRHLAAALASPAFAISSPASWDRTVDVDGSEVTTPAGTGPYRWADAAETAELT +RAHPGASGATFLVPSARHRGSDPAAHPVAVQAWGRASVRLRELRRGTADVIDVVAPGQLRPLVEAGTQVLPRDPLGVLYV +GMNLDHPLVHAQYLRQAIAYAVDRPRIAGSDVFLEGTRLAHDLVPPSLGVGDEEARRYDVNPGRAREFLGLAGYDGEPLE +FLYPAGTARPSLPEPERVYAMVARDLGAVGMHIVPVPVPEDQDYLHAVVSRPTRALHLMGRTGDYRDPHAFLEPFARSGR +AETGYRNPRVVEDVDAAAAETDDDTRRALFRRVVRAMALDLPALPLVYPISALATGPRVASYPTSPQLDEPFSRVRLTEG +>GCF_003691675_PROKKA_00555 +MQPTRRAFLGGGLGLLGLGVAGC----TTSPAAP-SSAAPSSSGPG-RLLVVGAPARALTRDPARALDVESFRLIRQVFE +TLLGVDADTGAPTPRLAERHEESDGGRLHTFHLVSGVVFDDGEPCDAAAVVANIERWAAAPAPVDGTVSPPSSFVSAFGG +YAGDADSAFAGVEAHGELEVRLRLHSPRRHLAAALASPAFAISSPASWDRTVDVDGSEVTTPAGTGPYRWADAAETAELT +RAHPGASGATFLVPSARHRGSDPAAHPVAVQAWGRASVRLRELRRGTADVIDVVAPGQLRPLVEAGTQVLPRDPLGVLYV +GMNLDHPLVHAQYLRQAIAYAVDRPRIAGSDVFLEGTRLAHDLVPPSLGVGDEEARRYDVNPGRAREFLGLAGYDGEPLE +FLYPAGTARPSLPEPERVYAMVARDLGAVGMHIVPVPVPEDQDYLHAVVSRPTRALHLMGRTGDYRDPHAFLEPFARSGR +AETGYRNPRVVEDVDAAAAETDDDTRRALFRRVVRAMALDLPALPLVYPISALATGPRVASYPTSPQLDEPFSRVRLTEG +>GCF_005280335_PROKKA_02107 +MQPSRRALLGAGLGALGLGLGGCAGTPTPAPSAS-GTAPATPSGPS-RLLVVGAPGRPFTRDSARAWDSESFRIIRQVLE +TLLGVDPDTGAPTPRLAERHEVSADGRVHAFHLVPGLVFDDGEPCDADAVVANIRRWAQAPAPVEGSVPMPSSFVSAFGG +HEGEEGSVYAGVEARGAHEVRLRLTSPLRHLAAALSSPAFAISSPASWERTVPVDGVETVTPAGTGPYRWATEAEVAELS +RDQPDGADVAYLVPSASHRGEEPAVRPVVVHPWGRATTRLRELRRGTADVIDVVAPGQLRPLVEAGTQVLPRDPLAVLYV +GMNLDHPRIRSQYLRQAIAYAVDRPRIAASDVFLEGTRLAHDLVPPALGVGDEEARRYDVNPAQARRLVELSGYDGEELE +FLYPAGTSSPSLPEPERVYAMVAQDLGAIGLHITPVPVPADHDYLRAVVSRPTRALHLMGRNGAYRDPHAFLEPFARSWR +AETGYRNPRVIQDVDAAASEQDDEARRGLFRRVVRAMALDLPALPLVYPISALATGPRVASYPTSPQLDEPFARVRLTEG +>GCF_020097155_PROKKA_01998 +MDASRRSVLSLGLAGLGLGLSAC----GAGRATPASSSSSAASAPAVRPLVLGAPGRPLTRTPALAWDTESLRLIAQVLE +PLLGVDQDTGAPTPLLAE-HRESEDGLTHTFVLTPDLRFSDGVACDADAVVANLRRWSEG-EPAE-AVAMPSPFVAAFGG +LAGEDSTAFRDATAADARTVRLRLRRRLRHLPAALASPRFAISSPASWKRTQDVDGAPVATPAGTGPHRWADPTESVEVL +EPLGGTGPATVLVPNEHARAGLPTPPTAVVHSWGRASTRLRELRRGNADVIDVVAPGQLRPLVEAGTQVLPRDPFSVLYL +GMNLDHPLLHSLYLRQAVAYAVDRPRLASSDVFLQGTALAHDLVPPALGVAVEDGPRYDVDPARARRLLELAGYRGEPLE +FLYPSGHAWPSLPEPERVFAMVSSDLGVVGLRVVPVPVPADQDYRRAVLGRRGRALHLMGRDGHYRDPHAFLEPFARSAR +TETGYVNAALTADVDAAASETDDERRRELHRRAGRTLLLDLPALPLVHPISALATGPRVASYPTSPQLDEPLAQVRLADS +>GCF_023573625_PROKKA_00792 +MQPTRRAFLGGGLGLLGLGVAGC----TTSPAVP-SSAAPSSSGPG-RLLVVGAPARALTRDPARALDVESFRLIRQVFE +TLLGVDADTGAPTPRLAERHEESDGGRLHTFHLVSGVVFDDGEPCDAAAVVANIERWASAPAPVDGTVAPPSSFVSAFGG +YAGDADSAFAGVEARGELEVRLRLHSPRRHLAAALASPAFAISSPASWDRTVDVDGSEVTTPAGTGPYRWADAAETAELT +RAHPGASGATILVPSARHRGSDPAAYPVAVQAWGRASVRLRELRRGSADVIDVVAPGQLRPLVEAGTQVLPRDPLGVLYV +GMNLDHPRVRSQYLRQAIAYAVDRPRIAGSDVFLEGTRLAHDLVPPSLGVGDEEARRYDVNPGRAREFLHLAGYDGEPLE +FLYPAGTARPSLPEPERVYAMVARDLGAVGMHIVPVPVPEDQDYLHAVVSRPTRALHLMGRTGDYRDPHAFLEPFARSGR +AETGYRNPRVVEDVDAAAAETDDDARRALFRRVVRAMALDLPALPLVYPISALATGPRVASYPTSPQLDEPFSRVRLTEG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000752.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000752.fa new file mode 100644 index 0000000000000000000000000000000000000000..4ed3c0e0f1e68af7230f3ee3c0f8060b022ce96f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000752.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00865 +MAKLLTIHGGKPLTGEVTVRGAKNLVPKAMVAALLGNSPSVLRNIPEIKDVDVVSSLLEI +HGVSVEWDKETGRITMDPAGVKSALTAEIDAHAGDSRIPILFCGPLMHAIGEAFIPDLGG +CKIGDRPIDYHLAVLRNFGAVVDKRPGGISISAPKGLHGAKLELPYPSVGATEQVLLTAV +KAEGITELKGAAVEPEIHDLIAVLQKMGAIITVQTDRTIRIEGVSEMRGYNHIALPDRNE +SASWASAALATRGDIYVRGAEQRDLTAFLNTYRKIGGEFDVVDDGIRFWHAGGDLNPLVL +ETDVHPGFMTDWQQPLVVALTQAKGVSIVHETVYENRFGFTDALVRMGASIQLHRECLGS +VPCRFGQRNFLHSAVISGPTPLHGVEFDIPDLRGGFSHLIAALTAEGTSTATGLEIINRG +YEHFMAKLEGLGADVELTERDR +>GCF_003691675_PROKKA_00587 +MAKLLTIHGGKPLTGEVTVRGAKNLVPKAMVAALLGNSPSVLRNIPEIKDVDVVSSLLEI +HGVSVEWDKETGRITMDPAGVKSALTAEIDAHAGDSRIPILFCGPLMHAIGEAFIPDLGG +CKIGDRPIDYHLAVLRNFGAVVDKRPGGISISAPKGLHGAKLELPYPSVGATEQVLLTAV +KAEGITELKGAAVEPEIHDLIAVLQKMGAIITVQTDRTIRIEGVSEMRGYNHIALPDRNE +SASWASAALATRGDIYVRGAEQRDLTAFLNTYRKIGGEFDVVDDGIRFWHAGGDLNPLVL +ETDVHPGFMTDWQQPLVVALTQAKGVSIVHETVYENRFGFTDALVRMGASIQLHRECLGS +VPCRFGQRNFLHSAVISGPKPLHGVEFDIPDLRGGFSHLIAALTAEGTSTATGLEIINRG +YEHFMAKLEGLGADVELTERDR +>GCF_005280335_PROKKA_02070 +MAKLLTIHGGKPLTGEVTVRGAKNLVPKAMVAALLGNTPSVLRSIPEIKDVDVVSSLLEI +HGVSVEWDKESGRITMDPAGVKSALTAEIDAHAGDSRIPILFCGPLMHAIGEAFIPDLGG +CKIGDRPIDYHLAVLRNFGAVVDKRPGGISISAPKGLHGAKLELPYPSVGATEQVLLTAV +KAEGITELKGAAVEPEIHDLIAVLQKMGAIITVQTDRTIRIEGVTEMRGYNHEALPDRNE +SASWASAALATGGDIFVRGASQRDLTAFLNTYRKIGGEFDVVDDGIRFWHAGGDLNPLVL +ETDVHPGFMTDWQQPLVVALTQAKGVSIVHETVYENRFGFTDALVRMGASIQLHRECLGS +VPCRFGQRNFLHSAVISGPTPLHGVEIDIPDLRGGFSHLIAALAAEGTSTATGLEIINRG +YEHFMDKLQGLGADVELSDRTR +>GCF_020097155_PROKKA_01964 +MAKLLTIHGGKPLQGEVTVRGAKNLVPKAMVAALLGTGPSVLRSIPEIKDVDVVSSLLEI +HGVTVDWDKESGTITMDPAGVKSALTAEIDAHAGDSRIPILFCGPLMHAIGEAFIPDLGG +CKIGDRPIDYHLAVLRNFGAVVDKRPGGISISAPKGLHGAKLELPYPSVGATEQVLLTAV +KAEGITELKGAAVEPEIHDLIHVLQKMGAIITVQTDRTIRIEGVPELRGYNHVAIPDRNE +SASWASAALATKGDIFVRGASQRDLTAFLNTYRKIGGEFEVTDEGIRFWHGGGELNPLVL +ETDVHPGFMTDWQQPLVVALTQATGVSIVHETVYENRFGFTDALVRMGASIQLHRECLGS +VPCRFGQRNFLHSAVISGPTPLHGVDFDVPDLRGGFSHLIAALAAEGTSHATGLEIINRG +YEHFMAKLQGLGADVELSERPR +>GCF_023573625_PROKKA_00824 +MAKLLTIHGGKPLTGEVTVRGAKNLVPKAMVAALLGNSPSVLRNIPEIKDVDVVSSLLEI +HGVSVEWDKETGRITMDPAGVKSALTAEIDAHAGDSRIPILFCGPLMHAIGEAFIPDLGG +CKIGDRPIDYHLAVLRNFGAVVDKRPGGISISAPKGLHGAKLELPYPSVGATEQVLLTAV +KAEGITELKGAAVEPEIHDLIAVLQKMGAIITVQTDRTIRIEGVSEMRGYNHIALPDRNE +SASWASAALATRGDIYVRGAEQRDLTAFLNTYRKIGGEFDVVDDGIRFWHAGGDLNPLVL +ETDVHPGFMTDWQQPLVVALTQAKGVSIVHETVYENRFGFTDALVRMGASIQLHRECLGS +VPCRFGQRNFLHSAVISGPTPLHGVEFDIPDLRGGFSHLIAALTAEGTSTATGLEIINRG +YEHFMAKLEGLGADVEPTERDR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000759.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000759.fa new file mode 100644 index 0000000000000000000000000000000000000000..7f30af3c2eb222b74cd074b7a31029efa819e536 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000759.fa @@ -0,0 +1,55 @@ +>GCF_002008305_PROKKA_00872 +MAAEAPVTDLPLSEVLGGKLPARLERELGLTTVGDLLDHVPRRWIERGELTPIAALPYDAEVTVVAVVESVTTRRMHSRP +GFIVDVTVADPSVAGVPGASLSMAFFNGHDARRRLAPGMTAMFQGRTTEYRGRITLNNPDFALLDDDVAPGEVDVRPVPL +YRATGKLPSWTVRSAVARVLETVDLGRIPELLTERIRAEAAAALDLDVPLPGTAQAYRDLHAPNDVAATGPARTALALRE +ALLVQAALAWRRNRERAVPAVPRPPRAGGLLEALDARLPFALTPGQVAVGEQLSAELARDAPMSRLLQGDVGAGKTLVAL +RAMLQVVDAGGQAALVAPTEVLAAQHHRALLRLMGPLA-EAGTLGAG--DGPATRIALVTGSLKTAARREALLALASGEA +GIAVGTHALLSEKVGFAELALAVVDEQHRFGVDQREALRRANPGTHLLVMSATPIPRSVAMTVFGDLDLSVLEGLPSGRQ +PVTTHVARMAHGPRVIGRVWELIAEHVAAGHQAFVVCPRIDPDDADPGHANVEEMTPRLRGLPALAGLRIDAVHGRMDQA +EQDAAMQAFARGETDVLVATTVVEVGVDVPNATVMAILDADDFGLSTLHQLRGRVGRGPGAAVCLLATRLPDGHPSLRRL +EVLAQEQDGMRIAQEDLAQRGVGDVLGAAQSGLASGLHHVDVIADAPLIAVAADAVAQVMAAGPGLSAHPALAAEVARWE +AEHLTAADYLEKG +>GCF_003691675_PROKKA_00594 +MAAEAPVTDLPLSEVLGGKLPARLEKELGLTTVGDLLDHVPRRWIERGELTPIAALPHDAEVTVVAVVESVTTRRMHSRP +GFIVDVTVADPSVAGVPGASLSMAFFNGHDARRRLAPGMTAMFQGRTTEYRGRITLNNPDFALLDDDVAPGEVDVRPVPL +YRATGKLPSWTVRSAVARVLETVDLGRIPELLTERIRAEAAAALDLDAPLPGTAQAYRDLHAPHDVAATGPARTALALRE +ALLVQAALAWRRDRERAVPAVPRPPRPGGLLEALDARLPFALTPGQVAVGEQLSAELARDAPMSRLLQGDVGAGKTLVAL +RAMLQVVDAGGQAALVAPTEVLAAQHHRALLRLMGPLA-EAGTLGAG--DGPATRVALVTGSLKTTARREALLALASGEA +GIAVGTHALLSEKVGFAELALAVVDEQHRFGVDQREALRRANPGTHLLVMSATPIPRSVAMTVFGDLDLSVLEGLPSGRQ +PVTTHVARMAHGPRVIGRVWELIAEHVAAGHQAFVVCPRIDPDDADPGHANVEEMTPRLRSLPALAGLRIDAVHGRMDQA +EQDAAMQAFARGETDVLVATTVVEVGVDVPNATVMAILDADDFGLSTLHQLRGRVGRGPGAAVCLLATRLPDGHPSLRRL +EVLAQEQDGMRIAQEDLAQRGVGDVLGAAQSGLASGLRHVDVIADAPLIAVAADAVTRVMAAGPGLSAHPALAAEVARWE +AEHLTAADYLEKG +>GCF_005280335_PROKKA_02063 +MGAEVRVTDLPLSEVLDGRLPARLDKELGLATVGDLLDHVPRRWIERGELTPIAALPWDAEVTVVAVVESVTTRRMHSRP +GFIVDVTVADPAADGAPGASLSMAFFNGHDARRRLAPGMTAMFQGRTTAYRGRITLNNPDFALLDDDVAPGDVDVRPVPL +YRATGKLPSWTVRSAVARVLADVDLTRIPELLTPRLRAEAAAALDLDAPLPDTARAYRDLHAPEEVEATGPARTALALRE +ALVVQAALAWRRDRERAVPAVPRPPRAGGLLDALDARLPFALTPGQAEVGEQLAAELTRDAPMSRLLQGDVGAGKTLVAL +RAMLQVVDAGGQAALVAPTEVLAAQHHRALLALMGPLA-EAGTLGAG--DGPATKVVLVTGSLKTQARREALLALASGEA +GIAVGTHALLSDKVGFAELALAVVDEQHRFGVDQREALRRSNPGTHLLVMSATPIPRSVAMTVFGDLDLSVLEGLPSGRQ +PVATHVARMDHGPRVIGRVWELIAEHAAAGRQAFVVCPRIDPDDADPGHANVEEMAPRLRSLPALAGLRIEAVHGRMDQA +EQDAAMQAFARGETDVLVATTVIEVGVDVPNATVMAVLDADDFGLSTLHQLRGRVGRGPDAAVCLLATRLPDEHPSLRRL +EVLAQEQDGMRIAQEDLATRGVGDVLGAAQSGLASGLRHVDVLRDAPLIAVAADAVGRIMAEGPGLSAHPALAAEVARWE +SEHLTAADYLEKG +>GCF_020097155_PROKKA_01957 +MAADG-VLDLPLGEVLSGRLPGRLEKELGLATVGGLLDHVPRRWVERGELTPIAALPVDAEVTVVARVEHVATRRMRSRA +GFIVDVTVADPSVAGTAGASLSMAFFNGHDAQRRLAPGVTAMFQGKTSLYRGAVTLNNPDFALLDDDVAPGEVDTRPVPI +YRATGRMPSWTVRSAVRRVLETVDLDAIPELLTEPIRARATLALGLPETLPGTAEAYRRLHAPDAVEQTGPARTALSLRE +ALVVQGALAWRRSREKAVPAVPRPRRAGGLLEALDARLPFELTPGQRAVGEELAAELSGPHPMSRLLQGDVGAGKTLVAL +RAMAQAVDAGGQAAFVAPTEVLAAQHHRALLALLGPLAREAGTLGAAAQEGPGTDVVLVTGSQRSAQRRAALLKLASGEA +GIAVGTHALLAERVQFAELALAVVDEQHRFGVDQREALRRANPGTHLLVMSATPIPRSVAMTVFGDLDLSVLEGLPSGRT +PVATHVARMAHGPRVIARVWEVVAEHCAAGRQAFVVCPRIDPDDADPAHANVTEMAERLRALPVLGGLRIGEVHGRMDQA +EQDAAMQAFARGETDVLVATTVVEVGVDVPNATVMAVLDADDFGLSTLHQLRGRVGRGQDAAICLLATRLADGHPSLRRL +EVLEATRDGMRIAQADLAQRGVGDVLGAAQSGLASGLTHVDVIGDADVIGVAADVVADLMAAAPGLSAHPALAAEVSRWE +AAHLTAADYLEKG +>GCF_023573625_PROKKA_00831 +MAAEAPVTDLPLSEVLGGKLPARLEKELGLTTVGDLLDHVPRRWIERGELTPIAALPYDAEVTVVAVVESVTTRRMHSRP +GFIVDVTVADPSVAGVPGASLSMAFFNGHDARRRLAPGMTAMFQGRTTEYRGRITLNNPDFALLDDDVAPGEVDVRPVPL +YRATGKLPSWTVRSAVARVLETVDLGRIPELLTERIRAEAAAALDLDAPLPGTAQAYRDLHAPHDVAATGPARTALALRE +ALLVQAALAWRRDRERAVPAVPRPPRAGGLLEALDARLPFALTPGQVAVGEQLSAELAREAPMSRLLQGDVGAGKTLVAL +RAMLQVVDAGGQAALVAPTEVLAAQHHRALLRLMGPLA-EACTLGAG--DGPATRVVLVTGSLKTAARREALLALASGEA +GIAVGTHALLSEKVGFAELALAVVDEQHRFGVDQREALRRANPGTHLLVMSATPIPRSVAMTVFGDLDLSVLEGLPSGRQ +PVTTHVAQMAHGPRVIGRVWELIAEHVAAGHQAFVVCPRIDPDDADPGHANVEEMTPRLRGLPALAGLRIDAVHGRMDQV +EQDAAMQAFARGETDVLVATTVVEVGVDVPNATVMAILDADDFGLSTLHQLRGRVGRGPGAAVCLLATRLPDGHPSLRRL +EVLAQEQDGMRIAQEDLAQRGVGDVLGAAQSGLASGLHHVDVIADAPLIAVAADAVAQVMAAGPGLSAHPALAAEVARWE +AEHLTAADYLEKG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000761.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000761.fa new file mode 100644 index 0000000000000000000000000000000000000000..aa46debf3f872814ac13ce3d10bcd74c3c70e5e4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000761.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00874 +MD------------GTQPTP---GAAPHDVD------VDAPWRRTAAAAGLLGDAGPVPT +VFETMTGLAVEHGAVNLGQGFPDADGPDALLRLAADAVLAGPNQYAPGTGDPALRQAVAE +HRRRHWGVTEDPATQVMITTGATEGIAATVLAFVRPGDEVVTVEPFYDSHAATIALAGAR +HVSVPVEAPDFLPDPARVAAAMTDRTRLLIVNTPHNPTGAVYPRELLEELVALCRSRGVL +ILSDEVYDHLVYEGEHVSLRSVAGAEDIALTVSSAGKAFAVTGWKVGWLTGPAELVGAAR +AVKQFLTYSSGPAFQRALGAYLPTDGAERHLAGQRERYRDARDRLVAGLREAGLDPVVPA +AGYFVVVDLAPWGVTDAAEAAVRWTREAGVTGIPVGALCRPDGGHLRSWLRLAFCKSPDA +IDEAMRRLAEAAPRLRA----A +>GCF_003691675_PROKKA_00596 +MD------------GTQPTP---GSARHDVD------VDAPWRRTAAAAGLLGDTGPVPT +VFETMTGLAVEHGAVNLGQGFPDADGPDALLRLAADAVLAGPNQYAPGTGDPVLRQAVAE +HRRRHWGVTEDPATQAMITTGATEGIASTVLAFVRPGDEVITVEPFYDSHAATIALAGGR +HVSVPVEAPDFLPDPARVADAITDRTRLLIVNTPHNPTGAVYPRELLEELVALCRSRGVL +MLSDEVYDHLVYEGEHVSLRSVAGAEDIALTVSSAGKAFAVTGWKVGWLTGPAELVGAAR +AVKQFLTYSSGPAFQRALGAYLPTDDAERHLAGQRERYRDARDRLVAGLREAGLDPVVPA +AGYFVVVDLAPWGVTDAAEAAVQWTREAGVTGIPVGALCRPDGGHLRSWLRLAFCKSPDA +IDEAMRRLAEAAPRLRA----P +>GCF_005280335_PROKKA_02061 +MNADASDRTRPPRTGPAPAP---ATGPAPADVAGTAFVAGPWRRTAAAAGLLDDGAPVPT +VFETMTGLAVEHGAVNLGQGFPDADGPDALLRLAAEAVLAGPNQYAPGTGDPVLRQAVAE +HRRRHWGVTEDPATQVMITTGATEGIAATVLAFVRPGDEVITVEPFYDSHAATIALAGGR +HVSVPVEAPDFLPDPARVADAITDRTRLLIVNTPHNPTGAVYPRELLEELVTLCRSRGVL +ILSDEVYDHLVYEGEHVSLRSVAGAEDIALTVSSAGKAFAVTGWKVGWLTGPAELVGAAR +AVKQFLTYSSGPAFQRALGAYLPTEDAKRHLAGQRERYRDARDRLVAGLRAADLDPVVPA +AGYFVVVDLAPWGVTDAAEAAVRWTREAGVTGIPVGALCRPDGGHLRSWLRLAFCKSPDA +IDEAMRRLAAAAPALDGRRPRP +>GCF_020097155_PROKKA_01955 +MS------------HDSPSPTDAAAAPSDVR------LAGPWRAASAAAGVLRDGAPVPT +VFETMTALAVEHGAVNLGQGFPDADGPPELLALAAEAVTTGPNQYAPGTGRADLRAAVAA +HRARHWGVAEDPDTQVLATTGATEAIAATVLALVRPGDEVITVEPFYDSHAAVVALAGGR +HVTVPVHAPDFLPDPARIAAAITPRTRLLIVNTPHNPTGAVYPRALLEELVALCRARDVL +MLSDEVYDHLVHEGRHVTLRAIPGAERIALTASSAGKSLAVTGWKVGWLTGPADLVAAVR +GVKQFLSYSSGPAFQQAVAAFLPR--ADDFLAGQLARHRRSRDLLVSGLRDIGLDPVVPA +AGYFTVVDLAPWGVRDAAAAARTWTERAGVAGIPVSALCRPDGDHLRSWLRLTFCKSEDT +VAEAVARLTRHAADLRA----G +>GCF_023573625_PROKKA_00833 +MD------------GTQPTP---RSAPHDVD------VDAPWRRTAAAAGLLGDAGPVPT +VFETMTGLAVEHGAVNLGQGFPDADGPDALLRLAADAVLAGPNQYAPGTGDPALRRAVAE +HRRRHWGVTEDPATQVMITTGATEGIAATVLAFVRPGDEVVTVEPFYDSHAATIALAGGR +HVSVPVEAPDFLPDPARVAAAMTDRTRLLIVNTPHNPTGAVYPRELLEELVALCRSRGVL +ILADEVYDHLVYEGEHVGLRSVAGAEDIALTVSSAGKAFAVTGWKVGWLTGPAELVGAAR +AVKQFLTYSSGPAFQRALGAYLPTDDAERHLAGQRERYRDARDRLVAGLREAGLDPVVPA +AGYFVVVDLAPWGVTDAAEAAVQWTREAGVTGIPVGALCRPDGGHLRSWLRLAFCKSPDA +IDEAMRRLAEAAPRLRA----A + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000777.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000777.fa new file mode 100644 index 0000000000000000000000000000000000000000..bb4f079c04d4ea41efb37ce5539cecb9772abb0f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000777.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_00904 +MFNSLSDRLTATFRSLKGKGRLSEADIDATAREIRRALLDADVAVPVVRQFIAQIKERALSAEVAQALNPGQQVVKIVNE +ELVGILGGETRRIQHAKTGTTVIMLVGLQGAGKTTLAGKLAHLLKSQGHTPLLVACDLQRPNAVKQLQVGGERAGVPVYA +PHPGVSSEFEAATGDPVQVARDGVAEANTKYHDVVIIDTAGRLGVDAELMQQAADIRAAVDPDEVLFVIDAMIGQDAVAT +AQAFNEGVGFTGVVLTKLDGDARGGAALSVRHVTGKPIMFASTGEGLKDFEVFHPDRMASRILDMGDVLSLIEQAEQNWD +RTEAEKMARKFADQEDFTLDDFLAQMQQLKKMGSLKKMLMMMPGAQGMRQQLEQFDESSIGRVEAIIHSMTPHERVAPKI +INGSRRARIARGSGVSVSEVNGLLERFAEAQKMMKRMAAGGGIPGMPGTPGGASRKGKGKGKNAKRDRVKSGNPAKAAAE +RKAIEERRARAAQAQAGAVFGRD-GA--GMDGFDPSTLNLPAGFEKYLKDR +>GCF_003691675_PROKKA_00623 +MFNSLSDRLTATFRSLKGKGRLSEADIDATAREIRRALLDADVAVPVVRQFIAQIKERALGAEVAQALNPGQQVVKIVNE +ELVGILGGETRRIQHAKTGTTVIMLVGLQGAGKTTLAGKLAHLLKSQGHTPLLVACDLQRPNAVKQLQVGGERAGVPVYA +PHPGVSSEFEAATGDPVQVARDGVAEANTKYHDVVIIDTAGRLGVDAELMQQAADIRAAVDPDEVLFVIDAMIGQDAVAT +AQAFNEGVGFTGVVLTKLDGDARGGAALSVRHVTGKPIMFASTGEGLKDFEVFHPDRMASRILDMGDVLSLIEQAEQNWD +RTEAEKMARKFADQEDFTLDDFLAQMQQLKKMGSLKKMLMMMPGAQGMRQQLEQFDESSIGRVEAIIHSMTPHERVAPKI +INGSRRARIARGSGVSVSEVNGLLERFAEAQKMMKRMAAGGGIPGVPGMPGGASRKAKGKGKNAKRDRVKSGNPAKAAAE +RKAIEERRARAAQAQAGAVFGRD-GA--GMDGFDPSTLNLPAGFEKYLKDR +>GCF_005280335_PROKKA_02038 +MFNSLSDRLTATFRSLKGKGRLTEADIDATAREIRRALLDADVAVPVVRQFIAQIKERALGEEVAQALNPGQQVVKIVNE +ELVGILGGETRRIRHAKTGTTVIMLVGLQGAGKTTLAGKLAHLLKAQGHTPLLVACDLQRPNAVKQLQVGGERAGVPVFA +PHPGVSSEFEAATGDPVQVARDGVAEANAKYHDVVIIDTAGRLGVDAELMQQAADVRAAVEPDEVLFVIDAMIGQDAVAT +AQAFNEGVGFTGVVLTKLDGDARGGAALSVRHVTGKPIMFASTGEGLKDFEVFHPDRMASRILDMGDVLSLIEQAEQNWD +RSEAEKMAKKFADQEDFTLDDFLNQMQQLKKMGSLKKMLMMMPGAQGMRQQLEQFDESSIGRVEAVIHSMTPHERVAPKI +INGSRRARIAKGSGVSVSEVNGLLERFAEAQKMMKRMAAGGGMPGMPGAPGGVSRKA--KGKNAKRNKVKSGNPAKAAAE +RKALEERQARAAQAQAGAVFGRDGGA--GMDGFDPSSLNLPAGFEKYLKDR +>GCF_020097155_PROKKA_01936 +MFTSLSDRLTATFRNLKGKGRLTEADIDATAREIRRALLDADVAVPVVRQFIAQIKERALGEEVSQALNPGQQVVKIVNE +ELVAILGGETRRIQHAKTGTTVIMLVGLQGAGKTTLAGKLAHLLKSQGHTPLLVACDLQRPNAVKQLQVNGERAGVPVFA +PHPGVSSEFEAATGDPVQVARAGIDEANTKYHDVVIIDTAGRLGVDAELMQQAADIRAAVQPDEVLFVIDAMIGQDAVAT +AQAFNEGVGFTGVVLTKLDGDARGGAALSVRHVTGKPIMFASTGEGLKDFEVFHPDRMASRILDMGDVLSLIEQAEQNWD +RAEAEKMAKKFADQEDFTFDDFLTQMQQLKKMGSMKKLLGMMPGAQGMRQQLEQFDESSIGRVEAIIHSMTPHERVAPKI +INGSRRARIAKGSGVQVTEVNALLERFAEAQKMMKKL-AGGGVPGMPGMGPGPGRKS--KGRNAKKTKVKSGNPAKAAAE +RRALEERRSRPA---AGGVFGQG-GTMPDMTDFDPSQLNLPAGFEKYLKDR +>GCF_023573625_PROKKA_00852 +MFNSLSDRLTATFRSLKGKGRLSEADIDATAREIRRALLDADVAVPVVRQFIAQIKERALGAEVAQALNPGQQVVKIVNE +ELVGILGGETRRIQHAKTGTTVIMLVGLQGAGKTTLAGKLAHLLKSQGHTPLLVACDLQRPNAVKQLQVGGERAGVPVYA +PHPGVSSEFEAATGDPVQVARDGVAEANTKYHDVVIIDTAGRLGVDAELMQQAADIRAAVDPDEVLFVIDAMIGQDAVAT +AQAFNEGVGFTGVVLTKLDGDARGGAALSVRHVTGKPIMFASTGEGLKDFEVFHPDRMASRILDMGDVLSLIEQAEQNWD +RSEAEKMARKFADQEDFTLDDFLAQMQQLKKMGSLKKMLMMMPGAQGMRQQLEQFDESSIGRVEAIIHSMTPHERVAPKI +INGSRRARIARGSGVSVSEVNGLLERFAEAQKMMKRMAAGGGIPGMPGMPGGASRKAKGKGKNAKRDRVKSGNPAKAAAE +RKAIEERRARAAQAQAGAVFGRD-GA--GMDGFDPSTLNLPAGFEKYLKDR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000805.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000805.fa new file mode 100644 index 0000000000000000000000000000000000000000..e3df24c964330e2b58e5f1a285849214f7c26e11 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000805.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_00933 +MTEQTTTVPVGAADIGVTGLAVMGANLARNFARHGYTVALHNRSRARTDQLVAEHGDEGAFVATETLAELVQSLAVPRRV +LIMVKAGAPVDAVIDQLVPLLDEGDIVIDAGNSHFEDTRRREAALAEKGLHFVGVGVSGGEEGALHGPAIMPGGPEKSYE +ALGPMLEKIAAQFEGEPCCAWVGTDGAGHYVKMVHNGIEYADMQVIGEAYDLLRRVGGLEPAEQAEVFTAWNQTDLASYL +IEITAEVLAQVDAATGRPLVDVIVDEAGQKGTGRWTAISGLDVGSPVAAIAESVFARSLSSQRAVREVARETLAAGVDEE +AQRAPQDTDAFVEDVRQALFASKLVAYAQGMDMLAAAAEEYGWSLDLGTIASLWRDGCIIRADLLDVIMQAFGGRDTSRH +PAPGTRAPGQPLNLLFAPEFAQAIAEALPAWRRVVGTAVAAGVPVPVFSSALAYYDGLRADRLPAALVQGQRDYFGAHTY +LRVDREGSFHTLWSGDRTEVDGEGVPVVMPQPTEGDPTQD--- +>GCF_003691675_PROKKA_00652 +MTEQTTTVPVGAADIGVTGLAVMGANLARNFARHGYTVALHNRSRARTDQLVAEHGDEGAFVATETLAELVQSLAVPRRV +LIMVKAGAPVDAVIDQLVPLLDEGDIVIDAGNSHFEDTRRREAALAEKGLHFVGVGVSGGEEGALHGPAIMPGGPEKSYE +ALGPMLEKISAQFEGEPCCAWVGTDGAGHYVKMVHNGIEYADMQVIGEAYDLLRRVGGLEPAEQAEVFTAWNQTDLASYL +IEITAEVLAQVDAATGRPLVDVIVDEAGQKGTGRWTAISGLDVGSPVAAIAESVFARSLSSQRAVRQVARETLAAGVDEE +AQRAPQDTDTFVEDVRQALFASKLVAYAQGMDMLAAAAEEYGWSLDLGTIASLWRDGCIIRADLLDVIMQAFGGRDTSRH +PAPGTRAPGQPLNLLFAPEFAQAIAEALPAWRRVVGTAVAAGVPVPVFSSALAYYDGLRADRLPAALVQGQRDFFGAHTY +LRVDREGSFHTLWSGDRTEVDGEGVPVVMPQPTEGDPTQD--- +>GCF_005280335_PROKKA_02007 +MTEQTTTVPVGAADIGVTGLAVMGANLARNFARHGYTVALHNRSHGRTDQFVAEHGDEGAFVATETLAELVQSLAVPRRV +LIMVKAGAPVDAVIDQLVPLLDEGDIVIDAGNSHYEDTRRREAALAEKGLHFVGVGVSGGEEGALHGPAIMPGGPEKSYE +ALGPMLEKISAQFEGEPCCAWVGTDGAGHYVKMVHNGIEYADMQVIGEAYDLLRRVGGLEPAEQAEVFTAWNQTDLASYL +IEITAEVLAQVDAATGRPLVDVIVDEAGQKGTGRWTAISGLDVGSPVAAIAESVFARSLSSQREVRAAAREVLQAGVDEA +AVPAVTDTDAFVEDVRQALFASKLVAYAQGMDMLAAAAEEYGWSLDLGTIASLWRDGCIIRADLLDVIMKAFGGRDTARH +PEPGTRAEGQPLNLLFAPEFAQAIAEALPAWRRVVGTAVAAGVPVPVFSSALAYYDGLRADRLPAALVQGQRDYFGAHTY +LRVDREGSFHTLWSGDRTEVDGEGVPVVMPQPAEGDPTQD--- +>GCF_020097155_PROKKA_01903 +MTETSTV--RGTADIGVTGLAVMGANLARNFARHGYTVALHNRSRAKTDALVAEHGHEGSFVATETLEELVGSLASPRRV +LIMVKAGAPVDAVIDQLVPLLDEGDIVIDAGNSHYEDTRRREAALAEKGLHFVGVGVSGGEEGALNGPAIMPGGPEESYA +ALGPLLEDIAASYDGEPCCAWIGTDGAGHYVKMVHNGIEYADMEVIGEAFDLLRRVAGIEPAEQAQVFDAWNQTELASYL +IEITAEVLQQVDAATGAPLVDVIVDEAGQKGTGRWTAISGLDVGSPVAAIAESVFARSLSAQTEVRATAREVLAAGVESA +PAVSPQDRDAFVEDVRQALFASKLVAYAQGLDMLSAAAIEYGWALDLGTIASLWRDGCIIRADLLDVIMKAFGGRDTSRH +PEPGTRAEGQPLNLLFAPEFAQAMAEALPAWRRVVGAAVAAGVPVPVFSSALAYYDGLRADRLPAALIQGQRDFFGAHTY +RRTDRDGSFHTLWSGDRTEVDGDGAPVVMPQPAEGDPTDETAR +>GCF_023573625_PROKKA_00882 +MTEQTTTVPVGAADIGVTGLAVMGANLARNFARHGYTVALHNRSRARTDQLVAEHGDEGAFVATETLAELVQSLAVPRRV +LIMVKAGAPVDAVIDQLVPLLEEGDIVIDAGNSHYEDTRRREAALAEKGLHFVGVGVSGGEEGALHGPAIMPGGPEKSYE +ALGPMLEKISAQFEGEPCCAWVGTDGAGHYVKMVHNGIEYADMQVIGEAYDLLRRVGGLEPAEQAEVFTAWNQTDLASYL +IEITAEVLAQVDAATGRPLVDVIVDEAGQKGTGRWTAISGLDVGSPVAAIAESVFARSLSSQRAVREVARETLAAGIDED +AQRVPQDTDAFVEDVRQALFASKLVAYAQGMDMLAAAAEEYGWSLDLGTIASLWRDGCIIRADLLDVIMQAFGGRDTSRH +PAPGTRAPGQPLNLLFAPEFAQAIAEALPAWRRVVGTAVASGVPVPVFSSALAYYDGLRADRLPAALVQGQRDYFGAHTY +LRVDREGSFHTLWSGDRTEVDGEGVPVVMPQPTEGDPTQD--- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000811.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000811.fa new file mode 100644 index 0000000000000000000000000000000000000000..8e4ee228172d229281c674f3a0d53624f0a9e4d0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000811.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00939 +MSGRVLQVEADGGSRGNPGVAGYGALVRDPATGEILRTDAAPLGKASNNVAEYSGLVAGL +RMARDLDPEARVHVLMDSKLVVEQMSGRWKIKHDDMRRLAAEARSVLPPERVSYEWIPRN +RNKDADRLSNEAMDAGARGEQWDAGASEVPVAAP-------AKASTTSASAVAESGLEAD +ADVRAVEADGPDAVASPEDATPAPAPTGRLHHVEIWVADLAAAEASLGWLFGELGYVPGE +GWAEGRTYQGAGEYLVLEAGPDVAAGAHERTRPGLNHLAFRAGSRARVDELTAAARDRGF +RLLFEDRHPHAGGPDHYAAYLETADGFEVELVAVED +>GCF_003691675_PROKKA_00658 +MSGRVLQVEADGGSRGNPGVAGYGALVRDPATGEILRTDAAPLGKASNNVAEYSGLVAGL +RMARDLDPEARVHVLMDSKLVVEQMSGRWKIKHDDMRRLAAEARAVLPPERVSYEWIPRN +RNKDADRLSNEAMDAGARGGQWDAGASEVPVAAP-------AEASTTSTSAVAESGLDAD +ADVRAVEADGPDAVASPEDATPGPAPTGRLHHVEIWVADLAAAEASLGWLFGELGYVPGE +GWAEGRTYQGAGEYLVLEAGPDVAAGAHERTRPGLNHLAFRAGSRSRVDELTAAARGRGF +RLLFEDRHPHAGGADHYAAYLETADGFEVELVAVED +>GCF_005280335_PROKKA_02000 +M----------------------------------------------------------- +------------------------------------------------------------ +--------------------------------------------------------LEAD +ADARAVEAEAPDAVGQDAAAPQAPTPTGRLHHVEVWVADLAAAEAGLGWLLGELGYVLGE +GWAEGRTYQGAGEYIVLESGPDVVGGAHERTRPGLNHLAFRAGTRARVDELTAAARERGF +RLLFADRHPHAGGADHYAAYLEAPDGFEVELVAVED +>GCF_020097155_PROKKA_01897 +MAERTLQVEADGGSRGNPGVAGYGALVRDPATGDVLMTDAAPLGKASNNVAEYSGLIAGL +EMAKTLDPDARVHVKMDSKLVVEQMSGRWKIKHEDMRRLAQQARAVLPPSRVTYEWIPRA +QNKDADQLSNEAMDAGARGGRWDAGASKVPVTAP-------SAPTSAGAPA-------AE +PDKEPLEEP-----PVPEERT-RPRPVGRLHHVEIWAADLDAAVESLGWLFEQVGYAPGD +AWAEGRVYRGAGDYLVLESGRDVAPGGHDRLRPGLNHLAFRAGTRADVDRIAAQAADHGF +TLLFEDRHPFAGGRDHYAAYLETADGFEVELVADPA +>GCF_023573625_PROKKA_00888 +MSGRVLQVEADGGSRGNPGVAGYGALVRDPATGEILRTDAAPLGKASNNVAEYSGLVAGL +RMARDLDPEARVHVLMDSKLVVEQMSGRWKIKHEDMRRLAAEARSVLPPERVSYEWIPRN +RNKDADRLSNEAMDAGARGEQWDAGASEVPVAAPAAAGSTAAEASTTSASAVAESCLDAD +ADVRAVEADGPEAVASPGDATPAPAPTGRLHHVEIWVADLAAAEASLGWLFGELGYVPGE +GWAEGRTYQGAGEYLVLEAGPDVAAGAHERTRPGLNHLAFRAGSRARVDELTAAARDRGF +RLLFEDRHPHAGGPDHYAAYLETADGFEVELVAVED + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000818.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000818.fa new file mode 100644 index 0000000000000000000000000000000000000000..c0cdcc100257762c511fd76681f2aa055445d298 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000818.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_00957 +MSVSTPRPSGSTAHRPEYVGVGGLRADPQVAGADWWPILVGTLGSLLLVVGSYSVGWLASASPINRWQWLIPWRTQETGV +LAGAALLTLGCWVMFWAWLRLGQTIRPFGRGALRTVNLATVLWCLPQVVALPIFSRDIFAYVGQGRLMEAGQDPYVDTIS +SLSNWFQLGADATWADSETPYGPIFLWIEQAVVAISGDMNPDLAIFLFRLVAVAGVALIMVFVPLLARRMGVNDAWAQWI +SVANPLFTISFVASGHNDALMVGLALAGTWCALRAGHPLRPQRPGQSVAWGVAGVVLVTLSLGIKPITLVLLPFIGLLWA +GPTARWPRRFAFWALTAGISFGLMALVGVLNGFGFGWVAVMVGTGTGTVPWGPIGMLSLITVGASELLGQGADVQAVEGV +YKTAGRVLSVLIVLALMFLGRQDRVMTRMTWAFTALVILSPIIQPWYLLWLLPFFAVIGIRDNWQIKWVVFTVGYFLAFG +ASDQLFTWQFLDIADQVKAVSLIVSAVCLLWILVVDRRTSRFVKDHWHVRPAVRAGLARLRGAP---------------R +PVEPG---------E +>GCF_003691675_PROKKA_00670 +MSVSTPRPSGSTAHRPEYVGVGGLRADPQVAGADWWPILVGTLGSLLLVVGSYSVGWLASASPINRWQWLIPWRTQETGV +LAGTVLLTLGCWVMFWAWLRLGQTIRPFGRGALRTVNLATVLWCLPQVVALPIFSRDIFAYVGQGRLMVAGQDPYVDTIS +SLSNWFQLGADATWADSETPYGPIFLWIEQAVVAISGDMNPDLAIFLFRLVAVAGVALIMVFVPLLARRLGVNDAWAQWI +SAANPLFTISFVASGHNDALMVGLALAGTWCALRAGHPLRPQRPGQSVAWGVAGVVLVTLSLGIKPITLVLLPFIGLLWA +GPTARWPRRFAFWALTAGISFGLMALVGVLNGFGFGWVAVMVGTGTGTVPWGPIGMLSLITVGASELLGQGADVQAVEGV +YKTAGRVLSVLIVLALMFLGRQDRVMTRMTWAFTALVILSPIIQPWYLLWLLPFFAVIGIRDNWQIKWVVFTVGYFLAFG +ASDQLFTWQFLDIADQVKAVSLIVSAVCLLWILVVDRRTSRFVKDHWHVRPAVRAGLARLRGAP---------------R +PVEPG---------E +>GCF_005280335_PROKKA_01930 +MSVTTPRPSGSTAGRPAHIGVGGLRADPKVAGGNTWPILVGTLGSLLLVAGSFSVGWLASASPINRWQWLIPWRTQETGV +IVGTILLTLGCWVMFWAWLRLGQTVRPFGRGSLRTVNLATALWCLPQVFALPIFSRDIFAYVGQGRLMVAGQDPYEDTIS +SLSNWFQLGADATWADSETPYGPIFLWIEQAVVAVSGDMNPDLAIFLFRLVAVAGVVLIMVFVPLLARRLRVNGAWAQWV +SAANPLFTISFVASGHNDALMVGLALAGTWCALRAGHPLRPQSAARSAAWGVAGVVLVTLSLGIKPITLVLLPFIGLLWA +GPTAGWIRRFVLWFLTAGISFGIMAVVGALNGFGFGWVAVMVGTGTGTVPWGPIGILSLLTVGISELVGQGADQQAVEGV +YKTAGRVLSVLIVLALMFLGRQDRVLTRMTWAFTALVILSPIIQPWYLLWLLPFFAVIGIRDDWQIKWVVFTVGYFLAFG +ASDQLFTWQFLAIADQVKAISLIVSAVCLAWILVVDRRTSRFVKDHWHVRPAVRAGLARLRRAP---------------R +TPEPG---------E +>GCF_020097155_PROKKA_01882 +MGVPAAGPSGSTAFRPEYIGVGGLRADPQVAGRPLWPILVGLLGSLMLVAGSFSVGWLASASPINRWQWLIPWRTQESGV +MTGTVLLTLGCWVMFWAWLRLGQTVRPFGPGALRTVNVATALWCLPMVFALPIFSRDIFAYVGQGRLMVNGQDPYTDAIS +SLNNWFQLGADATWAGSETPYGPVFLWIEEVVVRISGDMNPDLAIFLFRLVAVVGVVLTMVFVPLLARRLSVNGAWAQWV +SAANPLFTVSFVASGHNDALMVGLALAGTWCALRAGHPRGGQSTASHVGWGVAAVVLVTASLGVKPITLVLLPFIGLLWA +GPRAGWSRKFVYWAVTGGLSLALMVLVGRLNGFGFGWLEVMAGTGSGTSPWAPVGMMSIATRVLMEVLQLGPDLQAIEGF +YKSVCRLLSVLIVLALMFLGRQDRVFTRMTWAFTTLVVLSPIVQPWYLLWLLPFFAVIGLRDNWQIKWVVFTVGYFLAFG +AMDQLFTWQFLDIAEEVRAASLLVSGVSLVWILAVDRKTSRFIKDHWHVRPALREGVRRLRRRPTGGAAAPHTRPHPVER +LGESGSEDAAARGAR +>GCF_023573625_PROKKA_00903 +MSVSTPRPSGSTAHRPEYVGVGGLRADPQVAGADWWPILVGTLGSLLLVVGSYSVGWLASASPINRWQWLIPWRTQETGV +LAGTALLTLGCWVMFWAWLRLGQTIRPFGRGALRTVNLATVLWCLPQVVALPIFSRDIFAYVGQGRLMEAGQDPYVDTIS +SLSNWFQLGADATWADSETPYGPIFLWIEQAVVAISGDMNPDLAIFLFRLVAVAGVALIMVFVPLLARRLGVNGARAQWI +SAANPLFTISFVASGHNDALMVGLALAGTWCALRAGHPLRPQRPGQSVAWGVAGVVLVTLSLGIKPITLVLLPFIGLLWA +GPTARWPRRFAFWALTAGISFGLMALVGVLNGFGFGWVAVMVGTGTGTVPWGPIGMLSLITVGASELLGQGADVQAVEGV +YKTAGRALSVLIVLALMFLGRQDRVMTRMTWAFTALVILSPIIQPWYLLWLLPFFAVIGIRDNWQIKWVVFTVGYFLAFG +ASDQLFTWQFLNIADQVKAVSLIVSAVCLLWILVVDRRTSRFVKDHWHVRPAVRAGLARLRGAP---------------R +PVEPG---------E diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000826.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000826.fa new file mode 100644 index 0000000000000000000000000000000000000000..57c760b96e597bf2392715963009da2596be3638 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000826.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00972 +MPEGHSVHRLARQFTDVFGGRRIRATSPQGRFAEGAALLDGQVLKRARAHGKHFFADVSG +GHVLHVHLGMYGAWTFGGDQDFAAASSIGAPRRIGEREVHDDGAPAAEPARDADGWVQPP +PPAATVRLRLRAEHGWADLIGASRCRALTPAEAADVVAGLGPDPLSDDDPAPFYDLARRT +RRPIGVVLMDQAAVSGIGNIFRAEALFRVGIDPWRPARDVSASELESLWADNAALMREGV +RLGRIVTTRPEHRPGIPAEAAWPEHASYVYQRQGLACLVCGRETIVVEEMAARKLYRCLT +CQS +>GCF_003691675_PROKKA_00685 +MPEGHSVHRLARQFTDVFGGRRIRATSPQGRFAEGAALLDGQVLKRARAHGKHFFADVSG +GHVLHVHLGMYGAWTFGGDQDFAAASSIGAPRRIGEREVHDDGAPAAEPARDADGWVQPP +PPASTVRLRLRAEHGWADLIGANRCRALTRAEAADVVAGLGPDPLNDDDPAPFYDLARRT +RRPIGVVLMDQGAVSGIGNIFRAEALFRAGIDPWRPAREVSAPDLAFLWADNAALMREGV +RLGRIVTTRPEHRPGIPAEAAWPEHANYVYQRQGLACLVCGRETIVVEEMAARKLYRCLT +CQS +>GCF_005280335_PROKKA_01918 +MPEGHSIHRLARQFTDVFGGWPIRASSPQGRFAEGAARMDGQVLEAARAHGKHFFADLAD +GHVLNVHLGMYGAWSFGGDERFDAASSIGAPRRIGEREVHADGAAAAEPDRDDDGWVLPP +PPVPTVRLRVRAEHGWADLIGASTCRLLTPAEAGDVVAKLGPDPLNDDDPAPFLDLAGRT +RRPIGAVLMDQAAVGGIGNIFRAEALFRAGLDPWRPSNAVPREVLRRLWSDNAELMREGV +RLGRIVTTRPEHRPGVPAEQAWPEHANYVYQRQGSPCLVCGQDAIVVEGMAARKLYRCTV +CQR +>GCF_020097155_PROKKA_01866 +MPEGHSIHRLARQVQDVFGGQALAASSPQGRFADGAALLDGRVLERAWAHGKHFFADIEG +GLTLNVHLGMYGAMTFGGDEAFAAASSIGAPRRIGETE--DHGALAA---------AEPP +PARPTVRLRLRSAHGWADLIGAGTCRVLTPQELAEVTSKLGPDPLNDDDPAAFVARAART +GRPVGVVLMDQSMVGGIGNIYRAEVLFRAGLDPWTPARDVGADVLAALYADAQALMRDGV +RLGRIVTTAPEHRPGVAAEDAWPEHANYVYRRQGMPCRVCGQDAIVREEMAARNLFRCTD +CQR +>GCF_023573625_PROKKA_00915 +MPEGHSVHRLARQFTDVFGGRRIRATSPQGRFAEGAALLDGQVLKRARAHGKHFFADVSG +GHVLHVHLGMYGAWTFGGDQDFAAASSIGAPRRIGEREVHDDGAPAAEPARDADGWVQPP +PPAATVRLRLRAEHGWADLIGASRCRALTPAEAADVVAGLGPDPLSDDDPAPFYDLARRT +RRPIGVVLMDQAAVSGIGNIFRAEALFRAGIDPWRPAREVSASDLAFLWADNAALMREGV +RLGRIVTTRPEHRPGIPAESAWPEHANYVYQRQGLACLVCGRETIVVEEMAARKLYRCLT +CQS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000841.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000841.fa new file mode 100644 index 0000000000000000000000000000000000000000..bae7389f414acc1a11e40c11dc1fde5b79446167 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000841.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_00989 +MTVVMEDVGKSFGGPTPVLEDVSVRIEPGEFVCLLGASGCGKSTLLNLVARLEAPTAGVV +KTPREGAAFMFQDAALFPWLTARGNIELALRFAGVAAGERRERAGELLRLVHLDDAADLR +PHQLSGGMRQRVALARALAQDRPLLLMDEPFAALDAITRDLLHGELERVWRQTGRTVVFV +THNVAEAVRLGQRVLLLSSRPGRVVAEWDVPAAARHDAPAAAALTAAITARLGQEIRRHA +H +>GCF_003691675_PROKKA_00703 +MTVVMEDVGKSFGGPTPVLEDVSVRIEPGEFVCLLGASGCGKSTLLNIIARLEAPTAGVV +KTPREGAAFMFQDAALFPWLTARGNIELALRFAGVAAGERRERAGELLRLVHLDDAADLR +PHQLSGGMRQRVALARALAQDRPLLLMDEPFAALDAITRDLLHGELERVWRQTGRTVVFV +THNVAEAVRLGQRVLLLSSRPGRVVAEWDVPAAARHDAPAAAALTAAITARLGQEIRRHA +H +>GCF_005280335_PROKKA_01900 +MTVVMEDVGKSFGGPTPVLEDVSVRIEPGEFVCLLGASGCGKSTLLNLIARLEAPTAGVV +KAPRQGAAFMFQDAALFPWLTARGNIELALRFAGVPAAERRGRAGELLRLVHLGDAADLR +PHQLSGGMRQRVALARALAQDRPLLLMDEPFGALDAITRDLLHVELERVWRQTGRTVVFV +THNVAEAVRLGQRVLLLSSRPGRVVAEWDVPAAARHDAPAAAALTAAITARLGQEIRRHA +H +>GCF_020097155_PROKKA_01847 +MTVVMEDVGKSFGGPTPVLEDVSVRIEPGEFVCLLGASGCGKSTLLNLIARLEAPTAGVV +KTPREGAAFMFQDAALFPWLTARGNIELALRFAGVPAAGRRERAGELLRLVHLGDAADLR +PHQLSGGMRQRVALARALAQDRPLLLMDEPFAALDAITRDLLHVELERVWRQTGRTVVFV +THNVAEAVRLGQRVLLLSSRPGRVVAEWDVPAAAHHDAPAAAALTAAITARLGQEIRRHA +H +>GCF_023573625_PROKKA_00932 +MTVVMEDVGKSFGGPTPVLEDVSVRIEPGEFVCLLGASGCGKSTLLNLVARLEAPTAGVV +KTPREGAAFMFQDAALFPWLTARGNIELALRFAGVAAGERRERAGELLRLVHLDDAADLR +PHQLSGGMRQRVALARALAQDRPLLLMDEPFAALDAITRDLLHGELERVWRQTGRTVVFV +THNVAEAVRLGQRVLLLSSRPGRVVAEWDVPAAARHDAPAAAALTAAITARLGQEIRRHA +H + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000843.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000843.fa new file mode 100644 index 0000000000000000000000000000000000000000..c7b5a4c1089375bc9a27040b7f0c4ce9e5dd649d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000843.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_00991 +MTASDLYPTSLRLLGRPVLIVGGGRVAGRRVGALLDAGALVSVVAPEPGEEVERLAAAGL +LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVV +RAGDVTVAVNAGGDPRRARALKDAIALALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL +ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA +RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSAVSVPAAAGIPVTHRGVA +TGFTLVTGHEELAEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD +QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGAPAAGIPAPISTLNPTSEGA +RA +>GCF_003691675_PROKKA_00705 +MTASDLYPTSLRLLGRPVLMVGGGRVAGRRMGALLDAGALVTVVAPEPGEEVERLAAAGL +LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVV +RAGDVTVAVNAGGDPRRARALKDAITLALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL +ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA +RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSAVSVPAAAGIPVTHRGVA +TGFTLVTGHEELSEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD +QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGAPAAGVPAPISTLNSTSEGA +RA +>GCF_005280335_PROKKA_01898 +MTASDLYPTSLRLLGRPVLMVGGGRVAGRRVGALLDAGALVTVVAPEPGEEVERLAAAGL +LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVV +RAGDVTVAVNAGGDPRRARALKDAITLALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL +ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA +RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSAVSVPAAAGIPVTHRGVA +TGFTLVTGHEELSEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD +QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGARAAGVPAPILTLNPTSEGA +RA +>GCF_020097155_PROKKA_01845 +MTASDLYPTSLCLLGRPVLIVGGGRVAGRRVGALLDAGALVTVVAPEPGEEVERLAAAGL +LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVA +RAGDVTVAVNAGGDPRRARALKDAITLALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL +ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA +RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSAVSVPAAAGIPVTHRGVA +TGFTLVTGHEELAEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD +QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGAPAAGVPAPISTLNPTSEGA +RA +>GCF_023573625_PROKKA_00934 +MTTSDLYPTSLRLLGRPVLVVGGGRVAGRRMGALLDAGALVTVVAPKPGEEVERLAAAGL +LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVV +RAGDVTVAVNAGGDPRRARALKDAITLALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL +ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA +RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSVVSVPAAAGIPVTHRGVA +TGFTLVTGHEELSEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD +QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGAPAAGIPAPILTLNPTSEGA +RA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000857.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000857.fa new file mode 100644 index 0000000000000000000000000000000000000000..5f92bbd82aad430396b8c2ef3eebfa8c449cd7e1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000857.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01008 +MRLILLRHGETDWNVLDRYQGHTDIELNAEGERQARRAAGGPVGDLVEDAEELVAVCSPL +ARARRTAEIVLEARVGAASVAVDPELMELAGGEWEGLELSAIAERWPDEHRLWRAEPALD +AGPVGGETLRGGGERALRALRGHVPPHWADTPRDG---GAHTLLVVAHGALIRAATGLLL +RHEGEAFAAMERIGNARAAVLQGAFTADTGAEGWGDWTLEGYGI +>GCF_003691675_PROKKA_00722 +MRLILLRHGETDWNVLDRYQGHTDIELNAEGERQARRAAGGPVGDLVEDAEELVAVCSPL +ARARRTAEIVLEARVGAASVAVDPELMELAGGEWEGLELSAIAERWPDEHRLWRAEPALD +AGPVGGETLRGGGERALRALRGHVPPHWADTPRDG---GAHTLLVVAHGALIRAATGLLL +RHEGEAFAAMERIGNARAAVLQGAFTADTGAEGWGDWTLEGYGI +>GCF_005280335_PROKKA_01882 +MRLILLRHGETDWNAGDRYQGRTDVELNAVGERQARRAAVGPVGDLLEEAAELVAVASPL +ARARRTAEILLEARVGAADLALDEQLMELHGGDWEGLGLTAIAQRWPEEHRSWRAVPALD +AGPVGGETLRAAGERALGALRGRVPQHWA-VYAAA------------------------- +-------------------------------------------L +>GCF_020097155_PROKKA_01809 +MRLVLLRHGETDWNALDRYQGRTDVPLNALGERQAAAAAAGPVGELLRSAEDLVAVSSPL +IRARRTAEIVLEDAVGAVELAVDSRLVELGGGEWEGLDFTEIGARWPHEHHAWRTVPDLD +GGPVGGEVLRAGGERVLAAAAAHVPEDWS-TPRPARVPDARTLLIVAHGAVIRAAAGLAL +ALEGADFAHLARVSNARAVILDGTFA----GEGPGAWSLLGYDV +>GCF_023573625_PROKKA_00951 +MRLILLRHGETDWNALDRYQGHTDIELNAEGERQARRAAGGPVGDLLEDAEELVAVCSPL +ARARRTAEIVLQARVGAASVAVDPELMELAGGEWEGLELSAIAERWPDEHRLWRAVPALD +AGPVGGETLRGGGERALRALRGHVPPHWADTPRDG---GAHTLLAVAHGALIRAATGLLL +RHEGEAFAAMERIGNARAAVLQGAFAPAT--EGWGDWTLEGYGI + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000858.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000858.fa new file mode 100644 index 0000000000000000000000000000000000000000..1bfe679de59180034ff77af3660fe450a1de6085 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000858.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_01014 +MTTAPATAGRERRTSDVVVIGAGPAGLMAARTAKAQGLSVTVLEARRRVGGRTWNGLVEGADGKDHFIEIGGQWISPDQT +RLI--SLVEELGLPTFS-----RFRDGRNVYVDPRGERHVYDGLDFPVAEKTDREMDRL-IAKIDELTAEIDAAAP-WEH +PRAAE--LDKISFRHWLEQQSDDPEAIDNVSIYIASGMLTKPSHTFSLLQALLMSASAGSFRNLVDEDFILDKR--VEGG +MQSVSLAMAAEL---GDDVVLGQPVRTLRWAEPDPSTADEKNGVAADVRNGVAHDGAAGDVVALTDDYEVHARYAVLAVP +PNLYSRISFEP-----PMPREQQIAHQHISMGLVIKVHAVYETPFWREEGLSGTCFGGGRLVQEIYDNTNRGENLAGGAP +GKEDPHGTLVGFVSDVYAEQMWALPEEERKAAILGAMAEYLGPRTLEPIAFFLSDMAAEEWTRGAYATSYDLGGLSRWGH +LQNRPTGPIHYACSDIAAE-----GYQHVDGAIRMGEAAALAIAEREATDAGQPTG +>GCF_003691675_PROKKA_00728 +MTTAPATAGRERRTSDVVVIGAGPAGLMAARTAKAQGLSVTVLEARRRVGGRTWNGLVEGADGKDHFIEIGGQWISPDQT +RLI--SLVEELGLPTFS-----RFRDGRNVYVDPRGERHVYDGLDFPVAEKTDREMDRL-IAKIDELTAEIDAAAP-WEH +PRAAE--LDKISFRHWLEQQSDDPEAIDNVSIYIASGMLTKPSHTFSLLQALLMSASAGSFRNLVDEDFILDKR--VEGG +MQSVSLAMAAEL---GDDVVLGQPVRTLRWAEPDPSTADEKNGVAADVRNGVAHDGAAGDVVALTDDYEVHARYAVLAVP +PNLYSRISFEP-----PMPREQQIAHQHISMGLVIKVHAVYETPFWREEGLSGTCFGGGRLVQEIYDNTNRGENPAGGAP +GEEDPHGTLVGFVSDVYAEQMWALPEEERKAAILGAMAEYLGPRTLEPIAFFLSDMAAEEWTRGAYATSYDLGGLSRWGH +LQNRPTGPIHYACSDIAAE-----GYQHVDGAIRMGEAAALAIAEREATDAGQPTG +>GCF_005280335_PROKKA_01874 +MTTAPATAGRERRTSDVVVIGAGPAGLMAARTAKAQGLSVTVLEARRRVGGRTWNGLVEGADGKDHFIEIGGQWISPDQT +RLI--SLVEELGLPTFS-----RFRDGRNVYVDPRGERHVYDGLDFPVAEKTDREMDRL-IGNIDELTAEIDAAAP-WEH +PRAAE--LDTISFRHWLEQESDDPEAIDNVSIYIASGMLTKPSHTFSMLQALLMAASAGSFRNLVDEDFILDQR--VEGG +MQSVSLAMAAEL---GDDVVLGQPVRTLRWTEPDPSTADEKNGVAADVRNGVAHDGDAGDVVALTDDYEVHARYAVLAVP +PNLYSRISFEP-----PMPREQQIAHQHISMGLVIKVHAVYETPFWREEGLSGTCFGGGRLVQEIYDNTNRGENLAGGAP +GEEDPHGTLVGFVSDVYAEQMWALPEEERKAAILGAMAEYLGPRTLEPIAFFLSDMAAEEWTRGAYATSYDLGGLSRWGH +LQNRPTGPIHYACSDIAAE-----GYQHVDGAIRMGEAAALAIAEREATDAGQPTG +>GCF_020097155_PROKKA_01230 +METP----------SDVIVVGAGLAGLVAARTLAEAGLSVRVLEREAEVGGRQRTRTVDG-----FVLDRGFQLVNPAYP +ELPRHADVDALGLRPFGAGVRVRTRRGLALLADPRREPR--------LAARTLRDGVRHGLLDARELAALSRWAAPALAA +PRVAKHRMDAPLIEAWDRAGVRGPLR-DAVLEPFLRGVLADPDLT-----------TSSRFTELLVRMFVLGTPGVPARG +VAALPEQLAARVRAAGTRVTTGASVTAVRPA---------ADGVVVDVAGGAP----------------LHARAAVLAVG +PEAFTGLLPEAATDRLPVP----------SRGLTTWWFRAPSAPA-RERFLAVDGTGSGPLVHTAV--------MTAAAP +GLS-PDGTPLVEATALLDPSAPAVTDAQARA------------------------HAARIW--GVDASDWDLLARDDVPH +ALPVQAAPLRLRAEARVAERVYAAGDHRDTASIQGALVSGRRVAERLLHELPR--- +>GCF_023573625_PROKKA_00957 +MTTAPATAGRERRTSDVVVIGAGPAGLMAARTAKAQGLSVTVLEARRRVGGRTWNGLVEGADGKDHFIEIGGQWISPDQT +RLI--SLVEELGLPTFS-----RFRDGRNVYVDPRGERHVYDGLDFPVAEKTDREMDRL-IAKIDELTAEIDAAAP-WEH +PRAAE--LDKISFRHWLEQQSDDPEAIDNVSIYIASGMLTKPSHTFSLLQALLMSASAGSFRNLVDEDFILDKR--VEGG +MQSVSLAMAAEL---GDDVVLGQPVRTLRWAEPDPSTADEKNGVAADVRNGVAHDGAAGDVVALTDDYEVHARYAVLAVP +PNLYSRISFEP-----PMPREQQIAHQHISMGLVIKVHAVYETPFWREEGLSGTCFGGGRLVQEIYDNTNRGENLAGGAP +GKEDPHGTLVGFVSDVYAEQMWALPEEERKAAILGAMAEYLGPRTLEPIAFFLSDMAAEEWTRGAYATSYDLGGLSRWGH +LQNRPTGPIHYACSDIAAE-----GYQHVDGAIRMGEAAALAIAEREATDAGQPTG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000872.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000872.fa new file mode 100644 index 0000000000000000000000000000000000000000..595b7f3d3bde1c84196b6cdffd326081d488640f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000872.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01035 +MTILPASPPPSVILLGGASGSGKSYLARQHGRPHLSLDAFYRPQSDDGAAGGPGPVFPRT +PYGEIDWDHPGTWDEQAAVDAVVELLEEGATRVPDYDISTSSVRGHSTVALEPDGVIVAE +GIFAERMPAALDRAEVHYAAWYIDQARTTTAARRFVRDVAERRKPVPFLVQRGWSLYRTD +AARRAAAMAAGFTPRRKREIIADLT- +>GCF_003691675_PROKKA_00748 +-----------MILLGGASGSGKSYLARQHGRPHLSLDAFYRPQSDDGAAGGPGPVFPRT +PYGEIDWDHPGTWDEQAAVDAVVELLEEGATRVPDYDISTSSVRGHSTVALEPGGVIVAE +GIFAERMPAALDRAGVRYAAWYIDQARTTTAARRFVRDVAERRKPVPFLVQRGWSLYRTD +AARRAAAVAAGFTPRRKREIIADLTA +>GCF_005280335_PROKKA_01849 +-----------MILLGGASGSGKSYLARRHGRPHLSLDAFYRPQSDDGAAGGPGPVFPRT +PYGEIDWDHPGTWDEQAAVDAVVELLEEGATRVPDYDISTSSVRGHSTVALEPGGVIVAE +GIFAERMPAALDRAGVGYAAWYIDQARTTTAARRFVRDVAERRKPVPFLVQRGWSLYRTD +AARRAAAVAAGFTPRRKREIIADLTA +>GCF_020097155_PROKKA_01739 +MTILPASPPPSVILLGGASGSGKSYLARRHGRPHLSLDAFYRPQSDDGAAGGPGPVFPRT +PYGEIDWDHPGTWDEQAAVDAVVELLEEGATRVPDYDISTSSVRGHSTVALEPGGVIVAE +GIFAERMPAALDRAGVGYAAWYIDQARTTTAARRFVRDVAERRKPVPFLVQRGWSLYRTD +AARRAAAVAAGFTPRRKREIIADLTA +>GCF_023573625_PROKKA_00977 +MTILPASPPPSVILLGGASGSGKSYLARRHGRPHLSLDAFYRPQSDDGAAGGPGPVFPRT +PYGEIDWDHPGTWDEQAAVDAVVELLEEGATRVPDYDISTSSVRGHSTVALEPGGVIVAE +GIFAERMPAALDRAGVRYAAWYIDQARTTTAARRFVRDVAERRKPVPFLVQRGWSLYRTD +AARRAAAVAAGFTPRRKREIIADLTA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000875.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000875.fa new file mode 100644 index 0000000000000000000000000000000000000000..6bd6202af2e1450544d77f2f4dde522cd6c41a31 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000875.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01039 +MCGRYVMARATSDLVALGDAE-ANEDLVLRQSWNVAPTAEVPILVAHADDVGAGGTRGGD +GGAGVTRRIHVARWGLVPPWAKELSVGSRAFNARSETVASKPTFRAAVRARRCAVPVEGY +YEWKTPEPGAKGPDGRIAKKQPYYVHPAGAGDGEGPVIWFAGLYEWWQDPEAKAAGEDAW +VLSTTILTMAAPDADDDDPVLAALGQLHDRLPVPMDAETMDRWLAPDTLGSAEEADALVG +QVCAGAYDVAAGWSLRPVGSAVGNVRNNGPELIQEMREQQGTLL +>GCF_003691675_PROKKA_00752 +MCGRYVMARATSDLVALGDAE-ANEDLVLRQSWNVAPTAEVPILVAHADDVGAGGARGGD +GGAGVTRRIHVARWGLVPPWAKELSVGSRAFNARSETVASKPTFRAAVRARRCAVPVEGY +YEWKAPEPGAKGPDGRAAKKQSYYVHPAGAGDGEGPVIWFAGLYEWWQDPEAKAAGEDAW +VLSTTILTMAAPDADDDDPVLAALGQLHDRLPVPMDAETMDRWLAPDTLGSAEEADALVG +QVCAGAYDVAAGWSLRPVGSAVGNVRNNGPELIQEMREQQGTLL +>GCF_005280335_PROKKA_01846 +MCGRYVMARAAGDLVALGGGELPDERLELRRSWNVAPTSDVPILLEREAD---------- +--GAVRRELHVARWGLVPSWAKELAVGSRAFNARSETVASKPTFRAAVRARRCAVPVEGY +YEWKAPAPGAKGPDGKAAKKQPYYVHPAGAGDGEGPVIWFAGLYEWWQDPEAEAAGRDPW +VLSTTILTMAAPDADDEDEVLGSLGDLHDRLPVPLDAETMDAWLTPGRLGSAEEADALVG +QVCAGAYDVAAGWVLRPVGTAVGNVRNDGPELIQAEEPAQGTLL +>GCF_020097155_PROKKA_01736 +------MARAAGDLVALGGGLLPEEGLELRPNWNVAPTADVPILLEREDA---------- +--GVVRRELHVARWGLVPTWAKELSVGSRAFNARSETVTSKPTFRSAVRARRCAVPVEGY +YEWKAPEPGSTGPDGKAAVKQPFYVHPAGGGDGEGPVIWFAGLYEWWKDAGAEARGDDPW +VLSTTILTMPSP-ADDEPGVLGELADLHDRLPMPMGPAAMDSWLSPDKLGSADEAAALVD +EMTAQAYDVARGWELRPVGRAVGNVRNNGPELIAPPAEVQDALL +>GCF_023573625_PROKKA_00981 +MCGRYVMARATSDLVALGDAE-TNEELVLRQSWNVAPTAEVPILVAHADDV--------- +-GAGVTRRIHVARWGLVPPWAKELSVGSRAFNARSETVASKPTFRAAVRARRCAVPVEGY +YEWKTPEPGAKGPDGRAAKKQPYYVHPAGAGDGEGPVIWFAGLYEWWQDPEAKAAGEDAW +VLSTTILTMAAPDADDDDPVLAALGQLHDRLPVPMDAETMDRWLAPDTLGSAEEADALVG +QVCAGAYDVAAGWSLRPVGSAVGNVRNNGPELIQEMREQQGTLL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000883.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000883.fa new file mode 100644 index 0000000000000000000000000000000000000000..85c9899f30b0cfa25b70239e10e64e292d6ccc80 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000883.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01050 +MTENHAVPAALAEIIDDFAGVPDPEKLELLLEFSDELPALPERYDGHEAEMEQVVECQTP +LFLAVELEG--EPGPQAPVRLFITAPPEAPTTRGFASVLTQGLDGLSALEVVDVPEDIPT +RLGLAKALTPLRLRGMSAMLGRIKRNVREQAGIA +>GCF_003691675_PROKKA_00763 +MTENHAVPAALAEIIDDFAGVPDPEKLELLLEFSDELPALPERYDGHEAEMEQVVECQTP +LFLAVELEG--EPGPQAPVRLFITAPPEAPTTRGFASVLTQGLDGLSALEVVDVPEDIPT +RLGLAKALTPLRLRGMSAMLGRIKRNVREQAGIA +>GCF_005280335_PROKKA_01836 +MTQNHAVPAALAEIVDDFAGVPDAEKLELLLEFADELPALPERYDGHEAEMEQVVECQSP +LFLAVELEGEDEPGPESVVRLFITAPPEAPTTRGFASVLSQGLDGLTARQIVDVPEDIPS +RLGLAKALTPLRLRGMSAMLGRIKRNVREQTGVA +>GCF_020097155_PROKKA_01726 +MTDT-AVPANLAEIVDDFAGVPDPQKLELLLEFSDELPALPERYAGHEDEMEQVVECQSP +LFLAVELED-GATGDDAVVRLFISSPPEAPTTRGFASVLTQGLDGCTARQVLAVPEDIPS +RLGLQKALTPLRLRGMSAMLGRIKRNVREQAGIA +>GCF_023573625_PROKKA_00991 +MTENHAVPAALAEIIDDFAGVPDPEKLELLLEFSDELPALPERYDGHEAEMEQVVECQTP +LFLAVELEG--EPGPQAPVRLFITAPPEAPTTRGFASVLTQGLDGLSALEVLDVPEDIPT +RLGLAKALTPLRLRGMSAMLGRIKRNVREQAGIA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000885.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000885.fa new file mode 100644 index 0000000000000000000000000000000000000000..b9e76ed0183c3de14f6bbdf3805ac37c06f72265 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000885.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01052 +MAQIVHLADRSPQVTPDQLLAGFHPSYRFGTVSFDTYIPDPAHPTQAQAVERLRRFAADL +G--RG-GSGGGFLGGLF-GGKKRAAGPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTF +VEYTNLVGALSFRKAVDELKEYTLVCIDEFELDDPGDTVLMSRLMRELADAGVRLVATSN +TLPGSLGEGRFAAQDFKREIQVLADQFEVIRVDGEDYRHRGLSAAPSPLDDAAVEATAQE +NFPDAGVLAVDDFADLTAMLSRVHPSRYRELVKDVDVLALHDVHTITEQATALRFVVFAD +RLYDKDVPVLASGVPFDALFTQEMMHGGYMKKYFRTVSRMTALVREGQTGVAEHK +>GCF_003691675_PROKKA_00765 +MAQIVHLADRSPQVTPDQLLAGFHPSYRFGTVSFDTYIPDPAHPSQAQAVERLRRFAADL +G--RG-GSGGGFLGGLF-GGKKRAAGPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTF +VEYTNLVGALSFRKAVDELKEYTLVCIDEFELDDPGDTVLMSRLMRELADAGVRLVATSN +TLPGSLGEGRFAAQDFKREIQVLADQFEVIRVDGEDYRHRGLSAAPSPLDDAVVEATAQE +NFPDAGVLAVDDFADLTAMLSRVHPSRYRELVKDVDVLALHDVHTITEQATALRFVVFAD +RLYDKDVPVLASGVPFDALFTQEMMHGGYMKKYFRTVSRMTALVREGQTGVAEHK +>GCF_005280335_PROKKA_01834 +MAQIVHLADRSPQVTPDQLLAGFHPSYRFGEVSFDTYIPDPAHPSQAQAVERLRRFAAAL +G--RGSGSGGGFLSGLFGGGRKRAAGPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTF +VEYTNLVGALSFRKAVDVLKEYTLVCIDEFELDDPGDTVLMSRLMRELADAGVHLVATSN +TLPGSLGEGRFAAQDFQREIQVLAEQFEVIRVDGEDYRHRGLSAAPDPLPDDQVVSTAEA +NFPDSGVLAVDDFDALTAMLSRVHPSRYRELVKDVDVIALHDVKTITEQATALRFVVFAD +RLYDKDVPVVASGVPFDDLFTQEMMHGGYMKKYFRTVSRMTALVREGQLGIAEEK +>GCF_020097155_PROKKA_01724 +MPQTVHLADRSPQVSADQLLAGLHPSYRFGEVSFDSYIPDPAHPSQAQAVERLRRFAASL +GGPRGGSGGGGFLGGLFGGGRKRGPEPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTF +VEYTNLVGALSFRQAVDVLKGYTLVCIDEFELDDPGDTVLMSRLMRELADAGVRLVATSN +TLPGSLGEGRFAAQDFKREIQVLADQFEVIRVDGEDYRHRGLSAAPEPLADDAVESTAQA +NFPHADVVSVDDFAALTAMLSRVHPSRYRELVKDVDVAAFHDVQTITEQATALRFVVFAD +RLYDKDVPVVASGVPFDQLFTSEMMHGGYMKKYFRTVSRMTALVREGQTGETVEK +>GCF_023573625_PROKKA_00993 +MAQIVHLADRSPQVTPDQLLSGFHPSYRFGTVSFDTYIPDPAHPSQAQAVERLRRFAADL +G--RG-GSGGGFLGGLF-GGKKRAAGPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTF +VEYTNLVGALSFRKAVDELKEYTLVCIDEFELDDPGDTVLMSRLMRELADAGVRLVATSN +TLPGSLGEGRFAAQDFKREIQVLADQFEVIRVDGEDYRHRGLSAAPSPLDDAAVEATAQE +NFPDAGVLAVDDFADLTAMLSRVHPSRYRELVKDVDVLALHDVHTITEQATALRFVVFAD +RLYDKDVPVLASGVPFDALFTQEMMHGGYMKKYFRTVSRMTALVREGQTGVAEHK + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000888.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000888.fa new file mode 100644 index 0000000000000000000000000000000000000000..edd32bdd0fbbc8cadfdc1b799e8afc96f3be54ab --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000888.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01059 +M------------TAPT-PLRVLYAGTPETAVPVLRALLDSPHEVVGVLTRPDAPVGRRR +VLTPSPVAVVAEEAR--LPVLKADRLRGPEGADALQAIRALEADVAVVVAYGALVPAEAL +QTPRHGWLNLHFSALPAYRGAAPVQRAVMAGETEIAADVFQLEEGLDTGPVFARLTRPVA +ADETAGTVLTDLAERGGPLVIDVLDRLADGTATATPQRGEPTHAPKLTAADGLVDPARPA +AEVAARINGVTPEPGAWGWL--TADDGAAPARFKLDGVAPVRAGDDGWPSVLDAAVPGQI +LVAAKAAWLRTAGGAVRLSRVQPAGRKLMPAADWARGAAAGAALLAGEALAHHEEQARRD +AAARAAARQAARNATEQDEEARA +>GCF_003691675_PROKKA_00778 +M------------TAPT-PLRVLYAGTPETAVPVLRALLDSPHEVVGVLTRPDAPVGRRR +VLTPSPVAVVAEEAR--LPVLKADRLRGPEGADALQAIRALEADVAVVVAYGALVPAEAL +QTPRHGWLNLHFSALPAYRGAAPVQRAVMAGETEIAADVFQLEEGLDTGPVFARLTRPVA +ADETAGAVLTDLAERGGPLVIDVLDRLADGTATATPQRGEPTHAPKLTAADGLVDPARPA +AEVAARINGVTPEPGAWGWL--TADDGAAPARFKIDGVAPVRPGDDGWPTALDAAAPGQI +LVAAKAAWLRTTDGAVRLSRVQPAGRKLMPAADWARGAAPGAALLAGEALAHHEDQARQE +AAARAAARQAARNATAQDEEARA +>GCF_005280335_PROKKA_01827 +M------------TATT-PLRVLYAGTPETAVPVLRALLDSPHEVVGVLTRPDAPIGRRR +VLTPSPVAVVAEEAG--VPVVKADRLRGPAGEPALEAVRALEPDVAVVVAYGALVPAEAL +ALPRHGWLNLHFSALPAYRGAAPVQRAVMAGEPEIAADVFQLEEGLDTGPVHARLTRAVA +PDETAGQILADLAERGGPLVLELLGRIADGTAAPRPQEGEPSHAPKLTAADGLVDPARPA +AEVAARINGVTPEPGAWGWL--TVGEGGEPARFKLDGVAPATPADADWPADLDAAPPGAL +RTAGRAAWLRTADGAVRLGRVQPAGKKLMPAADWARGAADGAALLAGEALAAHTARLGQE +AAARAARREAARETEAH-----A +>GCF_020097155_PROKKA_01717 +MSIPETALSPDAGSAPARSLRVLFAGTPEAAVPVLRALVGSAHEVAGVLTRTDAPVGRKR +VLTPSAVARAAAESAPDVPVLKADRLRGPEAAEVLEAIRALEADVAVVVAYGALVPAEAL +TIPAHGWLNLHFSHLPAYRGAAPVQRALMDGVERTGADVFQLEEGLDTGPVFARIGRDVA +PEDTAGDLLAALAEDGGPLVLEVLDALAAGEARSVPQTGEPTHAPKLTAADGLVDAAAGT +REVAARINGTTPEPGAWGWLVPAGEADAAPARLKLGGVVPTHPGEDGWPEAAEAAAPGAI +VAAGGTAWLRTAGGAVRLDQVQPAGKKPMSAADWARGLTAPVRLLAGDELAAHLAALDAE +AARRAAQQAAARAAQAGEG---A +>GCF_023573625_PROKKA_01006 +M------------TAPT-PLRVLYAGTPETAVPVLRALLDSPHEVVGVLTRPDAPVGRRR +VLTPSPVAVVAEEAG--LPVLKADRLRGPEGADALQAIRVLEADVAVVVAYGALVPVEAL +QIPRHGWLNLHFSALPAYRGAAPVQRAVMAGETEIAADVFQLEEGLDTGPVFARLTRPVA +ADETAGAVLTDLAERGGPLVIDVLDRLADGTATATPQRGEPTHAPKLTAADGLVDPARPA +AEVAARINGVTPEPGAWGWL--TADDGAAPARFKLDGVAPVSAGDDGWPSALDAAAPGQI +LVAAKAAWLRTAGGAVRLSRVQPAGRKLMPAADWARGAAAGAALLAGEALAHHEEQARRE +AAARAAAREAARNATAQDEEARA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000889.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000889.fa new file mode 100644 index 0000000000000000000000000000000000000000..6ce4db8bcdf7e4df13cbd76655ea8e49cd906c29 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000889.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_01060 +MSREGQ-------AGQ--------------------GRGERGA-----RGERGRAPRPD--PQDRRDAQGRTRNRGRSGA +GRKYSAQAPSQRSRTADPARRVAFGVVRSVHAEDAYANLVLPARIRQARLDRRDAGFATELAYGTLRGLGLYDAILTRCV +DRPLEQIDPPVLDALRLGAHQLLGMRVPAHAALDATVSLVRAEIGAGASGFVNAVLRRVAERPLEEWLADVAPADGGDAA +LAVRASHPVWIVRALRQALAAHRGTRHIADRDAELAALLEADNAPPVVNLVALPVAGGAEALAAALDDGAEPGPLAPDSA +LHSGGDAGRLPGVREGVLRVQDAGSQLTARALAQAPVPAAEGR------AERWLDLCAGPGGKAALLAALAAERGATLVA +NEVAPHRADLVRQALAAVPADAWTVRTGDGRTIA-DAPEAAPAFDRVLVDAPCTGLGALRRRPESRWRRTPADLAELTGL +QAELLDAAVSVLAPGGVLAYVTCSPHVAETVVQVQDLVRRHPELELLDARTALDTVALDDLRLDEAEP-----AGAPKPG +D-VVARTAQLWPHRHGTDAMFLALLRAPG----------A +>GCF_003691675_PROKKA_00779 +MSRERQ-------PGQ--------------------GRGERGA-----RGERGRAPRPD--AQDRRDAQGRTRNRGRSGA +GRKYSAQAPSQRSRTADPARRVAFGVVRSVHAEDAYANLVLPARIRQARLDRRDAGFATELAYGTLRGLGLYDAILTRCV +DRPLEKIDPPVLDALRLGAHQLLGMRVPAHAALDATVSLVRAEIGAGASGFVNAVLRRVAERPLEEWLADVAPADGGDAA +LAVRASHPVWIVRALRQALAAHRGTRHTADRDAELAALLEADNAPPVVNLVALPVAGGAEALAAALDDGAEPGPLAPDSA +LHSGGDAGRLPGVREGVLRVQDAGSQLTARALAQAPVPAAEGR------AERWLDLCAGPGGKAALLAALAAERGATLVA +NEVAPHRADLVRQALAAVPAGAWTVRTGDGRTIA-DAPEAAPAFDRVLVDAPCTGLGALRRRPESRWRRTPADLAELTGL +QAELLDAAVAVLAPGGVLAYVTCSPHVAETVVQVQDLVRRHPELELLDARTALDAVALDDLRLDEAEP-----AGAPEPG +D-VVARTAQLWPHRHGTDAMFLALLRAPG----------A +>GCF_005280335_PROKKA_01826 +MSGEGQGRQGRGRGGSGGGSRGGAGGGSRGGSRNGSGGGPRGGSHGGPRGGSGGARRES-GGEERRDAQGRTRSRGRSGA +GRRYSAQAPAQRSRTADPARRVAFEVIRAVHAEDAYANLVLPGRIRQARLDRRDAGFATELAYGTLRGIGLYDAVLARCV +DRPLEKIDPPVLDALRLGAHQLLAMRVPAHAALDATVALVRAEIGAGPSGFVNAVLRRVAERPLEDWLADVAPAEGGDAA +LAVRASHPVWIVRALRQALAAHRGTRHVADRDAELGALLEADNASPVVNLVALPVPGGREGLSAALEDGAEPGPLAPDSA +LHAGGDAGRLTGVREGVLRVQDAGSQLTARALAAAPAAAAEGR------PERWLDLCAGPGGKAALLAALAAERGATLVA +NEVAEHRAELVRQALGAVPAAAWTVRAGDGRAIA-DAPEAAGGFDRVLVDAPCTGLGALRRRPESRWRRTPADLAELTGL +QSELLDAAAAVLAPGGVLAYVTCSPHVAETTVQVQDLLRRRPELELLDAGAVLSEVALGDLRLDEGEPGGDEAAGAAAPD +D-VAARTAQLWPHRHGTDAMFLALLRAPSDTPESPERTRG +>GCF_020097155_PROKKA_01716 +MSAGQDGSTGRG-AGQG-------------------GRGRGGA-----EGRQGPGGRQGAGGQDRRDAQGRQLNRGASGT +GRHRTTLAPKERARRADPARRVAFEVVRAVHAEDAYANLVLPARIRQGRLDRRDAGFATELTYGTLREQGLYDAVLARCV +DRALDALDAPVLDALRLGAHQLLGMRVPAHAALDATVALVRAEVGAGPAGFVNAVLRRVSERPREDWLAEVAPADGGDTA +RAVRHSHPAWIVRALRQALAGHPGTADVEDRDAELEALLVADNAAPVVNLVGLPVPGGREALASALGDGAEPHPLTPDAA +LHAGGDAGRLPGVREGVLRVQDAGSQLTARALAA--VPAASGRDAGGRKAERWLDLCAGPGGKAALLAALASERGATVLA +NEVAPHRADLVRSALAGVPASAWEVRTGDGRTIAEDAP--AGGFDRILVDAPCTGLGALRRRPESRWRRTPADLAELTGL +QAELLDAAVGVLAPGGVLAYVTCSPHVAETLVQVQDLLRRHPVLEQLDAPAALQDVAVADLGL-----------AAPEDA +DPVLARTAQLWPHRHGTDAMFLALFRAPV----------A +>GCF_023573625_PROKKA_01007 +MSRERQ-------PGQ--------------------GRGERGA-----RGERGRAPRPD--PQDRRDAQGRTRNRGRSGA +GRKYSAQAPSQRSRTADPARRVAFGVVRSVHAEDAYANLVLPARIRQARLDRRDAGFATELAYGTLRGLGLYDAILTRCV +DRPLEKIDPPVLDALRLGAHQLLGMRVPAHAALDATVSLVRAEIGAGASGFVNAVLRRVAERPLEEWLADVAPADGGDAA +LAVRASHPVWIVRALRQALAAHRGTRHIADRDAELAALLEADNAPPVVNLVALPVAGGAEALAAALDDGAEPGPLAPDSA +LHSGGDAGRLPGVREGVLRVQDAGSQLTARALAQAPVPAAEGR------AERWLDLCAGPGGKAALLAALAAERGATLVA +NEVAPHRADLVRQALAAVPADAWTVRAGDGRTIA-DAPEAAPAFDRVLVDAPCTGLGALRRRPESRWRRTPADLAELTGL +QAELLDAAVAVLAPGGVLAYVTCSPHVAETVVQVQDLVRRHPELELLDARTALDAVALDDLRLDEAEP-----AGAPKPG +D-VVARTAQLWPHRHGTDAMFLALLRAPG----------A diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000901.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000901.fa new file mode 100644 index 0000000000000000000000000000000000000000..9317fe4c8520fc411b0af2ae91350ca0bc5ee606 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000901.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01085 +M--SVLQEIIDGVREDLEPRRRALPEARLSELVAATPAPRDAHAALHGGRTDPAGIRVIS +EVKRASPSKGALAEIPEPATLARAYERGGASAVSVLTEARRFGGSLADLDAVRAAVDLPV +LRKDFTVTEYQIHEARAHGADLVLLIVAALDDAELAGFLQLTESLGMHALVEAHTPEEIE +RGVAAGARILGVNVRNLKTLDVDPARYAALADGLPEDVVRVAESGVESEEQIKAYAAAGA +DVVLVGEALVRHGAPEEALRAFRAASLTVR +>GCF_003691675_PROKKA_00804 +M--SVLQEIIDGVREDLEPRRRALPEARLAELVAAAPAPRDAHAALHGGRTDPAGIRVIS +EVKRASPSKGALAEIPEPATLARAYERGGASAVSVLTEARRFGGSLADLDAVRAAVDLPV +LRKDFTVTEYQIHEARAHGADLVLLIVAALDDAELAGFLQLTESLGMHALVEAHTPEEIE +RGVAAGARILGVNVRNLKTLDVDPARYAALADGLPEDVVRVAESGVESEEQIKAYAAAGA +DVVLVGEALVRHGAPEEALRAFRAASLTVR +>GCF_005280335_PROKKA_01812 +M--SVLQEIIDGVREDLAPRRRDVPEARLAELVAAAPAPRDAHAALLGGRTDPAGIRVIS +EVKRSSPSKGALAEIPEPAALARAYERGGASAVSVLTEARRFGGSLADLDAVRGAVDLPV +LRKDFTVTEYQIHEARAPGADLVLLIVAALDDAELTGFLQLTESLGMHALVEAHTPEEIE +RGVTAGARILGVNVRNLKTLDVDPARYAALADGLPEDVVRVAESGVESDEQIKAYAAAGA +DAVLVGEALVRHGAPEEALRAFRAASLTVR +>GCF_020097155_PROKKA_01700 +MPETVLDSIVAGVLEDLAPRREAVPEARLQELIAQAPAPRDAYAALRDGRSDPAGIHVIA +EVKRRSPSKGALAEITEPAALAASYADGGAGAISVLTEQRRFGGSLADLDAVRAAVARPV +LRKDFTVTEYQILEARAHGADLVLLIVASLDDARLRGFRELAESLGMHALVEAHTSEEIA +RGVDSGARILGVNVRNLKTLDVDPDRYAALAGDLPEDVVRVAESGVESEAQVRQYAAAGA +DAILVGEALVRHGAPADALRAFRAASLTVR +>GCF_023573625_PROKKA_01034 +M--SVLQEIIDGVREDLEPRRRALPEARLAELVAAAPAPRDAHAALHGGRTDPAGIRVIS +EVKRASPSKGALAEIPEPATLARAYERGGASAVSVLTEARRFGGSLADLDAVRAAVDLPV +LRKDFTVTEYQIHEARAHGADLVLLIVAALDDAELAGFLQLTESLGMHALVEAHTPEEIE +RGVAAGARILGVNVRNLKTLDVDPARYAALADGLPEDVVRVAESGVESEEQIKAYAAAGA +DVVLVGEALVRHGAPEEALRAFRAASLTVR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000904.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000904.fa new file mode 100644 index 0000000000000000000000000000000000000000..3e6451d96d5500db927f67a6a6033d021203e227 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000904.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01088 +MTALASLASPAALAPLAAFPAPGWDGFQLGPVKIHAYALCIILGIVLALWLAERRWRARG +GPEDRVLDIALWAIPFGFVGGRLYHVFSSPDRYFGPGFDGTGDPIQILYVWNGGLGIWGA +IALGAVGAWIACRRYGLRLTAFGDVVAPGILLAQAIGRWGNWFNQELFGGPTTLPWGLEV +DPASPNFPAGYAPDTLFHPTFLYECLWNLAGVALLLLVDRALHLRHGLMLWSYVAWYTAG +RTWIEMLRIDDAEMVTLFGVTQRLNVWTSLLVFVIALAFIVGILLRHRGAAAGPHAHQSV +WRAGHAPEGDDGV-----AVAAGR-----SGSHA---VGAAEDDAVRR +>GCF_003691675_PROKKA_00807 +MT--------AALAPLAAFPAPGWDGFQLGPVKIHAYALCIILGIVLALWLAERRWRARG +GPEDRVLDIALWAIPFGFVGGRLYHVFSSPDRYFGPGFDGTGDPIQILYVWNGGLGIWGA +IALGAVGAWIACRRYGLRLTAFGDVVAPGILLAQAIGRWGNWFNQELFGGPTTLPWGLEV +DPASPNFPAGYAPDTLFHPTFLYECLWNLAGVALLLLVDRALHLRHGLMLWSYVAWYTAG +RTWIEMLRIDDAEMVTLFGVTQRLNVWTSLLVFVIALAFIVGILLRHRGAAAGPHAHQSV +WRAGHAPEGDDGA-----AVAAGR-----SGSHA---VGAAEDDAVRR +>GCF_005280335_PROKKA_01808 +-------------------------------MKIYAYALSIILGIVLALWLAERRWKARG +GPEGRVLDVALWAIPFGFVGGRLYHVFSSPDRYFGPGFDGTGDPVQILHVWNGGLGIWGA +IALGAVGAWIACRRYGLRLSAFGDVVAPGILLAQAVGRWGNWFNQELFGRPTTAPWGLRV +DADHPNFPDGVAPDTLFHPTFLYESLWCLLGVAVLLLADRRWRLRRGAMVWAYVAWYTAG +RVWIETLRIDDAELVTLFGLTQRLNVWTSIVMLLLALVMLAVILVKHGPAAAGPRSDDSV +WLPGRGPALEAGAGAPVDAAVAGQGPDDGAGSTA---AGVRED----R +>GCF_020097155_PROKKA_01697 +MGS-------GALTPLAAFPAPVWDGFELGPMKIHAYALCIIAGIVVALWLSGRRWADRG +GPEGRVLDIALWAIPFGFVGGRLYHVFSSPDLYFGPGYDGTGDPIKILYVWNGGLGIWGA +IALGAVGAWIACRRYGLRLTAFADVVAPGVLLAQAIGRWGNWFNQELFGGPTTLPWGLTV +DPASPNFPAQYAPGTLFHPTFLYESLWNLLGVAVLLLVDRRLHLRHGAMLWSYVAWYTAG +RTWIEMMRIDDAELVTLFGVTQRLNVWTSLLMFAIALAFLIGILLRHRGAAAGPHARQSV +WRDGHGPVGEDVEGAGPAAAPAVRTTQGGSGSHAWDDVGA-------- +>GCF_023573625_PROKKA_01037 +MT--------AALAPLAAFPAPGWDGFQLGPVKIHAYALCIILGIVLALWLAERRWRARG +GPEDRVLDIALWAIPFGFVGGRLYHVFSSPDRYFGPGFDGTGDPIQILYVWNGGLGIWGA +IALGAVGAWIACRRYGLRLTAFGDVVAPGILLAQAIGRWGNWFNQELFGGPTTLPWGLEV +DPASPNFPAGYAPDTLFHPTFLYECLWNLAGVALLLLVDRALHLRHGLMLWSYVAWYTAG +RTWIEMLRIDDAEMVTLFGVTQRLNVWTSLLVFVIALAFIVGILLRHRGAAAGPHAHQSV +WRAGHAPEGDDGA-----AVAAGR-----SGSHA---VGAAEDDAVRR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000933.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000933.fa new file mode 100644 index 0000000000000000000000000000000000000000..5eb6a66fdadd16f784690fa732a1ab96f812b50d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000933.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01124 +MTKIAINGYGRIGRNIVRVLRDRGHENLELVAVNDLADPEDLFWLTQYDTILGRYPGELE +RTEKGFRIDGRDVAFFQEADPTKLPWGELGVDLVIECTGIFTTGPKAQAHLDAGAKKVLI +SAPAKEVDGTFVMGVNEHTYDAESMHIVSNASCTTNCLAPMAKVLNDEFGIVDGIMTTIH +AYTGDQNLHDNVHKKDRRRARAAAQNMVPTSTGAAKAIGEVIPELKGKLDGFAMRVPTIT +GSATDLTVELTRHVEVEEINAAFKKAAESGPLQGRLVYSEDPIVSSDIITSPAACTFDAP +LTKSIGQTVKIIGWYDNEYGYTSQLMDFADLIGSKL +>GCF_003691675_PROKKA_00843 +MTKIAINGYGRIGRNIVRVLRDRGHEGLELVAVNDLADPEDLFWLTKYDTILGRYPGELE +RTEKGFRIDGRDVAFFQEADPTKLPWGELGVDLVIECTGIFTTGPKAQAHLDAGAKKVLI +SAPAKEVDGTFVMGVNEHTYDAETMHIVSNASCTTNCLAPMAKVLNDEFGIVDGIMTTIH +AYTGDQNLHDNVHKKDRRRARAAAQNMVPTSTGAAKAIGEVIPELKGKLDGFAMRVPTIT +GSATDLTVELTRHVEVEEINAAFKKAAESGPLQGRLVYSEDPIVSSDIITSPAACTFDAP +LTKSIGQTVKIIGWYDNEYGYTSQLMDFADLIGSKL +>GCF_005280335_PROKKA_01769 +MTKIAINGYGRIGRNIVRVLRDRGYENLELVAVNDLADNEDLFWLTQYDTILGRYPGELE +LTETGFRIDGRDVAFFSEPDPAKLPWGELGVDIVIECTGFFTTGPKAKAHLDAGAKKVLL +SAPGKEVDGTFVMGVNEKNYDSATMDIVSNASCTTNCLAPMAKILNDEFGIVDGIMTTIH +AYTGDQNLHDSVHKKDRRRARAAAQNMVPTDTGAAKAIGEVIPELKGKLDGFAMRVPTIT +GSATDLTVELTRHVEVEEINAAFKKAAESGPLQGRLVYSEDPIVSSDIITSPAACTFDAP +LTKSIGQTVKIIGWYDNEYGYTSQLVDFADLIGSKL +>GCF_020097155_PROKKA_01662 +MTKIAINGYGRIGRNAVRVLLEQGHDDLELVAVNDLAATEDLFWLTKYDTILGRFPGELE +LTDKGFSINGKDVAFFAETDPANLPWGELGVDIVVECTGRFTTGPAAKAHLDAGAKKVLL +SAPGKEVDGTFVMGVNEGDYDSSTMHIVSNASCTTNCLAPMVKVLNDEFGIVDGIMTTIH +AYTGDQNLHDNVHKKDRRRARAAAQNMVPTSTGAAKAIGEVIPELKGKLDGFAMRVPTIT +GSATDLTVELTRHVEAEEVNEAFRRAAESGPLVGRLVYSTDPIVSSDIVTAPAACTFDAP +LTKSIGQTVKVIGWYDNEYGYTCQLMDMASHMASKL +>GCF_023573625_PROKKA_01074 +MTKIAINGYGRIGRNIVRVLRDRGHENLELVAVNDLADPEDLFWLTQYDTILGRYPGELE +RTEKGFRIDGRDVAFFQEADPTKLPWGELGVDLVIECTGIFTTGPKAQAHLDAGAKKVLI +SAPAKEVDGTFVMGVNEHTYDAETMHIVSNASCTTNCLAPMAKVLNDEFGIVDGIMTTIH +AYTGDQNLHDNVHKKDRRRARAAAQNMVPTSTGAAKAIGEVIPELKGKLDGFAMRVPTIT +GSATDLTVELTRHVEVEEINAAFKKAAESGPLQGRLVYSEDPIVSSDIITSPAACTFDAP +LTKSIGQTVKIIGWYDNEYGYTSQLMDFADLIGSKL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000940.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000940.fa new file mode 100644 index 0000000000000000000000000000000000000000..7e2e7d7b005df553634fab189132a3d6a0d7de65 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000940.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01131 +MSTPQNPNTAALAQAGVSIWLDDLSRTRLDEGTLEELIATRSVTGVTTNPSIFAVALADA +GAYQGQLRDLAAAGASVDEAVVALTTEDVRRAADVLAPVHERTGGADGFVSLEVDPRLAR +DAAGTVAQARELAAAVDRPNLMVKIPATVEGLSAIADVLGAGISVNVTLIFSLPRYRRVL +NAWLTGLEKARANGHDVRRLHSVASFFVSRVDTEVDARLRAI---GTPEAEALTGRAAVA +NARLAYRAFEQALDSERWRLLEAAGAPVQRPLWASTGVKDPALPDTLYVTELVAPHTVTT +LPEKTLEAVADHGVIAADTVTGAYAEADALLDAVGAAGVSYQDVVDVLETEGLEKFEAAW +DELLGSVRSGLDAHR +>GCF_003691675_PROKKA_00850 +MSTPQNPNTAALAQAGVSIWLDDLSRTRLDEGTLEELIATRSVTGVTTNPSIFAVALADA +GAYQGQLRDLAAAGASVDEAVVALTTEDVRRAADVLAPVHERTGGADGFVSLEVDPRLAR +DAAGTVAQARELAAAVDRPNLMVKIPATVEGLSAIADVLGAGISVNVTLIFSLPRYRRVL +NAWLTGLEKARANGHDVRRLHSVASFFVSRVDTEVDARLRAI---GTPEAEALTGRAAVA +NARLAYRAFEQALDSERWRLLEAAGAPVQRPLWASTGVKDPALPDTLYVTELVAPHTVTT +LPEKTLEAVADHGVIAADTVTGAYAEADALLDAVGAAGVSYQDVVDVLETEGLEKFEAAW +DELLGSVRSGLDAHR +>GCF_005280335_PROKKA_01761 +MSTQQNPNTAALAEAGVSIWLDDLSRKRLDEGTLEELMATRSVTGVTTNPSIFAVALADA +GSYEGQLRELAAAGADVDEAVTALTTQDVRRAADVLAPVHERTGGADGFVSLEVDPRLAR +DAEGTARQAQELAAAVDRPNLMVKIPATVEGLAAITDVLAEGISVNVTLIFSLPRYRQVL +NAWLAGLEKARENGHDLSRIHSVASFFVSRVDTEVDARLRAL---GTPEAEALTGQAALA +NARLAYRAFEQALDSERWRLLEAAGAPVQRPLWASTGVKDPALPDTLYVTGLVAPRTVTT +LPEQTLEAVADHGEVAGDTVTGGYAEADALLDAVGAAGVSYQDVVDVLETEGLQKFESAW +EELLGSVRDGLAAHR +>GCF_020097155_PROKKA_01655 +MTTETTPATAALAAAGVSLWLDDLSRTRLNEGSLERLIATRNVTGVTTNPSIFAAALKDA +GAYEAQLAELAAAGADVDAAVTALTTTDVRRACDLLAPVHQETGGRDGYVSIEVDPRLAR +DTAGTVAQARELVALVDRPNLMVKIPATVEGLPAITEVLGAGISVNVTLIFSLPRYREVL +NAWLSGLELARANGHDVSRIHSVASFFVSRVDTDVDAQLRALAEQGRPEAGELTGRAGLA +NARLAYRAFEQMKDTERWSLLEAAGAPVQRPLWASTGVKDPALADTLYVTALVAPDTVNT +MPEKTLEAYADHGELTAEPVVGGYAQADADLDAIGELGISYTELVDRLETEGLQKFEAAW +DELLASVRAGLAAHR +>GCF_023573625_PROKKA_01081 +MSTPQNPNTAALAQAGVSIWLDDLSRTRLDEGTLEELIATRSVTGVTTNPSIFAVALADA +GAYQGQLRELAAAGASVDEAVVALTTEDVRRAADVLAPVHERTGGADGFVSLEVDPRLAR +DAAGTVAQARELAAAVDRPNLMVKIPATVEGLSAIADVLGAGISVNVTLIFSLPRYRRVL +NAWLTGLEKARANGHDVRRLHSVASFFVSRVDTEVDARLRAI---GTPEAEALTGRAAVA +NARLAYRAFEQALDSERWRLLEAAGAPVQRPLWASTGVKDPALPDTLYVTELVAPHTVTT +LPEKTLEAVADHGVIAADTVTGAYAEADALLDAVGAAGVSYQDVVDVLETEGLEKFEAAW +DELLGSVRSGLDAHR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000949.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000949.fa new file mode 100644 index 0000000000000000000000000000000000000000..8f11e0bb27ea17fbb4728117ecbcf6160537d3df --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000949.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01140 +MATLQITDLHVQIATENGPKEILKGLSLTIETGETHAIMGPNGSGKSTLASTIAGHPRYE +VTSGSITLDGEDVLEMGVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTALDGEAPSLR +TWTKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV +DALRIVSEGVNRAQAQNEMGTLLITHYTRILNYIKPDHVHVLVDGRVAESGGPELAEQLE +AEGYARFEKAAAGA +>GCF_003691675_PROKKA_00859 +MATLQITDLHVQIETENGPKEILKGLSLTIETGETHAIMGPNGSGKSTLASTIAGHPRYE +VTSGSITLDGEDVLEMSVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTALDGQAPSLR +TWTKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV +DALRIVSEGVNRAQAQNEMGTLLITHYTRILNYIKPDHVHVLVDGRVAESGGPELAEQLE +AEGYARFEKAAAGA +>GCF_005280335_PROKKA_01752 +MATLQITDLHVQIETENGPKEILKGLSLTIETGQTHAIMGPNGSGKSTLASTIAGHPRYE +VTSGSITLDGEDVLEMGVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTALDGEAPSLR +TWTKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV +DALRIVSEGVNRAAEQNEMGTLLITHYTRILNYIKPDHVHVLVDGRVAESGGPELAAQLE +AEGYARFEKAAAGV +>GCF_020097155_PROKKA_01646 +MATLQITDLHVQIETENGPKEILKGLSLTINTGETHAIMGPNGSGKSTLASTIAGHPRYE +VTSGSITLDGEDVLEMSVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTAIDGEAPSLR +TWSKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV +DALRIVSEGVNRAAEANEMGTLLITHYTRILNYIKPQHVHVLVDGRVAESGGPELAARLE +SEGYARFEKAAAEA +>GCF_023573625_PROKKA_01090 +MATLQITDLHVQIATENGPKEILKGLSLTIETGETHAIMGPNGSGKSTLASTIAGHPRYE +VTSGSITLDGEDVLEMGVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTALDGQAPSLR +TWTKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV +DALRIVSEGVNRAQAQNEMGTLLITHYTRILNYIKPDHVHVLVDGRVAESGGPELAEQLE +AEGYARFEKAAAGA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000960.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000960.fa new file mode 100644 index 0000000000000000000000000000000000000000..6e3342c623c303a4c0be3326729bf85ef1196665 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000960.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01154 +---MTTLHGEYKVIGGKLVAADLSLADGRIATASINGDFYLEPDEALEDLNAAVAGLSAD +AEHRVIREAVERGLRPEAELFGVDAFAVASAVRRALGKATTWGDHEWEVIGPEPMPIALT +VALDEVLTRQVAEGRRKPTMRLWQWNEPAVVIGAFQSLANEVDPEGARRHGINVVRRISG +GGAMFMEADNCVTYSMHVPSSLVDGLETAESYPFLDEWTMDALSRLGVHAFYQPLNDIAT +DQGKIGGAAQKRVGTAGLLHHVTMSYDIDADKMLEVLRIGREKLRGKGVTSAKKRVDPLR +RQTGVSRAEIWETMMTTFEERYGARRVELDEATREEAEQLARTKFATPEWTARVP +>GCF_003691675_PROKKA_00873 +---MTTLHGEYKVIGGKLVAADLSLADGRIATASINGDFYLEPDEALEDLNAAVAGLSAD +AEHRVIREAVERGLRPEAELFGVDAFAVASAVRRALGKATTWGDHEWEVIGPEPMPIALT +VALDEVLTRQVAEGRRKPTMRLWQWNEPAVVIGAFQSLANEVDPEGARRHGINVVRRISG +GGAMFMEADNCVTYSMHVPSSLVDGLETAESYPFLDEWTMDALSRLGVHAFYQPLNDIAT +DQGKIGGAAQKRVGTAGLLHHVTMSYDIDADKMLEVLRIGREKLRGKGVTSAKKRVDPLR +RQTGVSRAEIWETMMTTFEERYGARRVELDEATREEAEQLARTKFATPEWTARVP +>GCF_005280335_PROKKA_01736 +---MTTHHGEYKVIGGKLVAADLTIDDGRIAAASINGDFFLEPDEALEDLNAAVTGLSAD +AEHRVIQAAVEAGLREDAELFGVDAHAIATAVRRALGKATTWEDHEWEIIPPEPLPIALT +VALDEVLTRQVAEGRRRPTMRLWQWNEPAVVIGAFQSLANEVDPEGASRHGINVVRRISG +GGAMFMEADNCVTYSLHVPRSLVDGLETAESYPFLDEWTMDALSRLGVQAFYQPLNDIAT +DQGKIGGAAQKRVGQDGLLHHVTMSYDIDADKMLEVLRIGREKLKGKGVASAKKRVDPLR +RQTGVARPEIWETMMATFEERYGARRVELDDATRAEAEELARTKFGTQEWTARVP +>GCF_020097155_PROKKA_01632 +MSTQTTHHGEFKVLGGKLVAADLEVQDGVIVRASVNGDFFLEPDDALEDINAALTGLPAD +TEHHVLAERVRAGLRPEARLFGFDAEAVATAVRRAVGLATTWESHRWEILPPEPLPIEMN +TALDQILTEDVAAGRRNPVMRLWQWTEPAVVIGAFQSLANEVDPDGVTRHGIHVVRRVSG +GGAMFMEADNCVTFALSAPASLVDGIDTAESYPFLDEWVMEALRELGVQAFYQPLNDIAT +DQGKIGGAAQKRFGATGLLHHVTMSYDIDADKMTEVLRIGREKLRGKGVASAKKRVDPLR +RQTGVPREQIWETMMAVFERRYGARRVELDADTRARAEELARTKFSSPEWTARVP +>GCF_023573625_PROKKA_01104 +---MTTLHGEYKVIGGKLVAADLSLADGRIATASINGDFYLEPDEALEDLNAAVAGLSAD +AEHRVIREAVERGLRPEAELFGVDAFAVASAVRRALGKATTWGDHEWEVIGPEPMPIALT +VALDEVLTRQVAEGRRKPTMRLWQWNEPAVVIGAFQSLANEVDPEGARRHGINVVRRISG +GGAMFMEADNCVTYSMHVPSSLVDGLETAESYPFLDEWTMDALSRLGVHAFYQPLNDIAT +DQGKIGGAAQKRVGTAGLLHHVTMSYDIDADKMLEVLRIGREKLRGKGVTSAKKRVDPLR +RQTGVSRAEIWETMMTTFEERYGARRVELDEATREEAEQLARTKFATPEWTARVP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000961.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000961.fa new file mode 100644 index 0000000000000000000000000000000000000000..4060aaeecb7bf12a22af0cb8571bbb99a4a7e7b5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000961.fa @@ -0,0 +1,65 @@ +>GCF_002008305_PROKKA_01156 +M--TDTTPDLDATNVTRAEAADRSRLLTVQDYVVDVDLSDARDAAADTYPVRTVIRFACAEPGAQTHLDWIHGGVESVAL +NGTALDVAEVVGEARVLLPDLAAQNVVELVGRSVYSRSGEGLHRFTDPADGEVYLYTQYEPADARRVFPDFEQPDLKAAF +TFSLTGPEDWVLASNRPEVSRTPTGDGVVRVEFAPTLPQSTYITTLLAGPYAQWEDAWDGHPASGAQAVPLRLFTRRTMA +DAFDPEAVFDVTKRGLTFFHDLFGVAYPWGKYDQAFVPEYNLGAMENPGLVTFTEDFVFTSRATAVQYEGRANVILHEMA +HMWFGDLVTMHWWDDLWLKESFADYMGALGVDEATDFRTAWVTFASRRKAWAYVQDQMPTTHPIVADIVDLEAARQNFDG +ITYAKGASVLKQLAAYVGRDAFLDAAHRYFAAHAWGNASLADFMAVLEAASGRDMRAWADAWLHTSGVPRLRVDVDGD-A +PVLRQEGADPVTGGPILRPHVLKVGVFTPGQDGVLRRTAQVTADVPGGAEGAAVPLPDLEVPGGVRLVLPNDEDLTYAAV +ALDAGSLRAALTHPIADPLAEATVWAALWSMTRDGELPVARFLDAVATLSARIATVGVHAQVLAQAAAAVGQYARAEDRD +ALRSRLGEVLAEQTRTLEAGSDRQRTAARTWATLARADVGMAAALEAALLG--------EDAAAFAPGLAVDAELRWLVL +QALAATGRADQDRLDAELEAGRTAQTVTWHRLAAAARPEAEVKAAAWEAVMSGRTTTGTELSNDLLSATAAGFAAGGVEL +LAPYESGFWPRLTSVWASRSNGLASRAIGGLFPGRQDAVAGGADAQESHPTLAAAQRWLDEHPDAPGALRRLVVEHTDAL +RRSLRVQAVQPAG +>GCF_003691675_PROKKA_00875 +M--TDTTPDLDATNVTRAEAADRSRLLTVQDYVVDVDLSDARDAAADTYPVRTVIRFACAEPGAQTHLDWIHGGVESVTL +NGTALDVAEVVGEARVLLPDLAAQNVVELVGRSVYSRSGEGLHRFTDPADGEVYLYTQYEPADARRVFPDFEQPDLKAAF +TFSLTGPEDWVLASNRPEVSRTPTGDGVVRVEFAPTLPQSTYITTLLAGPYAQWEDAWDGHPASGAQAVPLRLFTRRTMA +DAFDPEAVFDVTKRGLTFFHDLFGVAYPWGKYDQAFVPEYNLGAMENPGLVTFTEDFVFTSRATAVQYEGRANVILHEMA +HMWFGDLVTMHWWDDLWLKESFADYMGALGVDEATDFRTAWVTFASRRKAWAYVQDQMPTTHPIVADIVDLEAARQNFDG +ITYAKGASVLKQLAAYVGRDAFLDAAHRYFAAHAWGNASLADFMAVLEAASGRDMRAWADAWLHTSGVPRLRVDVDGD-A +PVLRQEGADPVTGGPILRPHVLKVGVFTPGQDGVLRRTAQVTADVPGGAEGAAVPLPDLEVPGGVRLVLPNDEDLTYAAV +ALDAGSLRAALTHPIADPLAEATVWAALWSMTRDGELPVARFLDAVATLSARIATVGVHAQVLAQAAAAVGQYARAEDRD +ALRSRLGEVLAEQTRTLEAGSDRQRTAARTWATLARADVGMAAALEAALLG--------EDAAAFAPGLAVDAELRWLVL +QALAATGRADQDRLDAELEAGRTAQTVTWHRLAAAARPEAEVKAAAWEAVMSGRTTTGTELSNDLLSATAAGFAAGGVEL +LAPYESGFWPRLTSVWASRSNGLASRAIGGLFPGRQDAVAGGADAQESHPTLAAAQRWLDEHPDAPGALRRLVVEHTDAL +RRSLRVQAVQPAG +>GCF_005280335_PROKKA_01733 +MPRPHAAVDLDATNVTRAEAAERSRLLTVSAYEVHVDVSGARDEAAETYPVEATLRFVCAEPGAAAHVDWIHAGVDAVVL +NGRELEPADVVGDARILLPELAAENELVLRGRSRYSRSGEGLHRFTDPADGQVYLYTQYEPADARRVFPDFEQPDLKAAF +TFALTGPADWVLASNRPEASRTEVRPGVVRVDFEPTLPQSTYITTLLAGPYASWEDRWDGHAGTDAPAVPLRLFTRQTMA +EAFDPEAVFDVTRRGLDLFHELFGVPYEWGKYDQAFVPEYNLGAMENPGLVTFTEDFVFTSRATAAQYEGRANVILHEMA +HMWFGDLVTMRWWDDLWLKESFADFMGTLGVDEATDFETAWVTFASRRKAWAYVQDQMPTTHPIVADIVDLEAARQNFDG +ITYAKGASVLKQLAAYVGRDAFLDAARRYFRAHAWGNAELTDFMAALEAASGRDMGAWADAWLHTSGVPRLRVEAGDDGA +SMLHQEGADPVTGRPVLRPHALKVGVFTPDEAGVLRRTAQVAADVPGGADGAAVVLEGLTVPAGVRLVLPNDEDLTYAAL +ALDEASLQAALTHPIADPLAEATVWAALWSMTRDGELSAARFLEAVERLSAGIETVGVHTQVLAQAAAAVSQFAAAADRP +SLRARLAETLAEQVRTLEAGSDRQRTAARTWALVARADADLARPLAAALLGGTGAGAADGEAGEDAPGLAVDAEIRWLVL +QALAATGQADEARLDAELAAGRTAQTVTWHRLATAARPEPAVKAAAWEAVMAGRTADGVELSNDLLSATAAGFAAGDVEL +LAEHEAGFWPRLEQVWASRSNGLASRAIGGLFPGHQDAVAGDAGAQESHPTLASAQRWLDEHPDAPGALRRLVVEHTDHL +RRSLRVQAAQPTA +>GCF_020097155_PROKKA_01631 +M--------TDSPTLTRDEARARARLITVHDYDVHVDVSGAADASAAAYPVTATIRFDCAEPGAETWLDWISASVESVEL +NGEALDPAVVASRSRVRLPDLAAQNTVTLRGTSLYSRSGEGLHRFVDPADGRTYLYTQYEPADARRVFPDFEQPDLKASF +TFRLTGPADWVLASNGAEVGREDAGEGAVTVAFAPTRRLSTYITALVAGPYAVVEDRWDGHAATGAEPLPLRVMCRRALA +EHLDADELFRITKAGLDFFHDLFGIPYEWGAYDQAFVPEYNLGAMENPGLVTFTEHYIHDTAPTRGQLEGRATTVLHEMA +HMWFGDLVTMRWWDDLWLKESFADYMGTLAADEAAGFDESWTTFASRRKAWAYVQDAYPTTHPIVADIVDLEAARQNFDG +ITYAKGASVLKQLAAFVGRDAFMEAARVYFHRHAWGNAELDDFLAVLGAASGRDMSAWADAWLRTAGVPALAVEVDGDGA +PVLVQSGVDPRTGEPIRRPHVLRVGVFTPDADGALTRTAQVDADIAAGAERTT--LPGLAVPDGPRLILPNDEDLTYAAV +ALDEASLDAVLTRPVADPLAQATVWAALWSMVREGTLPAARFVGAVQELSASVAGVAVYTQVVSQAAAAVELYATAAQRG +ALRAGLGEHLLSALRSLEAGGDRQRAAVRTLAVLARGDADLARRLETAVL---------EDAETGAPGLAVDAEIRWLVL +QALAATGSADRARLDAALAEERTAKTVVAHRLAVQAIPDPAVKRAAWDAVLAGEDAEGQALSNDLLSATASGFAAGGHDL +VDPFEPGFWGELEGLWSSRSNGLASRAISGLFPLHQDALPGDAAAQEAHPVLARAQAWLDEHTAAPGALRRLVVEQTDAL +RRSLRVQAAQPTP +>GCF_023573625_PROKKA_01106 +M--TDTTPDLDATNVTRAEAADRSRLLTVQDYVVDVDLSDARDAAADTYPVRTVIRFACAEPGAQTHLDWIHGGVESVTL +NGTALDVAEVVGEARVLLPDLAAQNVVELVGRSVYSRSGEGLHRFTDPADGEVYLYTQYEPADARRVFPDFEQPDLKAAF +TFSLTGPEDWVLASNRPEVSRTPTGDGVVRVEFAPTLPQSTYITTLLAGPYAQWEDAWDGHPASGAQAVPLRLFTRRTMA +DAFDPEAVFDVTKRGLTFFHDLFGVAYPWGKYDQAFVPEYNLGAMENPGLVTFTEDFVFTSRATAVQYEGRANVILHEMA +HMWFGDLVTMHWWDDLWLKESFADYMGALGVDEATDFRTAWVTFASRRKAWAYVQDQMPTTHPIVADIVDLEAARQNFDG +ITYAKGASVLKQLAAYVGRDAFLDAAHRYFAAHAWGNASLADFMAVLEAASGRDMRAWADAWLHTSGVPRLRVDVDGD-A +PVLRQEGADPVTGGPILRPHVLKVGVFTPGQDGVLRRTAQVTADVPGGAEGAAVPLPDLEVPGGVRLVLPNDEDLTYAAV +ALDAGSLRAALTHPIADPLAEATVWAALWSMTRDGELPVARFLDAVATLSARIATVGVHAQVLAQAAAAVGQYARAEDRD +ALRSRLGEVLAEQTRTLEAGSDRQRTAARTWATLARADVGMAAALEAALLG--------EDAAAFAPGLAVDAELRWLVL +QALAATGRADQDRLDAELEAGRTAQTVTWHRLAAAARPEAEVKAAAWEAVMSGRTTTGTELSNDLLSATAAGFAAGGVEL +LAPYESGFWPRLTSVWASRSNGLASRAIGGLFPGRQDAVAGGADAQESHPTLAAAQRWLDEHPDAPGALRRLVVEHTDAL +RRSLRVQAVQPAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000962.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000962.fa new file mode 100644 index 0000000000000000000000000000000000000000..8973ba0978e25ffd1280d516bacf6cab3d799510 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000962.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01157 +MVQKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGTYRLIDFALSNLVNSRYREIVVLTQ +YKSHSLDRHISETWRMSTLLNNYVASVPAQQRRGKDWFTGSANAIYQSMNLIHDARPDIV +VVIGADHVYHMDFQQMVDQHIASGAKATVAAVRQPLELASSFGVIETDPQDRTRISAFVE +KPETTPGLPDDPTQFLASMGNYVFDTDALVAALNQDEENPESNNDMGGDIIPLFVERGEA +GVYDFTANEVPGGTAGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNREWPLYTRQSVSP +PAKLVRSSTRRPGSANDSILSQGVVISGGTVAQSVLSTDVRVHNEAWVEQSVLLDSVVIG +EGAHVRNAILDKNVVVPPGARIGFDRAEDEANGYTVTESGLTVLSKGQPVPTPH +>GCF_003691675_PROKKA_00876 +MVQKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGTYRLIDFALSNLVNSRYREIVVLTQ +YKSHSLDRHISETWRMSTLLNNYVASVPAQQRRGKDWFTGSANAIYQSMNLIHDARPDIV +VVIGADHVYHMDFQQMVDQHIASGAKATVAAVRQPLELASSFGVIETDPQDRTRISAFVE +KPETTPGLPDDPTQFLASMGNYVFDTDALVAALNQDEENPESNNDMGGDIIPLFVERGEA +GVYDFTANEVPGGTAGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNREWPLYTRQSVSP +PAKLVRSSTRRPGSANDSILSQGVVISGGTVAQSVLSTDVRVHNEAWVEQSVLLDSVVIG +EGAHVRNAILDKNVVVPPGARIGFDRAEDEANGYTVTESGLTVLSKGQPVPTPH +>GCF_005280335_PROKKA_01732 +MVQKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGTYRLIDFALSNLVNSRYREIVVLTQ +YKSHSLDRHISETWRMSTLLNNYVASVPAQQRRGKDWFTGSANAIYQSMNLIHDARPDIV +VVIGADHVYHMDFQQMVDQHIASGAKATVAAVRQPLELASSFGVIETDPQDRTRISAFVE +KPQTTPGLPDDPTLFLASMGNYVFDTDALVAALNQDEENPESNNDMGGDIIPLFVERGEA +GVYDFTANEVPGGTAGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNRDWPLYTRQSVSP +PAKLVRSSTRRPGSANDSILSQGVVISGGTVAQSVLSTDVRVANEAWVEQSVLLDSVVIG +EGAHVRNAILDKNVVVPPGARIGFDRAEDEANGYTVTDSGLTVLAKDQSVPKPH +>GCF_020097155_PROKKA_01630 +MVEKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGEYRLIDFALSNLVNSRFREIVVLTQ +YKSHSLDRHISETWRMSTMLNNYVATVPAQQRRGKDWFTGSANAIYQSMNLISDARPDIV +VVIGADHVYHMDFQQMVDHHVASGAKATVAAVRQPLELADQFGVIETDATDPGRITAFVE +KPATTPGLADDPAQFLASMGNYVFDTDALVEALNADDANPESNNDMGGDIVPYFVGRGEA +GVYDFTTNEVPGGTPGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNRAWPLYTRQSVSP +PAKLVRSASRRPGTAGDSILAQGVVISGGTVAQSVLSTDVRVGNEAWVEQSVLLDSVTVG +EGAHVRNAIIDKNVVIPAGARIGFDRAEDEANGYTVTDSGLTVLSKNQRVPDPR +>GCF_023573625_PROKKA_01107 +MVQKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGTYRLIDFALSNLVNSRYREIVVLTQ +YKSHSLDRHISETWRMSTLLNNYVASVPAQQRRGKDWFTGSANAIYQSMNLIHDARPDIV +VVIGADHVYHMDFQQMVDQHIASGAKATVAAVRQPLELASSFGVIETDPQDRTRISAFVE +KPETTPGLPDDPTQFLASMGNYVFDTDALVAALNQDEENPESNNDMGGDIIPLFVERGEA +GVYDFTANEVPGGTAGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNREWPLYTRQSVSP +PAKLVRSSTRRPGSANDSILSQGVVISGGTVAQSVLSTDVRVHNEAWVEQSVLLDSVVIG +EGAHVRNAILDKNVVVPPGARIGFDRAEDEANGYTVTESGLTVLSKGQPVPTPH + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000970.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000970.fa new file mode 100644 index 0000000000000000000000000000000000000000..166343a7f05a46ad3fa4fc4e5d87dc34998d5e05 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000970.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01167 +---MREQLMSSTLDAISRGQKWEYLVMTVAAHESLADARRRLVEHAEYGQWELQRSVHYR +DGARRYWMRRRVMRVASTLQTL +>GCF_003691675_PROKKA_00886 +---MREQLMSSTLDAISRGQKWEYLVMTVAAHESLADARRRLVEHAEYGQWELQRSVHYR +DGARRYWMRRRVMRVASTLQTL +>GCF_005280335_PROKKA_01722 +---MREQLMSSTLDSIARGQKWEYLVITVSPDESLGDARRRLVEHAEYGRWELQRSVHFR +GGARRYWLRRRVVRVASTLASA +>GCF_020097155_PROKKA_01620 +MDGMREQLMSSTLDSIARGEKWEYLVITVAPHESLADARRRLVDHAEYGQWELQRSVHYR +GGTRRHWMRRRVIRVRSTLQS- +>GCF_023573625_PROKKA_01117 +---MREQLMSSTLDAISRGQKWEYLVMTVAAHESLADARRRLVEHAEYGQWELQRSVHYR +DGARRYWMRRRVMRVASTLQTV + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000971.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000971.fa new file mode 100644 index 0000000000000000000000000000000000000000..a6d504764a66aeb0775f58e723112218f821a1cc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000971.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01168 +MSSDARMALEALTTALNEHLVAAQNKRGEDDPAVEAAFFAVADAFEAYEDALYADTEEVT +PLDLFDDEDDDD--- +>GCF_003691675_PROKKA_00887 +MSSDARMALEALTTALNEHLVAAQNKRGEDDPAVEAAFFAVADAFEAYEDALYADTEEVT +PLDLFDDEDDDD--- +>GCF_005280335_PROKKA_01721 +MSSDARMALEALTTALNEHLVAAQNKRGEDDPAVEAAFFAVADAFEAYEDALYADTEEVT +PLEVFDDEEDDEA-- +>GCF_020097155_PROKKA_01619 +MSSDARVALEALTSALNEHLVAAQNRRGEDDPAVEAAFFAVADAFDAYEEALYAETEEVT +PLELFDDEDDLDEED +>GCF_023573625_PROKKA_01118 +MSSDARMALEALTTALNEHLVAAQNKRGEDDPAVEAAFFAVADAFEAYEDALYADTEEVT +PLDLFDDEDDDD--- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000975.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000975.fa new file mode 100644 index 0000000000000000000000000000000000000000..d5cbabf2b6aa0c63ece4d55c84336c45e065052f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000975.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01172 +MSRHP-APAPDDRARRLPRAVLWDMDGTLVDTEPLWNAVQRRLVVEHGGTWSEDLAASLV +GRPLDEGARRLQEAGLDLPVQRIIDLTMHEVVQGVVSGVPWRPGARELLVALAEAGVPGA +LVTMSHAPLARALAERAPAGTLDVVVSGDMVSRGKPDPEAYRLGLQLLAERTPGLTAADC +VAVEDSPVGVGAAMAAGLPTVGVPSVLPLPAGLATVEWTTLAGRTPADLAAVRQIAAARG +PGGDGAE------ +>GCF_003691675_PROKKA_00891 +MPRHP-APAPDDRARRLPRAVLWDMDGTLVDTEPLWNAVQRRLVAEHGGTWSDDLAASLV +GRPLDEGARRLQEAGLDLPVQRIIDLTMDEVVQGVVRGVPWRPGARELLVALAEAGVPGA +LVTMSHAPLARALAERAPAGTLDVVVSGDMVSRGKPDPEAYRLGLQLLAERTPGLTAADC +VAVEDSPVGVGAAMAAGLPTVGVPSVLPLPAGLATVEWTTLAGRTPADLAAVRRIAAARG +PGADGAG------ +>GCF_005280335_PROKKA_01717 +------------------------MDGTLADTEPLWNASQRRLLAEHGGVWSEALADSLV +GRPLDEGARRLQAAGLDLPVDEIIERTMGAVTRGVADRVPWRPGARELLAALAEAGVPGA +LVTMSHAPLARALAERAPAAALDVVVSGDLVARGKPDPEAYLLALDLLAARHPGLDAAGC +VAVEDSPVGVAAAVAAGLPTVGVPSVLPLPAGAATVEWDTLAGRAPADLAAVRDVAAGRA +EDAPAPAGPGGRA +>GCF_020097155_PROKKA_01615 +MPRTPAAPAP-----VLPAALLWDMDGTLVDTEPLWNAVQRRLVEEHGGTWSDGLAASLV +GRPLDEGARSLRAAGLRMEVPEIIEATMAEVARGVEAATPWRPGALELLTAQAEAGVPGA +LVTMSHAPLARVLAERAPAGALRVVVTGDRVSRGKPDPEAYLLALEELSAHVPGLRAEDC +VAVEDSPVGVAAAVAAGLPTVGVPSVLPLPEGAATVQWGTLAGRGLADLAAVRPGAAG-- +------------- +>GCF_023573625_PROKKA_01122 +MPRHP-APAPDDRARRLPRAVLWDMDGTLVDTEPLWNAVQRRLVVEHGGTWSEDLAASLV +GHPLDEGARRLQEAGLDLPVQRIIDLTMDEVVQGVVGGVPWRPGARELLVALAEAGVPGA +LVTMSHAPLARALAERAPAGTLDVVVSGDMVSRGKPDPEAYQLGLQLLAERTPGLTAADC +VAVEDSPVGVGAAVAAGLPTVGVPSVLPLPAGLATVEWTTLAGRTPADLAAVRRIAAARR +PGADEPG------ + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000976.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000976.fa new file mode 100644 index 0000000000000000000000000000000000000000..c70ac76061e19c19ff10dc7074fac06866b19148 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000976.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01173 +MSGPA-----SVRLGTIAGAPVRLSWSWLLIAAAITLAFGPQIQRALPSLGGGAYGVALG +YAVLLALSVLVHEAAHALTGRAFGQRTEEIALTLWGGHTQFRSPSARPLDTVLTAMAGPA +ANLVLAGLAHLAARAVAGPSVPALLLEVTVWANLLLAAFNALPGTPLDGGRMVESAVWAA +TGSRARGVEAAGWAGRVVAVGVLAAVLGPPILAGRAPDLFVVVLAAWVALTLWRGADDAV +RHGRWSRRLETLRLEQVEAPAVALPEHLSVAEALAQADDGRRAVVAVDGAGRPRGVLDLA +AAAGLTPERRTTTALAAVAVALAPGAVLVRDDVPAAGPDLAARL-------ADPQ----- +---TPVWVLTDAHGLVRSVVPRETILAAVDATRRP------- +>GCF_003691675_PROKKA_00892 +MSGPA-----SVRLGTIAGAPVRLSWSWLLIAAVITLAFGPQIQRALPLIGGGAYGVALG +YAVLLALSVLVHEAAHALTGRAFGQRTEEIALTLWGGHTQFRSPSARPLDTVLTAMAGPA +ANLVLAGLAHLAARAVAGPSVLALLLEVTVWANLLLAAFNALPGTPLDGGRMVESAVWAA +TGSRARGVEAAGWAGRVVAVGVLAAVFGPPTLAGRAPDLFVVVLAAWVALTLWRGADDAV +RHGRWSRRLETLRLEQVEAPAIALPEHLCVAEALAQADGGRRAVVAVDGAGRPRGVLDHT +AAAGLTPARRTTTALAAVAVALAPEAVLVRDDVPAAGPDLASRL-------ADPQ----- +---TPVWVLTDAHGLVRSVVPRETILAAVDATRRP------- +>GCF_005280335_PROKKA_01716 +MSGAAARRIGSLRLGSVAGAPVLLSWTWLLIAVAIVLALGPQIRRALPELGAGAYGVALG +YAVLLALSVLVHEVAHALAGRAAGQRAEEIALTLWGGHTQFRGAHAGPLGTVLTAMAGPA +ANLALAGLAHLAARAVDGPSVAALLLDVSVWANLLLAAFNALPGAPLDGGRMVESAVWAA +TGSRDRGVEASGWAGRVIAAGIVAAALLAPLLQGRTPDVLFTALLIWAALTLWRGAGDAV +ARGRWGRRLAGLRLADLELAAVAVPEHLSVAEALAHADGGRRAAVAVDGAGLPRGVLDRT +AVGRLDAAARAGTPVAAAAVALAPQAVLEREALPEAGPELAAVL-------ADPE----- +---TPVWVLTDVRGLVRSVVTRERILAAVHATRRP------- +>GCF_020097155_PROKKA_01614 +MSGPR-----ALTLGRIAGAPVRLSPAWVAVAGAVVLLFGPQVARALPGLGGAAWLVALG +YAALLALSVLVHEAAHAVAGRAFGQRPQEIVLTLWGGHTQFAAPQATPVGTVVTALAGPA +ANVVLAGLAWALGAAADARGVPGLLVDATVWANLLLAGFNALPGAPLDGGRMVESAVWAA +TGSRDRGVAAAGWTGRLIAAALVIGWVAVPLVRGERPGLVVSLLLVWVAVTLWRGASESV +ERGRWGRRLAGVRLADLAIPALAVPVDADASAVLAGVPAG-LAVVAVDEAGRPVGVLDRA +ALDGAAASARV--PVAAACRAVAPHAVLAADSLPPSGGALVASLATAAESAADPRPGVPG +LDSTPVWVLTDGHGAVRSVLPRERILTALATASRPDPEEPRP +>GCF_023573625_PROKKA_01123 +MSGPA-----SVRLGTIAGAPVRLSWSWLLIAAVITLAFGPQIQRALPSLDGGAYGVALG +YAVLLALSVLVHEAAHALTGRAFGQRTEEIALTLWGGHTQFRSPSARPLDTVLTAMAGPA +ANLVLAGLAHLAARAVPGPSVPALLLEVTVWANLLLAAFNALPGTPLDGGRMVESAVWAA +TGSRARGVEAAGWAGRVVAVGVLAAVFGPPTLAGRAPDLFVVVLAAWVALTLWRGADDAV +RHGRWSRRLETLRLEQVEAPAIALPEHLCVAEALAQADGGRRAVVAVDGAGRPRGVLDHT +AAAGLTPARRTTTALAAVAVALAPEAVLVRDDVPAAGPDLASRL-------ADPQ----- +---TPVWVLTDAHGLVRSVVPRETILAAVDATRRP------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000981.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000981.fa new file mode 100644 index 0000000000000000000000000000000000000000..a84e0e90d6a76fa1c76a6fca400f354be7bdc834 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000981.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01178 +MRLWTLHPRHLDRQGLTGAWREALLAQAVLAGRTRGYRDHPQLLRFREHPDPSGAIGAFL +SGLEAEATARGYRFDHSRIDRPCPAPDGAVR-IPPAGLAPIPATTGQRDLEWRHLCAKLA +ARSPAWLERWSDTPVPDVHPLFTIVPGPVASWERA +>GCF_003691675_PROKKA_00897 +MRLWTLHPRHLDRQGLTGAWREALLAQAVLAGRTRGYRDHPQLLRFREHPDPSGAIGAFL +SGLEAEATARGYRFDHSRIDRPCPAPDGAVR-IPPAGLAPIPATTGQRDLEWRHLCAKLA +ARSPAWLERWSDTPVPDVHPLFTIVPGPVASWERA +>GCF_005280335_PROKKA_01711 +MRLWTLHPRHLDRQGLTGAWREALLAQAVLAGRTRGYRDHPQLLRFREHPDPSGAVGAFL +SGLEAEATARGYRFDHSRIDRPCPAPDGAVR-IPTVGLAPIPATTGQRDLEWRHLCAKLA +ARSPAWLERWADTPVPDVHPLFTIVPGPVASWERA +>GCF_020097155_PROKKA_01609 +MRLWTLHPRHLDRQGLTGGWREALLAQAVLARRTKGYRDHPQLERFRGHGDPAAAIGAFL +SGIALEASARGYRFDVSKIDRPLLPADGAGELVLPFRIAPIEVTTGQVAHEWGHLRAKLA +ARSPGWLERWADVQTPDVHPLFEVVDGPIASWERP +>GCF_023573625_PROKKA_01128 +MRLWTLHPRHLDRQGLTGAWREALLAQAVLAGRTRGYRDHPQLLRFREHPDPSGAVGAFL +SGLEAEATARGYRFDHSRIDRPCPAPDGAVR-IPPAGLAPIPATTGQRDLEWRHLCAKLA +ARSPAWLEQWSDTPVPDVHPLFTIVPGPVASWERA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000983.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000983.fa new file mode 100644 index 0000000000000000000000000000000000000000..3c977e00438909db5718b3d84ad6d46f157ebb27 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000983.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01180 +MTDADRARRIFGLETEYGVQHWNPEGRALSPEEVVRYLFRPVVEWGRSSNVFVANGSRLY +LDVGSHPEYATAECSTLDELIASDGAGDLLLHDLVVQAEERMATDGVGGRIHLYRNNADS +SGSSYGSHENYLLRRRTEYRRLTEALVPFLVSRQILVGAGRVVPAGTWPEGEGPAHFAFS +QRADFVQDGVSSSTTRSRPIINTRDEPHADASEYRRLHVIVGDTNLSEHTHLLRFGATDL +LLRMIEAGFPLGDRVVAHPTRAVRQISHDLTGTARIALREGEASALELQEHYLERARTFV +AAEGAHHDRVGEVLTLWGEVLDAVRTGDRSRIEDRIDWAIKLRLLEDYRARHDLGWDAPR +LAQLDLAFHDIDPDRGLFRLLLRRGAVARLLPEDAARSAVETAPPTTRARVRADFVARAR +ERGLDYAVDWTTLKLTDHPLHAIVTKDPFDTSSAAVDRLFGRIA +>GCF_003691675_PROKKA_00899 +MTDADRARRIFGLETEYGVQHWNPQGRPLSPEEVVRYLFRPVVEWGRSSNVFVANGSRLY +LDVGSHPEYATAECSTLDELIASDGAGDLLLHDLVVQAEERMAADGVGGRIHLYRNNADS +SGSSYGSHENYLLRRRTEYRRLTEALVPFLVSRQILVGAGRVVPAGTWPEGEGPAHFAFS +QRADFVQDGVSSSTTRSRPIINTRDEPHADASEYRRLHVIVGDTNLSEHTHLLRFGATDL +LLRMIEAGFPLGDRVVAHPTRAVRQISHDLTGTARIALREGEASALELQEHYLERARAFV +AAEGAHHDRVGEVLTLWGEVLDAVRTGDRSRIEDRIDWAIKLRLLEDYRARHDLGWDAPR +LAQLDLAFHDIDPDRGLFRLLLRRGAVARLLPEDAARSAVEAAPPTTRARVRADFVSRAR +ERGLDYAVDWTTLKLTDHPLHAIVTKDPFDTSSAAVDRLFERIA +>GCF_005280335_PROKKA_01709 +MTDADRARRIFGLETEYGVQHWNPEGRPLSPEEVVRYLFRPVVEWGHSSNVFVSNGSRLY +LDVGSHPEYATAECSTLDELIASDAAGDLILHDLVTRAQERMAADGISGRIHLYRNNADS +SGSSYGSHENYLLRRRTEYRRLTEALVPFLVSRQILVGAGRVVPAGTWPEGDGAAHFAFS +QRADFVQDGVSSSTTRSRPIINTRDEPHADASEYRRLHVIVGDTSLSEHTHLLRFGATDL +MLRMIEAGFPLGDRVLAHPTLAVRQISHDLTGTARVALRDGDASALELQEHYLERARAFV +AAEGAHHERVEEILTLWEDVLEAVRTGDRSRIEDRIDWAIKLRMLEDYRARQNLDWGSAR +LAQLDLAFHDIDPDRGLFRLLLRRGAAARLLPEDAGRLAVDAAPPTTRARVRADFIARAR +QRGLGYAVDWTTLKLTDHPLHAIAAKDPFDASSDAVDRLFERIG +>GCF_020097155_PROKKA_01607 +MT--TDARRIFGLETEYGVQHWNPQARPLSPEEVVRYLFRPVLEWGRSSNVFVRNGSRLY +LDVGSHPEYATAECSTLDELIASDAAGDLMLLDLIARAEEAMAADGIGGRIYLYRNNADS +SGSSYGSHENYLLRRRTEYRRLTEALVPFLVSRQILVGAGRVIPAGVWPEGEGRAHFAFS +QRADFVQEGVSSSTTRSRPIINTRDEPHADASEYRRLHVIVGDTNLSEATTLLRFGATDL +MLRMIEAGYPLGDHRVAHPTLAIRQISHDLTGTVRVNLREGTASALDLQDHYLSRARAFV +ASEGAHHDRVEDVLDLWGTVVDAVRSQDFGPIEETIDWAIKLKLLRGYRDRYGLDWDAPR +LAQLDLAFHDIAPGRGLFPLLRERGGVRRVLPEGAARAAVDAAPPSTRATVRAEFIARAR +AAGMDYAVDWTTLKLNDHPIHAISTKDPFSTDATPVDRLFERVG +>GCF_023573625_PROKKA_01130 +MTDADRARRILGLETEYGVQHWNPQGRPLSPEEVVRYLFRPVVEWGRSSNVFVANGSRLY +LDVGSHPEYATAECSTLDELIASDGAGDLLLHDLVVQAEERMAADGVGGRIHLYRNNADS +SGSSYGSHENYLLRRRTEYRRLTEALVPFLVSRQILVGAGRVVPAGTWPEGEGPAHFAFS +QRADFVQDGVSSSTTRSRPIINTRDEPHADASEYRRLHVIVGDTNLSEHTHLLRFGATDL +LLRMIEAGFPLGDRVVAHPTRAVRQISHDLTGTARIALREGEASALELQEHYLERARAFV +AAEGAHHDRVGEVLTLWGEVLDAVRTGDRSRIEDRIDWAIKLRLLEDYRARHDLGWDAPR +LAQLDLAFHDIDPDRGLFRLLLRRGAVARLLPEDAARSAVETAPPTTRARVRADFVARAR +ERGLDYAVDWTTLKLTDHPLHAIVTKDPFDTSSAAVDRLFERIA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000984.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000984.fa new file mode 100644 index 0000000000000000000000000000000000000000..fd6173c6c47f7647e0186c17101c4a2ba10d1deb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000984.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01182 +MSFGQRDYDRTKPEIDFPGETPPTELVVEDLIEGSGPAVEAGSRVQVHYVGVAWSTGEEF +DASWNRGTPLPLTVGVGQVIAGWDQGLLGMKVGGRRRLEIPPHLGYGARGAGSAIGPNET +LIFVCDLVSVD +>GCF_003691675_PROKKA_00901 +MSFGQRDYDRTKPEIDFPGETPPTELVVEDLIEGSGPAVEAGSRVQVHYVGVAWSTGEEF +DASWNRGTPLPLTVGVGQVIAGWDQGLLGMKVGGRRRLEIPPHLGYGARGAGSAIGPNET +LIFVCDLVSVD +>GCF_005280335_PROKKA_01706 +MSFGQRDYDRTKPEIDFPGENPPAELVVEDLIAGSGPAVEAGSRVQVHYVGVAWSTGEEF +DASWNRGTPLPLTVGVGQVIAGWDQGLLGMQVGGRRRLEIPPHLGYGARGAGSAIGPNET +LIFVCDLVSVD +>GCF_020097155_PROKKA_01605 +MSFGQRDYDRTKPEIDFPGDTPPTELVVEDLIEGSGPAVEPGSRVQVHYVGVAWSTGEEF +DASWNRGTPLPLTVGIGQVIAGWDQGLLGMKVGGRRRLEIPPHLGYGARGAGSAIGPNET +LIFVCDLVSVD +>GCF_023573625_PROKKA_01132 +MSFGQRDYDRTKPEIDFPGETPPTELVVEDLIEGSGPAVEAGSRVQVHYVGVAWSTGEEF +DASWNRGTPLPLTVGVGQVIAGWDQGLLGMKVGGRRRLEIPPHLGYGARGAGSAIGPNET +LIFVCDLVSVD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000994.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000994.fa new file mode 100644 index 0000000000000000000000000000000000000000..de7ade96f4af57ac11a3211c3db8f5b9c16507de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000994.fa @@ -0,0 +1,50 @@ +>GCF_002008305_PROKKA_01192 +---MTSSPVAVSPLLQPITLGPLTLPNRVVMASMHMGLEDRHDDLPQLAAFYAERARGGVGLIVTGGLGVVPEGTVTLGG +GMLASEEDARAHRVVTDAVHAAGGRILAQLLHAGRYAPSPDLVSASAVRAPISRHTPREMTAADIERTVNAFARAATLAL +EAGYDGVEIMASEGYLLNQFLAPATNRRADEYGGDAERRRRFPVAVVAAVREALGERGVLSVRTSAADLVPDGQTRAEIA +DTARAFEAAGADVLMTGIGWHESRVPTIVTSVPRAAFLAASADLTAAVDIPVIASNRLTTPAEAEEALTSGAAALVGLAR +PLLADPDWMAAIGDPRARTLTPCIACNQACLDHVFTGAKVSCLMNPRAGRETEPEYAAPVPVALGRRRRIAVVGAGPAGL +TAAERAARFGHEVTLFDRHAEPGGQFRLARRIPGKEEFGPALEHLAARAAASGVTLVTGEEVSAQTLLTDDGRPGYDEVL +LTTGVRPRPVALPGTGEPGAPAVHAYDDVVLGHVDVGPRVAVIGAGGVGVDVAEALAA---GTERPDGTPETQEHWRARW +GVALTSQT-PGQLAKPAAADPGREVHLLQRSPGPIGVRLRPTTGWVHRAELRRHGVHLHSGVTYEGLGPDGLRVTAPS-- +-PEDPEARVALTLDVTDVVVCAGQESETDLVEDLVAAGYAPEAVRLIGGAAEARELDAYRAMDHAVRAVQG +>GCF_003691675_PROKKA_00911 +---MTSSPVAVSPLLQPITLGPLTLPNRVVMASMHMGLEDRHDDLPQLAAFYAERARGGVGLIVTGGLGVVPEGTVTLGG +GMLASEEDARAHRVVTDAVHAAGGRILAQLLHAGRYAPSPDLVSASAVRAPISRHTPREMTAADIERTVNAFARAATLAL +EAGYDGVEIMASEGYLLNQFLAPATNRRADEYGGDAERRRRFPAAVVAAVREALGERGVLSVRTSAADLVPDGQTRAEIA +DTARAFEAAGADVLMTGIGWHESRVPTIVTSVPRAAFLAASADLTAAVDIPVIASNRLTTPAEAEEALTSGAAALVGLAR +PLLADPEWMAAISDPRARTLTPCIACNQACLDHVFTGAKVSCLMNPRAGRETEPEYAAPVPVALARRRRIAVVGAGPAGL +TAAERAARFGHEVTLFDRHAEPGGQFRLARRIPGKEEFGPALEHLAARAAASGVTLVTGEEVSAQTLLTDDGRPGYDEVL +LTTGVRPRPVALPGAGEPGAPAVHAYDDVVLGHVDVGPRVAVIGAGGVGVDVAEALAA---GTERPDGTPETQEHWRARW +GVALTAET-PGQLAKPAAAHPGREVHLLQRSPGPIGVRLRPTTGWVHRAELRRHGVHLHSGVTYEGLGPDGLRVTAPS-- +-PEDPETRVPLTLDVTDVVVCAGQESETDLVEDLVAAGYAPEAVRLIGGAAEARELDAYRAMDHAVRAVQG +>GCF_005280335_PROKKA_01696 +---MTVAPAITSPLLEPITLGPLTLPNRVVMASMHLGLEDRHEDLPRLAAFYAERARSGVGLIVTGGVGVVPEGTVAPGG +GLLATAEDARAHRVVTDAVHAEGGRILVQLLHTGRYARGEDLVCASAVRAPISAHTPREMDEADLERTVAAFARAAALAL +EAGYDGVEVMASEGYLLNAFLAPVTNRRQDAYGGSAQARRRFPVRVVEAVRAALGERGVLSVRTSAADLVPGGQTREEVA +DTARAFEAAGADVLMTGIGWHESRVPTIVTSVPRATFLPATAALSAAVDIPVIAANRLTTPAEAEEAIASGAAALVGLAR +PLLADPDWMAGIGVDDAAALTPCIACNQACLDHVYTGAPVSCLMNPRAGRETDPAYARPVPVAIGRRRRVAVVGAGPAGL +TAAERAARFGHEVTLFDRHDEPGGQFRLARRIPGKEEFGPALEHLAARARASGVTVLTGEEVTVQTLLTPEGGPAFDEVL +LTTGVRPRRIALPGAGEPGAPAVHAYDDVVLGHAQLGPRVAVIGAGGVGVDVAEALTA---GAHRPDGTPESAEQWRARW +GVALDSPT-PGQLGEPTGEPPAREVHLLQRSPEPIGARLRPTTGWVHRAELRRHGVRLHSGVAYEGLSAAGLHVTVPD-- +-PERPEERTPLTLDVTDVVVCAGQESEDGLAGDLVAAGYPAEAVRLVGGAAEARELDAYRAMDHAVRAIQG +>GCF_020097155_PROKKA_01595 +MTHMTDAP-ASHRLLEPLTVRRTVLRNRVVMGSMHLGLEDSHADLPALAAFYAERAAGGVGLIVTGGVGVTPEGAVSPGG +GLLADAADAAAHRTLTDAVHAEGGRILVQLLHAGRYARGADLVSASATRAPISRHTAHALTEAEVEELVAAYARSARLAL +EAGYDGVEVMASEGYLLNQFLAPSTNLREDRYGGSAENRRRFPVAVVAAVREALGETGLLSVRTSLTDLVPGGQTSAEAL +DTARAFEAAGADLIMTGIGWHESRVPTVVTSVPRAAWAEASARVRAAVGIPVIAANRLTTPDDAEALLRGGAADLVAVAR +PLLADPDWVRTVGRAGAEHLTPCIACNQACLDHVMAGRPVSCLMNPRAGRETDPRYARPVPVEIGRRRRVAVVGAGPAGL +TAAHRAAGFGHDVTLFEATEEVGGQFRLARRIPGKEEFEPALRHLEARAVAAGVHLRRETRVTPRTLLTEDGRPAFDRVI +IATGVRPRDVDLPGVGEPGAPAVHRYDDVVAGRVRCGAAVAVIGAGGVGVDVAELLASPEGGAAL--GEPEPLEHWRARW +GVADDDPTAPGGLTRPEPAERARRVFLLQRSPEPVGSRLRPTTGWVHRLELRALGVEMLSGVSYERVDRDGLHVTAPAVG +GDGDP-GRRRLVLPVTDVVVCAGQESEDGLAGDLLAAGWDPEAVTVIGGARVAAEVDAYRAMDDAVLAVQD +>GCF_023573625_PROKKA_01142 +---MTSSPVAVSPLLQPITLGPLTLPNRVVMASMHMGLEDRHDDLPQLAAFYAERARGGVGLIVTGGLGVVPEGTVTLGG +GMLASEEDARAHRVVTDAVHAAGGRILAQLLHAGRYAPSADLVSASAVRAPISRHTPREMTAADIERTVNAFARAATLAL +EAGYDGVEIMASEGYLLNQFLAPATNRRADEYGGDAERRRRFPAAVVAAVREALGERGVLSVRTSAADLVPDGQTRAEIA +DTARAFEAAGADVLMTGIGWHESRVPTIVTSVPRAAFLAASADLTAAVDIPVIASNRLTTPAEAEEALTSGAAALVGLAR +PLLADPEWMAAISDPRARTLTPCIACNQACLDHVFTGAKVSCLMNPRAGRETEPEYAAPVPVALGRRRRIAVVGAGPAGL +TAAERAARFGHEVTLFDRHAEPGGQFRLARRIPGKEEFGPALEHLAARAAASGVTLVTGEEVSAQTLLTDDGRPGYDEVL +LTTGVRPRPVDLPGTGEPGAPAVHAYDDVVLGHVDVGPRVAVIGAGGVGVDVAEALAA---GTERPDGTPETQEHWRARW +GVALTSQT-PGQLAKPAAADPGREVHLLQRSPGPIGVRLRPTTGWVHRAELRRHGVHLHSGVTYEGLGPDGLRVTAPS-- +-PEDPEARVALTLDVTDVVVCAGQESETDLVEDLVAAGYAPEAVRLIGGAAEARELDAYRAMDHAVRAVQG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001009.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001009.fa new file mode 100644 index 0000000000000000000000000000000000000000..aa47cba7f15a698443c9b6542b68dfd3ddca347e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001009.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01208 +MFKRDKTPETAPAPSTHGSSAAPAEGAAVAEAGPRDRSQGKKGPTPRRRDQEAARRRTLV +PEDRKAARKAERQAMAQERMRQRAALETGDERGLPARDKGPQKRWVRDYVDARTGIGEWL +MPVVFAYVLLMFIPGREAQLILMISLYVLVALVLIESFLVSRHIKKGLTERFGTPEPGTG +FYGIMRALQFRRLRLPKPQVKRGEYPA +>GCF_003691675_PROKKA_00927 +MFKRDKTPETAPAPSTHGSSAAPAEG-AVSGAAPRDRSQGKKGPTPRRRDQEAARRRTLV +PEDRKAARKAERQAMAQERMRQRAALETGDERGLPARDKGPQKRWVRDYVDARTGIGEWL +MPVVFAYVVLMFIPGREAQLILMISLYALVALVLIESFLVSRHIKKGLTERFGTPEPGTG +FYGIMRALQFRRMRLPKPQVKRGEYPA +>GCF_005280335_PROKKA_01679 +----------------------------------------------------------MV +PEDRKAARKAAREAAAQDRMRQRVALETGDERGLPLRDRGPQKRWVRDYVDARTGIGEWL +MPVVFAYVLLMFLPGREVQLFLMISLYALVALVVIESLIVARRIKKGLTERFGEPESGTG +FYGVMRALQFRRLRLPKPQVKRGQFPA +>GCF_020097155_PROKKA_01577 +MLNRRKKTEN-DAPASHGSTALGAGNTPAAQPAPRDRSQGKTGPTPRRRDQEAARRRTLV +PEDRKAARKAERDAATAERMRQRQALETGDERNLPARDKGPQKRYVRDYIDARTGLGEWL +MPIVLVYVIAMFIPGTRAQVILMVTLYVIVGLVIAESFYISAQIKKRLTATFGTPEPGSR +FYGVMRALQFRRLRLPKPQVRRGEFPA +>GCF_023573625_PROKKA_01165 +MFKRDKTPETAPAPSTHGSSAAPAEGAAVAEAGPRDRSQGKKGPTPRRRDQEAARRRTLV +PEDRKAARKAERQAMAQERMRQRAALETGDERGLPARDKGPQKRWVRDYVDARTGIGEWL +MPVVFAYVLLMFIPGREAQLILMISLYVLVALVLIESFLVSRHIKKGLTERFGTPEPGTG +FYGIMRALQFRRLRLPKPQVKRGEYPA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001011.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001011.fa new file mode 100644 index 0000000000000000000000000000000000000000..e991590ae5d9b935ba74e471c70e5d29ee4e9c97 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001011.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01210 +MARDPI-QPPPPDPSAPHGAPAGGPTEEDTRPFLDDPPGLGWVPDGLPGFERCTLGLDTD +EQGQNLVTVVRPRTDAP-RDPARRPILSVHGWSDYFYNAPLAHAFEAAGYAFHAVDLRHY +GRSLRAGQTPGWTDDLTRYDADLEAAFETIAQDHPLPPILMGHSTGGLIAALWADRNPGR +LAALVLNSPWLEMQGSAGVRLLAKSIVGPVSAMKPYATLTLPRIDHYWRTLSDQAEGEWD +LHPLWRPPHAFEVPAAWLSAVLSGHRAVAGRLHVSVPILVLVSARGHRGTSYGEAMLTSD +IVLDPDAMARRSLRLGDRVTVHRLPDALHDVFASPASVREAAGAATLTWLGAYAPPSATE +AESGAPDDGAG +>GCF_003691675_PROKKA_00929 +MARDPL-QPPPPDPSAPHGAPAGGPTEEDTRPFLDDPPGLGWVPDGLPGFERCTLGLDTD +EQGQNLVTVVRPRTDAA-RDPARRPILSVHGWSDYFYNAPLAHAFEAAGYAFHAVDLRHY +GRSLRTGQTPGWTDDLARYDADLEAAFETIAQDHPLPPILMGHSTGGLIAALWADRNPGR +LAALVLNSPWLEMQGSAGVRLLAKSIVGPVSAMKPYAMLTLPRIDHYWRTLSDQAEGEWD +LHPLWRPPHAFEVPAAWLSAVLSGHRAVAGRLDVTVPILVLVSARGHRGTSYAEAMLTSD +IVLDPDAMARRSLRLGDRVTVHRLPDALHDVFASPASVREAAGAATLTWLGAYAPPSASE +A--GAPDDGAG +>GCF_005280335_PROKKA_01677 +MSIKPAEQPIPADESEPSRPPEGGPTDEDTRPLLDDPPGLGWVEDGMAGFERLTLGLDTD +EQGQNLVTVVRPQATGP-RDRTRRAILSVHGWSDYFYNAPLARAFEEAGYAFHAVDLRHY +GRSLREGQTPGWTDDLARYDADLEAALATIAEDHPLPPVLMGHSTGGLIASLWAHRNPGR +ISALVLNSPWLEMQGSAGVRLLAKTIVDPVSALKPYAMLTLPRIDYYWRTLSDQAEGEWD +LHPLWRPTHAFEVPAAWLSAVLKGHRTVARRLQVSAPILVLVSARGHRGTSYDEAMLASD +IVLDPDAMARRSLRLGDRVTVHRLPDALHDVFASPASVREAAGAATLTWLGAYAPPSASE +AESGAPDDGAG +>GCF_020097155_PROKKA_01575 +MTL----FPHVRGPWPRHG--LGLPADDAAAPPTPVDPEAGWTPDVLDGFERRSLALNAD +RQGRNVVTVVRRRAASRHRDPCRRPFVAVHGWSDYFYNTPLAEAVESAGYAFHAVDLRHH +GRSLRPGQTPGFVDRLDRHHEDLDAALALIAEDHPATPVVEAHSTGGLTTALWAADRPEA +ASALVLNSPWLQTHGGPLARAVAAPAVRRIARRDPYEILPLPRVDHYWRSLSAEADGEWD +LEPAWRDRWAFAVPAGWLAAVLDGHTTVARGLDLPVPVLVLVSDRGGLPLATRRRAASSD +VILSPRAQARAARRLGPGVVVHRCPGALHDVFASAPPVRRAALDATLSWLAETAPPRIA- +----------G +>GCF_023573625_PROKKA_01167 +MARDPI-QPPPPDPSAPHGAPAGGPTEEDTRPFLDDPPGLGWVPDGLPGFERCTLGLDTD +EQGQNLVTVVRPRTDAP-RDPARRPILSVHGWSDYFYNAPLAHAFEAAGYAFHAVDLRHY +GRSLRTGQTPGWTDDLTRYDADLEAAFETIAQDHPLPPILMGHSTGGLIAALWADRNPGR +LAALVLNSPWLEMQGSAGVRLLAKSIVGPVSAMKPYAVLTLPRIDHYWRTLSDQAEGEWD +LHPLWRPPHAFEVPAAWLSAVLSGHRAVAGRLDVSVPILVLVSARGHRGTSYAEAMLTSD +IVLDPDAMARRSLRLGDRVTVHRLPDALHDVFASPASVREAAGAATLTWLGAYAPPSATE +AESGAPDDGAG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001038.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001038.fa new file mode 100644 index 0000000000000000000000000000000000000000..698e725980ea7d81fdb0601b49a4494bed805478 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001038.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01239 +MALRQLSVQERAEARRKALQARQARAELKAAFAAGEVGLADIFARADADDAVARLRTVDL +LLALPGVGEVRAREAMAGCGISPRRRLGGLGRRQREALIAYIGR +>GCF_003691675_PROKKA_00958 +MALRQLSVQERAEARRKALQARQARAELKAAFAAGAVGLADVFARADTEDAVARLRTVDL +LLALPGVGEVRARETMAGCGISPRRRLGGLGRRQREALIAYIGR +>GCF_005280335_PROKKA_01649 +MALRQLSVEERAEARSKALAARQERAALKADFAAGQVSLAEVFSRADAEDAIGRLRTVDL +LQALPGVGEVRAREAMAGCGISPRRRLRGLGRRQREALIAYIGR +>GCF_020097155_PROKKA_01546 +MALRQLSVEERAEARAKALRARQERATLKTSFANRDLSLQEVFARADVDPAIGRLRTVDL +LQAMPGVGEVRASAVMEACEISPARRLKGLGRRQREALIAYIGR +>GCF_023573625_PROKKA_01197 +MALRQLSVQERAEARRKALQARQARAELKAAFAAGEVGLADIFARADADDAVARLRTVDL +LLALPGVGEVRAREAMAGCGISPRRRLGGLGRRQREALIAYIGR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001065.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001065.fa new file mode 100644 index 0000000000000000000000000000000000000000..f0442b22651148ac48e2321465d9eceba0a9097b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001065.fa @@ -0,0 +1,55 @@ +>GCF_002008305_PROKKA_01268 +MSEQDPT----------PVPVRPRGRIARLTGRHATEYSPLLEPLMRTVRQRATKTELADIVRAFEVARAAHEGQMRRSG +DPYITHPVAVATILAEIGVTGPTLLAALLHDTVEDTDYSLERLRADFGSDVALLVDGVTKLDKVTYGAAAQAETVRKMVI +AMAQDVNVLLIKLADRLHNARTWRYVSPESSARKAQETLDIYAPLAHRLGMNTVKWELEDLSFAALKPKMYAEIVRLVGE +RNPEREKHIAALRTVIEDHLREHRIRATVTGRPKHYYSIYQKMVTRGKDFDDIHDLTGIRVLVDSVRDCYAVLGAIHARW +NPVPGRFKDYIAVPKLNMYRSLHTTVMVPGGKPVEIQIRTQEMHRQAEYGVAAHWRYKAQAAGQAPV-QA--TPAWLRSV +MDWQADTRDPDEFLASLRTQIGADEVYVFTPKGEIRTLPAGSTPVDFAYAIHTDVGHRTIGARVNGKLVPLSTPLSHGDT +VEVFTSRAEDAGPSRDWLGFVVSPRARSKIRHHFATQRRGEQADRGRESLTRQLRKAGMTVQHVLGGEELVQLATDLGYA +DLDGLFVALGDGHVSAQSVQERVAERLAPPTPTQAEPEGELTVGEVDLQELVPAQARRAPARATNDAGVLVDGDGGVMAK +LARCCNPVPPDAIDGFVTRGSGVSVHRVDCPNLATLLAQEPERHTPVSWAPSRDTVYLVEIQIEALDRKSLLSDVTRVLS +ENHVNILSASVNTTRDRVAMSRFVFEMGDPRFLGHVIDAVRRIDGVFDVHRT +>GCF_003691675_PROKKA_00987 +MSEQDPTPAPARPAPARPAPVRPRSRIARLTGRHATEYSPLLEPLMRTVRQRATKTELAEIVRAFEVARAAHEGQMRRSG +DPYITHPVAVATILAEIGVTGPTLLAALLHDTVEDTDYSLERLRADFGSEVALLVDGVTKLDKVTYGAAAQAETVRKMVI +AMAQDVNVLLIKLADRLHNARTWRYVSPESSARKAQETLDIYAPLAHRLGMNTVKWELEDLSFAALKPKMYAEIVRLVGE +RNPEREKHIAALRTVIEEHLREHRIRATVTGRPKHYYSIYQKMVTRGKDFDDIHDLTGIRVLVDSVRDCYAVLGVIHARW +NPVPGRFKDYIAVPKLNMYRSLHTTVMVPGGKPVEIQIRTQEMHRQAEYGVAAHWRYKAQVAGQAPV-QA--TPAWLRSV +MDWQADTRDPDEFLASLRTQIGADEVYVFTPKGEIRTLPAGSTPVDFAYAIHTDVGHRTIGARVNDKLVPLSTPLSHGDT +VEVFTSRAEDAGPSRDWLGFVVSPRARSKIRHHFATQRRDEQADRGRESLTRQLRKAGMAVQQVLGGEELVQVATDLGYA +DLDGLFVALGDGHVSAQSVQERVAERLAPPTSTQAEPEGELTVGEVDLQELVPAQSRRAPARATNDAGVLVDGDGGVMAK +LARCCNPVPPDAIDGFVTRGSGVSVHRVDCPNLATLLAQEPERRTPVSWAPSRDTVYLVEIQIEALDRKSLLSDVTRVLS +ENHVNILSASVNTTRDRVAMSRFVFEMGDPRFLGHVIDAVRRIDGVFDVHRT +>GCF_005280335_PROKKA_01619 +MSEHDPT-----HAPARVAAVRPRGRIARLTGRHATEYSPLLEPLMRTVRQRATKAELADLIRAFEVARAAHEGQMRRSG +DPYITHPVAVATILAEIGVSGPTLLAALLHDTVEDTDYSLERLRADFGPEVALLVDGVTKLDKVTYGAAAQAETVRKMVI +AMAQDVNVLLIKLADRLHNARTWRYVSPESSARKAQETLDIYAPLAHRLGMNTVKWELEDLSFAALKPKMYAEIVRLVGE +RNPEREKHIAALRTVIEDHLREHRIRAEVTGRPKHYYSIYQKMVMRGKDFDEIHDLTGIRVLVDSVRDCYAVLGVIHARW +NPVPGRFKDYIAVPKLNMYRSLHTTVMGPGGRPVEIQIRTHEMHRQAEYGVAAHWRYKAQAAAESSS-SSSGTPAWLRSV +MDWQKDTRDPDEFLDSLRTQIGADEVYVFTPSGEIRSLPAGSTPVDFAYAIHTDVGHRTIGAKVNGKLVPLSTPLNHGDT +VEAFTSRAEDAGPSRDWLGFVVSPRARSKIRHHFATQRRDEQAERGRESLTRQLRRAGLAVQSVLGGEELAQVASDMGYA +DLDGLLVALGDGHVSAQAVQERVSERLAPPPPARTEPQGELTVGEVDLAELVPAQARRTPARATNDAGVLVDGDGGVMAK +LARCCNPLPPDAIDGFVTRGSGVSVHRLDCPNLATLLEQEPERRTPVGWAPSRHTVYLVEIQVEALDRKSLLSDVTRVLS +ENHVNILSASVNTTRDRVAMSRFVFEMGDPRFLGHVIAAVRRIDGVFDVHRT +>GCF_020097155_PROKKA_01514 +MTEQDRR----------PAAPPRRGRIARLTGRRATEYSPLLEPLMRTVRQSATHAEQEDIVRAFEVAERAHRGQMRRSG +DPYITHPVAVATILAELGVTGPTLLAALLHDTVEDTDYSLEQLTADFGPQVALLVDGVTKLDKVTYGAAAQAETVRKMVI +AMAQDVNVLLIKLADRLHNARTWRYVSPESSAKKARETLDIYAPLAHRLGMNTVKWELEDLSFAALQPKVYAEIVRLVGE +RNPEREKQLAALRGVLEEQLREQRVRATVTGRPKHYYSVYQKMVTQKKDFAQIYDLTGIRVLVDSVQDCYAVLGVVHARW +NPVPGRFKDYIAVPKLNMYRSLHTTVMGPEGKPVEIQIRTWEMHRQAEYGVAAHWRYKAGARGELEAGRSQQTPGWLRSV +MDWQEDTRDPDEFLAALRTQIGADEVYVFTPKGEIRSLPADSTPVDFAYAIHTDVGHRTVGARVNGRLVPLSTVLRHGDT +VEVFTSKAEDAGPSRDWLNFVVSPRAKSKIRHHFATRRRDEQIERGREAFTRQLRKAGLSVQRVLGGEDLGVVAGELGYH +DPDTLFAAMADGHVSPQAVTERLEARLAPP-PAPTAPDAELRVGEVDLAGLVPEKARRAPTRSTNEAGVLVNGDGGVLAK +LARCCNPVPPDEVVGFVTRGSGVSVHRGDCRNLATMLENEPERRVDVAWAPSRDAVYLVEIQVQALDRTSLLSDVTRVLS +ENHVNILSASVNTTRDRVAMSRFVFEMGDPKFLEHVVNAVRRIDGVFDVRRT +>GCF_023573625_PROKKA_01226 +MSEQDPTPAPARPAPARPAPVRPRSRIARLTGRHATEYSPLLEPLMRTVRQRATKTELAEIVRAFEVARAAHEGQMRRSG +DPYITHPVAVATILAEIGVTGPTLLAALLHDTVEDTDYSLERLRADFGSEVALLVDGVTKLDKVTYGAAAQAETVRKMVI +AMAQDVNVLLIKLADRLHNARTWRYVSPESSARKAQETLDIYAPLAHRLGMNTVKWELEDLSFAALKPKMYAEIVRLVGE +RNPEREKHIAALRTVIEEHLREHRIRATVTGRPKHYYSIYQKMVTRGKDFDDIHDLTGIRVLVDSVRDCYAVLGVIHARW +NPVPGRFKDYIAVPKLNMYRSLHTTVMVPGGKPVEIQIRTQEMHRQAEYGVAAHWRYKAQVAGQAPV-QA--TPAWLRSV +MDWQADTRDPDEFLASLRTQIGADEVYVFTPKGEIRTLPAGSTPVDFAYAIHTDVGHRTIGARVNDKLVPLSTPLSHGDT +VEVFTSRAEDAGPSRDWLGFVVSPRARSKIRHHFATQRRDEQADRGRESLTRQLRKAGMAVQQVLGGEELVQVATDLGYA +DLDGLFVALGDGHVSAQSVQERVAERLAPPTSTQAEPEGELTVGEVDLQELVPAQSRRAPARATNDAGVLVDGDGGVMAK +LARCCNPVPPDAIDGFVTRGSGVSVHRVDCPNLATLLAQEPERRTPVSWAPSRDTVYLVEIQIEALDRKSLLSDVTRVLS +ENHVNILSASVNTTRDRVAMSRFVFEMGDPRFLGHVIDAVRRIDGVFDVHRT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001070.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001070.fa new file mode 100644 index 0000000000000000000000000000000000000000..17e3ce5e195bcc293b853a797aaf09a5cf6f25ca --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001070.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01274 +-------------MDPGLTRCGIAVVDVDARRRAALVHVEVTGTPPTAPLDQRLLRIDEA +VSAVLAAHRPDRAAVERMFANTNTPTVLGTAQAAGVAIAAAARAGVPVGLHTPSEVKAAV +TGHGDAGKEQVTTMVTRILRLDAPPRPADAADALALAIAHGWRGTALGAAAGQTGLDTAD +LASRAGRSQFAAKAPARARQRGQLTAAQRAWLDAERSAGG--GRRR-- +>GCF_003691675_PROKKA_00993 +-------------MDPGLTRCGIAVVDVDARRRAALVHVEVTGTPPTAPLDQRLLRIDEA +VSAVLAAHRPDRAAVERMFANTNTPTVLGTAQAAGVAIAAAARAGVPVGLHTPSEVKAAV +TGHGDAGKEQVTTMVTRILRLDAPPRPADAADALALAIAHGWRGTALGAAAGQTGLDTAD +LASRAGRSQFAAKAPARARPRGQLTAAQRAWLDAERSAGG--GRRR-- +>GCF_005280335_PROKKA_01613 +------------------------MVDVDARRRAALVHVEVAGTPPTASLDQRLLRIDEA +VSAVLTAHAPDRAAVERMFANTNTPTVLGTAQAAGVAIAAAARAGIPVGLHTPSEVKAAV +TGYGDAGKEQVTTMITRILGLDAPPRPADAADALALAIAHGWRGTALGAAAGQTGLDTSD +LASRAGRSQFAAGTRSRGGRRGELTAAQRAWLDAERSAGG--GCR--- +>GCF_020097155_PROKKA_01508 +MTDRPAGVVRVLGVDPGLTRCGIAVVDVDARRRAELVHVEVAGTAPEESLDARLLCIDRA +VSAVLVRFRPERAAVERMFANNNTPTVLGTAQAAGVAIAAAARAGVPVGLHTPSEVKAAV +TGNGDAGKEQVTTMVTRILRLDAPPRPADAADALALAIAHAWRGTALGRAAGHTGLDTSG +LASRTGASRGAAGARVRRAPKAALTPAQQAWLAAERSAGARPGRRSAG +>GCF_023573625_PROKKA_01232 +-------------MDPGLTRCGIAVVDVDARRRAALVHVEVTGTPPTAPLDQRLLRIDEA +VSAVLAAHRPDRAAVERMFANTNTPTVLGTAQAAGVAIAAAARAGVPVGLHTPSEVKAAV +TGHGDAGKEQVTTMVTRILRLDAPPRPADAADALALAIAHGWRGTALGAAAGQTGLDTAD +LASRAGRSQFAAKAPARARPRGQLTAAQRAWLDAERSAGG--GRRR-- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001082.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001082.fa new file mode 100644 index 0000000000000000000000000000000000000000..928b56039a64379893fb63693a6b5b507b47fed9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001082.fa @@ -0,0 +1,50 @@ +>GCF_002008305_PROKKA_01287 +MEHLPPTSPGAPLLPQIARPADLSALTEDQLTALAAEIRAYLIAHVSKTGGHLGPNLGVVELTLAVHRVFESPKDAVIFD +TGHQSYVHKLLTGRQDFTTLRQEGGLSGYGDRTESEHDVVESSHASSSLSWADGIARAWAQTGQGDRTVVAVIGDGALTG +GMAWEAVNNIAAGRDRRVVIVVNDNGRSYAPTVGGVAEHLGGLRRGVLDKVRTHHRYEQTLDYLKRRLQEAGLAGELVYR +PLHAAKKGLKDLWAPQGLFEDLGMKYIGPVDGHDLTAMEEALEDARAYGGPVIVHAMTEKGHGYAPAVAHEADQFHAIGV +IDPSTGEPITSSTAQSWTSVFGEEMVAIADERPDVVAITAAMQNPVGLAPMALAHPDRVFDVGIAEQHAVTSAAGMAFGG +LHPVVAVYATFLNRAYDQVLMDVGLHRAGVTFVLDRAGVTGPDGPSHHGMWDLALLQSVPGLRISAPRDADTLREELREA +VAVEDAPTVVRFAKGSVGESVRALERLSDGTDVLARRGEAGGRDGAERDVLIVAVGAMAELGLDVAERLERHGISATVID +PRWVLPVARSVIDTAARHRIVVCLEDGVRAGGVGSRIRQEMRAAGVDTALNEVGLPVEFLAHGSREQVLARVGLTAQRIT +QDTVAQVLGAKVPYARPVPEDAAAPH-----------------HQEQA +>GCF_003691675_PROKKA_01006 +MEHLPPTSPGAPLLPQIARPADLSALTEDQLTALAAEIRAYLIAHVSKTGGHLGPNLGVVELTLAVHRVFESPKDAVIFD +TGHQSYVHKLLTGRQDFTTLRQEGGLSGYGDRTESEHDVVESSHASSSLSWADGIARAWAQTGQGDRTVVAVIGDGALTG +GMAWEAVNNIAAGRDRRVVIVVNDNGRSYAPTVGGVAEHLGGLRRGVLDKVRTHHRYEQTLDYLKRRLQEAGLAGELVYR +PLHAAKKGLKDLWAPQGLFEDLGMKYIGPVDGHDLTAMEEALEDARAYGGPVIVHAMTEKGHGYAPAVAHEADQFHAIGV +IDPSTGEPITSSTAQSWTSVFGEEMVAIADERPDVVAITAAMQNPVGLAPMALAHPDRVFDVGIAEQHAVTSAAGMAFGG +LHPVVAVYATFLNRAYDQVLMDVGLHRAGVTFVLDRAGVTGPDGPSHHGMWDLALLQSVPGLRISAPRDADTLREELREA +VAVEDAPTVVRFAKGSVGEPVRALERLSDGTDVLARRGEAGGRDGAERDVLIVAVGAMAELGLDVAERLERHGISATVID +PRWVLPVARSVIDTAARHRIVVCLEDGVRAGGVGSRIRQEMRAAGVDTALNEVGLPVEFLAHGSREQVLARVGLTAQRIT +QDTVAQVLGAKVPYARPVPEDAAAPH-----------------HQEQA +>GCF_005280335_PROKKA_01598 +MEHLPPTSPGAPLLPQIASPADLADVSEEQLTALAAEIRDYLIAHVSKTGGHLGPNLGVVELTLAVHRVFESPKDAVLFD +TGHQSYVHKLLTGRQDFTTLRQEGGLSGYGDRAESEHDVVESSHASSSLSWADGIARAWHQTGQGDRTVVAVIGDGALTG +GMAWEAVNNIAAGRDRRVVIVVNDNGRSYAPTVGGIADHLDGLRRGVLDKVRTHHRYEQTLDFLKRRLQEAGTAGEMVYR +PLHAAKKGLKDLWAPQGLFEDLGMKYIGPVDGHDLGELEEALEDAKAYGGPVIVHALTEKGHGYAPARAHEDDQFHAIGV +IDPSTGEPVTSSTAQSWTSVFGEEMLAIAEERPDVVAITAAMRNPVGLAPMALAHPDRVFDVGIAEQHAVASAAGMAFGG +LHPVVAVYATFLNRAYDQVLMDVGLHRAGVTFVLDRAGVTGPDGPSHHGMWDLALLQSVPGLRIAAPRDAETLREELREA +VAVEDAPTVVRFAKGSVGEPVRAIERLADGTDVLARRGEAGARDGAERDVLIVAVGALAELGLDVAERLERHGISSTVVD +PRWVLPVAESVIEAAARHRIVVCLEDGVRAGGVGSRIRQEMRAAGVDTALNEVGLPVEFLAHGSREQVLARVGLTAQRVT +QDTVAQVLGAKVPYARPVPQDEAARH-----------------PQEHA +>GCF_020097155_PROKKA_01494 +MSDTSRAPLGAPLLPGIHSPEDLALLSDAQLRALAAEIRAFLIQHVSQTGGHLGPNLGVVELTLAIHRVFDSPRDAVVFD +TGHQSYVHKLLTGRQDFSRLRQQGGLSGYGDRAESEHDVVESSHASSSLSWADGISRAWKQTGQGDRTVVAVIGDGALTG +GMAWEAVNNIAADRDRRVVIVVNDNGRSYAPTVGGIADHLGGLRRGVLDKVRMHHRYEQTLDYLKRRLQEAGTAGEMVYR +PLHAAKKGLKDLWAPQGLFEDLGMKYIGPVDGHDEHALEEALEDAKAYGGPVIVHAMTEKGHGYGPATSHEDDMFHAIGR +IDPETGRPISSPTAQSWTSVFGEEILDIARERPDVVAITAAMQNPVGLGPMAAEFPDRVFDVGIAEQHAVTSAAGMAFGG +LHPVVAVYATFLNRAFDQVLMDVGLHRAGVTFVLDRAGVTGPDGPSHHGMWDLALLQSVPGLRIAAPRDADTLREELREA +VAVDDAPTVLRFAKGSVGEPVRALERLSDGTDVLARLGAPTGADGAERDVLIVAVGSFAELGLDVARRLGQHGITATVVD +PRWVLPVARSVIELAGRHRIVVCLEDGVRAGGVGSRIRQEMRAAGVDTALNEVGLPVEFLAHATRDQVLERVGLTAQRIT +QDTVAQVLGAKVPYARALPRDAEHPEASAHPAGAPTTSAQAARPEEQA +>GCF_023573625_PROKKA_01245 +MEHLPPTSPGAPLLPQIARPADLSALTEDQLTALAAEIRAYLIAHVSKTGGHLGPNLGVVELTLAVHRVFESPKDAVIFD +TGHQSYVHKLLTGRQDFTTLRQEGGLSGYGDRTESEHDVVESSHASSSLSWADGIARAWAQTGQGDRTVVAVIGDGALTG +GMAWEAVNNIAAGRDRRVVIVVNDNGRSYAPTVGGVAEHLGGLRRGVLDKVRTHHRYEQTLDYLKRRLQEAGLAGELVYR +PLHAAKKGLKDLWAPQGLFEDLGMKYIGPVDGHDLIAMEEALEDARAYGGPVIVHAMTEKGHGYPPAVAHEADQFHAIGV +IDPSTGEPITSSTAQSWTSVFGEEMVAIADERPDVVAITAAMQNPVGLAPMALAHPDRVFDVGIAEQHAVTSAAGMAFGG +LHPVVAVYATFLNRAYDQVLMDVGLHRAGVTFVLDRAGVTGPDGPSHHGMWDLALLQSVPGLRISAPRDADTLREELREA +VAVEDAPTVVRFAKGSVGEPVRALERLSDGTDVLARRGEAGGRDGAERDVLIVAVGAMAELGLDVAERLERHGISATVID +PRWVLPVARSVIDTAARHRIVVCLEDGVRAGGVGSRIRQEMRAAGVDTALNEVGLPVEFLAHGSREQVLARVGLTAQRIT +QDTVAQVLGAKVPYARPVPEDAAAPH-----------------HQEQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001091.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001091.fa new file mode 100644 index 0000000000000000000000000000000000000000..a7eeaca541aa80917a89ab7e6dcc97b05c0501b4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001091.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01303 +MTDSAELPVPLHALDPGLAPPAYAQPGDAGADLRTAVDVTLAPGERALVPTGVALAIPEG +HAGFVHPRSGLAVRHGLSVVNAPGTIDAGYRGEIKVPLINLDPTEPIVLRRGDRIAQLVL +QPVVRARFEPVDALPDSERGAGGFGSTGGFTA---DNTPGRTS +>GCF_003691675_PROKKA_01026 +MTDSAELPVPLHALDPGLAPPAYAQPGDAGADLRTAVDVTLAPGERALVPTGVALAIPEG +HAGFVHPRSGLAVRHGLSVVNAPGTIDAGYRGEIKVPLINLDPTEPIVLRRGDRIAQLVL +QPVVRARFEPVDALPDSERGAGGFGSTGGFTA---DNTPGRTS +>GCF_005280335_PROKKA_01589 +MTDSAELPVPLHALDPDLAPPAYAQPGDAGADLRAAVDVTLAPGERALVPTGVALAIPEG +FAGFVHPRSGLAVRHGLSVVNAPGTIDAGYRGEIKVPLINLDPTDAVELRRGDRIAQLVI +QPVVRARFAPVDALPGSERGAAGFGSTGGFGT---ENAPGRTS +>GCF_020097155_PROKKA_01485 +MNGPREIDVPLRALDPQLPPPEYARPDDAGADLRAAEDVTLAPGERALVPTGVALAIPAG +FAGFVHPRSGLAVRHGLSVVNAPGTIDAGYRGEIKVPLINLDPTEPVVLRRGDRIAQLVV +QPVVQARFMAVDRLADSERGEAGFGSTGGFTPAAHDDAPGRTA +>GCF_023573625_PROKKA_01261 +MTDSAELPVPLHALDPGLAPPAYAQPGDAGADLRTAVDVTLAPGERALVPTGVALAIPEG +HAGFVHPRSGLAVRHGLSVVNAPGTIDAGYRGEIKVPLINLDPTEPIVLRRGDRIAQLVL +QPVVRARFEPVDALPDSERGAGGFGSTGGFTA---DNTPGRTS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001099.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001099.fa new file mode 100644 index 0000000000000000000000000000000000000000..41f3b71fb96ec76251a74d3cca9e69d2f4b03b2d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001099.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01312 +MAEALPVFWYVIIAVLWLGYLALEGFDLGAGMLMQAWARDERRRRVLLNVIGPVWEGNEV +WLITAIGAMFAAFPFWYASLLSTLYLPMLLLLLALILRAVSIEYRGKARTDRTRAVWTWC +LALGSFTAAFVVGAFLALTTTGLPIDANGDRVGGPFAWLNGWAVLGGLAVVGFSIAQAWA +FIGLKTDGAPRQAAARFLSRWTPVALAPLLVWAGAVLLRGDRPWTWALLAAGVAAAAGSV +VAARRGREGLALAGLTLFLVAAWSAVMIVQFPVLQPSTVDPAFDLTAEIAASGPYTLGIM +AVVSLVFVPIVLAYSAWSYWVFRRRVRETHIPEPHAVEPV +>GCF_003691675_PROKKA_01035 +MAEVLPVYWYVIIAVLWLGYLALEGFDLGVGMLVRFWARDEPRRRVLLNIIGPVWEGNEV +WLITAVGAMFAAFPFWYAAVFSTLYLPMLVMLFGLILRAVSIEYRGKAATDAGREIWTWT +LGIGSFLAAFMAGVLLVLTTTGLPLDANGDRVGGPFVWVTGPALLGGLAVVGFSLAQAWA +FIGLKTDGAPRRSAARFLSTWTPLAVLPLLVWAGLVVARGDRPWTWALLVLAVVAVAASV +VAARAGREGLAFTSLTLVLVLAWTAIMVTQYPVVLPSTVDPQFSLTAQLASSGPYTLGLM +AVISLIFVPIVLAYTGWSYWMFRRRLADTHIPEAHLVEPL +>GCF_005280335_PROKKA_01580 +MAEALPVFWYVIIAVLWLGYLALEGFDLGAGMLMQAWARDERRRRVLLNVIGPVWEGNEV +WLITAIGAMFAAFPFWYASLLSTLYLPMLLLLLALILRAVSIEYRGKARTDRTRAVWTWC +LALGSFTAAFVVGAFLALTTTGLPIDANGDRVGGPFAWLNGWAVLGGLAVVGFSIAQAWA +FIGLKTDGAPRQAAARFLSRWTPVALAPLLVWAGAVLLRGDRPWTWALLAAGVAAAAGSV +VAARRGREGLALAGLTLFLVAAWSAVMIVQFPVLQPSTVDPAFDLTAEIAASGPYTLGIM +AVVSLVFVPIVLAYSAWSYWVFRRRVRETHIPEPHAVEPV +>GCF_020097155_PROKKA_01476 +MTEALPVYWFVIIAVLWLGYLALEGFDLGVGMLMQAWARDERRRRVLLNIIGPVWEGNEV +WLITAIGAMFAAFPFWYAALLSTLYIPMLLLLFALILRAVSIEYRGKAQTDRVRGIWTWC +LAVGSFLAAFIVGAMLALTTTGLPLDAHGDRVGGPSAWLNGWAVLGGLAVVGFSIAQAWA +FIGLKTDGAPRVAAARFLRTWTPVAVLPMLVWALAVLVRGDRPGAWILLLLALAAVLVSV +LAARAGREGVALAGLTGFAAATWSAVMVAQFPVLTPSAVDRAYDLTAQVSSSGSYTLGVM +AVVSLVFVPIVLAYSAWSYWVFRHRVKETHIPESHIVEPV +>GCF_023573625_PROKKA_01270 +MAEVLPVYWYVIIAVLWLGYLALEGFDLGVGMLVRFWARDEPRRRVLLNIIGPVWEGNEV +WLITAVGAMFAAFPFWYAAVFSTLYLPMLVMLFGLILRAVSIEYRGKAATDAGREIWTWT +LGIGSFLAAFMAGVLLVLTTTGLPLDANGDRVGGPFVWVTGPALLGGLAVVGFSLAQAWA +FIGLKTDGVPRRSAARFLSTWTPLAVLPLLVWAGLVVARGDRPWTWALLVLAVVAVAASV +VAARAGREGLAFTSLTLFLVLAWTALMVTQYPVVLPSTVDPQFSLTAQLASSGPYTLGLM +AVISLIFVPIVLAYTGWSYWMFRRRLADTHIPEAHLVEPL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001101.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001101.fa new file mode 100644 index 0000000000000000000000000000000000000000..94771ea1c0184cc1cefdcb2b6c80866998d79610 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001101.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01316 +---MTNVSGNASYEYSRAALLAVTEVEAPLEVTSDDLDERLADVLRRLKLPPHLLQRVAG +VRARRNWDASQDFQEAAAQAGTAALAAAGIGPERVGLLINTSVTRATLEPSVAVRIHHMM +GLPTSATNFDITNACLGFVNGLMLASTLVDAGQVDYAVVVASEDASKVQDATVENLHAST +TNRGNFMEQFASLTLGCGAAAAVVGSIEDHPDAHRIVRGITRAGTDHHDLCVGDHRGMYT +DSTALLNDGLELVMDAWNDTPAEWAWKDADRFITHQVSQLHTNAISESAGLPLDRIPTTF +PVLGNVGPASLPITLVREMDELSAGDTVVCLGVGSGLNTAMLEIQW +>GCF_003691675_PROKKA_01037 +---MTNVSGNASYEYSRAALLAVTEVEAPVEVTSQDLDDQLAEVLTRLRLPGSLLERVAG +VRSRRNWDETEDFQEAAARAGVAALEQAGVPRERVGLLVNTSVTRATLEPSVAVRIHHLM +GLPTSATNFDITNACLGFVNGLMLASTLVDAGQIDYAVVVAAEDASKVQAATVANLHAET +THRGNFMEQFASLTLGSGAAAAVVGRIEDHPDAHRIVRGITRAGTDHHGLCVGDHHGMYT +DSTALLKDGLELVMDAWHDVPAEWAWPQADRFITHQVSQMHTDAIAESAHLDPARIPTTF +PTLGNVGPASLPITLVREMDALEDGDTVVCLGVGSGLNTAMLEIEW +>GCF_005280335_PROKKA_01576 +---MTNVSGNASYEYSRAALLAVTEVEAPLEVTSDDLDERLADVLRRLKLPPHLLQRVAG +VRARRNWDASQDFQEAAAQAGTAALAAAGIGPERVGLLINTSVTRATLEPSVAVRIHHMM +GLPTSATNFDITNACLGFVNGLMMASTLVDAGQVDYAVVVASEDASKVQDATVENLHAST +TNRGNFMEQFASLTLGCGAAAAVVGSIEDHPDAHRIVRGITRAGTDHHDLCVGDHRGMYT +DSTALLNDGLELVMDAWNDTPAEWAWKDADRFITHQVSQLHTNAISESAGLPLDRIPTTF +PVLGNVGPASLPITLVREMDELSAGDTVVCLGVGSGLNTAMLEIQW +>GCF_020097155_PROKKA_01472 +MVQVPHVSGNASFEFSRAALLSVTEVQAPLEVTSDDLDEQLADVLTRLRLPRHLLERVAG +VKVRRAWDAQKDFQQAAAEAGTAALAAAGVAPGQVGLLVNTSVTRATLEPSVAVRIHDLM +GLPTSATNFDITNACLGFVNGLMLASTMVDAGQIDYAVVVAAEDASKVQASTVANLHAET +TVRGNFMEQFASLTLGSGAAAAVVGRTDEHPDAHRILRGITRAGTDHHQLCVGDHNGMFT +DSNALLKDGLELVMDAWHDVPAEWGWDHAARYVTHQVSQMHTDAISESAGIPLEKLPTTF +PVLGNVGPASLPITLVREQDSLRRGDAVVCLGVGSGLNTAMLEIQW +>GCF_023573625_PROKKA_01272 +---MTNVSGNASYEYSRAALLAVTEVEAPVEVTSQDLDDQLAEVLTRLRLPGSLLERVAG +VRSRRNWDETEDFQEAAARAGVAALEQAGVPRERVGLLVNTSVTRATLEPSVAVRIHHLM +GLPTSATNFDITNACLGFVNGLMLASTLVDAGQIDYAVVVAAEDASKVQAATVANLHAET +THRGNFMEQFASLTLGSGAAAAVVGRIEDHPDAHRIVRGITRAGTDHHGLCVGDHHGMYT +DSTALLKDGLELVMDAWHDVPAEWAWPEADRFITHQVSQMHTDAIAESAHLDPARIPTTF +PTLGNVGPASLPITLVREMDALEDGDTVVCLGVGSGLNTAMLEIEW + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001102.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001102.fa new file mode 100644 index 0000000000000000000000000000000000000000..258041edfd56127e1d526c4b896bb62ff9b66444 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001102.fa @@ -0,0 +1,70 @@ +>GCF_002008305_PROKKA_01317 +MPQIPAAPAVLPPADRLPGWDPAWSRLVEIRSAADPEGTVRTLHVADTGPVLAAAGAEIVGTIVAVHGNPTWSWLWRSLL +AETVRRARRGMAAWRVVAPDQLDMGFSERLAHTGSPSASSMGRADDTYRTLGGRIADLDALLAALGLRDLAATGHPLITL +GHDWGGVVSLGWAARHPELVAGVATLNTAVHQPEGAPIPAPLQAALAGPVLPASTVTTDAFLSVTTSLATPALDRETRAA +YHLPYDTAARRGGVGGFVADIPADPGHGSHPELQRVGEDLAALGRTDVPALILWGADDPVFLDRYLDDLRDRLPHARVHR +YEGAGHLLVDDRDITAPLLQWAQLLRAGQLSDPASGLPGPVPHAT--------------ADP-GLEVDLGEEP--GAREP +GMVRLWDHLRDWGAPGSDHREYTALVDMAGAQAGRSLVGTARRPVAVTWGELQEMVSAIATGLWAAGMRPGDRVAMLVPP +GRDLSAALYAVLRVGAVAVVADQGLGVKGMTRAMKSARPRWIIGRTPGLTLARAQSWPGTRISVTEPGAAQRRLLDVSDS +LYAMVDRHRDPATGDAVDEHGTVLPEPALDADAAVLFTSGSTGPAKGVVYTHERLGRLVAMISRTLGIRPGGSLLAGFAP +FALLGPALGAASVSPDMDVTKPATLTARSLADAAIAGQSTVLFASPAALANVVATADGLDAARRDALDAVRLVLSAGAPV +HPQLMRQVRDLMPNAEVHTPWGMTEGLLLTDIDGETVQRLRGADDEGVCVGTALPTVSLAIAPLLEDGTAEDLILDPAQG +HGVLGEIVVSAPHLKDRYDALWHTDQQSKRDGLWRRDGRVWHRTADIGHFDAEGRVWLEGRLQHVITTPEGPLGPGGPEK +TVDALGPVRRSAVVGVGPRGTQAVVVVVEAAVPATRPARRAGQHRDGRPKQGLAPTALASAVRAALEPLPVAAVLVADEI +PTDIRHNSKIDRARVARWAEGVLAGGRAGAL +>GCF_003691675_PROKKA_01038 +MPQIPAAPAALPPADRLPGWDPAWSRLVEIRSAADPEGTVRTLHVADTGPVLAAAGAEIVGTIVAVHGNPTWSWLWRSLL +AETVRRARRGMAAWRVVAPDQLDMGFSERLAHAGYPSAASMGRAGDTYRTLGGRIADLDALLAALGLRDLAATGHPLITL +GHDWGGVVSLGWAARHPELVAGVATLNTAVHQPEGAPIPAPLQAALAGPVLPASTVTTDAFLSVTTSLATPALDRETRAA +YHLPYDAAARRGGVGGFVADIPADPGHGSHPELQRVGEDLASLGRTDVPALILWGADDPVFLDRYLDDLRDRLPRARVHR +YEQAGHLLVDDRDITAPLLQWAQLLRGGQLSDPASGLPGPVPHATTDAA----------ADP-GLEVDLGEEP--GARDP +GVVRLWDHLRDWGAPGSDHREYTALVDMAGAQAGRSLVGTARRPVAVTWGELQEMVSAIATGLWAAGMRPGDRVAMLVPP +GRDLSAALYAVLRVGAVAVVADQGLGVKGMTRAMKSARPRWIIGRTPGLTLARAQSWPGTRISVTEPGAAQRRLLDVSDS +LYAMVDRHRDPAAGDAVDEHGTVLPEPALDADAAVLFTSGSTGPAKGVVYTHERLGRLVALISRTLGIRPGGSLLAGFAP +FALLGPALGAASVSPDMDVTQPATLTAQKLADAAIAGQSSVLFASPAALANVVATADGLDAPQREALDAVRLVLSAGAPV +HPQLMRQVSDLMPNARVHTPWGMTEGLLLTDIDGDEVQRLRTADDAGVCVGSALPTVSLAIAPLLEDGSADDVILDPARG +HGVLGEIVVSAPHLKDRYDALWHTDQQSKRDGLWRRDGRVWHRTADVGHFDAEGRVWLEGRLQHVITTPEGPVGPGGPEK +TVDALGPVRRSAVVGVGPRGTQAVVVVVEAAVPATRPARRPGHHRDGRPKQGLAPTALASAVRAALEPLPVAAVLVADEI +PTDIRHNSKIDRARVADWAEAVLAGGKAGAL +>GCF_005280335_PROKKA_01575 +---------------------------MEIRSAADPEGTVRTLHVADTGPVLAAAGAEIVGTIVAVHGNPTWSWLWRSLL +AETVRRARRGMAAWRVVAPDQLDMGFSERLAHPGHPAAASMGRDGDTYRSLGARIEDLDALLETLGLRDLAATGHPLITL +GHDWGGVVSLGWAGRNPELVDGVATLNSAVHHPEGAPIPAPLQAALAGPVLPASTVLTDAFVSVTTSLAKPALASDVRAA +YHLPYETADRRGGVGGFVADIPAEPSHGSHAELRRVWEGVSALGRAGTPALILWGADDPVFLDRYLDDLRDRLPQARVHR +YEEAGHLLVDDRDVTAPLLQWAQLLRAGQLDDPGSGLPGPVPHAPAASP----------ADEDGLHVDLGEHA--APAGD +DVARLWDHLRDWGAPGSEHREYTALVDMAGAQTGRSLVGGARRPVAVSWGELQETVSAIATGLWAAGMRPGDRVAMLVPP +GRDLSAALYAVLRVGGVAVVADQGLGIAGMTRAMKSARPRWIIGRTPGLTLARAQSWPGARISVTEPGAAQKRLLDVSDS +IYAMIERHRDPAVGEPVDEHGSPLPEPALAADAAVLFTSGSTGPAKGVVYTHERLGRLVAMISRTLGIRPGGSLLAGFAP +FALLGPALGAASVSPDMDVTKPATLTARSLADAAIAGQSTVLFASPAALANVVASADGLDAARRDALDAVRLVLSAGAPV +HPQLMRQVRDLMPNAEVHTPWGMTEGLLLTDIDGETVQRLRGADDEGVCVGTALPTVSLAIAPLLEDGTAEDLILDPAQG +HGVLGEIVVSAPHLKDRYDALWHTDQQSKRDGLWRRDGRVWHRTADIGHFDAEGRVWLEGRLQHVITTPEGPLGPGGPEK +TVDALGPVRRSAVVGVGPRGTQAVVVVVEAAVPATRPARRAGQHRDGRPKQGLAPTALASAVRAALEPLPVAAVLVADEI +PTDIRHNSKIDRARVARWAEGVLAGGRAGAL +>GCF_020097155_PROKKA_01471 +MPRIPAAPAALPPFDQLPGWDPDWSRLVTIRSAADLPGVERTLHVADNGPQLAALGAELAGTILAVHGNPTWSYLWRALL +AETTRRARRGQQAWRVVAPDQLDMGYSERLEHPASPTPSEMGRARSTYRSLGDRLDDLDALTAALGLTDLAATGHPLITL +GHDWGGVVSLGWAGRHRDVVAGVSTLNTAVHQPPQAKIPAPLQAALAGPVLPASTVSTDAFIAVTTSLAKPSLAPEVRAA +YHLPYPSAERRGGVGGFVADIPVDASHGSHAALEEVSSGVSALGAQGTPALIQWGADDPVFLDRYLDDLRDRLPAARVHR +YEEAGHLLIDDRDVVTPLLTWAQLLTAGLLADPASGLPGPRPHADDAAPRTSALPLLPEASR-GVHVDIADHASEAGSPA +GLPRLWDRLEDWGAPDSPMREYTALVDMAGAETSRALFGGARRPVAVSWGEFQETVSAIATGLWEAGMRPGDRVSMLVPP +GRDLSAALYAVLRVGAVAVVADQGLGVSGMTRAMKSARPRWVIGKTAGLTLARAQNWPGTRLSVSTLAAPQRALLDVSDS +LYAMVDRHRAPELGVPRDAAGAPLPVPELGADAAVLFTSGSTGPAKGVVYTHERLGHLVRLIARTLDIRPGASLLAGFAP +FALLGPALGAASVSPVMDVTKPATLTAAALADAAIAGQSSVLFASPAALANVVATAGDLSGEQRTALRQVRQVLSAGAPV +HPALLRQVSALMPEAEVNTPYGMTEGLLLANIDGETIHALRRADDAGVCVGSPLPTVEFRIAPLAEDGTPEEVTLDPAAG +HGVLGEFVVSAPHLKDRYDALWFTDHQSKRDGLIRRDGRVWHRTADVGHFDAEGRVWIEGRAQHVLTTPDRPLAPGGPEG +VVDALGPVARSAVVGVGPAGTQAVVVVVEAAVPAARPPRRAGHHRDGRPKQGLAPTALAASVRSALEPLPVAAVLVADHI +PTDIRHNSKIDRPRVARWAEGVLAGGTVDGL +>GCF_023573625_PROKKA_01273 +MPQIPAAPAALPPADRLPGWDPAWSRLVEIRSAADPEGTVRTLHVADTGPVLAAAGAEIVGTIVALHGNPTWSWLWRSLL +AETVRRARRGMAAWRVVAPDQLDMGFSERLAHAGSPSAASMGRAGDTYRTLGGRIADLDALLAALGLRDLAATGHPLITL +GHDWGGVVSLGWAARHPELVAGVATLNTAVHQPEGAPIPAPLQAALAGPVLPASTVTTDAFLSVTTSLATPALDRETRAA +YHLPYDTAARRGGVGGFVADIPADPGHGSHPELQRVGEDLAALGRTDVPALILWGADDPVFLDRYLDDLRDRLPHARVHR +YEQAGHLLVDDRDITAPLLQWAQLLRGGQLSDPASGLPGPVPHATADAA----------ADP-GLEVDLGEEP--GAREP +GVVRLWDHLRDWGAPGSDHREYTALVDMAGAQAGRSLVGTARRPVAVTWGELQEMVSAIATGLWAAGMRPGDRVAMLVPP +GRDLSAALYAVLRVGAVAVVADQGLGVKGMTRAMKSARPRWIIGRTPGLTLARAQSWPGTRISVTEPGAAQRRLLDVSDS +LYAMVDRHRDPAAGDAVDEHGTVLPEPALDADAAVLFTSGSTGPAKGVVYTHERLGRLVALISRTLGIRPGGSLLAGFAP +FALLGPALGAASVSPDMDVTQPATLTAQKLADAAIAGQSSVLFASPAALANVVATADGLDAPRREALDAVRLVLSAGAPV +HPQLMRQVSDLMPNARVHTPWGMTEGLLLTDIDGAEVQRLRAADDEGVCVGSALPTVSLAIAPLLEDGSAEDVILDPARG +HGVLGEIVVSAPHLKDRYDALWHTDQQSKRDGLWRRDGRVWHRTADVGHFDAEGRVWLEGRLQHVITTPEGPVGPGGPEK +TVDALGPVRRSAVVGVGPRGTQAVVVVVEAAVPATRPARRPGHHRDGRPKQGLAPTALASAVRAALEPLPVAAVLVADEI +PTDIRHNSKIDRARVADWAEAVLAGGKVGAL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001109.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001109.fa new file mode 100644 index 0000000000000000000000000000000000000000..e6ba927abd771c500546c2fda6bbe4c20b446d89 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001109.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_01324 +MITLDRPTLTARALEDLTASALVVGVGTGPDGPVLLTDALPAEAATALEASFELLGVRGAADEVHRLPGLGGVPVPLLVL +AGVGGLDDDGEAADESLRRAAGAAVRSLAGTDAVALALPADTPARLAAVAEGAVLGAYAFTAQKSERARAETDTSRPVRE +VEVVTPLAAADADPVLRRAAVVGDAVCAVRDLVNTAPSHLYPATFADAVAEDLADSSVSVDVWDEDRLRAEGFGGILAIG +QGSSRPPRLVRIEHAPADAAAHIALVGKGITFDTGGISLKPAASMMTMKSDMAGAATVFAVVRAAAALDVPVKVTGWLAL +AENMPSGTAIRPSDVITMYGGKTVEVMNTDAEGRVVMADALVAATDERPDAVLDVATLTGAQLVALGVRHTGVMGDDALR +DEVVAAADAAGELAWGMPLPEQLRASLTSRVADISNMGDRFGGMMTAATFLREFVDAGRSEGDAA-ARTPWAHLDIAGPS +FNESAAYGYTPQDATGVMVRTLVGLIEGRAR +>GCF_003691675_PROKKA_01045 +MITLDRPTLTARALEDLTASALVVGVGTGPDGPVLLTDALPAEAATALEASFELLGVRGAEDEVHRLPGLGGVPVPLLVL +AGVGGLDDDGEASDESLRRAAGAAVRSLAGTDAVALALPADTPARLAAVAEGAVLGAYAFTAQKSERARAEADSSRPVRE +LEVVTPLAAADADPVLRRAAVVGDAVCAVRDLVNTAPSHLYPATFADAVAEDLADSSVSVDVWDEDRLRAEGFGGILAIG +QGSSRPPRLVRIEHAPADAAAHIALVGKGITFDTGGISLKPAASMMTMKSDMAGAATVFAVVRAAAALDVPVKVTGWLAL +AENMPSGTAIRPSDVITMYGGKTVEVMNTDAEGRVVMADALVAATDERPDAVLDVATLTGAQLVALGVRHTGVMGDDALR +DEVVAAADAAGELAWGMPLPEQLRASLNSRVADISNMGDRFGGMMTAATFLREFVDAGRPQDDDA-ARTPWAHLDIAGPS +FNESAAYGYTPQDATGVMVRTLVGLIEGRAR +>GCF_005280335_PROKKA_01567 +MITLDRPTLTARTLEDVSASALVVGVGTGPDGPVLLTDALDAPAASALEASFDLLGVRGAQDEVHRLPGLGGSPVPMLVL +VGVGPLDDDGEVSDEALRRAAGAAVRSLAGTDAVALALPADTAQRLSAVAEGASMGAYAFTALKSEKAREEAEKSRPVRG +LEFVTALGAEEAEAALRRAAVLGDAVCAVRDLVNTAPSHLYPGTFADAVAQDLSGSSVSVDVWDEERLTAEGFGGILAIG +QGSSRPPRLVRIEHAPAEAKAHIALVGKGITFDTGGISLKPAASMMTMKSDMAGAATVFAVVRAAAALDVPVKVTGWLAL +AENMPSDTAIRPSDVVTMYGGKTVEIMNTDAEGRVVMADALVAATDERPDAVLDVATLTGAQMVALGTRYTGVMGDDALR +TEVVEAADRVGELAWAIPIPENQRASLNSRVADISNMGDRFGGMMTAAAFLREFVDAGRTGEEDA-PRTPWAHLDIAGPS +FNESAAHGYTPQDATGVMVRTLMGLIEGRGR +>GCF_020097155_PROKKA_01463 +MISQERPTLIARSLAEVTAPAVVVGVGAGPDGPLLLTDALPDEAAVALESSLELLEVKGRPDEVHRLPGLSGSRWPLLVL +VGLGDLDQDGGADDEALRQASGAAVRSLAGTESVALALPADTPSRLAAVAEGAALGAYAFTAFTSA---GDTPGRAPVST +VELVTPLPASASEPVLRRAAVIGDAVCAVRDLVNTPPSHLYPASFADAVVGDLEGTDVDVRVWDEAQLAAEGFGGIVGIG +QGSSRPPRLVRVEHAPAGARAHVALVGKGITFDTGGISLKPPASMMTMKSDMAGAATVFAVVRAAAALEIPVRVTGWLAM +AENMPSDTALRPSDVLTMHGGKTVEVMNTDAEGRVVMADALVAATDERPDAVLDVATLTGAQLVALGVRHTGVMGDEALR +NEVVAAAGAAGELAWPMPIPEQLRPSLDSRVADISNMGERFGGMMTAAAFLREFVDAGRPAAERAESPTPWAHLDIAGPS +FNESAAYGYTPRDATGTMVRTLVGLIAGRAG +>GCF_023573625_PROKKA_01280 +MITLDRPTLTARALEDLTASALVVGVGTGPDGPVLLTDALPAEAATALEASFELLGVRGAEDEVHRLPGLGGVPVPLLVL +AGVGGLDDDGEAADESLRRAAGAAVRSLAGTDAVALALPADTPARLAAVAEGAVLGAYAFTAQKSERARAEADTSRPVRE +LEVVTPLAAADADPVLRRAAVVGDAVCAVRDLVNTAPSHLYPATFADAVAEDLADSSVSVDVWDEDRLRAEGFGGILAIG +QGSSRPPRLVRIEHAPADAAAHIALVGKGITFDTGGISLKPAASMMTMKSDMAGAATVFAVVRAAAALDVPVKVTGWLAL +AENMPSGTAIRPSDVITMYGGKTVEVMNTDAEGRVVMADALVAATDERPDAVLDVATLTGAQLVALGVRHTGVMGDDALR +DEVVAAADAAGELAWGMPLPEQLRASLNSRVADISNMGDRFGGMMTAATFLCEFVDAGRPEGDAA-ARTPWAHLDIAGPS +FNESAAYGYTPQDATGVMVRTLLGLIEGRAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001135.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001135.fa new file mode 100644 index 0000000000000000000000000000000000000000..ed6e666024f561e9a94e202a3dafeed7dc0abf79 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001135.fa @@ -0,0 +1,51 @@ +>GCF_002008305_PROKKA_01353 +MSRDESTRPAAEG-----RFADLGRVHLLGIGGVGVSGVARILQEQGVAVSGSDAKDLPV +MRELAAGGARITVGYDAAHLGRDVTTVIASSIAGPGNPEHDAAVARGLRVLHRSEGLALA +MRGHRVLAVAGTHGKTTTSSMAAMAFSDAGWDPTFAVGAAVAGLGTNARAGRGEWFIAEA +DESDGTLVNYPSTIGIVTTVEADHLDHYGTEEAVHQVFRDFAGGLPAAAQGGVLVACLDD +AGAADLAAWAREHAAADVVTYGSAPRDGVAPDLLVTDLAVEPGETGVGQRATFRMAGGPE +RTLHLQVPGRHNALNAAAVVLAAVRAGMAFEAAVRGVEAFRGTARRFEFRGAARGVRVFD +DYAHHPTEVAAAVSAGRAVAGDARVHVLFQPHLFSRTRDFAAEFAAALSGADAVRVLPVY +AAREEPMPGVDSSLIASRLTTGAAEDRVVAEDRAEAVRSLAAGATAGDVVLTMGAGDVTA +LGADLLAELGRDAAPGVAHP +>GCF_003691675_PROKKA_01073 +MSRDESTRPAAEG-----RFADLGRVHLLGIGGVGVSGVARILQEQGVAVSGSDAKDLPV +MRELAAGGARITVGYDAAHLGRDVTTVIASSIAGPGNPEHDAAVARGLRVLHRSEGLALA +MRGHRVLAVAGTHGKTTTSSMAAMAFSDAGWDPTFAVGAAVAGLGTNARAGQGEWFIAEA +DESDGTLVNYPSTIGIVTTVEADHLDHYGTEEAVHQVFRDFAGGLPAAAQGGVLVACLDD +AGAADLAAWAREHAAADVVTYGSAPRDGVAPDLLVTDLAVEPGETGVGQRATFRMAGGPE +RTLHLQVPGRHNALNAAAVVLAAVRAGMAFEAAVRGVEAFRGTARRFEFRGAARGVRVFD +DYAHHPTEVAAAVSAGRAVAGDARVHVLFQPHLFSRTRDFAAEFAAALSGADAVRVLPVY +AAREEPMPGVDSSLIASRLTTGAAEDRVVAEDRAEAVRSLAAGATAGDVVLTMGAGDVTA +LGPDLLAELGRDAAPGVAHP +>GCF_005280335_PROKKA_01539 +MSRDESTRPVAEG-----RFDELGRVHLLGIGGVGVSGVARILQDQGVAVSGSDAKDLPV +MRELAAAGARITVGYDAAHLGEDVTTVIASSIAGPGNPEHDAAVARGLRVLHRSEGLALA +MRGHRVLAVAGTHGKTTTSSMAAMAFASAGWDPTFAVGAAVAGLGTNARAGQGEWFIAEA +DESDGTLVNYPTTIAVVTTVEADHLDHYGTEEAVHQVFRDFAAGLPDAASGGVLVACLDD +DGAAGLAAWAREHAAARVLTYGTGPRDGVAPDLLVADLAVEPGESGVGQRATLRLASGPE +ATLHLQVPGRHNALNAAAVALAAVQAGMGFEDAVRGLEAFRGTARRFEFRGAGRGVKVFD +DYAHHPTEVTAAVSAGRAVAGDGRVHVLFQPHLFSRTREFAAEFAAALSAADVVRVLPVY +AAREEPMEGVDSSLIAGRLTTAADADRAVAEDRAVAVRELAAGAESGDVILTMGAGDVTA +LGADLVAALGPDAAPGAAGR +>GCF_020097155_PROKKA_01435 +M----TTQQTPEGRARRERVAALGRVHLLGIGGVGVSGVARILQDQGVAISGSDAKDLPV +MHDLAAGGARITVGYDAAHVGDDVTTVIASSIAGPGNPEHDAAVARGLRVLHRSEGLALA +MEGHRVLAVAGTHGKTTTSSMAAMAFTDAGWDPTFAVGAAVAGLGTNARAGAGEWFVAEA +DESDGTLVNYPTTIAVVTTVEADHLDHYGTEEAVHEVFRVFAGQLPAAEDGGALVACLDD +EGAAGLAAWAHEHARAAVVTYGTGPRDGVEPDLLVDGVTVEPGESGVGQRARFTLADGTS +AEVRLQVPGRHNALNAAAVALAAVRAGMSLREAVHGLEQFRGTARRFEFRGAERGVRVFD +DYAHHPTEVVAAVSAARAVAGEGRVHVLFQPHLFSRTRDFAAEFAAALSGADRVRVLPVY +AAREEPMEGVDATLITRALTTPDPADRTVAVDRAAAVRELAAGAREGDVILTMGAGDVTA +LGPDLVAALAADPSVDA--- +>GCF_023573625_PROKKA_01308 +MSRDESTRPAAEG-----RFADLGRVHLLGIGGVGVSGVARILQEQGVAVSGSDAKDLPV +MRELAAGGARITVGYDAAHLGRDVTTVIASSIAGPGNPEHDAAVARGLRVLHRSEGLALA +MRGHRVLAVAGTHGKTTTSSMAAMAFSDAGWDPTFAVGAAVAGLGTNARAGQGEWFIAEA +DESDGTLVNYPSTVGIVTTVEADHLDHYGTEEAVHQVFRDFAGGLPAAAQGGVLVACLDD +AGAADLAAWAREHAAADVVTYGSAPRDGVAPDLLVTDLAVEPGETGVGQRATFRMADGPE +RTLHLQVPGRHNALNAAAVVLAAVRAGMAFEAAVRGVEAFRGTARRFEFRGAARGVRVFD +DYAHHPTEVAAAVSAGRAVAGDARVHVLFQPHLFSRTRDFAAEFAAALSGADAVRVLPVY +AAREEPMHGVDSSLIASRLTTGAAEDRVVAEDRAEAVRSLAAGATAGDVVLTMGAGDVTA +LGPDLLAELGRDAAPGVAHP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001138.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001138.fa new file mode 100644 index 0000000000000000000000000000000000000000..48258ba51e793b20faf390e94723b38ab16bf18a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001138.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_01356 +MTGPASDAAPAPVRRPRADTARTADLTSWDAPGWAGLRVVVTGLGLTGFSVADTLAELGAAVVVVEGDDGPENRARAETL +RIVGVREVLLDRAATQALPEVDGAAADLVVTSPGWRPDQPLLMAAHAAGLPIWSDVELAWRLRERAGRKTADWVCLTGTN +GKTTTVTMVEAILRADGRRAVACGNVGTPVLDAIRDPQGFDVLALELSSFQLHWTHGLAPASSAVLNLAEDHVDWHGSME +EYAAAKGKVYANTRVACVFNEQDPLTRTLVERADVQEGCRAIGFTTDTPGLSDIGVVDGILVDRAFLDNRRHEAIALAER +ADLGPVAPRHTVANAAAAAALTRAVGVSPAAVAEGLRSYDRGEHRIQLVATSRDVMWVNDSKATNPHAADASLAAFSSVV +WLAGGLPKGVTYHELVAAHAHRLRAVVLLGRDTSALRAALAAHAPEVPVHAPLAAADGTGPADGAAVMAEAVRVADGLAR +PGDIVLMAPAAASMDQFRSYAARGDAFIEAVAGLMREHGWDVHDDAAPDAD +>GCF_003691675_PROKKA_01076 +MTGPASAAAPAPVRRPRADTARTADLTSWDAPGWAGLRVVVTGLGVTGFSVADTLAELGAAVVVVDGDDGPENRARAETL +RIVGVREVLLDRAATQVLPEVDGAAADLVVTSPGWRPDQPLLMAAHAAGLPIWSDVELAWRLRERAGRKTADWVCLTGTN +GKTTTVTMVEAILRADGRRAVACGNVGTPVLDAIRDPQGFDVLALELSSFQLHWTHGLAPASSAVLNLAEDHVDWHGSME +EYAAAKGKVYANTRVACVFNEQDPVTRTLVERADVQEGCRAIGFTTDTPGLSDIGVVDGILVDRAFLDNRRHEAIALAER +ADLGPVAPRHTMANAAAAAALTRAVGVSPAAVAEGLRSYDRGEHRIQLVATSRDIMWVNDSKATNPHAADASLAAFSSVV +WLAGGLPKGVTYHELVAAHAHRLRAVVLLGRDTSALRAALAAHAPDVPVHAPLAAADGTGPADGAAVMAEAVRVADGLAR +PGDTVLMAPAAASMDQFRSYAARGDAFIEAVAGLMREHGWDVHDDAAPDTD +>GCF_005280335_PROKKA_01536 +MS-ASENTALVPVRRPLADTGRTAALTSWDAEGWAGLRVVVAGLGVTGFSVADTLAELGAVVVVVDGNDGPENQARAETL +RIVGVHEVLLDAEATQSLPEVDGAPAELVVTSPGWRPDQPLLMAAHAAGLPIWSDVELAWRVRERAGRPTADWVCLTGTN +GKTTTVTMVEAILRADGRRAIACGNVGTPVLDAIRDPEGYDVLALELSSFQLHWTHRVAPASSAVLNLAEDHVDWHGSME +EYAAAKGKVYENTRVACVFNEHDPVTRTLVERADVQDGCRAVGFTTDTPGLSDVGVVDGILVDRAFTENRRHEAIALAER +TDLGPVAPRHTMANAAAAAALTRAVGVAPAAVAEGLRSYDRGEHRIQLVATSRDVMWVNDSKATNPHAADASLAAFTSVV +WIAGGLPKGVTYEELVGAHAHRLRAVVLLGTDASALRSALAAHAPDVPVHAPLADADGTGPADGAAVMAEAVRVADGLAR +PGDTVLMAPAAASMDQFRSYAQRGEAFIDAVAALMREHGWDTDAGTAAP-- +>GCF_020097155_PROKKA_01432 +MS--------APVMRPHADTDRTRGLRTWDDAGWAGLRVVVTGLGVSGFSAADTLAELGARVVVVDGRDSPENRAKADTL +RIVGVADVLLSEDATHSLPEVDGERPDLVVTSPGWRPDQPLLMAAHEAGLPIWSDVELAWRLRERAGRRTADWVCLTGTN +GKTTTVTMVEAILRADGRRALACGNVGTPVLDAVRDPEGFDTLAVELSSFQLHWTHSIVPASSAVLNLAEDHVDWHGSME +EYAAAKGKVYERTTVACVFNEADALTRTLVERADVAEGCRAVGFTTDTPGLSDVGVVDGIIVDRAFLENRRHEAIALAER +SDLGAVAPRHTVANACAAAALTRAVGVSPEAVAEGLRSYDRGEHRIQLVATSRDVMWVNDSKATNPHAADASLAAFSSVV +WIAGGLPKGVTYDELVSAHAGRLREVILLGTDTSELRRALAAHAPEVPVHAPLADADGHGSPDGRAVMAEAVRLADAHAC +PGDTVLMAPAAASMDQFRSYAERGDAFIAAVAELMREHGWDVDSEADAPA- +>GCF_023573625_PROKKA_01311 +MTGPASDAAPAPVRRPRADTARTADLTSWDAPGWAGLRVVVTGLGLTGFSVADTLAELGAAVVVVDGDDGPENRARAETL +RIVGVREVLLDRAATQVLPEVDGAAADLVVTSPGWRPDQPLLMAAHAAGLPIWSDVELAWRLRERAGRKTADWVCLTGTN +GKTTTVTMVEAILRADGRRAVACGNVGTPVLDAIRDPEGFDVLALELSSFQLHWTHGLAPASSAVLNLAEDHVDWHGSME +EYAAAKGKVYANTRVACVFNEQDPLTRTLVERADVQEGCRAIGFTTDTPGLSDIGVVDGILVDRAFLDNRRHEAIALAER +ADLGPVAPRHTMANAAAAAALTRAVGVSPAAVAEGLRSYDRGEHRIQLVATSRDIMWVNDSKATNPHAADASLAAFSSVV +WLAGGLPKGVTYHELVAAHAHRLRAVVLLGRDTSALRAALAAHAPDVPVHAPLAAADGTGPADGAAVMTEAVRVADGLAR +PGDTVLMAPAAASMDQFRSYAARGDAFIEAVAGLMREHGWDVHDDAAPDTD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001153.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001153.fa new file mode 100644 index 0000000000000000000000000000000000000000..329bc698883c2e4bc29807b885b90f1b2dd9406a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001153.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_01373 +MHEISEPYHHPRLSPEANITDFLERQATERPDHGLFAVPDAQDQWTDVSARDARERVRALAKGLIAAGIQPGETVGLLAS +TRLEWTLVDFAIWYAGAVTVPVYETSSVSQVSWIIEDSDVRAVVTGNEDLAKTVRDAVQREGLPELIGLWTMDPADGAPG +SGLEALVALGADVTDEELETRRSSAGLADLATIIYTSGTTGRPKGCELTHENFAELVNQTLSSSLGDVVREDTSTVLFIP +LAHVFARFVSVLTVAAGARCGHVSDIKRLSVSLQTFQPSFVLAVPRVFEKIYNAALLNAQSGGKEKIFRRGADVAIRWSR +ALDSGQMTAPLRLQRAFYSALVYRRIRTAMGGRLAYAVSGGGPLSTDLAHFFRGVGVTILEGYGLTETTAPITVGRPDRL +KIGTVGHPLGGNQVRIAEDGEILTRGTSLMRGYHNRPEANEEAF-EDGWFRTGDLGALDDDGFLTITGRKKELLVTAGGK +NVAPAMLEDAIRSDALVSQVMVVGDGKPFIAAIVTLDTDTLPAWLAANGLPKDLDVAAAAREDAVRRHIQEAVDKANSLV +SRAEGIREFRILDRDFSLEEGHVTPSLKMRRSAIMKDFAAQIADIYGEPAPQN +>GCF_003691675_PROKKA_01093 +MHEISEPY-HPRLSPEANITDFLERQATERPDHGLFAVPDAQDQWTDVSARDARERVRALAKGLIAAGIQPGETVGLLAS +TRLEWTLVDFAIWYAGAVTVPVYETSSVSQVSWIIEDSHVRAVVTGNENLAKTVRDAVQREGLPELIGLWTMDPADGAPG +SGLEALVALGTDVTDEELETRRSSAGLADLATIIYTSGTTGRPKGCELTHENFAELVNQTLSSSLGDVVRQDTSTVLFIP +LAHVFARFVSVLTVAAGARCGHVSDIKRLSVSLQTFQPSFVLAVPRVFEKIYNAALLNAQSGGKEKIFRRGADVAIRWSR +ALDSGQMTAPLRLQRAFYSALVYRRIRTAMGGRLAYAVSGGGPLSTDLAHFFRGVGVTILEGYGLTETTAPITVGRPDRL +KIGTVGHPLGGNQVRIAEDGEILTRGTSLMRGYHNRPEANEEAF-EDGWFRTGDLGALDDDGFLTITGRKKELLVTAGGK +NVAPAMLEDAIRSDALVSQVMVVGDGKPFIAAIVTLDTDTLPAWLAANGLPKDLDVAAAAREDAVRRHIQEAVDKANSLV +SRAEGIREFRILDRDFSLEEGHVTPSLKMRRSAIMKDFAAQIADIYGEPAPHN +>GCF_005280335_PROKKA_01519 +MREISEPY-HPRLSPESNITDFLERQAEERPDHGLFAVADEQDQWTDVSARDARERVRALAKGLIAAGVGAGDRVGLIAA +TRLEWTLVDFAIWYAGAVTVPIYETSSATQVAWIVEDADVCAVVAGDESLVKTVRDAVHREHLPELRGVWVMDVAGGEPG +SGLDELAALGADVSDEDLEARRSAANLEDLATIIYTSGTTGRPKGCELTHENFAELVNQTLSSSLGEVVRPDTSTVLFIP +LAHVFARFVSVLTVAAGARCGHVTDLKRLSNSLQTFQPSFVLAVPRVFEKIYNAALLNAQSGGKDKIFRRGADVAVRWSR +ALDSGKMTAPLRLQRAFYSALIYRRIRAAMGGRLEYAVSGGGPLSPDLAHFFRGVGLTILEGYGLTETTAPITVGRPGRL +KIGTVGLPLGGNAVRIAEDGEILTRGTSLMRGYHDRPEANEEAF-EDGWFRTGDLGSLDEDGFLTITGRKKELIVTAGGK +NVAPAMLEDAIRSDALISQVMVVGDAKPFIAAIVTLDADTLPSWLAAHGLPKDLDVAAAAKEERVRRHVQEIVDKASSAV +SRAEGIREFRILDRDFSMEEGHMTPSLKMKRAVIMQDFAAEIADIYGEAPAQG +>GCF_020097155_PROKKA_01414 +MRQISEPY-LPRLSPDAAITDFLRDQAVQHPERALFAVPREDGSWDDVTAAEAWDRVRALARGLVAAGVGPGDRVAIVSA +TRLEWTLADFAIWTAGAVTVPVYETSSASQIAWIFEDAGVGAAIADTPARAKSVSDAVHREGLPELKGLWVMDEDGGAPG +AGLDRLTDAGADVPADELDARREGVTLESLATIIYTSGTTGRPKGCELTHGNFAELVNQTLRSSLGEVVDEGASTLLFIP +LAHVFARFVSVLTVAAGARCGHVPDLSRLATSMDTYHPTFLLAVPRVFEKIYNASLLKAQAGGKEKIFRRGADVAVRWSR +ALEEGRMTAPLRLQRAFYSALLYRRIREAMGGHLKYAVSGGGPLSPDLAHFFRGVGVTILEGYGLTETTAPITVGRPGKL +KIGRVGQPLGGNEVRIDDDGEILTRGTSLFRGYRNRPEANAEAFTEDGWFRTGDLGELDDDGFLKITGRKKEIIVTAGGK +NVAPAQLEDAIRSDALVSQVMVVGEAKPFVAAIVTLDADTLPSWASAHGLDPQISMAEAAREPQVIAHVQKAVDRANDTV +SRAEGIREFRILDRDFSADEGHMTPSLKMRRTAILKDFQPVLDEIYGAGPARG +>GCF_023573625_PROKKA_01328 +MHEISEPYHHPRLSPEANITDFLERQATERPDHGLFAVPDAQDQWTDVSARDARERVRALAKGLIAAGIQPGETVGLLAS +TRLEWTLVDFAIWYAGAVTVPVYETSSVSQVSWIIEDSHVRAVVTGNENLAKTVRDAVQREGLPELIGLWTMDPADGAPG +SGLEALVALGTDVTDEELETRRSSAGLADLATIIYTSGTTGRPKGCELTHENFAELVNQTLSSSLGDVVRQDTSTVLFIP +LAHVFARFVSVLTVAAGARCGHVSDIKRLSVSLQTFQPSFVLAVPRVFEKIYNAALLNAQSGGKEKIFRRGADVAIRWSR +ALDSGQMTAPLRLQRAFYSALIYRRIRTAMGGRLAYAVSGGGPLSTDLAHFFRGVGVTILEGYGLTETTAPITVGRPDRL +KIGTVGHPLGGNQVRIAEDGEILTRGTSLMRGYHNRPEANEEAF-EDGWFRTGDLGALDDDGFLTITGRKKELLVTAGGK +NVAPAMLEDAIRSDALVSQVMVVGDGKPFIAAIVTLDTDTLPAWLAANGLPKDLDVAAAAREDAVRRHIQEAVDKANSLV +SRAEGIREFRILDRDFSLEEGHVTPSLKMRRSAIMKDFAAQIADIYGEPAPHN diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001162.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001162.fa new file mode 100644 index 0000000000000000000000000000000000000000..cb399e6bfecdf4f2252931a82b404d888dd51a69 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001162.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01403 +------------MSLI----R-RRPAALSLATLAALALAASGCAVD-DGETRAALQSAED +RLAQAEDRISELEADASDRV-DLGQLRQEAEDALEEADQR----AAEV------------ +-------------------------VEDLTRSLPSGSDIVDVEALREDGKVVIEYGQSLL +EADPQVLEDTMREAADRARDAIPDLEDVEFRVGDRTFTY +>GCF_003691675_PROKKA_01133 +------------MSLI----R-RRPAALSLATLAALALAASGCAVD-DGATRAALQSAED +RLAQAEDRISELEADASDRV-DLGQLRQEAEGALEEADQR----AAEV------------ +-------------------------VEDLTRSLPSGSDIVDVEALREDGKVVIEYGQSLL +EADPQVLEDTMREAADRARDAIPDLEDVEFRVGDRTFTF +>GCF_005280335_PROKKA_01492 +------------MTTL----RPRRPAVLSLAALAALSLALSGCGVD-EGDAQAALESAED +RLAQAEDRISELEADASNRV-DLGELQRQAEGALDGADQR----VGELLEDLRGRAEPLR +EITEQDLRDLELPRIEGLDLEAEAAVEDLMKSLPSGPDMADVEALREDGRVIVEYAESAL +EADPQVLEDTMREVAEQARNAIPDLKDVEFRVGDQSFRF +>GCF_020097155_PROKKA_01404 +MVVPGWPASLALMTTTPRASRASRPAA-ALLTLAGAALALTGCAAGPDQETADALASADE +RIASAEAEIADLK-DRMDRVPDTAAMQSQASEAVSSAVAQATGAAGSLGADAARRAQ--- +--------------------EA---VDGVS-GLPDAEAVQQVE---DGGRVIVEYAQDAL +PKDPAELQARLDEAADAVRRQVPDSAGVEFKVGDQTFTF +>GCF_023573625_PROKKA_01353 +------------MSLI----R-RRPAALSLATLAALALAASGCAVD-DGATRAALQSAED +RLAQAEDRISELEADASDRV-DLGQLRQEAEGALEEADQR----AAEV------------ +-------------------------VEDLTRSLPSGSDIVDVEALREDGKVVIEYGQSLL +EADPQVLEDTMREAADRARDAIPDLEDVEFRVGDRTFTF + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001166.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001166.fa new file mode 100644 index 0000000000000000000000000000000000000000..1329724221482d0321fb439474a519bce2036763 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001166.fa @@ -0,0 +1,50 @@ +>GCF_002008305_PROKKA_01412 +MATHDAPAEDRPSGAYADAHARSLRDPEGFWLDAARAIDWTVAPTRALDDSAAPLYRWFPDGELNTAFNCLDRHVEAGRG +DAVALIHDSAMTGEVTRYTYAELTDAVARLAGALAARGVGKGDRVLVYLPMIPQAPIAMLACARLGAVHSVVFGGFAPRE +LASRIDDAAPDVVLTCSGGIEPKRRVEYLPAVAEALETAAHPVRTVLVHHREGFETALADADGRGGASWEDWGEAVAAAE +PADCVPVRATDPLYVLYTSGTTGKPKGVVRDNGGHAVALRWTMEHIYDVGPGQAMCTASDVGWVVGHSYIVYGPLLAGAT +TVMYEGKPVGTPDAGAFWRLIEDHGVRSFFTAPTALRAIRRADPEGELLKAHDLSSLRHFFAAGERLDPETQRWIEGLLG +MPVIDHWWQTETGWAIAANPVGLEQLPVKIGSSSVPSPGVDLVVLDGLGEPVPAGTEGNIALRLPLPPGSLPTLWRDDQR +YIDSYLSAFPGHYATGDSGVVDEDGYVFVLGRTDDVINVSGHRLSTGVLEAALGSHPAVAECAVIGVADPLKGQRPSGYV +VLKSGVETPEPGSEAEAALLDELRQAVRREVGPVADFRDVVVVDALPKTRSGKILRKTMRQMADGEEYAVPSTIEDPAVL +EALAGVLRPAR +>GCF_003691675_PROKKA_01143 +MATHDAPAEDRPSGAYADAHARSLRDPEGFWLDAARAIDWTVAPTRALDDSAAPLYRWFPDGELNTAFNCLDRHVEAGRG +DAVALIHDSAMTGEVTRYTYAELTDAVARLAGALAARGVGKGDRVLVYLPMIPQAHIAMLACARLGAVHSVVFGGFAPRE +LASRIDDAAPDVVLTCSGGIEPKRRVEYLPAVAEALETAAHPVRTVLVHHREGFETALADADGRGGASWEDWGEAVAAAE +PADCVPVQATDPLYVLYTSGTTGKPKGVVRDNGGHAVALRWTMEHIYDVGPGQAMCTASDVGWVVGHSYIVYGPLLAGAT +TVMYEGKPVGTPDAGAFWRLIEDHGVRSFFTAPTALRAIRRADPEGELLKDHDLSSLRHFFAAGERLDPETQRWIEGLLG +MPVIDHWWQTETGWAIAANPVGLEQLPVKIGSSSVPSPGVDLVVLDGLGEPVPAGTEGNIALRLPLPPGTLPTLWGDDQR +YIDSYLSAFPGHYATGDSGVVDEDGYVFVLGRTDDVINVSGHRLSTGVLEAALAAHPAVAECAVIGIADPLKGQRPSGYV +VLKSGVETPEAGSEAEAALLDELRQAVRREVGPVADFRDVVVVDALPKTRSGKILRKTMRQMADGEEYAVPSTIEDPAVL +EALAGVLRPAR +>GCF_005280335_PROKKA_01487 +MM---PPPNPAPPAPTPPPTPAPLHDPEGFWLEAAEAIDWTVPPTRALDDSAAPLYRWFPDGELNTAFNCLDRHVEAGRG +DAVALIHDSAMTGEVTRFTYAELTDAVARLAGALAARGVGKGDRVLVYLPMIPQAHIAMLACARLGAVHSVVFGGFAPRE +LASRIDDAAPDVVLTCSGGIEPKRRVEYLPAVAEALETAAHPVRTVLVHHREGFETALADVDGRGGASWEDWGEAVAAAE +PAECVPVQATDPLYVLYTSGTTGKPKGVVRDNGGHAVALRWTMEHIYDVGPGQAMCTASDVGWVVGHSYIVYGPLLAGAT +TVMYEGKPVGTPDAGAFWRLIEDHGVRSFFTAPTALRAIRRADPEGELLQDHDLSSLRHFFAAGERLDPETQRWIEGLLG +MPVIDHWWQTETGWAIAANPVGLEQLPVKIGSSSVPSPGVDLVVLDGLGEPVPAGTEGNIALRLPLPPGTLPTLWRDDQR +YIDSYLSAFPGHYATGDSGVVDEDGYVFVLGRTDDVINVSGHRLSTGVLEAALASHPAVAECAVIGVADPLKGQRPSGYV +VLKSGVPVPEPGSEAEAALLDELRQAVRREVGPVADFRDVVVVDALPKTRSGKILRKTMRQMADGEEYAVPSTIEDASVL +DALAPVLRPGA +>GCF_020097155_PROKKA_01394 +MA----TDTTAAPRSYADVHRRSLEDRESFWLAAAEAIDWTVPPTRALDDSAAPLYRWFPDGVLNTAHNCLDRHVAAGRG +EELALVHDSAMTGEVTRFTYAELTAEVARLAGALAERGVGKGDRVLVYLPMIPQAPIAMLACARLGAVHSVVFGGFAPRE +LAARIDDATPDVVLTCTGGIEPKRRVEYLPAVAEALEIAEHPVRTVLVHHREGFATAREDVADRGGAEWEDWAEAVADAA +PAGCVDVAATDPLYILYTSGTTGRPKGVVRDHGGHAVALRWTMENIYDVGPGQVMCTASDVGWVVGHSYIVYGPLLAGAT +TVLYEGKPVGTPDAGAFWRLIQDHGVRSFFTAPTALRAVRKADPEAALLAEYDVSSLRHFFAAGERLDPETQKWIEGVLG +MPVIDHWWQTETGWAIAANPVGLEELPVKTGSSSVPSPGFDVVVVDGLGTPVAPGEEGNIAIRLPLPPGTLPTLWKADQR +YVDSYLTAFPGHYATGDSGIVDEDGYVFVLGRTDDVINVSGHRLSTGVLEAALASHPAVAECAVIGVADTLKGQRPSGYV +VLRAGVERPEPGGEAEEALLAELVQTVRREVGPVADFRDVAVVEALPKTRSGKILRKTMRQLADGEQVAVPSTIEDASVL +EDLAAVLRPAG +>GCF_023573625_PROKKA_01362 +MATHDAPTEDRPSGAYADAHARSLRDPEGFWLDAARAIDWTVAPTRALDDSAAPLYRWFPDGELNTAFNCLDRHVEAGRG +DAVALIHDSAMTGEVTRYTYAELTDAVARLAGALAARGVGKGDRVLVYLPMIPQAHIAMLACARLGAVHSVVFGGFAPRE +LASRIDDAAPDVVLTCSGGIEPKRRVEYLPAVAEALETAAHPVRTVLVHHREGFETALADADGRGGASWEDWGEAVAAAE +PADCVPVRATDPLYVLYTSGTTGKPKGVVRDNGGHAVALRWTMEHIYDVGPGQAMCTASDVGWVVGHSYIVYGPLLAGAT +TVMYEGKPVGTPDAGAFWRLIEDHGVRSFFTAPTALRAIRRADPEGELLQAHDLSSLRHFFAAGERLDPETQRWIEGLLG +MPVIDHWWQTETGWAIAANPVGLEQLPVKIGSSSVPSPGVDLVVLDGLGEPVPAGTEGNIALRLPLPPGTLPTLWRDDQR +YIDSYLSAFPGHYATGDSGLVDEDGYVFVLGRTDDVINVSGHRLSTGVLEAALAAHPAVAECAVIGVADQLKGQRPSGYV +VLKSGVETPEAGSEAEAALMDELRQAVRREVGPVADFRDVVVVDALPKTRSGKILRKTMRQMADGEEYAVPSTIEDPAVL +EALAGVLRPAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001183.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001183.fa new file mode 100644 index 0000000000000000000000000000000000000000..12403390003b6aef3cc584adcd474c9dc37b9169 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001183.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01433 +MAAPTTKIARQAAIREILATRGIRSQAELSDALGDRGLSVTQGTLSRDLVDLGAVRTRGP +AGMVYALPAEGDDGAVPGRGSDAQLNRLASMARELLVSAEPTANLVVLRTPPGAAQFLAS +VIDQARVEHVMGTIAGDDTILLITTGTTSAPAVAAHLLGLAG +>GCF_003691675_PROKKA_01165 +MAAPTTKIARQAAIREILATRGIRSQAELSDALGDRGLSVTQGTLSRDLVDLGAVRTRGP +AGMVYALPAEGDDGAVPGRGSDAQLNRLASMARELLVSAEPTANLVVLRTPPGAAQFLAS +VIDQARVEHVMGTIAGDDTILLITTGTTSAPAVAAHLLGLAG +>GCF_005280335_PROKKA_01465 +MAVPTTKTARQAAIREILATRGIRSQAELSDALGDRGLSVTQGTLSRDLVDLGAVRTRGP +GGMVYALPAEGDDGALPGRGSDAQLSRLSSMARELLISAEPTENLVVLHTPPGAAQFLAS +VIDQARVENVMGTIAGDDTILLITTGVSAAPVVAAHLLGLAG +>GCF_020097155_PROKKA_01373 +MATPATKTARQAAIRDVLQTRAIRSQAELSDALAERGLSVTQGTLSRDLVDLGAVRLRGA +EGMVYAVPADGEE-AVAGRSAESQTGRLASMARELLLSAEPTENLVVLRTPPGAAQFLAS +VVDQARVEGIVGTIAGDDTVLLITAGTREAPAVAARLLGMAG +>GCF_023573625_PROKKA_01383 +MAAPTTKIARQAAIREILATRGIRSQAELSDALGDRGLSVTQGTLSRDLVDLGAVRTRGP +AGMVYALPAEGDDGAVPGRGSDAQLNRLASMARELLVSAEPTANLVVLRTPPGAAQFLAS +VIDQARVEHVMGTIAGDDTILLITTGTTSAPAVAAHLLGLAG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001186.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001186.fa new file mode 100644 index 0000000000000000000000000000000000000000..0d5aad1f8a3e50319007adab0e6b0a5eeb40e518 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001186.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_01436 +M----TPHT---DP-ATAAAPVLSTADRLDRAESKAEVLVEALPWIRRFAGTVMVVKYGG +NAMVSEELRRAFAEDIVFLHHVGVHPVVVHGGGPQINAMLDRLGIASEFRGGLRVTTEEA +MDVVRMVLTGQVGRELVGLVNSHGPYAVGFSGEDAGLLRARRTGAVVDGQEVDLGLVGEV +TGVDPTAILDVIESGRIPVVSSVAPEINDDGEPTGQVLNVNADTAAAALAAALGAAKLVL +LTDVEGLYADWPDRDSLISSLTAAQLRALLPSLASGMIPKMAACLAAVDAGVQRAHVVDG +RRPHSMLLEVFTSAGVGTQVVPDAEPT-----APT--TPEEDA +>GCF_003691675_PROKKA_01168 +M----SPHT---DP-ATAAAPVLSTADRLDRAESKAEVLVEALPWIRRFAGTVMVVKYGG +NAMVSEELRRAFAEDIVFLHHVGVHPVVVHGGGPQINAMLDRLGIASEFRGGLRVTTEEA +MDVVRMVLTGQVGRELVGLVNSHGPYAVGFSGEDAGLLRARRTGAVVDGQEVDLGLVGEV +TGVDPTAILDVIESGRIPVVSSVAPEINDDGEPTGQVLNVNADTAAAALAAALGAAKLVL +LTDVEGLYADWPDRDSLISSLTAAQLRALLPSLASGMIPKMAACLAAVDAGVQRAHVVDG +RRPHSMLLEVFTSAGVGTQVVPDAEPT-----APT--TPEEDA +>GCF_005280335_PROKKA_01462 +MSQSSSRQP---DPVTTAAAPVLSAADRLDRAESKAEVLIEALPWIQRFAGSVMVIKYGG +NAMVSDELRRAFAEDVVFLHHVGVHPVVVHGGGPQINAMLDRLGIESEFRGGLRVTTEEA +MDVVRMVLTGQVGRELVGLVNSHGPYAVGFSGEDAGLLRARRTGAVVDGQEVDLGLVGEV +TGVDPTAILDVVRSGRIPVVSSVAPEIDEHGEPTGQVLNVNADTAAAALASALGAAKLVL +LTDVEGLYADWPDRESLISSLTAGQLRALLPSLASGMIPKMAACLAAVDAGVQRAHVVDG +RRPHSMLLEVFTSAGVGTPVVPDADTAGRP--APT--TVQEDA +>GCF_020097155_PROKKA_01370 +M----TGQPAPADP-TTPSVPVLSTAQRLERAASKAEVLVEALPWVQRFAGATMVIKYGG +NAMVSDELRRAFAEDVVFLHHVGVHPVVVHGGGPQINAMLERLGIESEFRGGLRVTTPEA +MEVVRMVLTGQVGRELVGLINSHGAYAVGSSGEDAGLFRARRTGAVVDGETVDLGLVGEV +TAVNPEAIRDVIDAGRIPVVSSVAPEIGDDGEPTGEVLNVNADTAAAALAAGLGAAKLVL +LTDVEGLYADWPDRDSLISSLTASQLRGLLPGLQSGMIPKMAACLHAVDSGVHRAHVVDG +RRPHSMLLEVFTSDGVGTQVVPDPTPATRPASAPTTATAQEDA +>GCF_023573625_PROKKA_01386 +M----SPHT---DP-ATAAAPVLSTADRLDRAESKAEVLVEALPWIRRFAGTVMVVKYGG +NAMVSEELRRAFAEDIVFLHHVGVHPVVVHGGGPQINAMLDRLGIASEFRGGLRVTTEEA +MDVVRMVLTGQVGRELVGLVNSHGPYAVGFSGEDAGLLRARRTGAVVDGQEVDLGLVGEV +TGVDPTAILDVIESGRIPVVSSVAPEIDDDGQPTGQVLNVNADTAAAALAAALGAAKLVL +LTDVEGLYADWPDRDSLISSLTAAQLRALLPSLASGMIPKMAACLAAVDAGVQRAHVVDG +RRPHSMLLEVFTSAGVGTQVVPDAEPT-----APT--TPEEDA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001197.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001197.fa new file mode 100644 index 0000000000000000000000000000000000000000..4c2e9fa6c114525999720bddfc9bcaed0c24ae29 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001197.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01449 +-----------------------------MGLALLDDVAAPTRLLAARRSAPAPLRGLWE +FPGGKVEPGEGVQEALLRECREELGVAVRLGPEVAAPEPDGWELANGARMRVFWGVLAEE +GTTPRALQDHDLLAWLPLAGPGVRHLDWIPADRPIVAEVLRGAATAFSAGR--- +>GCF_003691675_PROKKA_01181 +-----------------------------MGLALLDDVAAPTRLLAARRSAPAPLRGLWE +FPGGKVEPGEGVQEALLRECREELGVAVRLGPEVAAPEPDGWELANGARMRVFWGVLAEE +GTTPRALQDHDLLAWLPLAGPGVRHLDWIPADRPIVAEVLRGAATAFSAGR--- +>GCF_005280335_PROKKA_01450 +----------------------------MVGLALLDDAAAPSRLLAARRSAPAVLRGLWE +FPGGKVETGEGPREALAREVREELGVAVRLGAEVPSPDPEGWELANGARMRVLWGVLAEE +GAEPAALEDHDLLAWVPLSGAGAHHLDWIPADRPIVSAVVAGAATAFAAAP--- +>GCF_020097155_PROKKA_01354 +MSPATPQTPPVPSA-----------PRPVVGVALVDDAARPTALLAARRSAPASLAGLWE +FPGGKVEPEEGADAALHRELVEELGVRVRLGTEVAAPEGPGWELANGARMRVWFGVLRED +SGAPAALQDHDRLEWTPLTAEALHALDWIPADRPIVDALLA----AVEAGRLGL +>GCF_023573625_PROKKA_01399 +MTSATPAR-PAPAARPTTSPRDGARPRQVVGLALLDDVAAPTRLLAARRSAPAPLRGLWE +FPGGKVEPGEGVQEALLRECREELGVAVRLGPEVAAPEPDGWELANGARMRVFWGVLAEE +GATPRALQDHDLLAWLPLAGPGVRHLDWIPADRPIVAEVLRGAATAFSAGR--- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001208.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001208.fa new file mode 100644 index 0000000000000000000000000000000000000000..a84eb3689e26b6ed03e3e09edd24c00d302cdab9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001208.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01462 +MQRFLTLTDVAETLNISGQAARALVRSGELQAIQVGGRGQWRIEVSWLEDYVERQKEVTR +ARVREWTEADA-KAR +>GCF_003691675_PROKKA_01194 +MQRFLTLTDVAETLNISGQAARALVRSGELQAIQVGGRGQWRIEVSWLEDYVERQKEVTR +ARVREWTETDA-QAR +>GCF_005280335_PROKKA_01438 +MQRFLTLTDVAETLNISGQAARALIRSGELQAIQVGGRGQWRIEESWLQEYVDRQREATR +ARVQEWAEADA-KSR +>GCF_020097155_PROKKA_01341 +MPQFLTLTDVAEVLNVSVGQARTLVRTGQLQAIQVGGRGQWRIEAGWLDEYVERQRELTR +SRVAERTREDAGHGA +>GCF_023573625_PROKKA_01412 +MQRFLTLTDVAETLNISGQAARALVRSGELQAIQVGGRGQWRIEVSWLEDYVERQKEVTR +ARVREWTETDA-KAR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001224.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001224.fa new file mode 100644 index 0000000000000000000000000000000000000000..6b3dacb51518debff0fdc9fdfb674664b44f9452 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001224.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01481 +MPDSPTPPRP--------NPHEGADRAPAPGTPGFRILLLTPEIPGNTGNAIRLAALTGA +ELHLVEPLGFGFEDAHLRRAGLDYHDLAVVTVHPDLDAALAALAPARVLAFTARGSVRHD +RVAYRPGDVLLFGRESTGLPEEVLTDPRVTETVCLPMQPARRSLNLANAVSIAVYEAWRQ +HDFAGSAA-RPDSLD +>GCF_003691675_PROKKA_01213 +MPDSPAPPRP--------NPHEGADRAPAPGTPGFRILLLTPEIPGNTGNAIRLAALTGA +ELHLVEPLGFGFEDAHLRRAGLDYHDLAVVTVHPDLDAALAALAPARVLAFTARGSVRHD +RVAYRPGDVLLFGRESTGLPEEVLADPRVTETVCLPMQPARRSLNLANAVSIAVYEAWRQ +HDFAGSAV-RPDSLD +>GCF_005280335_PROKKA_01421 +------------------------------------------------------------ +----MEPLGFGFEDAHLRRAGLDYHDLAVVTVHPDLDAALAALAPARVLAFTARGRVRHD +RVDYRPGDVLLFGRESTGLPEEVVADPRVAETVALPMQPSRRSLNLANAVSIAVYEAWRQ +HGFAGAAS-ETDSLD +>GCF_020097155_PROKKA_01321 +MPQTPPDPSPAAPPPAARNPHLDAERAPAPGTPGFRILFHTPEIPGNTGNAIRLAAITGA +ELHLVEPLGFDFSDAHLRRAGLDYHDLAVMTVHPDLDTALAALAPARVFAFSARGRVRHD +RVAYEAGDVLLFGRESTGLPEDVLSDPRVTDTVSLPMQPSRRSLNLANAASIAVYEAWRQ +HGFAGAGSPAADSLH +>GCF_023573625_PROKKA_01431 +MPDSPTPPRP--------NPHEGADRAPAPGTPGFRILLLTPEIPGNTGNAIRLAALTGA +ELHLVEPLGFGFEDAHLRRAGLDYHDLAVVTVHPDLDAALAALAPARVLAFTARGSVRHD +RVAYRPGDVLLFGRESTGLPEEVLTDPRVTETVCLPMQPARRSLNLANAVSIAVYEAWRQ +HDFAGSAA-RPDSLD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001237.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001237.fa new file mode 100644 index 0000000000000000000000000000000000000000..bcf3f80a0fe01384708d7fd26c3cd1b1cb3d7478 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001237.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01519 +MDRQPLRLAALAAAAVPGLAPVSVEASPDDPADFSTAVVVDGEGQRWRVRSPRTPEAGIR +LETELQVLAGLTPAVRAGLPFRTPSVAGAVRLEGLRTFVYQDMPGRPVTLDELARLGEPA +VQDVGRVLAAIHTLPSDVVDHADLPSYTAEQIRQRHLHALDQAATSGRVPPLLLRRWEEA +MEEEALWRFTPVPVHGDLHEDNLLLERGRVVGVTGWTDLHVGDPAGDVAWLAAATDPDLA +DRVLDAYAARRADAGAADDGDAHLMRRAALLAEFALSQWLTRGLDRHDEGMVAEAEAMLA +ELE---GDVRAAQEAAARQAEADAAADAAEDARDAAEDAREA-AAVRSADPETGSLPAVE +VVRPINGGPGR-----P +>GCF_003691675_PROKKA_01228 +MDRQPLRLAALAAAAVPGLAPVSVEASPDDPADFSTAVVVDGEGQRWRVRSPRTPEAGIR +LETELQVLAGLTPAVRAGLPFRTPSVAGAVRLEGLRTFVYQDMPGRPVTLDELARLGEPA +VQDVGRVLAAIHTLPSDVVDHADLPSYTAEQIRQRHLHALDQAATSGRVPPLLLRRWEEA +MEEEALWRFTPVPVHGDLHEDNLLLERGRVVGVTGWTDLHVGDPAGDVAWLAAATDPDLA +DRVLDAYAARRADAGAADDGDAHLMRRAALLAEFALAQWLTRVLDRHDEAMVAEAEAMLA +ELA---GDVRAAQEAAARQAEADAAADAAEDARDAAEDAREA-AAARTADPETGPLPAAE +VVRPINGGPGR-----P +>GCF_005280335_PROKKA_01406 +-----------------------MEASPDDPADFSTAVVVDGEGQRWRVRSPRTPEAGIR +LETELQVLAGLTPAVRAALPFRTPSVAGAVRLEGLRTFVYQDMPGRPVSLDELARLGEPA +VQDVGRVLAAIHTLPDDVVDQADLPSYSAEEIRQRHLHALDQAATSGRVPPLLLRRWEEA +MEEEALWRFTPVPVHGDLHEDNLLLERGRVVGVTGWTDLHRGDPAADVAWLAAAEDPDLA +DRVLDAYESRRAAAGAADDGDTHLMRRAALLAEFALAQWLARGLDRHDAAMVTEAEAMLA +ELA---ADVRAAQEAEDRQDREQAAADAAEDA-DAAADARDD-AQRHAAVQEGSPPGGAE +P----GGASGRRRVTDA +>GCF_020097155_PROKKA_01305 +MHRQPLRLAALAAAAVPGLTPVSVEPSPDDSPDVAAALVVDDAGQRWLVRSPRSAEAGIR +LETELQVLAGFDPHLRAGLPFRVPSVAGAVRIDGLRTFVYQALPGEPATLEQIGGLGDAA +VQDLGRILAALHTLPLTVVEQADLPVYTADHVRERHLTELDRAAATGQVPPRLLRRWEET +LEEADLWDFSPVPVHGDLHEDGLLVSRGRVVGVSGWTDLHVGDPAEDFAWLAAAEDPALP +ERVLAAYAERLDSEGAAAP-DAHLLRRGALLAEFALARWLLRGVDRHDAETTADARALLT +ELAEAVGVAEATAPQAAPTADNVVGLHAAHDDRAPDWDEDDADGVVDVSDDDGRAGGTVS +VLRPVD----------- +>GCF_023573625_PROKKA_01446 +MDRQPLRLAALAAAAVPGLAPVSAEASPDDPADFSTAVVVDGEGQRWRVRSPRTPEAGIR +LETELQVLAGLTPAVRAGLPFRTPSVAGAVRLEGLRTFVYQDMPGRPVTLDELARLGEPA +VQDVGRVLAAIHTLPSDVVDHADLPSYTAEQIRQRHLHALDQAATSGRVPPLLLRRWEEA +MEEEALWRFTPVPVHGDLHEDNLLLERGRVVGVTGWTDLHVGDPAGDVAWLAAATDPDLA +DRVLDAYAARRADAGAADDGDAHLMRRAALLAEFALAQWLTRGLDRHDAGMVAEAEAMLA +ELE---GDVRAAQEAAARQAEADAAADAAEDARDAAEDAREA-AAARTADPETGPLPAVE +VVRPINGGPGR-----P + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001247.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001247.fa new file mode 100644 index 0000000000000000000000000000000000000000..6f3b89861d12ded29865673dcc13e69d246fe388 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001247.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01529 +MR---VLLTRQPAQAGDLEAGLAGTEVAGRRLRVGFLPLTDFALPDDDGPLRALLADWAG +ADGDAAGPVRSDGSRWLVVTSPNTVRALRAVGWDGHVPAGARIAVTGPGTARVLTEAGCD +AAPWLPPEDRSAEGLIAGLAALHPR----GARAWLPQSDRARSRLADGLRAAGWDVRTGL +AYRTVPYPAQAGRRLLDGAADEGRGDVVTPARLAAVAAGTAVVLTSSSAAEEFVA--AGL +TPLVGERVRLVAIGAPTRDTCARRGLPLLGTAPTPDAAGVLAVL-RAAA +>GCF_003691675_PROKKA_01239 +MR---VLLTRQPAQAGDLEAGLAGTEVAGRRLRVGFLPLTDFALPDDDGPLRALLADWAG +ADGDAAGPVRSDGSRWLVVTSPNTVRALRAVGWDGHVPAGARIAVTGPGTARVLTEAGCD +AAPWLPPEDRSAEGLIAGLAALHPR----GARAWLPQSDRARSRLADGLRAAGWDVRTGL +AYRTVPYPAQAGRRLLDGAADEGRGDVVTPARLAEVAAGTAVVLTSSSAAEEFVA--AGL +TPLVGERVRLVAIGAPTRDTCARRGLPLLGTAPTPDAAGVLAVL-RAAA +>GCF_005280335_PROKKA_01396 +MR---VLLTRQPAQAGDLEAGLAGAEVAGRRLRVGFLPLTDFALPDDDGPLRALLADWAG +ADGDAAGPGRSDGSRWLVLTSPNTVRALRAVGWDGHVPAGARIAVTGPGTARVLTEAGCD +AAPWLPPEDRSAEGLIAGLAALHPR----GGRAWLPQSDRARPRLADGLRAAGWDVRTGL +AYRTVPYPAQAGRRLLDAAADEGRGDVVTPARLAAVAAGTAVVLTSSSAAEEFLA--AGL +TPLVGERVRLVAIGAPTRDTCARRGLPLLGTAPTPDAAGVLAVL-RAAA +>GCF_020097155_PROKKA_01287 +MDGRPLVLTRQPAQAGTLEADLAA---AGR--RVAFCPLTDFELPPTPGGLRAVVEAVVG +GR-----------CAWLLVTSPNAVRALQAAGWTGAVGAGVRVAVTGAGTARVLADAGCA +VEPWM-PESASAAGILAEFPAAPAETGDGARRVLLPQSALATAELEEALTRRGWAVDRVE +AYRTVPYPADAARRLL--TEEPGDAGTVVP---VAELAGADVVLTSPSAARALAVHPALD +DPELRRTWRLVALGAPTAREARRLGLRLTGQAATPDATGILAALARPVG +>GCF_023573625_PROKKA_01456 +MR---VLLTRQPAQAGDLEAGLAGAEVAGRRLRVGFLPLTDFALPDDDGPLRALLADWAG +ADGDAVGPVRSDGPRWLVVTSPNTVRALRAVGWGGHVPAGARIAVTGPGTARVLTEAGCD +AAPWLPPEDRSAEGLIAGLAALHPR----GARAWLPQSDRARPRLADGLRAAGWDVRTGL +AYRTVPYPAQAGRRLLDGAADEGRGDVVTPARLAAVAAGTAVVLTSSSAAEEFVA--AGL +TPLVGKRVRLVAIGAPTRDTCARRGLPLLGTAPTPDAAGVLAVL-RGAA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001250.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001250.fa new file mode 100644 index 0000000000000000000000000000000000000000..00770e932de6234488cadfdbb387d5b4463c9450 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001250.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01532 +MTKDSTTTPAEAGKDWFTTYTVFARPQGEPGWLGLEGRDAKKAAKEFDEAVARVAQTGVT +VRGVYDVSGMREAGDVMVWMYGQVPEDLQAAIRELRRTRLLEGTTMVLSAMGADRMAEFN +KDHVPAFAMGRKALKWLCFYPFVRSYDWYLLDPKERARMLREHGQLGQDFPQVWANTTSA +FGLNDWEWLLGLEADELTDLVDMMRHLRNNETRLHVRSEVPFYTGRRLETAEIAEVLA +>GCF_003691675_PROKKA_01242 +MTKDSTTTPAEAGKDWFTTYTVFARPQGEPGWLGLEGRDAKKAAKEFDEAVARVAQTGVT +VRGVYDVSGMREAGDVMVWMYGQVPEDLQAAIRELRRTRLLEGTTMVLSAMGADRMAEFN +KDHVPAFAMGRKALKWLCFYPFVRSYDWYLLDPKERARMLREHGQLGQDFPQVWANTTSA +FGLNDWEWLLGLEADELTDLVDMMRHLRNNETRLHVRSEVPFYTGRRLETAEIAEVLA +>GCF_005280335_PROKKA_01393 +MTKDTATTPAEAGKDWFTTYTVFARPQGQPGWLGLEGRDAKKAVQEFDALVADLAKAGVT +VRGVYDVSGMREAGDVMVWMYGQVPEDLQAAIRRLRRTRLLERTTMVLSAMGADRLAEFN +KDHIPAFAMGRKALPWLCFYPFVRSYDWYLMEPKERARMLREHGQLGQEFPQVWANTTSA +FGLNDWEWLLGLEAPELKDLVDMMRHLRNNETRLYVRAEVPFYTGRRVETADLLEVLA +>GCF_020097155_PROKKA_01284 +M----SNTAAQPGQDWFTTYTVFARPQGEPGWLGLDGREAKKAVKEFDGVVKSLATRGVT +VRGVYDVSGMRAEGDVMVWMYAHAPEDLQAAIRDLRRTRLLDGTNMVLSAMGADRMAEFN +KDHIPAFAMGRKPLDWLCFYPFVRSYDWYTLDPKERARMLREHGKLGQDFPQVWANTTSA +FALNDWEWLLGLEAPKLNDLVDMMRHLRDNETRHYVREEVPFYTGRRLETSELPEVLA +>GCF_023573625_PROKKA_01459 +MTKDSTTTPAEAGKDWFTTYTVFARPQGEPGWLGLEGRDAKKAAKEFDEAVARVAQTGVT +VRGVYDVSGMREAGDVMVWMYGQVPEDLQAAIRELRRTRLLEGTTMVLSAMGADRMAEFN +KDHVPAFAMGRKALKWLCFYPFVRSYDWYLLDPKERARMLREHGQLGQDFPQVWANTTSA +FGLNDWEWLLGLEADELTDLVDMMRHLRNNETRLHVRSEVPFYTGRRLETAEIAEVLA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001260.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001260.fa new file mode 100644 index 0000000000000000000000000000000000000000..6029f9647e9f38a8222fd36767784e2255c0693f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001260.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01543 +MSIMMPNPQPGAEQGLPRGELLATYATYAQAREQVDRLAATDFPVSAVSIVGKDLRVVER +VRGRLNYAQVALSAGVRGVFFGGLIGVFLYLLAPEAGPGQILTSMLLGLAVWLIFGVIGF +AMRRGQHGFASSQAVVPTAFDLVVAFDHAARARQELGLGGAAA----------PTPPA-A +SQP----AP---------APAA-EAEDGSVQATP-APAPSSGGSHAAPAPGGPEAPARPA +PEAD--PAPTGLDRSYGVTLPPEEVAKLIEARGGHPPRPQDEPRG---------- +>GCF_003691675_PROKKA_01253 +MSFMMSNPQPGAEQGLPRGELLATYATYAQAREQVDRLAATDFPVSAVSIVGKDLRVVER +VRGRLNYAQVALSAGVRGVFFGGLIGVFLYLLAPEAGPGQILTSMLLGLAVWLIFGVIGF +AMRRGQHGFASSQAVVPTAFDLVVAFDHAARARQELGLGGAAA----------PTPQP-A +PQP----AP---------APAAEEAGGGSVQATP-AAAPSSGGSHAAPAPGGPEASARPT +PEAD--TAPTGLDRSYGVTLPPEEVAKLIEARGGHPPRPQDEPRG---------- +>GCF_005280335_PROKKA_01382 +MSFMMSSPPPGADRGLPRGELLATYASYADAREQVDRLAATDFPVSAVSIVGKDLRVVER +VRGRLNYAQVALSAGVRGVFFGGLIGVFLFLLTPEGGAGQILTSMLLGLAVWLIFGVIGF +GMRKGRHGFASSQAVVPTGYDLVVAFEHAARARTELGLGGAAATAAAAVSTSPATPAPAA +PQA----GPNQNGAGQVDAPRP-DAPQADAQHAPQAGAPSSGGSHAAPDADAQPAGAEAA +PAAG--AVPTGLDRSYGVTLPPEEVAKLIQARGGQASRPQEDPRD---------- +>GCF_020097155_PROKKA_01273 +--MMMSGPAAG---GLPQGELLATYSTYEQAREQVDRLAEADFPVTALSIVGKDLRVVER +VRGRLNYGRVALGAAVQGALFGAMIGAFLLLLDSSAGGMQIVTSALLGVAVWVIFGVVGF +ASRKGRHGFASTQALVPGGYDLVVAFEHAGRARQELGLGARGA----------ATPAP-A +PMPVQESAP---------APAPAPAPSGSAVSGP-------SGSHAAPASSAEPAPAHVD +GPAQDPAAPAGLDRSYGVTLPPEEVARLIEARGGRPRQDPQAPQGQPHPWDRPQS +>GCF_023573625_PROKKA_01470 +MSIMMPNPQPGAEQGLPRGELLATYATYAQARDQVDRLAATDFPVSAVSIVGKDLRVVER +VRGRLNYAQVALSAGVRGVFFGGLIGVFLYLLAPEAGPGQILTSMLLGLAVWLIFGVIGF +AMRRGQHGFASSQAVVPTAFDLVVAFDHAARARQELGLGGAAA----------PTPPA-A +SQP----AP---------APAA-EAEDGSVQATP-APAPSSGGSHAAPAPGGPEAPARPA +PEAD--PAPTGLDRSYGVTLPPEEVAKLIEARGGHPPRPQDEPRG---------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001297.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001297.fa new file mode 100644 index 0000000000000000000000000000000000000000..94ba6bc33ca3f4593b1ba3da3fa84d909c88486a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001297.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_01594 +MALHLQRYREIAHVMARNGLMATAVQAGLSRWLPLEEGEPHLGIDAEARPELFVRTFEELGVTFVKLGQLISARPDVFPE +AYCAAFARLTDSTSAVPFEAVARTVEEDLGADVDTLFAWFDRAPLATASIGQAHRARLHDGRAVVVKVRKPGVVEQVQAD +LEILRTLAATWSRASRTFADLDVPAMVDEFDRSLRAELDYVVEARACEEIAAGFRDTPGVRFPWIEWDLTTSRVLTMQEL +SGLRVDDLAGLDAAGIDREELAYRAADVLLAMVFEHGVFHADPHPGNLFIEPDGTVGFIDFGSVGRISPSLRRRFAGLAM +ALARQDTDGLVRALLDIAPPRGPVDRRRLRLEVARIVGRLEGRELEDIRVAQLISEIFALVRRHRLSLPPELVQLLRMLI +IVDGIGRRLHPGFDYTRVLDPFALRLVGEHLDPRRVAGRIGRATIAAAELGIDLPEYARKVMERIDDGGIDVTVRASELE +PLVTRLERTGDRVVAAMVVAAMITGGTNVLVAYKDRLGRFAGPVVAAGGAALTGGSAYLAWISRP---RRRPR- +>GCF_003691675_PROKKA_01306 +MALHLQRYREIAHVMARNGLRATAVQAGLSRWLPLEEGEPHLGIDAEARPELFVRTFEELGVTFVKLGQLISARPDLFPE +AYCAAFARLTDSTTAVPFEAVARTVEEDLGADVDTLFAWFDRAPLATASIGQAHRARLHDGRAVVVKVRKPGVVEQAQAD +LEILRTLAATWSRASRTFADLDVPAMVDEFDRSLRAELDYVVEARACEEIAAGFRDTPGVRFPWIEWDLTTSRVLTMQEL +SGLRVDDLAGLDAAGIDREELAYRAADVLLAMVFEHGVFHADPHPGNLFIEPDGTVGFIDFGSVGRISPSLRRRFAGLAM +ALARQDTDGLVRALLDIAPPRGPVDRRRLRLEVARIVGRLEGRELEDIRVAQLVSEIFALVRRHRLSLPPELVQLLRMLI +IVDGIGRRLHPGFDYTRVLDPFALRLVGEHLDPRRVAGRIGRATIAAAELGIDLPEYARKVMERIDDGGIDVTVRASELE +PLVTRLERTGDRVVAAMVVAAMITGGTNVLVAYKDRLGRFAGPVVAAGGAALTGGSAYLAWISRP---RRRPR- +>GCF_005280335_PROKKA_01327 +MPSRLHRSREIALILGRNGLQATALAAGLGRWLPAAD--ARTARDAVLRPDMLVDVFEQLGTTFVKLGQLISARPDMFPE +SICTAFARLTDDTTPVPFEAMAATVLEDFGASVDELYAWFDPVPLATASIGQAHRARLHDGRDVVVKIRKPGVVEQVRTD +LEILRTVASRLSRASRALQDMDVVSLVDEFDRALRAELDYLVEARACEQIAENLRDVPGVRVPWVDWATTSSRVLTMEEI +TGFRVDDLASLDAAGIDRADLAYRAAEVLMGMVFEDGLFHADPHPGNVFIEADGGIGFIDFGSVGRISSGMRRRFARMAM +ALVRQDPDGLVRALVAIAPPRGDLDRRALRLEVSRITGRLEGRDLADIRVDQLVGQIFGIVRRHRLALPPELVQLFRMLI +IVDGLGKRLHPGFDYTRVLNPFAVRVAGEELDPRRVAGRIGQAGLAAAELGLDLPEYARKVIDHLEDGGLDVTLRTGELE +PLVARMERTGDRVVAALVVAAMITGGTNVLVAYKDRLGRFAGPVVAAGGAALTGGSAYLAWTGRPRRMRRRPRG +>GCF_020097155_PROKKA_01215 +MALHLQRYREIAHVMARNGLDATARLAGLGRWLAPQDPTARRPLDAEARPELLVRTFEELGTTFVKLGQLISTRPDLFPE +SYCTAFARLTDRATPVPYAAIARTVEEDFGAPVDELFAEFDRTPLATASVGQVHGAVLHDGRDVVVKVRKPGVVEAVTAD +LEILRTLTGRLVRASRTLADMDVAGMVDQFDRSLRAELDFVVEARACEEIAAGFTGTPGVRFPWIAWELTSARVLTMERM +AGMRVDDLPALEAAGIDREELAYRAADVLMRMVFQHGVFHADPHAGNVFIEPDGTIGFIDFGSVGRIGPGVRERISGLAM +ALARQDVDGLVRALLEIAPPRGPVDRRRLRSEVGRIVARVDGRDLQDIKVPQLVSEVFAIVRRHRLSLPPELVQVFRMVL +IVDGLGRRLDPGFDYTRVLDPFVRRMVMDQLDPRRLARRLRRATITTADIGLELPQYLRTLMERIEDGGIDVNVRTSELE +PLVARVERTGDRVVAALVVAAMITGGTNVLVAYKDRLGPFAGPLVAAGGAALTSGSAYLAWISRP---RRAPRR +>GCF_023573625_PROKKA_01521 +MALHLQRYREIAHVMARNGLMATAVQAGLSRWLPLEEGEPHLGIDAEARPELFVRTFEELGVTFVKLGQLISARPDVFPE +AYCAAFARLTDSTSAVPFEAVARTVEEDLGADVDTLFAWFDRAPLATASIGQAHRARLHDGRAVVVKVRKPGVVEQVQAD +LEILRTLAATWSRASRTFADLDVPAMVDEFDRSLRAELDYVVEARACEEIAAGFRDTPGVRFPWIEWDLTTSRVLTMQEL +SGLRVDDLAGLDAAGIDREELAYRAADVLLAMVFEHGVFHADPHPGNLFIEPDGTVGFIDFGSVGRISPSLRRRFAGLAM +ALARQDTDGLVRALLDIAPPRGPVDRRRLRLEVARIVGRLEGRELEDIRVAQLISEIFALVRRHRLSLPPELVQLLRMLI +IVDGIGRRLHPGFDYTRVLDPFALRLVGEHLDPRRVAGRIGRATIAAAELGIDLPEYARKVMERIDDGGIDVTVRASELE +PLVTRLERTGDRVVAAMVVAAMITGGTNVLVAYKDRLGRFAGPVVAAGGAALTGGSAYLAWISRP---RRRPR- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001300.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001300.fa new file mode 100644 index 0000000000000000000000000000000000000000..3bb6b67fafa25285f057b5a49586770942861505 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001300.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01598 +MTKHRQPVPLSQTAARLGLGGFMTAAGLSHLTVARREFRAQVPSWVPLPADLVVLGSGVA +EIGLGAALLALPGQRRLTGTALAAFYTAIYPGNIGQYAERKDGFGLDTDGRRLARLFGQP +ALIAAALWAAGIPEREQGGRG +>GCF_003691675_PROKKA_01310 +MTKHRQPVPLSQTAARLGLGGFMTAAGLSHLTVARREFRAQVPSWVPLPADLVVLGSGVA +EIGLGAALLALPGQRRLTGTALAAFYTAIYPGNIGQYAERKDGFGLDTDGRRLARLFGQP +ALIAAALWAAGIPEREQGGRG +>GCF_005280335_PROKKA_01295 +MTKRRQSVPLSQTAARLGLG---------------------------------------- +------------------------------------------------------------ +----AALWAAGIPEREHGGRG +>GCF_020097155_PROKKA_01204 +MTKRRQSVPLSQTAARLGLGGFMTAAGLSHLTVARREFRAQVPSWVPLPADLVVLGSGVA +EIGLGAALLALPGQRRRTGTALAAFYTAIYPGNIGQYAERKDGFGLDTDGRRLARLFGQP +ALIAAALWAAGIPEREHGGRG +>GCF_023573625_PROKKA_01525 +MTKRRQSAPLSQTAARLGLGGFMTAAGLSHLTVARREFRAQVPSWVPLPADLVVLGSGVA +EIGLGAALLALPGQRRLTGTALAAFYTAIYPGNIGQYAERKDGFGLDTDGRRLARLFGQP +ALIAAALWAAGIPEREQGGRR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001305.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001305.fa new file mode 100644 index 0000000000000000000000000000000000000000..bae71b6b6f40788289eec1ea084160d8b7e66d4a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001305.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01610 +MATVLLVRHGRTTANATGLLAGRTPGVSLDDHGREQAARTGGRIAAVPVAAVVASPLERC +AQTARALLDRQPGTVPSLVDDDLTECDYGQWQGRALSDLATEPLWATVQTQPSAVVFPGG +ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGTHLDLFQRIEV +GPASVSIVSYGPARPRVWAMNTDAGDLSWLATLGPSDDAPVGGGAGTG--AGAVDERTPR +IVA +>GCF_003691675_PROKKA_01321 +MATVLLVRHGRTTANATGLLAGRTPGVSLDDHGREQAARTADRIAAVPVAAVVASPLERC +AQTARALLDRQPGTVPSLVDDDLTECDYGQWQGRALSDLATESLWATVQTQPSAVVFPGG +ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGTHLDLFQRIEV +GPASVSIVSYGPARPRVWAMNTDAGDLSWLATLGPSDDAPVGGGAGTG--TGAVDERTPR +IVA +>GCF_005280335_PROKKA_01288 +MATVLLVRHGRTTANASGLLAGRTPGVSLDEHGREQAARTADRIAAVPVTAVVASPLERC +AQTARALLDRQPGTVPSLVDDDLTECDYGQWQGRALSDLATEPLWATVQSRPSAVVFPGG +ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGMHLDMFQRLDV +GPASVSIVSYGSSRPRVLTVNTDAGDLSWLATKGPSGDAPVGGGAGTDPVADSANGRTPR +IDA +>GCF_020097155_PROKKA_01193 +MATVLLVRHGRTTANATGLLAGRTPGVSLDDHGREQAARTADRVAAVPVAAVVASPLERC +AQTARALLDRQSGAVPSLVDDDLTECDYGQWQGRALSDLATEPLWATVQTQPSAVVFPGG +ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGTHLDLFQRIEV +GPASVSIVSYGPSRPRVWATNTDAGDLSWLSSLGPSDDAPVGGGAGTG--PGAVDEQTPR +IVT +>GCF_023573625_PROKKA_01536 +MATVLLVRHGRTTANASGLLAGRTPGVSLDDHGREQAARTADRIATLPVAAVVASPLERC +AQTARALLDRQPGTVPSLVDDDLTECDYGQWQGRALSDLATESLWATVQTQPSAVVFPGG +ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGTHLDLFQRIEV +GPASVSIVSYGPARPRVWAMNTDAGDLSWLATLGPSDDAPVGGGAGTG--TGAVDEQTPR +IVT + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001333.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001333.fa new file mode 100644 index 0000000000000000000000000000000000000000..76d2c76abbc9f02007cf1b58dadf9737f7d1a353 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001333.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01652 +MTNQIEIGRGKRGRRAFSLDDVSVVPARRTRDPQDVSLTWRIDAYTFDMPVIGAPMDSVM +SPEAAIAMGRLGGLGVLNLEGLWTRHEDPRPLLEEIAALQAGPAGTEATRKLQEAYAAPI +RPDLITERLAQIREAGVVVAGSLTPQNTQEFYRTVVAAGVDLFVIRGTTVSAEHVSSTQE +PLDLKQFIYELDVPVIVGGAAGYTPALHLMRTGAAGVLVGFGGGASTTTRRAMGIRVPMA +TAISDIAEARRDYMDESGGRYVHVIADGGVSTSGEIVKAIAMGADAVVLGAALARATDAP +GGGWHWGLEAAHPELPRGHRTQVGQVAPLEEVLWGPGRHADGTSNLMGGLKRAMATCGYT +ELKDFQKVEVLVTPTQTV +>GCF_003691675_PROKKA_01357 +MTNQIEIGRGKRGRRAFSLDDVSVVPARRTRDPQDVSLTWRIDAYTFDMPVIGAPMDSVM +SPETAIAMGRLGGLGVLNLEGLWTRHEDPRPLLEEIAALEAGPAGTEATRMLQEAYAAPI +RPDLITERLAQIREAGVVVAGSLTPQNTQEFYRTVVAAGVDLFVIRGTTVSAEHVSSTQE +PLDLKQFIYELDVPVIVGGAAGYTPALHLMRTGAAGVLVGFGGGASTTTRRAMGIRVPMA +TAISDIAEARRDYMDESGGRYVHVIADGGVSTSGEIVKAIAMGADAVVLGAALARATDAP +GGGWHWGLEAVHPELPRGHRTHVGQVAPLEEVLWGPGRHADGTSNLMGGLKRAMATCGYT +ELKDFQKVEVLVTPTQTV +>GCF_005280335_PROKKA_01241 +MTNQIEIGRGKRGRRAFSLDDVSVVPARRTRDPKDVSLTWRIDAYTFEMPVIGAPMDSVM +SPETAIALGRLGGLGVLNLEGLWTRHEDPRPLLEEIAALEAGPDGTEATRRLQEAYAAPI +RAELITERLAQIREAGVVVAGSLTPQNTQEFYKTVLAAGVDLFVIRGTTVSAEHVSSSHE +PLDLKQFIYELDVPVIVGGAAGYTPALHLMRTGAAGVLVGFGGGSSTTTRRAMGIRVPMA +TAIADIAEARRDYMDESGGRYVHVIADGGVSTSGEIVKALAMGADAVVLGAALARATDAP +GGGWHWGLEAAHPELPRGHRTHVGQVAPLEEVLWGPGHHADGTSNLMGGLKRAMATSGYT +ELKEFQKVEVLVTPTQTV +>GCF_020097155_PROKKA_01152 +MTNQIEIGRGKRGRQAFSFDDVSVVPSRRTRDPKDVNLSWRIDAYTFDMPVMGAPMDSVM +SPETAIALGRLGGLGVLNLEGLWTRHEDPEPLLEEIAAMEAEAGSPEVTRRLQEIYSAPI +RADLITERLAQIRESGVVVAGSLTPQNTQQFSQTVLAAGVDLFVIRGTTVSAEHVSSTHE +PLDLKQFIYELDVPVIVGGAAGYTPALHLMRTGAAGVLVGFGGGASTTTRRAMGIRVPMA +TAIADIAEARRDYMDESGGRYVHVIADGGVGTSGEIVKAIAMGADAVTLGTALARATEAP +GRGWHWGLEAAHPELPRGHRTRVGQVAPLEEVLWGPGHTTDGTSNLMGALKRAMATSGYT +ELKDFQKVEVLVTGARTH +>GCF_023573625_PROKKA_01582 +MTNQIEIGRGKRGRRAFSLDDVSVVPARRTRDPQDVSLTWRIDAYTFDMPVIGAPMDSVM +SPETAIAMGRLGGLGVLNLEGLWTRHEDPRPLLEEIAALEAGPAGTEATRKLQEAYAAPI +RPDLITERLEQIREAGVVVAGSLTPQNTQEFYRTVVAAGVDLFVIRGTTVSAEHVSSTQE +PLDLKQFIYELDVPVIVGGAAGYTPALHLMRTGAAGVLVGFGGGASTTTRRAMGIRVPMA +TAISDIAEARRDYMDESGGRYVHVIADGGVSTSGEIVKAIAMGADAVVLGAALARATDAP +GGGWHWGLEAAHPELPRGHRTHVGQVAPLEEVLWGPGRHADGTSNLMGGLKRAMATCGYT +ELKDFQKVEVLVTPTQTV + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001336.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001336.fa new file mode 100644 index 0000000000000000000000000000000000000000..1fcce647eb506fda9a5c742978705d6eefa7f417 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001336.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01657 +MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGNRVPVD +VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVAK +>GCF_003691675_PROKKA_01362 +MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGNRVPVD +VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVTK +>GCF_005280335_PROKKA_01237 +MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGNRVPVD +VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVTK +>GCF_020097155_PROKKA_01148 +MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGTRVPVD +VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVTK +>GCF_023573625_PROKKA_01587 +MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGNRVPVD +VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVTK + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001338.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001338.fa new file mode 100644 index 0000000000000000000000000000000000000000..8c3600e2dd042485e11f678fe201452d449c7c76 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001338.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01660 +MAEPLATAPGRLPAPLGGATAAGPVDADAPRRSGAFVTAAERRRYAVVVAVLAAVAVLST +AGILLWGNEAEPGSRAFWMIARMRVESLGVIGIVALCHSFATVTFHTVTGNRIITPSIMG +FEALYTAVSTVAVYVLGAAGVAVLTGVGPFLAQAALMVALTTALYSWLLSRPYGSVHLML +LVGVVLGGGLAALSTFMQRLLDPNSFDLLSARLFGNISNARTEYVAIAAPIAVVVCALLW +LRSRRLNTVALGADAATNLGLHHRRELMVTLLLVSVLMAMTTALVGPMTFLGFLVATLAY +SLVDTHDHRFILPVAALAGYAVLTSAYFVLRHVFYAGGAVTVVIELIGGITFLVVVMRKG +RL +>GCF_003691675_PROKKA_01365 +MAEPLATAPGRIPAPPGGATAAGPVEADAPRRSGAFVTAADRRRYAVVVAVLAAVAVLST +AGILLWGNEAEPGSRAFWMIARMRVESLGVIGIVALCHSFATVTFHTVTGNRIITPSIMG +FEALYTAVSTVAVYVLGAAGVAVLTGVGPFLAQAALMVALATALYSWLLSRPYGSVHLML +LVGVVLGGGLAALSTFMQRLLDPNSFDLLSARLFGNISNARTEYVAIAAPIAVVVCALLW +LRSRRLNTVALGADAATNLGLHHRRELMVTLLLVSVLMAMTTALVGPMTFLGFLVATLAY +SLVDTHDHRFILPVAALAGYAVLTSAYFVLRHVFYAGGAVTVVIELIGGITFLVVVMRKG +RL +>GCF_005280335_PROKKA_01234 +-----------------------------------------------MVAVLAVVAVLST +AGILLWGNEAEPGSRAFWMIAGMRLDSLGVIAIVALCHSFATVSFHTVTGNRIITPSIMG +FEALYTAVQTGAVYVLGAAGIGVVTGTGPFLAQAALMVVLATVLYSWLLSRPYGSIHLML +LVGVVLGGGLAALSTFMQRLLDPNSFDVLSARLFGNISNARSEYVAIAAPIVVVVCLVLW +LRSRRMNVLALGADSATNLGLHHRRELMVTLLLVSVLMAMTTALVGPMTFLGFLVATLAY +SLVDTHDHRMVLPVAALGAYAVLTLAYFVLRHVFYAGGAVTVIIELVGGITFLIVVMRKG +RL +>GCF_020097155_PROKKA_01145 +MAEPLATAPGRIPAPSGGATAAGPVDADAPRRSGAFVTAADRRRYALVVAVLAAVAVLST +AGILLWGNEAEPGSRAFWMIARMRVESLGVIGIVALCHSFATVSFHTVTGNRIITPSIMG +FEALYTAVSTAAVYVLGAAGVAVLTGVGPFLAQAALMVALATALYSWLLSRPYGSVHLML +LVGVVLGGGLAALSTFMQRLLDPNSFDLLSARLFGNISNARTEYVAIAAPIAVVVCALLW +LRSRRLNTVALGADAATNLGLHHRRELMVTLLLVSVLMAMTTALVGPMTFLGFLVATLAY +SLVDTHDHRFILPVAALAGYAVLTSAYFVLRHVFYAGGAVTVVIELIGGITFLIVVMRKG +RL +>GCF_023573625_PROKKA_01590 +MVEPLATAPGRIPAPPGGATAAGPVDADAPRRSGAFVTAADRRRYAVVVAVLAVVAVLST +AGVLLWGNEAEPGSRAFWMIARMRVESLGVIGIVALCHSFATVSFHTVTGNRIITPSIMG +FEALYTAVSTAAVYVLGAAGVAVLTGVGPFLAQAALMVALATALYSWLLSRPYGSVHLML +LVGVVLGGGLAALSTFMQRLLDPNSFDLLSARLFGNISNARTEYVAIAAPIAVVVCALLW +LRSRRLNTVALGADAATNLGLHHRRELMVTLLLVSVLMAMTTALVGPMTFLGFLVATLAY +SLVDTHDHRFILPVAALAGYAVLTSAYFVLRHVFYAGGAVTVVIELIGGITFLVVVMRKG +RL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001375.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001375.fa new file mode 100644 index 0000000000000000000000000000000000000000..6149257c17488ef7c88b0d4a3d5967b94240a45d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001375.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01702 +MFEPTRKNIQPSDATLVITQTRGVTGSKQNHRDTLRSLGLKRIGHQVTRKADAVTVGMVN +TVPHLVSVEEVNNG +>GCF_003691675_PROKKA_01409 +MFEPTRKNIQPSDATLVITQTRGVTGSKQNHRDTLRSLGLKRIGHQVTRKADAVTVGMVN +TVPHLVSVEEVNNG +>GCF_005280335_PROKKA_01176 +MTEPTRKNIQPSDATLVITQTRGVTGTKQNHRDTLRSLGLKRIGHQVTRKADAVTVGMVN +TVPHLVSVEEVNNG +>GCF_020097155_PROKKA_01106 +MLQTTRKNIQPSDATLVITQTRGVTGTKQNQRDTLRSLGLKRIGHQVTRKADAATVGMVN +TVPHLVSVEEVNHG +>GCF_023573625_PROKKA_01631 +MFEPTRKNIQPSDATLVITQTRGVTGSKQNHRDTLRSLGLKRIGHQVTRKADAVTVGMVN +TVPHLVSVEEVNNG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001376.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001376.fa new file mode 100644 index 0000000000000000000000000000000000000000..ca505c0e208c21712d84fd9fb00844b36646399d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001376.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01703 +MTENINQKDTQVTESTETTVSETGSGSASQTTERATGGRGGRDGGRGGRDGDRRGGRRDD +RNRRGAQDDEKDQFLERVVGINRVSKVVKGGRRFSFTALVVVGDGDGTVGVGYGKAKEVP +AAIQKAVEEAKKSFFRVPRVGSTIPHLVQGEDAAGVVLLRPASPGTGVIAGGPVRAVLEC +AGIHDVLSKSMGSVNAINIVRGTVDALKKLEEPQAVAARRGKALDEIAPHAMLRTMENDR +AQKSA-KAGA +>GCF_003691675_PROKKA_01410 +MTENINQKDTQVTESTETTVSETGSGSASQTTERATGGRGGRDGGRGGRDGDRRGGRRDD +RNRRGAQDDEKDQFLERVVGINRVSKVVKGGRRFSFTALVVVGDGDGTVGVGYGKAKEVP +AAIQKAVEEAKKSFFRVPRVGSTIPHLVQGEDAAGVVLLRPASPGTGVIAGGPVRAVLEC +AGIHDVLSKSMGSVNAINIVRGTVDALKKLEEPQAVAARRGKALDEIAPHAMLRTMENDR +AQKSA-KAGA +>GCF_005280335_PROKKA_01175 +MTENNNQKDTQVTESTETTVSETASGSSSQTTERSAGGRGGRDGGRGGRDGDRRGGRRDD +RNRRGAQDDEKDQFLERVVAINRVSKVVKGGRRFSFTALVVVGDGDGTVGVGYGKAKEVP +AAIQKAVEEAKKSFFRVPRVGSTIPHLVQGEDAAGVVLLRPASPGTGVIAGGPVRAVLEC +AGIHDVLSKSMGSVNAINIVRGTVDALKKLEEPQAVAARRGKALDEIAPHAMLRTMENDR +AQKSA-KAGA +>GCF_020097155_PROKKA_01105 +MTETNDQKDTQVSETTETTVSETSAGSAGQSTERS-GGRGGRDGGRGGRDGDRRGGRRDD +RNRRGAQEDEKDAFLERVVAINRVSKVVKGGRRFSFTALVVVGDGDGTVGVGYGKAKEVP +AAIQKAVEEAKKSFFRVPRVGSTIPHLVQGEDAAGVVLLRPASPGTGVIAGGPVRAVLEC +AGIHDVLSKSMGSANAINIVRGTVDALKRLEEPQAVAARRGKALDEVAPHAMLRTMENDR +ASKGAQKAGV +>GCF_023573625_PROKKA_01632 +MTENINQKDTQVTESTETTVSETGSGSASQTTERATGGRGGRDGGRGGRDGDRRGGRRDD +RNRRGAQDDEKDQFLERVVGINRVSKVVKGGRRFSFTALVVVGDGDGTVGVGYGKAKEVP +AAIQKAVEEAKKSFFRVPRVGSTIPHLVQGEDAAGVVLLRPASPGTGVIAGGPVRAVLEC +AGIHDVLSKSMGSVNAINIVRGTVDALKKLEEPQAVAARRGKALDEIAPHAMLRTMENDR +AQKSA-KAGA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001378.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001378.fa new file mode 100644 index 0000000000000000000000000000000000000000..15eb203431ce7e40922cd5d79f0a14cb7c66d389 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001378.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01705 +MSRIGRLPITIPAGVDVTIDGDRVSVKGPKGQLEHSLPTPITATLEEGQVTVARPDDERE +SRSLHGLTRTLISNMVEGVTNGFSKQLEVVGTGYRVQAKGQDLEFALGYSHPVPVKAPQG +ITFTVEGNKVTVAGIDKQQVGETAANIRKLRRPDPYKGKGVRYAGEQIRRKAGKAGK +>GCF_003691675_PROKKA_01412 +MSRIGRLPITIPAGVDVTIDGDRVSVKGPKGQLEHSLPTPITVTLEEGQVTVARPDDERE +SRSLHGLTRTLISNMVEGVTNGFSKQLEVVGTGYRVQAKGQDLEFALGYSHPVPVKAPQG +ITFTVEGNKVTVAGIDKQQVGETAANIRKLRRPDPYKGKGVRYAGEQIRRKAGKAGK +>GCF_005280335_PROKKA_01173 +MSRIGRLPITIPSGVDVTIDGDRVSVKGPKGQLEHSLPTPITATLEEGQVTVARPDDERE +SRSLHGLTRTLISNMVEGVTTGFSKQLEVVGTGYRVQAKGQDLEFALGYSHPVPVKAPQG +ITFTVEGNKVTVAGIDKQQVGETAANIRKLRRPDPYKGKGVRYAGEQIRRKAGKAGK +>GCF_020097155_PROKKA_01103 +MSRIGRLPITVPSGVDVTIDGARISVKGPKGQLEHTLPSPITATLEEGQVIVARPDDERE +SRSLHGLSRTLINNMVLGVTEGFTKALEVVGTGYRVQAKGQDLEFALGYSHPVPVKCPEG +ISFTVEGNKVTVAGIDKQKVGETAANIRKLRKPDPYKGKGVRYAGEQIRRKAGKAGK +>GCF_023573625_PROKKA_01634 +MSRIGRLPITIPAGVDVTIDGDRVSVKGPKGQLEHSLPTPITVTLEEGQVTVARPDDERE +SRSLHGLTRTLISNMVEGVTNGFSKQLEVVGTGYRVQAKGQDLEFALGYSHPVPVKAPQG +ITFTVEGNKVTVAGIDKQQVGETAANIRKLRRPDPYKGKGVRYAGEQIRRKAGKAGK + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001379.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001379.fa new file mode 100644 index 0000000000000000000000000000000000000000..0c200467618fe8dcc01527612d2b6270c3748db0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001379.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01706 +MTMTDPVADMLTRLRNANSAYHDTVSMPSSKLKTRVAEILKAEGYIQDWREEEAEVGKKL +TIDLKFGPQRERAIAGLRRISKPGLRVYAKSTNLPHVLGGLGIAILSTSSGLLTNQQAAK +KGVGGEVLAYVW +>GCF_003691675_PROKKA_01413 +MTMTDPVADMLTRLRNANSAYHDTVSMPSSKLKTRVAEILKAEGYIQDWREEEAEVGKKL +TIDLKFGPQRERAIAGLRRISKPGLRVYAKSTNLPHVLGGLGIAILSTSSGLLTNQQAAK +KGVGGEVLAYVW +>GCF_005280335_PROKKA_01172 +MTMTDPVADMLTRLRNANSAYHDTVSMPSSKLKTRVAEILKSEGYIQDWREEEAEVGKKL +TIDLKFGPQRERAIAGLRRISKPGLRVYAKSTNLPHVLGGLGIAILSTSSGLLTNQQAAK +KGVGGEVLAYVW +>GCF_020097155_PROKKA_01102 +MTMTDPVADMLTRLRNANSAYHDTVSMPSSKLKVRVAEILKAEGYIQDWREEEAEVGKKL +TIDLKFGPQRERAIAGLRRISKPGLRVYAKSTNLPHVLGGLGIAILSTSSGLLTDRQASQ +KGVGGEVLAYVW +>GCF_023573625_PROKKA_01635 +MTMTDPVADMLTRLRNANSAYHDTVSMPSSKLKTRVAEILKAEGYIQDWREEEAEVGKKL +TIDLKFGPQRERAIAGLRRISKPGLRVYAKSTNLPHVLGGLGIAILSTSSGLLTNQQAAK +KGVGGEVLAYVW + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001384.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001384.fa new file mode 100644 index 0000000000000000000000000000000000000000..fc84a665015e4f168e073548c48fea68e4f81a71 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001384.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01711 +MAIGTKDLNVESLDGMDNARLLEALKSSKEELFNLRFQAATGQLDNASRLKAVKRDIARI +YTILRERELGIRGDVAAEAQAEKNEEAAK +>GCF_003691675_PROKKA_01418 +MAIGTKDLNVESLDGMDNARLLEALKSSKEELFNLRFQAATGQLDNASRLKAVKRDIARI +YTILRERELGIRGDVAAEAQAEKNEEAAK +>GCF_005280335_PROKKA_01167 +MAIGTKDLNVESLDGMDNARLLEALKSSKEELFNLRFQAATGQLDNSSRLKAVKRDIARI +YTILRERELGIRGDVAAEAQADNNEEAAK +>GCF_020097155_PROKKA_01097 +MAIGTKDLNVESLDGMDNARLLEALKSSKEELFNLRFQAATGQLEDSSRLKAVKRDIARI +YTILRERELGIRGDVET-AGAEKNEEAAK +>GCF_023573625_PROKKA_01640 +MAIGTKDLNVESLDGMDNARLLEALKSSKEELFNLRFQAATGQLDNASRLKAVKRDIARI +YTILRERELGIRGDVAAEAQAEKNEEAAK + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001413.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001413.fa new file mode 100644 index 0000000000000000000000000000000000000000..bddea7a65cf17695f5d1cf1a6365a499b1dc1861 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001413.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01741 +MRPDHP----AVGVLALGLARRLGLPDTALLPDDAPAAGAEPRRIEVARQGVAEAEVLAL +PWA--TVVAGPAWFTRACRGVPAEALGVESALLRTAVRAA------AGEAVRSRGEFTLY +AAEEPPPVDPSRTVAVSDDPAHVHAVVAQAPADDVAEAGVPSWESSVALVPDDGAGRAIE +AAVAAAGHRVTGGVLASLGTLTPPRLRGRGLGRYAVAVAMDRAALEGLLPFAEVPAGHTA +AHHVAIAVGLEAAGTRTVLAL---D +>GCF_003691675_PROKKA_01448 +MRPDHP----AVGVLALGLARRLGLPDTALLPGDAPAAGAEPRRIEVARQDVAEAEVLAL +PWA--TVVAGPAWFTRACRGVPAEALGVESALLRTAVRAA------AGEAVRSRGEFTLY +AAEEPPPVDPSRTVAVSDDPAHVHAVVAQAPADDVAEAGVPSWESSVALVPDDGAGRAIE +AAVAAAGHRVTGGVLASLGTLTPPRLRGRGLGRYAVAVAMDRAALEGLLPFAEVPAGHTA +AHHVAIAVGLEAAGTRTVLAL---D +>GCF_005280335_PROKKA_01136 +MSGAPS----FAGVLALGLARRLGLPDTALLPDDDGA--TKPRRLEAVREDAAEAEVLAL +PWA--TVVAGPAWFAAACRNVPAEVLGVESALLRTAAGAAPGAGSGGGAAVRSRGEFTLY +AAEEPPVLEPSRSVAVSEDPAHALAVAAQAPADDLAEAAAQAWTSSASLVPDDGAGHGLE +APVAAAGHRVSGGILAELGVLTVPRLRGHGLGRYAAAVAMDRATLEGLLPVAHLRAGHTA +AHHVAIAVGLEPVGSRTVLAL---G +>GCF_020097155_PROKKA_01065 +MTAAEPLPEHVRELVALAWGRALGVPDDV-----AALARATGRRVALPRPAGPETDILLL +EAAGLEVLAGPEPLLAAAADRATEELALESTLLRLA----------SGWGPRSRGEHTLL +HLDEPPEVAPSGRVAVSDDPADAAALARECPADDARAAGLDELHALRTLVPDDGAGRATG +TPLAAAGHATRAGLLADVRVLVRPELRGRGLGAYAAAVAAGAAWDEGLVPQARVPAAQDG +ALRLALGVGFVPTGRLTRVELTRAG +>GCF_023573625_PROKKA_01670 +MRPDHP----AVGVLALGLARRLGLPDTALLPGDAPAAGAEPRRIEVARQGVAEAEVLAL +PWA--TVVAGPAWFTRACRGVPAEALGVESALLRTAVRAA------AGEAVRSRGEFTLY +AAEEPPPVDPSRTVAVSDDPAHVHAVVAQAPADDVAEAGVPSWESSVALVPDDGAGRAIE +AAVAAAGHRVTGGVLASLGTLTPPRLRGRGLGRYAVAVAMDRAALEGLLPFAEVPAGHTA +AHHVAIAVGLEAAGTRTVLAL---D + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001414.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001414.fa new file mode 100644 index 0000000000000000000000000000000000000000..fbafd4d0ed9cab5742841bc131fe7b0ef9eb7b98 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001414.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01742 +MT------------TSRSPLLDLAVAEPQGPAGGAVEGRGPDAGVAAHYGRPLPEQRALA +RGRALVDLSHRAVLSVSGPDRLSWLHTLGTQHVETLPPGTSTEILFLDVQGRIEHAAHLL +EDGTAAWLVTDREDGPGLAAWLTSMRFSHDVTLRDHTGAVAVVGATAPVPGWEDRTVWLD +PWPRVGAGGWAYTADPDPATHPGADWSWREYLVTRADLEATVRALGTGVLAGWSLAGTTA +AEALRIEAGRPRRALDVDDRAIPHELDLLRTAVHLEKGCYRGQETVARVHNLGRPPRRLT +RLLLDGSGHALPEHGAPVILRPAEDTPEARAAARPVGTVTAAAQHHEAGAVALALLKRTV +PVDAELLVREDAPGE------DGVAEGGWIAASQEPLVSPDAGQVVGRPRGVGRLR +>GCF_003691675_PROKKA_01449 +MT------------TSRSPLLDLAVAEPQGPAGGAVEGRGPDAGVAAHYGRPLPEQRALA +RGRALVDLSHRAVLSVSGPDRLSWLHTLGTQHVETLPPGTSTEILFLDVQGRIEHAAHLL +EDGTAAWLVTDREDGPGLAAWLTSMRFSHDVTLRDHTGAVAVVGATAPVPGWEDRTVWLD +PWPRVGAGGWAYTADPDPATHPGADWSWREYLVTRADLEATVRALGTGVLAGWSLAGTTA +AEALRIEAGRPRRALDVDDRAIPHELDLLRTAVHLEKGCYRGQETVARVHNLGRPPRRLT +RLLLDGSGHALPEHGAPVILRPAEDTPEARAAARPVGTVTAAAQHHEAGAVALALLKRTV +PVDAELLVREDAPGE------DGVAEGGWIAASQEPLVSPDAGQVVGRPRGVGRLR +>GCF_005280335_PROKKA_01135 +MT--------GAEPAQRSPLLDLASAEPHGPAGGAVEGVGPDAGVAAHYGRPLPEQRALA +RGRALVDLSHRAVLSVSGPDRLTWLHTLGTQHVADLPAGTSTEILFLDAQGRIEHAAHLL +EDGTAAWLVTDREDGPGLAAWLASMRFSHQVTLRDHTGAVAVVGSTAPVPGWEDRTVWVD +PWPHVGVGGWAYTADPRPESHPGADWSWREHLVTRADLEATVRTLGTGPLEGWSLAGTTA +AEALRIEAGRPRMATDVDERALPHELDLLRTAVHLEKGCYRGQETVARVHNLGRPPRRLT +RLMLDGSVHALPPHGAPVILRPAEDTPQARAAARPVGAVTSSAQHHEAGAVALALLKRSV +PVDAELLVCEDLPGDAEAGDAADAAETGWIAAAQEPLVSPAAGQVVGRPRGVGRLR +>GCF_020097155_PROKKA_01064 +MTEPRPEPAPAVRAARRSPLLAPPPAAPGGPAEGAVEGVGQDAGVAAHYGRPLVEQRALA +RGRALVDLSQKTVVSVSGPDRLSWLHTLSTQHLKDRPAGTSTEALFLDANGRIEIAVHLL +EDGAAAWLIADPAHADVLVTWLRSMVFSHRVTLRDHTGVVAVVGAMAPVPGWEDRTVWLD +PWPRVDVGGWPYSPDPDPAAHPGAGWSWREYLVTRGDLVATVDRLGTGELEGWSLAGALA +AEALRIEAGRPRPAVDADARAIPHELDILRTAVHLEKGCYRGQETVARVYNLGRPPRRLT +QLLLDGSSHALPAAGAAVILRPEPDTADARAAARPVGTVTSAVQHHEAGAVALAVLKRAV +PVAAELLVREEA---------AGGGEPEWIAASQQALVSPDAGQVVGRPAGLSRRA +>GCF_023573625_PROKKA_01671 +MT------------TSRSPLLDLAVAEPQGPAGGAVEGRGPDAGVAAHYGRPLPEQRALA +RGRALVDLSHRAVLSVSGPDRLSWLHTLGTQHVETLPPGTSTEILFLDVQGRIEHAAHLL +EDGTAAWLVTDREDGPGLAAWLTSMRFSHDVTLRDHTGAVAVVGATAPVPGWEDRTVWLD +PWPRVGAGGWAYTADPDPATHPGADWSWREYLITRADLEATVRALGTGVLAGWSLAGTTA +AEALRIEAGRPRRALDVDDRAIPHELDLLRTAVHLEKGCYRGQETVARVHNLGRPPRRLT +RLLLDGSVHALPEHGAPVILRPAEDTPEARAAARPVGTVTAAAQHHEAGAVALALLKRTV +PVDAELLVREDAPGE------DGAAEGGWIAASQEPLVSPDAGQVVGRPRGVGRLR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001421.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001421.fa new file mode 100644 index 0000000000000000000000000000000000000000..0b753e19fff9856a5f1d06c21f907f3413b0c32c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001421.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01749 +MGRVSIPTPYEDLLADVMAHGAVKTDRTGTGTRSVFGRQLRFDLAESFPLITTKRVHFKS +VALELLWFLRGDSNVRWLQERGVRIWNEWADEDGELGPVYGVQWRSWPTPDGGHIDQIAK +VVEQIRTNPDSRRHIVTAWNPAEVDEMALPPCHALFQFYVSPGQDGAPGRLSCQLYQRSA +DLFLGVPFNIASYALLTVMVAQQTGLTPGEFVWTGGDVHIYANHEEQVREQLSREPYPYP +RLRLRRTPASIFDYDYEDFEVLDYRHHPTITAPIAV +>GCF_003691675_PROKKA_01456 +MGRVSIPTPYEDLLADVMAHGAVKTDRTGTGTRSVFGRQLRFDLAESFPLITTKRVHFKS +VALELLWFLRGDSNVRWLQERGVRIWNEWADEDGELGPVYGVQWRSWPTPDGGHIDQIAK +VVEQIRTNPDSRRHIVTAWNPAEVDEMALPPCHALFQFYVSPGQDGAPGRLSCQLYQRSA +DLFLGVPFNIASYALLTVMVAQQTGLTPGEFVWTGGDVHIYANHEEQVREQLSREPYPYP +RLRLRRTPASIFDYDYEDFEVLDYRHHPTITAPIAV +>GCF_005280335_PROKKA_01128 +---MSIPTPYEDLLADVMANGAVKSDRTGTGTRSVFGRQMRFDLSRSFPLITTKRVHFKS +VALELLWFLRGDSNVRWLQERGVRIWNEWADEDGELGPVYGVQWRSWPTPDGGHIDQIAK +VVEQIRTNPDSRRHIVTAWNPAEVDEMALPPCHALFQFYVSPGQDGAPGRLSCQLYQRSA +DLFLGVPFNIASYALLTVIVAQQTGLAPGEFVWTGGDVHIYANHEEQVREQLSREPYPYP +RLWLRRTPASIFDYDYEDFEVLDYRHHPTITAPIAV +>GCF_020097155_PROKKA_01053 +---MSIPTPYEDLLADVLAHGAVKADRTGTGTRSVFGRQLRFDLAESFPLITTKRVHFKS +VALELLWFLRGDSNVRWLQERGVTIWDEWADEGGELGPVYGVQWRSWPTPDGGSIDQIAK +VVEQIRTSPDSRRHLVTAWNPAEVDEMALPPCHAMFQFYVAPDVDGAPGVLSCQLYQRSA +DLFLGVPFNIASYALLTLMVAQQTGLTPGEFVWTGGDCHIYANHEEQVREQLSREPYPYP +TLRIRRTPESIFDYEYDDFELVDYRHHPAIKAPVAV +>GCF_023573625_PROKKA_01678 +MGRVSIPTPYEDLLADVMAHGAVKTDRTGTGTRSVFGRQLRFDLAESFPLITTKRVHFKS +VALELLWFLRGDSNVRWLQERGVRIWNEWADEDGELGPVYGVQWRSWPTPDGGHIDQIAK +VVEQIRTNPDSRRHIVTAWNPAEVDEMALPPCHALFQFYVSPGQDGAPGRLSCQLYQRSA +DLFLGVPFNIASYALLTVMVAQQTGLTPGEFVWTGGDVHIYANHEEQVREQLSREPYPYP +RLRLRRTPASIFDYDYEDFEVLDYRHHPTITAPIAV + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001437.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001437.fa new file mode 100644 index 0000000000000000000000000000000000000000..6e7028e4c1827de509f15e6467cc47d1d5115787 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001437.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01769 +MLYLIDPRGAVWSADTTIGRARARARVDGRPVDDLKFAKAAMLLTFDDHVDLALRHGVAA +PRGLLLDHGFVAQVLAPANLKAQRANQDAIAEQLAVVERRTEDVGSLRSHRHAAAYEGAD +QSLERRIKKAEEAARETLQAAPDEDLVRHWTRLGGAVPATLQAGRDR-- +>GCF_003691675_PROKKA_01476 +MLYLIDPRGAVWSADTTIGRARARARVDGRPVDDLKFTKAAMLLTFEDHVDLALRHGIAA +PRGLLLDHGFVAQVLAPANLKAQRANQDAIAEQLAVVERRTEDVGSLRSHRHAAAYEGAD +QDLERRIKKAEEAARETLQAAPDEDLVRHWTRLGGAVPATLQADRDR-- +>GCF_005280335_PROKKA_01108 +MLYLIDPRGAVWSADATIGQARARARVDGRPIDDLKFARAAMLLTLDDYVDLALRHGVEA +PRGILLDHGFVAQALAPANLKAQRANQDAMAEQLLPVERRTEDAGSLRGHRHDAAYEGAH +QDLDRRIKKAEETARETLQKTPDEDLIRHWRRLGGDVPATIEADRKD-- +>GCF_020097155_PROKKA_01034 +MLYLIDPRGAVWQSDVTLGRALARQKVDGRPVDDVPLKKAVLPIDEADVLDLGLRHGVAA +PRGILLDGGWVTQVLQPSQLKRQRANQDATADQLEPVELRTE-TDSLRSSRHAAVVEGAH +RDLDTRIEKAEKAAREALQAAPRRELVTHWRGMGGGLPATIQADLADAD +>GCF_023573625_PROKKA_01698 +MLYLIDPRGAVWSADTTIGRARARARVDGRPVDDLKFTKAAMLLTFEDHVDLALRHGIAA +PRGLLLDHGFVAQVLAPANLKAQRANQDAIAEQLAVVERRTEDVGSLRSHRHAAAYEGAD +QDLERRIKKAEEAARETLQAAPDEDLVRHWTRLGGAVPATLQADRDR-- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001441.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001441.fa new file mode 100644 index 0000000000000000000000000000000000000000..b289029a205b3a6fdb3cfb4f39431b181fd8120c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001441.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01774 +MTAPAPVSHAPDDYVCPFCGLVASDVSDPGNRCELGDTVYQDEDLLVLIAVDGFGDHEGH +AMVCPAEHYENLYDLPPRVLQRIALMAQQVALAMKRAWAPDGVSTRQHNEPAGNQHVWHY +HLHVFPRFEGDMLYRQLRHPVAPEVRAGKARELAAALDPAPTRLD +>GCF_003691675_PROKKA_01481 +MTAPAPVSHAPDGYVCPFCGLVAGDVSDPGNRCELGDTVYQDEDLIVLIAVDGFGDHEGH +AMVCPAEHYENLYDLPPRVLQRIALMAQQVALAMKRAWAPDGVSTRQHNEPAGNQHVWHY +HLHVFPRFEGDMLYRQLRHPVAPEVRAGKARELAAALDPAPTRLD +>GCF_005280335_PROKKA_01103 +MSGPRLRSHAPEGYVCPFCGLVAGDVSDPGNRCELADTVYQDEDLLVLIAVDGFGDHEGH +AMVCPAGHYENLYELPPRVLQRIALMAREVALAMKRAWSPDGVSTRQHNEPAGNQHVWHY +HLHVFPRFEGDLLYRQLRHPVSPEVRALKARELAAELDPAPTFLD +>GCF_020097155_PROKKA_01028 +MSA-QPLSHAPEGYVCPFCGLVAGDVSDPGNRCELEDTVYQDEDVLVLIAVDGFGEHDGH +AMVCPSGHYENLYDLPPRVLQRIALMAQQVALAMKRAWGPDGVSTRQHNEPAGNQHVWHY +HLHVFPRYEDDLLYRQLRHPVAPEVRAARARELAAALDPAPTLLD +>GCF_023573625_PROKKA_01703 +MTAPAPVSHAPDGYVCPFCGLVAGDVSDPGNRCELGDTVYQDEDLLVLIAVDGFGDHEGH +AMVCPAEHYENLYDLPPRVLQRIALMAQQVALAMKRAWAPEGVSTRQHNEPAGNQHVWHY +HLHVFPRFEGDMLYRQLRHPVAPEVRALKARELAAALDPVPTRLD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001444.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001444.fa new file mode 100644 index 0000000000000000000000000000000000000000..920aaa9d98a03e6bddeec07cbc8a6384ef2b0cc8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001444.fa @@ -0,0 +1,50 @@ +>GCF_002008305_PROKKA_01777 +MTSVDSLSVARAVATALIDAGMRDAVVCPGSRSAPLAYALAALEHAGQVRLHVRVDERSAGFLAHGLSLASGRPVGVLTT +SGTAVGNLVPALMESFHAGTRVIALTADRPPELHGTGANQTTDQRDVFGTHVRHAASLGCDAADGVDTEQHLRHVRATVR +RALLAAEGVVAET-DSDDG----APGPVTMAEAPAGPVHLNLHFRDPLVPSPEEAAAMGAA-AAAPHTPAPAVAPTGASP +AAAASAYRAPGAVLSGLPELDVARLDQRRTVVLACHGAGPVAAAFALSLGLPLLAEPSSNARFSANAIAAYPLLLGAAGG +RDAD--AHPLAARIQRVVLFGRPTLTRTVNALLARPDVATALHAPEPAPWFEPGRRRETPVETLEELAAFAGQGEPGWLA +AWQHASMRAQAAVEDVLVTTDAGDRLSPQTVAHVSAAMVRGPLVLGSSSVIRDVDLTWRPPSAPDAEVYANRGLAGIDGT +VSTAAGVALARGRRTVALLGDLTALHEAGGLLVGPTETEPDLDLVVLNDNGGAIFASLEHGAVAEAPGMADPVERLFGTP +HGVDLAALAAAYGVPHTRVTDRVDLVRALSDPVRGRRLLEVRCDRADRPRVAAALAAAVRATFPPACPVPDPAP-DAGPA +PAPPTAELAAEEAPQ +>GCF_003691675_PROKKA_01484 +MTSVDSLSVARAVATALIDAGMRDAVVCPGSRSAPLAYALAALERAGEVRLHVRVDERSAGFLAHGLSLASGRPVGVLTT +SGTAVGNLLPALMESIHAGTRVIALTADRPPELHGTGANQTTDQRGVFGTHVRHAASLGCDAADGVDAEQHLRHVRATVR +RALLAAEGVVAEA-GSDDG----APGPVTMAEAPAGPVHLNLHFRDPLVPSPEEAAAMG-A-AAAPHTPAPAVAPTGASP +AAAASAYRAPGAVLSGLPELDVARLDQRRTVVLACHGAGPVAAAFALSLGLPLLAEPSSNARFSANAIAAYPLLLGAAGG +RDAD--AHPLAARIERVVLFGRPTLTRTVNALLARPDVATALHAPEPAPWFEPGRRRETPVETLEELAAFAGQGEPGWLA +AWQHASMRAQAAVEDALVTTDAGDRLSPQTVAHVSAAMVRGPLVLGSSSVIRDVDLTWRPPSAPDAEVYANRGLAGIDGT +VSTAAGVALARGRRTVALLGDLTALHEAGGLLVGPTETEPDLDLVVVNDDGGAIFASLEHGAVAEAPGMADPVERLFGTP +HGVDLAALAAAYGLPHTRVTDRVDLVRALSDPVRGRRLLEVRCDRADRPRVAAALAAAVRATFPPACPVPDPAP-DAGPA +PAPPTAELAAEEAPQ +>GCF_005280335_PROKKA_01100 +MTSVDSLSVARAVADALIEAGMRDAVVCPGSRSAPLAYALAERERAGAVRLHVRVDERSAGFLAHGLSLASGRPVGVLTT +SGTAVGNLLPALMESFHAGTRVIALTADRPTELHGTGANQTTSQEGVFALHVRHAASIGCDAPAGRDADAHLRAVGAVVH +RALLAADGVVADGPGHDDGGHVPEPGPVTVGEAPAGPVHLNLQFRAPLVPAPDEAAAMGSARQSAPQSPADP-----ASE +AAVHSAYRAPGALLSGFPELDVARLTQRRTVVLACHGAGPVAAAFALALGLPLLAEPSSNARFSVDAIAAYPLLLGSAGG +RGPD--SHPLAGRIERVVLFGRPTLTRPVTALLAREDVETVLFAPEPAPWFEPGRRRERPIETLEELADFAGHGEAGWLS +AWQRASMRAQAAVEDVLVAEDLRHGLSPQSVAQVGAAVTRGPLVLGSSSVIRDVDLTWRPPTAPDAEVYANRGLAGIDGT +VSTAAGVALARGMRTVALLGDLTALHDVGGLLVGPTEVEPDLELVVVNDDGGAIFAGLEHGAVAAVPGLAAPVERLFATP +HGVDVAALAAAYGIPHVAVSDRVGLIHCLADPVRGRRIVEVRCSRADRPRVAAALAEAVRATFPAAA---DSAPADTDPA +PADP----AAEEAPQ +>GCF_020097155_PROKKA_01024 +MSSVDSTTLARTVAAALLEGGMREAVVCPGSRSAPLVYALAEAERRGRIRLHVRVDERSAAFLAHGISLATGRPVGVLTT +SGTAVGNLLPALMEAFHAGTRLVALTADRPAEMHGTGANQTTRQDGLFALHTRGAASISADLAPGEGAEEHLGRVAATVR +RLLVRAEGLVVD----------PAAARPDLAEAPAGPVHLNLPFRAPLVPDAGQLAAMA-----APAAPGDD-----ADR +PAEPAPWRAPGSDLTARVDLDVSRRPERRTVVLACHGAGPVAAAFAMALGLPLLAEPSSNARFTVNAVAAYPLLLGPAGG +APGSDQGHPLAECIERVVLFGRPTLTRTVTALLDRPDVEAVLYSPEPAPWFEPGRRPERVVTDLGELADFAGQGAAGWVP +AWQRASHRAQNAVEDALVRADRRHGLSPQSVAHVVPAVTRGPLVLGSSSLIRDVDLTWRPPTAPDAGVFANRGLAGIDGT +IATAAGVALGTGRRTVALIGDLTALHDAGGLLVGDGEPEPDLDVVVVNDAGGAIFAGLEHGQVAGHAGMADVVERFFGTP +HRVDLAALAAAYGVPHVLVEDRVELVHVLGAPERGRRLVEVRVHRADRPAVAAAIARAVAEAV-----AADPVP-ACTGA +--------AAPEEES +>GCF_023573625_PROKKA_01706 +MTSVDSLSVARAVATALIDAGMRDAVVCPGSRSAPLAYALAALERAGEVRLHVRVDERSAGFLAHGLSLASGRPVGVLTT +SGTAVGNLLPALMESIHAGTRVIALTADRPPELHGTGANQTTDQRGVFGTHVRHAASLGCDAADGVDAEQHLRHVRATVR +RALLAAEGVVAEA-GSDDG----APGPVTMAEAPAGPVHLNLHFRDPLVPSPEEAAAMG-A-AAAPHTPAPAVAPTGASP +APAASTYRAPGAVLSGLPELDVARLDQRRTVVLACHGAGPVAAAFALSLGLPLLAEPSSNARFSANAIAAYPLLLGAAGG +RDAD--AHPLAARIERVVLFGRPTLTRTVNALLARPDVATALHAPEPAPWFEPGRRRETPVETLEELAAFAGQGEPGWLA +AWQHASMRAQAAVEDVLVSTDAGGRLSPQTVAHVSAAMVRGPLVLGSSSVIRDVDLTWRPPSAPDAEVYANRGLAGIDGT +VSTAAGVALARGRRTVALLGDLTALHEAGGLLVGPTETEPDLDLVVVNDDGGAIFASLEHGAVAEAPGMADPVERLFGTP +HGVDLAALAAAYGLPHTRVTDRVDLVRALSDPVRGRRLLEVRCDRADRPRVAAALAAAVRATFPPACPVPDPAP-DAGPA +PAPPTAELAAEEAPQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001459.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001459.fa new file mode 100644 index 0000000000000000000000000000000000000000..bb05d9708a0a728f6fc1909bd63ef071fddba588 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001459.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01810 +MSGTSPTDPHGSQNPYGTDPYGAAPQGPTPGSPDPAGASPYGQNPY-------GAPPAAP +YGAPGQAGMPQA----PSPHGPAGWQSPGPVELPPRPRSLTAAFWLIVSGGLLLLATTLL +AAFAITQPEGQVAIQQELDRSVEQMNLPADQAEQMRTMMDGMLPALATTAAVFGVLAFLV +YLWVAFAIRGGSRAARIVGTVLASLSVLVLVSNAVMGAFSPLDLVWVGLGVAGIVLAYRP +DATEYMRLKTWQRFARR +>GCF_003691675_PROKKA_01507 +MSGTSPTDPHGSQNPYGTDPYGAAPQGPTPGSPGPAGASPYGQNPY-------GAPPAAP +YGAPGQAGMPQA----PSPHGPAGWQSPGPVELPPRPRSLTAAFWLIVSGGLLLLATTLL +AAFALTQPEGQAAIQQELDRSVEQMDLPADQAEQMRAMMDGMLPALATTAAVFGVVAFLV +YLWVAFAIRGGSRAARIVGTVLAALSVLVLVSNAVMGAFSPLDLVWVGLGVAGIVLAYRP +DATEYMRLKAWQRFARR +>GCF_005280335_PROKKA_01064 +MSGTSPTDPQRGQNPYGQEAP-----GPSPYGENPYGAHPYGQAPYGQGGPAQGQPGQG- +HPNPGHPAPSYADQGYPAQGGWPGQQAPGPLTAPRRPGAITASFWLILAGGLVLLASTLL +AAFAMTLPESRAMLEQQMRETYEQMGLPADQLAQMEQMTDQLLPVMSVVAAAFGVVAFLV +YLLIALKIRKGSRAARTVGTVLAALSVLMIVTNLMMGAFNPFDLLWVGLGVAGIVMAFRP +EASEYMRLKAWERAGTR +>GCF_020097155_PROKKA_00999 +MSGTE------NSNPYGRPAG-----QSGPQWPDAAAQAPYGQAPDASAQAPYGAPPQG- +WGAPQQWG------------GQPGWPAAAPVPA-RRPGPINAAFWLIVSAGVVFLASTVL +SALVATSDAGRRELEAAMTKVWGDYGMTPEQIREYQDMLPPMMPVMAGVMVAVGVLALLV +YLLIASKIRGGSRAARTVGTVLAVLSVLMVLAPLASGQFSPLDLLWCLLGVAGIATAYRK +EATEFMRLRAWERAARR +>GCF_023573625_PROKKA_01731 +MSGTSPTDPHGSQNPYGADPYGAVPQGSTPGSPDPAGASPYGQNPY-------GAPPATP +YGAPGQAGMPQA----PSPHGPAGWQSPGPVELPPRPRSLTAAFWLIVSGGLLLLATTLL +AAFALTQPEGQAAIQQELDRSVEQMDLPADQAEQMRAMMDGMLPALATTAAVFGVLAFLV +YLWVAFAIRGGSRAARIVGTVLAALSVLVLVSNAVMGAFSPLDLVWVGLGVAGIVLAYRP +DATEYMRLKAWQRFARR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001463.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001463.fa new file mode 100644 index 0000000000000000000000000000000000000000..d4bfc8543d393de4e7d96a74f2d69856c2474aa6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001463.fa @@ -0,0 +1,51 @@ +>GCF_002008305_PROKKA_01814 +MAGPRPTPHARRHGGVRRPGGLPRPGQASTLESSTDLRTVLRRSGRAVSSVVGGSPARAA +LSAFALMALVFTGLLALPWAAADGHATPLHDAMFTAVSAFSVTGLTTVNTAAHWSPAGQV +IILVAIQIGGLGILSIASLLTLAVSRHLGLRSKLATQQAGMTSGSLGEVGQLLRVVVVTV +LTAEAALALVLVPRFAAISGSWLTGLWHGVFYSVSAFNNAGFTLHVDGLPEIMHDPVIIT +VLGVGVFLGALGFPVVMVLLEKGWRFREWNLHTKLTVEVTLALLVLGAVALFFFEAGNPA +TQAGMGFWQRVGHSLFGSVMTRSGGFAIDDTNAHRPESLLLMDALMFVGGGSASTAGGIK +VTTLAIMFLAIVAEARGDREVTAHGRTIAPESLRVAIAVLALGATLVLVATLALVHITDE +SLQRPLFEVISAFGTCGLSVGVSAESPPAGKYVLTAMMFAGRVGTITFAAALALRQRRVL +YRYPVERPVIG +>GCF_003691675_PROKKA_01511 +MAGPRPTPHARRHGGVRRPGGLPRPGQASTLESSTDLRTVLRRSGRAVSSVVGGSPARAA +LSAFALMALVFTGLLALPWAAADGHATPLHDAMFTAVSAFSVTGLTTVNTAVHWSPAGQV +IILVAIQIGGLGILSMASLLTLAVSRHLGLRSKLATQQAGMTSGSLGEVGQLLRVVVLTV +LTAEAALALFLVPRFAAISGSWLTGLWHGVFYSVSAFNNAGFSLHVDGLPEIMHDPVIIT +VLGVGVFFGALGFPVVMVLLEKGWRFRQWNLHTKLTVEVTLALLVLGAVALFFFEAGNPA +TQAGMGFWQRVGHSLFGSVMTRSGGFAIDDTNAHRPESLLLMDALMFVGGGSASTAGGIK +VTTLAIMFLAIVAEARGDREVTAHGRTIAPESLRVAIAVLALGATLVLVATLALVHITDE +SLQRPLFEVISAFGTCGLSVGVSAESPPAGKYVLTAMMFAGRVGTITFAAALALRQRRVL +YRYPVERPVIG +>GCF_005280335_PROKKA_01060 +M---------------------------STLESSSELRTALRRSSRAVSSVVSGSPARAA +LSAFLLVSLVFTALLSLPWASADGRPTALHDAMFTAVSAVSVTGLTTLNTAEHWSVAGQV +IILVAIQIGGLGILSMASLLTLAVSRHLGLRSKLATQEAGMTTGNVGEVGRLLRVVVVTV +LTCEAALAVFLVPRFAAESGSWLTGLWHGVFYSVSAFNNAGFSLHVDGLSAVAHDPVILT +VIAVGVFAGALGFPVVMVLLDKGWRYRAWNLHTKLTVEVTLALLVLGAVLLFFFEAGNPG +TNGDLGVVERIWRSLFGSVMTRSGGFAIDDTNAHRPESLLLMDALMFVGGGSASTAGGIK +VTTLAVMFLAILAEARGDREVTAHGRTIAPETLRVAISVLALGATLVLVATLALVNIMDE +SLQRPLFEVISAFATCGLSVGVSAEAPPAGKYLLAAMMFAGRVGTITFAAALALRQRRVL +YRYPVERPILG +>GCF_020097155_PROKKA_00995 +M----PS------------GAL----------------SPARRVVTAVTGVVAGSPARAA +LSAFALGALLFTGLLMLPAAATDGRVTPLHDAMFTAVSAFSVTGLTTLDTAEHWTPLGQV +ILLAAMQIGGLGILSMASLLTLAVSRHLGLRTKLATQESGMTTGNMGEVGHLLKVVVLTV +LTCEGALAVILVPRFAALSDSWATGLWQGVFYSVSAFNNAGFTIHEGGTAAFMHDPVILT +VIAVGVFAGALGFPVVMVLVDKGWRFRSWNLHTKLTVEVTLVLLVVGAVALFFFEAGNPA +THGDMVVGQRIGHSFFGSVMTRSGGFAIDDTNSHRPESLLLMDALMFVGGGSASTAGGIK +VTTLAVMFLAIVAEARGDKEVTVHGRTIAPETLRVAISVLALGATLVLLATLALVSIVDQ +PLQRPLFEVVSAFGTCGLSVGVSAEAPPAGKYLLTAMMFAGRVGTITFAAALALRQRRVL +YRYPVERPILG +>GCF_023573625_PROKKA_01735 +MAGPRPTPHARRHGGVRRPGGLPRPGQASTLESSTDLRTALRRSGRAVSSVVGGSPARAA +LSAFALMALVFTGLLALPWAAADGHATPLHDAMFTAVSAFSVTGLTTVNTAEHWSPAGQV +VILVAIQIGGLGILSMASLLTLAVSRHLGLRSKLATQQAGMTSGSLGEVGQLLRVVVVTV +LTAEAALALVLVPRFAAISGSWLTGLWHGVFYSVSAFNNAGFTLHVDGLPEIMHDPVVIT +VLGVGVFLGALGFPVVMVLLEKGWRFREWNLHTKLTVEVTLALLVLGAVALFFFEAGNPA +TQAGMGFWQRVGHSLFGSVMTRSGGFAIDDTNAHQPESLLLMDALMFVGGGSASTAGGIK +VTTLAIMFLAIVAEARGDREVTAHGRTIAPESLRVAIAVLALGATLVLVATLALVHITDE +SLQRPLFEVISAFGTCGLSVGVSAESPPAGKYVLTAMMFAGRVGTITFAAALALRQRRVL +YRYPVERPVIG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001471.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001471.fa new file mode 100644 index 0000000000000000000000000000000000000000..6c70033cba861d8a02ac0947e963fb26c5d9cff7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001471.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01822 +MRDGRGLARTGLTPYPSDMTEHLDPALVDIWFAAWSRSRGYRTSQEAGRRAALRTPRPAH +MIPGGSGRATVDVPATWEHVVVNPSRAELEDLREAVRDQEQILLTVFGDAGEDPKAMGLK +AQAEPERFMTMDMDPELQDVEPPLLPEGYEARVDQPMEGSRRLRILAVGA-STAPEGEEE +LAALGWVTEEDGTAVYDRIWTSPNHRRRGLGSLVMRYLTSEVM-SEGEISRGLLVASPDG +QKLYRHLAWTDLGPVSIWGRGLAEDNPTAEHTGTMGA +>GCF_003691675_PROKKA_01519 +------------------MTEHLDPALVDIWFAAWSRSRGYRTSQEAGRRAALRTPRPAC +MIPGGSGRATVDVPATWEHVVVNPSRGELEDLREAVRDQEQILLTVFGDAGEDPKAMGLK +AQAEPERFMTMDMDPELQDVEPPLLPEGYEARVDQPMEGSRRLRILAVGA-STVPEGEEE +LAALGWVTEEGGTAVYDRIWTSPNHRRRGLGSLVMRYLTSEVM-SEGEISRGLLVASPDG +QKLYRHLAWTDLGPVSIWGRGLAEDNPAAEHTGTMGA +>GCF_005280335_PROKKA_01047 +------------------MSEHLDTALVDTWFAAWSRSRGYRTSPEAGRRAALRTRRPAR +MIPGGSGRATVDVPATWEYVVVDPTREQLEELREALRDEEQILLTVFGDAGADPKAMGLT +PQAEPERFMSMDMDPEVQDVEPPLLPDGYEARVDQPMEGSVRVRIMAVGA-STAPEGEEE +LAALGWVTREDGTAVYDRIWTSPNHRRRGLGSLVMRYLTSEVM-SDGEISLGLLVASPDG +RKLYEHLAWTDLGPVSIWGRGLAADTPTAEHTGTMGA +>GCF_020097155_PROKKA_00986 +------------------MTQSIDDTLVGTWFAAWSRSRGYETRIEDGMRSALRKKRSAQ +RIPGGAGRAAMDIPTTWEHVLVSPDADALAPALASLEEQPDRLVTVFGETDQDLTSAGLH +SAVLPERFMSMELDREVQDVEPPLLPEGYEAHVDEPRPGSRRVRFYAAGALSGVPEGEEE +LAALGWVTFEGETAVFDRIWTSPDHRRRGLGSLVMRHLTSEALGADDELERGLLVASPDG +QKLYGHLGWTDLGPVRIWTRADGE-APGAEHTGTMAR +>GCF_023573625_PROKKA_01743 +MRDGRGLARTGLTPYPSDMTEHLDPALVDIWFAAWSRSRGYRTSQEAGRRAALRTPRPAH +MIPGGSGRATVDVPATWEHVVVNPSRAELEDLREAVRDQEQILLTVFGDAGEDPKAMGLK +AQAEPERFMTMDMDPELQDVEPPLLPEGYEARVDQPMEGSRRLRILAVGA-STAPEGEEE +LAALGWVTEEDGTAVYDRIWTSPNHRRRGLGSLVMRYLTSEVM-SEGEISRGLLVASPDG +QKLYRHLAWTDLGPVSIWGRGLAEDNPTAEHTGTMGA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001481.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001481.fa new file mode 100644 index 0000000000000000000000000000000000000000..631b99afa08bd730739516ca9cf419b8c0e7984b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001481.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_01833 +MAFSTRSTGETMRATGPSAAAPSAAPVAGGAAGVVSTSLPVVAVDGSLPTPPYRQIVDAV +LAGVTSGSLARGDRLPPVRALAAELGVAPGTVARAYKELEAHGTIRTRGRAGTFVA---- +----ASADARADAAHQAVRRCLDTLLERLGYTPDEAVELV-------------RRDAAAR +A +>GCF_003691675_PROKKA_01530 +MAVSTRSTGETMRAPGPSAAAPSAAPVAGGAAGVVSASLPVVAVDGSLSAPPYRQIVDAV +LAGVASGSLARGDRLPPVRALAAELGVAPGTVARAYKELEAHGTIRTRGRAGTFVA---- +----ASADARADAAHQAVRRCLDTLLERLGYTPDEAVELV-------------RRDAAAR +A +>GCF_005280335_PROKKA_01035 +MTAT------------PSGAAPSPASAEGGAARVVSASLPVVAVDAALSAPPYRQITDAV +LAGVASGCLARGDRLPPVRALASELGVAPGTVARAYKELEARGTILTRGRAGTFVA---- +----ASADARADAAHQAVRRCLDTLLDRLGYTADEAVELV-------------RRDAAAR +A +>GCF_020097155_PROKKA_01055 +MNGVE----------------------------------PTLELDLRSPVPPFEQIRAGI +SAFVDAGVLAPGDRLPSVRALAADLGVAPNTVVRAYRELESAGVVRTARGKGTVVADRPR +GALTADDDGTARTLEAAVHSALAAGWDR------ERVQRVVEAALVSPPAPVDRKDT--- +P +>GCF_023573625_PROKKA_01754 +MAVSTRGTGESMRLPGPFA----AAPVADGAAGVVSASLPVVAVDASLPAPPYRQIVDAV +LAGVASGSLARGDRLPPVRVLAAELGVAPGTVARAYKELEAHGTIRTRGRAGTFVA---- +----ASADARADAAHQAVRRCLDTLLERLGYTPDEAVELV-------------RRDAAAR +A + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001482.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001482.fa new file mode 100644 index 0000000000000000000000000000000000000000..16df2b3302cecb54c21428b950562c07a341193c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001482.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01834 +MSTAAIVMMSLAILLVWGGLAVSAIHLLRHPDDSSGDLAIEDDLAPAVWERED--GLLDA +Q---HR- +>GCF_003691675_PROKKA_01531 +MSTAAIVMMSLAILLVWGGLAVSAIHLLRHPDDSSGDLAIEDELAPAVWERED--GRLDA +Q---HR- +>GCF_005280335_PROKKA_01034 +MSTAAIVMMSLAILLVWGGLALSAVHLLRHPDDSSGDLALGDRLAPAAWEREDELGREDV +RLGARRG +>GCF_020097155_PROKKA_00975 +MHTPALIMMVIAMLTVWGGLVLSAVHLLKHPDETSGTLA----------------DAVDV +D---HTL +>GCF_023573625_PROKKA_01755 +MSTAAIVMMSLAILLVWGGLAVSAIHLLRHPDDSSGDLAIEDELAPAVRERED--GRLDA +R---HR- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001488.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001488.fa new file mode 100644 index 0000000000000000000000000000000000000000..38f06e5942a17542e306c903e27cb19cd6ab769b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001488.fa @@ -0,0 +1,55 @@ +>GCF_002008305_PROKKA_01841 +MASRTT-RFPAPSSALGRLLAFVGLSAVAGLLVAALLLPVAGLAGVAAASGREMLDELPDELPTEPVSVPSRILSEDGEE +IAVFYEENRTPVPLDEISEHMQHAIVAIEDERFYDHDGVDARGLIRATVNNATSDSTQGASTLTQQFVNNMLVNVQQIRG +DSRLTLSGSKNIADKVKEIKLAVAVEKQMSKDEILEGYLNIVLFSGRAYGVEAASQYVFGKSAADLESWEAATLAGMVQS +PTRFNPARNPEEATERRNLVLNAMKDNGYLSQEEYDHAVAQPMEVVMESRPSGCLYAKFGTYFCDYVERQILADPTFGPD +VQSRQALLDRGGLTIRTTIDSTLQKETEKNLRASVPNNESLGAGHALTSVEAGTGNIRTMAQNTEYAIQDELGHTSLNFN +VDKQWGGGQGFQAGSTLKPFVALTWLRNGNRLVDSVDASRNVYPTGTRFAASCRPGGYTTIGG---TWQFKNVIPGMLRQ +VRVDEGLFWSVNTPTVATAYQLDLCDITSLTTQLGITRALDSSPLQPDDPSFLLGKDSVAPLSLAGAYAAIAANGLYCEP +RAILEVTDTVGNQYDVADPQCDQVIDPDHVRELMPVLRHIAGFNIAEEGAGYEFGGKTGTNDNVSSTWFVGFTSELATAV +WTGRYNNLKSMTGETVNGEVRNPFYSTSINGPSWLEYNQLAKEKFPPGELPEWDGPQSEDPGEAGEHPDGRQFHIDDLDR +GGPLPEAVPG-----------------------F +>GCF_003691675_PROKKA_01538 +MASRTT-RFPAPSSAPGRLLAFVGLSALAGLLVAALLLPVAGLAGVAAASGREMLDELPDELPAEPVSVPSRILSEDGEE +IAVFYEENRTPVPLDKISKHMQHAIVAIEDERFYDHDGVDARGLIRATVNNATSDSTQGASTLTQQFVNNMLVNVQQIRG +DSRLTLSGSKNIADKVKEIKLAVAVEKQMSKDEILEGYLNIVLFSGRAYGVEAASQYVFGKSAADLESWEAATLAGMVQS +PTRFNPARNPEEATERRNLVLNAMKDNGYLSQEEYDHAVAQPMEVVMESRPSGCLYAKFGTYFCDYVERQILADPTFGPD +VQSRQALLDRGGLTIRTTIDSTLQKETEKNLRASVPNNESLGAGHALTSVEAGTGNIRTMAQNTEYAIQDELGHTSLNFN +VDKQWGGGQGFQAGSTLKPFVALTWLRNGNRLVDSVDASRNVYPTGTRFAASCRPGGYTTIGG---TWQFKNVIPGMLRQ +VRVDEGLFWSVNTPTVATAYQLDLCDITSLTTQLGITRALDSSPLQPDDPSFLLGKDSVAPLSLAGAYAAIAANGLYCEP +RAILEVTDTVGNQYDVADPQCDQVIDPDHVRELMPVLRHIAGFNIAEEGAGYEFGGKTGTNDNVSSTWFVGFTSKLATAV +WTGRYNNLKSMTGETVNGEVRNPFYSTSINGPSWLEYNQLAKEKFPPGELPEWDGPQSEDPGEAGEHPDGRQFHIDDLDR +GGPLPEAVPG-----------------------F +>GCF_005280335_PROKKA_01027 +MASRTSRRLPEPSSALGRLLAFLGLSALAGLLVAALLLPLAGLTGVAAASGREMLDELPDELPAEPVSVPSRMISEDGEE +IAVFYEEDRIPVPLDQISEHMRNAIVAVEDERFYEHDGVDARGLIRATVNNATSDSTQGASTLTQQFVNNMLVNVQQIRG +DSRLTLSGTKNVSDKVKEIKLAVAVEEQMTKDEILEGYLNIVLFSGRAYGVEAASRYVFGKSAAELESWEAATLAGMVQS +PTRFNPARNPEEATERRNLVLGAMKKNGYLTEEEHAEAVAQPMEVVMESRPSGCLYSKFGSYFCDYVERQILADPAFGPD +PQSRQALLDRGGLTIRTTIDSELQKAAEENLRKSVPNNESLGAGHALTSVQAGTGNIVTMAQNTEYAIQDELGHTSLNFN +VDREWGGGQGFQAGSTLKPFVALTWLRNGNRMVDSVDASRNVYPTGTRFEASCRPGGYTTIGG---TWQFKNVIPGMLRQ +VRVDEGLFWSVNTPTVATAYQMDLCDITSLTTQLGITRALDSSPLQPDDPSFLLGKDSIAPLSLAGAYAAIAADGLYCEP +RAILEVTDTVGNQYDVAGPQCDQVVDPKHIAELMPVLRHIGAFNIAEEGAGYEFGGKTGTNDNVSSTWFTGFTTELATAV +WTGRYNNMKSMTGETVNGEVRNPFYSTSINGPSWLEYNQLAKEKYPPGELPDWDGPQSEDPGAEGEHPDGTAFRIDDLDR +GGPQPQAVPG-----------------------N +>GCF_020097155_PROKKA_00968 +MASRSS-RLPARSSALGRLLSFLGLSALAGLLVAGLMMPAAGATGIVFASGRDMLDELPDQLPAEPVSMPSKIYSADGEL +IATFFQENRQPVPLDQISPYMRNAIVAIEDERFYQHDGVDAKGLVRAMVNNVSSSSTQGASTLTQQFVNNMLINSQQVRG +DSRLTLSGTKQASDKVKEIKLAVAVEKQMSKDQILEGYLNLVLFQGRAYGIEAASQYVFGKPAKDLELWEAATLAGMVQS +PTRFNPARNPEGTTARRNTVLKAMLKNGYISQEEHDHAVAQPLTYTMKGQSTGCLSAAFGAYFCDYVERQILADPTFGPD +TASRQALLDRGGLTIRTTIDSNLQKKAEELTRRVIPNNESLGAGHSLISLRPGSGDIVTMAQNTEYSIQDELGKTTLNLN +VDAKWGGGTGFAAGSTFKPFIGLTWLRNGGKLIDSVDGSKDRYPPDARFQASCLPGGYTTAGGGTQGWQLNNVIDGMKKR +DRIDEGIFWSVNTPTVALAYQMDLCDIVNTLTQVGIVTARDGAPLSPAEPSFVLGKDDVSPMTMAGAYATLAANGKYCKP +RAITEVTDTTGNQYTVPAPECRQVLDPAQVAEVTPLLRHIAAHNIAPDGTGYEFAGKTGTNNNMSSTWFIGYTTELATAV +WAGRYTSQKTMRGETINGVVQKEFYGATVNGGTWLEWNDMAKRTFVPGELPEFDGPQSEDPALEGDHPDGRFYRPEDIDR +NGGTPTSSLGPAAGETAFSSAENAAKFESGVLTR +>GCF_023573625_PROKKA_01762 +MASRTT-RFPAPSSALGRLLAFVGLSAVAGLLVAALLLPVAGLAGVAAASGREMLDELPDELPTEPVSVPSRILSEDGEE +IAVFYEENRTPVPLDEISEHMQHAIVAIEDERFYDHDGVDARGLIRAAVNNATSDSTQGASTLTQQFVNNMLVNVQQIRG +DSRLTLSGSKNIADKVKEIKLAVAVEEQMSKDEILEGYLNIVLFSGRAYGVEAASQYVFGKSAADLESWEAATLAGMVQS +PTRFNPARNPEEATERRNLVLNAMKDNGYLSQEEYDHAVAQPMEVVMESRPSGCLYAKFGAYFCDYVERQILADPTFGPD +VQSRQALLDRGGLTIRTTIDSTLQKETEKNLRASVPNNESLGAGHALTSVEAGTGNIRTMAQNTEYAIQDELGHTSLNFN +VDKQWGGGQGFQAGSTLKPFVALTWLRNGNRLVDSVDASRNVYPTGTRFAASCRPGGYTTIGG---TWQFKNVIPNMLRQ +VRVDEGLFWSVNTPTVATAYQLDLCDITSLTTQLGITRALDSSPLQPDDPSFLLGKDSVAPLSLAGAYAAIAANGLYCEP +RAILEVTDTAGNQYDVADPQCDQVIDPDHVRELMPVLRHIGGFNIAEEGAGYEFGGKTGTNDNVSSTWFVGFTSKLATAV +WTGRYNNLKSMTGETVNGEVRNPFYSTSINGPSWLEYNQLAKEKFPPGELPEWDGPQSEDPGEAGEHPDGRQFTIDDLDR +GGPQPQAVPG-----------------------F diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001495.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001495.fa new file mode 100644 index 0000000000000000000000000000000000000000..78abb5b71a6fabc973422040913168770f0cb599 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001495.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_01851 +MFLALRDLRFATGRFALMGSVVALISLLLVMLSGLTAGLGGQNTAAIDRLGEQGVQRLVF +GGAAGQEPTASFTQSEFTVAQRDAWAATDGVASVEPLGVSQGRAIGLEHPVDTDPQGRAD +VSGEPTTGVATTAFIGLTPGGSDAPAGVELGQIVLSQDVADSLHAQAGDAVAVSGFVYTV +ADVVPTEYYSHSPVTWLALEDWNAISHTADDAVLGTAGLVRFDAGADVDAVAAAGDDAAG +TVAETVKGSYAALPSYRSENGSLMTMQGFLYGISALVVIAFLSIWTVQRTRDIAVLKALG +GSNGWVLKDSLAQAAFVLVGGVAVGTGLAAVIGAFAGRAVPFELSWATTAVPAAGVLVLG +MLAAVIAVYRVTRIDPLVALGGN +>GCF_003691675_PROKKA_01547 +MFLALRDLRFATGRFALMGSVVALISLLLVMLSGLTAGLGGQNTAAIDRLGEQGVQRLVF +DGAAGQEPTASFTQSEFTVAQRDAWAATDGVASVEPLGVSQGRAIGLEHPVDTDPPGRAD +VSGEPTTGVATTAFIGLTPGGSDAPAGVEPGQIVLSQDVADSLHAQEGDAVAVSGFVYTV +ADVVPTEYYSHSPVTWLALEDWNAISHTADDAVLGTAGLVRFDADTDVDAVAAAGDDAAG +TVAETVKGSYAALPSYRSENGSLMTMQGFLYGISALVVIAFLSIWTVQRTRDIAVLKALG +GSNGWVLKDSLAQAAFVLVGGVAVGTGLAAAIGAFAGRAVPFELSWATTAVPAAGVLVLG +MLAAVVAVFRVTRIDPLVALGGN +>GCF_005280335_PROKKA_01017 +MFLALRDLRFATGRFALMGSVVALISLLLVMLSGLTAGLGGQNTAALDRLEEQGVQRLVF +GGAAGQEATASFTQSKFTAEQRDAWAATDGVASVEPLGVSQGRAVGLAHGVETDEAGRAD +VADVPTTGVASTAFLGLVPGGADAPAALAPGEVVLSSDVADSLGAQAGDAVAVSGFVFTV +AEVVPNEFYSHSPVTWLALEDWRAISHTADDAVLGTAGLVRFAAGADPDAVAAAGDAAAG +TVSETVRGSYAALPSYRSENGSLMTMQGFLYGISALVVIAFLSIWTVQRTRDIAVLKALG +GTDGWVLKDALTQAAFVLLGGVLVGTALAAGIGVLAARGVPFELSWATTLVPAAGILVLG +MLAAVAAVFRVTRIDPLVALGGN +>GCF_020097155_PROKKA_00959 +MFLALRDLRFATGRFSLMGAVVALITVLLVMLSGLTAGLGHQNTAALDDLGARGTDRIVF +GGTAGQDPTASFTSSEVTAAQLDSWCAADGVARVEPVGVAQGRLTGVAGHVDTDAAGRPA +ETPE-VAGVGSASFVGLDPAAPQAPAGLEDGELVLSQALAEALEVEEGGQVESSGRVYTV +ASVAADSWYSHTPVAWTTLTDWRALSHTEDADVAGTAGLVTLVDGADADAVASAADDAAH +TVATDVKGAYAALPAYSSEHGSLTMMQGFLYGISALVVVAFLSIWTIQRTREIAVLKALG +ASTGWVLRDSLLQGGIVLAVGVGLGTALAAGAGWFAAQAVPFVLSPATTVLPALGVLALG +LAGSALAVARVTRIDPLIALGGN +>GCF_023573625_PROKKA_01771 +MFLALRDLRFATGRFALMGSVVALISLLLVMLSGLTAGLGGQNTAAIDRLGEQGVQRLVF +GGAAGQEPTASFTQSEFSVAQRDAWAATDGVASVEPLGVSQGRAIGLEHPVDTDPQGRAD +VSGEPTTGVATTTFIGLTPGGSDAPAGVEPGQIVLSQDVADSLHAQEGDAVAVSGFVYTV +ADVVPTEYYSHSPVTWLALEDWNAISHTADDAVLGTAGLVRFDAGADVDAVAAAGDDAAG +TVAETVKGSYAALPSYRSENGSLMTMQGFLYGISALVVIAFLSIWTVQRTRDIAVLKALG +GSNGWVLKDSLAQAAFVLVGGVAVGTGLAAVVGAFAGRAVPFELSWATTAVPAAGVLVLG +MLAAVVAVYRVTRIDPLVALGGN + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001509.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001509.fa new file mode 100644 index 0000000000000000000000000000000000000000..9a8535fdd15c16ddb73aa620d3289f50a5d77a52 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001509.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01866 +MSTQAPVSPAPAMKPGRARRRRRLSLIIQAAVFVLALVVLAVLIDWGALAENVLNFPAVA +PMFPNVILVGLGNTLFYTVTSFVVGLLGGIVLALMRLSSFGPYRWLATAYVEFFRGVPAL +LVFLAFGYGVPFAFGVSWPIPVVVMVALGMVSAAYIAETLRAGLQAVPRGQMEAARSLGM +PTWRAMVTIVIPQAFRIVLPPLTNEVILLTKDSSLVYVLGLAAHEYELTKFGRDGISALD +AGMTPILVAGLFYLVITVPLSLLARRFETRSTKKGH +>GCF_003691675_PROKKA_01562 +MSTQAPVSPAPAMKPGRARRRRRLSLIIQAAVFVLALVVLAVLIDWGALAENVLNFPAVA +PMFPNVILVGLGNTLFYTVTSFVVGLLGGIVLALMRLSSFGPYRWLATAYVEFFRGVPAL +LVFLAFGYGVPFAFGVSWPIPVVVMVALGMVSAAYIAETLRAGLQAVPRGQMEAARSLGM +PTWRAMVTIVIPQAFRIVLPPLTNEVILLTKDSSLVYVLGLAAHEYELTKFGRDGISALD +AGMTPILVAGLFYLVITVPLSLLARRFEARSTKKGH +>GCF_005280335_PROKKA_00994 +-------------------------------MFVLAIVVLALLIDWGTIGENVLNFPAVA +PLFPNIILVGLGNTLFYTATSFVVGLLGGIALALMRMSAFAPYRWLATAYVEFFRGVPAL +LVFLAFGYGVPFAFGVSWPIPVVVMTALGMVAAAYIAETLRAGLQAFPPGQMEAARSLGM +PAWQAMITIVIPQAFRIVLPPLTNEVILLTKDSSLVYVLGLAAHEYELTKFGRDGISALD +AGMTPILVAGLFYLVITVPLSLLARRFEARSTKKGH +>GCF_020097155_PROKKA_00932 +MSTQASPAPRTAAAPSRAGRRRTLSVAVQAAVFVLAIVVVALLADWQAIAENVLNFSAAG +PMFPNVILVGLGNTIFYTVTAFVVGLLGGMLLALMRMSSFAPYRWLATAYVEFFRGIPAL +LVFLAFGYGVPFAFGVSWPIPVVVMIALGMVSAAYIAETLRAGLQAVPKGQMEAARSLGM +PHWRAMLTIVIPQAFRVVLPPLTNEVILLTKDSSLVYVLGLAAHEYELTKFGRDGIAALD +AGMTPILVAGLCYLVITIPLSLLARRFEARSSRKAH +>GCF_023573625_PROKKA_01786 +MSTQAPVSPAPAMKPGRARRRRRLSLIIQAAVFVLALVVLAVLIDWGTLTENVLNFPAVA +PMFPNVILVGLGNTLFYTVTSFVVGLLGGIVLALMRLSSFGPYRWLATAYVEFFRGVPAL +LVFLAFGYGVPFAFGVSWPIPVVVMVALGMVSAAYIAETLRAGLQAVPRGQMEAARSLGM +PTWRAMVTIVIPQAFRIVLPPLTNEVILLTKDSSLVYVLGLAAHEYELTKFGRDGISALD +AGMTPILVAGLFYLVITVPLSLLARRFETRSTKKGH + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001537.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001537.fa new file mode 100644 index 0000000000000000000000000000000000000000..07ebdb6fdfab916437bc771a89e5f037fe98b757 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001537.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01903 +MPTTDPAVR------PDDHHGSGGREGARPAPGGPSRRGLLLGAGAVGGGLLGTALGYGA +GHASAS-TAPGASAAPGAGASPSEVMGDTGIEGDVGRAGWAEPGGQAARVAVSSPVGTDT +VPFHGPRQAGVDTPAQAHAVFLALDLREDADRVRIERMLRLLTDDAARLTQGRATIADTE +PELAAAPARLTVTFGFGPELVRRVAPDRAPAWLRPLPAFEQIDRLDPAFSDGDLLLQICG +DDRMSVAHTRRMLLKAARPFATERWVQEGFRSARGAHPTGTTMRNLFGQVDGTGNPAADT +PHLDRVVWGVGAE--QVGVTPWIPDGTSVVIRRIEMLMDTWDELDRPAKEKVIGRRLGTG +APLTGEQEHDEPDFDAVGPTGFPVISDIAHLRRARGEEPEYGMLRRGYNYDDPRGALEAG +SGLIFAAYQADVDRQFVPVQARLAESDHLNLWTVPVGSAVFAIPPGCAEGGFVGDALFA +>GCF_003691675_PROKKA_01599 +MPTTDPVVRSDDHHGPDDHHGPDGREGARPTPGGPSRRGLLLGAGAVGGGLLGTALGYGA +GHASAS-TAPGASAASGTGASPSEVMGDTGIEGDVGRAGWAEPGGQAARVAVSSPVGTDT +VPFHGPRQAGVDTPAQAHAVFLAFDLHEDTDRVRIERMLRLLTDDAARLTQGRATIADTE +PELAAAPARLTVTFGFGPELVRRVAPDRAPAWLRPLPAFEQIDRLDPAFSDGDLLLQICG +DDRMSVAHARRMLLKAARPFATERWVQEGFRSARGAHPTGTTMRNLFGQVDGTGNPAADT +PHLDRVVWGVGAE--QVGVTPWIADGTSVVIRRIEMLMDTWDELDRPAKEKVIGRRLGTG +APLTGEQEHDEPDFDAVGPAGFPVISDIAHLRRARGEEPEYGMLRRGYNYDDPRGALEAG +SGLIFAAYQADVDRQFVPVQARLAESDHLNLWTVPVGSAVFAIPPGCAEGGFVGDALFA +>GCF_005280335_PROKKA_00955 +----------------------------------------------MGGGLLGTALGYGA +GHASAAPAAPAASGAAGAGASPSEVMGDTGIEGEVGRAGWAEPGGQSARVAVSSPVGTDT +VPFHGPRQAGVDTPAQAHAVFLAFDLLPDTDRLGIERMLRLLTDDAARLTQGRATIADTE +PELAAAPARLTVTFGFGPELLARVAPDRAPAWLRPLPAFPQIDRLDPAFGDGDLLLQICG +DDRMSVAHARRMLIKAARPFAAERWAQEGFRASRGAHPTGTTMRNLFGQVDGTANPAAQT +PHLDRVVWGVGAE--QVGITPWIQDGTSLVVRRIEMLLDTWDELDRPGKERVIGRTLGTG +APLTGEQEHDEPDFVALGPAGFPVIPDISHLRRARMDVPEYGMLRRGYNYDDPRGAIESG +AGLIFAAYQADVDRQFVPVQERLAESDHLNLWTVPVGSAVFAIPPGCAEGGFVGDVLFA +>GCF_020097155_PROKKA_00895 +MPTTD-----------------------------PSRRGVLFGLGAVGGGLLGGAVGYGA +GAAQAT-PAPGG-APSGVDASPSGVMEDTGLEGEVGRAGWAEPGGEASRVAVSSPVGTDT +VPFHGPRQAGVDTPAQTHAMLVALDLLPETDRAGVRALLRLLSDDAARLTQGRATLADTE +PELAAAPARLTVTFGFGPELLARVAPERAPAWLKPLPAFPTIDALEDRWSGGDLLLQICG +DDRISVAHARRMLGKVARPFAEVRWVQEGFRAARGTHPTGTTMRNLFGQVDGTANPQGGS +PALERIVWGAGQEAADLGIAPWIPDGTSLVVRRIDMLMDTWDELDRPAKEKVIGRTLGTG +APLTGELETDAPDLEAIGPTGFPVIPDTAHLRRARGPEPEYGMLRRGYNYDDGAGASGTG +AGLIFAAFQADVDRQYIPVQERLAASDHLNLWTRPVGSAVFAIPPGCAEGGFVGDVLFA +>GCF_023573625_PROKKA_01823 +MPTTDPAVR------PDDHHGPDGREGARPAPGGPSRRGLLLGAGAVGGGLLGTALGYGA +GHASAS-TAPGASAAPGAGASPSEVMGDTGIEGDVGRAGWAEPGGQAARVAVSSPVGTDT +VPFHGPRQAGVDTPAQAHAVFLAFDLHEDTGRVRIERMLRLLTDDAARLTQGRATIADTE +PELAAAPARLTVTFGFGPELVRRVAPDRAPAWLRPLPAFEQIDRLDPAFSDGDLLLQICG +DDRMSVAHARRMLLKAARPFATERWVQEGFRSARGAHPTGTTMRNLFGQVDGTGNPAADT +PHLDRVVWGVGAE--QVGVTPWITDGTSVVIRRIEMLMDTWDELDRPAKEKVIGRRLGTG +APLTGEQEHDEPDFDAVGPTGFPVISDIAHLRRARGEEPEYGMLRRGYNYDDPRGALEAG +SGLIFAAYQADVDRQFVPVQARLAESDHLNLWTVPVGSAVFAIPPGCTEGGFVGDALFA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001544.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001544.fa new file mode 100644 index 0000000000000000000000000000000000000000..4caccd6915e5270f337f7b0dab5f626eb9b86b37 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001544.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_01910 +MAAHCQVTGAGPGFGHSISHSHRRTKRRFDPNIQKKTYWVPSLRRNVTLTLSAKGIKTID +VRGIDAVVADLIAKGVKL +>GCF_003691675_PROKKA_01606 +MAAHCQVTGAGPGFGHSISHSHRRTKRRFDPNIQKKTYWVPSLRRNVMLTLSAKGIKTID +VRGIDAVVADLIAKGVKL +>GCF_005280335_PROKKA_00948 +MAAHCQVTGAGPGFGHSISHSHRRTKRRFDPNIQKKTYWVPSLRRNVTLTLSAKGIKTID +VRGIDAVVADLIAKGVKL +>GCF_020097155_PROKKA_00888 +MAAHCQVTGAGPGFGHSISHSHRRNKRRFDPNIQKKTYWVPSLRRNVTLTLSAKGIKTID +VRGIDAVVADLISKGVKL +>GCF_023573625_PROKKA_01830 +MAAHCQVTGAGPGFGHSISHSHRRTKRRFDPNIQKKTYWVPSLRRNVTLTLSAKGIKTID +VRGIDAVVADLIAKGVKL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001548.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001548.fa new file mode 100644 index 0000000000000000000000000000000000000000..3196e9786876fab3dc36e1234e282ada98fd04bd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001548.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01920 +MTILVGYAPSKAADAALDTALDIARSTGEHVVVVNAGPGGEHRTKSLVTEEQQRGVQARL +DASGVTAEFRQYARGRSTVEEMKDVAAELDPSIVVIGVRRRGGFGRFVMGSVSDELLQEI +DQPVLCVKEYRQYGDHTPEAVSHVAETDPAAHGLPASEPMAERRRLTPVDSGDPTLER +>GCF_003691675_PROKKA_01616 +MTILVGYAPSKAADAALDTALDIARSTGEHVVVVNAGPGGEHRTKSLVTEEQQRGVQARL +DASGVTAEFRQYARGRSTVEEMKDVAAELGPSIVVIGVRRRGGFGRFVMGSVSDELLQEI +DQPVLCVKEYRQYGDHTPEAVSHVAETDPAAHGLPASEPMAERRRLTPVDSGDPTLER +>GCF_005280335_PROKKA_00940 +MTILVGYAPSTSADAALDTALDIARSTGERVVVVNAGPGGEHRTKSLVTEEQQRGVQARL +DASGVDAEFRQYARGRSTVQEMKDVAAELDPSIVVIGVRRRGGFGRFVMGSVSDELLQEI +DQPVLCVKEYTQYGDRTPEAVSHVAETDPATRGLPASEPMLEQHPLTPVKDQDPTRRG +>GCF_020097155_PROKKA_00875 +MTILVAYKPSETAKAALSTALDVARQTGEHVVVVNAGPGGEHRSPSLVTEAQQQEVQRLL +DDSGVSAEFRQYARGRSTADELKSVADELDPSIVVVGLRRRGGFGRFVMGSVSDELLQVI +DQPVLAVKEYR---GRTPDAVSSVAETDPATHGMPSAEPGHAPRPFTGEHAADDGR-- +>GCF_023573625_PROKKA_01840 +MTILVGYAPSKSADAALDTALDIARSTGEHVVVVNAGPGGEHRTKSLVTEEQQRGVQARL +DASGVTAEFRQYARGRSTVEEMKDVAAELDPSIVVIGVRRRGGFGRFVMGSVSDELLQEI +DQPVLCVKEYRQYGDHTPEAVSHVAETDPATHGLPASEPMAERRRLTPVDPGDPTLER + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001552.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001552.fa new file mode 100644 index 0000000000000000000000000000000000000000..ee1c3687100ba6e0cd3a3fe73d9e06bc7213c961 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001552.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01926 +MTLTHEPHTAAWDTDLSLGNLRSGLSAFPTGVVALAGLADDVPEVMVSSSFGVGISWEPA +LVSFSAQNSSRTWPRLRRAGAIGVSLLAADQTPLCRQLASREGDRFAGLDVHRSPHDALL +IGGSSLWLETRVHAEVPAGDHTVVLLEVTAFADHTDAAPPAALHRNLFHGLRAL +>GCF_003691675_PROKKA_01622 +MTLTHEPHTATWDTDLSLGNLRSGLSAFPTGVVALAGLADGVPEVMVSSSFGVGISWEPA +LVSFSAQNSSRTWPRLRRAGAIGVSLLAADQTPLCRQLASREGDRFAGLDVHRSPHDALL +IGGSSLWLETRVHAEVPAGDHTVVLLEVTAFADHTDAAPPAALHRNLFHGLRAL +>GCF_005280335_PROKKA_00935 +MTLTLDDRTRVWDTDLSHHNLRSGLSAFPTGVVAVAGLAEDRREVMVSSSFGVGISWEPA +LVAFSAQNTSRTWPRLRQAASLGISLLAADQTHLCRQLASREGDRFAGLDVHVSPNEALL +IEGAALWLETRLHAEVPAGDHTVVMLEVTGFADHTDEVAPAALHRNLFHGLRAL +>GCF_020097155_PROKKA_00866 +MTLIHAPHTAAWDTDLSLGNLRSGLSAFPTGVVALAGLADDVPEVMVSSSFGVGISWEPA +LVSFSAQNSSRTWPRLRRAGAIGVSLLAADQTPLCRQLAAREGDRFAGLDVHRSPHDALL +IGGSSLWLETRVHAEVPAGDHTVVLLEVTAFADHTDDAPPAALHRNLFHGLRAL +>GCF_023573625_PROKKA_01845 +MTLTHEPHTAAWDTDLSLGNLRSGLSAFPTGVVALAGLADDVPEVMVSSSFGVGISWEPA +LVSFSAQNSSRTWPRLRRAGAIGVSLLAADQTPLCRQLASREGDRFAGLDVHRSPHDALL +IGGSSLWLETRVHAEVPAGDHTVVLLEVTALADHTDAAPPAALHRNLFHGLRAL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001554.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001554.fa new file mode 100644 index 0000000000000000000000000000000000000000..9c6ffe3cd98114feadfb29cd4156ba6ed271b1b9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001554.fa @@ -0,0 +1,46 @@ +>GCF_002008305_PROKKA_01928 +M-----------------------------TLP--APAARR--PSAALLWVLLAAMGAGP +LFTYGVSASSTVVMERLDVTSGQLGTVMTVVFAAAAVTSLGLGRAADRLSARAQLSIIFG +GTAAALVLGAVAPSLPVLYAAAAVAGVTQAISNPTTNRIIRTVVPPERRIGWVGVKQSGV +QAAQLVGGLFFPAASLALGWTGAALGAAVLIGALWVLALVAAPPLPGAP--P-------- +-----------SATGPAG-------GRRR--RDTSPLPATVWFSAAIAFLTGLGMQATNT +YLPLFAVETLGMTLVAGGAAAAVSGVVGVLSRIGWSRRMSSGDRPTTLLTVICLGAVAGV +VVFLAADLLDLPALLWVGAAVHGLTVLGANVVVNAGLLSEVPAERLGRATGANSMGMYAG +FALGPLLMGVLRDVTGDYRAGFAVVALGYLLALGVVLLLRRHVGRRGA------A +>GCF_003691675_PROKKA_01624 +M-----------------------------TLP--APAARR--PSAALLWVLLAAMGAGP +LFNYGVSASSTVVMERLDVTSGQLGTVMTVVFAAAAVTSLGLGRAADRLSARAQLSIIFG +GTAAALVLGAVAPSLPVLYAAAAVAGVTQAISNPTTNRIIRTVVPPERRIGWVGVKQSGV +QAAQLVGGLFFPAASLALGWTGAALGAAVLIGALWVLALVAAPPLPGAP--P-------- +-----------PATGPVG-------GRRR--RDTSPLPATVWFFAAIAFLTGLGMQATNT +YLPLFAVETLGMTLVAGGAAAAVSGVVGVLSRIGWSRRMSSGDRPTTLLAVICLGAVAGV +AVFLAADLLDLPALLWVGAAVHGLTVLGANVVINAGLLSEVPAERLGRATGANSMGMYAG +FALGPLLMGVLRDVTGDYRAGFAVVALGYLLALGVVLLLRRHVGRRGA------A +>GCF_005280335_PROKKA_00931 +M-----------------------------TPPSSAPAAARSGPSTALLWVLLAAMGAGP +LFNYGISASSTVIIERLGVTSGQLGTVMTAVFAAAAVTSLGLGRAADRLSSRAQMSIIFG +GTAVALVMGAFAPSLPVLYAAAAVAGVTQAISNPTTNRIIRTVVPPERRIGWIGVKQSGV +QAAQLFGGLFFPAASLALGWTGAALVVAVLACVLWGFALWAAPPLPGTA--PTADPDAGR +ASAPDVDRASAPDAGPAAARARRRDGRRR--RGTTALPASVWFFAAIAFLTGLGMQATNM +YLPLFAVESLDLTLVAGGAAAAVSGVIGVFSRIWWSRRMAVGARPTTLLAAICLGALAGV +VVLLAADLAHLPALLWVGAAVHGLTVLGANVVTNAGLMSEVPAESLGRASGANAMGMYAG +FALGPLVMGVLRDLTGDYRAGFAAVGLGYILAFLVVLLLRRHVGRRAADPRAEAA +>GCF_020097155_PROKKA_00863 +MGDAGAGRRLTGSSGGPAAPGGPTLGAVTASPPS-RPADRA--PGTLLLWTLLAAMGAGP +VFNYAVSTSSTVIIERLGVTSGQLGTVMTVVFAAAAVTSVGLGRAADRLSSRTQMAIIFF +GSALALAVGGFAGSLWALYGAAVLAGVTQTISNPTTNRIIRTSVPAERRIGWIGVKQSGV +QASQLFAGLFFPVAALGLGWTGASLVAAALVGLLGVVALRAAPPLPGAPAAP-------- +-----------PTTTPDA-------GRPRAGRARAPLPATVWFFAGIAFLTGFGMQATNM +YLPLFAVESLDQTLVIGGAAAATSGVIGVFSRIWWSRRMAAGHRPTTLLAGIALGAVVGV +VVFLGADLLHAPALLWVGAAVHGLTVLGTNVVTNAGLMDAVPAHHLGRASGVNAMGMYAG +FACGPLVMGLMRDLTGDFRAGFLAVGVFYLLALAVVGLLRRHTDRQGA-PRA--A +>GCF_023573625_PROKKA_01847 +M-----------------------------TPP--APAARR--PSAALLWVLLAAMGAGP +LFNYGVSASSTVVMERLDVTSGQLGTVMTVVFAAAAVTSLGLGRAADRLSARAQLSIIFG +GTAAALVLGAAAPSLPVLYAAAAVAGVTQAISNPTTNRIIRTVVPPERRIGWVGVKQSGV +QAAQLVGGLFFPAASLALGWTGAALGAAVLIGALWVLALVAAPPLPGAP--P-------- +-----------PATGPVG-------GRRR--RDTSPLPATVWFFAAIAFLTGLGMQATNT +YLPLFAVETLGMTLVAGGAAAAVSGVVGVLSRIGWSRRMSSGDRPTTLLTVICLGAVAGV +VVFLAADLLDLPVLLWVGAAVHGLTVLGANVVINAGLLSEVPAERLGRATGANSMGMYAG +FALGPLLMGVLRDVTGDYRAGFAVVAAGYLLALGVVLLLRRHVGRRGA------A + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001566.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001566.fa new file mode 100644 index 0000000000000000000000000000000000000000..6bfb44554cc378d568ed75d76bf8d200226b54d3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001566.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_01943 +MPDQITHPTDAAA--HPSPAPEDTIGRVFARAVARSPQAVALRFEDRDWTYTQLRDGAHRVARRLQDTGLPAGTRVAAYA +TNSDAYALLFLACVTAGYVHVPVNFALKGGELAHALEDSGAELLVADAGMLERVDQVRAEGRASALRHVWTMLPAGHAEP +SVLETARDETLDAAAPEAEVSATDLAQLLYTSGTTSTPKGAMMSHRALVAEYLSSMIALDFTAEDRPLVAMPLYHSAAMH +VFLLPYLSLGATVRLLAAPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLRKAQYGASIMPVTVLQRLRQ +SQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHVEARVMTADGAPAAPGEPGEIQYRSPQLLSGYWNRPDAT +ADAFTDDGWFRSGDQVTQDAAGYIQVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVVGLPDERWIEAVTAVVVLK +EGAELTAETVRAHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR +>GCF_003691675_PROKKA_01639 +MPDQITHPTD-AG--HLSPAPEDTIGRVFARAVARSPQAVALRFEDRDWTYAQLRDGAHRVARRLQDTGLPAGTRVAAYA +TNSDAYALLFLACVTAGYVHVPVNFALKGGELAHALEDSGAELLVADAGMLERVDQVRAEGRASALRHVWTMLPAGHAEP +SVLETAQDETLDAAAPEAEVSATDLAQLLYTSGTTSTPKGAMMSHRALVAEYLSSIIALDFTAEDRPLVAMPLYHSAAMH +VFLLPYLSLGATVRLLAAPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLHKAQYGASIMPVTVLQRLRQ +SQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHVEARVMTADGAPAAPGEPGEIQYRSPQLLSGYWNRPDAT +ADAFTDDGWFRSGDQVTQDAAGYIQVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVIGLPDERWIEAVTAVVVLK +EGAELTAETVRTHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR +>GCF_005280335_PROKKA_00913 +M----TEQTSPAAPTADSPSPEDTIGRLFTRAAARHPETVALRFEDRDWTYAQLLDGVHRVARRLLATGLPRGTRVAAYG +ANSDAYAVLFLACVTAGYVHVPVNFALKGGELAHALEDSGAEVLVADAGMLERVEQVRADGGGAGLRHVWTMLPAGHAEP +SLLETARDEAADATAPDVPVTATDLAQLLYTSGTTSTPKGAMMSHRALITEYLSSIIALDFTAEDRPLVAMPLYHSAAMH +VFLLPYLSLGATVRLLATPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLRKAQYGASIMPVTVLQRLRQ +SQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHVEARVMTADGAPAAPGEPGEIQYRSPQLLSGYWNRPDAT +ADAFTDDGWFRSGDQVTQDAAGYIQVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVIGLPDERWIEAVTAVVVLK +EGAELTAETVRTHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR +>GCF_020097155_PROKKA_00851 +MPDQITHPTDAAA--HLSPAPEDTIGRVFARAVARSPQAVALRFEDRDWTYAQLRDGAHRVARRLQGTGLPAGTRVAAYA +TNSDAYALLFLACVTAGYVHVPVNFALKGGELAHALEDSGTELLVADAGMLERVDQVRAEGRASALRHVWTMLPAGHAEP +SVLETAQDEALDAAAPEAEVSATDLAQLLYTSGTTSTPKGAMMSHRALVAEYLSSIIALDFTAEDRPLVAMPLYHSAAMH +VFLLPYLSLGATVRLLAAPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLRKAQYGASIMPVTVLQRLRQ +SQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHVEARVMTADGVPAAPGMPGEIQYRSPQLLSGYWNRPDAT +ADAFTDDGWFRSGDQVTQDAAGYIQVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVIGLPDERWIEAVTAVVVLK +EGAELTAETVRTHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR +>GCF_023573625_PROKKA_01862 +MPDQITHPTD-AG--HLSPAPEDTIGRVFARAVARSPQAVALRFEDRDWTYAQLRDGAHRVARRLQDTGLPAGTRVAAYA +TNSDAYALLFLACVTAGYVHVPVNFALKGGELAHALEDSGAELLVADAGMLERVDQVRAEGRASALRHVWTMLPAGHAEP +SVLQTAQDETLDAAAPEAEVSATDLAQLLYTSGTTSTPKGAMMSHRALVAEYLSSIIALDFTAEDRPLVAMPLYHSAAMH +VFLLPYLSLGATVRLLAAPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLHKAQYGASIMPVTVLQRLRQ +SQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHVEARVMTADGAPAAPGEPGEIQYRSPQLLSGYWNRPDAT +ADAFTDDGWFRSGDQVTQDAAGYIQVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVIGLPDERWIEAVTAVVVLK +EGAELTAETVRAHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001578.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001578.fa new file mode 100644 index 0000000000000000000000000000000000000000..bf09d9e12d5e45778a7bd8ec7e19a5ea91bb0eae --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001578.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_01974 +MTVPPGSPAAPSAPASRRRRRALAAALAVAVVVQLVVLYLPGEQVPQAGFAAPGLDKAIH +VAVFALPAFLAVGRGRSAWWALPFAVHAPVSELVQHAWVPLRTGDPVDVVADLAGVVLGV +V---------------------AARSRRIGGSGASGV +>GCF_003691675_PROKKA_01668 +MTVPSGSPAAPSAPASPRRRRALAAALAVAVAVQLVVLYLPGEQVPEAGFTVPGLDKAIH +VAVFALPAFLAVGRGRSAWWALPFAVHAPVSELVQHAWVPLRTGDPVDVVADLAGVVLGV +V---------------------AARSRRIGGSGASGV +>GCF_005280335_PROKKA_00884 +MG--DARPRVPVCPSSRRRRRALAALLAVVVVVHLVVLYLPGSDVPQTGFEVPGLDKTIH +VLAFAAPTWAAVRLGSSWWWALPFAVHAPVSEAVQHAWVPLRTGDAWDMVADLAGVVLGA +ALAWRAVRREVEAPGEVGEVGEAGRGDRIGGSGRPGV +>GCF_020097155_PROKKA_00826 +MPARSSAPAAP--PPSAARRRTLALLLVIALAAHLVVLYLPGDDVPAVGFEVPGMDKAIH +VATFGVPALLGVLLARRVWPAAVLAVHAPLSEVLQAVQGLGRTGDPADAVADLAGVALGL +LAARAALRR-------------GPTGRPIGAAPGRGV +>GCF_023573625_PROKKA_01900 +MTVPSGSPAAPSAPASRRRRRAVAAALVVAVVVQLVVLYLPGEQVPEAGFAVPGLDKAIH +VAVFALPAFLAVGRGRSAWWALPFAVHAPVSELVQHAWVPLRTGDPVDVVADLAGVVLGV +L---------------------AARSRRIGGSGASGV + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001579.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001579.fa new file mode 100644 index 0000000000000000000000000000000000000000..bddc48ce6de2c4978195b243f4fb2ba9c8b64628 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001579.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_01978 +M--------------------SEAKAEILRRIREATADGPVADPVQRTYRRTSSRDRAEV +VEMLRDRLIDYRASVRDETEETVAAAIAELLGPDARYVVPAGLEPDWLPTDSRGAGRERI +TEPAVGHTGERAAVRGAHDGEREPLNVDALNEVDAVVTSSTVSCAETGTIFLSGRPDEGR +RAITLVPDHHVCIVPLDSVVELFPEALARVEATAPITMISGPSATSDIELERVEGVHGPR +RLDVILLDRAR +>GCF_003691675_PROKKA_01672 +M--------------------SEAKAEILRRIREATADGPVADPVQRTYRRTSSRDRAEV +VEMLRDRLIDYRASVRDETEETVAAAIAELLGPDARYVVPAGLEPDWLPADSRGAGRERI +TEPAVGHTGERAAVRGAHDGEREPLSVDALNEVDAVVTSSTVSCAETGTIFLSGRPDEGR +RAITLVPDHHVCIVPLDSVVELFPEALARVEATAPITMISGPSATSDIELERVEGVHGPR +RLDVILLDRAR +>GCF_005280335_PROKKA_00880 +MSEATPTTVPATPTPGPGGPGGEARAAILDRIRQALQDGPTPDPVERTYRRTSEAAPGDV +VEQLVDRLVDYKAGVHREDLTTVADRVADLLGEGARYVVPPGLDPAWLPGD--GQGRVRV +TEPATADAG--------------ALGVRELDELDAVVTGSTVSCSETGTIFLTGRPEEGR +RAISLVPDHHVCIVPLDTVVELFPEALARVEPTAAITMISGPSATSDIELERVEGVHGPR +RLDVILLDR-- +>GCF_020097155_PROKKA_00815 +M--------------------SEAKAEILRRIREATADGPVADPVQRTYRRTSSRDRAEV +VEMLRDRLIDYRASVRDETEETVAAAIAELLGPDARYVVPAGLEPDWLPADSRGAGRERI +TEPAVGHTGERAAVRGAHDGEREPLSVDALNEVDAVVTSSTVSCAETGTIFLSGRPDEGR +RAITLVPDHHVCIVPLDSVVELFPEALARVEATAPITMISGPSATSDIELERVEGVHGPR +RLDVILLDRAR +>GCF_023573625_PROKKA_01904 +M--------------------SEAKAEILRRIREATADGPVADPVQRTYRRTSSRDRAEV +VEMLRDRLIDYRASVRDETEETVAAAIAELLGPDARYVVPAGLEPDWLPADSCGAGRERI +TEPAVGHTGERAAVRGAHDGEREPLSVDALNEVDAVVTSSTVSCAETGTIFLSGRPDEGR +RAITLVPDHHVCIVPLDSVVELFPEALARVEATAPITMISGPSATSDIELERVEGVHGPR +RLDVILLDRAR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001598.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001598.fa new file mode 100644 index 0000000000000000000000000000000000000000..d17842e23d7cb88a731b54ef682c09342c9c496f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001598.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_02004 +M-AEHDGG-----P------VREGAPSQTLSRALTLLEAVVEAPEPPTIADLADGLGVHR +SVAYRMLRTFETHGLLRRDGLGRVHAAPGLAVLARRVEQDLRAAAMPHLTAVSTDLGMTA +FLVVWDGAHCLTLATAEPPSGNLVTQRPGTRHPLGVGAPGMAIAVALTGQEWARLPGEAA +PERPELDDVRERGWAVSSDEVITGVSSVAVPLRVPGQLPAALAVVYATRPEDPARLGDRL +GEAARAVAVAFGAA +>GCF_003691675_PROKKA_01714 +M-AEHDGG-----P------VREGAPSQTLSRALTLLETVVEAPEPPTIADLADGLGVHR +SVAYRMLRTFEAHGLLRRDGLGRVHAAPGLAVLARRVEQDLRAAAMPHLTAVSTDLGMTA +FLVVWDGAHCLTLATAEPPSGNLVTQRPGTRHPLGVGAPGMAIAVALTGQEWARLPGEAP +PERPELDDVRERGWAVSSDEVITGVSSVAVPLRVPGQLPAALAVVYATRPEDPARLGDRL +GEAARAVAVAFGAA +>GCF_005280335_PROKKA_00838 +M-AEDDGGPA---P------AREGAPSQTLSRALALLEAVVEAAEPPTIAELADGLGVHR +SVAYRVLRTFEAHGLLRRDPLGRVHSAPGLAVLARRVEQDLRTAAMPHLSAVSADLGMTA +FLVVGDGSTCLTLATVEPPRGNLVTQRPGTRHPLGIGAPGMAVALALPEQEWEQRRGDAA +PERPELGEARERGWAVSRDEVITGVSSVAVPLSVPGQLPAALAVVYATRPEDPERLGGRL +KEAAQAVAASLGAA +>GCF_020097155_PROKKA_00775 +MDPHDDSVPAVSAPPPSAPGVRPGAPSQTLSRALTMLELVADRPTPPSIAELADDLGVHR +SVAYRMLRTFEVHGLLRRDAAGLVHGAPGLVTLAGGVEQDLRAAAVTELSRVSDALAMTA +FLVVWDGRDCLTLATVEPPRGNLVTQRPGTRHPLGVGAPGIAIASVLPAE---------G +QDRPAVREARARGWAASRDEVITGVGSVAAPVPAAAGMPAALAVVFTSPAVDEEAVGAEL +AAAARRLGAVLGEG +>GCF_023573625_PROKKA_01942 +M-AEHDGG-----P------VREGAPSQTLSRALTLLETVVEAPEPPTIADLADGLGVHR +SVAYRVLRTFETHGLLRRDGLGRVHAAPGLAVLARRVEQDLRAAAMPHLTAVSTDLGMTA +FLVVWDGAHCLTLATAEPPSGNLVTQRPGTRHPLGIGAPGMAIAVALTGQEWARLPGEAP +PERPELDDVRERGWAVSSDEVITGVSSVAVPLRVPGQLPAALAVVYATRPEDPARLGDRL +GEAARAVAVAFGAA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001601.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001601.fa new file mode 100644 index 0000000000000000000000000000000000000000..004a5443653c9176f224c53999d5d550b6f986af --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001601.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_02008 +MTQTSSPQHLASVPSPEDAAGQENFDRLIAEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE +IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDELNEQLLSGRA +KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRASYGPYGRAMVRICKEESFHQRQG +WEILYELSHGTPEQKQMAQDAVNRFYGPALQMFGPTDEDSPNSRQSMAWKVKRFSNDDLR +QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDEFMSVIKGDGPMNTQRMARR +IQAHEDGAWVREAAAAYARRQAEQNAPAETHLIGA +>GCF_003691675_PROKKA_01718 +MTQTSSPQHLASVPSPEDAAGQENFDRLIAEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE +IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDELNEQLLSGRA +KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRASYGPYGRAMVRICKEESFHQRQG +WEILYELSHGTPEQKQMAQDAVNRFYGPALQMFGPPDEDSPNSRQSMAWKVKRFSNDDLR +QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDEFMSVIKGDGPMNTQRMARR +IQAHEDGAWVREAAAAYARRQAEQNAPAETHLIGA +>GCF_005280335_PROKKA_00834 +MTQTSSTTRLASVPSPEDAAGQENFDRLIAEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE +IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDVLNDQLLEGKA +KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRSSYGPYGRAMVRICKEESFHQRQG +WEILYELSHGTPEQKQMAQDAVDRFYGPALQMFGPPDEDSPNSKQSMAWKVKRFSNDELR +QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDELMSVIKGNGPMNTQRLARR +IQAHEDGAWVRDAAAAYARRQAEQHAPAETHLIGA +>GCF_020097155_PROKKA_00771 +MTQTSSSPHLASVPSPDDAAGQENFDRLIQEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE +IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDELNEQLLSGRA +KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRASYGPYGRAMVRICKEESFHQRQG +WEILYELSHGTPEQKQMAQDAVNRFYGPALQMFGPPDEDSPNSQQSMAWKVKRFSNDELR +QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDEFMSVIKGNGPMNTQRLARR +VQAHEDGAWVREAAAAYARRQAEQHVPADTQLIGA +>GCF_023573625_PROKKA_01946 +MTQTSSPQHLASVPSPEDAAGQENFDRLIAEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE +IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDELNAQLLSGRA +KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRASYGPYGRAMVRICKEESFHQRQG +WEILYELSHGTPEQKQMAQDAVDRFYGPALQMFGPPDEDSPNSRQSMAWKVKRFSNDDLR +QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDEFMSVIKGDGPMNTQRMARR +IQAHEEGAWVREAAAAYARRQAEQNAPAETHLIGA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001602.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001602.fa new file mode 100644 index 0000000000000000000000000000000000000000..15de9451ff6d6549fbab9cabaabe03c6f91083fd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001602.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_02009 +MSETTAASHAWPLWEVFVRANRGLSHVHAGSLHAPDATLALRNARDLYTRRNEGTSVWVV +PAEAIAASDPDSKGGFFESAQGKSYRHATYYQQSEGVPHL +>GCF_003691675_PROKKA_01719 +MSETTAASHAWPLWEVFVRANRGLSHVHAGSLHAPDATLALRNARDLYTRRNEGTSVWVV +PAEAIAASDPDSKGGFFESAQGKSYRHATYYQQSEGVPHL +>GCF_005280335_PROKKA_00833 +MGENTAASNAWPLWEVFVRANRGLSHVHAGSLHAPDASLALRNARDLYTRRNEGTSVWVV +PAEAIAASDPDSKGGFFESPQGKSYRHATYYQQSEGVPHL +>GCF_020097155_PROKKA_00770 +MTENTAPSNEWPLWEVFVRANRGLSHVHAGSLHAPDATMALRNARDLYTRRNEGTSVWVV +PADAVAASDPDSKGGFFESPQGKSYRHATYYQKSEGVPHL +>GCF_023573625_PROKKA_01947 +MSETTAASHAWPLWEVFVRANRGLSHVHAGSLHAPDATLALRNARDLYTRRNEGTSVWVV +PAEAIAASDPDSKGGFFESAQGKSYRHATYYQQSEGVPHL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001603.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001603.fa new file mode 100644 index 0000000000000000000000000000000000000000..b79b2fb37f49d98f22c96ffd4d04871ab60957b2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001603.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_02010 +MSFATNDSATRHSAGVAITAEEIAAGEQKANDDVARYALALGDDALMLGQRLSWWISRAP +EIEEDIALGNIALDLVGHARFLLSYAGTAWGKTEDELAYFRDEEEFRSVRLVEAENGDFA +KTIARQLYYSFYSYELYTRLRESTDPTLAAIADKALKEVLYHQDHAALWLQRLGLGTEES +KRRMQRGLDELWPYVAELFHDDDVVRALAEQGVAVLPSSLEEPTMTRIRAAIEEACLTVP +TTGTARGGDRSGAMSEYRGYILAEMQSLARRHPGATW +>GCF_003691675_PROKKA_01720 +MSFATNDSATRHSAGVAITAEEIAAGEQKASDDVARYALALGDDALMLGQRLSWWISRAP +ELEEDIALGNIALDLVGHARFLLSYAGTAWGKTEDELAYFRDEEEFRSVRLVEAENGDFA +KTIARQLYYSFYSYELYTRLRESTDSTLAAIADKALKEVLYHQDHAALWLQRLGLGTEES +KRRMQRGLDELWPYVAELFHDDDVVRALAEQGVAVLPSSLEEPTMTRIRAAIEEAGLTVP +TTGTARGGDRSGAMSEYRGYILAEMQSLARRHPGATW +>GCF_005280335_PROKKA_00832 +MSFATNDSATKHSAGVAITAEEIASGEQKASEETARYALYLGDDALMLGQRLSWWISRTP +ELEEDIALGNIALDLVGHARFLLSYAGTAWGQSEDELAYFRDEEEFRSVRLVEAENGDFA +KTIARQLYYSFYAFELYTRLKESTDATLAAIADKALKEVLYHQDHAALWLNRLGLGTDES +KFRMQRGLDELWPYLPELFHDDETTRPLAEQGIAVLPSSLEEPTMTRIREAIEAAGLEVP +TTGTARGGDRSGAMSEYRGYILAEMQSLARRHPGASW +>GCF_020097155_PROKKA_00769 +MSFATNDSATRHSAGVANTAEEIASGGQKASDEVARYAVYLGDDALMLGQRLSWWISRAP +ELEEDIALGNIALDLVGHARFLLSYAGTAWDKSEDDLAYFRDEEEFRSTRLVEAENGDFG +KTIARQLYYSVYAHGLYTRLKDSKDATLAAIADKALKEVEYHLDHAEQWVNRLGLGTEES +NARLQRGLDELWPYLPELFHDDELTRSLAEQGIAVLPSSLEESTMARIRAAIEGADLKVP +ETGAARGGDRSGQMSEYRGYILAEMQSLARRHPGASW +>GCF_023573625_PROKKA_01948 +MSFATNDSATRHSAGVAITAEEIAAGEQKASDDVARYALALGDDALMLGQRLSWWISRAP +ELEEDIALGNIALDLVGHARFLLSYAGTAWGKTEDELAYFRDEEEFRSVRLVEAENGDFA +KTIARQLYYSFYSYELYTRLRESADPTLAAIADKALKEVLYHQDHAALWLQRLGLGTEES +KRRMQRGLDELWPYVAELFHDDDVVRALAEQGVAVLPSSLEEPTMTRIRAAIEEAGLTVP +TTGTARGGDRSGAMSEYRGYILAEMQSLARRHPGATW + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001612.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001612.fa new file mode 100644 index 0000000000000000000000000000000000000000..b50025490c1b0948d4a737e15a6ed51105859c29 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001612.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_02022 +----------MRCGLDGLLRDPTVFSTPAAREAGVSAARLRRGDVVSLGWGLWGRRGIEP +DPMDHVRALQDLHPEGVFSHVTAARVLGLWLTGPLAADRSVHVATPRGHGTASSRAGVRS +HRLRADAPVRIVDGVRVTAPGWIFVDLAAQAGPLEHLVALGDSMVRTAPTEARRRRLPPG +VTDVAELRAAVEERGRVRGIRAAREALELVRPGADSPQESRLRVRLVLDGVPEPAVNPCI +RLATGQRLRVDLVWADAKVAVEYDGDQHRTDRRQWREDRERDAALRAEGWEVIRVTADVF +RPGHWELFVRQLRGLVAARTPPGRVPPSWI +>GCF_003691675_PROKKA_01731 +----------MRCGLDGLLRAPTVFSTPAARETGVSAARLRRGDVVSLGWGLWGLRGVEP +DPMDHLRALQDLHPEGVFSHVTAARVLGLWLTGPLAADRSVHVATPRGHGTASSRAGVRS +HRLRADAPVRIVDGVRVTAPGWIFVDLAAQAGPLDHLVALGDSMVRTAPTEARRRRLPPG +VTDVAELRAAVEERGRVRGIRAAREALELVRPGADSPQESRLRARLVLDGVPEPAVNPCI +RLATGQRLRVDLVWAEAKVAVEYDGDQHRTDRRQWREDRERDAALRAEGWEVIRVTADVF +RPGHWELFVRQLRGLVAARTPPGRVPPSWI +>GCF_005280335_PROKKA_00797 +----------MRCGLDETEREPTVFSTNAAQEAGVPPGRLRRSDLEPWGRGLWRVRDAVP +DVMDHLRALQDLHPEGVFTHVTAARVLGLWLTGPLARDPAIHLGAPRHHGTGSRREGVRS +HRLYGDVPVRIVDGVRVTATGWTFVDLAAAAATVETLVALGDSAVRSAPTERRRRDLPPG +VTSLEELRGAVAERPRVKGIRLARDAVDLVRPGADSPQESRLRVGLVLDGVPEPQVNPRI +VLSTGQWLRVDLAWPAARLVVEYDGDQHRTEQRQWREDRSRDAGLRADGWEVLRVTADVF +RPAEWELFVRRVRARL-GRDAAGRAAAG-- +>GCF_020097155_PROKKA_00758 +MPRSPAPLPPMRCGLDGLLRAPTVFSTPAAREAGVSAARLRRGDVVSLGWGLWGRRGVEP +DPLDHVRALQDLHPEGVFNHVTAARVLGLWLTGPLAADRSVHIATPRGHGTASSRAGIRS +HRLRADAPVRIVDGVRVTAPGWTFVDLAAQAGPLEHLVALGDSMVRTAPTEARRRRLPPG +VTDVAELRAAVEERGRVRGIRAAREALELVRPGVDSPPESRLRVRLVLDGVPEPAVNPCI +RLATGQRLRVDLVWAEAKVAVEYDGDQHRTDRRQWREDRERDAALRAEGWEVIRVTADVF +RPGHWELFVRQLRGLVAARTKPGRVPPSWI +>GCF_023573625_PROKKA_01959 +----------MRCGLDGLLRAPTVFSTPAAREAGVSAARLRRGDVVSLGWGLWGRRGVEP +DPMDHVRALQDLHPEGVFSHVTAARVLGLWLTGPLAADRSVHIATPRGHGTASSRAGIRS +HRLRADAPVRIVDGVRVTAPGWTFVDLAAHAGPLEHLVALGDSMVRTAPTEARRRRLPPG +VTDMAELRAAVEERGRVRGIRAAREALELVRPGADSPQESRLRVRLVLDGVPEPAVNPCI +RLATGQRLRVDLVWADAKVAVEYDGDQHRTDRRQWREDRERDAALRAEGWEVIRVTADVF +RPGHWELFVRQLRGLVAARTPPGRVPPSWI + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001616.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001616.fa new file mode 100644 index 0000000000000000000000000000000000000000..be3b8526cfb6160db44718c6441e43b3dc63bbb4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001616.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_02026 +MPQSSPTPRRGRPGYDRQTLLAECVELFNRHGYEATSMGMLATHLGISKSAIYHHVESKE +AILDHAVTEALDALEACLDDVVASGVDAGAQVEAAIRGTLGVLAEKQPEVTLLLRLRGNS +AVEVAAVERRREITRRFGDLLEAAQAAGAVRSDVTPRNLARLALGMINSIVDWYRPDRGV +PGQEGPGQMIDAVTGVVLGGLRG +>GCF_003691675_PROKKA_01735 +MPQSSPTPRRGRPGYDRQTLLAECVELFNRHGYEATSMGMLAAHLGISKSAIYHHVESKE +AILDHAVTEALDALEACLDDVVASGADAGAQVEAAIRGTLGVLAEKQPEVTLLLRLRGNS +AVEVAAVERRREITRRFGDLLEAAQAAGAVRSDVTPRNLARLALGMINSIVDWYRPDRGV +PGQQGPDQMIDAVTGVVLGGLRG +>GCF_005280335_PROKKA_00793 +MPHSSTAPRRGRPGYDRQTLLTVCVDVFNRHGYEATSMGMLAQHLGISKSAIYHHVESKE +AILEQALDDALDALEASLDGVMADFAGPGEQVEAAVRGTLRVLVEKMPEVTLLLRLRGNS +AVELAAMERRRAITRRLGEMIAAAQEAGAVRGDITPRNLARLALGMINSIVDWYRPESDS +PGHKSVTEMVDAVTRVVLGGLRG +>GCF_020097155_PROKKA_00754 +MPQSSPTPRRGRPGYDRQTLLAECVELFNRHGYEATSMGMLATHLGISKSAIYHHVESKE +AILDHAVTEALDALEACLDDVVASGADAGAQVEAAIRGTLGVLAEKQPEVTLLLRLRGNS +AVEVAAVERRREITRRLGDLLESAQAAGAVRSDVTPRNLARLALGMINSIVDWYRPDGAD +PGHKSVEEMVAAVTGVVMGGLRG +>GCF_023573625_PROKKA_01963 +MPQSSPTPRRGRPGYDRQTLLAECVELFNRHGYEATSMGMLAAHLGISKSAIYHHVESKE +AILDHAVTEALDALEACLDDVVASGADAGAQVEAAIRGTLGVLAEKQPEVTLLLRLRGNS +AVEVAAVERRREITRRFGDLLEAAQAAGAVRSDVTPRNLARLALGMINSIVDWYRPDRGV +PGQQGPDQMIDAVTGVVLGGLRG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001640.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001640.fa new file mode 100644 index 0000000000000000000000000000000000000000..fb3291ccbf167bc73bf24d9afeb18a807698896f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001640.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_02088 +M---CVRLPDMTQSTPGGPATDLPDFRPSGNQGVDPALYEIENAAMDREGALWAALQEAA +PWTGRTLLDLGAGTGFWLPRYADAAETIAVEPDARLLGAARARPGGARVLYGSAEQIPLP +EASVDVVHARFAYFFPHPRWDVRPGLDEVTRVLRPGGALVVIDNDTERGQFAELLRASTN +AAAQGQDTYAREWWAGIGAETREVMSSWTFDSRADLEAVLRLEFERGVADAWLAEHPAAT +SLSYGYLLHVWR--- +>GCF_003691675_PROKKA_01793 +M---CVRLPDMTQSTPGGPATDLPDFRPSGNQGVDPALYEIENAAMDREGALWAALQEAA +PWTGRTLLDLGAGTGFWLPRYADAAETIAVEPDARLLGAARARPGGARVLYGSAEQIPLP +EASVDVVHARFAYFFPHPRWDVRPGLDEVTRVLRPGGALVVIDNDTERGQFAELLRASTN +AAAQGQDTYAREWWAGIGAETREVMSSWTFDSRADLEAVLRLEFERGVADAWLAEHPAAT +SLSYGYLLHVWR--- +>GCF_005280335_PROKKA_00586 +M-----------TATP-----ELPDFVPASNQGGDPAVYEVENAALDREGTLWAALQEAA +PWAGRTLLDLGAGTGFWLPRYADAAEVIAVEPDTRLLDAARARPGGARVRRGSAERIPLA +EASVDVVHARFAYFFPHPQWDVRPGLEEVARVLRPDGALVVIDNDTERGEFAELLVRSDA +AADQGQDTYARRWWADVGAETREVMSSWTFDTRADLEAVLRLEFPAELAEEWLAAHPEAT +SLTYGYLLHVWRPRG +>GCF_005280335_PROKKA_00695 +M--------------------ELPDFRPSGNQGVDPALYEIENAAMDREGALWAALQEAA +PWAGRTLLDLGAGTGFWLPRYADAAETIAVEPDARLLGAARARPGGARVLYGSAEQIPLP +EASVDVVHARFAYFFPHPHWDVRPGLDEVTRVLRPGGALVVIDNDTERGQFAELLRASTN +AAAQGQDTYAREWWAGVGAETREVMSSWTFDSRADLEAVLRLEFERGVADAWLAEHPAAT +SLSYGYLFHVWR--- +>GCF_023573625_PROKKA_02027 +MEGGCVRLPGMTQSTPGGPATGLPDFRPSGNQGVDPALYEIENAAMDREGALWAALQEAA +PWAGRTLLDLGAGTGFWLPRYADAAETIAVEPDVRLLGAARARPGGARVLYGSAEQIPLP +EASVDVVHARFAYFFPHPRWDVRPGLDEVTRVLRPGGALVVIDNDTERGQFAELLRASTN +AAAQGQDTYAREWWAGVGAETREVMSSWTFDSRADLEAVLRLEFERGVADAWLAEHPAAT +SLSYGYLLHVWR--- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001644.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001644.fa new file mode 100644 index 0000000000000000000000000000000000000000..22b73f324832f9f96139b39f403a883084a6af31 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001644.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_02102 +MTFLDLVLVFVGFALAVLVGAALVGRVRGEHLRAVAATLVALWALTAVFDNVMIAAGLFD +YGHELLVGAYVGQAPVEDFAYPLGSALLLPALWLLLTSRGRAGRRGRRPGRRPHPGD--- +-----R +>GCF_003691675_PROKKA_01809 +MTFLDLVLVFVGFALAVLVGAALVGRVRGEHLRAVAATLVALWALTAVFDNVMIAAGLFD +YGHELLVGAYVGQAPVEDFAYPLGSALLLPALWLLLTSRGRAGRRGRRPGRRPHPGD--- +-----R +>GCF_005280335_PROKKA_00677 +MTFLDLILVFVGLAAAVLAAVALTGRVRARHAAAIAVAIAALAVLTAVFDNVMIAAGLFD +YGHDLLSGIYVGLAPIEDFAYPVGSALLLPAVWLLMTGRRRRGGERSPDGGAEPTGDGSS +TADAGR +>GCF_020097155_PROKKA_00592 +MTYLTISLPFLAVAAAVLLASALTGRLDRRRRLGLVLAVALLVVLTAVFDSVIIGLGIVD +YTQANINGARIGLAPVEDFLYPLAGVALLGGLWTLVRGGTR------------------- +------ +>GCF_023573625_PROKKA_02042 +MTFLDLVLVFVGFALAVLVGAALVGRVRGEHLRAVTATLVALWALTAVFDNVMIAAGLFD +YGHELLVGAYVGQAPVEDFAYPLGSALLLPALWLLLTSRGRAGRRGRRPGRRPHPGD--- +-----R + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001647.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001647.fa new file mode 100644 index 0000000000000000000000000000000000000000..a60f6db619a4114381d9b5fabacbb97f6db619f1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001647.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_02105 +MSARDTAL--------GPRTVVVGGGFAGLATAGLLARDGHRVTLLERGAVLGGRAGRWSEAGFTFDTGPSWYLMPEVID +RWFRLMGTSAAERLDLRRLDPGYRVYFEGHLHE--------------PPVDVRTGHAET--LFESLEPGAGRRLRAYLDS +ASRIYGLAKEHFLYTDFRRPAALAHPDVLRALPALGPQLLGGLRSHVAARFQDPRLRQILGYPAVFLGTSPDRAPAMYHL +MSHLDLADGVQYPLGGFAALVDAMAEVVREAGVEIRTGVEATAVEVVDRPAPAGRLGRLAARLPRPGAARGDEGRRRRPG +RVTGVAWRSDDGAAGRLDADVVVAAADLHHVQTRLLPPGRRVAESTWDRRDPGPSGVLVCVGVRGSLPQLAHHTLLFTAD +WEDNFGRIERGEDLAADTSIYVSRTSATDPGVAPEGDENLFILVPAPAEPGWGRGGIRVRDGQGWRVDRAGDAQVEAVAD +RALDQLARWAGIPDLAERIVVRRTYGPGDFAADVHAWRGSLLGPGHTLAQSAMFRPSVRDADVAGLMYAGSSVRPGIGVP +MCLISAEVVRDELRHDARR--VRP------------AGPGGSGT--- +>GCF_003691675_PROKKA_01812 +MSARDTAL--------GPRTVVVGGGFAGLATAGLLARDGHRVTLLERGAVLGGRAGRWSEAGFTFDTGPSWYLMPEVID +RWFRLMGTSAAERLDLRRLDPGYRVYFEGHLHE--------------PPVDVRTGHAET--LFESLEPGAGRRLRAYLDS +ASRIYGLAKEHFLYTDFRRPAALAHPDVLRALPALGPQLLGGLRSHVAARFQDPRLRQILGYPAVFLGTSPDRAPAMYHL +MSHLDLADGVQYPLGGFAALVDAMAEVVREAGVEIRTGVEATAVEVVDRPAPAGRLGRLAARLPRPGAARGDEGRRRRPG +RVTGVAWRSDDGAAGRLDADVVVAAADLHHVQTRLLPPGRRVAESTWDRRDPGPSGVLVCVGVRGSLPQLAHHTLLFTAD +WEDNFGRIERGEDLAADTSIYVSRTSATDPGVAPEGDENLFILVPAPAEPGWGRGGIRVRDGQGWRVDRAGDAQVEAVAD +RALDQLARWAGIPDLAERIVVRRTYGPGDFAADVHAWRGSLLGPGHTLAQSAMFRPSVRDADVAGLMYAGSSVRPGIGVP +MCLISAEVVRDELRHDARR--VRP------------AGPGGSGT--- +>GCF_005280335_PROKKA_00674 +MSAAPNVASGAAAHDDGPRAVVIGGGFAGLATAGLLARDGHRVTLLERNDGLGGRSGRWSAEGFAFDTGPSWYLMPEVID +RWFRLMGASAAERLDLRRLDPGYRVYFEDHLDA--------------PPVDVRTGHAEE--LVESLEPGAGERLRAYLDS +AGRVYELAKEHFLYTDFRRPADLARPAVLRALPSLGPQLLGGLRAHVAARFRDPRIRQILGYPAVFLGTSPDRAPAMYHL +MSHLDLRDGVQYPIGGFAALVDAMADLVREAGVEVVTGAEATRIEVEDA-----------------------ERRRRRRG +RVTGVVVRQ-DGTERRLSADVVVAAADLHHVQTALLPPAQRVAESAWDRRDPGPSGVLVCVGVRGALPQLAHHTLLFTAD +WEDNFGRIERGEDLAADTSLYVSRTSATDPGVAPDGDESLFVLVPAPAEPGWGRGGIRVREGDGWRVEREGDAQVEAVAD +RALDQLARWAGIEDLHERIVVRRTIGPGDFAADVHAWRGSMLGPGHTLAQSAMFRPSVRDADVAGLLYAGSSVRPGIGVP +MCLISAEVVREELRHAARRDALRAQRRGRSQDDDDGARRGRVAAS-- +>GCF_020097155_PROKKA_00590 +MTPTTPAARPAAAPSGSRRVVVIGGGFAGLATAGLLAQDGHRVTLLEKNPVLGGRSGRWSAEGFTFDTGPSWYLMPEVID +RWFRLMGTSADEALDLRALSPAYRVYFQEHAADDAAAPGDGSTPGARAPLDVVSGREESLALAEELEPGAGGRLAAYLDS +AERIYALAKRRFLYTDFQDLTELLRPDVLRALPALAPQLLGDLRGFVARRFEDGRLRRVLGYPAVFLGTSPGKAPAMYHL +MSHLDLADGVQYPIGGFAALVDAMAELVRAAGVEIVTAAEVTAVDVVSDPRPRGRLPRLLDGAPRPWEPRTPAGGRRRSG +HVRGVSWRDAEGGSHRLDADAVVAAADLHHVQTALLPGDQRVAERTWDRRDPGPSAVLVCVGVRGRLPELLHHTLLFTED +WDENFRRIDEGEDLQEETSLYVSMTSATDPGVAPEGDESLFLLVPAPAVPEWGRGGVRTPEE-----DRAGDAQVETVAD +RALAQLARWAGVPDLGERIVVRRTWGPADFTADVHAWRGSLLGPGHVLRQSALFRPPVRDPRVAGLVYAGSSVRPGIGVP +MCLISAELARDAVSG------VRP----------GGAAPGAPAMAGR +>GCF_023573625_PROKKA_02045 +MSARDTAL--------GPRTVVVGGGFAGLATAGLLARDGHRVTLLERGAVLGGRAGRWSEAGFTFDTGPSWYLMPEVID +RWFRLMGTSAAERLDLRRLDPGYRVYFEGHLHE--------------PPVDVRTGHAET--LFESLEPGAGRRLRAYLDS +ASRIYGLAKEHFLYTDFRRPAALAHPDVLRALPALGPQLLGGLRSHVAARFQDPRLRQILGYPAVFLGTSPDRAPAMYHL +MSHLDLADGVQYPLGGFAALVDAMAEVVREAGVEIRTGVEATAVEVVDRPAPAGRLGRLAARLPRPGAARGDEGRRRRPG +RVTGVAWRSDDGAAGRLDADVVVAAADLHHVQTRLLPPGRRVAESTWDRRDPGPSGVLVCVGVRGSLPQLAHHTLLFTAD +WEDNFGRIERGEDLAADTSIYVSRTSATDPGVAPEGDENLFILVPAPAEPGWGRGGIRVRDGQGWRVDRAGDAQVEAVAD +RALDQLARWAGIPDLAERIVVRRTYGPGDFAADVHAWRGSLLGPGHTLAQSAMFRPSVRDADVAGLMYAGSSVRPGIGVP +MCLISAEVVRDELRHDARR--ARP------------AGPGGSGA--- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001648.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001648.fa new file mode 100644 index 0000000000000000000000000000000000000000..73dc714c685596994129c286363d69863f3ff9f7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001648.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_02106 +MAA----PTP--------------SPAALYTRTAHTAAAQVIRRYSTSFSWACRTLPRQA +RQDVATIYAMVRVADEVVDGVAVAAGLDEAGVRAALDDYERACEAAMASGFATDPVLHAF +ADVARRHGITPELTRPFFASMRADLGIREHGAESLDAYIHGSAEVVGLMCLQVFLSLPGT +RARTPGQRQELRAQASRLGAAFQKVNFLRDLAADHHELGRTYLPGAAPGVLTEARKAELV +AEVRADLDAALPGIRVLDPGAGRAVALAHGLFAALVDRIEATPAAELAHRRVRVPDHQKA +RIAARVLA--------RGRR---------------GGRR- +>GCF_003691675_PROKKA_01813 +MAA----PTP--------------SPAALYTRTAHAAAAQVIRRYSTSFSWACRTLPRQA +RQDVATIYAMVRVADEVVDGVAVAAGLDEAGVRAALDDYERACEAAMASGFATDPVLHAF +ADVARRHGITPELTRPFFASMRADLGIREHGAESLDAYIHGSAEVVGLMCLQVFLSLPGT +RARTPGQRQELRAQASRLGAAFQKVNFLRDLAADHHELGRTYLPGAAPGVLTEARKAELV +AEVRADLDAALPGIRVLDPGAGRAVALAHGLFAALVDRIEATPAAELAHRRVRVPDHQKA +RIAARVLA--------RGRR---------------GGRR- +>GCF_005280335_PROKKA_00673 +M--------P--------------ADAPLYTRTARAAAGRVIRRYSTSFSWACRTLPREA +RRDVEAIYAMVRVADEAVDGVAQAAGLDSQRVRAALDDYERACEAAMASGFSTDLVLHAF +GDVARRHGITPELTRPFFASMRADLGVSEHGAESLAAYIHGSAEVVGLMCLQVFLSLPGT +RARTPAEREAIRAQAARLGAAFQKVNFLRDLAADHDGLGRTYLTGAAPDELTEARKAELV +AEVRADLAAALPGIRALDPRAGRAVALAHGLFAALADRIETTPAAELARRRVRVPDAQKA +RIAARVLAEQAGLAVARRRR---------------GGRR- +>GCF_020097155_PROKKA_00589 +MTGTTTPPAPAGPECGTVRARTGETDLELYTATALRVAGEVIGRYSTSFSWACRVLPPDA +RRDIAAIYAMVRVADEVVDGAAEEAGLPVARVAAGLDAYERACEDAMDTGFSTDLVLHAF +ADVSRRHGITAELTRPFFVSMRADLTVAEHGEDSLAAYIHGSAEVVGLMCLQVFLSMDGT +RADGPADRAALRAAASRLGAAFQKVNFLRDLAADHDALGRTYFSGAAPEALTEERKAELL +ADLDADLDASLPGILALDPRAARAVLLAHGLFAELSRRLAATPAAELARRRVRVPDPVKA +RIAVRVLAASP-VGIGRRGRPLPAGCAEDLAAHQDGDRRP +>GCF_023573625_PROKKA_02046 +MAA----PAP--------------IPAALYTRTAHAAAAQVIRRYSTSFSWACRTLPRQA +RQDVATIYAMVRVADEVVDGVAVAAGLDEAGVRAALDDYERACEAAMASGFATDPVLHAF +ADVARRHGITPELTRPFFASMRADLGIREHGAESLDAYIHGSAEVVGLMCLQVFLSLPGT +RARTPGQRQELRAQASRLGAAFQKVNFLRDLAADHHELGRTYLPGAAPGVLTEARKAELV +AEVRADLDAALPGIRVLDPGAGRAVALAHGLFAALVDRIEATPAAELAHRRVRVPDHQKA +RIAARVLA--------RGRR---------------GGRR- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001659.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001659.fa new file mode 100644 index 0000000000000000000000000000000000000000..5c0ad8fa3ce4c9b1ae32c30b73d2d625a472d229 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001659.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_02121 +MTTTDLKITGMTCGHCVASVQEELGEIAGVSAVDVDLNSGGVSTATVTSEAPLDPAAARA +AVEEAGYTLVEA +>GCF_003691675_PROKKA_01829 +MTTTDLKITGMTCGHCAASVREELGEIAGVSAVDVDLNAGGVSTATVTSEGPLDPAAARA +AVEEAGYTLVEA +>GCF_005280335_PROKKA_00659 +MTTTDLKITGMTCGHCVASVQEELGEIAGVTAVDVDLTAGGVSTATVTSESPLDPAAARA +AVEEAGYRLVEG +>GCF_020097155_PROKKA_00576 +MTTTDLKITGMTCGHCVASVREELGEIAGVSAVDVDLNAGGVSTATVTSEGPLGPAAARA +AVEEAGYTLVEG +>GCF_023573625_PROKKA_02059 +MTTTDLKITGMTCGHCAASVREELGEIAGVSAVDVDLNAGGVSTATVTSEGPLDPAAARA +AVEEAGYTLVEA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001663.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001663.fa new file mode 100644 index 0000000000000000000000000000000000000000..eb35da4bcee5d23be83d09978a18b56abd21be47 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001663.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_02127 +MTQTTSTPARLRARDGFVLAARHFAP-TTAPQARPAGAVVIAPATGVKATYYRRYAEFLA +GHGFHAVTFDYRGVGESREPFAVARQARWADWGALDADAVLGWARTHLPGPLLTVGHSYG +GFGIGLADEARHVARHVAVGGQHAHWRDYRARPGRARMWARWHAAMPVVTLARGHLPGRR +LGWLEDLPRGVALDWARSRRDFTASARTAAGRDELRRRLAAFTADALIVAPVDDDFGTEA +ALDRADAYSPGRRTVRWRVRPEELGVAEIGHFGLFHARFAPTFWPATLEWLRDGVAPDAA +R +>GCF_003691675_PROKKA_01835 +MTQTTSTPVRLRARDGFVLAARHFAPTTTTPPARPAGAVVIASATGVKATYYRRYAEFLA +GHGFHAVTFDYRGVGESREPFAVARRARWADWGALDADAVLGWARTRLPGPLLTVGHSYG +GFGIGLADEARHVARHVAVGGQHAHWRDYRARPGRARMWARWHAAMPAITLARGHFPGRR +LGWLEDLPRGVALDWARSRRDFTASARTTAGRDELRRRLAAFTADALIVAPVDDDFGTDA +ALDRADAYSPGRRTVRWRVRPEELGVAEIGHFGLFHARFAPAFWPATLEWLRDGVAPAAA +R +>GCF_005280335_PROKKA_00653 +MTQTTSTPVRLRAPDGFVLAARHFTPTTTTPPASPAGTVVIASATGVKATYYRRYAEFLA +GHGFHAVTFDYRGVGESREPFAVARRARWADWGVLDADAVLGWARTHLPGPLLTVGHSYG +GFGIGLADEARHVARHVAVGGQHAHWRDYRARPGRVRMWARWHAAMPAITLARGHFPGRR +LGWLEDLPRGVALDWARSRRDFTASARTAAGRDELRRRLAAFTADALIVAPVDDDFGTDA +ALDRADSYSPGRRTVRWRVRPEELGVAEIGHFGLFHARFAPTFWPATLEWLRDGVVPAAA +R +>GCF_020097155_PROKKA_00569 +MTQTTSTLVRLRARDGFVLAARHFAP-TTTPPARPAGAVVIAPATGVKATYYRRYAEFLA +GHGFHAVTFDYRGVGESRAPFAVARRARWADWGALDADAVLGWARTHLPGPLLTVGHSYG +GFGIGLADEARHVARHVAVGGQHAHWRDYRARPGRARMWARWHALMPMVTLARGHFPGRR +LGWLEDLPRGVALDWARSRRDFTASARTVAGRDELRRRLAAFTADALIVAPVDDDFGTDA +ALDRADSYSPGRRTVRWRVRPEELGVGEIGHFGLFHARFASTFWPATLEWLRDGVAPAGA +R +>GCF_023573625_PROKKA_02065 +MTQTTSTPARLRARDGFVLAARHFAP-TTAPQARPAGAVVIAPATGVKATYYRRYAEFLA +GHGFHAVTFDYRGVGESREPFAVARQARWADWGALDADAVLGWARTHLPGPLLTVGHSYG +GFGIGLADEARHVARHVAVGGQHAHWRDYRARPGRVRMWARWHAAMPAITLARGHFPGRR +LGWLEDLPRGVALDWARSRRDFTASARTAAGRDELRRRLAAFTADALIVAPVDDDFGTDA +ALDRADAYSPGRRTVRWRVRPEELGVTEIGHFGLLHARFAPTFWPATLEWLRDGVAPDAA +R + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001667.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001667.fa new file mode 100644 index 0000000000000000000000000000000000000000..a55b32c0951eb8c8d975d33e3078a69863711944 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001667.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_02131 +MTVPSSSAEHAPALEARPEMPGETVSRVAMTPAALELIRRLLPIHGPLMFHQSGGCCDGS +APMCYPAGDFTTGAADVLLGTFALPAEGDQAAVEIPFWMSAAQFEYWKHTHLTLDVVDGR +GSGFSVEAPEGKRFLIRSRLMAGSG +>GCF_003691675_PROKKA_01839 +MTVPSSSAEHAPALEARPEMPGETLSRVAMTSAALELIRRLLPIHGPLMFHQSGGCCDGS +APMCYPAGDFTTGAADVLLGTFALPAEGDQAAVEIPFWMSAAQFEYWKHTHLTLDVVDGR +GSGFSVEAPEGKRFLIRSRLMAGSG +>GCF_005280335_PROKKA_00649 +MTVPSSSAEHAPALEARPELPGETVSRVAMTPAALELIRRLLPIHGPLMFHQSGGCCDGS +APMCYPAGDFTTGAADVLLGTFALPAEGDQDAVEIPFWMSAAQFEYWKHTHLTLDVVDGR +GSGFSVEAPEGKRFLIRSRLMAGSG +>GCF_020097155_PROKKA_00565 +MTVSSSSAEHAPALEARPELPGETVSRVAMTPAALALIRRLLPIHGPLMFHQSGGCCDGS +APMCYPAGDFTTGAADVRLGTFVVPAEGDQAAVEIPFWMSAAQFEYWKHTHLTLDVVDGR +GSGFSVEAPEGKRFLIRSRLMAGSG +>GCF_023573625_PROKKA_02069 +MTVPSSSAEH--ALDARPELPGETVSRVAMTPAALELIRRLLPIHGPLMFHQSGGCCDGS +APMCYPAGDFTTGAADVLLGTFALPAEGDQAAVEIPFWMSAAQFEYWKHTHLTLDVVDGR +GSGFSVEAPEGKRFLIRSRLMAGSG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001669.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001669.fa new file mode 100644 index 0000000000000000000000000000000000000000..2c25a04b3a375490cd3d9d5e4a2ae12b77eaf3cd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001669.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_02133 +MSQTSQATGRLSAGHVIVKTLESHGVKRVYSVPGESYLDVLDGLHDSG-IENVVCRHEGGATYMAEADGKMNVVPGVAMV +TRGPGAANAHVGLHTAWQDSTALVLFVGLIPFEHRDREAFQEFDPHAWFGTGAKRVMVLDHPERASEIVAEAMFAASSGR +PGPVVVGLPEDVIREEIDAHLHPQIPVASGGMTVGDWKSLHAALKESRKPLFITGGNDWTDEGAQTLTTWLEEHKIPAAA +EWRTEGTVPFSSPSYVGPIGYGRPKPTYDMLEETDLIVFVGTVPGDVVTNGFTIRQNWDKKNFLVTIDPSLRGRSGPVSH +QIVAKPDGFIRDLVRMELEVKPEWEEWTSRMRGEQEKFAALPPAEPSEGQAKMATLMANLVPKLPKDSMISLGAGEHTNW +AHRYFPTEGYRSMISARNGSMGYSVPGAVAASLNFPDRTVVTIAGDGEFLMNGQELATAAQYGATPLVIVMDNQEYGTIR +THQERQYPGRVSGTQLKNPDFAAMAQAFGGFGVRVERDADVPAAVDAALKAVQEEGRFALIHLIVEQRVKAY +>GCF_003691675_PROKKA_01841 +MSQTSQATGRLSAGHVIVKTLESHGVKRVYSVPGESYLDVLDGLYDSG-IENVVCRHEGGATYMAEADGKMNVVPGVAMV +TRGPGAANAHVGLHTAWQDSTALVLFVGLIPFEHRDREAFQEFDPHAWFGTGAKRVMVLDHPERASEIVAEAMFAASSGR +PGPVVVGLPEDVIRQEIDAHLHPQIPVAPGGMTVEDWKSLHAALKESRKPLFITGGNDWTDEGAQTLTTWLEEHKIPAAA +EWRTEGTVPFSSPSYVGPIGYGRPKPTYDMLEETDLIVFVGTVPGDVVTNGFTIRQNWDKKNFLVTIDPSLRGRSGPVSH +QIVAKPDVFIRDLVRMELEVKPEWEEWTSRMRGEQEKFAALPPAEPSEGQAKMATLMANLVPKLPKDSMISLGAGEHTNW +AHRYFPTEGYRAMISARNGSMGYSVPGAVAASLNFPDRTVVTIAGDGEFLMNGQELATAAQYGAKPLVIVMDNQEYGTIR +THQEREYPERVSGTQLKNPDFAAMAQAFGGFGVRVERDADVPAAVDAALKAVQEEGRFALIHLIVEQRVKAY +>GCF_005280335_PROKKA_00647 +MSQTTEAGGRLSAGHVIVKTLESHGVRRIYSVPGESYLDVLDGLHDSQ-IENVVCRHEGGATYMAEADGKMNEVPGIAMV +TRGPGAANAHVGLHTAWQDSTALVLFVGLIPFEHREKEAFQEFDPHAWFGTGAKRVMVLDHADRASEIVAEAMFAATSGR +PGPVVVGLPEDVIREQIDATLHPVIPVATGGMTVEDWKSLHSALKESKKPLFITGGNDWTDEGAQQLTQWLEGHKIPAAA +EWRTEGTVPFSSPSYVGPIGYGRPKPTYDLLEETDLIVFIGTVPGDVVTNGFKIRQNWDKKNFLVTIDPSLRGRSGPVSH +QIVAKPDVFVRDLVRMDLDVKPEWEEWTSRMRGEQETFAALPPAEPSEGQAKMATLMANLMPKLPKDSMISLGAGEHTNW +AHRYFPTEGYRAMISARNGSMGYSVPGAVAASLNFPDRTVVTIAGDGEFLMNGQELATAAQYGATPLVIVMDNQEYGTIR +THQEREYPERVSGTQLKNPDFAGMAEAFGGLGIRVEKDADVPAAVDAALKAVQEEGRFALIHLIVEQRVKAY +>GCF_020097155_PROKKA_00563 +MSQNSEAPGRLSAGHLIVKTLESHGVRRVYSVPGESYLDVLDGLHDSAQIENVVCRHEGGATYMAEADGKMNEVPGIAMV +TRGPGAANAHVGLHTAWQDSTAMVLFVGLIPFEHRDREAFQEFDPHAWFDSGAKRVMVLDHPERASEIVAEAMFAAASGR +PGPVVVGLPEDIIRVEVDAHLHPQIPVAPGGMTVEDWKSLHAALKESQKPLFITGGNDWTDAGAEALTSWLEDHKIPAAA +EWRCEGTVPFSSPSYVGPIGYGRPDFTQHLLEETDLIVFVGTVPGDVVTDGFTIRQNWDKKNFLVTIDPSLRGRSGPVSH +QIVAKPDVFVRDLVRMDLAVKPEWEAWTSRLRGQQEEFAALPAAEPGDGQAKMATLMATLMPKLPKDSMISLGAGEHTNW +AHRYFPTEGYRAMISARNGSMGYSVPGAVAASLNFPDRTVVTIAGDGEFLMNGQELATAAQYGATPLVIVMDNQEYGTIR +THQEREYPERVSGTQLKNPDFAAMAEAFGGFGVRVEQDADVPAAVDAALKAVQEEGRFALIHLIVEQRVKAY +>GCF_023573625_PROKKA_02071 +MSQTSQATGRLSAGHVIVKTLESHGVKRVYSVPGESYLDVLDGLHDSG-IENVVCRHEGGATYMAEADGKMNVVPGVAMV +TRGPGAANAHVGLHTAWQDSTALVLFVGLIPFEHRDREAFQEFDPHAWFGTGAKRVMVLDHPERASEIVAEAMFAASSGR +PGPVVVGLPEDVIREEIDAHLHPQIPVAPGGMTVEDWKSLHAALKESRKPLFITGGNDWTDEGAQTLTTWLEEHKIPAAA +EWRTEGTVPFSSPSYVGPIGYGRPKPTYDMLEETDLIVFVGTVPGDAVTNGFTIRQNWDKKNFLVTIDPSLRGRSGPVSH +QIVAKPDGFIRDLVRMELEVKPEWEEWTSRMRGEQEKFAALPPAEPSEGQAKMATLMANLVPKLPKDSMISLGAGEHTNW +AHRYFPTEGYRSMISARNGSMGYSVPGAVAASLNFPDRTVVTIAGDGEFLMNGQELATAAQYGATPLVIVMDNQEYGTIR +THQERQYPGRVSGTQLKNPDFAAMAQAFGGFGVRVERDADVPAAVDAALKAVQEEGRFALIHLIVEQRVKAY diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001672.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001672.fa new file mode 100644 index 0000000000000000000000000000000000000000..44450d29698365d670677f384040faca836e0ad8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001672.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_02137 +M---QTPLEISSVVFKPILIRAVVALAFGLTTVFVAEPGLTWMKVMFALYLAFSGSAMWE +YLRRDPVPVAMRSPLSLAAAAWMLGVIVLLFLGSPAAVGVAAGAALVLGGVAELVAWARH +RREFIPARDQLWTGLVGLLSGGGVVVAALQGFGPHALLGIAGGGAILIGVLLMVSGLGFH +HEVRRDRGTARGL +>GCF_003691675_PROKKA_01845 +M---QTPLEISSVVFKPILIRAVVALAFGLTTVFVAEPGLTWMKVMFALYLAFSGSAMWE +YLRRDPVPVAMRSPLSLAAAAWMLGVIVLLFLGSPAAVGVAAGAALVLGGVAELVAWARH +RREFIPARDQLWTGLVGLLSGGGVVVAALQGFGPHALLGIAGGGAILIGVLLMVSGLGFH +HEVRRDRGTARGL +>GCF_005280335_PROKKA_00635 +M---QTPLEISSVVFKPILIRAVVALAFGLTTVFVAAPGLTWMKVSLALYLAFSGSAMWE +YLRREPVPVAMRSPLSMAAAASMLGVIVLLFLGTPAGVGLAAAAALVLGGAAELVAWARH +RREFIPARDQLWTGLVGLLSGLGVAFGALQGFGPHALLGIAGGGAIIIGVLLLVSGLGFH +HEVRRDRGTAKGL +>GCF_020097155_PROKKA_00559 +MTSPQTPLEISSEVFKPVLIRAGVALIFGLTTVFVQNPGLTWMKVAFALYLVFSGSALWE +YLRRDPVPVGMRSPLSLAAAAWMLGTVVLVIMGSPAAVGIVVGLALLAGGAAELTAWARF +RREFIPARDQLWTGLVGALSGLGVLVGAVQGFGPHALLGIAGGGAIIVGVLMLISGLGFH +HEVRRDRGTAKGL +>GCF_023573625_PROKKA_02075 +M---QTPLEISSVVFKPILIRAVVALAFGLTTVFVAEPGLTWMKVMFALYLAFSGSAMWE +YLRRDPVPVAMRSPLSLAAAAWMLGVIVLLFLGSPAAVGVAAGAALVLGGVAELVAWARH +RREFIPARDQLWTGLVGLLSGGGVVVAALQGFGPHALLGIAGGGAILIGVLLMVSGLGFH +HEVRRDRGTARGL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001682.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001682.fa new file mode 100644 index 0000000000000000000000000000000000000000..f39d704d754358e8efdeb04008699726260c5078 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001682.fa @@ -0,0 +1,45 @@ +>GCF_002008305_PROKKA_02148 +MLWTLLRRHGRRYRGDVAAVVVLQLISTLAMLYLPSLNARIIDEGVARGDTARIWDIGLVMLGVALVQVVAAIAAVWFGA +KASMGVGRDLRRAVYTRVDAFSAEELGRFGAATLITRGTNDVNQVQMLTLMALNFMVAVPIMAVGGIVMAIREDPGLSWL +VWVSVPVLLVIVAWIVARLMPLFQQMQDNIDDVNGVLREQIQGIRVVRAFVRERHETRRFTDANAALTETSVRIGRLFVL +LGPVITMILHLATAAVLWFGGQRVDAGLVQVGALTAFMQYLLQILMAVMMGTFMMMMLPRAVISARRIGEVLDTVPTLGE +PVRPVTPERRDGAVELRHVTFQYPGAEAPVLDDVSFAVAPGTTTAIIGSTGSGKSTLISLLPRLYDATSGEVLVDGVPVT +DLARAELTEAVALVPQKPYLFSGTVRENMQFGAPDASDERIWAALETAQAADFVRARTTGKGEAAASGLDSRLSQGGTDV +SGGQRQRLSIARALVAEPRILVFDDSFSALDVTTDARLRAALDRAAAGVTRIVVAQRVATITDADQIIVLDEGRVVGRGT +HAELLADNQTYREIVDSQLTAEDVA +>GCF_003691675_PROKKA_01856 +MLWTLLRRHGRRYRGAVAAVVVLQLISTLAMLYLPSLNARIIDEGVARGDTARIWDIGLVMLGVALVQVVAAIAAVWFGA +KASMGVGRDLRRAVYTRVDAFSAEELGRFGAATLITRGTNDVNQVQMLTLMALNFMVAVPIMAVGGIIMAIREDPGLSWL +VWVSVPVLLVIVAWIVARLMPLFQRMQDNIDDVNGVMREQIQGIRVVRAFVRERHETRRFTDANAALTETSVRIGRLFVL +LGPVITMILHLATAAVLWFGGERVDAGLVQVGALTAFMQYLLQILMAVMMGTFMMMMLPRAVISARRIGEVLDTVPTLAE +PVRPVTPARRDGAVELRHVTFQYPGAEAPVLDDVSFAVAPGTTTAIIGSTGSGKSTLISLLPRLYDATSGEVLVDGVPVT +DLARAELTEAVALVPQKPYLFSGTVRENMQFGAPDASDERIWAALETAQAADFVRARTTGKAETAASGLDSRLSQGGTDV +SGGQRQRLSIARALVAEPRILVFDDSFSALDVTTDARLRAALDRAAAGVTRIVVAQRVATITDADQIIVLDEGRVVGRGT +HAELLADNQTYREIVDSQLTAEDVA +>GCF_005280335_PROKKA_00621 +MLWTLLRRPRRPDLGAVTAVVVLQLISTLAMLYLPSLNARIIDEGVARGDTDRIWDLGLVMLGVALVQVVAAIVAVWFGA +KVAMGIGRDLRRAVYTRVDGFSAEELGRFGAPTLITRGTNDVNQVQMVTLMGLNFMVAVPIMAIGGIIMAVREDPGLSWL +VWVSVPVLLVIVAWIVAKLMPLFQRMQDDIDRVNGVMREQVMGIRVVRAFVREPHESARFSGANAALTRTSVLIGRLFVL +LGPVITMILHLATAAVLWFGGHRVADGLVEVGALTAFMQYLLQILMAVMMGTFMMMMLPRAVVSAGRIGEVLDTVPTLAE +PVNPVTPADPRGAVELRDVTFAYPGAEAPVLDGVSFTVAPGSTTAIIGATGSGKSTLVNLIPRLYDATSGQVLIDGVPVT +ELARAELTRAVALVPQKPYLFSGTVAENMRFGAPEATEEEIWAALETAQAAGFVRERTTGEGETAAGGLDSRLSQGGTDV +SGGQRQRLSIARALVARPRILLFDDSFSALDVATDARLRGALDATAAGTTRIVVAQRVATITEADQIIVLDEGRVVGRGT +HAELLAGNETYKAIVDSQVREEELA +>GCF_020097155_PROKKA_00546 +MLWTLLRRHLNPYAGAVTAVIVLQLVSTLAMLYLPSLNARIIDEGVARGDTARIWDLGLVMLGVAAVQVVAAISAVWFGA +KASMGVGRDLRRAVYTRVDGFSAEELGRFGAATLITRGTNDVNQVQMLTLMALNFMVAVPIMAVGGIVMAVREDAGLSWL +VWVSVPLLLVIVGFIVSRLMPLFQRMQDDIDAVNGVMREQVMGIRVVRAFVRQDHEAARFTDANQALTDTSVRIGRLFVL +LGPVITMVLHLATAAVLWFGGHRVDQGLVQIGSLTAFMQYLLQILMAVMMGTFMMMMLPRAVISARRIGEVLDTAPTLGE +PVHPVTPERREGRVELRDVTFAYPGAEAPVLDGVSFTAEPGTTTAIIGATGSGKSTLVNLIPRLYDATSGQVLVDGVPVT +DLARAELTDAVAIVPQKPYLFSGTVRDNMRFGAPEATDEQIWAALETAQAADFVRERTTGEGETAASGLDSSLSQGGTDV +SGGQRQRLSIARALVADPRILLFDDSFSALDVTTDATLRAALDASAAQTTRVVVAQRVATITDADQIVVLEAGRVVGRGT +HAELLAGNETYRQIVDSQVREEELA +>GCF_023573625_PROKKA_02086 +MLWTLLRRHGRRYRGAVAAVVVLQLISTLAMLYLPSLNARIIDEGVARGDTARIWDIGLVMLGVALVQVVAAIAAVWFGA +KASMGVGRDLRRAVYTRVDAFSAEELGRFGAATLITRGTNDVNQVQMLTLMALNFMVAVPIMAVGGIIMAIREDPGLSWL +VWVSVPVLLVIVAWIVAGLMPLFQRMQDNIDDVNGVMREQIQGIRVVRAFVRERHEARRFTDANAALTETSVRIGRLFVL +LGPVITMILHLATAAVLWFGGQRVDAGLVQVGALTAFMQYLLQILMAVMMGTFMMMMLPRAVISARRIGEVLDTVPTLGE +PARPVSPARRDGAVELRHVTFQYPGAEAPVLDDVSFAVAPGTTTAIIGSTGSGKSTLISLLPRLYDATSGEVLVDGVPVT +DLARAELTEAVALVPQKPYLFSGTVRENMQFGAPDASDERIWAALETAQAADFVRARTTGKGEAAASGLDSRLSQGGTDV +SGGQRQRLSIARALVAEPRVLVFDDSFSALDVTTDARLRAALDRAAAGVTRIVVAQRVATITDADQIIVLDEGRVVGRGT +HAELLADNQTYREIVDSQLTAEDVA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001687.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001687.fa new file mode 100644 index 0000000000000000000000000000000000000000..795949c550b52f0a9e93e047ce6b7f9f575cab40 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001687.fa @@ -0,0 +1,80 @@ +>GCF_002008305_PROKKA_02154 +MSQTLTPAAPQDLNARRHRLRRYRAVIFDMDGVITDTAGVHAQAWKELFDGALPAVGALPANAAVVAADPDVLRPFDAAA +DYLHHVDGRPREDGVRTFFASRGLRVPEADAPEADAAPELTVLALAERKQGYFEQVLERDGVRVFPEAQDLLERLRAKGV +PVALVTSSKNSRAVLTAGGVLDFFPVIVDGNTAVERGLPGKPDPAMFWEAARELGVDVADAMVLEDAVSGVKAAADGRFG +LVIGVDRE-PELGKGRLKAAGAHLVVQDYGTLHLEDRTTTPFDPAWVLRWDHFDPASEGTREVLSTLANGYWGTRGAVPG +TRISSVHYPGTYMAGVFNRLTSMVQGRVVETEHMVNIQDWTPLVVTPRHGRPLLPGEENLVEYGQEMDLRRGVLSRTMTF +EDEQGRRTTVHTRQFTSLANRHLAAIELTVVAENWSGDLTVRSKIEGRVANLNVSDDRTLANQHLEPVQAREIDGETVLL +ETATNQSGIHVAVATRTRQVAPVGHHEPIRRPVDGSDLVVGQDILLHVDEGVPLVLEKVAAVATSHDHASASVWESAVKD +AQRAQNFRNLLTLHEQRWGTNWDRFSVRIDLAEPYRHHRRSTAA-ETGGEYAPPVVAAGHSAPVGSAVPMGKDGASLRQQ +LALNLHTFHVLQTAYGRRRDLDASVGARGLHGEGYRGHIFWDEIYVYPMLTLRRPEITRGLLMYRYRRLNEARANAQAAG +WAGAMYPWQSGADGSEETPTELWNPRSRMWMPDNSHNQRHVSLDIAYSVLRYIEITKDTSFISDYGAEMLVEISRFFMSM +TLHNAVTDRYEIHGVMGPDEFHDGYPETPGSGLRNNAYTNVLTSWVLAETARLVRWLDTIDDGLPELMEISEEEIERWEE +VSTRLTVPFFEEGEEAGILAQFEGYQDLLEFDWEAYRAKYGNIGRMDLILQAEGDATNRYKLSKQADTLMLGYLFSSEEL +DRILRRMGYELPQEAFERMVTYYEARSTHGSTLSRLVHAWVAARTDPDRSWDLFTEALESDLSDTQGGTTKEGIHLGLMA +GTVDTVIRCYAGLETRDDVVRLHPRMPAQLPGARFTIRFRQQPVVIHMTQREVTVAAGEGMWHDVPMIIAGREHTLSPGE +KLTVPLD +>GCF_003691675_PROKKA_01867 +MSQTLTPAAPQDLNARRHRLRRYRAVIFDMDGVITDTAGVHAQAWKELFDGALPAVGALPANAAVVAADPDVLRPFDAAA +DYLHHVDGRPREDGVRTFFASRGLRVPEADAPEADAAPELTVLALAERKQGYFEQVLERDGVRVFPEAQDLLERLRAKGV +PVALVTSSKNSRAVLTAGGVLDFFPVIVDGNTAVERGLPGKPDPAMFWEAARELGVDVADAMVLEDAVSGVKAASDGRFG +LVIGVDRE-PELGKGRLKAAGAHLVVQDYGTLHLEDRTTTPFDPAWVLRWDRFDPASEGTREVLCTLANGYWGTRGAVPG +THISSVHYPGTYMAGVFNRLTSMVQGRVVETEHMVNIQDWTPLVVTPRHGRPLLPGEENLVEYGQEMDLRRGVLSRTMTF +EDEQGRRTTVHTRQFTSLANRHLAAIELTVVAENWSGDLTVRSKIEGRVANLNVSDDRTLANQHLEPVQAREIDGETVLL +ETATNQSGIHVAVATRTRQVAPVGHHEPIRRPVDGSDLVVGQDILLHVDEGVPLVLEKIAAVATSHDHANASVWESAVKD +VQRAQNFRNLLTLHEQRWGTNWDRFSVRIDLAEPYRHQRRSTAA-EAGGEYAPPVVDAGHSAPVGSAVPMGKDGASLRQQ +LALNLHTFHVLQTAYGRRRDLDASVGARGLHGEGYRGHIFWDEIYVYPMLTLRRPEITRGLLMYRYRRLNEARANAQAEG +WAGAMYPWQSGADGSEETPTELWNPRSRMWMPDNSHNQRHVSLDIAYSVLRYIEITKDTSFISDYGAEMLVEISRFFMSM +TLHNAVTDRYEIHGVMGPDEFHDGYPETPGSGLRNNAYTNVLTSWVLAETARLVRWLDTIDDGLPELMEISEEEIERWEE +VSTRLTVPFFEEGEEAGILAQFEGYQDLLEFDWEAYRAKYGNIGRMDLILQAEGDATNRYKLSKQADTLMLGYLFSAEEL +DRILRRMGYELPEEAFERMVTYYEARSTHGSTLSRLVHAWVSARTDPDRSWDLFTEALESDLSDTQGGTTKEGIHLGLMA +GTVDTVIRCYAGLETRDDVVRLHPRMPAQLPGARFTIRFRQQPVVIQMTQREVTVAAGEGMWHDVPMIIAGREHTLSPGE +KLTVPLG +>GCF_005280335_PROKKA_00609 +-----------------------------MDGVVTDTAGVHAQAWKELFDEALPAVGALPANAAAVAADPEALRPFDAAA +DYLHHVDGRPREDGVRTFFHSRGLRVPEADSPEAATTPQLTVLALAERKQGYFEQVLARDGVRVFPEAQDLLEKLRAKGV +PVALVTSSKNSRAVLGAGGVLDFFPVIVDGHTAIERGLPGKPDPAMFWEAARELGVDVADAMVLEDAVSGVKAAADGRFG +LVIGVDRE-PDLGKGRLKGAGAHLVVQDYGTLCLEQRTTTPFDPAWVLRWDEFDPASEGTREVLCTLANGYWGTRGAVPG +TRISDVHYPGTYMAGVFNRLTSMVQGRAVDTEHMVNIQDWTPLVVTPRGGRPLLPGEETLVDFSQEMDLRRGVLSRTMAF +EDEQGRRTSLHTRQFTSLANRHLAAIELTVVAENWTGELTVRSTIEGRVANLNVSDDRTLANQHLEPSQAREIDGETVLL +ETTTSQSRIDIAVATRTRQMAPVGHHEPIRRPVDGSDLRVGQDIRLHVEEGVPLVIEKIAAVATSHDHAQASVWESAVKD +VQRANNFRNLLTLHEQRWGTNWDRFSVRIDIAEPYRHQRRSAAA-AEGAEYAPPVVDAGRSASVGSAVPMGKDGASLRQQ +LALNLHTFHVLQTAYGRRRDLDASVGARGLHGEGYRGHIFWDEIYVYPMLTLRRPEITRGILMYRYRRLNEARANAQAEG +WAGAMYPWQSGADGSEETPTELWNPRSRMWMPDNSHNQRHVSLDIAYSVLRYIEITKDTSFISDYGAEMLVEVSRFFMSM +ALHNADTDRYEIHGVMGPDEFHDGYPETPGSGLRNNAYTNVLTSWVLSETARLVRWLDTLDDGLPEIMEITEEEIERWED +VSARLTVPFFEDGEEAGILAQFEGYQDLKEFDWEAYRAKYGNIGRMDLILQAEGDATNRYKLSKQADTLMLGYLFSAEEL +DGILRRMGYELPQEAFERMVTYYEARSTHGSTLSRLVHAWVAARTDPDRSWDLFTEALESDLSDTQGGTTREGIHLGLMA +GTVDTVIRCYAGLETREDVVRVDPRMPSQLPGASFTIRFRQQPVQIHMRRSEVTVRAGSGMWHDVPMIIAGQEHTLSPGA +EITVPLG +>GCF_020097155_PROKKA_00533 +MTQTLTPVDQQDRNARRHRLRRYRAVIFDMDGVITDTAGVHAAAWKELFDQALPAVGALDANRAAVAADPGVLRPFDPEA +DYLHHVDGRPREDGVRAFFASRGLTVPEVD--DADAPVDLTVLALAERKQGFFEKVLERDGVRVFPEATDLLEKLRDKGV +PVALVTSSKNSRAVLTAGGVLDYFPVIVDGHTAIERGLPGKPDPAMFWEAARELGVDVADAMVLEDAVSGVKAAADGRFG +LVIGVDREHGEGGKPRLKDAGAHIVVKDYGTLRLADRTTAPFDAAWVLRWDHFDPATEGTREVLCTLANGYWGTRGSIPG +TRISDVHYPGTYLAGVFNRLTSMVQGRQVETEHMVNMQDWTPLQVIPAGGRPLIPGEETLLDYHQEMDLRRGVLSRSMRF +EDAQGRITTLHTRQFQSLADRHLGAIELTVEAENWSGDLVVRTLVDGRVANLNVSDDRTLANQHLEPVAAREVDGETLLL +ETVTSQSRVHVAVAARTRQMAPKGHHQPIRRPVEGSDLMVGQDIHLHVEQDVPLVLEKVAAVANTHDHALASVDASAIKK +VQRAQNFRNLLTLHEQRWGMNWDRFSVRIDLAEEHRNQRRSTAVLAEGEEFEAPVFEAGRSASVGSAATMGKDGASLRQQ +LALNLHTYHVLQTAFGKRRDLDASVGARGLHGEGYRGHIFWDEIFVYPMLTLRRPEITRGILMYRYRRLNEARANAQAEG +WAGAMYPWQSGSDGREETPAELWNPRSHMWMPDNSHNQRHVSLDIAYSVLRYIEITKDASFISDYAAEMLVEISRFFTSM +TLHNAETGRYEIHGVMGPDEFHDGYPETPGSGLRNNAYTNVLTSWVLSETARLLRWLDTLDDGLPEVMEVTEEEIARWEE +IAAKLTVPFFTEGPEAGILAQFEGYQDLLEFDWEGYRAKYGNIGRMDLILQSEGDATNRYKLSKQADTLMLPYLFSGAEL +EQILGRMGYELHQEALERTVEYYEARSTHGSTLSRLVHAWVAARTDPDRSWDLFTEALESDLSDTQGGTTREGIHLGLMA +GTVDTVIRCYSGLETRDDVVRLDPRLPRQLPGARFTIRYHQQPVVIHMTQRDVTVTAGEGMWHEVPMVIAGREHTLEPGG +EVTVALG +>GCF_023573625_PROKKA_02097 +MSQTLTPAAPQDLNARRHRLRRYRAVIFDMDGVITDTAGVHAQAWKELFDGALPAVGALPANAAVVAADPDVLRPFDAAA +DYLHHVDGRPREDGVRTFFASRGLRVPEADAPEADAAPELTVLALAERKQGYFEQVLERDGVRVFPEAQDLLERLRAKGV +PVALVTSSKNSRAVLTAGGVLDFFPVIVDGNTALERGLPGKPDPAMFWEAARELGVDVADAMVLEDAVSGVKAAADGRFG +LVIGVDRE-PELGKGRLKAAGAHLVVQDYGTLHLEDRTTTPFDPAWVLRWDRFDPASEGTREVLCTLANGYWGTRGAVPG +THISSVHYPGTYMAGVFNRLTSMVQGRVVETEHMVNIQDWTPLVVTPRHGRPLLPGEENLVEYGQEMDLRRGVLSRTMTF +EDEQGRRTTVHTRQFTSLANRHLAAIELTVVAENWSGDLTVRSKIEGRVANLNVSDDRTLANQHLEPVQAREIDGETVLL +ETATNQSGIHVAMATRTRQVAPVGHHEPIRRPVDGSDLVVGQDILLHVDEGVPLVLEKIAAVATSHDHANASVWESAVKD +VQRAQNFRNLLTLHEQRWGTNWDRFSVRIDLAEPYRHQRRSTAA-EAGGEYAPPVVDAGHSAPVGSAVPMGKDGASLRQQ +LALNLHTFHVLQTAYGRRRDLDASVGARGLHGEGYRGHIFWDEIYVYPMLTLRRPEITRGLLMYRYRRLNEARANAQAAG +WAGAMYPWQSGADGSEETPTELWNPRSRMWMPDNSHNQRHVSLDIAYSVLRYIEITKDTSFISDYGAEMLVEISRFFMSM +TLHNAVTDRYEIHGVMGPDEFHDGYPETPGSGLRNNAYTNVLTSWVLAETARLVRWLDTIDDGLPELMEISEEEIERWEE +VSTRLTVPFFEEGEEAGILAQFEGYQDLLEFDWEAYRAKYGNIGRMDLILQAEGDATNRYKLSKQADTLMLGYLFSAEEL +DRILRRMGYELPQEAFERMVTYYEARSTHGSTLSRLVHAWVAARTDPDRSWDLFTEALESDLSDTQGGTTKEGIHLGLMA +GTVDTVIRCYAGLETRDDVVRLHPRMPAQLPGARFTIRFRQQPVVIHMTQREVTVAAGEGMWHDVPMIIAGREHTLSPGD +KLTVPLD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001702.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001702.fa new file mode 100644 index 0000000000000000000000000000000000000000..3dcaad19a1b9e33a97d0790b3a413924411e2d1f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001702.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_02179 +MSADGMIVAHTRVVSVEQPCRGFRRIVLAGPDLEAASGDLLGLLPPGVADLHALYRGARP +RRDAYVKLLIPPPGGTSADPDLSAGFRAGFLAIPEEERGWMRTYTVRSAGLVRLDGRQVP +SLTVDVVLHGDPDDPADPHQGPGLRWARAVQAGDAVNVLVPSAEAPAWSGWRQTGAHRVL +AVGDETAVPALVSVAEELADPFGGFDGEADLVLELPHDGQAADLIAERLAVPEPWDWRAV +TELTDRGRVRLHVGRRAPGAPSGSWAHARLAALLGVDPDDAGGPV-------APPAASVE +REWTVAALE---ADERPEAYVFLAGESAMVRALRRLSVGPGGVPKKHVSFMGYWREGQAE +S +>GCF_003691675_PROKKA_01893 +MSADGMIVAHTRVVSVEQPCRGLRRIVLAGPDLEAASGDLLGLLPPGVADLHALYRGARP +RRDAYVKLLIPPPGGTSADPDLSAGFRAGFLAIPEEERGWMRTYTVRSAGLVRLDGRQVP +SLTVDVVLHGDPDDPADPHQGPGLRWARAVQAGDAVNVLVPSAEAPAWSGWRQTGAHRVL +AVGDETAVPALVSVAEELADPFGGFDGEADLVLELPHDGQAADLIAERLAVPEPWDWRAV +TELTDRGRVRLHVGRRAPGAPSGSWAHARLAALLGVDPDDAGGPV-------APPAASVE +REWTVAALE---ADERPEAYVFLAGESAMVRALRRLSVGPGGVPKKHVSFMGYWRQGQAE +S +>GCF_005280335_PROKKA_00573 +M-SEGMFVAHTRVVSVEQPCRGFRRIVLAGPDLERASPDLMGLLPPGTADLHALYRGSRP +RRDAYVKVLIPPPGGVSADPDLSAGFRAGFLAIPEAERGWMRTYTVRSAGPVRLDGRPVP +SLTVDVVLHGDADDPADPHQGPGLRWARAVQAGDAVNVLVPSAEAPAWSAWRQTGARRVL +AVGDETAVPALVSVAEELADPFGGFDGVADLVLELPHDGQVADLIAERLAVPEPWDWRQV +TELADRGRVRLHVGRRAPGAPSGSWAHARLAALLGVDPDDAGGPV-------APPAASAD +REWSVAALA---EDERPEAYVFLAGESAMVRALRRLTVGPGGVPKAHVSFMGYWRQGQAE +S +>GCF_020097155_PROKKA_00500 +MSTEAMFVAHTRVVSTSQPCRGFRRIVLAGEDLEHASADLLGTLPPGVPDLHAIYRGSRP +RRDAYVKVLVPPPGGVSADPDLSAGFRAGFTAVPEDERGWMRTYTVRSAGRTRVDGREVP +ALTIDVVLHGDPDDAADPHQGPGLRWARTVAAGESVNVLVPTGEAPAWAGWRDTGARRVL +AVGDATAAPALLSVAEELADPFGGFDGEADLVLELPADAELADLIAERLAVPEPWDESRP +LDVAEHGRVRLHVGRTAPGRPVGAWAQARLGALLGLSGTARAGVVGVDGVVEAPPAEGAA +REWTLADLEPVTGVDRPDTYVFLAGESGMVRALRRLAVDGGDIPKKNVSFMGYWRQGQAE +S +>GCF_023573625_PROKKA_02124 +MSADGMFVAHTRVVSVEQPCRGFRRIVLAGPDLEAASRDLLGLLPPGVADLHALYRGARP +RRDAYVKLLIPPPGGTSADPDLSAGFRAGFLAIPEEERGWMRTYTVRSAGLVRLDGRQVP +SLTVDVVLHGDPDDPADPHQGPGLRWARAVQAGDAVNVLVPSAEAPAWSGWRQTGAHRVL +AVGDETAVPALVSVAEELADPFGGFDGEADLVLELPHDGQAADLIAERLAVPEPWDWRAV +TELADRGRVRLHVGRRAPGAPSGSWAHARLAALLGVDPDDAGGPV-------APPAASVE +REWTVAALE---ADERPEAYVFLAGESAMVRALRRLSVGPGGVPKKHVSFMGYWREGQAE +S + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001706.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001706.fa new file mode 100644 index 0000000000000000000000000000000000000000..1145a425ed4281c9150a4ce6a2fcd57419793d5a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001706.fa @@ -0,0 +1,31 @@ +>GCF_002008305_PROKKA_02183 +MTSPDPAPP-----------------------RPRVHVLTLRPDGARE--DTARRVG--I +VLAEAFATDPYTLGLVPEDRREARLERKFTAAVRHGLR----TGADGAPLGAVDVAVDAD +DGTLLGAAVWTSPAAPRGVDVPGLLAGLPTAV-------AVHGRHTLALKRIQAACERAR +PAGRHWYLEEVGAVPSARGRGAASALVRHGQRRA--SGLPVHLEASVPATVPFYERLGFR +ATGHVPVPGGEPLTCLRWEA-- +>GCF_003691675_PROKKA_01897 +MTSPDPAAP-----------------------RPRVHVLTLRPDGARE--DTARRVG--A +VLAEAFATDPYTLGLVPEDRRGPRLERKFTAAVRQGLR----AGADGAPLGAVDVAVDAA +DGTLLGAAVWTSPAAPRGVDVPGLLAGLPTAV-------AVHGRHTLALKRIQAACERAR +PAGRHWYLEEVGTVPSARGRGAASALVRHGQRRA--SGLPVHLEASVPATVPFYERLGFR +ATGHVPVPGGEPLTCLRWEA-- +>GCF_005280335_PROKKA_00567 +MTSPDRAAPPAPPTPAFGPAPEAPAADNAAPARRRLQVVSLRPEGLSE--DAVGRVA--E +LLAEAFAEDEFTLGLLPADRRAERLARMFALDVHDALRPARAAGGEAGPRGAVDVALDPE +DGTLLAAAVWDGPDAPRGTTVPGALAALPARL-------RVHGRRTWDAARTDAACERAR +PAAAHWHLTQLGTAPAARGRGAASALVRLRQRRAARAGVGIHLEASSAEAVPFYARLGFR +ETGTVRAHGTRDLTAMWWEAQA +>GCF_020097155_PROKKA_00492 +MSD---AAR-----------------------RPRPLVTSLRPAAAADHPDAAAVAGMAG +ALAEAFAEDPYTTSFLPPDRREERLRDYFDLLVRESLD----AAARGH--GAVDAAVDPR +TGEVLGVALWERPGAPR--PPAGLLGALRPAVPTAARRWRAFGRHALDHVRTVAACQAVR +PSEEHWYLLELGTVPSARGRGAGRALLERRRREARAAGVGIYLESSSAESTRFYEHVGFR +PHGTATVHGADDLTTMWWKD-- +>GCF_023573625_PROKKA_02128 +MTSPDPAAP-----------------------RPRVHVLTLRPGGARE--DTARRVG--A +VLAEAFATDPYTLGLVPEDRREARLERKFTAAVRHGLR----AGADGAPLGAVDVAVDAD +DGTLLGAAVWTSPAAPRGVDVPGLLAGLPTAV-------AVHGRHTLALKRIQAACERAR +PAGRHWYLEEVGTVPSARGRGAASALVRHGQRRA--AGLPVHLEASVPATVPFYERLGFR +ATGHVPVPGGEPLTCLRWEA-- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001725.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001725.fa new file mode 100644 index 0000000000000000000000000000000000000000..7e323a8827ed25c7a2823ae30d43bb5efd08756d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001725.fa @@ -0,0 +1,41 @@ +>GCF_002008305_PROKKA_02240 +MS-----------AAPPPPAFGTVLHHRAHGMAPGESISPPLVHASAFHLPGADPDGAPT +APGADVPFQYARWATPTWSALEAALGALEDADVAVVPSGMAAIAAVLLPLLHPGDRALLP +ADGYGPTRALAAEHLTPRGVHVDLVATQGLAHADLSGYDLVLVETPSNPGLRVADLADVA +ARAHANGRRDGAGALVVVDNTLLTPLGQRPLELGADVVVASDTKAVNGHTDALGGHVASR +DPQVMARVRGWRTLAGGILGTHEAWLIHRGLETLEVRFARMCASAQAVAELAAGHPAVRA +VVYPGLADHPDAEVVARQMTAAGGLVGLRFADAAAAERFIAAAQYVVPQTSFGGTHTAAE +RRARWGDDVPDGFVRLSVGVEPTAELLADLERAMTAAGGGPTA +>GCF_003691675_PROKKA_01942 +MS-----------AAPPPPAFGTVLHHRAHGMAPGESISPPLVHASAFHLPGADPDGAPT +APGADVPFQYARWATPTWSALEAALGALEDADVAVVPSGMAAIAAVLLPLLHPGDRALLP +ADGYGATRALAAEHLTPRGVHVDLVATQGLAHADLSGYDLVLVETPSNPGLRVADLADVA +ARAHANGRRDGAGALVVVDNTLLTPLGQRPLELGADVVVASDTKAVNGHTDALGGHVASR +DPQVMARVRGWRTLAGGILGTHEAWLIHRGLETLEVRFARMCASAQAVAELAAGHPAVRA +VVYPGLADHPDAEVVARQMTAAGGLVGLRFADAAAAERFIAAAQYVVPQTSFGGTHTAAE +RRARWGDDVPDGFVRLSVGVEPTAELLADLERAMTAAGGGPTA +>GCF_005280335_PROKKA_00505 +MPDSAARHSAARHDVPAPPPFGPVLHHRAHGMAPGDAISPPLVHASAFHLPGAGPDGAPA +EPAAQGGFQYARWGTPTWAALEAALGVLEDADVAVVPSGMAAIASVLLSHLRPGDRALLP +SDGYGATRALAAEHLSPIGVHVDLVPTPALASADLSAYDLVFVETPSNPGLRVADLADVA +ARAHANGRRGGAGALVVVDNTSLTPLGQRPLDLGADVVVASDTKALNGHSDALGGHVASR +DADVLARVRGWRTLTGAILGTHEAWLIHRGLETLEVRFARMCASALAVAELAAGHSAVRA +VAYPGLPDHPDAEVVARQTTAAGSVVGLEFADAAAAERFLAAARLVVPQTSFGGTHTSAE +RRARWGDDVPAGFVRLSVGVEPTAELLADVERALEAAG----- +>GCF_020097155_PROKKA_00441 +M------------ASPQPPAFGPVLHHRAHGMAPGDAISPPLVHASAFHLPGAGPDGAPV +APGADVAFQYARWGTPTWAALEAALGVLEDADVAVVPSGMAAIAAALLPVLRPGGRALLP +SDGYGATRALAAEHLVPAGVHVDFVSTPGLADAGFSAYDLVFVETPSNPGLRVADLADVA +ARAHANGRRDGKGALVVVDNTSLTPLGQRPLDLGADVVVASDTKALNGHTDALGGHVASR +DPELMTRVRGWRTLAGGILGTHEAWLIHRGLETLEVRFARMCASALAVAELAAGHPAVRA +VAYPGLPDHPDAAIVARQMTAAGGVVGLEFADAAAAERFIGAAAYVVAQTSFGGTHTAAE +RRARWGDDVPAGFVRLSVGVEPTAELLTDLARALDAAAG--PA +>GCF_023573625_PROKKA_02172 +MS-----------AAPPPPAFGTVLHHRAHGMAPGESISPPLVHASAFHLPGADPDGAPT +APGADVPFQYARWATPTWSALEAALGALEDADVAVVPSGMAAIAAVLLPLLHPGDRALLP +ADGYGPTRALAAEHLTPRGVHVDLVATQGLAHADLSGYDLVLVETPSNPGLRVADLADVA +ARAHANGRRDGAGALVVVDNTLLTPLGQRPLELGADVVVASDTKAVNGHTDALGGHVASR +DPQVMARVRGWRTLAGGILGTHEAWLIHRGLETLEVRFARMCASAQAVAELAAGHPAVRA +VVYPGLADHPDAEVVARQMTAAGGLVGLRFADAAAAERFIAAAQYVVPQTSFGGTHTAAE +RRARWGDDVPDGFVRLSVGVEPTAELLADLERAMTAAGGGPTA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001728.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001728.fa new file mode 100644 index 0000000000000000000000000000000000000000..670efe4c0826210a4a7e27f3ff1a67d62ac15423 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001728.fa @@ -0,0 +1,26 @@ +>GCF_002008305_PROKKA_02245 +M-TPRSLAGLALTVAALMSAFVLMAPTAPGLFVGVLTVGTFGFGPFYGEPSRQLVDRPWR +RDTRWRDLARRVRTDWLSRQLGAVGWNAAISRRITGRADLRRIRTAAVGSLVSHAASAGL +HAVAGVALAAVGHPVWGVVAVALGLVVHAWPALLQVSVLGRIDGLQTQIRGDQLLW---- +--- +>GCF_003691675_PROKKA_01947 +M-TPRSLAGLALTVAALMSAFVLMAPTAPGLFVGVLTVGTFGFGPFYGEPSRQLVDRPWR +RDTRWRDLARRVRTDWLSRQLGAVGWNAAISRRITGRADLRRIRTAAVGSLVSHAASAGL +HAVAGVALAAVGHPVWGVVAVALGLVVHAWPALLQVSVLGRIDGLQTQIRGDQLLW---- +--- +>GCF_005280335_PROKKA_00500 +M-TPRSLAGLALAVAALAAAFALMAPTAPGLFVGVLTAGTLGFGPFYGEPTRHLVDRPWR +RDRRWHELARRVRTDWLSRQLGAAGWNAAIRRRITGRADLRRIRTAAVGSLVSHAASVGL +HGIAALALAVVGHPGWGLLAVLLGLVVHAWPALLQVAVLGRIDGLQAQLRGDRLLW---- +--- +>GCF_020097155_PROKKA_00511 +MRIPAVCAAVAV-VTLLAWGFRQVVPASPGAYVAVLTAATVGFGPFYGVPTRAVVDLPWR +RLRRLRALAARAHTWWLARQLRVAGSDARIRRRIRSRADVLAFRREAVGRLLNHGLSAVL +HAAAGVALAAAGHPLWGVVAVVAGLLVHGWPGLLQVGVLGRVDELQATVQARRGVGGAAS +AGR +>GCF_023573625_PROKKA_02177 +M-TPRSLAGLALTVAALMSAFVLMAPTAPGLFVGVLTVGTFGFGPFYGEPSRQLVDRPWR +RDTRWRDLARRVRTDWLSRQLGAVGWNAAISRRITGRADLRRIRTAAVGSLVSHAASAGL +HAVAGVALAAVGHPVWGVVAVALGLVVHAWPALLQVSVLGRIDGLQTQIRGDQLLW---- +--- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001746.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001746.fa new file mode 100644 index 0000000000000000000000000000000000000000..045cf62f89ddbe73b8f5195d47602f8432e215f7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001746.fa @@ -0,0 +1,40 @@ +>GCF_002008305_PROKKA_02295 +MRPAPAHAATPSEPPTHA----------ADGAPSDAVTAPGAPAGRSADSAP----------------SGTLPAPGERGG +RFQLAGGLAAN----GPGRGTGSWAGPVALTGLLVALAAVVTVLQKSPCLLHGWGAPDVYYAGCYSDWAALYGGRGFAAD +PWAPFRAGSTFEYPVLMSVVGSVAAWITQALPFSPEQGTVVFWLVNLGFVVVLWAVVAVLTVRMAGRRWTDGLMVAVAPG +IVLAGTINWDLWAVALLACGMYAWSRGRSLTAGVLFGLGAAMKLYPLLILGPLLILAVRSRRWRPFLLAAGGTVAAWAAV +NVPLMAVNFQAWSVFFTFSGERGPGLSSVWHAWDVTAAQAGWAFVPEDSLTLLAYGTFAVCCLGIFVLGVRVRHTPRLAQ +LTFLVVAAFVLTNKVYSPQFVVWLIPLLALALPRWRDFWVWQTVEALHFFAVWMYLAKGVAETPPQHSMDDSVYVAAILA +HILAVLWLCGRVVWEMLHPAEDLVKRDHGGHPDADPLAGAYAGPAR-GRSG-RP-----------AAVQA +>GCF_003691675_PROKKA_01988 +MRPAPAHAATPSEPPTHA----------ADGAPCDAVADPGAPAGRSADSAP----------------SGALPAPGERGG +RFQLAGGLAAN----GPGRGTGSWAGPVALTGLLVALAAVVTVLQKSPCLLHGWGAPDVYYAGCYSDWAALYGGRGFAAD +PWAPFRAGSTFEYPVLMSVVGSVAAWITQALPFSPEQGTVVFWLVNLGFVVVLWAVVAVLTVRMAGRRWTDGLMVAVAPG +IVLAGTINWDLWAVALLACGMYAWSRGRSLTAGVLFGLGAAMKLYPLLILGPLLILAVRSRRWRPFLLAAGGTVAAWAAV +NVPLMAVNFQAWSVFFTFSGERGPGLSSVWHAWDVTAAQAGWAFVPEDSLTLLAYGTFAVCCLGIFVLGVRVRHTPRLAQ +LTFLVVAAFVLTNKVYSPQFVVWLIPLLALALPRWRDFWVWQTVEALHFFAVWMYLAKGVAETPPQHSMDDSVYVAAILA +HMLAVLWLCGRVVWEMLHPAEDLVKRDHGGHPDADPLAGAYAGPAR-GRSG-RP-----------AAVQA +>GCF_005280335_PROKKA_00441 +MRPAPAHAATPSEPPTHA----------VDG-PSWAGPDGRAEAGGSAVSAP-------PSRGPAAV-PAPVPAPGDRGG +RFQLPGGLAANRFTLGGRGGTGSWASPAALAGVLVALAAVVTVLQKAPCLLHGWGAPNVYYAGCYSDWAALYGGRGFAAD +PWAPFQAGSTFEYPVLMSLVGSVGAQLTQWLPFGAEHGTLVFWLVNLLFVVGLWAAVAVLTVRMAGRRWSDGLMVAVAPG +VILAGTINWDLWAVALLALGMYAWARERPLAAGVLIGLGAAMKIYPLLILGPLLILAVRSRRWRPFLLAAGGAVAAWAAV +NVPLMVANFEAWSVFFTFSGERGPGLSSVWHAWDVTAAQAGWAFVPEDSLTLLAYGAFAVCCLGIFVLGVRVRHTPRLAQ +LTFLVVAAFVLTNKVYSPQFVIWLIPLVALALPRWRDFWAWQTVEALHFFAVWMYLAKGASGSMPQHSMDDSVYVAAILA +HMLAVLWLCGRVVWEMLHPEDDLVRRDHTDLPGGDPLAGAY------------------------RSAQA +>GCF_020097155_PROKKA_00394 +MSSSPAPGAAPDDPPAPAPQARPDVPVGAHRAPRHALTTPPPGSAEGAPSAGSGAVESDEATPEGEVDPRVVPAPGDRGG +RFAIPGGLAAN----GRGRGTGAWAGPVALTALLVALGAIATVLQKSPCLLHGWGAPNVYYAGCYSDWAALYGGRGFAAD +PWAPFQAGSTFEYPVLMSLVASVGAQLTQWLPFPASVGTVVFWCVNLLFVVGLWAATAVLTVRTAGRRWTDGLMVAVAPG +IILAGTVNWDLWAVALMAWGMWVWLRGRPGWAGVLFGLGAATKLYPLLILGPLLILAVRSRRFGPFLKATGGAVAAWLAV +NLPLMLTHFESWKVFFTFSAERGPGLSSVWHAWDVVAAQAGWAAVPDERLGMYAYGAFAVCCLGIFVLGVVAKRPPRLAQ +LTFLVVAAFVLTNKVYSPQFVIWLIPLMALALPRWKDFWVWQTVEALHFFAVWMYLAKGASGSMPQHSMDDSVYVAAILA +HMLAVLWLCARVVLEILDPDDDLV-RGPGGDPARDP-EDPSAGPADPGMTGVRPVREAVAAGVGAASAQA +>GCF_023573625_PROKKA_02236 +MRPAPAHAATPSEPPTHA----------ADGAPCDAVADPGAPAGRSADSAP----------------SGTLPAPGERGG +RFQLAGGLAAN----GPGRGTGSWAGPAALTGLLVALAAVVTVLQKSPCLLHGWGAPDVYYAGCYSDWAALYGGRGFAAD +PWAPFRAGSTFEYPVLMSVVGSVAAWITQALPFSPEQGTVVFWLVNLGFVVVLWAVVAVLTVRMAGRRWTDGLMVAVAPG +IVLAGTINWDLWAVALLACGMYAWSRGRSLTAGMLFGLGAAMKLYPLLILGPLLILAVRSRRWRPFLLAAGGTVAAWAAV +NVPLMAVNFQAWSVFFTFSGERGPGLSSVWHAWDVTAAQAGWAFVPEDSLTLLAYGTFAVCCLGIFVLGVRVRHTPRLAQ +LTFLVVAAFVLTNKVYSPQFVVWLIPLLALALPRWRDFWVWQTVEALHFFAVWMYLAKGVAETPPQHSMDDSVYVAAILA +HMLAVLWLCGRVVWEMLHPAEDLVKRDHGGHPDTDPLAGAYAGPAR-GRSG-RP-----------AAVQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001776.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001776.fa new file mode 100644 index 0000000000000000000000000000000000000000..4abe28ea3e4e146b01734bf4be936616a38e18e1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001776.fa @@ -0,0 +1,33 @@ +>GCF_002008305_PROKKA_00073 +M-----------RHPAPLPAALLHGPFTAAQARAAGIDRNRLRRSDVERLARGLYRRREA +T-------PAAVERPAAGS---SPYRWSTPLSATQHELLLRLARHRATTVVSHQTAARAR +EIWLPERLDAGDGVHVSRPRDRGRLALPGVISHRTALPPADVERVRIGGLAW----HVTA +PPRLWVDLAALLDDDELVILGDHLVRRAKLSGGPGAAER--ARAALAQAAEASPSAHNRR +RRLRTAATLVRVGAHSPKETRLRLALTAAGLPEPALQLEARDPEFSLHHPATADLGYRQA +RVALHYDGGHHGADRQIDRDVQRNAAFERRGYRNITVSSSDARRGFTRVIVEVRRHLGDA +GDLSRKESEWGVNGTSERPLT +>GCF_003691675_PROKKA_02086 +M-----------RRPTPLPASLLDGPFTAAQARAAGIDHNRLRRSDVERLARGLYRRREA +A-------PAAVERPAAGS---SPYRWSTPLSATQHELLLRLARHRATTVVSHQTAARAR +EIWLPERLDAGDEVHVSRPRDRGRLALPGVTSHRTALPPADVERVRIGGLAW----YVTA +PPRLWVDLAALLDDDELVILGDHLVRRAELSGGPDAAER--TRAALTQAAETSPSAHNRR +RRLRTAATLVRVGAHSPKETRLRLALTAAGLPEPALQLEVWDPEFSLHHPATADLGYPQA +RVALHYDGGHHGADRQIDRDVQRNAAFERRGYRNITVSSSDARRGFTRVIVEVRRHLGDA +GGLSRKESEWGGDPASERHHA +>GCF_020097155_PROKKA_00261 +MERWPPHTDIMSRPPRDLPAVLRRGPFTTASALALGVPASRLRRSDVRRLRRGVLVWTGA +TDGGSTVDPALPPRPAAASGADTPWVLASRLTPSEQETLAGVLAAAPDATASHLTAARLT +GLWLPTRLAADRTLHVTRPPGTANSAPAGVRMHRRRPTSEGAQLVRGSGPPLDGPIPVTG +PARTWRDLASLLDLAELVVLGDRLV----CSSGPERADPLCSRAALVQAAARPGQRH--A +VLARDAAALVRDGAHSPPETRLRLALLDAGLPEPELQLEVWDPAFSRSRPATADLGWRRH +GVVLQYEGAGHDDPVQVRGDTLRDAAFQRRGVVVIRAAAADLAEGFRGTTALAEAALRRR +GWTPGRE-------------- +>GCF_023573625_PROKKA_00067 +M-----------RHPAPLPAALLHGPFTAAQARAAGIDLNRLRRSDVERLARGLYRRREV +T-------PAAVERPAAGS---SPYRWSTPLSATQHELLLRLARHRATTVVSHQTAARAR +EIWLPERLDAGDDVHVSRPRDRGQLSLPGVTSHRTALPPADVERVRIGGLAW----YVTA +PPRLWVDLSALLDDDELVILGDHLVRRAQLSGGPDAAER--TRAALAQAAEASPSAHNRR +RRLRTAATLVRVGAHSPKETRLRLALRAAGLPEPALQLEVWDPEFSLHHPATADLGYRQA +RVALHYDGGHHGADRQIDRDVQRNAAFERRGCRNITVSSSDARRGFTRVIVEVRRHLGDA +GDLSRKESEWGVNGTSERPLT + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001777.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001777.fa new file mode 100644 index 0000000000000000000000000000000000000000..f2aab0939dfea7d2af5c96f22fffb0db253e532d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001777.fa @@ -0,0 +1,17 @@ +>GCF_002008305_PROKKA_00083 +MRIMTVCLGNICRSPAAEAVLNRKLAEAGL-HDVEVTSAGTSDEHVGARPHHLTREVGGE +LGYEFPTVGVQLSADLVDEADLILVMDEANLADARRLATTDEQRDRIHLMGEFASDADSA +GVREVPDPYGYPRPQFEEMYRQIEDAADGVVAAIRDGRL +>GCF_003691675_PROKKA_02096 +MRIMTVCLGNICRSPAAEAVLNRKLAEAGL-DDVEVTSAGTSDEHVGARPHHLTREVGGE +LGYEFPTVGVQLSADLVDDADLILVMDEANLADARRLATTDEQRDRIHLMGEFASDADRA +GVREVPDPYGYPRPQFEEMYRQIEDAADGVVAAIRDGRL +>GCF_005280335_PROKKA_00309 +---MTVCLGNICRSPAAEAVLHRKLAEAGLADEVTVTSAGTADYHVGDRPHELTRAVGGE +LGYAFESVGVHLAAGHLDEADLVLVMDESNLADVRALAATDEQRAKVRMMGEFASDADTA +GVLEVPDPYGHPRAQFEDMYRQLEDAADGVVAAIRDGRL +>GCF_023573625_PROKKA_00077 +------------------------------------------------------------ +-------MGVQLSAELVDDADLILVMDEANLADTRRLATTDEQRDRIHLMGEFASDADSA +GVREVPDPYGYPRPQFEEMYRQIEDAADGVVAAIRDGRL + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001782.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001782.fa new file mode 100644 index 0000000000000000000000000000000000000000..b5e16c02174b8552e1619fbe5edfc0194cc2d0b2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001782.fa @@ -0,0 +1,37 @@ +>GCF_002008305_PROKKA_00145 +MAPVRRPSRPLALAAAVAVVAGFGAPHAALAQESAPAPDAPEVSSAVEDLSQPATTAEDA +RWNAARDALAAASADDPFYLPPTTLPSTPGALIRTEPTAFYLDPVRLVQVPAHATRIMYA +SQDAQGRPIAVTGTVLTPTAPWTGAGERPVIGYAVGTQGAADRCAPSRTLSTGVQYEGVG +ITSLLSRGHAVVVTDYEGLGTPGTHTYMVREAQAHAVLDAVRAAAQVAGSGVTATAPVAL +AGYSQGGGAAAAAAELAPDYAPELDLKGAYAGAPPADLVQVAGRIDGGLYAAFLLYAMAG +QLAAYDVDPATHLNETGLTALDGAAETCLAGSLAYAHLDSATLTHTGQDFPELVRSDAEL +AGILAEQRIGAQGRRPDVPVMIAHSVTDDVIPYRAGRDLGRRWCAEGARVRFDPLLTPTH +VGGHVASLPRMGAFLDATLADRWTADSCGWF +>GCF_003691675_PROKKA_02159 +MAPARRPSRPLALAAAVAVVAGFGAPHAALAQESAPAPDAPEVSSAVADLSQPATTAEDA +RWNAARDALAAASVDDPFYLPPAVVPATPGALIRSEPAAFYLDPVRLVQVPAHATRIMYA +SQDAQGRPVAVTGTVLTPTAPWTGGGERPVIGYAVGTQGAADRCAPSRTLSTGAQYEGVG +ITSLLSRGHAVVVTDYEGLGTPGTHTYMVREAQAHAVLDAVRAAAQVSGSGVTSTAPVAL +AGYSQGGGAAAAAAELASDYAPELDLKGAYVGAPPADLVQVADRIDGGLYAAFLLYAMAG +QLAAYDVDPATHLNETGLTALAGAAETCVAGSLAYAHLDSATLTHTGQDFPELVRSDAEL +AGILAEQRIGAPGRRPDVPVMIAHSVTDDVIPYRTGRDLGRRWCAEGARVRFDPLLTPTH +VGGHVASLPRMGAFLDATLADRWTADSCGWF +>GCF_005280335_PROKKA_00239 +MS-RRRRVRPLSTAAALAVVAGLCAP-GALAQDPVPAPDAPEVRSAVEDLSRPASPAEER +SWDAARAELAEDTAGDAFYRPPATIPARPGTLIRSEPSAFYLDPVKLIRVPARATRILYS +SVDAQGRPMAVSGTVLTPTAPWTGGGERPVIGYAVGTQGAADRCAPSRTLSTGEQYEGVG +ISSLLGRGHTVVVTDYEGLGTPGAHTYMVRESQAHAVLDSVRAAAQVDGAEVTASSPVAL +AGYSQGGGASAAAAELAPSYAPELDLKGAYAGAPPADLVQVADRIDGGSYSAFLLYAMSG +QLAAYDVDPAVYLNEHGRQVLTDAVETCVTDSGEHGSLDSSALTHTGQSFPQLVRTDPQL +AGILAEQKLGAEGRRPEVPVMIAHSLTDDVIPYRTGRELGLRWCAEGARVRFDPILTPTH +MGGYVAALPRMHSFLDAALADRWTPNSCGWF +>GCF_023573625_PROKKA_00153 +MA----PSRPLALAAAVAVVAGFGAPHAALAQESAPAPDAPEVSSAVADLSQPATTAEDA +RWNAARDALAAASADDPFYLPPATVPATPGALIRTEPTAFYLDPVRLVQVPAHATRIMYA +SQDAQGRPIAVTGTVLTPTAPWTGGGERPVIGYAVGTQGAADRCAPSRTLSTGVQYEGVG +ITSLLSRGHAVVVTDYEGLGTPGAHTYMVREAQAHAVLDAVRAAAQVSGSGVAATAPVAL +AGYSQGGGASAAAAELASEYAPELDLKGAYVGAPPADLVQVADRIDGGLYAAFLLYAMAG +QLAAYDVDPATHLNETGLTALAGAAETCMVGGLAYAHLDSATLTHTGQDFPELVRSDAEL +AGILAEQRIGAPGRRPDVPVMIAHSVTDDVIPYRTGRDLGRRWCAEGARVRFDPLLTPTH +VGGHVASLPRMGAFLDATLADRWTADSCGWF + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001788.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001788.fa new file mode 100644 index 0000000000000000000000000000000000000000..44919147ced94410efa1d927b547ca7795b9c3a9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001788.fa @@ -0,0 +1,37 @@ +>GCF_002008305_PROKKA_00201 +MDRTAPTP-PANALAPDLPEDIAREAIAFRRLLHGHPELDLHLPRTQAAVLERLEALRAE +AGEDAATGRPALETSVGRALSSVVVVLRGGAPLPEGARRPVVLLRGDMDALPVTEETGLE +YAPAVPGTMHACGHDLHTAGLYGALAWLVRRRGELTADVVAMFQPGEETGGGALHMIQEG +LLEAAGRPVDAAYAIHVSSGTYPRGVLRSRPGAIQAGCDDLVVTVHGRGGHGSVPHLAQD +PVPVAAEMVLALQSVVTRQFDAFDTVVATVGHLSAGTAANIIPDSATLALTLRTFSADAR +ARLRAAVERMVHGIAAAHGMSAQVRADCAFPVTANDADAVAFARGVVEDLYGADAYRELP +EPEPGSEDFSEVLQRVPGAYVLLGAVPEGVDPDEAPVNHSPQAVFDDAVVPRAAQVLAEL +ALRTAPVPAS +>GCF_003691675_PROKKA_02196 +MDRTAPTP-PANALAPDLPEDIAREAIAFRRLLHGHPELDLHLPRTQAAVLERLEALRAE +AGEDAATGRPALETSVGRALSSVVVVLRGGAPLPEGARRPVVLLRGDMDALPVTEETGLE +YAPAVPGTMHACGHDLHTAGLYGALAWLVRRRGELTADVVAMFQPGEETGGGALHMIQEG +LLEAAGRPVDAAYAIHVSSGTYPRGVLLSRPGAIQAGCDDLVVTVHGRGGHGSVPHLAQD +PVPVAAEMVLALQSVVTRQFDAFDPVVATVGHLSAGTAANIIPDSATLALTLRTFSADAR +ARLLSAVERLVHGIAAAHGMSAQVRTDCAFPVTANDPDAVAFVRGVVEDLYGADAYRELP +EPEPGSEDFSEVLQRVPGAYVLLGAVPEGMDPDEAPVNHSPQAVFDDAVVPRAAQVLAEL +ALRTAPGPAS +>GCF_005280335_PROKKA_00205 +M-----TPETADALAPRVPDGLAQDVIALRRDLHAHPELDLHLPRTQAAVLDRLAPLQER +AGQDARTGGPALEVSTGRELSSVVLVLRGAKPLPAGTRRPVVLLRGDMDGLPVTELTGLD +WAPPTPGTMHACGHDLHTAGLYGALAWLVERRDELAADVIGMFQPGEETDGGAARMIDEG +LLEAAGPHPDAAYAIHVYSGKYPHGALVSRTGAIQAGCDDLIVTVRGRGGHGSVPHLAQD +PVPVAAEMVLALQSLVARQFDAFDPVVATVGHLSAGSAANIIPDTATLAITLRTFSADAR +ERLVPAVRRMVDGIAAAHGMSAEVRADCAFPVTVNDGEKVDFARGVVEDLYGAEAWQELP +EPEPGSEDFSEVLVRVPGAYLLLGAVPPGVDPETAEGNHSPRAVFDDAVLPRAVEVLAEL +ALRTPPVPEG +>GCF_023573625_PROKKA_00203 +MDRTAPTP-PANALAPDLPEDIAREAIAFRRRLHGHPELDLHLPRTQAAVLERLEALRAE +AGEDAATGRPALETSVGRALSSVVVVLRGGAPLPEGARRPVVLLRGDMDALPVTEETGLE +YAPSVPGTMHACGHDLHTAGLHGALAWLVRRRGELTADVVAMFQPGEETGGGALHMIQEG +LLEAAGRPVDAAYAIHVSSGTYPRGVLISRPGAIQAGCDDLVVTVHGRGGHGSVPHLAQD +PVPVAAEMVLALQSVVTRQFDAFDPVVATVGHLSAGTAANVIPDSATLALTLRTFSADAR +ARLRAAVERMVHGIAAAHGMSAQVRTDCAFPVTANDADAVAFVRRTVEDLYGADAYRELP +EPEPGSEDFSEVLQRVPGAYVLLGAVPEGVAPDEAPVNHSPQAVFDDAVVPRAAQVLAEL +ALRTAPVSAS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001802.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001802.fa new file mode 100644 index 0000000000000000000000000000000000000000..7615794c00e1db1450e87e2b6af3f96d8dd31af7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001802.fa @@ -0,0 +1,29 @@ +>GCF_002008305_PROKKA_00327 +MKHRSLPLTAALAVAALGLTACGDSGSGGSGSSSAAGGDGSYTVGINQLVSHPALDGAAE +GFKEAFKDAGLDVTFEEQNAQGEQATVTSIASTFANDGDVDLVAAIATPAAQGTASAVKD +KPVVFMAVTDPQGAELVASDEAPGGNVTGVSDRNPVKEQLQLLKDVKPDATTVGIVYNSG +EANSKVQVDQAKEAGKELGLEVKEATITNSSEVQQGVQSLSGVDGIYVPTDNAVVSALET +VVGYGEEQRVPVISADIDSVERGALGTYGIDYTAHGKQAGEMAVKILKDGAKPAELPVGY +ADPANLQLVLNPKAAEAYGVEIPAELTDRADQLVEG +>GCF_003691675_PROKKA_00043 +MKHRSLPLTAALAVAALGLTACGDSGSGGSGSSSAAGGDGSYTVGINQLVSHPALDGAAE +GFKEAFKDAGLDVTFEEQNAQGEQATVTSIASTFANDGDVDLVAAIATPAAQGTASAVKD +KPVVFMAVTDPQGAELVASDEAPGGNVTGVSDRNPVKEQLQLLKDVKPDATTVGIVYNSG +EANSKVQVDQAKEAGKELGLEVKEATITNSSEVQQGVQSLSGVDGIYVPTDNAVVSALET +VVGYGEEQRVPVISADIDSVERGALGTYGIDYTAHGKQAGEMAVKILKDGAKPAELPVGY +ADPANLQLVLNPKAAEAYGVEIPAELTDRADQLVEG +>GCF_005280335_PROKKA_00008 +MKHRSLTLTAALAVTALGLTACGDSGDAG------AGGDEKYTVGINQLVSHPALDGARE +GFKEAFSDAGLEVTFEEQNAQGEQATVTSIASTFANDGDVDLVAAIATPAAQGTAAAVKD +KPVVFMAVTDPKGAELVASEEAPGGNVTGVSDRNPVQEQLQLLKDVNPDAKTVGIVYNSG +EANSAVQVEQAKEAGQELGLEIKEATVTNSSEVQQGVQSLSDVDGIYVPTDNAVVSALET +VVGFGEENDIPVISADIDSVDRGALGTYGIDYKAHGKQAGEMAVKILKDGANPGEIAVGF +ADPANLQLVLNPAAAEAYGVEIPAELSDEADRLVEG +>GCF_023573625_PROKKA_00334 +MKHRSLPLTAALAVAALGLTACGDSGSGGSGSSSAAGGDGSYTVGINQLVSHPALDGAAE +GFKEAFEDAGLDVTFEEQNAQGEQATVTSIASTFANDADVDLVAAIATPAAQGTASAVKD +KPVVFMAVTDPKGAELVASDEAPGGNVTGVSDRNPVKEQLQLLKDVKPDATTVGIVYNSG +EANSKVQVDQAKEAGKELGLEVKEATITNSSEVQQGVQSLSGVDGIYVPTDNAVVSALET +VVGYGKEQRVPVISADIDSVERGALGTYGIDYTAHGKQAGEMAVKILKDGAKPAELPVGY +ADPANLQLVLNPKAAEAYGVEIPAELTDRADQLVEG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001818.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001818.fa new file mode 100644 index 0000000000000000000000000000000000000000..441a85cdbcb58af0f97d5a118d7e18a6a22838f9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001818.fa @@ -0,0 +1,32 @@ +>GCF_002008305_PROKKA_00577 +MAAAVALVPIGYLFLRTAQGGFGPWLDAVVSPRVGALAATSLALTAVVTALCLVIGVGAAWLVTRTDTPGRGLLAVLLAL +PLAVPSYVAAFTWVSVSDLLPGVEAGRFEGFWAAVTVMTLYTYPYVYLPVAAALSRIDPGQEDVARSLGRGPAATLFTVT +LAQVRPAIAGGALLVALYVLSDFGAVAILRLDTFTRAIFTALEVGFNRQLALTLATVLVLLTVLVLWGESRTRRADDGVR +SGRTVRRVSVHRLGRSRWVGTGLLAVVTGAALGVPAVSLVRWMGEGTSLSAVRDRWLDAVSGSVVLAGAGAALTLALALP +IGILAARHPGRVSRIAERAAFLAHGLPGVVVGLSLVFLGVSLVPALYQTTWMVAFAYATLFLPLAVTSVAGAVAQSSPAL +EEAARSLGSSGAEVLRRVTLPLALPGVGAGVALVALTAMKELPATLLLRPTGMDTLATRLWNATSVGRYAEAAPYALTLV +LLAAVPTWVVVHRTGIVAAVRGRSSAPSTPNEVSE +>GCF_003691675_PROKKA_00309 +MAAAVALVPIGYLFLRTAQGGFGPWLDAVVSPRVGALAATSLALTAVVTALCLVIGVGAAWLVTRTDTPGRGLLAVLLAL +PLAVPSYVAAFTWVSVSDLLPGVEAGRFEGFWAAVTVMTLYTYPYVYLPVAAALSRIDPGQEDVARSLGRGPAATLFTVT +LAQVRPAIAGGALLVALYVLSDFGAVAILRLDTFTRAIFTALEVGFNRQLALTLATVLVLLTVLVLWGESRTRRADDGVR +SGRTVRRVSVHRLGRSRWVGTGLLAVVTGAALGVPAVSLVRWMGEGTSLSAVRDRWLDAVSGSVVLAGAGAALTLALALP +IGILAARHPGRVSRIAERAAFLAHGLPGVVVGLSLVFLGVSLVPALYQTTWMVAFAYATLFLPLAVTSVAGAVAQSSPAL +EEAARSLGSSGAEVLRRVTLPLALPGVGAGVALVALTAMKELPATLLLRPTGMDTLATRLWNATSVGRYAEAAPYALTLV +LLAAVPTWVVVHRTGIVAAVRGRSSAPSTPNEVSE +>GCF_005280335_PROKKA_02356 +MAAAVAVVPIGYLFLRTAQGGFGPWLDAVVSPRVGALAATSLALTAVVTALCLVIGVGAAWLVTRTDTPGRGLLAVLLAL +PLAVPSYVAAFTWVSVSDLLPGVEAGRFEGFWAAVTVMTLYTYPYVYLPVAAALSRIDPGQEDVARSLGRGPAATLFTVT +LAQVRPAIAGGALLVALYVLSDFGAVAILRLDTFTRAIFTALEVGFNRQLALTLATVLVLLTVLVLWGESRTRRADDGVR +SGRTVRRVSVHRLGRSRWVGTGLLAVVTGAALGVPAVSLVRWMGEGTSLSAVRDRWLDAVSGSVVLAGAGAALTLALALP +IGILAARHPGRVTRIAERAAFLAHGLPGVVVGLSLVFLGVSLVPALYQTTWMVAFAYATLFLPLAVTSVAGAVAQSSPAL +EEAARSLGSSGAEVLRRVTLPLALPGVGAGVALVALTAMKELPATLLLRPTGMDTLATRLWNATSVGRYAEAAPYALTLV +LLAAVPTWVVVHRTGIVAAVRGRSSAPSTPNEVSE +>GCF_023573625_PROKKA_00578 +MAAAVALVPIGYLFLRTAQGGFGPWLDAVVSPRVGALAATSLALTAVVTALCLVIGVGAAWLVTRTDTPGRGLLAVLLAL +PLAVPSYVAAFTWVSVSDLLPGVEAGRFEGFWAAVTVMTLYTYPYVYLPVAAALSRIDPGQEDVARSLGRGPAATLFTVT +LAQVRPAIAGGALLVALYVLSDFGAVAILRLDTFTRAIFTALEVGFNRQLALTLATVLVLLTVLVLWGESRTRRADDGVR +SGRTVRRVSVHRLGRSRWVGTGLLAVVTGAALGVPAVSLVRWMGEGTSLSAVRDRWLDAVSGSVVLAGAGAALTLALALP +IGILAARHPGRVSRIAERAAFLAHGLPGVVVGLSLVFLGVSLVPALYQTTWMVAFAYATLFLPLAVTSVPGAVAQSSPAL +EEAARSLGSSGAEVLRRVTLPLALPGVGAGVALVALTAMKELPATLLLRPTGMDTLATRLWNATSVGRYAEAAPYALTLV +LLAAVPTWVVVHRTGIVAAVRGRSSAPSTPNEVSE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001841.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001841.fa new file mode 100644 index 0000000000000000000000000000000000000000..e370598729e6aafabd6ea8db61f13b33675f3631 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001841.fa @@ -0,0 +1,36 @@ +>GCF_002008305_PROKKA_00958 +MR------------PAAPATTGARGPRPSRVAAQPEPEAAVRRGTWASVLITVGSWGVGWLPMTPDSVFSGTTLLNPLRV +YLPGVLLSTVLLAAGSLLLVRSWLELGRALRGRWEEHGRLVARAAWWWSAPLMLALPIFSRDVFSYLQQGRLLASGLDPY +SQGVSALPGWFMQGADSIWAESPSPYGPLFLLFAETTWRATGGNIELSVTAFRLLALAGLALCLWAVPRLAAVAGRCGPW +ATWVAVANPLFLLYMIAGAHNDALMSGLMLAGILLMVRLPRRRVHALWGIVLIALSVAIKPLTALVLPFVALLLPTGWAR +FRAADPRLRRRDRLGPWFTTAVISLAVLTILGAGSGLWFGWVPAMLTSGDAAFPYAPVGLLGLLLGAVVEAVTPLGARDV +AAAFYTVMTVSALGFTAWLALRRRPLDPVFSAAAVLVVAVATAPIVQPWYLLWVLPLLACALRPLPWGADHPRWLGWVTA +LAVLLLTGVGVVDQLSVAQWLPVLAVRVFTLVLMLAGIGWIIHRDPVTAPLFPGRRRPPLEVVEPRA------AAASPTP +PEAGVPPDAPPDGPPSTAAHPASSSTRIPQERP +>GCF_003691675_PROKKA_00671 +MR------------PAAPATTGARGPRPSRVAAQPEPEAAVRRGTWASVLITVGSWGVGWLPMTPDSVFSGTTLLNPLRV +YLPGVLLSTVLLAAGSLLLVRSWLELGRALRGRWEEHGRLVARAAWWWSAPLMLALPIFSRDVFSYLQQGRLLASGLDPY +SQGVSALPGWFMQGADSIWAESPSPYGPLFLLFAETTWRATGGNIELSVTAFRLLALAGLALCLWAVPRLAAVAGRCGVW +ATWVAVANPLFLLYMIAGAHNDALMSGLMLAGILLMVRPPRRRVHALWGIVLIALSVAIKPLTALVLPFVALLLPTGWAR +FRAADPRLRRRDRLGPWFTTAVISLAVLTILGAGSGLWFGWVPAMLTSGDAAFPYAPVGLLGLLLGAVVEAVTPLGARDV +AAAFYTAMTVSALGFTAWLALRRRPLDPVFSAAAVLVVAVATAPIVQPWYLLWVLPLLACALRPLPWGADHPRWLGWVTA +LAVLLLTGVGVVDQLSVAQWLPVLAVRVFTLVLMLAGIGWIIHRDPVTAPLFPGRRRPPLEVVEPRA------AAASPTP +PEAGVPPDAPPDGPPSTAAHPASSSTRIPQERP +>GCF_020097155_PROKKA_01881 +MTLAVDGARRDDGGPSGRGSRALNGP-----AAAPEPAAAVREGLWAALAVMVASWGVGWQPMTPLSVFSGSTLLVPLRT +GLAGVLLCAVLLAVGVFALVRAWLRLGRSLQGRWTADGHLAARAALFWSLPLLAALPIFSRDVFSYLQQGRLVALGLDPY +EDGISRLPGWFMHGADSIWAESPSPYGPLFLLSAEGIWRLTGGQVELSVAAFRLLALAGLALCLWAVPRLAAAAGREPAW +AVWVSVANPLFLLYMVAGAHNDALMTGLLLAGAALLVRVGRRRVVALAGLVLVALSVAIKPLTALTLPFLAMLLPGGWSR +FRVGARRLGRVERIGPWITAAVIAAAVLTVLGAGTGLWFGWVRAMTTSGDAAFPYAPVGLLGLGLGWAVDLVSDVPARQA +AGWFYSAMTCAALAFTAWMALRRSPREPLVASAAVLVVAIVTAPIIQPWYLLWFLPLLACAPRPLPGVVDHPRWLGWVLT +ALVLALCGVGVVDQISVAQWLPLGLVRVVAALACLVAAWALVRRDPSTAVLFPRRRRPPDETIEPRGRPAPRRALAAPTT +PTAPV------------------------QE-- +>GCF_023573625_PROKKA_00904 +MR------------PAAPATTGARRPRPTRAAAQPEPGAAVRRGTWASVLITVGSWGVGWLPMTPDSVFSGTTLLNPLRV +YLPGVLLSTVLLAAGSLLLVRSWLELGRALRGRWEEHGRLVAHAAWWWSAPLMLALPIFSRDVFSYLQQGRLLASGLDPY +SQGVSALPGWFMQGADSIWAESPSPYGPLFLLFAETTWRATGGSIELSVTAFRLLALAGLALCLWAVPRLAAVAGRCGPW +ATWVAVANPLFLLYMIAGAHNDALMSGLMLAGILLMVRPPRRRVHALWGIVLIALSVAIKPLTALVLPFVALLLPTGWAR +FRAADPRLRRRDRLGPWFTTAVISLAVLTILGAGSGLWFGWVPAMLTSGDAAFPYAPVGLLGLLLGAVVEAVTPLGARDV +AAAFYTVMTVSALGFTAWLALRRRPLDPVFSAAAVLVVAVATAPIIQPWYLLWVLPLLACALRPLPWGADHPRWLGWVTA +LAVLLLTGVGVVDQLSVAQWLPVLAVRVFTLVLMLAGIGWIIHRDPVTAPLFPGRRRPPLEVVEPRA------EAASSTP +PEAGVPPDAPPDGPPSTAAHPASSSTRIPQERP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001842.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001842.fa new file mode 100644 index 0000000000000000000000000000000000000000..81348353b94e575b580c29d9b06352877b337cd5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001842.fa @@ -0,0 +1,17 @@ +>GCF_002008305_PROKKA_00996 +MT-PDQPETGGATEQGRFGDEPWRPERETRAQRQWRPGTRRRRRSVRALFTSTILMLEAV +LIFFLGLMLFGMHRDEPGAWWFVAGYSALAVVAVLTCALVRKPVGIAIGWAIQAVLLASG +FWEYSMFVVGALFALTWAYAVIKGGAMDVENAQRDRLEAAWEAEHGR------ +>GCF_003691675_PROKKA_00710 +MT-PDQPETGGATEQGRFGDESWRPARETRAQRQWRPGTRRRRRSVRALFTSTILMLEAV +LIFFLGLMLFGMHRDEPGAWWFVAGYSALAVVAVLTCALVRKPVGIAIGWAIQAVLLASG +FWEYSMFVVGALFALTWAYAVIKGGAMDVENAQRDRLEAAWEAEHGR------ +>GCF_020097155_PROKKA_01840 +MSGPTEPRPGRPADE-RFGAEDWRPARETKTQRAWRPGQRKRARSVRAMFASTVLCLEAV +LLFFLGMTLFGLNRGADHAPWVAVAFTALAAVAVLDCALVRKPLGVAIGWAIQAVLIASG +FWEYSMFVIGPLFALTWWYAITKGDQIDRENAARARAQAAWEASHPEEAGPRT +>GCF_023573625_PROKKA_00939 +MT-DDQPETGGATEQGRFGDEPWRPARETRAQRQWRPGTRRRRRSVRALFTSTILMLEAV +LIFFLGLMLFGMHRDEPGAWWFVAGYSALAVVAVLTCALVRKPVGIAIGWAIQAVLLASG +FWEYSMFVVGALFALTWAYAVIKGGAMDVENAHRDRLEAAWEAEHGR------ + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001843.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001843.fa new file mode 100644 index 0000000000000000000000000000000000000000..9d7510c617986e5f20a64fb15ed36989ca1d0d85 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001843.fa @@ -0,0 +1,33 @@ +>GCF_002008305_PROKKA_01010 +MSRTDAPIRTALIGYGFAGKTFHVPLLHATEGLALTHVVSSRPDAVHADLPDVVVVPDVD +KLLARHDVDLVVIAAPNDQHAPLARTALRAGRHVVVDKPFTLSLAEARELRDLAVETGRV +LRVFQNRRFDSDFLGIAELVRSGRLGDVVHLESRIDRFRPTVRDRWREAAVPGGGIWFDL +GPHLVDQALLLFGVPERVDADLAALRPGAPVEDWAHCVLQYPGRRVVLQASMLVAGGSPR +FAVHGTRGSAVKELPDRQEVQLRAGLLPGAEGWGVDPDPILLHDGEGNTERVPAPIGAQQ +RSYAGVRDAILGRASSDAATPDQAVAVMAVLEAAVASAREGRAVEPALTAAERAAYPGVS +PAPTAAERHHRSAEPR +>GCF_003691675_PROKKA_00724 +MSRTDAPIRTALIGYGFAGKTFHVPLLHATEGLALTHVVSSRPDAVHADLPDVVVVPDVD +KLLARHDVDLVVIAAPNDQHAPLARTALRAGRHVVVDKPFTLSLAEARELRDLAVETGRV +LRVFQNRRFDSDFLGIAELVRSGRLGDVVHLESRIDRFRPTVRDRWREAAVPGGGIWFDL +GPHLVDQALLLFGVPERVDADLAALRPGAPVEDWAHCVLQYPGRRVVLQASMLVAGGSPR +FAVHGTRGSAVKELPDRQEVQLRAGLLPGAEGWGVDPDPILLHDGEGNTERVPAPIGAQQ +RSYAGVRDAILGRASSDAATPDQAVAVMAVLEAAVASAREGRAVEPALTAAERAAYPGVS +PAPTAAERHHRSAEPR +>GCF_005280335_PROKKA_01879 +MPPTDAPIRTALIGYGFAGKTFHVPLLHATDGLALTHVVSSRPDAVHADLPDVVVVPDVD +ALLARHDVDLVVIAAPNDQHAPLARTALGAGRHVVVDKPFALSLAEARELRDLAAATGRV +LRVFQNRRFDSDFLGIAELVRSGRLGDVVHLESRIDRFRPTVRDRWREAAVPGGGIWFDL +GPHLVDQALLLFGVPDRVDADLAALRPGAPVEDWAHCVLQYPGRRVVLQASMLVAGGSPR +FAVHGTRGTAVKELPDQQEAQLRAGLLPGAEGWGVDPDPILLHDGEGNIERAPAPTGAQQ +RSYAGVRDAILGRPNGDAATPDQAVAVMAVLEAAVASAREGRAVKPALTAVERAAYPGVS +LAPTAAERHHRSAAAR +>GCF_023573625_PROKKA_00953 +MSRTDAPIRTALIGYGFAGKTFHVPLLHATEGLALTHVVSSRPDAVHADLPDVVVVPDVD +ALLAWHDVDLVVIAAPNDQHTPLARAALRAGRHVVVDKPFTLSLAEARELRDLAAETGRV +LRVFQNRRFDSDFLGIAELVRSGRLGDVVHLESRIDRFRPTVRSRWREASVPGGGIWFDL +GPHLVDQALLLFGVPERVDADLAALRPGAPVEDWAHCVLQYPGRRVVLQASMLVAGGSPR +FAVHGTRGTAVKELPDQQEAQLRAGLLPGAEGWGVDPDPILLHDGEGNTERVPAPTGAQQ +RSYTGVRDAILGRPNGDAATPDQAVAVMAVLEAAVASAREGRAVEPALTAVERAAYPGVS +PAPTAAERHHRSAAAR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001872.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001872.fa new file mode 100644 index 0000000000000000000000000000000000000000..d268f13e48286d22f4c7b111e8b90076e45c3bf1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001872.fa @@ -0,0 +1,37 @@ +>GCF_002008305_PROKKA_01477 +MVGSFLVAIVTGTGALLLPASYQGRAPTPLEAAFTATSATTVTGLGVVDTQTFWTPLGQL +VILTLIKLGGLGVMTFTSLLGLVILRRLGLTQRLDAAASTRAEGIGDLPRVLRALILYST +AVEASVALLLSLRFWLGAGMSPGQALWQGVFHAVSAFNNAGFALFSDNLMGFVSDPFICL +PIAAAIILGGLGLPVVLTLRRDLRRPERWNLTVRLVLVGTAVLLVGGTLMYLVLEWSNPR +TLGGLDPASRVLAAFFQSVTTRTAGFNTLDYGQMHPVTLFATDVLMFIGGGPAGTASGVK +ITTASVLLFIVLAEIRGEGAVHAFGRRLSRTTHREAITVIMLSATAIAVATMALMGLSSF +TTDQILFECVSAFSTVGLSTGITAQLPPAAQGILMLLMFVGRIGPATVAGSLALTDRTRH +FEYPKERPLIG +>GCF_003691675_PROKKA_01209 +MVGSFLVAIVTGTGALLLPASYQGRAPTPLEAAFTATSATTVTGLGVVDTQTFWTPLGQL +VILTLIKLGGLGVMTFTSLLGLVILRRLGLTQRLDAAASTRAEGIGDLPRVLRALILYST +AVEASVALLLSLRFWLGAGMSPGQALWQGVFHAVSAFNNAGFALFSDNLMGFVSDPFICL +PIAAAIILGGLGLPVVLTLRRDLRRPERWNLTVRLVLVGTAVLLVGGTLMYLVLEWSNPR +TLGGLDPASRVLAAFFQSVTTRTAGFNTLDYGQMHPVTLFATDVLMFIGGGPAGTASGVK +ITTASVLLFIVLAEIRGEGAVHAFGRRLSRTTHREAITVIMLSATAIAVATMALMGLSSF +TTDQILFECVSAFSTVGLSTGITAQLPPAAQGILMLLMFVGRIGPATVAGSLALTDRTRH +FEYPKERPLIG +>GCF_020097155_PROKKA_01325 +MVGSFLVAIVTGTGALLLPASYQGRAPTPLEAAFTATSATTVTGLGVVDTQTFWTPLGQV +VILALIKLGGLGVMTFTSLLGLVILRRLGLTQRLDAAASTRAEGIGDLPRVLQALILYST +AVEASVALLLSLRFWLGAGMSPGQALWQGIFHAVSAFNNAGFALFSDNLMGFVSDPFICL +PIAAAIILGGLGLPVVLTLRRHLRRPERWNLTVRLVLVGTAVLLVGGTLMYLVLEWSNPR +TLGGLDPASRVLAAFFQSVTTRTAGFNTLDYGQMHPVTLFGTDVLMFIGGGPAGTASGVK +ITTASVLLFIVLAEIRGEGAVHAFGRRLSRTTHREAITVIMLSATAIAVATMAIMGLSSF +TTDQILFECVSAFGTVGLSTGITAQLPPTAQGILMLLMFVGRIGPATVAGSLALTDRTRH +FEYPKERPLIG +>GCF_023573625_PROKKA_01427 +MVGSFLVAIVTGTGALLLPASYQGRAPTPLEAAFTATSATTVTGLGVVDTQTFWTPLGQL +VILTLIKLGGLGVMTFTSLLGLVILRRLGLTQRLDAAASTRAEGIGDLPRVLRALILYST +AVEASVALLLSLRFWLGAGMSPGQALWQGVFHAVSAFNNAGFALFSDNLMGFVSDPFICL +PIAAAIILGGLGLPVVLTLRRDLRRPERWNLTVRLVLVGTAVLLVGGTLMYLVLEWSNPR +TLGGLDPASRVLAAFFQSVTTRTAGFNTLDYGQMHPVTLFATDVLMFIGGGPAGTASGVK +ITTASVLLFIVLAEIRGEGAVHAFGRRLSRTTHREAITVIMLSATAIAVATMALMGLSSF +TTDQILFECVSAFSTVGLSTGITAQLPPAAQGILMLLMFVGRIGPATVAGSLALTDRTRH +FEYPKERPLIG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001882.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001882.fa new file mode 100644 index 0000000000000000000000000000000000000000..c7fc444b1e41608682aa22473c11e88a10b7259c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001882.fa @@ -0,0 +1,17 @@ +>GCF_002008305_PROKKA_01669 +MTGHDHPRPESISAAVDEQMLADFLNQHLLGSRSGVKAFRAAEQTWAGTPQEAALRRLGD +AVQDDQDRLEALIGELGLRTPLVDRAAGAAAEVGGRLNPVNALRTRGSGWTQIELDLLQG +MLQAKSAMWDVLEQLAPHLPAVDAAEMQALRQRTADQQREVQRITSATLEGRFLAG +>GCF_003691675_PROKKA_01374 +MTGHEHPRPESTSAAVDEQMLEDFPNQHLLGSRSGVKAFRAAEQTWAGTPQEAALRRLGD +AVQDDQDRLEALIGELGLRTPLVDRAAGAAAEVGGRLNPVNALRTRGSGWTQIELDLLQG +MLQAKSAMWHVLEQLAPHLPAVDAAEMQALRQRAADQQREVQRITSATLEGRFLAG +>GCF_005280335_PROKKA_01225 +MTGHEHPRPEPLSAAVDEQMLEDFLNQHLLGSRSGVKAFRAAEQTWAGTPQEDALRRLGD +AVQDDQERLEALIGELGLRTPLVDRAAGAAAEVGGRLNPVNALRTRGSGWTQIELDLLQG +MLQAKAAMWHVLEALAPHEPVLDAGEMAALYERAQDQQRAVQRIAEDTLLERFLR- +>GCF_023573625_PROKKA_01599 +MTGHEHPRPESTSAAVDEQMLADFLNQHLLGSRSGVKAFRAAEQTWAGTPQEAALRRLGD +AVQDDQDRLEALIGELGLRTPLVDRAAGAAAEVGGRLNPVNALRTRGSGWTQIELDLLQG +MLQAKSAMWHVLEQLAPHLPAVDAAEMHALRQRTGDQQREVQRITSATLEGRFLAG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001898.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001898.fa new file mode 100644 index 0000000000000000000000000000000000000000..c66d3aaa52b46e48c42f99f21eef2757451bb901 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001898.fa @@ -0,0 +1,25 @@ +>GCF_002008305_PROKKA_01913 +MTTTTPLPPLDGATTPAQARERFRAGLVRPTSGIADGYAQANLVSIPQDHAYDVLLFAQR +NPQALPLLGVFEAGEVNGPALDGDVRTDVPQYVVYRDGVETDRPTDLLDVWRDDLVTFVI +GCSFTFESALVAEGIRMAHQDAGVNVPMYRTTRRCASAGRLSGPLVVSMRPLPADRVADA +VRITSRYPAVHGAPVHVGDPAGLGITDLSAPDFGDAVEVPQGHLPVFWACGVTPQAAIME +SRPPLAITHAPGHMLITDLPDRMFQVP +>GCF_003691675_PROKKA_01609 +MTTTTPLPPLDAATTPAQARERFRAGLVRPTSGIADGYAQANLVSIPQDHAYDVLLFAQR +NPKALPLLGVFEAGEVNGPALDGDVRTDVPQYVVYRNGVETDRPTDLLDVWRDDLVTFVI +GCSFTFESALVAEGIRMAHQDAGVNVPMYRTTRRCASAGRLSGPLVVSMRPIPADRVADA +VRITSRYPAVHGAPVHVGDPAGLGITDLSAPDFGDAVEVPQGHLPVFWACGVTPQAAIME +SRPPLAITHAPGHMLITDLPDRMFQVP +>GCF_020097155_PROKKA_00882 +------MTALHGGTGPAEARERFRAGLVRPTAGIADGFAQANLMVVPQDLAWDVLLFAQR +NPKALPLLGVLEAGEVRGPAVDGDVRTDVPQYVVYEDGVPVGRPTDLLEVWRDDLVTFLI +GCSFTFESALVAEGIRIAHQDAGVNVPMYRTTRRCVPAGRLSGPLVVSMRPIPADRVADA +VRITSRYPSVHGAPVHVGDPAALGIADLSAPDFGDAVEVPPGHLPVFWACGVTPQAAVME +SRPPLAISHAPGHMLITDIPDRTFQIP +>GCF_023573625_PROKKA_01833 +MTTTTPLPPLDGATTPAQARERFRAGLVRPTSGIADGYAQANLVSIPQDHAYDVLLFAQR +NPQALPLLGVFEAGEVNGPALDGDVRTDVPQYVVYRDGVETDRPTDLLDVWRDDLVTFVI +GCSFTFESALVAEGIRMAHQDAGVNVPMYRTTRRCASAGRLSGPLVVSMRPLPADRVADA +VRITSRYPAVHGAPVHVGDPAGLGITDLSAPDFGDAVEVPQGHLPVFWACGVTPQAAIME +SRPPLAITHAPGHMLITDLPDRMFQVP + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001921.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001921.fa new file mode 100644 index 0000000000000000000000000000000000000000..5449bf8fadc14bf5242ef5c052725afed731eda8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001921.fa @@ -0,0 +1,37 @@ +>GCF_002008305_PROKKA_02097 +MH-------------------RPSRSSTAAPAFAPSAPAPTAAPAFAPSVRSQVPPFTVM +SILGRVAALRAAGHDVVSLCAGEPGGGAPPAVDAAAAAVHASGRALTYTPALGLPELRAA +VAGHYRRWYGLDVRPEQVAITTGSSGAFMLGFLAAFSPGDRVLLPRPGYPAYRNILTALG +VEVVDVDVDAGTRYQPTVAHLEAALAEGPVAGLVLASPANPTGTMVSAAELAELARWCEE +RGVRLVSDEIYHGIVH-----TDG------------------------QGPGACAWRTSR +TALVVSSFSKYWGMPGWRLGWMLMPDDLATAVDGLAGSVALCPPAAAQEAAVHAFTEESY +AFCAEQAGGFTATRGVVLAALPRLAWADAAPADGAFYLWARLASGMLAEFGSAVGYCAAL +LEEAGVALTPGDDFDAVHGPESVRLSFAAGPDAVHEALERIAAWHAARGLA +>GCF_003691675_PROKKA_01804 +MR-------------------RPSRSSTADPA-STAAPAPTATPAFAPSARSQVPPFTVM +SILGRVAELRAAGHDVVSLCAGEPGGGAPPAVDAAAAAVHASGRAFTYTPALGLPELRTA +VAGHYRRWYGLDVRPEQVAITTGSSGAFMLGFLAAFPPGDRVLLPRPGYPAYRNILTALG +VEVVDVDVDAGTRYQPTVAHLEAALAEGPVAGLVLASPANPTGTMVSADELAELARWCEE +RGVRLVSDEIYHGIVH-----TDG------------------------EGLGACAWRTSR +TALVVSSFSKYWGMPGWRLGWMLMPDDLAAAVDGLAGSVALCPPAAAQEAAVHAFSEESY +AFCAEQAGGFTATRGVVLAALPRLGWADAAPADGAFYLWARLAPGMLAEFGSAVGYCAAL +LEEAGVALTPGDDFDAVHGPESVRLSFAAGPDAVHEALERIAAWHAARGLA +>GCF_005280335_PROKKA_00682 +MDPQPRLAPGTHHDVAALAPASPVADAAPEDQAAPGDPASPVAPAFAPSARSQVPPFTVM +TILGRVAELRAAGRDVISLCAGEPGGGAPPTVSAAAAEVHASGSPLTYTPALGLPELRAA +VAGHYRRWYGIDVRPEQVAITTGSSGAFMLGFLAAFSPGDRVVLPRPGYPAYRNILAALG +CEVVEVGVDASTRYQPTVAHLEAALAEGPVAGLVLASPSNPTGTMVDADELAALASWCEA +HGVRLVSDEIYHGIVHPRSGDDDGGPAGGGAAGGAPGASGAEGSRFPHESVGACAWATSR +TAMVISSFSKYWGMPGWRLGWMLMPEDLAGAIDGLAGSVALCPPAAAQRAAVEAFGEDAY +AFCEEQAGGFTATRGVVLAALPRLGWADAAPADGAFYLWARLGERQLAEFGDAVAYCTAL +LEEAGVALTPGADFDGVHGGEFVRMSYAADAGAVAEALERIAAWHAARGLA +>GCF_023573625_PROKKA_02037 +MR-------------------RPSRSSTADPA-STAAPAPTATPAFAPSARSQVPPFTVM +SILGRVAELRAAGHDVVSLCAGEPGGGAPPAVDAAAAAVHASGRAFTYTPALGLPELRTA +VAGHYRRWYGLDVRPEQVAITTGSSGAFMLGFLAAFPPGDRVLLPRPGYPAYRNILTALG +VEVVDVDVDAGTRYQPTVAHLEAALAEGPVAGLVLASPANPTGTMVSADELAELARWCEE +RGVRLVSDEIYHGIVH-----TDG------------------------EGLGACAWRTSR +TALVVSSFSKYWGMPGWRLGWMLMPDDLAAAVDGLAGSVALCPPAAAQEAAVHAFSEESY +AFCAEQAGGFTATRGVVLAALPRLGWADAAPADGAFYLWARLAPGMLAEFGSAVGYCAAL +LEEAGVALTPGDDFDAVHGPESVRLSFAAGPDAVHEALERIAAWHAGRGLA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001924.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001924.fa new file mode 100644 index 0000000000000000000000000000000000000000..2b64c79089f13929dd2a82163ad7330d8fab3947 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001924.fa @@ -0,0 +1,21 @@ +>GCF_002008305_PROKKA_02108 +MAFAALSRSARLAGLSAAALLALTACGGQDSSDADASASTTAPASASAQGAESSSASASS +LSAAPADYEAGTCFTAPLGARDLSSFETTDCEGAHTAEYLWAVPAVAEGEEADPAAAQTC +TAQAQRLSEEKEDQLNGAVLTSSELGNYGTDEKHCVVYGVSGEWEGQIVDPEITLETASA +DA--- +>GCF_003691675_PROKKA_01815 +MAFAALSRSARLAGLSAAALLALTACGGQDSSDADASASTTAPASASAQGVESSSASASS +LSAAPADYEAGTCFTAPLGARDLSSFETTDCEGAHTAEYLWAVPAVAEGEEADPAAAQTC +TAQAQRLSEEKEDQLNGAVLTSSELGNYGTDEKHCVVYGVSGEWEGQIVDPEITLETASA +DA--- +>GCF_005280335_PROKKA_00670 +MAFAALSRSARLAGLSAAALLALTACGGQDSSDADASASTTAPASESAQSSESSSASASS +LSAAPADYEAGTCFTAPLGARDLSTFETTDCEGAHIAEYLWAVPAVAEGEEADPAAAQTC +TAQAQRLSEEKEDQLNGAVLTSSELGNYGTDEKHCVVYGVSGEWEGQIVDPELTLDEAIA +ASAGA +>GCF_023573625_PROKKA_02048 +MAFAALSRSARLAGLSAAALLALTACGGQDSSDADAS------ASASAQGSESSSASASS +LSAAPADYAAGTCFTAPLGARDLSSFETTDCEGAHTAEYLWAVPAVAEGEEADPAAAQTC +TAQAQRLSEEKEDQLNGAVLTSSELGNYGTDEKHCVVYGVSGEWEGQIVDPEITLETASA +DA--- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001955.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001955.fa new file mode 100644 index 0000000000000000000000000000000000000000..92b5e42372a72515f2f41ad7df2d12402bb68de8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001955.fa @@ -0,0 +1,21 @@ +>GCF_003691675_PROKKA_00255 +MQKNTSTLSRRKVTAGIAWSVPAVAAVAAAPFAAASPTGCAAVTTGTAEKFPGGGHPDGI +KQAYGFTITITNTSPTPVYVDPGTVTVEFKGHPTRSGEALLYTASPCEGGTRLAAMDPEL +LLQPGESETYYYVVNQTGNSAQESGCVKGKLQLALPKGAPEGADLCNDGVVDFSNCFDTT +PPTAGC +>GCF_005280335_PROKKA_02418 +MQQNTSSLSRRKVTTGIAWSVPAVVAVAAAPFAAASPS-CITSSAGRVVKYPGNSSGYDL +KQAYGFTVTVTNPTRGKLRVTAKSVSLILDKKVLR-GSLLIYTADPCAGGVPVDPNSDLL +VLEPGESQTLFLVANNTGNSANTSGCIYAKLGVKLVDGSVPVANLCDEHDV-VEACFDET +SPTATC +>GCF_020097155_PROKKA_02300 +MQTTPKTVNRRTVSAGIAWSVPAVAAVAAAPFAAASPTGCVNVTSGTAEKFPGGGHPDGI +KQAYGFTITITNTSPTPVYVNPGTVTVVFGGHTTRNGEARLYTASPCRGGKRLAAMDPEL +LLQPGQSKTYYYVVNNTGNSAQESGCVKGKLQLALPKGAPEGADLCNGGIVEFKNCFETT +PPTAGC +>GCF_023573625_PROKKA_00534 +MQKNTSTLSRRKVTAGIAWSVPAVAAVAAAPFAAASPTGCAAVTTGTAEKFPGGGHPDGI +KQAYGFTITITNTSPTPVYVDPGTVTVVFGGHTTRNGEARLYTANPCRGGKRLAAMDPAL +LLQSGQSKTYYYVVNNTGNSANESGCVEGKLQLALPKGAPEGADLCNDGVVEFSNCFETT +PPTARC + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001963.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001963.fa new file mode 100644 index 0000000000000000000000000000000000000000..66971724909290a60a5055883fc577171a11bc14 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001963.fa @@ -0,0 +1,32 @@ +>GCF_003691675_PROKKA_01697 +M-------AWSEGLRDTLRFWPLVLVAFVHAVASCSLLGLSFQQASEAQEVDRHLQRWEQLGAASLRGFYLAAPG---HL +EGGGAAPGESQQEPP--EPDLSADSKAASADDGRRAAALLALLEDPHRTAYTMDPYGDRFGDDLPGALLVTEDFFAGSGL +AAAMSPTGQSPHRDADGTAAPYAVLGSDSSAKDPYALTVGGVLPPPTRVQFQDAMIPVTGRLAPGATALDPMMGSV-PLD +GAVLVVVPPSALASLYPPDALEAILLRTIVLGQDAVPALDAAGRALETDALVVNAEPLTPQSSALLQSLSASSRTLLVLF +GAAVLGAVVSLFGVLGVLARALAPTWRIAAMVGAARWQAAVRIIVPVLFAWVLPAAVGLTAG---ASALPGPPPT-GLTS +TALIAVMAIGAVATLSSWRALAATFGRRPRRHRPTKETARASSKSTTWTRRSSPAGRRCPSSGGPLCWFRPVRCTPSPGL +PGPGNPPCCGSSRAWTPRTRVASCSGANLSRSRGAGAGTGIGTSGAASSCRTSPSWSTPPHWRT +>GCF_005280335_PROKKA_00854 +M-------AWSDGLRDTLRFWPLVLVAFVHAVASCSLLGLSFQQASEAQEIGRHLQRWEQLGAASLRGFYLAGPG---DL +EGGGAAPGDSQQEPP--EPDFSAGSRADSADDGRRTAALLALLADPHRTAYTMDPYGDRFGDDLPGALLVTEDFFAGSGL +DETMSPTGQSSHRDAGGTAAPYAVLGSDSSAKDPYALTAGGVLPPTTRVQFQDAMIPVTGRLAPGATALDPMMGSV-PLD +EAVLVVVPPSMLASLYPPDALEALLLRTIVLGQDAVPALDAAGRALETDALLVTAEPLTPQSSALLQSLSASSRTLLVLF +GAAVLGAVVSLFGVLGVLARALAPTWRIAAMVGAARWQAAVRIIVPVLFAWVLPAAVGLTAG---ASALPGPPST-GLTS +TALIAVMAIGAVATLSSWRALAATFGRRPRR-RPTKETA----------------------------------------- +---------------------------------------------------------------- +>GCF_020097155_PROKKA_00791 +MSTRALAVALADGLNDAARFWPLILGAFLHAVVSCLLLGLSFQQVSEAGEVSAHLHRWEQQGAASLHGIYLAGVSARPAA +EGMTPTLQDGLDETPVLDPEGEAGAAS-------RTAGLLSLLEDPQRLAYTMDPYGDRFGDDLPGAMVVTEDFLRATGV +DDSMTPTGAAVPRDSDGAPAPYAVLGSASRAKDPHALLVDGAPPPTTRVQFQGAMIPVVGRLAQGATTLDPMMGSV-PLD +EAALIVLPAASLPGLYPAEELEALLLRTVVLGPDAVPVLDASARPFESERLLVAAQPLTAESSGLLQSLTSSSRTLVLLF +GSAVLGAVVSLFGALGVLARALAPTWRIAAMVGAARWQAAVRIAVPVLLAWVLPAGLGLLAG---AAAVPGPSPT-ALAA +VALALVLGVGCWAALSSWRALAATFG--PRRRTPTRTTTKEAA------------------------------------- +---------------------------------------------------------------- +>GCF_023573625_PROKKA_00736 +M--MAAMRAVADGLRDLFDTPGLLFLSLLHTTVASVVFGLALGVAGGVTTALEVLEDAESSGLVTARIL----------- +-----------------DPAVTTDLHPRAVDTVSRAFAAHVDGVDP-RAFLVTDAIGIE-DPRLQGAVIATPGLAREFGA +AAAVSP--------------------AEGVYFAPAAITSGG---PGGTVYVGSTPHSYAGPL-PGDAAAPRADGSLWPLG +ESPVIVTSTTTMAGLIEPAQLAA-VYGSVVARQDAASEVRAALDVLEDETGVVAELAPIASARSPIAREARGAALMVTAY +TAGLASAVVTVVSLLTTVTRRLTPTWLAHLTVGAPRRLIRLRIATSVAAVWGIPAVLGSLLGLGIASEAGGLRPAPAVVV +VGLAVVLAIAAACTRHPLRQL----------HRAVRTAALVEGT------------------------------------ +---------------------------------------------------------------V diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001964.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001964.fa new file mode 100644 index 0000000000000000000000000000000000000000..e4c5a9a3b502611bd8ddaceb4483472be9346f6e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001964.fa @@ -0,0 +1,29 @@ +>GCF_003691675_PROKKA_01698 +MTGRGLRTLGLLVTRAVLLVALCGLALSLVGSLSVHHRQYFGAAECGPAVWDVGIGGGGE +VWSVAEAATTGRNLTLMASGADPGVRHLAG-PAAPCL-AGIDVPTLESLRAARGFLLREG +SILADRAARSGELAGRPVALASAADWRGLP----SDGVIQPTPAFDNAAAYVGFLVGDPA +DLDGFLQNLRTAGLEVDAAPAP----SAMTASLGTPVLGVTSSLTGLTLMSVTAFWVLTL +RAGDRPSLRVLRLLGVSPLRAAVSRARVSLVPFLGAAGISAALWQGMVLTGAVTEPSPLV +ASGVILVVLLGDAVLVSATHVVALWM-RAPR +>GCF_005280335_PROKKA_00853 +M---GSRTLGLLVTRAVLLAAVCGLALSLVGSMSVHQRQYFGAAECGDAVWDVGIGGSGE +VWSATEAALTGRNLTLMANGADPRVRHLTG-PTAPCL-AGVDEQMLNSLRMERGFLVREG +SVLADRAAGEGELAGRPVALASSARWRGLP----SDGVIQPTPAFDNAAAYVGFLVGDPA +DLDGFLQNLRTAGLEVDAAPAP----TAMTASLGTPVLGVTSSLTGLTLMSVTAFWVLTL +RAGERPSLRVLRLLGVSPLRAAVSRARVSLVPFLGAAGISAALWQGMVLTGAVTEPSPLV +ASGVILVVLLGDAVLVAATHVVSLWM-RAPR +>GCF_020097155_PROKKA_00790 +M---GTGLLGRLLTRAVLLTALCGLALGIAGSMSVHRQQYFGAEGCGEAVWDVNVVGADR +VWSALEAALTGRDLTAMVTGADPGLFHVAG-PAASCL-TGVDEQTLGSTREAGGFLVRGG +GMLAARAGQDGELATRPAVVVPPDRWRGLP----SVSLIQPTPVFDDSSSYVGFLVGDAG +EIEDLVRRLRESGLEVEAAPAA----TAAEAALRAPTLSATTGLTALTCLSVTAFWALTL +HAGQRPAVRVLRLLGVSPLRAAASRWAASAVPFAAAAALAAALWLGMILSGTLTTPAPGT +AALIVAGAILADAALVALTHVGALWMKRVPR +>GCF_023573625_PROKKA_00737 +MTR-------MLVSRFLLLLITLGTAALLASYVGVEKEDRWRMDG---TVYEISAFPAGE +AWPMIRTSLTGPDSGSAATSTSPHVTALAGRPALDVLPDGV----------APTAVVPST +SPFAARAAA-GELSWPDVDRVVVRDLSSAPDRATEADLLVPFLSTD-SSSLAGVIGGSPA +QVDELVQSLRRAGVVVDVVPLPPPWEAAMRRSVHVPLLAV---IAGFALLGAQVVWRTTL +RSRLLPAVTSHRLVGASPLRAARLGVRPAMLAWATAAASAGGVWLVAWPRWDAEIGLTGD +TALLWSAVLVVDAILILGTTLSTLWVRRAHA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001966.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001966.fa new file mode 100644 index 0000000000000000000000000000000000000000..d48d0dde8ec06784ac1284ba38b0acc4b01a9353 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001966.fa @@ -0,0 +1,25 @@ +>GCF_003691675_PROKKA_01701 +MLEFVDTAAQAVSRITDGATVLIGGFGNAGQPMELIDALLESGATGLTVVNNNAGQADAG +LALLIKERRVAKIICSFPRHSDSWHFDEAYRAGEIELELVPQGNLAERLRAGGAGIGGFF +TPTGYGTQLAEGKEVREIDGTHYVLEAPIRGDVALIKAYAADRHGNLVYRKTARNFGPVM +AAAAATTIVQVDEVREEPIDPEHVVTPGIYTDTVVRIDTESGEKERAERAALAEGRPKPC +AATTTAAEPAAEGK +>GCF_005280335_PROKKA_00850 +MLEFVDTAAQAVSQVTDGATVLIGGFGNAGQPMELIDALLESGATGLTVVNNNAGQADAG +LALLIKERRVAKIICSFPRQSDSWHFDEAYRAGEIELELVPQGNLAERLRAGGAGIGGFF +TPTGYGTQLAEGKEVREIDGRHYVLESPIRGDVALIKAYAADRHGNLVYRKTARNFGPIM +AAAAEHTVVQVDEVRDEPIDPEHVITPGIYTDVIVRIETESGAKEREEREALAAGKPKPC +AATKTAAEKAAEGK +>GCF_020097155_PROKKA_00787 +MLEFVETAAEAVAQVRDGQTVLIGGFGNAGQPMELIDALLESGATGLTVVNNNAGQADAG +LALLIKERRVAKIICSFPRQSDSWHFDEAYRAGEIELELVPQGNLAERLRAGGAGIGGFF +TPTGYGTQLAEGKEVREIDGRHYVLESPIKGDVALIKAYAADRHGNLVYRKTARNFGPVM +AAAAATTIVQVDEISEEPLNPEHVITPSIYVDTVVRIQTESGVK---EREALAAGKPKPC +LATETAAGQAAEGK +>GCF_023573625_PROKKA_01929 +MLEFVDTAAQAVSRITDGATVLIGGFGNAGQPMELIDALLESGATGLTVVNNNAGQADAG +LALLIKERRVAKIICSFPRQSDSWHFDEAYRAGEIELELVPQGNLAERLRAGGAGIGGFF +TPTGYGTQLAEGKEVREIDGTHYVLEAPIRGDVALIKAYAADRHGNLVYRKTARNFGPVM +AAAAATTIVQVDEVREEPIDPEHVVTPGIYTDTVVRIDTESGEKERAERAALAEGRPKPC +AATTTAAEPAAEGK + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001978.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001978.fa new file mode 100644 index 0000000000000000000000000000000000000000..cf44a801a25da037ed33e083b8fe29d4bcd30fe9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001978.fa @@ -0,0 +1,29 @@ +>GCF_005280335_PROKKA_00733 +MIRFIDEHRDRFGVEAICRTLGATARGFITSRGYRAAKRRPASERALRDELLIEELERIH +AENYSVYGVRKMHQAMARAGWQIGRDQTARLMRAAGLQGVRRGRKPITTRPACEPDARPD +LVERRFAAERPHQLWVADITYVRILDGFCYVAFITDVFTRRIVGWAVSASLHTQGLPLLA +LEHALLSTGASRGREGLVHHSDRGAQ------------GGFNRSSQHPLGIIGGMGDG-- +--------------------------------------------QQGLG----------- +EEDQ------- +>GCF_005280335_PROKKA_00750 +MIRFIDEHRDRFGVEAICRTLGATARGFITSRGYRAAKRRPASERALRDELLIEELERIH +AENYSVYGVRKMHQAMARAGWQIGRDQTARLMRAAGLQGVRRGRKPITTRPACEPDARPD +LVERRFAAERPHQLWVADITYVRILDGFCYVAFITDVFTRRIVGWAVSASLHTQGLPLLA +LEHALLSTGASRGREGLVHHSDRGAQ------------GGFNRSSQHPLGIIGGMGDG-- +--------------------------------------------QQGLG----------- +EEDQ------- +>GCF_005280335_PROKKA_02328 +MIRFIDEHRDRFGVEAICRTLGATARGFITSRGYRAAKRRPASERALRDELLIEELERIH +AENYSVYGVRKMHQAMARAGWQIGRDQTARLMRAAGLQGVRRGRKPITTRPACEPDARPD +LVERRFAAERPHQLWVADITYVRILGGFCYVAFITDVFTRRIVGWAVSASLHTQGLPLLA +LEHALLSTGASRGREGLVHHSDRGAQYVSLAYSDALIAAGVSAS-------VGTVGDSYD +NALAETVNGLYKAELIHSKRVWESVEEVELATMGWVHWWNTARLHEALGYCTPAEVEATY +THDQDSAPVAS +>GCF_020097155_PROKKA_00415 +MIAFIDEHRDQFGVEAICRTLRATECGFITSRGYRAAKTRPRSSRTLRDEILVEELRRIH +AENYSVYGVRKMHHAMVRAGWQVGRDQVARLMRAAGLQGVRRGRKPITTRPAGEPDARPD +LVERRFAAERPHQLWVADITYVRTITGFCYVPFITDVYSRRIVGWAVSASLHTQGLPLLA +LEHALLSTGASRGRQGLIHHSDRGAQYVSLAYSDALITAGVSAS-------VGTVGDSYD +NALAESVNGLYKAELIHSKRVWESVEAVELATLKSVHRPRPRRRRSALP----------- +T---------- + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002000.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002000.fa new file mode 100644 index 0000000000000000000000000000000000000000..af966d636d611fdd1746c633df181db6331919db --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002000.fa @@ -0,0 +1,10 @@ +>GCF_002008305_PROKKA_00375 +MKTIRTIAFILFLCATAFGVMLTLHYLPIPEILPSEITSWVPARDTADATWLIVGMVVAV +VATAVGFSASHKAVERETQVTS +>GCF_005280335_PROKKA_02587 +MKTIRTIAFILFLCATAFGVMLTLHYLPIPEILPSEVTSWVPARDTADATWLIVGMVVAV +VATAVGFSASHKAVERETQVTS +>GCF_023573625_PROKKA_00382 +MKTIRTIAFILFLCATAFGVMLTLHYLPIPEILPSEITSWVPARDTADATWLIVGMVVAV +VATAVGFSASHKAVERETQVTS + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002016.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002016.fa new file mode 100644 index 0000000000000000000000000000000000000000..5fb504d7846d67ee3fd36584bb5c86e4db64d1a0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002016.fa @@ -0,0 +1,16 @@ +>GCF_002008305_PROKKA_00768 +MRLFLAIRPPRAALDHLEPALDGVRDRAGRALCWTEPEQRHLTLAFHPEVPAGAVDDVVA +VAGRIAAGHGPLDLHLAGAGEFSHRTLWVGVGGQVRELGALLAEPWLADDDGRDRRRAHL +TVARASGAAPRPRGRRRGEPRPPAPATVLLAEAVHALAVYRGPEWTADEVEVVASRLGEG +RSGGPLHEVLATVPLRG +>GCF_003691675_PROKKA_00498 +MRLFLAIRPPRAVLDHLEPAFDGVRDRAGRALCWTEPEQRHLTLAFHPEVPAGAVDDVVA +VAGRIAAGHGPLDLHLAGAGEFSHRTLWVGVGGQVRELGALLAEPWLADDDGRDRRRAHL +TVAPVSGAALRPRGRRRGEPRPPAPATVLLAEAVRALAVYRGPEWTADEVEVVASRLGEG +RSGGPLHEVLATVPLRG +>GCF_023573625_PROKKA_00732 +MRLFLAIRPPRAALDHLEPALDGVRDRAGRALCWTEPEQRHLTLAFHPEVPAGAVDDVVA +VAGRIAAGHGPLDLHLAGAGEFSHRTLWVGVGGQVRELGALLAEPWLADDDGRDRRRAHL +TVAPVSGAALRPRGRRRGEPRPPAPATVLLAEAVRALAVYRGPEWTADEVEVVASRLGEG +RSGGPLHEVLATVPLRG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002031.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002031.fa new file mode 100644 index 0000000000000000000000000000000000000000..1605b4ac88d773dc289f9cf22748fbcd999c7963 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002031.fa @@ -0,0 +1,22 @@ +>GCF_002008305_PROKKA_01390 +MSHPTVFFYPRPRVDVAEVPAASHAGAVLLTDTIHATGLASSLREALGSWTKPLAEHHAS +KVLLDLAMTLAVGGEVARDTDLLRCEPGLFGDVASAPTISRTLTTLAEDAPAVMTAIARA +RRTAREQAWALAGEHSPAEGTSAKTPLVIDLDATLINVHSEKEQAAPTFKRGFGYHPLYA +FLDHGSEGTGEPLAIHLRPGNAGSNTASDHIAVTRLALAQLPPALLGRGGRGSKKVLIRT +DGAGGPKDFAGWLERQRLAYSVGFTLPANTPDLLERIDEAKAWTPAYDTDTEGIRDGAWV +AELTGLLDLPGWPPECG +>GCF_003691675_PROKKA_01122 +MSHPTVFFYPRPRVDVAEVPAASHAGAVLLTDTIHATGLASSLREALGSWTKPLAEHHAS +KVLLDLAMTLAVGGEVARDTDLLRCEPGLFGDVASAPTISRTLTTLAEDAPAVMTAIARA +RRTAREQAWALAGEHSPAEGTSAKTPLVIDLDATLINVHSEKEQAAPTFKRGFGYHPLYA +FLDHGSEGTGEPLAIHLRPGNAGSNTASDHIAVTRLALAQLPPALLGRGGRGSKKVLIRT +DGAGGPKDFAGWLERQRLAYSVGFTLPANTPDLLERIDEAKAWTPAYDTDTEGIRDGAWV +AELTGLLDLPGWPPECG +>GCF_023573625_PROKKA_01341 +MSHPTVFFYPRPRVDVAEVPAASHAGAVLLTDTIHATGLASSLREALGSWTKPLAEHHAS +KVLLDLAMTLAVGGEVARDTDLLRCEPGLFGDVASAPTISRTLTTLAEDAPAVMTAIARA +RRTAREQAWALAGEHSPAEGTSAKTPLVIDLDATLINVHSEKEQAAPTFKRGFGYHPLYA +FLDHGSEGTGEPLAIHLRPGNAGSNTASDHIAVTRLALAQLPPALLGRGGRGSKKVLIRT +DGAGGPKDFAGWLERQRLAYSVGFTLPANTPDLLERIDEAKAWTPAYDTDTEGIRDGAWV +AELTGLLDLPGWPPECG + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002039.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002039.fa new file mode 100644 index 0000000000000000000000000000000000000000..c40e3dd7e7ed180dd6afd3f9f7d37bd97c0c9634 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002039.fa @@ -0,0 +1,24 @@ +>GCF_002008305_PROKKA_01617 +MTG------------------------IPFLLVFILAIALMIVMIS----RWKIHPFLSIMVVAFALGIIGGIPLVKSTG +AEGEAPVKGIADVIGEGFSGIFTSIGIVIILGTLIGLILERTGGAFRIADALVRVVGKRYPVLAMQLMGWVVS-IPVFCD +SGFVILNPIRKALARRTGASPVAMTVALAAGLYTSHVFIPPTPGPIAAAQNLG---IGDHLLLVIGLGVLVSIPALLVAY +LYALYIGKRVTSPEETGTEDADELEAAYDA--------LRRSYGRMPGTAASFAPIIAPILLMALGSLASVLKWTGPAGD +FARFLGTPMIAL----AVGTLCAVGLLFSVRRGETFYDLTEETLRVVGPILFITAAGGVLGRVIAATDLVTFIESNAAQL +SVIGLFFPFLVSAVLKTAQGSSTVALTTTSAMVFPMMPALGFETPVASALVVMAIAAGAMTVSHANDSYFWVVTNFSGMT +PSQGYRTQTMVTLLMGLTSIVFI-WLLGLVLV----------------------------- +>GCF_002008305_PROKKA_02039 +MSTDTRTATPHTRGSTRRGDRPMPVPRDPHPLVALLPLLALIALASASTLSWKIGMILPIVAGIVVAAVIG-----RLTG +HSWKDMEAAMTDGVSRAMPAVF----ILLIIGMIIGTWI--SGGV--IPTLIHYGLEFINPTFFLPMACLVTAFISLVLG +SSFTSIATVGLAFMAIGGGMGVPLPI--VAGAVISGAFFGDKLSPLSDTTNVAPAMVGEGLFDHIRHMLWDTIPGLVLSA +GLFWFIGLRVSPGGDVDTAARDTIQAGLSGQFTIHPALLLVVLATLVIIALRVPAIPALVLVAALGGLSGVLVQGRPVGA +VLKDATTGYTSTTGQESVDSLLTNGGVASM-------------FMTIGLVIVATALGGLLERTGVFRALIDPLVRRIRRT +G----------SLIAATVMASFLVGFSTGAQFLAVILPARG-----------MVDAYRRMGLSPLNLSRVVEAAGTVGIN +LVPWGVPAVFAAGVFGLEPMEFIPWILFAFIVPALNVLYGYTGLSIKRITPAEVDPEDQRD +>GCF_005280335_PROKKA_01279 +MTG------------------------IPFLLVFILAVALMIVMIS----RWKIHPFLSIMVVAFALGIIGGIPLVKSTG +AEGEEPVKGIADVIGEGFSGIFTSIGIVIILGTLIGLILERTGGAFRIADALVRVVGKRYPVLAMQLMGWVVS-IPVFCD +SGFVILNPIRKALARRTGASPVAMTVALAAGLYTSHVFIPPTPGPIAAAQNLG---IGDHLLLVIGLGVLVSIPALLVAY +LYALYIGKRVSSPEETGTEDADELEAAYDA--------LRRSYGRMPGTAASFAPIIAPILLMALGSLASVLKWTGPAGD +FARFLGTPMIAL----AVGTLCAVGLLFSVRRGETFYDLTEETLRVVGPILFITAAGGVLGRVIAATDLVTFIESNAAQL +SVIGLFFPFLVSAVLKTAQGSSTVALTTTSAMVFPMMPALGFETPVASALVVMAIAAGAMTVSHANDSYFWVVTNFSGMT +PSQGYRTQTMVTLLMGLTSIVFI-WVLGLVLV----------------------------- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002042.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002042.fa new file mode 100644 index 0000000000000000000000000000000000000000..a858f5a8dab69caa69f17148e7dccd9d1aef16e3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002042.fa @@ -0,0 +1,19 @@ +>GCF_002008305_PROKKA_01622 +MKTPVLSATDMRI---VEQVLDMGDGYVLDFSNRTFADFFADLDVEIEPE--DSGLSKAK +RLRAFFRSASTSECARVLHALLEYRGE-QDGDDESASIDKYRAIVSRLEGVAVPLSAAPV +APEVLTLAYVRELSDKAERRLAASDLEGAITVSRTLVEAVLEQLEIRLTGQSGNYAGDLQ +RQYKAVAKILRIDDKDDQVDEGFKQIARGLVQIVNGLAAIRNMASDGHA---RHVQPQAR +HARVAVNSAKTVASFLVEVYLAKRTGPTSPAAVRSGG +>GCF_003691675_PROKKA_00369 +MASTSPTLLPFRIDSLATSLFAKETG----FSGPHLHDFFARYTDMLGPYRWNGSPSRWQ +IFQTGLHSLPLPQQRAVLLELCSYDGEFKNGRPPEGELTRLRGML--LSAGTPGAHAAQE +SLQKLEDWEAVNRSWQAALTKVQDDPDGAITATRTTIESVCKHI-CDERGVKYEDGWDLA +RLYKATSSAMQV-APDQHSEQIIKQILSGAATLVGGLAAMRNALSDAHGRGKRSVGPAPR +HAKLAVNAGFAIAGFLIDTHVEKP--PVS-------S +>GCF_020097155_PROKKA_02204 +MASTSPTLLPFRIDSLATSLFAKETG----FSGPQLHDFFARYTDVLGPYRWNGSPSRWQ +IFQTGLHSLPLPQQRAVLLELCSYDGEFKNGRPPEGELTRLRAML--LSAGTPGAQAAQE +SLQKLEDWEAVNRSWQAALTKVQDDPDGAITATRTTIESVCKHI-CDERGVKYEDGWDLA +RLYKATSSAMQV-APDQHSEQIIKQILSGAATLVGGLAAMRNALSDAHGRGKRSVGPAPR +HAKLAVNAGFAIAGFLIDTHVEKP--PVS-------S + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002074.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002074.fa new file mode 100644 index 0000000000000000000000000000000000000000..b7abb80c7d1ebb00c0e2e2b30b36a94f6f5bed29 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002074.fa @@ -0,0 +1,24 @@ +>GCF_003691675_PROKKA_00101 +MTTIPIHEAQVRHQPLHAYVEEHAQVSPDRTAIVCGGSQLTFGQLQSQVEQLSAYLSEQGVSHGDTVALFMQNSPQFVVS +LLAVQRLGATAGPCNPMFKQWELEYQLNDLDTKVLITFDDLVPVFEKTDTGVQTVVLTRWSDVIEDVSQVPVEDGAEPVQ +QTKAPHTVRYAQIIGGERTVPPAAEIDLAQDPALIIYTSGTTGQPKGAMLSYRNVEFKTACTVQTYGFTSDDVFCAVMPI +FHIAGMTVCMNSPLMVGGTMVIEPRFEPGTMIRDLERHAVTVTYTTPPMNLALLDHPAMAEADLSAVRLSPGTSFGIKIT +REISDRWEEVTGAPLFEWAYGMSE-THTGDTQMPPEAIRYGSHGKPTFDTDVRISDPEDPSREMPQGELGEILVSSPSVF +LGYRGREEATQKTMHRHWYRSGDLGRIDSEGYLHFEGRNKDLIKSSGYSVFPEEVERMLVRHEAVAQAAVVGYPDPQRGE +SVRAFVILEEGQSVTPKELIEWSRERMAAYKYPRDVRIIQELPTTTTGKLQYAKLRD-------------LD +>GCF_003691675_PROKKA_02299 +M------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +---------------------------------------------------------NTTVSGARIPIRPDDVVLAVLPF +FHVYGLTSVLNICVRHACTMVLLPRFDAAAALDLVERHGITRISAVPTMLIGMVEDPDTGR-DLSSV--SQVVSGGSALP +QEVLRRFEAKFPRATILEGYGLSESTSSVAVNVSREERRVMSIGKPLWGTECRVVDAEGHLLGPGEDQVGELLFRGPTIM +KGYYRNPEATAATLVDGWLRTGDMGYRDEDGFIYVVDRKKELILRGGYNVYPREVEEVIATHPAVSEVAVVGRPHPSLGS +EVVAVVSTRPGMSVTPAGVIEHAKVSLAAYKYPREVVVVDSLPKTATGKIRKRDLATTLAEPASPESHSATP +>GCF_023573625_PROKKA_00283 +M------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +---------------------------------------------------------NTTVSGARIPIRPDDVVLAVLPF +FHVYGLTSVLNICVRHACTMVLLPRFDAAAALDLVERHGITRISAVPTMLIGMVEDPDTGR-DLSSV--SQVVSGGSALP +QEVLRRFEAKFPRATILEGYGLSESTSSVAVNVSREERRVMSIGKPLWGTECRVVDAEGHLLGPGEDQVGELLFRGPTIM +KGYYRNPEATAATLVDGWLRTGDMGYRDEDGFIYVVDRKKELILRGGYNVYPREVEEVIATHPAVSEVAVVGRPHPSLGS +EVVAVVSTRPGMSVTPAGVIEHAKVSLAAYKYPREVVVVDSLPKTATGKIRKRDLATTLAEPASPESHSATP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002075.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002075.fa new file mode 100644 index 0000000000000000000000000000000000000000..295844a10c0a1058c048cd3be8c8b1c42d0bd0e3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002075.fa @@ -0,0 +1,19 @@ +>GCF_003691675_PROKKA_00235 +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------MHHHGGAFTGIKKHHHAWAPLIEEMQED +VDAWVTGYRVPRSSEAAYFHGPLGRDVRKNFSLLLGFSGKIVRPGSPLTSEWLAEVERRL +DYYGSLLAQAPGNIYGDNPGYPVPWTRIGSQVFEPLTLKYREHIRIDPRLKPQLWGHR +>GCF_005280335_PROKKA_02429 +MA-LNAARRAKHQVW-----TLRKVSAQQARELLDTTA--QRLRPLSFNPHRYPLHR--- +------FLRFDAPMQ-ETLPAPERIFVLWTGLNEMPAIRAANLGRIRTIVGVPVEFVTPA +TLHEWTVEHHPLHPAYPHLSLTHSSDYLRAYLLHHHGGGYMDLKAPAGSWADMFTRLNGD +PEAWVLGYPEDSKGRIPPYGGHMERDLRIHFARVMGTMAMIARPRSPFTAEWFHEVERRL +DYFLPLLRDHPGGVRDEIDLYPVGWTQILADIAYPLPLKHHDHIRLEKGFTPPDEAYR +>GCF_020097155_PROKKA_02313 +MRLMYSARQAKHAAFVANKRTRRVLGAGKWRALTMVTPALSRVWPFRYDAQRYTGPNRGK +EGHDLSFLQLPPPIDAASSELPRRVFVLWTGNNPLPPNRSRNLAHLRKVIAVPVVLVTPQ +TLGGWLIPGHPLHPAYEHLSLVHRSDYLRAYLMHHHGGGYIDLKAPVGSWAPAFDRMERD +PSAWLSGYGEINANASARFPGPMGRDIATHWKSLVGTAAMIVRSHTPFTGEWIREVDRRM +DALAPRLAASPGLVRLGGPGYPVSWTDLLGKVYQPLQLKYFEHIRVDDDLLVNFTDYQ + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002086.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002086.fa new file mode 100644 index 0000000000000000000000000000000000000000..81e2eb0d4392aa8fb553f6f2fb0025fb5f496c49 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002086.fa @@ -0,0 +1,28 @@ +>GCF_003691675_PROKKA_01493 +MRPRSASAARTREALRDAVQIYAPSTVYAVGLGAMTPALAVAALALGLDAARAAAVVLLV +GLGSLVANGPASALAARAGERVTMVVSAGLGTVGAGLAWATTAGVSSGPSAAGVAEPGRL +ALFLAAVLAVGMAGAGFNLARQAYLAVAVPATHRARAMSTLGGTVRIGTFLGPFLGAAAQ +APLGLDGAFAAAAAAMAVGALLCLRIRDLP-----VPASDPAAGEEPGPAGRPRLLDVAR +ARRGALLTAGFGVVAVSAARAARNAVIPLWATHLGLDAATASLVFGLAGAADLLLFYPSG +RLMDRFGRRAVAVPCLTLLGAGFLAISLTREPTAFAAAAVLLGIGNGFGAGIVMTLGADH +SPPNARAPFLGLWRSMSDAGMLAGPLLLSGATAAAGLAVGVGSLAVVCGVGAVVFAAVLP +RGPGAVADPPPVVVRPR +>GCF_005280335_PROKKA_01090 +MPRRSASAARTRQALRGAVQIYAPSTVYAVGLGAMTPALAVAALALGLDAARAAAVVVLV +GLGSLVANAPASALAARAGERVTIVVSAFLGTAGAALAWATTAGLSSSPGREGVVEPGRL +ALYLTAVLAMGMAGSGFNLARQAYLAVAVPPSHRARAMSTLGGTIRIGVFLGPFLGAAVQ +AAMGLDGAFAAATAAMAVGALLCLRIRDLPASGAAAPGADP--GAQPVPAHRPRVADVAR +ARREVLLTAGFGVVAVSAARAARNAVIPLWATHLGMDAASASLVFGLAGAVDLLLFYPAG +RLMDRHGRRAVAVPCLAVLGAGFLAVSLTRDPAAFAAATVLLGIGNGFGAGIVMTLGADY +------------W-------LLGHP-------------VGLG------------------ +--------------RAG +>GCF_023573625_PROKKA_01715 +MRPRSASAARTREALRDAVQIYAPSTVYAVGLGAMTPALAVAALALGLDAARAAAVVLLV +GLGSLVANGPASALAARAGERVTMVVSAGLGTVGAGLAWATTAGVSSGPSAAGVAEPGRL +ALFLAAVLAVGMAGAGFNLARQAYLAVAVPATHRARAMSTLGGTVRIGTFLGPFLGAAAQ +APLGLDGAFAAAAAAMAVGALLCLRIRDLP-----VPASDPAAGEEPGPAGRPRLRDVAR +ARRGALLTAGFGVVAVSAARAARNAVIPLWATHLGLDAATASLVFGLAGAADLLLFYPSG +RLMDRFGRRAVAVPCLTLLGAGFLAISLTREPTAFAAAAVLLGIGNGFGAGIVMTLGADH +SPPNARAPFLGLWRSMSDAGMLAGPLLLSGATAAAGLAVGVGSLAVVCGVGAVVFAAVLP +RGPGAVADPPPVVVRSR + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002090.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002090.fa new file mode 100644 index 0000000000000000000000000000000000000000..a4dd3c7d61eb5e0495adf79c9d5c12a37c625fbe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002090.fa @@ -0,0 +1,16 @@ +>GCF_003691675_PROKKA_01709 +MRIDETTERTADGRLVPTPGQTIGPFFGYANGYEQVHLPWRDGHQLVPAGRADAMRLFGT +VYDGNGDPIPDAMIEIWQADAEGVISQEDGSLVQDGFTFTGWGRCAVDNAGRYTFSTVEP +GVVNEDRARFIHVVVFARGLLNKLHTRVYLPEDAEAIVQDAFLTSLDEDRRRTLIGTRND +DGSLEFDIWIQGPGEHAPKETVFLQFPGIEYPELD +>GCF_005280335_PROKKA_00843 +MRIDENSERDAQGRLIPTPGQTIGPFFGYADGYEQVHLPFRDGQNLVPPGRADALRLTGT +VYDGNGDPIPDAMLEIWQADAQGVISQEDGSLVRDGFTFTGWGRATVDNVGTYTFSTVEP +GATGEGTARFISMVVFARGLLNKLHTRVYLPEDTEALAADPLLQSLPEERRRTLIAERLD +DGSLRFDVWIQGRGEHADKETVFLQFPGIEYPQHD +>GCF_023573625_PROKKA_01937 +MRIDETTERTADGRLVPTPGQTIGPFFGYANGYEQVHLPWRDGHQLVPAGRADAMRLFGT +VYDGNGDPIPDAMIEIWQADAEGVISQEDGSLVQDGFTFTGWGRCAVDNAGRYTFSTVEP +GVVNEDRARFIHVVVFARGLLNKLHTRVYLPEDAEAIVQDAFLTSLDEDRRRTLIGTRND +DGSLEFDIWIQGPGEHAPKETVFLQFPGIEYPELD + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002100.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002100.fa new file mode 100644 index 0000000000000000000000000000000000000000..5e309ce94932475b4aae8ef776b76907c2451084 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002100.fa @@ -0,0 +1,10 @@ +>GCF_003691675_PROKKA_01928 +MSQN--DLTVYGADWCRDCLRTKRQLDELGVAYDYVDLVADPAQADAAERISGRKNIPVV +VFPDGDHQVEPTNEETAAKLTALGLI +>GCF_005280335_PROKKA_00526 +MTQNAPALTVYGADWCRDCLRTKRQLDELGVAYDYVDLVADPAQADVAERISGRKNIPVV +VFPDGEHQVEPTNEETAQKLTALGLL +>GCF_023573625_PROKKA_02154 +MSQN--VLTVYGADWCRDCLRTKRQLDELGVAYDYVDLVADPAQADAAERISGRKNIPVV +VFPDGDHQVEPTNEETAAKLTALGLI + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002102.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002102.fa new file mode 100644 index 0000000000000000000000000000000000000000..38978dd101aad87e3525064295fec4f2f17de70f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002102.fa @@ -0,0 +1,28 @@ +>GCF_003691675_PROKKA_02184 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------------------MVPTADDAPR +REPGAVWRGLLTIFLVSAGGSLMFYTWLIYLPTHAQVAHQMDKSTTLSASLVAQVIFLAA +ILGAGLLGDRVGRRPLVIAFGLLFVVLPFPLFGMLDGTFASFLLVQTIALLAVALLFGVN +GAVWSEALPTAVRAKGVATMLSLATAIFGGTAPYLITWLTAQGWTSAFPIYLMVVG---G +LTGLVMKETKDVDLAA +>GCF_020097155_PROKKA_00158 +MSTAATGAARPAPVPRTRPRSLKDMLAVNFGNALEWYDWNVYTIFAPVFAAQIFHADNPT +SELLATLAVFAVGFVARPIGGYVFGAYADRVGRKRSLFAAMMITALGSLIIAFTPTYGMV +GVLASVILVIARLLQGLAHGGEMGTSVTYLVERAPQGRRGLFGATSWVSVVVGTILATLV +GLTINTLLTHEQVASWGWRVAFGIGGVLGLYALYLRRSLTESEHFTAAQQVVPTADDAPR +RESGAVWRGLLTIFLVSAGGSLMFYTWLIYLPTHAQVAHHMDKSTTLSASLLAQVIFLAA +ILGAGLLGDRVGRRPLVIAFGLLFVLLPFPLFGMLDGTFASFLLVQTIALLAVALLFGVN +GAVWSEALPTAVRAKGVATMLSLATAIFGGTAPYLITWLTAQGWTSAFPIYLMVVGGLTG +LTGLVMKETKDVDLAA +>GCF_023573625_PROKKA_00185 +------------------------------------------------------------ +------------------------------------------------------------ +----------------------MGTSVTYLVERAPQGRRGLFGATSWVSVVVGTILATLV +GLAVNTLLSPEQVASWGWRVAFGIGGVLGLYALYLRRSLTESEHFTAAQQVVPTADDAPR +RELGAVWRGLLTIFLVSAGGSLMFYTWLIYLPTHAQVAHQMDKSTTLSASLLAQVIFLAA +ILGAGLLGDRVGRRPLVIAFGLLFVVLPFPLFGMLDGTFASFLLVQTIALLAVALLFGVN +GAVWSEVLPTAVRAKGVATMLSLATAIFGGTAPYLITWLTAQGWASAFPIYLMVVGGLTG +LTGLFMKETKDVDLAA + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002105.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002105.fa new file mode 100644 index 0000000000000000000000000000000000000000..dabd9951b5b97abd6708f8f6551930abc5f4dc3b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002105.fa @@ -0,0 +1,25 @@ +>GCF_005280335_PROKKA_00130 +MPFALYMLALAVFVMGTSEFMLAGLLPAIATELDVSVGTAGLLTSAFAVGMVVGAPVMAA +FARSWPPRLTLIVCLLVFAGSHVIGAMTPVFSLLLITRVLSALANAGFLAVALSTATTLV +PANQKGRALSILLSGTTIATVVGVPAGALLGTALGWRTTFWAIAILCIPAAVGVIRGVTN +NVGRSATSA-TSPRLRAELSQLAMPRLILAMALGALINGGTFAAFTFLAPVVTETAGLAE +AWVSVALVMFGIGSFLGVTIAGRLSDQRPGLVLAVGGPLLLTGWIVLAVVASHPVALIVL +VLVQGFLSFGVGSTLITRVLYAASGAPTMGGSYATAALNIGAAAGPVLGAFGLATGLGLL +APVWVASVLTAIALAIMLLTGRALTKTAAEA-N +>GCF_005280335_PROKKA_01507 +MPFALYLLALAVFAMGTSEFMLAGLVPDIAASVGVSVGTAGLLTSAFAVGMILGAPAMAA +LTRRWPARTTLLGCVVIFAACHVVAATAETFSVLFATRVVAAVANAGFLAVALSTATRLV +APSRKGRALAILLSGTTIAMVAGVPAGALLGTALGWRATFWAVAFLCVPAAIGILTGIRP +QPRDTQDEANDGLSLAFELAQLRVPRLFTAMLLAALVNGGTFAAFTFLAPVVTGTAGLGQ +VWVPVALVLFGIGSFMGVSIAGRLSDQHPRTLLVVAAPLLLVGWLLLAVLAGHSVPLLVL +VFLLGMLAFAVGSTMIARVLYAASEAPTMGGSYATAALNIGAAAGPALGAVALESSRA-- +---------------------RATLVPCGQRPR +>GCF_005280335_PROKKA_02340 +MPFVLYLLAMVVFAMGTSEFMLSGLVPDISAYFGVSVGTAGLLTSAFAIGMVIGAPAMAA +LTRRLPVKATLLGCVIVFALSHAVGALTPDFTVLFITRVIAAVVNAGFLAVALVAATKLV +APDAKGRAVAILLAGTTVATVAGVPAGALLGAVLGWQSTFWAIALLCVPAAVGIAAGFTA +QSDDSSREEPTSISLRAELSQLASPRLVLTMLLAALVNAGTFSTLTFLAPIVTHTAGLSQ +WWVSVALVLFGVGSFIGVTVAGRLSDARPRIVIVGGGSVLVLGWLALATFATNPIALLGL +VFAQGVLGFAVGSTLITRVLYAAAGAPSMAGSYATAALNVGAAAGPILAATALGVVPGAL +GPVWVAVIVTAAALLLAIPVLRLVAPAESEVIK + \ No newline at end of file diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002144.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002144.fa new file mode 100644 index 0000000000000000000000000000000000000000..4f09ed49612197fcd0139df46062a2a8ac579024 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002144.fa @@ -0,0 +1,12 @@ +>GCF_002008305_PROKKA_00950 +MANTSAIEWTEVTWNPVTGCDRVAAGCDNCYALTLAKRLKAMGAEKYQNDGNPVTSGPGF +GVTLHPKALGQPRSWKAPRVVFVNSMSDLFHAKVPLGFIRDIFDVMRETPQHTYQALTKR +SLRMARLADRLDWPANLWMGVSVEDETVTGRIDHLREVPAAVRFLSCEPLIGPLRDLDLA +GIDWVIAGGESGANHRPMDQAWVEDIRDQCVSADVAFFFKQWGGRTPKANGRLLEGRTWD +EMPTSRAALAG +>GCF_005280335_PROKKA_02104 +MAQTSAIEWTEVTWNPVTGCDRVAAGCDNCYALTLAKRLKAMGAAKYQQDGNPATSGPGF +GVTLHRQALDQPRSWKTPRVVFVNSMSDLFHAKVPLEFIQDIFDVIRETPQHTYQALTKR +SLRMARLADQLDWPPNLWMGVSVEDASVTNRIEHLRRVPAAVRFLSCEPLIGPVGALDLD +GIDWVIAGGESGANHRPMDEEWVTDIRDQCVAAGVAFFFKQWGGRTPKANGRVLAGRTWD +EMPNQPASMAV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002146.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002146.fa new file mode 100644 index 0000000000000000000000000000000000000000..37592f3c046ec82a8decae1776b6cb8b25ccc1bc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002146.fa @@ -0,0 +1,6 @@ +>GCF_002008305_PROKKA_00953 +MTTTTQAPACAGHLSVRDHMALQLWGRRWRHGAARDRAAEHLVGLQGTALAMRVATLAED +PVAIAAYPVITRRAREARQTRERAVRVPAA +>GCF_005280335_PROKKA_01934 +MTTTTQAPASAGHLSVRDHMVLQLWGRRWRHGAARDRAAEHLVGLRGTALAMRVAVLAED +PVAIAAYPVITRRAREARQTRERAVRAPAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002155.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002155.fa new file mode 100644 index 0000000000000000000000000000000000000000..e6f0856d1f6ebfb7c06fb2cead40e7e755e2b497 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002155.fa @@ -0,0 +1,8 @@ +>GCF_002008305_PROKKA_01494 +MTASTTKSERARRQRTVYSKRLELRLTERQLQLASETAQRLSAIRGKRVTVSDYVRLLID +DGGRGLVQRLERISQSPAGTLTQADADRVVAALQEVRDEVRRVGHNVNQMTVRAHQAKQV +VDDLDEVKASLSQIDAHVLDAAKTFLGYEGTDEDEG +>GCF_005280335_PROKKA_02202 +MTASTTKSGRARRQRTIFSKRLELRLTERQFRLASETAKRLSEIRDKKVTVSDYLRMLIE +DGGKGLIQGLERVSHAPAGILSQADVDRIVAALQEVRDEVRRVGHNVNQMTKVAHQSGQV +ADDLDGVKQALAGIDAHVLDAAKSFLGYEATDEEEG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002156.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002156.fa new file mode 100644 index 0000000000000000000000000000000000000000..21333ecd4f89c12a8da6b553e0f01ce148ac2816 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002156.fa @@ -0,0 +1,24 @@ +>GCF_002008305_PROKKA_01495 +MAAPIAAIVVASPTRNASRLLAYALNKKKGQTTDRFVVASGLNGAIPEVAAAQYRDNRKR +HGKNGERQVRVPDDKGGMRTITEGAYVQGYHVIQSFARDGEGALDPNDPEAWEEAHRLGR +KFALRLAGDGRMGVVVTQIDGRTGCIHNHLVLDSIDRQTGKSFASSNVKHKVLAQTHDEV +LREAGYAQQNELQSTAAERREPSEERARLRHEQWGANGRQGPEPFSVAVMKQRVREGMSD +PRSVSFETYAEVLAERGVRVERRGQDHPGLTYEMVLSDGKGGTVDPQPAYRRRASKLGRD +FMLATVEQALERNRTKQAVQPTGHRPLLDPSKYVALVGRADQVPAPAVTATPNADETERP +LLWRTYERMGLDWREARKVAPETEVEPAPTPDVAEPLPAPSAPAAEPIAAPTEPEDEAEA +QDEAQRAT-------------APAYRS-----PVRDRTVKRERSREFRERLAAADEHVVA +RLEAGEPVDDTVL-KGLGPDKIRSYRTSLHPQTQRALRRRQSMQGAAARAY--------- +--AAGQRELAQR------IRAEVAAGEYRWIEPAPDAVAQHEQDEPELGG---------- +------------------------------- +>GCF_005280335_PROKKA_02203 +MAQPIAAIVVASPTRNASRLIAYALNRKQGQTTDRFVAASGLNGAIPEIAAHQFRDNRKR +HGKNGERQVQVPDGEGGTVTVTEGVYVQGYHVIQSFARDGDGALDPSDPDAWEEAHRLGR +KLCRRLAGDGRMAVVVTQIDGATGCIHNHIVLDSIDRQTGKSFASSNVKHKMLAATHDEV +LAEAGYVQQNELQSTAAERREPSEDRALLKHQQWVAGGRQGPEPYSVAIVKHRIREAQGD +PRSVSFDTYAGVLLEHGVRVEKRGEKGAGLTYEMVLADGGGGVLKAQPAHRRRASKLGRD +FMLPAVEAACARNRARE-------------------VGRLRGLGAPVL---PPREESAVE +ALLRELTEARAKGRAGRR--------PGPT-------EAPAAPPRTP-----EPREPAEA +SQAAQRAAQAQQAAAVAAPVQSSAWRSRLWDLPPSNRTV---RTQQIIDAVAEWEPSARE +RLQSGERLDEPAIPKGVGARFLESYGQYLDPAVRTELEAREETRAQRREQFELEREHEEA +LQAVGRRPEAERTIYERGVRAQLDTARLRR-EAIEAAIAEGRYGRADVDGIVSEAEQAER +EASARRREQVAERAAAMRDEDRESDDPQPGD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002170.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002170.fa new file mode 100644 index 0000000000000000000000000000000000000000..e72f40610e029143af2aa263810f340c78db56c7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002170.fa @@ -0,0 +1,12 @@ +>GCF_002008305_PROKKA_01794 +MQIKDRTFLVTGGASGLGEATTRALLDRGGHVVVADRAGTAPEGAVFVEADVTDAVQVAH +AVAEATRQPGPLSGVVNCAGIGSAAKVISRDGPQPLADFERIVGVNLIGTFNVIRLAAAA +MAENEPDDDGGRGVIVNTASVAAYEGQVGQAGYSASKGGVVAMTLPIARELAAYGIRVNT +IAPGLFLTPMMHQLPEKARASLGEQVPYPSRLGDPAEYAHLVTHIVENQMLNGETIRLDG +AIRMAPR +>GCF_005280335_PROKKA_01082 +MQIKDRTFLVTGGASGLGEATTRALLDRGGHVVVADRAGTAPEGAVFVEADVTDAVQVAH +AVAEATRQPGPLSGVVNCAGIGSAAKVISRDGPQPLADFERIVGVNLIGTFNIIRLAAAA +MAENEPDDDGGRGVIVNTASVAAYEGQVGQAGYSASKGGVVAMTLPIARELAAYGIRVNT +IAPGLFLTPMMHQLPEKARASLGEQVPYPSRLGDPAEYAHLVTHIVENQMLNGETIRLDG +AIRMAPR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002176.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002176.fa new file mode 100644 index 0000000000000000000000000000000000000000..a7ff8de916fba51542d55dfcd9627107a7804006 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002176.fa @@ -0,0 +1,8 @@ +>GCF_002008305_PROKKA_02059 +MNQP------SMATLSS----------GKITLR---DARRGTTRDVELEPFEMAVHPLHD +RSTGRPLTPLTWFETINLCNELSNAEELQPAYTRAGDGRSVTWNTSADGYRLPTEAEWEY +ACRAGTTSPAYGPLEDIAWTGLDHLEGPQPVVRSENP +>GCF_020097155_PROKKA_02219 +MTPPAAEGHFSRATLTDLLCEKFIACRVKSSLHLDSDARRGTTRDVELEPFEMAVHPLHD +RSTGRPLTPLTWFETINLCNELSNAEELQPAYTRAGDGRSVTWNTSADGYRLPTEAEWEY +ACRAGTTSPAYGPLEDIAWTGLDHLEGPQPVVRSENP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002206.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002206.fa new file mode 100644 index 0000000000000000000000000000000000000000..90c87f69df83676119c54c18f9acf59c7ca142bf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002206.fa @@ -0,0 +1,24 @@ +>GCF_003691675_PROKKA_00767 +MTPVPPSSPSRLDALTAPTARHAHRLLVAKAIREFTHERLLTPVRGERVDDAGRHAYTLT +LGGVRWTFTARALPLEHLGVDPDSVCRAGDPDAVAVDRFVLDAAEVLGLAGEALDVYLEE +LASTFAARCHTLAGERPSAADLVDADYTAVEAAMSEGHPGFVATNGRIGWGATEYAMFAP +EGGRALHPVWLAFPSELGGRWTWPKTASAGAAVPAPPPPITEAVAGLWAERAAALDVDPE +AYTLIPVHPWQWEHRIQVAFAPDLAVGRLVHVGEDPDAFTAMQAVRTLFNASDPHAPQLK +TALSVQNMGFVRGLSPAYMSVTPAINAVVADLVDSDPLLARWGFGVLREYASAGYTGDAF +HAVGSKGPHTKMLAALWRESPLPRLAEGERVMTMAALLHRDGGGRSVAGALVERSGLTAA +QWLHGVVTAYVTPLVHLAAAYSTVFMPHGENIVLRLREGRVTGAFLKDIGEEVVVGADGV +PLTEQTRRIRIDLTDEDLSLSFFTDMLDGVLRHLADVMDADALLPAEEFYAVVGRVLAEY +TALGLADVERLGLDAEDFAHSCLNRLQLRNATQMVDLTDPSGSLLYAGRLANPVSAPLRR +ALAELRQDAAA +>GCF_023573625_PROKKA_00995 +MTPVP---PSRLDALTAPTARHAHRLLVAKAIREFTHERLLTPVRGERVDDAGRHAYTLT +LGGVRWTFTARALPLEHLGVDPDSVCRAGDPDAVAVDRFVLDAAEVLGLAGEALDVYLEE +LASTFAARCHTLAGERPSAADLVDADYTAVEAAMSEGHPGFVATNGRIGWGATEYAMFAP +EGGRALHPVWLAFPSELGGRWTWPKTASAGAAVPAPPPPITEAVAGLWAERAAALDVDPE +AYTLIPVHPWQWEHRIQVAFAPDLAAGRLVHVGEDPDAFTAMQAVRTLFNASDPHAPQLK +TALSVQNMGFVRGLSPAYMSVTPAINAVVADLVDSDPLLARWGFGVLREYASAGYTGDAF +HAVGSKGPHTKMLAALWRESPLPRLAEGERVMTMAALLHRDGGGRSVAGALVERSGLTAA +QWLHGVVTAYVTPLVHLAAAYSTVFMPHGENIVLRLREGRVTGAFLKDIGEEVVVGADGV +PLTEQTRRIRIDLTDEDLSLSFFTDMLDGVLRHLADVMDADALLPAEEFYAVVGRVLAEY +TALGLADVERLGLDAEDFAHSCLNRLQLRNATQMVDLTDPSGSLLYAGRLANPVAAPLRR +ALAELRQDAAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002214.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002214.fa new file mode 100644 index 0000000000000000000000000000000000000000..562ef1d3445b180f0edfb7883b9b443fc34bcabb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002214.fa @@ -0,0 +1,6 @@ +>GCF_003691675_PROKKA_01745 +MNAKPEKDLRRTVDILFRPARVAVLIDGCYWHGCPQHYIAPKANGGYWSDKVATNRARDL +ETTRILTERGWLVLRFWEHEDPAVVAERVVAVVNERRPRRTTGAS +>GCF_023573625_PROKKA_01973 +MNAKPEKDLRRTVDILFRPARVAVLIDGCYWHGCPQHYIAPKANGGYWSDKVATNRARDL +ETTRILTERGWLVLRFWEHEDPAVVAERVVAVVNERRPRRTTGAS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002216.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002216.fa new file mode 100644 index 0000000000000000000000000000000000000000..0f407db0e7c40062f8a807f5c81e71ada9c489c4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002216.fa @@ -0,0 +1,10 @@ +>GCF_003691675_PROKKA_01749 +MIGALRYVLSGGAPLAVETLREAEAEAAFGVPVREAYGLSESCGPVCFNPMDGPSRPGTV +GRPLEGVEFRIVTPEGVEVPERDTETPGELRIHRPVVMSGYLGLPEAGAAAFDDDGWLRT +GDLARRDEEGYYRIVGRLKDINIRNGYNVYPREVEDALYVHPDVAEAEFSAFVRERLLSY +KGPQPVTLMDSLPKNGTGKIVKDLLR +>GCF_023573625_PROKKA_01977 +MIGALRYVLSGGAPLAVETLREAEAEAAFGVPVREAYGLSESCGPVCFNPMDGPSRPGTV +GRPLEGVEFRIVTPEGVEVPERDTETPGELRIHRPVVMSGYLGLPEAGAAAFDDDGWLRT +GDLARRDEEGYYRIVGRLKDINIRNGYNVYPREVEDALYVHPDVAEAEFSAFVRERLLSY +KGPQPVTLMDSLPKNGTGKIVKDLLR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002217.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002217.fa new file mode 100644 index 0000000000000000000000000000000000000000..b766f1e217592bfd766949b52369da25302ff982 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002217.fa @@ -0,0 +1,8 @@ +>GCF_003691675_PROKKA_01782 +M-------------------------------ADDLAQCYLMSYPPDVAASDLDEAREEM +NATFRGDYGKLRADASTTAWVGGRLAGAIMVVTHSIWDEHLTGPFIIDLFIDPHARGKGI +GRALVQHAIATCCDAGDHTLSLRFGQGTSDAAMRIYQRLGFRPV------G +>GCF_020097155_PROKKA_01295 +MSTDLLTLRLPAAHAADHVRGDFEFRGLDTGTTDDLARCYLMGYPPGVAASGLAEAREEM +DATFRGDYGELRADASATAWVDGRLAGAIMVVTRSIWDADLAGPFIIDLFTDPAVRGKGV +GRALVQHAVDTCSAAGDAAVSLRFGEGTSEAAMGIYRRLGFRPRTGTQRGG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002230.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002230.fa new file mode 100644 index 0000000000000000000000000000000000000000..6077ac99729d257014fa7394c34ab1c8db8b32d5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002230.fa @@ -0,0 +1,6 @@ +>GCF_003691675_PROKKA_02229 +MNGPTC---RHCADWAYGYAEGYAQGHASGLAAGRVQGAAEGPAHPAIADSVARMFAGWD +GAEAAHARSAAGFRDWYAQARQEENAHDIAA +>GCF_005280335_PROKKA_00037 +MSTLETVAERVAADRAL-YAAAYAQGHADGLAEGLAQGA----AHPAITDSVARVFAGWG +GAEAAHARSVAAFRAWHTAARAELKE---AA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002235.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002235.fa new file mode 100644 index 0000000000000000000000000000000000000000..bde3467c2beb87733ceb4b9e2ba48eae46f5a053 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002235.fa @@ -0,0 +1,16 @@ +>GCF_003691675_PROKKA_02305 +MVQEAGVPEESGDAERRLREAWSALLEDADRIADEIAAATLGGDQGGAWSTPELRARLRR +STREHVRRGLRGLAGVPSGEGAGGRLVDTWRATGVERARQGVPLETVISTYTSGNRLLWE +ELGRRVREGRLDITTEELLEAGRRLWEDLSVTGEVLSAAYRRETARLTLRDLRRQEDCLA +GLLEGKGADPVYAEQAEEILGVRATAPLACVVALAEDPGSDVLHHPEDRMGRLGATSRWA +VREGALYGVVEPPSTDEEWLTEALGPLVEGQVGVAWARQGIPETAAAFRLATRAAHTLPP +GERRLAWASHRLPEVLLESSPEVAALLVEEVLGPLRALPADQRATLMETLRALLRRSGSA +TLAAEDLICHRNTVIYRTKRLVELTGCSLQDPRGRLMLELAVLAADRAGGPVRRARPISP +>GCF_023573625_PROKKA_00289 +MVQEAGVPEESGDAERRLREAWSALLEDADRIADEIAAATLGGDQGGAWSTPELRARLRR +STREHVRRGLRGLAGVPSGEGAGGRLVDTWRATGVERARQGVPLETVISTYTSGNRLLWE +ELGRRVREGRLDITTEELLEAGRRLWEDLSVTGEVLSAAYRRETARLTLRDLRRQEDCLA +GLLEGKGADPVYAEQAEEILGVRATAPLACVVALAEDPGSDVLHHPEDRMGRLGATSRWA +VREGALYGVVEPPSTDEEWLTEALGPLVEGQVGVAWARQGIPETAAAFRLATRAAHTLPP +GERRLAWASHRLPEVLLESSPEVAALLVEEVLGPLRALPADQRATLMETLRALLRRSGSA +TLAAEDLICHRNTVIYRTKRLVELTGCSLQDPRGRLMLELAVLAADRAGGPVRRARPISP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002236.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002236.fa new file mode 100644 index 0000000000000000000000000000000000000000..456ec22cd57b77bc9e66592e89cd02800beb527e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002236.fa @@ -0,0 +1,20 @@ +>GCF_003691675_PROKKA_02312 +MMAVEAQRSRLVVLVAEAFAIQREFKTFLGKPRRGDKALRPVYEAETSKVHQRMAWACEA +LHEGTVATASPLCDRPTGPRSLGEAANPVPVVAGIIGDMKYSESETAAYLKSTILRDFSA +PLSTEPRKDKGTYYSRRVGCYEAPVPVLLRYPFDLLGIQHTGPGEKFAWAVEFNYKGFPA +YLGYHKFGVKAGIICSLSRAESENHLNMMLDRIFSAAHVVEKLLSERAPEAIRQGNVTVA +NQYRRLRAPYEYHRDRAINPVFVADEREHRRFNGGQSWTHISGKMVMKMHASHDLVASTV +AFLSLLEHLFVLSLPFAGYNPESEDLTAFIGDRWGVKWERIIGDKNPEARDLRRRMSEVV +EQWRNPYSHGGFEKGHGSSLYVHTPGLGALPMGLTRVRESTFFSFNPAPKGDIESIYSLF +DEIESYLKSILPGAYTWIESGLDVRFDSEFAQELAEASQIDGGVEKLVDQYICRQEMIDN +MDYY +>GCF_023573625_PROKKA_00296 +MMAVEAQRSRLVVLVAEAFAIQREFKTFLGKPRRGDKALRPVYEAETSKVHQRMAWACEA +LHEGTVATASPLCDRPTGPRSLGEAANPVPVVAGIIGDMKYSESETAAYLKSTILRDFSA +PLSTEPRKDKGTYYSRRVGCYEAPVPVLLRYPFDLLGIQHTGPGEKFAWAVEFNYKGFPA +YLGYHKFGVKAGIICSLSRAESENHLNMMLDRIFSAAHVVEKLLSERAPEAIRQGNVTVA +NQYRRLRAPYEYHRDRAINPVFVADEREHRRFNGGQSWTHISGKMVMKMHASHDLVASTV +AFLSLLEHLFVLSLPFAGYNPESEDLTAFIGDRWGVKWERIIGDKNPEARDLRRRMSEVV +EQWRNPYSHGGFEKGHGSSLYVHTPGLGALPMGLTRVRESTFFSFNPAPKGDIESIYSLF +DEIESYLKSILPGAYTWIESGLDVRFDSEFAQELAEASQIDGGVEKLVDQYICRQEMIDN +MDYY diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002239.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002239.fa new file mode 100644 index 0000000000000000000000000000000000000000..b68d5b6c5c7fa32e5598b10b97d0165450977713 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002239.fa @@ -0,0 +1,16 @@ +>GCF_005280335_PROKKA_00082 +MTVRVAAAPDVLSWAAERAGWDDALAEKHFPRFHDWLTGTQQPTLKQLEEFAHKTHTPFG +ALFLPEPPRMDLPIPDLRT-VGGAGVSEPSPDLLDVVHECQLRQDWYRDEALRQGEEPVA +LVGSATVDDDPEAVGARLRHELAIQPVQNKAGAESFRRRLVARLEGLGLLVMISGIVGGN +TSRALDPQDFRGFALSDPVAPLIFVNGTDAPVAQHFTLLHETAHIVLGHSAVSGSRMRGG +TGEEA--WCNRVASAALVPLDEVRRARRDSAGVPLAELVEDLAARYCVSRSVIYLRLRVA +GLVSEDVVSRHFEEQDADAPGRTPRRRR------ESGGDYYRTATVRLGKPLIRAVLRST +REGHTSYREAMRLLGTHKIEVLHEMGRQAGV--E +>GCF_023573625_PROKKA_01542 +MTVRVSVSPDVLLWALDRSPDPDAVATA-FPGVDRWVSGEAEPTVKQLHAFAARTGTAYG +YFFLQAPPAIELPIEDFREGFEGERYRDPSVNLLAVLHQSLRRQDWYRDYAIENGFADVS +VVGRGA-GMSPLEAAADMRRELNYEVRSRVGNWSDQRKRLLAAFEALGGLTVVTSMVENN +THRPLDVDEFRGFSLIDDMAPLVFVNARQTINGQLFTLAHEFAHVWRGVGGISDEDLRYE +PRNEVEQWCNDVASEFLVPSNDLRERYAGVSSLRLTEQIERLASIYRCGTLVVLQALRRN +RLYD-------FEDFQTDYDAEVERLRRFERADSGPGGQFLYNQPYRIGTRLSRALISDA +MAGRTRFTDAARLMSFKSMKNFDSYASYLGTVRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002258.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002258.fa new file mode 100644 index 0000000000000000000000000000000000000000..01a34e59af70a87c18fde592a012c963f30a4f5b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002258.fa @@ -0,0 +1,6 @@ +>GCF_005280335_PROKKA_00396 +MPKKYTPELRERAARMVLERQAAQGGPRSHSIRAIAPQVGVGEETLRMWCNRHGHEITQA +PAGEDLQQENKRLKRELAEARRANEILKAASAFFARELDRPTTR +>GCF_020097155_PROKKA_00309 +MPKKYTPELRERAVRMVLERQVAEGGPRSHSIRAVAPQLRVGEETLRMWCNRHGHEITQA +PAGEDLQQENKRLKRELAEARRANEILKAASAFFAAD-----AR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002259.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002259.fa new file mode 100644 index 0000000000000000000000000000000000000000..84e6c04c004f6b429c7eefeeef5aef9f2f31bf03 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002259.fa @@ -0,0 +1,22 @@ +>GCF_005280335_PROKKA_00438 +-----MIDAEIAAAHPIQPIARIAAEAGIAEDLLIPYGRHMAKVDVHALTAPEDGRVVLV +TGISPTPAGEGKTTVTVGLADGLNMLAGQADAPAAVAGSRTVVALREPSLGPVFGIKGGA +TGGGHAQVVPMEAINLHFTGDFHAITSAHNLLCALVDNHVQQGNALGIDPRTIALKRALD +MNDRSLRDVVTGLGGRTQGVPREGGFEITVATETMAVFCLAADLADLKERLGRITVGHTY +DGEPVTASQIGPHGAQGAMAVLLKDAISPNLVQTLGGTPALVHGGPFANIAHGANSVIAT +RTARRLGDLVITEAGFGADLGGQKFMDITAVAGGFPPAAVVVVATVRALKLQAGLSLRDV +KAGAAETAAITGRDAEAVRAEHLDALRTGTANLARHVANMQEYGVPVVVGVNRFTQDEDA +ELEVLRAWGAEHGVPVAVADVWGGGGEGSLELARLLGEHLPAPGEPAAEVTRLWEEDMDV +EEHIQAVVRRVYRGARAELTPAARRQLAQLRDRGLDRLPVCMAKTQYSFSDDPALLNAPE +GFTVTVRELSAKTGAGFVVALTGAVMTMPGLPASPAADRMDVAEDGTVTGLF +>GCF_020097155_PROKKA_00391 +MTEAPLTDAQIAAAHPIRPIARIAAEAGIDEELVIPYGRHMAKVDVHALTAPEDGRVVLV +TGISPTPAGEGKTTVTVGLADGLNLLAGQEDAPAAVAGARAVVALREPSLGPVFGIKGGA +TGGGHAQVVPMEDINLHFTGDFHAVTSAHNLLCALVDNHIQQGNVLGIDPRTVSIKRALD +MNDRALRQVVTGLGGRAQGVPREGGFEITVATETMAVFCLAADLADLKARLGRITVGQTF +DGEPVTASQIGPHGAQGAMAVLLKDAMRPNLVQTLGGTPALVHGGPFANIAHGANSVIAT +RTARRLGEIVVTEAGFGADLGGQKFMDLTSVAGGFPPAAVVVVATVRALKLQAGISLTDV +KAGVAAAAERAGRPAAEVEAEHVAALRAGTANLTRHVENMQSYGAPVVVAVNRFAQDADA +ELDALRAWGAERGVAVAVADVHGGGGEGALELARTLGEALPAPGAPQAELTRLWTEEMDV +AQRIEAVVRRIYRGTGVEYSAVARRQLRDLADRGLDRLPVCLAKTQYSFSDDPALLNAPE +GFTVHVRELSAKTGAGFVVVLTGAVMTMPGLPASPAADRMDVSADGVVTGLF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002264.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002264.fa new file mode 100644 index 0000000000000000000000000000000000000000..632e602a066ccc4be922415a5ea022e6dbe94108 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002264.fa @@ -0,0 +1,10 @@ +>GCF_005280335_PROKKA_00507 +MTLTAALLSFALLALLITITPGLDNALVLRYAGRQGSGAAFAASAGICAGLFVWALAASL +GISALLAASEVAYTALRWIGAAYMVYLGVRMLISAIRGGYG-APGGSSVATVRSRDAFRT +GFTVNLLNPKVGAFYVALIPQFMVTGVAPAAMGVLLAVVHIAVCMAWFVVLIALVGVVSG +WLQRPSVQRGLDGVVGTALVGFGARLALAKA +>GCF_020097155_PROKKA_00443 +MTLTVALLSFALLALLITLTPGLDTALVLRYAGRQGSGAAFAASAGICAGLFVWAVAAAL +GVSALLAASELAYTALRWIGAAYMVYLGVRMLIAAVRGTSGDHDGDAAPALVRRGQAFRT +GFTVNLLNPKVGAFYVALIPQFMVPGVAPAVMGVLLAVVHIAVCLAWFVLLIALVGVVSG +WLRRPAVQRGMDGVVGTALVGFGARLALAKA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002279.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002279.fa new file mode 100644 index 0000000000000000000000000000000000000000..72a8c94bedc5ea8dfa1014710bfb8fc6d03f76a9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002279.fa @@ -0,0 +1,10 @@ +>GCF_005280335_PROKKA_00671 +M-----------------------------------------------GEARRGTEQARL +LRQVVLLHQEVRIHLCRLMGMHDTDYAALALLMRGRLGPSALASALGLSSAAATAVVDRL +EAAGHAERLPHPQDRRRTMVRLLPASQEPVQAEVDRMADATGALLEDFDERERAAIARYL +AGTRDALEQWRDDVAARVAARDDVAAVDAEAGR +>GCF_020097155_PROKKA_00587 +MARLLDFLEKGVDVPEAIQSLDAASTALRESPMLSPISEPAPAIRPVSGELKGVTSAART +LRRIIRLNAQIRVQMRLLMGLNETDYAALSVLMRAPTGPTELARNLHLTTAATTAVVDRL +VSGGHAVREPHPQDRRRTLVRALPESRSQAMAEVQPMVDMVGDAMSGMTDQDRAAVERFL +DSVADHMDAWRDDLTARVTQQAEQP-------- diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002280.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002280.fa new file mode 100644 index 0000000000000000000000000000000000000000..3e616861ac6ba87a466801ad931c604adc9ecb18 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002280.fa @@ -0,0 +1,34 @@ +>GCF_005280335_PROKKA_00710 +M----------------------------------------------------------- +------------------------------------------------------------ +------------------HQSLRAYASNRDLGHGAHAVTAAARTAGELTYDGLPREPLLY +AGIATALLTLGLIPLALWFRVRRRIDRLRRRLRSARTDLARVILDLEAVEVAVL-TTPEG +ASGGSSGRSSAPDLRGGLARLTDSAFALARGEEDLARRLRR-----------PDRGAEAD +LQGHESAVARVRGQAAGLHDA----------ATLQSRHAGAQTAADRLVAPLVMAAQAVV +SRARRVSDGRSPEAPSDRPRSDAVADRLQSAADALLQVAADAGSGDLTGLAPRVLEAEGE +LARASADLVQHLRAAAGPAGGPIDEAVTAVPSLRPDPEDAARRANAGLPAVGPADAPQAL +STAYAAVLVAGAADPQDVVAAVVDADRELRGSVAPTPDEWRAAVARVAE---ERRRAGER +ERSASSGPWWAAVGTAVGCLVLAGLIARPLAE----AATAEPGWDLAGSDEVASLVVDGM +PQGVLTEEHLSVEDVRGYLEETLPAGLDVTVAVRPAASHLVP--------DPSGPSSESI +MALDRSATLDGLARLKAEFPDLLEPGTGDLRPGAVIVPVFTTAGGQVIVDASLTGVVAYG +TESWLEGGGFERMNVSRGWEPDLTEVSVAHEI-EDVARGVQS------EG-AFESDVETS +TLWALLTVSGGIVLLMLALAARAVGGAMARRFGVGPARGTVARARG---RLERLMLDLDL +QRLDAVAVLGRGPAADAREAEQRLWESALVSAWREADEIERLPLPQQWDEDVKRRAAALA +ARVEDLAAHRSDVAARAE----------L +>GCF_005280335_PROKKA_00768 +MRAPVLAWIAGACALLTAVLVGLAAWVTTVEPRHTVRIEVAEGTPVGISQGTVDAVLAQR +PVRSWQPMTLRVTDEHLTFEETFRGEGLPEGVDVLLSTQTERLGAQRPDLDASERPERDA +AGVGIRPGLGLDEDHADGHDLERMYLAGLGAGQGPTAVVNVARAMGEASYAGPARVPALH +LGLALPALAGALVATALWARARRRQADVRRALDRGRASLARVLLEVEALEVSVAGVAPHA +LPTGHSQRR---------AELRRSLQHEARRERDLTDAVERLTARDAIRGTASDDDAGGR +PGGRGRGGRRRGGRSRGTRPASSWRDLGQRVAAFEDSTRGLEDAVEQLIDSADVLA-ATP +RRTRVVDRVLAPVAVEMLALTGLLREAPEGAVDPRIRRALDEAYDDLLAVA--------Q +HERLDRDAARRWRDAEKRLAGHARE-VTAQLERFPLGADAGRVAAA------PEDDSLA- +--ALRAGLGLSARPAGDLLTHLARARRTAVALLGPLTDEHRGAPSSSGEGAPGASRRADR +SDALASAPHLRRAAWAL-VTVLAVLVSVPFAQRAADAALPPDPYRLVGSEALRSVSVDGP +ADGI------DVERVAEHVDGTFPRALDVVVAVRAGEAYLTPRATRTDAEDGKGPWSELG +VDLDPTATAEGLRRVVAESGALLDPATGELRRDAVVLPVFVFEDGRRVMGRVPLNTVDTA +-EPWTVAG------VVLSSLPHAQGASLAGEVGSAVVRAGQAMQSADREGEAPAPDVEPA +VLTTVLTLGFAAALLTLALALESLATTAAGLRGLGSLTSSGRRLQAITRRLEALMLGLDD +SRLDAVAVLGRGPAGTAKEAGQRLYERELVAAWREAKALAGTSVVERLRGGMADRLDGLE +ATAAALEHREADVADRAAEVLERARRHPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002282.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002282.fa new file mode 100644 index 0000000000000000000000000000000000000000..0ba420d7e32bfce2843de58297acb2d896f9dd4d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002282.fa @@ -0,0 +1,6 @@ +>GCF_005280335_PROKKA_00735 +MLQRPLEPAQYVSLAYSDALIAAGVSASVGTVGDSYDNALAETVNGLYKAELIHSKRVWE +SVEEVELATMGWVHWWNTARLHEALGYCTPAEVEATYTHDQDSAPVAS +>GCF_005280335_PROKKA_00745 +MLQRPLEPAQYVSLAYSDALIAAGVSASVGTVGDSYDNALAETVNGLYKAELIHSKRVWE +SVEEVELATMGWVHWWNTARLHEALGYCTPAEVEATYTHDQDSAPVAS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002292.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002292.fa new file mode 100644 index 0000000000000000000000000000000000000000..455e56a391c45a4d00e734996027889021da4170 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002292.fa @@ -0,0 +1,10 @@ +>GCF_005280335_PROKKA_00909 +------------------------------------------------------------ +----------------------------------------------------------MD +GVRGTWAPGTVRGVLHASGVGAATGYPGVVLATPAATEHPAAQIADVPAQLLVSVDLPDH +WDRLDAFEGAGYRRVPAVVAL-DDDAVRPAYLYELVPDAVPPSA +>GCF_023573625_PROKKA_01868 +MALTGVPELGGWRVTPSPTPAGTTPPELTITYATDDFATALALANRIGEAAEAADHHPDL +TVSYGRLTVGMHSHDVRALTSRDVRLARTVARLASEVLAPHALAAYGTLAPGRSNAHVMD +GVRGTWIPGTLRGTLHASGIGAATGYPGVVLAGTA----PAHATTDVPAQVLVSADLPDH +WDRLDAFEGAGYRRVPGVVALEDDDAVRPAFVYELVPDAVPPSA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002294.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002294.fa new file mode 100644 index 0000000000000000000000000000000000000000..54045618c38abf4c552af97995b6860842c784fe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002294.fa @@ -0,0 +1,18 @@ +>GCF_005280335_PROKKA_00933 +M----------------------------------------------------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------AAGGFTLGLGQPLTMSLVTQA +VPADWRSSALAVRLMGNRAGQVVLPATAGLLAAPLGPAAAVWFACAVLAASGLERTAAAR +RRR------------------- +>GCF_020097155_PROKKA_00864 +MTESRTGAAAGERTTAGPGAGWLWALIGAAVLTQAATNLARPVTSYHLLSLGAPDAAVGL +ATAAYALLPLVGALWLGRVTDRLSSAAPLVVAGAAVVAAGAAGLALATDVAAVLAASAVL +GVGHLAFTIAGQAAIARRAPAHLLDGAFGWFTAAFSLGQMLGPLLSGGILTAVGGTPRDA +TTLALWVSAGLALAGALPVLLAPGAPPGTRDPAAREASAESGAAPGDDAGRPTVRAILAR +PGVGSAMLASLALLAVLDILTAFLPVVGERHGVSAAWVGALLALRGAGSLVSRVFLPRLR +RRFSRELLLAVALWASAATIAAVPVGMTSGLLWLAAAAAVAGGLTLGVGQPLTMSVISEA +VPHAWRSTALAVRLMGNRLGQVVLPAAAGLAAAPLGPSAAVWTACAVLAVSGAERAARSR +RRRPPRSVRSGGGRGGSASADQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002298.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002298.fa new file mode 100644 index 0000000000000000000000000000000000000000..fedb9452f4d0d9324f0e371c5d8f3e00db6be36f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002298.fa @@ -0,0 +1,10 @@ +>GCF_005280335_PROKKA_00978 +MG-----------PGQH---------------------AKLTMEGIAARAGVSKQTVYRW +WKTKVDVLVEAVG--AGYLVIPLPVIPDTGDLREDLAHWLREMQEEIDGGGATHLSQSLV +AAIATADSQSRQIHGMLVAPVREQLHARFRSARLGDGVDREMLAETVGAQLVMRVLFA-- +--------EPTDEEWVRRLLD------LVAPEGS-- +>GCF_020097155_PROKKA_00942 +MTSLTPPRAGTIRPGGRTARVRAEVLRATRELLTQQGASAMRMELIAERSGVHRSTLYRR +WKRPAGIIADLADDIAGTI-----AVPDTGDLGQDLRQLAGRLAHQLDGDGG-----ALV +RALLGWPDQEVQQH----------LEDFWRDRRADVGLVLQHHGIDADPALVTRLLASPL +HYRSLIERHPVDDETITAAVESTILAVLRTPRTSHR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002306.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002306.fa new file mode 100644 index 0000000000000000000000000000000000000000..d86434e9836eb2c42c26fa54800ffc0b274f3f51 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002306.fa @@ -0,0 +1,10 @@ +>GCF_005280335_PROKKA_01264 +MQD----ARRALEAVGSVPDLAGTAVAVMGVSGSGKTVLALRLAAALGVPFAEADEFHSP +EAVAKMAGGTPLTDADRLPWLHRIRDWTAVAAAERGAVVTCSALKRSYRDLLRDGPARVV +FLHVDAPQSEIRDRMARRRHYMPPTLLHSQAATLEPLGVDEPGAVLANDSTVEDLTERAL +RVLAAR +>GCF_020097155_PROKKA_01173 +MTGQAGPAR-------ALLDLAGTAVVVMGVSGSGKTVLAQRLAQALGVPFAEGDEFHSA +EAVARMAGGTPLTDEDRGPWLRRIRDWMGSGVAARGAVVTCSALKRSYRDVLREAPVRVV +FLHVETPAEQVLHRMERRRHFMPPALLPGQLATLEPLEADEEGVVLANDSTMEELTERAL +RALADL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002314.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002314.fa new file mode 100644 index 0000000000000000000000000000000000000000..ed856f1ab6afaf6f80b1fa402203dceeea22de13 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002314.fa @@ -0,0 +1,14 @@ +>GCF_005280335_PROKKA_01685 +MLSFGIREAAGSQPATGPRRTGRSPPLEASSGASGRQTHAPSSGSRRHPCTGACAGRTTS +VSHSVVSGFHPARTVATSSSSGRQRVAEARQPRAVRWTASHSWATQSRSGTTHRPALPFT +RCQSWPLEALTSRGTLRHSRTESSGLLILYVRRTPSTGVTAADPAPESSPLRSNPAGSCE +TLATMPTGIDHQILYRFAVGSAGVLPLRGLPPAAPPVPRPRGRLGGPGAADSGRLVPTGR +SSTGSPPAGRPSGEPALSPAHARSPVSGLHGRADPLPARPLRRDPASTSPPPPFRPEQHG +RVLPPPGPRGRGQRGPARADRPRLPDGTRRRAARW +>GCF_023573625_PROKKA_01156 +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------------------MRSNPAGTCE +TLATMATGIDHQIPYRFAVGSAGFLPLRGLPPAAPPAP---------------------- +------------------------------------------------------------ +----------------------------------L diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002315.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002315.fa new file mode 100644 index 0000000000000000000000000000000000000000..34f68dfbaa023602a306def28a2ebfc42da23516 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002315.fa @@ -0,0 +1,8 @@ +>GCF_005280335_PROKKA_01919 +MRVHIATDHAGMELSAHLVEHLRGKGYEMVDHGPEEYDALDDYPGFCINAARAVVADREK +GLDSLGIVLGGSGNGEQIAANKVAGVRAALAWNLDTAKLAREHNDANVVAVGGRQHSLEE +ATAIIEAFLAEPFSEDERHVRRIGKIAQYEQTGEVVM +>GCF_020097155_PROKKA_01867 +MRVHIATDHAGMELSAHLVEHLTAAGYEMVDHGPTEYDAQDDYPGFCINAARAVVADREQ +GLDSLGIVLGGSGNGEQIAANKVAGVRAALAWNLDTAKLAREHNDANVVAVGGRQHSLEE +ATAIIEAFLAEPFSEDERHVRRIGKIAHYEQTGEVVM diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002318.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002318.fa new file mode 100644 index 0000000000000000000000000000000000000000..e5ebd72957dd735cfb466dcc2481264b3c8047ac --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002318.fa @@ -0,0 +1,12 @@ +>GCF_005280335_PROKKA_02122 +MRAAAGGGPGPDRAALDRLAWRLPVRRVTEHPRSPADRGTWPATVPAVRQLLDEGLDLSA +ATVVVGANGAGKSTLVEAVAEAFGLNAEGGTRNVVHETRRTSSDLAEHLQLARGAQATRD +GVFLRAETMYGLFTYYESVFRGADHHRRSHGEAFLQFCAERAGLTGLWVLDEPESALSFD +GCLALIAHLRDILADGSQVILSTHSPVLAALPGARILLLDERGITPTEYDDLPFVYHHRS +FLDSPQRYLRHLYDA +>GCF_020097155_PROKKA_02013 +M---------PEVGIDATPTW--PVRQVSEHPRAPMPRESWPATVPAIAQVLDAGLDLGP +ATVLVGANGAGKSTLVEGIAEAFGLNAEGGTRNVRHETRRTTSPLAGHLLLTRSAGAPRG +GVFLRAETMYGLFTHLEQNLIGDVLHERSHGEAFLDYLQERAGVRGLWVLDEPESALSFD +GCMALLVLLADVLEGGSQVILSTHSPLLAALPGAQMLEVGPWGLRDTAWEDVEAVQHWRR +FLDSPERYLRHL--R diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002347.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002347.fa new file mode 100644 index 0000000000000000000000000000000000000000..fc2cbd3d302aadd7208bbcd5d665d929faae8255 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002347.fa @@ -0,0 +1,30 @@ +>GCF_020097155_PROKKA_00642 +MTSTTH-------HQEQPVSNRDVIRVRGARTNNLRDVDVDIPKKQLTVVTGVSGSGKSS +LAFDTIAAESQRLLAATYPAFVQNLMPHLPRPDVDTLEGLSASIVVDQAPLGANPRSTVG +TATDAWSLLRQLYAGHGTPPVPGPHALSFNAAT--------------------------G +MCPACEGTGRTATLDVDLVLDRSLSLNDGAITFPNFTVGSLFWKVYARSGAFDNDKPVQS +YTPAELEHLLTGTGPNVDTGTYPMAYEGVLTKITRLYLSKDPAALKPRLREALELAATTG +PCPGCAGTRLNSAARACTIDNTPITTCHTMPATDLHRWLADLDLPAAAPLIAQLQSLLAN +LTRVGLGYLALDRPTSTLSGGEGQRIRTVLHLDSALTDLTYVFDEPAAGLHAHDTAQVVT +LLHALRDKGNTVLVVEHHPDVITAADHVIDLGPGAGTDGGTITFQGTPAQLTHTHTPTAA +ALAARPTLNLTPRTPTGTLRIRDATTHNLHHLDVDIPLGVLTCITGVAGAGKTSLL-TNL +PRRDDLAVIDQRPIRGSRRSTPATYTGVMDWLRDAFAKAGSTPGHKLKPAMFSANSAGAC +PDCTGLGVTYLDAPGSGPVPVTCTTCNGARYTADVLTHTLDGLTIADVLGLPVADAATRY +TNTPAGPP-----LAGLVDVGLGYLTLGQPLSTLSGGERQRLRLATRIAQSATVYALDEP +TTGLHMSDVDTLTRLLHRLVDTGATVVVADHHLNLIATADHVIDLGPDAGPGGGHITYQG +-PAADLATTDTHTGRALAARLAL +>GCF_020097155_PROKKA_01228 +M-PTPHASAAPAPHTAHPADGHDVIRVHGARTHNLQDVSLELPKRRLTVFTGVSGSGKSS +LVFGTLAAESQRLVNETYPSFVQGFMAAMPRPDVDVLEGLTTAIVVGQERMGSNPRSTVG +TATDATALLRILFSRLGTPHIGSPQAFSFNVASVSGAGAVSTQKNGRTVKERREFSVTGG +MCERCEGTGRVSDIDLAALYDEELSLEDGALKIPGYSMDGWCGRIFRGAGLFPVDTPIKK +FTQRQLDALLHKEATTITVDGINLTYLGLIPQMERSMLSKDVESLQPHIRRFVESAVAFG +TCPDCHGTRLNERARSVTLGGASIDQVCALQITDAAAWLRGLDAGPAAPLVAGLQELLDA +FERIGLGYLSLDRATGTLSGGESQRVKMIRHLGSALTDVTYVFDEPSVGLHPHDLARVNA +LLTDLRDKGNTVLVVEHKPETIAIADHVVDMGPRAGADGGRVTFEGTVEELAASDTLTGR +HLKDRAALKGEVRTPTGVVEIRGASEHNLQDVDVDIPLGVLVAVTGVAGSGKSSLVHGSL +AGREGVVVIDQAPITGSRRSNPATYTGLLEPLRKAFAKANG-----VKPGLFSPNSDGAC +PACKGAGVIYTDLATLGGVESVCEECQGRRFLPEVLELTLAGRSIADVLEMSVDQAAAYV +AEGEARLPAAQKVLGRLQDVGLGYLTVGQPLTTLSGGERQRLKLAVQMGERAEVYVLDEP +TTGLHLADVDQLLALLDRLVDGGTSVVVIEHHQAVMAHADWIVDLGPGAGHDGGRIVFEG +TPAALVADASTLTGRHLKEYVGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002348.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002348.fa new file mode 100644 index 0000000000000000000000000000000000000000..172fe285fbab8dc7726965bfc010070500d8508e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002348.fa @@ -0,0 +1,10 @@ +>GCF_020097155_PROKKA_00666 +M-----------SAEPDGMRPHSPSAQEAYAARAVEYADLLGRMDAVADADKRLVEAWAQ +RTGGVLADVGCGPAHWTAYLHSLGHDVRGIEPVEEFVAHARRAHPEVRVERGSFETLPTA +AVDGILAWYSIIHTPPAEMPHLFEHAHRSLRPGGSMLLGFFAGDEVEPFDHAVTTTWHWP +VDALSRLLTTAEFTVVDRGTRQDPGARLHGWIEADRE +>GCF_020097155_PROKKA_00938 +MEAGTLDAEGGTTITADDVHGENISSCAAYGARAAEYAELLGTMAAVADDDRLLVEAWAH +ETGGSLADVGCGPAHWTAHLAALGHDIVGVEPVDEFVAHARRVHPGVRVETGSFRTLPAS +TFDGILAWYSMIHTPPPEATLLLEHAHEALRPGGSLLLGFFAGDRVEPFDHAVTTAWYWP +LDDLTSVLTAAGFTVTDRGTRLDPGTRRHGWMRAHRN diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002358.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002358.fa new file mode 100644 index 0000000000000000000000000000000000000000..aadfc530485da5e8b97ac03442ac259fcb3ea838 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002358.fa @@ -0,0 +1,18 @@ +>GCF_020097155_PROKKA_01195 +MGVLKDLKERFERERVELHLDDIQGLVLRERPEPYVGAHAMLTVEEAEGGRDFVRRLAEH +VTSAQDWADDLQSWTGVAISFAGLRALGLPEDPLASFPLPYQQGMAARAQQLMDTGPNAP +EHWDEAFTQDACHIALTIYAADADALDAALDQAQQVLDHSTGVTLVATHRFGVDELNKNP +FGFRDSISQPTVAGSGVRPQPGQERSISAGEFILGENSETGSPLAVPQPDVLGRNGTYVV +LRKFASRVGAFNEYLASQSPDPEEQHRIAAKMFGRWRSGAPLVLSPDHDDEALGNDPERR +NDFTFEDDPKGLMCPHSSHMRRLNPRDSDLSIMTDVNIKRIIRRSSTYGPGWSPEVTSAD +DAKEDRGIYFIFISARAFDTIEFMQQEWINGGNFVDLGSERDPIVGLHEDDPTQGRFTIP +AEPARKRINGITTFNRMAGGEYLFMPSLRALRWIGEAGWTSDQSDAEA +>GCF_023573625_PROKKA_01534 +MGVLKDLKERFDRERVELDLDDIQGLVLRSRPEPYVGAHAMLTVEEAEGGRDFVRRLAEH +VTSAQDWADDLQSWTGVAISYAGLRALGLPEDSLASFPLPYQQGMAARAQQLMDTGPNAP +EHWDEAFTQDACHIALTIYAADADALDAALDQAEEVLEHSTGVTLVATHRFGVDELNKNP +FGFRDSISQPTVAGSGVRPQPGQERSISAGEFILGENSETGSPLAVPQPDVLGRNGTYVV +LRKFASRVGAFNEYLASQSPDPEEQHRIAAKMFGRWRSGAPLVLSPDHDDEELGNDPERR +NDFTFEDDPKGLMCPHSSHMRRLNPRDSDLSIMTDVNIKRIIRRSSTYGPGWSPEVSSAD +DAKEDRGIYFIFISARAFDTIEFMQQEWINGGNFVDLGSERDPIVGLHEDDPTQGRFTIP +AEPARKRIDGITTFNRMAGGEYLFMPSLSALRWIGEGGWTSDQSAAEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002365.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002365.fa new file mode 100644 index 0000000000000000000000000000000000000000..8106cca5644bef347bc8f7ae244c2bbe42d96665 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002365.fa @@ -0,0 +1,16 @@ +>GCF_020097155_PROKKA_01888 +MWALVELGKRATSEPAAQLRLETLDDIEFDSAGSPAELLQIKHHTRGDGPLTAQAVDLWR +TLNVWMDLPSADKLVLRLVTTRTLSEESGLIRLRDGENRDTSVALEELLKAARTSTSKAT +DKWREKFLHLNETARVELVDRIIIDDGSLPAAHIDKELVRTFRYAYPTGRDDVFLHLLKG +WWSGVSVQLLSRTLEAVTGQDLIVQVTEIADQLKSDALPIDPAVMQEHDESISDLYKDRP +FVQQLLWIALENNRLWKAIRDYHRSFTQRSFWLRHQLLAETELDRFAFRLHDEWEQTFDS +RIAAMKREGRTDHDVVGQEILEELARESRARLRDRFDEPWFNRGMFHALADGELGYRVGW +HPDFESKLEEMLSHVSST +>GCF_023573625_PROKKA_00897 +MWALVELGKRATSEPAAQLRLETLDDIVFDSAGSPAELLQIKHHTRGDGPLTAQAVDLWR +TLNVWMDLPSADKLVLRLVTTRTLSEESGLIRLRDGENRDTSVALDELLNAARTSTSKTT +DKWREKFLHLNETARVELVDRIIIDDGSLPAAHIDKELVRTFRYAYPTGRDDVFLHLLKG +WWSGVSVQLLSRTLEAVTGQDLIVQVTEIADQLKSDALPIDPAVMQEHDESISDLYKDRP +FVQQLLWIALENNRLWKAIRDYHRSFTQRSFWLRHQLLAETELDRFAFRLHDEWEQTFDS +RIAAMKREGRTDHDVVGQEILEELARESRARLRDRFDEPWFNRGMFHALADGELGYRVGW +HPDFESKLEEMLSHVSST diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002367.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002367.fa new file mode 100644 index 0000000000000000000000000000000000000000..139615fbffd98315ef6966340e2e123a9d12e3a4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0002367.fa @@ -0,0 +1,14 @@ +>GCF_020097155_PROKKA_02314 +MNTRCLVLTSGRAADGPYGIDQLGQFGYDLVEVEPARTRVHRKLRDVVEHRSGRPMDKTV +RSVRQAWQADLVLAFLEKEALAASWAKRRGVAPFAGRPLVMIACWLADELQRMSPAQRTA +VVTSYSGVDLIIVLSRNQVEILVEAGFDASRIEAVSFGYNPDQFPVAAFEERRGIVSVGA +DRGRDFPTLLQAVE-GSDLQLHLYTGEGHLNDVELPAEAVLHGRVPFERYQEVIATASMV +AIPTHVMAYPSGQTVALEAAGTGACLILTDTPAMREYFTDETAVF-VPPGDADGWRTALT +ELTSDAEARRRLGRNAAAMVADHFTYADMWRQVDEAIR---RRGWSA----Q +>GCF_023573625_PROKKA_00520 +M----------------------------------------------------------- +------------------------------------------------------------ +-----EGVDRLLMFSSNQVRIFTDAGIDPKRLHPVLFGVDERFYHPSKEPRRFQVLAAGV +DRGRDWQTLVEAARLLPHIRFELYTRPETVAPLAVPSNMTVHAPVGIDEHRHNLQSSDLV +VVPTHDLAYPTGQSVMLEAMASGACVAVTATEAMADYQDDGVSTLALPLHDPEGVASVIE +MPIEDAALRRQIAESGRAAIEERFTFTRMWDEIRQVVRDVARDGASTASAFR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Putative_Xenologs/GCF_002008305.tsv b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Putative_Xenologs/GCF_002008305.tsv new file mode 100644 index 0000000000000000000000000000000000000000..5b5affc70e8b9c73997e94d20e725a1bc7350cf1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Putative_Xenologs/GCF_002008305.tsv @@ -0,0 +1 @@ +Orthogroup GCF_002008305 Other diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Putative_Xenologs/GCF_003691675.tsv b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Putative_Xenologs/GCF_003691675.tsv new file mode 100644 index 0000000000000000000000000000000000000000..3a149078b1eb9e8793fde81bd66c6607d1f7cdda --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Putative_Xenologs/GCF_003691675.tsv @@ -0,0 +1 @@ +Orthogroup GCF_003691675 Other diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Putative_Xenologs/GCF_005280335.tsv b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Putative_Xenologs/GCF_005280335.tsv new file mode 100644 index 0000000000000000000000000000000000000000..6b529510679169c5bfffa8f15097e77968ed6296 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Putative_Xenologs/GCF_005280335.tsv @@ -0,0 +1 @@ +Orthogroup GCF_005280335 Other diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Putative_Xenologs/GCF_020097155.tsv b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Putative_Xenologs/GCF_020097155.tsv new file mode 100644 index 0000000000000000000000000000000000000000..1afd5bc6772d8a7441e3d87294d86d1b280795e8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Putative_Xenologs/GCF_020097155.tsv @@ -0,0 +1 @@ +Orthogroup GCF_020097155 Other diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Putative_Xenologs/GCF_023573625.tsv b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Putative_Xenologs/GCF_023573625.tsv new file mode 100644 index 0000000000000000000000000000000000000000..06603a535f771636b2ac07e75a5c61e1be437c80 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Putative_Xenologs/GCF_023573625.tsv @@ -0,0 +1 @@ +Orthogroup GCF_023573625 Other diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000175.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000175.fa new file mode 100644 index 0000000000000000000000000000000000000000..d5b35c0474651c7bcbb5c103ce95240198521d9e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000175.fa @@ -0,0 +1,39 @@ +>PROKKA_00002 +MQLVKFTVERDILTDAVSWAARSLSPRPPVPVLSGLLITAEAGVVSIASFDYETSARLEI +EADVETAGQVLVSGRLLNDIVRSLPQAQVTVELDGGKVLVTCRSSRFALATMPVGDYPAL +PELPAPAGTVDGAAFAHAVAQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMK +EIRWTPADPSLSTSLLIKARTLTEVAKSLGSGGDLEILLGQTADLVGFASGGRRTTSVLV +DGEYPKIRSLFPESSPIQAVVDTAALVEASRRVALVAERNTALRMVFTDGQVTLDAGTGD +DASANESVPCTLEGEDITVAFNPSYLSEGLAVVDQPQVRFAFTSAPKPALLTGVNQEDGV +VSDYRYLVMPVRIA +>PROKKA_02007 +MQLVKFTVERDILTDAVSWAARSLSPRPPVPVLSGLLITAEAGVVSIASFDYETSARLEI +EADVETAGQVLVSGRLLNDIVRSLPQAQVTVELDGGKVLVTCRSSRFALATMPVGDYPAL +PELPAPAGTVDGAAFAHAVAQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMK +EIRWTPADPSLSTSLLIKARTLTEVAKSLGSGGDLEILLGQTADLVGFASGGRRTTSVLV +DGEYPKIRSLFPESSPIQAVVDTAALVEASRRVALVAERNTALRMVFTDGQVTLDAGTGD +DASANESVPCTLEGEDITVAFNPSYLSEGLAVVDQPQVRFAFTSAPKPALLTGVNQEDGV +VSDYRYLVMPVRIA +>PROKKA_00422 +MPVLSGLLITAEAGVVSIASFDYETSARLEIEADVETDGQVLVSGRLLNDIVRALPHAQV +TVELDGGKVVVTCRSSRFALATMPVGDYPALPELPTPAGTVDGAAFAHAVAQVTVAASKD +DTLPILTAVKVEIEGDTMTFLATDRYRLAMKEIRWTPADPSISTSLLVKARTLTEVAKSL +GAGGDLEILLGEGTDLVGFSSGGRRTTSVLVDGEYPKIRSLFPETSPIQAVVDTAALVEA +SRRVALVAERNTALRMVFTDGQVTLDAGTGDDASANESVPCTLEGEDITVAFNPSYLSEG +LAVVDQPQVRFAFTSAPKPALLTGVNQEDGVVSDYRYLVMPVRIA +>PROKKA_00375 +MKFTVARDILSDAVSWAARSLSPRPPVPVLSGLLVTAEAGLVSIASFDYETSARLQIEAD +VEDEGQVLVSGRLLNDIVRALPNAPVTLELDGGKVLVTCRSSRFQLATMPVADYPALPEL +PEPAGTVDGAAFAHAVNQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMTEIR +WNPADPAISTSLLIKARTLTEVAKSLGGGGRLEIMFGSSHDLVGFSSGGRRTTSVLVDGE +YPKIRSLFPETSPIQAAVDTEELIAASRRVALVAERNTALRMVFTDGQVTLDAGTGDDAT +ANESVPCTLEGEEITVAFNPAYLSEGLAVVDQPQVRFSFTAAPKPALLTGVHEEDGTVSD +HRYLVMPVRLT +>PROKKA_00002 +MQLVKFTVERDILTDAVSWAARSLSPRPPVPVLSGLLITAEAGVVSIASFDYETSARLEI +EADVETAGQVLVSGRLLNDIVRSLPQAQVTVELDGGKVLVTCRSSRFALATMPVGDYPAL +PELPAPAGTVDGAAFAHAVAQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMK +EIRWTPADPSLSTSLLIKARTLTEVAKSLGSGGDLEILLGQTADLVGFASGGRRTTSVLV +DGEYPKIRSLFPESSPIQAVVDTAALVEASRRVALVAERNTALRMVFTDGQVTLDAGTGD +DASANESVPCTLEGEDITVAFNPSYLSEGLAVVDQPQVRFAFTSAPKPALLTGVNQEDGV +VSDYRYLVMPVRIA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000176.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000176.fa new file mode 100644 index 0000000000000000000000000000000000000000..6aa617886152c2e5239786650c3a237eaeba0c9f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000176.fa @@ -0,0 +1,41 @@ +>PROKKA_00003 +MYLSHLTVADFRSYRWADLELTPGSTVLLGANGVGKTNLVEAIGYLGAQQSHRVSSDAQL +VRFGRDRARIAGRVHRGSRAVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE +DLSLVTGEPGGRRRLLDQLMVQLRPALGEAAADYERVLRQRNALLKSSRGSRRWGPEEDA +TLAVWDEHLCAAGARLLHGRLHVLRLLARPLQEMYAALTNGSKAAAYAYESTVPLARGTH +AEVPAVADLAVDMRRTLETQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL +ALALRMAAYDVLVADDPDPDARPVLILDDVFAELDAARRRRLAALVHRAEQVIVTAAALE +DVPEELTAHRVLIRQDAEGSEAVAAAAPVEGDIREPRREGGADG +>PROKKA_02008 +MYLSHLTVADFRSYRWADLELTPGSTVLLGANGVGKTNLVEAIGYLGAQQSHRVSSDAQL +VRFGRDRARIAGRVHRGSRAVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE +DLGLVTGEPGGRRRLLDQLMVQLRPALGEAAADYERVLRQRNALLKAGRGSRRWGPEEDA +TLAVWDEHLCAAGARLLHGRLHVLRLLARPLQEMYAALTNGSKAAAYAYESTVPLARGTH +AEVPAVADLAVDMRRTLETQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL +ALALRMAAYDVLVADDPDPDARPVLILDDVFAELDAARRRRLAALVHRAEQVIVTAAALE +DVPEELTAHRVLIRQDAEGSEAVAAAAPVEGDIREPRREGGADG +>PROKKA_00421 +MHLSHLTVADFRSYRWADLELGPGSTVLLGANGVGKTNLVEAVGYLGSHQSHRVSSDAQL +VRFGQDRARIAGRVHRGSRTVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE +DLNLVTGEPGGRRRLLDQLMVQLRPALGEAAADFERVLRQRNALLKSARKARRWGPEEEA +TLEVWDEHLCAAGARLLHGRLHVLRLLAHPLREMYGALTNGSKAATYAYESTVPLARGTH +AEVPPVAELAADMRRALVAQRDEEQARALTLVGPHRDELALFLGPAPARGYASHGETWSL +ALALRLAAYDVLVADDPDPDGRPVLILDDVFAELDAARRRRLAALVGRAEQVIVTAAALE +DVPAELAGPRVLIRQDAEGSEAVPAAAPVEGDIRAPRGAGGTEGEAPGARRGRRRRRRHA +PADPAEDDPDG +>PROKKA_00374 +MHLSHLTVQDFRSYRWADLELSPGSTVLLGANGVGKTNLVEAIGYLGSHQSHRVSQDAQL +VRFGQDRARIAGRVHRGARSVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE +DLGLVTQDPGGRRRFLDQLMVQLRPALGQAAADYERVLRQRNALLKSARKARRWGAEEDA +TLAVWDEHLCAAGARLLHGRLHVLRLLAHPLQEDYAALTNGSKTATYSYESTVPAARGTH +VQAPPVAELAASMHAALVEQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL +ALALRLAAYDVLVADDSDPEGRPVLILDDVFAELDAARRERLAGLVGRAEQVIVTAAALA +DIPASLAGHRVLIRQDAEGSEAVAAAEPVEGDIRAPRPGAAPGAAASEAEEPEDGDARA +>PROKKA_00003 +MYLSHLTVADFRSYRWADLELTPGSTVLLGANGVGKTNLVEAIGYLGAQQSHRVSSDAQL +VRFGRDRARIAGRVHRGSRTVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE +DLSLVTGEPGGRRRLLDQLMVQLRPALGEAAADYERVLRQRNALLKSSRGSRRWGPEEDA +TLAVWDEHLCAAGARLLHGRLHVLRLLARPLQEMYAALTNGSKAAAYAYESTVPLARGTH +AEVPAVADLAADMHRTLEAQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL +ALALRMAAYDVLVADDPDPDARPVLILDDVFAELDAARRRRLAALVHRAEQVIVTAAALE +DVPEELTAHRVLIRQDAEGSEAVAAAAPVEGDIREPRREGGADG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000177.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000177.fa new file mode 100644 index 0000000000000000000000000000000000000000..022609b66cebc4bca0035bc973faf26d40cd32de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000177.fa @@ -0,0 +1,23 @@ +>PROKKA_00004 +MAETPAPFEPDRPDLALVQLRRVREAARERGEAPLRARGTGAGLAGAMAGTPSAGRERQD +RRRPFGGADRDPATVSTVFGRLIRDRGWSTPVAVGSVLTRWAELVGPEIALHCRPESFED +SVVRVRTSSTAWATQLRLMSPVLLQRFDEALGPGVVTRIEVAGPQAPSWRKGPRTVRGGR +GPRDTYG +>PROKKA_02009 +MAETPAPFEPDRPDLALVQLRRVREAARERGEAPLRARGTGAGLAGAMAGTPSAGRERQD +RRRPFGGADRDPATVSTVFGRLIRDRGWSTPVAVGSVLTRWAELVGPEIALHCRPESFED +SVVRVRTSSTAWATQLRLMSPVLLQRFDEALGPGVVTRIEVAGPQAPSWRKGPRTVRGGR +GPRDTYG +>PROKKA_00420 +MSSVFGRLIRDRGWSTPVAVGSVLTRWDELVGPEIALHCRPESFEDSVVRVRTSSTAWAT +QLRLMTPVLLQRFDDALGPGVVTRLEVAGPQAPSWRKGPRTVRGGRGPRDTYG +>PROKKA_00373 +MRERSPEPDALAELPPDRPDLALVQLRRVRDAARQRGEAPLNRRGTAAGLAQSMAGSEAA +AAAGGAVARSGHRRPGAPADRDPAVVSSVFGRLIRDRGWSTPVAVGSVLTRWADLVGPEI +ALHCRPESFEDSVVRVRTSSTAWATQLRLMSPMLLSRFDEALGPGVVTRIDVAGPAAPSW +RHGPRTVRGGRGPRDTYG +>PROKKA_00004 +MAETPAPFEPDRPDLALVQLRRVREAARERGEAPLRARGTGAGLAGAMAGTTSAGRERQD +RRRPFGGADRDPATVSTVFGRLIRDRGWSTPVAVGSVLTRWAELVGPEIALHCRPESFED +SVVRVRTSSTAWATQLRLMSPVLLQRFDEALGPGVVTRIEVAGPQAPSWRKGPRTVRGGR +GPRDTYG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000179.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000179.fa new file mode 100644 index 0000000000000000000000000000000000000000..288e30942dc76c37602bfd745cc3d631987bdd0d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000179.fa @@ -0,0 +1,82 @@ +>PROKKA_00006 +MSDETTPQTPDEPVEGAPTPQPPQTGLDIEVEHYVLPEGAADKVEPVDLESEMKRSYLDY +AMAVIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRAFNKSARVVGDVMGNYHPHGDTA +IYDALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTVD +MQDNYDGKQQEPVVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEAT +REELLEALLARVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVT +ELPYMTNPDNLAAKIAEMVRDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLY +KHTELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIDVIVRRTAFRKRKAEERAHILR +GLLKALDMLDEVIATIRRSASAEVAREALKELLDIDDVQAQAILQMQLRQLAALESQKIQ +DEYDDLMAKIAEYNRILESPQRQREVISEELAEIVAKHGDDRRTEIMAGFDGDMSIEDLI +PEEEMVVSITRGGYVKRTRIDQYRSQARGGKGVRGATLRGDDVVEHFLTVSTHHWLLFFT +NFGRVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQIQPLVDYGRAPYLVLATRGGL +VKKTPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISHKGQSLRFTATDEALR +PMGRATSGVTGMKFRDDDSLLTMDVVEEDGYVFTVTDGGFAKRTHVDEYRPQNRGGLGIK +VAKLVDDRGELAGGLVVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDR +IVAVTLNNEQEMEAKADAEAEAGPDVPLDADIDPTDPVAAPEDALTQDAGEGADGGEQ +>PROKKA_02011 +MSDETTPQTPDEPVEGAPTPQTGLDIEVEHYVLPEGAADKVEPVDLESEMKRSYLDYAMA +VIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRAFNKSARVVGDVMGNYHPHGDTAIYD +ALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTVDMQD +NYDGKQQEPVVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEATREE +LLEALLARVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVTELP +YMTNPDNLAAKIAEMVRDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLYKHT +ELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIDVIVRRTAFRKRKAEERAHILRGLL +KALDMLDEVIATIRRSASADVAREALKELLDIDDVQAQAILQMQLRQLAALESQKIQDEY +DDLMAKIAEYNRILESPQRQREVISEELAEIVAKHGDDRRTEIMAGFDGDMSIEDLIPEE +EMVVSITRGGYVKRTRIDQYRSQARGGKGVRGATLRGDDVVEHFLTVSTHHWLLFFTNFG +RVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQIQPLVDYGRAPYLVLATRGGLVKK +TPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISRKGQSLRFTATDEALRPMG +RATSGVTGMKFRDDDSLLTMDVVEEDGYVFTVTDGGFAKRTHVDEYRLQNRGGLGIKVAK +LVDDRGELAGGLVVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDRIVA +VTLNNEQEMEAKADAEAEAGPDVPLDADIDPTDPVAAPEDALTQDAGEGADGGEQ +>PROKKA_00418 +MSDETTPQTPDESAEVPETPETGQDVAVEQYVLPEGAADKVEPVDLESEMKRSYLDYAMA +VIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRSFNKSARVVGDVMGNYHPHGDTAIYD +ALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTVDMQD +NYDGKQQEPAVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEATREE +LLEALLTRVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVTELP +YMTNPDNLAAKIAEMVRDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLYKHT +ELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIDVIVRRTVFRKRKAEERAHILRGLL +KALDMLDEVIATIRRSASADVAREALKELLDIDDVQAQAILQMQLRQLAALESQKIQDEY +DELMARIAEYDRILESPQRQREVISEELGEIVAKHGDDRRTEIMAGYDGDMSMEDLIPEE +EMVVSITRGGYVKRTRIDQYRSQGRGGKGVRGATLRGDDIVEHFLTVSTHHWLLFFTNFG +RVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQIQPLTGYDRAPYLVLATRNGLVKK +TPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISHKGQSLRFTATDEALRPMG +RATSGVTGMKFRDDDALLTMDVVEEDGYVFTVTDGGFAKRTHVDEYRLQNRGGLGIKVAK +LVDDRGELAGGLVVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDRIVA +VTLNNEHEMEAQADAEAAEDPVSEGSAAAAGVLPEGEPEALVGAEATAGAAADADVRLDA +DIDPTDPAAAPEGLFEEDADGEGADGGEQ +>PROKKA_00370 +MSDETTPGTAPGTPQDGHDADQTPQIGQDVAVEHYVLPEGAADKVEPVDLESEMKRSYLD +YAMAVIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRSFNKSARVVGEVMGNYHPHGDT +AIYDALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTV +DMQENYDGKQLEPTVLPARFPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEA +TREELLAALMQRIKGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVV +TELPYMTNPDNLAAKIAEMVRDGKIAGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNL +YKHTELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIEVIVRRTAFRKKKAEARAHIL +QGLLKALDMLDEVIATIRRSASAEVAREALKTLLDIDDEQAQAILQMQLRQLAALESQKI +QDEYDELMARIAEYTAILESPQRQREVVSDELGELVAKHGDERRTEIVAGFDGDMSIEDL +IPEEEMVVTITRGGYVKRTRIDQYRSQARGGKGVRGAALRGDDVVEHFLTVSTHHWLLFF +TNLGRVYRIKTYELQEAGRDAKGQHVANLLAFQPDERIAQIQPLAGYDGDAPYLVLATRN +GLVKKTPLEDYDTNRQAGLIAIKLREGDELVSARVVSAQDDLLLISRQGQSVRFTATDEA +LRPMGRATSGVTGMKFRGDDALLAMDVIRAGDEDSYVFTVTDGGFAKRTHVDEYRTQGRG +GLGIKVARLVDDRGELAGGLVVGEDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVVFAKP +DKRDRIVAVTLNNEDEIEATADERAAAEGAAPEAAGAADGAGVPLDAVNDQTDPAAAAEA +EAAGEDADGGEQ +>PROKKA_00006 +MSDETTPQTPDEPVEGAPTPQTGLDIEVEHYVLPEGAADKVEPVDLESEMKRSYLDYAMA +VIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRAFNKSARVVGDVMGNYHPHGDTAIYD +ALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTVDMQD +NYDGKQQEPVVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEATREE +LLEALLARVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVTELP +YMTNPDNLAAKIAEMVRDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLYKHT +ELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIDVIVRRTAFRKRKAEERAHILRGLL +KALDMLDEVIATIRRSASADVAREALKELLDIDDVQAQAILQMQLRQLAALESQKIQDEY +DDLMAKIAEYNRILESPQRQREVISEELAEIVAKHGDDRRTEIMAGFDGDMSIEDLIPEE +EMVVSITRGGYVKRTRIDQYRSQARGGKGVRGATLRGDDVVEHFLTVSTHHWLLFFTNFG +RVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQIQPLVDYGRAPYLVLATRGGLVKK +TPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISHKGQSLRFTATDEALRPMG +RATSGVTGMKFRDDDSLLTMDVVEEDGYVFTVTDGGFAKRTHVDEYRLQNRGGLGIKVAK +LVDDRGELAGGLVVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDRIVA +VTLNNEQEMEAKADAEAEAGPDVPLDADIDPTDPVAAPEDALTQDAGEGADGGEQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000181.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000181.fa new file mode 100644 index 0000000000000000000000000000000000000000..26defa0d436bbe710ab5bdf248c6f58a55dff3f1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000181.fa @@ -0,0 +1,10 @@ +>PROKKA_00009 +MGRLARVALVVSAAAAAYGARLWRENSARKDVWATATDDLPEDADGVEPAPED +>PROKKA_02014 +MGRLARVALVVSAAAAAYGARLWRENSAGKDVWATATDDLPEDADGVEPAPED +>PROKKA_00415 +MGRLARVALVAGAAAAAYGARLWQQNREGKDIWATATDDLPEDAEGVEPAPED +>PROKKA_00367 +MRLARIATLVAGAAAAYGVRSWRQQREDKAVWASATDSLEPRKAPAEDGRGEDEETPQG +>PROKKA_00009 +MGRLARVALVVSAAAAAYGARLWRENSAGKDVWATATDDLPEDADGVEPAPED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000182.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000182.fa new file mode 100644 index 0000000000000000000000000000000000000000..45f9b8a022914464831d979a3e163a5cd39ac7c1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000182.fa @@ -0,0 +1,30 @@ +>PROKKA_00011 +MNTTIDTPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYGPTVPVI +SDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAALTYTVVS +WTTPVEGFEVWDQALAPMLRITVAGVVAFLVGSLLNASIVVRLKERMKERHVAFRLILST +VVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRALKRREPT +YRAPGFEIHRDDDPALAPAASR +>PROKKA_02029 +MNTTTHAPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYGPTVPVI +SDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAALTYTVVS +WTTPVEGFEVWDQALAPMLRITVAGFVAFLVGSLLNASIVVRLKERMKERHVAFRLILST +VVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRALKRREPT +YRAPGFEIHRDDDPALAPAASR +>PROKKA_00386 +MVLDGPVNTTIDTPSPDQPVSGQGTPAYARVPASYYDIFVGVFVALLILSGVTAAKLFYG +PTVPVFSDVFYGGGPLIFDGGAFLFPFAYIIGDILAEVYGWRRARRAILLGFAMLVLAAL +TYTVVSWTTPVEGFEVWDQALAPMLRITVAGFVAFLAGSLINATIVVRLKERMRERHVAF +RLILSTIVGQFFDTLIFCTIAFAGTITLLELANYTFTGFLYKTLVEILIVPITLLVIRRV +KASEPTYRPASSPARAAADAA +>PROKKA_02181 +MNTTPASRSEPTSGQGAAASAAAPHSHYDIFVGVFVALLILSGVTAAKLFYGPTVPGVSD +VFYGGGPLIFDGGAFLFPLSYVVGDILAEVYGLRRARRAIYIGFAMLVVAALTYRLVALT +TPVEGFEAWDQALAPTLRITLAGLAGYIVGSLLNATVVARMKARMAERAVAWRLIASTLV +GEFFDTLIFCLVAFAGTITLADLANYTVTGYVYKCLVEICIVPVTLLVIRWLKRHEPTYR +AQPTPAPVSAPTA +>PROKKA_00011 +MNTTIDTPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYGPTVPVI +SDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAALTYTVVS +WTTPVEGFEVWDQALAPMLRITVAGFVAFLVGSLLNASIVVRLKERMRERHVAFRLILST +VVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRALKRREPT +YRAPGFEIHRDDDPALAPAASR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000186.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000186.fa new file mode 100644 index 0000000000000000000000000000000000000000..e7c2bbb0139cda10ac82a9c2d00fdb099b74dcc5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000186.fa @@ -0,0 +1,15 @@ +>PROKKA_00017 +MAAPAGKRKDSARRKREELEAARRSRSAVRTDLGDVDPGPKPLSPVYKAVMFGLLILGLL +WIIVYYLTQGLLPIVQIGGWNILVGFGIALVGFLMMSRWSE +>PROKKA_02035 +MAAPAGKRKDSARRKREELEAARRSRSAVRTDLGDVDPGPKPLSPVYKAVMFGLLILGLL +WIIVYYLTQGLFPIVQIGGWNILVGFGLALVGFLMMSRWSE +>PROKKA_00380 +MAAPSGKRKDSARRKHEELEDARRGARRGSSAVTTDLGDVDPGPKPLSPVYKAVMFGLMI +VGLLWIVVYYLTQGLFPIVAIGGWNILVGFGIALVGFLMMSRWSE +>PROKKA_00361 +MATTSGKRKDSARRKRRELEQARSRRGRTASVSTDLGDVDATPAPLPRWYKAVMFGLLIL +GLLWIVVYYLSQGLFPIPDAGGWNILIGFGIALVGFLMMSRWSE +>PROKKA_00017 +MAAPAGKRKDSARRKREELEAARRSRSAVRTDLGDVDPGPKPLSPVYKAVMFGLLILGLL +WIIVYYLTQGLFPIVQIGGWNILVGFGIALVGFLMMSRWSE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000188.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000188.fa new file mode 100644 index 0000000000000000000000000000000000000000..f43db27f9c3f7617cc0a4a6b03933c0cdb147560 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000188.fa @@ -0,0 +1,66 @@ +>PROKKA_00019 +MDEQRTLNGRYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRKEA +RSAASLNHPSIVSVYDTGEVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGPDRAV +AWTRGVLEALEHAHEEDIVHRDVKPANVMVTDTGTVKVMDFGIAHALADTSATTSQTQAV +VGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPPAP +SDVDPDLPPAFDPVVLRALRKDPQDRFPTGAAFLAALEEAAADPHAGPGRHTPPLDAVHP +ALVGAGGAVLGATPAEHGADVADVPTAAVPLTRPAPSVPAEPDTAQPQAVNHAVAGAGLP +GAASAAQLAAAAAMDGPRPVTGGQPVTPGAAATPRPEPPPRDTPAPATATPRRVRRRVRR +RTLLAAGVVLVALALVLAPWLAAALRTTAEVPAVVGLQQDEAVAALEDAGLVAVVSSAYM +ADAPDGTVTQSDPPTGTEVPRGAEVRIRVSRGEEGIALSDSLHGLSEDAARRELERLGLR +VSSVQYQDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARRQL +ALSAPELRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTTSSWIAPTAEPSEPAP +PSSEAPEPTPSASTSPSPPSSESPEPSESPEPSESAEPSPSPSASATPSPEPTTTATPSP +TQSPSPPSAAPSTSSEPTEQSPSTSPTATPVDPLPTLTPDPEPSIDPPPST +>PROKKA_02037 +MSVDEQRTLNGRYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRK +EARSAASLNHPSIVSVYDTGEVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGTDR +AVAWTRGVLEALEHAHEEGIVHRDVKPANVMVTETGAVKVMDFGIAHALADTSATTSQTQ +AVVGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPP +APSDVDPDLPPAFDPVVLRALRKDPEDRFPTGTAFLAALEEAAADPHAGPGRHTPPLDAF +PPALVGAVLGAAAAEHGADVPTAAVPLTRPTPSVPAEPDAAQPQAANHAVAGAGLPGAAS +AAQLAAAAAMDGPRPVTVGQPVMPGAAATPWPEPQGDTPAPATATPRRVRRRLRRRTLPA +AGVVLVALALVLTPWLAAALRTTVEVPAVVGLQQDEAVVALEDAGLLAVVSSAYMADAPD +GTVTQSDPPTGTEVPRGAEVRIRVSRGKEGIALSDSLHGLSEDAARRELERLGLRVSSVQ +YQDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARRQLALSAP +ELRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTASSWIAPTAEPSEPAPPYSEA +PEPTPSASASPSPPPSESSEPSESAEPSPSPSASATPSPEPTTTATPSPTQSPSPTSAAP +SEPTEQPPSTSPTATPVDPLPTLTPDPEPSIDPPPST +>PROKKA_00377 +MEEQWTLNGRYRIDALIGRGGMADVFRGTDLRLHRPVAVKLMRRDLARDPHFQARFRKEA +RSVASLNHPSIVSVYDTGEVSLEDGHHPVDCPYLVMELVTGRSLREVLHAEGAVGTERAV +AWTREVLEALEHAHQEGIVHRDVKPANVMVTDAGSVKVMDFGIAHALADTSATTSQTQAV +VGTALYLAPEQATGRTVDGRADLYATGCVLFELLTGRPPFTGDTPLAVAYQHVREAPPAP +SEVDPDLPRAFDPVLLRALEKDPEDRFPTGAAFREALEAAAADPHAAVDADTAALDLVRA +GAAGAGGAAVAAGREVRRDGARDSADVPTAAVPLTPAPAPAAPAEPAEPPGGEPRRGRGR +AARRRLRRPAGGRRLRGRPAPGHRLPTPPSRGPRRPAPRPPPGSALPPPLPPPDGAAAGG +AACRSPGCCWPASSC +>PROKKA_00359 +MQGQRILHERYRVDELIGRGGMADVFRGHDLRLNRTVAVKMMRPDLARDPAFQARFRTEA +RHAAALNHPNIVSVYDTGDALLDDGPQSVECPYLVMEHVDGRTLRELLDAGEVAWRDAVE +WTRGLLHALDHSHRQRIVHRDVKPANVMVTRDGGVKVMDFGIARALSDTSAHTGQTQAVV +GTALYLPPEQAQGARVDARSDLYAAGCVLFELLTGRPPFTGETPLAIAYQHVREEPPAPS +AVDPSLSTEFDSVVLRALQKDPGLRHQHAREFLSALDFAAARAARAADDDAPTRVVPASG +AAPLATGSGALAAAVAGSTAAGPTASGSTALGAGGAPEARPATGPPATTPLGAAAGPTEP +LIAGHAVAGAAVPGAPSASQLAAAEAVETAPAAASTTGGSAGAGATSGAERAGRRHRLSW +AVLAAVAAVAAVAAILALGAALLIGSRDPGPVTVPALAGRTEAEAVSALTGLGLRSAISP +DYHSTEPDGRVLKVHPGAGAAVEPGSTVNLSVARGGEGVVLPTSLRGASEARVRQELARL +GLNVASVEDTPSGELDRGALVQTDPVLGSRVPPGSAVVLHLADGTARVPSLVGMTGADAR +TTLAALDPEMTVRFQGAAGADPDTGVVVLQDPAAGTVVDNTAMITLITSAEATPTASAVT +VAPPDPALPSATTTTAPAEPSPGVPAPTTPAAPAVDTPAPAPATTPAPAPESSSTPGAGT +DPAPTESAPTPDDGPGSTGTPSTEAPTEAPTDPVGTPAPSPSGEPVPQPSPSVEPLPEPT +APTEAPTADPAG +>PROKKA_00019 +MDEQRTLNERYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRKEA +RSAASLNHPSIVSVYDTGEVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGTDRAV +AWTRGVLEALEHAHEEGIVHRDVKPANVMVTDTGTVKVMDFGIAHALADTSATTSQTQAV +VGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPPAP +SDVDPDLPPAFDPVVLRALRKNPQDRFPTGAAFLAALEEAAADPHAGPGRHPPPLDAVHP +ALVGAVLGATPAGHGADVPTAAVPLTRPTPSVPAEPDTTQPQAANHAVAGAGLPGAASAA +QLAAAAAMDGPRPVTAGQPVTAGQPVTPRPEPPPGDTPAPATATPRRVRRRVRRRTLLAA +GMVLVALALVLAPWLAAALRNTVEVPAVVGLQQDEAVAALEDAGLVAVVSSAYMADAPDG +AVTQSDPQTGTEVPRGAEVRIRVSRGEEGIALSDSLHGLSEDAARRELERLGLRVSSVQY +QDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARRQLALSAPE +LRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTASSWIAPTAEPSEPAPPSSEAP +EPTPSASAPPSPPPSESPEPSESAEPSPSPSASATPSPDPTSATPSPTQSPSPPSAAPST +SPEPTAQSPSTSPTGTPVDPLPTLTPDPEPSIDPPPST diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000189.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000189.fa new file mode 100644 index 0000000000000000000000000000000000000000..fab61160b8a48754d71b8125520161cc5967231f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000189.fa @@ -0,0 +1,64 @@ +>PROKKA_00020 +MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRA +EAQHTALLNHPGVANVYDYGEEKGSAYLVMELVPGQPLSSILEKEKVLSPERTLRIIAQT +AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA +PEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPPLPDTVPAPV +RALIMCMLSKDPKERPSDATALSEAADALRRKDTRGAVEAVPGLAVFLEEQGVADPSGAE +TAPLDYDGLRTTHPRTEGIRTDGSPATAALPVTAAQPRTDDAARGPGAAGAAAVGAAGAA +ASASTRDHEIAAVRDQQTRPGDVVDPGPPAGGGSAPARRRRANPWPLWALLGLVVFALLG +ALLWPLLTGGRGDGGSAPATSQEESSVNVDPEAYKGRPVSEVRAELEGLGLAVREEDRDA +QSPQGTVEEINPVGALQRGETVTLAVSTGEGVIPEGLVGQPVDSAIQTLRDRGFTVDRVD +DPSADGADGEVVRVVPGEGERHRYDTHVQLIVATGGSDAAPTREASQPASEPVPSASEEP +SSEPSPSASDEPSPSPTAESPTATADPEPTQEPTEEPTTPTGDPTTESSGESTAPTGEPT +TDPSADARGAEASSADATPSA +>PROKKA_02038 +MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRNTAVKILKEEYTGDPNFLRRFRA +EAQHTALLNHPGVANVYDYGEEEGSAYLVMELVPGQPLSSILEKEKVLSPERTLGIIAQT +AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA +PEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPPLPDTVPAPV +RALIMCMLSKDPKERPSDATALSEAADALRRKDTCGAVEAVPGLAVFLEEQGVADPSGAE +TAPLDYDGMRTTHPRAEGTRADGSPATAALPVTAAQPRTDDAARGPGAAGAAAVGAAGAA +GAAGAVASTRDHEIAAVRDQQTRPGDVVDPAPPAGGGSAPARRRRANRWPLWALLGLVVF +ALLGALLWPLLTGGRGIGGSAPATSQDESSVRVDPEAYRGRPVSEVRTELEGLGLAVREE +DRDAQSPQGTVEEINPVGALRRGETVTLAVSTGEGVIPEGLVGQPVESAIQTLRDRGFTV +DRVDDPSADGADGEVVRVVPGEGERHRYDTHVQLIVATGGSDAAPTREASQPASEPEPSA +SEEPSTEPSPSASDEPSPSPTAESPTATADPEPTPEPSEEPTTPTGDPTTESSGESTAPT +GESTTDPSADARGAEASSADATPSA +>PROKKA_00376 +MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRA +EAQHTALLNHPGVANVYDYGEEKGSAYLVMELVPGQPLSAILEKEKVLSPERTLRIIAQT +AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA +PEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDAPPPLPSTVPAPV +RALIMCMLSKDPKERPTDATAASEAADALRRKDTRAAVEAVPGLAAFLAAEGVADPSGAE +TAPLDYDGMRTAHPRPEGTRADGTPATAALPVTAAQPRTDDGARGSAATAAGAAGAAGLA +GAAAAGARPANEEIAAVRDPQTRPSDVVQEAPPAGQGSAPVKRRRANRWPVFALLGLVLF +ALLGALLWPWITGDRTPGGSTPSGTSQASSVSVDPEAYKGRPAAEVRAELERLGLVVREE +DRDARNPRGTVEEVNPVGSLQRGETVTLAVSTGEGVVPDGLVGQPVDSAIQLLRDRGFTV +DRVDDPSADGAEGEVVRVVPGEGQRHRYDTHVQLIVAGGAGGDEPAPTPEPSEPAEPTAE +PSDEPTTEPTSEPTEEPTTEPTAPSEEPTEEPTEEPTTEPTSDPTGEPTGEPTADPTDDA +GGSASPTAEESPTA +>PROKKA_00358 +MRPTSGITLGGRYALTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRA +EAQHTALLNHPGVANVYDYGEEKGSAYLVMELVPGQPLSAILEKDRTLSTDRTLSIIRQT +AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA +PEQATGQQATGSSDIYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPALPDTISAPV +RALIMCMLSKNPKDRPANATALSEAAEALRRKDVAGAVAAVPTLAAFLADQGVHSTGGPG +DAETTALDAAPRTAPQPTVPLGTTTEPAAPATAALPVAAARPDVAATRSPRAAEPARSVP +AAAPADPAPRTAKPRRRNRWPLFALLALVAFAVLGALLYPLLSGESGAGAGASSSTGTDA +QVEVDAAAYRGRPADEVRAELEGRGLAVEEEQRDANDPQGTVVEVTPTGTLRRGDTVTLA +VSTGQGTIPQDLVGQPADTVVGILRDRGFSVDRVDDPNADGATGQVVRVVPGEGQTHRFD +TPVQVIVAGGTGSSPVTQSVVTAPTAAPASESPAEPAPASSSSGDPAPSSAQPTPSEAST +EPSPESPAPTSESAAPSTEPSAGTPSTPDASGPSSQGSDAGSPSTDPAG +>PROKKA_00020 +MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRA +EAQHTALLNHPGVANVYDYGEEEGSAYLVMELVPGQPLSSILEKEKVLSPERTLGIIAQT +AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA +PEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPPLPDTVPAPV +RALIMCMLSKDPKERPSDATALSEAAEALRRKDTCGAVEAVPCLAVFLEEQGVADPSGAE +TAPLDYDGMRTTHPRAEGIRTDGSPATAALPVTAAQPRTADDARGPGAAGAAAVGAAGAA +GAAASTRDHEIAAVRDQQTRPGDVVDPGPPAGGGSAPARRRRANRWPLWALLGLVVFALL +GALLWPLLTGGRGVGGSAPATSQEESSVHVDPEAYRGRPVSEVRTELEGLGLAVREEDRD +AQSPQGTVEEINPVGALRRGETVTLAVSTGEGVIPEGLVGQPVESAIQTLRDRGFTVDRV +DDPSADGADGEVVRVVPGEGERHRYDTHVQLIVATGGSDAAPTREASQPASEPEPSASEE +PSTGPSPSASDEPSPSPTAESPTATADPEPTPEPSEEPTTPTADPTTESSGESTAPTGEP +TTDPSADARGAGASSADATPSA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000190.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000190.fa new file mode 100644 index 0000000000000000000000000000000000000000..988c3b3dafba064d426e317ecc5fd226eefdeadc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000190.fa @@ -0,0 +1,50 @@ +>PROKKA_00021 +MNEAIRRTWTVMAAMILVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE +PIAESVPSDDAYHYQRVYHEPELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA +MEIITGATPEGDQVELTIDPELQRLAYDALPDGVRASAVVTDPTTGEILAMVSKPSFDSN +ALSSHSPAEAQAAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT +VDIPAAWTLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVELGQDRIREVA +ERFGFNDSFDYPLPVTGSVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM +EPQLIKAVRRSDLTTVQEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA +AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGVGHQTIVSGMKAIMEAVVT +E +>PROKKA_02039 +MNEAIRRTWTVMAAMILVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE +PIAESVPSDDAYHYQRVYHEPELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA +MEIITGATPEGDQVELTIDPELQRLAYDALPDGVRASAVVTDPTTGEILAMVSKPSFDSN +ALSSHSPAEAQAAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT +VDIPAAWTLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVELGQDRIREVA +ERFGFNDSFDYPLPVTGSVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM +EPQLIKAVRRSDLTTVQEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA +AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGVGHQTVVSGMKAIMEAVVT +E +>PROKKA_00375 +MNEAIRRTWTVMAAMMLVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE +PIAESVPSDDAYHYQRVYHDPELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA +MEIITGATPEGDQVELTIDPELQRVAYDALPDGVRASAVVTDPTTGEILAMVSKPGFDSN +ALSSHSATEAQSAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT +VDIPAAWPLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVKLGQDRIREVA +ERFGFNDSFDYPLPVTASVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM +EPQLIKAVRRPDLTTVEEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA +AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGIGHQTIVSGIKAITEAVVT +E +>PROKKA_00357 +MNEAIRRTWTVMVAMFLVLAVAASVIQVVAADSLKENKLNNRQLFLEFGAPRGPILVDGT +PVAQSVPSGDAYNYQRVYRDSLLYAPLTGHYSLAYGTAGMEKAMNGELAGTSSSQFLDRA +LEIVTGSTPEGDQVELTLDSELQKLAYESIPDGVKGSVVATDPKTGRVLAMASKPSYDAN +TISSHTRSEATAAMSAYEGVPGLTVGQNRPTQQRVAPGSTFKLIDLVAMLESGDYAPDQV +LDVPAAWTLPGTRTQMSNFDGGRCNGVGRATLTWIVANSCNTPFAQAAVALGQDEIRSVA +ERFGFNQDGSMPLPVTASVFPEDLDDAALAQSAIGQRDVQATALQMNMVAAGIANDGMVM +EPNLVQAVRRPDLTTVSEFSPREHGRAMDPDVAHQVRDMMVATVEDGTASAAKSSTLQIA +AKTGTAEKDGTANVNTWVTGFAPAQDPKVAVTIVYEDQNSSSAHTQAVESMQRIMEAVVA +E +>PROKKA_00021 +MNEAIRRTWTVMAAMLLVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE +PIAESVPSGDAYHYQRVYHETELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA +MEIITGATPEGDQVELTIDPELQRLAYDALPDGVRASAVVTDPTTGEILAMVSKPGFDSN +ALSSHSPAEAQSAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT +VDIPAAWTLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVELGQDRIREAA +ERFGFNDSFEYPLPVTASVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM +EPQLIEAVRRSDLTTVQEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA +AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGVGHQTVVSGMKAIMEAVVT +E diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000199.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000199.fa new file mode 100644 index 0000000000000000000000000000000000000000..2c12f084d083d33776957275c826f2d7a86d5d7f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000199.fa @@ -0,0 +1,33 @@ +>PROKKA_00040 +MAKGVKPAGRAGGEGRRRPAPAPPADLPVPPETLFLATIPGATPSTWVERFTTRQRTVQL +VNHDDAAQLAHLAHDDAGQPRHFLPQLGYVRRRRDVSAEEFLRAGDVDPRHVHLVGVYSE +LPVVCVGRDHLLAAWDVDADGPVPPAELDPDEELDPARFAPAPSPEPMDAAELPGAGERM +ALEIAASGAGHVVLPMSVARMFGRKDVIVLPLASTLDDTVGLSRADREAAATRSALADEQ +ARAEAEAGAAVVDGADPAGHGDDDARHPVWDVALAWLKAADSELVQAFVGVARGRRGASS +R +>PROKKA_02053 +MAKGVKPAGRAGGEGRRRPAPAPPADLPVPPETLFLATIPGATPSTWVERFTTRQRTVQL +VNHDDAAQLAHLAHDDAGQPRHFLPQLGYVRRRRDVSAEEFLRAGGVDPRHVHLVGVYSE +LPVVCVGRDHLLAAWDVDADGPVPPAELDPDEELDPARFAPAPSAEPMDAAELPGAGERM +ALEIAASGAGHVVLPMSVARMFGRKDVIVLPLASTLDDTVGLSRADREAAATRSALADEQ +ARAQAEAGAAVVDGADPAGQGDDDARHPGWDVALAWLKAADSELVQAFVGVARGRRGASS +R +>PROKKA_00360 +MGPRRGLPEGEGPLSGARGGRGAGRQRASRGGPARSTRTGGRAGAKGGGPQRAGSGSRAG +GEGRRRAPSAPADLAAPPETLFLATIPGATPSTWVDRFTTRQRVVQLVNHDEASQLAHLA +HDDAGMPRHPLPQLGYVRRRRDVEAEEMLRAAGVDPRRVHLVGVYAELPVVCVGRDHLLA +AWDAEADGPVPLAELDSHEELDPARFAAAPVEDPLDSAELPGAGERMALEIAASGAGHVV +LPMSVARMFGRKDVVVLPLASALDDTVGMSRADREAAATRAEVEADAGDAGTAAAGPGEA +DDDAARHPGWDVALAWLKEADSELVQSFVGVARGRRGNSSR +>PROKKA_00301 +MPAAPADLPTPPETLFLATIPGATPSTWVQRFSSRARTVQLVNHEEAQQAAHLAHDAAGA +PLHPLPQLGYVRWLRDAGVESVLRESGVDPRFVHVVGVYSELPVVCVGKEHLLAAWDLEA +DGPVPLAELDPAEHMDPARFAPEPGAASNPLDSAELPGAGERMALEIVASGVGHVVLPQS +VARVFGRKDVVVLPVACELDDVVGLSRADREAAATRAEVAEEGDGVVPDGADAPATTAPR +HPGWDVGLAWLKEQDSELVQSFVGVARGRRGGTSR +>PROKKA_00035 +MKPAGRAGGEGRRRPAPAPPADLPVPPETLFLATIPGATPSTWVERFTTRQRTVQLVNHD +DAAQLAHLAHDDAGQPRHFLPQLGYVRRRRDVSAEEFLRAGDIDPRHVHLVGVYSELPVV +CVGRDHLLAAWDVDADGPVPPAELDPDEELDPARFAPAPSPEPMDAAELPGAGERMALEI +AASGAGHVVLPMSVARMFGRKDVIVLPLASTLDDTVGLSRADREAAATRSALADEQARAE +AEAGAAVVDGADPAGQGDDEARHPGWDVALAWLKAADSELVQAFVGVARGRRGASSR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000200.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000200.fa new file mode 100644 index 0000000000000000000000000000000000000000..8f231adc37afbb25ba3f29f3aa47333c74c5fa69 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000200.fa @@ -0,0 +1,45 @@ +>PROKKA_00042 +MSPTPTRPSRGPGWRLHGDGRTITPGTVVAPDERLSWPRTVGIGVQHVMAMFGATVLVPA +LTGMPATTALLFSGLGTLLFLVITGNRLPSYLGSSFAFIAPLTAATTIGGTGAALGGILV +TGLLLTVIGVIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQEVPVTTFGTAL +AVVLTAVAFRGLLGRLSILVGIVVGYVLALAQGQVDFAAVREAAWIGLPPFHGPELRWDL +LPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTMLSGAGGGVGTTTYA +ENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAGIILYGMIGMMG +VRIWVQNRVDFSNTVNLMAAGAGLIIAIADPQLVVGGLVFGGITLGTVAALVVYHLMTAI +ARARGTEPVPEDEEQFEASEAGRLG +>PROKKA_02055 +MSPTPTRPSRGPGWRLHGDGRTITPGTVVAPDERLSWPRTVGIGVQHVMAMFGATVLVPA +LTGMPATTALLFSGLGTLLFLVITGNRLPSYLGSSFAFIAPLTAAAAIGGTGAALGGILV +TGLLLTVIGAIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQEVPVTTFGTAL +AVVLTAVTFRGLLGRLSILVGIVVGYVLALAQGQVDFAAVGEAAWIGLPPFHGPELRWDL +LPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTMLSGAGGGVGTTTYA +ENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAGIILYGMIGMMG +VRIWVQNRVDFSNTVNLMTAGAGLIIAIADPQLVVGGLVFGGITLGTVAALVVYHLMTAI +ARARGTEPVPEDEEQFEASEAGRLG +>PROKKA_00358 +MSSSPSRPAPGFGWRLHGDGRTITSGTVVAPDERLSWPRTVGIGVQHVMAMFGATVLVPA +LTGMPATTALLFSGVGTLLFLLLTGNRLPSYLGSSFAFIAPITAATTAGGVGAALGGVLV +TGVLLAVIGLIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQEVPLTTFGTAL +AIVLTAVLFRGLLGRLSILVGIVVGYLLALAQGQVDFTAVGEAGWLGLPPFHAPELHWNL +LPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTTLSGLGGGVGTTTYA +ENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAGIILYGMIGVMG +VRIWVQNRVDFSSTINLMTAGAGLIIAIADPQLVLGGLVFGGITLGTIAALVVYHLMTAI +ARVRGTEPVSEDDEAYEASEAGRLG +>PROKKA_00300 +MSSSPTPSAPRAGHVPGPGPAVRSWRLHGDGRTITPGTVVAPDERLSWGRTVGIGVQHVM +AMFGATVLVPAITGMPATTALLFSGLGTLLFLLITGNRLPSYLGSSFAFIAPLTAASASH +GVGAALGGIAATGVLLMVIGVVVGWAGTGWIHALMPPAVMGTIVALIGLNLAGATTQAMQ +EVPLTTFGTALAVVLTAVLFKGLLGRLSILVGIVVGYLLALAQGQVDFTAVGQAAWVGLP +PFHTPELHWSLLPLFLPVVLVLIAENIGHVRTVGLMTKRDLDPLTGRALLADGLATTLSG +LGGGVGTTTYAENIGVMASSKVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAG +IILYGMIGVMGVRIWVQNRVDFSNTINLMTAGAGLIVAIANPELVVGGLVFGGITLGTLT +ALVVYHLMTLVARVRGTEPVDEDTEDPASYRAAEAGRLG +>PROKKA_00037 +MSPTPTRPSRGPGWRLHGDGRTITPGTVVAPDERLSWPRTVGIGVQHVMAMFGATVLVPA +LTGMPATTALLFSGLGTLLFLVITGNRLPSYLGSSFAFIAPLTAAAAIGGTGAALGGILV +TGLLLTVIGAIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQEVPVTTFGTAL +AVVLTAVTFRGLLGRLSILVGIVVGYVLALAQGQVDFAAVGEAAWIGLPPFHGPELRWDL +LPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTMLSGAGGGVGTTTYA +ENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAGIILYGMIGMMG +VRIWVQNRVDFSNTVNLMTAGAGLIIAIADPQLVVGGLVFGGITLGTVAALVVYHLMTAI +ARARGTEPVPEDEEEFEASEAGRLG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000204.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000204.fa new file mode 100644 index 0000000000000000000000000000000000000000..b4cd40a4b335148706edaf75ca34440c41d9775e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000204.fa @@ -0,0 +1,25 @@ +>PROKKA_00046 +MSERTTYLLIDGENIDATLGTSILQRRPQPDERPRWKRLLGYLEDRWDQPVKGLFFLAID +GEIPIPFVQALTALGFQPIMLRGEGKVVDIGIQRTAEALLGREDDVVLVSHDADFAPQLT +DLAATPGRRTGIMGFEEFLSHELRRIPGVEFFDLEHAVGAFDSSLPRLRVIDVEAFDPYE +FL +>PROKKA_02059 +MSERTTYLLIDGENIDATLGTSILQRRPQPDERPRWKRLLGYLEDRWDQPVKGLFFLAID +GEIPIPFVQALTALGFQPIMLRGEGKVVDIGIQRTAEALLGREDDVVLVSHDADFAPQLT +DLAATPGRRTGIMGFEEFLSHELRRIPGVEFFDLEHAVGAFDSSLPRLRVIDVEAFDPYE +FL +>PROKKA_00349 +MGRRADAPAGPGRAVVVPTTTSSPAPASAPVHTPAPAPATSSAPAGSLGQVSESTTYLLV +DGENIDATLGTSILQRRPQPDERPRWNRLLSFMGEHWDQPVKGLFFLAIDGDIPVPFVQA +LTAIGYKPIMLRGAGKVVDIGIQKTMEALQEREDDVVLVSHDADFAPQLTDLAATPDRRT +AIIGFEEFLSHELRRIPDVEFFDLEYGVGAFDTPLRRLRVIDIDEFDPLEFL +>PROKKA_00294 +MSRRADLPTGPATAVPAAPAAPVSPTAEDRSAATPADTLDTMSARTTYLLVDGENLDATL +GMSVLNRRPNPEERPRWNRVLRHVERAWGQEVRPLFFLAVDEDGDIPFGFVQALTTMGYQ +PILLRGAGKVVDIGIQRMAEALIGRDADVVLASHDADFAPQMLDLAAHGHKIAVMGFDEF +MSAELRAVNGMEVWDLEHDVAAFDVPLPRLRVIDIDDFDPRDFL +>PROKKA_00041 +MSERTTYLLIDGENIDATLGTSILQRRPQPDERPRWKRLLGYLEDRWDQPVKGLFFLAID +GEIPIPFVQALTALGFQPIMLRGEGKVVDIGIQRTAEALLGREDDVILVSHDADFAPQLT +DLAATPGRRTGIMGFEEFLSHELRRIPGVEFFDLEHAVGAFDSSLPRLRVIDVEAFDPNE +FL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000205.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000205.fa new file mode 100644 index 0000000000000000000000000000000000000000..5744dd4725f8165fadaa10a7cd5854ab8fc18679 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000205.fa @@ -0,0 +1,40 @@ +>PROKKA_00047 +MPAPSSHAPAATHTARGRLVWVDVARGLALVAMMVAHTAPAGGPGGVLHLSEHLTAPLFA +ALVGVGARLEAEWLGRGRAVPRALVRAAALCGAAWLTGHFGAAVVNVLAHLAVLTVIMAL +LAALPLAAHLVLAVLAGGGGLLLAATPTADVVDRLVPLAQALGLSRATLTPYVSAFLTDG +PYRLPLFLTWALLGAVLVRTVHGTTTAAPARSARLTGLAWAAGGIALAGVVLALSRTQTG +AAPVPYTATPAEALLDTGLVLTVLGACAALAPRRAGLLAVPGAMTLSVYVAHLWYLGWVR +RLGPGPWRSATGTDDTWFNLAVLVAGALLLPLLWRAVVRIGPFRAGPLEGVVRLLTAPFD +RAR +>PROKKA_02060 +MPAPSSHAPAATHTARGRLVWVDVARGLALVAMMVAHTAPAGGPGGVLHLSEHLTAPLFA +ALVGVGARLEAEWLGRGRAVPRALVRAAALCGAAWLTGLFGAAVVNVLAHLAVLTVLMAL +LAALPLAAHLVLAVLAGGGGLLLAATSTADVVDRLVPLAQALGLSRATLTPWVSAFLTDG +PYRLPLFLAWALLGAVLVATVHGTTTAAPARRARLTGLAWAAGGIALAGVVLALSRTQTG +AAPVPYTATPAEALLDTGLVLAVLGACAALAPRRAGLLAVPGAMTLSVYVAHLWYLGWVR +RLGPGPWRSATGADDTWFNLAVLVVGALLLPLLWRAVVRVGPFRAGPLEGVVRLLTAPFD +RAR +>PROKKA_00348 +MPRVSSRPHTGRDRLVWVDVARGVALVSMFVAHVAPSGGPAGVLNLSEHLTAALFAALVG +VSARLEVQGLGVGRALVRAMVRAAALLGAAWLTSLFDAAVVDVLTHLAVITVLMALLAAL +PLAVHLVLALLAGGGGILLTASGTLAVADALAPAARALGLDPAELVPAVAGFLTAGPYRL +TAFLGWALLGAVLVRTVHGTTTALPRSGRLVGLGWGVGGVVLAGLVILLSRVQTGAAPVP +YTGTAAEILVDTGLVLGVLGLCAAVVPSRPSPATDLLAVPGSMTLSVYVAHQAYLGWVLT +AGPGPWVDGRGADDTWFNLAVLLAGGILLPLLWRGLVRVRPFRAGPLEGVVRLVTDPIGR +RSRGEH +>PROKKA_00295 +MTLAAGHRLTWVDVARGLALVSMFVAHTAPTGGPGGVLNLSEHLTAALFAALVGVSAHLE +QRRHGFWRAFLRAVVRAAALCGAAWLTSHFGAAVVDVLTHLAVLTVLMSVLALLPGLVQL +LLVPAAAWAGVRVGALTADDVAARLEPARALVPAQVRPGPAVVAEQAAAFFTVGPYFLLF +FTAWALLGAVVVRSVQGGGLRAALRLGGHPGPGLGGRAAGGVWAGVGLLVGGAGVALARQ +RTEDSPVPYEATWDYALLAAGLVLIVLGACAAVVPSHVPWLTAVLAVPGSMTLSVYVAHQ +AYLGWVLRAGPGPWLSELGTDDTWFNVGALCAAGLLLPLLWRALVRAEPWRRGPLEGPVA +LVTHGLARR +>PROKKA_00042 +MPAPSSHAPAATHTARGRLVWVDVARGLALVAMMVAHTAPAGGPGGVLHLSEHLTAPLFA +ALVGVGARLEVEWLGRGRAVPRALVRAAALFGAAWLTGLFGAAVVNVLAHLAVLTVLMAL +LAALPLAAHLVLAVLAGGGGLLLAATPTADVVDRLLPAAQALGLSRATLTPWVSAFLTDG +PYRLPLFLAWALLGAVLVATVHGTTTAAPARRARLTGLAWAAGGIALAGVVLALSRTQTG +AAPVPYTATPAEALLDTGLVLIVLGACAALAPRRAGLLAVPGAMTLSVYVAHLWYLGWVR +RLGPGPWRSATGADDTWFTLAVLVAGALLLPLLWRAVVRIGPFRAGPLEGVVRLLTAPFD +RAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000206.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000206.fa new file mode 100644 index 0000000000000000000000000000000000000000..25f9b9d92d14a56b68c1e8bcf241999c5c2be86e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000206.fa @@ -0,0 +1,25 @@ +>PROKKA_00050 +MAALTDRAVLIAGATSASGRAAARTLLDAGAHVVATGRDAAKLAPLAGLGAETATLDLTD +ETAVRGLVEDLHARGTRIDGLLHLVGGWRGGGGLAGQTEADYRALEASFTALRHVSRALD +DDLRASSAGRLAIVSSTAVTRPLAGGANYAAVKAASEAWTRAVAQGWAKATRDAETPLRS +AAVVFRVKSLAGLEERLAEEYARLWKAEAGALNDAVLTLQEKGT +>PROKKA_02063 +MAALTDRAVLIAGATSASGRAATRTLLDAGAHVVPTGRDAAKLAPLAALGAETAALDLTD +EAAVRGLVEDLHARGTRIDGLLHLVGGWRGGGGLTGQTEDDYRALEASFTALRHVSRALD +DDLRASSAGRLAIVSSTAVTRPLAGGANYAAVKAASEAWTRAVAQGWAKAARDAEAPLRS +AAVVFRVKSLAGLEERLAEEYARLWKAEAGALNDAVLTLQEKGTD +>PROKKA_00353 +MGTLTGRTVLISGATSASGLAAARALLAAGADVVATGRSPERLAPLAALGADTAALDLSD +EAAVRGLVEDLHARGVRVDGLLHLVGGWRGGGGLAGQSEEDYRALESSLTALRHVSRALD +DDLRASSAGRLAIVSSTAVARPLAGGAAYAAVKAASEAWTRAVAQGWDKAARDAGTELRG +AAVVLRVKSLAGLEDRLAEQFVRLWSADAAQLNDSILAVQEKETA +>PROKKA_01218 +MSAPAAPDLTGALVLVTGASSGIGSALARGLAAAGADLVLVARRAGRLAALADELRAAHR +TEVTVLPRDLAAPDAGPALRAELSSRGPRVTGLVNNAGFGSGLPFGREDPARLEAMPAEE +ERGRERVLCVSPSSTGTEFFDVAGTPGAGGGFARRAAPDDVAAAVLRVLARRGGPAEVVP +HDRAVTVAARLLPRTVLRGMGAMHRRGAARR +>PROKKA_00045 +MAALTDRAVLIAGATSASGRAAARTLLDAGAHVVATGRDAAKLAPLAELGAETAALDLTD +ETAVRGLVEDLHARGTRIDGLLHLVGGWRGGGGLAGQTEEDYRALEASFTALRHVSRALD +DDLRASSAGRLAIVSSTAVTRPLAGGANYAAVKAASEAWTRAVAQGWAKAARDAEAPLRS +AAVVFRVRSLAGLEERLAEEYARLWKAEAGALNDAVLTLQEKGTD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000208.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000208.fa new file mode 100644 index 0000000000000000000000000000000000000000..704a36f023ff8987a9f3c73470a8546ca3b7a538 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000208.fa @@ -0,0 +1,55 @@ +>PROKKA_00055 +MTENTAALPAAERPGTPALPQDLIDVDALLEAYHTGHPDVTDPAQKVVFGTSGHRGSAFT +TSFNDDHIAAITQAVVEYRAHHGITGPVLVGRDTHALSGPAQDTAVEVLLGNDVEVLVDS +RGGYTPTPAVSHAILHLNAGRELSPSGFAVDGDNAGLVDGLVITPSHNPPADGGFKYNPP +HGGPADTEATTWIADRANELLAAGLAGVHRVASADVAGHAKLGGFDFLDRYVSDLPQVID +VEAIREAGVRIGADPMGGASVAYWGEIADRHGLDLTVVNPEVDPRFGFMTLDWDGKIRMD +CSSPNAMASLIERMTPDADGHAPFDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYL +YRHRQQWPQSAGVGKTLVSSSMIDRVAGDLGRELVEVPVGFKWFVPGLLTGTGVFGGEES +AGASFVQFDGSPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGDPAYARIDAPA +TAEQKAKLKTLSPDDVPVTELAGETILATLTNAPGNDAPIGGLKVVTQHAWFAARPSGTE +DVYKIYAESFRGPEHLKQVQAEAQKLVDAVIG +>PROKKA_02068 +MTENTAALPAAERPGTPALPQDLIDVDALLEAYRTGHPDVTDPAQKVVFGTSGHRGSAFT +TSFNDDHIAAITQAVVEYRAHHGITGPVLVGKDTHALSGPAQDTAVEVLLGNDVEVLVDS +RGGYTPTPAVSHAILHLNAGRELSPSGFAVDGDNAGLVDGLVITPSHNPPADGGFKYNPP +HGGPADTEATTWIADRANELLAAGLAGVHRVASADVAGHAKLGGFDFLDRYVSDLPQVID +VEAIREAGVRIGADPMGGASVAYWGEIADRHGLDLTVVNPEVDPRFGFMTLDWDGKIRMD +CSSPNAMASLIERMTPDADGQAPFDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYL +YRHREQWPQSAGVGKTLVSSSMIDRVAGDLGRELVEVPVGFKWFVPGLLTGTGVFGGEES +AGASFVQFDGSPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGDPAYARIDAPA +TAEQKAKLKTLSPDDVPVTELAGETILATLTNAPGNDAPIGGLKVVTQHAWFAARPSGTE +DVYKIYAESFRGPEHLTQVQAEAQRLVDAVIG +>PROKKA_00342 +MTEHTAAPPASERPGTPALPQDLIDVDALLTAYRTGRPDVSDPAQKVVFGTSGHRGSALK +TSFNDDHIAAITQAVVEYRAEHGITGAVLVGKDTHALSGPAQDTAVEVLLGNDVEVLVDS +RGGYTPTPAVSHAILHLNAGRDLTPAGFSADGDNAGLVDGLVITPSHNPPADGGFKYNPP +HGGPADTEATTWIADRANALLAAGLEGVRRVAAADVDGHAKLGGFDFLDRYVTDLPDVID +VEAIREAGVRIGADPMGGASVAYWGEIARRHGLDLTVVNPDADPRFGFMTLDWDGKIRMD +CSSPHAMASLIERMTPDADGQAPYDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYL +YRHRERWPADAGVGKTLVSSSMIDRVAGDLGRELVEVPVGFKWFVPGLLTGTGVFGGEES +AGASFVKLDGGPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGSPAYARIDAPA +TAEQKARLKTLSPDDVTVTELAGETILATLTNAPGNDAPIGGLKVVTQNAWFAARPSGTE +DVYKIYAESFRGPEHLKQVQEEAQRLVDAVIG +>PROKKA_00281 +MSTPAAGRAGTPALPEDLIDVEALLAAYRDLHPDPADPAQKVVFGTSGHRGSALKSSFND +DHIAAITQAVVEYRAEHGITGAILVGKDTHALSGPAQDTAVQVLLANDVEVLVDSRGGFT +PTPAVSHAILHLNAGRDLTAAGFSADGDNAGLVDGLVITPSHNPPADGGFKYNPPHGGPA +DTDATSWIAARANDLLAARLDGVTRLAPEDVEGHAKLGSFDFLDRYVTDLPQVIDLDAIR +EAGVRIGADPMGGASVAYWGEIGRRHGLDLTVVNPDVDPQFGFMTLDWDGKIRMDCSSPN +AMASLIERMTPDADGHAPFDVATGNDADSDRHGIVTPDGGLMNPNHFLAVSIDYLYRNRS +QWPQNAGVGKTLVSSSMIDRVATDLGRELVEVPVGFKWFVPGLLSGTGVFGGEESAGASF +VKFDGGAWSTDKDGLLLCLLAAEIQAVTGQSPSERYRDLVALHGDPAYARIDAPATAEQK +AALKALSPDDVTATELAGETILAALTNAPGNDAPIGGLKVVTKNAWFAARPSGTEDVYKI +YAESFLGEEHLKQVQQEAQAIVDAVIS +>PROKKA_00050 +MTENTAALPAAERPGTPALPQDLIDVDALLEAYHTGHPDVTDPAQKVVFGTSGHRGSAFT +TSFNDDHIAAITQAVVEYRAHHGITGPVLVGKDTHALSGPAQDTAVEVLLGNDVEVLVDS +RGGYTPTPAVSHAILHLNAGRELSPSGFAVDGDNAGLVDGLVITPSHNPPADGGFKYNPP +HGGPADTEATTWIADRANELLAAGLAGVHRVASADVAGHAKLGGFDFLDRYVSDLPQVID +VEAIREAGVRIGADPMGGASVAYWGEIADRHGLDLTVVNPEVDPRFGFMTLDWDGKIRMD +CSSPNAMASLIERMTPDADGQAPFDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYL +YRHREQWPQSAGVGKTLVSSSMIDRVAGDLGRELVEVPVGFKWFVPGLLTGTGVFGGEES +AGASFVQFDGSPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGDPAYARIDAPA +TAEQKAKLKTLSPDDVPVTELAGETILATLTNAPGNDAPIGGLKVVTQHAWFAARPSGTE +DVYKIYAESFRGPEHLTQVQAEAQKLVDAVIG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000211.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000211.fa new file mode 100644 index 0000000000000000000000000000000000000000..a6041f4dc439a1de617d7e4755cfa533b7703d48 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000211.fa @@ -0,0 +1,65 @@ +>PROKKA_00058 +MVSFSHTDDGTSEAAWAEGGVGELPELRLPVWDAQTLLLVAVAHPDDETLAATGLIRSAL +RDGARVHVLVATAGEASHPHSPTHTPEDLVRLRRDEMEHALDALAAGLPASAGPGSPARD +RLTWASLALPDSGVAEHEDAVRDAVAAALDAHPGPAVLASHDPGDGHADHEAVGRAVGAV +AGECDLPLYAFPIWFWHWADPADLPARRYRRLPLTDDDRAARRAALDAHASQVRPLSAAP +GDEAILGPAVLAHHERPFEAHRVSGPDDADAHRAAAVFDRLYRAQEDPWRYLSSSYEARK +RALTLAALPRPRYGTVVEAGASIGVLTADVAARADRVVGLEASSTAVERAAARLAGAPHA +EVRRAVLPADWPADVAGADLVIASEIGYFLQPEELDALIDDADAALAPGGELLLCHWRHP +IEGWPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHAVVVVPAKDEQERLP +AALAALAAALDRWEEHHAQGTAAVVVAADRCDDATVAAALEARAADPRIHVLELGEPTAG +QAGVGRARLEGARRARALFPDVPAERLWLASTDADSRVPADWLLAQTVAAGHDEVLVLGT +VDVHQGPLRQAWLRGYRHEEGHPHVHGANLGLPWSLYEAVGGFPPVAEHEDVGLAEAVRA +LAGERDGGDGRRVRVIATDTTRVLTSSRLEGRTPGGFSGYLKAVGRPG +>PROKKA_02071 +MVSFSHTDDGTSEAAWAEGGVGELPELRLPVWDAQTLLLVAVAHPDDETLAATGLIRSAL +RGGARVHVLVATAGEASHPHSPTHTPADLVRLRRDEMEHALDALAAGLPASAGPGSPARD +RLTWASLALPDSGVAEHEDAVRDAVAAALDAHPGPAVLASHDPGDGHADHEAVGRAVGAV +AGECDLPLYAFPIWFWHWADPADLPARRYRRLPLTDDDRAARRAALDAHASQVRPLSAAP +GDEAILGPAVLAHHERPFEAHRVSGPDDADAHRAAAVFDRLYRAQEDPWRYLSSSYEARK +RALTLAALPRPRYGTVVEAGASIGVLTAAVAARAGRVVGLEASPTAVERAAARLAGAPHA +EVRRAVLPADWPADVAGADLVIASEIGYFLQPEELDALIDDADAALAPGGELLLCHWRHP +IEGWPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHAVVVVPAKDEQERLP +AALAALTAALDRWEEHHAQGTAAVVVAADRCDDATVAAALEARAADPRIHVLELGEPTAG +QAGVGRARLEGARRARALFPDVPAERLWLASTDADSRVPADWLLAQTVAAGRDEALVLGT +VDVRQGPLRQAWLRGYRHEEGHAHVHGANLGLPWSLYEAVGGFPPVAEHEDVGLAEAVRA +LAGERDGGEGRRVRVIATDTTRVLTSSRLEGRTPGGFSGYLKAVGRPG +>PROKKA_00337 +MVSFSHTDAGTSEEAWAAAGVGALPVLESPAWDADTLLLVAVAHPDDETLGATGLIRSAL +RGGARVHVLVATAGEASHPDSPTHAPEDLVRLRRAEMEHALDALAADLPGPGEDRRSALT +WESLGLPDSGVAGREDAVRAAVVAALAAHPGPAVLASHDPGDGHADHEAVGRAVGELAGE +RDLPLCAFPIWFWHWADPAELPARRYRRLALTDDDRAARRAALDAHASQVRPLSDAPGDE +AVLGPQVLAHHDRPFEAHRLSGPDDADAHRAAAVFDRLYREHEDPWRYLSSPYEARKRAL +TLAVLPRPRYGTVVEAGASIGVLTGEVAARADRVVGLEASPTAVERAAARLADTPHAEVR +RAVLPGHWPDDVAGADLVIASEIGYFLQPEELDALVDDADAALAPGGELLLCHWRHPIEG +WPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHAVVIVPAKDEQERLPAAL +AALGAALDRWEEHHAQGSAAVVVAADRCDDATVAAAVAARHADPRVHVLELGEPGPGEAG +VGRARAEAARRARALFPDVPAQRLWLASTDADSRVPADWLLAQTTAAGPDGALVLGTVDV +REGALRRAWVRDYRHEEGHPHVHGANLGLPWSLYEAAGGFPPVAEHEDVRLVEAVRALAE +ARVRATDTTRVLTSSRLTGRTPGGFAGHLQEVGGEAVPRRGAQARP +>PROKKA_00277 +MVSFDHRDDGTAEAVWMAAGVGELPALPARAWTRADTLLVAVAHPDDETLGAAGLIRAAL +RGGAAVHVAVATAGEASHPDSPTHTPADLVRLRRAEMDHALAALADGLGPDAGALTWESL +ALPDGGLTDRPDEVRAALERVLAGRTPAEEGGGAVVLVSHDPDDGHGDHDAVGAAAAALA +ADHDLELYAFPLWLWHWGAPEDLAPRRYRRLELAAGDDAARLAALDAHASQTRPLSAAPG +DEAILPERMIAHFTRGFETYRRTAPDDADASRASAVFDRLYREHEDPWRYLTSPYEARKR +ALTLAVLPRPRYGTVVEAGASIGVLTAALAERAERVVGLEASQVAVERAAAHLAEIPHAE +VRRAVLPADWPADVGPAEEGAGAPADLVVASEIGYFLQPEELDALVDAADASLGAGGELL +LCHWRQPITGWPLDGDAVHDRVAADPRWRLLSEHVEADLRLSVHARAAAATHAVAVVPAM +DEAEHLPAGLDALSAALDLWEAQHTQGSAAVVTVVPADDAPTLEAAHAARARDPRIRVLE +LAPGAGGVGRARAAAARHARGLFPDVPAEALWLASTDADTRVPADWLVGQPALAARRRAD +GQVLVLGTVDLPAHADDDLAHRWRADYEHREDHPHVHGANLGLPWGLYERAGGFAEVAEH +EDVRLAEAVRALGEDRVLATDRVRVHTSSRLEGRTPGGFAGFLRGLLEEGAAEG +>PROKKA_00053 +MVSFSHTDDGTSEAAWAEGGVGELPELRLPVWDAQTLLLVAVAHPDDETLAATGLIRSAL +RGGARVHVLVATAGEASHPHSPTHTPEDLVRLRRDEMEHALDALAAGLPASAGPGSPARD +RLTWASLALPDSGVAEHEDAVRDAVAAALDAHPGPAVLASHDPGDGHADHEAVGRAVGAV +AGECDLPLYAFPIWFWHWADPADLPARRYRRLRLTDDDRAARRAALDAHASQVRPLSAAP +GDEAILGPAVLAHHERPFEAHRVSGPDDADAHRAAAVFDRLYRAQEDPWRYLSSSYEARK +RALTLAALPRPRYGTVVEAGASIGVLTADVAARADRVVGLEASPTAVERAAARLAGAPHA +EVRRAVLPADWPADVAGADLVIASEIGYFLQPEELDALIDDADAALAPGGELLLCHWRHP +IEGWPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHAVVVVPAKDEQERLP +AALAALTAALDRWEEHHAQGTAAVVVAADRCDDATVAAALEARAADPRIHVLELGEPTAG +QAGVGRARLEGARRARALFPDVPAERLWLASTDADSRVPADWLLAQTVAAGRDEALVLGT +VDVRQGPLRQAWLRGYRHEEGHAHVHGANLGLPWSLYEAVGGFPPVAEHEDVGLAEAVRA +LAGERDGGDGRRVRVIATDTTRVLTSSRLEGRTPGGFSGYLKAVGRPG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000213.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000213.fa new file mode 100644 index 0000000000000000000000000000000000000000..2eca68ed1a95229b22eccb76b170a3343232115a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000213.fa @@ -0,0 +1,15 @@ +>PROKKA_00061 +MSAFETVDVNEIPADAAILDVREDDEWALGRAAGAQHIPLGQLPDRLEELDPDTDYYLIC +RTGGRSARAAEFMTGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK +>PROKKA_02074 +MSAFETVDVNEIPADATILDVREDDEWALGRAAGAQHIPLGQLPDRLEELDPDTDYYLIC +RTGGRSARAAEFMTGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK +>PROKKA_00334 +MSAFETVDVNEIPADAAILDVREDDEWALGRAAGAQHLPLGQLPDRLEELDPDTDYYVIC +RTGGRSARAAEFMVGRGYTAINVAGGSGAWLEAGKPMEADGGAEPTVK +>PROKKA_00275 +MSHFETVTVDQIPADAAILDVREDDEWALGRAAGAQHLPLGQLPERIEELDPDTDYYVIC +RTGGRSARAAEYMVGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK +>PROKKA_00056 +MSAFETVDVNEIPADAAILDVREDDEWALGRAAGAQHIPLGQLPDRLEELDPDTDYYLIC +RTGGRSARAAEFMTGRGYSAINVAGGSGAWLEAGKPMEADGDAEPTVK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000214.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000214.fa new file mode 100644 index 0000000000000000000000000000000000000000..81a5bf3b59d7ab2556ba0b82c66781b031b3265b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000214.fa @@ -0,0 +1,35 @@ +>PROKKA_00062 +MTGTDSADATPSRLRYAFLGPAGTFTEAALRKVADPAEAEFVPAGSVLSAVAALRRGEVD +RAVVPIENSVEGGVSATVDEIALGETLQILAEVHVAISFVLVGRPGVAIEDVRRVTTHPH +AWAQVRGWAETALPGVEFTPAPSTAAGAGLVAQGDFDAAVCAPLVAEQTGLPVLAERIED +VPGAVTRFVLLSRPTALPAPTGADKTTLVVPLPEDRPGALGQILAEFTTRGVNLSRIESR +PTGEGIGRYFFSLDLEGHLAEARVGDALAALYREYPDLRFLGSYAQAEPVPTRVPAEFTD +AAYRSGRAWVESLRSR +>PROKKA_02075 +MTGTGSADATPSRLRYAFLGPAGTFTEAALRKVADPAEAEFVSAGSVLSAVAALRRGEVD +RAVVPIENSVEGGVSATVDEIALGETLQILAEVHVPISFVLVGRPGVAMEDVRRVTTHPH +AWAQVRGWAETALPGVDFTPAPSTAAGAGLVAQGDFDAAVCAPLVAEQTGLPVLAERIED +VPGAVTRFVLLSRPTALPAPTGADKTTLVVPLPEDRPGALGQILAEFTTRGVNLSRIESR +PTGEGIGRYFFSLDLEGHLAEARVGDALAALYREYPDLRFLGSYAQAEPVPTRVPAEFTD +AAYRSGRAWVESLRSR +>PROKKA_00333 +MTRDDAAPLGRCTFLGPAGTFTEAALRAVPGAEQAELIPATSVPAALAAVRAGEADHAMV +PIENSVEGGVSATLDDIASGDDLQILREELVQISFVLVGRPGVELADVRRVSTHTHAWAQ +VRGWVEANLPGVEYTPSGSTAAAARALADAEPGSEPFDAAVCAPLVAEQTGLPVLARAIE +DVTGAVTRFVLVGRPGPLPAHTGSDKTTLTVPLPDDHPGALREILDQFATRGINLSRIES +RPTGEGMGKYFFSIDLEGHLAEERVAAAMGALHRIFPGVRFLGSYPRAEHRPVAVRRHTS +DDAYRAGRAWVDGLLAR +>PROKKA_00274 +MSPAPRYAFLGPAGTFTEAALRQVASPEDVDLLPASSVLAALAAVRVGEAERAVVPIENS +VEGGVTATLDDIGADEPLQILAEVLVPISFVLVGRPGVALEDVRRVTTHTHAWAQVRGWM +EAHLPGVEFTPAGSTAAGARALLPSAGGDGAVASFDAAVCAPLVAEQTGLPVLAEAIEDV +TGAVTRFVLVSRPGPVPEPTGADKTTLTVPLPDDHPGALREILDQFATRGINLSRIESRP +TGEGMGRYFFSIDLEGHVAEERVGAALAALHRTFPGVRFLGSYPRAEGRPPTVPEHVTDA +AYRRGTAWVRGLRSR +>PROKKA_00057 +MTGTDSADATPSRLRYAFLGPAGTFTEAALRKVADPAKAEFVSAGSVLSAVAALRRGEVD +RAVVPIENSVEGGVSATVDEIALGETLQILAEVHVPISFVLVGRPGVAIEDVRRVTTHPH +AWAQVRGWAETALPGVEFTPAPSTAAGAGLVAQGDFDAAVCAPLVAEQTGLPVLAERIED +VPGAVTRFVLLSRPTALPAPTGADKTTLVVPLPEDRPGALGQILAEFTTRGVNLSRIESR +PTGEGIGRYFFSLDLEGHLAEARVGDALAALYREYPDLRFLGSYAQAEPVPTRVPAEFTD +AAYRSGRAWVESLRSR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000218.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000218.fa new file mode 100644 index 0000000000000000000000000000000000000000..80722fcdf276cdcfabe310fe8082823b0663db0d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000218.fa @@ -0,0 +1,46 @@ +>PROKKA_00069 +MGQVDTGRTGRRDRRTERPRSRSLHAVLLAALAAVLVACGPVTAPPAPSSAPASSTTAAP +TSSSPSAGPTAAEVAAAVEPGLETSPGTASAEFRDLATGEVLYARDADEPVAPASSLKVL +AAAAIVSALGPETTLQTTVVAQPTADDAATELVLVGGGDVLLGTGASDSTHVSGRAGLRT +LAQRTVAGLVEDGVTGQVVVSTDLRLFTDRTALNPRWTSDIPESGNIAPVQPLATYGGRE +APGTGEDRIEDPAQFAALTFQAALDDAVAASGADLEVGLRDTLPATEVPRATVLAAAPVA +AVESASVGEQVAYLLAHSENQVVEALAHTAAPATDLPATHEGATRLLTATVEDLGVDTAG +MALVDSSGLSPDNRVSAGQLAGVVAGVARTPALATVLEGLPRPGEDSTLGDRFPDAPARQ +AVAAKTGTLDQTVSLTGTVTTTSGRVLAFSIICSDLQWKLEPARAAVDEAVSAVAGL +>PROKKA_02082 +MGQVDTGRAGRRDRRTEHRRSRSLPAVLLAALAAVLVACGPVTAPTAPSSASASTSTAAP +TSSSPSAGPTAAEVAAAVEPGLETSPGTVSAEFRDLATGEVLYARDADEPVAPASSLKVL +AAAAIVSALGPETTLQTTVVAQPTADGAATELVLVGGGDVLLGTGASDSKAVSGRAGLRT +LAERTVAGLVEDGVTGRVVVSTDLRLFADRTALNPRWTSDIPESGNIAPVQPLATYGGRE +APGTGEDRIEDPAQFAALTFQAALDDAVAASGADLEVGLRDTFPATEVPRATVLAAAPVA +AVESAPVGQQVAYLLAHSENQVVEALAHTAAPATDLPATHEGATQLLTATAEDLGVDTAG +MALVDSSGLSPDNRVSAGQLAGVVAGVARTPALGTVLEGLPRPGEDSTLGDRFPDAPARQ +AVAAKTGTLDQTVSLTGTVTTTSGRVLAFSIICSDLQWKLEPARAAVDEAVSAVAGL +>PROKKA_00323 +MTPGSPFASLLAALAAALLSAAPVLTPLAGPAALAPGNPVTAEAVAAPSPDARALASAVD +AALDASPGRVAAQVRDAATGEVLHARDADFLAAPASSLKVLTAAAALRTLGPERTLRTRV +VAVPAADDGATELVLVGGGDVLLGDGASDPDAVAGRAGLRTLAERTVAGLAEAGVSGDVV +VSVDLRLFDGAAVNPAWTPDLLEDGHVSAVQPLATWGGREVPGVDEERIEDPAGHAALVF +QRLLDEEIERTGADLDLGLRDSIPATTAVRDDVVAAEPTAQVESAPVAEVAAYMLAHSEN +QVAEALGHLSAYAVGRPATHEGAADLLEDVAADLGADTAGMAVLDASGLAEGSLVSPAQL +AAVVSAASRVPWLAPVLDGLPRPGEDSTLDERFRGTAAEGAVAAKTGTLDHTVSLTGTVT +TQDGRVLAFSIVASDLDWRLDEAREAVDAAVTAMAGL +>PROKKA_00265 +MTPSNRAARVAAVTRVLLALAICALLGLLAHDVLLPRLPTPAAPAASAPSAPVPAASPSG +GATAPSSTALASVAPVDPADVAAAVAPALAQAPGTASAEVRDAATGEVLYARSADQAVAP +ASALKILTAVTAVDVLGADRALTTSVVALPGGGATELVLVGGGDALLGAGASDPGRVDGR +AGLRTLARRTVAGLRERGVTGPVAVSTDLRLFTDASPLNPAWSAGLVESGNITAVQPLAT +YGGRTAPGTGEDRIADPAAFAALAFQRELTAAVADSGADLSVRARDVVPATSAPRGDVLA +TEPVARVESAPVGQQVAYLLAHSENQVAEVLARVAAAADGRPATHAAVPGLLRDRAAAHG +VDTAGMRLVDASGLSPQNRVTAHQLAGLVEAVQADPALAPVRDGLPRPGEDSTLAERFPG +SPAREAVAAKTGTLDQTVSLTGTVTTGSGRVLAFSIVCSGVDWRIAPARAAIDEAVSALA +AL +>PROKKA_00063 +MGQVDTGRAGRRDRRTEHRRSRSLPAVLLAALAAVLVACGPVTAPPAPSSAPAASTTAAP +TSTSPSAGPTAAEVAAAVEPGLATSPGTVSAEFRDLATGEVLYARDADEPVAPASSLKVL +AAAAIVSALGPETTLQTTVVAQPTADGAATELVLVGGGDVLLGTGASDSTHVSGRAGLRT +LAERTVAGLVEDGVTGQVVVSTDLRLFTDRTALNPRWTSDIPESGNIAPVQPLATYGGRE +APGTGEDRIEAPAQFAALTFQAALDDAVAASGADLEVGLRDTLPATEVPRATVLAAAPVA +AVESASVGEQVAYLLAHSENQVVEALAHTAAPATDLPATHEGATRLLTATAEDLGVDTAG +MALVDSSGLSPDNRVSAGQLAGVVAGVARTPALATVLEGLPRPGEDSTLGDRFPDAPARQ +AVAAKTGTLDQTVSLTGTVTATSGRVLAFSIICSDLQWKLEPARAAVDEAVSAVAGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000221.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000221.fa new file mode 100644 index 0000000000000000000000000000000000000000..02cd2fba391699a79628748ddadd40f6b6221bba --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000221.fa @@ -0,0 +1,25 @@ +>PROKKA_00072 +MDAQDVQNDLTHVLMSREDVQDTITDLARQIDRDYADKDLLIVAVLKGAVMVVADLTRAL +HSHVELDFMAVSSYGSGTKSSGVVRILKDLDADLTGRHVLIVEDIIDSGLTLSWLKANLE +SRGPASVEICTLLRKPEAMKVDIDVKYVGRDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH +VYS +>PROKKA_02085 +MDAQDVQNDLTHVLMSREDVQDTITDLARQIDRDYADKDLLIVAVLKGAVMVVADLTRAL +HSHVELDFMAVSSYGSGTKSSGVVRILKDLDADLTGRHVLIVEDIIDSGLTLSWLKANLE +SRGPASVEICTLLRKPEAMKVDIDVKYVGRDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH +VYS +>PROKKA_00320 +MDAQDVQNDLTHVLMRREEVQETVKDLAAQIDRDYEGKDLLIVAVLKGAIMVVADLTRAL +HSHVQIDFMAVSSYGSGTKSSGVVRILKDLDADLTGRDVLIVEDIIDSGLTLSWLKANLE +SRGPASVEICTLLRKPDAMKVEIDVKYVGRDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH +VYS +>PROKKA_00262 +MDAQDVQNDLTHVLMSKEEVQDTIRDLAAQIDRDYEGKDLLIVAVLKGAVMVVADLTRAL +HSHVEMDFMAVSSYGSGTKSSGVVRILKDLDADLTGRHVLIVEDIIDSGLTLSWLKANLE +TRGPASVEICTFLRKPDAMKVDIDVKYVGKDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH +VYS +>PROKKA_00066 +MDAQDVQNDLSHVLMSREDVQDTITDLARQIDRDYADKDLLIVAVLKGAVMVVADLTRAL +HSHVELDFMAVSSYGSGTKSSGVVRILKDLDADLTGRHVLIVEDIIDSGLTLSWLKANLE +SRGPASVEICTLLRKPEAMKVDIDVKYVGRDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH +VYS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000222.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000222.fa new file mode 100644 index 0000000000000000000000000000000000000000..e6a6faeb4cfa27e8c193bf2b88997f11c0437db1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000222.fa @@ -0,0 +1,65 @@ +>PROKKA_00074 +MKKLFNKPYVWILLGLLVLAVAIPLTTSQSGRTMVDTNVGMALLKDDKAAQARVVDGDQR +VDLTLREPYKQDDRDLGKEVYFYFATARATDVVTAVDDSALDGYTDEPVRSNWFLSLLGF +MVPFLLIALLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE +IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV +GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD +ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVDAPDLEGRAKILEVHAQGKPIALDVDL +RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH +ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL +AYAMGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGSSEPFVG +GAAGGSSREYSEELAYLVDAEVRTLLDQAHAEAHWVLTENRDVLDRLAYELLEKETLTQE +AIAAIFADVRKRPERGVWLASDDRLPQDIPPVLSPSERRSRHDGGEQTPVGVEGTTVPVR +PEGAPPSSLGGDAAGPGLPPHGGPSNTPGPGEGPTF +>PROKKA_02087 +MKKLFNKPYVWILLGLLVLAVAIPLTTSQSGRTMVDTNVGMALLKDDKAAQARVVDGDQR +VDLTLREPYKQDDRDLGKEVYFYFATARATDVVTAVDDSALDGYTDEPVRSNWFLSLLGF +MVPFLLIALLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE +IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV +GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD +ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVDAPDLEGRAKILEVHAQGKPIALDVDL +RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH +ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL +AYAMGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGSSEPFVG +GAAGGSSREYSEELAYLVDAEVRTLLDQAHAEAHWVLTENRDVLDRLAYELLEKETLTQE +AIAAIFADVRKRPERGVWLASDDRLPQDIPPVLSPSERRSRHDGGQQTPVGVEGTTVPVR +PEGAPPSSLGGDAAGPGLPPHGGPSNTPGPGEGPTF +>PROKKA_00319 +MKKLFNKPYIWILLGLLVLAVAIPLATSQTGRTMVDTNVGMAMLQDDKAAQARVVDGDQR +VDLTLREPYSQDGRDLGKEVYFHFATARASDVVTAVDDSALDGYTDEPVRSNWLLSLLGF +MIPFLLIALLFWFLLSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE +IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV +GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD +ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVEAPDLEGRAKILEVHAQGKPIALDVDL +RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH +ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL +AYALGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGNSEPFVG +GGGGGSSREYSEELAYLVDAEVRGLLDGAHAEAHWVLTENRDVLDRLAYELLEKETLTQE +AIAEIFRDVRKRPERDVWLASDERLPQDIPPVLSPSERRSRHEGGEQTPVGVEGTTVPVH +PEGAPPSSLGGDAPTPGLPPHGGPSSSPGAGEGPTY +>PROKKA_00260 +MKKQFNKPYIWILLGLLVLGLVIPLTTAQSGRGMVDTNVGMALLRDDKVAQARVVDGEQR +VDLTLREPLSQDGRDLGRDVYFQFSAARAQDVVRTVQDSSVDGYQDEPVRDSWLLSLLGL +MIPFLLISLLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELHE +IKEFLTEPERFHAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV +GVGASRVRDLFEQAKANAPAIIFVDEIDAVGRSRGVGIGGGNDEREQTLNQMLVEMDGFD +ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVEAPDLDGRAKILEVHAQGKPIALDVDL +RSLAKRTPGYTGADLANVINEAALLTARSRNNVIDNAALDEAVDRVMAGPQKRTRLMNEH +ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPENDKYSVTRNELLDQL +AYAMGGRVAEEVVFKDPSSGAANDIQKATETARKMVTDYGMSSKVGAVKLGSANTDPFLG +GGGAASREYSEELAYLVDAEVRALLDGAHAEAHWVLTENRDVLDRLAAELLEKETLTQEQ +IAEIFKDVRKRPERPLWLAADDRPPHDVPPVLTARERASRLEGEQPEAVGVEGTTVPDAP +EGAPPTALGGAGGSAGGPGDLPGQHSPTPGPTY +>PROKKA_00068 +MKKLFNKPYVWILLGLLVLAVAIPLTTSQSGRTMVDTNVGMALLKDDKAAQARVVDGDQR +VDLTLREPYKQDDRDLGKEVYFYFASARATDVVTAVDDSALDGYTDEPVRSNWFLSLLGF +MVPFLLIALLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE +IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV +GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD +ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVDAPDLEGRARILEVHAQGKPIALDVDL +RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH +ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL +AYAMGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGSSEPFVG +GAPGGSSREYSEELAYLVDAEVRTLLDQAHAEAHWVLTENRDVLDRLAYELLEKETLTQE +AIAAIFADVRKRPERGVWLASDDRLPQDIPPVLSPSERRSRHDGGEQTPVGVEGTTVPVR +PEGAPPSSLGGDAAGPGLPPHGGPSNTPGPGEGPTF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000223.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000223.fa new file mode 100644 index 0000000000000000000000000000000000000000..d5c90e0aa7f15c5158eba76c5b0c98940966a244 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000223.fa @@ -0,0 +1,25 @@ +>PROKKA_00075 +MTAHTPDDAVPGTFDPDSTAVDRPRIEAAVREILLAIGEDPDREGLADTPARVAKAYAEF +FAGLHQSPDQVLGTTFDIAHEELVLVKDIPFYSTCEHHLVPFHGTAHIGYIPSAEGRVTG +LSKLARLVELYARRPQVQERLTTQVVEALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAK +TVTSAVRGQLRDPSTRSEAMSLIMHG +>PROKKA_02088 +MTAHTPDDAVPGTFDPDSTAVDRPRIEAAVREILLAIGEDPDREGLADTPARVAKAYAEF +FAGLHQSPDQVLGTTFDIAHEELVLVKDIPFYSTCEHHLVPFHGTAHIGYIPSAEGRVTG +LSKLARLVELYARRPQVQERLTTQVVEALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAK +TVTSAVRGQLRDPSTRSEAMSLIMHG +>PROKKA_00318 +MTEQTHHDDAARGPVPAADGSAAAPTASTPAAAGVPGTFDPDSTAIDRPRIEAAVREILL +AIGEDPDREGLQDTPKRVAKAYAEFFAGLHQGPEQVLGTTFDIAHEELVLVKDIPFYSTC +EHHLVPVHGTAHIGYIPSAAGRVTGLSKLARLVELYARRPQVQERLTTQVVEALMEHLAP +RGAIVVVEAEHMCMSMRGVRKPGAKTVTSAVRGQLRDPSTRSEAMSLIMHG +>PROKKA_00259 +MTEQHRDAALADAHLHRPHEAAADVAPTTGAGAALAGAVPGVPGTFDPDQDTVDRPRIEA +AVREILLAIGEDPDREGLQDTPKRVAKAYAEFFAGLHQRPEQVLGTTFDLSHEELVLVKD +IPFYSTCEHHLVPFHGAAHIGYIPSAEGRVTGLSKLARLVELYARRPQVQERLTTQVVEA +LMEHLQPKGAIVVVEAEHMCMSMRGVRKPGAKTVTSAVRGQLRDPSTRAEAMSLIMHG +>PROKKA_00069 +MTAHTPDDAVPGTFDPDSTAVDRPRIEAAVREILLAIGEDPDREGLADTPARVAKAYAEF +FAGLHQSPDQVLGTTFDIAHEELVLVKDIPFYSTCEHHLVPFHGAAHIGYIPSAEGRVTG +LSKLARLVELYARRPQVQERLTTQVVEALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAK +TVTSAVRGQLRDPSTRSEAMSLIMHG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000224.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000224.fa new file mode 100644 index 0000000000000000000000000000000000000000..bf20fa33419637acca2092981d894bdf505648a9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000224.fa @@ -0,0 +1,20 @@ +>PROKKA_00077 +MSARDRIRLAGLSAVGHHGVFDHERRDGQPFVTDVVLHLDAGPAAAGDDLARTANYAEVA +DTVVRLVTGEPVDLIETLADRIARAVLAEQPVVTAVEVTVHKPQAPIPHDFADAAVTVHR +TREDLA +>PROKKA_02090 +MSARDRIRLAGLSAVGHHGVFDHERRDGQPFVTDVVLHLDAGPAAADDDLARTANYAEVA +DTVVRLVTGEPVDLIETLADRIARAVLAEQPVVAAVEVTVHKPQAPIPHDFADAAVTVHR +TREDLA +>PROKKA_00316 +MSARDRIRLTGLSAVGHHGVFDHERRDGQPFVTDVVLHLNAGPAAAGDDLARTANYAEVA +DTVVRLVTGEPVDLIETLAERIARAVLAEQPVVEAVEVTVHKPQAPIPHDFADAAVTVHR +TRRDAS +>PROKKA_00257 +MSDVIRLTGLTATGRHGVFEHERRDGQPFTTDVALTLDAGPAAARDDLARTANYAEVAET +VVRLVTGEPFDLIETLAVRIAEAVLAEQPVVTAVEVTVHKPQAPIPHDFTDVSVTVARRR +GA +>PROKKA_00071 +MSARDRIRLAGLSAVGHHGVFDHERRDGQPFVTDVVLHLDAGPAAAGDDLARTANYAEVA +DTVVRLVTGEPVDLIETLADRIARTVLAEQPVVAAVEVTVHKPQAPIPHDFADAAVTVHR +TREDLA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000225.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000225.fa new file mode 100644 index 0000000000000000000000000000000000000000..952afb1e66c3cc258a6b401da9faee801284a400 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000225.fa @@ -0,0 +1,25 @@ +>PROKKA_00078 +MSTVDWSHLAEGPAPVPALGARPDAPVAAVLALGANLREPAQTLDAAVAALSALPHITDV +RASPRAVTAPVGGPPGQPDYLNQVVTLRTDLAPWELLAVAHRLEQDHHRRREVRWGARTL +DVDVIAYGDVRSDHPDLTLPHPRAAERAFVLLPWLWLDADATLAGTPVADLAAVAADAPG +VRRQEPERHRLLAGTDDVVPLRPACPDALGREDT +>PROKKA_02091 +MSTVDWSHPAEGPAPIPELGARPDAPVAAVLALGANLREPAQTLDAAVAALSALPHITDV +RASPRAVTTPVGGPPGQPDYLNQVVTLRTDLAPWELLAVAHRLEQDHHRRREVRWGARTL +DVDVIAYGDVRSDHPDLTLPHPRAAERAFVLLPWLWLDADATLAGTPVADLAAVAADAPG +VRRQEPERHRLLAGTDDVAPLRPARPDALGREAT +>PROKKA_00315 +MSGVDWRHPAEDPAPTPALGARPAEPVAAVLALGANLREPAQTLDAAVAALSALPHVTDV +QASPRAVTAPVGGPPGQPDYLNQVLTLRTTLSAWELLAVAHRLEQEHHRRREVRWGARTL +DVDVIAYGDLVSDHPDLTLPHPRAAERGFVLLPWLWLDPDAVLAGRPVAELAALAADAPG +VRRAEPERHRLLAGRDDVVPVRPRAVRAPGRDAIDGSGP +>PROKKA_00256 +MSRPEAAHPAEGPAPTPELAARPSSPVTAVLALGANLGDPSETLDASVAVLTVTPGIEAV +AASPRALTAPVGGPPGQPDYLNQVVRIRTALSPWELLGVAHRLEQDHHRRRTVRWGARTL +DVDLIVYGDLTSDHPDLVLPHPRAAERGFVLLPWAWLDPEAELAGESVAELGARAADAPH +VRREPARTAHLDGPRPDVLRPDSTPGLPSAPLPDGAAIARPWSDPT +>PROKKA_00072 +MSTVDWSHPAEGPAPIPELGARPDAPVAAVLALGANLREPAQTLDAAVAALSALPHITDV +RASPRAVTTPVGGPPGQPDYLNQVVTLRTDLAPWELLAVAHRLEQDHHRRREVRWGARTL +DVDVIAYGDVRSDHPDLTLPHPRAAERAFVLLPWLWLDADATLAGTPVADLAAVAADAPG +VRRQEPERHRLLAGTDDVAPLRPARPDALGREAT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000227.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000227.fa new file mode 100644 index 0000000000000000000000000000000000000000..5cf93e8d1407b09939c7e836809e0692f0b9807c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000227.fa @@ -0,0 +1,20 @@ +>PROKKA_00080 +MPGIDLSGVAFTPASPRLTTVKLIATTIGHLIWLAAFSVPLILKLTGPWAGMAAWVAWGL +PAVVVVSWIVDLILIPRRVRAMGWAEREDDVLWREGILFRSVHAVPYGRLQYVDVSDGPL +LRRVGLQTLTLKTAAAGGDVTLEGVPRERAEELREVLMARGQARLAGL +>PROKKA_02093 +MPGIDLSGVAFTPASPRLATVKLIATTIGHLIWLAAFSVPLILKLTGPWAGMAAWVAWGL +PAVVVVSWIVDLILIPRRVRAMGWAEREDDVLWREGILFRSVHAVPYGRLQYVDVSDGPL +LRRVGLQTLTLKTAAAGGDVTLEGVPRERAEELREVLMARGQARLAGL +>PROKKA_00313 +MPGIDLTGVTFAPASPKLTPVKLISSSIGHLIWLVVFSVPLVLKLLGPWEGLWAWTAWGL +PAIVVVSWLVDLVLIPRRVRAMGWAEREDDVLWREGLLFRSVHAVPYGRLQYVDVSDGPL +LRRVGLQTLTLKTAASGSDVTLEGLPRETADELREVLMARGQARLAGL +>PROKKA_00254 +MPGIDLQGVEFTPVSPALVRVEAVRELIALVIWLAVVSVPLVLKLTGVWPDMWSWTAWGL +PALVLAWSLVELVLIPRRVVAKGWAEREDDVLWREGILFRRVVAVPYGRLQYVDVTDGPL +LRWAGLQKLTLKTAGGADVELVGLPRETCDRLREVLMARGQARLAGL +>PROKKA_00074 +MPGIDLSGVAFTPASPRLATVKLIATTIGHLIWLAAFSVPLILKLTGPWAGMAAWVAWGL +PAVVVVSWIVDLILIPRRVRAMGWAEREDDVLWREGILFRSVHAVPYGRLQYVDVSDGPL +LRRVGLQTLTLKTAAAGGDVTLEGVPRERAEELREVLMARGQARLAGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000228.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000228.fa new file mode 100644 index 0000000000000000000000000000000000000000..de653a4f3ba2200833ba9e977579becc200a61a5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000228.fa @@ -0,0 +1,56 @@ +>PROKKA_00081 +MSAAAPPPADDAGWVRVHPASPWVRGWTFLLLILFFAGRNAVEDFAAGRLSGEDAPGGGD +GSLLVAGGILLGVTLLISLVFFFSWWFTRFRCGEDRIELRQGWLFRSRRQMRYDRIQAVD +LQHPLVARLLGLATVKVEAADGGESALELSFLRRAEAEAVRREILDRASGMLGGAGADAS +APERAAEPGLPDADAADAGELMLQVPAGRLLGSVLLSGGVLGVLAGSLIWLGGLALVVAL +LPEAVLDEGETLTGIGAAASLPALFSVAGVAWSRLNAGWGFQVRRSTDGLRLRHGLTETT +HQTVPPGRVQGVTVSQPLFWRPFGWYRVNMAVAGYLQESDGARDVALPVGPWEDVLRVLT +VVAPDPGLDGDPRAAQGLTPAGLMHLGVHGTGTEGGFQHVPRRGRWWFNWFAWRRTGFTT +TRSLLVVRSGWLNRRLQTLQHERMQAAELAQGPVQRRLGLATVRVWVAGANAVVRDLDED +VAVDLYAREARHAAVSRRLADRDQWMRPEELARFEQRTREVAATEVGRRELARAGVVGGA +VVGEESGAHVPAVRGEEER +>PROKKA_02094 +MSAAAPPPADDAGWVRVHPASPWVRGWTFLLLILFFAGRNAVEDFAAGRLSGEDAPGGGD +GSLLVAGGILLGVTLLISLVFFFSWWFTRFRCGEDRIELRQGWLFRSRRQMRYDRIQAVD +LQHPLVARLLGLATVKVEAADGGESALELSFLRRAEAEAVRREILDRASGVLGGAGADAS +APERAAEPGLADADPDAVDADAGELLLQVPAGRLLGSVLLSGGVLGVLAGSLIWLGGLAL +VVALLPEAVLDEGETLTGIGAAASLPALFSVAGVAWSRLNAGWGFQVRRSTDGLRLRHGL +TETTHQTVPPGRVQGVTVSQPLFWRPFGWYRVNMAVAGYLQESDGARDVALPVGPWEDVL +RVLTVVAPDPGLDGDPRAAQGLTPAGLMHLGVHGTGTEGGFQHVPRRGRWWFNWFAWRRT +GFTTTRSLLVVRSGWLNRRLQTLQHERMQAAELAQGPVQRRLGLATVRVWVAGANAVVRD +LDEDVAVDLYAREARHAAVSRRLADRDQWMRPEELARFEQRTREVAATEVGRRELARAGV +VGGAVVGEESGAHVPAVRGEEER +>PROKKA_00312 +MSAAAPVPATRPADDDGWARVHPASPWVRGWTFLLLILFFLGRNAVEDFAAGRFGAGAGG +GSGEGEGSLLVAGGILLGVTLLVSLAFFFSWWFTRFRIGEDQIELRQGWLFRTRRQMKYD +RIQAVDLQHPLVARLLGLAVVKVEAADGGESALELSFLPKARAEQVRREILDRASGVLVG +PASAPRIAEGADAAAGVIPGVMPGVMPGAEAGPGVAPPGADADPTTPRADAPEGAAPSSS +DPGLARRADDEGELMLRVPSGRLIGSVLLSGGVAGTVAVYLVVVLGTSLFFALAPGTWLE +GEDTPLTGIVVAWGLPLAFAVVGQAWSGLNGGWGFQVRRSADGLRLRHGLTETTHQTVPP +GRVQGVTVSQPLFWRPFGWHRVKVSVAGYGEDAAGKRSTALPVGPWEDVLRVLTVVAPDP +GLDGDPREAEGLTPARLMHLGLHGSGTEGGFHHIPHRGRWWFNWFAWRRRGFTTTRALLV +VRSGRWNRVLQTLQHERVQTAALDQGPVQRRLRLATVHVRTAGGRAVLPDLDEAVALELF +AEEARHAAVSRRLADRDRWMRPEELARFEQRTREVAATEVGREELARAGVARPAAPAGGV +AGTDPEPRTSHEERP +>PROKKA_00253 +MSAPAPRPEGLASGPSPEDGRIAPAPAADDAGWVRVHPASPWIRGWVMVATFLFFALRDV +VERWIGGLFGADAGGGPGVDGRGLLIGGGIALGVLLLVGLAFFFSWWFTRFRIGAEEIEL +KQGWLFRSRRQMHYDRLQAVDLQHPLPARLIGLAVVKVEAADGGGDSALELAYLPKAQAA +AVRRQILDRASGAAAARPVPSAAPEAAGGPAAAGPVRGLLVDPEEQGPVLLRVPAGRLIG +SVLLSSTVMGLLGAVVAVPAVLSLLLLLFPDANAGEEAGVWAVTLGSTFPLLFSLAGAVW +SGLNKGWGFTVRDSSDGLRLRYGFTETVSQTVPPGRVQGVEISQPLFWRPFGWHRVKVSV +AGYGGLEAEGRRRDVALPVGPWEDVLRVLQVVAPDPGLGGDARAAGELMRTAMTGSGEEG +GFRHVPRRAAWWWHWLTWRRHGYALTPTLLVVRHGRLSRSVQTVQHERLQAVALTQGPVQ +RRLRVATLRVHMAGGAARLRGLDEDVLAELFEVESRHAAVSRRLTDRNRWMLPEELERFE +RRTAEVARTEVGRAEMAAAGVVPMETGPRPGDTPPVATTEHRGEETA +>PROKKA_00075 +MSAAAPPPADDAGWVRVHPASPWVRGWTFLLLILFFAGRNAVEDFAAGRLSGEDAPGGGD +GSLLVAGGILLGVTLLISLVFFFSWWFTRFRCGEDRIELRQGWLFRSRRQMRYDRIQAVD +LQHPLVARLLGLATVKVEAADGGESALELSFLRRAEAEAVRREILDRASGMLGGAGADAS +APERAAEPGLPDADAADAGELMLQVPAGRLLGSVLLSGGVLGVLAGSLIWLGGLALVVAL +LPEAVLDEGETLTGIGAAAALPALFSVAGVAWSRLNAGWGFQVRRSTDGLRLRHGLTETT +HQTVPPGRVQGVTVSQPLFWRPFGWYRVNMAVAGYLQESDGARDVALPVGPWEDVLRVLT +VVAPDPGLDGDPRAAQGLTPAGLMHLGVHGTGTEGGFQHVPRRGRWWFNWFAWRRTGFTT +TRSLLVVRSGWLNRRLQTLQHERMQAAELAQGPVQRRLGLATVRVWVAGANAVVRDLDED +VAVDLYAREARHAAVSRRLADRDQWMRPEELARFEQRTREVAATEVGRRELARAGVVGGA +VVGEESGAHVPAVRGEEER diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000229.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000229.fa new file mode 100644 index 0000000000000000000000000000000000000000..c4c8251758e4df6426a91febfb9d11ced3ff0f8c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000229.fa @@ -0,0 +1,35 @@ +>PROKKA_00082 +MTGGLDLSLDPHDPAQRPGRLGVGVVSAGRVGAVLGSALRAAGHTITGVHAVSEASRDRA +EMLLPGVPVLEIPEILRRSEMVVFAVPDDALGELVAGLAAAGHVQTGHLLVHTSGRYGVG +VMEPVRAHGAIPLAIHPAMTFTGLSLDVARLQDCVFGVTADPVVLPVAQALVVEMGGEPV +VVKEADRAAYHLALSHGSNHLVTLTAQARQILETIGVADPERVLRSLMTAALENALTDGD +GALTGPVARGDVDTLRTHRETLGELEAGGLPPDVRAVWETLARATTDRAETRGTLRADTA +ARLREVLDDSDDPHDD +>PROKKA_02095 +MTGGLDLSLDPHDPAQRPGRLGVGVVSAGRVGAVLGSALRAAGHTITGVHAVSEASRDRA +EMLLPGVPVLEIPEILRRSEMVVFAVPDDALGELVAGLAAAGHVQTGHLLVHTSGRYGVG +VMEPVRAHGAIPLAIHPAMTFTGLSLDVARLQDCVFGVTADPVVLPVAQALVVEMGGEPV +VVKEADRAAYHLALSHGSNHLVTLTAQARQILETIGVADPERVLRSLMTAALENALTDGD +GALTGPVARGDVDTLRTHRETLGELEAGGLSADVRAVWETLARATTDRAETRGALRADTA +ARLREVLDDSDDPHDD +>PROKKA_00311 +MTGGLDLTLDPTDPTQRPGRLGVGVVGAGRVGAVLGAALRNAGHTITGVHAVSEASRTRA +EALLPEAPVLEIPEILRRSEMVLFAVPDDVLPELVAGLAAAGHVQTGHLVVHTSGRHGVG +ALNPVRAHGAIPIALHPAMTFTGLSLDLARLQDCVFGVTADPVVLPVAQALAVEMGGEPV +VIKEADRGVYHAALSHGSNHLVTLTAQAAQLLRSIGVQDTERLLRPLMHASLENALADGD +GALTGPVARGDVETVRGHRETLRELVAEGMPADVLAVWETLARATADRAEARGALRPDVA +ARLREALAPDA +>PROKKA_00252 +MSRMDMSPELTGADPADRPGRLGVGVIGAGRVGAVLGAALRGAGHTITGVHAVSEASRTR +AEALLPGVPVLELPEILRRSEMVLFAVPDDALPELIAGLAAAGHIQTGHLLVHTSGRHGV +RVMDPVRAHGAIPLAVHPAMTFTGLSLDLARLQDCVFGVTADPVVLPVAQALVVEMGGDP +VVVKEADRAAYHLALSHGSNHLVTVTAQARQILEEIGVAEPERMLRPLMQASLENALTDG +DGALTGPVARGDVETVRGHRDTLRELVDGGMPADVLAVWESLARATAQRAARRGALRADA +AERILAVLDGADDGPDATG +>PROKKA_00076 +MTGGLDLSLDPHDPAQRPGRLGVGVVSAGRVGAVLGSALRAAGHTITGVHAVSEASRDRA +EMLLPGVPVLEIPEILRRSEMVVFAVPDDALGELVAGLAAAGHVQTGHLLVHTSGRYGVG +VMEPVRAHGAIPLAIHPAMTFTGLSLDVARLQDCVFGVTADPVVLPVAQALVVEMGGEPV +VVKEADRAAYHLALSHGSNHLVTLTAQARQILETIGVADPERVLRSLMTAALENALTDGD +GALTGPVARGDVDTLRTHRETLGELEAGGLSADVRAVWETLARATTDRAETRGALRADTA +ARLREVLDDSDDPHDD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000231.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000231.fa new file mode 100644 index 0000000000000000000000000000000000000000..d6fd4c80a0e70dd907651589bde98e38fef6aa3a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000231.fa @@ -0,0 +1,41 @@ +>PROKKA_00086 +MTSVRRHAARGLVALAAAVAVSAPLAAPAAAAPAAPTTPAAAQSVTGKPVVRPDVVGHRG +ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRK +TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER +LSARYGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEYGLNKRNAPATVQSFELANLRD +LNENLGLKAETVFLSSVTGAPYDSVAAGDGLRDYDFYETAAGMREVRAAGVDTLGPAFAQ +IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDPNARGDMVGMIQ +PFLDAGIDGFFTDHPDLGVQAVDTWMQGKKEHPGRGVGKTAQRGLKVR +>PROKKA_02099 +MTSVRRHAARGLVALAAAVAVSAPLAAPAVAAPAATETPAAAQSVTGKPVVRPDVVGHRG +ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRR +TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER +LSARHGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD +LNENLGLKAETVFLSSVTGAPYDSVAAGDELRDYDFYETAAGMREIRAAGVDTLGPAFAQ +IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDRNAQGDMVGMIQ +PFLDAGIDGFFTDHPDLGVQAVDVWMQGKKEHPGRGVGKTAQRGLQGR +>PROKKA_00305 +MISVRRHAARGLVALAAAVAVSAPLAAPAVAAPAAPTAPAAAQSATGKPVVRPEVVGHRG +ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRK +TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYNGRYQVPTFEEVLELRER +LSDRYGRQIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD +LNENLGLKAETVFLSSVTGTPYDSVAAGDTVRDYDFYETAAGMREVRAAGVDTLGPAFAQ +VITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSADSNAQGDMVGMIQ +PFLDAGIDGFFTDHPDLGVQAVDTWMQGKKEHPGRGVGKSAQRGLQVR +>PROKKA_00250 +MTALRTTARGLAALTAAVAVAAPLAVPASAAIPAKEPITQAERPDVVAHRGASAYRPEHT +LAAYELAVAQGADVIEPDLVSTKDGVLVDRHENDITGTTDVSERPEFADRKTTKTVDGVE +ITGWFTEDFTLAELKTLRAKERLPEARPGSAAYDGMYQVPTFEEDLKLREELSAKYGREI +GIIPEIKHPSYFDGIGLSQEEEVIELLEEHGLNHADGRAVVQSFEFSNLAEMNTRLGLQA +DTAYLLWYEGSGYDAVLSGDTARDYAYFSTPAGAAEAAFNGIDIYGPELRQVIALNQDGS +LGAPTGLVEVAHDAGLTVVPYTFRAENQSLPLQFRSSENPVEHGDLAAYITEVLDAGVDG +FFTDFPDVGVAARDAWLAEKPAEQPSEQPSDGSHAVPGKVQTGDAAAWLPAGLAAAAAGV +LVALRRRLTAAR +>PROKKA_00081 +MTSVRRHAARGLVALAAAVAVSAPLAAPAVAAPAATETPAAAQSVTGKPVVRPDVVGHRG +ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRR +TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER +LSARHGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD +LNENLGLKAETVFLSSVTGAPYDSVAAGDELRDYDFYETAAGMREIRAAGVDTLGPAFAQ +IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDRNAQGDMVGMIQ +PFLDAGIDGFFTDHPDLGVQAVDVWMQGKKEHPGRGVGKTAQRGLKGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000232.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000232.fa new file mode 100644 index 0000000000000000000000000000000000000000..2f5afac13d5fc272c081c10e439ae7f2d2d15ed6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000232.fa @@ -0,0 +1,30 @@ +>PROKKA_00087 +MTTNTPKNAHGSSAEGRDAKDQAKDKAQQAAGEAQGQAKAVAQDAKDKAQDLAATAKHEA +GQVKDEAADQVQSLVGSAQEQVGAQVQTQQERFAGQVRSYTDDLHRVVSGEQPQTDLVRQ +GVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRDA +VQPDSAASTSPRRHTTRPDAVHADVTPHHLDSQAPAYSSDSLSQADGRVADGAGPRRAAG +VGDTPYGTQAPVQQGLTAERPFDQTRPGGDA +>PROKKA_02100 +MTTNTPKNAHGSSAEGRDAKDQAKGKAQQAAGEAQGQAKAVAHDAKDKAQDLAATAKHEA +GQVKDEAADQVQSLVGSAQEQVGAQVQTQQERLAGQVRSYTDDLHRVVSGEQPQTDLVRQ +GVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRDA +AQPDSTASTSPRRHETRPDAVHADVTPHHLDSQAPAYSSDSLSQADGRVADGAGPRRAAG +VGDVPYGTQAPVQQGLTAERPFDQTRPGGDA +>PROKKA_00304 +MTTNTPKNAHGSSAEGRDAKDQAKDKAQQAAGEAQGQAKAVANDAKDKVQDLAATAKHEA +GQVKDEAADQVQSLVGSAQEEVGAQVQTQQERLAGQVRSYTDDLHRVVSGEQPQTDLVRQ +GVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRDA +AQPDAAAPTAPRRRDTRPEAVHADVTPHHLDSQAPAYSSDSLSQADGRVASGAGPRRAAG +VGDTPYGVEAPEQHGLTAERPFDRSQPGGRA +>PROKKA_00249 +MAKNHSARAADPQQSETRQKAEAAAGAAQDQAAGVAQDAKAHAQDLAQSAQQEAVAVKDE +AVQHAKSLAGSLQDQAAQQASTQQGRLAEQSRGITDDLHRLLSGEQPQGDAVRQAVAAVA +DRAETLTQRLETAQPMDLVDDVRRFAARRPGTFLAIALGAGVLAGRMTRGVRDASQDGPA +SLSSAPRTPQHRRELEPQGVQADVTPHHLDSQIPAHTGDDAPRPVSDTAAGLPYGTEPLP +TIDPLTGEPVAEDPYDQTRDGGRA +>PROKKA_00082 +MTTNTPKNAHGSSAEGRDAKDQAKGKAQQAAGEAQGQAKAVAHDAKDKAQDLAATAKHEA +GQVKDEAADQVQSLVGSAQEQVGAQVQTQQERLAGQVRSYTDDLHRVVSGEQPQTDLVRQ +GVASVADRAEALTQRLETASPQDLLQDVRGFAARRPGTFLALALGAGLVAGRLTRGIRDA +AQPDSTASTAPRRHETRPDAVHADVTPHHLDSQAPAYSSDSLSQADGRVADGAGPRRAAG +VGDVPYGTQAPVQQGLTAERPFDQTRPGGDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000235.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000235.fa new file mode 100644 index 0000000000000000000000000000000000000000..d825fc3c95e6b5d904ff109c8d4105280aa23b3a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000235.fa @@ -0,0 +1,35 @@ +>PROKKA_00090 +MTPLDRVPDQRPVPAGTGLTLEDALPAPVTAEADGVSARPRLARTVAEMRSALRELVAHA +TDDGDAEPVTVGLIPTMGALHGGHAALVRRARAENDVVAVSIFVNPLQFGDPADLEHYPR +TLDADLDLLAAAGADVVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGASRPGHFDGVAT +VVAKLWNIVRPAVPALRSYFGQKDAQQLTVLRRLATDLDIDVDVRAVPIVRSPEGLALSS +RNTRLDAAGLEHALVLSRALRSLADAAAAGEPVDVQAARRMVEDEPGVELDHLVVVDRDT +FAELGPELLCQPLRREALALVAAHVPPVRLIDTMVLPVAGPLP +>PROKKA_02103 +MTPLDRVPDQRPVPAGTGLTLEDALPAPVTAEADGVSARPRLARTVAEMRSALRELVAHA +TDDGDAEPVTVGLIPTMGALHGGHAALVRRARAENDVVAVSIFVNPLQFGDPADLEHYPR +TLDADLDLLAAAGADVVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGASRPGHFDGVAT +VVAKLWNIVRPAVPALRSYFGQKDAQQLTVLRRLATDLDIDVDVRAVPIVRSPEGLALSS +RNTRLDAAGLEHALVLSRALRSLADAAAAGEPVDVQAARRMVEDEPGVELDHLVVVDRDT +FAELGPELLCQPLRREALALVAAHVPPVRLIDTMVLPVAGPLP +>PROKKA_00301 +MTPLDRVPDRTPVPPRTGLTLEDQVPEAGGTRPRLTTTKADFRAAVAELVGRAAAEDPGE +EVSVGLVPTMGALHGGHAALARQARSENDVVAASIFVNPLQFGDRADLEHYPRTLEADLD +LLGAVGVDVVFAPSVDEMYPGHPDAPIVSVSAGRMGEVLEGASRPGHFDGVCTVVAKLWN +LSMPPAPAVLRSYFGQKDAQQLAVLRRLAHDLDVAVDVRAVPIVRSPEGLALSSRNTRLD +EAGLHAALVLNRALTRLEEAAVAGRVLDVQAAREEVAAEPGVTLDHLVVVDRETLEELGA +ELLCQPLRRDALALVAAHVPPVRLIDNRVLPAAGPLP +>PROKKA_00246 +MTPLDRTPDRRPVPAGTGLTLEDALPVADGARRPRLARTVAEARAALRELTAAAGQERGG +APVVVGMVPTMGALHGGHAALIRQARAENDVVVASIFVNPLQFGDPADLENYPRTLEADL +DLLGAAGADLVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGVSRPGHFDGVVTVVAKLW +NIVRPAVPALRSYFGQKDAQQLAILRRLAHDLDVDVEVRAVPIVRSPEGLALSSRNTRLD +ADGLEHALVLSRALRALVDAAEAGEPIDVRAARQMVSDEPGVTLDHLVVVDRETLEELGP +ELLCQPLRREALALVAAHVPPVRLIDNMVLPAAGPLP +>PROKKA_00085 +MTPLDRVPDQRPVPAGTGLTLEDALPAPVTAEADGVSARPRLARTVAEMRSALRELVAHA +TDDGDAEPVTVGLIPTMGALHGGHAALVRRARAENDVVAVSIFVNPLQFGDPADLEHYPR +TLDADLDLLAAAGADVVFAPDVQEMYPGYPDAPIVTVSAGRMGEVLEGASRPGHFDGVAT +VVAKLWNIVRPAVPALRSYFGQKDAQQLTVLRRLATDLDIDVDVRAVPIVRSPEGLALSS +RNTRLDAAGLEHALVLSRALRSLADAAAAGEPVDVQAARRMVEDEPGVELDHLVVVDRDT +FAELGPELLCQPLRREALALVAAHVPPVRLIDTMVLPVAGPLP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000238.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000238.fa new file mode 100644 index 0000000000000000000000000000000000000000..b4bc6b0cc19e9e627612b837ce7cce4c047446f5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000238.fa @@ -0,0 +1,65 @@ +>PROKKA_00093 +MTATAEPEVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVR +EVGTGFDPAQARVQATAAAGAHRDVPLAPLDEEDAEGTEHPELKRRIAALYASFMDDETV +EARGLEPIASDLAAVATVSTPAELLALSGRLQRQGVSGLINTGALNDAGNPDRMLLHLLQ +GGLGLPDESYYRDEAYAEILEQYTEHTGRLLALAGIGADRDEAAALGVRVVELEKRIAAL +HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGL +LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAF +VNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRSIEELEWMGEETRQRALEKLA +MFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHITPQTV +NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGR +LEDWWTEEDRAAFTERTSRLVAQYNALSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRAL +EIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVTRIASDPHSPNEFRCNQVVKN +LDAFHEAFGTREGDPMWLAPEERVTIW +>PROKKA_02106 +MTATAEPRVPSPREDLYRHVNTGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEGAVR +EVGAGFDPAQARVQATAAAGAHRDAPLAPLDAEDTEGMEHPELKRRIAALYASFMDDETV +EARGLEPIASDLAAVATVTTPAELLTLSGRLQRQGVSGLINTGALNDAGNPDRMLLHLLQ +GGLGLPDESYYRDEAYAEILEQYTEHTGRLLTLAGIGADRDEAAALGVRVVELEKRIAAL +HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGL +LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAF +VNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRSIEELEWMGEETRQRALEKLA +MFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHMTPQTV +NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGR +LEDWWTEEDRAAFTERTSRLVAQYNALSPVEAPDHRVNGEFTLGENIGDLGGLGIAHRAL +EIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVTRIASDPHSPNEFRCNQVVKN +IDAFHEAFGTREGDPMWLAPEERVTIW +>PROKKA_00298 +MTATAEPRVPAPREDLYRHVNAAWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVR +EVGAGFDPAQARVDATAAAGAEHHTPLEPLDAEETEGMELPEVKRRIAALYASFMDDETV +EARGLEPVATDMAAVASVQTPAELLELSGRLQRQGVSGLVNTGALNDAGNPDRMLLHLLQ +GGLGLPDESYYRDEAYAEILEQYTEHAGRLLGLAGIGADSAEAAEAGVRVVELEKRIAAL +HWDVVRSRDAVARYNLMTHEQLVELFPLAEAWLEGVDAAGERSREVVVWQPDFLSGVQAL +LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRHRWKRAVAF +VNGAAGEDVARLYVDRHFPEGHVAAMDELVNLLQEAYRRSIDELEWMSEETRQRALEKLS +MFRPMVGRPVRWVDYSSLEVHAGDLLGNARAASEFEWERDLRKIEDGPDPEEWHITPQTV +NAYYSPLENAIVFPAAILQPPFFDPEKSMAANLGAIGAVIGHEIGHGFDDQGSRYDGSGR +LEDWWTQEDRAAFTELTSRLVAQYNVLSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRAL +EIWRDEGDGASLDAAAGDREFFSAWAAVWRQLTRPETMVTRIASDPHSPNEFRCNQVVKN +IDAFHEAFGTQEGDPMWLAPEERVTIW +>PROKKA_00243 +MTATAEPRVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRRIAEDAAR +DAAMAAPAPEVEAPAQDEASQDPAAAERAARERIAVLWSAFMDEEAVEAAGILPLAADLE +AVDAVASPAELLALSGRLQREGVSGLIGTGALNDAGDPERMLLHLIQSGLGLPDESYYRE +EAYAEILAQYTEHVGRLFALAGVGGDEAGAAALGERVVALEKRIAAHHWDVVRSRDAVAR +YNLLTRDQLLELLPLAPGWLEGIGAADARADEVVVWQPDFLTGVQALLEGPDAADLADWK +AWLTLQVLRSRAGFLPDAFVQENFSFYGRRLAGTQEVRPRWKRAVAFVNGGVGEDVGRLY +VARHFPEGHVAAMDQLVGLLLEAYRRSIDALDWMGEQTRQSALEKLAMFRPMVGFPETWR +DYSALELTPGDLVGCARAVDRFEWDRDLAKIETGPDPREWHMTPQTVNAYYTPLENAIVF +PAALLQPPFFDPERSMAANLGGIGAVIGHEIGHGFDDQGSRYDGSGRLHDWWTEQDREAF +AERTGRLVAQYSALSPAEAPDRQVNGEFTLGENIGDLGGLGIAHQALEIWREEQDGSTED +ESSGDREFFQAWAAVWRQLTRPETMVTRIASDPHSPNQFRCNQVVKNLDAFHTAYGTREG +DPMWLAPEERVTIW +>PROKKA_00088 +MTATAEPEVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVR +EVGTGFDPAQARVQATAAAGAHRDVPLAPLDEEDAEGTEHPELKRRIAALYASFMDDETV +EARGLEPIASDLAAVATVSTPAELLALSGRLQRQGVSGLINTGALNDAGNPDRMLLHLLQ +GGLGLPDESYYRDEAYAEILEQYTEHTGRLLALAGIGADRDEAAALGVRVVELEKRIAAL +HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGL +LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAF +VNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRSIEELEWMGEETRQRALEKLA +MFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHITPQTV +NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGR +LEDWWTEEDRAAFTERTSRLVAQYNALSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRAL +EIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVTRIASDPHSPNEFRCNQVVKN +IDAFHEAFGTREGDPMWLAPEERVTIW diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000239.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000239.fa new file mode 100644 index 0000000000000000000000000000000000000000..df21e8ae2d4a77183652cd4de49970612ba90fab --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000239.fa @@ -0,0 +1,21 @@ +>PROKKA_00094 +MADGAPDPGGGGDDAGFEAAVQGLEQAFSRLVLQHRQVMVRYAAALSPALSVGAMKAFMM +LANEGTMTPSAVAEGLLVDRAQVSRMVRDLEAAGLITREPDPRDRRSALLSASPEGLARL +DAVRGGPAGRGLRDDLARWDREDIRTLTRLLDRLAAERQTRMQDPAESE +>PROKKA_02107 +MVDGAPDPGGGGDDAGFEAAVQGLEQAFSRLVLQHRQVMARYAEALSPTLSVGAMKAFMM +LANEGTMTPSAVAEGMLVDRAQVSRMVRDLEAAGLITREPDPRDRRSALLSASPEGLARL +DAVRGGPAGRGLRDDLARWDREDIRTLTRLLDRLAAERQTRMQDPAESE +>PROKKA_00297 +MAERGHGDDRGLDGVGAERGDAGGEIDGFEAAVRGLEDAFARMVRQHRQVVTRQAAALKP +GLSAGAMKAFITLCNAGTMTPSTLAEHLLLDRAQVSRMVRDLEDEGLITREPDPVDRRSA +LLTATEEGRARLDAVRGGPAGEGLRADLAHWDRADIHTLVRLLGRLVEEQQARVDRTPDA +G +>PROKKA_00242 +MADPADHGSDGRGTGADAFAPEAFDAAVRELEGSFNRLVRQYRATLARQAEAVHPGLPLG +AMKAFVAICHRGPLTPSDLAEHLMLDRTQISRVLKDLEGDGLIHREPDPRDRRSALLTAT +DEARARLDAVRQGPAGGGTRARLQRWDLEDVRALSALLRRFVDEREDPAADDACRP +>PROKKA_00089 +MADGAPDPGRGGDDAGFEAAVQGLEQAFSRLVLQHRQVMVRYAAALSPALSVGAMKAFMM +LANEGTMTPSAVAEGLLVDRAQVSRMVRDLEAAGLITREPDPRDRRSALLSASPEGLARL +DAVRGGPAGRGLRDDLARWDREDIRTLTRLLDRLAAERQTRMQDPAESE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000240.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000240.fa new file mode 100644 index 0000000000000000000000000000000000000000..2dc1b4aca1716fe7a7b20b79001fc1b2e7411023 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000240.fa @@ -0,0 +1,61 @@ +>PROKKA_00095 +MTPTSPAPEAVAPAGAPSLERAAADAARHRSVLQALTGLLLGMFVSMIANTVVSTSMPVI +IHDIGGDQTAYTWVITSALLATAIATPIWGKLADLVNRKVLFQVALAIFVAASAAAGFTH +DPTFLIVCRTVQGLGGGGLVALSQVIMADIISPRERGRYMGLFGAVMAVATVGGPLAGGV +ITDLWGWRWNFFVAVPFAVVALVMVQRTLHLPHRERQKVSIDYLGIVFLTAATALLLIWV +TSAGRDFDWASTTSAWMLGGAAVATVLFVVTELRVAEPLIPLTLFRDRTFTLATIASIAT +GLAMFGSSVYLAQYMQLARGATPTQAGLMTIPMILGLLVSSTVIGGLITRTGVWKRWLVI +GAVLLIAGTALLGTLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQMGVASS +GVTFFRTLGGSIGVAVMGAVVSNVVPDRIEERRADLAAALRSLGPDAAEWSESLQSSTLP +RVAEMPDSLRVIFEDVYAQGIALAFLVAVPLAIVALIAILFLPNLPLGRMTTSERLHATR +ADLATHATAEAMQTLPATGPIPVVTAAQGQHPAEDPEESRSVSAERPATAVADRPVVPAA +LAVAGTALLAAVVTALVRARRG +>PROKKA_02108 +MTPTSPAPEAVAPAGAPSLERAAADAARHRSVLQALTGLLLGMFVSMIANTVVSTSMPVI +IHDIGGDQTAYTWVITSALLATAIATPIWGKLADLVNRKVLFQVALAIFVAASAAAGFTH +DPTFLIVCRTVQGLGGGGLVALSQVIMADIISPRERGRYMGLFGAVMAVATVGGPLAGGV +ITDLWGWRWNFFVAVPFAVVALVMVQRTLHLPHRERQKVSIDYLGIVFLTAATALLLIWV +TSAGRDFDWASTTTAWMLGGAAVATVLFVVTELRVAEPLIPLTLFRDRTFTLATIASIAT +GLAMFGSSVYLAQYMQLARGATPTQAGLMTIPMILGLLVSSTVIGGLITRTGVWKRWLVI +GAVLLIAGTALLGTLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQMGVASS +GVTFFRTLGGSIGVAVMGAVVSNVVPDRIEERRADLAAALRSLGPDAAEWSESLQSSTLP +RVAEMPDGLRSIFEDVYATGISHAFLVGVPLAIVALIAILFLPNIPLGRMTTSERLHATR +ADLATHATAEAMQTLPATGPIPVVTAAQGQHPAEDPEESRSVSAERPATAVADRPVVPAA +LAVAGTALLAAVVTALVRARRG +>PROKKA_00296 +MIDHRQSLTAVNHSDDPAEGPHEPHLPAVAGTAPAGAPSLERAAADAARHRAVLQALTGL +LLGMFVSMIANTVVSTSMPVIISDIGGNQNDYTWVITAALLATAVSTPVWGKLADLMDRK +MLFQVALVIFVGASAAAGFTNDPTFLIVCRVVQGLGGGGLAALSQVIMADIISPRERGRY +MGLFGAVMAVATVGGPLAGGVITDLWGWRWNFFVAVPFALVALVMVQRTLHLPAREPRKV +SIDYLGIVLLGVATSLLLIWVTTAGQQFPWASWTTAWMVGGAVLAAALFVVVELKVTEPL +IPLTLFRNRTFTLATIASIATGLAMFGAGVYLAQYMQLARGATPTQAGLMTIPMIAGLLI +TSTVIGRVITRTGVWKRWLIVGAVLLTAGMALLATLHYDTPFVLVSLHMLLLGAGVGMTM +QNLVLVVQNTTDPRQMGVASSGVTFFRSLGGSVGVAAMGAVVANVVPSRFEARGADLAAA +LQSLGADGPVWAQRLQSGTLPRVAEMPEPLRVVVEDVYATGISQAFLVGVPLAVVAVVAI +VFLPNIPLGRMTTSERLDASRADLATVTAPAAMQKVPATGEIPVVAPAAGGAGGTDDACT +AEDADGTEGVPAAQGPTTAPAEPTAERAERPAVQPAAESVPARVVAPAAAAPSTAAASGR +SGGARPGARAAAAVALLTAIAVLMRQARRG +>PROKKA_00241 +MSTTTAPPATAGPAAVGNSPAVPSLERAADDAARHRTVLRALTGLLLGMFVSMIANTVVS +TSMPVIISDIGGDQTAYTWVITAALLATAIATPIWGKLADLVDRKVLFQVALVLFVAASA +AAGFTTDPTFLIVCRVIQGLGGGGLAALSQVIMADIISPRERGRYAGLFGAVMAVATVGG +PLAGGIITDLWGWRWNFFVSLPFALVALVMVQRTLHLPARESRKVSIDYLGIVLLSTATA +LLLIWVTNAGHQFDWASATTAWMLGGAALAAVLFVVVELTVAEPLIPLTLFRDRTFTLGT +IASIATGLAMFGASVYLSQYMQLARGATPTQAGLMTIPMIVGLLVSSTVIGGVITRTGVW +KRWLVIGAVLLIAGAAMLGTLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQ +MGVASSGVTFFRSLGGTIGVAVMGAVVANVVPDQVEQRRTDIGAALASLGPAGAEWAQRL +QSGSLPRVAEMPDALRVIFEDVYATGISQAFLVGVPLAVVALAAILFLPNIPLGHMTTTE +RIDAERADLATVSVPQAMQTLPATGSTPVVAQAQVQEAAPASTTTTPAPAARALRVPAGL +RERRIAPAGTGRSTAWRATASALAAGAAAAAFVPLLRRSRRG +>PROKKA_00090 +MTPTSPAPEAVAPAGAPSLERAAADAARHRSVLQALTGLLLGMFVSMIANTVVSTSMPVI +IHDIGGDQTAYTWVITSALLATAIATPIWGKLADLVNRKVLFQVALAIFVAASAAAGFTH +DPTFLIVCRTVQGLGGGGLVALSQVIMADIISPRERGRYMGLFGAVMAVATVGGPLAGGV +ITDLWGWRWNFFVAVPFAVVALVMVQRTLHLPHRERQKVSIDYLGIVFLTAATALLLIWV +TSAGRDFDWASTTTAWMLGGAAVATVLFVVTELRVAEPLIPLTLFRDRTFTLATIASIAT +GLAMFGSSVYLAQYMQLARGATPTQAGLMTIPMILGLLVSSTVIGGLITRTGVWKRWLVI +GAVLLIAGTALLGTLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQMGVASS +GVTFFRTLGGSIGVAVMGAVVSNVVPDRIEERRADLAAALRSLGPDAAEWSESLQSSTLP +RVAEMPDGLRSIFEDVYATGISHAFLVGVPLAIVALIAILFLPNIPLGRMTTSERLHATR +ADLATHATAEAMQTLPATGPIPVVTAAQGQHPAEDPEESRAVAAERPATASPVAGRPVAP +AALAVAGTALLAAVVTALVRARRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000241.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000241.fa new file mode 100644 index 0000000000000000000000000000000000000000..28b922556ec396bb1da82b7cef4293d6edd5a1ce --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000241.fa @@ -0,0 +1,35 @@ +>PROKKA_00096 +MTPRFLLMTRLPEPGLGMLREAGEVVDGADVGGDAALARLVASGDYDVVVAALDQKFTAD +VLADARIRGIANYAVGYNNVDVAAATRRGIAVGNTPDVLTDATADIAMLLILGVTRRAPE +GERMVREGRFHGWAPDLLVGRDVRGATLGLAGFGRIGKAVAERALAFGMEVVFAPRPPAH +REVAAAELGDLAGRVRQVRWEELVEVADVLSLHVPLTDDTHHLVDADVIAKMKDDAVLVN +TARGPVVDEAALVTALREGRLFGAGLDVYEDEPALAPGLAELENVMLLPHLGSATRDTRA +AMAELAARNAIAMATGAEAPALVNPEVRG +>PROKKA_02109 +MTPRFLLMTRLPEPGLGMLREAGEVVDGADVGGDAALARLVASGDYDVVVAALDQKFTAD +VLADARIRGIANYAVGYNNVDVAAATRRGIAVGNTPDVLTDATADIAMLLILGVTRRAPE +GERMVREGRFHGWAPDLLVGRDVRGATLGLAGFGRIGKAVAERALAFGMDVVFAPRPPAH +REVAAEELGDLAGRVRQVRWEELVEVADVLSLHVPLTDDTHHLVDAEVIAKMKDDAVLVN +TARGPVVDEVALVTALREGRLFGAGLDVYEDEPALAPGLAELENVMLLPHLGSATRDTRA +AMAELAARNAIAMATGAEVPALVNPEVRG +>PROKKA_00295 +MSPRFLLMTEIPEPGLGMLREAGEVTLGSEVGGNDALPALAASGDYDVVVCALAQKFDAD +VLAQARLKGIANYAVGYNNVDVAAATEAGIAVGNTPDVLTDATADIALLLILGVSRRAHE +GEAMMRAGEFTGWRADLLVGKDVKGATLGLAGFGRIGKAVAERALAFGMDVVFAPRPPAH +REVAPEELGELAGRVEQVRWEELVERSDFLSLHVPLTADTEHLVDADVLARMKDDAVLIN +TARGPVVDEAALVEALRAGRLFGAGLDVYEDEPAMAPGLAELDNVMLLPHLGSATRDTRA +AMAELTARNAIAMATGGEVPALVNPDVRR +>PROKKA_00240 +MSPRFLLMADLPEPGLGMLREAGEVVRGGDVGGNAALADLCASGEYDVVVGALDQRYDAD +LLARARVKGIANYAVGFDNVDVPAATEHGILVGNTPDVLTAATADIALLLILGVTRRAVE +GERMMREGRFEGWRADMLVGKDVVGATLGLAGFGRIGRAVAERALAFGMEVVFAPRPPAH +REVPAEELGDLAGRVRQVRWEELVETADVLSLHVPLTEDTRHLVDEDVIARMKDDAVLVN +TARGPVVDEAALVTALREGRLFGAGFDVYEDEPAMAEGLAELPNVMLLPHLGSATRDARA +AMAELTARNAIGMATDGEAPALVNPEARG +>PROKKA_00091 +MTPRFLLMTRLPEPGLGMLREAGEVVDGADVGGDAALARLVASGDYDVVVAALDQKFTAD +VLADARIRGIANYAVGYNNVDVAAATRRGIAVGNTPDVLTDATADIAMLLILGVTRRAPE +GERMVREGRFHGWAPDLLVGRDVRGATLGLAGFGRIGKAVAERALAFGMDVVFAPRPPAH +REVAAEELGDLAGRVRQVRWEELVEVADVLSLHVPLTDDTHHLVDAEVIAKMKDDAVLVN +TARGPVVDEVALVTALREGRLFGAGLDVYEDEPALAPGLAELENVMLLPHLGSATRDTRA +AMAELAARNAIAMATGAEVPALVNPGVRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000243.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000243.fa new file mode 100644 index 0000000000000000000000000000000000000000..49fcfa215b98d80cb5bf72b95ca9b94df4a99d9e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000243.fa @@ -0,0 +1,15 @@ +>PROKKA_00098 +MAAFWDYFSVLAPSIGLGLIFWLVMRSLLRSDTGERESQARRLSGADARAAREEAEAREW +AARRRAEGGPGADPEDRAR +>PROKKA_02111 +MADFWDYFSVLAPSIGLGLIFWLVMRSLLRSDTGERESQARRLSGADARAAREEAEAREW +AARRRAEGGPGADPEDRAR +>PROKKA_00293 +MATFWEYFSVLAPSIGLGLIFWLVMRSLLRSDTAERESMGRRSTGEDARAAREEADAREW +ARRRGGDDVPRRGDDSR +>PROKKA_00238 +MAAFWEYFSVLAPSVGIGLVFWLVMRSLLRSDTAEREARQRRGEDARAAREEAEAREWAA +RRRGDAPAGPGGAERP +>PROKKA_00093 +MAAFWDYFSVLAPSIGLGLIFWLVMRSLLRSDTGERESQARRLSGADARAAREEAEAREW +AARRRAEGGPGADPEDRAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000244.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000244.fa new file mode 100644 index 0000000000000000000000000000000000000000..86be830b3523691952516df6e83026c1ca715b51 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000244.fa @@ -0,0 +1,80 @@ +>PROKKA_00100 +MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR +EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA +AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR +NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG +DVPETLRDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG +AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVAEPSVEDAT +EILRGLRDRYEAHHKVSITDGALKAAAGLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT +VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLGDERREKEQAWRTGADADV +ATVDEDLIAEVLSKSTGIPVFKLTEEETDRLRNMEDELHRRVIGQDEAIKSLSRAIRRTR +AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG +APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD +FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD +VIVFPQLQKHEIVEIVDLFVSRLGKRLAEQDLSIELTQSAKDLLADRGYDPAMGARPLRR +TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFAFSGGREALEGADLAELESG +AGDPVDADRSV +>PROKKA_02113 +MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR +EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA +AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR +NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG +DVPETLRDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG +AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVAEPSVEDAT +EILRGLRDRYEAHHKVSITDGALKAAAGLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT +VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLGDERREKEQAWRTGADADV +ATVDEDLIAEVLSKSTGIPVFKLTEEETDRLRNMEDELHRRVIGQDEAIKSLSRAIRRTR +AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG +APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD +FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD +VIVFPQLQKHEIVQIVDLFVSRLGKRLAEQDLSIELTQSAKDLLADRGYDPAMGARPLRR +TIQQMVEDQLSEKILFGEIPAGSLITVDTTGEGEGAELTFAFSGGREALEGADLAELEPG +AGDPVDADRSA +>PROKKA_00291 +MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR +EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA +AQVLVKLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR +NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG +DVPETLKDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG +AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVPEPSVEDAT +EILRGLRDRYEAHHRVSITDGALKAAATLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT +VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLEDERRQKEEAWRTGADSDV +ATVDEELIAEVLSKSTGIPVFKLTAEETDRLRTMEDELHKRVIGQDEAIKSLSRAIRRTR +AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG +APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD +FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD +VIVFPQLQKHEIVEIVDLFVSRLGKRLAEQDLSIELTQAAKDLLADRGYDPAMGARPLRR +TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFGFSGGREALEGAELPELEPG +SGETVEAGRSA +>PROKKA_00237 +MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLAAVR +EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA +AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGSEGQNAGSVVLDQFGR +NLTAAAHDGKLDPVIGRAQEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIERG +DVPETLKGKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG +AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVPEPSVEDAT +QILRGLRDRYEAHHKVSITDGALSAAASLADRYISDRHLPDKAIDLIDEAGARLRIRRMT +VPPEVKAYEERIAEVKAQKEAAIDGQDFEGAARLRDQEKQLEEEREQKEQAWRAGQDAAV +ATVDEDLIAEVLSLSTGIPVFKLTEEETDRLRNMEAELHQRVIGQDEAIKSLSRAIRRTR +AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG +APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHADLFNSLLQILEDGRLTDSQGRVVD +FKNTVIIMTTNLGTRDISKGVMTGFQSSTDTSTGYERMKGKVREELRQHFRPEFLNRVDD +VIVFPQLQKHEIVEIVDLFVSRLAKRLAEQDLSIELTPAAKDLLADRGYDPAMGARPLRR +TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFAFAGGRAALEGDDAAEPAAL +PAAADAPVEGREAPGADVPRGDDAGQDGPEAGGALGARLD +>PROKKA_00095 +MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR +EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA +AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR +NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG +DVPETLRDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG +AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVAEPSVEDAT +EILRGLRDRYEAHHKVSITDGALKAAAGLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT +VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLGDERREKEQAWRTGADADV +ATVDEDLIAEVLSKSTGIPVFKLTEEETDRLRNMEDELHRRVIGQDEAIKSLSRAIRRTR +AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG +APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD +FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD +VIVFPQLQKHEIVEIVDLFVSRLGKRLAEQDLSIELTQSAKDLLADRGYDPAMGARPLRR +TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFAFSGGREALEGADLAELEPG +AGDPVDADRSV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000245.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000245.fa new file mode 100644 index 0000000000000000000000000000000000000000..1fb7b117bcbd8070f68d004f963fb253ec0cf28b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000245.fa @@ -0,0 +1,12 @@ +>PROKKA_00101 +MGIGDLNNLANQHSDKIDEAVDNAQEQHGDKLGEHGDTVNKGVDGAQEKFLSGDEGEQQA +>PROKKA_02114 +MGIGDLNNLANQHSDKIDEAVDNAQEQHGDKLGEHADTVNKGVDGAQEKFLSGDEGEQQA +>PROKKA_00289 +MGIGDLNNLANQHSDKINEAVDGAQEQHGDKLGEHADTVNKGVDGAQEKFLSGEKNEGEQ +QA +>PROKKA_00235 +MVGFDDVKNLANENSDKINEQVDAAQAQHSDKLGQHADLADKGIDGAQDKFLNGQSAENE +GEQQA +>PROKKA_00096 +MGIGDLNNLANQHSDKIDEAVDNAQEQHGDKLGEHGDTVDKGVDGAQEKFLSGDEGEQQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000248.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000248.fa new file mode 100644 index 0000000000000000000000000000000000000000..cc09d4247ba155331ca6c205d2779ed268412484 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000248.fa @@ -0,0 +1,31 @@ +>PROKKA_00104 +MPSRPTSPGSKPSPAVYRRRRLVAALLALVLLLLVGWAVVALVRAGIGAFSSEDADPSAA +PTPVHSPSPAPATDAESSSASPTVALEDAAECQPSDLRIAASADRSEYQRGEEAELRLGI +TNLSSTPCRTDVGTARQEFTIRTAEGDDVFSTRICQADPAEAQRVLYPHEELTAVYRWSG +RASSQDCGRLGALAEPGPHLLTVSLGDVTSRPVALKILEELAPGAQDSSSSAAPSSATPS +SATPSSSGSASPSGSASDPASASTTDPSPSSSR +>PROKKA_02117 +MPSRPTSPGSKPSPAVYRRRRLVAALLALVLLLLVGWAVVSLVRAGIDAFSSEDADPSAA +PTPVHSPSPAPATDAESGSASPTVALEDAAECQPSDLRIAASADRSEYQRGEEAELRLGI +TNLSSTPCRKDVGTARQEFTIRTAEGDDVFSTRICQADPAEAPRVLYPHEELTAVYRWSG +RASSQDCGRPGALAEPGPHLLTVSLGDVTSRPVALKILEELAPGAQDSSSSAAPSSATPS +SATPSSSGSASPSGSASDPASASTTDPSPSSSR +>PROKKA_00286 +MPSRPSSPGPKPSAAVYRRRRLVAALLALILLLLVGWGLWSLIRLGMGALSGDDAEPSVS +APPTPVHSPSPAPPSGATPGSAAPTVALEDAAECQPSDLRLVASADKAQYLRGEEAVLRL +GVTNLSSSPCRADVGTARQEFTVRTAEGDDVFSTRVCQADPTSSERVLTPHEELTAVYRW +SGHASNEDCGTPGALAAAGPHLLTVTLGEQTSRPVALRIQEEAAPGAWDGASSGAPASGS +PAPSTPASPSASPSATGSAPAASSPAPASGSPAASTPATPSASPSR +>PROKKA_00232 +MPSASPAPRPRPSAAVLRRRRVVAGCLAAAFLLLVGWGIGALVNALLPSGRPDAEPSAAP +TPVSSPTPAAARSLDAQAGQTQDPASVESCAPMDLRLVAAADRERYAPGEEAVLRLEVTN +LSGRPCRTDVGTAQQEFRVTDASEQQVMSTRVCQADPTHEDVVLEPRDQKAAVYRWNGRA +SSADCARLGPAVEPGEYRLTVTLGEVTSRPVALTVTDGTKSAAPASSPAASSAAPGPSAT +TAPASAETSSASPSASSSSAQPSSPAPRASEPTSSAPTSSPAGSGRASSSPAAPSSSAAS +PTR +>PROKKA_00099 +MPSRPTSPGSKPSPAVYRRRRLVAALLALVLLLLVGWAVVSLVRAGIDAFSSEDADPSAA +PTPVHSPSPAPATDAESGSASPTVALEDAAECQPSDLRIAASADRSEYQRGEEAELRLGI +TNLSSTPCRTDVGTARQEFTIRTAEGDDVFSTRICQADPAEAPRVLYPHEELTAVYRWSG +RASSQDCGRLGALAEPGPHLLTVSLGDVTSRPVALKILEELAPGAQDGGSSATPSSATPS +SSGSASPSASASAPASASASASASASASASPSAAPATTTDPSPSPSR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000251.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000251.fa new file mode 100644 index 0000000000000000000000000000000000000000..132eab656920d7106d091c4a55e9a2e23a0e9a6c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000251.fa @@ -0,0 +1,35 @@ +>PROKKA_00108 +MSSTTNEAAPKPSSLRGPRRGAAGDKLLSGGALAAAVLILLVLAFVAVFLLTEAWPALQP +GAELVSADSFFQYVWPLMAGTVMVSIIALLIATPVAIGVALFISHYAPPRIAQSVGFVID +LLAAIPSVVYGVWGWLTLAPLMVPIYGWLNENLGFIPFFGGSATTTGRTLLTSGVVLAVM +VLPIITALCREIFTQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIISSIMLGLGRALG +ETMAVTMVLSGGVFSWSLVESGRNQTIPSEIALNFPEAFNMRLHELIAAGLMLFIITLAV +NMIARAIVNKHKEFSGAN +>PROKKA_02121 +MSSTTNEAAPKPSSLRGPRRGAAGDKLLSGGALAAAVLILLVLAFVAVFLLTEAWPALQP +GAELVSADSFFQYVWPLMAGTVMVSIIALLIATPVAIGVALFISHYAPPRIAQSVGFVID +LLAAIPSVVYGVWGWLTLAPLMVPIYGWLNENLGFIPFFGGSATTTGRTLLTSGVVLAVM +VLPIITALCREIFTQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIISSIMLGLGRALG +ETMAVTMVLSGGVFSWSLVESGRNQTIPSEIALNFPEAFNMRLHELIAAGLMLFIITLAV +NMIARAIVNKHKEFSGAN +>PROKKA_00282 +MTSPATEAPPRATTLKSSRGGAAGDKVFSGLSLAAGVLILLTLAFVAIFLVVRSLPALFP +DAYGTQLKSADTFFQYVWPLMAGTIMAAVIALLLATPVAVGVALFISHYAPPKIAQPVGY +VIDLLAAIPSVIYGIWGWLTLAPVMVPIYQWLNEYLGFIPFFGGPVTGTGRVIMTSGVVL +AVMILPIITALCREIFRQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIVSSVMLGLGR +ALGETMAVTLVLSAGGFSLSLIEEGRNATIPSEIALNFPEAYGIRLNELIAAGLMLFVIT +LVVNMTARWIVNKHKEFSGAN +>PROKKA_00223 +MSHTATEAAPSSSALKSSRAGAAGDKVFSGLALAAGVLILLILAFVAIFLVSEAWPALFP +AEGANLESGDSFWGYVWPLMAGTVMAAIIALLLATPVAVGVALFISHYAPPKIAQPVGYV +IDLLAAIPSVVYGIWGWLTLAPLMVPIYEWLNEYLGWLPFFGGSVTSTGRVLMTSGIVLA +VMVVPIITALCREIFSQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIVSSIMLGLGRA +LGETMAVTMVLSPGKFSPSVIEEGRNATIPSEIALNFPEAYGIRLNELIAAGLMLFVITL +VVNMVARWIVNKHKEFSGAN +>PROKKA_00103 +MSSTTNEAAPKPSSLRGPRRGAAGDKLLSGGALAAAVLILLVLAFVAVFLLTEAWPALQP +GAELVSADSFFQYVWPLMAGTVMVSIIALLIATPVAIGVALFISHYAPPRIAQSVGFVID +LLAAIPSVVYGVWGWLTLAPLMVPIYGWLNENLGFIPFFGGSATTTGRTLLTSGVVLAVM +VLPIITALCREIFTQTPKLHEEAALGLGATRWEMIKMTVFPFARAGIVSSIMLGLGRALG +ETMAVTMVLSGGVFSWSLVESGRNQTIPSEIALNFPEAFNMRLHELIAAGLMLFIITLAV +NMIARAIVNKHKEFSGAN diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000252.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000252.fa new file mode 100644 index 0000000000000000000000000000000000000000..3c6626d3cc4fc00837c53acab1dddba19d742a6c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000252.fa @@ -0,0 +1,40 @@ +>PROKKA_00109 +MSTVSTSPRATEDSVTPRRHSLTEGQKPGWTWMAVAAAAAVVAAGLTVLLSGAFNVVGFV +IIAAILYIAGLYVATRVMENRRRAADGLCRNLVWLAFLVALVPLVSVLWSVLSAGLPTLI +ANPQIMAYDMKGITGIDDSAWVEDGKPAGGLAGGFGHALIGTVVITIIATLISVPIGMLT +SIYLVEYSRGGWFSRAIVFFVDVMTGIPSIVAGLFAYAAITWVLTLVTGSKSTALQSVQM +GLTAAIALSVLMIPVVVRSTEEMLRVVPNELREGAYALGVRKWQTIAKVVLPTAISGIAS +GVTLAIARVAGETAPILVTAGFATSINWNPFDNWMTALPVYIYRQLVAPTSPTAADPSTA +RAWAAALLLVTIVMLLNLAARFIAKAFAPKKGR +>PROKKA_02122 +MSTVSTSPRATEDSVTPRRHSLTEGQKPGWTWMAVAAAAAVVAAGLTVLLSGAFNVVGFV +IIAAILYIAGLYVATRVMENRRRAADGLCRNLVWLAFLVALVPLVSVLWSVLSAGLPTLI +ANPQIMAYDMKGITGIDDSAWVEDGKPAGGLAGGFGHALIGTVVITIIATLISVPIGMLT +SIYLVEYSRGGWFSRAIVFFVDVMTGIPSIVAGLFAYAAITWVLTLVTGSKSTALQSVQM +GLTAAIALSVLMIPVVVRSTEEMLRVVPNELREGAYALGVRKWQTIAKVVLPTAISGIAS +GVTLAIARVAGETAPILVTAGFATSINWNPFDNWMTALPVYIYRQLVAPTSPTAADPSTA +RAWAAALLLVTIVMLLNLAARFIAKAFAPKKGR +>PROKKA_00281 +MSTAIDDVSTRQDTPPSKHRQNSLTAGQKPGWVWMAIAAAAVLLGLGIEALLSGAAPFSE +DFSLARFVVLAGVLYIAGMYLVTRVMENRRRASDGLWKNLVWTAFLIALVPLVSVIWTVL +EGGGPTLLSNPQVLWNDMDGVTGATDAAYDQAGSPAGGLPGGFAHALIGTLVITIIATLI +AVPIGLLASIYLVEYGRDGWLSRAITFFVDVMTGIPSIVAGLFAYAAMTVLLELIMGPGP +AALQAVKMGFTAAVALTVLMIPVVVRSTEEMLRVVPNELREGSYALGVRKWRTIFKVVLP +TAISGIASGVTLAIARVTGETAPILVTAGYAMTTNWNAFDNWMTALPVYIYRQIVSPTSP +TAADPSMARAWSAALVLIFIVMALNLLARVIAKAFAPKTGR +>PROKKA_00222 +MSTALNDTPTRENTPASKHTQNSLTAGQKPRWTWMAVAAGAVVLGLGLEALLAGGFADFS +IARFIILAAILFVAGMYVATRVLENRRQATDGLWRNLVWAAFLIALVPLISVLWSVVADG +GATLFGNPQLLVNDMQGVTGVTDAQYVQAGEPMGDLPGGFAHALVGTFLITVIATVIAVP +IGLLTSIYLVEFGRDGWLSRAIIFFVDVMTGIPSIVAGLFAFAAMSVVLEMVMGSGPKAL +QSVKMGLTAAIALTVLMIPVVVRSTEEMLRVVPNELREGSYALGVRKWRTIFKVVLPTAI +SGIASGITLAIARVTGETAPILVTAGFASAVNWNPFDNWMTALPVYIYRQLVAPTSPTAM +DASTSRAWAAALVLIIIVMVLNLLARIVAKAFAPKTGR +>PROKKA_00104 +MSTVSTSPRATEDSVTPRRHSLTEGQKPGWTWMAVAAAAAVVAAGLTVLLSGAFNVVGFV +IIAAILYIAGLYVATRVMENRRRAADGLCRNLVWLAFLVALVPLVSVLWSVLSAGLPTLI +ANPQIMAYDMKGITGIDDSAWVEDGKPAGGLAGGFGHALIGTVVITIIATLISVPIGMLT +SIYLVEYSRGGWFSRAIVFFVDVMTGIPSIVAGLFAYAAITWVLTLVTGSKSTALQSVQM +GLTAAIALSVLMIPVVVRSTEEMLRVVPNELREGAYALGVRKWQTIAKVVLPTAISGIAS +GVTLAIARVAGETAPILVTAGFATSINWNPFDNWMTALPVYIYRQLVAPTSPTAADPSTA +RAWAAALLLVTIVMLLNLAARFIAKAFAPKKGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000255.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000255.fa new file mode 100644 index 0000000000000000000000000000000000000000..525d7335646159938b2c86bf70515f7eb8b0ae08 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000255.fa @@ -0,0 +1,25 @@ +>PROKKA_00112 +MSPRMPWLVTRDTPALRHMADLAEALHRSVHLVAQVAGTRGPEADRAARELEELDSSSSA +TLMAFLTALRSAYVTPLPRQDLYRLASGVHATTRRVVSAGVLIQRADLEELPTHALDVLE +TVGRQAELLARGAAEMRDLDALEATWMQLLRASRRTERIMVEWLADLGMDLLQRDYNRQR +EVAWALHAALEALSRVNMDLGMVLVRES +>PROKKA_02125 +MSPRMPWLVTRDTPALRHMADLAEALHRSVHLVAQVAGTRGPEADRAARELEELDSSSSA +TLMAFLTALRSAYVTPLPRQDLYRLASGVHATTRRVVSAGVLIQRADLEELPTHALDVLE +TVGRQAELLARGAAEMRDLDALEATWMQLLRASRRTERIMVEWLADLGMDLLQRDYNRQR +EVAWALHAALEALSRVNMDLGMVLVRES +>PROKKA_00278 +MSPRMPWPVTRDTPALRHIVDLAEALRRSVHLVAQVAGARGPEADRTARELEDLDAASTA +SLMSFLTALRSAYVTPLPRQDLYRLAGGVHAATQRVVSAGVLIQRADLEHLPAHALDVLE +TVGRQAELLGRSTTELRDLDALEATWMQLLRASRRTERIMVQWLADLGMDLLQRDFNRQR +EVAWALQSALEALGRVNTDLGMVLVRES +>PROKKA_00219 +MTPRPAWLVTRDSPALGHLTDLCDTLGRAVRAVAQAVAADGSERDRVERDLSALDAAATA +ALMAFLTALRSAYVTPVPRPDLYRLADGVKTAAHRVVGAGVLVHRADLDALPRNAVELLE +TLGRQAELLAHGTRQLRDLDALEDTWMQLERGIRRMERLMVDWLAALGTDLLQRDYNRQR +EIASALRDAVLALDRVNTDLGVVLVRES +>PROKKA_00107 +MSPRMPWLVTRDTPALRHMADLAEALHRSVHLVAQVAGTRGPEADRAARELEELDSSSSA +TLMAFLTALRSAYVTPLPRQDLYRLASGVHATTRRVVSAGVLIQRADLEELPTHALDVLE +TVGRQAELLARGAAEMRDLDALEATWMQLLRASRRTERIMVEWLADLGMDLLQRDYNRQR +EVAWALHAALEALSRVNMDLGMVLVRES diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000256.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000256.fa new file mode 100644 index 0000000000000000000000000000000000000000..f0b0ec6111d9c1fad61309c47d25c27ec4da3c9d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000256.fa @@ -0,0 +1,25 @@ +>PROKKA_00113 +MARHRLPAGRGASSSASGVLRPHRPRLSEPQELTHFAGGEDPQEVAAAASRLAHALVAGG +RAEEDPAIVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATTRDGERWAAW +YRAGHAAYASRVVAGAVEPPGPAELRRLTDTILTGAYRSEIDVAFERAAAYARVVALGQV +EHAEGSEAAAPDRAAALTRRAARLVSTADALEAAGRAFRDGSLD +>PROKKA_02126 +MARHRLPAGRGASSSASGVLRPHRPRLSEPQELTHFAGGEDPQEVAAAASRLAHALVAGG +RAEEDPAIVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATTRDGERWAAW +YRAGHAAYASRVVAGAVEPPGPAELRRLTDTILTGAYRSEIDVAFERAAAYARVVALGQV +EHAEGSEAAAPDRAAALTRRAARLVSTADALEAAGRAFRDGSLD +>PROKKA_00277 +MARHRQTTGRGASSSASGLVRPHRPRLSEPDELAHFAGGEDPQEVAAAASRLAHALVAGG +RAEEDPEVVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATARDGERWAAW +YRAGHAAHAARAVAGAVEPPGPDELRRLTDTILTGAYRSEIDVAFERAGAYGRVVALGQV +EHAEAAEAADPALAAGLTRRAARLVSTSEALEEAARAFRNGSLD +>PROKKA_00218 +MAHHRAPAGRGASSTASGLVRPHRPRLTDPGLIADLADGEDPQEIAAAASRLAHALVAGG +RAEEDPDVVARLVGLVREVGVETLAGLWADAPAVSLAGALWRLYALQEATARDGERWAAW +YRAGHAAHAARAVAGAVEPPGPEELRRLTDTILTGAYRSELDVALERAGAYARVVALGQA +EHAAAAEHADPAHAARLTLRAARMISTAEALEAAARSWRDGSLD +>PROKKA_00108 +MARHRLPAGRGASSSASGVLRPHRPRLSEPQELTHFAGGEDPQEVAAAASRLAHALVAGG +RAEEDPAIVERLVGLVRELGVETLAELWADAPPVSLAGALWRLYALQEATTRDGERWAAW +YRAGHAAYASRVVAGAVEPPGPAELRRLTDTILTGAYRSEIDVAFERAAAYARVVALGQV +EHAEGSEAAAPDRAAALTRRAARLVSTADALEAAGRAFRDGSLD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000258.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000258.fa new file mode 100644 index 0000000000000000000000000000000000000000..69b6c8417aa56f3c1f44e0540cc07021fd5c5297 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000258.fa @@ -0,0 +1,30 @@ +>PROKKA_00116 +MAKNSTIGRYASGKVKDFGLKSALDENGEPTEGFEKALSTVLAVQRPLVLKNIQRMAAKH +PGESPERLAERLGQQYLTTVTGAGAAVGGTAIVPGIGTVAALGLSGAAVAGFMEATALYA +QSLAELHGITTQDPQRAQALVMGLMLGDDAKELLREAAAKAGRPYDPQSSLNALAGTASG +TGISAFVVDRLKRTFMRKMLLRQGAGFVGRAVPFGVGAVIGGVGNRAMGKAVMENAAELF +GPLPMVIPGEIREGVAQGRAGGESAGAKDDGGVLGAIRRALPGGKDEKDDRQKKGKPAA +>PROKKA_02129 +MAKNSTIGRYASGKVKDFGLKSALDENGEPTEGFEKALSTVLAVQRPLVLKNIQRMAAKH +PGESPERLAERLGQQYLTTVTGAGAAVGGTAIVPGIGTVAALGLSGAAVAGFMEATALYA +QSLAELHGITTQDPQRAQALVMGLMLGDDAKELLREAAAKAGRPYDPQSSLNALAGTASG +TGISAFVVDRLKRTFMRKMLLRQGAGFVGRAVPFGVGAVIGGVGNRAMGKAVMENAAELF +GPLPMVIPGEIREGAAQGRAAGESEGTKDYGGVFGAIRRALPGGKDEKDKPAA +>PROKKA_00271 +MAKNSMIGRYTSGKVKDFALKSALDENGEPTEGFEKVVSKVLGIQRPLVLKHIQNVAAKN +PELTAEQIAERLGQQYLNTVTGAGAAVGGTAIVPGVGTVAALGLSAAATVGFMEATALYA +QSLAELHGITMEDPQRAETLVMALMLGDDAKELLREAAAKAGRPFDPNASLNALAGSAAG +TGGGAGISAFVMDRLKRTFMKKMLVRQGAGFLGRAVPFGVGAVIGGVGNRAMGKAVMENA +QELFGPLPTVIPGEIREGAARQAQEDDGEGGVFAAIRRALPGGDDKKDAAKA +>PROKKA_00203 +MAKNSIIGRYASGKAKDFAMKSAFDENGNPTEGFEKLVFTTLDIQRPLVLKNIQRLHESH +PGETPEQLAERLADQYVTASTGAGAAVGGTAIVPGIGTVAALGLSAAATVAFLEATALYA +QSLAELHGLTTKDPARSKALVMAVMLGDDTKELLKDISRKSGVKNTGTPDSAAGLAAMMN +GGAAGQAAGGAGLGAVAIEQLKKQFVKKVLVRQGAGFLGRAVPFGVGAVIGGVGNRAMAK +AVVKNSRDLFGPLPAQIPGEIVAASAKGQDVGQSAEDGKGGLVSGLIKALPLGKKDEKKA +>PROKKA_00121 +MAKNSTIGRYASGKVKDFGLKSALDENGEPTEGFEKALSTVLAVQRPLVLKNIQRMAAKH +PGESPERLAERLGQQYLTTVTGAGAAVGGTAIVPGIGTVAALGLSGAAVAGFMEATALYA +QSLAELHGITTQDPQRAQALVMGLMLGDDAKELLREAAAKAGRPYDPQSSLNALAGTASG +TGISAFVVDRLKRTFMRKMRLRQGAGFVGRAVPFGVGAVIGGVGNRAMGKAVMENAAELF +GPLPMVIPGEIREGAAQGRADGTKDDGGVFGAIRRALPGGKDEKDDRQKKGKPAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000259.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000259.fa new file mode 100644 index 0000000000000000000000000000000000000000..507e9c5e3da2e51fc2db3664f467a94db1c06b33 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000259.fa @@ -0,0 +1,45 @@ +>PROKKA_00117 +MSLSPDPAQQLLSAGALERAAGLRRMKAVALGLLILLAVVFVVAFPLQDTHPVWGYVRAA +AEGGMVGALADWFAVTALFRHPMGVPVPHTALIPRKKDQLGAALTEFVQENFLDSEVAHE +KVDGLKVAEAAGGWLRREENAARTAREIATAARGAMAAADDDAVQELLRQLMERHMVAPD +WSPTLAGVLEDVVAGRHHERVVDLVVAHTGDWVAAHPELFVETVRRRSPEWSPDLVDRLL +AERLHAETLKYLAGIRRDREHEARRAVDDWLDRLADEMRNEPATRASVERFKRNLFADER +LRAWAGRAWVSLRDSLLDALEDPSSDLHRALVAALRDLGARLQEDPELRDRVDGHARRAA +AYALSSYGPALTGVIEETVARWDGEQTARTLELFVGKDLQFIRINGSVVGALAGLAIHGV +ATLFL +>PROKKA_02130 +MSLSPDPAQQLLSAGALERAAGLRRMKAVALGLLILLAVVFVVAFPLQDTHPVWGYVRAA +AEGGMVGALADWFAVTALFRHPMGVPVPHTALIPRKKDQLGAALTEFVQENFLDSEVAHE +KVDGLKVAEAAGGWLRREENAARTAREIATAARGAMAAADDDAVQELLRQLMERHMVAPD +WSPTLAGVLEDVVAGRHHERVVDLVVAHTGDWVAAHPELFVETVRRRSPEWSPDLVDRLL +AERLHAETLKYLAGIRRDRQHEARRAVDDWLDRLADEMRNEPATRASVERFKRNLFADER +LRAWAGRAWVSLRDSLLDALEDPSSDLHRALVAALRDLGARLQEDPELRDRVDGHARRAA +AYALSSYGPALTGVIEETVARWDGEQTARTLELFVGKDLQFIRINGSIVGALAGLAIHGV +ATLFL +>PROKKA_00270 +MSLSPDPARQLLSAGTLERERGLRRMKAVALGLLVALAVVFAVAFPLQDVHPVWGYVRAA +AEGGMVGALADWFAVTALFRHPMGIPVPHTALIPRKKDQLGAALTEFVQENFLDSDVARE +KVEGLEVAAAAGGWLRRPENAERAAREVATAARGAMAAADDDAVQELLRQLMQRHMVEPE +WSPTLAGVLQDVVTGRHHERVVDLVVEHTGDWVAAHPEMFVETVRRRSPEWSPDLVDRLL +AERLHAEALKYLAGIRDDRDHEARRAVDDWLTRLSAEMRDDPHTRASVERFKHSLFADER +LRAWAGRAWTSLRDSLLDALEDPASDLHRALVAALRDLGARLQEDPVLRDRVDGHARAAA +AYALSTYGPAVTGVIEETVARWDGDQTARTLELFVGRDLQYIRINGSIVGALAGLTIHAV +ATLFL +>PROKKA_00201 +MAPSPVPADSPFPLTPAALERAAGLRRMKAVALGLLIVLAVVFAVAFPLQRVHPAWGFVR +AAAEGGMVGALADWFAVTALFRRPLGLPIPHTALIPEKKDQLGAALTEFVQENFLDSDVA +REKVAGLQVARAAGGWLRERPHAVHAAGEIAMAARGAVAATDDDAVQDLLQQLMQRHMVE +PDWSPTLAGVLEDVLAGRHHEKVVDLVVEHTGDWVATHPEMFLETVRRRSPEWSPDLVDR +LLAERLHAETLKYLAGVRADRDHEARRSVDDWLARLAGNMRDDPATRASAERFKADLFAD +EQLRAWAGRAWITLRDSLLAALEDQDSDLHRALVDALVDLGVRLQEDPALQASVDGRARA +AASYALSSYGPALTGVIEETVARWDGRQTADTLENLVGRDLQFIRINGSVVGALAGLAIH +TLASLVF +>PROKKA_00122 +MSLSPDPAQQLLSAGALERAAGLRRMKAVALGLLILLAVVFVVAFPLQDTHPVWGYVRAA +AEGGMVGALADWFAVTALFRHPMGVPVPHTALIPRKKDQLGAALTEFVQENFLDSEVAHE +KVDGLKVAEAAGGWLRREENAARTAREIATAARGAMAAADDDAVQELLRQLMERHMVAPD +WSPTLAGVLEDVVAGRHHERVVDLVVAHTGDWVAAHPELFVETVRRRSPEWSPDLVDRLL +AERLHAETLKYLAGIRRDRQHEARRAVDDWLDRLADEMRNEPATRASVERFKRNLFADER +LRAWAGRAWVSLRDSLLDALEDPSSDLHRALVAALRDLGARLQEDPELRDRVDGHARRAA +AYALSSYGPALTGVIEETVARWDGEQTARTLELFVGKDLQFIRINGSIVGALAGLAIHGV +ATLFL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000260.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000260.fa new file mode 100644 index 0000000000000000000000000000000000000000..524b4570ac20c22d919eace26ecaccf4e18044c2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000260.fa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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000261.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000261.fa new file mode 100644 index 0000000000000000000000000000000000000000..d3816331adbc43a4a1c42e326839e93f5bbc9487 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000261.fa @@ -0,0 +1,18 @@ +>PROKKA_00123 +MIVAFSVAPSGQPADSAHLPGDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGDWD +EVMEVVRGAVDAVSSYGSRVSLVLKADIRPGHSGELDGKLERLEAALAEDGNGDAADAR +>PROKKA_02137 +MIVAFSVAPSGQPADSAHLPGDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGDWD +EVMEVVRGAVDAVSSYGSRVSLVLKADIRPGHTGELDGKLERLESALAEDEGRRAAPAPH +DGDAG +>PROKKA_00262 +MIVAFSVAPSGTPADAAHQPGDEDSASVHRAVAAAVAVVRESGLPHRTSSMFTEIEGDWD +EVMDVVRGAVDAVAPYGSRVSLVLKADIRPGHTGELDGKLARLEAALASDDVS +>PROKKA_00196 +MIVAFSVSPSGAPADAAYAPSSDGDSASVHRAVAAAVAVVRASGLPHRTSSMFTEVEGEW +DEVMGVVKRAVEAVEPYGSRVSLVLKADIRRGRTGELDGKLERLEAALTDGTPATPDRFR +A +>PROKKA_00131 +MIVAFSVAPSGQPADAEHLPGDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGEWD +EVMEVVRAAVDAVSPYGTRVSLVLKADIRPGRTGELDGKLERLESALAEDEGRRAAPAPR +DGDAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000262.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000262.fa new file mode 100644 index 0000000000000000000000000000000000000000..da1e1545779bc7dea2914d8c8a104f62bd368bce --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000262.fa @@ -0,0 +1,23 @@ +>PROKKA_00124 +MAVTVRPATSDDVEPLLRVKAQAWREAYGGLLPAAHLDAVDAGVPEQVPGWAALVGSDRE +LWVADDGGRLLGMALAGPRRSQGGGLPDLELMALYVLAEAYGTGLGALLLDAVVGKRPAV +LRVLAENPRAVAFYAKHGFAPEGGPEPMTGPWAGLHEQLMVRRG +>PROKKA_02138 +MPESVTVRPAAPGDVEALLRVKARSWREAYGALLPSAYLDAIEARIPEDVPAWTALIGPD +RDLWVADDGGRLLGVALAGPRRSAAETGRTGADDAAASPADLPDVELMVLYVLAEAYGTG +LGARLLDAVVGERPAMLRVLAENPRAVAFYAKHGFAAVGAPEPMTGPWAGLHEQLMVRRR +PHDGGAA +>PROKKA_00261 +MAVVVRPARREDAEALLRVKAQSWREAYGAHLPAEVFDRADARVPQDAPAWAALVGSDRD +LWVAEDDDGGRLVGVALAGPSRIEDEGLPPRELMVLYVLAEAHGTGVGARLLDAVVGDGP +AVLDVLAENPRARAFYAKHGFEDHGAPAPMDGAWAGLHEQRMVRRG +>PROKKA_00195 +MRETDGASDAVVRDVNPPSAPAPTVRPAGADDLPAVLAMKNAAWRETYAHLLEPGFLAAQ +EAELPRAVEAWTRLLGEPGMEVWLAEGAGVVVGMAAAGPADDPALGPEGRELIALYVRAR +LHGAGLGAALLRAAVGGRPARLDVLVGNERAIAFYERHGFVAVGEPAVLGGPWGDAREQR +MVRR +>PROKKA_00132 +MPESVTVRPAAPGDVEALLRVKARSWREAYGALLPSAYLDAIEDRIPEDVPVWTALIGSD +RDLWVADDGGRLLGVALAGPRRSAAETGRTGADDAAASPADLPDVELMVLYVLAEAYGTG +LGARLLDAVVGDRPAVLRVLAENPRAVAFYAKHGFASVGAPEPMTGPWAGLHEQLMVRRL +PHDGGAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000263.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000263.fa new file mode 100644 index 0000000000000000000000000000000000000000..4f2c76a1794eff07469bd343d2da6a252bb596cd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000263.fa @@ -0,0 +1,34 @@ +>PROKKA_00125 +MSRRSGRSSGRSSAASSSSRGSAARRGRAAEPEGIVPGVHEISHGTAEIREDPYEPGAFV +LYVNGVESSPLDPDHPERMGFEYMRWAVAAVRAHWPEPTPLRALHLGGAGCALARWVDHA +HPGSHQTAVEIDAGLAALARERFGLPRAPALRIRVADAAEVLATAHPASRDLIIRDVFAP +DPTDLTGARHITPPGLTGLDAARAAARVLAPGGLYVLNVGGGPDLTSVRADVAAVVAAFE +HVEVIADPPMLKGRRRGNVIVAASDAPVARPAADAPPGSDPRDRLARALRMDAFPARLAE +DPRGFPAGVAPGITGLVPGPEA +>PROKKA_02139 +MSRRSSARRGRAAGGSAGPAGIEPGVHAITHGTAEIREDAFEPDAFILYVNGVESSPLDP +ERPERMAFEYMRWAAAAVRAHWPEPTPLRALHLGGAGCALARWVDHAYPGSHQTAVEIDA +GLAALARERFGLPRAPALRIRVADAAEVLATAHPASRDLIIRDVFAPDPTDLTGARHITP +PGLTGLDAARAAARVLAPGGLYVLNVGGGPDLTSVRADVAAVVAAFEHVEVIADPPMLKG +RRRGNVIVAASDAPVARPAADAPPGSDPRDRLARALRMDAFPARLAEDPRGFPAGVAPGI +TGLVPGPEA +>PROKKA_00260 +MITPGVFAISSGTAEILPDPWTDGVYLLKVNGVESSQLNPDRPETLGFEYMRWAAAVLAH +RFAPDAERLRVLHLGGAGCTFARWVTHTWPQAHQLAVELDAGLAELARTHFDLPRAPQLK +IRVGEAGQVLAGLREATREVVFRDVFAPADPLSLAPDSPHVTPAHLTGADAAAHAARVLV +PGGVYVLNIGGGPDLASVRREVAALRTAFAHVEVMADPAMLKGRRRGNVIAAASSVPLAA +EELGGRAALARALRSDALPAQLVDDVARFAGGLAPDPTPLVQASDGTSEGASTQASPGPA +Q +>PROKKA_00194 +MITPGTFPISSGTAEIVPDPWTDGVFLLKVNGVESSQLNPDRPETLGFEYMRWAAAVLTH +RFAPDARLRVLHLGGAGCTFARWVTHTYPASHQLAVELDAGLAAVAREHFDLPRAPQLKI +RVGEAGEVLAGLRDATREVVFRDVFAPDPADPTGALHVTPAHLTGLDAAAHAARVLTPGG +VYLLNIGGGPDLTSVRREVAALTETFAHVEVMADPAMLKGRRRGNVIAAASSAPLSADGL +GGRSALARALRSDALPAQLLDDVVAFTAGLTPDATPLVTPAEG +>PROKKA_00133 +MSRRSSARRGRAAGGAAGPAGIEPGVHAITHGTAEIRENAFEPGAFILYVNGVESSPLDP +ERPERMAFEYMRWAAAAVRAHWPEPTPLRALHLGGAGCALARWVDHAYPGSHQTAVEIDA +GLAALARERFGLPRAPALRIRVADAAEVLATAHPASRDLIIRDVFAPDPTDLTGARHITP +PGLTGLDAARAAARVLAPGGLYVLNVGGGPDLTSVRADVAAVVAAFEHVEVIADPPMLKG +RRRGNVIVAASDAPVARPAADAPPGSDPRDRLARALRMDAFPARLAEDPRGFPAGVAPGI +TGLVPGPEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000267.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000267.fa new file mode 100644 index 0000000000000000000000000000000000000000..92cd359532f3d7d195763d9c080fa53fd594f9f9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000267.fa @@ -0,0 +1,60 @@ +>PROKKA_00133 +MSDPTPPSTEPMIPEQPGNHPSSATAPDAGVAPATSAAAGRDRVLLPWVFWPSAVIVLSF +VGATLLAPAQMTVGIGLVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGDITLGKPDEK +PEFSTLSWFSLLFAAGMGIGLVFFGMTEPLMHFTSPRPDLAAANPTQAEAAQSALATTFL +HWGLQPWAIYAVVGVAVALAIHRRGRPLALRWAFEPLIGERRVRGGWGHLIDNIALIGTV +FGVATSLGLGVTQMSAGLRALGIVPEDSPWLEYVMIGAVTCVVLYTVVSGVERGMKWLSN +TNLILAAGLLLFIAIVGPTAFLFKEMVQSLGSYMQYFFANSLNVSAFYGAEGDAWQAGWS +AYYWGWWMSWTPFVGIFIARISRGRTVREFIAGVLLVPTLVCVVWFGILGGTAIFLETTR +PAGYTSVVGADGAIDSNTALFQVLEQLPAGMMLVVGAIILSGIFFITSADSGSLVMGMLA +TGGDVNPKATVKIFFAIATSLMAAALLAAGGLSAIQVLAITIGLPFSVLMLLICLATFRS +LGYSVARVEAVRRQAMLASIKDRLGLESDDDEVVDAGPVAASQWWASLSRDHQQRIADAA +AGVPASEGPRRPRLRRHEH +>PROKKA_02147 +MSDPTPPSTEPMIPEQPGNHPSSATAPDAGVAPATSAAADRDRVLLPWVFWPSAVIVLSF +VVATLLAPEQMTVGISLVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGDITLGKPDEK +PEFSTLSWFSLLFAAGMGIGLVFFGMTEPLMHFTSPRPDLAAANPTQAEAAQSALATTFL +HWGLQPWAIYAVVGVAVALAIHRRGRPLALRWAFEPLIGERRVRGGWGHLIDNIALIGTV +FGVATSLGLGVTQMSAGLRALGIVPEDSPWLEYAMIGAVTCVVLYTVVSGVERGMKWLSN +TNLILAAGLLLFIAIVGPTAFLFKEMVQSLGSYMQYFFANSLNVSAFYGAEGDAWQAGWS +AYYWGWWMSWTPFVGIFIARISRGRTVREFIAGVLLVPTLVCVVWFGILGGTAIFLETTR +PAGYTSVVGADGAIDSNTALFQVLEQLPAGMMLVVGAIILSGIFFITSADSGSLVMGMLA +TGGDVNPKATVKIFFAIATSLMAAALLAAGGLSAIQVLAITIGLPFSVLMLLICLATFRS +LGYSVARVEAVRRQAMLASIKDRLGLESDDDEVVDAGPVAASQWWASLSRDHQQRIADAA +AGVPASEGPRRPRLRRHEH +>PROKKA_00252 +MSESIPPSHPSAPPGPASAHPAAPAAGAADAREASGAVAPASSDAATGARVLLPWVFWPS +TIVVLLFVGATLLFPEPMTAAIGTVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGAIT +LGKPDEKPEFSTLSWFALLFAAGMGIGLVFFGMTEPLMHFVSPRPDLAATDPNPAQAAQA +ALATTFLHWGLQPWAIYAVVGVAVGLAIHRRGRPLALRWAFEPLLGERRVRGGWGHLIDN +IALIGTVFGVATSLGLGVTQMSAGLRSLGVVPEESAWVEYAMIGLVTLVVLYTVVSGVER +GMKWLSNVNLVLAAGLLLFIAIVGPTAFLFKEMVQSFGAYLQTFFGASLNVSAFQGAEGD +AWQAGWSAYYWGWWMSWTPFVGIFIARISRGRTVRQFLAGVLLVPTLIGVVWFGVLGGTA +IYLETVRPDGYTSVVGADGSIDSNTALFQVVEQLPAGALLVIGAIMLSAIFFVTSADSGA +LVMGMLATGGDVNPKVPVKIFFAIATALMSAALLAAGGLSAIQTLAITIGLPFSVLMLVM +CLATFRSLGYSVARVEAVRRQAMLASIKDRFGLDTDDDEVVDGGPVAASQWWASLSRDRQ +RTIAQAASAGPDDEIRLAGSSAEEPAGSPDARR +>PROKKA_00188 +MTPAPAGRDADAPAANRPHRTGPDPDVKHPAPATADQADRGHAGLLPWVFWPSTLIVLLF +VVATLAFPAQMTDVIGDVQAAIIRNFSWWYAIVAFAFVVFCAYLVFSRKGSITLGKPDEK +PEFSTMSWFALLFAAGMGIGLVFFGMTEPLMHFTSPRPDLAAANPTEAQAAQSALATTFL +HWGLQPWAIYAVVGVAVGLAIHRRGRPLSLRWAFEPLLGERRVRGGWGHLIDNIALIGTV +FGVATSLGLGVTQMAAGLRSLGIVPADSPWLEYAMIAAVTCVVMYTVVSGVERGMKWLSN +INLVLAAGLLLFIALVGPTPFLLKETVQSFGAYLQNFFADSLNVSAFYGAEGDAWQAGWT +AYYWGWWMSWTPFVGIFIARISRGRTVREFLMGVLLVPTLVCVVWFGILGGTAIWLETVR +PAGYTSVVGADGAIDSNSALFQVLEQLPAGLLLVIGAIILSGIFFVTSADSGALVMGMLA +TGGDVNPKTAVKIFFAIATAFMAAALLAAGGLSAIQTLAITIGLPFSVLMLVMCVATFRS +LGYSAARVEAVRRQAMLASIQDRLGKDTDDDEVVEGGPVAASQWWASLSRDHQRTIARLA +SPGPDDEIRLHEDATATSARPDTTRGGSTAR +>PROKKA_00141 +MSDPTPPLKNPLDPERADTRPSSAPTADGAVAPATSAAAARDRVLLPWVFWPSAVIVLSF +VGATLLAPEQMTVGISLVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGDITLGKPDEK +PEFSTLSWFSLLFAAGMGIGLVFFGMTEPLMHFTSPRPDVAAANPTQAEAAQSALATTFL +HWGLQPWAIYAVVGVAVALAIHRRGRPLALRWAFEPLIGERRVRGGWGHLIDNIALIGTV +FGVATSLGLGVTQMSAGLRALGIVPEDSPWLEYAMIGAVTCVVLYTVVSGVERGMKWLSN +TNLILAAGLLLFIAIVGPTAFLLKEMVQSLGSYMQYFFANSLNVSAFYGAEGDAWQAGWS +AYYWGWWMSWTPFVGIFIARISRGRTVREFIAGVLLVPTLVCVVWFGILGGTAIFLETTR +PAGYTSVVGADGAIDSNTALFQVLEQLPAGMMLVVGAIILSGIFFITSADSGSLVMGMLA +TGGDVNPKATVKIFFAIATSLMAAALLAAGGLSAIQVLAITIGLPFSVLMLLICLATFRS +LGYSVARVEAVRRQAMLASIKDRLGLESDDDEVVDAGPVAASQWWASLSRDHQQRIADAA +AGVPASEGPRRTRLRRHGH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000268.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000268.fa new file mode 100644 index 0000000000000000000000000000000000000000..fac8be1cc954580811c5d9eb5b74fa2463c7f89b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000268.fa @@ -0,0 +1,59 @@ +>PROKKA_00135 +MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLG +VDAIWLSPFYLSPQHDAGYDVADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHT +SSEHAWFQAALAAGPGSPERARYHFAEGRGEHGELPPNNWESTFGGGAWTRVTEADGTPG +QWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS +RMGMVTDAGEDADPTFDPDTFEPLTPFMDQDRVHEVYRDWRRVLDSYDHEPMMVAEAWVA +PLSRMFRYVRPGEMHQTFNFTYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTV +RHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMVELGLPGSAYIYQGDELGLPE +HTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA +PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWSEHHDPTRGVLAF +TVTSGGGRHLGSGEPIPARTVLVMANLSTEPVDLPANHSRALFSLEEAEAVQDGRLAHDA +AAWLLMD +>PROKKA_02149 +MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLG +VDAIWLSPFYLSPQHDAGYDVADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHT +SSEHAWFQAALAAGPGSPERARYHFAEGRGEHGELPPNNWESTFGGGAWTRVTEADGTPG +QWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS +RMGMVTDAGEDADPTFDPDTFEPLTPFMDQDRVHEVYRDWRRVLDSYDHEPMMVAEAWVA +PLSRMFRYVRPGEMHQTFNFTYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTV +RHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMVELGLPGSAYIYQGDELGLPE +HTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA +PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWSEHHDPTRGVLAF +TVTSGGGRHLGSGEPIPARTVLVMANLSTEPVDLPANHSRALFSLEEAEAVQDGRLAHDA +AAWLLMD +>PROKKA_00250 +MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLG +VDAIWLSPFYLSPQHDAGYDVADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHT +SSEHAWFQAALAAGPDSPERARYHFAEGRGEHGELPPNNWESTFGGGAWTRVTEADGTPG +QWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS +RMGMVTDAGEDADPTFDPDTFEPLTPFLDQDRVHEVYRDWRRVLDSYGHEPMMVAEAWVA +PLSRMFRYVRPGEMHQTFNFTYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTV +RHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMVELGLPGSAYIYQGDELGLPE +HTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA +PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWSEHHDPARGVLAF +TVTSGGGRHLGSGEPIPARTVLVMANLSTDPVDLPTGHSRALFSLEEAEAVQDGRLAHDA +AAWLLMD +>PROKKA_00185 +MTTQRLTTPPSEARNRPETPWWVDAVVYQVYPRSFADGDGNGMGDLPGVTAKIPYLSRLG +VDAIWLSPFYLSPQHDAGYDVADYRTVDPRFGTLADADALIDAAHAADIRVIVDLVPNHT +SSEHPWFQAAMAAGPGSRERARYHFTEGRGEHGELPPSNWESTFGGGAWSRVTEADGTPG +QWYLHLFDTTQPDLNWENPEVREEFESILRFWLDRGVDGFRVDVAHGLVKKPGYPDADHT +RMGMVTDAGEDQDPDFDVDAFEPAMPFLDQDGVHEVYRQWRRVLDSYPHEPMMVAEAWVS +PLPRTFRYVRPGEMHQAFNFTYLMAGWDAESLTSAIDRSFTEAEKVGAPNTWVLSNHDTV +RHTSRYGLSDPTAYPAGITAEDEQPDEALGRRRARAAAMIELALPGSAYIYQGDELGLPE +HTTLPAELREDPYFFRTGGAEPGRDGCRIPLPWAADEPALGFSGPDADAAPWLPQPDSFR +VLAADRQVGVEGSHFELYRHLLQIRAELDLGTGTFAWSAEHHRPEQGVLAFTVSSGGGRH +LGSGVPIPARTVLVMANIGDTPVALPGDHVRAQFSLPESEAVVDDRLAPDAAAWLLLR +>PROKKA_00143 +MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLG +VDAIWLSPFYLSPQHDAGYDVADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHT +SSEHAWFQAALAAGPGSPERARYHFAEGRGEHGELPPNNWESTFGGGAWTRVTEADGTPG +QWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS +RMGMVTDAGEDADPTFDPDTFEPLTPFMDQDRVHEVYRDWRRVLDSYDHEPMMVAEAWVA +PLSRMFRYVRPGEMHQTFNFTYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTV +RHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMVELGLPGSAYIYQGDELGLPE +HTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA +PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWSEHHDPARGVLAF +TVTSGGGRHLGSGEPIPARTVLVMANLSTDPVDLPAGHSRALFSLEEAEAVQDGRLAHDA +AAWLLMD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000269.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000269.fa new file mode 100644 index 0000000000000000000000000000000000000000..b1a0eb4247498ae0b9f58cce6128bc7c11b3406c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000269.fa @@ -0,0 +1,31 @@ +>PROKKA_00136 +MTHDDGGPPPGVARGTAHLRVFQPLAAFPDAVQARLIAGGHRTRAEVEAEAAERARRRLA +RPVADPFPEPGEDDLVRVLQDEHRSAFYCPDERGLRAEMAAAMLEETMLPRLHSAAIPPA +ARAMNRGRALVALEDEWGLSPDPDAAVEDPQDEDGAPEHHRVQTRTATWGVPHGWLTVFD +PEEPVQRLVDGERTAYRRAPIVAARERAGHAAAVLARHAPDAELIGELTVMVEWLGAFHP +DSWVELDYGGLTRHVWPDDSVFDLWTLIDALEEGDEATAGVAQERLNRRWATVGMLARLT +>PROKKA_02150 +MTHDDGGPPPGVARGTAHLRVFQPLATFPDAVQARLIAGGHRTRAEVEAEAAERARRRLA +RPVADPFPEPGEDDLVRVLQDEHRSAFYCPDERGLRAEMAAAMLEETMLPRLHEAAIPPA +ARAMNRGRALVALEDEWGLSPDPDAAGQDPQDEGGAPEHHRVQTRTATWGVPHGWLTVFD +PEEPVKRLVDGERTAYRRAPIVAARERAGHAAAVLARHALDAELIGELTVMVEWLGAFHP +DSWIELDYGGLTRHVWPDDSVFDLWTLIDALEEGDEATAGVAQERLNRRWAAVGMLARLT +>PROKKA_00248 +MVHDDGADGPAPGGGRVPGGAPPPGIAHGTAHLRVFQPLAAYPDAVQARLIAGAHRTRAE +VEAEAAERARRRLARPVTDPFPEPGEDDLVRVLQDEQGSAFYCPDEFGLRAEMAAAQLEE +TMLPLAYEAAVPTAARAMNRGRVLVALEEEWGLSPDPDADRAHPDEEDGPGRDEDGPSGR +HRVQTRTATWGVPHGWLAVFDPEEPVRRLVDGERTAYRRAPALAALERAGHAAAVLSRHA +PDAELIAELTVMVEWLGAFHPDSHVELDYGGLTRHVWPDDSVFDLWTLIDALGEGDEATA +GVAQGRLNRRWAAVGMLARLT +>PROKKA_00182 +MRTAAANLRVFQPLSAYPDAVAARMVAAAHRTRAEVEAEAAERARRRLLRLPADPFPAPG +EDDLVRVLERGGSAFYCPDELALRMEMAAEMLEASAPEALYAAAVPAAARAMNRGRALVA +LEDEWGLSPDPDAPAPDDPQDAAHQDQDADAGTHRLQTRTSLWGVPHAWLAAFDPEEPAR +RLVDGEDVAYRRTPVAEAVERVGHAAAVLAGAAPDAELLGELAVMIPWLQAFHPDAVLEL +DYGRALTSLVWPDDSVFDLWTLLDALEEGDEVGAGMAQERLNRRWARVGMHAHDG +>PROKKA_00144 +MTHDDGGPPPGVARGTAHLRVFQPLAAFPDAVQARLIAGGHRTRAEVEAEAAERARRRLA +RPVADPFPEPGEDDLVRVLQDEHRSAFYCPDERGLRAEMAAAMLEETMLPRLHEAAIPPA +ARAMNRGRALVALEDEWGLSPDPDAAGQDPQDEGGAPEHHRVQTRTATWGVPHGWLTVFD +PEEPVKRLVDGERTAYRRAPIVAARERAGHAAAVLARHAPDAELIGELTVMVEWLGAFHP +DSWIELDYGGLTRHVWPDDSVFDLWTLIDALEEGDEATAGVAQERLNRRWAAVGMLARLT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000272.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000272.fa new file mode 100644 index 0000000000000000000000000000000000000000..a9e1827b4b867b6058d73e9040115b481f564d0a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000272.fa @@ -0,0 +1,20 @@ +>PROKKA_00139 +MSEIQHDDAVQHPSGLPLAHWLTLTEGLIAARVAESLEEHGLTRAQWQLLNTLTVAPQSR +AELEAGFEEEQRGAVSGQIEELVESRWVTVEGDLYTLTATGRTAGARVGEAVEALRAEAT +ADVPRDQIDDAVRVLRRIARNLGHPDA +>PROKKA_02153 +MSEIPHDDAPVQHPSGLPLAHWLTLTEGLIAARVAESLEEHGLTRVQWQLLNTLTVAPQS +RAELEAGFEEEQRGAVSGQIEELVESHWVTVEGDLYTLTATGRTAGARVGEAVEALRAEA +TADVPRDQIDDAVRVLRRIARNLGHPDA +>PROKKA_00245 +MSEIPHDDAAVQHPSGLPLAHWLTLTEGLIAVRVAESLEEHGLTRAQWQLLNTLTVAPQS +RAELEAGFEEEHRGAVSGQIEELVESRWVTVEGDLYTLTATGRTAGARVGEAVEALRAEA +TADVPRDQIDDAVRVLRRIARNLGHPDA +>PROKKA_00179 +MTDNTQTPENRQTQAPRRDSHPSGLPLSHWLTVAEGLLAARVAASLEEHGLTRAQWQSLN +ALTAAPLSAAEIGAGFEPEVRGAVVEQLDELVDAGWVTVEGDLFTLTSTGRTAGERVGEA +VERLRGEATADLPAEHYEVTVATLRTIARNLGHPDA +>PROKKA_00147 +MSEIQHDDAVQHPSGLPLAHWLTLTEGLIAARVAESLEEHGLTRAQWQLLNTLTVAPQSR +AELEAGFEEEQRGAVSGQIEELVESRWVTVEGDLYTLTATGRTAGARVGEAVEALRAEAT +ADVPRDQIDDAVRVLRRIARNLGHPDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000274.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000274.fa new file mode 100644 index 0000000000000000000000000000000000000000..4e322ad9bf33892bb19aa8d970a6fdb2318f23f0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000274.fa @@ -0,0 +1,37 @@ +>PROKKA_00141 +MIDNAVYVDGRRVHAPSTLEDTWEECERTGGMAWLGLYRPDVAELQAVAEELRLHPLAVE +DALAGGERAKLDRYGEDSFMVLHPARYIDRTETVEFGELSVFTGEHYVVTVRHAEEPDLA +AVRRSLETEGRERLAMGPWQVTLEILDRVVDDYFPVADGLEQDIAEIEDQVFAGDGHVSR +RIYELSREVLNFQHAIRALPSIVEQLQEEVRTRLHEDTRRLDADGLPRRDDAHAWEDEEL +SEQARLEVENLRRLRDVHDHAVQINERVMTMRQMLNSALELDSTLASKRLAEQSIAQNEQ +VKQISSWAAIIFAPQLVGSVYGMNFDGMPELHWAFGYPFALGLMLAVALTLFVLFKRADW +L +>PROKKA_02155 +MIDNAVYVDGRRVHAPSTLEDTWEECERTGGMAWLGLYRPDVAELQAVAEELRLHPLAVE +DALAGGERAKLDRYGEDSFMVLHPARYVDRTETVEFGELSVFTGEHYVVTVRHAEEPDLA +AVRRSLETEGRERLAMGPWQVTLEILDRVVDDYFPVADGLEQDIAEIEDQVFAGDGHVSR +RIYELSREVLNFQHAIRALPSIVEQLQEEVRTRLHEDTRRLDADGLPRRDDAHAWEDEEL +SDQARLEVENLRRLRDVHDHAVQINERVMTMRQMLNNALELDSTLASKRLAEQSIAQNEQ +VKQISSWAAIIFAPQLVGSVYGMNFDGMPELHWAFGYPFALGLMLAVALTLFVLFKRADW +L +>PROKKA_00243 +MIDNAVYVDGRRVHAPSTLEDTWEAAEASGGMAWLGLYRPDADELRAVADELHLHPLAVE +DALEGGERAKLDRYGEDLFMVLHFQHAIRALPVIVEQLQGGARARLREEEHRREVGAPRT +GDVHEWDQDELSEEGVFEVENLRRLRDVHDHAVQINERVAAMRQMLANALELDSTLASKR +LAEQSIEQNEQVKQISSWAAIIFAPQLVGSIYGMNFDGMPELHWAFGYPFALGLMLAVAL +TLFVLFKRADWL +>PROKKA_00177 +MTLIDNAVYVDGRRVFAPTSLSDTWDAIERTGGMAWLGLYRPHPDELQEVADELPLHPLA +VEDALTPGQRAKLERYGDDWFMVLHPARYIDATETVEFGELDVFTGKDYVVTVRHAEEPD +LADIRAGMEQRHTDRLAQGPSQVAFEILDHVVDAYFPVAEGLEQDIREIEDQIFSGDAAV +SRRIYELSREIIGFERATRPLPRMIEQLQEDMRARLGDAANGSHASHLEAPEPEPGEEER +AELVETLRALRDIHDHAVQVTDRVAAMRQMLENALELDSTLASKRLAEQSIAQNEQVKRI +SSWAAIIFAPQLIGSVYGMNFQHMPELEWPLGYPWALGLMLGVAVALYALFKKADWL +>PROKKA_00149 +MIDNAVYVDGRRVHAPSTLEDTWEECERTGGMAWLGLYRPDVAELQAVAEELRLHPLAVE +DALAGGERAKLDRYGEDSFMVLHPARYVDRTETVEFGELSVFTGEHYVVTVRHAEEPDLA +AVRRSLETEGRERLAMGPWQVTLEILDRVVDDYFPVADGLEQDIAEIEDQVFAGDGHVSR +RIYELSREVLNFQHAIRALPSIVEQLQEEVRTRLHEDTRRLDADGLPRRDDAHAWEDEEL +SDQARLEVENLRRLRDVHDHAVQINERVMTMRQMLNNALELDSTLASKRLAEQSIAQNEQ +VKQISSWAAIIFAPQLVGSVYGMNFDGMPELHWAFGYPFALGLMLAVALTLFVLFKRADW +L diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000275.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000275.fa new file mode 100644 index 0000000000000000000000000000000000000000..1eb50beaf460973a64759cbc9c8d8cd6a3be2c68 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000275.fa @@ -0,0 +1,20 @@ +>PROKKA_00142 +MKTPRHAPPVVRDGKTLLPAHAVSTAPVTAFGLIGGYLTARETGIRPLGGVVLAAAGLYA +GRTWLAKRGPAVAGGLAALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDRSEA +GR +>PROKKA_02156 +MKTPRHAPPVVRDGKTLLPAHAVSTAPVTAFGLIGGYLTARETGIRPLGGVVLAAAGLYA +GRTWLATRGPAVTGGLAALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDRSEA +GR +>PROKKA_00242 +MNSPRHAAPVVRDGRTLLPAHAVTTAPIAAFGLIGGYLTARETGIRPLGGVVLAAAGAYA +GRTWLAKRGPAVAGGLTALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDREGA +R +>PROKKA_00176 +MSKDTSTPVARDGKTLLPADAVTTAPIAALGLVGGYLVARETGIRWLGGVVLGAAGLYAG +RTWAAKGGPAVAGTLGALYLGGFGASHPLAKKIGAWPSVLSVAAASAGAAYAAVDRKDGR +R +>PROKKA_00150 +MKTPRHAPPVVRDGKTLLPAHAVSTAPVTAFGLIGGYLTARETGIRPLGGVVLAAAGLYA +GRTWLAKRGPAVAGGLAALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDRSEA +GR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000276.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000276.fa new file mode 100644 index 0000000000000000000000000000000000000000..abeedb8767d45f27be39ef436f1bed1b85d1a66e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000276.fa @@ -0,0 +1,23 @@ +>PROKKA_00143 +MAIENWQHDLNIGTVVRTANAFNAAGVHIIGRRRWNRRGAMVTDRYLHVRHHETVAAFTE +WAAGEGLPVLGVDLFPESVPVETFDFPRACVLVFGQEGPGLSAEVRAASSAVLSIAQYGS +TRSINAGVAAGIAMHAWIRQHAAVP +>PROKKA_02157 +MLDHYRYWSLEAIVADLDARRHPFHVAIENWQHDLNIGTVVRTANAFNAAGVHIIGRRRW +NRRGAMVTDRYLHVRHHETVAAFTEWAAGEGLPVLGVDLFPESVPVETFDFPRACVLVFG +QEGPGLSAEVRAASSAVLSIAQYGSTRSINAGVAAGIAMHAWIRQHAAVP +>PROKKA_00241 +MGPGTSENSPETREKREEREGREEREVGVGPWEGPWPEDPRYDPELLRDGDRRNVVDGYR +YWTLEAIVADLDARRHPFHVAIENWQHDLNIGTVVRTANAFNAAGVHVIGRRRWNRRGAM +VTDRYLHVRHHATVEEFTAWAAAEGLPVLGVDLFPESVPLESFELPRECVLVFGQEGPGL +SEEVRAASAAVLSIAQYGSTRSINAGVAAGIAMHAWVRQHGGVPTSSS +>PROKKA_00175 +MGSGEGVDAREVGREVGAPPWEGPWPEDPRYDPALLRDGDRRNVADRYRYWTVEAIVADL +DRTRHPFHVAIENWQHDLNIGTVVRTANAFNAAGVHIIGRRRWNRRGAMVTDRYLHVHHH +ETVEAFTAWAAGEGLPVLGVDLFPESVPVETFDFPRACVLVFGQEGPGLSEEVRAASEAV +LSIAQYGSTRSINAGVAAGIAMHAWIRQHGGPAPV +>PROKKA_00151 +MPREVGVGPWLGPWPEDPRYDPELLAHGDRRNVLDRYRYWRLEAIVADLDARRHPFHVAI +ENWQHDLNIGTVVRTANAFNAAGVHIIGRRRWNRRGAMVTDRYLHVRHHETVAAFTEWAA +GEGLPVLGVDLFPESVPVETFDFPRACVLVFGQEGPGLSAEVRAASSAVLSIAQYGSTRS +INAGVAAGIAMHAWIRQHAAVP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000278.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000278.fa new file mode 100644 index 0000000000000000000000000000000000000000..cecd077883da5931ef1221628d185a167f650606 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000278.fa @@ -0,0 +1,35 @@ +>PROKKA_00146 +MPIASPEKYAEMIDAAKNGAFAYPAINVTSSQTLNAAIRGFAEAGSDGIIQVSTGGAAYF +SGSSVKDMVAGSLAFAAFAREVAKKHSVNIALHTDHCPQDKLEDFVLPLLDASEAEVKAG +RDPIFNSHMWDGSAETLEENLRIGRELLARTHANKQILEVEIGVVGGEEDGVAHEINEKL +YTTVADGIATVEALGLGENGRYLTALTFGNVHGVYKPGNVKLRPEILQEIQQAVGEKFGR +ERPFDLVFHGGSGSAAQEIADSVEYGVVKMNVDTDTQYAFTRPVAGHMFENYDGVLKVDG +EVGDKKQYDPRVWGAKAEEAMAARVVQACTELNSAGKSIG +>PROKKA_02160 +MPIASPEKYAEMIDAAKNGAFAYPAINVTSSQTLNAAIRGFAEAGSDGIIQVSTGGAAYF +SGSSVKDMVAGSLAFAAFAREVAKKYSVNIALHTDHCPQDKLEGFVLPLLDASEAEVKAG +RDPIFNSHMWDGSAETLEENLRIGRELLARTHANKQILEVEIGVVGGEEDGVAHEINEKL +YTTVADGIATVEALGLGEHGRYLTALTFGNVHGVYKPGNVKLRPEILQEIQQAVGEKFGK +ERPFDLVFHGGSGSAAQEIADSVEYGVVKMNVDTDTQYAFTRPVAGHMFENYDGVLKVDG +EVGDKKQYDPRVWGAKAEEAMAARVVQACTELNSAGKSIG +>PROKKA_00238 +MPIASPDKYAEMIDAAKNGAFAYPAINVTSSQTLNAAIRGFAEAGSDGIIQVSTGGAAYF +SGASVKDMVTGSLAMAAFAREVAKNYSVNIALHTDHCPKDKLDAFVMPLLDASEAEVKAG +RDPIFNSHMWDGSAETLEENLRIGKELLARTHANKQILEVEIGVVGGEEDGVAHEINDKL +YTTVEDGIATIEALGLGEQGRYLTALTFGNVHGVYKPGNVKLRPQILEDIQKAVGEKFGK +ERPFDLVFHGGSGSAAQEIADSVSYGVVKMNVDTDTQYAFSRPVAGHMFENYAGVLKVDG +EVGDKKMYDPRVWGAKAEEAMAARVVQACQELNSAGTSIG +>PROKKA_00173 +MPIASPDKYAEMIDAAKNGAFAYPAINVTSSQTLNAAVRGFAEAGSDGIIQVSTGGAAYF +SGSSVKDMVAGSLAMAAFAREVAKKYSVNIALHTDHCPKDKLDGFVKPLLDASEAEVKAG +RDPLFNSHMWDGSAETLEENLRIAQELLARTHANKQILEVEIGVVGGEEDGVANEINDKL +YTTVEDGIATIEALGLGENGRYLTALTFGNVHGVYKPGGVKLRPQILQDIQQAVGEKFGR +QRPFDLVFHGGSGSAAQEIADSVSYGVVKMNVDTDTQYAFSRPVAGHMFENYDGVLKVDG +EVGNKKMYDPRVWGAKAEDGMAARVVQACQELNAAGKSIG +>PROKKA_00154 +MPIASPEKYAEMIDAAKNGAFAFPAINVTSSQTLNAAIRGFAEAGSDGIVQVSTGGAAYF +SGSSVKDMVAGSLAFAAFAREVAKKYSVNIALHTDHCPQDKLEGFVLPLLDASEAEVKAG +RDPIFNSHMWDGSAETLEENLRIGRELLARTHANKQILEVEIGVVGGEEDGVAHEINEKL +YTTVQDGIATVEALGLGEHGRYLTALTFGNVHGVYKPGNVKLRPEILQEIQQAVGEKFGK +ERPFDLVFHGGSGSAAQEIADSVEYGVVKMNVDTDTQYAFTRPVAGHMFENYDGVLKVDG +EVGDKKQYDPRVWGAKAEEAMAARVVQACTELNSAGKSIG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000279.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000279.fa new file mode 100644 index 0000000000000000000000000000000000000000..c1eb66c73de0b5f7e60eb09dca303207b467dcf7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000279.fa @@ -0,0 +1,50 @@ +>PROKKA_00147 +MDHGNGPPLVKNVTFFPKHVISSPVPSTVPRMMTRPLPEDSATVDTVALGRRVRHLRKQA +GLTLDQLAERTGVSGSHLSLVENARREPRLSLVQRIAEVLGVPVEDLLTGRAPTRRAELE +IEVERFARSEHYASLGLPPLRIGPRTPTEVLEVIAGLEAELRRRLEEQAATPEEARRANA +QLRARMRAVDNHYPDLEAEAHRLLDAIGHTGGPLGLHAVSELAEHLGFTLRFVPDLPHST +RSVTDLKHGRIHISGSRSSDHDRRTVVLQALAAAVLGHGEPRDYEDFLAQRVAVNYLAGA +LLMPQRAASSLLRAAQKRRDLSVDDLKDAFGVSYEAAAHRFTNLATVDLGIRCHFQKVHE +TGVIHKAYENDGIVFPADHTGAIEGQQACRKWGARQAFSRNDRFRAHAQYTDSPNGTFWC +TSMIENGPDGLFALSVGTPFEHARYFRGADTRHRVTSTCPDPRCCRRPDPELEAAWGGHV +WPAARMHAHLLAAMPTQTFPGVDEREVFEFLQAQEEREG +>PROKKA_02161 +MMTRPLPEDSATVDTVALGRRVRHLRKQAGLTLDQLAERTGVSGSHLSLVENARREPRLS +LVQRIAEVLGVPVEDLLTGRAPTRRAELEIEVERFARSEHYASLGLPPLRIGPRTPTEVL +EVIAGLEAELRRRLEEQAATPEEARRANAQLRARMRAVDNHYPDLEAEAHRLLDAIGHTG +GPLGLHAVSELAEHLGFTLRFVPDLPHSTRSVTDLKHGRIHISGSRSSDHDRRTVVLQAL +AAAVLGHGEPRDYEDFLAQRVAVNYLAGALLMPQRAASSLLRAAQKRRDLSVDDLKDAFG +VSYEAAAHRFTNLATVDLGIRCHFQKVHETGVIHKAYENDGIVFPADHTGAIEGQQACRK +WGARQAFSRNDRFRAHTQYTDSPNGTFWCTSMIENGPDGLFALSVGTPFEHARYFRGADT +RHRVTSTCPDPRCCRRPDPELEAAWGGHVWPAARMHAHLLAAMPTQTFPGVDEREVFEFL +QAQEEREG +>PROKKA_00236 +MMTRPLPEDSATVDAVALGRRVRHLRKQAGLTLDQLADRTGVSGSHLSLVENARREPRLS +LVQRIAEVLGVPVEDLLTGRAPTRRAELEIEVERFARSEHYASLGLPPLRIGPRTPTEVL +EVIAGLEAELRRRLEEQAATPEEARRANAQLRARMRAVDNHYPDLEAEAQRLLDAIGHTG +GPLGLHAVSSLAEHLGFTLSFVANLPHSTRSVTDLKHGRIHVSGGRASDHDRRTVVLQAL +AAAVLGHGEPRDYEDFLSQRVAVNYLAGALLMPQRPASALLRAAQKRRDLSVDDLKDAFG +VSYEAAAHRFTNLATVDLGIRCHFQKVHETGVIHKAYENDGLVFPADHTGAIEGQAACRR +WGARQAFGRSDRFRAHTQYTDAPNGTYWCTSMVEHGPDGLFALSVGTAFEHARHFRGADT +RHRITSTCPDPRCCRLPDPALEAEWGGHVWPAARMHAHLLAAMPTQAFPGVDEVEVFEFL +ESQRDRTPGAPGADAPDGAGGVTP +>PROKKA_00821 +MATPTDPAHEPPRVDPLVLGRRLRHLRRVSGATLSDVAEKVGVTASHLSLVENGHREPRL +TLLTALADVHGVGVEDLLTPEAPSRRAALEVAVERAQRGPLFQRLGLPALKIGPRTPDEV +LEVIAGLQAELDRQMAERVSTPEEARRANSALREEMRACGNHYADLERRAQELREAVDVA +DGPLTHHHVSALAEHLGFAVRFVPDLPHSTRSVTDLKNRRIYLARARRPDHDPRAVLLQA +VCSSVLGHGEPADYADFLRQRVYTNYLAAAMMMPERGTVRALREAKERRDLSVDDLRDRF +GVSWESAAHRFTNLATEHLGLTCHFAKVHESGVFHKAYENDGIPFPTDHIGAIEGQTACR +HWTSRQVFSVADHLGAFPQYTDTPAGTYWSAAVVEPTSTGFYSLTVGVPFDDAKWFRGRE +TSARTRSTCPDPKCCRLPSAELEAAWGGQAWPAARANAHLLAAMPGGAFPGVEEVQVFEF +LQTQESRWPPEGSGAA +>PROKKA_00155 +MMTRPLPEDSATVDTVALGRRVRHLRKQAGLTLDQLAERTGVSGSHLSLVENARREPRLS +LVQRIAEVLGVPVEDLLTGRAPTRRAELEIEVERFARSEHYASLGLPPLRIGPRTPTEVL +EVIAGLEAELRRRLEEQAATPEEARRANAQLRARMRAVDNHYPDLEAEAHRLLDAIGHTG +GPLGLHAVSELAEHLGFTLRFVPDLPHSTRSVTDLKHGRIHISGSRSSDHDRRTVVLQAL +AAAVLGHGEPRDYEDFLAQRVAVNYLAGALLMPQRAASSLLRAAQKRRDLSVDDLKDAFG +VSYEAAAHRFTNLATVDLGIRCHFQKVHETGVIHKAYENDGIVFPADHTGAIEGQQACRK +WGARQAFSRNDRFRAHTQYTDSPNGTFWCTSMIENGPDGLFALSVGTPFEHARYFRGADT +RHRVTSTCPDPRCCRRPDPELEAAWGGHVWPAARMHAHLLAAMPTQTFPGVDEREVFEFL +QAQEEREG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000282.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000282.fa new file mode 100644 index 0000000000000000000000000000000000000000..69edb53d41aa1171c8c01d3a10ab294e99ee6b0a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000282.fa @@ -0,0 +1,39 @@ +>PROKKA_00150 +MTHPAPARRRAPLAVGVAALALALAGCGSAGQSGEPASSTAAAPSGSAASAAAGSATESP +TDPASAAASRVREALASESAEGTPRAEPRQAFETVGPGIKDGAATEAWKNTAAVRNDTVS +VMDCTRDVLDQRTLDAVATHIPDSSNIEIVQLFASQDETHEFLTCVYNGYFEYSPGMPLA +QVHYQHNLDGSRLEWCQEEPAAVADEYTFDPKTGKGLLALLRPGMVGGQDGAPLLPQRTA +WACSEDGSEMVSVTMGSMEGFGDANGGLTQVKNSPVAQSTTLVTETRDHLADTVLKDAGD +FQEVIKLSSPFFLNAQMDEETLAQAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPP +RPFQGAAREAAESQRAAEASASASASPSPTKSASASASPSPSTSGD +>PROKKA_02164 +MTHPAPARRRAPLAVGVAALALALAGCGSAGQSGEPASSTAAAPSGSAASAAAGSATESP +TDPASAAASRVREALASESAEGTPRAEPRQAFETVGPGIKDGAATEAWKNTAAVRNDTVS +VMDCTRDVLDQRTLDAVATHIPDSSNIEIVQLFASQDETHEFLTCVYNGYFEYSPGMPLA +QVHYQHNLDGSRLEWCQEEPAAVADEYTFDPKTGKGLLALLRPGMVGGQDGAPLLPQRTA +WACSEDGSEMVSVTMGSMEGFGDANGGLTQVKNSPVAQSTTLVTETRDHLADTVLKDAGD +FQEVIKLSSPFFLNAQMDEETLAQAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPP +RPFQGAAREAAESQRAAEASASASASPSPTKSASASPSPSTSGD +>PROKKA_00233 +MREARESASAEGTPRAQPRQALETLGPGIRDGAATTAWENTAAVRNDTVSVMDCTRDVLD +QRTLDAVATHIPDGSNIEIVQLFAAQDETHEFLTCAYNGYFEYSPGMPLAQVQYQHNLDS +TRLDWCEDEPATVADEYTFDPETGKGLLALLRPGMIGGQDGAPLMPQRTAWACSEDGTEL +VSVTMGSMEGYGDANGGLTQVENSPVAGSTTLVTEARDHLADTVLKDASRFHEVIKLSSP +FFLNASMDEESLAKAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPPRPFQGAAREA +AESQRAAEASASAAEASASRAASGSGTPSPSSTPASRTPSPSGTGG +>PROKKA_00172 +MTHPTSAPHRAAAALGAAALALTLAGCSDSGQPSPASSTSTATAAAGSSASATGDPQSPA +SAAASEIRAARASEKADGSERPQPREALETQGPGITSGAASAGWKSVAARYNDTVSVMDC +TQDVLDQTTLDAVATHIPVANDIGIVQLFASRDQTHEFLTCQYQGSSSRSEGAPLVMVHY +QHNLDGRRLEWCRPEAPVMADEYSYDESTRKGLLALLRPGMVGGADGAPLLPQRTAWACN +EDGTQLVSVTFGAMKGYGSVNEGLTQVTNSPIANSTTLATQARDHLADTVLKDPSDFQAD +IETSSPFFLNAQTDQETLDKAKGLPTGIIPQDQLSDQSTIDRPEGAPEPVAPGQPPRPFV +GAARDAAESAAAESAASSSGSDSASPSDDGDGNPVVSESGTPSPSNTTD +>PROKKA_00158 +MTHPAPARRRAPLAVGVAALALALAGCGSAGQSGEPASSTAAAPSGSAASAAAGSATESP +TDPASAAASRVREALASESAEGTPRAEPRQAFETVGPGIKDGAATEAWKNTAAVRNDTVS +VMDCTRDVLDQRTLDAVATHIPDSSNIEIVQLFASQDETHEFLTCVYNGYFEYSPGMPLA +QVHYQHNLDGSRLEWCQEEPAAVADEYTFDPKTGKGLLALLRPGMVGGQDGAPLLPQRTA +WACSEDGSEMVSVTMGSMEGFGDANGGLTQVKNSPVAQSTTLVTETRDHLADTVLKDAGD +FQEVIKLSSPFFLNAQMDEETLAQAREIPTGRVPDELLNNQSTIDRPEGAPGPVAPGQPP +RPFQGAAREAAESQRAAEASASASASPSPTKSTSASPSPSTSGD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000283.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000283.fa new file mode 100644 index 0000000000000000000000000000000000000000..d96c92d44733283eb0eb20ac8ad712200e72db2f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000283.fa @@ -0,0 +1,20 @@ +>PROKKA_00151 +MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDIVPVAPESSLVWALMAEDAWAEGR +TVDSYAYARVGYHRGLDALRRAGWRGAGPVPYAHEPNRGFLRALYALGRAAAGIGESEEV +ERIRTFLRDSDPTAAEQIEAGQGRARG +>PROKKA_02165 +MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDIVPVAPESSLVWALMAEDAWAEGR +TVDSYAYARVGYHRGLDALRRAGWRGAGPVPYAHEPNHGFLRALYALGRAAAGIGESEEV +ERIRTFLRDSDPTAAEQIEAGQGRAQG +>PROKKA_00232 +MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDVVPVAPESSLVWALMAEDAWSEGR +TVDSYAYARVGYHRGLDALRKAGWRGAGPVPYDHEPNRGFLRALYSLGRAAAGIGESEEV +ERIRTFLKDSDPTAAEKIEATQGRSGS +>PROKKA_00171 +MSESLIGKNLMEPPATLLPEEPEVLARLDAGDLPEDLVPLAPESSLVWALMAEDAWSEGR +AVDSYAYSRVGYHRGLDALRRAGWRGAGPVPWSHEPNRGFLRALYALGRAAAGIGESAEV +DRIRTFLKDSDPTAAQQIEAAQA +>PROKKA_00159 +MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDIVPVAPESSLVWALMAEDAWAEGR +TVDSYAYARVGYHRGLDALRRAGWRGAGPVPYAHEPNRGFLRALYALGRAAAGIGESEEV +ERIRTFLRDSDPTAAEQIEADQGRAQG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000284.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000284.fa new file mode 100644 index 0000000000000000000000000000000000000000..4e9beed7b195028219a800c8f31fbcfbdb0bcddc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000284.fa @@ -0,0 +1,25 @@ +>PROKKA_00152 +MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEGDVVSRLGVTRAVDF +LVPAGADVRELFRRHATGDDPDALVGHVEAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG +VPVIAYGLRTDFRTRSFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVDPATGAEHF +VFEGDQVAIDGVQVTYESLCGTCYLAESGGALG +>PROKKA_02166 +MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEGDVVSRLGVTRAVDF +LVPAGADVRELFRRHATGDDPDALVGHVEAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG +VPVIAYGLRTDFRTRSFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVDPATGAEHF +VFEGDQVAIDGVQVTYESLCGTCYLAESGGALG +>PROKKA_00231 +MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEDEVVSRLGVTRTVDF +LVPAGAGVRELFRRHASGDDPDALVDHVDAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG +VPVIAYGLRTDFRTRCFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVNPATGAEHF +VFEGDQVAIDGVEVTYESLCGSCYLAESGGRLG +>PROKKA_00170 +MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPAVDTKGDAAVVSRLGVTRAVDF +LVPAGADVLALFRAHAAGDDPDALVDHVDAPPVACLLVDEAQFLEAGQVDDLLRIAVLED +VPVMAYGLRTDFRTHSFPGSARLLELAHSLEELKTICRCGRKAVLNTRKVVDAATGRSRF +VFEGDQVAIDGVEVTYESLCAACYLEESGGRLG +>PROKKA_00160 +MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEGDVVSRLGVTRAVDF +LVPAGADVRELFRRHATGDDPDALVGHVEAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG +VPVIAYGLRTDFRTRSFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVDPATGAEHF +VFEGDQVAIDGVQVTYESLCGTCYLAESGGALG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000285.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000285.fa new file mode 100644 index 0000000000000000000000000000000000000000..cb20b7eae51c6dd3aeb4c2b833e76c6522a32637 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000285.fa @@ -0,0 +1,25 @@ +>PROKKA_00154 +MATPLLELAASRGVCFPLRARRLTLTPFRGLDAPAVWSFCRLEQVWSWTSGRPESENALR +ESYLGAGDRLTVRAGDVIVGVGKVAVQDAWSQDGPQEEARDAQAELGWTIDPRQAGQGYG +TELARALLGFAFDDLGVRRVEAHAFADNAPSLRIMEKVGMRHEGTFKEESLHLTRGWVDG +ATYAMLASEFHSPLTQE +>PROKKA_02168 +MATPLLELAASRGVCFPLRTRRLTLTPFRGLDAPAVWSFCRLEQVWSWTSGRPESENALR +ESYLGAGDRLTVRAGDVIVGVGKVAVRDAWSQGGPREEGRDAQAEIGWTIDPRQAGQGYG +TELARALLGFAFDDLGVRRVEAHAFADNAPSLRIMEKVGMRHEGTFKEESLHLTRGWVDG +ATYAMLASEFHSPLTQE +>PROKKA_00470 +MATPLLDLAARRGVVFPLRTERLTLTSFAADDAPAVFDFCRLEEVWTWTSGRAGSAGELR +ESYLAAGDRLTVRAGEAIIGVGKLAVQDAWSQGGPREEARDAQAEIGWTIHPTHADQGYA +TELAGALLKLAFTGLGVHRVEAEAFADNAPTLRVMEKVGLRHEGTFREESLHLTRGWVDG +VTYAMLASEFLARV +>PROKKA_00420 +MATPLLDLAARRGVAFPLRTERLTLTPFTAVDAPAVWDFCRLEEVRTWTSGRAGSAAELR +EEYLATGDRLTVRDGAGDVVGVGKLAVQDAWSQGGPHPDARDAQAELGWTVAPEHAGRGY +ATEIGRALLDLAFRGLGVRRVEAGAFADNAPSLRVMAKIGLRHEGTFLGESLHLTRGWID +GVTFALLASEYEGGAAASRA +>PROKKA_00167 +MAPPLLELAASRGVCFPLRARRLTLTPFRGLDAPAVWGFCRLEQVWSWTSGRPESEGALR +ESYLAAGDRLTVRVGDVIVGVGKAAVQDAWSQGGPREEARDAQAEIGWTIDPRQAGQGYG +TELARALLGFAFNDLGVRRVEAHAFADNAPSLRIMEKVGMRHEGTFKEESLHLTRGWVDG +ATYAMLASEFHSPLTQE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000287.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000287.fa new file mode 100644 index 0000000000000000000000000000000000000000..6a9d3c4c5cd5f0048983682b084f0d68373b6c7a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000287.fa @@ -0,0 +1,25 @@ +>PROKKA_00178 +MSTAAPHTQHSDFPSPTPTRKGPSVGTWRPWAVLPWALALLALPLIALALRSNFGANGWM +TVIYMVFGALPHELVLMVLVGSLFLLPRVNPQDEQRGGIRLGRLLHTLLGVSWGSFALAA +IIFPDGGDHPDSGATTPVLMDLLGKSTAMDVGIVGGLALVAVSALTGLAVIVVCVVRRIR +AVR +>PROKKA_02174 +MSTAAPGTQHSDFASPTPTRKGPSVGTWRPWAVLPWALALLALPLIALALRSNFGANGWM +TVIYMVFGALPHELALVLMVGSLFLLPRVNPQDEQRGGIRLGRLLHTLLGISWGSFALAA +IIFPDGGDHPDSGATTPVLMDLLGKSTAMDVGLVGGLALVAVSALTGLAVIVVCVVRRIR +AVR +>PROKKA_00223 +MSTAAPHTQHSDSASPAPTRKGPSVGTWRPWAVLPWALALLALPLIALALRSNFGANGWM +TVIYMVFGALPHELFLMLMVGSLFLLPRVNPLDEQRGGIRLGRLLHTLLGVSWGSFALAA +ILFPDAGDHPDSAATTPVLMDLLGKSTAMDVGSVAGLALAAVSALTGLAVIVVCVVRRIR +AVR +>PROKKA_00169 +MAVPHPVMPPPGTPLPHQLRPAGPSVGTPRWLPAVLWIVAFALLPLCVIVGRFATENGGW +LLFTYIMFGWMVQGGLGVLAAASLFLLPRVNPPVERRAGVRTGVVVHLLLGASWLTGLLG +MLAFGDYGDAPGSETAPAPLVDLYGMDRAVEIGDAVGPPLVGISLLTGLAAVVLVVVRRL +AAAVRS +>PROKKA_00175 +MSTAAPGTQHSEFASPAPARKGPSVGTWRPWAVLPWALALLALPLIALALRSDFGANGWM +TVIYMVFGALPHELVLMVLVGSLFLLPRVNPQDEQRGGLRLGRLLHTLLGVSWGSFALAA +IIFPDGGDHPESGATTPVLMGLLGTSTAMDVGIVGGLALVAVSALTGLAVIVVCVVRRIR +AVR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000289.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000289.fa new file mode 100644 index 0000000000000000000000000000000000000000..8d7fbf82338d460134c39d312f21da104919ab52 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000289.fa @@ -0,0 +1,70 @@ +>PROKKA_00180 +MTTQQPDIPGTPGPITPDLEEHTALTHPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAA +QGCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGA +HGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGT +WDLVGNNIPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTLW +NMSDRGIPRSYRMMEGFGVHTYRLIAADGSTVLVKFHWKPMLGVHSVTWEEALLTNGMDP +DFHRRDLADAIEAGAFPEWELGVQVFEDNEEQMFEGIDLLDPTKLVPEELAPVQPLGRMT +LNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWNQLPIN +RPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHAFIEHPEPLPASVKER +AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLA +QQVADGLGIPVPAPTETPADVQPSPVLSQIGGAWPLDGRQVGVVVGESVDEKELDALVQG +IHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVVVASPAAPAADAAPGLDQKAG +AADPEAVDPRVIKVLQEMWRHSKAILALEPAEAVLAAAQVSGKGVESAADGASAVSRLTE +LLPAHRVWDRFPTTGRLAD +>PROKKA_02176 +MTTQQPDIPGTPGPITPDLEEHTALTHPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAA +QGCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGA +HGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGT +WDLVGNNIPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTLW +NMSDRGIPRSYRMMEGFGVHTYRLIAADGSTVLVKFHWKPMLGVHSVTWEEALLTNGMDP +DFHRRDLADAIEAGAFPEWELGVQVFEDNEEQMFEGIDLLDPTKLVPEELAPVQPLGRMT +LNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWNQLPIN +RPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHAFIEHPEPLPASVKER +AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLA +QQVADGLGIPVPAPTETPADVQPSPVLSQIGGAWPLDGRQVGVVVGESVDEKELDALVQG +IHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVVVASPAAPAADAAPSLDQKAG +AADSEAVDPRVVKVLQEMWRHSKAILALEPAEAVLAAAQVSGKGVESAADGASAVSRLTD +LLPAHRVWERFPTTGRLAD +>PROKKA_00221 +MTTQQPDIPGTPGPRTPDLEERTAPTSSDDAAMPAPDQRGPASVSPTGQDTGADPATAAQ +GCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGAH +GMFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGTW +DLVGNNMPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTIWN +MSDRGIPRSFRMMEGFGVHTYRLIAADGSTVLVKFHWKPKLGVHSVTWEEALITNGADPD +YHRRDLADAIEAGAFPEWELGVQVFEDTEEQMFEGIDLLDPTKLVPEELVPVQPLGRMTL +NANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWTQLPINR +PHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHALIEHPEPLPASVKERA +HAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLAQ +QVADGLGIPVPAPTETPADVQPSPVLSQIGGVWPLDGRQVGVVVGESVDEKELDALVQGI +HGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVVVASPAAPAADAAPGLDEKAGA +AASEAVDPRVVKVLQEMWRHSKAILALEPAEGVLAAAQVSGKGVESAADGASAVSRLTEL +LPAHRVWERFGTTGRFAD +>PROKKA_00166 +MAEQPKIPGTPGPITPDLEEHTALTDPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAAQ +GCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGAH +GVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGTW +DLVGNNMPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTIWN +MSDRGIPRSFRMMEGFGVHTYRLIAADGSTVLVKFHWKPKLGVHSVTWEEALITNGADPD +YHRRDLADAIEAGAFPEWELGVQVFEDNEEQMFEGIDLLDPTKLVPEELVPVQTLGLMTL +NANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWTQLPINR +PHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHALIEHPEPLPASVKERA +HAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEETIRVRQLQNLGAIDPRLAQ +QVADGLGMPVPAPADAPADVQPSAALSQVGGTWPLDGRQVGLVVGPQVDEKELGDAVQGI +HGAGMVPLVIAPKGGPVAGEVVAQRAYLTAASIELDAVVVLGATPPAGDAQHGLDAKAAA +DAPDAVDPRVAKLVQEAWRHAKAIVAVGEGTSVLDELGLTGTPGVLTVDAGADAVAQLKE +LMPAHRVWERFPTTGRLAD +>PROKKA_00177 +MTTQQPDIPGTPGPITPDLEEHTALTHPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAA +QGCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGA +HGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGT +WDLVGNNIPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTLW +NMSDRGIPRSYRMMEGFGVHTYRLIAADGSTVLVKFHWKPMLGVHSVTWEEALLTNGMDP +DFHRRDLADAIEAGAFPEWELGVQVFEDNEEQMFEGIDLLDPTKLVPEELAPVQPLGRMT +LNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWNQLPIN +RPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHAFIEHPEPLPASVKER +AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLA +QQVADGLGIPVPAPTETPADVQPSPVLSQIGGAWPLDGRQVGVVVGESVDEKELDALVQG +IHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVVVASPAAPAADAAPGLDQKAG +AADSEAVDPRVVKVLQEMWRHSKAILALEPAEAVLAAAQVSGKGVESAADGASAVAALKQ +LLPAHRVWDRFPTTGRLAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000290.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000290.fa new file mode 100644 index 0000000000000000000000000000000000000000..62928a7b76a5b7166780ca6a72b5114e2344dd84 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000290.fa @@ -0,0 +1,30 @@ +>PROKKA_00181 +MRISVGQFGPVGDVEENLAVMARLAARAAGEGADLLVLPEEAMLGAREVGEEFPDAVAAA +WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH +RESDRITPGDGGVAAIELGGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK +VEHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVAELADEREAVATAEVTR +ERIDEVREFLPSLANRRTDVL +>PROKKA_02177 +MRISVGQFGPVGDVEANLAVMARLAARAAGEGADLLVLPEEAMLGAREVGEEFPDAVAAA +WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH +RESDRITPGDGGVAAIELGGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK +VDHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVAELADEREAVVTAEVTR +ERIDEVREFLPSLANRRTDVL +>PROKKA_00220 +MRISVGQFGPVGDVEANLAVMARLAARAAGEGAELLVLPEEAMLGAREVGEEFPDAIAAA +WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH +RESDRISPGDGGVAAIELDGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK +VEHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVVELADEREAVVTAEVTR +ERIDEVRKFLPSLANRRTDVL +>PROKKA_00165 +MRIAVGQFGPTGRVEDNLEAMGRLAARAAAEGAGLLVLPEEAMLTFREVEDEFAHAVAGS +WEPFTEGLARLARQHGLAIVAGGYEPSATDRPYNTLVAVDADGAVAGAYRKLHLYDAFEH +RESELITPGDRGLVTVEVGGLTVGLQTCYDLRFPEVSRALALAGAQVLAIPAAWFAGEHK +VDHWRTLLRARAVENTVWVAAADTASAATVGHSAIIDPLALTLAEADDDAAPETLLCADV +TAERVEEVRRTVPVLANRRTDVLTPPVDVEPGG +>PROKKA_00178 +MRISVGQFGPVGDVEANLAVMARLAARAAGEGADLLVLPEEAMLGAREVGEEFPDAVAAA +WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH +RESDRITPGDGGVAAIELGGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK +VDHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVAELADEREAVVTAEVTR +ERIDEVREFLPSLANRRTDVL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000292.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000292.fa new file mode 100644 index 0000000000000000000000000000000000000000..63c3100076094594ea5a604d61d8c79a61587ca3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000292.fa @@ -0,0 +1,25 @@ +>PROKKA_00183 +MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD +DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVATPPDSAVYLAIV +EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV +VGALSTLVPAYRCTDELADRCGAALVAATHELAHLLGAADTPRERPADSPGKPKARS +>PROKKA_02179 +MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD +DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVTTPPDSAVYLAIV +EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV +VGALSTLVPAYRCTDELADRCGAALVAATGELAHLLGAADTPRERPADSPGKPKASS +>PROKKA_00218 +MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD +DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVTTPPASAVYLAIV +EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV +VGALSTLVPAYRCTDELADRCGAALVAATDELAHLLGAADTPRERPADSPGKPKASS +>PROKKA_00163 +MPTTPPASTRTVDRALALLAAVVAQPRLSLAEAARATDLPASTALRLLRSLETAGFVDRQ +EEGEYRPGARLIQLGARAFSREPLVRLARAPMDGVAEATGESVYLSLRNGAQEAVYIAIV +EGTHSVRHASWVGRTVPLEGTAVGEVYRGEVPPGGYAHGGHSVEQDVTALSSPVVVGGRV +VAALSALVPDYRCTAEHADRCGRALAGATTRLASALGEEAPPEDAD +>PROKKA_00180 +MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD +DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVTTPPDSAVYLAIV +EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV +VGALSTLVPAYRCTDELADRCGAALVAATHELAHLLGAADTPRERPADSPGKPKASS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000293.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000293.fa new file mode 100644 index 0000000000000000000000000000000000000000..4571e7a858dc2f59fc5fa730af9c534b24f40d0e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000293.fa @@ -0,0 +1,55 @@ +>PROKKA_00184 +MAVGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA +ARSWEAYDAIVATLKDLEEDETLLVQSGKPVGVFRTNKWAPRVLIANSNLVGDWATWPEF +RELEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKRYDGSLQGTLTLTGGCGGM +GGAQPLAVTLNGGVCLIVDVSEDRLRRRMGKRYLDEVETDIDKAVERVMQAKNDGEAVSV +GLVGNAAEVFPELLERQKAGTVEIDIVTDQTSAHDPLSYLPIEIDEKDWHAEAEADPDTF +TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC +EGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY +GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA +LTATSSGATWVSIHHGGGVGIGRSIHAGQVGVADGTELAAAKLEALLTNDPGMGVIRHVD +AGYSRAAEVAKERGVRVPMEATIRD +>PROKKA_02180 +MAEGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA +ARSWEAYDAIVATLKDLEEDETLLVQSGKPVGVFRTNKWAPRVLIANSNLVGDWATWPEF +RKLEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKRYDGSLQGTLTLTGGCGGM +GGAQPLAVTLNGGVCLIVDVSEDRLRRRMGKRYLDEVETDIDKAVERVMQAKRDGEAVSV +GLVGNAAEVFPELLERQKAGTVEIDIVTDQTSAHDPLSYLPIEIDEKDWHAEAEADPDTF +TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC +EGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY +GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA +LTATSSGATWVSIHHGGGVGIGRSIHAGQVGVADGTELAAAKLEALLTNDPGMGVIRHVD +AGYSRAVEVAAERGVRVPMEATIRD +>PROKKA_00217 +MAVGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA +ARSWEAYDAIVATLKDLEEDETLLVQSGKPVGVFRTNKWAPRVLIANSNLVGDWATWPEF +RKLEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKRYDGSLKGTLTLTGGCGGM +GGAQPLAVTLNGGACLIVDVSEGRLRRRMGKRYLDEVVTDIDKAVERVMQAKRDGEAVSV +GLVGNAAEVFPELLERQKRGEIEIDIVTDQTSAHDPLSYLPIEIDEADWQAEAEGDPETF +TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC +EGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY +GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA +LTATSSGATWVSIHHGGGVGIGRSIHAGQVGLADGTELAAAKLEALLTNDPGMGVIRHVD +AGYSRAAEIAAERGVRVPMEATIRD +>PROKKA_00162 +MAAGFTQHDPSRTIRAPRGTELNAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA +ARSWEAFDAIVETLKDLEEDETLLVQSGKPVGVFRTNVWAPRVLIANSNLVGDWADWKTF +RELEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKKYDGTLKGTLTLTGGCGGM +GGAQPLAVTLNGGVCLIVDVSEERLRRRMGKRYLHEVETDIDAAIARVMQAKRDGEAVSV +GLVGNAAEVFPELLKRQKAGEVEIDIVTDQTSAHDPLSYLPIEIEEKDWHAEAEADPDTF +TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC +EGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY +GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA +LTATSSGATWVSIHHGGGVGIGRSIHAGQVGLADGTELAAAKLTALLTNDPGMGVIRHVD +AGYSRAVEVAAERGVRIPMEPTVRD +>PROKKA_00181 +MAVGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA +ARSWEAYDAIVATLKDLEEDETLLVQSGKPVGVVKTNVWAPRVLIANSNLVGDWADWKTF +RELEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKRYDGSLKGTLTLTGGCGGM +GGAQPLAVTLNGGVCLIVDVSEDRLRRRMGKRYLDEVETDIERAVERVMQAKRDGEAVSV +GLVGNAAEVFPELLERQKAGTVEIDIVTDQTSAHDPLSYLPIEIDEKDWHAEAEADPDTF +TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC +EGLGPFRWAALSGDPEDIRVTDAALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY +GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA +LTATSSGATWVSIHHGGGVGIGRSIHAGQVGVADGTELAAAKLEALLTNDPGMGVIRHVD +AGYSRAAEVAKERGVRVPMEATIRD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000295.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000295.fa new file mode 100644 index 0000000000000000000000000000000000000000..534fa380ce3afa0f35b7306779e94994204d3f97 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000295.fa @@ -0,0 +1,40 @@ +>PROKKA_00186 +MRSTLITDIAELTTVDPEGRVLTDAAVVVEDERIAWIGPAADAPEADDRVSVEGRAVLPG +WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDARLAELVRGRVADAVA +GGTTYLETKTGYGLTVEEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV +GPMLAAVREHVGWVDVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE +FGAASVDHVNHLSDADVEALAGTWADWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL +LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGALGLRAQDRVG +SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV +>PROKKA_02182 +MRSTLITDIAELTTVDPEGRVLTDAAVVVEDERIAWIGPAADAPEADDRVSVEGRAVLPG +WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDARLAELVRGRVADAVA +GGTTYLETKTGYGLTVAEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV +GPMLAAVREHVGWVDVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE +FGAASVDHVNHLSDADVEALAGTWADWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL +LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGAIGLRAQDRVG +SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV +>PROKKA_00215 +MRSTLITDIAELTTVDPEGRVLTDAAVVVEDERIAWIGPAADAPDADDRVSVEGRAVLPG +WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDDRLAELVRGRVADAVA +GGTTYLETKTGYGLTVEEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV +GPMLEAVREHAGWADVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE +FGAASVDHVNHLSDTDVEALAGTWTGWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL +LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGALGLRAQDRVG +SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV +>PROKKA_00160 +MASTLITDIAELTTVDPEGRVLRDAAVVLDDEDVAWIGPAAQAPAADERVSVAGRAVLPG +WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGLTMEATRAASDERLRELVLGRVADAVR +GGTTYLETKTGYGLTVEEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDVEDYLDDVV +GPMLEAVREHVGWVDVFCDTGAFDAAQTRRVLAAGVAAGLRARLHGNQIEQGPGVALAVE +FGAASVDHVNHLSDADVEALAGTWSGWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL +LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGAIGLRAQDRVG +SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV +>PROKKA_00183 +MRSTLITDIAELTTVDPEGRVLQDAAVVVEDERIAWIGAAADAPDADDRVSVGGRAVLPG +WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDDRLAELVRGRVADAVA +GGTTYLETKTGYGLTVAEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV +GPMLEAVREHAGWVDVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE +FGAASVDHVNHLSDADVEALAGTWTGWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL +LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGAIGLRAQDRVG +SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000296.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000296.fa new file mode 100644 index 0000000000000000000000000000000000000000..3ec58d759c2485f86b3dc01d2f6dd7482cf69a4c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000296.fa @@ -0,0 +1,50 @@ +>PROKKA_00187 +MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV +STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR +PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGTDGALRPAGEA +LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR +VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR +DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER +RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ +EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV +PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH +>PROKKA_02183 +MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV +STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR +PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGEDGALRPAGEA +LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR +VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR +DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER +RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ +EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV +PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH +>PROKKA_00214 +MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV +STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR +PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGADGALRPAGEA +LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR +VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR +DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER +RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ +EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV +PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAWKSEGTEAEGH +>PROKKA_00159 +MTTTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGVSTG +FGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVRPVV +VETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGADGALRPAGEALAE +AGIEPVELREKEGLALVNGTEGMLGMLIMALADLDELVDTVDLTAAMSVEALLGTDRVFV +PELHLPLRPHPGQAASADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLRDTL +AYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSERRTD +RMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQEDH +VSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGVPGP +GPDQYMAPQLAAAEQALRDGSVLAAVAEALAGASADAEPQDLAEESAGAEAEGH +>PROKKA_00184 +MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV +STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR +PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGTDGALRPAGEA +LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR +VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR +DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER +RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ +EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV +PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000297.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000297.fa new file mode 100644 index 0000000000000000000000000000000000000000..9b9f9bf0605015fd10eae7d1a39b247bf1a23e78 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000297.fa @@ -0,0 +1,36 @@ +>PROKKA_00192 +MTSELPSSSLSPAWTGRTDGDTPEHLRWHQVVRPADGRGEPTTPQRDPGAGAPTSGARST +ALIGFASDEGVRRNHGRVGAEDGPEALRGALASLAYLEGTGALVDAGDVSVDRGDDDAPG +ELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYASITGLTGSTRVAAGTRVGILNLDAH +FDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGISEANNTRALFDTARERGVTWVTDE +QAQTADVTGVRRWVRSFINAVDVLYLTIDLDVLPAAVAPGVSAPAGFGVPYEVIHACALE +ATQSGKLALADVVELNPALDVDGRTAKAAARLIHTIVSRHRTDASLLA +>PROKKA_02188 +MTSELPSPSLSPAWTGRTDGDTPEHLRWHQVVRPADGRGEPTTTQRHPGAGAPTSGARST +ALVGFASDEGVRRNHGRVGAEDGPEALRGALASLAYLEGTGALVDAGDVSVDRGDDDAPG +ELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYASITGLTGSTRVGAGTRVGILNLDAH +FDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGISEANNTRALFDTARERGVTWVTDE +QAQTADVTGVRRWVRSFINAVDVLYLTIDLDVLPAAVAPGVSAPAGFGVPYEVIHACALE +ATQSGKLALADVVELNPALDVDGRTAKAAARLIHTVVSRHRTDASLLA +>PROKKA_00208 +MTSELPSPSLSSAWAGRTDGDAPEHLRWHQVVRPADGRGEPTTTQRHPGAGAPTSGARST +ALVGFASDEGVRRNHGRVGAEDGPEALRGALASLAYLEGTGALVDAGDVSVDRGDDDAPG +ELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYASITGLTGSTRVGEGTRVGILNLDAH +FDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGISEANNTRVLFDTAREHGVTWVTDE +QAQIADVTGVRRWVRSFIDAVDVLYLTVDLDVLPAAVAPGVSAPAGFGVPYEVIHACAVE +AATSGKLALADVVELNPSLDVDGRTAKAAARLIHTIVSRHRTDASLLA +>PROKKA_00155 +MSGVVRPSLRTRPSMAWNGAMTADRASELPSAALSPAWTGRTDGDAPEHLRWHQVVRSAD +GGAPAQTVDAAPARSTALVGFASDEGVRRNHGRVGAEDGPDALRGALASLAYLEGTGALV +DAGDVSVDRGDDDAPGELEAGQAELATVVSGLLNAHDLAVVLGGGHETAYASITGLTGST +RVAAGTRVGILNLDAHFDLREAPRPSSGTPFLQALRDAEEAEHQLSYAVVGISEANNTRA +LFDTARERGVTWVTDEQAQTADVTGVRRWVRSFIDAVDVLYLTIDLDVLPAAVAPGVSAP +AGFGVPYEVIHACTLEATQSGKLALADVVELNPALDVDGRTAKAAARLIHTIVSRHRTDA +SLLA +>PROKKA_00192 +MTSELPSSSLSPAWTGRTDGDTPEHLRWHQVVRPADGRGEPTTTQRHPGAGAPTSGARST +ALIGFASDEGVRRNHGRVGAEDGPEALRGALASLAYLEGTGALVDAGDVSVDRGDDDAPG +ELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYASITGLTGSTRVGAGTRVGILNLDAH +FDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGISEANNTRALFDTARERGVTWVTDE +QAQTADVTGVRRWVRSFINAVDVLYLTIDLDVLPAAVAPGVSAPAGFGVPYEVIHACALE +ATQSGKLALADVVELNPALDVDGRTAKAAARLIHTIVSRHRTDASLLA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000298.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000298.fa new file mode 100644 index 0000000000000000000000000000000000000000..79287d44e418796e294ec57dd78ef1adfc6a125a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000298.fa @@ -0,0 +1,20 @@ +>PROKKA_00193 +MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN +PVLAAAGKEILGHRVYASLDGLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW +NEDAARQAEAAGLEVVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR +>PROKKA_02189 +MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN +PVLAAAGKEILGHRVYASLDDLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW +NEDAARQAEAAGLEVVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR +>PROKKA_00207 +MSATHPERTWTGPSAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN +PVLAAAGQEILGHRVYASLDDLPVTPDLVEVFRKASDAPEMVADAARVGARTVWLQLGIW +NEDAARQAEAAGLEIVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR +>PROKKA_00154 +MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN +PVLAAAGKEILGHRVYASLDDLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW +NEDAARQAEAAGLEIVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR +>PROKKA_00193 +MSTTHPERTWTGPGAPERLAILRRTRSIAIVGASDKPARASYFVATYLLSSTTYDVYFVN +PVLAAAGKEILGHRVYASLDDLPVTPDLVEVFRKSSDAPEVVADAARVGARTVWLQLGIW +NEDAARQAEAAGLEVVMDRCVKIEHARFHGGLNLAGFVTGVISSRRQELDR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000299.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000299.fa new file mode 100644 index 0000000000000000000000000000000000000000..87ea18adf59d4253360a4640752ef43f5fdd6e51 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000299.fa @@ -0,0 +1,49 @@ +>PROKKA_00194 +MITQPALHATGRRRVTLCDVPTLPPARLARDNGADCPEASIERTPVADHEFGFRTQALHA +GAVPDAVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRIGNPTVAAFEERVATL +EGGIGAVATASGMAAEFVTFAALAAAGDHIVASSKLYGGTITQLDVSLRRFGVETTFVDS +AEAADFEAALQPNTKTVYTEIVANPSGDVVDLPGLADVAHRHGVPLVVDATLTPPYLIRP +IEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTEPVPSYGGVSWWGNFG +EYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLANAQAVAQWLDEDPRVS +WVRYAGLPDHPHHARAQQLLPRGVGSVFSIGVAPAATDTDDGASGPEAGRATASRFISAL +QLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPEDLIRISVGIEDTEDILWDLDQ +ALTEATGRTRDDDGAPAAPKEA +>PROKKA_02190 +MITQPALHGTGRRRVTLCDVPTLPPAHLARDNGRDCPEASIERTPVADHEFGFRTQALHA +GAVPDTVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRIGNPTVAAFEERVATL +EGGIGAVATASGMAAEFVTFAALAAAGDHIVASSKLYGGTITQLDVSLRRFGVETTFVDS +AEAADFEAALQPNTKTVYTEIVANPSGDVVDLPGLADVAHRHGVPLVVDATLTPPYLIRP +IEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTEPVPSYGGVSWWGNFG +EYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLANAQAVAQWLDEDPRVS +WVRYAGLPDHPHHARAQQLLPRGVGSVFSFGVAPAATDTDDGASGPEAGRATASRFISAL +QLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPEDLIRISVGIEDTEDILWDLDQ +ALTEATGRTRDDDGAPAAPKEA +>PROKKA_00206 +MADHEFGFRTQALHAGAVPDAVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRI +GNPTVAAFEERVATLEGGIGAVATASGMAAEFVTFAALAGAGDHIVASSKLYGGTITQLD +VSLRRFGVETTFVDSVEAADFEAALQPNTKAVYTEIVANPSGDVVDLPGLADVAHRHGVP +LVVDATLTPPYLIRPIEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTE +PVPSYGGVSWWGNFGEYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLAN +ARAVATWLDEDPRVSWVRYAGLPDHPHHARAQQLLPRGVGSVFSFGVAPAATDTDDGASG +PEAGRATASRFISALQLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPADLIRIS +VGIEDLEDILWDLDQALTEATGRTRDGAVVPAEQEA +>PROKKA_00153 +MITQPALHGTGLRRVTLCDVPTLPPAHLARDNGTDCPEASIERTPVADHEFGFRTQALHA +GAVPDAVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRIGNPTVAAFEERVATL +EGGIGAVATASGMAAEFVTFAALAGAGDHIVASSKLYGGTITQLDVSLRRFGVETTFVDS +AEAADFEAALQPNTKAVYTEIVANPSGDVVDLPGLADVAHRHGVPLVVDATLTPPYLIRP +IEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTEPVPSYGGVSWWGNFG +EYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLANARAVATWLDEDPRVS +WVRYAGLPDHPHHARAQQLLPRGVGSVFSFGVAPAATDTDDGASGPEAGRATASRFISAL +QLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPADLIRISVGIEDLEDILWDLDQ +ALTEATGRTRDGAVVPAEQEA +>PROKKA_00194 +MITQPALHGTGRPRVTLCDAPTLPPAHLARDNGTDCPEASIERTPVADHEFGFRTQALHA +GAVPDAVHGSRAVPIHQTSSFVFESAEDAANLFALQKYGNIYSRIGNPTVAAFEERVATL +EGGIGAVATASGMAAEFVTFAALAGAGDHIVASSKLYGGTITQLDVSLRRFGVETTFVDS +AEAADFEAALQPNTKAVYTEIVANPSGDVVDLPGLADVAHRHGVPLVVDATLTPPYLIRP +IEHGADIVIHSATKFLGGQGTTLGGVVVESGRFPWDNGKFPSMTEPVPSYGGVSWWGNFG +EYGFLTKLRSEQLRDFGPSLAPQSAFQLLLGVETLAPRMDAHLANAQAVAQWLDEDPRVS +WVRYAGLPDHPHHARAQQLLPRGVGSVFSFGVAPAATDTDDGASGPEAGRATASRFISAL +QLASHLANIGDAKTLVLHPATTTHQQLTAEQLVAAGIPADLIRISVGIEDLEDILWDLDQ +ALTEATGRARDGAVVPAEQEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000300.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000300.fa new file mode 100644 index 0000000000000000000000000000000000000000..16274fa2fed16245c11f95156c707c9a0e5c54e3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000300.fa @@ -0,0 +1,35 @@ +>PROKKA_00195 +MTARTPLPSTLAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGIPDPCAPDGAAAL +VRLTGGVVSHVSAALWHGLPLPPRLARPAGLHLTFDRSARTHRTDLDGVVSHRVRLPSDH +VLELPDGQRVTTAARTWFDLAGMLRPHEVDWLIADGDHLVRPPWTPTGRADPVATVSELS +EVLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPASP +VVDLGYRGARLALQYDGAGHRTAQQQARDARRDAYCLEREWTTLRCTWEDQRAGFGRIVG +LVRRRLARTR +>PROKKA_02191 +MTARTPLPSTLAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGIPDPCAPDGAAAL +VRLTGGVVSHVSAALWHGLPLPPRLARPAGLHLTFDRSARTHRTDLDGVVSHRVRLPSDH +VLELPDGQRVTTAARTWFDLAGMLRPHEVDWLIADGDHLVRPPWTPTGRADPVATVSELS +EVLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPASP +VVDLGYRGARLALQYDGAGHRTAQQQARDARRDAYCLEREWTTLRCTWEDQRAGFGRIVG +LVRRRLARTR +>PROKKA_00204 +MTARAPLPPALARAAFGVDELLDAGLPWDRTRAADLHRIWRGVYTAADPAALTWDRAAAL +CRVTGGVISHTTAAAWHGIPLPRRLEASEELHLTVDRGRRQHRSARPGVVTHRLRLPPQE +IRQVGGGLRVTSPERTWLDLAVLLRPWELDWLVVAGDHLVHHPWHPDGRRPSATTPALLD +AALGRHVGRHGIRRAREALADVRVGADSAPETRLRLALIRAGLPEPALQIAVDPSDPRSP +EADLGYRDARIALQYDGAAHRTPEQQARDARREAYCLELDWLPLRCTQEDLREGFIRVIG +LVRRRLGPRGAFGATSRR +>PROKKA_00152 +MTARTPLPPALAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGVPDPCAPDGAAAL +ARLTGGVVSHVSAALWHGLPLPPRLARPAGLHLTFDRSARTHRSDLGGVVSHRVRLPSDH +VLELPDGQRVTTAARTWFDLAGMFRPHEVDWLIAAGDHLVRPPWTPTGRADPVATVPGLS +EVLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPASP +VVDLGYRAARLALQYDGAGHRTAQQQARDARRDAYCLEREWTTLRCTWEDQRAGFGRIVG +LVRRRLARTR +>PROKKA_00195 +MTARTPLPSTLAAGAFTTAELHAAGLPWRRTLAADLARICRGVHTAGVPDPCAPDGAAAL +VRLTGGVVSHVSAALWHGLPLPPRLTRPAGLHLTFDRSARTHRTDLGGVVSHRVRLPSDH +VLELPDGQRVTTAARTWFDLAGMLRPHEVDWLIAAGDHLVRPPWTPTGRAHPVATVPGLS +EVLARCRGRPGVRLARAALAEVRVGADSPPETFLRLALIRAGLPEPELQVAVDPADPASP +VVDLGYRGRAWPSSTTAPATARLSSRRGTPVGTRTASSGNGRPCAAPGRTSALGSGGSWG +WSGVGSPARADPPPRPTRVELSRVPSNAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000301.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000301.fa new file mode 100644 index 0000000000000000000000000000000000000000..9512bf968d17e6f3c427de2b1e8a24d3643b6cd5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000301.fa @@ -0,0 +1,20 @@ +>PROKKA_00196 +MPDDVAVRLLLIADTHIPRRARALPAQVWAEVARADVVLHAGDWVTEDVLDDLDARAARL +VGVWGNNDGPKLRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS +HIPWDTVAGPDTANPGLRLLNPGSCTDRRRQPVCTLMRAVVRGGRLEDVELVSVDRTP +>PROKKA_02192 +MPDDVAVRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDARAARL +VGVWGNNDGPGPRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS +HIPWDTVAGPETANPGLRLLNPGSCTDRRRQPVCTLIRAVARDGRLEDVELVPVDRTP +>PROKKA_00203 +MTTETRLLLLADTHIPPRARAMPAQVWDEVARADVVLHAGDWVEESVLDELEARSRRLVG +VWGNNDDGALRARLPEVARVEIGGVRIAMVHETGAARGRERRMAEAFPDADVLVFGHSHI +PWDTVAGPETANPGLRLLNPGSPTDRRRQPVCTLMRAVVRDGGLADVELVPVDRTP +>PROKKA_00151 +MTTRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDAQAARLVGVW +GNNDGPRLRARLPEVARVEIGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHSHIPW +DTVAGPETANPGLRLLNPGSCTDRRRQPVCTLMRAVVRGGRLEDVELVPVDRTP +>PROKKA_00196 +MPDDVAVRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDARAARL +VGVWGNNDGPGPRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS +HIPWDTVAGPETANPGLRLLNPGSCTDRRRQPVCTLIRAVARDGRLEDVELVPVDRTP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000306.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000306.fa new file mode 100644 index 0000000000000000000000000000000000000000..de65e30244a442ac2952ac41c1182a6967879d16 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000306.fa @@ -0,0 +1,27 @@ +>PROKKA_00208 +MAAAPCLGRQQPQEENMQRRRAVRAAGLGVVGALALAGCASEPQSAGEAWHQARTQLDEA +ETVRLETAYTTGRQGPHSVRWDIAGRLDGGDAESKGVMQVGRDSHITMESRQVGEDVFVR +VDVDGSDVPDDVQVMYSDPQWRRVPAGEGQEPPLKALLDQVGFPAADALDGAEVRAEEVD +WDDGTAYRYAVPEEVADAAMVEGDATRVHSFTVDDDGELVALTVDDGRATQQYALSDWNQ +IEPAEAPEEVAE +>PROKKA_02201 +MQRRRAVRAAGLGVVGALALAGCGSEPQSVGEAWHQARTQVDEAETVRLETAYTTGRQGP +QSVRWDIAGRLDGGDAESKGVMQVGRDSHITMESRQVGEDVFVRVEVDGSDVPDDVQLMY +ADPQWRRVSAGEGQEPPLKSLLDQVGFPAADALDGAEVRAEEVDWDGGTAYRYAVPEEVA +DAAMAEGDATRVHSFTVDDDGELVALTVDDGRATQQYALSDWNQIEPAEAPEEVAE +>PROKKA_00183 +MQRRRAVRAVGLGVAGVLALAGCAAEPQSAGEAWQQARTQLDEAQTVRLETAHTTGRQGP +NTVRWDIAGRLDGSNGDAKGVIQAGHESHMTMETRTVGEDSYVRVSIDGADFADDVQLAY +ADPQWRRTPAGQEQERPLKELLEQIGLPSADALEGAEVRAEEVGWAGETAHRYAVPQEVA +AAAMGQGDSTLLHSFTVDDDGGLLALTVDDGRSLRQYALSDWNEIDPAEAPEEVAE +>PROKKA_00129 +MQRRRAVHAAGLGVVAALTLAGCGTDQQDVGEAWQHARAQIDGAESVRMTMASVNDSQGP +SVVAWDVAGPLEGADGTTTGRMQVGRDSWMTVRSVSADGKTWARVDTEGQDVPEQIASMY +RTDGWTETQQSGQNALRATLDAVGLPAADALDGVDVQPEKVDWSGGTAYRYAMPGDVASA +ARGDSQFSVRAFTVDEDGDLVGLRVEDGGVIQEFALSDWNEIEPAEAPEEAQH +>PROKKA_00208 +MAAAPCLGRQQPQEENMQRRRAVRAAGLGVVGALALAGCASEPQSAGEAWHQARTQLDEA +ETVRLETAYTTGRQGPHSVRWDIAGRLDGGDAESKGVMQVGRDSHITMESRQVGEDVFVR +VDVDGSDVPDDVQVMYSDPQWRRVPAGEGQEPPLKALLDQVGFPAADALDGAQVRAEEVD +WDGGTAYRYAVPEEVADAAMAEGDATRVHSFTVDDDGELVALTVDDGRATQQYALSDWNQ +IEPAEAPEEVAE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000307.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000307.fa new file mode 100644 index 0000000000000000000000000000000000000000..8fa1773af3247fac7a532c5ac5b78c3bfca642f9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000307.fa @@ -0,0 +1,30 @@ +>PROKKA_00209 +MRQRQTQTRRTRRGLSLAALGAAALLLTGCASGDDAPGAWDRARTQLEEADSVRMVTELR +SEAPSNGRAVPDAVDISGPVDGSSMRYVSVYKDDGLITRDESRIVDGTAYSRFTVERVGA +SGEDHPAYAERWTATPYEGDPSATGMGAMVSSLLGSLPESGGLDDVEADADGIRRSGQDA +IRYVLDEPVSGPQEGVELTAFTVSKEDGRLLTVETESAGTKAVVTLSEMGGVDPVQAPPA +DEVLKQDG +>PROKKA_02202 +MRQRQTQTRRTRRGLSLAAVGAAALLLTGCASGDDAPGAWDRARTQLEEADSVRMVTELR +SEAPSNGRAVPDSVDISGPVDGSSMRYVSVYQDDGLITRDESRIVDGTAYSRFTVERAGA +SGEDRPAYVERWTATPYESDPRATGMGAMVSSLLGSLPESGGLDDVEADADGIRRSGQDA +IRYVLDEPVSGPQEGVELTAFTVSKEDGRLLTVETESAGTKAVVTLSEMGGVDPVQAPPA +DEVLKQDG +>PROKKA_00182 +MPRQNPTGRARRGLPLAALGAAAALVLTGCGASGEDASAAWDRARTQLEETDSVRMVTEL +RSDAPQAGNRTPESVDLSGPVDGSSMRYVSTYEDGDLITRDESRVVDGTAYSRFTVERRG +ASGEDRPAYVERWTAAPHTGDPRATGMGAMVSSLLGSLPESGGLEDVAVDADGIRRSGQD +AVRYVLDEPLSVADDGVAMTAFTVSEEDGRLLTVETESAGTKAVVTVSEMGDVEPLQAPP +SDEVLPQQQGQGAPGAVPPGGAPQDGTAPGGTPAEPVPPTDG +>PROKKA_00128 +MRPTTPRTPAPHGGARRRALSLAALGAAAALSLSACGASGEDASAAWDAARTQLQDASSV +RLTTEARNDSGAAPGTPDGVEIAGDVHSSDLSYTGVFRTDGYITRDESRTVGGQRYERFT +LEQPGGVSGEGRPAFAEKWKKAEPLPGDASMRSILDGVLTAVPQAGALQGADVRATDIRR +QGRDATRYVLDTPVKGGTTDSSLTAFTVADDDGTLLTVETTGPGTRGTVTFSDWNAVEPV +TAPATEDMAQDTATAK +>PROKKA_00209 +MRQRQTQTRRTRRGLSLAAVGAAALLLTGCASGDDAPGAWDRARTQLEEADSVRMVTELR +SEAPSNGRAVPDSVDISGPVDGSSMRYVSVYQDDGLITRDESRIVDGTAYSRFTVERAGA +SGEDRPAYVERWTATPYESDPRATGMGAMVSSLLGSLPESGGLDDVEADADGIRRSGQDA +IRYVLDEPVSGPQEGVALTAFTVSKEDGRLLTVETESAGTKAVVTLSEMGEVDPVQAPPA +DEVLKQDG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000309.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000309.fa new file mode 100644 index 0000000000000000000000000000000000000000..862a9828eef8879b693bd271fae41a30f535571b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000309.fa @@ -0,0 +1,70 @@ +>PROKKA_00211 +MSQQFNIETVADAQATPDVEQPWAELGLKENEYAEIKKILGRRPTAAELAMYSVMWSEHC +SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ +GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI +GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA +SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS +NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEYSWL +GEVTGDGRLIITWDGEVIVDVDPRTVAHDGPVYERPYARPAWQDELQADTFRSSEAGQDL +PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTALAAPDDAGVVRVDEETGIGVA +LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPEDPDVMWQFAEA +VRGLADGCQTLGIPVTGGNVSLYNQTGSTPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG +QAIYLLGETADELDGSEFARLRGHLGGLPPKVDLKKERLLGELLVNMSRDGMIDAAHDVS +GGGLAATLSEMVLRFGVGARVVLDEVLRRAGVDLFTALFSETQARAVVAVPRTEEVRFTD +MTTARGYAAVRIGVVDADSAALEVQDAFTLPIAELREAWEATLPKHFG +>PROKKA_02204 +MSQQFNIETVADAQATPDVEQPWAELGLKENEYAEIKKILGRRPTAAELAMYSVMWSEHC +SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ +GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI +GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA +SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS +NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEYSWL +GEVTGDGRLIITWDGEVIVDVDPRTVAHDGPVYERPYARPAWQDELQADTFRSSEAGQDL +PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTALAAPDDAGVVRVDEETGIGVA +LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPEDPDVMWQFAEA +VRGLADGCQTLGIPVTGGNVSLYNQTGSTPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG +QAIYLLGETADELDGSEFARLRGHLGGLPPKVDLKKERLLGELLVNMSRDGMIDAAHDVS +GGGLAATLSEMVLRFGVGARVVLDEVLRRAGVDLFTALFSETQARAVVAVPRTEEVRFTD +MTTARGYAAVRIGVVDADSAALEVQDAFTLPIAELREAWEATLPKHFG +>PROKKA_00175 +MSQQFSIETVADAAANPDIEQPWAELGLKENEYAQIREILGRRPTAAELAMYSVMWSEHC +SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ +GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI +GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGLGNKVVLFGARTGGDGIGGASVLA +SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFAGSLVEGIQDLGAAGISCATSELAS +NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPDNVAAFEAVMAKWDVEYSWL +GEVTGDGRLVITWDGEVIVDVDPRTVAHDGPVYERPYARPGWQDRVQADTFRASEAGADL +PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTAMAAPDDAGVVRVDEETGMGVA +LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPENPDVMWQFAEA +VRGLADGCQVLGIPVTGGNVSLYNQTGATPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG +QAIYLLGETADELDGSEFARLRGHLGGVPPKVDLAKERLLGELLVNMSRDGMIDAAHDVS +GGGLAATLSEMVLRHGVGARVVLDEVLRRDGVDLFTALFSETQARAVVAVPRTEEVRFTD +MTTARGYTVTRIGVVDADSAALEVQDAFTLPIAELREGWEATLPKHFG +>PROKKA_00124 +MSTQFTIETVEQAAANPDVAQPWAELGLKEDEYARIREILGRRPTAAELAMYSVMWSEHC +SYKSSKVHLRQFGDTLTEEMKEHMMVGIGENAGVTDLGDGWAVTFKVESHNHPSFVEPYQ +GAATGIGGIVRDIISMGARPVAVMDPLRFGAVDHPDTARVVHGVVAGIGGYGNSLGLPNI +GGEVAFDPSYQGNPLVNALAVGVLRHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA +SESFDDGGKPAKRPSVQAGDPFAEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS +NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEHSWL +GEVTGDGRLVITWDGETIVDVDPRTVAHDGPVYERPCHRPSFQDALQADTFRSSAAGQDL +PATGEELKAAVVELMASPNMADVSWITRQYDRYVRGNTALASPDDAGVVRVDEETGMGVA +VATDCNDRYAYLDPYAGAQLSLAEAYRNVTTTGAVPLAVTDCLNFGSPEDPEVMWQFAEA +VRGLADACQVLGVPVTGGNVSLYNQTGGVAIHPTPTVGVLGRFDDVLRRTPSGFGTDADG +QAVYLLGVTADELDGSEYANLRGHLGGVPPKVDLAQERLLGELLVNMSRDGMVDAAHDVS +KGGLAATLADMVLRFGVGARIVLDEVVRRDGVDVFTALFSETQGRTVVSVPRTEEVRFTD +MTTARGYTVTRIGVVDAQSDALEVQGQFTLPIAELREAWEATLPKHFG +>PROKKA_00211 +MSQQFNIETVADAQATPDVEQPWAELGLKENEYAEIKKILGRRPTAAELAMYSVMWSEHC +SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ +GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI +GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA +SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS +NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEYSWL +GEVTGDGRLIITWDGEVIVDVDPRTVAHDGPVYERPYARPAWQDELQADTFRSSEAGQHL +PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTALAAPDDAGVVRVDEETGMGVA +LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPEDPDVMWQFAEA +VRGLADGCQTLGIPVTGGNVSLYNQTGSTPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG +QAIYLLGETADELDGSEFARLRGHLGGLPPKVDLKKERLLGELLVNMSRDGMIDAAHDVS +GGGLAATLSEMVLRFGVGARVVLDEVLRRDGVDLFTALFSETQARAVVAVPRTEEVRFTD +MTTARGYAAVRIGVVDADSAALEVQDAFTLPITELREAWEATLPKHFG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000310.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000310.fa new file mode 100644 index 0000000000000000000000000000000000000000..6d25701ebfe6cbefe0b66879dd71804f6709b238 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000310.fa @@ -0,0 +1,30 @@ +>PROKKA_00212 +MTELPLIGDYSTPATPLSGARIGVITFPGTLDDVDALRAVRLAGAEPVSLWHADADPQRT +LAGVDAVVIPGGFSYGDYLRAGAIARFAPMMDAVATAAGGPEGEADGLPVLGICNGFQIL +TESHLLPGSMIKNDHLHFICRDQELVVESTDTVWTRDFEQGQTITVPLKNQDGQYVADET +TLDALEAEGRVVFRYQGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVETGFGPDTAAGP +RSGVDGLGFFTSVLTTLASRGGHA +>PROKKA_02205 +MTELPLIGDYSTPTTPLSGARIGVITFPGTLDDVDALRAVRLAGAEPVSLWHADADPQRT +LAGVDAVVIPGGFSYGDYLRAGAIARFAPMMDAVATAAGGPEGEADGLPVLGICNGFQIL +TESHLLPGSMIKNDHLHFICRDQELVVESTDTVWTRDFEQGQTITVPLKNQDGQYVADET +TLDALEAEGRVVFRYQGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVETGFGPDTAAGP +RSGVDGLGFFTSVLTTLASRGGHA +>PROKKA_00174 +MTTDLPLIGDYSTPTTPLNGARIGVITFPGTLDDVDALRAVRLTGAEPVSLWHADEDPQR +TLAGVDAVVIPGGFSYGDYLRAGAISRFAPMMDAVATAAGGPEGAADGLPVLGICNGFQI +LTESHLLPGSMIKNDHLHFICRDQELTVENTDTAWTRDYERGQTITVPLKNQDGQYVADD +ATLDALEAEGRVVFRYRGWNPNGSRRDIAGIANAAGNVVGLMPHPEHAVEPGFGPDTADG +PRTGTDGLGFFTSVLTTLASRGGHA +>PROKKA_00123 +MTEIPLIGDYSTPSTPLNGARIGVITFPGTLDDVDALRAVRLTGAEPVSLWHAEADAAAT +LATVDAVVIPGGFSYGDYLRAGAISRFAPMMGAVAQAAGGPEGSEDGLPVLGICNGFQIL +TESHLLPGSMIKNDHLHFICRDQQLAVESTDTAWTRDFEQGEVITVPLKNQDGQYVADEK +TLDALEAEGRVVFRYVGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVEAGFGPDTEAGP +RSGTDGLGFFTSVLTTLATRGGAA +>PROKKA_00212 +MTELPLIGDYSTPTTPLSGARIGVITFPGTLDDVDALRAVRLAGAEPVSLWHADADPQRT +LAGVDAVVIPGGFSYGDYLRAGAIARFAPMMDAVATAAGGPEGEADGLPVLGICNGFQIL +TESHLLPGSMIKNDHLHFICRDQELVVESADTVWTRDFEQGQTITVPLKNQDGQYVADET +TLDALEAEGRVVFRYQGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVEPGFGPDTAAGP +RSGVDGLGFFTSVLTTLASRGGHA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000311.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000311.fa new file mode 100644 index 0000000000000000000000000000000000000000..5d5247259631484636a65ae98e97162e2451458e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000311.fa @@ -0,0 +1,15 @@ +>PROKKA_00213 +MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTDEILAQAR +TAAEEMLSNPVIEDVVNVAVLDEAEGAR +>PROKKA_02206 +MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGKVTDEILAQAR +TAAEEMLSNPVIEDVVNVAVLDEAEGAR +>PROKKA_00173 +MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTDAVLDQAR +RAAEELLSNPVIEDVVNVAVLDEAEGAR +>PROKKA_00122 +MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTEEVLAAAR +TAAEEMLSNPVIEDVVNVAVLDEDAA +>PROKKA_00213 +MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTDEILAQAR +TAAEEMLSNPVIEDVVNVAVLDEAEGAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000316.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000316.fa new file mode 100644 index 0000000000000000000000000000000000000000..01cba00d5aa26f30855adb7332748ac8e8946261 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000316.fa @@ -0,0 +1,45 @@ +>PROKKA_00222 +MSLIVQKFGGSSVADAAGIQRVARRIADTVRAGNRVCVVVSAMGDTTDELLDLAAELTQD +APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMLTDTSYGRARIVKVNPHR +VQEALDAGRVAIVAGFQGMSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY +SADPRVVPTARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPLHVRSSFSDHEGTW +IMPDPNDTITLQEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAVSNVNI +DMIVQNISREGSGRTDISFTLPIVEGKDAMAALRAAQDRIGFQDIVSDPEIGKLSLIGAG +MRSNPGVSATFFKALADAGVNVDLISTSEIRISVVTAESKLDDAVRAVHAAFGLDAEEEA +TVYGGTGR +>PROKKA_02235 +MSLIVQKFGGSSVADAAGIQRVARRIADTVRAGNRVCVVVSAMGDTTDELLDLAAELTQD +APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMLTDTSYGRARIVKVNPHR +VQEALDAGRVAIVAGFQGMSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY +SADPRVVPTARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPLHVRSSFSDHEGTW +IMPDPNDTITLQEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAVSNVNI +DMIVQNISREGSGRTDISFTLPIVEGKDAMAALRAAQDRIGFQDIVSDPEIGKLSLIGAG +MRSNPGVSATFFKALADAGVNVDLISTSEIRISVVTAESKLDDAVRAVHAAFGLDAEEEA +TVYGGTGR +>PROKKA_00158 +MSLIVQKFGGSSVADAAGIQRVARRVADTVRAGHRVCVVVSAMGDTTDELLDLAAELTQD +APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMMTDTSYGRARIVKVNPHR +VQEALDAGGVAIVAGFQGVSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY +SADPRVVPSARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPIHVRSSFSDHEGTW +IMPDPNDTITLKEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAESNVNI +DMIVQNVSREGSGTTDISFTLPIVEGKDAMAALRAAQERIGFQDIVSDKEIGKLSLIGAG +MRSNPGVSATFFKALSDAGVNVDLISTSEIRISVVTAEDKLDDAVRAVHTAFGLDAEEEA +TVYGGTGR +>PROKKA_00116 +MRLIVQKFGGSSVADAEGIQRVARRIVATQQAGNQVCVVVSAMGDTTDELLDLAAELTAD +APAREMDILLSAGERISMSLLAMAIDAQGVPARSFTGSQAGMMTDAAYGRARIIEVNPHR +VRAALDEGAVAIVAGFQGMSRESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY +SADPRVVSSARKLPQLSSEETLELAASGAKVLHLRSVEYARRFGVPIHVRSSFSDHEGSW +IMPDPNDTIHLKEGAPMEQPIVAGVAHDRSEAKVTIVGVPDVPGKAAEIFRVIAESNVNI +DMIVQNVSRQDSGRTDISFTLPIVEGKAAIEALRAAQESIGFEEIVPNKEIGKLSLIGAG +MRSNPGISATFFKALSDAGVNVDLISTSEIRISVVTSEDKLDDAVRAVHTAFGLDTDVEA +TVYGGTGR +>PROKKA_00223 +MSLIVQKFGGSSVADAAGIQRVARRVADTVRAGNRVCVVVSAMGDTTDELLDLAAELTQD +APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMLTDTSYGRARIVKVNPHR +VQEALDAGRVAIVAGFQGMSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY +SADPRVVPTARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPLHVRSSFSDHEGTW +IMPDPNDTITLQEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAVSNVNI +DMIVQNISREGSGRTDISFTLPIVEGKDAMAALRAAQDRIGFQDIVSDPEIGKLSLIGAG +MRSNPGVSATFFKALADAGVNVDLISTSEIRISVVTAEDKLDDAVRAVHAAFGLDAEEEA +TVYGGTGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000317.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000317.fa new file mode 100644 index 0000000000000000000000000000000000000000..a34d7c7fafb985be9a014f218f02befe844f49bc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000317.fa @@ -0,0 +1,40 @@ +>PROKKA_00224 +MSTAVATSIHDRRPPQPQPGGRLGAAQAVATVVGMELRQRLRSRGWYVLLGVFFVVVGAV +TLGALGLRGLGVAEMEASGLEPELAEQQMRALGRTLFDGVLLFVLTLSLLVSPALAANAI +SGDRAGGTLAITQVTLLRTGHLMAGKWLAAWIASAAFPAAALPWLAVAAVVGRVSPWAVL +VGLVMILVEFGMIAGIGVAVSAIAGRTLFAVVVTYLIVAALTIGTLVAFGLSLQFLQTEV +RANEADYGSTTAEPFTEAELEKMTPEEAEQAWAEWEAAHPELYDGIADRCVGPVTTRTIP +DPRRSGWLLAANPYAVLADASPWEGGLLEDGTRAEPGPLNLLSVGLRWTQRDPVRDVECL +DGELRGLDQSGVPDRQGTWPVWPLGLAMQGVLVAGLGWWGHRRLDTPAGRLPAGTRVA +>PROKKA_02237 +MSTAVATSIHDRRPPQPQPGGRLGAAQAVATVVGMELRQRLRSRGWYVLLGVFFVVVGAV +TLGALGLRGLGVAEMEASGLEPELAEQQMRALGRTLFDGVLLFVLTLSLLVSPALAANAI +SGDRAGGTLAITQVTLLRTGHLMTGKWLAAWIASAAFLAAALPWLAVAAVVGRVSPWAVL +VGLVMILVEFGMIAGIGVAVSAIAGRTLFAVVVTYLIVAALTIGTLVAFGLSLQFLQTEV +RANDAEYGSMTAEPFTEAELEKMTPEEAEQAWAEWEAAHPELYDGIADRCVGPVTTRTIP +DPRRSGWLLAANPYAVLADASPWEGGLLEDGTRAEPGPLNLLSVGLRWTQRDPVRDVECL +DGELRGLDSTGVPDRQGTWPVWPLGLAMQGVLVAGLGWWGHRRLDTPAGRLPAGTRVA +>PROKKA_00156 +MSTVVADPTRQGPPPLRPPGGGRLSTASAVRTVVGMELRQRLRSRGWYVLLGVFFLVVGA +VTLGALGLRATTLGDLQSQGMDPAAAEVQMRSAGQWLFDGVLLFVLTLSLLVSPVLAANA +ISGDRAGGTLAITQVTLLRTGQLMAGKWIAAWIASAAFLVAALPWLAVAAVVGRVSPLFV +LVGLLMILVEFGVITGIGVAVSAIAGRTLFAVVVTYLIVAALSIGTLVAFVLSLQFLQTD +VRANMPEHDGMTMADPLEGQDVENMTQAEIDAAWAEWERQNPDAYDGIADACVGPVGVQS +VPDPRRVGWLLAANPYAVLADASPWDPTGASMQFTPETGPLNMMSAALRLTQQDPAETTE +CLDGQLRRIDTTSVPDREGTWPVWPLGLAMQAALTGGLLWWGHRRLDTPAGRLPAGTRVA +>PROKKA_00114 +MSAVLHTPPPAAAPAGGPTPLGSGRLGVVDALRTLVGMELRQRLRSRGWYILLGVFFLLV +GGVTLGALGLHAWTGGNSPDSTMVFGRWLYDGVLLFVLTLCLLVSPALSANAISGDRSAG +TLAITQVTLVSTWQLMLGKWLAAWIAAVAFLVAAAPWLIVAAVVGQVPPLAVLAGLAMIL +VEFAVVTGIGVAVSAITGRTLFAVVVTYLLVAMMTIGSLIAFTISLQFIETRLQTNQVTY +GYAEDAGSTKSCAGPLRDTTVPDPRRVAWLLAGNPYVVVADAVPLPELREDSAGEEFGAL +NLISLGMRVAQIDPREYTDCVDGQVNEGSVTDSPVTLVDRTWPTWPLGMLLQGGFLAALL +WWGRRRLDTPAGRLPTGTRVA +>PROKKA_00225 +MSTAVATSIHDRRPPQPQPGGRLGAAQAVATVVGMELRQRLRSRGWYVLLGVFFVVVGAV +TLGALGLRSLGVTEMEASGLEPELAEQQMRALGRTLFDGVLLFVLTLSLLVSPALAANAI +SGDRAGGTLAITQVTLLRTGHLMAGKWLAAWIASAAFLAAALPWLAVAAVVGRVSPWAVL +VGLVMILVEFGMIAGIGVAVSAIAGRTLFAVVVTYLIVAALTIGTLVAFGLSLQFLQTEV +RANDAEFGSMTAEPFTEAELEKMTPEEADQAWAEWEAANPELFDGIADRCVGPVTTRTIP +DPRRSGWLLAANPYAVLADASPWEGGLVEDGTWAEPGPLNLLSVGLRWTQRDPVRDVECL +DGELRGLDQSGVPDRQGTWPVWPLGLAMQGVLVAGLGWWGHRRLDTPAGRLPAGTRVA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000320.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000320.fa new file mode 100644 index 0000000000000000000000000000000000000000..0cf06bcd1be3b7c59f683f8a2d7be13fbd9f8c82 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000320.fa @@ -0,0 +1,35 @@ +>PROKKA_00228 +MPAGRYAPSPTGSLHLGNLRTALVAWLAARATNRAFLLRVEDLDRVRSGAEADQRADLAA +VGLDWDAEPVRQSERTALYDAAVAALRAVHGPDAVYECFCSRKDIAEATSAPHPRPDDGA +PASGGAVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDVAKVAGLPAGETPRATAVD +VLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAEAL +CAARGEPTPAVEYLHVPLVLNAEGRRLAKRDGAVTLEDLSAQDPAWTPERVRDRLLESLG +LPAGPLAAAVPAFDPAALPRVPWVFTGL +>PROKKA_02241 +MPAGRYAPSPTGSLHLGNLRTALVAWLAARATDRAFLLRIEDLDRVRSGAEAGQRADLAA +VGLDWDAEPVRQSERTALYDAAVAALRAAHGADAVYECFCSRKDIAEATSAPHPRPDDGA +PASGGAVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDAAKVAGLPAGEIPRATAVD +VLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAEAL +CDGRGEPTPAVEYLHVPLVLNAEGRRLAKRDGAVTLEDLAAQDPAWTPERVRDRLLESLG +LPAGPLAAAVPAFDPAALPRDPWVFTGL +>PROKKA_00153 +MPAGRYAPSPTGALHLGNLRTAIVAWLAARATDRTFLLRVEDLDRVRSGAEAAQLSELAA +VGLDWDAEPVRQSERTGLYDDAVAALRAAHGADAVYECFCSRKDIAEATSAPHPAPADDD +GAPGPAGAAPLRPPGFYPGTCRGLTAAQRAERRRVRPAALRIDAVQVAGLPEGEIPRAEA +VDLLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSTPRQRWLAA +ALCAARGEALPQTSYLHVPLVLNAEGRRLAKRDGAVTLEDLAAADPSWTPERVRDRLLSS +LGLPPGPPADAVPAFARMLEDGSLPREPWMFDPAAFAGA +>PROKKA_00110 +MPAGRYAPSPTGTLHLGNLRTALVAWLAARATGRTFLLRIEDLDRVCSGAEAGQLADLAA +VGLDWDGEPVHQSERTALYDAAVAALRAAHGADAVYECFCSRKDIAEATSAPHPRPDDGA +PASGGTVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDAAKVAGLPAGEIPRATAVD +VLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAEAL +CVARGEPTPAVEYLHVPLVLNAEGRRLAKRDGAVTLGDLAAQDPAWTPARLRDRLLESLG +LPAGPLAVAVRAFDPAALPRDPWVFTGL +>PROKKA_00229 +MPAGRYAPSPTGSLHLGNLRTALVAWLAARATDRAFLLRVEDLDRVRSGAEAGQRADLAA +VGLDWDAEPVRQSERTALYDAAVAALRAAHGADAVYECFCSRKDIAEATSAPHPRPDDGA +PASGGTVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDVAKVAGLPAGEIPRATAVD +VLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAEAL +CSARGEPTPAVEYLHVPLVLNAAGRRLAKRDGAVTLEDLAAQDPAWTPERVRDRLLESLD +LPPGPLAAAVPAFDPAALPRDPWVFTGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000325.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000325.fa new file mode 100644 index 0000000000000000000000000000000000000000..3a7a9c68d678076d6738cd110b8fbed0dd471b70 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000325.fa @@ -0,0 +1,39 @@ +>PROKKA_00234 +MPLARLRAALPAAALSLLLLTGCTATDDGVTPASDADTSASVSTMPITSTPSVDAAATSR +AAASSLAASSSAAQSSRAAASSSSGAAESRAAEGSRSAEPAAPAAPADVEGDVVTVESIS +DGDTLRVTLGEVSTRVRLLNIDTPETHHPSKPVECMGPEATAALKSMISPGDTVVLRYDR +RLYDRYDRLLAGVYADGVLLNAEMARLGYGEPAVFDGNDRFLPEVEAAWEQARANGVGRF +SGECGTAAEPIPEAAPAPAPEAAPAAGDAGPVSGADSVCPDSHPVKANDNSGIYHMPGQQ +HYGKTNARHCYASASAAQAGGYRAARR +>PROKKA_02247 +MPLARLRAALPAAALSLLLLTGCTATDDGVTPESAADTSASVSTMPTTPTPSVDAAATSR +AAASSLAASSSAAQSSRAAASSSSGAAESRAARAAEESRTAEGSRSAEPAAPAAPADVEG +DVVTVESISDGDTLRVTLGEVSTRVRLLNIDTPETRHPSKPVECMGPEATAALKSMISPG +DTVVLRYDRRLYDRYDRLLAGVYADGVLVNAEMARLGYGEPAVFDGNDRFLPEVEAAWEQ +ARANGVGRFSGECGAAAEPIPEAAPAPAPEAAPASGDAGPVRGADSVCPDSHPVKANDNS +GIYHMPGQQHYGKTNARNCYASAAAAQADGYRAARR +>PROKKA_00137 +MTPRLFPRAGLVAAAALSLVLTGCTPAASGDDVAAPASAGAPSSGAAATTAAPAVSSTAS +AEAADRSRAAESSRAAAQASEAEQSRRAEESRAAEARRAEESRAAEASREAERSRRAEES +RAAAAAAAEEEDLDAAGSAEDAAWGGTAGVEGDVAVVQSVADGDTLRVSLDGVSTPVRLL +NIDTPETVHPSKPVQCQGPEATAALKSMIGPGDTVVLRYDRRVYDRYDRLLAGVFADGRL +VNAEMARLGLGEPVVFDGNVRFLPEVEAAWEQARADGVGLFSGECAVEEAPEPVEDEAPT +AVAEPAPAPAAGSGPVPGADFVCPDDFPVKGNDNSFIYHVPGQQHYGRTNARNCYASAAA +AEVDGYRAAKR +>PROKKA_00102 +MPSSRPPAPRVRTRLLVSAALVLLAATGCTASPATSSSTSSTSSAAPAALAASASPPASG +ASSAAAVEGDAATVVRVVDGDTVDVRRGAEDVRVRLLNIDTPETKHPSRPVECLGPEATR +KLEELLRPGDEVVLQYDEERFDRYGRTLAGVVEGETLVNAEIVRAGLGVPVVFEPNRRFL +PPVEAAWAEAQREGAGLNQPGLECSLQTLQESVAQDPAPAAVSELAQALEAVEAEGQEWM +KVHYAAVIPLAVSLVQQHGGRADVPSAGAASVAPRASTAPAVPAAPQAPAVGAGSDAAER +DRQRAAEAQAAADRAERKRQAEARAEAQRQAQAQEQVQARERAAQASREAEAAASAREKQ +KGASSGSSTAKGFADTSARDTSSGSPSSSGGTSQKAPNRCYAPGGETFVYCGEGSTGSSS +GGSSSSASAGASSSGAGTSSGGAGGPVSGADGVCPAGYPVKVSSSGKYHVPGGQYYDDTS +AKRCYASTAAAAADGAVASKR +>PROKKA_00235 +MPLARLRAALPAAALSLLLLTGCTATDDGVTPESDADTSASVSTMPTTPTPSVDAAATSR +AAASSLAASSAAQSSRAAASSSIEAAQSRAARAAEESRTAEGSRSAEPAAPAAPADVEGD +VVTVESISDGDTLRVTLGEVSTRVRLLNIDTPETHHPSKPVECMGPEATAALKSMISPGD +TVVLRYDRRLYDRYDRLLAGVYAEGVLLNAEMARLGYGEPAVFDGNDRFLPEVEAAWEQA +RANGVGRFSGECGTAAEPIPEAAPAPAPEAAPAAGDAGPVSGADSVCPDSHPVKANDNSG +IYHMPGQQHYGKTNARHCYASASAAQAGGYRAARR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000328.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000328.fa new file mode 100644 index 0000000000000000000000000000000000000000..9f8bec473d98c99252d54ef79ebad668e4210759 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000328.fa @@ -0,0 +1,30 @@ +>PROKKA_00238 +MKILVLAKQVPDTWQERELSLETGWVVRDGAAEPVPDEISERVMEVALGWRDAGADIEVV +ALTVGPEDSSKTLRKMLAMGADSAVQITDDALVGSDAVQTARVIAAAVEKEGADLVLAGT +VSTDGGTGVVPAMVAELLERPYLPHAEAPELADGELIGTVATSDADVRAAVALPAVASLT +EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGEKI +TDDGTAAERLVEFLAGRGLV +>PROKKA_02251 +MKILVLAKQVPDTWQERELSLETGWVVRDGAAEPVPDEISERVMEVALGWRDAGADIEVV +ALTVGPEDSSKTLRKMLAMGADSAVQITDDALVGSDAVQTARVIAAAVEKEGADLVLAGT +LSTDGGTGVVPAMVAELLERPYLPHAEAPELADGELTGTVATSDADVRAAVALPAVAGLT +EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGEKV +TDDGTAAERLVEFLAGRGLV +>PROKKA_00133 +MKILVLAKQVPDTWQERELSLDTGWVVRDGAAEPVPDEISERVMEVALGWRDAGTDAEIV +ALTVGPEDSSKTLRKMLAMGADAAVQVTDDALVGSDAVETARVIAAAVEREGADLVLAGT +VSTDGGTGVVPAMVAELLDRPYLPHAEAPQLADGELTGTVATSDADVRAAVALPAVAGLT +EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGAKV +SDDGTAAQQLVDFLAGRGLV +>PROKKA_00098 +MKIAVLAKQVPDTWQERTLDMETGMAVRDGAAEPVPDEIGERVMEVALAAREAGLEAEIV +AVTMGPADATKTLRKMLAMGADSAVHVVDDALDWSDAVQTARVLAAAVEHLGVDLVLAGS +ESTDGATGVVPAMVAELLDRPLLPSVEAVEITPEEVRGVLVTEDARLRASVPVPAVVALT +EKTAEPRFPNFKSIMAAKKKPLETLTLADLGLTAGPLDADRRSVMVSAAARRERAAGEKI +VDDGTAGEQVAAFLAARGLV +>PROKKA_00239 +MKILVLAKQVPDTWQERELSLETGWVVRDGAAEPVPDEISERVMEVALGWRDAGADIEVV +ALTVGPEDSSKTLRKMLAMGADSAVQITDDALVGSDAVQTARVIAAAVEKEGADLVLAGT +LSTDGGTGVVPAMVAELLERPYLPHAEAPELADGELTGTVATSDADVRAAVALPAVAGLT +EKTAEPRFPNFKNIMAAKKKPLTVLSLADLGIAAGPAEAAYRSVMVSADTRPERAAGEKV +TDDGTAAERLVEFLAGRGLV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000329.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000329.fa new file mode 100644 index 0000000000000000000000000000000000000000..c41825d0ee08dc610a7f8e7c91cf6940ae411860 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000329.fa @@ -0,0 +1,35 @@ +>PROKKA_00239 +MSANVEETEMTTQTDAANSGQTVLVHAEIGADGALRPVVAELLGAAATVGVPEAVLVTGA +EGRDAAVARLGEYGATRVHVLVADDAATTLGDAAVQALAAAAARTAPVAVLLSGSPESRA +VAGRLSVRARGPVCTDAVGLRWADDEVIARHSVFGGDYLSESTGEGGPRIITMRPGAVAD +RAPAVEAPEVVELAAAELGPVTAGARVLEVNARTQNSARPPLRGAKTVVAGGRGVGSEEG +FAIVEQLADELGAAVGASRAAVDSGYTAAERQVGQTGVIVSPNLYIALGISGAIQHLAGM +KTAKTIVAIDKNEDAEIFEHADFGVVGDIFQVVPQVIEQLRTRRG +>PROKKA_02252 +MSANVEETEMTTQTDAANSGQTVLVHAEIGADGALRPIVAELLGAAATVGVPEAVLVTGA +EGRDAAVARLGEYGATRVHVLVADDAATTLGDAAVQALAAATARTAPVAVLLSGSPESRA +VAGRLSVRARGPVCADAVGLRWADDEVIARHSVFGGDYLSESTGEGGPRIITVRPGAVAD +RAPAVEAPEVVELAAAELGPVTAGARVLEVNARTQNSARPPLRGAKTVVAGGRGVGSEEG +FAIVEQLADELGAAVGASRAAVDSGYTAAERQVGQTGVIVSPNLYIALGISGAIQHLAGM +KTAKTIVAIDKNEDAEIFEHADFGVVGDIFQVVPQVIEQLRTRRG +>PROKKA_00132 +MSANVEESEMTMQNDAANSGQTVLVHAELGADGALRPVVAELLGAAATVGVPEAVLVTGA +ASQDAAVARLGELGAARVHVLVAEDAAGTLGDAAVQALAAVTARTAPVAVLLSGSPESRA +VAGRLSVRARGPVCADAVALRWADDEVIARHSVFGGDFLSESTGEGGPRIITMRPGAVSD +RAPAVASPEVVEVAAAELGAVTAGARVLETTRRVQQADRPALRGAKTVVSGGRGVGSEEG +FAIVEELADALGAAVGASRAAVDAGYTAADRQVGQTGVIVSPNLYIALGISGAIQHLAGM +KTAKTIVAIDKNEDAEIFEYADFGVVGDIFKVVPQVIEQLRARRG +>PROKKA_00097 +MTDLPVTPVLVLAELTAAGDLRPAVAEALGAAARVGVPHAVLVTDADADDALVARLGELG +AAVVHTAVAQDPAELGTAQVAALAAAVDAVLPEAVVLPNTPESRAVAGRLAVRARGAVTA +DAVGLHRADGEIVARHSVFGGDVLAESTVEGGPNIVTLRPGAVADRARPVAAPEVRPLDV +AGRTVTAGARILSSEPAAPSADRPDLRTARAVVAGGRGVGSAEGFTTLVEPLADALGAAV +GASRVAVDSGFTAPEGQIGQTGVTVAPDLYVALGISGAIQHLVGMKTSGTIVAVDSDEDA +AIFEHADLGVVGDVNEVVPQLIAALAARRG +>PROKKA_00240 +MSANVEETEMTTQTDAANSGQTVLVHAEIGADGALRPIVAELLGAAATVGVPEAVLVTGA +EGRDAAVARLGEYGATRVHVLVADDAATTLGDAAVQALAAATARTAPVAVLLSGSPESRA +VAGRLSVRARGPVCADAVGLRWADDEVIARHSVFGGDYLSESTGEGGPRIITVRPGAVAD +RAPAVEAPEVVELAAAELGPVTAGARVLEVNARTQNSARPPLRGAKTVVAGGRGVGSEEG +FAIVEQLADELGAAVGASRAAVDSGYTAAERQVGQTGVIVSPNLYIALGISGAIQHLAGM +KTAKTIVAIDKNEDAEIFEHADFGVVGDIFQVVPQVIEQLRTRRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000330.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000330.fa new file mode 100644 index 0000000000000000000000000000000000000000..6bcc730a5993a0594676c06f80149d59d8f77585 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000330.fa @@ -0,0 +1,52 @@ +>PROKKA_00240 +MPKQRMAGYVPLKGAPAETEPAPAPAQDTTTAAPASAAAAVPVAPTAPTSGLTPLSARRR +MAGYVPFAREAEWLGGAPAPAAGSIPAAAPARSVAPEPIAASASPTRAPAPAETEPVVPD +VAAVVASATGAPAAAGVGAPVESDLVPLAKRRRMAGYVPFAREGEWFTELAAVGGPTAPE +MVAQEVDAPEQATAEPTAEPAAAAPARPVVAELADVEPADAEPAVAAPVAAASAPEPAPT +APDTRSAPPASAVQPPRAATGTPARTAETDAAESAVPSRLRKALPAVAGVVVLALLAVLA +ARWLRSLDPVADFIATYDGHPVLPEGTPEGMPWWMGWQHFLNMFLMVLIIRTGLQIRHET +RPPANFTPTKDGLFSARGNTPKKFSLTIWMHQALDALWLLNGLIFVVLLIATGHWARIVP +TDPHVFQHALSAGIQYLSLDWPTENGWVHYNALQMLSYALVVFVAAPLAALTGWRMSSWF +PTEAKGLNKAFPMEVARKVHFPVMVFFVAFIVVHVFLVAFTGLLTNLNHMYTSRGGATDA +WGLVVFLVSVAVTAAAWFFLKPAFTAPVASRFGTVGR +>PROKKA_02253 +MPKQRMAGYVPLKGAPAETEPAPAPGQDTTTAAPASAAAAVPVAPTAPTSGLTPLSARRR +MAGYVPFAREAEWLGGAPAPAAGSIPAAAPARSVAPEPIAASASPTRAPAPAETEPVVPD +VAAVVASATGAPAAAGVGAPVESDLVPLAKRRRMVGYVPFAREGEWFTELAAVGGPTAPE +TAAQEVVAEPATAEPAAAEPADAEPAVAAPVAAAPAAEPAPTAPDTRSAPPASTAQPPRA +APGAATGTPARAAETDAAESAAPSRLRKALPAVAGVVVLALLAVLAGRGLRSLDPVADFI +ATYDGHPVLPEGTPEGMPWWMGWQHFLNMFLMVLIIRTGLQIRHETRPPANFTPTKDGLF +SARGNTPKKFSLTIWMHQALDALWLLNGVIFVVLLIVTGHWARIVPTDPHVFQHAVSAGI +QYLSLDWPTENGWVHYNALQMLSYSLVVFVAAPLAALTGWRMSSWFPTKATGLNKAFPME +VARKVHFPVMVFFVAFILVHVFLVAFTGLLTNLNHMYTSRGGATDAWGLVVFLVSVAVTA +AAWFFLKPAFTAPVASRFGTVGR +>PROKKA_00131 +MARRRRRPGGRSGLGHPAGAPAAAPAPIAASASPTQSPRPAEPAAAQPRLAEQDVAAAVA +RPAAAAPVAVESDLVPLGQRRRMGGYVPLAREGEWFAELAAADAAPAGETAEPTVLEAAH +DDAAPAAEAAVTEPAAPTTTAAAAAATTAAAQAPAAPAQPAAAAAAPTAPDTRSAPPASA +AQPPRAEPAAASGRPARATKKTDAAEEAPAPSRLRKALPLVAGVVVLALVAVLAARWLRT +LDPVADFIAAYDGHPALAEGTPVGMPPWLGWQHFLNMFLMVLIIRTGLQIRNETRPPANF +TPKKDGAFSARGNTPKKFSLTIWTHQALDALWLLNGVVFVVLLFVTGQWARIVPTDPYVF +HHAFSAGIQYLSLDWPTENGWVHYNALQMLSYTLVVFVAAPLAALTGWRMSSWFPTEAKG +LNRAFPMEAARKVHFPVMLFFVLFILTHVFLVFFTGALKNLNHMYTSRGDATDAWGLVVF +LVSVAVTAAAWFLLRPSFTAPAASKFGTVGR +>PROKKA_00096 +MPQRMQGYTEFRGEPWPPRDRVPQAPAPTTTPAVAADERRPGRRMVGYTAFRGEPWPPVR +EAAQPAPAPAAAASPAEVTEAAAAAVPLEATAPAGIAVPGRRMAGYTAFRGEPWPPARVG +AAPQAPEPAPMATVEPAVATGPTPTVEPVAAGAPETTPKPAPSTGRRVAAAVGGVVVLGL +LAVLGARWLLTLPEVAAFVARYPGVPRHPEVTPVGIPAWLAWQHFLNLFLLVLVVRTGLQ +VRHETRPPATFTPHQPGPFAPRSATGGTYSLTVWIHQALDALWLLNGLVFVVLLFATGHW +MRLIPTDPQTPQHMVSTALQYLSLQWPEHDGWLHYNALQMVTYAGVVFVLAPLAALTGFR +MSSWWPSRNTALSRGFPMELARRLHYPTMLAFVLFVVVHVVLVLFSGVLHELNAMFLARN +AADAWGLAAFLVGCAVIAAGWVLLKPAIVAPVAERFGRVSR +>PROKKA_00241 +MPKQRMAGYVPLKGAPAETEPAPAPAQDTTTAAPASAAAAVPVAPTAPTSGLTPLSARRR +MAGYVPFAREAEWLGGAPAPAAGSIPAAAPARSVAPEPIAASASPTRAPAPAETEPVVPD +VAAVVASATGAPAAAGVGAPVESDLVPLAKRRRMAGYVPFAREGEWFTELAAVGGPTAPE +MVAQEVVAEPATAEPAAAEPADAEPAVAAPVAAAPAAEPAPTAPDTRSAPPASTAQPPRA +VPGAATGTPARAAETDAAESAAPSRLRKALPAVAGVVVLALLAVLAGRWLRSLDPVADFI +ATYDGHPVLPEGTPEGMPWWMGWQHFLNMFLMVLIIRTGLQIRHETRPPANFTPTKDGLF +SARGNTPKKFSLTIWTHQALDALWLLNGVIFVVLLIVTGHWARIVPTDPHVFQHALSAGI +QYLSLDWPTENGWVHYNALQMLSYALVVFVAAPLAALTGWRMSSWFPTEAKGLNKAFPME +VARKVHFPVMVFFVAFIVVHVFLVAFTGLLTNLNHMYTSRGGATDAWGLVVFLVSVAVTA +AAWFFLKPAFTAPVASRFGTVGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000333.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000333.fa new file mode 100644 index 0000000000000000000000000000000000000000..49a85280494241fce92baf69c3c43946d35a7c5f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000333.fa @@ -0,0 +1,43 @@ +>PROKKA_00246 +MTTVLFLGLGHMGGPMAANLAAAGHRVLGFDLVPEALEKARAAGVETVTDTAAAAAEADV +VLTMLPHGRLVLDVYRGEDGDGGLLAAARPGTVFLDCSTIDVAEAREAAAAAEAAGMRAA +DAPVSGGQVGAEAGTLAFMVGASDEVYAEVLPLLEVMGARIVHCGAAGLGQAAKICNNMV +LGVTQIAVAEAFVLGERLGLQHQALYDVMSKASGQCWSLTTNCPVPGPVPGSPVNRDFQP +GFAGALMAKDLGLALAALDEQGVAADLGRLAQAKYAEYAAGEGAARDFSGIIEDIRASHT +DRSEA +>PROKKA_02258 +MTTVLFLGLGHMGGPMAANLAAAGHRVLGFDLVPEALEKARAAGVETVTDTAAAAAEADV +VLTMLPHGRLVLDVYRGEDGDGGLLAAARPGTVFLDCSTIDVAEAREAAAAAEAAGMRAA +DAPVSGGQVGAEAGTLAFMVGASDEVYAEVLPLLEVMGARIVHCGAAGLGQAAKICNNMV +LGVTQIAVAEAFVLGERLGLQHQALYDVMSKASGQCWSLTTNCPVPGPVPGSPANRDFQP +GFAGALMAKDLGLALAALDEQGVAADLGRLAQAKYAEYAAGEGAARDFSGIIEDIRASHT +DRSEA +>PROKKA_00123 +MSEKTATTTTAPVIPHFVHGERVDGSSGRHSDVYHPATGQVEGRVPLASVEEIDAALASS +EKGFAAWSALNPQRRGRILLKWVDLINENVDELATLLSQEHGKTVPDAKGDIQRGVEVVE +FAAGAPHLLKGEFSSNAGSGIDVHSIRQPLGIAVGITPFNFPAMIPLWKAGIALAAGNAF +VLKPSERDPSVPVRLAELALEAGMPAGALNVVHGDKTAVDALIEDPRVKAVGFVGSTPIA +QSIYAHAGRMGKRAQCFGGAKNHAVIMPDADLEMAADALVGAAFGSAGERCMAISVAVPV +GEETADRLVALLSERIRRLKVGPSLDESSDFGPVVSKDAKERIEGYIAAGAAAARRPGRG +RPRRRRRGPRGRLLRGRHPLRPRHRGHEHLPRGDLRPGALRGPRRGLRGGAHPRQRARVR +QRRGHLHPRRRRRPRLRHPRGDRHGGRQRADPRPDRLLHLRRLEGLRLRRPEPARHRRPE +VLHQDQDHHHALALGRARGRQLRDARRLLTAVHPLPQEDPMTTVLFLGLGHMGGPMAANL +AAAGHRVLGFDLVPEALEKARMAGIETVTDTAAAAAEADVVLTMLPNGRLVLDVYRGREG +APGLLDAARPGTVFLDCSTIDVAEAREAAQAAEAAGMRAADAPVSGGQVGAEAGTLAFMV +GAADEVYAEVLPLLEVMGGRIVHCGGSGLGQAAKICNNMVLGVTQIAVAEAFVLGERLGL +EHQALYDVMSKASGQCWALTTNCPVPGPVPGSPANRDFQPGFAGALMAKDLGLALAALDE +QGVAADLGRLAQAKYAEYAAGEGAARDFSGIIEDIRASHTDRSEA +>PROKKA_00092 +MSQSQTPSASLPGTVAFIGLGNMGGPMAANLVAAGVTVRGFDLVPAAVEAARATGVEIAD +DAASAVPGADVVITMLPNGALVRGVYEGTADAPGLLGAADPDTLFLDCSTISTSEAQEVA +ALAEAAGHRAADAPVSGGVVGAQAGTLAFMVGGSVEVFEEIRPLLEVMGSRIVHCGGNGL +GQAAKVCNNMLLAISQIGVAEAFVLGERLGLEHQVLFDVMSEATGRCWSLTANCPVPGPV +PTSPANRDFEGGFAGALMAKDLGLALKALDEQHVGAEMGRLAQRTYAAYADGEGARKDFS +GIIETVREAGKDTAA +>PROKKA_00246 +MTTVLFLGLGHMGGPMAANLAAAGHRVLGFDLVPEALEKARAAGVETVTDTAAAAAEADV +VLTMLPHGRLVLDVYRGEDGDGGLLAAARPGTVFLDCSTIDVAEAREAAAAAEAAGMRAA +DAPVSGGQVGAEAGTLAFMVGASDEVYTEVLPLLEVMGARIVHCGGAGLGQAAKICNNMV +LGVTQIAVAEAFVLGERLGLQHQALYDVMSKASGQCWSLTTNCPVPGPVPGSPANRDFQP +GFAGALMAKDLGLALAALDEQGVAADLGRLAQAKYAEYAAGEGAARDFSGIIEDIRASHT +DRSEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000336.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000336.fa new file mode 100644 index 0000000000000000000000000000000000000000..12e603f027f55414b547c960b652398a5b6ffadb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000336.fa @@ -0,0 +1,41 @@ +>PROKKA_00251 +MTAIADRPVPAPGAPAVTPGLPHVDLLRLRDRLEPVERARLDAIEDHLQTRVRPHLTRYW +DAEEFAFDLLPGLAELGLGRLVLDGSSSLFQQLVHAEIARVDLSLSALVGIHNELNLGMI +AGLGSERQKATWQGRLESFDALGAFCLTEPDHGSDIAGGLATTATRDGDEWVIRGAKRWI +GAGTIADVALVWARDTADGEIKGFVVPTDTPGYEATKISGKMGLRIMQNADITLDVRLPA +DAILPGATTFAATRALLRDSRMWVGWQGVGAQMGVLDVLRSYALRREQFGRPLAAFQLIQ +AQIAEVAGNLAASAGMMLQVDALRQEGRMEMMHAAMAKATSTRLARSSAALARDALGGNG +LLTEHEIAKIMGDVEAIYSYEGSYGMNTLIVGRALTGVSAFV +>PROKKA_02263 +MTALADRPLPATGAPAVPPGLPHVDLLRLRDRLEPVERARLDAIEDHLQTRVRPHLTRYW +DAEEFAFDLLPGLAELGLGRLVLDGSSSLFQQLVHAEIARVDLSLSALVGIHNELNLGMI +AGLGSERQKATWQGRLESFDALGAFCLTEPDHGSDIAGGLATTATRDGDEWVIRGAKRWI +GAGTIADVALVWARDTADGEIKGFVVPTETPGYEATKISGKMGLRIMQNADITLDVRLPT +DAILPGATTFAATRALLRDSRMWVGWQGVGAQMGVLDVLRSYALRREQFGRPLAAFQLIQ +AQIAEVAGNLAASAGMMLQVDALRQEGRMEMMHAAMAKATSTRLARSSAALARDALGGNG +LLTEHEIAKIMGDVEAIYSYEGSYGMNTLIVGRALTGVSAFV +>PROKKA_00119 +MTPHADLPHVDLLRLRDGLDPAERTRLEEVEEHLQTAVRPRLAPYWDAEEFAFDLLPGLA +GLGLGRLVLDGSSSLFQQLVHAEIARVDLSLSALVGIHNELNLGMIAHLGSDAHRDRWQA +RLESFDALGAFCLTEPEHGSDVAGGLATTATLDGDEWVIRGAKRWIGAGMIADVALVWAR +DTADGEIKGFVVPTDTPGYEATKITGKMGLRIMQNADITLDVRLPADAQLPGAATFDAAR +DLLRDSRMWVGWQGFGAQMGLLDSLRSYALEREQFGRPLAKFQLIQSAIAEVAGNLAATS +GMMLQVDALRQEGRMEMMHAAMAKATSTRLARASAALARDALGGNGLLTEYEVSKMMGDV +EAIYSYEGSYGMNTLIVGRALTGVSAFV +>PROKKA_00087 +MTPSPTPSPASAEPAASPATGVLTVAAAVHPGHAAAPAAAVTDGLPDVDLFDLRSLLSAE +ERAHLERIEAHLEEHVRPHLAEPWNTETLPMEMLPGLASVGLGELDFLGASRLFQNLVHV +AIARVDLSFSALVGIHNELNIGSIERFGTEEQKQRWVPALRRFEALGAFCLTEPDHGSDI +AGGVETTATPDGDGWILRGTKRWIGAGTVAAVALVWAKDVSDGEVKCFLVPTDAPGFSAS +KITGKTGLRIMQNADMVFDDVRLGPEALLPGAGSFDATREMLRDSRAWVGWQGVGVQQGI +LRTLREYALTRTQFGRPLAKFQLIQAAIAQVAGNLAAATGLMMQVQRLQDDGTLKMVHAA +AAKATSTRLARESAALARDAMGGNGIVASYEMARFMGDVEAIYTYEGTQSINALLVGRAL +TGVSAFV +>PROKKA_00251 +MTALADRPLPATGAPAVPPGLPHVDLLRLRDRLEPVERARLDAIEDHLQTRVRPHLTRYW +DAEEFAFDLLPGLAELGLGRLVLDGSSSLFQQLVHAEIARVDLSLSALVGIHNELNLGMI +AGLGSERQKATWQGRLESFDALGAFCLTEPDHGSDIAGGLATTATRDGDEWVIRGAKRWI +GAGTIADVALVWARDTADGEIKGFVVPTDTPGYEATKISGKMGLRIMQNADITLDVRLPA +DAILPGATTFAATRALLRDSRMWVGWQGVGAQMGVLDVLRSYALRREQFGRPLAAFQLIQ +AQIAEVAGNLAASAGMMLQVDALRQEGRMEMMHAAMAKATSTRLARSSAALARDALGGNG +LLTEHEIAKIMGDVEAIYSYEGSYGMNTLIVGRALTGVSAFV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000340.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000340.fa new file mode 100644 index 0000000000000000000000000000000000000000..fdf639b57d6403f9938e4cbc7c2da5a26eb95e6e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000340.fa @@ -0,0 +1,20 @@ +>PROKKA_00261 +MTTPAPVASAARARRRAARSGPRPQLRMGLNGFLVAWLLPNLVMAAVVAVLAVVPGLQAF +GSLTPLLTVVGVAGLVVGLPLCLLVNWAFRHVLNQWVHVLAYALIGMLYGLVVLTQGAAG +ILPMLIPVIGFPAAVLMALGRTAARPLVRTVTPEPSPAEPA +>PROKKA_02274 +MTTPAPVASAARARRRAARSGPRPQLRMGLNGFLVAWLLPNLVMAAVVAILAVVPGLQAF +GSLTPLLTVVGVAGLVVGLPLCLLVNWAFRHVLNQWVHVLAYALIGMLYGLVVLTQGAAG +ILPMLIPVIGFPAAVLMALGRTAARPLVRTVTPEPSPAEPA +>PROKKA_00106 +MGLNGFLVAWLLPNLVMAALVAVLAVLPGLQAFGSLTPLLTVVGIAGLVVGLPLCLLVNF +AFRHVLNQWVHVLAYALIGMLYGLVVLTQGAAGILPMLIPVIGFPAAVLMALGRMAARPL +VQVVTPGQEAEARSAAQTASPADPEPSERAARGA +>PROKKA_00076 +MTTPAPVKSTARARRKAARAVSGPRPRLRMGLNGFLVAWLLPNLLMAAVVLALTLIPSLQ +RFGTLTPLLTVVGIAGLVIGLPLCLLVNRAFRHVLNQWVHVLAYALVGMLYGLVVLAQGV +GGVLPMLIPVIGFPAAVLMGLGRLAARPLVDVVPGAEPRS +>PROKKA_00259 +MTTPAPVASAARARRRAARSGPRPQLRMGLNGFLVAWLLPNLVMAAVVAVLAVVPGLQAF +GSLTPLLTVVGVAGLVVGLPLCLLVNWAFRHVLNQWVHVLAYALIGMLYGLVVLTQGAAG +ILPMLIPVIGFPAAVLMALGRTAARPLVRTVTPEPSPAEPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000341.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000341.fa new file mode 100644 index 0000000000000000000000000000000000000000..0992987b83c892843b2f201f24362f8861311d03 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000341.fa @@ -0,0 +1,35 @@ +>PROKKA_00262 +MKLPSPAPSAPGEVHHSASSVPVDGVEAVFPALRQRALAPGGRLYGLAAAAAVGGLTLLD +PHARRGRERRALAELEAAVSGTVLAAETANALHTAAIADGEVAPSPAARALRGLGGLAVG +GAVAAVALRTAGLNDRIDGAVVRGLQRVGVPAPRVALAAAASLAMLLANEDARRTRRDAV +ELAVTGPAGLDEDPVDEVEPEATAELPVEVRVLLETLLDPALAEGRDLPGAEALRSQLPH +ARTVASVAEAIREAGEVPDWVPLVVQTDDDVRRAVPNDCVWPVRGRFASGSAGGHELELR +LQVIDGEIGALTVTLPADAEADSDAWDAFQEIESFPGVEDLAFHVDGDRRA +>PROKKA_02275 +MKLPSPAPSAPGEVHHSASSVPVDGVEAVFPALRQRALAPGGRLYGLAAAAAVGGLTLLD +PHARRGRERRALAELEAAVSGTVLAAETANALHTAAIADGEVAPSPAARALRGLGGLAVG +GAVAAVTLRATGLNDRIDGALVRGLQRVGVPAPRVALAAAASLAMLLANEDARRTRRDAV +ELAVTGPAGLDEDPVDEVEPEATAELPVEVRVLLETLLDPALAEGRDLPGAEALRSQLPH +ARTVASVAEAIREAGEVPDWVPLVVQTDDDVRRAVPNDCVWPVRGRFASGSAGGHELELR +LQVIDGEIGALTVTLPADAEADSDAWDAFQEIESFPGVEDLAFHVDGDRRA +>PROKKA_00105 +MRQNSPVPGSLPARYVDDPAAAFPALRQRALAPGGRPYGLLAAAVVGALTLVDPHRMGAA +ERRGLARTEAAASGAFVAAEAASSLRLAGLPGRVGPAAGGLAAGAATAALALSTVPLNDR +IDGALVRFLERAGASAPRAVLAGTAALSVLAGNESVRRERRNALEEAAWPAWDDLSEEEQ +SEPTAPLPVEVRVLLETLLDPALAEGRELPGAAALRAQLPHVRTVASMAEAIRDEDEVPD +WTPLVVETDGPVDRAVPHDHVWPVRGRFAVGEDGHEVELRLQVIDGELGALVITLPADED +ADPDAWDAFQELEAFPGVEDLTFQVDGERRD +>PROKKA_00075 +METPRTPETRTDPPADRLAEPQHPAHADAPVVHDTAVPESERIERTVSTRTGETRPPVVR +TVVTESERIERPVVEVRDARVPGRLLWWIGGGTLAAGSLAALVRVLRERLATPEPTPLER +LADAGRGAGLPLALSLAGTAAGVGVSLRARRRRRTEEVLAAPAVPFLLGEAVSAEAGEDD +VDGLPPVNEASDAYPAGALETEALPLEVVVLLDTLLDPSLDEGRELPGAAALRAQLPHVR +TAASVAEEIREDGKVPDWTPLVVEEETGVARAIPNDMVWPVRGRFTTEDGHELELRLQVI +DGELGALVITLPEDVEDGVAAWDAFQELEAFPGVEELTFTVDGDRRP +>PROKKA_00260 +MKLPSPAPSVPGEVHHSASSVPVDDAEAVFPALRQRALAPGGRLYGLAAAAAVGGLTLLD +PHARRGRERRALAELEAAVSGTFLAAETAGALHTAAIAEGEVAPSPAARALRGLGGLAVG +GAVAAVALRATGLNDRIDGAVVRGLQRVGVPAPRVALAAAASLAMLLANEDARRTRRDAV +ELAVTGPAGLDEDAVDEVEPEATAELPVEVCVLLETLLDPALAEGRDLPGAEALRSQLPH +ARTVTSVAEAIREAGEVPDWVPLVVETDDDIRRAVPNDCVWPVRGRFASGSAGGHELELR +LQVIDGEIGALTVTLPADAEADSDAWDAFQEIESFPGVEDLTFHVDGDRRV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000344.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000344.fa new file mode 100644 index 0000000000000000000000000000000000000000..75f60299a16d203ad4fbe5e2b6e00665b0f38eb2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000344.fa @@ -0,0 +1,15 @@ +>PROKKA_00265 +MDGMILINLKFTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYFLLEGF +TDEGAQAHVASPHFQEGLDAMRPLLASTPQIISEQVGAEGFGPMGELQID +>PROKKA_02278 +MDGMILINLKFTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYFLLEGF +TDEGAQAHVASPHFQEGLDAMRPLLASTPQIISEQVGAEGFGPMGELQID +>PROKKA_00098 +MDRMILINLKYTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYLLIEGF +TDEGAKAHVESPHFQEGIDAMRPLLASTPQIISEHVDAEGFGPMGELQID +>PROKKA_00069 +MILINLKFTVKPELADQWMDAVAKYIADVRSEPGNMFFEWYKPVEGGDNEFFLLEGFTDE +GAQAHVASPHFQEGIDAMRPLLQSTPQIISEQIGAEGFGPMGEIQID +>PROKKA_00263 +MDGMILINLKFTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYFLLEGF +TDEGAQAHVASPHFQEGLDAMRPLLASTPQIISEQVGAEGFGPMGELQID diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000347.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000347.fa new file mode 100644 index 0000000000000000000000000000000000000000..0581c3f44b0721354dc3b165b856a637cac45440 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000347.fa @@ -0,0 +1,40 @@ +>PROKKA_00268 +MTETLPTVEPEYDVATPLDTDFYLALADVSDAEKDVWRRARAFALEPDVLPRIREAWDRH +EYPLDLVARLGQADLLRDGVPVDGLPEISRVAAGLAMMELSRLDGSIATMTGVQGGLAMR +SIQLCGSEEQRAEHLPAMARGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLHGHKKW +IGNGAAGGVTVVWARSAEDEKVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVFV +PDADVLPEARSFKDTSRVLFATRVGVAWSALGKAVGCYEAAVHYAGQRVQFGRPLAAAQS +VQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASMAKYSATRAARSIAANARDLLGG +NGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV +>PROKKA_02281 +MTETLPTVEPEYDVATPLDTDFYLALADVSDAEKDVWRRARAFALEPDVLPRIREAWDRH +EYPLDLVARLGQADLLRDGVPVDGLPDVSRVAAGLAMMELSRLDGSIATMTGVQGGLAMR +SIQLCGSEEQRAEHLPAMARGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLHGHKKW +IGNGAAGGVTVVWARSAEDEKVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVFV +PDADVLPEARSFKDTSRVLFATRVGVAWSALGKAVGCYEAAVHYAGQRVQFGRPLAAAQS +VQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASMAKYSATRAARSIAANARDLLGG +NGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV +>PROKKA_00095 +MTENLPTAEPEYDVAAPLDTDFYLALGDVSDDEKEVWRRARAFALEPDVLPRIREAWDRH +EYPLDLVARLGAADLLRDGVPVDGLPEVSRVAAGLAMMELSRLDGSIATVAGVQGGLAMR +SIQLCGSDEQRAELLPAMSRGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLRGHKKW +IGNGAAGGVSVVWARSAEDEQVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVFV +PDADVLPEARSFKDTSRVLFATRVGVAWSALGQAVGCYEAAVQYAGQRIQFGRPLAAAQT +VQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASLAKYSATRAARSIAANARDLLGG +NGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV +>PROKKA_00066 +MTETLPTAEPDYSTITGPLDTDAYAVFAELPDEDLALARAARAFLTPEVQKRLQEAWDTG +EYPTELIAGLAEADLLRDGVAVEGKPAQSRLACGLAAMETSRIDGSLATVVGVQGGLAMR +SIEMCGSDEQKAKYLPAMDRGELFGAFALTEPTHGSDSVSLQTTATKVEGGWRISGHKKW +IGNGAAGGITVTWARSAEDGQVKGFIVQQDAEGYSAEVIRGKMSLRAIHQAHITYDDVFV +PDEDVMPGAQSFKNTAAVLFATRLGVAWAAVGHALGCYEAAVQYAKQRVQFGRPLAESQI +VQERLARMLSELTQVQLLVLRAARLEDAGKLTGPQASLAKYSATRTARSIAANARDLLGG +NGILLENEVGKHFADIEAIHTYEGTETVQALIVGRDITGVGAFA +>PROKKA_00266 +MTETLPTVEPEYDVATPLDTDFYLALADVSDAEKDVWRRARAFALEPDVLPRIREAWDRH +EYPLDLVARLGQADLLRDGVPVDGLPDVSRVAAGLAMMELSRLDGSIATMTGVQGGLAMR +SIQLCGSEEQRAEHLPAMARGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLHGHKKW +IGNGAAGGVTVVWARSAEDEKVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVFV +PDADVLPEARSFKDTSRVLFATRVGVAWSALGKAVGCYEAAVHYAGQRVQFGRPLAAAQS +VQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASMAKYSATRAARSIAANARDLLGG +NGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000349.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000349.fa new file mode 100644 index 0000000000000000000000000000000000000000..3ca17be1ba8a7b67897112f96654f9f2759a8e97 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000349.fa @@ -0,0 +1,45 @@ +>PROKKA_00270 +MPDTPQPPAVPAHPDHFGFEVTHRLETPGHDGAPLGRTGVITTPHGRIQTPAFIPVATQA +TVKAVLPESMKDLGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGPTFTDSGGFQVM +SLGSGFKKVIDMKGPGAPEGQGADDAVAPGKERLANVDDDGVWFKSHLTGDRHRFTPEVS +VGIQHNLGADIMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARLTGVRAARPYQA +LFGVIQGAQYEDLRRKACRDLAGMRAEFPAAGELDGVTSGFDGYGVGGALEKENLGTIVG +WCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFYTRDGRYNLPGA +KYRRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLLSIHNERFTVSLVDRIRAAM +QDGTLAELKAETLGRYYAPKG +>PROKKA_02285 +MPDTPQPPAVPAHPDHFGFEVTHRLETGGADGAPLGRTGVITTPHGRIQTPAFIPVATQA +SVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGPTFTDSGGFQVM +SLGSGFKKVIDMKGPGAPEGQGADDAVAPGKERLANVDDDGVWFKSHLTGDRHRFTPEVS +VGIQHNLGADIMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARLTGVRAARPYQA +LFGVIQGAQYEDLRRKACRDLAGMRAEFPAAGELDGVTSGFDGYGVGGALEKENLGTIVG +WCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFYTRDGRYNLPGA +KYRRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLLSIHNERFTVSLVDRIRAAM +QDGTLAELKAETLGRYYAPKG +>PROKKA_00087 +MPDTSPGPAPSSSSSGAPAHPSHFGFEVTHRLEAGGVDGAPLGRTGVISTPHGQIQTPAF +IPVATQATVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGPTFTD +SGGFQVMSLGSGFKKVIDMKGPSAPDGQGADDAVAPGKERLANVDDDGVWFKSHLTGDRH +RFTPEVSVGIQHRLGADVMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARLTGVR +AARPYQALFGVIQGAQYEDLRRKACRDLAAMRADFPSAGELDGVTSGFDGYGVGGALEKE +NLGTIVGWCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFYTRDG +RFNLPGAKYRRDFGPLDPACDCYTCAHYSRAYIRHLFKAKEMVAHTLISIHNERFTVSLV +DRIRAALQDGTYAELKEETLGRYYAPKG +>PROKKA_00064 +MPETSAPGTAGPTSSSAVTSDPAHPDHLGFEVRERLDAPGADGIALGRTGVLRTPHGEIQ +TPAFIPVATQATVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGP +TFTDSGGFQVMSLGSGFKKVIDMKGPAAPEGQGADDAVAPGKERLANVDDDGVWFKSHLT +GDRHRFTPERSLQIQHNLGADVMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARL +TAERAGRPYQGLFGVIQGAQYEDLRRKACRDLSGMTAEFAAAGERPATAHGFDGYGIGGA +IEKENLGTIVGWCAQELPEDRPRHLLGISEPDDLFRAVENGADTFDCVSPTRVARTGAFY +TRDGRYNLPGATYKRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLISIHNERFT +VSLVDRIRASIQAGTFAELKAETLGRYYAPKG +>PROKKA_00268 +MPDTPQPPAVPAHPDHFGFEVTHRLETGGADGAPLGRTGVITTPHGRIQTPAFIPVATQA +SVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGPTFTDSGGFQVM +SLGSGFKKVIDMKGPGAPEGQGADDAVAPGKERLANVDDDGVWFKSHLTGDRHRFTPEVS +VGIQHNLGADIMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARLTGVRAARPYQA +LFGVIQGAQYEDLRRKACRDLAGMRAEFPAAGELDGVTSGFDGYGVGGALEKENLGTIVG +WCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFYTRDGRYNLPGA +KYRRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLLSIHNERFTVSLVDRIRAAM +QDGTLAELKAETLGRYYAPKG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000350.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000350.fa new file mode 100644 index 0000000000000000000000000000000000000000..cb341c1739fe3ef27c8dff5963654f7312c0351d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000350.fa @@ -0,0 +1,30 @@ +>PROKKA_00275 +MTTPTGAIPSPHPRPFLLVQTRPEDDAAAAEVEAVQRLGGYPEGRLRVLRLDRVVQRPDV +ATHGLDWEAELADVAAVILPGSPFTGSDPEETKSPVQRAVEAELGRMLDVVRRRDLPFLG +CCYGVGTLGRHAGGVVDNAYGESAAPVEVTLTDEGAADPLLAGVPRTFAAYVGHKEAMSA +LPPGAVLLAAGTDCPVQMFRLGTRQYATQFHPELDQAGILERLEIYRDHGYFAPGEYEPT +VAGLAAVDPEHPRRILANFRTLFG +>PROKKA_02290 +MTTPTGAIPSPHPRPFLLVQTRPEDDAAAAEVEAVQRLGGYPEGRLRVLRLDRVVQRPDV +ATHGLDWEAELADVAAVILPGSPFTGTDPEETKSPVQRAVEAELGRMLDVVRRRDLPFLG +CCYGVGTLGRHAGGVVDNAYGESAAPVEVTLTDEGAADPLLAGVPRTFAAYVGHKEAMSA +LPPGAVLLAAGADCPVQMFRLGTRQYATQFHPELDQAGILERLEIYRDHGYFAPGEYEPT +VAGLAAVDPEHPRRILANFRTLFG +>PROKKA_00080 +MSTPSAPQPAPSADAPPSGRPFLLIQTRPEDEAARAEEEAVRRLGGFAEHQLAALRLDRT +LDADPDARQDWAALVAGHAGVILSGSPYTSSVPQETKDELQVAVELELGRMLDAVLDADA +PFLGCCYGVGTLGAHAGGTVDGTHAEPAGPTDVTLTEAGAADPLLEGLPPRFTAYVGHKE +GLTVPPPGAVVLATGEACPTQMFRLGRRQYATQFHPELDQVGLVERLRIYLHHGYVDPED +AEDTFARIESTPAPVPPRILENFRRVFG +>PROKKA_00063 +MTETTAPAADAAAPRPFLLVQTRPEEDAAAAEAESVRRLGGYDDATLRVLRLDRRVLDAE +GEAHAGAVDWEAELADVAGVILPGSPFTGSDPEESKSDLQVAVEAELGRLMALVLARQTP +FLGCCYGVGTLGRAAGGVVDTTYRELPGPIDVALTSEGLRDPLLEGMPAEFAAYVGHKEA +VRELPPGAVLLATGQACPVQMFRVGEHLYATQFHPELDQAGLLERLEIYADHGYFAAHEA +DDMFAAIRAREAPIPPRILERFRAIYG +>PROKKA_00273 +MTTPTGAVPSPHPRPFLLVQTRPEDDAAAAEVEAVQRLGGYPEGRLRVLRLDRVVQRPDV +ATHGLDWEAELADVAAVVLPGSPFTGSDPEETKSPVQRAVEAELGRMLDVVRRRDLPFLG +CCYGVGTLGRHAGGVVDNAYGESAAPVEVTLTDEGAADPLLAGVPRTFAAYVGHKEAMSA +LPPGAVLLAAGADCPVQMFRLGTRQYATQFHPELDQAGILERLEIYRDHGYFAPGEYEPT +VAGLAAVDPEHPRRILANFRTLFG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000353.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000353.fa new file mode 100644 index 0000000000000000000000000000000000000000..dfecc11dc4c38e0cc66b3fcf76d27d8d4354401a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000353.fa @@ -0,0 +1,15 @@ +>PROKKA_00280 +MPSYRARLQIGDLLPGHRPEEVMDLAEAAVQATHVLAAKDIEVVARVPRIVLRFTVPGSH +RAGEDAEAAEVARRMAEAVSGVAVTGRLDVLRRDGGRWVPVPAGLGR +>PROKKA_02295 +MPSYRARLQIGDLLPGHRPDEVMDLAEAAVQATHVLAAKDIEVVARVPRIVLRFTVPGSH +RAGEDAEAAEVARRMAEAVSGVAVTGRLDVLRRDGGRWVPVPAGLGR +>PROKKA_00073 +MPSYRARLQIGDLLPGHRPEEVMDLAEAAVQATHVLAAKDIEVVARVPRIVLRFTVPGSH +RAGEDAEAAEVARRMAEAVSGVAATGRLDVLRRDGGRWVPVPAGPGR +>PROKKA_00059 +MPSYRARLQIGDVLPGHRPEEVLDTAEAAIGATHEVAAKDVEVVARVPRIVLRFTVPAAH +RAAEDAEAAAVAGRMAEAVADVATVGRLDVLRREGGRWLPVSAR +>PROKKA_00279 +MPSYRARLQIGDLLPGHRPDEVMDLAEAAVQASHVLAAKDIEVVARVPRIVLRFTVHGSH +RAGEDAEAAEVARRMAEAVSGVAVTGRLDVLRRDGGRWVPVPAGPGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000354.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000354.fa new file mode 100644 index 0000000000000000000000000000000000000000..19806a4182a5cecae4222bed84506c486715cc3d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000354.fa @@ -0,0 +1,74 @@ +>PROKKA_00281 +MQDASSESRAALERLRAASAPRPDDAETRAPAARPRRALAAPGEISRRDLRRHERALRSG +RSETAAERRVREDHRADVHRAMDRLRTPGAPAEQRPRRDLSEILDRLGSPDLARFADPLV +GTVERILPAPGRDPEKAAEAARRRTAAEERRRARLRAGRAAEHERPVAEAAAAAQARDAA +RARDAAALQARLDEEARRAQAARVARRRREEEKQRRRREAERRRRVAAEEKARAAAEAEA +RRREREERRRREAEVAAERARVQAERRAREEAALAERERLRLEAEAEAERRRQAAEAERR +RLEAERVEAERRRRAEEAERRRREAEEAARLEAERRRRQAARVRAHTVLHAERALAQARL +LEDRAREAERRAAEDAARRRREHEERESRALARAARELEGPEVFPAAADRPLLSDPEERL +TDEELFARARVALPEWRRRQRLSTKAQAVRAEATAHSSAGPVTGALPLIPGYTPAPPEEP +AGSPTAADRRGQALLTVVWALFVLSGAWGLGLAGRVPGLGALDAGAYPLTADGRHGPGAS +VFGLSPLHPAIWPVLWLLTGMYVLRQWGRGQGASPRHRRIRGAIAGALLALALWFPLAVL +APGGFDVVPWLLALVLMLRVVRRLGARPAARRVARVAEDGALGVLLGTLLAGAPTAVGAA +LHAWGVHVGWFPTELLALLVLVALLLAALRLVLGGRGRMGVALGMAWTLLCLALPRLLPS +PLGAQQSVWVGLAAAFGALLLVTAAAVRRSWARQIERDAARRPHPAGA +>PROKKA_02296 +MQDASSESRAALERLRDASAPRPDDDATRAPAERPRRALAAPGEISRRDLRRHERALRSG +RPETAAERRVREDRRADVHRAMDRLRTPGAPAQQRPRRDLSEILDRLGSPDLARFTDPLV +GTVERILPAPGRDPEKAAEAARRRTAAEERRRARLRAGRERAAEAARRRAAEHERPVAEA +AAAAQARDAARARDAAALQARLDEEARRAQAARVARRRREEEKQRRRREAERRRRVAAEE +KARAAAEAEARRREREERRRREAEVAAERARVQAERRAREEAALAERERLRLEAEAEAER +RRQAAEAERRRLEAERVEAERRRRAEEAERRRREAEEAARLEAERRRRQAARVRAYTVLH +AERALAQARLLEDRAREAERRAAEDAARRRREHEERESRALARAARELEGPEVFPAAADR +PLLSDPEERLTDEELFARARVALPEWRRRQRLSTKAQAVRAEATAHSSAGPVTGALPLIP +GYTPAPPEEPAGSPTAADRRGQALLTVVWALFVLSGAWGLGLAGRVPGLGALDAGAYPLT +ADGRHGPGASVFGLSPLHPAIWPVLWLLTGMYVLRQWGRGQGASPRHRRIRGAIAGALLA +LALWFPLAVLAPGGFDVVPWLLALVLMLRVVRRLGARPAARRVARVAEDGALGVLLGTLL +AGAPTAVGAALHAWGVHVGWFPTELLALLVLVALLLAALRLVLGGRGRMGVALGMAWTLL +CLALPRLLPSPLGAQQSAWVGLAAAFGALLLVTAAAVRRSWARQIERDAARRPHPAGA +>PROKKA_00072 +MQDPSSESHAALERLRGAPKPVPAPEEAAGAPRTPDQDDDGAATAEDPVPAAARTPADDP +APAPSPSPPQDAETAPAPDASPASDADAPADVEADVEAPRPARRATPPRPRRPRPDLPPR +PAPPRARPAHRLSPRRPMRGACARAAARTSTRRWSGRAPPAPPRSSAPRRDLSDILDRLG +SPDLARFTAPLVGTVERILPAPGADPQKAAQAARRREEAEARRRARLQSGRERAAESARR +RAAEHDRLAAEAAEREAALRDDDARSEARRADEEAAAAKEACRQERLRERRTAGRAAAEE +RARLAAEAVEADRERERREAEEAAAAAAREEAALQARLQEEARARRERAEQEERLAQERA +AEEARLAQAARIARRRREEERERQRREAERRRRLAQEAKARAAADQEKRRQQEQERRRRE +AKVAEERARVQAERRAREEAELAERERRRLEAEAEAERRRQAQEAERRRREAERAEAERR +ARAEEAERRRREAEEAARRAAEARRLHAERTRAHTVLHAERALAQARLLEDRARDAERRA +AEEEARRLREHQDRESRALYRAARELEGPEVIPAASQRPLLARPEEGLTDEELVARARQA +LPEWRHRQRLATKARAVGAETAAGRSAGPPTGPVPLIPGYTPAAPEEPAGPATVRDRRGQ +LVLTLAWAAFVLAGVWGLGLFRFVPGLDALDAGPYPAAGDGRHGSGATVFSLFPLHPVIW +PVLWLLTGLHVARQWGPGQGAAPRHRRTRGPMAGTLLALALWFPLTVLVPWGLESVLWLV +ALALMLGAVRRLGARPAAGRLARLAEDGAPGALLGTLLAGAPTALAATLHAWGVHVGRFP +TELVAALVLLTLLPGAVRLVLGGRGRMGVAVGMAWTLLCLALPRLLPSPLGAQQSAWVGF +AAAFGALLLLTAAAVRRSWVRQIERDAARRPPPAVA +>PROKKA_00058 +MTSQDDDAPRPAPPAPRHAARPRRALAEPGRLAPEQLERHTRRLRGEPLPPETPEEAAAR +AGRRHDLAAALDRLPAESAPAAPRPRADLSDLLDRIGTPDLARFADPLLGTVGRILPSGP +SPERAAAAARRRAEHEGRRRAERAAGRARAAEAARRRAEETARREAEAAERARAARTVEE +SRAEAVRAAEDAAREAERHRAERLRERREAARAAAADKARRVAEAAERARVEEEALLAVE +ADAQAREVAAAQAEPDALARERRERADQEERRRRAALLARRRRDEERRRRRREAERARRE +AEEQRERAARAERSAAEAARRRQAEEAAEAERRQMAVEAARARAEAERLAQEAARERRRR +IAAARALPRTVAARHIAAGTAAEDRRRQAAARASEEAARVLAAHHDRETRALMAAARELD +GPDVVPPAHLRPLLADPAEGLDDAALLERARAALPQWRRTGRLLTKADAVRAQTAHGAAD +GTGPATGAFPIVPGYVPPSGPPEPRAPATREDRRHQLELTGAWLLFVLASAWGLGLFRLV +PGLRVVDQGSYTAAHGGRYAFTTSVLSLFPLHPAVWPVLWLALGVYVAHQWGPGQGAAAR +QRQTRRSVAGALALTALWFPLAVLVPWGLEFMVWLAALALMIRVMRGLTAVPARTRAAQT +CTDGVLGGFLGLLLAAAPTTLASPVAATGVFWGWFPSALVAAALLWAVVLTGARLALQDR +GRLGLALGMAWTLLCLALPRLLPSPLGAWQSAWVGLSAVAGGLGVLLLVVVRRTWVREIE +EQAAAAPQGVPAGRVNGR +>PROKKA_00280 +MQDASSESRAALERLRGASAPRPDDDATRAPAARPRRALAAPGEISRRDLRRHERALRSG +RPETAAERRVREDRRADVHRAMDRLRTPGAPAEQRPRRDLSEILDRLGSPDLARFADPLV +GTVERILPAPGRDPEKAAEAARRRAAAEERRRARLRAGRERAAEVARRRAAEHERLAAEA +AAAAQARDAARARDAAALQARLDEEARRAQAARVARRRREEEKQRRRREAERRRRVAAEE +KARAAAEAEARRREREERRRREAEVAAERARVQAERRAREEAALAERERLRLEAEAEAER +RRQAAEAERRRLEAERVEAERRRRAEEAERRRREAEEAARLEAERRRRQAARVRAHTVLH +AERALAQARLLEDRAREAERRAAEDAARRRREHEERESRALARAARELEGPEVFPAAADR +PLLSDPEERLTDEELFARARVALPEWRRRQRLSTKAQAVQAEATAHSSAGPVTGALPLIP +GYTPAPPEEPAGSPTRADRRGQTLLTVAWALFVLSGAWGLGLAGRVPGLGALDAGAYPLT +ADGRHGPGASVFGLSPLHPAIWPVLWLLTGMYVLRQWGPGQGASPRHRRIRGAVAGTLLA +LALWFPLAVLAPGGLDVVPWLLALVLMLRVVRRLGARPAARRLARVAEDGALGVLLGTLL +AGAPTAVGAALHAWGVHVDWFPTELLALLVLMALLLAALRLVLGGRGRLGVALGMAWTLL +CLALPRLLPSPLGAQQSAWVGLAAAFGALLLVTAAAVRRSWARQIERDAARRPHPAGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000356.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000356.fa new file mode 100644 index 0000000000000000000000000000000000000000..3aece0d0ac32e0c746faeff1be28b0ed29dc9095 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000356.fa @@ -0,0 +1,47 @@ +>PROKKA_00284 +MADPFPKDPEGAVVALVLAGGTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLR +DVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQGRAEEGFARGNGHAIAQQLPL +LEQFGAETVVVLSADHLYQLDLRPVLAEHARSGAELTVVTTETDEDPSRFGVVQVDDDGA +VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSS +LGDYGESIIPAFVARGRVREHRLVGYWRDIGTLDAYVRAHREILDGTGLDLAAEGWPLIT +NPHQAPPAWVAPDARVSGSLLSPGCRIAGEVSDSVVGPGVVVAAGATVRGSLLLGDCEVP +AGAVLDTVVVDVGGAVPAREVTGRAAPAEEVVVLTPQDRGPAEDETTGSGRPGRSD +>PROKKA_02306 +MADPFPTDPEGAVVALVLAGGTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLR +DVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQGRAEEGFARGNGHAIAQQLPL +LEQFGAETVVVLSADHLYQLDLRPVLAEHARSGAELTVVTTETDEDPSRFGVVQVDDDGA +VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSS +LGDYGESIIPAFVARGRVREHRLVGYWRDIGTLDAYVRAHREILDGTGLDVAAEGWPLLT +NPHAAPPAWVAPEATVTGSLLSPGCRIAGEVTDSVVGPSVVVEAGAVVRGSILLGECTVP +SGAVLDTVIADVGAAIPAEGATGRAEPADEVVVLEPGERGPASSDETTGSGAPVRD +>PROKKA_00069 +MPEGDSLVRLAHRLRPVLAGRALTHADLRVPQHATADLTGWTVVEVEPRGKYLLMRLTPP +AGRPAARPLTLVSHLKMEGRWLVSALDARWGAPAWQVRAVLETADHRVLGAQLGMLTLVP +TDREDTVLGHLGPDLLDPAWDGSEEAAAALLAEGTRRLTARPERPVGLALLDQRTTCGIG +NIYRCESLLLAGIDPHRPVGAVPDVPGLLTIARDLLRANVPPAAPFLGWPRTTTGVRANP +DRPYGIEVVVADRGFPPGLPAAVGSGTAADPAADPGADRTASGPALGRPPARPPADPGAA +GRRRTGCTGTTAPPACAAAGACARRTSAPPRTTRGSCGGARPASGEPRPNRGPGGGAPYA +ERRPSPQGRSARPPTPRRTRVADPFPDDPRSAVVALILAGGRGSRLAPLTDARSKPAVPF +AGQYRLIDVALTTVAHSGLQDAWIVEQYRPFTLNQHVAGGRPWDLDGTRHGLRVLPPAQG +RDEEGFAQGNGHAIHQQLAPLRRFGAKTVVIMSADHLYRMDLRPVLERHRERDAELTVVT +TQVAEGASRFGVVSSDADGRVTAYDYKPDEPATDVVATEVFVADVDALTEVIESLLDSAS +EEQVDDDDPAGAQLGDYGETIIPALVERGRVHEFRHEGYWKDVGTIDAYYQAHMALLRGD +GLDLDDPRWPLISNFHPRPPAFIHPEAEVNGSMLCPGSRVRGTVTESVIGPGVVVEAGAT +VHRSVLLGSATVPAGARLDAVIADVGARIPEGATGQTKPGPGNITVLTPDDRSTAEGDET +TGHA +>PROKKA_00049 +MADPFPKDPAGSTVALVLAGGRGSRLDPLTAARSKPAVPFAGQYRLIDVVLSNLAHSGLK +DVWIAEQYRPFTLNQHLAGGRPWDLDGTRHGLRILPPAEGREEEGFSAGNGHALAQQVPI +LRSFGAERVVVLSADHLYQLDLRPVLAAHADSGAELTMVTTVTDEDPSRFGVVQADEDGA +VTAYDYKPEDPEGRLVATEVFVFDVAALHEVVAELVAREKAAGEHADGEEDEDGDPVASS +LGDYGETIIPAFVERGRVREHRLEGYWRDIGTLDAFYRAHMELLDGAGLDLAAPGWPLLT +NPPAAPPARVGPRAEVSNALLSPGCVVKGTVEDSVLGPGVVVERGAHVRRSVLFGECIVP +RGARLDAVIADVGAHIPAEEVGRSRPGPGNLTVLTPATRDPDSEDETTGGAAAKDG +>PROKKA_00290 +MADPFPKDPEGAVVALVLAGGTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLR +DVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQGRAEEGFARGNGHAIAQQLPL +LEQFGAETVVVLSADHLYQLDLRPVLAEHTRSGAELTVVTTETDEDPSRFGVVQVDDDGA +VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSS +LGDYGESIIPAFVARGRVREHRLVGYWRDIGTLDAYVRAHREILDGTGLDVAAEGWPLLT +NPHAAPPAWVAPEATVTGSLLSPGCRIAGEVTDSVVGPSVVVEAGAVVRGSILLGECTVP +SGAVLDTVIADVGAAIPAEGATGRAEPADEVVVLEPGERGPASSDETTGSGAPVRD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000357.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000357.fa new file mode 100644 index 0000000000000000000000000000000000000000..7bc431403f00d3366d8b8e629a81413bb743d205 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000357.fa @@ -0,0 +1,20 @@ +>PROKKA_00288 +MSVRVLAIGKKHEAWVVDGIDRYERRLKKPYDLSWRLLPHSARQEEAARTEESDRILGAV +GADEHLILLDERGTAFDSPGLARHLQSRFDVGAPVTMVIGGAYGVDARVHARADRVWSLS +PLVFPHQLVRLILAEQVYRAQEISAGRPYHHA +>PROKKA_02310 +MSVRVLAIGKKHEAWVVDGIDRYERRLKKPYDLSWRLLPHSARQEEAARTEESDRILGAV +GADEHLILLDERGAAFDSPGLARHLQSRFDVGAPVTMVIGGAYGVDARVHARADRVWSLS +PLVFPHQLVRLILAEQVYRAQEISAGRPYHHA +>PROKKA_00066 +MSVRVLAIGKKHEAWVSEGIDRYERRLKKPYDLSWRLLPHSARQEEAARTEESDRILGAV +GADEHLILLDERGTAFDSPGLARHLQSRFDVGAPVTVVIGGAYGVDARVHARADRVWSLS +PLVFPHQLVRLILAEQVYRAQEISAGRPYHHA +>PROKKA_00045 +MMVLMAVRVVAIGKRHESWVSEGITRYEKRLKKPWDLTWQLLPHSSRQEDAARAEESERI +LAKVGPDEQLILLDERGRGFDSPGLSAHLQGQFDLGRTVTLVIGGAYGVDASVHARADRV +WSLSGLVFPHQLVRLILAEQVYRAQEIAGGRPYHHA +>PROKKA_00294 +MSVRVLAIGKKHEAWVVDGIDRYERRLKKPYDLSWRLLPHSARQEEAARTEESDRILGAV +GADEHLILLDERGAAFDSPGLARHLQSRFDVGAPVTMVIGGAYGVDARVHARADRVWSLS +PLVFPHQLVRLILAEQVYRAQEISAGRPYHHA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000359.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000359.fa new file mode 100644 index 0000000000000000000000000000000000000000..65b7f3d4dc54a4944c953c984f10b557c4b7f172 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000359.fa @@ -0,0 +1,20 @@ +>PROKKA_00291 +MGLALRAARAAGAAGDVPIGAALVAGDGTVLAVVGNEREQHHDPTAHAEVLALRRGAELR +AAAGAGDGWRLTDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP +RFNHQVQVRAGVRSEESAALLRGFFAAQRD +>PROKKA_02314 +MGLALRAARAAGAAGDVPIGAALVAGDGTVLAVVGNEREQHHDPTAHAEVLALRRGAELR +AAAGAGDGWRLTDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP +RFNHRVQVRAGVRSEESAALLRGFFAAQRD +>PROKKA_00063 +MGLALDAARAAGEAGDVPIGAVLVAGDGTVLAAVGNEREQHHDPTAHAEVLALRRGARAL +AEAGEADGWRLSDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP +RFNHAVQVRAGVRAEESAALLRGFFAVQRG +>PROKKA_00042 +MGLALDAARTAGEAGDVPIGAVLVDGDGRVLAAVGNEREQHHDPTAHAEVLALRRGAAAL +AARGDADGWRLAECTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP +RFNHTVQVRAGVRGDECAALLVDFFAARRPGG +>PROKKA_00298 +MGLALRAARVAGAAGDVPIGAALVAGDGTVLAVVGNEREQHHDPTAHAEVLALRRGAELR +AAAGAGDGWRLTDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVIRDP +RFNHQVQVRAGVRAEESAALLRGFFAAQRS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000360.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000360.fa new file mode 100644 index 0000000000000000000000000000000000000000..5cb0d67ee82e0987259ffde3ac3cc444ce73196d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000360.fa @@ -0,0 +1,26 @@ +>PROKKA_00292 +MDGTVGAMRVHIVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVR +IETPVTETTGFRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY +AERLPADLSGRHVFVLDPMLATGGTLIEAIRFLYQRGAARVTCLCLLGAPEGIERLEASL +GDVEVDLYLAAVDERLDERSYIVPGLGDAGDRLYGLAE +>PROKKA_02315 +MGGTVGAMRVHIVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVR +IETPVTETTGFRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY +AERLPADLSGRHVFVLDPMLATGGTLIEAIRFLYQRGAARVTCLCLLGAPEGIERLEASL +GDVEVDLYLAAVDERLDERSYIVPGLGDAGDRLYGLAE + +>PROKKA_00062 +MRVHLVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVEIQTPVAT +TTGLRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTYAERLPAD +LSGRHVFVLDPMLATGGTLIESIRFLYERGAARVTCICLLGAPEGIARLEESLGDVEVDL +YLAAQDERLDENAYIVPGLGDAGDRLYGLAE +>PROKKA_00041 +MRLHVVDHPLVAHKLTVLRDERTPSMIFRQLTEELVMLLAYEATRGVAVTEVEVKTPVAT +TVGTTLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTYAERLPAD +LTGRHVFVLDPMLATGGTLIEAIRFLYERGAERVTCLCLLGAPEGVARLEEALGDVDVEL +YLAAVDERLNEKSYIVPGLGDAGDRLYGLAE +>PROKKA_00299 +MGGTVGAMRVHIVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVR +IETPVTETTGFRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY +AERLPADLSGRHVFVLDPMLATGGTLIEAIRFLYQRGAARVTCLCLLGAPEGIERLEASL +GDVEVDLYLAAVDERLDERSYIVPGLGDAGDRLYGLAE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000361.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000361.fa new file mode 100644 index 0000000000000000000000000000000000000000..6242f06c82c1a3714bec3d0131b343f5e32c7e4b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000361.fa @@ -0,0 +1,30 @@ +>PROKKA_00293 +MGQSAGYVHISVRNAQRRADGMSRRGQARAGLRLAGGTDAPDSQTAPTPVLAPNGIPGPQ +AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGA +EGRDIEVVRQVLGDPTVQGGTRPDLAQAPAPVSTRQPGVLIDLSRREVQLDGESLNLTFK +EFELLNYLVENGERTVGREELLDALWRNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR +GQGYRFYRHPEVVVWAAPEYSI +>PROKKA_00001 +MGQSAGYVHISVRNAQRRADGMSRRGQARAGLRLAGGTDAPDSQTAPTPVLAPNGIPGPQ +AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGA +EGRDIEVVRQVLGDPTVQGGTRPDLAQAPAPVSTRQPGVLIDLSRREVQLDGESLNLTFK +EFELLNYLVENGERTVGREELLDALWRNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR +GQGYRFYRHPEVVVWAAPEYSI +>PROKKA_00061 +MGQSAGYVHISVRNAQRRADGMSRRGQARADLRLAGGTDAPAAQTAPTPVLAPNGIPGPQ +AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGSESHAAVALAPSGA +EGRDLEVVRQVLGDPTVQGGAHPDLAQAPAPVSTREPGVLIDLSRREVQLDGESLNLTYK +EFELLNYLVENGERTVGREELLEALWHNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR +GQGYRFYRHPEVVVWAAPEYSI +>PROKKA_00040 +MGETAGYVHISVRNAQRRANVSRARRGDLRLAGGTSHEPTPPQTAPTPVLAPSGIPGPQA +VARENEARGFVIYVGMDELMASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGAA +GRDLEVVRQVLGDPTVQGAARPDLAQAPAPVSTRQPGVLIDLSRREVQLDGEALNLTFKE +FELLNYLVENGERTVGREELLDALWKNSDEVPNERTIDVHIRRLRAKLGRLANTVRTVRG +QGYRFYRHPEVVVWAAPEYSI +>PROKKA_00300 +MGQSAGYVHISVRNAQRRADGMSRRGQARAGLRLAGGTDAPDSQTAPTPVLAPNGIPGPQ +AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGA +EGRDIEVVRQVLGDPTVQGGTRPDLAQAPAPVSTRQPGVLIDLSRREVQLDGESLNLTFK +EFELLNYLVENGERTVGREELLDALWRNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR +GQGYRFYRHPEVVVWAAPEYSI diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000362.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000362.fa new file mode 100644 index 0000000000000000000000000000000000000000..73056925af87e1124c3efa5dc4153cd059e4a933 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000362.fa @@ -0,0 +1,20 @@ +>PROKKA_00294 +MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPAAGDWLREHGLVPDAVVCSDA +LRTRQTCVWVCERLGELAPTPYLDPRLYGADAARALAVVNETEETTRRLLVVGHMPWVQE +LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWAELDGRDAALTHFVVPGR +>PROKKA_00002 +MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPAAGDWLREHDLVPDAVVCSDA +LRTRQTCVWVCERLGELAPTPYLDPRLYGADAARALAVVNETEETTRRLLVVGHMPWVQE +LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWAELDGRDAALTHFVVPGR +>PROKKA_00060 +MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPAAGDWLRENGLVPDAIVCSDA +LRTRQTCVWVCERLGELAPTPYLDPRLYHADAAKALAIVNETEETTRSLLVVGHMPWVQN +LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWVELDGRDAALTHFVVPGR +>PROKKA_00039 +MSPADAKTLVLLRHAKADWPAGVDDHDRPLAPRGHAQAPAAGDWLLEHGIAPEAAVVSDA +LRTRQTWVWVAQRLGERAPTAYLDRRLYEADAARALAVVNETEETVRSLIVVGHMPWLQN +LGMRLMSLDSDQDAALEMAEHLPTLGLQVFRVDTPWAELDGRDAALTHFAVPGR +>PROKKA_00301 +MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPTAGDWLREHDLVPDAVVCSDA +LRTRQTCVWVCERLGELAPTPYLDPRLYGADAARALAVVNETEETTRRLLVVGHMPWVQE +LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWAELDGRDAALTHFVVPGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000365.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000365.fa new file mode 100644 index 0000000000000000000000000000000000000000..6962a036ebef8cf37924092f18d190d2e4e645af --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000365.fa @@ -0,0 +1,70 @@ +>PROKKA_00299 +MDATSHPDAGPRLPETSVPGGDAALHEEALAVLRRLVDRPDARFKDGQFEAIEALVAHRR +RALVVQRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSS +ANATEWDEVRARLAADEVDVLLISPERLTNPRFRDEQLPDLVARMGLLVVDEAHCISDWG +HDFRPDYRRIRDLIGLLPAEGPRAVPVLATTATANARVVADVVEQLGVASEQDVFVLRGP +LARASLRLGVLRMPSPAARLAWLLDHLGDLPGSGIVYALTVSAAEDTARALREAGHEVVA +YTGRTDPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHFGAPGSPVAYYQQVG +RAGRGTDHADVLLLPGPEDRRIWEYFATASMPDEEQARAVLGALADHGGALSVAALEPAV +RIKRTALELLLKVLAVDGAVERVGGGWRATGREWTYDAERYARVAEARRAEERLMLDYQT +TDRCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDGAARERAEAALRRTGVPIEPRRM +WPSGMDRLGVPVKGRIAPESQAEEGRALARLTDLGWGTVLRDLLDREDAPVPEEVLRGAV +DVLAGWGWRTRPIAVVAMPSRTRPQLVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGN +SAYRLGSVYGRFAVPEAMAQMLRTAPDAGRHGPVLLVDDLVDSRWSLAEAARVLREAGAQ +GVLPLVLAQAG +>PROKKA_00007 +MDATSHPDAGPRLPETSAPGGDAALHEEALAVLRRLVDRPDARFKDGQFEAIEALVAHRR +RALVVQRTGWGKSAVYFVASLLLRARDAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSS +ANATEWDEVRARLAADEVDVLLISPERLTNPRFRDEQLPGLVARMGLLVVDEAHCISDWG +HDFRPDYRRIRDLIGLLPAEGPRAVPVLATTATANARVVADVVEQLGVASEQDVFVLRGP +LARASLRLGVLRMPSPAARLAWLLDHLADLPGSGIVYALTVSAAEDTARALREAGHEVVA +YTGRTDPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHFGAPGSPVAYYQQVG +RAGRGTDHADVLLLPGPEDRRIWEYFATASMPDEEQARAVLGALADHGGALSVAALEPAV +RIKRTSLELLLKVLAVDGAVERVGGGWRATGREWTYDAERYARVAEARRAEERLMLDYQT +TDRCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDGAARERAEAALRRTGVPIEPRRM +WPSGMDRLGVPVKGRIAPESQAEEGRALARLTDLGWGTVLRDLLDREDAPVPEEVLRGAV +DVLAGWGWRTRPIAVVAMPSRTRPQLVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGN +SAYRLGSVYGRFAVPEAMAQMLRTAPDAGRHGPVLLVDDLVDSRWSLAEAARVLREAGAQ +GVLPLVLAQAG +>PROKKA_00055 +MDTTQHPDAGPLPSESTAPIGPYGSGAAAPGAAAAREPELHAEALAVLRRLVDRPDAQFK +DGQFEAIEALVAHRRRALVVQRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQV +AAAARAGVRAVSVSSANATQWDEVRARLAADEVDVLLISPERLTNPRFREEQLPDLVARM +GLLVVDEAHCISDWGHDFRPDYRRIRDLIGLLPSTGPRAVPVLATTATANARVVGDVVEQ +LGVDSAQDVFVLRGSLARASLRLGVLRMPSPAARLAWLLDHLEDLPGSGIVYALTVSAAE +DTARALREAGHEAVAYTGRTDPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVH +FGAPSSPVAYYQQVGRAGRGTDHADVLLLPGPEDRRIWEYFATASMPDEEQARAVLQALA +QHGGALSVAALEPAVRIKRTALELLLKVLAVDGAVERVGGGWRATGREWVYDAQRYARVA +EARRAEERLMLDYQTTDTCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDTSARERAE +AALRRTGVPIEPRRMWPSGMDRLGVPVKGRMAPEIQAEEGRALARLTDLGWGTVLRELLD +KEDAPVPEDVLQGAVGVLAGWGWQTRPIAVVAMPSRTRPLLVGSFAEGIARIGRLPFLGS +LEHARGGPTAGPGGNSAYRLGSVHGRFEVPEAMAHLLRTASDAGRHGPVLLVDDLVDSRW +SLAEASRVLREAGAQGVLPLVLAQAG +>PROKKA_00033 +MSTSPQDPARPAAVADPALYAEALGVLRALVGRPDAEFKDGQYEAVEALVAHRRRALVVQ +RTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAASLSSANATEW +EDVRRSLEADEVDVLLISPERLTNPRFRDEQLPDLVSRMGLLVVDEAHCISDWGHDFRPD +YRRIRDLIRLLPSSGPRAVPVLATTATANARVVQDVVEQLDVESRQDVFVLRGPLARASL +RLGVLRLPSPAARLAWLLQHLGELPGSGIVYALTVSAAEDTARALREAGHEVVAYTGRTD +PEQRARIEQDLKDNRVKAVIATSALGMGFDKPDLTFVVHLGAPSSPVAYYQQVGRAGRGT +DHADVLLLPGQEDRAIWEYFATASMPDEVQARAVLEALEESGGAMSVAALEPVVSVKRTA +LELLLKVLSVDGAVERVGGGWRATGSPWTYDAERYARVAEARRAEERLMLDYQTTQTCRM +EFLARTLDDPTAAPCGRCDVCAGPWYPTGWDGAAREQADRALRRTGVPLEPRRMWPSGMD +RLHVPVKGRISPAEQAEEGRALARLTDLGWGSRLRELLAAPDAPVPEEVLQAAVRVLAEW +GWQERPIAVVAMPSRGRPQLVDSLARGLAGQGRLPFLGPLELVGGGPTAGPGGNSAYRLA +SVHGRFAVPEGMARMLATAPDAGRHGPVLLVDDLADSRWSLAEAARVLRGTGAQGVLPFV +LAQNG +>PROKKA_00306 +MDATSHPDAGPRLPETSAPGGDAALHEEALAVLRRLVDRPDARFKDGQFEAIEALVAHRR +RALVVQRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSS +ANATEWDEVRARLAADEVDVLLISPERLTNPRFRDEQLPDLVARMGLLVVDEAHCISDWG +HDFRPDYRRIRDLIGLLPAEGPRAVPVLATTATANARVVADVVEQLGVASEQDVFVLRGP +LARASLRLGVLHLPSPAARLAWLLDHLGDLPGSGIVYALTVSAAEDTARALREAGHEVVA +YTGRTDPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHLGAPGSPVAYYQQVG +RAGRGTDHADVLLLPGPEDRRIWEYFATASMPDEEQARAVLGALADHGGALSVAALEPDV +RIKRTSLELLLKVLAVDGAVERVGGGWRATGREWTYDAERYARVAEARRAEERLMLDYQT +TDRCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDGAARERAEAALRRTGVPIEPRRM +WPSGMDRLGVPVKGRIAPESQAEEGRALARLTDLGWGTVLRDLLDREDAPVPEEVLRGAV +DVLAGWGWRTRPIAVVAMPSRTRPQLVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGN +SAYRLGSVYGRFAVPEAMAQMLRTAPDAGRHGPVLLVDDLVDSRWSLAEAARVLREAGAQ +GVLPLVLAQAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000367.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000367.fa new file mode 100644 index 0000000000000000000000000000000000000000..150fab95e1488f536ee7df3bbf09d03a4426fab5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000367.fa @@ -0,0 +1,42 @@ +>PROKKA_00301 +MPPTTPPPPAGPPAVPPSGPAPAAPGEAAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSD +DLGVPADRAALLVSASTLGLALSVVPWSVAGDRWGRRRAMVVSMVSASACALAGVLAPTF +EAMLRLRLLEGMAHGGVAGLAVALLAEEVAPHAVAAAAGTYIAGTTLGGLSGRLLALPVA +EASSWRGGMLAVTVVGVLCTVGFLAITPRARRFTPSPTSPATLVRIVRGHLRSPELVAVY +LQGALLMGGFVALYNFVGYRLLGPPFSWTPTAAGLVFLAYLAGTWSSPRAGRLAARVGRL +PVLAGATAAMAAGVALTSVPHPAVLVPALVLVTGAFFAAHAVASAWSGTAAPTGRAQSTS +LYNFAYYAGSSLFGWLGGVFHESHGWPGTVLMVLALVLTALASAVVVLRGRGTAPAR +>PROKKA_00009 +MPPTTPPPSAGPPAVPPSGPAPAAPGEPAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSD +DLGVPADRAALLVSASTLGLAVSVVPWSVAGDRWGRRRAMVVSMVSASACALTGVLAPTF +EAMLGLRLLEGMAHGGVAGLAVALLAEEVVPHAVAAAAGTYIAGTTLGGLSGRLLALPVA +EASSWRGGMLTVTVVGVLCTVGFLAITPRARRFTPSPTSPATLVRIVRGHLRSPELVAVY +LQGALLMGGFVALYNFVGYRLLDPPFSWTPTAAGLVFLAYLAGTWSSPRAGRLAARVGRL +PVLAGATAAMAAGVALTSVPHPAVLVPALVLVTGAFFAAHAVASAWSGTAAPTGRAQSTS +LYNFAYYAGSSLFGWLGGVFHESHGWPGTVLMVLALVLTALVSAVVVLRGRGTAPAR +>PROKKA_00053 +MPPQPPPAGPPAVPPSGPAPLAPGDPAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSADL +GVGAHRAALLVSAGTLGLALSVVPWSMAGDRWGRRRAMVVSMVSASLFALAGVLAPTFEA +MLGLRLLEGMAHGGVAGLAVALLAEEVAPRAVATAAGTYIAGTTIGGLSGRLIALPVAEA +FTWRTGMLAVTVVGVACTAAFLAVTPQARRFTPSPTSVARLVRIVRGHLGSAELVAVYLQ +AALLMGGFVALYNFVGYRLLGPPFSWAPTAAGLVFLAYLAGTWSSPRAGRLAARFGRLPV +LTGATAAMAAGAALTLVPHPAVLVGALVLTTGAFFAAHSVASAWSGTAAPHGRAQSTSLY +NLAYYAGSSLFGWLGGVFHESHGWTGTVLMVVALALTALAIAVVVLRGRGTAPARCAGAV +RGAGRRGIRRISRGRLRRRRWPSGAGRARPRGPRGPAARASRPSAGRSRSRCPARRTPPA +WSAPRPG +>PROKKA_00031 +MPPALPAPLEPGTPLYRRLLLGLFLAGVATFAQLYAPQGLLPLVSSDLGVPSHRAALLVS +AGTLGLALSVVPWSLAGDRWGRRPVMVASLVSASVLALVGVFMPSIELLMGMRLLEGMAH +GGVAGLAVTLLAEEVAPRVVPVAAGTYVAGTTLGGLSGRLLAMPVGEWAGWRAGMLAVTA +AGAACTVAFLFVTPPARRSTPVRLSLARLGRIIGGHLRTPGLVALYLQAALLMGGFVALY +NYIGYTLLAPPFGWPPTAVGLVFLAYLAGTWSSPRAGRLAVRVGRLKVLTGSTALMAVGV +VLTLVPSPFVLVPALVVATGAFFAAHSVASGWAGTAAPTGRAQSTSLYNLAYYAGSSLFG +WLGGVFHEGVGWAGTVFMVAGLAAVALVVALVVLRGREDAGPPPPSAVAEGAAA +>PROKKA_00308 +MPPTTPPPSAGPPAVPPSGPAPAAPGEPAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSD +DLGVPADRAALLVSASTLGLAVSVVPWSVAGDRWGRRRAMVVSMVSASACALTGVLAPTF +EAMLGLRLLEGMAHGGVAGLAVALLAEEVAPHAVAAAAGTYIAGTTLGGLSGRLLALPVA +EASSWRGGMLAVTVVGVLCTVGFLAITPRARRFTPSPTSAAALVRIVRGHLSSPELVVVY +LQGALLMGGFVALYNFVGYRLLDPPFSWTPTAAGLVFLAYLAGTWSSPRAGRLAARVGRL +PVLAGATAAMAAGVALTSVPHPAVLVPALVLVTGAFFAAHAVASAWSGTAAPTGRAQSTS +LYNFAYYAGSSLFGWLGGVFHESHGWPGTVLMVLALVLTALASAVVVLRGRGTAPAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000368.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000368.fa new file mode 100644 index 0000000000000000000000000000000000000000..a2bc322c0feaccb1060d82ff95b388935e2af138 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000368.fa @@ -0,0 +1,30 @@ +>PROKKA_00303 +MEYLVPVLAVVVIGALAFAAARWMSAGRARQAADQRTPSGRGLDIGPERARLAAGLLDED +AHRRVYGHIAQSRVMEAVRDYRAHTGRGLKDAVMDVQSLAVHPQVYSEPAQEPDATSAGA +AGPVPADHEEPHRDDTAPAETPGPERPGQDSSGRGEPDAQTPDREPSDAVAEDDARQDTD +HASAAPRPTATPADELTTLTVPAEWTAAPAEEELPFEVEVMRGTESVRLSSRDLPPWLRD +QLSAMVRDGNLESAAVQLSSHSELSVPEAYELLRRMREHRGEG +>PROKKA_00011 +MEYLVPVLAVVVIGALAFAAARWMSAGRARQAADQRTPSGRGLDIGPERARLAAGLLDED +AHRRVYGHIAQSRVMEAVRDYRAHTGRGLKDAVMDVQSLAVHPQVYSEPVQEPDATSAGV +AGPVPGGHGEPHRDDAAPADTPGPKRPGQDSSGRGEPDAQTPDRETSDAVAEDDARQDSD +HASAAPRPTAPSADELTTLTVPAEWTAAPAEEELPFEVEVMRGTESVRLSSRDLPPWLRD +QLAAMVRDGNLESAAVQLSSHSELSVPEAYELLRRMRERRGEG +>PROKKA_00051 +MEYLVPVLAVVLIGALAFAVSRWMSAARDRQTAGPRTPSGRPLEIGPERARQAAALLDED +AHRRVYGHIAQSRVMEAVRDYRAHTGRSLKDAVMDVQSLAVHPQVYSVPATEQEAPEEAE +VRDPRTRPTPPEPARDEAADGERQGTERADVVEEGADDPAADDEPRPEAESDLSAEEGRV +DDGAASGTEPRPGTSEPARADELTALTVPADWSAAPAEEEPPFEVEVMRGMDSVRLSSQD +LPPWLRDQLSAMVRDGNLESAAVQLSSHSQLSVPEAYELLRRMRERRGED +>PROKKA_00030 +MEYLVPILAVVVIGGITLLVARRLSGRSQAPTRSATGTGADTVEASPERARTAARRLDEA +THRAVYGHIAQGRPFEAVRDYRRATGRGVRDAILDIQSLTLHPQVWSLPVQAEPADDASP +AAADMPSGPPRGPSDGRGRDGESSARPRLRRAEPSEAGPAPDAEPAPGGDAAADPEADGA +TSRRPGRQAPEELTTLTVPEGWTADPAPEEPPFEVEVMRGEESVRLASQDLPPWLRDQLS +AMVRDGNLESAAVQLSSHSSLSVPEAFELLRRMKERREGRG +>PROKKA_00310 +MEYLVPVLAVVVIGALAFAAARWMSAGRARQAADQRTPSGRGLDIGPERARLAAGLLDED +AHRRVYGHIAQSRVMEAVRDYRAHTGRGLKDAVMDVQSLAVHPQVYSEPVQEPDATSAGV +AGPVPDDHGEPHRDDAAPAETPGPKRPGQDSSGRGEPDAQTPDREPSDAVAEDDAQQDTD +HASAAPRPTATPADELTTLTVPAEWTAAPAEEELPFEVEVMRGTDSVRLSSQDLPPWLRD +QLSAMVRDGNLESAAVQLSSHSELSVPEAYELLRRMRERRGEG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000371.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000371.fa new file mode 100644 index 0000000000000000000000000000000000000000..25189e84130d2daaeeabc023ff4ca7077c5ac582 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000371.fa @@ -0,0 +1,84 @@ +>PROKKA_00307 +MTPLPRFAARTAVTTAALALLAPAVALPSQASPAGDSLVINEAYTNGGSANAVYTHKFVE +LYNPTDQPINLDGWSLQYRSAAGTAATQGTVALSGTVPAKGHFLVSGGSNGTAGAALPQA +DLVAGGAFNPAGTKGTIVLARQAGTVTDLPVGSVVTGQVPGVADVLGYGATNTFETAAAG +APSANSDPKSLTRTNGVDTDDNSADFTVTGQVTPTNAAATGGEPTPEPEPQPTPSERITI +AQLQGTGTATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGDTPDATPGASDGVFVY +SPDTVGSVTLGDHVQVTGEAAEHYGLTQIKVAADGVLPVAEPGAVAPTPVEFPLEEADRE +ALEGMVLAPQGDWTVTDNYSLNQYGSLGVVPGTKPLDNPTSVARPGAEAQAVAAANAQQL +IVLDDGASTNFMRSPGNQNPLPYLDADQPVRVGAGLEFSTGVILDWRFDAWSFQPLGHLT +DATAAAVQPVTIEDTRPAEAAPEAVGGNVTVGSFNVLNYFTTLGQDVAGCGAYRDRAGTP +VTTNGCLPRGAYTPEAFARQQEKIAAAINGLGTSVVALEEIENSEKFGLDRDHALAHLVE +ALNAQAGEQRWAYVASPSARPALADEDVIRSAFIYQPAEVTPLGESVILDDQTNFDNARE +PMAQLFRAADGTAEGAAGTEFVAITNHFKSKGGSGATGDNVDAGDGQGAYNADRVGQAEA +LVAFAERMKAETGTDRVLLMGDFNAYEKEDPIRVLEAAGYVSQGALTGEYSYAFGGAVGS +LDGIYASPSAAAAITGQDIWMINANESVALEYSRHNYVAEDLYSADQWRSSDHNPILVGL +QLDAPVTEPTPEPEPEPTPGETCDGVTDPRGVPGKPANSVREWLRCIGATPGHGGDHPGK +GHGGDHPGKGRGPVRP +>PROKKA_00022 +MTPLPRFAARTAVTTAALALLAPAVALPSQASPAGDSLVINEAYTNGGSANAVYTHKFVE +LYNPTDQPINLDGWSLQYRSAAGTAATQGTVALSGTVPAKGHFLVSGGSNGTAGAALPQA +DLVAGGAFNPAGTKGTIVLARQAGTVTDLPVGSVVTGQVPGVADVLGYGATNTFETAAAG +APSANSDPKSLTRTNGVDTDDNSADFTVTDQVTPTNAAATGGEPTPEPEPQPTPAERITI +AQLQGTGTATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGDTPDATPGASDGVFVY +SPDTVGSVTLGDHVQVTGEAAEHYGLTQIKVAAGGVLPVAEPGAVAPTPVEFPLEEADRE +ALEGMVLAPQGDWTVTDNYSLNQYGSLGIVPGTTPLDNPTSVARPGAEAQAVAAANAQQL +IVLDDGATTNFMRSPGNQNPLPYLDADQPVRVGAGLEFTTGVILDWRFDAWSFQPLGHLT +DATAAAVQPVTIEDTRPAEAAPEAVGGNVTVGSFNVLNYFTTLGQDVAGCSAYRDRAGTP +VTTNGCLPRGAYTSEAFARQQEKIAAAINGLGTSVVALEEIENSEKFGLDRDHALAHLVE +ALNAQAGEQRWAYVASPATRPALADEDVIRSAFIYQPAEVTPVGESVILDDQTNFDNARE +PMAQLFRAADGTSEGAAGTDFVAITNHFKSKGGSGATGDNVDAGDGQGAYNADRVGQAEA +LVAFAERMKAETGTDRVLLMGDFNAYEKEDPIRVLEAAGYLSQGALTGEYSYAFGGAVGS +LDGIYASPSAATAITGQDIWMINANESVALEYSRHNYVAEDLYSADQWRSSDHNPILVGL +QLDAPVTEPTPEPEPSPGETCDGVTDPRGVPGKPANSVREWLRCVGATPGHGGDHPGKGH +GPEHPGKGRGPVRP +>PROKKA_00030 +MTQRTFRLSRPAVALAALTLLAPAVVAGPAHAAPTGDGLVINEVYTNGGSANAVFTHKFV +ELYNPTDTPISLDGWSLQYRSATGTAAPNGVVALSGTVPAKGHFLIQGGSNGTTGAALPR +PDLNAGGAFNPAGARGTVVLSDQAGALTALPVGSVTTGQAEGVADLLGYGTSNTFETAAA +GAPSSNSDPKSLTRTDGVDTDDNAADFTVTAQVTPTSSTGEAPVDPIPDPEPDPEPAPAL +TIAQIQGDGAATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGSAEDATPGASDGLF +VYSPDTVGSVALGDHVQVTGEAAEHYGLTQVRVGAAGVTPVAEPAAVAPTAVDFPLSEAD +REALEGMLLAPTGEWTVTDNYDLNQYGSLGIVPGTEPLPNPTSVAAPGAEAQAVAADNAS +RLIVLDDGASTNFMRSPGNENPLPYLDADRPVRVGAGLDFTTGVILDYRFDAWSFQPLGH +LTDATAAAVQPVAVEDTRPEEASPEAVGGNVSVGSFNVLNYFTALGQDFPGCRAYTDRFG +EPVTTNGCLPRGAYTPEAFARQQEKIAAAIDGLDASVVALEEIENSAKFDLDRDRALAHL +VDALNAQAGEQKWAYVASPADRPALSEEDVIRNAFVYQPAEVTPVGESVILRDEVNFDNA +REPLAQHFRAADGTEAGVAGTDFVAVTNHFKSKGGSGAAGDNADSGDGQGAYNGDRTRQA +QALVAFAEQVADDAGTDRVLLLGDFNAYEKEDPIRVLEEAGYVSQGALTGEYSYTFDGAV +GSLDGVYASPAASAVVTGQDIWMINANESVALEYSRHDYVAEDLYAPDQWRSSDHNPLLV +GLQLDAPVVEPEPQPGAGHPGKGKGLDKGAGHPGKGKGLDKGAGHPGHGRVPEAARP +>PROKKA_00026 +MPTPRLRLVRTAATLAAATLLAPAVLALPAQASPAGDSLVINEAYTNGGSAGALFTHKFV +ELYNPTDQPISLDGWSLQYRSATGTTAPSTTVALSGTVPAKGHFLIQGGSNGATGAALPT +PDLTTSFNPAGTKGTIVLADQAGTVAGLPTGSVVTDQVAGVADVLGYGATNTFETAASGA +PAANSDPKSIARTGGADTDDNAADFTVAADVTPQNAAGGGTAPVDPVDPVDPTPAPAPSV +TVAEIQGTGATSPLEGRRVSTTGVVTAVYSTGGYDGFYIQTAGTGGAEDATPGASDGVFV +YAPAEVGSVTLGQTVTVTGDVAEYYGLTQVKAEAGGVRQAAEAGAPVTARELAFPLTEAE +KEAHEGELLAPAGAWTVTDNYDVNQYGSLGLAPGTSPLPNPTSVALPGADAQAVAADNAQ +RLIVLDDGASTNFFRSPGNQNALPYIDADAPARVGSAVDFRTPVILDYRYGAWSFQPLGH +LTDANKAEVQPVDIADTRPAEAVREDLGGNVTVGSFNVLNYFTTLGEDVPGCGYYADKDG +APVSTKGCLPRGAYTEEAFLEQQAKIATAINGMDTSVVALEEIENSEKFGLDRDHALAHL +VDALNAQAGYAKWAYVASPTVRPALADEDVIRSAFIYQPAEVTPVGESVILDDQVNFANA +REPMAQAFRVADGSAGGVVGTEFVAITNHFKSKGGSGATGDNVDTGDGQGAYNGDRTRMA +QALVAFAEQMKVQAGTDRVLLMGDFNSYEKEDPIRVLEAAGYISQGAKTGEYSYTFDGAV +GSLDGIYASPAADATVTGQDIWMINANESVAFEYSRDNYVGEEFYAPDQWRSSDHNPVLV +GLQLDAPAAPVVPTPGTRPTPPADQCALITSPRGAKASAGFSASEWMRCAGVHPGKGRGR +G +>PROKKA_00314 +MTPLPRFAARTAVTTAALALLAPAVALPSQASPAGDSLVINEAYTNGGSANAVYTHKFVE +LYNPTDQPINLDGWSLQYRSAAGTAATQGTVALSGTVPAKGHFLVSGGSNGTAGAALPQA +DLVAGGAFNPAGTKGTIVLARQAGTVTDLPVGSVVTGQVPGVADVLGYGATNTFETAAAG +APSANSDPKSLTRTNGVDTDDNSADFTVTDQVTPTNAAATGGEPTPEPEPQPTPAERITI +AQLQGTGTATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGDTPDATPGASDGVFVY +SPDTVGSVTLGDHVQVTGEAAEHYGLTQIKVAAGGVLPVAEPGAVAPTPVEFPLEEADRE +ALEGMVLAPQGDWTVTDNYSLNQYGSLGIVPGTTPLDNPTSVARPGAEAQAVAAANAQQL +IVLDDGATTNFMRSPGNQNPLPYLDADQPVRVGAGLEFTTGVILDWRFDAWSFQPLGHLT +DATAAAVQPVTIEDTRPAEAAPEAVGGNVTVGSFNVLNYFTTLGQDVAGCSAYRDRAGNP +VTTNGCLPRGAYTSEAFARQQEKIAAAINGLGTSVVALEEIENSEKFGLDRDHALAHLVE +ALNAQAGEQRWAYVASPATRPALADEDVIRSAFIYQPAEVTPVGESVILDDQTNFDNARE +PMAQLFRAADGTSEGAAGTDFVAITNHFKSKGGSGATGDNVDAGDGQGAYNADRVGQAEA +LVAFAERMKAETGTDRVLLMGDFNAYEKEDPIRVLEAAGYLSQGALTGEYSYAFGGAVGS +LDGIYASPSAATAITGQDIWMINANESVALEYSRHNYVAEDLYSADQWRSSDHNPILVGL +QLDAPVTEPTPEPEPSPGETCDGVTDPRGVPGKPANSVREWLRCVGATPGHGGDHPGKGH +GPEHPGKGRGPVRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000373.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000373.fa new file mode 100644 index 0000000000000000000000000000000000000000..d754b6d5595b58c083493d8061e84f8d08928b26 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000373.fa @@ -0,0 +1,20 @@ +>PROKKA_00311 +MRGPFARFRQERADDRELGTGLWRRAHDRLGRAMDRYWQVLAGQRGTDVLSPEERNGVVH +AGNVLTERLPAVRALCVRLHRDHEGDGEHIPAEAADVHRELSRAAHELAATAQALALYRL +GQGSAESVGRHAERTLGHLDRAEELGAGL +>PROKKA_00026 +MRGPFARFRQERADDRELGTGLWRRAHDRLSRALDRYWQVLEGQRGTDVLSPEERNGVVH +AGNVLTERLPAVRALCVRLHRDHEGDGEHIPAEAADVHRELSRAAHELAATAQALALYRL +GQGSAESVGRHAERTLGHLDRAEELGAGL +>PROKKA_00026 +MRGPFARFRQSCSDDRELGTGLWRRAHDRFVRAMDRYWQVLEGDRGPDLLRTEQRNGVVH +AGNVLAERLPAVRALCVRLHRDHAGDGEHIPPEAADVHRELSRAAHELAATAQALAMHRL +GQGSSDSVGRHAERTLAHLDRAEELAARL +>PROKKA_00022 +MIRGPFARFRQGRSDDRELGTGLWRRSHDRYVRALDRYWQVLEDGRSAGGFTPEERNGLV +HAGNVLAERVPAVRALAARLHAAHPGDGEQHIPPVTAPVHRELSRASHELAAAAQAVAMF +RRGVSGSEAVSRHAQRTLDHLDRAEGLAADL +>PROKKA_00318 +MRGPFARFRQERADDRELGTGLWRRAHDRLGRALDRYWQVLEGQRGTDVLSPEERNGVVH +AGNVLTERLPAVRALCVRLHRDHEGDGEHIPAEAADVHRELSRAAHELAATAQALALYRL +GQGSAESVGRHAERTLGHLDRAEELGARL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000374.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000374.fa new file mode 100644 index 0000000000000000000000000000000000000000..fd1a2cb5edf85acedfc0c6dc0c66e7d76db653f7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000374.fa @@ -0,0 +1,30 @@ +>PROKKA_00313 +MSLPHAPRTPAPPAAASSAVPLRLAVVDMSGTSIVEHGLQDTAFARSLDQHGVPAGTPEH +DDAARRFRALRPTSRTAVFPRVFADRAVAAAATRTFEATFDALLAEHGVRAVPGAEEALI +RLRALGLHVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMILTALLGLD +LEDVRSVLVVGDTAEDMTAGRRAGAGLVVGVRTGRDADHVLLAAGSDRVVPGLADVPDLV +VRTR +>PROKKA_00028 +MSLPHAPRTPAPPAAASSAAPLRLAVVDMSGTSIVEHGLQDTAFARTLDQHGVPAGTPEH +DDAARRFRALRPTSRTAVFPRVFADRAVAAAATRTFEAAFDALLAEHGVQAVPGAEEALV +RLRALGLHVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMILTALLGLD +LDDVRSVLVVGDTAEDMTAGRRAGAGLVVGVRTGRDADDVLLAAGADRVVPGLADVPDLV +VRTR +>PROKKA_00024 +MSLPPRPPPRGRAPRADGPPAPPLRLAVVDMSGTSIVERGLQDAAFAHALETHGLAADAP +AHADAVRVFRARRATSRTAVFAQVFPDRPAAAAAARTFEEAFDSLLAEHGVQPVPGAEEA +LLRLRALGLRVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPFPDMILTALLG +LDLDDVRGVLVVGDTAEDMTAGRRAGAGLVAGVRTGRDADAALLAAGAHHVVDGLADVPA +LVGAGG +>PROKKA_00020 +MSLSTAVPALSVGTPVPLRLAVVDMSGTSVVEGGLQDRAFAEVVAARGLAEGSPEHERAA +RLFRERRGTSRTAVFQALFEGRTAALEATRAFEAAFDRLLAEHGVTAVPGAEGALVRLRE +AGLDLCLITGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMVLTALLALDHDDV +RSVLTVGDTAADILAGRRAGAGLVVGVRSGQDTGGVLAGAGADQVVDSLAQVPDLVATLR +G +>PROKKA_00320 +MSLPHAPRTPAPPAAASSAVPLRLAVVDMSGTSIVEHGLQDTAFARTLDQHGVPAGTPEH +DDAARRFRALRPTSRTAVFPRVFADRAVAAAATRTFEATFDALLGQHGVQAVPGAEEALV +RLRALGLHVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMILTALLGLD +LDDVRSVLVVGDTAEDMTAGRRAGAGLVVGVRTGRDADDVLLAAGADRVVPGLADVPDLV +VRTR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000375.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000375.fa new file mode 100644 index 0000000000000000000000000000000000000000..b8803b22a4120d609ff039c1473ee30cd2d2ad7d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000375.fa @@ -0,0 +1,40 @@ +>PROKKA_00314 +MTASAPVPPVFADLAGQEAAVAQLRRAAAEDRPTHAWMFTGPPGSGRSTAARAFAAALQC +EVADPAARGCGECHACRTVLGGTHPDVTVLATEAVSYRIEDVRALVEAGQSTPATGRWRI +FLMEDADRMTERATNVLLKAIEEPPARTIWMLCTPSPADVLPTVRSRCRLITLSIPAVEQ +VAELLHRRDGLDRETALTTARISQSHVGMARRLARDPEALERRERILSLPLQATAVSDAM +ALAATLAEVSKAEAESAAEARDAEELEALRRSLGLEPGEPVPPKLRHHVKRLEEDQTRRR +RRAVRDSLDRAMIDVMGLFRDVLRVQLGADGELINEHRRDEIEAYARGTAGDSAEVLARI +DAVTTTRERIAANVPEQLALEAMMLALLPRRVRTPRRR +>PROKKA_00029 +MTAPAPAVFADLAGQEAAVAQLRRAAAEDRPTHAWMFTGPPGSGRSTAARAFAAALQCEV +ADPAARGCGECHACRTVLGGTHPDVTVLATEAVSYRIEDVRALVEAGQSTPATGRWRIFL +MEDADRMTERATNVLLKAIEEPPARTIWMLCAPSPADVLPTVRSRCRLITLSIPAVEQVA +ELLHRRDGLDRETALTTARISQSHVGMARRLARDPEALERRERILSLPLQATAVSDAMAL +AATLAEVSKAEAESAAEARDAEELEALRRSLGLEPGEPVPPKLRHHVKRLEEDQTRRRRR +AVRDSLDRAMIDVMGLFRDVLRVQLGADGELINEHRRDEIEAYARGAAGDSAEVLARIDA +VTTARERIAANVPEQLALEAMMLALLPRRVRTPRRR +>PROKKA_00023 +MTALPDAVPAVFADLAGQGSAVEQLRRAAAEDRPTHAWMFTGPPGSGRSTAARAFAAALQ +CEAPDPAARGCGRCHACRTVLAGTHPDVTVLATEAVTYRIEDVRSLVEAAQSTPATGRWR +IFLMEDADRMTERATNVLLKAVEEPPARTVWMLCTPSPADVLPTVRSRCRLVTLSIPAVE +DVADLLHRRDGLDRETALTTARISQSHVGMARRLARDPEALERRERILSLPLEATSVSDA +MALAATLADVSKAEAESSAEARDAEELETLRRSLGLEPGEPVPPKLRQHVKRLEEDQTRR +RRRSVRDSLDRAMIDVMGLFRDVLRVQLGAEGELINEHRRAEVEAYARGAAGDSAEVLAR +IDAVATARERIAANVPEQLALEAMMLALLPRRVRTPRRR +>PROKKA_00019 +MTGAPDVYSDLAGQDAAVAQLRRAATEDRPTHAWLFTGPPGSGRSTAARAFAAALQCEQP +DPANRGCGACHACRTVLGGTHPDVTVLATEAVSYRIEDVRALVEAAQSTPATGRWRIFLM +EDADRMTERATNVLLKAIEEPPPRTIWMLCSPSPADVLPTIRSRCRLVTLRIPAPEDVAA +LLHRRDGLDEATALMTARISQSHVGMARRLARDPEALARREDVLSLPLQATAVSDAMAMA +ARLAEVSHAEAESSAAARDAEELAALRRQLGVAEGEAVPPKLRQQVKRLEEDQSRRRTRV +TRDALDRAMIDVIGLFRDVLRVQLGAGGDLVNEHRRAEIERYAAGAAGSSAEVVARIDAV +HLARERLGQNVPEQLALEAMMLALLPARVRTPRGRR +>PROKKA_00321 +MTAPAPAVFADLAGQEAAVAQLRRAAAEDRPTHAWMFTGPPGSGRSTAARAFAAALQCEV +ADPAARGCGECHACRTVLGGTHPDVTVLATEAVSYRIEDVRALVEAGQSTPATGRWRIFL +MEDADRMTERATNVLLKAIEEPPARTIWMLCAPSPADVLPTVRSRCRLITLSIPAVEQVA +ELLHRRDGLDRETALTTARISQSHVGMARRLARDPEALERRERILSLPLQATAVSDAMAL +AATLAEVSKAEAESAAEARDAEELEALRRSLGLEPGEPVPPKLRHHVKRLEEDQTRRRRR +AVRDSLDRAMIDVMGLFRDVLRVQLGADGELINEHRRDEIEAYARGAAGDSAEVLARIDA +VTTARERIAANVPEQLALEAMMLALLPRRVRTPRRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000377.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000377.fa new file mode 100644 index 0000000000000000000000000000000000000000..faba5b348f985350e38c43a92938d8c2d36faf2f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000377.fa @@ -0,0 +1,15 @@ +>PROKKA_00316 +MHVALLFDHWLFRVLAIAALVLEVWALVDVVRRRPDDFARIGGRDRSFWLILTGVAAVVG +LLGVLAGGGMGMFGLVAACVACVYLAGPRQDMGPALRR +>PROKKA_00031 +MHFALLVDHWLFRVLAIAALVLEVWALVDVVRRRPDDFARIGGRDRSFWLILTGVAAVVG +LLGVLAGGGMGMFGLVAACVACVYLAGPRQDMGPALRR +>PROKKA_00021 +MHLALTFDQWLFRILAIVGLVLEVWAFLDALRRSPGDFARIGGRDKSFWMILTGVAAAVG +VLGVLSGGGMGMFGLLAACVACVYLAGPRQEMGPATRR +>PROKKA_00017 +MHLAIVAGNWLFYALAVVAFLLELWAFADAARTSQETFLRTGGRTKGFWLALTGAAAAVG +LVGVLLGPTGGFGILGLAAVCVASVYLAGPRDDLRFYGGRRGR +>PROKKA_00323 +MHFALLVDHWLFRVLAIAALVLEVWALVDVVRRRPDDFARIGGRDRSFWLILTGVAAVVG +LLGVLAGGGMGMFGLVAACVACVYLAGPRQDMGPALRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000384.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000384.fa new file mode 100644 index 0000000000000000000000000000000000000000..3b0bf80842a11c3fe0a7c6b2ba5c5513791421a3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000384.fa @@ -0,0 +1,45 @@ +>PROKKA_00324 +MPTALVIAAAGAGTRLGAGLPKALAPLADGRTLLRHCLESVAAARAAGLDLDAVVVLTPP +AGADAGRVAAEVDAGPRLDVPVHCVPGGAERADSVRAGLAAASHALADLAPAGAPRRVLV +HDAARALTPPSVFGAVTAALETGAVAAIPGLPLTDTVKQVTPGRGGVDVVAATPARAGLR +AIQTPQGFDLDTLLAAHEAVRTDPTLDAAALTDDAMVMEAAGHEVVVVTGDPAAFKVTAP +ADLDLARLELARRAPQEEAPMDQPARPAAAPAPLPRVGIGTDVHAWAPEDAPRPLWLGGI +HWPGERGVAATSDGDVAAHAACNALLSAAGLGDLGAVFGVDRPEMADASGADMLREVLRL +LTEAGLAVGNVAVQVVAPRPKVGARRAEMEAALSAALGGAPVSVSAATTDRLGFIGRKEG +LVGIATALVIPAA +>PROKKA_00039 +MPTALVIAAAGAGTRLGAGLPKALAPLADGRTLLRHCLESVAAARAAGLGLDAVVVLTPP +AEADAGRVAAEVDAGPRLDVPVHCVPGGAERADSVRAGLAAASGALADLAPAGAPRCVLV +HDAARALTPPSVFGAVTAALGTGAVAAVPGLPLTDTVKQVTPGRGGVDVVAATPARAGLR +AIQTPQGFDLDTLLAAHEAVRTDPTLDAAALTDDAMVMEAAGHEVVVVTGDPAAFKVTAP +ADLDLARLELARRAPQEEAPMDQPARPAAAPAPLPRVGIGTDVHAWAPEDAPRPLWLGGI +HWPGERGVAATSDGDVAAHAACNALLSAAGLGDLGAVFGVDRPEMADASGADMLREVLRL +LTEAGLAVGNVAVQVVAPRPKVGARRAEMEAALSAALGGAPVSVSAATTDRLGFIGRKEG +LVGIATALVIPAA +>PROKKA_00013 +MPTALVIAAAGAGTRLGAGMPKALVPLADGRTLLRHCLDSVAAARAAGAAVDAVVVLAPP +AEEDAARVAAEVDAGPGLGAPVACVPGGAERADSVRAGLAAAADALNALGPAAGPRRVLV +HDAARALTPPAVFAAVEAALDAGAVAVVPGIAVTDTVKQVAPGPGGAEVVTTTPPRAALR +AVQTPQGFDLDALLAAHEAVRADPALDAAALTDDAMVMEAAGHPVAVVAGDAAAFKVTAP +ADLELARLELARRADAPTPEEDPAMDQYGTAPGTGPEADAATDPAGPRPGAALPRVGVGT +DVHRWAPEDAPRPLWLGGVHWPGERGVAATSDGDVAAHAACNALLSAAGLGDLGAVFGVD +RPEMADASGTAMLAEVLRLLTEAGLAVGNVAVQVVAPRPKVGTRRAEMEAALSAALGGAP +VSVSAATTDRLGFIGRGEGLVGIATALVAPTA +>PROKKA_00009 +MPTALVIAAAGSGTRLGAGVPKALAPLTDGRPLLDHCLESVAAARATGLGLDALVVLVPP +AADHARAVADVVARHETAVGAPVTCVPGGVERADSVRAGLAAADAALADRGHPAGQGVRH +VLVHDAARAFTPPAVFEAVAGALVSGEVAAVPGLPLTDTVKEVTGADGREVVVATPARSA +LRAVQTPQGFDLDVLLAAHAAAQADPAADAAALTDDAMAMEAAGHAVVVVPGDERAFKVT +SPADLEAAARILAVRDAQSGPGTPSPAAVPAAPPLPRTGIGTDVHRWAPDDAPRPLWLGC +VEWPGQNGVAATSDGDVAAHAACNALLSAAGLGDLGAVFGVDRWEMRGASGAAMLAEVLR +LVTEAGCRIGSVAVQVVAPRPKVGTRRAEMEAAMSAALGGAPVAVSAATTDGLGFIGAGE +GLVGLATALVVPAA +>PROKKA_00331 +MPTALVIAAAGAGTRLGAGLPKALAPLADGRTLLHHCLASVATARAAGLALDAVVVLTPP +AEADAGRVAAEVDAGPRLDVPVHCVSGGAERADSVRAGLAAASYALADLAPAGAPRRVLV +HDAARALTPPSVFGAVTAALETGVVAAVPGLPLTDTVKQVTPGRGGVDVVAATPARAGLR +AIQTPQGFDLDTLLAAHEAVRTDPTLDAAALTDDAMVMEAAGHEVVVVTGDPAAFKVTAP +ADLDLARLELARRAPREEAPMDQPARPAAAPAPLPRVGIGTDVHAWAPEDAPRPLWLGGI +HWPGERGVAATSDGDVAAHAACNALLSAAGLGDLGAVFGVDRPEMADASGADMLREVLRL +LTEAGVAVGNVAVQVVAPRPKVGTRRAEMEAALSAALGGAPVSVSAATTDRLGFIGRREG +LVGIATALVVPAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000385.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000385.fa new file mode 100644 index 0000000000000000000000000000000000000000..1421da20ae6c31f31ec4185e31ecf3759d57d494 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000385.fa @@ -0,0 +1,50 @@ +>PROKKA_00325 +MAQRFYDTRTAQVRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDILIRWLEATGL +RVTSVRNVTDIDDKILERSAASHEAGFEASDLYPAREPWWALAYRFEKAFDAAYLALGVR +RPTYEPRATGHVPEMFALIERLMERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ +DAPDADPRGKRDPRDFALWKGAKPGEPATAVWESPWGAGRPGWHLECSAMSTKYLGTEFD +IHGGGLDLRFPHHENELAQSAAAGDGFARLWLHNGLVTYGGEKMSKSVGNTISPEEMLGM +ARPTAVRYFLGQAHYRSQLDYRPGALDEAEAAVERIEGFTARARAAGAVPPAPDGALADR +VPAAFRAAMEDDLNVPQALAALHEAVRAGNSALAGQDLDAAAARLAEVEAMTAVLGLDDV +PEGDDAAAGPVSDALDSLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGADGAT +WRLAD +>PROKKA_00040 +MAQRFYDTRTAQVRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDILIRWLEATGL +RVTSVRNVTDIDDKILERSAASYEAGFEASDLYPAREPWWGLAYRFEKAFDAAYLALGVR +RPTYEPRATGHVPEMFALIERLMERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ +DAPDADPRGKRDPRDFALWKGAKPGEPATAVWESPWGAGRPGWHLECSAMSTKYLGTEFD +IHGGGLDLRFPHHENELAQSAAAGDGFARFWLHNGLVTYGGEKMSKSVGNTISPEEMLGM +ARPTAVRYFLGQAHYRSQLDYRPGALDEAEAAVERIEGFTARARAAGAVPPAPDGALADR +VPAAFRAAMEDDLNVPQALAALHEAVRAGNSALAGQDLDAAAARLAEVEAMTAVLGLDDV +PEGDDAAAGPVSDALDSLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGADGAT +WRLAD +>PROKKA_00012 +MAQRFYDTRTAQIRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDVLIRWLEATGL +RVTSVRNVTDIDDKILDRSAASHEEGFEPSALYPAREPWWALAYRFEKAFDAAYLALGVR +RPTYEPRATGHVPEMFALIERLVERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ +DAPDADPRGKRDPRDFALWKGAKEGEPATAVWTSPWGAGRPGWHLECSAMATKYLGAQFD +IHGGGLDLRFPHHENELAQSAAAGDGFARFWLHNGLVAYGGEKMSKSVGNTISPEEMLGM +ARPKAVRYFLGQAHYRSQLDYRPGALEEAEAAVERIENFTARARTAGAVPPAVDGALADR +VPAAFRAAMEDDLNVPQALAALHEAVRAGNSALAAQDLESAAARLTEVEAMTAVLGLDDV +PEGDGDGTGPAADALDSLVRSQIEARAQARAEKDWAAADRIRDALAAAGVVVEDGADGAT +WRLAD +>PROKKA_00008 +MAQRFYDTRSAEIRDFVPLVPGQASVYYCGATVQGMPHVGHVRSAIVFDVLIRWLEATGL +RVTSVRNVTDIDDKILDRSAASQEPGFEPSEMYPADEPWWALAFRFENAFDAAYLALGVR +RPTYEPRATGHVPEMLALIERLIERGHAYPAADGSGDVYFDVRSWDRYGELTRQRVEDMQ +DAPDADPRGKRDPRDFALWKGAKEGEPVTAVWSSPWGAGRPGWHLECSAMSTKYLGGEFD +VHGGGLDLRFPHHENELAQSAAAGDPFARFWLHNGLVTYQGEKMSKSVGNTISPQEMLAM +ARPKAVRYFLGQAHYRSQLDYRPGALEEAEAAVERIENFVQRAAAALGAPELTAPLAEHV +PAAFRAAMEDDLAVPQALAVLHEAVRAGNSALAAGDDAAARARLAEVAAMTAVLGLDDVP +EASAGGSGPEAAALDSLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGAQGATW +HLAG +>PROKKA_00332 +MAQRFYDTRTAQIRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDILIRWLEATGL +RVTSVRNVTDIDDKILDRSAASHEAGFEASDLYPAREPWWALAYRFERAFDAAYLALGVR +RPTYEPRATGHVPEMFALIERLIERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ +DAPDADPRGKRDPRDFALWKGAKPGEPATAVWESPWGAGRPGWHLECSAMSTKYLGAEFD +IHGGGLDLRFPHHENELAQSAAAGDGFARFWLHNGLVTYGGEKMSKSVGNTISPEEMLGM +ARPTAVRYFLGQAHYRSQLDYRPGALDEAEAAVERIEGFTARARAAGAVPPAPDGALADR +VPAAFRTAMEDDLNVPQALAALHEAVRAGNSALAGQDLDAAAARLAEVEAMTAVLGLDDV +PEGDDAAAGPVSDALDLLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGADGAT +WRLAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000386.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000386.fa new file mode 100644 index 0000000000000000000000000000000000000000..783cd68343ad48b7574c9ef9cb3cef71af754d07 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000386.fa @@ -0,0 +1,35 @@ +>PROKKA_00326 +MSTAPRSGGSRKPKGKKGPMKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA +KRGPVKDQVRGRVKLTDETVSGRNPVLEALRAGIPAKALHVAVRIEMDDRVKEALRLCLE +QGVPVLENTKPELDRLSGEAVHQGIVLQIPPYEYADATALALDALAKHEKGHLRTPPLLI +ALDGITDPRNLGAIIRAGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQAGNLN +TTLVDLHKAGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRMVREHCQQIVSIP +IDSTMESLNASMAVGISLYEISVQRAGGR +>PROKKA_00042 +MSTAPRSGGSRKPKGKKGPMKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA +KRGPVKDQVRGRVKLTDETVSGRNPVLEALRAGIPAKALHVAVRIEMDDRVKEALRLCLE +QGVPVLENTKPELDRLSGEAVHQGIVLQIPPYEYADATALALDALAKHEKGHLRTPPLLI +ALDGITDPRNLGAIIRAGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQAGNLN +TTLVDLHKAGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRMVREHCQQIVSIP +IDSTMESLNASMAVGISLYEISVQRAGGR +>PROKKA_00009 +MSTAPRSGGSRKPKGKKGPMKGTGGHGRKALEGKGPTPKAEDRVYHKAYRAKQLSERSAA +KRGGPVRPSRPKLTDETVSGRNPVVEALRAGIPAKALHVAVRIEMDDRVKEALRLCLEQG +VPVMENTKPELDRLSGEAIHQGLVLQIPPYEYADAMTLATDALEKHEKGHLRTPPLLIAL +DGITDPRNLGAIIRSGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQAGNLNTT +LVELHRAGYFVLGLDGGGDVSLPGLSLATEPLVLVVGAEGKGLSRMVREHCQQIVSIPIN +SDMESLNASMAVGISLYEISVQRAGGR +>PROKKA_00007 +MSTAPRSGGSRAPKGKKGPQKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA +KHGGGRVPVRDQVRGRVKLTDETVSGRNPVVEALRAGIPAKALHVATRIEVDDRVKEALR +LCAENKVPVMENTRPELDRMSGEAVHQGLVLQIPPYQYADALTLGREAMEAQEKGHLRTP +PLLIALDGITDPRNLGAIIRSASAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQA +GNLNTTLVELHRMGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRMVREHCQQI +VSIPIQSEMESLNASMAVGISLYEIAVGRAGGRPVAS +>PROKKA_00333 +MSTAPRSGGSRKPKGKKGPVKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA +KRGPVKDQVRGRVKLTDETVSGRNPVLEALRAGIPAKALHVAVRIEMDDRVKEALRLCLE +QGVPVLENTKPELDRLSGEAVHQGIVLQIPPYEYADATALALDALAKHEKGHLRTPPLLI +ALDGITDPRNLGAIIRAGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQAGNLN +TTLVDLHKAGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRLVREHCQQIVSIP +IDSTMESLNASMAVGISLYEISVQRAGGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000387.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000387.fa new file mode 100644 index 0000000000000000000000000000000000000000..8f2e2a671eb4e2a9e25d52b2e4876930b4e7d550 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000387.fa @@ -0,0 +1,65 @@ +>PROKKA_00330 +MKPDTQSATAADVRLQTVTGRIPVTDVQPVVLDGRFPAKAVVGEDIPVRATVFREGHDSV +RATVRLLDPAGAEVQRVQMRPGRPGLDEVVATLRPAEPGLHQFVVEGWDDPVGTWKHAAT +VKIAAGIDVELMLAEGAALFRRAAEDAERSAEDRAVFEEVVRGLEDESLIPAQRLASAES +AEVSAVLHARPVREHLTSSELYPLDVQRELAGRGAWYEFFPRSEGARFDEASGTWSSGTF +ATAADRLPAVARMGFQVVYLPPIHPIGTTHRKGPNNTLTAGPQDPGSPWAIGGPEGGHDA +AHPDLGTVEDFEAFVAAAADEGLEVALDLALQCSPDHPWVTAHPEWFTTRVDGTIAYAEN +PPKKYQDIYPLNFDNDPDGLAQAVLDVVRGWVARGVHIFRVDNPHTKPLWFWEWLIAKVR +AEEPRVVFLAEAFTRPAMMHALGKVGFQQSYGYFTWRNTAEELAEYLQEISHETPAFYRP +NLFVNTPDILTEYLQHGGPGAFRIRAVVAATASPLWGVYAGFELFEHVARPGAEEYIDNE +KYEYRPRDWEGAEAAGASLAPYLTRLNEIRAAHPALGDLQNLTLHASTHPDLLVFSKTRS +ARPEGAHRDAEAVTDAGPAEDTLIVVVTTNPHDVAEATLDLDLEALRLRPEDRDASGAVE +VEDLLTGQRWRWGRTPYVRLDPHVEPAHVLRIVRNG +>PROKKA_00046 +MKPDTQSATAADVRLQTVTGRIPVTDVQPVVLDGRFPAKAVVGEDIPVRATVFREGHDSV +RATVRLLDPAGAEVQRVQMRPGRPGLDEVVATLRPAEPGLHQFVVEGWDDPVGTWKHAAT +VKIAAGIDVELMLAEGAALFRRAAEDAERSAEDRAVFEEVVRGLEDESLIPAQRLASSES +AEVSAVLHARPVREHLTSSELYPLDVQRELAGRGAWYEFFPRSEGARFDEASGTWSSGTF +GTAADRLPAVARMGFQVVYLPPIHPIGTTHRKGPNNTLTAGPQDPGSPWAIGGPEGGHDA +VHPDLGTVEDFEAFVAAAADEGLEVALDLALQCSPDHPWVTAHPEWFTTRVDGTIAYAEN +PPKKYQDIYPLNFDNDPDGLAQAVLDVVRGWVARGVHIFRVDNPHTKPLWFWEWLIAKVR +AEEPRVVFLAEAFTRPAMMHALGKVGFQQSYGYFTWRNTAEELAEYLQEISHETPAFYRP +NLFVNTPDILTEYLQHGGPGAFRIRAVVAATASPLWGVYAGFELFEHVARPGAEEYIDNE +KYEYRPRDWEGAEAAGASLAPYLTRLNEIRAAHPALGDLQNLTLHASTHPDLLVFSKTRS +ARPEGAHRDAEAVTDAGPAEDTLIVVVTTNPHDVVEATLDLDLEALRLRPEDRDASGAVE +VEDLLTGQRWRWGRTPYVRLDPNVEPAHVLRVVRNG +>PROKKA_00005 +MSNSKQAAQSTPVPDVRLQTVTGRIPVTGVQPVVQDGRFPAKAVVGEDIPVRATVFGEGH +DAVRATVRLLDPSGAEVQRVHMRPGRPGLDEFLATLRPSETGVHHFVVEGWHDPVGTWLH +AATVKLAAGVDVELMLAEGAALFRAAAEDAERSAQDRAAFEETARVLADEGLVPAQRLAG +AESAELAAVLGARPLREHVTSSELLPLDVQRELAGRGGWYEFFPRSEGARFDEAAGTWSS +GTFTTAARRLPAVARMGFQVVYLPPIHPIGTAHRKGPNNTLTAGPQDPGSPWAIGAAEGG +HDAVHPDLGTIADFEDFVAAAADEGLEVALDLALQCSPDHPWVAEHPEWFTTRVDGTIAY +AENPPKKYQDIYPLNFDNDPEGLAQAVLEVVQGWVGRGVHIFRVDNPHTKPLWFWEWLIA +RVRAEEPRVVFLAEAFTRPAMMHALGTVGFQQSYGYFTWRNTAAELAEYLEEISHETPAF +YRPNFFVNTPDILTEYLQHGGPGAFRIRAVVAALANPLWGVYAGYELFEHVARPGAEESI +DNEKYEYRPRDWEGAEAAGASLAPYLTRLNEIRAAHPALRDLQNLTLHRSTHQDLLVFSK +TRTARPEGEHRDAEAVTDAGAHEDTVITVVTVNPHHVAEATLDLDLSALRLRPEDLDESG +SFEVEDLLTGQRWRWGRTPYVRLDPHVEPAHVLRVVRHG +>PROKKA_00006 +MSTSKPRPAAHPAPPAPALPDVRRTTLTGRIPVSNVQPTVEEGRFPAKAIVGEDVPVRAN +VYREGHDAVRATVRLLGPDGAEVQRVHMRPGRPGLDEAVATLRPSEPGVHHFVVEGWDDP +VGTWRHNASVKLAAGVDVELMLDEGAALFRAAAQDPERGAADRAVFEEAVRGLEDASLAP +VQRFAVTQSAEVSAVLDARPVRRWVTSSELYPLDVQRPLAGRGAWYEFFPRSEGARYDEA +AGLWHSGTFRTAAERLPAVAAMGFQVVYLPPIHPIGVAHRKGPNNTLTAGPQDPGSPWAI +GGEAGGHDAIHPGLGTFEDFDAFQERVRELGMELALDLALQCSPDHPWVTEHPEWFTHRV +DGSIAYAENPPKKYQDIYPLNFDDDADGLARAVLDVVLGWVRRGVHIFRVDNPHTKPLWF +WEWLIREVRAVEPEVVFLAEAFTRPAMMHGLGRVGFQQSYGYFTWRNTREELEEYLEEIT +AETAGFYRPNFFVNTPDILTDYLQHGGPGAFKARAVIAATSNPLYGVYAGFELFEHVARP +GAEEYIDNEKYEFRPRDWAGEEAAGRSLAPYLTRLNRIRAEHPALQDLQNLTLHSATDPE +LLVFSKTRSALPEGDHRDAAAVTDAGSAEDTVVVVVACDPHRVAEATLRLDAEALRVRPE +DRDEEGRFEVEELLTGARWRWDEQPYVRLDPAVEPAHVLRVVRRG +>PROKKA_00337 +MKPDTQSATAADVRLQTVTGRIPVTDVQPVVLDGRFPAKAVVGEDIPVRATVFREGHDSV +RATVRLFDPAGAEVQRVQMRPGRPGLDEVVATLRPAEPGLHQFVVEGWDDPVGTWKHAAT +VKIAAGVDVELMLAEGAALFRRAAEDAERSAEDRAVFEEVVRGLEDESLIPAQRLASAES +AEVSAVLHARPVREHLTSSELYPLDVQRELAGRGAWYEFFPRSEGARFDEASGTWSSGTF +ATAAGRLPAVARMGFQVAYLPPIHPIGTTHRKGPNNTLTAGPQDPGSPWAIGGPEGGHDA +VHPDLGTVEDFEAFVAAAADEGLEVALDLALQCSPDHPWVTAHPEWFTTRVDGTIAYAEN +PPKKYQDIYPLNFDNDPGGLAQAVLDVVRGWVARGVHIFRVDNPHTKPLWFWEWLIAKVR +AEEPRVVFLAEAFTRPAMMHALGKVGFQQSYGYYTWRNTAEELAEYLQEISHETPAFYRP +NLFVNTPDILTEYLQHGGPGAFRIRAVVAATASPLWGVYAGFELFEHVARPGAEEYIDNE +KYEYRPRDWEGAEAAGASLAPYLTRLNEIRAAHPALGDLQNLTLHASTHPDLLVFSKTRS +ARPEGAHRDAEAVTDAGPAEDTLIVVVTTNPHDVVEATLDLDLEALRLRPEDRDASGAVE +VEDLLTGQRWQWGRTPYVRLDPHVEPAHVLRIVRNG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000389.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000389.fa new file mode 100644 index 0000000000000000000000000000000000000000..6a00828e2183df9cc56ef2e99029c6f12ef2af4c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000389.fa @@ -0,0 +1,21 @@ +>PROKKA_00335 +MSWWPFPRPSASPSPDDDGAPAAAELEEAVAALRQLLRAERHRLRPDSWALAWEMVEQAA +EYAPAWTRLQRTRPVETQELVLALTGRLEPLLCDFLALPDSEKPTHADAVHARLREQGTE +HGRLRRRLTRALTARLRAGEEL +>PROKKA_00051 +MSWWPFLRSSASPSPDDDGAPAAAELEEAVAALRRLLRAERHRLRPDSWALAWEMVEHAA +EYGPAWTRLQRTRPVETQELVLALTGRLEPLLRDFLALPDSEKPAHADAVHARLREQSTE +HGRLRRRLTRALTARLRAGEEL +>PROKKA_02680 +MAWWPFRGPSGAPRDDDASTAGRASLEAAVHSLRALMTAERHRLRPDSRDLAWTITERAA +EYGPAWDRVSAQRPAEAQELLLLLSHRLEPALRDFLDLPDSQKPRHADELHGRLSELQTE +AQRLGRRLTRALSSRLRARGEL +>PROKKA_02492 +MAWWARRRLSSSGPAPLGKPPLVAAEELRRLTDELSEILQRESARIRPDAAAVLRSFLNR +SRALLPAWDRTAPARSAEALAAYELLRDRVLPGLQDWLCLPDHLKPVHADDLLADAQAWE +GDLSHHAARLTQVLTARGRAVRELDERQ + +>PROKKA_00342 +MSWWPFLHSSASPSPDDDGAPAAAELEEAVAALRRLLRAERHRLRPDSWALAWEMVEHAA +EYGPAWTRLQRTRPVETQELVLALTGRLEPLLRDFLAIPDSEKPAHADAVHARLREQSTE +HGRLRRRLTRALTARLRAGEEL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000390.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000390.fa new file mode 100644 index 0000000000000000000000000000000000000000..9926a64ba10e9de2394d17b119551e53b1284cf1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000390.fa @@ -0,0 +1,17 @@ +>PROKKA_00337 +MTEQTPSLEHPQVRKNAERYEIVVDEAGTVAGYTVAIDYDTGDGPTQRIFPHTKVDHGYE +GRGLASTLVREALKDTVAAGRRIVPVCPYVKDWVNEHDDVAGEVDPAGPEHLQFLESRQD +>PROKKA_00053 +MTEQTPSLEHPQVRKNAERYEIVVDDAGTVAGFTVAIDDDTADGPAQRIFPHTKVDHQYE +GRGLASTLVREALKDTVAAGRRIVPVCPYVKDWVDEHDDVAGEVDPARPEHMQFLESRQD +>PROKKA_02676 +MTENTPTLDAPQVRKVGEKYEIVVDGDGTVAGYTLAIDYEGTDGVAQRIFPHTKMAEEYG +GRGLASVLVREALKDSVAAGFRIVPVCPYVKQWTQKHDDVAGDVDQARPEHLQFLEEHAR +RRSEG +>PROKKA_02488 +MTEQTSSLDHPQVRKNAEKYEIVVDADGTVAGYTLAIDYTAEDGTAEDGTEQRIFPHTKL +EDAYEGKGLASTLVREALRDTEAAGRRIVPVCPYVKQWADKHADEVEGQVDQPRPEHLQF +LEKHAQERKQG +>PROKKA_00344 +MTEQTPSLEHPQVRKNGERYEIVVDDAGTVAGFTVAIDDDTADGPAQRIFPHTKVDHEYE +GRGLASNLVREALKDTVAAGRRIVPVCPYVKDWVDEHDDVAGEVDPARAEHLQFLESRQD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000391.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000391.fa new file mode 100644 index 0000000000000000000000000000000000000000..74920839b02788a42649c6ae46b7eed580c1ba4c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000391.fa @@ -0,0 +1,20 @@ +>PROKKA_00338 +MTAADTPAPRQDPLAFFLDKAVPEAWHAVGPLASAARGAAEQAGLDRQLVELVNLRVSQL +NGCVFCLDRHTRQGADAGLSVQRLGLLPAWREAGAVYSEQERAALELAEAVTDLPEQEQL +NYVQASTAAVLTDAQYAAVQWVAIVMNLTNRISILSHHPVRRRDG +>PROKKA_00054 +MTAADTPAPRQDPLAFFLDKAVPEAWHAVGPLASAARAAAEQAGLDRQLVELVNLRVSQL +NGCGFCLDRHTRQGADAGLSVQRLGLLPAWREAGAVYSEQERAALELAEAVTDLPEQEQL +NYVQASTAAVLTDAQYAAVQWVAMVMNLTNRISILSHHPVRRRDD +>PROKKA_02674 +MSAAENPATRKDPLAFYLDKAVPDAWKAVGGLAAAVRTAAEEAGLDRQLVELVNLRVSQI +NGCGFCLDLHAREGAKAGLNAQRMALLPAWREAEAVYSEQERAALELAEAVTELPEQEQL +HYVQASTAAALTDAQYAAVQWAAMVMNLTNRISILSHHPVRRRED +>PROKKA_02486 +MSSPHDDAAPARKDPLAFYLDKAVPEAWVAVGGLAAAARRAAVEAGLDEQLMELVNLRVS +AINGCAYCLDVHTRKGVGAGLSDQRRGLLSAWREAPEVYTELERAALELAEAVTELPEQE +QQQYVQLSTHGVLTDAQYAAVQWLAIVMNVTNRISILSHHPVRRHDS +>PROKKA_00345 +MTAADTPAPRQDPLAFYLDKAVPEAWHAVGPLASAARDAAEQAGLDRQLVELVNLRVSQL +NGCVFCLDRHTRQGADAGLSVQRLGLLPAWREAGAVYSEQERAALELAEAVTDLPEQEQL +NYVQASTAAVLTDAQYAAVQWVAIVMNLTNRISILSHHPVRRRDG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000397.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000397.fa new file mode 100644 index 0000000000000000000000000000000000000000..324602748703ba71701769bd3d8a490850d27824 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000397.fa @@ -0,0 +1,75 @@ +>PROKKA_00344 +MSTSTVRSAPASTYRLQVSPDLPLESVAGLVPYLRRLGVDWLYLSPLLEAEPGSDHGYDV +VDPTRLDAARGGAEGLDAVARAAHEAGMGVLVDIVPNHVGVATPQANPAWWDVLTHGPEA +AHAAWFDVDWAAGGGSLLIPVLGDGPDGDADAELNRLVVDEGRLRYWDNVYPLAPGSLEA +AEAETGLRAAEVFAEADPAKESTAERARLARAVHDRQHYRLVGWRRGDAELNYRRFFTVT +TLAGVRVDEPEVFDAVHAEPARWVREGLVDGLRVDHPDGLADPAGYARRLRSHVLPEGYL +VVEKILEPGEALPADWPVDGTTGYDALGEVERVFMHPEAAGDAAEDARRRREWDEAVVRA +KHDVATGSLAAETARLVREVRAVHALGAHPDEDVAAAFAAVLARLPVYRTYLPVGLAVLE +GALADAAEAEPALAAVLGDLRPELTDPDSPVARRFQQTSGMVMAKGVEDRSFYRYTRWAN +LNEVGGDPSHVALSLADFHAAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEPDR +WAAELAELRRLHPLGHPDAERLLWESIVGVWPTDGTAPEEERILGFLQKASREAALATSW +TDQDPEFEARLAALAAAVTSPEGPARGVLQAVADRIAEPGLVVQLGHKLVQLAAPGVPDV +YQGTEVPFPTLVDPDNRRPVDFAARADLLDRLDAGHTPGLDDPAAAKLAVVAAVLRTRRD +RPELFTGHRPLDVSGPAAEHAIAFDRGGALAVATRWPVRLAAAGGWGETVVTVPAGRWED +AVTGHPVHPDARGAVRLDELLSTLPVALLVPAHAPSDRRERTAP +>PROKKA_00060 +MSTSTVRSAPASTYRLQVSPDLPLESVAGLVPYLRRLGVDWLYLSPLLEAEPGSDHGYDV +VDPTRLDAARGGAEGLDMVARAAHEAGMGVLVDIVPNHVGVATPRANPAWWDVLTHGPEA +AHAAWFDVDWAAGGGSLLIPVLGDGPDGDADAELNRLVVDEGRLRYWDNVYPLAPGSLEA +AEAETGLRAAEVFAEADPASEPTAEQARLARAVHERQHYRLVGWRRGDAELNYRRFFTVT +TLAGVRVDEPEVFDAVHAEPARWVREGLVDGLRVDHPDGLADPAGYARRLRSHVLPEGYL +VVEKILEPGEALPADWPVDGTTGYDALGEVERVFMHPEAAGDAAEDARRRREWDEAVVRA +KHDVATGSLAAETARLVREVRAVHALGAHPDEDVAAAFAAVLARLPVYRTYLPVGLAVLE +GALADAAAAEPGLADVLGDLRPELTDPDSPVARRFQQTSGMVMAKGVEDRSFYRYTRWAN +LNEVGGDPSHVALSLADFHSAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEPDR +WAAELAELRRLHPLGHPDAERLLWESIVGVWPTDGTAPEEERILGFLQKASREAALATSW +TEQDPEFEARLAALAAAVTSPEGPARGVLQAVADRLAEPGLVVQLGHKLVQLAAPGVPDV +YQGTEVPFPTLVDPDNRRPVDFAARADLLDRLDAGHTPGLDDPAAAKLAVVAAVLRARRD +RPELFTGHRPLDVSGPAAEHAIAFDRGGALAVATRWPVRLAAAGGWGETVVTVPAGRWED +AVTGHPVHPDARGAVRLDELLSTLPVALLVPAHAPSDRRERTAP +>PROKKA_02625 +MSTSTERPVPSSTYRLQVGPDLPLESVAGLVPYLRRLGVGWLYLSPILEAEPGSDHGYDV +VDPTRLDAARGGAEGLEAVARAAREAGLGVLVDIVPNHVGVATPEANPAWWDLLAHGSEA +AHAPWFDVDWTAGEGRVLLPVLGDGPDGEAEAELDRLVVETGDDGGRLRHWDTRYPLAPG +SLAAAEEETGLRAADVFAGAEPAHEPTPERARLARAVHARQHYRLIGWRRGDAELNYRRF +FTVTTLAGVRVEDPEVFDAVHAEPARWVREGLVQGLRVDHPDGLADPAGYVRRLRSHVLP +EGYLVVEKILEPGEELPADWDVDGTTGYDALGEVERVFMHPVAAGGPNEDERRRRDWDEV +VAEAKRDVATGSLVAETARLVREVRGVHALGAHADEDVAAAFAAVLSRLPVYRTYLPVGL +AVLERALADAGEAEPALAPVLADLGPELADPDSPVARRFQQTSGMVMAKGVEDRSFYRWT +RWANLNEVGGDPAHVQLSLDAFHAAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAE +EPDRWAGELAGLRALHPLGDEGAERLLWESIVGVWPTDGTAPSTERILGFLQKASREAAL +STTWTDQDPEFEGRLEDLARAVTAPDSPARGAVQAVADRIAEPGLVVQLGHKLVQLAAPG +VPDVYQGTELPVPSLVDPDNRRPVDFHARADLLDRLDAGHVPGLDDADAAKLAVVAAVLR +ARRDRPELFTRHRRLDVSGPAAEHAVAFDRGGALAVATRWPVHLAAAGGWGETVVTLPPG +RWEDAVTGRPVHPDARGAVRLDELLSTLPVALLVPARAEEATP +>PROKKA_02477 +MSHTDAVSAPASTYRLQVGPDLPLDSVAGLVPYLRRLGVDWLYLSPILAADPGSDHGYDV +VDPARVDPARGGPEALAALAAAAHEAGMRLLVDVVPNHLGVATPLANPAWADLLAHGPEA +AHAAWFDVDWEAGDGRVLLPVLGDGPEGDPRGAEAGLDQLIVDPSAGEHGVLRHWDTAYP +LAPGSLAAAEEETGLRAAEVFAGADPAAPTDDAARLGRAVHDRQHYRLVHWRRGDAELNY +RRFFTVTTLAGLRVEDPEVFDATHVEIGRWVSEGLVHGLRIDHPDGLTDPGAYLRALRER +VLPEGYLVVEKILEPGEDLPAAWPVDGTTGYDALGELERVFMPADPDGPAADDAARAAWE +ALIAEAKRDVATGSLAAETARLVREARAAVVLGAHSDEALTEAFADVLASLDVYRTYLPV +GAERLAAAVARARAAHPEPADVLDDVARVLADPDSPVARRFQQTSGMVMAKGVEDRSFYR +WTRWANLNEVGGDPAHLDLPLAGFHALQRARQASWPTTMTALTTHDTKRSEDVRARITAL +AEEPASWEDALARLRTAHPLDAPGLEELVWESIVGVWPTDGTAPEADRLEEFLLKSAREG +QEHTSWTAQDDAYEGRLRALAADVVAPDSAARAVVQEIADRIAEPGLTVQLGRKLVQLAA +PGVPDVYQGTEIPFPTLVDPDNRRAVDFEARADLLDRLDAGHAPTLDEPEAAKLLVVSRA +LRARRDRPELFHGYRPLDVDGPAAAHLIAFSRGGALALATRLPLTLAAAGGWRETVVSLP +PGRWRCAVTGRAVTPDARGAVRVDDVLSQLPVALLLPEEETA +>PROKKA_00351 +MSTSTVRSAPASTYRLQVSPDLPLESVAGLVPYLRRLGVDWLYLSPLLEAEPGSDHGYDV +VDPTRLDAARGGAEGLDMVARAAHEAGMGVLVDIVPNHVGVATPPANPAWWDVLTHGPEA +AHAAWFDVDWAAGDGSLLIPVLGDGPDGNADAELDRLVVDAEGGRLRYWDNVYPLAPGSL +EAAETETGLRAAEVFAAADSAKEPTAEQARLARAVHDRQHYRLVGWRRGDAELNYRRFFT +VTTLAGVRVEEPEVFDAVHAEPARWVREGLVDGLRVDHPDGLADPAGYARRLRSHVLPEG +YLVVEKILEPGETLPADWPVDGTTGYDALGEVERVFMHPEAAGDAAEDARRRREWDEAVV +RAKHDVATGPLAAETARLVREVRAVHALGAHPDEDVAAAFAAVLARLPVYRTYLPVGLAV +LEGALADAAEAEPGLADVLGDLRPELTDPDSPVARRFQQTSGMVMAKGVEDRSFYRYTRW +ANLNEVGGDPSHVALSLADFHAAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEP +DRWAAELAELRRLHPLGHPDAERLLWESIVGVWPTDGTTPEEERILGFLQKASREAALAT +TWTDQDPEFEARLAALAAAVTSPEGPARGVLQAVADRIAEPGLVVQLGHKLVQLAAPGVP +DVYQGTEVPFPTLVDPDNRRPVDFAARADLLDRLDAGHTPGLDDPAAAKLAVVAGVLRAR +RDRPELFTGHRPLDVSGPAAEHAIAFDRGGALAVATRWPVRLAAAGGWGQTVVTVPAGRW +EDAVTGHPVHPDARGAVRLDELLSTLPVALLVPAHAPSDRRERTAP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000400.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000400.fa new file mode 100644 index 0000000000000000000000000000000000000000..c738d888e7bcb4b30135ffd280ee938765fb6c1d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000400.fa @@ -0,0 +1,56 @@ +>PROKKA_00349 +MQSSTPRSTRRIGALVAGAVLAGGTLTSSPALAAPSGAAPAAPAASPTVASPLAAAQVED +PNADGYDSFIVTYKETAANAHAKGRANAWGKAAKEAGVSVKELRETALGSRVVTVDRKLD +QAESAKFMADLKASGAVEAVEPDAILTATGLSPVDALYSQQWGFTGTHGMRVPGAWDRTT +GSGATVAVIDTGITSHPDLDRNVVPGYDFISDSAAARDGGGRDSNPRDEGDWYAAGECGT +AGASDSSWHGTHVAGTVAAVADSQGVVGVAPNAKIQPIRVLGKCGGSLSDIADAVVWAAG +GTVAGVPANPNPADVINMSLGGSGMCGTTYQNAINAAVSRGVPVVVAAGNENQPAANVRP +ANCQNTIVVAASTSQGARASFSNYGSAVDVTAPGANIISTVNNGATTPTTAGHAAYNGTS +MATPHVAGLAALLLAAQPSLTPAQVESTLRSTARSMPVTCSAGCGAGLADASAAVSSLGG +AQTEPGPAPVASLIVNGGFESGSTGWTGTPTGFVRTDAAKAASGQAFAQLNGVGRRNTTT +VEQKVTVPASGATLTYALQVDTAETTASRSYDLLDVQVVTGATGTYTVASHSNLDKGGYA +TRTVDLSRFAGTTVTLRFRGTEDSSAATTFRIDEVAVTAR +>PROKKA_00065 +MQSSTPRSTRRRIGALVAGAVLAGGTLTSSPALAAPSGGAPAAPAASPTAASPLAAAQAE +DPNADGYDSFIVTYKETAANAHAKGRANAWGKAAKEAGVSVKELRETALGSRVITADRKL +DQAESAKFMADLKASGAVEAVEPDALLTATGLSPVDALYSQQWGFTGSHGMRVPGAWDRT +TGSGATVAVIDTGITSHPDLDRNVVPGYDFISDSAAARDGGGRDSNPRDEGDWYAAGECG +TAGASDSSWHGSHVAGTVAAVADSQGVVGVAPNAKIQPIRVLGRCGGSLSDIADAVVWAA +GGTVAGVPANPNPADVINMSLGGSGVCGTTYQNAINAAVSRGVPVVVAAGNENQPAANVR +PANCRNTIVVAASTPQGARASFSNYGSAVDVTAPGANIISTVNNGATTPTTAGHAAYNGT +SMATPHVAGLAGLLLATKPSLTPANVESTLTSTARSMPVTCSAGCGAGLADAARAVSSLG +GSS +>PROKKA_02612 +MKSSVQHSTRRRVGALLAGAVLAGGALTSSPAFAAPAEGARAEQAPRPVAAAPLATVDAA +DPNADGYDSFIVTYKETAQNNNGKGRALAWGKAAKAAGVSVKELRETALGSHVVQADRKL +DQSESARFMADLKASGAVEDVEPNAIMTATGLSPADALYSQQWGFTGTNGMRVPGAWDYN +TGSGVTVAVLDTGITSHPDLDRNVVAGYDFISSSAAARDGNGRDSNPRDEGDWYAAGECG +ASQPGNSSWHGTHVAGTVAAVTDTQGVVGVAPNAKIQPVRVLGKCGGSLADIADAIVWAS +GGSVTGVPANANPADVINMSLGGSGTCGTTYQNAINAAVNRGVPVVVAAGNENQPAANAR +PANCSNVITVAASTSQGARSSFSNYGSAVDVTAPGSSIISTINRGLTTPTTAGHASYNGT +SMATPHVAGLTALMLAQQPGITPAQVESTLKSTARSMPVACSAGCGAGLVDATRAVAALG +GGSTTPTPTGVIVNGGFESGATGWTGTPSDFVGNTAGYARSGSNYGVLNGYGRSNTGTVE +QRVTVPASGASLSYWLQVGSDETTTRSQYDTLAVQVVDGSQTTTVKSHSNLEKGTSYAQH +TVDLSAYKGKTVTLRFRGVEDYSNSTVFRIDDVAVTAK +>PROKKA_02471 +MTALTSPSARRRVGSLLAAAVLAGTALTAAPTLAAAERPAEPARTSPAAAAPLADPNADG +YDSFIVTYRETAANSTAQGRAKAWGRAAREAGVSVKELRETALGSRVIATDEKLTQEESA +AFMADLRASGAVEAVEPNVIMTRAALSPADPYYADQWGFTGVNGMRVPGAWDVSTGTGAI +VGVIDTGQTDHADLNANTVPGYDFISDATTARDGGGRDADPRDEGDWYLAGECGQSRASN +SSWHGSHVAGTVAAVANTQGVVGVAPGAKVQHARVLGKCGGTLADIADAIVWSSGGSVPG +VPANPTPVDVINMSLGGQGTCGTTYQNAINAAVGRGVPVVVAAGNENQSAANARPANCQN +TITVAATDVNGNRASYSNYGSAVDVAAPGSGIISTVNAGTTTPTAGAYAQYNGTSMATPH +VAGTVALMLAEDATLTPAEVESSLKTNSRPIPGVCAEGCGAGLVDAAKTLASLRGGTTDP +HPVTPVPGAEKLVNGGFESGLTGWTATGRVAASSTAGLSATGSLHAALNGKGGTSTATLT +QKAVLPAGAAATLSYAVRVDSAETTTARQWDKLTVSVSDGATTTTLRTHSNLDKGRGYLA +QAADLSAYAGKTVTISFSGTEDGSGATTFRIDDVSVKAG +>PROKKA_00356 +MQSSPPRSTRRRIGALVAGAVLAGGTLTSSPALAAPSGDAPAAPAATPTAASPLAAAQVE +DPNADGYDSFIVTYKETAATAHAKGRANAWGKAAKEAGVSVKELRETALGSRVIKADRKL +DQAESAKFMADLKASGAVEAVEPDAILTATGLSPVDALYSQQWGFTGTHGMRVPGAWDRT +TGSGVTVAVIDTGITSHPDLDRNVVPGYDFISDGRAARDGGGRDSNPRDEGDWYAAGECG +TAGASDSSWHGTHVAGTVAAVADSQGVVGVAPNAKIQPIRVLGKCGGSLSDIADAVVWAA +GGTVAGVPANPNPADVINMSLGGSGMCGTTYQNAINAAVSRGVPVVVAAGNENQPAANVR +PANCRNTIVVAASTSQGARASFSNYGSVVDVTAPGANIISTVNNGATTPTTAGHAAYNGT +SMATPHVAGLAALLLAEQPSLTPAQVESTLTSTARSMPVTCYAGCGAGLADATRAVSSLG +GSS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000402.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000402.fa new file mode 100644 index 0000000000000000000000000000000000000000..9bfc038ca1b268c50dd4469da93ad207778ab677 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000402.fa @@ -0,0 +1,25 @@ +>PROKKA_00352 +MEFIAPLDPGWEAALAPQAAAFEQVGERLRARRAGGEQVLPAPEHILRAFRQSFADVRVL +VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLANIHRELHDDLGITPPAHGDLSAWTDQGV +LLLNRALSVRAGAPGSHRGLGWEQITEAAVRALCARGTPLVGLLWGADARRMAPLLTAAG +AGVVESPHPSPLSAHRGFFGSRPFSRVNRLLEAAGAAPVDWRLPD +>PROKKA_00068 +MEFIAPLDPGWEAALAPQAAAFEQVGEALRARRAAGEQVLPAPEHILRAFRQPFADVRVL +VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLANIHRELHDDLGITPPAHGDLSAWTDQGV +LLLNRALSVRAGAPGSHRGLGWEQITEAAVRALCARGTPLVGLLWGADARRMAPLLAAAG +AGVVESPHPSPLSAHRGFFGSRPFSRVNRLLEAAGAAPVDWRLPD +>PROKKA_02609 +MELIAPLDPGWEAALAPQAAALEQVGAALTQRRAAGEQVLPAPEHILRVFRRPFEDVRVL +VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLVNIHRELQDDLGIAPPAHGDLSAWADQGV +MLLNRALTVRAGAPGSHRGLGWEQITEAAVRALCERGTPLVGLLWGADARRMAPLLTQAG +AGVVESPHPSPLSAHRGFLGSRPFSRVNRLLEEAGAEPVDWRLPD +>PROKKA_02468 +MDLISPLDPGWAAALADQEEALVRVGAELTARRAAGEHVLPAPEHILRAFRQPFADVKVL +IVGQDPYPTPGHPIGLCFACDRHVRPLPRSLANIHRELHDDLGVPPAAHGDLSAWTDQGV +LLLNRVLTVRAGAAGSHRGIGWEQITEAAVRALVARGTPLVGLLWGNDARRLAPLLTAGG +AGVVESAHPSPLSASRGFFGSRPFSRVNALLEAAGASPVDWRLPD +>PROKKA_00359 +MEFIAPLDPGWEAALAPQAAAFEQVGERLRARRAAGEQVLPAPEHILRAFRQPFADVRVV +VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLANIHRELHDDLGIAPPAHGDLSAWTDQGV +LLLNRALSVRAGAPGSHRGLGWEQITEAAVRALCARGTPLVGLLWGADARRMAPLLTAAG +AGVVESPHPSPLSAHRGFFGSRPFSRVNRLLEAAGAAPVDWRLPD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000404.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000404.fa new file mode 100644 index 0000000000000000000000000000000000000000..a8229ca6c43881bb5f57cfa1899861af05f588d3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000404.fa @@ -0,0 +1,35 @@ +>PROKKA_00354 +MAYQPDRFDEVPEYTDQRGAHRESFAVAGATATGGGRRLSPLLWVAGLVLLAGLFVGVVL +PWLTGDRSEPVAAESSTTAPAAAPSTSASSVSSSASSASASTASATESATPSEDAVEASR +SAAAAESSRAAQEAAAAEAAESSQAAASSRAAAEAQAAEASRSEAAAQSAEASRAAAEAQ +AAEASRSEAAAQSAEASRSAAAVQAAESSRAAASRSAAAAEASRSQSAAASSSRAAAQSA +AASSSRAAAQSAAVRGTHVTVYNATRTQGLAASYAQRLTGAGYTSVDAKNWSGYGIQSST +VLYNGSANKAAAEAVGKELGFPVMQTPNLQVNGIAVVVTS +>PROKKA_00070 +MAYQPDRFDEVPEYTDQRGAHRESFAAAGATAAGGGRRLSPLLWVAGLVLLAGLFVGVVL +PWLTGDRSEPVAAESSTTAPAVEPSPSTSTSASSESSSASSASASTASATESATPSEDTA +EASRSAAAAAAESSRVAQEAAAAEAAESSRAAESSRAAAEAAESSRAAAEAQAAEASRSE +AAAQSAEASRSAAAVQAAESSRAAASRSAAAAEASRSQSAAASSSRAAAQSAAASSSRAA +AQSAAVRGTHVTVYNATRSQGLAASYAQRLTSAGYTSVDAKNWSGYGIQSSTVLYNGSAN +KAAAEAVGKELGFPVMQTPNLQVNGVAVVVTG +>PROKKA_02607 +MAYQPDRFDEVPEYTDQRGAHRASFAAPAGAAAAGGGARRFSPLLLVAGLVLLAGLFVGV +VLPWLTGDRSEPVAAESSASSPAADPSTSSEPASPTEGAATTEPASPSEDAAAAEASRSQ +AAAQSAAEQSAAEAAAASSRAAEEAAAAEASRSAEAAQAAEASRSAAAAAEASRSAGAAQ +AAEASRSAEAAQAAEASRSAAAAAEASRSAEAAQAAEASRSAAAAAEASRSAEAAQAAEA +SRSAAAQAAEASRSAAAQAAAAARSTNVTVYNATRTTGLAASYAQRLRSAGFTSVSAQNW +GGYGIQSSTVLYNGSGNQAAAEAVAAELGFPVLQTPNLQVNGVAVVVTG +>PROKKA_02466 +MAYPADRFDDVPEYTDQSGAHRESFAAAPAAAGAAGATAAGTEAAAGGGILKWLLAAAAA +VLLVGLFLGLVLPRLNGGDDKPVAGAASSSSSSEPAADASSSSSDAPSSDASSSAGPDSA +APAAPSSDAGAESAAAPSSDAAVESRAAAESSQAAAESSQAAADAQRSRDDAARAASESA +QAAADASSADAAARERAASESAQAAADASRAAEASRSAEASRSAEASRSAEASRSAEASR +SAEASRSAAASRSAAAQESADRAVKSTPVNVYNATRRNGLAASYADRLTGAGYTRVTADN +WPGFRVTSNTVMYNGADKRAAAEAVGRELGMPVQQVPNLQVPGIAVVVVR +>PROKKA_00361 +MAYQPDRFDEVPEYTDQRGAHRESFAAAGATAAGGGRRLSPLLWVAGLVLLAGLFVGVVL +PWLTGDRSEPVAAESSTTAPAVEPSTSASSESSSASSASASTASATESATPSEDTAEASR +SAAAAAAESSRVAQEAAAAEAAESSQAAASSRAAAEAQAAEASRSEAAAQSAEASRSAAA +VQAAESSRAAASRSAAAAEASRSQSAAASSSRAAAQSAAASSSRAAAQSAAVRGTHVTVY +NATRTQGLAASYAQRLTGAGYTSVDAKNWSGYGIQSSTVLYNGSANKAAAEAVGKELGFP +VMQTPNLQVNGIAVVVTS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000407.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000407.fa new file mode 100644 index 0000000000000000000000000000000000000000..b8d6605a61846f910a45566244dd12d4afd9f346 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000407.fa @@ -0,0 +1,59 @@ +>PROKKA_00358 +MRARLDAAAARVRHPRAWLRGAWQGQSLRTKLVVMIAALMLALVAVTAVATAVLFRQEAV +RQLDEDMAANRDTVSMYLANVAQTGEYYMPQLPILRFYGVVWDNEGARVVQTPVMPGADE +PALPDITPAEALERGSASFEVPGTQPDSSGWRVQLYGLSSGDGTMAVALPLQSVTSSVER +VTSIVVTIGLLATAGTVIVANLAVQRAFRTLNRVERTAAKIAAGDLSQRVESAAPDTEVG +RLSRSLNAMLAHIESAFRDKEISEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGLREE +EDVAAAMQRIESEATRMTRLVEDLLTLARLDEQRPLEHAPVDLLILAMDSMMDASVNAPD +RKVTLVGPDGDRAAPAPILGDENRMRQVVVNLMANALRYTPAGTPIEIAVGTVDHLGGQA +GADGAGRSSVIEIRDHGPGVSEEDRARIFERFYRADTSRHRETGGTGLGLAIVAAIVAQH +GGSVRLLETEGGGATFSVHLPWAPFEDEADEDVEDERLPARDTDDDAAGPPTGPLALAAP +SGAGASAADAARSSRLLRAAERFRRASAERRRRASAPAQAPQADPPSPGEDDPAAERDAR +P +>PROKKA_00074 +MRARLDAAAAHVRHPRAWLRGTWQGQSLRTKLVVMIAALMLALVAVTALATAALFRQEAV +RQLDEDMAANRDTVSMYLANVAQTGEYYMPQLPILRFYGVVWDNEGARVVQTPVMPGADE +PALPDITPAEALERGSASFEVPGTQPDSSGWRVQLYGLSSGDGTMAVALPLQSVTSSVER +VTSIVVTIGLLATAGTVIVANLAVQRAFRTLNRVERTAAKIAAGDLSQRVESAAPDTEVG +RLSRSLNAMLAHIESAFRDKEISEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGLREE +EDVAAAMQRIESEATRMTRLVEDLLTLARLDEQRPLEHAPVDLLILAMDSMMDASVNAPD +RKVTLVGPDGDRAAPAPILGDENRMRQVVVNLMANALRYTPAGTPIEIAVGTVDHLGGQA +GADGAGRSSVIEIRDHGPGVSEEDRARIFERFYRADTSRHRETGGTGLGLAIVAAIVAQH +GGSVRLLETEGGGATFSVHLPWAPFEDEADEDVEDERPSARDTDDDAAGPPTGPLAQTAP +SGAGASAADAARRSRLLRAAERFRRASAERRRRVSAPAQAPQADAPSPGGDDPAAGRDAR +P +>PROKKA_02603 +MSGRLDAAAARARLPRAWLSSAWRGQSLRTKLVMMITVLMLALVAVTAIATAALFRQEAV +RQLDEDMAANRDTVSMYLANVAQTGEYYMPQLPILRYYGVVWDNDGDRVVQTPVVPGSDE +PDLPSITPERALEIGSASFEVAGTQDESSRWRVQLYGLSSGDGTMAVALPLEGVRSSVER +VTSLVVTIGLLGTAGTVIVANLAVQRAFRALNRVERTAAKIAAGDLTQRVESAAPDTEVG +RLSRSLNAMLAHIESAFRDKEVSEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGLREE +EDVAAAMQRIESEATRMTRLVEDLLTLARLDEQRPLELAPVDLLILAMDSMMDASVNAPD +RKVTLVGLDGGRAGSAPIVGDENRMRQVVVNLMANALRYTPAGTPIEIAVGTVDPLGGPG +AAGDGEGRTSVIEIRDHGLGVSEEDAARIFERFYRADTSRHRETGGTGLGLAIVAAIVAQ +HGGSVRLLETEGGGATFSVHLPWAPFEDDDDLEDEDDAGPVSESENAAEVSHTGPLGLVA +PSGAGASVVDAARRSRLLRAGERFRRASAERRPRAGTPAQAPAEGAASPGEEEPGPAAPD +RP +>PROKKA_02462 +MGPRLGVAAARLRHPRTWLWGWWGARPLRTKLVVMITALMMVLVAVIALVTAVLFRTELL +RQLDDDLSHNRDEVSIYLTTMSQTGGYYTPQQSILRFYGVVWDTSGRAVVSTPLMPGADG +PALEGMTPEQVDAQGSASFEVPGTTAGSDGWRVQLYHLRSGEGSLAIALPLHGVRTSVER +VVTLVVTIGLLGTAVSVVASNLLVERAFRALNRVERTAAKIAAGDLSQRVAYAPPSTEVG +RLSRSLNAMLAHIETAFRDKEASEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGITRE +EDVAAAMGRIESEAGRMHRLVEDLLTLARLDEQRPLEHEPVDLLVLGMDSMMDASVNAPD +RKVSLVGLDGGPAGSAPLMGDENRMRQVVVNLMTNALRYTPEGTPIEIAVGTRDAFGGDS +GVDGTRHSVIEIRDHGAGVSEEDAARIFERFYRADASRHRETGGTGLGLAIVAAIVAQHG +GSVRLLETEGGGATFSVHLPWAALEDDADDDLDLEDDDARPGAGVPAGRPPTGGSTAAGS +AGALETGQRRRLAWAGERFRRASAARRQAQAGTSPAQAARDGA +>PROKKA_00365 +MRARLDAAAARVRHPRAWLRGAWQGQSLRTKLVVMIAALMLALVAVTAVATAVLFRQEAV +RQLDEDMAANRDTVSMYLANVAQTGEYYMPQLPILRFYGVVWDNEGARVVQTPVMPGADE +PALPDITPAEALERGSASFEVPGTQPDSSGWRVQLYGLSSGDGTMAVALPLQSVTSSVER +VTSIVVTIGLLATAGTVIVANLAVQRAFRTLNRVERTAAKIAAGDLSQRVESAAPDTEVG +RLSRSLNAMLAHIESAFRDKEISEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGLREE +EDVAAAMQRIESEATRMTRLVEDLLTLARLDEQRPLEHAPVDLLILAMDSMMDASVNAPD +RKVTLVGPDGDRAAPAPILGDENRMRQVVVNLMANALRYTPAGTPIEIAVGTVDHLGGQA +GADGAGRSSVIEIRDHGPGVSEEDRARIFERFYRADTSRHRETGGTGLGLAIVAAIVAQH +GGSVRLLETEGGGATFSVHLPWAPFEDEADEDVEDERPSARDTDDDAAGPPTGPLAQTAP +SGAGASAADAARRSRLLRAAERFRRASAERRRRVSAPAQAPQADAPSPGGDDPAAGRDAR +P diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000408.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000408.fa new file mode 100644 index 0000000000000000000000000000000000000000..5373bade36824078173626147cc5ac09a09228d8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000408.fa @@ -0,0 +1,14 @@ +>PROKKA_00360 +MTSQDSPTRVAGMPRTSTLPAPAPADHRGGRGVVLVLGVAVTAVSALALVALLVAYFLAW +PASPALFALALFGLPVGFGLMLLHVVLGAVRRSRP +>PROKKA_00076 +MTSQDSPTRVAGMPRTSTLPASAPAADPADHRGGRGVVLVLGVAVTAVSALALVALLVAY +FLAWPASPALFALALFGLPVGFGLMLLHVVLGAVRRSRP +>PROKKA_02601 +MLGVTVTAVSFVALLGLLAAYFFSWPAVPALYALAMFGLPVGFSLMLLHVVLGAVRRSRL +>PROKKA_02460 +MPSPRTSPQPRPDAAPAPSGARRALRVLLTAGVVLTVVSGLGLLGALAAYFLHATPAFLP +ALYAVSLFGLPLGFTLMVLHVVLSAVLRARS +>PROKKA_00367 +MTSQDSPTRVAGMPRTSTLPASAPAADPADHRGGRGVVLVLGVAVTAVSALALVALLVAY +FLAWPASPALFALALFGLPVGFGLMLLHVVLGAVRRSRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000412.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000412.fa new file mode 100644 index 0000000000000000000000000000000000000000..f28d1253770bc668b1965ab6f0e78eaa5c023ad4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000412.fa @@ -0,0 +1,23 @@ +>PROKKA_00364 +MTDLIDTTEMYLRTILELEEEGIPPLRARIVERLEHSGPTVSQTVARMERDGLVHVGMDR +RLELTVAGRERAVSVLRKHRLAERLLADVIGLEWELVHEEACRWEHVMSDQVERRLLTLL +ENPTETPYGTPIPPRPEQASAEDWSRDMGLAGTRLSEEAATAGRFRVRGLAEGVQTDPDL +LAQLAGAGVTPGRVVRAEAARDAGYIRVEGEAEDGAAADGGALELAAATAAHVWVERLDG +>PROKKA_00080 +MTDLIDTTEMYLRTILELEEEGIPPLRARIVERLEHSGPTVSQTVARMERDGLVHVGTDR +RLELTVAGRERAVSVLRKHRLAERLLADVIGLEWELVHEEACRWEHVMSDQVERRLLTLL +ENPTETPYGTPIPPRPEQASAEDWSREMGLAGTRLSEEAATAGRFRVRGLAEGVQTDPEL +LAQLAGAGVTPGRVVRAQAARDAGYIRVEGEAEDGAAADGGALELAEATAAHVWVERLDG +>PROKKA_02597 +MGLAGTRLSEEAATPGRFRVRGLAEGVQTDPELLAQLAAAGVTPGRTVTAQAAIDPGYVR +VEGEAADGAPESGALELAVETAAHVWVERLDA +>PROKKA_02456 +MTDLIDTTEMYLRTILELEEEGTVPLRARIVERLEHSGPTVSQTVARMERDGLVHVGSDR +RLLLTDEGRERAVAVLRKHRLAERLLSDVIGLDWAYVHDEACRWEHVMSDRVEQRLLEVL +ENPTATPYGTPIPPRPEAQSAGEWSRDLGLAGEPLATAAATPGRFRVGSLSEGVQADPEL +LAELQDAGVLPGGVLEAQPALEAGYVRVQGEGSAEALELSAGTAAHVWVQRL +>PROKKA_00371 +MTDLIDTTEMYLRTILELEEEGIPPLRARIVERLEHSGPTVSQTVARMERDGLVHVGADR +RLELTVAGRERAVSVLRKHRLAERLLADVIGLEWELVHEEACRWEHVMSDQVERRLLTLL +ENPTETPYGTPIPPRPEQASAEDWSRDMGLAGARLSEEAATAGRFRVRGLAEGVQTDPEL +LAQLAGAGVTPGRVVRAEAARDAGYIRVEGEAEDGAAADGGALELAEATAAHVWVERLDG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000413.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000413.fa new file mode 100644 index 0000000000000000000000000000000000000000..aa4d5cf879ac244af9a1b5736da4ad558664e47f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000413.fa @@ -0,0 +1,20 @@ +>PROKKA_00365 +MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR +VPHTDAAPVSRKGVLRRDGHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNGAK +ADRSLEALGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA +>PROKKA_00081 +MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR +VPHTDAAPVSRKGVLRRDGHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNGAK +ADRSLEALGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA +>PROKKA_02596 +MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR +VPHTDAAPVSRKGVLRRDAHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNALK +ADRSLESMGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA +>PROKKA_02455 +MRTLVLNAGYEPVSVVSDRRALLLVATGKASVLEDGDAPMHSPTRAWGRPLVILLHQYVR +VPHADAAAVSRKGVLRRDGHRCAYCGAHATTVDHVHPRSRGGQNTWENLVACCLRCNSAK +ADRSLDALGWRLRVVPTRPCGVQWRLRELERPAPAWEGWLQFAA +>PROKKA_00372 +MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR +VPHTDAAPVSRKGVLRRDGHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNGAK +ADRSLEALGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000416.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000416.fa new file mode 100644 index 0000000000000000000000000000000000000000..65b17b238ed69b0159f36545a60d715d84716ad1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000416.fa @@ -0,0 +1,40 @@ +>PROKKA_00371 +MDLYEYQARDLFEAHGVPVLAGIVAQTPDEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK +VAKTADEAYEHAKAILGMDIKGHTVHQVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE +GGMEIEQLAEERPEALAKVPVSALTGIDAETAQKIVTEAGFPEELRADVAEVIQKLWEVF +EKEDATLVEVNPLVKTGDGTILALDGKVSLDDNAQFRHEDHAALVDERTEDPLEAKAKAN +GLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEQHGGVKPANFLDIGGGANAEVMANGLD +VILGDEQVKSVFVNVFGGITACDQVANGIVKALEILGDTATKPLVVRLDGNAVEEGRRIL +QEANHPLVTLAATMDEGADKAAELAHSAN +>PROKKA_00087 +MDLYEYQARDLFEAHGVPVLAGIVAQTPDEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK +VAKTADEAYEHAKAILGMDIKGHTVHQVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE +GGMEIEQLAEERPEALAKVPVSPLTGIDAETAQKIVTEAGFPEELRADVAEVIQKLWEVF +EKEDATLVEVNPLVKTGDGTILALDGKVSLDDNAAFRHEGHAALVDERTEDPLEAKAKAN +GLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEKHGGVKPANFLDIGGGANAEVMANGLD +VILGDEQVKSVFVNVFGGITACDQVANGIVKALEILGDTATKPLVVRLDGNAVEEGRRIL +QEANHPLVTLAATMDEGADKAAELAHSAN +>PROKKA_02591 +MDLYEYQARDLFEAHGVPVLAGIVAQTPEEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK +VAKTADEAYEHAKAILGMDIKGHTVHQVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE +GGMEIEQLAEERPEALAKVPVSPLTGIDAETAQKIVAEAGFPEELRADVADVIQKLWVVF +EKEDATLVEVNPLVKTGDGKILALDGKVSLDDNAEFRHEGHAALVDERTEDPLEAKAKAN +DLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEQHGGVKPANFLDIGGGANAEVMANGLD +VILGDEQVKSVFVNVFGGITACDAVANGIVKALEILGDAATKPLVVRLDGNAVEEGRRIL +QEANHPLVTLAATMDEGADKAAELAHSAN +>PROKKA_02450 +MDLYEYQARDLFEKHGVPVLQGIVAETPEEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK +VAKTADEAYEHAKAILGMDIKGHTVNKVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE +GGMEIEQLAEERPEALAKVPVSALTGLDQATADTIVAEAGFPEELRADVAAVIVKLGEVF +KNEDATLVEVNPLVKTGDGTILALDGKVSLDDNAEFRQADHAGLVDKTTEDPLEAKAKAN +DLNYVKLDGQVGIIGNGAGLVMSTLDVVAYAGENHGGVKPANFLDIGGGANAEVMAAGLD +VILGDEQVKSVFVNVFGGITACDAVANGIVKALEILGDSATKPLVVRLDGNAVEEGRRIL +QEADHPLVTLAATMDEGADKATELAHSAN +>PROKKA_00378 +MDLYEYQARDLFEAHGVPVLAGIVAQTPDEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK +VAKTADEAYEHAKAILGMDIKGHTVHRVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE +GGMEIEQLAEERPEALAKVPVSALTGIDAETAQKIVAEAGFPEELRADVAEVIQKLWEVF +EKEDATLVEVNPLVKTGDGTILALDGKVSLDDNAAFRHEGHAALVDERTEDPLEAKAKAN +GLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEKHGGVKPANFLDIGGGANAEVMANGLD +VILGDEQVKSVFVNVFGGITACDAVANGIVKALEILGDTATKPLVVRLDGNAVEEGRRIL +QEANHPLVTLAATMDEGADKAAELAHSAN diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000417.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000417.fa new file mode 100644 index 0000000000000000000000000000000000000000..42a80e8a59d97339e48863df444ade4cd18ed117 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000417.fa @@ -0,0 +1,35 @@ +>PROKKA_00372 +MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDKDGNAVEL +PVFGTVKEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDTAEFFAL +SQSKTGEDGKPKTRIIGPNCPGVITPGEALAGITPATITGSGPIGLVSKSGTLTYQMMYE +LRDFGFSTAIGIGGDPVIGTTHIDALEAFEADPDTQAIVMIGEIGGDAEERAAEFIKANV +TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETAQLMRE +ILQAQA +>PROKKA_00088 +MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDKDGNAVEL +PVFGTVKEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDTAKFFAL +SQSKTGEDGKPKTRIIGPNCPGIITPGEALAGITPATITGTGPIGLVSKSGTLTYQMMYE +LRDFGFSTAIGIGGDPIIGTTHIDALEAFEADPDTQAIVMIGEIGGDAEERAAEFIKANV +TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETAQLMRE +ILEG +>PROKKA_02590 +MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDKDGNAVEL +PVFGSVTEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDSAKFFAL +SQSKTGEDGKPKTRIIGPNCPGVITPGEALAGITPATITGSGPIGLVSKSGTLTYQMMYE +LRDFGFSTAIGIGGDPVIGTTHIDALEAFEADPDTQAIVMIGEIGGDAEERAAEFIKANV +TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETAQLMRE +ILQAQA +>PROKKA_02449 +MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDEDGNAVEL +PVFGSVAEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDSAEFFAL +SQSKTGEDGKPKTRIIGPNCPGIITPGEALAGITPATITGSGPIGLVSKSGTLTYQMMYE +LKDFGFSTAIGIGGDPVIGTTHIDALEAFEADPETKAIVMIGEIGGDAEERAAEFIKANV +TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETADLMRE +IMKGL +>PROKKA_00379 +MSIYLNKDSKVIVQGITGGEGTKHTRLMLKAGTNIVGGVNARKAGTTVSHEDKDGNAVEL +PVFGTVKEAMEKTGADVSVAFVPPAFAKDAAIEAIEAEIPLLVVITEGIPVQDSAEFFAL +SQSKTGEDGKPKTRIIGPNCPGIITPGEALAGITPATITGSGPIGLVSKSGTLTYQMMYE +LRDFGFSTAIGIGGDPVIGTTHIDALEAFEADPDTQAIVMIGEIGGDAEERAAEFIKANV +TKPVVGYVAGFTAPEGKTMGHAGAIVSGSAGTAQAKKEALEAAGVKVGKTPSETAQLMRE +ILQAQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000421.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000421.fa new file mode 100644 index 0000000000000000000000000000000000000000..159ee35fad0d20b80f9218dcf1d8ec881d8427f5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000421.fa @@ -0,0 +1,40 @@ +>PROKKA_00379 +MSPAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER +RHEQHWRALLGEHAENPPRPSLHRILLRWLARIFGSVFVLALAQRAESDTPYAEDQDAPE +GMVADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL +FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELKLVYLARG +MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA +SGALIPILPYIFGMSGLWALGLAAAMVGVALLFTGGVVGLLSGSSPLARGLRQLAIGFGA +AAVTYVLGLLFGANVG +>PROKKA_00103 +MSAAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER +RHEQHWRILLGEHAENPPRPSFRRVLLRWLARIFGSVFVLALAQRAESDTPYEKDQDAPE +GMAADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL +FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELKLVYLARG +MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA +SGALIPILPYIFGMSGLWALGLAAAMVGAALLFTGGVVGLLSGSSPLARGLRQLAIGYGA +AAVTYVLGLLFGANVG +>PROKKA_02576 +MSPAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER +RHEQHWRALLGEHAENPPRPSVHRILLRWLARIFGSVFVLALAQRAESDTPYAKDQDAPE +GMVADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL +FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELTLVYLARG +MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA +SGALIPILPYIFGMSGLWALGLAAAMVGVALLFTGGVVGLLSGSSPLARGLRQLAIGYGA +AAVTYVLGLLFGANVG +>PROKKA_02448 +MSPAHAATPAALPEPTREQVRRWRRYLADEIAEGQIYRDIAASKDGVERDILIGLAEAEK +RHEEHWRALLGEHAAHPPRPSVHRILLRALARVFGSVFVLALAQRAESDTPYAKDQDATE +HMAADEQIHEEVVRGLASRGREQLAGSFRAAVFGMNDGLVSNLALVMGIGATGVASSVVL +FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAEHLDLDRNELELVYLARG +MTPEDAKHRALERLGYLSCDCNPQFSARPDGSKGPVDHSESFAEIGSAWGASLSSFCFFA +SGALIPILPYLFGMTGLGALVVAAVLVGIALLFTGGVVGLLSGSSPLWRGLRQLMIGYGA +AAVTYLLGLLVGGSIG +>PROKKA_00385 +MSPAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER +RHEQHWRALLGEHAENPPRPSLHRILLRWLARIFGSVFVLALAQRAESDTPYAEDQDAPE +GMVADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL +FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELKLVYLARG +MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA +SGALIPILPYIFGMSGLWALGLAAAMVGVALLFTGGVVGLLSGSSPLARGLRQLAIGFGA +AAVTYVLGLLFGANVG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000422.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000422.fa new file mode 100644 index 0000000000000000000000000000000000000000..f5be29f32a1c4ac51ec265a6a766eacf48702a13 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000422.fa @@ -0,0 +1,20 @@ +>PROKKA_00380 +MDAAETPDGPETAAHDGGRPAWQHRLLAGGEEPDPRFTLANERTFLAWVRTALALLAGGV +AVEAFTGALFAPPVRVVLSTVLLVLAALLALGAGARWLRVERAMRRGRPLPLPLIVPVLA +GGVVLAVVVLLAAVVLPRG +>PROKKA_00104 +MDAAETPDGPETAAHDGGRPAWQHRLLAGGEEPDPRFTLANERTFLAWVRTALALLAGGV +AVEAFTGALFAPPVRVVLSTVLLVLAALLALGAGARWLRVERAMRRGRPLPLPLIVPVLA +GGVVLAVVVLMLAVVLPRG +>PROKKA_02575 +MDAAETPEGPEATAYDGGRPAWQHRLLAGGDEPDPRFTLANERTFLAWVRTALALLAGGV +AVEAFTGALFAPPVRVALSTVLLVLAALLAVGAGARWLRVERAMRRGRPLPLPLIVPVLA +GGVVLAVVVLMLAVVLPRG +>PROKKA_02447 +MDAAETPDGPEAAAYDGGRPAWQHRLLAGGDEPDPRFTLANERTFLAWVRTALALLAGGV +AVEAFTGALFAPPVRVALSTVLLVLAALLALGAGARWLRVERAMRRGRPLPLPLIVPVLA +GGVVLAVVVLMLAVVLPRG +>PROKKA_00386 +MDAAETPDGPETAAHDGGRPAWQHRLLAGGEEPDPRFTLANERTFLAWVRTALALLAGGV +AVEAFTGALFAPPVRVVLSTVLLVLAALLALGAGARWLRVERAMRRGRPLPLPLIVPVLA +GGVVLAVVVLLAAVVLPRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000423.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000423.fa new file mode 100644 index 0000000000000000000000000000000000000000..a94fd1a5f77462d9aafc442331b1d2a5acb34877 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000423.fa @@ -0,0 +1,15 @@ +>PROKKA_00381 +MRLHHDPGLQPERTVMSWGRTALALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT +QRRRYVAHADGIAREQARPALASVACMVALVVGLAALGITATLLHAA +>PROKKA_00105 +MRLHHDPGLQPERTVMSWGRTVLALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT +QRRRYVAHADGIARERARPALASVACMVALVVGLAALGITATLLHAA +>PROKKA_02574 +MRLHHDPGLQPERTVMSWGRTVLALGVLSLMFLRWWPAVGAWAFGPAVVAAVGGAAVLAT +QRRRYVAQSRGIAGEWARPALASVAGMVALVVGLAALGITATLLHAA +>PROKKA_02446 +MRLHHDPGLQPERTVMSWGRTVLALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT +QRRRYVAQADGIAREQARPALASVACMVALVVGLAVLGITATLLHAA +>PROKKA_00387 +MRLHHDPGLQPERTVMSWGRTVLALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT +QRRRYVAHADGIAREQARPALASVACMVALVVGLAALGITATLLHAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000424.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000424.fa new file mode 100644 index 0000000000000000000000000000000000000000..edd13c3c349da5015f4175268d137d81fa29086e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000424.fa @@ -0,0 +1,40 @@ +>PROKKA_00382 +MTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHGVILKIVATNICGSDLHIYRGSFP +APEGMVLGHEMTGQVLEVGSDVQFLQEGDLVSVPFNVACGRCRNCRAGRTEICETANPDQ +ACAAYGFNLGGFQGGQAEYLFVPYADFQLLRFPDQEQAMEKILDLTVLSDILPTAFHGLV +EAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVGDQDASRLELVRKHGCETIDLSTT +ENLQDAVSDILGEPMVDCAVDCVGSEAHGLGSASDEMQPIAAVNQVLDITRPGGATGIIG +IYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQAPVMRYNRQLMMSILWDRMPYLTE +MVNPRVISLDEAPQAYAEFDQGSLEKFVIDPHGMIAR +>PROKKA_00106 +MTTENRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHGVILKIVATNICGSDLHIYRGSFP +APEGMVLGHEMTGQVLEVGSDVQFLQEGDLVSVPFNVACGRCRNCRAGRTEVCETTNPEQ +ACAAYGFNLGGFQGGQAEYLFVPYADFQLLRFPDQEQAMEKILDLAVLSDILPTAFHGLM +EAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVGDQDASRLELVRKHGCETIDLSTT +ENLQDAVNDILGEPMVDCAVDCVGSEAHGLGSASDEMQPIAAVNQVLDVTRPGGATGIIG +IYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQAPIMRYNRQLMMSILWDRMPYLTE +LVNPRVITLDEAPQAYAEFDQGSVEKFVIDPHGMIAR +>PROKKA_02573 +MSPRGRSGSRLTQASLETEGNSFMTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHG +VILKIVATNICGSDLHIYRGSFPVPEGMVLGHEMTGQVLEVGSDVQFLKEGDLVSVPFNV +ACGRCRNCRAGRTEVCETANPEQACAAYGFNLGNFQGGQAEYLFVPYADFQLLRFPDQEQ +AMEKILDLAVLSDILPTAFHGLMAAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVG +DQDASRLELVRKHGCETIDLSVTENLQDAVNDILGEPMVDCAVDYVGSEAHGLGSESDEM +QPIAAVNQVLDITRPGGATGIIGIYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQA +PIMRYNRQLMMSILWDRMPYLTEMVNPRVISLDEAPQAYAEFDQGSVDKFIIDPHGMIAR +>PROKKA_02445 +MTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHGVILKIVATNICGSDLHIYRGSFP +VPEGMVLGHEMTGQVLEVGSDVQFLKEGDLVSVPFNVACGRCRNCRAGHTEICETANPEQ +ACAAYGFNLGNFQGGQAEYLFVPYADFQLLRFPDQEQAMEKILDLAVLSDILPTAFHGLM +AAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVGDQDASRLELVRKHGCETIDLSVT +ENLQDAVNDILGEPMVDCAVDYVGSEAHGLGSESDEMQPIAAVNQVLDITRPGGATGIIG +IYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQAPIMRYNRQLMMSILWDRMPYLTE +MVNPRVISLDEAPQAYAEFDQGSVDKFIIDPHGMIAR +>PROKKA_00388 +MTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHGVILKIVATNICGSDLHIYRGSFP +APEGMVLGHEMTGQVLEVGSDVQFLQEGDLVSVPFNVACGRCRNCRAGRTEICETANPEQ +ACAAYGFNLGGFQGGQAEYLFVPYADFQLLRFPGQEQAMEKILDLAVLSDILPTAFHGLM +EAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVGDQDASRLELVRKHGCETIDLSVT +ENLQDAVNDILGEPMVDCAVDCVGSEAHGLGSASDEMQPIAAVNQVLDITRPGGATGIIG +IYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQAPIMRYNRQLMMSILWDRMPYLTE +MVNPRVISLDEAPQAYAEFDQGSLEKFVIDPHGMIAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000430.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000430.fa new file mode 100644 index 0000000000000000000000000000000000000000..5a53e2b73ada0d9ebfd736efb63c1041488f560c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000430.fa @@ -0,0 +1,41 @@ +>PROKKA_00391 +MPAASDAPTPAPRRGRLAPSGDPTPVENVATHLQEGWNRWHRARALRAGNVPTVMAFTGY +GSTSWVRILSRVVIASDEEFMNGRRLSKVVADGVRGWRNFVAPPMAYAEVEVQVGDLRTT +VRTDRMGVVDVVLDVELEPGWQTATLHVGGQEEHAVMDLYICEPGARIGLVSDIDDTVVV +TSLPRPLLAAWNSFVIDEHARTPTPGIAVLLRRIAELEPKAPVLYLSTGAWNVAQTLTRF +LGRNLYPLGALLLTSWGPTRDRWFRSGQEHKRVQLERLAEQFPDIQWILVGDDGQHDPEI +YAEFAQRHPDRVKAIVIRQLTPSQALLAGGRAEDTRRSTPGIPWCYGPDGATLSNQLEDL +GILPVEFVDVQPEAWREDILGDDEAPATLDAAAQRDDRSTDEEAAR +>PROKKA_00115 +MPAASDAPTPAPRRGRLAPSGDPTPVENVATHLQEGWNRWHRARALRAGNVPTVMAFTGY +GSTSWVRILSRVVIASDEEFMNGRRLSKVVADGVRGWRNFVAPPMAYAEVEVQVGDLRTT +VRTDRMGVVDVVLDVELEPGWQTATLHVGGQEEHAVMDLYICEPGARIGLVSDIDDTVVV +TSLPRPLLAAWNSFVIDEHARTPTPGIAVLLRRIAELEPKAPVLYLSTGAWNVAQTLTRF +LGRNLYPLGALLLTSWGPTRDRWFRSGQEHKRVQLERLAEQFPDIQWILVGDDGQHDPEI +YAEFAQRHPDRVKAIVIRQLTPSQALLAGGRAEDTRHSTPGIPWCYGPDGATLSNQLEDL +GILPVEFVDVQPEAWREDILGDDEAPATLDAPGQRDGRPADEEAAR +>PROKKA_02565 +MSAVSDAAPVSPRRTRLAALGDPTPVENVATHLQEGWNRWHRSRALRAGHVPTIMAFTGY +GSTSWVRILSRVVIAPDEEFLNGRRISKVVADGVRGWRNFVAPPMAYAEVEVEVGGTRTT +VRTDRMGVVDAVLDVEMEPGWRTATLHVGDDEHVTMDLYICHPDARIGLVSDIDDTVVVT +SLPRPLLAAWNSFVIDEHARTPTPGMAVLLRRVAELEPKAPVLYLSTGAWNVAQTLTRFL +GRNLYPLGALLLTSWGPTKDRWFRSGQEHKKTQLERLAEQFPDIKWILVGDDGQHDPEIY +ADFAQRHPDRVAAIVIRQLTPSEALLAGGRAEDTRRSTPGIPWCYGPDGASLSNQLEDLG +ILPVGFVDVQPEGWKEDILGDDEVLSAAEHGAAALGDEADAPDTAAEPRVPAGEAAVGDG +AADEAEAAEAGGSR +>PROKKA_02436 +MPASESASIAAQNDPARRQRLAAAGGPTPAENVATHLQEQWNRWHRSRALRRGFVPTVMA +FTGYGTTSWVRVLSRVVLAKDEDFLNGRRLSKVVADGVHGWRNFVAPPMAYAEVEVEVGD +LVTTVRADRMGVVDVVLDVELEPGWRTAVLRVGDEEEVTTDLYIASPDAKVGLVSDIDDT +VVVTSLPRPLLAAWNSFVIDEHARTPTPGMAVLLRRIAAAEPMAPVLYLSTGAWNVAQTL +TRFLGRNLYPLGALLLTSWGPTKDRWFRSGQEHKVTQLERLAQQFPDLQWILVGDDGQHD +PEIYADFATKHPDKVKAIVIRQLTPSEALLAGGRAEATRHSTPGIPWCYGPDGAALSNQL +EDLGILPVDFVDVHPEGWLEDILGEDEASAAGRDGDEHGVHGGRADQDEARDVDVSAQD +>PROKKA_00397 +MPAASDAPTPAPRRGRLAPSGDPTPVENVATHLQEGWNRWHRARALRAGNVPTVMAFTGY +GSTSWVRILSRVVIASDEEFMNGRRLSKVVADGVRGWRNFVAPPMAYAEVEVQVGDLRTT +VRTDRMGVVDVVLDVELEPGWQTATLHVGGQEEHAVMDLYICEPGARIGLVSDIDDTVVV +TSLPRPLLAAWNSFVIDEHARTPTPGIAVLLRRIAELEPKAPVLYLSTGAWNVAQTLTRF +LGRNLYPLGALLLTSWGPTRDRWFRSGQEHKRVQLERLAEQFPDIQWILVGDDGQHDPEI +YAEFAQRHPDRVKAIVIRQLTPSQALLAGGRAEDTRHSTPGIPWCYGPDGATLSNQLEDL +GILPVEFVDVQPEAWREDILGDDEAPATLDAAAQRDGRSADEEAAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000434.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000434.fa new file mode 100644 index 0000000000000000000000000000000000000000..32f890a3df61a0c7e3b509bc7ab672b30f869c50 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000434.fa @@ -0,0 +1,40 @@ +>PROKKA_00396 +MRVVVVAESFLPHMNGVTNSILQVLRHLRERGDEAMVVAPAASWSAGWTQRAGAGEAPRE +VEGFPVRTLPSVPLTGYTSVRVAAGTVGRLRGMLADFAPDVVHIASPFVLGWRAVQAAEE +LGIPSVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNMATLTLAPSSFTVRQLHRQGVR +RVHLWGRGVDSRRFHPAKRDEALRAELAPNGEKLVGFVGRLAHEKQVGDLRVLSDLPGTR +LVVIGSGPLREQLERELPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS +GVPVVAVGRGGPLDIVDASRTGWLYPPGELDELRRHVADLVYDDVKRAAFADAAWASVQG +RTWPVLCEQLMGYYEKAIAVQERRRVELARRLLTAPALLAARVFG +>PROKKA_00120 +MRVVVVAESFLPHMNGVTNSLLQVLRHLRERGDEAMVVAPAASWSAGWTQRAGAGEAPRE +VEGFPVRTLPSVPLTGYTSVRVAAGTVGRLRGMLADFAPDVVHIASPFVLGWRAVQAAEE +LGIPSVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNMATLTLAPSSFTVRQLHRQGVR +RVHLWGRGVDSRRFHPAKRDEALRAELAPNGEKLVGFVGRLAHEKQVGDLRVLSDLPGTR +LVVIGSGPLREQLERELPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS +GVPVVAVGRGGPLDIVDASRTGWLYPPGELDELRRHVADLVYDDVKRAAFADAAWASVQG +RTWPVLCEQLMGYYEKAIAVQERRRVELARRLLTAPALLAARVFG +>PROKKA_02561 +MVAESFLPHMNGVTHSILQVLRHLRERGDEAIVIAPAASWSAGWTQRAGEGQAPREVEGF +PVHALPSVPLSGYSSVRVAAGTVGRLRGILTAFGPDVVHIASPFVLGWRAVQAAEELGIP +SVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNTATLTLAPSSFTVRQLHAAGLRRVHL +WGRGVDTRRFHPVKRDDALRAELAPHGERLIGFVGRLAHEKQVEDLRVLSDLPGTRLVVI +GSGPLREQLERRLPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMASGVPV +VAVGRGGPLDIVDPSRTGWLYPPGELDELRRHVADLAHDDVKRSAFAQAAWASVQGRTWP +VLCEQLVGCYEKAVAVQDRRRRELARRLLAMPSQLTARVFG +>PROKKA_02432 +MRVAVIAESFLPHMNGVTNSILQVLKHLRSRGDEAVVIAPAASWSAGWTQRAGAGQAPSE +VEGFPVITLPSMPLSGYASVRVAAGTVLRLRSLLADFAPDVVHIASPFVLGWRAVQAAEE +LGIPSVAVYQTEVPRYAAKYGAPWLEDVLWNHVTRLHNTATLTLAPSSFTLRQLHHVGVR +RVHLWGRGVDSTRFHPAKRDEALRAELAPNGERLIGFVGRLAHEKQVADLRVLADLPDTR +LVIIGSGPLRDQLERRLPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS +GVPVVAVGRGGPLDIVDSSRTGWIYQPGDLGELRARVADLAYDDAKRAAFAEAAWASMQG +RTWPVLCEQLVGYYEKAIHVQRRRRGELSRRLLGAPGAVASRAYRVFG +>PROKKA_00402 +MRVVVVAESFLPHMNGVTNSILQVLRHLRERGDEAMVVAPAASWSAGWTQRAGAGEAPRE +VEGFPVRTLPSVPLTGYTSVRVAAGTVGRLRGMLADFAPDVVHIASPFVLGWRAVQAAEE +LGIPSVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNMATLTLAPSSFTVRQLHRQGVR +RVHLWGRGVDSRRFHPAKRDEALRAELAPNGEKLVGFVGRLAHEKQVGDLRVLSDLPGTR +LVVIGSGPLREQLERELPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS +GVPVVAVGRGGPLDIVDASRTGWLYPPGELDELRRHVADLVYDDVKRAAFADAAWASVQG +RTWPVLCEQLVGYYEKAIAVQERRRVELARRLLTAPSLLAARVFG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000435.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000435.fa new file mode 100644 index 0000000000000000000000000000000000000000..b2c03f4ef8ce07a843005d9fab94a6cc695f0437 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000435.fa @@ -0,0 +1,46 @@ +>PROKKA_00397 +MSSRPAAPRLLRPVPLPLWLQGVVEALVTAMISLLAVMVPTLAVWATGGFERPTIEGAVQ +VGGVLWLALHAVPVTVTTAMPTAPDHLITGTAWLVPWGLTLLPLALSWRAGRRLARASYR +DQAWQAFVGAVGAYALVGLAVAFLPGTDELTAHPAPAALLPALLFGVAALAGARREAGTW +AHLIGLDLTERISRRSQYERWAGSYAWSVVRAAAVAVLALTGLNALLVAGRLAVEWTAVV +TVAEAIGGGPLGGLLLALLQIGWLPTFTAWSIAWTAGPGFSVGADSLYSVFGATPATAPA +LPALGALPGTWSPWQLLLLAVPIGAGAVAGVWLLREGENHLDDWLHTRHGSRAVSLTLST +LALAVLTGLLTGLLLLVPLALTSGTLGLGALTDLGSHVWAVSAAVAGWVALGCAAGYLTA +LAVAGHRDGTTTVPRSGDRASGLRDRPSPRRARD +>PROKKA_00121 +MSSRPAAPRLLRPVPLPLWLQGVVEALVTAMISLLAVMVPTLAVWATGGFERPTIEGAVQ +VGGVLWLALHAVPVTVATAMPTAPDHLITGTAWLVPWGLTLVPLALSWRAGRRLARASYR +DQAWQAFVGAVGAYALVGLAVAFLPGTDELTAHPAPAALLPALLFGVAALAGARREAGTW +AHLIGLDLTERISRRSQYERWAGSYAWSVVRAAAVAVLALTGLNALLVAGRLAVEWTAVV +TVAQAIGGGPLGGLLVALLQIGWLPTFTAWSIAWTAGPGFSVGADSLYSVFGATPATAPA +LPALGALPGTWSPWQLLLLAVPISAGVVAGVWLLREGENHLDDWLHTRHGSRAVSLTLST +LALAVLTGLLAGLLLLVPLALTSGTLGLGTLTDIGPHVWAVCAAVAGWVALGCAAGYLTA +LAVAGHRDGTTTVPRSGDRASGLRDRPSPRRARD +>PROKKA_02560 +MTALLSLLAVMIPTLVVWATGGFQRPTIEGALQVGGTLWLALHAVPVTVATVLPTAEGHV +LSGTAWLVPWGLTLIPLLLSWRAGRRLARASYRDQAWQAFAGAVVGYALAGLTVAFLPGT +PELRVSPWAAALLPALLFGIAALAGARREAGTWAHLIGLDLTERIARRSQYERWAGSYAW +SVVRAAVVALLVLAALSALLVAVRLAVEWPAVVTLAQAIDAGPFGGLLLAVLQIGWLPTL +TGWAIAWTAGPGFSVGSDSLYSVFGATPAAAPALPALGALPAAWAPWHPLFLAVPIAAGV +AAGVWLLREGENHLDDWLDARTGHRAVSLALSTLALAVLTGLLAGLLLLVPLALTSGTLG +VGTLTDIGANVWAVCAAVAGWVALGCAAGYLVALALAGRRFIPPAEAAVAAERPRPRRSR +D +>PROKKA_02431 +MSPRVPSLLRPVPLPLWLQGVVEALVTALTSLALVLVPTLAVWITGGFSSTRIEDVLQTG +GALWLGLHAVPLAVTTVVAQADTPTVTGTVWLVPWALTALPVWLSWRAGRRLARASYREQ +AWQALAGAVAAYAVVALACALLPGEGRITVHPLPSVLLPCLLFTTSAVAGARREAGTWAH +LIGLDLTERIARRSQYERWAGTYAWSVLRGAGVGLAALAGLHALLVTVAVLVRWPRIIEV +QQMVGAGPVGGLMLALLEIGWLPTFTAWAVAWTAGPGFAVGADGHYSVFGTTPAPVPALP +LLEALPAPWAPWHPAFLLVPVLAGAVAGWWLLREGENHLDDWIDSRITARWASLTLSTLA +LALLLGLVSGVAVLVPLALTNGTLGVGSMREIGSNAPLVALAVAGWMALGCALGYLVALA +VVDRPVRGRRRISLPLPGSAPRAVTGRARRLPPRRLPRGVADAEADEPEVAAPAAAREEI +PGRETPAQETPSEEPPAAARPAPRRAGAPRVPRVPRPAPRRARD +>PROKKA_00403 +MSSRPAAPRLLRPVPLPLWLQGVVEALVTAMISLLAVMVPTLAVWATGGFERPTIEGAVQ +VGGVLWLALHAVPVTVATAMPTAPDHLITGTAWLVPWGLTLVPLALSWRAGRRLARASYR +DQAWQAFVGAVGAYALVGLAVAFLPGTDELTVHPAPAALLPALLFGVAALAGARREAGTW +AHLIGLDLTERISRRSQYERWAGSYAWSVVRAAVLAVLALTGLNALLVAGRLAVEWTAVV +TVAEAIGAGPLGGLLLALLQIGWLPTFTAWSIAWTAGPGFSVGADSLYSVFGATPATAPA +LPALGALPGTWSPWQLLLLAVPIGAGAVAGVWLLREGENHLDDWLHTRHGSRAVSLTLST +LALAVLTGLLTGLLLLVPLALTSGTLGLGTLTDIGSHVWAVCAAVAGWVALGCAAGYLTA +LAVAGHRDGTTTVPRSGDRASGPRDRPSPRRARD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000436.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000436.fa new file mode 100644 index 0000000000000000000000000000000000000000..664023ab3e22eff8bfbd8c0d19a9549899da0e71 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000436.fa @@ -0,0 +1,19 @@ +>PROKKA_00398 +MSAPVPSSPPRPPQGAPDPGRVRTGRALLWQSVALLGMVLSFSLVLPWKLIALALGLVAL +VLGVRVWVTSRGAERSGLPRAVASAGMAMALMGMTTAALPLLAWDATVQLEQCGASALTV +RAQQACADEFTRQVEERTGVPQLRP +>PROKKA_00122 +MSAPVPSSPPRPPQGAPDPGRVRTGRALLWQSVALLGMVLSFSLVLPWKLIALALGLVAL +VLGVRVWVTSRGAERSGLPRAVASAGMAMALMGMTTAALPLLAWDATVQLEQCGASALTV +RAQQACADEFTRQVEERTGVPQLRP +>PROKKA_02559 +MVLSLSLVLPWKLAALVLGLVALVLGVRVWLTSRGERRAGLPRAVAAGGMALALFGTTTA +ALPLLAWDATVELERCTSSALTVRAQQACADAFTRAVEERTGVPQLRP +>PROKKA_02430 +MSALPPVPPSAPDRRPADAAARARVGRLLVAQSAALLAMLGAFTLVLPFKVLTLAAALAA +LVLGVLVFTASRRTAQSLVPRAAAGAGMALALMGLTVGVFPLLLWNETAGFERCTASAVT +VRAQQTCADDFTATVERRTGVAQLGG +>PROKKA_00404 +MSAPVPSSPPRPPQGAPDPGRVRTGRALLWQSVALLGMVLSFSLVLPWKLIALALGLVAL +VLGVRVWVTSRGAERSGLPRAVASAGMAMALMGMTTAALPLLAWDATVQLEQCSASALTV +RAQQACADEFTRQVEERTGVPQLRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000438.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000438.fa new file mode 100644 index 0000000000000000000000000000000000000000..e11a7fb7d5ab8f4b082d899b125a4ab84be575c3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000438.fa @@ -0,0 +1,45 @@ +>PROKKA_00400 +MSSATPPRPSADGAHPGPAPDVVAPDAALPTGEAVVQELPWRWSVQGRIFLIGGLGFMFD +AWDVTLNGVMIPLLREEWALDKADAAWIGTANLIGMAVGAFLWGTIADRIGRKAAFAWTL +AIFSVFTIAGALTDSLLWFALFRFVAGMGLGGTIPVDYALVGEFTPRRLRGRVLAAMDGW +WPVGAALCGLVSAWLVGTWGDWRLPLLAMVLPALLVFVVRLGIPESPLFLMSRGREAQAR +AVIDRMVAATGAPRRPYTMPPAEPARSSGVGAQLAAVWRFSPRITAVAWALFVAIMLVYY +IALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATALIEVTGRRWLLAVSAVVASA +LTVWLASVLDVPAAVLPLVLTFGFVVQVAIPVLYTYVSELYPTTLRASGFGWASAASRVG +AGLGPLLFVGTLVPALGLPGAFAVTGGLVVLACAAMLALAPETRGRALEVSAD +>PROKKA_00124 +MSSATPPRPSADGAHPGPTPDVVSPDAALPTGEAVVQELPWRWSVQGRIFLIGGLGFMFD +AWDVTLNGVMIPLLREEWALDKADAAWIGTANLIGMAVGAFLWGTIADRIGRKAAFAWTL +AIFSVFTIAGALTDSLLWFALFRFVAGVGLGGTIPVDYALVGEFTPRRLRGRVLAAMDGW +WPVGAALCGLVSAWLVGTWGDWRLPLLAMVLPALLVFVVRLGIPESPLFLMSRGREAQAR +AVIDRMVAATGAPRRPYTMPPAEPARSGGVGAQLAAVWRFSPRITAVAWALFVAIMLVYY +IALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATALIEVTGRRWLLAVSAVVASA +LTVWLASVLDVPAAVLPLVLAFGFVVQVAIPVLYTYVSELYPTTLRASGFGWASAASRVG +AGLGPLLFVGTLVPALGLPGAFAVTGGLVVLACAAMLALAPETRGRALEVSAD +>PROKKA_02557 +MQGRIFLIGGLGFMFDAWDVALNGVMIPLLREEWALAPADAAWIGTANLIGMAVGAFLWG +TIADRIGRKAAFAWTLAIFSVFTLAGALTDSLLWFAVFRFVAGVGLGGTIPVDYALVGEF +TPRRLRGRVLAAMDGWWPVGAALCGLVSAWLVGTWGDWRLPLLAMVLPALLVFVVRLGIP +ESPLFLMSRGREAEARKVIDRMVEATGAERREYVMPPVEQERAGGVLAQLAAVWRFSPRI +TAVTWALFVAIMVVYYIALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATVLIEV +TGRRWLLGVSAVVASALLVWLASVLGVPSAVLPLVLAFGFVVQIAIPVLYTYVSELYPTT +LRASGFGWASAASRVGAGLGPLFFVGTLVPAMGLPAAFAVTGGLVLLACVAMLALAPETR +GRALEVSAD +>PROKKA_02427 +MPPTGSHAASAAPTGEQVVQELPWRWPVQGRIFLIGGLGFMFDAWDVTLNGVMIPLLTEE +WGLSKADAAWIGTANLIGMAVGAFLWGTVADQIGRKAAFTWTLLIFSVFTLAGALTDSLL +WFAVFRFMAGIGLGGTVPVDYALVGEFTPRRLRGHVLTAMDGWWPIGAALCGVVSAWLVG +TWSDWRLPLLAMVLPALLVFLVRLGIPESPLYLMSRGREREARAVIDRMVERTGAEPRPY +VMPAADSRAHGGLLAQLAAVWRFSPRITATAWLLFVAVMLIYYIALQWLPTFLIEAGFAQ +SRAFITTSGMAAAGLVGVAVSAVLVEATGRRRLLAVSGVVASGLLVWLASVLGVPGAALP +LVLAYGFVIQIAVPVLYTYVSELYPTTLRASGFGWASAASRVGAGLGPLFFVGTLVPALG +LPGAFGVTAGLVVVAVLVMFAWAPETRGRALEVAED +>PROKKA_00406 +MSSATPPHPSADGAHPGPTSDVVAPDATLPTGEAVVQELPWRWSVQGRIFLIGGLGFMFD +AWDVTLNGVMIPLLREEWALDKADAAWIGTANLIGMAVGAFLWGTIADRIGRKAAFAWTL +AIFSVFTIAGALTDSLLWFALFRFVAGMGLGGTIPVDYALVGEFTPRRLRGRVLAAMDGW +WPVGAALCGLVSAWLVGTWGDWRLPLMAMVLPALLVFVVRLGIPESPLFLMSRGRETQAR +AVIDRMVAATGAPRRPYTMPPAEPARSGGVGAQLAAVWRFSPRITAVAWALFVAIMLVYY +IALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATALIEVTGRRWLLAVSAVVASA +LTVWLASVLDVPAAVLPLVLTFGFVVQVAIPVLYTYVSELYPTTLRASGFGWASAASRVG +AGLGPLLFVGTLVPALGLPGAFAVTGGLVVLACAAMLALAPETRGRALEVSAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000444.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000444.fa new file mode 100644 index 0000000000000000000000000000000000000000..ac293a5ff28a2fee7d3fe2258f9eb2534043618d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000444.fa @@ -0,0 +1,81 @@ +>PROKKA_00410 +MVPMPTPVDPVTVPSALSAALGRLSAGLTFAAALPDLEAALDARGAAVVEAPPGTGKTTV +VPPALAVRLADHGGGRVLVTQPRRVAVRAAWRRLRTAVLAAAADSHPGADPDARARLADA +AVGYAVRGDAVGGGASAVEFVTPGLLLRRLLADPGLDGVGAVVLDEVHERDLDTDVLFAL +LADLRQLRPELALVAMSATVDAAALAARWARGMGEAPLPVVSTPAVLHPLREEHAPFRGH +RLTAEGRVDRAFLDHVAATAARAHAKALEADPTVDALVFLPGVAEVETVAGRVAALAPDT +EVRVLHGRQEPADQDAALAGRTDPAVPRVVVATAVAESSLTVPGVRLVVDSGLAREPRRD +RGRGMAGLVTVQASRAAAGQRAGRAARLGPGTVVRCHTAAALGTAPAAPTPALAVVDLAP +VALAFAAWGAPGGRGLTLPEDPPADAMAAAERTLASLGAVDADGRITPHGAVLAELPLDP +PLGHALLRAAPLTGPRPAAEATAALALDLRAPGADLEALVAALRDGRHPEAGRWHREADR +LERLARRHAHHAPETREPDEPGPEAATAPRHSAGLVAALAFPAWIARRAGEEGAYLLASG +TRAALPRDAVGGLAGQEWLAVAEVARVAGDAAGTGAAIRAAAPIDRSLVERAGAGLRRTE +DTAEWRGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRDALAADGLARFDPRGRAERL +RRRVHLLHRVLGAPWPDLSDTALPDLDTLVDGLAADLAAGRPLARLDAEALLRGALPWPE +AGRLDELAPERLPVPSGRAVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREPVVL +HLLSPAGRPLAVTADLPSFWAGPYAQVRAENRGRYPKHPWPEDPAVAEPTARTNRRAL +>PROKKA_00130 +MDPMPTPVDPVAVPSALSTALGRLSAGLTFAAALPELGSALDARGAAVVEAPPGTGKTTV +VPPALAVRLADHGGGRVLVTQPRRVAVRAAWRRLRTAVLAAAADAQPGADPDARARLADA +AVGYAVRGDAAGGGASAVEFVTPGLLLRRLLADPGLDGVDAVVLDEVHERDLDTDVLFAL +LADLRQLRPELALVAMSATVDAAALAARWARGMGEAPLPVVSTPAVLHPLREEHAPFRGH +RLTAEGRVDRAFLDHVAATAARAHAEALEADPTVDALVFLPGVAEVEAVAGRVAALAPDT +EVRVLHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRRD +RGRGMAGLVTVQASRAAAGQRAGRAARLGPGTVVRCHTAAALGTAPAAPTPALAVVDLAP +VALAFTAWGAPGGRGLTLPEDPPADAMAAAERTLASLDAVDADGRITPHGAVLAELPLDP +PLGHALLRAALWTGPRPAAEATAALALDLRAPGADLEALVASVRDGRHPEAGRWRREADR +LERLARRHAHHSLETRAPGEPGPEATAAARRHPAGLVAALAFPAWIARRAGEAGAYLLAS +GTRAALPRDAAGGGLAGQEWLAVAEVARVAGDAAGTGAAIRATAPIDRTLAELAGAGLRR +TEDTADWRGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRAALAADGLARFDPSGRTE +RLRRRVHLLHRVLGAPWPDLSDAALPGLDALVDGLAADLAAGRSLARLDAEALLRGALPW +PEAGRLDELAPERLPVPSGRAVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREPV +VLHLLSPAGRPLAVTADLPSFWAGPYAQVRAENRGRYPKHPWPEDPAAAEPTARTNRRAR +>PROKKA_02549 +MPAPSPHSSRPASVDTAVAPALSAALERLGSGLTFVAALPDLEAALDARGAAVVEAPPGT +GKTTVVPPALAVRLADHGGGRVLVTQPRRVAVRAAWRRLRSAVLDAADRTSAPDALADAA +VGYAVRGDAVGGGASAVEFVTPGLLLRRLLADPGLDGVDAVVLDEVHERDLDTDVLFALL +ADLRQLRPELALVAMSATVDAAALAARWARGMGEEAPLPVVSTPAVLHPLREEHAPFRGR +RLTAEGRVDRAFLDHVAATAARAHAAALDADPTVDALVFVPGVAEVEAVAGRVAARAPDT +EVRVLHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRRD +RGRGMAGLVTVQASRAAAGQRAGRAARLGPGTVVRCHTAAALGAAPAAPTPALAVVDLAP +VALAFAAWGAPGGRGLTLPKDPPADAMAAAERTLASLGAVDTDGRITPHGAVLAELPLDP +PLGHALLRAAPLTGPRPAAEATAALALDLRASGADLEALVAALRDGRHPESRRWRREADR +LERLARRHAHRAPETREPDGPGPEAATARRHPAGLVAALASPAWIARRAGEAGAYLLASG +TRAALPRNAVVGGLAGQEWLAVAEVARAAGDAAGTGAAIRAAAPIDRPLAELAGAGLRRT +EDTADWRGDRLTGRRVDRMGALVLAETPAPVAPDAAAQAVRAALAADGLARFDPSGRAER +LRRRVHLLHRVLGAPWPDLSDTALPGLDALVDGLAADLAAGRSLAHVDAEALLRGALPWP +EAGRLDELAPERLPVPSGRGVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGRELVV +LHLLSPAGRPLAVTADLPSFWAGPYAQVRAENRGRYPKHPWPEDPAAAEPTARTNRRVR +>PROKKA_02417 +MSTSSASHSTPDLRAALAAASARLGADLAFSASLPALEAALDARAGAVVHAPPGTGKTTA +VPPAVALWLARRAESGGEGGRVLVTQPRRVAVRAAWRRLHGAVADALGPESGPDTGRLPD +AVVGYAVRGDAVGRGASAVEFVTPGLLLRRLLGDPGLEGVGAVVLDEVHERDLDTDVLFA +LLADLRQLRPELALTAMSATLDADALAARWATGMGEDPVPVVRTPSVQHPLTVEHAPFGG +PRTTADGRVDRDFLDHVAATAARAHAEALDADPTVDALVFVPGVAEVEAVAGRVAALAPD +TEVRVLHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRR +DRGRGITGLATVQASRAAADQRAGRAARLGPGTAVRCHTAAALGAAPAAPTPALAVADLA +SVVLAFAVWGAPGGDGLVLPEDPPADAMAAAERTLASLDAVDTDGRITPHGTVLAELPLD +PPLGHALLRAAPLTGPRSAAEATAALALDLRAPGADLEALVAALRDGRHPEAGRWRREAD +RLERLARRHAHRAPETREPDEPGPAATATARRHPAGLVAALAFPAWIARRAGEEGAYLLA +SGTRAALPRDAVGGGLAGQEWLAVAEVARVAGDAAGTGAAIRAAAPIDRPLAELAGAGLR +RTEDTAEWRGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRVALAADGLARFDPSGRA +ERLRRRVHLLHRVLGAPWPDLSDATLPGLDALVDGLAADLAAGRSLTRLDAEALLRGALP +WPEAGRLDELAPERLPVPSGRGVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREP +VVLHLLSPAGRPLAVTADLPSFWAGPYAQVRAENRGRYPKHPWPEDPAAAEPTDRTNRRA +R +>PROKKA_00413 +MPTPVDPVSVPSALSAALGRLSAGLTFAAALPDLEAALDARGAAVVEAPPGTGKTTVVPP +ALAVRLADHGGGRVLVTQPRRVAVRAAWRRLRTAVLAAAADAQPGADPDAQARLGDAAVG +YAVRGDAAGGGASAVEFVTPGLLLRRLLADPGLDGVGAVVLDEVHERDLDTDVLFALLAD +LRQLRPELALVAMSATVDAAALAARWARGMGEDAPLPVVSTPAVLHPLREEHTPFRGHRL +TAEGRVDRAFLDHVAATAARAHAEALDADPTVDALVFLPGVAEVEAVAGRVAALAPDTEV +RVLHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRRDRG +RGMAGLVTVQASRAAAGQRAGRAARLGPGTVVRCHTAAALGTAPAAPTPALAVVDLAPVA +LAFAAWGAPGGRGLTLPEDPPADAMAAAERTLASLDAVDADGRITPHGAVLAELPLDPPL +GHALLRAAPWTGPRPAAEATAALALDLRAPGADLEALVAAVRDGRHPEAGRWRREADRLE +RLARRHAHHAPGEPGPEAAATVRRHPAGLVAALAFPAWIARRAGEAGAYLLASGTRAALP +RDAAGGDLTGQEWLAVAEVARVAGDAAGTGAAIRAAAPIDRTLAELAGAGLRRTEDTADW +RGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRAALAADGLARFDPSGRTERLRRRVH +LLHRVLGAPWPDLSDAGLPGLDALVDGLAADLAAGRPLTRLDAEALLRGALPWPEAGRLD +ELAPERLPVPSGRAVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREPVVLHLLSP +AGRPLAVTADLPSFWAGPYAQVRAENRGRYPKHPWPEDPAAAEPTARTNRRAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000445.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000445.fa new file mode 100644 index 0000000000000000000000000000000000000000..8f5d145edbe5654ee99d72ce94927720ea18245f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000445.fa @@ -0,0 +1,45 @@ +>PROKKA_00411 +MRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTNPDDGGQAKIAAQCTDAA +NGRYRVETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFVPELAEPGFLAPVPEEMQ +AYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAAGLDMSQPVTWDQLIEAA +RSQDKDLAVQGARAESMTVWLNALIEGGGEQIVPNAEAPTDEVTTNLDSEAGRTAARIIS +TIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATLGSVEEGSLPEDLPEDIG +WAVYPRTVEGEDAAPPVGGINLGVGAKSEHQDLAWDAISCITTTEHQSQYFVENGNPPAD +PAAYDAPEVAEKYPMADTIRESLELGAPRPQTPYYNEVSTAIQQRYAPPSGVSESTPAET +DDFIQEVLRGERLL +>PROKKA_00131 +MRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTNPDDGGQAKIAAQCTDAA +NGRYRVETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFVPELAEPGFLAPVPEEMQ +AYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAAGLDMSQPVTWDQLIEAA +RSQDKDLAVQGARAESMTVWLNALIEGGGEQIVPNAEAPTDEVTTNLDSEAGRTAARIIS +TIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATLGSVEEGSLPEDLPEDIG +WAVYPRTVEGEDAAPPVGGINLGVGAKSEHQDLAWDAISCITTTEHQSQYFVENGNPPAD +PAAYDAPEVAEKYPMADTIRESLELGAPRPQTPYYNEVSTAIQQRYAPPSGVSESTPAET +DDFIQEVLRGERLL +>PROKKA_02548 +MRHDTRARQRRRATLAGAVVAGALILAGCAPAEQTPTLTWYTNPDDGGQAKIAAQCTDAA +NGRYRIETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFVPELAEPGFLAPVPEEMQ +AYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAAGLDMSQPVTWDQLIEVA +RSQDKDLGVQGARAESMTVWLNALIEGGGEQIIPNAEAPTDEVTTNLDSEAGRTAARIIS +TIGKEGLGSAGLPTQDENASMLLFQGNNGSFMVNWPFVWPATLGSVEEGSLPEDLPEDIG +WAVYPRTVEDKDAAPPVGGINLGVGEKSEYQDLAWDAISCITTTEHQSQYFVENGNPPAD +PAAYDAPEVAEKFPMADTIRESLELGAPRPQTPYYNEVSTAIQQRYAPPSGVSESTPAET +DDFIQEVLRGERLL +>PROKKA_02416 +MGDDGRHIRLASNEVPLVRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTN +PDDGGQAKIAAQCTDAANGRYRIETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFV +PELAEPGFLAPVPEEMQAYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAA +GLDMSKPVTWDQLIEVARSQDKDLGVQGARAESMTVWLNALIEGGGEQIIPNAEAPTDQV +TTNLDSEAGRTAARIISTIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATL +GSVEEGSLPKDLPEDIGWAVYPRTVEDKDAAPPVGGINLGVGAKSEHQDLAWDAISCITT +TEHQSQYFVENGNPPADPAAYDAPEVAEKFPMADTIRESLELGAPRPQTPYYNEVSTAIQ +QRYAPPSGVSESTPAETDDFIQEVLRGERLL +>PROKKA_00414 +MRDDGRHIRLASIEVPLVRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTN +PDDGGQAKIAAQCTDAANGRYRVETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFV +PELAEPGFLAPVPEEMQAYAKDNALEGALAAASWKDEIVTVPFWANTQLLWYRKSVAEAA +GLDMSQPVTWDQLIEAARSQDKDLAVQGARAESMTVWLNALIEGGGEQIVPNAEAPTDEV +TTNLDSEAGRTAARIISTIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATL +GSVEEGSLPEDLPEDIGWAVYPRTVEGKDAAPPVGGINLGVGAKSEHQDLAWDAISCITT +TEHQSQYFVENGNPPADPAAYDAPEVAEKYPMADTIRESLDLGAPRPQTPYYNEVSTAIQ +QRYAPPSGVTESTPAETDDFIQEVLRGERLL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000448.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000448.fa new file mode 100644 index 0000000000000000000000000000000000000000..6c9518b2a59161d343ec3901092fe3410daf8b68 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000448.fa @@ -0,0 +1,20 @@ +>PROKKA_00416 +MAHIITVAGATPRIHESVFLAPTAAITGDVEMAERSSAFYGVSARGDSAPIRVGAGTNLQ +DNVVLHADEGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA +LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKKNAATYLRLSAAHRDAVAG +>PROKKA_00136 +MAHIITVAGATPRIHESVFLAPTAAITGDVEMAERSSAFYGVSARGDSAPIRVGAGTNLQ +DNVVLHADEGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA +LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKKNAATYLRLSAAHRDAVAG +>PROKKA_02544 +MAHIITVAGAGPRIHESVFLAPTAAITGDVEMAERSSAFYGVSARGDSAPIRVGERTNLQ +DNVVLHADKGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA +LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKVNAATYLELSAAHREATAER +>PROKKA_02412 +MGHLVTVLGRTPRVDPSAFVARTAVLSGDVELGPRASAFYGVSARGDSAAIRVGEGSNLQ +DNVVLHADAGFPCTLGAGVSVGHAAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA +VVLEGTQVPPGSLVAGVPAKVRRGLTEEERASLTVNARTYLDLAAAHRAAEEAEQAGV +>PROKKA_00419 +MAHIITVAGATPRIHESVFLAPTAAITGDVEMAEHSSAFYGASARGDSAPIRVGAGTNLQ +DNVVLHADEGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA +LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKKNAATYLRLSAAHRDAVAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000450.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000450.fa new file mode 100644 index 0000000000000000000000000000000000000000..ad257debb28fecb8d4fb8bfc32d15d05beb64300 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000450.fa @@ -0,0 +1,50 @@ +>PROKKA_00419 +MTEYQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERR +PHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFAL +RFYSEEGNYDLVGNNTPIFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAH +QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA +GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVG +TLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLP +VNRPKNAVHNYAFDGQMWYDHTGDRSTYAPNSNGDSWSDETGPVDDGWEADGTLTREAQA +LRADDDDFGQAGTLVREVFSAQEREDFVETVAGALKGVRQDVQARAFEYWKNVDTAIGQR +IEDEVKRHEGDGIPGVEAGGEARI +>PROKKA_00140 +MTEYQKKTPHATGSTRQNGAPAISDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERR +PHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFAL +RFYTEEGNYDIVGNNTPIFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAH +QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA +GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVG +TLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLP +VNRPKNAVHNYAFEGQMWYDHTGDRSTYVPNSNGDSWSDETGPVDDGWEADGTLTREAQA +LRADDDDFGQAGTLVREVFSDQERDDFVETVSGALKGVRQDVQARAFEYWKNVDATIGQR +IEDEVKRHEGDGIPGVEAGGEARI +>PROKKA_02540 +MTENQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLVETHQHFNRMNIPERR +PHAKGSGAFGEFEVTEDVSKYTKALVFQPGAKTETLLRFSTVAGELGSPDTWRDVRGFAL +RFYTDEGNLDVVGNNTPVFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNTPESAH +QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNFSNEEAEAMA +GKNADYHRQDLFESIAKGDYPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVG +TLTLNRNPENHFAQIESAAFNPGNMVPGVGLSPDRMLLGRSFAYHDAQLYRVGAHVNQLP +VNRPKNEVHNYAFDGQMWYDHTGSRSTYAPNSNGDSWSDETGPVDDGWEADGTLTREAQA +LRKDDDDFGQAGTLVREVFTDAERDAFVETVAGALDGVREDVQARAFQYWKNVDATIGQR +IEDEVNKGQGDDIPGAAGGGEARI +>PROKKA_02409 +MTEYQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERR +PHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFAL +RFYSEEGNYDIVGNNTPVFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAH +QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA +GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISQKDYPRIKVG +TLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLP +VNRPKNAVNNYAFDGQMWYDHTGDRSTYAPNSNGDSWSDETGPVDDGWEADGTLTREAQA +LRADDDDFGQAGTLVREVFSDQERDDFVETVAGALKGVRQDVQARAFEYWKNVDATIGQR +IEDEVKRHEGDGIPGVEAGGEARI +>PROKKA_00422 +MTEYQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERR +PHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFAL +RFYSEEGNYDLVGNNTPIFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAH +QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA +GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVG +TLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLP +VNRPKNAVHNYAFDGQMWYDHTGDRSTYAPNSNGDSWSDETGPVDDGWEADGTLTREAQA +LRADDDDFGQAGTLVREVFSAQEREDFVETVAGALKGVRQDVQARAFEYWKNVDTAIGQR +IEDEVKRHEGDGIPGVEAGGEARI diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000454.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000454.fa new file mode 100644 index 0000000000000000000000000000000000000000..42fc6131a8cd18d7a3f44ab0014ceaaf93dc11b2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000454.fa @@ -0,0 +1,49 @@ +>PROKKA_00424 +MTPRPPHPADPASGAFTPDQRRILTALLMPLFLALMSVSVVNVALPAIESGLDATSADLQ +WVLAGYTLTFGTVLVAAGRAGDLWGRKNLFLAGITLYMLGSLLSGLAGDTLLLNAGRLLT +GLGAGVFNPQVIGFIQSNFHGRARGRAYGLFGTVVGLGVAVGPLLGGLFLGAFGPEWGWR +STFLMNVPVGLAAVAMGALWLPPPTRVHGLPPAPGPRGIAALDPVGALLLGAGGVSLMVP +FIVPGTAWLLVLAAALVTAWWLWEKRVKARASATGVQPMVDPALFRRPSFTIGALESTIY +LATMPAVFAIVAIFLQRGMGFTPLEAGLVGLPGAVVVASLSPWVGSMVQRRGPVLVLLGA +LVGLVSLGVLALAFERSAAGAWSPWIVGVGLIVQSASQALLLTSTQVLMMDDVAGHEAGA +AGGVAQTAQRLGTALGLSVVTGAFFAALAGAAGESAGPPSAAAYAHAASTAMGMVAVCWA +LTAAVAALDVVRRRRAARAA +>PROKKA_00145 +MTPRPPHPADPASGAFTPDQRRILTALLMPLFLALMSVSVVNVALPAIESGLDATSADLQ +WVLAGYTLTFGTVLVAAGRAGDLWGRKNLFLAGITLYMLGSLLSGLAGDTLLLNAGRLLT +GLGAGVFNPQVIGFIQSNFHGRARGRAYGLFGTVVGLGVAVGPLLGGLFLGAFGPEWGWR +STFLMNVPVGLAAVAMGALWLPPPTRVHGLPPAPGPRGIAALDPVGALLLGAGGVSLMVP +FIVPGTAWLLVLAAALVTAWWLWEKRVKARASATGVQPMVDPALFRRPSFTIGALESTIY +LATMPAVFAIVAIFLQRGMGFTPLEAGLVGLPGAVVVASLSPWVGSMVQRRGPVLVLLGA +LVGLVSLGVLALAFERSAAGAWSPWIVGVGLIVQSASQALLLTSTQVLMMDDVAGHEAGA +AGGVAQTAQRLGTALGLSVVTGAFFAALAGAAAESAGPPSAAAYAHAASTAMGMVAVCWA +LTAVVAALDVVRRRRAVRAA +>PROKKA_02533 +MGGPVAATARRPANRRAGPVVVRAYPEAVTPRPRSADGDAAPAAFTPEQRRILTALLMPL +FLALMSVSVVNVALPAIESGLHATSADLQWVLAGYTLTFGTVLVASGRAGDLWGRKSLFL +VGIGLYVAGALVSGFAADPLMLNAGRLVTGVGAGVFNPQVVGFIQSNFSGRARGRAYGLF +GTVIGLGVAVGPMLGGLLLGALGPEWGWRSTFLMNAPVGLAAIVMGVLWLPAPTRVHGLP +AAPGPRGIAALDPVGALLLGLGAVCLMVPFIVPGTAGLLVLAAALVTAWWLWEKRVKARA +SATGVQPMVDPALFRRLSFTIGALESTIYLATMPAVFAIVAIFLQRGMGFTPLEAGLVGL +PGAVVVASLSPWVGSMVQRRGPVLVLLGALVGLVSLGVLALAFERSAAGAWSPWIVGVGL +IVQSASQALLLTSTQVLMMDDVAGHEAGAAGGVAQTAQRLGTALGLSVVTGAFFAALAGA +AAEGAGPPSAAAYAHAASTAMGMVAVCWALTAVVAALDVVRRRRAVRAA +>PROKKA_02403 +MTLPSPAAAESGAFTADQRRILTVLLIPLFLALMSVSVVNVALPSIEGGLGASSADLQWV +LSGYTLTFGMVLVAAGRAGDLWGRRPLFLAGIALYVLGSLLSGLAPDPLWLNAGRLLTGL +GAGVFNPQTIGFIQSHFTGRARGRAYGLFGMVVGLGVAVGPLLGGLLLGALGPDWGWRST +FLMNVPVGVLAIVMATAWLSPDTRVKGAAGRSGGPRGIAALDPVGALLLGGASLCLMVPF +IAPGTWALLAGAAVLGVGWWLWELRVKRRAAATGVEPMVDPALFRRASFSIGAAESTIFL +SSMPAVFAVTAVFLQQGMGFSPLASGLATLPGAVVQAVASPWAGSKVPSQGARMVFGGGV +VGLASLAILALAFERSAAGAWSPWIVGAALAVMAVSQALILTTTQVLMMEDVAGHEAGAA +GGVAQTAQRMGTALGLSVVMGAFYAALAGAAGPGGAPSAAGFAHAASAAVLMVGACWLVT +TAIAAADLVRRRRTAR +>PROKKA_00427 +MPLFLALMSVSVVNVALPAIESGLDATSADLQWVLAGYTLTFGTVLVAAGRAGDLWGRKS +LFLAGITLYMLGSLLSGLAGDTLLLNAGRLLTGLGAGVFNPQVIGFIQSNFHGRARGRAY +GLFGTVVGLGVAVGPLLGGLFLGAFGPEWGWRSTFLMNVPVGLAAVAMGALWLPPPTRVH +GLPPAPGPRGIAALDPVGALLLGAGGVSLMVPFIVPGTAWLLVLAAALVTAWWLWEKRVK +ARAWATGVQPMVDPALFRRPSFTIGALESTIYLATMPAVFAIVAIFLQRGMGFTPLEAGL +VGLPGAVVVASLSPWVGSMVQRRGPVLVLLGALVGLVSLGVLALAFERSAAGAWSPWIVG +VGLIVQSASQALLLTSTQVLMMDDVAGHEAGAAGGVAQTAQRLGTALGLSVVTGAFFAAL +AGAAAESAGSPSAAAYAHAASTAMGMVAVCWALTAVVAALDVVRRRRAARAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000457.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000457.fa new file mode 100644 index 0000000000000000000000000000000000000000..119f187557d0665cc290ecc286ec5fc80442f362 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000457.fa @@ -0,0 +1,35 @@ +>PROKKA_00427 +MTMKKNSVQDVLAQDAAATAHLAGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD +FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV +LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH +VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP +KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAVSGTPIPQLEEEFVGKMYGHLKV +AVADAVVERLAPVRERALALLDDPAELDRILAAGAEKARAVATPVLEDVYAKVGFLPPLR +>PROKKA_00148 +MTMKKNSVQDVLAQDAAATAHLPGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD +FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV +LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH +VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP +KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILAAVSGTPIPQLEEEFVGKMYGHLKV +AVADAVVERLAPVRERALELLADPAELDRILASGAEKARAVATPVLEDVYAKVGFLPPLR +>PROKKA_02530 +MKKNSVQDVLAQDVSATAHLAGASDRHRVLSGMQPSADSLHLGNYLGALTNWVRTQDDFE +AFFFIPDLHAITVPQDPAALAQRTRVAAAQFIAAGIDPERSTLFVQSQVPEHAQLAWVLT +CMTGMGEAMRMTQFKDKSAKQGAEAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQHVE +LTRDLAQRFNHRHGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINVMDDPKR +TAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAMTDVPVAELEGRYVGRMYGHLKVDV +ADAVVERLAPVKARTEELLADPAELDRILAAGAAKARAVATPVLEDVYAKVGFLPPLR +>PROKKA_02400 +MTMKKNSVQDVLAQDAAATAHLAGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD +FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV +LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH +VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP +KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAVSDRPIPELEAEFEGKMYGHLKV +AVADAVVERLAPVRERALGLLDDPAELDRILAAGAAKAREVATPVLEDVYARVGFLRPLR +>PROKKA_00430 +MTMKKNSVQDVLAQDAAATAHLAGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD +FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV +LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH +VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP +KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAVSGTPIPQLEEEFVGKMYGHLKV +AVADAVVERLVPVRERALALLADPAELDRILAAGAEKARAVATPVLEDVYAKVGFLPPLR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000458.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000458.fa new file mode 100644 index 0000000000000000000000000000000000000000..2ee77ee6b6a9a0fb27eb9a55f6346ce83bb727b8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000458.fa @@ -0,0 +1,30 @@ +>PROKKA_00428 +MSTAVPIPAVAEVPPGAEPVLETENLVKVYGRGASRFDALKGITLQIQRGESLAVVGKSG +SGKSTLMHLLALLDQPSAGVVAMDGRPVSQLKAAEISQLRNERFGFVFQQFFLNPNQTVL +ENTVLPLKIAGVGRAERARRGMAVLERLELADKAKNKATDLSGGQKQRVCIARALVNNPT +VLFADEPTGNLDSATSAAVEDILFGLHRDEGITLVVVTHDDDLAAKCDRRVELQDGVVIA +DERVGTERDGARA +>PROKKA_00149 +MSTAVPIPAVAEVPPGAEPVLETENLVKVYGRGASRFDALKGITLQIQRGESLAVVGKSG +SGKSTLMHLLALLDQPSAGVVAMDGRPVSQLKAAEISQLRNERFGFVFQQFFLNPNQTVL +ENTVLPLKIAGVGRAQRTRRGMAVLERLELADKAKNKATDLSGGQKQRVCIARALVNNPT +VLFADEPTGNLDSATSAAVEDILFGLHRDEGITLVVVTHDDDLAAKCDRRVELQDGVVIA +DERVGTERDGARA +>PROKKA_02529 +MHTVQQAAGAHAPAGREPVLETENLVKVYGRGESRFDALKGVTLQIQAGESVAIVGKSGS +GKSTLMHLLALLDRPSAGVVAMDGRPVQDVSPAEVARLRNETFGFVFQQFFLNPAQTVLE +NTVLPLKISGVPRAERRERGMAVLERLELADKAGNKATDLSGGQKQRVCIARALVNRPTV +LFADEPTGNLDSATSAAVEDILFGLHRDEGITLVVVTHDDDLAARCDRRLVMQDGMIVDE +TTTAGAQA +>PROKKA_02399 +MSTVHTHPPETQASRGEEPVLETENLVKVYGRGASRFDALKGVTLQIHRGESVAVVGKSG +SGKSTLMHLLALLDVPTSGVVAMDGRPVSQLKAAEVAHLRNERFGFVFQQFFLNADQTVL +ENVVLPLKIAGVPRHEREARGREVLERLEIADKAKNRANDLSGGQKQRVCIARALINRPT +VLFADEPTGNLDSATSRSVEEILFGLHRDEGITLVVVTHDDDLAAQCDRRLVMQDGVIVA +AEGAGRAVAAGTGARA +>PROKKA_00431 +MSTAVPIPAVAEVPPGAEPVLETENLVKVYGRGASRFDALKGITLQIQRGESLAVVGKSG +SGKSTLMHLLALLDQPSAGVVAMDGRPVSQLKAAEISQLRNERFGFVFQQFFLNPNQTVL +ENTVLPLKIAGVGRAQRTRRGMAVLERLELADKAKNKATDLSGGQKQRVCIARALVNNPT +VLFADEPTGNLDSATSAAVEDILFGLHRDDGITLVVVTHDDDLAAKCDRRVELQDGVVID +DERVGTEQDGARA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000459.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000459.fa new file mode 100644 index 0000000000000000000000000000000000000000..aaf5a693d0cccf1d10d86a7a93231a03a70ceab0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000459.fa @@ -0,0 +1,45 @@ +>PROKKA_00429 +MKATDVAGTALANTMRSKLRTFLTVVAIVIGAFTLTLTTGLGAGINKYVDNVVEGFGKPG +ELTVMKQQDMSSAGAASGSPQEYAEQDAAGGEMFGMPLLTQEDLAAIEDTEHVTEVKTYR +VAEPEYIQGPDDRKWQTGFMGSSGEIDMLTFSAGRAPEAGAAEIVMPESWVEDLGAGDAE +DLVGTELTVVAATPLQEHKSVTATVVGVTKAAASGAGTAPTPSESLEQEIYDITTEGLPE +SQRDTYFQATAIVADPEANEDAVKQALADQGLLAQTLEEQLGVIRGIIDAVTWVLTGFAL +IALLAASFGIINTLLMAVQERTREIGLMKALGMTGGKIFGLFTMEAVVIGLLGSLVGIGL +GVAVGLIANQVLTTGPLSGVTGLVLFAVNPLALLLILLLIVAIAFIAGTLPALRAARKDP +IEALRHE +>PROKKA_00150 +MKATDVAGTALANTMRSKLRTFLTVVAIVIGAFTLTLTTGLGAGINKYVDNVVEGFGKPG +ELTVMKQQDMSSAGAASGSPQEYTEQDAAGGEMFGMPLLTQEDLAAIEDTEHVTEVKTYR +VAEPEYIQGPDDRKWQTGFMGSSGEIDMLTFSAGRAPEAGAAEIVMPESWVEDLGAGDAE +DLVGTELTVVAATPLQEHKSVTATVVGVTKAAASGAGTAPTPSESLEQAIYDITTEGLPE +SQRNTYFQATAIVEDPEANEDAVKQALADQGLLAQTLEEQLGVIRGIIDAVTWVLTGFAL +IALLAASFGIINTLLMAVQERTREIGLMKALGMTGGKIFGLFTMEAVVIGLLGSLVGIGL +GVAVGLIANQVLTTGPLSGVTGLVLFAVNPLALLLILLLIVAIAFIAGTLPALRAARKDP +IEALRHE +>PROKKA_02528 +MKATDLAGTALANTMRAKLRTFLTVVAIVIGAFTLTLTSGLGAGINKFVDNMVEGFGSPD +QLTVMKQVDPTSFAAGGAPQEYEPDEAAAGEMFGLPLLTAADLDRIRDTEHVTEVETARL +VEPEYIEGEDGRQWQVPFMGSSFEIGALSLAAGREPAADAAEVTVPQDWVEALGGQTPED +VLGQTVTLVAADPLGKQDGVEAEVVGVTEPMASGSGSGPVPSGEVETRLHEIQTAGLPEA +QRDTFFSASVTVADMAANEAAVKAALAEEGYSAQTLEDQLGPIRGIIDAVTWVLNGFALI +ALLAASFGIINTLLMAVQERTREIGLMKALGMTGRKIFGLFTMEAVVIGLLGSLIGVGLG +VAVGVVANQVLTEGALSGVTGLVLYAVEPLSLALIVLLIVAIAFLAGTLPAARAARKDPI +EALRYE +>PROKKA_02398 +MKAPDLIRTALGNTARAKLRTFLTVIAIMIGAFTLTLTSGLGAGINKYVDNMVAGFGAPD +ELTVSKPAGNQMAGMTGGAPTEYEDSAAAGEMYGMPLLTQEDLDRIGATEHVTGVETVRI +VEVQDLRGADGRRWSVPMMGGTYEIGKLSVKAGREPAADGGAMELTVPTEWVESLGGTAP +EDVLGQEVTLTTKTPLQQERTVQAEVVGVTERLPSGVGANPVPSAALEQGLHDIQTEGLP +EEQRNTYFQATAIVEGMPGNEAAVKAALSEQGYQAQTLEDQLGSIRGIISAVTWVLNGFA +LIALLAASFGIINTLLMAVQERTREIGLMKALGMTSGRIFGLFTLEAVVIGLLGSLLGVG +LGVAVGVGVNAWLTTGGPLEDVAGLVLYAVDPLALLLIVLLIVAIAFVAGTLPAARAARK +DPIEALRHE +>PROKKA_00432 +MKATDVAGTALANTMRSKLRTFLTVVAIVIGAFTLTLTTGLGAGINKYVDNVVEGFGKPG +ELTVMKQQDMSSAGAASGSPQEYTEQDAAGGEMFGMPLLTQEDLAAIEDTEHVTEVKTYR +VAEPEYIQGPDDRKWQTGFMGSSGEIDMLTFSAGRAPEAGAAEIVMPESWVEDLGAGDAE +DLIGTELTVVAATPLQEHKSVTATVVGVTKAAASGAGTAPTPSESLEQEIYDITTEGLPE +SQRDTYFQATAIVADPEANEDAVKQALADQGLLAQTLEEQLGVIRGIIDAVTWVLTGFAL +IALLAASFGIINTLLMAVQERTREIGLMKALGMTGGKIFGLFTMEAVVIGLLGSLIGIGL +GVAVGLIANQVLTTGPLSGVTGLVLFAVNPLALLLILLLIVAIAFIAGTLPALRAARKDP +IEALRHE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000460.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000460.fa new file mode 100644 index 0000000000000000000000000000000000000000..3fb960607358686b68eb7d04f88d49bc6a4d25c2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000460.fa @@ -0,0 +1,26 @@ +>PROKKA_00430 +MTTDRPNPDPNPEQPAVGSRYGTQPYAAPGYGAQPGSPYGIVPEPAAFPALLTLTLTSLA +LYVLSSLPALFGGEESIERMRDSLRQSGLTPEQVEEIAPVVGASVTVGTIIVLLIGVALY +ALVYFNLRGAKNWARILGIVVGILGTLSAVGGIFSFVTYPGIGGVLASVLSLALVIVNIL +WLVKAFNPQVAAYTRQGRRA +>PROKKA_00151 +MTTDRPNPNPEQPAAGSRYGTQPYAAPGHGAQPGSSYGIVPEPAAFPALLTLTLTSLALY +VLSSLPALFGGEESIERMRDSLRQSGLTPEQVEEIAPVVGASVTVGTIIVLLIGVALYAL +VYFNLRGAKNWARILGIVVAILGTLSAVGGIFSFVTYPGIGGVLASVLSLALVIVNILWL +VKAFNPQVAAYTRQGRRA +>PROKKA_02527 +MSNQNPDFTNPAYNPANPPFEGESGQAGQAPQQGQPGQAAQYGQPGPYGQAPQYGQPGQY +PATGTRYGTQPYGVDGRYGTVPEPRGFRTLLTLTLVSAALWVLSSLPAMFTMDDMMDVVM +RDAASQPGVTAEDMEMVSSFMRTAGITSIVISLIIGLGLYALVYFNLRGVKNWARILGIV +FAILGALAIFSGIGFLFSGSTMLILSGALTLAYAVVNIIWVITAFRSDVAEWFRQGRPAA +A +>PROKKA_02397 +MTDQNTPYPQNPQGGQPAPQYGQPGQAAPQYGQPGEGSRFGTQAYGAPGLQYGAPLAEPA +KFRTLLKLTLASAVVYVLSALPGLFVDQDALVRDQLRAQGMSAEQIDQAMQNAGMFSAMA +GIGAVVGLLIALGLYALVYFGLRAGKNWARVLGIVLAILGTLSAVFGLFSLGSFPAGVMI +ASLVLSVLFIAVNVLWLVNAFNKDVAAYTKQGRLPAA +>PROKKA_00433 +MTTDRPNPDPNPEQPAAGGPGPYPGQNPAYGQPTAGSRYGTQPYAAPGYGAQPGSPYGIV +PEPAAFPALLTLTLTSLALYVLSSLPALFGGEESIERMRDSLRQSGLTPEQVEEIAPVVG +ASVTVGTIIVLLIGVALYALVYFNLRGAKNWARILGIVVAILGTLSAVGGIFSFVTYPGI +GGVLASVLSLALVIVNILWLVKAFNPQVAAYTRQGRRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000472.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000472.fa new file mode 100644 index 0000000000000000000000000000000000000000..8b70442a5805d67ad4b714012230295be238034d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000472.fa @@ -0,0 +1,20 @@ +>PROKKA_00443 +MADGQHTTTAPRVDWDRLRAAALAATEHAYVPYSGFRVGAAALTDDGRLVSGCNIENASY +GLTLCAECALLAELRMGGGGRLAAFVCVDGAGVLTMPCGRCRQLLYEFRAPGLVLLTPAG +ERGIDAVLPDAFGPADLERADRP +>PROKKA_00164 +MADGQHTTTAPRVDWDRLRAAALAATEHAYVPYSGFRVGAAALTDDGRLVAGCNIENASY +GLTLCAECALLADLRMGGGGRLAAFVCVDGAGVLTMPCGRCRQLLYEFRAPGLVLLTPAG +ERGIDAVLPDAFGPADLERADRP +>PROKKA_02514 +MAAEGTTTAPGVDWDRLRRAALAATEHAYVPYSGFRVGAAALTEDGRLVTGCNIENASYG +LTLCAECALLADLRMGGGGRLAAFVCVDGQGVLTMPCGRCRQLLHEFRAPDMVLLTPAGE +RTMGQVLPDAFGPEDLERAAAR +>PROKKA_02385 +MTGTTTPPACAAPVAEADWDRLRAAAADAMERAYAPYSGFRVGAAALTEDGRLVSGCNVE +NAAYGVALCAECALVGQLHMTGGGRLRAFLCVGGDGRLITPCGRCRQLLWEFRAPGLAVL +TAAGVTTVEALLPEAFGPDALEA +>PROKKA_00446 +MADGQHTTTAPRVDWDRLRAAALAATEHAYVPYSGFRVGAAALTDDGRLVSGCNIENASY +GLTLCAECALLADLRMGGGGRLAAFVCVDGDGVLTMPCGRCRQLLYEFRAPGLVLLTPAG +ERGIDAVLPDAFGPADLERADRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000475.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000475.fa new file mode 100644 index 0000000000000000000000000000000000000000..71b75f479400205bc6c8d989a04860830e337726 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000475.fa @@ -0,0 +1,40 @@ +>PROKKA_00446 +MTTTQLPDTASPSPLEVDLAVLPKVSLHDHLDGGLRVGTVLDLAREAGVEVPADTVEGLA +EWIAEHANGESLEKYLQVFALTTAVMQTREQLRRVAREFVEDLVADGVVYGEIRWAPEQH +LAGGLSLDEAVEAVQAGLDEAVEADAAAGHAIRVGQLVTAMRHADRAQEIAELAVRHRAA +GVVGFDIAGAEAGFPPSRFADTFTWLAAHHLPVTVHAGEGDGLDSVRSALVDGRALRLGH +GVRLAEDISVEYGGVDEDGEQLDELTGLVDLGETAAWVRDRQIALEVCPSSNLQTGAVDA +AAGIAGHPIDLLVQLGFRVTVNTDNRLVSDVSLTDELYLLAETFGYSLSELLDLQLNAAE +AAFLSVDEREDLAEILVAGWGEVISGDAVGPVLEELDDEDEDD +>PROKKA_00167 +MTTTQLPDTASPSPLEVDLAVLPKVSLHDHLDGGLRVGTVLDLAREAGVEVPADTVEGLA +EWIAEHANGESLEKYLQVFALTTAVMQTREQLRRVAREFVEDLVADGVVYGEIRWAPEQH +LAGGLSLDEAVEAVQAGLDEAVEAADAAGHVIRVGQLVTAMRHADRAQEIAELAVRHREA +GVVGFDIAGAEAGFPPSRFADTFTWLAAHHLPVTVHAGEGDGLDSVRSALVDGRALRLGH +GVRLAEDISVEYGGVDEDGEQLDELTGIVDLGETAAWVRDRQIALEVCPSSNLQTGAVDA +AAGIAGHPIDLLVQLGFRVTVNTDNRLVSDVSLTDELYLLAETFGYSLSELLDLQLNAAE +AAFLSVDEREDLAEILVAGWGEVISGDAVGPVLEELDDEDEDD +>PROKKA_02511 +MTATQLPDTASPSPLEVDLAALPKVSLHDHLDGGLRVGTVLELATEAGVDVPADTVEGLA +EWIAEHANGESLEKYLQVFALTTAVMQTREQLRRVAREFVEDLVADGVVYGEIRWAPEQH +LAGGLSLDEAVEAVQEGLDEAVDAAEAQGRLIRVGQLVTAMRHADRAQEIAELAVRHRER +GVVGFDIAGAEAGFPPSRFAETFTWLAAHHLPVTVHAGEGDGLDSVRSALVDGRALRLGH +GVRLAEDISVEFGGVDEDGEQLDELTGLVDLGETAAWVRDRQIALEVCPSSNLQTGAVDA +EAGIAGHPIDLLVQLGFRVTVNTDNRLVSDVSLTDELYLLAETFGYSLAELLDLQLNAAE +AAFLAVDEREDLAEILVAGWGEVISGDDAGPVLEELDEDDEDEDA +>PROKKA_02382 +MTISSQTPADAAPSPLTIDLGALPKVSLHDHLDGGLRVATVLELAREAGVEVPADTVDGL +ADWFAEHANGESLEKYLETFALTTSVMQTHEQLRRVAREFVEDLVADGVVYGEIRWAPEQ +HLASGLTLDEAVEAVQEGLDEAVDAADEAGHVIRVGQLVTAMRHADRAQEIAELAVRHRD +RGVVGFDIAGAEIGFPPSRFADTFTWLAQQHLPVTVHAGEAEGLSSIQDALVSGRALRLG +HGVRIADDIQVEFGGLDEDGVPVDADTGIVDLGETAAWVRDRQIALEICPSSNLQTGAVD +AAAGIAGHPIDLLVQLGFRVTVNTDNRLVSNVSLTDELYLLAETFGYSLSELLDLQLNAA +EAAFLAVDEREDLAEILVSGWGEVISGAGGTVALEELEADTDDEADA +>PROKKA_00449 +MTTTQLPDTASPSPLEVDLAVLPKVSLHDHLDGGLRVGTVLDLAREAGVEVPADTVEGLA +EWIAEHANGESLEKYLQVFALTTAVMQTREQLRRVAREFVEDLVADGVVYGEIRWAPEQH +LAGGLTLDEAVEAVQAGLDEAVEAADAAGHVIRVGQLVTAMRHADRAQEIAELAVRHREA +GVVGFDIAGAEAGFPPSRFADTFTWLAAHHLPVTVHAGEGDGLDSVRSALVDGRALRLGH +GVRLAEDISVEYGGVDEDGEQLDELTGLVDLGETAAWVRDRQIALEVCPSSNLQTGAVDA +AAGIAGHPIDLLVQLGFRVTVNTDNRLVSDVSLTDELYLLAETFGYSLSELLDLQLNAAE +AAFLSVDEREDLAEILVAGWGEVISGDAVGPVLEELDDEDEDD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000477.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000477.fa new file mode 100644 index 0000000000000000000000000000000000000000..5bfd75fba271e0f4d0c3c0a22cf83f555c779009 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000477.fa @@ -0,0 +1,27 @@ +>PROKKA_00449 +MSPRRPRVPRVDPTTGAPRRTAVAAPAAPTTASPKADAPTPTPEATTPTPAATGAEVIDL +HSVQERRQAGHHGHLDGHPDADRADTAPAAPASPSAPPRRTAPARPAGRRTRPAPRRAAS +AAATAARRRAPLPEPVPARQITGRSLIVVAVLLVAAVLVAPTLRAFLNQQLEISAAREEI +ATMQAQREDYERRIQLWDDPAYVTQQARERLELVMPGETLYSVTGRPSETETETDTEAED +TPAARADEVVNTRLPWAEGLWDSAVRAGLE +>PROKKA_00170 +MSPRRPRVPRVDPTTGAPRRTAVAAPAAPTTAFPEADTPTPTPAAPTPAPAATDAEVIDL +QSIQERRQAGHPDVDRADTAPAGDTAAPASPSAPPRRTAPARPAGRRPRPAPRGAASAAA +TAARRRAPLPEPVPARQITGRSLIVVAVLLVAAVLVAPTLRAFLNQQLEISAAREEIATM +QAQREDYERRIQLWDDPAYVTQQARERLELVMPGETLYSVTGRPSETDTATETEDTPAAG +ADEVVNTRLPWAEGLWDSAVRAGLE +>PROKKA_02507 +MAARRRAPLPDPVPARQITGRSLLVVAVLLVAAVLVAPTLRAFLNQQLEIAAAEEEIAAM +QAQREDYEERIRLWDDPGYVTQQARERLQLVMPGETLYSVTGVPEEAPRDPRPEAPAGEP +VNTRLPWAEGLWDSAVRAGPRVSPGPRPDPGSGPARP +>PROKKA_02379 +MSARRPRVPRVAVPDTAPERATPAVVEPVVVEPAPVAPAAPEAPAPPAPPGPQVIDLQEA +AQRRRHEATRPSPRPDAERAAAQRVARLREERRRATVREHAAARRRVPLPEPVPARQLTG +RSLVVLAVLIIAAVLVAPTARLMLNQQLEISAAQQDIAEQQRRKAEYEEQIRRWDDPGYV +AQQARQRLELVMPGETLYTVTGLPDESGAVPADSVPQEKVNDRLPWVEGLWDSAVRAATE +>PROKKA_00452 +MSPRRPRVPRVDPTTGAPRRTAVAAPAAPTTAFPEADTPTPTPAAPTPAPAATDAEVIDL +QSVQERRQAGHPGHLDGHPDADRADTAPAGDTAAPASPSAPPRRTAPARPAGRRPRPAPR +RAASAAATAARRRAPLPEPVPARQITGRSLIVVAVLLVAAVLVAPTLRAFLNQQLEISAA +REEIATMQAQREDYERRIQLWDDPAYVTQQARERLELVMPGETLYSVTGRPSETDTATET +EDTPAAGADEVVNTRLPWAEGLWDSAVRAGLE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000479.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000479.fa new file mode 100644 index 0000000000000000000000000000000000000000..5b87940aa159b769f7fe2f17b3b052887e94b2b3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000479.fa @@ -0,0 +1,45 @@ +>PROKKA_00451 +MSLTPELSPKPRLLIVGGGYAGFQLAKELQTKVKDRGGVVTVVDPLPYMTYQPFLPEVVG +GHIVGRNVVVDLATHLKDAEVLRGTVVKVEHARRVATVRGEDGHEFELPYQDIAMTAGAT +TRVFPIKGLGEHGIGLKTVEEAVTLRNQILERLDAASLMVDAEARRRALTFVVVGGGFAG +IETVGEMEHLIRTAVARNPRLSQSEVRIVLVEAMGRIMPEVGEDQAVGVVEHLKDRGIEV +LLNTSLGDATDGIMTLVDMKDKSEKEKFGADTLVWTAGVAANAVAKQTDFPVEERGRIEV +TPTLQVKDGENGVFEGAWGCGDVCAVPDLTGAGPGGFCVPNAQHAGRQAKQLAANYMAVR +HGEGEVQEYVHKSLGAVAGLGFFKGVGNPLGVKISGPAAFLAHRGYHAYAMPTLDRRFRI +LSGWVAETLFGRDSTSVAGLDTPFNPFRRAAGVELEPGRFERQRALESSKG +>PROKKA_00172 +MSLTPELSPKPRLLIVGGGYAGFHVARELQKKVAERGGVVTVVDPRPYMTYYPFLPEVVG +GHIEGRHVNVDLQTHLKDAEVVRGAVVSVDHAGRTAVVRGEGGDEFEIPYQDIVMTAGAV +TRVFPIPGLGEQGIGLRSVEEAVQLRNQILERLDAGSLMTDAEERKRALTFVVVGGGFAG +IEAIAEMENLIRNAVERNERLSQSEIRIVLVEAMGRIMPEVSEEQAQGVVEHLKDRGIEV +LLNTSLGDATDGVMKLVAMPSKEEAETFAADTLVWCAGVVANSVVKSTDFPVDDRGRVEA +TPTLQIKDGEAGALEGAWACGDVSAVPDLTGAGPGGFCVPNAQHAIRQAKRLAANYMAVR +HGEGEVQEYVHKSLGTVAGLGFGRGVGNPLGTKIAGIPAFLAHRGYHGYAMPTLERKFRI +LSGWVAETLFGRDSTSVAGLDTPFNPFRRAAGVELEPGRFERQRALESSKG +>PROKKA_02505 +MSLTPELSPKPRLLIVGGGYAGFHIAKELQKKVKDAGGVVTVVDPLPYMTYQPFLPEVVG +GHIDGRNVVVDHATHLKDAEVLRGTVVKVEHARRVATVRGEDGHEFEVPYQDVVMTAGAT +TRVFPIAGLGEHGIGLKTVEEAEALRNQILERLDAASLMVDAEARRRALTFVVVGGGFAG +VETVGEMEHLIRTAVSRDPRVSQSEVRIALVEAMGRIMPEVSEDQAAGVVEHLKDRGIEV +LLNTSLGDATDGIMTLVDMKDKSEKEKFGADTLVWTAGVAANSVAKQTDFPVEERGRIEV +TATLQVKDGQGGVLEGAWGCGDVCAVPDLTGAGPGGFCVPNAQHAGRQAKQLAANYLAVR +HGEGEVQEYVHKSLGTVAGLGFFKGVGNPLGVKISGPAAFLAHRGYHAYAMPTLDRRFRI +FAGWVAETLFGRDSTSVEGQDRPFNAFRRAAGVELEPGRFERKRALESSKG +>PROKKA_02377 +MSITPDLSPKPRLLVVGGGYAGFHIAQTLQSKVKDRGGVVTVVDPRPYMTYQPFLPEVVG +GHIEGRHVIVDLQTHLKDTEVVRGAVTKVEHARKVAVVRGEDGAEFEVPYQDIVMTAGAN +TRVFPIPGLAEQGIGLKTVEEAVALRNQILERLDAAALMTDAEQRRAALTFVVVGGGFAG +IEAIAEMENLIRTAVSRNENLSQTEVRIVLVEAMGRIMPEVSEDQAQAVVAHLKGRGIEV +LLNTSLGDATGGVMKLVNMADKSEADSFRADTLVWTAGVAANGVAKQTDFPVEDRGRIEV +TPTLQIKDGEGVLEGAWACGDVAAVPDLTGAGPGGFCVPNAQHAGRQAAQLAKNYMAVRH +GEGEVQEYVHKSLGAVAGLGFLKGVGNPMGVKLFGVPAFLAHRGYHAYAMPTLERRFRIV +SGWIAETLFGRDSTSVDGQETPFNAFRVAAGAEPVPSTLEKKRAGELAAK +>PROKKA_00454 +MSLTPELSPKPRLLIVGGGYAGFHVARELQKKVAERGGVVTVVDPRPYMTYYPFLPEVVG +GHIEGRHVNVDLQTHLKDAEVVRGAVVSVDHAGRTAVVRGEGGDEFEIPYQDIVMTAGAV +TRVFPIPGLGEQGIGLRSVEEAVQLRNQILERLDAGSLMTDAEERKRALTFVVVGGGFAG +IEAIAEMENLIRNAVERNERLSQSEIRIVLVEAMGRIMPEVSEEQAQGVVGHLKDRGIEV +LLNTSLGDATDGVMKLVAMPSKEEAETFAADTLVWCAGVVANSVVKSTDFPVDDRGRVEA +TPTLQIKDGEAGALEGAWACGDVSAVPDLTGAGPGGFCVPNAQHAIRQAKRLAANYMAVR +HGEGEVQEYVHKSLGTVAGLGFGRGVGNPLGTKIAGIPAFLAHRGYHGYAMPTLERKFRI +LSGWVAETLFGRDSTSVAGLDTPFNPFRRAAGVELEPGRFERQRALESSKG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000482.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000482.fa new file mode 100644 index 0000000000000000000000000000000000000000..528a1e961b210d7582096c2df7f1e91b277ed306 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000482.fa @@ -0,0 +1,40 @@ +>PROKKA_00458 +MSSTLAAQTKINKDVPYGLTVAAAWSWRLVAVVIGIGVVVYLLGFVSLVVIPILVAALLA +TLLAPVFQAMRRIKVPGVAAALLCVLLLVVVVVGLMGLAGQQIVQGFAELGDQLGQAVDD +AIAWLAGVGVEIPRSGAGLEGLWQTLRDNSATVMNSAVSLGSTAVNIGAGLFIALFSLIF +FLYDGDRIWRFLLIFVPKAHRATVGRAGRSGWQSLGSYVRVQIFVAFIDAVGIGIGALIL +GVPLAIPLAVLVFLASFIPMIGATLTGAMAVLLALMSNGLVNALLMLGVVLLVQQIESNV +LQPLVMGKAVALHPLAVFLAVAAGSTVLGLAGAVFAVPVLAFVNSFVRALTADTPEELTE +RTGHALEPGGAEDETAGSHRYRPSAHDDAALASEADAGTRHGDDA +>PROKKA_00176 +MSSTLAAQTKIDKDVPYGLTVAAAWSWRLVAVVIGIGVVVYLLGFVSLVVIPILVAALLA +TLLAPVFQAMRRIKVPGVAAALLCVLLLVVVVVGLMGLAGQQIVQGFAQLGDQLGQAVDD +TIAWLAGVGVEIPRSGAGLEGLWQTLRDNSATVMNSAVTFGSTAVNIGAGLFIALFSLIF +FLYDGDRIWRFLLIFVPKAHRATVGRAGRSGWQSLGSYVRVQIFVAFIDAVGIGIGALIL +GVPLAIPLAVLVFLASFIPMIGATLTGAMAVLLALMSNGLVNALLMLGVVLLVQQIESNV +LQPLVMGKAVALHPLAVFLAVAAGSTVLGLAGAVFAVPVLAFVNSFVRALTADTPEELTE +RTGHALEPGGAEDEAAGSHRYRPSAHDDAALASEADAGTRHGDDA +>PROKKA_02489 +MSSTLAAQTKINKDVPYGLTVAAAWSWRLVAVLVGLGILWWLLSFVSLVLIPVLVAALLA +TLLAPLFEGMRRIGIPGIAASLLCVVLLIVVVVGLVVVAGQQIAQGFSDLGDKLTQAVDG +AIAWLASIGVELPTAGGGLEGLWQTLRDNSGTLLDSAMTFGSTAVNIGAGFFIALFSLIF +FLYDGDRIWRFILVFVPKAHRATVGRAGQTGWRALGNYVRVQIFVAFVDAVGIGLGALIL +GVPLAIPLAVLVFLASFIPMIGATVTGAIAVLFALMSNGLVNALLMLGVVLLVQQIESNV +LQPLVMGKAVALHPLAVFLAVAAGSAVLGLAGAVFAVPVLAFVNSFIRALTADPPEQLTD +RSDQALAPGSAADEAVGSHVFEPTKHDDAALASEDDAGTSGDLR +>PROKKA_02373 +MSSTLSTDAKLEKDIPYGLTVAAGWSWRVIAVAAMLWVVWHFAGFASLVIIPVLVAALLA +VLLAPIYRALRRARIPGVLAAVLSIVLLLAAVVLLAWVAGLELVQGFSDLSDQLGASVEH +LVTWVQGMGVPVSFDAAALDNVWSTVKDNSGVLVDGALAFGSTAANVLTGLFIALFTLIF +FLFDGERIWRFLLAFVPHTSRSRVDVAGRTGWNALGSFVRVQIVVAFIDAVGIGLGAWLL +GVPLALPVAVIVFLFSFVPTIGAIASGALACVLALTANGLVNALLMLGVVILVQQIESNL +LQPLIMGRAVSLHPLAVFLGVAAGGVALGLVGAVFAVPLLAFANAFVQALRAKGPGEEIL +PGEKVFRPSDEVIAAARRDAKLDPKLDPTSFDDDSGPDGDVEDGRTGSTRTELKP +>PROKKA_00458 +MSSTLAAQTKIDKDVPYGLTVAAAWSWRLVAVVIGIGVVVYLLGFVSLVVIPILVAALLA +TLLAPVFQAMRRIKVPGIAAALLCVLLLVVVVVGLMGLAGQQIVQGVAQLGDQLGQAVDD +AIAWLAGVGVEIPRSGAGLEGLWQTLRDNSATLMNSAVSFGSTAVNIGAGLFIALFSLIF +FLYDGDRIWRFLLIFVPKAHRATVGRAGRSGWQSLGSYVRVQIFVAFIDAVGIGIGALIL +GVPLAIPLAVLVFLASFIPMIGATLTGAMAVLLALMSNGLVNALLMLGVVLLVQQIESNV +LQPLVMGKAVALHPLAVFLAVAAGSTVLGLAGAVFAVPVLAFVNSFVRALTADTPEELTE +RTDHALEPGGAEDEAAGSHRYRPSTHEDAALASEADAGTRHGDGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000485.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000485.fa new file mode 100644 index 0000000000000000000000000000000000000000..0b582cfc759a9895b0bbd2a3179a710dfa216c4d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000485.fa @@ -0,0 +1,20 @@ +>PROKKA_00461 +MTTSQSDAPWLTQEAYDRLSKELEYISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ +SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAADDESL +EVYSERSPLGEAINGAKKGDKVSYTAPNGKDIKVEVKDVQPYSG +>PROKKA_00179 +MTTSQSDAPWLTQEAYDRLSKELEYISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ +SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAADDESL +EVYSERSPLGEAINGAKKGDKVSYTAPNGKDIKVEVKDVQPYSG +>PROKKA_02486 +MTTSQSDAPWLTQEAFDRLSKELEHISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ +SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAEDDEHL +EVYSERSPLGEAINGAAKGDKVTYTAPNGKEIKVEIKDVKPYSG +>PROKKA_02370 +MATTPSDAPWLTQEAFDRLSKELAHISGPGRQEIIERIEAAREEGDLKENGGYHAAREEQ +SKNEGRIAELKHLLETARVGETQAADGVVTPGTVVTAVVAGDEMTFLFGNREIAADGEDL +EVYSERSPMGEAINGAKQGDKVTYTAPNGKDIAVEITDVKPYQA +>PROKKA_00461 +MTTSQSDAPWLTQEAYDRLSKELEHISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ +SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAADDESL +EVYSERSPLGEAINGAKKGDKVSYTAPNGKDIKVEVKDVQPYSG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000487.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000487.fa new file mode 100644 index 0000000000000000000000000000000000000000..471ab934385dda9dd90364c5bc4330b23ca3274b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000487.fa @@ -0,0 +1,20 @@ +>PROKKA_00464 +MTPLSGLPLVLTALAAASPAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMAIIVL +RVMVRSVRRVQQRSPQAEAMLVERHQQHLPDEVRAGGEHLDADSEDRLRRLQEKYPGYLQ +EPAPEPQAPDTGRD +>PROKKA_00182 +MTPLSGLPLVLTALAAASPAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMAIIVL +RVMVRSVRRVQQRSPEAEAMLVERHQQHLPDEVRAGGEHLDADSEDRLRRLQEKYPGYLQ +APAPEPQAPDTGRD +>PROKKA_02483 +MSPLSGLPLVLTALAAASPAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMAIIVL +RVMVRSVRRVQQRSPEAEAMLVDRHQQHLPEDVRELAPEDEERDAQDRLRHLQEKYPGYL +QEPAPRPQSPDDGRS +>PROKKA_02367 +MSLAPLALSAVSLAASVSPSAPMPAVPEPTLKPGLDKQDISPGIEGFLFTALMVVMAIIV +FRLMVRSVRRVQQRSPEAEAMLVDRHQQHLPEEVREGGERLDGDAHDRIERLRRRYPGYL +QDPTPEPESPDTGREPR +>PROKKA_00464 +MTPLSGLPLVLNALAAASPAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMAIIVF +RVMVRSVRRVQQRSPQAEAMLVERHQQHLPDEVRAGGEHLDADSEDRLRRLQEKYPGYLQ +EPAPEPQAPDTGRD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000488.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000488.fa new file mode 100644 index 0000000000000000000000000000000000000000..3b756e39590749e1979c10a5b1dc8ba810421151 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000488.fa @@ -0,0 +1,26 @@ +>PROKKA_00465 +MTPLRETDAARRLRWRIERIRDPDHPLYKPRLRGWIHAVMAPLTLAAGIVLIVLAPTATL +RWASAVYAVTGLLLFAVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYTPLSLALLAP +DRARVLLTLVWVGAVAGVAFRVLWTDAPRWLYTPVYVALGLAALLYLGDFFAADAAAGWL +IVAGGVAYITGAVCYALQAPTIHREWFGFHELFHAFTVAGFVCHAVAIYRAVLVVA +>PROKKA_00183 +MTPLRETDAARRLRWRIERIRDPDHPLYKPRLRGWIHAVMAPLTLAAGIVLIVLAPTATL +RWASAVYAVTGLLLFAVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYTPLSLALLAP +DRARVLLTLVWVGAVAGVAFRVLWTDAPRWLYTPVYVALGLAALLYLGDFFAADAAAGWL +IVAGGVAYITGAVCYALQAPTIHREWFGFHELFHAFTVAGFVCHAVAIYRAVLVVT +>PROKKA_02482 +MDPLTPAREPEAARRLRWRIERIRDPEHPLFKPRLRGWIHAAMAPLTLAAGIVLIVLAPT +ATLRWASAVYAVTGLLLFGVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYTPLSLAL +LPPGKAHLLLTLVWAGAVAGVAFRLLWTDAPRWLYTPVYVVLGLAALLYIGDFFAADVAA +GWLIVAGGAAYIVGAVFYALRAPTIHREWFGFHELFHVFTVGGFVCHAVAIYRAVLVVA +>PROKKA_02366 +MWEHGGMVTRAPSVENRTGRPLKWRIERIRDPEHPLYKPRLRGWVHAVMAPLVLVAGIVL +IVLAPGATLTWACVVYVVTGLLLFGVSATYHLVQWNETVSRVLKRLDHTNIMLVIAGTYT +PLSLAMLPADKAWTLVTAVWVGAALGVAFRLLWTDAPRWLYTPVYVALGLAAVVYLGDFF +AASVPAAVLICAGGAAYIVGAVFYALKAPTIHREWFGFHELFHVFTVGGFVCHYIAVMMA +VLAA +>PROKKA_00465 +MTPLRETDAARRLRWRIERIRDPDHPLYKPRLRGWIHAVMAPLTLAAGIVLIVLAPTATL +RWASAVYAVTGLLLFGVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYTPLSLALLAP +DRARVLLTLVWVGAVAGVAFRVLWTDAPRWLYTPVYVALGLAALLYLGDFFAADAAAGWL +IVAGGVAYITGAVFYALQAPTIHREWFGFHELFHAFTVAGFVCHAVAIYRAVLVVA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000492.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000492.fa new file mode 100644 index 0000000000000000000000000000000000000000..fcaa5fdaf6bb5d74c5818f4b0afcc86548234c90 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000492.fa @@ -0,0 +1,20 @@ +>PROKKA_00469 +MSGVGWAWTHGAPATAVLWSLGLVWFAVCAGVLVRTDLREHRLPNRWTLRLALGGLTMMT +GGALLAGRGDLTLCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV +LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA +>PROKKA_00187 +MSGVGWAWTHGAPATAVLWTLGLAWFAVCSGVLVRTDLREHRLSNRWTLRLALGGLAMMT +GGALLAGRGDLALCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV +LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA +>PROKKA_02478 +MDGVGWAWAQGLPATAVLWSAGLAWFAVCAAVLVRVDLREHRLPNRWTLRLALGGLAAMA +GGAALAGRADLVLSSVLGGLGYAAAMLVLHVLSRGSLGMGDVKLAAGLGAYTGVLGGSAV +VAAGLGAILLGGAVAAVLVAARRASRSTALPFGPPMILAAAAVLAFAPAGG +>PROKKA_02362 +MTWWTGAWEAGERLTAMLWAAGLVWFLLCSVVLARTDLREHRLPNRWTGRLALGGVVAMG +GGAVLGGLWSVVASCLLGGLGYALAMLALHVLTRGGLGLGDVKLAAGLGLYCGVAGLAAV +LAAAVLAVLLGGVVAVVLVLARRADRHTALPFGPAMVAGALGVLLLA +>PROKKA_00469 +MSGVGWAWTHGAPATAVLWTLGLAWFAVCSGVLVRTDLREHRLSNRWTLRLALGGLAMMT +GGALLAGRGDLALCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV +LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000495.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000495.fa new file mode 100644 index 0000000000000000000000000000000000000000..8ed5a47af4c22806b36004813005f3113f2274ee --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000495.fa @@ -0,0 +1,25 @@ +>PROKKA_00472 +MLTVSSADPHAPAPRPVLTATQAQRARQPWMAMVLSLAALLAIVAVVLLLNPEPPQRPRE +DRVDVAAEAATIPHDDGDLPALAPEVPESWYANYARLQKLDGVSTWDVGWVVTDTVFAGL +QQAEDVDPTWVSLRVDQVPTSETIEIDGIAWDLHADPKKPERRLVAEVDGSTVVLTTTGD +QAVLEDLAHGVAKETR +>PROKKA_00190 +MLTVSSADPHAPAPRPVLTATQAQRARQPWMAMVLSLAALLAIVAVVLLLNPEPPQRPRE +DRVDVAAEAATIPHDDGDLPALAPEVPESWYANYARLQKLDGVSTWDVGWVVTDTVFAGL +QQAEDVDPTWVSLRVDQVPTSETIEIDGIAWDLHADPKKPERRLVAEVDGSTVVLTTTGD +QAVLEDLAHGVAKETR +>PROKKA_02475 +MLTVSSTHPTDPTDPNAPAPRPVLTAKQAQRARQPWIGMVLSVVALLALVAVVLILNPEP +PQRPREDRVDVAAAAATVPHDDGVLPALAPEVPESWYANFARLQTMDGVSTWDVGWVVTD +TVFAGMQQAHDVDPTWVTLRVDSVPATETLEIDGLAWDLHADPRAPEKRLVTEVEDTTVV +LTTTGDRAVLEDLARGVAKETR +>PROKKA_02359 +MPGMSSPDPAAPPAPRPVLTPKQAQRARAPWIAMVLSTLAVLGIVLVALMVNQPPPAPAQ +ADRVDVAAAASTVPHDDGALPALAPDVPEPWDSTYARVERLQGVDTWDVGWAVNDAVFAG +LKQTSRADPTWLALRVGSAPAVGTVDVDGITWDHYAPQDSKDQHLVAEVRGSTLVLTTSG +DQAVLEDLARAVAKEIR +>PROKKA_00472 +MLTVSSADPHAPAPRPVLTATQAQRARQPWMAMVLSLAALLAIVAVVLLLNPEPPQRPRE +DRVDVAAEAATVPHDDGDLPALAPEVPESWYANYARLQKLDGVSTWDVGWVVTDTVFAGL +QQAEDVDPTWVSLRVDHVPTSETIEIDGIAWDLHADPKKPERRLVAEVDGSTVVLTTTGD +RAVLEDLAHGVAKETR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000499.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000499.fa new file mode 100644 index 0000000000000000000000000000000000000000..027e0c1c3c7bd94648bbe97f5c1c264a6c4fdc73 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000499.fa @@ -0,0 +1,43 @@ +>PROKKA_00477 +MMAGAAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPT +EHLRALQEAGVAVRPDPEALQHAQDKLVMRAAVERLGLPNPAWAPVDDLEAVLAFGDEHG +WPMILKTARGGYDGKGVLKLDDADDARASAADGTLAAWLGAGITPLLAEALVPFSRELSA +QVARTPSGEVAVYPVVDSVQVAGVCDLVVAPAQDLDPAVAAAATAAAVRLAEELDVTGML +AVELFETPGVGPGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGETAPRGAG +VVMKNVLGGAREDLHAGSVAALAAHPQAKVHLYGKDVRPGRKVGHVNVVADHGLSLEEAV +RTAESAAALLRDDAPTTGTETEARP +>PROKKA_00195 +MMAGAAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPT +EHLRALQEAGVAVRPDPEALQHAQDKLVMRAAVERLGLPNPAWAPVDDLEAVLAFGDEHG +WPMILKTARGGYDGKGVLTLDDADDARASAADGTLAAWLGAGIAPLLAEALVPFSRELSA +QVARTPSGEVAVYPIVDSVQVAGVCDLVVAPAQDLDPAVAAAATAAAVRLAEELDVTGML +AVELFETPGVGPGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGETAPRGAG +VVMKNVLGGAREDLHAGSVVALAAHPQAKVHLYGKDVRPGRKVGHVNVVADHGLSLEEAV +RTAESAAALLRDDAPTTGTETEARP +>PROKKA_02470 +MMAGPAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPT +EHLRVLQEVGVAVRPGPEALQHAQDKLVMRAAVERLGLPNPAWAAVRDLDEVLAFGDEHG +WPMILKTPRGGYDGKGVLKLDDADDARASASDGTLGTWLGAGIAPLLAEALVPFTRELSA +QVARTPSGRVAAYPVVDSVQVAGVCDLVVAPARDLDPAVAEAATAAAVRLAEELDVTGML +AVELFETPGVGPGFQINELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGDTAPRGAG +VVMKNLLGGAREDLHAGLADALAAHPQAKVHLYGKAVRPGRKVGHVNVVADHGLTLEQAV +RAAESAAAVLRDGAAPDAVDASPSSPATPHPAGGPPMTATPQNPAQPLQDDAPVVSVVMG +SDSDWPVMSAAAEALRELDVPVEVGVVSAHRMPHEMVEFGARAHERGIRVIVAGAGGAAH +LPGMLASVTPLPVIGVPVKLKSLDGLDSLLSIVQMPAGVPVATVSVDGARNAGLLAARIL +ASADTEEGERLRAALTEHAAELNAQAQAKGARLRERMAADR +>PROKKA_02354 +MIGGGQLARMMAGPAAELGVPFRVLAEAPDASAAQVAPHMVGDHASLEDLRAFAATVDVV +TFDHEHVPTEHLRTLEAAGVAVRPGPDALQYAQDKLLMRGLVERLGLPNPAWAPVSSLEE +VIAFGDEHGWPMILKTARGGYDGKGVLKVDSADDARSGAADGTLGTWLGAGIAPLLAEAM +VPFARELSAQVARRPSGEVAAYPVVASLQTQGVCDVVTAPAPDLAPAVAEAASGAAVRIA +EELDVTGMLAVELFETPGTDAGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDMPL +GGTAPRGDGTVMKNVLGGAHEDLHSGFSEALAAHPEAKVHVYGKGVRPGRKVGHVNVVAE +HGLSLADAERIAESTAAVLRDATAPSAPTPKA +>PROKKA_00477 +MMAGAAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPT +EHLRALQEAGVAVRPDPEALQHAQDKLVMRAAVERLGLPNPAWAPVDDLEAVLAFGDEHG +WPMILKTARGGYDGKGVLKLDDADDARASAADGTLAAWLGAGITPLLAEALVPFSRELSA +QVARTPSGEVAVYPVVDSVQVAGVCDLVVAPAQDLDPAVAAAATAAAVRLAEELDVTGML +AVELFETPGVGPGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGETAPRGAG +VVMKNVLGGAREDLHAGSVAALAAHPQAKVHLYGKDVRPGRKVGHVNVVADHGLSLEEAV +RTAESAAALLRDDAPTTGTETEARP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000501.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000501.fa new file mode 100644 index 0000000000000000000000000000000000000000..37bfcea5322bf0578c39e14f2a6566594e94d479 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000501.fa @@ -0,0 +1,25 @@ +>PROKKA_00479 +MVSLSAPRSTGPLVLRLASSPRPALVQEPGAPDEPGAVDQRIELSGRVTVNWAAKFAGLL +GAEGIGAGDAVALDLPVHWLSHALALGVLCAEAEPALEGDSPAAVLTDRPEAWPDPSVAV +FAVALPRGLEPEFDGPAVDPAVVDVAAEIRAQPDALPGPVDHVRPASIPAGADVAPDDDG +PRPRLTWAGVRAALEAWDAGRAVTVRP +>PROKKA_00197 +MVSLSAPRSTGPLVLRLASSPRPALVQEPGAPDEPGAVDQRIELSGRVTVNWAAKFTGLL +GAEGIGAGDAVALDLPVHWLSHALALGVLCAEAEPALEGDSPAAVLTDRPEAWPDPSVAV +FAVALPRGLEPEFDGPATDPAVVDVAAEIRAQPDALPGPVDHVRPASIPAGTDVAPDDDG +PRPRLTWAGVRAALEAWDAGRAVTVRP +>PROKKA_02468 +MVSLSAPRSTGPLVLRLASSPRPALVQEPGAPGEHGAVDQRIELSGRVTVNWAAKTAGLL +ADEGLGPGDPVALDLPAHWLSHALALGVLCAGAEPADDGAAPAAVLTDRPERWTDPATAV +FAVALPRGLELPTGGAVADPSVVDVAAEILGQPDALPGPVDHVRPEALPAADVAAADGDA +RTDEDQDDDGPRPRLTWAGMRAVLQAWDAGRAVQVRP +>PROKKA_02352 +MVSLSAPRPDGPLVTRLASSPRPALVQEPAPAGEAAGAAHGAVDQRIELSGSVTVNWAAK +AAGLLLDEGVAPGDAVLLDLPDHWLSRALALGVLCAGARPAFVAGPADRAQEAPDDAAAV +LTDRPEHWDDPVLTVVAVRLPRGIEPDFGDDDAGDPSVVDLAAEIRAQPDALPGRVDHVT +VDAVPADPADAAGPLTEGGVGVGRARLDAPALRASLEAWDAGRAAHVPA +>PROKKA_00479 +MVSLSAPRSTGPLVLRLASSPRPALVQEPGAPDEPGAVDQRIELSGRVTVNWAAKFAGLL +GAEGIGAGDAVALDLPVHWLSHALALGVLCAEAEPALEGDSPAAVLTDRPEAWPDPSVAV +FAVALPRGLEPEFDGPAVDPAVVDVAAEIRAQPDALPGPVDHVRPASIPAGADVAPDDDG +PRPRLTWAGVRAALEAWDAGRAVTVRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000504.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000504.fa new file mode 100644 index 0000000000000000000000000000000000000000..6cfebeceb559db386f3c52de46af5b4a1a6d7632 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000504.fa @@ -0,0 +1,16 @@ +>PROKKA_00482 +MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRRAEPHTYDLCGEHARRTTAPRGWEVLR +LELPEHYEAVDADGGVRTVPTRPMAVPPARPGLRVVRDGD +>PROKKA_00200 +MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRRAEPHTYDLCGEHARRTTAPRGWEVLR +LELPEHYEAVDADGGVRTVPTRPMAVPPARPGLRVVRDGD +>PROKKA_02465 +MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRLAEPHTYDLCAEHARRTTAPRGWEVLR +LELPGHYEAVAPDGTVHTVPTAPRAVPAAPPADVASRPSLAAPRPAPAVPPVDADEPEAP +APPTRPGLRLVRDDDPLPPA +>PROKKA_02349 +MRRCSKTGCQEPAEATLTYNYAGSQVVIGPLAQRAEPHAYDLCAAHAARTTAPRGWEVLR +LAPAAPAAPGVAAPTHPALRLVTDPVEGTAG +>PROKKA_00482 +MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRRAEPHTYDLCGEHARRTTAPRGWEVLR +LELPEHYEAVDADGGVRTVPTRPMAVPPARPGLRVVRDGD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000505.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000505.fa new file mode 100644 index 0000000000000000000000000000000000000000..358eb74042cd4b6179b41bdc91fd678c62798bb3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000505.fa @@ -0,0 +1,50 @@ +>PROKKA_00483 +MTETSAEFRTPDVDPAFANRTTVPGASFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLRE +EYGEAQPLKGARIAGSLHMTVQTAVLIETLIALGAEVRWASCNIFSTQDEAAAAVVVGSG +TPEDPQGVPVFAWKNESLEDYWWTASQILTWPGADEDPERGPNMILDDGGDATLLVHKGV +EFEAAGAVPSATEDDPEEYRIILETLRRSLARDPQHWTRTAGTLRGVSEETTTGVLRLYQ +LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGK +GAAEALRGQGARVIVTEIDPICALQAAMDGYQVARLEDVVGEGDIFVTTTGGKDIIMAEH +MAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQVHEWTLGGGTEAERSIIVLSE +GRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK +VARLHLDALGVGLTELTKAQAEYLGVDVAGPYKADHYRY +>PROKKA_00201 +MTETSAEFRTPDVDPAFANRTTVPGASFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLRE +EYGEAQPLKGARIAGSLHMTVQTAVLIETLIALGAEVRWASCNIFSTQDEAAAAVVVGSG +TPEDPQGVPVFAWKNESLEDYWWTASQILTWPGADEDPERGPNMILDDGGDATLLVHKGV +EFEAAGAVPSATEDDPEEYRIILETLRRSLARDPQHWTRTAGTLRGVSEETTTGVLRLYQ +LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGK +GAAEALRGQGARVIVTEIDPICALQAAMDGYQVARLEDVVGEGDIFVTTTGGKDIIMAEH +MAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQVHEWTLDGGTEAERSIIVLSE +GRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK +VARLHLDALGVGLTELTKAQAEYLGVDVAGPFKADHYRY +>PROKKA_02464 +MTETPAESRTPDVDPAYANRATVPGAAFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLRE +EYGESQPLAGARIAGSLHMTVQTAVLIETLTALGAEVRWASCNIFSTQDEAAAAVVVGSG +TPEDPQGVPVFAWKNETLEDYWWTASQILTWPGAAEDPERGPNMILDDGGDATLLVHKGV +EFEAAGAVPSATEDDPEEYRIILETLRRSLAEDPQRWTRTASTLRGVSEETTTGVLRLYQ +LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGK +GAAEALRGQGARVIVTEIDPICALQAAMDGYQVARLEDVVGQGDLFVTTTGGKDIIMAEH +MAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQVHEWTLDAGTDSERSIIVLSE +GRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK +VARLHLDALGVGLTELTKSQAEYLGVDVAGPYKADHYRY +>PROKKA_02348 +MTETSSARPTPDVDPAFANRSTVPGATFDFAVRDLSLAEAGRHQIRLAEHEMPGLMALRE +EYGESQPLKGARIAGSLHMTVQTAVLIETLTALGAEVRWASCNIFSTQDEAAAAIVVGSG +TPDAPAGVPVFAWKGESLEEYWWTASQILTWPGAAEDPDRGPNMILDDGGDATLLVHKGV +EFEAAGAVPSATEDDPEEYRIILETLRRSLAEDPQRWTRTASTLRGVSEETTTGVLRLYQ +LAQEGTLLFPAINVNDSVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGK +GAAEALRGQGARVIVTEIDPICALQAAMDGYQVARLEDVVEQGDLFVTTTGGKDIIMAED +MLRMKDKAIVGNVGHFDNEIDMAGLGRVDGVVKTEIKPQVHEWTFDTGTEDERSIIVLSE +GRLLNLGNATGHPSFVMSASFTNQVMAQIELYDGSTGQGALTGEHYEKQVYTLPKVLDEK +VARLHLDALGVGLTELTKAQAEYLGVDVAGPYKADHYRY +>PROKKA_00483 +MTETSAEFRTPDVDPAFANRTTVPGASFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLRE +EYGEAQPLKGARIAGSLHMTVQTAVLIETLIALGAEVRWASCNIFSTQDEAAAAVVVGSG +TPEDPQGVPVFAWKNESLEDYWWTASQILTWPGADEDPERGPNMILDDGGDATLLVHKGV +EFEAAGAVPSATEDDPEEYRIILETLRRSLARDPQHWTRTAGTLRGVSEETTTGVLRLYQ +LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGK +GAAEALRGQGARVIVTEIDPICALQAAMDGYQVARLEDVVGEGDIFVTTTGGKDIIMAEH +MAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQVHEWTLDGGTEAERSIIVLSE +GRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK +VARLHLDALGVGLTELTKAQAEYLGVDVAGPYKADHYRY diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000509.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000509.fa new file mode 100644 index 0000000000000000000000000000000000000000..f27cff3c96b68838bba069695e7ce548d5392dfb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000509.fa @@ -0,0 +1,30 @@ +>PROKKA_00487 +MPEGRIVLAATPIGNLGDASARLRDLLAEADVIAAEDTRTARRLCAGLGVTPAGRVVAHH +EHNEAASAQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVTCAPGPSAVT +TALALSGLPTDRFAFDGFVPRKDGERRRWLTSLLTEARTVVAFESPQRLADALAVVAEVL +GAERPVCVARELTKLHEEVVRGTAAGVHAWAAERHAGEGIRGEIVLVIGPAAPGAEGEAS +EADAVAEVAVLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAARG +>PROKKA_00207 +MTGRIVLAATPIGNLGDASARLRELMAEADVIAAEDTRTARRLCAGLGVTPAGRVVAHHE +HNEAASTQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVTCAPGPSAVTT +ALALSGLPTDRFAFDGFVPRKDGDRRRWLTSLLTEARTVVAFESPQRLADALAVVVEVLG +AERPVCVARELTKLHEEVVRGTAADVHAWAAERHAGEGIRGEIVLVIGPAAPGAEGEASE +ADAVAEVAVLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAARS +>PROKKA_02459 +MTPRPTDLPSPSGRIVLAATPIGNLGDASARLRELLAEADVIAAEDTRTARRLCQGLGVT +PAGRVVAHHEHNEAASTQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVT +CAPGPSAVTTALALSGLPTDRFAFDGFVPRKDGERRRWLTSLLTEARTVVAFESPQRLAD +ALAVVVEVLGAERPVCVARELTKLHEEVVRGTAAEVHAWAAERHAGEGIRGEIVLVIGPA +SPDAASAGGATEADAVAEVGVLVDSGTRLKEAVATVAAAHGLRSRTLYQAVLAARG +>PROKKA_02343 +MSLPAASGRIVLAATPLGNLGDATGRLRELLATADVIAAEDTRNTRRLCQGLGITPAGRL +MAHHEHNEAASAAGLLERVRAGETVVMVSDAGMPTVSDPGFRLVEAAVAAGLPVTCAPGA +SAVTTALALSGLPSDRFAFDGFLPRKDGERRRRLEEIRTDPRTVVYFESPQRTASALAVI +AEVLGGARPVCVARELTKLHEEVVRGTADELVAWAVEREAGEGIRGEVAIVVGPAAPDAG +AGADEADVLAEVAALTDSGTRLKEAVAAVAAAHGLRSRELYQAVLDARRG +>PROKKA_00487 +MPEGRIVLAATPIGNLGDASARLRDLLAEADVIAAEDTRTARRLCAGLGVTPAGRVVAHH +EHNEAASAQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVTCAPGPSAVT +TALALSGLPTDRFAFDGFVPRKDGERRRWLTSLLTEARTVVAFESPQRLADALAVVVEVL +GAERPVCVARELTKLHEEVVRGTAAGVHAWAAERHAGEGIRGEIVLVIGPAAPGAEGEAS +EADAVAEVAVLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAARG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000515.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000515.fa new file mode 100644 index 0000000000000000000000000000000000000000..37fc03e6ecc59f017589377005b55d23c52fd835 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000515.fa @@ -0,0 +1,50 @@ +>PROKKA_00497 +MSQPSARPSAVIVLAAGQGTRMKSTTPKIMHAIGGRSLVGHALAAAWSLSPEHLVAVVRH +ERARVAEHIETVAAQLGIDALAIADQDDVPGTGRAVELGLAALPADLEGTVVVTYGDVPL +LTPETLARLVADHEADGNAVTVLTATLEDATGYGRIVRDAEGLVERIMEHKDALAHAEAT +GDDSFVAIREVNSGIYAFDAALLRRTLPEISTDNVQGEKYLTDVLGMARAEGGRVASVGT +DDVWEVEGANDRRQLSDLGRQLNDRVLRGWMKEGVTVVDPSSTWVDVTVSLASDVTLKPG +TQLHGATSVATGAVVGPDSTLTDTQVGEGAVVKRTDATEAVIGAGATVGPFTYLRPGTVL +GEDGKIGAFYETKNVTVGRGAKLSHLGYAGDAEIGEYTNIGCGNITANYDGVNKHRTVIG +AHVRTGSNTVFTAPVTVGDGAYTGAGAVVREDVPAGALALNAVSQRTLEGWVPAKRPGTS +SAEAARAAGAEGSGAQG +>PROKKA_00218 +MSQPSARPSAVIVLAAGQGTRMKSTTPKIMHAIGGRSLVGHALAAAWSLAPEHLVAVVRH +ERARVADHLETVAAQLGIDALAIADQDDVPGTGRAVELGLAALPADLEGTVVVTYGDVPL +LTPETLARLVADHEADGNAVTVLTATLEDATGYGRIVRDAEGLVERIMEHKDALAHAEST +GDDSFVAIREVNSGIYAFDAALLRRTLPEISTDNVQGEKYLTDVLGMARAEGGRVASVGT +DDVWEVEGANDRRQLSDLGRQLNDRVLRGWMKEGVTVVDPSSTWVDVTVSLASDVTLKPG +TQLHGATSVATGAVVGPDSTLTDTQVGEGAVVKRTDATEAVIGAGATVGPFTYLRPGTVL +GEDGKIGAFYETKNVTVGRGAKLSHLGYAGDAEIGEYTNIGCGNITANYDGVAKHRTVIG +AHVRTGSNTVFTAPVSVGDGAYTGAGAVVRDDVPAGALALNAVAQRTIEGWVPAKRPGST +SAQAARAAGAEGSGAQG +>PROKKA_02450 +MPQSSVRPSAVIVLAAGQGTRMKSTTPKIMHPIGGRSLVGHALAAAHSLAPEHLVAVVRY +ERDRVAEHIESVAEGLGIASLAIADQDEVPGTGRAVELGLAALPKDLEGTVVVTYGDVPL +LTPETLERLVAAHEADGNAVTVLTAALEDATGYGRIVRDGEGLVERIMEHKDALAHAEST +GDSSFVEIREVNSGIYAFDAALLRRTLPAISTDNVQGEKYLTDVLGMARAEGGRVASVGT +DDVWEVEGANDRRQLSDLGRRLNDRVLRHWMKEGVTVVDPSSTWVDVTVSLASDVTLKPG +TQLHGATQVATGAVVGPDTTLTDTRVGERAVVKRTDATEAVIGADATVGPFTYLRPGTVL +GEEGKIGAFYETKKVTIGRGAKLSHLGYAGDAEIGDYTNIGCGNITANYDGEKKHRTVIG +AHVRTGSNTVFTAPVTVGDGAYTGAGAVVREDVPAGALALNAVSQRTIEGWVPAKRPGTS +SAQAAQAADAQGDAPQG +>PROKKA_02334 +MPQTAVRPSAVIVLAAGQGTRMKSATPKIMHAIGGRSLVGHALAAAQSLAPEHLVTVVRH +ERDRVAAHIEEAAADLGVTGLAIADQDEVPGTGRAVELGLAALPEDLEGTVVVTYGDVPL +LTPETLQRLVAAHEADGNAVTVLTATLADATGYGRIVRDADGLVERIMEHKDALAHAEAT +GDSSYVEIAEVNSGIYAFDAALLRRTLPQLSTENVQGEKYLTDVLGMARAEGGRVASVGT +DDVWEVEGANDRRQLSDLGRQLNERVLRRWMKDGVTVVDPSSTWVDVTVELAADVTLKPG +TQLHGSTTVATGAVVGPDSTLVDTRVGERGTVKRTDATEAVIGDDATVGPFTYLRPGTVL +GEEGKIGAFYETKKVTIGRGAKLSHLGYAGDAEIGEYTNIGCGNITANYDGVDKHRTVIG +SHVRTGSNTVFIAPVTVGDGAYTGAAATVRQDVPAGALALNAVDQRNVDGWVVSRRAGTA +SAEAAQAAGAVGRDQATEAAQD +>PROKKA_00496 +MSQPSARPSAVIVLAAGQGTRMKSTTPKIMHAIGGRSLVGHALAAAWSLAPEHLVAVVRH +ERARVAEHLETVAAQLGIDALAIADQDDVPGTGRAVELGLAALPADLEGTVVVTYGDVPL +LTPETLARLVADHEADGNAVTVLTATLEDATGYGRIVRDAEGLVERIMEHKDALAHAEST +GDDSFVAIREVNSGIYAFDAALLRRTLPEVSTDNVQGEKYLTDVLGMARAEGGRVASVGT +DDVWEVEGANDRRQLSDLGRQLNDRVLRGWMKEGVTVVDPSSTWVDVTVSLASDVTLKPG +TQLHGATSVATGAVVGPDSTLTDTQVGEGAVVKRTDATEAVIGAGATVGPFTYLRPGTVL +GEDGKIGAFYETKNVTVGRGAKLSHLGYAGDAEIGEYTNIGCGNITANYDGVNKHRTVIG +AHVRTGSNTVFTAPVTVGDGAYTGAGAVVREDVPAGALALNAVSQRTLEGWVPAKRPGTS +SAEAARAAGAEGSGAQG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000516.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000516.fa new file mode 100644 index 0000000000000000000000000000000000000000..7e85abe65e5c07fbcdfab67dfb0fec6e2f3340d4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000516.fa @@ -0,0 +1,35 @@ +>PROKKA_00500 +MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD +VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV +ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADHIRSSVEGEEVTVVSPDTG +RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA +GAVQILKDAGAKDVIIAATHPVFSDPAAQRLGECGAREVVVTNTLPIPEEKRFETLTVLS +IAPLIARAIREVFEDGSVTSLFDGVA +>PROKKA_00221 +MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD +VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV +ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADHIRSSVEGEEVTVVSPDTG +RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA +GAVQILKDAGAKDVIIAATHAVFSDPAAQRLGECGAREVVVTNTLPIPEEKRFETLTVLS +IAPLIARAIREVFEDGSVTSLFDGVA +>PROKKA_02449 +MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD +VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV +ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADYIRTRVEGEEVTVVSPDTG +RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA +GAVQILKEAGAKDVIIAATHAVFSEPAAQRLGECGAREVVVTNTLPILEEKRFETLTVLS +IAPLIARAIREVFEDGSVTSLFDGDA +>PROKKA_02333 +MTELSRSEDKRLVLAAGRAHPGLAQEIAEALGTELLPMSAYDFANGEIYVRSGESVRGKD +VFVIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV +ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADYIRGQVEGEKVTVVSPDTG +RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA +GAVRILKEAGAKDVIIAATHAVFSDPAAQRLGESGAREVVVTNTLPIPEEKRFDNLTVLS +IAPLIARAIREVFEDGSVTSLFDGDA +>PROKKA_00499 +MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD +VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV +ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADHIRSSVEGEEVTVVSPDTG +RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA +GAVQILKDAGAKDVIIAATHPVFSDPAAQRLGECGAREVVVTNTLPIPEEKRFETLTVLS +IAPLIARAIREVFEDGSVTSLFDGVA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000517.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000517.fa new file mode 100644 index 0000000000000000000000000000000000000000..f053fea6835f142a98a3677ed63ba461572ca86d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000517.fa @@ -0,0 +1,30 @@ +>PROKKA_00501 +MAERVEPAHGEDGGAVAAPQPHRPRLPFWASLLLNVVVALAVVAVVQALWVKVYSVPSGS +MENTLEVGDRMLVNRTAYPDGAADAQDVVVFTANEDWAHPMPPEGAVENAVRTFGDLTGI +GRSHEQALVKRVIGTAGQTVECCTAEGAVTVDGEPLDEPYIHNDLPFIRDELDCESEVMS +ARCFGPVTVPEDSMLVLGDHRSNSADSVIACRGIPADQAGDCARFVTREDIVGEVFVTVW +PPTHWGGH +>PROKKA_00222 +MAERVEPAHGEDGGAVAAPQPHRPRLPFWASLLLNVVVALAVVAVVQALWVKVYSVPSGS +MENTLEVGDRMLVNRTAYPDGMADAQDVVVFTANEDWAHPMPPEGAVENAVRTFGDLTGI +GRSHEQALVKRVVGTAGQTVECCTAEGAVTVDGEPVDEPYIHNDLPFIRDELDCESEVMS +ARCFGPVTVPEDSMLVLGDHRSNSADSVIACRGIPADQAGDCARFVTREDIVGEVFVTVW +PPTHWGGH +>PROKKA_02448 +MAERVEPVRGEDGDDGSVAAPERRRSRLPGWASVLLNVVVAIAVVAVVQALWVKVYSVPS +GSMEQTLEVGDRMLVNRTAYPDGMAASQDVVVFNANEDWAQPLPPEGPVENAVRTFGDIT +GIGRSHDQALVKRVVGTEGQTVECCTSEGRVTVDGQPLDEPYLHNDLPFAPGRLDCESDV +MSARCFGPITVPEDSMLVLGDHRSNSADSVIGCRGLPAEQAEGCARFVTREDVVGEVFVT +IWPPSNWGGH +>PROKKA_02332 +MAHTPDAVPARDEAACDEAVRDDAAPAPASSAAAPGRRRRVQLPFWASVLLNVAVALLVV +SVVQALWVKVYSVPSGSMEQTLQVGDRMLVNRTAYPDGVAERQDIVVFDANETWGVDTVG +EEGPVEGAVRTFGDLTGIGRSHENALVKRVIGLPGETVECCTSQGAVTVGGTPLEEDYLY +EDLPFVPGTLDCTTTPRSSRCFGPVTVPERSMLVMGDHRSNSADSVYQCRGLTAEQAGDC +AHFVRDEDVVGRVFSTVWPPSNWSGH +>PROKKA_00500 +MAERVEPAHGDDVDGGAVAAPQPHRPRLPFWASLLLNVVVALAVVAVVQALWVKVYSVPS +GSMENTLEVGDRMLVNRTAYPDGAADSQDVVVFTANEDWAHPMPPEGAVENAVRTFGDLT +GIGRSHEQALVKRVVGTAGQTVECCTAEGAVTVDGEPLDEPYIHNDLPFIRDELDCESEV +MSARCFGPVTVPEDSMLVLGDHRSNSADSVIACRGIPADQVGDCARFVTREDIVGEVFVT +VWPPTHWGGH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000519.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000519.fa new file mode 100644 index 0000000000000000000000000000000000000000..92b1e70b60df6ed3f44ccc5ccd1899cb2f4dc929 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000519.fa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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000521.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000521.fa new file mode 100644 index 0000000000000000000000000000000000000000..d4f52b786b101f33211f93b217778269151a0a6e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000521.fa @@ -0,0 +1,40 @@ +>PROKKA_00506 +MTDAPLFWRSEDLPRWHAWQRAQWPLTRRAADTARSTVRGVAGALTRRRSTGDDAPRLLL +PAGDVHTLVALESFGPTQLAALASPVAALATARPEAAAGVGWVLPAGDAPALPGAVGHRE +HAATADVVTDRLPGLRRVLVAGEYLPSGRAAVRWARQRGARVGVVQHGLLAVSTPPVPRD +ATLYAFTSADADWWTQGRADVEAVAVGSALLEQARRAAPAPSDTAGDGPGVFLGQLHGAE +LPRRDFAAAAEQYVRATGAAYRPHPAERDRLSRGQHAAWRRAGVRIDDAGAPLVATRGPV +AAVFSTGILEAAQAGRPAWAVHPDPPAWLEGFWRRYGMTRWRPGRTPEPTPPLASPTADP +AAAIAEHVWKESA +>PROKKA_00226 +MTDAPLFWRSGDLPRWHAWQRAQWPLTRRAADTARSTVRGVAGALARRGSTGDDVPRLLL +PPGDVHTLVALESFGPTQLAALASPVAALATARPEAAAGVGWVLPAGDAPALPGAAGHRE +HAATADVVTDRLSGLRRVLVAGEYLPSGRAAVRWARQRGARVGVVQHGLLAVSTPPVPQD +ATLYAFTSADADWWTQGRADVEAVPVGSALLEQARRTAPALSGAGDDGPGVFLGQLHGAE +LPRRDFAAAAEQYVRATGAAYRPHPAERDRLSRGQHAAWRRAGVRIDDAGAPLVATRGPV +AAVFSTGILEAAQAGRPAWAVHPDPPAWLEGFWRRYGMTRWRPGRVPEPTPPLASPTTDP +AAAIAEHVWKESA +>PROKKA_02444 +MSGVGSGDVPLFWRPEDLPAWQRWQRAQWPASRRLADTARRLARAGRGALAAGRGAAPAP +ESGLRLVLPAGDVHTLVGVESAAPTQRAALVEPVRALAEGRAGHAAADAARTAAGVGWVV +PADVVAAQLPDLPGSDALSVHAVDDVMVAERLGGLRCVLVAGEYLPAGRAAVRWARERGA +RVGVVQHGLLAVSTPPVPRDVALYAFTDHDAHWWTQGRTDVQAVAVGSALLEAARRMASH +AVADAVPRAAGPGVFLGQLHGAELPRTDFARAAQEYVRATGAAYRPHPAERDRLSLAQHE +AWRKAGMRIDATAGPLASTAGPVAAVFSTGILEAAQAGRPAWAVHPDPPAWLEGFWERYG +MTRWRPGVETEPTPPLASPSADPAAAIAAHLWKETA +>PROKKA_02328 +MTRAVAQPPLFWRAEQLDAWRRWQRTQWPLARRAADLVRGGVARSRGAVQAPDAGLRLLL +PAGDVHTLIAVESAGPTQRAALVEPTRALAEGRTGLDAAARTRLLGGVAWVVPADVAGAL +LPDLPAAAQLTGHAADPDTVGTRLAGLERVLVAGEYLPAGRAAVRWAHERGASVHVVQHG +LLAVSTPPVPRDATLYAFTARDADWWTQGRADVRAVPVGSALLEAARRGAASADPTATGS +TGPGPGLFLGQLHGAELPRAQFAAAAEQYVRTTGAVYRPHPAERDRLSRAQHARWEGAGI +AVDRSGAPLTQTAGPVAAVFSTGILEAAQTGRPAWAVHPDPPRWLVEFWDRYGITRWMPG +ADPTPTPALVAPTADPAAAIARDLWKEHA +>PROKKA_00505 +MTDAPLFWRSEDLPRWHAWQRAQWPLTRRAADTARSTVRGVAGALTRRRSTGDDAPRLYL +PAGDVHTLVALESFGPTQLAALASPVAALATARPEAAAGVGWVLPAGDAPALPGAVGHRE +HAATADVVTDRLSGLRRVLVAGEYLPSGRAAVRWARQRGARIGVVQHGLLAVSTPPVPQD +ATLYAFTSADADWWTQGRADVEAVPVGSVLLEQARRTAPALSGAGDDGPGVFLGQLHGAE +LPRRDFAAAAEQYVRATGAAYRPHPAERDRLSRGQHAAWRRAGVRIDDAGAPLVATRGPV +AAVFSTGILEAAQAGRPAWAVHPEPPAWLEGFWRRYGMTRWRPGRTPEPTPPLASPTADP +AAAIAEHVWKESA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000524.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000524.fa new file mode 100644 index 0000000000000000000000000000000000000000..3af78b613e0a2ef80b6bc8997e8694dc594795a0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000524.fa @@ -0,0 +1,35 @@ +>PROKKA_00511 +MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAADGFDVVRL +GGPGRLGYLRALRAWDRGRGKDDVVWCNGLLPATALAGRPRRIVHLHQVPEKPLLRVFSA +LARPGALAVLAPSRFAADRIRGARVLHNWVPAPTTPQAGRARDADEPLTVGFLGRLSEDK +GIVTLLEAAALLRKTDPGAFVFRVAGESRFVADDEAERLATALKAAGEDVQVLGWQDTAE +FLASVDVLAVPSQWAEVFGLVTAEAMAAGVPVVASDAGAVPEVVGSEHPFVFPQRDAAAL +ADRLQAVRAVDLGAVAHSQQRRWESLFSPEAGRAAVAELLDDLSL +>PROKKA_00231 +MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAADGFDVVRV +GGPGRLGYMRALRVWDRGRGGDDVVWCNGLLPATALAGRPRRIVHLHQVPEKPLLRVFSA +LARPGALAVLVPSRFAADRIHGARVLHNWVPGPTTPQAGRARGTDEPVTVGFLGRLSEGK +GIVTLLEAAALLRRTDPGAFVFRIAGESRFVAEDEAERLATALKAAGEDVQVLGWQDTGE +FLTSVDVLAVPSQWAESFGLVAAEAMAAGVPVVASDAGAVPEVVGSDHPFVVPQRDAAAL +ANCLRAVRAVDLGEVAHSQRHRWASLFSPEAGRAAVAELLDDLSL +>PROKKA_02440 +MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAANGFDVVRV +GGPGRLGYLRALRAWDRDRGNDDVVWCNGLLPATALAGRPRRIVHLHQVPEKPLLRVFSA +LARPGALAVLAPSRFAADRIRGARVLHNWVPGPTTPPARRARDADEPVTVGFLGRLSEDK +GIVTLLEAAALLRKTDPGAFVFRVAGESRFVAEDEAERLATALKAAGEDVQVLGWQDTAE +FLASVDVLAVPSQWAEVFGLVTAEAMAAGVPVVASDAGAVPEVVGNDHPFVFPQRDAAAL +ADRLQAVRAGDLGAVAHSQRRRWASLFSPEAGRAAVAELLDDLSL +>PROKKA_02323 +MTRRIWIAANQGEVGGGEVMLHHLATALHELGRDIAVVAPAAPSATAARLEADGFTVDRV +GGPGRAGYMRALRRWHNGHREDVVWCNGLLPATALAGRPRRIVHLHQWLIRPRDRVLGTL +AMRGALAVIAPSESVAREIPGCRVLHNWVPRPLPLSGAAPARRRPGEGGALRVGYLGRLS +FDKGFHLLMDVAEELHREQPDEWRFFVAGEPRFTTGDDAREIRERLAASRAVTALGWQAP +GDFLPTVDVLVVPSLAPESFGLVAAEAMAAGVPVAVSDSGALPEVAGDDHPLLFECDDHE +ELAAALRRARQIDLAPLVAAQHRRWEALFSPEAGRAGVAALLEELHV +>PROKKA_00510 +MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAADGFDVVRV +GGPGRLGYLRALRAWDRGRDGDDVAWCNGLLPATALAGRPRRIVHLHQVPEKPVLRVFSA +LARPGALAVLVPSRFAANRIRGARVLHNWVPAPTAPQTRPARGADDPVTVGFLGRLSEDK +GIVTLLEAAALLRKTDPGAFVFRVAGESRFVAEDEADRLATALKAAGEDVQVLGWQDSGE +FLATVDVLAVPSQWAEVFGLVTAEAMAAGVPVVASDAGAVPEVVGSDHPFVVPQRDAAAL +ANCLRAVRAIDLGAVAHSQRHRWESLFSPEAGRAAVAELLDDLSL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000526.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000526.fa new file mode 100644 index 0000000000000000000000000000000000000000..393243d9d2d3c60316af2678c7c67332e1fcfcc1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000526.fa @@ -0,0 +1,40 @@ +>PROKKA_00513 +MTDMTRGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTFPEFKDARIITS +PLNRVGVLRKDPRRALPLLPLASSLLHVKEPVAVVSTSGWAHGFRYDGATLVYCHTPARW +VYLLDDYLGEGGRNSIKGRIARALRPGLRRWDRAAVRRRSRYVANSTVVKERIEDVYGLD +GVDLVFPPHSVSTDGPQEPIPGAERLAEDGFLLSVARLMPYKHVDVAIEAAARAGRPLVV +IGKGPEEARLRAMAGEDVVFGQDLTDAQLRWAYAHAIALIAASHEDFGITPLEASAWGVP +TVALRAGGYLDTIVDGVNGTFVLDASIDAVGEGIKKLQAARWDTAAMRRHVEKFSEREFA +LRIRALVEGLPGA +>PROKKA_00233 +MSEQTPATIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTFPEFEDAHIVTS +PLNRVGVLRKDPRRALPLLPLASSLMHVKEPIAVVSTSGWAHGFRYDGATLVYCHTPARW +VYLLDDYLGEDGRNSIKGRIARVLRPGLRRWDRAAVRRRSRYVANSTVVKKRIDDVYGLD +GVDLVFPPHSVSTDGPQGPIPGAEQLAEDGFLLSVARLMPYKHVDVAIEAAARAGRPLVV +IGKGPEEARLRAMAGEDVVFGQDLTDAQLRWAYAHATALIAASHEDFGITPLEASAWGVP +TVALRAGGYLDTIVDGVNGVFVEEPTVDAVAGGVERLLAHDWDRAAMQAHAERFSEAQFG +RRIRALVAESPAGPAHRGRQ +>PROKKA_02438 +MTDTTRGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTFPEFKDARIITS +PLNRVGVLRRDPRRALPLLPVASSLMHVKEPVAVVSTSGWAHGFRYHGDTLVYCHTPARW +VYLLEDYLGEEGQKSMKGRVARVLRPGLRAWDRAAQRRRTRYVANSTVVKERIEEAYGLT +DVPIVFPPHSVSTDGSQEPIPGAEHLAEGGYLLSVARLMPYKHVDVAIRAAERTGLRLLV +IGKGPDEARLKAMAGDGVVFAQDLTDAQLRWAYAHATALIAASHEDFGITPLEASAWGVP +TVALRAGGYLDTITEGVNGVFVEAPTVEAVTDGVEQALARDWDPPAMRAHAERFSEDQIA +RQVRTQLGQLQNHARNKGAM +>PROKKA_02321 +MKIHASRPLSARRASQPGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYNPEGTF +PEFKKARIITSPLNRVGVLRSDPRRALPLLPLASSLMHVKEPLAVVSTSGWAHGFRYEGD +TLVYCHTPARWVYLLEDYLGEGGQRSLKGRVARALRPALRAWDSAAQLRRTRYVANSTVV +KRRIEEVYGVANVDLVFPPHSVSTDGPQAPIPGAEDLAEGGYLLSVARLMPYKHVDVAIR +AAERTGRRLLVIGKGPEEARLRALAGQGVVFAQDLTDAQLRWAYAHAVALIAASHEDFGI +TPLEASAWGVPTVALRAGGYLDTIVEGVNGVFVPEPTVEAVTDVVEQVLAQDWDRGAMQA +HAEHFSEVAFRERLARLLDDPHGAV +>PROKKA_00512 +MTDTTRGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTFPEFKDARIITS +PLNRVGLLRKDPRRALPLLPLASSLMHVKEPIAVVSTSGWAHGFRYDGATLVYCHTPARW +VYLLDDYLGEGGRDSIKGRIARVLRPGLRRWDRAAVRRRSRYVANSTVVKERIEEVYGLI +DVPVVFPPHSVSTDGPQEPIPGAEHLAEGGYLLSVARLMPYKHVDVAIRAAERTGLRLLV +IGKGPEEARLKAMAGDGVVFAQDLTEAQLRWAYAHATALIAASHEDFGITPLEASAWGVP +TVALRAGGYLDTIVEGVNGVFVNGTSVAAVAGGIEWVRAHNWDRAAMRSHARRFSEFEFG +QQVQAQLGWIGISR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000531.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000531.fa new file mode 100644 index 0000000000000000000000000000000000000000..771b9f6cab59511e61a4db4c3fcf2f67a7644b68 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000531.fa @@ -0,0 +1,20 @@ +>PROKKA_00529 +MAFSAQQSIPHPPAAVAAALASEDFHRSVVESFGGSLVSFSVEGSPEGPMTVTAVRSLPA +DRIPDRVPDMARKLIGSALQVEQVERWDAPAADGSRAGTTTITVPSAKATADGALRLTAA +GEGSQFSVDGTLVCRIPLVGSKLAAKAEPMVGKVVNRQARALSSWLERDGGAARG +>PROKKA_00250 +MAFSAQQSIPHPPAAVAAALASEDFHRSVVESFGGSLVSFSVEGSPEGPMTVTAVRSLPA +DRIPDRVPDMARKLIGSALQVEQVERWDAPAADGSRAGTTTITVPSAKATADGSLRLTAA +GEGSQFSVDGTLVCRIPLVGSKLAAKAEPMVGKVVDRQARALSSWLERDGGAARS +>PROKKA_02423 +MAFSAQQSIPHPPAAVAAALASEEFHRSVVEQLGGSLVSFRVEGSPEGPMTVTTVRSAPA +DRLPEMARKFIGSSLQVEQVERWEAPAADGSRVGTTTITVPAAKATAEGAQRLTAAGEGS +QYSVDGTVTCKIPLVGSKLAAKAEPMVGKVVNRQARALTSWIGRDGGAAGA +>PROKKA_02305 +MAFSAQQTIPHPPAAVAEALFSEDFHRSVAESLGGGLVSFARQDQADGGVELTIVRSGPT +DRLPDMVRKVVGENLNIEQVERWSAPAADGSRTGTTTIRVPKAKATAEGTLRLAAAPAGT +EYGVNGDLQVKIPLVGSKMAQMAEPMVGKVVARAGREVSAWIDRGGRG +>PROKKA_00529 +MAFSAQQPIPHPPSAVAAALASEDFHRSVVESFGGSLVSFSVEGSPEGPMTVTAVRSLPA +DRIPDRVPDMARKLIGSALQVEQVERWDAPAADGSRTGTTTITVPSAKATADGSLRLTAA +GEGSQFSVDGTLVCRIPLVGSKLAAKAEPMVGKVVNRQARALSSWLERDGGAARG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000534.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000534.fa new file mode 100644 index 0000000000000000000000000000000000000000..ad0845bcf036d406098f9dc35b2bef535c1f0915 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000534.fa @@ -0,0 +1,16 @@ +>PROKKA_00532 +MTVETTEGWTLAPNIAWARTAGGQAAVMTLEAGQPLLLGASGDVIWDVLVGGRTPEDDLV +ADPPASLSTTDVTVQVAEAFGLAPADVAADVHAFLEMLEAHGVLVRVRTA +>PROKKA_00253 +MTVETTEGWALAPDIAWARTAGGQTAVMTLEAGQPLLLSASGDVIWDVLVGGRTPADDLV +ADPPAPLSTTDVTVQVAKAFGLYPADVAADVHAFLEMLEAHGVLVRVRTA +>PROKKA_02420 +MAADRLPAPFGMTSERGSAWAVAPGVAWALTDGGDAAVMHLEHGVPLLLSPTGHAVWDVL +VGGRTPEDDLTAAPPIPLPEEAVAAETAAAFGLAPEDVAADVGAFLAMLEQHGVVVRVGG +VLPRP +>PROKKA_02302 +MSDAEHPPFAQAPAARAWRVAPTTAWVRSGEHQVTVMDLDEGNPQVLSPTGSAVWELLLD +GRTPEDDLAADPPKPVEEEALCGAVAEAFGVDVEVVAADTRAFLGMLAGHRLVVPAVLP +>PROKKA_00532 +MTVETTEGWALAPDIAWARTAGGQAAVMTLEAGQPLLLSASGDVIWDVLVGGRTPEDDLI +ADPPVPLSTTDVTVQVAEAFGLDPADVAADVHAFLEMLEAHGILVRVRTA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000537.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000537.fa new file mode 100644 index 0000000000000000000000000000000000000000..aba08d61ca90a9fb0bf970433d9a3e5f5902489c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000537.fa @@ -0,0 +1,35 @@ +>PROKKA_00535 +MDALRLVSIAAVVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVWGRFRS +LMVPYLVWAALMSVAAFAWFADDPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFTTVL +RRFLERFPSAVAWAVGLAGLAWAHLVPDSAIARTPLGVGLALPCLLFVLSGEMFRRRVQP +HVRRHRTLIGVGLVLLGMVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFGSTV +ERLLRSFARRTGTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALALAL +SWLAGLALLATPLSKPFTGARRRWHPVHRLRHVEPPHPVTSALPRVTTASERTHP +>PROKKA_00259 +MVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVWGRFRSLMVPYLVWAAL +MSVAAFAWFADDPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFTTVLRRFLERFPSAV +AWAVGLAGLAWAHLVPDSAIARTPLGVGLALPCLLFVLSGEMFRRRVQPHVRRHRTLIGV +GLVLLGMVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFGSTVERLLRSFARRT +GTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALALALSWLAGLALLAT +PLSKPFTGARRRWHPVHRLRHVEPPHPVTSALPRVTTASERTHP +>PROKKA_02414 +MDALRLVSIAAVVLGHAYLADLTFSRYLEIWRMPLFFFLTGYFWTRGRPVARDARGRFKA +LMVPYLVWAVVMSAAALAWFGDDPERLQRLMAAGWYGGADQEPPWWAFWFISVLFFATVL +RRFLERFPTAVAWGVGLAGLAWAYLVPESAIARTPLGVGLALPCLLFILSGEAFRRRVQP +RIRRHRTLLGLALVGLGLAAVALGLEPHNIKFGGFGTPLLTPLVGVLMSAGMVLVFGAAV +ERILREFARRTGSGQALRRVITALVRTGTVVVLLHGWVLMWVMRQGVEDNLLKFVLALGI +SWLVGLALLATPLSKPLTGARRRWFPLHRLRGEEPPHPPTSALPRVTTASERTHP +>PROKKA_02296 +MDALRLVSISAVVLGHAYLADLTFSPYLEIWRMPLFFFLTGYFWTRGRPWAADALSRFRS +LMVPYLLWSVLMTLVVLSWSRRSQIDGVTLADLVSAGWYGGADQPPPWWAFWFISVLFFV +ALLRRALERAPSWAGWAVALAGLAAAELVPESAIARTPLGIGLAAPCLFYVLAGEAFRRR +VQPRIRRHRTLIGVALVAAGVGAVALGLPPHNIKWGGFGLFPWTPLTGIAMAAGMVLVFG +AFVERRLRAFARDTGTGRAIRAGITALTRTGTVVVLLHGLVLMEAMRVGIEDNLMKFVVA +LTVSWAVGLALLATPLARPLTGVPQQWFPFGREAGA +>PROKKA_00538 +MDALRLVSIAAVVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVRGRFRS +LMVPYLVWAALMSVAAFAWFADDPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFTTVL +RRFLERFPSAVAWAVGLAGLAWAHFVPDSAIARTPLGVGLALPCLLFVLSGETFRRRVQP +HVRRHRTLIGVGLVLLGLVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFGSTV +EGLLRSFARRTGTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALALAL +SWLAGLALLATPLSKPFTGARRRWHPVHRLRRVEPPHPVTSALPRVPTASERTHP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000538.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000538.fa new file mode 100644 index 0000000000000000000000000000000000000000..e0e6f9181828b8bf0c114add506a0a5278ac9fd9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000538.fa @@ -0,0 +1,25 @@ +>PROKKA_00537 +MTVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELAGS +DVLTCTVIGFPLGANASEVKAFEARQAIDAGADEVDMVLDVAAARAGDRDRLVADVRAVA +EAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH +VALMRRTVGERIGVKASGGVRTRADALAMIEAGATRIGASSALAILGSD +>PROKKA_00261 +MTVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELADS +DVLTCTVIGFPLGANTSEVKAFEARQAIDAGADEVDMVLDIAAARAGDRARLVADVRAVA +EAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH +VALMRRTVGEDIGVKASGGVRTREDALAMIEAGATRIGASSALAILGSD +>PROKKA_02412 +MTRTLSTAELAQYIDATALKTETSEADVRRLVAEARQAGVKSVCVNPRWVPLVSAELAGS +DVLTCTVIGFPLGANASEVKTFEARQAIEAGAHEVDMVIDVAAARAGDRARLVEDVRAVA +EAAHAAGPAGQGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH +VALMRRTVGEHVGVKASGGVRTREDALAMIEAGATRIGASSALAILGTD +>PROKKA_02294 +MSETPQLTTAELAKHIDHTLLKPEASREDILRVVAEAREAGVKSVCVNPRWVREVRAGLE +GSDVLTCTVIGFPLGASSSAVKAFETTQAIADGADEVDMVIDIAAARAGDRARLEEDVRA +VVAAAHASGPAGRAGTLVKVIIETALLDDAAKVLACEAAVAAGADFVKTSTGFSTGGATV +EDVALMRRTVGPEIGVKASGGVRSREDALAMITAGATRIGASSALAILGDD +>PROKKA_00540 +MTVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELAGS +DVLTCTVIGFPLGANASEVKAFEARQAIDAGADEVDMVLDVAAARAGDRDRLVADVRAVA +EAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH +VALMRRTVGERIGVKASGGVRTRADALAMIEAGATRIGASSALAILGSD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000540.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000540.fa new file mode 100644 index 0000000000000000000000000000000000000000..09684f9c3faf1be83ba0598089c46d3037e6157b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000540.fa @@ -0,0 +1,30 @@ +>PROKKA_00539 +MTDQTSIPSPDSPLTGDHPGFAEARAAADTIARATGVAEHRVAVVLGSGWGEAAGLIGDE +VAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTVRTA +AAAGARTVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLVGATFVDLTDLYSPRLRAI +AREVDPSLREGVYVQFAGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVFGIS +LVTNLGAGISETPLSHAEVVEAGQAAGPRIARLLADIVGRL +>PROKKA_00263 +MTDQTSIPSPDSPLTGDHPGFAEARAAADTIARATGVAEHRVAVVLGSGWGEAAGLIGEE +VAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTVRTA +AAAGARTVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLAGATFVDLTDLYSPRLRAI +AREVDPSLREGVYVQFAGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVFGIS +LVTNLGAGISETPLSHAEVVEAGQAAGPRIARLLADIVGRL +>PROKKA_02410 +MSEQTFSPSPASPLAGDHPGFDQARAAAAVIADATGVAEHRIAVVLGSGWGEAAGLIGEE +VAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTVRTA +AAAGAKTVVLTNGCGGLDPEIAPGTPVLISDHLNLTGATPLVGATFVDLTDLYSPRIRQI +AREVDPSLREGVYVQFSGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVFGMS +LVTNLGAGISETALSHGEVVEAGQAAGPRISRLLADIVWRL +>PROKKA_02292 +MSEQSTPTPTPASLARLAGDHPGFAEARAAAEAIAEATGCAEHRIAVVLGSGWGEAAELI +GVERARIDLADVPGFHAPKVPGHNAVIRSVELADGSRALVFGSRTHFYESRDAQAVAHTV +RTAAAAGAATVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLVGATFVDLTDVYSPRI +RAIAQEVDPTLTEGVYVQFSGPQYETPAEVRMATALGGDLVGMSTALDAIAARHAGLEVF +GISLVTNHGAGIQETPLSHQEVVEAGQAAGPRISRLLAEIVGRL +>PROKKA_00542 +MTDQTSIPSPDSPLTGDHPGFAEARAAADTIARATGVAEHRVAVVLGSGWGEAAGLIGDE +VAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTVRTA +AAAGARTVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLVGATFVDLTDLYSPRLRAI +AREVDPSLREGVYVQFAGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVFGIS +LVTNLGAGISETPLSHAEVVEAGQAAGPRIARLLADIVGRL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000541.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000541.fa new file mode 100644 index 0000000000000000000000000000000000000000..87862113a1b4c0a9207f4d4281526941d410791f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000541.fa @@ -0,0 +1,45 @@ +>PROKKA_00540 +MEPVSEENSTFIPSLTIIGGGPGGYEAAMVAAKLGARVTLVERQGLGGAAVLTDVVPSKT +LIAAADSMRRVGASVDLGVDLGGADVHADMGRVGHRILNLAHEQSSDIRAGLERVGVRVI +DGVGRVVGPHEVSVRALDDADAGAEPEIITSDAILVAVGASPRELPTAVPDGERIFNWKQ +VYNLKELPEHLIVVGSGVTGAEFASAYNRLGAKVTLVSSRDRVLPGEDADAAELLEKVFE +GNGLRVVSRSRAESVERTETGVRVHLSGEGAEDTPSIEGSHALVAVGGVPNTAGLGLDDV +GVKLTGSGHVLVDGVSRTSVPSIYAAGDCTGKLALASVAAMQGRIAVAHLLGDALKPLRP +HLLASNIFTSPEIATVGVTQAQVDSGQYQADVLRLDFHTNPRAKMSGAEEGFVKIFARQG +SGTVIGGVVVSPRASELIYALALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRI +>PROKKA_00264 +MEPVTEENSTFIPSLTIIGGGPGGYEAAMVAAKLGARVTLVERQGVGGAAVLTDVVPSKT +LIAAADSMRRVGASVDLGVDLGGAEAHADMGRVGHRILNLAHEQSSDIRAGLERVGVRVI +DGVGRVVGPHEVSVRALDDADAGAEPEIITSDAILVAVGASPRELPTAVPDGERIFNWKQ +VYNLKELPEHLIVVGSGVTGAEFASAYNRLGAKVTLVSSRDRVLPGEDADAAELLEKVFE +GNGLRVVSRSRAESVERTETGVRVHLSGEGAEDTPSIEGSHALVAVGGVPNTAGLGLDDV +GVKLSGSGHVLVDGVSRTSVPSIYAAGDCTGTLALASVAAMQGRIAVAHLLGDALKPLRP +HLLASNIFTSPEIATVGVTQAQVDSGQYQADVLRLDFHTNPRAKMSGAEEGFVKIFARQG +SGTVIGGVVVSPRASELIYALALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRI +>PROKKA_02409 +MVAAKLGARVTLVERQGVGGAAVLTDVVPSKTLIATADSMRRVGLAEDLGVDLGDAEPRA +DMRQVDRRILDLAGEQSRDIRAALERRGVRVIDGVARVVGPNEVSVRTLQDADAEPEVIT +SDAILVAVGASPRELPTAVPDGERIFNWKQLYAMTELPEHLIVVGSGVTGAEFASAYNRL +GAKVTLVSSRDRVLPGEDADAAELLEKVFQDNGLTVVARSRAEAVERTETGVRVELSGEG +AADTPYVEGSHALVAVGGIPNTAGLGLEDVGVELTESGHVKVDGVSRTTVPSIYAAGDCT +GNLALASVAAMQGRIAVAHLLGDALKPLRPHLLASNIFTSPEIATVGVTQAQVDSGQYQA +DVLRLDFATNPRAKMSGVQEGFVKIFARQGSGTVIGGVVVSPRASELIYALALAVTHKLH +VDDLADTFTVYPSMSGSIAEAARRLHVRI +>PROKKA_02291 +MNVTEENTTFLPSLTIIGGGPGGYEAALVAAKLGARVTVVERAGMGGSAVLTDVVPSKTL +IATADSMRRVMAASGLGVDLGEAQPHADMHAVDRRILELAGQQSSDIHRALEKRGVRVVI +GDAVVTGPHEVTVRRRGIEEGEEPEVITSDAILVAVGASPRELPTARPDSERIFNWKQVY +ALQDLPEHLIVVGSGVTGAEFASAYNQLGAAVTLVSSRDRVLPGEDPDAAELLEDVFAQN +GLDVAGRCRAESVERTETGVRVHLSGEGADGRPYIDGSHCLLAVGGVPNTAGLGLEEVGV +ELTESGHVKVDGVSRTTVPSIYAAGDCTGQLALASVAAMQGRIAVAHLLGDALKPLRPHL +LASNIFTSPEIATVGVTQAQVDSGQYQADVIRLDFATNPRAKMQGVSTGFVKIFARQGSG +TVIGGVVVAPRASDLIYSLALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRV +>PROKKA_00543 +MEPVSEENSTFIPSLTIIGGGPGGYEAAMVAAKLGARVTLVERQGLGGAAVLTDVVPSKT +LIAAADSMRRVGASVDLGVDLGGGDVHADMGRVGHRILNLAHEQSSDIRAGLERVGVRAI +DGVGRVVGPHEVSVRALDDADAGAEPEIITSDAILVAVGASPRELPTAVPDGERIFNWKQ +VYNLKELPEHLIVVGSGVTGAEFASAYNRLGAKVTLVSSRDRVLPGEDADAAELLEKVFE +GNGLRVVSRSRAESVERTETGVRVHLSGEGAEDTPSIEGSHALVAVGGVPNTAGLGLDDV +GVKLTGSGHVLVDGVSRTSVPSIYAAGDCTGKLALASVAAMQGRIAVAHLLGDALKPLRP +HLLASNIFTSPEIATVGVTQAQVDSGQYQADVLRLDFHTNPRAKMSGAEEGFVKIFARQG +SGTVIGGVVVSPRASELIYALALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRI diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000542.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000542.fa new file mode 100644 index 0000000000000000000000000000000000000000..e40afc7fa24ed84777f52637f436481fbf9c192b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000542.fa @@ -0,0 +1,45 @@ +>PROKKA_00541 +MSHSTPPVNPGAPTDLTSDAVATAEEVPRSRVIIASLVGTSIEFYDFYIYATAAVSVFPL +IFFAGGDDNTALLASMATFGAAFIARPLGAVVFGHLGDRVGRKTTLIGSLLTMGIATFLI +GLLPTYFQIGLWAPAMLTLLRFFQGLGLGGEWSGAALLATEYAKDGKRAQAAMWPQLGAP +IGFLLANGLFLALVLGFDHDSTNPVLDGPFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP +VFQRALDRDQRVKAPLSEVFRRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKPANGF +LGVPYAEFLVLQLVGILFFAAFVPVSGLLADRFGRRPTLIVISVLMVLFGLSFGLWLSPE +NMGVGAELNGPLMVAFLATGMTLMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA +ALTPFIAAWLVQKFDVSYVGYYLAAASAITVIALVLSPETRHTDLDTVTSARERRAAR +>PROKKA_00265 +MSHSTPPVNPGAPTDLTSDAVATAEEVPRSRVIIASLVGTSIEFYDFYIYATAAVSVFPL +IFFAGGDDNTALLASMATFGAAFIARPLGAVVFGHLGDRVGRKTTLIGSLLTMGIATFLI +GLLPTYFQIGLWAPAMLTLLRFFQGLGLGGEWSGAALLATEYAKDGKRAQAAMWPQLGAP +IGFLLANGLFLALVLGFDHDSTNPVLDGPFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP +VFQRALDRDQRVKAPLGEVFRRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKPANGF +LGVPYAEFLVLQLVGILFFAAFVPVSGLLADRFGRRPTLIVISVLMVLFGLSFGLWLSPE +NMGVGAELNVPLMLAFLATGMTLMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA +ALTPFIAAWLVQKFDVAYVGYYLAAASAITVIALALSPETRHTDLDTVTSARERRAAR +>PROKKA_02408 +MSRTTTPADGTAAGLEAAAEVPRGRVITASLVGTSIEFYDFYVYATAAVSVFPLIFFPGD +DQTTALLASFAVFGTAFVARPIGSVLFGHFGDIMGRKVTLIGSLLTMGIATFLIGLLPTA +FQIGLWAPAMLVVLRFCQGLGLGGEWSGAALLATEYAAEGKRARAAMWPQLGAPIGFFLA +NGLFLALVIGFGHDSTNPDHDGAFLNWVWRLPFLLSIVMVAVGLYVRVKLEETPVFQRAI +ANDTRVKAPLGEVFKRNWWELILGTFIMYATYVLFYLMTTWILSYAIGKTENGMLGVPYA +EFLVLQLIGILFFAAFVPASGWLADRFGRKPTLLTVSALMVLFGLSFGLWLSAERMGTGA +GVNVPLMLAFLAVGMALMGLTFGPMSAVLPELFPTNTRYTGSGISYNVSSILGAALTPFL +AAWLVKEYGVAYVGYYLAAASVITMIALALAPETRHTDLDGVTSARERRAASV +>PROKKA_02290 +MSHTTARSAEAPSVEDVPKSRVILASLVGTSIEFYDFYVYATAAVSVFPLIFFPGDDPTT +ALLASFAVFGTAFVARPIGSILFGHFGDRMGRKVTLIGSLLTMGIATFLIGLLPTAFQIG +LWAPAMLVVLRFCQGLGLGGEWSGAALLATEYADHGKRARAAMWPQLGAPIGFLLANGLF +LILVRAFGHDSTNPQLEGSFLTWVWRVPFLLSIVMVAVGLYVRVKLEETPVFQRALEDDT +RVKAPLGEVFKRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKTQNGMLGVKYADFLV +LQLVGILFFAAFVPVSGWLADRFGRKPTLLVVSGLMVVFGLSFGAWLSPAAMGQGDALNV +PSMLAFLAVGMALMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGAALTPFLAGWL +VKEFGVATVGWYLAIASVITMAALALSPETRHADLHEVTSARERRAAAR +>PROKKA_00544 +MSHSTPPVNPGAPTDLTSDAVATAEEVPRSRVIIASLVGTSIEFYDFYIYATAAVSVFPL +IFFAGGDDNTALLASMATFGAAFIARPLGAVVFGHLGDRVGRKTTLIGSLLTMGIATFLI +GLLPTYFQIGLWAPAMLTLLRFFQGLGLGGEWSGAALLATEYAKDGKRAQAAMWPQLGAP +IGFLLANGLFLALVLGFDHDSTSPVLDGPFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP +VFQRALDRDQRVKAPLGEVFRRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKPANGF +LGVPYAEFLVLQLVGILFFAAFVPVSGLLADRFGRRPTLIVISVLMVLFGLSFGLWLSPE +NMGVGAELNVPLMLAFLATGMTLMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA +ALTPFIAAWLVQRFDVSYVGYYLAAASAITVIALALSPETRHADLDTVTSARERRAAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000546.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000546.fa new file mode 100644 index 0000000000000000000000000000000000000000..58b39d220ae8af980786fe5ec51ebd943b369282 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000546.fa @@ -0,0 +1,50 @@ +>PROKKA_00546 +MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELD +ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ +EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA +YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE +DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLEVIASIV +DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAF +NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS +KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN +PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL +>PROKKA_00271 +MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELD +ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ +EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA +YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE +DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLAVIASIV +DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAF +NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS +KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN +PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL +>PROKKA_02401 +MSDPDLTTTAGRLADLHRRLEATAAPGGEGAVERQHARGKHTARERIDLLLDEGSFVELD +ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ +EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA +YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNSTSGTAHYMASSEE +DAIAYVQELLELLPSNNLAEAPTFEAADPETTDEDLALDEIVPDSANQPYDMLEVIGAIV +DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPQQLAGTLDIAASEKAARFVRFCDAF +NIPILTLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS +KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATQDAGGDVDARRAEIVADYEAELLN +PYQAAELGYVDAVVPPHATRGALIRALRATLHKREARPAKKHGNMPL +>PROKKA_02284 +MSAPELSTTAGRLADLHRRLEATAAPGGEAAVERQHSRGKHTARERIDLLLDEGSFVELD +ALATHRTTAFGMDAKHPAGDGVVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ +EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVMASGMIPQISLIMGPSAGGAA +YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNSTTGTAHYMATSEE +DAIAYVQDLLEYLPSNNLAEAPVFEAESLEETEQDLALDTIVPDSANQPYDMLEVIAALV +DDGHLLQLQEMYAPNVITGLARLDGMSVGVVANQPQQLAGTLDIAASEKASRFVRFCDAF +NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS +KKLGADLNLAWPSAQIGVMGPQGAVNILYRRELAAAEAAGEDVEARRAQIVADYEAELLN +PYQAADLGYVDAVVPPRQTRAHLVRALRATFHKREARPAKKHGNMPL +>PROKKA_00549 +MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELD +ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ +EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA +YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE +DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLEVIASIV +DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAF +NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS +KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN +PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000550.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000550.fa new file mode 100644 index 0000000000000000000000000000000000000000..9c09f20338505247bb3144e69ec25c95967f788e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000550.fa @@ -0,0 +1,35 @@ +>PROKKA_00552 +MSARTTVPGLLVVAKAAARAGADVLARRWTGHHPAVPLGIEEIGAQTKSSGSDWVTDYDR +RAEQAVREVVAGYRPSDEITGEEYGATRPAEPSGYRWSIDPLDGTTNFVRGLPQFCTSVA +VTGPVDAETADLLGVAEGTERWLAGVVAAPALGRTWYASAGRGAFSTADATTAGVDLPDR +DAAPVRLTGPLPGRSGRLLATGFGYDPARRALQVRALAALLPAFGDVRRIGSAALDLCMV +ADGTLDAYAEFGTQEYDWAAGALVAEEAGVAVTRPASADGTAHPDWMVAGDVDGSALAAM +TGERA +>PROKKA_00277 +MSARTTVPGLLVVAKAAARAGADVLARRWTGHHPAVPLGIEEIGAQTKSSGSDWVTDYDR +RAEQAVREVVAGYRPSDEITGEEYGATRPAEPSGYRWSIDPLDGTTNFVRGLPQFCTSVA +VTGPVDAETADLLGVAEGTERWLAGVVAAPALGRTWYASAGRGAFSTADATTAGVDLPDR +DAAPVRLTGPLPGRSGRLLATGFGYDPARRALQVRALAALLPAFGDVRRIGSAALDLCMV +ADGTLDAYAEFGTQEYDWAAGALVAEEAGVAVTRPASADGTAHPDWMVAGDVDGSALAAM +TGERA +>PROKKA_02393 +MSSPTRVAHVPSQPPGISGLLVVAKAAARAGADVLARRWTGHHPAVPLGREEIGAETKTS +GSDWVTDYDRRAEQAVREVLVAYRPQDEITGEEYGATVPAEPSGLRWSIDPLDGTTNFVR +GLPQFCTSVAVTGPVDEETAALLGVPAGTRRWLAGVVAAPALGRTWFASAGRGAFSTADA +TTAGVDVPDRDAAPVRITGPAPGRSGRLLATGFGYDPARRAMQVRALAALLPAFGDVRRI +GSAALDLCMVADGTLDAYAEFGTQEYDWAAGALIAEEAGVRVRRPASGDGTAHPDWMVAG +DVDEAALAAAQEETA +>PROKKA_02278 +MSAAPARPASPAGLLVIAKAAARAGADVLAERWAGHHPAVPLTSDELGADTKSSGSDWVT +DYDRRAEDAVRAVLTGYRPHDEITGEEHGSTAPVEPSGYRWSIDPLDGTTNFIRGLPQFG +TSVAVEGPVDEETAALLGVLPGSRRWLAGVVAAPALGRTWFASAGRGAFSTADATTAGVA +VPDRDAAPVRLTGPVPGRSGRLLATGFGYHPGRRAMQLRALAALLPAFGDVRRIGSAALD +LCMVADGTLDAYAEFGTQEWDWAAGALIADEAGVPVDRPASGDGTGHPDWMTAGDVDAAA +LAAAKEATA +>PROKKA_00555 +MSARTTVPGLLVVAKAAARAGADVLARRWTGHHPAVPLGIEEIGAQTKSSGSDWVTDYDR +RAEQAVREVVAGYRPSDEITGEEYGATRPAEPSGYRWSIDPLDGTTNFVRGLPQFCTSVA +VTGPVDAETADLLGVAEGTERWLAGVVAAPALGRTWYASAGRGAFSTADATTAGVDLPDR +DAAPVRLTGPLPGRSGRLLATGFGYDPARRALQVRALAALLPAFGDVRRIGSAALDLCMV +ADGTLDAYAEFGTQEYDWAAGALVAEEAGVAVTRPASADGTAHPDWMVAGDVDGSALAAV +TGERA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000551.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000551.fa new file mode 100644 index 0000000000000000000000000000000000000000..78d69453307ba4cd6609304f92e4895645734d74 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000551.fa @@ -0,0 +1,20 @@ +>PROKKA_00553 +MRRIVGDPWFYPVLFVAGGLTFMIAGTRLQQVGMIVAGLVLAGYAVTYRWAVRVRSRPFA +GAQAHVERGGVVVFWRPGCPFTRRLVKELTAQERDRAYWVNIWQEPAAATFLEGLHESRD +GHPHQAVPTAWLRRRDYVVATDATRARLKDTLRQHAGGDA +>PROKKA_00278 +MRRIVGDPWFYPVLFVAGGLTFMIAGTRLQQVGMIVAGLVLAGYAVTYRWAVRVRSRPFA +GAQAHVERGGVVVFWRPGCPFTRRLVKELTAQERDRAYWVNIWQEPAAATFLEGLHESRD +GHPHQAVPTAWLRRRDYVVATDATRARLKDTLRQHAGGDA +>PROKKA_02392 +MRRLVGDPWFWPVLFGSAGLVFLVWGTLRRDVVVLVAALAMLWMLRRHLPQLRVRSRPLA +GAQAHVQDGGVVVFWRPGCQYCQALLRDLDPAQRDAVYWVNIWTDKDAVPVLRRLHAGRD +GHAHEAVPTVWARRKDFVAADEASRSRLKDMLRDARPAGGPRTREEGPR +>PROKKA_02277 +MRRLVGDPWFWPVLFGAAGVVFLVWGTVRRDVIAIVAGVAMLWMVWQYLPALRVRSCPMA +GAQAHVDAGGVVVFWRPACRYCLALIKDLDPAQRAAVYWVNIWTDPDAVPVLHRLHATRD +GHAHEAVPTVWSRRRDFVVKDEATRRRLTDMLGAVRHIPESGR +>PROKKA_00556 +MRRIVGDPWFYPVLFVAGGLTFMIAGTRLQQVGMIVAGLVLAGYAVTYRWAVRVRSRPFA +GAQAHVERGGVVVFWRPGCSFTRRLVTELTAQERERAYWVNIWQEPAAATFLAGLHEARD +GHPHQAVPTAWLRRRDYVVATDATRARLKDTLRQHAGGDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000555.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000555.fa new file mode 100644 index 0000000000000000000000000000000000000000..1e1bacc2d00893a87405635512c1d6881093d446 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000555.fa @@ -0,0 +1,36 @@ +>PROKKA_00558 +MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL +RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLASALAERDVSWAVPVALSDPVSAG +PGAAVLQRFLPGGPYPPHEGDPDVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPAR +ARHVAALPGAVAARLGAWEGHDVDARLGAEAWPDAVAALTDAVTTWTAAPPVPPSLVHGD +LAGHNMRWRAVPEDEDPRAPLRWALAGVLDWDLACAWGPALNVAYLALWHGEQKVPDLAR +DAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLRKTLPRVARALTALDG +>PROKKA_00283 +MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL +RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLAAALAERRVPWTVPIALSDPVPAG +PGAAVLQRFLPGGPHPPHEGDPAVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPER +ARHVAALPGAVAARLGAWEGHDVDARLGAEAWPDAVAALADAVTTWTAAPPVPPSLVHGD +LAGHNMRWRAVPEDEDPRAPLRWALAGVLDWDLACAWDPALNVAYLALWHGEEKVPDLAR +DAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLRKTLPRVARALTALDG +>PROKKA_02385 +MASDPVDSELELVHRALGRLRPHVSPADARALHEADWSAGTVEEGGQFNRVLVCAGAGVL +RMTRAHEVGAAPAARWSPERDPARQLGRRMALLDGLDAALAEQGVAWTVPVALSDPVPAG +TGAAVLQRYLPGGPHPPHEGDPAVLRRLLDEIAAVDVADPRIAPHLGRPFSFRGPWTAQR +AEHVAGIPGRLAPRLGAWPGDDVDARTGADAWADAVARVTRAVTAWTEEPPVPPSLVHGD +LAGHNMRWRAMPAADDAPGEVRWELAGVLDWDLACAWDPALNVAYLSLWHGEDQVERLAV +DAGEAARARVWLGAMALETLDDAAARDELVGGLPNGSWRRLLRKALPRVARALTALG +>PROKKA_02269 +MASDPARSELDLVAAALQRLRPGLDDGVAARLRGADWSAGRVEEGGQFHRVLVLEDVGVL +RMTRVHEAGAAPAARWTPERDPAVHLPRRLALLDGLAAVLAEAGVRWSLPTALSAVVEDG +PGAAVLQRYVPGFPHPPHEGDPAVLRGVLADLAAVDVADPRVAPHLGRPFTFRGPWTPER +AAHVAGLPARLAPRLGAWPGDALGHAGDETAAGEAAVRLRADAWGESVTALTGVVSAWTR +EPPVPPALVHGDLAGHNMRWRVVPAAATPDAEVPDAPVRWELAGVLDWDLACAWDPALNV +AYLGLWHGEDLVEAIAADPAEARRARVWLGAMALETLDDAGARDVLVGGLAESSWRRLLR +KTLPRVGRALAAAAA +>PROKKA_00561 +MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL +RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLAAALAERRVPWTVPIALSDPVPAG +PGAAVLQRFLPGGPHPPHEGDPAVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPER +ARHVAALPGAVAARLGAWEGHDVDARLGAEAWPDAVAAVTDAVTAWTAAPPVPPSLVHGD +LAGHNMRWRAVPEDEDPRAPLRWALAGVLDWDFACAWDPALNVAYLALWHGEEKVPDLAR +DAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLRKTLPRVARALTALDG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000561.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000561.fa new file mode 100644 index 0000000000000000000000000000000000000000..1a515ff340963f4dd4479b5c3456bf5ae722e208 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000561.fa @@ -0,0 +1,25 @@ +>PROKKA_00564 +MPLARLAGVNANPTPAVEPVVRWSRPEGERTEDLLIVLHGYGANEDDLFGLVPHLPEHVT +VAAVRAPLPLQPGSHAWFPLSQDPVTGELGSTAEPVREAVEALHAWVQAVRGDFRTVSLL +GFSQGMAMATSLLRLDPEAYACTVALSGFVVDPELDEPRLRELFTRDDDVARVRPKVFWG +RGQEDPIISEPRVEETHAWLNAHVDLMKIVYAGLGHAINEQELGHVKEYLAHMVPPRG +>PROKKA_00289 +MNANPTPAVEPVVRWSRPEGERTEDLLIVLHGYGANEDDLFGLVPHLPEHFTVAAVRAPL +PLQPGSHAWFPLSQDPVTGELGSTAEPVREAVEALHAWVQAVRGDFRTVSLLGFSQGMAM +ATSLLRLDPEAYACTVALSGFVVDPELTEPRLRELFTRDDDVARVRPKVFWGRGQEDPII +SEPRVEETHAWLNAHVDLMKIVYAGLGHAINEQELGHVKEYLAHMVPPRG +>PROKKA_02379 +MNNDTANTAPSSETAPFTVRWSRPEGERTEDLLILLHGYGANEDDLFGLVPHLPERFTVA +AVRAPMTLQPGGYAWFPLSQDPVTGEIGSDAASVRTAIEDLHAWVGAVREGFRTVSLLGF +SQGMALATSLLRLDPTAYAATVALSGFVVDPTREESGLAGLFDGDDEVARVRPKVFWGRG +QDDPIISEARVEASHAWLNAHVDLMKIVYAGLPHAINQQELGHVKEYLEHMVR +>PROKKA_02263 +MNDTTPRDPAPFAVRWSRPEGERTEHLLVLLHGYGADEDDLFGLVPQLPEAFTALAVRAP +MDLPQGGAAWFPLTQDPATGEIGSDAGAVRAAVEDLHAWLPGVSGGFRTVSLLGFSQGMA +MATSLLRLDPAAYAATVALSGFVVDPLHVEPELEGLFPADETVDAVTPKVFWGRGQEDPI +ISAQRVEESHGWLTAHTDLTKVVYAGLPHAISPQELGHVREYLTHVVL +>PROKKA_00567 +MPLARLAGVNANPTPAVEPVVRWSRPEGERTEDLLIVLHGYGANEDDLFGLVPHLPEHVT +VAAVRAPLPLQPGSHAWFPLSQDPVTGELGSTAEPVREAVEALHAWVQAVRGDFRTVSLL +GFSQGMAMATSLLRLDPEAYACTVALSGFVVDPELAEPQLRELFTRDDDVARVRPKVFWG +RGQEDPIISEPRVEETHAWLNAHVDLMKIVYAGLGHAINEQELGHVKEYLAHMVPPRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000562.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000562.fa new file mode 100644 index 0000000000000000000000000000000000000000..f78f057c3738a0963e174a1c034542da8758eea0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000562.fa @@ -0,0 +1,15 @@ +>PROKKA_00565 +MTETNAPDAQPLPIRDESIRLGQALKLASLVEDGAMARDVVTDGLVTVNGAVETRRGAQL +HDGDVVEFAGEAFVVQAEQA +>PROKKA_00290 +MMDTMTETNAPDAQPLPIRDESIRLGQALKLASLVEDGAMARDVVTDGLVTVNGAVETRR +GAQLHDGDVVEFNGEAFVVQAGQA +>PROKKA_02378 +MMDTMTETNPADARPLPIRDASIRLGQALKLAALVEDGAMARDVVQDGLVTVNGAVETRR +GAQLKDGDVVEFHGEAVVIEAGSAD +>PROKKA_02262 +MTSSSDVQPLPIRDESIRLGQALKLASLVEDGAMARDVVQDGMVSVNGEVETRRGRQLHD +GDVVEFNGEEIVVEAGQS +>PROKKA_00568 +MTETNAPDAQPLPIRDESIRLGQALKLASLVEDGAMARDVVTDGLVTVNGAVETRRGAQL +HDGDVVEFAGEAFVVQAEQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000563.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000563.fa new file mode 100644 index 0000000000000000000000000000000000000000..ad741b8e1fbc7cbfc9200f868e8ace6c06acccd1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000563.fa @@ -0,0 +1,45 @@ +>PROKKA_00566 +MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE +DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHRRHRQDHLLEAFEAKKGRPAEGMA +EIVCPDCGTQGAWTEPQLFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGAARK +KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAGQHFDRWVEDCWDWFID +LGIDPAHLRKFDVPADERAHYSDATIDLEYDFGFTGGDGWGELMGIANRTDYDLGRHTEH +SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGVDVRTVLKLD +PRLAPVKAAVLPLSKKPELQPTTQSLAAELRTLWNIETDDSGAIGRRYRRQDEIGTPFCI +TVDFDTLEDQAVTIRERDTMAQERVALSQVKSYLLERLVK +>PROKKA_00291 +MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE +DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHRRHRQDHLLEAFEAKKGRPAEGMA +EIVCPDCGTQGAWTEPQLFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGAARK +KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKQHFDRWVEDCWDWFID +LGIDPAHLRKFDVPAEDRAHYSDGTIDLEYDFGFTGGDGWGELMGIANRTDYDLGQHTTH +SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGVDVRTVLKLD +PRLAPVKAAVLPLSKKPELQPATQSLAAELRGLWNIETDDSGAIGRRYRRQDEIGTPFCI +TVDFDTLEDQAVTIRERDTMAQERVALSQVKSYLLERLVK +>PROKKA_02377 +MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE +DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHKRHRQDHLLEAFEAKKGRPSASMD +EIVCPDCGTKGAWTEPQMFSGLVKTFLGPVDNEEGLHYMRPETAQGIFVNFLNVLGASRK +KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKQHFDTWVEACWDWFID +LGIDPENLRRLDVPEEERAHYSDGTIDLEYRFGFGGGDGWGELMGVANRTDYDLGRHTEH +SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGTDVRTVLKLD +PRLAPVKAAVLPLSKKPELQPATQALAAELRALWNIETDDSGAIGRRYRRQDEIGTPFCI +TVDFDTLEDQAVTIRERDTMSQERVALSQVKSYLLERLVK +>PROKKA_02261 +MAAKSPLDNVINLAKRRGFVFQAGDIYGGSRSAWDYGPLGVELKENIKAEWWRTFVRSRE +DMVGLDSSIILPRQVWEASGHVATFTDPLVECQQCHRRHRQDHLLEAFEAKKGRAAAGME +EITCPDCGTTGKWTEPQMFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGASRK +KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKEHFDTWVEACWDWFID +LGIDPANLRKFDVPEEERAHYSDGTIDLEYRFGFAGGDGWGELMGVANRTDYDLTSHANA +SGAKLQYFDQANDVHYTPYVIEPSFGLTRSMMAFLVDAYTEDEAPNAKGGVDVRTVLKLD +PRLAPVKAAVLPLSKKLELQEPSQRLAAELRAHWNIETDDSGAIGRRYRRQDEIGTPFCI +TVDFDTLEDQSVTIRERDTMSQERVALAQVRAYLAERLTK +>PROKKA_00569 +MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE +DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHRRHRQDHLLEAFEAKKGRPAEGMA +EIVCPDCGTQGAWTEPQLFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGAARK +KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKQHFDRWVEDCWDWFID +LGIDPAHLRKFDVPADERAHYSDATIDLEYDFGFTGGDGWGELMGIANRTDYDLGRHTEH +SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGVDVRTVLKLD +PRLAPVKAAVLPLSKKPELQPATQSLAAELRTLWNIETDDSGAIGRRYRRQDEIGTPYCI +TVDFDTLEDQAVTIRERDTMAQERVALSQVKSYLLERLVK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000569.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000569.fa new file mode 100644 index 0000000000000000000000000000000000000000..88f755f63dce0d9b06a6b48f129c42773e44f495 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000569.fa @@ -0,0 +1,34 @@ +>PROKKA_00579 +MADPHPVLAASAPVLADPHPVLAASAPDLDPDALDAVRALVAAAERPVVLSGAGMSAESG +IPTFRDARTGLWERFSAEELATEEAFLADPALVWSWYRWRARMVRARRPNPGHDAVAAWQ +RRTPGLEVVTQNVDDLHERAGARVLAHLHGSLFEHRCAECWAPADVDPGAPADEATAGSE +ADLEAMLREAPPACTVCGDGLIRPGIVWFGEMLPAEPWDRAFAALEDCDLCVVVGTSGIV +QPAASLPFVALGAGAAVVEVNPVETELSGAVTHVLRGPAGAVLPALVAGVWPGPSGALST +ARHVTW +>PROKKA_00311 +MADPHPVLAASAPVLAASAPVLAASAPDLDPGALDAVRALVAAAERPVVLSGAGMSAESG +IPTFRDAQTGLWERFSAEQLATEEAFLADPALVWSWYRWRARMVRARRPNPGHDAVAAWQ +RRTPDLEVVTQNVDDLHERAGARVLAHLHGSLFEHRCAECGAPADVDPGAPSDVDAAGSE +ADLEAMLREAPPACPACGTGRIRPGVVWFGEMLPQEPWERAYEALERCDLALVVGTSGLI +QPAASLPFVALGAGVAVVEVNPVKTELSGAVTHALRGSAGAVLPALVAGVWPGPSGALST +ARHVTW +>PROKKA_02354 +MPVEPGRDDVGPAGEAGRAVVGAGQRRRVVNPVAATPPSYLGRHYPVPMSHPSPGDLSET +VPTADLDAVRALVAQARRPVVLTGAGMSAESGIPTFRDAQTGLWERYSPEQLATEDAFLA +DPDLVWSWYRWRARMVRARRPNPGHDAVAHWQRAVPGLEVVTQNVDDLHERAGARVLAHL +HGSLFEHRCAECGAPADVDPGAPADAEAAGSEADLEAMLREAPPTCPACGTGRIRPGVVW +FGEMLPQEPWERAYEALERCDLALVVGTSGLVQPAASLPFVALGAGAAVVEVNPVETELS +GAVTHALRGSAGAVLPALVAGV +>PROKKA_02248 +MSPTQPSDPAALGAVRRLILEAERPVVLTGAGVSAESGVPTFRDAQTGLWERYSPEQLAT +AEAFAADPSLVWSWYLWRARMVRAVEPNAGHRALAAWQARTPALRIVTQNVDDLHERAGA +DVLSHLHGSLFAFRCAECDTPADVDPSAVVALAESAAPGSEAGLEALMHLEPPLCAACRR +GRVRPDIVWFGELLPERAWGDAQAALEECDLCVVVGTSGVVQPAASLPFLALGAGAPVVE +VNPDRTALSDAMTHVLRGPAGTVLPALLG +>PROKKA_00580 +MADPHPVLAASAPVLADPHPVLAASAPDLDPGALDAVRALVAAAERPVVLSGAGMSAESG +IPTFRDAQTGLWERFSAEQLATEEAFLADPALVWSWYRWRARMVRARRPNPGHDAVAAWQ +RRTPDLEVVTQNVDDLHERAGARVLAHLHGSLFEHRCAECGAPADVDPGAPSDVDAAGSE +ADLEAMLREAPPACPACGTGRIRPGVVWFGEMLPQEPWERAYEALERCDLALVVGTSGLI +QPAASLPFVALGAGVAVVEVNPVETELSGAVTHALRGSAGAVLPALVAGVWPGPSGALST +ARHVTW diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000570.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000570.fa new file mode 100644 index 0000000000000000000000000000000000000000..bcd83a4dac1f6273be5505926cb9db81499a0187 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000570.fa @@ -0,0 +1,50 @@ +>PROKKA_00580 +MPTAPAPSEAAATPLHVAVRTLDAAALAAAGHTAATAVAAVYAHAVVRGAASFWLDSALP +DPAEARWSVAGDGLDVLGEEQGRVPSPGPRLVRHDDPADPDRAWAGLAAAAAPRPVVGGE +GLPLRGGLVGWLGYELGLADLGVTPPSRRAEDPAPLPAQFWVRPSRYVVADHAAGVLHCC +VVSLDPTTAEAGADRWAADVRRALAAARRALETAAGDAVVPPPQDAVPGPRADEEAPGTW +REDRAAYAEQIARCRAALHAGDSYELCLTTRFDADPGLRVDPLVLFHELAAHQPAPYAAL +LEHGTGSRRWAVVSASPERFLSGREGRYSTKPIKGTAARLADPAGDAEAARALAADPKTR +AENLMIVDLLRNDLSRVCEPGSVQVPSLMAVESYASVHQLVSTVTGTARAGIEPVDVVRS +LFPGGSMTGAPKRRSVELLAAWEASPRGVYSGALGMLSADGTTSLSVVIRTAVLAGGRWS +VGAGGAIVADSDPAAEHDEVLLKARGLRRALARAAGTGLPTTAPDIA +>PROKKA_00313 +MPTAPAPSVAAATPLHVAVRTLDAAALAAAGHTAATAVAAVYAHAVVRGAASFWLDSALP +DPAEARWSVAGDGLDVLGEEQGRTPSPGPRLVRHDDPADPDRAWADLAAAAAPRPVVGGE +GLPLRGGLVGWLGYELGLADLGVTPPSPRPGDPASLPAQFWVRPSRYVVADHAAGVLHCC +VVSLAPTAAETGADRWAADVRRALAAARRALETASGDVVVPPPRDAGPGPQADEEAPGTW +REDRAAYAEQIARCRAALHAGDSYELCLTTRFDADPGLRVDPLVLFHELAAHQPAPYAAL +LEHGTGARRWAVVSASPERFLAGRAGRYSTKPIKGTAARLADPVADAEAARALAADPKTR +AENLMIVDLLRNDLSRVCEPGSVEVPSLMAVESYASVHQLVSTVTGTARAGVEPVDVVRS +LFPGGSMTGAPKRRSVELLAAWEASPRGVYSGALGMLSADGTTSLSVVIRTAVLAGGRWS +VGAGGAIVADSDPAAEHDEVLLKARGLRRALARAAGTGVPTTAPDVA +>PROKKA_02353 +MAAVYAHAVQRGAGSFWLDSALPDPAEARWSVAGDGLDVLGEEQGRVPSPGPRLVRHADP +ADPERAWSDLAAAAAPRRVVGGEGLPLRGGLVGWLGYELGLADLGVRPPSRRAGDPAALP +AQFWVRPSRYAVADHAAGTLSCCVVALDAAAAEAAADRWAADVRRALDAARRATQAAADD +AAASEVRADVAPEAGTGEAAGAWREDRAAYDEHIARCHAALHAGDSYELCLTTRFDADPA +LRVDPLALFLELAAHQPAPYAALMEHGTGPRGWAVVSASPERFLAGRDGRYSTKPIKGTA +ARLPDPAADAEAARALAADPKTRAENLMIVDLLRNDLSRVCEPGSVQVPSLMAVESYATV +HQLVSTVTGTARAGVAPVDVVRSLFPGGSMTGAPKRRSVELLAQWEDSPRGVYSGALGLL +GADGAVSLSIVIRTAVLAAGRWGIGAGGAIVADSTAEAEHEEVLLKARGLRRALARADGT +ARTTTAPPRSR +>PROKKA_02247 +MPTAPGRPDASPAPLHVAVRTLDIATLAAVGHTAATAAGAVYAHAVQRGTASFWLDSALP +DGGEARWSMVGDGVDVLGEEEGRIPSPGLRLIRHGDPADPDRAWADLAAAAAPREVHGGE +GLPLRGGLVGWLGYELGLADLGVTPPPPRPGDPAALPAQFWVRPSRYAVADHVAGALSCC +VVSLDADAAEAAADRWEADVRRALEAARTSTEEVEVDVDAPEAPGVWREDGAAYAEQIAR +CRAALHAGDSYELCLTTRFDADPALRVDPLALFRDLAAHQPAPYAALMEHGTGAERWAVV +SASPERFLSGRDGRYSTKPIKGTAARLPDPTEDAAAAAALAADPKTRAENLMIVDLLRND +LSRVCEPGTVQVPALMAVESYATVHQLVSTVTGVARAGVAPVDVVRSLFPGGSMTGAPKR +RTVELLAAWEGSPRGVYSGALGMLGADGTVELSIVIRTAVLSPTTPDAPARWSVGAGGAI +VADSDAHAEHEEVLLKARGLRRALTRAAGTA +>PROKKA_00581 +MPTAPAPSEAAATPLHVAVRTLDAAALAAAGHTAATAVAAVYAHAVVRGAASFWLDSALP +DPAEARWSVAGDGLDVLGEEQGRVPSPGPRLVRHDDPADPDRAWADLGAAAAPRSVVGGE +GLPLRGGLVGWLGYELGMADLGVSPPSRRPEDPAPLPAQFWVRPSRYAVADHAAGVLHCC +VVSLDPTAAEAGADRWAADVRRALAAARRDLETAAGDAVVPPPEDAGPEPRADEEAPGTW +REDRAAYAEQIARCRAALHAGDSYELCLTTRFDADPGLRVNPLVLFHELAAHQPAPYAAL +LEHGTGARRWAVVSASPERFLAGREGRYSTKPIKGTAARLPDPAADAAAARALADDPKTR +AENLMIVDLLRNDLSRVCEPGSVEVPSLMAVESYASVHQLVSTVTGTARAGVEPVEVVRS +LFPGGSMTGAPKRRSVELLAAWEASPRGVYSGALGMLSADGTTSLSVVIRTAVLAGGRWS +VGAGGAIVADSDPAAEHDEVLLKARGLRRALARAAGTGVPTTAPDIA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000571.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000571.fa new file mode 100644 index 0000000000000000000000000000000000000000..442c90e9e1dc1b7ff0f2a16ffcbb5ac2c7568c14 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000571.fa @@ -0,0 +1,60 @@ +>PROKKA_00583 +MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY +HCFGCGAHGDVISFLMELEHTTFTETVERLASRVGVELHYEDGGTGPDKAETGRRRRLFE +ANKVADEFFRRALGSPEAQAARDFLTQRGFTQEHATQFGLGYAPQGWSHLLDHLRQRGFR +DEELRASGLVSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP +LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKVA +RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTFVAVEPSGMDPCDLRMQKG +DEAVRALIASRRPLFEFAIRAGLKDYDLDTVEGRAGALRHAVPIVAGIKDAVLRPGYERE +LAGWLGLDPNAVHRAVAAAGRAPRRGPEPEARPAPADDGQAIGPQGRHGEAAAPAPRIVV +PVDPRDPVARRERESLEVVLQHPTLLSAEQWTALYAARFTVPQYAAVHQGVKMAGSAGAT +PQRWVDAVRDAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFALQIVHRKEELL +GRLQRLGPEGDPAEFTRLNSELMELEARRRALRADD +>PROKKA_00316 +MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY +HCFGCGAHGDVISFLMELEHTTFTETVERLASRVGVELHYEDGGTGPDKAETGRRRRLFE +ANKVADEFFRRALGSPEAQAARDFLTQRGFTQEHAVQFGLGYAPQGWSHLLDHLRQRGFR +DEELRASGLVSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP +LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKVA +RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTFVAVEPSGMDPCDLRMQKG +DEAVRALIASRRPLFEFAIRAGLKDYDLNTVEGRAGALRHAAPIVAGIKDAVLRPGYERE +LAGWLGLDPNAVHRAVAAAGRAPRRGPEPEARPAPADDGQAIGPTGRHGEAAAPAPKIVV +PVDPRDPVARRERESLEVVLQHPTLLSAEQWTALYAARFTVPQYAAVHQGVKMAGSAGAT +PQRWVDAVRDAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFALQIVHRKEELL +GRLQRLGPEGDPAEFTRLNSELMELEARRRALRADD +>PROKKA_02351 +MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY +HCFGCGEHGDVISFLMELEHTTFTETVERLAARVGVELHYEDGGTGPDKAETGRRRRLLE +ANKVADEFYRRALGSAEAQTGRDFLTQRGFTQEHAEQFGLGYAPQGWSHLLDHLRQKGFR +DEELRASGLFSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP +LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKMA +RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTYVAVEPSGMDPCDLRMQQG +DEAVRALIASRRPLFEFAIRAGLKDYDLDTVEGRAGALRHAAPIVAGIKDAVLRPGYERE +LAGWLGLDPNAVHRAVAAAGRGQRRGGGSEPRREPERGPEPDQAPGQGRGPAPEGPSVGP +QGRHGEAAAPAPQVLVPVDPRDPVARCERESLEVVLQHPTLLSAEQWTALYAARFTIPQY +AAVHHGVKVAGSSGATPQRWVDAVRYAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIM +NRLFALQIVHRKEELLGRLQRLGPDGDPAEFTALNSELMELEARRRALRADD +>PROKKA_02246 +MVRMAGLIVRKDIDLVRERADLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGV +GTYHCFGCGEHGDVISFLMEMEHTTFTETVERLAARAGVELHYEDGQGPDRAETSRRRRL +LEANKLADEFYRARLAAPDAQPGRDFLTGRGFTQEHAEQFGLGYAPQGWSALLDHLRQQG +FRDDELRASGLFSEGQRGLYDRFRGRLLWPIRDMTGNTIGFGARKLFEDDPGPKYLNTPE +TPLYKKSQVLYGIDLAKRAIAKERQLVLVEGYTDVMAAHLSGVETAVATCGTAFGADHIK +IARRLISDDGTGGEVIFTFDGDAAGQKAALKAFDEDHRFLAKTFVAVEPNGLDPCDLRMQ +QGEEAVRALIASRRPLFEFAISAGLKDYDLNTVEGRAGALRHAAPIVAGIKDSVLRPGYE +RELAGWLGMDPNVVSRAVAQELRGRRRGGPSGGSAERTPAPERAPEGANAGQAPGEEPAA +PRPALIVPVDPRDPAARRERESLEVVLQHPTLLSAEQWTAFYQARFTIPQYAAVHHAVKV +AGTAGATPSRWVDAVRDAAPGEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFSLQIV +HRKEELLGQLQRLGPEGDHDEFMRLNAELMELETRRRALRADD +>PROKKA_00584 +MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY +HCFGCGAHGDVISFLMELEHTTFMETVERLASRVGVELHYEDGGTGPDKAETGRRRRLFE +ANKVADEFFRRALGSPEAQAARDFLTQRGFTQEHAVQFGLGYAPQGWSHLLDHLRQRGFR +DEELRASGLVSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP +LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKVA +RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTFVAVEPSGMDPCDLRMQKG +DEAVRALIASRRPLFEFAIRAGLKDYDLNTVEGRAGALRHAAPIVAGIKDAVLRPGYERE +LAGWLGLGPNAVHRAVAAAGRAPRRGPEPEARPTPASDGQAVGPTGRHGEAAAPAPRIVV +PVDPRDPVARRERESLEVVLQHPTLLSAEQWTALYAARFTVPQYAAVHQGVKVAGSAGAT +PQRWVDAVRDAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFALQIVHRKEELL +GRLQRLGPEGDPAEFTRLNSELMELEARRRALRADD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000572.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000572.fa new file mode 100644 index 0000000000000000000000000000000000000000..258763a70229158ad1f21a786be267721583ff9c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000572.fa @@ -0,0 +1,25 @@ +>PROKKA_00584 +MTITTLTRKTALTGTGMLAALALAACGTTSDNGDDGSASPEVDASSSLASTPATDDASGS +ATSSSASSASASSTAAAAGSDSATGQADDPAYAVIDAVLEKYGDGIIVAVDADDDDTTWE +VDVVVGEEVKELDVTADGDITETDRESDLEDVQKAKDAEVTAQQALDTAREGRDGVTLDE +MDLDDDNGTLQWEVGFDREDGSDGPEVEIDATSGEVLTVDEH +>PROKKA_00317 +MTITTLTRKTALTGTGVLAALALAACGTTADNGDDGSVSPEVDASSAVASTPATDDASTT +SASASSSASSTSASSTAAAASSGSGTGQADDPAYAVIDAVLEKHGDGIIVEVDANDDDTT +WEVDVVVGEEVKELDVTADGDITETDRESDLEDVQKAKDAEVTAQQALDTAREGRDGVTL +DEMDLEDDNGTLQWEVGFDREDGSDGPEVEIDATSGEVLTVDER +>PROKKA_02350 +MNATSLARKTALTGTGLLAALALAACGTADDDTAANPQETAVQQSPTQAATTAPASASGS +ASASASGSASASASGSASPAAASGSVERQGDDPAYAAIDAILGLHDDGVIVEMDLDDDDA +KWEVDVVVGDDVKEYDVTTGGQVSEGVRPQIDDDVRRAGEAQVTAETAISTALQGRTDQT +VDEVDLDEEGGTLVWKVELDRENGEDGAEVKIDAKTGDVIEVEEG +>PROKKA_02245 +MTITTLTRKTALTGTGVLAALALAACGTTADNGDDGSASLEVDASSAVASTPATEDASTT +SASASSASSAPASSTAAAAGRDSATGQADDPASAVIDAVLEKYGDGIIVGVDANDDDTTW +EVDVVVDKEVKELDVTADGDITETDRESDPEDVQKAKDAEVTAQQALDTARKGRDGVTLD +EMDLDDDNGTLQWEVEFDREDGSDGPEVEIDATSGEVLTVDEH +>PROKKA_00585 +MTITTLTRKTALTGTGMLAALALAACGTTSDNGDDGSASPGVDASSAVASTPTTDDASGS +ASSSASSASASSTAAAAGSGSATGQADEPAYAVIDAVLEKYADGIIVAVDANDDDTTWEV +DVVVGEGAKELDVTADGDITETDRESDPEDVQKAKEAEVTAQQALDTAREGRDGVTLDEM +DLEDDNGTLQWEVRFDREDGSDGPEVEIDATSGEVLTVDER diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000578.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000578.fa new file mode 100644 index 0000000000000000000000000000000000000000..2b704e3aca87da538da84e68dd952cef600c9949 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000578.fa @@ -0,0 +1,36 @@ +>PROKKA_00641 +MDTTRFDDDLRAMLGEVESDRRGEPSDYLEDVAGQHVDGLAVAVCTVDGHQAAAGETEHA +FALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGAILV +HSLLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGRLPI +SAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQTMSVMLTCGM +YDASGQWVAEVGVPAKSGVSGALLGAVPGALGLAAWSPRLDEQGNSRRGIGLFEGLSARW +DLHVLQHRGALRGLSGPR +>PROKKA_00378 +MDTTRFDDDLRAMLDEVESDRRGEPSDYLEDVAGQHVDGLAVAVCTVDGHQAAAGETEHA +FALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGAILV +HSLLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGRLPI +SAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQAMSVMLTCGM +YDASGQWVAEVGVPAKSGVSGALLGAVPGALGLATWSPRLDEQGNSRRGIGLFEGLSARW +DLHVLQHRGALRGLSGPR +>PROKKA_02321 +MDTTRLDDDLRAMLAEVESDRRGEPSDYLEDVAGQHVDGLAAAVCTVDGHQAAAGETDHA +FALQSVSKALTYAVVLQEVGLDAVLERVGVEPSGEAFNHLSLHDDGRPYNPLINAGAIMA +HALLPAGDHEERVALLVRRYSALAGAELEVSQDVLDAELTRADRNLGLAHLLADAGQLPV +SAREAVAGYLAQCSVTVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQTMSVMLTCGM +YDATGQWVAEVGVPAKSGVSGALLGAVPGALGIATWSPRLDERGNSRRGIGIFEGLSARW +DLHVLQHRGALRGLRASR +>PROKKA_02184 +MGIGSLIATMLPSSIAFLPACTGMVIGWRWLGLPLGPNARSSAHRDRPGARPRPGRPSTT +VTGMDTTRFDDDLRAMLGEVESDRRGEPSDYLEDVAGQHVDGLAVAVCTVDGHQAAAGET +EHAFALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGA +ILVHSLLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGR +LPISAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQTMSVMLT +CGMYDASGQWVAEVGVPAKSGVSGALLGAVPGALGLAAWSPRLDEQGNSRRGIGLFEGLS +SRWDLHVLQHRGALRGLSGPR +>PROKKA_00611 +MDTTRFDDDLRAMLDEVESDRRGEPSDYREDVAGQHVDGLAAAVCTVDGHQAAAGETEHA +FALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGAILV +HALLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGRLPI +SAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQAMSVMLTCGM +YDASGQWVAEVGVPAKSGVSGALLGAVPGALGIATWSPRLDEQGNSRRGIGLFEGLSARW +DLHVLQHRGALRGLSGPR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000580.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000580.fa new file mode 100644 index 0000000000000000000000000000000000000000..25fd1389e86f57a45b8eb7782f3192d02aeb7e27 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000580.fa @@ -0,0 +1,35 @@ +>PROKKA_00643 +MTARLLADVDTGIDDACALLHLVGAHRLGAGPELAAVTTTGGNATARDCALNTAAVLDLA +GRADVEVAVGAETPLRRPAVTTPETHGDGGLGHARIVRRPERLSPRPAVDVWLDELRAHP +GETAILCTAPLTNLALALRTEPRLPFLARGIVIMGGSFYHPGNTTPTAEWNTWVDPDAAK +EVFAAVEGLPEDRLPIVCALETTERIEYTPALLDGLLADAGAHPVGWSADRPRVAGPDAA +TGSPVLDVLADALRFYFEFHHDYDQGYIAHLHDLFAAQVAAGQARIATRATVVDVEADSE +LLRGTTVHDTRDIWGRRPNAQLVTANDPAEVFAAFARAVGAVVAGERTLDGGSPAR +>PROKKA_00380 +MTARLLADVDTGIDDACALLHLVGAHRLGVGPELAAVTTTGGNATARDCALNTAAVLDLA +GRADVEVAVGAETPLRRPAVTTPETHGDGGLGHARIVRRPERLSSRPAVDVWLDELRAHP +GETTILCTAPLTNLALALRTEPRLPFLARGIVIMGGSFYHPGNTTPTAEWNTWVDPDAAK +EVFAAVEGLPEDRLPIVCALETTERIEYTPALLDGLLADAGARPVGWSADRPRVAGPDAA +TGSPVLDVLADALRFYFEFHHDYDQGYIAHLHDLFAAQVAAGQARIATRATVVDVEADSE +LLRGTTVHDTRDIWGMRPNAQLVTANDPAEVFAAFARAVGAVVAGERTLDGGSPAR +>PROKKA_00385 +MGARILADMDTGIDDACALLQLVGAGAELAAVTTTGGNATARECALNTAALLDLMGRTDV +EVAVGAEAPLQRPPETTPETHGDGGLGYARLAHRPERLSARSAVDVWVEELRARPGRTTI +LCTAPLTNLALALRAEPALPELAAGVVIMGGAFYYPGNTTPTAEWNTWCDPDAAKEVFAA +FEGLPEDRLPLLCPLETTERIEYTPALLDALLTGVGHAPTGWSVDRARHAGPQADTGSPV +LDVLADALRFYFEFHHDYDQGYVAHLHDLFAAQVALGTAQIRTQATVVDVEADSDLLRGT +TVHDDRHIWGRRPNARRVVDADPAGVFAAFAQAASAAARAGDDAGR +>PROKKA_02182 +MAAVTARLLADVDTGIDDACALLHLVGAHRLGAGPELAAVTTTGGNATARDCALNTAAVL +DLAGRADVEVAVGAETPLRRPAVTTPETHGDGGLGHARIDRRPERLSPRPAVDVWLDELR +AHPGETTILCTAPLTNLALALRAEPRLPFLARGIVIMGGSFYHPGNTTPTAEWNTWVDPD +SAKEVFAAVEGLPEDRLPIVCALETTERIEYTPALLDGLLADAGARPARWDVARPRVSGP +AADTGHPVTDVLADALRFYFEFHHDYDQGYIAHLHDLVAAQVAAGQADVTLQATVVDVEA +DSELLRGTTVHDDRRIWGRRPNARRVTGCDPRRVFEDFAQAVGALTGAGVG +>PROKKA_00613 +MAAVTARLLADVDTGIDDACALLHLVGAHRLGAGPELVAVTTTGGNASARDCALNTAAVL +DLAGRADVEVAVGAETPLRRPAVTTPETHGDGGLGHARIVRHPERLSPRPAVDVWLDELR +AHPGETTILCTAPLTNLALALRTEPRLPFLARGIVIMGGSFYHPGNTTPTAEWNTWVDPD +AAKEVFAAVEGLPEDRLPIVCALETTERIEYTPALLDGLLADAGARPVGWSADRPRVAGP +DAATGSPVLDVLADALRFYFEFHHDYDQGYIAHLHDLFAAQVAAGQARIATRATVIDVEA +DSELLRGTTVHDTRDIWGRRPNAQLVTANDPAEVFAAFARAVGAVVAGERTPDGGAPAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000581.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000581.fa new file mode 100644 index 0000000000000000000000000000000000000000..85d7656e9fbe2967ba37a7d5fa176954e175839c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000581.fa @@ -0,0 +1,35 @@ +>PROKKA_00645 +MSHQAPPADASKVRAPRTAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELELAKRHVAAK +GKKAGIGAGIAVVGLFFLALMVVALVVTLIGAFADPTFWFPALMVALAFLVLGLIFAGVG +LMMVKGAMPLVPQEIVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAAREAERKK +VEKEENKKARKNGEAAPHPDRADASEAEIRRRADLRRRHLGDIRSGLDEKTSVKGQLAAF +AAQRKGRGVTPETAHATEQTAPFTGAARAGERTAEAEDYVKDNWQPLALLGASSAAFVAL +AGRLRRR +>PROKKA_00382 +MSHQAPPADASKVRAPRTAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELELAKRHVAAK +GKKAGIGAGIAVVGLFFLALMVVALVVTLIGAFADPTFWFPALMVALAFLVLGLIFAGVG +LMMVKGAMPLVPQEIVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAAREAERKK +VEKKENKKARKNGEAAPHPDRADASEAEIRRRADLRRRHLGDIRSGLDEKTSVKGQLAAF +AAQRKGRGVTPETAHATEQTAPFTGAARAGERTAEAEDYVKDNWQPLALLGASSAAFVAL +AGRLRRR +>PROKKA_02318 +MSHQAPPADALKAGAPRPAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELALAKGHVVAK +GKKAGIGAGVTVVGLFFLALVVVALVVALIGAFADPTFWFPALMVAAAFLVLGAIFAGIG +LFMVKGAMPLVPQETVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAKRAEERRK +VEKEENKKARKNGEAAPHPDRDEASEAEIRRRADLRRRHLGDIRSGLEEKTSVKGQLAAF +AAQRKGRGVTPQTAHATDQTAPFTGAARAGEKAAEAEDYVKDNWQPLALLGASSAAFLAL +AGRLRRR +>PROKKA_02177 +MSHAAPTAAPRAPRPTTPVTPQTRASSLTDLLAAVVRLLPLQLKDELALAKGQAAAKGKK +AGIGAALAVVGLFFLALMTIALVVALIGAFANPPFWFPALMVALVFLVLGLVLAGVGAMQ +IKGAMPLVPQETVRNLEYDLGYLKEGNDFDPAEYDRLKAERAEAKRLEKQREAERKKVEK +EENKQARKDGLAAPHPAKDDASEDEVRRRAELRRRHLGDIRSGLDEKTSVKGQVAAFTAQ +RKLRGTTPDTAHATEQTAPFTTAARAGEQTAAAEDYVKERWQPLALLGASGTAFAVLASR +LRGRKG +>PROKKA_00615 +MSHQAPPADASKARAPRTAVPVTPQTRASSLTDLLGAVVRLLPLQMKDELALAKGHVAAK +GKKAGIGAGVAVVGLFFLALMVVALVVTLIGAFADPSFWFPALMVALAFLVLGLIFAGVG +LVMVKGAMPLVPQETVRNLEYDLGYLKEGNAFDPAEYDRLKAERAEAKRVEAAREAERKK +VEKEENKKARKNGEAAPHPDRDDATEAEIRRRADLRRRHLGDIRSGLDEKTNVKGQLAAF +AAQRKGRGVTPETTHATEQTAPFTGAARAGERTAEAEDYVKDNWQPLALLGASSAAFVAL +AGRLRRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000583.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000583.fa new file mode 100644 index 0000000000000000000000000000000000000000..4c94cc44e73dbc404699847ab2cc0f674f178f39 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000583.fa @@ -0,0 +1,30 @@ +>PROKKA_00649 +MSVTSSHAAVRRAPRTAAASVALALGAAALTGVGTVSVAETAQAAETAYTVRSGDGWWII +AQRTGVSMSRLQSLNGMTAATVLHPGMVLKTSGTATPTPAPAPSTSGSTYTVLAGDGWWI +ISYRTGVSASILQSINGMSSSTMLHPGMVLKTTSVSTSSAPAVAPAPAPASKQAAVDYVR +SAVRNPSSYYVWGGNGPSGFDCSGLTQQAMARAGISIPRRAGDQYLAAKSYVPISQAQPG +DLVFYANQSTGRIYHTAMYMGGGQLAHALNEDAGLVFTSTTIMKSDMLAVAARY +>PROKKA_00386 +MSVTSSHAASRRAPRTAAASVALALGAAALTGVGTVSVAETAQAAETTYTVRSGDGWWII +AQRTGVSMSTLQSLNGMTAATVLHPGMVLETSGTATPAPAPAPSTSGSTYTVLAGDGWWI +ISYRTGVSASILQSINGMTSSTMLHPGMVLKTTSVSTSSAPALAPASAPASKQAAVDYVR +AAVRNPSSYYAWGGNGPSGFDCSGLTQQAMAQAGISIPRRAGDQYLAAKSYVPISQAQPG +DLVFYANQSTGRIYHVAMYMGGGQLAHALNEDAGLVFTSTTIMKSDMLAVAARY +>PROKKA_02314 +MSVTSSRAASRRAPRTAAASLALALGAGALAGVGSVTAAETAQAVETTYTVRAGDGWWVI +SQRTGVSMSTLQSLNGMTSATMLHPGMVLKTSGTAAPAPAPAPSASTYTVLAGDGWWIIS +YRTGVSASVLQSINGMTSSTVLHPGMVLKTSVVASSAPAPAPAPVTNGKQAAVDFVRSTV +QNPSSYYLWGGNGPYGFDCSGLTQQAMAKAGISIPRRAGDQYNAAKSYVPISQAQPGDLV +FYANQSTGRIYHVAMYMGGGQLAHALNEDAGLLFTSTTIMKSDMLAVAARY +>PROKKA_02171 +MPEALLTPARRPRAAAASLALALGAGAGVTAGAAVIAPQAVAAETYTVQAGDGWWIISQR +TGVSMATLMQLNGMTSADMLHPGMVLKTSGTVTAAAGTYTVKAGDGWYAISRATGVPVST +LTSLNGMTITSMLYPGMVLKTTGTPASTAPAPAPAPAPVVRQSSKQAAIDFAVAKVNDPN +TYYAWGGNGPYGYDCSGLTKAAFAAAGITIPRVSHDQYVNAPAYAPLSQAQPGDLVFWAN +QSTGRVYHVAVYIGNGKVAHALNTTDDLVITSTDVMTSNRLAVVGRY +>PROKKA_00619 +MSVTSPHAAARRAPRTAAASVALALGAAALTGVGTVSVAETAQAAETTYTVRSGDGWWII +AQRTGVSMSTLQSLNGMTAATVLHPGMVLKTSGTATPAPAPAPSTSGSTYTVLAGDGWWI +ISYRTGVSASVLQSINGMTSSTMLHPGMVLKTTSVSTSSAPAPAPAPASKQAAVDYVRSA +VRNPSSYYVWGGNGPSGFDCSGLTQQAMARAGISIPRRAGDQYLAAKSYVPISQAQPGDL +VFYANQSTGRIYHTAMYMGGGQLAHALNEDAGLVFTSTTIMKSDMLAVAARY diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000584.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000584.fa new file mode 100644 index 0000000000000000000000000000000000000000..d78da01a1b9e8296c80c792819f46cbc2dac6967 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000584.fa @@ -0,0 +1,25 @@ +>PROKKA_00651 +MTPRTHLPRPLPRPHIAGCVAAALLAWLVLASGVGGLDAVPRATSAPSGRDALLLVAASP +AGPGSTAAPVAWHAPVAGAAPDDVLRAFVAPERPWGRGHRGVDLAVPSGAAIRAPAAGRV +VFAGVVVDRPVLTLEHEDGTRSSLEPVEADVAVGAVVAAGDPVGRLAGAPPHCTRACVHW +GVREPDGWRVGDAAFDRYLDPLVLIGWSGPSVLWPHAAPHPARP +>PROKKA_00388 +MTPRTLLPRPLPRPRIAGCVAAALLAWLVLALEMGDLGPASRATPAPSTRDALLLVAASP +AGPGATAAPVAWHPPVAGAAPDDVLRAFVAPERPWSRGHRGVDLAVQTGAPIQAPAAGRV +VFAGVVVDRPVLTLEHADGTRSSLEPVEADVAVGAVVDAGDPVGRLAGAPPHCPRACVHW +GVREPDGWRVGDAAFDRYLDPLVLIGWSGPSVLWPHAAPHPARP +>PROKKA_02312 +MTARSPAPRRARPAASPHRLLAVLLLCVLGLALAFALGPGIGAATPSSIRAEDGPTADAR +LAVAATPARAWTAPAAGVRPGDVLRPFAAPERPWGRGHRGVDLAVSPGAAVLAPAAGTVV +FAGTVVDRPVVTLEHADGTRSSLEPVEAAAPVGARLERGAPLGTVADAPAHCAVPCVHWG +VRVPDGWRFGDATFDRYLDPLVLIGWSGPSVLWPHAAPPPAGPAPARE +>PROKKA_02169 +MNEASTPPPRLRAAAVLAVALLATASAARAEDAPAAPPVTGALLAPTPGAGPSDVLRGFA +GPERPWSRGHRGVDLATSSGLVTAPAAGTVRFVGSVAGRGVLTLAHPDGTLSSFEPVTSD +LTAGQAVAAGQEVARVQEGAAHCPVRCVHWGVRREDAWAVGAARFDRYLDPLLLLGWSGP +SVLWPVGDAG +>PROKKA_00621 +MTPRTLLPRPLPRPRIAGCVAAALLAWLVLALGMGDLGPVSRATPAPSTRDALLLVAASP +AGPGATAAPVAWHPPVAGAAPDDVLRAFVAPERPWSRGHRGVDLAVQTGAPIQAPAAGRV +VFAGVVVDRPVLTLEHEDGTRSSLEPVEADVAVGAVVAAGDPVGRLAGAPPHCTRACVHW +GVREPDGWRVGEAAFDRYLDPLVLIGWSGPSVLWPHAAPHPARP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000586.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000586.fa new file mode 100644 index 0000000000000000000000000000000000000000..f0db01de6d95eff87ae05675c16f0a73aa2f4a6e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000586.fa @@ -0,0 +1,30 @@ +>PROKKA_00653 +MANYTAADIKALRERTGAGMMDVKKALDEADGDAEKAIEIIRVKGLKGATKREGRSAAEG +LVAATVENGVGVMIELNCETDFVAKADKFIALGDVVLRAAVASGATDVDGLLASEHEGRT +LGDYVTEEGALLGEKVAVRRLARVEGAYVDAYLHKTSKDLPAQVGVLLAVDADSAEAKTA +AHDIAVHVAAYSPTYLTREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK +EIVLVDQPFAKDPKQTVGKVASDAGTNVTGFARFRVGN +>PROKKA_00390 +MANYTAADIKALRERTGAGMMDVKKALDEANGDAEKAIEIIRVKGLKGATKREGRSAAEG +LVAATVENGVGVMIELNCETDFVAKADKFIALGDVVLRAAVASGATDVDGLLASDYEGRT +LGDYVTEEGALLGEKVAVRRLARVEGAFVDAYLHKTSKDLPAQVGVLLAVDADSADAKTA +AHDIAVHTAAYSPTYLTREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK +EIVLVDQPFAKDPKQTVGKVASDAGTNVTGFARFRVGN +>PROKKA_02310 +MANYTAADIKALRERTGAGMMDVKKALDEANGDAEKAIEIIRVKGLKGATKREGRSAAEG +LVAATVENGVGVMIELNCETDFVAKAEKFITLGDVVLRAAVASGAADVESLLASEHEGRT +LGDHVIEEGALLGEKVAVRRLARVEGALVDAYLHKTSKDLPAQVGVLLAVDADSAEAKTA +AHDIAVHTAAYSPTYLSREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK +EIVLEDQPFAKDPKQTVGKVASDAGTKVTGFARFRVGN +>PROKKA_02167 +MANYTAADIKALRERTGAGMMDVKKALDEANGDADKAVEIIRVKGLKGATKREGRSAAEG +LVAATVENGVGVMIELNCETDFVAKADKFISLGDVVLKAAVASGAADVDSLLASDHEGRT +LGDYVTEEGALLGEKVAVRRVARVEGAHVDAYLHKTSKDLPAQVGVLLAVDADSDAAKTA +AHDIAVHTAAYSPTYLTREDVPAETVENERRIAEESARAEGKPEQALAKIVEGRLTGFFK +EGVLVDQPFAKDPKTTVGKVASEAGTAVTGYARFRVGN +>PROKKA_00623 +MANYTAADIKALRERTGAGMMDVKKALDEANGDAEKAIEIIRVKGLKGATKREGRSAAEG +LVAATVENGVGVMIELNCETDFVAKADKFIALGDVVLRAAVASGATDVDGLLASDYEGRT +LGDYVTEEGALLGEKVAVRRLARVEGAFVDAYLHKTSKDLPAQVGVLLAVDADSADAKTA +AHDIAVHTAAYSPTYLTREDVPAETVENERRIADETARAEGKPEQALPKIVEGRLTGFFK +EIVLVDQPFAKDPKQTVGKVASDAGTNVTGFARFRVGN diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000590.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000590.fa new file mode 100644 index 0000000000000000000000000000000000000000..f1df45c94665be74c12c2c5cf98417e3c6588930 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000590.fa @@ -0,0 +1,40 @@ +>PROKKA_00658 +MTLVDHTRPTGGQSAGSPPPAGPAEAVMLQVLDTEGRRRPQPELDPWIEDVDADALAALY +RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALRPDDFVFPSYRENGVALL +RGVPALDLLRVWRGSTFSSWDPNETRVATQQIIIGAQALHAVGYAMGVQRDQADVATIVY +FGDGATSQGDVNEAMVFSASYQSPVVFFCQNNHWAISEPVRLQTRRSIADRPWGFGIPSM +RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA +RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALEALEEDGADRLFDEIYAEPH +QELERQRREHALYLQQFGDEEAGA +>PROKKA_00395 +MTLVDHTRPTGGQSAGSPLPAGPAEAVMLQVLDTEGRRRPQPELDPWIEDVDADALAALY +RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALRPDDFVFPSYRENGVALL +RGVPALDLLRVWRGSTFSSWDPNETRVATQQIIIGAQALHAVGYAMGVQRDQADVATIVY +FGDGATSQGDVNEAMVFSASYQSPVVFFCQNNHWAISEPVRLQTRRSIADRPWGFGIPSM +RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA +RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALEALEEDGADRLFDEIYAEPH +QELERQRREHALYLQQFDDEEAGA +>PROKKA_02305 +MTLVDHTRPAGGEAATSPPPGEPAEAPMLQVLDAEGRRHAQPELDPWIEDVDADALAALY +RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALREDDFVFPSYRENGVALL +RGVPALDLLRVWRGSTFSGWDPQATGVATQQIIIGAQALHAVGYAMGVQRDQADAATIVY +FGDGATSQGDVNEAMVFSASYRSPVVFFCQNNHWAISEPVKLQTRRSIADRPWGFGIPSL +RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA +RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALESLVEDGAELLFDEIYAEPH +QELERQRREHALYLQQFDDEEAGA +>PROKKA_02161 +MTDVHLPEQDAPPRSDRPAEQLQVLTPDGRRSPSPELDPWLTDVDEEMLARLHRELTLVR +RLDTEATHLQRQGRLALWPPLRGQEASQVGAAAALRPADHVFPSYRENGLCLLRGVEAGE +LLRVWSGSSFSGWDPAATGVATQQLVIGAQTLHAVGYAMGVQRDAADVSTLVCFGDGATS +EGDVHEAMVFAASYQAPVVFFCQNNHWAISEPVGLQARRSIADRAWGYGIPALRVDGNDV +LAVLAAVRRGVDRAAAGAGPMFVEAVTYRMGAHTTADDPTRYQDPAELEAWARRDPLERL +TAHLRDVGADADAVVDASEAAADDLAARMRADLDALPEEGPEALFAHVYAEPHQELARQQ +RDLQLHLDGLDAGEEQA +>PROKKA_00628 +MTLVDHTRPTGGQSAGSPPPAGPAEAVMLQVLDAEGRRRPQPELDPWIEDVDADALAALY +RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALRPDDFVFPSYRENGVALL +RGVPALDLLRVWRGSTFSSWDPNETRVATQQIIIGAQALHAVGYAMGVQRDQADVATIVY +FGDGATSQGDVNEAMVFSASYQSPVVFFCQNNHWAISEPVRLQTRRSIADRPWGFGIPSM +RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA +RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALEALEEDGADRLFDEIYAEPH +QELERQRREHALYLQQFDDEEAGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000593.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000593.fa new file mode 100644 index 0000000000000000000000000000000000000000..139d9b5d054f8f2bc5a692f563699f1449d94925 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000593.fa @@ -0,0 +1,20 @@ +>PROKKA_00661 +MAGTRDGDAVEPRPERSTAVLLRDVRPEDLDEFFLHQQDEQANLMSAFAPRNPRDRGVFD +YHWAHLLGDEDTVVRTIEHEGRAVGALVCTQQDGVGELSFWTAQDYWGLGLTTAAVDRFL +EEHTARPLRAHVPEDNVGSVKVLSRRGFETVGEEKVFSNARAEVITELVMELPAAD +>PROKKA_00398 +MLLRDVRPEDLDEFFLHQQDEQANLMSAFAPRNPRDRGVFDYHWAHLLGDEDTVVRTIEH +EGRAVGALVCIQQDGVGELSFWTAQDYWGLGLTTAAVDRFLEEHTARPLRAHVPEDNVGS +VKVLSRRGFETVGEEKVFSNARAEVITELVMELPAAD +>PROKKA_02302 +MLLRDVRPEDLDEFFLHQQDEQASLMSAFAPRNPRDRGVFDYHWSSLLAAETAVVRTIEH +EGRAVGAIVCTEHDGVGELSFWTAQDYWGLGLTTAAVDAFLREHTRRPLRAHVPEDNAGS +VKVLSRRGFETVGQEKVFSNARAEVITELVMELPAGAE +>PROKKA_02158 +MPLRDVRPDDLDAFFLHQQDERANLMSAFAPRNPSDRGVFDYHWAHLLGDDATEVRTIEH +EGRPVGALVCTRVDGVDELSFWVAREFWGQGLTTSAVDEFLSTHRERPVRAHVPEDNLGS +VKVLTRRGFREVGREKVFSNARAEVVEELVLELPGA +>PROKKA_00631 +MLLRDVRPEDLDEFFLHQQDEQANLMSAFAPRNPRDRGVFDYHWAHLLGDEDTVVRTIEH +EGRAVGALVCTQQDGVGELSFWTAQDYWGLGLTTAAVDRFLEEHTARPLRAHVPEDNVGS +VKVLSRRGFETVGEEKVFSNARAEVITELVMELPAAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000594.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000594.fa new file mode 100644 index 0000000000000000000000000000000000000000..889dace09a8b5be2924d66fe0c64b3cc6a07831c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000594.fa @@ -0,0 +1,25 @@ +>PROKKA_00662 +MPAADPASPAAPATPPTAREAAKARRRVDLLAAAARLFAARGFDAVRLEDIGAAVGISGP +AIYRHFAGKAAVLTAILDTASQDLLDGGLAAEAQHAPGAETLRALIGFQADFALAQRDVI +RVQDRDMSALPDGARTAITRTQRAYIDVWARQLQVVHPREDQATAVFRAQAVLGLLNSTP +RSVRRTAADRAARRATLVAMAWAAATAPGPLSGED +>PROKKA_00399 +MPAVDPASPAAPATPPTAREAAKARRRVDLLAAAARLFAARGFDAVRLEDIGAAVGISGP +AIYRHFAGKAAVLTAILDTASQDLLDGGLAAEAQHAPGAETLRALIGFQADFALAQRDVI +RVQDRDMSALPDGARTAITRTQRAYIDVWARQLQVVHPHEDQATAVFRAQAVLGLLNSTP +RSVRRTAADRAARRATLVAMAWAAATAPGPLSGED +>PROKKA_02301 +MPAAVDPSAPAASAAAPTSRVAAKARRREDLLAAAARLFAARGFDAVRLEDIGAEVGISG +PAIYRHFAGKAAVLVAILATASQDLLEGALATEREHDAGEDALRALIAFQTDFALAQRDV +IRVQDRDMSALPEDERAAVTGTQRAYIDVWARQLRVVHPSEDQATAVFRAQAVLGLINST +PRSVRRTAADRAARRATLVAMAWAAATAPGPAADRP +>PROKKA_02157 +MPHAPDTAAPGPTGTPRERAKARRRAELLAAAARLFAAHGYEATRLEDIGAAAGISGPGI +YRHFAGKAAVLVEILSSASLFLLDGAEAVAARGLSGAEAVHDLIAFHTDFALANRDVIRV +QGRDMSSLPPADGAEITRVQRRYIDLWGAQLRRLHPGEDHATARFRTQALLGLINSTPFS +VRRSRADRGARRDALIGMAWAAARTPGGTARPEPPVVP +>PROKKA_00632 +MPAVDPASPAAPATPPTAREAAKARRRVDLLAAAARLFAARGFDAVRLEDIGAAVGISGP +AIYRHFAGKAAVLTAILDTASQDLLDGGLAAEAQHAPGAETLRALIGFQADFALAQRDVI +RVQDRDMSALPDGARTAITRTQRAYIDVWARQLQVVHPHEDQATAVFRAQAVLGLLNSTP +RSVRRTAADRAARRATLVAMAWAAATAPGPLPGGD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000598.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000598.fa new file mode 100644 index 0000000000000000000000000000000000000000..c1332221c68bd445a008532174ddd0b0b92698e6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000598.fa @@ -0,0 +1,44 @@ +>PROKKA_00670 +MTHGSLTDYTLPAPAPAHDGGAPRAVALIGSTGSIGTQGLDVIAQDPARLRAVALAGGAN +TTLLAEQAVRFEVEAVGSAAAGEEELRAALADAAARLGRPAPRPVLFTGPRAAEQIAAWP +GADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAARPGQLVPVDSEHS +ALAQALRGGTADEVRRLVLTASGGPFRGLDRAALHAVTPAQALAHPTWDMGRVVTTNSAS +LVNKALEVIEAHLLFDVPLDRIDVVVHPQSVVHSMVEFVDGSTLAQASPPDMRLPIALGL +CWPRRLPGAAPACDWTRAATWTFEPLDEEAFPAVRAAKEAAAASPTHMAVFNAANEESVD +AFHAGALPFDGIVDTVRAVVADYAPEHVLAAAGHDPAPTGLTVDAVLAAEAWARRAARAR +W +>PROKKA_00407 +MTHGSLTDYTLPAPAPADDDGAPRAVALIGSTGSIGTQGLDVIAQDPTRLRAVALAGGAN +TTLLAEQAVRFEVEAVGSAAAGEEELRAALADAAARLGRPSPRPVLFTGPCAAEQIAAWP +GADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAAAPGQLVPVDSEHS +ALAQALRGGTADEVRRLVLTASGGPFRGLDRAALHAVTPAQALAHPTWDMGRVVTTNSAS +LVNKALEVIEAHLLFDVPLDRIDVVVHPQSVVHSMVEFVDGSTLAQASPPDMRLPIALGL +CWPRRLSGAAPACDWTRAATWTFEPLDEEAFPAVRAAKEAAAASPTHMAVFNAANEESVD +AFHAGALPFDGIVDTVRAVVADYAPEHVLAAAGHDPAPTGLTVDAVLAAEAWARRAARAR +W +>PROKKA_02292 +MTHGSLTDYTLPAAGAPSASNAHDDGAPRAVALIGSTGSIGTQGLDVIAQDPARFRAVAL +SGGANTGLLAEQAVRFEVQAVGSATATEDELRAAIADAAARLGLKPAPRPALFTGPTAAE +RIAAWKGADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAAAPGQLVP +VDSEHSALAQALRGGTADEVRRLVLTASGGPFRGLDRAALAEVTPAQALAHPTWDMGRVV +TTNSASLVNKALEVIEAHLLFDVPLERIDVVVHPQSVVHSMVEFTDGSTLAQASPPDMRL +PIALGLAWPARVPGAAAGCDWTRAATWAFEPLDEDAFPAVRAAKEAAAASPTHMAVFNAV +NEEAVDAFHDGRIRFDAIVDTVRAVVGEYEPARVLGAAGHGHVAQDLTVEAVLAAEDWAR +TAARARW +>PROKKA_02154 +MTHGSLTDYTFPADHGPGASDGACRAVALVGSTGSIGTQGLDVIAQAPERFRAVALSGGA +NTALLAEQAVAHGVEAVGSAAASEEELRAALADAAARLRRPDPRPALFTGPEAAARIAAW +EGADTVLNGITGSIGLAPTLAALRAGHRLALANKESLIVGGALVKAAAAPGQLVPVDSEH +SALAQALRGGTAGEVRRLVLTASGGPFRGFSAAQLAEVTPAQALAHPTWDMGRVVTTNSA +SLVNKALEVIEAHLLFDVPLERIDVVVHSQSVVHSMVEFTDGSTLAQASPPDMRLPIALG +IGWPHRVLGAAAGCDWTQAAQWTFEPLDEAAFPAVSLAKEAAASSDTHMAVFNAANEEAV +DAFHGGRIRFDQIVETVRAVLGEYRPDGVLAAAGADPDELTVEAVLAAEDWARAAARGRW +>PROKKA_00640 +MTHGSLTDYTLPAPAPADDDGAPRAVALIGSTGSIGTQGLDVIAQDPARLRAVALAGGAN +TTLLAEQAVRFEVEAVGSAAAGEEELRAALADAAARLGRPAPRPVLFTGPRAAEQIAAWP +GADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAARPGQLVPVDSEHS +ALAQALRGGTADEVRRLVLTASGGPFRGLDRAALHAVTPAQALAHPTWDMGRVVTTNSAS +LVNKALEVIEAHLLFDVPLDRIDVVVHPQSVVHSMVEFVDGSTLAQASPPDMRLPIALGL +CWPRRLPGAAPACDWTRAATWTFEPLDEEAFPAVRAAKEAAAASPTHMAVFNAANEESVD +AFHAGALPFDGIVDTVRAVVADYAPEHVLAAAGHDPAPTGLTVDAVLAAEAWARRAARAR +W diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000601.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000601.fa new file mode 100644 index 0000000000000000000000000000000000000000..cf672f22d0384f53d25cf0dafeab43c3b48d652d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000601.fa @@ -0,0 +1,34 @@ +>PROKKA_00673 +MTRLPPVPRWSPSTDREVRAATGDRVRLLTDADTAALAALSARAPVSNVFVDSLLEAGRL +AGPRGGAAGTLFLGIDDDAPGAGALRAAVWIGSNVVPVAASEAPDAGWAPGDAEALGAAA +AALRRRYGSIYGPAGPVLAAGEALAAAGHRSRSVRPDQPLLVLGTAGGIDPNPHVVQAQP +HDFARVLPASAAMFEEELGFSPFAGGAAQYRDRVERLIHTGRVFIDPGPRDAGGPLRFKA +DIGLLSSRCAQIQGVWMAPAARGRGLAASAMAAVVDYVRLQAPVVSLYVNAYNTPALRTY +ERVGFERRGTFATVLY +>PROKKA_00410 +MTRLPPVPRWSPSTDREVRAATGDRVRLLTDADTAALAALSARAPVSNVFVDSLLEAGRL +AGPRGGAAGTLFLGIDDDAPGAGALRAAVWIGSNVVPVAASEAPDAGWAPGDAEALGAAA +AALRRRYGSIYGPAGPVLAAGEALAAAGHRSRSVRPDQPLLVLGTAGGIDPNPHVVQAQP +HDFARVLPASAAMFEEELGFSPFAGGAAQYRDRVERLIHAGRVFIDPGPRDAGGPLRFKA +DIGLLSSRCAQIQGVWMAPAARGRGLAASAMAAVVDYVRLQAPVVSLYVNAYNTPALRTY +ERVGFERRGTFATVLY +>PROKKA_02289 +MTRLPPVPRWSPSTDRQVRAATGGRVRLLTDADTPALAALSARAPVSNVFVDSLLEAGRL +AGPRGGAAGTLFLGIDAGEGRDDDGAPVAGLRAALWVGSNVVPVAAAETPDAGWAPGDAE +ALGAAAVALRRRYGSLYGPAEPVLAVGSALAAAGHRARSVREDQPLLVLGADGAAETSPH +VVQAHPRDFERVLPASAAMFEEELGFSPFLGGAAQYRDRVERLIRAGRVFIDPGPADAGG +PLRFKADIGLLSSRCAQIQGVWMAPAARGRGLAAAAMAAVVEYVRLQAPVVSLYVNAYNT +PALRTYERVGFERRGTFATVLY +>PROKKA_02151 +MDLAAASDGRVRVLTDADTPALTALAAADPVANVHAASLLEAGRLAGPRGGRADGTLFLG +VEDPDRPGALRSACWVGSTVVPLAGHDDDVPALAASVAALRRRFASVYGPAVTVLAVGRT +LRDAGHRPRAVREEQPLMVHARTPGDLVPDPAVRAAAPGEWESVVPASAAMFEEELGFSP +FLTGAAQYRDRVRRLVADGRVFTAPGEPVVDDPTSGVRFKADIGLLSASCVQVQGVWLHP +SRRGRGEAAPAMAAAVALMARRAPAVSLYVNGFNTPALRTYERVGFERVGTFATVLY +>PROKKA_00643 +MTRLPPVPRWSPSTDREVRAATGDRVRLLTDADTAALAALSARAPVSNVFVDSLLEAGRL +AGPRGGAAGTLFLGIDDDAPGAGGLRAAVWIGSNVVPVAASEAPDAGWAPGDAEALGAAA +AALRRRYGSIYGPAGPVLAAGEALAAAGHRSRSVRPDQPLLVLGTAGGIDPNPSVVQAQP +RDFARVLPASAAMFEEELGFSPFAGGAAQYRDRVERLIQAGRVFIDPGPRDAGGPLRFKA +DIGLLSSRCAQIQGVWMAPAARGRGLAVSAMAAVVDYVRLQAPVVSLYVNAYNTPALRTY +ERVGFERRGTFATVLY diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000604.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000604.fa new file mode 100644 index 0000000000000000000000000000000000000000..2af3aef3ee28f8d59263ff61bfad45e908817995 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000604.fa @@ -0,0 +1,25 @@ +>PROKKA_00676 +MDSTDRRDDLAELRTRVEEALAADDVVVEQVRATGTAEHRTVEVVLDRASGTQGLSLDDV +ARLSGRVSAALDALGDHVPGVGAGEYLLEVTTAGVDRPLTEPRHFARNVGRLVEVSVDGA +APVTARLKDVTDDDVELAVVRPPAKKGMKAKELPAERVALDRLGPAIVQVEWSPAQQAGD +ADAAAGEDTAEHTEA +>PROKKA_00413 +MDSTDRRDDLAELRTRVEEALAADDVVVEQVRATGTAEHRTVEVVLDRASGTQGLSLDDV +ARLSGRVSAALDALGDHVPGVGAGEYLLEVTTAGVDRPLTEPRHFARNVGRLVEVSVDGA +APVTARLKDVTDDDVELAVVRPPAKKGMKAKELPAERVALDRLGPAIVQVEWSPAQQAGD +ADAAAGEDTAEHTEA +>PROKKA_02286 +MDSTDRHDDAASLRARVEEALASADVVVEEVRVAGAAAHPTVEVVVDRASGTEGLSLDEL +AGLSGRVSAALDALGDHVPGVGAGEYLLELTTAGVDRPLTQPRHFARNVGRLVEVAVDGG +EPFTARLLAADEDAVELAEVRPGAKKGMKAKELPAQRVELARLGPAVVQVEWTPAQQAAD +AAAAGEQTAEHTEA +>PROKKA_02148 +METVPAALTELVEGAVSHRGVVVESVRVAGAADAPTVEVVLDRLEGTEGLSLDEVAELSG +LVSDALDACGDEVPGVGAGEYLLEVSTAGVDRPLTGPRHWLRNVGRLVEVSIDAALPVTA +RVLGVEASGVELEVVRPGAKKGMPAKVLPAEHVDFSRLGPGQVQVEWSTAAEQSGAEQTA +EQTEA +>PROKKA_00646 +MDSTDRRDDLAELRTRVEEALAADDVVVEQVRATGAAEHRTVEVVLDRASGTQGLSLDDV +ARLSGRVSAALDALGDHVPGVGAGEYLLEVTTAGVDRPLTEPRHFARNVGRLVEVSIDGA +APVTARLKDVTDDDVELAVVRPPAKKGMKAKELPAERVALDRLGPAIVQVEWSPAQQAGD +ADAAAGEDTAEHTEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000610.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000610.fa new file mode 100644 index 0000000000000000000000000000000000000000..f07a45f8c4d581d5fae49ab49c85c5c8a47b4d3a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000610.fa @@ -0,0 +1,20 @@ +>PROKKA_00683 +MAPSDGAPARNQGLGRIIVMVYAVFALSASARSLFQILTQFDAAPVAYTLSAVAAVVYIV +ATFALARSGARAWAVALGAVLVELAGVVGVGLWTVLDPGMFAHDTVWSRFGAGYGYVPLV +LPVVGLIWLLTHRPARPAEAGAL +>PROKKA_00420 +MAPSDGAPARNQGLGRIIVMVYAVFALSASARSLFQILTQFDAAPVAYTLSAVAAVVYIV +ATFALARSGARAWAVALGAVLVELAGVVGVGLWTVLDPGMFAHDTVWSRFGAGYGYVPLV +LPVVGLIWLLTHRPARPAEAGAL +>PROKKA_02280 +MARTRTASGAARPGAAAPARNQGLGRIIVMVYAVFALSATARSLFQILTDVEAAPVAYSL +SAFAATVYIVATLALARSGARAWAVALGAVLVELIGVVGVGLWTVLDPGLFAEETVWSRF +GAGYGYVPLVLPVVGLAWLLAHRPSRPTAEEMAR +>PROKKA_02141 +MVEQHPVADDGAPARPRRNQGLGRIIVMVYAVFALSASARSLFQILDHFWVAPFAYVLSA +FAAVVYIVATLALARSGPTAWKVAVAAVGVELAGVVGVGLLTVLDPQLFADATVWSRFGA +GYGYVPLVLPMVGLAWLLSHRPSREGRVR +>PROKKA_00653 +MAPSDGAPARNQGLGRIIVMVYAVFALSASARSLFQILTQFDAAPVAYTLSAVAAVVYIV +ATFALARSGARAWAVALGAVLVELAGVVGVGLWTVLDPGMFAHDTVWSRFGAGYGYVPLV +LPVVGLIWLLTHRPARPAEAGAL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000616.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000616.fa new file mode 100644 index 0000000000000000000000000000000000000000..16f7dd25683ab9d670895eb9e9b1535d25970eff --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000616.fa @@ -0,0 +1,45 @@ +>PROKKA_00689 +MSVHREIPLDFDGVLADEGNGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSRDES +PEGYGATHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDLPMA +VEVLTDMLTSSLIDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRPIGG +TPETIRAVTRDHVVGHYTHWYRPDELVVTAAGHLDHDEVCRLVLAALRASGWELTQGALP +APRRAVDTAGAAASRVRTGTHTVTKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLGGGM +SSRLFQEIRERRGLAYNTYSFSAGYSDAGYWGLYAGCQPDRVDEVAALMEAELDRMAEAD +VTGEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLARVREVDAGQVR +AVAARLAAGDRARVVVAPA +>PROKKA_00426 +MSVHREIPLDFDGVLADEGNGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSRDES +PEGYGATHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDLPMA +VEVLTDMLTSSLIDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRPIGG +TPETIRAVTRDHVVGHYTHWYRPDELVVTAAGHLDHDEVCRLVLAALRASGWELTQGALP +APRRAVDTAGAAASRVRTGTHTVTKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLGGGM +SSRLFQEIRERRGLAYNTYSFSAGYSDAGYWGLYAGCQPDRVDEVAALMEAELDRMAEAD +VTGEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLARVREVDAGQVR +AVAARLAAGDRARVVVAPA +>PROKKA_02266 +MAGMSIHREIPLDFTGVLADEGHGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSR +DESPEGYGSTHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDL +PMAVEVLTDMLTSSLLDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRP +IGGTPETIRAVTREHVAGHYARWYRPDELVVTAAGNLDHDEVCRLVLAALQASGWELAPG +ALPAPRRAVDTEGAAASRVLTGTHTVAKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLG +GGMSSRLFQEVRERRGLAYSTYSFSAGYSDAGYWGLYAGCQPDRVDEVSALMEAELDRMA +AEVVTEEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLERVRAVDAA +QVRAVAARLAAGERARVVVAPA +>PROKKA_02135 +MAGMTVQREIPLDFSGVLAEDRGAVVCRSVLPGGVRVLTESMPDQRSVTVGYWVAVGSRD +ESPEGYGSTHFLEHLLFKGTPTRTAMDIASAFDRVGGESNAGTAKESTVYHAHVLDEDLP +MAVEVLTDMVTSSLIDADELETERGVILEELAMDADDPVDVAHERLAAVLMDGHPLGRPI +GGTPETIRAVTREHVVAHYRHWYRPQELVITAAGNLDHDDVCRLVLDALERSGWDLAEGA +APAPRRTADAAGAGAVLAGTHTVAKQVEQANVIVGGQSLSTTDPDRFALGVMMSVLGGGM +SSRLFQEIRERRGLAYSTYSFSAGYSDGGYFGLYAGCQPERVDEVAALMEAELERMAAAE +VTAEELDRAHGQICGGTVLGMESTGARMSRLGRAELVTGEFVDLSASLARVRAVDAGRVR +AVAARLAAGERARVVVAPA +>PROKKA_00659 +MSVHREIPLDFDGVLADEGNGSVVRRSVLPGGVRVLTEAMPDQRSVTIGYWVAVGSRDES +PEGYGATHFLEHLLFKGTPTRTAMDIAAAFDRVGGESNAGTAKESTVYHARVLDEDLPMA +VEVLTDMLTSSLIDPDELETERGVILEELAMDADDPVDVAHEKLAEVMLDGHPLGRPIGG +TPETIRAVTRDHVVGHYTHWYRPDELVVTAAGHLDHDEVCRLVLAALRASGWELTPGALP +APRRAVDTAGAAASRVRTGTHTVTKAVEQANVLVGGRSLSTTDPDRFALGVMQSVLGGGM +SSRLFQEIRERRGLAYNTYSFSAGYSDAGYWGLYAGCQPDRVDEVAALMEAELDRMAEAD +VTGEELARAHGQICGGTVLGMESTGARMSRLGRAELVTGEYVDLAASLARVREVDAGQVR +AVAARLAAGDRARVVVAPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000618.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000618.fa new file mode 100644 index 0000000000000000000000000000000000000000..22ff44496d009469625077af3443ae1dcab5593d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000618.fa @@ -0,0 +1,20 @@ +>PROKKA_00691 +MDWTDTWTLAEPSRTPDDGAVGPPAPAVRARRSTVMSKVWVGFVCLLVLLFAGFALNASV +ALVRAPQPLAKAIGAGVILVVLVTVAVLAREVWFGRQTERLADQLEAEGGLPEDDLPRSP +GGRIDREAADAQFELYRVEAEAAPRDWRARYRLALAYDASGDRRRAREAAREAVRLHRAG +>PROKKA_00428 +MAEPSRTPDDGAVGPTEHAARARRSTVMSKVWVGFVSLLVLLFAGFALNASVALVRAPQP +LAKAIGAGVILVVLVTVAVLAREVWFGRQTERLADQLEAEGGLPEDDLPRSPGGRIDREA +ADAQFELYRVEAEAAPRDWRARYRLALAYDASGDRRRAREAAREAVRLHRAG +>PROKKA_02264 +MADRAPRPAEQTVADPAEHAARARRSTLMSKLWVGFVSLLVLFFASFAVYVAVAFIRAPQ +LLAKGIGVGVIFVVLVTVAVLAREVWFGQQTERLADLLEAEGGLPEDDLPRSPGGRIDRA +AADAQFEVYRVEAEAAPRDWRTRYRLALAYDASGDRRRAREAAREAVRLHRQG +>PROKKA_02132 +MASTDPRPGVDREQAPRAGSSTGAKLWVLFVAALTLFFAFFVVRAAVVFIAAGGVLPAVI +GVAVILVVLVGLGLLGREMLFGLQTERLARTLEAEGGLPADDLPRSPGGRIDRDAADAAF +ADAADEVRAAPEDWRARYRLSLAYDAAGDRRRAREAARQAISLASRRG +>PROKKA_00661 +MAEPSRTPDDGAVGPTEHAARARRSTVMSKVWVGFVSLLVLLFAGFALNASVALVRAPQP +LAKAIGVGVILVVLVTVAVLAREVWFGRQTERLADQLEAEGGLPEDDLPRSPGGRIDREA +ADAQFELYRVEAEAAPRDWRARYRLALAYDASGDRRRAREAAREAVRLHRAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000622.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000622.fa new file mode 100644 index 0000000000000000000000000000000000000000..cc9b95a8eec46edaad8f13e32de135c22f640606 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000622.fa @@ -0,0 +1,25 @@ +>PROKKA_00696 +MSAAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWGGDSLVARWVALALFAAAMY +TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT +LMRFVVIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPVVGGWWPWAGWVVIGAATVLTV +LTGLEYVKDAWVLRRDALAAQRGA +>PROKKA_00433 +MSTAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWGGDSLVARWVALALFAAAMY +TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT +LMRFVVIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPLVGGWWPWAGWVVIGAATVLTV +LTGLEYVKDAWVLRRDALAAQRGA +>PROKKA_02258 +MSTGGEAERVSAWNLPNILTSVRILMVPLFAWALWAGGPWGGDSATARWIAVALFAAAMY +TDKLDGDIARARGLITDFGKIADPIADKLLTGAALVLFSLLGELWWWVTVVILVREWGIT +LMRFVVIRYGVMPAGRGGKLKTVLQAVGIGLLLMPLAPVVGGWWPWVGWTVIGAATVLTV +LTGLEYVKDAWILRRDALAAPRGA +>PROKKA_02129 +MNAQPERVSAWNLPNILTTVRILMVPFFVWAVWAGGPWGQDSLTARWIAVALFAAAMYTD +KLDGDIARSRGLITDFGKIADPIADKLLTGSALVLFALLGELWWWVVIVILVREWGITAM +RFVVIRYGVMPAGRGGKLKTVLQAVGIGLLLMPLAPVLGGWWPWLGWTVIGAALALTVVT +GVEYVRDAVRLRADWLASHPEARR +>PROKKA_00666 +MSTAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWSGDSLLARWVALALFAAAMY +TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT +LMRFVMIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPLVGGWWPWAGWVVIGAATVLTV +LTGLEYVKDAWVLRRDALAAQRAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000623.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000623.fa new file mode 100644 index 0000000000000000000000000000000000000000..866c2e1937a252bffbf9d81c75b9af64213fc5ad --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000623.fa @@ -0,0 +1,22 @@ +>PROKKA_00697 +MAGAQDVVHALAHAGRTVATGESLTAGLLAARLADVPGASAVLHGGVVAYQNAVKTGLLG +VPEDLLARVGAVDADVARRMALGARAALGADVGVATTGVAGPEPHQGQPVGTVWLGLAVP +DADANALDVLGGERDGAATAILLRLDGDRAAIREATVAAALQALTRLLAVRGH +>PROKKA_00434 +MAAARDVVHALADAGLTVATGESLTAGLVAARLADVPGASAVLHGGVVAYQNAVKTGLLG +VPEDLLARVGAVDADVARRMALGARAALGADVGVATTGVAGPEPHQGQPVGTVWLGLAVP +DADASALDVFGGERDGAATAILLRLDGDRAAIREATVAAALQALTRLLAGRGH +>PROKKA_02257 +MAAQETVRALAGAGLTVATAESLTAGLVAARLADVPGASAVLQGGVVAYQNSVKAGLLGV +PADLLERVGAVDPEVARRMAEGARAGLGADVGVATTGVAGPEPHQGRPVGTVWLGVAVPE +RLTAALDGLGGERRGAATAIPLALDGDRRAIREATVAAALAALTRLGAPVGERATGEGAA +GEPCAGA +>PROKKA_02128 +MSTGVGAVAAEGEAADPARAAVRALTTAGLTVATAESLTAGLVAARLADVPGASAALQGG +VVAYQNHVKAGLLGVDAGLLTARGAVDPEVARQMACGARRAAGADVGVATTGVAGPEPHQ +GKPVGTVFVGVAVPAELAPALAGLDGEPGAGEAAPGEAGSGGSEAGVAAAAFALTLPGNR +AEIRAATVETVLDLLAALGTTGRGMPDEAPALS +>PROKKA_00667 +MTTAAARDVVHALADAGLTVATGESLTAGLVAARLADVPGASAVLHGGVVAYQNAVKTGL +LGVPEDLLARVGAVDADVARRMALGARAALGADVGVATTGVAGPEPHQGQPVGTVWLGLA +VPDADASALDVLGGERDGAATAILLRLDGDRAAIREATVAAALQALTHLLAGPGH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000624.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000624.fa new file mode 100644 index 0000000000000000000000000000000000000000..51557407c31526e229497b0ca4468031c0775229 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000624.fa @@ -0,0 +1,17 @@ +>PROKKA_00699 +MPLLRHEIGDVLRDVRQLQGRTLREVSHDARVSLGYLSEVERGQKEASSELLASICQALD +IPLSYLLREVSDRLVEQEGMVVPDTLPDDLTDPSLGSLAGR +>PROKKA_00436 +MPLLRHEIGDVLRDVRQLQGRTLREVSHDARVSLGYLSEVERGQKEASSELLASICQALD +IPLSYLLREVSDRLVEQEGMVVPDTLPDDLTDPSLGSLAGR +>PROKKA_02255 +MMRHPVQAHGITRWVDDQPRPRATTPDIKERSMPLLRHEIGDVLRDVRQLQGRTLREVSH +DARVSLGYLSEVERGQKEASSELLASICQALEIPLSYLLREVSDRLVDQEGIQVPDTLPE +DLTDAADPSLGTLAGR +>PROKKA_02127 +MMRHPVQAHGITRWVDSQPRPSQPTPELKERSMPILRHEIGDVLRDVRQRQGRTLREVSH +DARVSLGYLSEVERGQKEASSELLASICDALQIPLSFLLREVSDRLAEQEGVVVPDTVPA +DMAEDGAADVAPLAVR +>PROKKA_00669 +MPLLRHEIGDVLRDVRQLQGRTLREVSHDARVSLGYLSEVERGQKEASSELLASICQALD +IPLSYLLREVSDRLVEQEGMVVPDTLPDDLTDPSLGSLAGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000628.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000628.fa new file mode 100644 index 0000000000000000000000000000000000000000..28c70406c6ce8d0ece55f2c18d0b935cee7728af --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000628.fa @@ -0,0 +1,49 @@ +>PROKKA_00706 +MTLTDPTPRTTPLAQDGAAARPHEGLTYEVRTFGCQMNVHDSERISGLLESTGYAPVAED +AQADLVVFNTCAVRENADNRLYGNLGNLRAVKDAHPGMQIAVGGCLAQKDQAAIQRRAPW +VDVVFGTHNIGSLPVLLERSRHNAEAEIEILESLEVFPSTLPTKRDSTHSGWVSISVGCN +NTCTFCIVPSLRGKEKDRRPGEILAEVQALVDAGAVEVTLLGQNVNTYGVEFGDRGAFAK +LLRACGEIEGLERVRFTSPHPAAFTDDVIDAMAETPNVMPQLHMPLQSGSDKVLKDMRRS +YRSAKFLRILEKVRERIPHAAITTDIIVGFPGETEEDFAETMRVVEASRFSSAFTFQYSI +RPGTPAGEMDHQVPKAVVQERFERLVALQDRISAEEMATLVGTRQELLVTADSGSKAAER +GRLSGRAPDNRLVHFSVPAGAETPRPGDFVTVTVTEAHPFFAVADPTAQDYVLRRSRAGD +AWDRAQAESCGAPAPGTAGGSGATSLGMPTLRPRS +>PROKKA_00440 +MTLTDPTPRTTPLAQDGAAARPHEGLTYEVRTFGCQMNVHDSERISGLLESTGYAPVAED +AQADLVVFNTCAVRENADNRLYGNLGNLRAVKDAHPGMQIAVGGCLAQKDQAAIQRRAPW +VDVVFGTHNIGSLPVLLERSRHNAEAEIEILESLEVFPSTLPTKRDSTHSGWVSISVGCN +NTCTFCIVPSLRGKEKDRRPGEILAEVQALVDAGAVEVTLLGQNVNTYGVEFGDRGAFAK +LLRACGEIEGLERVRFTSPHPAAFTDDVIDAMAETPNVMPQLHMPLQSGSDRVLKDMRRS +YRSAKFLRILEKVRERIPHAAITTDIIVGFPGETAEDFAETMRVVEASRFSSAFTFQYSI +RPGTPAGEMDHQVPKAVVQERFERLVALQDRISAEEMATLVGTRQELLVTADSGSKAAER +GRLSGRAPDNRLVHFSVPAGAETPRPGDFVTVTVTEAHPFFAVADPTAQDYVLRRSRAGD +AWDRAQAESCGAPAPGTAGGSGATSLGMPTLRPRS +>PROKKA_02251 +MNVHDSERISGLLESTGYAPVPQDAQADLVVFNTCAVRENADNRLYGNLGNLRAVKDARP +GMQIAVGGCLAQKDQATIQRKAPWVDVVFGTHNIGSLPVLLERSRHNAEAEIEILESLEV +FPSTLPTKRDSTHSGWVSISVGCNNTCTFCIVPSLRGKEKDRRPGEILAEVQALVDAGAV +EVTLLGQNVNTYGVEFGDRGAFAKLLRACGQIEGLERVRFTSPHPAAFTDDVIDAMAETP +NVMPQLHMPLQSGSDTVLKAMRRSYRSKRFLGILEKVRERIPHAAITTDIIVGFPGETEE +DFQDTMRVVEASRFSSAFTFQYSIRPGTPAGEMADQVPKAVVQERFERLVALQDRISAEE +MATLVGTRQELLVTADSGTKASERGRLSGRARDNRLVHFSVPAGAPTPRPGDFVTVTVTE +AHPFFAVADPAPEDYSLRRSRAGDAWDRAQAESCGVPTPGASGGAGATSLGMPTLRPRS +>PROKKA_02123 +MTLTDPTTHLPALGTAPDAHAGLTYEVRTFGCQMNVHDSERISGLLESTGYTPAEDGTQP +DLVVFNTCAVRENADNRLYGNLGNLRPVKDAHPGMQIAVGGCLAQKDQATIQEKAPWVDV +VFGTHNIGSLPALLERSRHNAEAEMEILESLEVFPSTLPTKRESTHSGWVSISVGCNNTC +TFCIVPSLRGKEKDRRPGEILAEVQALVDAGAVEVTLLGQNVNTYGVEFGDRGAFAKLLR +ACGEIDGLERVRFTSPHPAAFTDDVIDAMAETPNVMPQLHMPLQSGSDKVLKDMRRSYRS +AKFLRILEKVRERIPHAAITTDIIVGFPGETEEDFAETMRVVEASRFSSAFTFQYSIRPG +TPAGEMDHQVPKAVVQERFERLVALQDRISAEEMATLVGTRQELLVTADSGSKATERGRL +SGRAPDNRLVHFSVPAGAETPRPGDFVTVTVTEAHPFFAVADPTAQDYVLRRSRAGDAWD +RAQAESCGAPAPGAAGGSGATSLGMPTLRPRF +>PROKKA_00673 +MTLTDPTPRTTPLAQDGAAARPHEGLTYEVRTFGCQMNVHDSERISGLLESTGYAPVAED +AQADLVVFNTCAVRENADNRLYGNLGNLRAVKDAHPGMQIAVGGCLAQKDQAAIQRRAPW +VDVVFGTHNIGSLPVLLERSRHNAEAEIEILESLEVFPSTLPTKRDSTHSGWVSISVGCN +NTCTFCIVPSLRGKEKDRRPGEILAEVQALVDAGAVEVTLLGQNVNTYGVEFGDRGAFAK +LLRACGEIEGLERVRFTSPHPAAFTDDVIDAMAETPNVMPQLHMPLQSGSDKVLKDMRRS +YRSAKFLRILEKVRERIPHAAITTDIIVGFPGETEEDFAETMRVVEASRFSSAFTFQYSI +RPGTPAGEMDHQVPKAVVQERFERLVALQDRISAEEMATLVGTRQELLVTADSGSKAAER +GRLSGRAPDNRLVHFSVPAGAETPRPGDFVTVTVTEAHPFFAVADPTAQDYVLRRSRAGD +AWDRAQAESCGAPAPGTAGGSGATSLGMPTLRPRS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000631.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000631.fa new file mode 100644 index 0000000000000000000000000000000000000000..55de8b692d4b265f5a26cf50fd0689609bc8acbc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000631.fa @@ -0,0 +1,25 @@ +>PROKKA_00709 +MVAVSSASHYFDADPSAPERRRTVRTRLAGRDVEVQTANGIFSPDGLDKGTAALFSAVPA +PPARGRFLDVGAGWGPIALTLALRSPEAEVTAVEVNDRSLQLTRDNAAALGLDNLVALRP +EDVPEGAEFDLIWSNPPIRIGKPALHALLERWLPRLAPGGEAWLVVQKNLGADSLLPWIG +RMLEERAPGRFTAERADSVKGFRILRVARAR +>PROKKA_00443 +MVAVSSASHYFDADPSAPERRRTLRTRLAGRDVEVQTANGIFSPDGLDKGTAALFSAVPA +PPATGRFLDVGAGWGPIALTLALRSPEAEVTAVEVNDRSLQLTRDNAAALGLDNVVALRP +EDVPEDAEFDLIWSNPPIRIGKPALHALLERWLPRLAPGGEAWLVVQKNLGADSLLPWIG +RMLEERAPGRFTAERADSVKGFRILRVVRAR +>PROKKA_02246 +MVAVTSPAHYFSPDPGTPERRRSVDVELAGRRVTLQTANGVFSPDGIDKGTAALLSAVPA +PPARGAFLDVGAGWGPLALTLALASPEAEVTGVEVNERSLALARDNAAAVGASNARFLTP +EQIPDDARFDLIWSNPPIRIGKAALHDLLAQWLPRLAPGGEAWLVVQKNLGADSLLPWIA +GMLQEQAPGEFTATRAATVKGFRILRISRAAESSS +>PROKKA_02119 +MDAVTSPAHYFSPDPGTPERRRRVDVEIAGRRVTLQTANGVFSPDGIDKGTAALLSAVPA +PPARGAFLDVGAGWGPLALTLALTSPEAEVTGVEVNERSLALARDNAAAVGAQNARFLTP +EQVPDDARFDLIWSNPPIRIGKAALHDLLAQWLPRLAPGGEAWLVVQKNLGADSLLPWIS +GMLQERAPGEFTATRAATVKGFRILRISRAAESSS +>PROKKA_00676 +MVAVSPASHYFDADPSAPERRRTLRTRLAGRDVEVQTANGIFSPDGLDKGTAALFSAVPA +PPATGRFLDVGAGWGPIALTLALRSPEAEVTAVEVNDRSLQLTRDNAAALGLDNVVALRP +EDVPEDAEFDLIWSNPPIRIGKPALHALLERWLPRLAPGGEAWLVVQKNLGADSLLPWIG +RMLEERAPGRFTAERADSVKGFRILRVVRAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000632.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000632.fa new file mode 100644 index 0000000000000000000000000000000000000000..66b84cd4a27f698b09f8e8c477cfa8a102fc08ab --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000632.fa @@ -0,0 +1,37 @@ +>PROKKA_00710 +MGRTQWPLTDEFAGQRVVIVGMGVSATQLLAEISTVADTLWVTRREPRWQDSAAPGALAE +SVRGVDERTRAGLPPGSVVGATGMHRSSWVREAESRGVLVRHPMFTAVEPDGVRMPDGSF +EPADVILWATGFRPAIRHLAPLRLRTPAGGIRVAGGRALDEPRLFLLGYGPSQSTVGANR +AGRDAVRAILADLAGPASG +>PROKKA_00444 +MGVECTGRRVWATGAPAPGPLTTRTYPAGMTASPSPAPPRPGRTGRATVVVIGAGQAGLS +AAYHLRRRGFVGLGPNDDGAAGVPDDAPGTFVVLDAETAPGGAWQHRWDSLTMATVNHIH +ELPGDPVPPADPAAHANTLLPAYFADYEARFALPIRRPVRVRRVERIGEPGRARGFFVRT +DGAPGTWRADFVVNATGTWTSPRWPSVPGMRSFRGRQLHTRDYVSKDEFAGQRVVIVGMG +VSATQLLAEISTVADTLWVTRREPQWQDSAAPGALAESVRGVDERTRAGLPPGSVVGATG +MHRSSWVREAETRGVLVRHPMFMAVEPDGVRMPDGSFEPADVILWATGFRPAIRHLAPLR +LRTPAGGIRVAGGRALDEPRLFLLGYGPSQSTVGANRAGRDAVRAILADLAGPASG +>PROKKA_02245 +MRTILAADRRRRHPSPVGEHAPAVPTLGRMTPHPDRHVTVLVVGAGQAGLSAAHHLRRRG +FQPVGPGEAPRPAPEGSPGTFAVLDAEDRPGGAWLHRWDTLTMGSVNHIHELPGHPVPPA +DPAARANAVLPAYFAEYEERFDLRVHRPVRVSRVERIGEPGAAEGFRVHTDAGTWTCGFL +VNATGTWTSPHWPAVPGRREFRGRQLHTHDYRDPEEFARRRVVVVGMGVSATQHLAEVSR +VADTLWVTRREPRWIDDPDPGHLAESVEGVDERTRLGLAPRSVVSATGMFRSDWVREAQA +RGVLERHPMFERIEPDGVRMPDGSLERADVILWATGFRPAVRHLAPLRLRTPDGGIRAAH +GRALDEPRLFLIGYGPSQSTVGANRAGRDAVRAILADLRAAGAA +>PROKKA_02118 +MTPHPDRHVTVLVVGAGQAGLSAAHHLRRRGFLPVGPGEAPGPAPGGSPGTFAVLDAEDR +PGGAWLHRWDTLTMGSVNHIHELPGHPVPPADPDAQANAVLPAYFAEYEERFDLRVHRPV +RVSRVERIGEPGAAEGFRVHTDTGTWTCGFLVNATGTWTSPHWPAVPGRREFRGRQLHTH +DYRGPQEFAGRRVVVVGMGVSATQHLAEVSRVADTLWVTRREPRWIDDPDPGHLAESVEG +VDERTRLGLAPRSVVSATGMFRSDWVREAQARGVLERHPMFERIEPDGVRMPDGSLERAD +VILWATGFRPAVRHLAPLRLRTPDGGIRAAHGRALDEPRLFLIGYGPSQSTVGANRAGRD +AVRAILADLRAAGAA +>PROKKA_00677 +MGVECTGRRVWATGAPAPGPLTTRTYPAGMTASPSPAPPRPGRTGRATVVVIGAGQAGLS +AAYHLRRRGFVGLGPNDDGAAGVPDDAPGTFVVLDAETAPGGAWQHRWDSLTMATVNHIH +ELPGDPVPPADPAAHANTLLPAYFADYEARFALPIRRPVRVRRVERIGEPGRARGFFVRT +DGAPGTWRADFVVNATGTWTSPRWPSVPGMRSFRGRQLHTRDYVSKDEFAGQRVVIVGMG +VSATQLLAEISTVADTLWVTRREPQWQDSAAPGALAESVRGVDERTRAGLPPGSVVGATG +MHRSSWVREAETRGVLVRHPMFMAVEPDGVRMPDGSFEPADVILWATGFRPAIRHLAPLR +LRTPAGGIRVAGGRALDEPRLFLLGYGPSQSTVGANRAGRDAVRAILADLAGPASG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000639.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000639.fa new file mode 100644 index 0000000000000000000000000000000000000000..dcbffdf1c730331ceab76cfe3584dd899b94cac3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000639.fa @@ -0,0 +1,25 @@ +>PROKKA_00720 +MARPTTVPGVRPRVAVLDYGSGNVHSALRAVERAGAEVELTRDPQAVQEADGLLVPGVGA +YASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERTAGMGEWPGVVAE +LPAEVLPHMGWNTVRPPEGSALFAGIEDERFYFVHSYGVLEWEFDQTISAMRPPQVTWAH +HGADFIAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL +>PROKKA_00451 +MARPTTVPGVRPRVAVLDYGSGNVHSALRAVERAGAEVELTRDPQAVQEADGLLVPGVGA +YASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERTAGMGEWPGVVAE +LPAEVLPHMGWNTVRPPEGSALFAGIEDERFYFVHSYGVLEWEFDQTISAMRPPQVTWAH +HGADFIAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL +>PROKKA_02238 +MARPTSVPGVRPSVAVLDYGSGNVHSAVRALERAGADVELTRDPEAVQSADGLLVPGVGA +FASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERAEGMGEWPGVVEA +LPAEVLPHMGWNTVRPPEGSALFAGIEDERFYFVHSYGVLRWEFDQTISAMRPPQVTWAH +HGADFVAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL +>PROKKA_02110 +MASPTSVPGVRPTVAVLDYGSGNVHSAVRAVEHAGARVELTKDPDAVLGADGLVVPGVGA +FASVMEALRSSGGTRWIGRRVAGGRPVLGICVGHQVLFEAGVEHGVRTEGMGEWPGVVEP +LPAATVPHMGWNTVRPAEGSALFAGIEDERFYFVHSYAVQSWEFDQGNEAMRPPQVTWSH +HGADFIAAVENGPLSATQFHPEKSGDAGQALLRNWLETL +>PROKKA_00684 +MARPTTVPGVRPRVAVLDYGSGNVHSALRAVERAGAEVELTRDPQAVQEADGLLVPGVGA +YASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERTAGMGEWPGVVAE +LPAEVLPHMGWNTVRPAEGSALFAGIEDERFYFVHSYGVLEWEFDQTISAMRPPQVTWAH +HGADFIAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000640.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000640.fa new file mode 100644 index 0000000000000000000000000000000000000000..b73c0c70d4f29e5f0e2351d7fc00e5a08bf86e73 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000640.fa @@ -0,0 +1,10 @@ +>PROKKA_00721 +MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVGA +>PROKKA_00452 +MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVGA +>PROKKA_02237 +MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVAR +>PROKKA_02109 +MPYWSVLYLGLGGILLGAAWSMRTQKAPTWAVVIALVLAAMAVAAAFLTV +>PROKKA_00685 +MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000641.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000641.fa new file mode 100644 index 0000000000000000000000000000000000000000..105cac119d56ad6e19ec50cab85617a7a1905352 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000641.fa @@ -0,0 +1,30 @@ +>PROKKA_00722 +MTPNAPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPVTAALDWQRAGAEWIHLVDLDA +AFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPDWTAR +VIERFGDRVAVGLDVRGTTLAARGWTKEGGDLWEVLARLEDAGCARYVVTDVTKDGTLKG +PNTELLAQVCAKTAKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQAL +AVAGGATVEQARSEQPGPVAP +>PROKKA_00453 +MTPNAPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPVTAALDWQRAGAEWIHLVDLDA +AFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPDWTAR +VIERFADRVAVGLDVRGTTLAARGWTKEGGDLWEVLARLEDAGCARYVVTDVTKDGTLKG +PNTELLAQVCAKTAKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQAL +AVAGGATVEQARSEQPGPVAP +>PROKKA_02236 +MTPNPAAPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPLTAALDWQRAGAEWIHLVDL +DAAFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPAWT +ARVIERFGDKVAVGLDVRGTTLAARGWTQEGGDLWEVLARLEDAGCSRYVVTDVTKDGTL +KGPNTELLAQVCARTDKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQ +ALAVAGGATVEQARAEQPGPVAE +>PROKKA_02108 +MTETTPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPLTAALDWQDAGAEWIHLVDLDA +AFGRGDNRDVLRRVVDEIGVKIELSGGIRDDASLENALAMGAARVNLGTAALEDPAWTAR +AIERFGNRVAVGLDVRGTTLAARGWTQDGGDLWEVLARLEEAGCARYVVTDVTKDGTLRG +PNRELLARMCAATDKPVVASGGISSLEDIAALAAMVPQGVEGAIMGKALYAGRFSLEQAL +AVAAGATVERAREQHPFQAAP +>PROKKA_00686 +MTPNAPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPVTAALDWQRAGAEWIHLVDLDA +AFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPDWTAR +VIERFADRVAVGLDVRGTTLAARGWTKEGGDLWEVLARLEDAGCARYVVTDVTKDGTLKG +PNTELLAQVCAKTAKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQAL +AVAGGATVEQARSEQPGPVAP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000647.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000647.fa new file mode 100644 index 0000000000000000000000000000000000000000..e89616ec5cbcc65bf240f176fe6a77e174f3f1c6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000647.fa @@ -0,0 +1,25 @@ +>PROKKA_00728 +MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD +VVDGDDGRVLFRLADPATFGRDRFAILDADGLPFANLVRQIAFLRTSVNVEVVDGTCFAV +TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA +LDLIRAKDRRSNG +>PROKKA_00459 +MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD +VVDGDDGRVLFRLADPATFGRDRFAILDADGLPLAHLVRQFAFLRTSVNVEVVDGTCFAV +TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA +LDLIRAKDRRSNG +>PROKKA_02229 +MNTAFDAGRLGRTDVLTLQQVTSFMSNDMQVTGPDGQTVATVVTTGGGLGRMVLGSRTFD +VVDGEDGRVLFRLADPATFGRDRYAIVDADGLPLANLVREFALFRTSVSVEVVDGTRFAV +TGNLWDHDYTMTVGQAPIARATATFGGFMNALAGRSRYELRLDPGMPPVVRCAVLGTAIA +LDLIRAKDRRRNN +>PROKKA_02102 +MTTFDAGRLALVNSLALQQVTSFLSNDMQVLGPDGEVVATVQTQGGGLSRMLMGSRRLLV +CDGDDGRPLFELQDPATFGRDRFQVLDPAGLPLANLRREVAFFRTAVSVEVVDGTVFRVE +GDLFDHDYRMIAGEVPIARAVSQWSGFGNALLGRSRYRLELDPAMPPVVRCAVLGTAIAL +DLLRAKDARRND +>PROKKA_00692 +MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD +VVDGDDGRVLFRLADPATFGRDRFAILDADGLPFANLVRQIAFLRTSVNVEVVDGTCFAV +TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA +LDLIRAKDRRSNG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000648.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000648.fa new file mode 100644 index 0000000000000000000000000000000000000000..112533f4480442252d3513584b2801d166ebc98f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000648.fa @@ -0,0 +1,46 @@ +>PROKKA_00729 +MDFGAYGRLLQDPRIRHLLAVGFIARFPHTAAGVILTLHVALTLGLGYGQAGLAGAAMTL +GIAVGSPWRGRVVDAKGLRRALLPSVIAEAVIWPIVPWLPFWPMLLAVFLGGVFSLPIFS +VVRQGLGVLTHGKDRQTAFALDSIVTETIFMMGPALGAVVAATWSSALGLTIVGLSSALG +GILLMWFNPPTRSSQLAVVGPATEDPYTEEQDRQEAIAQAVTAAPMHVEMAAPSLATGAL +PAITEAIPLVTGSLPVIAADGSGPTTAPRRARAERLRQWRRTHFSWVGPEVLGVLVVSMA +AGIVMVGTEVSMVAELESQGAAASVGLVYAFWCGASAVGGLFYGAWGRQVHPYLLMALFA +VATVPLALVDGVWALALASIPSGLLTAPTLASASSRLSHLVVEERRGEAMGFYGSAMTAG +AAMGAPLAGVFIDGVAPSAGYVFAAAAGFVLVLLAALATVMRGRRPA +>PROKKA_00460 +MDFGAYGRLLQDPRIRHLLAVGFIARFPHTAAGVILTLHVALTLGLGYGQAGLAGAAMTL +GIAVGSPWRGRVVDAKGLRRALLPSVIAEAVIWPIVPWLPFWPMLLAVFLGGVFSLPIFS +VVRQGLGVLTHGKDRQTAFALDSIVTETIFMMGPALGAVVAATWSSALGLTIVGLSSALG +GILLMWFNPPTRSSQLAVVGPATEDPYTEEQDRQEAIAQAVTAAPMHVEMAAPSLATGAL +PAITEAIPLVTGSLPVIAADGSGPTTAPRRARAERLRQWRRSHFSWVGSEVLGVLVVSMA +AGIVMVGTEVSMVAELESQGAAASVGLVYAFWCGASAVGGLFYGAWGRQVHPYLLMALFA +VATVPLALVDGVWALALASIPSGLLTAPTLASASSRLSHLVEEERRGEAMGFYGSAMTAG +AAMGAPLAGVFIDGVAPSAGYVFAAAAGFVLVLLAALATVARGRRSA +>PROKKA_02226 +MGFIARFPHTAAGVILTLHVALTLDLGYGQAGLAAAAMTLGIAVGSPWRGRVVDAKGLRR +ALLPSVIAEALIWPLVPWLPFWLMLVAVFFGGVFALPIFSVVRQGLGVLTHGRDRQTAFA +LDSIITETIFMVGPALGAVVAATWSSALGLTIVGLSSALGGVLLMWFNPPTRSSQLAVVG +PETEDPYTEDEDREEAVAQTVHGAPMHVEMTAPSLATGALPVVTEAIPLVTGALPVIAAD +GSGPATPTPGLTRAERLRLWRARHFAWVGPEALGVLVVSMAAGLVMVGTEVTMVAELEHA +GMAGSVGVVYAFWCGASAVGGLFYGAWGRQVHPYLLMGLLALLTLPMAFVDGLWALALAA +IPSGLFTAPTLASASSRLSTLVPEERRGEAMGFYGSAMTAGAAMGAPLSGVFIDAIHPAA +GYVFAGLAGAVLVLAAALVTLARRRRVGGTSA +>PROKKA_02100 +MDFRAYGRLLQDPRIRNLLAVGFIARFPHTAAGVILTLHVAVTLGLGYGQAGLAAAAMTL +GIACGSPWRGRAIDRDGLRRALLPSVVAEAVIWPVVPWLPFGFLLVAVFFGGLFAVPIFS +VVRQGLGVLTHGADRQTAFTLDSIITELVFMVGPALGAVIAATGSTALGLTVVGLSGALS +GALLMWFNPPTRSTQLAADGPSAGDPFTEEEDREQALSQAVHTAPVRATVAAADLATGAL +PVVTEAVPIVTGSLPVIAADGSGPVSPAPRAGRHDDGRAADGLTRDERWRLWRVRHFGWV +TPEVLGVLVVAMAAGIALVGTEVTMVAELEHAGQEASVGVVYAFWCGASALGGLFYGAWG +RQVHPYLLGALFALAVAPMAFVDGLWALAWASVPSGLLTAPTLAAASSRISLLVSEERRG +EAMGYYGSAMTAGSALGAPVVGLVIDGVGPGAGYVGAAGAAVVMIGAAAILTAARRRRSP +ARG +>PROKKA_00693 +MDFGAYGRLLQDPRIRHLLAVGFIARFPHTAAGVILTLHVALTLGLGYGQAGLAGAAMTL +GIAVGSPWRGRVVDAKGLRRALLPSVIAEAVIWPIVPWLPFWPMLLAVFLGGVFSLPIFS +VVRQGLGVLTHGKDRQTAFALDSIVTETIFMMGPALGAVVAATWSSALGLTIVGLSSALG +GILLMWFNPPTRSSQLAVVGPATEDPYTEEQDRQEAIAQAVTAAPMHVEMAAPSLATGAL +PAITEAIPLVTGSLPVIAADGSGPTTAPRRARAERLRQWRRTHFSWVGPEVLGVLVVSMA +AGIVMVGTEVSMVAELESQGAAASVGLVYAFWCGASAVGGLFYGAWGRQVHPYLLMALFA +VATVPLALVDGVWALALASIPSGLLTAPTLASASSRLSHLVVEERRGEAMGFYGSAMTAG +AAMGAPLAGVFIDGVAPSAGYVFAAAAGFVLVLLAALATVMRGRRPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000649.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000649.fa new file mode 100644 index 0000000000000000000000000000000000000000..d4c5a5b7aa4c04b88523e930b3c729029f18d0e9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000649.fa @@ -0,0 +1,25 @@ +>PROKKA_00730 +MAQIVLFHHALGLTDGVRALAEQIASGGHTVHTPDLYDGRTFATVDEGVAHAQHLGFEEI +GRRGMRACAEHQEASVVAGISMGVMPAWRAAQVVPGFRACIAMAGVLALDAYAPLWQPHT +ALQIHLGTRDPWALEGDLATARSYAATAEHPDRPADLFEYDTDRHLFMNSSTADFDADLT +AVLVRRIHELLA +>PROKKA_00461 +MAQIVLFHHALGLTDGVRALAEQIAGGGHTVHTPDLYDGRTFATVDEGVAHAQHIGFEEI +GRRGMRACAEHQEASVVAGISMGVMPAWRAAQVVPGFRACIAMAGALALDAYAPLWQPHT +ALQIHLGTRDPWALEGDLETARSYAATAEHPDRPADLFEYDTDRHLFMDSSTADFDADLT +AVLVRRIHELLA +>PROKKA_02223 +MAQILLFHHALGLTDGVRALAAQIEAGGHTVHTPDLYDGALFTDVEEGIAHVESLGGFDV +IAERGMRAAAQHPQASVVAGISMGVVAAHKAAQAVPAFRACIDIAGIVPLDAFAPLWQPH +TALQVHLATRDPWVMDEDLPLARSVAATEEDPDKPAVLFEYDTDAHLFMDSSTDGHDPAL +TEVLVRRIHELLA +>PROKKA_02099 +MAQIILFHHARGLTEGVLALAEQIEQASGHHVHTPDLFGGAVLPTVEDGLAHLQQIGQDE +VMTRAMHACAEHKEASVVAGISMGVMPAWKAAQTAPGFRACIAMSSALPLDAYARLWQPH +TSLQIHLAAQDPWVKDEDLPLARTYAATAEHPDRPADLFEYETASHLFMDSSTDQYDARH +TEVMVERIRELLA +>PROKKA_00694 +MAQIVLFHHALGLTDGVRALAEQIASGGHTVHTPDLYDGRTFATVDEGVAHAQHLGFEEI +GRRGMRACAEHQEASVVAGISMGVMPAWRAAQVVPGFRACIAMAGVLALDAYAPLWQPHT +ALQIHLGTRDPWALEGDLETARSYAATAEHPDRPADLFEYDTDRHLFMDSSTADFDADLT +AVLVRRIHELLA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000650.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000650.fa new file mode 100644 index 0000000000000000000000000000000000000000..272d7701b1cd6caa3880ae736f327f25be02ca4d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000650.fa @@ -0,0 +1,40 @@ +>PROKKA_00732 +MDAVRILEDEIREIVRRQGIDPQREHARVLTLIQDAAADYESRAMVSSLPDLEDPVAARQ +DLFDRIAGLGPLQRLMDDPSVEEIWLNAPDAVYCARSGRSELTGIVLTEEEVQDLVEVML +KSSGRRLDLSMPFVDAALPDGSRLHVAIPDITRRHWAVNIRKFIARARRLDDLVRGGSLT +PTAARFLDAAVDAGMNILVSGATQAGKTTLLNCLASAIGPRERVITVEEIFELQIPVRDV +VGLQCRQPNLEGHGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI +HANSAADALTKLCTLPLLAGENISRDFVVPTVATCIDVVVHCERDRQGRRRVREILTVGS +RVEGGVIETSALFQRDAEGDLRLNEGANLEFEALARRGVDVHELVGLR +>PROKKA_00463 +MDAVRILEDEIREIVRRQGIDPQREHARVLTLIQDAAADYESRAMVSSLPDLEDPVAARQ +DLFDRIAGLGPLQRLMDDPSVEEIWLNAPDAVYCARSGRSELTGIVLTEEEVQDLVEVML +KSSGRRLDLSMPFVDAALPDGSRLHVAIPDITRRHWAVNIRKFIARARRLDDLVRGGSLT +PTAARFLDAAVDAGMNILVSGATQAGKTTLLNCLASAIGPRERVITVEEIFELQIPVRDV +VGLQCRQPNLEGHGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI +HANSAADALTKLCTLPLLAGENISRDFVVPTVATCIDVVVHCERDRQGRRRVREILTVGS +RVEGGVIETSALFQRDAEGDLRLNEGANLEFEALARRGVDVHELVGLR +>PROKKA_02221 +MDAVRILEDEIREVVRRQGIDPQREHARVIALIQDAAADYESRAEVSALPDLEDPAAARQ +DLFDRIAGLGPLQRLMDDPSVEEIWLNAPDAVYCARAGRSELTGIVLTEEEVHDLVEVML +KSSGRRLDLSMPFVDAALPDGSRLHVAIPDITRRHWAVNIRKFISRARRLEDLVRSGSLT +PTAARFLDAAVDVGMNVLVSGATQAGKTTLLNCLASSIGARERVITVEEIFELQIPVRDV +VGLQCRQPNLEGHGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI +HANSAADALTKLCTLPLLAGENISRSFVVPTVATCIDVVVHCERDWDGRRRVLEVLTVGA +RVEDGVIETSTLFQRDSAGDLRLNEAASLEFDAFARRGVDVHELVGLR +>PROKKA_02097 +MDAVRMLEDELRELVRRRGVDPRVEGHRIRTMIAEATLDYESRSLVSSLPPLEDPEAARQ +ELFDRIAGLGPLQRLMDDPTVEEIWLNAPDQVYCARAGRSELTGIVLSEEQVRDLVELML +KSSGRRLDLSMPFVDASLPDGSRLHVAIPDITRRHWAVNIRKFISRAHRLDDLVRSESLT +TPAARFLDAAVDAGMNILVSGATQAGKTTMLNCLSASIGARERVITVEEIFELQIPVRDV +VGLQCRQPNLEGTGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI +HANSASDALTKLCTLPLLAGENISRNFVVPTVATCIDVVVHCERDREGRRRVREILTVGS +RVEGGVIETSTLFRRDAHGDLVLNPSADLEFEAFARRGLDPRDLVEVR +>PROKKA_00696 +MDAVRILEDEIREIVRRQGIDPQREHARVLTLIQDAAADYESRAMVSSLPDLEDPVAARQ +DLFDRIAGLGPLQRLMDDPSVEEIWLNAPDAVYCARSGRSELTGIVLTEEEVQDLVEVML +KSSGRRLDLSMPFVDAALPDGSRLHVAIPDITRRHWAVNIRKFIARARRLDDLVRGGSLT +PTAARFLDAAVDTGMNILVSGATQAGKTTLLNCLASAIGPRERVITVEEIFELQIPVRDV +VGLQCRQPNLEGHGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI +HANSAADALTKLCTLPLLAGENISRDFVVPTVATCIDVVVHCERDRQGRRRVREILTVGS +RVEGGVIETSALFQRDAEGDLRLNEGANLEFEALARRGVDVHELVGLR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000653.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000653.fa new file mode 100644 index 0000000000000000000000000000000000000000..77f5f51d582a65e096933be7cfe5e9ff4ba53ac8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000653.fa @@ -0,0 +1,15 @@ +>PROKKA_00735 +MLHHHAITVLAALRALIHDDVRDERGDVPGWVMITLMSAVLVAGLLALALPALQGLFNQA +ISQVSQGG +>PROKKA_00466 +MLHHHAITVLAALRALIHDDVRDERGDVPGWVMITLMSAVLVAGLLALALPALQGLFNQA +ISQVSQGG +>PROKKA_02195 +MLHHHVISILTALRGLLHDDVRDDRGDVPGWVMITLMSAVLVAALLTLALPALTDLFDQA +ISQVTQGE +>PROKKA_02094 +MLTNAYLTVVSALTSLLHDDARDERGDVPGWVMITLMSAALVVALLGLAMPALKAMFDQA +ITQVNNAAG +>PROKKA_00699 +MLHHHAITVLAALRALIHDDVRDERGDVPGWVMITLMSAVLVAGLLALALPALEGLFNQA +ISQVSQGG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000662.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000662.fa new file mode 100644 index 0000000000000000000000000000000000000000..212ed017e40cd40ee434996ae01e23af1950d8d7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000662.fa @@ -0,0 +1,20 @@ +>PROKKA_00745 +MGKNSKGKAAKQPAPGERQVIANNKKARHDYTILDTYEAGMVLTGTEVKSLREGKASLVD +GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL +SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRMRNRRAGVA +>PROKKA_00476 +MGKNSKGKATKQPAPGERQVIANNKKARHDYTILDTYEAGIVLTGTEVKSLREGKASLVD +GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL +SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRMRNRRAGVA +>PROKKA_02184 +MGKNSKGKAAKQPAPGERQVIANNKKARHDYTILDVYEAGLVLTGTEVKSLREGKASLVD +GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL +SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRIRNRRAGVA +>PROKKA_02082 +MGKNSKGKAAKQPAPGERQVIANNKKARHDYTILDTYEAGMVLTGTEVKSLREGKASLVD +GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL +SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRMRNRRAGVA +>PROKKA_00710 +MGKNSKGKAAKQPAPGERQVIANNKKARHDYTILDTYEAGMVLTGTEVKSLREGKASLVD +GFAVFYRDELWLEQVYIPEYLNGSWTNHAARRRRKLLLHRAELTKISRQIQDPGLTIVPL +SLYFLNGRVKVEIGVARGNREYDKRHKLREQQDNREAQRAMRMRNRRAGVA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000664.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000664.fa new file mode 100644 index 0000000000000000000000000000000000000000..2566fb28aa2563dd6e46d947844da6904c9d6390 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000664.fa @@ -0,0 +1,40 @@ +>PROKKA_00751 +MARRLDPSAWDESDVRVRPSKRGTRPRTKERPKHEDAEVGMVTTVDRGRYAVVLPERLDE +RITAMRARELRRTPIATGDRVAVVGDLSGEEGTLARIVRVEERSTVLRRSADDSDEVERV +VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPDALVAHYEAL +DLEVMTSGAATFEAETGDTALDASLVARVAERLIGHTSAFVGPSGVGKSTLLNALTGAER +ATGHVNAVTGRGRHTSSSALALPLTGDDGVPLPDTWVVDTPGIRSFGLGWVEPDRVVEAF +DDLAGGLADCPRGCTHTADSPGCGLDAWVAAGHAGPSGAARLASLRRLLGNRLAPSGAED +AASSED +>PROKKA_00481 +MARRLDPSAWDESDVRVRPSKRGTRPRTKERPKHEDAQVGMVTTVDRGRYAVVLPDRLDE +RITAMRARELRRTPIATGDRVAVVGDLSGDEGTLARIIRVEERSTVLRRSADDSDEVERV +VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPDALVAHYEAL +DLEVMTSGAATFEAETGDTALDASLVARVAERLIGHTSAFVGPSGVGKSTLLNALTGAER +ATGHVNAVTGRGRHTSSSALALPLTGDDGAPLPDTWVVDTPGIRSFGLGWVEPDRVVEAF +DDLAGGLADCPRGCTHTADSPGCGLDAWVAAGHAGPSGAARLASLRRLLGNRLAPSGAED +AASSED +>PROKKA_02179 +MGRRVDPGAWDESDVRVRPSKRGTRPRTKERPKHEDAVVGMVTTVDRGRYTVVLPERLDE +RITAMRARELRRTPIATGDRVAVVGDLSGDEGTLARVVRVEERSTVLRRSADDSDEVERV +VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPAALMAHYESL +DLEVMTSGAAVFEAETGDTALDGALVARVAERLQGHTSAFVGPSGVGKSTLLNALTGAER +ATGHVNAVTGRGRHTSSSALALPLTDDDGVPLADTWVVDTPGIRSFGLGWVEPDRVVEAF +DDLAGGLADCPRGCAHTADSPGCGLDGWVAAGHAGPSGAARLASLRRLLGNRLGPAGAED +SASSED +>PROKKA_02074 +MGRSLDPSAWDESHVRVRPSKRGTRPRTKQRPQHEDAQTGLVTTVDRGRYTVVLPGRAHA +PVTAMRARELRRTPIATGDRVDVVGDLSGDEGSLARIVRVQERDTVLRRSADDSDAVERV +VVANADTLMVMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPAELVAHYEAL +DLEVMTSGASRFEAESGDTDLDDGLVERVAERLAGHTAAFVGPSGVGKSTLLNALTGAGR +ATGHVNAVTGRGRHTSSSALAMSLPGPDGEPVPDTWVVDTPGIRSFGLGWVEPDRVVEAF +EDLAGGLEGCPRGCTHLADSPGCGLDAWVAEGHAGEAGPARLASLRRLLGNRTTAEAGGS +ASSED +>PROKKA_00715 +MARRLDPSAWDESDVRVRPSKRGTRPRTKERPKHEDAEIGMVTTVDRGRYAVVLPDRLDE +RITAMRARELRRTPIATGDRVAVVGDLSGDEGTLARIVRVEERSTVLRRSADDSDEVERV +VVANADLLVIMVAAANPEPRTGFIDRALVACYDAGIHPVLLITKTDLRDPAALVAHYEAL +DLEVMTSGAATFEAETGDTALDASLVARVAERLIGHTSAFVGPSGVGKSTLLNALTGAER +ATGHVNAVTGRGRHTSSSALALPLTGDDGAPLPDTWVVDTPGIRSFGLGWVEPDRVVEAF +DDLAGGLADCPRGCTHTADSPGCGLDAWVAAGHAGPSGAARLASLRRLLGNRLAPSGAED +AASSED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000668.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000668.fa new file mode 100644 index 0000000000000000000000000000000000000000..94ceed1ed345cfb2677e2481f9f5fd3666b7d68a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000668.fa @@ -0,0 +1,25 @@ +>PROKKA_00755 +MHNRRIRIAAVGDQLLAGAGDARAIGWWGRVLARTQAPDVELENYVLAVPHETTEDLNER +WWGEASRRFSEETENRLVVALSDADLDLEATSTARSRLNLANVLDTASQRNIPVLVVGPT +PTLDEQRNARLAELNAAYLDVADRRNHVYVDTFTPLVGHEQWRSDLASGQGRPGQAGHGL +IAWLVLHRGWYQWLGLPEPTA +>PROKKA_00485 +MHNRRIRIAAVGDHLLAGAGDARAIGWWGRVLARTQAPDVELENYVLAVPHETTEDLNER +WWGEASRRFSEETENRLVVALSDADLDLEATSTARSRLNLANVLDTASQRNIPVLVVGPT +PTLDEQRNARLAELNAAYLDVADRRNHVYVDTFTPLVGHEQWRSDLASGQGRPGQAGHGL +IAWLVLHRGWYQWLGLPEPTA +>PROKKA_02175 +MNDRRIRIAAVGDHLLAGAGDARAIGWWGRVLARTQAPGVELENYVLAVPHETTEDLNER +WWGEASRRYSEDTENRLVVALSDADLDLEASSTARSRLNLANVLDTASQRGIPVLVVGPT +PTLDEERNARLAELNAAYLDVADRRSHVYVDTFTPLQGHEQWRADLAAGEGRPGQAGHGL +IAWLVLHRGWYQWLGLPEPTA +>PROKKA_02070 +MQNRRIRIAAVGDHILAGAGDPRSIGWWGRVLARTAAPEVTLENYVLAVPHETTEQLNER +WWGEASRRFSESAENRLVVALSDADLDLEASSSARSRLNLANVLDTASQRGITALVVGPV +PTLDEARNDRLADLNTAYQDVAARRGHLYVDAFTPLRTHEQWRADLAAGDGVPGQAGHGL +IAWLVLHRGWYQWLGVPEPTA +>PROKKA_00719 +MHNRRIRIAAVGDHLLAGAGDARAIGWWGRVLARTQAPDVELENYVLAVPHETTEDLNER +WWGEASRRFSEETENRLVVALSDADLDLEATSTARSRLNLANVLDTASQRNIPVLVVGPT +PTLDEQRNARLAELNAAYLDVADRRNHVYVDTFTPLVGHEQWRSDLASGQGRPGQAGHGL +IAWLVLHRGWYQWLGLPEPTA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000669.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000669.fa new file mode 100644 index 0000000000000000000000000000000000000000..d119584a7da931a3facf0521c6ba90d457afaea3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000669.fa @@ -0,0 +1,110 @@ +>PROKKA_00756 +MPELTSDRLAQEFPGNERLVAEIYRKYREDSGSVDRQWAQIFARLEASAPAAEAEPKAAA +KTEPKTAAKAEPKATAKVTEPKAATAPARGAQPKETSVSTGPKPKKTPAAQAVPSEPADT +ATTTADEKQEKATVLKGMAKAVATNMDASLSMPTATTVRDLPAKVLIDNRVVINSHLART +RGGKVSFTHFIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLPRPDGTRA +LVVPNVKAAETLDFRGFWKAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGTVHSVPRL +SQGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSGEFLKIVH +GLLLGEDGFYDEVFHSLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN +VDPLEYSMAYHPDLDIREHGLTLWDLDRKWPTGGFGGAGSLTLRKILGVLRDAYCRTIGV +EYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE +GGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA +SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRLDLGGQRP +DSFSVLPILVHGDAAFAGQGVVTEVLQLSQLPGYRTGGTIHVVVNNQVGFTTPPTQARSA +VYSTDVAKTIQAPIFHVNGDEPESVVHVAQLAFEYRQRFNKDVVIDLVCYRRRGHNEGDD +PSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADSALKDYQQQLERVFAETHEDAP +ASGGEGLRPAEDRDAAPEAPASTAISAETLRAIGQAHIDVPEGFTVHPKLAALLERRAKM +AVDGGIDWGFAELAAFGSLLMERVPVRLAGQDSQRGTFTQRHSVFHDRITGDTWAPLRHL +SEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFVNGAQTIIDEFISSAD +QKWSQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSTGANHFHLLREHA +YARPRRPLIVFTPKQLLRLKAAANSVEDFTEGGFQPVIPDAGVDAKDVTRVLLVSGRLYY +DLLARRQKSGDTSTAIVRVEQLYPLPLDEIRKALRAYPVADVTWVQDEPANQGPWPFMAL +NLVPQLDVPVTLVSRPASAATSAGTKGRHDQELSTLLDAAFGR +>PROKKA_00486 +MPELTSDRLAQEFPGNERLVAEIYRKYREDSGSVDRQWAQIFARLEASAPAAEAEPKAAA +KTEPKTAAKAEPKATAKVTEPKAATAPARGAQPKETSVSTGPKPKKTPAAQAVPSEPADT +ATTTADEKQEKATVLKGMAKAVATNMDASLSVPTATTVRDLPAKVLIDNRVVINSHLART +RGGKVSFTHLIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLPRPDGTRA +LVVPNVKAAETLDFRGFWKAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGTVHSVPRL +SQGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSGEFLKIVH +GLLLGEDGFYDEVFHSLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN +VDPLEYSMAYHPDLDIREHGLTLWDLDRQWPTGGFGGASSLTLRKILGVLRDAYCRTIGV +EYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE +GGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA +SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRLDLGGQRP +DSFSVLPILVHGDAAFAGQGVVAEVLQLSQLPGYRTGGTIHVIVNNQVGFTTPPTQARSA +VYSTDVAKTIQAPILHVNGDEPESVVHVAQLAFEYRQRFNKDVVIDLVCYRRRGHNEGDD +PSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADSALKDYQQQLERVFAETHEDAP +ASGGEGLRPAEDRDAAPEAPASTAISAETLRAIGQAHIDVPEGFTVHPKLAALLERRAKM +AVDGGIDWGFAELAAFGSLLMEGVPVRLAGQDSQRGTFTQRHSVFHDRITDETWAPLKHL +SEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFVNGAQTIIDEFISSAD +QKWSQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSTGANHFHLLREQA +YARPRRPLVVFTPKQLLRLKAAANSVEDFTEGRFQPVIPDAGVDAKDVTRVLLVSGRLYY +DLLARREKSGDTSTAIVRVEQLYPLPLEEIRKALRAYPDADVAWVQDEPANQGPWPFMAL +NLVPQLDVPVTLVSRPASAATSAGTKGRHDQELSTLLDAAFGR +>PROKKA_02174 +MLRKRRYTVPELTSDRLAQEFPGNERLVAEIYRKYRADSGSVDRQWAQIFARLEASAPAP +AEKAPAQAAAKAAPKAEPQAEAKVTEPKAKPAPARGAQPKETSTSTGPKVKKTPAAQAVP +SEPADPSKDAAKEEKQEKATVLKGMAKAVATNMDASLSMPTATTVRDVPAKVLIDNRVVI +NSHLARTRGGKVSFTHLIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLP +RPDGSRSLVVPNVKAAETLDFRGFWQAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGT +VHSVPRLSKGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSG +EFLKIVHGLLLGEDGFYDEVFHSLRIPYEPVRWAQDLQVNPEEQVGKVARVQQLIHAYRD +RGHLMANVDPLEYSMPYHPDLDIREHGLTLWDLDRQWPTGGFGGASTLTLRKILGVLRDA +YCRTIGVEYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIG +QKRFSLEGGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYGQVFREFE +GATPGGTSGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRL +DLGGQRPDSFSVLPILVHGDAAFAGQGVVTEVLQLSQLPGYRTGGTIHVIVNNQVGFTTP +PTQARSAVYSTDVAKTIQAPILHVNGDEPESVMHVAELAFEYRQRFNKDVVIDLVCYRRR +GHNEGDDPSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADTALKDYQQQLERVFA +ETHEGSASSGGEGIRPAEDRDQAPEAPETTAISAETLRAIGQAHIDVPEGFTVHPKLAAL +LERRAKMAVDGGIDWGFAELAAFGSLLMEGVPVRLAGQDSQRGTFTQRHSVFHDRITGDE +WAPLKNLSEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFINGAQTIID +EFISSAEQKWAQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPTTGANHF +HLLREQAYARPRRPLVVFTPKQLLRLKAAANSVEDFTEGRFQPVIPDAGVDPKKVTRVQL +VSGRLYYDLLARRNKDGDETTAIVRVEQLYPLPLDELRAALEAYPQAEVVWVQDEPANQG +PWPFMALNLLPQLDREVRLVSRPASASTSAGTKGRHDQELSTLLDAGFAR +>PROKKA_02069 +MPELTSDRLSQEFPGNEDLVAQIYRKYREDQGAVDRQWAQIFARLEASQPQPEPAAAAPK +ATSSATAEPAPAVKPAVKRGAATPADPQAAAKKSGPTDVSAPAQRKRSVSEAVPSEPARD +AAAGASEKQDKATVLKGMAKAVATNMDASLSMPTATTVRDLPAKLLIDNRTVINSHLART +RGGKVSFTHLIGYAVVRALKAMPSMNTLYEERDGKPTMVEPAHVNFGLAIDLPKPDGTRA +LVVPNIKAAETLSFRQFWEAYDDLVKRGRANKLTMDDYAGTTVSLTNPGGIGTVHSVPRL +SKGQAAIIGVGALTYPAAFQGAAESTLNSLAISKTITLTSTYDHRVIQGAGSGEFLKLIH +GYLLGEDGFYDDVFHDLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN +VDPLEYRMPTHPDLDIREHGLTLWDLDREWPTGGFGGADTLTLRRILGVLRDAYCRTVGV +EYMHIQNPAERAWFQDKLERPYEKPSREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE +GGESLIPLLDSILGDAADEGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA +SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVARAKQDRLEAAGESG +AAFPVLPILVHGDAAFAGQGVVTEVLNLSQLPGYRTGGTIHVVVNNQVGFTTSPAEGRSS +VYATDVAKTIQAPILHVNGDEPESVLRVARLAYEYRQRFHKDVVIDLVCYRRRGHNEGDD +PSMTQPRMYTLIEQKRSTRKLYVESLVGRGDITQEEADTALKDYQQQLERVFAETHAAET +GQAVATTGLEPARDRDAARPAPSTTAISPDTLRRIGDVHLEVPEDFTVHPKLSQLLEKRA +KMAVDGGIDWGFAELAAFGSLLMEGVPVRLSGQDSQRGTFTQRHSVFHDRVTDETWTPLN +HLSESEAPFWVYNSLLSEYAVLGFEYGYSVERSDALVLWEAQFGDFINGAQTMIDEFISS +AEQKWSQNSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSHGANHFHLLRE +QAYSRPRRPLVVFTPKQLLRLKAAADPVEAFTQGGFRKVIGDASVDAAQVERVILVSGRL +YYDLLARREKSGDTSTAIVRVEQLYPLPAEEIRAELAKYPGAQVRWVQDEPANQGPWPFM +ALNLLPQLDREVTLVSRPALAATSAGTKGRHDEELSTLLDTAFGA +>PROKKA_00720 +MPELTSDRLAQEFPGNERLVAEIYRKYREDSGSVDRQWAQIFARLEASAAAAEAEPKAAA +EAEPKAAARAEPKATAKVTEPKAATAPARGAQPKETSVSTGPKAKKTPAAQAVPSEPADT +ATTTADEKQEKATVLKGMAKAVATNMDASLSMPTATTVRDLPAKVLIDNRVVINSHLART +RGGKVSFTHLIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLPRPDGTRA +LVVPNVKAAETLDFRGFWKAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGTVHSVPRL +SQGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSGEFLKIVH +GLLLGEDGFYDEVFHSLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN +VDPLEYSMAYHPDLDIREHGLTLWDLDREWPTGGFGGASSLTLRKILGVLRDAYCRTIGV +EYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE +GGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA +SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRLDLGGQRP +DSFSVLPILVHGDAAFAGQGVVTEVLQLSQLPGYRTGGTIHVIVNNQVGFTTPPTQARSA +VYSTDVAKTIQAPIFHVNGDEPESVVHVAQLAFEYRQRFNKDVVIDLVCYRRRGHNEGDD +PSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADSALKDYQQQLERAFAETHEDAP +TSGDEGIRPAEDRDAAPKAPASTAISAEMLRAIGQAHLDVPEGFTVHPKLAALLERRAKM +AVDGGIDWGFAELAAFGSLLMEGVPVRLAGQDSQRGTFTQRHSVFHDRITGDTWAPLKHL +SEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFVNGAQTIIDEFISSAD +QKWSQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSTGANHFHLLREHA +YARPRRPLIVFTPKQLLRLKAAANSVEDFTEGRFQPVIPDAGVDAKDATRVLLVSGRLYY +DLLARRQKSGDTSTAIVRVEQLYPLPLEEIRKALRAYPDADVAWVQDEPANQGPWPFMAL +NLVPQLDVPVTLVSRPASAATSAGTKGRHDQELSTLLDAAFGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000672.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000672.fa new file mode 100644 index 0000000000000000000000000000000000000000..71886b7e8026e37be9af9ed72c260bc20941d604 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000672.fa @@ -0,0 +1,36 @@ +>PROKKA_00759 +MNGDVVGLLWLVVLLAANAFFVAGEFAVMGARRAQIEPRAEAGSRQAQVALYAMEHVSQM +LAVCQLGITVCSLLILNVSEPALHHLLVVPMAALGVPSAAADVTAFVLALLVVTFLHVTL +GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPVVAALNWTANLVLHALRIEPKDEVASS +YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHRAGDVMVPLERVVTVPEGITPHDFE +WTVGRVGFSRFVVEDPDGGYTGYLHLKDVLTVGPSGHDEPIPLTRVRSLANVRLEDEVED +ALALMQRTGSHLARVITPEGETAGILFLEDVLEELVGEINDVTQSPRRFRPA +>PROKKA_00489 +MNGDVVGLLWLVVLLAANAFFVAGEFAVMGARRAQIEPRAEAGSRQAQVALYAMEHVSQM +LAVCQLGITVCSLLILNVSEPALHHLLVVPMAALGVPSAAADVTAFVLALLVVTFLHVTL +GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPVVAALNWTANLVLHALRIEPKDEVASS +YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHRAGDVMVPLERVVTVPEGITPHDFE +WTVGRVGFSRFVVEDPDGGYTGYLHLKDVLTVGPSGHDEPIPLTRVRSLANVRLEDEVED +ALALMQRTGSHLARVITPEGETAGILFLEDVLEELVGEINDVTQSPRRFRPA +>PROKKA_02171 +MNEDVIGLLWLVVLLVANAFFVAGEFAVMGARRSQIEPKAEAGSRPAQVALYAMEHVSQM +LAVCQLGITVCSLLILNVSEPALHHLLVGPMTALGVPDAAADVTAFVLALLVVTFLHVTF +GEMVPKNAAVSFADRAVMILARPLVGLSKLLHPIVTVLNWAANVVLRAFRIEPKDEVASS +YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHTAGDVMVPLEKVVTVPEGITPHDFE +WTVGRVGYSRFVVEDPDGGYTGYLHLKDVLTVGPSGHEEPIPLTRVRSLANVRLEDEVED +ALALMQRTGSHLARVITPEGETAGVLFLEDVLEELVGEINDVTQSPRRFRPA +>PROKKA_02066 +MSQDVVGLLWLAVLLAANAFFVAGEFAVMGARRSQIEPRAEAGSRQAQVALFAMEHVSQM +LAVCQLGITVCSLLILNVSEPALHHLLAAPMEALGLPLAAADVVAFVLALLIVTFLHVTM +GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPLIVVLNWAANTVLRAFGIEPKDEVASS +FTLEEVQTIVAESTRSGTLEDESGVLHSALEFSSYTAGDVMVPIEKVVSVPEDVTPQQFE +WAVGRVGYSRFVVEDSQGGYAGYLHLKDVLAGGPSRYADPVPVTRVRSLANVRVADEVED +ALGLMQRTGSHLARVISEDGATVGVLFLEDVLEELVGEIHDVTQSPRRFRPTTGSHAAPE +PTRMRDLPAR +>PROKKA_00723 +MNGDVVGLLWLVVLLAANAFFVAGEFAVMGARRAQIEPRAEAGSRQAQVALYAMEHVSQM +LAVCQLGITVCSLLILNVSEPALHHLLVVPMGALGVPAAAADVTAFVLALLVVTFLHVTL +GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPVVAALNWTANLVLHALRIEPKDEVASS +YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHRAGDVMVPLERVVTVPEGITPHDFE +WAVGRVGFSRFVVEDPDGGYTGYLHLKDVLTVGPSGHDEPIPLTRVRSLANVRLEDEVED +ALALMQRTGSHLARVITPEGETAGILFLEDVLEELVGEINDVTQSPRRFRPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000673.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000673.fa new file mode 100644 index 0000000000000000000000000000000000000000..7d0e5765a5cd605fdab0913b7ecc2202590e8230 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000673.fa @@ -0,0 +1,35 @@ +>PROKKA_00760 +MLRRRRLPALTGALAALTLSLAACGGTSGDSAGAQAAGASADSGSGSAAGAPVAVATTTQ +LGSVLDRVVACADARSATVMGPGDDPHDFSASSAQVKDMVSSGLVFSNGLGLEGGMESAL +ANAEADGATVVEVAPQLDPLPFGGHDHAEEGAGHEGHDHGSEDPHVWMDVARMARAAELM +GDTLAQERGDERFAECGATVRGELEQTDAQVREILAGVPEDRRTLVTDHDAYGYFSDAYD +FTVSGVVVPGGSTDGEPSSQEIAELARSIRDGGADAVITSVGARNSLVDTVAEEAGNLPV +IEVYESGVGPKDTPEADYAEAMLANARTLADALEG +>PROKKA_00490 +MLRRRRLPALTGALTALTLSLAACGGTSGDSAGEQAAGASAAAGSGSAAGAPVAVATTTQ +LGSVLDRVVACADARSVTVMGPGDDPHDFSASSAQVKDMVSSGLVFSNGLGLEGGMESAL +ANAEADGATVVEVAPQLDPLPFGGHDHAEEGAGHEGHDHGSEDPHVWMDVARMARAAELM +GDTLAQERGDERFAECGATVRGELEQTDTQVREILAGVPEDRRTLVTDHDAYGYFSEAYD +FTVSGVVVPGGSTDGEPSSQEIAELARSIRDGGADAVITSVGARNSLVDTVAEEAGDLPV +IEVYEGGVGPKDTPEADYAEAMLLNARTLADALEG +>PROKKA_02170 +MHRTPRRRAAAALTLASALALAGCGADSGGDGQAGSGEPAAVATTTQLGSVLGDVARCAG +ATTATVMGPGDDPHDFAPSSQQVAQMARAGLVFANGFGLEAGMASALENAAQDGAQVLEV +APRLDPLPFGAGEGAADGHAGETADEHAAHAEEGSAGAHDGHDHGSQDPHVWMDVARMAR +AAEVMGDALAEHTGEDRFADCGRQVRGELEATDAEVREILAAVPEDRRRLIADHDAYGYF +AAAYGFEVAGVVVPGGSTDGEPSSQRIAELTQAVAEAGADALVTSAGGGAPTVETIAADG +GGSTPVVELYEGGVGPADGEPAGYAEAMLHNARVLADALGE +>PROKKA_02065 +MSRSSPTPRLAAPAVVAALGVALAGCSVADSSSPSAAEEGAVTASSSAAGPVVAVATTTQ +LASVADRVARCGGGSVVSVMGPGDDPHDVAASSDQVAQMVHSGLVFTNGLGLEGGMDSAL +DNARQDGAVVVEVAPRLDPLPFGEHDADHAGHEGADAHAGHEHGSQDPHVWMDVARMAAA +ARVVGDELAAETGEQKYAECGATVEGELEETDRQVREILAAVPQERRTLVTDHDAYGYFS +AAYGFTIEGVVVPGGSTDAEPSSRELAALTQQVKDHGAAALLTSTGTPNGLVETVAREAG +GLPVVQLYEGGVGPVGTPEADYAQAMLHNARTLADALKG +>PROKKA_00724 +MLRRRRLPALTGALTALTLSLAACGGTSGDSSGAQAAGASADAGSGSAVGEPVAVATTTQ +LGSVLDRVVACAGARSATVMGPGDDPHDFSASSAQVKDMVSSGLVFSNGLGLEGGMESAL +ANAEADGATVVEVAPQLDPLPFGGHDHAEEGAGHEGHDHGSEDPHVWMDVARMARAAELM +GDTLAQERGDEQFAECGATVRGELEQTDTQVREILAGVPEDRRTLVTDHDAYGYFSEAYD +FTVSGVVVPGGSTDGEPSSQELAELARSIRDGGADAVITSVGARNSLVDTVAEEAGDLPV +IEVYEGGVGPKDTPEADYAEAMLVNARTLADALEG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000674.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000674.fa new file mode 100644 index 0000000000000000000000000000000000000000..b520e738a1d9f22d413b62b37051746a97c86da4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000674.fa @@ -0,0 +1,31 @@ +>PROKKA_00761 +MDWLLEPFQMGFQQRALVGGLIAVVMCSVVGTWLVLRGMSFFGDAFVHGVLPGIALAVVT +GGSPHLGAAVAAVVMMAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISKSDSYTGSLT +SILFGDVLGVSVDGIVTQAVIAVVVIALALLLYRPLLALSFSEVKARSLGMRPGLTHTLL +LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRSVPQMMLVSVVIGAACVVTGLTLS +YRLGTAGSATMALMPILLFFVVLAVRAAVLALLGRHVRSRAQRERETPVVALPGAEVAR +>PROKKA_00491 +MDWLLEPFQMGFQQRALVGGLIAVVMCSVVGTWLVLRGMSFFGDAFVHGVLPGIALAVVT +GGSPHLGAAVAAVVMMAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISKSDSYTGSLT +SILFGDVLGVSVDGIVTQAVIAVVVIALALLLYRPLLALSFSEVKARSLGMRPGLTHTLL +LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRSVPQMMLVSVVIGAACVVTGLTLS +YRLGTAGSATMALMPILLFFVVLAVRAAVLALLGRHVRSRAQREQEAPVVALPGAEAPR +>PROKKA_02169 +MDWLIEPFLLGFQQRALVGGLIAAALCAVVGTWLVLRGMSFFGDAFVHGVMPGIALSVVL +GFDAHLGAALAALVMLAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISLSDSYTGSLT +AILFGDALGVTWEGIVRQAVIAALVLVLALVLYRPLMALSFSPAKARSLGMRPRLTHALL +LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRTVPQMMALAVLLGAAGVTIGLVLS +YHLGTAASATMALVPIAMFFVVLAGRAGLRALRSRRVRADRRRAVVETPSRRSVSP +>PROKKA_02064 +MDWLIDPFLLGFQQRALLGGLIAALMCSAVGTWLVLRGMSFFGDAFVHGVLPGIALAVLL +GGSPHLGAALAAVLMMGGISLVHRTTTLKEDTAIGLLFVGMMALGVVIISLSSSYTGSLT +AILFGDALGVTPENLLVQAAIGVVVVVLALVLYRPLLALSFSEAKSQALGMRPRLTHTLL +LVLIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRTVPQMMALSAGIGALSVVAGLVLS +YHWGTAASATMALVPVVLFFVVLLGRSAVQAAAGRRRRTRGAASAPTPAGDDDAESRRET +EGSPAR +>PROKKA_00725 +MDWLLEPFQMGFQQRALVGGLIAVVMCSVVGTWLVLRGMSFFGDAFVHGVLPGIALAVVT +GGSPHLGAAVAAVVMMAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISKSDSYTGSLT +SILFGDVLGVSVDGIVTQAVIAVVVIALALLLYRPLLALSFSEVKARSLGMRPGLTHTLL +LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRSVPQMMLVSVVIGAACVVTGLTLS +YRLGTAGSATMALMPILLFFVVLAVRAAVLALLGRHVRSRAQREQEAPVVALPGAEAAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000676.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000676.fa new file mode 100644 index 0000000000000000000000000000000000000000..006d32f6c6e071b1f2a51c14beb55f3061e1da42 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000676.fa @@ -0,0 +1,36 @@ +>PROKKA_00764 +MHSETPDPSPVPDRDGAAPDRPDPLIVVDEGQARVVPAPTAAPSSSHDAGGDPDADTDGV +DPEAAEPPTLVTVDVLAGWLGLAPVEDLPPVPEGPAYAQPGRCRPNRVILLDVRFRATAG +GPDHAAYLQGHLPGAVYVSLPSQLAGHAGPAAGRHPLPDARQFAETVRMWGIDEGDTIVV +YDDDHGLSAARAWWLLRHAGLRDSMLLDGGLEAWRAAGLPLQPGEVIPVPGTARPSWGRM +PVVDTAGAEAMASGGLLLDARAAERYRGEVEPFDPVAGHIPGARNVPTAESIAEDGRLRP +AAELAERFDAVGVDDATPVAVYCGSGITAAHAVLTLAVAGRPGVALYPGSWSAWVQDPSN +AVAVGPEPDGASGRD +>PROKKA_00494 +MHSETPDPSPVPDRDGAAPDRPDPLIVVDEGQGRVVPAPTAAPSSSHDAGGDPDADIDGV +DPEAAEPPTLVTVDVLAGWLGLAPVEDLPPVPGGPAYAQPGRCRPNRVILLDVRFRATGG +GPDHAAYLQGHLPGAVYVSLPSQLAGHAGPAAGRHPLPDARQFAETVRMWGIDEGDTIVV +YDDDHGLSAARAWWLLRHAGLRDSVLLDGGLEAWRAAGLPLQPGEVIPVPGTARPSWGRM +PVVDTAGAEAMASGGLLLDARAAERYRGEVEPFDPVAGHIPGARNVPTAESIAEDGRLRP +AAELAERFDAVGVDDATPVAVYCGSGITAAHAVLTLAVAGRPGVALYPGSWSAWVQDPSN +AVAVGPEPDGASGRD +>PROKKA_02165 +MWGIDDGDTVVVYDDDRGLSAARAWWLLRHAGLRDSMLLDGGLAAWRAGGLPLQPGEVIP +MPGSARTSWGRMPVVDTAGAEAMASGGLLLDARAAERYRGETEPIDPVTGHIPGARSLPT +AGSLAEDGRLRPAEELAARFDAVGVDDETPVAVYCGSGVTAAHAVLTLAVAGRPGVALYP +GSWSAWIQDPSNAVAVGPDPHGEPGRD +>PROKKA_02061 +MKDSTEGRPPSPASSPAADAPTDQTPLAELAEDATAPDPAAAEPPSLVDVGVLAGWLGLT +PAEPVPAPPPGPVFDRRVDPGRVILLDVRYAVAGAGGSGHDAYLRGHLPGAVFVSLPNQL +AGHAGPRQGRHPLPDPVQFAHSLRMWGIDDGDTVVVYDDDRSLAAARAWWLLRHAGLRDS +VLLDGGLGAWRAAGLPLQPGEVIPQPGSVHPSWGRMPVVDTDGAEAIAAGGLLLDARSAE +RYRGEEEPLDPVAGHIPGARSLPTSGNVAADGRLLDPAALAARFEDAGLSDEVPAAVYCG +SGVTAAHQVLALAVAGRHGVALYPGSWSAWIQDPDRPVATGPRPEGD +>PROKKA_00728 +MHSETPDPSPVPDRDGAAPDRPDPLIVVDEGQGRVVPAPTAAPSSSHDAGGDPDADIDGV +DPEAAEPPTLVTVDVLAGWLGLAPVEDLPPVPGGPAYAQPGRCRPNRVILLDVRFRATGG +GPDHAAYLQGHLPGAVYVSLPSQLAGHAGPAAGRHPLPDARQFAETVRMWGIDEGDTIVV +YDDDHGLSAARAWWLLRHAGLRDSVLLDGGLEAWRAAGLPLQPGEVIPVPGTARPSWGRM +PVVDTAGAEAMASGGLLLDARAAERYRGEVEPFDPVAGHIPGARNAPTAESIAEDGRLRP +AAELAERFDAVGVDDATPVAVYCGSGITAAHAVLTLAVAGRPGVALYPGSWSAWVQDPSN +AVAVGPEPYGASGRE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000677.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000677.fa new file mode 100644 index 0000000000000000000000000000000000000000..5a8b742bfd6d0f70da1daa32ba042b870b3332ca --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000677.fa @@ -0,0 +1,20 @@ +>PROKKA_00765 +MATVFSRIIAGELPARFVWQDQTCVAFLSAAPLQPGHALVVPRAEVDEWVEVDPALVTHL +TTVAQQIGKAQVAAFSARRAGLMIAGYEIPHLHVHVWPSTSLADFDLARVDNAPDPADLD +DAAARLRAALRDLGHGEVVPQD +>PROKKA_00495 +MATVFSRIIAGELPARFVWQDQTCVAFLSAAPLQPGHALVVPRAEVDEWVEVDPALVTHL +TTVAQQIGKAQVAAFSARRAGLMIAGYEIPHLHVHVWPSTSLADFDLARVDNAPDPADLD +DAAARLRAALRDLGHGEVVPQD +>PROKKA_02164 +MASVFSRIIAGELPARFVWQDETCVAFLSTGPLNPGHALVVPREEVDAWVDADPALVMHL +MTVAQQLGKAQVRAFSAQRAGLMVAGYEILHLHVHVWPSNSLADFDLNRVDNSPDPAEMD +DAAARLRAALRELGHGEVVPQD +>PROKKA_02060 +MATVFSRIIAGELPARFVWQDEQCVAFLSLGPLAQGHTLVVPREEVDQWVDADPDLLAHL +TRVAQAIGRVQVRAFGAQRAGLMVAGYEIPHLHVHVWPSNSMNDYDMARVDNAPEPESLD +EAAAAIRAGLREDGHGDVVPQD +>PROKKA_00729 +MATVFSRIVAGELPARFVWQDQTCVAFLSAAPLQPGHTLVVPRAEVDEWVEVDPALVTHL +TTVAQQIGKAQVAAFSARRAGLMIAGYEIPHLHVHVWPSTSLADFDLARVDNAPDPADLD +DAAARLRAALRDLGHGEVVPQD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000678.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000678.fa new file mode 100644 index 0000000000000000000000000000000000000000..b08e9b29e8a26dee3e1f816b1fa8d631d1a0366f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000678.fa @@ -0,0 +1,121 @@ +>PROKKA_00766 +MTQTPPPSTPAAQPSATPHDAVAITFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKT +TQLPKMCLALGLGEAGSIGHTQPRRIAARSVAERIAQELGEEIGQTVGYQVRFTAQTSKA +TRVKVMTDGILLAEIPHDPQLRRYSVIIVDEAHERSLNIDFLLGYLRNLLPQRPDLKVII +TSATIDPERFARHFGRPLAEGEDHADAVEADDGGRVVPAPIIEVSGRTYPVEIRYRPLTD +EPSPDDPEDDADDAAETRDPLDAIGDAVLELASEPPGDILVFLPGEREIREAADHLTGVV +AGTTRLAGTEILPLFGRLSMAEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDT +GTARISRYSHRTKVQRLPIERVSQASANQRSGRSGRTSDGIAIRLYSEEDYLSRPEFTDP +EILRTSLASVILQMLSLGVARTPGDVKEFPFVQPPDGRQVTDGATTLTELGALEAGGARA +GTITRVGRRLARLPVDPRLGRMILEAGERGCVREVMVIAAALTIQDPRERPTEQREAADE +LHRRFADENSDFSAILNLWAYLRERQQELSGSQFRKLCRREHINWLRVQEWQDLVRQLRQ +LAKDVGLTVEAGPVDPVGRHEAVHKSLLTGLLAQIGAYDERRREYAGARGTRFAVFPGSA +LFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEVAGHLVKRAYNEPHWSRRAGSVVAR +EKVTLFGVTLIPDRSVRYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDAL +ETRLRRRDLRIGDEDLFAFYDARIPANVVSERHFDAWWKKARQEQPDLLDLDVAALLTAD +AEDLDTDAFPTTFSYPMPGGDVELDLEYTFDPTGAAGTDGVTVAVPILLLNQVSPGPFAW +LVPGLRVELVTALIKALPKAVRKNLVPAPDVAQQLVADLEAHADPLRDELPEALSAAVRR +VRGVVVEPGLWAPDAVPLHLRMDYRVVDARGAVMGAGQDLPALQARLAQANRSAIAARLA +GTDDPASARPGPRGTGRGGRAQADARAGAEGRRRPEGPGRSGATPAFEERHRLTSWSIGT +VPKTVSTAAGARGPAITGYPSLVPETTPDGGPAAGLTVARSAEDQAAWHRAGVIRLLLAT +LPSPQRYVLDHLDNREKLTFTQNPHGSVDSLVADCTQAAVDRLVGDELPFDEAAFRALFD +RVRADLIDTVFAVTSLVEQVLSRAAQVRRRLKGSVSLALAPALSDVKAHLEQLVFPGFVA +ATGWERLQHLPRYLQGMLTRLDRLDAGGHLQRDGQHMAVVQGLEDEFDAAVAAHRARFAG +TPVPAELERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALARATRA +>PROKKA_00496 +MTQTPPPSTPAAQPSATPHDAVAITFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKT +TQLPKMCLALGLGEAGSIGHTQPRRIAARSVAERIAQELGEEIGQTVGYQVRFTAQTSKA +TRVKVMTDGILLAEIPHDPQLRRYSVIIVDEAHERSLNIDFLLGYLRNLLPQRPDLKVII +TSATIDPERFARHFGRPLAAGEDHADAVEADDGGRVVPVPIIEVSGRTYPVEIRYRPLTD +EPSPDDPEDDADDAAETRDPLDAIGDAVLELAAEPPGDILVFLPGEREIREAADHLTGVV +AGTTRLAGTEILPLFGRLSMAEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDT +GTARISRYSHRTKVQRLPIERVSQASANQRAGRSGRTSDGIAIRLYSEEDYLSRPEFTDP +EILRTSLASVILQMLSLGVARTPGDVKEFPFVQPPDGRQVTDGATTLTELGALEAGGARA +GTITRVGRRLARLPVDPRLGRMILEAGERGCVREVMVIAAALTIQDPRERPTEQREAADE +LHRRFADENSDFSAILNLWAYLHERQKELSGSQFRKLCRREHINWLRVQEWQDLVRQLRQ +LAKDVGLTVEAGPVDPVGRHEAVHKSLLTGLLSQIGAYDERRREYAGARGTRFAVFPGSA +LFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEVAGHLVKRAYNEPHWSRRAGSVVAR +EKVTLFGVTLIPDRSVRYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDAL +ETRLRRRDLRIGDEDLFAFYDARIPGNVVSERHFDAWWKKARQDQPDLLDLDVAALLTAD +AEDLDTDAFPTTFAYPMPGGDVELDLEYTFDPTGAAGTDGVTVAVPILLLNQVSPGPFAW +LVPGLRVELVTALIKALPKAVRKNLVPAPDVAQQLVADLEAHADPLRDELPDALSAAVRR +VRGVVVEPGLWAPDAVPLHLRMDYRVVDARGAVMGAGQDLPALQARLAQANRSAIAARLA +GTDDPASARPGPRGTGRGGRAPADARAGAEGHRRPEGPGRSGATPVFEERHGLTSWSIGT +VPKTVSTAAGARGPAITGYPSLVPETTPDGGPAAGLTVARSAEDQAAWHRAGVIRLLLAT +LPSPQRYVLDHLDNREKLTFTQNPHGSVDSLVADCTQAAVDRLVGDELPFDEAAFRALFD +RVRADLIDTVFAVTSLVEQVLSRAAQVRRRLKDSVSLALAPALSDVKAHLEQLVFPGFVA +ATGWERLQHLPRYLQGMLTRLDRLDAGGHLQRDGQHMAVVQGLEDEFDAAVAAHRARFAG +TPVPAELERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALARATRA +>PROKKA_02163 +MTETPTPPAAASSAPAIVFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKTTQLPKMC +LALGLGEAGVIGHTQPRRIAARSVAERIAEELGEDIGRTVGYQVRFTAQTSKATRVKVMT +DGILLAEIPHDPQLRRYSVVIVDEAHERSLNIDFLLGYLRTLLPQRPDLKVIITSATIDP +ERFARHFGRALAEGEEHEDAVPADDGGLVVPAPVIEVSGRTYPVEVRYRPLTGEPSPDDP +EDDSDDAAETRDPLDAIGEAVLELAAEPPGDILVFLPGEREIRDAADHLSGVVASSKRLA +GTEVLPLFGRLSMAEQHRVFGRAAAGVRRRIVLATNVAETSLTVPGIKYVIDTGTARISR +YSHRTKVQRLPIERVSQASANQRAGRSGRTSPGIAIRLYSEEDYLSRPEFTDPEILRTSL +ASVILQMLSLGVAATPADVQGFPFVQPPDGRQVSDGATTLTELGALHPPRPSGAKDGHDG +GRGRGGRAPEPGTITPIGRRLARLPVDPRLGRMILESGERGCVREVMVLAAALTIQDPRE +RPVEQREAADELHRRFADENSDFSAILNLWAYLQEQQKELSGSQFRKLCRREHINWLRVH +EWQDLVRQLRQLAKDVGVAVHAGPVDPVGQHEAVHRSLLTGLLSQIGSYDERRREYAGAR +GTRFAVFPGSALFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEAAGGLVKRTYNEPH +WSRRAGAVVAREKVTLFGVTLIPDRSVKYGRIDPELSRELFIRHALVEGDWRTRHRFFAR +NRAALEEVDALETRLRRRDLRIGDEDLFAFYDARVPANVVSERHFDAWWKKARQERPDLL +DLDVAALLTADAEDLDTDAFPTVFPYPLSGGDVDLDLEYTFDPTGASGTDGVTVSVPVLL +LNQVSPGPFAWLVPGLRVELVTALIKALPKAVRKQLVPAPDVARQLVADLDAHADPLADE +LTEALSAAVRRVRGIVVEPGLWAPDAVPAHLRMDYRVVDARGAVMGAGQDLAALQARLAK +ANRSAIAARLAGTDDPANARPGPGRQGGRRDGGGNDGGAGRRGSGRGVRGRGRDGTGRPE +AGAQGAGGAAAAFAERHGLTSWSIGTVPRRITTDPGARGPAITGYPALVPETTAEGGPAA +GLTVARSAEDQAAWHRAGVIRLLLATLPSPQRYVLDHLDNREKLTFTQNPHGSVDSLVAD +CSQAAVDRLVGDELPFDEAAFRALFDRVRADLIDTVFAVTRLVEQVLSRAAEVRRRLKGS +VSLAMAPALSDVKAHLEQLVFPGFVAATGWERLQHLPRYLQGILVRLDRLDAGGHLQRDG +QHMAVVQRLEDEFDAAVQAHRARFSGVPVPADLERVRWLIEELRVSFFAQELGTAVSVSE +KRVRQALAQAARA +>PROKKA_02059 +MTDFPQPPAAAPVITFPAHLPVAERREEIMDAVRENQVVIVAGETGSGKTTQLPKMLLAL +GLGGAGVVGHTQPRRIAARSVAERIAEELGEDVGRTVGYQVRFTAQTSTRTRVKVMTDGI +LLAEIPHDPDLRKYSAIIVDEAHERSLNIDFLLGYLKRLLPRRPDLKVIITSATIDPERF +ARHFGTEDEPAPIIEVSGRTYPVEIRYRPLTEEPSPDDPDDDADDHAETRDPIDAVGDAV +LELAGEAPGDILVFFPGEREIREAADHLAGVVASTPRLAGTEVLPLYGRLSMAEQHRVFG +RAGAGVRRRIVLATNVAETSLTVPGIKYVIDTGTARISRYSHRTKVQRLPIERISQASAN +QRSGRSGRTSDGIAIRLYSEEDFLSRPEFTDPEILRTSLASVILQMLSLGVADTPREVMD +FPFVQPPDSRQVTDGAATLTELGALHADAPTRGGGRGRGKGAGNRSAAGTITDIGRRLAR +LPVDPRLGRMILESGRRDCTREVMVLAAALTIQDPRERPVEQRQAADELHARFADDRSDF +SAYLNLWEYLREQQRELSGSQFRKLCRREHINWLRVHEWQDLVRQLRQLSKDVGVSVHPG +PVDPVGKHDDVHKSLLTGLLSQIGAYDERRREYQGARNTRFAVFPGSALFKKRHPFVMAA +ELVETSRLWARAVARIEPEWIEEVAGDLVLRSYAEPHWSRKAGAAVAMEKVTLFGVTIVP +ERSVRYGRIDPVLSRELFLRHALVEGDWRTRHRFFARNRRLLEEVDELETRLRRRDLRVG +DEELFAFYDARVPANVVSERHFDAWWKKARQETPDLLDLDLDALLTQDADELDTDAFPTA +FRYPLPGGDADLALDYTYDPTGASGTDGVTVAVPILLLNEVAPGPFAWLVPGLRGELVTA +LIKALPKAVRKNLVPAPDVARLLVEDLDAHADPLRDELPAALSSAVRRVRGAVVEPELWR +LDAVPDHLRMDYRVVDARGAVMGAGQDLPALQARLAKANRSAIAARLAGTDDPRNARPGQ +GAGRGRGKTEPKGGDGGARGPAADTGRPGPSRTADGAPAFRERHGLTSWTVGEVPRQITT +APGDRGPAITGYPSLIPETTADGSPAAGLVVARSAQDQAAWHRAGVIALLLATLPSTHRY +VLDHLDNKEKLTFTQNPHGSVESLVRDATHVAVDRLVGTDLPFTEVGFRALFDRVRADLI +DTVFAVTALVEQVLSRAAEVRRRLKGGVSLAMAPAKSDVQAHLEQLVFPGFLAATGWQQL +QHLPRYVQGMLARLDKLDAGGHLQRDGQHMAVVQGLEDEFDAAVTAHRSRFPGTPVPAEL +ERVRWLLEELRVSYFAQELGTAVSVSEKRVRQALAQARQG +>PROKKA_00730 +MTQTPPPSTPAAQPSATPHDAVAITFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKT +TQLPKMCLALGLGEAGSIGHTQPRRIAARSVAERIAQELGEEIGQTVGYQVRFTTQTSKA +TRVKVMTDGILLAEIPHDPQLRRYSVIIVDEAHERSLNIDFLLGYLRNLLPQRPDLKVII +TSATIDPERFARHFGRPLAAGEDHADAVEADDGGRVVPAPIIEVSGRTYPVEIRYRPLTD +EPSPDDPEDDADDAAETRDPLDAIGDAVLELAAEPPGDILVFLPGEREIREAADHLTGVV +AGTTRLAGTEILPLFGRLSMAEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDT +GTARISRYSHRTKVQRLPIERVSQASANQRAGRSGRTSDGIAIRLYSEEDYLSRPEFTDP +EILRTSLASVILQMLSLGVARTPGDVKEFPFVQPPDGRQVTDGATTLTELGALEAGGARA +GTITRVGRRLARLPVDPRLGRMILEAGERGCVREVMVIAAALTIQDPRERPTEQREAADE +LHRRFADENSDFSAILNLWAYLHERQKELSGSQFRKLCRREHINWLRVQEWQDLVRQLRQ +LAKDVGLTVEAGPVDPVGRHEAVHKSLLTGLLSQIGAYDERRREYVGARGTRFAVFPGSA +LFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEVAGHLVKRTYNEPHWSRRAGSVVAR +EKVTLFGVTLIPDRSVRYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDAL +ETRLRRRDLRIGDEDLFAFYDARIPGNVVSERHFDAWWKKARQDQPDLLDLDVAALLTAD +AEDLDTDAFPTTFTYPMPGGDVELDLEYTFDPTGAAGTDGVTVAVPILLLNQVSPGPFAW +LVPGLRVELVTALIKALPKAVRKNLVPAPDVAQQLVADLEAHADPLRDELPDALSAAVRR +VRGVVVEPGLWAPDAVPLHLRMDYRVVDARGAVMGAGQDLPALQARLAQANRSAIAARLA +GTDDPASARPGPRRTGRGGRAQADGRAGAEGRRRPEGPGRSGATPAFEERHGLTSWSIGT +VPRTVSTAAGARGPAITGYPSLVPETTPDGGPAAGLTVARSADDQAAWHRAGVIRLLLAT +LPSPQRYVLDHLDNREKLTFTQNPHGSVDSLVADCTQAAVDRLVGDELPFDEAAFRALFD +RVRADLIDTVFAVTSLVEQVLSRAAQVRRRLKGSVSLALAPALSDVKAHLEQLVFPGFVA +ATGWERLQHLPRYLQGILTRLDRLDAGGHLQRDGQHMAVVQGLEDEFDAAVAAHRARFAG +TPVPAELERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALARATRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000682.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000682.fa new file mode 100644 index 0000000000000000000000000000000000000000..17036e75660e72d01c4818f98d7cd91dfe6f1026 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000682.fa @@ -0,0 +1,40 @@ +>PROKKA_00772 +MSHVTESSPAHPGRAEESAPLRPTSPLGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG +TGALVIAGALFFLLAVIVLRLAQKLRTTDIHRIVNPTTSRVPTWFADLSITTSLLGTLVI +MLAGAGAAVHTAFGLPSLVGSLVMATVCVVSVLAGITGLVRVQAVVVPLIIVVAVGVAVW +GLANPGAAVDDVAALVTSSPLINQWWLSGVLYVAFNIQLAYAVLAPIGEESSSSGRSLVA +GAGLGALGLVVMAGAVMAAMTAHAQLIGRAELPMVELAAMIGGWAALLYTVVLLLAQFTT +AVSCLYGGVERIALLSSMRRVPGWVIAVVTALAATLLSSVGFSDLVGTVYPVLGYAGLVI +IVMLVVTWIVERSTVRRRAARAARA +>PROKKA_00503 +MSHVTESSPAHPGRAEESTPLRPTSPLGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG +TGALVIAGALFFLLAVIVLRLAQKLRTTDIHRIVNPTTSRVPTWFADLCITTSLLGTLVI +MLAGAGAAVHTAFGLPSLVGSLVMAAVCVVSVLAGITGLVRVQAVVVPLIIVVAVGVAVW +GLANPGAAVDDVAALVTSSPLINQWWLSGVLYVAFNIQLAYAVLAPIGEESSSSGRSLVA +GAGLGALGLVVMAGAVMAALTVHAQLIGRAELPMVELAAMIGGWAALLYTVVLLLAQFTT +AVSCLYGGVERIALLSSMRRVPGWAIAVVTALAATLLSSVGFSDLVGTVYPVLGYAGIVI +IVMLIVTWIVERTTVRRRAARAARA +>PROKKA_02158 +MSPVTESSPAHRGRAEESAPLRPTSRLGIAATFIGTTIGAGYASGNEILQYFVSFGFWGG +TLALVIAGALFFLLSAIVLKMAQKLRTTDIHRLVNPTTSRVPTWFADLCITASLLGTLVI +MLAGAGAAVNTSFGLPTMVGSLLMAAVCVLSVLAGISGLVRVQAVVVPLIIVVAVGVAWW +GLANPGAPVEDVASLVTSSPLINQWWMSGILYVAFNFQLAYAVLAPIGRDSSSSGRTLVA +GAGLGAVGLVVMAGAIMFAMAAHAHLIGRADLPMVELAAMIGGWAALVYTVILLLAQFTT +AVSCLFGGVERIALLSPLRRVPGWAIAVATALAATLLSSVGFSDLVGTVYPVLGYAGIAI +IVMLIITWIAERTLVRRRAARAARA +>PROKKA_02053 +MSHVAQSTHENRPAQDGGNGLRPMSALGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG +TGALVIAGVLFFLLSAIVLKMAQQLRTTDIHRLVNPTSSRIPTWFADLCITASLLGTLVI +MFAGAGAALDTWLGLPAWAGAALMAAVCVLTVLGGISGLVKVQGLVVPLIILVAVGVAWW +GLTHPGAGADDVASLVTSSPLINTWWMSGILYVAFNFQLAYAVLAPIGKGSSSPGTSLVA +GAGLGAIGLVVMAGAIMAAMGAHATLIGRAELPMVELAGMVAPWVAAVYTVILLLAQFTT +AVSCLFGGVERIALLSPLRDVPGWLIAVVTAVVAVLLSSVGFSDLVGIVYPVLGYAGIAI +VAMLIATWILDRTLVRRRAARADRA +>PROKKA_00739 +MSHVTESSPAHPGRAEESAPLRPTSPLGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG +TGALVIAGALFFLLAVIVLRLAQKLRTTDIHRIVNPTTSRVPTWFADLCITTSLLGTLVI +MLAGAGAAVHTAFGLPSLVGSLVMAAVCVVSVLAGITGLVRVQAVVVPLIIVVAVGVAVW +GLANPGAAVDDVAALVTSSPLINQWWLSGVLYVAFNIQLAYAVLAPIGEESSSSGRSLVA +GAGLGALGLVVMAGAVMAAMTAHAQLIGRAELPMVELAAMIGGWAALLYTVVLLLAQFTT +AVSCLYGGVERIALLSSMRRVPGWVIAVVTALAATLLSSVGFSDLVGTVYPVLGYAGIVI +IVMLVVTWIVERSTVRRRAARAARA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000683.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000683.fa new file mode 100644 index 0000000000000000000000000000000000000000..0fd7fba8d162d597455229e06e147b09898775b1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000683.fa @@ -0,0 +1,31 @@ +>PROKKA_00773 +MTSAVPRVLSIAGSDSGGGAGVQADLKTIAAWGGYGMTAITAITAQNTQGVQAVHPLPVD +VVRAQLDSVAADIAVDAVKIGMLGTVELMRAVAGWLEETRPAVVVLDPVMVASSGDALTA +VGDDDGRAAWARLLRVAHLVTPNLPELARLTGRDATDWDAALDAARGLAAEHGVTVLLKG +GHLDETEAPEAAAAEVPDAVVRVGGAVHEVRGPRVTTRASHGTGCTLSSALATLAGAGLS +WDDALERAKPWLADAMRAGEALAVGDASRPTWHGPVDHGHAQRG +>PROKKA_00504 +MTPAVPRVLSIAGSDSGGGAGVQADLKTIAAWGGYGMTAITAITAQNTQGVQAVHPLPVD +VVRAQLDSVAADIAVDAVKIGMLGTVELMRAVAGWLEETRPAVVVLDPVMVASSGDALTA +VGDDDGRAAWARLLRVAHLVTPNLPELARLTGRDATDWDAALDAARGLAAEHGVTVLLKG +GHLDETEAPEAAAAEVPDAVVRVGGAVHEVRGPRVTTRASHGTGCTLSSALATLAGAGLS +WEDALERAKPWLADAMRAGEALAVGDASRPTWHGPVDHGHAQRG +>PROKKA_02157 +MLSIAGSDSGGGAGVQADLKTIAVWGGYGMTAITAITAQNTQGVQAVHPLPVDVVRAQLD +SIAADIAVDAVKIGMLGTAELMGAVAGWLEETRPAVVVLDPVMVASSGDALTAVGDDDGR +AAWSRLLRAAHLVTPNLPELARLTGRDSTDWEAALDAAGGLAAEHEVTVLLKGGHLDEAA +AAEVPDAVVRVAGAVHEVRGPRVATRASHGTGCTLSSALATLAGAGLSWEDALERAKPWL +ADAMRAGEALAVGDASRPTWHGPVDHGHARRG +>PROKKA_02052 +MAPSPSTPPSSSPAAEGPAVPRVLSIAGSDSGGGAGIQADLKTIAEWGGYGMTAITAITA +QNTQGVQAVHPLPAEVVRAQLDSVASDIAVDAVKVGMLGTAELMRVVADWLEEARPAVVV +VDPVMAATSGHALTPVGDAEAHAAWGRLLRAAHLVTPNLPELARLAGRPLDSWAAALDAA +RELAAAHAVTVLAKGGHLADLTRADPEGAEAGDDPDAEGGVPDALVRPDGSVHEVRGPRV +ESGATHGTGCTLSAALATLAAGGLGWEDAIERAKPWLAQAMVAGEALAVGDRTRPTWHGP +VDHGHARRG +>PROKKA_00740 +MTSAVPRVLSIAGSDSGGGAGVQADLKTIAAWGGYGMTAITAITAQNTQGVQAVHPLPVD +VVRAQLDSVAADIAVDAVKIGMLGTVELMRAVAGWLEETRPAVVVLDPVMVASSGDALTA +VGDDDGRAAWARLLRVAHLVTPNLPELARLTGRDATDWDAALDAARGLAAEHGVTVLLKG +GHLDETEAPEAAAAEVPDAVVRVGGAVHEVRGPRVTTRASHGTGCTLSSALATLAGAGLS +WEDALERAKPWLADAMRAGEALAVGDASRPTWHGPVDHGHAQRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000684.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000684.fa new file mode 100644 index 0000000000000000000000000000000000000000..5c5fad74733a1d071519a35f3f6e7b1285181b96 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000684.fa @@ -0,0 +1,30 @@ +>PROKKA_00775 +MHSPDPLLMTAAGRDDGGTGPGARRRARLAASRLYVCTDLQRFLRPDGTLDTAAFADFCA +AAFRGGVDVIQVRDKAVDVAVELAAFATLVPLAREHGALSAANDRADVAALAGVDVFHTG +QTDLTTAQCRALLGPDVVLGRSCHTEAQVRGARAEDGLDYFCTGPVWATPTKPGRAAVGL +ELPTLAARLDAEDPAGARPWFAIGGVDADRLPEVRAAGAERIVVVRAVTQAEDPEAAART +LRAGLPG +>PROKKA_00506 +MHSPDPLLMTAAGRDDGGTGPGARRRARLAASRLYVCTDLQRFLRPDGTLDTAAFADFCA +AAFRGGVDVIQVRDKAVDVAVELAAFATLVPLAREHGALSAANDRADVAALAGVDVFHTG +QTDLTTAQCRALLGPDVVLGRSCHTEAQVRGARAEDGLDYFCTGPVWATPTKPGRAAVGL +ELPTLAARLDAEDPAGARPWFAIGGVDADRLPEVRAAGAERIVVVRAVTQAEDPEAAART +LRAGLPG +>PROKKA_02155 +MHSPDPLLMAAAGRDDGDTGPGTGRRARLAASRLYVCTDLQRFLRPDGTLDTVAFADFCA +AAFRGGVDLIQVRDKAVDVAVELAAFAVLVPLARAHEALSAANDRADVAALAGVDVFHTG +QTDLTTVQCRALLGPDVVLGRSCHTEAQVRAARAEDGLDYFCTGPVWATPTKPGRAAVGL +ELPSHAARLDAEDPAGARPWFAIGGVDADRLTEVRAAGADRIVVVRAVTQAEDPEAAART +LRAGLPG +>PROKKA_02050 +MHSPDPLLMTAAGRDDGDTGPGAGRRARLAASRLYVCTDLQRFLRPDGTLDTAAFGGFCA +AAFRGGVDLIQVRDKAVDVAVELAAFAVLIPLAREHGALSAANDRADVAALAGVDVFHTG +QTDLTTAQCRALLGPNVVLGRSCHTPDHVRAARAEDGLDYFCTGPVWATPTKPGRAAVGL +GLPTLAARLDAEDPAGARPWFAIGGVDAERLPEVRAAGAGRIVVVRAVTQAADPEAAARE +LRAGLPA +>PROKKA_00742 +MHSPDPLLMAAAGRDDGGTGPGAGRRARLAASRLYVCTGLQRFLRPDGTLDTAAFADFCA +AAFRGGVDVIQVRDKAVDVALELAAFAVLVPLAREHGALSAANDRADVAALAGVDVFHTG +QTDLTTAQCRALLGPNVVLGRSCHTEAQVRAARAEDGLDYFCTGPVWATPTKPGRAAVGL +GLPSLAARLDAEDPAGARPWFAIGGVDADRLPEVRTAGAERIVVVRAVTQAEDPEAAART +LRAGLPG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000687.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000687.fa new file mode 100644 index 0000000000000000000000000000000000000000..c8d38285ea58c893ef9f8c72ea742dc16231d3d9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000687.fa @@ -0,0 +1,30 @@ +>PROKKA_00778 +MAEHRTPPAAPAIPPLRIGGYDLASRLIMGTGGITDLTALEGALVASGTTLTTVALRRWS +ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP +DVVETLEATERLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL +ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG +FHARRAGRIPRREHALASSPMAGRVTAEEDER +>PROKKA_00509 +MAEHRTPPAAPAIPPLRIGGYDLASRLIMGTGGITDLTALEGALVASGTTLTTVALRRWS +ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP +DVVETLEATERLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL +ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG +FHARRAGRIPRREHALASSPMAGRVTAEEDER +>PROKKA_02152 +MAEHRTPPATPAIPPLRIGGYDLAARLIMGTGGITDLTALEGALVASGTTLTTVALRRWS +ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP +DVVETLEATELLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL +ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG +FHARRAGRIPRREHALASSPMAGRVTAEEDER +>PROKKA_02047 +MAPHDTTERRRAREASTAVPPLRIGGYELSSRLIMGTGGITDLAALEGALVASETTLTTV +ALRRWSTDARDGLIALLDRLGIDVLPNTAGCRTARDAVLTARLGREALETELVKVEVIAD +DRTLLPDVVETLDATEQLAAAGFTVLAYTSDDPAMALRLEHAGAAAVMPLGSPIGSGLGI +LNRTNLELIVSRAGVPVVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACR +LALEAGYHAHRAGRIPRRLHALASSPMAGRIGGAEERA +>PROKKA_00745 +MAEHRTPPAAPAIPPLRIGGYDLASRLIMGTGGITDLTALEGALVASGTTLTTVALRRWS +ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP +DVVETLEATERLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL +ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG +FHARRAGRIPRREHALASSPMAGRVTAEEDER diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000691.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000691.fa new file mode 100644 index 0000000000000000000000000000000000000000..086af3a97aa8a684bc560e0e6e12a5cbe9ffa959 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000691.fa @@ -0,0 +1,45 @@ +>PROKKA_00782 +MPQHTDAPTALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAVRDTGATRDW +QADPALYTTDAEALVDGADVVIELMGGIEPARTLILRALAAGTSVVTGNKALLAQHGEEL +YAAAAATGAQLSFEAAVAGAIPILRPLRDSLGGDRVTRVMGIANGTTNFILDRMDSEGAD +FDDALAEAQRLGYAEADPTADVEGHDAAAKAAILATIAFGAPYTLDQVAVAGITAITAED +NAAAAEAGYVIKLLAIAERGRAADGAQGAVLRVHPTLLPREHPLASVRGAFNAVFVEAEN +AGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVTALPALDPAEAHTSFMV +VLRAADQPGVLRRVAGVFEEHGVSIETLRQVPSEREDAPGASLRLITHRARQRDLDATVE +ALAALDVVHEVASVLRVEGN +>PROKKA_00513 +MPQHTDAPTALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAVRDTGATRDW +QADPALYTTDAEALVDGADVVIELMGGIEPARTLILRALAAGTSVVTGNKALLAQHGEEL +YAAAAATGAQLSFEAAVAGAIPILRPLRDSLGGDRVTRVMGIANGTTNFILDRMDSEGAD +FDDALAEAQRLGYAEADPTADVEGHDAAAKAAILATIAFGAPYTLDQVAVAGITAITAED +NAAAAEAGYVIKLLAIAERGRAADGAQGAVLRVHPTLLPREHPLASVRGAFNAVFVEAEN +AGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVTALPALDPAEAHTSFMV +VLRAADQPGVLRRVAGVFEEHGVSIETLRQVPSEREDAPGASLRLITHRARQRDLDATVE +ALAALDVVHEVASVLRVEGN +>PROKKA_02148 +MPQHTDAPTALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAVRNTGATRDW +QADPALYTTDAEALVDGADVVIELMGGIEPARTLILRALAAGTSVVTGNKALLAQHGEEL +YAAAAATGAQLSFEAAVAGAIPILRPLRDSLAGDRVTRVMGIANGTTNYILDKMDSEGAG +FDEALAEAQRLGYAEADPTADVEGHDAAAKAAILATLAFGAPYTLDQVAVSGITAITAED +NEAAADAGYVIKLLAIAERARAADSAEGAVLRVHPTLLPREHPLASVRGAFNAVFVEAEN +AGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVAELPALDPAEAVTSCLV +VLRVADEPGVLRRVAGVFEEQGVSIETLRQVQSDRDDAPGASLRLITHRARQRDLDATVE +ALAALDAVHEVASVLRVEGN +>PROKKA_02042 +MAEPTASAAQTAPAPARDALRVALLGGGTVGSQAARILTEDAAVLADRVGVRLELTGIAV +RDTAAVRDWQADPSLYTTDAEALVDGADLVIELMGGIEPARSLIRRALQVGTSVVTGNKA +LLAEHGEELYRLASETGAQLSFEAAVAGAIPILRPLRDSLSGDTVNRVMGIANGTTNFIL +DRMDTEGASFADALAEAQRLGYAEADPTADVGGFDAAAKAAILATLAFGSSYTLDQVSVE +GITEVTAEDNAAAADAGYVIKLLAIAERDTARDGTAGAILRVHPTLIPREHPLGSVRGAY +NAVFVEAENAGQLMFYGPGAGGAPTASAVMGDAVAIGQRIVRGGPARLRTPVAALPALDV +SEARTSCMVVLRVADQPGVLRRVAGVFEEHGVSIETLRQVQGADDAAGASLRLITHRARQ +RDLDDVVAELTTLDAVHEVASVLRVEGN +>PROKKA_00749 +MPQHTDAPTALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAVRDTGATRDW +QADPALYTTDAEALVDGADVVIELMGGVEPARTLILRALAAGTSVVTGNKALLAQHGEEL +YAAAAATGAQLSFEAAVAGAIPILRPLRDSLGGDRVTRVMGIANGTTNFILDRMDSEGAD +FDDALAEAQRLGYAEADPTADVEGHDAAAKAAILATIAFGAPYTLDQVAVAGITAITAED +NAAAAEAGYVIKLLAIAERGRAADGAQGAVLRVHPTLLPREHPLASVRGAFNAVFVEAEN +AGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVTALPALDPAEAHTSFMV +VLRAADQPGVLRRVAGVFEEHGVSIETLRQVPSEREDAPGASLRLITHRARQRDLDATVE +ALAALDVVHEVASVLRVEGN diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000692.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000692.fa new file mode 100644 index 0000000000000000000000000000000000000000..bfd39fa55c85fb1e0ef53f0ed0731260a8ddba98 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000692.fa @@ -0,0 +1,40 @@ +>PROKKA_00783 +MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS +FKDRGMTMAITAAVADGAKAVVCASTGNTSASAAAYAAQAGITCAVLVPEGKISMGKMSQ +AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDTLGDAP +DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDAELPAVATKTPVMWGFQAAGAAPI +VQGHPVTDPDTIATAIRIGNPASWEQAEAARDESGGMIDSVTDEEILEAHRWLSAKEGVF +VEPASAAGVAGLLKHHAAGNVPAGKSWVITVTGHGLKDPQWALRGADGADVTPRSVPFDV +VTVAQALGLS +>PROKKA_00514 +MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS +FKDRGMTMAITAAVADGAKAVVCASTGNTSASAAAYAAQAGITCAVLVPEGKISMGKMSQ +AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDTLGDAP +DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDAELPAVATKTPVMWGFQAAGAAPI +VQGHPVTDPDTIATAIRIGNPASWEQAEAARDESGGMIDSVTDEEILEAHRWLSAKEGVF +VEPASAAGVAGLLKHHAAGNVPAGKSWVITVTGHGLKDPQWALRGADGADVTPRSVPFDV +VTVAQALGLS +>PROKKA_02147 +MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS +FKDRGMTMAITAAVDQGAKAVVCASTGNTSASAAAYAAQAGLTCAVLVPEGKISMGKMSQ +AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDALGDAP +DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDEELPAVSTKTPVMWGFQAAGAAPI +VLGHPVTEPDTIATAIRIGNPASWEQAEAARDGSGGMIDSVTDEEILAAHRWLSAKEGVF +VEPASAAGVAGLIKHHAAGNVPAGKSWVITVTGHGLKDPQWALRDADGEDVTPRTVPFDV +VTVAQALGLA +>PROKKA_02041 +MAHVWRGVIREYAGRLPVTEDTRVVSLGEGGTPLIRAPHLSELVEGEVYVKFEGMNPTGS +FKDRGMTMAITAAVENGAKAVVCASTGNTSASAAAFAAQAGLTCAVLVPEGKISMGKMSQ +AVAHGAEILQVQGNFDNCLDIARKLSENYPVFLVNSVNPARIEGQKTAAFEVVDLLGDAP +DYHLLPVGNAGNITAYWKGYQEYSRPYVNPHPGTSDEELPAVATKTPVMWGFQAAGAAPL +VLGHPVTEPETIATAIRIGNPASWDQATAARDASGGMIDSVTDEEILAAHRWLSSKEGVF +VEPASAAGVAGLIKHHAAGNVPAGKTWVITVTGHGLKDPQWALKGADGDDVTPRSVPFDV +VTVAEALGLT +>PROKKA_00750 +MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS +FKDRGMTMAITAAVADGAKAVVCASTGNTSASAAAYAAQAGITCAVLVPEGKISMGKMSQ +AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDTLGDAP +DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDAELPAVATKTPVMWGFQAAGAAPI +VQGHPVTDPDTIATAIRIGNPASWEQAEAARDESGGMIDSVTDEEILEAHRWLSAKEGVF +VEPASAAGVAGLLKHHAAGNVPAGKSWVITVTGHGLKDPQWALRGADGADVTPRSVPFDV +VTVAQALGLS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000694.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000694.fa new file mode 100644 index 0000000000000000000000000000000000000000..ff093cb7b41b1e4f095ac71173494b62ec42f6e7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000694.fa @@ -0,0 +1,65 @@ +>PROKKA_00785 +MTESTEQTTPTNGGGLASLKLAQLQALASQLGIAGGSRMRKADLVTAISDHQRGGSVADR +DAAERAAQAPAAPAAEAAPAAASSQDAAPAAERPARRRSRRADADTSAPAAAQDGQPQAE +AREDQTEQAPRETASDQDRSEGSETRDEGEGRPQSERRSRGRRAGDDDAQQGQDRRSDGA +QGEDGADRRGDREDRDDNGRENGRGRNGRNGRDRDNGRDRENGRENNRDRENGRDGSREQ +RGDKSEDGGRGDGGRGDRSRRDDRDDEGGRNRRNRRNRNERGRNRRGRGGPEVDETELTE +DDVLQPVAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKYGLRKGDAVVGAIRAPRDG +EKQQHHGGGSNRQKFNALVKISSVNGQPAVEHPQRVEFGKLVPLYPQERLRLETDPKLIG +PRVIDLVSPIGKGQRGLIVSPPKAGKTMILQSIANAIKTNNPEVHLMMVLVDERPEEVTD +MQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLDSMTRLGRAYNLAA +PASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKGT +GNMELRLSRHLAERRIFPAVDVNASGTRREEALLSQEEVKIMWKLRRVLSGLEQQQALDL +LTNKIKDTASNAEFLMLVSKTTLGSKGDD +>PROKKA_00516 +MTESTEQTTPTNGGGLASLKLAQLQALASQLGIAGGSRMRKADLVTAISDHQRGGSVADR +DAAERAAQAPAAPAAEAAPAAASSQDAAPAAERPARRRSRRADADTSAPAAAAQDGQPQA +EAREDQTEQAPRETASDQDRSGGSEARDEGEDRPQSERRSRNRRRAGDDDAQQGQDRRSD +GAQGEDGADRRGDREDRDDNGRENGRGRNGRNGRDRENGRDRENGRENNRDRENGRDGSR +EQRGDKSEDGGRGDGGRGDRSRRDDRDDEGGRNRRNRRNRNERGRNRRGRGGPEVDETEL +TEDDVLQPVAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKYGLRKGDAVVGAIRAPR +DGEKQQHHGGGSNRQKFNALVKISSVNGQPAVEHPQRVEFGKLVPLYPQERLRLETDPKL +IGPRVIDLVSPIGKGQRGLIVSPPKAGKTMILQSIANAIKTNNPEVHLMMVLVDERPEEV +TDMQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLDSMTRLGRAYNL +AAPASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFK +GTGNMELRLSRHLAERRIFPAVDVNASGTRREEALLSQEEVKIMWKLRRVLSGLDQQQAL +DLLTNKIKDTASNAEFLMLVSKTTLGSKGDD +>PROKKA_02145 +MTESTEQTTPTTGGGLAALKLAQLQALASQLGIPGGSRMRKADLVTAISDHQRGGSVADR +AAAERAAKAAAAPAAEAAPAADKAAEQPAEAAERPARRRSRRADADTSAAAQSAESGKDQ +AERRAEQPAEGRDAEGSQDSGDRAQDSGDRTQGERRSRGRRRAGDDDARGQDRRRQDGED +AGQDQAHDSAEDRGGDREDGGRENGRGNRGRNGRDNGRDRENGNGRDRDNGNGRDRDGSR +EQKQDKSEDGGRDGGRNDRNRRDDRDDEGGRGRRNRRNRNERGRNRRGRGGPDVDETELT +EDDVLQPVAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKHGLRKGDAVVGAIRAPRE +GEKPQHQGGGSNRQKFNALVKISSVNGQPAVEHPERVEFAKLVPLYPQERLRLETDPKQV +GPRVIDLVSPIGKGQRGLIVSPPKAGKTMILQSIANAIKTNNPEVHLMMVLVDERPEEVT +DMQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLDSMTRLGRAYNLA +APASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKG +TGNMELRLSRHLAERRIFPAVDVNASGTRREEALLSPEEVKIMWKLRRVLSGLEQQQALE +LLTNKIKDTGSNAEFLMLVSKTTLGAKGED +>PROKKA_02039 +MTESPDQTTAGGGLASLKLAQLQALASQLGITGGSRMRKSDLVAAISDHQRGGSVADRDA +AAQAAAAPAAQAEAAEAPAAEQAPRSRRRSRRADSDGAVAADQPAEATQAPADEQPAAET +EDAPARAEASAESGAQEAGSGRSRRRRGDRAARDEQQDGAQDEKQESGRGAGEETRREQD +GDEERAEGRSRSRRGRGDRDRGERQNADRQNGERANGERANGQGEDRSQGGRREDREEES +GRGQGGDGQKRSDRGNGRREDRDEDGRRGRNRRNRNDRGRNRRSRGPEVDDVEVTEDDVL +QPVAGILDVLDNYAFVRTSGYLPGEKDVYVSLAMVKKFGLRKGDAVVGAIRAPREGEKPH +SGGGRNQKFNALVKVTTVNGQPAEENPQRVEFGKLVPLYPTERLRLESDHKLVGPRVIDL +ISPIGKGQRGLIVSPPKAGKTMILQSIANAITRNNPEVHLMMVLVDERPEEVTDMQRSVA +GEVIASTFDRPAEDHTTVAELAIERAKRLVEMGRDVVVLLDSMTRLGRAYNLAAPASGRI +LSGGVDSAALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKGTGNMELR +LSRQLAERRIFPAVDVNASGTRREEVLLSPEEVKIMWKLRRVLSGLDTQQALELLTNKIK +DTASNAEFLMLVSKTTLGSKGDD +>PROKKA_00752 +MTESTEQTTPTNGGGLASLKLAQLQALASQLGIAGGSRMRKADLVTAISDHQRGGSVADR +DAAERAAQAPAAPAAEAVPAAASSQDAAPAAERPARRRSRRADADTSAPAAVAQDGQPQA +EAREAQTEQGPRETASDQDRSGGSETRDEGEDRPQSERRSRGRRRAGDDDAQQGQDRRSD +GAQGEDGADADRRGDREDRDDNGRENGRGRNGRNGRDRDNGRDRDNGRDRENGRDGSREQ +RGDKSEDGGRGDGGRGDRSRRDDRDDEGGRNRRNRRNRNERGRNRRGRGGPEVDETELTE +DDVLQPAAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKYGLRKGDAVVGAIRAPRDG +EKQQHHGGGSNRQKFNALVKISSVNGQPAVEHPQRVEFGKLVPLYPQERLRLETDPKLIG +PRVIDLVSPIGKGQRGLIVSPPKAGKTMILQSIANAIKTNNPEVHLMMVLVDERPEEVTD +MQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLDSMTRLGRAYNLAA +PASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKGT +GNMELRLSRHLAERRIFPAVDVNASGTRREEALLSQEEVKIMWKLRRVLSGLEQQQALDL +LTNKIKDTASNAEFLMLVSKTTLGSKGDD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000695.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000695.fa new file mode 100644 index 0000000000000000000000000000000000000000..e6f654baa9e6cab9aebfd81f01c9907d8f10e4fb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000695.fa @@ -0,0 +1,40 @@ +>PROKKA_00786 +MFDSEQRREAVDRLLAEHRELTARLSDPAVHQDPALARRLNRRFAELGAVVTAHRAWSAA +AEELADARELAAAGDDDAAAFAAEVPGLEAAEAEAAERLRRLLIPRDPDDARDVILEIKG +GEGGEEAALFAGDLLRMYLRYADSRGWKTEVLSATHSDLGGYKDVHVAVRGSAADPADGV +YARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVHLDPNDLKVDVFRSSG +PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAEQDAEDS +AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVIASCLALDEER +RLAALGGDA +>PROKKA_00517 +MFDSEQRREAVDRLLAEHRELTARLSDPAVHQDPALARRLNRRFAELGAVVTAHRAWSAA +AEELADARELAAAGDDDAAAFAAEVPGLEAAEAEAAERLRRLLIPRDPDDARDVILEIKG +GEGGEEAALFAGDLLRMYLRYADSRGWKTEVLSATHSDLGGYKDVHVAVRGSAADPADGV +YARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVHLDPNDLKVDVFRSSG +PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAEQDAEDS +AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVIASCLALDEER +RLAALGGDA +>PROKKA_02144 +MFDSEERREAVDRLLAEHRELTARLSDPAVHQDPVLARRLNRRFAELGAVVTAHAAWREA +AAELADARELAAAGDDDAAAFAAEVPCLEEAETAAAERLRRLLIPRDPDDARDVILEIKG +GEGGEEAALFAGDLLRMYLRYAESRGWKTEVLSATHSDLGGYKDVHVAIRAGATDPAEGV +FARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVRIDPNEVKTDVFRSSG +PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAAMRVLRSRLLERRRAEQDAEDS +AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVVASCLALDEER +RLAALGGDA +>PROKKA_02038 +MFESVERLLAEHRELAGQLSDPALHADAARARRVGRRYAELGAVVAAHREWEQAVADRDD +ARELAAAPGEDAAAFAAEVPALEAAADEAAERLRRLLIPRDPDDGRDVILEIKGGEGGEE +AALFAGDLLRMYLRYAESRGWRTEVLSATHSDLGGFKDVHVAVRGSAQDPAEGVYARLKH +EGGVHRVQRVPVTESAGRIHTSAAGVLVLPEADAPDEVQIDPNDLKTDVFRSSGPGGQSV +NTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAERDAEDSAARSAQ +VRTMDRSERIRTYNFPENRIADHRTGFKAHNLDAVLDGALDPVIDSCVALDEQRRLARLG +EEAR +>PROKKA_00753 +MFDSDQRREAVDRLLAEHRELTARLSDPAVHQDPALARRLNRRFAELGAVVTAHRAWSAA +AEELADARELAAAGDDDAAAFAAEVPGLEAAEAEAAERLRRLLIPRDPDDARDVILEIKG +GEGGEEAALFAGDLLRMYLRYAESRGWKTEVLSATHSDLGGYKDVHVAVRGSAADPADGV +YARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVHLDPNDLKVDVFRSSG +PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAEQDAEDS +AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVIASCLALDEER +RLAALGGDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000697.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000697.fa new file mode 100644 index 0000000000000000000000000000000000000000..b1d0408d0de6a0021d823439f8e3444110a04111 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000697.fa @@ -0,0 +1,40 @@ +>PROKKA_00789 +MRAYLVLVMVTAVACGALTPLMRRLGLRARVFTPLRQRDVHRHPVPKLGGVAMAAAVLVG +FAVGGVVPFLQGIYADDAAMRGLLVAVAVVLVVGIADDMWDLRWWVKMAGQVLAGLAVAL +GGIRIEAMPVGWIPVGNETTQVILTVFAVVLTMNAINFVDGLDGLAAGVALIGGSAFFVY +SYLLTRTINQFDYANLATLLMALLVGACVGFLPWNLAPARIFMGEVGAMLIGLLMAAAAV +AVTADVNALDGMRFRNVPAYMPILLPVAVLALPLADLALAVLRRTAKGTSPFSADRGHLH +HKLVDGGYTQAQAVGLLWLWAFLVAWGAVSLNFVDHMVVLPVLAVALAGAGYLTLHPIVE +RRRADRNDAAAHPDERGDA +>PROKKA_00520 +MRAYLVLVMVTAVACGALTPLMRRLGLRARVFTPLRQRDVHRHPVPKLGGVAMAAAVLVG +FAVGGVVPFLQGIYADDAAMRGLLVAVAVVLVVGIADDMWDLRWWVKMAGQVLAGLAVAL +GGIRIEAMPVGWIPVGNETTQVILTVFAVVLTMNAINFVDGLDGLAAGVALIGGSAFFVY +SYLLTRTINQFDYANLATLLMALLVGACVGFLPWNLAPARIFMGEVGAMLIGLLMAAAAV +AVTADVNALDGMRFRNVPAYMPILLPVAVLALPLADLALAVLRRTAKGTSPFSADRGHLH +HKLVDGGYTQAQAVGLLWLWAFLVAWGAVSLNFVDHMVVLPVLAVALAGAGYLTLHPIVE +RRRADRNDAAAHPDERGDA +>PROKKA_02142 +MRAYLVLVVVTALACGALTPLMRRIGLRARVFTPVRQRDMHRRPIPKLGGVAMAAAVLVG +LAVGGTVPFLQGIYADDAAMVGLLVAVAVVFVVGIADDLWDLRWWVKMAGQVCAGLAVAL +GGIRIEAMPVGWIPVGSEAMQIALTVFAVVLTMNALNFVDGLDGLAAGVALIGGSAFFVY +SYLLTRTINQFDYANLATLLMALLVGACLGFLPFNRFPARIFMGEVGAMLLGLLMAAAAV +AVTADVKALDGMRFRNVPAYMPILLPIAVLALPLLDLALAVVRRTARGASPFSADRGHLH +HKLVDGGYTHAQAVWLLWLWAFLVAWGAVSLNFVDDMIVLPVLGLALLGAGYLTLRTPVR +RRRAGAPAAGPALDPEEGA +>PROKKA_02035 +MRAYLLVAAVTALTCLALTPWVRRVGVRARAYTPHRDRDVHRAPVPKLGGVAMVAAVLAG +LAVAGTVPFLGGIFTDASAMRGLLAALGIILVLGVVDDLVDLRWWAKLGGQSLAALAVAL +GGIRIAALPVGWIHVGSEAVQVALTVFVVVLTMNAINFIDGLDGLAAGVALIGGSAFFVY +SYLLTRTIDQFDYSNLATLLMALLIGACAGFLPYNRHPARIFMGESGALLLGLLLSTAAV +AVTADLDALEGFRFRNVPAYMPVLLPIAVLALPLADLTISVIRRAAHGESPFGADRGHLH +HRLVDGGFTHAQAVRVLWLWSFIVAWGVLSLNFADDAVVLLLAAAGLAVATWLTVHPLRA +RAARPASRPDAQPKDQP +>PROKKA_00756 +MRAYLVLVVVTAVACGALTPLMRRLGLRARVFTPLRQRDVHRHPVPKLGGVAMAAAVLVG +FAVGGVVPFLQGIYADDAAMRGLLVAVAVVLVVGIADDMWDLRWWVKMAGQVLAGLAVAL +GGIRIEAMPVGWIPVGNETTQVILTVFAVVLTMNAINFVDGLDGLAAGVALIGGSAFFVY +SYLLTRTINQFDYANLATLLMALLVGACVGFLPWNLAPARIFMGEVGAMLIGLLMAAAAV +AVTADVNALDGMRFRNVPAYMPILLPVAVLALPLADLALAVLRRTAKGTSPFSADRGHLH +HKLVDGGYTQAQAVALLWLWAFLVAWGAVSLNFVDPMIVLPVLAVALAGAGYLTLHPIVE +RRRAVRNDAAAHPDERGDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000698.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000698.fa new file mode 100644 index 0000000000000000000000000000000000000000..71e0bab6008bc34441e6ecf920e6e6dad45fdc6f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000698.fa @@ -0,0 +1,20 @@ +>PROKKA_00790 +MTGAGGRRRRRRWENRRGWWGILGWSLAAAGVALAITCAAWLLSVGGEAAGSALLGGGAV +LALSALTGVTTALVWDRAREAALPVSVGLFVLKIAVFAVLLGVLPRPGWVRADAAAIAAL +VTILVWQAAEVLVFARTRRGIYAD +>PROKKA_00521 +MTGAGGRRRRRRWENRRGWWGILGWSLAAAGVALAITCAAWLLSVGGEAAGSALLGGGAV +LALSALTGVTTALVWDRAREAALPVSVGLFVLKIAVFAVLLGVLPRPGWVRADAAAIAAL +VTILVWQAAEVLVFARTRRGIYAD +>PROKKA_02141 +MSPRTAPDAAPRSARARRRPRRRRWENRRGWWGILAWSLAATAAAVAVVCAVALAAGGPD +AAASALLGGGAVLVLSALTGATTALVWDRAREAALPVSVGLFVLKIAVFAVLLGTVPRPD +WILPDAAAIAALVAILVWQGVEVLVFARTRRGIYAD +>PROKKA_02034 +MTASARPARRRWENRAGWWGILRWCCAATAVGVLACGAVAAVLHGGPAGLSALTGGGAVL +VLSALTGATTAVAWDRARAAALPLSVGAFVVKLVLYALLLATLRMPEWMSGTAVAVGALV +GVVVWQAVEVLVFARTRRGIYAD +>PROKKA_00757 +MTGAGGRRRRRRWENRRGWWGILGWSLAAAGAALAITCAAWLLSAGGEAAGSALLGGGAV +LALSALTGATTALVWDRAREAALPVSVGLFVLKIAVFAVLLGVLPRPGWVRADAAAIAAL +VTILVWQAAEVLVFARTRRGIYAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000699.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000699.fa new file mode 100644 index 0000000000000000000000000000000000000000..2a7eed5bdb2236996ffc64583ecc6a95f4ee5a0c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000699.fa @@ -0,0 +1,30 @@ +>PROKKA_00791 +MLTLVLANASFVPPTISDGHLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP +RLVPGKAQWLAESGYSFVRNDIAKDILGEKNFKQWVPLLFAIFFFVLLNNLFGAIPVLQL +PTFSHAGAAYGLALIVYAIWIGVGIKRHGVRYLKLAVVPSGVPGWILPLLVPLEIISNFI +VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVILGSVALYFLELL +IMYLQAFVFTLLTAIYIQGAIDANDH +>PROKKA_00522 +MLTLVLANASFVPPTISDGHLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP +RLVPGKAQWLAESGYSFVRNDIAKDILGEKNFKQWVPLLFAIFFFVLLNNLFGAIPVLQL +PTFSHAGAAYGLALIVYAIWIGVGIKRHGVRYLKLAVVPSGVPGWILPLLVPLEIISNFI +VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVILGSVALYFLELL +IMYLQAFVFTLLTAIYIQGAIDANDH +>PROKKA_02140 +MLTLVLANASFVPPTISDGNLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP +QLVPGKAQWLAESGYSFVRNGIAKDILGEKNFRQWVPLLFAIFFFVLLNNLFGAIPVLQL +PSFSHAGAAYGIALIVYAIWIGVGLKRHGIRYLKLAVVPSGVPSWILPLLVPLEIISNFI +VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVIIGSVALYFLELL +IMYLQAFVFTLLTAIYIQGAIDANDH +>PROKKA_02033 +MLPLVLANAEFVPPSVSDAHLPDLLPWGAEYGTGFGKQMLLVLLSVVLITGFFAWAMRKP +KLVPGRAQWIAESGYAFVRNGIGRDVMGEKHFKQWVPLLFAIFFFVLLNNLFGAIPLLQM +PSFSHAGSAYAIALIVYAIWIGVGVKHHGVKYFKLAVVPSGVPGWILPLLVPLEFISNFI +VRPLTHSLRLMAVMLAGHMIVMLAGAGAAFLITQTGNPLLAGTGVLVILASVALYLLEIL +LMYLQAFVFTLLTALYIQGAIDANDH +>PROKKA_00758 +MLTLVLANASFVPPTISDGHLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP +RLVPGKAQWLAESGYSFVRNDIAKDILGEKNFKQWVPLLFSIFFFVLLNNLFGAIPVLQL +PTFSHAGAAYGLALIVYAIWIGVGIKRHGVRYLKLAVVPSGVPGWILPLLVPLEIISNFI +VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVILGSVALYFLELL +IMYLQAFVFTLLTAIYIQGAIDANDH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000701.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000701.fa new file mode 100644 index 0000000000000000000000000000000000000000..4c433698811b0672df53194a21b7592d733b7ae0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000701.fa @@ -0,0 +1,25 @@ +>PROKKA_00793 +MISNGLILAAAEGANPLIPNPWEILVVVVGFALLMFIVIKFIVPTLEKSYQDRVEAIEGG +LAKAEKAQAEANAMMADYESQLADARTEANRIREDARTEAAEIVAEARERATAEARRISE +QAQAQIAAERQQAAAQLKGEVGSLATTLAGKIVGESLEDDARSQRVVDRFLADLDRHQSA +GVAE +>PROKKA_00524 +MISNGLILAAAEGANPLIPNPWEILVVVVGFALLMFIVIKFIVPTLEKSYQDRVEAIEGG +LAKAEKAQAEANAMMADYESQLADARTEANRIREDARTEAAEIVAEARERATAEARRISE +QAQAQIAAERQQAAAQLKGEVGSLATTLAGKIVGESLEDDARSQRVVDRFLADLDRHQSA +GVAE +>PROKKA_02138 +MISNGLILAAGANPLIPNPWEILVVVVGFALLMFIVIKFIVPTLEKSYQDRVEAIEGGLA +KAEKAQAEANAMMADYESQLADARTEANRIREDARTEAAEIVAEARERATAESTRISEQA +QAQIAAERQQAASQLKGEVGTLATTLASKIVGESLEDDARSQRVVDRFLADLDRHQSAGV +AE +>PROKKA_02031 +MISNGLILASAEGANPLVPNPWEILVTTVGFAVLMFIVVKFVVPALEKSYTDRVEAIEGG +LEKAEKAQAEANKMMADYEGQLADARQEANRIREEARTEGAQIVAEARERAAAEAARITE +QAQTQIAAERTQAAAQLKGEVGTLATTLASKIVGESLDDDARSQRVVDRFLADLDRHQSA +GVSE +>PROKKA_00760 +MISNGLILAAAEGANPLIPNPWEILVVVVGFALLMFIVIKFIVPTLEKSYQDRVEAIEGG +LAKAEKAQAEANAMMADYESQLADARTEANRIREDARTEAAEIVAEARERATAEATRISE +QAQAQIAAERQQAAAQLKGEVGSLATTLAGKIVGESLEDDARSQRVVDRFLADLDRHQSA +GVAE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000702.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000702.fa new file mode 100644 index 0000000000000000000000000000000000000000..bc429dc05f00e4e74590eb20c9f7ca2fbe087e8f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000702.fa @@ -0,0 +1,30 @@ +>PROKKA_00794 +MMTGASRDSLAASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH +GLVDSLFGARVTPGALQVLKDLAGRRWSAERDLGDALETVAVHAAAAEAARGGHAGLAAL +LGELLAFNRTVEDSHELQRALTDQHAPLEARAALAGRLLGESASPAGRLLVERAVSAPRG +LKPSAAIRKAADAVAERQRQWIAEVTVARPLEAEQQERLALGLRRAFGRDLVMDVTVDPH +VVGGVRVQVGDDVVDGSMASRLHDLQRRMAG +>PROKKA_00525 +MMTGASRDSLAASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH +GLVDSLFGARVTPGALQVLKDLAGRRWSAERDLGDALETVAVHAAAAEAARGGHAGLAAL +LGELLAFNRTVEDSHELQRALTDQHAPLEARAALAGRLLGESASPAGRLLVERAVSAPRG +LKPSAAIRKAADVVAERQRQWIAEVTVARPLEAEQQERLALGLRRAFGRDLVMDVTVDPH +VVGGVRVQVGDDVVDGSMASRLHDLQRRMAG +>PROKKA_02137 +MMTGASRDSLTASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH +GLVDSLFGARVTPGALQVIKDLAGRRWSAERDLGDALETVAAHAAAAEAGRGGHAGLAAL +SGELLAFNRTVEDSHEVQRALTDQHAPVEARAALARRLLGESASPAGQLLVERAVAAPRG +VKPAAAVRQAADVVAERQRQWIAEVTVARPLGAEQQERLALGLRRAFERDLVMDVTVDPH +VVGGIRVQVGDDVVDGSMASRLNDLQRRMAG +>PROKKA_02030 +MMTGASGDSLTASLESVRTVLDEGGVALARELFAALDVVDQQGALRRALTDPAWSTERRH +GVLDSLFGGRVSPGALQVLKDLAGRRWSAERDFGDALEAVAADAAAGEAARGGHAGLAAL +SGELLGFQRVFQDSHEVERALTDQRAPRESRSGLARRLLGAQASPAAVLLVERAVTDGRG +VKPATALRSYADVVATRQRQWIAEVTVARPLEDGQRERLAAGLRRAFGRDLVLDVNVDPT +VVGGIRVQVGDDVIDGSMASRLNDLQRRMAA +>PROKKA_00761 +MMTGASRDSLAASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH +GLVDSLFGARVTPGALQVLKDLAGRRWSAERDLGDALETVAAHAAAAEAARGGHAGLAAL +SGELLAFNRTVEDSHEVQRALTDQHAPLEARAALAGRLLGESASPAGRLLVERAVSAPRG +LKPSAAVRKAADVVAERQRQWIAEVTVARPLEAEQQERLALGLRRAFGRDLVMDVTVDPH +VVGGIRVQVGDDVVDGSMASRLHDLQRRMAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000707.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000707.fa new file mode 100644 index 0000000000000000000000000000000000000000..fb1112014bd684127d7e2ce069ff6fb9b3989516 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000707.fa @@ -0,0 +1,20 @@ +>PROKKA_00799 +MQGPVLIASATVAAVIVLSALALVMRRRALARVTAAFPAVLEREGPGRERVIGVYDESRL +RLTGRWRLSRERWSADRSRLQIDRLPADEAGRTVLELSAGARPVRVVVDPDDAGALRAWS +EAGPSAASSFWRR +>PROKKA_00530 +MLIASATVVAVIVLSALALVMRRRALARVTAAFPAVLEREGPGRERVIGVYDESRLRLTG +GWRLSRERWSADRSRLQIDRLPADEAGRAVLELSAGARPVRVVVDPDDAGALRAWSEAGP +SAASSFWRR +>PROKKA_02132 +MLIALAGVLAVFALSASALAVRRRALLRTSAAFPAVLQGHGRPRERVIGVYDETRLLFTG +RWMIRRERWSVGRCDLQIDRLPVAEDGRAVLELDGGRGSVTVVVDPDDAGALRAWSEAGP +SAASSFWRR +>PROKKA_02025 +MRGPVLLLSGALAVFALLALAGWARHRALVRGPGRFAGVLVTDGGRRCRVVGCFRSHELV +LSHHLLPERRLWSAERWRLEVDRLPAAEAGHTRLRITDASGRSDDAVDLEVEDDVAGAVR +AWTEAGPSQAGQSWWRPPGAA +>PROKKA_00766 +MEGPVLIASATVVAVIVLSALALVMRRRALARVTAAFPAVLEREGPGRERVIGVYDESRL +RLTGGWRLSRERWSADRSRLQIDRLPADEAGRAVLELSAGTRPVRVVVDPDDAGALRAWS +EAGPSAASSFWRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000708.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000708.fa new file mode 100644 index 0000000000000000000000000000000000000000..4db9930951937f0f9664699239ba8bf072009719 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000708.fa @@ -0,0 +1,25 @@ +>PROKKA_00800 +MRLVIARCSVTYEGRLNAHLPTATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE +PSPDQADQGVTQVWRVQAKKSDDRLIVLIEEVLADDSHELGVDPGLVKDGVEADLQRLLA +EQISLLGDGHTLVRREYMTAIGPVDILARDADGGTVAVELKRRGDIDGVEQLTRYLELMN +RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF +>PROKKA_00531 +MRLVIARCSVTYEGRLNAHLPTATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE +PSPDQADQGVTQVWRVQAKKSDDRLIVLIEEVLADDSHELGVDPGLVKDGVEADLQRLLA +EQISLLGDGHTLVRREYMTAIGPVDILARDADGGTVAVELKRRGDIDGVEQLTRYLELMN +RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF +>PROKKA_02130 +MRLVIARCSVTYEGRLNAHLPPATRLLMVKADGAVLVHSDGGSYKPLNWMSPPATLHTTA +PTAEQAEQGVVEVWRVQAAKSDDRLMILIEEILADQSHELGADPGLVKDGVEADLQRLLA +EQIGLLGDGHTLVRREYMTAIGPVDILARDPEGGTVAVELKRRGDIDGVEQLTRYLELMN +RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF +>PROKKA_02023 +MRLVIARCSVTYEGRLNAHLPSATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE +PTEEQAAAGVTQVWRVQAKKSDDRLLVLLEEVLADETHELGVDPGLVKDGVEADLQRLLA +EQIGLLGDGHTLVRREYMTAIGPVDILAKGPGGQTVAVELKRRGDIDGVEQLTRYLDLMN +RDPLLAPVTGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDADARLF +>PROKKA_00767 +MRLVIARCSVTYEGRLNAHLPTATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE +PFPDQADQGVTQVWRVQAKKSDDRLIVLIEEVLADDSHELGVDPGLVKDGVEADLQRLLA +EQISLLGDGHTLVRREYMTAIGPVDILARDADGGTVAVELKRRGDIDGVEQLTRYLELMN +RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000710.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000710.fa new file mode 100644 index 0000000000000000000000000000000000000000..122574f62e4a85f0a1e32d008b56b27da66968aa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000710.fa @@ -0,0 +1,43 @@ +>PROKKA_00802 +MEEKEPASGPDAPSVADVRAPAEPEGAEQQPVGGIPVEPAGAAAAPPSHGPTPAGRRRRL +RLGSVLRRRRPFLEEDRVDPEPDPADGAEDPAVAAVALESPVLTGFLLAVGVTLAIGIVS +VLRTNGQLIVWIAAALFIALGLDPLVRRVESWGAPRWVGVLTAALGLAAVAGAFVALLVP +TVIEQSTQLVQDLPAIIDGVMRAEWFVQLDEEFHLQEAVRAQTERLAADGVAITDLFGGL +LGLGQTVLNAVFSVLVVVVLTLYFLSSLPHMKYWAYRLAPRSRRPRIEALSEQITSSVGH +YVMGQSFVAALNGAVAFTALAIAGAPFAVLLAAIAAFMAFIPLVGAAIGGTLLTLVSLLT +SWQTAAVFAAIYFVYLQIEAYVISPRVMARAVPVPAAVAVIAVIAGGALLGVLGALMAIP +LAAALALLVREVFIPRQDAR +>PROKKA_00533 +MSLGPTVASRARRGQAGALTYAERVEEKETASGPDVAGVADVRGPAEPEGAEQPPVAGVP +VEPVGVAAAPPSHGPTPAGRRRLPRLGSVLRRRRPFLEEDRVDPESVPVDGAEDPAVAAV +ALESPVLTGFLLAVGVALAIGVVSVLRTNGQLIVWIAAALFIALGLDPLVRRVESWGAPR +WVGVLTAALGLAAVAGAFVALLVPTVIEQSTQLVQDLPAIIDGVMTAEWFVQLDEEFHLQ +EAVRAQTERLAADGVAVTDLFGGLLGFGQTVLNAVFSVLVVVVLTLYFLSSLPHMKYWAY +RLAPRSRRPRIEALSEQITSSVGHYVMGQSFVAALNGAVAFTALAIAGAPFAVLLAAIAA +FMAFIPLVGAAIGGTLLTLVSLLTSWQTAAVFAAIYFVYLQIEAYVISPRVMARAVSVPA +AVAVIAVIAGGALLGVLGALMAIPLAVALLLLVREVFIPRQDAR +>PROKKA_02128 +MEPVDPTAAPASAAPAPLPASGRVPRRRRRRGRLIPLRGVLRRRRPVFLAEDRVDPDPEH +PEPEPTGEPPVTAVTVESPVATGFLLTVGVALALAVVWVLRTNGQLLVWIAAALFIALGL +DPLVRRVESWGAPRWAGVLTAALGLAAVASAFVALLVPTVVEQSRQLVEGLPGTIEDVMT +SAWFIELDQEFHIQEAVRAQTDRLTTDGAAVTDLFGGLLGIGQTVLNAFFSVFVVVVLTL +YFLASLPHMKYWAYRLAPRSRRPQVERLSEKITSSVGHYVMGQSFVAALNGTVAFTALAV +AGTPFAVLLAAFAAFMAFIPLVGAVIGGTVLTLLSLLTSWQTAAVFAAIYFVYLQIEAYV +VSPRVMARAVAVPAAVAVIAVIAGGALLGVLGALMAIPLAAALSMLVREVFIPRQDAR +>PROKKA_02021 +MDHIEDSPAPSGPSRGARRLRLGSLVRRREAFLPNERVDPLPPGSPDAAPAEPEVPELAL +RAPVAAGFLLTMGVCLAAVLVWVVLENTQLLVWIAAALFIALGLDPVVRLVERWGAPRWV +GVLLAALGLAAVAGAVVGMLVPAVVQQSTQLITGLPDTITQIMATPWFREVDRQLQIQHA +VQSWLDGLTKDGAAVTQLFGGLVGIGQTVMNAVFSTIVVVVLALYFLASLPHLKYWGYRL +APRSKRLRVEALGEEITLSVGHYVMGQTVVAVLNGTVAFIALSVAGGPFPVLLAFVAAVM +AFIPLVGALIGGTILTAVCLLESWQAAALFAAIYFVYLQIEAYVVSPRVMARAVAVPAAV +GVIAVIAGGTLLGVLGALMAIPTAAAVLLIVREVLIPRQDAR +>PROKKA_00769 +MSLRPTVASPARRGQAGALTYAERVEEKETASGPDAAGVADVRAPAEPEGTEQPPVAGIP +VEPVGVAAAPPSHGPTPAGRRRLPRLGSVLRRRRPFLEEDRVDPESVPVDGAEDPAVAAV +ALESPVLTGFLLAVGVALAIGVVSVLRTNGHLIVWIAAALFIALGLDPLVRRVESWGAPR +WVGVLTAALGLAAVAGAFVALLVPTVIEQSTQLVQDLPAIIDGVMTAEWFVQLDEEFHLQ +EAVRAQTERLAADGVAVTDLFGGLLGFGQTVLNAVFSVLVVVVLTLYFLSSLPHMKYWAY +RLAPRSRRPRIEALSEQITSSVGHYVMGQSFVAALNGAVAFTALAIAGAPFAVLLAAIAA +FMAFIPLVGAAIGGTLLTLVSLLTSWQTAAVFAAIYFVYLQIEAYVISPRVMARAVSVPA +AVAVIAVIAGGALLGVLGALMAIPLAAALLLLVREVFIPRQDAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000712.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000712.fa new file mode 100644 index 0000000000000000000000000000000000000000..2a434fb312271fbf9b958a7b4f47f350a3dbd7cc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000712.fa @@ -0,0 +1,30 @@ +>PROKKA_00804 +MTPHASEPAPTHLAAATRRRAVDAPDPDLALVTRGLTQRFGDKLALDALDLDVPAGSFFG +VVGPNGAGKTTALSMATGLLRPDHGRAWIHGVDVWEQPLEAKRRVGVLADGVRTFDRLTG +AQLVTYAGLLHGLDADTVAERTADLLRVMDLEDAGRTLVADYSAGMTKKVSLAAAMVHAP +DLLVLDEPFEAVDPVSAANIRDILHSYVERGGTVIVSSHVMDLVQRMCTHVAVIAAGTLR +AAGTLEEVRDGRDLEDRFVELVGGRHGSEGLAWL +>PROKKA_00535 +MTPHAPEPAPAHLAAAARRRAADAPDPDLALVTRGLTQRFGDKLALDALDLDVPAGSFFG +VVGPNGAGKTTALSMATGLLRPDHGRAWIHGVDVWEQPLEAKRRVGVLADGVRTFDRLTG +TQLVTYAGLLHGLDADTVAERTADLLRVMDLEDAGRKLVADYSAGMTKKVSLAAAMVHAP +DLLVLDEPFEAVDPVSAANIRDILHSYVERGGTVIVSSHVMDLVQRMCTHVAVIAAGTLR +AAGTLEEVRDGRDLEDRFVDLVGGRHGSEGLAWL +>PROKKA_02126 +MSEHPAEPHRTAPSSAEAPHAGPAPAEAPAVVPSAAARRRAVDAPDPDLALVTRGLTKRF +GDKTALDGLDLDVPAGSFYGVVGPNGAGKTTALSMATGLLRPDLGQAWIHGVDVWAQPLE +AKRRVGVLADGVRTFDRLTGAQLVTYAGLLHGVDADTVAARTEDLLRVMDLADAGRKLVV +DYSAGMTKKISLAAAMVHAPDVLVLDEPFEAVDPVSAANIRDILHDYVGRGGTVIVSSHV +MDLVQRMCSHVAVIAGGTLRAAGTLEEVRAGRDLEDRFVDLVGGRHEQEGLAWL +>PROKKA_02019 +MRAQDAPDPNLALVTRGLAKRFGEKVALAGLDLEVPAGSFFGVVGPNGAGKTTALSMATG +MLRPDAGRVWIHGVDVWEQPLEAKRRVGVLADGVRTFDRLTGAQLITYAGLLHGLDRDTV +DVRTADLLRVMDLEEAGRKLVVDYSAGMTKKVNLAAAMVHAPDVLVLDEPFEAVDPVSAA +NIRDILHDYVGRGGTVIVSSHVMDLVQRMCSHVAVIAGGVLRAAGTLEEVRAGRDLEERF +VDLVGGRHTGEGLAWL +>PROKKA_00771 +MTPHAPEPAPAHLAAAARRRAVDAPDPDLAFVTRGLTQRFGDKLALDALDLDVPAGSFFG +VVGPNGAGKTTALSMATGLLRPDHGRAWIHGVDVWEQPLEAKRRVGVLADGVRTFDRLTG +AQLVTYAGLLHGLDADTVAERTTDLLRVMDLEDAGRKLVADYSAGMTKKVSLAAAMVHAP +DLLVLDEPFEAVDPVSAANIRDILHSYVERGGTVIVSSHVMDLVQRMCTHVAVIAAGTLR +AADTLEEVRDGRDLEDRFVDLVGGRHGSEGLAWL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000714.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000714.fa new file mode 100644 index 0000000000000000000000000000000000000000..0263e0c40fe18a4e60f96fec9c86f3f531d795ff --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000714.fa @@ -0,0 +1,15 @@ +>PROKKA_00806 +MSVTGEPDLNDPFAPAGGGTSVLEREELRQEIEPGDHERFAHYVRKEKITESAVTGAPVI +ALCGKVWVPGRDPNKFPVCPTCKEIYEGLREPQDGGDGDGGGKRGGWFGGRGRG +>PROKKA_00537 +MSVTGEPDLNDPFAPAGGGTSVLEREELRQEIEPGDHERFAHYVRKEKITESAVTGAPVI +ALCGKVWVPGRDPNKFPVCPTCKEIYEGLREPQDGGDGDGGGKRGGWFGGRGRG +>PROKKA_02124 +MSVTGEPDLTDPFSPAGGGTSVLEREQQLQDVEPGDHERFAHYVRKEKITESAVTGAPVI +ALCGKVWVPGRDPQKFPVCPTCQEIYEGLREPQDGDDAGAGGGRRGGWFGGRGRG +>PROKKA_02017 +MSISDPFQNDPLSPSGGGTSVLEREEQLQDVEPGDHERFAHYVRKEKIMESALSGEPVIA +LCGKVWVPGRDPNKFPVCPLCQEIYDGLRDPQDGDDAGSGGGRRGGFFGRGRG +>PROKKA_00773 +MSVTGEPDLNDPFAPAGGGTSVLEREELRQEIEPGDHERFAHYVRKEKITESAVTGAPVI +ALCGKVWVPGRDPNKFPVCPTCKEIYEGLREPQDGGDGDGKRGGWFGGRGRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000719.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000719.fa new file mode 100644 index 0000000000000000000000000000000000000000..129fcea83195f6f4825936aa50ec2709a2e84288 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000719.fa @@ -0,0 +1,30 @@ +>PROKKA_00812 +MAERFRWTRRGYTAQLELPEVRLLRGLVRDVVALLEGRRADVRPAEADPAEAPAAEDGVD +TPEDPPAAPPSVSAAQDAGPVAGLDASDAAFWGLVSGLHLSQDPEPQRSAPTDPAVARLL +PDAMPQAGAAEQGAHRALTEDALSEGKLADARLALELLRSTRVEVPHDQAPAFGRALNDV +RLVLAARLGVETEEDAARVHAVDDWRSAEDVESTMALLYNFTSWLLETLMTEMLSELPEG +ADESAPGAGDAEDEQ +>PROKKA_00544 +MAERFRWTRRGYTAQLELPEVRLLRGLVRDVVALLEGRRADVRPAEADPAEAPAAEDGVD +TPEDPPAAPPSVSAAQDAGPVAGLDASDAAFWGLVSGLHLSQDPEPQRSAPTDPAVARLL +PDAMPQAGAAEQGAHRALTEDALSEGKLADARLALELLRSTRVEVPHNQAPAFGRALNDV +RLVLAARLGVETEEDAARVHAVDDWRSAEDVESTMALLYNFTSWLLETLMTEMLSELPEG +SDESAPGAGDAEGEQ +>PROKKA_02118 +MAERFRWTRRGYTAQLEKPEVRLLRGLVKDVITLLEGRRRNVLSEADDLPADAPGAPEPS +ADVAPVPQGPEAGAGPAAGLDEADAAFWELVSGLHLSQDRVPHRAAPADPAVARLLPEAM +PQADAQERGAHRALTEDALSEGKLADARLALELLRSTRVEVPHHQAPAFGRALNDVRLVL +AARLGVETEEDAERVHAVDDWRSAEDVESTMALLYNFTTWLLETLMTEMLSELPEGADED +APGADEAGDDA +>PROKKA_02009 +MAQRFRWTRRGYVAELEDAELRLLRGLVKDVVTLLENRQDEVAPPGSDAGTAEDAPEAGA +EPVADARPGDAVGPGEETPHDAAFWALVGGLDLVADPVAERSAPEDPAVARLLPDAMPHA +EPAERARQRALTEDALTAAKLADARRALEALRSVRVTVPHEHAVSFGRALNDVRLVLAAR +LGIETEQDAARVHAVDDWRDAQDVEATMALLYNFTTWLQETLMAEMLSELPLEGAAGPDE +EERA +>PROKKA_00781 +MAERFRWTRRGYTAQLELPEVRLLRGLVRDVVALLEGRRADVRPAEADPAEAPAAEDGVD +TPEDPPAAPPSVSAAQDAGPVAGLDASDAAFWGLVSGLHLSQDPEPQRSAPTDPAVARLL +PDAMPQAGAAEQGAHRALTEDALSEGKLADARLALELLRSTRVEVPHDQAPAFGRALNDV +RLVLAARLGVETEEDAARVHAVDDWRSAEDVESTMALLYNFTSWLLETLMTEMLSELPEG +SDESAPGAGDAEGEQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000720.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000720.fa new file mode 100644 index 0000000000000000000000000000000000000000..fc7a9b0827a93deb711bfe6c04313463b404fd33 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000720.fa @@ -0,0 +1,35 @@ +>PROKKA_00813 +MSGQRAAVDAAAPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTEHSPYGPRPIAEVRA +LALAIMDELVARGVKALVIACNSASAAVLRDARERYTGGHGIPVIEVIQPAVRRAVAATR +TGRIGVIGTEATVGSRAYEDSFSAAPHLEITSVACPRFVEFVEAGITTGPELLETAREYT +APLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEHPHS +AAGSGQATRHRFAATGDPDHFQALARRFLGPEVESVRRLETIGAPRPAAAPVPTRSTAFV +PLGAEQEGVT +>PROKKA_00545 +MSGQRAAVDAAAPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTEHSPYGPRPIAEVRA +LALAIMDELVARGVKALVIACNSASAAVLRDARERYTGGHGIPVIEVIQPAVRRAVAATR +TGRIGVIGTEATVGSRAYEDSFSAAPHLEITSVACPRFVEFVEAGITTGPELLETAREYT +APLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEHPHS +AAGSGQATRHRFAATGDPDHFQALARRFLGPEVESVRRLETIGAPRPAAAPVPTRSAASV +RPGPEQEGVT +>PROKKA_02117 +MSAPPQARPEVSASSPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTAHAPYGPRPIAQ +VRALALGIMDELVDAGVKALVIACNSASAAVLRDARERYTGRHGIPVVEVIQPAVRRAVA +ATRSGRIGVIGTQATVGSRAYDDSFSAAPHLQVTSAACPRFVEFVEAGITTGPELLATAQ +EYTEPLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEH +PHSAAGSGQDTRHRFAATGDPEHFQALARRFLGPEVGAVRRLDTVRERYPTAALAQLTPD +LIARLGAEQERET +>PROKKA_02008 +MSATADTAQTGAGPSSPIGVFDSGVGGLTVARAIMDQLPHEPIIYVGDTAHSPYGPRPIA +QVRALALGVMDELVEAGVKALVIACNSASAAVLRDARERYTGRLGIPVVEVIQPAVRRAV +AATRNGRVGVIGTQATVGSRAYEDSFSAAPHLQITSVACPRFVEFVEAGITTGPELLETA +EEYVAPLKAAGVDTMVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRALVRHGLE +HPHSAAGSAAAPEHRFAATGDPEHFAALARRFLGPEVGPVRQIQEIRERYPTAALTALTP +DVLARLRAEMEEDGAR +>PROKKA_00782 +MSGQRAAVDAAAPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTEHSPYGPRPIAEVRA +LALAIMDELVARGVKALVIACNSASAAVLRDARERYTGGHGIPVIEVIQPAVRRAVAATR +TGRIGVIGTEATVGSRAYEDSFSAAPHLEITSVACPRFVEFVEAGITTGPELLETAREYT +APLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEHPHS +AAGSGQATRHRFAATGDPDHFQALARRFLGPEVESVRRLETIGAPRPAAAPVPTRSAASV +RPGPEQEGVT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000721.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000721.fa new file mode 100644 index 0000000000000000000000000000000000000000..a8ceae5d6be1975b834d7b2d203686562abd9d26 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000721.fa @@ -0,0 +1,30 @@ +>PROKKA_00814 +MKLTIIGASGSFPGPGSPASCYLLTAEGVAEDGVTPRTWRILLDLGNGALGVLQRYVELE +DLDGILLSHLHPDHFMDLCGMHVAIRWNPAGWDRGRLPVYGPAGTADRIAEAYGMDPEPG +MHQDFEFRCWAAGRTERLGPFRFTPVPVRHPIDEAYAIRVEVDRVDDDGDVTTRVLTYSG +DTDACEGLVEAARDADVFLCEAAFHEGRDDGIDGVHLTGRRAGETAAQAGARKLLLTHLP +VWNDPQRAVQEARAVYDGPLAVAVSGLSYGV +>PROKKA_00546 +MKLTIIGASGSFPGPGSPASCYLLTAEGVAEDGVTPRTWRILLDLGNGALGVLQRYVELE +DLDGILLSHLHPDHFMDLCGMHVAIRWNPAGWGRGRLPVYGPAGTADRIAEAYGMDPEPG +MHQDFEFRCWAAGRPERLGPFRFTPVPVRHPIDEAYAIRVEVDRVDDDGDVTTRVLTYSG +DTDACEGLVEAARDADVFLCEAAFHEGRDDGIDGVHLTGRRAGETAAQAGARKLLLTHLP +VWNDPQRAVQEARAVYDGPLAVAVSGLSYGV +>PROKKA_02116 +MKLTVIGASGSFPGPGSPASCYLVTAQGVAEDGVTPRTWRILLDLGNGSLGVLQRYIELE +ELDGILLSHLHPDHCMDLCGMHVAIRWNPEGWHRDRMPVYGPTATADRIAEAYGMDPEPG +MHEDFDFRVWRPGRTERFGPFRLTPVPVRHPIDEAYAIRVEADEPDGEGGTVTRVLTYSG +DTDACEGLVEAARDADLFLCEAAFHEGRDDGIDGVHLTGLRAGQTAAQAGAKKLLLTHLP +VWNDPQRAVLEAREAYEGPMAVAVSGLSYGV +>PROKKA_02007 +MKLTVIGASGSFPGPGSPASCYLVTADGPDGNGGTRPWRILLDLGNGSLGVLQRHIELEQ +IDGVLLSHLHPDHCIDLCGLHVAVRWNPEGWDAGRIPVYGPAATATRIAEAYGMDPEPGM +QEDFDFRAWEAGRTEGLGPFRLTPFAVRHPIDEAYAIRVETTEPGPDGEPVTRVLAYSGD +SDTCDGLVEAARDADLFLCEAAYHEGRDDHIDGVHLTGRRAGQMAAEAGARKLLLTHLPV +WNDPQRCAQEAREAYVGPLAVAVSGLSYGL +>PROKKA_00783 +MKLTIIGASGSFPGPGSPASCYLLTAEGVAEDGVTPRTWRILLDLGNGALGVLQRYVELE +DLDGILLSHLHPDHFMDLCGMHVAIRWNPAGWGRGRLPVYGPAGTADRIAEAYGMDPEPG +MHQDFEFRCWAAGRPERLGPFRFTPVPVRHPIDEAYAIRVEVDRVDDDGDVTTRVLTYSG +DTDACEGLVEAARDADVFLCEAAFHEGRDDGIDGVHLTGRRAGETAAQAGARKLLLTHLP +VWNDPQRAVQEAREVYDGPLAVAVSGLSYGV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000724.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000724.fa new file mode 100644 index 0000000000000000000000000000000000000000..bfdf4e4f7cf25ef2c55fcc350f56938b6d457a79 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000724.fa @@ -0,0 +1,39 @@ +>PROKKA_00817 +MSGGRVPVPGLDFTAIDFETANGFRGSPCAVGAVRVRDGVMVDRAEWLIRPPVGFDRFDP +RNVRIHGITEDRVLDAPRFAQVYDELADFVGTDVLAAHNAGFDVGVIESGLEVSGRDVPG +LEFVCTLVLARRVYDLPSYALPSAAREAGFTPGRHHDALADAEACAAILVDIGRRVLGAP +PADADVLPGLTDAPAGRGVDRLMRAQGLGVSVLAPRAAGAGAESKATRQARRTEGVFDAR +VPLRDERAMPDFMRWPDEGVNPLPNPAADPGHPLFGQTVVFTGGIGMSRQRAKTRAAAHG +AQTANRVGAATTMLVVGDGFEAADLHRPRAEDGAPQAVTTALAHRKTRDALRRRDRG +>PROKKA_00549 +MSGGRAPVPGLDFTAIDFETANGFRGSPCAVGAVRVRDGVMVDRAEWLIRPPVGFDRFDP +RNVRIHGITEDRVLDAPRFAQVYDELADFVGTDVLAAHNAGFDVGVIESGLEVSGRDVPG +LEFVCTLVLARRVYDLPSYALPSAAREAGFTPGRHHDALADAEACAAILVDIGRRVLGAP +PADAEILPGLTDAPAGRGVDRLMRAQGLGVSVLAPRAAGSGAESKATRQARRTEGVFDAR +VPLRDERAMPDFMRWPDEGVNPPPNPTADPGHPLFGQTVVFTGGIGMSRQSAKTRAAAHG +AQTANRVGAATTMLVVGDGFEAADLHRPRAEDGAPQAVTTALAHRKTRDALRRRDRGQAI +ALVSEGEFLQMLDGNWPDAAR +>PROKKA_02113 +MSGVLAPVPGLDFTAIDFETANGFRGSPCALGAVRVRDGVMVERAEWLIRPPVGFDRFDP +RNVRIHGITEDRVLDAARFADVYDELAGFVGADVLAAHNAGFDVGVIESGLEVSGRDVPR +LDFVCTLVLARRVYDLASYALPSAAREAGFAPGPHHDALADAEACAAILVDVARRVLGTE +AGDGAAVAPAGARGLPEPFDVPRLMRAQGLTVNTLAQRAAGEGPESKATRQARRAQGVFD +ARVPLKDERAMPDFLRWPDEGTNPVPNPDADPGHPLHGQTVVFTGGIGMSRQTAKVRAAR +LGAQTANRVGAATTMLVVGDGFEAADLDRPAPAPGTREAVTTALAHRKTRDALRRRERGQ +HISLVSEGEFLQMLDGNWPDAAR +>PROKKA_02004 +MTAGIAPVRQPGLDFTAIDFETANGFRGSACQLGAVRVRDGLPASRAVWLMRPPAGFDRF +DPRNVRIHGIHADRVVDAPRFAEVYDAFAAFAGDDVLVAHNAGFDLGVIESGLEVSGRDV +PAHDYACTLTLARRIYDLPSYSLPSAAREAGFVPGRHHDALADAEACAAILVDLARRVCP +PGEATVDALLASQGLRRSRLTARAAGTGRESRATRQARTMPGLFDATIPLADDRTLPDLM +RWPDEGVNPEPAADADPGHPLYGQVVVFTGGIGMSRQEAKNRAAQRGAATANRVNGRTTM +LVVGDGVDPAELVGAPEVHGVVVDPGATDPAGRGVDPGGAVTHRKTREALQRRAKGQAIA +LVSEAEFLQMVDGAWPAGAR +>PROKKA_00786 +MSGGRVPVPGLDFTAIDFETANGFRGSPCAVGAVRVRDGVMVDRAEWLIRPPVGFDRFDP +RNVRIHGITEDRVLDAPRFAQVYDELADFVGTDVLAAHNAGFDVGVIESGLEVSGRDVPG +LEFVCTLVLARRVYDLPSYALPSAAREAGFTPGRHHDALADAEACAAILVDIGRRVLGAP +PADAEILPGLTDAPAGRGVDRLMRAQGLSVSVLAPRAAGSGAESKATRQARRTEGVFDAR +VPLRDERAMPDFMRWPDEGVNPLPNPAADPGHPLFGQTVVFTGGIGMSRQSAKTRAAAHG +AQTANRVGAATTMLVVGDGFEAADLHRPRAEDGAPQAVTTALAHRKTRDALRRRDRGQAI +ALVSEGEFLQMLDGNWPDAAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000725.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000725.fa new file mode 100644 index 0000000000000000000000000000000000000000..5fafa5bdd60fa2aac0a35825a92ac714859a9f69 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000725.fa @@ -0,0 +1,40 @@ +>PROKKA_00818 +MSATAPEPTASSSTPLPGPEHADRVLALLAAGAAGDALGGVVEFTPASGIAAVHGPAGVT +DAADLLAQEGAHALPITDDTQLTLYVLDGLLEWIEWQNDGVPADPAACVWLACLRWFATQ +DGALPEGAPPAPPRWIDAHAELKVRRAPGTACLTGLAEPGMGLPGDPHNPGSKGCGTVMR +SAPYGMVPGLEDPHVVSLARQGAVLTHGHPTAWVAAAAYALVIAALLRGLDLAAAVAHAR +AWLDTLGEEAEETRAAVTAAVDLAGTVDADPGAPGALPTALGEGWVAEEALAIALYAALT +AQAAHPADPAAALALALRIGVNHDGDSDSTASLAGQVLGAAHGTAVFGAHDPADRAAAEA +SVPGWIAEREVVLEAARRWSAATT +>PROKKA_00550 +MSATAPEPTASSSTPLPGPEHADRVLALLAAGAAGDALGGVVEFTPASGIAAVHGPAGVT +DAADLLAQQGAHALPITDDTQLTLYVLDGLLEWIEWQNDGVPADPAACVWLACLRWFATQ +DGALPEGAPPAPPRWIDAHAELKVRRAPGTACLSGLAEPGMGLPGDPHNPGSKGCGTVMR +SAPYGMVPGLEDPHVVSLARQGAVLTHGHPTAWVAAAAYALVIAALLRGLDLAAAVAHAR +AWLDTLGEEAEETRAAVTAAVDLAGTVDADPGAPGALPTALGEGWVAEEALAIALYAALT +AQAAHPADPAAALALALRIGVNHDGDSDSTASLAGQVLGAAHGTAVFGAHDPADRAAAEA +SVPGWIAEREVVLEAARRWSAATT +>PROKKA_02112 +MTETPAAPSLPGPEHATRVAALLAAGAAGDALGYTVEFDADAAVRARHGAEGLTTGEAAL +AVVGGEALPISDDTQMTLYVLDGLLEWIEWQNDGQAADPAACVWLACLRWWATQHGGALP +DGAPPVPPRWLEDHPELRARRAPGNACLSGLDSAAMGLPGDPRNPDSKGCGTVMRSAPYG +MVPGLEDVHVVSFARQGAVLTHGHPTAWVAAAAYSLMIAALLRGAGLEDAVAHARVWVDS +LDPAEGGETAAALASAVELAASPADDAGRPGTLPAALGEGWVAEEALAIAVHAALVAQAR +HEDPADMLALALRIGANHAGDSDSTASLAGQLLGAAHGPAVFGADAAADGPAGLVPAWVA +EREVVAEAARRWSAATT +>PROKKA_02003 +MTDAAPSPRTDVSYPSRVLGLLAAGAAGDALGYAVEFDSVDRILGRLGAAGVTDGPALAA +VSGVSALPVSGDTQMTLYVLDGMLEWIEWQNAGQASDPAACVWLACLRWLRTQDGALPDG +APPAQDRWIDAHTELHAQRAPGMACLSGLRSSGMGVVPDPKNPDSKGCGAVMRSAPYGMV +PGLEDHHVASFARQGAVLTHGHPTGWTAAAAFALTVSALFDGAELRGALEHPRTWLDSTG +EDGAETRAALDGALAEAARAVEAGDDVGAPGTLPASLGEGWVAEEALAIAAYAALVAEAR +AEDPAAALGLALRIGANHDGDSDSTAALAGQLVGARHGMAVFGSRGQDADSVPAWITERE +VVAEAARRWIAATT +>PROKKA_00787 +MSATAPEPTASSSTPLPGPEHADRVLALLAAGAAGDALGGVVEFTPASGIAAVHGPAGVT +DAADLLAQEGAHALPITDDTQLTLYVLDGLLEWIEWQNDGVPADPAACVWLACLRWFATQ +DGALPEGAPPAPPRWIDAHAELKVRRAPGTACLTGLAEPGMGLPGDPHNPGSKGCGTVMR +SAPYGMVPGLEDPHVVSLARQGAVLTHGHPTAWVAAGAYALVIAALLRGLDLAAAVAHAR +AWLDGLGEEAAETRAAVTAAVDLAGTVDADPGAPGALPTALGEGWVAEEALAIALYAALT +AQAVHPADPAAALALALRIGVNHDGDSDSTASLAGQVLGVAHGTAVFGAHDPADRAAAEA +SVPGWVAEREVVLEAARRWSAATT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000727.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000727.fa new file mode 100644 index 0000000000000000000000000000000000000000..c7a38a973ba0877dededa39e59efdf4a315926ad --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000727.fa @@ -0,0 +1,91 @@ +>PROKKA_00820 +MRIHRMRLEGLGPYAQAQDVDFDRLNAGGLFLLDGPTGAGKSTVLAALCFALYGTVPGGR +SAESLVTTLREPGAVIPEVQVEFTVQGRRFEVVRSPKHERPRRRRSAAGGATVTTQATVS +LRERVAGEWTAPLTRADEVGQQIAAVLHLDAEQFMQVVLLPQGQFAQFLTAKSDERRALL +RRLFGTQRFDGVEEHLRVETARLDTAVAVDADVARTARAQLAEALHEALGPDWHAPEPSP +DTDDRLLALAAERAGRAHEDARADLATARAAEQRARVTARELETRGRDLAAAEAWASRRR +DHDAEAETAAARRRAVDAHERAGRVLAAAQRATAAADAAGTASETVTEALAHVEDEPTAA +AWLAAARADGAADAPASRQALGEAERAAEAVARAVQDRARMGELEQEAAAAAERRAEIGR +DRAALVESRPEREAAVAAHRAAVERGTERLGAREAVDRAVSEAAARRTAAEAAAARAVEA +ETAARAHREAQERRREAAERHVGLLRARYEQAASELAERLVPGEPCAVCGSPEHPAPAAT +ADTAVTEADVRDAEQARTAADRAATDAETALRAAEQTLRTAREAAAGLAPEAAREALERA +EAERAALDQAAKDLAADRRRLTAAEKTLAGADETAAALAAEDGRLAEAAAHRAARLTELR +DAVEAARGDAETLDARRDQVTAARRVLAALAAAQDEDARARAVADETDQALTAALAEQHF +DDVDAARAARLEETEAAARTAAVQEWHAERARLAELEASEPVRRGRALAEAGVEPPTEEQ +TRAAAEALAAAEAASSSRATAVGRLDSLVATVRRQSAALTEVLERSAGLIAEHTRVRGLL +DLVRGGGENLLKMPLTSYVLAGRLEEVAAAATERLLAMTDQRYSIEYSDAVGGRGNKGLE +LVIRDHYVDETRHPATLSGGETFMASLALALGLADTVQAEAGGIELDTLFVDEGFGSLDA +DTLDDVLDVVDTLRTGGRTVGLVSHVERMRQEIGVRLEVRKDRRGSSLAVHDGA +>PROKKA_00552 +MRIHRMRLEGLGPYAQAQDVDFDRLNAAGLFLLDGPTGAGKSTVLAALCFALYGTVPGGR +SAESLVTTLREPGAVIPEVQVEFTVQGRRFEVVRSPKHERPRRRRSAAGGATVTTQATVS +LRERVAGEWTAPLTRADEVGQQIAAVLHLDAEQFIQVVLLPQGQFAQFLTAKSDERRVLL +RRLFGTQRFDGVEEHLRVETARLDTAVAVDADVARTARAQLAEALHEALGPDWHAPEPSP +DTDDRLLALAAERAGRAHEDARADLATARAAEQRARVTARELETRGRDLAAAEAWASRRR +DHDAEAETAAARRRAVDAHERAGRVLAAAQRASAAADAAGTASEAVTEALAHVEDEPTAA +AWLAAARADGAADAPASRQALGEAERAAEAVARAVRDRDRMRELEQEAAAAAERRAEIDR +DRAALVESRPEREAAVAAHRAVVERGTERLGAREAVDRAVSEAAARRTAAEAAAARAVEV +ETAARAHREAQERRREAAERHVGLLRARYEQAASELAERLVPGEPCAVCGSPEHPAPAAT +ADTAVTEADVRDAEQARTAADRAATDAETALRAAEQTLRSAGEAAAGLAPEAAREALERA +ETERAALDQAAKDLAADRRRLTAAEKTLAGADETAAALAAEDGRLAEAAAHRAARLTELR +DAVEAARGDAETLDARRDQVTAARRVLAALAAAQDEDARARAVADETGQALTATLAEQRF +DDVDAARAARLEETEAADRTAAVQEWDAERARLAELEASEPVRRGRALAEAGVEPPTEEQ +TRAAAEALAAAEAASSSRATAVGRLDSLVATVRRQSAALTEVLERSAGLIAEHTRVRGLL +DLVRGGGENLLKMPLTSYVLAGRLEEVAAAATERLLAMTDQRYSIEYSDAVGGRGNKGLE +LVIRDHYVDETRHPATLSGGETFMASLALALGLADTVQAEAGGIELDTLFVDEGFGSLDA +DTLDDVLDVVDTLRTGGRTVGLVSHVERMRQEIGVRLEVRKDRRGSSLAVHDGA +>PROKKA_02110 +MRIHRMRLQGIGPYAEAQDVDMDRLNDAGLFLLDGPTGAGKSTVLAALCYALYGSVPGGR +SPESLVTTLRPPGAVVPEVLVEFTVQGRRFEVVRSPRHERLKKRRSASGKDTTPTPAAVS +LREHVDGAWQEPLTRNDEVGVQVADVMHLDAAQFMQVVMLPQGRFAEFLTARSDERQRLL +RRLFGTQRFDGVEEHLKAEAERLGSRAAADAKVAASAREQLREAVAAELGEDWHAPEPFP +ATDEELVERTAERTREAVDAARAGRDAAAAEEAAARGTQAELRATGEALAAAAAWTERER +AHREGAEAAAGDRTAVAAHERAGRVLGAADRSESARAAEDRAREADGTAQAAAAEDPLSA +GWLEQARRDAAETPADDAAETSADAAALPRDAVALAERAVEEVVRAVRDRAAAERLEETE +RTEAARRTQIVAEREAAEAERSGREEGLAAVREAVEAASARLGAQADVDRRVAEAEQGLA +AAREAERHALAADAADRAREAARTGRDAAAQHRLGLLRSRYEQAAADLAADLEDGTPCAV +CGSPEHPDPAPRVGTAVTEADVAAAEEGLAAAEAVLADAETARTAAHERVRASSAAAGGR +TPAQAEEALAAARTEHAELAAVRKALAADRRRLRALETERDEAAAAETARTAEDARLQEA +ARQRHERLLELRAGIERARGDAPDLDARGALVRAARGRLEALAGAVEVRERAVAVAADAD +RALAAALREQEFEDVGAARAARLPAEDAAARTARVRAWDDEQARLAELAQSDAVRRGREL +QDQQATAPTPEDLEAAAARLLEAERSRREQDEALGRRTAVAAAVERQAALLRGVLDRSAA +LLAEHERVTGLLALVRGGGENRLKMPLASYVLAGRLEEVAAAATERLLAMTDGRYSIEYS +DDSAGRGNKGLELVVRDHYVDETRHPSTLSGGETFMASLALALGLADTVQAEAGGVELDT +LFVDEGFGSLDSDTLDDVLDVVDGLRSGGRTVGLVSHVERMKQEIPVRLAVTKEREGSSL +AVHVDA +>PROKKA_02001 +MRIHRMRLEGIGPYAEPQDLDLDPLNDAGLFLLDGPTGAGKSTVLAALCFALYGSVPGGR +TPESLVTTLRPPGAVVPQVLVEFTVQGRRFEVLRSPRHARPKKRGGGTTATQASVSLRER +VDGAWTAPLTRADEVGRQVAEVLRLDAAQFMQVVSLPQGRFAEFLTARSDDRQRLLRRLF +GTQRFDGVEDRLKECAEALGTRVAADAAEAAGARAQLLEQARLELGEDWHAPDPAPEEGE +DERLVELTRTRADAALAEARTAQQAADAAEAAARAAQDRLTADTEALRALAAWEGREREH +RQAADHVAADRSAVALHERASHVLGAATRAEQTRAAHASTAERARAAAEAVAADALAAAW +LDEAEDADAARRRADRETDALARAVRDRDALTRLEAEGTQADAERERLEDEARSAREKGK +RRAAQIAELHDTVDAAAARLGAEDEVARRLAEATERAAAAGQAAERAVAQERARAARDER +RDAQRGAAQARLDLLRSRFEQAAAELAAGLEDGSPCPVCGSAEHPDPAPRADGAVTEADV +AAADRALEAADAALAEAEQALAAASEEHRAARERAGGQDVAAAEEALSAVRAEHEALAAA +RTALATDRRALARRESEQRTADEAATARTAALARLSEAQARRTERAAELTAAVAAAQGDA +ADLDARTAHVRTATRALSALVEAGDAAARAAAVAEDAAQALAGALAEQDFADVAAARAAA +LPPDDAAARAARVRSWDVEEARLAEAAASEPLVRGRALREAGTSEPTAEEFAAAQETLRE +ATAARTARAAVVGRREALVASLERQARRLRAVLERSSELLAEHERATGLLALVRGQGENR +LKMPLASYVLAGRLEEVAAAATERLLAMTDRRYSIEYSDEATGRGNKGLELVIRDHYVDE +TRHPSTLSGGETFMASLALALGLADTVQAEAGGVELDTLFVDEGFGSLDADTLDDVLDVV +DGLRAGGRTVGLVSHVERMKQEIPVRLEVTKSRAGSTLAIHDGG +>PROKKA_00789 +MRIHRMRLEGLGPYAQAQDVDFDRLNAGGLFLLDGPTGAGKSTVLAALCFALYGTVPGGR +SAESLVTTLREPGAVIPEVQVEFTVQGRRFEVVRSPKHERPRRRRSAAGGATVTTQATVS +LRERVDGEWTAPLTRADEVGQQIAAVLHLDAEQFMQVVLLPQGQFAQFLTAKSDERRVLL +RRLFGTQRFDGVEEHLRVETARLDTAVAVDADVARTARAQLAEALHEALGPDWHAPEPSP +DTDDRLLGLAAERAGRAHEDARADLATARAAEQRARVTARELETRGRDLAAAEAWASRRR +DHDAEAETAAARRRAVDAHERAGRVLAAAQRATAAADAAGTASETVTEALAHVEDEPTAA +AWLAAARADGAADAPASRQALGEAERAAEAVARAVQDRARMGELEQEAAAAAERRAEIGR +DRAALVESRPEREAAVAAHRAAVERGTERLGAREAVDRAVSEAAARRTAAEAAAARAVEA +ETAARAHREAQERRREAAERHVGLLRARYEQAASELAERLVPGEPCAVCGSPEHPAPAAT +ADTTVTEADVRDAEQARTAADRAATDAETALRAAEQTLRTAREAAAGLAPEAAREALERA +EAERAALDQAAKDLAADRRRLTAAEKTLAGADETAAALAAEDGRLAEAAAHRAARLTELR +DAVEAARGDAETLDARRDQVTAARRVLAALAAAQDEDARARAVADETDQALTAALAEQHF +DDVDAARAARLEETEAAARTAAVQEWHAERARLAELEASEPVRRGRALAEAGVEPPTEEQ +TRAAAEALAAAEAASSSRATAVGRLDSLVATVRRQSAALTEVLERSAGLIAEHTRVRGLL +DLVRGGGENLLKMPLTSYVLAGRLEEVAAAATERLLAMTDQRYSIEYSDAVGGRGNKGLE +LVIRDHYVDETRHPATLSGGETFMASLALALGLADTVQAEAGGIELDTLFVDEGFGSLDA +DTLDDVLDVVDTLRTGGRTVGLVSHVERMRQEIGVRLEVRKDRRGSSLAVHDGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000728.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000728.fa new file mode 100644 index 0000000000000000000000000000000000000000..24cd7299bea462681c373ddbad58dd0f3d1ec88a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000728.fa @@ -0,0 +1,98 @@ +>PROKKA_00821 +MGALARFSLGRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVV +DAQVGEPLETALQAVEGLESSRSTSQSGFNAVQLEFAYGTDLNRARSQVDRVVANLGPQL +PEEAETSSFAGSVSDFPVVFLALSGDEDLNTLRRRAEDVLAPRLQKIDGVRGADVLGGTD +ENVSVVPDPAALAAAGLTTSDITDALEENAGLFPVGQVTEGATTYPVQAGAAVEDLEGLR +GIVVAPSGDGEPRTLDEVADVTLVAAAPTSLTRTDGVPTLSVSVTATPDADLVAVSQAVR +DALPELASLVGGGADLTVVFDQAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSVRSTLV +TAVSIPLSLLAALIGVAAFGYSLNTLTLGALTISIGRVVDDAIVVVENIRRHLGLGADRR +TAILDGTREVATAITASTLVSVAVFLPIAFVGGLAGELFRPFAVTATVALLASLVVALTI +VPVLCWWFLRSPRRGAETTAAPAVPGDRPVAAGGWLTRAYRPVLRWTQRHTVVTLAAALA +LLAGTAALVPLIPTNLLGDSGQNSFVVTAEQEPGTSLETTAAAAERIERVLLDTDGVETV +QWTAGTAAGPMGAFGGSSADRARFTVVTDPDADQVALQDGVRAELTGLDGVGDVSVSTQQ +GPSGGQDIEVAVSAPDPQALTAAADQVAEALRPVEGAREVTTPASDLRPTFQVDVDTVAA +ARLGLTEEAVAGQAAAALQAVPVGDVRFGFESFAVQLGDPEPVESLDALRQVPVETAEGP +VPLADLAEVSRVSVPARVTSSNGERTAVVTVTPDDEDLGAVSRRVTQAVAELDLPEGVTA +AVGGAAEQQAQTFRDLGLALLAAVATVYVVLVATFNSLRQPLVLLVSIPFAATGVFLALL +ATGTPLGLSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMPLDEAIEVGALNRVRPVVM +TALATVLAMTPMALGVTGHAGFISQPLAVAVVGGLVSSTLLTLVLVPVLYRLTEVRGERR +LQEERRVAAAWEAQRVAAERAAKQERRAEQGSAAPSELDAGRLGRLRQRLRRRWRRA +>PROKKA_00553 +MGALARFSLGRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVV +DAQVGEPLETALQAVEGLESSRSTSQSGFNAVQLEFAYGTDLNRARSQVDRVVANLGPQL +PEEAETSSFAGSVSDFPVVFLALSGDEDLNTLRRRAEDVLAPRLQKIDGVRGADVLGGTD +ENVSVVPDPAALAAAGLTTSDITDALEENAGLFPVGQVTEGATTYPVQAGAAVEDLEGLR +GIVVAPSGDGEPRTLDEVADVTLVAAAPTSLTRTDGVPTLSVSVTATPDADLVAVSQAVR +DALPELASLVGGGADLTVVFDQAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSVRSTLV +TAVSIPLSLLAALIGVAAFGYSLNTLTLGALTISIGRVVDDAIVVVENIRRHLGLGADRR +TAILDGTREVATAITASTLVSVAVFLPIAFVGGLAGELFRPFAVTATVALLASLVVALTI +VPVLCWWFLRSPRRGAETTAAPAVPGDRPVAAGGWLTRAYRPVLRWTQRHTVVTLAAALA +LLAGTAALVPLIPTNLLGDSGQNSFVVTAEQEPGTSLETTAAAAERIERVLLDTDGVETV +QWTAGTAAGPMGAFGGSSADRARFTVVTDPDADQVALQDGVRAELTGLDGVGDVSVSTQQ +GPSGGQDIEVAVSAPDPQALTAAADQVAEALRPVEGAREVTTPASDLRPTFQVDVDTVAA +ARLGLTEEAVAGQAAAALQAVPVGDVRFGFESFAVQLGDPEPVESLDALRQVPVETAEGP +VPLGDLAEVSRVPVPARVTSSNGERTAVVTVTPDDEDLGAVSRRVTQAVAELDLPEGVTA +AVGGAAEQQAQTFRDLGLALLAAVATVYVVMVATFNSLRQPLVLLVSIPFAATGVFLALL +ATGTPLGLSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMTLDEAIEVGALNRVRPVVM +TALATILAMTPMALGITGHAGFISQPLAVAVVGGLVSSTLLTLVLVPVLYRLTEVRGERR +LQEERRVAAEREAQRVAAERAAEQARRAEERWAAPSELDAGRLGRLRQRLRRRWRRA +>PROKKA_02109 +MGALARFSLRRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVV +DSLVGEPLETALQAVEGLESSGSTSQASFNSIQLQFAYGTDLNRARSQVDRVVSNLASQL +PEEAETSSFAGSVSDFPVVFLALSGDEDLNELRRRAEAVLAPRLQKLEGVRGADVLGGTE +EHVSVVPDPEALAAAGLSTQDITTALEENAGLFPVGQVTEGESTYPVQAGAAVEDLEGLR +GIVVTPAEGGQGAAPQDRTADGGPVGGGGGPPADAEATPAAPAEPAGDGEPRTLGEVAEV +SLQAAEPTSVTRTDGADTLSVSVTATPDADLVAVSEAVREALPELESVVGGGADLTVVFD +QAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSLRSTLVTAVSIPLSLLAALIGVAVFGY +SLNTLTLGALTISIGRVVDDAIVVVENIRRHLDLGADRRTAILIGTREVATAITASTLVS +VAVFLPIAFVGGLAGELFRPFAVTATIALLASLVVALTIVPVLCWWFLRTPRRPAGDESP +ADAAEGGAPAVPAGEHGHDAHPSAAGGWLARAYRPVLRWTQRHTVATLAGAVAVLAGTAA +LVPLIPTNLIGDTGQNSFVVTADQEPGTSLEATAAAAGVIERTLLETEGVETVQWTAGTA +GGPAGAFGGSSADRARFTVVTDENADQTALQDGVRADLAALEGVGEVSVSTQQGPGGGQD +IEVSVSAPDPQALATAADEVAGALRGVEGAREVTTPAADVRPTFQVDVDTEAAARLGLTE +EAVAGQAAAALQAVPVGDVRFGFEQFQVRLGDPDPVESLEALRQVAVQTGSGPVPLEELA +SVERVDVPARVTSSNGERTAVVTVTPDDQDLGAVSRRVTEAVDGLALPEGVTATVGGAAE +QQAATFRELGLALLAAIATVYVVMVATFNSLRQPLVLLVSIPFAATGVFLALLATGTALG +LSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMGLDEAIEVGALNRVRPVVMTALATIL +AMVPMALGLTGHSGFISQPLAVAVVGGLLSSTLLTLVLVPVLYRLTEARGERRIQAERAE +QARRDEEARRRAAEAEQAAAEQAESARAGLLARRRTGGAPAASAAAGMADDGGRRPGPLG +RLRARLGGLVGRARRA +>PROKKA_02000 +MGALARFSLSRRALVALVTAFIAVFGVLSAGLLKRELIPSLELPVISVSTTYPGASPEVV +DAEIGQPLEQALQAVEGLDSSASTSATSFNSVQLRFRYGTDLTRARSQVDRVISNLASQL +PEEAQTTSFAGSVSDFPVVFLALSGDEDLNALKRRAEDVLVPRLQRIDGVRGAQVLGGTE +EYVSVVPDAAKLAAAGLTTQDVTTALEENAGLFPIGQATSGTVTYPVQAGAPVGSVADLE +QVTVTPGGGQSSTGAADQGAGAGAGGGPGAATGTPARLGDVAAVSMQAADPTSVTRTDGA +PTLSLSVTATPDADLVAVSHAVADALPELESLAGSGAKLTVVFDQAPFIEQSIRTLFVEG +LLGLAMAILVIAVFLLSARSTMVTAVSIPLSLLTALIGVAVFGYSLNTLTLGALTISIGR +VVDDAIVVVENIRRHLGLGADKRTAILEGTREVATAITASTLVSVAVFLPIAFVDGLAGE +LFRPFAVTTSIALLASLVVALTIVPVLCWWFLRAPRAAAAPGGAEGVSSPVEDAAQDTWL +ARAYRPVLRWTQRHAVATLAGAAALLAGTVALAPLIPTNLLGDSGQNSFVVTAQQAPGTS +LEATTAIAGRIEAALRDTPGVRTVQFTAGSAGGAMGAFGRGSADRATFTVVTDPDADQTA +LQDEVRGRLAGLGDVGEVDVSAQQGPAGGQDITVSVTAPDPEALADGIDRVAEALRGLDG +VLQASTPSSDVRPTFQVDVDTLAAAERGLTEKAVSGQVAAALQAVPAGTVRFGFQEFTVR +LGDPDPVESLGALRAVPISTPSGPVPLSELADVRRADVPAQVTSSNGQRTAEVTVTPDPA +DLGGVSRRVSDALEGVALPDGVEATVGGAATEQAKTFRDLGLALLAAIAAVYVVMVATFN +SLRQPFVLLVSIPFAATGVVLALLASGTALGVATMIGLLMLVGIVVTNAIVLIDLINQYR +RRHGMALDEAIERGALHRVRPVVMTALATVLAMTPMALGITGHAGFISQPLAVAVVGGLA +SSTVLTLVLVPVLYRLTEARGERRIQAERAAREAEERELAEREARERELAEREAAARAVA +GPAAAAHPAPAGRLSRRRGWRGWIRRATS +>PROKKA_00790 +MGALARFSLGRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVV +DAQVGEPLETALQAVEGLESSRSTSQSGFNAVQLEFAYGTDLNRARSQVDRVVANLGPQL +PEEAETSSFAGSVSDFPVVFLALSGDEDLNTLRRRAEDVLAPRLQKIDGVRGADVLGGTD +ENVSVVPDPAALAAAGLTTSDITDALEENAGLFPVGQVTEGATTYPVQAGAAVEDLEGLR +GIVVAPSGDGEPRTLDEVADVTLVAAAPTSLTRTDGVPTLSVSVTATPDADLVAVSQAVR +DALPELASLVGGGADLTVVFDQAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSVRSTLV +TAVSIPLSLLAALIGVAAFGYSLNTLTLGALTISIGRVVDDAIVVVENIRRHLGLGADRR +TAILDGTREVATAITASTLVSVAVFLPIAFVGGLAGELFRPFAVTATVALLASLVVALTI +VPVLCWWFLRAPRRGAETTAAPAVPGDRPVAAGGWLTRAYRPVLRWTQRHTVVTLAAALA +LLAGTAALVPLIPTNLLGDSGQNSFVVTAEQEPGTSLETTAAAAERIERVLLDTDGVETV +QWTAGTTAGPMGAFGGSSADRARFTVVTDPDADQVALQDGVRAELTGLDGVGDVSVSTQQ +GPSGGQDIEVAVSAPDPQALTAAADQVAEALRPVEGAREVTTPASDLRPTFQVDVDTVAA +ARLGLTEEAVAGQAAAALQAVPVGDVRFGFESFAVQLGDPEPVESLDALRQVPVETAEGP +VPLGDLAEVSRVPVPARVTSSNGERTAVVTVTPDDEDLGAVSRRVTQAVAELDLPEGVTA +AVGGAAEQQAQTFRDLGLALLAAVATVYVVMVATFNSLRQPLVLLVSIPFAATGVFLALL +ATGTPLGLSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMTLDEAIEVGALNRVRPVVM +TALATILAMTPMALGITGHAGFISQPLAVAVVGGLVSSTLLTLVLVPVLYRLTEVRGERR +LQEERRVAAEREAQRVAAERAAEQARRAEERWAAPSELDAGRLGRLRQRLRRRWRRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000731.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000731.fa new file mode 100644 index 0000000000000000000000000000000000000000..e533dabbcbba33811966ed0e2d1bd7ebd064f25a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000731.fa @@ -0,0 +1,20 @@ +>PROKKA_00825 +MTDTTQHRLQPGDTAPAFTLQDQEGRPVSLRDSAGKHTIVYFYPAASTPGCTTQACDFRD +SLASLTAAGYVVLGISPDPIGKIIRFAEQEGLTFPLLSDEDHAVAEAYGAWGEKKNYGRT +FEGLIRSTIVVGPDGKVTHAQYNVKATGHVARLRRTLGLDEA +>PROKKA_00557 +MTDTTQHRLQPGDTAPAFTLQDQEGRPVSLRDSAGKHTIVYFYPAASTPGCTTQACDFRD +SLASLTAAGYVVLGISPDPIGKIIRFAEQEGLTFPLLSDEDHAVAEAYGAWGEKKNYGRT +FEGLIRSTIVVGPDGKVTHAQYNVKATGHVARLRRTLGLDEA +>PROKKA_02097 +MSDTTQNRLQPGDIAPSFTLQDQDGRPVSLRDSAGKSTIVYFYPAASTPGCTTQACDFRD +SLASLTAAGYVVLGVSPDPIGKIIRFAQKEGLTFSLLSDEDHAVAEAYGAWGEKKNYGRT +YEGLIRSTVVVGPDGRVTHAQYNVKATGHVARLRRTLGLDEA +>PROKKA_01996 +MTENTAAPARLSPGDVAPEFTLQDQDGRPVSLRDSAGKSTIVYFYPAASTPGCTTQACDF +RDSLASLTAAGYRVLGISPDPIGKIIRFAQNEGLTFSLLSDEDHAVAAAYGAWGEKKNYG +RTSEGLIRSTVVVGPDGKVTLAQYNVKATGHVARLRRELGLDD +>PROKKA_00794 +MTDTTQHRLQPGDTAPAFTLQDQEGRPVSLRDSAGKHTIVYFYPAASTPGCTTQACDFRD +SLASLTAAGYVVLGISPDPIGRIIRFAEQEGLTFPLLSDEDHAVAEAYGAWGEKKNYGRT +FEGLIRSTIVVGPDGKVTHAQYNVKATGHVARLRRTLGLDEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000732.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000732.fa new file mode 100644 index 0000000000000000000000000000000000000000..aa1a883c99cdc926d6ad1bde193114bb3069cc71 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000732.fa @@ -0,0 +1,24 @@ +>PROKKA_00827 +MTRADGSAYVGPMDTPTLHRRLRRVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLE +MLLCPFDPTSTPDDHDRRAPGVAEDDPHGPVTEASADRADVVEVGLANVATVADTGSGYQ +VETVTGFRTWFDVPEHTRVPVGDLTEDGTAELDQAEDATDFHAFMTAFMDELDRLYATPE +TDATDVTPPDLHGV +>PROKKA_00559 +MDTPTLHRRLRRVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLEMLLCPFDPTSTP +DDHDRRAPGVAEDDPHGPVTEASADRADVVEVGLANVATVADTGSGYQVETVTGFRTWFD +VPEHTRVPVGDLTEDGTAELDQAEDATDFHAFMTAFMDELDRLYATPETDATDVTPPDLH +GV +>PROKKA_02095 +MDSPTLQRRLRGVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLEMLLCPFDPTSTP +DDAPADAPAADAPEEDPHGPVAEPSSHGTDVVGVALGNVATVADTGSGYQVETVTGFRTW +FDVPEHARVPVGDLTEDGTAGLDQAEDAVDFHAFMTAFMDELDRLYAAPEAGGTDVTGPD +LHAR +>PROKKA_01994 +MDSPTLARRIRGAFDARVFNHGDYNLVYGQRSGGSLPLVIGYRHSPLEMLLCPLDPVEAV +AAVPEEVALANVATVADTGSGYQVETVTGFRTWFEVVDRPRVPVGEASEDGLAELDQADD +AADFHAFMTAFMDELDRLYAEPADPDLHPPQKSV +>PROKKA_00796 +MDTPTLHRRLRRVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLEMLLCPFDPTSTP +DDHDRRAPGVAEDDPHGPVTEASADRADVVEVGLANVATVADTGSGYQVETVTGFRTWFD +VPEHTRVPVGDLTEDGTAELDQAEDATDFHAFMTAFMDELDRLYATPETDATDVTPPDLR +GV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000733.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000733.fa new file mode 100644 index 0000000000000000000000000000000000000000..7a2827acb6a8cd203cf19d0c0b4e109736466854 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000733.fa @@ -0,0 +1,55 @@ +>PROKKA_00828 +MLTRLRGMDSAASTPSTPSAAPDIKPRSRDVTDGMERTAARGMLRAVGMGDEDFGKPQIG +IASSWNEITPCNLSLDRLAQASKDGVHAAGGYPLEFGTVSVSDGISMGHEGMHFSLVSRE +VIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSIMPGVARLTDG +TERQVTIIDAFEAVGACARGLMSEEDLLRIEKSIAPGEGACGGMYTANTMASIGEALGMS +LPGSAAAPSADRRRDAFARRSGKAVVNMLRQGITARDIMTKPAFENAIAVTMAFGGSTNA +VLHLLAIAREAGVDLQLSDFNRIADRTPHIADLKPFGQYVMTDVDRIGGVPVVMKALLDE +GLLHGDTLTVTGKTLAENLAALDPDPVDGKVIRTMDDAMHPNGGIAILHGSLAPEGAVVK +SAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPKGGPGMREMLAITGAI +KGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAAEGGPIGLVQDGDRIRVDIAGRTMDLL +VDEAELAARRESWEPVEPKFTTGVLGKYAKLVHSAAEGAYLG +>PROKKA_00560 +MLTRLRGMDSAASTPSTPSAAPDIKPRSRDVTDGMERTAARGMLRAVGMGDEDFGKPQIG +IASSWNEITPCNLSLDRLAQASKDGVHAAGGYPLEFGTVSVSDGISMGHEGMHFSLVSRE +VIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSIMPGVARLTDG +TERQVTIIDAFEAVGACARGLMSEEDLLRIEKSIAPGEGACGGMYTANTMASIGEALGMS +LPGSAAAPSADRRRDAFARRSGKAVVNMLRQGITARDIMTKPAFENAIAVTMAFGGSTNA +VLHLLAIAREAGVDLQLSDFNRIADRTPHIADLKPFGQYVMTDVDRIGGVPVVMKALLDE +GLLHGDTLTVTGKTLAENLAALDPDPVDGKVIRTMDDAMHPNGGIAILHGSLAPEGAVVK +SAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPKGGPGMREMLAITGAI +KGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAAEGGPIGLVQDGDRIRVDIAGRTMDLL +VDEAELAARRESWEPVEPKFTTGVLGKYAKLVHSAAEGAYLG +>PROKKA_02094 +MDTAASTPRTPSAAPDMKPRSRDVTDGMERAASRGMLRAVGLGDADFAKPQIGIASSWNE +ITPCNLSLDRLAQAAKEGVHADGGFPLEFGTVSVSDGISMGHEGMHFSLVSREVIADSVE +TVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSTMPGHARLSDGTEKQVTI +IDAFEAVGACARGLMSEEDLLRIEKAIVPTEGACGGMYTANTMASVGEALGMSLPGSATP +PSPDRRRDDFARRSGAAVVNLLRQGITARDIMTKEAFENAIAVTMAFGGSTNAVLHLLAI +AREAGVDLSLEDFNRVGDRTPHIADLKPFGRYVMTDVDRVGGVPVVMKALLDEGLLHGDA +LTVTGRTVAENLAELAPDPVDGDVIRTMDRPMHPNGGIAILHGSLAPEGAVVKSAGFDAD +VFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPRGGPGMREMLAITGAIKGAGLGK +DVLLLTDGRFSGGTTGLCIGHIAPEAADGGPIGLVRDGDRIRVDIAGRTLDVQVAEEELE +ARRREWTPVPPKFTTGVLGKYAKLVHSAAEGAYLG +>PROKKA_01993 +MDTSAADRTPQDVVTAPDMKPRSRDVTDGMERTAARGMLRAVGLGDEDFAKPQIGIASSW +NEITPCNLSLDRLAQASKDGVHAAGGFPLEFGTVSVSDGISMGHEGMHFSLVSREVIADS +VETVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSIMPGVARLTDGTEKQV +TIIDAFEAVGACARGLMSEEDLLRIEKAIAPGEGACGGMYTANTMASIGEALGMSLPGSA +AAPSADRRRDAFARRSGEAVVNMLRLGITARDVMTKPAFENAIAVTMAFGGSTNAVLHLL +AIAREAGVDLQLSDFNRIADRTPHIADLKPFGQYVMTDVDRVGGVPVVMKALLDEGLLHG +DTLTVTGKTLAENLAALDPDPVDGTVIRTMENALHPNGGIAILHGSLAPEGAVVKSAGFD +ADVFEGTARVFDRERAAMDALEEGVIQAGDVVVIRYEGPKGGPGMREMLAITGAIKGAGL +GKDVLLITDGRFSGGTTGLCIGHIAPEAADGGPIGLVRDGDRIRVDIASRTLDLLVEEAE +LEARRTSWQPVPPKFTTGVLGKYAKLVHSAAEGAYLG +>PROKKA_00797 +MLTRLRGMDSAASTPSTPSAAPDIKPRSRDVTDGMERTAARGMLRAVGMGDEDFGKPQIG +IASSWNEITPCNLSLDRLAQASKDGVHAAGGYPLEFGTVSVSDGISMGHEGMHFSLVSRE +VIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSIMPGVARLTDG +TERQVTIIDAFEAVGACARGLMSEEDLLRIEKSIAPGEGACGGMYTANTMASIGEALGMS +LPGSAAAPSADRRRDAFARRSGEAVVKMIRQGITARDIMTKPAFENAIAVTMAFGGSTNA +VLHLLAIAREAGVDLQLSDFNRIADRTPHIADLKPFGQYVMTDVDRIGGVPVVMKALLDE +GLLHGDTLTVTGKTLAENLAALDPDPVDGKVIRTMDDAMHPNGGIAILHGSLAPEGAVVK +SAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPKGGPGMREMLAITGAI +KGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAAEGGPIGLVQDGDRIRVDIAGRTMDLL +VDEAELAARRESWKPVEPKFTTGVLGKYAKLVHSAAEGAYLG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000736.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000736.fa new file mode 100644 index 0000000000000000000000000000000000000000..60f9806f921e8eeeff1b8ac9ea01a64a645ea34c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000736.fa @@ -0,0 +1,20 @@ +>PROKKA_00832 +MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTEVEGLSRITVVVDADTDLLEQ +VTKQLNKLINVIKVVELTPDSSVQRDHLLVKVRADAATRGQVVQAADLFRAHVVDVAPES +LTLEATGTRDKLEAFLEMMEPYGVRELVRSGTLALARGPRSMTDRALAR +>PROKKA_00564 +MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTEVEGLSRITVVVDADTDLLEQ +VTKQLNKLINVIKVVELTPDSSVQRDHLLVKVRADAATRGQVVQAADLFRAHVVDVAPES +LTLEATGTRDKLEAFLEMMEPYGVRELVRSGTLALARGPRSMTDRALAR +>PROKKA_02092 +MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTEVEGLSRITVVVDADTDLLEQ +VTKQLNKLINVIKVVELTPDSSVQRDHLLVKVRADAATRGQVVQAADLFRAHVVDVAPES +LTLEATGTRDKLEAFLEMMEPYGVRELVRSGTLALARGPRSMTDRALAR +>PROKKA_01991 +MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTQVPGISRMTVVVDADAHLLEQ +VTKQLNKLINVIKVVELAGDSSVQRDHLLVKVRADASTRGQVVQAADLFRAHVVDVAPDS +LTFEATGTREKLEAFLEMMEPHGIRELVRSGTLALARGPRSMTDRALAR +>PROKKA_00802 +MERHTLSVLVEDVPGTLTRVAGLFARRAFNIHSLAVGVTEVEGLSRITVVVDADTDLLEQ +VTKQLNKLINVIKVVELTPDSSVQRDHLLVKVRADAATRGQVVQAADLFRAHVVDVAPES +LTLEATGTRDKLEAFLEMMEPYGVRELVRSGTLALARGPRSMTDRAVAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000737.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000737.fa new file mode 100644 index 0000000000000000000000000000000000000000..3370f46626123474e056ace89904108d22be3e09 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000737.fa @@ -0,0 +1,35 @@ +>PROKKA_00833 +MTVKKFYDDDADLSIIQGRTVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSKSRAKAEA +EGLRVVDVATAAAEADLIMILTPDQVQADVYDQHIAGNLQKGDALFFAHGFNVRFGYIQA +PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEKDASGQAHALALSYAKAVGGTRAGV +IETTFTEETETDLFGEQAVLCGGASQLVQYGFETLTEAGYQPEIAYFEVLHELKLIVDLM +VEGGIAKQRWSISDTAEYGDYVSGPRVITPDVKENMKAVLADIQSGAFAQRFMDDQKAGA +PEFKELRARGEAHPIEKTGRELRQMFSWLKDADDDYTEGTAAR +>PROKKA_00565 +MTVKKFYDDDADLSIIQGRTVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSKSRAKAEA +EGLRVVDVATAAAEADLIMILTPDQVQADVYDQHIAGNLQEGDALFFAHGFNVRFGYIQA +PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEKDASGQAHALALSYAKAVGGTRAGV +IETTFTEETETDLFGEQAVLCGGASQLVQYGFETLTEAGYQPEIAYFEVLHELKLIVDLM +VEGGIAKQRWSISDTAEYGDYVSGPRVITPDVKENMKAVLADIQSGAFAKRFMDDQKAGA +PEFKELRARGEAHPIEKTGRELRQMFSWLKDADDDYTEGTAAR +>PROKKA_02091 +MTVKKFYDDDADLSIIQGRTVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSKSRAKAEA +EGLRVVDVATAAAEADLIMILTPDQVQADVYDQHIAGNLQEGDALFFAHGFNVRFGYIQA +PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEKDASGQAHALALSYAKAVGGTRAGV +IETTFTEETETDLFGEQAVLCGGASQLVQYGFETLTEAGYQPEIAYFEVLHELKLIVDLM +VEGGIAKQRWSISDTAEYGDYVSGPRVITPDVKENMKAVLADIQSGAFAQRFMDDQKAGA +PEFKELRAKGEAHPIEKTGRELREMFSWLKDADDDYTEGTAAR +>PROKKA_01990 +MTAQKFYDDDADLSIIQGRTVAVIGYGSQGHAHSLSLRDSGVDVRIGLAEGSKSRAKAEA +EGLRVVDVATAAAEADLIMILTPDQVQADVYDEHIAPNLQEGDALFFAHGFNVRFGYIQA +PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEQDASGQAEALALSYAKAIGGTRAGV +IKTTFTEETESDLFGEQAVLCGGASQLIQYGFEVLTEAGYQPEIAYFEVLHELKLIVDLM +VEGGIAKQRWSISDTAEFGDYVSGPRVITPEVKDHMKEVLADIQNGAFAKHFMDDQKAGA +PEFTELRAKGESHPIEKTGRELRQMFSWLKDTDDDYTEGTAAR +>PROKKA_00803 +MTVKKFYDDDADLSIIQGRTVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSRSRAKAEA +EGLRVVDVATAAAEADLIMILTPDQVQADVYDQHIAGNLQEGDALFFAHGFNVRFGYIQA +PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEKDASGQAHALALSYAKAVGGTRAGV +IETTFTEETETDLFGEQAVLCGGASQLVQYGFETLTEAGYQPEIAYFEVLHELKLIVDLM +VEGGIAKQRWSISDTAEYGDYVSGPRVITPDVKENMKAVLADIQSGAFAKRFMDDQKAGA +PEFKELRARGEAHPIEKTGRELRQMFSWLKDADDDYTEGTAAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000738.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000738.fa new file mode 100644 index 0000000000000000000000000000000000000000..f5d618e8cfe78c7f43ec5e41d1a86f6d2ce6e4f9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000738.fa @@ -0,0 +1,50 @@ +>PROKKA_00834 +MSAAQPVVLIAEELSPATVEALGPDFEIRRTDGADRARLLEDLRDVDAVLIRSATQMDAE +AIAAAPQLKVIARAGVGLDNVDVPAATEAGVMVVNAPTSNIISAAELTCGHILAAARNIA +AAHGSLKAGEWKRSKYTGVELYGKRLGVIGLGRIGALVAERMKAFGMEILAYDPYVTTAR +AQQLGASLVELDELLERADVVTIHMPKTPETVGMIGDEQFARMKDTAIIVNVARGGLVDE +DALARALEAGTIGGAGIDVFSSEPATDLAFFAHDSAVVTPHLGASTAEAQEKAGVAVAGS +VRLALSGELVPDAVNVAGGAIHEDVRPGLPLAEKLGRVLTALVGEQSITAVEVEIAGEIS +EHDVSAMRLAALKGVFTDIVSDQVSYVNAPVLAEQRGVECRLTTTAVSESYRNTVTVRAA +TAQGAQTAVTGTLTGPRQVQKLVGVDRHELEVPLADHLLVFAYQDRPGVIGVLGQALGVQ +GVNIAGMDVSRDDEGAALAVLTLDGALSGDTAATLAAAIGAARAAEVDLSV +>PROKKA_00566 +MSAAQPVVLIAEELSPATVEALGPDFEIRRTDGADRARLLEDLRDVDAVLIRSATRMDAE +AIAAAPQLKVIARAGVGLDNVDVPAATEAGVMVVNAPTSNIISAAELTCGHILAAARNIA +AAHGSLKAGEWKRSKYTGVELYGKRLGVIGLGRIGALVAERMKAFGMEILAYDPYVTTAR +AQQLGASLVELDELLERADVVTIHMPKTPETVGMIGDEQFARMKDTAIIVNVARGGLVDE +DALARALEAGTIGGAGIDVFSSEPATDLAFFAHDSAVVTPHLGASTAEAQEKAGVAVAGS +VRLALSGELVPDAVNVAGGAIHEDVRPGLPLAEKLGRVLTALVGEQSITAVEVEIAGEIA +EHDVSAMRLAALKGVFTDIVSDQVSYVNAPVLAEQRGVECRLTTTAVSESYRNTVTVRAA +TAQGTQTAVTGTLTGPRQVQKLVGVDRHELEVPLADHLLVFAYQDRPGVIGVLGQALGVQ +GVNIAGMDVSRDDEGAALAVLTLDGALSGDTAATLAAAIGAARAAEVDLSA +>PROKKA_02090 +MSAAQPVVLIAEELSPATVEALGPDFEIRRTDGADRARLLEDLRDVDAVLIRSATRMDAE +AIAAAPQLKVIARAGVGLDNVDVPAATAAGVMVVNAPTSNIISAAELTCGHILATARNIA +AANRSLKAGEWKRSKYTGVELYGKKLGVIGLGRIGALVAERMRAFGMEILAYDPYVTTAR +AQQLGATLVELDQLLERADFVTIHMPKTPETVGMIGDDQFARMKDTAVVVNVARGGLVDE +DALARALDSGAIAGAGIDVFSTEPATDLAFFAQDSAVVTPHLGASTAEAQEKAGVAVAGS +VRLALSGELVPDAVNVAGGVIHEDVRPGLPLAEKLGRVLTSLVGEQSLTAVEVEIAGEIA +EHDVSAMRLAALKGVFTDIVSDQVSYVNAPMLAEQRGVECRLTTTPVSESYRNTVTLRAA +TAQGTQVSVTGTLTGPRQIQKLVGVDRHELEVPLADHLLVFTYEDRPGVIGVLGQALGVQ +GVNIAGMDVSRDDEGEALAVLTLDGALSGDTATALAAAIGASRVAEVDLSA +>PROKKA_01989 +MSAAKPVVLIAEELSPATVEALGPDFEIRHTDGADRARLLADLPGVDAVLIRSATTMDAE +AIAVAKDLKVIARAGVGLDNVEVPAATAAGVMVVNAPTSNIVSAAELTCGHILSVARNIA +PANRALKAGEWKRSKYAGVELFEKKLGVIGLGRIGALVAERMKAFGMEILAYDPYISAAR +AQQLGATLLDLDELLAQSDFITVHMPKTPETVGMISDAQFATMKDTAFIVNVARGGLIDE +DALDRALESGAIAGAGVDVFSSEPATDLAFFRHDTAVVTPHLGASTAEAQEKAGVAVAKS +VRLALAGELVPDAVNVAGGVIHEDVRPGLPLAEKLARVLRALAGERSLASVDVEVAGEIA +VHDVKALRLAALKGVFTDVVSDQVSYVNAPVLAEQRGVGGQLTTAAEAGSYRNTVTVAAV +TDEGERLSVTGTLTGPKQVEKLVGVGRHEMEVALAEHMLLFRYADRPGVVGVLGQSLGEQ +GVNIAGMDVSRDEQGSALAVLTLDAALAPGTAPTLAAAIDADRAAEVNLAD +>PROKKA_00804 +MSAAQPVVLIAEELSPATVEALGPDFEIRRTDGADRARLLEDLRDVDAVLIRSATRMDAE +AIAAAPQLKVIARAGVGLDNVDVPAATEAGVMVVNAPTSNIISAAELTCGHILAAARNIA +AAHGSLKAGEWKRSKYTGVELYGKRLGVIGLGRIGALVAERMKAFGMEILAYDPYVTTAR +AQQLGASLVELDELLERADVVTIHMPKTPETVGMIGDEQFARMKDTAIIVNVARGGLVDE +DALARALEAGTIGGAGIDVFSSEPATDLAFFAHDSAVVTPHLGASTAEAQEKAGVAVAGS +VRLALSGELVPDAVNVAGGAIHEDVRPGLPLAEKLGRVLTALVGEQSITAVEVEIAGEIA +EHDVSAMRLAALKGVFTDIVSDQVSYVNAPVLAEQRGVECRLTTTAVSESYRNTVTVRAA +TAQGTQTAVTGTLTGPRQVQKLVGVDRHELEVPLADHLLVFAYQDRPGVIGVLGQALGVQ +GVNIAGMDVSRDDEGAALAVLTLDGALSGDTAATLAAAIGAARAAEVDLSA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000739.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000739.fa new file mode 100644 index 0000000000000000000000000000000000000000..3a5e35153e89ec721693c96fa3226f07f8ca15ab --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000739.fa @@ -0,0 +1,54 @@ +>PROKKA_00847 +MTDARAPYYLTTAISYPNGEPHIGHAYEYIASDAMARFQRLDGRDVRFLTGTDEHGQKME +QTAQQQGVSALELATRNAAVFKEMDDDVLDISYDRFIRTTDTDHAEAVREIWRRMEANGD +IYLGSYAGWYSVRDERYFGEDETEVGQDGVRRAVETGTEVTWTEEESYFFRLSKYQQPLL +DHYREHPDFAAPRYRFNEVIRFVEAGLEDLSISRTSFQWGIDLPAPADPDAADADRRADH +VTYVWVDALTNYLTGAGWPAEDPEAFARYWPADLHVIGKDISRFHCIFWPAFLMSAGLEL +PRRVMIHGFLNNNGAKMSKSLGNVVHPREWVARYGLDAIRFFLLREFPFGADGSYSHEAV +VSRKNADLANNLGNLAQRSLSMVAKNCGAAVPEPGEFTEADRAVLAQVDALLERSRSAYA +VQDFHDALEETWRVLGEINAYFADQAPWVLRKTDEPRMRTVLYVTLQAVRRVALLAQPVM +PGSASRLLDLLGVPAEGDAGRTGASGTGPRSFAAFHEDLVPGTPLPAPQPVFPRHEEPAE +D +>PROKKA_00569 +MTDARAPYYLTTAISYPNGEPHIGHAYEYIASDAMARFQRLDGRDVRFLTGTDEHGQKME +QTAQQQGVSALELATRNAAVFKEMDDDVLDISYDRFIRTTDTDHAEAVREIWRRMEANGD +IYLGSYAGWYSVRDERYFGEDETEVGQDGVRRAVETGTEVTWTEEESYFFRLSKYQQPLL +DHYREHPDFAAPRYRFNEVIRFVEAGLEDLSISRTSFQWGIDLPAPADPDAADADRRADH +VTYVWVDALTNYLTGAGWPADDPEAFARYWPADLHVIGKDISRFHCIFWPAFLMSAGLEL +PRRVMIHGFLNNNGAKMSKSLGNVVHPREWVARYGLDAIRFFLLREFPFGADGSYSHEAV +VSRKNADLANNLGNLAQRSLSMVAKNCGAAVPEPGEFTEADRAVLAQVDALLERSRSAYA +VQDFHDALEETWRVLGEINAYFADQAPWVLRKTDEPRMRTVLYVTLQAVRRVALLAQPVM +PGSASRLLDLLGVPAEGDAGRTGASGTGPRSFAAFHEDLVPGTPLPAPQPVFPRHEEPAE +D +>PROKKA_02088 +MTDARAPYYLTTAISYPNGEPHIGHAYEYIATDAMARFQRLDGRDVRFLTGTDEHGQKME +QTAQREGVTALELATRNAAVFKEMDDEVLDISYDRFIRTTDADHAEAVQEIWRRMEANGD +VYLGSYAGWYSVRDERYFGEDETAVGEDGVRRAVETGTEVTWTEEESYFFRLSKYQEPLL +EHYRRNPEFAAPRYRFNEVIRFVEDGLEDLSISRTSFDWGVPLPAPVDPDAEVADRRADH +VTYVWVDALTNYLTGAGWPGRDPEAFGRYWPADLHVIGKDISRFHCIFWPAFLMSAGIEL +PKRVMIHGFLNNNGAKMSKSLGNVVHPRDWVARYGLDAIRFFLLREFPFGADGSYSHEAV +VGRKNADLANNLGNLAQRSLSMVAKNCEAAVPQPGPLTAEDEAVLAQVDALLERSRTAYA +VQDFHDALEETWRVLGEVNAYFADQAPWVLRKTDEARMRTVLYVTLQAVRRVALLVQPVM +PASASRLLDLLGVPAEGDAGRTGASGQGPRSFAAFHEDLVPGTALPKPEGVFPRHEEPAE +A +>PROKKA_01988 +MTDTRAPYYVTTAIHYPNGEPHIGHAYEVVGADALARFMRLDGRDVFFLTGTDEHGQKMA +QTAERLGVTPMELATRNSAAFKAMDDEVLGVSYDRFIRTTDEDHHRASQEIWRRMEANGD +VYLDRYAGWYSVRDERFFDEDETEVREDGQRYAAETGTEVTWTEEESWFFRLSKYQEPLL +ALYRDDPEFAAPRSRFNEVIRFVEGGLEDLSISRTSFDWGIDVPAPADGAASDAHHVMYV +WVDALTNYLTGVGFPDESSESFRRFWPADVHVIGKDISRFHCVFWPAFLMSAGIELPKRV +MIHGFLNNNGEKMSKSLGNVVAPRDWVARYGLDAVRFFLLREFPFGADGSYSHEAVVGRK +NADLANNLGNLAQRSLSMVAKNCGGGVPEPGSLTEADTAVLAQVDALLEHSRAAYTVQDF +HGALEETWRVLGEVNAYFADQAPWVLKKTDEPRMRTVLYVTLQAVRRVALLVQPVMPASS +SRLLDLLGVPAEGDAGATAASNAGPRSFAAFGEDLMPGTALPRPEGVFPRHEDPAEG +>PROKKA_00806 +MTDARAPYYLTTAISYPNGEPHIGHAYEYIASDAMARFQRLDGRDVRFLTGTDEHGQKME +QTAQQQGVSALELATRNAAVFKEMDDDVLDISYDRFIRTTDTDHAEAVREIWRRMEANGD +IYLGSYAGWYSVRDERYFGEDETEVGQDGVRRAVETGTEVTWTEEESYFFRLSKYQQPLL +DHYREHPDFAAPRYRFNEVIRFVEAGLEDLSISRTSFQWGIDLPAPADPDAADADRRADH +VTYVWVDALTNYLTGAGWPAEDPEAFARYWPADLHVIGKDISRFHCIFWPAFLMSAGLEL +PRRVMIHGFLNNNGAKMSKSLGNVVHPREWVARYGLDAIRFFLLREFPFGADGSYSHEAV +VSRKNADLANNLGNLAQRSLSMVAKNCGAAVPEPGEFTEADRAVLAQVDALLERSRSAYA +VQDFHDALEETWRVLGEINAYFADQAPWVLRKTDEPRMRTVLYVTLQAVRRVALLAQPVM +PGSASRLLDLLGVPAEGDAGRTGASGTGPRSFAAFHEDLVPGTPLPAPQPVFPRHEEPAE +D diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000744.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000744.fa new file mode 100644 index 0000000000000000000000000000000000000000..8b4cc25d834ca8a16f774fc43deb94e1cb59cf53 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000744.fa @@ -0,0 +1,30 @@ +>PROKKA_00852 +MRIARFVDQAEPTYGIVEGPADADPAELTVTALQGDPFFHGIQPTGTTHRLEDVRLVAPI +IPRSKIVGVGRNWADHAKELGNEVPASPQFFLKPNTAVVGPNEPVTLPSWSDEVSYEAEL +AVVIGTICKDVPVSRVDDVVFGYTVGNDLTARDAQRTDLQWARAKGFDGACPLGPWIETE +LDVEPAGGLRITSRLDGETRQDGTTTDMVFGVRELVAAASEMFTLLPGDVILTGTPGGVG +TVQEGQRVEAEVEGIGVLATVFRR +>PROKKA_00574 +MRIARFVDQAEPTYGIVEGPADADPAELSITALQGDPFFHGIQPTGTTHRLEDVRLVAPI +IPRSKIVGVGRNWADHAKELGNEVPASPQFFLKPNTAVVGPNEPVTLPSWSDEVSYEAEL +AVVIGTICKDVPVSRVDDVVFGYTVGNDLTARDAQRTDLQWARAKGFDGACPLGPWIETE +LDVEPTGGLRITSRLDGETRQDGTTADMVFGVRELVAAASEMFTLLPGDVILTGTPGGVG +TVQEGQRVEAEVEGIGILATVFRR +>PROKKA_02082 +MRIARFVDQAEPTYGVVEGPADADLSELTITALQGDPFFHGIQPTSTVHRLEDVRLVAPI +IPRSKIVGVGRNWADHAKELGNETPASPQFFLKPNTSVVGPGEPVTLPSWSDEVSYEAEL +AVVIGTICKDVPVSRVDDVVFGYTVGNDLTARDAQRTDLQWARAKGFDGACPLGPWIETE +LDVEPAGGLRITSRLDGQTRQDGTTADMVFGVRELVAAASEAFTLLPGDVILTGTPAGVG +TVAEGQRVEAEVEGIGVLATVFRR +>PROKKA_01977 +MRIARFVDQAEPTYGVVEGPADADLSALTVTALQGDPFFHGIQPTGTTHRLEDVRLVAPI +IPRSKIVGVGRNWADHAKELGNEVPSSPQFFLKPNTSVVGPDEPVTLPSWSEEVSYEAEL +AVVIGTICKDVPLSRVDDVVFGYTVANDLTARDAQRTDLQWARAKGFDGACPLGPWIETE +LDVEQAGGLRVTSRLAGETRQDGTTADMVFGVKELVAAASEMFTLLPGDVILTGTPAGVG +TVEAGQRVEAEVEGIGVLGTHVRR +>PROKKA_00811 +MRIARFVDQAEPTYGIVEGPADADPAELSITALQGDPFFHGIQPTGTTHRLEDVRLVAPI +IPRSKIVGVGRNWADHAKELGNEVPASPQFFLKPNTAVVGPNEPVTLPSWSDEVSYEAEL +AVVIGTICKDVPVSRVDDVVFGYTVGNDLTARDAQRTDLQWARAKGFDGACPLGPWIETE +LDVEPTGGLRITSRLDGETRQDGTTADMVFGVRELVAAASEMFTLLPGDVILTGTPGGVG +TVQEGQRVEAEVEGIGILATVFRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000745.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000745.fa new file mode 100644 index 0000000000000000000000000000000000000000..d200a09b297f413e2d92e9a78397f75be0539d81 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000745.fa @@ -0,0 +1,50 @@ +>PROKKA_00853 +MTDATAPVSENAPAPFADVPQVDAETPVRVRFAPSPTGTPHVGLIRTVLFNWGWARHTGG +TLVFRIEDTDAKRDSEESYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGQIYADVIE +KLKAGGYIYPSYSSPEETEARHRAAGRDPKLGYDGHDRDLTDEQIAAFEAEGRAPVWRLR +MPDEDITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGEDLL +SSTPRQIALYRALHAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQANLFLHRDNGFIPEG +LLNYLGLLGWSLSADEDIFTPQQFVEHFDVHKVLANPARFDEKKAIAINGTHVRMLDVAD +FRDRLVPYLHAAGLVGEHLTEREMQILTAAAPLVQERVQLLGEAVEMLAFLFTADRDVRT +AEGALKGMPADLGAAVAAAREALAALPEDEFTTERIEAALRAALIDGLGLKPRQAFGPVR +VAVTGRKVSPPLFESLEILGRDSALARLDRFAAEQGLDQGRPTDA +>PROKKA_00575 +MTDATAPVSENAPAPFVDVPQVDAETPVRVRFAPSPTGTPHVGLIRTVLFNWGWARHTGG +TLVFRIEDTDAKRDSEESYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGQIYADVIE +KLKAGGHIYPSYSSPEETEARHRAAGRDPKLGYDGHDRDLTDEQIAAFEAEGRAPVWRLR +MPDEDITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGEDLL +SSTPRQIALYRALYAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQANLFLHRDNGFIPEG +LLNYLGLLGWSLSADEDIFTPQQFVEHFDVHKVLANPARFDEKKAIAINGTHVRMLDVAD +FRDRLVPYLHAAGLVGEHLTEREMEVLTAAAPLVQERVQLLGEAVEMLAFLFTADRDVRT +AEGALKGMPADLGAAVAAAREALAALPEEEFTTERIEAALRAALIDGLGLKPRQAFGPVR +VAVTGRKVSPPLFESLEILGRDSALARLDRFAAEQGLDQDQPTDA +>PROKKA_02081 +MDAETPVRVRFCPSPTGTPHVGLIRTALFNWGWARHTGGTLVFRIEDTDAKRDSEESYQQ +LLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGEIYAEVIEKLKAGGHIYPSYSSPEETEAR +HRAAGRDPKLGYDGFDRDLTDEQVAAFEAEGRAPVWRLRMPDTDITFTDLVRGEITFKAG +TVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGEDLLSSTPRQIALYRALHAVGVAAY +MPVFGHLPYVMGEGNKKLSKRDPQANLFLHREHGFIREGLLNYLALLGWSLSADEDIFTP +EQFVEHFDVHKVLANPARFDEKKAIAINGSHVRMLDADDFRERLVPYLHAAGLVDAEPTE +REREILAAAAPLVQERVQLLGEAVEMLAFLFTADADVATSEGALKGMPADLGAAVAAARD +ALAALPEDGFTTERIEEALRAALIDGLGLKPRQAFGPVRVAVTGRKVSPPLFESLEILGR +DSALARLDRFAAEQGLDQGLPTDA +>PROKKA_01976 +MTEPTTASDTAAENAPAVFADVPQVDADTPVRVRFCPSPTGTPHVGLIRTALFNWGWARH +TGGTLVFRIEDTDAKRDSEESYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGEIYAE +VIEKLKAGGHIYPSYSTPEETEARHRAAGRDPKLGYDGADRDLSAEQVEAYEAEGRRPVW +RLRMPDADITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGE +DLLSSTPRQIALYRALHAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQSNLFLHRDRGFI +PEGLLNYLALLGWSLSADEDIFTPEQFVEHFDIHKVLANPARFDEKKATAINGTHVRMLE +PADFRARLVPYLQAAGLVGERLTEREERILDAAAPLVHERVALLGEAVDMLAFLFTPDAE +IATAEGALKGMPADLPTAVAAAREALAGIDEAEFTTAAVEEALRAALIDGLELKPRQAFG +PVRVAVTGKKVSPPLFESLEILGKESALARLDRFAAEQAAA +>PROKKA_00812 +MTDATAPVSENAPAPFVDVPQVDAETPVRVRFAPSPTGTPHVGLIRTVLFNWGWARHTGG +TLVFRIEDTDAKRDSEESYQQLLEAMRWLGIDWDEGVEVGGPHEPYRQSQRGQIYADVIE +KLKAGGHIYPSYSSPEETEARHRAAGRDPKLGYDGHDRDLTDEQIAAFEAEGRAPVWRLR +MPDEDITFTDLVRGEITFKAGSVPDFVVVRADGSPLYTLVNPVDDALMGITHVLRGEDLL +SSTPRQIALYRALYAIGVARYMPVFGHLPYVMGEGNKKLSKRDPQANLFLHRDNGFIPEG +LLNYLGLLGWSLSADEDIFTPQQFVEHFDVHKVLANPARFDEKKAIAINGTHVRMLDVAD +FRDRLVPYLHAAGLVGEHLTEREMEVLTAAAPLVQERVQLLGEAVEMLAFLFTADRDVRT +AEGALKGMPADLGAAVAAAREALAALPEEEFTTERIEAALRAALIDGLGLKPRQAFGPVR +VAVTGRKVSPPLFESLEILGRDSALARLDRFAAEQGLDQDQPTDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000746.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000746.fa new file mode 100644 index 0000000000000000000000000000000000000000..7e6fed15028a54e742e6e3e4611c82d036a5fe56 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000746.fa @@ -0,0 +1,52 @@ +>PROKKA_00859 +MSRRDTPALAPRLDALGEAAELAAGRLPEDVVAGADAVVRAAGERQALSAEHTVVGFFGA +TGSGKSSLFNALTGRDLARVAATRPTTSEPLAAVWGVGRGQGLDPDAEHGDGTGEGGGAA +ALLDWLGVRRRHLLDEAPVLDDGRPGFLGFGRRDGADATGLILLDLPDIDSVERGNREIT +SRLAGHVDVLVWVVDPEKYADAVLHREFLATMGSHAAVTLVLLNQVDRLSVRDRDVVLAS +LRRMLSGHGLGDVRVLPVSARTGEGLEEVGRQVAAIVAQRGAAAERLGADVAARAADLAA +ASGEGEPAGVGPGDEQRLGRELAVAGGVPAVVRAVEGSYRLRSAKRTSWPVLRWMHSFRA +DPLRRLHLMPESAAPRRDRDEVARDPALHRTSLPERSGTQRAVVDGAVRTLAAAAGAGAS +EPWAAAIRRAGREHAEELPGAVDQAIAATDLGAGRGSWWHPVLDVLQWLALLTAVVGAGW +LGVLALAGYLQFPLPPAPTVEGFPLPTLLLVGGLALGVLLALLAIPLTRWTAAARGRHAR +RRLEEATTDVGRRLVVDPVRAEVDRFRAFRDALARASGAPVRRGRR +>PROKKA_00581 +MSRRDTPALAPRLDALGEAAELAAGRLPEDVVAGADAVVRAAGERQALSAEHTVVGFFGA +TGSGKSSLFNALTGRDLARVAATRPTTSEPLAAVWGVGRGQGLDPDAEHGDGTGEGGGAA +ALLDWLGVRRRHLLDEAPVLDDGRPGFLGLGRRDGADATGLILLDLPDIDSVERGNREIT +SRLAGHVDVLVWVVDPEKYADAVLHREFLATMGSHAAVTLVLLNQVDRLSVRDRDVVLAS +LRRMLSGHGLGDVRVLPVSARTGEGLEEVGRQVAAIVAQRGAAAERLGADVAARAADLAA +ASGEGEPAGVGPGDEQRLGRELAVAGGVPAVVRAVEGSYRLRSAKRTSWPVLRWMHSFRA +DPLRRLHLMPASTAPRRDRDEVARDPALHRTSLPERSGTQRAVVDGAVRTLAAAAGTGAS +EPWAAAIRRAGREHAEDLPGAVDQAIAATDLGAGRGSWWHPVLDVLQWLALLTAVVGAGW +LGVLALAGYLQFPLPPAPTVEGFPLPTLLLVGGLALGVLLALLAIPLTRWTAAARGRRAR +RRLEEATTDVGRRLVVDPVRAEVERFHAFRDALARASGVPVRRGRR +>PROKKA_02076 +MELSNREITSRLAGHVDVLVWVVDPEKYADAVLHREFLATMGSHAAVTLVLLNQVDRLSV +RDRDTVLASLRRMLSGHGLGDVRVLPVSARTGEGLEEVGRQIAAIVERRGAAAERLGADV +AARARDLDAASGEGEPAGVGPGDEQRLGRDLATAGGVPAVVRAVEGSYRLRSAKQTSWPV +LRWMHSFRADPLRRLHLMPDRPAVRRDRDEVGRDPALHRTSLPERTGTQKAVVDGAVRTL +VTAAAAGAPEPWAASVRRAGRAHAEQVPDAVDQAIAATDLGAGRGSWWHPVLNVLQWLAL +LTAVVGAGWLGVLALAAYLQFPLPPAPVVEGFPIPTLLLVGGLALGVLLALLAIPLTRIT +AASRGRRARRRLEEGTTDVGRRLVVDPVRAEVDRFHAFRDAVARAAGATARRGRR +>PROKKA_01970 +MSRPAAPTLAQRLDALGTAAELARDRLPDAVVADAQAAVRAAEERQSLSAEHTVVGFFGA +TGSGKSSLFNALTGRELAGVAATRPTTSEPLAAVWGVGRGENLDGEGGGAAALLDWLGVR +RRHLLDDAPVLDGGRPVFLGLGHREGADATGLILLDLPDIDSVQRSHRDVTARLAGHVDV +LVWVVDPEKYADAVIHRDFLATMASHAAVTLVLLNQVDRLTVTDRDAVLASLRRMLSGHG +MGDVRVLPVSARTGEGLEEVGRQIAAIVSRRGAAAERLGADVSARARALDEASGPGEPAG +AGDDDAVRLGRDLAVAGGVPAVVRAVEGSYRLRSAKRTSWPVLRWMHSFRADPLRRLHLL +PERAVARRDRDPVDRDPALHRTSLPERTQTQRAVVEGAVRTLVTSASAGASEPWAASVRR +AGREHLDELPAAVDHAIAGTDVEAGRGSWWWPVLDVLQWLALAVAVAGAGWLGAYALAAW +LQFPLPPAPTTQGFPIPTLLLIGGLALGLLLALLAVPLTRLTAASRGRRARRRLEEAAVR +VGRELVVDPVNAEAARHREFRSALAAAQGSGVRSRSRR +>PROKKA_00818 +MSRRDTPALAPRLDALGEAAELAAGRLPEDVVAGADAAVRAAGERQALSAEHTVVGFFGA +TGSGKSSLFNALTGRDLARVAATRPTTSEPLAAVWGVGRGQGLDPDAEHGDGTGEGGGAA +ALLDWLGVRRRHLLDEAPVLDDGRPGFLGVGRRDGADATGLILLDLPDIDSVERGNREIT +SRLAGHVDVLVWVVDPEKYADAVLHREFLATMGSHAAVTLVLLNQVDRLSVRDRDVVLAS +LRRMLSGHGLGDVRVLPVSARTGEGLEEVGRQVAAIVAQRGAAAERLGADVAARAADLAA +ASGEGEPAGVGPGDEQRLGRELAVAGGVPAVVRAVEGSYRLRSAKRTSWPVLRWMHSFRA +DPLRRLHLMPESAAPRRDRDEVARDPALHRTSLPERSGTQRAVVDGAVRTLAAAAGAGAS +EPWAAAIRHAGREHAEELPGAVDQAIAATDLGAGRGSWWHPVLDMLQWLALLTAVVGAGW +LGVLALAGYLQFPLPPAPTVEGFPLPTLLLVGGLALGVLLALLAIPLTRWTAAARGRRAR +RRLEEATTDVGRRLVVDPVRAEVDRFHAFRDALARASGVPVRRGRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000747.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000747.fa new file mode 100644 index 0000000000000000000000000000000000000000..aa2f4f19d0b25af99419e0245fee215dee69f966 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000747.fa @@ -0,0 +1,40 @@ +>PROKKA_00860 +MTVRDPAAAAGATVGDLTEAELLEVVLTGLAPAVRDGHWPAGTVAPGDDAALVPAPRGGT +LISTDAMGEGTDFLHRWPAGPRTRGHDAGWKAVAQNLSDVNAMGGSASALVTALTLPPTT +PVAWVRSFAAGIVGAVRHLGAPDCRVAGGDLGTGGRVHAAVTVLGDPHPGGVLCRTPAAA +DRDRVLAEGADLVHAQAVPDGPRAAAPPGPGWAAAGLAVLLTDRAELERRADALPAADRP +SPRELARAVRAQLRPRPPLALGPAAVTAGLLTLMDVSDGLGKDAHRMAAATGGAGPAPAP +WLDEAWLAQAAAPLRRVAALAGTSPEALVTGGGEDYGLLGLAWPETELPRGFTRIGRLVP +AGARAPAGHRPLPGSGWDPFAG +>PROKKA_00582 +MTVRDPAAAAGATVGDLTESELLEVVLTGLAPAVRDGHWPAGTVAPGDDAALVPAPRGGT +LISTDAMGEGTDFLPRWPAGPRTRGHDAGWKAVAQNLSDVNAMGGTASALVTALTLPPTT +PVAWVRSFAAGIVGAVRHLGAPDCRVAGGDLGTGGRVHAAVTVLGDPHPGGVLCRTPAAA +DRDRVLVEGADLVHAQAVPDGPRAAAPPGPGWAAAGLTLLLTDRAELERRADALPAADRP +SPRELARAVRAQLRPRPPLALGPAAVTAGLLTLMDVSDGLGKDAHRMAAATGGAGPAPAP +WLDEAWLAEAAAPLRRVAALAGTSPEALVTGGGEDYGLLGLAWPETELPRGFTRIGRLVP +AGARPPAGHRPLSESGWDPFAG +>PROKKA_02075 +MTPAGGRPADGRTVGEVTEAQLLRVVLDGLAPAVRPGHWPPGTVAPGDDAALVPAPRGGT +LVSTDAMGEGTDFLHRWPAGVRTRGHDAGWKAVAQNLSDVNAMGGTASALVTALTLPPTT +PLAWVRSFAAGVVGAVDRLGAPGCRVAGGDLGTGERVHAAVTVLGDPHPAGVLRRAPAPA +ARERVLAEGADLVHAQDAPGSSGAARSGALRPSAARPGPGWAAAGLALLLTDRDELARRA +AALPPEDRPGARDLARAVRAQLRPRPPLALGPAAVEAGILTLMDVSDGLGRDAHRMAAAT +GAAASAEAPPPVPWIDAAWLAEAAAPLRGVAALAGVSAESLVTGGGEDYGLLGLAWPETA +LPAGFVRIGRLEPAGAPAPAGHRELPEAGWDPFGG +>PROKKA_01969 +MSTPASTASAGGRPAPARTVGEASEAELLDLIQDALAPVARDVPWPAGTVPPGDDCAVVP +APRGLVAVSTDAMGEGTDFLRRWPAGVRTRGHDVGWKAAAQNLSDVNAMGATPSALVTAL +ALPAPTPLDWVASLAGGFTAAVRALGADRCRVAGGDLGAGESVQVAVTALGDPDPAGALR +RAAGGERGARIARRGADLVLAAGSPRAAAAGEGQDSAWGPAGPGWAAAGLALLLTDRAVL +TRRWADLAAHERPSARELARAVRGQLRPRPPLAAGPAAARAGLAALMDVSDGLGRDGHRL +ARASSAPGAPLVPWVDRRWLAEAAEPLRRVASLAGTTPEALVLGGAEDYGLLGLAEPGLA +LPSGFRRVGRLAPAGETPDGHVRLPEAGWDHFDAGRG +>PROKKA_00819 +MTMRDPAAAAGATVGDLTEAELLEVVLTGLAPAVRDGHWPAGTVAPGDDAALVPAPRGGT +LISTDAMGEGTDFLHRWPAGPRTRGHDAGWKAVAQNLSDVNAMGGTASALVTALTLPPTT +PVAWVRSFAAGIVGAVRHLGAPDCRVAGGDLGTGGRVHAAVTVLGDPHPGGVLRRTPAAA +DRDRVLAEGADLVHAQAVPDGPRAAAPSGPGWAAAGLTLLLTDRAELERRADALPAADRP +SPRELARAVRAQLRPRPPLALGPAAVTAGLLTLMDVSDGLGKDAHRMAAATGGAGPAPAP +WLDEAWLAEAAAPLRRVAALAGTSPEALVTGGGEDYGLLGLAWPETELPRGFTRIGRLVP +AGARPPAGHRPLSESGWDPFAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000748.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000748.fa new file mode 100644 index 0000000000000000000000000000000000000000..55421a619edbb15e07a4a6e233dc0eee264aaee8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000748.fa @@ -0,0 +1,50 @@ +>PROKKA_00861 +MTETTAPAAPAEQEAAPRLSVIGTGYLGATHAACMAELGFEVLGVDVDPAKIERLARGEV +PFHEPGLPELLRTHVASGRLRFTTDVAEAARWADVHFIGVGTPQKVGETAADLSYVDAAV +ASLAAAIDRDALIVGKSTVPVGTARRLAELVRTVRAEAGLPGEVELAWNPEFLREGFAVR +DTLTPDRLVIGMHGPRAEGILRRVYARQLAADTPWISTDLETAELVKVAANAFLATKISF +INAFSEITENVGGDIGTLADAIGHDARIGRRFLNAGVGFGGGCLPKDIRALQARVSELGL +DRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARDGRIRRAEASGPAPTPASVQVLNGTRI +AVLGVTFKPDSDDVRDSPALDVANRLYTAGADVRVYDPEGNANAAARFPRLDYVDSLEAA +VDGAELTLLLTEWRQFREMDPDTVGARVASRLLIDGRNVLDVAAWREHGWDVIGLGHRFD +PERLLRAA +>PROKKA_00583 +MTETTAPAAPAEQEAAPRLSVIGTGYLGATHAACMAELGFEVLGVDVDPAKIERLARGEV +PFHEPGLPELLRTHVASGRLRFTTDVAEAARWADVHFIGVGTPQKVGETAADLSYVDAAV +ASLAAAIDRDALIVGKSTVPVGTARRLAELVRTVRAEAGLPGEVELAWNPEFLREGFAVR +DTLTPDRLVIGTHGPRAEGILRRVYARQLAADTPWISTDLETAELVKVAANAFLATKISF +INAFSEITENVGGDIGTLADAIGHDARIGRRFLNAGVGFGGGCLPKDIRALQARVSELGL +DRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARDGRIRRAEASGPAPTPASVQVLNGTRI +AVLGVTFKPDSDDVRDSPALDVANRLYTAGADVRVYDPEGNANAAARFPRLDYVDSLEAA +VDGAELTLLLTEWRQFREMDPDTVGARVASRLLIDGRNVLDVAAWREHGWDVIGLGHRFD +PERLLRAA +>PROKKA_02074 +MTHPSAPAEQDRAPRLSVIGTGYLGATHAACMAELGFEVLGVDVDPEKIARLSRGEVPFH +EPGLPELLRTHVESGRLRFTTDVAEAARWADVHFVGVGTPQKVGESGADLRYVDAAVASL +AAAIDRDALIVGKSTVPVGTARRLAAMVRRVRAEAGLPGEVELAWNPEFLREGFAVKDTL +TPDRLVIGTDGPRAEQVLRRVYARQLAADTPWISTDLETAELVKVAANAFLATKISFINA +FSEITEAVGGDIGTLADAIGHDARIGRRFLNAGVGFGGGCLPKDIRALQARVSELGLDRT +MRFLAEVDDINLRRRDRVVDLAVQVLSAARDAGRGEAAAYGGKTTASGVEVLRGARIAVL +GVTFKPDSDDVRDSPALDVANRLYTAGADVRVHDPEGNANAAARFPRLDYVDSLEEAVEG +AELTLLLTEWQAFREMDPAAVGALVDARLLIDGRNVLDLAAWAEHGWTVVGLGHRFDPAA +LGA +>PROKKA_01968 +MTETAVVPAAAESEEAPARPRLSVIGTGYLGATHAACMAELGFEVLGVDVDPAKIERLAR +GEVPFHEPGLPELLRAHVASGRLRFTTDVAEAASWADVHFIGVGTPQKVGEAAADLTYVD +AAVESLARAIDRDALIVGKSTVPVGTARRLAARVAEIRAAEGLPGEVELAWNPEFLREGY +AVKDTLTPDRLVIGTHGPRAELLLRTVYATPLAAGTPWISTDLETAELVKVAANAFLATK +ISFINAFSEITETVGGDIGTLADAIGHDGRIGRRFLNAGVGFGGGCLPKDIRALQARVSE +LGLDRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARQGVVRSAPGGARTAPTPAGVQVLN +GTRIAVLGVTFKPYSDDVRDSPALDVANRLFTAGAEVAVYDPEGNANAAARFPRLGYVDS +LDAALQGAELVLLLTEWDEFRQMDPAAAGELVAQRILIDGRNVLDVDAWGEHGWTVLGLG +HRFDPAALNGGRPGDDAQA +>PROKKA_00820 +MTETTAPAAPAEQEAAPRLSVIGTGYLGATHAACMAELGFEVLGVDVDPAKIERLARGEV +PFHEPGLPELLRTHVASGRLRFTTDVAEAARWADVHFIGVGTPQKVGETAADLSYVDAAV +ASLAAAIDRDALIVGKSTVPVGTARRLAELVRTVRAEAGLPGEVELAWNPEFLREGFAVR +DTLTPDRLVIGTHGPRAEGILRRVYARQLAADTPWISTDLETAELVKVAANAFLATKISF +INAFSEITENVGGDIGTLADAIGHDARIGRRFLNAGVGFGGGCLPKDIRALQARVSELGL +DRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARDGRVRRADASGTAPTPASVQVLNGTRI +AVLGVTFKPDSDDVRDSPALDVANRLYTAGADVRVYDPEGNANAAARFPRLDYVDSLEAA +VDGAELTLLLTEWRQFREMDPDAVGARVASRLLIDGRNVLDAAAWREHGWDVIGLGHRFD +PERLLRAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000749.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000749.fa new file mode 100644 index 0000000000000000000000000000000000000000..00afe4944c58fdf4f9f5466c8d08807438f78cb5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000749.fa @@ -0,0 +1,30 @@ +>PROKKA_00862 +MTTEPVRPPTEDDLIGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVIATGIARPTL +HRLAAALTHHRMVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV +FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT +PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRLHAD +AVVSAATRLTELIRAGEA +>PROKKA_00584 +MTTEPVRPPTEDDLIGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVIATGIARPTL +HRLAAALTHHRMVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV +FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT +PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRLHAD +AVVSAATRLTELIRAGEA +>PROKKA_02073 +MTAEPARAQADDDVLGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVTATGIARPTL +HRLAAALTHHRLVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV +FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT +PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRNHAD +AVVAAATRLTELIRAGEA +>PROKKA_01967 +MTTTPLPDAGADIGPALHVHPSGVGVVDKSVAILDALESGPATLAQLVTATGIARPTLHR +LAAALTHHRLVAKDLQGRYVLGSRLAELASAAGEDRLTSAAGPVLQWLRDACGESAQVFR +RQADSRVCVASAERPWGLRDTIPVGTRMSMKAGSAAQVLLAWEDNERLVDGLVGAVFTPT +VLAAVRRRGWAQSLAEREPGVASVSAPVRGPNGKVIAALSISGPLERLSRQPGRLHAGSV +VAAADRLTELIRAGEA +>PROKKA_00821 +MTTEPVRPPTEDDLIGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVTATGIARPTL +HRLAAALTHHRMVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV +FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT +PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRLHAD +AVVSAATRLTELIRAGEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000750.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000750.fa new file mode 100644 index 0000000000000000000000000000000000000000..782780af338f6190cc30fc80ecadf55d72b349ee --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000750.fa @@ -0,0 +1,50 @@ +>PROKKA_00863 +MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR +PVRRPDLTIATEDHNTPTLDIDQPIADATSRTQIETLRANCAEFGVRLHPLGDAEQGIVH +VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAVT +VDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAGAR +AGMVAPDETTFAYLKGRPHAPEGDDWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPFVT +WGTNPGQGVSLNDTVPAPEDFADPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSCTN +SRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM +CLGMNPDQLSPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT +PQEA +>PROKKA_00585 +MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR +PVRRPDLTIATEDHNTPTLDIDQPIADPTSRTQIETLRANCAEFGVRLHPLGDAEQGIVH +VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAVT +VDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAGAR +AGMVAPDETTFAYLKGRPHAPEGADWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPFVT +WGTNPGQGVSLNDTVPAPEDFTDPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSCTN +SRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM +CLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT +LQEA +>PROKKA_02072 +MTSETTRPRTLAEKVWDEHVVVRGEGEGSSRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR +PVRRPDLTIATEDHNTPTLEIDKPIADPTSRTQIETLRANAAEFGVRLHPLGDAEQGIVH +VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAIT +VDGTLRPGVTAKDVILAVIAKIGTGGGQGFVLEYRGEAIRSLSMEGRMTICNMSIEAGAR +AGMVAPDETTFAYLKGRPHAPEGADWDAAVEHWRTLATDEGAEFDAEVVIDADELEPFVT +WGTNPGQGVSLNGAVPAPEDFDDPVAQESARKALGYMDLTPGTPMKEVAVDTVFMGSCTN +SRIEDLRAFAEVVKGRKKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM +CLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT +PQEA +>PROKKA_01966 +MSTQTQTPRPRTLAEKVWDEHVVVRGEGEGARRTPDLLYIDLHLVHEVTSPQAFDGLRLA +DRPVARPELTIATEDHNTPTLEIDRPIADETSRVQIETLRANAEEFGVRLHSLGDREQGI +VHVVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLRLKPFRTMA +ITVDGTLRPGVTAKDVILAVIAKIGTGGGQGYVLEYRGEAIRSLSMEGRMTLCNMSIEAG +ARAGMVAPDDTTFEYLKGRPHAPQGADWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPF +VTWGTNPGQGVSLNDAVPAPEDFSDPAAQEAARKALSYMDLTPGTPMKDVAVDTVFMGSC +TNSRIEDLRAFAEVVKGRTKADGLRVMVVPGSARVRLQAMDEGLDKVFEDFGAEWRFAGC +SMCLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPLVAAATAVLGRLASPSDLPA +LENQEA +>PROKKA_00822 +MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR +PVRRPDLTIATEDHNTPTLDIDQPIADATSRTQIETLRANCAEFGVRLHPLGDAEQGIVH +VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAVT +VDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAGAR +AGMVAPDETTFAYLKGRPHAPEGDDWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPFVT +WGTNPGQGVSLNDTVPAPEDFADPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSCTN +SRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM +CLGMNPDQLSPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT +PQEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000755.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000755.fa new file mode 100644 index 0000000000000000000000000000000000000000..1629ce77f323786c5275221c943a4b889d28f0cd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000755.fa @@ -0,0 +1,40 @@ +>PROKKA_00868 +MTATPAPEAAADARPRVLLLFGGRSSEHPISCVTAAGVLHAADRQRWDVVPVGVARSGLW +SHDELDVASFRLDGDALPEVPEPEAPVSLRALPDGTVELTAADGSSLGPVDVVFPLLHGP +WGEDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITARDWARD +PEAALARAGALAYPLFVKPARAGSSFGITRVTEPAGLRAAVEEARRFDPKVVVEAGIVGR +EIECAVLDGHGSAAPRASLPGEIVVAHDEGETQFYDFESKYQDTGTTQLSCPAELPEEEI +ERLRALAIRAFEAVDGSGLGRCDFFFTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSY +DDLISELLDLALERGVGLH +>PROKKA_00590 +MTATPAPEAAADARPRVLLLFGGRSSEHPISCVTAAGVLHAADRQRWDVVPVGVARSGLW +SHDELDVASFRLDGDALPEVPEPEAPVSLRALPDGTVELTAADGSSLGPVDVVFPLLHGP +WGEDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITARDWARD +PEAALARAGALAYPLFVKPARAGSSFGITRVTEPAGLRAAVEEARRFDPKVVVEAGIVGR +EIECAVLDGHGAAAPRASLPGEIVVAHDEGETQFYDFESKYQDTGSTQLSCPAELPEEEI +ERLRALAIRAFEAVDGSGLGRCDFFFTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSY +DDLISELLDLALERGVGLH +>PROKKA_02067 +MLLLFGGRSSEHPISCVTAAGVLHAADPQRWDVVPVGVARSGLWSHDELDVAAFRLDGET +LPEVPEPEAPVSLRTLPDGTVELTAEDGSSLGRVDVVFPLLHGPWGEDGTLQGMFESLGL +PYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITDRDWARDPEAALARAGALAFPLF +VKPARGGSSFGITRVSDPADLRAAVEEARRFDPKVVVEAGIVGREIECAVLDGHGSDAPR +ASLPGEIVVKHDEGDLQFYDFQAKYQDDDAAQLSCPAELPEEQTRRLRELAVRAFEAVDG +SGLGRCDFFHTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSYDALISELLDLALERGV +GLH +>PROKKA_01961 +MTQPPETAPGRRPRVLLLFGGRSSEHPISCVTAAGVLHAADRERWDVVPVGVAHSGLWSH +GEVDAAAYALGDGELPSVPEPERPVSLRARADDAVELVGADGEDLGVVDVVFPLLHGPWG +EDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAGGLEVGPWETITDRQWRNDPE +AALERAGALDYPLFVKPARGGSSFGITKVDAPEDLRAAVEEARRFDPKVVVEAGILGREI +ECAVLDGHGAESPRASLPGEIVVKGAESGHQFYDFEAKYQDASAAQLSCPAELPEEAIER +LREQAVRAFEAVDGAGLGRCDFFYTPDGRWVVNEINTMPGFTSISMYPAMWERTGLPYGE +LISELLDLALERGVGLH +>PROKKA_00827 +MTAIPAPEAAAGARPRVLLLFGGRSSEHPISCVTAAGVLHAADRQRWDVVPVGVARSGLW +SHDELDVASFRLDGGALPEVPEPEAPVSLRALPDGTVELTAADGSSLGPVDVVFPLLHGP +WGEDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITARDWARD +PEAALARAGALAYPLFVKPARAGSSFGITRVTEPAGLRAAVEEARRFDPKVVVEAGIVGR +EIECAVLDGHGSAAPRASLPGEIVVAHDEGETQFYDFESKYQDTGTTQLSCPAELPEEEI +ERLRALAIRAFEAVDGSGLGRCDFFFTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSY +DDLISELLYLALERGVGLH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000756.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000756.fa new file mode 100644 index 0000000000000000000000000000000000000000..e0daf4ea4818ab23f111233cf4e67125a4e28779 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000756.fa @@ -0,0 +1,20 @@ +>PROKKA_00869 +MESRRLRRLVPLLTAIALGATACTGRVATVEAAPHAADPACAPAMVAMPDALGDLDLRPT +DSQATAVWGDPAAVVLRCGAEVPGPTTDRCISVDGIDWVVRDEDENWRITTYGRDPAVEV +LFGKDQASSDTVMVGLSSAVAQIEPSGGCVGVQDATPVG +>PROKKA_00591 +MESRRLRRLVPLLTAIALGATACTGRVATVEAAPHAADPACAPAMVAMPDALGDLDLRPT +DSQATAVWGDPAAVVLRCGAEVPGPTTDRCISVDGIDWVVRDEDENWRITTYGRDPAVEV +LFGKDQASSDTVMVGLSSAVAQIEPSGGCVSVQDATPVG +>PROKKA_02066 +MESRPLRPLRRLVPLLTAIALGATACSGRVATVEAAPDAANPECAPAMVAMPDALGDAAL +RPTDSQATAVWGDPAAVVLRCGAPVPGPTTDRCISVDGVDWVIRDEDENWRIVTYGRDPA +VEVLFGKDKASSDTVMVGLASAVAQIDADGGCVNLQDATPVG +>PROKKA_01960 +MPRLPRPVILAPALAAAALGLTACSGPVVSVEAAPGAADPACAPAMVAVPDVLGGQDRRE +TDSQATAAWGEPAAVVLRCGVPTPGPTTDRCVSVDDIDWVVRDEDDHWRITTYGRTPAVE +AVFGKSEVSSDSVMTGLGSAVAQIPSQRRCVNIEDATPVG +>PROKKA_00828 +MESRRLRRLVPLLTAIALGATACTGRVATVEAAPHAADPACAPAMVAMPDALGDLDLRPT +DSQATAVWGDPAAVVLRCGAEVPGPTTDRCISVDGIDWVIRDEDENWRITTYGRDPAVEV +LFGKDQASSDTVMVGLSSAVAQIESSGGCVSVQDATPVG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000758.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000758.fa new file mode 100644 index 0000000000000000000000000000000000000000..88472308d67222ed7744b0ee633d53370292f406 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000758.fa @@ -0,0 +1,35 @@ +>PROKKA_00871 +MGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADACPAQDDAGAVLAHAGAAALDSA +RGNSGMLLAVSLAGMAEPLRGRERVDAFALAAAFGAADRAARQALSDPREGTILTVLSAA +ARSLARSSTQAPDTPAVAGDADPAVRLGPAVTLMLADCVQAVEETESLLAPLTRAHVVDA +GAVGLLWVFEALRAVVTGTPVDEELATALPGYGEGAHAAEAEPAAAAEAPAEGAVEVMGT +LALTPLAAAELRRRLTEVGDAVILAPLGTARDGQGRVPWRVHVHVPRAEDAIGPLRAAGD +VEGLTVTDLAGPSHGDDAAPDGCHGR +>PROKKA_00593 +MSTPSRPSLVRHWLALAEELVGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADACP +AQDDAGAVLAHAGAAALDSARGNSGMLLAVSLAGMAEPLRGRERVDAFALAAAFGAADRA +ARQALSDPREGTILTVLSAAARSLARSSTQAPDTPAVAGDADPAVRLGPAVTVMLADCVQ +AVEETESLLAPLTGAQVVDAGAVGLLWVFEALRAVVTGTPVDEELATALPGYGEGVHAAE +GEPAAAAEAPAEGAVEVMGTLTLTPLAAAELRRRLADVGDAVILAPLGTARDGQGRVPWR +VHVHVPRAEDAIGPLRAAGDVEGLTVTDLAGPSHGDDAAPDGCHGR +>PROKKA_02064 +MSTPPRPSLVRHWLALAEELVGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADACP +AQDDAGAVLARAGAAALDLARGNSGTLLAVALAGMAEPLRGRARADAFALAAAFGAADRA +ARQALSDPREGTILTVLSAASRSLARSATQAPDSPAVAADVDPAVRLGPAVTAMMADCLR +AVEQTESQLAPLAQARVVDAGAVGLLWVLEALRAAVTDTAPDEELATALHGYVEGVRPGP +EPAGEDAVEVMGTLALTPLAAADLRRRLAETGDSVILAPVGTERDEHGRVPWRVHVHVPR +AADAVELMRAAGEVQGLAVTELSGDAAGPDADGCHGR +>PROKKA_01958 +MIRARLRGALAWLRGAEAALAQAAPRLDALNLFPVPDADTGSNMLATVRAARQAAERSAG +TDMSAVLRDAGAAALDSARGNSGTLLAVALVGLAAPLTPDAPLTTAELAAGARAADRAAR +AALSDPREGTILTVLREAATVLEAAAAGGREPAEALGSVVEAARRAVEDTEGQLAPLTRA +RVVDAGAVGLLLVLEALRAEVTRTPFDEGVVAALHGWADGPGAAGEDPQADGREAPGVEV +MCSIDLTPVDAAGLRRGLEEAGDSVILAPLSRAVDGAGRLRWRVHVHVARAEDAVALLEA +AGAPEEVAVTDLWDPAHRHPDDPAEGDAASPAPDGHGR +>PROKKA_00830 +MSTPSRPSLVRHWLALAEELVGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADACP +AQDDVGAVLAHAGAAALDSARGNSGMLLAVSLAGMAEPLRGRERVDAFALAAAFGAADRA +ARQALSDPREGTILTVLSAAARSLARSSTQAPDTPAVAGDADPAVRLGPAVTVMLADCVQ +AVEETESLLAPLTRAHVVDAGAVGLLWVFEALRAVVTGTPVDEELATALPGYGEGVHAAE +GEPAAAAETPAEGAVEVMGTLALTPLAAAELRRRLADVGDAVILAPVGTARDGQGRVPWR +VHVHVPRAEDAIGPLRAAGDVEGLAVTDLAGPSHGDAAPDGCHGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000763.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000763.fa new file mode 100644 index 0000000000000000000000000000000000000000..78d39a8a38c8f24172d2306e8d97559a1e02e72a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000763.fa @@ -0,0 +1,35 @@ +>PROKKA_00876 +MTVPPPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVTEARRAGLADV +LMITGRNKRALEDHFDRHPALEAALEHKGDTKRLAQIHESDLVGDIHYVRQGEALGLGHA +VNCARRHVGEEPFAVLLGDDIIGDGEALLERMIDVQQRLGGSVIALMEVPEEAVSAYGVA +AVQAVPGEGDDVVRVTDLVEKPAREDAPSTLAIIGRYVLAPQVFDVLDETPPGRGGEIQL +TDALQRLATEDGEGRGVHAVVFDGRRYDTGDKLGYLQAVIEFGTRHEDLGADLRAWLREF +TAGL +>PROKKA_00598 +MTVPPPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVTEARRAGLADV +LMITGRNKRALEDHFDRHPALEAALEHKGDAKRLAQIHESDLVGDIHYVRQGEALGLGHA +VNCARRHVGEEPFAVLLGDDIIGDGEALLERMIDVQQRLGGSVIALMEVPEEAVSAYGVA +AVEAVPGEGDDVVRVTDLVEKPAREDAPSTLAIIGRYVLAPQVFDVLDETPPGRGGEIQL +TDALQRLATEDGEGRGVHAVVFDGRRYDTGDKLGYLQAVIEFGARHEDLGADLRAWLREF +TAGL +>PROKKA_02059 +MTVPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVAEARRAGLQDVLM +ITGRNKRALEDHFDRHPALEATLERKGDATRLAQIRESDLVGDIHYVRQGEALGLGHAVN +CARRHVGDEPFAVLLGDDIIGDGEALLARMIDVQQRLGGSVVALMEVPEEAVSAYGVAAV +EAVPGEGEDVVRVTGLVEKPAREDAPSTLAVIGRYVLASQVFDVLDRTPPGRGGEIQLTD +ALQTLADDDGEGGGVHAVVFDGRRYDTGDKLGYLQAVVEFGTRHEELGGDLRAWLKAFAA +GL +>PROKKA_01953 +MTEQSTAASPTRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVAEAVSAG +LGDVLMITGRNKRALEDHFDRHPALEQVLEAKGDTKRIDLIRASDLVGDIHYVRQGEALG +LGHAVGCARRHVGDEPFAVLLGDDLIGEDEGLLARMIDVQHRLGGSVIALMEVPEDAVSA +YGVAAVAPVDGEDDDVVAVTSLVEKPARGDAPSNLAIIGRYVLAPQVFEVLERTAPGRGG +EIQLTDALQTLAAGEGEGFGVHAVVFRGRRYDTGDKLGYLQAVVELGVRHPELGGDLREW +LKGFAAGL +>PROKKA_00835 +MTVPPPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVTEARRAGLADV +LMITGRNKRALEDHFDRHPALEAALEHKGDATRLAQIHESDLVGDIHYVRQGEALGLGHA +VNCARRHVGEEPFAVLLGDDIIGDGEALLERMIDVQQRLGGSVIALMEVPEEAVSAYGVA +AVQAVPGEGDDVVRVTDLVEKPAREDAPSTLAIIGRYVLAPQVFDVLDETPPGRGGEIQL +TDALQRLATEDGEGRGVHAVVFDGRRYDTGDKLGYLQAVIEFGTRHEDLGADLRAWLREF +TAGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000766.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000766.fa new file mode 100644 index 0000000000000000000000000000000000000000..66eeb25211ed0fe37ac2d23e9944415d2ca32e07 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000766.fa @@ -0,0 +1,26 @@ +>PROKKA_00879 +MHITAGTLERALTHRSFAYEQGGLPTNERLEFLGDSVLGYVVTDHIFTVYPDLAEGDLAR +RRAAVVSTRALAKVARRIGIGPFVRLGTGERRTGGADKDSILADTLEALIGAVYVDHGAV +AAAALVHRHVVPLLDEPDLLRESTDWKTVVAEAASRHGLGAVRYAIEGQGPAHDPRYRAT +LVVGEREYGSAVASSKKQAERDAAAASWPALEADLPAAGR +>PROKKA_00601 +MHITAGTLERALTHRSFAYEQGGLPTNERLEFLGDSVLGYVVTDHIFTVYPDLAEGDLAR +RRAAVVSTRALAKVARRIGIGPFVRLGTGERRTGGADKDSILADTLEALIGAVYVDHGAV +AAAALVHRHVVPLLDEPDLLRESTDWKTVVAEAASRHGLGAVRYAIEGQGPAHDPRYRAT +LVVGEREYGSAVASSKKQAERDAAAASWPALEAGLPAAGR +>PROKKA_02056 +MHVTAETLERALTHRSYAYEQGGLPTNERLEFLGDSVLGYVVTDHIFTVHPDLAEGDLAR +RRAAVVSTRALAKVARRIGIGPFVRLGTGEGRTGGADKDSILADTLEALIGAVHVDHGLV +AASALVHRHVVPLLDEPDLVRESTDWKTVVAEAANRHGLGAVRYAIEGQGPAHDPRYRAT +LVVGEREYGSAVASSKKQAERDAAAASWPALEADLPAAGR +>PROKKA_01950 +MASPQTRTGSVPVPESSALLERLGVHITAGTLERALTHRSYAYEHGGLPTNERLEFLGDS +VLGFVVTDHLFTAFPDLPEGDLARRRAAIVSTRALAKVARRIGVGPHVRLGTGETRTGGA +DKDSILADTFEALIGAVYRDHGAVAAAALVHRHVVPLLDEPGLLRESTDWKTVVAEAASR +HGLGEVRYDIEGQGPAHDPRFRATLTVGGRAFGSAVASSKKQAERDAAAEGWPELSATLP +AAGS +>PROKKA_00838 +MHITAGTLERALTHRSFAYEQGGLPTNERLEFLGDSVLGYVVTDHIFTVYPDLAEGDLAR +RRAAVVSTRALAKVARRIGIGPFVRLGTGERRTGGADKDSILADTLEALIGAVYVDHGAV +AAAALVHRHVVPLLDEPDLLRESTDWKTVVAEAASRHGLGAVRYAIEGQGPAHDPRYRAT +LVVGEREYGSAVASSKKQAERDAAAASWPALEAGLPAAGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000768.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000768.fa new file mode 100644 index 0000000000000000000000000000000000000000..6b25fd8ad1d76595939050da7a2ae274c7857972 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000768.fa @@ -0,0 +1,40 @@ +>PROKKA_00881 +MSHPPAASWTPEPLPRPEPPRDDAPPVARRRRRWPWVVGLLAVLLAALLGLGAWYTSSLG +RTFDDHRQTVDVGALEQAAGNGPLNVLVLGSDSREGEGEQDMGQRSDTMMLVHIPADRRQ +VYVMSVLRDSWVTVPGHGEAKINSAFDTGGYTLAVDTVELLLGVSIHHVLEVDFQGFRGV +TNALGGVEVCNPRAFSSGQANPSYYPRGHILLQDTAALRYVRERHAFDDGDVTRVENQQR +YLAGAMDRFLSPQILGNPARTTEVVATFSDHLGVDEGLTSGVIASLAWQLRDVRGEDVEM +FTVPRKGFAEGPNGDAIVELDEDKLADLRSALADDDVQRYVDEHEPTKEKKAQAAGGPAP +VLTLLTGTTPAPVLGEDPCDD +>PROKKA_00603 +MSHPPAASWTPEPLPRPEPPRDDAPPVARRRRRWPWVVGLLAVLLAALLGLGAWYAGSLG +RTFDDHRQTVDVGALEQAAGDGPLNVLVLGSDSREGEGEQDMGQRSDTMMLVHIPADRRQ +VYVMSVLRDSWVTVPGHGEAKINSAFDTGGYALAVDTVELLLGVPIHHVLEVDFQGFRGV +TNALGGVEVCNPQAFSSGQANPSYYPRGHILLQDTAALRYVRERHAFDDGDVTRVKNQQR +YLAGAMDRFLSPQILGNPARTTEVVATFSDHLGVDEGLTSGVIASLAWQLRDVRGEDVEM +FTVPRKGFAEGPNGDAIVELDEDKLADLRSALADDDVQRYVDEHEPEKEKKAQAAGGPAP +VLTLLTGTTPAPALGENPCDD +>PROKKA_02054 +MSQPPAASWTPEPLPRPARSPEPPRPARRRRWPWVLGVLAAVLVVLLALGAWYAVSLART +FDDHRQTVDAGALEQAGGGEPVNVLVLGSDSRGGEGEEDMGERSDAMMLVHLPADRSQVF +VMSVLRDSWVEIPGHGEAKVNAAFDLGGYPLAVDTVEQLLGVPVHHVVEMDFQGFRGVTN +ALGGVEVCNPVAFSSGQTSPSYYPRGPVLLQDTAALRYVRERHAFDDGDVSRVQNQQRYL +AGAVERFLSPQILGNPARTTEVVATFSDHLGVDAGLTSGVVASLAWQLRGVRAGDVEMFT +VPRAGFGYSPDGDSIVELDEAKLADLRSALKDDDVQRYVAEHESEDGQDASAAGADPAPV +LALLAQPAPTPAVGEDPCAD +>PROKKA_01948 +MTQPPQQPWIPPERPGGAADPLEGLRGPAPAAPPTSTPPATRRSGGGRARRRRPLRRFLA +VLGVLALLLVVALGAYGLLLARTFDGHRQTVSAAAFADPGNDGPVNFLVLGSDSRAAEDS +AETSQRSDTMMLVHVPADRRHVYVISVLRDSLVEIPGRGQRKANAAYELGGPELTAAMLD +KLLGVPVHHLAELDFQGFRGMTTALGGVEVCNPHAFSSGQKNPSFYPRGRIELKDTAALR +YVRERHAFPEGDVMRVQNQQRFVRGAVAAFLDPAVVLNPPRAVDVVAGLSDHLTVDEGLD +SATLASLAWQLRGVDRSALTMFTVPRAGYGTSPDGQDVVLLDADRMAALRDALQRDDVES +YLRAHDPEALAAGEDVQPALAAAPGATPLLTELAAAPPAGEGTLLGEDPCGG +>PROKKA_00840 +MSHPPAASWTPEPLPRPESPRDDASSVARRRRRWPWVVGVLAVLLAALLGLGAWYAGSLG +RTFDDHRQTVDVGALEQAAGNGPLNVLVLGSDSREGEGEQDMGQRSDTMMLVHIPADRRQ +VYVMSVLRDSWVTVPGHGEAKINSAFDTGGYALAVDTVELLLGVPIHHVLEVDFQGFRGV +TNALGGVEVCNPQAFSSGQANPSYYPRGHILLQDTAALRYVRERHAFDDGDVTRVKNQQR +YLAGAMDRFLSPEILGNPARTTEVVATFSDHLGVDEGLTSGVIASLAWQLRDVRGEDVEM +FTVPRKGFAEGPNGDAIVELDEDKLADLRSALADDDVQRYVDEHEPTKEKKAQAAGGPAP +VLTLLTGTTPAPALGEDPCDD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000770.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000770.fa new file mode 100644 index 0000000000000000000000000000000000000000..617f49026b341014355c53e3a691b95acdd4ccf3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000770.fa @@ -0,0 +1,41 @@ +>PROKKA_00885 +MKKIETVAVIGLGYIGLPTAAILAENGVRVLGVDVSDRTVDAVNAGTVPFVEPDLAGFVA +RGVEKGLLSASTTTPAADAYIVAVPTPFKDGHSPDLGYIEAAARGLAPQLTGDELVILES +TSPPGATEYMAEVIFAERPELREAELDFAHCPERVLPGRVMVELVTNDRIVGGSTRRAAE +RARDLYRTFCEGEILLTDTRTAEMAKLVENSFRDVNIAFANELSVICAEQGIDVWELIEL +ANHHPRVNILQPGPGVGGHCIAVDPWFIVDAAPQTARLIRAAREINDGKPQWVIDQVKAA +AFDVQQATGRAPVVAALGLAFKPNIDDLRESPALNIAAELAGQFSGSDVLVVEPHVTELP +AALQGKDNVRLVAVDEALEAADIVVLLVDHSAFADLGDRVADKRVIDTRGQWRTDPSL +>PROKKA_00607 +MKKIETVAVIGLGYIGLPTAAILAENGVKVLGVDVSDRTVDAVNAGTVPFVEPDLAGFVA +RGVEKGLLSASTTTPAADAYIVAVPTPFKDGHSPDLGYIEAAARGLAPQLTGDELVILES +TSPPGATEYMAEVIFAERPELREAELDFAHCPERVLPGRVMVELVTNDRIVGGSTRRAAE +RARDLYRTFCEGEILLTDTRTAEMAKLVENSFRDVNIAFANELSVICAEQGIDVWELIEL +ANHHPRVNILQPGPGVGGHCIAVDPWFIVDAAPQTARLIRAAREINDGKPQWVIDQVKAA +AFDVQQATGRAPVVAALGLAFKPNIDDLRESPALNIAAELAGQFSGSDVLVVEPHVTELP +AALQGKDNVRLVAVDEALEAADIVVLLVDHSAFADLGDRVADKRVIDTRGQWRTDPSL +>PROKKA_02051 +MTTQIKDVAVIGLGYIGLPTAAILAENGVRVHGVDVSQRTVDAVNAGTVPFVEPDLADFV +ERNVKAGRLSASLKTPQADAYIVAVPTPFKDGHSPDLGYIEAAARGLAPQLRGGELVILE +STSPPGATEHMAAVIREARPDLDGATLDFAHCPERVLPGRVMIELVTNDRIVGGSTPEAA +QRAKQLYETFCQGEILVTDCVTAEMAKLVENSFRDVNIAFANELSLICSDLGIDVWELIE +LANHHPRVDILQPGPGVGGHCIAVDPWFIVDAAPQTARIIRAAREINDGKPKWVVDQAKA +AAFDVQQATGRAPVVAVLGLAFKPNIDDLRESPALNIATEVAQQFTGSRILVVEPHVEEL +PAALAGRDNVELVPAEDGIREADVVLLLVDHDAFASLGTTTEGKKVIDTRGQWR +>PROKKA_01945 +MMGTPPALRCRDVNARMGIQNVTQIKTVAVIGLGYIGLPTAAILAENGLTVHGVDVSPRT +VDAVNAGKVPFVEPDLADFVERNVAAGRLDASLETPKADAYIVAVPTPFQGDHAPDLSYI +EAAARGLAPQLTGDELVILESTSPPGATDHMADVIREVRPDLKDAPLDFVHCPERVLPGR +VMVELVTNDRIVGGSTPAAAERARDLYRSFCEGEILLTDCRTAEMAKLVENSFRDVNIAF +ANELSLICAEQGIDVWELIGLANHHPRVNILQPGPGVGGHCIAVDPWFIVDAAPQTARII +RAAREINDAKPQWVIERAKAAAFDVQQKEGRPAVVAALGLAFKPNIDDLRESPALNIAAQ +LADEFSGSTVLVSEPHVDELPAKLQGKENVRFVPAEQAVAEADVVLLLVDHDAFAGLGEQ +TAGKRVIDTRGQWR +>PROKKA_00843 +MTTQIKDVAVIGLGYIGLPTAAILAENGVRVHGVDVSQRTVDAVNAGTVPFVEPDLADFV +ERNVKAGRLSASLKTPQADAYIVAVPTPFKDGHSPDLGYIEAAARGLAPQLRGGELVILE +STSPPGATEHMAAVIREARPDLDGVTLDFAHCPERVLPGRVMIELVTNDRIVGGSTPEAA +QRAKQLYEAFCQGEILVTDCVTAEMAKLVENSFRDVNIAFANELSLICSDLGIDVWELIE +LANHHPRVNILQPGPGVGGHCIAVDPWFIVDAAPQTARIIRAAREINDGKPKWVVDQAKA +AAFDVQQATGRAPVVAVLGLAFKPNIDDLRESPALNIAIEVAQQFTGSRILVVEPHVEEL +PAALAGRDNVELVPAEDGIREADVVLLLVDHDAFASLGATTEGKKVIDTRGQWR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000772.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000772.fa new file mode 100644 index 0000000000000000000000000000000000000000..5a7c8e00a7dd34845a52d9d69a6368232752595c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000772.fa @@ -0,0 +1,29 @@ +>PROKKA_00896 +MSDTGDPRVPSGTAVLTVDGATLRRVGARPGLARYLASLWEYRSFILFDSRSRIAGANSV +NALGRVWMVLNPILDGAAYFLVFGLLLGTGRGVPNFLGYLIIGVFLFRYTSSAITAGSRS +ISTNLSIVRAFRFPRATLPIATNIRELMLFGPTLVVMLVLVLAIPPMEQITWRWLLLIPL +LALQTLFNVGASLLLARYVARWSDLSNLIAFGTRIWLYVSAVFFSADRFADFPPMMTAMH +LNPLFCVLDIARQSLLYASDADPMRWVVLAAWTAALLVVGTVVFWRAEETYGEER +>PROKKA_00618 +MADTGDPRVPSGTAVLTVDGATLRRVGARPGLARYLASLWEYRSFILFDSRSRIAGANSV +NALGRVWMVLNPILDGAAYFLVFGLLLGTGRGVPNFLGYLIIGVFLFRYTSSAITAGSRS +ISTNLSIVRAFRFPRATLPIATNIRELMLFGPTLVVMLVLVLAIPPMEQITWRWLLLIPL +LALQTLFNVGASLLLARYVARWSDLSNLIAFGTRIWLYVSAVFFSADRFADIPPLMTAMH +LNPLFCVLDIARQSLLYASDADPMRWIVLAAWTAALLVVGTVVFWRAEETYGEER +>PROKKA_02043 +MSGTGMAASGPVNTVVVDAAPLGVVGARPSLRDYVLSLFRYRSFILFDSRSRISGANAVN +TLGRLWMVLNPILDGGAYFLVFGVLLGTGRGIPNFIAYLIIGVFFFRYSSQAITAGSKAV +SSNLTLVRAFRFPRATLVLATNLRALLEFVPTLAVMVVLILAIPPLEVFTWRWLLLVPLL +ILQTLFNVGLSLVLARFVAHWPDLANMIAFGMRIWLYLSAVFFSVERFDGQPIVQTAMHL +NPLYCVLDIARQSLLYGQDAEPHRWLVLAGWAALVAVVGLVVFWRAEETYGEER +>PROKKA_01941 +MTDRVEATSPPVELRVDESRLERVGRRPSLGDYVTRLWRLRHYVRYDAVAAVQAQNRRHR +LGNVWLLLNPILNGATYFLVFGVLLRTSLGVENFIGYLTVGVFMFTFTTRAVTALSRSLT +ARNNVADAFQLPRAVLPLTALAREVLAYGFTLAAMLLAVLILPPHAQVTWWWLLFPVVVA +LQLMLVAGVGLLLARAVSRVRDLSQIVGFGIRLWMYGSAVFYSFDRFVSQPNVLAVLQLN +PMYQVLDISRDLLLYGRSPSPVAWGILAAWSVGLLVVGVVVFWLGEERYAKDLNR +>PROKKA_00847 +MLDAIFYWLIFGLLLRFDHGMDNFVAFVIVGVFMFQMTSAALTSGTRTIASNLSLTRAFR +FPRMALPLADLVYDVLQRLPAIAVMFILVIAIPPHETPEWSWLVFPGVLGLHVILNFGIM +LLLARLSTLLPDVSRMVPFVSRLLMYGSGVIFPITRFTDNHPALHAIIQLNPLYVLITMY +RQVIIEGVTPPASSWAMLAAYAVCLTIVGGIVFWLGEESYGRDQYR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000773.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000773.fa new file mode 100644 index 0000000000000000000000000000000000000000..5411ae7d5eee7c8fcdb1edbe2ee76215fe7cd0cf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000773.fa @@ -0,0 +1,40 @@ +>PROKKA_00897 +MPKVMPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDLN +IIQPRQTLNGVFARTLDGLDAVLEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEAG +LRSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAAEDIYVTGNTVIDALLE +AVGHQVPFEDERLAELEASGRRVVLVTTHRRENQGDAMRGVGRALARLAADHPEVTFVLP +AHRNPVVREAILPEIEGRENVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAPSLGKPV +LVMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLLTDEAAYTAMSQAVNPYGDGRAAER +TVSAIAELLGVGERLPAFDGGDPA +>PROKKA_00619 +MPKVMPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDLN +IIQPRQTLNGVFARTLDGLDAVLEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEAG +LRSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAPEDVYVTGNTVIDALLE +AVSHQVPFEDERLAGLEASGRRVVLVTTHRRENQGDAMRGVGRALARLAADHPEVTFVLP +AHRNPVVREAILPEIEGRENVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAPSLGKPV +LVMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLLTDEAAYSAMSQAVNPYGDGRAAER +TVSAIAELLGVGERMPEFAPDDRG +>PROKKA_02044 +MKVMPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDLNI +IQPRQTLNGVFARTLDGLDAILEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEAGL +RSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAPEDVYVTGNTVIDALLEA +VGHQVPFEDERLAELEASGRRVVLVTTHRRENQGDAMRGVGRALARLAADHPEVTFVLPA +HRNPVVREAILPEIEGRANVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAPSLGKPVL +VMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLLTDEAAYTAMSQAVNPYGDGRAAERT +VSAIAELLGVGERLPAFDGA +>PROKKA_01942 +MPLKIMPIYGTRPEAIKMAPIVNALRADDRFECFTTVTGQHREMLDQVNAIFGITPDADL +DIMRPNQTLNGIMSVMLEGLDELLVRERPDAVVVQGDTTTSTAGAIAAFYRGIPVVHAEA +GLRSGDLFSPFPEEANRKITSQIASLHLAPTSVSRANLEREAIDSAAITVTGNTVIDALL +ETVAQQLPFTDPRLAELAERRAADPQSRVLLVTTHRRENQGEAMRGVGRALARLAQSHPN +LTIVLPAHRNPVVREAVLPTLEGIDSVIVTEPLPYGEFTRMMDLADVVLTDSGGVQEEAP +SLGKPVLVMRDNTERPEAVHAGTVRLIGTDEERLVEETSLLLTDPDAYAAMAHAVNPYGD +GRAGLRTVAAIAQLLGVGDRLDEFGA +>PROKKA_00848 +MPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDLNIIQP +RQTLNGVFARTLDGLDAVLEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEAGLRSF +DILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAAEDIYVTGNTVIDALLEAVSH +QVPFEDERLAELEASGRRVVLVTTHRRENQGDAMRGVGRALARLAADHPEVTFVLPAHRN +PVVREAILPEIEGRENVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAPSLGKPVLVMR +ENTERPEAVTAGTVRLIGTDEEVVVTEVTRLVTDEAAYTAMSQAVNPYGDGRAAERTVSA +IAELLGVGERLPAFDGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000774.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000774.fa new file mode 100644 index 0000000000000000000000000000000000000000..f104d2fb248c9be8bc54cd09e0a0ec5f5f64cbba --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000774.fa @@ -0,0 +1,45 @@ +>PROKKA_00900 +MPSSPPAARVPLPTEIKVMVAAAFVIAIGFGIIAPLLPQYAEMFASDFANPATAVAAVVS +AFGLTRLLFAPVSGRLTNRLGETPVYMTGVLIVAASMFLIAFAQDYTQLLLYRALGGVGS +TLFTVSAMAFLASKSPPTIRGRVSGAYASAFLIGNIVGPIVGSVLAVFGFRVPFLIYGTS +LVIAAGIVFVMLRDTRLQDRARGETRPVMPLRAALGHRSYRAALTSMFANGWATFGVRNA +ITPLFAASAFTGTALLGWGITEENRQLMAGLALSVFAAGNVLAVASSSRLSDLHGRKPLI +LVGLAVMAVFTGAIGWLESPLLFLVSCALAGAGTGTLNAPQQAAVADLVGQDRKAGPVMS +AAQMSGDLGAILGPLLVGLVVDAAGYGWGFVVTGAVIAVGALAWARAPETNLPVAPGGPR +TGSLPKVDPDVDPCRMEGRELG +>PROKKA_00620 +MAVMPSSSARSSRVPLPREIKVLVAAAFIIAIGFGIIAPLLPQYAATFDASAVGVAAVVS +AFGLTRLLFAPVSGKLTNRLGETPVYMTGVLIVAASMFLVAFAQTFPQLLLFRALGGVGS +TLFTVSAMAFLARKSPPTMRGRISGAYASAFLIGNIVGPIVGSALSVFGYRAPFLIYGSS +LVVAAALVFFLLKDTRLADRAVRDVRPAMPVREALSNPSYRAALVSFFANGWATFGVRNS +VMPLFAATAFAGTGLLGWQVDGAMMAGLALSVFALGNVVAVSFSSRLSDVHGRKPLILTG +LLVMAVTTGAIGWVGTPSLFLIACLVSGAGTGILNAPQQAAIADVVGQDRRSGSVMSSAQ +MSADLGAIVGPLAAGLVVDVAGYGWAFVVTGAVILLGAIAWWRAPETNLPVVPGGPRTGA +LPKIEPEDARPPHREDG +>PROKKA_02041 +MPSSSSRTARAPLPREIKVLVAAAFIIAIGFGIIAPLLPQYAASFNASATAVAAVVSVFG +LTRLLFAPLSGRLTNRLGETPVYMTGVLIVAASMFLIAFAQTFAQLLAFRAIGGVGSTLF +TVSAMAFLARKAPPSMRGRVSGAYASAFLIGNIVGPIVGSALAVFGYRAPFLIYGTSLVI +AAALVFFMLKDTRLADRAARDARPAMPVKEALENPSYRAALVSFFANGWATFGVRNSVMP +LFAASAFAGSGLLGWQVDGALMAGLALSVFALGNVVAVTFSSRLSDMHGRKPLILTGLLV +MAVTTGVLGWMQSPLLFLLACLVSGAGTGVLNAPQQAAIADVVGQGRRSGAVMSSAQMSA +DLGAIIGPLLAGLVVDAAGYGWAFVLTGGVILLGALAWWRAPETNLPIVPGGPRTGSLPL +VRPEDARVTPREDG +>PROKKA_01939 +MPTTPSAARAPLPREIKVLVAAAFVIAIGFGIIAPLLPQYAERFASDFANPATAVAAVVS +AFGLTRLLFAPLSGRLTNRLGETPVYMTGVLIVAASMYLIAFAQDYTQLLVFRGLGGVGS +TLFTVSAMAFLASKSPPSMRGRVSGAYASAFLIGNIVGPIVGSVLSVFGYRVPFLIYGTS +LVIAAAIVFFMLKDTRLHDRAAADSRPVMRLREALDHPSYRAALVSMFANGWATFGVRNA +VTPLFAASAFTGTALLGWTVTQENQALMAGLALSVFAAGNVAAVTFSSRLSDVRGRKPLI +LLGLAVMAVCTGVIGWMTSPLLFLVACLLAGAGTGTLNAPQQAAVSDLVGQGRKAGPVMS +VAQMAADLGAISGPMLVGLVVDGAGYGWAFAVTGAVLAVGFLAWLRAPETNLPIVPGGPR +TGSLPKIAPEDVAPPHHREA +>PROKKA_00849 +MAVMPSSSARSSRVPLPREIKVLVAAAFIIAIGFGIIAPLLPQYASSFNASATAVAAVVS +AFGLTRLLFAPLSGRLTNRLGETPVYMTGVLIVAASMFLIAFAQTFEQLLLFRALGGVGS +TLFTVSAMAFLAAKSPPTMRGRVSGAYASAFLIGNIVGPIVGSALAVFGFRAPFLIYGTS +LVIAAGMVFVLLRDTRRADRGTGDPRPTMPLKEAFGLPSYRAALASFFANGWATFGVRNS +VMPLFAATAFAGTGLLGWQVDGAFMAGLALSVFALGNVVAVTFSSRLSDVHGRKPLILTG +LLTMAATTGVIGWMSSPALFLLACLLAGAGTGTLNAPQQAAIADVVGQGRRSGAVMSAAQ +MSADLGAISGPLLAGLVVDTAGYGWAFVLTGGVILLGALAWWRAPETNLPIVPGGPRTGS +LPLVRPEDARVTPREDG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000776.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000776.fa new file mode 100644 index 0000000000000000000000000000000000000000..68e4b09084752fb4dc41a4f8dbdeac63bc9a5d52 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000776.fa @@ -0,0 +1,43 @@ +>PROKKA_00903 +MNEMTLDAGTVWMVVSAGLVLLMTPGLALFYGGMTRSKSALNMMMMSFVSMGLVGVVWIL +WVSGMTGGEGWLGLVGSPLADPGLTTAMEEGGLIAAGFGATFAIITVALISGAVADRARF +LTWCVFVPVWVTLVYAPLAYMVWGGGLLAEEGAIGSRLGEALDFAGGLVVHISAGVAALV +LALMMGKRKGFGVDPGHKPHNVPFTMLGAALLWFGWFGFNGGAAGDTGQLGLIWINTLAA +AAAGMLGWVVVEWVRRGRPTSIGTASGIVAGLVGITPACAFVSPLGALVIGVASGAASAL +AVNLKYRLGFDDSLDVVGVHLTAGILGTVLIGFFALPSEGPAGLFYGGDGRLLLAQTVAV +VVAVVFTAVLTFLIALVLKATLGLRVSEEDEERGVDLTLHDESAYHYDVGFGGVPVPADA +QAHRGGAAG +>PROKKA_00622 +MEESNVLDAGTVWMVTSAAMVLLMTPGLAIFYGGMTRAKSSLNMIMMSFVSMGLVGVVWV +LWVHGMTGGDGWAGVVGNPAGDLGLTGTMAEGGLVAAAYGATFAIIAVALISGAVADRFK +FVTWCVFVPVWTTVVYAPLAYMVWGGGLLSEDGAIGARLGEALDFAGGLVVHISAGVAAL +VLALLLGKRHGFGVDPGHRPHNVPFTMLGAALLWFGWFGFNGGAAGGVDELGLIWVDTLA +AGAAGMLGWVFVEWLRRGRPTSIGTASGIVSGLVAITPACAYVSPLGAVVIGLVSGAASA +LAVNLKYRLGFDDSLDVVGVHLTSGILGTVLIGFFALPGEGRAGLFYGGDAGLLVAQTVA +VLVAVVFTAVVTTAIALVLRGTMGLRVSKEDEERGVDLTLHDESAYDVGFGGVPVPAEAR +>PROKKA_02039 +MNEMTLDAGTVWMVVSAGLVLLMTPGLALFYGGMTRSKSALNMMMMSFVSMGLVGVVWIL +WVSGMTGGEGWLGLVGSPLADPGLTTAMEEGGLIAAGFGATFAIITVALISGAVADRARF +LTWCVFVPVWVTLVYAPLAYMVWGGGLLAEEGAIGSRLGEALDFAGGLVVHISAGVAALV +LALMMGKRKGFGVDPGHKPHNVPFTMLGAALLWFGWFGFNGGAAGDTGQLGLIWINTLAA +AAAGMLGWVVVEWVRRGRPTSIGTASGIVAGLVGITPACAFVSPLGALVIGVASGAASAL +AVNLKYRLGFDDSLDVVGVHLTAGILGTVLIGFFALPSEGPAGLFYGGDGRLLLAQTVAV +VVAVVFTAVLTFLIALVLKATLGLRVSEEDEERGVDLTLHDESAYHYDVGFGGVPVPADA +QAHRGGAAG +>PROKKA_01937 +MTETTPLDAGAVWTVTAAALVLLMTPGLALFYGGMTRAKSALNMMMMSFVSMGLIGVAWI +LWAYGMTSGDGLAGIVGSPLNDLGAVQSMADGDLISVGFSATFAIIAVALISGAVADRAK +FSTWCVFVPVWVTLVYAPLAYMVWGGGLLSADGAIGARLGEALDFAGGLVVHISAGVAAL +VLAMMMGKRQGFGVDAAHRPHNVPFTMLGAALLWFGWFGFNSGAASDVEQLGLTWVTTLV +AAAAGMLGWVLVEWLRRGRPTSIGTASGIVSGLVAITPACAFVSPLGAVVIGLVAGAACA +LAVNLKYRWGFDDSLDVVGVHLTAGILGTLLIGLFALPETGHAGLFHGGDGSLLLAQTVA +VVVAVVFTAVVTAVIAFVLRATLGLRVSVEEEERGVDLTLHDETAYDVGFGGVPVPTDAQ +ARSTAAAE +>PROKKA_00851 +MEESNVLDAGTVWMVTSAAMVLLMTPGLAIFYGGMTRAKSSLNMIMMSFVSMGLVGVVWV +LWVHGMTGGDGWAGVVGNPAGDLGLTGTMAEGGLVAAAYGATFAIIAVALISGAVADRFK +FVTWCVFVPVWTTVVYAPLAYMVWGGGLLSADGAIGARLGEALDFAGGLVVHISAGVAAL +VLALLLGKRHGFGVDPGHRPHNVPFTMLGAALLWFGWFGFNGGAAGSVDELGLIWVATLA +AGAAGMLGWVFVEWLRRGRPTSIGTASGIVSGLVAITPACAYVSPLGAVVIGLVSGAASA +LAVNLKYRLGFDDSLDVVGVHLTAGILGTVLIGFFALPDEGRAGLFYGGDAGLLVAQTVA +VLVAVVFTAVVTTAIALVLRGTMGLRVSKEDEERGVDLTLHDESAYDVGFGGVPVPAEAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000778.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000778.fa new file mode 100644 index 0000000000000000000000000000000000000000..112c8007d73014708b1a2b4340c308592d4514f1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000778.fa @@ -0,0 +1,20 @@ +>PROKKA_00905 +MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL +SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE +APAESEQAAEAPAAEAPAEDAEKSE +>PROKKA_00624 +MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL +SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE +APAESEQAAEAPAEEAAEAPAEDAEKSE +>PROKKA_02037 +MAVKIRLKRFGKIRAPYYRIVVADSRTRRDGRAIEEIGKYHPTEEPSYIEVDSERAQYWL +SVGAQPTEQVAALLKITGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKAEE +PKAKESAEAETPAEEAPEAPAEDAEKSE +>PROKKA_01935 +MAVKIRLKRFGKIRAPYYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL +SVGAQPTEQVAALLKITGDWQKFKGEAGAEGTLKTKGEKEAFVAPAKESVILPEEPKQEE +APAESAEAEAPVEEAADAEAPAEDAEKAE +>PROKKA_00853 +MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL +SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE +APAESEQAAEAPAEEAAEAPAEDAEKSE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000780.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000780.fa new file mode 100644 index 0000000000000000000000000000000000000000..d3853aae3642355b18619b149c6ae7adbd72b8d1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000780.fa @@ -0,0 +1,25 @@ +>PROKKA_00907 +MSPAAQDDLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGERLVVRDGAPGLPAELTVT +RARWNKQILVVGFEESPDRNVAETLRGAQLFAVPAAPEESDEWYEEDLVDLEVRVDGERV +GVVTALTTGAVQDLLHVALDGVEEEALVPFVEEIVPEIDPEAGVLVLTPPPGLLELATGE +DEGAADGPTDADAED +>PROKKA_00626 +MSPAAQDDLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGERLVVRDGAPGLPAELTVT +RARWNKQILVVGFAESPDRNVAETLRGAQLFAVPAVPEESDEWYEEDLVDLEVRVEGERV +GVVTALTTGAVQDLLHVALDGVEEEALVPFVEEIVPEIDSEAGVLVLTPPPGLLELATGE +DEGAVDGPADADAED +>PROKKA_02035 +MSPAPQDGLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGATLTVRDGGPSLPAELTVT +RARWNKQILVVGFEQSPDRNTAETLRGAQLFAAPAAPEESDEWYEDDLVDLEVRVDGRRV +GVVTALTTGAVQDLLHVALDGVDEEALVPFVEEIVPEIDPEAGVLVLTPPPGLLELASGE +AEQDDDAAASDAEADADAGREG +>PROKKA_01933 +MSPAPQPAETEGQVRVARIGKPHGIRGEVTVQLFTDDPEARFAADSRLEVRQGPPGAPAA +LTVTRARWNKAILVVGFAEVPDRNAAEALRGAQLYAAPLEKVEDDAWYEDDLLDLEVHVD +GARVGVVTGLLTGTVQDLLQVRLDATGDDALVPFVEEIVPEVDQEAGVVVVAPPPGLLEL +ASETTAGEG +>PROKKA_00855 +MSPAAQDDLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGERLVVRDGAPGLPAELTVT +RARWNKQILVVGFAESPDRNVAETLRGAQLFAVPAAPEESDEWYEEDLVDLEVRVEGERV +GVVTALTTGAVQDLLHVALDGVEEEALVPFVEEIVPEIDSEAGVLVLTPPPGLLELATGE +DEDAADGPADADAED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000782.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000782.fa new file mode 100644 index 0000000000000000000000000000000000000000..74e09e00f1121797baf331373b3608cbbbab9f7b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000782.fa @@ -0,0 +1,15 @@ +>PROKKA_00909 +MHILDSFDKKTLRDDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGHGVRETFRV +RKVSFGIGVERVFPVHSPVIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRVDAK +>PROKKA_00628 +MHILDSFDKKTLRDDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGYGVRETFRV +RKVSFGIGVERVFPVHSPVIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRADAK +>PROKKA_02033 +MHILDSLDSNSLRSDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRNGYGVRETFRV +RKVSFGVGVERVFPVHSPVIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRVDAK +>PROKKA_01931 +MHILDSFDKASLREDIPAFGPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGHGVRETFRV +RKVSFGVGVERVFPVHSPVIDKIEVLTKGDVRRAKLYYMRDRHGKAARIREKRADAK +>PROKKA_00857 +MHILDSFDKKTLRDDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGYGVRETFRV +RKVSFGIGVERVFPVHSPIIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRVDAK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000783.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000783.fa new file mode 100644 index 0000000000000000000000000000000000000000..e91b42507628f9a597ce7ba3fa03d424b50fef80 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000783.fa @@ -0,0 +1,29 @@ +>PROKKA_00910 +MRTSEPRDPRRSRGSVASGAGSSPGTTAAPASGASRWWAWLGLTVVAAVVVAAVLRALTG +PVYLIPSGSMEPTLQPGDRVRVDAAAAGGQGLHHGDVVVFDGAGSLAPYRSAGSLERGLE +DVARWWGVGAAEDVFVKRVLALPGDRLECCAPDGRLLREGEPLDEPYLGRPVTADEPAAA +GTWSFEVPDGRMVVLGDHRAASRDSRALLGAPGGGLIPLERVEGRAAEIVWPLSRRGTVD +APSGDTP +>PROKKA_00629 +MRTSEPRDPRRSRGSVASGAGSSSGPTAAPASGTSRWWAWLGLTVVAAVVVAAVLRALTG +PVYLIPSGSMEPTLQPGDRVRVDAAAAGGQGLHHGDVVVFDGAGSLAPYRSAGSLERGLE +DVARWWGVGAAEDVFVKRVLALPGDRLECCAPDGRLLRNGEPLDEPYLGRPVTADEPAAA +GTWSFEVPDGRMVVLGDHRAASRDSRALLGAPGGGLIPLERVEGRAAEIVWPLSRRGTMD +APSGDTP +>PROKKA_02032 +MSHPEPRDPRRSRGSAVSRSVAPGSGRGTTPARGSGGTAWWAWIGLTVAAAVGAAAVLRA +LTGPVYLIPSGSMEPTLHPGDRVRVDASAAGGEGVRRGDVVVFDGAGSLAPYRSVGSLER +GLEDVARSWGLGASGDAFVKRVLALPGDRLECCAPDGRLLRDGAPVDEPYLGRPVTAQDP +AADGSWTFEVPEGRMVVLGDNRSASRDSRALLGGAGGGLIPLKRVEGRAAEVVWPLDRRG +PVDASAPEAAPGAAP +>PROKKA_01930 +MRAQEPRDRNRSRGSRASGEAGRPWWALVLLTLAGAVVAAALLRAFTGPVYLVPSGSMEP +TLLPGDRVHVDTAAADGAGLEHGDVVVFDGAGSLAPYRSRTALDRGLEDVAAFWGVGAAQ +DVYVKRVLALPGDTLSCCTADGRLERNGAPLDESYLGRTVDAAAPASRSTWAFEVPEGRM +VVLGDNRDVSRDSRALLGAPGGGLIPVEKVIGRVDSVAWPLDRRGDVPAGAQDGSRG +>PROKKA_00858 +MRTSEPRDPRRSRGSVASGAGSSSGPTAAPASGTSRWWAWLGLTVVAAVVVAAVLRALTG +PVYLIPSGSMEPTLQPGDRVRVDAAAAGGQGLQRGDVVVFDGAGSLAPYRSAGSLERGLE +DVARWWGVGAAEDVFVKRVLALPGDRLECCAPDGRLLREGEPLDEPYLGRPVTADEPAAA +GTWSFEVPDGRMVVLGDHRAASRDSRALLGAPGGGLIPLERVEGRAAEIVWPLSRRGTVD +APSGDTP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000787.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000787.fa new file mode 100644 index 0000000000000000000000000000000000000000..9a5d2868fa974a97dd59eb6a3904cf6fd4b3d449 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000787.fa @@ -0,0 +1,20 @@ +>PROKKA_00914 +MTGTAEQVGAQPPGERRASRAHTALGRFGEDAAARWLAERGYVIADRNWRGEAGELDIVA +HHAGWWVGVEVKTRSGLAFGDPFESIDRRKLTRLHRLTAAWVRAHAADRRGTPWRVDAVA +VLVPRTGGIRFDLLQDVRP +>PROKKA_00633 +MTGTAERIGAQPPGDRRASRAHTALGRFGEDAAARWLAERGYVIADRNWRGEAGELDIVA +HHAGWWVGVEVKTRSGLAFGDPFESIDRRKLTRLHRLTAAWVRAHAADRRGTPWRVDAVA +VLVPRTGGIRFDLLQDVRP +>PROKKA_02028 +MTGTAEKVGADSPGGGRGSRAHTALGRFGEDAAARWLADRGYVIADRNWRGEAGELDLVA +HHAGWWVGVEVKTRSGLAFGDPLESIDRRKLLRLHRLTAAWVRAHGEGRRAERWRVDAVA +VLVPRTGGIRFDLLQDVRP +>PROKKA_01926 +MVPLDTTTTTPAARRGSTAHTALGRYGEDAAARWLAERGYQIVARNWRGEDGELDLVARH +GPWWVGVEVKTRSGLAYGDPLEAIGRRKLLRLHRLTAAWVREAAAREGRPLRSQQWRVDA +VAVLVPRTGGVHFDLVQDVRP +>PROKKA_00862 +MTGTAEQVGAQPPGERRASRAHTALGRFGEDAAARWLAERGYVIADRNWRGEAGELDIVA +HHAGWWVGVEVKTRSGLAFGDPFESIDRRKLTRLHRLTAAWVRAHAADRRGTPWRVDAVA +VLVPRTGGIRFDLLQDVRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000789.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000789.fa new file mode 100644 index 0000000000000000000000000000000000000000..4a5598bf4ba315763405c550ac7a42d42dede21a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000789.fa @@ -0,0 +1,44 @@ +>PROKKA_00916 +MTTHVTPAADHVAGPRRPDAARLARAALTRLVEPGDALAVQTVTALGPERALALLTGRET +IQPAERDLLADLAGAPDTLPRRWAAGLARWAPRAARLEPERDLVTLHRLGGGLLIPEDDA +WPAALADLGEEAPLGLWFRGSGTLPPADRMLAVVGSREATAYGRTVTARCAAHAVQQGAC +VISGGAYGIDGAAHRAALQAPAAPEDAADRDGVPPTVAVLAGGLDRFYPAGHEDLLRAVM +AAGLLVSEMPPGASPTRYRFLQRNRVIAALAGAVLVVEARWRSGAQNTAGHAFGLGREVG +VVPGPVTSPSSAGCHRLLQESPARLVTTEQEALALLGQGPARSGDTGGRTSARAAPEPAA +RPTDGLTMEEALVHEALPLRQAVPADRITVSAGLALPTVLACLSRLQRAGLAERVEDRWR +RG +>PROKKA_00635 +MTTYVTPAADHVAGPRRPDAARLARAALTRLLEPGDALAVQTVTALGPERALALLTGRET +IQPAERDLLADRAGAPDTLPRRWAAGLARWAPRAARLEPERDLVTLHRLGGGLLIPEDDA +WPAALADLGEEAPLGLWFRGSGTLPPADRMLAVVGSREATAYGRTVTARCAAHAVQQGAC +VISGGAYGIDGAAHRAALQALAAPGDAADRDGVPPTVAVLAGGLDRFYPAGHEDLLRAVM +AAGLLVSEMPPGASPTRYRFLQRNRVIAALAGAVLVVEARWRSGAQNTAGHAFGLGREVG +VVPGPVTSPSSAGCHRLLQESPARLVTTEQEALALLGQAPARSGGAGGRASTRAAPEPAT +RPTDGLTMEEALVHEALPLRQAVPADRITVSAGLALPTVLACLSRLQRAGLAERVEDRWR +RG +>PROKKA_02026 +MTADTAHDHPVAAAQGPDTQRPDAHRPDTQRPDAQRPDTQRPDAARIARAALTRLVEPGD +ALAVHAVAALGPERALVLLTGREAIQPAERDLLAEHAGAPDTLARRWSAGLDRWAPRAAR +LDPVRDLVALHRLGGGLLVPEDEAWPAALDDLGEAAPLGLWFRGPGTLPPASRALAVVGS +REATAYGRAVTTRLAAHAVQQGVCVVSGGAYGIDGAAHRAALAAPVGPEDPDAHDGPGGA +SDRVPPTVAVLAGGLDRFYPAGHEDLLREVMAAGLLVSEMPPGASPTRYRFLQRNRVIAA +LAGAVLVVEARWRSGAQNTAGHAFGLGREVGAVPGPVTSPSSAGCHRLLQETPARLVTSE +TEALALLDGGAPAPRPGGTGGGNTAPPGDAPAPPPGGTGEGTRRPPRPPPPPRPCGSRTG +>PROKKA_01924 +MTTAGETAQNARPDGPRVARAALTRLVEPGDDLALATVAALGPERALTLLTGAARIEAAE +RDLLADRLGQDAFARRWSAGLARWAPRSARLDPVRDLVALHRLGGGLLIPEDPAWPAGLD +DLGDAAPVGLWFRGRGTLPPLPRALAVVGSREATAYGRQVTRDVVACASAAGVCIVSGGA +YGIDGAAHEAALETAAAAGRRSGPGSHDDAAPGVPPTVAVLAGGLDRFYPAGHERLLRAV +MEEGLLLSEMPPGATPTRYRFLHRNRLIAALSGAVVVVEARWRSGAQNTAGHAHGLGREV +GAVPGPVTSPSSAGCHRLLQEGPTRLIADPAQALTLLEPPRPGEPPAASPATTTRGEASR +SPGRPTDGLTVEELLVHEALPLRRAVPVDNLTSSAGLALPTVLAVLTRLEGRRLAERRGD +LWRRAPE +>PROKKA_00864 +MTTHVTPAADHVAGPRRPDAARLARAALTRLVEPGDALAVQTVTALGPERALALLTGRET +IQPAERDLLADLAGAPDTLPRRWAAGLARWAPRAARLEPERDLVTLHRLGGGLLIPEDDA +WPAALADLGEEAPLGLWFRGSGTLPPADRMLAVVGSREATAYGRTVTARCAAHAVQQGAC +VISGGAYGIDGAAHRAALQALAAPGDAADRDGVPPTVAVLAGGLDRFYPAGHEDLLRAVM +AAGLLVSEMPPGASPTRYRFLQRNRVIAALAGAVLVVEARWRSGAQNTAGHAFGLGREVG +VVPGPVTSPSSAGCHRLLQESPARLVTTEQEALALLGQGPARSGGAGGPSSTRAAPEPAA +RPTDGLTMEEALVHEALPLRQAVPVDRITVSAGLALPTVLACLSRLQRAGLAERVEDRWR +RG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000790.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000790.fa new file mode 100644 index 0000000000000000000000000000000000000000..ec4fa5567a5cd2780518b7137b84250966095933 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000790.fa @@ -0,0 +1,35 @@ +>PROKKA_00917 +MAPSSSVRPAPAPRAPSPRDTAWLEAFEEHLRHERNRSPQTVRAYLADLHSLIDYVAGTA +ATAGTPPVDDDAPARHGPSAPDVLPELDIEDLRGWLAAMSGSGLARATLARRVAAVRTFT +AWLRREGLRSDDPALRLRSPRPEGTLPHVLQEQQATRLLAAAQERVDAAAAGDDPAAHAL +ALRDAALLELLYATGARVAELSALDVDDLEAGRGVVRLTGKGDRQRTVPYGAPAGRALQA +WERLGRPRLARPDSGPALFLGARGGRLGVRQARTVVDRALEGLGDTAARGPHALRHTAAT +HLLDGGADLRSVQELLGHASLRTTQVYTHVSIDRLREGYRQAHPRA +>PROKKA_00636 +MAPSSSARPAPAPRAPSPRDTAWLEAFEEHLRHERNRSPQTVRAYLADLRALIDHVAGTA +GTSGSPAADDDAPARHVPSAPDVLAELDIEDLRGWLAAMSGAGLARATLARRVAAVRTFT +AWLRREGLRSDDPALRLRSPRPEGTLPHVLQEQQATRLLAAAQDRVDAAAAGDDPAAHAL +ALRDAALLELLYATGARVAELSALDVDDLEAGRGVVRLTGKGDRQRTVPYGAPAGRALQA +WQRLGRPRLARPDSGPALFLGARGGRLGVRQARTVVDRALEGLGDTAARGPHALRHTAAT +HLLDGGADLRSVQELLGHASLRTTQVYTHVSIDRLREGYRQAHPRA +>PROKKA_02024 +MASSSSSARPAAARAFAPSPRDAAWLEAFEEHLRHERNRSPQTVRAYATDLRDLVAHVAS +GTWGGHPGTATSEAAVEADAVAPDVFAEVDVEDLRGWLAAMTDAGLARTTLARRVAAVRT +FTGWLRREGLREDDPALRLRSPRPAATLPHVLQEQQAERLLAGAQARVAEAAVGDDPAAH +ALALRDAALLELLYATGARVAELSALDVDDLEPGRAVARLTGKGDRQRTVPYGAPAARAL +DAWLRLGRPRLARDGSGPAVFLGVRGGRLGVRQVRAVVDRALEGLGDTAARGPHALRHTA +ATHLLDGGADLRSVQEVLGHSSLRTTQVYTHVSIDRLREGYRQAHPRA +>PROKKA_01923 +MHPPHAHHAPGAPLPPASARDEAWLEAFAEHLLHERGRRPRTVRAYLADLRHLAAHVTDD +GADAFAEVDLEDLRRWLARMRDQGLSRATVARRVAAARTFLGWLHRSGLRPDDPTLRLRA +PAPDSRLPQVLQAEQAQRLLQAAEERVHEARRADDLHGAALAARDVALFELLYATGARVA +EVAALDVDDLDLDRRTARLTGKGDRQRTVPFGAPAAAAVERWLRVARPVLATEHSGVALL +LGARGGRADVRVLRGAVDRALERLGDTAARGPHALRHTAATHLLDGGADLRSVQELLGHS +SLQTTQRYTHVSVDRLRDGYRRAHPRA +>PROKKA_00865 +MTPSSSARPAPVPRDPSPRDTAWLEAFEEHLRHERNRSPQTVRAYLADLHSLIDHVAGTA +GTSDTPAVDDDAPARHASSAPDVLAELDIEDLRGWLADMSGSGLARATLARRVAAVRTFT +AWLRREGLRSDDPALRLRSPRPEGTLPHVLQEQQATRLLAAAQERVDAAAAGDDPAAHAL +ALRDAALLELLYATGARVAELSALDVDDLEAGRGVVRLTGKGDRQRTVPYGAPAGRALQA +WQRLGRPRLARPDSGPALFLGARGGRLGVRQARTVVDRALEGLGDTAARGPHALRHTAAT +HLLDGGADLRSVQELLGHASLRTTQVYTHVSIDRLREGYRQAHPRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000795.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000795.fa new file mode 100644 index 0000000000000000000000000000000000000000..f4501bfb418e14f1d7573284354fc5546cbab270 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000795.fa @@ -0,0 +1,35 @@ +>PROKKA_00922 +MLAIVCPGQGSQTPGFLAPWLELDGTRDLLASLSDAAGVDLIRHGTESDEETIKDTAVAQ +PLIVAAGLVAAAALEADAAAPKSTVVAGHSVGEVTAAAVTGVLSPAEALSLVRVRATGMA +RAAAATPTGMAAVVGGDQDEVLAAIDAAGLAPANVNGAGQIVAAGTAEALGALAESAPAR +ARVIPLKVAGAFHTEHMRPAVDDLATHVAGLSPSDPRLPLLSNRDGETVESGTDVLARIV +DQVTRPVRWDLCMATMAARQVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA +FLAEHSA +>PROKKA_00641 +MLAIVCPGQGSQTPGFLAPWLELDGTRDLLASLSDAAGVDLIRHGTESDEETIKDTAVAQ +PLIVAAGLVAAAALEADAAAPKSTVVAGHSVGEVTAAAVTGVLSPAEALSLVRVRATGMA +RAAAATPTGMAAVVGGDQDEVLAAIDAAGLTPANVNGAGQIVAAGTAEALGALAESAPAR +ARVIPLKVAGAFHTEHMRPAVDDLAAHVAGLSPSDPRLPLLSNRDGEAVESGTDVLARIV +DQVTRPVRWDLCMATMATRQVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA +FLAEHSA +>PROKKA_02019 +MLAIVCPGQGSQTPGFLSPWLELDGTRALLESLSDAAGVDLVRHGTESDEETIKDTAVAQ +PLIVAAGLVAAAALEADAAAPASTLVAGHSVGEITAAAVTGVLSPADALALVRVRATGMA +RAAAATPTGMAAVVGGDQDEVLAAIEAADLAPANVNGAGQIVAAGTAEALAALGESAPAR +ARVIPLKVAGAFHTEHMRPAVEELAAHVAGLSPADPRLTLLSNRDGQAVDAGAEVLSRIV +DQVTRPVRWDLCMEAMAEREVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA +FLAEHTA +>PROKKA_01918 +MLAIVCPGQGSQTPGFLAPWRELEGVPSLLDRLSAAAGVDLTAHGTVSDEETIKDTAVAQ +PLIVAAGLVAADVLGLDALAPDRVLAAGHSVGEITAAAVAGVLSPEDALALVRVRATGMA +EAAAATPTGMAAVVGGDQDEVLAAVEAAGLTPANVNGGGQIVAAGTQDALDALAAQPPAR +ARVIPLKVAGAFHTEHMRPAVDALAAHVTGLSPADPRLTLLSNREGAAVASGTEVLERIV +NQVTRPVRWDLCMEAMAERGVTGIMEVLPGGTLAGLAKRGLKGVPSLAVKAPDDLDAARA +FIAEHTA +>PROKKA_00870 +MLAIVCPGQGSQTPGFLAPWLELDGTRDLLASLSDAAGVDLIRHGTESDEETIKDTAVAQ +PLIVAAGLVAAAALEADAAAPKSTVVAGHSVGEVTAAAVTGVLSPAEALSLVRVRATGMA +RAAAATPTGMAAVVGGDQDEVLAAIDAAGLAPANVNGAGQIVAAGTAEALGALAESAPAR +ARVIPLKVAGAFHTEHMRPAVDDLAAHVAGLSPSDPRLPLLSNRDGEAVESGTDVLARIV +DQVTRPVRWDLCMATMATRQVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA +FLAEHSA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000796.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000796.fa new file mode 100644 index 0000000000000000000000000000000000000000..ba37abf61a4322cfb7ea3f47dc8f2e8e58a31b38 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000796.fa @@ -0,0 +1,40 @@ +>PROKKA_00923 +MPEPRPAAPRPVSTDGLARLRSHLGALNTAVLQRLDATLPWYRRLTPDERSALGLVAQRA +LQGFLTWFERPTSTGHVLQDVFGPAPTDLTRAISLQRALQLIRTMVDVVETRVPELLAER +DQAPVREHILHYSREVAFALADVYARAAEMRGAMDSRLESVLLDAVLRGQDPDEIRHRAT +ALGWRGDHDVMVMAGLAPGQDKPAFIPDLRRAAARLDCDLLVGVQSERLVLVVGSVRDAR +AVGEALAPWFAPGPVIVGPVVDSLVSAHVSARHTLAGLSAAAAHPRASRPTPAEDLLPER +ALLGDPTAREALVDGVFTPLADAGTSLLETVDAYGALGHSLEGTARELFVHANTVRYRLK +RVAEVTGWDPLVPRDAYVLQTAITLGRLAGARPTTGTGSD +>PROKKA_00642 +MPEPRPAAPRPVSTDGLARLRSHLGALNTAVLQRLDATLPWYRRLTPDERSALGLVAQRA +LQGFLTWFERPTSTGHVLQDVFGPAPTDLTRAISLQRALQLIRTMVDVVETRVPELLAER +DQAPVREHILHYSREVAFALADVYARAAEMRGAMDSRLESVLLDAVLRGQDPDEIRHRAT +ALGWRGDHDVMVMAGLAPGQDKPAFIPDLRRAAARLDCDLLVGVQSERLVLVVGSVRDAR +AVGEALAPWFAPGPVIVGPVVDSLVSVHVSARHTLAGLSAAAAHPRASRPTPAEDLLPER +ALLGDPTAREALVDGVFTPLADAGTSLLETVDAYGALGHSLEGTARELFVHANTVRYRLK +RVAEVTGWDPLVPRDAYVLQTAITLGRLAGARPTTGAGSD +>PROKKA_02018 +MPEPRSAASRPVSTEGRARLRSHLGALNTAVLQRLDATLPWYRGLTPDERSALGLVAQRA +LQGFISWFDRPKTTGHVLQDVFGPAPTDLTRAISLQRALQLIRTMVDVVETRVPELLAER +DQAPIREHVLHYSREVAFALADVYARAAEMRGAMDSRLEAVLLDAVLRGQDPDEIRHRAT +ALGWRGDHRVMVMAGLAPGQDQPAFIPGLRRAAAKLDCDLLVGVQAERLVLVIGSVTDAQ +VVGEALTPWFAPGPVILGPVVDSLVEAHVSARHTLAGLGAAPAHPRAIRPTPAEDLLPER +ALLGDPTACEALVEGVYAPLADAGTALLDTVDAYGALGHSLEGTARELFVHANTVRYRLK +RVAEVTGWDPLVPRDAYVLQTAVTLGRLAGSRPGVAEASA +>PROKKA_01917 +MPAPRPSAPRRVSADGLARLRAHLGTFNTATLRRLDETLPWYRELTPDERSALGLIAQRA +LQGFITSFERPQTTTVDVLRDVFGQSPTELTRAISLHRALQLIRTIVDVVETGVPDAVSE +ADQPVVAEHVLHYSREIAFAIADVYARAAELRGAMDSRLEAVLLDAVLRGQEPDEIQHRA +TAFGWRGGDGVMVMAGSARDGATAAFLPGLRRDAARLQCELLVGVQSRRLVLVVGSVSDP +DAVAEALLPWFADGPVIVGPVVDSLLEAHVSAHHALAGLGAAAAHPRAGRPARSDDLLPE +RALAGDATACAALVDGVYAALADAGPSLLETVDVYTACGHSLEGTARELYVHANTVRYRL +RRAAEVTGWDPQRPRDAYVLQTAVALGRLSEGAPRL +>PROKKA_00871 +MPEPRPAAPRPVSTDGLARLRSHLGALNTAVLQRLDATLPWYRRLTPDERSALGLVAQRA +LQGFLTWFERPTSTGHVLQDVFGPAPTDLTRAISLHRALQLIRTMVDVVETRVPELLAER +DQAPVREHILHYSREVAFALADVYARAAEMRGAMDSRLESVLLDAVLRGQDPDEIRHRAT +ALGWRGDHDVMVMAGLAPGQDKPAFIPDLRRAAARLDCDLLVGVQSERLVLVVGSVRDAR +AVGEALARWFAPGPVIVGPVVDSLISAHVSARHTLAGLSAAAAHPRACRPTPAEDLLPER +ALLGDPTAREALVDGVFTPLADAGTSLLETVDAYGALGHSLEGTARELFVHANTVRYRLK +RVAEVTGWDPLVPRDAYVLQTAITLGRLAGARPTTGTGSD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000801.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000801.fa new file mode 100644 index 0000000000000000000000000000000000000000..95b702e900b9a272709eca69c1145a1cc80c0006 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000801.fa @@ -0,0 +1,15 @@ +>PROKKA_00929 +MTGAAYLVAAAVVAGLVTFCLRAVPFALLQPLRESVLAARLAVWMPAGVLTILALVMLLD +AAALAPGEPVDGTRVAHALFAAAVTVVVHLLAGRRTLVSIAAGTLAYVLLVNLA +>PROKKA_00648 +MTGAAYLVAAAVVAGLVTFCLRALPFALLQPLRESVLAARLAVWMPAGVLTILALVMLLD +AAALAPGEPVDGTRVAHALIAAAVTVVVHLLAGRRTLVSIAAGTLAYVLLVNLA +>PROKKA_02011 +MTDAAYLVAVAVVAGAVTFALRALPFALLRPLRESVLAARLAVWMPAGVLTILAVVMLLD +AAALAPGAPVDPRRVAHALIAAVVTVAVHLLGGRRTLLSIAAGTLAYVLLVNLA +>PROKKA_01910 +MIDGVVHPGYIVAAALVAGGVTFLLRALPFVLLRPLRESRLVARLAVWMPAGILTILAVV +MVLDSAALAPGDPVDWPRVGCTLAAGAVTVLVHLLGGRRTLLSIGAGTLAYVLLVNLAL +>PROKKA_00877 +MTGAAYLVAAAVVAGLVTFCLRALPFALLQPLRESVLAARLAVWMPAGVLTILALVMLLD +AAALAPGEPVDGARVAHALIAAAVTVVVHLLAGRRTLVSIAAGTLAYVLLVNLA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000802.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000802.fa new file mode 100644 index 0000000000000000000000000000000000000000..131789e932e2d2c8a8e76fd5e4edfd7d75d4f901 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000802.fa @@ -0,0 +1,25 @@ +>PROKKA_00930 +MGLLRDLLTRRSARDRSSDPPATLGRHLDNAAAIVAAARRADVPLAVAAALAELESGGRN +VFGHDAGGVHSAPRGTDVLVTRERYEELVARVAQGETSNGVGPAQITWPPYFAQAAERGL +HLWEPEDNLAFGLEILRGHLRGDLSAEGIARAGTLYNAGTLSDGVTAYGRRLAAASRAWA +ERLGEPAPPPVRPG +>PROKKA_00649 +MGLLRDLLTRRSARDRSSDPTATLGRHLDNAAAIVAAARRADVPLAVAAALAELESGGRN +VFGHDAGGVHSAPRGTDVLVTRERYEELVARVAQGEKSNGVGPAQITWPPYFAQAAERGL +HLWEPEDNLAFGLEILRGHLRGDLSAEGIARAGTLYNAGTLSDGVTAYGRRLAAATRAWA +ERLGESAPPPVRPG +>PROKKA_02010 +MATTPSVGRMSWFPRRRAASAPRALAARLENADAIAAAARRADVPLPVAAALAQLESGGR +NVFGHDAGGVHAAPRGTDVPVTRELFEELEARVAAGETSNGVGPAQITWPPYFAQARRRG +LRLWEPEDNMAFGLEILRGHLGGDLTEEGIARAGTLYNAGTLQGGVTDYGRRLARASRDW +ARRLGEPAPPSSSPGRGAGRDGDRGRARSGAPGRTHVIEPGDTLWAIARANGTDVATLRR +LNPDLVPEALAVGAPVRLP +>PROKKA_01908 +MDPVTVLSASLAHPEAIVAAAGRARVPVSVAAALAELESGGRNVFGNDVGGVFSSPGAPD +VEVTPERVAELRRRVADGERSNGVGPAQITWPPLFDRADAEGLDLADPEDNMTLGLSLLR +DSARGDFSVAGLERAGTLYNAGTLAGGVTDYGRRLAAAAAAWERRLTARG +>PROKKA_00878 +MGLLRDLLTRRSARDRPSDPTATLGRHLDNAATIVAAARRADVPLPVAAALAELESGGRN +VFGHDAGGVHSAPRGTDVPVTRERYEELVARVAQGETSNGVGPAQITWPPYFAQAAERGF +RLWEPEDNLAFGLEILRGHLRGDLSAEGIARAGTLYNAGTLTHGVTAYGRRLAAATRVWA +ERLGELAPPPVRPG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000803.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000803.fa new file mode 100644 index 0000000000000000000000000000000000000000..37957d82c5fb02e2172de4e5973b3a0134543b93 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000803.fa @@ -0,0 +1,20 @@ +>PROKKA_00931 +MSATPLGFWKLPARPDGAARHLAVITGGEAQQTMLFLQDGQWSILALFQDELAGKAAART +LDALLQSVTCLRMGGRDVLDGADTPRPGIEWAGYDREFEEADVAEQRDVEPRGRIWILPA +TDGASVGLKLPGHRRYDDAVAQFADVDAARAAVAAIDELLGVGPRG +>PROKKA_00650 +MSATPLGFWKLPARPDGAARHLAVITGGEAQQTMLFLQDGQWSILALFQDELAGKAAART +LDALLQSVTCLRMGGRDVLDGADTPRPGIEWAGYDREFEEADVAEQRDVEPRGRIWILPA +TDGASVGLKLPGHRRYDDAVAQFADVDAARAAVAAIDELLGVGPRG +>PROKKA_02009 +MLFLQDGQWSILGLFQDELAGKATARTLDALLQSVTCLRMGGRDVLDGADTPRPGVEWAG +YDREFEEADVAESRDVEPHGRIWILPATDGATVGLKLPGHRRYHDAVAQFADVDAARAAV +AAIDELLGVGPRG +>PROKKA_01907 +MPATPHGFWKLPAPSDAGPRHLAVITGGEAEQTMLFLQDAAGWHVLALFQDELAGRTTAR +TLDRLLQSVTYLRMGGADLMDGADTERPGVEWAGYDREFEEQDAADETAADPAARLWILP +ATDGASVGLKLPGHPRYADAVAQFVDAGTARAAVDAVDALIGARRPGAARPAAD +>PROKKA_00880 +MSATPLGFWKLPARPDGAARHLAVITGGEAQQTMLFLQDGQWSILALFQDELAGKAAART +LDALLQSVTCLRMGGRDVLDGADTPRPGIEWAGYDREFEEADVAEQRDVEPRGRIWILPA +TDGASVGLKLPGHRRYDDAVAQFADVDAARAAVAAIDELLGVGPRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000812.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000812.fa new file mode 100644 index 0000000000000000000000000000000000000000..5b7dddc2f5c3afce833762518c03c9aef0c17cdf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000812.fa @@ -0,0 +1,30 @@ +>PROKKA_00940 +MLILLPPSEGKTAPRSGAPLDLDALALADDAAVTGARADLLTRLAAVSAAPDALAALGVG +ASLTGEVEANTRLASAPAAPGHRVFTGVLFDALDHASLSAAAKRRARASVLVFSALFGAT +ALADRIPAFRLPVGAKLPGLPGLAAHWRPVLTPALDALAARDGGPVVDCRSGGYAAQWRA +PAERTLAVDVFQLRDGERTVVSHFAKHTRGLVARALLEAGARETSTLERVADVVARAGDG +HGWEVELARPSGAKPGALRVILPEG +>PROKKA_00659 +MLILLPPSEGKTAPRSGAPLDLDSLALADDAAVTGARADLLTRLAAVSAAPDALTTLGVG +ASLAGEVEANTRLAVAPAAPGHRVFTGVLFDALDHASLSAAAKRRARLSVLVFSALFGAT +ALADRIPAFRLPVGAKLPGLPGLAAHWRPVLTPALDALAARDGGPVVDCRSGGYAAQWRA +PAEQTLAVDVFQLRDGERTVVSHFAKHTRGLVARALLEAGARETSTLDRVADVVARAGDG +PGWEVELARPSGGKPGALRVILPEG +>PROKKA_01999 +MLILLPPSEGKTAPRSGAPLRLEDLALAEHDAVTAARRDLLARLAEASAAPDALETLGVG +ASLAGEVAANTSLATAPAAPGHRVFTGVLFDALDHASLSPGAKRRARDAVLVFSALFGAT +SLADRIPAHRLSVGARLPGLPGLAAHWRPVLAPALDAVAQADGGPIVDCRSGGYAAMWKA +PAERTATVDVFQLRGGEPTVVSHFAKHTRGLVARALLEAGARATGALDRAAEVVAAAGAG +DVEGRRWDVELVAPSGAKPGSLRVVLPEA +>PROKKA_01896 +MLILLPPSEGKTGPRSGRPLDLSSLTLADDDAVTAARAELLPRLAEASARPDALDILGVG +ASLADEVAANTRLATAPSAPARKVYTGVLFEALDLTSLSPAAKRRAASDVLVFSALFGAT +TPGDRIPAYRLPVGARLPGMPGLAAWWRPRLAPALDGYAEARGGVVVDCRSGGYAAQWKA +PAERSLAVDVFQLRAGRRTVVSHFAKHTRGLVARALLEAGSRAAGTPATAADVVARAGDG +GVPGQRWEVELVPPTGRKAGSLQVILPEE +>PROKKA_00889 +MLILLPPSEGKTAPRSGAPLDLESLALADDAAVTGARADLLTRLAAVSAAPDALTALGVG +ASLAGEVEANTCLASAPAAPGHRVFTGVLFDALDHVSLSSAAKRRARASVLVFSALFGAT +ALADRIPAFRLSVGAKLPGLPGLAAHWRPVLTPALDALAARDGGPVVDCRSGGYAAQWRA +PAERTLAVDVFQLRDGERTVVSHFAKHTRGLVARALLEAGARETSTLERVADVVARAGDG +HGWEVELARPSGAKPGALRVILPEG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000813.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000813.fa new file mode 100644 index 0000000000000000000000000000000000000000..106099e0d4bfdd4264763dcfdf264e9b46586ed5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000813.fa @@ -0,0 +1,14 @@ +>PROKKA_00941 +MTAMNVFGVVYPFVLLVIAAAVWLGIRSSGRERTHASAVEQRLRERTFTGQDRVTLEWPR +DRRRPSLAKVVSIGESYGYRLLDKREREHVVELEFERILDDEGF +>PROKKA_00660 +MTAMNVFGVVYPFVLLVIAAAVWLGVRSSGRERTHASALEHRLRERTFTGQDRVTLEWPR +DRRHPSLAKVVSIGESYGYRLLDKREREHVVELEFERILDDEGF +>PROKKA_01997 +MTLEWPRDRRRPTPAKVVAIAESYGYRLLEKRERDHVIELDFERIRDDEGF +>PROKKA_01895 +MQTIPVMGWVFPVVLLVIAAAFWLGVRSSGGARGDSDLERRLRERTFTGAPRARLEWPRD +RRRPTLAQLVRIGASHGYRLVSRTEAEHVYILDFQRVEDDDL +>PROKKA_00890 +MTAMNVFGVVYPFVLLVIAAAVWLGIRSSGRERTHASAVEQRLRERTFTGQDRVTLEWPR +DRRRPSLAKVVSIGESYGYRLLDKREREHVVELEFERILDDEGF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000817.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000817.fa new file mode 100644 index 0000000000000000000000000000000000000000..98aeacaf85e91cf32fd2bf88a89fab9741e48d54 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000817.fa @@ -0,0 +1,25 @@ +>PROKKA_00956 +MSETSTPTPESAPLVWIDCEMTGLHPQVDELVEVAVLITDAELNILDEGIDLVIRPSAAA +LEQMDPFVRDMHTTSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNTVGQDKLF +LARYMPAVVDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIKDSITELRYY +RAAVMAPAPGPTTEEARAIAEVVSGAQA +>PROKKA_00669 +MSETSTPAPESAPLVWIDCEMTGLHPQVDELVEVAVLITDAELNTLDEGIDLVIRPSAAA +LEQMDPFVRDMHTTSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNTVGQDKLF +LARYMPAVVDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIKDSITELRYY +RAAVMAPAPGPTTEEARAIAEVVSGAQA +>PROKKA_01931 +MSETSTPAPENAPLVWIDCEMTGLHPHVDELVEVAVLITDAELNILDEGIDLVIRPSEAA +LAQMDPFVRDMHTTSGLLPELEHGLTLENATARVMEYLTARVPAGKALLAGNTVGQDKLF +LSAYMPAVVEHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIRDSITELRYY +RAAVMAPSPGPTSEEAQAIARVVAEAQA +>PROKKA_01883 +MSETSTPAPESAPLVWIDCEMTGLDPDVDVLVEVAVLITDSELNVLDEGLDLVIRPTPEA +LAQMDPFVRDMHTSSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNSVGQDKLF +LARYMPAVIDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIRDSITELRYY +REAVMVPAPGPTSEEARAIAEVVSGAQA +>PROKKA_00902 +MSETSTPTPESAPLVWIDCEMTGLHPQVDELVEVAVLITDAELNILDEGIDLVIRPSEAA +LEQMDPFVRDMHTTSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNTVGQDKLF +LARYMPAVVDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIKDSITELRYY +RAAVMAPAPGPTTEEARAIAQVVSGAQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000819.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000819.fa new file mode 100644 index 0000000000000000000000000000000000000000..1e658d355dc7a097cf86106d0b454865a32f5856 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000819.fa @@ -0,0 +1,55 @@ +>PROKKA_00959 +MTSHPRSPAPSRPSGRWVGLLVGLTVVAAAVGVLTKQWCRVNGWAAPGVHAHMCYSDFAQ +LFPTRGLSDGHFPFYTPLPPEQWMEYPALLAVVAGVTMWLVPASGDLHERTVTYFDVNAI +GVVLCWIVLVVATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAGR +PTLAGLLIGLGTATKLYPLFFFGAIFVLALRTGRWAGFVKAALAGAAAWLAVNLPFMLTA +FDQWSRFYTFSGDRAVSFSSTWLALAWTGWSGETFTTLQNGLFLVCCVGIAYLALAARHR +PRMAQLCFLIVASFILWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGVWME +SARITSDGAFAGGAWWITAWYASGIVAHIVALVWLMTTVVKDILDPVRDPVRRTALDQGA +PEIAPGVAEDPHAGVFTGARDRLLLPPAGLGLQPLGESAGR +>PROKKA_00672 +MTSHPRSPAPSRPSGRWVGLLVGLTVVAAAVGVLTKQWCRVNGWAAPGVHAHMCYSDFAQ +LFPTRGLSDGHFPFYTPLPPEQWMEYPALLAVVAGVTMWLVPASGDLHERTVTYFDVNAI +GVVLCWIVLVVATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAGR +PTLAGLLIGLGTATKLYPLFFFGAIFVLALRTGRWAGFVKAALAGAAAWLAVNLPFMLTA +FDQWSRFYTFSGDRAVSFSSTWLALAWTGWSGETFTTLQNGLFLVCCVGIAYLALAARHR +PRMAQLCFLIVASFILWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGVWME +SARITSDGAFAGGAWWITAWYASGIVAHIVALVWLMTTVVKDILDPVRDPVRRTALDQGA +PEIAPGVAEDPHAGVFTGAPDRLLLPPAGRGLQPLGGSADR +>PROKKA_01929 +MRRAGLAPTPAPPGLPERETAPPEPAVAVRQGTWAAVLIMVGSWGVGWLPMTPDSVFSGS +TLLNPLRVNLPGVLASTLLLASGSLLLVRAWLVLGRSLRGRWEGHGRLVSRAAWQWSAPL +MLALPIFSRDVFSYLQQGRLFALGLDPYTQGVSALPGWFMQGADSIWAESPSPYGPLFLL +CAEAIWRVTGGQIELSVTAFRLLALAGLALCLWAVPRLAEAAGRCGAWAAWVCVANPLFL +LYMIAGVHNDALMSGLMLAGIVLMVRVPRRRLHALWGIVLIALSVAIKPLTALVLPFVGL +LLPTGWDRFRRADPGLRRRDRLGPWITTAAIALAVLTILGAGSRLWFGWVPAMLTSGDAA +FPYAPVGVLGLLLGAAADGLAGLPARAVAGGFYTLMTLAALGFGAWLALRRRAPEPVSAA +AAVLFVAVVTAPIVQPWYLLWVLPLLACALRPLPWGADHPRWLGWVTALAVLLLTGVGVV +DQISVAQWLPVAAVRALTAVVVLAGIAWIVVRDPATAPLFPGRRRPPREVVEPREAVGPR +EPGAPPGPPTAAPDAEFPPDALAADPDRRRRPAPDRRPARPGETVTSQPRRPADTRTGSA +AAPPSPAALRPGPRWIGILVGLTAVAAVVGLLTKQWCRVNGWAAPGVHVHMCYSDFAQLF +PTRGLSDGYFPFYTPLPPEQWMEYPALLAVVAGVTMWLVPDSGDLHERTVMYFDVNALGV +VLCWVVLVIATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAHRPT +LAGLLIGLGTALKLYPLFFFGAILVLALRTGRWRGLITSLAAGVAAWLAVNVPFMLTAFD +QWSRFYTFSGDRAVSFSSTWLSLAWTGWSGETFSTLQNGMFALFCAGIAWLGLSARHRPR +MAQLCFLIVASFLLWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGVWMESA +RITSGGAFADGAWWITAWYASGIVAHIVALVWLMVTVVKDILDPSRDPVRRTALAQGAPT +IAPGVAEDPHAGVYAGAPDRLVLPPAGRGLQPAEGATSGS +>PROKKA_01880 +MSSHPRAADAAPRPAAGLRPAGRPSPRWIGVLIAVTAAAAVVGLLTKQWCRLNGWATPGV +HVHMCYSDFAQLFPTRGLSDGYFPFYTPLPEEQWMEYPALLAVVAGASSWLVPSTGTLAE +RTVTYFDVNAAGVVLCWMAVVVATAFTARGRSKDALLVAVAPGIILTSMLNWDLWAVMLA +ALALWAWSEDRPVLSGLLLGLGAAMKLYPLFFFGALLVLALRTGRWRGFLGALAAGAAAW +LAVNVPFMLTAFDQWSRFYTFSGDREVSFSSMWLAFTWTGLSGSAFSVISNGLFALCCVG +VAYLGLSSRHRPRLAQLCLLIVAAFLLLGKVYSPQFVMWLIPLVVLATPRRKQFWIWQAA +EFFHWAGVWMESARITSGGEFGGTWVTVWYASGIVLHMATLIWICVTVIRDIRDPERDPV +RRSALEQGVEPLAPGVAEDPNAGVFTGAADRFLLPPAGHGLQPTR +>PROKKA_00905 +MTSHPRSPAPTRPSARWVGLLVGLTVVAAAVGVLTKQWCRVNGWAAPGVHAHMCYSDFAQ +LFPTRGLSDGHFPFYTPLPPEQWMEYPALLAVVAGVTMWFVPASGDLHERTVTYFDVNAI +GVVLCWIVLVVATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAGR +PTLAGMLIGLGTATKLYPLFFFGAIFVLALRTGRWAGFVKAAVAGAAAWLAVNLPFMLTA +FDQWSRFYTFSGDRAVSFSSTWLALAWTGWSGETFTTLQNGLFLVCCVGIAYLALAARHR +PRMAQLCFLIVASFILWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGVWME +SARITSDGAFAGGAWWITAWYASGIVAHVVALVWLMTTVVKDVLDPVRDPVRRTALDQGA +PEIAPGVAEDPHAGVFTGARDRLLLPPAGRGLQPLGESAGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000824.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000824.fa new file mode 100644 index 0000000000000000000000000000000000000000..2665f8f04372f64b697231f19e4d377cfe108578 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000824.fa @@ -0,0 +1,37 @@ +>PROKKA_00966 +MKHTFSLRTEWTGDRGSGTSGVRDYDRSVVIQDAAVGEIQASAARPFRGDDSKWNPETLL +LGALAECHVLSYLHVAATSGVVVTGMTCGVEGELEVDGDGAGRFTAITLRPEVTLQDEAD +RERAEALHAEAHRLCFIANSLSAPVAVEPVRPEALPTGAPTLPDHSARLGAPLAVLRPRV +AKGPSRVTGLAERPTEVEPVMQEGTPAPVEQVRARDAAAGPAGATPGTPAAPGQAASFYD +AVGGRPTFDRLTAEFYARVREDEILAPMYPQDDFEGAQRRLLMFLEQYWGGPRTYSEERG +HPRLRMRHAPYRIDPAARNAWLRHMRAAVDTLELSPLHEAELWDYLERAAHSLQNSA +>PROKKA_00679 +MKHTFSLRTEWTGDRGSGTSGVRDYDRSVVIQDAAVGEIQASAARPFRGDDSKWNPETLL +LGALAECHVLSYLHVAATSGVVVTGMTCGVEGELEVDGDGAGRFTAITLRPEVTLQDEAD +RERAEALHAEAHRLCFIANSLSAPVAVEPVRPEALPTGTSTLPDHSARLGAPLAVLRPRV +AKGPSRVTGLAERPTEVEPVMQEGTPAPVEQVRARDAAAGPTGATPGTPAVPGQATSFYD +AVGGRPTFDRLTAEFYARVREDEILAPMYPQDDFEGAQRRLLMFLEQYWGGPRTYSEERG +HPRLRMRHAPYRIDPAARDAWLRHMRAAVDTLELSPLHEAELWDYLERAAHSLQNSA +>PROKKA_01921 +MKHTFALRTEWTGNRGTGTSGVRDYDRSVVIQDAAVGEIHASAARPFRGDDSKWNPETLL +LGALAECHVLSYLHVAATSGLVVTGMACAAEGVLEVDGDGAGRFAAVTLRPEVALQDEAD +RERADALHAEAHRLCFIANSLSAPVSVEPAVAGSGAAASGGPALPDHSSRLGAPLAVLRP +RVAKRPSQVTGLAERPTEVEPVMKAGAPAPVDQMQARDAAAGRAASPATPAPAAETAAPG +QAASFYEAVGGRETFDRLTAEFYARVREDELLSPMYPQDDFEGAQRRLLMFLEQYWGGPR +TYSEERGHPRLRMRHAPYRIDPAARDAWLTHMRAAVDTLGLSPLHEAELWDYLERAAHSL +QNSA +>PROKKA_01869 +MKHTFSLRAEWTGDRGTGTTGVRDFDRSVVIQESEVGEIHASAARPFRGDAAKWNPETLL +LGALAECHVLSYLHAAATGGLVVTGMTCAAEGTLEVDSDGAGRFASITLRPEVALRDEAD +RARADELHAEAHRMCFIANSISAPITVEAGPGSSPTRGDGAALPDHSARLGAPLAVLRPR +VANRPTRVTGLADRPTEAEPVVRADAPSGAEQARARDEATARGERPPSATPIATPAPGAT +PAASPATAAPGQATSFYEAVGGHPTFEKLVHVFYQGVREDPLLAPMYPHQDWDGAEERLR +MFLEQYWGGPRTYSERRGHPRLRMRHMPFTVDPAARDAWLRHMRAAVDAVELSPLHEAEL +WDYLERAAHSLQNSA +>PROKKA_00912 +MKHTFSLRTEWTGDRGSGTSGVRDYDRSVVIQDAAVGEIQASAARPFRGDDSKWNPETLL +LGALAECHVLSYLHVAATSGVVVTGMTCGVEGELEVDGDGAGRFIAITLRPEVTLQDEAD +RERAEALHAEAHRLCFIANSLSAPVTVEPVRPEALPTGTPTLPDHSARLGAPLAVLRPRV +AKGPSRVTGLAERPTEVEPVMQEGTPAPVEQVRARDAAAGPAGATPGTPAAPGQATSFYD +AVGGRPTFDRLTAEFYARVREDEILAPMYPQDDFEGAQRRLLMFLEQYWGGPRTYSEERG +HPRLRMRHASYRIDPAARDAWLRHMRAAVDTLELSPLHEAELWDYLERAAHSLQNSA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000827.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000827.fa new file mode 100644 index 0000000000000000000000000000000000000000..5aa1fc32ee4f4243017609dcff0b4bdbe82d2739 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000827.fa @@ -0,0 +1,31 @@ +>PROKKA_00974 +MMHGSRPALRRAASALAGRRPLSLRGATVLVTGGASGIGRLIALGAARRGAGRVVVWDLD +LQGAEAVAAEIRSQGADAQAERVDVTDAAAVEAAAARAGEVDVAVNNAGVVTGVRLEDAT +EEGIRRTFEVNALAPYWLTRAVLPGMRARDRGAVVTVASAAGLVGVARQTDYSATKHAAV +GFAESLAAELRKDGSRVTSLAVCPFYIDTGMFAGVRSRVPWLLPVLDPRHVAQEVLDAVE +AGRTRLLLPRAVGLIAPLRALPAPVFDRAMDVLGVNATMDGFTGRRSRLFAGRETAR +>PROKKA_00688 +MHGSRPALRRAASALAGRRPLPLHGATVLVTGGASGIGRLIALGAAHRGAGRVVVWDLDL +QGVEAVAAEIRSQGADARAERVDVTDAAAVEAAAAGAGEVDVAVNNAGVVTGAPLEDATE +EGIRRTFEVNALAPYWLTRAVLPGMRARDRGAVVTVASAAGLVGVARQTDYSATKHAAVG +FAESLAAELRKDGSRVTSLAVCPFYIDTGMFAGVRSRVPWLLPVLDPHHVAQEVLDAVEA +GRTRLLLPRAVGLIAPLRALPAPVFDRAMDVLGVNATMDGFTGRRSRLFAGRETAR +>PROKKA_01916 +MPRSRTPRPALRALAGALPRRRRLPLRGTAVLITGGASGIGRLMALGAARRGAARVVVWD +LDLSAAEAVAAEARALGAEAVAERVDVTDAAAVEAAAARAGAVDVAVNNAGVVTGARLED +ATEEGIRRTFEVNALAPYWLTRAVLPGMKARDRGAVVVIASAAGLVGVARQTDYSATKHA +AVGFAESLSAELRKDGSAVTALAVCPFYIDTGMFDGVRSRIPWLLPVLRQEEVAEQVLDA +VEAGRTRLPLPRAVGLLAPLRALPTPVFDRAMDVMGVNDTMDGFTGRRPAVDVPAPDPRV +FAPDGAAR +>PROKKA_01863 +MTPILNRLRGRRPLPLAGRAVLITGAGSGIGRLMALEAARRGAAVVHVWDRDDAAARTVA +AEVAALGARGEAACVDVTDTAAVEAAAARAEAVDVLVNNAGVVTGTPLLETTEEGIRRTF +EVNALAGYWTTRALLPGMLERGRGAVVTVASAAGLVGVARQTDYSASKHAAVGFAESLRA +ELRRADAPVTSLVVCPFYISTGMFAGVRTKVPALLPILEPEAVAAQVVDAVEAGRERLVL +PPAVQLIAPLRALPVPAFDRVMDVLGVNRAMDGFTGRR +>PROKKA_00917 +MMHGSRPALRRAASALAGRRPLSLRGATVLVTGGASGIGRLIALGAARRGAGRVVVWDLD +LQGAEAVAAEIRSQGADAQAERVDVTDAAAVEAAAARAGEVDVAVNNAGVVTGVRLEDAT +EEGIRRTFEVNALAPYWLTRAVLPGMRARDRGAVVTVASAAGLVGVARQTDYSATKHAAV +GFAESLAAELRKDGSRVTSLAVCPFYIDTGMFAGVRSRVPWLLPVLDPRHVAQEVLDAVE +AGRTRLLLPRAVGLIAPLRALPAPVFDLAMDVLGVNATMDGFTGRRSRLFAGRETAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000833.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000833.fa new file mode 100644 index 0000000000000000000000000000000000000000..a985ace8786db10fb6b11ea5c878db07227a2169 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000833.fa @@ -0,0 +1,20 @@ +>PROKKA_00981 +MRPTPDPAPAGRRACDSSARRMSAALAAMGVLHFVRPEPFDGLIPPFLPGSARAWTHGSG +VAELAVAGLLAVPRTRRAGGRAAQALFLGVWPGNAWMAWRWRRRPWPAQLVSLGRLPLQV +PLIRAAGRVARS +>PROKKA_00695 +MRPTPDPAPAGRRACDSSARRMSAALAAMGVLHFVRPEPFDGLIPPFLPGSARAWTHGSG +VAELAVAGLLAVPRTRRAGGRAAQALFLGVWPGNAWMAWRWRRRPWPAQLVSLGRLPLQV +PLIRAAGRVARS +>PROKKA_01908 +MRRASAPRTDTAGATGTGARRMAAALAGMGVLHFARPKPFDGLIPPALPGPARAWTVGSG +VAELAVAGMLAAPRTRRAGGRAAQALFLGVWPGNAWMAWRWRGRSWPWRALALGRLPLQV +PMIRAAGRIARG +>PROKKA_01856 +MKPTPDPAPAGRRASDGSARRMSAALAAMGVLHFVRPEPFDGLIPPFLPGSARAWTHGSG +VAELAVAGLLAVPHTRRAGGRAAQALFLGVWPGNAWMAWRWRRRPWPAQLVSLGRLPLQV +PLIRAAGRVARR +>PROKKA_00924 +MRPTPDPAPAGRRACDSSARRMSAALAAMGVLHFVRPEPFDGLIPPFLPGSARAWTHGSG +VAELAVAGLLAVPRTRRAGGRAAQALFLGVWPGNAWMAWRWRRRPWPAQLVSLGRLPLQV +PLIRAAGRVARS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000835.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000835.fa new file mode 100644 index 0000000000000000000000000000000000000000..1b1670bfe8bdb1fcb12daf0d08e3c60e4d67f141 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000835.fa @@ -0,0 +1,30 @@ +>PROKKA_00983 +MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG +VSGDVVPAALDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGDGDRADWEWMYR +VNVLGTLTMCQAFLPMLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE +EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP +HHVNLDQIVMRPVAQAAQHKVIRR +>PROKKA_00697 +MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG +VSGDVVPAALDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGVGDRADWEWMYR +VNVLGTLTMCQAFLPMLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE +EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP +HHVNLDQIVMRPVAQAAQHKVIRR +>PROKKA_01906 +MDVSHTTENQSPRAAVVTGATTGIGRATALELARRGWRVYAVGRRAERLDALAAQAREEA +VPGEVVPAPLDVTDEAAVAGLVARVDTDGGIDTLVNIAGGARGTDFVGAGNREDWEWMYR +ANVLGTLAMCQAFLPGLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTAALRLE +EAEHNVRVIEVLPGMVHTEEFSLMRLGGDAAAAEKVYAGVEKPLTAEDVAEVCVHAVELP +HHVNLDQIVIRPVAQAAQHKVIRR +>PROKKA_01853 +MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG +VSGDVVPAPLDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGDGDRADWEWMYR +VNVLGTLTMCQAFLPMLRTHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE +EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP +HHVNLDQIVMRPVAQAAQHKVIRR +>PROKKA_00926 +MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG +VSGDVVPAALDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGDGDRADWEWMYR +VNVLGTLTMCQAFLPMLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE +EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP +HHVNLDQIVMRPVAQAAQHKVIRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000836.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000836.fa new file mode 100644 index 0000000000000000000000000000000000000000..330a26ca30cea8468f7e262d768d505c9cd04f39 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000836.fa @@ -0,0 +1,30 @@ +>PROKKA_00984 +MSAPVLHVIACAHGTHDAAGRDVIDGLRADLAALLAAEGPGAQVHEAYVDVQSPSLDEVV +AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPGTIAAAPLAGAGDDVEPRLVTVLAER +VARAVPAGEAATSDVILAAAGTRAADGQAQVHALAGALARATGLPVTAAFGAAATPRVPD +AVARVHAAGRRAVVAAHLLAPGYFHDRLGEAGADAVTDPLLPHPLVARIALDRLRSALVE +APRGAAGGR +>PROKKA_00698 +MSAPVLHVIACAHGTHDAAGRDVIDGLRADLAALLAAEGPGAQVHEAYVDVQSPSLDEVV +AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPGTIAAAPLAGAGDDVEPRLVTVLAER +VAQAVPAGEAATSDIILAAAGTRAADGQAQVHALAGALARATGLPVTAAFGAAATPRVPD +AVSRVRAAGRRAVVAAHLLAPGHFHDRLGESGADAVTDPLLPHPLVARIALDRLRSALAE +APRGAAGGR +>PROKKA_01905 +MSAPVLHVIACAHGTHDAAGRVVIDGLRADLAALLDAEGPGAQVHEAYVDVQSPSLDEVV +AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPDTIAAAPLAGAGDDVEPRLVAVLAER +VAQAVPAGEAATSEVILAAAGTRAADGQAQVHALAAALARATGLPVTAAFGAAATPPVPD +AVSRVRATGRRAVAAAHLLAPGYFHDRLGESGADAVTDPLLPHPLVARIALDRLRSALAE +APRGAAGGR +>PROKKA_01852 +MSAPVLHVIACAHGTHDAAGRVVIDGLRADLAALLDAEGPGAQVHEAYVDVQSPSLDEVV +AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPDTIAAAPLAGAEDDVEPRLVTVLAER +VAQAVPAGEAATSDIILAAAGTRAADGQAQVHALAAALARATGLPVTAAFGAAATPRVPD +AVARVRATGRRAVVAAHLLAPGYFHDRLGESGADAVTDPLLPHPLVARIALDRLRSALAE +APRGAAGGR +>PROKKA_00927 +MSAPVLHVIACAHGTHDAAGRDVIDGLRADLAALLAAEGPGAQVHEAYVDVQSPSLDEVV +AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPGTIAAAPLAGAGDDVEPRLVTVLAER +VARAVPAGEAATSDVILAAAGTRAADGQAQVHALAGALARATGLPVTAAFGAAATPRVPD +AVARVHAAGRRAVVAAHLLAPGYFHDRLGEAGADAVTDPLLPHPLVARIALDRLRSALVE +APRGAAGGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000837.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000837.fa new file mode 100644 index 0000000000000000000000000000000000000000..d75136278bcc9dfb002dda8825af9c986c014cd9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000837.fa @@ -0,0 +1,48 @@ +>PROKKA_00985 +MTQVNETSRPARTPRRPSAKPHGQWKVDGTAPLNHNEEFKQQDDGLNVRERIEQVYAHEG +FDSIPSDDLHGRFRWWGLYTQRRQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQL +RVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRLESVGLSTTEACGDVPRVILG +SPVAGIAADEIIDPTPVIREIADRWIGDLEISNLPRKFKTAITGHPSQDVVHEINDVSLI +GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNK +ARMKYLLEDWGPERFRTVLEEEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAP +VVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVERDRVDAVVAGLKELGLDPEPS +VFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA +RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDY +VERVVRRYDEQREPGETFARWAHRVDEEALR +>PROKKA_00699 +MTQVNETSRPARTPRRPSAKPHGQWKVDGTTPLNHNEEFKQQDDGLNVRERIEQVYAREG +FDSIPSDDLHGRFRWWGLYTQRRQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQL +RVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRLESVGLSTTEACGDVPRVILG +SPVAGIAADEIIDPTPVIREIADRWIGDLEVSNLPRKFKTAITGHPSQDVVHEINDVSLI +GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNK +ARMKYLLEDWGPERFRTVLEEEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAP +VVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVERDRVDAVVAGLKELGLDPEPS +VFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA +RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDY +VERLVRRYDEQREPGETFARWAHRVDEEALR +>PROKKA_01904 +MVLDVEGDRVDAVVAGLKELGLDPEPSVFRRSTIACTGLEFCKLAIVDTKDTATAAIAQL +EERLADLADRLPERLSLHVNGCPNSCARIQTADIGLKGQLLPDDDGGQTPGFQIHLGGGL +ASVDRAEAGLGRSVRGLKVRADGLVDYVERLVRRYDEQREPGETFARWAHRVDEEALR +>PROKKA_01851 +MTQVNETSRPARTPRRPSAKPHGQWKVDGTAPLNHNEEFKQQDDGLNVRERIEQVYAREG +FDSIPSDDLHGRFRWWGLYTQRKQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQL +RVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRLESVGLSTTEACGDVPRVILG +SPVAGIAADEIIDPTPVIREIADRWIGDLEVSNLPRKFKTAITGHPSQDVVHEINDVSLI +GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNK +ARMKYLLEDWGPERFRTVLEEEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAP +VVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVERDRVDAVVAGLKELGLDPEPS +VFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA +RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDY +VERLVRRYDEQREPGETFARWAHRVDEEALR +>PROKKA_00928 +MTQVNETSRPARTPRRPSAKPHGQWKVDGTAPLNHNEEFKQQDDGLNVRERIEQVYAHEG +FDSIPSDDLHGRFRWWGLYTQRRQGIDGGKTATLEPHELEDRYFMLRVRIDGGDLTTEQL +RVIGGISTDFGRDTADITDRQNVQLHWIRVEDVPEIWRRLESVGLSTTEACGDVPRVILG +SPVAGIAADEIIDPTPVIREIADRWIGDLEISNLPRKFKTAITGHPSQDVVHEINDVSLI +GVVHPELGPGYDLWVGGGLSTKARLADRIGAFVSAERAPEVWHAVVSIFRDYGYRRLRNK +ARMKYLLEDWGPERFRTVLEEEYLGYALPDGPAPAPPTRPGDHVGVHEQKDGRFYIGAAP +VVGRSSGTTLTALADLLEAHGSTRLRTTPHQKIVVLDVERDRVDAVVAGLKELGLDPEPS +VFRRSTIACTGLEFCKLAIVDTKDTATAAIAQLEERLADLADRLPERLSLHVNGCPNSCA +RIQTADIGLKGQLLPDDDGGQTPGFQVHLGGGLASVDRAEAGLGRSVRGLKVRADGLVDY +VERVVRRYDEQREPGETFARWAHRVDEEALR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000838.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000838.fa new file mode 100644 index 0000000000000000000000000000000000000000..7260b08007126bcf181785a60891cc73ce7cf231 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000838.fa @@ -0,0 +1,30 @@ +>PROKKA_00986 +MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL +PHLVAQRMPGVDVLFLDTGYHFTETLATRDEVARRLAVTVVDVLPELTVAEQDERHGKDL +FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA +PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH +V +>PROKKA_00700 +MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL +PHLVAQRMPGVDVLFLETGYHFTETLATRDEVARRLDVTVVDVLPELTVAEQDERHGKDL +FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA +PWSLDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH +V +>PROKKA_01903 +MSTVPPTRPTEELERLQALAESGAAELGWDAPAAAVVDWAARHVDLRRAAVACSMADAVL +PHLVAQRMPGVDVLFLETGYHFTETLATRDEVARRLDVTVVDVLPELTVAEQDERHGKDL +FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA +PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWTGTAKTECGIH +V +>PROKKA_01850 +MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL +PHLVAQRMPGVDVLFLETGYHFTETLATRDEVARRLDVTVVDVLPELTVAEQDERHGKDL +FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA +PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH +V +>PROKKA_00929 +MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL +PHLVAQRMPGVDVLFLDTGYHFTETLATRDEVARRLAVTVVDVLPELTVAEQDERHGKDL +FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHSMVKVNPVA +PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH +V diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000839.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000839.fa new file mode 100644 index 0000000000000000000000000000000000000000..6b4413da12b14f01e1a9fcfd7146c076161756dd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000839.fa @@ -0,0 +1,35 @@ +>PROKKA_00987 +MTLTHAPDPGTVSPAGPDVQDALEAEAIHIIREVVAEFERPAMLFSGGKDSVVMLHLAAK +AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR +NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY +NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPSIYYAHEREVFRRDGMWRAVGEHSR +PAEGEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA +AMEDRKKDGYF +>PROKKA_00701 +MTLTHAPDPGTVSPAGPDVQDALEAEAIHIVREVVAEFERPAMLFSGGKDSVVMLHLAAK +AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR +NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY +NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPSIYYAHEREVFRRDGMWRAVGEHSR +PAENEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA +AMEDRKKDGYF +>PROKKA_01902 +MTLTHAPDPGTVSPAGPDVLDALEAEAIHIIREVVAEFERPAMLFSGGKDSVVMLHLAAK +AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR +NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY +NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPPIYYAHEREVFRRDGMWRAVGEHSR +PAEGEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA +AMEDRKKDGYF +>PROKKA_01849 +MTLTHAPDPGTVSPAGPDVQDALEAEAIHIIREVVAEFERPAMLFSGGKDSVVMLHLAAK +AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR +NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY +NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPSIYYAHEREVFRRDGMWRAVGEHSR +PAEGEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA +AMEDRKKDGYF +>PROKKA_00930 +MTLTHAPDPGTVSPAGPDVQDALEAEAIHIIREVVAEFERPAMLFSGGKDSVVMLHLAAK +AFWPGRIPFPVVHVDTGHNFPEVLEFRDRTVERLGLRLVVGSVQEYIDRGELRERADGTR +NTLQTTPLLDTIRTNRFDAVFGGGRRDEDKARAKERIISLRDAFGQWDPRNQRPELWNLY +NGRHTPGQHVRAFPISNWTELDVWRYIAREGIELPSIYYAHEREVFRRDGMWRAVGEHSR +PAEGEEVTTRTVRYRTVGDMSCTGAVLSEAATVEDVVLEVAASTLTERGATRADDRISEA +AMEDRKKDGYF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000840.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000840.fa new file mode 100644 index 0000000000000000000000000000000000000000..2944c71e0ff7d6307d83f3d1792d4d8dfd7fdeb1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000840.fa @@ -0,0 +1,45 @@ +>PROKKA_00988 +MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG +GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST +ADAVVLLVDARKGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYAEEVFTAIAEDVRRV +ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP +VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA +AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ +VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR +TGAFLVIDPHDGATLAAGMVRGGDEA +>PROKKA_00702 +MSTALLDRRAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG +GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST +ADAVVLLVDARKGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYAEEVFTAIAEDVRRV +ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP +VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPVRTTTVVGVDA +AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ +VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR +TGAFLVIDPHDGATLAAGMVRGGDEA +>PROKKA_01901 +MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG +GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST +ADAVVLLVDARSGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYSEEVFTAIADDVRRV +ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP +VQLVLRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA +AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ +VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR +TGAFLVIDPQDGATLAAGMVRGGDEA +>PROKKA_01848 +MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG +GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST +ADAVVLLVDARKGVVEQTRRHLSVVALLRVPQVIVAVNKIDLVDYSEEVFTAIAEDVRRV +ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP +VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA +AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ +VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR +TGAFLVIDPQDGATLAAGMVRGGDEA +>PROKKA_00931 +MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG +GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST +ADAVVLLVDARKGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYAEEVFTAIAEDVRRV +ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP +VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA +AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ +VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR +TGAFLVIDPHDGATLAAGMVRGGDEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000845.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000845.fa new file mode 100644 index 0000000000000000000000000000000000000000..7522f0e6a6225976424fc743b266d726ff8a26da --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000845.fa @@ -0,0 +1,53 @@ +>PROKKA_00995 +MRGDAPGTVEEVYRDLLARAPENKMQPRLEPMRRVLALLGDPQHAAPVIHLTGTNGKTST +ARMVEAVLRAYGLRTGRYTSPHLQRVTERISIDGAPVADETFVRVWGEILPIVQTVDAEL +EAAGEVPLTYFEAVTTLGFAVFADEPVEVVVLEVGLGGVTDATNVADAVVSVVTPISLDH +TDLLGETEAEIAEEKAGIIKPGGALVSAAQERDAAQVLLEAAQAADVPFRFEGVEFGVLE +RSLAVGGQQVSVRGLAAEYRDLFLPLLGEHQAQNLAVAVAALEMFLGGGERPLDEELLRE +GLSQVTSPGRLEVLRTAPTLIVDAAHNPDGVRATARAVQEAFGFTRLSLVVGILQEKDAP +GMLAALYRAFGDDVEDLAVTQSSSARAIPAGELARMAVDAGWPEDDVYATESVPDALEWA +VGRAEALETSADELASGTGGGVLVLGSITLAAEVRTLVGEPRHAGPVTVAARGLDPADLL +DAVGLADADEDDLDPEILELLEDRDDAGARRRPEEDR +>PROKKA_00709 +MRGDVPGTVEEVYRDLLARAPENKMQPRLEPMRRVLALLGDPQHAAPVIHLTGTNGKTST +ARMVEAVLRAYGLRTGRYTSPHLQRVTERISIDGAPVADETFVRVWGEILPIVQTVDAEL +EAAGEVPLTYFEAVTTLGFAVFADEPVEVVVLEVGLGGVTDATNVADAVVSVVTPISLDH +TDLLGETEAEIAEEKAGIIKPGGALVSAAQERDAAQVLLEAARAADVPFRFEGVEFGVLE +RSLAVGGQQVSVRGLAAEYRDLFLPLLGEHQAQNLAVAVAALEMFLGGGERPLDEELLRE +GLSQVTSPGRLEVLRTAPTLIVDAAHNPDGVRATARAVQEAFGFTRLSLVVGILQEKDAP +GMLAALYRAFGDDVEDLAVTQSSSARAIPAGELARMAVDAGWPEDDVYATESVPDALEWA +VGRAEALETSADELASGTGGGVLVLGSITLAAEVRTLVGEPRHAGPVTVAARGLDPADLL +DAVGLADADEDDLDPEILELLEDRDDAGARRRPEEDR +>PROKKA_01894 +MSGAPAPQTVEQVYADLLARAPENAMEPRLEPMRRVLALLGDPQHAAPVIHLTGTNGKTS +TARMIEAVLRSYGLRTGRYTSPHLQSVTERISIDGAPVSDETFVRVWGEILPIVQAVDAE +LEAEGRPRLTYFEAVTTLGFAVFADEPVEVVVLEVGLGGITDATNVADGAVSVVTPISLD +HTDLLGETEAEIAEEKAGIVKPGGALVSAVQERDAAQVLLEAARAADVPFRFEGVEFGVL +ERSLAVGGQQVSVRGLAAEYRDLFLPLHGEHQAQNLAVAVAALEMFLGGGDRPLDEELLR +EGLAQVASPGRLEVLRTAPTLIVDAAHNPDGVRATARAVQEAFGFTRLALVVGILREKDA +PAMLEALFRAFGDDVEDLALTQSSSPRAIPAGDLARMAVDAGWPEADVFAAESVPDALEW +AVGRAEALETSADELASGTGGGVLVLGSVTLAAEVRALVGEPRHAGPVTVAARGLDPADL +PRRRRPGRGGRGRPGPRDPRAARGPRRRRLPPPHRGGPMSTPQPGTGRTPEEDERFGDES +WRPERETRAQRAWRPGTRRRRRSVRALFTSTVLMLEAVVIFFLGMMLFGMNRDQPGAVWF +IAGYTLLAAVAVLTCALVRRPVGIAIGWAIQAVLVLSGFWEYSMFVVGALFALTWAYAVI +KGGGMDVENAERDRLQAEWEAEHGQ +>PROKKA_01841 +MSAPAEGRVPGTVEEVYADLLARAPEHRMEPRLDPVRRVLALLGDPQHAAPVIHLTGTNG +KTSTARMIEAVLRAYGLRTGRYTSPHLERVTERISVDGEPVADEDFVRVWGEILPMVHTV +DAELEAAGEPRLTYFEAVTVLGFAVFADAPVEVVVLEVGLGGITDATNVADGAVSVVTPI +SLDHTDLLGDTEAEIAEEKAGIIKPGGFLVSAAQDADAAQVLLEAARAADVPFRFEGVEF +GVLERRLAVGGQQVDVRGLADEYRELFLPLHGAHQAENLAVAVAALEAFLGGGQRPLDVE +LLREGLAQVTSPGRLEVLRTAPTVVVDAAHNPDGVAVTARAVQEVFSFTRLALVVGVLQE +KDARTMLEVLHREFGDLISDVALTQSASPRAIPAGDLAALAVDAGWPEDDLFITESVPDA +LEWAVGRAEAVETSADALASGTAGGVLVLGSITLAAEVRSLLGAPAHAGPVTVAARGMDP +ADLLAAVGLEDDDADAVDPEVLELLDDREEHTR +>PROKKA_00938 +MRGDVPGTVEEVYRDLLARAPENKMQPRLEPMRRVLALLGDPQHAAPVIHLTGTNGKTST +ARMVEAVLRAYGLRTGRYTSPHLQRVTERISIDGAPVADETFVRVWGEILPIVQTVDAEL +EAAGEVPLTYFEAVTTLGFAVFADEPVEVVVLEVGLGGVTDATNVADAVVSVVTPISLDH +TDLLGETEAEIAEEKAGIIKPGGALVSAAQERDAAQALLEAARAADVPFRFEGVEFGVLE +RSLAVGGQQVSVRGLAAEYRDLFLPLLGEHQAQNLAVAVAALEMFLGGGERPLDEELLRE +GLSQVTSPGRLEVLRTAPTLIVDAAHNPDGVRATARAVQEAFGFTRLSLVVGILQEKDAP +AMLAALYRAFGDDVEDLAVTQSSSARAIPAGELVRMAVDAGWPEDDVYATESVPDALEWA +VGRAEALETSADELASGTGGGVLVLGSITLAAEVRTLVGEPRHAGPVTVAARGLDPADLL +DAVGLADADEDDLDPEILELLEDRDDAGARRRPEEDR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000847.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000847.fa new file mode 100644 index 0000000000000000000000000000000000000000..1b42a4f96726196f7b8cf0320154b572d729e78a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000847.fa @@ -0,0 +1,25 @@ +>PROKKA_00998 +MPATPLTDDIRLSPADDIPAEEARLTWYARPAGTAALLLITSLVALTATIIIIVERTLLT +ADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLLAGARFARW +YWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNLQTGTLPA +PAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID +>PROKKA_00712 +MPATPLTDDIRLSPADDIPAEEARLTWYARPAGTAALLLITSLVALTATIIIIVERTLLT +ADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLLAGARFARW +YWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNLQTGTLPA +PAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID +>PROKKA_01892 +MPSTPTADRVRPAQPAETPASDGTLSWYARPAGMAWTLLVTSLVALTATIVIIVERSILA +ADPGHRTSCDLNPWVSCGRVMQSWQAMTFGFPNTYIGIVAFSVLITVAVSLFAGARFARW +YWLLMNVGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNIQTGTLPA +SPGAARLARELAWPVILILYVLVFATILLELGFGVIGLD +>PROKKA_01838 +MDVTETAENPPAPRAHHAAHALPEDRSLSWYARPLGTAWMLLITSIVAVTATIIIIVERS +ILAENPNYRTSCDINPWLSCGTVMQSWQAHTFGFPNTFVGIVAFPVLITVAVSLFAGARF +ARWYWVLMNVGILAGFAFAAWLWYSAVYSIGTLCLYCMIVWAMVILQLVLVTSRNLQTGA +LPSSPGLARLAQDFAWPVIVLLYALVFASILLQLGLGVIGIR +>PROKKA_00941 +MSMPTTPPTDDVRLSPADDVPAEEARLTWYARPAGTAALLLITSLVALTATIVIIVERAL +LTADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLLAGARFA +RWYWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNLQTGTL +PAPAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000848.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000848.fa new file mode 100644 index 0000000000000000000000000000000000000000..3e4d8b39008fb6651db9e760a1be0ef96dba28cb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000848.fa @@ -0,0 +1,96 @@ +>PROKKA_00999 +MAANNEDTTRADERVEETAEQAVTQTAADTADGAEPERTAASDDAADPAEEPSAPTLQVD +PTDPFAVPANLIEVLRTETTSRQRSEDEDAGESEDRAEGAVVSRRRRRRRRGEVDMELDG +GEAGDPEHTVTRVRAPRQAVGTASDTVQSVKGSTRLEAKRQRRRDSRSGGRRRTVITEAE +FLARREAVDRKMLVRQRDQRIQIAVLEDGVLAEHFVSHTTQDSMIGNVYLGKVQNVLPSM +EAAFVDIGRGRNAVLYAGEVNWDAAQLDGKPRKIENALKSGDTVLVQVTKDPVGHKGARL +TSQVSLPGRYLVYVPGGSMTGISRKLPDVERSRLKKILKDHLPQDAGVIVRTAAEGTSEQ +ELQNDINRLRAQWEGIQEKASGTKVLAPELLYAEPDLTIKTVRDVFNEDFSAMLVQGEAT +WDNIEAYVTYVAPHLLGRLHHWVPEDHDGEDLYATHRVDEQLHKALERKVYLPSGGSLVI +DRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEIVRQLRLRDIGGIIVIDFIDMVL +EANRDLVLRRLVECLGRDRTKHQVAEVTSLGLVQMTRKRMGTGLVEVFSETCEHCAGRGI +LIQDTPVERGRSGGEQRGEAEGRRRRRRRGDGEGEHAHAAAATTTGAEHADSEDERQRRE +RAEAARVALHSIAKASGKVAEDEAPAQESAPAEQAADAAEDSAAEAVEAASAGPAEAGQP +AGTDEEETPRRRRRRGRRRSRGRAEESGDTGAEDAGSEDAARSHDDGPAESAGQTRQTEE +EAAEPAAAAAPEHQDPVVQAEEAVAAVAEAEADAEAESPEDAAEQDDRPRRSRRRRGGRG +RSRRGGEAASTEADADAEDHGAERATPSRHEAADADSSVAVSSEVASEPVPAEDAPAPVP +AEDAPAPRRRRSRRASSDGVVRPAAGADASAERTADRTDAAPVEATEPSPEESTDATEVH +EQPAAPAAVEEAVMVEPAATEPTAEPTADADQASAADAPTEAQAAPTAPVPGSPRRRSRR +AVSSDGVHVQVQAAPGGAQGGRFTAAVAEASTPAEPQGAAPVMLGVGVKAADLARRGR +>PROKKA_00713 +MAANNEDTTRADERVEETAEQAVTQTAADTADGAEPERTAASDDAADPAEEPSAPTLQVD +PTDPFAVPANLIEVLRTETTSRQRSEDEDAGESEDRAEGAVVSRRRRRRRRGEVDMELDG +GEAGDPEHTVTRVRAPRQAVGTASDTVQSVKGSTRLEAKRQRRRDSRSGGRRRTVITEAE +FLARREAVDRKMLVRQRDQRIQIAVLEDGVLAEHFVSHTTQDSMIGNVYLGKVQNVLPSM +EAAFVDIGRGRNAVLYAGEVNWDAAQLDGKPRKIENALKSGDTVLVQVTKDPVGHKGARL +TSQVSLPGRYLVYVPGGSMTGISRKLPDVERSRLKKILKDHLPQDAGVIVRTAAEGTSEQ +ELQNDINRLRAQWEGIQEKASGTKVLAPELLYAEPDLTIKTVRDVFNEDFSAMLVQGEAT +WDNIEAYVTYVAPHLLGRLHHWVPEDHDGEDLYATHRVDEQLHKALERKVYLPSGGSLVI +DRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEIVRQLRLRDIGGIIVIDFIDMVL +EANRDLVLRRLVECLGRDRTKHQVAEVTSLGLVQMTRKRMGTGLVEVFSETCEHCAGRGI +LIQDTPVERGRSGGEQRGEAEGRRRRRRRGDGEGEHAHAAAATTTGAEHADSEDERQRRE +RAEAARVALHSIAKASGKVAEDEAPAQESAPAEQAADAAEDSAAEAVEAASAGPAEAGQP +AGTDEEETPRRRRRRGRRRSRGRAEESGDTGAEDAGSEDAARSHDDGPAESAGQTRQTEE +EAAEPAAAAAPEHQDPVVQAEEAVAAVAEAEADAEAESPEDAAEQDDRPRRSRRRRGGRG +RSRRGGEAASTEADADAEDHGAERATPSRHEAADADSSVAVSSEVASEPVPAEDAPAPVP +AEDAPAPRRRRSRRASSDGVVRPAAGADASAERTADRTDAAPVEATEPSPEESTDATEVH +EQPAAPAAVEEAVMVEPAATEPTAEPTADADQASAADAPTEAQAAPTAPVPGSPRRRSRR +AVSSDGVHVQVQAAPGGAQGGRFTAAVAEASTPAEPQGAAPVMLGVGVKAADLARRGR +>PROKKA_01891 +MAANEDTTGAEERAEQTEQTTAETSAAVAGQAAAESPVEDGGTVTQAQADAAEGADAPER +TAEAADIEDEAETDTAAEPEPDEAPGAPALQFDPTDPFAVPANVMEILRTEKSERRPARD +ERPARGAEDEEEAPGRSRRRRRPSRDRDQAETEAGAEDEAVETAEGEQDAETAERGEGAV +VSRRRRRRRRGDVDMELDGGEDGDPENTVTRVRAPRQALSTGSDAVQGVKGSTRLEAKRQ +RRRDSRSGGRRRTVITEAEFLARREAVDRKMLVRQREHRIQIAVLEDGVLAEHFVSNTTQ +DSLIGNVYVGKVQNVLPSMEAAFVDIGRGRNAVLYAGEVNWDAAQLDGKPKKIENALKSG +DTVLVQVTKDPVGHKGARLTSQVSLPGRYLVYVPGGSMTGISRKLPDVERSRLKKILKDH +LPQDAGVIVRTAAEGTSEQELQNDINRLRAQWEGIQEKASSTKVLAPELLYAEPDLTIKT +VRDVFNEDFSAVLVQGEATWDNIEAYVTYVAPHLLDRLHHWVPQDHDGEDLYATHRVDEQ +LHKALERKVYLPSGGSLVIDRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEVVRQ +LRLRDIGGIIVIDFIDMVLEANQDLVLRRLVECLGRDRTKHQVAEVTSLGLVQMTRKRMG +TGLVEVFSETCEHCAGRGILIHDTPVERGRSGGEPRGEGEGRRRRRRKGAGEGEQAQPAE +STTTAGGEEVDAEDERQRRERAEAARAALHSIAKASGKVSEDEDPAEQAAPAEQAADAAE +DQAAEAVEAARQDAAEETGEAGAQDGEGAEDEDEAPRRRRRRGRRRGRGRSEEAAEAAEA +ASEDGSRDADAAPAGQAPAADEEEAPAADPVAQAEAAVTAVAEAEADAESGGEEREAEPA +GDEEGARPRRARRRRGGRGRSRRGADREASTADADDEAAQPAQEPAQADAGAAGDRARAS +RAGRVGAARAARVRPGRGRGGRRAASRPAPPPFAPRFERRCRAPGRGPGRRPGVVRPGDP +VPRGGGRRRGDRAHRGAVHGRHRGARAPGRPRPGGGGRDGRAGGGRPRPGRAGRARPAAR +PELRARRPPSPGAVGPVARCPRTACACRSRTPPGRHGADASRRPPPSPRPPPSRAPRRP +>PROKKA_01819 +MAADESTTQDTHETAEGSTTPVEATEEETAAEVAESPAGEAAEATAAPDVRFDPTNPFAV +PEGLLPLIEAETVERRRRRPAADPVPEGAADDAHADDEDDEDRPAVSRRRRRRRRGTVDM +ELAGGEDGDPEDTVTRVRAPRRALSTGPEAVQGVKGSTRLEAKRQRRRESRSGGRRRTVI +TEAEFLARRESVDRKMLVRQREHRIQIAVLEDGVLAEHFVSNTTQDSMIGNVYLGKVQNV +LPSMEAAFVDIGRGRNAVLYAGEVDWDAAQLDGKAKKIENALKSGDTVLVQVTKDPVGHK +GARLTSQISLPGRYLVYVPGGTMTGISRKLPDVERARLKKILKDHLPQDAGVIVRTAAEG +TSEQELQNDINRLRVQWEGIQEKASSTKTLAPELLYAEPDLTIKTVRDVFNEDFSAMLVQ +GEATWDSIEAYVTYVAPHLLDRLHHWVPEDHDGEDLYATHRVDEQLHKALERKVYLPSGG +SLVIDRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEVVRQLRLRDIGGIIVIDFI +DMVLESNQDLVLRRLVECLGRDRTKHQVAEVTSLGLVQMTRKRMGTGLVEVFSEVCEHCG +GRGILIQDTPVERNRWGHEHRAEPEARRRNKRRRGTESGEGGPAEPTAAELTEEERLRAE +RAAAARTALMSIAKASGKAADEEPSEEAAPRAEDAPEEAADEVRPSPAGDAEEQGESESG +GRRRKRRGRRRGRGRGGDDAARSAEEQDAPAEHPAEAAGEPAPAEAGAPDPAETATEDAD +ADSASDAPAAQAEADEDGRSGGRRRSRRRGGRRAESPQGSGAPASAPEASVEAEQDPEEP +AGAAEAEEALAAEEAPASPEPAAVVTFDGEPVAVPRRRRSRRATSDGVSAPRPSGMDALE +AAVDRRAEDAAAAAQRSPATPAATPTAAPEPAPAPVAGEGPAAAAPRRRSRRAVSADGAT +VQVQEGAAAGGGRFTAQAAQAAPAGETAAPVMLGVGVKAADIVRGE +>PROKKA_00942 +MAANNEDTTRADERVEETAEQAVTQTAADTAAGAVQPERTPASDDAADAPEEPSAPTLQV +DPTDPFAVPANLIEVLRTETTSRQRSEDEDDPDTSGRSRRRRRPSREDDRAEEGAADASA +DAEDREDASESEDRAEGAVVSRRRRRRRRGEVDMELDGGEAGDPEHTVTRVRAPRQAVST +ASDTVQSVKGSTRLEAKRQRRRDSRSGGRRRTVITEAEFLARREAVDRKMLVRQRDQRIQ +IAVLEDGVLAEHFVSHTTQDSMIGNVYLGKVQNVLPSMEAAFVDIGRGRNAVLYAGEVNW +DAAQLDGKPRKIENALKSGDTVLVQVTKDPVGHKGARLTSQVSLPGRYLVYVPGGSMTGI +SRKLPDVERSRLKKILKDHLPQDAGVIVRTAAEGTSEQELQNDINRLRAQWEGIQEKASG +TKVLAPELLYAEPDLTIKTVRDVFNEDFSAMLVQGEATWDNIEAYVTYVAPHLLDRLHHW +VPEDHDGEDLYATHRVDEQLHKALERKVYLPSGGSLVIDRTEAMTVVDVNTGKFTGSGGN +LEETVTKNNLEAAEEIVRQLRLRDIGGIIVIDFIDMVLEANRDLVLRRLVECLGRDRTKH +QVAEVTSLGLVQMTRKRMGTGLVEVFSETCEHCAGRGIIIKDTPVERGRSGGEQRGEAEG +RRRRRRRGNGEGEHAHAAAATTTGAEHADSEDERQRRERAEAARVALHSIAKASGKVAED +ETPAQEPAPAEQAADAAEDSVAEAVEAASTGPAEAGQPAAADEEETPRRRRRRGRRRSRG +RAEESGDTGAEDAGSEDAARSHDDGPAESAGQTRQTEEEAAEPAAAAAPEHQDPVVQAEE +AVAAVAEAEADAEAESPEDAAEQGDRPRRSRRRRGGRGRSRRGGEAASTEADADAEDHGA +ERATPSRHEAADADSSVAVSSEVASEPVPAEDAPAPVPAEDAPAPRRRRSRRASSDGVVR +PAAGADASAERTADRTDAAPVEATEPSPEESTDATEVHEQPAAPAAVEEAVMVEPAATEP +TAEPTADADQASAADAPTEAQAAPTAPVPGSPRRRSRRAVSSDGVHVQVQAAPGGAQGGR +FTAAVAEASTPAEPQGAAPVMLGVGVKAADLARRGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000849.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000849.fa new file mode 100644 index 0000000000000000000000000000000000000000..ae82519469deb6b581a5cf73c7daa6d2ad92e47c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000849.fa @@ -0,0 +1,15 @@ +>PROKKA_01000 +MVYAIVRAGGRQEKVSVGDLVTLDRVPAETGGSVELPALMLVDGDEVKAGADAAGVKVTA +EVVSHSRGKKVVIMKYKNKTGYKKRQGHRSELSTVKITGIA +>PROKKA_00714 +MVYAIVRAGGRQEKVSVGDLVTLDRVPAETGGSVELPALMLVDGDEVKAGADAAGVKVTA +EVVSHSRGKKVVIMKYKNKTGYKKRQGHRSELSTVKITGIA +>PROKKA_01890 +MVYAIVRAGGRQEKVSVGDLVTLDRVPAETGGSVELPALMLVDGDKVTAGADAAGVKVTA +EVVSHSRGKKVVIMKYKNKTGYKKRQGHRSELSTVKITGIA +>PROKKA_01818 +MVYAIVRAGGRQEKVSVGDLVTLDRVPAEEGGSVELPALMLVDGDKVKAGADAADVKVTA +EVVSHSRGKKIVIVKYKNKTGYKKRQGHRSELSTVKITGIA +>PROKKA_00943 +MVYAIVRAGGRQEKVSVGDLVTLDRVPAETGGSVELPALMLVDGDEVKAGADAAGVKVTA +EVVSHSRGKKVVIMKYKNKTGYKKRQGHRSELSTVKITGIA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000852.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000852.fa new file mode 100644 index 0000000000000000000000000000000000000000..19e50003413ba4a86e0a4626a357c74c5e95bbd3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000852.fa @@ -0,0 +1,40 @@ +>PROKKA_01003 +MSVRRTVVTRYPTPATRGSEDPQANPVTSRETMQAARRVVVKIGSSSLTTPDGLDVAAID +RLVDVLAAERQKGTQVVLVSSGAIAAGFPHLGLSRRPKDTATQQASAAVGQSKLMAHYTT +SFGRHDTEVAQVLLTAEELMRRTQYTNAHRALARLLTLDVMPIVNENDAVATREIRFGDN +DRLAALTANLCKADLLVLLSDVDALYTGHPSNPDARRIPEVTSDDDLSGVDVRVPGSAGV +GTGGMVTKVDAAGIAATTGIPTLLTSAANAGAAFAGEDVGTWFSATGRRRSARAAWLGLT +AEVRGRLIIDDGAVAGAIDRGRSLLAAGITGCTGAFTPGDVVEIVDAHGRVRARGLVQYS +SSQLPAMLGRTTADLREDLGAGYDGVVVHADDWVRLAPPQR +>PROKKA_00717 +MSVRRTVVTRYPTPATRGSEDPQANPVTSRETMQAARRVVVKIGSSSLTTPDGLDVAAID +RLVDVLAAERQKGTQVVLVSSGAIAAGFPHLGLGRRPKDTATQQASAAVGQSKLMAHYTT +SFGRHDTEVAQVLLTAEELMRRTQYTNAHRALSRLLTLDVMPIVNENDAVATREIRFGDN +DRLAALTANLCKADLLVLLSDVDALYTGHPSHPDARRIPEVTSDDDLAGVDVRVPGSAGV +GTGGMVTKVDAAGIAATTGIPTLLTSAANAGAAFAGEDVGTWFSATGRRRSARAAWLGLT +AEVRGRLIIDDGAVAGAIDRGRSLLAAGITGCTGAFTPGDVVEIVDAHGRVRARGLVQYS +SSQLPAMLGRTTADLREDLGAGYDGVVVHADDWVRLAPPQR +>PROKKA_01887 +MSARRTVVTRYPTPATRGAEDPRANPVTTRDTMAAARRVVIKIGSSSLTTATGLDVAAID +RLVDVIAELRGRGTQVVLVSSGAIAAGFPHLGLDRRPKDTATQQAAAAVGQGRLLAHYTH +SFGRHETEVAQVLLTAEELMRRTQYTNAHRALARLLTLDVMPIVNENDAVATREIRFGDN +DRLAALTANLVKADLLVLLSDVDALYTGHPSLPDSRRIPVVATDADLEGVDVHVPGSAGV +GTGGMVTKVDAAGIAATTGIPTLLTSAPNAGSAFAGEDVGTWFEATGRRRSARAAWLGLT +AEVRGQLVIDDGAVAGAIDRGRSLLAAGIIGLSGRFTPGDVVEILDATGRVLARGLVQYS +SSQLPRMLGRSTSDLKEDLGAGYDGVVVHADDWVRLAPPRR +>PROKKA_01815 +MARRPSTVHRHATPSSRGAEDPKANPVHTRADIGAARRVVIKVGSSSLTTGTGLNTDAID +ALVELVARLRGRGTQVVLVSSGAIAAGFPALGLSRRPKDTATQQAAAAVGQNRLVAYYSQ +SFARFDTTVAQVLLTAEELMRRGQYINAHRALARLLTLDVLPIVNENDAVATREIRFGDN +DRLAALTANLVKADLLVLLSDVDALYTGHPSRPGSRRIDTVTAETDLGGVDVRTPGSAGV +GTGGMVTKVDAAGIAATTGIPTLLTSAALASAALDGEDVGTWFSAAGRRRTARAAWLGLT +AQVRGRLTIDDGAVAGAIDRGRSLLAAGITAAEGDFTAGDVVEIADAQGTVLARGLAAYS +SSQLPRMLGRQTAQLKEEIGAGYDGVVVHADDWVRLAPTHSAFR +>PROKKA_00946 +MSVRRTVVTRYPTPATRGSEDPQANPVTSRETMQAARRVVVKIGSSSLTTPDGLDVAAID +RLVDVLAAERQKGTQVVLVSSGAVAAGFPHLGLGRRPKDTATQQASAAVGQSKLMAHYTT +SFGRHDTEVAQVLLTAEELMRRTQYTNAHRALSRLLTLDVMPIVNENDAVATREIRFGDN +DRLAALTANLCKADLLVLLSDVDALYTGHPSNPDARRIPEVTSDDDLAGVDVRVPGSAGV +GTGGMVTKVDAAGIAATTGIPTLLTSAANAGAAFAGQDVGTWFSATGRRRSARAAWLGLT +AEVRGRLVIDDGAVAGAIDRGRSLLAAGITGCTGDFTPGDVVEIVDTHGRVRARGLVQYS +SSQLPAMLGRTTADLREDLGAGYDGVVVHADDWVRLAPPQR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000853.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000853.fa new file mode 100644 index 0000000000000000000000000000000000000000..6d8e11ba7c667f4a66d2e213ada8161538c70f98 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000853.fa @@ -0,0 +1,45 @@ +>PROKKA_01004 +MQTTESTAPQDQSGRQDAEAPTPEVEEAVRQRAEWARQAVPELAVAGRARKDAVLRHMAE +ALRANTAAILTANREDRSRGRETGTSAAMLDRLKLDEARVEALALALETLAGLPDPVGTV +VRGGPLPNGVRMSQVRVPLGVVGAVYEARPNVTVDIAGIALKSGNGVILRGGSAAESTNA +VLIQVLREALVDQGFDANIIQGIDDLGRPGVAALMAARGAVDVLVPRGGRELIQRVVREA +RVPVIETGEGNVHLYVDASAPKQMAVDIALNSKTHRTSVCNAAETLLLHRDAEETGREVL +RALTRAGVLLHVDEAARAWLPTLADRGDHARDAVDATEEDWGTEYLDMEMAVRVVDSLGQ +AIEHIGRWSTGHTEAIVTNDLAAAERFITEVDAAAVIVNASTRFTDGGELGLGAEVGIST +QKMHARGPMGLEELTTTKWILRGDGQIRR +>PROKKA_00718 +MQTTESTAPQDQSGRQDAEAPTPEVEEAVRQRAEWARQAVPELAVAGRARKDAVLRHMAE +ALRANTAAIITANREDRSRGRETGTSAAMLDRLKLDEARVEALALALETLAGLPDPVGTV +VRGGPLPNGVRMSQVRVPLGVVGAVYEARPNVTVDIAGIALKSGNGVILRGGSAAESTNA +VLIQVLREALVDQGFDANIIQGIDDLGRPGVAALMAARGAVDVLVPRGGRELIQRVVREA +RVPVIETGEGNVHLYVDASAPKQMAVDIALNSKTHRTSVCNAAETLLLHRDAEETGREVL +RALTRAGVLLHVDEAARAWLPTLADRGDHARDAVDATEEDWGTEYLDMEMAVRVVDSLGQ +AIEHIGRWSTGHTEAIVTNDLAAAERFITEVDAAAVIVNASTRFTDGGELGLGAEVGIST +QKMHARGPMGLEELTTTKWILRGDGQIRR +>PROKKA_01886 +MENQESTAPQDQSAGQEAEAPSQEVVDAIRQRAEWARLAVPELATAGRTRKDAVLRHMAE +SLRSNAAAIITANQEDRARGAEAGTSAALLDRLKLDEPRVEALALGLEALAALPDPVGAV +VRGGTLPNGVRMTQTRVPLGVVGAVYEARPNVTVDIAGIALKSGNGVILRGGSAAQSTNA +VLIQVLREALADQGFDPNVVQGIDDLGRPGVAALMATRGAVDVLVPRGGRELIQRVVREA +RVPVIETGEGNVHLYLDASAPKDMAVEIALNAKTHRTSVCNAAETLLIHREAEETGREVL +RALMRGGVLLHVDEAAKAWLPGPTDRGDHARDAVDATEEDWGTEYLDMDMAVRIVDSLDQ +AIEHIGRWSTGHTEAIVTNDLAAAEQFITEVDAAAVIVNASTRFTDGGELGLGAEVGIST +QKMHARGPMGLEELTTTKWILRGDGQVRR +>PROKKA_01814 +MTTEHTETEPAERVQQTPTPEQGASADGRPGADVVAEVRSRSARARAAAPELARAGRERK +DALLRSMADAVRAAAASILAANAEDLARGEENGTSAAMLDRLRLDEPRLESLAVALEDLA +SLPDPVGAVVRGGDLPNGIHMQQVRVPLGVVGAVYEARPNVTVDIAGIALKSGNAVLLRG +GSAAEHTNAVLIQVLREALRDQGFESDLVQGIDDLGRPGVAALMSTRGAVDVLIPRGGRE +LIQRVVAEARVPVIETGEGNVHLFIDASAPADMAVDIALNAKTHRTSVCNAAETLLLHKD +AERAGREVLRALTRAGVLLHVDEASRARLPSPADRGQDAREPQAASDEDWGREYLDMEMA +VRTVDSIDEAMEHVRRWSTGHTEAIVTNDLANADRWVSEVDAAAVIVNASTRFTDGGQLG +LGAEVGISTQRMHARGPMGLEELTTTKWVLRGAGQVRR +>PROKKA_00947 +MQTTESTAPQDQSGRQDAEAPTPEVEEAVRQRAEWARQAVPELAIAGRARKDAVLRHMAE +ALRANTAAILTANREDRGRGRETGTSAAMLDRLKLDEARVEALALALETLAGLPDPVGTV +VRGGPLPNGVRMSQVRVPLGVVGAVYEARPNVTVDIAGIALKSGNGVILRGGSAAESTNA +VLIQVLREALVDQGFDPNIIQGIDDLGRPGVAALMAARGAVDVLVPRGGRELIQRVVREA +RVPVIETGEGNVHLYVDASAPKQMAVDIALNAKTHRTSVCNAAETLLLHRDAEETGREVL +RALTRAGVLLHVDEAARAWLPTLADRGDHARDAVDATEEDWGTEYLDMEMAVRVVDSLDQ +AIEHIGRWSTGHTEAIVTNDLAAAERFITEVDAAAVIVNASTRFTDGGELGLGAEVGIST +QKMHARGPMGLEELTTTKWILRGDGQIRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000854.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000854.fa new file mode 100644 index 0000000000000000000000000000000000000000..dae6b263cdaf0fceffbeaddf001244ac1ccb18fb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000854.fa @@ -0,0 +1,15 @@ +>PROKKA_01005 +MLNTSLILAAAEGHHVVNELPMDPIWYGLLVFALLMAALAATMSMRSRALRLPEPTTAVQ +HHGTGRGSHTSGH +>PROKKA_00719 +MLNTSLILAAAEGHHVVNELPMDPIWYGLLVFALLMAALAATMSMRSRALRLPEPTTAVQ +HHGTGRGSHTSGH +>PROKKA_01885 +MLNTSLVLAAAEGPHVVNELPIPTVWYGIIVFALLMAALLATMSMRSRALRLPEPTTAVQ +HHGTGHGSHTPGH +>PROKKA_01813 +MLNSALVLAAAEEGHHVVNELPIPPVWFGIIVFLLLMAGLLAILSMRSVGLRHAEPTTAV +QHHGTHGTGSHSAGH +>PROKKA_00948 +MLNTSLILAAAEGHHVVNELPMDPIWYGLLVFALLMAALAATMSMRSRALRLPEPTTAVQ +HHGTGRSSHTSGH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000859.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000859.fa new file mode 100644 index 0000000000000000000000000000000000000000..c637182f0ed8e85bca73d82942f70ec7e52c8599 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000859.fa @@ -0,0 +1,16 @@ +>PROKKA_01017 +MYPTPMTFDVARAGRALAQVSARTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALLK +YGVGLVPEDEFGGAGVRRIFSAEKSRRIKAMENEGGPAYEDDI +>PROKKA_00731 +MYPTPITFDVARAGRALAQVSVRTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALLK +YGVGLVPEDEFGGTGVRRIFTAEKSRRIEAMENEGGPAYEDDI +>PROKKA_01870 +MYPTPMTFDVARAGRALAQVSVRTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALRK +YGVGLVPEDEFGGTGVRRIFTAEKSRRLEAMENEGGPAYEDDI +>PROKKA_00705 +MESQHISNGDMTRAARILVKVSAQYIAREANVTKEELRDFEKGRHDLSEKKQERVRAALE +ELGAEFLPDGPNGGYGIRLKFGRSRIYSLERCEGEGGPRLTTESDRRTQAHVPFSEPDSN +LPFHLEDRTTASLRILVPLRLGRLWPSHLASVPGMEARAR +>PROKKA_00961 +MYPTPMTFDVARAGRALAQVSVRTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALRK +YGVGLVPEDEFGGAGVRRIFTAEKSRRLEVLENEGGPAYEDDI diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000860.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000860.fa new file mode 100644 index 0000000000000000000000000000000000000000..6d676b1f5b4c03ea9369e228964f8422300d0a78 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000860.fa @@ -0,0 +1,45 @@ +>PROKKA_01018 +MTATPDLEQTRHLATELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGNR +LIDLASGIAVTSVGASHPRVVAAVQDQVAQFTHTSFMITPYEGYVAVAEQLDRTSPIPGE +TRTALFNSGAEAVENAVKVARAYTGKQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGPF +APEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEGF +LPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVTG +RAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIREHFEQNADD +RIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRATGVILLTCGTYGNVVRFLPPLT +IGEDLLKEGLSEVTKALQSA +>PROKKA_00732 +MTATPDLEQTRHLATELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGNR +LIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTSPIPGE +TRTALFNSGAEAVENAVKVARAYTGKQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGPF +APEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEGF +LPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVTG +RAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIREHFAQNADD +RIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRAAGVILLTCGTYGNVVRFLPPLT +IGEDLLKEGLSEVTNALQSA +>PROKKA_01869 +MSSTPDLEQSRHLATALPGPRSQALAERQKAAVPAGVATTMPVYAARAAGGILEDVDGNR +LIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTAPISGQ +TRTALFNSGAEAVENAVKVARSYTGKQAVAAFDHAYHGRTTLTMALTAKNMPYKHHFGPF +APEVYRVPGSYPLRDGLSGAEAARRAIGALETQIGAENLAAVIMEPIQGEGGFIVPAEGF +LPAVVEWCRANDVLFIADEVQSGVARTGSWFACEAEGVEPDLMTTAKGIAGGMPLSGVTG +RAEVMDSVHPGGLGGTYGGNPVAAAAALAVFEAIEDEDLLAKATRIEEVIREHFAAHADD +RIAEVRGRGAMMAIELVEPGTGEPDAALTAAVAAAVRATGVILLTCGTYGNVIRFLPPLT +IGEDLLKEGLSEVTKALQSA +>PROKKA_01761 +MTSPVTAPEQSRHIATELPGPKSRELAARQAGAVPAGVATTMPVFASRAGGGIIEDVDGN +RLIDLGSGIAVTSVGASHPKVVEAVQEQVADFTHTCFMITPYEGYVAVAEKLGEKAPISG +ETRTALFNSGSEAVENAVKVARAYTRKQAVVAFDHAYHGRTTLTMSLTAKSMPYKHSFGP +FAPEVYRVAGSYPLRDGLNGAAAAKKAISAMEKQIGADNLAAVIMEPLQGEGGFIVPAEG +FLQAIVEWCTANDVLFIADEVQSGFARTGAWSASELEGIEPDLMCTAKGIAGGMPLSAVT +GRAEVMDAVHPGGLGGTYGGNPVATAASLAVFEAIEEDGLLQEAQMIERVIREHFEQNAD +ERIAEVRGRGGMMAIEFVDPASGEPDAALTGKLAAAVRAAGVVLLTCGTYGNVVRFLPPL +TIGEELLREGLAEVTTALQSA +>PROKKA_00962 +MTATPDLEQTRHLVTELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGNR +LIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTCPIPGE +TRTALFNSGAEAVENAVKVARAYTGRQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGPF +APEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEGF +LPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVTG +RAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIRDHFEQNADD +RIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRATGVILLTCGTYGNVVRFLPPLT +IGEDLLKEGLSEVTKALQSA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000862.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000862.fa new file mode 100644 index 0000000000000000000000000000000000000000..ababf092e5eeae7aea013d2bc06727b4bc72f2ae --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000862.fa @@ -0,0 +1,31 @@ +>PROKKA_01020 +MNTTVRRALWVVLVLLCLGLVFLALRGVLAVGAVPISAAPTLSATASATPSPSPSPSSAR +FTPSPATTATPTPTPSPSSASPTREAAVPVETQELAGTPTPSEEPTPTEEPAPSEEPAPS +EEPTPAAAAHLSGPAAPWDEVTATPVHVDVHQDGEQIVGAGIDLTQLDEGGDLDPEPQTV +GWYGPPQWGTTPGERSRYAGVLAGHVVYHGVRDVFWNLGDVRAGAVVVVTYDDGTQAAFE +ADSDAVSVEKEALTQDPANRWAWEPGGDDAKVTLITCDLVPGTGMAGNAFNNWVVQATRV +A +>PROKKA_00734 +MNTTVRRALWVVLVLLCLGLVFLALRGVLAVGAVPISAAPTLSATASATPSPSPSPSSAR +FTPSPAPTATPIPTPSPSSASPTREAAVPVETQELAGTPTPSEEPTPTEEPAPSEEPAPS +EEPTPAAAAHLSGPAAPWDEVTATPVHVDVHQDGEQIVGAGIDLTQLDEGGDLDPEPQTV +GWYGPPQWGTTPGERSRYAGVLAGHVVYYGVRDVFWNLGDVRAGAVVVVTYDDGTQAAFE +ADADAVSVEKEALTQDPAHRWAWEPGGDDAKVTLITCDLVPGTGMAGNAFNNWVVQATRV +A +>PROKKA_01867 +MTGPAAPWESIDAAPVHVEVHQDGERIVGASVEHTQMNEAGELDPDPQTVGWYGAPQWGT +DPGERSPYAGILAGHVVYYGVKDVFWNLDAVRAGDVVVLTYDDGSQAVFEADADAVSVEK +EALTQDPANRWAWEPGGDDARLTLITCDLVPGTGMAGNAFNNWVVQATRVA +>PROKKA_01763 +MSTTVKRAVWALLLLICLGVGAFALRGMFAFGDVPISAAPTVSARASTASSTPSAATGSP +SSTSASASAGPSVPAATSASSAAASTTTPASPTSSTTTPASPTSSTTPASTEAAAPAVGA +ASSTATASSSATPTGTDSRMTKPAASWERITAAPVHIDVYADGEQVVGAPVELVQTRDDG +ELNPDPQMAGWYGPPQWTTTPGERSAHPGVIAGHVIHSGLKDVFWNLQTLKAGSIVVITY +DDGTQAEFRTDFDVRSMDKDDLTQSPDYAWAWELPEAGNKVTLITCDLVDGSGMTGWSTN +NWVTQATRIG +>PROKKA_00964 +MNTTVRRALWVVLLLLCLSLVFLALRGVLAVGAVPISAAPTLSATASVSPSSAATTREAA +VPVETQELAGTPTPSEEPTPTEEPAPSEEPTPAAAAHLSGPAAPWDEVTATPVHVDVHQD +GEQIVGAGIDLTQLDEGGDLDPEPQTVGWYGPPQWGTTPGERSRYAGVLAGHVVYHGVRD +VFWNLGDVRAGAVVVVTYDDGTQAAFEADADAVSVEKEALTQDPSHRWAWEPGGDDAKVT +LITCDLVPGTGMAGNAFNNWVVQATRVA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000863.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000863.fa new file mode 100644 index 0000000000000000000000000000000000000000..96116a850f907b95f7d8f0192711202fcfddb8b8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000863.fa @@ -0,0 +1,33 @@ +>PROKKA_01021 +MSRADIAPARVRPRRWSVAVGGALLSITLATGGCSVAEEPGQTGGTEAGNTYLEGVLASP +SQTSADPLAADIQFAGLLLRNHRDAIQQSDQVLGKDGVDQEIRATAERMKSEHEERAGRL +ESMLEGWGVPSDDVRGAGAESTPSAQPESTEDAEPTQIVGDELRAGLLSDREKNVLAAAE +PEEAGRIYLLQMRRLYQGALTISATEAEDGSDDAAKELASSVVEGHRKELESLAATLGEM +GVIGSSGARTAEPSGFTGPIKIEGTGADGGSVPSDFVPEPLQRVRSFRATQKPVLPSSSS +PSSSSASGSASASGRDAEDQRGRDAASASPSPSPADTAQATPRPSSGASPSPSASR +>PROKKA_00735 +MSRADIAPARVRPRRWSVAVGGALLSITLATGGCSVAEEPGQTGGTEAGNTYLEGVLASP +SQTSADPLAADIQFAGLLLRNHRDAIQQSDEVLGKDGVDQEIRATAERMKSEHEERARRL +ESMLEGWGVPSDDVRGAGAESTPSAQPESTEDAEPTQIVGDELRAGLLSDREKNVLAAAE +PEEAGRIYLLQMRRLYQGALTISATEAEDGSDDAAKELASSVVEGHRKELESLAATLGEM +GVIGSSGARTAEPSGFTGPIKIEGTGADGGSVPSDFVPEPLQRVRNFRATQKPVLPSSSS +PSSSSASGPASASGRDAEDQRGRDAASASPSPSPADTAQATPRPSSGASPSSSASR +>PROKKA_01866 +MPVTGDELRAGLLSEREKNVLAAADAEDAGRIYLLQMHRVYQGALTISATEAESGTDEEA +KALAASVVADHQEDMQRMVEVLADMGAIGADASHTALPSGYTGPIKIEGTGADGGPVPSD +FVPEPVQRVQSFRATQRPVLPTSSSPGDAEDRRGRDSATASPSPTPADTARPSPSPSSAA +SPSPSATTGSPSGTNR +>PROKKA_01762 +MNRATDATAPVCPVRWSAAAGGLLGLSLVLAGCGTSAQPVPAGSGSNTYLEGVLATPSAT +KADPLAADQRFVASLLQNQYQVVQEADHVLSRPDMDGEVRDMAQQHKDVANQRIGDLSSR +LQAWGLEVPAAPEPLVDDTKPSGRPTGDPSEIQASKGQQAAADIRAGLLTASDQSALVTA +DDDAAGRIYLLQVHRLLQGGVSLAGTESDEGTDEETKKIASDLIDADRPRMQRILEKLGE +NGVVAAVPSPTAPNSGYQGPISLPSQAGGDGANVDYTPSALYEMWSTLPPPATSSSADGS +STGPSPSAQPTPTPADTASPRPTPGASAQPGAASSTASTTGAASTRNG +>PROKKA_00965 +MSRADIAPARVHPRRWSVAVGGALLSITLATGGCSVVEEPGQTGDTEAGNTYLEGVLASP +SQTSADPLAADIQFAGLLLRNHRDAIQQSDQVLGKDGVDQEIRATAERMKSEHEERAGRL +ESMLEGWGVPSDDVRGAGAEATPSAQPESTEDAEPAEIVGDELRAGLLSDREKNVLAAAE +PEEAGRIYLLQMRRLYQGALTISATEAEDGSDDAAKELASSVVEGHRKELESLAATLAEM +GVIGSSGARTAEPSGFTGPIKIEGTGADGGSVPSDFVPEPLQRVRNFRATQKPVLPSSSS +PSSSSASGSASASGRDAEDQRGRDTASASPSPSPADTAQATPRPSSGASPSPSASR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000865.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000865.fa new file mode 100644 index 0000000000000000000000000000000000000000..0988a3e3bf10c2104abed2f9a5b84ac872e88797 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000865.fa @@ -0,0 +1,15 @@ +>PROKKA_01023 +MSTSPTVTRNDAESRYELHDGGTLLAVLDFRDNGAAVSLNRAFTIPVHRGRGHAAALTAG +AVEDIATNGGPAGGRRIVPMCWYVAQWFDEHPEKSALLAPR +>PROKKA_00738 +MSTSPTVTRNDAESRYELHDGGTLLAVLDFRDNGAAVSLNRAFTIPVHRGRGHAAALTAG +AVEDIETNGGPAGGRRIVPMCWYVAQWFDEHPEKSALLAPR +>PROKKA_01865 +MTARDAAGGPAVTRNDAESRYELHDGGTLLAVLDYRDNGTAVALTRAFTIPVHRGHGHAA +TLTAGAVEDIEARGGAAGGRQIVPLCWYVAQWLEEHPEKAHLVAPR +>PROKKA_01758 +MDASDSPTTFTRNDAASRYELHDASGELLAALDYRDNGTAVSLTRAFTVPVHRRQGHAAT +LTAGAVADIEARGGAAGGTTVVPMCWYVARWFEEHPEKAGLLDAR +>PROKKA_00967 +MTTGGCPGMSTSPTVTRNDAESRYELHDGGTLLAVLDFRDNGAAVSLNRAFTIPVHRGRG +HAAALTAGAVEDIATNGGPAGGRRIVPMCWYVAQWFDEHPEKSALLAPH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000867.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000867.fa new file mode 100644 index 0000000000000000000000000000000000000000..090170c7b77547280e6643d9c3882cd6bbf4ae4d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000867.fa @@ -0,0 +1,20 @@ +>PROKKA_01025 +MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREPT +LGATAPYVLMTPTYGGGSGPGAVPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLAGY +IISRKCQVPLMYKFELMGTPDDVERVRGGLEGMWT +>PROKKA_00740 +MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREPT +LGATAPYVLMTPTYGGGSGPGAVPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLAGY +IISRKCQVPLMYKFELMGTPDDVERVRGGLEGLWT +>PROKKA_01860 +MTVAADPGHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVQKLELPEDRVARLPLITREPT +LGATAPYVLLTPTYGGGDGPGAVPKQVIKFLNVPGNRTWIRGVIASGNTNFHEAYCLAGY +IIARKCQVPLMYKFELMGTPEDVDSVRGGLEGLWT +>PROKKA_01750 +MTTATAGPNHMRDAEAQGLVPTDARLIYFSSASGYTHRFVEKLGLPLGQAARLPLLTREP +TLGATAPYVLLTPTYGGGGDTGGEVPKQVIKFLNVPGNRALIRGVIASGNTNFSGAYAAA +GYIISRKCQVPLMYKFELMGTPEDVVAVREGLERLEEGQHA +>PROKKA_00969 +MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREPT +LGATAPYVLMTPTYGGGSGPGAVPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLAGY +IISRKCQVPLMYKFELMGTPDDVERVRGGLEGLWT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000869.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000869.fa new file mode 100644 index 0000000000000000000000000000000000000000..2163c138f508f47e45d014e4057b66aca505d59c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000869.fa @@ -0,0 +1,35 @@ +>PROKKA_01027 +MCPAVTETQQSHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDEE +RLLSMRVFTGLTLLDTIQGTVGAVSLIPDAMTPHEEAVLTNIAFMESVHAKSYSSIFSTL +ASTPEIDEAFRWSRENRNLQAKARLIVERYDGQDPYKKKIASTLLESFLFYSGFYWPMYL +SGHARLTNTADLIRLIIRDEAVHGYYIGYKYQRSIETLPEEKREELKAFTFELLFELYEN +EVEYTHDLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSDE +NHDFFSGSGSSYVIGKAENTEDEDWDF +>PROKKA_00742 +MCPAVTETQQSHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDEE +RLLSMRVFTGLTLLDTIQGTVGAVSLIPDAMTPHEEAVLTNIAFMESVHAKSYSSIFSTL +ASTPEIDEAFRWSRENRNLQAKAGLIVERYDGQDPYKKKIASTLLESFLFYSGFYWPMYL +SAHARLTNTADLIRLIIRDEAVHGYYIGYKYQRSIETLPEEKREELKAFTFELLFELYEN +EVEYTHDLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSDE +NHDFFSGSGSSYVIGKAENTEDEDWDF +>PROKKA_01858 +MTEVTDTVKTNHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDEE +RLLSMRVFTGLTLLDTIQGTVGAVSLIPDAITPHEEAVLTNIAFMESVHAKSYSSIFSTL +ASTKEIDEAFRWSRENENLQRKASLIVERYDGEDPYKRKIASTLLESFLFYSGFYWPMYL +SAHARLTNTADLIRLIIRDEAVHGYYIGYKYQRNIETLPEEKREELKAFTFELLFELYEN +EVEYTHDLYDAVGLSEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSDE +NHDFFSGSGSSYVIGKAENTEDADWDF +>PROKKA_01745 +MTEPHHGPSVHDHLVEAINWNRIQDEKDNEVWQRLVNNFWLPEKVPLSNDVQSWNQLTDD +ERLLSMRVFTGLTLLDTIQGTVGAVSLIPDAITPHEEAVYTNIAFMESVHAKSYSSIFST +LASTKEIDEAFRWSRENPNLQRKAQLILERYDGEDPYKKKIASTLLESFLFYSGFYWPMY +LSSHARLTNTADLIRLIIRDEAVHGYYIGYKYQRNIETLPEERREELKAFTFELMFELYE +NEVEYTHSLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTDVNPAILSALSPNSD +ENHDFFSGSGSSYVIGKAEATEDEDWDF +>PROKKA_00971 +MCPAVTETQQSHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDEE +RLLSMRVFTGLTLLDTIQGTVGAVSLIPDAMTPHEEAVLTNIAFMESVHAKSYSSIFSTL +ASTPEIDEAFRWSRENPNLQAKARLIVERYDGQDPYKKKIASTLLESFLFYSGFYWPMYL +SAHARLTNTADLIRLIIRDEAVHGYYIGYKYQRSIETLPEEKREELKAFTFELLFELYEN +EVEYTHDLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSDE +NHDFFSGSGSSYVIGKAENTEDEDWDF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000871.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000871.fa new file mode 100644 index 0000000000000000000000000000000000000000..b53984467c9f5f64afbf54b08a17d7ad78311779 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000871.fa @@ -0,0 +1,30 @@ +>PROKKA_01032 +MSVAPRLRWAVQERTLGAVEDLDWAMGELAVFRAAAAEGRALDDLIRVYVPEPTVAFGQR +DARLPGFAAAAAAARAHGFAPAVRRAGGRAAAYHHGCLVVDHLSQQEDAALTQQARFAEF +ADLFVRAFARMDVPASVGEIPGEYCPGEFSVQGPAPTYPVKLAGSAQRVVKGAFLFSTHV +VVSDPAPLRAVLVDVYRELGLDMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAAGI +EVVAEQLAVLGARTSG +>PROKKA_00747 +MSAAPRLRWAVQERTLGAVEDLDWAMDELAVFRAAAAEGRALDGLIRVYVPEPTVAFGQR +DARLPGFEAAAAAARAHGFEPVVRRAGGRAAAYHHGCLVVDHLSQQEDAALTQQARFAEF +ADLFVRAFARMDVPASVGEIPGEYCPGEFSVQGPAPTYPVKLAGSAQRVVKGAFLFSTHV +VVSDPAPLRAVLVDVYRELGLDMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAGLE +VVDEQLAVLTAGTAG +>PROKKA_01850 +MSAAPRLRWAVQERTLGATDDLDWAMDELAVFRAAAAEGRALDDLIRVYVPEPTVAFGQR +DARLPGFEAAAAAARTHGFEPAVRRAGGRAAAYHHGCLVVDHLSQQEDAALTQQARFAEF +ADLFVRAFARMGVPASVGEIPGEYCPGEFSVQGPAPTYPVKLAGSAQRVVKGAFLFSTHV +VVSDPAPLRAVLVDVYRELGLDMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAAGL +KVVDEHLAVLAAGTSG +>PROKKA_01740 +MSAAPRLRWAVQERTLGAADDLDWAMGELAVFRAAAAEGRALDDLIRVYVPEPTVAFGQR +DARLPGFEAAAAAARAHGFEPAVRRAGGRAAAYHHGCLVVDHLSQQEDATLTQQARFAEF +ADLFVRAFARMGVPASVGEIPGEYCPGEFSVQGPAPAYPVKLAGSAQRVVKGAFLFSTHV +VVSDPAPLRAVLVDVYRELGLGMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAAGL +EVVDEQLAVLGAGTSG +>PROKKA_00976 +MSAAPRLRWAVQERTLGAVEDLDWAMGELAVFRAAAAEGRALDDLIRVYVPEPTVAFGQR +DARLPGFAAAAAAARAHGFAPAVRRAGGRAAAYHHGCLVVDHLSQQEDAALTQQARFAEF +ADLFVRAFARMDVPASVGEIPGEYCPGEFSVQGPAPTYPVKLAGSAQRVVKGAFLFSTHV +VVSDPAPLRAVLVDVYRELGLDMDPRTAGAAEDVRPGVSVPAFAAALREEYTAWAAAAGI +EVVAEQLAVLGARTSG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000873.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000873.fa new file mode 100644 index 0000000000000000000000000000000000000000..4eda628c8b506b09e2b4f401974fb0cc9b111ba5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000873.fa @@ -0,0 +1,25 @@ +>PROKKA_01036 +MARIDHLVTSGTFSLDGETFDVDNNVWIVGGAEQCVVIDPAHDASAVWKKVNGRQVLAIV +LTHGHDDHIRQVQEFRQMVDAPALLHPADRMLWDDVFPDEEPDGALAEGDVLRVAGVELR +VLHTPGHSPGSVCLYAPALGEAGDDGAPTGVVFSGDTLFQGGPGATGRSYSDFDTIIESI +RERLLSLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH +>PROKKA_00749 +MARIDHLVTSGTFSLDGETFDVDNNVWIVGGAEQCVVIDPAHDASAVWKKVNGRQVLAIV +LTHGHDDHIRQVQEFRQMVDAPVLLHPADRMLWDDVFPDEEPDGALAEGDVLRVAGVELR +VLHTPGHSPGSVCLYAPALGEAGDDGAPTGVVFSGDTLFQGGPGATGRSYSDFDTIIESI +RERLLPLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH +>PROKKA_01848 +MARIDHLVTSGTFSLDGETFDVDNNVWLVGGAEQCIVIDPAHDASAVWKKVNGRQVLAIV +LTHGHDDHIRQVQEFRQMVDAPVLLHPADRMLWDDVFPDEEPDGALAEGDVLRVAGVELR +VLHTPGHSPGSVCLYAPALGEAGDDGGATGVVFSGDTLFQGGPGATGRSYSDFDTIIESI +RERLFPLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH +>PROKKA_01738 +MARIDHLVTSGTFSLDGETFDVDNNVWIVGGAEQCVVIDPAHDASAVWKKVNGRQVLAIV +LTHGHDDHIRQVQEFRQMVDAPVLLHPADRMLWDDVFPDEEPDGALAEGDVLRVAGVELR +VLHTPGHSPGSVCLYAPALGEAGDDGAPTGVVFSGDTLFQGGPGATGRSYSDFDTIIESI +RERLFPLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH +>PROKKA_00978 +MARIDHLVTSGTFSLDGETFDVDNNVWIVGGAEQCVVIDPAHDASAVWKKVNGRQVLAIV +LTHGHDDHIRQVQEFRQMVDAPVLLHPADRMLWDAVFPDEEPDGALAEGDVLRVAGVELR +VLHTPGHSPGSVCLYAPALGEAGDDGAPTGVVFSGDTLFQGGPGATGRSYSDFDTIIESI +RERLFPLPEATVVHTGHGDSTTIGTEKPHLQEWIDRGH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000876.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000876.fa new file mode 100644 index 0000000000000000000000000000000000000000..6d4e63285fb9b9062e74878c7d1a03576d29f51d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000876.fa @@ -0,0 +1,28 @@ +>PROKKA_01043 +MSLTAPGRALRRHRFAQAGTLSVALALALTACGGQSEPAESSTTSPSSAKPAVETSAPAS +TSETAGVSSSPTATESGSGEYVPASADGPARSVPKPEMPADMKEETKEGAEAAIRYFWDV +HYYAEQTGDTELLDSLYSEYCEFCQFSSNDLQMIYKDGGWYTGTEVQIDSILTHRSETGY +VSTLLVTTGTGTGYTKGGVVPENGDVEAASKQPWIAEVSFNPESSHWIVDEMSYEGSIGS +N +>PROKKA_00756 +MSLTAPGRALRRHRFAQAGTLSVALALTLTACGGQSEPAESSTTSPSSAKPAVETSAPAS +TSATAGVSSSPTATESGSGEYVPASADGPARNVPKPEMPAAMKEETKEGAEAAIRYFWEA +IYYTDQTGETADFDSTYSEYCELCQAVSDSTAQHYKEGGWSTGEHTSIKSLTLTPSEFGY +TATLVRDASAVDVFDSQGVRDDSASGAETHDETWLADVVYEPSKGHWVIDEMQNQQDAQ +>PROKKA_00543 +MSFTAPRRVLRRHRLTQVGALGAGLALLLTACGGGSEPAESSSPAPTGSSSSPAEATTAS +PSAESSPTTSPSGSVGSTAAAGSSGSGGAYVPASAEGPARNVPKPEMPAVTKEETQEGAE +AAVEYFWEAAYYLQQTGDSEYQESVSSPTCKFCDLQRTSMEGHYRDGGWMKVEAVNIASM +VTRPSANGYMSTLLLDMPKEEAFASQGGKAESIGTQPALEESPWIAETSFSEEAGHWVIE +AMIAGGS +>PROKKA_01734 +MTLPAPRRTLRRRRLARTGALSGALLLALTACAGGGADSGASSASTTTTAPAASSTSAAA +SSSTGGASASESDATTSGAAGEYVPASSKGPAQNVPKPVMPAAVKENTPEGAEAAVKYWW +EAVNYLQQTNDPEPLKSISMEECNLCSAHIKTIKRIYGDGGWATGENFAVNSVSMEKKKD +FTLATVAISTDDSATFNADGVKVDQAPADAGTDAPWGVLLKFDSNKGQWVVREAEYDFQE +G +>PROKKA_00984 +MSLTAPGRALRRHRFAQAGTLSVALALALTACGGQSEPAESSTTSPSSAKPAVETSAPAS +TSETAGVSSSPTATESGSGEYVPASADGPARNVPKPEMPAAMKEETKEGAEAAIRYFWEA +IYYTDQTGETADFDSTYSEYCELCQAVSDSTAQHYKEGGWSTGEHTSIKSLTLTPSEFGY +TATLVRDASAVEVFDSQGVRDDSASGVETHDETWLADVVYEPSKGHWVIDEMQNHQDAQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000879.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000879.fa new file mode 100644 index 0000000000000000000000000000000000000000..cfcbb11d7299d837ebcec62e3c2b24a6980ab723 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000879.fa @@ -0,0 +1,65 @@ +>PROKKA_01046 +MSEPKNILLTVDGELREVTHGTTGLDLFREKPTTAVMRVDGLLWDLAREIPAGASVESVD +ITEPEGLEVLRHSTAHVMAQAVQQLRPGAKLGIGPYITDGFYFDFDVDEPFTPEDLKQIS +SLMQKIVKSGQTFRRRVVDEETARAEMAEEPYKLELLGKKDAADTAGEGASVEVGAGEIT +IYDNVDRKTGDAVWCDLCRGPHLPSTKLIGNGFALTRSAAAYWLGNEKNKQLQRIYGTAW +ASKDDLKAYQERLAEAERRDHRKLGAELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSR +RRHTEAGYEFVYTPHITKQHLYEVSGHLDWYADGMFPPMHIDEVRDPETGEITRQGQNYY +LKPMNCPMHNLIYRSRGRSYRELPLRLFEFGSVYRYEKSGVVHGLTRVRGMTQDDAHIYC +TREQMKEELTTTLNFVLDLLKDYGLNDFYLELSTKDPEKFVGSDEIWEEATRTLAEVAEA +SGLQLVPDPGGAAFYGPKISVQARDAIGRTWQMSTIQLDFNLPERFDLEYQAADGTRQRP +VMIHRALFGSIERFLGVLTEHYAGAFPAWLAPEQVVAIPVAEAFNDYLDDVVAKLRAEGI +RARLDDSSDRFPKKIRTAAKEKAPFVLIAGGEDREANAVSFRFRDGTQDNGVPVEEAIER +IVKAVREREVTP +>PROKKA_00759 +MSEPKNILLTVDGELREVTHGTTGLDLFREKPTTAVMRVDGLLWDLAREIPAGASVESVD +ITEPEGLEVLRHSTAHVMAQAVQQLRPGAKLGIGPYITDGFYFDFDVDEPFTPEDLKQIS +SLMQKIVKSGQTFRRRVVDEETARAEMADEPYKLELLGKKDAADTAGEGASVEVGAGEIT +IYDNVDRKTGDAVWCDLCRGPHLPSTKLIGNGFALTRSAAAYWLGNEKNKQLQRIYGTAW +ASKDDLKAYQERLAEAERRDHRKLGAELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSR +RRHTEAGYEFVYTPHITKQHLYEVSGHLDWYADGMFPPMHIDEVRDPETGEITRQGQNYY +LKPMNCPMHNLIYRSRGRSYRELPLRLFEFGSVYRYEKSGVVHGLTRVRGMTQDDAHIYC +TREQMKEELTTTLNFVLDLLKDYGLNDFYLELSTKDPEKFVGSDEIWEEATRTLAEVAEA +SGLQLVPDPGGAAFYGPKISVQARDAIGRTWQMSTIQLDFNLPERFDLEYQAADGTRQRP +VMIHRALFGSIERFLGVLTEHYAGAFPAWLAPEQVVAIPVAEAFNDYLDDVVAKLRAEGI +RARLDDSSDRFPKKIRTAAKEKAPFVLIAGGEDREAGAVSFRFRDGTQDNGVPVEEAIER +IVKAVREREVTP +>PROKKA_01842 +MSEPNNILLTVDGQMREVAHGITGLELFRDQSTTVVMRVDGVLWDLSREIPGGASVESVD +ITEQDGLDVLRHSTAHVMAQAVQQLRPDAKLGIGPYITDGFYFDFDVAEPFTPEDLRTLE +KMMQKIINSGQAFRRRVVTEDEARAEMADEPYKLELLGKKNDAATAGEGASVEVGAGEIT +IYDNVDRKSGDAVWCDLCRGPHLPQTKLISNAFALTRSAAAYWLGNQDNKQLQRIYGTAW +PTKADLKAYQERLAEAERRDHRRLGSELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSR +RRHTEAGYEFVYTPHITKQHLYETSGHLDWYADGMFPPMQIDEQRDPETGEVTRQGQNYY +LKPMNCPMHNLVFRSRGRSYRELPLRLFEFGAVYRYEKSGVVHGLTRVRGMTQDDAHIYC +TREQMKDELTTTLNFVLDLLKDYGLDDFYLELSTRDPEKSVGSDEIWEEATRTLDEVARA +SGLDLVPDPGGAAFYGPKISVQAKDAIGRTWQMSTIQLDFNLPERFDLEYQAPDGSRQRP +VMIHRALFGSIERFLGVLTEHYAGAFPAWLAPEQVVAIPVAEAFADYLGDVVKRLRAEGI +RARLDDSSDRFPKKIRTASKEKVPFVLIAGGEDAEAGAVSFRFRDGSQDNGVPVDEAIER +IVRAVREREATP +>PROKKA_01730 +MSESNPILLTVDGEMREVTHAITGAELFKDQPTTVVMRVDGQLWDLSRELHGGEAVESVD +ITEQDGLNVLRHSTAHVMAQAVQELRPDAKLGIGPFITDGFYFDFDVAEPFTPEDLKQLE +KMMQRIVKSGQTFRRRVVTEDEARAEMADEPYKLELLGKKDDAEAAGEGATVEVGAGEIT +IYDNVDRKSGDAVWCDLCRGPHLPTTKLIGNGFALTRSAAAYWLGNEKNKQLQRIYGTAW +PTKEDLKAYQERLAEAERRDHRKLGAELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSR +KRHAAAGYEFVYTPHITKQHLYEVSGHLDWYADGMFPPMQIDEVRDPETGQITKQGQNYY +LKPMNCPMHNLIYRSRGRSYRELPLRLFEFGSVYRYEKSGVVHGLTRVRGMTQDDAHIYC +TREQMKDELTTTLNFVLDLLKDYGLDDFYLELSTKDPEKFVGSDEIWEEATRTLAEVAEA +SGLELVPDPAGAAFYGPKISVQARDAIGRTWQMSTIQLDFNLPERFDLEYQAADGSRQRP +VMIHRALFGSIERFLGVLTEHYAGAFPAWLAPEQVVAIPVAEAFNDYLADVVATLKAEGI +RVRLDESSDRFPKKIRTASKEKVPFVLIAGGEDAEAGAVSFRYRDGSQDNGVPVDEAVAR +IVKAVREREVTP +>PROKKA_00987 +MSEPKNILLTVDGELREVTHGTTGLDLFREKPTTAVMRVDGLLWDLAREIPAGASVEAVD +ITEPEGLEVLRHSTAHVMAQAVQQLRPGAKLGIGPYITDGFYFDFDVDEPFTPEDLKQIS +SLMQKIVKSGQTFRRRVVDEETARAEMADEPYKLELLGKKDAADTAGEGASVEVGAGEIT +IYDNVDRKTGDAVWCDLCRGPHLPSTKLIGNGFALTRSAAAYWLGNEKNKQLQRIYGTAW +ASKDDLKAYQERLAEAERRDHRKLGAELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSR +RRHTEAGYEFVYTPHITKQHLYEVSGHLDWYADGMFPPMHIDEVRDPETGEITRQGQNYY +LKPMNCPMHNLIYRSRGRSYRELPLRLFEFGSVYRYEKSGVVHGLTRVRGMTQDDAHIYC +TREQMKEELTTTLNFVLDLLKDYGLNDFYLELSTKDPEKFVGSDEIWEEATRTLAEVAEA +SGLQLVPDPGGAAFYGPKISVQARDAIGRTWQMSTIQLDFNLPERFDLEYQAADGTRQRP +VMIHRALFGSIERFLGVLTEHYAGAFPAWLAPEQVVAIPVAEAFNDYLDDVVAKLRAEGI +RARLDDSSDRFPKKIRTAAKEKAPFVLIAGGEDREANAVSFRFRDGTQDNGVPVEEAIER +IVKAVREREVTP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000881.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000881.fa new file mode 100644 index 0000000000000000000000000000000000000000..c50ed604e872126722f023168dff9ced304c96ef --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000881.fa @@ -0,0 +1,25 @@ +>PROKKA_01048 +MLDRHARDLTTRLFTPVAHTLLRAGVSPDTVTVVGTLGVSLGALVLFPLGHLFWGTLFIT +AFVFSDLVDGIMAREAGSTGRWGAFLDSTLDRVQDAAVFLGLCLWGFGVGAAPAVGALSG +ACLALGMLVSYVRAKAEALGWSAHVGIAERAERLVAALVVAGLTGLGLPPVVLAVTLGLL +AAASLVTVGQRMAAVRRQARDDA +>PROKKA_00761 +MLDRHARGVTTRLFTPVARTLLRAGVSPDTVTVVGTLGVSLGALVLFPLGHLFWGTLFIT +AFVFSDLVDGIMAREAGSTGRWGAFLDSTLDRVQDAAVFLGLCLWGFGVGAAPAVGALSG +ACLALGMLVSYVRAKAEALGWDAHVGIAERAERLVATLVVAGLTGLGLPPVVLAVTLGLL +AAASLVTVGQRMVAVRRQARDDA +>PROKKA_01840 +MLDRHARGATTRVFTPVARALLRAGVSPDAVTVVGTLGVSLGALVLFPLGELFWGTLFIT +AFVFSDLVDGIMAREAGTTGRWGAFLDSTLDRVQDAAVFLGLSLWGFGVGGEPAVGTLAA +VCLALGMLVSYVRAKAEALGLTANVGIAERAERLVAALVLAGLTGLGLPPAFLAATLGLL +AAASLVTVGQRVAAVRSQTRRAA +>PROKKA_01728 +MLDRRARGTTTALFTPLARRLLRAGVTPDAVTVAGTVGVSAAALLLYPAGHLFWGTIVIT +LFVFSDVLDGVMAREAGTTGPWGSFLDSTLDRVQDAAIFLALSWWGFGVGAHPAVGVLAG +VCLALGMLVSYARAKAESLGFTAAGGIAERAERLIVTLVFAGLTGLGLPSAVLTAVLGLL +ALASLITVAQRVAGVRRQSRTA +>PROKKA_00989 +MLDRHARGVTTRLFTPVARTLLRAGVSPDTVTVVGTLGVSLGALVLFPLGHLFWGTLFIT +AFVFSDLVDGIMAREAGSTGRWGAFLDSTLDRVQDAAVFLGLCLWGFGVGAAPAVGALSG +ACLALGMLVSYVRAKAEALGWDAHVGIAERAERLVATLVVAGLTGLGLPPVVLAVTLGLL +AAASLVTVGQRMAVVRRQARDDV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000884.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000884.fa new file mode 100644 index 0000000000000000000000000000000000000000..f5c18039f49e3b10900d613002f6e4b0a5dbc38c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000884.fa @@ -0,0 +1,30 @@ +>PROKKA_01051 +MTDTAAKFSEYAHPEKLVSTQWVADHVGDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE +LNDPVTRDFVGPEAFAEFAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD +GGRDKWIAEGRETTREVPTVARAEYPVIERDDHTERAAREDVLQAIGTTPLIDVRSRPEY +TGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRAGAGLQEGDD +VIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR +>PROKKA_00764 +MTDTAAKFSEYAHPEKLVSTQWVADHVDDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE +LNDPVTRDFVGPEAFAEVAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD +GGRDKWIAEGRETTREVPTVARAEYPVIERDDHTERAAREDVLQAIGTTPLIDVRSRPEY +TGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRTDAGLREGDD +VIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR +>PROKKA_01835 +MTETATEFSQYAHPEKLVSTQWVADHVGEEGVVVLESNEDALLYATGHIPGAQRIDWHTE +LNDPVTRDFIGPEAFAEMAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDVRLMN +GGRDKWIAEGRETTREVPTVARGEYPVVPRDDTTERAAREDVLQAVGTTPLIDVRSRPEY +TGETTHMDGYPQEGTLRGGHIPTAASVPWAQAANEDGTFKSREELEAVYRDGAGLKDGDD +VIAYCRIGERSSHTWFVLKHLLGHENVRNYDGSWTEWGNSVRLPIVVGEEPGAAPAR +>PROKKA_01725 +MTETPAEFAEYAHPEKLVSTQWVADHIDDEGVVVLESNEDTLLYSTGHIPGAVKIDWHTE +LNDPVSRDFVGPEAFAELVASKGIGPDTTVVFYGDKSNWWAAYALWVFTLYGHRDVRLMN +GGRDKWIAEGRPTTREVPEVTPAPSYPVSQRDDATDRAAREDVLAAIGSTPLVDVRSPKE +YTGETTHMDGYPQEGTLRGGHIPTAASVPWAKAANEDGTFKSRAELEEIYKEGAGLGESD +SVIAYCRIGERSSHTWFVLKQLLGYENVRNYDGSWTEWGNGVRLPIALGDEPGEAPAR +>PROKKA_00992 +MTDTAAKFSEYAHPEKLVSTQWVADHVGDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE +LNDPVTRDFVGPEAFAEFAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD +GGRDKWIAEGRETTREVPTVARAEYPVIERDDHTDRAAREDVLQAIGTTPLIDVRSRPEY +TGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRAGAGLQEGDD +VIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000886.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000886.fa new file mode 100644 index 0000000000000000000000000000000000000000..85891a965916c7da490448084cc35a1b1fae1ee8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000886.fa @@ -0,0 +1,34 @@ +>PROKKA_01057 +MYARSLSGLPEVPSITTVIGMEKTDLDGWVGWMAAQSVTQDPRLAESVGSAARLKQVARQ +SADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTMAEARARLIEHGEGAYADRFDEWW +DLYDVRPIAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTGRDGRVKALDPKVVM +QLTAGLKAEESLVDPEAGTWEEWRHGQAEMLLGVALGETEVAVHQANPGVLPRHWHKFWA +LRQVWKHAQAVDDAGPALRVIGPPPPSVPVSAATGLQAVRAAAFGGGSHAAPAVAPDGLS +SRPASAEGGDRVTA +>PROKKA_00776 +MYARSLSGLPEVPSITTVIGMEKTDLDGWVGWMAAQSVTQDPRLAESVGSAARLKQVARQ +SADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTMAEARARLIEHGEGAYADRFDEWW +DLYDVRPIAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTGRDGRVKALDPKVVM +QLTAGLKAEESLVDPEAGTWEEWRHGQAEMLLGVALGETEVAVHQANPGVLPRHWHKFWA +LRQVWKHAQAVDDAGPALRVIGPPPPSVPVSAATGLQAVRAAAFGGGSHAAPAVAPDGSS +SRPASAEGGDRVTA +>PROKKA_01829 +MTQPRLAHQTPLGRMYARSLTGLPEVPSITTVIGMERTDLDGWIGWMAAQSVTQDPRLAE +SVGSAARLKQVARQSADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTLAETRAKLIE +HGEGAYADRFDEWWDLYDVRPLAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTG +RDGRVKALDPKVVMQLTAGLKAEESLVDAEAGTWEEWRHGQAEMLLGVALGETEVAVHQA +NPGVLPRHWHKFWALRQVWKHAQAADDAGPALRVIGPPPPSVPLHRG +>PROKKA_01719 +MYARSLSGLPEVPSITTVIGMERTDLDGWVGWMAANAVAQDPRLGESLGSPARLRQVAKQ +SADAAARYRDAAAERGDRVHDYAEQVALRALGRPHTMAASREELQRHGEGAYADRFDEWW +DLYDVQPVAAEITVWNHSVGYAGTLDLVARIGGRLCLIDYKTKGTGRDGRVKALDPKVVM +QLTAGLKAEESLVDAEAGTWEPWAHGGAEMLLGVALGETEVAVHQANNAALPRHWHKFWA +LRQVWKHALAVDDAGPALRVIGPPPVSVPGAAGGLSAARAAAFGAPPAVAHDPGTSAPAD +RLQP +>PROKKA_01004 +MYARSLSGLPEVPSITTVIGMEKTDLDGWVGWMAAQSVTQDPRLAESVGSAARLKQVARQ +SADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTMAEARARLIEHGEGAYADRFDEWW +DLYDVRPIAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTGRDGRVKALDPKVVM +QLTAGLKAEESLVDPEAGTWEEWRHGQAEMLLGVALGETEVAVHQANPGVLPRHWHKFWA +LRQVWKHAQAVDDAGPALRVIGPPPPSVPASAATGLQAVRAAAFGGGSHAAPDVAPDGSS +SRPASAAEGGDRVTA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000887.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000887.fa new file mode 100644 index 0000000000000000000000000000000000000000..dfcb05db608c0e1d29c6513479d74bf2ac713fe5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000887.fa @@ -0,0 +1,25 @@ +>PROKKA_01058 +MTVLPVRTIPDPVLRTAASPVPAGADVRALVADMIETMHAVGGVGLAAPQVGVGLRVFVF +DVAGVAGHVVNPVLETAGQALREPGEGCLSVPGLRYHPARAAEAVVRGTDVDGNPVEHRG +TGLLARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRAARRIGAARAAAVSSVF +GAPGAPAAGTGAAR +>PROKKA_00777 +MTVLPVRTIPDPVLRTAASPVPAGADVRALVADMIETMHAVGGVGLAAPQVGVGLRVFVF +DVAGVAGHVVNPVLETAGQALREPGEGCLSVPGLRYHPARAAEAVVRGTDVDGNPVEHRG +TGLLARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRAARRIGAARAAAVSSVF +GAPAVPAAGTGAAR +>PROKKA_01828 +MSVLPVRTVPDPVLRTPARPVPAGMDVRALVADMVETMHAVGGVGLAAPQVGVGLRVFVF +DVQGVAGHVVNPVLETGEETVREPGEGCLSVPGLRYHPARAAEAVVRGVNVDGHPVEHRG +TGLVARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRTARRVGAERAAAVGSVF +AAPAAPPTPARAPRGGTR +>PROKKA_01718 +MTVLTLRTVPDPVLRTPAAPVAAGQDVRALVEDMVETMHAVGGVGLAAPQVGVGLRVFVF +DCAGASGHVLNPVLETFGSPVREPGEGCLSVPGLRYHPARAERAVVRGVDVDGNPVEHRG +EGLLARCLQHETDHLDGILYVDRLDGDDRREARRRLRADAPDPEAERIRARRDALAGSVF +GARPSVSPSAARTTPRRGAQ +>PROKKA_01005 +MTVLPVRTVPDPVLRTAASPVPAGADVRALVADMIATMHAVGGVGLAAPQVGVGLRVFVF +DVAGVAGHVVNPVLETAGQALREPGEGCLSVPGLRYHPTRAAEAVVRGTDVDGNPVEHRG +TGLLARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRAARRIGAARAAAVSSVF +GAPAVPAAGTGAAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000890.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000890.fa new file mode 100644 index 0000000000000000000000000000000000000000..4e833bd484c3e4f32a0a3b0a9662cdb50e647f52 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000890.fa @@ -0,0 +1,25 @@ +>PROKKA_01061 +MTARPPRLHPSILSADFARLADDLARIPSADAVHVDVMDNHFVPNLTLGLPVVEAIRRAT +DLPLDLHLMIEDADRWAPGYAEAGAESVTFHAEASAAPVRLARELRAAGAKAGMALRPAT +AVEPYLDMLPELDMLLLMTVEPGFGGQAFLDVVLPKIRRARRALDGGPAPLALQVDGGVN +RETIERAAEAGADVFVAGSAVFGAEDPDAALAGLRTAAARACH +>PROKKA_00780 +MTARPPRLHPSILSADFARLADDLARIPSADAVHVDVMDNHFVPNLTLGLPVVEAIRRAT +DLPLDLHLMIEDADRWAPGYAEAGAESVTFHAEASAAPVRLARELRAAGAKAGMALRPAT +AVEPYLDMLPELDMLLLMTVEPGFGGQAFLDVVLPKIRRARRALDGGPAPLALQVDGGVN +RETIERAAEAGADVFVAGSAVFGAADPDAALVGLRTAAARACH +>PROKKA_01825 +MSPRAPRLHPSILSADFAHLAEELGRIRGADAVHVDVMDNHFVPNLTLGLPVVEAIRRAT +DLPLDIHLMIEDADRWAPGYAEAGAESVTFHAEASAAPVRLARELRAAGARAGMALKPAT +PVEPYLDMLPELDMLLLMTVEPGFGGQAFLDVVLPKIRRARRALDGAAAPLALQVDGGVN +AETIERAAEAGADVFVAGSAVFGAEDPDAAVDGLRRAAARACC +>PROKKA_01715 +MSAHPCIHPSILSADFARLADELARIPGSDAVHVDVMDGHFVPNLTLGLPVVEAIRAATD +LPLDIHLMIEDADRWAPAYADAGAESVTFHAEAARAPIVLARSLRAAGAQAGLAVRPATP +IEPYLDLLPELDMLLIMTVEPGFGGQSFLDVTLPKIRRARQALDGAPVPVRLQVDGGVNR +ETILRAAEAGADVFVAGSAVFGADDPGAAIAGLRDLAAGVAPACHTR +>PROKKA_01008 +MTARALRLHPSILSADFARLADELARIPSADAVHVDVMDNHFVPNLTLGLPVVEAIRRAT +DLPLDLHLMIEDADRWAPGYAEAGAESVTFHAEASAAPVRLARELRAAGAKAGMALRPAT +AVEPYLDMLPELDMLLLMTVEPGFGGQAFLDVVLPKIRRARRALDGGPAPLALQVDGGVN +RETIERAAEAGADVFVAGSAVFGAEDPDAALAGLRTAAARACH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000891.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000891.fa new file mode 100644 index 0000000000000000000000000000000000000000..c58977c6d29003f013e287e0884938c01d887418 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000891.fa @@ -0,0 +1,25 @@ +>PROKKA_01062 +MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARRVWAWPVGILGNLILLTVFL +ASLFTGADHATLLGQAGRQVMFIAVSVYGWARWRQARRGHAEDAPAITPEWAGWRGRVFL +VTAMAVGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV +PLLWSTGYYASAVMYAFYGAFTLIGFFVWLRATDRDKPAVETLLPDGPEGDVAR +>PROKKA_00781 +MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARRVWAWPVGILGNLILLTVFL +ASLFTGADHATLLGQAGRQVMFIAVSVYGWARWRRARRGHAEDAPAITPEWAGWRGRVFL +VTAMAVGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV +PLLWSTGYYASAVMYAFYGAFTLIGFFVWLRATDRDKPAVETLLPDGPEGDVAR +>PROKKA_01824 +MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARKVWAWPVGILGNLILLTVFL +ASLFTGADHATLLGQAGRQVMFIAVSVYGWVRWNEARRGRSEHATAITPEWAGLGGRAFL +VLGMLIGTLALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLVWVAVDVVGV +PLLWSTGYYASAVMYAFYGAFTLVGFFVWLRAKDRDKPAVETLLPDGPEEHAAR +>PROKKA_01714 +MQWLVDVFNWTIPVAGGGLLMREVVGNVFGLASALGGMARKVWAWPVGILGNLLLLTVFL +ASLFNDAPHATLLGQAGRQVMFIAVSVYGWKRWRDAQRGRADHAPAITPEWAGWGNRAFL +AVALVLGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV +PLLWSSGYYASAVMYAFYGVFTLTGFFVWMRARDRDKPAVETLLPDGPAPEEAAR +>PROKKA_01009 +MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARRVWAWPVGILGNLILLTVFL +ASLFTGADHATLLGQAGRQVMFIAVSVYGWVRWRQARRGHAEDAPAITPEWAGWRGRVFL +VTAMAVGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV +PLLWSTGYYASAVMYAFYGAFTLIGFFVWLRATDRDKPAVETLLPDGPEGDVAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000892.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000892.fa new file mode 100644 index 0000000000000000000000000000000000000000..a606efe931ff35edd52d95ac50cf9c039ed95011 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000892.fa @@ -0,0 +1,43 @@ +>PROKKA_01063 +MNAAETPSADPMDLAVGAALRGVRGANPLVGAVLTDAAGRILAVGHHRGRGTAHAEVDAL +TRWRAARAADPALATLDPAGLTLHVTLEPCDHTGSTGPCSQAVLDAGIGALRYAVADPTG +HDGGGAARLAAHGVHVTGPTGEAAALTLTARWREVRDAGRPWVTGHLAQSLDGHAAAADG +TSQWITGPDSRVHAHEVRSRVDAIVVGTGTVLADDPRLTARDAAGAELAHQPVPVVQGHR +PVPDGAALRTHPVLLHVPDHDPHAVLAALAAHPGPWPHGRRAEHVLIEGGPRVLGAWLRA +GLVDELMVYTAPLLLGPGRAAVAGLDVATLSEGPRWHPDPAEGGPARALGVDVWTHLSPV +PAPRLPTAPAPTRFQED +>PROKKA_00782 +MSAAETPSADPMDLAVRAALRGVRGANPLVGAVLTDEAGRVLAVGHHRGRGTAHAEVDAL +TRWRAARATDPALAALDPAGLTLHVTLEPCNHTGSTGPCSQAVLDAGVGALRYAVADPTG +HDGGGAARLAAHGVRVTGPTGEVAALALTARWREARDAGRPWVTGHLAQSLDGHAAAADG +TSQWITGPDSRVHAHEVRSRVDAIVVGTGTVLADDPRLTARDAAGAELAHQPVPVVQGHR +PVPDGAALRAHPVLLHVPDHDPHAVLAALAAHPGPWPHGRRAEHVLIEGGPRVLGAWLRA +GLVDELMVYTAPLLLGPGRAAVAGLDVATLSEGPRWHPDPAEGGPARALGDDVWTHLSPV +PAPRLPTAPAPTRFQED +>PROKKA_01823 +MSGAPDPMALAVGAALRGVRGANPLVGAVLTDDAGRVLAAGHHRGRGTAHAEVDALARWE +AARAADPALAALDPAGLTLHVTLEPCDHTGSTGPCSGAILASGVGAVRYAVADPTGVDGG +GAARLAAHGVRVSGPTGEPAALALTERWRRARDAGRPWITGHLAQSLDGHAAAADGTSRW +ITGAASRAHAHRVRARVDAIVVGTGTVLADDPRLTVRDAAGAETGPQPVPVVQGRTPIPA +GAALRARPETLHVPAHEPEAVLAALAARPGPWPHGGARPGHVLIEGGPRVLGAWIRAGLV +DELMVYTAPLLLGAGRPAVAGLDVGTLADGLRWHPDPAEDGPVRALGEDVWTHLAPVPAP +APEGPDPQEDCMFTGIVTHLGTVLALEPDPAADTARLVLDAGGALEGLPAGGSLAVDGVC +LTALDGPGAEPGVFRADLMGQTLRMTSLGGRTPGDRVNLERCLRPTDHLDGHVVQGHVDG +VGEVLSVTPQGAWTTVRIGLPAALARYVPAQGAIALQGVSLTVSAVSEPGADAHWFEVGL +IPATLEATTLGALRPGDRVNLETDVLARYAERLALLPAAPAASPSAAPAEEVRP +>PROKKA_01713 +MSAPAARHDDAGRPAEPLDLAAAAALAGVRGANPLVGAVITGPDGAVLAVGHHRGRGTAH +AEVDALNRWAAARAADPSLHVDPAACTIHVTLEPCDHTGSTGPCAGAILDAGLGAVRYAV +ADATGTAGGGAARLTRAGLRVEGPTGHAASAALTARWRRVRDAGRPWITVHLAQSLDGRA +AAADGTSRWITGPASRAHAHAVRARVDAVVCGTGTVAADDPRLTARDAAGEQLPVQPVPV +VMGERDLPAGAALAARADLIHVRSHDPRAVLAALASRPGPWPHGGSRPGHVLIEGGPHVL +GAWLAAGLVDEVFAYTAPVLLGDGLPGVAGLDVPTLAAGHRWAPDPAEDGPVRALGDDVL +THLAPVTDPAD +>PROKKA_01010 +MNAAETPSADPMDLAVRAALRGVRGANPLVGAVLTDEAGRVLAVGHHRGRGTAHAEVDAL +TRWRAARATDPALAALDPAGLTLHVTLEPCDHTGSTGPCSQAVLDAGIGALRYAVADPTG +HDGGGAARLAAHGVHVTGPTGEAAALTLTARWREVRDAGRPWVTGHLAQSLDGHAAAADG +TSQWITGPDSRVHAHEVRSRVDAIVVGTGTVLADDPRLTARDAVGAELAHQPVPVVQGHR +PVPDGAVLRTHPVVLEVLDHDPHAVLAALAAHPGPWPHGRRAEHVLIEGGPRVLGAWLRA +GLVDELMVYTAPLLLGPGRAAVAGLDVATLSEGLRWHPDPAEGGPVRALGVDVWTHLSPV +PAPRLPTAPAPTRFQED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000893.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000893.fa new file mode 100644 index 0000000000000000000000000000000000000000..1aa205a9ce78a116f447bf1bcaf35f85332c6415 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000893.fa @@ -0,0 +1,20 @@ +>PROKKA_01066 +MSGAGAPTFTPDPAAASGLNVAIVAAQWHTEIMDGLIAGAQAAAADLGLEPVLVRVPGTV +ELTVAAARLAERFDVVVVLGVVVRGDTPHFDYVCQSVTQGVTEVSVRTGVPVGFGVLTVD +TEQQARDRAGLPGSREDKGREALEAAVLTELALRSVTPRD +>PROKKA_00785 +MSGAGAPTFTPDPAAASGLNVAIVAAQWHTEIMDGLIAGAQAAAADLGLEPVLVRVPGTV +ELTVAAARLAERFDVVVVLGVVVRGDTPHFDYVCQSVTQGVTEVSVRTGVPVGFGVLTVD +TDQQARDRAGLPGSREDKGREALEAAVLTELALRSVTPRD +>PROKKA_01821 +MAVVAAQWHTEIMDGLIAGARAAAADLGLEPVLVRVPGTVELSVAAARLAEDFDAVVVLG +VVVRGDTPHFDYVCQAVTQGVTEVSVRTGTPVGFGVLTVDTEQQARDRAGLPGSREDKGR +ESLEAAVLTELALRDVQA +>PROKKA_01710 +MSGAGAPTLALTTLTDADRAAAGSLRVAVVAAQWHTEIMDGLIAGSRAAAADLGIDVDLV +RVPGTVELSVAAARLAATHDVVVVLGVVVRGGTPHFDYVCQSVTQGVTEVSVRTGVPVGF +GVLTVDTVEQARDRAGLPGSQEDKGREALEAAVLTELALRAALG +>PROKKA_01013 +MSGAGAPTFTPDPAAASGLNVAIVAAQWHTEIMDGLIAGAQAAAADLGLEPVLVRVPGTV +ELTVAAARLAERFDVVVVLGVVVRGDTPHFDYVCQSVTQGVTEVSVRTGVPVGFGVLTVD +TDQQARDRAGLPGSREDKGREALEAAVLTELALRSVTPRD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000894.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000894.fa new file mode 100644 index 0000000000000000000000000000000000000000..c217e64d1f4a4dbc154a41e2d30a3a7f0bbd78d2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000894.fa @@ -0,0 +1,15 @@ +>PROKKA_01078 +MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE +EISQLLYHVQTMMIARGISLEDVYRHL +>PROKKA_00797 +MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE +EISQLLYHVQTMMIARGISLEDVYRHL +>PROKKA_01820 +MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE +EISQLLYHVQTMMIARGIALEDVYRHL +>PROKKA_01707 +MKTFEELFAELTRKVAERPEGSGTVAQIDAGVHAIGKKIVEEAAEVWMAAEYESHDAAAE +EISQLLYHVQTMMIAKGIGLKDVYRHL +>PROKKA_01027 +MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE +EISQLLYHVQTMMIARGISLEDVYRHL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000895.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000895.fa new file mode 100644 index 0000000000000000000000000000000000000000..471e6bd358676e35e3998259e0cbd0b39698ad8e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000895.fa @@ -0,0 +1,30 @@ +>PROKKA_01079 +MLRIAVPNKGALSESAREILTEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG +TLDVGLTGRDLFCDAQVGDTAEEIMALGFGRSVFRLAAPVGSFTSAEQLAGKRIATSYDG +LLSDYLARTGLDATVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMEVFGEPILDSE +AVLIGRAGERPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEAATAVTPGLESPTVSPL +RDETMVAVRSMVRKPDANRVMDELYALGARGILISAIHAIRL +>PROKKA_00798 +MLRIAVPNKGALSESAREILTEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG +TLDVGLTGRDLFCDAQVGDTAEEIMALGFGRSVFRLAAPVGSFTSAEQLAGKRIATSYDG +LLSDYLARTGLDATVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMEVFGEPILDSE +AVLIGRAGERPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEAATAVTPGLESPTVSPL +RDETMVAVRSMVRKPDANRVMDELYALGARGILISAIHAIRL +>PROKKA_01819 +MLRIAVPNKGALAEAAREILQEAGYRQRRDSRELVLVDPENQVEFFYLRPRDIAVYVGQG +TLDVGLTGRDLFRDAQVDGGAEEIMALGFGRSVFRLAAPVGAFSSEAELSGKRIATSYDG +LLSAYLERTGLDAEVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMETFGESILDSE +AVMIARVGARPEGLDVLLRRLKGVLVARRWVMIDYDVRRELLEQATAVTPGLESPTISPL +RDESMVAVRSMVRKADANRAMDDLYALGARGILISAIHAIRL +>PROKKA_01706 +MLRIAVPNKGALSESAREILIEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG +TLDVGLTGRDLFRDARVGETAEEIMALGFGKSVFRLAAPVGSFTSAEELAGRRIATSYDG +LLTEYLAESGLDARVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMETFGEPILDSE +AIMIARVGARPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEQATAVTPGLESPTVSPL +RDESMVAVRSMVRKADANRAMDDLYDLGARGILISAIHAIRL +>PROKKA_01028 +MLRIAVPNKGALSESAREILTEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG +TLDVGLTGRDLFCDAQVGDTAEEIMALGFGRSVFRLAAPVGSFTSAEQLAGKRIATSYDG +LLSDYLARTGLDATVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMEVFGEPILDSE +AVLIGRAGERPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEAATAVTPGLESPTVSPL +RDETMVAVRSMVRKPDANRVMDELYALGARGILISAIHAIRL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000897.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000897.fa new file mode 100644 index 0000000000000000000000000000000000000000..6d8f3727ea4ecb1fc5415a0c70fa08baf8d2bf71 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000897.fa @@ -0,0 +1,20 @@ +>PROKKA_01081 +MSISPPDDLVASVTFDDRGLVPAIAQQEGTGEVLMMAWMNEESLRATLETGWATYWSRSR +GELWRKGETSGHLQRVRAVHADCDGDTLLLTVDQTGPACHTGTRTCFTGRELVMPPAAVD +PEEAAR +>PROKKA_00800 +MSISPPDDLVASVTFDDRGLVPAIAQQEGTGEVLMMAWMNAESLRATLETGWATYWSRSR +GELWRKGETSGHLQRVRAVHADCDGDTLLLTVDQTGPACHTGTRTCFTGRELVMPPAAVD +PEEAAR +>PROKKA_01816 +MSISSHHDLVASLAFDDRGLVPAIAQQEGTGEVLMMAWMNAESLRLTLETGWATYWSRSR +GELWRKGETSGHLQRVLAVHADCDADTLLLTVDQTGPACHTGTRSCFTDRLLAEPAAPAG +DQAEGAGR +>PROKKA_01704 +MSPSDVVADLPPLIFDERGLIPAIAQQHDSGEVLMMAWMNEESLRRTLEDGWATYWSRSR +QEYWRKGETSGHLQRVLAVAADCDGDTLLLTVDQTGPACHTGTTSCFTDRRFAAPTAADE +DPQTEDAEAVR +>PROKKA_01030 +MSISPPDDLVASVTFDDRGLVPAIAQQEGTGEVLMMAWMNAESLRATLETGWATYWSRSR +GELWRKGETSGHLQRVRAVHADCDGDTLLLTVDQTGPACHTGTRTCFTGRELVMPPAAVD +PEEAAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000899.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000899.fa new file mode 100644 index 0000000000000000000000000000000000000000..0e809f272ba4f1ab2c40a12af04f1f36623514de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000899.fa @@ -0,0 +1,25 @@ +>PROKKA_01083 +MRRRTVVLAALAAGALVLLTAGRTWVTATGLSGGIASEATTSGGAAAPVATAMALVVMAG +ALALTTARRLGAVIVGVLMALAGVVIASTSVTAALDPATTAAAAVADATGTTALAQDYAV +TAWPWVAAAGGVLAALCGVVAALAGRGWRSSRRYEKAPAASEPGPAAAGEQPAQSAREAA +QRRRVDQMDAWDELSRGNDPT +>PROKKA_00802 +MRRRTVVLAALAAGGLVLLTAGRTWVTATGLSGGIASEATTSGGAAAPVATAMALVVMAG +ALALTTARRLGAVIVGVLMALAGVVIASTSVTAALDPATTAAAAVADATGTTALAQDYAV +TAWPWVAAAGGVLAALCGVVAALAGRGWRSSRRYEKAPAASEPGPAAAGEQPAQSAREAA +QRRRVDQMDAWDELSRGNDPT +>PROKKA_01814 +MRRRTVVLAALAAGSLVLLAAGQTWVVGSGLTGGLSEEATTSGGAAAPGATAMALVVLAG +ALALTTARRVGVVVVGALLVLAGIVIVTGAAGAALDPAGTAASAVAEATGTTAAAGSYAV +TAWPWVAVTGGVLAALCGAVAALAGRGWVSVRRYEKAEATDAAEPAAPGRAAAPGRTEAE +RRRTEQMDAWDELSRGNDPT +>PROKKA_01702 +MRRRWIVLAALLAGVLVLAATGQTWVTASGLEGSPVPQATAGGGRVAPVATALALVVMAG +ALALTTARRVGVVLVGVLMTLAGVVIASTAVTAALDPVAAAAGAVSELTGTTAPAAAYAV +SAWPWVSAAGGVMAAVLGVATLVVGPRWAASRRFESPATADEPAAAAPPSRHVDRMDAWD +ELSRGEDPT +>PROKKA_01032 +MRRRTVVLAALAAGGLVLLTAGRTWVTATGLSGGIASEATTSGGAAAPVATAMALVVMAG +ALALTTARRLGAVIVGVLMALAGVVIASTSVTAALDPATTAAAAVADATGTTALAQDYAV +TAWPWVAAAGGVLAALCGVVAALAGRGWRSSRRYEKAPAASEPGPAAAGEQPAQSAREAA +QRRRVDQMDAWDELSRGNDPT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000902.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000902.fa new file mode 100644 index 0000000000000000000000000000000000000000..d5f1b6dca9c1c14c25483dd607ce23188329cf51 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000902.fa @@ -0,0 +1,45 @@ +>PROKKA_01086 +MSADRPSTEPAIEFEGPYQGQAGPYFGDYGGQWMPESLMAALQELTRTYEEARQDPAFEA +ELRTLFRDYVNRPSLLSEVPRFAADTPGVRIFLKREDLNHTGSHKINNVIGQALLARRMG +KTRLIAETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVVPVAIG +ARTLKDAINEALRDWVASVDTTHYLMGTVTGPHPFPAMVRYFHSVIGEEAREQILAQAGR +LPDAVAACVGGGSNAMGLFHGFLDDPGVELYGFEAGGEGLETGRHAASITLGRTGVLHGA +RTYLMQDEDGQTIDSHSISAGLDYPAVGPEHAFLHDTGRAVYEPVSDTECMDAFLRLTRT +EGITPAIESAHALAGALRLARRWADEGLVGPDAPEGQERIIIVNLSGRGDKDVATAAAWF +GLGTATEEKDPLEEMTPGEEQ +>PROKKA_00805 +MSADRPSTEPAIEFEGPYQGQAGPYFGDYGGQWMPESLMAALQELTRTYEQARQDPAFEA +ELRTLFRDYVNRPSLLSEVPRFAADTPGVRIFLKREDLNHTGSHKINNVIGQALLARRMG +KTRLIAETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVVPVAIG +ARTLKDAINEALRDWVASVDNTHYLMGTVTGPHPFPAMVRYFHSVIGEEAREQILAQAGR +LPDAVAACVGGGSNAMGLFHGFLDDPEVELYGFEAGGEGLETGRHAASITLGRTGVLHGA +RTYLMQDEDGQTIDSHSISAGLDYPAVGPEHAFLHDTGRAVYEPVSDTECMDAFLRLTRT +EGITPAIESAHALAGALRLARRWADEGLVGPDAPEGEERIIIVNLSGRGDKDVATAAAWF +GLGTAAEEKDPLEEMTPGEEQ +>PROKKA_01811 +MSADRPSTEPTVEFEGPYQGQSGPYFGDYGGQWMPESLMAALQEVQRTYEEARQDPAFEG +ELRTLFRDYVNRPSLLSDVPRFAADSPGVRIMLKREDLNHTGSHKINNVIGQALLARRMG +KTRLIAETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVVPVAIG +ARTLKDAINEALRDWVASVDTTHYLLGTVTGPHPFPAMVRYFHSVIGEEARQQVLAQTGR +LPHAVAACVGGGSNAMGLFHGFLDDPEVELYGFEAGGDGLETGRHAASITLGRTGVLHGA +RTYLMQDEDGQTIDSHSISAGLDYPAVGPEHAFLNDTGRAVYEPVTDTECMDAFLRLTRT +EGITPAIESAHALAGALRLARRWADEGLVGPDTPEGEERIIVVNLSGRGDKDVATAAAWF +GLGQADAEKDPLEELTPGEEQ +>PROKKA_01699 +MTSTESVDVAGPFQDQPGPYFGRYGGQWMPESLMAALKEVADTYEAARQDPEFLAELEDL +YANYVNRPSLLTEAPRFAAEVPGVRIFLKREDLNHTGSHKINNVIGQALLARRMGKTRLI +AETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVIPVTIGARTLK +DAINEALRDWVASVDTTHYLMGTVTGPHPFPAMVRYFHSVIGEEAREQILAQTGRLPDAV +AACVGGGSNAMGLFHGFLDDPEVELYGFEAGGDGVETGRHAASITLGRTGVLHGARTYLM +QDEDGQTIDSHSISAGLDYPAVGPEHAFLNDTGRATYEPVTDTECMDALLRLTRTEGITP +AIESAHALAGALRLARRWRDEGLVGEGTPEGEERIIIVNLSGRGDKDVATAAAWFGLGEA +DEQKDPLEEMTPGEEQ +>PROKKA_01035 +MSADRPSTEPAIEFEGPYQGQAGPYFGDYGGQWMPESLMAALQELTRTYEQARQDPAFEA +ELRTLFRDYVNRPSLLSEVPRFAADTPGVRIFLKREDLNHTGSHKINNVIGQALLARRMG +KTRLIAETGAGQHGVATATAAALFGMECTVYMGEEDTRRQALNVARMQMLGAEVIPVAIG +ARTLKDAINEALRDWVASVDNTHYLMGTVTGPHPFPAMVRYFHSVIGEEAREQILAQAGR +LPDAVAACVGGGSNAMGLFHGFLDDPEVELYGFEAGGEGLETGRHAASITLGRTGVLHGA +RTYLMQDEDGQTIDSHSISAGLDYPAVGPEHAFLHDTGRAVYEPVSDTECMDAFLRLTRT +EGITPAIESAHALAGALRLARRWADEGLVGPDAPEGQERIIIVNLSGRGDKDVATAAAWF +GLGTAAEEKDPLEEMTPGEEQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000906.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000906.fa new file mode 100644 index 0000000000000000000000000000000000000000..2c06556dfcb1d5a110762b87b2d31c0fd810e33b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000906.fa @@ -0,0 +1,50 @@ +>PROKKA_01090 +MADPRGFLKNRERVDRPTRPVPVRIMDFKDVYVRQDEAIVRTQAGRCMDCGIPFCHSGCP +LGNLIPEWNDLVRRRRWDEAAARLHSTNNFPEVTGRICPAPCEDSCTLGINQPAVTIKQT +EVAIAEQIFDNDWLEPVVPARLNGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDERLG +GLLRLGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGVDLPWDQLKARFDAVIVATGAP +VARELPVPGRGLDGIHLAMDYLVQSNRAVAGDEVPDQISAEGRHVVILGGGDTGADCIGT +AHRQGAASVTTLAIGQQLPVERPVHQPWPTIPKVHQQTTADAEGGARAHLASTVEFLGDE +HGRVRALRVAETEYREDGTRGPKAGTEREVQADLVLLALGFTGIEEGLLTQQLGVHVTRG +LVARKDGYETDEPGVFACGDAGRGASLVVWAIAEGRACAQEVDESLERWSRLPHPVDPDD +RGLVLG +>PROKKA_00809 +MADPRGFLKNRERVERPTRPVPVRIMDFKDVYVRQDEAIVRTQAGRCMDCGIPFCHSGCP +LGNLIPEWNDLVRRRRWDEAAARLHSTNNFPEVTGRICPAPCEDSCTLGINQPAVTIKQT +EVAIAEQIFDNDWLEPVVPARLNGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDERLG +GLLRLGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGVDLPWDQLKARFDAVIVATGAP +VARELPVPGRGLDGIHLAMDYLVQSNRAVAGDEVPDQISAEGRHVVILGGGDTGADCIGT +AHRQGAASVTTLAIGQQLPVERPVHQPWPTIPKVHQQTTADAEGGARAHLASTVEFLGDE +HGRVRALRVAETEYREDGTRGPKAGTEREVQADLVLLALGFTGIEEGLLTQQLGVHVTRG +LVARKDGYETDEPGVFACGDAGRGASLVVWAIAEGRACAQEVDESLERWSRLPHPVDPDD +RGLVLG +>PROKKA_01806 +MADPRGFLKHRERVARPSRPVPVRIMDFKDVHVRQDEAIVRTEASRCMDCGVPFCHAGCP +LGNLIPEFNDLVYRDDWDEAGARLEATNNFPEFTGRICPAPCEASCVLGINQPAVSIKQV +EQSIADHLFDAPSLTPHPPQRQNGLTVAVVGSGPAGLAAAQQLTRSGYTVVVYEKDEALG +GLLRFGIPDFKLEKHLIDRRIAQMTEEGTRFRTGVRIGTDMSWEALQRRYDAVVLATGAP +VGRELPLPGRGLDGIHLAMDYLVPVNRRVAGGEPEPISAQGRHVVILGGGDTGADCIGTA +HRQGAASVTTLAIGRRPPEQRPEHQPWPTVPTLFEVASAHAEGGERTYLASTVEFLGDAE +GRVRALKVAETEIRADGTRGPRAGTEHEIPADLVLLALGFTGADLDELVDRSAVSLERGL +VVRDETYATQAPGVFACGDVSRGASLVVWAIAEGRAVAAEVDRFLTGDTMLPAPVRPSDH +GFVLR +>PROKKA_01695 +MADPRGFLKNRERVERPTRPVPVRIMDFKDVYVRQDEAVVRTQASRCMDCGIPFCHSGCP +LGNLIPEWNDLVRRGRWEDAAARLHSTNNFPEVTGRICPAPCEDACTLGINQPAVTIKQT +EVAIAEQIFDHDWLEPVVPTRINGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDDRPG +GLLRYGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGRDLAWDALKARFDAVIVATGAP +VGRELPVPGRGLDGIHLAMDYLVQSNHATAGDDVPGQITAEGRHVVVLGGGDTGADCIGT +AHRQGAASVTTLAIGQQLPVDRPVHQPWPTVPKVHQMTTADAEGGQREHLASTVEFLGDE +NGRVRALRVAETEYRADGTRGPKAGTEREVKADLVLLALGFTGVEEEALTAQLAVRTERG +LVARAGTYETDEPGVFVCGDAGRGASLVVWAIAEGRACAQAVDESLESWSRLPHPVDPTD +RGLVLG +>PROKKA_01039 +MADPRGFLKNRERVERPTRPVPVRIMDFKDVYVRQDEAIVRTQAGRCMDCGIPFCHSGCP +LGNLIPEWNDLVRRGRWDEAAARLHSTNNFPEVTGRICPAPCEDSCTLGINQPAVTIKQT +EVAIAEQIFDNDWLEPVVPARLNGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDERLG +GLLRLGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGVDLPWDQLKARFDAVIVATGAP +VARELPVPGRGLDGIHLAMDYLVQSNRAVAGDEVPDQISAEGRHVVILGGGDTGADCIGT +AHRQGAASVTTLAIGQQLPVERPVHQPWPTIPKVHQQTTADAEGGARAHLASTVEFLGDE +HGRVRALRVAETEYREDGTRGPKAGTEREVQADLVLLALGFTGIEEGLLTQQLGVHVTRG +LVARKDGYETDEPGVFACGDAGRGASLVVWAIAEGRACAQEVDESLERWSRLPHPVDPDD +RGLVLG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000908.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000908.fa new file mode 100644 index 0000000000000000000000000000000000000000..28cff291b87f7800cad4465e9f9ebeda8d7775ba --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000908.fa @@ -0,0 +1,25 @@ +>PROKKA_01092 +MSTLTPPEETGLRAVVAEDETLIRLDLVEVLTGAGYRVVAEAGDGRAAVEAVREHRPDIV +VMDVKMPVMDGIAAAGEIAGERLAPVVMLTAFSQRELVERARTAGAMAYVVKPFTEADLV +PAIELAVARFDELRSLEAEVRDLGDRLETRKIVDRAKALLQERMRLTEAESFRWIQKTSM +DRRLTMREVAQAVIDQVG +>PROKKA_00811 +MSTLTPPEETGLRAVVAEDETLIRLDLVEVLTGAGYRVVAEAGDGRAAVEAVREHRPDIV +VMDVKMPVMDGIAAAGEIAGERLAPVVMLTAFSQRELVERARTAGAMAYVVKPFTEADLV +PAIELAVARFDELRSLEAEVRDLGDRLETRKIVDRAKALLQERMRLTEAESFRWIQKTSM +DRRLTMREVAQAVIDQVG +>PROKKA_01804 +MPMTTPAEGTGLRAVVAEDETLIRLDLVEVLTGAGYEVVAEAGDGAAAVAAVREQRPDIV +VMDVQMPVMDGIAAASEIAQDRLAPVVMLTAFSQRDLVERARTAGAMAYVVKPFTEHDLV +PAVELAVARFEELRSLESEVRDLGDRLETRKLVDRAKSVLQDRLRLSEAESFRWIQKTSM +DRRLTMREVAQAVIDQVR +>PROKKA_01693 +MTIPAESADPTAGLRVVVAEDEALIRLDVVETLTHAGHTVVAEVGDGQAAVAAVREHRPD +IVVMDVMMPVMDGIAAAGEIAAERLAPVVMLTAFSQRDLVERASQVGAMAYVVKPFTEKD +LLPAMELAVARFDQLRGLEEEVRGLEDRLATRKLVDRAKSLLQAHMGLSEAESFRWIQKT +SMDRRLTMREVAQTVVDQIGA +>PROKKA_01041 +MSTLTPPEETGLRAVVAEDETLIRLDLVEVLTGAGYRVVAEAGDGRAAVEAVREHRPDIV +VMDVKMPVMDGIAAAGEIAGERLAPVVMLTAFSQRELVERARTAGAMAYVVKPFTEADLV +PAIELAVARFDELRSLEAEVRDLGDRLETRKIVDRAKALLQERMRLTEAESFRWIQKTSM +DRRLTMREVAQAVIDQVG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000909.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000909.fa new file mode 100644 index 0000000000000000000000000000000000000000..314532499e0093f1cac0b88abf812998e50709ce --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000909.fa @@ -0,0 +1,77 @@ +>PROKKA_01094 +MLLTSLLLTLLSVVAAVPASRALGRDAGWVLAAPLLAAAGVLIAAWTGDVRTEHHPWIPA +VGVDLDLRLNGLALVFAMIVLVIGAAILAYSSRYLSRDRTESRPGSFYLLMTAFAASMLL +LVLADNIVVLFVAWEFTSFTSFFLIGRSGDHARDPAIRTLLVTVGGGLALLAAVALMAVR +TGTASLSGVLASDVWSEAGFTTTVAVLLAVAAFTKSAQFPFQAWLPDSMVAISPVSAYLH +AAAMVKAGIFLLLVFSPVLAGNPVWSALLIGSGLITALLGAVSAIRRHDLKGLLAYSTMS +QLGLLVTAIGIGTPVALTAAIVHTVAHALFKSALFMLIGVVDHEAGTRDLRELAARHVRM +PVTGTAIAVAALSMAGIPPLFGFISKEGLVEAALGTPGPAWLPVLVTAGIALTSVFTVAY +SGRLVLGALGLWGPSPDGAAHSWPTGREDEVHEASATFWGVPVLAAAAGVALGLLPGVLD +TPVSYAAEAASGAEVHAHLALWHGVNTALLVSAAIIVLGLLLVALRRPVERVASHAALPF +SALDAVDEVRHRLIGVGAVVSRASGTLAPRPHLLIPALVLGLLAVAGVATIEDLPAVVGQ +PSRWHDWVLVVLVGAGVIATIRAKTRIAAMVVVGVVGFGMTLWFLTLGAVDVALTQLMVE +VLTVCVMVLLLRRLPARFSDEPTPRRMQAVLAASVAGVAATLGVLAFTGRSSMSEIAHFY +LTQSYAQAGGTNVVNVILVDFRAVDTWGEMTVLGATALTIAALLLNRRPTPPQPSAVDMR +SPLAHVRENLVHIRVFGRVFGVLIILLSAFLLLRGHYEPGGGFIAALVAGAGYALLYLAA +DSDTAPELRWPYLAFIGSGIAVGTATGIVGYLTGKGFLGAAGVKVLDYGLSTTLAFDMGV +YLAVIGLIVAAFSLLGPERPGEDPLRASSRDPGVAPAAPSSDPSAPTTTTAREEVTR +>PROKKA_00813 +MLLTSLLLTLLSVVAAVPASRVLGRDAGWVLAAPLLAAAGVLIAAWTGDVRTEHHPWIPA +VGVDLDLRLNGLALVFAMIVLVIGAAILAYSSRYLSRDRTESRPGSFYLLMTAFAASMLL +LVLADNIVVLFVAWEFTSFTSFFLIGRSGDHARDPAIRTLLVTVGGGLALLAAVALMAVR +TGTASLSGVLASDVWSEAGFTTTVAVLLAVAAFTKSAQFPFQAWLPDSMVAISPVSAYLH +AAAMVKAGIFLLLVFSPVLAGNPVWSALLIGSGLITALLGAVSAIRRHDLKGLLAYSTMS +QLGLLVTAIGIGTPVALTAAIVHTVAHALFKSALFMLIGVVDHEAGTRDLRELAARHVRM +PVTGTAIAVAALSMAGIPPLFGFISKEGLVEAALGTPGPAWLPVLVTAGIALTSVFTVAY +SGRLVLGALGLWGPSPDGAAHSWPTGREDEVHEAPATFWGVPVLAAAAGVALGLLPGVLD +TPVSYAAEAASGAEVHAHLALWHGVNTALLVSAAIIVLGLLLVALRRPVERVASHAALPF +SALDAVDEVRHRLIGVGAVVSRASGTLAPRPHLLIPALVLGLLAVAGVATIEDLPAVVGQ +PSRWHDWVLVVLVGAGVIATIRAKTRIAAMVVVGVVGFGMTLWFLTLGAVDVALTQLMVE +VLTVCVMVLLLRRLPARFSDEPTPRRMQAVLAASVAGVAATLGVLAFTGRSSMSEIAHFY +LTQSYAQAGGTNVVNVILVDFRAVDTWGEMTVLGATALTIAALLLNRRPTPPQPSAVDMR +SPLAHVRENLVHIRVFGRVFGVLIILLSAFLLLRGHYEPGGGFIAALVAGAGYALLYLAA +DSDTAPELRWPYLAFIGSGIAVGTATGIVGYLTGKGFLGAAGVKVLDYGLSTTLAFDMGV +YLAVIGLIVAAFSLLGPERPGEDPLRASSRDPGVAPAAPSSDPSAPTTTTAREEVTR +>PROKKA_01801 +MDEARHGLVRLGALVDRASGSVAPRVHLLIPACVLGAFALAGVFTVDDLPAVVGTPSRWH +DWALVVLVGAGVVATIRAKTRISAMVVVGVVGFGVTLWFFTLGAVDVALTQLLVEVLTVC +VMVLLLRRLPGRFRDEEAPRRVQAVVAATIAGVAATVGVLAFTGRSEMSEIAHFYLTQTY +AQAGGVNVVNVILVDFRALDTLGEMTVLGATGLTVAALLLNRRPAPPQRSAVDLRSPLAH +VRENLVHIRVFGRVFGVLIIALSVLLLLRGHYEPGGGFIAALVAGAGYALLYLAADHDTD +RRLQWPYLTLIGGGIALGALTGVAGYLTGKGFLGAAGVKILGYGLSTTLAFDLGVYLAVL +GLIVAAFSLLGPERSETEAGAEPDPTSPIADPAAEQTTGQTTEPTTAPGTAPTPAAAREE +TSR +>PROKKA_01691 +MLLTSLLLTLLAVVLAAPLGRTLGRDAGWVLALPLLTSAGALVSARAGGGGETVVERRPW +IPSLGAHLDLRLDGLAFVFALLVLVVGAGILAYSSRYLPRDRDEARAGSFYTLMTAFAAS +MLLLVLADNLVVLFVAWEFTSFASFLLIARSGDHARRPAIRTLLVTVGGGLCLLAAVALT +AARTGTASLSGALASDAWADPGFAAPVAALLAVAAFTKSAQFPFQSWLPDSMVAISPVSA +YLHAAAMVKAGIYLLLVFSPVLAGTPVWSALLIGSGLTTALLGAVSAIRRHDLKGLLAYS +TMSQLGLLVTAIGVGTPTALAAAVVHTVAHALFKSTLFMLIGVVDHEAGTRDLRDLAARH +VRMPVTGAAIAVAAASMAGLPPLLGFVSKEGLLDAALGAQGPAWLPGLVTAGIALTSVFT +VAYSGRLVLGALGVWGTAPAGAADMWSAGRGEDVHEAPAAFWAVPVLGVVVTLVLGLVPG +VLDEAVAAAATAAAGAPVHAHLALWHGVTPALLVSAGVIAAGLALVAARRPVERVASHAG +LPFSGLGVVDGILRGAVSLGAAVSRVSGGIAPRAHLLMPALVLGAFAVAGVVASPDLPAV +VGQPSRWHDWALVALVGVGVAATLRARTRIAAMVVVGTVGFGVTLWFFTLGAVDVALTQL +MVEVLTVCVMVLLLRRLPARFSAESTPHRAGAVAAAVIAGVASTLSVLAFTGRREISDIA +QYYLDRTYPDAGGHNVVNVILVDFRALDTLGEMTVLGVTGLTVAALLMNRRPAPPQPSAV +DVRSPLAAVHENLVYARTFGRALGPIILVLSVLLLLRGHYEPGGGFIAALVGGAGYALLH +LSADTDDEPRLRWPYLALIGGGVTLGTVAGLAGYLTGKGFLGSASVKVLGYSLGTTLAFD +MGVYLAVLGLIVAAFRLLGPDNATADDAAPAPTTGGESAREEAAR +>PROKKA_01043 +MLLTSLLLTLLSVVAAVPASRVLGRDAGWVLAAPLLAAAGVLIAAWTGDVRTEHHPWIPA +VGVDLDLRLNGLALVFAMIVLVIGAAILAYSSRYLSRDRTESRPGSFYLLMTAFAASMLL +LVLADNIVVLFVAWEFTSFTSFFLIGRSGDHARDPAIRTLLVTVGGGLALLAAVALMAVR +TGTASLSGVLASDVWSEAGFTTTVAVLLAVAAFTKSAQFPFQAWLPDSMVAISPVSAYLH +AAAMVKAGIFLLLVFSPVLAGNPVWSALLIGSGLITALLGAVSAIRRHDLKGLLAYSTMS +QLGLLVTAIGIGTPVALTAAIVHTVAHALFKSALFMLIGVVDHEAGTRDLRELAARHVRM +PVTGTAIAVAALSMAGIPPLFGFISKEGLVEAALGTPGPAWLPVLVTAGIALTSVFTVAY +SGRLVLGALGLWGPSPDGAAHSWPTGREDEVHEAPATFWGVPVLAAAAGVALGLLPGVLD +TPVSYAAEAASGAEVHAHLALLHGVNTALLVSAAIIVLGLLLVALRRPVERVASHAALPF +SALDAVDEVRHRLIGVGAVVSRASGTLAPRPHLLIPALVLGLLAVAGVATIEDLPAVVGQ +PSRWHDWVLVVLVGAGVIATIRAKTRIAAMVVVGVVGFGMTLWFLTLGAVDVALTQLMVE +VLTVCVMVLLLRRLPARFSDEPTPRRMQAVLAASVAGVAATLGVLAFTGRSSMSEIAHFY +LTQSYAQAGGTNVVNVILVDFRAVDTWGEMTVLGATALTIAALLLNRRPTPPQPSAVDMR +SPLAHVRENLVHIRVFGRVFGVLIILLSAFLLLRGHYEPGGGFIAALVAGAGYALLYLAA +DSDTAPELRWPYLAFIGSGIAVGTATGIVGYLTGKGFLGAAGVKVLDYGLSTTLAFDMGV +YLAVIGLIVAAFSLLGPERPGEDPLRASSRDPGVAPAAPSSDPSAPTTTTAREEVTR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000911.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000911.fa new file mode 100644 index 0000000000000000000000000000000000000000..b0aa9c8f8fd67fe133e10fedca5c9dce36785c93 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000911.fa @@ -0,0 +1,55 @@ +>PROKKA_01096 +MSAVPLGQLLPLFAAVPLLSAGLLVLAGERPRLHRAVLFAVLGLVTTGGLALGVHALDGS +VLATSLGGWPGGIGIGFAADMLSALMLVLTSALTIVGAAFAYGSRVANSQFFAPLLLILI +GGVNGALLTADLFNLFVFIEVMLVPSYGLYVLSANRREPLRRVDGARLYVTLNLLTSTIL +LVGVGFVYGLTGSVNLAMLAGSAAADPRIAIAAGMVLFALSIKASVAPLHGWLAWAYSST +SPAVTALFAALHTKVAVYGLYRIYSVMYDGDARLLPLILVLSLATLVVGALASVGEHGVR +AVLSWQMVSGIGGILVGLGLSTRLGLAAGLFYLVHHMVAMGCLLMAAGAIEVRYGTGRLA +DLQGLARREPLIAVAFFVGLLSLVGIPPFSGFVGKLMLVSAGLDAGRGVTAALVLGASLV +SLWVLLRVWDAWFWGAPTAPHGHRERLATAAMPIVGRAGSVPSPSGRGSSTDHERTESWA +SQETLDPPTGVLPVTVDPDEDVTRSRIPGRLAAPAVVLAMATLALGLGGQALWTVTDLAA +QGLMDPSRYIEAVLNP +>PROKKA_00815 +MSAVPLGQLLPLFAAVPLLSAGLLVLAGERPRLHRAVLFAVLGLVTTGGLALGVHALDGS +VLATSLGGWPGGIGIGFAADMLSALMLVLTSALTIVGAAFAYGSRVANSQFFAPLLLILI +GGVNGALLTADLFNLFVFIEVMLVPSYGLYVLSANRREPLRRVDGARLYVTLNLLTSTIL +LVGVGFVYGLTGSVNLAMLAGSAAADPRIAIAAGMVLFALSIKASVAPLHGWLAWAYSST +SPAVTALFAALHTKVAVYGLYRIYSVMYDGDARLLPLILVLSLATLVVGALASVGEHGVR +AVLSWQMVSGIGGILVGLGLSTRLGLAAGLFYLVHHMVAMGCLLMAAGAIEVRYGTGRLA +DLQGLARREPLIAVAFFVGLLSLVGIPPFSGFVGKLMLVSAGLDAGRGVTAALVLGASLV +SLWALLRVWDAWFWGAPTAPHGHRERLATAAMPIVGRAGSVPSPSGRGSSTDHERTESWA +SQETLDPPTGVLPVTVDPDEDVTRSRIPGRLAAPAVVLAMATLALGLGGQALWTVTDLAA +QGLMDPSRYIEAVLNP +>PROKKA_01799 +MSPEALGQLLPLFVAVPLITAGLLTLAGDRPRVHRLVVALVLCLTAGAGALIVARSLDGD +VLATSVGGWPGGIGIGFAADMLTGLMLLLTSLLTLVGVNLAHGTRVVNSLYFGPLMLVLM +AGVNGALLTADLFNLFVFIEVMLLPSYGLYVLSANRREPLRRVDGARLYVTLNLLTSTIL +VVAVGFLYALTGTVNLAVMAGAAARDERVAIAGGLVLFALSIKASVVPLHGWLARAYPST +SPAVTAIFAALHTKVAVYALYRVFSVLFDNDARFLPLLLALAGLTLAVGALASVGVHGVR +LVLSWQMVSGIGGILVGLGLSTQLGLSAGLFYLVHHMVAMGCLLAATAAVEVRYGTGRLA +DLRGLARREPLIAVVFFVGLLSIVGIPPFSGFVGKLMLVTAGVEAGRLVTVAVVLVGSLV +SLWALLRVWDAWFWGEPGTPHGLRERLATAALPVVGRGAERTGPSGRGSSTDHERTESWT +STQTIDPPTGVLPVTFAADEDVTRSRIPVRLAMPGVVLAAATLVLGLAGQALWTLTDVAA +QGLLDPARYIEAVLAP +>PROKKA_01689 +MSDHAVGLLLPLFVAVPLLSAGLLVVAGSRPRLHRAVLAAVLAGGTVGGGLLMARAADGS +VAAAGVGGWPDGIAIAFAADMLTGLMVALTAGLTLVGAWFAYGSRVANSAHFAPFMLVLM +AGVHGALLTADLFNLFVFIEVMLLPSYGLYVLSANRREPLRRVDGARMYVTLNLLTSTIL +VTGVGFVYALTGSVNMAVLAGAARGDVRVALAAGLVLFALSIKASMLPMHGWLARAYPST +SPAVTAIFAALHTKVAVYAMYRIYMVVYDGDPRLLGLILTLCLATLMVGAVASVGEHGAR +AVLSWQMVSGIGGIMVGLGLATQAGLSAGLFYLVHHMVVMACLLTATGAIEVRYGSGRLA +DLQGLAVREPLIAAAFFVGMLSLVGIPPFSGFAGKLALVLAGVAAGRTVTVVLVLVASLI +SLWALLRIWDAWFWGRPRAPHGHRERLDTAALPLVHGDGVMPAAGAPVHPAGRGSSTDSE +RAEAWASTETLDTPTGVLPVVVDPDEDHTASRIPLRLAGPAALMAAATLALGLGAEGLWS +VTDQAARGLADPTAYIEAVLGR +>PROKKA_01045 +MSAVPLGQLLPLFAAVPLLSAGLLVLAGERPRLHRAVLFAVLGLVTTGGLALGVHALDGS +VLATSLGGWPGGIGIGFAADMLSALMLVLTSALTIVGAAFAYGSRVANSQFFAPLLLILI +GGVNGALLTADLFNLFVFIEVMLVPSYGLYVLSANRREPLRRVDGARLYVTLNLLTSTIL +LVGVGFVYGLTGSVNLAMLAGSAAADPRIAIAAGMVLFALSIKASVAPLHGWLAWAYSST +SPAVTALFAALHTKVAVYGLYRIYSVMYDGDARLLPLILVLSLATLVVGALASVGEHGVR +AVLSWQMVSGIGGILVGLGLSTRLGLAAGLFYLVHHMVAMGCLLMAAGAIEVRYGTGRLA +DLQGLARREPLIAVAFFVGLLSLVGIPPFSGFVGKLMLVSAGLDAGRGVTAALVLGASLV +SLWALLRVWDAWFWGAPTAPHGHRERLATAAMPIVGRAGSVPSPSGRGSSTDHERTESWA +SQETLDPPTGVLPVTVDPDEDVTRSRIPGRLAAPAVVLAMATLALGLGGQALWTVTDLAA +QGLMDPSRYIEAVLNP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000914.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000914.fa new file mode 100644 index 0000000000000000000000000000000000000000..63a98b40332e564e5ba7adedcb7100aa6b4f1cae --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000914.fa @@ -0,0 +1,20 @@ +>PROKKA_01099 +MDVVLTAAGSVLVVIGALAFVTAGLGLIRFPDPYTRVSAVGTAGGVGMILIVVGALLLAP +GVAAFVKVALIVVLQLGSASVATMALGRSAYLTGVPMNPGHYDELAEDTPGREHGEPAPR +APDEV +>PROKKA_00818 +MDVVLTAAGSVLVVIGALAFVTAGLGLIRFPDPYTRVSAVGTAGGVGMILIVVGALLLAP +GVAAFVKVALIVVLQLGSASVATMALGRSAYLTGVPMNPGHYDELAEDTPGREHGEPAPR +APDEV +>PROKKA_01796 +MDLVLTVIGSVLVVAGALVFVTAGLGLIRFPDPYTRISATGTAGGVGMILIVVGGLVLAP +SVANVVKVALIVVLQLGSAAVATMALGRSAYLTGVPMNPGHYDELAEDTPGREHGEPAPR +TPDAS +>PROKKA_01686 +MDLVMTVAGSVLAVAGAVVFLGAAVGLIRFPDPYTRISATGTAGGVGMILIVTGGLLLMP +SVANLVKVVLIVVLQLGTAAIATMALGRSAYLTGVPMNLAHYDELAEDTPGREHGEPAPR +HPED +>PROKKA_01048 +MDVVLTAAGSVLVVIGALAFVTAGLGLIRFPDPYTRVSAVGTAGGVGMILIVVGALLLAP +GVAAFVKVALIVVLQLGSASVATMALGRSAYLTGVPMNPGHYDELAEDTPGREGGRAAPR +LPDMD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000916.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000916.fa new file mode 100644 index 0000000000000000000000000000000000000000..d3560fe90e15f95ccb4965aadcbb569e078ee52c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000916.fa @@ -0,0 +1,85 @@ +>PROKKA_01101 +MAADPTPEAPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR +PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTLEGYEA +DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVKAKYG +VAPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLKQYGDLDGVLAHAHEITGKKGEALR +EHLEDVRRNRRLNALVRDLDLPIGLETMRLEMPEREPVEELFDALQFHRIRERVFEVFGE +RVGEDAPPPEVEAAPEFTEATTAEDVRAFLAAEAGNLLGVHVDVEGPALLPRRKVPVPGT +FGTPVGVALVGEHAGLHVTLDGDAPDPALVAAVREALGEGGLAKAVHDLKRTLKALAAPT +EGDGLGPDAALDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLTAPRESAQQRAQGS +FDLDGGQAAAERADRAADAVRAAWVVRRLSTQFTPQVLDRGAQRLLQELEIPLSRLLARM +ELTGIAVDVDALTGLREDFTDAADAAKESAWASVAEETGGMQVNLGSPKQLQEVLFERLN +MPRTRKTKTGYSTDVDSLQDLLEQTRHPFLENLMAHRDATKLRQTVEGLLETVAPDGRIH +TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIREVFVADEVAGEQAVLLSADYSQIEMR +IMAHLSEDEGLIQAFREGEDLHSFVGSQVFGVDPDDVTAEQRAKVKAMSYGLAYGLSSFG +LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARQDGYTSTIEGRRRYLPDLSSDN +RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLEEHGLASRLLLQVHDELILEVPAAE +LEKATALLKERMGRAAELSVPLDVHVGQGRSWHDAAH +>PROKKA_00820 +MAADPTPEAPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR +PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTLEGYEA +DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVMAKYG +VAPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLKQYGDLDGVLAHAHEITGKKGEALR +EHLEDVRRNRRLNALVRDLDLPIGLEAMRLEMPEREPVEELFDALQFNRIRERVFEVFGE +RVGEDAPPPEAEAAPEFTEATTAEDVRSFLAAEAGNLLGVHVDVEGPALLPRRKVPVPGT +FGTPVGVALVGEHAGLHVTLDGDAPDPALVAAVREALGEGGLAKAVHDLKRTLKALAAPT +EGDGLGRDAALDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLTAPREPAQQRAQGT +FDLDGGQAAAERADRAADAVRAAWVVRRLSTQFTPQVLDRGAQRLLQELEIPLSRLLARM +ELTGIAVDVDALTGLREDFTDAADAAKESAWASVAEETGGMQVNLGSPKQLQEVLFERLN +MPRTRKTKTGYSTDVDSLQDLLEQTRHPFLENLMAHRDATKLRQTVEGLLETVAPDGRIH +TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIREVFVADEVAGEQAVLLSADYSQIEMR +IMAHLSEDEGLIQAFREGEDLHSFVGSQVFGVDPDDVTAEQRAKVKAMSYGLAYGLSSFG +LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARQDGYTSTIEGRRRYLPDLSSDN +RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLEEHGLASRLLLQVHDELILEVPAAE +LEQATALLKERMGRAAELSVPLDVHVGRGRSWHDAAH +>PROKKA_01794 +MAADPTPEDPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR +PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTITLEGYEA +DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVMAKYG +VSPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLTQYGDLDGVLAHADEIKGKKGEALR +AHLDDVRRNRRLNALVRDLDLPIGLEAMALEMPEREPVEELFDALQFNRIRERVFEVFSE +RIGETAPAAQVEEAPEFTEAATAQDVADFLAAEAGNLLGVHVDVEGPALLPKRKVPVPGT +FGTAVGVALVGEHAGLHVSLDADAPDPALLAALREALGEGGLSKAVHDLKRVLKAIAEPA +EATALEAGTPLDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLAAPREPAEADAQGA +FDLDGGAAAAERAARAADAVRAAWVVRRLSVLFTPQVLERGAQRLLQELEIPLARLLARI +ELTGIAVDAQALETLRADFSEAAAAAQESAWASVAEETGGMKVNLGSPKQLQEVLFEHLD +MPRTRKTKTGWSTDVDSLQDLLEQTRHPFLENLMRHRDATKLRQTVEGLLETVAPDGRIH +TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIREVFVADRVAGEDAVLLSADYSQIEMR +IMAHLSEDAGLIQAFREGEDLHSFVGSQVFGVAPDEVSSEQRAKVKAMSYGLAYGLSSFG +LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARRDGYTSTIEGRRRYLPDLSSDN +RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLAEHGMASRLLLQVHDELILEVPAAE +LEQATALLQERMGRAAELAVPLDVHVGQGRSWHDAAH +>PROKKA_01684 +MGENSTEARPRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTSMLLTMIRQQAP +THVAVAFDLSGPTFRSAEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTKEDFEAD +DIVATLSAQAEAQGWDVCVVSGDRDAFQLISERTQVLYPKKGVSDIPPMTAADVEAKYGV +RPEQYPELAALVGESADNLPGVPGVGPGFAAKWLQKYGDLDGVLAHADEITGKKGEALRA +HLDDVRRNRRLNALVRDLDLDVSLDAMELTMPEREVVEELFDALQFQRIRERVFEVFAER +LGSAAPAAPVAEAPAAVLAATADDVHAFVSAHAGTLLGLHVEIDGPDLLPKRKVPVPGTF +GTPVGLALAAEDAALYVDLTDADADPGLVAALGDLLAEDGAAKAVHDLKRTLKAIAVPTG +PTALPADTSLHGVVDDVALSAYLIQPDRRDTDLATLSQAHLQEPLEAPESAAAGAQGAFD +LDGAQEEAERTARAARAARSAWVVRRLSQAFTPQVLERGAQRLLQEMEIPLARLLARMEL +AGIAVDGDALSALLADFTDRAEAAKESAWASVAEETGGMKVNLGSPKQLQEVLFEHLDMP +KTRKTKTGWSTDVDSLQDLLEQTQHPFLENLMAHRDATKLRQTVEGLRETVAPDGRIHTT +YSQTVAATGRLSSLHPNLQNIPVRTEAGRRIREAFVAAPVDGEPAELLSADYSQIEMRIM +AHLSEDAGLIEAFNSGEDLHSFVGSQVFGVDPDDVTSEQRSKVKAMSYGLAYGLSSFGLS +KQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARRDGFTSTIEGRRRYLPDLTSDNRQ +LRDMAERAALNAPIQGSAADIIKRAMLDVQAGLVEQGLRSRLLLQVHDELILEVPASELD +AATALLQERMGRAADLSVPLDVHVGHGGTWHAAAH +>PROKKA_01050 +MAADPTPEAPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR +PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTLEGYEA +DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVKAKYG +VAPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLKQYGDLDGVLAHAHEITGKKGEALR +EHLEDVRRNRRLNALVRDLDLPIGLEAMRLEMPEREPVEELFDALQFNRIRERVFEVFGE +RVGEDAPPPEVEAAPEFTEATTAEDVRAFLAAEAGTLLGVHVDVEGPALLPRRKVPVPGT +FGTPVGVALVGEHAGLHVSLDGDAPDPALVGAVREALGEGGLAKAVHDLKRTLKALAAPT +EGDGLGRDAALDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLTAPREPAQQRAQGT +FDLDGGQAAAERADRAADAVRAAWVVRRLSTQFTPQVLDRGAQRLLQELEIPLSRLLARM +ELTGIAVDVDALTGLREDFTVAADAAKESAWASVAEETGGMQVNLGSPKQLQDVLFERLN +MPRTRKTKTGYSTDVDSLQDLLEQTRHPFLENLMAHRDATKLRQTVEGLLETVAPDGRIH +TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIRGVFVADEVAGEQAVLLSADYSQIEMR +IMAHLSEDEGLIQAFREGEDLHSFVGSQVFGVDPDDVTAEQRAKVKAMSYGLAYGLSSFG +LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARQDGYTSTIEGRRRYLPDLSSDN +RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLEEHGLASRLLLQVHDELILEVPAAE +LEQATALLKERMGRAAELSVPLDVHVGRGRSWHDAAH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000917.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000917.fa new file mode 100644 index 0000000000000000000000000000000000000000..ddb65a5f6e4e27dcbd1f43441e7b64fa01a13434 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000917.fa @@ -0,0 +1,50 @@ +>PROKKA_01103 +MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG +VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE +EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN +NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS +WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV +TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS +LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVETNEWMEGFETERAAWEQQY +ADAQARWEAHKEQVRRSLQEEATAGADAGAGLGGSSYSSEAPSSDGGTLASDEALAALRE +KLTGN +>PROKKA_00822 +MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG +VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE +EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN +NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS +WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV +TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS +LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVETNEWMEGFETERAAWEQQY +ADAQARWEAHKEQVRRSLQEEATAGADAGAGLGGSSYSSEAPSSDGGTLASDEALAALRE +KLTGN +>PROKKA_01791 +MTTTSNAPQVAINDIGTAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG +VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE +EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN +NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS +WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV +TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS +LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVESNEWMEGFESERAAWEQQY +ADAQSRWEQHKEQVRRSFEEEANAGADTGAGMGGSSYSSEAPASDGGTLASDEALAALRE +KLTGN +>PROKKA_01682 +MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG +VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKVKE +EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN +NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRQGTVSSIVNFGAFVDLGGVDGLVHVSELS +WKHIDHPSEVVEVGQDVTVEVLDVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV +TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDQLFVKVIDIDLERRRISLS +LKQANEGVDPEGTEFDPALYGMAAEYDDEGNYKYPEGFDVETNEWMEGFESERASWEQQY +ADAQTRWEAHKEQVRRSLEEEAQAPAGNASTASSYSSEAPASDGGTLASDEALAALREKL +TGN +>PROKKA_01052 +MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG +VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE +EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN +NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS +WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV +TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS +LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVETNEWMEGFETERAAWEQQY +ADAQARWEAHKEQVRRSLQEEATAGADAGAGLGGSSYSSEAPSSDGGTLASDEALAALRE +KLTGN diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000918.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000918.fa new file mode 100644 index 0000000000000000000000000000000000000000..ca5970e429c184698cebe24d301a9e78b50ae2b1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000918.fa @@ -0,0 +1,37 @@ +>PROKKA_01104 +MSEPLPRGVTPDVAHGGLPDDLTAGVDFAALDRWPLPPEPDRQAHDAADLLLLDTLAGWI +ASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDANLAAWRAAGRLGGEA +GELERTATPEDAARGARTVLLPLPRSLDELDRLSRIVAAAADPGVVLLAGGRDKHMSPRM +NAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTPRPPEEADRDVPGVGSLHLVAHAGAFG +GAAADPGSRLLLASLADDPRPPGRLVDLGCGNGLLSVGAARLWPHVTVLATDQSAVAVAS +TLATARANRVADRVRAVRDDALATWPDGTEECVLLNPPFHDGNAVDPSVAHRLVAAAARV +LEPGGRLWCVWNSHLRYRPVLEDLVGPTRQTARDRTFTVTVSERR +>PROKKA_00823 +MSEPLPRGVTPDVARGGLPDDLTAGVDFAALDRWPLPTEPDRQAHDTADLLLLDTLAGWI +ASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDANLAAWRAAGRLGGET +GELERTATPEEAARGARTVLLPLPRSLDELDRLSRIVSAAADPGVVLLAGGRDKHMSPRM +NAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTARPPEEADRDVPGVGRLHLVAHAGTFG +GAAADPGSRLLLASLADDPRPPGRVVDLGCGNGLLSVGAARLWPHVTVVATDQSAVAVAS +TLATARANRVADRVRAVRDDALATWPDGEEECVLLNPPFHDGNAVDPSVAHRLVAAAARV +LEPGGRLWCVWNSHLRYRSVLEDLVGPTRQTARDRTFTVTVSERR +>PROKKA_01790 +MDLGCGNGLLGVGAARLWPHVRVLATDQSAVAVASTLATARANGVADRLEAVRDDALAGR +PDASEECILLNPPFHDGNAVDPAVAHRLVAEAARVLAPGGRLWCVWNSHLRHRPVLEAEV +GPTRQVARDRTFTVTVSTRR +>PROKKA_01681 +MDAIAQTPPRDPGPARLTATELVTPDAAGRGLPRDWTAEFPFERLGRWPLPESRERQAHD +AADLLLVDTLAGWTADGRVPGPVAVLHDQHGAVSLPLLARGLNVRLGLDEASAARSVERN +LDLFRDADGALPAGWGRLTVGGVDAATLADARTVLLLLPRALDALHLTAARIAVHAAPDV +LVLGAGRDKHMTPSMNDVLARSFAAVVPGRGRSKSRVITAARPVDDATEPAPRRAQHRLG +RLGAVTLVGGWATFGGAAADPGSLLLAGTLADRAPALPVPAPHRMRTDSGLGVDIPWATR +AGAPDVVDAGSGNGMLSVVAARVWPEAAVLASDQSADAVASSAATAEANGLAERITAVQD +DALGALPDASVRAVLLNPPFHDGTAVDPTVAHRMIEAAGRILAPGGELWCVWNSHLRHRP +VLETAVGPTRQVARNRTFTVTVSTRR +>PROKKA_01053 +MSEPLPRGVTPDVARGGLPDDLTAGVDFAALDRWPLPTEPDRQAHDAADLLLLDTLAGWI +ASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDANLAAWRAAGRLGGET +GELERTATPEEAARGARTVLLPLPRSLDELDRLSRIVSAAADPGVVLLAGGRDKHMSPRM +NAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTARPPEEADRDVPGVGRLHLVAHAGTFG +GAAADPGSRLLLASLADDPRPPGRVVDLGCGNGLLSVGAARLWPHVTVVATDQSAVAVAS +TLATARANRVADRVRAVRDDALATWPDGEEECVLLNPPFHDGNAVDPSVAHRLVAAAARV +LEPGGRLWCVWNSHLRYRSVLEDLVGPTRQTARDRTFTVTVSERR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000921.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000921.fa new file mode 100644 index 0000000000000000000000000000000000000000..ae026bd87451234cf419e9ce74da26bd32371756 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000921.fa @@ -0,0 +1,65 @@ +>PROKKA_01108 +MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW +LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK +DSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGAEMDRDV +LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG +QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDRLLEAQRLRMRTTY +DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE +GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII +RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV +EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT +SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRI +ADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSLDRAPATGEGAEAPAVDPASL +PAKDLADLIEQMSQQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ +>PROKKA_00827 +MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW +LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK +DSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGAEMDRDV +LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG +QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDKLLEAQRLRMRTTY +DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE +GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII +RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV +EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT +SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRI +ADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSLDRDATTGEGTEAPAVDPASL +PAKDLADLIEQMSKQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ +>PROKKA_01785 +MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW +LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK +DSSVNEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGEEMDRDV +LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG +QVVREETEMYIFPASHYVAGDERMGRAVTAIEDELRERLQELESQDRLLEAQRLRMRTTY +DLEMMQQMGYCNGIENYSRHIDGRPDGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE +GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII +RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLDAGVKV +EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT +SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIEETERRRAVQIAYNEEHGIDPQPLRKRI +ADITDQLAREDADTADFLKGMGGVKSGFDYGMGHRGLSSLDREEGQERAGGGPAVDAASL +PAKDLADLIEQMSLQMHQAAADLQFELAARLRDEVGELKKELRQMRREQ +>PROKKA_01677 +MSLAKQINRVVAPFEVVSPYQPSGDQPTAIAEIAERVQAGEKDVVLMGATGTGKSATTAW +VIEQLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK +DSSINEEVERLRHSATNALLTRRDVVVVATVSCIYGLGTPEEYIAQMVTLRRGQEMDRDA +LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEVESIQTLHPLTG +QVVREEEEMYIFPASHYVAGDERMGRAIATIEDELRERLQELESQDKLLEAQRLRMRTTY +DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE +GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGQYELSQADGVVEQII +RPTGLVDPTVVVKPTQGQIDDLLEQIRTRTEKDERVLVTTLTKRMAEDLTEYLLEAGVKV +EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVSILDADKEGFLRSTT +SLIQTIGRAARNVSGEVHMYADRVTDSMRRAIEETERRREVQIRYNAEHGIDPQPLRKKI +ADITDALAREDADSADFLKGMGGVKAGFDYGMGHRGLGSLDHEPPAGEVPSGSPAVDPAA +LPAKDLAQLIEQMSAQMHQAAADLQFELAARLRDEIGDLKKELRQMKREQ +>PROKKA_01057 +MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW +LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK +DSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGAEMDRDV +LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG +QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDKLLEAQRLRMRTTY +DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE +GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII +RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV +EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT +SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRI +ADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSLDRDATTGEGTEAPAVDPASL +PAKDLADLIEQMSKQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000922.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000922.fa new file mode 100644 index 0000000000000000000000000000000000000000..bc8b8bf7e621d74e84c082dfb17b3595fed56812 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000922.fa @@ -0,0 +1,25 @@ +>PROKKA_01109 +MSAAPPVAAVIADIVGSRALPDRDRAQEQILAAFAAAEQDVPPLRPAWASVGDEFQALHR +TWPDALRLTVRVTLALPPGLDLRFGIGLGQRRALDAGGDGIEDGPAWYRAREAVERAHER +AVGAATAFRAADPSLTAAVDGLVLLRDHVLGRLKARERRIAAALLGGATQAEAARAERIT +QSAVSQAVARSGIDRLLELDAELAAAATEVAP +>PROKKA_00828 +MSAAPPVAAVIADIVGSRALPDRERAQEQILAAFAAAEQDVPPLRPAWASVGDEFQALHR +TWPDALRLTVRVTLALPPGLDLRFGIGLGQRRALDAGGDGIEDGTAWYRAREAVEHAHER +AAGAATAFRAADPSLTAAVDGLALLRDHVLGRLKARERRIAAALLGGATQAEAARAERIT +QSAVSQTVARSGIGRLLELDAELAAAATEVAP +>PROKKA_01783 +MTRAPQAAAVIADIVGSRRLPDREAAQEQILAAFAVAEKDVPPLRAAWATVGDEFQALHG +VWPQAVRAVVRVSLALPPGLELRFGIGVGERRSLDDGAGDRIEDGTAWYRARAAVERAHA +RADGAATAFVAADPSLTAAVDGVLLLRDHVLGRLKARERRLAAALLGGATQTQAARAERI +TQSAVSQAVTRSGIDRLLELDAALAEAAAGRPGHAGAAGEGAGDEGDAG +>PROKKA_01676 +MSLTDEGPVRGTAVIADIVGSRGLRDRAAAQEAILAAFAAAEEAVPARIPAWATVGDEFQ +ALHADWAAAVRATLRVAVALPEGVELRFGLGDGVHREVTGAADDDGRPILDGSAWHRARE +ALEAAEHRTRGLAGAYRGPDADLTAAVDGQLLVRDHVLRRLKARERRIAAALLAGRTQAE +TATAERITQGAVSQAVARSGVRELLALDAALGALPGAGRGAKATAEEDRP +>PROKKA_01058 +MSAAPPVAAVIADIVGSRALPDRERAQEQILAAFAAAEQDVPPLRPAWASVGDEFQALHR +TWPDALRLTVRVTLALPPGLDLRFGIGLGQRRALDAGGDGIEDGTAWYRAREAVEHAHER +AAGAATAFRAADPSLTAAVDGLALLRDHVLGRLKARERRIAAALLGGATQAEAARAERIT +QSAVSQTVARSGIGRLLELDAELAAAATEVAP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000924.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000924.fa new file mode 100644 index 0000000000000000000000000000000000000000..794c4a82e496cf1f1f9a67cbd210a2ab5339ff16 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000924.fa @@ -0,0 +1,50 @@ +>PROKKA_01113 +MAGDPRGFAPLEPARHRVGERTELYDGTVTVDHWFSVPIDHALGLAEAEAQDAAGTGVGP +HGRGTLTVFAREIRAKDDPEGERPWALYLQGGPGSAGPRPARLSGWLGALAESHRVLLLD +QRGTGRSTPATVATLTAPGAFATDEARAEHLVHLRAPSIVRDAEMLRLALGAGPWTTLGQ +SFGGFCTLSYLSFHPEGLQRSLVTGGLAPLTGHADRVYRATYARMRARTEEFFDRHPADR +DAWSEAVGLIRAAEAAGAPIPLPGGGPLTVGRAQGLGMLLGGNTRVDRLHWVLAEAVDRT +GPAPRLSETFLAAVADQDDRLVNPLYTVLHEAIYAQPADLAGGRADTGWSASRMLAEHPD +FDPEATTVPLPTGEHVMPWSVEVDPRLRPLAGTARLLAERTQWGPLYDVAALAQNTVPVA +AAVYADDVYVDRDLSLETARRVRGLQVWETDAFHHDGIADDGPAILERLLAMTAPDGAGT +TTAPDPVD +>PROKKA_00832 +MAGDPRGFAPLEPARHRVGERTELYDGTVTVDHWFSVPIDHALGLAEAEAQDAAGTGVGP +HGRGTLTVFAREIRAKDDPEGERPWALYLQGGPGSAGPRPARLSGWLGALAESHRVLLLD +QRATGRSTPATVATLTAPGAFATDEARAEHLVHLRAPSIVRDAEMLRLALGAGPWTTLGQ +SFGGFCTLSYLSFHPEGLQRSLVTGGLAPLTGHADRVYRATYARMRARTEEFFDRHPADR +DAWSEAVGLIRAAEAAGAPIPLPGGGPLTVGRAQGLGMLLGGNTRVDRLHWVLAEAVDRT +GPAPRLSETFLAAVADQDDRLVNPLYTVLHEAIYAQPADLAGGRADTGWSASRMLAEHPD +FDPEATTVPLPTGEHVMPWSVEVDPRLRPLAGTARLLAERTQWGPLYDVAALAQNTVPVA +AAVYADDVYVDRDLSLETARRVRGLQVWETDAFHHDGIADDGPAILERLLAMTAPDGAGT +TTASDPVN +>PROKKA_01780 +MSAPAPRVPGDPRGFAPLEPARHRVGERTELYDGTVAVDHWFTVPVDHALTLAEAEAQDA +AGTGVGPHGRGTLTVFAREIRAAGDADGARPWALYLQGGPGGAGPRPARGGGWIGALASE +HRVLLLDQRGTGRSTAASVAALTAPGAFASDEALAEHLVHLRAPSIVRDAEMVRLALGAA +PWTTLGQSFGGFCTLTYLSFHPEGLRRCLVTGGLAPLTGHADRVYQATYARMRDRAHEFF +ARHTGDRAAWAEAVALIRAAEQAGEPVRLPDGGLLTVARAQALGMLLGGNTRVDRLHWIL +AEAVDRSGPAPRLSETFLAAVAEQNDRHVNPLYTVLHESIYAQPAELAGGRAATDWSAAR +VLAEHPDFDPDAADAPLPTGEHVMPASLELDPHLRPLRGAARLLAERTDWGPLYDVEALA +RNIVPVAAAVYTDDVYVDRDLSLETAGRVRGLRVWETDAFHHDGLADDGPAIVRRLLEMT +GEGAAPAAAEGAERSDSAPAASETTTAPGPVD +>PROKKA_01673 +MTRTGTGDAAFVPGDPRGFAPVGPAAHREGERTVLFDGTVAVDHWFTVPVDHALTLAEAL +AQDAAGTGLGPGGRGTLEVFAREVRHPEDPEGERPWLLYLQGGPGSGGPRPARLGGWQCE +LAQHHRLLLLDQRGTARSTPVTAATLAGLPDDAARAAYLTHLRAPQIVQDAEMIRVALGA +PPWTTLGQSFGGFCTLSYLSWRAEGLERCLVTGGLAPLTGHADRVYRATTARMHARWQEF +LERHPQDAGHWAEAVALIRAAQDDGDPYVLPDGTALTVGRAQQLGMLLGGNTRVDGLHWV +LAEAVDRSGGEPRLSPGFLAAVAAQTTRAVNPLYAVLHEAIYAQPAALTDGRGATAWSAQ +RVLAEHPDSSPAADPAPVPTGEHVLPWSFETEPELRALAGVAALLAAKDDWGALYDLDAL +AANEVPVAAAVYTDDVYVDRDLSLETAARVRGLQVWETDAFHHDGLADDGPGIVRRLRGM +LGA +>PROKKA_01063 +MAGDPRGFAPLEPARHRVGERTELYDGTVTVDHWFSVPIDHALGLAEAEAQDAAGTGVGP +HGRGTLTVFAREIRAKDDPEGERPWALYLQGGPGSAGPRPARLSGWLGALAESHRVLLLD +QRGTGRSTPATVATLTAPGAFATDEARAEHLVHLRAPSIVRDAEMLRLALGAGPWTTLGQ +SFGGFCTLSYLSFHPEGLQRSLVTGGLAPLTGHADRVYRATYARMRARTEEFFDRHPADR +DAWSEAVGLIRAAEAAGAPIPLPGGGPLTVGRAQGLGMLLGGNTRVDRLHWVLAEAVDRT +GPAPRLSETFLAAVADQDDRLVNPLYTVLHEAIYAQPADLAGGRADTGWSASRMLAEHPD +FDPEATTVPLPTGEHVMPWSVEVDPRLRPLAGTARLLAERTQWGPLYDVAALAQNTVPVA +AAVYADDVYVDRDLSLETARRVRGLQVWETDAFHHDGIADDGPAILERLLAMTAPDGAGT +TTAPDPVD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000925.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000925.fa new file mode 100644 index 0000000000000000000000000000000000000000..be8ec912e79bd821677dc3a34b2bfdc052978662 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000925.fa @@ -0,0 +1,80 @@ +>PROKKA_01114 +MTSAATNPPSLTDRIDALPPAPDADDVFGAFAAWTEDRGISLYPAQEEAALELVQGRHVI +LATPTGSGKSLVALAAHADALAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS +TVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQVPLLELPQAR +FLLMSATLGDTTRLEADLTERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEEFVSTHQA +PVYIVHFSQLDAVETAQGLSSISVTSREEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGV +HHAGMLPKYRRLVEKLAQDGLLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQA +REFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAAAKFANVKDEAERAKRMKQSV +KSGKRKTPPAGFVSWGPATFERLVSAEPEPLVSRMRITHSMLLNILDRPGDPVIAVRRLL +RGTHETPARQAVLMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLS +PFALAALDLLDPADPDHALDVVSVIEATLDPPRQVLSAQVKHAKGEAVAAMKAEGMDYND +RMRALDEITHPRPLAELLEQQFELYRQDAPWLAEFELTPKSVVRDMFERAMGFGDYVRFY +GIARSEGVLLRYLTDAVKALRHTVPEAARTEELQVLLDWLDEMVKQTDSSLLEEWEDLVA +GDIDELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEALARLSGELSA +DDWADALDAYFDDHEDIDDGPAARGPELFRVAAAPDVAAPLELAGPRWWAVRQVLKDPDG +DLDHGINAVVDLDASDEAGHPVIRVVSVGAPESGWGL +>PROKKA_00833 +MTSAATNPPSLTDRIDALPPTPDADDVFGAFAAWTEDRGISLYPAQEEAVLELVQGKHVI +LATPTGSGKSLVALAAHADALAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS +TVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQVPLLELPQAR +FLLMSATLGDTTRLEADLTERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEELVSTHQA +PVYIVHFSQLDAVETAQGLSSISVTSREEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGV +HHAGMLPKYRRLVEKLAQDGLLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQA +REFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAAAKFANVKDEAERAKRMKQSV +KSGKRKTPPAGFVSWGPATFERLVSAEPEPLVSRMRITHSMLLNILDRPGDPVIAVRRLL +RGTHETPARQAVLMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLS +PFALAALDLLDPADPDHALDVVSVIEATLDPPRQVLSAQVKHAKGEAVAAMKAEGMDYND +RMRALDEITHPRPLAELLEQQFELYRQDAPWLAEFELTPKSVVRDMFERAMGFGDYVRFY +GIARSEGVLLRYLTDAVKALRHTVPEAARTEDLQVLLDWLDEMVKQTDSSLLEEWEDLVA +GDIDELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEALARLSGELSA +DDWADALDAYFDDHEDIDDGPAARGPELFRVAAAPDVAAPLELAGPRWWAVRQVLKDPDG +DLDHGINAVVDLDASDEAGHPVIRVVSVGAPESGWGL +>PROKKA_01779 +MTSPATNPPSLTDRIDALPPTPDADDVFGAFAAWTEVRGISLYPAQEEAALELVQGRHVI +LATPTGSGKSLVALAAHADALAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS +TVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQVPLLELPQAR +FLLMSATLGDTTRLEADLIERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEELVSTHQA +PVYIVHFSQLDAVETAQGLSSISVTSKEEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGV +HHAGMLPKYRRLVEKLAQDGLLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQA +REFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAAAKFANVKDEAERAKRMKQSV +KSGKRKSPPAGFVSWGPATFERLVAAEPEPLVSRMQITHSMLLNILDRPGDPVVAVRRLL +RGTHETPARQAILMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLS +PFALAALELLDPAEPDHALDVVSVIEATLDPPRQVLSAQVKKAKGEAVAAMKAEGMDYND +RMRALDEVTHPQPLADLLEQQFEVYRASAPWLAEFELTPKSVVRDMFERAMGFGDYVRFY +GIARSEGVLLRYLTDAVKALRQTVPEASRTEELQVLLDWLDEMVKQTDSSLLEEWEDLVA +GDIEELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEELARLSGDLSA +DDWADALDAYFGDHEDIDDGPAARGTELFRVAESPDVAPPVELAGSRWWAVRQVLKDPDG +VHDHGVNAVVDLDASDEAGHPVIRVVSVGAPESGWGL +>PROKKA_01672 +MTPSATNPPSLTDRLDALPASPDADDVFGAFAAWTEDRGISLYPAQEEAVLELVQGRHVI +LATPTGSGKSLVALGAHADALAHGKVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS +SVNADAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQLPLLELPQAR +FLLMSATLGDTSMLERDLAERTGREVAVVAHAERPIPLSFEWSEVPLQEKVEELVSTHQA +PVYIVHFSQLDAVETAVGLASISVTTKEEKEAIAERIAGFRFSAGFGKTLNRLVRAGIGV +HHAGMLPKYRRLVEKLAQEGRLKVISGTDTLGVGINVPIRTVLLTALSKFDGEKTRILQS +REFHQIAGRAGRAGFDTQGYVVVQAPEHVIENKAAERKAAAKFAGIKDEAERAKRMKQSV +KGSKRKTPPQGFVSWGPATFDKLVASEPEPLVSRMRITHSMLLNILDRPGDPVLAVRRLL +RATHETPARQAQLMRRALGIFRELLATGVVEVLPEPDAEGRTVDLTVDLQPDFALNQPLS +PFALAALDLLDPAAPDHHLDVVSVIEATLDAPRQVLSAQVKKAKGEAVAAMKAEGMDYSD +RMRALDEVTHPQPLAELLEQAFERYRQDAPWLAEFELSPKSVVRDMFERAMGFGDYVRFY +GLARSEGVLLRYLTDAVKALRQTVPQEDRTEDLQVLLDWLDEMVKQTDSSLLEEWEDLMS +GDIAELRRDLESLEPTPPPRLTDNAAVFRVMVRNAMFHRVRLFGDEQDARLAELSGDLSA +NDWADALDAYFDEHEDIDDGPDARGQEFFRVATAPGARCPVELEGSRWWAVRQVLKDHDG +DHDHGINAVVDLEASDEAGHPAIRVVSVGAPVPGWDL +>PROKKA_01064 +MTSAATNPPSLTDRIDALPPTPDADDVFGAFAAWTEDRGISLYPAQEEAVLELVQGKHVI +LATPTGSGKSLVALAAHADALAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS +TVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQVPLLELPQAR +FLLMSATLGDTTRLEADLTERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEELVSTHQA +PVYIVHFSQLDAVETAQGLSSISVTSKEEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGV +HHAGMLPKYRRLVEKLAQDGLLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQA +REFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAAAKFANVKDEAERAKRMKQSV +KSGKRKTPPAGFVSWGPATFERLVSAEPEPLVSRMRITHSMLLNILDRPGDPVIAVRRLL +RGTHETPARQAVLMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLS +PFALAALDLLDPADPDHALDVVSVIEATLDPPRQVLSAQVKHAKGEAVAAMKAEGMDYND +RMRALDEITHPRPLAELLEQQFELYRQDAPWLAEFELTPKSVVRDMFERAMGFGDYVRFY +GIARSEGVLLRYLTDAVKALRHTVPEAARTEDLQVLLDWLDEMVKQTDSSLLEEWEDLVA +GDIDELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEALARLSGELSA +DDWADALDAYFDDHEDIDDGPAARGPELFRVTAAPDVAAPLELAGPRWWAVRQVLKDPDG +DLDHGINAVVDLDASDEAGHPVIRVVSVGAPESGWGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000926.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000926.fa new file mode 100644 index 0000000000000000000000000000000000000000..c6a3151ad8ce5a15b8d265b08efdad44e111e0ed --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000926.fa @@ -0,0 +1,34 @@ +>PROKKA_01115 +MSQIAPESPHPDTDAVVGDVTGRQGGGFTWDPAQYEGFAEHRARPFHDLVGRVRAEAPRV +VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLERAREQAARTGAPANLRFEAVDASQW +RPSGATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED +PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR +PSLQALARWDAEEGAAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF +MAGQKPA +>PROKKA_00834 +MSQIAPESPHPDTDAVVGDVTGRQGGGFTWDPAQYEGFAEHRARPFHDLVGRVRAEAPRV +VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLERAREQAARTGTPANLRFEAVDASQW +RPSRATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED +PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR +PSLQALARWDAEEGSAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF +MVGQKPA +>PROKKA_01778 +MSQIAPESPHPDTDAVAGDVTGRQGGGFTWDPAQYESFAEHRARPFHDLVGRVRAEAPRV +VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLKRAREQAARTGAPANLRFEAVDASQW +RPSRATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED +PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR +PSLQALARWDAEECSAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF +MVGQKPA +>PROKKA_01671 +MSTVPAVTGRETAGFTWDPAQYEGFAEHRARPFHDLVARVEAEAPRVVVDLGCGPGTLTR +TLAERWPAAEVIGLDDSPAMLERAREGAADADLPNLRFDRVDASQWRPGPEVDVIVSNAM +LQWIPTHRRLIRRWLGDLHPGAWFGAQLPRPYQQASHATIVALADEPVFSEALHGVETTR +TVAPPEEYTRLFLEAGWTPSVWETEYQQVLTGPDPVLRWTSGAALRPSLQALAAWDAEEG +AAEGAGLLELFVARYRQAMREAYPPVPGVSDADGGPLTVFPVRRMFLVGRKPGE +>PROKKA_01065 +MSQIAPESPHPDTDAVVGDVTGRQGGGFTWDPAQYEGFAEHRARPFHDLVGRVRAEAPRV +VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLERAREQAARTGTPANLRFEAVDASQW +RPSRATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED +PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR +PSLQALARWDAEEGSAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF +MVGQKPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000927.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000927.fa new file mode 100644 index 0000000000000000000000000000000000000000..d4b96112bc6d85dc2450d75b8c8b3f3ff982dd89 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000927.fa @@ -0,0 +1,25 @@ +>PROKKA_01116 +MPETARNRLLHDLPAVTVRTCSVSEMDNNVYLLTSKTTGAQVLIDAAAEAEAIRDLIASA +ADDTPCEPRLEMIVTTHRHWDHVRALPALASLTGARTAAGEDDADAIAEATGVAPDVRLR +HGDTVGADGLRLEVVALRGHTPGSIALVCRPEADEPAVLFTGDSLFPGGVGNTEGDDGRF +RQLFTDVSDRIFDAFDDDVVVHPGHGASTTLGAERPHLPEWAERSW +>PROKKA_00835 +MPETARNRLLHDLPAVTVRACSVSEMDNNVYLLTSKTTGAQVLIDAAAEAEAIRDLIASA +ADDTPCEPRLEMIVTTHRHWDHVRALPALASLTGARTAAGEDDADAIAEATGVAPDVRLR +HGDIVGVDGLRLEVLALRGHTPGSIALVCRPEADEPAVLFTGDSLFPGGVGNTEGDDGRF +RQLFTDVTERIFDAFDDDVVVHPGHGASTTLGAERPHLPEWAERGW +>PROKKA_01777 +MPETARNRLLHDLPAVTVRTSSVSEMDNNVYLLTSKTTGAQVLIDAADDAEAIRDLIASA +AGDTPCEPRLEMIVTTHRHWDHVRALPALASLTGARTAAGEDDADAIAEATGVAPDVRLH +HGDIVGADGLRLEVVALRGHTPGSIALVCRPEADEPAVLFTGDSLFPGGVGNTEGDDGRF +RQLFTDVSERIFDAFDDDVVVHPGHGASTTLGAERPHLPKWAERGW +>PROKKA_01670 +MPATAEPRLLHDLPAVTVRAVSVSEMDNNAYVLTSKTTGAQVLIDAAAEPETLRDLLASA +AADTPCELRLELIVTTHRHWDHVRALPALATVTGARTAAGEDDADAIAAETGVTPDVRLA +HGSRTGAEGIELEVIALRGHTPGSVALAYRPEADEPAVLFTGDSLFPGGVGNTQGDAERF +ASLIRDVEDRVFAAFDDDVVVHPGHGASTTLGAERPHLQEWRERGW +>PROKKA_01066 +MPETARNRLLHDLPAVTVRACSVSEMDNNVYLLTSKTTGAQVLIDAAAEAEAIRDLIASA +ADDTPCEPRLEMIVTTHRHWDHVRALPALASLTGARTAAGEDDADAIAEATGVAPDVRLR +HGDIVGVDGLRLEVLALRGHTPGSIALVCRPEADEPAVLFTGDSLFPGGVGNTEGDDGRF +RQLFTDVTERIFDAFDDDVVVHPGHGASTTLGAERPHLPEWAERGW diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000928.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000928.fa new file mode 100644 index 0000000000000000000000000000000000000000..ed65360a55bbef223c34d4c3cbb431f0d1b93186 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000928.fa @@ -0,0 +1,60 @@ +>PROKKA_01119 +MPVADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLSSYFQDPARLATKTR +TMVFTAAAVEWTVVGSELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQ +VMRGDRKPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRARAQDRPCLLGYIGK +CSAPCVGRISPADHRALAQDFCDFMAGDANRFIRELEKAMARAVEELRYEDAARLRDDIA +ALRRVFERNAVVLPENTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVAEP +EMVAHLLQQVYGDLEGPERIPHEILVPVEPDDAAQLTEWLSGLRGSRVAVRVPRRGSKAD +LMETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEITEPLLRIECYDISHSQGTNV +VGSMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARLAKERAEGAPLSGQVE +ADDQEAGRRFAYPPSLVVVDGGPPQVAAAAAVLEELGLDDLPVVGLAKRLEEVWLPGDEF +PVVLPRTSEGLYLLQRIRDESHRFAIAGHRSRRSKAMTVSALDGIPGLGPAKRTALLNHF +GSVAEIRAAGVDRLTEVAGIGPRLAEAVHTALTADTPADTVES +>PROKKA_00838 +MADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLSSYFQDPARLATKTRAM +VFTAAAVEWTVVGSELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQVM +RGDRKPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRARAQDRPCLLGYIGKCS +APCVGRISPADHRALAQDFCDFMAGDANRFIRELEKAMARAVEELRYEDAARLRDDIAAL +RRVFERNAVVLPENTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVAEPEM +VAHLLQQVYGDLEGPERIPHEILVPVEPDDAAQLTEWLSGLRGSRVAVRVPRRGSKADLM +ETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEVTEPLLRIECYDISHSQGTNVVG +SMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARLAKERAEGAPLSGQVEGD +DQEAGRRFAYPPSLVVVDGGPPQVAAAAAVLAELGLDDLPVVGLAKRLEEVWLPGDEFPV +VLPRTSEGLYLLQRIRDESHRFAIAGHRSRRSKAMTVSALDGIPGLGPAKRTALLNHFGS +VAEIRAAGVDRLTEVAGIGPRLAEAVHTALTADTPADTVES +>PROKKA_01774 +MADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLGSYFQDPARLTTKTRTM +VFTAAAVEWTVVGSELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQVM +RGDRRPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRARAQDRPCLLGYIGKCS +APCVGRISPAEHRELAQDFCDFMAGDAQRFIRELERAMQGAVEELRYEDAARLRDDIAAL +RRVFERNAVVLPESTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVSEPEM +VTHLLQQVYGDLAGEDRIPHEILVPAEPDDAAQLVEWLSGLRGARVNVRVPRRGTKADLM +ETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEIAEPLLRIECYDISHSQGTNVVG +SMVVMEDGLPKKKDYRRFNVTGEAARDDTASMKDVLSRRFARLAEERAEGAPLSGQLEGE +EEGRDRRFAYPPSLVVVDGGPPQVAAAAAVLEELGLDDLPVVGLAKRLEEVWLPGDEFPV +VLPRTSEALYLLQRIRDESHRFAIAGHRGRRAKAMTASALDGISGLGPAKRTALLNHFGS +VAQIRAAGVERLTEVAGIGPTLAQTVHAALAPAEPTDTVEP +>PROKKA_01667 +MADPRTYRPAPGEISTSPGVYRFRDPDGRVIYVGKAKNLRARLSSYFQDPARLATKTRTM +VFTASAVEWTVVASELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNERFPRVQVM +RGDKRPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRAQAQDRPCLLGYIGKCS +APCVGRISPDEHRALAQDFCDFMAGDADRFVRELEKAMAGAVEELRFEDAARLRDDIAAL +RRVFERNAVVLAESTEADVFALHSDELETAVQVFHVRQGRIRGQRGWIMERVEDVGEDEA +VAELLTQVYGDVPDTERIPHEVLVPVLPAGAEQVTEWLSGLRGARVQVRVPQRGPKADLM +GTVRENAEMALKLHKTRRSGDLTTRSAALRELQDALEIDEPLLRIECYDISHSQGTNVVG +SMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARMAEDRREGGVLTGQIDAE +EAEGERRRFAYPPSLVVVDGGPPQVAAAAEVLAELGLDDLPVVGLAKRLEEVWLPGDEFP +VVLPRTSEGLFLLQRIRDESHRFAIAGHRSRRTKAMTASALDDVPGLGPTRRRALLTHFG +SVERMRQAGPAGLTEVAGIGPALAEAVHAALTASDGGDTVAP +>PROKKA_01069 +MPVADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLSSYFQDPARLATKTR +TMVFTAAAVEWTVVGSELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQ +VMRGDRKPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRARAQDRPCLLGYIGK +CSAPCVGRISPADHRALAQDFCDFMAGDANRFIRELEKAMARAVEELRYEDAARLRDDIA +ALRRVFERNAVVLPENTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVAEP +EMVAHLLQQVYGDLEGPERIPHEILVPVEPDDAAQLTEWLSGLRGSRVAVRVPRRGSKAD +LMETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEITEPLLRIECYDISHSQGTNV +VGSMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARLAKERAEGAPLSGQVE +GDDQEAGRRFAYPPSLVVVDGGPPQVAAAAAVLEELGLDDLPVVGLAKRLEEVWLPGDEF +PVVLPRTSEGLYLLQRIRDESHRFAIAGHRSRRSKAMTVSALDGIPGLGPAKRTALLNHF +GSVAEIRAAGVDRLTEVAGIGPRLAEAVHTALTADTPADTVES diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000929.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000929.fa new file mode 100644 index 0000000000000000000000000000000000000000..4b8727cb4256b5f4a57192fc86e5c8f5f112f568 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000929.fa @@ -0,0 +1,30 @@ +>PROKKA_01120 +MTEETLQPEKPPTSEVLVIAGMSGAGRTTAAHALEDHGWDVVENMPPALFGTLAELIARS +PEAFPRLAIVVDVRSRSYFEELYAALQHLANSGVEYRTVFLDAEDHVLLQRFEAGRRPHP +MQGNARLLDGIRAERDVVEPLKARADVVVDTTELNVHGLATEITELFSESGPVTLRLTIM +SFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAAVADYVLSRPGVEDFLRTYVAM +LGPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVHVQHRDMGRE +>PROKKA_00839 +MTEETLQPEKPPTSEVLVIAGMSGAGRTTAAHALEDHGWDVVENMPPALFGTLAELIARS +PEAFPRLAIVVDVRSRSYFEELYAALQHLANSGVEYRTVFLDAEDHVLLQRFEAGRRPHP +MQGNARLLDGIRAERDVVEPLKARADVVVDTTELNVHGLATEITELFSESGPVTLRLTIM +SFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAAVADYVLSRPGVEDFLRTYVAM +LGPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVHVQHRDMGRE +>PROKKA_01773 +MSEESLRPEKPPTSEVLVITGMSGAGRTTAAHALEDHGWYVVENMPPPLFITLADLVARS +PEAFPRLAIVVDVRSRAYFPELHAALQQLENNGVEYRMVFLEADEHVLVRRFEAGRRPHP +LQGNASLLDGIRAERDMLAELKARADVVVDTTELNVHGLATEITELFSVSGPVTLRLTLM +SFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAEVSDYVLTRPGVEDFLRSYTAM +LAPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVQVQHRDMGRE +>PROKKA_01666 +MSADEHLQPDKPPSSEVLVITGMSGAGRTTAAHALQDHGWYVVENMPPQLLGTLSDLVAR +SPEAFPRLAIVVDVRSRSYFNELRTALQQLESTGVEFRTVFLEASDEVLVRRFEAGRRPH +PLQGNARLLDGIQAEREILSELKERADIVVDTSALNVHGLATEVTQLFSEDGPVTVRLNV +MSFGFKYGLPSDANFVADMRFVANPHWVPELRSKTGLDPEVSGFVLGQPGVQEFLSNYLA +ALGPVVEGYRRENKHYATLAVGCTGGKHRSVAVAEELARRVAQWPRVSVHVDHRDVGRE +>PROKKA_01070 +MTEETLQPEKPPTSEVLVIAGMSGAGRTTAAHALEDHGWDVVENMPPALFGTLAELIARS +PEAFPRLAIVVDVRSRSYFEELYAALQHLANSGVEYRTVFLDAEDHVLLQRFEAGRRPHP +MQGNARLLDGIRAERDVVEPLKARADVVVDTTELNVHGLATEITELFSESGPVTLRLTIM +SFGFKYGVPADANFVADMRFIPNPHWVPALRPHTGTEAAVADYVLSRPGVEDFLRTYVAM +LGPVFEGYRRENKHYATLAIGCTGGKHRSVAVAEELARRLAQVPHVTVHVQHRDMGRE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000935.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000935.fa new file mode 100644 index 0000000000000000000000000000000000000000..616a2cb9c262eb8186810e93a1a64153e58b61de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000935.fa @@ -0,0 +1,30 @@ +>PROKKA_01126 +MAEQTTRVPLIAGNWKMNLDHLEAVTLVQRLTWLLSDADHDQEAVEVAVFPPFTGLRSVQ +TLVTGDRLDLVYGAQDLSPEDAGAYTGDVSGAFLAALGCRYAIVGHSERRTLHGEDDALV +ARKAAAALRHGLTPVICVGEGLEVRQAGRHVEHTLAQLEGSIAGLSAQDVAGVVVAYEPV +WAIGTGEVAGPEDAQQMCAALRARVAALHGDDVAAGLRILYGGSVKSSSAPALLAQPDVD +GALVGGASLDADEFAKIVRFDQA +>PROKKA_00845 +MAEQTTRVPLIAGNWKMNLDHLEAVTLVQRLTWLLTDADHDQEAVEVAVFPPFTGLRSVQ +TLVTGDRLDLVYGAQDLSPEDAGAYTGDVSGAFLAALGCRYAIVGHSERRTLHGEDDALV +ARKAAAALRHGLTPVICVGEGLEVRQAGRHVEHTLAQLEGSIAGLSAQDVAGVVVAYEPV +WAIGTGEVAGPEDAQQMCAALRARVAALHGDDVAAGLRILYGGSVKSSSAPALLAQPDVD +GALVGGASLDADEFAKIVRFDQA +>PROKKA_01766 +MAETAARVPLIAGNWKMNLDHREAVTLVQRLAWLLTDADHDHEDVEVAVFPPFTDLRAVQ +VLVTGDRLDVAYGAQDLSPEDSGAYTGDVSGAFLAALGCRYAIVGHSERRTIHGEDDALV +ARKAAAALRHGLSPVVCVGEGLDVRQAGRHVAHTVAQLEGSLVGLSAEDVARTVVAYEPV +WAIGTGEVAGAGDAQEMCAALRARVGELHGDDVAAGLRILYGGSVKSTSAPELLAQPDVD +GALVGGASLDAEEFARIVRFDQA +>PROKKA_01660 +MSVVQPVRVPLIAGNWKMNLDHQEAVTLVQRLGWLLGDADHEQGNVEAAVFPPFTDLRSV +QTLVAADRIGVAYGAQDVSAEDSGAFTGEVSGAFLAKLGCAYAIVGHSERRTLHHEDDAL +VARKAAAALRHGLVPVVCVGEGLDVRQAGRHVEHTVAQLRGSLDGLSSEDVARVVVAYEP +VWAIGTGEVASAADAQEMCAALRADLAERHGAEVAERVRVLYGGSVKSSSAPELLAQPDV +DGALVGGASLDADEFARIVRSDAAH +>PROKKA_01076 +MAEQTTRVPLIAGNWKMNLDHLEAVTLVQRLTWLLTDADHDQEAVEVAVFPPFTGLRAVQ +TLVTGDRLDLAYGAQDLSPEDAGAYTGDVSGAFLAALGCRYAIVGHSERRTLHGEDDALV +ARKAAAALRHGLTPVICVGEGLEVRQAGRHVEHTLAQLEGSIAGLSAQDVAGVVVAYEPV +WAIGTGEVAGPEDAQQMCAALRARVAALHGDDVAAGLRILYGGSVKSSSAPALLAQPDVD +GALVGGASLDADEFAKIVRFDQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000936.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000936.fa new file mode 100644 index 0000000000000000000000000000000000000000..ed28899a924ff7034cd47c7e9ebfcac07ed38898 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000936.fa @@ -0,0 +1,15 @@ +>PROKKA_01127 +MDVLTLALQILVVVLSVVIVLLILLHKGRGGGVSDMFGGGVTSSMSSSGSAQRLLTRLTV +GSVVAWGVVIALLGVLPRLTMES +>PROKKA_00846 +MDVLTLALQILVVVLSVVIVLLILLHKGRGGGVSDMFGGGVTSSMSSSGSAQRLLTRLTV +GSVVAWGVVIALLGVLPRLTMES +>PROKKA_01765 +MDMLTLILQILVVVLSVVIVLLVLLHKGRGGGVSDMFGGGVTTSMSSSGSAQRLLTRLTV +GTVAAWALLIVTLGVLPRLAMES +>PROKKA_01659 +MDILTLLLQIAVVALSVVIIMLVLLHKGRGGGVSDMFGGGVTTSMSSSGSAQRLLTRVTV +SATVLWGLAIVALALIARFSVES +>PROKKA_01077 +MDVLTLALQILVVVLSVVIVLLILLHKGRGGGVSDMFGGGVTSSMSSSGSAQRLLTRLTV +GSVVAWGVVIALLGVLPRLTLES diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000938.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000938.fa new file mode 100644 index 0000000000000000000000000000000000000000..2a7954c549d4c1e4a9bef198cafc5899a150bf45 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000938.fa @@ -0,0 +1,50 @@ +>PROKKA_01129 +MAGESRTAPRNPLRDPRDRRLTRIAGPSALVLFGVTGDLAKKKLLPAMYDLAQRGLLPPA +FSLVGFGRRSWSDEEFADYVRAAVEASSRTTFDETVWDQFQGGLRFVSGAFDDEAAYVRL +DEVLAELETSRGTRGNTAFYLSIPPDWFEAVSRHLADQGLADRSQPAEGPWRRVVIEKPF +GHDLASAQELNAVIERVFPSDAVFRIDHYLGKETVQNILAFRFANRMFEPLWNAEHVDHV +QITMAEDIGIGGRASYYDGVGAARDVIQNHLLQLLAFTAMEEPISFDADHLRAEKEKVLE +AVTVPDTPEGLAAASARGQYTSGWQGGERVTGFLDEEGFNPASVTETYAALKVGIRTRRW +QGVPFYLRAGKRLGRRVTEIAVVFKKPPHLLFPVHDGDEFGQNIIVIRVQPDEGVTIRFA +SKVPGTQTEIRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQAEVELSWRIVD +PFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRSWRRP +>PROKKA_00848 +MAGESRTAPRNPLRDPRDRRLTRIAGPSALVLFGVTGDLAKKKLLPAMYDLAQRGLLPPA +FSLVGFGRRSWSDEEFADYVRAAVEASSRTTFDETVWDQFQGGLRFVSGAFDDEAAYVRL +DEVLAELETSRGTRGNTAFYLSIPPDWFEAVSRHLADQGLADRSQPAEGPWRRVVIEKPF +GHDLASAQELNAVIERVFPSDAVFRIDHYLGKETVQNILAFRFANRMFEPLWNAEHVDHV +QITMAEDIGIGGRASYYDGVGAARDVIQNHLLQLLAFTAMEEPISFDADHLRAEKEKVLE +AVTVPDTPEGLAAASARGQYTSGWQGGERVTGFLDEEGFNPASVTETYAALKVGIRTRRW +QGVPFYLRAGKRLGRRVTEIAVVFKKPPHLLFPVHDGDEFGQNIIVIRVQPDEGVTIRFA +SKVPGTQTEIRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQAEVELSWRIVD +PFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRSWRRP +>PROKKA_01763 +MPGESKAAARNPLRDPRDRRLTRIAGPSALVLFGVTGDLAKKKLLPAMYDLAQRGLLPPS +FSLVGFGRRDWSDEEFAEYVRAAVEASARTTFDETVWDQFRGGLRFVSGAFDDEAAYVRL +GEVLGELESSRGTRGNTAFYLSIPPDWFEDVSRHLADQGLADRSQPADGPWRRVVIEKPF +GHDLASAQELNAVIERVFPPDAVFRIDHYLGKETVQNILAFRFANRMFEPIWNAEHVDHV +QITMAEDIGIGGRAGYYDGVGAARDVIQNHLLQLLAFTAMEEPISFDADHLRTEKEKILE +AVQVPDTPAGLEAASARGQYTSGWQGGERITGFLDEEGFNPESVTETYAALKVGIRTRRW +QGVPFYLRAGKRLGRRVTEIAVVFKKPPHLLFPVHEGDEFGQNVIVIRVQPDEGVTIRFA +SKVPGTQSEVRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQAEVELSWRIVD +PFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRAWRRP +>PROKKA_01657 +MRPEPGGPARRNPLRDPRDRRLTRIAGPSALVLFGVTGDLARKKLLPAMYDLAHRGLLPP +SFSLVGFGRRDWSEAEFADYVRAAVEAGSRTAFNETVWDQFRGGLRFVSGAFGDADAYAR +LDEVLTELESSRGTGGNTAFYLSIPPDWFEDVSRHLADQGLADRSQPADGPWRRVVIEKP +FGHDLASAHELNAVIERVFPPDAVFRIDHYLGKETVQNILAFRFANRIFEPLWSAEHVDH +VQITMAEDIGIGGRAGYYDGVGAARDVIQNHLLQLLALTAMEEPISFDAAHLRAEKEKVL +AAVRVPCTPEGLEAASARGQYTSGWQGGEQVTGFLDEEGFNPASVTETFAALKVDIGTRR +WQGVPFYLRAGKRLGRRVTEIAVVFKSPPHLLFPVHPGDEFGQNVIVIRVQPDEGVTIRF +ASKVPGTQHEVRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQEEVELSWAIV +DPFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRTWRRP +>PROKKA_01079 +MAGESRTAPRNPLRDPRDRRLTRIAGPSALVLFGVTGDLAKKKLLPAMYDLAQRGLLPPA +FSLVGFGRRSWSDEEFADYVRAAVEASSRTTFDETVWDQFQGGLRFVSGAFDDEAAYVRL +DEVLAELETSRGTRGNTAFYLSIPPDWFEAVSRHLADQGLADRSQPAEGPWRRVVIEKPF +GHDLASAQELNAVIERVFPSDAVFRIDHYLGKETVQNILAFRFANRMFEPLWNAEHVDHV +QITMAEDIGIGGRASYYDGVGAARDVIQNHLLQLLAFTAMEEPISFDADHLRAEKEKVLE +AVTVPDTPEGLAAASARGQYTSGWQGGERVTGFLDEEGFNPASVTETYAALKVGIRTRRW +QGVPFYLRAGKRLGRRVTEIAVVFKKPPHLLFPVHDGDEFGQNIIVIRVQPDEGVTIRFA +SKVPGTQTEIRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQAEVELSWRIVD +PFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRSWRRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000941.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000941.fa new file mode 100644 index 0000000000000000000000000000000000000000..ba1ab461bd71484ffebf82f98ee719dec0d9fbae --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000941.fa @@ -0,0 +1,69 @@ +>PROKKA_01132 +MTDAAQPSTPPTLDRVAPARGFVYSEQDRRMVDTLKALSADAVEKAGHGHPGTAISLAPV +AWQLYQNVMHLDPTDDRWEGRDRFILSAGHASLIQYLQLFAAGAGLEIEDIQGLRTEGSR +TPGHPEYGHTHGVEVTTGPLGQGLAMGVGFAYEQRRVRGLMDPDAAPGTSPFDHHVFVLA +SDGDIQEGVAAEASSLAGHQELGNLVVVYDANRISIEDDTDIAFTEDVVRRYEAYGWHVQ +EVDWTNGAQGHAVTEYTEDVEALYDALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGIH +GSKLGTDEVAGLKESLGLDPTKTFDVDPELLARARSIAERSAEYRRGWEVAFQAWREANP +ENARLYDRLAGRELPAGFADAFPSWDADEKGLATRAASGEVLTALAPVMPELWGGSADLA +GSNNTTMKGEPSFIPARRSTATWQGHEYGRTLHFGVREFAAGAIVNGITIGGLTRAYVGT +FLTFSDYMRPAVRLAALMGTPSTYVWTHDSIGLGEDGPTHQPVEHLAALRAIPGLDVVRP +ADANETAWAWRTVLEHRDRPAGLVLSRQSLPVLPRDTDGFAPASGVARGAYVLIDATDAD +GAPTPARALLIATGSEVSVAVRARALLQADGVPTRVVSAPCLEWFAEQDEAYRAEVLPDG +PDAPVRVSVEAGIAMPWFEHTVTASSPGARVSLEHYGESADGARLMEKYGFTGEHVAEVT +RGLL +>PROKKA_00851 +MTDAAQPSTPPTLDRVAPARGFVYSEQDRRMVDTLKALSADAVEKAGHGHPGTAISLAPV +AWQLYQNVMHLDPTDDRWEGRDRFILSAGHASLIQYLQLFAAGAGLEIEDIQGLRTEGSR +TPGHPEYGHTHGVEVTTGPLGQGLAMGVGFAYEQRRVRGLMDPDAAPGTSPFDHHVFVLA +SDGDIQEGVAAEASSLAGHQELGNLVVVYDANRISIEDDTDIAFTEDVVRRYEAYGWHVQ +EVDWTNGAQGHAVTEYTEDVEALYDALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGIH +GSKLGTDEVAGLKESLGLDPTKTFDVDPELLARARSIAERSAEYRRGWEVAFQAWREANP +ENARLYDRLAGRELPAGFADAFPSWDADEKGLATRAASGEVLTALAPVMPELWGGSADLA +GSNNTTMKGEPSFIPARRSTATWQGHEYGRTLHFGVREFAAGAIVNGITIGGLTRAYVGT +FLTFSDYMRPAVRLAALMGTPSTYVWTHDSIGLGEDGPTHQPVEHLAALRAIPGLDVVRP +ADANETAWAWRTVLEHRDRPAGLVLSRQSLPVLPRDTDGFAPASGVARGAYVLIDATDAD +GAPTPARALLIATGSEVSVAVRARALLQADGVPTRVVSAPCLEWFAEQDEAYRAEVLPDG +PDAPVRVSVEAGIAMPWFEHTVTASSPGARVSLEHYGESADGARLMEKYGFTGEHVAEVT +RGLL +>PROKKA_01760 +MTDAQHPSTAPALDRTAPARDFVYSEQDRRMVDTLKVLSADAVEQAGHGHPGTAISLAPV +AWQMYQNVMHLDPQDDRWEGRDRFILSAGHASLIQYLQLFAAGAGLELEDIRALRTEGSK +TPGHPEYGHTHGVEVTTGPLGQGLAMGVGFAYEQRRLRGLMDPDAAPGTSPFDHHVFVLA +SDGDIQEGVAAEASSLAGHQELGNLVVVYDANRISIEDDTDIAFTEDVSARYEAYGWHVQ +EVDWTNGALGHAVTEYTEDVEALYEALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGVH +GSKLGAEELAGLKEGLGFDPAESFDVDPEVLANSRSIAERSAAYRRTWEGAFQAWREAHP +ENARLYDRLAGRELPEGFAEAFPSWDADEKGLATRAASGEVLTALAPVMPELWGGSADLA +RSNNTTMKGEPSFIPARRSTATWQGDEHGRTLHFGIREFAAGAIVNGITIGGLTRAYMGT +FLTFSDYMRPAVRLAALMGTPSVYVWTHDSIGLGEDGPTHQPVEHLAALRAIPGLDVVRP +ADANETAWAWRTVLENRDRPAGMVLSRQNLPVLPRDTDGFASAEGVARGAYVLVDAVGGS +GAPAPARVLLIATGSEVSVAVHARELLQAEGVPTRVVSAPCLEWFAEQDEAYRAEVLPDG +PDAPVRVSVEAGIAMPWFEHTVTAVSRGARVSLEHYGESADGARLMEKYGFTGEAVAQAA +RGLL +>PROKKA_01654 +MTDTASTALDRTLPARDFVYDEQDRRMVDTLKVLAADAVEKAGHGHPGTAISLSPVAWQL +YQNVMHLDPSDDRWEGRDRFILSAGHASLIQYLQLFAAGAGLELEDIAALRTEGSLTPGH +PEYGHTHGVEVTTGPLGQGLAMAVGFAYEQRRLRGLMDPDAAPGTSPFDHHVFVLASDGD +IQEGVSSEASSLAGHQELGNLVVVYDANRISIEDDTDISFTEDVAKRYKAYGWHVQEVDW +SNGAQGHEVTEYTEGVQDLYEALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGIHGSKL +GGDEVVGLKEALGFDPQKSFDVDPEVLAHARSISERSAAYRETWEAAFAAWREAHPENAR +LYDRLASRELPAGFEDAFPSWDADEKGVATRAASGKVLTALAPVMPELWGGSADLAGSNN +TTMEGEPSFIPAHRSTAAWQGDPFGRTLHFGIREFAAGAIVNGITIGGLTRAYMGTFLTF +SDYMRGAVRLAALMGTPAVYVWTHDSVGLGEDGPTHQPVEHLAALRAIPGLDVVRPADAN +ETAWAWRTILQHRDRPAGLVLTRQNVPVLPRGTEGFAPADGVARGAYVLVDGADASGAAA +PARVVLIATGSEVSVAVGARELLQAEGVPTRVVSAPCLEWFAEQDEAYRAEVLPDGPGAP +VRVSVEAGIAMPWHELTVTQSSRGARVSLEHYGESADGPHLLKKYGFSPENVADTARGLL +>PROKKA_01082 +MTDAAQPSTPPTLDRVAPARGFVYSEQDRRMVDTLKALSADAVEKAGHGHPGTAISLAPV +AWQLYQNVMHLDPTDDRWEGRDRFILSAGHASLIQYLQLFAAGAGLEIEDIQGLRTEGSR +TPGHPEYGHTHGVEVTTGPLGQGLAMGVGFAYEQRRVRGLMDPDAAPGTSPFDHHVFVLA +SDGDIQEGVAAEASSLAGHQELGNLVVVYDANRISIEDDTDIAFTEDVVRRYEAYGWHVQ +EVDWTNGAQGHAVTEYTEDVEALYDALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGIH +GSKLGTDEVAGLKESLGLDPTKTFDVDPELLARARSIAERSAEYRRGWEAAFQAWREANP +ENARLYDRLAGRELPAGFADAFPSWDADEKGLATRAASGEVLTALAPVMPELWGGSADLA +GSNNTTMKGEPSFIPARRSTATWQGHEYGRTLHFGVREFAAGAIVNGITIGGLTRAYMGT +FLTFSDYMRPAVRLAALMGTPSTYVWTHDSIGLGEDGPTHQPVEHLAALRAIPGLDVVRP +ADANETAWAWRTVLEHRDRPAGLVLSRQSLPVLPRDTDGFAPASGVARGAYVLIDATDAD +GAPTPARALLIATGSEVSVAVRARALLQADGVPTRVVSAPCLEWFAEQDEAYRAEVLPDG +PDAPVRVSVEAGIAMPWFEHTVTASSPGARVSLEHYGESADGARLMEKYGFTGEHVAEVT +RGLL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000944.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000944.fa new file mode 100644 index 0000000000000000000000000000000000000000..23241a81462bd499d280bf52846d3229d9f7ce03 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000944.fa @@ -0,0 +1,30 @@ +>PROKKA_01135 +MSTPVVDHRAPAGTGAHAGAAPLAARVLRQAGYETGTALRNGEQLLVTVVLPLLALVGVH +VTGLLDAPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALATTPLGTLGLV +AGKALAVVALLLVQVSVIGGVGLALGWRPDPEGILPALVALALGAAAFTALGLLLAGTAR +PEATLAVANLLWVLFGAVGGTVFPARVPGVDLLPSGALGTALRAALLDGAWSPVPLLVLT +LWGAVAVAAALRWFRWRP +>PROKKA_00854 +MSTPVVDHRAPAGTGAHAGAAPLAARVLRQAGYETGTALRNGEQLLVTVVLPLLALVGVH +VTGLLDAPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALATTPLGTLGLV +AGKALAVVALLLVQVSVIGGVGLALGWRPDPEGILPALVALALGAAAFTALGLLLAGTAR +PEATLAVANLLWVLFGAVGGTVFPARVPGVDLLPSGALGTALRAALLDGAWSPVPLLVLT +LWGAVAVAAALRWFRWRP +>PROKKA_01757 +MSAPIAPGSAEPRTAGQVPEPGTAPHAGAAPLATRVLRQAAYETGTALRNGEQLLVTVVL +PLLALVGVHVTGLLDEPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALAT +TPLGTLGLVAGKALSVVALLLVQVAVIGGVGLALGWRPEAAGILPAVVALALGAAAFTAL +GLLLAGTARPEATLAAANLLWVLFGAVGGTVFPSRVPGVDLLPSGALGSALRAALVDGAG +APIPLLVLALWCAVAVAAALRWFRWRP +>PROKKA_01651 +MSAPAAPIPASHAGAAPLGARILAQARYETVTALRNGEQLLVTLVLPLLALVGVHVTGLL +DAPGRNGLDLAVPGVLALAVISAAFTATAISTGFERRYDVLAALATTPLGTGGLVAGKAA +AVAAVLLLQTIVIGGVGLALGWSPDPAGIPPAVVALLLGAAAFTALGLLLAGTARPEATL +AVANLVWVLLGALGGTVFPSRWAWMDLLPSGALGTALRSALQDGAWAPSALAVLAAWTVM +AVAAALRWFRWRP +>PROKKA_01085 +MSTPVVDHRAPAGTGAHAGAAPLAARVLRQAGYETGTALRNGEQLLVTVVLPLLALVGVH +VTGLLDAPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALATTPLGTLGLV +AGKALAVVALLLVQVSVIGGVGLALGWRPDPEGILPALVALALGAAAFTALGLLLAGTAR +PEATLAVANLLWVLFGAVGGTVFPARVPGVGLLPSGALGTALRAALLDGAWSPVPLLVLT +LWGAVAVAAALRWFRWRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000945.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000945.fa new file mode 100644 index 0000000000000000000000000000000000000000..e0ec07b66d76985b4709b5893bec08f56019997c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000945.fa @@ -0,0 +1,35 @@ +>PROKKA_01136 +MPRDEPVLRLSDVHRSLGRGRSRTPVLRGVDLTARAGAVTVLLGPNGAGKSTTLGLCHGM +DRPDAGTVRVFGADPWRASADLRARIGVMWQEGGLPPAIPARRFVGHVASLYRDPLPVEP +LLERLLIAEVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLDPETRPVVHDVV +REQTDRGAAVLLTTHLLDDAERLADDVAILRAGRVVRSGSLAELTRVAEGDVVDVDFGDA +SPDAVRAWADTLPAPLRAAGLDESARLRVAGVRGPDDLAVLAASWREHALMPTRFERAGL +RLEQILRETAA +>PROKKA_00855 +MPRDEPVLRLSDVHRSLGRGRSRTPVLRGVDLTARAGAVTVLLGPNGAGKSTTLGLCHGM +DRPDAGTVRVFGADPWRASADLRARIGVMWQEGGLPPAIPARRFVGHVASLYRDPLPVEP +LLERLLIAEVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLDPETRPVVHDVV +REQTDRGAAVLLTTHLLDDAERLADDVAILRAGRVVRSGSLAELTRVAEGDVVDVDFGDA +SPDAVRAWADTLPAPLRAAGLDESARLRVAGVRGPDDLAVLAASWREHALMPTRFERAGL +RLEQILRETAA +>PROKKA_01756 +MVPRPVLTPDPAPRDEPVLRLRDVHRSLGRGRARTPVLRGVDLTARAGAVTVLLGPNGAG +KSTTLGLCHGMDRPDAGAVRVFGADPWRAPADLRARIGVMWQEGGLPPSVPARRFVGHVA +SLYRDPMPVEPLLERLLIADVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLD +PETRPVVHEVVREQTARGAAVLLTTHLLDDAERLADDVAILRAGRVVRAGSLADLTRVAE +GDVVDVDFGDAAPEAVRAWADALPEPLRAAGLAEPARLRVAGVHGPAELAALAASWHRHA +LMPTRFERAGLRLEQILRETAA +>PROKKA_01650 +MPETSPHPDAPALRLHEVRRTLGRGAARTEVLRGVDLEARRGAVTVLLGPNGAGKSTTLA +LCHGSDRPDSGTVRVFGRDPWRADADLRARLGVMWQEGGLPPSVTARRFVRHVASLHGDP +LDPDALLGRLRIDRVADRPIRRLSGGQRQRVALAAAVVGRPDLLFLDEPTAGLDPETRPV +VHDVVREHTARGAAVLLTTHLLDDAERLADDVAILRAGRVVRAGTLAELTRVQDGDVVDV +RFDEARAADVRAWVAAAPASFRAVASAGAPAARVAGVRSPADLEALAASWTRAGLFPTRL +ERAVLRLEELLQSPDADTPSPERSR +>PROKKA_01086 +MPRDEPVLRLSDVHRSLGRGRSRTPVLRGVDLTARAGAVTVLLGPNGAGKSTTLGLCHGM +DRPDAGTVRVFGADPWRASADLRARIGVMWQEGGLPPAIPARRFVGHVASLYRDPLPVEP +LLERLLIAEVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLDPETRPVVHDVV +REQTDRGAAVLLTTHLLDDAERLADDVAILRAGRVVRSGPLSELTRVAEGDVVDVDFGDA +SPDAVRAWADTLPAPLRAAGLGESARLRVAGVRGPDDLAVLAASWREHALMPTRFERAGL +RLEQILRETAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000950.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000950.fa new file mode 100644 index 0000000000000000000000000000000000000000..7ef07985907ba503ac8bac6bbe866ecb35d54654 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000950.fa @@ -0,0 +1,15 @@ +>PROKKA_01141 +MTETANQVPTEDIREALKDVIDPELGVNVVDLGLLYGLHYADDGALLVDMTLTTAACPLT +DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI +>PROKKA_00860 +MTETTNQAPTEDIREALKDVIDPELGVNVVDLGLLYGLHYADDGALLVDMTLTTAACPLT +DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI +>PROKKA_01751 +MTETANQVPTEDVREALKDVIDPELGVNVVDLGLLYGLHYAEDGALLVDMTLTTAACPLT +DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI +>PROKKA_01645 +MTDTAAQTPVEDIREALKDVIDPELGVNVVDLGLLYGLHYAEDGALLVDMTLTTAACPLT +DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGKDQMRALGFNI +>PROKKA_01091 +MTETTNQAPTEDIREALKDVIDPELGVNVVDLGLLYGLHYADDGALLVDMTLTTAACPLT +DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000953.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000953.fa new file mode 100644 index 0000000000000000000000000000000000000000..af873860073fc21af2dfe44fa1adfdb1607462cd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000953.fa @@ -0,0 +1,35 @@ +>PROKKA_01144 +MSIPAPMTDPTARDAERLPALRFGFLATGPWILGFVVCVLFAFLCHALAQWQWDRRVEVQ +HRVNRVLENYDDDPVPFAEASRLFTAFQTDDEWTPVTLTGEYLVDETLIVRNRPRAGQPG +YEVLVPFRTDEGPVVVVDRGWLPVGNSPGQPDAVPAPPAGHAEVVVRVKPGEPALDRDAP +DGQVPSIDLAEIADTVGGPVAGTAYGIMVTEDPAVEPMPQKLVEPTLDEGPHLSYAIQWY +LFAAMGFGVWGYSAWMRARNDRADALDDAADDGLLSAHRVPRAKPARRRRDGRLTDEEAE +DALFD +>PROKKA_00863 +MSTPAPMSAPTARDAERLPPLRFGFLATGPWILGFVLCILFAFLCHALAQWQWDRRVEVQ +HRVNRVLENYDDDPVPFAEASRLFTAFQTEDEWTPVTLTGEYLVDETLIVRNRPRAGQPG +YEVLVPFRTDEGPVVVVDRGWLPVGNSPGQPDAVPAPPAGHAEVVVRVKPGEPALDRDAP +DGQVPSIDLAEIADTVGGPVAGTAYGIMVTEDPAVESMPQKLVEPTLDEGPHLSYAIQWY +LFAAMGFGVWGYSAWMRARNDRADALDDAADDGLLSAHRVPRAKPARRRRDGRLTDEEAE +DALFD +>PROKKA_01747 +MTAPAPATGFRRDPGSARPPRLRFDFLATPPWILGFVLCILFAFACHYLAQWQWERRVQV +QHQVNRVLENYDDAPVPFAQASRMFTDFDAQDEWTPVTLSGEYLAEETLVVRNRPRAGRP +GYEVLVPFRTDEGPVVVVDRGWLPVGNTPGRPDAVPAPPAGPAEVVVRVKPGEPALDRDA +PEGQVPSIDLAEIRGHVGGPVADTAYGIMVEEDPAVQDLPQKLVEPTLDEGPHLSYAIQW +YLFAAMGFGVWGYSAWMRARNDRADALEGVRDDGMLTARRAPRPKPVRRRRDGRPTDEEA +EDALFD +>PROKKA_01642 +MTPAPAPTDTPDAPGAERLPPLRFGFLASGPWILGFVVCILFAFLCHGLAQWQWDRRVQV +MHDVNRVLANYDDDPVPFAEAPRLFTDFDSEDEWTPVTLTGRYETDETLVVRNRPRAGAP +GYEVLVPFVTEEGVTVIVDRGWLPIGSQPGRPDAIPAPDPAAGEVVVRVKPGEPALDRDA +PEGQVPSIDLAAIERILGRPIADTAYGLMVSESPAAATVPNQLVAPTLDEGPHLSYAIQW +YIFAAMGFAVWGYSAWMKARNDRADALEDAEDDGLLAARRAPRPKARRRRRGGRPSDEEV +EDALQEDVLRDRPGQASEIRSR +>PROKKA_01094 +MSTPAPMSAPTARDAERLPPLRFGFLATGPWILGFVLCILFAFLCHALAQWQWDRRVEVQ +HRVNRVLENYDDDPVPFAEASRLFTAFQTEDEWTPVTLTGEYLVDETLIVRNRPRAGQPG +YEVLVPFRTDEGPVVVVDRGWLPVGNSPGQPDAVPAPPAGHAEVVVRVKPGEPALDRDAP +DGQVPSIDLAEIADTVGGPVAGTAYGIMVTEDPAVESMPQKLVEPTLDEGPHLSYAIQWY +LFAAMGFGVWGYSAWMRARNDRADALDDAADDGLLSAHRVPRAKPARRRRDGRLTDEEAE +DALFD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000954.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000954.fa new file mode 100644 index 0000000000000000000000000000000000000000..0e736836c984898962d052cc10347074560702d4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000954.fa @@ -0,0 +1,20 @@ +>PROKKA_01146 +MTSSAAGSRAGRPARAGRGTTPEVQGVTTAAAGRSADREARMRVYLVQMLVRTACFVAAL +FTHGWWQLGFILGAVVLPYVAVVRVNNTGPQQAGTLRAVPAQGPALAPRPDDTAAPEPVV +LTGDLVDDPRDRAPRALGRGSSSAGSPGLPGRGGA +>PROKKA_00865 +MTSSAAGSRAGRPARAGRGTTPEVQGVTTAAAGRSADREARMKVYLVQMLLRTACFVAAL +FTHGWWQLGFILGAVVLPYVAVVRVNNTGPQQAGTLRAVPAQGPALAPRPDDTAAPKPVV +LTGDLVDDPRDRAPRALGRGSSSAGGPGLPGRGAA +>PROKKA_01746 +MTSSAAGSRAGRPARAGRSTGPQVQGVTTASAARSEDREARMKVYLVQMLIRTVCFGAAL +FTTGWWQLLFILGAVALPYVAVVQVNNAGPRQAGSLRAVPAEGPELTARPADAPGPASPV +VLTGDVVDDPREVGPRALPPGSPSEGARRLPGRGAA +>PROKKA_01640 +MAAIVREPDAVQGVTTAAAPRSADRDARTRVYVVQMAVRTACFIAALFTHGWWQILFILG +AVVLPYVAVVRVNNTGPREAGRRRDVARTAPAVPALPAEPSPVPTGPVVLVGEVVEDDDP +AARRALPAGSPGETGRGRP +>PROKKA_01096 +MTSSAAGSRAGRPARAGRGTTPEVQGVTTAAAGRSADREARMKVYLVQMLLRTACFVAAL +FTHGWWQLGFILGAVVLPYVAVVRVNNTGPQQAGTLHAVPAQGPALAPRPDDTAAPKPVV +LTGDLVDDPRDRAPRALGRGSSSAGGPGLPGRGAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000956.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000956.fa new file mode 100644 index 0000000000000000000000000000000000000000..eb7b062b20343e8d57fbb89bfde1da188beaacca --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000956.fa @@ -0,0 +1,30 @@ +>PROKKA_01149 +MSTLRRLVVTADPALLVTDAPPAGVPDDAERLTDDGLLGWRFAADEWAAAPEPGSGWDVL +TVPATVAAAPAPLVVTDVDSTLIRQEVIELLAAHAGREAEVAEVTERAMRGELDFAASLH +ARVEALAGLPVGVVADVVRAIRPTDGALALIEAVTAAGGRVCAVSGGFTQVLAPLAEAWG +VHAYCANELEVQDGHLTGKVLGDVVDRAAKAAMLRAWAEDAGLTPEQAVGVGDGANDIDL +LEAAGCGVALCAKPILREHADVVVDVPSFTPLRWLLGL +>PROKKA_00868 +MSTLRRLVVTADPALLVTDAPPAGVPDDAERLTDDGLLGWRFAADEWAAAPEPGSGWDVL +TVPATVAAAPAPLVVTDVDSTLIRQEVVELLAAHAGREAEVAEVTERAMRGELDFAASLH +ARVEALAGLPVGVVADVVRAIRPTDGALALIEAVTAAGGRVCAVSGGFTQVLAPLAEAWG +VHAYCANELEVRDGHLTGKVLGDVVDRAAKAAMLRAWAEDAGLTPEQAVGVGDGANDIDL +LEAAGCGVALCAKPILREHADVVVDVPSFTPLRWLLGL +>PROKKA_01743 +MSTLRRLVVTADPALLADRTPPAGVPDDAERLLEDGLLGWRFAADEWAAAPEPGPGWAVH +TLPAAVAEAPVPLVVTDVDSTLIRQEVIELLAAHAGREAEVAAVTERAMRGELDFAASLH +ARVEALAGLPVGVVDDVVRAIRPTAGALALIEAVTAAGGRVCAVSGGFSQVLAPLAQAWG +VHAYCANELEVHDGHLTGRVAGDVVDRAAKAAMLRAWAEDAGLSPEQAVGVGDGANDIDL +LDAAGAGVALCAKPVLREHADVVVDVPSFTPLRWLLGL +>PROKKA_01637 +MTQARHLLYRAVPAGTDSPVAPAWAPLPADAEHLAADGLAGLRWEGSVPSAEEATALPED +WALASLPQSVAAAPTPLVVTDVDSTLIQQEVIELLAAHTGREAEVAAVTERAMRGELDFA +QSLHARVEALAGLPASVVDDVVARVRPTDGAVELIAAVNAAGGRVCAVSGGFTQVLAPLA +EAWGVHAYCANELEVRDGHLSGKVLGDVVDRAAKAAMLRAWAEDAGLSPEQAVGVGDGAN +DIDLLEVAGCGVALCAKPILREHADVVIDVPSFTPLRWLLGL +>PROKKA_01099 +MSTLRRLVVTADPALLVTDAPPAGVPDDAERLTDDGLLGWRFAADEWAAAPEPGSGWDVL +TVPATVAAAPAPLVVTDVDSTLIRQEVVELLAAHAGREAEVAEVTERAMRGELDFAASLH +ARVEALAGLPVGVVADVVRAIRPTDGALALIEAVTAAGGRVCAVSGGFTQVLAPLAEAWG +VHAYCANELEVRDGHLTGKVLGDVVDRAAKAAMLRAWAEDAGLTPEQAVGVGDGANDIDL +LEAAGCGVALCAKPILREHADVVVDVPSFTPLRWLLGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000963.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000963.fa new file mode 100644 index 0000000000000000000000000000000000000000..89fb00a1b7e4b00839a9d14081d043738a00c65e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000963.fa @@ -0,0 +1,40 @@ +>PROKKA_01158 +MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGAPRDPDYHGARVLTYPNPP +GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANLAGHLGKLLHQTPHVLSAHSLEPL +RPWKAEQLGGGYALSSWAERTAYLGADAVIAVSDGMRRDILACYPDVDPAKVHTVHNGID +TQVWTPQTGTAALEKYGIDPDKPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP +DTAELAHEVNELISELRRTRQGVVVIEGMIPRHEVMEILTAATVFACPSVYEPLGIVNLE +AMACGTAVVASAVGGIPEVVQDGETGLLVPFEQVDDGTGAPVDEERFAADFAAALTRVVE +DPERARAMGEAGRARAIEHFSWETIAERTIEVYEAVLR +>PROKKA_00877 +MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGAPRDPDYHGARVLTYPNPP +GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANLAGHLGKLLHQTPHVLSAHSLEPL +RPWKAEQLGGGYALSSWAERTAYLGADAVIAVSDGMRRDILACYPDVDPAKVHTVHNGID +TQVWTPQTGTAALEKYGIDPDKPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP +DTAELAHEVNELIAELRRTRQGVVVIEGMIPRHEVMEILTAATVFACPSVYEPLGIVNLE +AMACGTAVVASAVGGIPEVVQDGETGLLVPFEQVDDGTGAPVDEERFAADFAAALTRVVE +DPERARAMGEAGRARAIEHFSWETIAERTIEVYEAVLR +>PROKKA_01731 +MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGEPRDPDYHGARVLTYPNPP +GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANMAGHLGKLMHGVPHVLSAHSLEPL +RPWKAEQLGGGYALSSWAEKTAYLGADAVIAVSDGMRRDILACYPEVDPEKVHTVHNGID +TEAWTPQTETDALEKYGIDPTRPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP +DTPELAHEVNGLIAELRRTREGVVVIEGMIPRREVTQILSAATVFACPSVYEPLGIVNLE +AMACGTAVVASAVGGIPEVVQDGETGLLVPIEQVADGTGAPADEDAFAADFAAALTRVLE +DPERATAMGEAGRARAIEHFSWEAIAERTIEVYEAVLR +>PROKKA_01629 +MRIDIVTKEFPPTIYGGAGVHVAELTRVLSSRADVHVHAFGGAREPDYHGATVTSYAQPA +GFESANGAVQTLVTDLDIVGDLDGADVIHSHTWYANMAGHLGGLMHGVPHVLSAHSLEPL +RPWKAEQLGGGYALSSWAESTAYHGAAAVIAVSEGMRRDILRCYPDVDPAKVHTVHNGID +TQLWTPQTGTDALTKYGIDPDRPSVAFVGRITRQKGVPHLLRAALQLPEDVQLVLCVGAA +DTPELAREVEGLIGRLRAEREGVVVVEGMIPRGEVTQILSAATVFACPSIYEPLGIVNLE +AMACGTAVVASAVGGIPEVVDDGVTGLLVPVEQADDGTGTPVDEEKFAADLAKALSTVLA +DPERATAMGEAGRARAIEHFSWETIADRTMEVYAAVAR +>PROKKA_01108 +MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGAPRDPDYHGARVLTYPNPP +GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANLAGHLGKLLHQTPHVLSAHSLEPL +RPWKAEQLGGGYALSSWAERTAYLGADAVIAVSDGMRRDILACYPDVDPAKVHTVHNGID +TQVWTPQTGTAALEKYGIDPDKPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP +DTAELAHEVNELISELRRTRQGVVVIEGMIPRHEVMEILTAATVFACPSVYEPLGIVNLE +AMACGTAVVASAVGGIPEVVQDGETGLLVPFEQVDDGTGAPVDEERFAADFAAALTRVVE +DPERARAMGEAGRARAIEHFSWETIAERTIEVYEAVLR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000965.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000965.fa new file mode 100644 index 0000000000000000000000000000000000000000..351c8ca05d74a944cd3553f6da630e77e6ea5ca0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000965.fa @@ -0,0 +1,45 @@ +>PROKKA_01161 +MTHHETPASETASRPAVAGGALRPAVILGGNRIPFARANTAYAEVGNQEMLTATLDGLVA +RFGLQGERLGQVTAGAVLKHPRNFNLTREAVLGSALSAATPAADVQVACATGMEALGTLA +NKIRLGQLDSAIGGGVDSISDAPVSLSDGARRVLLQLNTAKTMKDRLRALAQLRPGQLVP +EPAGAGEPRTGMSMGEHQALTTHKWGITRQTQDELAAASHRNLGAAYAAGYMDDLVTPFH +GLARDNNLRPDSTPEKLAGLKPAFGRQLGDEATMTAANSTPLTDGASAVLLSSEEWAAER +GLPVLAEFVDMENAAVDFVDGHEGLLMAPAYAVPRLLARHGLTLDDLDFVEIHEAFAGTV +LSTLAAWEDEEYCRERLGLPGALGSVDRARLNVHGSSLAAGHPFAATGGRIVALLAKMLH +EKGEGSLGLISVCAAGGQGIVALLRGR +>PROKKA_00880 +MTHHETPASETASRPAVAGGALRPAVILGGNRIPFARANTAYAEVGNQEMLTATLDGLVA +RFGLQGERLGQVTAGAVLKHPRNFNLTREAVLGSALSAATPAADVQVACATGMEAVGTLA +NKIRLGQLDSAIGGGVDSISDAPVSLSDGARRVLLQLTTAKTMKDRLRALAQLRPGQLVP +EPAGAGEPRTGMSMGEHQALTTHKWGITRQAQDELAAASHRNLGAAYAAGYMDDLVTPFH +GLARDNNLRPDSTPEKLAGLKPVFGRQLGDEATMTAGNSTPLTDGASAVLLSSEEWAAER +GLPVLAEFVDMENAAVDFVDGHEGLLMAPAYAVPRLLARHGLTLDDLDFVEIHEAFAGTV +LSTLAAWEDEEYCRERLGLPGALGSVDRARLNVHGSSLAAGHPFAATGGRIVALLAKMLH +EKGEGSLGLISVCAAGGQGIVALLRGR +>PROKKA_01729 +MTQPETTARPAVAGGALRPAVVVGGNRIPFARANTAYAEVGNQEMLTAALEGLVARFGLQ +GERVGQVSAGAVLKHPRNFNLTREAVLGSALASDTPAADLQVACATGMEAIGTLADKIRL +GRIDSAIGGGVDSISDAPVSLSDGARRALLRLNAAKTMKDRLAALKDLRPGHLAPEPAGA +GEPRTGMSMGDHQALTTHRWGITRQAQDELAAASHRNLGAAYAAGYMDDLVTPFRGLDRD +NNLRPDSTPEKLAGLKPAFGRHLGEEATMTAGNSTPLTDGASAVLLSSEDWAAERGLPVL +AEFVDVENAAVDFVDGDEGLLMSPAYAVPRLLARHGLTLQDLDFVEIHEAFAGTVLSTLA +AWEDEEYCRERLGLPGALGSVDRAKLNVHGSSLAAGHPFAATGGRIVALLSKMLHEKGEG +SLGLVSVCAAGGQGIVALLRGR +>PROKKA_01626 +MSTESPRVPAETARPAIAGGELRPAVVVGSNRIPFARAFTAYAEVGEQEMLTAAIDGLVA +RLGLQGERLGQVSAGAVMKHPKDFNLTREAVMGSALSSETPAADIQVACATGMEAIGTLA +DKIRLGRIDSAIGGGVDSISASPMTVSESARRVLLQLNSAKTVKDRLKALSSLRPGQLVP +EPAAAGEPRTGMSMGEHQALTTHQWGITRQAQDELAAASHRNLGASYASGYQDDLVTPFR +GLAKDNNLRPDSTVEKLAGLKPAFGRHLGDEATMTAGNSTPLTDGASAVLLSSEDWAVQR +NLPVLAEIVDMENAAVDFVDGEDGLLMSPVYAVPRLLARHGLTLDDLDFVEIHEAFAGTV +LATLAAWEDEEFGRTRLGLPGAYGSVDRAKLNVNGSSLAAGHPFAATGGRIVGLLSKMLH +EKGEGSLGLVSVCAAGGQGIVALLRGR +>PROKKA_01111 +MTHHETPASETASRPAVAGGALRPAVILGGNRIPFARANTAYAEVGNQEMLTATLDGLIA +RFGLQGERLGQVTAGAVLKHPRNFNLTREAVLGSALSAATPAADVQVACATGMEALGTLA +NKIRLGQLDSAIGGGVDSISDAPVSLSDGARRVLLQLNTAKTTKDRLRALAQLRPGQLVP +EPAGAGEPRTGMSMGEHQALTTHKWGITRQAQDELAAASHRNLGAAYAAGYMDDLVTPFH +GLARDNNLRPDSTPEKLAGLKPAFGRQLGDEATMTAANSTPLTDGASAVLLSSEEWAAER +GLPVLAEFVDMENAAVDFVDGHEGLLMAPAYAVPRLLARHGLTLDDLDFVEIHEAFAGTV +LSTLAAWEDEEYCRERLGLPGALGSVDRARLNVHGSSLAAGHPFAATGGRIVALLAKMLH +EKGEGSLGLISVCAAGGQGIVALLRGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000966.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000966.fa new file mode 100644 index 0000000000000000000000000000000000000000..c5d5b712de2bb38bb7b218b6c8d3158b2d31c618 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000966.fa @@ -0,0 +1,45 @@ +>PROKKA_01162 +MTDRYGTFVASPLGRRLTGALGLPQPVELRRHTPGDPVLPGSVLVLGATPAAADARTLLA +SWGLEVADAPREGARHAAIVACFDGVATPADLGAVALEIGGALRSLGSSSRVVTVFEDPE +AATDPTLRAARQGVTGLTRSIAHEMRRGGTANGLVLGEGVPLTAPGAAGALAFLLSGRAA +YVSGQFVPVATADGAVPADAARPLAGKVAVVTGAARGIGAAIVRTLARDGAVVVGVDVPA +AGEALAEVVNEVGGTALALDITAPDAGARILEHCRTRHGRMDAVVHNAGITRDRMLANMD +AARWDSVLAVNTTAQLAMNEAFLAEDARDVAGQGLRIVGLASISGIAGNRGQTNYAASKA +GVIGLTAASAPVLAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNALQQGGLPQDVA +ETVAWLASDAAGGTNGATLRVCGQSKLGA +>PROKKA_00881 +MTDRYGTFVASPLGRRLTGALGLPQPVELRRHTPGDPVLPGSVLVLGATPAAADARTLLA +SWGLEVADAPREGARHAAIVACFDGVATPADLGAVALEIGGALRSLGSSSRVVTVFEDPE +AATDPALRAARQGVTGLTRSIAHEMRRGGTANGLVLGEGVPLTAPGAAGALAFLLSGRAA +YVSGQFVPVSTADGAVPADAARPLAGKVAVVTGAARGIGAAIVRTLARDGAVVVGVDVPA +AGETLAKVVNEVGGTALALDITAPDAGARILEHCRTRHGRMDVVVHNAGITRDRMLANMD +AARWDSVLAVNTTAQLAMNEAFLAEDARDVAGHGLRIVGLASISGIAGNRGQTNYAASKA +GVIGLTAASAPVLAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNALQQGGLPQDVA +ETVAWLASDAAGGTNGATLRVCGQSKLGA +>PROKKA_01728 +MTDRYGAFAASALGRRLTGALGLPQPVELRRHAPGEPVLHGSVLVLGAGPAAADARTLLA +SWGLEVADAPREGARLAGVVACFDDAAAPGDLGETVLQIGGALRSLGASSRVVTVSVDPE +AAAEPAVRAARQGVQGLTRSLAQEMRRGGTANGIVLGEGVPLTAPGAAGALAFLLSGRSA +YVSGQFLPVTTRDGATPADAARPLADKVAVVTGAARGIGAAIVRTLARDGATVVGVDVPV +AGESLAAVVNEVGGTALALDITAPEAGARILEHCRARHGRMDVVVHNAGITRDRMLANMD +AARWDSVIAVNTASQLAMNEAFLADDAREVTGEGLRIIGLASISGIAGNRGQTNYAASKA +GVIGLTAASAPALAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNSLQQGGLPQDVA +EAVAWFASDAAGGTNGATLRVCGQSKLGA +>PROKKA_01625 +MPANDPYGDLVRTRLGRRLTGALGLPQPAELRRHTAGDPAVRGTVLVLGATSAADAARAL +VTAEGARAVAHPAEGERLAAVIACFDGVAAPGDLSDTALALGGALRSLEPSAHVVTVVED +PEEAEVPAVRAARAGVMGLTRSLAHEMRRGGVANGLLLRGGARLGDAGPAGALRFLLSGR +AAFVSGQFLPAAAGAGSAPASADARPLEGRVAVVTGAARGIGAAILRTLARDGATVVGVD +LPAAGEDLVRIVNELGGTALPLDITAPDAGARIVEHARARHGRLDVVVHNAGITKDKLLA +NMDAARWDAVLAVNTASQLAINEVLLSAEAADVVSPDIRIVGLASISGIAGNRGQTNYAA +SKAGVIGLTAATAPDLAARGGGITAVAPGFIETEMTAKIPLVTRELGRRVNSLQQGGRPE +DVAEAVAFLSSPAASGINGTTLRVCGQSMLGA +>PROKKA_01112 +MTDRYGTFVASPLGRRLTGALGLPQPVELRRHTPGDPVLPGSVLVLGATPAAADARTLLA +SWGLEVADAPREGARHAAIVACFDGVATPADLGAVALEIGGALRSLGSSSRVVTVFEDPE +SATDPTLRAARQGVTGLTRSIAHEMRRGGTANGLVLGEGVPLTAPGAAGALAFLLSGRAA +YVSGQFVPVATADGAVPADAARPLAGKVAVVTGAARGIGAAIVRTLARDGAVVVGVDVPA +AGEALAEVVNEVGGTALALDITAPDAGARILEHCRTRHGRMDVVVHNAGITRDRMLANMD +AARWDSVLAVNTTAQLAMNEAFLAEDARDVAGQGLRIVGLASISGIAGNRGQTNYAASKA +GVIGLTAASAPVLAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNALQQGGLPQDVA +ETVAWLASDAAGGTNGATLRVCGQSKLGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000969.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000969.fa new file mode 100644 index 0000000000000000000000000000000000000000..f546955d07b6e55815820a120f749dfbbf2a9b4b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000969.fa @@ -0,0 +1,45 @@ +>PROKKA_01166 +MVENIVNPARSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAEYCARLMAEAGMTPRF +FESAPGRVSVVGHLPGWDPEAPGLVIHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV +DMKGMDAMVLAVLLHLARTGRRPRRPLTVAFFADEEAGGVYGARWVVDHHPEVFDGCTEA +ISEVGGFSTEVHGSRAYLVQTAEKGLAWLNLTAEGAPGHGSAPHPDNAVTRLAGAMTRIG +GHEWPLVYTKTTRALLEQVAEIMGVDFDEADPTPQLDALGQARSWVAGTLRTSSNPTGLT +AGYKHNVIPSSATGTVDVRLIPGEEESALATIAELAGPEVTIAPEHRDVALETPFSGDLV +ELMIASLQAEDPEAQVLPFMLGGGTDNKSLSRLGITGYGFAPMRLPADLAFTSLFHAIDE +RVPVDALEFGCRVLERMLEPR +>PROKKA_00885 +MVENIVNPARSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAEYCARLMAEAGMTPRF +FESAPGRVSVVGHLPGWDPEAPGLVIHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV +DMKGMDAMVLAVLLHLARTGRRPRRPLTVAFFADEEAGGVYGARWVVDHHPEVFDGCTEA +ISEVGGFSTEVHGSRAYLVQTAEKGLAWLNLTAEGAPGHGSAPHPDNAVTRLAGAMTRIG +GHEWPLVYTKTTRALLEQVAEIMGVDFDETDPTPQLDALGQARSWVAGTLRTSSNPTGLT +AGYKHNVIPSSATGTVDVRLIPGEEESALATIAELAGPDVTIAPEHRDVALETPFSGDLV +ELMIASLQAEDSEAQVLPFMLGGGTDNKSLSRLGITGYGFAPMRLPADLAFTSLFHAIDE +RVPVDALEFGCRVLERMLEPR +>PROKKA_01723 +MIQNAHDTPVSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAALCARLMEEAGMRPRL +FESSPGRVSVVGHLPGWDEDAPGLVVHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV +DMKGMDAMVLSVLLHLTRTGRRPRRPLTVAFFADEEAGGVYGARWLVEHHPELFDGCTEA +ISEVGGFSTEVHGSRAYLVQTAEKGIAWLNLRAEGAPGHGSAPHPDNAVTRLAGAMTRIG +GHEWPLVYTKTTRALLEQVAEIMGVDFDEQDPTPQLDALGQARSWVAGTLRTSSNPTGMT +SGYKHNVIPSTATGTVDARLLPGEEEAALATLQELAGPGVSIEPEHRDVALETPFSGDLV +ELMVASLQAEDPGAEVLPFMLGGGTDNKSLARLGITGYGFAPMRLPADLAFTSLFHGIDE +RVPVDALEFGCRVLERMLEPR +>PROKKA_01621 +MDASTPSTAPSTADADVVEICRDLIRIDTTNHGGGRSVGEPEAAELCAAWMRKAGMEPEL +IESAPGRVSVVGRLEGWDPEAPGLVLHGHTDVVPAEPDEWTVDPFGAEFRDGMIWGRGAV +DMKGMDAMILSVLVHLARTGRRPRRPVVVAFFSDEEAGGVFGAQWLVAHRPELFAGCTEA +ISEVGGFSTDVAGTRAYLVQTGEKGLAWLNLRAQGAPGHGSAPHTDNAVTRLAGAMERIG +RHPWPLTYTKTTRQLLEEVAEITGTPFDERDPTPQLQALGHARDWVAGTLRTSSNPTGLT +AGYKHNVIPSTATGTVDVRLIPGEEEQTLAELADLAGDGIEISPEHQDTGLEVPFSGDLV +ERMASALDAEDPGAHVLPFMLGAGTDNKSLHRLGIAGYGFSPLQLPSGLEFTRLFHGIDE +RVPVESLRFGCRVLEHVLEPRA +>PROKKA_01116 +MVENIENPARSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAEYCARLMTEAGMTPRF +FESAPGRVSVVGHLPGWDPEAPGLVIHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV +DMKGMDAMVLAVLLHLARTGRRPRRPLTVAFFADEEAGGVYGARWVVDHHPEVFDGCTEA +ISEVGGFSTEVHGSRAYLVQTAEKGLAWLNLTAEGAPGHGSAPHPDNAVTRLAGAMTRIG +GHEWPLVYTKTTRALLEQVAEIMGVDFDETDPTPQLDALGQARSWVAGTLRTSSNPTGLT +AGYKHNVIPSSATGTVDVRLIPGEEESALATIAELAGPDVTIAPEHRDVALETPFSGDLV +ELMIASLQAEDPEAQVLPFMLGGGTDNKSLSRLGITGYGFAPMRLPADLAFTSLFHGIDE +RVPVDALEFGCRVLERMLEPR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000974.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000974.fa new file mode 100644 index 0000000000000000000000000000000000000000..bb3b491f1a932f9b4cadd1f80eedf093714d7ccc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000974.fa @@ -0,0 +1,35 @@ +>PROKKA_01171 +MTDATSEDQPDDALGPLRTHLTATVDALEAGRRAPTVLLLAFEGWNDAGEAATGALGALR +EQWDAADAGRVCDGEFYDYQVTRPLVRRDADGLGTLDWPAVTLHEAFLDREGRPVAGEAA +PPDGVRVLLAVGVEPNVRWRAFLEELFTAADAHDVDAVVTLGALLADVPHTRPLRARPTS +PLVDVRVAVGADRPVYEGPTGIIGVIADEAARRGLPSLSLWGTVPHYVAQAPSPKTLLGL +VEAVEDLLHVSVSTRGLEDDARAWQRGVDELAAEDPDVAAYVRQLEEAQDTQQLPEASGE +SIAREFERYLRGRGGR +>PROKKA_00890 +MTDATSEDQPDDVLGPLRTHLTATVDALEAGRRAPTVLLLAFEGWNDAGEAATGALGALR +EQWDAADAGRVCDGEFYDYQVTRPLVRRDADGLGTLDWPAVTLHEALLDREGRPVAGEAA +PPDGVRVLLAVGVEPNVRWRAFLEELFTAADARDVDAVVTLGALLADVPHTRPLRARPTS +PLVDVRVAVGADRPVYEGPTGIIGVIADEAARRGLPSLSLWGTVPHYVAQAPSPKTLLGL +VEAVEDLLHVSVSTRGLEDDARAWQRGVDELAAEDPDVAAYVRQLEEAQDTQQLPEASGE +SIAREFERYLRGRGGR +>PROKKA_01718 +MTDASSADQPDDALGPLRTHLTATVDDLEAGLRAPTVLLLAFEGWNDAGDAASGALDALR +EQWDAAEAGRICDGEFYDYQVTRPVVRRDADGLGTLEWPAVRLHEAQLDAQGRPVAGEAA +PPDGVRVLLAVGVEPNVRWQAFAEELFAAAAARQVDAVVTLGALLADVPHSRPLRARPTS +PLVDVRVAVGADRPAYEGPTGIVGVIADEAARRGLPSVSLWGAVPHYVAQAPSPKTLLGL +VEAIEDLLHVSVSTCELEDDAQAWQRGVDELAAEDPDVAAYVRQLEEAQDTQQLPEASGE +AIAREFERYLRGRGGR +>PROKKA_01616 +MDEQTDPGSLDGAPSPEDRLGALRAHLTATVPEVEDGSRPPAVLLLAFEGWNDAGEAATG +ALAELSAQWEAAPAGVVCDGEYYDYQVTRPVVHRDADGLGTLEWPALRVHEARLDAHGAP +VPDGEAVPADGLRVLLASGVEPNVRWRAYVEELLRWAEAEGVDAVLTLGALLADVPHSRP +LRARPTSPLVAVRVAVDAGLPAYEGPTGIVGVVTDEAARRGTASLSLWGAVPHYVAQAPS +PKTLLGLVEAVEDLLHVELLTHALRDDAQAWQRGVDELAREDPEVASYVRRLEESQDAQE +LPEASGEAIAREFERYLRGRGRD +>PROKKA_01121 +MTDATSEDQPDDVLGPLRTHLTATVDALEAGRRAPTVLLLAFEGWNDAGEAATGALGALR +EQWDAADAGRVCDGEFYDYQVTRPLVRRDADGLGTLDWPAVTLHEALLDREGRPVAGEAA +PPDGVRVLLAVGVEPNVRWRAFLEELFTAADARDVDAVVTLGALLADVPHTRPLRARPTS +PLVDVRVAVGADRPVYEGPTGIIGVIADEAARRGLPSLSLWGTVPHYVAQAPSPKTLLGL +VEAVEDLLHVSVSTRGLEDDARAWQRGVDELAAEDPDVAAYVRQLEEAQDTQQLPEASGE +SIAREFERYLRGRGGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000977.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000977.fa new file mode 100644 index 0000000000000000000000000000000000000000..2e413dd77f3d9015bcb80a1168b6c48f7ddb02ca --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000977.fa @@ -0,0 +1,36 @@ +>PROKKA_01174 +MTEPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGEFHSYQGVLRHDDLIGGFEGVV +VENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIVQQADIFPGAVVVEAGVGSGAL +SMSLLRAVGDHGRLHSYERRPEFADVARANVEAFFGAEHPAWSVHLGDAQEEMPKVHEPG +SVDRVVLDMLAPWECLDAVAEVLAPGGVWLNYVATATQLSRVAEAIRDSGRFTQVEANET +LVRGWHLDGLAVRPDHRMVAHTGFLLTARRLASGEEALRLKKRSKVSEFRAEDVEAWQPA +DEARWTPEALGERPITDKKARKAAKEARLMAARSRAAEQGVDAYGGRTPTGEQD +>PROKKA_00893 +MTEPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGEFHSYQGVLRHDDLIGGFEGVV +VENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIVQQADIFPGAVVVEAGVGSGAL +SMSLLRAVGDHGRLHSYERRPEFADVARANVEAFFGAEHPAWSVHLGDAQEEMPKVHEPG +SVDRVVLDMLAPWECLDTVAEVLAPGGVWLNYVATATQLSRVAEAIRDSGRFTQVEANET +LVRGWHLDGLAVRPDHRMVAHTGFLLTARRLASGEEALRLKKRSKVSEFKAEDVEAWQPA +DEARWTPEALGERPVTDKKARKAAKEARLMAARSRAAEQGVDAYGGRTPTGEQD +>PROKKA_01715 +MTEPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGEFHSYQGVLRHDDLIGGFEGVV +VENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIVQQADIFPGAVVVEAGVGSGAL +SMSLLRAVGDHGRLHSYERREEFADVARANVEAFFGAEHPAWSIHLGDAQEQMTRVHEPG +SVDRVVLDMLAPWECLDAVAEVLAPGGVWLNYVATATQLSRVAEAIRDSGRFTQVEANET +LVRGWHLDGLAVRPDHRMVAHTGFLLTARRLATGEEALRLKKRSKVSEFKAEDVEAWQPA +DEARWTPEALGERPVTDKKARKAAKEARLMAARSRAAERGVDAYGGSIQEQDQD +>PROKKA_01613 +MSDATAPETPAAPTTPDTAAPAGRPAGVTARRGPLRAGQRVQIKDAKGRLNTITLLPGGE +FHSYQGVLRHDDLIGGPEGIVVQNSSGHAYQVLRPLLNDFVLSMPRGATVVYPKDAGQIV +QQADIFPGAVVVEAGVGSGALSMSLLRAVGDAGRLHSYERRAEFAEIARGNVESFFGGVH +PAWSIHLGDAQEEMPKVHEPHSVDRVVLDMLAPWECLDAVATVLAPGGVWLNYVATATQL +SRVAEAIRASGKFTQIEATETLVRGWHLDGLAVRPDHRMVAHTGFLLTARRLAAGEDALV +MKKRLKVSEFTTEDVEAWTPSDGARWTPQALGERTVTDKKARKAAKEARLTARRARAALE +GRDPRTVGQDKD +>PROKKA_01124 +MTEPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGEFHSYQGVLRHDDLIGGFEGVV +VENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIVQQADIFPGAVVVEAGVGSGAL +SMSLLRAVGDHGRLHSYERRPEFADVARANVEAFFGAEHPAWSVHLGDAQEEMPKVHEPG +SVDRVVLDMLAPWECLDAVAEVLAPGGVWLNYVATATQLSRVAEAIRDSGRFTQVEANET +LVRGWHLDGLAVRPDHRMVAHTGFLLTARRLASGEEALRLKKRSKVSEFKAEDVEAWQPA +DEARWTPEALGERPVTDKKARKAAKEARLMAARSRAAEQGVDAYGGRTPTGEQD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000982.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000982.fa new file mode 100644 index 0000000000000000000000000000000000000000..cb45e28012655aae7973418085523f6e4cbd751d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000982.fa @@ -0,0 +1,15 @@ +>PROKKA_01179 +MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQRLDSLLDEIDSVLESNAEEFVKGFVQK +GGQ +>PROKKA_00898 +MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQRLDSLLDEIDSVLESNAEEFVKGFVQK +GGQ +>PROKKA_01710 +MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQGLDSLLDEIDSVLESNAEEFVKGFVQK +GGQ +>PROKKA_01608 +MAQEQIRPRPAGGPEDEGAAAQAQAKAAPQDTGLDGLLDEIDSVLESNAEEFVKGFVQKG +GQ +>PROKKA_01129 +MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQGLDSLLDEIDSVLVSNAEEFVKGFVQK +GGQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000986.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000986.fa new file mode 100644 index 0000000000000000000000000000000000000000..c4a1316ae1ea50a56c517ecbe335dd804b7a93af --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000986.fa @@ -0,0 +1,15 @@ +>PROKKA_01184 +MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEGKGTTDERSGA +GSTAADEPVEGRVVERDETDPRDPR +>PROKKA_00903 +MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEGKGTTDERSGA +GSTAADEPVEGRVVERDETDPRDPR +>PROKKA_01704 +MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEDKGAKDGKDAR +SGSGSTAADEPVEGRVVERDETDVRPRDER +>PROKKA_01603 +MRFTPTHLIVLIIVVLLLFAAPKLPALARNLGQSMRIFSSEVKQMKEENTTKKAEGAATA +DAPSQGAGSTAAEPVEGRVVDRDVRDDR +>PROKKA_01134 +MAGLQGWQLVIIILLAILLFAAPKLPAMARNLGQSMRIFSSEVKQMRTEGKGTTDERSGA +GSTAADEPVEGRVVERDETDPRDPR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000989.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000989.fa new file mode 100644 index 0000000000000000000000000000000000000000..553abdc7e4c575b831d45ee2362499e4fb686e2d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000989.fa @@ -0,0 +1,39 @@ +>PROKKA_01187 +MSAHLLTRGIIHSTTDPYAQALLVRDGMIAWLGADDSADRVADPGDERRDLDGAVVVPVF +VEPLARPADARDALSRGTAVVTVLAGPEDTGAAPADEDVQTVVYRHADRVDAEAAGVWLP +VGTDTDPATLTGLLTASTQAGEQAYLVPDGGADAGPAAQDVALTALRSVAEELGTAALGR +VRHRLVVTHPVTAEDRAFLAAAGVSATVVPDADGVLHAPVASLLADAVTVCLGAGPAGDP +WAAVRSALSHPDPDERISARSAFAAATRTPLRALPDAPAARLSVAPRLSVSAPAVFGVWD +ADAVAVQSPDGRVAAWSTDTRAGTPLLPALDAETALPRWRATWVDGRIAAEDVARDAHDA +ATPA +>PROKKA_00906 +MSAHLLTRGIIHSTTDPYAQALLVRDGMIAWLGADDSADRVADPGDERRDLDGAVVVPVF +VEPLARPADARDALSRGTAVVTVLAGPEDTGAVPADEDVQTVVYRHADRVDAEAAGVWLP +VGTDTDPATLTGLLTASTQAGEQAYLVPDGGADAGPAAQDVALTALRSVAEELGTAALGR +VRHRLVVTHSVTAEDRAFLAAAGVSATVVPDADGVLHAPVASLLADAVSVCLGAGPAGDP +WAAVRSALSHPDPDERISARSAFAAATRTPLRALPDAPAAGLSVAPRLSVSAPAVFGVWD +ADAVAVQSPDGRVAAWSTDTRAGTPLLPALDAETALPRWRATWVDGRIAAEDVARDAHDA +ATPA +>PROKKA_01701 +MGRVTAHLLTTGIIHSVTDPYAQALLVRDGVIAWLGADDSAERVADPADARTDLDGAVVV +PAFVEPLARPEDARDALSRGTAVVTVLAGPAGDVAPAEGVQAVVYRHAEGPAEGAVGVWL +PVAADADAADLAAALAEATRAGEQAYLVPAADAAGHGDAEAPAAAQAAAIAALRRVAEEL +GAPALGRVRHRLVVTSPVTAEDRAFLASVAVSATVVPAADGTLRAPVASLLADAVPVALG +AGPGRDPWAAVRAALSHPEEAERISARSAFAAATRTPLRALPDAADADLVAAPRLAVSAP +GVFGVWEAEAVAVQSPDGRVAAWSTDTRAGTPLLPALDDQTPLPRWRATWVGGRIAAEAA +DGDARGTGDHA +>PROKKA_01600 +MSSTLFLNGIVHSASDPYATAALVSDGVVAWLGDDSSADRVADPDVPRVDLAGAVLAPAF +VEPGGPSVDPAQALRHGVAIVTVLAEPGQTAQALQAAADPALQTVVYRAADTVDAEAAGV +WLPAEGEALAALVVASTRAGEQVHLVPPAGGDPSEGQAAALAALRSAAEELGAPALGRVR +HRVVLTAPITAEDRALLAAISASVTVGPEADGLLRAPLGTLLAEGVPVCLSTAGEAGPWA +AVRAALSHPDEAERISARSAFTAATRTPLRVLPDAPGATVQAAPRLTVSAPATFAVWEAD +AVAVQSPDGRVAAWSTDTRAGTPLLPALDAETALPRWRATWVDGRPAAVEVADA +>PROKKA_01137 +MSAHLLTRGIIHSTTDPYAQALLVRDGMIAWLGADDSADRVADPGDERRDLDGAVVVPVF +VEPLARPADARDALSRGTAVVTVLAGPEDTGAAPADEDVQTVVYRHADRVDAEAAGVWLP +VGTDTDPATLTGLLTASTQAGEQAYLVPDGGADAGPAAQDVALTALRSVAEELGTAALGR +VRHRLVVTHPVTAEDRAFLAAAGVSATVVPDADGVLHAPVASLLADAVTVCLGAGPAGDP +WAAVRSALSHPDPDERISARSAFAAATRTPLRALPDAPAARLSVAPRLSVSAPAVFGVWD +ADAVAVQSPDGRVAAWSTDTRAGTPLLPALDAETALPRWRATWVDGRIAAEDVARDAHDA +ATPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000993.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000993.fa new file mode 100644 index 0000000000000000000000000000000000000000..f62a5092f529ff73e3428c247e61ad29afe2b52d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000993.fa @@ -0,0 +1,20 @@ +>PROKKA_01191 +MEWIEANAGWLWLVLAAGLAGVELLTLDLVFLMIAAGAGAAGVVALVGGPLALQLAAFAA +VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITGDAGTLAVDGDTWSARV +EPGAPEVAPGDEVTVLRIDGATLVVRPLPRIDWEADGA +>PROKKA_00910 +MEWIEANAGWLWLVLAAGLAGVELLTLDLVFLMIAAGAGAAGVVALVGGPLALQLAAFAA +VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITGDAGTLAVDGDTWSARV +EPGAPDVAPGDEVTVLRIDGATLVVRPLPRIDWQADGA +>PROKKA_01697 +MDWIEANAGWLWLVAAAGLIGVELLTLDLVFLMIAAGAGAAGVVALAGGPLPLQLAAFAV +VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITAEAGTLTVDGDTWSARV +EDGAPDAAPGAEVTVLRVEGATLVVRPLPQIDWEDGRS +>PROKKA_01596 +MEWIEANADWLWLVLALGLVGAELLSLDLVLAMLAAGALSAGVAALAGAPLGLQLGVFVV +VSLLTLVAVRPAAMRRLHPDPAVGASWLDGLSGRRLTATGPVTDEGGRIDVDGETWSARV +EPGAAPAAHGQGVTVLRVEGAHLILRPDPVIDWDAPAHD +>PROKKA_01141 +MEWIEANAGWLWLVLAAGLAGVELLTLDLVFLMIAAGAGAAGVVALVGGPLALQLAAFAA +VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITGDAGTLAVDGDTWSARV +EPGAPEVAPGDEVTVLRIDGATLVVRPLPRIDWEADGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000998.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000998.fa new file mode 100644 index 0000000000000000000000000000000000000000..e97ddae27a7934f4858c9d67154ea7d880bfc5ef --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000998.fa @@ -0,0 +1,15 @@ +>PROKKA_01196 +MVTAIVLIKTDKSSIPETAETLAALEGVGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL +SKVDGIQDTETMLAFRAYSSEDLGEGWALGFDS +>PROKKA_00916 +MVTAIVLIKTDKSSIPETAETLAALEGVGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL +SKVDGIQDTETMLAFRTYSSEDLGEGWALGFDS +>PROKKA_01691 +MVTAIVMIKTDKSSIPETAETLAALEGIGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL +SKVEGIQDTETMLAFRTYSSEDLGEGWALGFED +>PROKKA_01589 +MVTAIVMITTDKSTIPETAQAIASLEGVSSVYSVTGAWDLVAMVKLKRYEDLADVIADQL +SKVDGIEDTETMLAFRTYSTEDLEEGWALGFDG +>PROKKA_01150 +MVTAIVLIKTDKSSIPETAEALAALEGVGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL +SKVDGIQDTETMLAFRTYSSEDLGEGWALGFDS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000999.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000999.fa new file mode 100644 index 0000000000000000000000000000000000000000..9abc478844fe065896676ebb5aa35321104c2026 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0000999.fa @@ -0,0 +1,35 @@ +>PROKKA_01197 +MSTPENTAAVLGTSWPEVFRALTVGEDLSDDVAAWAMGEMMAGDATEGQVGGFLLALAAK +GVTVPELRGLTEAMVQAANPVHVPGETLDVVGTGGDRLGTVNLSTMSSLVAAGAGARIVK +HGNRGASSTAGAADVIEALGVDLSMPTRKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQ +LGVPTVFNFLGPLSNPAQVTAQALGCSSQAMVPLLAQVLADRGVRGFVFRGADGRDKITT +SGPSTVMEVRDGVRTHELDPRELGIDLAPVQALAGRDGAYNATLVRALLAGEKGPIRDAV +LLNAAAGLTAWDRGADAPLMERLAANMARAAESIDSGAARDVLDRWVAFSRS +>PROKKA_00917 +MSTPENTAAVLGTSWPEVFRALTVGEDLSDDVAAWAMGEMMAGDATEGQVGGFLLALAAK +GVTVPELRGLTEAMVQAANPVHVPGETLDVVGTGGDRLGTVNLSTMSSLVAAGAGARIVK +HGNRGASSTAGAADVIEALGVDLSMPTRKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQ +LGVPTVFNFLGPLSNPAQVTAQALGCSSEAMVPLLAQVLADRGVRGFVFRGADGRDKITT +SGPSTVMEVRDGVRTHELDPRELGIDLAPVQALAGRDGAYNATLVRALLAGEKGPIRDAV +LLNAAAGLTAWDRDADAPLMERLAANMARAAESIDSGAARDVLDRWVAFSRS +>PROKKA_01690 +MSIPNTTAAAPETTWPDVFRALTFGEDLSDEAAAWAMGEMMAGDATEGQVGGFLLALAAK +GVTVPELRGLTEAMVQAARPVQVTGETLDIVGTGGDRLGTVNLSTMSSLVAAGAGARIVK +HGNRGASSTAGAADVIEALGVDLSMPREKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQ +LGVPTVFNFLGPLSNPAQVSAQALGCSSEVMVPLLARVLADRGVRGFVFRGSDGRDKITT +SGPSTVIEVRHEVTAHELDPRDFGIELAPVEALAGRDGAYNATLVHALLAGEKGPIRDAV +LLNAATGLTAWDTEAQGPLADRLAANMARAAESLDSGAARDVLDRWVAFSRS +>PROKKA_01587 +MRETVTHTWPEVFRRLTLGQDLDDAAAEWAMGEMMSGDATEGQVGAFLLALAAKGETVPE +LRGLTDAMVAKARRVHVSGETLDIVGTGGDRLGTVNLSTMSSLVAAGAGARIVKHGNRGA +SSTAGAADVIEALGVDLSMPPAKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQLGVPTV +FNFLGPLSNPAQASAQALGCSSEEMVPLLAQVLADRGVRGFVFRGSDGRDKITTSGPSTI +MEVRGGVTAHEIDPRDFGIELAPVEALAGRDGAYNATLVRGLLAGEHGPIRDAVLLNAAA +GLTAWDVEAEGPLMDRLRTNMARAAESIDSGAAADVLERWVQFSRS +>PROKKA_01151 +MSTPENTAAVLGTSWPEVFRALTVGEDLSDDVAAWAMGEMMAGDATEGQVGGFLLALAAK +GVTVPELRGLTEAMVQAANPVHVPGETLDVVGTGGDRLGTVNLSTMSSLVAAGAGARIVK +HGNRGASSTAGAADVIEALGVDLSMPTRKAEECAEAVGITFLFAQNYHPSMKYVAPVRKQ +LGVPTVFNFLGPLSNPAQVTAQALGCSSEAMVPLLAQVLADRGVRGFVFRGADGRDKITT +SGPSTVMEVRDGVRTHELDPRELGIDLAPVQALAGRDGAYNATLVRALLAGEKGPIRDAV +LLNAAAGLTAWDRDADAPLMERLAANMARAAESIDSGAARDVLDRWVAFSRS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001001.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001001.fa new file mode 100644 index 0000000000000000000000000000000000000000..a0b621cc87042435486b22f11aaa4ac82fba6d2c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001001.fa @@ -0,0 +1,30 @@ +>PROKKA_01199 +MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDISEGEKLF +NANCASCHGTGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAQVKPNQFNDEQTA +QLAAYVASLGAGPAVPEDEYLDVNHEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKYA +PSLQGVEEKHIYEAMETGPQNMPVFSDSNIKPEDKRDIIAYLKTIENQGSPGGLALGSLG +PVSEGLFIWTAGLALIIGFMVWLTSRSS +>PROKKA_00919 +MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDITEGEKLF +NANCASCHGMGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAPAKPNQFNEEQTA +QLAAYVASLGAGPAIPEDEYLDVNHEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKYA +PSLQGVDEKHIYEAMETGPQNMPVFSDSNIKPEDKRDIIAYLKTIENQGSPGGLTLGSLG +PVSEGLFIWTAGLALIIGFMVWLTSRSS +>PROKKA_01688 +MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDITEGEKLF +NANCATCHGMGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAPAKPNQFNEEQTA +QLAAYVASLGAGPAIPEDEYLDINNEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKFA +PSLQGVEEKYIYEAMETGPQNMPVFSDANIKPEDKRDIIAYLKTIENQGSPGGLSLGSLG +PVSEGLFIWTAGLALIIGFMVWLTSRSS +>PROKKA_01585 +MKALSQNRRHPLVGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAAAADDITAGEKLF +NANCASCHNMGATGTADGPSLVGVGAAAVDFQVGTGRMPMQMNGPQAQRKPNQFSEEQTA +QLAAYVASLGAGPAVPADEDLDPNAEGVNIAKGGDLFRINCAMCHNAAAAGGALTRGKFA +PSLEGVSEKHIYEAMETGPQNMPVFSDANLKPEDKRDIIAYLKTIEANGSPGGLQLGSLG +PVAEGLFIWTAGLALIVGFMVWLTSRSS +>PROKKA_01153 +MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDISEGEKLF +NANCASCHGTGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAQVKPNQFNDEQTA +QLAAYVASLGAGPAVPEDEYLDVNHEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKYA +PSLQGVEEKHIYEAMETGPQNMPVFSDSNIKPEDKRDIIAYLKTIENQGSPGGLALGSLG +PVSEGLFIWTAGLALIIGFMVWLTSRSS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001003.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001003.fa new file mode 100644 index 0000000000000000000000000000000000000000..74c937c7e0489788f295035d03bef69c52ead942 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001003.fa @@ -0,0 +1,55 @@ +>PROKKA_01201 +MSTTVNEFQPATSTGRIANFVDTRTGMSPIVKFFARKIFPDHWTFMFGEVALYSFVILLL +SGAFLTFFFDPSMSEVVYNGAYAPLRGIEMSAAYASTLDISFDVRGGLFMRQLHHWAALM +FVAAMSVHMLRVFFTGAFRRPRELNWLVGCFLLMAGWAAGFTGYSLPDEVLSGNGLRIID +GILKSLPLVGTYLSAFFFGGEFPGHSVIGRLYALHIMIVPAAILLLIGIHLFMVVVHKHT +QYPGPGRTEDNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINANWNYGPYDPSPVQ +AGTQPDWYIGVFDGALRLMPGMIGDYSFLWNIPMPWGSSVSLPMGVLVPLIPVGVLLVGM +CAWPWIERWITKDDTEHHLLDRPRNAPARTGIGVAAVVWYCVMWAAASSDLIATHFHLSL +NDVLYVLRALFFLGPVIAFIVTRRICLSLQRKDRELVLHGHEAGVIEMSPEGGFHERHRP +LTDYELYRLVAFEDRRPVPAIPGRNGKVGALEKARAGLNRMFYQERVAPVSREELVEART +HGQHGHEEHPVELGHGSDAPRLER +>PROKKA_00921 +MSTTVNEFQPATTTGRIANFVDTRMGMSPIVKFFGRKIFPDHWTFMFGEVALYSFVILLL +SGAFLTLFFDPSMSEVVYDGAYAPLRGIEMSAAYASTLDISFDVRGGLFMRQLHHWAALM +FVAAMSVHMLRVFFTGAFRRPRELNWLVGCFLLMAGWAAGFTGYSLPDEVLSGNGLRIID +GILKSLPLVGTYLSAFFFGGEFPGHSVIGRLYALHIMIVPAAILLLIGIHLFMVVVHKHT +QYPGPGRTEDNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINANWNYGPYDPSPVQ +AGTQPDWYIGVFDGALRLMPGMIGDYSFLWNIPMPWGSSVSLPMGVLVPLIPVGVLLVGM +CTWPWIERWITKDNTEHHLLDRPRNAPARTGIGVAAVVWYCVMWAAASSDLIATHFRLSL +NDVLYVLRALFFLGPVIAFIVTRRICLSLQRKDRELVLHGHEAGVIEMSPEGGFHERHRQ +LTDYELYRLVSFEDRRPVPAIPGRNGKVGMLEKARAGLNRMFYQDRVAPVSREELVEART +HGQHGHEEHPVELEHGSHAPHLDR +>PROKKA_01686 +MSTTVNEFQPATSTGRIANFVDTRMGMSPIVKFFARKIFPDHWTFMFGEVALYSFVILLL +SGAFLTFFFDPSMSEVVYNGAYAPLRGIEMSAAYASTLDISFDVRGGLFMRQLHHWAALL +FVAAMSVHMLRVFFTGAFRRPRELNWLVGCFLLMAGWAAGFTGYSLPDEVLSGNGLRIID +GILKSLPIVGTYLSAFFFGGEFPGHSIIGRLYALHIMVVPAAILLLIGIHLFMVVVHKHT +QYPGPGRTENNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINANWNYGPYDPSPVQ +AGTQPDWYIGVFDGALRLMPGMIGDFSFLWNIPMPWGSSVSLPMGVLVPLIPIGVLIVGM +CAWPWIERWITKDDTEHHLLDRPRNAPTRTGIGVAAVIWYCVMWAAASSDLIATHFRLSL +NDVLYALRTLFFLGPVIGFIVTRRICLSLQRKDRELVLHGHEAGVIEMSPDGGFHERHRQ +LTDHELYRLVSFEDRRPVPALPNRSGKVGMIEKARAGLNRMFYQDRVAPVTREELVEARA +HGHHGVEDGGHHELGADPSSHNPKIDG +>PROKKA_01583 +MSTATHEYQPATGTGRLANFLDTRVGLSPIVKFFGRKTFPDHWTFMFGEVALYSFVILLL +SGAFLTFFFDPSMSHVTYDGAYAPLRGIEMSAAMASALDISFDIRGGLFMRQLHHWSALL +FVASMSVHMLRIFFTGAFRRPRELNWVVGCFLLMAGWAAGFTGYSLPDDVLSGNGLRIID +GILKAMPLVGSYLSAFLFGGEFPGYSVIGRLYALHIMIVPAIILLLIAVHLFMVVVHKHT +QYPGPGRTENNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINSIWIYGPYDPSPVS +AGTQPDWYIGPFDGALRLMPGMIGDFSFLWNIPMPWGSRVSLPMGVLTPLIPVGVILVGM +ISWPWIERWITKDDREHHLLDRPRNAPARTGIGVGMMIMWCTMWAAASSDLIATHFHLSL +NDVLYFLRALFILGPILGFIVTRRICISLQRRDRETVLHGHESGVVEMSPEGGFSERHRQ +LTDYEMYRLVSFEDRRPVPATPGRNGKVSGAERMRAGLNRMFYQERVAPVSREELVEART +HGHGEHVGAVQGGSHSAELGH +>PROKKA_01155 +MSTTVNEFQPATTTGRIANFVDTRMGMSPIVKFFGRKIFPDHWTFMFGEVALYSFVILLL +SGAFLTLFFDPSMSEVVYDGAYAPLRGIEMSAAYASTLDISFDVRGGLFMRQLHHWAALM +FVAAMSVHMLRVFFTGAFRRPRELNWLVGCFLLMAGWAAGFTGYSLPDEVLSGNGLRIID +GILKSLPLVGTYLSAFFFGGEFPGHSVIGRLYALHIMIVPAAILLLIGIHLFMVVVHKHT +QYPGPGRTEDNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINANWNYGPYDPSPVQ +AGTQPDWYIGVFDGALRLMPGMIGDYSFLWNIPMPWGSSVSLPMGVLVPLIPVGVLLVGM +CTWPWIERWITKDNTEHHLLDRPRNAPARTGIGVAAVVWYCVMWAAASSDLIATHFHLSL +NDVLYVLRALFFLGPVIAFIVTRRICLSLQRKDRELVLHGHEAGVIEMSPEGGFHERHRQ +LTDYELYRLVSFEDRRPVPAMPGRNGKVGALEKARAGLNRMFYQDRVAPVSREELVEART +HGQHGHEDGGHHELGADPSSHNPKIDG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001006.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001006.fa new file mode 100644 index 0000000000000000000000000000000000000000..e98f1c7669ebed7b845823080dbb47b963d3b3f6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001006.fa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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001007.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001007.fa new file mode 100644 index 0000000000000000000000000000000000000000..b95b9ce5e09bb47ca9668da5cdcfe4ce5687d1ac --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001007.fa @@ -0,0 +1,20 @@ +>PROKKA_01206 +MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS +GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAG +GSCACGDSFH +>PROKKA_00925 +MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS +GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAG +GSCACGDSFH +>PROKKA_01681 +MALSADETGVEIGATQDSEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS +GLIYQLYFDERVLDGDTVRDYDGVQVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAV +GSCACGDSFH +>PROKKA_01579 +MALSAEETGVEIGATEDATGLPPHEVELTDVAAAKVRALLEQEGRTDLRLRVAVQPGGCS +GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAV +GSCACGDSFH +>PROKKA_01163 +MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS +GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYIMGATIDFEDTISKQGFTIDNPNAG +GSCACGDSFH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001008.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001008.fa new file mode 100644 index 0000000000000000000000000000000000000000..3dc828cc4cb321cfeafa6b6182a7161ee07c3ace --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001008.fa @@ -0,0 +1,45 @@ +>PROKKA_01207 +MTDITSRAPQDAALVSAVREAVEARFPTTLQTLTDLVAIPGIAWDSADRAQLERSAEAVA +GLLREAGLQDVEIVSEIRDDGRPGGPAVIGEKPGTSDKPTVLFYAHHDVQPIGDEDLWDT +PPLVATERGGRLYGRGAADDKAGIMVHLAALAALRDVLPDAGVGVRVFIEGEEEAGSPTF +RTFLEKHRARLDADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP +VLDAVVLLSRLIATLHDADGAVAVPGLEPRQTAGLDYPEDVFRADAGVLDGVTLAGRGPV +ADRLWNAPALSIIGIDAPSVAESSNTIQPAARAKFSMRLGPGMEPAEAFEALRTHLEAQS +AAVLGAEITVTAGEFGQPFTTDTSAPAAAAMMAALEDAWGVEPRAIGMGGSIPFTADLAE +VFPEATLLITGVEDPDTRAHSANESLHIDDFQRAVVAEALWLARLSA +>PROKKA_00926 +MTDITSRAPQDAALVSAVREAVEARFPTTLQTLTDLVAIPGIAWDSADRTQLERSAEAVA +GLLRAAGLQHVEIVTETRDDGRPGGPAVIGEKPGASDKPTVLLYAHHDVQPIGDEDLWDT +PPLVATERGGRLYGRGAADDKAGIMVHLAALAALRDVLPDAGVGVRVFIEGEEEAGSPTF +RTFLEKHRARLDADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP +VLDAVVLLSRLIATLHDADGAVAVPGLEPRQTAGLDYPEDVFRADAGVLDGVTLAGRGPV +ADRLWNAPALSIIGIDAPSVAESSNTIQPAARAKFSLRLGPGMDPAEAFEALRTHLEAQS +AAVLGAEITVTAGEFGQPFTTDTSATAAAAMMAALEDAWDVEPRAIGMGGSIPFTADLAQ +VFPEATLLITGVEDPDTRAHSANESLHIDDFQRAVVAEALWLARLSA +>PROKKA_01680 +MTETTPPVRDDAALVAAVRDAVDARFPQTLQTLTDLVAIPGIAWDSADRAQLERSSEAVA +ALLRQAGLQGVEIVTETREDGRPGGPAVIGEKPGASDKPTVLLYAHHDVQPIGDEALWDT +EPLVATEKGGRLYGRGAADDKAGIMVHLAALAALKDVLPDAGVGVRVFIEGEEEAGSPTF +RTFLENHRARLEADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP +VLDAVVLLSRLIATLHDADGAVAVPGLEPRRSASLDYPEDVFRADAGVLDSVTLAGRGPV +ADRLWNAPALSVIGIDVPSVAESSNTIQPQARAKFSLRLGPGMDPAEAFEALKAHLEAQS +AAVLGAEITVEAGEFGQPFDTDTSDPLAAAMMGALGDAWGVAPKEAGMGGSIPFTADLAE +VFPDATILITGVEDPDSRAHSANESLHIEDFRRAVVAEALWFARLAG +>PROKKA_01578 +MTQSTQNTPVGAAPDPELVSAIRAAVDRRFPETLQSLKDLVSIPGIAWDSMDREPLERSA +AAVADLLRTAGLEGVETAVEERADGRPGGPAVIGGRPAVGDKPTVLLYAHHDVQPLGEEG +LWDTPPLVATERDGRLYGRGAADDKAGIMVHLAALAALDEVCPDAGVGVRVFIEGEEEAG +SPTFRPFLERHRDRLAADAIVVADSSNWAVGEPALTTSLRGVVSATVTVRALDHAVHSGM +FGGPVLDAVVLMSRLIATLHDADGAVAVPGLEPRHHADVDYPEDAFRADSGILPGTRLAG +RGALADRLWNGPALSVIGLDAPSVDTSSNTIQPAARAKISLRLGPGMDPAASLDALRAHL +EAQSDAVLGAEITVEPGELGQPFSTDTSAPAAAAMMGALGAAFATPARETGLGGSIPFTA +DLKELFPEATILITGVEDPDSRAHSANESLHLEDFRRAIVAEALWLAAMGA +>PROKKA_01164 +MTDITSRAPQDAALVSAVREAVEARFPTTLQTLTDLVAIPGIAWDSADRTQLERSAEAVA +GLLREAGLQEVEIVTETRDDDRPGGPAVIGEKPGASDKPTVLLYAHHDVQPIGDEDLWDT +PPLEATERGGRLYGRGAADDKAGIMVHLAALAALRDVLPDAGVGVRVFIEGEEEAGSPTF +RTFLEKHRARLDADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP +VLDAVVLLSRLIATLHDADGAVAVPGLEPRQTAGLDYPEDVFRADAGVLDGVTLAGRGPV +ADRLWNAPALSIIGIDAPSVAESSNTIQPAARAKFSLRLGPGMEPAEAFEALRTHLEAQS +AAVLGAEITVTAGEFGQPFTTDTSAPAAAGMMAALEDAWGVEPRAIGMGGSIPFTADLAE +VFPEATLLITGVEDPDTRAHSANESLHIDDFQRAVVAEALWLARLSA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001014.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001014.fa new file mode 100644 index 0000000000000000000000000000000000000000..d4d8ee962d6713bab1d2184f81a1bc015ba7a8ee --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001014.fa @@ -0,0 +1,35 @@ +>PROKKA_01214 +MTDLVDPARAADGFRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH +REDFQLVLVDTPGLHRPRTLLGERLNDLVAETLNEVDAVGMCLPADEAIGPGDRFIAQQL +SYLHRTPVVAVVTKTDKVGPEQLMAQLVAVTALGDEVLGPENGGEGFAAVVPVSAVAGRQ +VDDVLGVFAGLLPAGPPLYPDGELTDEPEAVMVAELIREAALEGVRDELPHSVAVMVEEM +SLREDRPADRPLMDVWANVFVERDSQKGIIIGKGGSRLREIGAQARAGIERMLGTKVHLD +LRVKVAKEWQRDPKQLGRLGF +>PROKKA_00933 +MTDLVDPARAADGFRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH +REDFQLVLVDTPGLHRPRTLLGERLNDLVAETLNEVDAVGMCLPADEAIGPGDRFIAQQL +SYLHRTPVVAVVTKTDKVGPEQLMAQLVAVTALGDEVLGPENGGEGFAAVVPVSAVAGRQ +VDDVLGVFAGLLPAGPPLYPDGELTDEPEAVMVAELIREAALEGVRDELPHSVAVVVEEM +SLREDRPADRPLMDVWANVFVERDSQKGIIIGKGGSRLREIGAQARAGIERMLGTKVHLD +LRVKVAKEWQRDPKQLGRLGF +>PROKKA_01674 +MTDLVDPARAADGHRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH +REDFQLVLVDTPGLHRPRTLLGQRLNDLVAETLGEVDAVGFCLPADEAIGPGDRFIAQQL +AHLHRTPVVAVVTKTDKVGPEQLMAQLLAVTALGEEVLGPENGGEGFAAVVPVSAVAGRQ +VDDVLEVLRGLLPEGPPLYPDGELTDEPEAVMIAELIREAALEGVRDELPHSVAVVVEEM +ALREGRPDDRPLMDVWANLFVERDSQKGIIIGKGGSRLREIGARARAGIERMLGTKVHLD +LRVKVAKEWQRDPKQLGRLGF +>PROKKA_01571 +MTSLLDPAVPEGHRSGFACLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVHR +PDFQLVLVDTPGLHRPRTLLGERLNALVQETLSEVDVVGFCLPADEKIGPGDRFIAQQLA +ALRRTPVVAIVTKTDKTDPQRVAEQLLAVTALGDEVLGPENGGRGFAAVVPVSAVAGRQV +EDVESVLAQLLPDGPPLYPDGELTDEPEAIMVAELIREAALEDVRDELPHSVAVVVEEMN +PREGRPEERPLLDVYANVFVERDSQKGIIIGKGGSRLRAIGTQARTGIERMLGTPVHLDL +RVKVAKDWQRDPKHLNRLGM +>PROKKA_01171 +MTDLVDPARAADGFRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH +REDFQLVLVDTPGLHRPRTLLGERLNDLVAETLNEVDAVGMCLPADEAIGPGDRFIAQQL +SYLHRTPVVAVVTKTDKVGPEQLMAQLVAVTALGDEVLGPENGGEGFAAVVPVSAVAGRQ +VDDVLGVFAGLLPAGPPLYLDGELTDEPEAVMVAELIREAALEGVRDELPHSVAVVVEEM +SLREDRPADRPLMDVWANVFVERDSQKGIIIGKGGSRLREIGAQARAGIERMLGTKVHLD +LRVKVAKEWQRDPKQLGRLGF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001019.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001019.fa new file mode 100644 index 0000000000000000000000000000000000000000..47b3cd0dc13b398c927ffcf4879b9bbad818c642 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001019.fa @@ -0,0 +1,40 @@ +>PROKKA_01219 +MTDHYETLGVSRDASTEEIRRAYRKLARTHHPDVNPDPEAAEQFKRISHAYEVLSDEGRR +RAYDTTGNENGQAGFPGGFGGAGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT +ARIDLRDAVFGGEQTIELDTAVRCDRCEGSCCEPGTQPETCQTCHGHGMIQRPVRSLLGT +VMATEACPACQGFGTVIPTPCHECDGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP +GGGPNGDLYVEIAVRPDETFRREGDHLATTVTVPMAAAALGTTVTLDTLDGKQSLSLDPG +VQSGHVEVLHGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRQLLERLAEVRGEEVVHGA +PQAKGMFARLRENLRNL +>PROKKA_00938 +MTDHYETLGVSRDASTEEIRRAYRKLARTHHPDVNPDPEAAEQFKRISHAYEVLSDEGRR +RAYDTTGNENGQAGFPGGFGGAGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT +ARIDLRDAVFGGEQTIELDTAVRCDRCEGSCCEPGTQPETCQTCHGHGMIQRPVRSLLGT +VMATEACPACQGFGTVIPTPCHECDGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP +GGGPNGDLYVEIAVRPDETFRREGDHLATTVTVPMAAAALGTTVTLDTLDGKQSLSLDPG +VQSGHVEVLHGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRQLLERLAEVRGEEVVHGA +PQAKGMFARLRENLRNL +>PROKKA_01669 +MTDHYATLGVSRDASTEEIRRAYRKLARTHHPDVNPDPESAEQFKRISHAYEVLSDEGRR +RAYDTTGNENGQSGFPGGFGGGGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT +APIDLEDAVFGGEQTITLDTAVRCKRCEGSCCEPGTEPETCQTCQGHGMIQRPMRSLLGT +VMATEACPACQGFGTVIPDPCHECAGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP +GGGPNGDLYVEIAVRPHETFRREGDHLATTVTVPMAAAALGTTVTLATLDGEQTVRLEPG +VQSGHVETLAGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRELLERLAELRGEEVVHGT +PPARGMFARLRENLRNL +>PROKKA_01566 +MADHYATLGVSRDASAEEIKRAYRKLARQHHPDVNPSEEAAEEFKRISHAYEVLSDEDKR +RVYDQTGNENGTAGGFGGGGFGGAGFGGFADIFETFMNAAGTPGGGRGPMPRARRGQDAL +VTARIELRDAVFGGEATLQLDTAVTCERCSGTCCEPGTHPETCSTCQGQGMTQRPVRSML +GTIMAAETCPVCRGFGTVIPHPCTECSGQGRVRVQQPLTIRIPAGVDDGTRIHLAGRGEA +GPGGGPNGDLYVEVQVRPDEVFRREGDHLATTVTVPMAAAALGTSVTLETLDGPQEVDIE +PGTQSGHVETLRGLGVGRLRGAGRGDLKVDVVVTTPTDVTDEQRALLEQLAGLRGEEVVH +GAPPQSKGMFARLRENLKNL +>PROKKA_01177 +MTDHYETLGVSRDASTEEIRRAYRKLARTHHPDVNPGPEAAEQFKRISHAYEVLSDEGRR +RAYDTTGNENGQAGFPGGFGGAGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT +ARIDLRDAVFGGEQTIELDTAVRCDRCEGSCCEPGTQPETCQTCHGHGMIQRPVRSLLGT +VMATEACPACQGFGTVIPTPCHECDGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP +GGGPNGDLYVEIAVRPDETFRREGDHLATTVTVPMAAAALGTTVTLDTLDGKQSLSLDPG +VQSGHVEVLHGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRQLLERLAEVRGEEVVHGA +PQAKGMFARLRENLRNL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001022.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001022.fa new file mode 100644 index 0000000000000000000000000000000000000000..2bfc9dcbac56836cf7d0ce96fb400919503e66a0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001022.fa @@ -0,0 +1,20 @@ +>PROKKA_01222 +MNTRAQPDAGRTGHGPPAWLVSAGGRGAPLTAKQDRDRAALAHLSLAFGVLGPLVVWLLY +RDRGPFTSQESREALNFSGPPTLITLLFFFLSLLPVVGPIFAILGALTWAAMAVYGVMGA +SHVSKGRPFRYPFNLRILR +>PROKKA_00941 +MNTRAQPDAGRTGHGPPAWLVSAGGRGAPLTAKQDRDRAALAHLSLAFGVLGPLVVWLLY +RDRGPFTSQESREALNFSGPPTLITLLFFFLSLLPVVGPIFAILGALTWAAMAVYGVMGA +SHVSKGRPFRYPFNLRILR +>PROKKA_01666 +MNPSAQPDAGRPGHEPPAWLASAGGRATPLTAKQDRDRAALAHLSLAFGVLGPLVVWLLY +RDRGPFTSQESKEALNFSGPPTLITTLFFFLALLPVIGAIFAILGALSWAVMAVYGVMGA +SNVSKGRPFRYPFNLRILR +>PROKKA_01563 +MATTPSTTPAGETATPRRAAGGSAAHEAPAWLRDAAGGRAPLTAKQDRDRAALSHLSLAC +GLPGPLVMWLLYRDRGPFTAQESREALNFSLAPTLLIVLLFLLGGVPLLGGLLAILGALL +WIALALYGVMGASQVAKGRPFRYPFSPRLLR +>PROKKA_01180 +MNTRAQPDAGRTGHGPPAWLVSAGGRGAPLTAKQDRDRAALAHLSLAFGVLGPLVVWLLY +RDRGPFTSQESREALNFSGPPTLITLLFFFLSLLPVVGPIFAILGALTWAAMAAYGVMGA +SHVSKGRPFRYPFNLRILR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001025.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001025.fa new file mode 100644 index 0000000000000000000000000000000000000000..f6348772c1328145a3975d63c92beb4c58765967 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001025.fa @@ -0,0 +1,15 @@ +>PROKKA_01226 +MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEPEAAAAALRTASRKLDK +AASKGVIHKNQAANRKSGIAARVKALLG +>PROKKA_00945 +MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK +AASKGVIHKNQAANRKSGIAARVKALLG +>PROKKA_01662 +MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK +AASKGVIHKNQAANRKSGIAARVKALLG +>PROKKA_01559 +MANIKSQKKRILTNEKARQRNIAVKSELKTAIRAVDKAVAAGEQDAAVEALRTASRKLDK +AASKGVIHKNQAANRKSGIAARVKALLG +>PROKKA_01184 +MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK +AASKGVIHKNQAANRKSGIAARVKALLG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001029.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001029.fa new file mode 100644 index 0000000000000000000000000000000000000000..d76aa96a8961dad92f7391132da311ca0c729797 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001029.fa @@ -0,0 +1,35 @@ +>PROKKA_01230 +MASIEQWRDDALVRLRSRRSQLAGRARYGLRPPRRDRTAVVTDSAAALPGAVLGHGLAAG +IRQVALPVMVGEQIHTEGTDELALELPLALAAGTPVRTSRPSPGAFRTVYAELARAGYAR +ILSVHLSGELSGTVEAARLAAADAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMPVARI +RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLLGTLLQVRPVMAVDDGAIGLVDRPR +SAARAVDRLVELAVERAGEDPVRIAVHEYGDPETAMQLAERLQPISTTPVPVVELPAVLA +AHLGLGALGVVICPLESPTGGSGD +>PROKKA_00949 +MASIEQWRDDALVRLRSRRSQLAGRARYGLRPPRRDRTAVVTDSAAALPGAVLGHGLAAG +IRQVALPVMVGEQIHTEGTDELALELPLALAAGTPVRTSRPSPGAFRTAYAELARAGYAR +ILSVHLSGELSGTVEAARLAAAEAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMPVARI +RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLLGTLLQVRPVMAVDDGAIGLVDRPR +SAARAVDRLVELATERAGEDPVRIAVHEYGDPETAVQLAERLQPVSTTPVPVVELPAVLA +AHLGLGALGVVICPLESPTGGSGD +>PROKKA_01658 +MATIEQWRDDALVRLRSRRSQLVGRARYGLKPPRRDRTAVVTDSAAALPAAALGHSLAAG +IRQVPLPVMVGDQIHAEGTDDLALELPLALAAGTAVRTSRPSPGAFRSVYAQLAREGYAR +ILSVHLSGELSGTAEAARLAAVDAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMTVARI +RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLIGTLLHVRPVLAVDDGAISLVDRPR +SAARAVDRLVELATERAGDVPVRIAVHEYGDPETAAALAERLTPVSTTPVPVVELPAVLA +AHLGLGALGVVVCPLESPTGGSGD +>PROKKA_01555 +MASTSQWLEDAVERLRARRGQLVGRARYGLKPARRDRTGIVTDSAAALPVEVFAHPFAAG +IRQVALPVMVGEQIHVEGDADLDLELQLALAAGTPVRTSRPAPGAFRAAYADLAQAGCAR +ILSVHLSGELSGTVEAARLAAADAPVPVVVLDSRTAGLALGHAVLDAAVEAGFGRPLDQV +AAIAQACADQSSVLFTVPHLEQLRRGGRIGAVPSLLGALLQVRPVLGLQDGSVHLVDRAR +TSPRALERMVDLARERAAGGPARIAVHEYGDPAGATALAERLQSASATPVPVVPLPAVLA +AHLGLGTLAVVLSPLEPVPSTSSSPAQAN +>PROKKA_01188 +MASIEQWRDDALVRLRSRRSQLAGRARYGLRPPRRDRTAVVTDSAAALPGAVLGHGLAAG +IRQVALPVMVGEQIHTEGTDELALELPLALAAGTPVRTSRPSPGAFRTAYAELARAGYAR +ILSVHLSGELSGTVEAARLAAAEAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMPVARI +RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLLGTLLQVRPVMAVDDGAIGLVDRPR +SAARAVDRLVELATERAGEDPVRIAVHEYGDPETAVQLAERLQPVSTTPVPVVELPAVLA +AHLGLGALGVVICPLESPTGGSGD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001031.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001031.fa new file mode 100644 index 0000000000000000000000000000000000000000..cc8f83d637f360ead9797c8c4a5364db2e74e37d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001031.fa @@ -0,0 +1,43 @@ +>PROKKA_01232 +MQHPVALRSLKIALAFVGLLVGAGFATGAEVIQYFVGFGWIGIVGAGLAGLLVTAGGAVI +LQLGSVFLAADHKVVFRSVSHPVMARILDVVVTVTLFAIGVVMLAGAGSTLAQQFGWPTW +AGSTLMTLLVLVTGMLDVEKVSAIISLITPLVVVAVVAGFVHVLVTRDGGFTAHESLAVQ +ATTPVDPWWLSSVNYFGLVVVMAVSMCLVIGGSITHPREAFLGGLTGGLMYTALLLMAST +LLYLGYAEIGRADVPMLRLFASIAPWLGWAMVVVIYLMIFNTAIGMFYALGRRLTADRPG +RYRPVFAGVTLLAFAVSFVGFGDLINVVYPALGHLGIVLALVLLVWWLTHRRQISAESGL +RLRLLALLRLREHPEKTFTAQHAVQLQEAVGDSVAAPDAVTEALEDEVAQVLEEDDALTS +EGARPGPDAGPERPAGGSHSA +>PROKKA_00951 +MQHPVALRSLKIALAFVGLLVGAGFATGAEVIQYFVGFGWIGIVGAGLAGLLVTAGGAVI +LQLGSVFLAADHKVVFRSVSHPVMARILDVVVTVTLFAIGVVMLAGAGSTLAQQFGWPTW +AGSTLMTLLVLVTGMLDVEKVSAIISLITPLVVVAVVAGFVHVLVTRDGGFTAHESLAVQ +ATTPVDPWWLSSVNYFGLVVVMAVSMCLVIGGSITHPREAFLGGLTGGLMYTVLLLMAST +LLYLGYAEIGRADVPMLRLFASIAPWLGWAMVVVIYLMIYNTAIGMFYALGRRLTADHPG +RYRPVFAGVTLLAFAVSFVGFGDLMNVVYPALGHLGIVLALVLLVWWLTHRRQISAESGL +RLRLLALLRLREHPEKTFTAQHAVQLQEAVGDSVAAPGAVTEALEDEVAQVLEEDDAVTP +DEVHPGPDAGPERPAGGSHSA +>PROKKA_01656 +MVFRSVSHPVMARILDVTVTVTLFAIGFVMLAGAGSTLAQQLGWPTWAGAGLMTALVLVT +GMLDVEKVSAIISLITPLIILAVVAGFVHVLLTHEGSFTANEALAVQAATPVAPWWLSSV +NYFGLVVVMAVSMCLVIGGSITNPREAFAGGLTGGVLYTVLLLLASVLLYLGYAEIGRAD +VPMLQLFASIAPWLGWTMVVVIYLMIYNTAIGMLYALGRRLTAERPGRYRPVFIGVTLLA +FAVSFVGFGDLMNVVYPALGYLGIVLALVLIAWWVLHRRQISAESGLRLRLRALLRLREH +PEKTFTAQHAVLLQEAADESVAATAVVTEAVEEEVVQAIEADEPYGDPRRS +>PROKKA_01553 +MQKSAALRSVQLALAFVGLLVGAGFATGAEVIQYFVGFGEVGIGGALLAGVLVAVGGAVA +LQLGSLFLAADHKVVFRSVSHPVMARILDAVVTVTLFAIGFVMLAGAGSTLAQQLGWPVW +AGAALMTAMVIVTGMLDVEKVSAIIGMITPLIIIAVVAGFAYVVATHEGPFTVNDSLAVQ +AVTPVSPWWLSSINYFGLVVVMAVSMCVVIGGSTSSPREAFVGGLVGGVVYTVLLVLASV +LLYLGYAELGTADVPMLQLFASIHPALGWAMVVVIYLMIYNTAIGMFYALGRRLTAERPG +LYRPAFVGVTLAAFAVSFLGFGDLMNYVYPALGYLGIVLAVVLLVWWAAHRDDIAAESGL +RLRLLALLRLREHPEKTFTRQHAVILQETAEESVAPTETVTEMMEADAVAVIEAEDPDLL +PAADETAGRGGADHGGADGSAAARG +>PROKKA_01190 +MQHPVALRSLKIALAFVGLLVGAGFATGAEVIQYFVGFGWIGIVGAGLAGLLVTAGGAVI +LQLGSVFLAADHKVVFRSVSHPVMARILDVVVTVTLFAIGVVMLAGAGSTLAQQFGWPTW +AGSTLMTLLVVVTGMLDVEKVSAIISLITPLVVVAVVAGFVHVLVTRDGGFTAHESLAVQ +ATTPVDPWWLSSVNYFGLVVVMAVSMCLVIGGSITHPREAFLGGLTGGLMYTALLLMAST +LLYLGYADIGRADVPMLRLFASIAPWLGWAMVVVIYLMIFNTAIGMFYALGRRLTADRPG +RYRPVFAGVTLLAFAVSFVGFGDLMNVVYPALGHLGIVLALVLLVWWLTHRRQISAESGL +RLRLLALLRLREHPEKTFTAQHAVQLQEAVGDSVAAPGAVTEALEDEVAQVLEEDDALTS +GGARPGPDAGPERPAGGSHSA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001034.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001034.fa new file mode 100644 index 0000000000000000000000000000000000000000..7f95241e679e39ccc7c9be2f3dc6196b25f9c574 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001034.fa @@ -0,0 +1,40 @@ +>PROKKA_01235 +MTDAASLSPARHADPYSGVGGGELRLFTSESVTAGHPDKICDQISDAILDAILAADPSAK +VAVETLTTTGLVQVAGEVNTSAYVEIPKIVRETILDIGYDSSANGFDGAQCGVNISIGQQ +SSDIFAGVSRSLETREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL +TAVRRAENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHEWVTQEQLRADVEEH +VIRPVIERSGLDTSGMRIIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG +KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTATVPEEK +IIEAVNAVFDLRPAAIVKELNLLRPIYRRTAANGHFGRDDADFTWERTDRVEQLRAAAGL +>PROKKA_00954 +MTDAASLSPARHADPYSGVGGGELRLFTSESVTAGHPDKICDQISDAILDAILAADPSAK +VAVETLTTTGLVQVAGEVNTSAYVEIPRIVRETILDIGYDSSANGFDGAQCGVNISIGQQ +SSDIFAGVSRSLEAREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL +TAVRRAENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHEWVTQEQLRADVEEH +VIRPVIERSGLDTSGMRIIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG +KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTATVPEEK +IIEAVNAVFDLRPAAIVKELNLLRPIYRRTAANGHFGRDDADFTWERTDRVEQLRAAAGL +>PROKKA_01653 +MTDAAQPSPARHADPYTGVGGGELRLFTSESVTEGHPDKICDQISDAILDAILAADPAAK +VAVETLTTTGLVQVAGEVNTSAYVEIPRIVRETILDIGYDSSANGFDGAQCGVNISIGQQ +SSDIFAGVTRSLEAREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL +TAVRRQENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHDWVGQEQLRKDVEEH +VIRPVIERSGLDTSGMRVIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG +KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTAVVPEER +IIQAVNEVFDLRPAAIVKELNLLRPIYRKTAANGHFGRDDADFTWERTDRVERLRAAAGL +>PROKKA_01550 +MSDTPTPTPSAAAQPYRGVGGGDLRLFTSESVTSGHPDKMCDQISDAILDAILAADPSAK +VAVETLSTTGLVQVAGEVNTSAYVEIPHIVRETILDIGYDSSANGFDGAQCGVNVSIGQQ +SSDIFAGVSRSLEAREQGSADEVDEQGAGDQGIMFGYATNETPSYMPTPIYLAHRLSERL +TAVRRQENTPMPYLLPDGKTQVTVGYDADHRPRTVETVVVSTQHHDVVTQEQLRADVAEH +VIRPVIERSGLDVSNARFIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG +KDPSKVDRSAAYALRWVAKNVVAAGLAGRAEFQVAYAIGSARPVGLYVDTFGTNAVPEET +IIAAVNEVFDLRPAAIVKSLNLLRPIYRKTAAHGHFGRDDADFTWERTDKVEELRRAAGV +>PROKKA_01193 +MTDAASLSPARHADPYSGVGGGELRLFTSESVTAGHPDKICDQISDAILDAILAADPSAK +VAVETLTTTGLVQVAGEVNTSAYVEIPRIVRETILDIGYDSSANGFDGAQCGVNISIGQQ +SSDIFAGVSRSLEAREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL +TAVRRAENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHEWVTQEQLRADVEKH +VIRPVIERSGLDTSGMRIIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG +KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTATVPEEK +IIEAVNAVFDLRPAAIVKELNLLRPIYRRTAANGHFGRDDADFTWERTDRVEQLRAAAGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001039.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001039.fa new file mode 100644 index 0000000000000000000000000000000000000000..61479259b6ecf4f554c32507c168de081c66cebc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001039.fa @@ -0,0 +1,31 @@ +>PROKKA_01240 +MTTTATGGAGPRAPFGRRLAHAMETAGPLCLGVDPHPGLLRQWGLSDTPAGLEAFSLTAL +EAAVGPEGPRVAAIKPQVALYERHGSAGLAALERLLAAARDAGVLTIADAKRGDIGSTMD +GYAAAWIADASPLAADAVTLSPYLGFGTLVPTIRAAHEVGRGVFVLALTSNPEGREVQHV +GEGSAEGSVARRIAAAAAAENAALRGDDAWGPVGLVLGATVAAEADRLGLDLPALGGPLL +APGFGAQGATARGMRADFGTAWPQVLATSSRGILSAGPSVASLVDTIEENRAALR +>PROKKA_00959 +MTTTATGGAGPRAPFGRRLAQAMETAGPLCLGVDPHPGLLRQWGLSDTPAGLEAFSLTAL +EAAVGPEGPRVAAIKPQVALYERHGSAGLAALERLLAAARDAGVLTIADAKRGDIGSTMD +GYAAAWIADASPLAADAVTLSPYLGFGTLVPTIRAAHEAGRGVFVLALTSNPEGREVQHV +GEGSAEGSVARRIAAAAAAENAALRGDDAWGPVGLVLGATVAAEADRLGLDLPALGGPLL +APGFGAQGATARGMRADFGTAWPQVLATSSRGILSAGPSVASLVDTIEENRAALR +>PROKKA_01648 +MAQAGPLCLGVDPHPSLLRQWGLPDTPAGLEAFSLTGLEAAVGPDGPRVAAIKPQVALYE +RHGSAGLAALERLLAEARDAGVLTIADAKRGDIGSTMDGYAAAWTSDASPLAADAVTLSP +YLGFGTLVPTIEAAHAAGRGVFVLALTSNPEGREVQHVGRDAGEGAVARRIAAAAADLNA +ALRAEDEWGPVGLVLGATVAEDAERLGLDLPGLAGPLLAPGFGAQGATAAGMREGFGRAW +PQVLATSSRGILAGGPTVAALVERIERDRADLG +>PROKKA_01545 +MSVPAASMTREPFGRRLAAAMAAAGPLCLGIDPHPSLLQAWGLPDTAAGLESFGLTALEA +AAGDGAARVAAVKPQVALFERHGSAGLAVLERLLAEARDAGVLTIADAKRGDIGSTMDGY +AAAWLDDASPLAADAVTLSPYLGYGTLTASIERAAAAGRGVFVLALTSNPEGASVQHVGA +SEGQGAVAARIVTSAAADDARLAGLDGWGPVGLVVGATVAGHARELGIDLAALRGPLLAP +GFGAQGATGAGMREAFGAAWPQVLATSSRGILAAGPTVTSLTRAIDAARADLGVEGPDPR +HAAGRDA +>PROKKA_01198 +MTTTATGGAGPRAPFGRRLAHAMETAGPLCLGVDPHPGLLRQWGLSDTPAGLEAFSLTAL +EAAVGPEGPRVAAIKPQVALYERHGSAGLAALERLLAAARDAGVLTIADAKRGDIGSTMD +GYAAAWIADASPLAADAVTLSPYLGFGTLVPTIRAAHEAGRGVFVLALTSNPEGREVQHV +GEGSAEGSVARRIAAAAAAENAALRGDDAWGPVGLVLGATVAAEADRLGLDLPALGGPLL +APGFGAQGATARGMRADFGTAWPQVLATSSRGILSAGPSVASLVDTIEENRAALR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001040.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001040.fa new file mode 100644 index 0000000000000000000000000000000000000000..b38d2d94899ce4bf92559a4aab2765315a61fe93 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001040.fa @@ -0,0 +1,100 @@ +>PROKKA_01241 +MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPEL +ADATYVEPITPAVVAKIIEKERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANI +EAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVEDLKYPVVVRPSFTMGGLGSG +MAYDEADLYRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV +GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPVDGRVVVIEM +NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR +FAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRSLEQKGSELAFPQDADPQALL +AAASTATTDRLSQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADEIRDAEVLDEA +LLRRAKRHGFSDAQIGSLRHMDAAVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY +DLETEVAPHEGESVIILGSGPNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVST +DYDISDRLYFEPLTLEDVLEVIAAEEASGGVRGVFVQLGGQTPLKLAQQLADAGVPILGT +SPAAIDLAEHRGEFALVLERAGLVAPKNGTAVSFDDAKRVADEIGYPVLVRPSYVLGGRG +MEIVYSEEALAHYVEHATEITPDQPMLVDRFLEDAIEIDVDALYDGTELYLGGVMEHIEE +AGIHSGDSACVLPPVTLGPDVLERVHRATERIAAGVGVRGLINIQFALASDVLYVIEANP +RASRTVPFVSKATGVQLAKAAARIGVGESIADLRAAGMLPTAYDGGTLPIGAPVAVKEAV +LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDKHFDTAFAKSQSAAGGPLPTSGRVFVSV +ANRDKRTLVGQAKRLVDLGFQVVSTGGTAEVLRRNGIPAEVVAKIADAGHEDGAGTVLEQ +LHAGTVDLVLNTPSGGDARTDGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRSYEWSV +TSLQEHDARLQQAVAGPEAAA +>PROKKA_00960 +MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPEL +ADATYVEPITPAVVAKIIEKERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANI +EAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVEDLKYPVVVRPSFTMGGLGSG +MAYDEADLYRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV +GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPVDGRVVVIEM +NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR +FAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRSLEQKGSELAFPQDADPQALL +AAASTATTDRLSQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADEIRDAEVLDEA +LLRRAKRHGFSDAQIGSLRHMDAAVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY +DLETEVAPHEGESVIILGSGPNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVST +DYDISDRLYFEPLTLEDVLEVIAAEEASGGVRGVFVQLGGQTPLKLAQQLADAGVPILGT +SPAAIDLAEHRGEFALVLERAGLVAPKNGTAVSFDDAKRVADEIGYPVLVRPSYVLGGRG +MEIVYSEEALAHYVAHATEITPDQPMLVDRFLEDAIEIDVDALYDGTELYLGGVMEHIEE +AGIHSGDSACVLPPVTLGPDVLERVHRATERIAAGVGVRGLINIQFALASDVLYVIEANP +RASRTVPFVSKATGVQLAKAAARIGVGESIADLRAAGMLPTAYDGGTLPIGAPVAVKEAV +LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDKHFDTAFAKSQSAAGGPLPTSGRVFVSV +ANRDKRTLVGQAKRLVDLGFQVVSTGGTAEVLRRNGIPAEVVAKIADAGHEDGAGTVLEQ +LHAGTVDLVLNTPSGGDARTDGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRSYEWSV +TSLQEHDARLQQAVAGPEAAA +>PROKKA_01647 +MPKRPDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPEL +ADATYVEPITPAVVAKIIEKERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANI +EAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVEDLKYPVVVRPSFTMGGLGSG +MAYDEADLHRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV +GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPADGRVVVIEM +NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR +FAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRSLEQKGSELAFPQDADPRELL +RRARTATTDRLAQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADQIRDAEVLDES +LLRHAKRHGFSDAQIGSLRHMGADVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY +DLETEVAPHEGRSVIILGSGPNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVST +DYDISDRLYFEPLTLEDVLEVIAAEEASGGVLGVYVQLGGQTPLKLAQQLADAGVPILGT +SPEAIDLAEHRGEFARVLDRAGLVAPKNGTAVSFEDAKRVADEIGYPVLVRPSYVLGGRG +MEIVYSEEALAHYVEHATEITPDQPMLVDRFLEDAIEIDVDALYDGERMYLGGVMEHIEE +AGIHSGDSACVLPPVTLGPDVLERVHRATEQIAAGVGVRGLINIQFALASDVLYVIEANP +RASRTVPFVSKATGVQLAKAAAMIGVGKSIADLQAEGVLPTAYDGATLPLGAPVAVKEAV +LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDRHYDTAFAKSQAAAGGPLPTSGRVFVSV +ANRDKRTLVGQAKRLVDLGFQIVSTGGTAEVLRRNGIPAETVAKIAEAGGEDGAGTVLEQ +LHAGTVDLVLNTPSGGDARTDGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRAYEWSV +TSLQEHDARLQQAVEASA +>PROKKA_01544 +MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVILVNSNPATIMTDPEL +ADATYVEPITPEVVAKIIEKERPDAVLPTLGGQTALNTAIALDKDGVLEKFGVELIGANI +AAIELGENRELFKGVVERAGGESARSHIVHTMEEAFAAVEDLKYPVVVRPSFTMGGLGSG +MAYDEADLRRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV +GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPEDGRVVVIEM +NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR +FAFEKFPAADATLTTTMKSVGEAMAIGRSFSEALQKALRSLEQKGSELSFDRDADPASLL +ASARTATTQRLAQTQRALYAGATLEEAFEATAIDPWFLDQLMLINEVADEVREAPQLDEA +VLRRAKRHGFSDAQIGSLRHMDPAVVRGLRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY +DLESEVDEHAAPSVVILGSGPNRIGQGIEFDYSCVHATLALREAGYETVMVNCNPETVST +DYDISDRLYFEPLTLEDVLEVIAAEEATGGVAGVFVQLGGQTPLKLAQQLADAGVPILGT +SPEAIDLAEHRGEFARVLDEAGLIAPKNGTAVSFEDARRVADEIGYPVLVRPSYVLGGRG +MEIVYTEEALAHYVTNATEITPTQPMLVDRFLEDAIEIDVDALYDGHELYLGGVMEHIEE +AGIHSGDSACVLPPVTLGPDVLERVRTATEKIAAGVGVRGLINIQFALASDVLYVIEANP +RASRTVPFVSKATGVQLAKAAAMIGMGRTIAELRAAGTLPTAFDGASLPMGASVAVKEAV +LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDRHFDTAFAKSQAGAGGPLPTEGRVFVSV +ANRDKRAVVGQAKRLVDLGFEIVSTGGTAEVLRRNGVPAEVVAKIADASDADGAGTVLEQ +LHEGRVDLVLNTPSGGEARTDGYEIRAAATSLGVPVITTTAEFAACLQAIEAMRTYEWSV +TSLQEHEERLAQAVAAEASA +>PROKKA_01199 +MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPEL +ADATYVEPITPAVVAKIIEKERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANI +EAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVEDLKYPVVVRPSFTMGGLGSG +MAYDEADLYRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV +GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPVDGRVVVIEM +NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR +FAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRSLEQKGSELAFPQDADPQALL +AAASTATTDRLSQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADEIRDAEVLDEA +LLRRAKRHGFSDAQIGSLRHMDAAVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY +DLETEVAPHEGESVIILGSGPNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVST +DYDISDRLYFEPLTLEDVLEVIAAEEASGGVRGVFVQLGGQTPLKLAQQLADAGVPILGT +SPAAIDLAEHRGEFALVLERAGLVAPKNGTAVSFDDAKRVADEIGYPVLVRPSYVLGGRG +MEIVYSEEALAHYVEHATEITPDQPMLVDRFLEDAIEIDVDALYDGTELYLGGVMEHIEE +AGIHSGDSACVLPPVTLGPDVLERVHRATERIAAGVGVRGLINIQFALASDVLYVIEANP +RASRTVPFVSKATGVQLAKAAARIGVGESIADLRAAGMLPTAYDGGTLPIGAPVAVKEAV +LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDKHFDTAFAKSQSAAGGPLPTSGRVFVSV +ANRDKRTLVGQAKRLVDLGFQVVSTGGTAEVLRRNGIPAEVVAKIADAGHEDGAGTVLEQ +LHAGTVDLVLNTPSGGDARTDGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRSYEWSV +TSLQEHDARLQQAVAGPEAAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001041.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001041.fa new file mode 100644 index 0000000000000000000000000000000000000000..e5de797b64bb0d6a761d61f5132317b85a7564a0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001041.fa @@ -0,0 +1,40 @@ +>PROKKA_01242 +MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT +SPHIGNTGVNDADRESRAIFAAGYVVRDAARRPSNWRAERTLDEELEAFGVVGIREVDTR +AITRRLRTEGSMRAGVFSGEHAARPEAELLAEVRAQPSMAGARLAESVTTEQPYVIEPAE +HGWEGEPIAEIAALDLGIKAATPRHLASRGIRVHVLPAATDLAGIRAVDPDGVFLSNGPG +DPATADAQVELLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVLDKATG +RVAITSQNHGFAVAAPLGEPIEAPESRFGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP +ESAAGPNDTLDLFDRFVQLLTEHRAATTPATEGA +>PROKKA_00961 +MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT +SPHIGNTGVNDADRESRAIFAAGYVVRDAARRPSNWRAERTLDEELETFGVVGIREVDTR +AITRRLRTEGSMRAGVFSGEHAARPEAELLAEVRAQPSMAGARLAESVTTEQPYVIEPAE +HGWEGEPIAEIAALDLGIKAATPRHLASRGIRVHVLPAATDLAGIRAVDPDGVFLSNGPG +DPATADAQVELLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVLDKATG +RVAITSQNHGFAVDAPLGEPIEAPESRFGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP +ESAAGPNDTLDLFDRFVQLLTEHRAATTPATEGA +>PROKKA_01646 +MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT +SPHIGNTGVNDTDRESRAIFAAGYVVRDAARRPSNWRAERTLDEELEAFGVVGIREVDTR +AITRRLRTEGSMRAGVYSGEHAGRPEAELLAEVREQPSMAGARLAETVTTEQPYVIEPAA +HGWEGEPLAEIAALDLGIKAATPRHLASRGIRVHVLPATAGLEEIRAVSPDGVFLSNGPG +DPATADAQVALLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVMDNATG +RVAITSQNHGFAVDAPLGEPVEAPETRYGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP +ESAAGPNDTLDLFDRFVRMLTEHRDAAAPAATEGA +>PROKKA_01543 +MSTPTPETALLVLEDGTVHRGRAYGARGSTLGEAVFTTGMTGYQETLTDPSYARQIVVQT +APHIGNTGVNDEDAESRAIWVAGYVVRDAARRPSNWRSQRTLDEELAAHGVVGIQDVDTR +AITRALRTEGSMKAGIFSGEAAQRPEAELLAEVREQPSMAGARLAETVSAPSAYVVEPSD +HGWDGEPIADVAALDLGIKAATPHHLAARGIRVHVLPADSDFAAIQAVRPDGVFMSNGPG +DPATADAQVAVLREVLDAGLPYFGICFGNQIFGRALGFGTYKLPFGHRGPNQPVMDKATG +RVEITSQNHGFAVDAPIGEVVEAPEARYGRVEVSHWSLNDDVVEGLRLLDRPAFSVQFHP +EAAAGPHDSLGLFDRFAHTLTERRAAAPSATPEGA +>PROKKA_01200 +MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT +SPHIGNTGVNDADRESRAIFAAGYVVRDAARRPSNWRAERTLDEELEAFGVVGIREVDTR +AITRRLRTEGSMRAGVFSGEHAARPEAELLAEVRAQPSMAGARLAESVTTEQPYVIEPAE +HGWEGEPIAEIAALDLGIKAATPRHLASRGIRVHVLPAATDLAGIRAVDPDGVFLSNGPG +DPATADAQVELLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVLDKATG +RVAITSQNHGFAVAAPLGEPIEAPESRFGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP +ESAAGPNDTLDLFDRFVQLLTEHRAATTPATEGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001047.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001047.fa new file mode 100644 index 0000000000000000000000000000000000000000..cb795493a95ac5ad6ada4d2586eb9fa5395e3996 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001047.fa @@ -0,0 +1,40 @@ +>PROKKA_01249 +MTDREPDITEQETPGAAPAAAPAAPEDVTVIPVAGGHEAAVHGGYDVVVGRGLLARLPDL +LGPTVRRVLVIHPRALRATGDVVKNDLEAVGLTALTAEIPDAEEGKHLQVAGFCWQVLGQ +NDFTRSDAIVSVGGGAVSDLAGFVAATWLRGIRVVHMPTTLLGMVDAAVGGKTGINTAEG +KNLVGAFHNPAGVLADLDTLLTLPANELISGLAEVVKCGFIADPAILDLIEEDPAQAQNP +HSPRLRELIERSIRVKADVVSRDPRESGAREALNYGHTMGHAIELAERYQWRHGAAVSVG +LVFAAELARSLGRLDDATADRHWSVLTALGLPVSYRGDRWQTLLEGIRRDKKNRGDQLRF +VLLDGLAQPTTVDIPDASLLFAAYQEIAE +>PROKKA_00968 +MTDREPDITEQETPGAAPAAAPAAPEDVTVIPVAGGHEAAVHGGYDVVVGRGLLARLPDM +LGPTVRRVLVIHPRALRATGDVVKNDLEAVGLTALTAEIPDAEEGKHLQVAGFCWQVLGQ +NDFTRSDAIVSVGGGAVSDLAGFVAATWLRGVRVVHMPTTLLGMVDAAVGGKTGINTAEG +KNLVGAFHNPAGVLADLDTLLTLPANELISGLAEVVKCGFIADPAILDLIEEDPAQAQNP +HSARLRELIERSIRVKADVVSRDPRESGAREALNYGHTMGHAIELAERYQWRHGAAVSVG +LVFAAELARSLGRLDDATADRHWSVLTALGLPVSYRGDRWQTLLEGIRRDKKNRGDQLRF +VLLDGLAQPTTVDIPDASLLFAAYQEIAE +>PROKKA_01639 +MTDRHPDPAEPEIPGEPPAAEPAAAGQEDVTVIPVSGGQEAAAHGGYDVVVGRGLLARLP +EMLGPGVQRVLVIHPRALRATGDVVKNDLEAVGLTALTAEIPDAEEGKHLQVAGFCWQVL +GQNDFTRSDAVVSVGGGAVSDLAGFVAATWLRGVRVVHMPTTLLGMVDAAVGGKTGINTS +EGKNLVGAFHPPAGVLADLDTLLTLPANELISGLAEVVKCGFIADPAILDLIEQDPAQSQ +NPHSARLRELIERSIRVKADIVSRDLRESGEREALNYGHTMGHAIELAERYQWRHGAAVS +VGLVFAAELARSLGRLDDATADRHWSVLTALGLPVSYRGDRWQTLLEGIRRDKKNRGDQL +RFVLLDGLAQPSTVDIPDPSLLFAAYQEIAE +>PROKKA_01536 +MTEHQPDQSDPIAEHSAAAPEQDVTVIPVAGGPENRAGGGYDVVVGRGLLGRLPAVLGPQ +VRRVLVIHPRALRATGDVVKNDLEAAGLVSLTAEIPDAEEGKHLQVAGFCWQVLGQNDFT +RSDAIVSVGGGAVSDLAGFVAATWLRGIRVVHMPTTLLGMVDAAVGGKTGINTAEGKNLV +GAFHPPAGVLADLDTLLTLPSNELVSGLAEVVKCGFIADPRILELIEEAPEQAQNPHSAV +LRELIERAVRVKAEVVSGDLREAGPREALNYGHTLGHAIEHAERYQWRHGAAVSVGLVFA +AELARSLGRLDDATADRHWSVLQSLGLPVSYRGDRWQTLLEGIKRDKKNRGDQLRFVLLD +GLARPTTVDIPDASLLFAAYQEIAE +>PROKKA_01207 +MTDREPDITEQETPGAAPAAAPAAPEDVTVIPVAGGHEAAVHGGYDVVVGRGLLARLPDM +LGPTVRRVLVIHPRALRATGDVVKNDLEAVGLTALTAEIPDAEEGKHLQVAGFCWQVLGQ +NDFTRSDAIVSVGGGAVSDLAGFVAATWLRGVRVVHMPTTLLGMVDAAVGGKTGINTAEG +KNLVGAFHNPAGVLADLDTLLTLPANELISGLAEVVKCGFIADPAILDLIEEDPAQAQNP +HSARLRELIERSIRVKADVVSRDPRESGAREALNYGHTMGHAIELAERYQWRHGAAVSVG +LVFAAELARSLGRLDDATADRHWSVLTALGLPVSYRGDRWQTLLEGIRRDKKNRGDQLRF +VLLDGLAQPTTVDIPDASLLFAAYQEIAE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001048.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001048.fa new file mode 100644 index 0000000000000000000000000000000000000000..c6cd602f5603bc9fe86bc2d14e122f862d3941f3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001048.fa @@ -0,0 +1,25 @@ +>PROKKA_01250 +MTDTPGTAPAPGPDPSTRPVPGPVTVCPWEGMTGALEARLTAAATVAAAADEDPAARPAR +RVVLVGPMGAGKTTVGRALAAVTGLPFVDSDELFTQVHGPIPEFFAEHGEAAFRAEEARV +IGHVLGRPTPCVLSCGGGAVLHPGTRRALAGPDSDVVYLAVGEEEALRRVGGGAGRPVLA +GDPAGTWRRILAEREGLYREVADLVLDTTGLTAAEAAWRIVGDAHRPRRSESHP +>PROKKA_00969 +MTDTPGTAPAPGPDPSTRPVPGPVTVCPWEGMIGALEARLTAAATVAAAADEDPAARPAR +RIVLVGPMGAGKTTVGRALAAVTGLPFVDSDELFTQVHGPIPEFFAEHGEAAFRAEEARV +IGHVLGRPAPCVLSCGGGAVLHPGTRRALAGPDSDVVYLAVGEEEALRRVGGGAGRPVLA +GDPAGTWRRILAEREGLYREVADLVLDTTGLTAAEAAWRIVGDAHRPRRSESHP +>PROKKA_01638 +MPGPVSLCAWEAMTGALEARLATAAAAADGAPAPRIVLVGPMGAGKTTVGRALAATTGLP +FVDADELFVQVHGPIPEFFAARGEAAFREEEARVIAHVLGRPSPCVLSCGGGAVLHPATR +RALRGPGSDVVHLAVDEAVALRRVGGGAGRPVLAGDPAGTWRRILAEREPFYREVADLVV +DTTGLTAAEAAWRIVEGVHRPRRSESHP +>PROKKA_01535 +MSAQPAPTDGVPSWEAMVRGLDGRLAETSRDPGPVVVLVGPMGAGKTTVGRALAEATGRV +FVDSDALFEDAFGSIPAYFTSRGEPEFRRQEERVIAHVLAHPAPCVLACGGGAVLSAATR +ARLADPRAVVVSLQVAEPEALRRLGGGAGRPVLAGDPAGRWKAVLAERAPLYAEVADLTL +DGTGHRPGDIASRIVEAIPTLPRRHTRP +>PROKKA_01208 +MTDTPGTAPAPGPDPSTRPVPGPVTVCPWEGMIGALEARLTAAATVAAAADEDPAARPAR +RIVLVGPMGAGKTTVGRALAAVTGLPFVDSDELFTQVHGPIPEFFAEHGEAAFRAEEARV +IGHVLGRPAPCVLSCGGGAVLHPGTRRALAGPDSDVVYLAVGEEEALRRVGGGAGRPVLA +GDPAGTWRRILAEREGLYREVADLVLDTTGLTAAEAAWRIVGDAHRPRRSESHP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001052.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001052.fa new file mode 100644 index 0000000000000000000000000000000000000000..6a15bb90ef59140b01ee46cefbba11953f659820 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001052.fa @@ -0,0 +1,85 @@ +>PROKKA_01255 +MKSQEIARRWTAFFESRGHRVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRVV +SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKETAIPMAWELLTSSVEDGGFGLD +PERLWVTVYREDDEAERIWREDVGVRPERIQRMGKEDNYWHTGQPGPGGPCSEIFYDRGP +AYGVDGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDVAGELEHKNIDTGLGLERLAMI +LQGVENMYETDQVRPVLDRAAQLAGRSYTSTEDPADPHYDDDVRLRMVADHVRSALMLIS +DGVRPGNEGRGYVLRRLIRRVVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERI +ARIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPDAFELHDTYGFPIELTLEIAE +EAGVAVDEAGFRALMAEQRDRARADAKAKKSGHTDTAVYQRLRAEGQTHFTGYTEHTTES +VVRGLLQNGEEVPSAGAGTELELVLDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPV +KGLSVHRVKVLDGEVAAGAQALGAIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGS +FNKEGYLRFDFRWAESLSAGARSEVEDVVNIAIRDDHTVLTQEMSLEEARALGAMSLFGE +KYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH +LAAERTLVSELSEMFKAPAEELKDRIGATLDRLKAAEKQVAELRAQALQAQAGQLAAQAR +DVTTSGGTSVRVLAHHAGDVAGDQLRSLALDLRARIESAGGNAAGTPVFVALTAEAKGRP +LVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQGGGQDVTRVGDALDAVVAAV +RAA +>PROKKA_00974 +MKSQEIARRWTAFFESRGHRVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRVV +SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKETAIPMAWELLTSSVEDGGFGLD +PERLWVTVYREDDEAERIWREDVGVRPERIQRMGKDDNYWNTGQPGPGGPCSEIFYDRGP +AYGVDGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDIAGELEHKNIDTGLGLERLAMI +LQGVENMYETDQVRPVLDRAAQLAGRSYTSTEDPADPHYDDDVRLRMVADHVRSALMLIS +DGVRPGNEGRGYVLRRLIRRVVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERI +SRIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPDAFELHDTYGFPIELTLEIAE +EAGVAVDEAGFRALMAEQRDRARADAKAKKAGHTDTAVYQRLRAEGQTHFTGYTEHTTES +VVRGLLQNGEEVASAGAGTELELVLDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPV +KGLSVHRVKVLDGEVAAGAQALGAIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGS +FNKEGYLRFDFRWAEALSAGARSEVEDVVNIAIRDDHAVLTQEMSLEEARALGAMSLFGE +KYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH +LAAERTLVSELSEMFKAPAEELKDRIGATLDRLKAAEKQVAELRAQALQAQAGQLAGQAQ +DVTTSAGTSVRVLAHHVGDVAGDQLRSLVLDLRARIESAGGNAAGTPVLVALTAEAKGRP +LVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQGGGQDVTRVGDALEAVVAAV +RAA +>PROKKA_01633 +MKSQEIARRWIAFFESKGHQHVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRAV +SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKEKAIPMAWELLTTSVEDGGYGLD +PERLWVTVYEEDDEAARIWEESVGVRPERIQRMGKDDNYWNTGQPGPGGPCSEIFYDRGP +EYGADGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDVAGELENKNIDTGLGLERLAML +LQGVENMYETDQVRPVLDRAAELSGREYTSTEDPTDPHYEDDVRLRMVADHVRSALMLIG +DGVRPGNEGRGYVLRRLIRRVIRALRLMGVTEPVLPELLPVSRDAMKGSYPVVADEFERI +SRIAYAEEKAFLRTIAAGTARLDAAVGQARTAGGGIAGADAFELHDTYGFPIELTLEIAE +ESGVAVDEAGFRALMAEQRDRARADAKAKKSGHTDTALYQRLRAEGQTHFTGYTEHTTES +VVRGLLLDGEEVASASAGTELEVILDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPV +RGLSVHRVKVLDGEVPAGAEALGAIDLQRRLDGEKAHSGTHLVHAALHQVLGPEATQSGS +FNKEGYLRFDFRWAESLSAGARSEVEDVVNIAIRDDHTVLTQEMSLEEARALGAMSLFGE +KYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH +LAAERTLVSELSEMFKAPAEELKDRIAASMDRLKAAEKQIAELQAKALQAQAGELAAQAQ +DVTTASGVSVRVLARHVGEVAGDQLRGLVLDLRSRIESAGGNAAGTPVLVALTGEAKGRP +LVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQGGGQDVTRVGDALDAVVAAA +RAA +>PROKKA_01530 +MKSHEIARRWTAYFEKQGHLVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRAT +SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKEKAIPMAWELLTTSVEDGGYGLD +PERLWVTVYEEDDEAARIWREDVGVRPERIQRMGKADNYWNTGQPGPGGPCSEIFYDRGP +EYGVEGGPEADDTRYIEIWNLVFMQYRLSQVRSKYDFDVAGELEHKNIDTGLGLERLAMI +LQGVENMYETDQVRPVLDRAAELAGKSYTSTEDPADPHYDDDVRLRMVADHVRSALMLIS +DGVRPGNEGRGYVLRRLIRRVVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERI +SRIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPDAFELHDTYGFPIELTLEIAE +EAGVAVDEAGFHALMAEQRDRARADAKAKKSGHTDTAVYQRLRAEGQTHFTGYTEHTTES +VVRGLLQNGEEVASAGAGTELELVLDATPFYAESGGQAADTGVITGDGFSLEVLDVQAPV +KGLSVHRVKVLDGEVPVGAEAVGRIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGS +FNKEGYLRFDFRWAEAVSAMARSEIEDVVNIAIRDDHQVLTQEMSLDEARAMGAMSLFGE +KYGDRVRVVEINGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH +LAAERTLVSDLSEMFKAPADQLKDRITATMDRLKAAEKQVADLQAKALQAQAGTLAAQAQ +DVTTTSGASVKVLAHHAGEVAGDQLRSLVLGLRSRIESAGGNAAGTPVLVALTGEAKGRP +LVVVATNEAARGAGLKAGAMVKLATAALGGGGGGKDDVAQGGGQDVTAVAAALDAVLDAV +RDA +>PROKKA_01213 +MKSQEIARRWTAFFESRGHRVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRVV +SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKETAIPMAWELLTSSVEDGGFGLD +PERLWVTVYREDDEAERIWREDVGVRPERIQRMGKDDNYWNTGQPGPGGPCSEIFYDRGP +AYGVDGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDIAGELEHKNIDTGLGLERLAMI +LQGVENMYETDQVRPVLDRAAQLAGRSYTSTEDPADPHYDDDVRLRMVADHVRSALMLIS +DGVRPGNEGRGYVLRRLIRRVVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERI +SRIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPDAFELHDTYGFPIELTLEIAE +EAGVAVDEAGFRALMAEQRDRARADAKAKKAGHTDTAVYQRLRAEGQTHFTGYTEHTTES +VVRGLLQNGEEVASAGAGTELELVLDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPV +KGLSVHRVKVLDGEVAAGAQALGAIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGS +FNKEGYLRFDFRWAEALSAGARSEVEDVVNIAIRDDHAVLTQEMSLEEARALGAMSLFGE +KYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH +LAAERTLVSELSEMFKAPAEELKDRIGATLDRLKAAEKQVAELRAQALQAQAGQLVGQAQ +DVTTSAGTSVRVLAHHVGDVAGDQLRSLVLDLRARIESAGGNAAGTPVLVALTAEAKGRP +LVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQGGGQDVTRVGDALEAVVAAV +RAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001054.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001054.fa new file mode 100644 index 0000000000000000000000000000000000000000..b72fae447aaabb91a9b220842b2521197daaa920 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001054.fa @@ -0,0 +1,25 @@ +>PROKKA_01257 +MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL +RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEQRLDALVLRAGFARTIQQARQLVVHR +HIMVDGKRVDVPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIDKL +RATLTRRPKRSEVPVTCEEQLVVEYYAR +>PROKKA_00976 +MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL +RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEQRLDALVLRAGFARTIQQARQLVVHR +HILVDGKRVDVPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIDKL +RATLTRRPKRSEVPVTCEEQLVVEYYAR +>PROKKA_01630 +MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL +RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEMRLDALVLRAGFARTIQQARQLVVHR +HIMVDGKRVDIPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIDKL +RATLTRRPKRSEVPVTCEEQLVVEYYAR +>PROKKA_01528 +MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL +RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEMRLDALVLRAGFARTIQQARQLVVHR +HIMVDGKRVDIPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIEKL +RATLTRRPKRSEVPVTCEEQLVVEYYAR +>PROKKA_01215 +MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL +RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEQRLDALVLRAGFARTIQQARQLVVHR +HILVDGKRVDVPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIDKL +RATLTRRPKRSEVPVTCEEQLVVEYYAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001058.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001058.fa new file mode 100644 index 0000000000000000000000000000000000000000..981ef350fe479b9775114d676909fdc1777fe01c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001058.fa @@ -0,0 +1,55 @@ +>PROKKA_01261 +MPRLARLATAVTAAALSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHET +GVFGESAAEIPAFDAVSGRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVT +DKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTTTLRYLGGVRVGALPDSLAFSPNG +AYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTALPAG +VRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLED +LWALTPTDWSTEGVLDASDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGR +EWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLKVLTDLGYDSERECHSSLTTLGGR +SFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPEPES +VVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGA +EGLTFVPADESPSGTALLIVANEVSGSTTVYEVNPTRRQ +>PROKKA_00980 +MPRLARLATAVTAATLSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHET +GVFGESAAEIPAFDAVSGRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVT +DKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTTTLRYLGGVRVGALPDSLAFSPNG +AYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTALPAG +VRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLED +LWALTPTDWSTEGVLDASDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGR +EWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLKVLTDLGYDSERECHSSLTTLGGR +SFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPEPES +VVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGA +EGLTFVPADESPSGTALLIVANEVSGSTTVYEVNPTRRQ +>PROKKA_01627 +MRTLSRLAAATSMVALSAAVVAPLTVAAPAANPSGRSIELTAAGTHATGVFDASAAEIPA +FDKTTGRLFVVNAQKGAIDVLTVGEDAEPAAESVLSVAGLPAADGSVTGAGAVVNSVAVA +GAVMAATVEAEDKTGHGWLVFFDTRTLGFLGGVRVGALPDSVALAPNGAYAVVANEGEPA +DDFSSDPEGTISVVSVPKNARQFARLGQDAVRTVDFRAYDEGAALPEGVRVFGPDVAVPS +GHEEAGRIARNLEPEYASIDPTGRTAYVSVQEANAVVAVDLASASLADFWALHLTDWSTE +GVLDVSDKDGAISPAYQPVLGVPMPDGLATYKHRGQTLVVTANQGDSREWGDFVDAERVK +DLELCGDVFPHAKALQKNEALGRLNVLTDLGYDAERGCHTELHALGGRGFSIYTADGQRL +FDSSGMLEEQIARLIAAGELPAHAFNANNDETPSFDSRSDDKGVEPESVVVGEVQGRQYA +FVGLERIGGVMVFDITDPTDARYVDYINERAWDAVGEDGDAGLGDMGAEGLAFVPASDSP +SGTALLIVATEVSGSTTVYEVDPVKGGKRT +>PROKKA_01524 +MSRIVRLTRLGAAAGALALSAAVVAPSAVSAPVTATAAAANPSGKTVELSLAGTHETGVF +GESAAEIPAFDAATGRLFVVNAEKGAVDVLRVGADGAPAAETVLSAEGLRTADGSVTDGG +ATVNSVAVSGGVLAVAVEAADKTGLGWVAFFDTTTLSYLGGVRVGALPDSIAFSPDGAYA +VVANEGEPADDFSADPEGTISVISVPKNVRQFARLTQAAVRTVDFRAYDAGTALPEGVRV +FGPDVQVPEGQEPAGRIARNLEPEYVTIDDTGRTAYVSVQEANAVVAVDLKSATLKDFWA +LQLTDWSKEGVLDASNEDKAITLRNQPVLGVPMPDGVDTYRYRGQDLVVTANEGDSREWG +DFVDAARVKDLELCTAEYPDAKALQKKPALGRLNVVTDLGYDADRDCFSQLHAFGGRSFS +IYTADGTRLFDSAGMIEEQIAQLIADGELPESAFNANNDETPSFDSRSDDKGPEPEAVVV +GRVQGRTYAFVGLERIGGVMVFDITDPTKATYVDYVNERNWDAEGDDAAAGLGDMGAEGL +TFVPANESPSGTALLVVANEVSGSTTVYEVNPVRR +>PROKKA_01219 +MPRLARLATAVTAATLSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHET +GVFGESAAEIPAFDAVSGRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVT +DKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTTTLRYLGGVRVGALPDSLAFSPNG +AYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTALPAG +VRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLED +LWALTPTDWSTEGVLDASDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGR +EWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLKVLTDLGYDSERECHSSLTTLGGR +SFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPEPES +VVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGA +EGLTFVPADESPSGTALLIVANEVSGSTTVYEVNPTRRQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001060.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001060.fa new file mode 100644 index 0000000000000000000000000000000000000000..aa80663b0ac6c9c67b961fd9e41c8a93c1188787 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001060.fa @@ -0,0 +1,60 @@ +>PROKKA_01263 +MLRTHSLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVRDEADFDPLR +NEWVLQVTGTVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARL +RHRYLDLRRPQPSRIMRLRSEVNRTARELLHGEGFVEVETPTLTRSTPEGARDFLVPARL +APGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADRQPEFTQLDIEASFVEQD +DVIALGEKIVKALWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKDT +PFRVFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGELTGPVSKNI +SEEEKAGLAAAVGANPGDCVFFAAGKPKESRALLGAARVEIGRRCGLFTDAGDGVAAKDA +DWAFVWVVDAPMFEPAADAVASGDVAVGAGAWTAVHHAFTSPKPEFADTFDTDPGAALAY +AYDIVCNGNEIGGGSIRIHRQDVQERVFEVMGLSPEEANEKFGFLLEGFKYGAPPHGGIA +FGWDRVVALLAGTDSIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAQPEPKQAEA +EPEA +>PROKKA_00982 +MLRTHSLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVREEADFDPLR +NEWVLQVTGTVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARL +RHRYLDLRRPQPSRIMRLRSEVNRTARELLHGEGFVEVETPTLTRSTPEGARDFLVPARL +APGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADRQPEFTQLDIEASFVEQD +DVIALGEKIVKALWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKHT +PFRVFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGELTGPVSKNI +SEEEKAGLAAAVGANPGDCVFFAAGKPKESRALLGAARVEIGRRCGLFTDAGDGVAAKDA +DWAFVWVVDAPMFEPAADAVASGDVAVGAGAWTAVHHAFTSPKPEFADTFDTDPGAALAY +AYDIVCNGNEIGGGSIRIHRQDVQERVFEVMGLSPEEANEKFGFLLEGFKYGAPPHGGIA +FGWDRVVALLAGTDSIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAQPEPKQAEA +EPEA +>PROKKA_01624 +MNPTISSGRSPDGEDAFVLRTHQLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDAS +GFAQVVVRDEADFDPLRNEWVLQVSGVVERRPEGNENPNLPSGEIELIAETVTVLNTAAA +LPFQVDEHVEVGEEARLRHRYLDLRRPEPSRIMRLRSEVNRTAREMLHGEGFTEVETPTL +TRSTPEGARDFLVPARLAPGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADR +QPEFTQLDIEASFVEQDDVIALGEKIVKAVWALVGVDVPTPIRRMTYAEAMEKYGSDKPD +LRFGLELTDLTAYFKDTPFRVFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAY +VLIQEDGSLTGPVSKNISDEEKAGLAAAVGANPGDCVFFAAGKPKESRALLGAARVEIGR +RCELFTDAGNGVEAKDADWAFVWVVDAPMFEPAADAVASGDVAVGSGAWTAVHHAFTSPK +PEFADTFDTDPGSALAYAYDIVCNGNEIGGGSIRIHRQDMQERVFSVMGLSQEDAQEKFG +FLLEGFKYGAPPHGGIAFGWDRVVALLAGTESIREVIAFPKTGGGFDPLTAAPAPITAQQ +RKEAGVDAKPEPKKAEGEKAEAAGQPQA +>PROKKA_01521 +MLRTHHLGELNASLIGQTVTVTGWVAKRRDHGGVAFVDLRDASGRAQVVVRDEADFDPLR +NEWVLQVTGTVERRPEGNENPNLPTGEVELIADDVVVLNTAAALPFQIDEHVEVGEEARL +RHRYLDLRRPQPARIMRLRSEANRVARELLNEQGFVEVETPTLTRSTPEGARDFLVPARL +APGSWYALPQSPQLFKQLLQVGGLEKYYQIARCYRDEDFRADRQPEFTQLDIEASFVEQD +DVIALGEQIVKALWGLVGVEVQTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKDT +PFRVFQNEYVGAVVMPGGASQPRRTLDAWQEWAKQRGAKGLAHVLIQEDGTLTGPVSKNI +TDEEKAGLAAAVGANPGDCVFFAAGKAKESRALLGAARVEIGRRCELFTDAGDGVEAKDA +DWAFVWVVDAPLFEPAADAVASGDVAVGAGQWTAVHHAFTSPKPEFMDTFDTDPGSALAY +AYDIVCNGNEIGGGSIRIHRQDVQKRVFSVMGLSEEDANEKFGFLLEGFKYGAPPHGGIA +FGWDRVVALLAGTESIREVIAFPKTGGGYDPLTAAPAPITPQQRKEAGVDAKPEAKKAEG +AASEGAEAQAKANDEKTAADEAQLR +>PROKKA_01221 +MLRTHSLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVRDEADFDPLR +NEWVLQVTGTVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARL +RHRYLDLRRPQPSRIMRLRSEVNRTARELLHGEGFVEVETPTLTRSTPEGARDFLVPARL +APGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADRQPEFTQLDIEASFVEQD +DVIALGEKIVKALWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKDT +PFRVFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGELTGPVSKNI +SEEEKAGLAAAVGANPGDCVFFAAGKPKESRALLGAARVEIGRRCGLFTDAGDGVAAKDA +DWAFVWVVDAPMFEPAADAVASGDVAVGAGAWTAVHHAFTSPKPEFADTFDTDPGSALAY +AYDIVCNGNEIGGGSIRIHRQDVQERVFEVMGLSPEEANEKFGFLLEGFKYGAPPHGGIA +FGWDRVVALLAGTDSIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAQPEPKQAEA +EPGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001061.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001061.fa new file mode 100644 index 0000000000000000000000000000000000000000..594526213538af72db148725e8756c6ca124352c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001061.fa @@ -0,0 +1,45 @@ +>PROKKA_01264 +MTAALQRRLTLLHAVAIGLGSMIGAGVFTAIGLAAALTGGHPGLLYGALAVAAVAALCNA +LSTAQLATVHPESGGAYVYGRRQLHPWAGFVAGWGFVTGKTASVAAVAATLGLYLVPDDA +AAARWTGVAAVVVLTGVAMAGVTRTAQATLAILVPVLAVLVLAIGAGLAREAPGGSAAAL +GVDSPVQGVLMGAGVLFFAFAGYARVATMGEEVIDPARTIPRAILIALAVTVALYLLLAT +ALISGLGTSGLARSPAPVRELLETALGSGWGWVAVAGAALAAAGAMLTLLTGISRTALAM +AREADLPRPLARVHAGTGTPWTAQLTVAAAVVLLLLTTDILTVVGFSSFGVLVYYAVANL +SALTLRGDDHGHRPARPRPLRVPRAVNVLGLALCLLLAFSLPPMSVAAMAGVFLIGVGGR +AFVRAGRRGG +>PROKKA_00983 +MTAALQRRLTLLHAVAIGLGSMIGAGVFTAIGLAAALTGGHPGLLYGALAVAAVAALCNA +LSTAQLATVHPESGGAYVYGRRQLHPWAGFVAGWGFVTGKTASVAAMAATLGLYLFPDDD +AAARWTGVAAVVVLTGVAMAGVTRTAQATLAILVPVLAVLVLAIGAGLAREAPGGSAAAL +GVDSPVQGVLMGAGVLFFAFAGYARVATMGEEVIDPARTIPRAILIALAVTVALYLLLAT +ALISGLGTSGLARSPAPVRDLLETALGSGWGWVAVAGAALAAAGAMLNLLTGISRTALAM +ARESDLPRPLARVHAGTGTPWTAQLTLAAAVILLLLTTDILTVVGFSSFGVLVYYAVANL +SALTLRGDDDGRRPARPRPLRPLRVPRAVNVLGLALCLLLALSLPPMSVAAMAGVFLIGV +GGRAFVRAGRRGR +>PROKKA_01623 +MLQRRLTLTHAVVIGLGSMIGAGVFTAIGLAAALTGGHPGLLYAALALALLTALCNALST +AQLATVHPESGGAYVYGRRQLHPLAGFVAGWGFVTGKTASVAAMAATIGLYLFPDDAAAA +RLTGVAAVVVLTAVAMAGVTRTAQATMAILVPVAAVLALAIGAGLALGAPSEADAFAGVA +DSPVTGVLMGAGILFFAFAGYARVATMGEEVIDPRRSIPRAILIALGLTAGLYVLLTAAL +FAGLGPTGLALSPAPVRELLETTLGATWGWAALAGAALAAAGAALNLLTGISRTALAMAR +ESDLPRPLARVNARTGTPWVGQLTIAVAVILLLLTTDILTVVGFSSFGVLVYYAVANLAA +ATLRGGEDGRDPALPRPLRVPRAVNVLGLVLCAVLAATLPPMAVVAMLAVFLVGVGGRAF +VLAGRGRPGRRGAVAP +>PROKKA_01520 +MTATSPAPRGLPLRGALAIGVGSMVGAGAFTSLGLAALLTGGHVGALAAALGLAVAVATC +NALSTAQLAAVHPASGGTYVYGRRQIGPTAGFVAGWGFVTGKTASVAAMATTAGLYLFPD +SPLAARLAGAAAVVILTAVALRGITRTAQATVAILVPVLAVLGLTIVAGLAGGRAAADTP +VSAADPAGVLAAAGVLFFAFAGYARVATMGEEVEDPRRTIPRAVLGALAFTVVLYALLAA +ALVAALGGTGLAASEAPVRATLEASLGAGWGWAAVVGAVLACAGAMLNLLAGISRTGMAM +AREGDLPRPLARVDERTAVPWAGQVTVAVAVILLVLTTDVLTVVGFSSFGVLVYYAVANL +SALTLRPEQRTLRVPRAVNVLGLGLCLVIAFTLPPASVAAMVGVFLIGLGGRWFVRSRRP +DRIG +>PROKKA_01222 +MTAALQRRLTLLHAVAIGLGSMIGAGVFTAIGLAAALTGGHPGLLYGALAVAAVAALCNA +LSTAQLATVHPESGGAYVYGRRQLHPWAGFVAGWGFVTGKTASVAAMAATLGLYLFPDDA +AAARWTGVAAVVVLTGVAMAGVTRTAQATLAILVPVLAVLVLAIGAGLAREAPGGSAAAL +GVDSPVQGVLMGAGVLFFAFAGYARVATMGEEVIDPARTIPRAILIALAVTVALYLLLAT +ALISGLGTSGLARSPAPVRDLLETALGSGWGWVAVAGAALAAAGAMLNLLTGISRTALAM +ARESDLPRPLARVHAGTGTPWTAQLTVAAAVILLLLTTDILTVVGFSSFGVLVYYAVANL +SALTLRGDDDGRRPARPRPLRVPRAVNVLGLALCLLLALSLPPMSVAAMAGVFLIGVGGR +AFVRAGRRGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001062.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001062.fa new file mode 100644 index 0000000000000000000000000000000000000000..f1b2cbb192072604e457ab4fecfe4dcf9c63ca0d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001062.fa @@ -0,0 +1,45 @@ +>PROKKA_01265 +MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE +VYAVSRLAEDEEVAAGRREPKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ +KVWRGERPQEGRAREFTQADIDVVGDGALSPRYDADVALVMAEALGALPIGDFLIRVNNR +KLAEGFYRGIGLEDTAGVLRSIDKLEKVGPEEVARLLQEEVGASPEQAAQALALADIRTS +DTSFVERVRALGVTHELLEEGLTELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET +VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQQMAVASRSVPTAV +YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFMGRDDAG +ARVHEVKDIRSGEQHAVDPADWTPPTEDLLPQITRTQD +>PROKKA_00984 +MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE +VYAVSRLAEDEEVAAGLRDPKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ +KVWRGERPQEGRAREFTQADIDVVGDGALSPRYDADVALVMAEALGALPIGDFLIRVNNR +KLAEGFYRGIGLEDTAGVLRSIDKLEKVGPEEVARLLQEEVGASPEQAAQALALADIRTS +DTSFVERVRALGVTHELLEEGLTELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET +VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQQMAVASRSVPTAV +YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFMGRDDAG +ARVHEVKDIRSGEQHAADPADWTPPAEDLLPQVARAQD +>PROKKA_01622 +MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE +VYAVSRLAEDEEVAAGRREAKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ +KVWRGERPQEGRAREFTQADIDVVGDGELSPRHDADVALVMAEALGALPIGDFLIRVNNR +KLAEGFYRGIGLTDAAGVLRSIDKLEKIGADEVARLLQEEVGASPEQARQALALAAIRTE +DVSFVEQVRALGVSDPLLEEGLAELADVVETLHRRAPGRAVADLSIARGLDYYTGTVYET +VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQEMAQASRSVPTAV +YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFLGRDDAG +ARVHEVKDIRSGDQHPADPADWTPPSEDLLPQVTRTESTEG +>PROKKA_01517 +MSRKQSLSGFHEWLPAERIVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE +VYAVSRLAEDQEVAEGVREAKDPSDPKRLALHFDLTVPFARYVTENAGHLAFPFRRHQIQ +KVWRGERPQEGRAREFTQADIDVVGDGELSPRYDADVALVMAEALGALPIGDFRIRVNNR +KLAEGFYRGIGLEDAAGVLRSIDKLEKVGAEEVARLLQEEVGATAEQAAQALKLAEIRTP +DTAFVEQVRALGVEDPLLEEGLAELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET +VLVGHEQLGSICSGGRYDALATKGNRAFPGVGLSIGVTRLVMRMLSQEMAVASRAVPTVV +YVALTHDDDWSRAQDVAAGLRGRGIAAEVAVSAEKFGKQIKYADRRGIPFVWFLGAEGAS +DEVKDIRSGEQVPADAATWAPPAEDLVPQVTESPRAED +>PROKKA_01223 +MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE +VYAVSRLAEDEEVAAGLRDPKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ +KVWRGERPQEGRAREFTQADIDVVGDGALSPRYDADVALVMAEALGALPIGDFLIRVNNR +KLAEGFYRGIGLEDTAGVLRSIDKLEKVGPEEVARLLQEEVGASPEQAAQALALADIRTS +DTSFVERVRALGVTHELLEEGLTELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET +VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQQMAVASRSVPTAV +YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFMGRDDAG +ARVHEVKDIRSGEQHAADPADWTPPAEDLLPQVARAQD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001064.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001064.fa new file mode 100644 index 0000000000000000000000000000000000000000..83df129dc8ab857937cf6b74498d7dcd9a1bd659 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001064.fa @@ -0,0 +1,25 @@ +>PROKKA_01267 +MTTVTIEETAPAGALMLAGDPFTEPELQALGARGAVRPLLPGVWARPDAADDPAVRAAAL +WTLGGPLLAAGWTAIGPSAAWILAGGAAPGRLHAAVPHFHRRPAGGGQLPWTLTQSDVAA +DATGVAPAEQDVLRFGPVRVTTPARTVEDLLLSADPDAARRAAAVIGAHGAAGLRERLAR +RTRRAGVVAARRRLGALLTALDVPD +>PROKKA_00986 +MTTVTIEETAPTGALVLAGDPFTEPELQALGARGAVRPLLPGVWARPDAADDPAVRAAAL +WTLGGPLLAAGWTAIGPSAAWILAGGAAPGRLHAAVPHFHRRPAGGGLLPWTLTQSDVAA +DATGVAPAEHDVLRFGPVRVTTPARTVEDLLLSADPDAARRAAAVIGAHGAAGLRERLAR +RTRRAGVVAARRRLGALLAALDVPD +>PROKKA_01620 +MEGLILAGEPFTPAELQALGSRGVVVPLVPGVWARPEAARRPGVRAEALWMLGGPVLAGG +WTAIGSSAAWVLTGGAVPERLHAAVPHFHRLPAGGSPLPWTLTQSDVAAGPDGRAPAEED +VLRIGPLRVTTPERTVEDLLLSPDPDAARTAAAVIAAHGAAGLRERLARHSRRSGVVAAR +RRLDVLLGALEAAG +>PROKKA_01515 +MHQGHGSRGGAAWELAGMTFTEPELRLLAARGTLEAVLPGVYRPVDVPSEPAGRAAALGL +LGGPVLASGWTAVGPSAAWVHVGGPAPHRLHAAVPHFHRLPAGGAAPAWRLVQSDVAAGP +TGAAPAEEDVQVLEGVRVTVPARTVEDLLLTGDPDDARRAARVIAAHGAEGLRDRLDRPS +RRPGSVGARRRLRMLLDALGADG +>PROKKA_01225 +MTTVTIEETAPTGALVLAGDPFTEPELQALGARGAVRPLLPGVWARPDAADDPAVRAAAL +WTLGGPLLAAGWTAIGPSAAWILAGGAAPGRLHAAVPHFHRRPAGGGLLPWTLTQSDVAA +DATGVAPAEHDVLRFGPVRVTTPARTVEDLLLSADPDAARRAAAVIGAHGAAGLRERLAR +RTRRAGVVAARRRLGALLAALDVPD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001066.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001066.fa new file mode 100644 index 0000000000000000000000000000000000000000..553b60ae1e8bfb33024e909872ab07e44cceecf1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001066.fa @@ -0,0 +1,35 @@ +>PROKKA_01269 +MNRFADWGNALYSGRISYPFIQRWRRWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF +TVSQTASTDVAAGERAVTDVLADGHATVTNVAPGTVRVQTEQLDDAQTRAVAANLQEAYG +VGQDQVTSTFVGPTWGAAVSQQALIGLVIFVVLVTLFMAVYFRTWKMSLAAVLGMLYVVA +LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGAEEDPERSFVENVNL +AVNQTLVRSITTSVVGILPVGSILFIGAGLLGAGTLRDIALALFVGIIVGTLSTLFLQAP +LYALLRRNDPDVRDHDARAAARAARERASEAVTDPDVAPWDDGARL +>PROKKA_00988 +MNRFADWGNALYSGRISYPFIQRWRRWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF +TVSQTASTDVAAGERAVTDVLADGHATVTNVAPGTVRVQTEQLDDAQTRAVAANLQEAYG +VGQDQVTSTFVGPTWGAAVSQQALIGLVIFVVLVTLFMAVYFRTWKMSLAAVLGMLYVVA +LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGAEEDPERSFVENVNL +AVNQTLVRSITTSVVGILPVGSILFIGAGLLGAGTLRDIALALFVGIIVGTLSTLFLQAP +LYALLRRNDPDVRDHDARAAARAARERASEAVTDPDVAPWDDGARL +>PROKKA_01618 +MNRFADWGNALYSGRVSYPFVQRWRLWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF +TVSQTAATDIAAGERAVTDVLAGGHATVTNIAPGTVRVQTEQLDDAQTRQVAANLQDAYG +VGQDQVTSTFVGPTWGAAVSQQALLGLVIFVVLVTLFMAFYFRTWKMSLAAVIGMLYVVA +LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGQEEDPERTFEQNVNL +AVNQTLVRSITTSIVGILPVGSILFIGAGLLGAGTLRDIALAIFVGIIVGTLSTLFIQAP +LYALLRRGDEDVRDHDARAAARAARENRGDTVTDPDVAPWEDGARL +>PROKKA_01513 +MNRFADWGNALYSGRISYPFVRKWKTWFLIAAALLAVAFGLTALRGGFNLGIDFRGGSEF +TVSDAASSELDPGRAAVTDVVAGAEPTVTQVAPGTMRVQTEQLDDAQTRQVAQNLQQAYG +VTGDHVTSTFVGPTWGQAVSQQAVIGLVIFVVLVTLFMALYFRTWKMSLAAVVGMLYVVA +LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTRGVEEDPDRTFDGSVNL +AVNQTLVRSITTSIVGLLPVGSILFIGAGLLGAGTLRDISLAIFVGIIVGTLSTLFIQAP +LYALLRRGDADVVAHDARVGADHDEREQEEDLADARGAVL +>PROKKA_01227 +MNRFADWGNALYSGRISYPFIQRWRRWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF +TVSQTASTDVAAGERAVTDVLADGHATVTNVAPGTVRVQTEQLDDAQTRAVAANLQEAYG +VGQDQVTSTFVGPTWGAAVSQQALIGLVIFVVLVTLFMAVYFRTWKMSLAAVLGMLYVVA +LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGAEEDPERSFVENVNL +AVNQTLVRSITTSVVGILPVGSILFIGAGLLGAGTLRDIALALFVGIIVGTLSTLFLQAP +LYALLRRNDPDVRDHDARAAARAARERASEAVTDPDVAPWDDGARL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001069.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001069.fa new file mode 100644 index 0000000000000000000000000000000000000000..ef3ac7737dfbbfe92c83366853b257af4340db17 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001069.fa @@ -0,0 +1,25 @@ +>PROKKA_01273 +MIASLSGTVEHVALDRAVIAVGGLGVQFSATPQTLSTLHEGRPGAVQTHLVVKEDALTLY +GFADRDEREVFEVLITANGVGPRLALAILSVHHPETVRRAVTEEDEKTLTRVPGIGPKMA +RKIIVELSGRLAPTGEPVPEAEAEASAEPTVEALWHADVVQAMAGLGWSEKEALKAVEAT +VAARPELDEGRDVAALLRATLRDVGMAGSVRGGR +>PROKKA_00992 +MIASLSGTVEHVALDRAVIAVGGLGVQFSATPQTLATLHEGRPGAVQTHLVVKEDALTLY +GFADRDEREVFEVLITANGVGPRLALAILSVHHPETVRRAVTEEDEKTLTRVPGIGPKMA +RKIIVELSGRLAPTGEPVPEAEAEASAEPTVEALWHADVVQAMAGLGWSEKEALKAVEAT +VAARPELDEGRDVAALLRATLRDVGMAGSVRGGR +>PROKKA_01614 +MIASLSGTVEHVALDRAVIAVGGFGVQFSATPQTLATLHEGRTGSVQTHLVVKEDALTLF +GFADRHEREVFEVLITANGVGPRLALAVLSVHHPEAVRRAVTEEDENALTRVPGVGPKLA +RKIIVELSGRLTPTGEQVPAPEEPAAPETPEAAWHADVVQAMTGLGWSEKEALKAVEATV +AARPELDEARDVAALLRATLRDVGTAGTVRGGR +>PROKKA_01509 +MIASLSGTVEHVGLDHAVIAVGGVGLSFSATPQTLSHLHEGRDGAVQTHLVVKEDSLTLF +GFADRAEREVFEVLLGANGVGPRLALAILAVHRPEAVRRAVTDEDEKALTLVPGIGPKMA +RKIIVDLAGRLAPTGEVEPEAAVVEPEAAADAWHADVVQAMTGLGWSEKEAAKAVAATVA +THPDVDASGDVAALLRATLRDVGAAAAVRGGRRA +>PROKKA_01231 +MIASLSGTVEHVALDRAVIAVGGLGVQFSATPQTLATLHEGRPGAVQTHLVVKEDALTLY +GFADRDEREVFEVLITANGVGPRLALAILSVHHPETVRRAVTEEDEKTLTRVPGIGPKMA +RKIIVELSGRLAPTGEPVPEAEAEASAEPTVEALWHADVVQAMAGLGWSEKEALKAVEAT +VAARPELDEGRDVAALLRATLRDVGMAGSVRGGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001073.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001073.fa new file mode 100644 index 0000000000000000000000000000000000000000..fe158ca8d3d67b4b082e42f4311be25599c80de0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001073.fa @@ -0,0 +1,44 @@ +>PROKKA_01277 +MAARPRRPRPHPADLPPALAAAVTVAARRAGSRESRVRRAGRLVRRGVTGSVRGGVAVAS +PVARWAPPVLSVAAAYAFVLAGASSALAGVFARTVVTPVRRHAESTPILAVVDTPAGQDV +ILQADEYTTVPGQYSLTFDDGAGCARIGEITSFDPRDGTVQRAVEEVFSGDLTTATRGRF +TGFVYPTPADAGLDAEDVQVPVPGGHARAWRIAPYPSEDGEPRPAEGLWAVMVHGRGARR +NEGIRAVPTARRLGMTSLLISYRNDGDAPDAADARYGLGTTEWEDVEAAIRYALDHGARD +VVLFGWSMGGAVVLQTVDRSALAPHVRGVVLTGPVIDWVDVLRHQARLNRIPEAVGLLGQ +WLLANRAGRFITGLAAPVDLKALDWVTRADHVRVPTLILHSEDDEYVPVGPSQDLAERNP +DLVRFVRFHQARHTREQNVDPRKWDTAVRGWLRAVLSAPRPGGRGR +>PROKKA_00996 +MAARPRRPRPHPADLPPALAAAVTVAARRAGGRDSRVRRAGRLVRRGVTGSVRGGVAVAS +PVARWAPPVLSVAAASAFVLAGASSALAGVFARTVVTPVRRHAESTPILAVVDTPAGQDV +ILQADEYTTVPGQYSLTFDDGAGCARIGEITSFDPRDGTVQRAVEEVFSGDLTTATRGRF +TGFVYPTPADAGLDAEDVQVPVPGGHARAWRIEPDPSEDGEPRPAEGLWAVMVHGRGARR +NEGIRAVPTARRLGMTSLLISYRNDGDAPDAADARYGLGTTEWEDVEAAIRYALDHGARD +VVLFGWSMGGAVVLQTVDRSPLAPHVRGVVLTGPVIDWVDVLRHQARLNRIPEAVGLLGQ +WLLANRAGRFITGLAAPVDLKALDWVTRADHVRVPTLILHSEDDEYVPVGPSQDLAERNP +DLVRFVRFHQARHTREQNVDPRKWDTTVRGWLRAVLSAPRPGGRGR +>PROKKA_01610 +MRTGVKAASPLARWTPPVLSVLASSAFVLAGASSALAGVFARTVVTPVRRHTETTAVLAV +VDTPTGPEVILKADEYTTVPGVYSLTFDGGAGCARIGRISSFDPRDGTVQRVVEEVYFGD +LAAATRGRLTGFVYPTPADAGLDAEEVLVPVPGGHAPAWLVGPDPDDDGAARPAAGIWAI +MVHGRGARRNEGIRTVPTAQRLGMTSLLISYRNDGDAPDAADSRYGLGTTEWEDVEAAIR +YALDNGASDVVLFGWSMGGAVVLQAVDRSDLAPQVRGVVLTGPVVDWVDVLQHQARLNRI +PEAVGVLGQWLLSNRAGRFITGLAAPVDLKSLDWVTRAEHVRVPTLIIHSEDDEYVPVGP +SQDLAERNPGLVRFVRFHQARHTREQNVDPKRWDTTVRGWLRAVLNADRPGAAER +>PROKKA_01505 +MACPRRHSPRLRARPDLRDALLGSLRGSAAVARPAARLAPAAASVAASAAFVLAGASAGL +AGVFARTVVTPVRSRPEHTAVLAVLDTGDGMDVILPADEHTTVPGTYSLTFHGGEGCARI +GAIRSYDPRDGTVQRVVEEVYSGDLRSAVRGRFTAFIWPGPAEAGLEAADVEVPVPGGAA +PAWRIDPPPAEDGEERAGEGMWAVMVHGRGAVRNEGLRAVPTAARLGMTSLLVSYRNDGD +APDAEDARYGLGTTEWEDVEAAVRYALDHGARDVVLFGWSMGGAVVLQTADRSDLTSRVR +GIVLTGPVVDWMDVLRHQARLNRIPEGIGLLGQWLLSNRAGRLVTGLAAPVDLKALDWVT +RADHVRVPTLILHSEDDEYVPVGPSQDLAERNPALVRFVRFHQARHTREQNVDPVKWDRS +VRGFLRAVLTAPRPGAVSPPGAPQAPSGSSPRRRSSGSSSASRPRNAR +>PROKKA_01235 +MAARPRRPRPHPADLPPALAAAVTVAARRAGGRDSRVRRAGRLVRRGVTGSVRGGVAVAS +PVARWAPPVLSVAAASAFVLAGASSALAGVFARTVVTPVRRHAESTPILAVVDTPAGQDV +ILQADEYTTVPGQYSLTFDDGAGCARIGEITSFDPRDGTVQRAVEEVFSGDLTTATRGRF +TGFVYPTPADAGLDAEDVQVPVPGGHARAWRIEPDPSEDGEPRPAEGLWAVMVHGRGARR +NEGIRAVPTARRLGMTSLLISYRNDGDAPDAADARYGLGTTEWEDVEAAIRYALDHGARD +VVLFGWSMGGAVVLQTVDRSPLAPHVRGVVLTGPVIDWVDVLRHQARLNRIPEAVGLLGQ +WLLANRAGRFITGLAAPVDLKALDWVTRADHVRVPTLILHSEDDEYVPVGPSQDLAERNP +DLVRFVRFHQARHTREQNVDPRKWDTTVRGWLRAVLSAPRPGGRGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001075.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001075.fa new file mode 100644 index 0000000000000000000000000000000000000000..ad183fdf89bb48471d8f71fdf9cf02f015002316 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001075.fa @@ -0,0 +1,25 @@ +>PROKKA_01279 +MSVIGPRRLSAAPGAVEAPVPPGVFRRALADLRDARPRTEVRLREIPAPEGQAPFAVALA +ADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLAGAVAW +TWLVEALERHHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLGSHLEA +WSDMICAFAGLPPEHAADVHTAGP +>PROKKA_00998 +MSVIGPRRLSAAPGAVEAPVPPGVFRRALADLRDARPRTEVRLREIPAPEGQAPFAVALA +ADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLAGAVAW +TWLVEALERRHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLGSHLEA +WSDMICAFAGLPPEHAADVHTAGP +>PROKKA_01607 +MTVIGPRRLAPVTGPRGAVAPAPAPLPAAFRRALADLRTARPRPEVRLREIAAPAGQAPH +AVALAAEVCGSPGADDVLATGRFVLLHDPSPAARWPGGFRAVTWIRASLEPDVALDQLAG +AVAWTWLVEALERRHAEHTQAGGTATRSIAEGFGTLGTAPDATDIELRASWTPAPRDLGA +HLEAWSDMIGAFAGLPPR +>PROKKA_01502 +MTESGPRAPAPAAGGASGAFADALADLRAAHPRPEVRLRPIPDPPGLAPFAVTLAADVLD +PHGAEADPLATGRFVLLHDPAGSPVWRGDFRVVTYIRASLEPDVATDHLAGAVAWDWLAE +ALERRHAAHTEAGGTATRQLAEHFGTLALEPGWTDIELRASWTPGPRDLGAHLEAWSDMI +CAFAGLPPLADDDVPAAVPLRP +>PROKKA_01237 +MSVIGPRRLSAAPGAVEAPVPPGVFRRALADLRDARPRTEVRLREIPAPEGQAPFAVALA +ADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLAGAVAW +TWLVEALERRHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLGSHLEA +WSDMICAFAGLPPEHAADVHTAGP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001077.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001077.fa new file mode 100644 index 0000000000000000000000000000000000000000..3611b4cfd927d33addaefe374239545b3328088d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001077.fa @@ -0,0 +1,69 @@ +>PROKKA_01281 +MTSVSLASFDHLPALAPDEVVTTVTVTDHALPEGAGTLALLTLDNGQGPRRPATLGPATL +LGLGRVLDEQAARAAAGEIQALAVTGVEGTFAAGADLSLIASITDDVGRDLALLGHAVYD +RLAALEIPTVALVNGLALGGGLELALAAGHRVVAADAKGFGLPEVRLGLIPGWSGVWRVP +HLIGPEAAVDVVLKNPLDDNRMLDARAAHGLGLMDRIVEGDLLDAGLELAAALVTGDESV +AAELAAHRDRDVSDAAWDRALAALERLQAARPGRHLPARRHLEALFTGARTRTRAESAQA +EADALGTLLHSPEFRRTVYAFLGLVQGRAKRPAGDPGRELAREVRKVGIVGAGLMAGQLA +LVFARHLRVPVVMTDIDAERVERGLAGVRAQVEKMVSRGRLSAEDGQALAGLITADTDKA +VYADADIVIEAVFEELEVKRTVFRELEGIVREDAILMTNTSSLSVAAMAEVLERPERLVG +FHFFNPVAVMPLVEIVRTEATTDEVVATAFELTRRLRKTGVLVHDATAFVVNRVLLRMMG +EVQNSFDEGTDAHEADHALDPLALPMTPFTLLAMVGIPVAQHVSESLSASFGAERFPVSA +NLQRLIDAGKTAIWAKDVRPDRRDEEAAGATGEQIPEATAALLEQGSTPQTSEELLRRVE +DALAEEIGLLLDERVVAAPEDVDLCMILGANWPLHLGGITPYLDDCGAAERVNGRRFHPA +AQA +>PROKKA_01000 +MTSVSLASFDHLPALAPDEVVTTVTVTDHALPDGAGTLALLTLDNGQGPRRPATLGPATL +LGLGRVLDEQAARAAAGAIQALAVTGVEGTFAAGADLSLIAGLTDDVGRDLALLGHAVYD +RLAALEIPTVALVNGLALGGGLELALAAGHRVVAADAKGFGLPEVRLGLIPGWSGVWRVP +HLIGPEAAVDVVLKNPLDDNRMLDARAAHGLGLMDRIVEGDLLDAGLELAAALVAGDESV +AAELAAHRDRDVSDAAWDRALAALERLQAARPGRHLPARRHLEDLFTGARTRTRAESAQA +EADALGTLLHSPEFRRTVYAFLGLVQGRAKRPAGDPGRELAREVRKVGIVGAGLMAGQLA +LVFARHLRVPVVMTDIDAERVERGLAGVRAQVEKMVSRGRLSAEDGEALAGLITADTDKA +VYADADIVIEAVFEELEVKRTVFRELEGIVREDAILMTNTSSLSVAAMAEVLEHPERLVG +FHFFNPVAVMPLVEIVRTEATTDEVVATAFELTRRLRKTGVLVHDATAFVVNRVLLRMMG +EVQNSFDEGTDAHEADHALDPLALPMTPFTLLAMVGIPVAQHVSESLSASFGAERFPVSA +NLQRLIDAGKTAIWAKDVRPDRRDEEAAGATGEQIPEATAALLEQGSTPQTSEELLRRVE +DALAEEIGLLLDERVVAAPEDVDLCMILGANWPLHLGGITPYLDDCGAAERVNGRRFHPA +AQA +>PROKKA_01605 +MTFTPAPLAPFESLLPLVPDEVLTHVAATDHVLPGGAGTLVLLTLDNGQGPRRPATLGPA +SLLELGRAVDAQAERARAGEVQALALTGVEGTFAAGADLSLIAGIEDRTVGRDLARLGHA +VHDRIDAFPAPTLALVNGTALGGGLELALAADHRVVAADARGFGLPEVRLGLIPGWSGVW +RVPHLIGPEAAVEVVLKNPLDNNRMLDARTAHGLGLMDEVAEGDLLEAGLAFAARIVAGD +DAALAAVRDHRDRDVSDAAWDRALEAMEALQAGRPGRDLPARRALQELFAGARTRTREES +AEAEAEALHGLIGSDEFRRTVYAFLDLLQRRAKRPVGDPGKELAREVTKVGVVGAGLMAG +QLALVFAQHLRVPVVMTDMDQERVDRGLAGVRGQVEKMVSRGRITAEQGEALAGLITAST +DKSVYADADVVIEAVFEELEVKRTVFRELEPIVREDAVLMTNTSSLSVAAMAEVLEHPER +LVGFHFFNPVAQMPLIEVVRVAETSDEAVATAFELSRRLRKTGVLVHDAAAFVVNRVLLR +MMGEVQASFDEGTDAHTADHALDPLALPMTPFTLLAMVGIPVAQHVSESLQAAFGAERFP +VSANLQRLIDAGKTAIWAKDVRRDKVEEEAAGATGETIPAGTAALIERGSSPQTAEELRR +RVEDALAEEIGLLLAEGVVAAPEDVDLCMILGAGWPLHLGGITPYLDDCGAAERVNGTRF +HG +>PROKKA_01500 +MSHTPAPLDQFEHLSTIAPDEILTRATATDHALPDGAGTLALITLDNGQGPRRPATLGSA +SLLELARAVDEQAARASAGEIQALGITGVEGVFAAGADLALVASLPADAETGRALGRLGH +AVYDRIDAFPVPTVALVNGTALGGGLELALACDRRVIAPEVKALGLPEVRLGLIPGWSGV +WRAPHLVGPEAAVALLLTNPLDNGRMIGAADAVRLGLMDSLAEGDLLAAGLTAAADAVAG +RTVQRTADVSDAAWDRALQAFGAAQSARPGRDLPARRHLEELFAGARTRTRAESAEAEAD +ALADLIGSAEFRRTVYAFLGLVQGRAKRPAGDPGVEQAHTVHRVGVVGAGLMAGQLALLF +ATALRVPVVMTDLDQERVDRGLAYVRSQLERSVTKGRMKAEDAEAVAGLITGATDVSAHA +EAEFVIEAVFEELEVKRTVFRQLEQVVSPTAILATNTSSLSVAGMAEVLEHPERLVGFHF +FNPVAQMPLVEIVRVAETTDAAVATAFELARRLRKTAVLVNDAAAFVVNRVLLRMMGEIQ +NSFDQGTDAHTADHALDPLAFPMTPFTLAAMVGLPVAQHVSESLQAAFGAERFPVSENLQ +RLIEAKKTAIWAKDVKSPEEAGGATGETIPADTAALIEQGDTPQTADELRVRVEDALAEE +IGLLLDEGVVAAPDDVDLCMILGAGWPLHLGGITPYLDDCGASERVRGARFHQA +>PROKKA_01239 +MTSVSLASFDHLPALAPDEVVTTVTVTDHALPEGAGTLALLTLDNGQGPRRPATLGPATL +LGLGRVLDEQAARAAAGEIQALAVTGVEGTFAAGADLSLIAGLTDDVGRDLALLGHAVYD +RLAALEIPTVALVNGLALGGGLELALAAGHRVVAADAKGFGLPEVRLGLIPGWSGVWRVP +HLIGPEAAVDVVLKNPLDDNRMLDARAAHGLGLMDRIVEGDLLDAGLELAAALVAGDESV +AAELAAHRDRDVSDAAWDRALAALERLQAARPGRHLPARRHLEDLFTGARTRTRAESAQA +EADALGTLLHSPEFRRTVYAFLGLVQGRAKRPAGDPGRELAREVRKVGIVGAGLMAGQLA +LVFARHLRVPVVMTDIDAERVERGLAGVRAQVEKMVSRGRLSAEDGEALAGLITADTDKA +VYADADIVIEAVFEELEVKRTVFRELEGIVREDAILMTNTSSLSVAAMAEVLEHPERLVG +FHFFNPVAVMPLVEIVRTEATTDEVVATAFELTRRLRKTGVLVHDATAFVVNRVLLRMMG +EVQNSFDEGTDAHEADHALDPLALPMTPFTLLAMVGIPVAQHVSESLSASFGAERFPVSA +NLQRLIDAGKTAIWAKDVRPDRRDEEAAGATGEQIPEATAALLEQGSTPQTSEELLRRVE +DALAEEIGLLLDERVVAAPEDVDLCMILGANWPLHLGGITPYLDDCGAAERVNGRRFHPA +AQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001078.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001078.fa new file mode 100644 index 0000000000000000000000000000000000000000..7ca855dd7510f2ba3e0936b14385b35d3696e1f7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001078.fa @@ -0,0 +1,25 @@ +>PROKKA_01282 +MTDPAPRPTGAARFDLTPFERWEAVTLDDVHVGFLHRVLEDGVLTTRTGFAPTTAQRAAR +DGLPERYLAQTQVGFTPDGDGWAWTTHEDSAGAQRVRIDRERAGIDAAVLPSYAEYLLLA +RVAAEGPLAVDRLEEASPLQGGLRVPRAELRPADAGGSDVRVAVVADGVELGAHLVREGA +VVASDWGGGTASTPVADQAAATAGLDAHVVTFAGLPIA +>PROKKA_01001 +MTHPAPRPTGAARFDLTPFERWEAVTLDDVHVGFLHRVLEDGVLTTRMGFAPTPAQRAAR +GGLPERYLAQTQVGFTPDGDGWAWTTHEDSAGAQRVRIDRERAGIDAAVLPSYAEYLLLA +RVAAEGPLAVDRLEEASPLQGGLRVPRAELRPADAGGSDVRVAVVADGVELGAHLVREGA +VVASDWGGGTASTPVADQAAATAGLDAHVVTFAGLPIA +>PROKKA_01603 +MTDPAPVRPSLDLTPFERWEAVTLDGEHVGFLHRVLDGTLLTTRMGFAPTPAQRRARPEL +PERYLAQSQVSFTADGTSWDWTSHEDSAGAQRVRIDRERAGLDADVLPSYAEYLLLAVAA +ADGPVVVAARLEESSPLQGGLRMPRAELRPADAGDGDVSVTVVADGAALGAHLVRDGAVV +ASDWGGGTASTPVAGRAEATEGLDEHVVTFSGMPLV +>PROKKA_01499 +MSARYDLTPFETWEAVALDGVHAGFLHRRLADGILTTRMAFQPTGAQRRERADLPQRYLA +QARVRFSADGSTWEVCDFEDSLTTQNVRIARERAGLGAEVVPSWAEHLLITAQRTPEHDG +APYLRLEESSPLQGPVRMPPAVLRIGAREAVPAAGPAGSEAGQARPEGLRVEVVSEGHVL +AVHWLGEPATEGRRPLVASDWGGGTVSVPVATAAEALEGLPADLHTFAQLPTD +>PROKKA_01240 +MTHPAPRPTGAARFDLTPFERWEAVTLDDVHVGFLHRVLEDGVLTTRMGFAPTPAQRAAR +GGLPERYLAQTQVGFTPDGDGWAWTTHEDSAGAQRVRIDRERAGIDAAVLPSYAEYLLLA +RVAAEGPLAVDRLEEASPLQGGLRVPRAELRPADAGGSDVRVAVVADGVELGAHLVREGA +VVASDWGGGTASTPVADQAAATAGLDAHVVTFAGLPIA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001079.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001079.fa new file mode 100644 index 0000000000000000000000000000000000000000..9006ca0d2b3129413b1a9434d397239d429fa640 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001079.fa @@ -0,0 +1,21 @@ +>PROKKA_01283 +MTTQDSPLTPNSSRSACCGGHARPDTSRRTVLGRGAAVAAAGAGALALTGCTDQLREKDT +AQDHYTGSDAVDALPAAELPVGASREVQVQGRTLMMHRVDETTVTAFTNVCTHQGCLLQV +VDRQEGPAYACPCHGSHFDVTSGKPFGGPARQALMDYDAAVVDDRIVVKL +>PROKKA_01002 +MTTQDSPLTPNSSRSGCCDDHARPDTSRRTVLGRGAAVAAAGAGTLALAGCTDRLREKDT +AQDHYTGSDAVDALPAAELPVGASREVQVQGRTLMMHRVDETTVTAFTNVCTHQGCLLQV +VDRQEGPAYACPCHGSHFDVTSGKPFGGPARKALMDYDAAVVDDRIVVKL +>PROKKA_01602 +MTAQDSTPTPDPSAVAPPSAPAGCCGGRAAADAARPEASRRTVLGRGAAVAAAGAGALAL +SGCTEQLREKENAQDHFAGADAVEALPAADLPVGAAREVEVEGRTLMMHRVDETTVTAFT +NVCTHQGCLLQVVDRAEGPSFACPCHGSHFDVQTGKPFGGPARQPLMDYEAVVDGDRIVV +KL +>PROKKA_01498 +MTSQDPAPHTSASPCCSGCSAEPAGSSRRSVLGAGSLVALAGAGSVVLSGCTQQLKDEAA +AGDHHVGSETTDAMALAELPVGGTTSVQVQGRTLLLHRADESTVTAFSNVCTHQGCLVQV +VDRPEGTAYACPCHGSNFDVATGEPFGGPAKAPLTDYQAAIEGDRIVVKL +>PROKKA_01241 +MTTQDSPLTPNSSRSGCCDDHARPDTSRRTVLGRGAAVAAAGAGTLALAGCTDRLREKDT +AQDHYTGSDAVDALPAAELPVGASREVQVQGRTLMMHRVDETTVTAFTNVCTHQGCLLQV +VDRQEGPAYACPCHGSHFDVTSGKPFGGPARKALMDYDAAVVDDRIVVKL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001081.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001081.fa new file mode 100644 index 0000000000000000000000000000000000000000..37b1a58ce494f4d7a036f20ac77860e06d1bfd47 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001081.fa @@ -0,0 +1,21 @@ +>PROKKA_01286 +MSIVRLYRESVGDDGARLFEYREAWADAEAGEFVVHHGRVGQPGTVGEQPLADQAEGDQL +LAAFVAQGAEEGFAEADPATFAVLPVAYRLRGREATAIERRTVERLRVEMTHQLAWRGLG +EVEDVVEEVGALVLRVRTPHARKAAAEIPAAAKRADGVQPNKVDVRTAEQEG +>PROKKA_01005 +MSIVRLYRETVGDDGTRLFEYREAWADAEAGEFVVHHGRVGQPGTVGEQPLADQVEGDQL +LAAFVAQGAEEGFAEADPATFAVLPVAYRLRGREATVIERRTVERLRVEVTHQLAWRGLG +EVEDVVEEAGALVLRVRTPHARKAAAEIPAAAKRADGVQPNKVDVRTAEQEG +>PROKKA_01599 +MSIVRLYRETTNEDGSRLFEYREAWADVEGGEFVVHHGRVGHPGTVGEQPLADEAEGEEL +LAAFLAQGAEEGFAEADPAGFALLPVAFRLRGREASDIERRNVEHLRVEVTHQLAWRGLG +EVEDVTEEPGALVLAVRTPHARKAAAEIPVAARRADGVQPNKVEVRSAVQED +>PROKKA_01495 +MSISRLYRDRTEEDGRRSFEYREAWIDPSGELFTVHHGRVGHPGTVGDQPLTSEAEGAEL +MDAFLAQGEADGFAPADEDAFDVLEVAYRLRGRAITEIERRHGRTLREEVTHQLAWRGLG +EVTDVVDGDGELVLVVRTPHAPKAAAEVPAAAKRAHGIQPNKVEVRRVDAPRTPAGAAPD +ADGEG +>PROKKA_01244 +MSIVRLYRETVGDDGTRLFEYREAWADAEAGEFVVHHGRVGQPGTVGEQPLADQVEGDQL +LAAFVAQGAEEGFAEADPATFAVLPVAYRLRGREATVIERRTVERLRVEVTHQLAWRGLG +EVEDVVEEAGALVLRVRTPHARKAAAEIPAAAKRADGVQPNKVDVRTAEQEG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001083.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001083.fa new file mode 100644 index 0000000000000000000000000000000000000000..ffb2303ca0a68c08d2af35364d3e69d8ce9d2b2d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001083.fa @@ -0,0 +1,80 @@ +>PROKKA_01295 +MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAQKLPYSLKVLLENLLRTEDGANVTADQIK +ALAAWDPNAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE +LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN +IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM +LIPRVVGFKLTGSIPSGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG +NMSPEFGSTAAIFPIDEVTLDYLRLTGRSEEQVALVEAYTKEQGMWHDPSSEVAYSEYLE +LDLSTVVPSISGPKRPQDRIELTDSKDQFRKDLHNYATQDEAGEGRPSKLVDVAMPDGRQ +FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY +YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR +INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDTEGNDVFLKDIWPDPTEVQQIID +ASIDTEMFTSQYATIFDGDERWQSLETPSGSTFEWDEKSTYVRKPPYFEGMTMQPDPVSD +ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGRYLLENGVQRKDFNSYGSRRGNHEVMIR +GTFANIRIKNQLLDGVEGGFTRDFTQEGAPQAYVYDAAQNYAEQGTPLVVLGGKEYGSGS +SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS +GITALNEGTTPKTVKVTATGEDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA +>PROKKA_01018 +MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAQKLPYSLKVLLENLLRTEDGANVTADQIK +ALAAWDPNAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE +LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN +IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM +LIPRVVGFKLTGSIPSGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG +NMSPEFGSTAAIFPIDEVTLDYLRLTGRSEEQVALVEAYTKEQGMWHDPSSEVAYSEYLE +LDLSTVVPSISGPKRPQDRIELTDSKDQFRKDLHNYATQDEAGEGRPSKLVDVAMPDGRQ +FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY +YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR +INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDTEGNDVFLKDIWPDPTEVQQIID +ASIDTEMFTSQYATIFDGDERWQSLETPSGSTFEWDEKSTYVRKPPYFEGMTMQPDPVSD +ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGRYLLENGVQRKDFNSYGSRRGNHEVMIR +GTFANIRIKNQLLDGVEGGFTRDFTQEGAPQAYVYDAAQNYAEQGTPLVVLGGKEYGSGS +SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS +GITALNEGTTPKTVKVTATGEDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA +>PROKKA_01597 +MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAEKLPYSLKVLLENLLRTEDGANVTAEQIK +ALASWNPDAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE +LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN +IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM +LIPRVVGFKLTGSIPAGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG +NMSPEFGSTAAMFPIDEVTLDYLRLTGRTAEQVDLVEAYTKEQGMWHDPSSEVKYSEYLE +LDLSTVVPSISGPKRPQDRIELSDSKDQFRKDLHNYATQDEAGEGRPSKLVDVSMEDGRQ +FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY +YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR +INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDSEGNDVFLKDIWPDPTEVQKIID +ESIDTEMFTSQYGTIFDGDERWQSLETPSGSTFEWDEQSTYVRKPPYFEGMTMQPDAVSD +ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGKYLLENGVERKDFNSYGSRRGNHEVMIR +GTFANIRIKNQLLDGVEGGFTRDFTQDGAPQAYVYDAAQNYAAAGTPLVVLGGKEYGSGS +SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS +GITALNEGTTPKTVKVTATGGDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA +>PROKKA_01493 +MTTVDSFGSKGVLDVNGSEYEIFRLNAVEGAQKLPYALKVLLENLLRTEDGANVTAEQIK +ALASWDPTAEPDTEIQFTPARVIMQDFTGVPCIVDLATMREAIADLGGDPSRVNPLSPAE +LVIDHSVQIDSFGNDAAVERNMDIEYQRNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN +IENLARAVMVRDVDGVKRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM +LIPRVVGFKLTGQIPAGATATDVVLTITEQLREHGVVGKFVEFYGEGVGAVPLANRATIG +NMSPEFGSTAAMFPIDDVTLDYLRLTGRSEEQVALVEAYTKEQGLWHDPSAEVQYSEYLE +LDLSTVVPSISGPKRPQDRIVLSDSKDQFRKDLHNYATQDEAGEGRPSKLVDVHMEDGRE +FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLTAKPWVKTSVAPGSRVVTDY +YEKSGLNASLDALGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR +INPDVKMNYLASPPLVVAYALAGTMDCDFENEALGTDQDGNDVFLKDIWPDPAEVQRIID +ESIDTEMFTSQYGTIFDGDERWQSLETPTGKTFEWDEASTYVRKPPYFEGMPAQPEPVQD +IAGARVLLKLGDSVTTDHISPAGSFKSDTPAGQYLLANGVERKDFNSYGSRRGNHEVMIR +GTFANIRIKNQLLDGVEGGFTRDFTQDGAPQAYVYDAAQNYAAAGTPLVVLGGKEYGTGS +SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPAGESADSLGLTGTETFAIS +GIAELNEGRTPKTVKVTATAEDGKVTEFDAVVRIDTPGEADYYRNGGILQYVLRQIAAKA +>PROKKA_01253 +MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAQKLPYSLKVLLENLLRTEDGANVTADQIK +ALAAWDPNAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE +LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN +IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM +LIPRVVGFKLTGSIPSGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG +NMSPEFGSTAAIFPIDEVTLDYLRLTGRSEEQVALVEAYTKEQGMWHDPSSEVAYSEYLE +LDLSTVVPSISGPKRPQDRIELTDSKDQFRKDLHNYATQDEAGEGRPSKLVDVAMADGRQ +FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY +YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR +INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDTEGNDVFLKDIWPDPTEVQQIID +ASIDTEMFTSQYATIFDGDERWQSLETPSGSTFEWDEKSTYVRKPPYFEGMTMQPDPVSD +ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGRYLLENGVQRKDFNSYGSRRGNHEVMIR +GTFANIRIKNQLLDGVEGGFTRDFTQEGAPQAYVYDAAQNYAEQGTPLVVLGGKEYGSGS +SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS +GITALNEGTTPKTVKVTATGEDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001084.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001084.fa new file mode 100644 index 0000000000000000000000000000000000000000..a6cf0c40387ab7da61949a74920342f242afb798 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001084.fa @@ -0,0 +1,50 @@ +>PROKKA_01296 +MAVVDTSTDVTGIGRTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEDG +ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF +RDTVHRIADLAVEPEVCFAGSEDEPTGQRWRTRNAFAVTPQGHIAMHAYRSATLLPVRNM +PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEVKLGRLRTRIRQ +AANACGVDVSTGLALPGPKQFQPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH +QHAPATLVDAVLEDARVEPGQVVADLYGGAGLFSAYLADAVGPEGRVYSVEASRQASKDA +RRNLHDQPQASVLNGPTDKVLGSWLKYPERPVADGGLGGAALDTVVLDPPRAGAGRRAIE +RILALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPAAQ +SAPAAAVVEI +>PROKKA_01019 +MAVVDTSTDVTGIGRTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEDG +ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF +RDTVHRIADLAVEPEVCFAGSEDEPTGQRWRTRNAFAVTPQGHIAMHAYRSATLLPVRNM +PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEVKLGRLRTRIRQ +AANACGVDVSTGLALPGPKQFQPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH +QHAPATLVDAVLEDARVEPGQVVADLYGGAGLFSAYLADAVGPEGRVYSVEASRQASKDA +RRNLHDQPQASVLNGPTDKVLGSWLKYPERPVADGGLGGAALDTVVLDPPRAGAGRRAIE +RILALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPAAQ +SAPAAAVVEI +>PROKKA_01596 +MAVIDTSTGVTGIGGTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEEG +ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF +RDTVHRIAGLTVEPEVCFAGPEDEPTGQRWRTRNAFTVTPQGHIAMHAYRSATLLPVRNM +PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEAKLGRLRTRIRQ +AANACGVDVSTGLALPGPKRHSPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH +RHAPATLVDAVLEDARIEPGQTVADLYGGAGLFSAYLADAVGPEGRVFSVEAAGQASKDA +RRNLHGQPQATVLNGPTDKALGSWIKYPERTVADGGLEGASLDTVVLDPPRAGAGRRAIE +RLLALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPATQ +LAAVPAIVEI +>PROKKA_01492 +MDTSTEVVAPGGVIEVEAGAMAHGGHCVARHEGRVVFVRHAIPGEIVRVALTEAEPGARF +WRGDVVEVVRPSEFRRIHQWKLADSLRAHASGRLPVGGAEYGHIVVHHQRRLKAQVFRDT +VARIAGVTIEPEALHAGHEDEPTGQHWRTRTAFAVTPQGRIAMHAHRSAVLLPVRNMPLG +VHALDALALWDWDFTGAARVDVATPADGTQPLVLATPTPQTLADEARLGKLRTRIRQAAN +ACPVDVSTGFAVPGPKKFSPTGIQRITGRTWVHETVSSERGGERTFRVTGDGFWQVHQHA +PATLVDAVLEDVDPQPGEVIADLYAGAGLFSAFLSDAVGEEGRVYSVEASRQASKDARRN +LLSLPQAGVLNGPTDKVLGSWIKEPERTTRDGGLDGDRLDAVVLDPPRAGAGRRAIERIL +ALAPGRICYVSCDPASFARDLAWLREGGYEVERARVFDLYPDTHHLESVTLLRPAGEVEQ +TTL +>PROKKA_01254 +MAVVDTSTDVTGIGRTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEDG +ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF +RDTVHRIADLAVEPEVCFAGSEDEPTGQRWRTRNAFAVTPQGHIAMHAYRSATLLPVRNM +PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEVKLGRLRTRIRQ +AANACGVDVSTGLALPGPKQFQPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH +QHAPATLVDAVLEDARVEPGQVVADLYGGAGLFSAYLADAVGPEGRVYSVEASRQASKDA +RRNLHDQPQASVLNGPTDKVLGSWLKYPERPVADGGLGGAALDTVVLDPPRAGAGRRAIE +RILALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPAAQ +SAPAAAVVEI diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001085.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001085.fa new file mode 100644 index 0000000000000000000000000000000000000000..efe39f087b1bfb06fd28a790de58606c460a77f3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001085.fa @@ -0,0 +1,61 @@ +>PROKKA_01297 +MATLSSLLRRGLLGRPVTSHAADEPRMNRWRALPVTSSNALSSLAYAPDEVILTLVAAGT +SALALGPAVGWAVVAVMLLIVVSFRAAVAAVPHGGIYHMAGMKLGPRAGVVASAALLLDF +VFTAAVSVAAFAHFVAALAPGLTVGSRVLVASAALVGVLLAALRGVRLSRWVLPVLVSVF +VALTALLVLAGLWQEGRGLLGAAPTAGWTQEGAGVGGTVGTVATALLALRAFSAGSVLLT +GVEVPVSSTRLMARPAVPTVRWVLTVMALTLGALTVGVMHLAQRTGVVVGLELENLRDAA +GAEVTPDRAPAPVLAQLADTVYGPGSILSVATIAATALLLLFAAKSAFRSFPALAARVAE +DGYLPRQLRVRSDRLVHTWSVLGMGAVALSLVLFFEARTALLVQLYVIGVLLAFTLAQAG +MLRLWRRRLVHTPGARARAAVRLRLIITAVAWVVTALAGVVVLVTRFTQGAWVALLAIVL +GSLVMGRIRRHYADVDRELAPDPQDDARALPSRVHVVVVVTTLDRPALRALAYARASRPS +SLEAVVVDAERAATLEVIDAWERAGLPMSLTVIASPYRDTVAPLVRHVREHRRRSPRDLT +MVFIPEYVVRPGWRTLLHNRTATRQTRRLQREPGVMVGSVPWQVHEGQGS +>PROKKA_01020 +MATLSSLLRRGLLGRPVTSHAADEPRMNRWRALPVTSSNALSSLAYAPDEVILTLVAAGT +SALALGPAVGWAVVAVMLLIVVSFRAAVAAVPHGGIYHMAGMKLGPRAGVVASAALLLDF +VFTAAVSVAAFAHFVAALAPGLTVGSRVLVASAALVGVLLAALRGVRLSRWVLPVLVSVF +VALTALLVLAGLWQEGRGLLGAAPTAGWTQEGAGVGGTVGTVATALLALRAFSAGSVLLT +GVEVPVSSTRLMARPAVPTVRWVLTVMALTLGALTVGVMHLAQRTGVVVGLELENLRDAA +GAEVTPDRAPAPVLAQLADTVYGPGSILSVATIAATALLLLFAAKSAFRSFPALAARVAE +DGYLPRQLRVRSDRLVHTWSVLGMGAVALSLVLFFEARTALLVQLYVIGVLLAFTLAQAG +MLRLWRRRLVHTPGARARAAVRLRLIITAVAWVVTALAGVVVLVTRFTQGAWVALLAIVL +GSLVMGRIRRHYADVDRELAPDPQDDARALPSRVHVVVVVTTLDRPALRALAYARASRPS +SLEAVVVDAERAATLEVIDAWERAGLPMSLTVIASPYRDTVAPLVRHVREHRRRSPRDLT +MVFIPEYVVRPGWRTLLHNRTATRQTRRLQREPGVMVGSVPWQVHEGQGS +>PROKKA_01595 +MATLSSLLRRGLLGRPVASHDVAEPRMSRWQALPVTSSNALSSLAYAPDEIVLTLVAAGT +AALALGPLVGWGVVVVMLLIVASFRAAVAAVPQGGIYQMARTKLGPRAGVVASAALLLDF +VFTAAVSVAAFAHFAAALLPGLGLESRVLVACAALVGVLLTSLRSARLSRWALPVLVSAF +VALTALLVAAGLWQEGQGLLGRAATSGWTQEGAGIGGTVGAVATALLALRAFSAGSVLLT +GVEVPVSSSSAMARPAVATVRWVLAVMALTLGALTLGVMHLAQRTGVVVALDPARLRDAA +GRPVAEADTPAPVIAQLADTVFGPGSVLSLATIAATALLLLFAARSAFRSFPALASRLAE +DGYLPRQLRVRGDRLVHTWGVLALGAAALALVLLFRAQTALLVQLYVIGVLLAFTLAQAG +MLRLWRRRLAQTPGARARAAVRLRLTITAVAWVVTALAGVVVLVTRFAQGAWVALLAIVL +GSLVMGRIRRHYEDVGRELAPDPEDDARALPSRVHVVVVVSTLNRPALRALAYARATRPS +SLEAVVVDAERAVTEDVIDAWSRAGLPVPLTVVAAPYRDTVVPLVRHLRERRRRSPRDLT +MVFIPEYVVRPGWRTLMHNRTATRQKRRLQREAGVMIGSVPWQIHEGQGDGQRSTTV +>PROKKA_01491 +MSTPPSTLRRLLLGRPVASGARPAPRRGRWLALPATASNALSSLAYAPDEVILTLVASGT +GALALGPLVGWAVVAVMVLIVLAFRAAVVAVPRGGIYRMARTKLGPRSGVVAAAALLLDF +VFTAAVSVAAFAHHASALVPALRGHVGIVSAVALVLVLVSALRGERGSGALVTVLVAAFV +GLLGTLVAVGLWQSGQGTLAAAPSAGLHVDGAGLGPVGDAATALLALRAFSAGSVLLSGV +EVPLSATDRMARPAVRTARWVLTVLAVVVGTLTVGVMHLAQRTGVVVALHPDRLRTADGA +PLAPDTAPAPVVAQLAETVFGAGSPGAVATVAVTSLLLLVAARGAFRSFPTLTARLAEDG +WLPRQLRVRGDRMVHTGGTLALATATLLLLVLFRGRTALLVQLYVIGVLLAFALALVGML +RLWRLKLAHTPGARARASVRVKLVVTAVGLGATALAGVVVLVTRFAQGAWVALLAIGVSA +VVMGRIRRHYRAVEAELAPDPQDDARALPSRVHAVVVVSTLNRPALRALAYARATRPATL +EAVVVDADRRQTERVVEDFARAGLPVPLTVIAAPYRDTVVPLVRHVRGRRLRSPRDLTMV +FIPEHVVRGGWRRLLHNRTASRQKARLQREAGVMVGSVPWQIREGDPHRPVEGGIVACAA +PGDVPEGVESS +>PROKKA_01255 +MATLSSLLRRGLLGRPVTSHAADEPRMNRWRALPVTSSNALSSLAYAPDEVILTLVAAGT +SALALGPAVGWAVVAVMLLIVVSFRAAVAAVPHGGIYHMAGMKLGPRAGVVASAALLLDF +VFTAAVSVAAFAHFVAALAPGLTVGSRVLVASAALVGVLLAALRGVRLSRWVLPVLVSVF +VALTALLVLAGLWQEGRGLLGAAPTAGWTQEGAGVGGTVGTVATALLALRAFSAGSVLLT +GVEVPVSSTRLMARPAVPTVRWVLTVMALTLGALTVGVMHLAQRTGVVVGLELENLRDAA +GAEVTPDRAPAPVLAQLADTVYGPGSILSVATIAATALLLLFAAKSAFRSFPALAARVAE +DGYLPRQLRVRSDRLVHTWSVLGMGAVALSLVLFFEARTALLVQLYVIGVLLAFTLAQAG +MLRLWRRRLVHTPGARARAAVRLRLIITAVAWVVTALAGVVVLVTRFTQGAWVALLAIVL +GSLVMGRIRRHYADVDRELAPDPQDDARALPSRVHVVVVVTTLDRPALRALAYARASRPS +SLEAVVVDAERAATLEVIDAWERAGLPMSLTVIASPYRDTVAPLVRHVREHRRRSPRDLT +MVFIPEYVVRPGWRTLLHNRTATRQTRRLQREPGVMVGSVPWQVHEGQGS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001086.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001086.fa new file mode 100644 index 0000000000000000000000000000000000000000..beb40baa20e743f010789b31625da9b13ffa04e2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001086.fa @@ -0,0 +1,25 @@ +>PROKKA_01298 +MAHYVIVGGGRVGTRLAAALDAAGHGVALVDRDPRTVEGLAPGFSGELVAGVGFDRSALL +AAGIDRAQGLAAVTADDNTNIIAARVARETFHVDHVVARIYDADRARLYQRLGIPTVASI +QWTADQVLHRLLPAGTADAEHRDASGRLLVTELVPHSSWWGRRLTDVESTVGMRIAYLTR +LGDGQLPRPGDRLQEGDVLHAVYPVDRRDRVEAALQGEARVPDGTDEDEEGRA +>PROKKA_01021 +MAHYVIVGGGRVGTRLAAALDAAGHGVALVDRDPRTVEGLAPGFSGELVAGVGFDRSALL +AAGIDRAQGLAAVTADDNTNIIAARVARETFHVDHVVARIYDADRARLYQRLGIPTVASI +QWTADQVLHRLLPAGTADAEHRDASGRLLVTELVPHSSWWGRRLTDVESTVGMRIAYLTR +LGDGQLPRPGDRLQEGDVLHAVYPVDRRDQVEAALQGEARVPDGTDEDEEGRA +>PROKKA_01594 +MAHYVIVGGGRVGTRLACALDAAGHSVALVDRDPRTVDGLVPGFSGELVAGVGFDRAALL +AAGVDRAQGLAAVTAEDNTNIIAARVARETFHVEHVVARIYDADQAKVYQRLGIPTVASI +QWTADQVLHRLLPAGTADVERRDASGRLLVTGLVPHPSWWGRRLTDVESGAGLRIAYLTR +RGEGLLPRPGDRLQEGDLLHAVYPVDRRDQVEAALQGEAVRSDRDAEDEDEEGRA +>PROKKA_01490 +MAHYVIVGAGRVGTRLAGALDTAGHSVAVIERSPELTAGLGPDFGGTVVAGIGFDRDALR +RAGIEQAQGLAAVTTEDTTNVIAARVARETFGVQHVVARIYDAQRARVFQRLGIPTVASV +EWTADQVLHRLLPAGTAEPSRRDASGRLAMGDYMPHRSWWGSPLHAVEAAVGARIAYLTR +YGEGVLPSPDGVLQEGDVLHVAYPAARRDRVEAALQGEAGDVRAGEDEDQEEDA +>PROKKA_01256 +MAHYVIVGGGRVGTRLAAALDAAGHGVALVDRDPRTVEGLAPGFSGELVAGVGFDRSALL +AAGIDRAQGLAAVTADDNTNIIAARVARETFHVDHVVARIYDADRARLYQRLGIPTVASI +QWTADQVLHRLLPAGTADAEHRDASGRLLVTELVPHSSWWGRRLTDVESTVGMRIAYLTR +LGDGQLPRPGDRLQEGDVLHAVYPVDRRDQVEAALQGEARVPDGTDEDEEGRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001088.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001088.fa new file mode 100644 index 0000000000000000000000000000000000000000..2c1c780bbfb65529a61906cf0cd45ddd5d9469bb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001088.fa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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001090.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001090.fa new file mode 100644 index 0000000000000000000000000000000000000000..2874fb2e40f18689a8de8dd1abb73de7e672b1fc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001090.fa @@ -0,0 +1,30 @@ +>PROKKA_01302 +MIFGRNRTVRHEQVSLPAELLEERDLEIAAAPEAADVGPHDVATRPDPAGMIDLGSLRLR +AVQGMKLRLDVEDATKRIVAATVSLGRSALQVQAFSAPRRTGLWDDLRAELHDSLSTTAH +ATVQEQTGRFGIEILTRVPAALPDGSPGWNVARFVGVDGPRWFVRGVFHGEAAFQPEAAE +PLEQVFSDLVVVRGDEPLPPRELLPLRPPPNARPLQRRRPAPDEGRDVLADTATGPGDGA +APEATALPERGPEITETR +>PROKKA_01025 +MIFGRNRTVRHEQVSLPAELLEERDLEIAAAPEAADVGPHDVATRPDPAGMIDLGSLRLR +AVQGMKLRLDVEDATKRIVAATVSLGRSALQVQAFSAPRRTGLWDDLRAELHDSLSTTAH +ATVQEQTGRFGIEILTRVPAALPDGSPGWNVARFVGVDGPRWFVRGVFHGEAAFQPEAAE +PLEQVFSDLVVVRGDEPLPPRELLPLRPPPNARPLQRRRPAPDEGRDVLADTATGPGDGA +APEATALPERGPEITETR +>PROKKA_01590 +MIFGRNRKVRHEQVSLPEELLEERDHEVAALPEAAETGPHDVATRPDPAGAIDLGSLRMR +AVQGMKLRLDVEDSTKRIVAATITLGRSALQVQAFSAPRRAGLWDEVREELRDSLDTTPN +ATVQEQAGRFGTEILTRVPAALPDGSPGWNVARFVGVDGPRWFVRGVFHGEAAFQPEAAA +QLEQVFSDIVVVRGDEPMPPRELLPLRPPANARPVQRRRPGAARDAGRDVLADTERGPQE +APALPERGPEITEIR +>PROKKA_01486 +MIFGRNRNVRHEQVAVPEQLKDERDRLVEARPAPAAEGDRGPFDVEAAPSGRPSVDLGAL +RVPAVQGMQLRLDVEDATQRIVAVTVTLERSALQIQAFSAPRAAGVWDDLRAEIKEALVG +TPGAQVQEQSGGFGPEVLTRIPATLPDGSPGWNVARFVGVDGPRWFVRGVFHGEAAYLPD +AARALEDVFAGVVVVRGDAPLPPRELLPLRPPADAQPVRRRPRPHAGGEPDVHARRPDDA +PETGAETLPERGPEITEIR +>PROKKA_01260 +MIFGRNRTVRHEQVSLPAELLEERDLEIAAAPEAADVGPHDVATRPDPAGMIDLGSLRLR +AVQGMKLRLDVEDATKRIVAATVSLGRSALQVQAFSAPRRTGLWDDLRAELHDSLSTTAH +ATVQEQTGRFGIEILTRVPAALPDGSPGWNVARFVGVDGPRWFVRGVFHGEAAFQPEAAE +PLEQVFSDLVVVRGDEPLPPRELLPLRPPPNARPLQRRRPAPDEGRDVLADTATGPGDGA +APEATALPERGPEITETR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001092.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001092.fa new file mode 100644 index 0000000000000000000000000000000000000000..86cefc90262c1c4b44999abf4f5c4201273dabb1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001092.fa @@ -0,0 +1,20 @@ +>PROKKA_01304 +MRDPQQHPVADASRRAPGGAAAGPDPVLFEERLTPSPGVWAVALMLAALTILVFAPIDLG +VGIAAAVAFFAVEVLILVATTPRIVVRERTLQVGRASIERHHVGQVTGYRGEDARAQRGP +LLHGLAFVNVRGWIAPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMARQEGTAEGR +>PROKKA_01027 +MRDPQQHPVADASRRAPGGAAAGPDPVLFEERLTPSPGVWAVALMLAALTILVFAPIDLG +VGIAAAVAFFAVEVLILVATTPRIVVRERTLQVGRASIERHHVGQVTGYRGEDARAQRGP +LLHGLAFVNVRGWIAPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMARQEGTAEGR +>PROKKA_01588 +MREPQQHPVSDAPVDRPQDPAQGSDRVLFEERLTPSAGVWVVALMLASLTILVFAPIDLW +FGVAAAVVFFGLEALLLLTTTPRIVVRERTLQVGRASIERRHVGEVTGHRGEDARRQRGP +LLHGLAYVVVRGWISPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMVQEDPADEDR +>PROKKA_01484 +MQDASATPDHHAPRTVAASADPVQYEERLSPSVGVWLVALLLAGLCIFVLAPVALWAGFL +AAAVFFVVEAVVLLASTPRIVVRERTLQVGRAQIERRHLGAVTGHRGEAARAQRGPLLHG +LAYVCVRGWISPVVRIQIEDERDATPYWLASTRHPEDLVAALGGRMAGEG +>PROKKA_01262 +MRDPQQHPVADASRRAPGGAAAGPDPVLFEERLTPSPGVWAVALMLAALTILVFAPIDLG +VGIAAAVAFFAVEVLILVATTPRIVVRERTLQVGRASIERHHVGQVTGYRGEDARAQRGP +LLHGLAFVNVRGWIAPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMARQEGTAEGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001094.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001094.fa new file mode 100644 index 0000000000000000000000000000000000000000..66d0dbbfcc687e6c77d072fc5a68d2e720beb001 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001094.fa @@ -0,0 +1,40 @@ +>PROKKA_01307 +MTGPALPAGVVPADRALRSVLTSAAAALGVPGCENALAVPAGRRVVVALVDGLGRSLLKR +FGGHAPTLRSAMADGGRVLEVAVPTTTAASLTSLGTGLDVGEHGVAGYDVLDPDRDVVIN +QLGGWDEATDPVGWQPKPTVFERAAAAGVDAVTVSLPAFERSALTRAGLRGGRFVAGRTL +IARAQAAERALKDARVPTLVYFYVNELDRAGHRDGVGSDRWLHALEEIDAAVRRLVDRVP +AGTVVLATGDHGMVDVPPSRRVDYAALDEAGELADAALLEGVAHTAGEPRLVQLHFRSDA +GPDVRARVRRAWAERYGAHAWVLTRDEAVDAGWFGAVVEDRVRARIGDLLVAVHGDLALY +DGRRVPPHAFEMVGQHGAPTRAEREVPLLTWHR +>PROKKA_01030 +MTGPALPAGVVPADRALRSVLTSAAAALGVPGCENALAVPAGRRVVVALVDGLGRSLLKR +FGGHAPTLRSAMADGGRVLEVAVPTTTAASLTSLGTGLDVGEHGVAGYDVLDPDRDVVIN +QLGGWDEATDPVGWQPKPTVFERAAAAGVDAVTVSLPAFERSALTRAGLRGGRFVAGRTL +IARAQAAERVMKDARVPTLVYFYVNELDKAGHRDGVGSERWLHALEEIDAAVRRLVDRVP +AGTVVLATGDHGMVDVPPSRRVDYAALDEAGELADPALLEGIAHTAGEPRLVQLHFRSDA +GPDVRARVRRTWAERYGAHAWVLTRDEAVDAGWFGAVVEDRVRARIGDLLVAVHGDLALY +DGRRVPPHAFEMVGQHGAPTRAEREVPLLTWHR +>PROKKA_01585 +MSGPAVPVGVVPPERALRSVLTSAAAALGVPGCENALGVPASRRVVVALVDGLGRSVLKR +FGGHAPTLRAAMADGGRVLQAAVPTTTAASLTSLGTGLDVGEHGVAGYDVLDPERDAVVN +QLGGWDEATDPVAWQPRPTVFERAGAAGVDAVTVSLPAFEHSGLTRAGLRGGRFVAGRGL +LARAQAAERVLKDAREPTLVYFYVNELDKAGHRDGVGSDRWLHALEEIDGALRRLVDRVP +AGTVVLATGDHGMVDVPPTRRVDYAAADESGALADPALLEGIAHTAGEPRLVQLHFRPDA +DADVRARVRRAWEDRFGAHAWVLTRDEAVAAGWFGTVVEERVRGRIGELLVAVHGDLALY +DGRRVAPHAFEMVGQHGSPTRAEREVPLLTWRR +>PROKKA_01481 +MTGPDAAAPAGPGLPPGPVPPERALRSVLTSAAAALGVPGCANALGVPVTRRVVVALVDG +LGRGVLKRFSGHAPTLRAAMADGGRVLTAATPTTTAASLTSLGTGLDVGEHGVAGYDVLD +PDRGVVVNMLGGWDEATDPLAWQPHPTVFERAVEAGVDAVTVSLPEFEHSALTRAGLRGG +RFVGGRGLLARAGHAERVLADACVPTLVYFYVNELDKAGHRDGVGSRSWLHALEEVDAAL +RRLVSRVPAGTVVLATGDHGMVDVAESRRVDYAALGDDGAPVRPGLLAGVAHTAGEPRLV +QLHFAPTATPAEREGTRRAWEDAYGDQAWILTRDEAVAAGWFGERVADRVLPRIGDLLVA +CHGELALYDGRRVSPRAFAMVGQHGSPTRAEREVPLLTWRR +>PROKKA_01265 +MTGPALPAGVVPADRALRSVLTSAAAALGVPGCENALAVPAGRRVVVALVDGLGRSLLKR +FGGHAPTLRSAMADGGRVLEVAVPTTTAASLTSLGTGLDVGEHGVAGYDVLDPDRDVVIN +QLGGWDEATDPVGWQPKPTVFERAAAAGVDAVTVSLPAFERSALTRAGLRGGRFVAGRTL +IARAQAAERVMKDARVPTLVYFYVNELDKAGHRDGVGSERWLHALEEIDAAVRRLVDRVP +AGTVVLATGDHGMVDVPPSRRVDYAALDEAGELADPALLEGIAHTAGEPRLVQLHFRSDA +GPDVRARVRRTWAERYGAHAWVLTRDEAVDAGWFGAVVEDRVRARIGDLLVAVHGDLALY +DGRRVPPHAFEMVGQHGAPTRAEREVPLLTWHR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001096.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001096.fa new file mode 100644 index 0000000000000000000000000000000000000000..90cd840ee6be239f353aad8331e013e7b629425f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001096.fa @@ -0,0 +1,85 @@ +>PROKKA_01309 +MGETEADRGYPSHWEADVVLRDGATAHLRPISPEDAAELQRMHAGQSENSIYLRYFTYKS +ELSAKDLDRFTHVDHRDRVAFVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLG +SILMEHLAAAARENGIRRFTAEVLPENRKMLSVFQESGFEVTRRFEDGVVAVEFPIDPTA +RWRAVVESREHRAESRSVAELVEPASVAVVGASRDPQAVGSLVLRHVLEAGFTGTVHAVN +RAAEDVQGLTAHRSLADIGEPVDLVVVAVPADEVEALIPEAAAAGAQGLVVLTSGYADAG +AEGLEAQRRLVSLARAHGMRVIGPASTGLVRTDPAIRLNASPSPGLAQRGPVSLFSQSGA +VGAMVSAGVKRRGVGISTSISAGNRADVSGNDAMQFFEADPHTAAVGVYLESFGNPRKFS +RIARRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGTVDSMLDQTGVLEAHTHEAMLD +ILMAVASQPLPTGHRVVLVADSLALDRLGRDAAAEAGLEVTATVGLVGSEQGIAPPADTL +VSAVRDAVCHEQADAVVVLARLGLHQADDEPERLAHALADATREARIPVLGCLTDVVSPR +YRGATLGAAGPVDDDAEPGSLQPGLPFYPSPQQAMAVLGALADYVHWRHQEVGEPLEPTG +LHPHEAEELVEAAAARAEGTELVRLSDEETETLLGHYGITVLPSVRFETAEEAVAAAERL +GFPVALKAVDPHLRHRLDLGGVRLNVVDADSLRRNVEHMRRLLAPFGVRELEVQAMAPAG +QACMLTALEDPLLGPVVSFGIAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAVKLRGT +GGVPPVDLAALEDLVGRVSVLKDDLPQVARLRFAPVLAAPERVTVLQAEVHVANAARRTD +SARRALRGR +>PROKKA_01032 +MGETEAVRGYPSHWEADVVLRDGATAHLRPISPEDAAELQRMHAGQSENSIYLRYFTYKS +ELSAKDLDRFTHVDHRDRVAFVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLG +SILMEHLAVAARENGIRRFTAEVLPENRKMLSVFQESGFEVTRRFEDGVVAVEFPIDPTA +RWRAVVESREHRAESRSVAELVEPASVAVVGASRDPQAVGSLVLRHVLEAGFTGAVHAVN +RAAEDVQGLTAHRSLADIGEPVDLVVVAVPADEVEALIPEAAAAGAQGLVVLTSGYADAG +AEGLEAQRRLVSLARAHGMRVIGPASAGLVRTDPAIRLNASPSPGLAQRGPVGLFSQSGA +VGAMVSAGVKRRGVGISTSISAGNRADVSGNDAMQFFEADPHTAAVGVYLESFGNPRKFS +RIARRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGTVDSMLDQTGVLEAHTHEAMLD +ILMAVASQPLPTGHRVVLVADSLALDRLGRDAAAEAGLEVTATVGLVGSEQGIAPPAETL +VSAVRDAVRHEQADAVVVLARLGLHQADDEPERLAHALADATRDARIPVLGCLTDVVSPR +YRGATLGAAGPVDDDAEPGSLQPGLPFYPSPQQAMTVLGALADYVHWRRQEVGEPLEPTG +LHPHEAEELVEAAAARAEGTELVRLSDEETETLLGHYGITVLPSARFETADEAVAAAERL +GFPVALKAVDPHLRHRLDLGGVRLNVVDADSLRRNVEHMRRLLAPFGVRELEVQAMAPAG +QACMLTALEDPLLGPVVSFGIAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAVKLRGT +GGVPSVNLAALEDLVGRVSVLKDDLPQVARLRFAPVLAAPEGVTVLQAEVHVANAARRTD +SARRALRGR +>PROKKA_01583 +MGDTEPVRDYPSHWEADVVLRDGATARLRPITPEDADELQRMHAGQSENSIYLRYFTYKS +ELSAKDLDRFTHVDHKDRVAFVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLG +SILMEHLAVAAREHGIRRFTAEVLPENRKMLSVFQESGFEVTRRFEDGVVAVEFPIDPTA +RWRAVVESREHRAEARSVAELVAPESVAVVGASRDPQAVGSMVLRHILEGGFAGPVHAVN +RAAGEVQGLTAHASLAEIGEEVELVVVAVPVDQVEALVPEAAAAGAAGLLVLTSGYADAG +AEGLEAQRRLVSLARAHGMRVIGPASAGLVRTDPAVRLNASPSPGLAQRGPVGLFSQSGA +VGAMVSAGAKRRGVGVSTSISAGNRADVSGNDAMQFFEADPHTAAVGVYLESFGNPRKFT +RITRRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGAVDSMLDQTGVLEVHTHEAMLD +LLMAVASQPLPTGRRVVLVADSLAVDRLARDAAAEAGLDVVATVGLAGSEQGVAPPAETL +VASVREAVAHEQADAVVVVGRLGLHQEDDDPETVARALAEATAGARMPVLVCLTDVVSPR +YAGATLGASGPVADDAEPGSLQPGVPFYPSPQQAMSVLGALADYVRWRGEEAGEPLEPAD +VRLHAAEDLVEAAAARAEGTELVRLSAAETEELLGHYGIAVLPSARFETADEAVAAAERL +GFPVAVKAVDPHLRHRLDLGGVRLNVVDAASLRRNVEQMRRVLAPFGVTELEVQAMAPAG +QACMVTALEDPLLGPVVSFGIAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAAKLEGR +GGVPAVDLAALEDLVGRVSVLKDDLPQVARLRFSPVLASPEGVTVLQAEVDVANAAGRTD +SARRALRGS +>PROKKA_01479 +MAEPDTETAYPSQWEADVVLRDGATARLRPIREDDVDGLRALHAGQSESSIYLRYFTFKS +ELSAKELERFTHVDHRDRVALVIERGGRILGVGRYDRYGDSDAAEVAFNISDAAQGQGLG +SILMEHLAVAAREQGIRRFTAEVLPENRKMLSVFQDSGFEVARHFEDGVVAVEFPIDPTA +RWRAVVESREHRAEARSVAELVEPESVAVVGASRDPHAVGSIVLRHILEAGFTGRVHAVN +RAAEDVQGLTAHASLKDIGEPVDLVVVAVPVAEVDAVVAEAAEAGAQGLLVLTSGYADAG +EDGLRAQRRLVARARARGMRVIGPASAGLVRTAPDVRLNASPSPGLASRGPVGVFSQSGA +VGAMITAGMKRRGVGMSTSLSAGNRADVSGNDAMQFFEDDPHTAAVGVYLESFGNPRKFS +RIARRLSRTKPVVVVRSDVTGRALPPGHETRTTQAPEGAVDSMLEQTGVLEAATHEDMLD +LLMAVATQPLPTGRRVTLVADSLALDRLGRDAAAVAGLEVVATHGLGGSEQGIAPTADDV +VASVEAALAAGDTDAVVVVTRLGLHQDEDAAHEVAQALARVAEGATVPVLGCLTDVVSAR +YGGARVGGAAAPAADAEPGALQPGLPLYPSPRKAMTVLGRLCDYVAWRREDAGEPIELTD +VDVRAAEALVDRALERALGTELIRLTGAETEELLRIYGIGVLRSRRFTTPDEAVAAAEEL +GFPVAVKAVDPYLRHRLDLGGVRLNLEDAESLRQNVRQMRAVLAPFGVTELEVQSMAPSG +QPCMVTALEDPLLGPVVSFGMAGDATDLLGDWVHRVPPLTDQDVRRMVRSPRAAVKLDGV +GGVPAVDLDALEDLLARVSCLKDDLPAVARLRFAPVLAAPTGTTVLSAEVDVANAAGRTD +SARRALRAS +>PROKKA_01267 +MGETEAVRGYPSHWEADVVLRDGATAHLRPISPEDAAELQRMHAGQSENSIYLRYFTYKS +ELSAKDLDRFTHVDHRDRVAFVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLG +SILMEHLAVAARENGIRRFTAEVLPENRKMLSVFQESGFEVTRRFEDGVVAVEFPIDPTA +RWRAVVESREHRAESRSVAELVEPASVAVVGASRDPQAVGSLVLRHVLEAGFTGAVHAVN +RAAEDVQGLTAHRSLADIGEPVDLVVVAVPADEVEALIPEAAAAGAQGLVVLTSGYADAG +AEGLEAQRRLVSLARAHGMRVIGPASAGLVRTDPAIRLNASPSPGLAQRGPVGLFSQSGA +VGAMVSAGVKRRGVGISTSISAGNRADVSGNDAMQFFEADPHTAAVGVYLESFGNPRKFS +RIARRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGTVDSMLDQTGVLEAHTHEAMLD +ILMAVASQPLPTGHRVVLVADSLALDRLGRDAAAEAGLEVTATVGLVGSEQGIAPPAETL +VSAVRDAVRHEQADAVVVLARLGLHQADDEPERLAHALADATRDARIPVLGCLTDVVSPR +YRGATLGAAGPVDDDAEPGSLQPGLPFYPSPQQAMTVLGALADYVHWRRQEVGEPLEPTG +LHPHEAEELVEAAAARAEGTELVRLSDEETETLLGHYGITVLPSARFETADEAVAAAERL +GFPVALKAVDPHLRHRLDLGGVRLNVVDADSLRRNVEHMRRLLAPFGVRELEVQAMAPAG +QACMLTALEDPLLGPVVSFGIAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAVKLRGT +GGVPSVNLAALEDLVGRVSVLKDDLPQVARLRFAPVLAAPEGVTVLQAEVHVANAARRTD +SARRALRGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001100.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001100.fa new file mode 100644 index 0000000000000000000000000000000000000000..de5f84a9b526ddea4ccc73f337df20f532aabbd4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001100.fa @@ -0,0 +1,50 @@ +>PROKKA_01313 +MDPLDLARWQFGITTVYHFLMVPLTIGLGLVVAVMQTLWVRTGREQYLRMTKFWGKLFLI +NFIMGVATGIVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGVWIFGWGRV +PRRLHLAAIWCAVIGAHLSAYFIMTANAFMQHPVGYEVVDGRPVLNDIGAVLANPIVLTH +FPHTIAGSWAVAGGFLLGISWYHLWKRRRDGIDTVDEHGRVVVGTTGSKARDRLDHRVWI +TSLRAGAAVAIVGFLGTAFTGHAQAQQMIEFQPTKMASAEAACHDGTAFSVLTLGDLGAG +DRTTCTDVTTVIELPGLLSYLAYEDFTTPVPGLNSLLPDFEERYGTHLPDDPLYGERAGA +PIDYQPLMEVTYWGFRLMITFGGLGALAGALTLWMTRRGTVPDSRGWTATAVASIGAPFA +ANVAGWVFTEMGRQPFVVYPNPAMGVDEVYMFTAAAVSPGVSAQEVLASLIVLVGIYAVL +LVVEVVLMVRYVRGGVPAGMPELTADEHRDPDEDRHDRDDVLAFAY +>PROKKA_01036 +MDPLELARWQFGITTVYHFLMVPLTIGLGLVVAVLQTLWVATGKDHYLRMTKFWGKLFLI +NFIMGVATGLVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGIWIFGWDRI +PRRLHLAALWCAVLGINLSAYFIMVANGFMQHPVGYEVVDGRPVLNDLGAVLTNPIVLTH +YPHTIFGSWAVAGGFLVGIAWYHLWKRRRDGIDVVDEAGRVVVGDAGTAARDRTDHRVWL +TSLRAGAAVALIGFVGTAFSGHAQAQQMIHFQPTKMAAAEAACHDGTAFSVLTLGDVRSG +GATTCEDVQGVIEVPGLLSYLAYEDFTTPVRGINTLLPEFEQKYGTHLPDSELYGDRAGS +EISYLPLMEVTYWGFRLMILFGGLGALAALGALWFSRRGTVPASRGWMRLAVASIGAPFA +ANMTGWVFTEMGRQPFVVYPNPAMGVDQVYMFTAAAVSPGVTGEEVLVSLIVLVGIYAVL +LGVEVFLLTRFVRGGVPAAMPELTAAEHSDEQKRDRDDVLAFAY +>PROKKA_01579 +MDPLDLARWQFGITTVYHFLMVPLTIGLGLVVAVMQTLWVRTGREQYLRMTKFWGKLFLI +NFIMGVATGIVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGVWIFGWGRV +PRRLHLAAIWCAVIGAHLSAYFILTANAFMQHPVGYEVVDGRPVLNDIGAVLANPIVLTH +FPHTIAGSWAVAGGFLLGISWYHLWKRRRDGIDTVDEHGRVVVGTTDSKARDRLDHRVWI +TSLRAGAAVAIVGFLGTAFTGHAQAQQMIEFQPTKMASAEAACHDGTAFSVLTLGDLGAG +DRTTCTDVTTVIELPGLLSYLAYEDFTTPVPGLNSLLPDFEERYGTHLPDDPLYGERAGA +PIDYQPLMEVTYWGFRLMITFGGLGALAGALTLWMTRRGTVPDSRGWTATAVASIGAPFA +ANVAGWVFTEMGRQPFVVYPNPAMGVDEVYMFTAAAVSPGVSAQEVLASLIVLVGIYAVL +LVVEVVLMVRYVRGGVPAGMPELTADEHRDPDEDRHDRDDVLAFAY +>PROKKA_01475 +MDPLELARWQFGITTVYHFLMVPLTIGLGLVVAVLQTLWVRTGREHYLRMTKFWGKLFLI +NFIMGVATGLVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGMWIFGWDRL +PRRLHLAAIWCAVIGAHLSAYFIMAANAFMQHPVGYEVVDGRPVLNDIVAVLTNPIVLTH +FPHTIAGSWAVAGGFLLGISWYHLWKRRRDGIDTVDAEGRVVVGTTGSKARDALDHRVWI +TSLRAGAAVVIVGFLGTAFTGHAQAQQMIHYQPTKMASAEAACHDGTAFSVLTLGDVNTP +GATTCDDVTGVIEIPGLLSFLAYSDFTTPVPGITTLLPQFEARYGTQLPDDPMYGERAGQ +EISYLPLMEVTYWGFRLMITFGGLAALAGALTLWMTRKGTVPDSKPWMITAVASIGASFA +ANVAGWVFTEMGRQPFVVYPNPAMGVDEVYMFTAAAVSPGVSGEEVLTSLIVFVVLYAVL +LVVEVALLARYVRGGVPAGMPELTADEHRDPDDDRHDRDDVLAFAY +>PROKKA_01271 +MDPLELARWQFGITTVYHFLMVPLTIGLGLVVAVLQTLWVATGKDHYLRMTKFWGKLFLI +NFIMGVATGLVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGIWIFGWDRI +PRRLHLAALWCAVLGINLSAYFIMVANGFMQHPVGYEVVDGRPVLNDLGAVLTNPIVLTH +YPHTIFGSWAVAGGFLVGIAWYHLWKRRRDGIDVVDEAGRVVVGDAGTAARDRTDHRVWL +TSLRAGAAVALIGFVGTAFSGHAQAQQMIHFQPTKMAAAEAACHDGTAFSVLTLGDVRSG +GATTCEDVQGVIEVPGLLSYLAYEDFTTPVRGINTLLPEFEQKYGTHLPDSELYGDRAGS +EISYLPLMEVTYWGFRLMILFGGLGALAALGALWFSRRGTVPASRGWMRLAVASIGAPFA +ANMTGWVFTEMGRQPFVVYPNPAMGVDQVYMFTAAAVSPGVTGEEVLVSLIVLVGIYAVL +LGVEVFLLTRFVRGGVPAAMPELTAAEHSDEQKRDRDDVLAFAY diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001103.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001103.fa new file mode 100644 index 0000000000000000000000000000000000000000..286d3fafe2f149a816b971cc1f1f2197222b6e8c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001103.fa @@ -0,0 +1,35 @@ +>PROKKA_01318 +MSGFGYDVGLDEAGMPELVERLESRRVLVTGASGLLGAGVARVLADAGNDVVTLQRRPSG +VAGARDVQGSVTDPAAVEEALTGADTVVHVAAKVSVSGPEHEYEAVNVEGTRILLHAAQR +HGVRRFVHVSSPSVAHAGDSIVGEGAGAASPEHARGPYARTKAAGERLALAADRDDFRVL +VLRPHLMWGPGDLQLTDRIVQRARAGRMPVLGTGAPLVDTLYTANAVEAVVAAVSAADVH +HGEALVVTNGEPRPVGELIRQIALAGGAAEPERRVPAGLARRAGALIERAWERDLFGLRS +RGVGSDDGEPPLTEFLAEQLSTAHWFDQRRTREVLSWTPTVSIDEGLHRVAAYYRDR +>PROKKA_01039 +MSGFGYDVGLDAAGMPDLVERLESRRVLVTGASGLLGAGVARVLADAGNDVTTLQRRPSG +VPGARDVRGSVTDPAAVEEALTGADTVVHVAAKVSVSGPEHEYEAVNVEGTRILLHAAQR +HGVRRFVHVSSPSVAHAGDSIVGEGAGAASPEHARGPYARTKAAGERLALAADRDDFRVL +VLRPHLMWGPGDLQLTDRIVQRARAGRMPVLGTGAPLVDTLYTANAVEAVVAALSAADVH +HGEALVVTNGEPRPVGELIRQIALAGGAAEPERRVPAGLARRAGALIERAWERDLFGLRS +RGVGSDDGEPPLTEFLAEQLSTAHWFDQRRTREVLAWTPTVSIDEGLHRVAAYYRDR +>PROKKA_01574 +MSGFGYDVGLDEAGMPELVERLESRRVLVTGASGLLGAGVARVLADAGNDVVTLQRRPSG +VAGARDVQGSVTDPAAVERAVAGVDTVVHVAAKVSVSGPEHEFEAVNVEGTRILLHAAQR +HGARRFVHISSPSVAHAGDSIVGEGAGPASPEHARGPYARTKAAGERLALAADRDDFRVL +VLRPHLMWGPGDMQLTDRIVQRARAGRMPVLGTGAPLIDTLYTGNAVEAVVAAVSAADHH +HGEALVVTNGEPRPVGELVRQIALAGGAEEPERHVPAGLARRAGALIERAWERDLFGLRS +RGVGSDDGEPPLTEFLAEQLSTAHWFDQRRTREVLDWTPSVSIGEGLHRLAAYYRAR +>PROKKA_01470 +MGFEVHLGDDGLLQLAERVEHRRVLVTGASGLLGSGVARVLAEAGNPVTTLQRRPSGVPG +AVDVLGSVTDPAAVERALEGVDTVVHVAAKVSVSGPEEEFAAVNVEGTRILVHAARRRGV +HRFVHVSSPSVAHAGASIVGEGAGPADPEHARGPYARTKAAGELIALGADADDFRVLALR +PHLMWGPGDLQLTDRIVQRAREGRMPVLGSGAALVDTLYTGNAVEAVVAAVSAVDHTHGE +ALVVTNGEPRPVGELIRRIALAGGAPEPERTVPAGVARRAGALIERAWERDLFGVRSSGR +GSADGEPPLTEFLAEQLSTSHWFDQRRTREVLDWTPSVSMDEGLLRLAAYYRDR +>PROKKA_01274 +MSGFGYDVGLDAAGMPDLVERLESRRVLVTGASGLLGAGVARVLADADNDVTTLQRRPSG +VPGARDVRGSVTDPAAVEEALTGADTVVHVAAKVSVSGPKHEYEAVNVEGTRILLHAAQR +HGVRRFVHVSSPSVAHAGDSIVGEGAGAASPEHARGPYARTKAAGERLALAADRDDFRVL +VLRPHLMWGPGDLQLTDRIVQRARAGRMPVLGTGAPLVDTLYTANAVEAVVAAVSAADVH +HGEALVVTNGEPRPVGELIRQIALAGGATEPERRVPAGLARRAGALIERAWERDLFGLRS +RGVGSDDGEPPLTEFLAEQLSTAHWFDQRRTREVLAWTPTVSIDEGLHRVAAYYRDR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001104.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001104.fa new file mode 100644 index 0000000000000000000000000000000000000000..18a670f23f810b740cf163fd198ea40fe5f84c5e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001104.fa @@ -0,0 +1,66 @@ +>PROKKA_01319 +MSGPRSRLDRPLSSTERPAPVPANTEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHC +LWEIIDNSVDEALAGFGQSIEITLHPDGSVEVEDNGRGIPVDVEPRTGLSGVEVVFTKLH +AGGKFGGGSYAASGGLHGVGASVVNALSSRLDVQVLRGGKVHQMSFRRGEPGRFQDGSRP +SPDAPFEPSTDASPLDVVGKAKRGQTGTRVRYWADEQIFVKDATFSAEELQARARQTAYL +IPGLRITVKDLRRRPGTPGADGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGTFK +ERVPVLGEDGRTSMQDVQRTCEVDVALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAAL +LKVFRAQVEANARRLKAGSDKVEKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTSAVRRI +VSQVVEKQLTARLTSTARAQKQQVHTLLEKVVAEMKSRISARTHKENQRRKNALETSTMP +AKLADCRSNDVASSELFIVEGDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILAN +AECAALIQVVGGGAGRSFDLDAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAG +RVYAAVPPLHRIEAVTRGVKEREVIYTYSEQELHATLARLEREGRSYREPIQRYKGLGEM +DADQLAETTMDPRHRMLRRVNIAEVEAAERVFDLLMGSAVAPRKDFIVSHADELDRARID +A +>PROKKA_01040 +MPANTEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGFGQSI +EITLHPDGSVEVEDNGRGIPVDVEPRTGLSGVEVVFTKLHAGGKFGGGSYAASGGLHGVG +ASVVNALSSRLDVQVLRGGKVHQMSFRRGEPGRFQDGSRPSPAAPFEPSTDASPLDVVGK +AKRGQTGTRVRYWADEQIFVKDATFSAEELQARARQTAYLIPGLRITVKDLRRRPGTPGA +DGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGTFKERVPVLGEDGRTSMQDVQRT +CEVDVALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAALLKVFRAQVEANARRLKAGSD +KVEKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTSAVRRIVSQVVEKQLTARLTSTARAQ +KQQVHTLLEKVVAEMKSRISARTHKENQRRKNALETSTMPAKLADCRSNDVASSELFIVE +GDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILANAECAALIQVVGGGAGRSFDL +DAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVYAAVPPLHRIEAVTRGVK +EREVIYTYSEQELHATLARLEREGRSYREPIQRYKGLGEMDADQLAETTMDPRHRMLRRV +NIAEVEAAERVFDLLMGSAVAPRKDFIVSHADELDRERIDA +>PROKKA_01572 +MPANSEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGYGQSI +EITLHPDGSVEVEDSGRGIPVDVEPRTGLSGVEVVFTKLHAGGKFGGGSYAASGGLHGVG +ASVVNALSSRLDVQVLRGGKVHQMSFRRGEPGRFQDGSRPSPDAPFEPSTDASPLDVVGK +AKRGQTGTRVRYWADEQIFIKDAAFSADDLHARARQTAYLIPGLRITVKDLRRRPGTPGA +EGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGSFKERVPVLGEDGRTAMQDVQRT +CEVDLALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAALLKAFRTQVESNARRLKAGSD +KVEKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTSAVRRIVAQVVEKELTARLTATARAQ +KQQVHVLLEKVVAEMKSRISARTHKENQRRKNALETSTMPAKLADCRSNDVASSELFIVE +GDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILANAECAALIQVVGGGAGRSFDL +DAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVFAAVPPLHRIEAVTKGVK +EREVIYTYSEQELYATLARLEKEGRSYKEPIQRYKGLGEMDADQLAETTMDPRHRTLRRV +NIAEVEAAERVFDLLMGSSVAPRKDFIVSHADELDRERIDA +>PROKKA_01468 +MPANTEYSARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGFGQSI +DVTLHPDGSVEVADNGRGIPVDVEPRTGLTGVEVVFTKLHAGGKFGGGSYAASGGLHGVG +ASVVNALSSRLDVQVVRGGKVHQLSFRRGEPGRFQDGSRPTPDAPFEPAADAAPLDVVGK +AKRGQTGTRVRYWADEQIFTPDATFSMEDLQARARQTAYLIPGLRIAVTDLRRLTGTAGE +AGPVQEVYQYDGGIAEFVDHLTPAKPVTDVWRIQGSGTFTERVPVLGEDGRTQMQDVQRT +CEVDVALRWDVGYETVFRSFVNIIATPKGGTHQSGFESALLKVFRAQVEAGARRLKAGSD +RPDKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTPAVRRIVARVVEKELTALLTSTARGQ +KQQVGALLEKVVAEMKSRISARTHKENQRRKNALETSTMPAKLADCRSNDVAASELFIVE +GDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILSNAECAALIQVVGGGAGRGFDL +DAARYGKVILMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVYAAVPPLHRIEAVTRGKK +EREVIYTYSEAELHEVLARLEAEGRTYREPIQRYKGLGEMDADQLAETTMDPRHRMLRRV +TISEVEAAERVFELLMGSSVAPRKAFIVSNADELDRERIDA +>PROKKA_01275 +MPANTEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGFGQSI +EITLHPDGSVEVEDNGRGIPVDVEPRTGLSGVEVVFTKLHAGGKFGGGSYAASGGLHGVG +ASVVNALSSRLDVQVLRGGKVHQMSFRRGEPGRFQDGSRPSPDAPFEPSTDASPLDVVGK +AKRGQTGTRVRYWADEQIFVKDATFSAEELQARARQTAYLIPGLRITVKDLRRRPGTPGA +DGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGTFKERVPVLGEDGRTSMQDVQRT +CEVDVALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAALLKAFRAQVEANARRLKAGSD +KVEKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTSAVRRIVSQVVEKQLTARFTSTARAQ +KQQVHTLLEKVVAEMKSRISARTHKENQRRKNALETSTMPAKLADCRSNDVASSELFIVE +GDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILANAECAALIQVVGGGAGRSFDL +DAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVYAAVPPLHRIEAVTRGVK +EREVIYTYSEQELHATLARLEREGRSYREPIQRYKGLGEMDADQLAETTMDPRHRMLRRV +NIAEVEAAERVFDLLMGSAVAPRKDFIVSHADELDRERIDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001105.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001105.fa new file mode 100644 index 0000000000000000000000000000000000000000..27837f3a4aea30ea6669b57a0bde643660e8124c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001105.fa @@ -0,0 +1,15 @@ +>PROKKA_01320 +MSITAVAEPAALTRSDRCDRCGAQAYVRAVLHSGGALQFCAHHARAVEDALRPQAALWQD +ETDRLTAGA +>PROKKA_01041 +MSITAVAEPAALTRSDRCDRCGAQAYVRAVLHSGGALQFCAHHARAVEDALRPQAALWQD +ETDRLTAGA +>PROKKA_01571 +MSITAVAEPAALTRSDRCDRCGAQAYVRAVLPSGGALQFCGHHARAVEDALRPQAAHWQD +ETDRLTAGA +>PROKKA_01467 +MSITAVAEPAALTRADRCDRCGAQAYVRAVLPSGGELLFCGHHARGVEASLRPQAALWQD +QTEELDGSTAA +>PROKKA_01276 +MSITAVAEPAALTRSDRCDRCGAQAYVRAVLHSGGALQFCAHHARAVEDALRPQTALWQD +ETDRLTAGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001107.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001107.fa new file mode 100644 index 0000000000000000000000000000000000000000..eaba508297817e7a73a4e08cdabd3cffd51cd63f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001107.fa @@ -0,0 +1,33 @@ +>PROKKA_01322 +MEAPTSLDVPVLPARGPEDLLAYVGHALGRLPEGSLVLLTLRDGRLRAVVRVDLPPEEVD +VGAWACAVAEVCRRDAAADATLCLALPDGARATLARPGWAAALDDALASAGRPLTAAWTC +ARGRARPWWGSGVAEEGPLDPRAAPLSLHLMTRGSVWDRAAVPDPVPRRGPAAARADDAR +WRPPEQDAPAARRAWLAQWESVLTGAARDRGAPAPAVLGSPLTRPAWRDGLLLHAAAPSG +AATGDPGDEERILTAASGRAPAWDRLDALRAGLRALVPVATPAVAAQALALAGWVGWARG +HGSDADAHLTAAAALSPDDPFVSVLRRIVAAGCVAGWATDPATAWRPDGGRP +>PROKKA_01043 +MEAPTSLDAPVLPARGPEDLLAYVGHALGRLPEDSLVLLTLHDGRLRAVVRVDLPPEEVD +VDAWACAVAEVCRRDAAADATLCLALPDGARATLTRPGWAAALDDALASAGRPLAAAWTC +AHGRARPWWGSSIAEEGTLDPRAAPLSLHLMTRGSVWDRAAVSDPVPRRGPAAARPDDAR +WRPPEQDAPPARRAWLAQWEPVLTGTARGRGAPAPAVLGSPLTRPAWRDGLLLHAAAPSG +AATGDPGDEERILTAASRRAPAWDRLDALRAGLRALVPVATPAVAAQALALAGWVGWARG +HGSDADAHLTAAAALSPGDPFVSVLRRIVAAGCVAGWATDPATAWRPDGGRP +>PROKKA_01569 +MWLSQWESVLAGERGAAGPVTAEGTAPVSGTEEHPSADAAVLGAPLTLPSWRDALVLHAA +VRPGDPPPEPAERERFLIAGSEQAPPWERLDRLRAGLRRLVPAAPPPAAAQALALAGWVG +WARGQGSDAAAHLAAAAELAPDDPFVTLMRRVVDTGCVAGWAAHPDTAWRPGA +>PROKKA_01465 +MRPRTLEGMDHPPAVPSAVPAGVTPPHLPVLRARGVDDLLGYAFHVLGTEPRESILLVTL +ARARLRAVVRVDRPGRETPPAARHWAEAVAAVARRDAAADAVVCVSLTGRAGGLEPPGWW +PPLVRALRDRGIPAREGWGVVAGHAARWPVEPGAGPGPLEEVDPRHSDLSLHLIGAGSVW +GLRAGHRSVPTPAALDPAAPDRPHWTAARARPEAPGPWLAAWERVLDGGGLPERPAGRAR +LGAGLEHPARRDALLIAAAGAAADELPAAERAALLTGTRDPGPDWRRLDRLWDALRALAA +DAPAPCAAPALALAAWICWARGEGTAAGAHLDVARRLAPRDPLVGVLRRILDAGAVCAWA +ADPRRAWTPWDPQDPASGMRG +>PROKKA_01278 +MEAPTSLDVPVLPARGPEDLLAYVGHALGRLPEGSLVLLTLRDGRLRAVVRVDLPPEEVD +VGAWACAVAEVCRRDAAADATLCLALPDGARATLARPGWAAALDDALASAGRPLTAAWTC +ARGRARPWWGSGVAEEGPLDPRAAPLSLHLMTRGSVWDRAAVPDPVPRRGPAAARADDAR +WRPPEQDAPAARRAWLAQWESVLTGAARDRGAPAPAVLGSPLTRPAWRDGLLLHAAAPSG +AATGEPGDEERILTAATGRAPAWDRLDALRAGLCALVPAATPAVAAQALALAGWVGWARG +HGSDADAHLTAAAALNPGDPFVSVLRRIVAAGCVAGWATDPATAWRPDGGGP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001111.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001111.fa new file mode 100644 index 0000000000000000000000000000000000000000..d72b4f7f0412c48e2feafa3ad91dcc92f35d9c13 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001111.fa @@ -0,0 +1,60 @@ +>PROKKA_01326 +MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEIL +VEEDDTVEVGAPLATIGDGSGGGSADASEDDAAAEEPAVEEAQQDDAQQEPAGEPAPEER +ASTDQGSDGAPSAGGEASEVTLPALGESVTEGTVTRWLKSVGDEVEVDEPLLEVSTDKVD +TEIPSPVAGTLLEIRAEEDDTVEVGAVLALVGSGSAGGGSAPSEGSSGQDEASAEEIEDK +ATEAEAPEETEEAAEAAGAEKSEKTPEASPSEEASRRESAERDSAQAESAEAPSATEPGQ +GYVTPLVRRLAHQNNVDLSTVRGTGVGGRIRKQDVLAAALASQAAAGGSEAPAEQASEAA +APSSAPAAASAPAASSSVDPSVRGEVEKAPRIRQVIAQRMRESLDLSAQLTQVHEVDVTR +IVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEITYHASEDIA +IAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVG +ALFDTPIINQPQVAILGIGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAG +RFLRTLRQRLEGGEFANELGL +>PROKKA_01047 +MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEIL +VEEDDTVEVGAPLATIGDGSGGGSADASEDDAAAEEPAVEEAQQDDAQQEPAGEPAPEER +ASTDQGSDGAPSAGGEASEVTLPALGESVTEGTVTRWLKSVGDEVEVDEPLLEVSTDKVD +TEIPSPVAGTLLEIRAEEDDTVEVGAVLALVGSGSAGGGSAPSEGSSGQDEASAEEIEDK +ATEAEAPEETEEAAEAAGAEKSEKTPEASPSEEASRRESAERDSAQAESAEAPSATEPGQ +GYVTPLVRRLAHQNNVDLSTVRGTGVGGRIRKQDVLAAALASQAAAGGSEAPAEQASEAA +APSSAPAAASAPAASSSVDPSVRGEVEKAPRIRQVIAQRMRESLDLSAQLTQVHEVDVTR +IVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEITYHASEDIA +IAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVG +ALFDTPIINQPQVAILGIGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAG +RFLTTLRQRLEGGEFANELGL +>PROKKA_01565 +MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLQEIL +ADEDETVEVGAPLATIGDGDGGGSSESDDDAQAEESEEPAAEEAQEDEEQQEPEGEPAPE +ERSSTQDSEEKSSGGASGGDASEVTLPALGESVTEGTVTRWLKAVGDEVEVDEPLLEVST +DKVDTEIPSPVAGTLLEIRAEEDETVEVGAVLALVGSGSAGGSSDSSDDSAKDDSAPDEA +SAEEIEDKATEAETGEETEEAAQDAGEEKEEKAPEASASENASREESAEQEKAAAADAPE +ATSPGQGYVTPLVRRLAHQNDVDLSTVRGTGVGGRIRKQDVLAAALAQQAGSAESAPAQE +QGSKEQAAAASSAPAVASSVDPSVRGEVEKAPRIRQVIAQRMRESLDLSTQLTQVHEVDV +TRIVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEITYHASED +IAIAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGS +VGALFDTPIINQPQVAILGTGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGAD +AGRFLTTLRQRLEGGEFANELGL +>PROKKA_01461 +MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEIL +VEEDDTVEVGAPLATIGDGSGGGSADASEDDAAAEEPAVEEAQQDDAQQEPAGEPAPEER +ASTDQGSDEAPSAGGEDSEVTLPALGESVTEGTVTRWLKSVGDEVEVDEPLLEVSTDKVD +TEIPSPVAGTLVEILANEDDTVEVGAVLARVGSGAAPAASQDPAPAADTASPEEIEDKAT +EAPTGEQTEEAAEQAGDVKQEQAPAASPAETASAAPAASAPAAETSASEPGPGYVTPLVR +RLAKQNGVDLSTVRGTGVGGRIRKQDVLAASLANQASSGSASPAAAEEQQTPAAASAPAP +AAVRGETEKAPRIRQVIAQRMRESLDLSTQLTQVHEVDMTRIVQLRGKAKASFQEKNGVK +LTYLPFITQAVTEALKQHPKLNASFSEDNKEITYHASEDIAIAVDTDRGLLVPVVKDAGT +LNLAGLAQKIADVAERTRTNKINPDELSGGTFSITNIGSVGALFDTPIINQPQVAILGTG +AIVKRPMVVADADGNDTIAIRHMMYLSLTYDHRLVDGADAGRFLQTLKARLEGGEFAAEL +GL +>PROKKA_01282 +MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEIL +VEEDDTVEVGAPLATIGDGSGGGSADASEDDAAAEEPAVEEAQQDDAQQEPAGEPAPEER +ASTDQGSDEAPSAGGEASEVTLPALGESVTEGTVTRWLKSVGDEVEVDEPLLEVSTDKVD +TEIPSPVAGTLLEIRAEEDDTVEVGAILALVGSGSAGGGSAPSEGSSGQDEASADEIEDK +ATEAEAPEETEEAAEAAGAEKSEETPEASPSEEASRRESAERDSAQGESAEAPAATEPGQ +GYVTPLVRRLAHQNNVDLSTVRGTGVGGRIRKQDVLAAALASQAAAGGSEAPAEQASEAA +APSSAPAAASAPAASSSVDPSVRGEVEKAPRIRQVIAQRMRESLDLSTQLTQVHEVDVTR +IVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEITYHASEDIA +IAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVG +ALFDTPIINQPQVAILGTGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAG +RFLTTLRQRLEGGQFADELGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001113.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001113.fa new file mode 100644 index 0000000000000000000000000000000000000000..25ed1090c5e448359937c9d9a2d7a9813185ffdf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001113.fa @@ -0,0 +1,55 @@ +>PROKKA_01328 +MRDWDEADGGAAGRVGGGPETEPERSSEPGTAAPRAPGWEPVRLLGAGAQAEVWLVEDGR +GVRAALKVPRAGAAPDALAAEAQAGRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDM +VQRVGPLSPGQAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVV +GGASGAGATPGFAAPEALAAVEGAGAEPGASPAVGAPSDVHAWAALGWYALTGRAPGAAG +HRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATARPEPVPLGEAAPAEV +AHLLPTVLPGSGPTRRRRGRRAAPRRRALARRRGAAPRRGVLVAAGLATALAVGGGTAGL +WWPASLGDATEGAPEPAGAVPAGTSVDAARPADGTPESGTPARVPDAGAPGEDAAGEDAV +DVGEALAAVGHARTAALIDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGLEVTV +EQAGPARRAGDDALRVDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGEGPEGR +DGGAAGRTWRVETVDPR +>PROKKA_01049 +MRDWDEADGGAAGRVGGGPETEPERSSEPGTAAPRAPGWEPVRLLGAGAQAEVWLVEDGR +GVRAALKVPRAGAAPDALAAEAQAGRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDM +VQRVGPLSPGQAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVV +GGASGAGATPGFAAPEALAAVEGAGAEPGASPAVGAPSDVHAWAALGWYALTGRAPGAAG +HRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATARPEPVPLGEAAPAEV +AHLLPTVLPGSGPTRRRRRRAAPRRRALALRRGAAPRRGVLVAAGLATALAVGGGTAGLW +WPASLGDATEGAPEPAGAVPAGTSVDAARPADGTPESGTPARVPDAGAPGEDAAGEDAVD +VGEALAAVGHARTAALIDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGLEVTVE +QAGPARRAGDDALRVDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGEGPEGRD +GGAAGRTWRVETVDPR +>PROKKA_01563 +MRDWDEADDGAVGRVGGGPETEPERTSELGTAAPRAPGWAPVRLLGAGAQAEVWLVEDGR +GVRAALKVPRAGAAPDALAAEAQAGRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDM +VQRVGPLSPGHAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVV +GGASGAGATPGFAAPEALAAVQGAGAEPEASPAVGAPSDVHAWAALGWYALTGRAPGAAG +HRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATARPEPVPLGEAAPAEV +AHLLPTVLPGSGPTRRRRRRAGPGRRALVGRRGAAPRRGVLLAAGLATALAVGGGTAGLW +WPAAPGSAAEGAPAEGAPEPAGTEPTGTPVDAARPADGTPESGTPARATDTGAPGEDAAG +ADAVDVGEALAAVGQARTAALTDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGL +EVTVEQAGPARRAGDDALRVDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGED +PEARDGGAAGRTWRVETVDPR +>PROKKA_01459 +MEAEDAERSGGVPPVGRPATDDWFADGGRDVSAWADPPRGGEGPAAVEPGVGDVGSPAEL +GPADRPPQAPGLRVVSRIGMGGQAEAWLVRREDGTECVLKVPRADGDPDAVAKEAAVYGH +LRHPHLLRVLGTVDTDRGTGVLSERLPAGSLASMVHDAGPLRPGQAVTVLVPVAQALAHL +HEHGVVHGDVSPGNVLFGVDGRPALADLGVARVVGGPRGRGGTPGFTAPEDEAGVGEGGA +AADVYAWGALGWFALTGRAPGPREHRAPLPVLVPDVPVELALLLSAALDPDPAGRPGAAE +AAVAAYDAAPPEPVPLHESAPAEVAHLLPTVVPPARPGGSGDARRSRPRAGGRRDAGRGR +GGRKRRNRSPRSRGWHPVMLVGAAVLAGTVVSAAVGGLTDRPEDQGEGAGSRAVAAPPTS +PTAAPANPRASVTPTGAADPKDAITPTRDGGVPSAAGTGPAAVLPAEDAAAALAAVAEGR +TAALTDPDPARVDAYAVPDGPAWRRDRAIQDQLREGGSAFSGLVVTLEAVGRPRPAEAGG +SGGAEAGWVVVPAVLRMSAHTVLDDAGSVVGEVPASEEDVSVTLVPGGEGRWRAAAVDPR +>PROKKA_01284 +MRDWDEADGGAAGRVGGGPETEPERSSEPGTAAPRAPGWAPVRLLGAGAQAEVWLVEDGR +GVRAALKVPRAGAAPDALAAEAQAGRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDM +VQRVGPLSPGQAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVV +GGASGAGATPGFAAPEALAAVQGAGAEPGASPAVGAPSDVHAWAALGWYALTGRAPGAAG +HRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATARPEPVPLGEAAPAEV +AHLLPTVLPGSGPTRRRRRRAGPGRRALARRRGAAPRRGVLVAAGLATALAVGGGTAGLW +WPASLGDATEGAPEPAGAVPAGTSVDAARPADGTRESGAPARVPDTGAPGEDAAGEDAVD +VGETLAAVGHARTAALTDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGLEVTVE +QAGPARRAGDDALRVDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGEGPEGRD +GGAAGRTWRVETVDPR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001114.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001114.fa new file mode 100644 index 0000000000000000000000000000000000000000..150b790a46edcca509b1a22e7817e78522bff8e6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001114.fa @@ -0,0 +1,25 @@ +>PROKKA_01329 +MPETLLPPLRLLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE +DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF +GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG +IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA +>PROKKA_01050 +MPETPLPPLRVLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE +DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF +GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG +IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA +>PROKKA_01562 +MPETLLPPLRVLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE +DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF +GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG +IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA +>PROKKA_01458 +MPHALLPPVRVLGLAPDLIDYEEGWALQRTLHADVVAGRSDGEILLLEHEAVYTAGRRTE +DADRPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEEVLIRTAAEF +GVTAVRVDGRAGIWITAREGDPRPDRKLGAIGLSIHDGVSMHGFSFNCSNSLTPYETIIA +CGIADASTTTLSVETGREVTPVDVLPVLVRHLEDLGPEHIALTPTEGTPA +>PROKKA_01285 +MPETLLPPLRVLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE +DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF +GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG +IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001115.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001115.fa new file mode 100644 index 0000000000000000000000000000000000000000..4be4f7d43ebf8a4f9ea23a6d68d4e2e6e8fd7616 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001115.fa @@ -0,0 +1,35 @@ +>PROKKA_01330 +MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC +PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMEEPQKVAENIREMDLRYATV +TGVARDDQKDGAAWLYAETIRRIHALNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN +LETVPRIFKRIRPAFTYEKSLRVLTMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG +CDIITITQYVRPSKLHHPIDRWVKPQEFVQWSQRAEEIGFQGVMAGPLVRSSYRAGKLYA +QAMQRLGRTLPENLAHLAGEKTARQEASAVVAQMS +>PROKKA_01051 +MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC +PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMEEPQKVAENIREMDLRYATV +TGVARDDQKDGAAWLYAETIRRIHALNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN +LETVPRIFKRIRPAFTYEKSLRVLTMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG +CDIITITQYVRPSKLHHPIDRWVKPQEFVHWSQRAEEIGFQGVMAGPLVRSSYRAGKLYA +QAMQRLGRTLPENLAHLAGEKTARQEASAVVAQMS +>PROKKA_01561 +MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC +PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMDEPQKVAENIREMDLRYATV +TGVARDDQKDGAAWLYAETIRRIHAFNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN +LETVPRIFKRIRPAFTYEKSLKVLSMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG +CDIITVTQYVRPSKLHHPIDRWVKPQEFVEWSRRAEEIGFQGVMAGPLVRSSYRAGKLYA +QAMQRLGRTLPENLEHLAGEKTARQEASAVVAQMS +>PROKKA_01457 +MTTAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNTVKGSGLHTVCEEAGC +PNIFECWEDREATFLIGGDICTRRCDFCDIASGRPLPLDMDEPQKVAENIREMDLRYATV +TGVARDDQKDGAAWLYAETIRRIHELNPSTGVEILPPDFGAVPELVQQVFDARPEVFAHN +LETVPRIFKRIRPAFTYEKSLRVLTMAKEQELVTKSNLILGMGETDEEIDQALVDLHEAG +CDIITITQYVRPSKLHHPIDRWVKPQEFVAWSQRAEEIGFAGVMAGPLVRSSYRAGKLYA +QAMERLGREVPEHLAHLRGERTARQEAAAVVARMS +>PROKKA_01286 +MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC +PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMEEPQKVAENIREMDLRYATV +TGVARDDQKDGAAWLYAETIRRIHALNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN +LETVPRIFKRIRPAFTYEKSLRVLTMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG +CDIITITQYVRPSKLHHPIDRWVKPQEFVQWSQRAEEIGFQGVMAGPLVRSSYRAGKLYA +QAMQRLGRTLPENLAHLAGEKTARQEASAVVAQMS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001116.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001116.fa new file mode 100644 index 0000000000000000000000000000000000000000..b6d8f44db2c9ee2924573b3f255f0cd78396b828 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001116.fa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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001117.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001117.fa new file mode 100644 index 0000000000000000000000000000000000000000..4bb5bb6d28cc9bb4df4c281649772526dec26476 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001117.fa @@ -0,0 +1,21 @@ +>PROKKA_01332 +MARRAPDPAQEPEPTRRDEPLITRRDLAGWVDGPGGGLAGGRWPGDLLGLPEHGPTSMAT +AARRAVALVIDWFLALGVSWLLFDSDAIATLMVFATMHILGITLLATTVGKAVCRTQVVR +LGGRTAPVHRVVVRTALLCLVLPAVVVGPDGRGMHDKVAGTVEIRM +>PROKKA_01053 +MARRAPDPAQEPEPTRRDEPLITRRDLAGWVDGPGGGLAGGRWPGDLLGLPEHGPTSMAT +AARRAVALVIDWFLALGVSWLLFDSDAIATLMVFATMHILGITLLATTVGKAVCRTQVVR +LGGRTAPVHRVVVRTALLCLVLPAVVVGPDGRGMHDKVAGTVEIRM +>PROKKA_01559 +MARRAPDPAQEPEPTRRDEPLITRRDLAGWVDGPGGGLAGGRWPGDLLGLPEHGPTSMAT +AARRAVALVIDWFLALGVSWLLFDSDAIATLMVFATMHILGITLLATTVGKAVCRTQVVR +LGGRTAPVHRVVVRTALLCLVLPAVVVGPDGRGMHDKVAGTVEIRM +>PROKKA_01455 +MSCVFPACNASSGPDYPGGVAHRASDPAPRDRSERDAAGRAEPLISRADLAGWIDGPGGG +RAGGRWPGDLLGLPEHGPASMATAARRAGALMIDWALALVVSNLAFGGDAIATLLVFAAM +HVVGLTLLATTVGKALCRIQVVREGTGGTAPVHRVLIRTALLCLVLPAVVVGPDGRGMHD +RVAGTVELHM +>PROKKA_01288 +MVAHYAGGVARRAPDPQDRTETTGRAEPLITRRDLAGWVDGPGGGRAGGRWPGDLLGLPE +RGPASMATAARRMGALVLDWFIALGISWLAFDADAIATLLVFAAMHVIGLTLLATTVGKA +VCRIQVVRVGGRPAGLLRILLRTALLCLVLPAVVVGPDGRGMHDKLADTVEIRM diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001118.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001118.fa new file mode 100644 index 0000000000000000000000000000000000000000..a338ef802bed75016da6d16f6136da9f1c291581 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001118.fa @@ -0,0 +1,45 @@ +>PROKKA_01333 +MFTSPADVLAYIKDEGIEFVDVRFTDLPGMQHHFNVPASSVDEDFFVTGQLFDGSSIRGF +AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS +SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG +GYFPVSPTDKQADLRDEICSVLAEVGLEVERSHHEVGAAGQAEINYRFNTLTHSADDLQK +FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW +YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR +IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD +EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV +>PROKKA_01054 +MFTSPADVLAYIKDEGIEFVDVRFTDLPGMQHHFNVPASSVDEDFFVTGQLFDGSSIRGF +AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS +SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG +GYFPVSPTDKQADLRDEICSVLAEVGLEVERSHHEVGAAGQAEINYRFNTLTHSADDLQK +FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW +YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR +IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD +EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV +>PROKKA_01558 +MFTSPADVLAYIKEEGIEFVDIRFTDLPGMQHHFNVPASTVDEDFFTTGQLFDGSSIRGF +AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS +SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG +GYFPVSPTDKQADLRDEICSVLAEVGLEVERSHHEVAAAGQAEINYRFNTLTHSADDLQK +FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW +YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR +IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD +EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV +>PROKKA_01454 +MFTSVEDVLAYIKDEGVEFVDIRFTDLPGMQHHFNVPASTVDEDFFVTGQLFDGSSIRGF +AGLAESDMQLIPDVTTAFVDPFRVRKTLAMNFSIVNPRTGEDYRRDPRGVAQRAEAYLAS +TGIADTAFFAPEAEFYVFDDVRYESSARSSFYRVDSTEAHWNTSRDEEGGNLGHKTPRQG +GYFPVTPVDKQADLRDEICAVLAEVGLEVERSHHEVGSAGQAEINYRFNTLTHSADDLQK +FKYVVKNVAEMFGKSVTFMPKPVFGEAGSGMHCHQSLWLGGEPLFYDEKGYANLSDTARW +YIGGLLQHASAVLAFTNPTVNSYRRLVPGFEAPVSMVYSQGNRSAGVRIPVTGSNPKAKR +LEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPPEEAADIQKAPTSLE +EALNALEEDHEFLLAGDVFTEELIRTWIDYKREMELTPLAARPNPYEFELYYSC +>PROKKA_01289 +MFTSPQEVLTYIREEGVEFVDVRFTDLPGLQHHFNVPASSVDEDFFVTGQLFDGSSIRGF +AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS +SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG +GYFPVSPTDKQADLRDEICAVLAEVGLTVERSHHEVGAPGQAEINYRFNTLTHSADDLQK +FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW +YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR +IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD +EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001119.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001119.fa new file mode 100644 index 0000000000000000000000000000000000000000..f043e72e37cdaf34b0598ba640e0024e1285f18a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001119.fa @@ -0,0 +1,95 @@ +>PROKKA_01335 +MSSLSTTGALPAVPDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRA +LLLWVRLAEREPRVHHALRDPETTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAAT +APALAQPDPADGEPWGDASATLRRLLLDSVGADPDTDRPVAAVTGKDAAVALRRAYRRQL +AAIALRDLDSAEPTAAMPSVGRWLADLAGATVDAALAVSRAVLTEREGPVVDRVDLAVIG +MGKCGAGELNYVSDVDVVFAHAVREAADGADPDAEVPDGPRAAALAAELAAGIGRVIQGA +APEPGLWEVDANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGER +YIAEIWPRVWESSSRDGFVESVRAMRARVLDTLAPAEREREIKLGPGGLRDVEFTAQLLQ +LVHGRADESLRVRGTLDAVRALHAASYITTRDARAFDEHYRWLRTLEHRIQLVHLRRTHL +MPVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALS +AEDVRLSAEAVRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGAD +PDGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLSGSRFVGDLLEHSPEAVAWVG +DDRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVALADISGLLDLE +AVTGALSDIDQVTVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVH +RPRPGVDEGRAREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGRQGPLVRTLD +SYREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAGDLTTADAREIRRIKA +RVEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGTLPALRAIARH +GLLPEAEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTAGGELE +ERYLRVTRLARQVFETRFYGL +>PROKKA_01056 +MSALPDAATADAPDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRAL +LLWVRLAEREPRVHHALRDPGTTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAATA +PALAQPDPTAGEPWGDASAALRRLLLDSVGADPDADRPLAAVTGKDAAVALRRAYRRQLA +AIALRDLDSAEPTAAMPSVGRWLADLAGATVDAALAVSRAVLTEREGPVVDRVDLAVIGM +GKCGAGELNYVSDVDVVFAHAVREAADGADPDAQVPDGPRAAALAAELAAGIGRVIQGAA +PEPGLWEVDANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGERY +IAEIWPRVWESSARDGFVESVRAMRARVLDTLAPAEREREIKLGPGGLRDVEFTAQLLQL +VHGRADESLRVRGTLDAVRALHAASYVTTRDARAFDEHYRWLRTLEHRIQLVHLRRTHLM +PVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALSA +EDVRLSAEAVRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGADP +DGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLSGSRFVGDLLEHSPEAVAWVGD +DRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVALADISGLLDLEA +VTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVHR +PRPGVDEGRAREQAEEVVRTLMALLQKPVAPPLPGERRLEVDADLRPEGRQGPLVRTLDS +YREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAQDLSAADAREIRRIKAR +VEAERLPRGADPARHVKLGRGGLSDVEWLVQSMQLKHAGQIEDLRVTGTLPALRAIARHD +LLPESEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTTGGELEE +RYLRVTRLARQVFETRFYGL +>PROKKA_01556 +MSALPDAATADAPDRRALAQAGVADARRVQSLLASPEFEGADVAPLVKRLGHAADPDRAL +LLWVRLAEREPRVHRALRDPETTARLLRLLGASEALGEFLIRRPEHLDLVLEPESAAATA +PALAQPDPADGEEWADEPAALRRLLLEAVEADPDADRPRAGLTGADAAVALRRAYRRQLA +AIALRDLDSADPAAVMPSVGRWLADLAGAAVDAALAVSRATLAEREGPAVDRVDLAVIGM +GKCGARELNYISDVDVVFVHELLDPGPDAAGEAGADGADGEASDAVDGTRAAVLAAELAA +GIGRVIQAAAPEPGLWEVDANLRPEGKDGALSRTLDSHAEYYRRWAHGWEFQALLKARPI +AGSADLGARYLERIWPRVWESSAREGFVDSVRAMRSRVLETIAPAEREREIKLGSGGLRD +VEFTAQLLQLVHGRADESIRVRGTLDAVRALHEASYISTRDAAAFDEHYRWLRTLEHRIQ +LVHLRRTHLMPVKDEALRIVARSLRGAQETGPATGEDLQAAFTRVRRAVRGLHETVFYRP +LLSTTAALSDDEVRLSAEAVRERLAALGYRDPKGALRHIEALTQGVSRRAAIQRQLLPAM +LGWFAEGADPDGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLAASRFVGDLLEH +SPEAVAWVGDDRELEPRGTVQLWRQADARLDRRIEAQETPAAVRHVRQVRRSETLRVALA +DISGLLDLEAVTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYG +SDLDALFVHRPRPGVDEGRAREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGR +QGPLVRTLDSYREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAGDLTTAD +AREIRRIKARVEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGTL +PALRAIARHGLLPEAEVAVLEEAWLLASRIRAAVLLWTGKVGDVLPTNMRDLEAIARLSG +VGTAGGELEERYLRVTRLARQVFEARFYGL +>PROKKA_01452 +MAPTPDSHVPGPRRALVHAGVADLTRAERLLSSPELAEQDADAALAALAHAADPDSALLL +YIRLAERDPQVHRVLAEADRARDLLRLLGASEALGEFLIRRPEHLDLVLDPARAAATAPA +LAQQDPTDGGDWHDEPAALRALLLEAVGADPAADQPVAGLTGADASVALRRAYRRQLTAI +ALADLASREPTLVMPAVGRWLADLAGAALEAALAVSRAELRAREGAAVDCVELAVIGMGK +CGARELNYVSDVDVVFVHDVLEPGAPDAPSAQEAARLAAELAAGISRVLSGPAPEPGLWE +VDANLRPEGRDGALSRTLDSHVEYYRRWAHGWEFQALLKARPVAGSPALGERYVAAVWPR +VWESSAREGFVENVRAMRTRVLDTIARDERDREIKLGAGGLRDVEFTAQLVQLVHGRADE +SVRVRGTLDALRVLHAASYISSRDMRAFDAAYRWLRLLEHRIQLVHLRRTHLMPVKEGPR +RVVARSMRGAGDVHPVAGDDLQDRFSRVRREVRALHETVFYRPLLSTTAALSDEDVRLSA +DAVQARLSALGYRDPRRALAHIEALTRGVSRRAAVQRQLLPAMLGWFADGADPDAGLLAF +RRLSESLGSSPWFLRMLRDSTDAARRLCLVLAGSRRVGDLLEHAPESVAWIGETRELAPR +GLSALTSEVTARLDRRSPEESAAQVIRHVRQIRQREILRTALADITGVVGLEEVGHALAD +VDQAAVQGALRVAGQAVLDGADPLTEVVVVAMGRQGGREIAYGSDLDAMFVHRPLAGADE +TAAAAQAEAVARQLMALLQQPAAPPLPSEQPLDVDADLRPEGRQGPLVRTLDSYREYYAR +WAEVWERQALLRARVVAGPAGLAEEFTAWADGVRYGDELSAGDAREIRRIKARVEAERLP +RGADPARHVKLGRGGLSDVEWLVQSLQLRHAHDEPELRVTGTLPALRALARLDLLPPSEA +ALLEEAWLLATRVRSALVLWTGKGSDVLPTNARDLGALARLAGDACGGGVAFEERYLRVT +RQARQVFEQRFYGL +>PROKKA_01291 +MSALPDAATADAPDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRAL +LLWVRLAEREPRVHHALRDPGTTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAATA +PALAQPDPTAGEPWGDASAALRRLLLDSVGADPDADRPLAAVTGKDAAVALRRAYRRQLA +AIALRDLDSAEPTAAMPSVGRWLADLAGAAVDAALAVSRAVLTEREGPVVDRVDLAVIGM +GKCGAGELNYVSDVDVVFAHAVREAADGADPDAQVPDGPRAAALAAELAAGIGRVIQGAA +PEPGLWEVDANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGERY +IAEIWPRVWESSARDGFVESVRAMRARVLDTLAPAEREREIKLGPGGLRDVEFTAQLLQL +VHGRADESLRVRGTLDAVRALHAASYVTTRDARAFDEHYRWLRTLEHRIQLVHLRRTHLM +PVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALSA +EDVRLSAEAVRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGADP +DGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLSGSRFVGDLLEHSPEAVAWVGD +DRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVALADISGLLDLEA +VTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVHR +PRPGVDEGRAREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGRQGPLVRTLDS +YREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAGDLTTADAREIRRIKAR +VEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGTLPALRAIARHG +LLPEAEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTAGGELEE +RYLRVTRLARQVFETRFYGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001120.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001120.fa new file mode 100644 index 0000000000000000000000000000000000000000..a5b52d5e9105e300cd8ea8d0deaf1bace65fe5b3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001120.fa @@ -0,0 +1,45 @@ +>PROKKA_01336 +MDRQQDYVLRTIEDRDVRFVRLWFTDVIGTLKSVALSPAEVENAFTEGLGFDGSSIDGYT +RISESDMLLQPDPSTFQILPWRGDQGQSSRMFCDVLTPDGRPAPADPRHVLRRVLDRAAD +RGFTCFTHPEIEFYLLQSDQPGPDGEPVPVDRAGYFDNVPGSDAADFRRDAVSLLEGMGI +SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSHHPG +SGMHTHFSLFEGDANAFYDPADEFRLSVTGRRFIAGLLRHSVEITAVTHQFVNSYKRLWG +GGEAPSYTSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLIAAGLKGI +EEGYEVPEAAAEDISALTTHERRVLGHVPLPGTLHDALRTAEESEFVASVLGEHVFDALL +RNKRQEWDDYRVEVTPYELRRYLSGL +>PROKKA_01057 +MDRQQDYVLRTIEDRDVRFVRLWFTDVIGTLKSVALSPAEVENAFTEGLGFDGSSIDGYT +RISESDMLLQPDPSTFQILPWRGDQGQSSRMFCDVLTPDGRPAPADPRHVLRRVLDRAAD +QGFTCFTHPEIEFYLLQSDQPGPDGEPVPVDRAGYFDNVPGSDAADFRRDAVSLLEGMGI +SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSEHPG +SGMHTHISLFEGDSNAFYDPADEFRLSVTGRRFIAGLLRHSVEISAVTHQFVNSYKRLWG +GGEAPSYVSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLIAAGLKGI +EEGYELPESAAEDVSALTTHERRVLGHVPLPGTLHDALRAAEESEFVASVLGEHVFDALL +RNKRQEWDDYRVEVTPYELRRYLSGL +>PROKKA_01555 +MDRQQDYVLRTIEDRDVRFVRLWFTDVVGTLKSVALSPAEVENAFAEGLGFDGSSIDGYT +RISESDMLLQPDPATFQILPWRGDGGQSSRMFCDVLTPDGRPAPADPRHVLRRVLEKASD +MGFSCFMHPEIEFYLLTSDQPGPDGRPVPVDRAGYFDNVPGSDAADFRRDAVTLLESMGI +SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSEHPG +SGMHTHISLFEGDSNAFYDPADEFRLSVTGRRFIAGLLRHSVEISAVTHQFVNSYKRLWG +GGEAPSYVSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLLAAGLKGI +EEGYELPESAAEDVSALTTHERRVLGHDPLPGTLHDALRAAEESEFVASVLGEHVFDALL +RNKRQEWDDYRVEVTPYELRRYLSGL +>PROKKA_01451 +MDRQQDFVLRTIEDRDVRFVRLWFTDVIGTLKSVALAPAEVEAAFTEGLGFDGSSIDGYT +RISESDMLLQPDPATFQILPWRGEAGQTSRMFCDVLTPDGRPAPADPRNVLRRVLDKASD +MGFSCYTHPEIEFYLLASDRPGPDGRPVPVDSAGYFDHVPGGAAQDFRRDAVTLLEDMGI +SVEFSHHENGPGQNEIDLRAADALTTADNVQTFRTIMKEVAARQGHYATFMPKPFGDQPG +SGMHTHFSLFEGDSNAFYDPADEFRLSVTGRRFIAGLLKHSVEISLVTHQFVNSYKRLWG +ADEAPAYVSWGHNNRSALVRVPLYKPDKAGSARIEYRGLDASANPYLAYALLLAAGLKGV +EENYDLPEPASEDVGALTPQERRVLGHVSLPGTLHDAVRAAEESEFVADVLGEHVYEALL +RNKRQEWDDYRVEITPYELRRYMTGL +>PROKKA_01292 +MDRQQDYVLRTIEDRDVRFVRLWFTDVIGTLKSVALSPAEVENAFTEGLGFDGSSIDGYT +RISESDMLLQPDPSTFQILPWRGDQEQSSRMFCDVLTPDGRPAPADPRHVLRRVLDRAAD +RGFTCFTHPEIEFYLLQSDQPGPDGEPVPVDRAGYFDNVPGSDAADFRRDAVSLLEGMGI +SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSHHPG +SGMHTHFSLFEGDANAFYDPADEFRLSVTGRRFIAGLLRHSVEITAVTHQFVNSYKRLWG +GGEAPSYTSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLLAAGLKGI +EEGYELPESAAEDVSALTTHERRVLGHVPLPGTLHDALRAAEESEFVASVLGEHVFDALL +RNKRQEWDDYRVEVTPYELRRYLSGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001121.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001121.fa new file mode 100644 index 0000000000000000000000000000000000000000..3cb736af15e79cf65282bd15009fcd9ee1db3da0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001121.fa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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001123.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001123.fa new file mode 100644 index 0000000000000000000000000000000000000000..28d189bf475c658ab86fa6a8e5c8f780ed3343b2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001123.fa @@ -0,0 +1,35 @@ +>PROKKA_01340 +MSQRQNPVAPSSHNGPRPAGPTAPEPGSFAPVGTLTPGAPSPAPPVPAAIPRPEYVGKAT +PDEGKASDVYDAAGVERIRAAGRLAAQAMEHTAAHIRPGVTTDELDRIAHAFLVERGAYP +SCLGYRGFPRSICTSINEVICHGIPDGTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV +DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH +SGLVIPHYDAAPAHDRLLVPGMVFTIEPMLTLGTIEWDQWDDGWTVVTRDRRRTAQFEHT +IVVTDDGAEILTLP +>PROKKA_01060 +MSQRQNPAVPSSHNGPRPAGPTAPEPGSLAPVGTLTPGAPSPAPPVPAAIPRPEYVGKAT +PDEGNASDVYDAAGIERIRAAGRLAAQAMEHTAAHIRPGVTTDELDRIAHAFLVERGAYP +SCLGYRGFPRSICTSINEVICHGIPDGTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV +DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH +SGLVIPHYDAAPAHDRLLVPGMVFTIEPMLTLGTIEWDQWDDGWTVVTRDRRRTAQFEHT +IVVTDDGAEILTLP +>PROKKA_01552 +MSHRQSTASPSSHNGPRPEGPAAPQPGSLAPVGTLTPGAPSPAPPVPASIPRPEYVGRAT +ADEGNASDVYDAAGIERIRAAGRLAARAMEHTAAYIRPGVTTDELDRIAHAYLVEHGAYP +SCLGYRGFPRSICTSMNEVICHGIPDSTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV +DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH +SGLVIPHYDAAPAHDRLLEPGMVFTIEPMLTLGTIDWDQWDDGWTVVTRDRRRTAQFEHT +LVVTDDGAEILTLP +>PROKKA_01448 +MSTTARPTSQPSHNGPRPEGPPAPEPGSRAPLGTLTPGAPSPAPAVPASIVRPEYVGRAT +ADEGNASDVYDTEGIGRIREAGRIAAQAMEHTAEHIRPGITTDELDRIAHEFIVAAGAYP +SCLGYRGFPRSICTSVNEVICHGIPDGTVLEDGDIVNLDITAYKDGVHGDHNRTYLVGDV +DEESRLLVERTEEALRRGIKAVKPGREINVIGRAIESYARRFGYGVVRDFIGHGVGVDFH +SGLVIPHYDAAPAHNRLMVPGMVFTIEPMITLGGIDWEQWDDGWTVVTKDRRRTAQFEHT +LVVTEDGAEILTLP +>PROKKA_01295 +MSQRQNPAVPSSHNGPRPAGPTAPEPGSLAPVGTLTPGAPSPAPPVPAAIPRPEYVGKAT +PDEGKASDVYDAAGIERIRAAGRLAAQAMEHTAAHIRPGVTTDELDRIAHAFLVERGAYP +SCLGYRGFPRSICTSINEVICHGIPDGTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV +DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH +SGLVIPHYDAAPAHDRLLVPGMVFTIEPMLTLGTIEWDQWDDGWTVVTRDRRRTAQFEHT +IVVTDDGAEILTLP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001124.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001124.fa new file mode 100644 index 0000000000000000000000000000000000000000..ca2c4a5e8832f50714185fe5d2725ea7b3291921 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001124.fa @@ -0,0 +1,20 @@ +>PROKKA_01342 +MHCPFCRHEDSRVVDSRSLDDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR +SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRATGNAEVDAHDVGLAILDPLRRLDQVA +FLRFASVYRDFESLDDFEEAIAELRAGDGDDRGRPAVQPRLFTR +>PROKKA_01062 +MHCPFCRHEDSRVVDSRSLDDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR +SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRATGNAEVDAHDVGLAILDPLRRLDQVA +FLRFASVYRDFESLDDFEEAIAELRAGDGDDRGRPAVQPRLFTR +>PROKKA_01550 +MHCPFCRHEDSRVVDSRSLEDGSAIRRRRQCQSCGKRFTTMETTALTVVKRSGVAEPFDR +SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRASGNAEVDAHDVGLAILDPLRRLDQVA +FLRFASVYRDFESLDDFADAIAELRAGTDERGRPAVQPRLFSR +>PROKKA_01446 +MHCPYCRHEDSRVVDSRSLEDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR +SKVINGVRKACQGRPVSSDDLAVLAQEVEEAVRASGNAEVDAHEVGLAILGPLRRLDQVA +YLRFASVYRDFESLSDFEDAIAELRAQEGEAPGRPAVQPRLFSR +>PROKKA_01297 +MHCPFCRHEDSRVVDSRSLDDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR +SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRATGNAEVDAHDVGLAILDPLRRLDQVA +FLRFASVYRDFESLDDFEEAIAELRAGDGDDRGRPAVQPRLFTR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001126.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001126.fa new file mode 100644 index 0000000000000000000000000000000000000000..bad322cd3045195299b37d06ac9d89c3e73ddf52 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001126.fa @@ -0,0 +1,35 @@ +>PROKKA_01344 +MGMRPGLTERLEVTEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA +KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG +PTVVGALAALGYDITTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK +VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLEDGRPSVTHYETLEVFGRATLLEVHL +ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLAFPHPVTGEPVTI +TSPYPDDLAHALAALRGDED +>PROKKA_01064 +MGMRPGLTERLQVAEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA +KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG +PTVVGALAALGYDITTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK +VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDDGRPSVTHYATLEVFGRATLLEVHL +ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLAFPHPVTGEPVTI +TSPYPDDLAHALAALRGDED +>PROKKA_01548 +MEPIPGATARIEVTPDRAGRRADAVLAEVLGLSRSALADWFSRGLVRAESRTGRRDRVLA +KSAKAVAGEVLAVDVPDDPDPLEVRAERVDALRILHEDEHLIAVDKPTGVAAHPSPGWAG +PTVVGALAALGHDISTSGAPERQGIVHRLDVGTTGVMVVAKTEQAYAALKDQFRRRVPEK +VYHALVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDGGRPSVTHYETLEVFGRATLLEVHL +ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLSFPHPVTGEPVSV +TSEHPDDLAHALARLRRDGS +>PROKKA_01444 +MGLRPGLTERLAVTEDDAGRRADAVLADAFGVSRASLADLFSRGLVRAESRTGRRDRVLA +KSAKAVAGETLAVDVPVDPDPLEVRAERVDAMTVLYEDDDLLAVDKPTGVAAHPSPGWFG +PTVVGGLAGLGRRISTSGAPERQGIVHRLDVGTTGVMVVAKSERAYTALKDQFRERVPEK +VYHAVVQGMPDPLEGTIDAPIGRDPNHHWRFAVLEGGRPSVTHYETVEAFGRATLLEIHL +ETGRTHQIRVHTSALRHPCAGDLTYGADPRLAAELGLTRQWLHAHRLALPHPATGERLEI +VSPYPDDLAHALRVLRGEDRGAAPDA +>PROKKA_01299 +MGMRPGLTERLEVTEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA +KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG +PTVVGALAALGRDISTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK +VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDDGRPSVTHYETLEVFGRATLLEVHL +ETGRTHQIRVHTSALRHPCVGDLTYGADPRMAAELGLTRQWLHAHRLAFPHPVTGEPVTI +TSPYPDDLAHALAALRGDAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001128.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001128.fa new file mode 100644 index 0000000000000000000000000000000000000000..88296ad82181260f54d9c867804c77fc787bd45d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001128.fa @@ -0,0 +1,25 @@ +>PROKKA_01346 +MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA +APAAGPAADTPEAAATPASAEESAPAAAPESADAAATSAAGVLAMAQRLHDEHVAAGEQR +STELVAEAEATAARLVSDAEEQKARTLEALAEEKAGLEGEVEQLRSFETDYRSRLTSYIE +GQLREIRAQKRVEPPTPTA +>PROKKA_01066 +MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA +APVADTPEAAETPSPVEEPAPAAAPEAADAAATSAAGVLAMAQRLHDEHVAAGEQRSTEL +VAEAEATAARLVSDAEEQKARTLEALAEERAGLEGEVEQLRSFETDYRSRLTSYIEGQLR +EIRAQKRVEPPTPTA +>PROKKA_01546 +MALSWEDVVNKQFQPTKFREGYDQGEVDDFLDEIVGELKRLQGLNEQLTAENEALRAGGA +VPDADAAVDAPVADADAAAVVDAGQSPAPAALADAEPGLEVEPTPSSADPASASAAGVLA +MAQRVHDEHVAAGEQRRDELISEAEARAEALVAEAEETRTRTLEELAADKAGLEAEVEQL +RGFETDYRSRLTAYIEGQLREIRSQERVEPAQRPA +>PROKKA_01442 +MVLSWEDVVNKEFQLTKFREGYDREEVEDFLDEVVEELKRLTEENDRLRSDLDACREGAP +AQAEASAPAAGEAAPALQAPAPVAPVEPSAPGEPVAPTDSATSAAGVLAMAQRLHDEYVA +EGEQRRDRIIADAEAEATTVVRQAEETRTRTLSDLESRRKGLEADVERLRAFETDYRSRL +TAYIEGQLREITAQERLEPAKGTV +>PROKKA_01301 +MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA +APAAAPAADTPEAAATPASVEEAAPAAAPESADAAATSAAGVLAMAQRLHDEHVAAGEQR +STELVAEAEATAARLVSDAEEQKARTLEALAEEKAGLEGEVEQLRSFETDYRSRLTSYIE +GQLREIRAQKRVEPPTPTA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001131.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001131.fa new file mode 100644 index 0000000000000000000000000000000000000000..c89d6faf131f924b2e303b2888346c3e9c81bd07 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001131.fa @@ -0,0 +1,30 @@ +>PROKKA_01349 +MTAPATAGPTPTDPRAREIADALAAVHARIADAARDAGREAEPALVVVTKTHPAEDVVRL +AALGVTDVGENRDQEARPKAEAVAAALGADAPRWHFVGQLQTNKAKYVVRYASVVESVDR +PELAEALSRALVLRREREPEAAIPDLECLVQVDVDDRADEDRPEGIGPRGGARPEDVPAL +ADVIAGLPGLRLGGLMCVAPRGLDPEHAFRRLAALGARLRQTHPEATALSMGMSADLEAA +VRAGATQVRIGSDVLGARDAVG +>PROKKA_01069 +MTAPATAGPTPTDPRTREIADALAAVRARLADAARDAGREAEPALVVVTKTHPAEDVVRL +AALGVTDVGENRDQEARPKAEAVAAALGADAPRWHFVGQLQTNKAKYVVRYASVVESVDR +PELAEALSRALLLRREREPEAAIPDLECLVQVDVDDRADEDRPEGIGPRGGARPEDVPAL +TDAIAGLPGLRLGGLMCVAPRGLDPEDAFRRLAALGAHLRQTHPEATALSMGMSADLEAA +VRAGATQVRIGSDVLGARDAVG +>PROKKA_01543 +MSTPEQHPTPHDAAAETRTREIAAGLAAVRERIARAAREAGRADEPALVVVTKTHPAEDV +VRLAGLGVAAVGENRDQEARPKAAAVAEALGDAAPRWHFIGQLQTNKAKHAARYASVVES +VDRTELAEALSRALVLRREREPGVEVPDLECLVQVDVDDRADEDRPEGIGPRGGAAPEDV +PALAAAIAALPGLRLGGLMCVAPRGLDPEASFRRLAALGEELRSAHPDASTLSMGMSADL +ESAVRAGATQVRIGSDVLGARPAVG +>PROKKA_01439 +MAEPLQDDPRVAEIAAGLDGVRRRIADAAAAAGRADLPELIVVSKTHPAEDVVALAGLGV +RQVGENRDQEARPKAAAVAEALGGAGVPAPAWHFIGQLQTNKAKHVARYASAVHSVDRLD +LVDALSRAVVLRREREGADAVSALDCLVQVDVDDRADEDRPEGIGPRGGAAPEDVPELAR +AIAAADGLRLRGLMCVAPRAADPAAAFARLAALSARVRAEHPDADALSMGMSGDLEAAVA +AGATHVRVGSDILGARGAVG +>PROKKA_01304 +MTAPATAGPTPTDPRAREIADALAAVRARIADAARDTGRAAEPALVVVTKTHPAEDVVRL +AALGVTDVGENRDQEARPKAEAVAAALGADAPRWHFVGQLQTNKAKYVVRYASVVESVDR +PELAEALSRALLLRREREPEAAIPDLECLVQVDVDDRADEDRPEGIGPRGGARPEDVPAL +ADVIAGLPGLRLGGLMCVAPRGLDPEDAFRRLAALGAGLRQTHPEATALSMGMSADLEAA +VRAGATQVRIGSDVLGARDAVG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001132.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001132.fa new file mode 100644 index 0000000000000000000000000000000000000000..4d6277a8cded738ff0288aa5a8864afde18b3d46 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001132.fa @@ -0,0 +1,30 @@ +>PROKKA_01350 +MTAAEGPAGTARVPAGPFVHRETVRTATGAVHVAWTSVAAGNLALHVVPPDEAEGLARVS +AARRALERVMGVPEGATLYLDQVHSADVVWADGPGRGGASAPVADAAVSRDGSRPLAVMV +ADCLPVVVVDETTGATAVAHAGRRGLLDGVLEATVDRLLSLRPEADRTGPGLRAWIGPGV +CGRCYEVPAAMRDEAAARLPATAATTSWGTPALDLPAGAAEVLRARGVATATIDVCTRED +ERLFSHRRAPGEGRFAGLVWRADPDATVPRGDA +>PROKKA_01070 +MTAAGGPAGTARVPAGPFVHRETVRTATGAVHVAWTSVAAGNLALHVVPPDEAEGPARVS +AARRALERMMGVPEGATLYLDQVHSADVVWADGPGRGGAPAPVADAAVSRDGSRPLAVMV +ADCLPVVVVDETTGATAVAHAGRRGLLDGVLEATVDRLLSLRPETDRTGPGLRAWIGPGV +CGRCYEVPAAMRAEAAARLPATAATTSWGTPALDLPAGAAQVLRARGVATATIDVCTRED +ERLFSHRRAPGEGRFAGLVWRADPDATTPRGEA +>PROKKA_01542 +MTAAEGPVGTVPVPAGPFVHREAVATAGGTVHVAWSGVAAGNLGLHVVADEDAAGRRAVG +EARRGLERAMGVPVGSTLYLDQVHSADAVWADGPGWGEEAGPTADAAVSRDGGRALAVMV +ADCLPVVLVDEATGATAVAHAGRRGLVDGVLEGTVDRLLSLRPADRRDAPGLRAWIGPGV +CGRCYEVPEQMRAEAAERVPATAATTAWGTPGLDLPAGAVAILRGRGADVAVVQACTLED +ERLFSHRRAPGQGRFAGLVWRADEDASTPTRAA +>PROKKA_01438 +MSLAGGPVGTQPVPSGPFVHREDLRADARGRVAHVAWTSAEAGSLAFHILGAEQEQARAD +VVAARHRVEDAMGVPRGSVFYLEQVHSVDVVTAGPGWEEGFAPTADASVSPDGHTPLAVM +VADCLPVVFVDGLTGATAVAHAGRRGLLDGVLENTVDALLALRPEGSAGAFGLKAWIGPG +ISGESYEVPQAMQDEAVARIPELEATTSWGTPALALASGAQAVLRARGVAVERIALDTFT +DERVFSHRRAPGRGRFAGLVWTTPADVDQDHDAGDARG +>PROKKA_01305 +MTAAEGPAGTARVPAGPFVHRETVRTATGAVHVAWTSVAAGNLALHVVPPDEAEGLARVS +AARRALERAMGVPEDATLYLDQVHSADVVWADGPGRGGAPAPVADAAVSRDGSRPLAVMV +ADCLPVVFVDETTGATAVAHAGRRGLLDGVLEATVDRLLSLRPETDRTGPGLRAWIGPGV +CGRCYEVPAAMRTEAAARLPATAATTSWGTPALDLSAGAAQVLRARGVTTATIDVCTRED +ERLFSHRRAPGEGRFAGLVWRTDLDATTPRGEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001133.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001133.fa new file mode 100644 index 0000000000000000000000000000000000000000..0d680670d714b07d1145097376b745cf89361356 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001133.fa @@ -0,0 +1,41 @@ +>PROKKA_01351 +MAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLDVGR +ELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARIARS +LGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVMDAF +RQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKAAEL +AIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDDALG +DEVRVTVIAAGFDKVDVTSAPAAPQAVQQQAAPQRAAAPAQPQPAAQPQPAAPAQPQQAE +RPAVRGTVPLAPQEQQPRRQQDLPTVVEPDLGAGSSDLDVPDFLK +>PROKKA_01071 +MAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLDVGR +ELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARIARS +LGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVMDAF +RQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKAAEL +AIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDDALG +DEVRVTVIAAGFDKVDVTSAPAAPQAAQQQAAPQRAAAPAQPQPVPAQPQQAERPAVRGT +VPLAPQEQQPRRQQDLPTVVEPDLGAGSSDLDVPDFLK +>PROKKA_01541 +MDTVAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLD +VGRELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARI +ARSLGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVM +DAFRQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKA +AELAIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDD +ALGDEVRVTVIAAGFDKVDATSAPASPQAGQFQQAPQRPAQQAQPQQQAPAPQQHQAQPA +QQEQPQQVQPQSVRGTVPLAPQQPQQTEQRRQQDLPTVVEPDLGAGSSDLDVPDFLK +>PROKKA_01437 +MDTVAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLD +VGRELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARI +ARSLGALTIGVVTRPFTFEGRRRAGSAENGIDALRDEVDTLIVIPNDRLLSISDRNVSVM +DAFRQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKA +AELAIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDD +ALGDEVRVTVIAAGFDKVDATSAPAAPFQQQAAPQRAAAPQQPAQQAQQAPVSQQAAPQR +PSVPGTMPLNSSSAFGGAPAQPAATQQPAAPQQPAAPQRAQQDLPTVVEPEFGSSDLDVP +DFLK +>PROKKA_01306 +MAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLDVGR +ELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARIARS +LGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVMDAF +RQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKAAEL +AIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDDALG +DEVRVTVIAAGFDKVDVTSAPAAPQAVQQQAAPQRAAAPTQPHPVPAQPQPAPAQPQPAP +AQPQQAERPAVRGTVPLAPQEQQPRRQQDLPTVVEPDLGAGSSDLDVPDFLK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001136.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001136.fa new file mode 100644 index 0000000000000000000000000000000000000000..df87517607f838f8b927414dbbcc1bbc61c250b1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001136.fa @@ -0,0 +1,40 @@ +>PROKKA_01354 +MTQTSHPSGPLRVVLAGGGTAGHISPMLAIARALEGDGGGPVECTMVGTASGMETRLVPE +AGYELDLIDRVPMPRRPSMDVVRFPARMRAAVATAARILRDRRADVVVGVGGYVATPVYL +AAFRAGVPVVVHEANARPGLANRIGALRATHVGTALPDTRLRGARWVGMPMRPEISGLDR +AAARRAAREALGLDPDRTTVVVTGGSSGALAVNRTVRAALGDLLDAGLQVFHLTGRDKAL +TEDDGSLLVRDGYVQREYLAGMEQAYAAADLIVARSGAGTVCEVSAVGLPAVYVPLPIGN +GEQALNARPVVEAEGALLVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV +TMAGLVRSAAQEGARR +>PROKKA_01074 +MTQTSHPSGPLRVVLAGGGTAGHISPMLAIARALEGDGGGPVECTMVGTASGMETRLVPE +AGYELDLIDRVPMPRRPSMDVVRFPARMRAAVATAARILRDRRADVVVGVGGYVATPVYL +AAFRAGVPVVVHEANARPGLANRIGALRAAHVGTALPDTRLRGARWVGMPMRPEISGLDR +AAARRAAREALGLDPDRTTVVVTGGSSGALAVNRTVRAALGDLLDAGLQVFHLTGRDKAL +TEDDGSLLVRDGYVQREYLAGMEQAYAAADLIVARSGAGTVCEVSAVGLPAVYVPLPIGN +GEQALNARPVVEAEGALLVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV +TMAGLVRSAAQEGARR +>PROKKA_01538 +MPQTPDPARELRVVLAGGGTAGHISPMLAIARALESDDAGPVRCTMVGTASGMETRLVPE +AGYELDLIERVPMPRRPSMDVVHFPARMRAAVAAAGRILAERRADVVVGVGGYVATPVYL +AAFRAGVPVVVHEANARPGLANRIGALRAAHVGTALPDTRLRGARWVGMPMRPEISGLDR +AAQRRAARAALGLDPERTTVVVTGGSSGALAVNRTVRDSLDDLLGAGLQVFHLTGRDKAL +TEADGTPLRREGYVQREYLDGMEQAYAAADLLVARSGAGTVCEVSAVGLPAVYVPLPIGN +GEQALNARPVVEAEGALTVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV +TMAGLVRSAAEEGARR +>PROKKA_01434 +MTTPNDASRPLRVVLAGGGTAGHISPMLAIARALGRQDPSTVCTMVGTDSGMETRLVPQA +GYELDFVERVPMPRRPSMDVVRFPGRFQASVRQAGEILRRRGADVLVGVGGYVSTPMYLA +ASRAGVPVVVHEANARPGLANRVGALRAARVGTALPDTRLPKAQWVGMPMRPEISGLDRA +AARDAARAELGLDPERTTVVVTGGSSGALNVNRTVRESLDDLLGAGLQVFHLTGRGKELT +DEAGQRVTRPGYVQREYLDGMEKAYAAADLIVARSGAGTVCEIAAVGLPAVFVPLPVGNG +EQALNARPVVDAGGALLVRDETFRADWVRRELIPLATDPQRLAAMGEAAARLGVRDADVR +TADLVREAAREGARR +>PROKKA_01309 +MTQTSHPSGPLRVVLAGGGTAGHISPMLAIARALEDDGGGPVECTMVGTASGMETRLVPE +AGYELDLIDRVPMPRRPSMDVVRFPARMRAAVATAARILRDRRADVVVGVGGYVATPVYL +AAFRAGVPVVVHEANARPGLANRIGALRATHVGTALPDTRLRGARWVGMPMRPEISGLDR +AAAGRAAREALGLDPDRTTVVVTGGSSGALAVNRTVRAALGDLLDAGLQVFHLTGRDKAL +TEDDGSLLVRDGYVQREYLAGMEQAYAAADLIVARSGAGTVCEVSAVGLPAVYVPLPIGN +GEQALNARPVVEAEGALLVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV +TMAGLVRSAAQEGARR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001137.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001137.fa new file mode 100644 index 0000000000000000000000000000000000000000..845b00b1918282ac9e4379722d97e52b7f56bbea --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001137.fa @@ -0,0 +1,45 @@ +>PROKKA_01355 +MSPIELRPVRPRAADDAPEHRERILRRMWRVLEGRRALDLSVLLISGCTALLTVLGLVMV +LSSSSVEAIGTGGGSYALFLRQSAWAVAGVAALLVFSRLPVRVLKALAWPAFGVAVILLA +LVAFSPLGVTVGGNRNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALIPV +LPGGLLLLVLVMAGSDLGTAIILAIVLATVLYVAGTHWGVFLTFLALSVLGILALTLLAP +HRMVRVQAWMGDCSDATDPCFQPAHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT +ILGEELGLVGTLVVLLAYLGLAIGIYRVAAGTTSTFIRLSTWGILAWLVGQAAVNIAMVS +GVIPVVGVPLPFISYGGSALTLSLSAVGIVLAFARHERRRAAQPDARPQADEPDTDPLPV +IPTPALQEPR +>PROKKA_01075 +MSPIELRPVRPRADDDAPEHRERLLHRMWRVLEGRRALDLSVLLISGCTALLTVLGLVMV +LSSSSVEAIGTGGGSYALFLRQSAWAVAGVAALLVFSRLPVRVFKALAWPAFGVAVILLA +LVAFSPLGVTVGGNRNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALIPV +LPGGLLLLGLVMAGSDLGTAIILAIVLATVLYVAGTHWGVFLTFLALSVLGILALTLLAP +HRMVRVQAWMGDCSDATDPCFQPAHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT +ILGEELGLVGTLVVLLAYLGLAIGIYRVAAGTTSTFIRLSTWGILAWLVGQASVNIAMVS +GVIPVVGVPLPFISYGGSALTLSLSAVGIVLAFARHERRRAAQPDARPQADEPDTDPLPV +IPTPALQEPR +>PROKKA_01537 +MSPTELHPVRTPADEEETEARSRPLQRLWRLVEGRRALDLSVLLIGGSTFLLTALGLVMV +LSSSSVEAIGTGGGSYGLFLRQTMWAVAGLAALLLFSRLPIGWIKALAWPAFGLAVVLLS +LVAFTPLGVTVGGNTNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALVPV +LPGGLLLIGLVMAGSDLGTAIILALVLAAVLFVAGTHHGVFIAFSAVTVVGAIALTLLAP +HRMVRVQAWLGDCSDASDPCFQPDHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT +ILGEELGLVGTLGVLLAYLALAVGMYRVAAGTTSPFIRLATWGIMAWLVGQAFVNIAMVS +GVIPVVGVPLPFISYGGSALTLSLTAVGIVLAFARHERRRAEEPDARPDADDPDTDPLPV +IPAPASQES +>PROKKA_01433 +MPSTATRPEASSRASARTAVRPRLAGFWGALEGRRALDWAALLIGLCTAVLTVLGLVMVL +SASSVEAISSSGGSYGLFLRQGGWALGGAVLLAVLRRLPVDLYRRLAWAAYLFAFLLLAL +VAFTPLGKEVNGNTNWLQLGPVTFQPSEAAKLAMALWAAAVLQRKERLVHLVSHALVPVL +PFGVALILLVLKGRDLGTALILAFILAVILFVAGTPGRVFAVLAGIGVVAALGMTVFAAN +RMERVQAWLFGCEGLQGDPCMQPDHGIYALASGGWWGVGLGQSRQKWNYIPEAENDFIFT +ILGEELGLVGTLLVLACFVGLAVGMYRVAAGASSTFVRLATWGILAWIVGQAAMNIAMVT +GLLPVVGVPLPFISYGGSALTLSLAAVGVVLSFARHERDLLPAAEASAADPASSASPQES +R +>PROKKA_01310 +MSPIELRPVRPRADDDAPEHRERLLPRMWRVLEGRRALDLSVLLISGCTALLTVLGLVMV +LSSSSVEAIGTGGGSYALFLRQSAWAVAGVAALLVFSRLPVRVFKALAWPAFGVAVILLA +LVAFSPLGVTVGGNRNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALIPV +LPGGLLLLILVMAGSDLGTAIILAIVLATVLYVAGTHWGVFLTFLALSMLGILALTLLAP +HRMVRVQAWMGDCSDATDPCFQPAHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT +ILGEELGLVGTLVVLLAYLGLAIGIYRVAAGTTSTFIRLSTWGILAWLVGQAAVNIAMVS +GVIPVVGVPLPFISYGGSALTLSLSAVGIVLAFARHERRRAAQPDARPQADEPDTDPLPV +IPTPALQEPR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001140.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001140.fa new file mode 100644 index 0000000000000000000000000000000000000000..cbf96c69c042f4615b5d747f7c19532aae5e98d1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001140.fa @@ -0,0 +1,55 @@ +>PROKKA_01359 +MTTPSDPPAPLTPAQQDAAFRPSHTPAAAWPALAQALAEAGIAAHVHGAAPADGVTGVSL +DSRVVRPGDLYVAVPGARAHGAAFAATALEAGAVGVLTDAAGRALLAEQGLADVPVLEVD +AVRTAAGTVAARVYGGGGDTGPRLLGVTGTNGKTTTSFLAAALLEALGRRSGIVGTILIR +AGEREVPSTLTTPEATQLHALMALMREEEVDTAVMEVSSHAVAYQRIAGLRYAVAGFTNL +TQDHLDMHGSMQEYFAAKAGLFDPARTDHAVITLDGGEGPRWGVAMARAAGAPVTTLALG +PAAPTPGALAEHDPGLRADWEVAELAPDGLGHRFTLRHAATGRELRASVGLPGRFNVANA +ALAVLLVLHAVGEEHLDALAAVLDVPAGEGPLAAAVPGRMEVVGREPDAVVDFAHNPDGM +VQALRSLADARAAAGTRGRTLIVFGSAGDRDRDKRPVMGAIAARAADVLIVTDDTPHSED +PAPIRAHILAGARAEADRIAREEGRTVVIEEVADRATAIRRAVELAGPQDGILLAGRGHE +TTMDYDGELVPLDDRVALREALAARVAAASASGSGPAREGKVIES +>PROKKA_01079 +MTTPSDPPAPLTPAQQDAAFRPSHTPATPWPALAQSLAGAGIAAHVHGAAPADGVTGVSL +DSRVVRPGDLYVAVPGAHAHGAAFAARALEAGAVGVLTDAAGRALLAEQDLADAPVLEAD +AVRTAAGTVAARVYGGGGDAGPRLVGVTGTNGKTTTSFLAAALLEALGHRSGIVGTILIR +AGEREVPSTLTTPEATQLHALMALMREEQVDTAVMEVSSHAVAYQRIAGLRYAVAGFTNL +TQDHLDMHGSMQEYFAAKAGLFDPARTDHAVITLDGGEGPRWGVAMARAAGAPVTTLALG +PAAPTPGALAEHDPGVRADWEVAELAPDGLGHRFTLRHAATGRELRASVGLPGRFNVANA +ALAVLLVLHAVGEEHLDALAAVLDVPAGEGPLAAAVPGRMEVVGREPDAVVDFAHNPDGM +VQALRSLADARAAAGTRGRTLIVFGSAGDRDRDKRPVMGAIAARAADVVIVTDDTPHSED +PAPIRAHILAGARAEADRIAREEGRTVVIEEVADRAAAIRRAVELAGPQDGILLAGRGHE +TTMDYDGELVPLDDRVALREALAAGAAVASASVSGPVREGKVIES +>PROKKA_01534 +MSSQPAQPQPLTPAQQDDAFRPSRTPATPWDELTRALQAAGVAARTHGRGPAAGVTGACL +DSRVVRPGDLYVALPGARSHGADFARAAVDAGAAGVLTDAEGRARLAEQGLDGSAVIEVD +SVRTAAGVVAARVYGGGQDAGPRLIGITGTNGKTTTSFLAAALLEALDRRSGVIGTILIR +AGGREVPSTLTTPESTQLHALMALMREEQVDTAVMEVSSHAVAYQRIAGLRYAVAGFTNL +TRDHLDMHGSMEEYFEAKAGLFDPERTARAVITVDGGEGPRWGLSMARAVRTPVTTLALG +PAAPHPGALAEEDPDFRADWEIAELVPDGLGHRFTLRHGATGRALRASVGLPGRFNAANA +ALAVLLVLYAVGEEHLDALAAVLDVPAGEGPLAAAVPGRMEVVGRAPDAVVDFAHNPDGM +VQALRSLADAREAAGRSGRTLIVFGSAGDRDREKRPIMGEIAARAADVVIVTDDTPHTED +PAPIRAQILEGARAEAARLLQAEGRTVLVEEVADRAVAIRRAAELAAPQDGILVAGRGHE +TTMDYDGELVPLDDRQALREALAARAAAASPRASDPGSGAPRGGKVDES +>PROKKA_01429 +MTDDAPQTTAPLTPAEQDAAFRPAAVTPVAWAEVAAALRAAGQDVRERSAAAAPAVTGAA +LDSRVVRPGDLYVALPGARAHGAAFAAAAREAGAAGVLTDGDGVALLAEQGLDDLPVLEV +ESVRAAAGVAAARIYGGGPDAGPRLLGVTGTNGKTTTSFLAASIVEALGERSGIIGTILT +RAGDRQVPSTLTTPESAQLHALMALMRQEGVDTAVMEVSSHAVEYRRIAGLHYAVAGFTN +LTQDHLDQHGTMEGYFRAKLGLFEADRTDRAVVVLDGGEGPRWGVKTARRAGAPVTTLAL +GAASPTPGALAEEHPDVVPDWQVTDLVADGLGHRFALVHAATGRRLPASVGLPGLFNVAN +AALAALMVLESIGEDRLDELAAVLDVPAGTGPLAAAVPGRMEVVGREPDAVVDFAHNPDG +MVQALRALGDARAAAGRAGRTLIVFGAAGDRDATKRPLMGRIAAEHADVVIVTDDTPHTE +DPAPIRAQLLEGAREEAARAAAAGREVRVEEFADRAAAIRRAAELAAPEDGILVAGRGHE +TEMDYDGTLVPLDDRVALRDALAARRPGDAQEPGVAGGKVAGK +>PROKKA_01314 +MTTPSDPPAPLTPAQQDAAFRPSHTPATPWPALAHALAEAGIAAHVHGAAPADGVTGVSL +DSRVVRPGDLYVAVPGARAHGAAFAATALEAGAVGVLTDAAGRALLAEQGLVDVPVLEVD +AVRTAAGTVAARVYGGGGDAGPRLVGVTGTNGKTTTSFLAAALLEALGRRSGIVGTILIR +AGEREVPSTLTTPEATQLHALMALMREEEVDTAVMEVSSHAVAYQRIAGLRYAVAGFTNL +TQDHLDMHGSMQEYFAAKAGLFDPARTDHAVITLDGGEGPRWGVAMARAAGAPVTTLALG +PAAPTPGALAEHDPGLRADWEVAELAPDGLGHRFTLRHAATGRELRASVGLPGRFNVANA +ALAVLLVLHAVGEEHLDALAAVLDVPAGEGPLAAAVPGRMEVVGREPDAVVDFAHNPDGM +VQALRSLADARAAAGTRGRTLIVFGSAGDRDRDKRPVMGAIAARAADVLIVTDDTPHSED +PAPIRAHILAGARAEADRIAREEGRTVVIEEVADRATAIRRAVELAGPQDGILLAGRGHE +TTMDYDGELVPLDDRVALREALAARVAAASASGSGPAREGKVIES diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001141.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001141.fa new file mode 100644 index 0000000000000000000000000000000000000000..8f05f91bcd9115f59f80193837e848ea295a0efd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001141.fa @@ -0,0 +1,57 @@ +>PROKKA_01360 +MRTRILLLLVFVLLGGLALRLVYVQGIDPTGQAAAAMDQRLTHQETLPQRGSILDRDGDV +LAASVRRYDIVVDQRLVKDFNEWDREARETVLVDVDSRLASLAEVLGMSEEEVREATIGS +RPYAVVRRSVTPEVRDAAMALNVPGLLSEAVDRRTYPNGSVAGSIIGFMGGDGTALEGLE +LSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPAVDGADLRLTVDKDAQWFAQETLGAL +AAEYEAEWANAVVMDVKTGDVIVMADSTTVDPADPDATEGNFRTSTVMSTPYEPGSTGKA +LPIAAAVDAGKVTATDGFTVPGSQDFDGQTIRDFSPHPTFDMTVAGIYARSYNTGTVQIA +EKITDEQRYEYMRSFGVGQPIDLGLPQQAGSVLVPPEQWDGRQRLTTAFGQGYTQTTLHT +AQMYQALANGGVLIPARLIDATVDGDGAEKRWESSAEPHRVVSEETAAQMLRMMETVVTQ +GTSKAAAIPGYRVGGKSSTAEAASDTGTYDGYNLGFTAVAPLDDPRFVVSVSMHRPPSKQ +GSRDVSVAAATIMEYMLRQADVPATGAEPNDYRVFVDDPQDRPW +>PROKKA_01080 +MRTRILLLLVLVLLGGLALRLVYVQGIDPTGQAAAAMDQRLTHQETLPQRGSILDRDGDV +LAASVRRYDIVVDQRLVKDFNEWDREARETVLVDVDSRLASLAEVLGMSEEEVREATIGS +RPYAVVRRSVTPEVRDAAMALNVPGLLSEAVDRRTYPNGSVAGSIIGFMGGDGTALEGLE +LSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPAVDGADLRLTVDKDAQWFAQETLGAL +AAEYDAEWANAVVMDVKTGDVIVMADSTTVDPADPDATEGNFRTSTVMSTPYEPGSTGKA +LPIAAAVDAGKVTATDGFTVPSSQDFDGQTIKDFSPHPTFDMTVAGIYARSYNTGTVQIA +EKITDEQRYEYMRSFGVGQPIDLGLPQQAGSVLVPPEKWDGRQRLTTAFGQGYTQTTLHT +AQMYQALANGGVLIPARLIDATVDGEGAEKRWESSAEPHRVVSEETAAQMLRMMETVVTQ +GTSKAAAIPGYRVGGKSSTAEAASDTGTYDGYNFGFTAVAPLDDPRFVVSVSMHRPPSKQ +GSRDVSVAAATIMEYMLRQADVPATGAEPNDYRVFVDDPQDRPW +>PROKKA_01533 +MTDRPAFSSPRGGSTVGPAPGLPDARIRGLLLLVLVLLGGLALRLVYVQGVDPTGQAAAA +MDKRLTHQETLPERGSILDRDGDVLASSVRRYDMVVDQRLVKDFNEWDREARKTVLVDVD +SRLASLAEVLELPEEQVREATIGSRPYNVVKRSVTPEMRDAAMALKVPGLLAEPVDRRVY +PNGSVAGSIVGFMGGDGTPLEGLELSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPAV +DGADLRLTLDKDAQWFAQETMGALAAEHDAEWANAVVLDAKTGDVLVMADSTTVDPADPE +GTEPYFRSSTVMSTPYEPGSTGKALPIAAALDAGAVTATDGYTVPSSQEFDGQTIRDFAP +HETYDMTVAGIFARSYNTGTVQVAEEISDELRYEYMRSFGVGKPIDLGLPRTAGGVLVPP +GEWDGRQRLTTAFGQGYTQTTLHTAQMYQAMANGGVMEPARLIDATVDGDGAEKRWEPAA +EPHRVVSEATAADMLRMMETVVTQGTSKAAAIPGYRVGGKSSTAEAASDTGRYDGYNFGF +TAVAPLDDPRFVVSVSMHRPPSQLGSRAVTSAAAQIMEHMLRQADVPADGAAPQDYDVFV +DDPQDRPW +>PROKKA_01428 +MPVSRSRVSGAGSRTAPPIGTARVRSRTVLLLLLALVTVLGLRLVWVQGIDASGAAATAM +SERLKTQEIRPERGAITDRDGAVLASTVRRYDIVVDQRLVKDFKEWDAEKRQSVLVSIDS +RLSSLAEALGMSEDEVRAAAIGDRPWAVLKRSVTPEVRDRVLALKVPGVLADAVDRRTYP +SGAVAGSLVGFMSSDGTPLEGLEKSQDAVLSGTPGTRTFEVGATGIRIPNAPEDVTPAVD +GATLRLTLDKDAQWYAQEAMARLADTYSAQWANAVVMDAKTGEVLALADSATVDPGDPQA +ADARARTPGVVYTPYEPGSTGKTATMAAALDMGLVTPETGLEVPDRLELKGQPPIRDASP +HETYTMTVAGVYARSYNTGTVMVAEKMSDEQRYEYMRSFGIGRPIDLGLPQPARSVLAAP +GDWDGRQRLVTAFGQGYTVTTLHTAQMFQAIANGGVLEPARLIAATVGADGTEHRWDPGV +ASRRVVSEQTAEEMLRMMETVVTQGTSTVAQLPGYRVGGKSSTAQVAGETGTYDGYNYGF +TAVAPLDDPRYVVSVSMNRPSAGGSSKVVAAAAADVMQHMLRQGGVPPGGAEPDDYRVFV +DDPQERPW +>PROKKA_01315 +MRTRILLLLVFVLLGGLALRLVYVQGIDPTGQAAAAMDQRLTHQETLPQRGSILDRDGDV +LAASVRRYDIVVDQRLVKDFNEWDREARETVLVDVDSRLASLAEVLGMSEEEVREATIGS +RPYAVVRRSVTPEVRDAAMALNVPGLLSEAVDRRTYPNGSVAGSIIGFMGGDGTALEGLE +LSQDDVMTGTPGTRTFEVGADGIRIPNAPLEEVPAVDGADLRLTVDKDAQWFAQETLGAL +AAEYEAEWANAVVMDVKTGDVIVMADSTTVDPADPDATEGNFRTSTVMSTPYEPGSTGKA +LPIAAAVDAGKVTATDGFTVPGSQDFDGQTIRDFSPHPTFDMTVAGIYARSYNTGTVQIA +EKITDEQRYEYMRSFGVGQPIDLGLPQQAGSVLVPPEQWDGRQRLTTAFGQGYTQTTLHT +AQMYQALANGGVLIPARLIDATVDGDGAEKRWESSAEPHRVVSEETAAQMLRMMETVVTQ +GTSKAAAIPGYRVGGKSSTAEAASDTGTYDGYNLGFTAVAPLDDPRFVVSVSLHRPPSKQ +GSRDVSVAAATIMEYMLRQADVPATGAEPNDYRVFVDDPQDRPW diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001142.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001142.fa new file mode 100644 index 0000000000000000000000000000000000000000..31f1fc2620257b842ff3968540b37c42963df123 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001142.fa @@ -0,0 +1,25 @@ +>PROKKA_01361 +MTLHEEMSMAAHARIAESLRPGSTPVAPARPTPQERTPLSVVPAPLPRSRSGVTVLCVLV +VLAALAAVLVMNITMSNRQYALLDLRQEQQAVTETNERLAEQVGHLEAPQNLAARADALG +MVAPAGTASVDAGTGQFSGEAQAAQDGDISATYVAPPADADAVRQGTAGDGQDEIEGPRT +LGGEDASAAPDQDAADR +>PROKKA_01081 +MTLHEEMSMAAHARIAESLRPGSTPVAPARPAPQERTPLSVVPAPLPRSRSGVTVLCVLV +VLAALAAVLVMNITMSNRQYALLDLRQEQQAVIETNERLAEQVGNLEAPQNLAARADALG +MVAPAGTASVDAGTGEFGGEAQAAQDGDVSATYVAPPADADVVRQGASAEGQDEIEGPRT +LGGEDASAAADQDAADR +>PROKKA_01532 +MTLHEEMSMAAHARIAEPLRHTGAPARPAPQERTPLSVVPAPLPRSRSGMTVLCVVVLLA +ALAAVLVMNITMSNRQYALLDLRQEQQAVTEVNERLAEQVGYLEAPQNVAARADALGMVA +PAGTASVDAATGEFRGEAQPAREGEISATFVAPPVNADAVRQGSAGSADADRGDIEGPRT +LGAPAAAPGAAASDDRDASDR +>PROKKA_01427 +MTAYEETGMSAQAWRDEARTAWPRTGATPEREHRQRTPLSVVPTPLPRSGSGVAVLCGLV +LLVALGLVLVMNITMSNRQFTLLDLRAQQTTLTETNERLAEQAGYLDAPQNLAARAGAMG +MVSPGATSTVDVASGAVAGPSTGAGSTTLPEGRIAPPADADLARQGEAQGQIPGPRTVDP +AAPTAAPSGETAPTPAPTDAPAGR +>PROKKA_01316 +MTLHEEMSMAAHARIAESLRPGSTPVAPARPTPQERTPLSVVPAPLPRSRSGVTVLCVLV +VLAALAAVLVMNITMSNRQYALLDLRQEQQAVTETNERLAERVGHLEAPQNLAARADALG +MVAPAGTASVDAGTGQFSGEAQAAQDGDISATYVAPPADADAVRQGTAGDGQDEIEGPRT +LGGEDASAAPDQDAADR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001143.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001143.fa new file mode 100644 index 0000000000000000000000000000000000000000..bd8e80de1a2f5bbc79545f255407dc921910d0c7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001143.fa @@ -0,0 +1,35 @@ +>PROKKA_01362 +MDAGQPRPEDRHLPVMRDRVVDLLAPAVQAALEAGRTPVAVDGTLGMGGHTEALLTRFPH +LRVIGIDRDVHAQAMAVERLGPLAERLIPFHGTYDRVPEAMAAAGVTKVDAALYDLGVSS +YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEQELRRIIRRDGEERFAGPIAR +AIVRARDEAPIETTGRLVEVIRSAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP +AILDALHVGGRLVVMSYHSLEDRITKRHLSAWATSTAPPGFPVVLEEHEPVVRVLTRGTE +KPTEEEISENRRASSARVRAVEKIRTSRTTA +>PROKKA_01082 +MDAGQPRPEDRHLPVMRDRVVDLLAPAVQAALEAGRTPVAVDGTLGMGGHTEALLTRFPH +LRVIGIDRDVHAQAMAAERLGPLADRLIPFHGTYDRVPEAMAAAGVTKVDAALYDLGVSS +YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEQELRRIIRRDGEERFAGPIAR +AIVRARAEAPIETTGRLVEVIRSAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP +AILDALHVGGRLVVMSYHSLEDRITKRHLSAWATSTAPPGFPVVLEEHEPVVRVLTRGTE +KPTEEEISENRRASSAKVRAVEKIRTSRTTA +>PROKKA_01531 +MDADQLRPEDRHVPVMRDRVVDLLAPAVQAALDAGRAPVAVDGTLGMGGHTEAMLTRFPE +LTVIGIDRDAHAQALAAERLGPLAERLVPFHGTYDLVPEAMAAAGVEKVDAALYDLGVSS +YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEHELRRIIRRDGEERFAGPIAR +AIVRARAEAPIETTGRLVEVIRTAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP +AILDALHVGGRLVVMSYHSLEDRIAKRHLSAWAASTAPPGFPVVLEEHEPVVRTLTRGTE +KPTEEEILENRRASSAKVRAVEKIRTSRTPA +>PROKKA_01426 +MDPTQPLPRDRHVPVMRDRVVDLLAPAVEAAAAAGRTPVAVDGTLGMGGHTEVLLRRFPT +LRVVGIDRDPNALAMAQERLGPLAERLVPFHGTYDQVPEALAAAGAERMDAALYDLGVSS +YQLDARERGFAYSYDAPLDMRMDTTAPVTAADLVAELDEQSLRRIIRRDGEDRFAGPIAR +AIVRAREEEPILTTGRLVDVIRAVVPVSAGNKGGHPAKRTFQALRIAVNEELDILDAAVP +AVLDALEVGGRLVVMSYHSLEDRIAKRHLQEWAASTAPPGFPVELPEHRPLVKVLTRGTE +KPTEEEIEENRRASSAKVRAVEKIRTSRTTA +>PROKKA_01317 +MDAGQPRPEDRHLPVMRDRVVDLLAPAVQAALEAGRTPVAVDGTLGMGGHTEALLTRFPH +LRVIGIDRDVHAQAMAVERLGPLAERLIPFHGTYDRVPEAMAAAGVTKVDAALYDLGVSS +YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEQELRRIIRRDGEERFAGPIAR +AIVRARDEAPIETTGRLVEVIRSAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP +AILDALHVGGRLVVMSYHSLEDRITKRHLSAWATSTAPPGFPVVLEEHEPVVRVLTRGTE +KPTEEEISENRRASSARVRAVEKIRTSRTTA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001145.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001145.fa new file mode 100644 index 0000000000000000000000000000000000000000..b88370a7de1d80ea5b021f925075fc51c09fdd99 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001145.fa @@ -0,0 +1,20 @@ +>PROKKA_01364 +MPLSEHEQRMLDQLEQQLRTEDPRLATQMADTGRHRLPVGRVVAGAVLAVVGLLVVVLGV +ANHAILLGVLGVVVIGAGIFLLTTRPRAVASGASGPEARRSGAPRRQGGGDFMGRLERRW +DERRAGGD +>PROKKA_01084 +MPLSEHEQRMLDQLEQQLRTEDPRLATQMADTGRHRLPVGRVVAGAVLAVVGLLVVVLGV +ANHAILLGVLGVVVIGAGIFLLTTRPRAVASGASGPEARRSGAPRRQGGGDFMGRLERRW +DERRAGGD +>PROKKA_01529 +MPLSEHEQRMLDQLEHQLRTEDPRLATQMADTRRDPVPVKRVVLGAVLAVVGLLVIVMGV +ANQLVPVGVLGALVVGAGIFLVTTRPRGGRAAGADRPGPGRGGRPGGGRPEGGRPGGDFM +GRLERRWDARREQGD +>PROKKA_01424 +MPLSDHEQRVLDELERQLHADDPSLASQLSTPRGPAPVRRIVLGAAMMLAGLAVVLVGVS +THLVVVGVLGAVLLGGGILVLTSRRVSASRAPGAPVAGDGGPHAGRRRGGLMDRLDREWD +SRGRADT +>PROKKA_01319 +MPLSEHEQRMLDQLEQQLRTEDPRLATQMADTGRHRLPVGRVVAGAVLAVVGLLVVVLGV +ANHAILLGVLGVVVIGAGIFLLTTRPRAVASGASGPEARRSGAPRRQGGGDFMGRLERRW +DERRAGGD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001146.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001146.fa new file mode 100644 index 0000000000000000000000000000000000000000..02f76255a5a1f79acade50fa24611eaab015eb67 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001146.fa @@ -0,0 +1,44 @@ +>PROKKA_01365 +MSETAPAAPRDEATILHVDMDAFFLSVELRERPDLEGRPAAVAAPSGRSVVLSASYAARA +YGVRSAMPLAHARALCPPLVVIPPRQQLYRAVSAEVMAVLADVTPVMEQLSVDEAFLDVA +GARRRLGPPEHIGHLIRERVRSALGLPCTVGGSAVKFVAKTASTAAKPDGLLIVPPERTL +DFLHPLPVGRLWGVGPKAAERLARRGVATIGDLARVDPARLEASFGAAGREWASLARGID +PRPVAPRPAARSIGADHTFDVDPVDVAGVDPEVLRLCHRVAARLRAEQATAGAVTVRLKA +PDGSVRSRTARLARPTATGHDLLGPARRLVRELHAERPHPVRLVGVRAERLGDEADQPPA +QEALFGGPAWGTEGEASEAGDWAGAEAALDAVARRFPTAAVRPASLLGRREARADARRDA +PRPGPGGPDRE +>PROKKA_01085 +MSESAPAAPRDEATILHVDMDAFFLSVELREQPDLEGRPAAVAAPSGRSVVLSASYAARA +YGVRSAMPLAHARALCPPLVVIPPRQQLYRAVSAEVMAVLADVTPVMEQLSVDEAFLDVA +GARRRLGPPEHIGHLIRERVRSALGLPCTVGGSAVKFVAKTASTAAKPDGLLIVPPQRTL +DFLHPLPVGRLWGVGPKAAERLARRGVATIGDLARVDPARLEASFGAAGREWASLARGID +PRPVAPRPAARSIGADHTFDVDPVDVAGVDPEVLRLCHRVAARLRAEQVTAGAVTVRLKA +PDGSVRSRTARLARPTATGHDLLGPARRLVRELHAERPHPVRLVGVRAERLGDEADQPPA +QEALFGGPAWGTEGEASEAGDWAGAEAALDAVARRFPTAAVRPASLLGRREARADARRDA +PRPGPGGPDRE +>PROKKA_01528 +MSDTAAAQARPEASILHVDMDAFFLSVELRERPDLTGRPAAVAAPSGRSVVLSASYEARA +YGVRSAMPLAHARALCPPLVVVPPRQDVYRSVSADVMALLGQVTPVLEQLSVDEAFLDVA +GARRRLGPPARIGGLIRRRVREELGLPCTVGAAGVKFVAKMASTAAKPDGLLVVPPERTL +EFLHPLPVGRLWGVGPKAAEALRRRGMATIRDLAAADPEQLERAFGAAGRSWAQLSRGID +PRPVAPRPAARSIGADHTFDVDPLDVAGVDLEVLRLCHRVAARLRAEEVAAGAVTVRLKD +PDGRVRSRTARLARPTTTAHGLLGPARRLVAELHAQRPHPVRLVGVRAERLTDADEPAPE +QEALFGGSGFGDDDAAEGGAGDWAGAEAAADAVARRFPTAAVRPASLLRRAAGRPDTRRD +VPGP +>PROKKA_01423 +MSAPDPGPAPSSPPPPRREPSILHVDMDAFFLSVERRERPELRGVPAAVAHPEGRSVVLS +ASYEARAYGVRSAMPLAQARALCPPLRVTPPRQELYRSTSARVMDLFGRVTPVVEQLSVD +EAFLDVAGARRLLGPPERIAALIRERVRAELGLPCTVGGAGVKFVAKMASTAAKPDGMLL +VPPQCTLAFLHPRPVGALWGVGPQAARRLRERGVETIGDLAARDPRWLREAFGAAGAAWA +ELAAGRDPRPVAPREPARSVGADHTFDVDARDPAALDREVLSLCHRVAARLRSGGHTAAA +VTVRVKDPALATRARTVRLPAPTASGRVLHAHAGPAVAGLLTERPHPVRLVGVRAERLSD +AEAHGAVQEALFAPEGHEGPTDDAGWRRAEEAADAVARRFPGAGVRPASLLGPPEGS +>PROKKA_01320 +MSETAPAAPRDEATILHVDMDAFFLSVELREQPDLEGRPAAVAAPSGRSVVLSASYAARA +YGVRSAMPLAHARALCPPLVVIPPRQQLYRAVSAEVMAVLADVTPVMEQLSVDEAFLDVA +GARRRLGPPEHIGHLIRERVRSELGLPCTVGGSAVKFVAKTASTAAKPDGLLIVPPERTL +DFLHPLPVGRLWGVGPKAAERLARRGVATIGDLARVDPARLEASFGAAGREWASLARGID +PRPVAPRPAARSIGADHTFDVDPVDVAGVDPEVLRLCHRVAARLRAEGVTAGAVTVRLKA +PDGSVRSRTARLARPTATGHDLLGPARRLVRELHAERPHPIRLVGVRAERLGGEADQPPA +QEALFGGPAWGTEGEASEAGDWAGAEAALDAVARRFPTAAVRPASLLGRREARADARRDA +PRPGPGGPDRE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001147.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001147.fa new file mode 100644 index 0000000000000000000000000000000000000000..e35acec6d8726e448dea8e7568b543e081a4280f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001147.fa @@ -0,0 +1,40 @@ +>PROKKA_01366 +MPADVAVPRPRPADQDRFRAAVADALDRLLAEHRDLARDVHPLTAPLVDAIADLTAGGKR +LRAVLAWLGWRAAGGEAEDPRIAEAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRRFE +SLHREAGWRHAAEHFGVSAAILAGDVALGMSETAFARVLAGTPREDRARAELERMRFGVM +AGQYLDVVAEMAPAARDAREAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDGLVTAFA +RVSLPFGMAFQYRDDLLGVFGDPATTGKPAGDDLREGKQTVLIARAVELLAPDEAAALDA +DLGDPDLGADRVAHWQGVLEACGARRAVEERVAALSHEAAGAVAGLLAHGVPEDVSAELT +QLIDAYTSRRH +>PROKKA_01086 +MPADVAVPRPRPRPADQDRFRAAVADALDRLLAEHRELARDIHPLTAPLVDAIADLTAGG +KRLRAVLAWLGWRAAGGEAEDPRIAEAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRR +FESLHREAGWRHAAEHFGVSAAILAGDVALGMSETAFARVLAGTPREDRARAELERMRFG +VMAGQYLDVVAEMAPAARDAREAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDGLVTA +FARVSLPFGMAFQYRDDLLGVFGDPATTGKPAGDDLREGKQTVLIARAVELLAPDEAAAL +DADLGDPDLGADRVAHWQAVLEACGARRAVEERVAALSHEAAGAVAGLLAHGVPEDVSTE +LTRLIDAYTPRRH +>PROKKA_01527 +MPVDAAVTRPRPADQDRFRAAVAEELTRTLDEHRERARAVHPLTVPLVDAVGDLAAGGKR +LRAVLGWLGWRAAGGDPENPRIARTGAALELFQAAALIHDDILDRSDTRRGMPSVHRRFE +AEHRASGWRHDAGHFGVSAAILAGDVALGMSETAFAAALEGAGRPARARDEFERMRFGVM +VGQYLDVAAEMAPPATDPAEAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDALVAAFA +EVSLPFGLAFQYQDDLLGVFGDPAATGKPAGDDLREGKRTVLIARAVALLSPADAAALDA +DLGDPGLSAERIAHWQRALEECGARQAVTDRVAALSARAAEAVGALEAHGVPADVRAELT +ALIEAATTRRH +>PROKKA_01422 +MPTPETASVSDFRAAVAERLTAVLDGHARGAARIHPDADPVVEAVSVLTSGGKRLRAVLC +WLGWRAAGGSPTDPRAAVAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRRFEARHREH +GWRHEAEHFGVSAAILAGDVALALSDSMFSRAIEGTPRAERARREMERMRFEVMVGQYLD +VAAEMAPPAADPAAAERAARAVVEHKSARYSAVHPLALGALLAGADDDLVAAFEAVSLPF +GMAFQLQDDLLGVFGDPAHTGKPAGDDLREGKRTVLVARAEALLPRGEAAALDAELGDPA +LSAERVAHWQRRLEEVGARTAVADEVDRLSAEARRGLERLAALGVGTDVRGELAELIDAY +TVRTA +>PROKKA_01321 +MPADVAVPRPRPADQDRFRAAVADALDRLLAEHRERARDVHPLTAPLVDAIADLTAGGKR +LRAVLAWLGWRAAGGEAEDPRIAEAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRRFE +SLHREAGWRHAAEHFGVSAAILAGDVALGMSETAFARVLAGTPREDRARAELERMRFGVM +AGQYLDVVAEMAPAARDAREAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDGLVTAFA +RVSLPFGMAFQYRDDLLGVFGDPATTGKPAGDDLREGKQTVLIARAVELLAPDEVAALDA +DLGDPDLGADRVAHWQAVLEACGARQAVEERVAVLSHEAAGAVAGLLAHGVPEDVSAELT +RLIDAYTSRRH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001149.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001149.fa new file mode 100644 index 0000000000000000000000000000000000000000..cddeaac0be7fb38cd8acdd0cf967f1dea0d4e250 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001149.fa @@ -0,0 +1,40 @@ +>PROKKA_01368 +MPRSAVPHTPVRSRCLRSVLTGGAVPLLLLTGLPAQAHAQEAAVHTVRPGDSLTRISAAR +GVSVADLLRFNGLGLETVLYPGDELRLTGAAAPAPAAGTYTVQPNDGWWVIARRTGVSAA +QLQRLNGMSASSMLHPGMVLTTQRTAAAPKAPASPAPTTTPATAPASTTPTAAGGTVRYT +VVSGDSLWGISQRFEVSIPRLRELNGLTRASTLHPGDVLVISDGTLEVEPVSAVQAVGDT +FLGRTYAPHVTASANENLRLLRAVPQPTPEQMQQIVRETAERMGVDPRLALGHAYTESRF +RMASVSPGNAVGAMQVIPITGEFASELVGRELNLLDPHDNAVAGVAFIKYVQDRTPTLDE +GIGAYYQGLGGVLDSGLNPEARDYVAKVRAAMAMF +>PROKKA_01088 +MPRSAVSHTPVRSRRLRSVLTGGAVPLLLLTGLPAQAHAQEAAVHTVRPGDTLTRISAAR +GVSVADLLRFNGLGLETVLYPGDELRLTGAAAPAPAVGTYTVQPNDGWWIIARRTGVSAA +QLQRLNGMSASSMLHPGMVLTTQRTAAAPKTPASTAPATTPASAPASTAPAAAGGTVRYT +VVSGDSLWGISQRFEVSIPRLRELNGLTRASTLHPGDVLVISDGTLEVEPVSAVQAVGDT +FLGRTYAPHVTASANENLRLLRSVPQPTPEQMQQIIRETAERMGVDPRLALGHAYTESRF +RMASVSPGNAVGAMQVIPITGEFASELVGRELNLLDPHDNAVAGIAFIKYVQDRTPTLDQ +GIGAYYQGLGGVLDSGLNPEARDYVAKVRAAMAMF +>PROKKA_01525 +MPRSSVSHTPSRRLRHALAGGAVPLLLLTGLPAQAQAQEAPVHTVRPGDTLTAISAAHGV +PLVDLFRLNGLDHESIIYPGDAIRLTGEAAPAAAAGTYTVQPDDGWWIIARRTGVSAAEL +QRLNGMSASTMLHPGMVLTTAGKAAAPAPTPAPPRCSLAPATRDVVRYAVVSGDSMWGIS +QRFEMSIPRLRELNGLTRSSMLHPGQVLVISDGTLEVEPVSDVQPIGDTFLGRTYPAHVT +ASANENLRLLQSVPQPSPEQMREIVRETAVRMDVDPRLALGHAYTESRFRMASVSPANAI +GAMQVIPITGEFASELVGRELNLLDPYDNAVAGVAYIKYVQDRTPTLDTGIGAYYQGLGG +VLQGGLSAEGRTYVATVRAAMAMF +>PROKKA_01420 +MPPARKVTPLMPQPAAPRASATTARRSLGLVAGGVVPLLMTGALPVAAQAAEAAHAAPRT +HTVRAGENPYRIAEAEGVRLSDLLRLNGLRADSVIYTGQVLALTGAPAPAAAPGTVEVER +GEGWWQVSRRAGVDAAVLQRINGLGARSMLHPGQILLTEAPARPTTPATPVAAAPAPVRQ +AAPTTYTVRNGDSMWSISQRVEVSIPRLRELNGLTWRSVLHTGDVLVIADGTEQAPVIDG +PVGSTFLSTTYAPHVTASANDNLRALQAVPQPSPAEVQALVRQTALELGVDPALALGHAY +TESRFQHASVSPGNAIGAMQVIPITGEFASQLVGRELNVLDVRDNVTAGVVLIKYLQEHT +DTVDQGISAYFTGLGGSDDPVKQQEARNYVARVKAAAAMF +>PROKKA_01323 +MPRSAVPHTPVRSHRLRSVLTGGAVPLLLLTGLPAQAHAQEAAVHTVRPGDSLTRISAAR +GVSVADLLRFNGLGLETVLYPGDELRLTGAAAPAPAAGTYTVQPNDGWWVIARRTGVSAA +QLQRLNGMSASSMLHPGMVLTTQRTAAAPKAPASPAPTTTPATAPASTAPTAAGGTVRYT +VVSGDSLWGISQRFEVSIPRLRELNGLTRASTLHPGDVLVISDGTLEVEPVSAVQAVGDT +FLGRTYAPHVTASANENLRLLRSVPQPTPEQMQQIVRETAERMGVDPRLALGHAYTESRF +RMASVSPGNAVGAMQVIPITGEFASELVGRELNLLDPHDNAVAGVAFIKYVQDRTPTLDE +GIGAYYQGLGGVLDSGLNPEARDYVAKVRAAMAMF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001150.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001150.fa new file mode 100644 index 0000000000000000000000000000000000000000..5617450aee7f2ac0640f60ea52999d2ee14b764d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001150.fa @@ -0,0 +1,45 @@ +>PROKKA_01370 +MTEDPREKILAFGTAISEGAADIPGLDHWRSLPIAQAPSWADEADHRAAVAELSALPPLV +FAGEVDLLRARLADVAQGRAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM +PVVKMGRIAGQFAKPRSSDTETRDGVTLPSFRGEIVNGYEFTEQARRHDARRMVQAYHTS +ASTLNLVRAFTQGGFADLRSVHQWNQGFMANPAYAQYEEMAAEIDRAVRFMNAAGVDFEA +MRRTEFYSAHEALLLDYERALTRVDSRSGDPYATSAHFLWIGERTRQVDGAHVDFLSRVR +NPIGVKLGPTTTVADALELAERLDPEREPGRLTFITRMGAERIRDVLPGIVEGVRDAGLE +PVWVTDPMHGNTVTAANGYKTRRFEDVMDEVSGFFEVHRELGTHPGGMHVELTGDDVAEC +LGGSDPINEADFDARYETLCDPRLNHQQSLEMAFKVTEALSHPERRAPRA +>PROKKA_01090 +MTEDPREKILAFGTAISEGAADIPGLDHWRSLPIAQAPSWADEADHRAAVAELSALPPLV +FAGEVDLLRARLADVAQGRAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM +PVVKMGRIAGQFAKPRSSDTETRDGVTLPSFRGEIVNGYEFTEQARRHDARRMVQAYHTS +ASTLNLVRAFTQGGFADLRSVHQWNQGFMANPAYAQYEEMAAEIDRAVRFMNAAGVDFEA +MRRTEFYSAHEALLLDYERALTRVDSRSGDPYATSAHFLWIGERTRQVDGAHVDFLSRVR +NPIGVKLGPTTTTADALELAERLDPEREPGRLTFITRMGAERIRDVLPGIVEGVRDAGLE +PVWVTDPMHGNTVTAANGYKTRRFEDVMDEVSGFFEVHRELGTHPGGMHVELTGDDVAEC +LGGSDPINEADFDARYETLCDPRLNHQQSLEMAFKVTEALSHPERRAPRA +>PROKKA_01522 +MTEDPREKILAFGTAISEGAADIPGLDHWRSLPVAQAPSWADEAEHRAAVAELSQVPPLV +FAGEVDLLRARLADVAQGRAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM +PVVKMGRIAGQFAKPRSSDTETRDGVTLPSFRGEIVNGYEFTEEARRHDARRMVQAYHTS +ASTLNLVRAFTQGGFADLRSVHQWNQGFMANPAYAQYEEMAAEIDRAVRFMNAAGVDFEA +MRRTEFYSAHEALLLDYERALTRVDSRSGDPYATSAHFLWIGERTRQVDGAHVDFLSRVR +NPIGVKLGPTTSAADALELAERLDPEREPGRLTFITRMGAERIRDVLPGIVEGVRDAGLE +PVWVTDPMHGNTVTAANGYKTRRFEDVMDEVSGFFEVHRALGTRPGGMHVELTGDDVAEC +LGGSDPINEADFDARYETLCDPRLNHQQSLEMAFKVTEALSHPERVAPRR +>PROKKA_01418 +MHEDPRDQIMAFGTAISEGAAPDPALDAWRELPIKQAPTWADEDDFRAAVAELSQVPPLV +FAGEVDVLRTRLADVARGQAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM +PVVKMGRIAGQYAKPRSSDTETRDGVTLPSFRGEIVNGFEFTEEARRHDARRMVTAYHTA +SSTLNLVRAFTQGGFADLRSVHQWNRGFMENPAYAQYEQIAAEIDRAVRFMDAAGADFEA +MRRTEFYAAHEALLLDYERALTRLDSRTGLPYATSAHFLWIGERTRDVDGAHVDFLSRVR +NPIGVKLGPTTTVDDVRALADRLDPEREPGRLTFITRMGADKVRDVLPGIVAGVRDEGLQ +PVWVTDPMHGNTVTAANGYKTRRFEDVMDELTGFFEVHRELGTHPGGMHVELTGDDVAEC +LGGSDPVDEADFDEHYETLCDPRLNHQQSLELAFKVTDALAHPHQD +>PROKKA_01325 +MTEDPREKILAFGTAISEGAADIPGLDHWRSLPIAQAPSWADEADHRAAVAELSALPPLV +FAGEVDLLRARLADVAQGRAFLLQGGDCAETFAGSTANRISARVKTILQMAAVLTYGASM +PVVKMGRIAGQFAKPRSSDTETRDGVTLPSFRGEIVNGYEFTEQARRHDARRMVQAYHTS +ASTLNLVRAFTQGGFADLRSVHQWNQGFMANPAYAQYEEMAAEIDRAVRFMNAAGVDFEA +MRRTEFYSAHEALLLDYERALTRVDSRSGDPYATSAHFLWIGERTRQVDGAHVDFLSRVR +NPIGVKLGPTTTVADALELAERLDPEREPGRLTFITRMGAERIRDVLPGIVEGVRDAGLE +PVWVTDPMHGNTVTAANGYKTRRFEDVMDEVSGFFEVHRELGTHPGGMHVELTGDDVAEC +LGGSDPINEADFDARYETLCDPRLNHQQSLEMAFKVTEALSHPERRAPRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001152.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001152.fa new file mode 100644 index 0000000000000000000000000000000000000000..239e5c6d177bfd77f0b1795ff9b0f0b9901c20f1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001152.fa @@ -0,0 +1,30 @@ +>PROKKA_01372 +MPRPVAVAPEDLPLRLMPAAPARRDHCVVLLHGFTSTPASVRAWAEGLAAGGSPVSVPLL +PGHGTRWEDLAATGADEIRAAVRAVVDLELARHGRVVMAGISMGGALALDAAAHRPVAGV +LVVNPALRFASPLAPFAPLLAPFVPTVAPIADDIADPTARERAYPRTPVAGVAALGRIQR +AARRALPRITAPVTVYRSARDAVVPASSHRTLVRGLRQAPVEVVGLPRSRHVATLDYDLP +LLIDHGRSAVAAMTTH +>PROKKA_01092 +MPRPVAVAPEDLPLRLMPAAPARRDHCVVLLHGFTSTPASVRAWAEGLAAGGSPVSVPLL +PGHGTRWEDLAATGADEIRAAVRAVVDLELARHGRVVMAGISMGGALALDAAAHRPVAGV +LVVNPALRFASPLAPFAPLLAPFVPTVAPIADDIADPTARERAYPRTPVAGVAAVGRIQR +AARRALPRITAPVTVYRSARDAVVPASSHRTLVRGLRQAPVEVVGLPRSRHVATLDHDLP +LLIDHGRSAVAAMTTH +>PROKKA_01520 +MDRPVPPVEPAPPAVPAPAVDPVHLPLRLAPGSGAGADRCVVVLHGFTSGPDSVRAWAEG +IAAGGSHVSVPLLPGHGTRWQDLAATGADEIRGAVRETVDRELSRHRHVVVAGISMGGAL +ALDAAAHRPVSAAIVVNPALRFASPLAPLAPALAPFVPSVAPIANDIADPDARELAYPRT +PVAGVAAVGRIQRAARRALPRITAPVTVFRSARDAVVPAASHRTLLRGLRRAPVDVVPLP +RSRHVATLDYDLPLLIERSRAAVEAATRA +>PROKKA_01416 +MTRLRPAAPDRRPAPGVDPAQRPFRLPATSLPGVAVVMLHGFTSGPDSVRAWAEGVAAGG +AAVHVPLLPGHGTRWEDLGTTDADELRAAVRDAVDAALATHRRVVVAGISMGGALALDAA +AHRDVAGVLVVNPALRFGSPLAVAAPLLRHVVPSVPSIAGDIADPDARELAYERAPVAGV +AQVGRIQTAARRGLGRITAPVTVFRSAEDAVVPERSHHTLLRGLTAAPVEVVRLLHSRHV +ATLDRDLPLLVARSRDAVAAAAR +>PROKKA_01327 +MPRPVAVAPEDLPLRLMPAAPARRDHCVVLLHGFTSTPASVRAWAEGLAAGGSPVSVPLL +PGHGTRWEDLAATGADEIRAAVRAVVDLELARHGRVVMAGISMGGALALDAAAHRPVAGV +LVVNPALRFASPLAPFAPLLAPFVPTVAPIADDIADPTARERAYPRTPVAGVAALGRIQR +AARRALPRITAPVTVYRSARDAVVPASSHRTLVRGLRQAPVEVVGLPRSRHVATLDYDLP +LLIDHGRSAVAAMTTH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001158.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001158.fa new file mode 100644 index 0000000000000000000000000000000000000000..58b94e345307110e06bc0404d0c6a241b928fdb0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001158.fa @@ -0,0 +1,30 @@ +>PROKKA_01378 +MIDPRPLPDAVPTARPAGRLGIGEVVAALEAEFPGVTASKVRFLEDRGLVLPERTPAGYR +RFRPEDVDRLRFVLALQRDHFLPLKVIADHLAALDRGERPTGLPGTAAVPASSDAARLGR +EVAGGRRSWTRAELAAESGAGEELLAELDQYSLLPVDPDGGYPSHAMDVARAAVVLAGHG +LEPRHLRPLRAAADRELGLVERAVAPLQARRDAGTRPRVARSAREIAQASLRLHAALVAV +GLEQWDD +>PROKKA_01098 +MTDPRPRPDAVPTARPAGRLGIGEVVASLEVEFPGVTASKVRFLEDRGLVLPERTSAGYR +RFRPEDVDRLRFVLALQRDHFLPLKVIADHLAALDRGERPTGLPGTAAAPASSDAERLGR +EVAGGRRSWTRAELAAESGAGEELLAELDQYSLLPVDPDGGYPSHAMDVARAAVVLAGHG +LEPRHLRPLRAAADRELGLVERAVAPLQARRDAGTRPRVARSAREIAQASLRLHAALVAV +GLEQWDD +>PROKKA_01514 +MTEPQHADAGPRTRPAGRLGIGEVVAALKSDFPGVSASKVRFLEDRGLVLPERTPAGYRR +YRPEDVDRLRFVLTVQRDHFLPLKVIAAQLAALDRGEVPADLPGGVVAPGASDASRLGRE +VAAGRRGWTRSELAEESGAGEELLAELDQYSLLPADEDGAYSSHAMEVARAAVVLAGHGL +EPRHLRPFRAAADRELGLVERAVAPLQARRDANMRPRVARSAQEIAQASLRLHSALVAEG +LEQWDDGAVG +>PROKKA_01409 +MSAPHEPSAAPPPAGAALGIGDLVAALEPSFPGVSASKVRFLEDRGLVRPERTAAGYRRY +RPADVDRIRLVLTLQRDRFLPLKVIREHLDALDRGERPEDLGEAPAAAQEAVRLGHGIAD +PDRRWTRAELAREAEVPAPLVDELDQYALLPRAEDGLHPPAALGVVRAAGRLAAHGIEPR +HLRPFRAAADRELGLVQSAVAPLATRRDAGTRERAARTAEEIATACLALHAALVRAGLES +LDG +>PROKKA_01333 +MTDPRPRPDAVPTARPAGRLGIGEVVASLEVEFPGVTASKVRFLEERGLVLPERTSAGYR +RFRPEDVDRLRFVLALQRDHFLPLKVIAEHLAALDRGERPTGLPGTAAAPASSDAERLGR +EVAGGRRSWTRAELAAESGAGEELLAELDQYSLLPVDPDGGYPSHAMDVARAAVVLAGHG +LEPRHLRPLRAAADRELGLVERAVAPLQARRDAGTRPRVARSAREIAQASLRLHAALVAV +GLEQWDD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001159.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001159.fa new file mode 100644 index 0000000000000000000000000000000000000000..dec85a8512aa6193672571401495ea800b8fc105 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001159.fa @@ -0,0 +1,20 @@ +>PROKKA_01379 +MNQPGREPDLSTSAINLTELAPLVSADLTREESDAIRALPAGSALLLAHEGPDQSARFLL +DKDVVSVGRHPDADIFLDDVTVSRRHAEFRAEDGGHRLVDLNSLNGTFVNHDRVDEILLR +SGMHVQIGKYRLTYYAAPARG +>PROKKA_01099 +MNQPGREPDLSTSAINLTELAPLVSADLTREESDAIRALPAGSALLLAHEGPDQSARFLL +DEDVVSVGRHPDADIFLDDVTVSRRHAEFRAEDGGHRLVDLNSLNGTFVNHDRVDEILLR +SGMHVQIGKYRLTYYAGPARG +>PROKKA_01513 +MNQPGREPDLSTSSINLTELAPLVAADLSAEESDAIRALPAGSALLLADGGPEKAARFLL +DQDVVTVGRHPDADIFLDDVTVSRRHAEFRAEAGGHRLVDMNSLNGTFVNHDRVDDVLLR +SGTHVQIGKYRLTYFTSTQRG +>PROKKA_01408 +MTQQEPSLHTSSISLTDLAPVAETGLSPEETAAVRALPAGAALLVAHEGPDAGARFLLDT +PVVTVGRHPESDILLDDVTVSRRHAEFRAVDGGHELVDLSSLNGTYVNNDRVDQVRLRTG +MQLQIGRYRLSYHAAEPA +>PROKKA_01334 +MNQPGREPDLSTSAINLTELAPLVSADLTREESDAIRALPAGSALLLAHEGPDQSARFLL +DEDVVSVGRHPDADIFLDDVTVSRRHAEFRAEDGGHRLVDLNSLNGTFVNHDRVDEILLR +SGMHVQIGKYRLTYYAGPARG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001160.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001160.fa new file mode 100644 index 0000000000000000000000000000000000000000..754909c6424780875f75934e7e3c17d9795f7536 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001160.fa @@ -0,0 +1,20 @@ +>PROKKA_01380 +MSSIPEGLKYSAEHEWIAEAGAAGTVRVGITDFAQDALGDVVYVDLPEVGTEVTAGTAVG +EVESTKSVSDIYAPVSGTVAAVNDELDGEPGLVNSAPYEGGWLFEITLADEAQLEGLMDA +EGYASHTS +>PROKKA_01100 +MSSIPEGLKYSAEHEWIAKAGAAGTVRVGITDFAQDALGDVVYVDLPEVGTEVTAGTAVG +EVESTKSVSDIYAPVSGTVAAVNDELDGEPGLVNSAPYEGGWLFEITLADEAQLEGLMDA +EGYASHTS +>PROKKA_01512 +MSSIPEGLKYSAEHEWIAEAGQAGTVRIGITDFAQDALGDVVYVDLPEVGSEVTAGTAVG +EVESTKSVSDIYAPVTGTVAAVNEDLDGEPGLVNSAPYEGGWLFEVTLADEAQLEGLLDA +EGYASHTS +>PROKKA_01407 +MSSIPEGLKYSTDHEWAQDAAEPGVVRVGITDFAQDALGDVVYVDLPSVGDEVTAGAAIG +EVESTKSVSDIMAPVSGTVTAVNEELDGEPALVNSAPYEGGWLVEIKLSDPAEVDGLLDA +AGYAAHVG +>PROKKA_01335 +MSSIPEGLKYSAEHEWIAEAGAAGTVRVGITDFAQDALGDVVYVDLPEVGTEVTAGTAVG +EVESTKSVSDIYAPVSGTVAAVNDELDGEPGLVNSAPYEGGWLFEITLADEAQLEGLMDA +EGYASHTS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001164.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001164.fa new file mode 100644 index 0000000000000000000000000000000000000000..ac72de05181e4cfdb5d6f4392b04f4e8d3f7928a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001164.fa @@ -0,0 +1,40 @@ +>PROKKA_01406 +MSAPAESAAKLGDGPAGIPQPVLVRGTGLLGASIGIGLSAAGVDVRLHDPSPAALAVAAD +IRAGRPARLDAEGDDLDVAPGLVVVAAPPDVTADVVVDSLRRWPAAVVVDIASVKEAVAA +GVRAAVDDGRLAPQDADRYLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTHPGALA +AGRALARTLQATPYRMAARAHDESVALISHLPQIAASLVASRLQDTPDQALALAGNGLRD +TTRIAASDPQLWVQILSGNAGRIVPALHGLRADLDRLIRTLEDPSAPGARLDMAQLIAEG +NAGRARVPGKHGAPPQAFAVVTVIVDDAPGQIAALLDEVGRTDVNVEDLRLEHASGHRVG +MVEISVLPGRRDELVAALTAAGWKVV +>PROKKA_01136 +MSAPAESAAKLGDGPAGIPQPVLVRGTGLLGASIGIGLSAAGVDVRLHDPSPAALAVAAD +IRAGRPARLDAEGDDLDVAPGLVVVAAPPDVTADVVVDSLRRWPAAVVVDIASVKEAVAA +GVRAAVDDGRLAPQDADRYLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTHPGALA +AGRALARTLQATPYRMAARAHDESVALISHLPQIAASLVASRLQDTPDQALALAGNGLRD +TTRIAASDPQLWVQILSGNAGRIVPALHGLRADLDRLIRTLEDPSAPGARLDMAQLIAEG +NAGRARVPGKHGAPPQAFAVVTVIVDDAPGQIAALLDEVGRTDVNVEDLRLEHASGHRVG +MVEISVPPGRRDELVAALTAAGWKVV +>PROKKA_01490 +MSAAAETAAAVPGALPAGIPQPVLVRGTGLLGASIGIGLSAAGADVLLHDLSPAALAVAA +DIGAGRPMRIDDDGADAGPAPALVVVAAPPDVTADVVVDSLRRWPEALVLDIASVKEAIA +AGVRAAVDDGRLGPSDPDRHLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTLPAAV +QAGRALALALRATPYRMDARAHDESVAMISHLPQIAASLVAARLQDTPDQALALAGNGLR +DTTRIAASDPQLWVQILSGNAERIVPALHGLRDDLDRLIRTLEAPGAPGSRLDMARLIAE +GNAGRARVPGKHGAPPQAFAVVTVIVDDTPGQIAAVLDEVGRTDVNVEDLRLEHASGHRA +GMVDISVLPGRRDELVAALSAAGWKVV +>PROKKA_01401 +MIPAEGGAGPAGLSGPVLVRGTGLLGASIGLGLRAAGADVLLDDPSPTALAVARDIGAGA +VVDLDDPALAPGLVVVGAPPDVTPAVVVDSLRRWPHAVVTDIASIKGAILAEVREAATRG +DIAPGDVARYLPGHPMAGSERSGPVAARGTLFTASPWVLCPAAETDPAALAAGEALARTL +QATVHRMSAADHDASVALISHLPQIAASLVASRLQDAPDPSLALAGNGLRDTTRIAASDP +HLWVQILAGNAPQIVPTLHGLREDLDRLIGTLEAPSAPGARLDVARLIAEGNAGRARIPG +KHGAPPQAFALVTVIVDDTPGQLAALFEEIGRAGVNVEDIRLDHASGYRVGMVDVSVLPG +RKDELVSALTDAGWKVV +>PROKKA_01356 +MSAPAESAAKLGDGPAGIPQPVLVRGTGLLGASIGIGLSAAGVDVRLHDPSPAALAVAAD +IRAGRPARLDAEGDDLDVAPGLVVVAAPPDVTADVVVDSLRRWPAAVVVDIASVKEAVAA +GVRAAVDDGRLAPQDADRYLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTHPGALA +AGRALARTLQATPYRMAARAHDESVALISHLPQIAASLVASRLQDTPDQALALAGNGLRD +TTRIAASDPQLWVQILSGNAGRIVPALHGLRADLDRLIRTLEDPSAPGARLDMAQLIAEG +NAGRARVPGKHGAPPQAFAVVTVIVDDAPGQIAALLDEVGRTDVNVEDLRLEHASGHRVG +MVEISVLPGRRDELVAALTAAGWKVV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001170.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001170.fa new file mode 100644 index 0000000000000000000000000000000000000000..b705a9fbeca3a9fa4e49f41706aa73e33fcaacbc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001170.fa @@ -0,0 +1,40 @@ +>PROKKA_01416 +MTETEIKKGLAGVVVDTTAISKVNPETNSLLYRGYPVQDLAAQLSFEAVALLLWTGELPT +DEELAAFEHFERAHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE +LEKAQALFAAFPAVVAYDQRRRRGQDVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS +MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK +EESRQDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML +GLYDGLQSAMDEAKQIKPNLDYPAGPTYHLMGFDTEMFTPLFIASRITGWTAHIMEQRAA +NALIRPLSAYDGPEQRELPAG +>PROKKA_01147 +MTETEIKKGLAGVVVDTTAISKVNPETNSLLYRGYPVQDLAAQLPFEAVALLLWTGELPT +DEELTAFERFERTHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE +LEKAQALFAAFPAVVAYDQRRRRGQEVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS +MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK +EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML +GLYDGLEQAMDEAKQIKPNLDYPAGPTYHLMGFDTELFTPIFIASRITGWTAHIMEQRAA +NALIRPLSAYDGPEQRELPAG +>PROKKA_01483 +MTETEIKKGLAGVVVDTTAISKVNPDTNSLLYRGYPVQDLAAKLPFESVALLLWNGELPT +DEELAEFQRFERAHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE +LEKAKALFAAFPAAVAYDQRRRRGQDVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS +MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK +EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML +GLYDGLQSAMDEAKQIKPNLDYPAGPTYHLMGFDTEMFTPLFIASRITGWTAHIMEQRAA +NALIRPLSSYDGPEQRELPAG +>PROKKA_01390 +MTETEIKKGLAGVVVDTTAVSKVNPETNSLLYRGYPVQDLAAQLPFEAVALLLWNGELPT +DAELEEFQRFERAHRALDPEVKAAVDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE +LEKAKALFAAFPAVVAYDQRRRRGQEVVEPRADLDYAQNFLWMSFGEEAAPEVVDAFRVS +MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK +EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML +GLYDGLEQAMDEAKQIKPNLDYPAGPTYHLMGFDTEMFTPIFIAARITGWTAHIMEQRAA +NALIRPLSAYNGPEQRELPGK +>PROKKA_01366 +MTETEIKKGLAGVVVDTTAISKVNPETNSLLYRGYPVQDLAAQLSFEAVALLLWTGELPT +DEELAAFERFERAHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE +LEKAQALFAAFPAVVAYDQRRRRGQDVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS +MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK +EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML +GLYDGLEQAMDEAKQIKPNLDYPAGPTYHLMGFDTELFTPIFIASRITGWTAHIMEQRAA +NALIRPLSAYDGPEQRELPAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001171.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001171.fa new file mode 100644 index 0000000000000000000000000000000000000000..6dd0b0ccb5068e5e2699541256290283bbacff52 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001171.fa @@ -0,0 +1,35 @@ +>PROKKA_01418 +MSADPAPRGSRGGRGAESALAAPFRRHLEHLAVERGLAANTLAAYRRDLERYRRWLEAQG +VRAPADVDPGHVSGFLRALGTGEDGGRPLAVRSAARVLAAVRGLHRFWALEGLTPADPAL +DVHPPKPGARLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARISEVVGLDVD +DVVGLAQTGDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGRPTIMAGAARSTPA +LFVNACGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLAGGADVRVVQELLG +HASVTTTQVYTLVTVDSLREVYSAAHPRAR +>PROKKA_01149 +MSTDPAARGSGEAEARGGRGAESALAAPFRRHLEHLAVERGLAANTLAAYRRDLERYRRW +LEAHGVRAPADVDPGHVSGFLRALGTGEDGGRPLAVRSAARVLAAVRGLHRFWALEGLTP +ADPARDVHPPKPGDRLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARISEVV +GLDVDDVVGLAQTGDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGRPTIMTGVT +RSTPALFVNARGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLAGGADVRVV +QELLGHASVTTTQVYTLVTVDSLREVYSAAHPRAR +>PROKKA_01481 +MSTDPAARGSGEAEARGSRGGRGAESALAAPFRRHLEHLAVERGLAANTLAAYRRDLERY +RRWLEAHGVRAPADVDPGHVSGFLRALGTGEDGGRPFAVRSAARVLAAVRGLHRFWALEG +LTPADPARDVHPPKPGDRLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARIS +EVVGLDVDDVVGLAQTGDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGRPTIMT +GAARSTPALFVNARGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLAGGADV +RVVQELLGHASVTTTQVYTLVTVDSLREVYAAAHPRAR +>PROKKA_01389 +MSASPELHRALDRHLDHLAVERGLASATLAAYRRDLGRYLAWLEASRVDRPADVDPGHVA +GFLSALGTGDDGGRPLGARSAARVLSAVRGMHRFWALEGLTPTDPAADVAPPRPPERLPK +ALPVETVTRILEAVPTAEPADLRDRALLEFLYGTGARVSEAVGLDVDDVVGVAGDRGAGR +GDDDRLPVVRLFGKGSKERLVPVGSHAADALAAWLVRGRPALAAAATRPVPALFLNLRGG +RLSRQSAWSILKAAAERAGVAQDVSPHTLRHSFATHLMQGGADVRVVQELLGHASVTTTQ +VYTRVTAEALREVYASAHPRARWTT +>PROKKA_01368 +MSPHAPQTSALAAPFRRHLDHLAVERGLAENTLAAYRCDLARYRRWLEAAGVRAPGDVDP +GHVAGFLQALATGDDGGRPLAVRSAARVLAAVRGLHRFWALEGLTPADPARDVHPPKPGD +RLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARISEVVGLDVDDVVGLAQTG +DDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGRPTIMTGVTRSTPALFVNARGGR +LSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLAGGADVRVVQELLGHASVTTTQV +YTLVTVDSLREVYSAAHPRAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001173.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001173.fa new file mode 100644 index 0000000000000000000000000000000000000000..d0b4b22125c678c81171e1688c7f8ed37ddf5c96 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001173.fa @@ -0,0 +1,55 @@ +>PROKKA_01420 +MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSS +RAVVDAGVRVTADHAALRLAQEAGAVVDEGDNGTHDLVLSRSVTASGDGTRSRATAGGRS +VPVGLLSEIGATLVAVHGQNDQVRLQGADAQRHALDAFGGAELAAALRAYRADHAAWTAA +RREREELTAHRQERAREAEALQRSLEEIDLAEPREGEDEELRALIRRLEDVEELRAASGE +AHARLAGPDVDAMDETPGAVSLVEAARQAVLAAPGDDPDLAAAAARLAEAAVVLTDIAGD +LARYTADLDADAASDLDAAQSRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGR +LEELEAEVDRLDAALRERAATLTALRTAAAERLETAVTEELHALFMPDASFHVGLTPVAG +DGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV +DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV +TLTADERVEELARMLAGHGDSAAAREHARELLESSARERG +>PROKKA_01151 +MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSS +RAVVDAGVRLPEAHAALALAEDAGAVLDEADEGVRELVLSRSVTASGEGTRSRAAAGGRT +VPVGLLAEIGATLVAVHGQNDQVRLQGADAQRHALDAFGGAELAAALRAYRADHAAWTAA +RREREELTAHRQERAREAEALQRSLEEIDLAEPQEGEDEELRALIRRLEDVEELRAASGE +AHARLAGPDVDTMDETPGAVSLVEAAQQAVLAAPGDDPELAAAAARLAEAAVVLTDIAGD +LARYTADLDADAASDLDAAQSRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGR +LEELEAEVDRLDAALRERAATLTALRTAAAERLETAVTEELHALFMPDASFHVGLTPVAG +DGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV +DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV +TLTADERVEELARMLAGHGDSAAAREHARELLESSARERG +>PROKKA_01479 +MIEHLRISGLGVIGEATVDLDPGLTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGAA +RAVVDAGVRLPEAHAALALAEDAGAVLDEADDGVRELVLSRSVTASGEGTRSRAAAGGRT +VPVGLLAEIGATLVAVHGQNDQVRLQGAEAQRRALDAFGGAELAASLRAYRADHAAVSAA +RRERDELTAHRQERAREAEALQRSLEEIDLAEPLAGEDAELRELIRRLEDVEELRAASGE +AHARLAGAEMDALEETPGAVSLVEGARQAVLAAPGDDPALAAAAERLAEAAVVLTDIAAD +LARYTADLDTDAASDLDAAQSRLAELTRLQRLYGPELEDVIGWAETQRPRLDELQGDSGR +LEELEGELERLESALRERAAALTALRTAAAGRLEEAVTQELHALFMPDASFHVDLAPVGG +DGLGPHGAEDVALALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV +DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV +TLSAEERVEELARMLAGHGDSAAAREHARELLEASARERG +>PROKKA_01387 +MIDWMQITGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGRRADAGAVRRGSR +RAAVDAGVRLPADHPALSLAVEAGAVLDDAGDGSADLVLSRSVTASGDGTRSRAGLGGRA +VPVGVLAEVGSALVAVHGQNDQVRLQSAAAQRHALDAFGGPQLVAAAAAYRADHTAYVAA +RRERDLLVERQQERAREAEALQRGLEEIDRAEPEAGEDETLRALIRRLEDVEELRAAADG +GHAHLAGPDIESGDDLPGAITLVESARAAVQAAPGDDPELAAAAGRLAEASVILGDIAAD +LARFSADLDGDAVSDLDAAQTRLAELSRLQRLYGPELTDVLAWAEAQRPRLEELQGDSGR +IDELEADLARLDASRRERAAELTTLRTAAAGRLEQAVTAELHALFMPDASFHVSLVPLDD +GDPGPHGAEDVALALRPHAGAEPRPLGRGASGGELSRVMLALEVVLAETDPVPTFVFDEV +DAGVGGEAAVSIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPEAGVTTSDVV +TLGQQERVDELARMLAGHGDSAAARAHARELLEASAAERA +>PROKKA_01370 +MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSS +RAVVDAGVRLPEAHAALALAEDAGAVLDEADEGVRELVLSRSVTASGEGTRSRAAAGGRT +VPVGLLAEIGATLVAVHGQNDQVRLQGADAQRHALDAFGGAELAAALRAYRADHAAWTAA +RREREELTAHRQERAREAEALQRSLEEIDLAEPQEGEDEELRALIRRLEDVEELRAASGE +AHARLAGPDVDAMDETPGAVSLVEAARQAVLAAPGDDPELAAAAARLAEAAVVLSDIAGD +LARYTADLDADAASDLDAAQSRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGR +LEELEAEVDRLDAALRERAATLTALRTEAAERLETAVTEELHALFMPDASFHVGLTPVAG +DGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV +DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV +TLTADERVEELARMLAGHGDSAAAREHARELLESSARERG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001174.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001174.fa new file mode 100644 index 0000000000000000000000000000000000000000..abc68ecfcd367415a73a6bca4535dfe890afdb7c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001174.fa @@ -0,0 +1,40 @@ +>PROKKA_01421 +MPYTPGRRILVLTHTGREDAISAALQATRMFAEEGLVTVMLEQDVAAIRAAAGDPPEFAP +ETLGVDCELEDITLGLVLGGDGSVLRAADFVRGYNVPLLAVNLGHVGFLAESERTDLHRT +VQAIASESYVVIERMALDVVVHVEGREVARTWALNEASVEKSHRERMLEVVVSVDNSPLT +SFGCDGVVLATPTGSTAYAFSAGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD +VLTRTRETGVLWCDGRRTVELPPQARVEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG +WRGPVTAQERAGVLHEVETVEPRHAGPRPDVVEPATMPLSVPSPADIQRHRDRGARHPGE +DA +>PROKKA_01152 +MPYTPGRRVLVLTHTGREDAISAALQATRMFAEEGLVSVMLEQDVAAIRAAAGDPPEFAP +EALGVDCELEDITLGLVLGGDGSVLRAADFVRGHNVPLLAVNLGHVGFLAESERTDLHRT +VQAIASESYVVIERMALDVVVLVEGREVARTWALNEASVEKSHRERMLEVVVSVDNSPLT +AFGCDGVVLATPTGSTAYAFSGGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD +VLTRTRETGVLWCDGRRTVELPPQARIEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG +WRGPVTAQERAGVLHAVETVEPRHAGPRPDVVEPATMPLSVLSPADIQRHRDRGARHPGE +DA +>PROKKA_01478 +MPHNPGRRVLVLAHTGREDAISAALQATRILEEEGLVSVMLEQDVAAIRENADAPAGFAP +QTLGVDCGLEDIVLGLVLGGDGSVLRAADFVRGYDVPLLAVNLGHVGFLAESERTDLQRT +VQAIASEAYVVIERMALDVVVRVEDREVARTWALNEASVEKSNRERMLEVVISVDNAPIS +SFGCDGVVLATPTGSTAYAFSGGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD +VLTRTRETGVLWCDGRRTVELPPQARIEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG +WRGPVTAQEREAVLREVETVEPRHAGPRPDVVEPATMPLSVLSAADIQRYRDRGARYPGE +DA +>PROKKA_01386 +MSETPSRRVLVLAHTGRADAIAAALQATAMLAEEGLDTVMLAEDVAAILESGTDAVGFRP +LTLGRDCTLDDVQLGLVLGGDGSVLRAADFVRGHGIPLVAVNLGHVGFLAESERTDLHRT +VKAIADGAYVVIERMALDVTVRVEGREVARTWALNEASVEKSNRERMLEVVVSVDDSPLT +SFGCDGVVLASPTGSTAYAFSAGGPVVWPGVEALLCVPISAHALFSRPLVVGPHSTVAVD +VLTRTRETGVLWCDGRRTVELPPRARIEVTRSAEPVRLARLRPTPFAERLVRKFRLPTEG +WRGPVTEADRRTGPLAEVETVEPRHAAPRPDVVPPPSEPLTVLSPEALARYRGRDGREGD +RTS +>PROKKA_01371 +MPYTPGRRVLVLTHTGREDAISAALQATRMFAEEGLVSVMLEQDVAAIRAAAGDPPEFAP +EALGVDCELEDITLGLVLGGDGSVLRAADFVRGHNVPLLAVNLGHVGFLAESERTDLHRT +VQAIASESYVVIERMALDVVVLVEGREVARTWALNEASVEKSHRERMLEVVVSVDNSPLT +AFGCDGVVLATPTGSTAYAFSGGGPVVWPSVEALLCVPISAHALFTRPLVVGPRSTIGVD +VLTRTRETGVLWCDGRRTVELPPQARIEVSRSAEPVRLARLNPTPFAERLVRKFRLPTDG +WRGPVTAQERAGVLHAVETVEPRHAGPRPDVVEPATMPLSVLSPADIQRHRDRGARHPGE +DA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001175.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001175.fa new file mode 100644 index 0000000000000000000000000000000000000000..1eb9944ac0b6d1a703b645cea6f9bb26bbcf47d8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001175.fa @@ -0,0 +1,30 @@ +>PROKKA_01422 +MAETARADVALAARGLARSRTEGAALIRAGQVLLDGRPVRRPADRVAADATLRLRDPGPR +YVSRAAHKLVSALEAFPDVGVAGRRALDAGASTGGFTQVLLERGAERVAAVDVGHNQLAP +PVRADPRVLVREGLNIRDLTAEDIDGPVDLVVSDLSFISLRLVLAPLASVCRPGAELLLM +VKPQFEVGRRALPRSGVVTDPDARRHAVVGVTAAALGAGLAPRGLARSGLAGQDGNAEFF +LRLRRPDATAADNPAGGTSPAPPAGERAAGWVRGAHIDWS +>PROKKA_01153 +MAETARADVALAARGLARSRTEGAALIRAGQVLLDGRPVRRPSDRVAADATLRLRDPGPR +YVSRAAHKLVSALEAFPDVAVAGRRALDAGASTGGFTQVLLERGAERVAAVDVGHDQLAP +PVQADPRVLVREGLNVRDLRAEDIDGPVDLVVSDLSFISLRLVLAPLAGVCRPGAELLLM +VKPQFEVGRRALPRSGVVTDPDARRDAVAGVAAAALGAGLAPRGLTRSGLAGQDGNAEFF +LRLHRPDATAADDPAGRTSPATPADERAAGWVRGAHIDWS +>PROKKA_01477 +MAEAVRADVALAARGLARSRTEASALIRAGQVLVDGRPVRRASERVAPTASLTLADDGPR +WVSRAAHKLVSALEAFPDVAVRGRRALDAGASTGGFTQVLLEGGAARVAAVDVGHGQLVD +LVRTDPRVLVREGLNVRDLTVQDVEGEVDLVVSDLSFISLRLVMDALAGVCRPGADLLLM +VKPQFEVGRAALPRTGVVTDPAARRDVVAAVAAAALDSGLELRGLARSGLPGQDGNVEFF +LRLRRPAADAAGAPGTGLDDDAPAAEAVAAAWTAAAEVDWA +>PROKKA_01385 +MGEARRADVALAADGLARSRTEAAALVKEGVVLVDGTPVRRPSQPVASGAVLSLLDQGPR +WVSRAAHKLVSALEAFPVPVAGRRALDAGASTGGFTQVLLERGAARVAAVDVGHGQLVQE +LRADPRVLVREGLNVRDLTATDVEGSVDLVVSDLSFISLRLVLDALAGVCRPDADLLLMV +KPQFEVGRAALPRTGVVTDPRARRSAVEGVVAAALGTGLAARGVARSGLPGQDGNVEFFL +HLRAPAAPRDGGAVAGDADEDERRRRAAALVAAADVDWS +>PROKKA_01372 +MAETARADVALAARGLARSRTEGAALIRAGQVLLDGRPVRRPSDRVAADATLRLRDPGPR +YVSRAAHKLVSALEAFPDVAVAGRQALDAGASTGGFTQVLLERGAERVAAVDVGHDQLAP +PVRADPRVLVREGLNVRDLRAEDIDGPVDLVVSDLSFISLRLVLAPLAGVCRPGAELLLM +VKPQFEVGRRALPRSGVVTDPDARRDAVAGVAAAALGAGLAPRGLTRSDLAGQDGNAEFF +LRLHRPDATAADDPAGRTSPATPADERAAGWVRGAHIDWS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001176.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001176.fa new file mode 100644 index 0000000000000000000000000000000000000000..017b6ec82455cf65ce19ef55a047ea1286b7185c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001176.fa @@ -0,0 +1,30 @@ +>PROKKA_01423 +MSTTFFDGHDGLLCDLDGVVYAGDGAIAGAVETLSTLQERGVPVGFVTNNASRAPESVAE +HLRTLGVPAEAGQVFGSAPAGVDLLEETLGRRTGRVLVVGSAYLRAVVEERGYEVVASAA +QCPDAVIQGFDPGLGWADLAEAAYAVRAGATWVATNLDTSIPRAEGIAPGNGALVEAVGR +ATGTAPVAAGKPEPRLFRTAADALGLARPLVVGDRLDTDIRGGNAAGFDTVLVLTGIDTR +ETAAAAPGPDRPTWVRAHLPALLAGGAEASADPRRG +>PROKKA_01154 +MSATFFAGHDGLLCDLDGVVYAGGGAIAGAVETLSTLQERGVPVGFVTNNASRAPESVAE +HLRTLGVPAQAGQVFGSAPAGVDLLEETLGRRTGRVLVVGSAYLRAVVEERGYEVVASAA +QRPDAVIQGFDPGLGWADLAEAAYAVRAGATWVATNLDTSIPRAEGIAPGNGALVEAVGR +ATGTAPVAAGKPEPRLFRTAAEALGLARPLVVGDRLDTDIRGGNAAGFDTVLVLTGIDTR +ETAAAAPGPDRPTWVRAHLPALLAGGAEAFADPRRG +>PROKKA_01476 +MSPTLPRGHDGLLCDLDGVVYAGGGAVPGAVETLTALAERGVPVGFVTNNASRAPESVAE +HLRSLGVPARPEQVFGSAPAGVDLLEETLGARTGRVLVVGSDYLRQVVRDRGFEVVAASQ +DRPDAVIQGFDPGVGWAELAQAAYAVNAGAAWVATNLDASIPRAEGIAPGNGALVGAVGQ +ATGTAPAAAGKPEPLLFRTAARALGLTRPLVVGDRLDTDIRGGNAAGFDTVLVLTGIDTR +ENAGSAPEADRPTWIVEDLPALLSEPDGQAGTADGRRG +>PROKKA_01384 +MTDPAASTFFGGHDGLLCDLDGVVYAGGEAIPGAVETVSALAERGVPVGFVTNNASRPPE +AVAEQLRRFGLEVSPSHVFGSAPVGVDLLEERLTAAGHEGPARVLVVGSVHLADLVAARG +HHVVETAAERPDAVLQGFDPRVDWSRLAEAAYAVNAGAAWVATNLDLSIPRAEGVAPGNG +ALALAVTQATGVIPVAAGKPEPRLFHTAAAALGLQAPLMVGDRLDTDIRGGNAAGMETVL +VLTGVGSRHAAGEAPEEDRPTWIVDDMTALLGEPAEAARG +>PROKKA_01373 +MSATFFAGHDGLLCDLDGVVYAGGGAIAGAVETLSTLQERGVPVGFVTNNASRAPESVAE +HLRTLGVPAQAGQVFGSAPAGVDLLEETLGRRTGRVLVVGSAYLRAVVEERGYEVVASAA +QRPDAVIQGFDPGLGWADLAEAAYAVRAGATWVATNLDTSIPRAEGIAPGNGALVEAVGR +ATGTAPVAAGKPEPRLFRTAAEALGLARPLVVGDRLDTDIRGGNAAGFDTVLVLTGIDTR +ETAAAAPGPDRPTWVRAHLPALLAGGAEAFADPRRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001177.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001177.fa new file mode 100644 index 0000000000000000000000000000000000000000..f53e3b13b8c21b76b7d21482474bd3282b3605fd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001177.fa @@ -0,0 +1,36 @@ +>PROKKA_01424 +MTGKELDRGTLKEINGLDERAASWVAKHLVMAGRYLDVDPTLAFQHALAASRKGGRLSRV +REAVALTAYAAGEYADALREFRTYRRMTGDDTHIAAQVDSERALGRTEKALQLAAEVDAS +RLDRAARAELAMVVSGIREDAGDLQGAHEALQIPELDRRRGYPFSPRLFQRQADVLLALG +RRDEARLWARAVRVAEKALGVGGFADPEIIDVDTEPVEDPRNRRPSPRERRHERYAAEAG +AEPTADGSPAEEPEAAAEPTLVPRQEAVAQPPAAVDTPDEVDPNQLSLFDALEAPEADER +>PROKKA_01155 +MTGQELDRGTLKEINGLDERPASWVAKHLVMAGRYLDVDPALAFQHALAASRKGGRLSRV +REAVALTAYAAGEYADALREFRTYRRMTGDDTHIAAQVDSERALGRTEKALQLAAEVDAS +RLDRAARAELAMVVSGIREDAGDLQGAHEALQIPELDRRRGYPFSPRLFQRQADVLLALG +RRDEARLWARAVRVAEKALGVGGFADPEIIDVDTEPVEDPRDRRPSPRERRHERYAAEAG +AEPTADGSPAEEPEAATEPTEAPRPEAAAEPPAAVDAPDEVDPNQLSLFDALEAPEADER +>PROKKA_01475 +MAEDTPRGRRDDRRSPGDGAGRSRGGSGDARRFGGPRDGRRSGGSGEGRSGQDRRDRSSE +GFRGGRSGDGPRRERSSDGPRRERSSDGFRRDRSSDGPRGERSGDGPRGPRAGGDRRQSG +AGSARGGFEGRRGGERREGAGGERRDRRSASSSPRWEGRGQDRTERTERRERPAHNPRDL +RAANRVDQERSPDIDADVTGQELDRGTLKEVNGLDERPASWVAKHLVMAGRYIDVDPALA +FQHALAASRKGGRLSRVREAVALTAYAAGEYADALREFRTYRRMTGDDTHVAAQVDSERA +LGRPAKALQLAAEIDTARLDRAARVELAMVVSGIREDAGDLQGAHDALQIPELDRRRGYP +FSPRLFQRQADVLLLLGRADEARLWARAVRVAEKALGIGGFAEPEIVDVDTEPVDDRRER +GPSPRERRYAENAAPAAEEVPDTPEADDEVAADADTEAPASTESELDAPPAAVAQADEVD +PNQMSLFDELDGGEGEGR +>PROKKA_01383 +MAERSAREPRDDRRGDGHDGTRSGTPRGRRDGDGGRRQGEGRPFRPHRDGEGVGRSRNVG +GRDGAAPRPGRPERAQRERPAHSPSDLRAANRVDQQRSPDIDGDVTGKELDRGTLKEIGG +LDERPATWVAKHLVMAGRYIDEDPELAFQHALAASRKGGRLARVREAVALTAYAAGEYHE +ALREFRTYRRMTGDDTHIAAQVDSERALGRHEKALQLAGEVDTSRLDRAARVELAMVVSG +VREDLGDLEGALAALKIPELDRRRGYPFSPRLFQRQADVLTALGRTQEAAVWQRSVHVAE +RALGIGGFAEPEIVDVEVEPAEDDRPVRGHRERHTGPRVSDASQSSAESAPVGEGSAEEH +GQAAPAERES +>PROKKA_01374 +MTGQELDRGTLKEINGLDERPASWVAKHLVMAGRYLDVDPALAFQHALAASRKGGRLSRV +REAVALTAYAAGEYADALREFRTYRRMTGDDTHIAAQVDSERALGRTEKALQLAAEVDAS +RLDRAARAELAMVVSGIREDAGDLQGAHEALQIPELDRRRGYPFSPRLFQRQADVLLALG +RRDEARLWARAVRVAEKALGVGGFADPEIIDVDTEPVEDPRDRRPSPRERRHERYAAEAG +AEPTADGSPAEEPEAATEPTEAPRPEAAAEPPAAVDAPDEVDPNQLSLFDALEAPEADER diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001178.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001178.fa new file mode 100644 index 0000000000000000000000000000000000000000..ab633632ccdc4c25005ac9722ca8dac97407cc07 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001178.fa @@ -0,0 +1,45 @@ +>PROKKA_01428 +MAPQNEERAARLRAQANDPSFENVWQELRWRGLVHVSTDEAALEQALAGEPVSYYCGFDP +TAPSLHLGHLVQLLTLRRLQLAGHRPYALVGGATGLIGDPRQTSERVLNSQETVAAWVES +LRAQIEPYLSFEGENAATMVNNLDWTAGMSALDFLRDVGKNFRVGTMVKKEIVAKRLNSD +EGISYTEFSYQVLQGNDFLELHRRHGVTLQTGGSDQWGNLTAGTELIRKVEGTHAHALGT +PLITNADGTKFGKSEGNAVWLDAEMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE +YAQKVADEPFRREAQRRLAWEVTALAHGEETTTKVIEASQAVFGGGDLTTVDPDTLTAVL +AELPQADRTQWEGEPGTVTAVELLVSTGLVASRSEARRTVRDGGASVNNVRVTDADQVFT +RDDALAGRHLLVRRGKKNMAGADLGEA +>PROKKA_01159 +MAPQNEERAARLRAQANDPSFENVWQELRWRGLVHVSTDEAALEQALAGEPVSYYCGFDP +TAPSLHLGHLVQLLTLRRLQLAGHRPYALVGGATGLIGDPRQTSERVLNSQETVAAWVES +LRAQIEPYLSFEGENAATMVNNLDWTAGMSALDFLRDVGKNFRVGTMVKKEIVAKRLNSD +EGISYTEFSYQVLQGNDFLELHRRHGVTLQTGGSDQWGNLTAGTELIRKVEGTHAHALGT +PLITNADGTKFGKSEGNAVWLDAKMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE +YAQKVADEPFRREAQKRLAWEVTALAHGEETTTKVIEASHAVFGGGDLTTVDPDTLTAVL +AELPQADRTQWEGEPGTVTAVELLVSTGLVASRSEARRTVRDGGASVNNVRVTDADQVFT +RDDALAGRHLLVRRGKKSMAGADLGEG +>PROKKA_01471 +MAPDNEERAARLRAQANDPSFENVWQELLWRGLVHVSTDEAALEEALAGEPISYYCGFDP +TAASLHLGHLVQLLTLRRLQLAGHRPMALVGGATGLIGDPRQTSERVLNSQETVAGWVES +LREQIQPYLSFEGENAATMVNNLDWTAGMSALDFLREVGKNFRVGTMMKKEIVAKRLNSE +EGISYTEFSYQVLQGNDFLELYRRHGVSLQTGGSDQWGNLTAGTELIRKVEGVPAHALGT +PLITNADGTKFGKSEGNAIWLDAAMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE +YAQKVADEPFRREAQKRLAWEVTSLAHGEEATTKVIEASQAVFGGGDLGEVDAETLGAIL +SELPQADRTQWEGEPGTVTAVELLVSTGLVGSKSEARRTVKEGGASVNNERVSDADRVYT +REDALAGRHLLVRRGKKNMAGADFGSQDADRG +>PROKKA_01378 +MAETTVTRAERLRQQANDPSFENVWQELTWRGLVHVSTDEAALEEALAGEPISYYCGFDP +TAPSLHLGHLVQLLLMRRLQLAGHRPVALVGGATGLIGDPRQTSERVLNTREVVQEWVES +LRAQIEPYLAFEGDNGARMVNNLDWTASMSALDFLREVGKNFRVGTMVKKEIVAKRLHSE +EGISYTEFSYQVLQGNDFLELYRQHGVTLQSGGSDQWGNLTSGTELIRKVEGAHVHALGT +PLITNSDGTKFGKSEGNAIWLDADMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE +YAAKVDAEPFRREAQKRLAWEVTALAHGEEAARTVIDASAAVFGGGDLSEVDVDVLSAVL +AELPQADAAQWGAAGKPTAVELLVSTGLVSSNSEARRTIKEGGASVNNVKVADAEQVFGA +DEALAGRYLLVRRGKKNMAAADLRSGE +>PROKKA_01378 +MAPQNEERAARLRAQANDPSFENVWQELRWRGLVHVSTDEAALEQALAGEPVSYYCGFDP +TAPSLHLGHLVQLLTLRRLQLAGHRPYALVGGATGLIGDPRQTSERVLNSQETVAAWVES +LRAQIEPYLSFEGENAATMVNNLDWTAGMSALDFLRDVGKNFRVGTMVKKEIVAKRLNSD +EGISYTEFSYQVLQGNDFLELHRRHGVTLQTGGSDQWGNLTAGTELIRKVEGTHAHALGT +PLITNADGTKFGKSEGNAVWLDAEMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE +YAQKVADEPFRREAQRRLAWEVTALAHGEETTTKVIEASQAVFGGGDLTTVDPDTLTAVL +AELPQADRTQWEGEPGTVTAVELLVSTGLVASRSEARRTVRDGGASVNNVRVTDADQVFT +RDDAFAGRHLLVRRGKKNMAGADLGEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001179.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001179.fa new file mode 100644 index 0000000000000000000000000000000000000000..632ea8b7a33453966512fc417b28d4082f5e108c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001179.fa @@ -0,0 +1,70 @@ +>PROKKA_01429 +MTDTVSVRQSELDLERGRVAERYARLDALREEKERQLAAVRRTGPQGSLQNHSERDAFAS +LYEDRLAQLYAVDDRLVFGRLDLDAEREGGADEQRYIGRIGLTTEDHERLLVDWRAAEAG +AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDILDPTLLGEDGVRADAQGALLAAVTARR +TGRMGDIVATIQAEQDEVIRAPLPGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG +VLIVGPSTAFMRYIERVLPSLGETGVVMSSLGTLMPGVRAVPERDLDAAAVKGRLDMVDA +VAHAVAQRQRLLVEPRRLMIDGTAVKLKPAMVRRARDKARATRKPHNEARVTFVKILVRE +LAEKLRKKLEKSSGTPVQRDLLLEDVRTSRDVRIALNLCWMPLTPEKLIGDLLTREDLLR +AAAPWLSDAEVGALLRPADAPWTEADVPLLDEAAELLGRLDTPGRGGESAAQHERNLENA +RASLENMHQTLADLGVDGVVDAEQLAAANEARGVRRTTAETAAHDRTWTYGHVVVDEAQE +LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLAPEFGDRWRLEELTVNYRSP +ARVMRWAAQVARAAGLEVSHPRAVREGDHRPRLVTEPGGDVAALALDAVEAERDRVPEAL +TAVIAPAERTGELLTALRERWGEAAVDTAPLPGVEIVVATPWETKGLEFDTVVLVLPERI +VADARGVVGDLYVAMTRATQSLSVVAGTDAAALPAGLADVPE +>PROKKA_01161 +MTDTVSVRQSELDLERGRVAERYARLDALREEKERQLAAVRRTGPQGSLQNHSERDAFAS +LYEDRLAQLYAVDDRLVFGRLDLDAEREGGADEQRYIGRIGLTTEDHERLLVDWRAAEAG +AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDILDPTLLGEDGVRADAQGALLAAVTARR +TGRMGDIVATIQAEQDEVIRAPLPGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG +VLIVGPSTAFMRYIERVLPSLGETGVVMSSLGTLMPGVRAVPERDLDAAAVKGRLDMVDA +VAHAVAQRQRLLVEPRRLMIDGTAVKLKPAMVRRARDKARATRKPHNEARVTFVKILVRE +LAEKLRKKLEKSSGTPVQRDLLLEDVRTSRDVRIALNLCWMPLTPEKLIGDLLTREDLLR +AAAPWLSDVEVGALLRPADAPWTEADVPLLDEAAELLGRLETPGRGGESAAQHERNLENA +RASLENMHQTLADLGVDGVVDAEQLAAANETRGVRRTTAETAAHDRTWTYGHVVVDEAQE +LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLAPEFGDRWRLEELTVNYRSP +ARVMRWAAQVARAAGLEVSHPRAVREGDHRPRLVTEPGGDVAALALEAVEVERDRVPEAL +TAVIAPAGRTGELLTVLRERWGEAAVDTAPLPGVEIVVATPWETKGLEFDTVVLVSPERI +VADARGVVGDLYVAMTRATQSLSVVAGTDAAALPAGLADVPE +>PROKKA_01470 +MTDAVSVRQSELELERARVAERYARLDALREEKERQLAAVRRTGLEGSLQNHSERDAFAS +LYEDRLAQLLAVDDRLVFGRLDLDPERAGDPDEERYIGRIGLTTEEHERLLVDWRAAEAG +AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDVLDPDLLGQEGVRADAQGALLAAVTARR +TGRMGDIVATIQAEQDEVIRAPLAGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG +VLIVGPSTAFMRYIERVLPSLGETGVVMASLGTLMPGVQAGPERDLDAAAVKGRLEMAQV +IAHAVAQRQRLLAQPRRLMIEGTAVKLKPAAVRRARDRARATGKPHNEARVTFVKILVRE +LAEKLSKKLEKSSGAPVQRDLLLEDVRTSRDVRVALNLCWMPLTPQKLVGDLLTREHLLR +AAAPWLSDGEVGALLRPADAPWTEADVPLLDEAAELLGRLEAPAKGGESAAQHERNLENA +RASLENMHQTLADMGVDGVVDAEQLAAANEARAVRRTTAETAAHDRTWTYGHVVVDEAQE +LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLEPEFGDRWRLEELTVNYRSP +ARVMRWASQVAQAAGLEVSRPRAVREGEHAPRLTVRPGADLVALTLDAVAGERDRVPEGL +VAVITAAAHAPELLAALRERWGRARVDTAPLPGVEIVVATPWETKGLEFDAVVLAAPERL +VDDARGVVGDLYVAMTRATQSLSVVSTAAVAALPAGLADPPA +>PROKKA_01377 +MTDTVSSRQAELELERERVAVRYARLDALRAEKEEQLARVRRSGLQGSVQNHSERDAFAS +LYEDRLAQLYAVDERLVFGRLDLDADDAGDVEQRYIGRIGLTDEGQERLLVDWRAQEAGA +FYQATAARRLGVGRRRHLLLRGREVRDFEDDVLDPSLIAEGAAGAQSQGALLAAVTARRT +GRMGDIVATIQAEQDEVIRADTSGALVVQGGPGTGKTAVALHRAAYLLYTHRDRLAKSGV +LVVGPSNAFMRYIERVLPSLGETGVVMASLGTLMPGVQAGPDRSARAAELKGRLEMADVV +AAAVAQRQRLIPETRRLEIEGTVVKLKPAMVRRARDRARATGKPHNEARTTFVKILVREL +AEKLRKKLEKSSGVPVQRDLLLEDVRTARDVRVALNLCWMPLTPQKLVGDLLTKEHLLRA +AAPGLSDGDVAALLRTDPDAWVESDVPLLDEAAELLGELEEPHRPGESEAQHRRNVENAQ +ASLENMHQTLAELGVDGVVDAEQLAAANEVRAVRRTTAEQAAHDRTWTFGHVVVDEAQEL +SPMQWRLLARRCPLKSFTVVGDIAQASRRGGARSWKDVLGPEFGDRMRLEELTVNYRSPA +RITRWAAQVAQAAGLEISSPEAVREGEHEPLLTVEPGADPTRLAQRVVEAERGRVGDGLV +AVIVPADDAAEHLTHLQDRWGSLVDRAPAPGVEVVVVTARETKGLEFDAVVLVSPERIVA +DADGVVGDLYVAMTRCTQSISVVSGAAEEELPAGLMPVPA +>PROKKA_01379 +MTDTVSVRQSELDLERGRVAERYARLDALREEKERQLAAVRRTGPQGSLQNHSERDAFAS +LYEDRLAQLYAVDDRLVFGRLDLDAEREGGADEQRYIGRIGLTTEDHERLLVDWRAAEAG +AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDILDPTLLGEDGVRADAQGALLAAVTARR +TGRMGDIVATIQAEQDEVIRAPLPGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG +VLIVGPSTAFMRYIERVLPSLGETGVVMSSLGTLMPGVRAVPERDLDAAAVKGRLDMVDA +VAHAVAQRQRLLVEPRRLMIDGTAVKLKPAMVRRARDKARATRKPHNEARVTFVKILVRE +LAEKLRKKLEKSSGTPVQRDLLLEDVRTSRDVRIALNLCWMPLTPEKLIGDLLTREDLLR +AAAPWLSDAEVGTLLRPADAPWTEADVPLLDEAAELLGRLETPGRGGEFAAQHERNLENA +RASLENMHQTLADLGVDGVVDAEQLAAANEARGVRRTTAETAAHDRTWTYGHVVVDEAQE +LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLAPEFGDRWRLEELTVNYRSP +ARVMRWAAQVARAAGLEVSHPRAVREGDHRPRLVTEPGGDVAALALDAVEVERDRVPEAL +TAVIAPAGRTGELLTVLRERWGEAAVDTAPLPGVEIVVATPWETKGLEFDTVVLVSPERI +VADARGVVGDLYVAMTRATQSLSVVAGTDAAALPAGLADVPE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001180.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001180.fa new file mode 100644 index 0000000000000000000000000000000000000000..8810e7db05d5ef3cd3adc5eecd0f745f52390b2d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001180.fa @@ -0,0 +1,50 @@ +>PROKKA_01430 +MTENTDARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA +GLLSADDLDGMIAALDRLEADVRSGAYTPAASDEDVHGSLERGLIERAGPELGGRLRAGR +SRNDQVATLGRMFLRDHARIIARGVIATVDALLDQARAHPHAPMPGRTHLQHAQPVLLSH +HLLAHAWAFARDLQRLVDWDARAAVSPYGSGALAGSSLGLDPNAVATELGFESAVWNSID +GTAARDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVTLHDAYSTGSSIMPQKKNPD +VAELARGKSGRLIGDLTGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA +TLEFQTERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVKAAEARGVELWDLTD +DEYAAISPALTPQVREVLSTEGSLASRDAQGGTAPTAVAAQIGALEDALEPLRRWADTPG +SVVDAR +>PROKKA_01162 +MTENTDARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA +GLLSADDLDGMIAALDRLEADVRSGAYTPAASDEDVHGSLERGLIERAGPELGGRLRAGR +SRNDQVATLGRMFLRDHARIIARGVIATVDALLDQARAHPYAPMPGRTHLQHAQPVLLSH +HLLAHAWAFARDLQRLVDWDARAAVSPYGSGALAGSSLGLDPNAVAAELGFESAVWNSID +GTAARDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVRLHDAYSTGSSIMPQKKNPD +VAELARGKSGRLIGDLTGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA +TLEFQTERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVMAAEARGVELWDLTD +DEYAAISPALTPQVREVLSTEGSLASRDAQGGTAPTAVAAQIGALEDALAPLRRWADTPG +SVVDAR +>PROKKA_01469 +MTENPEARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHAA +GLLGAEDLEGMIAALDRLETDVRSGAYAPADSDEDVHGSLERGLIERAGPELGGRLRAGR +SRNDQVATLGRMFLRDHARIIARGLVATVDALLSQVQAHPYAPMPGRTHLQHAQPVLLSH +HLLAHAWAFARDLQRLVDWDARTAVSPYGSGALAGSSLGLDPEAVAAELGFDSAVWNSID +GTASRDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVKLHDAYSTGSSIMPQKKNPD +VAELARGKSGRLIGDLAGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA +TLEFETERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVKAAEARGVELWDLTD +EEYAAISPALTPQVREVLSTEGSLNSRDAQGGTAPAAVAAQVEALERTLEPLRRWAQTPG +SVVDAR +>PROKKA_01376 +MSENSTPRHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA +GLLTADELAGMIDALDRLEADVRSGAYAPAESDEDVHGSLERGLIERAGAELGGKLRAGR +SRNDQVATLGRMFLRDHARVVARGVLATVDALVEQAEAHPFAPMPGRTHLQHAQPVLLSH +HLLAHAWAFTRDLQRLVDWDARAAVSPYGSGALAGSTLGLDPNAVAAELGFDSAVWNSID +GTAARDVYAEFAWVAGMIGVDLSRISEEVIFWATKEAGFVRLHDSYSTGSSIMPQKKNPD +VAELARGKAGRLIGDLAGLMATLKGLPLAYNRDLQEDKEPVFDAVDTLELLLPAVSGMIA +TLSFNTERMAALAPQGFALATDIAEWLVRQGVPFRVAHELSGEAVQVAESRGVELWDLTD +EEYAGISAHLTPAVREVLSTEGSLNARRGQGGTAPEAVAEQLAALKAALEPLRAFAASAG +SVVDAR +>PROKKA_01380 +MTENTDARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA +GLLSADDLDGMIAALDRLEADVRSGAYTPAASDEDVHGSLERGLIERAGPELGGRLRAGR +SRNDQVATLGRMFLRDHARIIARGVIATVDALLDQARAHPYAPMPGRTHLQHAQPVLLSH +HLLAHAWAFARDLQRLVDWDARAAVSPYGSGALAGSSLGLDPNAVATELGFESAVWNSID +GTAARDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVTLHDAYSTGSSIMPQKKNPD +VAELARGKSGRLIGDLTGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA +TLEFQTERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVKAAEARGVELWDLTD +DEYAAISPALTPQVREVLSTEGSLASRDAQGGTAPTAVAAQIGALEDALAPLRRWADTPG +SVVDAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001181.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001181.fa new file mode 100644 index 0000000000000000000000000000000000000000..6ce5c223b3f025a840372db1d84dd21cde05da81 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001181.fa @@ -0,0 +1,40 @@ +>PROKKA_01431 +MKERIILAYSGGLDTSVAIGWIAEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY +VADARDEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG +KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTREKAIEYAQRNDLPIVTTKKNPFSIDQNV +WGRAVETGFLEDIWNGPTKDVYDYTDDPAFPPAPDVVTIAFERGVPTALDGRALSPLEII +EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK +HVDQRWTELVYDGQWYSPLKRNLDTFIDATQEHVNGEIRLELHGGRATVQGRRSETGLYD +FNLATYDEGDSFDQSSARGFIDIFGLSAKTASEREQRLRGSDDLQDVARLSND +>PROKKA_01163 +MKERIILAYSGGLDTSVAIGWIAEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY +VADAREEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG +KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTREKAIEYAERNDLPIVTTKKNPFSIDQNV +WGRAVETGFLEDIWNGPTKDVYDYTDDPAFPPAPDVVTIAFERGVPTALDGRALSPLEII +EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK +QVDQRWTELVYDGQWYSPLKRNLDTFIDATQEHVNGEIRLELHGGRATVQGRRSETGLYD +FNLATYDEGDSFDQSSARGFIDIFGLSAKTASEREQRLRGGDDLQDVARLSND +>PROKKA_01468 +MKERIILAYSGGLDTSVAIGWIAEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY +VADARDEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG +KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTRDKAIDYAERNELPIVTTKKNPFSIDQNV +WGRAVETGFLEDIWNGPTKDVYDYTDDPAFSPAPDVVTIAFERGVPTALDGRALSSLEII +EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK +TVDQRWTELVYDGQWFSPLKRNLDTFIDATQEHVNGEIRLELHGGRATVQGRRSETGLYD +FNLATYDEGDSFDQSSARGFIDIFGLSAKTASERDQRLRGGDDLKDVARLANS +>PROKKA_01375 +MKDRIVLAYSGGLDTSVAIGWIGEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY +VADARDEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG +KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTREKAIEYAERNELPIATTKKNPFSIDQNV +WGRAVETGFLEDIWNGPTKDVYDYTDDPAFPPAPDVVTIAFEQGVPTALDGRALSALEII +EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK +QVDQRWTELVYDGQWFSPLKKSLDTFIDDTQKHVNGEIRLELHGGRATVQGRRSETGLYD +FNLATYDEGDSFDQSSARGFIDIYGLSAKTASEREQRLGGAADLADVARLSND +>PROKKA_01381 +MKERIILAYSGGLDTSVAIGWIAEATGAEVVAVAVDVGQGGESLETIRQRALDCGAVEAY +VADARDEFAEQYCMPTLKANALYMDAYPLVSAISRPVISRHLVAAARQFGASTVAHGCTG +KGNDQVRFEVSIQTLGPDLKCIAPVRDLALTREKAIEYAERNDLPIVTTKKNPFSIDQNV +WGRAVETGFLEDIWNGPTKDVYDYTDDPAFPPAPDVVTIAFERGVPTALDGRALSPLEII +EELNRRAGAQGVGRIDIVEDRLVGIKSREIYEAPGAMALIAAHRELENVTLEREQARFKK +HVDQRWTELVYDGQWYSPLKRNLDTFIDATQEHVNGEIRLELHGGRATVQGRRSETGLYD +FNLATYDEGDSFDQSSARGFIDIFGLSAKTASEREQRLRGGDDLQDVARLSND diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001182.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001182.fa new file mode 100644 index 0000000000000000000000000000000000000000..44f06ebce07428c5666458b9b83fb38b56f090aa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001182.fa @@ -0,0 +1,33 @@ +>PROKKA_01432 +MDTMTLFTTSATRSRRATASIVAGMTLAGAAAVGFSAPAQAATVDTWDRLAECESSGTWD +INTGNGFYGGVQFTLSSWQAVGGEGYPHQASKAEQIKRAEILQDLQGWGAWPLCSQKLGL +TQADADAGDVDAAPVAVERTATVQRQSAADETAADQAAAEQAAADQAAAEQAAADQAAAE +RWAAKQAAADQAAAERWAAKQAAAEQAAADKAAAQRAAAAEKAAAQKAAAAEKAAAQKAA +AAEKAAAQKAAAAEQAAAAEQAVVAEAETIVVKSGDSLWKLANEYEVEGGWTALYEANKG +AVSDAAVIYVGQELVLPQA +>PROKKA_01164 +MDTMTLFTTSATRSRRATASIVAGMTLAGAAAVGFSAPAQAATVDTWDRLAECESNGTWD +INTGNGFYGGVQFTLSSWQAVGGEGYPHQASKAEQIKRAEILQDLQGWGAWPLCSQKLGL +TQADADAGDVDATEAAPVAVERTATVQRQSAADEAAAEQAAAEQAAADQAAAERWAAEQA +AADQAAAERWAAEQAAAEQAAAERWAAKQAAAEQAAADKAAAQRAAAAEKAAAQKAAAAE +KPAAQKAAAAEKAAAQKAAAAEQAAAAEQAVVAEAETIVVKSGDSLWKLANEYEVEGGWT +ALYEANKGAVSDAAVIYVGQELVLPQA +>PROKKA_01467 +MDTMTLFTSTRTRRTTASVAAGMTLMGAAAVGFSAPAQAATEETWDAIAFCESTNRWDIN +TGNGFYGGLQFTLSSWQGVGGQGYPHQASKAEQIKRAEMLQDLQGWGAWPKCAAGLTQAD +ADATDAAPVAVERTSSVQRQAAAEQAAAEEAAAEQAAAEEAAAEQAAAEQWAAEQAAAEQ +AAAERAEAKRAAAAEKAAAKKAAAAERAAAHQAAAEQAVVAEAETIVVKAGDSLWKLAAE +HEVEGGWTALYEANKDTVSDAAMIYVGQELVLPQA +>PROKKA_01374 +MTFFTTSSRRATATALTGMTLVGAAAAFAAPAQAASVETWDKIAACESNGNWAINTGNGY +YGGLQFSLTSWRGVGGTGYPHEASKAEQIKRAEILQDMQGWRAWPVCSVKAGLSGADTAP +DAYSTTPVQRQSTQASASAAQDWAAEQSAAEQRAAEKAAAQRAAAAAHTPKSVLKAAEKA +NTENATELAAAEDTVFVKPGDSLWKIAKTHKVAGGWKALHEANKDIIEDASVIYVGQELV +LPTA +>PROKKA_01382 +MDTMTLFTTSATRSRRATASIVAGMTLAGAAAVGFSALAQAATVDTWDRLAECESNGTWD +INTGNGFYGGVQFTLSSWQAVGGEGYPHQASKAEQIKRAEILQDLQGWGAWPLCSQKLGL +TQADADAGDVDATEAAPVAVERTATVQRQSAADEAAAEQAAAEQAAADQAAAERWAAEQA +AADQAAAERWAAEQAAADQAAAERWAAEQAAAEQAAADKAAAQRAAAAEKAAAQKAAAAE +KAAAQKAAAAEQAAAAEQAVVAEAETIVVKSGDSLWKLANEYEVEGGWTALYEANKGAVS +DAAVIYVGQELVLPQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001184.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001184.fa new file mode 100644 index 0000000000000000000000000000000000000000..a8db7a3bda434481af6c41c68812c41d087009a5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001184.fa @@ -0,0 +1,35 @@ +>PROKKA_01434 +MTPAAAVRHFLVDTDLTPAEQAEVLDLAAQMKADRFRHRPLAGPRTGIVFFDKTSTRTRV +SFAAGIAELGGTPLIVNPGESQLGHKESVADTARVLERMVGVIVWRTFAQAGLEEMAAHS +SVPVVNALSDDYHPCQILADLLTVREHLGGTAGRTLTYLGDAANNMAHSYLLGCATAGMH +VRVAGPEGHLPAEDVVAAARQRAAETGGSVLVTTDAAEALAGADVVVTDTWVSMGQEEEK +EARLALFRDYQVDAAAMARAADDAIFLHCLPAYRGYEVTAEVIDGPRSVVFDEAENRLHA +QKALIAWLLYRSGLAEEPR +>PROKKA_01166 +MTPAAAVRHFLVDTDLTPAEQAEVLDLAAQMKADRFRHRPLAGPRTGIVFFDKTSTRTRV +SFAAGIAELGGTPLIVNPGESQLGHKESVADTARVLERMVGVIVWRTFAQAGLEEMAAHS +SVPVVNALSDDYHPCQILADLLTVREHLGGTAGRNLTYLGDAANNMAHSYLLGCATAGMH +VRVAGPEGHLPAEDVVAAARQRAAETGGSVLVTTDAVEALAGADVVVTDTWVSMGQEEEK +EARLALFRDYQVDAAAMARAADDAIFLHCLPAYRGYEVTAEVIDGPRSVVFDEAENRLHA +QKALIAWLLYRSGLAEEPR +>PROKKA_01464 +MTPAPTPAPAAVRHFLVDTDLTPGEQAEVLDLAAQMKTDRFAHRPLAGPRTGVVFFDKTS +TRTRVSFAAGIAELGGSPLIVNPGESQLGHKESVADTARVLERMVGIIVWRTFAQSGLEE +MAAHSRVPVVNALSDDYHPCQILADLLTVREHLGGTQGRVLAYLGDAANNMAHSYLLGCA +TAGMHVRIAGPAGHLPAEHVVAAARERAAETGGSVLVTTDAAEALDGADVVVTDTWVSMG +QEDEKEARLALFRDYQVDAAAMARAGSDAIFLHCLPAYRGYEVSAEVIDGPQSVVFDEAE +NRLHAQKALMAWLLYRSGLAEDPR +>PROKKA_01372 +MTAAPGTDVPVRHFLVDTDLSPAEQAEVLDLALEMKADRFRHRPLAGPQTGIVFFDKTST +RTRVSFAAGIADLGGTPLIVNPGESQLGHKESIADTARVLERMVGVIVWRTYAQSGLEEM +AAHSRVPVVNALSDDYHPCQLLADLLTVREHKGRTRGLTMAYLGDAANNMANSYLLGGVT +AGMHVRVAGPEGFLPDPAVVRAAEERAGETGGSVLVTTDAAAALDGADVVVTDTWVSMGQ +EDEKEERLRLFADYRVDAAAMARAASDAVFLHCLPAYRGYEVTEDVIDGPQSVVFDEAEN +RLHAQKALMAWLLYRSGLAQDPR +>PROKKA_01384 +MTPAAAVRHFLVDTDLTPAEQAEVLDLAAQMKADRFRHRPLAGPRTGIVFFDKTSTRTRV +SFAAGIAELGGTPLIVNPGESQLGHKESVADTARVLERMVGVIVWRTFAQAGLEEMAAHS +SVPVVNALSDDYHPCQILADLLTVREHLGGTAGRNLTYLGDAANNMAHSYLLGCATAGMH +VRVAGPEGHLPAEDVVAAARQRAAETGGSVLVTTDAVEALAGADVVVTDTWVSMGQEEEK +EARLALFRDYQVDAAAMARAADDAIFLHCLPAYRGYEVTAEVIDGPRSVVFDEAENRLHA +QKALIAWLLYRSGLAEEPR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001188.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001188.fa new file mode 100644 index 0000000000000000000000000000000000000000..575e5904695939b1ca9915932c8d5b484012e33a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001188.fa @@ -0,0 +1,35 @@ +>PROKKA_01438 +MTHTVAVSGASGYAGGEALRLLAGHPSVTVGAITAHSNAGERLGALQPHLHALADRVLAE +TTAEVLAGHDVVILALPHGASGALAAEIAERSPDTLVIDAGADHRLESAADWEAFYGTAH +AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT +SGAGKALKPHLLGAEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVRVSFTPTLAPMPR +GILATATARLRPGVAAADVRAAWAAAYGGERFVHLLPEGQWPTTKAVLGSNHVQLQLAVD +ERAGRVIVCAVLDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP +>PROKKA_01170 +MTHTVAVSGASGYAGGEALRLLAGHPSVTVGAITAHSNAGERLGALQPHLHALADRVLAE +TTADVLAGHDVVILALPHEASGALAAEIAERSPDTLVIDAGADHRLESAADWEAFYGTAH +AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT +SGAGKALKPHLLGAEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVRVSFTPTLAPMSR +GILATATARLRPGVAAADVRAAWAAAYGGERFVHLLPEGQWPTTKAVLGSNHVQLQLAVD +ERAGRVIVCAALDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP +>PROKKA_01460 +MTHTVAVSGASGYAGGEALRLLAGHPDVAVGAITAHSNAGERLGALQPHLHSLADRVLEE +TTADVLAGHDVVILALPHGASGALAAQIAERSPETLVIDAGADHRLESAADWEAFYGSEH +AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT +SGAGKAAKPHLLGSEVMGGMSPYGVGGGHRHTPEIEQGLSQAAGERVQISFTPTLAPMAR +GILATATARLRPGADPAAVRGAWERAYADERFVHLLPEGLWPATKSVLGSNHVQMQLAVD +ERAGRVIVTAALDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP +>PROKKA_01368 +MTFTVAVSGASGYAGGEVLRLLAGHPEVQIGAISAHSNAGERLGSLQPHLHALADRVLDD +TTADVLAGHDVVVLALPHGASAAVAAELAERSPRTLVIDAGADHRLESAADWERFYGTDH +AGTWPYGLPELPGQRERLAGATRIAVPGCYPTTSILALAPGFAAGLLETRDVVIVAASGT +SGAGRAAKPHLLGSEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVQISFTPTLAPMPR +GILATATARLKEGVTADRVRAAWEDAYGPERFVHLLPEGQWPTTKAVVGSNHVVMQLAVD +PHAGRVIVTAALDNLTKGTAGGALQSMNIALGLPEQLGLEIQGVAP +>PROKKA_01388 +MTHTVAVSGASGYAGGEALRLLAGHPSVTVGAITAHSNAGERLGALQPHLHALADRVLAE +TTAEVLAGHDVVILALPHGASGALAAEIAERSPDTLVIDAGADHRLESAADWEAFYGTAH +AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT +SGAGKALKPHLLGAEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVRVSFTPTLAPMSR +GILATATARLRPGVAAADVRDAWAEAYGGERFVHLLPEGQWPTTKAVLGSNHVQLQLAVD +ERAGRVIVCAALDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001189.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001189.fa new file mode 100644 index 0000000000000000000000000000000000000000..76ea2d25f85e318f79fe3b89d19015f4c4fe6804 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001189.fa @@ -0,0 +1,35 @@ +>PROKKA_01439 +MTTANTPAVPRTHHAVVVSATGGPEVLQWTETEVPSPAPGHVLVRTAAAGLNFIETYQRS +GVYTMDLPFTPGTEGSGEVVALGEGVDAGLLGARVATATATGAYAEHFTAPADRLLTVPE +GIDLAEAAALPLQGMTAHYLCRSTFPVEEGHTVVVTAGAGGVGLLLTQLATARGARVVTT +ASTEEKRELSRGAGAVAAVDYPDLAATVAELTDGEGAHVVYDGVGKDTFDTSLEVLRVRG +TLVLFGGASGQVPPFDLQRLNAAGSLYVTRPSLVHYTRTGEETRWRGGEVFGAWASGELD +VRIGERFPLADAAAAHAALESRSTTGKVLLTLS +>PROKKA_01171 +MTTANTPAVPRTHHAVVVSATGGPEVLQWTETEVPSPAPGHVLVRTAAAGLNFIETYQRS +GTYAMDLPFTPGTEGSGEVVALGEGVDAALLGARVATATATGAYAEHFTAPADRLLAVPE +GIDLAEAAALPLQGMTAHYLCRSTFPVEEGHTVVVTAGAGGVGLLLTQLATARGARVVTT +ASTEEKRELSRGAGAVAAVDYPDLAATVAELTDGEGAHVVYDGVGKDTFDTSLEVLRVRG +TLVLFGGASGQVPPFDLQRLNAAGSLYVTRPSLVHYTRTGEETRWRGGEVFGAWASGELD +VRIGERFPLADAAAAHAALESRSTTGKVLLTLS +>PROKKA_01459 +MPHASSPAVPRTHHAVVVAETGGPEVLRWTQADVPAPGPGRVLVRTAAVGLNYIETYQRA +GVYPMDLPFVPGTEASGTVVGLGEGVDPTLLGARVATATAQGAYAEHFTAPADRLLTVPE +GVDLADAAALPLQGMTAHYLCRSTFPVEEGQTVVVTAGAGGVGLLLTQLAAARGARVITT +ASTEAKRELSRAAGAAAAVDYPELAATVDRLTDGHGAHAVFDGVGKDTFETSLRVLRVRG +TLVLFGGASGQVPPFDLQRLNAAGGLYVTRPSLVHYTRTEEETRGRSDELFAAWAAGELD +VRIGERIPLAEAAAAHAALESRATTGKVLLTLG +>PROKKA_01367 +MSTHAEIPARHHAIIAEEVGGPEVLRWTETAVPTPGAGEVLVRTAAAGLNFIETYQRSGV +YAVPHPFTPGSEGSGVVVALGPGVDEALRGARVATAAGRGTYAEHFTAPADQLLHVPAGV +DLADAAALPLQGMTAHYLCRSTFPVEPGHVVALTAGAGGVGLLLTQLAAARGATVITAAS +TEDKRALSAAAGASAAVPYAELRQTVLDATGGEGAHAVFDGVGADTFEDSLASLRVRGTL +VLFGGASGQVPPFDLQRLNSGGGLYVTRPSLAHYTRTAEETAWRGRELFDAWSAGALDVR +IGARVPLAEAGRAHTLLASRATTGKVLLPLS +>PROKKA_01389 +MTTANTPAVPRTHHAVVVSATGGPEVLQWTETEVPSPAPGHVLVRTAAAGLNFIETYQRS +GVYTMDLPFTPGTEGSGEVVALGEGVDAGLLGARVATATATGAYAEHFTAPADRLLTVPE +GIDLAEAAALPLQGMTAHYLCRSTFPVEEGHTVVVTAGAGGVGLLLTQLATARGARVVTT +ASTEEKRELSRGAGAVAAVDYPDLAATVAELTDGEGAHAVYDGVGKDTFDTSLEVLRVRG +TLVLFGGASGQVPPFDLQRLNAAGSLYVTRPSLVHYTRTGEETRWRGGEVFGAWASGELD +VRIGERFPLADAAAAHAALESRSTTGKVLLTLS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001190.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001190.fa new file mode 100644 index 0000000000000000000000000000000000000000..0d3a83aa98e20fbe4f1003ca133e08f5db18f408 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001190.fa @@ -0,0 +1,45 @@ +>PROKKA_01441 +MSTDPYVPGVGTDAATVEHIALDLDVRLAANRVSGTAVLRVRLTKQSRRIELDLYRLRVS +RVDAVVDGRAVASSFTQPGRAPSRLVVDLDESRPEGTLVELTVVYAGTPTLRRSPWGTIG +WEELTDGVLVAGQPHGASTWLPCVDSPTSRSTAEITLTCDAGYLPVANGVGAPVRTRGSR +VTWRWRLHQRVPAYLLSVQIGRYRLVDAAPPAEGLPPLRLVVSPRTEQRALRALAPQPAM +MATFIDAYGPYPFEDYTAVVADEELEIPLEAASMSLFGTNHLDGSWESERLIAHEMSHQW +FGNAVTLGRWSDLWLHEGFACWSEWLWAEASGRSSITSMARRAWQKLAAHPVEQALAEPG +PEEMFEDWVYKRGALTVEALRHLLGTDLFGSMLRAWVREHRFGTVDSLGLRTHVHAWAPH +AGVSRAQVDELFDAWTLRPELPPFPG +>PROKKA_01173 +MSTDPYVPGVGTDAATVEHIALDLDVRLAANRVSGTAVLRVRLTKQSRRIELDLYRLRVS +RVDAVVDGRAVASSFTQPGRAPSRLVVDLDESRPEGTLVELTVVYAGTPTLRRSPWGTIG +WEELTDGVLVAGQPHGASTWLPCVDSPTSRSTAEITLTCDAGYLPVANGVGAPVRTRGSR +VTWRWRLDQPVPAYLLSVQIGRYRLVDAAPPAEGLPPLRLVVSPRTEQRALRALAPQPAM +MATFIDAYGPYPFEDYTAVVADEELEIPLEAASMSLFGTNHLDGSWESERLIAHEMSHQW +FGNAVTLGRWSDLWLHEGFACWSEWLWAEASGRSSITSMARRAWQKLAAHPVEQALAEPG +PEEMFEDWVYKRGALTVEALRHLLGTDLFGSMLRAWVREHRFGTVDSLGLRTHVHAWAPH +AGVSRAQVDELFDAWTLRPELPPFPG +>PROKKA_01457 +MSTDPYVPGVGTDAAVIEHVVLDLDVRLAANRVSGTAVLSVRLTRQSRRIELDLHRLRVS +KVGAAVDGRALPASFSQPRRWPSRLVVDLGESRPEGTLVELTVAYAGTPTPRRSPWGTIG +WEELTDGVLVAGQPHGASTWLPCVDSPVSRSTADITLTCDAGYLPVANGVGAPVRTRGSR +VTWRWRLTQPVPAYLLTVQIGRYRLVDAAAPADGLPPLRLVASTRTEQRARAALATQPAM +MAAFIAAYGPYPFEEYTAVVADDVLEIPLEAAGMSLFGTNHLDGSWESERLIAHEMAHQW +FGNAVTLGRWADLWLHEGFACWSEWLWAEASGRSSIASMARRAWQRLAEDPVEHVLTEPG +AAEMFEDWVYKRGALTVEALRVLLGREVFGSMLRAWVDEHRFGTVDTAGLRAHVHAWAPR +AQVTPEQVDELFEAWTRRPELPPFPG +>PROKKA_01365 +MSTDPYIPGVGSDTATIEHLRVELDVRLASNRVAGVAELHVRLCRQSDTVELDLHRLAVD +GAAGTHDGRPLKVRATTPRNRPHRVVVHLGASLPEGSLVVLRLSYSGHPRPRRSPWGTIG +WEELTDGVLVAGQPHGASTWVPCIDSPAVRQTADITVTCDAGYLPVANGRGTRLRSRGSR +ETWRWVMDRPVPAYLLTLQIGRYRQVTAPGSGTPESAAAGGVPPLRLVVSPRLQARAEAA +MAGQGRMMEAFTAAYGPYPFDDYAAVVADDVLEIPLEAAGLSLFGVNHLDGSWESERLIA +HEMAHQWFGNAVTLGRWSDLWLHEGFACYSEWLWAEASGRAALRHEAKQAWHGLKRQGED +LVLAAPGAADMFDDRVYKRGALTVLAVRTLLGDAVFGEMLRDWVARHRFATVDTPGFRAH +VLAWAPRADVAPEDVDALFDAWTLRPELPAFPG +>PROKKA_01391 +MSTDPYVPGVGTDAATVEHIALDLDVRLAANRVSGTAVLRVRLTKQSRRIELDLYRLRVS +RVDAVVDGRAVASSFTQPGRAPSRLVVDLDESRPEGTLVELTVVYAGTPTLRRSPWGTIG +WEELTDGVLVAGQPHGASTWLPCVDSPTSRSTAEITLTCDAGYLPVANGVGAPVRTRGSR +VTWRWRLDQPVPAYLLSVQIGRYRLVDAAPPAEGLPPLRLVVSPRTEQRALRALAPQPAM +MATFIDAYGPYPFEDYTAVVADEELEIPLEAASMSLFGTNHLDGSWESERLIAHEMSHQW +FGNAVTLGRWSDLWLHEGFACWSEWLWAEASGRSSITSMARRAWQKLAAHPVEQALAEPG +PEEMFEDWVYKRGALTVEALRHLLGTDLFGSMLRAWVREHRFGTVDSLGLRTHVHAWAPH +AGVSRAQVDELFDAWTLRPELPPFPG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001192.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001192.fa new file mode 100644 index 0000000000000000000000000000000000000000..7c56784ccdb0bf4778bea183a407ac57485a2444 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001192.fa @@ -0,0 +1,80 @@ +>PROKKA_01443 +MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPAAELQGPIVVGQVLSKEPEP +QKNGKTINWCSVRVVPEGAAQPLTGEGIEPSGVQGIVCGAHNFEVGDKVVVALPGAVLPG +DFRISPRKTYGHVSAGMIASSTELGMGDDGTDGIIVLGDLGLDPEPGTDARDVLDLHGEA +AEINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAAVHPPAADDAGPAVRIDDDAPIHGE +PGATRFVARTVSGVDATRPTPPWLAARLRLAGIRTISLPVDISNYVMWELGQPLHFYDAD +TLSGEIVVRRARAGETLTTLDGKERELDPEDLLITDDSGPIGLAGVMGGAATEVTDATTT +IVVESANFDPVSIARTRRRHRLPSEASKRNERGVDWEIADEAAERAVQLLVELAGGTAEP +GVTDVGTRPQPAVVEMAADFPSALVGVAYTTDEVVETLRALGAEVAVAEAAADVAPRLTV +TAPSWRTDLRIPEDLAEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGL +TEVLAYPFVSEEQNRRFGADSDAQGQALAMVALANPIASQYRYLRLSLLPGLVETARRNL +GRGFRDLALYEMGLVFLPGAQLGSATIPPRAVHPSAEVLADLEAGIPAQPWHVAGLYAGH +DSAPGPDHDPRPVDWQDAIAGALDVADVLGVELTVRQGRHHAFHPGRVAELVVVTEHGDR +VVGVAGELHPQWLEAEDLPARTSVWELDLDALCAAAPEIVVAAPLSTFPVSTQDVALVVD +EAVVAGDVRATLAEGAGELLEAVELFDVYRGAGVPEGRKSLAFSLRFRAPDRTLTAEEVS +EARAAATALAAQRHGAVQR +>PROKKA_01175 +MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPAAELQGPIVVGQVLSKEPEP +QKNGKTINWCSVRVVPEGAAQPLTGEGIEPSGVQGIVCGAHNFEVGDKVVVTLPGAVLPG +DFRISPRKTYGHVSAGMIASSTELGVGDDGTDGIIVLGDLGLDPEPGTDARDVLDLHGEA +AEINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAAVHPPAADDAGPAVRIDDDAPIHGE +PGATRFVARTVSGVDATRPTPPWLAARLRLAGIRTISLPVDISNYVMWELGQPLHFYDAD +TLSGEIVVRRARAGETLTTLDGKERELDPEDLLITDDSGPIGLAGVMGGAATEVTDATTT +IVVESANFDPVSIARTRRRHRLPSEASKRNERGVDWEIADEAAERAVQLLVELAGGTAEP +GVTDVGTRPQPAVVEMAADFPSALVGVAYTTDEVVETLRALGAEVAVAEAAADVAPRLTV +TAPSWRTDLRIPEDLAEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGL +TEVLAYPFVSEEQNRRFGADSDAQGQALAMVALANPIASQYRYLRLSLLPGLVETARRNL +GRGFRDLALYEMGLVFLPGAQLGSATIPPRAVHPSAEVLADLEAGIPAQPWHVAGLYAGH +DSAPGPDHDPRPVDWQDAIAGALDVADVLGVELTVRQGRHHAFHPGRVAELVVVTEHGDR +VVGVAGELHPQWLEAEDLPARTSVWELDLDALCAAAPEIVVAAPLSTFPVSTQDVALVVD +EAVVAGDVRATLAEGAGELLEAVELFDVYRGAGVPEGRKSLAFSLRFRAPDRTLTAEEVS +EARAAATALAAQRHGAVQR +>PROKKA_01455 +MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPSDELRGPIVVGQVLSKEPEP +QKNGKTINWCTVRVVPEGAEQTLTGEGIDPSGVQGVVCGAHNFEVGDKVVVTLPGAVLPG +DFRISPRKTYGHVSAGMIASVRELGIGDDHDGILVLSTLGLDPEPGTDALEVLDLQGEAA +EINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAALTPPAADDAGHPVRIADDAPIYGAP +GATRFVARTVSGVDASRPTPPWMAARLRLAGIRSISLPVDISNYVMWELGQPLHFYDAQK +LAGEIVVRRARAGETLRTLDDKERTLDPEDLLITDDSGPIGLAGVMGGLATEVTDATTTI +VIESANFDPISIARTRRRHRLPSEASKRNERGVDWEIADEAAERAVQLLVELAGGTAEPG +VTDVGTRPELAVVEMAADFPTALVGVEYTADEVAETLRALGAQVEAAEAADGAAPRLRVT +APSWRTDLRIPEDLVEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGHT +EVLAYPFVSAEQNRRFGVDSEEQGEALEMVALANPISSQYRYMRLSLLPGLVEIARRNLG +RGFRDLALYEAGLVFLPGTQLGSASIPPRAAHPAPEVLADLEAGIPAQPWRVAGLYAGHD +SAPGPDHAPRPVDWQDAVSGALAVADVLGVELAVRQGRHHAFHPGRVAELVVLGERGDQV +VGVAGELHPQWLEAEDLPARTSVWELDLDALCAAAPPAVVAVPLSTYPMSTQDVALVVEE +AVVAGDVRASLAEGAGELLESVELFDVYRGPGVPEGSKSLAFSLRFRAPDRTLTAEEASE +ARAAATALAAQRHGAVQR +>PROKKA_01363 +MRIPLDWLREFAQVPADATAEDVLADLVTVGLEEEDVHRPSDELTGPLVVGQVLTREPEP +QKNGKTINWCSVRVVPEGAEQTLTGEGIDPSGVQGIVCGAHNFEVGDKVVVCLPGAVLPG +DFRISPRSTYGHVSAGMMASARELGLGDDHDGIIVLGDMGLDPEVGTDVVDLFHLREEAA +EVNVTPDRSYAFSIRGIAREYAHATGTAFTDPAAAVTAPEANDAGPAVTLADGAGIYGVP +GCDRFVARVVEGIDPAAATPPWMAARLRLAGIRPHSLAVDVSNYVMWELGQPLHFYDADR +LTGGITVRRAAAGETLRTLDDKERTLDPEDLVIADESGAIGLAGVMGGAATEVSEGTTRV +LIESAHFDAVSIARTRRRHRLPSEASKRNERGVDWEIADEAAERAVQLLVELAGGTPAQG +VTDVGTRPEPVVVELDPEYPARRIGVDYPRERVVELLTGLGASVEDAGDLLQVTAPTWRH +DLRIPEDLVEEVARLDGYANIPSTLPVAPPGRGLTRAQVHRRRVADTLAAAGLTEVLDYP +FVSEGQNRLFGSATPEEGAAQRMVRLANPISSEFGWMRTTLLPNLLETVRRNVSRGFKDV +ALFEVGAVFLPGDGALGSPSNEPIGVKPSAETLAELDAGIPAQPRHVAGAFAGHEAAPGA +GFAPRAFDWQDPIAAALAVGRAVGVELTVVQGTHQAFHPGRTATLSLPDGTAVGVAGELL +PAWLEDADMPARTGAFELDLDAVLAAAADRVVARPLSTYPASQQDVALVVADDVVAGDVR +ATLAEGAGELLEEVALFDVYAGKGVPEGHKSLAFSLRFRAPDRTLTADEASEAREAATAL +AAERHGAVQR +>PROKKA_01393 +MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPAAELQGPIVVGQVLSKEPEP +QKNGKTINWCSVRVVPEGAAQPLTGEGIEPSGVQGIVCGAHNFEVGDKVVVTLPGAVLPG +DFRISPRKTYGHVSAGMIASSTELGMGDDGTDGIIVLGDLGLDPEPGTDARDVLDLHGEA +AEINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAAVHPPAADDAGPAVRIDDDAPIHGE +PGATRFVARTVSGVDATRPTPPWLAARLRLAGIRTISLPVDISNYVMWELGQPLHFYDAD +TLSGEIVVRRARAGETLTTLDGKERELDPEDLLITDDSGPIGLAGVMGGAATEVTDATTT +IVVESANFDPVSIARTRRRHRLPSEASKRNERGVDWEVADEAAERAVQMLVELAGGTAEP +GVTDVGTRPQPAVVEMAADFPSALVGVAYTTDEVVETLRALGAEVAVTEAADGAAPRLTV +TAPSWRTDLRIPEDLAEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGL +TEVLAYPFVSEEQNRRFGADSDAQGQVPAMVALANPIASQYRHLRLSLLPGLVETARRNL +GRGFRDLALYEMGLVFLPGAQLGSATIPPRAVHPSPEVLADLEAGIPAQPWHVAGLYAGH +DSAPGPDHAPRPVDWQDAVAGALDVADVLGVELTVRQGRHHAFHPGRVAELVVVTEHGDR +VVGVAGELHPQWLEAEDLPARMSVWELDLDALCAAAPETVVAAPLSTFPVSTQDVALVVD +EAVVAGDVRATLAEGAGELLEAVELFDVYRGAGVPEGRKSLAFSLRFRAPDRTLTAEEAS +EARAAATALAAQRHGAVQR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001196.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001196.fa new file mode 100644 index 0000000000000000000000000000000000000000..478d4e99f71d90206a700a140801f1c906cefdd9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001196.fa @@ -0,0 +1,37 @@ +>PROKKA_01448 +MRWEAQTLRSEGGAQRATAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNSV +PSASAMPFRWTVNPYRGCTHACRYCYARSTHTFLELDAGADFDRQIVVKVNVAEVLRAEL +ARPTWGREAVALGTNTDPYQRAEGRYALMPGIIRALADSGTPFSVLTKGTLLARDVPLLQ +AASRQVPVQVSLSLAMLDPAIAAAVEPGTPSPTARLRLIERLAAAGADVTVMAMPLLPWL +TDGDREIDALMRALADAGAARVMPGALHLRPGAKEWYLDWIRREHPDLLAGYEQMYARSA +YAPESYRRMLTRMAGEAAARHGLARGGAHGIRREDGPPARRRPASRPSAPAAQPALF +>PROKKA_01180 +MRWEAQTLRSEGGAQRATAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNSV +PSASAMPFRWTVNPYRGCTHACRYCYARSTHTFLELDAGADFDRQIVVKVNVAEVLRAEL +ARPTWGREAVALGTNTDPYQRAEGRYALMPGIIRALADSGTPFSVLTKGTLLARDVPLLQ +AASRQVPVQVSLSLAMLDPAIAAAVEPGTPSPTARLRLIERLAAAGADVTVMAMPLLPWL +TDGDREIDALMRALADAGAARVMPGALHLRPGAKEWYLDWIRREHPDLLAGYEQMYARSA +YAPESYRRMLTRMAGEAAARHGLARGGAHGIRREDGPPARRRPASRPSAPAAQPALF +>PROKKA_01451 +MRWEAQTLRSESGAQRAAAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNAV +PAASAMPFRWTVNPYRGCTHACRYCYARSTHAFLDLDAGEDFDRQIVVKVNVAQVLRAEL +ARPTWGREAVALGTNTDPYQRAEGRYSLMPGIIEALADSGTPFSVLTKGTLLARDVPLLQ +AASRSVPVQVSLSLAMLDPAVAAAVEPGTPSPAARLRLIERLAAAGADVTVMAMPLLPWL +TDGDRDLDALMRALAAAGAARVMPGALHLRPGAKEWYLRWIRQEHPDLLAGYEQMYARSA +YAPESYRRTLARAAGEAAARHGLTRGGAHGIRREDGPVARPVPRSTPVAVPAPAAPAQPA +LF +>PROKKA_01355 +MRWEAQTLRTGGGAQRPGAGTPAGSPATLPLPGLQRIVSPPEFAGVTFHEVLARSALNKV +PASSAMPFRWTVNPYRGCTHACVYCYARGTHRYLDLGPGEDFDRQIVVKTNAPEVLRAEL +SRPGWTREPVALGTNTDPYQRAEGRYRLMPGIITALADTGTPFSILTKGTLLGRDAPALQ +AAAAQTSVQVGLSLALLDPSLAAAVEPGTPSPAARLRLISRLAEAGVEVSVMAMPLLPWL +TDSDRQLDRLMAALADAGAHSVLAGTLHLRPGAREWFLGWIDREHPHLAADYRRMYARSA +YAPQAYRRVVSQAAREAAARHGLRHGGAHTITREDGPGPRGGASAPLSAPAGTTGAEQAD +TAADAVRPVIAQPTLF +>PROKKA_01398 +MRWEAQTLRSEGGAQRATAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNSV +PSASAMPFRWTVNPYRGCTHACRYCYARSTHTFLELDAGADFDRQIVVKVNVAEVLRAEL +ARPTWGREAVALGTNTDPYQRAEGRYALMPGIIRALADSGTPFSVLTKGTLLARDVPLLQ +AASRQVPVQVSLSLAMLDPAIAAAVEPGTPSPTARLRLIERLAAAGADVTVMAMPLLPWL +TDGDREIDALMRALADAGAARVMPGALHLRPGAKEWYLDWIRREHPDLLAGYEQMYARSA +YAPESYRRMLTRMAGEAAARHGLARGGAHGIRREDGPPARRRPASRPSAPAAQPALF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001203.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001203.fa new file mode 100644 index 0000000000000000000000000000000000000000..3d254f1393a490a16b5eb31b959f53e13877c4e1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001203.fa @@ -0,0 +1,20 @@ +>PROKKA_01457 +MAQSRRPDPVAPSESSGADATTVPPRPGRGLPVAVLVVAAALVLEAGALLWLAVDAVVHA +ADGVLPAGARVMLVVIYALLTLWILATAVALLRGRAWSRGAAVAIQLFGVLLSSWLFSVD +AAALGGPLLAVSGVALLTLFTTPVTRHLTPAPEASTDA +>PROKKA_01189 +MAQSRRPDPVAPSESSGADATTVPPRPGRGLPVAVLVVAAALVLEAGALLWLAVDAVVHA +ADGVLPAGARVMLVVIYALLTLWILATAVALLRGRAWSRGAVVAIQLFGVLLSSWLFSVD +AAALGGPLLAVSGVALLTLFTTPVTRHLTPAPEASTDA +>PROKKA_01443 +MAQSRRPDPVDPREAPAAPAPEGPRTGGRAPVAALVVAAALALQAAALLWLAGDAIAHLG +DGVLPAGARVMLIVIYVLLGLWILVTSVALLRGRAWSRGAATAVQLFGVLLSSRLLSVGE +PVVGGVLLAVSGIALVTLFSRPVTAHLSQAAREPSAE +>PROKKA_01346 +MSSSIPASPSGRRRMPAQAVVVAGVLGLEALTLVWLAVDGVAHLGAGALPTAAGVFLVVV +YVLLAAWVGAVCGGMVRGRRFSRGAAVAIQLFAVILSTWLMSIGAPIAGGLLLVGSGAAL +LCLFSGAVQAHLAGPDAGRPDAGRPDVG +>PROKKA_01407 +MAQSRRPDPVAPSESSGADATTVPPRPGRGLPVAVLVVAAALVLEAGALLWLAVDAVVHA +ADGVLPAGARVMLVVIYALLTLWILATAVALLRGRAWSRGAVVAIQLFGVLLSSWLFSVD +AAALGGPLLAVSGVALLTLFTTPVTRHLTPAPEASTDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001205.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001205.fa new file mode 100644 index 0000000000000000000000000000000000000000..fad2f705c0efd9ae51254316cda526745bc89020 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001205.fa @@ -0,0 +1,50 @@ +>PROKKA_01459 +MVSSLAQDPLTSHPDIGDEDRAWLQRLVGDWQLVADLALADLVLWCPVPRRDEAGGFVAL +AQVRPFTAPTLFHRDIVGSRARADLRAVVGQTWHGGERAEGAGPVEAPGGTLQVRLWPVV +RAGRVIAVVSAHADPNGRPARSVIEENYSRTASTLLDMMQHGRWPAPEEPSGLWAGGTPR +VGDGLVVLGPDSVAEFTSPNAVSALRRLGIASTLEGHRLTDVLASTEAARVPTDEGTWAV +LTGLRAGRREVQSGGASLTVRSVPLLGPDGWQGALLLLRDVTELRRQEQRLLTKDATIRE +IHHRVKNNLQTVGSLLRMQARRTSSPEAERALRQAMQRVDTIALVHQTLSEEIEDQVPVD +GLLQRQFRLAVEVAGDGRPLQVAVTGEFGELPSHVTTPLALVLNELAANAVEHGTAPGGG +CVGLHADRESTPAGTVLVVSVTDGGPAAPDGWVPGESPRAGEGSGLGLRIVHSLVEGDLR +GTLRWERSDDGGTRVVLRLPLT +>PROKKA_01191 +MVSSLAQDPLTSHPDIGDEDRAWLQRLVGDWQLVADLALADLVLWCPVPRRDEAGGFVAL +AQVRPFTAPTLFHRDIVGSRARADLRAVVGQTWHGGERAEGAGPVEAPGGTLQVRLWPVV +RAGRVIAVVSAHADPNGRPARSVIEENYSRTASTLLDMMQHGRWPAPEEPSGLWAGGTPR +VGDGLVVLGPDSVAEFTSPNAVSALRRLGIASTLEGHRLTDVLASTEAARVPTDEGTWAV +LTGLRAGRREVQSGGASLTVRSVPLLGPDGWQGALLLLRDVTELRRQEQRLLTKDATIRE +IHHRVKNNLQTVGSLLRMQARRTSSPEAERALRQAMQRVDTIALVHQTLSEEIEDQVPVD +GLLQRQFRLAVEVAGDGRPLQVAVTGEFGELPSHVTTPLALVLNELAANAVEHGTAPGGG +CVGLHADRESTPAGTVLVVSVTDGGPAAPDGWVPGESPRAGEGSGLGLRIVHSLVEGDLR +GTLRWERSDDGGTRVVLRLPLT +>PROKKA_01441 +MVSSLAQDPLTSHPDLADEDRSWLQLLVGDWQLVADLALADLVLWCPAPRPDPAEGFVAV +AQVRPFTAPTLFHRDIVGSRARADLRAVVASTWSGGERPEGAGPVETPDGTLQVRLWPVV +RRGRVVAVLSAHGDPNGRPSRSVIEENYIRTADSLLDMMQHGRWPAPEESAGLWAGGTPR +VGDGLVVLGPDSVARFTSPNAVSALRRLGIGATLEGHRLTDVLAGTDAARQPSEEGTWAV +LTGLRAGRREVQSRGASLTVRSVPLLGPDGWHGALLLLRDVTELRRQEQRLVSKDATIRE +IHHRVKNNLQTVGSLLRMQARRTSSPEADRALRQAMRRVDTIALVHQTLSEEIDGQVPVD +DLLKRQFRLAVEVSGDGRPLEAAASGEFGELPSHVTTPLALVLNELAANAVEHGTAPAGG +RVELHAERELTPAGSVLVVSVTDGGSGVQDGWSPGEFQPAADGAGLGLRIVQTMVEGDLR +GTLRWERLPDGGTRVVLRIPTA +>PROKKA_01344 +MVSTIASDPLNTHPDLGAEDRAWLQQLVGDWQLIADLALADLVLWCPLPVEVDGTGHLAM +AQVRPFTAPTLFHRDIVGSRARADLRALVDRVWAAGAPADGTGPLVEPGATLKVRLWPVV +RAGRVVGVVSAHEDPRTRPARSAVEDNYRTSADTLLDMVQHGRWPNPEDPPAYWIGGTPR +VGDGLVVLGDDSRATFTSPNAVSALRRLGLPTTLAGHSLTELLGGTEAARRPVEEGSWAM +LNGQRAGRTEVQANGATLTVRSVPLRNRDGWCGALIMLRDVTELRRQEQRLISKDATIRE +IHHRVKNNLQTVGSLLRMQARRSDSPETGRALRQAMQRVDTIALVHQTLSEQIDAQLSVD +ALMARQFRLAVEVAGDGRPLGTRVEGTFGELASHVVTSVALVLNELATNAVEHGTGEEGG +VVSLQAHREDTPAGDVLVFSVTDGASVEDGPGEGFVPQPAPNGLGLRIVHSLVEGDLRGS +IQWRRMPDGGTRVTVRLPVE +>PROKKA_01409 +MVSSLAQDPLTSHPDIGDEDRAWLQRLVGDWQLVADLALADLVLWCPVPRRDEAGGFVAL +AQVRPFTAPTLFHRDIVGSRARADLRAVVGQTWHGGERAEGAGPVEAPGGTLQVRLWPVV +RAGRVIAVVSAHADPNGRPARSVIEENYSRTASTLLDMMQHGRWPAPEEPSGLWAGGTPR +VGDGLVVLGPDSVAEFTSPNAVSALRRLGIASTLEGHRLTDVLASTEAARVPTDEGTWAV +LTGLRAGRREVQSGGASLTVRSVPLLGPDGWQGALLLLRDVTELRRQEQRLLTKDATIRE +IHHRVKNNLQTVGSLLRMQARRTSSPEAERALRQAMQRVDTIALVHQTLSEEIEDQVPVD +GLLQRQFRLAVEVAGDGRPLQVAVTGEFGELPSHVTTPLALVLNELAANAVEHGTAPGGG +CVGLHADRESTPAGTVLVVSVTDGGPAAPDGWVPGESPRAGEGSGLGLRIVHSLVEGDLR +GTLRWERSDDGGTRVVLRLPLT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001210.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001210.fa new file mode 100644 index 0000000000000000000000000000000000000000..88c97c35fdf11ce2468d3344b660aaafaf25fca2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001210.fa @@ -0,0 +1,31 @@ +>PROKKA_01464 +MERSTSPAGPAPTRPVDAADAVGLTVLLLAGPGLLACAAALLQTGTSAPGAELTRVLGLG +AGLAGLGLLAWWAVGLIGLALVALGRRAGRPAWARLGRSLTPALLGRVAGAVVGAQLLAA +PAAWADAAHPVPDASWTVAAVPAHATGVEAPAPDAAWTPRPPAPAPPGAGTGRADPDHPT +VTVRRGDCLWHLAAAELGPDATPREIDARWRRWYEANRRVIGDDPHLLLPGTVLTSPVFT +PHAGVDGPRP +>PROKKA_01196 +MERSTSPAGPAPTRPVDAADAVGLTVLLLAGPGLLACAAALLQTGTSAPAAELTRVLGLG +AGLAGLGLLAWWAVGLTGLALVALGRRAGRPAWARLGRSLTPALLGRVAGAVVGAQLLAA +PAAWADAAHPVPDASWTVAASPTHATGVEAPAPDAAWTPRPPAPAPPGAGTGRADPDHPT +VTVRRGDCLWHLAAAELGPDATPREIDARWRRWYEANRRVIGDDPHLLLPGTVLTSPVFA +PHAGVDGPRP +>PROKKA_01436 +MQRITEPARRGRAALSEADGHRADGHRVDTVDAVGLVVLALAAPALLIGAAALLEPGEGA +ASSELVRLLGLGAGIAGLGLVAWWAVGLLGLVLATVGRRTGRLGFARLGARLTPALLGRV +AGAVLGAHMLAAPAAWAEQPAVGPVPDAGQTVSHAAPASTTASAPAAVPEAAWTPRTPVP +APPGATAARNLSDRPTVTVRRGDCLWDIAAAELGPDATPREIDARWRRWHEANRRVIGDD +PHLLLPGTVLTAPVFSPHAAPQEGLAMTPRPRTTPTTTRPQEPAMTALAARPPSPPSTAA +PAVSPGTPTVAPTVPPPRCCTVPPTARPCCPAARRSPAGPPSSRAGRSCVGSAPWPR +>PROKKA_01339 +MSFVASQPPAAGVHAPRASALDVAALAVLAAAVPALGWAAATLLGPAAPTPDAALGRALG +LGAAGLGLALAAWWALGLLGLAALALGRRTGHRGWSRLGERMTPALLRRAGAAVLGAQLL +AAPAAWADAPPAPSAAVVDASWTSAAASPTLPDAAWTPGAPPTPQPGSPAAPRDTGDRPT +VTVRAGDCLWDIAADELGPDATPREVDRRWREWHRHNRDLIGEDPNLILPGTVLTAPDFT +PHVQRGGTP +>PROKKA_01414 +MERSTSPAGPAPTRPVDAADAVGLTVLLLAGPGLLACAAALLQTGTSAPGAELTRVLGLG +AGLAGLGLLAWWAVGLIGLALVALGRRAGRPAWARLGRSLTPALLGRVAGAVVGAQLLAA +PAAWADAAHPVPDASWTVAAVPAHATGVEAPAPDAAWTPRPPAPAPPGAGTGRADPDHPT +VTVRRGDCLWHLAAAELGPDATPREIDARWRRWYEANRRVIGDDPHLLLPGTVLTSPVFT +PHAGVDGPRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001212.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001212.fa new file mode 100644 index 0000000000000000000000000000000000000000..bbb17b5793afe803122133822a293b712863350a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001212.fa @@ -0,0 +1,85 @@ +>PROKKA_01466 +MPSIIDRVLKISDNRVLKRMQATVDAVNLLEDDFRALSDAELRAETDTLRARHADGESLD +LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL +SGRGVHVVTVNDFLASYQADLMGRVFRFLGMQTGVIVAGQTPAVRREQYAADITYGTNNE +FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA +RLVRRLEADTDYEVDHKKRTVGILGPGIEKVEDHLGITNLYETQNTTLIQFLNNAVKAKE +LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ +NYFRGYEKLAGMTGTAETEAAEFTSTYGLGVVVIPPNRERQRVDRNDVVYKNEKVKFDAV +VDDIAERHAKGQPVLVGTTSVEKSEYLSTLLAKRGVRHEVLNAKNHAREAAIVAQAGRPG +AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLAQAEAAVED +AHRAVIEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA +QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLKYDDVMNRQREAIYTDR +RSILEGEDLQDRVRRFVEDAVGNIVDAATEEGHATDWDLDQLWRDLAELYPVGISQEDVL +DEVGGRGRLKAEVLKRELVSDALLAYEDREAQVGSEALREAERRVVLATIGRRWQEHLYE +MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAAIREDAVRTLFQAQISAAPASTSLP +GVQDARAVTMAPQISVEGIDAPQQPAQLRFTGPSEDGQSAVTRSGTDSGATVAAGTNRRS +RRQAERRGRRG +>PROKKA_01198 +MPSIIDRVLKISDNRVLKRMQATVDAVNLLEDDFRALSDAELRAETDTLRARHADGESLD +LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL +SGRGVHVVTVNDFLASYQADLMGRVFRFLGMQTGVIVAGQTPAVRREQYAADITYGTNNE +FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA +RLVRRLEANTDYEVDHKKRTVGILGPGIEKVEDHLGITNLYETQNTTLIQFLNNAVKAKE +LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ +NYFRGYEKLAGMTGTAETEAAEFTSTYGLGVVVIPPNREPQRVDRNDVVYKNEKVKFDAV +VDDIAERHAKGQPVLVGTTSVEKSEYLSTLLAKRGIRHEVLNAKNHAREAAIVAQAGRPG +AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLAEAEAAVED +AHRAVIEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA +QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLKYDDVLNRQREAIYTDR +RSILEGEDLQDRVRRFVEDAVGNIVDAATEEGQATDWDLDQLWRDLAEIYPVGVSQEDVL +DEVGGRGRLTAEVLKRELVSDALLAYEDREAQVGSEALREAERRVVLATIGRHWQEHLYE +MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAAIREDAVRTLFQAQISAAPAPTSLP +GVKDARAVTMAPQISVEGIDAPQQPAQLRFTGPSEDGQSAVTRSGTDSGATVAAGTNRRS +RRQAERRGRRG +>PROKKA_01434 +MPSIIDRVLKISDNRVLRRMQGTVDAVNLLEEDFRALSDAELRAETDTLKARHADGESLD +LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL +TGRGVHVITVNDFLASYQAELMGRVFRFLGMETGVVVAGQLPAVRREQYAADITYGTNNE +FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA +RLVRRLEEGSDYEVDHKKRTVGVLGPGIEKVEDHLGIANLYETQNTTLIQFLNNAVKAKE +LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ +NYFRGYDKLAGMTGTAETEAAEFTSTYGLGVVVIPPNRERQRVDRNDVVYKNEKVKFDAV +VEDIAERHERRQPVLVGTTSVEKSEYLSTLLAKRGIRHEVLNAKNHAREAAIVAQAGRPG +AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPQVLAEAEAAVED +ANREVLEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA +QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLKYDDVMNRQREAIYADR +RSILEGEDLKDRVRRFVEDAVGNIVDATTEEGHAADWDLDQLWRDLSELYPVGITQEDVL +EEVGGRGRLKAEDLRRELVSDALLAYEDREAQVGSEALREAERRVVLSAIGRRWQEHLYE +MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAGIREDSVSTLFKAQITAAPAPTSLP +GIKDARGLTMTPQISVEGVEAPQRPSQLRFTGPSEDGQGAVTRAGTETGATVEAGTNRRS +RREAERRERRS +>PROKKA_01337 +MPSIIDRVLKISDNRVLKRMRGTVDAVNLLEDDFRALSDAELRAETDSFKKRLADGETLD +LLLPEAFAAVREAAGRTLGQRHYDVQLLGGLALHQGNIAEMKTGEGKTLVATAPAYLNAL +TGKGVHVVTVNDFLASYQADLMGRVYRFLGMETGVIVSGQDPATRRAQYAADITYGTNNE +FGFDFLRDNMAWSKEELVQRGHHFAIVDEVDSILIDEARTPLIISGPAQGDISRWYGEFA +RLVRSLERGTDYEVDEKKRTVGVLEPGIEKVEDHLGIANLYESQNTTLVQFLNNAVKAKE +LFKRDKDYVVLDGEVQIVDEHTGRVLAGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ +NYFRGYEKLSGMTGTAETEAAEFTSTYGLGVVVIPPNREKQRVDRNDLVYKNEKVKFDAV +VKDIAERHATGQPVLVGTTSVEKSEYLSTLLTKAGVRHEVLNAKNHAREAAIVAQAGRPG +AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLEQAEAAVQD +AREKVREAGGLYVLGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDDLMRNFNPGAA +QRIMNSASIPDDMALEFKMVSSAIQNAQSQVEGRNAEQRKNVLKYDDVMNRQREAIYADR +RAILEGDSLGERVRGFVEDAVGAVVDAATEEGAPVDWDLEKLWETLREVYPVGISPEDVL +EQVGGRGRLKAADLKRELVSDALLAYDDREAQVGSEALREAERRVVLAMIGRHWQEHLYE +MDYLKEGIGLRAMAQREPLVEYQREGFTMFQAMLAAIKEDSARTLFHAQIAAAPAPTQLP +GVKDARAMTMVPQISVEGVETPRQPARLHLSGPSEDGEGVEEKDLAADGAQTPAGANRAS +RRAEARRRRRGED +>PROKKA_01416 +MPSIIDRVLKISDHRVLKRMQATVDAVNLLEDDFRALSDAELRAETDALRARHADGESLD +LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL +SGRGVHVVTVNDFLASYQADLMGRVFRFLGMQTGVIVAGQTPAVRREQYAADITYGTNNE +FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA +RLVRRLEADTDYEVDHKKRTVGILGPGIEKVEDHLGITNLYETQNTTLIQFLNNAVKAKE +LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ +NYFRGYEKLAGMTGTAETEAAEFTSTYGLGVVVIPPNRERQRVDRNDVVYKNEKVKFDAV +VDDIAERHAKGQPVLVGTTSVEKSEYLSTLLAKRGVRHEVLNAKNHAREAAIVAQAGRPG +AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLAEAEAAVED +AHRAVIEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA +QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLQYDDVMNRQREAIYTDR +RSILEGEDLQDRVRRFVEDAVGNIVDAATEEGHATDWDLDQLWRDLAELYPVGISQEDVL +DEVGGRGRLKAEVLKRELVSDALLAYEDREAQVGSEALREAERRVVLATIGRRWQEHLYE +MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAAIREDAVRTLFQAQISAAPAPTSLP +GVKDARAVTMAPQISVEGIDAPQQPAQLRFTGPSEDGQSAVTRSGTDSGATVAAGTNRRS +RRQAERRGRRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001215.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001215.fa new file mode 100644 index 0000000000000000000000000000000000000000..ec40f47c0b13f5d6131cccec8a0239f03152f941 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001215.fa @@ -0,0 +1,55 @@ +>PROKKA_01469 +MTTVDPQPPRPPRVAVVAVIVALVLALSGCTQIPQSSEVRSADPVDGASAAADAPQFHPP +GPAESDTAEEAIRGFLLAGTSPQDDYAVAREFLDGPAATQWTPGQRTLVYSAEPRITRGD +GDGDYQIQVEVDSEIDEYGLRTVAPPGTTRAWAVTVQERPQGMRITSTENGTLLSQAQFG +QLFAPHELAFYDTAKRYIVPDVRWFVNRGTTVTAVTRALLRGPAPYLAGAVETAFPLRTG +TDLAAPTVPVDDDGVAHVDLTQAAAEGADAERRHRMREQLELTLRGLQSVKEVEVTVAGA +QLSTSGDDGPAPVQTDPAVRSVQVGIDAATGGLVYVQGSSVTPVGGAPDVTALDPVRPTM +SGDRSRFAFVTGDRTAVHVAGTDGSLREVLRGTGLTVPSLDLLGWVWAADRGTTSRIRAV +SAQPGGQERIVTATWLRPGERIVDLRLARSGARAAMLVDDGQRTTLRVSGVVRGSDGVPN +ALTEPILLPSSGSEDSVEWAGDTNLLVSAYAEKPDERVVPRIVSIDGTVRELNPLGGLRG +ISAGDDGAYYAETEELVFLLVGSSWRAQELDRGVRDLSFPD +>PROKKA_01201 +MTTVDPQSPRPPRLAVVGVIVALMLALSGCTQIPQSSEVRSADPVDGATADADAPQFHPP +GPAESDTAEEAIRGFLLAGTSPQDDYAVAREFLDGPAATQWTPGQRTLVYSAEPRITRGD +GAGDYQIQVEVDSEIDEYGLRTIAPPGTTRAWAVTVQERPQGMRITSTENGTLLSQAQFG +QLFAPHELAFYDTAKRYVVPDVRWFVNRGTTVTAVTRALLRGPAPYLAGAVDTAFPLRTG +TDLAAPTVPVDDDGVAHVDLTQAAAEGADAERRHRMREQLELTLRGLQSVKEVEVTVAGA +QLSTSGDDGPAPVQTDPAVRSVQVGIDAATGGLVYVQGSSVTPVGGAPDVTALDPVRPTM +SGDRSRFAFVTGDRTAVHVAGTDGSLREVLRGTGLTVPSLDLLGWVWAADRGTTSRIRAV +SAQPGGQERIVTATWLRPGERIVDLRLARSGARAAMLVDDGQRTTLRVSGVVRGSDGVPN +ALTEPILLPSSGSEDSVEWAGDTNLLVSAYAAKPDERVVPRIVSVDGTVRELNPLGGLRG +ISAGDDGAYYAETEEFVFLLVGSSWRAQELDRGVRDLSFPD +>PROKKA_01431 +MSPTRPTGPRRARRLAGVGLAAALALALGGCTQIPQSSDVRSAEPLDGATAAPEAPQFRP +PGPSADDTAEDVIRGFLLAGTSPQDDYAVAREFLDGPAAARWAPGQRTLVYSAQPRITRG +EGTGNYQVQVEVDSEIDEFGLRTIAPEGTTRAWQVSVQERPEGMRITATENGTLLSQSQF +GQLFAPHELAFYDTAQRYAVPDVRWFVNRGTTVTAVTRALLRGPAPYLTGAVETAFPLRT +GADLAGPTVPVDEDGVAHVDLTEAAAEGADADRRHRMREQLEITLLGLQSVSDVRVTVDG +AELSASGENPPPPVQDEPTTGSVQVGIDSATGDLAYFQGMSVGPVGGAPDVSALDPVDPT +MSRDRSRFAFVTRDRTAVHVAGTDGSLREAMRGTGLTSPSIDGLGWVWAADGAETSRVRA +VPAEPGQEARIVTATWLRPAERIVDLRVSRSGARAALLVDDGDRRTVRVAGIVRGSDGVP +SALTEPILLPSTGRAASVEWAGDTNLLVSPRAATPDERVVPRIVSIDGTVRELNPLGGLT +GVSAGDGGALYAETDELVFLLVGSSWRAQELERGVRDLSFPG +>PROKKA_01333 +MRPSGPARPRRRLCAAALAGALALAGCAQIPQSSPVRSGAPLDVGSRAADAPQFRPPGPA +EDATAEQLVRGFAQAGIAPEDGYAIARQYLSAEASDGWEPDRGVVVYSGEPTVTRGLGEG +TYEVQLEVESEVDEFGQRTMAPPNTTQAREVTVEEVDGVLRITGVQDGVLLSRSQFAQLY +APHPLYFFDQSQAFAVPDVRWFVNRGTAVTALTRALLRGPAPYLTGAVATAFPLRTGADL +TGPSVPVAEDGTAAVDLTGATVDGADPARLSRMREQLERTLTGVSGVERVEVTVEGRSLT +SSAPSGSVPSARIGEDPGTVQVGVSDAGELVFFQGLDAVPVGGLPSVADLGPEDPAMDRE +RRRFVFLDRTRTVLHGVGTDGGEHRLLDGGRLTAPSLDSSGWAWTVDRARSSRISVVRAD +GSEPARVVTTPWLAEGESIVALHIGPAGARAALIVDDGQQRTLRVAGVVRGGDGVPTALT +PPVYIPTLDPPDDVEWMGDGSLVSTPLAPDAETRVRPEVVSLDGTSRQLNPLAGLTGISA +REEGTLYAETAEDVFLLVGSSWRAQDVATPVHDLAFPD +>PROKKA_01419 +MTTVDPQPPRPLRVAVFAVIVALVLALSGCTQIPQSSEVRSADPVDGATAAADAPQFHPP +GPAESDTAEEAIRGFLLAGTSPQDDYAVAREFLDGPAATQWTPGQRTLVYSAEPRITRGD +GAGDYQIQVEVDSEIDEYGLRTVAPPGTTQAWAVTVQERPQGMRITSTENGTLLSQAQFG +QLFAPHELAFYDTAKRYVVPDVRWFVNRGTTVTAVTRALLRGPAPYLAGAVDTAFPLRTG +TDLAAPTVPVDDDGVAHVDLTQAAAEGADADRRHRMREQLELTLTGLQSVKEVEVTVAGA +QLSTSGDDGPAPVQTDPAVGSVQVGIDTATGGLVYVQGTSVTPVGGAPDVTALDPVRPTM +SGDRSRFVFVTRDRTAVHVAGTDGTLREVLRGTGLTVPSLDLLGWVWAADRETTSRIRAV +PAQPGGQERIVTATWLRPGERIVDLRLSRSGAQAAMLVDDGQRTTLRVSGVVRGSDGVPN +ALTEPILLPSSGSEDSVEWAGDTNLLVSAYAEKPDERVVPRIVSIDGTVRELNPLGGLRG +ISVGDDGAYYAETEELVFLLVGSSWRAQELDRGVRDLSFPD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001217.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001217.fa new file mode 100644 index 0000000000000000000000000000000000000000..5893c332d31223ae65dba9a487531489391c5742 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001217.fa @@ -0,0 +1,40 @@ +>PROKKA_01472 +MTEAAHDDGATGPVALGGTPWRGTDVAEAQRVTLGELGADHWPVLPELPDRGPGADATGR +SAALLQQLAVDLQPHGWRVSPPGAAGSGRDRRRAVSLWREDAHRWADTAGAEGAVVERLA +VRVRGPLSLLACLWLPGGERVLGDHGARRDVAESYLEGLQDALPRLRRATGAGRLGVVVD +EPWAAAVLAGTLPTASGYRTVRSLPREEARGLWRAALDGLTALPDVARVWLAPGRRAASP +GAELPGPAALSTLTGESLPRPDAAADAPAPAPVSLVVGVGALDDGADGTPGTREAWEAAA +GWADIGRGLTLAPEPGVRPVEVVRTWERLGVDPGRVGDVGLTAAGLHDPVVLHTLRRDAE +ELTARLAELRG +>PROKKA_01204 +MTEAAHDDGATGPVALGGTPWRGTDVAEAQRVTLGELGADHWPVLPELPDRGPGADATGR +SAALLQELAVDLQPHGWRVSPPGAAGSGRDRRRAVSLWHEDAHRWADTAGAEGAVVERLA +VRVRGPLSLLAGLWLPGGERVLGDHGARRDVAESYLEGLQDALPRLRRATGAGRLGVVVD +EPWAAAVLAGTLPTASGYRTVRSLPREEARGLWRAALDGLTALPDVARVWLAPGRRAASP +GAELPGPAALATLTGESLPRPDAAADAPVPAPVSLVVGVGALDDGADGTPGTREAWEAAA +GWADIGRGLTLAPEPGVRPVDVVRTWERLGVDPGRVGDVGLTAAGSHDPAVLRTLRRDAE +ELTARLAELRG +>PROKKA_01428 +MPEAHDDGARPVALGGSPWAGTDAAEAQRVTLGELGAEHWPVLPELPSRGPGADATGRSA +ALLSELAVDLQPHGWRVSPPGAAGSGMDRRRAASFWREDAHRWADTAGAEGAVVERLAVR +VRGPLSLLGGLWLPGGERVLADHGARRDVAASYLEGLLEAVPRLRAATGAAGLGLLVDEP +WAAAVLAGALPTASGYRTVRSLPRDEARGLWRELLAGLTALPGVASVWLAPGRRTASAAD +VPATAELAALAGECLPAAGGEDDDAGAPVRLVVPVGDLDDGPDGTAGTRAAWESAAGWAD +AGRGLTLSPAAHLRPADVVTTWERLGADPAHLRGTGLTAPGRHDATVLRRLRTDAAELAA +RLDDALG +>PROKKA_01330 +MPEASDDVGAVRVAALGGAPWRGTDAAEAQLATLGELGAEHWPVLPELPDRGPGADATGR +SAALLHELAVDLQPHGWRVSPPGVVGSGMDRRRAASFWREDAHRWADTAGAEGAVVERLG +VRLRGPLSLLGSLWLPGGERVLVDHGARRDVAASYVEGLRDAVPRLAAATGARTLGVVLD +EPWAAAVLAGALPTASGYRTVRSVPRDEVRALWRDALAALADLPGVGRVWLAPGRRSAGV +DVPLPDVSALAALAGESLPAAAPSADDDAPAPTRVDLVVPVGALDPGPDGTGGTRAGWET +AAGWTDAGRGLTLSTATGVRPADVARTWERLGADPGHLAGVGLTVPGPHDAAVLGRLRAD +AEELAARVGELLG +>PROKKA_01422 +MTEAAHDDGATGPVALGGTPWRGTDVAEAQRVTLGELGADHWPVLPELPERGPGADATGR +SAALLQELAVDLQPHGWRVSPPGAAGSGRDRRRAVSLWREDAHRWADTAGAEGAVVERLA +VRVRGPLSLLAGLWLPGGERVLGDHGARRDVAESYLEGLQDALPRLRRATGAARLGVVVD +EPWAGAVLAGTLPTASGYRTVRSLPREEARGLWRAALARLTALPDVARVWLAPGRRAASP +GAELPGPAALATLTGESLPRPDAAADAPARAPVSLVVGVGPLDDGADGSPGTREAWEAAA +GWADVGRGLTLAPEPGVRPVDVVRTWERLGVDPGRVGDVGLTAAGPHDPAVLRTLRRDAE +ELAARLAELRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001220.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001220.fa new file mode 100644 index 0000000000000000000000000000000000000000..0f9d10b62f6d923fe0f2240b61ddc17798b80b6f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001220.fa @@ -0,0 +1,41 @@ +>PROKKA_01475 +MTTPDRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLRLEEARERIAAAL +GAHPTEVILTSGGTEADNLAIQGLYRARRAAAPERTRIVLTGIEHHAVLDVVDWLAAHEG +AEPVLVPVDDDGRVDLAAWGAALATAPERTALATLMWANNEIGTVQPVAEAARLAADHGV +PLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALLVRRDVTLEAVVHGGGQER +RLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLTGPRDLDP +ATGQALSPGTRRLPGNVHITVPGRTADALLFSFDMAGLDTSSGSACTAGVAEPSHVVAAL +PGRTEADARATQRFTLGRTTTPAEAAALIDALRTLLGPGV +>PROKKA_01207 +MTTPDRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLHLEEARERIAAAL +GAHPPEVILTSGGTEADNLAVQGLYRARRAVAPERTRIVLTGIEHHAVLDVVDWLAAHEG +AEPVLVPVDDDGRVDLAAWGAALAAAPERTALATLMWANNEIGTVQPVAEAARLAADHGI +PLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALFVRRDVTLEAVVHGGGQER +RLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLTGPRDLDP +ATGEPLPPGTRRLPGNVHITVPGRTADALLFSFDMAGLDTSSGSACTAGVAEPSHVVAAL +PGRTEADARATQRFALGRTTTPAEAAALIDALRTLLGPGV +>PROKKA_01425 +MPSAATPRPLGERVHLDHAATTAVRPSALAALAEAAALPGNPASLHASGRRAKLALEQAR +EAVAAALGAHPSEVVLTSGGTEADNLAVQGLFRARRAADPQRLRIVLTGAEHHAVLDAVD +WLAAHEGAEPVIVPVDADGVVDLAAWEAALAAAPERTALAALMWANNEIGTVQPVAEAAR +IAAAHGVPLHTDAVQAVGAVPVDFAASGAATLAVSGHKAGAPVGVGALLVRRDVALTPVV +HGGGQERRLRSGTVSVALAAALAAALTEAVAEQPAEAVRLGVLRDRVIEAVEALETVVLT +GPRDADPATGEPLPPGTRRLPGNVHVTVPGRTADALLFTFDTAGLDTSSGSACTAGVAEP +SHVVAALPGRTEADARATQRFTLGRTSTSADVDALIAALRALAPAPRRGAPTPKGAPTTK +EESR +>PROKKA_01327 +MTTPDRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLHLEEARERIAAAL +GAHPTEVILTSGGTEADNLAVQGLYRARRAAAPERTRIVLTGIEHHAVLDVVGWLAAHEG +AEPVLVPVDDDGRVDLAAWGAALAAAPERTALATLMWANNEIGTVQPVAEAARLAADHGV +PLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALLVRRDVTLEAVVHGGGQER +RLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLTGPRDLDP +ATGEPLPPGTRRLPGNVHITVPGRTADALLFFFDMAGLDTSSGSACTAGVAEPSHVVAAL +PGRTEADARATQRFTLGRTTTPAEAAALIDGLRTLLGPASRLDRPSVVERGVRP +>PROKKA_01425 +MTTPDRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLHLEEARERIAAAL +GAHPSEVILTSGGTEADNLAVQGLYRARRAVAPERTRIVLTGIEHHAVLDVVDWLAAHEG +AEPVLVPVDDDGRVDLAAWGAALAAAPERTALATLMWANNEIGTVQPVAEAARLAADHGI +PLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALFVRRDVTLEAVVHGGGQER +RLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLTGPRDLDP +ATGEPLPPGTRRLPGNVHITVPGRTADALLFSFDMAGLDTSSGSACTAGVAEPSHVVAAL +PGRTEADARATQRFALGRTTTPAEAAALIDALRTLLGPGV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001221.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001221.fa new file mode 100644 index 0000000000000000000000000000000000000000..ec38cfba4da0d4717ae969d969e84ce2816d7ec6 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001221.fa @@ -0,0 +1,35 @@ +>PROKKA_01478 +MSREGNIVLPGRTVTVRRRWLNGRVPTPSVPLVHPVHRFAHHEIDFRRRIVTMAVVNRTP +DSFYDDGAGAVLEDALAQAHAAADAGAEWVDVGGVPFAPGAELDPTEEAARVVPLIAALR +SGDGAGSSEASRRLILSADTFQPAVAEAALAAGADVVNDTTGLFHADLGRVVAAAGAHLV +VTHSLAHVRGPRAVVPRPTYGDVVREVRDHLRRTVDRAVALGVPEERIIVDPGHDLNKNT +RHTLEITRRLDEIATLGLPVLAAVSNKDFIGESLDRHRHERLPGSLAAAAACVYGGARIL +RMHDADASVSAARMLECVFGWRQPARLVHNMGAENPPPDRSTLAGHRAHRGGRA +>PROKKA_01210 +MSREGNIVLPGRTVTVRRRWLNGRVPTPSVPLVHPVHRFAHHEIDFRRRIVTMAVVNRTP +DSFYDDGAGAVLEDALAQAHAAADAGAEWVDVGGVPFAPGAELDPTEEAARVVPLIAALR +SGDGAGSSEASRRLILSADTFQPAVAEAALAAGADVVNDTTGLFHADLGRVVAAAGAHLV +VTHSLAHVRGPRAVVPRPTYGDVVREVRDHLRRTVDRAVALGVPEERIIVDPGHDLNKNT +RHTLEITRRLDEIATLGLPVLAAVSNKDFIGESLDRHRHERLPGSLAAAAACVYGGARIL +RMHDADASVSAARMLECVFGWRQPARLVHNMGAENPPPDRSTLAGHRAHRGGRA +>PROKKA_01424 +MRQNVAMALTELALRHPVRRFARREVDFRRRILTMAVVNRTPDSFYDDGAAFALEAAVDQ +ARAAAEAGAEWVDVGGVPFAPGPALDPGEEARRVVPLIAALRGEAAEHSEAVAGLILSAD +TFEPAVAEAAIAAGADVVNDTSGLVHADLGRVVAASQAHLVLTHSLAHVHGPRAVVPRPR +YGDVVAEVREHLLRTVERAVALGVPEERIIVDPGHDLNKNTLHTLEITRRLDEIAGLGLP +VLAAVSNKDFIGESLDQHRHERLAGSLAAAVACVHGGARILRMHDAAASVSAARLLECVF +GWREPARLVHNMGEANPAPDRTSLAEHRAGRVRAGGTR +>PROKKA_01324 +MPTPSVPLAHPVHRFAHHEIDFRRRIVTMAVVNRTPDSFFDDGAGFAFDAALAQVHTAAD +AGAEWVDVGGVPFAPGRELDPAEEAARVAPFVAAVRAGRGEGASEAARRLILSADTFQPA +VAEAAIDAGADVVNDTTGLYYPDLGRVVAASNAHLVVTHSLAHVSGPRTVVPRPRYDDVV +AEVREHLLRTVDRAVALGVPEERIIVDPGHDLNKTTVHTLEVTRRLDEIADLGFPVLAAV +SNKDFIGESLDRHRHDRLAGTLASAAFCALAGARILRMHDADASVSTAHMLECILGWREP +LLAVHNTGDVNPAADRTTPADRVPADRPPAAVPAPTHDPEEARP +>PROKKA_01428 +MSREGNIVLPGRTVTVRRRWLNGRVPTPSVPLVHPVHRFAHHEIDFRRRIVTMAVVNRTP +DSFYDDGAGAVLEDALAQAHAAADAGAEWVDVGGVPFAPGAELDPTEEAARVVPLIAALR +SGDGAGSSEASRRLILSADTFQPAVAEAALAAGADVVNDTTGLFHADLGRVVAAAGAHLV +VTHSLAHVRGPRAVVPRPTYGDVVREVRDHLRRTVDRAVALGVPEERIIVDPGHDLNKNT +RHTLEITRRLDEIATLGLPVLAAVSNKDFIGESLDRHRHERLPGSLAAAAACVYGGARIL +RMHDADASVSAARMLECVFGWRQPARLVHNMGAENPPPDRSTLAGHRAHRGGRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001222.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001222.fa new file mode 100644 index 0000000000000000000000000000000000000000..5478cd40623294d4fa249d223e8a1a1d310b37e8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001222.fa @@ -0,0 +1,30 @@ +>PROKKA_01479 +MRRLTETGPGLDDDALRTALAAPAAEDTGPGPWVRVVFIASADGAATLDGRAGGLGSPAD +QRLLSLSRHDADVVLVGAGTIRAEGYEGALLSEEDRRRRAEAGGPADPPVAVVSGSLDLD +PASAFFTAAPVRPWILTSRAALAAEPERAAALAARADVLAVGEEHVDPQTVVATLHARGA +RVVHCEGGPRLFGSLAAAGLVDEVHLTVAPLLAGPAAGRVLTGEDGPGLPARLQLVQVLH +DDGMLFLRLHHERHASPGPDPTP +>PROKKA_01211 +MRRLTETGPGLDDDALRTALAAPAAEDTGPGPWVRVVFIASADGAATLDGRAGGLGSPAD +QRLLSLSRHDADVVLVGAGTIRAEGYEGALLSEEDRRRRAEAGGPADPPVAVVSGSLDLD +PASAFFTAAPVRPWILTSRAALAAEPERAAALAARADVLAVGEEHVDPQTVVATLHARGA +RVVHCEGGPRLFGSLAAAGLVDEVHLTVAPLLAGPAAGRVLTGEDGPGLPARLQLVQVLH +DDGMLFLRLHHERHASPGPDPTP +>PROKKA_01423 +MRRLAAVGPELSDEDLLALRRAPSTQDAPGPWVRAVFVSSLDGATALDGRSGTLGSPADR +RQFALARTDADVILVGAGTVRAEGYAGPLVDAAARARRAARGLPEHPAVAVVTGSLDLDP +DGEFFRAAPVRPWVIASERAVAAQPERAAALAEVADVLTAGVRDVEPRELLALLAGRGAR +VVHCEGGPTLLGALAAAGAVDELLLTLSSLLAGGAGPRLIPAVEGIGLPARMLPHHVLTQ +DGDLYLRLLHERHAALLADAPGLDGRAGTGR +>PROKKA_01323 +MRLLTATGPEIDDDALLALRRAPAPDLVPGPWVRAVFVSSLDGAATLDGRAGGLGSPADQ +RQFTLARTDADVVLVGAGTVRAEGYEGPLVGPAARARREEAGLPAHPGIAVVSGALGLDP +DGDFLRQAPVRPLILTTQTALERCPDRAEALAARADVVASGAEVVEAPALVDALTARGHR +VLHCEGGPRLFGTLAAADLVDELLLTISPLLAGGDGPRVLSGGDGPGLPTRLRPHHVLTE +DGELYLRLVHERHAAVLAEAPGLEADPADADPAPGAP +>PROKKA_01429 +MRRLTETGPGLDDDALRTALAAPAAEDTGPGPWVRVVFIASADGAATLDGRAGGLGSPAD +QRLLSLSRHDADVVLVGAGTIRAEGYEGALLSEEDRRRRAEAGGPADPPVAVVSGSLDLD +PASAFFTAAPVRPWILTSRAALAAEPERAAALAARADVLAVGEEHVDPQTVVATLHARGA +RVVHCEGGPRLFGSLAAAGLVDEVHLTVAPLLAGPAAGRVLTGEDGPGLPARLQLVQVLH +DDGMLFLRLHHERHASPGPDPTP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001225.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001225.fa new file mode 100644 index 0000000000000000000000000000000000000000..1100038143c9e0f902c42dde45dda821f405f0cf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001225.fa @@ -0,0 +1,47 @@ +>PROKKA_01482 +MQTPDASEPHADRPDDAGQPALDTLLRRSAEGDRAAFSAFYDATVPWVHGLAEAMFGPGD +DAAAATVRTYLTAWEEASEAGLDLSEQDDATHRERQVFTWLEVLAHRVMTSLRRAGGSAA +ERGRRPGPAGPAALPEDLMDRVDPDAFEAVRLAWLGGCTDREVADRLDLPADRARTLLRD +GVRQVVAARRDITQDAARPSAPAPATGPALGADVREDVDAGRALELADLSAVHALDTAGH +TAAFSAVQRRGGELARWRSRVDGARQAVAWAFRSVTAEPPSALLDEVLRRLPAQDVGMDL +IGDESTPAGPPRDRLRWLKVTALLLLAALVLGIGGWTVWSQFTRPGIVHRIDQSKDLFTT +SEYPAQDGGTVQAFLSREQNSGYLTISGMPQLPEGQSYQLWLYPSDGTAPASLGTYDANG +FGEPVTFRGLDRFAAMGISVEPSSGSEVPTSEPIVGVDLDPTAQTGPRYGGRPSTN +>PROKKA_01214 +MQTPDASEPHVDRPDDAGQPALDTLLRRSAEGDRAAFSAFYDATVPWVHGLAEAMFGPGD +DAAAATVRTYLTAWEEASEAGLDLSERDDATHRERQVFTWLEVLAHRVMTSLRRAGGSAA +ERGRRPGPAGPAPLPEDLVGRVAPDAYEAVRLAWLGGCTDREVADRLGLPADEARTLLRD +GVRQVVAARRDLTQDAARPSAPAPATGPALGADVREDVDAGRALELADLSAVHALDTAGH +TAAFSAVQRRGGELARWRSRVDGARQAVAWAFRSVTAEPPSALLDEVLRRLPAQDVGMDL +IGDESAPAGPPRDRLRWLKVTALLLLAALVLGVGGWTVWSQFTRPGIVHRIDQSKDLFTT +SEYPAQDGGTVQAFLSREQNSGYLTISGMPQLPEGQSYQLWLYPSDGTAPASLGTYDANG +FGEPITFRGLDRFAAMGISVEPSSGSEVPTSEPVVGVDLDPTAQTGPRYGGRPSTN +>PROKKA_01420 +MQTPDASEPRADRSAAAGAPALDTLLRRSAEGDRAAFSAFYDATVPWVHGLASAMFRSAD +DAAEATTLTYLTAWEEASEAGLDLSEHDAASHRERQVFTWLEVLAHRVMTTLLRSDGLPE +AGHGLLPDRAGPGSAGPAERPEDLDSRVDPAAFEAVRLAWLGGLSDRQVAARMGRPVAES +RTLLRDGVRQVVEAHRALTRDAADRSPETSARPALATSVREDVEAGHALELADLSAVHAL +ETAGHTAAVSAVQRRGGDLPRWRSRVDGARQAVAWAFRSVTAEPPSAVLDDVLRRLPAQD +VGMDLIGEEAAPARPPKDRLRWLKITVMVLLAALVLGVGAWTVWSQFTRPGIVHRVDQSE +DLFTTSENPARDGGTAQAFLSRDQNSGYVTVSGMPQLPDGQAYQVWLYPDDGTAPASLGT +FDANGFGEPVTFRGLDRFAAVGITVEPSSGSEVPTTDTLVGVDLDPTAHTGPRYGGRPST +N +>PROKKA_01320 +MQTPQHPETPGADASTAPQQPSRRGVDELLHASARGDRAAFSAFYDATVPWVHGMATAMF +RSRRDAAEATAQTYLAAWSEAPEAELDLSDRDAAAARERRVFAWLEVLAHRVMTGLLRTD +ALPEQGRRLLPERAGLGTGGPTALPATLEGSVSPETHRAVRLAWLGGRTDAQVAEALDVP +VDRARTLLRDGVQELVAAHRADQGLPAPVAGARPALAATTREDVDAGRGAELADLSALHA +LDAAGHTAAAAAAQQRGAGELALWRTRVDAGRRAVAWAFRDVVAEPPSDLLDGVLRRLPA +QDMGLELVEETAAPRGAAERRRGLKTVLLGLLALVVLALGVYAGWSQFSRDGITHRVHGA +KDLYTTSEYPAAGGGTMQGFLSDSENSGYVTVSGMPQLEDGQTYQVWLYPKDGSAPSSLG +TYDADGFDDPISFRGLDRFAAVSMTVEPSGGSPEPTADDVLLGLDLDPSNQSGPQYGGMP +SNN +>PROKKA_01432 +MQTPDASEPHADRPDDAGQPALDTLLRRSAEGDRAAFSAFYDATVPWVHGLAEAMFGPGD +DAAAATVRTYLTAWEEASEAGLDLSERDDATHRERQVFTWLEVLAHRVMTSLRRAGGSAA +ERGRRPGPAGPAPLPEDLVDRVAPDAYEAVRLAWLGGCTDREVADRLGLPADQARTLLRD +GVRQVVAARRDLTQDAARPSAPAPATGPALGADVREDVDAGRALELADLSAVHALDTAGH +TAAFSAVQRRGGELALWRSRVDGARQAVAWAFRSVTAEPPSALLDEVLRRLPAQDVGMDL +IGDESAPAGPPRDRLRWLKVTALLLLAALVLGVGGWTVWSQFTRPGIVHRIDQSKDLFTT +SEYPAQDGGTVQAFLSREQNSGYLTISGMPQLPEGQSYQLWLYPSDGTAPASLGTFDANG +FGEPVTFRGLDRFAAMGISVEPSSGSEVPTSEPVVGVDLDPTAQTGPRYGGRPSTN diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001226.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001226.fa new file mode 100644 index 0000000000000000000000000000000000000000..fd39035955744a8f8b9ccb0f1e4fb5163ab9b231 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001226.fa @@ -0,0 +1,29 @@ +>PROKKA_01483 +MAVGAHPDDLDFGAAATLAGFSAAGLHIELCIVTDGDAGGFDSEGAEAMTARRHAEQRAA +AAVVGAAEVHFLGERDGHLEPDHGVRRKLVALMRRVRPDVVLSTHPERDWERMQAAHPDH +LACGEAVVRAAYPAVENPYAYPELAAEGLEAFKIRNLLLYAAPAARRNTVVDVTGLAEQK +LRALDAHLSQHPDVDAMRRHVLAQMAEHHRHAAGPAAGPGHAEAFHLVTVNGPGTIAGF +>PROKKA_01215 +MTTTLTTPAALAAHHGWRRVLAVGAHPDDLDFGAAATLAGFSAAGLHIELCIVTDGDAGG +FDSEGPEAMTARRHAEQRAAAAVVGAAEVHFLGERDGHLEPDHGVRRKLVALMRRVRPDV +VLSTHPERDWERMQAAHPDHLACGEAVVRAAYPAVENPYAYPELAAEGLEAFKVRNLLLY +AAPAARRNTVVDVTGLAEQKLRALDAHLSQHPDVDAMRRHVLAQMAEHHRRAAGPAAAPG +HAEAFHLVTVNGPGTIAGF +>PROKKA_01419 +MTTPITPAALAAEHGWRTVLAVGAHPDDLDFGAAATLAGLSAAGLRVELCVVTDGDAGGF +DSEGPEAMTARRHAEQRAAAAVVGAHEVHFLGERDGHLEPDHGVRRKLVALMRRVRPDVV +LSTHPERDWELMQAAHPDHLACGEAVVRAAYPAVENPYAYPELAAEGLEAFKIRHLLLYS +APAARRNTVVDVTGLEDVKLRALDAHISQHPDVAAMRRHVLAQMTEHHRRAAGPAAAPGL +AEAFHLVTVNGPGTISGF +>PROKKA_01319 +MSAVPESLPTPADLAVRHGWRTVLAFGAHPDDLDFDASATLAGLAAAGVRVELCVVTDGD +AGGFDSDGPEAMTARRHAEQRAAAAVIGAADVHFLGERDGHLEPTHEVRRRIVELMRRVR +PDVVLCPHPERDWESMQASHPDHLACGEAVVRAAYPAVENPYAYPELADAGLDAFRIRHL +MLYTAPAARRNLTVDVTGLEDVKLRALDAHVSQHPDAPAMREAVRAKLTRRHREAAGPDA +PAGSGEAYHLVTVNGDGVIAGF +>PROKKA_01433 +MTTTLTTPAALAAHHGWRRVLAVGAHPDDLDFGAAATLAGFRAAGLHIELCIVTDGDAGG +FDSEGPEAMTARRHAEQRAAAAVVGAAEVHFLGERDGHLEPDHGVRRKLVALMRRVRPDV +VLSTHPERDWERMQAAHPDHLACGEAVVRAAYPAAENPYAYPELAAEGLEAFKVRNLLLY +AAPAARRNTVVDVTGLAEQKLRALDAHLSQHPDVDAMRRHVLAQMAEHHRRAAGPAAAPG +HAEAFHLVTVNGPSTIAGF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001229.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001229.fa new file mode 100644 index 0000000000000000000000000000000000000000..c0e64e8888c57fac2d8ff445766d775780d11e3f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001229.fa @@ -0,0 +1,30 @@ +>PROKKA_01486 +MVKQSIFGRISTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMI +EDDYREDQDASRSWGQKALAASQKADDFRAKGDTASADKFDNLAKVAIERQMDFERQAKS +AEPTIASQREIVERLKTGLDQMKVKRQQLVAKRDELTARAKSAHAQSAVADAVKSIDLLD +PTSEVSRFEEKVRREEARVRGQQEIAASSLDAQFESLEDLGEKTEVEARLAALKAGGAGQ +AALTSGDVDADETLTLDYAAEGTAEETGTARG +>PROKKA_01218 +MVKQSIFGRISTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMI +EDDYREDQDASRSWGQKALAASQKADDFRTKGDTASADKFDNLAKVAIERQMDFERQAKS +AEPTIASQREIVERLKTGLDQMKVKRQQLVAKRDELTARAKSAHAQSAVADAVKSIDLLD +PTSEVSRFEEKVRREEARVRGQQEIAASSLDAQFESLEDLGEKTEVEARLAALKAGGAGQ +AALTSGDVDADETLTLDYAAEGTAEETGTARG +>PROKKA_01416 +MVKQSIFGRISTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMI +EDDYREDQDAARSWGQKALAASQKADDFRTKGDAASAEKFDNLAKVAIERQMDSERQAKS +AEPTITSQREIVERLKTGLDQMKVKRQQLVSKRDELTARAKSAHAQSAVADAVKSIDLLD +PTSEVSRFEEKVRREEARVRGQQELAASSLDAQFESLEDLGEKTEVEARLAALKSGGAGQ +SALTAGGSEGSDLALDYGAETTAEQGAEQTRVERG +>PROKKA_01316 +MVKQSILGRITTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMM +EDDYREDQEAARSWGQKALAASQKADEFRTKGEAANADKFDNLAKVAIERQMDAERQAKT +AEPTITSQREIVDRLKTGLDQMKVKRQQLVSKRDELTARSRTAEAQTKVNEAVKSIDIMD +PTSEISRYEEKVRREEARVRGQQELAASSLDAQFESLEDLGEQTEVEARLAALKSGSAPS +ALTAGSEELTLDYSGAETGTQTGTAERA +>PROKKA_01436 +MVKQSIFGRISTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMI +EDDYREDQDASRSWGQKALAASQKADDFRTKGDTASADKFDNLAKVAIERQMDFERQAKS +AEPTIASQREIVERLKTGLDQMKVKRQQLVAKRDELTARAKSAHAQSAVADAVKSIDLLD +PTSEVSRFEEKVRREEARVRGQQEIAASSLDAQFESLEDLGEKTEVEARLAALKAGGAGQ +AALTSGDVDADETLTLDYAAEGTAEETGTARG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001230.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001230.fa new file mode 100644 index 0000000000000000000000000000000000000000..bdffeb6f4f1f49c089d3678c6c3e78921b94e372 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001230.fa @@ -0,0 +1,41 @@ +>PROKKA_01487 +MQEQFTAWSVLVDAGLIGALLAVGTLARAVITPLQTLMIPASVIAGILGLVLGPNGLGWL +PFSSQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGAFASYGVLIYASQVAIGALVTLV +LLQPLFDAPDSFAALLFAGWAGGFGSAAAVGQAYAANGDATVTSLAYTSATVGMIVGVVG +GIIQAKIGAQRGHAREFAGLTSIPEELRTGVLNQVEERPVIGRHTFSAASVESLAFQVGV +VAMIAAAAHGVVSWITSVWPSVVGEDGPQLIIPAFAIAFLLGLIARVLFQATKTAKFLDP +GSLNSVSGTATDILIVCGIAAIAPTVVVDYWQPLLLLFVIGLALALFLGIVVAPRVMTDA +WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL +LAGLSWAVVGIWGAIAVIAIIAAVWLRRTDPGRRTPAQQAVRASSR +>PROKKA_01219 +MQEQFTAWSVLVDAGLIGALLAVGTLARAVITPLQTLMIPASVIAGILGLALGPNGLGWL +PFSSQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGAFASYGVLIYSSQVAIGALVTLV +LLQPLFDAPDSFAALLFAGWAGGFGSAAAVGQAYAANGDATVTSLAYTSATVGMIVGVVG +GIIQAKIGAQRGHAREFAGLTSIPEELRTGVLNQVEERPVIGRHTFSAASVESLAFQVGV +VAMIAAAAHGVVSWITAVWPSVVGEDGPQLIIPAFAIAFLLGLIARVLFQATKTAKFLDP +GSLNSVSGTATDILIVCGIAAIAPTVVVDYWQPLLLLFVIGLALALFLGIVVAPRVMTDA +WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL +LAGLSWAVVGIWGAIAVIAIIAAVWLRRTDPGRRTPAQQAVRASSR +>PROKKA_01415 +MQEQFTAWSVLVDAGLIGALLAVGTLARAVIKPLQTLMIPASVIAGILGLVLGPNVLGWL +PFSTQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGSFASYGVLIYASQVAIGALVALL +VLQPLFSTPDSFAALLFAGWAGGFGSAAAVGQAYAANGDMTVTSLAYTSATVGMIVGVVG +GIIQAKIGARRGHAKEFAGLTSIPDELRTGVLDQVQERPVIGRHTFSAASVESLAFQVGV +VAMIAAAAHGVVTWITAVWPNIVGEDGPKLIIPAFAVAFILGLIGRVVFQATKTAKFLDP +GSLNSVSGTATDILIVCGIASIAPTVVVDYWQPLLVLFVIGLALALFLGLVVAPRVMTDA +WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL +IAGLSWAVVGIWGAIAIAAILAAIWLRRTDPGVRSPAQQAVRAASR +>PROKKA_01314 +MTWFQGVWPSIVGPEGPKLMIPAFAVAFVLGIIGRLLLQVTKTATFLDSASLNSVSGTAT +DILIVCGIASIAPKVVLDYWQPLLILFVVGLALAVLLGLVVAPHVMTESWFEKQLFTWGW +ATGAVATGVAMLRIVDPKLKSGTMEQFGVAYITVVPVEIAAVSFVPLLIIAGLSWAVVGI +WDAIAEAAIIAAVFLVRSDPARKSAVPA +>PROKKA_01437 +MQEQFTAWSVLVDAGLIGALLAVGTLARAVITPLQTLMIPASVIAGILGLALGPNGLGWL +PFSSQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGAFASYGVLIYSSQVAIGALVTLV +LLQPLFDAPDSFAALLFAGWAGGFGSAAAVGQAYAANGDATVTSLAYTSATVGMIVGVVG +GIIQAKIGAQRGHAREFAGLTSIPEELRTGVLNQVEERPVIGRHTFSAASVESLAFQVGV +VAMIAAAAHGVVSWITAVWPSVVGEDGPQLIIPAFAIAFLLGLIARVLFQATKTAKFLDP +GSLNSVSGTATDILIVCGIAAIAPTVVVDYWQPLLLLFVIGLALALFLGIVVAPRVMTDA +WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL +IAGLSWAVVGIWGAIAIIAIIAAVWLRRTDPGRRTPAQQAVRASSR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001234.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001234.fa new file mode 100644 index 0000000000000000000000000000000000000000..3cd12ff1fd169acd360c7008eafd96af03f8cf80 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001234.fa @@ -0,0 +1,30 @@ +>PROKKA_01516 +MRTVAETVTTVPHDAAASALEPGAWAPPTDVHVAGLDAVGAAIAHALAGAGALRLALWDP +RPVDAADLGTGLLPGDLGRPRAGALARRLGDVAPGLRLYAHHGPVPVLVGQATVAVGSVL +DADLAAHALAADHPLLPVTVGPRAVTVGPWCAPVVRGCPLCRWPADPAGVPGAPTAPGPS +AHRGQVDGLAALRAAVLTVDALRTGPAPGVLRADRVTGRTRRVKVRPRPGCACDPDALGW +AF +>PROKKA_01225 +MRTVAETVTTVPHDAAASALEPGAWAPPTDVHVAGLDAVGAAIAHALAGAGALRLALWDP +RPVDAADLGTGLLPGDLGRPRAGALARRLGDVAPGLRLYAHHGPVPVLVGQATVAVGSVL +DADLAAHALAADHPLLPVTVGPRAVTVGPWCAPGVRGCPLCRWPADPAGVPGAPTAPGPS +AHRGQVDGLAALRAAVLTVDALRTGPAPGVLRADRVTGRTRRVKVRPRPGCACDPDALGW +AF +>PROKKA_01409 +MPAAPSSALSDALSSAEPGAVRPEVEPGPPGAGWEPPVDVHVAGLDAVGVAVAHALAGAG +AHRMALWDPRPVDAADLGTGLLPGDLGRPRARALERRLLDVAPGLRVYAHHGPLPVLVGQ +ASVAVGDVLDADLAAQALAADHPLLPVHVGPRAVTVGPWCAPDVVGCPLCSLPADPVGPP +GRRSARGRATSSGESGAAAVDALTAQRAAVLVADALRAGPSAGVVRADRASGRTRRARVR +PRAGCACDPDALAWGT +>PROKKA_01308 +MATTDAHGPRESGLLADPAGIQVAGLGPAGGALAAALAAGGVAALALWDPTPVGASDLGL +GLLPADLGRPRDRAWEARLSRTWPALPVYAGAGTRPGALGAATVAVDLPGLPDLAARAIA +AQHPLLPVRTDLHGVSAGPWTGGGAPGCVLCTEDVPGTALTAPPAAPPRRDPGAAREPGH +ALRAVVLALDVLTGRRDATSAVLRVDAATGRLTRIPVRTRPGCGCADLLAGDGTGDDWAA +ALAAVEESLDGALADARP +>PROKKA_01443 +MRTVAETVTTVPHDAAASALEPGAWAPPTDVHVAGLDAVGAAIAHALAGAGALRLALWDP +RPVDAADLGTGLLPGDLGRPRAGALERRLGDVAPGLRVFAHHGPVPVLVGQATVAVGSVL +DADLAAQALAADHPLLPVTVGPRAVTVGPWCAPGVRGCPLCRWPADPAGVPGVPTAPGPS +AHRGQVDGLAALRAAVLTVDALRTGPAPGVLRADRVTGRTRRVKVRPRPGCACDPDALGW +AF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001236.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001236.fa new file mode 100644 index 0000000000000000000000000000000000000000..aa09f52026ebdf034becdbfbf69416adb64e9c46 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001236.fa @@ -0,0 +1,35 @@ +>PROKKA_01518 +MASCPPSSSDPTVAPPLALPLAREELDRGAVARLDPGHLAASWAREGTEVLWLQGGRAPV +ADGRLVFTAPSGPVPAEAAYLGRGTAADRGPHGREREVVSVAVEPPAALPEDAATALADA +VWVGLRDAAAALSDADTGLFVAAVANANWHATHRFCAFCGGVTDVEAAGWVRRCRDCSRE +QFPRTDPAVIVAVIDPAGRILLGRNAAWPEGLYSCLAGFVEPGESLEHAVVREIAEESGV +TVTQPRYRGSQPWPFPRSLMLGFTALAPAGAEPVPDGEEILSVRWFEREELARLAREGDV +TLPGAVSIARALIEDWYGGTLPDAQTLIT +>PROKKA_01227 +MASCPPSSSDPTAAPPLALPLAREELDRGAVARLDPGHLAASWAREGTEVLWLQGGRAPV +ADGRLVFTAPSGPVPAEAAYLGRGTAADRGPHGREREVVSVAVEPPAALPEDAATALADA +VWVGLRDAAAALSDADTGLFVAAVANANWHATHRFCAFCGGVTDVEAAGWVRRCRDCSRE +QFPRTDPAVIVAVIDPAGRILLGRNAAWPEGLYSCLAGFVEPGESLEHAVVREIAEESGV +TVTQPRYRGSQPWPFPRSLMLGFTALAPAGAEPVPDGEEILSVRWFEREELARLAREGDV +TLPGAVSIARALIEDWYGGTLPDAQTLIT +>PROKKA_01407 +MPVPDPAAPAPEPRHDPAPAPAPAAPLALPLAREEVDRGAVARLDPGHLAAAWEREGTEV +LWLQGGRAPVADGRLRFTTPSGPVPPQAAYLGRGTAADLGPGGRERAVVAVALEPPAVLP +PDAAAALGDAAWVGLRDAAAALSDADAGLFVAAVANANWHAAHRFCSFCGGATAVEAAGW +VRRCEACGREHFPRTDPAVIVAVTDPDGRILLGRNAAWPAGRYSCLAGFVEPGESLEHAV +VREVAEESGVTVADPRYRGSQPWPFPRSLMLGFTAQAPAGAEPVADGTEILSVRWFEREE +LAALAREGEITLPGAVSIARALIEDWYGGTLPDAQTLIT +>PROKKA_01306 +MPVPSAPDAVPAALPHLTLAREALDRSGAEREDPGLLGRLAADPATGVLHLVGGRAPVRD +GALVLVPPAGPFPPEAVFLGRRLTDAAAPSAAGRPLVLVARESAPGSSGDGGPTRPAEPT +DAPTRDPLAGAAWLGLRDVAAGLSDADTGLFVEAVAIANWHAGHGFCSRCGGRTDTESAG +WVRRCRDCSARHFPRTDPAVIMAVMDDQDRILLGSNAAWPAGRHSCLAGFVEPGESLEHA +VAREVLEEAGIVVVDAAYRGSQPWPFPRSLMVGYRAHALPGQEPVADGHEIRSVRWFTRD +ELAAEVRAGAVTLPGAVSIARALIEDWYGGTLPDPTTLIS +>PROKKA_01445 +MASCPPSSSDLTAAPPLALPLAREELDRGAVARLDPGHLAAVWAREGTEVLWLQGGRAPV +ADGRLVFTAPSGPVPAEAAYLGRGTAADRGPHGREREVVSVAVEPPAALPEDAATALADA +VWVGLRDAAAALSDADTGLFVAAVANANWHATHRFCAFCGGVTDVEAAGWVRRCRDCSRE +QFPRTDPAVIVAVTDPAGRILLGRNAAWPEGLYSCLAGFVEPGESLEHAVVREIAEESGI +TVTQPRYRGSQPWPFPRSLMLGFTALAPAGAEPVPDGEEILSVRWFEREELAHLAREGDV +TLPGAVSIARALIEDWYGGTLPDAQTLIT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001240.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001240.fa new file mode 100644 index 0000000000000000000000000000000000000000..250fa87d596ba1aee5381ebce5dee35f42b52e7d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001240.fa @@ -0,0 +1,20 @@ +>PROKKA_01522 +MTDHPVLPGARHRDDGPLTLGEGLEALARLVPPGRAVSYGGLAGLLGVGGPRQAGRAMAE +SSPGTPWWRVVRADGSLPPELAARAAVEHEREAMPRTPAGRVDLPRARWEPDDGAARAIR +AIADRIVSGPGARMRP +>PROKKA_01231 +MTDHPVLPGARHRDDGPLTLGEGLEALARLVPPGHAVSYGGLAGLLGVGGPRQAGRAMAE +SSPGTPWWRVVRADGSLPPELAARAAVEHEREATPRTPAGRVDLPRARWEPDDGAARAIR +AIADRIVSGPGARMRP +>PROKKA_01403 +MTTPPADPRPVPDGPLTLGEGLEAVARLVPAGRAVSYGDLAGLLGVGGPRQAGRAMAKSA +PGTPWWRVVSADGSLPGELARRAAVEHAREGTPVRPGGRVDLPRARWEPDEAALGAVAAI +AARIVSGPGARMQA +>PROKKA_01302 +MSPVPSTPPDPDPHLPTDGPVTLGEALAAAARLIPSGRAASYGALAGLLGRGGPRQAGRA +MAESEPGTPWWRVVRADGSLPEPLRRQARERWAAEGTPVRGSGTVRDQRVDLAQAGWEPD +AAARAALADLAARVG +>PROKKA_01449 +MTDHPVLPGARHRDDGPLTLGEGLEALARLVPPGRAVSYGGLAGLLGVGGPRQAGRAMAE +SSPGTPWWRVVRADGSLPPELAARAAVEHEREGTPRTPAGRVDLRRARWEPDDGAARAIR +AIADRIVSGPGARMGP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001241.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001241.fa new file mode 100644 index 0000000000000000000000000000000000000000..32223393192172f0f4bbe385641722c112ff92e5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001241.fa @@ -0,0 +1,25 @@ +>PROKKA_01523 +MTWHESIRAGFDLETTGRDPRTALIVTATLVMVDEQGRAASSAEWLVDPGVPIPAEAAEV +HGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARHHGLTPL +EARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALAARY +EQLRVAPVDLHERQVRWKAEQAESFEQYLRRKDPQATVSRHWPVEAER +>PROKKA_01232 +MTWHESIRAGFDLETTGRDPRTALIVTATLVMVDEQGRAASSAEWLVDPGVPIPAEAAEV +HGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGLTPL +EARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALAAQY +EQLRVAPADLHERQVRWKAEQAESFEQYLRRKDPQATVSRHWPVDAER +>PROKKA_01402 +MSPVNWHQSIRAGFDLETTGRDPRSALIVTATLVMVDAQGRATASAEWLLDPGVPIPAEA +AEVHGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGL +APVEARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALA +ERHEQLRVDPAELHERQVRWKAEQAESFEEYLRRKDPQATVSRDWPVESGR +>PROKKA_01301 +MSWNEQIRAGFDLETTGRDPRQARIVTATIVMVDAAGKAVSSAEWLLDPGVPIPEEAAAV +HGVTTERARAEGLEARRGVSEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGVAPL +EPRPVVDPYVVDKQVDRFRKGKRTLGAVSEHYDVVLEDAHTSAADALAAVQVMDELVRRH +PKADLPLDELHAAQARWKAEQAESFEEYLRRKDPQATVSRAWPVEPDV +>PROKKA_01450 +MTWHESIRAGFDLETTGRDPRTALIVTATLVMVDEHGRAASSAEWLVDPGVPIPAEAAEV +HGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGLTPL +EARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALAARY +EQLRVAPTDLHERQVRWKAEQAESFEQYLRRKDPQATVSRHWPVEAER diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001243.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001243.fa new file mode 100644 index 0000000000000000000000000000000000000000..5b1df0dfd8020ead734eb8336c36d80e68d00b9d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001243.fa @@ -0,0 +1,35 @@ +>PROKKA_01525 +MSFPLHRPRRLRRSAAMRRLAAETRLHPAELILPAFIKEGAAEPVPIASMPGVVQHTADS +LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRDVKAEVGDGLVVMSDL +CLDEFTDHGHCGVLTAEGAVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA +LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALLEVALDLE +EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV +LSIRRAGADSVLTYWAAELGRWMKEGSL +>PROKKA_01234 +MSFPLHRPRRLRRSAAMRRLVAETRLHPAELILPAFIKEGAAEPVPIASMPGVVQHTADS +LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRDVKAEVGDGLVVMSDL +CLDEFTDHGHCGVLTAEGTVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA +LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALLEVALDLE +EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV +LSIRRAGADSVLTYWAAELGRWMKEGSL +>PROKKA_01400 +MSFPLHRPRRLRRSAAMRRLVAETRLHPAELILPAFIKEGAPEPIAIASMPGVVQHTSDT +LKAAAAEAAELGLGGIMLFGVPETRDAVGSISLDPEGVLNQAIRDVKSEVGDALVVMSDL +CLDEFTDHGHCGVLTEDGAVDNDATLEIYAQMGVAQAEAGADVLGPSGMMDGQVRVIREA +LDAAGHVDTGILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRTEALHEVALDLE +EGADMVMVKPAMSYLDIVRDVAELADVPVSAYQISGEYAMIEAAAANGWIDRKASIVESV +LSIRRAGADTVLTYWATELGRWMKEGSL +>PROKKA_01299 +MSFPLNRPRRLRQSAAMRRLVAETRLHPNELILPAFIKEGAAEPVPIASMPGVVQHTTDT +LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRDVKAEVGDGLVVMSDL +CLDEFTDHGHCGVLTAEGTVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA +LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALREVALDLE +EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV +LSIRRAGADSVLTYWAAELGRWMKEGSL +>PROKKA_01452 +MSFPLHRPRRLRRSAAMRRLVAETRLHPAELILPAFIKEGAAEPVPIASMPGVVQHTADS +LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRGVKAEVGDGLVVMSDL +CLDEFTDHGHCGVLTAEGTVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA +LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALLEVALDLE +EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV +LSIRRAGADSVLTYWAAELGRWMKEGSL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001249.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001249.fa new file mode 100644 index 0000000000000000000000000000000000000000..8af1983ec0a340366812f5b81c63b74f990c5480 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001249.fa @@ -0,0 +1,45 @@ +>PROKKA_01531 +MTTAPEPRADAPVHTGPDAGVAPALRTPEKAAAGVDYDVCGVMAPKDYDALLLASFGGPE +GQDDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALKAAIEAELAARGLD +LPVYWGNRNWEPYFPDTLARMHADGHRRILTVTTSAYSCYSSCRQYREDMGMAMEQTGLT +GKVDLDKTRQYFNHPGFIEPFRDGLRADLASLRAELGDDARIHVLFATHSIPTSDAAAAG +PRGLAADLRAQAGAEPGDEGADVYSAQHLDVAREILAGVPEAADVPWSLVYQSRSGPPSV +PWLEPDINDAMEHLAGEGAETDAQGRAVAGFVVVPLGFVSDHMEVVWDLDTEAKETAEGL +GVGFRRSPTPGTDPRFVAGLVDIVEERLGRREGRAAVGCFPAWYDVCRPDCCVKVMRDGS +TRPTTSAVDAAVRGLAEHEAGAAAPAEEA +>PROKKA_01241 +MTTAPEPRADAPVHTGPDAGVAPALRTPEKAAAGVDYDVCGVMAPKDYDALLLASFGGPE +GQDDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALKAAIEAELAARGLD +LPVYWGNRNWEPYFPDTLARMHADGHRRILTVTTSAYSCYSSCRQYREDMGMALEQTGLT +GKVDLDKTRQYFNHPGFIEPFRDGLRADLASLRAELGDDARIHVLFATHSIPTSDAAAAG +PRGLAADLRAQAGAEPGDEGADVYSAQHLDVAREILAGVPEAADVPWSLVYQSRSGPPSV +PWLEPDINDAMEHLAGEGAETDAQGRAVAGFIVVPLGFVSDHMEVVWDLDTEAKETAEGL +GVGFRRSPTPGTDPRFVAGLVDIVEERLGRREGRAAVGCFPAWYDVCRPDCCVKVMRDGS +TRPTTSAVDAAVRGLAEHEAGAAAPAEEA +>PROKKA_01394 +MSTAPENAAAASPAPEPRADAPVHAGPRAGVAPTLRAPEEAAAGVDFDVCGVMAPKEYDA +LLLASFGGPEGQDDVIPFLRNVTRGRGIPDERLEEVATHYRANDGVSPINAQNRALKAAI +EAELAARGLALPVYWGNRNWEPYVPDTLERMHADGHRRILTVTTSAYSCYSSCRQYREDM +GMALRRTGLEGVVDLDKTRQYFNHPGFIEPFRDGLRADLASLREELGEDARIHVLFATHS +IPTSDAAAAGPRGLAADLRAQAGAEPGEEGADVYSAQHLDVAREILAGVPEAADVPWSLV +YQSRSGPPSVPWLEPDINDAMEHLAGEDAEADAAGRAVAGFVVVPLGFVSDHMEVLWDLD +TEARQTAADLGVAFRRSPTPGTDPRFVSGLVDIVEERMGRREGRASLGCFGAWYDVCRPD +CCSKVMRDGTVRPTTSAVDADVRGLAEHEAGTAPAGRTEES +>PROKKA_01285 +MTAVPTHRVPEDARRPVHEPERAAAGVDYDACGAMAPKAYDALILASFGGPEGQEDVIPF +LRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALISAIEAELVRRGLELPVYFGNR +NWEPYFPDALQRAYDDGHRRILTVTTSAYSCYSSCRQYREDMGLAMERTGLEGKVDLDKT +RQYFNHPGFVEPFAEGLRADLASLREEVGEDARVHLLFATHSIPTADAAAAGPRGLAAAL +REQAGGEPGDVEGADAYSAQHLDVIREVLARVPEAEGVDWSLVYQSRSGAPHVPWLEPDI +NDALEALAGPDAPADADGRALAGVVVVPVGFVSDHMEVVWDLDTEAKDTAAELGVAFRRT +PTPGTDPRFVSGLVDIVEERLGRREGREAVGCFPAWYDVCRPDCCVKVMRDGSVRPTTSA +VDAPVRGLAEHRGEQDGADDAGAQDS +>PROKKA_01458 +MTTAPEPRADAPVHTGPDAGVAPALRTPEKAAAGVDYDVCGVMAPKDYDALLLASFGGPE +GQDDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALKAAIEAELAARGLD +LPVYWGNRNWEPYFPDTLARMHADGHRRILTVTTSAYSCYSSCRQYREDMGMAMEQTGLT +GKVDLDKTRQYFNHPGFIEPFRDGLRADLASLRAELGDDARIHVLFATHSIPTSDAAAAG +PRGLAADLRAQAGAEPGDEGADVYSAQHLDVAREILAGVPEAADVPWSLVYQSRSGPPSV +PWLEPDINDAMEHLAGEGAETDAQGRAVAGFVVVPLGFVSDHMEVVWDLDTEAKETAEGL +GVGFRRSPTPGTDPRFVAGLVDIVEERLGRREGRAAVGCFPAWYDVCRPDCCVKVMRDGS +TRPTTSAVDAAVRGLAEHEAGAAAPAEEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001252.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001252.fa new file mode 100644 index 0000000000000000000000000000000000000000..e8d6db5441d15760538e0e2ec664249b426e1de5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001252.fa @@ -0,0 +1,40 @@ +>PROKKA_01534 +MSALSQTPETPAAVPALPAEHPLRTEDPSRSTVASPLLRALRGQRPDRHPVWFMRQAGRS +LPEYRRVREGIGMLDSCLMPDLVREITMQPVRRHDVDAAIFFSDIVVPLRLAGVDVEIQP +GVGPVLGQAVRTADDVAALPVLEDAALDVIREAVAATVAELGPRPLIGFAGAPFTLAAYM +VEGRPSRDHFGPRRMMHADPETWAALAGWAATVSGQFLRAQLESGASAAQLFDSWAGSLS +ADDYLEHVQPHSTAALAHVADLAGPGVPDGAPLLHFGTGTGEFLHHMRDAGATAVGVDHR +LTLAEAHRRLSANPGPDGRGAVPLQGNIDPALLAAPWEVLEAHVRDVVASGAVAPGHVVN +LAHGVPPETDAAVLTRVVELIHSLPVPEREGQDPAPGAETAEREERA +>PROKKA_01244 +MSALSQTPETPAAVPALPAEHPLRTEDPSRSTVASPLLRALRGQRPDRHPVWFMRQAGRS +LPEYRRVREGIGMLDSCLMPDLVREITMQPVRRHDVDAAIFFSDIVVPLRLAGVDVEIQP +GVGPVLGQAVRTADDVAALPVLEDAALDVIREAVAATVAELGPRPLIGFAGAPFTLAAYM +VEGRPSRDHFGPRRMMHADPETWAALAGWAATVSGQFLRAQLESGASAAQLFDSWAGSLS +ADDYLEHVQPHSTAALAHVADLAGPGVPDGAPLLHFGTGTGEFLHHMRDAGATAVGVDHR +LTLAEAHRRLSANPGPDGRGAVPLQGNIDPALLAAPWEVLEAHVRDVVASGAVAPGHVVN +LAHGVPPETDAAVLTRVVELIHSLPVPEREGQDPAPGVETAEREERA +>PROKKA_01391 +MSDLSQTSEIRAGAPALPADHPLRTQDPARSTAASPLVRALRGQRPDRHPVWFMRQAGRS +LPEYREARAGIGMLESCLMPDLVREITLQPVRRHDVDAAIFFSDIVVPLRLAGVDVEIQP +GVGPVLGRAVRTAEDVAALPVLEDSALDVIREAVSSTVAELGPRPLIGFAGAPFTLAAYM +VEGRPSRDHFGPRRMMHGDPEAWAALAGWAATVSGQFLRAQLEAGASAAQLFDSWAGSLA +AEDYLEHVQPHSRAALAHVDDLAGPGVDGGAPLLHFGTGTGEFLHHLRDAGASAVGVDHR +LTLSEAHRRLSERPGPDGRTVVPLQGNIDPALLAAPWPVVEAHVRDVVASGAAAPGHVVN +LAHGVPPETDPTVLTRVVELIHSLPVPEREGQDPAPPAGAAAGEGRA +>PROKKA_01282 +MSAMTTPPGLPAEHPLSTADPARSTADAPLVCALRGRRPHRHPVWFMRQAGRSLPEYRKA +REGVGMLESCLRPELAAEITLQPVRRHDVDAAIFFSDIVVPLKLAGVGVEIVPGVGPVLD +HPVRTAEDAAALPELEDSALDVIREAVSRTVAELGPTPLIGFAGAPFTLAAYMVEGRPSR +DHLGPRRMMHGDPQTWAALAAWAATVSGQFLRAQLEAGASAAQLFDSWAGSLSAADYRKH +VQPHSAAALSAVSDLAGPGVEGGAPLLHFGTGTGEFLDLMRDAGASAVGVDHRITLAEAH +RRLSSRPGPDGRAAVPLQGNIDPALLGAPWEVLEAHVREVVASGAAAPGHVVNLAHGVPP +ETDPEVLTRVVELIHSIPVADGAEK +>PROKKA_01461 +MSALSQTPETPAAVPALPAEHPLRTEDPSRSTVASPLLRALRGQRPDRHPVWFMRQAGRS +LPEYRRVREGIGMLDSCLMPDLVREITMQPVRRHDVDAAIFFSDIVVPLRLAGVDVEIQP +GVGPVLGQAVRTADDVAALPVLEDAALDVIREAVAATVAELGPRPLIGFAGAPFTLAAYM +VEGRPSRDHFGPRRMMHADPETWAALAGWAATVSGQFLRAQLESGASAAQLFDSWAGSLS +ADDYLEHVQPHSTAALAHVADLAGPGVPDGAPLLHFGTGTGEFLHHMRDAGATAVGVDHR +LTLAEAHRRLSANPGPDGRGAVPLQGNIDPALLAAPWEVLEAHVRDVVASGAVAPGHVVN +LAHGVPPETDAAVLTRVVELIHSLPVPEREGQDPAPGAETAEREERA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001253.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001253.fa new file mode 100644 index 0000000000000000000000000000000000000000..c2e2f44676a5c81fd1de09bba41ac575971bf02b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001253.fa @@ -0,0 +1,45 @@ +>PROKKA_01535 +MTVFSLVASHHDLDLDTVARLSAGATGVGPALPGSGAAGAVVLATCNRVEIYAEADAAGV +EAARAGLLSAVAASTSLPDEDVHAAFRTLDADATARHLFEVGAGLDSAVVGEREIAGQVR +RALTAAQEAGTASGPLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLAEELRGLTDA +AAQRDFWAGATILLIGTGAYAGTTLAQLADRGATTVGVHSASGRAEQFVADRGGWALALG +GEAVAGAVAEADVIIGSSGGERQISPERLQELRKGGRRPLTVVDLALSRDFDPAVADLPD +VDLITLESVRLAAPEQAQVAVAEARALVDDAVEEYRAAQRGRSADAAIKALRRHTLGVLD +RELERVRARHGCTAAAEEVEFALRRMVNQLLHEPSVRAKRLAAEGRLDRYEDALEAVFGI +EAPGRPAPAVGTVEAVCPAHEDEGGAARIA +>PROKKA_01245 +MTVFSLVASHHDLDLDTVARLSAGATGVGPALPGSGAAGAVVLATCNRVEIYAEADAAGV +EAARAGLLSAVAASTSLPDEDVHTAFRTLDADATARHLFEVGAGLDSAVVGEREIAGQVR +RALTAAQEAGTASGPLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLAEELRGLTDA +AAQRDFWAGATILLIGTGAYAGTTLAQLADRGATTVGVHSASGRAEQFVADRGGWALALG +GEAVAGAVAEADVIIGSSGGERQISPERLQELRKGGRRPLTVVDLALSRDFDPAVADLPD +VDLITLESVRLAAPEQAQVAVAEARALVDDAVEEYRAAQRGRSADAAIKALRRHTLGVLD +RELERVRARHGCTAAAEEVEFALRRMVNQLLHEPSVRAKRLAAEGRLDRYEDALEAVFGI +EAPGRPAPAVGTVEAACPAHEDDGGAARIA +>PROKKA_01390 +MADVVTVFSLVASHQHLDLDTVARLSAGATGVGPALPGSGAAGAVVLATCNRVEIYAEAD +ESGVEAAREGLVAAVAAHSSLPDEAVRSAFRVLDSEATARHLFEVGAGLDSAVVGEREIA +GQVRRALSMARESGTASGSLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLTEELRG +LADDDAKAAFWADASVLLIGTGAYAGTTLAQLAERGATAVAVHSASGRAEQFVEDRGGWA +LALGGGAVAGAVAEADVIIGSSGGERQISPERLQELREDVDRPLTVVDLALSRDFDPAVG +DLPDVDLITLESVRLAAPEQARAAVAEARVLVDGAVAEYRAAQRGRSADASIKALRRHTL +AALDREMERVRARHGCTAAAEEVEFALRRMVNQLLHEPIVRAKRLAAEGRLDRYEDGLEA +VFGIEPPGSTSSPAERPDAGCPAHEDEAGTARIA +>PROKKA_01281 +MDVAVTVFSLVASHKDLSLDTVARLSAGSAGVGSALASSTDDGAVVLATCNRVEVYADAR +DADAARERIVAAIAEQSGLPEDAVRSAFRVLDDDASARHLFEVGAGLDSAVVGEREIAGQ +VRRALVDARDAGTATGSLTRLFESATRTAKDVGSHTALGATGRSVVSVALDLAEELRGLT +DAMARRTFWQEANVLLIGTGAYAGTTLAQLADRGAQAVGVHSASGRAAQFVADRGGWALA +LGGADVAGAVAEADVIIGSSGGDRQISPERMAGLRRGAERPVTVVDLALSRDFDPAVGEL +EGVDLITLESVRLAAPEQAQAAVAEARGLVETALEEYTSARRGRTADAAIKALRGHTMAA +LDREMERVRARHGCTAAADEVQFALRRMVNQLLHTPSVRARELAAQGRLDEFEHALEVLF +DIPVPGTRPADAPGDACPATEADDARRTA +>PROKKA_01462 +MTVFSLVASHHDLDLDTVARLSAGATGVGPALPGSGAAGAIVLATCNRVEIYAEADGAGV +EAARTGLLSAVAASTSLPDEDVHTAFRTLDADATARHLFEVGAGLDSAVVGEREIAGQVR +RALTAAQEAGTASGPLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLAEELRGLTDA +AAQRDFWAGATILLIGTGAYAGTTLAQLADRGATTVGVHSASGRAEQFVADRGGWALALG +GEAVAGAVAEADVIIGSSGGERQISPERLQELREGGRRPLTVVDLALSRDFDPAVADLPD +VDLITLESVRLAAPEQAQVAVAEARALVDDAVEEYRAAQRGRSADAAIKALRRHTLGVLD +RELERVRARHGCTAAAEEVEFALRRMVNQLLHEPSVRAKRLAAEGRLDRYEDALEAVFGI +EAPGRPAPAVGTVEAACPAHEDDGGAARIA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001255.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001255.fa new file mode 100644 index 0000000000000000000000000000000000000000..6fce951474d4faa2b0784f21f3a313f587f402a1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001255.fa @@ -0,0 +1,15 @@ +>PROKKA_01537 +MEIRIGVQHVGREVVIDSEQSADEVRSLVDAAVSDGTPLVLADAKGRQVVVPGDRIGFVE +IGAKKSGPLGFAAS +>PROKKA_01247 +MEIRIGVQHVGREVVIDSEQSADEVRSLVDAAVADGTPLVLADAKGRQVVVPGDRIGFVE +IGAKKSGPLGFAAS +>PROKKA_01388 +MEIRIGVQHVGREVVIESEQPAEEVRSLVDAAVADGSTLVLADAKGRQVVVPGDRIGFVE +INAKKSGPLGFAAS +>PROKKA_01279 +MEIRIGVQHVGREVVLESDHTAQEVRALVDAALADGTTLALTDTKGRQVIVPADRIGFVE +IGAKKSAPLGFAAV +>PROKKA_01464 +MEIRIGVQHVGREVVIDSEQSADEVRSLVDAAVADGTPLVLTDAKGRQVVVPGDRIGFVE +IGAKKSGPLGFAAS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001256.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001256.fa new file mode 100644 index 0000000000000000000000000000000000000000..6b1861e4050da35ea9000d3a880939f6181182e1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001256.fa @@ -0,0 +1,50 @@ +>PROKKA_01538 +MTPHALGLRGPADPTLLERLAALRTELELPPAFPAPVLAEAEAAAREVHAGLTGSPDHAD +RTALPFVTVDPAGSTDLDQALLLTPADDDGILVRYAIADVPAFVTPGGAVDGEARRRGQT +VYLPDGRVPLHPEVLSEDAASLLPDREHPAFVWTFLLDAAGAVVETGLERARIRSRAQLT +YGQVQAFLDAQPGAQAPTTPRPGVTDADRAAAEGWPAEVRDSLALLPEVGRRRAAQEAAR +GGASLNLPDQEVRVTEDGAHELVHRAPLPAEEHNAQLSLLTGMAAAELMLAAGVGILRTM +PAPDTDAVAAFRERTRALGAPWDEGQDYGAYLRSLDPADARHLAVLHAATGLFRGAGYTA +FDAQAEDPALRTPPDEPAQAALAAPYAHATAPLRRLVDRFVLALCHAHAIGAPAPAWVRS +ALPALPALMADSSRRASAASRTAADLVEAAALESRVGAELEGIAVREAKDGTEVWLLDPA +VSLRVPGSVPAGTRVRVRIEGVDRASGAITAAGVDWPHSSR +>PROKKA_01248 +MSSHALGLRGPADPALLERLAALRTELELPSAFPTPVLAEAEAAAHGVHVGLAGSPDHAD +RTALPFVTVDPAGATDLDQALLLTPSDDDGILVRYAIADVPAFVAPGGAVDAEARRRGQT +VYLPDGRVPLHPEVLSEDAASLLPDRERPAFVWTFLLDAAGAVVETGLERARVRSRAQLT +YGQVQAFLDARPGAQAPATPRPGVTDADRAAAEGWPAEVRDSLALLPEVGRRRAAQEAAR +GGASLNLPDQEVLVTEDGAHELVHRAPLPAEEHNAQLSLLTGMAAAELMLAAGVGILRTM +PAPDADAVAAFRERTRALGVPWDEGQDYGAYLRSLDPADARHLAVLHAATGLFRGAGYTA +FDAQAEDPALRTPPAEPAQAALAAPYAHATAPLRRLVDRFVLALCHAHASGAPAPAWVRS +ALPELPALMADSSRRASAASRTAADLVEAAALESRVGAELEGIAVREAKDGTEVWLLDPA +VSLRVPGSVPAGTRVRVRIEGVDRASGAITAAGVDWSHSSR +>PROKKA_01387 +MPHRAVALRGRPDPALIERLAALRTELELPAGFPPEVLEEADAAARDVLAALASDPAYAD +RTDVPFVTVDPAGSTDLDQALYLEAADGDAITVRYAIADVPAFVAPGGAVDVEARRRGQT +VYLPDGRVPLHPEALSEDAASLLPDRERPAFVWTFVLDAAGAVVDTSLERARIRSRAQLT +YAQVQAFLDALPDAKAPAAPRPGLDEADHAAHRGWDAPLRDSLALLPEVGRRRAAQEAAR +GGASLNLPDQEVHVAEDGRHCLVQRAPLPAEDHNAQLSLMTGMAAARLMLEAGVGILRTM +PAPDAEAVAAFRSRTRALGAPWEEGQDYGAYLRTLDPADPGHLAVLHEATSLFRGAGYTA +FDAHAEDPELRTPPSEPEQAALAAPYAHATAPLRRLVDRFVLALCHAHATGAPAPEWARA +ALPEVPALMTESSRRTSAADRAATDLVEAAALQDHVCAELEGIAVRRVKGGAEVWLLDPA +VTLRVPGEAEPGTRVRVRIEGVDRASGEVTASGVDWPHSSR +>PROKKA_01278 +MPHHALEVRGGPDAALAARLRALRAELDVPGEFPADVLTEAERAAAEVPGRVAADPDRAD +LTAVPFVTVDPAGSTDLDQALHLQAGPGRDELTVRYAIADVPGFVAPEGAVDAEARRRGQ +TVYLPDGRVPLHPEVLSEDAASLLPEVERPTFVWTFVLDAEGAVASTDLVRARIRSRAQL +AYPQVQALLDDDAAPEAADWPAEVRASLALLPEVGARRTAQEAARGGASLSMPDQEISVV +DGAYTLVQRVPLAAEDHNAQLSLMTGMAAARIMLEAGVGILRTMPAPDPDAVDAFRARTR +ALGLPWGEELDYGAYLRTVDPTDPRGLAVMHAATTLFRGAGYTAFDRGSVDPALRALPED +PEQAALAAPYAHTTAPLRRLVDRFVLVLCHAHVAGEPVPDWVRRALPDLPALMAESGRRA +SAADRAATDLVEAALLAARVGSVLEGTAVRTSEKGTDVQLTDPAVSLRVPGRAEPGTVVR +VRVDAVDVAAGKVTASGVDWPHSAR +>PROKKA_01465 +MSSHALGLRGPADPALLERLAALRTELELPSAFPTPVLAEAEAAAHGVHVGLAGSPDHAD +RTALPFVTVDPAGATDLDQALLLTPSDDDGILVRYAIADVPAFVAPGGAVDAEARRRGQT +VYLPDGRVPLHPEVLSEDAASLLPDRERPAFVWTFLLDAAGAVVETGLERARIRSRAQLT +YGQVQAFLDAQPGAQAPTTPRPGVTDADRAAAEGWPAEVRDSLALLPEVGRRRAAQEAAR +GGASLNLPDQEVRVTEDGAHELVHRAPLPAEEHNAQLSLLTGMAAAELMLAAGVGILRTM +PAPDTDAVAAFRERTRALGAPWDEGQDYGAYLRSLDPADARHLAVLHAATGLFRGAGYTA +FDAQAEDPALRTPPDEPAQAALAAPYAHATAPLRRLVDRFVLALCHAHAIGAPAPAWVRS +ALPALPALMADSSRRASAASRTAADLVEAAALESRVGAELEGIAVREAKDGTEVWLLDPA +VSLRVPGSVPAGTRVRVRIEGVDRASGAITAAGVDWPHSSR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001257.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001257.fa new file mode 100644 index 0000000000000000000000000000000000000000..38e0e81e22146da6fd977fe9030dbc3cc0338664 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001257.fa @@ -0,0 +1,30 @@ +>PROKKA_01540 +MAAMARYDLHTHSTESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWAEAAQAARETGL +TLVPGMEMSCTSADGVSVHVLSYLHDPEDPALLREVGRARDARLTRAQEMVRRLGADFSI +TWELVQEHAAENATIGRPHLADALVTIGAVPDRSAAFREILAGRSKYYVPHFAPDPAEAV +ALIRAAGGVPVFAHPRARMRGRVVGDEVFEQMAEAGLAGVEVEHRDNPAEERTWLRAFAD +RHGLFVTGSSDYHGTGKPNPIGEHTTGAEVLAEIERQGTGTAIIRG +>PROKKA_01250 +MAAMARYDLHTHSTESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWAEAAHAARETGL +TLVPGMEMSCTSADGVSVHVLSYLHDPEDPALLREVGLARDARLIRAQEMVRRLGADFPI +TWELVQEHAAENATIGRPHLADALVTIGAVPDRSAAFREILAGRSKYYVPHFAPDPAEAV +ALIRAAGGVPVFAHPRARMRGRVVGDEVFEQMAEAGLAGVEVEHRDNPAEERTWLRAFAD +RHGLFVTGSSDYHGTGKPNPIGEHTTGAEVLAEIERQGTGTAIIRG +>PROKKA_01385 +MSRYDLHTHSVESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWEAAAEAALAEGIAFV +PGMEMSCMAADGTSVHVLSYLHDPADPSLLREIGTARSARLTRAQEMVHRLARDYPITWE +LVQEHAAEGATIGRPHLADTLVTLGVVEDRSAAFAHILTGRSKYYVPHYAPDPAIAVELI +RSAGGVPVFAHPRAVTRGRVVGVEVIEEMIDAGLAGLEADHRDNPEEERSWLREVAARHD +LFVTGSSDYHGTGKPNLLGEFSTGEDVLAEIERQGTGAAVVRG +>PROKKA_01276 +MSTARYDLHTHSTESDGTEPAADVVHAAALAGLDGLALTDHDTTAGWAAAADAARETGLL +LVPGMEMSCMAADGTSVHLLSYLHDPADPSLLAELGASRDARLTRAQSMTDRLAEDFPIT +WDLVREHASENATIGRPHIADALVTIGAVPDRSAAFSSILRGGSKYYVPHYAVDPVEAVR +LVRAAGGVPVFAHPRARLRGRIVGDDVLEAMIEAGLAGLEADHRDNPEQERTWLRETATR +HGLFVTGSSDYHGAGKPNLIGEFTTGPEVLAEIEHQGTGAAVVRG +>PROKKA_01467 +MAAMARYDLHTHSTESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWAEAAHAARETGL +TLVPGMEMSCTSADGVSVHVLSYLHDPEDPALLREVGLARDARLIRAQEMVRRLGADFPI +TWELVQEHAAENATIGRPHLADALVTIGAVPDRSAAFREILAGRSKYYVPHFAPDPAEAV +ALIRAAGGVPVFAHPRARMRGRVVGDEVFEQMAEAGLAGVEVEHRDNPAEERTWLRAFAD +RHGLFVTGSSDYHGTGKPNPIGEHTTGAEVLAEIERQGTGTAIIRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001258.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001258.fa new file mode 100644 index 0000000000000000000000000000000000000000..315830f242fd615fb7ddc3a9063f80e5a2269cd4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001258.fa @@ -0,0 +1,50 @@ +>PROKKA_01541 +MTDAAQHPAQTTPDQPAATPEAGADGTGAVNPQPLAERVDNRSQRPASNAFRDFMASDWA +PSSQALPDPDASAPYAARRRAAVSARFPGERIVVPAGRLKVRSNDTDYRFRAHSAFAHLT +GLGVDHEPDAVLVLEPTDPGAGDDGTDHTATLYFRPLAGRDTEQFYADSRSGEFWIGPRP +TLAGLAARTGLRTAGLEELESAVTKNVAADGTAVRLLAETDQDVDALLAAVRTEAGVDLA +AAAEADAQTAEFLSELRLVKDAWEVDRMRASVAATIAGFEDVVRALPRAVGHDRGERVVE +GAFFARARLEGNDLGYDTIAASGNNATILHWIRNTGAVRPGELLLLDAGVEDDSLYTADI +TRTLPVSGTFTDVQRRIYQAVLDAADAAFAIVRPGIRFRELHAEAMRVLVDRLDGWGLLP +VSAEVALSDEGQHHRRWMPHGTSHHLGLDVHDCAQAKRELYLDGVLEPGMVFTIEPGLYF +KEEDLAVPEEYRGIGVRIEDDILVTEDGAENLSAALPRTPDEIEAWMARLQA +>PROKKA_01251 +MTDAAQHPAQTTPDQPAATPEAGADGTGAVNPQPLAERVDNRSQRPASNAFRDFMASDWA +PSSQALPDPDASAPYAARRRAAVSARFPGERIVVPAGRLKVRSNDTDYRFRAHSAFAHLT +GLGVDHEPDAVLVLEPTDPGAGDDGTDHTATLYFRPLAGRDTEQFYADSRSGEFWIGPRP +TLAGLAARTGLRTAGLEELESAVTKNVAADGTAVRLLAETDQDVDALLAAVRTEAGVDLA +AAAEADAQTAEFLSELRLVKDAWEIERMRASVAATIAGFEDVVRALPRAVGHDRGERVVE +GAFFARARLEGNDLGYDTIAASGNNATILHWIRNTGAVRPGELLLLDAGVEDDSLYTADI +TRTLPVSGTFTDVQRRIYQAVLDAADAAFAIVRPGIRFRELHAEAMRVLVDRLDGWGLLP +VSAEVALSDEGQHHRRWMPHGTSHHLGLDVHDCAQAKRELYLDGVLEPGMVFTIEPGLYF +KEEDLAVPEEYRGIGVRIEDDILVTEDGAENLSAVLPRTPDEIEAWMARLQA +>PROKKA_01384 +MTDAAQHPAQHADQDRPQDPAATPEAGVDAEGAVSPQPLAQRVENRSQRPSSDAFRAFMG +ADWAPSSDELPAQDASAPHAARRRAAVSARYPGERIVVPAGRLKVRSNDTDYRFRAHSAF +AHLTGLGVDHEPDAVLVLEPTDPGAGDGGSDHAATLYFRPLAGRDTEQFYADARAGEFWI +GPRPTLAGLAARTGLRTAGLEELESAVTKNVCADGTAVRLLREADQDMDALLAGVRAEAG +MDAEAAASADAQVAEFLSELRLVKDAWEVERMRASVAATIAGFEDVVRALPRAVGHDRGE +RVVEGAFFARARLEGNDLGYDTIAASGNNATILHWIRNTGTVREGDLLLLDAGVEDDSLY +TADITRTLPVSGSFTDVQRRIYQAVLDSADAAYAIVRPGIRFREIHAEAMRVLVERLADW +GLLPVSAEVALSEDGQHHRRWMPHGTSHHLGLDVHDCAQAKRELYLDGVLEPGMVFTIEP +GLYFKEEDLAVPEEYRGIGVRIEDDILVTEDGAENLSAALPRTPDEIEAWMARLQA +>PROKKA_01275 +MTDASAQQNDDLAPEAAADSGAALSPQPLAERVENRSQKPTSDAFRAFMASQWAPASREL +PGPDASAPFAARRRAAVSAMFPGERIVVPAGRPKVRSNDTDYRFRAHSAFAHLTGLGVDH +EPDAVLVLEPTDAGAGDAGTDHAATLYFRPLAGRDTEQFYSDPRAGEFWIGPRPTLAELA +ARTGLRTAGLEELENAVTKDVAATAVRLLREADQDMDAVVAAARADAGVDAQAAGAADAA +LAEALSELRLVKDEWEVERMRASVASTIAGFEDVVRALPRAVGHARGERVVEGAFFARAR +EEGNDLGYDTIAASGNNATVLHWIRNTGRVREGELILVDAGVEDDSLYTADITRTLPVSG +TYSDVQRRVYQAVLDAADAAFALVKPGIRFREIHAEAMRVLAGRLHGWGLLPVSPEEALS +EAGQHHRRWMPHGTSHHLGLDVHDCAQARRELYLDAVLEPGMVFTIEPGLYFKAEDLAIP +EEYRGIGVRIEDDILVTEDGAENLSAALPRTPEDVEAWMARLQG +>PROKKA_01468 +MMGGMTDAAQHPAQTAPDQPAATPEAGADGTGAVNPQPLAERVDNRSQRPASNAFRDFMA +SDWAPSSDALPDADASAPYAARRRAAVSARFPGERIVVPAGRLKVRSNDTDYRFRAHSAF +AHLTGLGVDHEPDAVLVLEPADPGTGDDGTDHTATLYFRPLAGRDTEQFYADSRSGEFWI +GPRPTLAGLAARTGLRTAGLEELESAVTKNVAADGTAVRLLAETDQDVDALLAAVRTEAG +VDLTAAAEADAQTAEFLSELRLVKDAWEVERMRASVAATIAGFEDVVRALPRAVGHDRGE +RVVEGAFFARARLEGNDLGYDTIAASGNNATILHWIRNTGAVRPGELLLLDAGVEDDSLY +TADITRTLPVSGTFTDVQRRIYQAVLDAADAAFAIVRPGIRFRELHAEAMRVLVDRLDGW +GLLPVSAEVALSDEGQHHRRWMPHGTSHHLGLDVHDCAQAKRELYLDGVLEPGMVFTIEP +GLYFKEEDLAVPEEYRGIGVRIEDDILVNEDGAENLSAALPRTPDEIEAWMARLQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001259.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001259.fa new file mode 100644 index 0000000000000000000000000000000000000000..b5d6fbbf2ac01d59bfdeaceb7d58e58378d2bfe1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001259.fa @@ -0,0 +1,59 @@ +>PROKKA_01542 +MGIDLTTELTALRDRLLSAEAEHADLISRVRDRHRASARNLVHYVALRGTDLRPLQEALS +DAGLSSLGRMEAGVLGHVDAVLAAARALDGDLATAPEDDALTSAEGRAILARNAASLLGP +ARGDRDARIMVTMPSEAATDPELVARIAEAGMDLARVNCAHDDEQAWAAMIAAVRRCAGA +GRPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPARDPSGIVTEPSRVWLAAGPHDAVAVAD +RPDGAVVVPLAAPDGKTLAGLQRGDEIELTDARGAHRRLEVERVSGEGVLVRADKTVYWA +TGTALTTPHGPLEVGPLPPLEQSMRVHEGEQIVLTRSLEPVPAVDTPPYRIGLTLAQAFA +DATVGDRVSLDDGRIGTRITGVSDDEITLEVTQAGPRGAKLKAEKGVNFPDTHLDIPALT +DEDLAHIPFAARHADMVNMSFVRSAEDVAQLIDALEAEDAPDVDITLKIETVEAFRQLPR +MLLEAMRWRDVGVMIARGDLAVEAGFARMAELQEEILWLCEAAHVPAIWATQVLESLAKT +GLPSRAEITDAAMAQRAEAAMLNKGPYIDRAVTVLGDILGRMHGHASKKRDMLRRLESWS +L +>PROKKA_01252 +MGIDLTTELTALRDRLLSAEAEHADLISRVRERHRASARNLVHYVALRGTDLRPLQEALS +DAGLSSLGRMEAGVLGHVDAVLAAARALDGDPAPAPEDDALTSAEGRAILARNAASLLGP +ARGDRDARIMVTMPSEAATDPELVARIAEAGMDLARVNCAHDDEQAWAAMIAAVRRCAGA +GLPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPARDPSGIVTEPSRVWLAAGPHDAVATAD +RPDGAVVVPLADPEGTTLAVLQRGDEIELTDARGAHRRLEVEQVDGEGVLVRAEKTVYWA +TGTALTTPHGPLEVGPLPPLEQSMRVHEGEEIVLARSLEPVPAVDTPPYRIGLTLAQAFA +DAAVGDRVSLDDGRIGARITAVSADEITLEVTQAGPRGAKLKAEKGVNFPDTHLAIPALT +DEDLAHIPFAARHADMVNMSFVRSAEDVAQLIDALEAEDAPDVDITLKIETVEAFRQLPR +MLLEAMRWRDVGVMIARGDLAVEAGFARMAELQEEILWLCEAAHVPAIWATQVLESLAKT +GLPSRAEITDAAMAQRAEAAMLNKGPYIDRAVTVLGDILGRMHGHASKKRDMLRRLESWS +L +>PROKKA_01383 +MDIDLTTELTALRDRLLSAEAEHADLISRVRDRHRASARNLVHYVALRGTDLRPLQDALS +DVGLSSLGRMEAGVLGHVDAVLAAARALDGEDAPSPDDDALTPARGREILARDADRLLGP +ARPDRAARIMVTLPSEAAQDPDLVARMAEAGMDLARVNCAHDDEAAWAAMIEAVRACATP +ERPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPARTPAGLVTEPSRVWLAAAGAADAPAGA +VVVPVTEAGAEVLAGLAAGDEVELTDARGSHHVLTVEQAGAAGALVRADKTVYWGTGLAV +DTPRGTLTVGELAPLEQSMRVRRRDQVVLTRSLDPVPAASAPPYRIGLTLAQAFEDVAVG +DRVSIDDGKIDAVVRAANADEITLEVTEAGPNGTKLKAEKGVNFPDTALSIPALTDEDLA +HIPFVARHADMVNLSFVRSAEDVAQLIDALAAEDATDVDITLKIETVGAFEQLPRMLLEA +MRWRDVGVMIARGDLAVEAGFERMAELQEEILWLCEAAHVPAIWATQILESLAKTGLPSR +AEITDAAMAQRAEAAMLNKGPYIEEAITALGDILGRMGGHARKKRDMLRRLESWSL +>PROKKA_01274 +MSTLPENAPDSRPTAESPVVAPGAAVTELIEAIDALRARIVAAEQAHAERLDRVADRHRA +SARNLVHYVTLRGEDLRPLQDALSAVGLSSLGRMEAGVLGHLDAVRTALHPLGGRPAPDP +ADDDPLSPAEGRALLAANAESLLGPSRPGRETRIMVTMPSEAATNAALVQGMADAGMDLA +RVNAAHDGEAAWAAMVANIRGVARDGGRPAPRICMDLAGPKLRTGPLEPGPGVVKVKPRR +DVDGTVLERSRVWLGEADAPEAADAVVLPLDPAGSGHSPVLSALRPGDHAMLTDARDSDR +TLHVLAATEAGVLLACRKTVYWHTGLEVDTPRGTLVVGALPSVPQAMRVHAGDEIVLTRS +MDPRPAVSEGPFTIGCSLPQAFQDVRPGERVLIDDGKITGEVVSNDGEAITLTVTEAGPT +GAKLRAEKGVNFPDTDLRLPALTDEDRSHLPFAAAHADVVNMSFVRSPADVAALIDALDA +EDARGVGVSLKIETVGAFERLPAMLLEAMRWNDVGVMIARGDLAVEAGFERMAELQEEIL +WLCEAAHVPAVWATQILETLAKQGLPSRAEITDAAMAQRAEAAMLNKGPYIDEAIGALSD +ILTRMGGHADKKRDMLRRLRSWSL +>PROKKA_01469 +MGIDLTTELTALRDRLLSAEAEHADLISRVRERHRASARNLVHYVALRGTDLRPLQEALS +DAGLSSLGRMEAGVLGHVDAVLAAARALDGDPAPAPEDDALTSAEGRAILARNAASLLGP +ARGDRDARIMVTMPSEAATDPELVARIAEAGMDLARVNCAHDDEQAWAAMIAAVRRCAGA +GRPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPTRDPSGTVTEPSRVWLAAGPHDAVAAAD +RPDGAVVVPLADPEGTTLAVLQRGDEIELTDARGAHRRLEVEQVDGEGVLVRAEKTVYWA +TGTALTTPHGPLEVGPLPPLEQSMRVHEGEQIVLTRSLEPVPAVDTPPYRIGLTLAQAFA +DATVGDRVSLDDGRIGTRITGVSDDEITLEVTQAGPRGAKLKAEKGVNFPDTHLDIPALT +DEDLAHIPFAARHADMVNMSFVRSAEDVAQLIDALEAEDAPDVDITLKIETVEAFRQLPR +MLLEAMRWRDVGVMIARGDLAVEAGFARMAELQEEILWLCEAAHVPAIWATQVLESLAKT +GLPSRAEITDAAMAQRAEAAMLNKGPYIDRAVTVLGDILGRMHGHASKKRDMLRRLESWS +L diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001266.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001266.fa new file mode 100644 index 0000000000000000000000000000000000000000..0515c4b0fc64967634777b5831bedce2029fa0bf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001266.fa @@ -0,0 +1,10 @@ +>PROKKA_01550 +MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQA +>PROKKA_01260 +MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQA +>PROKKA_01375 +MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQG +>PROKKA_01266 +MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEAKELQQCLEGVTQA +>PROKKA_01477 +MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001267.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001267.fa new file mode 100644 index 0000000000000000000000000000000000000000..a11f2460ae06b94930562d12e6ee28c4a1e92bfa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001267.fa @@ -0,0 +1,18 @@ +>PROKKA_01551 +MRAPLGGEGRRVSGPQWIVLVAVLVVVLAALAAALAGRLTLRADDPAGRTPGHPVLLPER +PRAADVDLLRLAVAVPGYQRDQVDAVLLRLRDALAQCEDEVTALRARVAELEAADPSRSD +PAGRA +>PROKKA_01261 +MRAPLGGEGRRVSGPQGIVLVAVLVVVLAALAAALAGRLTLRADDPAGRTPGHPVLLPER +PRAADVDLLRLAVAVPGYQRDQVDAVLLRLRDALAQREDEVTALRARVAELEAADPSRSD +PAGRA +>PROKKA_01374 +MSTPLWIAVIAALVVVVAALAAAAAGRLTLRAGEPAGQAPVHPVALPERPRADDVAFVRL +AVAVPGYQRDQVDAVLLRLRDALADHEDEVAALRARLAELEADAARDAERTGPR +>PROKKA_01265 +MTQPIWIAVLVVAVVAVAALAAAALGRALPRPADPAGQAPPHPVLLPEHPRAADVDRLRL +ATAVPGYQRDQVDEVLARLRAALAADEERIAALEARLGEGDGVGR +>PROKKA_01478 +MRAPLGGEGRRVSGPQGIVLVAVLVVVLGALAASLAGRLTLRADDPAGRTPGHPVLLPER +PRAADVDLLRLAVAVPGYQRDQVDAVLLRLRDALAQREDEAAALRARLAELEAADPSRSD +PAARA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001268.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001268.fa new file mode 100644 index 0000000000000000000000000000000000000000..a2f55b44224f2cfc257160e48f54c8468772cc63 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001268.fa @@ -0,0 +1,30 @@ +>PROKKA_01552 +MAPHEHPSGGDVAAKPQRVRRGGQVLRGDAAHTPTFDQLLLDGRRPGDAARPAADVASTT +SEAWRVLRIQAEFVEGFGTLAGLGPAVSVFGSARTPEGSAEYALAHEVGTRLARAGYTVI +TGGGPGTMAAANRGAHEAGGESVGLGIDLPFETGLNPWVHVGVDFRYFFVRKVMFLKYAQ +GFIVLPGGLGTLDELFEALTLVQTGTVTRFPVVLVDRGFWSPLVDWIRGTLVERGMISPE +DPDLFHLVDTAEEAVACVLRSAGRADA +>PROKKA_01262 +MAPDEHPLDGDVAEPEHVRRGGQVLRGEAERTPTFDQLLLDGRQPGDATQPAADIASTTS +EAWRVLRIQAEFVEGFGTLAGLGPAVSVFGSARTPEGSAEYALAHEVGTRLARAGYTVIT +GGGPGTMAAANRGAHEAGGESVGLGIELPFETGLNPWVHVGVDFRYFFVRKVMFLKYAQG +FIVLPGGLGTLDELFEALTLVQTGTVTRFPVVLVDRGFWGPLVDWIRGTLVERGMISPED +PDLVQLVDTAEEAVACVLRSAGRADA +>PROKKA_01373 +MDPDQHPRTDAVPAPERVRRGGQVLRGEAARRPTSDQLLLDARRPGDALPPAADLASTTS +EAWRVLRIQAEFVEGFGTLAGIGPAVSVFGSARTPEASPEYALAREVGARLAEAGFTVIT +GGGPGSMAAANRGAHEAGGESVGLGIELPFEAGLNEWVHVGVDFRYFFARKVMFLKYAQG +FVVLPGGFGTLDELFEALTLVQTGTVTRFPVVLVDSTFWGPVVDWIRGTLVERGMISPGD +PEIFHVVETAEEAVDCVQRVCGPGAP +>PROKKA_01264 +MTDKPDPARADRVDRHRVHRGGQILRGDAAASPTFDQLLLDARRAPAGKTRTPSTSSTSD +AWRVLRIQSEFVEGFGTLADLGPAISVFGSARTGEGTDEYALGVEIGRRLAEEGWAVITG +GGPGAMESANRGADEAGGVSVGLGIELPFETGLNPWVGIGVDFRYFFARKVMFLRYAQGF +VVLPGGFGTLDELFEALTLVQTGTVTRFPVVLVGTEFWGPLVDWIRGTLTARGMISPGDA +DLITVVDTAEEAVAHVSATCGGARA +>PROKKA_01479 +MAPHEHPSGGDVAAKPQRVRRGGQVLRGEAARTPTFDQLLLDGRRPGDATQPAADIASTT +SEAWRVLRIQAEFVEGFGTLAGLGPAVSVFGSARTPEGSAEYALAHEVGTRLARAGYTVI +TGGGPGTMAAANRGAHEAGGESVGLGIELPFETGLNPWVHVGVDFRYFFVRKVMFLKYAQ +GFIVLPGGLGTLDELFEALTLVQTGTVTRFPVVLVDRGFWGPLVDWIRGTLVERGMISPE +DPDLVQLVDTAEEAVACVLRSAGRADA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001269.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001269.fa new file mode 100644 index 0000000000000000000000000000000000000000..74082d437e3711a6e9169dfacabde6317bb2f441 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001269.fa @@ -0,0 +1,30 @@ +>PROKKA_01553 +MTQITPEQPHGAHLPDEAGVRRRRGAAGDDLIVLEGVNKHFGDFHALRQIDLRIPRGQVA +IVLGPSGSGKSTLCRTINRLETIDDDGGRILIDGRPLPTEGRQLAQLRAEIGMVFQSFNL +FAHKSILENVTLGPIKVKGKRRADAERHAMELLERVGVAQQARKMPAQLSGGQQQRVAIA +RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF +MADGAILEDTDPDTFFTNPRHERAQDFLGKILAH +>PROKKA_01263 +MTQITPEQPHGAHLPDEAGVRRRRGAAGDDLIVLEGVNKHFGDFHALRQIDLRIPRGQVA +IVLGPSGSGKSTLCRTINRLETIDDDGGRILIDGRPLPTEGRQLAQLRAEIGMVFQSFNL +FAHKSILENVTLGPIKVKGKRRADAERHAMELLERVGVAAQARKMPAQLSGGQQQRVAIA +RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF +MADGAILEDTDPDTFFTNPRHERAQDFLGKILAH +>PROKKA_01372 +MTQITPEEPHGAHARDEAAPRRPRAAPGDDLIVLENVNKHFGDFHALKDIDLRIPRGQVA +IVVGPSGSGKSTLCRTINRLETIDDDGGRILLDGQPLPAEGKQLAQLRAEVGMVFQSFNL +FAHKSILENVTLGPIKVKGKRKADAERHAMELLERVGVAQQAKKMPAQLSGGQQQRVAIA +RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF +MADGAILEDTDPESFFTAPQHERARDFLGKILAH +>PROKKA_01263 +MSEITSGTVHGSTAASGPAPAAASDALIRLEHVNKHFGEFHALKDIDLAIPRGQVAIVLG +PSGSGKSTLCRTINRLETIDDDGGRILIDGRPLPSEGRELARLRAEVGMVFQSFNLFAHK +SILENVTLGPIRVKGRKKAEAERHALELLERVGVAHQAKKMPAQLSGGQQQRVAIARALA +MEPQALLFDEPTSALDPEMVQEVLDVMVGLAREGMTMVVVTHEMGFARKAGDRVVFMADG +EILEDTDPESFFTRPQHPRAQEFLGKILVH +>PROKKA_01480 +MTQITPEQPHGAHLPDEAGVRRRRGAAGDDLIVLEGVNKHFGDFHALRQIDLRIPRGQVA +IVLGPSGSGKSTLCRTINRLETIDDDGGRILVDGRPLPTEGRQLAQLRAEIGMVFQSFNL +FAHKSILENVTLGPIKVKGKRRADAERHAMELLERVGVAQQARKMPAQLSGGQQQRVAIA +RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF +MADGAILEDTDPDTFFTNPRHERAQDFLGKILAH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001270.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001270.fa new file mode 100644 index 0000000000000000000000000000000000000000..52d4c78998560ae5ee8a9fe7728204bb9857f681 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001270.fa @@ -0,0 +1,30 @@ +>PROKKA_01554 +MLRTKLLTLSAVTAAAALSLTACAPSSSQGGGGDAAGSSSAGESTSSGSGESLRIGIKFD +QPGLGYREGSAQPTGFDTDVARYVADKLGVAEQDIEWVQTPSANRENALENGEVDMIFAT +YSITDARKERVAFAGPYFVAGQDLLVRADDTAITGPESLDGKNLCSVTGSTSAQKIKDQF +ASGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAAADANKGKFKVVGNTFTTERYG +VGLPKDSERCEDINEAIKEMKDSGEWEKALESNTEGTGYTYDETLNSGEDAEFEPCA +>PROKKA_01264 +MLRTKLLTLSAVTAAAALSLTACAPSSSQGGGGDAAGSSSAGESTSSGSGERLRIGIKFD +QPGLGYREGSAQPTGFDTDVARYVADKLGVAEKDIEWVQTPSANRENALENGEVDMIFAT +YSITDARKERVDFAGPYFVAGQDLLVRADDTAITGPESLEGKNLCSVTGSTSAQKIKDQF +ASGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAAADANKGKFKVVGNTFTTERYG +VGLPKDSERCEDINEAIKEMKDSGEWEKALESNTEGTGYTYDETLNSGEDAEFEPCA +>PROKKA_01371 +MFRKKLLTLSAVTAAAALSLTACSPSAQQGGGEGSGSASAGGSQSAGSGEGLRIGIKFDQ +PGLGFREGSGAPTGFDTDVARYVADKLGVAEGDIEWVQTPSANRENALENGEVDMIFATY +SITDARKERVDFAGPYFVAGQDLLVRADDTEITGPDALDGKNLCSVTGSTSAQKIKDQFA +SGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAATDANKGKFKVVGNTFTTERYGV +GIAKGDDRCEDINDAIKEMKDSGAWKESLDANTEGTGYEYDEALNSGADAEFESCS +>PROKKA_01262 +MARSRILSVAAVAAAAALSLSACSPSSSGGSGSASSASGSTAAQSGSSDTLRIGIKYDQP +GLGFREGQNAPTGFDTDVARYVAGKLGVAEDKIEWVQTPSANRENALENGEVDMIFATYS +ITDARKQRVDFAGPYFVAGQDLLVRQDDTSITGPDSLNGKNLCSVTGSTSAQKIKDNYAS +GVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAATDANKGKFKVVGQPFTTERYGVG +LQKGSDKCKDINEAIKAMKDSGEWEKSLKANTEGTGYEYSEDKNSGADAEFEPCA +>PROKKA_01481 +MLRTKLLTLSAVTAAAALSLTACAPSSSQGGGGDAAGSSSAGESTSSGSGESLRIGIKFD +QPGLGYREGSAQPTGFDTDVARYVADKLGVAEQDIEWVQTPSANRENALENGEVDMIFAT +YSITDARKERVAFAGPYFVAGQDLLVRADDTAITGPESLDGKNLCSVTGSTSAQKIKDQF +ASGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAAADANKGKFKVVGNTFTTERYG +VGLPKDSERCEDINEAIKEMKDSGEWKKALESNTEGTGYTYDETLNSGEDAEFEPCA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001271.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001271.fa new file mode 100644 index 0000000000000000000000000000000000000000..349de6fd145d3f670d51136a7a6bebb0051cc06e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001271.fa @@ -0,0 +1,25 @@ +>PROKKA_01555 +MESISSLLADYGADIPLAFWMNIRLAFLATLGSFVLGVVLALFRISPVPSLRALGAGYVN +VVRNTPLTIIMLLGVLAVWGQLKISFSSDFTLNFFIYAVIALSLYHAAFMCEAIRSGVNT +VPLGQAEAARSIGLGFLPAARHVILPQALRGAITPLGNTVIALTKNTTVAAAASVAEASG +LMKRMIEFSPDVMVAIFLTFAIGFCLIVIPIGLLTTWASEKWAVAR +>PROKKA_01265 +MESISSLLADYGADIPLAFWTNIRLAFLATLGSFVLGVVLALFRISPVPSLRALGAGYVN +VVRNTPLTIIMLLGVLAVWGQLKISFSSDFTLNFFIYAVIALSLYHAAFMCEAIRSGVNT +VPLGQAEAARSIGLGFLPAARHVILPQALRGAITPLGNTVIALTKNTTVAAAASVAEASG +LMKRMIEFSPDLMVAIFLTFAIGFCLIVIPIGLLTTWASEKWAVAR +>PROKKA_01370 +MESISSLLADYGADIPLAFWTNIRLAFLATLGSFVLGVVLALFRISPVPSLRAIGTAYVN +VVRNTPLTIVMLLGVLAVWGQLKITFSSDFTLNFFIYAVIALSLYHAAFMCEAIRSGVNT +VPLGQAEAARAIGLGFLPAARHVILPQALRGAITPLGNTVIALTKNTTVAAAASVAEASG +LMKRMIEFSPDVMVAIFLTFAIGFCLIVIPIGLLTTWASDKWAVAR +>PROKKA_01261 +MESLSTLVEQYGAAVPQAFWMNIRLAALATLGAFVLGVLLALCRISPVPSLRAVGAGYVH +IVRNTPLTIIMLIGVLAVWGQLKVTFAPDFKVNFFVYAVLALSLYHAAFMCEAIRSGVNT +VPLGQAEAARAIGLGFLPAARLVILPQALRGAITPIGNTVIALTKNTTVAAAASVAEASG +LMKTMIEFRPDAMVAIFLTIAIGFCLIVIPIGLLTTWASDKWAVSR +>PROKKA_01482 +MESISSLLADYGADIPLAFWTNIRLAFLATLGSFVLGVVLALFRISPVPSLRALGAGYVN +VVRNTPLTIIMLLGVLAVWGQLKISFSSDFTLNFFIYAVIALSLYHAAFMCEAIRSGVNT +VPLGQAEAARSIGLGFLPAARHVILPQALRGAITPLGNTVIALTKNTTVAAAASVAEASG +LMKRMIEFSPDLMVAIFLTFAIGFCLIVIPIGLLTTWASEKWAVAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001272.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001272.fa new file mode 100644 index 0000000000000000000000000000000000000000..0be6435d706ed15bb10ce1ccf11a2c3536c6ad17 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001272.fa @@ -0,0 +1,30 @@ +>PROKKA_01556 +MSAQASVLFDAPGPIARRRILLANLVSLAAVLVVAVLVLIQMNATGQLSGRRWLAAVDGN +AWRNYYLPGLQFTLQSAGIAVVSSVVFGLVFGFLRLAPVGPVRWLAAVVVEFFRAVPVLV +MMVFFYQLFAQVARSGAIQPQDGPYYAVIAALTLYNGSVIAELVRSGVRSLPRGQREAAA +AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGNG +NILQSLVVAAMIFIVINFLLTWAATRLSRRLSSRTAGDASAPTTPRVGAPTDTAG +>PROKKA_01266 +MSAQASVLFDAPGPIARRRILLANLVSLAAVLVVAVLVLIQMNATGQLSGRRWLAAVDGN +AWRNYYLPGLQFTLQSAGIAVVSSVVFGLVFGFLRLAPVGPVRWLAAVVVEFFRAVPVLV +MMVFFYQLFAQVARSGAIQPQDGPYYAVIAALTLYNGSVIAELVRSGVRSLPRGQREAAA +AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLHYARQLGSGNG +NILQSLVVAAMIFIVINFLLTWAATRLSRRLSSRTAGDASAPTTPRVGAPTDTAG +>PROKKA_01369 +MSSQASVLFDAPGPLARRRILIANLVALAAVLALAVAVLMRMADADQLEARRWTAALDAN +AWTNYYLPGLQFTVQAAAIAVLTSVVFGLVLGFLRLAPFAPVRGAAGLVVEFFRAVPVLI +MMVFFYQVFAQVARTGVIAPADGPYYAVIVALTLYNGSVIAELVRSGVRSLPKGQREAAA +AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGQG +NILQSLVVAALIFIVINFLLTWVATRLSRRLSSRTAGDAGAPTTPVVGAPTDKPA +>PROKKA_01260 +MSAQASVLFDAPGPATRRRILIVNLVALALVLAVAVVVGMALQDRGQLEPRRWLAALDAN +AWTNYYLPGLQFTLQSAGIAVVTSVVFGLVFGFLRLAPVAPVRWLAAVVVEFLRAVPVLV +MMVFFYQAFALAARGGAINAADSPYYAVIVGLTLYNGSVIAELVRSGVTGLPKGQREAAA +AIGMTPNQSLRLVEVPQALVAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGQG +NILQTLVVAAVIFILINMLLTWLATLLSRRLSSRTSGRTKPHAGSTAVTIGKD +>PROKKA_01483 +MSAQASVLFDAPGPIARRRILLANLVSLAAVLVVAVLVLIQMNATGQLSGRRWLAAVDGN +AWRNYYLPGLQFTLQSAGIAVVSSVVFGLVFGFLRLAPVGPVRWLAAVVVEFFRAVPVLV +MMVFFYQLFAQVARSGAIQPQDGPYYAVIAALTLYNGSVIAELVRSGVRSLPRGQREAAA +AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGNG +NILQSLVVAAMIFIVINFLLTWAATRLSRRLSSRTAGDASAPTTPRVGAPTDTAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001273.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001273.fa new file mode 100644 index 0000000000000000000000000000000000000000..4261d12c179081cb5d7e614ac284bac3b1a832d9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001273.fa @@ -0,0 +1,40 @@ +>PROKKA_01557 +MSLTPNTLPDLADPDLDVAALTATLLDVRSVSGEEGPLADAVEQALRALGGLEVRRFGDA +VVARTALGRSTRVILAGHLDTVPLPTVPGSRGTVPSAWDGDVLYGRGAVDMKSGVAVQLA +LAGRFGRADGPTPVHDVTWVFYDHEEVSSDLSGLARVARQAPELLEGDFAVLLEPTDGVV +EGGCNGTCRYRVTFSGVAAHSGRAWRGDNAIHKLAPVLTALAAYEPATVTVEGLEYREGL +HAIRVAGGVAGNVIPDEASVDLNYRFAPDKTLEQAHAHVRAVLEGAGVDWDAQVRIDDAS +PAARPGLDRPAAAAFVAAVGGEPQPKYGWTDVARFSQLGVPAVNFGPGDALLAHTDDEHV +SREAVHACLAALTAWLAG +>PROKKA_01267 +MSLTPVSLPDLADPDLDVAALTATLLDVRSVSGEEGPLADAVEHALRALGGLEVRRFGDA +VVARTALGRPTRVILAGHLDTVPLPTVPGSRGTVPSAWDGDVLYGRGAVDMKSGVAVQLA +LAGRFGRADGPTPVHDVTWVFYDHEEVSSDLSGLARVARQAPELLEGDFAVLLEPTDGVV +EGGCNGTCRYRVTFSGVAAHSGRAWRGDNAIHKLAPVLTALAAYEPATVTVEGLEYREGL +HAIRVAGGVAGNVIPDEASVDLNYRFAPDKTLEQAHAHVRAVLEGAGVDWDAQVRIDDAS +PAARPGLDRPAAAAFVAAVGGEPQPKYGWTDVARFSQLGVPAVNFGPGDALLAHTDDEHV +SREAVHACLAALTAWLAG +>PROKKA_01368 +MTETSAPALPDLADPGLDVAELTAVLLDVPSVSGDEGPLADAVETALRALGGLEVRRFGD +AVVARTDLGRDTRVILAGHLDTVPLPTVPGSRGTVPSAWEGDVLYGRGAVDMKSGVAVQL +ALAGRYGRADGPAPAHDVTWVFYDHEEVASDLSGLARVARQAPELLEGDFAVLLEPTDGV +VEGGCNGTCRYRVSFSGVAAHSGRAWRGENAIHKLGAVLTALAAHEPATVTVEGLDYREG +LNAIRVAGGVAGNVIPDAAHVDVNYRFAPDKTLEQAHARVREVLEGAGVDWDAQVRIDDA +SPAARPGLDRPAAAAFVAAVGGEPQPKYGWTDVARFSELGVPAVNFGPGDALLAHTDDEH +VHRAAVHACLDALDAWLAG +>PROKKA_01259 +MTDAVAPVLPDLAAADLDVAALTATLLDAPSVSDDEGPLADAVEAALARLPRLGVRRFGD +AIVARTELGLPGRVILAGHLDTVPLPTAPGARGTVPSAWEGDVLYGRGAVDMKSGVAVQL +ALAGLFGRADGPDPVHDVTWVFYDHEEVDSARSGLARIARQAPELLEGDFAVLLEPTDGV +VEGGCNGTCRYRVRFEGVAAHSGRAWRGDNAIHKLGALLSALAAYEPATVTVEGLDYREG +LNAIRVSGGVAGNVIPDAAATEVNYRFAPDKTLEQAHAHVREVFAAAGVDWDAQVEVTDA +SPAARPGLDRPAAAAFVAAVGGEPMPKYGWTDVARFSELGVPAVNFGPGDALLAHTDDEH +VERAAVERCRDALEAWLRG +>PROKKA_01484 +MSLTPVSLPDLADPDLDVAALTATLLDVRSVSGEEGPLADAVEQALRALGGLEVRRFGDA +VVARTALGRSTRVILAGHLDTVPLPTVPGSRGTVPSAWDGDVLYGRGAVDMKSGVAVQLA +LAGRFGRADGPTPVHDVTWVFYDHEEVSSDLSGLARVARQAPELLEGDFAVLLEPTDGVV +EGGCNGTCRYRVTFSGVAAHSGRAWRGDNAIHKLAPVLTALAAYEPATVTVEGLEYREGL +HAIRVAGGVAGNVIPDEASVDLNYRFAPDKTLEQAHAHVRTVLEGAGVDWDAQVRIDDAS +PAARPGLDRPAAAAFVAAVGGEPQPKYGWTDVARFSQLGVPAVNFGPGDALLAHTDDEHV +HREAVHACLAALAAWLAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001275.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001275.fa new file mode 100644 index 0000000000000000000000000000000000000000..824d6bd415fdb723503bdcca9c87b33dcb99d9b8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001275.fa @@ -0,0 +1,45 @@ +>PROKKA_01560 +MTHHESVRLTVGEQSLDLGVEHATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTF +IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL +KLFFNGFPRDAHPMPVLSSSVSALSTFYPDSLDPHDQEQVHISTVRLLGKLPVLASYAFK +KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYDIDPDVVKALDLLLMLHADHEQNASTST +VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRKIKSEGITPEDFMEKVKNKED +GVRLMGFGHRVYKNYDPRAKIIKKTAEDILGKMGGNDELLEIAQRLEEKALADDYFVERK +LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPAAKIGRPRQIYVGE +QLRQYPQR +>PROKKA_01270 +MTHHESVRLTVGEQSLDLGVEHATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTY +IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL +KLFFNGFPRDAHPMPVLSSSVSALSTFYPDSLDPHDPEQVHISTVRLLGKLPVLASYAFK +KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYDIDPDVVKALDLLLMLHADHEQNASTST +VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRKIKSEGITPEDFMEKVKNKED +GVRLMGFGHRVYKNYDPRAKIIKKTAEDILGKMGGNDELLEIAQRLEEKALADDYFVERK +LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPATKIGRPRQIYVGE +QLRQYPQR +>PROKKA_01366 +MTQNESVRLTVGEQSLDLGVERATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTF +IDGDEGILRYRGYAIEDLAANSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL +KLFFNGFPRDAHPMPVLSSSVSGLSTFYPDSLDPHDPEQVHISTVRLLGKLPVLASYAFK +KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYEIDPDVVKALDLLLMLHADHEQNASTST +VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRTIQSDGIKPEDFMEKVKNKED +GVRLMGFGHRVYKNYDPRAKIIKKTAEDILSKMGGNDELLEIAQRLEEKALADDYFVERK +LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPATKIGRPRQIYVGE +PLRQYPQR +>PROKKA_01257 +MSEIESARLTVGEKTLDLGVEKAAEGNDGIVVAPLLKETGKVTYDPGFMNTANAKSAITY +IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKEALEAWETNILRHNMVHEDL +KMFFNGFPRDAHPMPVLSSSVSALSTFYADSLDPKDPEQVHISTVRLLGKLPVLASYAFK +KSLGQPFMYPHNNLNYVENFLRLCFGVPAEEYEIDPDMVKALDLLLMLHADHEQNASTST +VRLVGSTDANLFASVSAGINALYGPLHGGANEAVLNMLRRIQAEGIKPEDFMEKVKHKED +GVRLMGFGHRVYKNYDPRAKIVKKTAEDILAKLGGNDELLEIAMRLEEKALADDYFVERR +LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELTEDPATKIGRPRQIYVGE +QLRQYPQR +>PROKKA_01487 +MTHHESVRLTVGEQSLDLGVEHATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTF +IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL +KLFFNGFPRDAHPMPVLSSSVSGLSTFYPDSLDPHDPEQVHISTVRLLGKLPVLASYAFK +KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYDIDPDVVKALDLLLMLHADHEQNASTST +VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRKIKSEGITPEDFMEKVKNKED +GVRLMGFGHRVYKNYDPRAKIIKKTAEDILGKMGGNDELLEIAQRLEEKALADDYFVERK +LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPATKIGRPRQIYVGE +QLRQYPQR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001276.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001276.fa new file mode 100644 index 0000000000000000000000000000000000000000..719466d6a5a48210a2708a5f7dae11c62b29b278 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001276.fa @@ -0,0 +1,40 @@ +>PROKKA_01561 +MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPALIRRALTEAADAHGYPTTHG +TDDLRRAVVDWYARRRGVSGLDPAAVVPTVGSKEFIAWLPTLLGLGAGDVVVHPEAAYPT +YAVGALLAGAEAVAADDLDALAPEVRERVRLVWTNSPANPTGAVLDAAALRRTVDAARDV +GAVVCGDECYAELGWDAWDGAVVPCILSDEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA +GDPQLVATLINTRKHAGMIVPAPVQHAMAVALADDAHVAEQKDRYRRRRDALRTALEASG +HTVDHSEAGLYLWTRRADLDPADATAQDSWDLLGELADLGIIAGPGVFYGAGGDGYVRVA +ITATDEAVARAAARLTARGPRTG +>PROKKA_01271 +MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPALIRRALTEAADAHGYPTTHG +TDALRRAVVDWYARRRGVSGLDPAAVVPTVGSKEFIAWLPTLLGLGAGDVVVHPEAAYPT +YAVGALLAGAEAVAADGLDALAPEVRERVRLVWTNSPANPTGAVLDAAALRRTVDAARGV +GAVVCGDECYAELGWDAWDGAVVPCILSDEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA +GDPELVATLVNTRKHAGMIVPAPVQHAMAVALADDAHVAEQKDRYRRRRDALRTALEASG +HTVDHSEAGLYLWTRRADLDPADATAQDSWDLLGDLADLGIIAGPGVFYGAGGDGYVRVA +ITATDEAVARAAARLTARGPRTG +>PROKKA_01365 +MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPELIRRALTEAADAHGYPTTHG +TADLRRAVVDWYARRRGVAGLDPEAVVPTVGSKEFIAWLPTLMGLGAGDVVVHPEAAYPT +YAMGALIAGAEAVAADDLASLAPEVRERVRLVWTNSPANPTGAVLDAAALKRVVDDARAL +GAVVCGDECYAELGWDEWDGELVPCILSEEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA +GDPGLVATLVNTRKHAGMIVPAPVQHAMAVALADEGHVAQQKDRYRRRRDALRAALEASG +HAVDHSEAGLYLWTRRADTDPAAATEQDSWDLLGELADLGIIAGPGVFYGAGGHGYVRVA +ITASDEAVEQAARRLAARGPLRR +>PROKKA_01256 +MLTLPDYPWDTLAPYRERAAAHPEGTVDLSIGTPVDPTPALIRDALTAAADAHGYPTTHG +TAELRQAVVDWFARRRGVPGLDPEAVLPTVGSKELIAWLPTLLGLGAGDVVVFPATAYPT +YAIGAQIAGAEAVAADTLAELDDDVRSRVRLVWTNSPANPTGAVLDAAELRAIVDDARAL +GAVVCGDECYAELGWDEWEDRVVPCILAPEVSGGDLTGLLSVYSLSKQSNLAGYRAAFVG +GDPELIAPLTNTRKHAGMIVPGPVQHAMAVALRDDAHVAAQRDLYRERRAALKAALESAG +YAVDHSEAGLYLWTRRADLAPGQGTAQDSWDLLGELAELGIVAGPGVFYGAAGHGHVRVA +ITASDEAVAAGAARLTARGPLPR +>PROKKA_01488 +MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPALIRRALTEAADAHGYPTTHG +TDALRRAVVDWYARRRGVSGLDPAAVVPTVGSKEFIAWLPTLLGLGAGDVVVHPEAAYPT +YAVGALLAGAEAVAADDLDALAPEVRERVRLVWTNSPANPTGAVLDAAALRRTVDAARGV +GAVVCGDECYAELGWDAWDGAVVPCILSDEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA +GDPELVATLVNTRKHAGMIVPAPVQHAMAVALADDAHVAEQKDRYRRRRDALRTALEASG +HTVDHSEAGLYLWTRRADLDPADATAQDSWDLLGDLADLGIIAGPGVFYGGDGYVRVAIT +ATDEAVARAAARLTARGPRTG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001277.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001277.fa new file mode 100644 index 0000000000000000000000000000000000000000..639b1499bca1132fe18d573f946867770828da47 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001277.fa @@ -0,0 +1,15 @@ +>PROKKA_01562 +MTYVIALPCVDVKDKACIDECPVDCIYEGERMLYIHPDECVDCGACEPVCPVEAIYYEDD +TPEEWAEYYKANVEFFDDLGSPGGAAKLGMIAKDHPIISALPLQNADA +>PROKKA_01272 +MTYVIALPCVDVKDKACIDECPVDCIYEGERMLYIHPDECVDCGACEPVCPVEAIYYEDD +TPEEWAEYYKANVEFFDDLGSPGGAAKLGMIAKDHPIISALPLQNADA +>PROKKA_01364 +MTYVIALPCVDVKDKACIDECPVDCIYEGERSLYIHPDECVDCGACEPVCPVEAIYYEDD +TPEEWADYYKANVEFFDDLGSPGGAAKLGMIAKDHPIIAALPPQNADA +>PROKKA_01255 +MTYVIALPCVDVKDKACIDECPVDCIYEGERSLYIHPDECVDCGACEPVCPVEAIYYEDD +VPEEWADYYKANVEFFDDLGSPGGAAKLGQIAKDHPLISALPPQGEGA +>PROKKA_01489 +MTYVIALPCVDVKDKACIDECPVDCIYEGERMLYIHPDECVDCGACEPVCPVEAIYYEDD +TPDEWAEYYKANVEFFDDLGSPGGAAKLGMIAKDHPIISALPLQNADA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001280.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001280.fa new file mode 100644 index 0000000000000000000000000000000000000000..f51f9cecab7fd9c5b58d82064b86ff66e3c7824c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001280.fa @@ -0,0 +1,40 @@ +>PROKKA_01566 +MTTNNSSMTGAQLDEKQIFDLAEAEDAKLRAKAGKSYSQGALVRKRFFRHRAAMISLIVL +VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD +TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSLLMRLTDLIIVI +PLLVLAAVLGQMASGMKMGILPLAVVLGLVSWTSLARLVRGEVLSLREKEFVAAAVAMGA +KPGRLIFKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISDYQNA +FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGGGAHRRLRFFGRRAAATEAGAT +TAGGLAAAPTAGRIEAPVEEAGGSARISDADEDGQR +>PROKKA_01276 +MTTNNSSMTGAQLDEKQIFDLAEAEDAKLRAKAGKSYSQGALVRKRFFRHRAAMISLIVL +VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD +TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSVLMRLTDLIIVI +PLLVLAAVLGQMASGMKMGILPLAVVLGLVSWTSLARLVRGEVLSLREKEFVAAAVAMGA +KPGRLIFKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISDYQNA +FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGAGAHRRPRFFGRRAAATEAGAT +TAGGLAAAPTAGRIEAPVEAAGGSARISDADEDGQR +>PROKKA_01360 +MTTNNSSTTGAQLDEKQIFDLAEAEDAKLRVKAGKSYSQGALVRKRFFRHKAAMISLIVL +VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD +TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSVLMRLTDLIIVI +PLLVLAAVLGQMASGANMGILPLALVLGLVTWTSLARLVRGEVLSLREKEFVAAAVAMGA +KPGRVIGKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISLYQNS +FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGAAAGRKRGLFSRRAAKTDAGAT +TAGGLGTAPTARDGEADDLIADPDAPEHRRGGAGGPAGGVGQ +>PROKKA_01251 +MTMSHSAQQNPRSTSPAVVDLAEAEDLKLQQKTGKSYSQGALIRMRFFRHKAAMVSLVVL +AFIALMAFTSIGFAGIPGWWDESYSAASTVVDGGRPTLSVVPQFLGGEGLRWGAHPFGQT +STGTDFFALVMRGTQQSLIIAFIVGLISTAIGALVGAASAYFGGWVDSVLMRLTDLIIVI +PLLVLAAVLGKMAGGLQLGILPLAFVLGIVSWTSLARLVRGEILSLREKEFVAAAVAMGA +KPGRIIGKHLLPNTIGVIVVNATFAIAGAVLLETSLSYLGFGVKSPDSSLGLLISDYQTA +FTTRPWLFWWPGMTILAIALSVNFLGDGLRDAFDPRQSGSGRRKRGLFSRRAAVTEATPT +TAGGLQASPASAPAGHADVVTDSRGLDAPAAWTVTDADGTSRPAGDDVDTTEGDAR +>PROKKA_01493 +MTTNNSSTTGAQLDEKQIFDLAEAEDAKLRAKAGKSYSQGALVRKRFFRHKAAMISLIVL +VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD +TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSVLMRLTDLIIVI +PLLVLAAVLGQMASGMKMGILPLAVVLGLVSWTSLARLVRGEVLSLREKEFVAAAVAMGA +KPGRLIFKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISDYQNA +FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGAGAHRRPRFFGRRAAATEAGAT +TAGGLAAAPTAGRIEAPVEEAGGSARISDADEDGQR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001282.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001282.fa new file mode 100644 index 0000000000000000000000000000000000000000..b06011cf7437c6c74aa2d91b7501e57c4c7db39b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001282.fa @@ -0,0 +1,60 @@ +>PROKKA_01568 +MKYTKLSAAAALAAGSALILSACAPGGGNAGDSSSNSASGASQGGDSGAGNVIEGDKGQK +LTAEASGPGKADLGDVKTQDGSIAYSVGADDFLSYNGLQSNTYTTYNSAVADRMFSSFWY +FGTDGSIIPDKDFGTYEKTSDDPLTVKYTISDDAKWSDGTPVTAGDFIVHWAANNDTIKA +EGAETPLFDSISFEQGKYIPEAPEGEADGKEFTVTYPEPYADWEILISTALPAHIVAKEA +GMSFEELVTAAKEKDVEALTPAAEFWNDGWDFSPGELPDASLVPSMGPYKFKDGGWQAGQ +SITLEANPEYWGTPAATKELVLRFADPKTHVQALQNGDLDVIEPQATVDTLQQLEGLGED +VNVQTGDQLTWEHVDYNRGEGSVFADSPELREAFALCLPRQQIVDNLIKPIYADAQVMNL +REVFPFQDKYQEVVDAAYPKEMDQPNIEKAKELVEKSGVSKPTVRLGYQAGNQRRTETVA +LIKSSCDQAGFDVQDANSPVFFKEVMPAGDYDAALFAWAGSGQKASGANIYQSDGAQNQQ +SYNNPEVDAAWDKLATSLDENEQLEQVKTIEKLLWEDFQAIPLYAHPGLVGHKADVANVR +DTAAQSGALWNVEQWVRVQE +>PROKKA_01278 +MKYTKLSAAAALAAGSALILSACAPGGGNAGDSSSNSASGASQGGDSGAGNVIEGDKGQK +LTAEASGPGKADLGDVKTQDGSIAYSVGADDFLSYNGLQSNTYTTYNSAVADRMFSSFWY +FGTDGSIIPDKDFGTYEKTSDDPLTVKYTISDDAKWSDGTPVTAGDFIVHWAANNDTIKA +EGAETPLFDSISFEQGKYIPEAPEGEADGKEFTVTYPEPYADWEILISTALPAHIVAKEA +GMSFEELVTAAKEKDVEALTPAAEFWNDGWDFSPGELPDASLVPSMGPYKFKDGGWQAGQ +SITLEANPEYWGTPAATKELVLRFADPKTHVQALQNGDLDVIEPQATVDTLQQLEGLGED +VNVQTGDQLTWEHVDYNRGEGSVFADSPELREAFALCLPRQQIVDNLIKPIYADAQVMNL +REVFPFQDKYQEVVDAAYPKEMDQPNIEKAKELVEKSGVSKPTVRLGYQAGNQRRTETVA +LIKSSCDQAGFDVQDANSPVFFKEVMPAGDYDAALFAWAGSGQKASGANIYQSDGAQNQQ +SYNNPEVDAAWDKLATSLDENEQLEQVKTIEKLLWEDFQAIPLYAHPGLVGHKADVANVR +DTAAQSGALWNVEQWVRVQE +>PROKKA_01358 +MKYTKLSAAAALAAGSALILSACAPGGGDDADNTASSGNGGASGSASQGGEAGAPEVTEG +DKGQKLTAPVDGPGMADLGDVETQDGSIAYSVGADDFLSYNGLQSNTYTTYNSAVADRMF +SSFWYFGTDGSIIPNKDFGTYEKTSDDPLTVKYTISDDAKWSDGTPVTAGDFIVHWAANN +ETVKAEGSETPLFDSISFEQGKYIPEAPEGEADGKEFTVTYPEPYADWEILISTALPAHI +VAKEAGMSFEELVTAAKEKDVEALTPAAEFWNDGWDFSPGELPDASLVPSMGPYKFKDGG +WQAGQSITLEANPEYWGTPAATKELVLRFADPKTHVQALQNGDLDVIEPQATVDTLQQLE +GLGDDVNVQTGDQLTWEHVDFNRGEGSVFADSPELREAFALCLPRQQIVDNLIKPIYADA +QVMNAREVFPFQENYQEVVDAAFPEEMDQPNIEKAKELVEKSGVSKPTVRLGYQAGNQRR +TETVALIKSSCDQAGFDVQDANSPVFFKEVMPAGDYDAALYAWAGSGQKASGANIYQSDG +AQNQQSYNNPEVDAAWDKLATSLDEDEQLEQVKTIERLLWEDFQAIPLYAHPGLVGHKAD +VANVRDTAAQSGALWNVEQWVRVQE +>PROKKA_01249 +MKHTKLSAAAALAFGSALVLSACAPAGPAASGSSSNGGGSSAASGSSAASGSDAAGGVTT +GEKGEKLTAPADGPGMADLGDVKTEEGSVAYSVGKDDFLSYNGVQANTYSTYNSAIVDRL +FSGFYYFGTDGTIVRNEEFGTFEKISDDPLKVKYTINEDATWSDGTPVTAADFIVQWAAD +NPNIVDESGKADPKTGQKPQLFESITSEPGKYIPEAPEGDPKGKEFTVTYAEPYADWEIL +ITTALPAHVIAKGADMSLDDLVAAAKAKDSTKLVPAAKFWNNGWDFNPGELPSADMIPSM +GPYKIKDGGWVAGQSITLEANDKYWGTPAATKNLVIKFAAPETHVQALQNKELDVIEPQA +TVDTVSQLEGLGDSVNIQKGDQLTWEHLDFNRGTGSTFADSKELREAFALCVPRQQIVDN +LVKPINPDATVMNAREVFPFQDNYQEVVDAAYPKEMDQPNIEKAKELVAKSGVSKPTVRL +GYQAGNQRRAETVKLIKASCDQAGFDVQDANSNVFFKEVMPTGDYDVALYAWSGSGQKAS +GANIYQSDGEQNQQSYSNKTVDEAWDKLAGSLDEKEQLEQVKVIEKALWEDFQAIPLYAH +PGVVAHQADLANVRDTVAQQGALWNVEQWKRVS +>PROKKA_01495 +MKYTKLSAAAALAAGSALILSACAPGGGNADDSSSNGSGASQGGDSGAGNVVEGDKGQKL +TAEASGPEMADLGDVETQDGSIAYSVGADDFLSYNGLQSNTYTTYNSAVVDRMFSSFWYF +GTDGSIIPNEDFGTYEKTSDDPLTVKYTISDDAKWSDGTPVTAGDFIFHWAANNDTVKAE +GSETPLFDSISFEQGKYIPEAPEGEADGKEFTVTYPEPYADWEILISTALPAHIVAEEAG +MSFEELVTAAKEKDVEALTPAAEFWNDGWDFSPGELPDASLVPSMGSYKFKDGGWQAGQS +ITLEANPEYWGTPPATKELVLRFADPKTHVQALQNGDLDVIEPQATVDTLQQLEGLGDDV +NVQTGDQLTWEHVDYNRGEGSVFADSPELREAFALCLPRQQIVDNLIKPIYADAQVMNLR +EVFPFQDKYQEVVDEAYPKEMDEPNIEKAKELVEKSGVSTPTVRLGYQAGNQRRTETVAL +IKSSCDQAGFDVQDANSPVFFKEVMPAGDYDAALYAWAGSGQKASGANIYQSDGAQNQQS +YNNPEVDAAWDKLATSLDENEQLEQVKTIEKLLWEDFQAIPLYAHPGLVGHKADVANVRD +TAAQSGALWNVEQWVRVQE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001284.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001284.fa new file mode 100644 index 0000000000000000000000000000000000000000..74f4b3635a1710786199c9e6c7724976f057d640 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001284.fa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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001285.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001285.fa new file mode 100644 index 0000000000000000000000000000000000000000..f253eb1f6cfdcc14d37c51916affce4d78ccb19d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001285.fa @@ -0,0 +1,20 @@ +>PROKKA_01572 +MATTHMKSTPVHTVGELPQVGSPAPDFTLTGADLSPVTLRELRGRRVILNIFPSLDTGVC +AASVREFDSRVADLGDTTVVAVSADLPFAAARFCSVEGIDHVRSGSVFRSSFGGDYGVRM +TDGPLEGLLARAVVMVDADGVVRHAQLVPEISEEPDYEAALAAARG +>PROKKA_01282 +MATTHMKSTPVHTVGELPPVGAPAPDFTLTGADLSPVTLRELRGRRVILNIFPSLDTGVC +AASVREFDSRVADLEDTTVVAVSADLPFAAARFCSVEGIDHVRSGSVFRSSFGDDYGVRM +TDGPLEGLLARAVVVVDADGVVRHAQLVPEISEEPDYEAALAAARG +>PROKKA_01352 +MATTHMKSTPVQTVGDLPEVGAPAPDFTLTGADLSPVTLQELRGRRVILNVFPSLDTGVC +AASVREFNSRATDLEDTTVLAVSADLPFAAARFCSAEGIENVRSGSVFRSSFGDDYGVTM +VDGPLEGLLARAVVVVDAEGVVRHAQLVPEITEEPDYEAALAAAQA +>PROKKA_01245 +MATTHFKGTSVHTVGELPEVGSAAPEFTLTGSDLSSVTLADLKGRTVVLNIFPSLDTGVC +AASVRRFNQEAAGLEDTTVLAVSADLPFAAGRFCSAEGIENVVTGSVFRSDFGTAYGAEL +ADGPMRGLLARAVVVVDAEGTVAYTELVPEITTEPDYEAALAVVRG +>PROKKA_01499 +MATTHMKSTPVHTVGGLPQVGAPAPDFTLTGADLSPVTLRELRGRRVILNIFPSLDTGVC +AASVREFDSRVADLGDTTVVAVSADLPFAAARFCSVEGIDHVRSGSVFRSSFGDDYGVRM +TDGPLEGLLARAVVVVDADGVVRHAQLVPEISEEPDYEAALAAARG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001286.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001286.fa new file mode 100644 index 0000000000000000000000000000000000000000..5045d1f5d247d1d4467f6e8a846d3844c5472f83 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001286.fa @@ -0,0 +1,31 @@ +>PROKKA_01573 +MTEPMTSNVTDTALLFEGGGMRAALTSAVVAELLRERIHVDFVAGISAGSSNAVNYLSRD +PARARRSFVDFADDPRFGNWLSFVRGKGLFNAEYIYEHAGLPEADLPYDFATFRANPARL +VLGGFDAASGETRWWDRSDMTTLTDLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG +IPLTAAEDAGFEKVLVVLTRERGYVKRPERFPSFYQRTFRRYPAVADALLTRWRRYNATR +ERLFEMERQGRAYLFAPETMPIANGERSVAKLAAAHELGLDQVRREMPAIRAFLGLPASR +>PROKKA_01283 +MTEPMTSNVTDTALLFEGGGMRAALTSAVVAELLRERIHVDFVAGISAGSSNAVNYLSRD +PARARRSFVDFADDPRFGNWLSFVRGKGLFNAEYIYEHAGLPEADLPYDFATFRANPARL +VLGGFDAASGETRWWDRSDMTTLTDLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG +IPLTAAEDAGFEKVLVVLTRERGYVKRPERFPSFYQRTFRRYPAVADALLTRWRRYNATR +ERLFEMERQGRAYLFVPATMPISNGERSVAKLAAAHELGLDQVRREMPAIRAFLGLPASR +>PROKKA_01351 +MRTPMTSNVTDTALLFEGGGMRASLTSAVVAELLRERIHVDFVAGISAGSSNSVNYLARD +PERARRSFVDFADDPRFGNWLSFVRGKGLFNAEYIYEHAGLPEADLPYDFATFQANPARL +VLVGFDAVTGQTRWWDRSDMGTLADLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG +IPVTAAEEAGFEKLFVVMTRERSYVKRPERFPAFYQRTFRRYPAVAEALISRWRRYNETR +ERLFEMERQGRAYLFVPESMPVSNGERSVAKLAAAHELGLAQVRREMPAIREFLGL +>PROKKA_01244 +MAEQQDHTAEALTSNVTDTALLFEGGGMRASHTSAVVAELLRAGVHVDFVAGISAGSSNA +VNYLARDPLRARQAFVDFADDPRFGNWRTFLRGKGMFNAEYIYEHAGLPEADLPYDFAAY +RANPARLALAGFDAVTGETRWWGREDMTTLQDLMVRVRASSTMPILMPPVHLEDTVYVDG +ALGVDGGIPVTAAEEAGLAKLLVVMTRERSYVKRPERFPAFYQRAFRRYPAVAEALVTRW +QRYNATRERLFEMEREGTAYLFVPEVMPVSNGERSVAKLAAAHELGLAQARREMPAIKEF +LGL +>PROKKA_01500 +MTEPMTSNVTDTALLFEGGGMRAALTSAVVAELLRERIHVDFVAGISAGSSNAVNYLSRD +PARARRSFVDFADDPRFGNWLSFLRGKGLFNAEYIYEHAGLPEADLPYDFAAFRANPARL +VLGGFDAASGETRWWDRSDMTTLTDLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG +IPLTAAEDAGFKKVLVVLTRERGYVKRPERFPSFYQRTFRRYPAVADALLTRWRRYNATR +ERLFEMERQGRAYLFAPETMPIANGERSVAKLAAAHELGLDQVRREMPAIRAFLGLPASR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001288.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001288.fa new file mode 100644 index 0000000000000000000000000000000000000000..3d8ea72c10a9c518efc71f5ac889899d5b4e6c5a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001288.fa @@ -0,0 +1,19 @@ +>PROKKA_01575 +MKLTDDLLQKFNDQITLEFEASMVYRQLAIAADDLDLSGMAAWLRHQADEEIVHANKFID +HVADRDSFPTIGAIPAPPVQAGLSALEIFRAALAHEQKVSEAIRELYRATESAGDLNSRP +LLNWFLDEQIEEEATVSEIVGQLELVGDDGSGLLRIDGRLGSRPVETTENDA +>PROKKA_01285 +MKLTDDLLQKFNDQITLEFEASMVYRQLAIAADDLDLSGMAAWLRHQADEEIVHANKFID +HVADRDSFPTIGAIPAPPVQAGLSALEIFRAALAHEQKVSEAIRELYRATESAGDLNSRP +LLNWFLDEQIEEEATVSEIVGQLELVGDDGSGLLRIDGRLGSRPVETTENDA +>PROKKA_01349 +MTGVTAADGLDLSGMAAWLRHQADEEIVHANKFIDHVTDRGSDAAGDLSSRPLLNWFLEE +QIEGEATPPL +>PROKKA_01242 +MSIDKDLTRKFNEQITLEFEASMVYRQLAIAADMQDLSGMAAWLRHQADEEIVHANKFID +HVVDREASAVIGAIPAPDVPEHITPVQIFEAALAHERKVSEAIRELYRAAEAAGDLSSRP +LLNWFLEEQIEEEATVGEIVGQLKLVGEDGSGLLRIDSALGARPVETTENAG +>PROKKA_01502 +MKLTDDLLQKFNDQITLEFEASMVYRQLAIAADDLDLSGMASWLRHQADEEIVHANKFID +HVADRDSFPTIGAIPAPPVQAGLSALEIFRAALAHEQKVSEAIRELYRATESAGDLNSRP +LLNWFLDEQIEEEATVSEIVGQLELVGDDGSGLLRIDGRLGSRPVETTENDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001289.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001289.fa new file mode 100644 index 0000000000000000000000000000000000000000..c160f4dec6607d2ba4c603f81a72bb617f91c0ec --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001289.fa @@ -0,0 +1,35 @@ +>PROKKA_01576 +MVGLVALLDDVAALARLAAASVDDVAAGAGRAAAKAAGVVVDDAAVTPQYMAGAAAAREL +PMIWRITKGSLRNKLVFILPALLLLDWLAPWILPWLLLAGGTYLSYEGAHKVWGKLTGHG +HADDEEPAVERGPEAEDTVVRGAITTDFILSLEIMVISMNEVADLGFWMQAAVLAVVAVL +ITVGVYGAVGLIVKMDDVGLHLHQNASTSGGRSFGAGLVKAMPHVLRVVTVIGTVAMLWV +GGHIALVELDALGVPWPYAVQHGIVEPVTHAAGAFLGWLTETATSAVWGLLWGSVALGVV +LLVGRLRGNKAAPAH +>PROKKA_01286 +MVGLVALLDDVAALARLAAASVDDVAAGAGRAAAKAAGVVVDDAAVTPQYMAGAAAAREL +PMIWRITKGSLRNKLVFILPALLLLDWLAPWILPWLLLAGGTYLSYEGAHKVWGKLTGHG +HADDEEPAVERGPEAEETVVRGAITTDFILSLEIMVISMNEVADLGFWMQAAVLAVVAVL +ITVGVYGAVGLIVKMDDVGLHLHQNASTSGGRSFGAGLVKAMPHVLRVVTVIGTVAMLWV +GGHIALVELDALGVPWPYAVQHGIVEPVTHAAGAFLGWLTDTATSAVWGLLWGSVALGVV +LLVGRLRGKKAAPAH +>PROKKA_01348 +MSGLVALLDDVAALARLAAASVDDVAAGAAKASAKAAGVVVDDAAVTPQYMAGAAANREL +PMIWRITKGSLRNKLLIILPALLLLDWLAPWVLPWLLLAGGTYLAYEGAHKVWGKLTGHS +PERDEPAVEKGPEAEDKVVRGAITTDFILSAEIMVISMNEVADVDFWLKAVILVVVAILI +TAVVYGAVALIVKMDDVGLHMTQNGRTAGGRRFGAGLVKAMPHVLTAITVIGTVAMLWVG +GHIVLVELAALGVPWPYDVQHGIVHAVEAAGGFVAWLVETLTSALWGLIWGSLALGVVLV +VNRLRGKKDTLAH +>PROKKA_01241 +MSGLVALLDDVAALARLAAASVDDVAAGAAKASAKAAGVVVDDAAVTPQYMEGAAAQREL +PMILRIVRGSLRNKLVFILPGLLLLDWLAPWALPWLLLAGGTYLSFEGAEKVWHKLTGHH +EPQEDTPAVEQGPEAEDKVVRGAITTDFILSLEIMVISMNEVSDQGFWMKAAILAIVAVV +ITVAVYGAVALIVKMDDVGLHMHENAHTSGARRFGLGLVKAMPVVMGVISVIGTVAMLWV +GGHIVLMELATLGLPWLYELQHTIVHAVEGAGSVIAWLVETLTSAIWGLVWGSLVVAVVG +LVRRLRT +>PROKKA_01503 +MVGLVALLDDVAALARLAAASVDDVAAGAGRAAAKAAGVVVDDAAVTPQYMAGAAAAREL +PMIWRITKGSLRNKLVFILPALLLLDWLAPWILPWLLLAGGTYLSYEGAHKVWGKLTGHG +HADDEEPAVERGPEAEDTVVRGAITTDFILSLEIMVISMNEVADLGFWMQAAVLAVVAVL +ITVGVYGAVGLIVKMDDVGLHLHQNASTSGGRSFGAGLVKAMPHVLRVVTVIGTVAMLWV +GGHIALVELDALGVPWPYAVQHGIVEPVTHAAGAFLGWLTDTATSAVWGLLWGSVALGVV +LLVGRLRGKKAAPAH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001290.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001290.fa new file mode 100644 index 0000000000000000000000000000000000000000..2698d0d9ff076c0d2bb8328210b30207e90d24c4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001290.fa @@ -0,0 +1,30 @@ +>PROKKA_01577 +MNTTAAASDPSDAPLASTRIGEGPRGVAFLHGLMGRGRNFTGPAKELGDDFTVELIDLPD +HGASPWTDRVDYREIADRVAAHLRAGLAADGPVHLLGHSMGGKVAMVLALRHPELVDRLI +VEDISPRLSPQATDEFVHLLGTMLRMDLDAYDSRAEADAAMAEHVHDARVRGFLLQNLRR +TAGHFAWQPNVAMLFEHLREIGSFPDPVVPEDPERVFDHPVLWLAGAESDYVQDEDVPRM +KELFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD +>PROKKA_01287 +MNTTAAASDPSDAPLASTRIGEGPRRVAFLHGLLGRGRNFTGPAKELGDDFTVELIDLPD +HGASPWTDRVDYREIADRVAAHLRAGLAADGPVHLLGHSMGGKVAMVLALRHPDLVDRLI +VEDISPRVSPQATDEFVHLLGTMLRMDLDAYDSRAEADAAMAEHVHDARVRGFLLQNLRR +TAGHFAWQPNVAMLFEHLREIGSFPDPVVPEDPERVFDHPVLWLAGAESDYVQDEDVPRM +KELFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD +>PROKKA_01346 +MTISDQGSPRRLPDSLERVSTPDPSASAAPSDAALASDVIGDGPHRVAFLHGLMGRGRNF +TGPAKALADDFTVELLDLPDHGRSPWTDRVDYQEIADRVAEHLRAGLAADGPVHVLGHSM +GGKVAMVLALRHPDLVDRLIVEDISPRLLPQATDEFVHLLGTMLRMDLDSYESRAEADAV +MAKHVHDARVRGFLLQNLRREGGRFAWQPNVAMLFEHLEAVGSFPDPAAPEDPDRVFDRP +VLWLAGANSDYVRDEDVPRMKDLFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD +>PROKKA_01239 +MPTWSRASLSRVNTTAASAPSDAPLASTRIGEGSRRVAFLHGLMGRGRNFTGVATALADD +FTVELIDLPDHGQSPWTDAVDYQDMADRVADHLRAGLAADGPVHLLGHSMGGKVAMVLAL +RHPELVERLVVVDISPRMSPSATGEFVHLLGTMLRMDLASYTSRAEADAAMAEHVHDARV +RGFLLQNLRREDGHFAWQPNVRMLFEHLDEIGAFPDPVVPEDPDRVFDRPVLWLGGADSD +YIRDGDAPEMKALFPRVVRVTVRGASHWVHADQPEAFVSAVRTFLTAD +>PROKKA_01504 +MNTTAASAPSDAPLASTRIGEGPRRVAFLHGLMGRGRNFTGPAKELGDDFTVELIDLPDH +GASPWTDRVDYREIADRVAAHLRAGLAADGPVHLLGHSMGGKVAMVLALRHPELVDRLIV +EDISPRLSPQATDEFVHLLGTMLRMDLDAYDSRAEADAAMAEHVHDARVRGFLLQNLRRT +AGHFAWQPNVAMLFEHLREIGSFPDPVVPEDPERVVDHPVLWLAGAESDYVQDEDVPRMK +ELFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001291.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001291.fa new file mode 100644 index 0000000000000000000000000000000000000000..87e141ebb0443f05cace3bec26f63afed2113fb7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001291.fa @@ -0,0 +1,30 @@ +>PROKKA_01578 +MPVAEARVSVAVSTAVFGVRPDPHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD +VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPVLDDDGAAPASRPDPD +VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR +AVHEAVLGRGLDAANFRRATLAAGTLEETGEVRGGTPHRPPKLYRYRPAGPGTDPDPAGP +DARR +>PROKKA_01288 +MPVAEARVSVAVSTAVFGVRPDPHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD +VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPALDDDGAAPASSPDPD +VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR +AVHEAVLGRGLDAANFRRATLAAGALEETGEVRGGTPHRPPKLYRYRPAGPGTDPDPAGP +DARR +>PROKKA_01345 +MPAPEARVTVAVSTAVFGVRPDPSGAPRLHVALVPRMREPFLDRWALPGTWLAADEELAD +AAARVAAETVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPALDDDGAAPSHGGGLD +VAGLPAGVHVRWQRADAPPAMAFDHAEILTAAVARLRADLPRAGVAHALLGPSFTLAELR +AVHEAVLGRTLDAANFRRATLATGVLEETGEVRAGTRHRPPKLYRYRPADGAPPPAAPDD +PGDLS +>PROKKA_01238 +MPVAEARVSVAVSTAVFGVRPDAHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD +VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPTLDDDGAAPASRPDPD +VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR +AVHEAVLGRGLDAANFRRATLAAGTLEETGEVRDGTPHRPPKLYRYRPAGPGTDPNPAGP +DASR +>PROKKA_01505 +MPVAEARVSVAVSTAVFGVRPDPHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD +VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPALDDDGAAPASSPDPD +VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR +AVHEAVLGRGLDAANFRRATLAAGTLEETGEVRGGTPHRPPKLYRYRPAGPGTDPDPAGP +DARR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001292.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001292.fa new file mode 100644 index 0000000000000000000000000000000000000000..ac14649f2829cda4ba1f33fbb1e44de16f64e1c2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001292.fa @@ -0,0 +1,45 @@ +>PROKKA_01579 +MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA +PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR +ASQGRPEAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL +EAVYGTEPDDDGRVPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL +FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALRDAKVLLWHGFCSVHRRFTVA +QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ +RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPASVAEPART +ALERMLAVAPKQSAAQSAGAGT +>PROKKA_01289 +MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA +PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR +ASQGRPEAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL +EAVYGTEPDDDGRVPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL +FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALRDAKVLLWHGFCSVHRRFTVA +QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ +RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPASVADPART +ALERMLAVAPKQSAAQSAGAGT +>PROKKA_01344 +MTATPETTASVARTLTLVARDPARGSACSSDLTTGPWAFDAGLPAYGPGASQDDAIPADA +PVQGRIPEEYQQASDEELHARIAAAKAALGDRAVVLGHFYQRDEVVRHADFVGDSFQLAR +ASQGRPEAEAIVFCGVHFMAETADLLSTPEQAVILPNLAAGCSMADMADLDSVQDAWEQL +EEVYGTEPDADGRVPLLPVTYMNCSAALKGFVGERGGIVCTSSNASAVLEWAFERAQRVL +FFPDQHLGRNTGRAMGIELERMPMWNPRLPLGGNTEETLRDARVLLWHGFCSVHRRFTVA +QIEQARAEHPDVRVIVHPECPLPVVEAADESGSTDHIVKAIQAAPAGSTFAIGTEINLVQ +RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPDAVADPARA +ALERMLAVAPRQSVAQGAGA +>PROKKA_01237 +MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA +PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR +ASQGRPAAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL +EAVYGTEPDDDGRMPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL +FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALREAKVLLWHGFCSVHRRFTVA +QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ +RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPVSVADPART +ALERMLAVAPKQSAAQSAAQSAGAGT +>PROKKA_01506 +MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA +PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR +ASQGRPEAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL +EAVYGTEPDDDGRVPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL +FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALRDAKVLLWHGFCSVHRRFTVA +QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ +RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPASVADPART +ALERMLAVAPKQSAAQSAGAGT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001294.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001294.fa new file mode 100644 index 0000000000000000000000000000000000000000..d509e046992ceb75b76f16bde8d95111912ab1e8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001294.fa @@ -0,0 +1,43 @@ +>PROKKA_01587 +MSRSHSDALDASGPDSGGAVAVPRRRFGLLPRILVAIVAGVLVGLVAPTWLVQAFATFNG +LFSNFLGFIVPVLILALVAPAIGDIGRGAGKLLALTGGIAYGSTLVGGFGALLVCLLVFP +LILTPGSFEGMANPEDALLGPLFEVQMDPPFGVMTALLLAFVLGIGLTMLPRGALHESFD +QLRSIIERVVMGLIVPLLPVYIFGVFLNMTAAGEVFKVITTFLGVILLVFGLTVVLLLLQ +YVVAGTIAGRNPFTALKTMLPAYATALGTSSSAATIPVTLRQTLLLGVRRPIASFVVPLC +ATIHLAGSTVKIVSFSIAVLFLSGQSIDVPVFVGFIFMLGVTMIAAPGVPGGAIVAASGL +LTSMLGFTEPQVALMVATYIAIDSFGTATNVTGDAAIAMIVDKIAGDRLIEDSEDEGLER +LDDEGAATGADAG +>PROKKA_01298 +MSRSHSDALDASGPDSGGAVAVPRRRVGLLPRILVAIVAGVLVGLVAPTWLVQAFATFNG +LFSNFLGFIVPVLILALVAPAIGDIGRGAGKLLALTGGIAYGSTLVGGFGALLVCLLVFP +LILTPGSFEGMANPEDALLGPLFEVQMDPPFGVMTALLLAFVLGIGLTMLPRGALHESFD +QLRSIIERVVMGLIVPLLPVYIFGVFLNMTAAGEVFKVITTFLGVILLVFGLTVVLLLLQ +YVVAGAIAGRNPFTALKTMLPAYATALGTSSSAATIPVTLRQTLLLGVRRPIASFVVPLC +ATIHLAGSTVKIVSFSIAVLFLSGQSIDVPVFVGFIFMLGVTMVAAPGVPGGAIVAASGL +LTSMLGFTEPQVALMVATYIAIDSFGTATNVTGDAAIAMIVDKIAGDRLIEDSEDEGLER +LDDEGAATGADAG +>PROKKA_01335 +MSHASSGAAAPSDRAPQGAVSESCRRRRFGLLPRILVAIVAGVLVGLVAPTWLVQAFATF +NGLFSNVLGFIVPVLILALVAPAIGDIGRGAGKLLALTGGIAYGSTLFGGFGALLVCLLV +FPLILTPGSFEAMANPEDALLGPLFEVQMDPPFGVMTALLLAFVLGIGLTMLRRGALHEG +FDQLRSIIERVVMGLIVPLCATIHLAGSTVKIVSFSIAVLFLSGQSIDVPVFVGFIFMLG +VTMVAAPGVPGGAIVAASGLLSSMLGFTEPQVALMVATYIAIDSFGTATNVTGDAAIAMI +VDKIAGDRLIEDSEDEGLERLDDEEAATGADAG +>PROKKA_01233 +MSHAAPSSSVPPAPPSSSATDGTAAPEKAPRRGLRRLGLLPRVLLGIVLGVVVGLVSPEW +LTRTAVTGTSLFSAFLGFIVPVLIVALVAPAIAELGRGAGRWLSVTAAIAYGSTLFGGFL +SLGVALALFPRILTPGSISGVTDPSEGGATPFFEIAMDPPFGVMTALLLSFVLGIGMTLI +PRGVLQQGFEELRTIIERVVTGIVVPLLPFYIFGIFLAMAASGGVFEVIGTFLGVILIVF +ALTVVLLLVQYAVAGVIAHRNPLTALKAMMPAYATALGTSSSAATIPVTLRQVVSLGVRQ +PIAAFVVPLAATIHLAGSTVKIVAFSTAVIILTGGQVDVGLMVGFIFMLGITMVAAPGVP +GGAIVAASGLLSSMLGFTEPQVALMVATYIAIDSFGTATNVTGDGAIALIMDRIAGDRIA +ADPGVAEESPAA +>PROKKA_01514 +MSRSHSDALDASGPDSGGAVAVPRRRFGLLPRILVAIVAGVLVGLVAPTWLVQAFATFNG +LFSNFLGFIVPVLILALVAPAIGDIGRGAGKLLALTGGIAYGSTLVGGFGALLVCLLVFP +LILTPGSFEGMANPEDALLGPLFEVQMDPPFGVMTALLLAFVLGIGLTMLPRGALHESFD +QLRSIIERVVMGLIVPLLPVYIFGVFLNMTAAGEVFKVITTFLGVILLVFGLTVVLLLLQ +YVVAGAIAGRNPFTALKTMLPAYATALGTSSSAATIPVTLRQTLLLGVRRPIASFVVPLC +ATIHLAGSTVKIVSFSIAVLFLSGQSIDVPVFVGFIFMLGVTMVAAPGVPGGAIVAASGL +LTSMLGFTEPQVALMVATYIAIDSFGTATNVTGDAAIAMIVDKIAGDRLIEDSEDEGLER +LDDEGAATGADAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001296.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001296.fa new file mode 100644 index 0000000000000000000000000000000000000000..82627b9d588e8986f8dfa62aeca6e7c3a079cf32 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001296.fa @@ -0,0 +1,20 @@ +>PROKKA_01591 +MAEPRPGDVRVTPGPGAPRGLVIPAGELVERFSHASGPGGQGVNTADSRVQLSLDLAATS +ALDDVQRARVLARLAPRLAGTVLTVSVAEHRAQRRNRVAARERLAALLREALAPPTPRRA +TKPTRGSRRRRLEAKHRRSEVKRTRRRPGLD +>PROKKA_01303 +MAEPRPGDVRVTPGPGAPRGLVIPAGELVERFSHASGPGGQGVNTADSRVQLSLDLAATS +ALDDVQRARVLARLAPRLAGTVLTVSVAEHRAQRRNRVAARERLAALLREALAPPTPRRA +TKPTRGSRRRRLEAKHRRSEVKRTRRRPGLD +>PROKKA_01300 +MADLRVEPGPGAPRGLVIPAAELMERFSHASGPGGQGVNTADSRVQLSLDLATTTALDES +QRARALAVLGPRLAGTVLTVAAEEHRAQRRNRVAARERLAAMLREALIPETPRRATRPTR +GSRRRRLEAKRQRSETKQLRRRPGV +>PROKKA_01219 +MDDLRVPPGPGVPRGLRIPAAELSERFSHGSGPGGQGVNTADSRVQLSLDLAATTALTDA +QRIRLLEGLAPRLAGTVLTVDAAEHRAQRRNRTAARERLAALLREALVPETPRRATKPTR +GSQRRRLQAKARRSEVKQSRRRPRMD +>PROKKA_01518 +MAEPRPGDVRVTPGPGAPRGLIIPAGELVERFSHASGPGGQGVNTADSRVQLSLDLAATS +ALDDVQRARVLARLAPRLAGTVLTVSVAEHRAQWRNRVAARERLAALLREALAPPTPRRA +TTPTRGSRRRRLEAKRRRSEVKRTRRRPGLD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001302.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001302.fa new file mode 100644 index 0000000000000000000000000000000000000000..553b4e38e4547b4fe9d291717395587433e8e52e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001302.fa @@ -0,0 +1,20 @@ +>PROKKA_01600 +MDAAPTPSLALEDQLCFALHRAARAVTRGYGPLLSRLGLTYPQYLVMLTLWQAEGDASAE +TEASTPDAGALGVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDEG +RALRASARTVPVDALTRIPLDTTERQVLMDLLNRITEAAGPR +>PROKKA_01312 +MDAAPTPSLALEDQLCFALHRAARAVTRGYGPLLSRLGLTYPQYLVMLTLWQAESDASAE +TEASTSDAAGALGVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDE +GRALRASARTVPVDALTRIPLDTTERQVLMDLLNRITEAAGPR +>PROKKA_01293 +MDAAPTPSLALEDQLCFALHRATRAVTRGYGPLLSRIGLTYPQYLVMLTLWQVEGDASAE +TEAPTPGAGALAVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDEG +RALRASARTVPADALTRIPLDATERQVLMCLLNRITEAVGPR +>PROKKA_01202 +MDAAPTPSLALEDQLCFALHRATRAVTRGYGPLLSRLGLTYPQYLVMLTLWQVEGDASAE +TDAPTPGAGALAVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDEG +RALRESARTVPADALTRIPLDATERQVLMGLLNRITEAAGPR +>PROKKA_01527 +MDAAPTPSLALEDQLCFALHRAARAVTRGYGPLLSRLGLTYPQYLVMLTLWQVESDASAE +TEASTSDAAGALGVGALRDRLGMDNGTITPLVRRLAGMGLVTRERDVHDERRVLVRLTDE +GRALRASARTVPVDALTRIPLDTTERQVLMDLLNRITEAAGPR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001308.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001308.fa new file mode 100644 index 0000000000000000000000000000000000000000..3bd233bf753acf1c2c79c9440b255ff9bbc2110b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001308.fa @@ -0,0 +1,61 @@ +>PROKKA_01620 +MARRAAKAKPAKTLEQTLWDAADKLRGNQEPSEYKHVVLGLVFLKYVSDRFEERREQLKD +ELAAEGIKPERIESFLEDRDEYASQNVFWVPSLARWGYVQSVAKQPEIGQQIDQAMDLIE +KENPSLRGVLPRNYGRDGLDKRRLGELVDLIGSIGFTETDDHGADDVLGRVYEYFLGQFA +GKETGKDAGAFYTPRSVVKTLVEMLEPFKGRVYDPAVGSGGMFVQSAEFVKAHGGKRTDI +SVYGQEFTDTTWKLAKMNLALRGVEADMGSHSADSFTEDLHLDLRADYVIANPPFNVSDW +WDAKLADDPRWKYGTPPKGNANFAWVQHFLHHLAPHGTAGFVLANGSLSSKSSGEGEIRQ +RLVEAGLVDCIVAMPDKLFFNTGIPVSLWFISKGRDGNGHRARKGEVLFIDARKLGAMQS +RRLRVLSDDDIAQIADTYHEWRNHDGCYEDVPGFAKSATIGEIEKHEFVLTPGRYVGAAE +AEVDDEPIDEKIERLTNELLAEFERGRELENEVRLRMGSLS +>PROKKA_01648 +MTIPATRGAASAPHRSPQNLSNFVWGIADQLRGVFKPNQYGTLVLPLTILRRMEAVMAPH +REFFAELAAKGHPDFVLDNLVESRTGLTFYNLSPFTLDRILQEPDLLRTNLLAYVDGFSQ +NVADLFTYYEFDKTVAKLDEHDRLFLVLQQFASIDLSPETVSNAEMGTLFEDLIRRFAAA +SNETAGEHFTPRDAVKLLVDLLTANDDDVLTGYPVRTVYDPTAGTGGMLSVLDERLRRMN +PNAEVRLFGQELNDQSYAICKSELLGKGQAADGIARGDTLKNDAHMTERFDYVLSNPPYG +GDWKASRAAVEKEIAAGGATNRFPGGTPAISDGQMLFLQLVASKLRPVSEGGGRAGIVLN +GSPLFTGGAGSGPSEIRRWLLESDLVDVIVALPTDMFYNTGIATYVWVLDNNKPADRRGR +AQLIDARTFFTKLRRNVGSKNKELSKADRQRVLDIYRDFDAQSEANAEFSKVLTAQDFGY +REITVERPLQLRFEVEDATIAAALATKPADKLPDDGRSALEAALASLRGRVWDHQPTFVL +DLKKALKEHGVTAGAPLVKALTGAIGVHDPKAEVVTNKKGEPEPDTSLRDTELVPFGRDI +HEYFEAEVAPHVPGAWIDESKTKIGYEIPFTRLFYTYVPPRPLEEIDADLKQLTAEIIEL +LQEVER +>PROKKA_00900 +MTTPATPGAASAARRSPQNLSNFVWGIADQLRGVFKPNQYGTLVLPLTILRRMEAVMAPH +REFFAELAAKGHPDFVLDNLVESRTGLTFYNLSPFTLDRILQEPDLLRTNLLAYVDGFSQ +NVADLFTYYEFDKTVAKLDEHDRLFLVLQQFASIDLSPDTVSNAEMGTLFEDLIRRFAAA +SNETAGEHFTPRDAVKLLVDLLTANDDDVLTGYPVRTVYDPTAGTGGMLSLLDERLRRMN +PNAEVRLFGQELNDQSYAICKSELLGKGQDADGIARGDTLKNDVHLTERFDYVLSNPPYG +GDWKASRTAVEKEIAAGGATNRFPGGTPAISDGQMLFLQLVASKLRPVSEGGGRAGIVLN +GSPLFTGGAGSGPSEIRRWLLESDLVDAIVALPTDMFYNTGIATYVWVLDNNKSAERRGR +VQLIDARTFFTKLRRNVGSKNKELSKADRQRVLDIYRDFDAQSEANAEFSKVLTAQDFGY +REITVERPLQLRFEVEDATIAAALATKPVDKLPDDGRSALETALASLRGRVWDHQPTFVL +DLKKALKEHGVTAGAPLVKALTGAIGVHDPEAQIVTNKKGEPEPDTSLRDTELVPFGRDI +HEYFAAEVAPHVPGAWIDESKTKIGYEIPFTRLFYTYVPPRPLDEIDAELKQLTAEIIEL +LQEVER +>PROKKA_00838 +MPSPQNLSNFVWGIADQLRGVFKPNQYGTLVLPLTILRRMEAVMAQHREFFAELAAKGHP +DFVLDNLVQSRTGLTFYNLSPFTLDRILQEPDLLRTNLLAYVDGFSQNVADLFTYYEFDK +TVAKLDEHDRLFLVLQQFASIDLSPETVSNAEMGTLFEDLIRRFAAASNETAGEHFTPRD +AVKLLVDLLTANDDDVLTGYPVRTVYDPTAGTGGMLSLLDERLRRMNPNAEVRLFGQELN +DQSYAICKSELLGKGQDADGIARGDTLKNDAHLTERFDYVLSNPPYGGDWKASRTAVEKE +IAAGGATNRFPGGTPAISDGQMLFLQLVASKLRPVSEGGGRAGIVLNGSPLFTGGAGSGP +SEIRRWLLESDLVDAIVALPTDMFYNTGIATYVWVLDNNKSAERRGKVQLIDARTFFTKL +RRNVGSKNKELSTADRQRVLDIYRDFDAQSEANAEFSKVLTAQDFGYREITVERPLQLRF +EVEDATIAAALATKPADKLPVDGRSALGAALASLRGRVWDHQPTFVLDLKKALKEHGVTA +GAPLVKALTGAIGVHDPKAEVVMNKKGEPEPDASLRDTELVPFGRDIHEYFEAEVVPHVS +GAWIDESKTKIGYEIPFTRLFYTYVPPRPLEEIDAELKQLTAEIIELLQEVER +>PROKKA_01879 +MTTPATRGAASAPHRSPQNLSNFVWGIADQLRGVFKPNQYGTLVLPLTILRRMEAVMDPH +REFFAELAEKGHPDFVLDNLVQSRTGLTFYNLSPFTLDRILQEPDLLRTNLLAYVDGFSQ +NVADLFTYYEFDKTVAKLDEHDRLFLVLQQFASIDLSPDTVSNAEMGTLFEDLIRRFAAA +SNETAGEHFTPRDAVKLLVDLLTANDDDVLTGYPVRTVYDPTAGTGGMLSLLDERLRRMN +PNAEVRLFGQELNDQSYAICKSELLGKGQDADGIARGDTLKNDAHLTERFDYVLSNPPYG +GDWKASRTAVEKEIAAGGATNRFPGGTPAISDGQMLFLQLVASKLRPVSEGGGRAGIVLN +GSPLFTGGAGSGPSEIRRWLLESDLVDAIVALPTDMFYNTGIATYVWVLDNNKPADRRGR +VQLIDARSFFTKLRRNVGSKNKELSTADRQRVLDIYRDFDAQSEDNAEFSKVLTAQDFGY +REITVERPLQLRFEVEDATIAAALATKPVDKLPDDGRSALESALASLRGRVWDHQPTFVL +ELKKALKKHGVTAGAPLAKALTGAIGVHDPDAEVVKDKKGEPEPDTSLRDTELVPFGRDI +HEYFEAEVAPHVPGAWIDESKTKIGYEIPFTRLFYTYVPPRPLEEIDAELKQLTAEIIEL +LQEVER diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001309.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001309.fa new file mode 100644 index 0000000000000000000000000000000000000000..2353c9fd704f983a0231e37614eca662f1496e18 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001309.fa @@ -0,0 +1,20 @@ +>PROKKA_01626 +MARPIDPFREMERLVNGLTPRATGTVSMPMNLYREGDVFVAEVELPGVDPASIDVDVEER +TLTVRAERKEDPAREDRRWLTRERSAGTFARQLTLGEGLALDRIQADYSDGVLTLTIPVA +EQAKPRKISVTHGGAAPVAGQTVEGETAETTGE +>PROKKA_01332 +MARPIDPFREMERLMTGFARTSGAASMPMNLYREGDVFVAEVELPGVDPSSIDVDVEERT +LTVRAERKEAPAGEDRRWLTKERPAGTFARQLNLGQGLALDKIEADYSDGVLLLTIPVAE +QAKPRKIQVKHTGSAAQVEGEAVEGEAVEGSAAEASGE +>PROKKA_01271 +MARPIDPFREMERPFREMERLVNGLTRTSGTASMPMNLFREGDRFVAEVELPGVDPASID +VDVEERTLTVRAERKESPAGEDRRWLTRERSAGTFARQLTLGEGLALDRIEADYEDGVLT +LTIPVAEQAKPRKISVKHSGAGAGAGQTVPGETAEVEERSAEQEAAQNGGAPQA +>PROKKA_01181 +MARPIDPFREMERPFREMERLVNGLTTRATGTASMPMNLYREGDAFVAEVELPGVDPASI +DVDVEERTLTIRAERKEAAASEGRQWLTRERSSGTFARQLTLGQGLALDRIEADYRDGVL +VLSIPVAEQAKPRKIQVKHSAADQVEGQEVAGQESVQDSAAVEAPQQPSGE +>PROKKA_01555 +MARPIDPFREMERLVNGLTPRATGTVSMPMNLYREGDVFVAEVELPGVDPASIDVDVEER +TLTVRAERKEDPAREDRRWLTRERSAGTFARQLTLGEGLALDRIQADYSDGVLTLTIPVA +EQAKPRKISVTHGGTAPVAGQTVEGETAETTGE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001310.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001310.fa new file mode 100644 index 0000000000000000000000000000000000000000..d70c0ff153434a6fb39c41fb7ff29633681e23be --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001310.fa @@ -0,0 +1,23 @@ +>PROKKA_01628 +MQLTIAPGDITATHADAVVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPEGL +PAGQAVATTAGRLPARWVIHTVGPVWAKTIDKSDTLASCYRESLKVAAGLGARTVAFPAI +SAGIYGWPMEDAARIAVETCHAMADEVGDTVDEVLFVPYGETAEAAFRAALGHLEAPQTT +DDEGDTGR +>PROKKA_01333 +MQLTIAPGDITATHADAVVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPEGL +PAGQAVATTAGRLPARWVIHTVGPVWAKTIDKSDTLASCYRESLKVAAGLGARTVAFPAI +SAGIYGWPMEDAARIAVETCHAMADEVGGTVEEVLFVPYGDTAEAAFRTALDRVERG +>PROKKA_01268 +MELLIAPGDITATTADVVVNAANSTLLGGGGVDGAIHRRGGPEILAACRRLRETELPDGL +PVGQAVATTAGRLPARWVVHTVGPVWAKTIDKSATLASCYRESLRVAAELGARSVAFPAI +SAGVYGWPMDDAARIAVTTCREVAAQGAGSVERVLFVPFGERAEAAFRAALDAPDETGAP +AAS +>PROKKA_01176 +MKLSIAPGDITATHADAIVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPDGL +PAGQAVATTAGRLPARWVIHTVGPVWAKTIDKSDTLASCYRESLRVARELGARTVAFPAI +SAGVYGWPMDDAARIAVETSHAMADEVGDVVEEVLFVPFGDRAEAAFRAALEHLT +>PROKKA_01557 +MQLTIAPGDITATRADAVVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPEGL +PAGQAVATTAGRLPARWVIHTVGPVWAETIDKSDTLASCYRESLKVAAGLGARTVAFPAI +SAGIYGWPMEDAARIAVETCHAMADEVGGTVDEVLFVPYGETAEAAFRAALGHLEDPQAT +DDEGDTGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001312.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001312.fa new file mode 100644 index 0000000000000000000000000000000000000000..3860231b055874a62ef778a8ed1f43a51a7427b0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001312.fa @@ -0,0 +1,42 @@ +>PROKKA_01630 +MEILSLLLALTLGLVLGALLGAWLMWRRAADGGEEARRAQAELAALRTEHQGAREALAAA +RAEQRALTAARAEDAERQRAESQVMSTLAPLGQRLAALQEQVSVLERDRASQFGRLGEQL +RAAAATDRDLLNQTTSLMATLKSTSARGHWGEAQLRRVVEAAGMLHHVDFTEQATLSGRD +GERLRPDLVVSLPGGKAMAVDAKAPIGDALAAEALADEPGEEAYERRQALAAQHAAAVRR +HVDQLSAKSYWDGLEHSPELVLCFLPAESLLAAALDADPGLLDHAFSRNVALVAPVSLLT +ALKSVAYAWRQDTLAENAHTVVASAKDLYERLGTLGTHLDRMGGSLKTAVDRYNQLVGSV +ESRVLPAARRLRDADPGLAPTPDIRTLESAPRPLAAPELVAGVEEDELRRRRAESAREA +>PROKKA_01335 +MEILSLLLALILGLVLGALVGAWLMWRRAAGGGEEARRAQAELAALRTEHQGAREELAAA +RAEQRALTAARAEDAERQRAESQVMSTLAPLGQRLAALQEQVGVLERDRASQFGRLGEQL +RAAAATDRDLLNQTTSLMATLKSTSARGHWGEAQLRRVVEAAGMLHHVDFTEQATLSGKD +GERLRPDLVVSLPGGKAMAVDAKAPIGDALAAEALADEPGEEAYERRQALAGQHAAAVRR +HVDQLSAKSYWAGLEHSPELVLCFLPAESLLAAALDADPGLLDHAFSRNVALVAPVSLLT +ALKSVAYAWRQDTLAENAHTVVASAKDLYERLGTLGTHLDRMGGSLKTAVDRYNQLVGNV +ESRVLPAARRLRDADPGLAPTPDIRTLESAPRPLAAPELVAGVEEDELRRRRAESAREA +>PROKKA_01266 +MDILSLLLALALGLVVGALTGAWLMWRRAAGGGEEARRAEQELAALRVEHQGAREELAAA +RAEHRAVAAARAEDVERQRSEARVLSTLTPLGQQLTALQEQVGVLERDRAAQFGRLGEQL +RAAAATDRDLLNQTTSLMATLRSTSARGHWGEAQLRRVVEAAGMLHHVDFSEQSTLSGRD +GERLRPDLLVSLPGGKSMAVDAKAPIGDALAAEALADEPGEEAWERRQALAAQHAAAVRR +HVDQLSAKAYWAGLEHSPELVLCFLPAESLLAAALDADGGLLDHAFSRNVALVAPVSLLT +ALKSVAYAWRQDTLAENAHTVVASAKDLYERLGTLGTHLDRMGGSLKTTVDRYNQLVGNV +ESRVLPAARKLREADPGLAPTPDIRTLESAPRVLSAPELVEGVEQDELRRRREDPAREEA +VREDPAREA +>PROKKA_01174 +MDFLTLVITLALGLLVGAAVGAWLMWRRMDGAADGSAGAELDALRREHAAVREELAGARA +ESRALTQQRAEDAERARTDARVLETLAPLGRQLGALQEQVGVLERDRAAQFGRLGEQLRT +AAANDRDLLNQTASLMATLKSTSARGHWGEAQLRRVVEAAGMLHHVDFSEQTTMTGRDGE +RLRPDLLVSLPGGKTLAVDAKAPIGDALAAGALAEEPGEEAAERRAALNARHAAAVRRHV +DALSAKAYWTGLERSPELVLCFLPAESLLAAALDADGALLDHAFSRNVALVAPVSLLTAL +KSVAYAWRQERLAENAQLIVSGARELYDRLGTMGSHLDRMGGSLRAAVDGYNRLVGNVES +RVLPAARTLREADPGLPALADVRSVDNAPRPLTAPELVDGDGPVDEGWTPAGSAAAEDRP +EPAPAFEESPLWEDDEWTEDAAWDTDRRTA +>PROKKA_01559 +MEILNLLLALILGLVLGALVGAWLMWRRAAGGGEEARRAQAELAALRTEHQGAREELAAA +RAEQRALTAARAEDAERRRAESQVMSTLAPLGQRLAALQEQVSVLERDRASQFGRLGEQL +RAAAATDRDLLNQTTSLMATLKSTSARGHWGEAQLRRVVEAAGMLHHVDFTEQATLSGRD +GERLRPDLVVSLPGGKAMAVDAKAPIGDALAAEALADEPGEEAYERRQALAAQHAAAVRR +HVDQLSAKSYWDGLEHSPELVLCFLPAESLLAAALDADPGLLDHAFSRNVALVAPVSLLT +ALKSVAYAWRQDTLAENAHTVVASAKELYERLGTLGTHLDRMGGSLKTAVDRYNQLVGNV +ESRVLPAARRLRDADPGLAPTPDIRTLESAPRPLAAPELVAGVEEDELRRRRAESAREA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001316.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001316.fa new file mode 100644 index 0000000000000000000000000000000000000000..3ee65f5db3fc29d094d99980c183fc25038bd701 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001316.fa @@ -0,0 +1,45 @@ +>PROKKA_01634 +MDQPVTEGASAASDVPVSAPARAGETSAERPWPLRRLSENLKAHIERAPATWIEGQLIEF +KNNRGNVYMTMRDLEEEVSLPLTAWRNVAMTLDGTVQQGSRVVARVKPNFWLKAGRLSMN +VQEMRPVGLGDLLARVELLRRALAEEGLTSPARKRPLPLLPRRIGLITGRDSDAKKDVLR +NTLLRWPAAEFEIREVAVQGAEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS +DEALVRAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQEAAGLADA +RLRLAAAVERRVRAEAEGLAALRSRPVLARPHVMVDTRQEETDRWRERGRSALGHRLVRE +EDALTQLRARVRALSPQRTLDRGYAVVQHAGQVVRDADQVAPDDRLDILVAAGRIAADVV +ATHRTTPTPSHERTRQA +>PROKKA_01339 +MDQPVTEGASAASDVPVSAPARAGETSAERPWPLRRLSENLKAHIERAPATWIEGQLIEF +KNNRGNVYMTMRDLEEEVSLPLTAWRNVATTLDGTVQQGSRVVARVKPNFWLKAGRLSMN +VQEMRPVGLGDLLARVELLRRALAEEGLTSPARKRPLPLLPHRIGLITGRDSDAKKDVLR +NTLLRWPAAEFETREVAVQGAEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS +DEALVRAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQEAAGLADA +RLRLAAAVERRVRAEAEGLAALRSRPVLARPHVMVDIRQEETDRWRERGRSALGHRLVRE +EDALTQLRARVRALSPQRTLDRGYAVVQHAGQVVRDADQVAPDDRLDILVAVGRIAADVV +ATHRPTPTPSHERTRQA +>PROKKA_01261 +MDPSSTAHVEADALLDAGVPATASQTSAERPWPLRRLSENLKLHIERAPATWIEGQLIEY +KTNRGNVYMTMRDLEEEYSLPVTAWRNVAVTFEGTVQQGSRVVARVKPNFWTKAGRLSMV +VQEMRPVGLGDLLARVELLRRRLGEEGLLDPARKRPLPLLPGLVGLITGRDSDAKKDVLR +NAQLRWPAVRFEVREVAVQGPEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS +DEALVRAVAAARTPVVSAIGHEADRPVLDDVADVRASTPTDAAKRIVPDAAQEAAGIAEA +RRRLAAAVERRVQREGEGLAQLRSRPVLADPVVMVDGREQDLHAWRERARRATAHRLTRE +RDAVEHLVARVRALSPQQTLDRGYAVVQQEGRLIRDAAQVAPGEDVDILVASGRISAEVT +AVRPGRVGGVGTVQDEDEQAGTKEQA +>PROKKA_01170 +MEESAAREEGTVVVPATASETSPERPWPLHRLSENLKLHIERAPATWIEGQLIEHKNNRG +NLYMTMRDLEEEVSLPLTAWRAVAAGIDPSVQQGSRVVARVKPNFWVKGGRLSMVVQEMR +PVGLGDLLARVELLRRRLAEEGLTSPARKRQLPVLPGVIGLITGRDSDALKDVVRNTHLR +WPAAVFEVREVAVQGPDAPRQVAAALAELDARPEVEVIVIARGGGALEEVVLPFSDEALV +RAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQESVGIREARLRLA +GAVERRVRGEADALAALRSRPVLAHPHVMVDTRTEDLGRWQERGRVALGHRLAREADAVS +ALRAQVRALSPQQTLDRGYAVVQHAGHVVRRAEDVTPGDDLDVLVAAGRIEAYVTDVTPV +ETPSPTQEDA +>PROKKA_01563 +MDQPVTEGASAAPDVPVSAPARAGETSAERPWPLRRLSENLKAHIERAPATWIEGQLIEF +KNNRGNVYMTMRDLEEEVSLPLTAWRNVAMTLDGTVQQGSRVVARVKPNFWLKAGRLSMN +VQEMRPVGLGDLLARVELLRRALAEEGLTSPARKRPLPLLPHRIGLITGRDSDAKKDVLR +NTLLRWPAAEFEIREVAVQGAEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS +DEALVRAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQEAAGLADA +RLRLAAAVERRVRAEAEGLAALRSRPVLARPHVMVDTRQEETDRWRERGRSALGHRLVRE +EDALTQLRARVRALSPQRTLDRGYAVVQHAGQVVREADQVATDDRLDILVAAGRIAADVV +ATHRTTPTPSHERTRQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001320.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001320.fa new file mode 100644 index 0000000000000000000000000000000000000000..789e933d722565241de35f2afe7ba63dbff8c6bc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001320.fa @@ -0,0 +1,38 @@ +>PROKKA_01639 +MSRPAHRRPTALAASALALSLALGACARQADAPPTPSASGTPITVVHGGEGLEGAVAAVL +ARHLRLHGHAVADEDGVAVEQPAWSAAGGDTVAVVDTLALAVAADPAVALPSPPPPTSTP +SSTPTGTEAGPSADAVPTPSATASTAVPSPTALPVGDPAADAQAAGRVLETLLAEETAAA +GTPQDEAPAVLSSSAGVLRLTAVVTQTTAARLELESITDLNGWCESLTAVAPPPLTAAAD +PDAATALRARLDRLAGCRPETWLADTEDPSAALVADEAQVALLTDTDPEIDANTLVPLED +DGRVLPEGRLTAVGSAATLDDDAERRIAEVMSALDGDGLRELERLTTGADPLPAAEAAQY +WLVDHGLEDAPEDWFVPRGSWF +>PROKKA_01344 +MSRPAHRRPTALAASALALSLALGACARQADAPPTPSASGAPITVVHGGEGLEAAVAAVL +ARHLRLHGHAVADEDGVAVEQPAWSAAGGDTVAVVDTLALAAAADPAAALPSPPTPTPTP +TPTGTEAGTSTGTVPTPSATASTAAPSPTALPVGDPAADAPAAGRVLETLLAGQTAAAGT +PQDEAPAALSSSAGVLRLTAVVTQTTAARLELESITDLNGRCESLTAVAPPALTSAADAA +TALRARLDRLAGCRPETWLADTEDPTAAVVADEAQVALLTGTDPEIDANTLIPLEDDGRV +LPEGRLTAVGSAATLDDDAERRIAEVMSALDGDGLRELERLTTGADPLPVAEAAQYWLVD +QGLEDAPEDWFVPRGSWF +>PROKKA_01256 +MPTASESSDAADASATPEPTPLPDGEPAADAAEAGRVVERLLQGDAEAGASPEPGDAVAV +LGSSAGVLRLSAVVTATTAARLELDALEDLNGRCEGLTAALPAGLAGDPQANAALHARLD +RLAGCRPGTWREEDASAAAVVVADQAQLGLLSATDPEIPASMLVPLEDPERVLPEGRLAA +VGAPDALDDDAQRRIEEVLSALDEDGLRELERITTGADALPPAEAARYWLVDQGLEDVPE +GWFMPRDSWF +>PROKKA_01165 +MTRPAERPRTSRVRAAAGASALSLALALSGCGAPRAGAPADPTGAPVTVVHTSDPLDSAV +AAVVARHLRHRGHPVTLEDAGDATPWSAAAGDTVAVVDTLRLALQADPAAVLPPEPEDAA +ASRAAAAPTPSESSLEPIDPSAPARVPATGSATPSPTPLASGLPAADADAAQAVVDAALS +RVAAGADAAAPTPAASRSAATPTGPSPRVLADSAGTLRLAAVVTATTASREGLDSIDDLD +GRCGDLTLAVPAALAAAVSDGLLAHRLDDFAGCRPADWRTDAADVGPAVVADAAQVGLTY +RTDPDIPPNGLVLLEDPDRVLPEGRIAVVGERETLDDDAQSALGEVMDRLDDDGIAELAR +LTEGGDALPADEAAQYWLVSQRLEDAPEDWVVPADPWF +>PROKKA_01568 +MSRPAHRRPTALAASALALSLALGACARQADAPPTPSASGTPITVVHGGEGLEGAVAAVL +ARHLRLHGHAVADEDGVAVEQPAWSAAGGDTVAVVDTLALAAAADPAAALPSPPSPTSTP +SSTPTGTEAGTSADAVPTASTAAPSPTALPVGDPAADAPAAGRVLETLLAEETAAAGTPQ +AEAPAVLSSSAGVLRLTAVVTQTTAARLELESITDLNGRCESLTAVAPPTLTAAADADAA +TALRTRLDRLAGCRPETWLADTEDPTAAVVADEAQVALLTGTDPEIDANTLVLLEDDGRV +LPEGRLTAVGSAATLDDDAERRIAEVMSALDGDGLRELERLTTGDDPLPVAEAAQYWLVD +HGLEDAPEDWFVPRGSWF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001321.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001321.fa new file mode 100644 index 0000000000000000000000000000000000000000..11664f255a0ebc189ea60be8e1b6684039678982 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001321.fa @@ -0,0 +1,20 @@ +>PROKKA_01640 +MSTTPAAPDAAGAHPAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIELGES +PEEACLREVWEETGHTAELTGLLGVTTGTIPVEKRLRGEPLPLLTVQVLYTARITGGVLR +PEVGGSSTDARWFDLAELSELRTASWVTEALARAGVDT +>PROKKA_01345 +MSTTPAAPDAAGAHPAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIELGES +PEEACLREVWEETGHTAELTGLLGVTTGTIPVERRLRGEPLPLLTVQVLYTARITGGVLR +PEVGGSSTDARWFDLAELSGLRTASWVTEALARAGVAT +>PROKKA_01255 +MSPTPVPDAEPARADAPAGPFQTRAGAYALIVDGGRVLLSSWQGPEHLVWTLPGGGIELG +ESPEEACRREVWEETGHTAELTGLLGVTTGVIPAERRLRGEALPLLTVQVLYTARITGGV +LRPEVGGSSTDARWFDLAGLDAVRTAPWVREALARAGAAA +>PROKKA_01164 +MSAASPTAASTAPGPFETRAGAYALIVEDGRVLMSAWAGPTGIVWTLPGGGIELGESPEE +ACVREVEEETGHTAELTGLLGVTTGTIPVERRLRGEPLPLLTVQVLYTARLTGGVLRPEA +DGSSVDAAWFALDGLADVRTSAWVDRALALAGLAADDAAGTAR +>PROKKA_01569 +MSTTPAAPDAAGAHPAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIELGES +PEEACLREVWEETGHTAELTGLLGVTTGTIPVEKRLRGEPLPLLTVQVVYTARITGGVLR +PEVGGSSTDARWFDLAELSELRTASWVTEALARAGVDT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001324.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001324.fa new file mode 100644 index 0000000000000000000000000000000000000000..8cb9e66dd0419eea08e681324db0b4df70b8c8de --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001324.fa @@ -0,0 +1,33 @@ +>PROKKA_01643 +MDETTAPTRAVQAALDALADARVSASLVIVALVAFLAWRLVLRRHRLASAPARPSMPRSF +MHRLQSSPAVRALTARFSGRLSAAADAARAARGRTGLHIRWGRTALFLAALVALLVFLVA +GLAAAFGAGTLALAGWSLLFAVAGLAGLRALAVRDRTRRARPAAVVVPERPAAPAAEERQ +APPADPERDRRVLETVLAFETEAPRPAAAPAAPRVEPVVVTASAAAPAADRVVTIPAVPR +PTYLDAPEMARPLPAPLETPAPTGADTRLTDAARTADDQISAAAEQDIAALDLDNVLARR +RAC +>PROKKA_01348 +MDETTPPTTAVQAALDALADARVSASLVIVALVAFLAWRLVLRRHRLASAPARPSMPRSF +MHRLQSSPAVRALTARFSGRLGAAADAARAARGQTGLHIRWGRTALFLAALAALFVFLVA +GLAAAFGAGTLSLAGWSLLFAVAGLAGLRALAVRDRTRRARPAADVVPARPAAPAAEERQ +APPADPERDRRVLETVLAFETEAPRPAAAPAASRVEPVVVTASAAAPAADRAVTIPAVPR +PTYLDAPEMARPLPAPLETPAPTGADTRLQDAASTADDRISAAAEQDIAALDLDNVLARR +RAC +>PROKKA_01250 +MEDTTAPASAGRAALDALADARVSASFVILALVAYFAWRLVVRRRRVESAPARPTMLRST +MHRLQSSPAVRALTERLSGRVSGLADSARAAGRRTAGLQVRWGRTALFLAALAALAVALV +AGVAAAFGAGTAGLAGACLLFAVAAVAGLRALAVRDRARRAPAAVVEAPAEAAPHAAPEA +PRVDPERDRRVFETVLGLEDEAARVSAAAPAAPAAAPTVVAASAVRAPEATDTVTLPVVP +RPTYLDAPEMLRPAPAPLTAPEAAGSDVRLKDAARAAEHEEALSATAEQDVAALDLDHVL +ARRRAS +>PROKKA_01161 +MTETPSPREDARLDAEPGHADSGFHVHWDRASLFLVGVGALAVALVTALCALAGLPTAGL +AGWSLLVTVGAVVGLRVLAARDQREHHDDLADDADEPNLAEEDLDTHELPVVPDPERDRR +VLAAALSLTDEAEDEEPAAEPVPVVVDALQRRRAPRIPLGGIVIPEVPRPTYLDAPEAPA +AEAQAEYPAEDDAVATRPEAEEQAASAEVVEIPEPAARAVVLDLDGVLARRRAS +>PROKKA_01573 +MDETTAPTRAVQAALDALADARVSASLVIVALVAFLAWRLVLRRHRLASAPARPSMPRSF +MHRLQSSPAVRALTARFSGRLSAAADAARTARGRTGLHIRWGRTALFLAALVALLVFLVA +GLAAAFGAGTLSLAGWSLLFAVAGLAGLRALAVRDRTRRARPAAVVVPERPTAPAAEERQ +APPADPERDRRVLETVLAFETEAPRPAAAPAAPRVEPVVVTASAAAPAADRAVTIPTVPR +PTYLDAPEMARPLPAPLETPAPTGADTRLTDAARTADDQISAAAEQDIAALDLDNVLARR +RAC diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001325.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001325.fa new file mode 100644 index 0000000000000000000000000000000000000000..83c99c4c58678e763e064569b2e755af0b1e9e95 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001325.fa @@ -0,0 +1,25 @@ +>PROKKA_01644 +MSWQRSPWPVTLRHGTLALRPLRRRDREAWEEQRAHNREWLTPWDATSPVPGAGPASFGQ +MVRWHGRQGRDGSAYTWGMALDDDRPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREAG +RGLTPTAVAMATDWAFRSAGLHRVEVNIRPENAASLRVVAKLGLRDEGLRRAYLHVDGAW +RDHRTFAVTAEEVPDGLLAGWLATRPRP +>PROKKA_01349 +MSWQRSPWPVTLRHGTLALRPLRRRDREAWEEQRAHNREWLTPWDATSPVPGAGPASFGQ +MVRWHGRQGRDGSAYTWGMVLDDDDRPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREA +GRGLTPTAVAMATDWAFRSAGLHRVEVNIRPENAASLRVVAKLGLRDEGLRRAYLHVDGA +WRDHRTFAVTAEEVPDGLLARWLASRPRA +>PROKKA_01249 +MSWQRSPWPVTLRHGTLSLRPLRRRDRDAWEAQRAHNHAWLTPWDATSPVPGAGPSSFGQ +MVRWHGRQGREGSSFTWGVALDDDAPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREAG +RGLTPTAVAMAADWAFRSAGLHRVEVNIRPENAASLRVVEKLGLRDEGVRRSYLHVDGDW +RDHRTFAITAEEVPEGLLARWLASRPRA +>PROKKA_01160 +MDVSGSLWPVALRHGTLTLRPLRRGDRRAWEEQRAANRDWLTPWDATSPVPGAAPASFAQ +MVRWQHRQARAGTSYTWGMALDDDAPGRDRLIGLLSLGGVQHGSVMSGAVGYWIDRRQAG +RGLTPTAVAMATDWAFHGLGLHRVEVNIRPENTASLRVAEKLGLREEGLRRAYLHVDGAW +RDHLSFAVTAEEVPEGLLPRWLARREAAAGTAEPRDTAHTPGVAGDVPGPSGR +>PROKKA_01574 +MSWQRSPWPVTLRHGTLALRPLRRRDREAWEEQRAHNREWLTPWDATSPVPGVGPASFGQ +MVRWHGRQGRDGSAYTWGMVLDDDRPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREAG +RGLTPTAVAMATDWAFRSAGLHRVEVNIRPENAASLRVVAKLGLRDEGLRRAYLHVDGAW +RDHRTFAVTAEEVPDGLLARWLATRPRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001328.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001328.fa new file mode 100644 index 0000000000000000000000000000000000000000..bd1d9e16cd645859594f0dba5fa92efa3c210f3e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001328.fa @@ -0,0 +1,15 @@ +>PROKKA_01647 +MPADGAPRRRGPRRADAPGTGPASADGREPRLPGMPRLIGQAGTSPATAPTGDVAGVESG +PAEAERDRWLREQRPPHWG +>PROKKA_01352 +MSADGAPRRRGPRRADAPGTGPAAADGREPRLPGMPRLAGQAGTSPVTAPTGDVAGVESG +AAEAERDRWLREQRPPHWG +>PROKKA_01246 +MGAEVPDPAPRRRGPRRADAPGTGPASADAPEPRLPGVGAGTDGARGAEGVRGAGGVRGA +VGVRGAAGEPTADERDRWLLEQRPPHWG +>PROKKA_01157 +MRTTPTASPEPGRRRGHRRADAAGTGPASADGPEPTLPEPTLPGPALPGAQTAGDATPSR +PAVSRGRAVTSAAGADRPQPADELGRWLLEQRPPHWG +>PROKKA_01577 +MSADGAPRRRGPRRADAPGIGPAAADGREPRLPGMPRLAGTSPATAPTGDAAGVESGPAE +AERDRWLREQRPPHWG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001330.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001330.fa new file mode 100644 index 0000000000000000000000000000000000000000..c8da3067ebda1883b5d7322d619e4bcd714b6b5e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001330.fa @@ -0,0 +1,50 @@ +>PROKKA_01649 +MTQNAPHPDTPAPLSDVMPTVLVLDFGAQYAQLIARRVREANVYSEVVPASTPAAQILER +KPAALILSGGPSSVYEPGAPQLDPALLEAGVPVLGLCYGFQSIAHALGGTVAQTGTREYG +STRLDSVDADSVLFAGQDLEQVVWMSHGDAVTQAPEGFAVTASTAGAPVAAFEDRERRIY +GVQWHPEVGHSSHGQRVLEQFLHVGAGLGADWTVSNVIEEQVERIREQIGDKRAICGLSG +GVDSAVAAALVQRAIGDRLTCVYVDHGLMREGESAEIEQAFGEAHGGARLVMVDAREDFL +SALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESEHDPDATEVRFLVQGTLYPDVVESG +GGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG +LGIRIIGEVTQERLDLLRRADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY +GHPVVLRPVTSEDAMTADWARIPDDVLSRISNRITNEVDGVNRVVLDVTSKPPGTIEWE +>PROKKA_01354 +MTQNAPHPDTPAPLSDVMPTVLVLDFGAQYAQLIARRVREANVYSEVVPASTPAAQILER +KPAALILSGGPSSVYEPGAPQLDPALLEAGVPVLGLCYGFQSIAHALGGTVAQTGTREYG +STRLDSVDADSVLFADQDLEQVVWMSHGDAVTQAPEGFAVTASTAGAPVAAFEDRERRIF +GVQWHPEVGHSSHGQRVLEQFLHVGAGLGADWTASGVIEEQVERIREQIGDKRAICGLSG +GVDSAVAAALVQRAIGDRLTCVYVDHGLMREGESAEIEQAFGEAHGGARLVMVDAREDFL +SALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESEHDPDATEVRFLVQGTLYPDVVESG +GGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG +LGIRIIGEVTQERLDLLRRADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY +GHPVVLRPVISEDAMTADWARIPDDVLSRISNRITNEVDGVNRVVLDVTSKPPGTIEWE +>PROKKA_01244 +MTENAPHSDAPAPLSDVMPTVLVLDFGAQYAQLIARRVREANVYSEVVPASTPAAQILER +RPAALILSGGPSSVYEPGAPTLDPALLEAGVPVLGLCYGFQSIAHALGGTVAKTGTREYG +STRLDSVDADSVLFAGQDLEQVVWMSHGDAVTQAPEGFAVTASTAGAPVAAFEDAERRIY +GVQWHPEVGHSSHGQQVLEHFLHQGAGLGSDWTASNVIEEQVERIREQIGDKRAICGLSG +GVDSAVAAALVQRAIGDRLTCVYVDHGLMRQGESAEIEQAFGEAHGGARLVMVDAREDFL +SALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESEHDPEATEVRFLVQGTLYPDVVESG +GGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG +LGIRIIGEVTQERLDLLRSADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY +GHPIVLRPVTSEDAMTADWARIPDDVLSRISNRITNEVDGVNRVVLDVTSKPPGTIEWE +>PROKKA_01155 +MTQNEPTRDQPAPLHDVLPTVLVMDFGAQYAQLIARRVREANVYSEVVPSSTPAQEILDR +RPAALILSGGPSSVYEAGAPQLDPALLEAGVPVLGLCYGFQSIAHALGGTVARTGTREYG +STRLESADGGSVLLAGQDAAQVVWMSHGDAVTEAPEGFAVTAVTAGAPVAAFEDRERRIF +GVQWHPEVGHSERGQEILANFLTEGAGLSQDWTAENVIEEQVARIREQIGDARAICGLSG +GVDSAVAAALVQRAIGDRLTCVYVDHGLMRQGESDEIERAFGEAHGGAKLVMVDAREDFL +AALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESAHDPNAPEVRFLVQGTLYPDVVESG +GGDGTANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG +LGIRIIGEVTQERLDLLRQADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY +GHPVVLRPVTSEDAMTADWARIPSEVLSRISNRITNEVDGINRVVLDVTSKPPGTIEWE +>PROKKA_01579 +MTQNAPHPDTPTPLSDVMPTVLVLDYGAQYAQLIARRVREANVYSEVVPASTPAAQILER +EPAALILSGGPSSVYEPGAPQLDPALLEAGVPVLGLCYGFQSIAHALGGTVAKTGTREYG +STRLDSVDADSVLFADQDLEQVVWMSHGDAVTQAPEGFAVTASTAGAPVAAFEDRERRIY +GVQWHPEVGHSSRGQRVLEQFLHVGAGLGADWTASGVIEEQVERIREQIGDKRAICGLSG +GVDSAVAAALVQRAIGDRLTCVYVDHGLMREGESAEIEQAFGEAHGGARLVMVDAREDFL +SALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESEHDPDATEVRFLVQGTLYPDVVESG +GGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG +LGIRIIGEVTQERLDLLRRADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY +GHPVVLRPVTSEDAMTADWARIPDDVLSRISNRITNEVDGINRVVLDVTSKPPGTIEWE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001334.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001334.fa new file mode 100644 index 0000000000000000000000000000000000000000..400b74f7ee49425e05ba52f10722cb457616cd8e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001334.fa @@ -0,0 +1,50 @@ +>PROKKA_01653 +MARTRVAGLTPGHRIAETPVPKGVFVTTTSTGPSPEPVHSSSDPFGFFGLTYDDVLLLPN +ATDVIPADADPGTRLTRNIRLNIPIVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQ +ARHVDTVKRSESGMIKDPVTIGPDATLADLDELCAQYRVSGLPVVAEDMTLLGIITNRDT +RFIPREEWATRTVDTAMTRMPLVTAQEGVSRAETIRLFSQNRVEKLPLVDDAGRLTGLIT +IKDFDKAEQYPDAAKDDEGRLRVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGV +LDMIARLKKEKAAAHVDVIGGQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGV +PQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGADSVMLGSLLAGTAESPGDLV +FYQGKQFKTYRGMGSLGAMQTRNGTRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPVA +SVVHQLVGGLRQTMFYTGASTVTDLKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR +>PROKKA_01358 +MARTRVAGLTPGHRIAETPVPKGAFVTNTSTGPSPEPVHSSSDPFGFFGLTYDDVLLLPN +ATDVIPADADTGTRLTRNIRLNIPIVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQ +ARHVDTVKRSESGMIKDPVTIGPDATLADLDELCAQYRVSGLPVVAEDMTLLGIITNRDT +RFIPREEWATRTVDTAMTRMPLVTAQEGISRAETIRLFSQNRVEKLPLVDDAGRLTGLIT +IKDFDKAEQYPDAAKDDEGRLLVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGV +LDMIARLKKEKAAAHVDVIGGQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGV +PQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGADSVMLGSLLAGTAESPGDLV +FYQGKQFKTYRGMGSLGAMQTRNGTRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPIA +SVVHQLVGGLRQTMFYTGASTVADLKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR +>PROKKA_01240 +MARTRVAGLTPGHRIAETPVPKGAFVTTTSTGPSSEPVHSSADPFGFFGLTYDDVLLLPS +ATDVIPAEADTSTQLTRNIRLNIPVVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQ +ARHVDTVKRSESGMIKDPVTIGPKATLADLDELCAQYRVSGLPVVAEDMTLLGIITNRDT +RFIPHEEWETRTVDTAMTRMPLITAREGISREETIRLFSQNRVEKLPLVDEAGRLTGLIT +IKDFDKAEKYPDAAKDDEGRLRVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGV +LDMIARLKKEKAAAHVDVIGGQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGV +PQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGAESVMLGSLLAGTAESPGDLV +FYQGKQFKAYRGMGSLGAMQTRNGKRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPIA +SVVHQLVGGLRQTMFYTGASTVDELKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR +>PROKKA_01151 +MSTSTGPSSDPVYASEDPFGFFGLTYDDVLLLPNATDVIPADADTSTQLTRNIRLNIPVV +SAAMDTVTEAPLAIAIARQGGMGIIHRNLSIEDQAKHVDTVKRSESGMISDPVTIGPKAT +LAELDELCAQYRVSGLPVVAEDMTLLGIITNRDTRFIPHEEWDTRTVDTAMTRMPLITAQ +DGISREEVLHLFSQNRVEKLPLVDDAGRLTGLITIKDFDKAEKYPDAAKDDEGRLRVGGA +VGFFGDGWERAMTLVEAGVDALVVDTANGHTHGVLDMIARLKKEKAAAHVDVIGGQAATY +AGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGVPQITAIYEAAKATRPAGVPLIADGGL +QHSGDIGKALVAGADSVMLGSLLAGTAESPGDLVFYQGKQFKAYRGMGSLGAMQTRNGTR +SFSKDRYFQADVPDEDKLIPEGIEGQVPYRGPIASVVHQLVGGLRQTMFYTGAPTIVDLK +ENGRFVRITTAGLKESHPHDIMMTVEAPNYRSK +>PROKKA_01583 +MARTRVAGLTPGHRIAETPVPKGAFVTNTSTGPSPEPVHSSSDPFGFFGLTYDDVLLLPN +ATDVIPADADTGTRLTRNIRLNIPIVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQ +ARHVDTVKRSESGMIKDPVTIGPDATLADLDELCAQYRVSGLPVVAEDMTLLGIITNRDT +RFIPREEWATRTVDTAMTRMPLVTAQEGISRAETIRLFSQNRVEKLPLVDDAGRLTGLIT +IKDFDKAEQYPDAAKDDEGRLLVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGV +LDMIARLKKEKAAAHVDVIGGQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGV +PQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGADSVMLGSLLAGTAESPGDLV +FYQGKQFKTYRGMGSLGAMQTRNGTRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPVA +SVVHQLVGGLRQTMFYTGASTVADLKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001339.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001339.fa new file mode 100644 index 0000000000000000000000000000000000000000..eb05bc27dec79451e16d41b03b234b422c708eee --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001339.fa @@ -0,0 +1,35 @@ +>PROKKA_01661 +MTLDVRHHVADAPPRLEEPGRGDRVCWVPPAVLRPERTRWQRTWPLLVGVVVTAALIVVS +LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE +WAGLGLLVTMVLVPGAGLVTRMAGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA +VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFVIADRFTVAGL +GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRMNL +PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG +>PROKKA_01366 +MILDVRHHVADAPPRLEEPGRGDRVCWVPPAVLRPERTRWQRTWPLLAGIVVTAVLVVVS +LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE +WAGLGLLVTMVLVPGAGLVTRMAGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA +VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFVIADRFTVAGL +GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRTNL +PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG +>PROKKA_01233 +MTDLHPGVADARTRLPEPGPGERVCWVPPTVLRPQRSRWQRTWPLLAGVAVTVLLAVVSL +FVGVYDVGAEGGREMFAITRVPRTVALVLAGAAMAMCGLIMQLMTQNRFVEPSTTGTTEW +AGLGLLVTMILIPGASIVTRMTGAVLFAFVGTMVFFLFLRRVRLQSSLIVPIVGIMLGAV +VGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLVVCVAVFVIADRFTVAGLG +KDVATNVGLNYNAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNIVSMVRGDNLRTNLP +WVVMVGIWVVIVCDLIGRTVIAPFEVPISLILGLVGAVVFLGLLIRQAKHG +>PROKKA_01144 +MTLDVRHHVADAPPRLEEPGRGDRVCWVPPAVLRPERTRWQRTWPLLVGVLVTAALIVVS +LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE +WAGLGLLVTMVLVPGSGLVTRMVGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA +VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFVIADRFTVAGL +GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRTNL +PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG +>PROKKA_01591 +MILDVRHHVADAPPRLEELGRGDRVCWVPPAVLRPERTRWQRTWPLLVGVVVTAALIVVS +LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE +WAGLGLLVTMVLVPGAGLVTRMVGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA +VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFLIADRFTVAGL +GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRTNL +PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001340.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001340.fa new file mode 100644 index 0000000000000000000000000000000000000000..a679e72df83f80b2638abd0a8b14d0fc94a147e8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001340.fa @@ -0,0 +1,36 @@ +>PROKKA_01662 +MPRSVSAPRLARLALTSVAALALVGCSAGGAATGSSSASASGESSASASAAGGSSAASGG +IAAGVTVTDMSGAEVTLPEEVDSVIATDNRAFRTLDDWGVELSAAPKQIMYKGEGGPSYL +QDDSVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAAVVDTDFDVTQTP +MDEGLKELTTLLGEATGHEADAEKLIADFDAATQRAKDAYDPEQTVMGLIASGGELSYVA +PSTGRAIGPFFDMLELTPALEQSGTDNHQGDDISVEAIAKSNPDWLIVMDRDAAIGEENA +TAAELIERSEALQDVTAVKEGNIVYLPADFYVAEDIQNHTTVMEDLAKAFEGAQ +>PROKKA_01367 +MPSSARAPRLARLALTSVAALALVGCSAGGAATGSSSASASGESSASASASGESSASASA +AGGSSAASGGIATGVTVTDMSGAEVTLPEEVDSVIATDNRTFRTLDDWGVELSAAPKQIM +YKGEGGPSYLQDDSVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAAVV +DTDFDVTQTPMDEGLKELTTLLGEATGHEADAEKLIADFDAATQRAKDAYDPEQTVMGLI +ASGGELSYVAPSTGRAIGPFFDMLELTPALEQSGTDNHQGDDISVEAIAKSNPDWLIVMD +RDAAVGEENATAAELIERSEALQDVTAVKEGNIVYLPTDFYVAEDIQNHTTVMEDLAKAF +EGAQ +>PROKKA_01232 +MQRSPRTPRLKALALASVAALALVGCSAGGAAEGPASGSADTGSAAGSGSASAPAGDGVA +AGATVTDMSGAEITLPEEIDSVITTDNRTFRTLDEWGVELSAAPKQLMFKGEGGPGYLQD +DEVADIGNHREPDMEVFVTAEPDVVFNGQRFNERKAEIDELTGDAAVIDTDFDPKQKPMD +EGLKELTTLLGEATGHQDDAAALNKEFDDAVAKAKGAYDSEQTVMGLISTGGELSYVAPG +TGRSIGPMFDILGLTPALEQAGSDNHQGDDISVEAIAQSNPDWLIVMDRDAATGEANATA +AELIERSEALKDVTAVKEGNIVYLPQDFYVAEDIQNYTTVMDDLAKAFEGAR +>PROKKA_01143 +MRTARLSTAAALASLAALTLAGCGAGGPAAEGSSPASSAASSSPASSAASSSATAGGVAA +GVTVTDMSGTEVTLPEEVDSVIATDNRIFRTLDDWGVELSAAPKQIMYKGEGGPSYLQDD +SVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAAVVDTNFDVTQTPMDE +GLKKLTTLLGEATGHEADAEKLIADFDAATQLAKDAYDPEQTVMGLIASGGELSYAAPST +GRSIGPFFDMLDLTPALDQSGTDNHQGDDISVEAIAKSNPDWLIVMDRDAAVGEENATAA +ELIERSEALQDVTAVKEGNIVYLPADFYVSEDIQNHTTVMEDLAKAFEGAQ +>PROKKA_01592 +MPRSARAPRLARLALTSVAALALVGCSAGGAATGSSSASASGESSASASASGGSSAASGG +IATGVTVTDMSGAEVTLPEEVDSVIATDNRIFRTLDDWGVELSAAPKQIMYKGEGGPSYL +QDDSVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAAVVDTNFDVTQTP +MDEGLKELTTLLGEATGHEADAEKLIADFDAATQRAKDAYDPEQTVMGLIASGGELSYVA +PSTGRAVGPFFDMLELTPALEQSGTDNHQGDDISVEAIAKSNPDWLIVMDRDAAIGEENA +TAAELIERSEALQDVTAVKEGNIVYLPADFYVAEDIQNHTTVMEDLAKAFEGAQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001341.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001341.fa new file mode 100644 index 0000000000000000000000000000000000000000..fa2382ed158d9397190068c3735648bf5bbc796c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001341.fa @@ -0,0 +1,43 @@ +>PROKKA_01663 +MARPRPAARPSRPSAAASEEDDTALAPVLESEGRALLDSLAGYREADALAVSSRLRAAGH +PPERVAAALTQAALRSRAEARLGPEARRMLFTRDGLEQATRPLVAGLHADRLAAAGARRV +ADLGCGLGLDARAFADRGLDVVAVERDAVVAAAAEVNLAGHRGARVVHGDAVAWARAHVP +AEADAVWLDPARRQVGGGGSARVFDPEAFSPPLSVVTDIAATGVPVGVKLGPGLPHEAVP +AGAEAEWVSVDGDVVEAALWFNAAARPGVRRAARVMTVHGGKTTTAQLVSGADFGDSPEV +EAVGEEGMAGLVGAVLHEPDGAVIRAGLVTDLAVSWPVPTRQLDPHLAYLVAPEPVHDGL +ARAHRIEAVHGFHLASLRRWAKETGVGRLDVKKRGIRETPEEVRRAVLGGAKPGRRGGAG +RHATLVLARVGRSRFALEVTPLD +>PROKKA_01368 +MARPRPASRSPRPTAAASEADDTALAPVLEPEGRALLDSLAGYREADALAVSSRLRAAGH +PPERVAAALTQAALRSRAEARLGPEARRMLFTRDGLEQATRPLVAGLHADRLAAAGARRV +ADLGCGLGLDARAFADRGLDVVAVERDAVVAAAAEVNLAGHRGARVVHGDAVAWARAHVP +AEADAVWLDPARRQVGGGGSARVFDPEAFSPPLSVVTDIAATGVPVGVKLGPGLPHEAVP +EGAEAEWVSVDGDVVEAALWFNAAARPGVRRAARVMTVRGGETTTAQLVSGADFGDSPEV +EAVGEEGMAGLVGAVLHEPDGAVIRAGLVTDLAASWPVPTRQLDPHLAYLVAPEPVRDGL +ARAHRIEAVHGFHLASLRRWAKETGVGRLDVKKRGIRETPEEVRRAVLGGAKPGRRGGAG +RHATLVLARVGRSRFALEVTPLD +>PROKKA_01231 +MLTQADLRARAVPRLGPDARGMLFTRDGLEQATRPVVAALHAQRMAAAGARTVADLGCGL +GLDARAFADAGLGVVAVERDAVVAAAAEVNLTDRPGARVVHGDAVPWAREHVPAQADAVW +LDPARRQVGGGGSARVFDPEAFSPPLSVVEELAATGVPVGVKLGPGLPHEAVPAGAEAEW +VSVDGDVVEAALWFNAAARPGVRRAARVIDTRGGQATTAELVSGADFGDSPGVEAVGEEG +MPGLVGRCSTSRTAPSSGPGSSRTWRSPGRRRPASWTRTWPIWWPPSTRPTRWPGRTGST +RSTISTSSLCAGGRRRRGSAAWT +>PROKKA_01142 +MARSQRPARPSRPRPRPADRPGRPRAAESAADATRLEPVLDPAGRVLLDGLGDVSGQDPL +ALSSRLRAAGHDADTVAAALTQAGLRHAGRAKLGALADGMLLTRDGLEQATRAVVAEHRA +RRLQEAGVRSLADLGCGIGADALVYARAGLDVTAVERDPTVAAAAAANLATLAPAGAASV +VTGDAEAWAAAHADEVDALWLDPARRRLGSSGTARVFDPEAFSPPLSFVLGLADGGRPVG +VKLGPGLPHEHVPAAAEAEWVSVDGDVVEVTLWFGPLAQAPGRRTATLLDTRGSAVHRLV +PAAASSPAVEAVGEEGVDGLVGQVLLEPDGAVIRAGLVTDLAVELGPAVRLLDPHLAYLV +APDAAPHPLARGYRVLAVHEFRTKALARWARETGVGRLDVKKRGVRETPEQVRAAVLGRG +TPGGRHATLVLARVGERRVAFEVEPLPAG +>PROKKA_01593 +MARPRPASRSPRPTAAASEADATALTPVLEPEGRALLDSLAWYREADALAVSSRLRAAGH +PPERVAAALTQAALRSRAEARLGRQARRMLFTRDGLEQATRPLVAGLHADRLAAAGARCV +ADLGCGLGLDARAFADRGLDVVAVERDAVVAAAAEVNLAGHRGARVVHGDAVAWARAHVP +AEADAVWLDPARRQVGGGGSARVFDPEAFSPPLSVVTDIAATGVPVGVKLGPGLPHEAVP +AGAEAEWVSVDGDVVEAALWFNAAARPGVRRAARVMTVRGGETTTAQLVSGADFGDSPEV +EAVGEEGMAGLVGAVLHEPDGAVIRAGLVTDLAASWPVPTRQLDPHLAYLVAPEPVHDGL +ARAHRIEAVHGFHLASLRRWAKETGVGRLDVKKRGIRETPEEVRRAVLGGAKPGRRGGAG +RHATLVLARVGRSRFALEVTPLD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001342.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001342.fa new file mode 100644 index 0000000000000000000000000000000000000000..4771ccc19b404eab9a39f5d79e02823e5b642710 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001342.fa @@ -0,0 +1,40 @@ +>PROKKA_01664 +MTLPFADSAQSTLGIEWELALVDAVSGELRSEAPDLLRALHVTEGLAEDDVNPHMTSELL +QNTVELVTGVHERVDAATADLGRIAARVADAAAERGISLFCQGTHPFADAIAQPSTPSER +YDRMLDLTQYWGRQLLIFGVHVHVGLDDVSKAMPVVNGLVNRVPHLLALSASSPFWAGTD +TGYQSQRTLLFQQLPTAGLPFQFQEWEGFERCVAQMEQVGMIADVTECRWDVRAVPRLGT +VEMRACDGLATLEEIAAVTAYTQCLVDDLSASLERGETVEVLPPWHVQENKWRAARYGMD +ATVIVDARGTQVPLAEHLPAEIERLTPVAERLGCAAELAGVQAMIDDGGAARQRRVEAQA +LAGPPAAGEDADDAVAPLRAVVLDAAARTRASLDGRAG +>PROKKA_01369 +MTLPFADSAQSTLGIEWELALVDAVSGELRSEAPDLLRTLHATEGLAEDDVNPHMTSELL +QNTVELVTGVHERVDAATADLGRIAARVADAAAARGISLFCQGTHPFADAIAQPSTPSER +YDRMLDLTQYWGRQLLIFGVHVHVGLDDVSKAMPVVNGLVNRVPHLLALSASSPFWAGTD +TGYQSQRTLLFQQLPTAGLPFQFQEWEGFERCVAQMEQVGMIADVTECRWDVRAVPRLGT +VEMRACDGLATLEEIAAVTAYTQCLVDDLSASLERGETVEVLPPWHVQENKWRAARYGMD +ATVIVDARGTQVPLAEHLPAEIERLTPVAERLGCAAELAGVQAMIDDGGAARQRRVEAQA +LAGPPAAGEDTDDAVAPLRAVVLDAAARTRASLDGRTG +>PROKKA_01230 +MNLPFADSTQSTLGIEWEVALVDAATGDLRSEAPAILHELHKEAGLAEGEDHPHVTGELL +QNTVELVTGVHEAVPTAVAELGTIAARVARAAADRGLALYCQGTHPFGEAMTQPITPKER +YGRMVDLTQYWGRQMLIFGVHVHVGLDDPAKAMPAVNRLISRFPHLLALSASSPFWVGAD +TGYQSQRTQLFQQLPTAGLPFQFETWAEFEACVQQMTDVGMVEDVTECRWDVRAVPRLGT +VEMRACDGMATLEEIAAVAAYTQCLVHELSADVERGRHMEILPPWYTQENKWRASRYGMD +ATVIVDAAGTQVPLAEHLGADLERLAPIAEELGCAAELAHARVLMEHSPADRQRAVEAEA +LAGPPAEGESAHDAAAPLRAVVLDAAARTRESLERVGG +>PROKKA_01141 +MSLPFADSAQSTLGIEWELALVDPLTGDLRSEAPGILEELRAEAGLDADADHPHVTGELL +QNTVELVTGVHGSVPDAVADLGGIAARVQRAAADRGLALFCQGTHPFGEAMTQPITPKAR +YGRMVDLTQYWGRQMLIFGVHVHIGLDDRAKAMPAVNRLISRLPHLLALSASSPFWVGAD +TGYQSQRTQLFQQLPTAGLPFQFETWEGFEHCVEQMTGVGMVEDVTECRWDVRAVPRLGT +VEMRVCDGMATLEEIGAVAAYAQCLVHELSAQVEDDEPVAILPPWYTQENKWRAARYGLE +ATVITDDAGTQVPLAEHLAADLERLAPVAEELGCAAELAHARVLMEHSPADRQRRVAAEA +AAGPPRTGEDPADPVAPLRAVVRDAADRTRESLRAFQG +>PROKKA_01594 +MTLPFADSAQSTLGIEWELALVDAVSGELRSEAPDLLRALHVTEGLAEDDVNPHMTSELL +QNTVELVTGVHERVDAATADLGRIAARVADAAAERGISLFCQGTHPFAEAIAQPSTPSER +YDRMLDLTQYWGRQLLIFGVHVHVGLDDVSKAMPVVNGLVNRVPHLLALSASSPFWAGTD +TGYQSQRTLLFQQLPTAGLPFQFQEWEDFERCVAQMEQVGMIADVTECRWDVRAVPRLGT +VEMRACDGLATLEEIAAVTAYTQCLVDDLSASLERGETVEVLPPWHVQENKWRAARYGMD +ATVIVDARGTQVPLAEHLPAEIERLTPVAERLGCAAELAGVQAMIDDGGAARQRRVEAQA +LAGPPAAGEDADDAVAPLRAVVLDAAARTRTSLDGRTG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001343.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001343.fa new file mode 100644 index 0000000000000000000000000000000000000000..6cd472497897d1f2ca19bbea9797edd7ff8bb798 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001343.fa @@ -0,0 +1,40 @@ +>PROKKA_01665 +MRALTWQGKRNVVVEDVPDPRIQEPTDAIIEVTSTGICGSDLHLYEVLGPFMDAGDVIGH +EPMGIVREVGSEVTHIRPGDRVVVPFTISCGRCWMCQRGLQSQCETTQVREQGCGAALFG +YSRLYGSVPGGQAELLRVPHADYGPVKVPHTGPDEQWLFLSDVVPTAWQGVQYANVPDGG +TLAVLGLGPIGQLAARIGVHLGYRVIGVDPVPERRAMAARHGIEVLDADGGEAEVLRERT +GGRGPDAVLDAVGMEAHASPVGHAAHTAVGLLPDALGRAAMKTAGVDRLSALHTAIDAVR +RGGTVSISGVYGGMKDPMPMLTLFDKQVTLTMGQCNVRRWVDDLLPLLDDPSDPLGVLDL +TTHTAPLEDAPALYETFQKKEDGCVKVVLKP +>PROKKA_01370 +MRALTWQGKRNVAVEDVPDPRIQEPTDAIIEVTSTGICGSDLHLYEVLGPFMDAGDVIGH +EPMGIVREVGSEVTHIRPGDRVVVPFTISCGRCWMCQRGLQSQCETTQVREQGSGAALFG +YSRLYGSVPGGQAELLRVPHADYGPVKVPHTGPDEQWLFLSDVVPTAWQGVQYANVPDGG +TLAVLGLGPIGQLAARIGVHLGYRVIGVDPVPERRAMAARHGIEVLDADGGEAEVLRERT +GGRGPDGVVDAVGMEAHASPAGHAAHTAVGLLPDALGRAAMKTAGVDRLSALHTAIDAVR +RGGTVSLSGVYGGMKDPMPMLTLFDKQVTLTMGQCNVRRWVDDLLPLLDDPSDPLGVLDL +ATHTAPLEDAPALYETFQKKEDGCIKVVLKP +>PROKKA_01229 +MRALTWQGKRNVAVEDVPDPRIQEPTDAIVEITSTGICGSDLHLYEVLGPFMDAGDVIGH +EPMGIVREVGAEVTHIKPGDRVVVPFNIACGRCWMCERGLQSQCETTQVREQGSGAALLG +YSRLYGSVPGGQAEYLRVPHADYGPVKVPHTGPDEQWLFLSDVVPTAWQGVQYAQVPRGG +TLAVIGLGPIGQLAARIGVHQGLRVIGVDPVPERRAMAARHGVEVLDSSDGGVAELLREC +TQGRGPDGVVDAVGMEAHGSPVAKAAHTVVGLLPDALGRAAMKTAGVDRLDALHTAIDAV +RRGGTVSLSGVYGGMQSPMPLLTMFDKQVTLAMGQCNVRRWVDDLLPLLDDPSDPLGVLD +LTTHTAPLEDAPALYETFQKKEDGCIKVVLKP +>PROKKA_01140 +MRALTWQGKRSVSVEDVPDPRIQEPTDAIIKVTSTGICGSDLHLYEVLGPFMDKGDVIGH +EPMGIVEEVGSAVTNLSPGDRVVIPFNISCGHCWMCQHGLQSQCETTQVKEQGSGAALLG +YSRLYGSVPGGQAEYLRVPHADYGPIKVPHTGPDTQWLFLSDVVPTAWQAVQYANVSKGD +TLAVLGLGPIGQMSARIGVHLGCRVIAVDPVPERRHMAARHGVEVLDMEGSGTGVPDLLR +QATGGRGPDGVVDAVGMEAHGAPVAAAAQTAAGMLPGPLARAAVKTSGIDRLTALHTAIE +SVRRGGTVSLSGVYGGMQDPMPLLTMFDKQIQFTMGQCNVRRWVDDLLPLMDDPSDPLGV +LDLVTHTAPLEDAPAMYEKFQKKQDGCIKVVLTP +>PROKKA_01595 +MRALTWQGKRNVTVEDVPDPRIQEPTDAIIEVTSTGICGSDLHLYEVLGPFMDAGDVIGH +EPMGIVREVGSEVTHIRPGDRVVVPFTISCGRCWMCQRGLQSQCETTQVREQGSGAALFG +YSRLYGSVPGGQAELLRVPHADYGPVKVPHTGPDEQWLFLSDVVPTAWQGVQYANVPDGG +TLAVLGLGPIGQLAARIGVHLGYRVIGVDPVPERRAMAARHGIEVLDADGGEAEVLRERT +SGRGPDGVVDAVGMEAHASPAGHAAHTAVGLLPDALGRAAMKTAGVDRLSALHTAIDAVR +RGGTVSLSGVYGGMKDPMPMLTLFDKQVTLTMGQCNVRRWVDDLLPLLDDPSDPLGVLDL +TTHTAPLEDAPALYETFQKKEDGCIKVVLKP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001345.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001345.fa new file mode 100644 index 0000000000000000000000000000000000000000..9871e720806b2e110f4f8a2e6c260589932e7374 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001345.fa @@ -0,0 +1,20 @@ +>PROKKA_01667 +MRTRTLTRRAALTGLLGSAALGFTACTSSGYPADPDGTLDRVTGGVLRVGVVHHPPHVDV +SGAEPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHA +SITRDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR +>PROKKA_01372 +MTITRRAALAGLLGGAALGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDASGA +EPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHASIT +RDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR +>PROKKA_01227 +MTITRRAALTGLLGGAVLGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDASGA +EPVGPEPDLIRGFAAAHDAEIAWTVSGEEALLTALEKGDVDLVAGGLTSDSPWTTHASLT +RDYAEAAGPDGEPVKLVMAVPPGENQMLAALEAHLDAQAREAGR +>PROKKA_01138 +MQTPRRTLLTGALAAAGVVLTGCTSSGYPADPDGTLDRITGGTLRVGASHHPPHVDAAGA +EPQGPEPDLVRAFAAERDARVEWTVSGEEALMTALKQGDLDLVVGGLTKKSPWTTDAGLT +RPYAETTGPDGEKAELVMAVPLGENQFQSALERFLDAHGEEAGA +>PROKKA_01597 +MTITRRAALAGLLGGAALGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDASGA +EPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHASIT +RDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001346.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001346.fa new file mode 100644 index 0000000000000000000000000000000000000000..587ce0700fa41fa10d14b467101c7ffb23e6f471 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001346.fa @@ -0,0 +1,35 @@ +>PROKKA_01668 +MTRRDTRETGPSGRRFGATELPPEIERVVQQAKRLEWATLGVIVVTIVLVAFVMGSSQAM +RAAWIEDLLSLIPPIAFLVALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLVG +DSLLGLVTAEHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLKLAEQLHDRVL +YADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAILVGVSIVLDGWKNLKEAVTNLAD +RRAATIDGARPHPLIDRAERVAWAEPWVRHAGARVRDEGHVFHVEMFVVPHEGADVTVAR +CCALRDAIAALDWKLQDVVVAPVDELPAEVHGGRSGEHQTGEE +>PROKKA_01373 +MTRQDTRETGPSGRRFGATELPPEIERVVQQAKRLEWVTLGVIVVTIVLVAIVMGSSQAM +RAAWIEDLLSLIPPIAFLIALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLVG +DSLLGLVTAEHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLTLAEQLHDRVL +YADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAIFVGVSIVLDGWKNLKEAVTNLAD +RRATTIDGARPHPLIDRAERVAWAEPWVRHAGARVRDEGHVFHVEMFVVPHEGADVTVAR +CCALRDAIAALDWKLQDVVVAPVDELPAEVHGGRSGEHQTGEE +>PROKKA_01226 +MTHHASTTHRSPGGRRFGATELPPEIERALRRAVRLEWATLAVLAVTIALVAVVMGSSQA +MRAAWIEDLLSLVPPIAFLVAVRVTRRHPTRARPYGSHRSVGVGHLVAAVALSVMGVILV +ADSALGLVTGEHPPIGTLDLFGHTVWQGWFMMAVMALSIPGPVLLGRAKLKLAEQLHDRV +LYADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAIFVGVSIVLDGWRNLREAVGNLA +DRRATTIDGDRPHPLIDRAERVAWAQPWVRHAGTRVRDEGHVLHVEMFVVPHEGAGATVG +RCAQLREEIVALDWKLEDVVVVPVAELPAEVHGGASGDEQSGEE +>PROKKA_01137 +MSEKRTIGRAELPDDVARAAHQAVVLEWVSLGWLVLTVSLVAVVMGSSQAMRAAWIEDLL +SLIPPIAFLVALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLVGDSLLGLLTA +EHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLKLAEQLHDRVLYADADMNKA +DWQTGVATIVGVAGIGLGWWWADAAAAIFVGVSIVLDGWKNLKEAVTNLADRRATTIDGA +RPHPIIDRAERVAWAQPWVRHAGARVRDEGHVFHLEMFVVPRHGADVTVGRCADLRERIE +ELDWKLEDVVVVPVAELPEEVHGGRSGDEQSKGSE +>PROKKA_01598 +MTRRDTRETGPSGRRFGATELPPEIERVVQQAKRLEWATLGVIVVTIVLVAIVMGSSQAM +RAAWIEDLLSLIPPIAFLVALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLVG +DSLLGLVTAEHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLKLAEQLHDRVL +YADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAIFVGVSIVLDGWKNLKEAVTNLAD +RRAATIDGARPHPLIDRVERVAWAEPWVRQAGARVRDEGHVFHVEMFVVPHEGADVTVGR +CCALRDAIAALDWKLQDVVVAPVDELPAEVHGGRSGEHQTGEE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001349.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001349.fa new file mode 100644 index 0000000000000000000000000000000000000000..615828763c415e359de0b0d3ef6c6c9d4ae47399 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001349.fa @@ -0,0 +1,25 @@ +>PROKKA_01672 +MALLLAIDSSAAASVAVLRDGEELARWATDDTHAHAEVLAPAVQTVLGEAGVTGTALDAL +AVGVGPGPFTGLRAGLATAAALGLAWDVPVHGVRSLDALAHEAGVDAFRHGIEEFVVATD +ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPVYGAGAGLYPEALRAVPDWESATP +SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRAGA +>PROKKA_01377 +MALLLAIDSSAAASVAVLRDGEELAHWATDDTHAHAEVLAPAVQTVLGEAGVTGTALDAL +AVGVGPGPFTGLRAGLATAAALGLAWDVPVHGVRSLDALAHAAGVDAFRHGIEEFVVATD +ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPVYGAGAGLYPEALRAVPDWETATP +SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRAGA +>PROKKA_01206 +MALLLALDSSAAASVAVLRDGEALARWATEDTHAHAEVLAPAVRAVLAEAGVAGAGLDAV +AVGVGPGPFTGLRAGLATAAALGLAWDVPVRGVRSLDALAHDAAVDAFRHGAEEFVVATD +ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPAYGAGAGLYPEALRAVPGWETATP +SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRAGA +>PROKKA_01134 +MPLLLALDSSSAASVALLRDGEPLAAWSTADTTSHAEVLAPAVRQVLAEAGVAGGDLDGI +AAGVGPGPFTGLRAGLATAEALGFAWDVPVHGIRSLDALAHRAGTDAFAHAVEEFVVVTD +ARRREVYWAHYAQVGGQPTLLHGPFVTPAAEVTPLPAYGAGAGLYPEALHAVDGWEGAVP +DAVSLGRVDELALRRGRGVLPPTPLYLRESDATVPAPRTPARPAGA +>PROKKA_01602 +MALLIAIDSSAAASVAVLQDGEELARWATDDTHAHAEVLAPAVQAVLGEAGVTGTALDAL +AVGVGPGPFTGLRAGLATAAALGLAWDVPVHGVRSLDALAHEAGVDAFRHGIEEFVIATD +ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPVYGAGAGLYPEALRAVPDWETATP +SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRAGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001352.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001352.fa new file mode 100644 index 0000000000000000000000000000000000000000..396aad1d9248262e2ecc7e6e843b1dfc1d369181 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001352.fa @@ -0,0 +1,50 @@ +>PROKKA_01675 +MTADDLTRIAVTGSAVRTAEEPLLAAGRGPELMRAAAWALAEHAAALLRERGPVAGTTVA +ALVGPGNNGGDALFALAFLRRRGVAAVAVPVRRDDDGAPRWHAEGWAALRAAGGRRADAV +PPEAALVVDGVLGTGFTGEYELPAAARALPAEALVLACDVPSGVDADTGEVRGEALRAAA +TVTFGALKSGLVLGEGAGRAGTVHVADIGLGPHLPTSPAARLGVMDEAAARAAHPAPAAA +AHKYTRGVVAVVAGSERYPGAAVLASAGALHTGAGMVHHAGPQTTRDLVLAAHPEALVSA +EGPEPSRADAWVAGPGLDTEHDARRRWAGVLAALEERPEAALLADASALDLVTAAELRSL +RAAGTPVVLTPHAGEWSRLRERVPADGADAADPLAALRAWTAEHGATVLLKGPRTLVVAP +DGEAWAVTGGGPDLAMGGTGDVLSGAIGAVLAADVARRSRARRAGEDPGPAPTARLAAAA +AWLHAQAGAEQARAGRITTATLPAALGARVARLWWPDDAEPEAVR +>PROKKA_01380 +MTADDLTRIAVTGSAVRTAEEPLLTAGRGPELMRAAAWALAEHAAALLRERGPVAGATVA +ALVGPGNNGGDALFALAFLRGRGVAAVAVPVRRDDDGAPRWHAEGWAALRAAGGRRADAV +PPEAALVVDGVLGTGFTGEYELPAAARALPAEALVLACDVPSGVDADTGEVRGEALRADT +TVTFGALKSGLVLGEGAARAGTVHVVDIGLGPHLPTSPAARLGVMDEAAARTAHPAPAAE +AHKYTRGVVAVVAGSERYPGAAVLASAGALHTGAGMVHHAGPQTTRDLVLAAHPEALVSA +EGPEPSRADAWVAGPGLDTEHDARRRWAGVLAALEERPEAALVADASALDLVTAAELRSL +RAAGTPVVLTPHAGEWSRLRERVPADGADAADPLAALRAWTSEHGATVLFKGPRTLVVAP +DGEAWVVTGGGPDLAMGGTGDVLSGAIGAVLAADVARRSRARRAGEDPGPAPTARLAAAA +AWLHARAGADQARAGRITTATLPTALGARVAHLWWPDDAEPEAVR +>PROKKA_01203 +MSVEELRRVAVAGSAVRAAEAPLLAAGRGPAMMRDAAWALAEHAAALLRARGPVAGTTVA +ALVGPGNNGGDALFALAFLRRRGVAAVAVPVRHDDDGAPRWHAEGWAALRAAGGRRADAV +PAAAALVIDGMLGTGFAGELTLPPAARALPRDAVVLACDVPSGVDADTGEVRGEALRADA +TVTFGALKTGLLVGEGAALAGEVHPVDIGLGPQLPTSPAARLYLADEAAVRAAHPAPAPD +AHKYTRGLVAVAAGSPRYPGAAVLSCSGALHAGAGMVHHAGPEATRDRVLAEHPEALVSA +EGPAPDRADAWVAGPGLDTQDDARRRWEGVLSALAERPEAALVADASALELVTAAQLRAL +REGGTPVVLTPHAGEWARLRERLPADGADAADPLAALRSWSAAHGATVLLKGPRTLTVQP +DGEAWLVADGGPELAMGGTGDVLAGALGAVLAADVARRSRARRAEQAPGPVPTAALAAAA +AWLHARAGAEQARAGRLTTRTLPAALGAVTARLWRAGDENGRTRG +>PROKKA_01131 +MRAHTGTDVRAAERPLLDEGRGEALMRTAAWGLAEHVAAELRARGPVAGATVAALVGPGN +NGGDALWALAFLRRRGVEAVAVPVRRNEAGEPVWHAAGWAALQAAGGRRSTAVPARAAVV +VDAMLGTGARGGFTLPEPARHLPSGAAVVACDLPSGVDADTGAVPGEALAADLTVTFGAS +KTGLLLGAGPGRAGRVVCVDIGLGPHLPADPAAGLHVVDDDAVARLHPVPARDAHKYTRG +VVGVVAGSERYPGAAVLAVGGVLAGGAGMAHHGGPARAGDLVLAAHPAALTSADGPAPER +ADAWVLGPGLGDGDGARERVRATVAAVLASGADGDRGPAALVVDASALDLVTGEDLAALA +AVDARTVITPHAGEWARLRDRLPVPAADAVDVDEDGAGELARLRAWTAARGVTVLLKGPA +SLAVAPDGQAWLMRDGGPQLGVAGTGDVLAGALGAVLAAETARARRGGDERHGAARGGRP +SPAALAAAAAWLHARAGVRQAADGRATADTLPAALGDVVARRWWENDAHGRRP +>PROKKA_01605 +MTADDLTRIAVTGSAVRTAEEPLLAAGRGPELMRAAAWALAEHAAALLRERGPVAGATVA +ALVGPGNNGGDALFALAFLRRRGVAAVAVPVRRDDDGAPRWHAEGWAALQAAGGRRADAV +PPEAALVVDGVLGTGFTGEYELPAAARALPAEALVLACDVPSGVDADTGEVRGEALRADA +TVTFGALKSGLVLGEGAARAGTVHVVDIGLGPHLPTSPAARLGVMDEAAARTAHPAPAAE +AHKYTRGVVAVVAGSERYPGAAVLASAGALQTGAGMVHHAGPQTTRDLVLAAHPEALVSA +EGPEPSRADAWVAGPGLDTEHDARRRWAGVLAALEERPEAALVADASALDLVTAAELRSL +RAAGTPVVLTPHAGEWSRLRERVPADGADATDPLAALRAWTAAHGATVLLKGPRTLVVAP +DGEAWVVTGGGPDLAMGGTGDVLSGAIGAVLAADVARRSRARRAGEDPGPAPTARLAAAA +AWLHAQAGADQARAGRITTATLPTALGARVARLWWPDDAEPESVR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001353.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001353.fa new file mode 100644 index 0000000000000000000000000000000000000000..20db8abf68a91dfd25f5d8a5993ed6eb4811bbb7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001353.fa @@ -0,0 +1,19 @@ +>PROKKA_01676 +MIVGVGVDVVDVPRFRAQLERTPALRARLFTEDERDLPLRSLAARFAAKEAIAKAMGAPP +GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEALGITHWHLSLSHDGDVATAYVVAERRA +AEEESA +>PROKKA_01381 +MIVGVGVDVVDVPRFRAQLERTPALRARLFTEDERDLPLRSLAARFAAKEAIAKAMGAPP +GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEALGITHWHLSLSHDGDVATAYVVAERRA +AEEESA +>PROKKA_01202 +MIVGVGMDVVDVPRFRAQLERTPALRERLFTEDERDLPLRSLAARFAAKEAIAKAMGAPP +GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEAQGITHWHLSLSHDGDVAAAYVVAERRA +GEDGA +>PROKKA_01130 +MIVGIGVDVVDVPRFERQLARTPALRERLFTEEERDLSLRSLAARFAAKEAIAKALGAPP +GMMWHHCSIPRPAHGDGRPEVRLTDSVRDRADELGVTHWHLSLSHDGDVAVAYVVAERHD +>PROKKA_01606 +MIVGVGVDVVDVPRFRAQLERTPALRARLFTEDERDLPLRSLAARFAAKEAVAKAMGAPP +GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEALGITHWHLSLSHDGDVATAYVVAERRA +AEEESA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001355.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001355.fa new file mode 100644 index 0000000000000000000000000000000000000000..34bac03608e0523ff5468eca0758b549f188d45e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001355.fa @@ -0,0 +1,65 @@ +>PROKKA_01678 +MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHA +HVAGIGHGQRYGYRVHGPWDPARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPD +RIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYETHVKGMTKLHPAVPEELRGT +YAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS +SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEG +DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD +MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGLWSEWNGMYRDAVRDFWRGEP +GTLGEFATRLTGSADLYEGDGRGPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG +EAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNV +YCQDNEISWIDWSAMDDSLVAFTRDLIALRRDHAVFRRRHHFDGRPAARDVEAPLPDIVW +LEPDATAKTEDDWGAEARSIGFYLNGHMLTRGDEEGEEPYRDFYVLMNAWWEPVPYTLPG +PTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQVPEGA +>PROKKA_01383 +MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHA +HVAGIGHGQRYGYRVHGPWDPARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPD +RIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYETHVKGMTKLHPAVPEELRGT +YAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS +SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEG +DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD +MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGLWSEWNGMYRDAVRDFWRGEP +GTLGEFATRLTGSADLYEGDGRGPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG +EAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNV +YCQDNEISWIDWSAMDDSLVAFTRDLIALRRDHAVFRRRHHFDGRPAARDVEAPLPDIVW +LEPDATAKTEDDWGAEARSIGFYLNGHMLTRGDEEGEEPYRDFYVLMNAWWEPVPYTLPG +PTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQVPEGA +>PROKKA_01200 +MHTVDIGQPYPLGATVDETGTNFAVALAREAESVELCLVDEDGVETRLPVVERHGTTWHV +HVAGVGHGQRYGYRVTGPWDPSRGLWHNPAKILVDPYARAFAGEHEWGQQHHSYDFDEPD +RMDTSDNLGTTMLGVVTDDDFDWGEDAPPNIEMTDTVVYETHVKGMTMRHPAVPEELRGT +YAGMAHPEVVRHLTDLGVTAVELMPVHQFVDDATLQEKGLSNYWGYNTLGFFAPHAAYAA +SQEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSMRGLDNAGYYHLVEA +DERHYMDYTGTGNSVDLSSPKALQLVMDSLRHWVTEMHVDGFRFDLATTLTRVEGEQGPD +MFSAFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGIWSEWNGMYRDTVRDFWRGEP +GTLGEFATRLTGSADLYEGDGRSPGASVNFVTAHDGFTLRDLVSYNEKHNAANGEDNNDG +ESHNRSWNCGVEGETDDPEVLTLRARQQRNFLATLLISQGVPMISHGDELGRTQGGNNNV +YCQDNEISWIDWSAVDDSLVAFTRDLIALRHDHAVFRRRHHFDGRPAARDVEAPLPDIVW +LEPDATAKTEDDWGAEARSIGFYLNGHTLTRGDEDEEGPYRDFYVLMNAWWEPVPYTLPG +PLFPETWEVVVDTSSHVAPSGSRPRVRAGEVLEVPARSTVILRQVPEGA +>PROKKA_01128 +MHTVDIGQPYPLGATVDEAGTNFAVAVGREVEAVELCLIAEDGSEERIPVTERHDTTWHV +HVAGIGGGQRYGWRVHGPWDPARGLWHNPHKLLADPYARAFTGDYAWGQQHFSYAFDEPD +RMDTADSRGTSMVGVVVDDDFDWGDDAPPQRLLTDTVVYETHVKGLTALHPDVPEELRGT +YAGVAHPSVLEHLTSLGVTAVELMPVHQFVNDSILQEKGLSNYWGYNSLGYLAPHAAYSS +ADTVGGQVHEFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPLLSFRGFDNAGYYHLVEG +DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD +MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGIWSEWNGMYRDTVRDFWRGEP +GTLGEFATRLTGSADLYEGDGRNPGASVNFVTAHDGFTLRDLVSYNEKHNHANGEDNNDG +DSHNRSWNCGVEGETDDPEVLTLRARQQRNFLTTLMVSEGVPMLSHGDELGRTQKGNNNV +YCQDNELSWIDWSTRDDALIAFTRDVIALRRDHAVFRRRQHFDGRPAERDVEAPLPDIVW +LEPDATAKTEADWGAEARSIAFYLNGHDLQRREGEPDEAFRDFYVLMNAWWEPVPYTLPG +PLFPGEWEIVVDTSSHVAPAGTRPHVVAGEVIEVPGRSTMILREVVRQEQG +>PROKKA_01608 +MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHA +HVAGIGHGQRYGYRVHGPWDPARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPD +RIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYETHVKGMTKLHPAVPEELRGT +YAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS +SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEG +DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD +MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGLWSEWNGMYRDTVRDFWRGEP +GTLGEFATRLTGSADLYEGDGRSPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG +DAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNV +YCQDNEISWIDWSAMDDSLVAFTRDLIALRRDHAVFRRRHHFDGRPAARDIEAPLPDIVW +LEPDATAKTEDDWGAEARSLGFYLNGHTLPRGDEEGEEPYRDFYVLMNAWWEPVPYTLPG +PTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQVPEGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001359.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001359.fa new file mode 100644 index 0000000000000000000000000000000000000000..edfada3ff62ca0fde179a8d77211fea19f2afcca --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001359.fa @@ -0,0 +1,14 @@ +>PROKKA_01685 +MTSDAAPRPRRWTLFAGLLAGLAVLWSAAFLAVDAPVCARQSAPVEWLPCLDPDRQDSEV +APDAGSSADRTTSRP +>PROKKA_01389 +MTSDAAPRPRRWTLFAGLLAGLAVLWSAAFLAVDAPVCARQSAPVEWLPCLDPDRQDSEV +APDAGSSADRTTSRP +>PROKKA_01193 +MSSEAVPRPPRWSPFGALLAGLAVLWGAAFLAVDAPVCERHGAPVEWLPCLDRDRGDPDV +APQR +>PROKKA_01123 +MSPRRDPGRLRPLAGPAALLAALWVAAWLAVSVPVCDRGGPADWLPCVDPGRSVPAPGAP +>PROKKA_01614 +MTSDAAPRPRRWTLFAGLLAGLAVLWSAAFLAVDAPVCARQSAPVEWLPCLDPDRQDSEV +APDAGSSADRTTSRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001360.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001360.fa new file mode 100644 index 0000000000000000000000000000000000000000..2a88f409eb9b1360fdf9d3a48d10c4415a466621 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001360.fa @@ -0,0 +1,45 @@ +>PROKKA_01686 +MSRLFGTDGVRGLANETLTVELSVQLAQAASPVLGAEAFDAGRRPVAVVARDPRISGEFI +TAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLDADFGVMISASHNPAPDNGIKFLARGG +EKLTDAQEDEIIRHLEGVTPRRPQGADVGRVRVFADAEDRYVLHLLQTLPHRLDGLKVVL +DCAHGAAAGCSPEAFRAAGAEVVVIGASPDGLNINDGYGSTHLEKLQAAVREHGADLGIA +HDGDADRCLAVDERGEVVDGDQIMGVMAVALKDRGVLRDDTLVVTVMSNLGLKLAMGREG +VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLASRVAETGTP +LSELAAVMDRLPQVLVNVRGVDKSRAAEDEAVQAAVAEAEARLGETGRVLLRPSGTEPVV +RVMVEAPDEETAGREAQVLADVVQRELRLHD +>PROKKA_01390 +MSRLFGTDGVRGLANETLTVELSVQLAQAASPVLGAEAFDAGRRPVAVVARDPRISGEFI +TAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLDADFGVMISASHNPAPDNGIKFLARGG +EKLTDAQEDEIIRHLEGVTPRRPQGADVGRVRVFADAEDRYVLHLLQTLPHRLDGLKVVL +DCAHGAAAGCSPEAFRAAGAEVVVIGASPDGLNINDGYGSTHLEKLQAAVREHGADLGIA +HDGDADRCLAVDEHGEVVDGDQIMGVMAVALKDRGVLRDDTLVVTVMSNLGLKLAMGREG +VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLASRVAETGTP +LSELAAVMDRLPQVLVNVRGVDKSRAAEDEAVQAAVAEAEARLGETGRVLLRPSGTEPVV +RVMVEAPDEETAGREAQVLADVVQRELRLHD +>PROKKA_01192 +MSRLFGTDGVRGLANETLTVELSVQLAQAAAPVLGAEALEAGRRPVAVVARDPRISGEFI +AAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLGADFGVMISASHNPAPDNGIKFLARGG +EKLTDAQEDEIIRHLEGVEPRRPQGADVGRVKVFSDAEDRYVVHLLQALPHRLEGLKVVL +DCAHGAAAGCSPEAFRDAGAEVVVIGASPDGLNINEGYGSTHLEKLQAAVLEHGADLGIA +HDGDADRCLAVDERGEVVDGDQIMGVMAVAMKDRGVLRDDTLVVTVMSNLGLKLAMGREG +VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLAARVAETGRP +LSALAAVMDRLPQVLVNVRGVDKSRAAEDVAVQAAVAEAEARLGETGRVLLRPSGTEPVV +RVMVEAPDEETAGREAEALADVVQRELRLHV +>PROKKA_01122 +MSRLFGTDGVRGLANDVLTVELSVQLAQAAAPVLGADALAAGRRPVAVVARDPRISGQFI +AAAVIAGLASSGVDVHDAGVVPTPAAAFLVGDLDADFGVMISASHNPAPDNGIKFLARGG +EKLTDEQEDEIIQHLESEHPLRPTGAEVGRVRTFSDAEDRYVVHLLQTLPHRLDGLTVVL +DCAHGAASGCSPDAFRDAGAQVIVIGAEPDGLNINEGVGSTHLEKLQAAVKEHGADLGIA +HDGDADRCLAVDELGEVVDGDQIMGIMALALKDRGQLKEDTLVVTVMSNLGLKLAMRGAG +IELVETQVGDRYVLAGMRLGEYSLGGEQSGHVIFADHATTGDGVLTGLQIAARVAETGTP +LSQLAAVMTRLPQVLVNVRGVDKSRAAEDAAVQSAVREAEARLGETGRVLLRPSGTEPVV +RVMVEAPDEETARREAEALAEVVQRELRLHD +>PROKKA_01615 +MSRLFGTDGVRGLANETLTVELSVQLAQAASPVLGAEAFDAGRRPVAVVARDPRISGEFI +AAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLDADFGVMISASHNPAPDNGIKFLARGG +EKLTDAQEDEIIRHLEGVTPRRPQGADVGRVRVFADAEDRYVLHLLQTLPHRLDGLKVVL +DCAHGAAAGCSPEAFRAAGAEVVVIGASPDGLNINDGYGSTHLEKLQAAVREHGADLGIA +HDGDADRCLAVDERGEVVDGDQIMGVMAVALKDRGVLRDDTLVVTVMSNLGLKLAMGREG +VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLASRVAETGTP +LSELAAVMDRLPQVLVNVRGVDKSRAAEDEAVQAAVAEAEARLGETGRVLLRPSGTEPVV +RVMVEAPDEETAGREAQVLADVVQRELRLHD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001365.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001365.fa new file mode 100644 index 0000000000000000000000000000000000000000..cb88e76235edb1b3e591d4ca1a4641e753efeb7d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001365.fa @@ -0,0 +1,30 @@ +>PROKKA_01692 +MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPYAERLITFAKKGDL +PARRKVQGLIAAKNRTNKAVVHELFTVIGPAMAERNGGYTRITKIGNRHGDNAPMAVIEL +IMDPISGKQAVVREAEQAAASAPAAPAESTPVEAVDPAATEEVTVAESQETAAEIDGAVP +TTEDGSAPAEATIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGEAAQK +MA +>PROKKA_01399 +MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPYAERLITFAKKGDL +PARRKVQGLIAAKNRTNKAVVHELFTVIGPAMAERNGGYTRITKIGNRQGDNAPMAVIEL +IMDPISGKQAVVREAEQAAASAPAAPAESTPVEAVDPAATEEVTVAESQETAAEIDGAVP +TTEDGSAPAEATIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGEAAQK +MA +>PROKKA_01186 +MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPYAERLITFAKKGDL +PARRKVQGLIAAKNRTNKSIVHELFTVIGPAMAERNGGYTRITKIGNRQGDNAPMAVIEL +IMEPISGKQAVVREAEQAAASAPAAETAPVQETAPVEAVDPAAAEDVTVAESQEAAAEID +GAVATTEDGSAPEGASIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGE +AAQKMAD +>PROKKA_01116 +MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPHAERLITIAKKGDL +PARRKVQGIIAAKSRTNKSIVHELFTVIAPAMAERNGGYTRITKIGNRQGDNAPMAVIEL +VMEPVSGKQAVVREAEQAAASAPAAAPVEETPVEVVDPAATEEVTVAESEETAAEIDGAV +ATTEDGSAPEGATIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGEAAQ +KMA +>PROKKA_01621 +MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPYAERLITFAKKGDL +PARRKVQGLIAAKNRTNKAVVHELFTVIGPAMAERNGGYTRITKIGNRHGDNAPMAVIEL +IMDPISGKQAVVREAEQAAASAPAAPAESTPVEAVDPAATEEVTVAESQETAAEIDGAVP +TTEDGSAPAEATIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGEAAQK +MA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001367.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001367.fa new file mode 100644 index 0000000000000000000000000000000000000000..1e4104508292a5b2ab476c3e4a6e6524118c05f2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001367.fa @@ -0,0 +1,20 @@ +>PROKKA_01694 +MPPKTRASAARKPRRKANKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS +RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP +MAHNGARPAKRRRV +>PROKKA_01401 +MPPKTRASAARKPRRKANKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS +RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP +MAHNGARPAKRRRV +>PROKKA_01184 +MPPKTRASAARKPRRKDKKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS +RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP +MAHNGARPAKRRRV +>PROKKA_01114 +MPPKTRSAVRKPRRKDKKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGSR +KSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTPQ +AHNGARPAKRRRV +>PROKKA_01623 +MPPKTRASAARKPRRKANKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS +RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP +MAHNGARPAKRRRV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001370.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001370.fa new file mode 100644 index 0000000000000000000000000000000000000000..a16678e2bd386d28c8f5ca7dcaa7aad7d5683bde --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001370.fa @@ -0,0 +1,15 @@ +>PROKKA_01697 +MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV +VVELSPYDLNRGRIVYRYK +>PROKKA_01404 +MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV +VVELSPYDLNRGRIVYRYK +>PROKKA_01181 +MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV +VVELSPYDLNRGRIVYRYK +>PROKKA_01111 +MAKKEGVIEVEGTVTEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRVVVELSP +YDLNRGRIVYRYK +>PROKKA_01626 +MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV +VVELSPYDLNRGRIVYRYK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001371.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001371.fa new file mode 100644 index 0000000000000000000000000000000000000000..9eccdc859de49f31b1dcab7cf79d9de536936e67 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001371.fa @@ -0,0 +1,30 @@ +>PROKKA_01698 +MIGRRSLELKTAPQLQAMQRAGVVLSEALDATLAAAAPGVTTAELDAVFAGVLAERGATS +NFLGYYDFPASICTSVNDEVVHGIPGDRVLQTGDVLKVDGGAIVDGWHADSARTVILGSS +EAGTAGPADERLSAITREALWVGIAAFASATHVGDIGDAIDDFVSAQPGEELGILEEYVG +HGIGSAMHLPPDVFNYRTGHRGPKIRPGLALAIEPMLVRGSIDTKVLADDWTVVTLDGAR +ASQWEHSVCRHDGGVWVLTAPDGGASELARFGVVPVPPGE +>PROKKA_01405 +MIGRRSLELKTAPQLQAMQRAGVVLSEALDATLTAAAPGVTTAELDAVFAGVLAERGATS +NFLGYYDFPASICTSVNDEVVHGIPGDRVLQTGDVLKVDGGAIVDGWHADSARTVILGSS +AAGTADPADERLSAITREALWVGIAAFASATHVGDIGDAIDDFVSAQPGEELGILEEYVG +HGIGSAMHLPPDVFNYRTGHRGPKIRPGLALAIEPMLVRGSIDTKVLADDWTVVTLDGAR +ASQWEHSVCRHDGGVWVLTAPDGGASELARFGVVPVPPGE +>PROKKA_01180 +MVGRRSLELKTTPQLQTMRRAGVVLSEALDATLAAAAPGVTTAELDAVFAGVLAEHGATS +NFLGYYDFPATICASVNEEVVHGIPGDRVLQAGDVLKVDGGAIVDGWHADSARTLVLGSS +EAGTADEGDERLSAITREALWVGIAAFATAKHVGDIGDAIDDFVSAQPGEPLGILEEYVG +HGIGSSMHMPPDVFNYRTGHRGPKVRPGLALAVEPMLVRGGIETRVLEDDWTVVTVDGAR +ASQWEHSVCRHAGGLWVLTAPDGGASELERFGVVPVPPGE +>PROKKA_01110 +MFSRRSIELKTTPQLQTMQRAGVVLSEALDAAVAAAAPGVTTAEVDAVFADVLAQHGATS +NFLGYYGYPATVCASVNEEVVHGIPGERVLQQGDVLKIDGGAIVDGWHSDSARTLILGSS +EAGTADPEDERLSEITRQALWVGIAAFAQARHVGEIGDAVDDFVTSQPGAPLGILEDYVG +HGIGSAMHLAPDVFNYRTGHRGPKVQHGMALAIEPMLVRGGIETRTLEDEWTVVTTDGAR +ASQWEHTVCRHPGGVWVLTAPDGGAAELAAHGVVPVPPGE +>PROKKA_01627 +MIGRRSLELKTAPQLQAMQHAGVVLSEALDATLTAAAPGVTTAELDAVFAGVLAERGATS +NFLGYYDFPASICTSVNDEVVHGIPGDRVLQTGDVLKVDGGAIVDGWHADSARTVILGSS +AAGTADPADERLSAITREALWVGIAAFASATHVGDIGDAIDDFVTAQPGEELGILEEYVG +HGIGSAMHLPPDVFNYRTGHRGPKIRPGLALAIEPMLVRGSIDTKVLADDWTVVTLDGAR +ASQWEHSVCRHDGGVWVLTAPDGGASELARFGVVPVPPGE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001372.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001372.fa new file mode 100644 index 0000000000000000000000000000000000000000..e9fe1e5763888729b791469a79ff29859633ff5c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001372.fa @@ -0,0 +1,25 @@ +>PROKKA_01699 +MTRMLLMGPPGSGKGTQATRIADKLGIVPISTGDIFRHNVKSMTPLGVEAKKYIDNGDFV +PDEVTNRMVADRIAQADAEHGFLLDGYPRTKGQVEALDAMLAEAGLSLSAVVELEVPDEE +LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETESVIQEYVERGIVARVDGTGQIDDVTE +RLLQAVYSVRAATGSLPVIQPGAES +>PROKKA_01406 +MTRMLLMGPPGSGKGTQAARIADKLGIVPISTGDIFRHNVKSMTPLGVEAKKYIDNGDFV +PDEVTNRMVADRIAQADAEHGFLLDGYPRTKGQVEALDAMLAESGQSLSAVVELEVPDEE +LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETESVIQEYVERGIVARVDGTGQIDDVTE +RLLQAVYSVRAATGSLPVIQPGAES +>PROKKA_01179 +MTRMLLMGPPGSGKGTQATRIADKLGIVAISTGDIFRHNVKSMTPLGVEAKKYIDNGDFV +PDDVTNRMVADRIAQPDAEHGFLLDGYPRTKGQVEALDAMLTEAGLALSAVVELEVPDAE +LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETEAVIQEYVERGIVARVDGTGQIDDVTE +RLLQSVYAVRAATGSLPVIAPDTES +>PROKKA_01109 +MTRMLLMGPPGSGKGTQATRIADKLGIVAVSTGDIFRHNVKNMTELGKEAKRYMDAGDFV +PDEVTNRMVADRLSQSDAETGFLLDGYPRTAGQVDALDAMLKDTGQALSAVVELEVPDAE +LVARLLKRAEIEGRADDTEEVIQHRLDLYHRETESVIESYAERGIVARVDGTGQIDDVTE +RVLQSVYSVRAATGTLPIITPDTQA +>PROKKA_01628 +MTRMLLMGPPGSGKGTQAARIADKLGIVPISTGDIFRHNVKSMTPLGVEAKRYIDNGDFV +PDEVTNRMVADRIAQADAEHGFLLDGYPRTKGQVEALDAMLAEAGQSLSAVVELEVPDEE +LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETESVIQEYVERGIVARVDGTGQIDDVTE +RLLQAVYSVRAATGSLPVIQPGAES diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001380.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001380.fa new file mode 100644 index 0000000000000000000000000000000000000000..712074d7de3e1c0c5a6173913c284e594c6d1c03 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001380.fa @@ -0,0 +1,25 @@ +>PROKKA_01707 +MTEVQQTEKVTPRLKTKYRDEIRGALQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII +DGAVADLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR +IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL +KALGFPFKTDQ +>PROKKA_01414 +MTEVQQTEKVTPRLKTKYRDEIRGALQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII +DGAVADLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR +IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL +KALGFPFKTDQ +>PROKKA_01171 +MTEVQQTEKVAPRLKTKYREEIRATLQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII +DGAVTDLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR +IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL +KALGFPFKTDQ +>PROKKA_01101 +MTEVQQTEKVTPRLKTKYREEIRASLQEQFEYANVMQVPGLVKVVVNMGVGEAAKDSKII +DGAIADLTAITGQKPMVTKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR +IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL +KALGFPFKTDK +>PROKKA_01636 +MTEVQQTEKVTPRLKTKYRDEIRGALQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII +DGAVADLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR +IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL +KALGFPFKTDQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001381.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001381.fa new file mode 100644 index 0000000000000000000000000000000000000000..3a2ac9d906e84af18262421bedf399d3b86359b4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001381.fa @@ -0,0 +1,15 @@ +>PROKKA_01708 +MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGL +QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKDGVSKTVKVRFAKASGKEL +>PROKKA_01415 +MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGL +QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKDGVSKTVKVRFAKASGKEL +>PROKKA_01170 +MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGR +QVAEAPIHISNVAVVDPETKKPTRVGYRFETVEKNGESKTVKVRFAKASGKEL +>PROKKA_01100 +MAKIKKDDLVQVLSGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQNNNGSTEGGL +QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKNGEQVTVKVRFAKASGKEL +>PROKKA_01637 +MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGL +QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKDGVSKTVKVRFAKASGKEL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001383.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001383.fa new file mode 100644 index 0000000000000000000000000000000000000000..772a4102cb7dcd24531bc1430821c91e13057820 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001383.fa @@ -0,0 +1,15 @@ +>PROKKA_01710 +MTEQTPAVSEERGYRKALRGIVVSDKMDKTIVVEVEDRKKHSLYGKVLKTSKRVKAHDED +NTAGVGDRVRLAETRPLSASKRWRLVEIVERAK +>PROKKA_01417 +MTEQTPAVSEERGYRKALRGIVVSDKMDKTIVVEVEDRKKHSLYGKVLKTSKRVKAHDED +NTAGVGDRVRLAETRPLSASKRWRLVEIVERAK +>PROKKA_01168 +MTEQTPAVSEERGYRKALRGVVVSDKMDKTIVVEVEDRKKHSLYGKVMKTSKRVKAHDED +NTAGIGDRVRIAETRPLSASKRWRLVEIVERAK +>PROKKA_01098 +MTEQTAAPVEERNYRKSLRGVVVSDKMDKTIVVEVEDRKKHALYGKVMKTSKRVKAHDED +NTAGVGDRVLIVETRPLSADKHFRLVEIVERAK +>PROKKA_01639 +MTEQTPAVSEERGYRKALRGIVVSDKMDKTIVVEVEDRKKHSLYGKVLKTSKRVKAHDED +NTAGVGDRVRLAETRPLSASKRWRLVEIVERAK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001385.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001385.fa new file mode 100644 index 0000000000000000000000000000000000000000..7f1fb1cd25ded07c5fdaafbbcbd670f13657517d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001385.fa @@ -0,0 +1,20 @@ +>PROKKA_01712 +MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR +GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVTEDVAREALRL +AIHKLPLKARIIRREGGE +>PROKKA_01419 +MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR +GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVTEDVAREALRL +AIHKLPLKARIIRREGGE +>PROKKA_01166 +MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR +GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVSEEVAREALRL +AIHKLPLKARVIRREGGE +>PROKKA_01096 +MLIPRRVKHRKQHHPKRSGMAKGGTTVTFGEWGIQALSPAYVTNRQIEAARIAMTRYIKR +GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVSEEVAREALRL +AIHKLPLKARIIRREGGE +>PROKKA_01641 +MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR +GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVTEDVAREALRL +AIHKLPLKARIIRREGGE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001390.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001390.fa new file mode 100644 index 0000000000000000000000000000000000000000..ffa3edf05b8e2bd9b16caa51c894da015d3366a3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001390.fa @@ -0,0 +1,15 @@ +>PROKKA_01717 +MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKSEIKQAVERIFNVDVASVN +TLNRSGKRRRTRFGWGQRKSTKRAIVTLKDGTIDIFGGPLA +>PROKKA_01424 +MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKSEIKQAVERIFNVDVASVN +TLNRSGKRRRTRFGWGQRKSTKRAIVTLKDGTIDIFGGPLA +>PROKKA_01161 +MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKSEIKQAVERIFNVDVASVN +TLNRSGKRRRTRFGWGQRKSTKRAIVTLKDGTIDIFGGPLA +>PROKKA_01091 +MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKTEIKQAIERIFDVSVASVN +TLNRPGKRRRTRFGWGQRKSTKRAIVSLKDGATIDIFGGPLAS +>PROKKA_01646 +MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKSEIKQAVERIFNVDVASVN +TLNRSGKRRRTRFGWGQRKSTKRAIVTLKDGTIDIFGGPLA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001391.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001391.fa new file mode 100644 index 0000000000000000000000000000000000000000..4bc5b1923837cc5b19a41480884ff77a6b07d1cf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001391.fa @@ -0,0 +1,25 @@ +>PROKKA_01718 +MAENSVKTVQVDLPAELFDVQSNVPLMHQVVVAQLAAARQGTHKTKRRGEVSGAGRKPFK +QKGTGRARQGSIRAPHMTGGGVVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI +EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY +DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ +>PROKKA_01425 +MAENSVKTVQVDLPAELFDVQSNVPLMHQVVVAQLAAARQGTHKTKRRGEVSGAGRKPFK +QKGTGRARQGSIRAPHMTGGGVVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI +EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY +DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ +>PROKKA_01160 +MAENSVKTVQVDLPAEIFDVQSNVPLMHQVVVAQLAAARQGTHKVKRRGEVSGAGRKPFK +QKGTGRARQGSIRAPHMTGGGIVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI +EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY +DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ +>PROKKA_01090 +MAENTVKTVQVELPAEIFDVQANVPLMHQVVVAQLAAARQGTHKVKRRGEVSGAGRKPFK +QKGTGRARQGSIRAPHMTGGGIVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI +EALVSGTTPSTKAAKAGLESLNTGRKNVLLVIDRADDLTALSARNLPAVHTLYADQLNTY +DVLVSDDVVFTKVAYEAYVAQASGAKKEDAQ +>PROKKA_01647 +MAENSVKTVQVDLPAELFDVQSNVPLMHQVVVAQLAAARQGTHKTKRRGEVSGAGRKPFK +QKGTGRARQGSIRAPHMTGGGVVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI +EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY +DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001393.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001393.fa new file mode 100644 index 0000000000000000000000000000000000000000..3547e3bd65debb5f6905aba6f0826a2a01dbf102 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001393.fa @@ -0,0 +1,15 @@ +>PROKKA_01720 +MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD +SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL +>PROKKA_01427 +MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD +SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL +>PROKKA_01158 +MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD +SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL +>PROKKA_01088 +MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD +SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL +>PROKKA_01649 +MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD +SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001395.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001395.fa new file mode 100644 index 0000000000000000000000000000000000000000..b3b0deab07e4a4aaa4d6467cb6479d21689582db --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001395.fa @@ -0,0 +1,10 @@ +>PROKKA_01722 +MSDDGAAAAARLGSMPELILLIAVLAVVVVAVRWALRTFRPEIDRARRIRRANRGGELER +>PROKKA_01429 +MSDDGAAAAARLGSMPELLILIVVLAVAVVAVRWALRTFRPEIDRARRIRRANRGGELER +>PROKKA_01156 +MPELLITLLVLAAAVVAVVWALRTFRPEIDRARRIRRANRNGELRR +>PROKKA_01086 +MEWLIALVVIAAVVAGGLWARRAFAPEIERARRIRRAERGGRLER +>PROKKA_01651 +MSDDGAAAAARLGSMPELILLIAVLAVVVVAVRWALRTFRPEIDRARRIRRANRGGELER diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001396.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001396.fa new file mode 100644 index 0000000000000000000000000000000000000000..30bb7f5e4eedf73b10876053f3a26c8fecdac533 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001396.fa @@ -0,0 +1,40 @@ +>PROKKA_01723 +MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEARDFATIDSAPEERQ +RGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE +HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQDFDGDEAPVIRTSGLKA +LEGDAQWVKSVEDLMEAVDEFIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLK +INSEVEIVGIRDVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVEPGS +ITPHTNFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE +MSVELIQPIAMEEGLGFAIREGGRTVGSGRVTKITK +>PROKKA_01430 +MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEARDFATIDSAPEERQ +RGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE +HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQDFDGDEAPVIRTSGLKA +LEGDPQWVKSVEDLMEAVDEFIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLK +INSEVEIVGIRDVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVEPGS +ITPHTNFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE +MSVELIQPIAMEEGLGFAIREGGRTVGSGRVTKITK +>PROKKA_01155 +MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEARDFATIDSAPEERQ +RGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE +HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQEFDGDDAPVIRTSGLKA +LEGDAQWVKSVEDLMDAVDEYIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLA +INSEVEIVGIRDVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVAPGS +ITPHTNFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE +MTVELIQPIAMEEGLGFAIREGGRTVGSGRVTKITK +>PROKKA_01085 +MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEKRDFASIDSAPEERQ +RGITINISHVEYQTDKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE +HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQEFDGDEAPVIRTSGLKA +LEGDAQWVKSVEDLMDAVDEYIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLA +INSEVEIVGIRPVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVQPGS +ITPHTDFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE +MSVELIQPIAMEEGLGFAIREGGRTVGSGRVTKINK +>PROKKA_01652 +MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEARDFATIDSAPEERQ +RGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE +HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQDFDGDEAPVIRTSGLKA +LEGDAQWVKSVEDLMEAVDEFIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLK +INSEVEIVGIRDVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVEPGS +ITPHTNFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE +MSVELIQPIAMEEGLGFAIREGGRTVGSGRVTKITK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001400.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001400.fa new file mode 100644 index 0000000000000000000000000000000000000000..acd72c49fb718878efe2996e70beef4d3e7ba2a9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001400.fa @@ -0,0 +1,115 @@ +>PROKKA_01727 +MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC +ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL +APKDLEKVIYFAAYMITSVDEEARHRDLANLQAEYDQETRVLADQRDSDIAAVAADLEKD +LAKLESEGAKAAEKKKARDAADKTMAQIRKRADADLDRKEQVWDRFKNLKVADLEGDEGL +YRAMRDKYGQYFEGSMGAEAIQRRLQTFDLEAESEMLRETIKTGKGQRKTRALKRLKVVN +AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL +GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK +RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR +PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ +MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDEVGAGN +LYATVGEAIMAFDGGDLHLNAPARIGVEGFVPSADVPAPEGWSEGEIALIETTLGKVLFN +ELLPDDYPWLDKQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS +DITSDFDKAAIMEGYEEQAQRVQQQYDKGLIADDERRSELIDIWNKATDEVAAAMKDGLP +ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH +GARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTERGLSVTIAAPNADGELVAHE +QVENSAFARTLAQDVTGEDGTVLASAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT +CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ +ELFEARTPKGVAPISEVAGRVTIEDTETSVRLLLTPDDGSEEIAYPVLRRARILVADGEH +VPVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQSQGVGIHDKHVEVIVRQMLRR +ITVIESGDTDLLPGELTDRARFVAANRAAVAEGRQPASGRDELMGITKASLATDSWLSAA +SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFA +SPAGFADFDYPGLDQSLGENDFHAVSLDDYGRGGDFRA +>PROKKA_01434 +MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC +ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL +APKDLEKVIYFAAYMITSVDEEARHRDLANLQAEYDQETRVLADQRDSDIAAVAADLEKD +LAKLESEGAKAAEKKKARDAADKTMAQIRKRADADLDRKEQVWDRFKNLKVADLEGDEGL +YRAMRDKYGQYFEGSMGAEAIQRRLQTFDLEAESEMLRETIKTGKGQRKTRALKRLKVVN +AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL +GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK +RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR +PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ +MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDEVGAGN +LYATVGEAIMAFDGGDLHLNAPARIGVEGFVPSADVPAPEGWSEGEIALIETTLGKVLFN +ELLPDDYPWLDKQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS +DITSDFDKAAIMEGYEEQAQRVQQQYDKGLIADDERRSELIDIWNKATDEVAAAMKDGLP +ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH +GARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTERGLSVTIAAPNADGELVAHE +QVENSAFARTLAQDVTGEDGTVLASAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT +CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ +ELFEARTPKGVAPISEVAGRVTIEDTEASVRLLLTPDDGSEEIAYPVLRRARILVADGEH +VPVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQSQGVGIHDKHVEVIVRQMLRR +ITVIESGDTDLLPGELTDRARFVAANRAAVAEGRQPASGRDELMGITKASLATDSWLSAA +SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFA +SPAGFADFDYPGLDQSLGENDFHAVSLDDYDRGGDFRA +>PROKKA_01151 +MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC +ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL +APKDLEKVIYFAAYMITSVDEEGRHRDLANLQAEYDQETRVLADQRDADIAAVAADLEKD +LAKLESEGAKAAEKKKARDAADKTMSQIRKRADAELDRKEQVWDRFKNLKVADLEGDEGL +YRTMRDKYGQYFEGSMGAEAIQRRLQTFDLAAESEMLRETIKTGKGQRKTRALKRLKVVN +AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL +GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK +RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR +PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ +MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDAVGAGN +AYATVGEAVMAFDGGDLHLNAPVKIGVDGFVPSTAVPAPEGWSEGELAVIETTLGKVLFN +ELLPADYPWLDTQATKGSLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS +DITSDFDKAAIMEGYEEQALRVQQQYEKGLIADDERRSELIDIWNKATDEVAAAMKDGLP +ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH +GARKGLADTALKTANSGYLTRRLVDVSQDVIVREEDCGTERGLSVTIAVPNADGELVAHE +QVENSAFARTLAQDVTGEDGSVLASGGADVGDVLIDQLVGAGVSEIKVRSVLTCESAVGT +CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ +ELFEARTPKGVAPISEVAGRVTIEDTDASVRLLLTPDDGSEEIAYPVLRRARILVADGEH +VAVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQSQGVGIHDKHVEVIVRQMLRR +ITVIESGETDLLPGELTDRARFVAANRSAVAEGRQPASGRDELMGITKASLATDSWLSAA +SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFA +SPAGFADFDYPGLDQQLGESDFHAVSLDDYGRGGDFRS +>PROKKA_01080 +MTTENPFGLMRIGLATADDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC +ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL +APKDLEKVIYFAAYMITSVDEEARHRDLPNLQAEHDQETRVLEDQRDADIAAVAADLEKD +LAKLEAEGAKAAEKKKARDAADKTMAQIRKRADAELDRKAQVWDRFKNLKVADLEGDEGL +YRAMRDKFGAYFEGSMGAEAIQRRLQTFDLAAESELLRETIKTGKGQRKTRALKRLKVVN +AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL +GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK +RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNVKSAKRMVERFR +PQVWDVLEEVISEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ +MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRAEGKGAGR +QFATVGEAVMAFDNGELHLNAPATIGVEGFVPSAAVAAPEGWTEGEVALIETTLGKVIFN +DLLPADYPWLDTQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS +DITSDFDKASIMQGYEDQAQRVQAQYDKGLIADDERRSELIDIWNKATDEVAAAMKAGLS +ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH +GARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTGRGLSVTIAEPNHDGELVVRE +QVENSAFARTLAQAVTAEDGTVLAEAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT +CAKCYGRSMATGKLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ +ELFEARTPKGVAPISEVAGRVTIEDTDASVRLILTPDDGSEEIAYPVLRRARLLVADGEH +VAVGTQLVAGAVDPKQVLRVLGPRAAQRFLVQEVQDVYQSQGVGIHDKHVEVIVRQMLRR +ITVIESGETDLLPGELTDRSRFVAANRAAVAEGKQPAAGRDELMGITKASLATDSWLSAA +SFQETTRVLTQAAMEGKEDPLLGLKENVIIGKLIPAGTGLDRYTQTTVEPTEEAKANLFA +APVGFADFDYPGLDQPLGEAEFHAVSLDDYGRGGDFRA +>PROKKA_01656 +MSTDNSFGLMRIGLATAEDIRRWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWEC +ACGKYKRVRFKGIICERCGVEVTRSKVRRDRMGHIELAAPVTHIWYFKGVPSRLGYLLDL +APKDLEKVIYFAAYMITSVDEEARHRDLANLQAEYDQETRVLADQRDSDIAAVAADLEKD +LAKLESEGAKAAEKKKARDAADKTMAQIRKRADADLDRKEQVWDRFKNLKVADLEGDEGL +YRAMRDKYGQYFEGSMGAEAIQRRLQTFDLEAESEMLRETIKTGKGQRKTRALKRLKVVN +AFLTTDNSPEGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDL +GAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGK +RVDYSGRSVIVVGPQLKLHQCGLPKQMALELFKPFVMKRLVDLNHAQNIKSAKRMVERFR +PQVWDVLEEVITEHPVLLNRAPTLHRLGIQAFEPQLVEGKALQLHPLVCSAFNADFDGDQ +MAVHLPLSPEAQAEARLLMLSSHNILKPSDGRAVAVPAQDMIIGLNHLTTVRPDEVGAGN +LYATVGEAIMAFDGGDLHLNAPARIGVEGFVPSADVPAPEGWSEGEIALIETTLGKVLFN +ELLPDDYPWLDKQATKGTLGQLVNDLAERYPMVVTAQTLDNLKDAGFHWGTWSGVTVAIS +DITSDFDKAAIMEGYEEQAQRVQQQYDKGLIADDERRSELIDIWNKATDEVAAAMKDGLP +ELNTINRMVSSGARGNWLQVRQIAGIRGLVANPKGEIIPRPIKSSYREGLSVLEYFSATH +GARKGLADTALKTANSGYLTRRLVDVSQDVIVREDDCGTERGLSVTIAAPNADGELVAHE +QVENSAFARTLAQDVTGEDGTVLASAGADVGDVLIGELVAAGVTEIKVRSVLTCESAVGT +CAKCYGRSMATGQLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVASADDITQGLPRIQ +ELFEARTPKGVAPISEVAGRVTIEDTETSVRLLLTPDDGSEEIAYPVLRRARILVADGEH +VPVGTQLVAGAVDPKQVLRVLGPRAAQRFLVDEVQNVYQSQGVGIHDKHVEVIVRQMLRR +ITVIESGDTDLLPGELTDRARFVAANRAAVAEGRQPASGRDELMGITKASLATDSWLSAA +SFQETTRVLTQAAMEGKSDPLLGLKENVIIGKLIPAGTGLDRYTKTVVEPTEEAKANLFA +SPAGFADFDYPGLDQSLGENDFHAVSLDDYGRGGDFRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001402.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001402.fa new file mode 100644 index 0000000000000000000000000000000000000000..00b7dc83466a09790ace4b8ca4dfff53830737ca --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001402.fa @@ -0,0 +1,20 @@ +>PROKKA_01729 +MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAGGAAGGAEAAAAEEK +DEFDVVLEAAGDKKIGVIKEVRAITSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE +GAGATVTLK +>PROKKA_01436 +MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAGGAAGGAEAAAAEEK +DEFDVVLEAAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE +GAGATVTLK +>PROKKA_01149 +MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAAGAAGGDAAAAEEKD +EFDVVLESAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLEG +AGATVTLK +>PROKKA_01078 +MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAMAAAGAPAGGDAAAAEEKD +EFDVILEAAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLEG +AGATVTLK +>PROKKA_01658 +MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAGGAAGGAEAAAAEEK +DEFDVVLEAAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE +GAGATVTLK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001403.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001403.fa new file mode 100644 index 0000000000000000000000000000000000000000..af0646621ad58b3137b0deb5478dc44023c484b7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001403.fa @@ -0,0 +1,20 @@ +>PROKKA_01730 +MATSAKESAVAELTDLFRESSAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA +AKDAGLEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI +KQLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAAQGEAA +>PROKKA_01437 +MATSAKESAVAELTDLFRESSAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA +AKDAGLEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI +KKLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAAQGEAA +>PROKKA_01148 +MATSAKESAVAELTDLFRESNAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA +AKEAGVEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI +KKIADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAQQGEAA +>PROKKA_01077 +MATSAKESAVAELTDLFRSSSAAVLTEYRGLTVSELKQLRDSIRQDATYSVAKNTLTEIA +AKEAGVEGLDAHLAGPTAIAFVTGDPVTVAKALRDFAKDHDKLVLKGGYMDGQPLDEAGI +EKLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTARTVEALRAQQDQAA +>PROKKA_01659 +MATSAKESAVAELTDLFRESSAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA +AKDAGLEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI +KKLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAAQGEAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001405.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001405.fa new file mode 100644 index 0000000000000000000000000000000000000000..60b6bc58541d8ac8a48cbecc5f8efff39e4fd565 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001405.fa @@ -0,0 +1,20 @@ +>PROKKA_01732 +MAPKKKVTGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI +TVYEDRSFTFVTKTPPAAELIKKAAGVAKGSATPHTAKVGTLTQAQCEEIAQTKMEDLNA +NDVQAAAKIIAGTARSMGITVEG +>PROKKA_01439 +MAPKKKVTGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI +TVYEDRSFTFVTKTPPAAELIKKAAGVAKGSATPHTAKVGTLTQAQCEEIAQTKMEDLNA +NDVQAAAKIIAGTARSMGITVEG +>PROKKA_01146 +MAPKKKVSGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI +TVYEDRSFTFITKTPPAAELIKKAAGVAKGSATPHTAKVGKLTQAQCEEIAQTKMEDLNA +NDVKAAAKIIAGTARSMGITVEG +>PROKKA_01075 +MAPKKKVAGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATEAQRGNVIPVEI +TVYEDRSFTFITKTPPAVELIKKAAGVQKGSSTPHTAKVGTLTQAQCEEIAQSKMEDLNA +NDVKAAAKIIAGTARSMGITVEG +>PROKKA_01661 +MAPKKKVTGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI +TVYEDRSFTFVTKTPPAAELIKKAAGVAKGSATPHTAKVGTLTQAQCEEIAQTKMEDLNA +NDVQAAAKIIAGTARSMGITVEG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001406.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001406.fa new file mode 100644 index 0000000000000000000000000000000000000000..4a34ee9404b84bc76525735e9129c0b588f90048 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001406.fa @@ -0,0 +1,30 @@ +>PROKKA_01733 +MSEQELDRQPAEESVPMSEDAVAEETAETAQDAGTPVEDALDEVAGSGDETAEATVQEAD +LAVAEGEDAPTPVEEQSDDEPAVDPAEELRTRLRRQPGDWYVVHTYAGYEKRVKTNLEAR +ILTQDMEDSIYEIEVPMEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTPGV +TGFVGNDAHHPQPLSLDEVYDMLAPSVIQEAARAAEKAGLAVPAAAESGAPAAPAIHVDF +EVGESVTVNDGPFETLPATISEIKPEAQQLVVLVSIFERETPVTLSFNQVTKAI +>PROKKA_01440 +MSEDAVAEETAETAQDAGTPVEDALDEAAGSGDETAEATVQEADLAVAEGEDAPTPVEEQ +ADDEPAVDPAEELRTRLRRQPGDWYVVHTYAGYEKRVKTNLEARILTQDMEDSIYEIEVP +MEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTPGVTGFVGNDAHHPQPLSL +DEVYDMLAPSVIQEAARAAEKAGLAVPALVESGAPAAPAIHVDFEVGESVTVNDGPFETL +PATISEIKPEAQQLVVLVSIFERETPVTLSFNQVTKAI +>PROKKA_01145 +MSEQELDRQAAEESVSVQEDGAVEETVETAQDAPAPAEDAAGETAVDGEEAAEATEATAQ +EADPAAVEQAEEEPAVDPGEELRTRLRRQPGDWYVVHTYAGYEKRVKTNLEARILSQDME +DAIYEIEVPMEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTPGVTGFVGND +AHHPQPLSLDEVYDMLAPSVIQEAARAAEKAGLAVPASAESGAAAAPAIHVDFEVGESVT +VNDGPFETLPATISEIKPEAQQLVVLVSIFERETPVTLSFNQVTKVI +>PROKKA_01074 +MSEQELDRQDVEETAVAEDSTALEAPVEDTAAEEAEQTVQEADLAIAEGDQDAAEAPSAE +ELDAAGQAPAQPDVEAAEQLRTRLRRQPGDWYVVHTYAGYEKRVKTNLEARIQTQDMEDS +IYEIEVPMEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTSGVTGFVGNDAH +HPQPLTLDEVYDMLAPSVVQEAVREAEKAGLVPVAVAESGAAGAPAIHVDFEVGESVTVD +DGPFETLPATISEIKPETQQLVVLVSIFERETPVTLSFNQVTKVI +>PROKKA_01662 +MSEDAVAEETAQDAGTPVEDALDEPAGSGDETAEATVQEADLAVAEGEDAPTPVEEQSDD +EPAVDPAEELRTRLRRQPGDWYVVHTYAGYEKRVKTNLEARILTQDMEDSIYEIEVPMEE +VVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTPGVTGFVGNDAHHPQPLSLDEV +YDMLAPSVIQEAARAAEKAGLAVPAAAESGAPAAPAIHVDFEVGESVTVNDGPFETLPAT +ISEIKPEAQQLVVLVSIFERETPVTLSFNQVTKAI diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001409.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001409.fa new file mode 100644 index 0000000000000000000000000000000000000000..978242491431eae56b74b6554851bb1a0746a416 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001409.fa @@ -0,0 +1,25 @@ +>PROKKA_01737 +MTDPAPRTAVNVDDHAIFRSGLRADLDPDRLAIVGEAGDVDEAVRAVLDLAPDVVLLDVH +LPGGAGGGGAEVAERVLARRPAQRFLALSVSDAAEDVVAVIRAGARGYITKTASGAEVAD +AAVRVADGDAVFSPRLAGFVLDAFRGTAPASPPVPAAATSGAAAPDEDLDRLSAREREVM +RLIARGYTYREAGAELFISDRTVETHVSSVLRKLQLSNRHELTRWAARRGYA +>PROKKA_01444 +MTDPAPRTAVIVDDHAIFRSGLRADLDPDRLAIVGEAGDVDEAVRTVLDLVPDVVLLDVH +LPGGAGGGGAEVAERVLARRPAQRFLALSVSDAAEDVVAVIRAGARGYITKTASGVEVAD +AAVRVADGDAVFSPRLAGFVLDAFRGTAPASPPVPAAATSGAAAPDEDLDRLSAREREVM +RLIARGYTYREAGAELFISDRTVETHVSSVLRKLQLSNRHELTRWAARRGYA +>PROKKA_01141 +MSVPAPRTAVIVDDHAIFRSGLRADLDPARLAIVGEAGDVDEAVRAVLELAPDVVLLDVH +LPGGAGGGGAEVAERVLARRPAQRFLALSVSDAAEDVVAVIRAGARGYITKTASGAEVVD +AAVRVAGGDAVFSPRLAGFVLDAFRGAAAPAAAPASPAVPDEDVDRLSAREREVMRLIAR +GYTYREAGAELFISDRTVETHVSSVLRKLQLSNRHELTRWAARRGYA +>PROKKA_01070 +MTVHADPVVPTAVVVDDHAIFRSGLRADLDASRLRIVGEAGDVDEAVRVVLQLAPDVVLL +DVHLPGGAGGGGAEVASRVLAERPGQRLLALSVSDAAEDVVAVIRAGARGYITKSAAGAE +VVEAALRVAGGDAVFSPRLAGFVLDAFRGLPTESAPAGPAPSEGDLDRLSAREREVMRLI +ARGYTYREAGAELFISDRTVESHVSSVLRKLQLSNRHELTRWAARHGWA +>PROKKA_01666 +MTDPAPRTAVIVDDHAIFRSGLRADLDPDRLAIVGEAGDVDEAVRTVLDLAPDVVLLDVH +LPGGAGGGGAEVAERVLARRPAQRFLALSVSDAAEDVVAVIRAGARGYITKTASGAEVAD +AAVRVADGDAVFSPRLAGFVLDAFRGTAPAPPLVPAAAASGAAAPDEDLDRLSAREREVM +RLIARGYTYREAGAELFISDRTVETHVSSVLRKLQLSNRHELTRWAARRGYA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001410.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001410.fa new file mode 100644 index 0000000000000000000000000000000000000000..5aa027f0ecdbba03b600de33ee069f1953f3bc08 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001410.fa @@ -0,0 +1,42 @@ +>PROKKA_01738 +MPTPSAPAPAPRPPLMRHGADRPVSGVAAGLARHLGMPAGRVRAALALLSLLGGAGLALY +VWLWLLVPEEGPDGAPAADAPTLRGRAPEVLERVREGGWPVLLAAVVLGVGVLTVADGLG +LAVDWALVGPVAVLVIGLGLAWMQLDLAGGPRAGRSGRLVRLVLGTALVLLAVLAIVLGA +VSSGELWRALLAAVAMLAGAALVAMPYVLAWLRRRDAERTAFAVQAQRAEIAAHLHDSVL +QSLALIQRRAQDADAVARVARAQERELRQFLALDSRGGPHSLAEALEQHAAAVEDAHGAR +VEVVAVGRAAGAWLEPLAAAAREAMQNAARHAGDAQVFAEAGEDDRGRTVAEVFVRDRGP +GFDLPTVPADRLGVRESILGRMGRAGGTARIRSGPGGTEVHLTLAEPEGARARTGQEHP +>PROKKA_01445 +MPTPSAPAQAPRPPLMRHGADRPVSGVAAGLARHLGVPVGRVRAALALLSLMGGAGLALY +VWLWLLMPEEGPDGAPAADAPTLRGRAPEVLERVREGGWPVLLAAVVLGVGVLTVADGLG +LAVDWALVGPVAVLVIGLGLAWMQLDLAGGPRAGRSGRLVRLVLGTALVLLAVLAIVLGA +VSSGELWRALLAAVAMLAGAALVAMPYVLAWLRRRDAERTAFAVQVQRAEIAAHLHDSVL +QSLALIQRRAHDADAVARVARAQERELRQFLALDSRGGPRSLAEALEEHAAAVEDAHGSR +VEVVAVGRAAGAWLEPLAAAAREAMQNAARHAGDAQVFAEAGEDDHGRTVAEVFVRDRGP +GFDLHTVPADRLGVRESILGRMERAGGAARIRSGPGGTEVHLTLTEPEGARARAGQEHP +>PROKKA_01140 +MPASAVPPSAPSGRAGPRRAAADDARTRPIGADPRTSEARASGTRAPLMRHRADRPVSGV +AAGAARHLGLSPRTARAGFAVLALAGGAGLALYVWLWLLMPEEGADGAPTGEAPSLRGRA +PEVLERVREGGWPVLLAAVVLGVGVITIADGLGLAVDWALVGPVAVLVIGLGLAWMQLDL +AGGPPAGRVGRVVRLALGTALVLLAVLAIVLGGVTSGDLWLGLLVAVALIAGVAMVAMPY +ALSWLRRRDAERTAFAVQAQRAEIAAHLHDSVLQSLALIQRRAHDPEAVARAARAQEREL +RRFLALDDRGGHDSLAATLREHAAAVEDAHGRRVEVVAVGEASGAWLEPLTAAAREAMLN +AARHAGDAQVFAEVAEDDDGRTVAEVFVRDRGPGFDPGAVPADRLGVRESVVGRMERAGG +AARIRSGPGGTEVHLTLTRPDRVPPHAAQERP +>PROKKA_01069 +MPAPAIPPPADLSARPALLRHAADRPVSGVAGGVARHLGLDPRLARAGFAVLALAGGAGI +ALYAWLWLLMPEEGPDGAPAGPAPTLRGRAPEVLERLREGGWPILLAVVVLGVGVLTVAD +GLGVPVDWALVGPVAVLVIGLGLAWMQLGAADGPEGGRWARRARLGLGTALVLLGVLAIV +VGAVTAGDLWLGLLVAVALLAGGALVAMPFVLARRRRRDEERTGAAVRAQRDEIAAHLHD +SVLQSLALIQRRADDPETVARVARAQERELRQFLALDSARAHGTLAEAVEDHAAAVEDAF +GRRVEVVSVGEASGPWLEPLASAAREAMVNAARHAGDVQVFVEVSEDDGGRTLAEVFIRD +RGTGFDLADVPADRLGVRESILGRMRRAGGTARIRSGPSGTEVQLSLADPGAPGVGLREG +RGRA +>PROKKA_01667 +MPTPSAPAPAPRPPLMRHGADRPVSGVAAGLARHLGMPAGRVRAALALLSLLGGAGLALY +VWLWLLMPEERPDGAPAADAPTLRGRAPEVLERVREGGWPVLLAAVVLGVGVLTVADGLG +LAVDWALVGPVAVLVIGLGLAWMQLDLAGGSRAGRSGRLVRLVLGTALVLLAVLAIVLGA +VSSGELWRALLAAVAMLAGAALVAMPYVLAWLRRRDAERTAFAVQAQRAEIAAHLHDSVL +QSLALIQRRAQDADAVARVARAQERELRQFLALDSRGGPHSLAEALEQHAAAVEDAHGAR +VEVVAVGRAAGAWLEPLAAAAREAMQNAVRHAGDAQVFAEAGEDERGRTVAEVFVRDRGP +GFDLHTVPADRLGVRESIVGRMERAGGTARIRSGPGGTEVHLTLTEPEGARARTGQEHP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001415.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001415.fa new file mode 100644 index 0000000000000000000000000000000000000000..75c630abddd737d79c4bdb5df13c13f1f3fd5cdf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001415.fa @@ -0,0 +1,25 @@ +>PROKKA_01743 +MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSAGTEIFYQRVDFTEHGLPFVEYRAESW +LCEADGTLLRPLTVESGFWQVDRARRDGDVGPGMRPADIVPAFRSAEDVERLRAGDEGFG +LTATITHPGSLSELYYGRIKGPQLQLATDAVLRGSAAGPYHRATRMAGLVNGQLFWRWDV +ADAAGAELEAHASAILDRMPSAAEGRLAPGAERPRGARGEQS +>PROKKA_01450 +MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSAGTEIFYQRVDFTEHGLPFVEYRAESW +LCEADGTLLRPLTVESGFWQVDRARRDGDVGPGMRPADIVPAFRSAEDVERLRAGDEGFG +LTATITHPGSLSELYYGRIKGPQLQLATDAVLRGSAAGPYHRATRMAGLVNGQLFWRWDV +ADAAGAELEAHASAILDRMPSAAEGRLAPGAERPRGARGEQS +>PROKKA_01134 +MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSDGTEIFYQRVDFTEHGLPFVEYRAESW +LCEADGTLLRPLTVESGFWQVDRERRDGDVGPGMRPADIVPAFRSAEDVESLRAGDEGFG +ITATITHPGSLAELYYGRIKGPQLQLVTDAVLRGSAAGDYHRATRMAGLVNGQLFWRWDS +SGSEGAELEAHASAILDRMPSESEGRLAPGAPRPRGAGGAEPGERP +>PROKKA_01063 +MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSEGTDIFYQRVDFVEHGLPFVEYRAESW +LCEADGTLLRPLTVESGFWQVDRARQDGDVGPGMVPADIVPAYRSAEDVEALRSEDGAFR +ITATITHPGSLAELYYGRIKGPQVQIVMDSLLRGAAAGEYARATRMAGLVNGQLFWRWDS +SPAVEGPMEVHASAILDRMPDPSEGRLAPGAPRPRGERGRAPEQGA +>PROKKA_01672 +MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSAGTEIFYQRVDFTEHGLPFVEYRAESW +LCEADGTLLRPLTVESGFWQVDRARRDGDVGPGMRPADIVPAFRSAEDVERLRAGDEGFG +LTATITHPGSLSELYYGRIKGPQLQLATDAVLRGSAAGPYHRATRMAGLVNGQLFWRWDV +ADAAGAELEAHASAILDRMPSAAEGRLAPGAERPRGARGEQS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001416.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001416.fa new file mode 100644 index 0000000000000000000000000000000000000000..a10dca7635c0b783a964a23aa6729a2665f0493e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001416.fa @@ -0,0 +1,10 @@ +>PROKKA_01744 +MDTLLALEIFFLALVVLAGLGMAAVAAVVISGLFKGQR +>PROKKA_01451 +MDTLLALEIFFLALVVLAGLGMAAVAAVVISGLFKGQR +>PROKKA_01133 +MDTLLALEIFFLALVVLAGLGMAAVAAVVVGGLFKGQR +>PROKKA_01062 +MDSIVALEIFFLVLVVLAGLGMAAVAALVVGGLFKGQR +>PROKKA_01673 +MDTLLALEIFFLALVVLAGLGMAAVAAVVISGLFKGQR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001417.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001417.fa new file mode 100644 index 0000000000000000000000000000000000000000..93590f7d83c55e45621a11dfdf923a6a0be11d30 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001417.fa @@ -0,0 +1,30 @@ +>PROKKA_01745 +MAREVRPAVARPGPSRCAPGRMGQVMRLSMALSAAVAALVLGGAALLGPVPAALAAAVVI +LVIAWGWPRQMGAPARLSLSVTLAVAGGAAVLLMLLWPPLEDGHSGAWTLFEPLAVVVAW +STMASFVVQLVRGTGRPLRLESTVATMGGAFMAVVTACWVAVSRWTDTPAVAGLVITLAV +TVAAVSLVGLTPWMQGRPGVLALVVIPLGTVLAWPVSALAGVGARDRPAVTAAALAVAVL +VSLTAATAPSSRPRPEDRPVGTTLRPRRAGYALALAPVGAAGVVAHVMVGFLA +>PROKKA_01452 +MAREVRPAVARPGPSRCAPGRMGQVMRLSMALSAAVAALVLGGAALLGPVPAALAAAVVI +LVIAWGWPRQMGAPARLSLSVTLAVAGGAAVLLMLLWPPLEDGHSGAWTLFEPLAVVVAW +STMASFVVQLVRGTGRPLRLESTVATMGGAFMAVVTACWVAVSRWTDTPAVAGLVITLAV +TVAAVSLVGLTPWMQGRPGVLALVVIPLGTVLAWPVSALAGVGARDRPAVTAAALAVAVL +VSLTAATAPSSRPRPEDRPVGTTLRPRRAGYALALAPVGAAGVVAHVMVGFLA +>PROKKA_01132 +MMRLSMALSAAVAALVLGGATLLGPVPAAVAAMAVILVIAWGWPRQMGAPARLSLSVTLA +AVGLVAVLLMLLWPPIEDGRSGAWTLFEPLAVALAWSTMASFVVQLVRGTGRPLRLESTV +ATMGGGLIAVMTACWVAVSRWTDAPAVAGLVLTLAISVAAFSLIGLIPGVQGRPGVLALV +VVPLGALLAWPVSALLGVGPQDRAAVVAAVVAVATLVSLTAATAPSARPRPEDRPVGTTL +RPRRAGYALALAPVGAAGVVAHVMVGFLA +>PROKKA_01061 +MMRLSMALSAALAALVLGGAALLGPVPAAVAACLVIAVIAFGWPRQMGAPARLSLTLTML +VAGVLGVLVMVLWPRGDAGPRGAWALFEPLAVVLAFGTMASFIVQLVRGTGRPLRLESTV +TTMGGVLVCLLAASWVPLAHHREAPGATGLVVTLAATLIVTSLIGLTPFMQGRPRVLALV +MVPASGVVAALVSLLLGAPAHTAWVYAAAALGTAGLVSLTAAAAPSSRPLPEDRVVGTTL +SPRRAGYALAMAPVGAAGVVGHVMLGFLA +>PROKKA_01674 +MMRLSMALSAAVAALVLGGAALLGPVPAALAAAVVILVIAWGWPRQMGAPARLSLSVTLA +VAGGIAVLLMLLWPPLEDGHSGAWTLFEPLAVVVAWSTMASFVVQLVRGTGRPLRLESTV +ATMGGAFMAVVTACWVAVSRWSDTPAVAGLVITLAVTVAAVSLVGLTPWMQGRPGVLALV +VIPLGTVLAWPVSALAGVGARDRPAVTAAALAVAVLVSLTAATAPSSRPRPEDRPVGTTL +RPRRAGYALALAPVGAAGVVAHVMVGFLA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001419.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001419.fa new file mode 100644 index 0000000000000000000000000000000000000000..eac076c1730f01b5b5f2ef91e0f5271b29a7339a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001419.fa @@ -0,0 +1,35 @@ +>PROKKA_01747 +MPSSHADRVARWSTEDRVSEGPRAEVLAAGMLPWRRVPGGLEVMVIHRPRYDDWSWPKGK +LDPGETLPECAVRELREEVGLELRPGIPLCVTAYEVPGKRGARQSKEVWYWAAEVDGQRA +LPDGDEVDEVRWVGPDEARRLLTNDSDHEPLDLLLRAASRGRLRTVPLLVLRHAKAKPRS +SWSRAEQERPLAATGRRQALAVEGLVSAWRPERLVSSPWRRCVETLAPLVKSSRLALKTK +GAFTETTAREKPQKTRKVMAELMGRSRPLVVCTHRPVLPTLFEVVEDAAAGRTDRVLRAL +PTEDPWLRPGAVLVAHRALDLDGDVVAVEVYDPWDD +>PROKKA_01454 +MPSSHADRVARWSTEDRVSEGPRAEVLAAGMLPWRRVPGGLEVMVIHRPRYDDWSWPKGK +LDPGETLPECAVRELREEVGLELRPGIPLCVTAYEVPGKRGARQSKEVWYWAAEVDGQRA +LPDGDEVDEVRWVGPDEARRLLTNDSDHEPLDLLLRAASRGRLRTVPLLVLRHAKAKPRS +SWSRAEQERPLAATGRRQALAVEGLVSAWRPERLVSSPWRRCVETLAPLVKSSRLALKTK +GAFTETTAREKPQKTRKVMAELMGRSRPLVVCTHRPVLPTLFEVVEDAAAGRTDRVLRAL +PTEDPWLRPGAVLVAHRALDLDGDVVAVEVYDPWDD +>PROKKA_01130 +MPSTPTERVARWSTEDRAADGPRAEVLAAGVVPWRRTPGGRLEVLVIHRPRYDDWSWPKG +KLDPGETLPQCAVRELREEVGLALRPGIPLCVTEYEVSGKRGARLTKEVWYWAADAGAQR +AVPDGDEVDEVRWVRPEEAEALLTNETDREPLELLVRADSRGRLRTLPLLVLRHAKAKPR +SSWSRAEQERPLAATGRRQALAVEGLVAAWAPDRLVSSPWRRCVETLAPLVKSSRLPLKT +KGAFTETAAKEKPKKTRKAMHELLGRQRAQVVCTHRPVLPVLFEVVEDAARRQERVLRAM +PREDPWLRPGAVLVVHRSLDGDVVAVEAYDPWDD +>PROKKA_01058 +MTRPLSWDGIPDPIPPEDPRTMSAHPDDRAAAWSTPDGAVTAPGAEVLAAGMIPWRPGAE +GLEVLVIHRPRYDDWSWPKGKVDDGETLPEAAARELAEEVALTLRPGLPLAVTRYDVPDR +KGKGMLSKEVWYWAGEATGQRPTPDGDEVDEARWVSSARAREMLSNATDLEPLDRLERAD +ARGHLRTVPLLVLRHAKAKPRSSWSRAEQERPLAATGRRQAHSVARLIAVWRPERVVSSP +WRRCVETLAPFVKATRLPLKTKSAFTETTAREKPKKTRRAFRDLLARRRPQVLCLHRPVI +PSILEEVDDAAARPASDVLAALPRRDPHLRPGGVLVLHQGLDAKGAVVAAEVYDPWSD +>PROKKA_01676 +MPSSHADRVARWSTEDRVSEGPRAEVLAAGMLPWRRVPGGLEVMVIHRPRYDDWSWPKGK +LDPGETLPECAVRELREEVGLELRPGIPLCVTAYEVPGKRGARQSKEVWYWAAEVDGQRA +LPDGDEVDEVRWVGPDEARRLLTNDSDHEPLDLLLRAASRGRLRTVPLLVLRHAKAKPRS +SWSRAEQERPLAATGRRQALAVEGLVSAWRPERLVSSPWRRCVETLAPLVKSSRLPLKTK +GAFTETTAREKPKKTRKVMAELMGRSRPLVVCTHRPVLPTLFEVVEDAAAGQADRVLRAL +PTEDPWLRPGAVLVAHRALDLDGDVVAVEVYDPWDD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001422.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001422.fa new file mode 100644 index 0000000000000000000000000000000000000000..ad3f67d2efa0be981cfea7b1e2f85dd637abe577 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001422.fa @@ -0,0 +1,25 @@ +>PROKKA_01750 +MRSDPMSRATRPTEPVIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR +TWESFPARFRPLPGRTNIVVSRTLTATEEAGAELRAAGAVVVPNFGAALAAAAEADGCDT +VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPPLDARWRRTAVDPAPDAWLDSASG +PRHRFERWERD +>PROKKA_01457 +MRSDPMSRATRPTEPVIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR +TWESFPARFRPLPGRTNIVVSRTLTATEEAGAELRAAGAVVVPNFGAALAAAAEADGCDT +VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPPLDARWRRTAVDPAPDAWLDSASG +PRHRFERWERD +>PROKKA_01127 +MRSDPMSRATRPTEPAIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR +TWESFPARFRPLPGRTNIVVSRTLTASEEAGAELRAAGAVVVPDFGAALAAAAEADGCDT +VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPVLDPRWRRTAVDPAPDAWLDSASG +PRHRFERWERD +>PROKKA_01052 +MARHHDDGARPRQTIAMIWAQTPDGVIGADGTMPWHLPEDLARFKALTLGHPVIMGRRTW +DSFPARVRPLPGRTNIVVSRTLTATPEAGEAVRAAGAVVVPDFGAALTAADEADGLDLVW +VIGGATLYEQALDVATRAEITVVDVDAPGDTHAPALDSRWRLVAADPSPDGWLDSAAGPR +RRDERWERD +>PROKKA_01679 +MRSDPMSRATRPTEPVIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR +TWESFPARFRPLPGRTNIVVSRTLTATEEAGAELRAAGAVVVPDFGAALAAAAEADGCDT +VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPLLDARWRRTAVEPAPDAWLDSASG +PRHRFERWERD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001423.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001423.fa new file mode 100644 index 0000000000000000000000000000000000000000..807b716d02ab115bec4418eeca50aaad3633def0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001423.fa @@ -0,0 +1,15 @@ +>PROKKA_01751 +MAPTDSDQRLLSPQAVSFLALVALPVLAFVCAVFGLILVLQGKTIAGLVFLLVLTQVFAV +GGLIAWNRRKRAQQGR +>PROKKA_01458 +MAPTDSDQRLLSPQAVSFLALVALPVLAFVCAVFGLILVLQGKTIAGLVFLLVLTQVFAV +GGLIAWNRRKRAQQGR +>PROKKA_01126 +MAPTDPQDRLFTPQAVTFLALVACPVLAFVCAVMGLILVLQGKTIAGLVFLIVLTQVFAV +GGLIAWNKRKRAQQGR +>PROKKA_01051 +MADLPSDEKAPLLDAQAVTFLTLIAFPVLAFVCAVMGLILVLQGKVVAGVVFLVVLTQVF +AAGGLITWNRRRRDRSGR +>PROKKA_01680 +MAPTDSDQRLLSPQAVSFLALVVLPVLAFVCAVFGLILVLQGKTIAGLVFLLVLTQVFAV +GGFIAWNKRKRAQQGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001427.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001427.fa new file mode 100644 index 0000000000000000000000000000000000000000..1798210c1579d2e1387858d43aef34924142def3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001427.fa @@ -0,0 +1,20 @@ +>PROKKA_01755 +MSVNPDVAGRSYPPAPPFQVGREAVRGFAEAVQAQHPAHHDVAAARALGHADLVAPPTFA +VVIAQRAEAAVVADPELGIDFSRVVHADERFVHHRPLVAGDEVVATVRVEAVKSLGGNRM +VTTVTEIADLDGAAVSTVTSTLLVRGEES +>PROKKA_01462 +MSVNPDVAGRSYPPAPPFQVGREAVRGFAEAVQAQHPAHHDVAAARALGHADLVAPPTFA +VVIAQRAEAAVVADPELGIDFSRVVHADERFVHHRPLVAGDEVVATVRVEAVKSLGGNRM +VTTVTEIADLDGAAVSTVTSTLLVRGEES +>PROKKA_01122 +MSVNPDVAGRSYPPAPPFQVGREAVRAFASAVQAQHPAHHDVEAARALGHADLLAPPTFA +VVIAQRAEAAAVNDPEVGIDFSRVVHADERFVHHRPLVAGDEVVATVRIASVKSLGGNDM +VTTVTEIADADGAPVSTVTSTLLVRGEES +>PROKKA_01047 +MSETESLVGRTYPPAPPYQVGREAVRAFADAVQAAHPAHTDVDAARALGYADVVAPPTFA +VVVAQRAEAAVVADPEAGIDFSRVVHADERFTHHRPIVAGDELTATVLIEAVKELGGNRM +VTTVTEIVDAAGAPVSDVASTLLVRGEES +>PROKKA_01684 +MSVNPDVAGRSYPPAPPFQVGREAVRGFAEAVQAQHPAHHDVAAARALGHADLVAPPTFA +VVIAQRAEAAVVADPELGIDFSRVVHADERFVHHRPLVAGDEVVATVRVEAVKSLGGNRM +VTTVTEIADLDGAPVSTVTSTLLVRGEES diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001429.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001429.fa new file mode 100644 index 0000000000000000000000000000000000000000..de7cb6da785d6c5f75e9dc8a21d927056c0db032 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001429.fa @@ -0,0 +1,66 @@ +>PROKKA_01759 +MSDILDPQTTAEVAPELAEAEQEATGTVPQVDAAPEAPAEPAAPEAPAEPAGPTFLDLGL +DARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETTD +VTGRADTPQVLVLAPTRELALQVADAFDSYAKHLDDVSVLAVYGGSPYGPQLAGLRRGAQ +VVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRMGFAEEVDRILASTPDTKQTALFS +ATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKFEALSRILETEEHDG +VIAFVRTRAGTEELAQKLTRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAAR +GLDVERISHVVNYDIPQDAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQ +VEEMAVPSVADVNAARKRRFADGITRTLERASEEELAVFGEIVAAYVDEHEAEPARVAAA +LGMMAQGGRPLLAREQEIPFGGARGRKDRDGGREGGRDGGRERGTSDGRGSRGPAREPAA +GNVTYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTSAQLEA +AANAEINGRRLGLRKDTGRPTRAERDGEDRGERRGGFRKDRGERGERGGFRGDRDGGQRG +GYRKDRDDRGSREDRGGFRKDRDDRSFRGDRRGRPGGRKPRWGAQERSDRGARR +>PROKKA_01466 +MSDILDPQTTAEVAPELAEAEQEATGTVPQVDAAPEAPAEPAAPEAPAEPAGPTFLDLGL +DARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETTD +VTGRADTPQVLVLAPTRELALQVADAFDSYAKHLDDVSVLAVYGGSPYGPQLAGLRRGAQ +VVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRMGFAEEVDRILASTPDTKQTALFS +ATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKFEALSRILETEEHDG +VIAFVRTRAGTEELAQKLTRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAAR +GLDVERISHVVNYDIPQDAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQ +VEEMAVPSVADVNAARKRRFADGITRTLERASEEELAVFGEIVAAYVDEHEAEPARVAAA +LGMMAQGGRPLLAREQEIPFGGARGRKDRDGGREGGRDGGRERGTSDGRGSRGPAREPAA +GNVTYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTSAQLEA +AANAEINGRRLGLRKDTGRPTRAERDGEDRGERRGGFRKDRGERGERGGFRGDRDGGQRG +GYRKDRDDRGSREDRGGFRKDRDDRSFRGDRRGRPGGRKPRWGAQERSDRGARR +>PROKKA_01118 +MSDALDPQTTPEAQVDAAELAEARQEAAEAAAPKAETPETAAAATETDSAPEAETAEEPE +APAEPAGPTFLDLGLDARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTG +AFALPALARLAETADVNGRADTPQVLVLAPTRELALQVADAFDSYAKHLEDVSVLAVYGG +SPYGPQLAGLRRGAQVVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRMGFAEEVDR +ILASTPDTKQTALFSATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWK +LEAFTRILETEDHDGVIAFVRTRAGTEELAQKLNRAGFKAVAISGDIAQKQREKTVEDLK +AGRVDILVATDVAARGLDVERISLVVNYDIPQDAESYVHRIGRTGRAGRQGDAVLFMTPR +ERFLLKQIERTTRQQVEEMAVPAVKDVNAARKRRFADGITRTLERASEEELAVFGEIVAA +YVEEHDAEPSRVAAALGMMAQGGRPLLAKEQEIPTGPRGRKERDGGRDGGREHGTADGRG +SRGPAREPAAGNATYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELP +ADLTPAQLEAAANIEISGRRLGLRKDTGRPTRAERDGDERRGGFRKDRGERGGHGGHRGG +FRKDRDERGFRGDREERGGFRGDRDDRGDRGGFRKDREDRGGFRKDREDRGDRGGFRKDR +EDRGGFRKDRDERGGFRGGKAGGRKPRWGAQERSDRGPRR +>PROKKA_01043 +MTPHETIPADDQAPVDLTEFDPELAETTAEAPAAEQDADDAEADAEPAGPTFLSLGLDAR +VLAAVEDLGYQRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETQDVNG +RSQAPQILALAPTRELALQVAEAFESYAKHLDDVSVLAVYGGAPYGPQLAGLRRGAQVVV +GTPGRVIDHLERGNLDLSQLQTLVLDEADEMLRMGFAEEVDRILAETPDSKQTALFSATM +PPAIRRISAQYLNDPEEVAVARQSTTGTNIRQRYLQIAHQWKFEAMTRILETEDHEGVIA +FVRTRAGTDELAQRLNQAGFSAVAISGDVAQKQREKTVDDLKAGRVDILVATDVAARGLD +VERISLVVNYDIPQDAESYVHRIGRTGRAGRSGDAVLFMTPRERFLLKQIERTTRQEVEE +MQVPTVAQVNEARTRGVVAGIGRTLETASEADLDTYARMVAEYVEANDVDPARAAAALAL +MAQGGRPLLTEADEVPAGGRVRRDRDRDDRRERGDRSERGDRDGRGSRGPRREPAAGNAT +YWIGVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHALVELPADLTAAQLDAAANT +EINGRRLNLRKDTGRPTRAERDGDGERGHRGPREDRGGFRRDRGDRGGFRRDRGERPERG +GFRKDRDDRGPREDRGGFRHDRDDRGGRPGARKPRWGSDDRRDRGPRR +>PROKKA_01688 +MSDILDPQTTAEAAPELAEAEQEATGTVPQVDAAEPAAPEAPAGPAGPTFLDLGLDARVL +AAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETTDVTGRA +DTPQVLALAPTRELALQVADAFDSYAKHLDDVSVLAVYGGSPYGPQLAGLRRGAQVVVGT +PGRVIDHLERGSLDLSDLQTLVLDEADEMLRMGFAEEVDRILASTPDTKQTALFSATMPP +AIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKFEALSRILETEEHDGVIAFV +RTRAGTEELAQKLTRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAARGLDVE +RISHVVNYDIPQDAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQVEEMA +VPSVADVNAARKRRFADGITRTLERASEEELAVFGEIVAAYVDEHEAEPARVAAALGMMA +QGGRPLLAREQEIPFGGARGRKDRDGGREGGRDGGRERGTSDGRGSRGPAREPAAGNATY +WIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTSAQLEAAANAE +INGRRLGLRKDTGRPTRAERDGEDRGGFRKDRGERGERGGFRGDRDGGQRGGYRKDRDDR +GSREDRGGFRKDRDDRSFRGDRRGRPGGRKPRWGAQERSDRGARR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001433.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001433.fa new file mode 100644 index 0000000000000000000000000000000000000000..f7f2e6e3bbd508574cb37cf115ff3f98fae1abb1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001433.fa @@ -0,0 +1,50 @@ +>PROKKA_01763 +MQYAENVLELIGHTPLVKLHSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEEAEREGL +LGPGGTVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLSAYGAELVVTPTAV +DPTSEESYYGVADRLVREIPGAYQPNQFFNPAAPASHYETTGPEIWEDTAGRVTHVVMGA +GTGGTITGTGRYLKEVSADRPSGAVRVIGADPSGSVYSGGAGRPYFVEGVGEDMWVDNYD +PAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARELGPEDVMVIVLPD +SGRGYLAKIFNDPWMDERGFDYDVRETVLPAWARGRTRSAVPQTDDDGATGAAGGAGTPV +EALEHADAEPATRAGAPAEADRWSATAGELLTEKADLFPGSVPTLVTAAPTTSVADAVAT +MNRYGVDALPVILEPRHDLRIGEVRGTVSSAALADALAEGRATAQTPVADVMGPVLPCLG +ARTPLRAVARRLAQDPVLLVLEAGRVQGVVTLHDVLAHVTA +>PROKKA_01470 +MQYAENVLELIGHTPLVKLHSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEEAEREGL +LGPGGTVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLSAYGAELVVTPTAV +DPTSEESYYGVADRLVREIPGAYQPNQFFNPAAPASHYETTGPEIWEDTAGRVTHVVMGA +GTGGTITGTGRYLKEVSADRPSGPVRVIGADPSGSVYSGGAGRPYFVEGVGEDMWVDNYD +PAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARELGPEDVMVIVLPD +SGRGYLAKIFNDPWMDERGFDYDVRETVLPAWARGRTRSAVPQMDDDGATGAAGGAGTPV +EVLEHADAEPATRAGAPAEADRWSATAGELLTEKADLFPGSVPTLVTAAPTTSVADAVAT +MNRYGVDALPVILEPRHDLRIGEVRGTVSSAALADALAEGRATAQTPVADVMGPVLPCLG +ARTPLRAVARRLAQDPVLLVLEAGRVQGVVTLHDVLAHVTA +>PROKKA_01114 +MQYAENVLELIGHTPLVKLNSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEDAEKAGK +LAPGGTVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLTAYGAEIVVTPTSV +APESEESYYGVANRLERDIPGAYQPNQFFNPAAPASHYETTGPEIWEDTAHRVTHVVIGA +GTGGTITGTGRYLKEVSADRESGPVRVIGADPSGSVYSGGTGRPYFVEGVGEDMWVDNYD +PAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARDLGPKDVMVIVLPD +SGRGYLAKIFNDPWMDERGFDYDVQDTVLPEWARGRTRSAAPEADDDGAQGAAGGAGTPV +EALEQADAAAGADAGQVADAPAEADRWAATAGELLAEKADLFPGSVPTLVTASPTTSVAD +AVATMNRYGVDALPVVAEPRHDLRIGEVRGTVSAAALGEALAAGRVHPGTPVAEAMGPVL +PCIGARTPLRAVARRLAQDPTLLVLSAGRVAGVVTLHDVLAHVTA +>PROKKA_01039 +MGAVNEINPAPAHGQPRWAENVLDLIGRTPLVKLNRVTEGVEATVLVKVEYLNPGGSVKD +RIALRMLEEAERDGKLAPGGTVVEPTSGNTGVGLALVAQQKGYRAVFVTPDKVGQEKRDV +LTAYGAEIVVTPTSVEPSSDESYYGVANRLEKEIPGAFQPNQFFNPAAPASHYETTGPEI +WEDTAGTVTHVVIGAGTGGTITGTGRYLKEVSADRASSPVRVIGADPEGSVYSGGTGRPY +FVEGVGEDMWPGNYDPSVPDEVIAVSDDAAFEMTRRLAAEEGLLVGGSSGMAVVAGLQAA +RELGPDDVMVIVLPDSGRGYLAKIFNDDWMDERGFHYAQEETVLPAWAQGRTRSAVATAP +SDSREGARGGVGTPVEAPGEGSPQDGAATATPAPGSRWDASLADVLADKEDLFPGSVPTL +VTASPDTTVADAVATLARYGVDALPVIAEPRHDLRINEVRGTVSAPALAAALAAGRVQPG +SAVSDVMEPALPSVGAAMTLRAAARRLQEDPILLVMDAGIVQGVVTLHDVLVYATA +>PROKKA_01692 +MQYAENVLELIGRTPLVKLHSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEEAEREGL +LGPGGTVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLSAYGAELVVTPTAV +DPTSEESYYGVADRLVREIPGAYQPNQFFNPAAPASHYETTGPEIWEDTAGRVTHVVMGA +GTGGTITGTGRYLKEVSADRPSGPVRVIGADPSGSVYSGGAGRPYFVEGVGEDMWVDNYD +PAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARELGPEDVMVIVLPD +SGRGYLAKIFNDPWMDERGFDYDVRETVLPAWARGRTRSAVPQTDDDGATGAAGGAGTPV +EVLEHADAELATRAGAPAETDRWSATAGELLTEKADLFPGSVPTLVTAAPTTSVADAVAT +MNRYGVDALPVILEPRHDLRIGEVRGTVSTAALADALAEGRATAQTPVADVMGPVLPCLG +ARTPLRAVARRLAQDPVLLVLEAGRVQGVVTLHDVLAHVTA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001435.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001435.fa new file mode 100644 index 0000000000000000000000000000000000000000..8d54921ac9d6a7412b762920bdfb66cd1d0aa401 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001435.fa @@ -0,0 +1,20 @@ +>PROKKA_01765 +MTTAFEPRPHTAAAPREPDPHGPGTPGSLRPGERGSVLIVTRHPDPDEAMRHAMAWITAF +EEDCGLVLDTDETALYAVGRAGDLGEALRRGPLVHEDGSPADTSAFVDAVLADGTWRLRD +ADPRAWSTTYRATILGAAPEAVCTIWDVFPLPAA +>PROKKA_01472 +MTTAFEPRPHAAAAPREPDPHGPGTAGSLRPGARGSVLIVTRHPDPDEAMRHAMAWITAF +EEDCGLVLDTDETALYAVGRAGDLGEALRRGPLVHEDGSPADTSAFVDAVLTDGTWRLRD +ADPRAWSTTYRATILGAAPEAVCTIWDVFPLPAA +>PROKKA_01112 +MTTAFEPRPHTGLAPREPEPHGPGTPGPLRPGVRGSVLIVSEHADPDTAMRHAMAWITAF +EDDCGLVLDADGTELYAVGLAGELGASLRRSPGVAEDGTPTDTSEFVDAILTGGVWRLRE +PDARAWSTAYRAAILGAAPHAVCTVWDVLPLPAA +>PROKKA_01037 +MTAQHAEPTRTDRAEPHGPGTPATLRPGERGSVLVLSPAGPPEAAMGHAVAWITAFEDDC +GLVLDRDATSLYAVSPADGLRREGDVPSDGGIAEHLDFVLAGDVWHHRGTCPPAPAGSDV +DGWALLVHRLQREAPRGALGTVWDVFPLPAAG +>PROKKA_01694 +MTTAFEPRPHTAAAPREPDPHGPGTPGSLRPGERGSVLIVTRHPDPDEAMRHAMAWITAF +EEDCGLVLDTDETALYAVGRAGDLGEALRRGPLVHEDGSPADTSAFVDAVLTDGTWRLRD +ADPREWSTTYRAAILGAAPEAVCTIWDVFPLPAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001436.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001436.fa new file mode 100644 index 0000000000000000000000000000000000000000..5f0663768dc207670f35909423f3ac837dad8245 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001436.fa @@ -0,0 +1,20 @@ +>PROKKA_01768 +MASDSTFDVVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMRASSEERVK +AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEATMKEGIDQPTAKKITKLIRDEGPK +SVKAQIQGDELRVSSKSRDDLQSVIAMLKDFEDADLQFVNFR +>PROKKA_01475 +MASDSTFDIVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKASSEERVK +AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEATMKEGIDQPTAKKITKLIRDEGPK +SVKAQIQGDELRVSSKSRDDLQSVIAMLKDFEDADLQFVNFR +>PROKKA_01109 +MASDSTFDVVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKASSEERVK +AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEASMKEGIDQPTAKKITKLIRDEGPK +SVKAQIQGDELRVSSKSRDDLQEVIAMLKDFEDADLQFVNFR +>PROKKA_01035 +MASDSTFDVVSKVDKQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKANSEERVK +AVLDVFESKLVKRGISLKSLDCGEPFASGKETRMEASIKEGIDQPTAKKITKLIRDEAPK +SVKAVIQGDELRVSSKSRDDLQETIALLKTFEDADLQFINFR +>PROKKA_01697 +MASDSTFDVVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKASSEERVK +AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEATMKEGIDQPTAKKITKLIRDEGPK +SVKAQIQGDELRVSSKSRDDLQSVIAMLKDFEDADLQFVNFR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001438.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001438.fa new file mode 100644 index 0000000000000000000000000000000000000000..faf48c440e21b955a5a2c3fd49c8ad982b36e045 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001438.fa @@ -0,0 +1,45 @@ +>PROKKA_01770 +MARLLVDITPLRVSPAYRRLWLGNTLAYVGTQLTLVAVSLEVFALTGSSFAVGLLGLAAL +VPLVVAGLYGGAIADRHDRRRVALTSSAVMWLTTVGIAAQAWAGFESVPVLYALVALHSG +ASGINQPTRGAIIPALVGLPLVPAANALNMMTFSVALMVGPVLGGVLVAAVGYAWTYSID +VVTFLAALYAVWRLPSLPPQQAEAAAASGTRGGLASVVEGLRFLGSRPNLRMTFLADIVA +MTTAFPRALLPAIGAVVLGGGEAAVGVLLAAMAAGAFLAGLFSAPFTRLHAQGWGVYVSI +LVWGGAVAAFGGVVWWAQSLPDGDPRLTLAFALAALCMAVGGAADSLSGVFRGSILQSAT +PDHLRGRLQGVFVVVVAGGPRLGELITGGASVVLGEGPTLLAGGVLCMLGVSALMRWQPG +FLRYDARNPTP +>PROKKA_01477 +MARLLVDITPLRVSPAYRRLWLGNTLAYVGTQLTLVAVSLEVFALTGSSFAVGLLGLAAL +VPLVVAGLYGGAIADRHDRRRVALTSSAVMWLTTVGIAAQAWAGLESVPVLYALVALHSG +ASGINQPTRGAIIPALVGLPLVPAANALNMMTFSVALMVGPVLGGVLVAAVGYAWTYSID +VVTFLAALYAVWRLPSLPPQRAETATASGTRWGLASVVEGLRFLGSRPNLRMTFLADIVA +MTTAFPRALLPAIGAVVLGGGEAAVGVLLAAMAAGAFLAGLFSAPFTRLHAQGWGVYVSI +LVWGAAVAAFGGVVWWAQSLPDGDPRLTLAFALAALCMAVGGAADSLSGVFRGSILQSAT +PDHLRGRLQGVFVVVVAGGPRLGELLTGGASVGLGEGPTLLAGGVLCMLGVTALMRWQPG +FLRYDARNPTP +>PROKKA_01107 +MARLLVDLTPLKVSPAYRRLWVGNTLSFVGTQLTLVAVSLEVFALTGSSFAVGLLGLAAL +VPLVVAGLYGGAVADRHDRRTVALASSAVMWLTTVGIAAHAWAGIESVPLLYALVALHSG +ASGINQPTRGAIIPALVGMKLVPAANALNMMTFSVAMMAGPVLGGVLVASVGYAWTYSID +VVTFLAALYAVWRLPSLPPQRAEGEAAPTGRVGVRSVVEGLRFLGSRPNLRMTFLADIVA +MATAFPRALLPAVGGVVLGGGEAAVGVLLAAMAAGAFLAGLFSGPFTRLHAQGWGVYVSI +LVWGASVAAFGGVVWWAQGLPDGDPRLTGAFVAAALCLAVGGAADSISGVFRTTILQSAT +PDHLRGRLQGVFVVVVAGGPRVGELLTGGASVAVGEGLTLLLGGLACVLGVSLLMRRQPE +FLKYDARSPTP +>PROKKA_01033 +MPRLLVDLAPLEASPAYRRLWLGNALAFVGTQLTLVAVSLEVFALTGSSFAVGMLGLAAL +IPLVVAGLYGGAVADRHDRRTVALASGAVMWAATALIAAHAWAGVESVGVLYGLVALHSA +ASGINQPTRGAIIPALVGPALLPAANALNMLTFSTAMMAGPLLGGVLVASVGYAWTYTVD +VVTFLAALWAVWRLPSLPPDRSAAPDDAGRGGLSSVLDGFRFLGTRRNVRMTFVADIVAM +ATAFPRALLPAVGGTILGGGEAAVGVLLASMAAGTFLAGLFSGTFTRVHRQGRGVAVAIA +AWGLSVAAFGAVVLWAAPLPDGDPRLGPALAACAACLVVAGAADSVSAVFRTTILQSATP +DHLRGRLQGVFVVVVAGGPRVGEMIQGTASAALGEGATLVLGGVLCVAGIALLMRVQPGF +LHYDARRPTP +>PROKKA_01699 +MARLLVDITPLRVSPAYRRLWLGNTLAYVGTQLTLVAVSLEVFALTGSSFAVGLLGLAAL +VPLVVAGLYGGAIADRHDRRRVALTSSAVMWLTTVGIAAQAWAGLESVPVLYALVALHSG +ASGINQPTRGAIIPALVGLPLVPAANALNMMTFSVALMVGPVLGGVLVAAVGYAWTYSID +VVTFLAALYAVWRLPSLPPQRGEAAAASGTRGGLASVVEGLRFLGSRPNLRMTFLADIVA +MTTAFPRALLPAIGAVVLGGGEAAVGVLLAAMAAGAFLAGLFSAPFTRLHAQGWGVYVSI +LVWGAAVAAFGGVVWWAQSLPDGDPRLTLAFALAALCMAVGGAADSLSGVFRGSILQSAT +PDHLRGRLQGVFVVVVAGGPRLGELLTGGASVGLGEGPTLLAGGVLCMLGVSALMRWQPG +FLRYDARNPTP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001439.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001439.fa new file mode 100644 index 0000000000000000000000000000000000000000..b68622e74f0afc90e1491830770f6aa9ac990e02 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001439.fa @@ -0,0 +1,35 @@ +>PROKKA_01772 +MVRVSPSSPAVRPGVTPDGAAPDTGALPTVSPAPADDPRGLALGFTAYFVWGLLPLYMAV +LAPAGALEIVVVRIGFALIFCLLLLTVMRRLRELGTALATPGRWGTTGLAAGIIAVNWLL +YAVSVTTGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWVAVGIAVAAVVVMSAAMGQ +VPWIALGLATSFGLYGFVKKRFPSPVHAVTAMTAETVVLIPVFVVGSVLLAQAGLLTTVT +EGPGHFWLMAGLGVLTAVPLILFSAAARSLTLTTLGMLQYTAPILQFLVAVTVLGEQMPA +ARWAGFGLIWLSLAVFTLDQLNASRLQRRAVRAGQGAHA +>PROKKA_01479 +MVRVSPSSPAVRPGVTPDGAAPDTGALPTVSPAPADDPRGLALGFTAYFVWGLLPLYMAV +LAPAGALEIVVVRIGFALIFCLLLLTVMRRLRELGTALATPGRWGTTGLAAGIIAVNWLL +YAVSVTTGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWVAVGIAVAAVVVMSAAMGQ +VPWIALGLATSFGLYGFVKKRFPSPVHAVTAMTAETVVLIPVFVVGSVLLAQAGLLTTVT +EGPGHFWLMAGLGVLTAVPLILFSAAARSLTLTTLGMLQYTAPILQFLVAVTVLGEQMPA +ARWAGFGLIWLSLAVFTLDQLNASRLQRRAVRAGQGAHA +>PROKKA_01105 +MARVSPSPASRRPGVPPDAAAPDTGALPAVSPAPANDPRGLALGFTAYFLWGLLPLYMAR +LAPAGAVEIVVVRVGFALVFCLVLLALMRRLRELRTSLATPARWGATALAAGFIGTNWLL +YAVSVTTGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWAAVGIAVAAVVVMSVAMGQ +VPWIALGLAFSFGLYGFVKKRFPTPVHAVTTMTAETVVLLPAFAVGMVWLGQAGLLTTFT +EGPAHFWLMAGLGVLTAVPLILFSAAAKALTLTTLGMLQYTAPILQFIVAVTVLGEQMPV +ARWAGFGLIWVSLLVFTLDQVRVSRLHRRAARAGHGARA +>PROKKA_01031 +MAQVSHSPSPSGPDAPRDGVPVEAAAPDTGALPTITPAPANDPRGLALGFAAYVIWGLLP +LYMAATAPAGAVEIVVVRVVFALIFCLLLLAVMRRLPELRTALATRARWGSITLAAAFIA +VNWLLYAHSVTSGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWIAVGIAVVAVVVMS +VAMGQVPWIALGLAFTFGMYGFVKKRFPVPVHAVTTMTAETVVLLPAFAVGMVFLVQAGL +LTTVSEGPGHFWMMAGLGVLTAVPLILFSAATQSLTLTTLGMLQYIAPIMQFLVAVAVLG +EHMPAARWAGFALIWLSLVVFTLDQANASRVQRRAARAAGRART +>PROKKA_01701 +MVRVSPSSPAVRPGVTPDGAAPDTGALPTVSPAPADDPRGLALGFTAYFVWGLLPLYMAM +LAPAGALEIVVVRIGFALIFCLLLLTVMRRLRELGTALATPGRWGTTGLAAGIIAVNWLL +YAVSVTTGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWVAVGIAVAAVVVMSAAMGQ +VPWIALGLATSFGLYGFVKKRFPSPVHAVTAMTAETVVLIPVFVVGSVLLAQAGLLTTVT +EGPGHFWLMAGLGVFTAVPLILFSAAARSLTLTTLGMLQYTAPILQFLVAVTVLGEQMPA +ARWAGFGLIWLSLAVFTVDQLNASRLQRRPVRVRRGAHA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001443.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001443.fa new file mode 100644 index 0000000000000000000000000000000000000000..4c9f652cf93bed4e9ff3cb4abd68d107b4003c30 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001443.fa @@ -0,0 +1,45 @@ +>PROKKA_01776 +MTDTPTSPAPDSTSAVVRRADVLISGCGPAGATAAAHLAAAGLDVVVLEKTAHPREKVCG +DGLTPQAVRELQLLGVPHRGEPGDDGGWRVIRGLRLRAGERSVDVPWAPTQTWPDYALTR +TRRDFDALLADLARTRGAEVRERHAVTGVVRDEAGRVVGLDAELIAPNGRKTGETARFTA +PIVLACDGVSARAAVSAGLHRREDRPMGVAVRAYYTAGAAVDGAIPAPPGDRGEWMESWL +RLPDAEGNPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLKSWTGALTADWGIA +EQTRTSRILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARLAADLAV +QAHAAGTDGAADAILSRYPVITQHLWGRHFALGARFARLIGDPRVMKAALGAGMAAPPLL +RAAVKVMGNTVDARGGDAVDRAVRVLEALTPALTTAGGAPLGRLAR +>PROKKA_01483 +MTGTPTSPAPASTPAVVRRADVLISGCGPAGATAAAHLAAAGLDVVVLEKTAHPREKVCG +DGLTPQAVRELQLLGVPHRGEPGDDGGWRVIRGLRLRAGERSVDVPWAPTQTWPDYALTR +TRRDFDALLADLARTRGAEVRERHAVTGVVRDEAGRVVGLDAELIAPNGRKTGETARFTA +PIVLACDGVSARAAVSAGLHRREDRPMGVAVRAYYTAGAAVDGAIPAPPGDRGEWMESWL +RLPDAEGNPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLKSWTGALTADWGIA +EQTRTSRILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARLAAELAV +QAHAAGTDGAADAILSRYPVITQHLWGRHFALGARFARLIGDPRVMKAALGAGMAAPPLL +RAAVKVMGNTVDARGGDAVDRAVRVLEALTPALTTAGGAPLGRLAR +>PROKKA_01101 +MTAAPSSSPSESAPPPVVRRADVLISGGGPAGATAAAHLAAAGLDVVVLEKTAHPREKVC +GDGLTPQAVRELQLLGVPHRGEPGDDGGWQVIRGLRLRAGERSVDVPWPETRSWPDYALT +RTRRDFDALLADLARERGAEVRERHAVTSVVRDDAGRVCGLDAELIAPNGRKTGETARFE +APVVLSCDGVSARAAVSAGIHRREDRPMGVAVRAYYTAGPAADGAVPAPPGDRGEWMESW +LRLPDAQGRPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLKSWSGALTPDWGI +SEQTRVSKILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARIAADLA +VQAHAAGSDAAADTVLSRYPVITQHLWGRHFALGARFARLIGDPRVMRASLGAGMAVPPL +LRAVVKVMGNTVDPERGDAVDRAVRVLEALTPALTTADSAPLGRLAR +>PROKKA_01025 +MTEHPTPAAAPVVRRADVLISGAGPAGATAAAHLAAAGLDVVVLEKSAFPREKVCGDGLT +PQAVQEIRNLGIEHQGGPGDDGGWHAVRGLRLRAGERSVDVPWPATQSWPDYALTRTRKD +LDALLADTARARGAEVRERHAVTGVTRDDAGRVDGLEAELIAENGRKTGERVRFAAPLVL +ACDGVSARAAVSMDVHRRTDRPMGVAVRAYYTAGPVGADGAVPRPPGDRVDWMESWLRLP +DEHGNPLPGYGWLFPLADGTVNVGLGILDTSPLFGKLDYRALLKQWSGALSEDWGISEET +RTSKILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARIAADLAVQAH +AAPNTPAADAVLARYPVITQHLWGRHFRLGTVFARLIGEPRVMRAALATGMAVPPLLRTV +ARVMGNVVDPSGGDAVDRAVRILESVTPSLTTADAPGVGRLAR +>PROKKA_01705 +MTGTPTSPAPASTPAVVRRADVLISGCGPAGATAAAHLAAAGLDVVVLEKTAHPREKVCG +DGLTPQAVRELQLLGVPHRGEPGDDGGWRVIRGLRLRAGERSVDVPWAPTQTWPDYALTR +TRRDFDALLADLARTRGAEVRERHAVTGVVRDEAGRVIGLDAELIAPNGRKTGETARFTA +PIVLACDGVSARAAVSAGLHRREDRPMGVAVRAYYTAGAAVDGAIPAPPGDRGEWMESWL +RLPDAEGNPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLRSWTGALTADWGIA +EQTRTSRILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARLAADLAV +QAHAAGTDGAADAILSRYPVITQHLWGRHFALGARFARLIGDPRVMKAALGAGMAAPPLL +RAAVKVMGNTVDARGGDAVDRAVRVLEALTPALTTAGGAPLGRLAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001446.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001446.fa new file mode 100644 index 0000000000000000000000000000000000000000..c74aca496140341f266702743de39f77f6cd5dcc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001446.fa @@ -0,0 +1,50 @@ +>PROKKA_01782 +MSNTFLLPDLGEGLTEADIVRWLVAEGDTVAVDQPMVEVETAKALVEVPSPYAGTVLTLH +GAEGETMDVGSPLITIGAAGESGEGSAPAAGTEALAVPPATGAAAAEAARPGALSYREEE +MAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHRATSRSRPSKRGRGAARPTPAP +TAGAGAPRVTSPIVRKLAREKGVDVAALTGTGPDGLITRADVLAAAEGSAPQAAPAQAPL +VAAVPAAEAAAQPGAVDGRTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVT +ALLELRASLKAKDSENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDGVHL +GLAVQTDRGLMVPSVEHAEKLSADELTAAVNDTVSRARAGRAAPAELTRGTFTLNNYGPL +GTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTFDHRVTDGATASAFLT +FVADCLHDPTAALARI +>PROKKA_01489 +MSNTFLLPDLGEGLTEADIVRWLVAEGDTVAVDQPMVEVETAKALVEVPSPYAGTVLTLH +GAEGETMDVGSPLITIGAAGESGEGSAPAAGTEALAVPPATGAAAAEAARPGALSYREEE +MAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHRATSRSRPSKRGRGAARPTPAP +TAGAGAPRVTSPIVRKLAREKGVDVAALTGTGPDGLITRADVLAAAEGSAPQAAPAQAPL +VAAVPAAEAAAQPGAVDGRTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVT +ALLELRAALKAKDPENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGQDEIVEVDGVHL +GLAVQTDRGLMVPSVEHAEKLSADELTAAINDTVSRARAGRAAPAELTRGTFTLNNYGPL +GTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTFDHRVTDGATASAFLT +FVADCLHDPTAALARI +>PROKKA_01096 +MSNTFLLPDLGEGLTEADIVRWLVAEGDEVVVDQPIVEVETAKALVEVPSPYAGTVLTLH +GAEGQTMEVGRPLITVGAAGESGEGSAPVAGTEAQAVPPATGEDAAEADRPGALSYREEE +MAGVQPKPDKARGGDGDVAGSDEEASGAVLIGYGTSGHSATSRTRPSKRGRRGAGTTTAG +GSGAASGQGEQAGQARAPRVTSPIVRKLAREQGVDVAALTGTGPDGLITRADVLSAAQGG +DAPQAAAAPAAQPAATAGAASTVGAGSADARTGLAVVARTPISGVRKVIADQLSRSRREV +PEVTAWLDVDVTALLELRAALKAKDAENAPSLLGLIARFTLAGLRRYPVMNARIEAGADG +KDEIVEVDGVHLGLAVQTDRGLMVPSVEHAERLSADELTAAINETVTRAREGKAAPAELT +RGTFTLNNYGPLGTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTFDHR +VTDGATASAFLTFVADCLNDPQSALARI +>PROKKA_01019 +MSNTFLLPDLGEGLTEADIVRWLVAEGDEVAVDQPMVEVETAKALVEVPSPFAGTVLTLH +GAEGETMEVGAPLITVGAVGESAGDAPPPSSAADAGTAPAADGAVPGALSYREEERAGVQ +PKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHTATSRSRPSKRARGGAGTTQAAAGAAP +AASGRAPRVTSPIVRKLARERGVDVATLTGTGPDGLITRADVLGAAGGASAPQDAQAPAP +VQTAPSAAAQAPAVAAGATDARTGLAVVARTPISGVRKVIADQLSRSRREVPDVTAWLDV +DVTALLELRAQLKAKDPENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDG +VHLGLAVQTDRGLMVPSVEHAEKMSADELTRAINDTVSRAREGRAAPAELTRGTFTLNNY +GPLGTDGATPILNIPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTFDHRVTDGATASA +FLTFVADCLNDPQAALARI +>PROKKA_01711 +MSNTFLLPDLGEGLTEADIVRWLVAEGDTVAVDQPMVEVETAKALVEVPSPYAGTVLTLH +GAEGETMDVGSPLITIGAAGESGEGSAPVAGTEALAVPPSTGADAAEAARPGALSYREEE +MAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHRATSRSRPSKRGRGATRPTPAP +TAWAGAPRVTSPIVRKLAREKGVDVAALTGTGPDGLITRADVLAAAEGSAPQAAPAQAPS +VAAVPAAEAAAQPGAVDGRTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVT +ALLELRAALKAKDPENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDGVHL +GLAVQTDRGLMVPSVEHAEKLSADELTAAVNDTVSRARAGRAAPAELTRGTFTLNNYGPL +GTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIMVRKVTEMTVTFDHRVTDGATASAFLT +FVADCLHDPTAALARI diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001447.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001447.fa new file mode 100644 index 0000000000000000000000000000000000000000..c0e41c0299c123c9878370e14001207bec3980ea --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001447.fa @@ -0,0 +1,35 @@ +>PROKKA_01783 +MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTARFGEERCFDTPLAE +SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPITIRIPYG +GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRSAIRLDDPVVFMEPKKMYWTK +AELDLDQLRAEFEEGWARVEDKKEHGEAWARAAVVREGTDVTLVSYGPSVPTCLAAAHAA +AEEGLSVEVVDLRTVNPLDEDTMAASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS +LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLDAEEARA +>PROKKA_01490 +MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTARFGEERCFDTPLAE +SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPITLRIPYG +GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRSAIRLDDPVVFMEPKKMYWTK +AELDLDQLRAEFEEGWARVEDKKEHGEAWARAAVVREGTDVTLVSYGPSVPTCLAAAHAA +AEEGLSVEVVDLRTVNPLDEDTMAASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS +LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLDAEEARA +>PROKKA_01095 +MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTKRFGEERCFDTPLAE +SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPMTIRIPYG +GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRAAIRLDDPVVFMEPKKMYWTK +AELDLEDLRAEFEERWGRVEEKKEHGEAWARAAVVRAGSDVTLVSYGPSVPTCLAAARAA +EEEGLSVEVVDLRTVNPLDEDTMVASVSKTGRAVVVAEPQGFASVASELVARIQQRCFHS +LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLDAEEARA +>PROKKA_01018 +MANLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTQRFGDERCFDTPLAE +SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQVASHVAKMRNRTKGGAPMPIVIRIPYG +GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYLMLRSAIRLDDPVVFMEPKKMYWTK +ADLDLDELRAEFDEQWARAQEKTAQGEAWARAAVVRQGADVTLVSYGPSVPTCLAAAQAA +AEEGLSVEVVDLRTVNPLDEDTMAASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS +LAAPVGRVTGFDIPFPAPKLEEHHLPNVDRILDAIDDLNWDLDAEEARA +>PROKKA_01712 +MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTARFGEERCFDTPLAE +SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPITIRIPYG +GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRSAIRLDDPVVFMEPKKMYWTK +AELDLDQLREEFEEGWARVEDKKEHGEAWARAAVVREGTDVTLVSYGPSVPTCLAAAHAA +AEEGLSVEVVDLRTVNPLDEDTMTASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS +LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLGAEEARA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001448.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001448.fa new file mode 100644 index 0000000000000000000000000000000000000000..101c425ffef3c29fcf70ac3cbeccd13ba22c0635 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001448.fa @@ -0,0 +1,40 @@ +>PROKKA_01784 +MSDPTPAVPGAARTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQGTE +PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLG +EDDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHAVG +MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ +SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAHTN +TDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQIARDAEDVAQQLRDAMNA +ETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA +>PROKKA_01491 +MSDPTPAVPGAVRTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQGTE +PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLG +EHDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHAVG +MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ +SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAHTN +TDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQITRDAEDVAQQLRDAMNA +ETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA +>PROKKA_01094 +MSDPTPAVSGSARTDQAEARPNAGAAFGISLEEYLLPATRRIQLIGEDGTLLSPEEQGAE +PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLG +KQDWLFPTYRDTVAVIARGVPPLEVMVSYQGTWHQGYDPNEHHVSVQSTPLTTQLLHAVG +MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ +SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVDLCRQGQGPFLVEADTYRMQAHTN +TDDPTRYREDAEVQEWEARDPLRRMTAYLESTGALTEEVSAEIAQAAEDVAKDLRDAMNA +EAELDPLELFDHVYSVQTPQLAAQRAQLTEELSRSENQEA +>PROKKA_01017 +MTSTRPGPATPDTRTEAAAAFGITLEEYLLPAARRIQLISPEGELLPAEEQGTAPGHEYP +LPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLGQDDWLF +PTYRDTVAVIARGVAPLDVMVSFQGTWHQGYDPKEHRVSVQSTPLTTQLLHAVGMAKAAR +LRGEDVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFLVQNNKFAISVPFAKQSAAPSL +AHKAVGYGLAGERVDGNDLAALLAVLGRAVDLCREGKGPFLVEADTYRMQAHTNTDDPTR +YREDSEVKEWEVRDPLRRMTAYLESTGALTAEVSTSIAKDAEDVAQQLRDAMNADVELDP +LELFDHVYSVQTPQLAAQRAQLAEELSRSENKEA +>PROKKA_01713 +MSDPTPAVPGAVRTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQGTE +PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVSLG +EDDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHAVG +MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ +SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAHTN +TDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQIARDAEDVAQQLRDAMNA +ETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001451.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001451.fa new file mode 100644 index 0000000000000000000000000000000000000000..a3a56f5025045e6adf3c12d718a347bf13a82abe --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001451.fa @@ -0,0 +1,70 @@ +>PROKKA_01798 +MPQTTSHAPVPPSASAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD +QAPLREAIVGEIKARTVETDRSVPARRDGWWYFVRTREGAEYPIHCRVPARDTGDLEADW +TPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPDATRVAYAVDHTGDERFTLRV +REIATGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVRAHVLGTDPAEDVLLHE +EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLAD +VEPVTDADGVRRLLVVHDRALDDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVK +VDGVMVTLTHAALAVRRETTPRVVVAELDAVLAGQAAHWREPAFDEELYACHLSATAAES +PFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPSSVTGE +DVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGG +GELGRRWYEDGKKLAKRHSFTDFVDATRHLVGLGWADPARVACMGGSAGGLLMGAVLNLA +PELYRACLAVVPFVDALTTILDPELPLSALEWEEWGNPIEDAAVYAAMRAYTPYENVRAV +DYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQATPLAEGGAPILLRTEMDGGHGGA +SGRYQGWEDTAWEYAFLLTALGATARIV +>PROKKA_01495 +MPQTTSHAPVPPSASAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD +QAPLREAIVGEIKARTVETDRSVPARRDGWWYFVRTREGAEYPIHCRVPARDTGDLEADW +TPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPDATRVAYAVDHTGDERFTLRV +REISTGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVKAHVLGTDPAEDVLLHE +EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLAD +VEPVTDADGVRRLLVVHDRALDDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVK +VDGVMVTLTHAALAVRRETTPRVVVAELDAVLAGQAAHWREPAFEEELYACHLSATAAQS +PFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPSSVTGE +DVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGG +GELGRRWYEDGKKLAKRHSFTDFVDATRHLVDLGWADPARVACMGGSAGGLLMGAVLNLA +PELYRACLAVVPFVDALTTILDPELPLSALEWEEWGNPIEDAAVYEAMRAYTPYENVRAV +DYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQATPLAEGGAPILLRTEMDGGHGGA +SGRYQGWEDTAWEYAFLLTALGATARID +>PROKKA_01078 +MPQTTSHAPVPPSVSAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD +QAPLRAAIFGEIKARTVETDRSVPSRRDGWWYFARTKEGAEYPVHCRVPAADTGDLEADW +TPPVVTPDAPLEGEQVILDGNAEAEGHPFFALGGLHISPDSTRVAYAVDHTGDERFTLRV +REIATGEDLPDVVENIAHGVRFDRSGARVLYTVWDDSWRPYQVKAHVLGTDPAQDQLLYE +ESDPGMWTGFTGTADRTQLLIGVGNSEVSETHVVDLPESPDAPLPAPRLLIPRAWGMLAD +VEPVTGADGVRRLLVVHDRTVARQDAADAGADAPAPNGMLSLVAEADVADRGAWRTVVPH +REDVKVDGVMVTLTHAALAVRRETTPRVVVAPLDSVLAGEAADWREPAFEEELYACHLAS +TAAESPFLRLAYTSWISPARVLDVSAATGEVHLRRETEVPGYDPSLYVAERVWAPASEPS +SVTGEPVRIPVTVIRRKDVAADGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVYAVA +HVRGGGELGRRWYEDGKKLAKRHSFTDFVDATRHLVDLGWADPARVACTGGSAGGLLMGA +VLNLAPELYRACLAVVPFVDALTSILDPELPLSALEWEEWGNPIEDPEVYAAMRDYTPYE +NVRAVDYPTIAAVTSLHDTRVLYVEPAKWVARLRRTVTSDQATPLAEGGAPVLLRTEMDG +GHGGASGRYQGWEDTAWEYAFLLTALGATQRVD +>PROKKA_01013 +MYETSLPTPPRAAARPTARTVHGETFTDDFEWMRAKTEQEVLDHLQAENAYTEAATADQA +DLRAAIYGEIKAHTVETDQSVPARRDGWWYFVRTVEGKDYAVHCRVPAQDTGDALADWTP +PVVPADAALPGEQVILDGNAEAAGHPFFSLGGMHISPDGALAAYAVDLAGDERYTLRVRE +IATGTDLPDVVRNIAPGVRFDRSGTRLIYTVWDETWRPYQVRVHTLGTDAAEDAVLYEES +DPGMWTGFDASADRTQLLIGVGNSEVSETWAVDLPVDASPLPAPRVLVPRTARMLADVEP +FDMDGRRRLLIVHDRLADGTTAPNGMLSIVDEADVADRDAWRPVVPHADDVRVDGVLVTR +THVGLAVRRDTTPRVLIAPLEGLREGSAPAWTEPSFDEELYMCRLAGVNLDSPFLRLSYA +SWTTPARVLDVVAATGEVRLRREVEVPGFDREDYVAERWWAPASEPSSLTGEQVRIPLTV +IRRRDVAQDGTAPAVVYGYGSYEMSMDPVFGVARLSLLDRGVVYVVAHVRGGGELGRAWY +EDGKKAAKRHSFTDFVDATRFVADSGWVDPARIACTGGSAGGLLMGAVLNLAPELYRACL +AVVPFVDALTSILDPDLPLSALEWEEWGNPIEDPEVYATMKAYTPYENVRAVDYPAIAAV +TSLNDTRVLYVEPAKWVAQLRRTVTSDQTTPIAAGGSPILLRTEMDGGHGGASGRYQGWE +DTAWEYAFLLTALGATARVD +>PROKKA_01717 +MPQTTTHAPVPPSVAAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD +QAPLREAIVGEIKARTVETDRSVPARRDGWWYFVRTREGAEYPIHCRVPARETGDLEADW +TPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPDATRVAYAVDHTGDERFTLRV +REIATGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVKAHVLGTDPAEDVLLHE +EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLAD +VEPVTDADGVRRLLVVHDRALDDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVK +VDGVMVTLTHAALAVRRETTPRVVVTELDAVLAGQAAHWREPAFDEELYACHLSATAAES +PFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPSSVTGE +DVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGG +GELGRRWYEDGKKLAKRHSFTDFVDATRHLVDLGWADPARVACMGGSAGGLLMGAVLNLA +PELYRACLAVVPFVDALTTILDPELPLSALEWEEWGNPIEDAAVYAAMRAYTPYENVRAV +DYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQARPLADGGAPVLLRTEMDGGHGGA +SGRYQGWEDTAWEYAFLLTALGATRRVV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001454.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001454.fa new file mode 100644 index 0000000000000000000000000000000000000000..2ce211de485115cdccc64887dea06e34d8170348 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001454.fa @@ -0,0 +1,40 @@ +>PROKKA_01801 +MPATADALARATDALAAAFDGGAPVELTADGAVLPRPEARDSRRCGDPDAVAVVRTSGST +GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP +GPFTPAAFATGAAALPDDAGPRLISLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL +DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVTAAVAPDGPDAPPRVRLAGPMV +AAGYLDDPARTAAHFVPAADGARAFLTEDTGILSPTDDGGVRLAVTGRLDDVVITGGVKV +SAAAVTAALEAHPGVAAAHVAGVPDPEWGARLCAAVVPVRPAAAPDEAVLRAHVRAALGA +AAVPKTWLLLEALPLLSTGKTDRQALAARFTAG +>PROKKA_01498 +MPATADALARATDALAAAFDGGDPVELTADGAVLPRPEARDSRRCGDPDAVAVVRTSGST +GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP +GPFTPAAFATGAAALPDNAGPRLVSLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL +DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVTAAVAPDGPDAPPRVRLAGPMV +AAGYLDDPARTAAHFVTAVDGARAFLTEDTGILSPTDDGGVRLAVTGRLDDVVITGGVKV +SAAAVTAVLEAHPGVAAAHVAGVADPEWGQRLCAAVVPADPASPVGENALRAHIRDALGA +AAVPKTWLALDALPLLSTGKTDRQALAARFTAAG +>PROKKA_01072 +MPATADALARATDALAAAFDGGDPVELTADGAVLPRPEARDPRRCGDPDAVAVVRTSGST +GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGIAVLSRSIAAGTAPVALPP +GPFTPAAFATGAAALPDHAGPRLVSLVPTQLARLLAADTDPAGRTALRSFDRVLVGGARL +DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVAVAVAPDGPDAPPRVRLAGPMV +AVGYLDDPARTAAHFVPAADGARAFLTEDTGVLSPTDDGGVRLAVTGRLDDVVITGGVKV +SAAAVTAVLEAHPGVAAAHVAGVADPEWGQRLCAAVVPADPASPVGENALRAHIRDALGA +AAVPKTWLALDALPLLSTGKTDRQALAARFAAAG +>PROKKA_01008 +MPATADALARATDALAAAFDGGAPVELTADGAVLPRPEARDPRRCGDPDAVAVVRTSGST +GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP +GPFTPAAFATGAAALPDDAGPRLVSLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL +DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVAVAVAPDGPDAPPRVRLAGPMV +AAGYLDDPARTAAHFVPAADGARAFLTEDTGVLSPTDDGGVRLAVTGRLDDVVITGGVKV +SAAAVTAVLEAHPGVAAAHVAGVPDPEWGARLCAAVVPAHPAAAPDEAVLRAHVRAALGA +VAVPKTWLVLDALPLLSTGKTDRQALAARFTAG +>PROKKA_01722 +MPATADALARATDALAAAFDGGAPVELTADGAALPRPEARDPRRCGDPDAVAVVRSSGST +GTPKQIVLTGAALRASAAATARRLGGEGAWLLALGVHYVAGLAVLSRSIAAGTAPVALPP +GPFTPAAFATGAAALPDDAGPRLVSLVPTQLARLLAADADPAGRAALRSFDRVLVGGARL +DPALRAAAEAAGVRLTATYGMAETCGGCVYDGVPLPGVAAAVAPDDPDAPPRVRLAGPMV +AAGYLDDPARTAAHFVTAADGTRAFLTEDTGVLSPTDDGGVRLAVTGRLDDVVITGGVKV +SAAAVTAVLEAHPGVAAAHVAGVPDPEWGARLCAAVVPAHEAAAPDEAVLRAHVRAALGA +AAVPKTWLVLEALPLLSTGKTDRQALAARFTAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001456.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001456.fa new file mode 100644 index 0000000000000000000000000000000000000000..08206b1c2d6364c89b9dfd9f206b278b3a594b51 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001456.fa @@ -0,0 +1,15 @@ +>PROKKA_01803 +MRIFFYGLVRVVLFVALWALFYYVMDLWMIFAVIAAAILAFAVSYLFLDRLRTGATEDLS +AAWEGRPGRRGRTETADADAEDAYTEGRFRE +>PROKKA_01500 +MRILYYGLLRVALFFVLWWVGLQLGLGMVMATLAAAILTFAVSYLFLGRLRRGATQDLSA +AWEGRPGRRGRTEAADAEAEDAYTQGRFRE +>PROKKA_01070 +MRILYYGLLRVALFFVLWWVGLQLGLGMVMATLAAAILTFAVSYLFLGRLRRGATQDLSA +AWEGRPGRRGRTEAADAEAEDAYTEGRFRE +>PROKKA_01006 +MRLFLYGLVRVVLFFVIWALCYYVFGLGMLFSTLAAVILTFAVSYLFLTRLRLDASTDLQ +NAWEGRPSRRGRTEAADAAAEDAYTDGRFPG +>PROKKA_01724 +MRIFFYGLVRVVVFVALWALFYYVMDLGMIFGVIAATILTFAVSYLFLGRLRAGATEDLS +AAWEGRPGRRGRTETADADAEDAYTEGRFRE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001461.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001461.fa new file mode 100644 index 0000000000000000000000000000000000000000..892f17e866b8316bf5191bd357c33a58ee8ab4ef --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001461.fa @@ -0,0 +1,10 @@ +>PROKKA_01812 +MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK +>PROKKA_01509 +MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK +>PROKKA_01062 +MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK +>PROKKA_00997 +MGSVIKKRRKRMAKKKHRKLLRKTRHQRRNKK +>PROKKA_01733 +MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001462.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001462.fa new file mode 100644 index 0000000000000000000000000000000000000000..221ffdf686258cefe66face827f1f3d8b51dd98e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001462.fa @@ -0,0 +1,40 @@ +>PROKKA_01813 +MSTTSTPPAPTPAAVVWDSSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVRIVEP +PVATDEQLALVHDPEYVAAVRRAAATSSAEDGRFGLGTEDCPVFPDLHESAARIAGGSLV +AAEAIWSGEVDRAVNFAGGMHHAARSSASGFCIYNDCAVAIQRLLDLGAERVAYVDVDAH +HGDGTQSIFYDDPRVLTISLHETGISLFPGTGFANEIGGSAAQGTAVNVALPPRTGDAGF +LRAAHAVVPPLLEAFAPDVLVSQHGCDGHLTDPLADLRLSVDGQRQLAFDVGDWADRFAY +GRWLATGGGGYNPLRVVPRAWAHLTAAVLQTPIPVRSEIPAAWIEHVRALTADELTGDMS +VHEGDDAERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRREVFPLHGLDPWFD +>PROKKA_01510 +MSTTSTPPAPTPAAVVWDSSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVRIVEP +PVATDEQLALVHDPEYVAAVRRAAATSSAEDGRFGLGTEDCPVFPDLHESAARIAGGSLV +AAEAIWSGEVDRAVNFAGGMHHAARSSASGFCIYNDCAVAIQRLLDLGAERVAYVDVDAH +HGDGTQSIFYDDPRVLTISLHETGISLFPGTGFANEIGGSAAQGTAVNVALPPRTGDAGF +LRAAHAVVPPLLQAFAPDVLVSQHGCDGHRTDPLADLRLSVDGQRQLAFDVGDWADRFAH +GRWLATGGGGYNPLRVVPRAWAHLTAAVLQTPIPVKSEIPAAWIEHVRTLTADELTGDMS +VHEGDDAERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRREVFPLHGLDPWFD +>PROKKA_01061 +MSTTSQRPAPTPAAVVWDPSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVSIIEP +PVATDAQLALVHDPDYIAAVRRASEAASDEDAPFGLGTEDCPVFPDLHEASARIAGGTLA +AAEAVWSGQVRRAVNFAGGMHHAARAKASGFCIYNDCALAIQRLLDLGAERVVYLDVDAH +HGDGTQAIFYDDPRVMTISVHETGISLFPGTGFANEIGGPDAQGTAVNVAVPPRTGDAGF +LRAVHAVVPQLLQGFDPDVIVSQHGCDGHHADPLADLRLSVDGQRQLAFDIGDWAEKFAD +GRWVATGGGGYNPLRVVPRVWTHLTAAVLQTPIPVKAEIPQSWIEHARTLTAEELTGDMS +LHEGDESERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRRELFPLHGLDPWFD +>PROKKA_00996 +MTSATSDCSQPAPSAVVWDPSLLKYRFSAQHPMAPLRLDLTHRLASSLGLLDAEHVRILQ +PPVATDEQLATVHDPAFIAAVRAASREDAEADEPHGLGSEDCPTFPDLHESAARIAGGSL +VAAEAVWSGEVSRAVNVAGGMHHAARAKASGFCIYNDCAVAIQRLLDLGAERVAYVDVDA +HHGDGTQSIFYDDPRVLTISLHETGISLFPGTGFANETGGPGAEGTAVNVALPPGTGDAG +FLRAVHAVVPQLLGAFQPDVLVTQHGADAHRGDPLADLRLSVDGQRQLAFDLGDWADRYA +HGRWLATGGGGYNHVRVVPRAWTHLIGAVTGQPVPSSTPVPESWLEHVRSLTPDDLEGDM +SLFEGAEEDRYPLTMTEDADVWWRSWEVGYDPADPVDQTIMATRREVFPIHGLDPWFD +>PROKKA_01734 +MSTTSTPPAPTPAAVVWDSSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVRIVEP +PVATDEQLALVHDPEYVAAVRRAAATSSAEDGRFGLGTEDCPVFPDLHESAARIAGGSLA +AAEAIWSGEVDRAVNFAGGMHHAARSSASGFCIYNDCAVAIQRLLDLGAERVAYVDVDAH +HGDGTQSVFYDDPRVLTISLHETGISLFPGTGFANEIGGAAAQGTAVNVALPPRTGDAGF +LRAAHAVVPPLLEAFAPDVLVSQHGCDGHRTDPLADLRLTVDGQRQLAFDVGDWADRFAH +GRWLATGGGGYNPLRVVPRAWAHLTAAVLQTPIPVKSEIPAAWIEHVRALTADELTGDMS +VHVGDDAERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRREVFPLHGLDPWFD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001464.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001464.fa new file mode 100644 index 0000000000000000000000000000000000000000..73b9d73af5779c9497a3f7ba65176d7d789668ff --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001464.fa @@ -0,0 +1,25 @@ +>PROKKA_01815 +MADTPQRTDPNAPVLVVGLGRFGAATAEELVAQGREVLAVERDPVLVQRYAPSLTHVVEA +DATDSEALRQLGAQDFSTAVVGVGTSIEASVLITVNLVDLEIPHIWVKAISEAHGTILKR +IGANHVIFPEHDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPAECVGFTLAESHVRSKY +GVTVVGVKTPGEDFTYAQPDTRVGPRDTLIVSGHTDLIDRFAARP +>PROKKA_01512 +MADTPQRTDPNAPVLLVGLGRFGAATAEELVAQGREVLAVERDPVLVQRYAPSLTHVVEA +DATDSEALRQLGAQDFSTAVVGVGTSIEASVLITVNLVDLEIPHIWVKAISEAHGTILKR +IGANHVIFPEHDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPAECVGFTLAESKVRSKY +GVTVVGVKTPGEDFTYAQPDTRVGPRDTLIVSGHTDLIDRFAARP +>PROKKA_01059 +MADPQRTDPNAPVLVVGLGRFGAATAEELVAQGREVLAIERDPVLVQRFAPSLTHVVEAD +ATDPEALRQLGAQDFSTAVVGVGTSIEASVLITANLVDLEIQHIWVKAISEAHGTILKRI +GANHVIFPEHDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPAECVGFTLGESNVRSKYG +VTVVGVKTPGEDFTYAQPDTRVGARDTLIVSGHTDLIDRFAARP +>PROKKA_00994 +MADQPRTDPNAPVLVIGLGRFGAATAEELVTQGREVLAIERDPVLAQRFAPTLTHVVEAD +ATDAEALRQLGAQDFDVAVVGVGTSIEASVLITANLVDLEIPHIWVKAISDAHGTILKRI +GAQHIIFPEKDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPTETVGFTLEESNVRQKYG +VTIVGVKTPGEDFTYAQPHTRVGPRDTLIVSGHTDLIDRFAARP +>PROKKA_01736 +MADTPQRTDPNAPVLVVGLGRFGAATAEELVAQGREVLAVERDPVLVQRYAPSLTHVVEA +DATDPEALRQLGAQDFSTAVVGVGTSIEASVLITVNLVDLEIPHIWVKAISEAHGTILKR +IGANHVIFPEHDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPAECVGFTLAESHVRSKY +GVTVVGVKTPGEDFTYAQPDTRVGPRDTLIVSGHTDLIDRFAARP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001465.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001465.fa new file mode 100644 index 0000000000000000000000000000000000000000..22a1df7f88bd9b64ff3ca05afe0cebfc5c812924 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001465.fa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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001467.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001467.fa new file mode 100644 index 0000000000000000000000000000000000000000..2e33f6e14db62d6b988a2149be58fa303f371d3b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001467.fa @@ -0,0 +1,35 @@ +>PROKKA_01818 +MRLGVLDIGSNTVHLLLVDAHPGARPVAYAEHKRSLPLIRYQDADGAITEEGQRELVDFV +REAAAFAEEHRAEDMISFCTSAIRESANGAAVLARVQAETGVHLSELTGDQESAMTYFAV +RRWQGWDAGSILNFDIGGGSFEIAYGQDELPSHALSLPLGAGRLTRDWVPEDPPSPKAVK +KLRKHVEKRLEEAYTVFPRIESPVVVTATSKTFRSLARITGAAPSAAGPFVKRHLRADDL +HLWVNRLAAMTIAERAELPGVSDVRAHQVFAGAIVALTAMRTFGIAQLEICPWALREGLI +LNRLDALMLEGHLTRDGLPGVGHVNLNPDTLLPGLSLGVR +>PROKKA_01515 +MRLGVLDIGSNTVHLLLVDAHPGARPVAYAEHKRSLPLIRYQDADGAITEEGQRELVDFV +REAAAFAEEHRAEDMISFCTSAIRESANGAAVLARVQAETGVHLSELTGDQESAMTYFAV +RRWQGWGAGSILNFDIGGGSFEIAYGQDELPSHALSLPLGAGRLTRDWVLEDPPSPKAVK +KLRKHVEKRLEEAYTAFPRIESPVVVTATSKTFRSLARITGAAPSAAGPFVKRHLRADDL +HLWVNRLAAMTVAERAELPGVSDVRAHQVFAGAIVALTAMRTFGIAQLEICPWALREGLI +LNRLDALMLEGHLTRDGRPGVGHVNLNPDTLLPGLSLGVR +>PROKKA_01052 +MRLGVLDIGSNTVHLLLVDAHPGARPSAYAEHKRSLPLIRYQDAEGAITEEGQHELVDFI +REAVAFAEEHRAEDMISFCTSAIRESANGAEVLARVDREAGVHLAELSGDQESAMTYFAV +RRWQGWDAGSILNFDIGGGSFEIAYGQDELPSHALSLPLGAGRLTRDWLPEDPPSPKAVK +KLRKHVEKRLEEAFAAFPPVEAPVAVTATSKTFRSLARLTGAAPSAAGPYVKRHLRADDL +HLWVNRLAAMTAAERADLPGVSEVRAPQVLAGAIVALAAMRTFGIAQLEICPWALREGLI +LNRLDALMLEGHLTHDGLPGVGHVNLNTDTLLPGLRLGVR +>PROKKA_00990 +MRLGVLDIGSNTVHLLLVEARAGARPTPYAEHKRSLPLIRYLDESGAINEEGQDELVGFI +GEAVAFAEEHRAEDMISFCTSAIREAENGPAVLARVEAETGVHLSELSGEQEASMTYFAV +RRWQGWGVGSILNFDIGGGSFEIAYGQDELPSHAVSLPLGAGRLTRERLPDDPPSPKAVK +KLHKHVSREIEAVFADFPPLEAPYVVTATSKTFRSLARLTGAAPSAAGPYVKRHLRADDL +QLWVNRLAAMTWEQRAELPGVSEVRAPQVLAGALVALAAMRTFGVAQLEICPWALREGLI +LNRLDALMLEGHLTREDGLGVGHVNLNTDSLLPGLSLGVR +>PROKKA_01739 +MRLGVLDIGSNTVHLLLVDAHPGARPVAYAEHKRSLPLIRYQDADGAITEEGQRELVDFV +REAAAFAEEHRAEDMISFCTSAIRESANGAAVLARVQAETGVHLSELTGDQESAMTYFAV +RRWQGWGAGSILNFDIGGGSFEIAYGQDELPSHALSLPLGAGRLTRDWVLEDPPSPKAVN +KLRKHVEKRLEEAYTAFPRIESPVVVTATSKTFRSLARITGAAPSAAGPFVKRHLRADDL +HLWVNRLAAMTVAERAELPGVSDVRAHQVFAGAIVALTAMRTFGIAQLEICPWALREGLI +LNRLDALMLEGHLTRDGRPGVGHVNLNPDTLLPGLSLGVR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001468.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001468.fa new file mode 100644 index 0000000000000000000000000000000000000000..9c8e9f7274443727ec9a428d70c36bd655b9f2ae --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001468.fa @@ -0,0 +1,85 @@ +>PROKKA_01819 +MSTSSASVTAPVPEGKKLVIVESPAKSKSIAKYLNAVGSGWVVDSSVGHIRDLPKPSDLP +ADMKKGPFGKFAVDTEHGFTPYYVVHPDKKKKVAELKRELKDAEALYLATDADREGEAIA +WHLLDTLKPTVPVYRMTFGEITQEGVRRGLENIRELDTALVDAQETRRILDRLFGYELSP +VLWRKVSRGLSAGRVQSVATRLVVERERERMAFVSAHYWGVEGTFTVAEGAQAADAVGSS +FTARLSTVDGERVATGRDFDDAGRLKASAGKKVTHLDEAGARSLAEGLRGADFTVDSVED +KPYTRRPAAPFTTSTLQQEAARKLRMSSRVSMQVAQRLYENGYITYMRTDSVNLSQEAVQ +AARRQATELYGADAVPAQPRVYAKRNETAQEAHEAIRPAGDSFRTPAQVKAELRPDEFRL +YELIWKRTVASQMADAKGYTATLRLSATAQDGRLAQFSASGTVITFKGFLDAYEEGRDAE +VDGENAEAKDRRLPQVAQGERLTGDPIEATGHETSPPARYTEASIVAELERREIGRPSTY +APTISTIMDRGYVSKRGTALVPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGE +LGREAWLQTFYFGAPAAETEKGVEGLKHVVDNLGEIDARAVNSLPITEDITLRVGQYGPY +LERSLPADAEAGATPPRANVPEDLAPDELTPAKAEELFATAQPSERELGTDPETGRTIVA +KDGRYGPYVTEVIPEMTEEELQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFTSMSV +DTVTLEQALQLMSLPRVVGADAEGEVITAQNGRFGPYLKKGSDSRSLESEDQIFSITQEQ +ALEIYAQPKQRGRGAAKPPLAEFGEDPVSGKKVTVKEGRFGPYITDGVTNITVPRGRRPE +ELTAEEAYQLLADKRAKGPATRGGAKKPAARKAPAKKTTARKKA +>PROKKA_01516 +MSTSSASVTAPVPEGKKLVIVESPAKSKSIAKYLNAVGSGWVVDSSVGHIRDLPKPSDLP +ADMKKGPFGKFAVDTEHGFTPYYVVHPDKKKKVAELKRELKDAEALYLATDADREGEAIA +WHLLDTLKPTVPVYRMTFGEITQEGVRRGLENIRELDTALVDAQETRRILDRLFGYELSP +VLWRKVSRGLSAGRVQSVATRLVVERERERMAFVSAHYWGVEGTFTVAEGAQAADAVGSS +FTARLSTVDGERVATGRDFDDAGRLKASAGKKVTHLDEAGARSLAEGLRGADFTVDSVED +KPYTRRPAAPFTTSTLQQEAARKLRMSSRVSMQVAQRLYENGYITYMRTDSVNLSQEAVQ +AARRQATELYGADAVPAQPRVYAKRNETAQEAHEAIRPAGDSFRTPAQVKAELRPDEFRL +YELIWKRTVASQMADAKGYTATLRLSATAQDGRLAQFSASGTVITFKGFLDAYEEGRDAE +VDGENAEAKDRRLPQVAQGERLTGDPIEATGHETSPPARYTEASIVAELERREIGRPSTY +APTISTIMDRGYVSKRGTALVPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGE +LGREAWLQTFYFGAPAAETEKGVEGLKHVVDNLGEIDARAVNSLPITEDITLRVGQYGPY +LERSLPADAEAGATPPRANVPEDLAPDELTPAKAEELFATAQPSERELGTDPETGRTVVA +RDGRYGPYVTEVIPEMTEEELQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFTSMSV +DTVTLEQALQLMSLPRVVGADAEGEVITAQNGRFGPYLKKGSDSRSLESEDQIFSITQEQ +ALEIYAQPKQRGRGAAKPPLAEFGEDPVSGKKVTVKEGRFGPYVTDGVTNITVPRGRQPE +ELTAEEAYQLLADKRAKGPATRGGAKKPAARKAPAKKTTARKKA +>PROKKA_01051 +MPTTPASVTASVPEGKKLVIVESPAKSKSIAKYLNAVGEGWVVDSSVGHIRDLPKPSDLP +ADMKKGPFGKFAVDTENGFAPYYVVHPDKKKKVTELKRELKDAVALYLATDADREGEAIA +WHLLDTLKPKVPVYRMTFGEITKEGVRRGLENIRELDTHLVDAQETRRILDRLFGYELSP +VLWRKVSRGLSAGRVQSVATRLVVERERERMAFVSAAYWGVEGTFTVAPGAQAADAVGSS +FTARLSTVDGERVATGRDFDDAGALKASAGKKVTHLDEAAASSLAQGLRGADFTVDAVED +KPYTRRPAAPFTTSTLQQEASRKLRMSSRVSMQVAQRLYENGYITYMRTDSVNLSQEAVQ +AARRQATELYGQDAVPAQPRVYAKRNESAQEAHEAIRPAGDSFRTPAQVKAELRPDEFRL +YELIWKRTVASQMADAKGYTATLRFSATAQDGRAAQFSASGTVITFKGFLDAYEEGKDAE +TEDEKAEAKDRRLPQVAEGERLVGEPIEATGHETSPPARYTEASIVAELERREIGRPSTY +APTISTIMDRGYVSKRGNALVPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGE +LGREAWLQTFYFGAPASETGKGVEGLQQVVENLGEIDARAVNSLPITDEITLRVGQYGPY +LEKPLPADAEAGSTPPRANVPEELAPDELTPAKAEELFATAKPSERELGTDPETGRAVVA +KDGRYGPYVTEVIPEMTEEQLQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFSSMSV +DTVTLEEALRLMSLPRVVGADAEGEVITAQNGRFGPYLKKGTDSRSLESEDQIFTITQEQ +ALEIYAQPKQRGRGAAKPPLAEFGEDPVSGKKVTVKEGRFGPYVTDGVTNITVPRGRQPE +ELTAEEAYQLLADKRAKGPATRKAPARKPAARKAPAKKSAPKKKA +>PROKKA_00989 +MPTASASTSSSVPQGKKLVIVESPAKSKSIAKYLNAVGEGWVVDSSVGHIRDLPKPSDLP +ADMKKGPYGKFAVDTEHGFTPYYVVHPDKKKKVTELKRELKDAEALYLATDADREGEAIA +WHLLDTLKPKVPVYRMTFGEITKEGVRRGLENIRELDTHLVDAQETRRILDRLFGYELSP +VLWRKVSRGLSAGRVQSVATRLVVERERERMAFVAAQYWGVEGTFTVGPDAKADGAAGSS +FTARLSTVDGARVATGRDFDDAGRLKESAGKKVAHLDEAAAASLAEGLDGKDFTVDSVED +KPYTRRPAAPFTTSTLQQEASRKLRMSARVTMQVAQRLYENGYITYMRTDSVNLSQEAVQ +AARRQATELYGQESVPTQPRVYAKRTENAQEAHEAIRPAGDSFRTPAQVKAELRPDEFRL +YELIWKRTVASQMADAKGYTATLRFSAQAEDGRTAQFAASGTVITFKGFLDAYEEGRDAE +PEEEKDAKDRRLPQVAEGETLTGAPIQPTGHETTPPARYTEASIVAELERREIGRPSTYA +PTISTIMDRGYVSKRGSALVPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGEL +AREAWLQTFYFGADSADTQKGVEGLKHVVENLGEIDARQVNSLPVTEDITLRVGQYGPYL +ERRLPEGAAEGTAPERANVPEDLAPDELTPAKAEELMAAGGADERELGVDPETGRTVVAK +DGRYGPYVTEVIPEMGEEELQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFKTMSVD +TVTLEQALQLMSLPRIVGADAEGEVITAQNGRFGPYLKKGTDSRSLESEDQIFTVTQEQA +LEIYAQPKQRGRGTAKPPLAEFGEDPVSGKKVTVKEGRFGPYVTDGVTNITVPRGRAPEE +LTAEEAYQLLADKRAKGSAKKPAAKKPAARKPAAKKTTTSTTTRKKA +>PROKKA_01740 +MSTSSASVTAPVPEGKKLVIVESPAKSKSIAKYLNAVGSGWVVDSSVGHIRDLPKPSDLP +ADMKKGPFGKFAVDTEHGFTPYYVVHPDKKKKVAELKRELKDAEALYLATDADREGEAIA +WHLLDTLKPTVPVYRMTFGEITQEGVRRGLENIRELDTALVDAQETRRILDRLFGYELSP +VLWRKVSRGLSAGRVQSVATRLVVERERERMAFVSAHYWGVEGTFTVAEGAQAADAVGSS +FTARLSTVDGERVATGRDFDDAGRLKASAGKKVTHLDEAGARSLAEGLRGADFTVDSVED +KPYTRRPAAPFTTSTLQQEAARKLRMSSRVSMQVAQRLYENGYITYMRTDSVNLSQEAVQ +AARRQATELYGADAVPAQPRVYAKRNETAQEAHEAIRPAGDSFRTPAQVKAELRPDEFRL +YELIWKRTVASQMADAKGYTATLRLSATAQDGRLAQFSASGTVITFKGFLDAYEEGRDAE +VDGENAEAKDRRLPQVAQGERLTGDPIEATGHETSPPARYTEASIVAELERREIGRPSTY +APTISTIMDRGYVSKRGTALVPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGE +LGREAWLQTFYFGAPAAETEKGVEGLKHVVDNLGEIDARAVNSLPITEDITLRVGQYGPY +LERSLPADAEAGATPPRANVPEDLAPDELTPAKAEELFATAQPSERELGTDPETGRTVVA +RDGRYGPYVTEVIPEMTEEELQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFTSMSV +DTVTLEQALQLMSLPRVVGADAEGEVITAQNGRFGPYLKKGSDSRSLESEDQIFSITQEQ +ALEIYAQPKQRGRGAAKPPLAEFGEDPVSGKKVTVKEGRFGPYVTDGVTNITVPRDRQPE +ELTAEEAYQLLADKRAKGPATRGGAKKPATRKAPAKKTTARKKA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001469.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001469.fa new file mode 100644 index 0000000000000000000000000000000000000000..e94d48ff831213d97b8a2a1ac29d7cf54ff9c3d5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001469.fa @@ -0,0 +1,55 @@ +>PROKKA_01820 +MSPVPTPPSPPAPRLTPATAVALAADLAALPFTTAAVEGLLGPVATLALDREHAEAARRV +VAGHLAGPGRHDDAAGPGDRPGTRGLAAAVGAWLLGDPVPAADLDAALPSLGLAGAVAAG +LVVEGPDGRVRGAVDLSPYEADEPGRMWIASDLTALQRRGPLPPEHVLGVGRASLTLAGA +TQRRPVARALDVGVGCGIQTLHLLAHADHVTATDLSERALAFTRFNLLLNADVLGLDRER +LEDRVRLAAGDLLAPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGREGDRIVAELI +AALPDVLAEGGTAQLLANWEIPAGDTADADTAPWDARPRSWVASGMQAWFIQRDRQDPAG +YAETWLQDSSLELDPPAYEAAYRGYLDDFAARGVAGVGFGHVWLRRPAADGSQGRGWVVA +EELTQAVDEALGTAWAAAVARRDRLTAGAGAGDAVGDPALAALRGLHLRVAADVTEERHQ +RFGAEHPEVILARQGSGFRRVARLDTATAGVLSASDGELSVGQLVGAVAALLELDDVGRA +GLLAALRELYEDGFLVEG +>PROKKA_01517 +MSPVPTPPSPPAPRLTPATAVALAADLAALPFTTAAVEGLLGPVATRALDREHAEAARRV +VAGHLAGPGRHDDAAGPGDRHGTRGLAAAVGAWLLGDSVPAADLDAALPRLGLAGAVAAG +LVVEGPDGRVRGAVDLSPYEADEPGRMWIASDLTALQRRGPLPPEHVLGVGRASLTLAGA +TQRRPVARALDVGVGCGIQTLHLLAHADHVTATDLSERALAFTRFNLLLNADVLGLDRDR +LEDRVRLAAGDLLAPVTGERFDLVVSNPPFVITPRTDPGAPVLIYRDGGREGDRIVAELI +AALPDVLAEGGTAQLLANWEIPAGDTANADTAPWDARPRSWVAPGMQAWFLQRDRQDPAG +YAETWLQDSSLELDPPAYEAAYRGYLDDFAARGVAGVGFGHVWLRRPAADGSQGRGWVVA +EELTQPVDEALGAAWAAAVARRDRLAAGAGAGDAVGDPALAALRGLHLRVAADVTEERHQ +RFGAEHPEVILARQGSGFRRVARLDTATAGVLSASDGELSVGQLVGAVAALLELDDVGRA +GLLAALRELYEDGFLVEG +>PROKKA_01049 +MKPPAPSPSSPSLPAPRLTPATAAALDADLAALPYTTAAVEELLGPVATAALDREHAEPA +RRVVARVLTAAPGDHTQALYDDGALGSGARPLEAGIGSPAARRALAALVSVWMLGDAADA +ADVAAALPALGLDGAREAGLVAEEGGGTVRGTVDLSPYEADEPGRMWVASDQTALQRRGP +LPEDHVLGIGRASLTLAGATQRRPVACALDVGVGCGIQTLHLLAHAEHVTATDLSERALE +FTRFNLLLNADVLGLDRERLEDRVRLAAGDMLAPVAGERFDLVVSNPPFVITPRTDPDAP +VLTYRDGGREGDRIVAELVAALPAHLTEGGTAQLLANWEIPAGAAAIPAAAAASADGDLA +DTAGPAPWDARPRSWIAPGMQGWIIQRDAQDPAGYAETWLQDSSLELDPHRYEAAYRGYL +EDFAARGVAGVGFGHVWLRRPVDDGAQGRAWTVAEELTQPVDEALGAAWAAAVARRDRLA +AGAPDGAGDPALAALRGLHLRVAEDVSEERHGRFGAEHPEVILARQGAGFRRTARLDTAT +AGVLSASDGELSVGQLVGAVAALLELDDAGRAGLLAAIRELYEDGFLVERAED +>PROKKA_00988 +MSLPAPHLSPAAAAALAADLTALPYTTDVVETLLGPVATAALDREHAVAARRVVAGVLAA +PAARDAAAASRPLAAVVGAFMLGEPVPAADLAAALPALGLDGAVEAGLVVLDGADTGAER +ARATVDLSPYAADEPGPMWVASDQTALQRRGPLPEDHVLGIGRASLTLAGATQRRPVARA +LDLGVGCGVQTLHLLAHAEHVTATDLSERALDFTRFNLLLNADVLRLDRERLEDRVRLAA +GDLLGPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGREGDRLVAELIAALPEHLVE +GGTAQLLANWEIPAGAAEIPAGAAEVPAGDDAPPAWDARPRSWVGPGMQAWFVQRDRQDP +AGYAETWLQDSSLELDPAAYEAAYRGYLDDFAARGVTGVGFGHVWLRRPAADRSQGRAWT +VAEELTQPLDEALGTAWAAAVARRDRLAAGPEAGATDAVVTGDPALAALRGLHLRVAEDV +TEERHSRFGAEHPEVILARQGAGFRRTARLDTATAGVLSASDGELSVGQLVGAVAALLEL +DDAGRAGLLAAVRELHEDGFLLEA +>PROKKA_01741 +MSPVPTPPSPPAPRLTPATAVALAADLAALPFTTAAVEGLLGPVATLALDREHAEAARRV +VAGHLAGPGRHDDAAGPGDRPGTRGLAAAVGAWLLGDPVPAADLDAALPSLGLAGAVAAG +LVVEGPDGRVRGAVDLSPYEADEPGRMWIASDLTALQRRGPLPPEHVLGVGRASLTLAGA +TQRRPVARALDVGVGCGIQTLHLLAHADHVTATDLSERALAFTRFNLLLNADVLGLDRER +LEDRVRLAAGDLLAPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGGEGDRIVAELI +AALPDVLAEGGTAQLLANWEIPAGDTADADTAPWDARPRSWVAPGMQAWLLQRDRQDPAG +YAETWLQDSSLELDPPAYEAAYRGYLDDFAARGVAGVGFGHVWLRRPAADGSQGRAWVVA +EELTQPVDEALGTAWAAAVARRDRLAAGAGAGDAVGDPALAALRGLHLRVAADVTEERHQ +RFGAEHPEVILARQGSGFRRVARLDTATAGVLSASDGELSVGQLVGAVAALLELDDVGRA +GLLAALRELYEDGFLVEG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001470.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001470.fa new file mode 100644 index 0000000000000000000000000000000000000000..6a706a9b545ee4d969b3dfacddf5b7603e884523 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001470.fa @@ -0,0 +1,35 @@ +>PROKKA_01821 +MSTAALSRIALYYRFTPLADPEAVRLWQRTLAASLGLTGRIIVSPQGINGTVGGPVDAVK +RYVRGTREHPAFRDLEVKWSDGSAADFPRLSVKLKPELVAFGAPERVTVDADGVVGTGER +LTPAQVDALVAERAGSANPVRFLDGRNTVEAAIGRFDGAVVPDAHTTRDLLAAVDSGALD +HLKDAPLITYCTGGVRCEVLSALLKDRGFAEVYQLDGGIVRYGEARGDAGLWRGELAVFD +RRLSTRFTADAETIGRCVTCEAPTSALRNCADPACTTLEVRCAACAVDDPERRCPVCVHH +PHPAERTEA +>PROKKA_01518 +MSTAPLSRIALYYRFTPLADPEAVRLWQRTLAASLGLTGRIIVSPQGINGTVGGPVDAVK +RYMRGTREHPAFRDLEVKWSDGSAADFPRLSVKVKPELVAFGAPERVTVDADGIVGTGER +LTPVQVDALVAERAGTANPVRFLDGRNTVEAAIGRFDGAVVPDAHTTRDLLAAVDSGALD +HLKDAPLITYCTGGVRCEVLSALLKDRGFAEVYQLDGGIVRYGEARGDAGLWRGELAVFD +RRLSTRFTADAETIGRCVTCHAPTSALRNCADPACTTLEVRCAACAVDDLEHRCPFCAHR +PHPAERTEA +>PROKKA_01048 +MSPAPVSRIALYYRFAPLADPEAVRLWQRTLAASLGLTGRIIVSPQGINGTVGGPVDAVK +QYVKGTREHPALKDLEVKWSDGSAADFPRLSVKVRPELVAFGVPERITVDEHGVVGTGER +LTPERLEALVAERAGTENPVRFLDGRNTVEAQIGRFDGAVVPAAHTTRDLLAAVDSGSLD +HLRDAPLVTYCTGGVRCEVLSALLKDRGFREVYQLDGGIVRYGEAFGDAGLWRGELAVFD +RRIALRFSEDAETIGRCVTCEAPTSALRNCSDPACTTLEVRCAACAAADPDRRCPVCTER +SAA +>PROKKA_00987 +MTAAAPAAPTPLPAPGGPGRIALYYRFTPLADPEAVRLWQRTLAVSLGLAGRIIVSPQGI +NGTVGGPAEAVKRYVRGTREHPAFRGLEVTWSDGSAADFPRLSVKVRPELVAFGAPERIR +VDEHGVVGTGEHLPADQLHALVAERAAQGRPVRFLDGRNSVEAAIGRFEDAVIPAAHTTR +DLLEAVDSGSLDHLKDQPVVTYCTGGVRCEVLSALLKDRGFSEVYQLDGGIVRYGEAHGD +AGLWHGRLAVFDRRLSLAFTDGAETLGRCVTCGGATSHLANCADPACTTLQVRCPDCVAA +HPDHVCPRCLERTPA +>PROKKA_01742 +MSTAALSRIALYYRFTPLADPEAVRLWQRTLAASLGLTGRIIVSPQGINGTVGGPVDAVK +RYVRGTREHPAFRDLEVKWSDGSAADFPRLSVKLKPELVAFGAPERVTVDADGVVGTGER +LTPAQVDALVAERAGSANPVRFLDGRNTVEAAIGRFDGAVVPDAHTTRDLLAAVDSGALD +HLKDAPLITYCTGGVRCEVLSALLKDRGFAEVYQLDGGIVRYGEARGDAGLWRGELAVFD +RRLSTRFTADAETIGRCVTCEAPTSALRNCADPACTTLEVRCAACAVDDPERRCPVCVHH +PHPAERTEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001472.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001472.fa new file mode 100644 index 0000000000000000000000000000000000000000..b7efdb6c6295eb47c1c553252742e2d105b0d57d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001472.fa @@ -0,0 +1,79 @@ +>PROKKA_01823 +MTGHLPEHDPWADPAGGWGPPGTADAAPPVDDAAPDSSGPEPQPVGEVVADVVAGLSVTA +PGDLCPDTPAGAGLRAALGRTGLPEQIRHVTELPARQARHTDWPADAPEGLVRAFAARGV +ERPWLHQVRAAALAGAGTHTVLATGTASGKSLGYQLAVGTRLAADPRATALYLAPTKALA +ADQLTSWRALERDGAPGLRSAPYDGDTAPQDRIWAREHASVLMTNPDMLHVGILPHHERW +ATFFRNLAFVVVDESHTYRGVFGSQVGILLRRLRRIAAHYRGDRPETVFIGASATSADPA +GHFARLIGAPAAAVTEDASPHGAVTVAFWEPELTDRRGENGAPVRRSAMAAAADLVTDLA +LQQVRTLAFIRSRRGAEAIASAAKRQLEEVEPGLGTRIAAYRSGYLPEERRELEADLRSG +RLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQQIGRAGRGGQDALAFFVASDDPL +DTFVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPITPEAFGWFGEPERVRALL +DVLVDQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAESGALLGTMDSPQTHYQ +AHPGAVYVHQDRTYLVEELDEDAHAVVVTRAWPDFTTQARDVTEVEIVAVHRRLDAREGT +LRWCLGDVQVRTQVVSFQRKALASGEVLGEEPLDLPARDLFTSAVWFQAASDELIAAGLT +TDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSPAVFVYDGRPGGAGFAE +RGFEQARRWVEATAGAIAACECAEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLMDHADH +LVPADASTDGSGGGASGGSSGGATDAAPGA +>PROKKA_01520 +MTGHLPEHDPWADPAGGWGPPGTADSAPPVDDAAPDFSGPEPQPVGAVLADVVAGLSVTA +PGDLRPDTPAGAGLRAALGRTGLPEQIRHVTELPARQARHTDWPADAPEGLVRAFAARGV +ERPWLHQVRAAALAGAGTHTVLATGTASGKSLGYQLAVGTRLAADPRATALYLAPTKALA +ADQLTSWRALERDGAPGLRAAPYDGDTAPQDRIWAREHATVLMTNPDMLHVGILPHHERW +AAFFRNLTFVVVDESHTYRGVFGSQVGILLRRLRRIAAHYRGDRPETVFIGASATSADPA +GHFARLIGAPATAVTEDASPHGAVTVAFWEPELTDRRGENGAPVRRSAMAAAADLVTDLA +LQQVRTLAFIRSRRGAEAIASAAKRQLEEVEPGLGTRIAAYRSGYLPEERRELEADLRSG +RLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQQIGRAGRGGQDALAFFVASDDPL +DTFVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPITPEAFGWFGEPERVRALL +DVLVEQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAESGALLGTMDSPQTHYQ +AHPGAVYVHQDRTYLVEELDEDAHAVVVTRAWPDFTTQARDVTEIEIVAVHRRLDAREGT +LRWCLGDVQVRTQVVSFQRKALVSGEVLGEEPLDLPARDLFTSAVWFQAASDELIAAGLT +TDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSPAVFVYDGRPGGAGFAE +RGFEQARRWVEATAGAIAACECTEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLMDHADH +LVPADASTDGSGGGASGGSADPAPGA +>PROKKA_01046 +MSTPPPEPAAAGVAFDPWADPAAGWGAPDDGPSDRRDAPADVDETDHPGDEAHPWDEPAP +LADAVADVVAGLSVSRPGDPVAGGEAADVLRGALGRHGLPEQIRHVVTLPAREARHADWP +SEAPEALVGAFAGRGIERPWAHQVRAATVAGAGTHTVVATGTASGKSLAYQLAAGIRLSG +DPHATVLHLSPTKALAADQLLAWRALERDGATWLRAAPYDGDTAPPDRIWAREHANVLMT +NPDMLHVGILPHHERWARFFRHLAFVVVDESHSYRGVFGSQVGILLRRLRRVAAHWRGDR +PEPVFIGASATSADPAGHFSRLIGAPATAVAEDASPHGAVTVAFWEPELTDRRGENGAPV +RRSAMAASADLLTDLALQQVRTLAFIRSRRGAEAIASAARRQLEELEAGLGSRIAAYRSG +YLPEERRALEADLRSGRLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQQIGRAGR +GGQDALAFFVASDDPLDTYVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPLTP +EAFERFGDPERVRALLDVLVEQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAE +SGTLLGTMDSPQTHYQAHPGAVYVHQDRTYLVEELDEDAHAVIVTRAWPDFTTQARDVTE +IEIVDVHRRLDAREGTLRWCLGDVQVRTQVVSFQRKALVSGEVLGEEPLELPARDLFTSA +VWFQASSEELIAAGLTMDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSP +AVFVYDGRPGGAGFAERGFAQARRWVEATAGAIAACECEAGCPSCVQSPKCGNRNSPLDK +AGALTVLRFLLGQADHLVPVVAEGSGETDGGTDDGVGVDGEDASGSGSSGTA +>PROKKA_00985 +MTGGPVPWPDDDPWAARGPAEDRSARDVPTPAPGGPGWEPPQELATGDPEARAAFAAALG +RRSLPAQIRHVTTIPARTPRSAPWPAGTPAGLVRAFAARGVQAPWEHQARGTAAALAGRH +TVLATGTASGKSLAYQLAVGATLAADPRATVLYLAPTKALAADQLASWRALERDGAAWLR +AAPYDGDTAPQDRIWAREHANVLLTNPDMLHVGILPHHERWAVFFRNLAYVVLDESHTYR +GVFGSQVGILLRRLRRVVAHYRGERPETVFIGASATSAAPAEHLATLIGAAPGEVEAVTE +DASPHGAVHVAFWEPELTDRRGENGAPVRRSATATAADLLTDLALQQVRTLAFIKSRRGA +ETIAGAAKRQLEEVEAGLGSRIAAYRSGYLPEERRALEEALRSGRLLGMASTPALEMGID +VAGLDAVVVAGWPGTRASFFQQIGRAGRGGQDALAFFVASDDPLDTFVVEHPGAVFDLGV +EDTVLDPANPHLLGPQLCAAAAELPLRPEDLPWFGGPERVRELLDVLVEQGLLRRRPAGW +FWTHTEHAASLVSLRDDGGGPMDIIDVESGALLGTMDSPQTHYQAHPGAVYVHQDRTFLV +EDLDEDAHAVLVQRAWPDFTTQARDVTEIEIVAVHRRLDAAGSSLRWCLGDVQVTTQVIS +FQRKALLSGEVLGEEPLDLPARDLFTSAVWFQAASEELVAAGLTMDRLPGALHAAEHAMI +GMMPLVASNDRWDIGGVSMVLHPDTGVPTVFVYDGRPGGAGFAERGFAQARRWVEATAGA +IAACECAEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLAERFDGLIEVPAHLPDVTA +>PROKKA_01744 +MTGHLPEHDPWADPAGGWGPPGTADAAPPVDDAAPDSSGPEPQPVGEVVADVVAGLSVTA +PGDLRPDTPAGAGLRAALGRTGLPEQIRHVTELPARQARHTDWPADAPEGLVRAFAARGV +ERPWLHQVRAAALAGAGTHTVLATGTASGKSLGYQLAVGTRLAADPRATALYLAPTKALA +ADQLTSWRALERDGAPGLRSAPYDGDTAPQDRVWAREHASVLMTNPDMLHVGILPHHERW +AAFFRNLAFVVVDESHTYRGVFGSQVGILLRRLRRIAAHYRGDRPETVFIGASATSADPA +GHFARLIGAPARAVTEDASPHGAVTVAFWEPELTDRRGENGAPVRRSAMAAAADLVTDLA +LQQVRTLAFIRSRRGAEAIASAAKRQLEEVEPGLGTRIAAYRSGYLPEERRELEADLRSG +RLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQQIGRAGRGGQDALAFFVASDDPL +DTFVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPITPEAFGWFGEPERVRALL +DVLVEQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAESGALLGTMDSPQTHYQ +AHPGAVYVHQDRTYLVEELDEDAHAVVVTRAWPDFTTQARDVTEIEIVAVHRRLDARAGT +LRWCLGDVQVRTQVVSFQRKALVSGEVLGEEPLDLPARDLFTSAVWFQAASDELIAAGLT +TDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSPAVFVYDGRPGGAGFAE +RGFEQARRWVEATAGAIAACECAEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLMDHADH +LVPADASSDGSGGASGGATDAAPGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001473.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001473.fa new file mode 100644 index 0000000000000000000000000000000000000000..1866dddc02381a214c0a96a0b8f5b65f657bc806 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001473.fa @@ -0,0 +1,20 @@ +>PROKKA_01824 +MTRGRAPARGERGSGTVSVLGTAALGAGLLLAVAALGQASATGSRAAGAADLAALAASDA +RRGLSDHEPCVLAGRTAERNGAAVVACEVREDGTVRVAVELARAPLPAATADAVAGPPRS +QAPGAASVAPPEDPPEAPPPEPSVEASAGTR +>PROKKA_01521 +MTRGRAPVRGERGSGTVSVLGTAALGAGLLLAVAALGQASVTGARAAGAADLAALAASDA +RRGLSDHEPCVLAGRTAERNGAAVVACEAREDGTVRVAVELARAPLPAATADAVAGPPRS +QAPGAGSADPPEAPPPEPSVEASAGTR +>PROKKA_01045 +MTGRAPGGVPRGAASETGSGTVSVLGTAALGAGLLLAVAALGQASVAGAQAAGAADLAAL +AASDARRGLSAGEPCLVAGQTAARNRAVVVECEVRENGTVRVSVERGRAPLPPALAAAVA +GPPRLQAPQAVPEDPLPDASSPSTPTPSSVPPSVSPDPSATTGTR +>PROKKA_00984 +MSGTATALGTALLGAGLLTGVLAVGHASATAARASGAADLAALAASDARRGLGAVPDAGV +LEPCPLAEESARRNGAEVTECVLLPDGSVRVAVVIAADPLPASTAVAVAGPPVGPRGPVA +GPGRDDAPEDAPDTPGAPPEAATP +>PROKKA_01745 +MTRGRAPARGERGSGTVSVLGTAALGAGLLLAVAALGQASVTGSRAAGAADLAALAASDA +RRGLSDHEPCVLAGRTAERNGAAVVACEVREDGTVRVAVELARAPLPAATADAVAGPPRS +QAPGAASVAPPEAPPEPSLEASAGTR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001474.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001474.fa new file mode 100644 index 0000000000000000000000000000000000000000..0430e70749ab92bbfd391c8e25452ac79a1f00b5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001474.fa @@ -0,0 +1,19 @@ +>PROKKA_01825 +MTEHPTSASPSGRRTGARTAGRPRALRGGETGAVTAEYAVLLPVIAFVLVSVLLAGAAAV +QQVRGQDAAASAARILARGDDEAAARDAVARMAGDDASLSHTVEGGWVTVEVVQPGPGPL +AWAEVLTLTAHAAAPDQRPGTPAAGPEDRS +>PROKKA_01522 +MTEHPTSAPPSARRTGARTAGRPRGLRGGETGAVTAEYAVLLPVIAFVLVSVLLAGAAAV +QQVRGQDAAASAARILARGDDEAAARDAVARMAGDDASLSHTVEGGWVTVEVVQPGPGPL +AWAEALTLTAHAAAPEQRPGTPAAGPEDRS +>PROKKA_01044 +MTAEYAVLLPVIAFVLAAVLLAGAAAVQQVRGQDAATAAARILARGDGEAEARRAVARMA +GDDAALAHTADGGWVAVEVSQPGPGPLAWAEALTLTARAAAPQQHPGAAVDPDGGRT +>PROKKA_00983 +MADLPAEAPRPGRLRGARAGASGTVAFRDAERGEGERGAVTAEYAVLLPAAVAVLVAVLL +AGVAAVHQVRAQDAAASAARILARGDAESLARDAVGRMAGGDAALEARTAEGWVTVTVTR +PGPGPLAAVTLSAEAVAPVQATSPTPPGRTPGITAPTGEAAP +>PROKKA_01746 +MTEHPTSASPSGRRTGARTAGWPRALRGGETGAVTAEYAVLLPVIAFVLVSVLLAGAAAV +QQVRGQDAAASAARILARGDDEAAARDAVARMAGDDASLSHTIKGGWVTVEVVQPGPGPL +AWAEALTLTAHAAAPDQRPGTPAAGPEDRS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001476.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001476.fa new file mode 100644 index 0000000000000000000000000000000000000000..6206e39978f4ad098bb213475220a5d115bd184c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001476.fa @@ -0,0 +1,37 @@ +>PROKKA_01827 +MLVGALRRWAALVAAGLTEEQAWRETACTLPACGSGPGEAGAACCAHHRARRRAEALAWD +VPASHAPTGEAARGGGTLPWRTPARDPGWALVDAALAAGARAGAAPAAVARRLAHSLEAD +VDAARARRSAAAGPGATSRLLQWLPLGGLGLAWLLGTSPWDLARSPFGAVVAAVGLLFWL +AGRSWTRLLLRAAAREPAAVGAAVVLDVLAALLSAGRSLPAALDDLGRTLPGARGLRATA +ALLLWGRDWDEAWAGLDTDPVWIETAARLRPLHRSGMAGARTLAETAAAVRQQTRRADER +AAEELAVRLVMPLGLCLLPAFVCWGVVPVVMALLGAGPG +>PROKKA_01524 +MSPTTATGPARRSHAGRAVALLPWRAGRVPPEEETEVLIGVLRRWAALVAAGLTEEQAWR +ETACTLPACGSEPSEAGTACCAHHHARRRAEALAWDVPAAHAPTGEAARRGGTLPWRTPA +RDPGWALVDAALAAGARAGAAPAAVARRLAHSLEADVDAARARRSAAAGPGATSRLLQWL +PLGGLGLAWLLGTSPGDLVRSPFGAVVAAVGLLFWLAGRSWTRLLLRAAAREPAAVGAAV +VLDVLAALLSAGRSLPAALDDLGRTLPGARGLRATAALLLWGRDWDEAWVGLDTDPVWAE +TAARLRPLHRSGMAGARTLAETAAAVRQQTRRADERAAEELAVRLVMPLGLCLLPAFVCW +GVVPVVMALLGAGPG +>PROKKA_01042 +MSTAAPEDATEELVVVLRRWAALVSAGLTEEAAWRETVRMLPDDDGHARHAARLRAERLA +WDAAGDLSTGRDAPDVRGLRRDEHPPGDTHDASPDRSRRRWCPPWRTPPPDPGWALVDAA +LAAGARAGAAPAVVVRRLAESLEADVDAARARRSAAAGPAATARLLQWLPLGGVGLAWLL +GSSPWETVSTPFGAVVAAVGLLFWLAGRSWTRLLLRSAAREPAALTAPVVLDVLAALLGA +GRSLPAALDDLARTLPGARGLRVTSALLLWGRGWDEAWAGIGEETVWAEAAARLRPLHRS +GMAGARTLAESAAAARQQGRRADERAAEELAVRLVMPLGLCLLPAFVCWGVIPVVMALLG +AGA +>PROKKA_00981 +MIALPGRAEERAEERAQEVVEALRRWAGLTAAGMTPAEAWTAVAQASSPCGRPTPGCCPR +HEALRRAALARWGGPGRGAEGGQPRPGERSPWDLADAALAAAARAGASFSRTAARLADAL +EADVDASRARRTAAAGPRATARLLSWLPVGGLGLAWLLGMGPADLLATGFGWVLLVLGGV +LTAAGRAWTRLALRRGARPLGEASPGVVVDVAAVLLGAGRSLPAALDDVSAHLPGAADLR +VVAVLLRWGADWDEAWAPVTEEPRWAALGERLRPLHRTGMAGEAVLHQTAAALRQETRRA +DERGAEELAVRLVVPLGLCQLPAFVCWGVAPMALALLGAR +>PROKKA_01748 +MLVGVLRRWAALVSAGLTEEQAWRETACTLPACGPGPSEAGTACCAHHRARRRAEALAWD +VPASHAPTGEAARGGGTLPWRTPARDPGWALVDAALAAGARAGAAPAAVARRLAHSLEAD +VDAARARRSAAAGPGATSRLLQWLPLGGLGLAWLLGTSPWDLARSPFGAVVAAVGLLFWL +AGRSWTRLLLRAAAREPAAVGAAVVLDVLAALLSAGRSLPAALDDLGRTLPGARGLRTTA +TLLLWGRDWDEAWAGLDTDPVWIETAARLRPLHRSGMAGARTLAETAAAVRQQTRRADER +AAEELAVRLVMPLGLCLLPAFVCWGVVPVVMALLGAGPG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001477.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001477.fa new file mode 100644 index 0000000000000000000000000000000000000000..99b3b61803bc0eb239f4457fd294ef73d948b544 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001477.fa @@ -0,0 +1,44 @@ +>PROKKA_01828 +MRPFVPAAPARPPRGRRRRPAPPEGGRRFPWPRTGPAEPERTQVAAPPLAAPAAGPDGLD +AAVVRRRVAEARASAADGAEPPLAPLIAEALDVPIDDPRVAALVDELDGFGPLAPWVRTP +GVTDVLVDGAGAVWTDGDGGLVRRPDRLDPETARALAVRLLHRAGRRLDAAVPLADARVG +GVRVHAVLPPVSGGGTLLSLRIPAAATPSLAALADGWPDGALWADALEALVRDRATVLVS +GATGAGKTTLLSAALGRVPGDERIVVVEDTAEAAPDHPHVVALQCRAANAEGAGEVGLAE +LVRHALRMRPDRLVVGECRGAEVADVLTALNTGHQGAWGTLHANAAAEVPARLTAMASLA +GWRPETVAAQARAGVDAVLHIARDGHGRHPVELAVPDLRADGFALLPALTWRPGTEATGG +RTVEGPGMPALAARLAGRSGR +>PROKKA_01525 +MRPFVPAAPARPPRGRRRRPAPPEGSRRFPWPRTDPAEPERTQVAAPPLAAPAAGPGGLD +AAVVRRRVAEARASAADGAEPPLAPLIAEALDAPIDDPRVAALVDELDGFGPLAPWVRTP +GVTDVLVDGAGAVWTDGDEGLVRRPGRLDPETARALAVRMLHRAGRRLDAAVPLADARVG +GVRVHAVLPPVSGGGTLLSLRIPAATTPSLAALADGWPDGALWADALEALVRDRATVLVS +GATGAGKTTLLSAALGRVPGDERIVVVEDTAEAAPDHPHVIALQCRAANAEGAGEVGLAE +LVRHALRMRPDRLVVGECRGAEVADVLTALNTGHQGAWGTLHANAAAEVPARLTAMASLA +GWRPETVAAQARAGVDAVLHVARDGHGRHPVELAVPDPRADGFALLPALTWRPGTEATGG +RTVEGPGVPALAARLAGRSGR +>PROKKA_01041 +MRRRVAEARAAAAEGQEPALAPLVAEAIGVSATDPRVAALVDELDGFGPLAGWVRAPGVT +DVLVDGSGAVWTDGAEGLLRRPQRLDPHAAQALAMRLVHRAGRRLDAAVPLADARVDGVR +VHAVLPPVSGGGTLLSLRIPAARTPSLAELAAGWPDGDLWGEALEALVRDRASVLVSGAT +GTGKTTLLAAALGCVPGDERILTVEDTAEAAPEHPHVVALQCRAANAEGAGAVGLAELIR +HALRMRPDRLVVGECRGAEVADFLTALNTGHQGAWGTLHANGAADVPARLTAMGSLAGWG +PDTVAAQARAGVDAVVHLVRDRHGRHPVELAVPDPDARGFALLPALTWTPGPGPGDGSTA +EGPGLRALAARLAGRGSR +>PROKKA_00980 +MPAWVPDAPRPARRPALLPAGLSLPAPLLPDLRRVGRRRPGSDRGEPAHVGPDPDARLRR +AVAEAQARADPHAPPPLRETVSRALADLAAEDGDTPPSGCPRPAGLRDPDAVLEELVGFG +PLAPWVRRTGVTDVLVDAAGSVWTDGVEGLVRRPLILPEPTARALAVRLIGLAGRRLDPA +CPVADARVDGVRVHAVLPPVSGGGTVLSLRVPAAEPPSLDALAADWPDGERWRDAVVALV +RGRASVLVSGATGTGKTTLLAAALGLAGADERIVLVEDTAEAAPAHPHVISLQARAPTAD +GAGEVTLAELIRQALRMRPDRLVVGECRGPEVADLLTALNTGHQGAWGTLHANAAADVPA +RLAAMGALAGWSASAVAAQARAGVDAVLHVRRDGRGRHPVELAVPAPAAHPDAPLSVLPA +LTWDGGGTRAGPGLEVLEARLSGRGHG +>PROKKA_01749 +MRPFVPAAPARPPRGRRSRLAPPEVGRRFPWPRTGAAEPERTQVAAPPLAAPAAGPCGLD +VAAVRRRVAEARASAADGAEPPLAPLIAEALDAPIDDPRVAALVDELDGFGPLAPWVRTP +GVTDVLVDGVGAVWTDGDEGLVRRPGRLDPETAGALAVRLLHRAGRRLDAAVPLADARVG +GVRVHAVLPPVSGGGTLLSLRIPAATTPSLAALADGWPDGALWADALEALVRDRATVLVS +GATGAGKTTLLSAALGRVPGDERIVVVEDTAEAAPDHPHVVALQCRAANAEGAGEVGLAE +LVRHALRMRPDRLVVGECRGAEVADVLTALNTGHQGAWGTLHANAAAEVPARLTAMASLA +GWRPETVAAQARAGVDAVLHLARDGHGRHPVELAVPDPRADGFALLPALTWRPGTEAAGG +RTIEGPGVPALAARLAGRSGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001478.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001478.fa new file mode 100644 index 0000000000000000000000000000000000000000..25f836b5c193312687c3991f1ec59d36dcaff07d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001478.fa @@ -0,0 +1,30 @@ +>PROKKA_01829 +MPETPASPRPTSRDAVGTSDASLAGARDQLADLVARWGAAPADAPGHHDPVSLTTVPPEA +VPMWGFDWPRSGDPRPSAVLILFGALDDVPARHDAERVHPHVDVLLTQRAATLRQHAGQI +AFPGGRVDPEDGDVVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGHVVHPVLGWWRD +PSRVAVVDQAEAAAVFRMPVADLVDPANRCRVARPGGRRGETPGFLVGERLVWGFTAALL +DRVLGLLGWDVPWDDSRVRDARTHEILRD +>PROKKA_01526 +MPETPASPHPTSRDAAGTSDASLAGAREQLADLVARWGAPPAEAPGHHDPASLTTVPPEA +VPMWGFDWPRSGDPRPSAVLILFGALDDVPARHDAGRVHPHVDVLLTQRAATLRQHAGQI +AFPGGRVDPEDGDVVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGHVVHPVLGWWRD +PSRVAVVDQAEAAAVFRMPVADLVDPANRCRVARPGGRRGETPGFLVGERLVWGFTAALL +DRVLALLGWDVPWDDSRVRDARTHRILRD +>PROKKA_01040 +MAAVRDRLAALVERHGVPADQAPRDALTEIPASAVSTWGFDWPRAQRARPSAVLILFGSL +DDVPAHHADDRVHPDVDVLLTQRAATLRTHAGQIAFPGGRVDPEDADVVATALREAEEET +DLDPDGVEVLGVLPPVPVVVSGHVVHPVIGWWRDPSRVAVVDQAEAAAVFRMPVGDLVDP +ANRCRVARPGGRRGETPGFLVGERLVWGFTAALLDRILTLLDWDTPWDSGRVIDAHTHAP +LRG +>PROKKA_00979 +MSIPPLPPSSPSSARADLQRIVAEHGVAPVAGDDEAGLTTIPASSVRVWGFDWPQAARPR +ASAVLILVGELDDVPAAHDGRACGVSPAVDVLLTQRAAGLRTHAGQVAFPGGGVEAQDAD +VVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGYVVHPVIGWWRDPSRVAVVDHNEAT +AVFRVPVADLAAPANRVRVRRPGGRRGETPGFLAGDRLVWGFTAALLSRVLELAGWDEPW +AGAPLIDAGSRAVLEG +>PROKKA_01750 +MPETPASPRPTSRDAAGTSEASLTGARDQLADLVARWGTAPADAPGHHDPASLTTIPPEA +VPMWGFEWPRSGDPRPSAVLILFGALDDVPARHDAERVHPHVDVLLTQRAATLRQHAGQI +AFPGGRVDPEDADVVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGHVVHPVLGWWRD +PSRVAVVDQAEAAAVFRMPVADLVDPANRCRVARPGGRRGETPGFLVGERLVWGFTAALL +DRVLALLGWDVPWDDSRVRDARTHEILRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001480.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001480.fa new file mode 100644 index 0000000000000000000000000000000000000000..053e1fd2d8acdea09a36f1134ef1e446940cdc46 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001480.fa @@ -0,0 +1,60 @@ +>PROKKA_01832 +MDEQIPTFPPPAEFAAQAVAGADLYEEAAEDRLAYWARRAREVLHWEQDFTDVLDWSDAP +FAKWFVGGTTNAAYNALDRHVEAGHGDRVAIHFEGEPGDTRTYTYADLAAEVRRAANAFE +SLGVTKGDRVAVYLPMIPEAVITMLACARIGAVHSVVFGGFSSDALRSRVDDAEAKLVVT +ADGSFRRGKPSMLKPAVDQALSAPGHTAEHVLVVRRNEAEVEMTEGRDLWWHDVVDAQSD +EHELVWHDAEHPLYILYTSGTTGKPKGILHTTGGYLVQAAATHHDTFDLHPESDVFWCTA +DVGWVTGHSYVAYAPLVNGATQVIYEGTPDSPHQGRWWEIVQKYGVSILYTAPTAIRTFM +KWGRHIPDEYDLSSLRVLGSVGEAINPEAWRWYHEVIGAGRCPIVDTWWQTETGAHMLTP +LPGVTTLKPGSAQRPVPGVVLEVVDELGEPMTDTSAGFLVVREPWPSMLRGIWGDRERFK +ETYWSRFPGMYFAGDGARYDEDGDIWLLGRVDDVMNVSGHRLSTTEIESSLVAHPSVAES +AVVGAKDETTGEAVVAFVLLTAVAVAADRDVAEVEEELRQHVGKDIGPIAKPKRVLVVPE +LPKTRSGKIMRRLLKDVAEGRDPGDSTTLADPTVMQRIVETLAPKA +>PROKKA_01529 +MDEQIPTFPPPAEFAAQAVAGADLYEEAAEDRLAYWARRAREVLHWEQDFTDVLDWSDAP +FAKWFVGGTTNAAYNALDRHVEAGHGDRVAIHFEGEPGDTRTYTYADLAAEVRRAANAFE +SLGVTKGDRVAVYLPMIPEAVITMLACARIGAVHSVVFGGFSSDALRSRVDDAEAKLVVT +ADGSFRRGKPSMLKPAVDQALSAPGHTAEHVLVVRRNEAEVEMTEGRDLWWHDVVDGQSD +EHELVWHDAEHPLYILYTSGTTGKPKGILHTTGGYLVQAAVTHHDTFDLHPESDVFWCTA +DVGWVTGHSYVAYAPLVNGATQVIYEGTPDSPHQGRWWEIVQKYGVSILYTAPTAIRTFM +KWGRHIPDEYDLSSLRVLGSVGEAINPEAWRWYHEVIGAGRCPIVDTWWQTETGAHMLTP +LPGVTTLKPGSAQRPVPGVVLEVVDELGEPMTDTSAGFLVVREPWPSMLRGIWGDRERFK +ETYWSRFPGMYFAGDGARYDEDGDIWLLGRVDDVMNVSGHRLSTTEIESSLVAHPSVAES +AVVGAKDETTGEAVVAFVLLTAVAVAADRDVAEVEEELRQHVGKDIGPIAKPKRVLVVPE +LPKTRSGKIMRRLLKDVAEGRDPGDSTTLADPTVMQRIVETLAPKA +>PROKKA_01036 +MDEQIPTFPPPAEFAAQAVAGADLYEEAAEDRLAYWARRAREVLHWEQDFTEVLDWSDAP +FAKWFVGGTTNAAYNALDRHVEAGNGDRVAVHFEGEPGDTRTYTYAELASEVRRTANAFE +SLGVAKGDRVAVYLPMIPEAVITMLACARIGAVHSVVFGGFSADALRSRVDDAEAKLVVT +ADGSFRRGKPSMLKPAVDEALSAPGHSVQHVLVVRRNEAEVSLVEGRDLWWHDVVPAQSD +EHELVWHDAEHPLYILYTSGTTGKPKGILHTTGGYLVQTAATHHDTFDLHPETDVYWCTA +DVGWVTGHSYVAYAPLVNGATQVIYEGTPDSPHQGRWWEIVQKYGVSILYTAPTAIRTCM +KWGRQIPDEYDLSSLRVLGTVGEAINPEAWRWYHEVIGGGRCPIVDTWWQTETGAHMLTP +LPGVTTLKPGSAQTPVPGVTLEVVDEIGEPMKDTSAGFLVAREPWPSMLRGIWGNPERFK +ETYWSRFPGMYFAGDGARYDEDGDIWLLGRVDDVMNVSGHRLSTTEIESSLVAHPSVAES +AVVGAADETTGEAVVAFVLLTEEAAAAGRDVAEVEEELRQHVGRDIGPIAKPKRVLVVPE +LPKTRSGKIMRRLLKDVAEGRDPGDATTLADPTVMQRIVETLAPGA +>PROKKA_00976 +MDETRATYPPSEQFAAQAVAGADLYEEAAADRLAYWARRAREHLHWEQDFTQVLDWSDAP +FARWFADGTTNAAYNALDRHVEAGRGDRTAIVFEGEPGDTRTYTYADLAAEVRRAANAFE +SLGVAKGDRVAVYLPMIPEAVITMLACARIGAVHSVVFGGFSADALRSRVDDAEAKLVVT +ADGSFRRGRPSMLKPAVDQALSAEGHTVEHVVVVRRNEADVDWTEGRDLWWHDVVPTASD +EHEVVWHEAEHPLFILYTSGTTGKPKGILHTTGGYLVQTAATHHDTFDLHADTDVYWCTA +DVGWVTGHSYVAYAPLVNGATQVIYEGTPDSPHQGRWWEIVQKHGVTILYTAPTAIRTFM +KWGRQIPDGYDLSSLRVLGTVGEAINPEAWRWFHDVIGGGRCPIVDTWWQTETGAHMLTP +LPGVTELKPGSAQRPVPGVVLEVVDELGEPMEGSTAPGFLVAREPWPSMLRGIWGDPERF +KETYWSRFPGMYFAGDGAQYDEDGDIWLLGRVDDVMNVSGHRLSTTEIESSLVAHPKVAE +SAVVGAADETTGEAVVAFVLLTEEATAAGEDVEAVQEELRQHVGKDIGPIAKPKRVLVVP +ELPKTRSGKIMRRLLKDVAEGRRPGDATTLADPTVMDRITEAVGS +>PROKKA_01753 +MDEQIPTFPPPAEFAAQAVAGADLYEEAAKDRLAYWARRAREVLHWEQDFTDVLDWSDAP +FAKWFVGGTTNAAYNALDRHVEAGHGDRVAIHFEGEPGDTRTYTYADLAAEVRRAANAFE +SLGVTKGDRVAVYLPMIPEAVITMLACARIGAVHSVVFGGFSSDALRSRVDDAEAKLVVT +ADGSFRRGKPSMLKPAVDQALSAPGHTAEHVLVVRRNEAEVEMTEGRDLWWHDVVDGQSD +EHELVWHDAEHPLYILYTSGTTGKPKGILHTTGGYLVQAAVTHHDTFDLHPESDVFWCTA +DVGWVTGHSYVAYAPLVNGATQVIYEGTPDSPHQGRWWEIVQKYGVSILYTAPTAIRTFM +KWGRHIPDEYDLSSLRVLGSVGEAINPEAWLWYHEVIGAGRCPIVDTWWQTETGAHMLTP +LPGVTTLKPGSAQRPVPGVVLEVVDELGEPMTDTSAGFLVVREPWPSMLRGIWGDRERFK +ETYWSRFPGMYFAGDGARYDEDGDIWLLGRVDDVMNVSGHRLSTTEIESSLVAHPSVAES +AVVGAKDETTGEAVVAFVLLTAVAVAADRDVAEVEEELRQHVGKDIGPIAKPKRVLVVPE +LPKTRSGKIMRRLLKDVAEGRDPGDSTTLADPTVMQRIVETLAPKA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001483.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001483.fa new file mode 100644 index 0000000000000000000000000000000000000000..dce359ecb0af1b6b8d7f993524e881c99ef4d331 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001483.fa @@ -0,0 +1,54 @@ +>PROKKA_01835 +MSSTVSAPATAPKRTREEFAGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI +ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTETVGWWQVLICVVIGIYYAAIIGWA +IMYTWFSVDQRWGDDPETFLMGDYLQVADDPSPSFDVVSGVFWPMLAVWVITLLIMGFGV +RRGVALASMVGIPLLIVMFLVLVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI +FFSLSVGFGIMITYASYLNRRTNLTGSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS +VSEVAGSGIGLAFIAFPTLISQAPLGALIGVLFFGSLVVAGFTSLISILEVVISAVKDKL +GWGRWTATIVVIGLSGVVSLALFSTTTGLQMLDTMDAFANNFGIVGAALLSVLLVTGALG +SARRITAHLNAVSSFKVGRGYVLLIGVLMPIVLAYIWLSWIMKVIAEGYEGYPGDFLGVF +GWGIALGSVALAVLLSLIPWSRKSNLYAEDLDSEIHGDLIPHNAVPEGTVPTGALPVVPV +ATTRKEL +>PROKKA_01532 +MSSTVSAPATAPKRTREEFTGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI +ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTETVGWWQVLICVVIGIYYAAIIGWA +IMYTWFSVDQRWGEDPETFLMGDYLRVADDPSPSFDFVSGVFWPMLAVWVITLLIMGFGV +RRGVALASMVGIPLLIVMFLILVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI +FFSLSVGFGIMITYASYLNRRTNLTGSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS +VSEVAGSGIGLAFIAFPTLISQAPLGALIGVLFFGSLVVAGFTSLISILEVVISAVKDKL +GWGRWTATIVVIGLSGVVSLALFSTTTGLQMLDTMDAFANNFGIVGAALLSVLLVTGALG +SARRITAHLNAVSSFKVGRGYVLLIGVLMPIVLAYIWLSWIMKVIAEGYEGYPGDFLGVF +GWGIALGSVALAVLLSLIPWSRKSNLYAEDLDSEIHGDLIPHNAVPEGTVPTGALPVVPT +AATRKEL +>PROKKA_01033 +MSSTVSAPAAAPTRTREEFAGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI +ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTESVGWWQVLICVVIAVYYAAIIGWA +IMYTWFSVDQRWGADPETFMMGEFLQVSETPNPTFDVVSGVFWPMLAVWVITLLIMGFGV +RRGVAMASMIGIPLLVVMFLVLVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI +FFSLSVGFGIMITYASYLKKRTNLTSSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS +VADVAGSGIGLAFIAFPTLISQAPVGALIGVLFFGSLVLAGFTSLISILEVVISAVKDKL +GWGRWTATIIVVGLAGVVSMALFSTTSGLHMLDTMDAFANNFGIVGAALVSVLLVTGVLG +SARRVTAHLNAVSSFKLGRGYVLLIGVLMPIVLAYIWLSWIMKVISEGYGGYPGDFLGVY +GWGVAIGSVVLAVVLSLIPWSRKSNLYAEEMETEIHGDLIPHNAVPEGTTPTGAIPLVPA +DHTRKEL +>PROKKA_00974 +MSTSTGATAAPSRTREEFTGRWAFILAAIGSAVGLGNIWRFPYVAYEHGGGAFVIPYLVA +LLTAGIPLLFLDYAIGHRFRGSAPMAFRRMSRWTEAIGWWQVLICAVIGVYYAAIIAWSI +MYTWFSLDQRWGDDPEGFLFSTYLQQVKDPNPSFDIVPGVFWPMVAVWGVLLLIMGLGIR +RGVALASMIGIPLLVVMFVVLVIISLTLPGAMQGLDALFTPNWAALKEPGVWIAAYGQIF +FSLSVGFGIMITYASYLKKRTNLTASGLVVGFSNSGFEILAGIGVFSALGFMAQASGVQV +SEVAGSGIGLAFIAFPTLITQAPAGALIGVLFFASLVIAGFTSLISILEVVVSAVKDKLG +WGRWTAVLVVVGISAVISISLFSTTTGVAMLDTMDAFANNFGIVGAALVAVIAVMWIARR +GGELVAHLNSVSSFRVGRVYRILVGVVMPVLLGWMWIEWIRENAATPYGGYPTDFLAVYG +WGLAIGSVVLAVLLSLIPWSHKSSLHAEESVNEIDHTAPVASKES +>PROKKA_01756 +MSSTVSAPATAPKRTREEFTGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI +ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTETVGWWQVLICVVIGIYYAAIIGWA +IMYTWFSVDQRWGEDPETFLMGDYLRVADDPSPSFDFVSGVFWPMLAVWVITLLIMGFGV +RRGVALASMVGIPLLIVMFLILVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI +FFSLSVGFGIMITYASYLNRRTNLTGSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS +VSEVAGSGIGLAFIAFPTLISQAPLGALIGVLFFGSLVVAGFTSLISILEVVISAVKDKL +GWGRWTATIVVIGLSGVVSLALFSTTTGLQMLDTMDAFANNFGIVGAALLSVLLVTGALG +SARRITAHLNAVSSFKVGRGYVLLIGVLMPIVLAYIWLSWIMKVIAEGYEGYPGDFLGVF +GWGIALGSVALAVLLSLIPWSRKSNLYAEDLDSEIHGDLIPHNAVPEGTVPTGALPVVPA +ATTRKEL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001485.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001485.fa new file mode 100644 index 0000000000000000000000000000000000000000..0d08e438b56b67bb44aed8e92078a0093d1e6174 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001485.fa @@ -0,0 +1,31 @@ +>PROKKA_01838 +MSADPAGLLLPVPGQEEDLTRQWLDRRFRQVRPARPGSSVVLVRDGDDGPEVFLRHRAGR +TPLGRVGLPGGALIESDADSCPWYGPEPSQWARTFGTTDRRRARQHVVAAVRELHDEAGV +LLAGRSDTDVVSTARIETWGGGRSSLEEGSESLPHLLAARGLGVRADLLRPVMRWRSAPH +VHRRFDTAVFATMTPPLQSAPASEEPGPELQAWVSARRALAGPLRLPGPAGAEGTAPFDQ +VATPLTQVIVRRVAAHRTAAAFLLSVTPCARRGPVPEYHLVTEAGDDGTPRMRVKRATRD +>PROKKA_01535 +MSADPAGLLLPVPEQEEDLTRQWLDRRFRQVRPARPGSAVVLVRDGDDGPEVFLRHRAGR +TPLGRVGLPGGALIESDADLCPWYGPEPSQWAHTFGTTDRRRARQHVVAAVRQLHDEAGV +LLAGRSDTDVVSTARVETWGGGRSSLEEGSESLPHLLASRGLGLRADLLRPVMRWHSAPH +VHRRFDTAVFATTTPPVQSAPASEEPGPELQAWVPACRALAGPLRLPGPAGAEGTAPFDQ +VATPLTQVIVRRVAAHRTAAAFLLSVTPCARRGPVPEYHLVTEAGDDGTPRMRVERATRD +>PROKKA_01030 +MVLVRDGEDGPEVFLRHRPGRTPLGRVGLPGGALSEADADACAWFGPDPAHWARVLGTTD +RRCARQQVVAAVRELHDEAGVLLAGRTDADVVLDARGETWGGGGSSLEEGAESLPRMLAA +RGLGLRTDLLRPVARWHSAPHAHRRFDTAVFAAAVPPLQRPLERPETAPALQAWVSARRA +VAGPVPLPGPAGEEGVAPLDQVATPLTQVLVRRVAAHRTAAAFLLSLTQGAGHGPVPEYR +LVTEAGDDGAPRMRVERVTRD +>PROKKA_00971 +MSAEPDAPRVRVPGHEEELTRQWLAQRHRQVRPARPASAVVLVRDGADGVEVLLRHRSGR +TPLGRIGLPGGSLVDSDADPCTWYGPAPDEWARALGLADRRRVRQHVVAAVRELFEESGV +LLAGPADMDLVQDARGETWGASRSSLEEGDESLPRLLGDRGLGLRTDLLRGVGRWLSAPH +SPRRFDTVVFAAALPPQQELVHRPEGPVLQGWFSARRLLSEPAALPGPDGWLGESGVVAL +EEVSTPMTQLVLRRVAEHRTAAGFLLSPAGCRGPVPVVKLRTEAEHDDLATGTLYTVAER +VDPVG +>PROKKA_01759 +MSADPAGLLLPVPEQEEDLTRQWLDRRFRQVRPARPGSAVVLVRDGDDGPEVFLRHRAGR +TPLGRVGLPGGALIESDADLCPWYGPEPSQWAHTFGTTDRRRARQHVVAAVRQLHDEAGV +LLAGRSDTDVVSTARVETWGGGRSSLEEGSESLPHLLASRGLGLRADLLRPVMRWHSAPH +VHRRFDTAVFATTTPPVQSAPASEEPGPELQAWVPACRALAGPLRLPGPAGAEGTAPFDQ +VATPLTQVIVRRVAAHRTAAAFLLSVTPCARRGPVPEYHLVTEAGDDGTPRMRVERATRD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001487.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001487.fa new file mode 100644 index 0000000000000000000000000000000000000000..536b2cb945a2c857fb471b74b2b190766287e361 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001487.fa @@ -0,0 +1,10 @@ +>PROKKA_01840 +MTQQTQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGNNPVAYLKRPKAA +>PROKKA_01537 +MTQQTQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGNNPVAYLKRPKAA +>PROKKA_01028 +MTEQTKWEYATIPLLIHATKQILDQWGEDGWELVAVVPGPDGPNPVAYLKRPKAA +>PROKKA_00969 +MTQRIQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGANPVAYLKRPKDA +>PROKKA_01761 +MTQQTQWEYATIPLLIHATKQILDQWGEDGWELVTVIPGPEGNNPVAYLKRPKAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001489.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001489.fa new file mode 100644 index 0000000000000000000000000000000000000000..1be90490e50815c45239c49ff7fba0feb50aeea3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001489.fa @@ -0,0 +1,35 @@ +>PROKKA_01842 +MPPAASPTRRMLRSAAPAAVGMAATAGLGLAWGLAEAEARTVRTHRLAVLPAGSAPLRVL +HLSDIHLLPRHRAKRAWLRGLDALEPDLVVNTGDNVSAAASVPLVLDALGPLLARPGVFV +PGSNDYYAPKAANPLRYFAGPSRMDEDRPRLPSDVLFGAFRAAGWADLTNRGAALAVPTR +AGTTLEVLAAGTDDPHLGLDAWAGFPGAAPDENAGRPGDDGRFRLGVTHAPYRRVLDAMT +ADGADLLLAGHTHGGQVCVPFLGALVTNCDLPRRQASGVSTWTAAGRTVPLEVSAGLGTA +PSAPVRFACRPEAVVLDLVPRG +>PROKKA_01539 +MPPAASPTRRMLRSAAPAAVGMAATAGLGLAWGLAEAEARTVRTHRLAVLPAGSAPLRVL +HLSDIHLLPRHRAKRAWLRGLDALEPDLVVNTGDNVSAAASVPLVLDALGPLLARPGVFV +PGSNDYYAPKAANPLRYFAGPSRMDEDRPRLPSDVLFGAFRAAGWADLTNRGAALAVPTR +AGTTLEVLAAGTDDPHLGLDAWAGFPGAAPDENAGRPGDDGRFRLGVTHAPYRRVLDAMT +ADGADLLLAGHTHGGQVCVPFLGALVTNCDLPRRQASGVSTWTAAGRTVPLEVSAGLGTA +PSAPVRFACRPEAVVLDLVPRG +>PROKKA_01026 +MRPSATAPRRLVRAGSRAAVGMGTAAALGLAWGLVEAEARVVRTHRLAVLPAGADPVRVL +HLSDIHLLPRNRSRMAWLRGLDALEPDLVVNTGDNISAAASVPLVLDALGPLLRRPGVFV +PGSNDYYEPKPANPFRYFAGPSRMDEDRARLPTEALFGAFRAAGWADLTNRGSVLSVPTR +AGTVLEVLAAGTDDPHLGLDAWGGFPAPAPAPAPAPGDAAASGPASAHDDGAARPGGDGR +FRLGVTHAPYRRVLDAMTVDGADLLLAGHTHGGQVCLPGFGALVTNCDLPRAQASGVSTW +TAAGRTVPLEVSAGLGTAPSAPVRFACRPEAVVLELLPCA +>PROKKA_00967 +MTDAPGPRLRRLTHTAAWAAGGASALGAGALVWGRVEAEARVVRTHTVPVLPAGARPLRV +LHLSDIHLLPRHRRRLEWLCSLADLEPDLVVDTGDNISSAASIPLLLDALAPLLAVPGVF +VPGSNDYFTPKPANPLRYLRGPSELEASRSRLPTEDLFSAFRAAGWTDLTDRAADVVVGS +GPDAVRIRAAGTDDPHLGLDRWPGFDLADEGAAGDAPLLRLGVTHAPYRRVLDAMTADGA +DLLLAGHTHGGQVCLPFAGALVTNCDLPRSQASGLSSWTAAGRTVPLEVSAGIGTAPSAP +VRTFCRPEAVVLDLVPRA +>PROKKA_01763 +MRPAASPARRMFCAAAPAAAGLAATAGLGLAWGLAEAEARTVRTHRLAVLPAGSAPLRVL +HLSDIHLLPRHRAKRAWLRGLDALEPDLVVNTGDNVSAAASVPLVLDALGPLLARPGVFV +PGSNDYYAPKAANPLRYFAGPSRMDADRPRLPSDVLFGAFRAAGWADLTNRGAALAVPTR +AGTTLEVLAAGTDDPHLGLDAWAGFPGSAPDGGAGRPGDDGRFRLGVTHAPYRRVLDAMT +ADGADLLLAGHTHGGQVCVPFLGALVTNCDLPRRQASGVSTWMAAGRTVPLEVSAGLGTA +PSAPVRFACRPEAVVLDLVPRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001490.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001490.fa new file mode 100644 index 0000000000000000000000000000000000000000..0506de95d9a07c95b7f0537c1a822c3a1eece396 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001490.fa @@ -0,0 +1,61 @@ +>PROKKA_01843 +MTRATSPDASSLRDALGGIAPYLEGVRARWVLGLASATAAGLVALAIPQVIHLLVDTVFT +QTVLAGPSSPDSRADVWRAAGLLTVLGLAEAAFIGLRRYFILPPAAGVENRARIALFERL +QRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVMLVVDVVTIAVGLVLLFLLSWQLA +LLYLAAAVPIMWASFGFRNDFRAASRLSQDQAGDLATSVEESVHGIRVLKAFGRGAHALD +GFRGRARTLQGTEVHKASVLARFIALIVALPETVLGLGLALGLWLVATGELTVGALAAYF +ATAAVLAGPVESVGQLMGMTLSARTAIDRHVDVLATPVDIASPTGEAAVVPPATGALAFR +GVRFRWPDADPGRGERDLLDGVDLELVPGETMALVGATGAGKSTLLQLVPRLLDVTAGSV +CVDGVDVRRMPLEELRRRVSVAFEDATLFSATIRQNVLLGAPADVLADGLHSPAADALLD +LALETAQAGFVADLADGVETEIGEEGLSLSGGQRQRIALARAIAARPDVLVLDDPLSALD +VRTEETVTARLREVLDGTTTLIVAHRPSTVALADRVAVLADGRIEDVGTHPELLARSAVY +RHIISSRPEEQA +>PROKKA_01540 +MTRATSPDASSLRDALGGIAPYLEGVRARWVLGLASATAAGLVALAIPQVIHLLVDTVFT +QTVLAGPSSPDSRADVWRAAGLLTVLGLAEAAFIGLRRYFILPPAAGVENRARIALFERL +QRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVMLVVDVVTIAVGLVLLFLLSWQLA +LLYLAAAVPIMWASFGFRNDFRAASRLSQDQAGDLATSVEESVHGIRVLKAFGRGAHALD +GFRGRARTLQGTEVHKASVLARFIALIVALPETVLGLGLALGLWLVATGELTVGALAAYF +ATAAVLAGPVESVGQLMGMTLSARTAIDRHVDVLATPVDIASPTGEAAVVPPATGALAFR +GVRFRWPDADPGRGERDLLDGVDLELVPGETMALVGATGAGKSTLLQLVPRLLDVTAGSV +CVDGVDVRRMPLEELRRRVSVAFEDATLFSATIRQNVLLGAPADVLADGLHSPAADALLD +LALETAQAGFVADLADGVETEIGEEGLSLSGGQRQRIALARAIAARPDVLVLDDPLSALD +VRTEETVTARLREVLDGTTTLIVAHRPSTVALADRVAVLADGRIEDVGTHPELLARSAVY +RHIISSRPEEQA +>PROKKA_01025 +MTRTATRPLPLREALQVVAPYLQGVRGRWVLGLLSAMAAGLVALAIPQVVQVLVNTVFAE +AAPGTAGTADPAAGVWWAAGALALFGLAEALFIWLRRFFILPPAADVENRARISIYRRLQ +RLPVAFHDAWASGQLLSRAQGDLALLRRWIAFGSVMLVVETVTIVVGLVLLFVMSWQLAL +LYLVAAVPIMIRSFRFRTDFRAASRLSQDQAGDLATTVEESVHGIRVLKAFGRGPDALDG +FRGEAETLQGTEVHKASVLAKFISLTVSLPELVLGVALGLGLYLVAVGDLTVGALAAYFA +TTAVLARPVEGVGQLMGMTLSAKTAIDRHLEVMRVPVAVASPAGTDAAEEEATSRAVASS +AAEDSPVVTDGLPPSSGRLAFRDVVFRYPDAPEDSRPLLAGVDLELTPGETMALVGVTGS +GKSTLVQLVPRLLDVTAGVVEVDGTDVRAYPLDELRRRVSIAFEDATLFSDTVRANVLLG +APAEVTADGLDSPRAQALLDLALDTAQAGFARDLPAGVDTEIGEEGLSLSGGQRQRIALA +RAIAARPDVLVLDDPLSALDVRTEEAVTGRLREVLAGTTTLIVAHRPSTVALADRVAVLQ +DGAIHDVGTHAELLARSAAYREIITTGAAEDRSLAGLADAAHDDAALAAATDAARPPAGA +ARPPAGRTAGREETR +>PROKKA_00966 +MTRTTTAAAPLPLRDAVRGIAPYLEGVRTRWVLGLLSALAAGLVALAIPQVIRLLVNTVF +AAPTTPGAPAAEDATASVWWAVGGLALLGAAEALFIWLRRFFILPPAADVENRARIAVYR +RLQRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVMLVVETVTLVVGVGLLFWLSWP +LALVYLAAALPIMWRSYGFRNDFRTASRLSQDQAGDLATTVEESVHGIRVLKAFGRGPHA +LEGFRGEAQTLQGTEVHKAGVLASFIAFTVSLAEVMLGVALALGVWLVATGQMTVGALAA +YFATTAVLARPVEGIGQLLGMTLSAKTAIDRHLEVMRQPVSIASPPGTDPAEEAATGASV +GEDPDPAVADAPVDVSALPPSRGGLAFRGARFRHPDTPDDAPDLLAGVDLELVPGETMAL +VGLTGSGKSTLLQLVPRLRDVTGGVVEVDGVDVRDYPLEELRRRVSIAFEDATLFSDTVR +ANVLLGAPAAEVADGPDSPAAEALLELALDTAQAGFVADLPQGVDTPIGEEGLSLSGGQR +QRLALARAIAARPDVLVLDDPLSALDVRTEEAVTARLREVLAGTTTLIVAHRPSTVALAD +RVAVLQDGRIADVGTHADLLARSGAYRQIITTDREDAR +>PROKKA_01764 +MTRATSPAASSLRDALGGIAPYLEGVRARWVLGLASATAAGLVALAIPQVIHLLVDTVFT +QTVLAGPSSPDSRADVWRAAGLLTVLGLAEAAFIGLRRYFILPPAAGVENRARIALFERL +QRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVMLVVDVVTIAVGLVLLFLLSWQLA +LLYLAAAVPIMWASFGFRNDFRAASRLSQDQAGDLATSVEESVHGIRVLKAFGRGAHALD +GFRGRARTLQGTEVHKASVLARFIALIVALPETVLGLGLALGLWLVATGELTVGALAAYF +ATAAVLAGPVESVGQLMGMTLSARTAIDRHVDVLATPVDIASPTGEAAVVPPATGALAFR +GVRFRWPDADPGRGERDLLDGVDLELVPGETMALVGATGAGKSTLLQLVPRLLDVTAGSV +CVDGVDVRRMPLEELRRRVSVAFEDATLFSATIRQNVLLGAPADVLADGLHSPAADALLD +LALETAQAGFVADLADGVETEIGEEGLSLSGGQRQRIALARAIAARPDVLVLDDPLSALD +VRTEEAVTARLREVLDGTTTLIVAHRPSTVALADRVAVLADGRIEDVGTHPELLARSAVY +RHIISSRPEEQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001491.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001491.fa new file mode 100644 index 0000000000000000000000000000000000000000..38b7feee2eac7966296ca6b06736a41afde9743f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001491.fa @@ -0,0 +1,50 @@ +>PROKKA_01847 +MKTLVLGNGGREHALLTALSRDPQVSALHAAPGNAGMADLATLHAVEATDPAAVVELARE +LGADLVVVGPEAPLAAGVSDALREAGFAVFGPSQAAAQLEASKAFAKEVMAAAGVPTAGS +RVCTTAAEAAAALDEFGAPHVVKDDGLAAGKGVVVTSDRAEALAHAEACFAAGGTVVIED +FLDGPEVSLFVICDGEDAVALTPAQDFKRIHDGDAGPNTGGMGAYTPLPWLPEGFTDEVM +DRVARPVLAEMARRGTPFTGVLFCGLAVTAKGVEVIEFNVRFGDPETQAVLARLETPLGG +LLADAAAGRLGADRRLEWSDDVAVDVVMASAGYPASSSTGDVITGLADAAALEGVHVIHA +GTAASGEDVVTAGGRVLAVVGRGADLAQARERAYAGVERIRFDGAQWRTDIGLKAERGEI +TVPGTGGAK +>PROKKA_01543 +MKTLVLGNGGREHALLTALSRDPQVSALHAAPGNAGMADLATLHAVEATDPAAVVELARE +LGADLVVVGPEAPLAAGVSDALREAGFAVFGPSQAAAQLEASKAFAKEVMAAAGVPTAGS +RVCTTAAEAAAALDEFGAPHVVKDDGLAAGKGVVVTSDRAEALAHAEACFAAGGTVVIED +FLDGPEVSLFVICDGEDAVALTPAQDFKRIHDGDAGPNTGGMGAYTPLPWLPEGFTDEVM +DRVARPVLAEMARRGTPFTGVLFCGLAVTAKGVEVIEFNVRFGDPETQAVLARLETPLGG +LLADAAAGRLGADRRLEWSDDVAVDVVMASAGYPASSSTGDVITGLADAAALEGVHVIHA +GTAASGEDVVTAGGRVLAVVGRGADLAQARERAYAGVERIRFDGAQWRTDIGLKAERGEI +TVPGTGGAK +>PROKKA_01021 +MKTLVLGNGGREHALLAALSRDPQVGELHAAPGNAGMAALAALHAVEATDPDAVVALARE +LAADLVVVGPEAPLAAGVSDALREAGFAVFGPSRAAAQLEASKAFAKEVMAAAGVPTAGS +RTCATAEEAAAALDEFGAPHVVKDDGLAAGKGVVVTSDRAEALAHAQACFDAGGTVVIED +FLDGPEVSLFVVCDGTDAVALTPAQDFKRIHDGDAGPNTGGMGAYTPLPWLPEGFAEEVM +DRVARPVLAEMARRGTPFTGVLFCGLAVTAKGVEVIEFNVRFGDPETQAVLARLTTPLGG +LLADAAAGRLGADRALEWSDDVAVDVVMASAGYPATSSQGDVITGLTDAEALEGVHVIHA +GTATSGDDVVTAGGRVLAVVGRGADLAQARERAYAGVERIRFDGAQWRTDIGLKAERGEI +AVPAAVGQAGQAGEDAR +>PROKKA_00963 +MKILVLGNGGREHALLRALSRDPQVGELHAAPGNAGMADAAVLHPVTATDPEAVVALARD +LAVDLVVVGPEAPLAAGVSDALREAGFAVFGPSQAAAQLEASKAFAKEVMAAAGVPTAGA +RVCATEAEVDAALTAFGAPHVVKDDGLAAGKGVVVTSDRAAALDHARACLSAGGTVVVED +FLDGPEVSLFVLCDGEHAVPLTPAQDFKRIHDGDAGPNTGGMGAYTPLQWLPEGFVDEVM +ERVARPVLAEMSRRDTPFAGVLFIGLAVTENGPEVIEFNVRFGDPETQSVLARLETPLGQ +LLADAAAGRLGADRELRWSDDVAVDVVLASAGYPASSHSGDVIAGLEDALALEGVDVLHA +GTARTEDGDVVTAGGRVLAVVGRGATLEQARERAYAGVAKIRFDGAQHRTDIAIKAERGE +ITVPERRRGYAGAEALELPGWRHVYSGKVRDLYEPADAEPGTSETLLVVASDRISAYDFV +LEPPIPGKGAVLTRLSLWWFEQLAGVANHVVSTDVPAEVAGRAMVVKRLDMHPIECIARG +YLTGSGLAEYREHATVTGIPLPDGLVDGSRLEPPIFTPSAKAEVGEHDENITFEQTVERV +GAPTAEALRAATLEVYTRAEAIARKAGIILADTKVEFGADPVTGELVLGDEVLTPDSSRF +WDAEAYEPGRAQASFDKQFVRDWLTSPESGWDRTSGEEPPALPADVVERTRARYVEAYER +LTGRRFEA +>PROKKA_01767 +MKTLVLGNGGREHALLTALSRDPQVSALHAAPGNAGMADLATLHAVEATDPAAVVELARE +LGADLVVVGPEAPLAAGVSDALREAGFAVFGPSQAAAQLEASKAFAKEVMAAAGVPTAGS +RVCTTAAEAAAALDEFGAPHVVKDDGLAAGKGVVVTSDRAEALAHAEACFAAGGTVVIED +FLDGPEVSLFVICDGEDAVALTPAQDFKRIHDGDAGPNTGGMGAYTPLPWLPEGFTDEVM +DRVARPVLAEMARRGTPFTGVLFCGLAVTAKGVEVIEFNVRFGDPETQAVLARLETPLGG +LLADAAAGRLGADRRLEWSDDVAVDVVMASAGYPASSSTGDVITGLADAAALEGVHVIHA +GTAASGEDVVTAGGRVLAVVGRGADLAQARERAYAGVERIRFDGAQWRTDIGLKAERGEI +TVPGTGGAK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001494.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001494.fa new file mode 100644 index 0000000000000000000000000000000000000000..3a3d411689391cc9eb4d1a74f80be53fe1e9bf78 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001494.fa @@ -0,0 +1,45 @@ +>PROKKA_01850 +MSVAPRAAVPPAPTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPEASSGPFPAT +TLVLLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVAHHGDFAWVA +FPLFFVVLHVVDRVARQAWVRHVVGPALVVAMAVVVVAGMAAGAGGVRVPAVIGPLVGAA +VAVVLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLTQG +LASIVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGTGAPSLIEAL +ERAVAGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLANVGAHAGARRAR +VTLGYLGDELTVDVADDGAGFDPAVVAARPRAGAAGADPGAGTGVGLASVRERLAAVGGE +ATVESAPGEGTVVALRVPLVAAGAGRSADPEQTESEETA +>PROKKA_01546 +MSVAPRAAVPPAPTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPDASGPFPATT +LVLLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVGHHGDFAWVAF +PLFFVVLHVVDRVARQAWVRHVVGPALVVAMAAVVVAGMAAGAGGVRVPAVIGPLVGAAV +AVVLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLTQGL +ASIVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGTGAPSLVEALE +RAVTGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLANVGAHAGARRARV +TLGYLGDELTVDVADDGAGFDPAVVVARARAGAAGADPGAGTGVGLASVRERLAAVGGEA +TVESAPGEGTVVALRVPLAAAGAGRSADPEQTESEETA +>PROKKA_01018 +MPTTRPSADTAGAPAETGAAAVLAGLRVALHVAFAVLLAVGLGRALADLSRTGAPAPAVL +ALTGCTALLAGVYLAGTLVERRRWGRGEDVGRGPALLWLALVLALWGLLVAQHRDFAWVA +FPLFFVALHVVARTARTAMARRIAGPVLVAAMAAVVVAGMAAGVDEGVRPAAVIGPLVGA +AVAVVLSGAYRALHQESERQRDVAEQLRAAQAELARTQHRAGVGEERERLAREIHDTLTQ +GLASIVLVSRAAQDALDAQDPALARTRMETVRTTAAENLDESRRFVRDLRATGGASLVAA +VERAVAGFAERQAAAGTPVAADVEVVGTPVPLAEAVEAALLRAVQASLANVAAHARATRA +RVTLAWMPGELAVDVADDGVGFRPEAVVTGDAGTQGTGAGTQGARAGRASRPGAGTGVGL +ASVRERLAGVGGHASVESAPGEGTVVALRVPLPAAAGRAEEDEGRERG +>PROKKA_00960 +MRTSDPADGPRGANGTAALLSGLRVAVHVGFAVLLALALVRALAGPDAGARLTGRPALAL +VGLTVVLAGVYLTGTVAERRLHAAGRAPGRTAAGTWLAVLLGVWALAVLRHPDMMWVAFP +LFFVALHAVHVILGRPRLALACVAAMTVVVVVASLERGTAPGAVLGPAVGAAVAVVVFHA +CRLLVVESERQRSVAEQLRATRAELAASERHAGVLAERERLAREIHDTLTQGLASIVLVS +RAAQDAVRAGDAALADERLETVRTTAAENLAESRAFVRGLRAPVDGVQGGADRAGSALEA +ALGAAVRGFRARRQALGRPVEAELAVVGEPVAVGEAVETVLVRAAQSSLANVDQHARTDR +CRVTLTWMDGEVALDVADDGVGFDPEAARARASRAAVSDPAAPRPAEEGTGVGLAGLAER +VAGVGGRVDVESAPGQGCVVAVRIPVPRQHERRGA +>PROKKA_01770 +MSVAPRAAAPTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPEASSGPFPVTTLV +LLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVAHHGDFAWVAFPL +FFVVLHVVDRVARQAWVRHVVGPALVVAMAVVVVAGMAAGAGGVRVPAVIGPLVGAAVAV +VLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLTQGLAS +IVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGTGAPSLIEALERA +VTGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLANVGAHAGAHRARVTL +GYLGDELTVDVADDGAGFDPAVVAARPRAGAAGADPGAGTGVGLASVRERLAAVGGEATV +ESAPGEGTVVALRVPLVAAGAGRSADPEQTESEETA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001496.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001496.fa new file mode 100644 index 0000000000000000000000000000000000000000..435798b74e9e5ebc8bdda8df9727a3eee5351bc8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001496.fa @@ -0,0 +1,35 @@ +>PROKKA_01853 +MTHATVAPAGETLALSDAVELVETVRNGFVESRTAGAAVVTGPDGRVLAGLGPADALIYP +RSTLKPFQAVASLRHGAALEGEALSIACGSHRGTLRHQALAERMLADAGLDASALQCPPA +WPADTSEVVAQVRRDGESAAATPLAFNCSGKHAGFLAACAASGHDVATYLDPAHPLQREV +DAVIAEYCGEPVAHTGVDGCGAPAAVISLAGLARGIGRVAAAPGRADADPHAAAVATAML +EHPWAVHGETSSNTVVMRELGLLAKAGADGVLVMAAPDGTAVAVKALDGGTRAGDLVALA +LLARFAPDHVDRATLPGVLAAVVPPVLGRGEPVGEIRLAAPVRDLVGDVLPAFEARA +>PROKKA_01549 +MTHATIAPAGETFALSDAVELVETVRNGFVESRTAGAAVVTSPDGRVLAGLGPADALIYP +RSTLKPFQAVASLRHGAALEGEALSIACGSHRGTLRHQALAERMLADAGLDASALRCPPA +WPADTSEVVAQVRRDGESAAATPLAFNCSGKHAGFLAACAASGHDVATYLDPAHPLQREV +DAVIAEYCGEPVAHTGVDGCGAPAAVISLAGLARGIGRVAAAPGRADADPHAAAVATAML +EHPWAVHGETSSNTVVMRELGLLAKAGADGVLVMAAPDGTAVAVKALDGGTRAGDLVALA +LLARFAPDHVDRATLPGVLAAVVPPVLGRGEPVGEIRLAAPVRDLVGDVLPTFEARA +>PROKKA_01015 +MTQTPSATFALADAVELVHVVRNGFVESRTPGAAVVTGPDGTVLAALGPVDALIYPRSTL +KPFQAIASLRHGARLEGQEVAIACGSHRGTAAHRELAARILAEAGLSAADLQCPPDYPAD +AAEIVRFAQDLEHGAEKTPLAYNCSGKHAGFLAACVAAGHEVGTYLEPDHPLQAEVERVI +EEYCGEPVAHTGTDGCGAPAAVLSLTALARGIGKVASAPSRRDAEIHAATVANAMLEHPW +AVHGQSSSNTVVMRELGLLAKLGADGVMVMAAPDGTAVAVKALDGGTRAGNLVALALLAQ +FAPDHVDADRLPAVLETVAPKILGKGEPVGAVRLARPVLDLLD +>PROKKA_00957 +MTQTSAAPAGQTFALADAVELVEVVRGGFVESRTAGAAVVTGPDGEVLAALGPADALVYP +RSTLKPFQAIASLRHGARLEGEALAIACGSHTGSEAHQQLAARVLADHGLAPEALQCPSA +LPEVAGEVARLAAQAGTAEIATPLAYNCSGKHAGFLAACAASGHDVGTYLDPEHPLQREV +DAVIAEYCGEPVAHTGVDGCGAPAAVVSLAGLARGIGAVSKAPGREGAEPHAAAVARAML +AHPWAVQGPGKANTVVMEELGLVAKLGADGVMVMGAPDGTAVAVKALDGGTRAGNLVALA +LLGRFAADQVDAGRLAEVSARVAPSILGRGAPVGEVRLAAPVRQLVGA +>PROKKA_01773 +MTHATVAPAGETFALSDAVELVETVRNGFVESRTAGAAVVTGPDGRVLAGLGPADALIYP +RSTLKPFQAIASLRHGAALAGEALSIACGSHRGTLRHQALAERMLADAGLDASALRCPPA +WPADTSEVVAQVRRDGEAAAATPLAFNCSGKHAGFLAACAASGHDVATYLDPAHPLQREV +DAVIAEYCGEPVAHTGVDGCGAPAAVISLAGLARGIGRVAAAPGRADADPHAAAVATAML +EHPWAVHGETSSNTVVMRELGLLAKAGADGVLVMAAPDGTAVAVKALDGGTRAGDLVALA +LLARFAPDHVDRATLPGVLAAVVPPVLGRGEPVGEIRLAAPVRDLVGDVLPAFEARA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001498.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001498.fa new file mode 100644 index 0000000000000000000000000000000000000000..7acd425b91cbe3124c766f52629beed3957c2201 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001498.fa @@ -0,0 +1,20 @@ +>PROKKA_01855 +MTSAPEPTPDQRAYTVRRAPRLTAVLAVALALGLLIALVITTAVHASPTPPADPYSGIPL +SFSETFGFASLLSMLGTSVLGLLVWLLLDRRSRSTARTVVLERTDDPAVADVRLDRVDAG +APPARTTPTERTPEQ +>PROKKA_01551 +MTSAPEPTPDQRAYTVRRAPRLTAVLAVALALGLLIALVITTAVHASPTPPADPYSGIPL +SFSETFGFAALLSMLGTGVLGLIVWLLLDRRSRSTARTVVLERTDDPAVADVRLDRVDAG +TPPARTTSTERTPEQ +>PROKKA_01009 +MTTGPERSQHQHAYTVRRAPRLAAVLAVALALGLVIALVITTAVHGSPTPPADPYSGIPL +SFSETFGFAALLSMLGTGVLGLVVWLLLDRRSRATTRTVVLERTDDPAAADIRLDRSAAD +ALRSRTAPTERTPEQ +>PROKKA_00953 +MTSGPERSTPSAPQQQEYVLRRAPRLSAAVIVSALVGVVLALLGTAAVHAGPQPPADPYS +GMPLSFASTFGYMVVAAVLACLVLGLLVWLLLDRRSRRTQRTVLLERTDDPAAADVALPR +PEAVAPAARPAADPSDGRTPEQ +>PROKKA_01775 +MTSAPEPTPDQRAYTVRRAPRLTAVLAVALALGLLIALVITTAVHASPTPPADPYSGIPL +SFSETFGFASLLSMLGTSVLGLLVWLLLDRRSRSTARTVVLERTDDPAVADVRLDRVDAG +APPARTTPTERTPEQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001499.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001499.fa new file mode 100644 index 0000000000000000000000000000000000000000..770d88dddcebfc6b6e978307fe1ef048050e5561 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001499.fa @@ -0,0 +1,50 @@ +>PROKKA_01856 +MIAPRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAG +IAVSDGGRIAVYKDIGLVSQVFDEATLTALSGHIAVGHCRYSTTGVNKWANAQPTLGATA +DDGTVALAHNGNLVNSAELLRMVHAADGRHTHGEMKQGNTTDTALVTALLHGAPGDRLEE +TALELLPKIRGAYCFVFMDEHTLYAARDPQGVRPLVLGRLERGWVVASEQSALATVGASF +IREVEPGEMIAIDEEGIRSTRFAESKPAGCVFEYVYLARPDATIAGRSVYESRVEMGRRL +ALEQPVEADVVIPVPESGTPAAVGYADASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIR +LKLNVESTVVAGKRVVVVDDSIVRGNTQRAVVRMLKEAGAAEVHVKISSPPVKWPCFYGI +DFATRAELIANGAAVDQIAASIGADSLAYISEEGMIEATGQPRERLCTACFTGDYPIPLA +DEGERGKGLLEPVAVSPASTVVLDEDGETTTVTATGCEPGPDADDEKLLTETDRTPL +>PROKKA_01552 +MIAPRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAG +IAVSDGGRIAVYKDIGLVSQVFDEATLTALSGHIAVGHCRYSTTGVNKWANAQPTLGATA +DDGTVALAHNGNLVNSAELLRMVHAADGRHTHGEMKQGNTTDTALVTALLHGAPGDRLEE +TALELLPKIRGAYCFVFMDERTLYAARDPQGVRPLVLGRLERGWVVASEQSALATVGASF +IREVEPGEMIAIDEEGIRSTRFAESKPAGCVFEYVYLARPDAAIAGRSVYESRVEMGRRL +ALEQPVDADVVIPVPESGTPAAVGYADASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIR +LKLNVQSTVVAGKRVVVVDDSIVRGNTQRAVVRMLKEAGAAEVHVKISSPPVKWPCFYGI +DFATRAELIANGAAVDQIAASIGADSLAYISEKGMIEATGQPRERLCTACFTGDYPIPLA +DEGERGKGLLEPVAVSPASTVVLDEDGETTTVTATGCEPGPDADDEKLLTETDRIPL +>PROKKA_01008 +MIASRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAG +IAASDGKRIGVYKDIGLVSQVFDESTLATFTGHIAVGHCRYSTTGANKWANAQPTLGATA +GGDTVALAHNGNLVNSGELLRMVQARDGLQLRGEMKQGNTTDTALVTALLHGEEGRKLEE +TALELLPKVRGAYCFVFMDEHTLYAARDPHGVRPLVLGRLERGWVVASEQSALATVGASF +IREVEPGEMIAIDEEGIRSTRFAEATPAGCVFEYVYLARPDASIAGRSVYESRVDMGRRL +ALEGPVDADVVIPVPESGTPAAVGYAEASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIR +LKLNVQPSVVAGKRVVVVDDSIVRGNTQRAIVRMLKEAGAAEVHVKISSPPVKWPCFYGI +DFASRAELIANGAGVAEIASSIGADSLGYISEEAMIAATGQPRERLCTACFTGTYPIELA +DESERGKSVLETDAGSAAVTVMAPDGDATTVASTGCEPGPDADDEKLLTETDRTPL +>PROKKA_00952 +MISARTRRGDGRLTAALDPQEAGPQDECGVFGVWAPGEEVAKLTYYGLYALQHRGQESAG +IAASDGKRIAVYKDMGLVSQVFDEPTLAALTGHVAVGHCRYSTTGVNKWANAQPTLGATA +DDGTVALAHNGNLVNSAELLRMVESKEGAHTLGEIKQGNTTDTALVTALLHGEKGVSVEE +TALELLPKVRGAYCFVFMTERTLYAARDPHGVRPLVLGRLERGWVVASEQSALATVGASF +IREVEPGEMIAIDEEGIRSTRFAEATPAGCVFEYVYLARPDAAINGRSVYESRVEMGRRL +AQEHPVDADVVIPVPESGTPAAVGYADASGIPFRQGFVKNAYVGRTFIQPSQTLRQLGIR +LKLNVQPSVVAGKRVVVVDDSIVRGNTQRAIVRMLKEAGAAEVHVKISSPPVKWPCFYGI +DFATRAELIANGAGVQEIASSIGADSLAYISEEGMIAATEQPRERLCTACFTGTYPIELA +DEKERGKAVLENGTPTAEATDVVSEDGTVTTVASTGCEPGPDSEDEKLLTQTDRTPL +>PROKKA_01776 +MIAPRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAG +IAVSDGGRIAVYKDIGLVSQVFDEATLTALSGHIAVGHCRYSTTGVNKWANAQPTLGATA +DDGTVALAHNGNLVNSAELLRMVHAADGRHTHGEMKQGNTTDTALVTALLHGAPGDRLEE +TALELLPKIRGAYCFVFMDEHTLYAARDPQGVRPLVLGRLERGWVVASEQSALATVGASF +IREVEPGEMIAIDEEGIRSTRFAESKPAGCVFEYVYLARPDATIAGRSVYESRVEMGRRL +ALEQPVDADVVIPVPESGTPAAVGYADASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIR +LKLNVQSTVVAGKRVVVVDDSIVRGNTQRAVVRMLKEAGAAEVHVKISSPPVKWPCFYGI +DFATRAELIANGAAVDQIAASIGADSLAYISEEGMIEATGQPRERLCTACFTGDYPIPLA +DEGERGKGLLEPVAVSPASTVVLDVDGETTTVTATGCEPGPDADDEKLLTETDRTPL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001501.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001501.fa new file mode 100644 index 0000000000000000000000000000000000000000..61ba4255daa4aa6516018b8ac10266ef49fdce9e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001501.fa @@ -0,0 +1,35 @@ +>PROKKA_01858 +MATSSLPLSDIVETGRPFTRGDLRAAGVSERLVRGGDVRRVTHGVHRLRSDHLGSWADLG +YVEAPAPFAPEETAAIVEASGGVASHLTALLLHRVPLPPFLAEDGTVHVSRPHPRGASVR +PEITSHARLVPAADVTALHGIRLTSLERSWADLAALLRPGMLEPVVAAGDALIHRPWSPE +GRRSPRTTTAALRSALLRAGRFKGVRTARAALELVRVGADSPQETALRLALLHAGLPEPE +LQLVLHPGRARSPDADLGWRQWRLVVHYDGGHHLDPAQLAVDSWRDEGWARAGWTQIWAT +VDDARDDFRRVVAEVQTHRARLGGRVFAS +>PROKKA_01554 +MVTSSLPLSDIAEAGRPFTRGDLRAAGVSERLVRGADVRRVTHGVHRLRSDHLGSWADLG +YVEAPAPFAPEETAAIVEASGGVASHLTALLLHRVPLPPFLAEDGTVHVSRPHPRGASVR +PEITSHARLVPAADVTALHGIRLTSLERSWADLAALLRPGMLEPVVAAGDALIHRPWSPE +GRRSPRTTTAALRSALLRAGRFKGVRTARAALELVRVGADSPQETALRLALLHAGLPEPE +LQLVLHPGRARSPDADLGWRQWRLVVHYDGGHHLDPAQLAVDSWRDEGWARAGWTQIWAT +VDDARDDFRRVVAEVQTHRARLGGRIFAS +>PROKKA_01006 +MSMSTSTSTSLPCPQDRRPPVPARPLDVVAAGGPLFTRADLSAAGLPADRLRAADVRRVT +HGVHRRADDVPGDWGALGYAEPPVAFAPEETAAIVTASRGVASHLSALLLHGIPVPPFLV +DDGRVHVSRPHSRGASERPEVRSHARSVPEADAVVLHGIRVTSVERTWADLAALVRPGHL +DPVVAAGDAVVTGIWTPQGRLPPRATILRLRAGLARSGRFKGARTARAALELIRAGADSP +PETALRLALLHAGLPEPELQLVLHRGRRRSPDADLGWRAWRLVVHYDGDPHLDPAQQAVD +AWRNGGWARAGWSQIVATVDDARDDFRRVVAEVLAHRARLGGRAYVA +>PROKKA_00950 +MALESLADVLGSAPLPIRAEGPPPLGLFTRSDLRAAGLGGHRVHGRDVRRVTHGVHRLAT +DPAGDWAVLGHRCPPAPFAPEETAAIVEAAGGVASHLTALLLHGVPLPPFLAEDGTVHVS +RPHARGASGRLEVTSHARSVPAADVTSLHGIRVTSLERTWADLASLVPPGLVDPVVAAGD +AVVRHPWTPQGRSAPRTTPARLAAALDRAGRFKGVRTARRALEAVRVGSDSPQETALRLA +LVHAGIPEPELQLVLHPGRERSPDADLGWRMWRLVVHYDGASHLEPAQRAVDARRHEGWE +RAGWAQIVATVDDARDDFRRVVAEVQAHRRRLGGRVYVC +>PROKKA_01778 +MATSSLPLPDIVETGRPFTRGDLRAAGVSERLVRGGDVRRVTHGVHRLRTDHLGSWADLG +YAEAPAPFAPEETAAVVEASGGVASHLTALLLHRVPLPPFLAEDGTVHVSRPHPRGASVR +PEITSHARLVPAADVTALHGIRLTSLERSWADLAALLRPGMLEPVVAAGDALIHRPWSPE +GRRSPRTTTAALRSALLRAGRFKGVRTARAALELVRVGADSPQETALRLALLHAGLPEPE +LQLVLHPGRARSPDADLGWRQWRLVVHYDGGHHLDPAQLAVDSWRDEGWARAGWTQIWAT +VDDARDDFRRVVAEVQTHRARLGGRIFAS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001505.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001505.fa new file mode 100644 index 0000000000000000000000000000000000000000..d99803e69456bb7bbbc2d0bc11d79c16d9bd5016 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001505.fa @@ -0,0 +1,80 @@ +>PROKKA_01862 +MDAKFTTKSQEALSAAAMNASTAGNPQVEPAHLLKALMDQRESVAVAVLKAAGADPDAVS +TAASSAIRRLPSTQGSTVAQPQFSRAALQVVQNARTQAEQRSDEFVSTEHLLLGVAADSG +EAGEALRSNGASLEALAAALTLVRGDSRVTTQDPETTFQSLEKYGTDLTEIARSGKLDPV +IGRDAEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLISL +DLGAMVAGAKYRGEFEERLKAVLEEIKAAEGQVVTFIDEIHTVVGAGASEGAMDAGNMLK +PMLARGELRLIGATTLDEYRENIEKDPALERRFQQVFVGEPSVDDTIAILRGLKERYEAH +HKVAIADSALVAAATLSHRYITGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDVLRRQVD +RLTMEELALEGETDPASIERLDALRAEKADREEELTALTARWDAEKATLNQAGDLRAKVD +ELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAREADRSATEPMVSEEVTADD +IAEVVSAWTGIPAGRMLTAESEKLLTMEEHLGERLIGQRDAVVAVADAVRRSRAGIADPN +RPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHSVSRLVGAPPGYVG +YDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVILI +LTSNLGSQFLVDPTLDEAAKRESVMSVVRGAFKPEFLNRLDEIVQFDALTVAELTRIVDL +QVESLQARLTDRRLTLEVSDAAKAWLAATGFDPAYGARPLRRLVQREIGDRLARGILAGE +IADGDTVVVDRVEGENGLTVTRKG +>PROKKA_01558 +MDAKFTTKSQEALSAAAMNASTAGNPQIEPAHLLKALMDQRESVAVAVLKAAGADPDAVS +TAASSAIQRLPSTQGSTVAQAQLSRAALQVVQNARTQAEQRSDQFVSTEHLLLGVAADPG +EAGEALRSNGASLEALAAALTQVRGDSRVTTQDPETTFQSLEKYGTDLTELARSGKLDPV +IGRDAEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLISL +DLGAMVAGAKYRGEFEERLKAVLEEIKAAEGQVVTFIDEIHTVVGAGASEGAMDAGNMLK +PMLARGELRLIGATTLDEYRENIEKDPALERRFQQVYVGEPSVDDTIAILRGLKERYEAH +HKVAIADSALVAAAALSDRYITGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDVLRRQVD +RLTMEELALEGETDPASVERLEALRAEKADREEELTALTARWDAEKATLNEAGDLRAKVD +ELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAREADRSSTEPMVSEEVTADD +IAEVVSAWTGIPSGRMLTAESEKLLTMEEHLGERLIGQRDAVVAVADAVRRSRAGIADPN +RPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHSVSRLVGAPPGYVG +YDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVILI +LTSNLGSQFLVDPTLDEAAKRESVMSVVRAAFKPEFLNRLDEIVLFDALTVDELTRIVDL +QVESLQARLTDRRLTLEVSDAAKAWLAETGFDPAYGARPLRRLVQREIGDQLARGILAGE +IADGDTVVVDRVEGENGLTVTRKG +>PROKKA_00998 +MDAKFTTKSQEALSAAAMNASTAGNPQIEPAHLLKALMDQRESVAVAVLKAAGADPDAVS +TAASSAIRRLPSTQGSTVAQAQLSRAALQVVQNARTQAEQRSDQFVSTEHLLLGVAADPG +EAGEALRSNGASLEALAAALTQVRGDSRVTTQDPENTFQSLEKYGTDLTEVARSGKLDPV +IGRDAEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLISL +DLGAMVAGAKYRGEFEERLKAVLEEIKAAEGQVVTFIDEIHTVVGAGASEGAMDAGNMLK +PMLARGELRLIGATTLDEYRENIEKDPALERRFQQVYVGEPSVDDTIAILRGLKERYEAH +HKVAIADSALVAAATLSHRYITGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDVLRRQVD +RLTMEELALEGETDPSSVERLEALRAEKADREEELTALTARWDAEKATLNEAGDLRAKVD +ELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAREADRSTTEPMVSEEVTADD +IAEVVSAWTGIPAGRMLTAESEKLLTMEEHLGERLIGQRDAVVAVADAVRRSRAGIADPN +RPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHSVSRLVGAPPGYVG +YDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVILI +LTSNLGSQFLVDPTLDEAAKRESVMSVVRAAFKPEFLNRLDEIVQFDALTVAELTRIVDL +QVESLQARLTDRRLTLEVSDAAKAWLAETGFDPAYGARPLRRLVQREIGDRLARGILAGE +IADGDTVVVDRAEGEEGLTVASA +>PROKKA_00945 +MNPSPQFTTKSQEALSAAAMNASTASNPAVEPAHLLKALMDQRDSVAVAVLKAAGADPDV +VSVAASTAIHGLPKASGATVSEARLSPAAGAVVKAAQQQASAHGDEYVSTEHLLLGLAAD +GGEAGRALTDAGASLAALQAAFTQVRGDERVTTPDPEATFQSLEKYGTDLTAVARSGKLD +PVIGRDQEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLI +SLDLGAMIAGAKYRGEFEERLKSVLEEIKKSDGQIVTFIDEIHTVVGAGASEGAMDAGNM +LKPMLARGELRLIGATTLDEYRENIEKDPALERRFQQVYVGEPSVDDTIAILRGLKERYE +AHHKVAIADSALVAAATLSDRYISGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDALRRQ +VDRITMEELALDGESDPGSVERLAGLRAEKADKEEELRALTARWEAEKASLNEAGDLRAR +VDELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAQEGQQGDVEAMVSENVTA +DDIAEVISAWTGIPAGRMLASETEKLLSMEEHLGDRLIGQKDAVRAVSDAVRRARAGIAD +PNRPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHAVSRLVGAPPGY +VGYDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVI +LILTSNLGSQFLVDQTMPEQARKDAVMDVVRAAFKPEFLNRLDEIVTFDALGVEDLARIV +DLQVASLGERLQQRRLTLDVTDAAREWLALTGYDPAYGARPLRRLVQREIGDQLARALLS +GAVQDGDTVVVDRAGEDTADGLTVAARRA +>PROKKA_01782 +MDAKFTTKSQEALSAAAMNASTAGNPQVEPAHLLKALMDQRESVAVAVLKAAGADPDAVS +TAASSAIRRLPSTQGSTVAQPQFSRAALQVVQNARTQAEQRSDEFVSTEHLLLGVAADSG +EAGEALRSNGASLEALAAALTLVRGDSRVTTQDPETTFQSLEKYGTDLTEIARSGKLDPV +IGRDAEIRRVVQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQRMVAGDVPESLRGKTLISL +DLGAMVAGAKYRGEFEERLKAVLEEIKAAEGQVVTFIDEIHTVVGAGASEGAMDAGNMLK +PMLARGELRLIGATTLDEYRENIEKDPALERRFQQVFVGEPSVDDTIAILRGLKERYEAH +HKVAIADSALVAAATLSHRYITGRQLPDKAIDLVDEAASRLRMEIDSAPEEIDVLRRQVD +RLTMEELALEGETDPASIERLDALRAEKADREEELTALTARWDAEKATLNQAGDLRAKVD +ELRSLAEKAQRDGDLAEASRLLYGEIPALEKQLEEADRAAREADRSATEPMVSEEVTADD +IAEVVSAWTGIPAGRMLTAESEKLLTMEEHLGERLIGQRDAVVAVADAVRRSRAGIADPN +RPTGSFLFLGPTGVGKTELAKALAEFLFDDERAMVRIDMSEYAEKHSVSRLVGAPPGYVG +YDEGGQLTEAVRRRPYSVVLLDEVEKAHPEVFDILLQVLDDGRLTDGQGRTVDFRNVILI +LTSNLGSQFLVDPTLDEAAKRESVMSVVRGAFKPEFLNRLDEIVQFDALTVAELTRIVDL +QVESLQARLTDRRLTLEVSDAAKAWLAATGFDPAYGARPLRRLVQREIGDRLARGILAGE +IADGDTVVVDRVEGENGLTVTRKG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001510.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001510.fa new file mode 100644 index 0000000000000000000000000000000000000000..be36896dd9fff3c9e11e9bcd009329399f3d1c92 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001510.fa @@ -0,0 +1,30 @@ +>PROKKA_01867 +MAQQNPITGSFGAVAAADAAGVHVAGLNKSFGANHVLRGIDLDVAPGEVVCLIGPSGSGK +STLLRCVNLLEKPDSGVVTVGEFTVTDEDVDLDVLRRHVGMVFQQFNLFPHLSVLENCTV +AQLKVLKRGKAEAVDIARRQLARVGLAELEDRYPDQLSGGQQQRVAIARALAMDPQLMLF +DEPTSALDPETVGDVLAIMRQLARDGMTMLVVTHEMGFAREVADRVVFMDGGVVVEAGPA +AAVISDPQQPRTQDFLRRVLHPTEIDL +>PROKKA_01563 +MAQQNPITGSFGAVAAADAAGVHVAGLNKSFGANHVLRGIDLDVAPGEVVCLIGPSGSGK +STLLRCVNLLEKPDSGVVTVGEFTVTDEDVDLDVLRRHVGMVFQQFNLFPHLSVLENCTV +AQLKVLKRGKAEAVDVARRQLARVGLAELEDRYPDQLSGGQQQRVAIARALAMDPQLMLF +DEPTSALDPETVGDVLAIMRQLARDGMTMLVVTHEMGFAREVADRVVFMDGGVVVEAGPA +AAVISDPQQPRTQDFLRRVLHPTEIDL +>PROKKA_00993 +MAQQTPQPAASAVDAAGVHVADLNKSYGSNHVLRGIDLDVAPGEVVCLIGPSGSGKSTLL +RCVNLLEKPDSGRITVGEFDVTDEDVDLDALRRHVGMVFQQFNLFPHLSVLENCTVAQVK +VLKRSKAEAAEVARRQLARVGLAELEDRFPDQLSGGQQQRVAIARALAMDPQLMLFDEPT +SALDPETVGEVLAIMRQLARDGMTMLVVTHEMGFAREVADRVVSMDAGVVVETGPAAALI +ADPQQPRTQDFLRRVLHPTEIDL +>PROKKA_00931 +MTEQTASPRPSDAGTAAGVHIAGLHKSYGSNHVLRGIDLDVAPGEVVCLIGPSGSGKSTL +LRCVNLLEVPDSGGVQVGEFTVTDPDVDLDRLRQHVGMVFQQFNLFPHLTVLENCTVAQV +KVLKRSAAEAADTARRQLARVGLGELEGRYPDQLSGGQQQRVAIARALSMDPRLMLFDEP +TSALDPETVGDVLAIMRKLAREGMTMLVVTHEMGFAREVADRVVFMDGGVVVEQGPASAV +ITDPQEPRTQDFLRRVLNPAGVDI +>PROKKA_01787 +MAQQNPITGSFGAVAAADAAGVHVAGLNKSFGANHVLRGIDLDVAPGEVVCLIGPSGSGK +STLLRCVNLLEKPDSGVVTVGEFTVTDEDVDLDVLRRHVGMVFQQFNLFPHLSVLENCTV +AQLKVLKRGKAEAVDVARRQLARVGLAELEDRYPDQLSGGQQQRVAIARALAMDPQLMLF +DEPTSALDPETVGDVLGIMRQLARDGMTMLVVTHEMGFAREVADRVVFMDGGVVVEAGPA +AAVISDPQQPRTQDFLRRVLHPTEIDL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001512.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001512.fa new file mode 100644 index 0000000000000000000000000000000000000000..b3cbd901883909f396d43e1916f17afe31a12c1a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001512.fa @@ -0,0 +1,30 @@ +>PROKKA_01869 +MLPLVAPLTVAAAAPTDYGWLGNIVVDIMEAVGPIGVGLAVFAENIFPPIPSEVILPLAG +FTAAGGAFSPHAALVWATVGSIVGALALYGLGAWLGRHRMYRLADRMPLVDMEDVAKTER +WFIRYGYWTVFLGRMVPVFRSLISIPAGIERMNLAKFTLFTALGSLIWNAIFVYGGYALG +ERFHVVSEYADVFSNIVLVLILAFLAIWVVLRLRRDARRRNDPDWRPPTADEMAARVEAI +LESSDHRK +>PROKKA_01565 +MLPLVAPLTVAAAAPTDYGWLGNIVVDIMEAVGPIGVGLAVFAENIFPPIPSEVILPLAG +FTAAGGAFSPHAALVWATVGSIVGALALYGLGAWLGRHRMYRLADRMPLVDMEDVAKTER +WFIRYGYWTVFLGRMVPVFRSLISIPAGIERMNLAKFTLFTALGSLIWNAIFVYGGYALG +ERFHVVSEYADVFSNIVLVLILAFLAIWVVLRLRRDARRRNDPDWRPPTADEMAARVEAI +LESSDHRK +>PROKKA_00991 +MLPAVTPLTLAASTVTADTDYGWLGNVVVDIMEAVGPVGVALAVFAENIFPPIPSELILP +LAGFTAAGGAFSPLAALLWATVGSVTGALALYGIGALLGRRRMYRIADRMPLVDVEDVAK +TERWFARYGYWTVFLGRMVPVFRSLISIPAGIERMHLGMFTLFTTLGSLIWNAIFVYGGY +ALGERFHLVSDYADVFSNVVVVLVLAFLVVWVVLRLRRNARRAKDPDWHQPTADEMAARV +DALLESSDHRK +>PROKKA_00929 +MIRRGRTTSDAAAVVVVENGGMSALSTLPLLAAAGTPDYGWLGNTIVAIMEAIGPVGVGL +AVFAENIFPPIPSEVILPLAGFTAAGGAFSPHAALIWATVGSVVGALALYGLGAWLGRRR +LYRIAAWMPLVDVSDVERTEKWFARYGYWTVFVGRMVPVFRSLISIPAGIERMNVAKFTL +FTALGSLLWNAIFVYGGYALGENFHVISDYADMFSNIVMVLILVFLAVWVVLRLRRNRGR +AADPAVDHEDPEAAAARVEAEIKALQHRK +>PROKKA_01789 +MLPLVAPLTVAAAAPTDYGWLGNIVVDIMEAVGPIGVGLAVFAENIFPPIPSEVILPLAG +FTAAGGAFSPHAALVWATVGSILGALALYGLGAWLGRHRMYRLADRMPLVDMEDVAKTER +WFIRYGYWTVFLGRMVPVFRSLISIPAGIERMNLAKFTLFTALGSLIWNAIFVYGGYALG +ERFHVVSEYADVFSNIVLVLILAFLAIWVVLRLRRDARRRNDPDWRPPTADEMAARVEAI +LESSDHRK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001513.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001513.fa new file mode 100644 index 0000000000000000000000000000000000000000..6556df3c0b210e2cb1f0b036e0ae35f9ff9fe338 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001513.fa @@ -0,0 +1,47 @@ +>PROKKA_01870 +MHPVLPSPRRGRAALGLAAVALVALSACARTEPQPEPAPATTAASALPSMDMAPFTVEVP +SHDLERVPEASVAVLEGEDPDHHGAWLQVSGAPAWTDAMAGAVRDQIDQYRRDTDPSADP +RLEIQPQLAVVAEDIAAARLLATERRGTDSVSTSHVIWYSAREDRVLETADLFTPDGWDA +FRAEVRQRMANDPDVIGSRLDSAVDAPEQVENRRVWDAVVFLPDGSLMLEADQASMAPAA +AGVLTVRIPRDTATAWLSDLGHVAADAASAPADLRLPDRSTPTPEEQQPEPAPEPEPETS +SWTEEATGAPVPPPSAPADTAAPTPSVTTPVPSSTAPSSSAPAPTRSATPSSPSSPPTSS +SPSGTGSGSPTPSTPDPTPTSATPTPTSPTPTSPSPSGPSTSASGPSTSAPATDPAPDPT +ESAPEPTATTASASASPTSGDRSSSTP +>PROKKA_01566 +MHPVLPSPRRGRAALGLAAVALVTLSACARTEPQPEPAPATTAASALPSMDMAPFTVEVP +SHDLERVPEASVAVLEGEDPDHHGAWLQVPGAPAWTEAMAEAVRAQIDQYRRDTDPSADP +RLEIQPQLAVVAEDIAAARLLATERRGTDSVSTSHVIWYSAREDRVLETADLFTPDGWDA +FRAEVRQRMANDPDVIGSRLDSAVDAPEQVENRRVWDAVVFLPDGSLMLEADQASMAPAA +AGVLTVRIPRDTATAWLSDLGHVAADAASAPADLRLPDRSTPTPEEQQPEPAPEPEPETS +SWTEEATGAPVPPPSAPADTAAPTPSVTTPVPSSTAPSSSAPAPTRSATPSSPSSPPTSS +SPSGTGSGSPTPSTPDPTPTSATPTPTSPTPTSPSPSGPSTSASGPSTSAPATDPAPDPT +ESAPEPTATTASASASPTSGDRSSSTP +>PROKKA_00990 +MSTPASPSARRARAALGLAAVALVALSACARTEPAPEPAPSTASATALPPMDMAPFTVDV +PSLDLDRVPGASIAVLEGTDPDHRGAWLQVPEAPAWTEAMAGSVRGQIDAYRRDTDRGAD +PRLEVQPRLAVVGEDIAAARLLSTETRGTDSVSSSHVVWYSAREDRVLETRDLFTDEGWD +AFRTEVRQRMKNDPDVVRERLASAVDSPELVENRRIWDAVVLLPDGSVMLEADQASMAPA +AAGVLTVRIPRDTAAPWLSDLGDAATDAARTPADLRLPDRSTPSPSTSAPEPAESSWTPE +ATGAPVPPRVPVPDPTTTAPSVDPGGDRDPSTSSAPPSSRPGTTAPSPVAGPQHPGPHHP +GPHHLRADRPGARPLDDDGAPAPGADQPDAHADADPVDSHADADAHDAHPDPDRDGDHGP +ADRPGAGARAGADDAAAERHERLRPRDPGRAGLSRPTPGCPGRPRTGACPARRRPAPPPH +GLT +>PROKKA_00928 +MHRLSPASTVRLRAGAGLLALGMLGLTACGSGDDAASSSPAPSSAAATQELPSMDMAPFT +LDVPSLDLDKVPGASLAVIQGQDPEYHAAWLQVPGAPAWTQAMDESVRGLVAQYQRDTDR +TASPVLDVQPRLAVAGRDVAAARLLSTERRGDRSVSAVHVVWYAAREDRVLSTEDLFTAD +GWAAFRREVGARMAGDPAVVQDRLRSAVDAPAQVENVRVWDALTFLPDGSALLEVDQAAM +SPADAGVLTARIPADTVRPWLSALGVSAQDAARSPEALVLPERPSAAPASEGGDAAVPAP +GQPSSDGATTSAPGQGSVPPAPGLPGAPAPGTPGTASQGGGSPGTAPQDTGSQHTGSQGT +GSQGTGASAPGASPSATRGDAGPAPTSSSAAPAPTGTGAPAPAPLPMPAPTTSSATPSGP +APAPTGGTPAPSPTTVAPTEPSPSADPTTSEPAPSSDPAPAPTDTASPAPTASSPSTPAD +VTGTATASGPLPATGGSTDPVTPTPAA +>PROKKA_01790 +MHPVLPSPRRGRAALGLAAVALVTLSACARTEPQPEPAPATTAASALPSMDMAPFTVEVP +SHDLERVPEASVAVLEGEDPDHHGAWLQVPGAPAWTEAMAEAVRAQIDQYRRDTDPSADP +RLEIQPQLAVVAEDIAAARLLATERRGTDSVSTSHVIWYSAREDRVLETADLFTPDGWDA +FRAEVRQRMANDPDVIGSRLDSAVDAPEQVENRRVWDAVVFLPDGSLMLEADQASMAPAA +AGVLTVRIPRDTAAPWLSDLGHVAADAASAPADLRLPDRSTPTLEEQQPEPETSSRTQEA +TDAPVPPPSAPADTAAPTPSATTPVPSSTVPSSTAPSSSVPTSTGSATPSSPTSPASSSS +PSGTGSGSPTPSTPDPSPTSATPTPTSPSPSGPSTSAPATAPAPDPTESAPEPTATTASA +PAPPTSGDRSSGTP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001518.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001518.fa new file mode 100644 index 0000000000000000000000000000000000000000..f4ae8b570cd5f343b1c7d2ec9d1edd75c75a9692 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001518.fa @@ -0,0 +1,25 @@ +>PROKKA_01875 +MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETGEPRVSAESAAEQAEDGDALAQAER +ILDEAGAQAGTEAPQPEASDREAELEADLRRLQAEYVNYKRRVDRDRDLARDAGVLKAVT +ALLPVLDDIDAARAAGDLTDGPFAAIATKLDTALAGLGLERHDQEALAGVEFDPAVHEAV +MRQPHAEVPADHVVQVFRNGYVRDGRVLRAAQVMVSAGDE +>PROKKA_01571 +MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETGEPRVSAESAAEQAEDGDALAQAER +ILDEAGAEAGTQAPQPAASDREAELETDLRRLQAEFVNYKRRVDRDRDLARDAGVLKAVT +ALLPVLDDIDAARAAGDLTDGPFAAIATKLDTVLAGLGLERHDQAALAGVEFDPALHEAV +MRQPHAEVPADHVVQVFRNGYVRDGRVLRAAQVMVSAGDE +>PROKKA_00984 +MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETGEPRVSAESAAEQAEDGDALTQAER +ILDEAGAQAGTEAPQPAASDREAELETDLRRLQAEYVNYKRRVDRDRALAQDLGVLKAVT +ALLPVLDDLDAARAAGDLTDGPFAAIATKLDTALAGLGLERHDQEALAGVEFDPSVHEAV +MRQPHAEVPADHVVQVFRNGYVRDGRVLRAAQVMVSAGDE +>PROKKA_00922 +MSENQNETPSPEEPVIRDRRRIDPETGQARTPGAGEDTVPAQEQGQAPQDSGDALSQAEQ +ILDEAGAAAEAEALPAAGSDREAELLEDLRRLQAEYVNYKRRVDRDRDVAKEQGVLKAVT +ALLPVLDDLDAARAAGDLEDGPFAAIAAKLMTALEGLGLEREDQEALAGVEFDPVRHEAV +MRQPHAEVPADHVVQVFRNGYARDGRVLRAAQVMVSAGQD +>PROKKA_01795 +MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETDEPRVSAESAAEQAEDGDALAQAER +ILDEAGAQAGTEAPQPEASDREAELEADLRRLQAEFVNYKRRVDRDRDLARDAGVVKAVT +ALLPVLDDIDAARAAGDLTDGPFAAIATKLDTALAGLGLERHDQEALAGVEFDPAVHEAV +MRQPHAEVPADHVVQVFRNGYLRDGRVLRAAQVMVSAGDE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001521.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001521.fa new file mode 100644 index 0000000000000000000000000000000000000000..eb49e9eeb14964daa88c4df1d14e0448bd605d4a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001521.fa @@ -0,0 +1,99 @@ +>PROKKA_01881 +MATLLYRLGLGAARRPLLVILAWVLALALAVGGFLAFGGTLSSTVTIPGTPTAQVTDRLK +EEFPEASRGRGQVVFTTEDGSPLTDAQREQITALLDDVAEQPAVEGVVNPFEAQAQQDDA +RTRLDEGRTELADGEQRLADGRQEIEDGRAELERRTAEADAAEQRLAEAAAQLEEGQAKL +DAARADLEERGLDALPAEALAPLREAEQQVAEGQEQLDAGRAELEEQAERLEAGQAKLDA +QRQELEAAQAELDARWAELEAGQAELDARAEQLAAGRAELEQARDAALAEAEAAGIPAEQ +VTEQFADQEAQLAAAEAQLAAGQDQADAARAQLEAAQAEADAGAEQLAAAQAEADDGAAR +LAAGRQQLQESEAELEAGREQVAAGRQQALDAAEAELDAQQQKIDEGRAEYERGVAELED +GRAQLAAGAERLDQAEADLADGRAELEDGRVEAERGERTLALAEDFRTVSEDGSTAVGIV +TFTTPTLDVTAEDKEAVTGALTGADIDGVAVHPSQELNATAPSLLGPGEVVGLVVAAIVL +VVMLGTLVGAGLPLVNALVGVGVGAAGALAFSSAVEMISVTPVLGVMLGLAVGIDYALFI +VNRHRQELRRGTGLHESIALANGTSGNAVVFAGITVIVALVGLNVTGIPFLGLMGTVGAV +CVAVAVLVAVTLTPALLSLAGMRILSKKERARLADEGPASVAEGSAAVRRAGRRSTMSTP +AAIASALAAVALLVLVALPVGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVV +TVDLPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVST +EELVRDLRATEPAGEASNLGVAGMTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRS +ILVPLIATGGFVLSMFAAMGGVVAIYQWGWLGSVFGVHNPGPVLSFLPTIMIGVLFGLAM +DYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPM +GFGLAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERAHAPAQ +PSVPAPDGGAHRA +>PROKKA_01577 +MATLLYRLGLGAARRPLLVILAWVLALALAVGGFLAFGGTLSSTVTIPGTPTAQVTDRLK +EEFPEASRGRGQVVFTTEDGSPLTDAQREQITALLDDVAEQPAVEGVVNPFEAQAQQDDA +RTRLDEGRTELADGEQRLADGRQEIEDGRAELERRTAEADAAEQRLAEAAAQLEEGQAKL +DAARADLEERGLDALPAEALAPLREAEQQVAEGQEQLDAGRAELEEQAERLEAGQAKLDA +QRQELEAAQAELDARWAELEAGQAELDARAEQLAAGRAELEQARDAALAEAEAAGIPAEQ +VTEQFADQEAQLAAAEAQLAAGQDQADAARAQLEAAQAEADAGAEQLAAAQAEADDGAAR +LAAGRQQLQESEAELEAGREQVAAGRQQALDAAEAELDAQQQKIDEGRAEYERGVAELED +GRAQLAAGAERLDQAEADLADGRAELEDGRVEAERGERTLALAEDFRTVSEDGSTAVGIV +TFTTPTLDVTAEDKEAVTGALTGADIDGVAVHPSQELNATVSSLLGPGEVVGLVVAAIVL +VVMLGTLVGAGLPLVNALVGVGVGAAGALAFSSAVEMISVTPVLGVMLGLAVGIDYALFI +VNRHRHELRRGTSLHESIALATGTSGNAVVFAGITVIVALVGLNVTGIPFLGLMGTVGAV +CVAVAVLVAVTLTPALLSLAGMRILSKKERARLADEGPASVAEGSAAVRRAGRRSTMSTP +AAIASALAAVALLVLVALPVGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVV +TVDLPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVST +EELVRELRATEPAGEASNLGVAGMTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRS +ILVPLIATGGFVLSMFAAMGGVVAIYQWGWLGSVFGVHNPGPVLSFLPTIMIGVLFGLAM +DYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPM +GFGLAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERGHAPAA +EAASAPAPEAGRTPAVDGGAHRA +>PROKKA_00977 +MAKLLYRLGLGAARRPLTVILAWVLALALAVGGFLAFGGTLSTNVTIPGTPTAQVTDRLQ +DEFPEASRGMGQVVFTTEDGQPFTDAQRDAVAALLDEVAGQDAVDAVVDPFEVQAQQDDA +RTALADGRQEIADGEQALVDGREQVDAGRAEIEEGRAQADAGEQELADAAAQLEDGQVQL +DAARADIEARGLDALPAEALAPLREAEQQIADGQAELDAGRAEIEEQAARLAAGQAEIDA +NREQLEAGQAELDARWGELDAAQAQLDAQREELEAGRAQLEQALAAALEQAEAAGIPAEQ +VTAQFAEQQAQLEAGQAQLDAAQEQADAGREQLVAAQAEADAGAEQLAEAQAQADAGAEQ +LAAGREQLEAAEAELESGREQLAAGRQQALDAAAAELDAQQARIDEGRAQHEQGVADLEA +GRAELAAGAERLDQAEADLATGRTELEDGRVAAERGERSLALVGGYRSVSEDGSTAVGIV +SFSQPSLDVTAEEKEAVTGALTGADIDGVAVHPSQELNATVPSILGPGEVVGLIVAAIVL +VVMLGTLVGAGLPLVNALVGVGVGAAGALAFSSVVEMISVTPVLGVMLGLAVGIDYALFI +VNRHRQELKRGTALHEAIALANGTSGNAVVFAGITVIIALVALNVTGIGFLGLMGTVGAV +CVAVAVLVAVTLTPALLSLAGTRILSRKERARLADEGPASAAEGSAAVRRAGRRSTMSTP +AAIASALAAIALLVLVALPFGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVV +TVDLPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVST +EELVRELRATEPAGEASNLGVAGMTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRS +ILVPLIATGGFVLSVFAAMGGVVAIYQWGWLGSVFGVHNPGPVLSFLPTIMIGVLFGLAM +DYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPI +GFGLAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERGHAPAA +EAASAPAPEAGRTPAVDGGAHRA +>PROKKA_00915 +MATLLHRLGLASARRPWAAILAWLIALALAVGAFLAFSGTLTTAVTIPGTPTAQVTDRLK +EQFPDAAKGTGQVVFATEDGSAFTEAQRRAVSDALRGVEGQDAVDSVVDPFDVARQQDEA +RTALEDGRRQIAEGEQKIAENEKALEDGRAQLAEAKDKAEAGQKELDAAAAQLDAGQEKL +DAARADLEARGLDALPAEATAPLTEAQQKLDAGQAEYDAGVAALEEQRPALEAAEAEIAK +QEAALEQAQARFEAGRAQAIAQAEAAGATPEQAAAAVDARLAPEREKLDAGAAQLEEARA +RTEAGRAEFDAGEEKLAAAAAELEQGRAQLAAGREKALTAARAELDAQQQKIDAGRAEHE +QGVRELEAGRAEIAQNEAKLADGPAQLEQARKDLAAGREKADRGQRMLTLTDGYRVVSED +GSAALGTVAFDRPSLDVTTEQKTAVIDALADADIPGVRAIPTQALNATMPSLIGPGEVVG +LAVAALVLVLMLGTLVGAGLPLVNALIGVGVGAAGALAFSGVVEMMSVTPVLGIMLGLAV +GIDYALFIVNRHRLELKRGTPLHASIALANGTSGNAVVFAGITVVIALVALNVTGIPFLG +LMGTVGAVCVAVAVLVAVTLTPALLSLAGMRILSRKERARRAAEAAPVADDAAAPSGSHA +AAPVSRSAARAVRDARRRRRMSTPAAVATVLASAAALIVVAIPFGSMRLGLPDGASEPVG +SDSQVSYELIADEFGEGYNGPLVVTVDLPSGLDETTAEDAQVQVGEQLKGLEHVAAVVPA +GFNQDRTTAMFQVLPEEGPNAISTGDLVHTLRDTEPAGEASNLGVAGVTSGFIDVSEKLS +AALPLYLGVVVGLSLLIMILVFRSILVPLIATGGFVLSVFAAMGGVVAIYQWGWLGGLFN +VHAPGPVLSFLPTIMIGVLFGLAMDYQLFIASGMREAYAHGQPARDAVMTGLRAGRAVVT +AAAIIMISVLGGFVFSHDAMIRPIGFGLAFGVLLDAFVVRLLLMPALMHLLGDAAWWLPK +WLDRILPDVDVEGAGLERHGAAGEAADAAPVGADRA +>PROKKA_01801 +MATLLYRLGLGAARRPLLVILAWVLALALAVGGFLAFGGTLSSTVTIPGTPTAQVTDRLK +EEFPEASRGRGQVVFTTEDGSPLTDAQREQITALLDDVAEQPAVEGVVDPFEAQAQRDDA +RTRLDEGRAELADGEQRLADGRQEIEDGRAELERRTAEADAGEQRLAEAAAQLDEGQAAL +DAARADLEERGLEALPADALAPLREAEQKVADGQEQLDAGRAELEEQAERLEAGQAEIDA +QRQELEAGQAELGDRWTELEAGQAELDAQAEQLAAGRAELEQARDAALAEAEAAGIPAEQ +VAAQFADQEAQLAAGEAQLAAGQDQADAARAQLEAAQAEADAGAEQLAAAQAEADDGAAR +LAAGRQQLQESEAELEAGREQVAAGRQQALDAAEAELDAQQQKIDEGRAEYERGVAELED +GRAQLAAGAERLDQAEADLADGRAELDDGRVEAERGERTLALAEDFRTVSEDGSTAVGIV +TFTTPTLDVTAEDKEAVTGALTGADIDGVAVHPSQELNATAPSLLGPGEVVGLVVAAIVL +VVMLGTLVGAGLPLVNALVGVGVGAAGALAFSSAVEMISVTPVLGVMLGLAVGIDYALFI +VNRHRQELRRGTGLHESIALANGTSGNAVVFAGITVIVALVGLNVTGIPFLGLMGTVGAV +CVAVAVLVAVTLTPALLSLAGMRILSKKERARLADEGPASVAEGSAAVRRAGRRSTMSTP +AAIASALAAVALLVLVALPVGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVV +TVDLPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVST +EELVRDLRATEPAGEASNLGVAGMTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRS +ILVPLIATGGFVLSMFAAMGGVVAIYQWGWLGSVFGVHNPGPVLSFLPTIMIGVLFGLAM +DYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPM +GFGLAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERAHAPAQ +PSVPAPDGGAHRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001525.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001525.fa new file mode 100644 index 0000000000000000000000000000000000000000..fa52fbb8184ff832245c77ddbe9cdbb3db114afb --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001525.fa @@ -0,0 +1,15 @@ +>PROKKA_01885 +MDPMDLATWAGGALLVVGAVGALYRIVRGPSLLDRAVATDVLLVVFSGMLVLEMAVHRHT +HHVVLVVLAATVGFVGSVTVARFAEDRRPDHSLEDQARVPGTTDVPGGEEGR +>PROKKA_01581 +MTDPFHLAAWIAGTLLFVGALGALYRIVRGPSLLDRAVATDVLLVVFSGMLVLEMAAHRH +THHVVLVVLAATVGFVGSVTVARFAEDRRPDHSLEDQARVPGTTDVPGGEEGR +>PROKKA_00973 +MTDPFHLAAWIAGTLLFVGALGALYRIVRGPSLLDRAIATDVLLVVLSSGLILDMAVRRH +TDNVVLVVLAATVGFVGSVTVARFVEDRRPDHSMEDQARVPGTSDVPGGEEGR +>PROKKA_00911 +MSLPLTLAAWIGGAMLFVGAVGALYRIARGPSLLDRAAATDVLLVVLSGALLLDMGVHRR +TDTVVLVLLAAAVGFMGSVMVSRFVEDRRPEHPQEHEALVPGTSDVPAPREDA +>PROKKA_01805 +MDPMDLATWAGGALLVVGAVGALYRIVRGPSLLDRAVATDVLLVVFSGMLVLEMAVHRHT +HHVVLVVLAATVGFVGSVTVARFAEDRRPDHSLEDQARVPGTTDVPGGEEGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001526.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001526.fa new file mode 100644 index 0000000000000000000000000000000000000000..03f1df51d693ee0a0542654d7dca95bfd02c61fd --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001526.fa @@ -0,0 +1,26 @@ +>PROKKA_01886 +MPGSDSARRGVVRPDRIRGIVAQWPLILVMVAVWCALWQDFAPHVALTGLAFALLIIGLF +PMPSIPFSGRLNPWWSLVFTVRFLVDVVRASVNVAGTVLLRGRRARGSIVGVPLRSHDDL +IITLVSHALALVPGSIVLDVDRVRSVLYLHVLDATTDEDVAGFRAKALDVEAGIIRAVGT +REDLELVRRFPSSAPPAARPPKEEA +>PROKKA_01582 +MPGSDSARRDVVRPDRVRGIVAQWPLILVMVAVWCALWQDFAPHVALAGLAFALLILGLF +PMPSIPFSGRLNPWWSLVFTVRFLVDVVRASVNVTGVVLLRGRRARGSIVGVPLRSHDDL +IITLVSHALVLVPGSIVLDVDRVRSVLYLHVLDATTDEDVEGFRAKALDVEAGIIRAVGT +REDLELVHRYPDTAPPEEESAERRRPAAPRPGGTAPIGSTADHAKEGT +>PROKKA_00972 +MPGTDPARDAAGAERPARPHRVRDMVGQWPLIAVLVLLWCAVWEDYSLHVALAGLAFSLL +VMVLFPMPRIPFSGRLNPWWFLVFTAQFLGDVVRSSVEVSKVVLLRGRAARSSIVGVRLR +SHDDLVITLVSHALALVPGSIVLDVDRARSILYLHVLDATTDEDIEDFRAKALRVEAGII +KAVGTREDLELVHRYPDTAPPEEESAERRRPAAPRPGGTAPIGSTADHAKEGT +>PROKKA_00910 +MPAAETTSPASAPTRPAPGGVRSVLRQWPLLLALVLMWCAVWQDFSAHVALTGLLFSLLV +VVLFPMPPIPFGGRFHPGHALVFTGRFLADVVASSLSVTRVILTRGRTVRSSVVRVPLRS +HDDIVLTLVSHALALVPGSIVLDMDRANGVLYLHVLDATTDADVADYRAKALRVEADIIR +AVGTRADVAVLRDHPDSAPDPEGVEERRRHPAYRAELLPDTPGPVAPAPVDARPEPDAPG +GDR +>PROKKA_01806 +MPGSDSARRGVVRPDRIRGIVAQWPLILVMVAVWCALWQDFAPHVALTGLAFALLIIGLF +PMPSIPFSGRLNPWWSLVFTVRFLVDVVRASVNVAGTVLLRGRRARGSIVGVPLRSHDDL +IITLVSHALALVPGSIVLDVDRVRSVLYLHVLDATTDEDVAGFRAKALDVEAGIIRAVGT +REDLELVRRFPSSAPPAARPPKEEA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001528.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001528.fa new file mode 100644 index 0000000000000000000000000000000000000000..503646a0f96c23085eb3279df922b55a376d4b81 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001528.fa @@ -0,0 +1,24 @@ +>PROKKA_01888 +MMTVDLALLLAMGVMFAGGIYLVLERSLTRILLGIVLINNGAIMLLFLSSGGTGLAPLFV +RGRDPHEYADTLPQALILTAIVIGFAVIAFLTAMIYRSWLLVREDEVEVDAEDVKIARMP +AWDAEDDAELVEESSEFLDDAADPNAHYEHATESRPHVRHASPTPPAHPGPASAVRAHRA +DGGPRP +>PROKKA_01584 +MMTVDLALLLAMGVMFAGGIYLVLERSLTRILLGIMLINNGAIMLLFLASGGVGLAPLFV +RGRDPHEYADTLPQALILTAIVIGFAVVAFLTAMIYRSWLLVREDEVEVDAEDVKIARMP +AWDAEDDAELVEESSEFLDDAADPNAHYEHATEARPQVQHATPAPQAPTGSGAASRGRRP +EGGERA +>PROKKA_00970 +MMTVDLALLLAMGVMFAGGIYLVLERSLTRILLGIMLINNGAIMLLFLASGGVGLAPLFV +RGRDPHEYADTLPQALILTAIVIGFAVTAFLTAMIYRSWLISREDEVEVDAEDVKIASQG +AWDAEDDSELVEEHSEFMDASTDPNAHYEHTTEARPQVQHVIPAPPTAAGSREAARGRRP +EGGERA +>PROKKA_00908 +MTPTVDLALLAVMGVLFATGIYLLLERSLTRILVGVMLINNAAVVLLFLTSGGAGLAPLY +DADTAPEDYADMLPQALILTAIVIGFATTAFLTAMIYRSWQLRREDDVATDVEDVKIAAQ +SGWDAEDDSVLTEEDSEFMDDASDPNAEYEFATAAAPRARAVRPGRATVQGGGGRP +>PROKKA_01808 +MMTVDLALLLAMGVMFAGGIYLVLERSLTRILLGIVLINNGAIMLLFLSSGGTGLAPLFV +RGRDPHEYADTLPQALILTAIVIGFAVVAFLTAMIYRSWLLVREDEVEVDAEDVKIARMP +AWDAEDDAELVEESSEFLDDAADPNAHYEHATEARPQVQHATPAPQAPTGSGAASRGRRP +EGGERA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001530.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001530.fa new file mode 100644 index 0000000000000000000000000000000000000000..9501ab4870d2d93d810b146b67723100f6e24e31 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001530.fa @@ -0,0 +1,45 @@ +>PROKKA_01890 +MTDVALPPVASAAPRRQVAAWALWDWGSAAFNAVMVTFVFGTYLASDAFGPDERGTAWLS +TAMAVAGVVIAVTAPVLGRRADGAGRRRLWLALTTGAVIACTAACFWVTPEESSLLLGVT +LIALGTVFFEFAEVQVNAILVHISTPATIGRISGIGWGAGYLGGILLLLIVFVGFVSGDA +HWFGVTEDAALNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPAADGGPRRESVLGSYREL +GATLARMWREDRNTLWFLVASAVFRDGVGAVFVYGAILGTTVYGLAASDVILFAIAANVV +AALGAFVGGRLDDAVGPRRVILGSLAAMVLVAGALFFASGTLAFWVGGLALCLFVGPVQS +ASRAFLGRLTTPRTAGEVFGLYATTGRAVGFITPALVTLALALHPDNRVVIPVIAVVLVA +GGLLFARVTEPITRSAESVR +>PROKKA_01586 +MTDVALPPVASAAPRRQVAAWALWDWGSAAFNAVMVTFVFGTYLASDAFGPDERGTAWLS +TAMAVAGVVIAVTAPVLGRRADGAGRRRRGLGLTTGAVIACTAACFWVTPEESSLLLGVT +LIALGAVFFEFAEVQVNAILVHISTPATIGRISGIGWGAGYLGGILLLLIVFVGFVSGDA +HWFGVTEDEGLNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPSPGGGPRRESLAASYRAL +GSTLARMWREDRNTLWFLLSSAVFRDGVGAVFVYGAILGTTVYGLAASDVILFAIAANVV +AALGAFVGGRLDDAVGPRRVILGSLAAMVLVAGALFFASGTLAFWVGGLALCLFVGPVQS +ASRAFLGRLTTPRTAGEVFGLYATTGRAVGFITPALVTLALALHPDNRVVIPVIAVVLVA +GGLLFARVTEPITRSAESVR +>PROKKA_00968 +MPGMDPAASAVPDAALPRLATAAPRRQVVAWALWDWGSAAFNAVMVTFVFGTYLASDAFG +PDERGTAWLSTALAVAGVVIALTAPVMGRRADGAGRRRLWLGVMTAAVIACTTACFLVTP +QESSLLLGVTMIALGTVFFEFAEVQVNAILVQISTPATIGRISGIGWGAGYLGGILLLLI +VFVGFVSGDAHWFGITGDEALNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPTPGGGPRR +ESLAASYRALGSTLARMWRQDRNTLWFLVSSAVFRDGVGAVFVYGAILGTTVYGLAASDV +ILFAIVANVVAAAGAFAGGRLDDAIGPRRVILGSLAAMVLVAAGLALASGTLAFWIGGLA +LCLFVGPVQSASRAFLGRLTTERTAGEVFGLYATTGRAVGFITPMLVTLALAAVPDNRVV +IPVIVLVLIVGGVLFARVTDPVTRSAEPAP +>PROKKA_00906 +MPRMSSPAPHAAPQPCPAPHGGAGPAPARVPRGRVVAWAAWDWGSAAFNAVMVTFVFGTY +LASDAFGPDDRGTQWLSAANALAGVVIALTAPALGRLADGTGRRRLWIALTTGAVIACTA +ACFLVTPEESMLGLGVTLIALGTVFFEIASVHINAILLQISTPATIGRVSGFGWGAGYLG +GIVLLLIVFVGFVSGDDHWFGVGEERALNIRVVALVAAAWFLVFALPVLAASPEPPAARG +ADGSPRRESLVESYRGLGRTLARMWRQDRLTLRFLAASAVFRDGVGAVFVYGAILGTTLY +GLAAQDVVLFAIVANVVAALGAFAGGRLDDALGPRRVILGSLAAMVVVAAALVLAEGTAA +FWAGGLALCLFVGPVQSASRAFLGRLTVPETAGEAYGLYATTGRAIGFITPALVSAALAV +WGDSRVIIPVIALVLLAGGALLLGVREPEGPTVAGARPGTGPRAAR +>PROKKA_01810 +MTDVALPPVASAAPRRQVAAWALWDWGSAAFNAVMVTFVFGTYLASDAFGPDERGTAWLS +TAMAVAGVVIAVTAPVLGRRADGAGRRRRGLALTTGAVIACTAACFWVTPEESSLLLGVT +LIALGTVFFEFAEVQVNAILVHISTPATIGRISGIGWGAGYLGGILLLLIVFVGFVSGDA +HWFGVTEDAALNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPAADGGPRRESVLGSYREL +GATLARMWREDRNTLWFLVASAVFRDGVGAVFVYGAILGTTVYGLATSDVILFAIAANVV +AALGAFVGGRLDDAVGPRRVILGSLAAMVLVAGALFFASGTLAFWVGGLALCLFVGPVQS +ASRAFLGRLTTPRTAGEVFGLYATTGRAVGFITPALVTLALALHPDNRVVIPVIAVVLVA +GGLLFARVTEPITRSAESVR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001531.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001531.fa new file mode 100644 index 0000000000000000000000000000000000000000..f1b8ea14681b874e5e41eac02ca7e00f62f58a73 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001531.fa @@ -0,0 +1,25 @@ +>PROKKA_01891 +MLLSDRDIRAELDSGRVGLDPLDPAMVQPASVDVRLDRFFRLFDNHRYAHIDPRQKQDEL +TRLVEVDPDEAFILHPGEFVLGSTYEQVTLPDDLAARLEGKSSLGRLGLLTHSTAGFIDP +GFSGHVTLELSNVATLPITLWPGMKIGQLCFFRLSSSAQSPYGTGANQNRYQGQRGPTAS +RAHRDFHLTRIER +>PROKKA_01587 +MLLSDRDIRAELDSGRVGLDPLDPAMVQPASVDVRLDRFFRLFDNHRYAHIDPRQEQDEL +TRLVEVDPDEAFILHPGEFVLGSTYEQVTLPDDLAARLEGKSSLGRLGLLTHSTAGFIDP +GFSGHVTLELSNVATLPITLWPGMKIGQLCFFRLSSAAQSPYGTGANQNRYQGQRGPTAS +RAHRDFHLTRIE +>PROKKA_00967 +MLLSDQDIRAELASGRVGLDPLDEAMVQPASVDVRLDRFFRLFDNHRYAHIDPRQEQDEL +TRLVEVDPDEAFILHPGEFVLGSTYEQVTLPDDLAARLEGKSSLGRLGLLTHSTAGFIDP +GFTGHVTLELSNVATLPITLWPGMKIGQLCFFRLSSPAASPYGTGANQNRYQGQRGPTAS +RAHLDFHLTRIDR +>PROKKA_00905 +MASVLLSDRDIRAELSSGRIGLDPLELSMVQPASVDVRLDRFFRLFDNHRYAHIDPAQPQ +EELTRLVEVEPDQPFVLHPGEFVLGATYEQITLPDDVAARLEGKSSLGRLGLLTHSTAGF +VDPGFTGHVTLELSNVATLPITLWPGMKIGQLCFFRMSSPAESPYGSGGNLNRYQGQRGP +TASRSHQDFHLTRIPR +>PROKKA_01811 +MLLSDRDIRAELDSGRVGLDPLDPAMVQPASVDVRLDRFFRLFDNHRYAHIDPRQEQDEL +TRLVEVDPDEAFILHPGEFVLGSTYEQVTLPDDLAARLEGKSSLGRLGLLTHSTAGFIDP +GFSGHVTLELSNVATLPITLWPGMKIGQLCFFRLSSSAQSPYGTGANQNRYQGQRGPTAS +RAHRDFHLTRIER diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001532.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001532.fa new file mode 100644 index 0000000000000000000000000000000000000000..36619b2f9a1c2ff9d4de15010bcc2ef30c21181c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001532.fa @@ -0,0 +1,35 @@ +>PROKKA_01896 +MTQVLSGFAVVWVIILVGVLVGRTGVLGEHGRTVLSRAAFFIGNPALLFVTLSRADVGAV +LGPQLWVATLSAFTAAALYLAVTVPLLKGRSASERIMSALSASLVNSANLGIPIAAYVLG +DAALAAPALIFQLAIYTPLYVAAMDAATAREARRRTTAGRRRAVRRSPGRAVADQVRHTV +TNPLILGSVAGLVFSLTGWSLQGPLMESVELIGGLSIPAMLLAFGMSLVGSRPLERAGGR +RADVLLASAVKLVVHPLLAWLLAQFVFGLDARHVFVAVVLASLPTAQNVFVTAVRYDTGL +RVSKDTILVTTIVAIPAMIAVALLLA +>PROKKA_01592 +MTQVLSGFAVVWVIILVGVLVGRTGVLGEHGRTVLSRAAFFIGNPALLFVTLSRADVGAV +LGPQLWVATLSAFTAAALYLAVTVPLLKGRSASERIMSALSASLVNSANLGIPIAAYVLG +DAALAAPALIFQLAIYTPLYVAAMDAATAREVRRRTTAGRRRAVRRSPGRAVADQVRHTV +TNPLILGSVAGLVFSLTGWSLPGPLMESVELIGGLSIPAMLLAFGMSLVGSRPLERAGGR +RADVLLASAVKLVVHPLLAWLLAQFVFGLDARHVFVAVVLASLPTAQNVFVTAVRYDTGL +RVSKDTILVTTIVAIPAMIAVALLLA +>PROKKA_00962 +MTQVLSGFVVVWVIIAVGFLVGRSGVLGEDARTVLSRTAFYIGSPALLFVTLSGADVAAV +LGPQLWVATLSALAAAALFLAISIPVFKQRPASERIMAALSASMVNSANLGIPIAAYVLG +DAALAAPVLIFQLAIYTPLYVAAMDVATTSEARARAAGGRPAVRRSRGQALAAQLRQTGT +NPMILGSAAGLLFSLNDWTLPGPLMQSVELIGGLSIPAMLLAFGMSLVGSRPLERAGGRR +ADVLLASGVKLLVHPLIAWVLAQFVLGLDAREVFVAVVLASLPTAQNVFVSAVRYDAGLR +VAKDTILITTIVAIPAMIAVALLLA +>PROKKA_00901 +MIEVLSGFSVVWVIILVGLLLGRTGVLGDEAREVLSRTAFFVGNPALLFVTLSRADVGAV +LGPQLWVACLSAFAAAVVFLGLSIPLLKGRPASERVMSGLSASLVNSANLGIPIATYVLG +DAALAAPALIFQLAIYTPVYVAVMDWATTHEAAARASSAGAAHDAGAPAPRTVRPRNPVL +AQLRQTATNPMILGAFGGLLLSFTGWTLPGPLMTSVELIGGLSIPAMLIAFGMSLAGSRP +LARDSGRRADVLLASAVKLVVHPLVAWMIAQFVFGLDARRVFVAVVLASLPTAQNVYVSA +VRYRAGETVSKDTILVTTIVAIPAMIAVALLLA +>PROKKA_01816 +MTQVLSGFAVVWVIILVGVLVGRTGVLGEHGRTVLSRAAFFIGNPALLFVTLSRADVGAV +LGPQLWVATLSAFTAAALYLAVTVPLLKGRSASERIMSALSASLVNSANLGIPIAAYVLG +DAALAAPALIFQLAIYTPLYVAAMDAATAREARRRTTAGRRRAVRRSPGRAVADQVRHTV +TNPLILGSVAGLVFSLTGWSLQGPLMESVELIGGLSIPAMLLAFGMSLVGSRPLERAGGR +RADVLLASAVKLVVHPLLAWLLAQFVFGLDARHVFVAVVLASLPTAQNVFVTAVRYDTGL +RVSKDTILVTTIVAIPAMIAVALLLA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001533.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001533.fa new file mode 100644 index 0000000000000000000000000000000000000000..3c3634e1b187923b1fb51ea55bd932e35d29690b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001533.fa @@ -0,0 +1,20 @@ +>PROKKA_01899 +MTTLIVTSSAHGSTREIAERVAEVLRTSQAVPTVVEDVEGAAAWLATADAVIVAAPVYTG +SFAADARAFLDTRRAELTDLPLVILASGGAPELARPVREKLESYGPREVAYFRGALFEER +LGRLEKLKLKLSRNEHYGDFRDWDAIEAWAKTLPGAGVR +>PROKKA_01595 +MTTLIVTSSAHGSTREIAERVAEVLRTSQAVPTVVEDVEGAAAWLATADAVIVAAPVYTG +SLAADARAFLDTRRAELADLPLVILASGGAPELAPPVREKLESYGPREVAYFRGALVEER +LGRLEKLKLKLSRNEHYGDFRDWDAIEAWAKTLSGAGVR +>PROKKA_00959 +MTTLIVTSSAHGSTREIAERVAEVLRTSQSVETVVEDVAGAAAWLATADAVIVAAPVYEG +SLAAEARHFLDSRRAELADKPLLFLASGGGYELDPKVREKLESYGPREIAFFRGALVEER +LGWLEKLKLKVSRNENYGDYRDWDAIEAWAKSLSGHGVR +>PROKKA_00899 +MTALIVTASRHGSTREIAERVAEVLRTTAQTDTVVEDVAGAAAWLDTADAVVVAAPVYGD +KLEKSAKAFLDSRRAELSQKSLVILYSGASPVPNRALADQLGTYGARDVKYLRGALVEER +LGALEKLQIKLVKGRYGDFRDWNAVEHWAKGLSAHGVN +>PROKKA_01819 +MTTLIVTSSAHGSTREIAERVAEVLRTSQAVPTVVEDVKGAAAWLATADAVIVAAPVYTG +SLAADARAFLDTRRAELADLPLVILASGGAPELARPVREKLESYGPREVAYFRGALVEER +LGRLEKLKLKLSRNEHYGDFRDWDAIEAWAKTLSGAGVR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001534.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001534.fa new file mode 100644 index 0000000000000000000000000000000000000000..58c5de85ae7b1118d3cd766a10a0f57d9c95c606 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001534.fa @@ -0,0 +1,65 @@ +>PROKKA_01900 +MMVGMTAPQTPNPVPSADAPAAVPRAATRVRASELVGRGWLNTGGEQVTLEDLRGKVVLL +DFWTFCCINCLHVLDELRPLEEEFADVLVTVGVHSPKFEHEADPDALAAAVERYAIEHPV +LDDPELTTWQAYSARAWPTLVVVDPEGYIAAHLSGEGHVAGLYGLVRELVAEHEAKGTLH +RGSGPYVPPAPVARDLSFPGKAVSLGGRGSRPGSFLVSDTGHHRLLEVAEDLTTVLRAFG +GGDPATADAGQAELAFPTPGEKGHADGGPDEALFNEPQGLALLPEDVAERVGYDVVVADS +VNHRLRGLRLSDGHVSTLAGNGVQKLIDSERAKEAAAVDDEGDIAVDLADLPGEPTAISL +SSPWDVVWHPALGRVVIAMAGTHQLFDFDPVTGALAVHAGTALEGLLDGDAGRAWFAQPS +GLSVGADGALWVADSETSAVRWVRTGEDGRREVGTAVGAGLFDFGHVDGEADRARLQHPL +GVTALPDGSVLIADTYNGAIRRYAPAGEDAAGRAVPATVTTVARGLLEPSDVLVEHDADG +NDTAIVVVESNAHRLTRLAVPEEFLTVDEGARQTQRPRTPVVAGDLDLTIGFAAPTGQKL +DDRWGDPTQLKISSSPEELLLEGAGTSTGLHRTLRLNPEVEEGVLHITARAAACDGEKGQ +PIPDHAACHLYQQDWGIPVTVHTPDRAPEGAETRLDLDLRGIH +>PROKKA_01596 +MMVDMTAPQTPNPAPTADAPAAVPRAATRVRASELVGRGWLNTGGEQVSLEDLRGKVVLL +DFWTFCCINCLHVLDELRPLEEEFADVLVTVGVHSPKFEHEADPDALAAAVERYAIEHPV +LDDPELTTWQAYSARAWPTLVVVDPEGYIAAHLSGEGHVAGLYGLVRELVAEHEAKGTLH +RGSGPYVPPAPVARDLSFPGKAVSLGGRGSRPGTFLVSDTGHHRLLEVAEDLTTVLRAFG +GGDPATADAGQAELAFPTPGEKGHADGGPDQALFNEPQGLALLPEDVAQRVGYDVVVADS +VNHRLRGLRLSDGHVSTLAGNGVQKLIDSERAKEAAAVDDEGDVAVDLADLPGEPTAISL +SSPWDVVWHPALGRVVIAMAGTHQLFDFDPVTDALAVHAGTALEGLLDGEAGRAWFAQPS +GLSVGADGTLWVADSETSAVRWVRTGEDGRREVGTAVGAGLFDFGHVDGEADRARLQHAL +GVTALPDGSVLIADTYNGAIRRYAPAGEDAAGRAVPATVTTVARGLLEPSDVLVEHDADG +NDTAIVVVESNAHRLTRLAVPEEFLTVDEGARQTQRPRTPVVAGDLDLTIGFAAPTGQKL +DDRWGDPTQLKVSSSPEELLLEGAGTSTGLHRTLRLNPEVEEGVLHITARAAACDGEKGQ +PIPDHAACHLYQQDWGIPVTVHTPDRAPEGAETRLDLDLRGIH +>PROKKA_00958 +MMVGMTDPQTPPAVSPDAAPSDAAPAAVPRAASRVRASELVGRGWLNTGGEQVTLEDLRG +KVVILDFWTFCCINCLHVLDELRPLEEEFADVLVTVGVHSPKFEHEADPDALAAAVERYT +IEHPVLDDPELTTWQAYSARAWPTLVVVDPEGYIAAHLSGEGHVAGLYSLVRELVAEHEA +KGTLHRGSGPYVPPAPVARDLKFPGKAISLAGRGTAPGTFLVADTGHHRLLEVAEDLTTV +LRAVGGGDPAGAGEEQAGLAFPTPGEKGHADGGPEQALFNEPNGLALLPEDVAERVGYDV +VVADTVNHRLRGLRLADGGVSTVAGNGVQKLIDSERAKEASAGDAEDVAVDLSDLPGEPT +AISLSSPWDVAWDPAAGRVVIAMAGTHQLFDFDPVAGALAVHAGTGLEGLLDGDAGSAWF +AQTSGLSLGPDGTLWAADSETSAVRWLRTGEDGRREVGTAVGTGLFDFGFVDGEAAQARL +QHPLGVTALPDGSVLIADTYNGAVRRYAPAGEDAAGRPVAAAVSTVARGLQEPSDVLVEH +DADGAPAAIVVVETNAHRLVRLAVPEEYLTVDEGARQTQRPRTPMVAGDVDLAIGFAAPS +GQKLDDRWGDPTQLKVSSSPEELLLEGAGTSTGLSRTLRLNPAVAEGVLHITARAAACDG +EKGQPIPDHAACHLYQQDWGIPVTVHAPEGAPEGAETRLDLDLRGIH +>PROKKA_00898 +MRRPLPADARRAWAMMEGMTEQQTSAPSVPRSGSRVRASSLVGRRWLNTGGTEVSLEDLR +GKVVILDFWTFCCINCLHVADELRPLEEEFSDVLVTVGVHSPKFEHEADPDALDAAVERY +DIAHPVLDDPTLVTWQAYSARAWPTLVVVDPEGYIVAHLSGEGHVAGLYSLVRELVAEHE +AKGTLHRGSGPYVAPAPVARDLKFPGGAVSLEGRGSRPGSFLVADTGHHRIVELAADLTT +VLRAIGGGDPAEAPAEAADLAFPTPATRGHRDGGPETALFSEPNGLLLLPEDVAARAGVD +VVVADTVNHRLRGIDLATGEVTTLAGNGVQKLIDSERVREAAAGDESAAADLSDLPGDPT +GISLSSPWDVAWDAAAGRVIVAMAGTHQLFSYDPVARVLAVHAGTGLEGLLDGPADTAWF +AQTSGLSFAQDGTLWLADSETSAVRWLRTAEDGTRQVGTAVGTGLFDFGYVDGAPEQARL +QHPLGVTALPDGSVLVADTYNGAIRRYAPAAEDAAGRPVEAAVSTVTRELKEPSDVLVEP +GEDGAPAEIVVVETGAHQLVRISVPAEYLTVDEGARQTARPSTDVAAGDLDLSVGFAAPA +GQKLDDRWGDPTQLKVSSSPEELLLDGAGTSVGLTRTLRLNPAVAEGVLHITARAAACDG +EKDGPIPDSAACHLYQQDWGIPVRVHAADQAPDGAETRLDLDLRGIH +>PROKKA_01820 +MMVDMTAPQTPNPAPTADAPAAVPRAATRVRASELVGRGWLNTGGEQVSLEDLRGKVVLL +DFWTFCCINCLHVLDELRPLEEEFADVLVTVGVHSPKFEHEADPDALAAAVERYAIEHPV +LDDPELTTWQAYSARAWPTLVVVDPEGYIAAHLSGEGHVAGLYGLVRELVAEHEAKGTLH +RGSGPYVPPAPVARDLSFPGKAVSLGGRGSRPGTFLVSDTGHHRLLEVAEDLTTVLRAFG +GGDPATADAGQAELAFPTPGEKGHADGGPDQALFNEPQGLALLPEDVAQRVGYDVVVADS +VNHRLRGLRLSDGHVSTLAGNGVQKLIDSERAKEAAAVDDEGDVAVDLADLPGEPTAISL +SSPWDVVWHPALGRVVIAMAGTHQLFDFDPVTSALAVHAGTALEGLLDGEAGRAWFAQPS +GLSVGADGTLWVADSETSAVRWVRTGEDGGREVGTAVGAGLFDFGHVDGEADRARLQHAL +GVTALPDGSVLIADTYNGAIRRYAPAGEDAAGRAVPATVTTVARGLLEPSDVLVEHDADG +NDTAIVVVESNAHRLTRLAVPEEFLTVDEGARQTQRPRTPVVAGDLDLTIGFAAPTGQKL +DDRWGDPTQLKISSSPEELLLEGAGTSTGLHRTLRLNPEVEEGVLHITARAAACDGEKGQ +PIPDHAACHLYQQDWGIPVTVHTPDRAPEGAETRLDLDLRGIH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001535.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001535.fa new file mode 100644 index 0000000000000000000000000000000000000000..3e54b06fa7f582780ffa8a6b222204a876ce54e1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001535.fa @@ -0,0 +1,30 @@ +>PROKKA_01901 +MSADRVRPLRRPAAPRRGRLRLVAAVAAGLLALTGCGAGDNDPAAASVPADGVHDDAGTA +VHTESAAPEGLGLGDRQDERMAEAAAERAATFGFVRQRAATAEEIDAAREDSRDRRADAD +RTTVQPAQCKAPLTALDFSPIALDGAEATRVDVGADTFTGTGTVEVARLTGQGRQDVERH +IQTVNALRADCREMTMTVQEGDATVDYRLEVSDAPLSDGTPAQSALVWERTVASESEPQL +TAQVLTAVTSDAVVMVSFVGRPEAGRKEFTLIAEEMLAAALAAD +>PROKKA_01597 +MSADRLPPLGRPAAPRRGRLRLAAAVAAGLLALTGCGAGDGDPAAASASADGVHGDAGTA +APTESAAPEGLGLGDRQDERMAEAAAERAATFGFVRQRAATAEEIDAAREDSRDRRADAD +RTTVQPAQCKAPLTALDFSPIALDEAEATRVDVGADTFTGTGTVEVARLTGQGRQDVERH +IQTVNALRADCREMTMTVQEGDATVDYRLEVSDAPLSDGTPAQSALVWERTVASESEPQL +TAQVLTAVTSDAVVMVSFVGRPEAGRKEFTLIAEEMLAAALAAD +>PROKKA_00957 +MLALTGCGAGDEPAPEQPSAPADALHGDVGGAAPAPEEGAEGLGLGDRQDERMAAAAAER +AVGFGFVRQRAAAPEEIDAAREDSRARRSDADRTTVQPAACKAPLTALDFSPISLDEGEA +TRVDVGADTFTGTGTVEVARLTGSGRQEVERHLQTVNGLLADCREMTMTVQDGDASVDYR +LAVSEAPLSEGTPAQSALVWERSLASADGPQLTAQVLTAVTADAVVMVSFVGQPEAGRKE +FTLIAEEMLAAALAAG +>PROKKA_00897 +MSADRTRPRPAVRRLAVASSGAALAAVLLAGCASGGDAAASSGAQAAGPSSSAATGGLDL +GDRVDQRRAEAAAARAASFGFTRQDAVGADQIAAARGDAADRAADDGRTTVEPARCQAPL +AALDFSPILLDQEEVSRVDVGTDSFAGTGTVEVATLDGPGRQRVEEHLQTVNTLLADCRD +MTVTTRDADGARTYRLQMSAAGLSDGSPAQSGLVWTQTPAGRDEPATAAQILTAVGPEDV +VMVSFTGQPQAAERQFTVMAEEMLAAAGTVTR +>PROKKA_01821 +MSADRVRPLRRPAAPRRGRLRLVAAVAAGLLALTGCGAGDNDPAAASVPADGVHDDAGTA +VHTESAAPEGLGLGDRQDERMAEAAAERAATFGFVRQRAATAEEIDAAREDSRDRRADAD +RTTVQPAQCKAPLTALDFSPIALDGAEATRVDVGADTFTGTGTVEVARLTGQGRQDVERH +IQTVNALRADCREMTMTVQEGDATVDYRLEVSDAPLSDGTPAQSALVWERTVASESEPQL +TAQVLTAVTSDAVVMVSFVGRPEAGRKEFTLIAEEMLAAALAAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001542.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001542.fa new file mode 100644 index 0000000000000000000000000000000000000000..86fcafab5a4425ab8e172fa91ec737d8d259e29a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001542.fa @@ -0,0 +1,15 @@ +>PROKKA_01908 +MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV +RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW +>PROKKA_01604 +MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV +RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW +>PROKKA_00950 +MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV +RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW +>PROKKA_00890 +MAKKSKIAKNEQRKVMVARNAEKRLELKKTLIDPNASDEAREAARVGLQKLPRDASPVRV +RNRDAIDGRPRGTFQRFGISRVRFREMAHRGELPGVTKSSW +>PROKKA_01828 +MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV +RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001543.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001543.fa new file mode 100644 index 0000000000000000000000000000000000000000..4a6564d52e9d63430f347d9e9a9dc274575fac8e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001543.fa @@ -0,0 +1,10 @@ +>PROKKA_01909 +MAKDKDVRPIIKLKSTAGTGFTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER +>PROKKA_01605 +MAKDKDVRPIIKLKSTAGTGFTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER +>PROKKA_00949 +MAKDKDVRPIIKLKSTAGTGYTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER +>PROKKA_00889 +MAKDKDVRPIIKLKSTAGTGYTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER +>PROKKA_01829 +MAKDKDVRPIIKLKSTAGTGFTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001545.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001545.fa new file mode 100644 index 0000000000000000000000000000000000000000..e3e6eeb3c72bf746c36c01f05404a35873653792 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001545.fa @@ -0,0 +1,30 @@ +>PROKKA_01911 +MSHTSEQSSPLADQVPPGGPDEPHAAEGVHARLNWLRAGVLGANDGIVSVAATVVGVAGA +TTALTPVLLAGAAAVVGGAFSMALGEYVSVSSSSDSQKSLIAKERRELEEDPEGELEELV +QLYEADGLSRATAEAAARELTEKDALAAHLRMELGMAEEDVVSPWAAAGASFLSFLVGAL +LPFLTVVLAPVDFRIPLTFGVTLVALAVTGWVGARLGDAPALRAAVRVVLGGALALGLTL +AVGSLLGASVA +>PROKKA_01607 +MSHTSEQSSPLADQLPPGGPDEPHAAGGVHARLNWLRAGVLGANDGIVSVAATVVGVAGA +TTALTPILLAGAAAVVGGAFSMALGEYVSVSSSSDSQKSLIAKERRELEEDPEGELEELV +QLYEADGLSRATAEAAARELTEKDALAAHLRMELGMAEEDVVSPWAAAGASFLAFLVGAL +LPFLTVVLAPVGLRVPFTFGVTLVALAVTGWVGARLGDAPALRAAVRVVLGGALALGLTF +AVGSLLGASVA +>PROKKA_00943 +MNESTAPSEPTVRDDVAASSGHDRPEPHAGGGLHERLNWLRAGVLGANDGIVSVAATVVG +VAGATTAVAPVAIAGVAAVVGGAVSMALGEYVSVSSSSDSQKALIAKERRELAEDPEGEL +EELVGLYEAEGLSRATAENVARELTEKDALKAHLRAELGMDETGVVSPWSAAGASFVAFL +LGALLPFLTIILAPVDIRVALTFVTTLVALAGTGYAGAWLGGAPPVRAMLRVVIGGALAL +ALTFAVGAWLGTTVA +>PROKKA_00884 +MSHSTAPAAPSSYPDEPHAQTGVHARLNWLRAGVLGANDGIVSVAATVVGVAGATTAVTP +VLLAGTAAVVGGAVSMALGEYVSVSSSSDSQKAMIAKERRELAEDPEGELEELVGLYEAE +GLSRDTAEQVARELTANDPVTAHLRMELGMAEEDVVSPLAAAGASFIAFLVGALLPFLAI +LLSPVGVRVPVTFGVTLVALAVTGYLGAWLGNAPAVRAMVRVVVGGALALALTFGVGTWL +GVGVA +>PROKKA_01831 +MSHTSEQSSPLTDQVPPGGPDEPHAAGGVHARLNWLRAGVLGANDGIVSVAATVVGVAGA +TTALTPILLAGAAAVVGGAFSMALGEYVSVSSSSDSQKSLIAKERRELEEDPEGELEELV +QLYEADGLSRATAEAAARELTEKDALAAHLRMELGMAEEDVVSPWAAAGASFLAFLVGAL +LPFLTVVLAPVGLRVPFTFGVTLVALAVTGWVGARLGDAPALRAAVRVVLGGALALGLTF +AVGSLLGASVA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001546.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001546.fa new file mode 100644 index 0000000000000000000000000000000000000000..ca48669ca88256a023bddb15a6d5383472e3ff09 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001546.fa @@ -0,0 +1,40 @@ +>PROKKA_01918 +MENQQTGQAADRGTIDTREGFTGNYVQSGAEFTRDTNYIADRIVADPEAVRALPVAEPST +VGRVGGGLTEGAEAWPVEEGRYRLVAARACPWANRTIIVRRLLGLEDAISLGTPGPTHDE +RSWTFDLDEGGKDPVLGTERIQENYFTRFPDYPRGITVPAIVDVPTGGVVTNDYPQITLD +LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIERVFTEVNNGVYRCGFAGSQEAYDAAYER +LWTAMDWLEERLTTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNRLTEMSALWG +YARDLFQTPGFGDTIDFAQIKEHYYVVHEDINPTGIVPAGPELASWLSEHGREAFGGDPW +GGGTAPGPVREGERVDPEHTPLR +>PROKKA_01614 +MENQQTGQAADRGTIDTREGFTGNYVQSGAEFTRDTNYIADRIVADPEAVRALPVAEPST +VGRVGGGLTEGAEAWPVEAGRYRLVAARACPWANRTIIVRRLLGLEDAISLGTPGPTHDE +RSWTFDLDEGGKDPVLGTERIQENYFTRFPDYPRGITVPAIVDVPTGGVVTNDYPQITLD +LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIERVFTEVNNGVYRCGFAGSQEAYDAAYER +LWTAMDWLEERLSTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNRLTEMPALWG +YARDLFQTPGFGDTIDFAQIKEHYYVVHEDINPTGIVPAGPELASWLSEHGREAFGGDPW +GGGTAPGPVREGERVDPEHTPLR +>PROKKA_00942 +MENQQTGQAADRGTIDTREGLKGNYVQSGAEFTRDTNYITDRIVADPEAVRALPVAEPST +VGRVGGGLTEGAEAWPVEAGRYRLVAARACPWANRAIIVRRLLGLEDAISLGTPGPTHDE +RSWTFDLDEGGKDPVLGTERLQENYFARFPDYPRGITVPAVVDVPTGDVVTNDYPQMTLD +LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIKRVFTEVNNGVYRCGFAGSQEAYDAAYDR +LWTAMDWLEERLTTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNRLTEMPALWG +YARDLFQTPGFGDTIDFAQIKEHYYVVHEDINPTGIVPAGPELASWLSEHGREAFGGDPW +GGGTAPGPVREGEEVEPAHTPLR +>PROKKA_00877 +MEDQQTGQAADRGTIDTREALTGNYVQSGAEFTRDTDYIADRIVADPEAVRALPVAEPST +VGRVGGGLTEGAEAWPVEAGRYRLVAARACPWANRTIIVRRLLGLEDAISLGTPGPTHDE +RSWTFDLDAGGKDPVLGTERLQENYFTRFPDYPRGITVPAIVDVPTGGVVTNDYPQITLD +LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIERVFTEVNNGVYRCGFAGSQEAYDAAYER +LWAAMDWLEERLTTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNKLTEMPALWG +YARDLFQTPGFGDTIDFAQIKEHYYVVHEDINPTGIVPAGPDLSGWTTEHGRADLGGDPW +GGGTAPGPVRDDERVDPEHTPLR +>PROKKA_01838 +MENQQTGQAADRGTIDSREGLKGNYVQSGAEFTRDTNYIADRIVADPEAVRALPVAEPST +VGRVGGGLTEGAEAWPVEAGRYRLVAARACPWANRTIIVRRLLGLEDAISLGTPGPTHDE +RSWTFDLDEGGKDPVLGTERIQENYFTRFPDYPRGITVPAIVDVPTGGVVTNDYPQITLD +LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIERVFTEVNNGVYRCGFAGSQEAYDAAYER +LWTAMDWLEERLTTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNKLTEMPALWG +YARDLFQTPGFGDTIDFVQIKEHYYVVHEDINPTGIVPAGPELASWLSEHGREAFGGDPW +GGGTAPGPVREGERVDPEHTPLR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001551.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001551.fa new file mode 100644 index 0000000000000000000000000000000000000000..f33e16b569b5259cf378e4100be8b6bb71c1dd4c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001551.fa @@ -0,0 +1,17 @@ +>PROKKA_01924 +MTLVEYTRRHPDADHLDPEKESVLEEAVGTGTQQITVDAQQGAVLRVIVLCPSDATGETE +ILTSRGGGGTKTWMAGSEALCGGWSAATPPVDEAGPMTFTVTVDNDKPFRMVLTAPSA +>PROKKA_01620 +MTLVEYTRQHPDADYLDPEKESVLEEAVGTGTQQITVDAQQGAVLRVIVMCPSDATGETE +ILTSRGGGGTKTWMAGSEALCGGWSAATPPVDEAGPMTFTVTVDNDKPFRMVLTAPSA +>PROKKA_00936 +MPHRRRRPCVPVALSVAAALGLSLSACASTTTAGVGSQSPAPSSAAGAASSAAGTSSAAP +TTSAALTTSGTAAEIAGDEAAAQAQDDAATRTALNRAVAEDGIPYAELDPSLTPVPDGAS +ILWEGLAVGAQSLRVDARAGEEYTVVLLCAEQDGSRRSLVMATVPGEDFSDVMAESPGCG +HWSAGLPAREADGPLTLTGVVPDGGPFRMVVYRSEG +>PROKKA_00868 +MTLEEYTRQNPDSDYLHPETESVLQEKVGTGTQQITVDAQEGAVLRVILLCPSDATGKTD +IHTSRGAEGEKTWMAGSEALCGGWSAATPPVEKAGPMTFSATVDNDKPFRMVLTAPAA +>PROKKA_01844 +MTLVEYTRRHPDADHLDPEKESVLEEAVGTGTQQITVDAQQGAVLRVIVLCPSDATGETE +ILTSRSGGGTKTWMAGSEALCGGWSAATPPPVDEAGPMTFTATVDNDKPFRMVLTAPSA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001556.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001556.fa new file mode 100644 index 0000000000000000000000000000000000000000..8729e905fff7d27467fb5772d687c7dab111e67f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001556.fa @@ -0,0 +1,25 @@ +>PROKKA_01930 +MHLIPRTIWVVARARRRPRAGLWEPTTLPMRALPTDVDMALHVNNGQYFGLFDLGRFDAM +VRTGLWDEIRRRGWTPVVQAEQIAFRRSVTLGQRFDVETRMIGLDERAVWFEQRVVVDGD +VAVRAYICTRLRKKDGRPVENDEVRAIAAAAGHDLAGEPTLPEWLHEWRRSVALPSARTP +LPHTWDLDTVRRG +>PROKKA_01626 +MHLIPRTIWVVARARRRPRAGLWEPTTLPMRALPTDVDMALHVNNGQYFGLFDLGRFDAM +VRTGLWDEIRRRGWTPVVQAEQIAFRRSVTLGQRFDVETRMIGLDERAVWFEQRVVVDGD +VAVRAYICTRLRKKDGRPVENDEVRAIAAAAGHDLAGEPTLPEWLHEWRRSVALPSARTP +LPHTWDLDTVRRG +>PROKKA_00928 +MHLIPRTLWVLARARRRPPLSIWDSASLPMRALPTDVDIAGHVNNGQYFGLFDLGRFDLM +ARSGLMRAVRRRGWLPVVQAEQIAFRRSVTLGTAFTLETRIIGLDERAVWFEQRVVVAGD +VAVRGYVCTRLRGRDGTPVGNDEVRALAVELGHDPAAEPELPGWLHDWREQVALPSARTP +LPHAWGR +>PROKKA_00862 +MLHLLPRTALVVVRARRRPRLGIWEASTLPLRALPTDVDFAGHINNGQYFGLFDLGRFDL +MVRAGVWDGAKRRGWLPVVQAEQIAFRRSVTLGTRFTVESRIIGLDERAVWFEQRAVVDG +DVAVRAFICTRLRAKDGTPVSNEDVRDLARELGHDLAAEPVLPEWLHGWRSDIALPSART +PLPHAWGTPAPAGV +>PROKKA_01849 +MHLIPRTIWVVARARRRPRAGLWEPTTLPMRALPTDVDMALHVNNGQYFGLFDLGRFDAM +VRTGLWDEIRRRHWTPVVQAEQIAFRRSVTLGQRFDVETRMIGLDERAVWFEQRVVVDGD +VAVRAYICTRLRKKDGRPVENDEVRAIAAAAGHDLAGEPTLPEWLHEWRRSVALPSARTP +LPHTWDLDTVRRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001557.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001557.fa new file mode 100644 index 0000000000000000000000000000000000000000..5e7170c393139eb535f19a5ac2c9769448e59af8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001557.fa @@ -0,0 +1,36 @@ +>PROKKA_01932 +MAAVDPAPTDARERRDLVVPVPGPEDPPERAWLVLPHRHPVPTLLEETRDAVVGLAETLA +AVLPVTVLAHPRDAGAARLVPPEVDLLRAPVGSPLLGRTGPSFVRRPEGLAAVAWRSAAG +LTGTGPLDGAAATAVAEAAGLPLLTPLLCAPRGAWVSDGEGTAVVAADPVLDGRINGAWT +PGQVAAEFAALLGITRVLWVPPAPRPDTGPWGGPGHLASWVRLQGDGEAAVHWRGDRFNP +EHPYAAAALRFLQGADDAAGRPLRVRTVTGAAQPAEYDPAERGPRSLLDTLPLGAAVLRP +AFEDAAGEEAAAAACAALHPGRPQLSFPAPPLLRLAGALNDLVLLQPRP +>PROKKA_01628 +MAAVDPAPTDARERRDVVVPVPGPEDPPERAWLVLPHRHPVPTLLDETRDAVVGLAETLA +AVLPVTVLAHPRDAGAARLVPPEVDLLRAPVGSPLLGRTGPSFIRRPEGLAAVAWRSAAG +LTGTGPLDGAAATAVAEAAGLPLLTPLLCAPRGAWVSDGEGTAVVAADPVLDGRINGAWT +PGQVAAEFAALLGITRVLWVPPAPRPGTGPWGGPGHLASWVRLRGDGEAAVHWRGDRFHP +EHPYAAAALRFLQGADDAAGRPLRVRTVTGAAQPAAYDPAERGPRSLLDTLPLGAAVLRP +AFEDAAGEEAAAAACAALHPGLPQLSFPAPPLLRLAGALNDLVLLQPRP +>PROKKA_00927 +MPAAETVPADAAGRPDARPRVPGPREQPERAWLALPRRHPVPALLDEARDAVAGLAETLA +EVLPVTVLTDPADHAVRSLIPPEVDLLAAPVDSPLLGRTGPGFVRRPEGLAAIAWRPAAG +AGGPGPRDAGVAAAVAAAAGLPLLTPMLRAPRDAWVADGEGTAVVAADPVLDGRTNPAWT +PEQVEAEFAALLGITRVAWLPPVPRIPTGPWGGAGHLGAWVRLLGGGEAAVHWRADRFHP +EHLHGAAALRILQDAPDAAGRPLRVRTVPGGALPPEHDPAEIGPRSLVDTVPLGSAVLRP +AFEDAATEEAAAAACAALHPGLRPVPFPGPPLLRLAGSLSDLVLVQPHP +>PROKKA_00861 +MSTPAVPEPPRAPAPWEVPERLWLALPAVHPVPGLLAEARDAVAGLAETLGAHAPVAVLT +DPDDADAARLLPGVVERVPVRGASPLPGREGPTFVHAAGTRGSVEAVHWRLPSDAAGTAG +RAAATADAVARSAGLPLRTPLFSAPAGTWAADGDGTAVVSAALLDPAVNEGWTRAQAEDA +LAGLLGAERVLWLPPVAGHAAGPWDGGGAAQPHPHPWLRFVAPGEVAVHWQPGRLHPDHA +ASAAALHALTGARDARGRALSVRTVRALPPGPDADLEARGPLSALDLLPLAPGVVLRPAH +ADPEADAATAEAAAALFPGAEQVPFPGPPLLRLLGTLSDLVLPQPPGARTRRPSPAPAHP +EGPRAAP +>PROKKA_01851 +MAAADPVPTDARERRDVVVPVPGPEDPPERAWLVLPHRHPVPTLLDETRDAVVGLAETLA +AVLPVTVLAHPRDAGAARLVPPEVDLLRAPVGSPLLGRTGPSFIRRPEGLAAVAWRSAAG +LTGTGPLDGAAATAVAEAAGLPLLTPLLCAPRGAWVTDGEGTAVVAADPVLDGRINGAWT +PGQVAAEFAALLGITRVLWVPPAPRPGTGPWGGPGHLASWVRLRGDGEAAVHWRGDRFHP +EHPYAAAALRFLQGADDAAGRPLRVRTVTGAVQPAEYDPAERGPRSLLDTLPLGAAVLRP +AFEDAAGEEAAAAACAALHPGLAQLSFPAPPLLRLAGALNDLVLLQPRP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001558.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001558.fa new file mode 100644 index 0000000000000000000000000000000000000000..26ef3796da187f456e7a6a353571969bee4ec48d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001558.fa @@ -0,0 +1,45 @@ +>PROKKA_01933 +MSAAQPAGVTPPPASSSPASDWDIRRPHRMWPRMLVIVLTLAGLVLVVQFFQGIASIAAP +VFLGLNLVIVAYPLQAWLIRRGLHPVLGAATTVLLVVAVMAVFGGMMVWSGLELVAELPK +YADRFQQIVLDVSHWLNERGVTPDMVSQQLASIDMSAVTGTAVSAITKIATNVYAVFGLL +VTVIMGMFFLAMDSMDVERRVRLLSTARHEFGHALVEFAQGVRRYWVVTTVFGLIVAVLD +VIALMLIGVPLALVWGVLSFLTNYIPNIGFIIGLLPPAVLGLAAGGWSDFLWVVVSYSVL +NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN +ARWINALIASDLKGMERRQSSLLERLRPAAWRSDAHGKDEDRAPTDGGDDDGPATDEVTG +GAGAAPGR +>PROKKA_01629 +MSAAQPAGVTPPSASSSPASDWDIRRPHRMWPRMLVIVLTLAGLVLVVQFFQGIASIAAP +VFLGLNLVIVAYPLQAWLIRRGLHPVLGAATTVLLVVAVMAVFGGMMVWSGLELVAELPK +YADRFQQIVLDVSHWLNERGVTPDMVSQQLASIDMSAVTGTAVSAITKIATNVYAVFGLL +VTVIMGMFFLAMDSMDVERRVRLLSTARHEFGHALVEFAQGVRRYWVVTTVFGLIVAVLD +VIALMLIGVPLALVWGVLSFLTNYIPNIGFIIGLLPPAILGLAAGGWSDFLWVVVSYSVL +NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN +ARWINALIASDLKGMERRQSSLLERLRPAAWRSDAHGGDEDRASADGGDDDGPATDEVTG +EAGAAPGR +>PROKKA_00926 +MSAAQPVGAAPTPSAAGPVSDWDIRRPHRMWPRMLVIVLTLAGLVLLVQFFQGIASIAAP +VFLGLNLVIVAYPLQAWLIRRGVHPVLGAAASVVVVVAVLGAFVGMIVWSGLELVAELPK +YSGQFQQIVLDVSNWLNARGVTPDMVSQQLASIDVSAVTSAAVSALTKIATNLYAVLGLL +VTVVMGMFFLAMDSMDVERRVRLLSTARLELGEALIDFAHGVRRYWVVTTVFGLIVAALD +VIALVLIGVPLALVWGVLSFLTNYIPNVGFIIGLIPPAILGLAAGGWTSFLWVVVSYSVL +NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN +SRWVNSLIASDLKGMERRQHSLLERLRVGRRGEGRAGKADAEAVAGADVAAAGVEAALDV +DDAAAGARRPEAAPTGSTLTEPARTEPGPAAPADAADGPGLTGGAAPAPGR +>PROKKA_00860 +MSASAPPAVTGTSTPATEWDNRRPHRMWPRMLVIVLTLAGLVVLVQFFQGIASIAAPVFL +GLNLVIVAYPLQAWLIRRGLHPVLGAATTVVVVCAVIAAFLGMIAWSGMELLTELPKYAG +QFQQIMHDASQWLSDHGVTPDMVNQQLASVDMSAVTGAAVSALTTIASNLYAVLGLLITV +IMGMFFLAMDSMAVERRVRLLSTARHELGQALIDFADGVRRYWIVTTVFGLIVAVLDMVA +LVIIGVPLALVWGVLSFLTNYIPNVGFIIGLVPPAILGLAAGGWPAFLWVVVSYSVLNFV +LQSIIQPKVAGDAVGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLVKAVLIDADPNSRW +VNSLIASDLKGMERRQSSMLERLRLPRELIRHGGSTASHATAADVQGDDDVAPERTAEDA +APAQDRRRVRAAAQEARLEGPPPSTLRAPRVDLPGEPEPATADGSAPPEAGAAPGR +>PROKKA_01852 +MSAAQPAGVTPPPASSSPASDWDIRRPHRMWPRMLVIVLTLAGLVLVVQFFQGIASIAAP +VFLGLNLVIVAYPLQAWLIRRGLHPVLGAATTVLLVVAVMAVFGGMMVWSGLELVAELPK +YADRFQQIVLDVSHWLNERGVTPDMVSQQLASIDMSTVTGTAVSAITKIATNVYAVFGLL +VTVIMGMFFLAMDSMDVERRVRLLSTARHEFGHALVEFAQGVRRYWVVTTVFGLIVAVLD +VIALMLIGVPLALVWGVLSFLTNYIPNIGFIIGLLPPAVLGLAAGGWSDFLWVVVSYSVL +NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN +ARWINALIASDLKGMERRQSSLLERLRPAAWRSDAHGGDEDRASADGGDDEGPAADEVTG +EAGAAPGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001559.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001559.fa new file mode 100644 index 0000000000000000000000000000000000000000..2089edec77fb1e79f48073dda794d4c2ceea94f5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001559.fa @@ -0,0 +1,36 @@ +>PROKKA_01934 +MSRTPHRALAALSVAALALTGCSVSGSSGDGASSSAAGAGGEPTTVTIMTHDSFNLPQEL +VQKFEQESGYTLKTTAPGDAGSVVNQLLLAKDEPTVDGVYGVEDHSAHRLVREGVVAEYT +PQDLPASAQDRMVEDRMTPVDQGQVCFNTDPAWFEAHDVEAPTSIDQLDDPEYAKLTVAT +SPVASSPGLALLAATTEKYGDDGWQDWWRGLKENGGKVADSWSDAYNSDFSGGEGKGRFP +VVLSYSSSPAFAPETEVIEDSCTPQVEYAGVLEGAKNPEGAQAFVDFMLTEEVQSALPES +MYMYPIDESVQLPEEWAQNAPLVEDAITPDPARIDERREDLLKEWTALAEASRR +>PROKKA_01630 +MSRTPHRALAALSVAALALTGCSVSGSSGDGASSSASGAGGGEPTTVTIMTHDSFNLPQE +LVQKFEQESGYTLKTTAPGDAGSVVNQLLLAKDEPTVDGVYGVEDHSAHRLVREGVVAEY +TPQDLPASAQDRMVEDRMTPVDQGQVCFNTDPAWFEAHDVEAPTSIDQLDDPEYAKLTVA +TSPVASSPGLALLAATTEKYGDDGWQDWWRGLMENGGKVADSWSDAYNSDFSGGEGKGRF +PVVLSYSSSPAFAPETEVIEDSCTPQVEYAGVLEGAKNPEGAQAFVDFMLTEEVQSALPE +SMYMYPIDESVQLPEEWAQNAPLVEDAITPDPARIDERREDLLKEWTALAEASRR +>PROKKA_00925 +MTTAPHRVRTRPRRHGALAALSVAALALTGCSVADRGGSGDQGSSSAEARTVTIMTHDSF +SLPDELIARFEQESGHTLVTTAPGDAGSVVNQLLLAKDAPTVDGVYGIEDHSAHRLVSEG +VIAEHVPADLPDSARDLVVDGRMTPVDQGQVCLNVDTPWFQEQGLAAPTTLEQVAAPEYA +ELTVVTSPVSSSPGLALLAATVAEFGEDGWQDWWRTALQGGMQVDASWSDAYNTSFSGGE +GTGTRPIVLSYSSSPAFAPDTDVVAASCTPQVEYAGVVEGAENPEGARAFVDFLLTEDVQ +AAIPDAMYMYPVDSSVPLPEAWAEHAPLVEDPIVPDAGLLDSRREDLLKEWTALHEEAAS +>PROKKA_00859 +MSVHRTATTRRGVLAAACLSALALTGCSVSAPSTGSSSSAASSSAAPSSASGSSSTSASG +TAAAGSKGTVTIMTHDSFALPKELIAQFEAESGYRLVTTAPGDAGAVVSQVLLSKDAPVA +DGVYGVENHSAHRLVDQGAVQDVAPADLPASAEDLVVDGKMIPVDQGQVCFNTDPAWFTE +HGVAEPTSIDQLRDPEYAKLTAVTSPVTSSPGLALLAATTEKYGDDGWQGWWEDLLKGGA +KVDSTWSDAYSTDFSGGEGKGEFPVVLSYSSSPAFAPQTAVIEDSCTPQVEYAGVLTGAE +NPEGAKAFVEFLLSKDVQAAIPENMYMYPVDDTVELPAEWAANGPLVEDPITPDPAEIDT +EREGLLKEWTALSESAGSR +>PROKKA_01853 +MSRTPHRALAALSVAALALTGCSVSGSSGDGASSSAAGAGGEPTTVTIMTHDSFNLPQEL +VQKFEQESGYTLKTTAPGDAGSVVNQLLLAKDEPTVDGVYGVEDHSAHRLVREGVVAEYT +PQDLPASAQDRMVEDRMTPVDQGQVCFNTDPAWFEAHDVEAPTSIDQLDDPEYAKLTVAT +SPVASSPGLALLAATTEKYGDDGWQDWWQGLMENGGKIADSWSDAYNSDFSGGEGKGQFP +VVLSYSSSPAFAPETEVIEDSCTPQVEYAGVLEGAKNPEGAQAFVDFLLTEEVQSALPES +MYMYPIDESVQLPEEWAQNAPLVEDAITPDPARIDERREDLLKEWTALAEASRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001560.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001560.fa new file mode 100644 index 0000000000000000000000000000000000000000..d820ee60e0e1b2828f1e7385f572d6febe16f4f1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001560.fa @@ -0,0 +1,55 @@ +>PROKKA_01935 +MSALTEVAAPGTDLPRRRARGRGDGLGPWWLVAAVLPVAFLLVFFAWPVAAMLWRGIGGD +ADAFTGAVDLTAFGETLARERTWRILGQTLGMAAAGTVVSVALGLPTAFVLHRRRVPGRA +VLRALVLVPFVLPTVVVGVAFRALLAPGGPLGFTGLDQTTTAVVLAMVFFNVSVVVRQVG +ALWNALDPRQTEAARTLGASPWRAFRTVTLPQLAPAIAASAALVFLFCASAFGIVQTLGR +PGYGTLESEIWVQTSVYLDLRTAAVFSVLQFAVVLVAVVVSGVTAARTQRALRLRETPPA +RLTRADAVPVAVMLAVVALVVAPILTLVVRSFHTRHGWGLGNYRLLSTSAGSGFVGGSTP +ARALEQSLRVAVDATLVTLVVAVPLALLLTRPFRSRAALAAQRALDGALLLPLGVSAVTV +GFGFVVSLRAAFPELAASGVLVPLAQAVVALPLAVRALVPVLAAVDPRLREAARTLGAGP +WRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLASPSAPTLPVLIARLLGRPGADN +YGMALAAATVLAVLSAGIMLVCERLRPRGPAGAGGL +>PROKKA_01631 +MSALTEVAAPGTDLPRRRARGRGDGLGPWWLVAAVLPVAFLLVFFAWPVAAMLWRGIGGD +ADAFTGAVDLTAFGQTLARERTWRILGQTLGMAAAGTVVSVALGLPTAFVLHRRRVPGRA +VLRALVLVPFVLPTVVVGVAFRALLAPGGPLGFTGLDQTTTAVVLAMVFFNVSVVVRQVG +ALWNALDPRQTEAARTLGASPWRAFRTVTLPQLAPAIAASAALVFLFCASAFGIVQTLGR +PGYGTLESEIWVQTSVYLDLRTAAVFSVLQFAVVLAAVVVSGVTAARTQRALRLRETPPA +RLTRADAVPVAVMLAVVALVVAPILTLVVRSFHTRHGWGLGNYRLLSTSAGSGFVGGSTP +AQALEQSLRVAVDATLVTLVVAVPLALLLTRPFRSRAALAAQRALDGALLLPLGVSAVTV +GFGFVVSLRAAFPELAASGVLVPLAQAVVALPLAVRALVPVLAAVDPRLREAARTLGAGP +WRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLASPSAPTLPVLIARLLGRPGADN +YGMALAAATVLAVLSAGIMLVCERLRPRGPAGAGGL +>PROKKA_00924 +MDGPARGGGLLTVGLTSVPAPVGGPGAPPGAPGPAASGGRRRRRTAGGDGIGAWWLLAAV +VPVAFLLVFFAWPVGAMLWRGVSAEGVLDLGAFAEVLGRERTWRIVGQTLGMAAAGTVLA +VALGLPAAFVLHRRAFPGRAALRAVITVPFVLPTVVVGVAFRALLAPGGPFGWTGLDQST +AAVVLAMVFFNVSVVVRQVGALWASLDPRQAEAARTLGSSGWRAFRTVTLPQLAPALASS +AALVFLFCASAFGIVQTLGRPGVGTLESEIWVQTVVYFDLGTAAVFSTLQFLVVLAAVLV +SGATARRTRRALRLRDAPVRRLTRADAAPVAVTLATALLVLAPLATLLVRSFHSSEGWGL +RNYRLLASSPGAGFSGGVTPAQALEHSLRIALDATLLTLLIGVPLALLLTRPVRSAAGRR +AQRGLDGALLLPLGVSAVTVGFGFVVSLRAEAPALAASGALVPIAQAVVALPLVVRSLVP +VLGAVDPRLREAARTLGAGPLRVLATVDGPFLLRGLGVAAGFAFAVSLGEFGATSFLSSP +DYQTLPLLIVKLLGRPGADNYGMALAAATVLAVLSAGTMMACERLGPRAAASRGGI +>PROKKA_00858 +MPTPAPARGRRRATLRPPRGRRAAGDGLAPLWLLSAAVPVAFLLVLFAWPVAAMLWRGVA +SVDAAGDPTGGLDLSAFAQTLGAPRTWRILGNTLGLAAAGTAASVALGVPTAFALHRRAF +PGRGLARAVVTVPFVLPTVVVGAAFRALLAADGPLGWTGLDQTSTAVVMAMVFFNVSVVV +RQVGGLWAALDPRQAEAARTLGASPWRAFRTVTLPQLAPAVAGAAALVFLFCASAFGIVQ +TLGRPGPGTLETEIWAQTTVYLDLRTAAVLSTVQLAVVLAAILASGAAAARARRALRLGE +APARPLTRADAVPAAVTLAVLALVVAPILALLAGSLHSAEGWGLRNYRLLATSPGTGFAG +GVTPAQALEQSLRTAVDATVVTLVVAVPLALVLTRPVRSRAGRAAQRALDGALLLPLGVS +AVTVGFGFIVSLRATAPDLAASGALVPLAQSVIAVPLAVRALVPVLGAVDPRLREAARTL +GAGPWRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLAAADRPTLPVLIARLIGRP +GADNHGMALAAAVVLAVLSAGALLACERLRPRGAAPSGGL +>PROKKA_01854 +MSALTEVAAPGTDLPRRRARGRGDGLGPWWLVAAVLPVAFLLVFFAWPVAAMLWRGIGGD +ADAFTGAVDLTAFRETLARERTWRILGQTLGMAAAGTVVSVALGLPTAFVLHRRRVPGRA +VLRALVLVPFVLPTVVVGVAFRALLAPGGPLGFTGLDQTTTAVVLAMVFFNVSVVVRQVG +ALWNALDPRQTEAARTLGASPWRAFRTVTLPQLAPAIAASAALVFLFCASAFGIVQTLGR +PGYGTLESEIWVQTSVYLDLRTAAVFSVLQFAVVLAAVVVSGVTAARTQRALRLRETPPA +RLTRADAVPVAVMLAVVALVVAPILTLVVRSFHTRHGWGLGNYRLLSTSAGSGFVGGSTP +AQALEQSLRVAVDATLVTLVVAVPLALLLTRPFRSRAALVAQRALDGALLLPLGVSAVTV +GFGFVVSLRAAFPELAASGVLVPLAQAVVALPLAVRALVPVLAAVDPRLREAARTLGAGP +WRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLASPSAPTLPVLIARLLGRPGADN +YGMALAAATVLAVLSAGIMLVCERLRPRGPAGAGGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001562.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001562.fa new file mode 100644 index 0000000000000000000000000000000000000000..ead2cc0a4b24b5d9ef211e91fe0ddcf98b2f14c9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001562.fa @@ -0,0 +1,20 @@ +>PROKKA_01937 +MTPPAPRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAGVLGVQASALYWHVPDKQSLLAR +VADRIVAEAEETVRARRVTDLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLHRLLT +EAADTPEDGERALALLLGTVSLRQQRAQAQALGVATGPDVQRHRTDPL +>PROKKA_01633 +MTPPAPRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAAVLGVQASALYWHVPDKQSLLAR +VADRIVAEAEETVRARRITDLAGRAEAAEAALLRHRDGADLVLSALALGLGGLGLHRLLT +EAADTPEDGERALALLLGTVSLRQQRAQAQALGVPTGPDVQRHRTDPL +>PROKKA_00922 +MSSPPRAGSSRGRLSATDVVDAAVGILQDFGMGDLSMRRVASVLGVQASALYWHVPDKQT +LLARVADRIVAEAEEAVRHRGIADLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLH +ALLTEAAPTPEEGERALALLLGGVSLRQQRAQAEALGVRVGPDVQRHRTDPL +>PROKKA_00856 +MSTSSARGRLSAEDVVDAAVGILQDFGMGDLSMRRVASMLGVQASALYWHVPDKQTLLAR +VADRIVADVERACAARRVEDLAGRAEEAEAVLLRHRDGADVVLSALALGLGGLGLHRLLV +DAAHTPEEGERALAALLGTAALRQQRNQAAALGLRLGPDVQARRTGAL +>PROKKA_01856 +MTPPAPRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAGVLGVQASALYWHVPDKQSLLAR +VADRIVAEAEETVRARRVTDLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLHRLLT +EAADTPEDGERALALLLGTVSLRQQRAQAQALGVATGPDVQRHRTDPL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001563.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001563.fa new file mode 100644 index 0000000000000000000000000000000000000000..c2ea2449d506935779479159b82bfeb0d84b2750 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001563.fa @@ -0,0 +1,45 @@ +>PROKKA_01938 +MGARINHPRTVVDRTLHHDVEPAHPAALVDVGWDFRGPGAKAEEQHRPLRVVRARRPRGT +PRDRNGVDLTRTGPVVPRPSPPRTRIRRDGVRVVASPLAMLPGVDHGPALRLDLHPTTGG +IVYVARELELRELGDDVRGHVYTGMVGTAHLSVFWSTVTVDLPPERPVIVRLRSDRDAEL +LSLLEVLAPVDTRVVSYRLDESPVGTQRSSYLLPDVDPETVAQTGAARIPLEAIEAAQEE +EDALRRSSGVFLSRRRTDRFLRRNLPGVTHSLTFADEADVTDVYVDGSVLRGSRIGGAAA +VAGPSMWAVQAVAGATMPLEVELEALVLGHVICAWAGTPGGRVTIHSDSRAALALLNAAR +RERLTLGGARGERIRRTLRRLLAAVDLAQAADVQVDTTWVKGHVGVHGNELADDLARAAA +RHASVGTPEGDLPERMGQLIQLRVEDDAAG +>PROKKA_01634 +MGARINHPRTVVDRTLHHDVEPAHPAALVDVGWEFRGPGAKAEEQHRPLRVVRARRPRGT +PRDRNGVDLTRTGPVVPRPSPPRTRIRRDGVRVVASPLAMLPGVDHGPALRLDLHPTTGG +IVYVARELELRELGDDVRGHVYTGMVGTAHLSAFWSTVTVDLPPERPVIVRLGSDRDAEL +LSLLEVLAPVDTRVVSYRLDESPVGTQRSSYLLPDVDPETVAQTGAARIPLEAIEAAQEE +EDALRRSSGVFLSRRRTDRFLRRNLPGVTHSLTFADEADVTDVYVDGSVLRGSRIGGAAA +VAGPSMWAVQAVAGATMPLEVELEALVLGHVICAWAGTPGGRVTIHSDSRAALALLNAAR +RERLTLGGARGERIRRTLRRLLAAVDLAQAADVQVDTTWVKGHVGVHGNELADDLARAAA +RHASVGTPEGDLPERMGQLIRLRVEDDAAAG +>PROKKA_00921 +MRVVAAPLAMLPGVDHGPALRMDLHPVPGGIVYVARDLVLRELGDDVRGHVHAGMVGTAQ +LHAFWSTVTVDLPPDRPVIVRLRSDRDAELLSLLEVLAPVEMRVVSYRLDESPVGTQRSS +YLLPDVDPEIVARAESPRVPLEAIEATQEEEDALRRSSGVFLSRRRTDRFLRRTLPTVTH +SLSFSDEADVADVYVDGSVLRSSRIGGAAAVGGPSMWAVQAVNGATTPLEVELEALVLGH +VVSAWAGVPGERVTIHSDSRAALALLNAARRERLTLGGARGERVRRTLRRLLAAVDLAQA +ADVRVETTWVKGHVGVQGNELADDLARAAARHAGVGTSEEDLRRRLDRLIDLHEEAEAEA +GQTPARAVAAEGHRPMPPGRRPGPRL +>PROKKA_00855 +MDNSSTHPREGQVRSLHFDTDASSPDALLDPMWAFTGPRASRAGAPAPDGADVLARRARP +AHPGAALVRAATSLFTLPGPPGMPHRSRSAALEAARAPAGYLSPVPHRLALPRPARPRPA +PPRMRVRQDGVRVVARPLAMLPGVDHGRALRLDLHPVRDGIVFVSRHLELRELGDDVKGL +VLTGVVPAARLGYFWDTVAGDLPEGRPVIVRLRSNDDAELLTLLRAIAPPWLRVVSYRLD +ESPVGSQRSSYLLPDVDGEAVAASGAERVPLETLREAHQASAEVERASRVFLARRRVDRF +VRRSVPDLMHSLSYTDPAEVRHVYVDGSVLRGTRTGGAAAVTRSGPWAAHALPGATIPLE +AELEALTLGHLMAAWSGTPDERVLIHSDSRAALALLREAHRERLTLGDARGERIRRALRR +LLAAVDLAGSAGVEVSTLWVKGHAGTHGNELADDLARSAARNTAAGVSADEMRRRMRHVV +QLWDATTHPQA +>PROKKA_01857 +MGARINHPRTVVDRTLHHDVEPAHPAALVDVGWDFRGPGAKAEEQHRPLRVVRARRPRGT +PRDRNGVDLTRTGPVVPRPSPPRTRIRRDGVRVVASPLAMLPGVDHGPALRLDLHPTTGG +IVYVARELELRELGDDVRGHVYTGMVGTAHLSVFWSTVTVDLPPERPVIVRLRSDRDAEL +LSLLEVLAPVDTRVVSYRLDESPVGTQRSSYLLPDVDPETVAQTGAARIPLEAIEAAQEE +EDALRRSSGVFLSRRRTDRFLRRNLPGVTHSLTFADEADVTDVYVDGSVLRGSRIGGAAA +VAGPSMWAVQAVAGATMPLEVELEALVLGHVICAWAGTPGGRVTIHSDSRAALALLNAAR +RERLTLGGARGERIRRTLRRLLAAVDLAQAADVQVDTTWVKGHVGVHGNELADDLARAAA +RHASVGTPEGDLPERMGQLIQLRVEDDAAG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001568.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001568.fa new file mode 100644 index 0000000000000000000000000000000000000000..2171a17af784f5ce58285e18e4d3266ab28a7384 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001568.fa @@ -0,0 +1,30 @@ +>PROKKA_01947 +MSTAPTPSSSDDAPAVLVETRPGVVRLTLNRPAKGNALGLTMAREVLAAIAAAEADESVH +VLTLTGAGRIFCGGGDVQAMAAAPAGPERRAMIQELGEAAGEVAVALTGSRLLVLAGVNG +TAAGAGLGLMLGGDVVLVREDAQLVTAFSALGMTPDTGVSYWLPRVLGPVRATQLLLGGR +RLNGTEAVGWGLATEAAAGDAFAARLAELEDELVAGPAHTYGPTKALTRGADVEALRAHV +RQEAASIAAASEHPEAVRRVEAFAGR +>PROKKA_01641 +MTTAPTPSPHDDAPAVLVETRPGVVRLTLNRPAKGNALGLTMAREVLAAIAAAEADESVH +VLTLTGAGRIFCGGGNVQAMAAAPAGPERRAMIQELGEAAGEVAVALTGSRLLVLAGVNG +TAAGAGLGLMLGGDVVLVREDAQLVTAFSALGMTPDTGVSYWLPRVLGPVRATQLLLGGR +RLNGTEAVAWGLATEAVAGGAFAARLAELEDDLVAGPAHTYGPTKALARGADVEALRAHV +RQEAASIAAASEHPEAVRRVEAFAGR +>PROKKA_00911 +MSGDGGAADVATVRVEARPGVVRLTLDRPAQGNALSLAMARELTAAVRASEADPDVHVLT +LTGAGRFFCGGGDLAAMGAASPAERPAVLRELADAASEVALALVRSRLLVVAGVNGTAAG +AGLGLVLNADVVLVGDDALLLAAYAGIGLVPDTGVSWWLPRAVGPVRAAELTLRGRRLTG +AEAVEWGVASEAVSGDEFEARLAALEDELAAGAVHAYGPTKALLRGPEIVGYAEHLDRET +AAISAASGHPEAVRRVDAFLRR +>PROKKA_00847 +MTTAPTPSSSDDAPAVLVETRPGVVRLTLNRPAKGNALGLTMAREVLAAIAAAEADESVH +VLTLTGAGRIFCGGGDVQAMAAAPAGPERRAMIQELGEAAGEAAVALTGSRLLVLTGVNG +TAAGAGLGLMLGGDVVLVREDAQLVTAFSALGMTPDTGVSYWLPRVLGPVRATQLLLGGR +RLNGAEAVAWGLATEAVAGDAFAARLTELEDELVAGPTHTYGPTKALARGADAEALRAHV +RQEAASIAAASEHPEAVRRVEAFAGR +>PROKKA_01866 +MSTAPTPSSSDDAPAVLVETRPGVVRLTLNRPAKGNALGLTMAREVLAAIAAAEADESVH +VLTLTGAGRIFCGGGDVQAMAASPAGPERRAMIQELGEAAGEVAVALTGSRLLVLTGVNG +TAAGAGLGLMLGGDVVLVREDAQLVTAFSALGMTPDTGVSYWLPRVLGPVRATQLLLGGR +RLNGAEAVAWGLATEAVAGDAFTARLAELEDELVAGPAHTYGPTKALARGADVEALRAHV +RQEAASIAAASEHPEAVRRVEAFAGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001569.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001569.fa new file mode 100644 index 0000000000000000000000000000000000000000..14ee19856fdb38618a98dcefc24be63df7b16000 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001569.fa @@ -0,0 +1,15 @@ +>PROKKA_01948 +MKIGLRKPSLKKSIKARTTGRAKRAIKRKVIPGYGRKGMGWLRDPKRAAYNAVYRRTTVG +LGDVLKMFK +>PROKKA_01642 +MKIGLRKPSLKKSIKARTTGRAKRAIKRKVIPGYGRKGMGWLRDPKRAAYNAVYRRTTVG +LGDVLKMFK +>PROKKA_00907 +MKIGLRKPSLKKSIKARTTGRAKRAIKRKVIPGYGRKGMGWLRDPKRAAYNAVYRRTTVG +LGDVLKMFR +>PROKKA_00846 +MKIGLRKPSLKKSIKARTTGRAKRAIKRKVIPGYGRKGMGWLRDPKRAAYNAVYRRTTVG +LGDVLKMFK +>PROKKA_01871 +MKIGLRKPSLKKSIKARTTGRAKRAIKRKVIPGYGRKGMGWLRDPKRAARNAVYKRTTFG +LGDVLRMFR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001572.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001572.fa new file mode 100644 index 0000000000000000000000000000000000000000..630f85c058b21d455039044dd0f3c7f5ed23c706 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001572.fa @@ -0,0 +1,36 @@ +>PROKKA_01966 +MHEDEGRRRHYGHFYGLEDLPEDDLLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVP +PAFEAQPDEVAHLERLLPRVKALVTQPIPHDYRGMPIGTDQLVARLPEDAAVVRIPVVYD +VSRFPWQVTLRNWKFAPGAAERPGEDPPVVPYHDLRVLAEAATGRRREVAPAAIREAAAA +SVQALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTLLTRVAERVAERLPGDVAVQPV +PASRVLLGGVRAPLEAPVVEALDLDAAPTEDWTVAGQTVPAEQLRQTHLDWYAQNPQAVE +VGMRKYADQLRLLGLTG +>PROKKA_01660 +MNEDEGRRRHYGHFYGLEDLPEGDLLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVP +PAFEAQPDEVEHLERLLPRVKALVTQPIPHDYRGMPIGTDQLVARLPKDAAVVRIPVVYD +VSRFPWQVTLRNWKVAPGAAERPGEDPPVLPYHDLRVLAEAATGRRRQVAPAAIREAAAA +SVQALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTLLTRVAERVAGHLPGDVAVQPV +PASRVLLGGVRAPLEAVVVEALDLDAEPTEDWTVAGQTIPAEQLRQTHLDWYAQNPQAVE +VGMRKYADQLRLLGLAA +>PROKKA_00893 +MHEDEGRRRHYGHFYGLEDLPEGDLLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVP +PAFEVQPDEVEHLERLLPRVKALVTQPIPHDYRGMPIGTDQLVARLPEDAAVVRIPVVYD +VSRFPWQVTLRNWKFAPGAAERPGEDPPVVPYHDLRVLAEAATGRRREVAPAAIREAAAA +SVQALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTVLTRVAERVAEHLPGDVAAQPV +PAARVLLGGVRAPLEAVVVEALDLDAEPTEDWTVGGETIPAEQLRQTHLDWYAQNPQAVE +VGMRKYADQLRLLGLAA +>PROKKA_00833 +MSEETPMDDQTRTAGAEPGDEGVQVRGAAERAPSSDLPADEGRRRHYAHFYGLEPLPEGE +LLTVMGGCQAEATRLLLCGEPGRAEGGTPASVRVPPMFELGPDDLPHLLALLKRTTVLVV +KPVRDDYQGLPLGLGQLESLLPAGARSIRVPALYDSSRFPWLVTLRHPTRPWEDPPVVPY +HDLRTVAEAAAEAGLIPWPAALGGPGEAGAYDAGPRLPLSAEALRGLAAESVARLRAREE +HFGTVRVSDAVADERGVGFHTVNHPDNPLLEALARTVLAELGVDKEVHAPDRLLLGHVLA +PIEEQVVDALGLQTAPRAAWRVGGAEVSDAEVRRAHLGWFRANPEALAPGLERHGALMRE +LGLLA +>PROKKA_01892 +MNEDEGRRRHYGHFYGLEDLPEGDLLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVP +PAFEVQPDEVAHLERLLPRVKALVTQPIPHDYRGMPIGTDQLVARLPEDAAVVRIPVVYD +VSRFPWQVTLRNWKFAPGAAERPGEDPPVVPYHDLRVLAEAATGRRREVAPAAIREAAAA +SVQALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTLLTRVAERVAERLPGDVAVQPV +PASRVLLGGVRAPLEAVVVEALDLDAEPTEDWTVAGQTVPAEQLRQTHLDWYAQNPQAVE +VGLRKYADQLRLLGLTG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001573.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001573.fa new file mode 100644 index 0000000000000000000000000000000000000000..8476e0107985405c17524460ee6393e433b95e9b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001573.fa @@ -0,0 +1,45 @@ +>PROKKA_01968 +MSAAVSVVVPYYRAQADLDRLTAALAAQRGVTGGLQLVVADDGSPVPPRVDPGLPFDVVT +VRQQDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLAAALAAVAEAPRDAAVVGRR +RHLAEAWLERAWADGWRPGHEVPADALLAEPAWLRDGYRATDDLRRADSTGYRYVISAVL +TVAREVYEDAGGFDPAFVGYGGEDWELAHRLWRVGAALRHAPDAVAWQAGADFGGRGDAA +EAARVKAREALVLVSRIPATTSRGHGLSLAGPLRAEARVRVPEGADGAAAAVVAVDAVLR +AAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAAPEDLPPTPARGDLDAVRSVPDW +SVDVQVPLRPAAAGARPDTDAVAAWLLRLERAGVERVEVLGEPGERAERDVLAVLTCARA +RWRPRRGGTARVWRVPASRLGWAPVAAVPDLEAWWGGWG +>PROKKA_01662 +MSAAVSVVVPYYRAQADLDRLTAALAAQRGLTGGLQLVVADDGSPVPPRVGPGLPFDVVT +VRQQDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLAAALAAVAEAPRDAAVVGRR +RHLAEAWLERAWVDGWRPGDEVPADARLAEPAWLREGYRATDDLRRADSTGYRYVISAVL +TVAREVYADAGGFDPAFVGYGGEDWELAHRLWRVGAALRHAPDAVAWQAGADFGGRGDAA +EAARVKAREALVLASRIPATTARGHGLSLAGPLRVEARVRVPEGADGAAAAVVAVDAVLC +AAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAASQDLPPTPARGDLDAVRSVPDW +SVDVHVPLRPAAAGARPDADAVAAWLLRLERAGVERVEVLGEPGERAERAVLAVLTCARA +RWRRRRGGTARVWRVPASRLGWAPVATVPDLEAWWGGWG +>PROKKA_00891 +MSAAVSVVVPYYRAQADLDRLTAALAAQRGVTGGLQLVVADDGSPVPPMVGPDLPFDVVT +VRQQDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLAAAVAAVAEAPRDAAVVGRR +RHLAEAWLERAWADGWRPGHEVPADARLADPAWLREGYRTTDELRRADSTGYRYVISAVL +TVAREVYEDAGGFDPAFVGYGGEDWELAHRLWRVGAALRHAPDAVAWQAGADFGGRGDAA +EAARVKAREALALASRIPATTARGHGLSLAGPLRVEARVRVPERADGAAAAVVAVDAVLR +AAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAASQDLPPTPARGDLDAVRSVPDW +SVDVRVPLRPAAAGARPDADAVAAWLLRLERAGVERVEVLGEPGERAERAVLAVLTCARA +RWRRRRGGTSRVWRVPASRLGWAPVAAVPDLEAWWGGWG +>PROKKA_00832 +MTAPVAGREAAAETAGPEASVPEVSVVVPHYRAPADLERVVAALAAQDHPASRLQLVVAD +DGSPEPPVLPAGLPFEAVVVAQEDHGFRASAARALGASAAEGRILAFLDGDMLPEPGYLT +AACAAPAASVDAVVVGRRRHLDPALLESGWRPGEPVPEAARLPEPAWLAEAYQRSGDLAA +ADSTSYRYVISAVLTVAREVYADAGGFDPAFVGYGGEDWELAHRLWRVGGAFRHQPAAVA +WQAGEDFGGRGDAAERTAVKQREALRLAARITATTARGHGLSLPGPLRVGARVRAEASGD +AAAVVGVDALLAAAPGARVGVTGLGSGAARAALADPRVWIMDGGGEAARADLPPAPARGD +LGAVRGIPDWSCDVRTPLRPAAPGARPDAARAADWLLRLERAGVERVEVLGEPQAAEEPG +EAGRGERPVLAVLTCSRALWRSRRGGDSRVWRVPAARLGWAPVARDVDLEAWWGGWG +>PROKKA_01894 +MSAAVSVVVPYYRAQADLDRLTAALAAQRGLTGGLQLVVADDGSPVPPRVDPGLPFDVVT +VRQPDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLAAALAAVAEAPRDAAVVGRR +RHLAEAWLERAWAHGWQPGHEVPADARLAEPAWLREGYRATDDLRRADSTGYRYVISAVF +TVAREVYEDAGGFDPAFVGYGGEDWELAHRLWRVGAALRHAPDAVAWQAGADFGGRGDAA +EAARVKAREALVLASRIPATTARGHGLSLAGPLRVEARVRVPEGADGAAAAVVAVDAVLC +AAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAADEDLPPTPARGDLDAVRSVPDW +SVDVHVPLRPAAAGARPDADAVAAWLLRLERAGVERVEVLGEPAEPGERAVLAVLTCARA +RWRHRRGGTARVWRVPASRLGWAPVATVPDLEAWWGGWG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001574.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001574.fa new file mode 100644 index 0000000000000000000000000000000000000000..7e4eb561ad50d276813434e98b4fb823ad9337be --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001574.fa @@ -0,0 +1,40 @@ +>PROKKA_01969 +MKGIVDVDSQPQGRVLYVTVGAPEHGVVRHGRQTAAALQRVGAEVELLTAEDVAAFRGLV +PLLEEARALGAAVHLDVTDALFGPTATAAADLLVDVLPAGTTLTLHDIPQPAEGDGRYRR +RGEAYARLAQAVAGVVVSSQHERALLADLVDVAADVVPLPVQDRRAAAARAEPVVPESMA +GLDQDLVLFGFVYPGKGHALALEALTELHRQWGPDSGAPRRLTALGPVSAGHDDLVAELT +RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRAIASAGR +YTEEMERLRPGTLRLVHPNGSPAFAMAEAIAEAVEDPERTWLDPAVDLSPGAEGCARMLF +DVLRRVHRWT +>PROKKA_01663 +MKGIVDVDSQPQGRVLYVTVGAPEHGVVRHGRQTAAALRRVGAEVELLTAEDVAAFRGLV +PVLEEARALGAAVHLDVTDALFGPTATAAADLLVDVLPEGTTLTLHDIPQPAEGDGRYRR +RGEAYARLAQAVDGVVVSSQHERALLADLVDVAADVVPLPVEDRRAAAARAEPVVPESMA +GLDRDLVLFGFVYPGKGHALALEALTELHRQWGPDSGAPRRLTALGPVSAGHDDLVAELT +RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRAIASAGR +YTEEMERLRPGTLRLVHPNGSPAFAMAEAIAEAVEDPERTWLGPGVDLSPGAEDCARMLF +DVLRRVHRWT +>PROKKA_00890 +MESQPQGRVLYVIVGPPEHGVVRHARQTAAALRRVGAEVELLTAEDVAAFHGLVPLMAEA +RSLGAAVHLDVTDALFGPTAAAAADLLVDVLPEGTTLTLHDIPQPAEGDGRYRRRGEAYA +RLARHAAGVVVSSQHERALLAELVDADADVVPLPVEDRRAEAARAESVVPENMAGLDQDV +VLFGFVYPGKGHALALEALTELHRQWGPNSGAPRRLTALGPVSAGHDDLVAELTRDAEAR +GLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRAIASAGRYTEEME +RLRPGTLRLVHPNGSPAFAMAEAIAEAVEDPEHTWLDPAVDLSPGAEDCARMLFDVLRRV +HRWT +>PROKKA_00831 +MTSHAQGRVLYLSVGSRGHGVVHHGLLTAEELAQVGLDVESLHTEDATGFVGLAPVLARA +REARRAVHVDVTDSLFGPSPAAAADTLSRILPDGATVTLHDVPQPAEGEARFLERAEAYV +RIAQAAAGVVVSSEHERALLHAIVDVDAHVVPLPVEDRRAAREAVRLPEALEGLDRDVVI +FGHLYPGKGHAEAIDALAELDRQWGPSPHRPRRVTALGAVAARHEFLVDELTARAEVSGL +QFRVTGFVPDEVLDPALRAAAVPLAAHHNVSASGSLASWMSVGRRPIVPAGRYTQEMARL +RPGTLRIVQVGTSGPEYALAEAVAEAVEEPSRTWQARGTSLAPGPRACARMLAAALADVH +GWAWPR +>PROKKA_01895 +MKGIVDVDSQPQGRVLYVTVGAPEHGVVRHGRQTAAALRRVGAEVELLTAEDVAAFRGLV +PVLEEARALGAAVHLDVTDALFGPTATAAADLLVDVLPEGTTLTLHDIPQPAEGDGRYRR +RGEAYARLAQAVDGVVVSSQHERALLADLVDVAADVVPLPVEDRRAAAARAEPVVPESMA +GLDRDLVLFGFVYPGKGHALALEALTELHRQWGPDSGAPRRLTALGPVSIGHDDLVAELT +RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRTIASAGR +YTEEMERLRPGTLRLVHPNGSPAFAMAEAIAEAVEDPERTWLDPAVDLSPGAEDCARMLF +DVLRRVHRWT diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001575.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001575.fa new file mode 100644 index 0000000000000000000000000000000000000000..abfb33d93ae909e4a8b07438dd5f8613d56c9525 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001575.fa @@ -0,0 +1,64 @@ +>PROKKA_01970 +MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPGAPAHQWWPPRALHAEWLAEHR +PDVLHVHFGFEHFSPAQLAAALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGR +ADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVAQGDDDAPGAEPGLLPPDASDD +GDGAAAPARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQDTVQDEDAL +AALRAGCAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAV +ADIGHIADQSGAWLTPDSLAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVA +AAHVAVYREALARARGALPGVSVLVITGHRDEHLARVIAGLERSHRRPDQVVVVFMGQPD +GRVPATDLPVTVGHVAAEAGLPLAQARNRAAELATGEILVFLDVDCIPAAETVGVLATEV +AAHPGSVVMGRPRYLRPGWTRDVGEADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHL +VWTLILALRRADLARIGGFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMT +PPLHHLEDILVNARRFRQVHGRWAMEGWLRAFADAGLIAWDPEGERLELLRHPTEAELTA +ARRDDAAY +>PROKKA_01664 +MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPDAPAHQWWPPRALHAEWLAEHR +PDVLHVHFGFEHFSPAQLAAALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGR +ADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVAQGDDDAPGLLPPDASDDGDGA +PVPARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQDTVQDEDALAALR +AGCAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAVADIG +HIADQSGAWLSPDSLAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVAAAHV +AVYREALARARGALPSVSVLVITGHRDEHLARVIAGLERSHRRPDQVVVVFMGQPDGRVP +ATDLPVTVGHVAADAGLPLAQARNRAAELAIGEILVFLDVDCIPAAETVGVLATEVAAHP +GSVVMGRPRYLRPGWTRDVGEADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHLVWTL +ILALRRADLARIGCFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMTPPLH +HLEDILVNARRFRQVHGRWAMEGWLRAFADAGLIAWDPEGERLELLRHPTEAELTAARRD +DAAY +>PROKKA_00889 +MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPGAPAHQWWPPRALHAEWLAEHR +PDVLHVHFGFEHFNPAQLAAALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGR +ADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVSQGDDDAPGLLPPDASDDGAAA +PARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQATVQDEDALAALRAG +CAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAVADIGHI +ADQSGAWLAPDSLAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVAAAHVAV +YREALARARGALPSVSVLVITGHRDEHLARVIAGLERSHRRPDQVVVVFMGQPDGRVPAT +GLPVTVGHVAAEAGLPLAQARNRAAELATGEILVFLDVDCIPAAETVGVLATEVAAHPGS +VVMGRPRYLRPGWTRAVEEADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHLVWTLIL +ALRRADLARIGGFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMTPPLHHL +EDILVNARRFRQVHGRWAMEGWLRAFADAGLIAWDPEGERLELLRTPTADELAVARRDDA +AY +>PROKKA_00830 +MSLTVQHVPAGHPYARSVRPLDGAAAPDVEFWPDPPVPGAAEGVWWPPRALDPAWIAEHR +PDVLHVHFGFEHFTPEQLRAALDAQHAHGGAVVVTVHDLQNPHLQDQDPHRARLRVLLDA +ADAVITLTPGAAAAVEAASGRAPLVLPHPHVVPLDALPDDGAADGERPGVDRPARLLMHA +KDLRAQVDPVGLLPVLAAARDALAARGLAVEVTVDVQDGVRDEAALAELEAGAEAHGFAL +WRHARLDDAELHAALRDADVSVLPYRVGTHSGWVEMCRDLGVPVAVAEVGHIADQARAWT +TPELLAAFDPDDPASLADALAALLTAAPDARAAAPAARAAQRRRVAAAHVAVYRQALAVR +RGTAATVSVLVITGHRDAHLARVLAGLERSHRRPDQVVVVFMGQPDGAVPATDLPVTVGH +VAADHGLPLATARNRAAELATGEVLVFLDVDCIPAADTVGVLAAEVAAHPGSLVMGAPRY +LAPDWTAALAAEGVDADAAPTDGDLRRHAVPHRARTHLRPGPSEEWALVWTLVMAIGAAD +LARIDGFDEGFAGYGAEDTDLAFRARDAGLTLRISPAEAFHQHHGVHRPPLHHVADIVVN +ARRFRTLHGTWPMGGWLAAFAERGLIRWDPDGDLLELVREPTPDDVAAARVDDAAY +>PROKKA_01896 +MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPGAPAHQWWPPRALHAEWLAEHR +PDVLHVHFGFEHFSPAQLAAALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGR +ADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVAQGDDDAPGALPPDASDDGDGA +AAPARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQDTVQDEDALAALR +AGCAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAVADIG +HIADQSGAWLSPDSLAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVAAAHV +AVYREALARARGALPGVSVLVITGHRDEHLARVIAGLERSHRRPDQVVVVFMGQPDGRVP +ATDLPITVGHVSAEAGLPLAQARNRAAELATGEILVFLDVDCIPAAETVGVLATEVAAHP +GSVVMGRPRYLRPGWTRDVGEADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHLVWTL +ILALRRADLARIGGFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMVPPLH +HLEDILVNARRFRQVHGRWAMEGWLRAFADAGLIAWDPEGERLELLRHPTEAELTAARRG +DAAY diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001577.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001577.fa new file mode 100644 index 0000000000000000000000000000000000000000..8738372b3b4f38c6b3f3e1acb34aa481c7715b4f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001577.fa @@ -0,0 +1,38 @@ +>PROKKA_01972 +MRISVLTHMLHPIRSPYEGGLEMHTAMTVEHLVRRGHDVTVYAREGTRVPGDVVAVLPAE +GAGPGRAGARVREEAARRACALILDDDSDAVLNNSLSPAPLELLRARPVVTVLHTPATLA +EVLAVVDAPGWTAPDHHRWASVSASNALAWQHRLPRVDVVPNGIELHQWVSDAVPVRGRA +VWSGRITAEKGLHVAIDAARIAGMELHFAGPISDEEYHAREVVPRLGPDTVYHGHLDHHA +LPHMLATGEVFLATPLWAEPFGLAVVEAMALGVPVAALLSGAMGEIVAPQAGALAVHHTA +QELAVSIRHARRKDRGRVRAWACRFSAETMVEGYVDLLEQAAEDARDLAAAEDAYGFDPH +GVPRPSADAADLESL +>PROKKA_01666 +MRISVLTHMLHPIRSPYEGGLEMHTAMTVEHLVRRGHDVTVYAREGTRLPGDVVAVLPAE +GAGPGRAGARVREAAARRACALILDDDSDAVLNNSLSPAPLELLRARPVVTVLHTPATLA +EVLAVVDAPGWTAPDHHRWASVSASNALAWQHRLPRVDVVPNGIELHHWVSDAVPVRGRA +VWSGRITAEKGLHVAIDAARIAGMELHFAGPISDEEYHAREVVPRLGPDTVYHGHLDHHA +LPHMLATGEVFLATPLWAEPFGLAVVEAMALGVPVAALLSGAMGEIVAPQAGALAVHHTA +QELAVSIRHARRKDRGRVRAWACRFSAETMVEGYVDLLEQAAEDARDLAAAEDAYGFDPQ +GVPRPSADAADLESL +>PROKKA_00887 +MRISVLTHMLHPIRSPYAGGLEMHTAMTVEHLVRRGHDVTVYAREGTRLPADVVPVLPAE +GAGPGKEGDRLREEATRRACEMVLADDSDAVLNNSLSPAPLELLRERPMITVLHTPATLA +EVLAVVDHPDWRAPQHHRWASVSASNALAWQHRLPRVDVVPNGIELHHWVSDAVPVRGRA +VWSGRITAEKGLHVAIDAARIAGMELHFAGPISDEEYHAREVVPRLGPDTVYHGHLDHQT +LPHMLATGEVFLATPLWAEPFGLAVVEAMALGVPVAALLSGAMGEIVAPQAGALAVHHTA +QELAVSIRHARRKDRGRVRAWACRFSAETMVEGYLDLLEQAAEDARDGELV +>PROKKA_00828 +MRIDVLTHPLHPIRSPYEGGLEMHTAMTVEHLVAAGHQVRVHARAGTRIPGADVVSLLAA +APDAPGAEGQAVREGALAGACQRILADAPDAVLNNSLSPQPLIRLRSLPMLTVLHTPATL +EPVLEVTDAPGWTPPAHHRWASVSVSNALAWRHRLPSVDVVPNGIDLDRWVSDRAPVPGR +AVWSGRITPEKGLHMAIDAARAVGMELHAAGPVSDPAYYAERVAPRLGEDVVHHGHLDHT +ALPDLLATGEVFLSTPLWAEPFGLATVEAMALGVPVAALLTGAMGEIVAPQAGALAVHHS +VEALADAIRYARRKDRARVADWARRFSADTMVAGYLDLLEQAVADHADDAELRKVPA +>PROKKA_01898 +MRISVLTHMLHPIRSPYEGGLEMHTAMTVEHLVRRGHDVTVYAREGTRLPGDVVAVLPAE +GAGPGRAGARVREAAARRACALILDDDSDAVLNNSLSPAPLELLRARPVVTVLHTPATLA +EVLAVVDAPGWTAPDHHRWASVSASNALAWQHRLPRVDVVPNGIELHHWVSDAVPVRGRA +VWSGRITAEKGLHVAIDAARIAGMELHFAGPISDEEYHAREVVPRLGPDTVYHGHLDHHA +LPHMLATGEVFLATPLWAEPFGLAVVEAMALGVPVAALLSGAMGEIVAPQAGALAVHHTA +QELAVSIRHARRKDRGRVRAWACRFSAETMVEGYVDLLEQAAEDARDLAAAEDAYGFDPQ +GVPRPSADAADLESL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001580.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001580.fa new file mode 100644 index 0000000000000000000000000000000000000000..6d9420c042e2dc7db6d461cd1a5de4c9d4da3b42 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001580.fa @@ -0,0 +1,54 @@ +>PROKKA_01979 +MSTAPTRVRLGMPTVRPVHGEGEILLNTPFPESAREQLGNGQMRANIRRATHTIRAKRAG +VVEELPDWQELRAAGSALKQSVMADLPALLERLESEVTARGGVVHWARDAAEANRIITEL +VTAKGVDEVIKVKSMATQEIGLDAALEHAGVAAVETDLAELIVQLGHDRPSHILVPAIHR +NRREIRDIFRREMPDTDESLTSEPADLAEAARRHLREKFLSTKVAISGANFGVAETGTLS +VVESEGNGRMCLTLPETLITVMGIEKLVPTFEDLEVFLQLLPRSSTGERMNPYTSMWTGV +TEGDGPQEFHLVLLDNGRSAVLSDPKGRSALHCIRCSACMNVCPVYEQTGGHAYGSVYPG +PIGAILSPQLTGVDAGENGTLPYASTLCGACYDVCPVAIDIPSILIHLRDEDVQATHAAR +KALRTEKDAAAGPLARAKAAVESVTPSQMDVAMKGASVVMSSGRRMSLAERGLGLGRVAA +GPDRVLGWLPGIAGGWTDERDVPAPPRESFRNWWARHKDETEHRTALDGVAGLDRQEDEH +VEEDGR +>PROKKA_01673 +MSTAPTRVRLGMPTVRPVHGEGEVLLKTPFPESAREQLGNDQMRANIRRATHTIRAKRAG +VVEELPDWQELRAAGSALKQSVMADLPALLERLESEVTARGGVVHWARDAAEANRIITEL +VTAKGVDEVIKVKSMATQEIGLDAALEHAGVAAVETDLAELIVQLGHDRPSHILVPAIHR +NRREIRDIFLREMPETDESLTSEPADLAEAARRHLREKFLSTKVAISGANFGVAETGTLS +VVESEGNGRMCLTLPETLITVMGIEKLVPTFEDLEVFLQLLPRSSTGERMNPYTSMWTGV +TEGDGPQEFHLVLLDNGRSAVLSDPKGRSALHCIRCSACMNVCPVYEQTGGHAYGSVYPG +PIGAILSPQLTGVDAGENGTLPYASTLCGACYDVCPVAIDIPSILIHLRDEDVQATHAAR +KALRTEKDAAGGPLARAKTAVESVTPSQMDVAMKGASVVMSSGRRMSLAERGLGLGRVAA +GPDRVLGWLPGIAGGWTDERDVPAPPRESFRNWWARHKDETEHRTALDGVAGLDRQEDEH +VEEDGR +>PROKKA_00879 +MTRTALGMPAVRPAHGHGNIVLDEPFPSAARTQLGNAQMRANIHHATHTIRGKRARVVGE +LPDWAELRQAGSALKQQVMADLPALLEQFEQRVTERGGVVHWARDAEEANRIITGLVKAK +GVDEVIKVKSMATQEIDLEHALQAEGIAAVETDLAELIVQLGHDKPSHILVPAIHRNREE +IREIFVREMPETDESLTSDPSALADVARVHLREKFLTTSVAISGANFGVAETGTLTVVES +EGNGRMCLTLPETLITVMGIEKIVPTFQDLEVFLQLLPRSSTGERMNPYTSMWTGVTPGD +GPQEFHLVLLDNGRSAVLSDPEGRPALHCIRCSACMNVCPVYEQTGGHAYGSVYPGPIGA +ILSPQLTGVQEGANGSLPYASSLCGACYDVCPVAIDIPSILVHLRDQDVRATHARKKEET +RVPLPSQMDLMMKGARTVMSSGTAMSLAERGLPLGRLAAGRDATLGWLPGIAGGWTDQRD +VPSPPRQSFRNWWRGNAEHTEERVARDGGRRDVAAEDETTTTDGQEQR +>PROKKA_00814 +MSTAPTRVRLGMPTLRPVHGEGEILLKTPFPESAREQLGNGQMRANIRRATHTIRAKRAG +VVGELPDWQELRAAGSALKQSVMADLPALLERLESEVTARGGVVHWARDAAEANRIITEL +VTAKGVDEVIKVKSMATQEIGLDAALAQAGVAAVETDLAELIVQLGHDRPSHILVPAIHR +NRREIRDIFLREMPETDESLTSEPADLAEASRRHLREKFLSTKVAISGANFGVAETGTLA +VVESEGNGRMCLTLPETLITVMGIEKLVPTFEDLEVFLQLLPRSSTGERMNPYTSMWTGV +TEGDGPQEFHLVLLDNGRSAVLSDPKGRSALHCIRCSACMNVCPVYEQTGGHAYGSVYPG +PIGAILSPQLTGVDAGENGTLPYASSLCGACYDVCPVAIDIPSILIHLRDEDVQATHAAR +KALRTEGDGDAGPLARAKAAVESVTPSQMDVAMKGASVVMSSGRRMSLAERGLGLGRVAA +GPDRVLGWLPGIAGGWTDERDVPAPPRESFRNWWARHKDETEHRTALDGVAGLDRQEDEH +VEEDGR +>PROKKA_01905 +MSTAPTRVRLGMPTVRPVHGEGEILLNTPFPESAREQLGNGQMRANIRRATHTIRAKRAG +VVEELPDWQELRAAGSALKQSVMADLPALLERLESEVTARGGVVHWARDAAEANRIITEL +VTAKGVDEVIKVKSMATQEIGLDAALEHAGVAAVETDLAELIVQLGHDRPSHILVPAIHR +NRREIRDIFLREMPETDESLTSEPADLAEAARRHLREKFLSTKVAISGANFGVAETGTLS +VVESEGNGRMCLTLPETLITVMGIEKLVPTFEDLEVFLQLLPRSSTGERMNPYTSMWTGV +TEGDGPQEFHLVLLDNGRSAVLSDPKGRSALHCIRCSACMNVCPVYEQTGGHAYGSVYPG +PIGAILSPQLTGVDAGENGTLPYASTLCGACYDVCPVAIDIPSILIHLRDEDVQATHAAR +KALRTDEDAAAGPLARAKAAVESVTPSQMDVAMKGASVVMSSGRRMSLAERGLGLGRVAA +GPDRVLGWLPGIAGGWTDERDVPAPPRESFRNWWARHKDETEHRVAMDGVAGLDRPEDEH +VEEDGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001581.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001581.fa new file mode 100644 index 0000000000000000000000000000000000000000..83d18beb1a820bd66b3de3597472bfcbd8c63b1f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001581.fa @@ -0,0 +1,30 @@ +>PROKKA_01980 +MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYMEDALPVVR +NHVRTFMKADYDLAVAPSASCVASLGHQQPDVARSGGDEGLARDAEVVASRTLELSQLLT +DVLGVTDAGAQLGSWFPHTVTYHPSCHGMRLLRLGSRQEDLLRTVADIDLRPLPDAEECC +GFGGTFSLKNPDVSAAIAEEKIEKVTASGASLCTGGDASCLLHLDGAMHRREARGQDGRP +LRTVHLAEILAATRENPLEVDGPVELSIPASAGARRGPSARVEEARR +>PROKKA_01674 +MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYMEDALPVVR +NHVRTFMKADYDLAVAPSASCVASLGHQQPDVARSGGDEGLARDAEVVASRTLELSQLLT +DVLGVTDAAAQLGSWFPHTVTYHPSCHGMRLLRLGSRQEDLLRTVADIDLRPLPDAEECC +GFGGTFSLKNPDVSAAIAEEKIEKVTASGASLCTGGDASCLLHLDGAMHRREARGQDGRP +LRTVHLAEILAATRENPLEVDGPVELSIPTSAGVRRGPSARVEEARR +>PROKKA_00878 +MRVALFATCIVDAMYPKVALATVRILERLGHEVVFPRGQGCCAQMHVNSGYLDDALPVVK +NHVRTFQGADYDVAVAPSGSCVASLGHQQPMVARAAGDEALARDAEEVAANTYELAALLT +DVLGVTDAAAQLGSWFPHTVTYHPSCHGMRLLRLGDRQERLLRSVADIDYRALPDAEECC +GFGGTFSLKNPDVSGAMAEEKIGNIERTQARLCTGGDASCLLHLGGVMSRRGTTAPDGSP +VTTLHFAEILAATRENPLDVSGPVDLSIPAQGPARRRRQKEATR +>PROKKA_00813 +MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYVEDALPVVR +NHVRTFMKADYDLAVAPSGSCVASLGHQQPDVARSCGDEGLARDAEVVASRTLELSQLLT +DVLGVTDAAAQLGSWFPHTVTYHPSCHGMRLLRLGTRQEDLLRTVADIDLRPLPDAEECC +GFGGTFSLKNPDVSAAIAEEKIEKVTASGASICTGGDASCLLHLGGAMHRREARGQDGRP +LRTVHLAEILAATRENPLEVDGPVELSIPASAGARRGPSARVEEAHR +>PROKKA_01906 +MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYMEDALPVVR +NHVRTFMKADYDLAVAPSASCVASLGHQQPDVARSGGDEGLARDAEVVASRTLELSQLLT +DVLGVTDAGAQLGSWFPHTVTYHPSCHGMRLLRLGSRQEDLLRTVADIDLRPLPDAEECC +GFGGTFSLKNPDVSAAIAEEKIEKVTASGASLCTGGDASCLLHLDGAMHRREARGQDGRP +LRTVHLAEILAATRENPLEVDGPVELSIPASAGARRGPSARVEEARR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001583.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001583.fa new file mode 100644 index 0000000000000000000000000000000000000000..512c4735d8944a97d101b4150e8e6f0380a3ce34 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001583.fa @@ -0,0 +1,30 @@ +>PROKKA_01982 +MTAAPAYTIVLDWLEAELRSGAVVVGDKLPGERTLAERFGISRASVREATRMLEAMGLIR +ASAGSGPNSGAVVVSEPSAALGWALRLHIATRSLPMADVVAARVLLETDAAQAAAATSGD +PESVAVLAEVETLLDRMDDPALPEEDFHLLDTEFHVRLATLGGNVVTAMMLDSLRQATIG +YVTETVAGLSDWPAVRAGLQADHRRILAASAAGDGRAAAQELREHVLGFAALAQAGRVPA +GG +>PROKKA_01676 +MTAAPAYTIVLDWLEAELRSGAVVVGDKLPGERTLAERFGISRASVREATRMLEAMGLIR +ASAGSGPNSGAVVVSEPSAALGWALRLHIATRSLPMADVVAARVLLETDAAQAAAATSGD +PESVAVLAEVETLLDRMDDPALPEEDFHLLDTEFHVRLATLGGNVVTAMMLDSLRQATIG +YVTETVAGLSDWPAVRAGLQADHRRILAASAAGDGRAAAQELREHVLGFAALAQAGRVPA +GG +>PROKKA_00876 +MTARPPTPPAEPEPGRRRAPGHAVILDWLEGELRSGRIQVGDKLPSERTLAERFGMSRSS +VREAGRVMDAMGLVRSATGSGPRAGAIVVSEPSAALAWALRMHVATRALPVADLVTTRVL +LETEAALEAAEHDVPGRGAILATAHAHLDRMDVPDFPAREFHRLDAEFHVLLSTLSGNVV +LETILRSLREATIGYVEEAMAGVEDWGAVRDELQRQHRDILAAAVERDGPRAAQAVREHI +HWFSRFTTAGPDAAGG +>PROKKA_00811 +MTAAPAYTIVLDWLEAELRSGAVAVGDKLPGERTLAERFGISRASVREATRMLEAMGLIR +ASAGSGPNSGAVVVSEPSAALGWALRLHIATRSLPMADVVAARVLLETDAAQAAAATSGD +PESVAVLAEVETLLDRMDDPALPEEDFHLLDTEFHVRLATLGGNVVTAMMLDSLRQATIG +YVTETVAGLSDWPAVRAGLQADHRRILAASAAGDGRAAAQELREHVLGFAALAQTGRVPA +AG +>PROKKA_01908 +MTAAPAYTIVLDWLEAELRSGAVVVGDKLPGERTLAERFGISRASVREATRMLEAMGLIR +ASAGSGPNSGAVVVSEPSAALGWALRLHIATRSLPMADVVAARVLLETDAAQAAAATSGD +PESVAVLAEVETLLDRMDDPALPEEDFHLLDTEFHVRLATLGGNVVTAMMLDSLRQATIG +YVTETVAGLSDWPAVRAGLQADHRRILAASAAGDGRAAAQELREHVLGFAALAQAGRVPA +GG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001588.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001588.fa new file mode 100644 index 0000000000000000000000000000000000000000..4555f970fd228077fb02c2f74e29606046c241cc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001588.fa @@ -0,0 +1,40 @@ +>PROKKA_01990 +MRNLRDHLSQRAVGVKQSAVRDVFDIAMDPNLVSLAGGNPWLADLPLDELGRIASDLMTR +FGTESLQYGPGQGTEEMRAAAATVMAADGIPDADPDLVVITPGSQAAIDTACRAFANPGD +VVVVEDPTFVGALTTFATWQLEAVATGTDDQGLVPAALDETLTRLAAEGRRVAFLYTIPS +FANPSGALLPPGRRAEVGAICEKHGVLIVEDNPYGQIAFDGEPVAPIAADHRDNVVHLGT +MSKIFSPGVRIGWALVPAALKREFYLCAESAYIHASTYSQMLSTAFVTQLDWQGHVRHVT +GLYRERAGALVDAVREHWDPGVEFITPQGGFFLWATLPAGVDTLEVMHRGIEAGAVFVPG +AAFTPVEGTHSTLRLAYSFVDAEKLVEGVRRLAPAVNESIARAR +>PROKKA_01684 +MRNLRDHLSQRAVGVKQSAVRDVFDIAMDPNLISLAGGNPWLADLPLDELGRIASDLMTR +FGTESLQYGPGQGTEAMRAAATAVMAADGIPDADPDLVVITPGSQAAIDTACRAFANPGD +VVVVEDPTFVGALTTFTTWQLEAVATGTDDHGLVPAALDETLTRLAAEGRRVAFLYTIPS +FANPSGALLPPGRRAEVGAICEKHGVLIVEDNPYGQIAFDGEPVAPIAADHRDNVVHLGT +MSKIFSPGVRIGWALVPAALKREFYLCAESAYIHASTYSQMLSTAFVTQLDWQGHVRHVT +GLYRERAAALVDAVREHWDPAVEFITPQGGFFLWATLPVGVDTLEVMHRGIEAGAVFVPG +AAFTPVEGTHSTLRLAYSFVAAEKLVEGVRRLAPAVNESIARAR +>PROKKA_00867 +MRHLRDHLSHRAVGVKQSAVRDVFDIAMDPNLVSLAGGNPWLADLPLDELGRIASDLMTR +FGTESLQYGPGQGTEEMRAAAAAVMAADGIPDADPELVVITPGSQAAIDTACRAFGNPGD +VVVVEDPTFVGALTTFNTWELDAVATGTDEHGLVPAALDETLTRLAAEGRRVAFLYTIPS +FANPSGALLPADRRAEVAAICERHGVLIVEDNPYGQIAFDGDPVAPIAAEHRDGVVYLGT +MSKIFSPGVRIGWALVPAELKREFYLSAESAFIHASTYSQMLSTAFVTQLDWQGHVRHVT +GLYRERAGVLVDAVREHWDPGVEFITPRGGFFLWATLPGGVDTIELMHRGIEAGAVFVPG +GAFTPVEGVHSTLRLAYPFVEAERLVEGVRRLAPVVNDAVARAR +>PROKKA_01757 +MSTLDPAGARAHLARRATTVQQSAVRDVFDIAMDPDLVSLAGGNPWLAGLPLEELGATAA +RLVAEQGTASLQYGPGQGLECMRVAACAVMAADGIPDADPELVVITPGSQAAIDTACRAF +ADPGDVVVVEDPTFVGALTSFQTWELEAVATPTDEHGLVPADLDATLARLEAEGRRVAFL +YTIPSFANPSGLLLPADRRDDVAAVCERHGVLIVEDNPYGQIAFDGAPVAPIAAAHRERT +VYLGTMSKIFSPGVRVGWALVPEALHREFYLCAESAFIHASTTSQMLSTAFVTEYDWQDH +VRGVTGLYRSRAQALQAAIAEHWDPGFTFTPPAGGFFLWGSLPAGVDAVELMHRGIAAGA +VFVPGAAFTPVPGTHSTLRLAYSFVDEETLAEGVRRLAPVVNTAVEGAR +>PROKKA_01916 +MRNLRDHLSQRAVGVKQSAVRDVFDIAMDPNLVSLAGGNPWLADLPLDELGRIASDLMTR +FGTESLQYGPGQGTEEMRAAATAVMAADGIPDADPDLVVITPGSQAAIDTACRAFANPGD +VVVVEDPTFVGALTTFTTWQLEAVATGTDDHGLVPAALDETLTRLAAEGRRVAFLYTIPS +FANPSGALLPPGRRAEVGAICEKHGVLIVEDNPYGQIAFDGEPVAPIAADHRDNVVHLGT +MSKIFSPGVRIGWALVPAALKREFYLCAESAYIHASTYSQMLSTAFVTQLDWQGHVRHVT +GLYRERAGALVDAVREHWDPGVEFITPQGGFFLWATLPAGVDTLEVMHRGIEAGAVFVPG +AAFTPVEGTHSTLRLAYSFVDAEKLVEGVRRLAPAVNESIARAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001589.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001589.fa new file mode 100644 index 0000000000000000000000000000000000000000..788c815fc8ec3b9b46ab197d6ec981027ed71fc4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001589.fa @@ -0,0 +1,46 @@ +>PROKKA_01991 +MTQSTPEPTPTVTEHDFTVRENRPGKVLAVHLNYPSRIAQRGRPPQAPGYFLKAGTSLAR +SGDTIERPAGTELLAYEGEIALIIGRTARRVSPEEGWSHVSGITAANDWGLYDLRHADKG +SNVKNKSGDGYTPLGPAVISAAGLDPAALRVRTWVNGEIVQDDTTEGLVFPFGRLVADLS +QLMTLEEGDVILTGTPAGSSVAQPGDVVEVEVDAPSAPGAPTTGRLVTTVVDSEHALAPF +GAQPQVDDVQREEAWGSREAAGLAPQAEAASSSAVDENGHWVASAPQPDRSLLTPELRAK +IDAIAVATLTAQLQKRGVQNATIDGPRPVHRGRRVLGYAKTLRYVPKREDLAKEFGGGFN +AQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLALRAQVNGANAVITDGGIRDSAAVAEVG +LQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDIIVGDDDGVVVIPPSLLQEVVDD +AYEQELQDAWAYEQVKAGYPVDGMFPPNAEWKAKFAEYRKTLPDAPAPEGDA +>PROKKA_01685 +MTQSTPDPTPTVTEHDFTVRENRPGKVLAVHLNYPSRIAQRGRSPQAPGYFLKAGTSLAG +SGDTIERPAGTELLAYEGEIALIIGRTARRVSPEEGWSHVSGITAANDWGLYDLRHADKG +SNVKNKSGDGYTPLGPAVISAAGLDPAALRVRTWVNGEIVQDDTTEGLVFPFGQLVADLS +QLMTLEEGDVILTGTPAGSSVAQPGDVVEVEVDAPSAPGAPTTGRLVTTVVDSEHSLAPF +GAQPQVDDVQREEAWGSREAAGLAPQAAAPSSSAVDENGHWVASAPQPDRSLLTPELRAK +IDAIAVATLTAQLQKRGVQNATIDGPRPIHRGRRVLGYAKTLRYIPKREDLAKEFGGGFN +AQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLALRAQVNGANAVITDGGIRDSAAVAEVG +LQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDIIVGDDDGVVVIPPSLLQEVVDD +AYEQELQDAWAYEQVKAGYPVDGMFPPNAEWKAKFAEYRKTLPDAPAPEGDA +>PROKKA_00866 +MDENGHWVASAPQPDRSLLTPELRAKIDAVAVATLTAQLQKRGIQNATIDGPRPIHQGRR +VLGYAKTLRYVPKREDLFKEFGGGFNAQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLAL +RAQVNGANAVITDGGIRDSAAVAEVGLQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQ +PGDVIVGDDDGVVVIPPSLLQEVVDDAYEQELQDAWAYEQVKAGHPVDGMFPPNAEWKAT +FDEYRKTLPDAPAPEGDA +>PROKKA_00804 +MTQNTSPATPSVTEHDFTVRQNRPGKVLALHLNYPSRIAQRGRSPQFPGYFIKAGTSIAR +SGDAVERPAGTELLAYEGEIALIIGRTARRVRPEEGWSYVSGITAANDWGLYDLRHADKG +SNVKNKSGDGYTPLGPAVIAAANLDPAALRVRTWVNGALVQDDTTEGLVFPFGQLVADLS +QLMTLEEGDVILTGTPAGSSVAQPGDVVEVEVDAPTAPGAPSTGRLITHVTDSDIPMADY +GHGPRVDDLQREEAWGSREAAGLAPVEDAPAQDDAAPASTAVDENGHWVASAPQPDRSLL +TPELRAKIDAIAVATLTAQLQKRGIQNATIDGPRPIHQGRRVLGYAKTLRYIPKREDLFK +EFGGGFNAQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLALRAQVNGANAVITDGGIRDS +AAVAEVGLQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDIIVGDDDGVVVVPPSL +LQEVVDDAYEQELQDAWAYEQVKAGHPVDGMFPPNAEWKAKFDEYRKTLPDAPAPEGDA +>PROKKA_01917 +MTQSTPDPTPTVTEHDFTARENRPGKVLAVHLNYPSRIAQRGRSPQAPGYFLKAGTSLAR +TGDTIERPAGTELLAYEGEIALIIGRTARRVSPKEGWSHVSGITAANDWGLYDLRHADKG +SNVKNKSGDGYTPLGPAVISAAGLDPAALRVRTWVNGEIVQDDTTEGLVFPFGQLVADLS +QLMTLEEGDVILTGTPAGSSVAQPGDVVEVEVDAPSAPGAPTTGRLVTTVVESEHALAPF +GAQPQVDDVQREEAWGSREAAGLAPQAAAPSSSAVDENGHWVASAPQPDRSLLTPELRAK +IDAIAVATLTAQLQKRGVQNATIDGPRPIHQGRRVLGYAKTLRYIPKREDLAKEFGGGFN +AQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLALRAQVNGANAVITDGGIRDSAAVAEVG +LQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDIIVGDDDGVVVIPPSLLREVVDD +AYEQELQDAWAYEQVKAGYPVDGMFPPNAEWKAKFAEYRKTLPDAPAPEGDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001591.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001591.fa new file mode 100644 index 0000000000000000000000000000000000000000..5b4eebec438ce92c20ccc137593d242509b11066 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001591.fa @@ -0,0 +1,50 @@ +>PROKKA_01993 +MTEKTSIEARKPAGLPDVLRHYIDGEFVDSIDGDTFEVLDPVTNEPYLTAASGKAADIDR +AVAAAKRAFESGEWSQALPRQRSRVLHAIADIMETRGNQLAEMECFDTGLPIKQARGQAA +RAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAI +ATGNSVVLKPAEFTPLSASLWGGIFEEAGLPKGVFNMVHGFGEEGYAGDPLVKHPDVPLI +SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERC +TAGSRILVQRSVYDEFVERYAAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKT +EARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDTEEEALQLAN +NTKYGLAAYIWTNDLKRAHNVAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS +IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG +>PROKKA_01687 +MTEKTSIEARKPEGLPDVLRHYIDGEFVDSIDGDTFEVLDPVTNEPYLTAASGKAADIDR +AVAAAKRAFESGEWSQALPRQRSRVLHRIADIMETRGDQLAEMECFDTGLPIKQARGQAA +RAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAI +ATGNSVVLKPAEFTPLSASLWGGIFEEAGLPQGVFNMVHGFGEEGYAGDPLVKHPDVPLI +SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERC +TAGSRILVQRSVYDEFVERYAAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKT +EARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDTEEEALQLAN +NTKYGLAAYIWTNDLKRAHNVAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS +IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG +>PROKKA_00864 +MTEINDRKPEGLPDLIRHYIDGQSVDSVDGDTFDVLDPVTNQPYIKAASGKTADVDKAVA +AAKAAFESGVWSQALPRERSRVLHKIADIMETRGDQLAAMECFDTGLPIKQAKGQAARAA +ENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAIATG +NSVVLKPAEFTPLSASLWPGIFEEAGLPKGVFNMVHGFGEEGFAGDPLVKHPDVPLISFT +GESRTGQIIFGNAAPHLKGLSMELGGKSPAVVFADADLDAAIDATIFGVFSLNGERCTAG +SRILVAREVYDEFVERYAAQASRVKVGMPNDETTEVGAIVHPEHFEKVMSYVEIGKSEAH +LVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDSDEEALELANNTK +YGLAAYIWTNDLKRAHNFAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRSIDF +YTDQQAVHINLGEVHNPVFGKQEQAAAKIDG +>PROKKA_00802 +MTEKTSIAARTPEGMPDVIRHYIDGEFVDSIDGDTFDVLDPVTNEPYIKAASGKSADVDA +AVAAAKRAFESGEWSQALPRQRSRVLHRIADIMETRGDQLAEMECFDTGLPIKQAKGQAA +RAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAI +ATGNSVVLKPAEFTPLSASLWGGIFEEAGLPTGVFNMVHGFGEEGYAGDPLVKHPDVPLI +SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERC +TAGSRILVQRSVYDEFVERYAAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKA +EARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDTEEEALQLAN +NTKYGLAAYIWTNDLKRAHNFAQDVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS +IDFYTDQQAVHINLGEVHNPVFGKQESKETGDA +>PROKKA_01919 +MTEKTSIEARKPQGLPDVLRHYIDGEFVDSIDGDTFEVLDPVTNEPYLTAASGKAADIDR +AVAAAKRAFESGEWSQALPRQRSRVLHRIADIMETRGDQLAEMECFDTGLPIKQARGQAA +RAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAI +ATGNSVVLKPAEFTPLSASLWGGIFEEAGLPKGVFNMVHGFGEEGYAGDPLVKHPDVPLI +SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERC +TAGSRILVQRSVYDEFVERYAAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKT +EARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDTEEEALELAN +NTKYGLAAYIWTNDLKRAHNVAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS +IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001592.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001592.fa new file mode 100644 index 0000000000000000000000000000000000000000..9f86acc23735d3eb67be4fd2873bc2c049d9c3cc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001592.fa @@ -0,0 +1,40 @@ +>PROKKA_01994 +MTNLESRQKTSSGFFVTKEVPIDPENPLPTPTSEAPDILRSASMELVVTDLAQSREFYVD +VLGLVVTEEDEETVYLRSMEEFIHHNLVLRQGETAAVAAFSYRVRTPEDLDKAVAFYEEL +GCRVERRKDGFVKGVGDSVRVEDPLGFPYEFFHDVEHVERLAWRYDLYTPGALVRLDHFN +QVTPDVPRAARYMQDLGFRVTEDIQDENGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVCF +ATHEKHNILAICDKLGALRMSDHIERGPGRHGVSNAFYLYLRDPDGHRVEVYTQDYYTGD +PDNPVVTWDVHDNQRRDWWGTPVVPSWYTDASRVLDLDGNLQPLVSRTDDSEMAVTIGAD +GFSYTREGQGEESLPEWKQGEYKLGNQL +>PROKKA_01688 +MTNLESRQKTSSGFFVTKEAPIDPENPLPTPTSEAPDILRCASMELVVTDLAASREFYVD +VLGLVVTEEDEETVYLRSMEEFIHHNLVLRQGETAAVAAFSYRVRTPEDLDKAVAFYEEL +GCRVERRKDGFVKGVGDSVRVEDPLGFPYEFFHDVEHVERLAWRYDLYTPGALVRLDHFN +QVTPDVPRAARYMQDLGFRVTEDIQDENGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVCF +ATHEKHNILAICDKLGALRMSDHIERGPGRHGVSNAFYLYLRDPDGHRVEVYTQDYYTGD +PDNPVVTWDVHDNQRRDWWGTPVVPSWYTDASRVLDLDGNLQPLVSRTDDSEMAVTIGAD +GFSYTREGQGEESMPEWKQGEYKLGNQL +>PROKKA_00863 +MSNYAGRTRTSVGTYVGQEGPVKTDNPIPTPKAEAPDVLRCASMELVVTDLEKSRQFYVD +VLDLVVTEEDEDTVYLRSMEEFIHHNLILRKGEIAAVAAFSYRVRTPEDLDKAVAFYTEL +GCRVERNKDGFVKGVGDSVRVEDPLGFPYEFFYEVDHVERLAWRYDLYSPGALVRLDHFN +QVTPDVPRAARYMQDLGFRVTEDIQDENGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVAF +ATHEKHNILAICDKLGSLRMSDAIERGPGRHGVSNAFYLYLRDPDGHRVEIYTQDYYTGD +PDNPVVTWDVHDNQRRDWWGTPVVPSWYTDASLVLDLDGNVKEVVARTDDSEMAVTIGAD +GFSYTRAEEGEDSMPEYKKGEYKLGNQL +>PROKKA_00801 +MSNLESRKKTSSGFFVTEEAPITPANPLPTPKAEAPDILRCASMELVVTDLAASRHFYVD +VLGLVVTEEDEETVYLRSMEEFIHHNLILRKGETAAVAAFSYRVRTPEDLDKAVAFYTEL +GCRVERNKDGFVKGVGDSVRVEDPLGFPYEFFFETEHVERLAWRYDLYTPGALVRLDHFN +QVTPDVPRAAKFMQDLGFRVTEDIQDEQGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVCF +ATHEKHNILAICDKLGALRMSDHIERGPGRHGVSNAFYLYLRDPDGHRVEVYTQDYYTGD +PDNPVVTWDVHDNQRRDWWGTPVVPSWYTDASRVLDLDGNLQPLVARTDDSEMAVTIGAD +GFSYTREDEGEESMPEYKQGEYKLGNQL +>PROKKA_01920 +MTNLESRQKTSSGFFVTKEVPIDPENPLPTPTSEAPDILRCASMELVVTDLAASREFYVD +VLGLVVTEEDEETVYLRSMEEFIHHNLVLRQGETAAVAAFSYRVRTPEDLDKAVAFYEEL +GCRVERRKDGFVKGVGDSVRVEDPLGFPYEFFHDVEHVERLAWRYDLYTPGALVRLDHFN +QVTPDVPRAARYMQDLGFRVTEDIQDENGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVCF +ATHEKHNILAICDKLGALRMSDHIERGPGRHGVSNAFYLYLRDPDGHRVEVYTQDYYTGD +PDNPVVTWDVHDNQRRDWWGTPIVPSWYTDASRVLDLDGNLQPLVSRTDDSEMAVTIGAD +GFSYTREGQGEESMPEWKQGEYKLGNQL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001595.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001595.fa new file mode 100644 index 0000000000000000000000000000000000000000..83bedad0bec23de6596c5490ee5093f795bd0d8b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001595.fa @@ -0,0 +1,44 @@ +>PROKKA_01999 +MSHDVEAPAGVPGSVAVVGGGVAGFAVVRELRRRGFAGEIALVDPQGVPYDRPPLSKEFL +TGDADARRLLLAPPTWFAEHGVELVEDAAVRVVPGGVHPDGGPAPHRVETASGRVLEADA +VVLATGGRPRALDVAGADHPDLITLRTRSDAEALRDRLTFGAEVAVVGGGFTGAEVAAAA +RRSLAAVTLVTGTDAPARAAVGPALAARLHRMHVEHGVAVEVGRAAWIEHRDADGGAALP +AAHRLHLHDGRTVDADVVVLAGGTVPDTALAEDAGLEVADGVLTDAMGRTTVPGILAVGD +AARARESAWATSRHWEPALRSGAAAAAALLGEQTDAPGAPWFWSDRYDAHVEAVGDMTVP +AGGRIVDREVRGVVVASFALAADGTLRGAASIDDPMTVKAARRIIDRGIVVDAAALADPA +VPVKSLARG +>PROKKA_01693 +MSHDVEAPAGVPGSVAVVGGGVAGFAVVRELRRRGFAGGIALVDPQGVPYDRPPLSKEFL +TGDADAHRLLLAPPAWFAEHGVELVEDEAVRVVPGGVHPDGGPAPHRVETASGRVLDADA +VVLATGGRPRALDVAGADHPDLITLRTRADAEALRDRLTFGAEVAVVGGGFTGAEVAAAA +RRSLAAVTLVTGTDAPARAAVGPALAARLHRMHAEHGVAVEVGRAAWIEHRDADGGAALP +AAHRLHLHDGRTVDADVVVLAGGTVPDTALAEDAGLEVADGVLTDAMGRTTVPGILAVGD +AARARESAWAPSRHWEPALRSGAAAAAAILGEEADAPGAPWFWSDRYDAHVEAVGDMTVP +AGGRIVDREVRGTVVASFALAADGTLRGAASIDDPMTVKAARRIIDRGIVVDAAALADPA +VPVKSLARG +>PROKKA_00858 +MSGDVDARAGAPASVVVVGGGVAGFGAVRELRRRGHTGSLALVEPQGVPYDRPPLSKDYL +TGETDAHRLLFAPPSWFAEHDVELVEEAAVRLTPGGAHPDGDPVPHRVELASGRVLEAEA +VVLATGGRPRPLDVEGATHPDLITLRTRADADALRERLHFGAEVAVVGGGFTGAEAASSA +RQALAGVTLVTATDAPALRAVGPALAARLHRMHAEHGVAVEVGRVARIEHRDDDGGAALP +AAHRLHLGDGRTVDADVVVLAGGTVPDTALAEEAGLEVADGILVDEAGRTSVPGILAVGD +TARATGSAWGPSPHWEPALRSGAAAAAALLGEEPEPPGAPWLWSDRHGCHVEAVGDMAVP +PGGASVDREARGAAVASFVLDAEGRMRGAASIDDPMTVKAARRIIDRGIVVDPQALADPT +VPLKSLARG +>PROKKA_00794 +MTVPASVLVVGGGVAGFGTVRELRRRGFEGKLTLVDPQGLPYDRPPLSKDFLTGETDAHR +LLFAPPAWFAEHAVELVTARVDRMDLTGEHPAAVLDDGTVRAADAVVLAPGGRPRPLDVP +GGDRPGVLVLRTRADAEAIAARLHFGARVVVVGAGLTGSEVASAAREAMAEVTLVSASPA +PAAAAVGPALAARLHALHAARGVDVVQGRVLRIEHADDAPGLDAPHRVHVALADGGEAAL +DADLVVAAVGILPDAALAAEAGLELAVDGGILVDAAQRTSDPRVLAVGDAARRRDAAYAA +PAMHWEPALQDAADAAAALLGEDLPERGAPWFWSDRHGVHVEGVGAMRPPEGGRIVDREV +RGTVVASFALAADGAMVGAASVDDPMAVKAARRIVDRGIVVDPERLADPSVPVKALLRG +>PROKKA_01925 +MSHDVEAPAGVPGSVAVVGGGVAGFAVVRELRRRGFAGGIALVDPQGVPYDRPPLSKEFL +TGDADAHRLLLAPPAWFAEHGVELVEDEAVRVVPGGVHPDGGPAPHRVETASGRVLDADA +VVLATGGRPRALDVAGADHPDLITLRTRADAEALRDRLTFGAEVAVVGGGFTGAEVAAAA +RRSLAAVTLVTGTDAPARAAVGPALAARLHRMHAEHGVAVEVGRAAWIEHRDADGGAALP +AAHRLHLHDGRTVDADVVVLAGGTVPDTALAEDAGLEVADGVLTDAMGRTTVPGILAVGD +AARARESAWAPSRHWEPALRSGAAAAAAILGEEADAPGAPWFWSDRYDAHVEAVGDMTVP +AGGRIVDREVRGTVVASFALAADGTLRGAASIDDPMTVKAARRIIDRGIVVDAAALADPA +VPVKSLARG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001600.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001600.fa new file mode 100644 index 0000000000000000000000000000000000000000..b67525a6918de05fd0dd0371ed5e662510eb730b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001600.fa @@ -0,0 +1,20 @@ +>PROKKA_02007 +MPPLIGPQQIATALRAVGLDDDAARLVAWADPARREREAAEQALADLAVAQTQLRAALGG +LVSAATDVRSAIQTGWRGEAAGAYGEAVRRAAALAAELEREAGEWLALRATAERDAEDAR +RNAEARQRAAEETALAVLRSLAVAA +>PROKKA_01717 +MSPLIGPQQIATALRAVGLDDDAARLAAWADPARREREAAEQALADLAAAQTQLRTALGG +LVSAATDVRSAMHTAWRGEAAGAYGEAVRRAATLAAELEREAGEWLALRATAERDAEDAR +RNAEARQRAAEETALAVLRSLAVAA +>PROKKA_00835 +MLQLIGPQHLAAALQAAGLDDDAARLLAWADPARRDRDAAQAALDELAVAQESLRGALAG +LVAAARDVRAGAAVAWRGPAAGEYADAVAEAVGAAEGLEREAGEWLALRATAEREAEDAR +QDAEARLRAAEETARAALRALAVAA +>PROKKA_00772 +MLLPPTAQALLRTLVAAGLDDDAARLAVGLTDAHADLQAARAAQDALADAAEDLRDLLAL +LEELTRGVAAALDVDWRSEAGAEYGERTDGLHRTATDRQDEAREWAGLLGRARSEAEQAE +RDAELRVRRAEEGASALLRAMAAA +>PROKKA_01945 +MSPLIGPQQIATALRAVGLDDDAARLVAWADPARREREAAEQALADLAVAQTQLRTALGG +LVSAATDVRSAMHTAWRGEAAGAYGEAVRRAATLAAELEREAGEWLALRATAERDAEDAR +RDAEARQRAAEETALAVLRSLAVAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001605.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001605.fa new file mode 100644 index 0000000000000000000000000000000000000000..690104d1f48affdab76117394c958cc3866f68c0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001605.fa @@ -0,0 +1,40 @@ +>PROKKA_02012 +MTETTDAPTTGKRRATFNTLEVSELRRLTEDSVEVTFAVPEELADDYDYVPGQYVALRKE +LDGAEVRRSYSICAVPKRGEIRVAVKKDIGGTFSTWANESLEVGEKIDVMNPQGAFTSRT +HVTSLNDAQKVAAEKVAEKKDTHLVAFAAGSGITPIMAIAKAVLAASETSRFDLVYANRS +AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDEDKLTTLLDRVIDVEGTD +EWFLCGPFELVQLTRETLAARGVPEDDVRFELFTTGRPENPQGHSGRVVEVDPKGDNVTI +EFNLDGLTAKVESPKSAHETVLNAALRVRSDVPFACAGGVCGTCRAKVVDGAYEMDENYA +LEKDEVEKGYVLTCQTRPTSDSITLDFDA +>PROKKA_01722 +MTETTDVPTTGKRRATFNTLEVSELRRLTDDSVEITFAVPEELADDYDYVPGQYVALRKE +LDGAEVRRSYSICAVPKRGEIRVAVKKDIGGKFSTWANESLEVGEKIDVMNPQGAFTSRT +HVTSLNDAQKVAAEKVAEKKDTHLVAFAAGSGITPIMAIAKAVLAASETSRFDLVYANRS +AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDEDKLTTLLDRVIDVEGTD +EWFLCGPFELVQLTRETLAARGVSEDDVRFELFTTGRPENPQGHSGRVVEVDPKGDNVTI +EFNLDGLTAKVESPKSAHETVLNAALRVRSDVPFACAGGVCGTCRAKVVDGAYEMDENYA +LEKDEVEKGYVLTCQTRPTSDSITLDFDA +>PROKKA_00830 +MTETTVTPATGKRRATFNTLEVSELRRLTDDSVEVTFAVPEELADDYDYVPGQYVALRKE +LDGQEVRRSYSICAIPKRGEIRVAVKKDIGGKFSTWANEVLEVGEKIDVMNPQGAFTSRS +HVTSLNDAEKVAAEKVAQNKNTHLVAFAAGSGITPIMAIAKAVLAASETSRFDLVYANRS +AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDAEKLTTLLDRVIDVDGTD +EWFLCGPFELVQLARETLSARGVDEDDVRFELFTTGRPENPQGHSGRVVEADPSGDNVTI +EFNLDGLSGKVESPKSAHETILNAALRVRSDVPFACAGGVCGTCRAKVTDGEYEMDENYA +LEKDEVEAGYVLTCQTRATSDSITVDYDA +>PROKKA_00767 +MTETTDAPITGKRRATFNTLEVSGLRKLTDDSVEVTFAVPEELADDYDYVPGQYVALRKE +LDGAELRRSYSICAVPQRGEIRVAVKKDLGGTFSTWANEVLEVGEKIDVMNPQGAFTSRT +NVTSMNDPEAVAAEAVKQDQTHLVALAAGSGITPIMAIAKSVLAASDSARFDLIYANRSA +MDVMFAEEIGDLKDKYPARFTVNHVLSREQRVAPLLSGRIDDEKLNTLLDRVIDVENTDE +WFLCGPFELVQLARDTLSERGVAEDDVRFELFTTGKPEAPQGQSGRGVEADPSGDNVTIE +FNLDGLSAKVESPKSAHETILNAALRVRSDVPFACAGGVCGTCRAKVTEGEFTMEENYAL +EKDEVEQGYVLTCQTRPTTDSIKVDFDA +>PROKKA_01950 +MTETTAAPTTGKRRATFNTLEVSELRRLTDDSVEVTFAVPEELADDYDYVPGQYVALRKE +LDGAEVRRSYSICAVPKRGEIRVAVKKDIGGKFSTWANESLEVGEKIDVMNPQGAFTSRT +HVTSLNDAQKVAAEKVAENKDTHLVAFAAGSGITPIMAIAKAVLAASESSRFDLVYANRS +AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDEDKLTTLLDRVIDVEGTD +EWFLCGPFELVQLTRETLAARGVSEDDVRFELFTTGRPENPQGHSGRVVEVDPKGDNVTI +EFNLDGLTAKVESPKSAHETVLNAALRVRSDVPFACAGGVCGTCRAKVVDGAYEMDENYA +LEKDEVEKGYVLTCQTRPTSDSITLDFDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001607.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001607.fa new file mode 100644 index 0000000000000000000000000000000000000000..88169a0f03cd5b46d0f5bddde852ff7c98167c4e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001607.fa @@ -0,0 +1,40 @@ +>PROKKA_02016 +MSAQSQALLVGGRRTPVGKYGGALSSVRPDDLAALTVKAVIEDAGIDPSVVDDVILGNAN +GAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAGGVE +SMSRAPWVMEKPTTAFAKPGAAFDTAIGWRFVNPRFADGEFGEKFTFSMPETAEEVGEVD +GITREDADAFAARSHERALAAIEAGRFADEIVPVVVTGRKGAETVVDTDEGPRPGSTPEV +LASLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLAPEI +MGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPETVNADGGAIALG +HPLGSSGSRLVVTLLGRMEREGADRGLATMCVGVGQGSAMLVERV +>PROKKA_01725 +MSAQSQALLVGGRRTPVGKYGGALSSVRPDDLAALTIKAVIEDAGIDPSVVDEVILGNAN +GAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAGGVE +SMSRAPWVMEKPTTAFAKPGAAFDTAIGWRFVNPRFADGEFGEKFTFSMPETAEEVGEVD +GITREDADAFAARSHERALAAIEAGRFADEIVPVVVTGRKGAETVVDTDEGPRPGSTPEV +LASLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLAPEI +MGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPETVNADGGAIALG +HPLGSSGSRLVVTLLGRMEREGADRGLATMCVGVGQGSAMLVEKV +>PROKKA_00805 +MTTPSPQPQALLVGGKRTAVGRYGGALSAVRPDDLAALTIKQVIEDAGIDPAAVDEVILG +NANGAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAG +GVESMSRAPWVMEKPTTAFAKPGAAFDTSIGWRFVNPRFADGEFGEKFTFSMPETAEEVG +EVDGITREDADAFAARSHGRAIAAIEAGRFKDEIVPVTVKGRKGAETVVDTDEGPRPGST +PEVLAGLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLA +PEIMGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPEIVNADGGAI +ALGHPLGSSGSRLVVTLLGRMEREGADRGLATMCVGVGQGSAMLVEKV +>PROKKA_00764 +MSAQSQALLVGGRRTPVGKYGGALSSVRPDDLAALTVKAVIEDAGIDPSVVDDVILGNAN +GAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAGGVE +SMSRAPWVMEKPTTAFAKPGAAFDTSIGWRFVNPRFADGEFGEKFTFSMPETAEEVGEVD +GITREDADAFAARSHERALAAIEAGRFADEIVPVVVTGRKGAETIVDTDEGPRPGSTPEV +LAGLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLAPEI +MGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPETVNADGGAIALG +HPLGSSGSRLVVTLLGRMEREGADKGLATMCVGVGQGSAMLVEKV +>PROKKA_01953 +MSAQSQALLVGGRRTPVGKYGGALSSVRPDDLAALTIKAVIEDAGIDPSVVDEVILGNAN +GAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAGGVE +SMSRAPWVMEKPTTAFAKPGAAFDTAIGWRFVNPRFADGEFGEKFTFSMPETAEEVGEVD +GITREDADAFAARSHARALAAIEAGRFADEIVPVVVTGRKGAETIVDTDEGPRPGSTPEV +LAGLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLAPEI +MGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPETVNADGGAIALG +HPLGSSGSRLVVTLLGRMEREGADRGLATMCVGVGQGSAMLVERV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001608.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001608.fa new file mode 100644 index 0000000000000000000000000000000000000000..133546bcd5b86574332cb0b6d158c8379a5038c1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001608.fa @@ -0,0 +1,30 @@ +>PROKKA_02017 +MTDFSHFSALHVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ +VESTREPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG +GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA +QEALELKLVTELHEPDALLDAADALADRIAQQDPLAVRLSKRVFHLPRGAHPHVDEIAQA +ILFESDAKFERMQAFLDRKKK +>PROKKA_01726 +MDDFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ +VESKCEPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG +GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA +QEALELKLVTELHEPEALLDAADALADRIAQQDPLAVRLSKRVFHLPREAHPHVDEIAQA +ILFESEAKFERMQAFLDRKKK +>PROKKA_00804 +MTDFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ +VESKREPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG +GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA +QEALELKLVTELHEPEALEVAAHALADRIAKQDPLAVRISKRVFHLPREAHPHVDEIAQA +ILFESEAKFDRMQAFLDRKKK +>PROKKA_00763 +MADFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ +VESKREPGRFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG +GGAELAYAADFRIATPALKMGQPETGLGITAAAGAQWRLKELVGEPVALELLLAGRILDA +QEALELKLVTELHEPDALLDAADALADRIAQQDPLAVRISKRVFHLPREAHPHVDEIAQA +ILFESQAKFERMQAFLDRKKK +>PROKKA_01954 +MTDFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ +VESTREPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG +GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA +QEALELKLVTELHEPDALLDAADALADRIAQQDPLAVRLSKRVFHLPREAHPHVDEIAQA +ILFESEAKFERMQAFLDRKKK diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001613.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001613.fa new file mode 100644 index 0000000000000000000000000000000000000000..f442e4cf554b2622fa1beb2e3ba20fcb83faff40 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001613.fa @@ -0,0 +1,65 @@ +>PROKKA_02023 +MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGARLTGVSTDGLDTAAAIEHART +VGQQALGALTIHERALKLKELALYLNSRVQELYDVSFATGATQRDHAFDVDGGIGTLFTF +SGKGRRELPNSNVIIDGDVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP +AFVAGVPTVVKPATPTGYVAQKCVELMLESGVLPEGSIQLISGSARDLLDHLDYRDHVAF +TGSAATAATLKKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVK +AGQKCTAIRRVIVPQDRVEAVTAALTERLAAKVVLGDPRVEGTTMGALASKEQQGEVRGA +VQRLVDAGGQVRLGGPEGSTGDADAESGAFFAPTVLTFEDARTPEVHSVEAFGPVTSVIG +YTDVADAVALAALGSGSLVATVATNDGETARAFAAGIGAHHGRVHVLNRQTATTTTGHGA +PVPVLIHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTRE +DVEAGTAVHPFYKSLAELTVGDQFASGLRTVTLEDITAFAEETGDRFYAHTDEEAAMANP +FFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFITPVTYDDAIRVTLTAKRITP +RVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG +>PROKKA_01732 +MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGARLTGVSTDGLDTAAAIEHART +VGQQALGELTIHERALKLKELALFLNSRVQELYDVSFATGATQRDHAFDVDGGIGTLFTF +SGKGRRELPNSTVIIDGDVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP +AFVAGVPTVVKPATPTGYVTQKCVELMLESGVLPEGSIQLISGSARDLLDHLDYRDHVAF +TGSAATAATLKKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVK +AGQKCTAIRRVIVPQDRVEAVTAALTERLAAKVVLGDPRVEGTTMGALASKDQQGEVRGA +VQRLVDAGGQVRLGGPEGSTGDADAESGAFFAPTVLTFEDARTPEVHSVEAFGPVTSVIG +YTDVADAVALAALGSGSLVATVATNDGETARAFAAGIGAHHGRVHVLNRQTAATTTGHGA +PVPVLIHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTRE +DVEAGTAVHPFYKSLAELTVGDQFASGLRTITLEDITAFAEETGDRFYAHTDEEAAMANP +FFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFITPVTYDDAIRVTLTAKRITP +RVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG +>PROKKA_00796 +MTVTLPSLPEILPSYVNGAWWTPQSPSKVTDVTDANTGERLTGVSTDGLDTAAAIEHART +VGRKSLGELTIHERALKLKELALYLNSRIQELYDVSFATGATQRDHAFDVDGGIGTLFTF +SGKGRRELPNSNVITDGPVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP +SFVAGVPTVVKPATPTGYVTQKCVELMLESGVLPEGSLQLISGSARDLLDHLDYRDHVSF +TGSAATAQTLRKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVK +AGQKCTAIRRVIVPQDRVDAVVEALSARLGKVVLGDPRVEGTTMGALASKEQQGEVRGAV +QRLVDAGGQVRLGGPDASTGDADAESGAFFAPTVLSFEDARTPEVHAVEAFGPVTSVVGY +TDVEDAVALAALGSGSLVATVATDDGETARAFAAGIGAHHGRVHFLNRQTATTTTGHGAP +VPVLVHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTRED +VEAGTAVHPFYKSLAELTVGDQFASGLRTVTLQDITDFAEETGDKFYAHTDEEAAMANPF +FPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFITPVTYDDAIRVTLTAKRITPR +VSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG +>PROKKA_00757 +MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGELMARVSTDGIDTAGAIEHART +VGQRNLGELTIHERALKLKELALYLNSRIQELYDLSFATGSTQRDHAFDVDGGIGTLFTF +SGKGRRELPNSNVIIDGDVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP +AFVAGVPTVVKPATPTGYVTEACVRMMVESGVLPEGSIQLISGSARDLLDHLDYRDHVAF +TGSAGTAQTLRQHENVLNGGVRFTAETDSLNAAILGPDAGVDTPEFEAFVKVVFQEMTVK +AGQKCTAIRRVIVPEAMVEDVTAALTERLSSTVVLGDPRAEGTTMGALASKEQQSEVRKA +VQTLVDAGGQVRLGGPEGSTGDADAEAGAFFAPTVLTFADADTPQVHSVEAFGPVTSVIG +YTDVADAVRLAALGSGSLVATLATNDGATASEFIAGIGAHHGRVHVLNRQTAKTTTGHGA +PVPVLIHGGPGRAGGGEELGGVRAVKHYMQRTAVQGSPDMLTAITGVWHQGAAAQTATRE +DVEAGKAKHPFYKALDELQIGDQFASGLRTVTIEDITAFAESTGDKFYAHTDEEAAMANP +FFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLDDLRFITPVTYDDAIRVTLTAKRITP +RVTDEYGEVAWDCRLHNQKDELVAQYDVLTLVAKTWPMPEAEPKA +>PROKKA_01960 +MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGARLTGVSTDGLDTAAAIEHART +VGQQALGALTIHERALKLKELALYLNSRVQELYDVSFATGATQRDHAFDVDGGIGTLFTF +SGKGRRELPNSTVIIDGDVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP +AFVAGVPTVVKPATPTGYVTQKCVELMLESGVLPEGSIQLISGSARDLLDHLDYRDHVAF +TGSAATAATLKKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVK +AGQKCTAIRRVIVPQDRVEAVTAALTERLAAKVVLGDPRVEGTTMGALASKEQQSEVRGA +VQRLVDAGGQVRLGGPEGSTGDADAESGAFFAPTVLTFEDARTPEVHSVEAFGPVTSVIG +YTDVADAVALAALGSGSLVATVATNDGETARAFTAGIGAHHGRVHVLNRQTATTTTGHGA +PVPVLVHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTRE +DVEAGTAVHPFYKSLAELTVGDQFASGLRTVTLEDITAFAEETGDRFYAHTDEEAAMANP +FFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFITPVTYDDAIRVTLTAKRITP +RVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001615.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001615.fa new file mode 100644 index 0000000000000000000000000000000000000000..9de06e85c69fb64a5c1152584ed6287e752cc3d0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001615.fa @@ -0,0 +1,33 @@ +>PROKKA_02025 +MTTSRLPLLGALAVGALALAGCAGGGAEPSSPAPSSASSTTTAASSASPAASSSTAPTSP +AASASTASMGGASASGSLSLEMPPALDGQRTLAVQAAVQRAAGPGSEVGLSAASPLERQT +ELRQRAAGLEQTVDAGASPASTRSAEQQACLDATRSDLERDAEAGAADLGLTAQPETAAT +TGGGPTSTPVPSFTASPDAEVTPLGVRVTVYPTEEAARAALEDARAAAQACTGVDLAGLG +VESVTRTEHEGGTAYTALPAPGGSVYSHLTAVQDGARTVAVAQADADGGVPADAEDRAAS +IVADVLAALDGEG +>PROKKA_01734 +MTTSRLPLLGALAVGALALAGCAGGGGAEPSSPAPSSASSTTTAASSAPTSPAASSSTES +TGAAESTAGASASGSLSLEMPPALDGQRTLAVQAAVQRAAGPGSEVGLSAASPLERQTEL +RQRAAGLEQAVDAGASPASTRSAEQQACLDATRSDLERDAEAGAADLGLTAQPETAATTG +GGPTTTPAPSFTASPDAEVTPLGVRVTVYPTEEAARAALEDARAAAQACTGVDLAGLDVE +SVTRTEHEGGTAYTALPAPGGSVYSHLTAVQDGARTVAVAQADADGGVPADAEDRAASIV +ADVLAALDGEG +>PROKKA_00794 +MTPSRLPLLGVLAVGALALAGCAGGGAEPSSPAPSPASSSASPTTTAASSASTSPAASAS +ASSTPTATALSLDLPEELSGESATRLRAVVQDAAGPAAELGQTFSSPLERRAALEEDAAI +VDALEEDAGDDAGRRACVDATRAAREADQASGAAQAAWYAQPQTASTTGGSTDGTAASGR +PGLQVEPLGVQVAVYPDEATARSVAEAARDAAEACEGQEMSSMGVSSVEPLTGAPGETAF +TVVPVSGSIIYAVSTVVQVGDRVYAVSQGEDGAGVPEGAEERAVALVEDLEAALEG +>PROKKA_00756 +MTHMTAVPSRRLRAGFALGAAALVLTGCAGGGGSASSSTAAGSPTAGGAGSSVTSPAASS +SAASSSALSLSMPDRFGNEARTGLTEAVTAAAPEGFEVTTRSVSPLERKTDLEDQATILT +DGPLEPAAEGSSASPTYTEAQQRCADAAAERFRTEAAAGGAQLRSDAMPTVAGGGYTSVR +ADVVAYPDVSAAVAALADGSAPIELCTDVQVPGAEQPTDIAPVTGIGDEAVGGELAGGRW +LAVRRGTDVVSVMVAGPGETAPAGAADQARALAEQVLEAVPAG +>PROKKA_01962 +MTTPRLPLLGALAVGALALAGCAGGGGAEPSSPAPSSASSTTTAASSASTSPAASSSTAP +TSPAASASTESTAGASASSSLSLEMPPALDGQRTLAVQTAVQRAAGPGSEVGLSAASPLE +RQTELRQRAAGLEQAVDAGASPAPTRSAEQQACLDATRSALERDAEAGAADLGLTAQPET +AATTGVGPTTTPAPSFTASPDAEVTPLGVRVTVYPTEEAARAALEDARAAAQACTGVDLA +GLGVESVTRTEHEGGAAYTALPAPGGSVYSHLTAVQDGARTVAVAQADADGGVPADAEDR +AASIVTDVLAALDGEG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001618.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001618.fa new file mode 100644 index 0000000000000000000000000000000000000000..c35c887085c59a2c50f2a9bb707286cb71843de7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001618.fa @@ -0,0 +1,19 @@ +>PROKKA_02028 +MTETAHHPMLAEDRVARWLGVTLEAAEKDHARIRMTLTEDQHNGFGLAHGGAVFAFADTC +FALTCNDPASDGSTLTVASGVDVNFLAATRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG +TPVAAFRGRSRTIPAPGR +>PROKKA_01737 +MTETAHHPMLAEDRVARWLGVTLEAAEKDHARIRMTLTEDQHNGFGLAHGGAVFAFADTC +FALTCNDPASDGSTLTVASGVDVNFLAATRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG +TPVAAFRGRSRTIPAPGR +>PROKKA_00791 +MTLTEDHHNGFGMAHGGAVFAFADSCFALTCNDPGGDGSTITVASGVDVNFLAGTRAGQT +LVAEGRLVAAAGRSAVYDITVTTDDGTPVAAFRGRSRTIPAPGR +>PROKKA_00752 +MTETPHHPALVGDRVARWLGVTLEAAEKDHARIRMTLGEEHHNAFGMAHGGVVFAFADCC +FALTCNDPASDGSTLTVASGVDVNFLSGTRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG +TLVAAFRGRSRTVAVKGA +>PROKKA_01965 +MTETAHHPMLAEDRVARWLGVTLEAAEKDHARIRMTLTEDQHNGFGLAHGGAVFAFADTC +FALTCNDPASDGSTLTVASGVDVNFLAATRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG +TPVAAFRGRSRTIPAPGR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001622.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001622.fa new file mode 100644 index 0000000000000000000000000000000000000000..abd4535e1bc09a29a250c8ddc39dce184ff616d2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001622.fa @@ -0,0 +1,36 @@ +>PROKKA_02036 +MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT +RDILLDRGLPASLENPVYLAPPLLVSLLVYVKVIHPNRLNLTITLFDAAGLALFTVSGVL +LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM +NGALNAFTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLARLRRLATQAQEAAARRV +ERTLERRLRSPGAPAFPDDDADGSYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRL +DRGTGVMDVTDLRTGRTRSFDDPEHDWIADDPEDEKG +>PROKKA_01743 +MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT +RDILLDRGLPASLENPVYLAPPLLVSLLVYVKVIHPNRLNLTITLFDAAGLALFTVSGVL +LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM +NGALNGYTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLERLRRLATQAQEAAARRV +ERTLERRLRSPGAPAFPDDDTHGSYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRL +DRGTGVMDVTDLRTGRTRSFDDPEHDWIADDPADPRD +>PROKKA_00780 +MDVQQFFADLSDVPWLLTTLDLIGIFFFATSGALLASRKEFDLVGSMALALLAGLGGGFT +RDILLDRGLPASLENPIYLAPPVLVSLLVYVKALHPNRLNLTITLFDAGGLALFTVSGVL +IAHSMDVHPVSTVVVAMVAALGGGVLRDIVANEVPSIFDPRGVYVMPTFVGATVATIAAM +NGVLNAFTGFLIAFLIFAVRMLAYRYQWRLFGADISQDKESLDRLRRLATQAQDAAARRV +ERARERRLRSASGPGGMDVGEAEAIADRAVHHPPAPAGYHYDAVEDAYTRDHAFDDDGEP +GSASYGPRQEYEDQVRVDEYDPETQTITVIDPASRQQVRLDPATGVMDVTDLRTGRTRSY +DDPEHDWIADDAEDDARG +>PROKKA_00747 +MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT +RDILLDRGLPASLENPVYLAPPVLVSLLVYVKLIHPNRLNLTITLFDAAGLALFTVSGVL +LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM +NGALNAFTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLERLRRLATQAQEAAARRV +ERTLERRLRAPGAPAFPDDDTHGSYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRL +DRGTGVMDVTDLRTGRTRSFDDPEHDWIADDPEDSRD +>PROKKA_01971 +MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT +RDILLDRGLPASLENPVYLAPPLLVSLLVYVKVIHPNRLNLTITLFDAAGLALFTVSGVL +LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM +NGALNGYTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLERLRRLATQAQEAAARRV +ERTLERRLRSPGAPAFPDDDTHGSYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRL +DRGTGVMDVTDLRTGRTRSFDDPEHDWIADDPADPRD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001628.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001628.fa new file mode 100644 index 0000000000000000000000000000000000000000..7d8801e2b519483f01f78c0b42f3cf6cb66199d1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001628.fa @@ -0,0 +1,25 @@ +>PROKKA_02056 +MLSLYIHGDSPLHHARAGLKTGLFAVWVLALTLLPLSRWTAGAAVVGAVTAYLVGFGLRR +GAAMIASDLHALWLFYVVLFAAQWIFTDAFAAGLMVARVLGLVLTAQVLTRTTRIADMAG +VAEAMLRPVERIPWAGPRLARAGFRADRVGLAMGLVLSSIGHLRALAEQIRHAQAARGVR +MAPWAWALPLLVLSFKHADDVGDALAARGID +>PROKKA_01762 +MLSLYIHGDSPLHHARAGLKTGLFAVWVLALTLLPLSLWTAGAAVVGAVTAYLVGFGLRR +GAAMIASDLRALWLFYVVLFAAQWIFTDAFAAGLMVARVLGLVLTAQVLTRTTRIADMTG +VAEAVLRPVERIPWAGPRLARAGFRADRVGLAMGLVLSSIGHLRALAEQIRHAQAARGVR +MAPWAWALPLLVLSFKHADDVGDALAARGID +>PROKKA_00764 +MISLYVPGDSPLHRAPAGLKLALFAAWALAVTLAPPTPWTAGAAVGMALAAYLTGFGPRR +GAAMLGRDLRALWVFYAFLFAAQWLFADLTAAALMVGRVLGLVLAAQVLTRTTRIAELVG +VAEAVLAPVERIPWLGPRLARVGLRPERVGLAMGLVLASIGHLRSVAEQVRQAQASRGVR +MAPWAWVLPLLVLSVKHADDVGDALAARGIE +>PROKKA_00728 +MLSLHVPGDSPLHRCPAGAKVAALAVWALVVTLAPVSALTAGASVVVGVGAYLLGFGLRR +GVRLLAADLRGLWVFYAVLFAAQWLFTDLPTAALTTARVLGLVLAAQVLTRTTRIAEMAG +VAEAVLGPVTRIPWLGPRLARAGVRPDRVGLAMGLVLASVGHLRGLAEQIRAAQAARGVR +MAPWAWVLPLLVLSLKHADDVGDALAARGID +>PROKKA_01990 +MLSLYIHGDSPLHHARAGLKTGLFAVWVLALTLLPLSLWTAGAAVVGAVTAYLVGFGLRR +GAAMIASDLRALWLFYVVLFAAQWIFTDAFAAGLMVARVLGLVLTAQVLTRTTRIADMTG +VAEAVLRPVERIPWAGPRLARAGFRADRVGLAMGLVLSSIGHLRALAEQIRHAQAARGVR +MAPWAWALPLLVLSFKHADDVGDALAARGID diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001629.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001629.fa new file mode 100644 index 0000000000000000000000000000000000000000..e001403f39d69a964910443be22fb15c581b48a9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001629.fa @@ -0,0 +1,29 @@ +>PROKKA_02057 +MSPDRSVTLTGVRVEADGPEGAVVLLDGVDLTLAAPRVAVIGENGSGKSTLARAIAGLAD +VVAGEVTVHGVDAVRDVKALRRTVGFVFANPAAQMVMPTVREDVELTVKSLRDDAGRRLT +KDDVAARVAAALQEHRLTALADRACLSLSSGQAQRLAMCSVMTAGPSLVIADEPTSLLDG +RHRRIVADRLLAADPSAPDGFQLLLVTHDLELARACDEAVWIHSGRVERTGPAEEVVEAY +ERFLDHAVAAELR +>PROKKA_01763 +MSPDRSVTLTGVRVEADGPEGVVVLLDGVDLTLTAPRVAVIGENGSGKSTLARAIAGLAD +VVAGEVTVHGVDAVRDVKALRRTVGFVFANPAAQMVMPTVREDVELTVKSLRDDAGRRLT +KDDVAARVAAALQEHRLTALADRACLSLSSGQAQRLAMCSVMTTGPSLVIADEPTSLLDG +RHRRIVADRLLAADPSAPDGFQLLLVTHDLELARACDEAVWVHGGRVERTGPAEDVVEAY +EHFLDHAVAAELR +>PROKKA_00763 +MEQTTGVRLRGARVEADGPEGVVALLQDVDLDLTAPRVAVVGENGSGKSTLARAVAGLVD +VVAGEVTVHGVDAVRDVKALRRVVGMVFANPAAQAVMPTVREDVELTVKSLRDDDGRRLS +KDDVAARVAAALAEHRLTELAERPCLALSSGQAQRLAMCSVMAGRPRLVIADEPTSLLDG +RHRRIIADRLLAADGFQLLLVTHDLELARACDDAVWVHEGRVRAVGPAGEVVDAYAAFLD +EAVAAESAEAAAGDPAAVNPAGASAEARP +>PROKKA_00727 +MTGRTPPTRAPHDDDAAVRLAGVQVAAPGGPVLLDGVDLHLTAPRVAVVGENGSGKSTLA +RAVAGLAEVTAGEVAVHGVDAVRDVKALRRTVGMVFANPAAQMVMPTVREDVELTVKALT +DDAGRRLSRAEVAARVDAALAEHRLTDLAERPCLSLSSGQAQRLAMCSVLVGAPRLVIAD +EPTSLLDGRHRRIVADRLLGGAERGEFQLLLVTHDLDLARACDAAVWVHSGRVERHGPAA +ETVAAYEAFLDDAVARELA +>PROKKA_01991 +MLLDGVDLTLTAPRVAVIGENGSGKSTLARAIAGLADVVAGEVSVHGVDAVRDVKALRRT +VGFVFANPAAQMVMPTVREDVELTVKSLRDDAGRRLAKDDVAARVAAALEEHRLTALADR +ACLSLSSGQAQRLAMCSVMTAGPSLVIADEPTSLLDGRHRRIVADRLLAADPSAPDGFQL +LLVTHDLELARACDEAVWIHGGHVERTGPAEDVVEAYERFLDHAVAAELR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001630.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001630.fa new file mode 100644 index 0000000000000000000000000000000000000000..34f66bbd9ec4f6d0975ae1a9de647526906fd63e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001630.fa @@ -0,0 +1,25 @@ +>PROKKA_02058 +MSTSVPSSHDGHVRPAATTTADRPTDAGRPRRGSAGGSLARIAVMTALMAVLGLVPPIAV +AGVPAPIVLQNIAVILAGVILGPWRGAASMALFAGLVALGLPLLSGGRGGLGVFAGPTAG +FILGWIPSALIVGLIFWALTSRARPGLDAGRVALGAAVAGLIGGVVMVYFFGVLGFVGIA +GMEFGAAVLSMAPFVPGDLIKLVVSVILIVGLWKAYPRAFR +>PROKKA_01764 +MSTSVPSSHDGHVRPAATTTADRPTDAGRPRRGSAGGSLARIAVMTALMAVLGLVPPIAV +AGVPAPIVLQNIAVILAGVILGPWRGAASMALFAGLVALGLPLLSGGRGGLGVFAGPTAG +FILGWIPSALIVGLIFWALTSRARPGLGAGRVALGAAVAGLIGGVVMVYFFGVLGFVGIA +GMEFGAAVLSMAPFVPGDLLKLVVSVILVVGLWKAYPRAFR +>PROKKA_00760 +MPTSDTLASGRPAHSTDDRRPRRSSAGSGLARVAVFAALMAVLGLVPPVPVAGIPAPIVL +QNLAVTLAGVILGPWRGAAAILLFNVLVALGLPLLTGGRGGLGVFVGPSSGFILGYVVAA +AAVGLVFWALTGRARPGLRPGRVLAAALVAGLVGMVVLYAAGAVGFIVAAHMEPGAAVLA +MGAFVPGDTVKVVLAALLVTGLWKAYPRAFR +>PROKKA_00723 +MTSPSAPQTAVVDAPATHRPRRSPGADLARIAVMAALIAVLGAMPGIPVPGIPTPITLQT +LGVMLAGLVLGAWRGAASVALFHLLVALGLPLLAGGRGGAAVFVGPSAGFLWGWIPGAFV +VGLLFHLYLRGRRDGRNTGGLVAAALTACVVGGIAVIYLFGIPGMNLFGGVPLDKAAIGS +LAFIPGDLLKAVVAALLAAGLWKAYPRAFA +>PROKKA_01994 +MSTSVPSSHDGHVRPAATTTADRPADAGRPRHGSAGGSLARIAVMTALMAVLGLVPPIAV +AGVPAPIVLQNIAVILAGVILGPWRGAASMALFNALVALGLPLLTGGRGGLGVFVGPSVG +FILGWIPSAMIVGLIFWALTSRSRPGLSAGRIALAAAVAGLIGGVIMVYVFGAFGFVGVQ +GMEFGAAMLSMAVFVPGDLTKLVIAVLLCAGLWKAYPRAFR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001632.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001632.fa new file mode 100644 index 0000000000000000000000000000000000000000..66feb5bf453f93ad38b355304301c58f4b4d3ca3 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001632.fa @@ -0,0 +1,29 @@ +>PROKKA_02080 +MNLDQLQALRAIADEGSFEAAAYELDVSASAVSQRIRALEREVGQVLLRRGTPCEPTEAG +IGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPADVLGTWFGPVLAEAADWEDTVLD +LHVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAGPLGSMRYVPLASPALLARHAADDVV +DLGAMPMMRYNAKDDLQRLALSGAGLDIAPPTHLAPSFDGFHRSVRAGLGWGMLVDAQAV +EDVRAGRLVRVPGLDDVLVPLYWQAATLPVTRLVRLTRAVREAAQRTLERG +>PROKKA_01784 +MPKLCFMNLDQLQALRAIADEGSFEAAAYELGVSASAVSQRIRALEREVGQVLLRRGTPC +EPTEAGVGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPADVLGTWFGPVLAEAADW +DDTVLDLHVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAEPLGSMRYVPLASPALRARH +AAGDVVDLGAMPMMRYNAKDDLQRLALSGAGLDVAPPTHLAPSFDGFHRSVRAGLGWGML +VDAQAVEDVRAGRLVRVPGLDDVLVPLYWQAATLPVTRLVRLTRAVREAAQRTLERG +>PROKKA_00704 +MNLDQLQVLLRRGTPCEPTEAGVGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPAD +VLGTWFGPVLAEAADWDDLVLDLHVEDQDHSAQLLRRGEVLAAVTTEPQPVQGCAAEPLG +SMRYVPLVAPALLARHAAGDVVDLGAMPMMRYNVKDDLQRLALSDAGLDVAPPTLPVTRL +VRLTRAVREAAQRTLEPG +>PROKKA_00614 +MNLDQLQALRAIADEGSFEAAAYELGVSASAVSQRIRALEREVGQVLLRRGTPCEPTEAG +VGLVRVARHMRVLEQEAWAGLGRMAAGRSVTSLAVPADVLGTWFGPVLAEAADWDDTVLD +LRVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAEPLGSMRYVPLASPALLARHAAGDVV +DLGAMPMMRYNAKDDLQRLALSGAGLDVAPPTHLAPSFDGFHRSVRAGLGWGMLVDAQAV +EDVRAGRLVRVPGLDDVLVPLYWQATTLPVTRLARLTQAVREAAQRTLERG +>PROKKA_02018 +MPKLCFMNLDQLQALRAIADEGSFEAAAYDLGVSASAVSQRIRALEREVGQVLLRRGTPC +EPTEAGVGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPADVLGTWFGPVLAEAADW +DDTVLDLHVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAEPLGSMRYVPLASPALLARH +AAGDVVDLGAMPMMRYNAKDDLQRLALSGAGLDVAPPTHLAPSFDGFHRSVRAGLGWGML +VGAQAVEDVRAGRLVRVPGLDDVLVPLYWQAATLPVTRLVRLTRAVREAAQRTLERG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001633.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001633.fa new file mode 100644 index 0000000000000000000000000000000000000000..655e478b88c2b65651b05f3ae7ddad1e44089f55 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001633.fa @@ -0,0 +1,25 @@ +>PROKKA_02081 +MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA +LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVVATTLALTWLN +PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPKAWRV +VDVVIAVVMAVLAVRLIAGSGVWG +>PROKKA_01785 +MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA +LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVIATTLALTWLN +PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPKAWRV +VDVVIAVVMAVLAVRLIAGSGVWG +>PROKKA_00703 +MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA +LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALHPQGLVAEQAPRTAGSVIATTLALTWLN +PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPTAWRV +VDVVIAVVMAVLAVRLIAGSGVWG +>PROKKA_00613 +MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA +LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVIATTLALTWLN +PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASILWFTALGYGARLLARVLADPKAWRV +VDLVIAVVMAVLAVRLIAGSGVWG +>PROKKA_02019 +MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA +LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVVATTLALTWLN +PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPKAWRV +VDVVIAVVMAVLAVRLIAGSGVWG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001634.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001634.fa new file mode 100644 index 0000000000000000000000000000000000000000..ce1d8f4b741055e6f4611d481bb57049abdc1c6d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001634.fa @@ -0,0 +1,20 @@ +>PROKKA_02082 +MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA +MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV +SYQQRKRGERRASLSDLVGEASSAGLYDQKAESYREALRQARADLRGERG +>PROKKA_01787 +MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA +MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV +SYQQRKRGERRASLSDLVGEASSAGLYDQKAESYREALRQARADLRGERG +>PROKKA_00701 +MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA +MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV +SYQRRKRGERRAALSDLVGEASSAGLYGQNAESYREALRQARADLRGERG +>PROKKA_00611 +MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA +MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV +SYQQRKRGERRAALSDLVAEASSAELYDQKAESYREALRQARADLRGERG +>PROKKA_02021 +MTATVNDKHTVLPPTDLEEMLDVGRFLDGLTQPAALVGPDGQKVPLPPEAFNVLRDVVEA +MRVGKAITVAPVDQLLTTQEAANFLGISRPTLVRLLEEGALPYERTTGGRHRRIRLQDVV +SYQRRKRGERRASLSDLVGEASSAGLYDQKAESYREALRQARADLRGERG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001638.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001638.fa new file mode 100644 index 0000000000000000000000000000000000000000..22e13c88d42f98cc75b0ac58d809c18d7b4a6e1a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001638.fa @@ -0,0 +1,45 @@ +>PROKKA_02086 +MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE +YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH +RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH +DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA +EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG +LPDHPGHALAARQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE +MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGAPPSSAVPRPA +PAHHRTTRARTPERTR +>PROKKA_01791 +MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE +YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH +RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH +DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA +EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG +LPDHPGHALAARQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE +MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGAPPSSAVPRPA +PAHHRTTRARTPERTR +>PROKKA_00697 +MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE +YSRGSNPTRNGFETQLAALEHGERAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH +RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH +DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA +EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG +LPDHPGHDLAARQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE +MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAVGRGTPSSSAVPRPA +PAHHRTTRVRTPERTR +>PROKKA_00607 +MTAVHHPTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE +YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH +RLITTVLEPWGVSNTPVDITDTTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH +DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA +EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG +LPDHPGHDLATRQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE +MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGTPSSSAVPRPA +PAHHRTTRVRTPERTR +>PROKKA_02025 +MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE +YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH +RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH +DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA +EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG +LPDHPGHALAARQMDGFGGIVSIRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE +MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGAPSSSAVPRPA +PAHHRTTHARTPERTR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001642.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001642.fa new file mode 100644 index 0000000000000000000000000000000000000000..717bb8754eb40f2144ed6eb35be67d8e6252da9f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001642.fa @@ -0,0 +1,43 @@ +>PROKKA_02095 +MSPSAPQRRAARAATFAATLAAAAIALTACGADAAPFSPASAPASASDGAESPAGEATAA +SSVSEEDRVDPTQTTEVSAVTPRILLSHEDGLTLLDAESGEVVKEQDVTGFTRLSNAGNG +KDVLVTTGNGWEVFSTGIQAKAHGDHVHHYESAPGMTGVTFPGEHPGHVVTHNGRTTLFA +DGTGAIRTFDSTHLDKATPDLMPVMTEAETEDPHHGVALELSDGALFTTQGTEDSRDALQ +VIDPKTGEVTAETDDCPGSHGEAAAQPTEAGDVVVMGCENGPVVYRDGEFHKVDVETEYQ +RSGNLFGLHDSPIVLGDHKVEEEPKEAVERPTEIALIDTRTDELTTVDLGSSYWFRSLGR +AEDGSAVVLTYDGEANVIDEETGEVTAEYPVIEPWKEKDEWQEPGPILKVAGNTAYVTDA +EAQKLVAVDLETGETVLEKDLEFAPVEMAVVTGQPESVKPDEAADAASGHDEHTDHDH +>PROKKA_01803 +MSHSAPQRRSARTAALSATLAAAAIALTACGADAAPSGPTSAPAPAADGAESPSGEARAA +SSVSEGDRVDPTRTTEVSAVTPRILLSHEGGLTLLDAESGEVVREQDVPGFTRLSNAGNG +KDVLVTTGNGWEVFSTGIQAKAHGDHVHHYESAPGMTGVTFPGEHPGHVVTHNGRTTLFG +DGTGAIRTFDSAHLDKATPDLMPVMTEAETEDPHHGVALELSDGTLFTTQGTEDSRNTLQ +VIDPKTSEVTAETDDCPGSHGEAAAQPTEAGDVVVMGCENGPVVYRDGEFHKVDVETEYQ +RSGNLFGLHDSPIVLGDHKVEEEPEEAVERPTAIALIDTRTDELTTVDLGSSYWFRSLGR +AEDGSAVVLTYDGEVTVIDEETGEVTAEYPVIEPWKEKDEWQEPGPILKVAGNTAYVTDA +EAQKLVAVDLETGETVLEKDLEFAPVEMAVVTGEPESVKPEEGADAESGHDEHADHDHGH +ESDEHTDHDH +>PROKKA_00683 +MSHSAPQCRSTRTAASDGAESTSGETTAASSVSEEERVDPTRTTEVSAVTPRILLSHEDG +LTLLDAESGEVVKEQDVPGFTRLSDAGNGKDVLVTTGNGWEVFSTGIQAKAHGDHVHNDE +SAPGMTGVTFPGEDPGHVVTHNGRTTLFADGTGAIRTFDATHLDKATPDLMPVMTEAETE +DPHHGVALELYDGTLFTTQGTEDSRDTLQVIDSTTGEVTAETDDCPGSHGEAAAQPTEAG +DVVVTGCENGPVVYRDGEFHKVEVETEYQRSGNLFGLHDSPIVLGDHKVEEEPTEAVERP +TAIALIDTRTDELTTVDLGSSYWFRSLGRAEDGSAVVLTYDGEVNVIDEETGEVTAEYAV +IEPWKEKDEWQEPGPILKVAGNTAYVTDAEAQKLVVVDLETGETVLEKDLDFAPVEMAVV +TGQPESVKPEEAADAESGHDEHTDHDH +>PROKKA_00598 +MTPRILLSHEDGLTLLDAESGEVVKEQDVAGFTRLSNAGNGKDVLVTTGNGWEVFSTGIQ +AKAHGDHFHNYESAPGMTGVTFPGEHPGHVVTHNGRTTLFADGTGAIRTFDSAHLDKATP +DLMPVMTEAETEDPHHGVALELSDGTLFTTQGTEDSRNTLQVIDPTAGEVKAETDDCPGS +HGEAAAQPTEAGDVVVMGCENGPVVYRDGEFHKVDVETEYQRSGNLFGLHDSPIVLGDYK +VEEEPKEAVERPTEIALIDTRTDELTTVDLGSSYWFRSLGRAEDGSAVVLTYDGEVNVID +EETGEVTAEYPVIEPWKEKDEWQEPGPILKVAGNTAHVTDAEAQKLVAVDLETGETVLEK +DLEFAPVEMAVVTGQRESVKPEEAADAESGHDEHTDHDH +>PROKKA_02034 +MTGVTFPGEHPGHVVTHNGKTTLFADGTGAIRTFDSAHLDKATPDLMPVMTEAETEDPHH +GVALELSDGALFTTQGTEDSRNTLQVIDPKTGEVTAETDDCPGSHGEAAAQPTEAGDVVV +MGCENGPVVYRDGEFHKVDVETEYQRSGKLFGLHDSPIVLGDHKVEEEPKEAVERPTEIA +LIDTRTDELTTVDLGSSYWFRSLGRAEDGSAVVLTYDGEVNVIDEETGEVTAEYPVIEPW +KEKDEWQEPGPILKVAGNTAYVTDAEAHKLVAVDLETGETVLEKDLEFAPVEMAVVTGQP +ESVKPEEGAHGDEDHDDDGHEGHDHGAEPSEGHEGHDH diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001643.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001643.fa new file mode 100644 index 0000000000000000000000000000000000000000..dafbd9a1780520d8bbedbf84e6f2fda4b4b3ed33 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001643.fa @@ -0,0 +1,54 @@ +>PROKKA_02099 +MASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRA +GARNPSDLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRI +ADIVGTAADTAGVAQLVYLSGLHPDTVPVAELSDHMRSRALVAERLERAATPALTFEAGV +IIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQACALPEPVQLRAQI +GNGHPQSFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLA +EEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPS +DPEWAGTTVYTDERERESDLPAQEVWPVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGL +TRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQLSTEPREGGGSVYRQ +RAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRL +PLRRNPLDRRARGAGGAQSRD +>PROKKA_01806 +MASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRA +GARNPSDLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRI +ADIVGTAADTAGVAQLVYLSGLHPDTVPVAELSDHMRSRALVAERLERAATPALTFEAGV +IIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQACALPEPVQLRAQI +GNGHPQSFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLA +EEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPS +DPEWAGTTVYTDERERESDLPAQEVWPVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGL +TRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQLSTEPREGGGSVYRQ +RAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRL +PLRRNPLDRRARGAGGAQSRD +>PROKKA_00680 +MGGRLIPELLAAGFDVRAGARNPSDLADRPWSEGVEAVELDLTEADLVEAAMQDVHTVLY +LVHSMGGGGDFVTQEQRIADIVGTAADTAGVAQLVYLSGLHPDTIPVAELSDHMRSRALV +AERLEQAATPALTFEAGVIIGSGSTSFEMIRHLAERLPVMPGPSWLKNRVEPLAIRDVLY +YLLQACALPEPVQLRAQIGNGHPQSFASVLVDYAKAAGLSRRIVIPTPFPLQTLAGFWIG +TVTPIPVAVALPLAASLAEEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDV +TFDADVHAAADPADPLPSDPAWSGTTVYTDERERESDLPPQDVWPVIESVGGANGWYSTP +MLWKVRGLADKLVGGPGLIRGRRDQDRLRRGDAVDWWRVEDVEHGRRLTLRAEMKAGGRA +WLQMSTEPRDGGGSVYRQRAIFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEAQRRTT +GGERRRPRSLARALVDRLPLRRNPLDRGASA +>PROKKA_00594 +MSTPSTSRGSGLTSAAASGDTPAGTGATTASLSPLGLALPDGHDRRVLVTGATGYVGGRL +IPELLAAGFRVRAGARTPRDLEDRPWSDRVEVVELDLEKPDLVKAAMQDVHTALYLVHSM +GAGGDFVEQEQKIADIVATAADEAGITQLVYLSGLHPAGKPVEELSDHMRSRALVAERLE +AAATPALTFEAGVVIGSGSASFEMIRHLSERLPIMPGPSLLKNRVEPIAVRDVLHYLVQA +CALEEPVQLHAQIGNGRPQSFASVLVDYAEVAGLSKRIVIPTPLPLSRLAGLWVGVVTPI +PVKVALPLAASLAEDAVVEDHAIRDVIPAPEGGLTSYKEAVRRALAAEKNGPLDVTFEAD +VYDSSDPAAPLPSDPEWAGHTVYTDDRERESDLAPEDVWPVIESIGGRNGWYSTPLLWKV +RGYMDKVVGGPGLMRGRRDQDHLRRGDAVDWWRVEEVDPGHRLTLRAEMKAGGRAWLQLT +TEPREQGGSVYRQRAIFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEAERRRTGGARR +RTRGLVRALADRLPLRRSPLDRRAG +>PROKKA_02039 +MASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRA +GARNPSDLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRI +ADIVGTAADTAGVAQLVYLSGLHPDTVPVAELSDHMRSRALVAERLERAATPALTFEAGV +IIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQACALPEPVQLRAQI +GNGHPQPFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLA +EEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPS +DPEWAGTTVYTDERERESDLPAQEVWPVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGL +TRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQLSTEPREGGGSVYRQ +RAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRL +PLRRNPLDRRARGAGGAQSRD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001649.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001649.fa new file mode 100644 index 0000000000000000000000000000000000000000..a64a81da57e31316ffb5ee8a5a328c82859ac31d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001649.fa @@ -0,0 +1,36 @@ +>PROKKA_02107 +MGEARTGGEAALSGVTAELDAALRHAAAQAPGSAAFAELLDSLHVHVGAGKLIRPRLVEL +GWRLATADPVPPSGRAAVDRLGAAFELLHTALLVHDDVIDRDVLRRGQPAVHASARHRLE +ARGVPAADAAHAGVAVALIAGDVLLTQAFRLAATCAADTARAAEAAAVVFDAAAVTAAGE +LEDVLLGLSRHTGEEPDPDRILAMQRLKTAHYTVGAPLRAGALLAGADPDLARAMGEAGA +DLGAAYQVIDDVLGVFGDPGETGKSADGDLREGKATVLTAHGRRIPAVRALLDAGPATPA +DIEAARRALEAAGAREHALDVAAELTVRARERIAALPLDETVRAEFADACHAVLTRRS +>PROKKA_01814 +MGEARTGGEAALSGVTAELDAALRHAAAQAPGSAAFAELLDSLHVHVGAGKLIRPRLVEL +GWRLATADPVPPSGRAAVDRLGAAFELLHTALLVHDDVIDRDVLRRGQPAVHASARHRLE +ARGVPAADAAHAGVAVALIAGDVLLTQAFRLAATCAADTARAAEAAAVVFDAAAVTAAGE +LEDVLLGLSRHTGEEPDPDRILAMQRLKTAHYTVGAPLRAGALLAGADPDLARAMGEAGA +DLGAAYQVIDDVLGVFGDPGETGKSADGDLREGKATVLTAHGRRIPAVRALLDAGPATPA +DIEAARRALEAAGAREHALDVAAELTVRARERIAALPLDETVRAEFADACHAVLTRRS +>PROKKA_00672 +MSAGREGVVAELEAALSRAAGLAPESAAFAELLAGLRTHAGAGKLIRPRLVELGWRAAAD +GPVPAAERPAVDRLGAAFELLHTGLLVHDDVIDRDVVRRGERTVHEATRRRLAARGVPEA +EAAHAGTAVALIGGDVLLVEALRLAMTCTPDPGRAAPVAAVVLDAATASAAGELEDVLLG +LARHTGEEPEPERILAMQRLKTAHYTVSAPLRVGGAAGGGGSRRRRGAGEAAAPTWAWPT +RWWTTCSGCSAPRSRPASPPTATCARARPPCSPRTAAATPPSAPCSTPAPATPEELEAAR +RALEAAGAREHALQVAEELTRRAAEHLAVLPLGEAACAEFADACHAVLTRSS +>PROKKA_00588 +MNPLAAGIGGAAPWSASAATPGLDDAGRARAAVRAELDRVFAETPLCADAPDSFHLLWAR +LREAVSGGKLVRPRLVDLGWRTVRRAPASSGVPRGGTGEEEAADLRAVARVGAAFELLHA +ALIVHDDVIDRDDLRRGRPTVAEQYRRDAVRDGVPAGEAEHVGRSAGIIAGDLLLTAAFR +LAAASGARVRAAEAAESVFRAASAAAAGELEDVLLALHRHTGHHPEAGRILTMERLKTAG +YSFEEPLRAGALLAGADPAHAEALAEAGALLGVAYQVVDDVLGTAGDPAVTGKPHDADLR +EGKATLLTAHGRRDPRARAALDRVARAERHGEDLGELAAAVAEARAALVDAGSVEHALGV +AEELVDQARALLDALPMAPAERAEFAATCGQILQREA +>PROKKA_02047 +MGEARTGGEAALSGVTAELDAALRHAAAQAPGSAAFAELLDSLHVHVGAGKLIRPRLVEL +GWRLATADPVPPSGRAAVDRLGAAFELLHTALLVHDDVIDRDVLRRGQPAVHASARHRLE +ARGVPAADAAHAGVAVALIAGDVLLTQAFRLAATCAADTVRAAEAAAVVFDAAAVTAAGE +LEDVLLGLSRHTGEEPDPDRILAMQRLKTAHYTVGAPLRAGALLAGADPDLARAMGEAGA +DLGAAYQVIDDVLGVFGDPGETGKSADGDLREGKATVLTAHGRRIPAVRALLDAGPATPA +DIEAARRALEAAGAREHALDVAAELTVRARERIAALPLDETVRAEFADACHAVLTRRS diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001653.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001653.fa new file mode 100644 index 0000000000000000000000000000000000000000..4c3fe02c625ef77c71cb75a3ebab36ab1fa7d494 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001653.fa @@ -0,0 +1,20 @@ +>PROKKA_02114 +MGTQDPRARLLEKLAKVNVCMLTTAEPDGTLVTRPMGLQQAEDGGTLWFLTRATSDVAAD +APQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNPATEAFFGEGSSPEDPQIVLVRV +DVQTAQFWESPGAVATAVELVKAKVTGGEAHPGDSETVRF +>PROKKA_01822 +MGTQDPRTHLLEKLAKVHVCMLTTAEADGTLVTRPMGLQQAEDGGTLWFMTRSTSDVAAD +APQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNSATEAFFGEGSSPEDPQIVLVRV +DVNTAQFWESPGAVATAVEMVKAKVTGGTAEPGDSETVRF +>PROKKA_00666 +MGHKDPRTHLLEKLEKSNVCMLTTSETDGTLTTRPMGLQKAEETGTLWFMTRAASDVASD +ASQRPVNVSVQDKDFWASVAGHGQVVRDDARKKEFWNPATEAFFGEGAKPEDPQIVLVRV +DVESAQYWESPGAVGTVVELIKAKVTGGEAHPGESTTVQF +>PROKKA_00582 +MTEQDPRTALLEKIEKAGVVMLTTAEEDGTLASRPMAVQEVEQEPGVLWFITRATGDAAQ +DSAGRPVNVAVQEKGFWASVAGHGEIVRDEARKTEYWNSATEAFFGEGARPEDPQIVLVR +VQADSAEYWDGGGAASVVEIVKAKVTGGEARPGDHDTVEF +>PROKKA_02052 +MGTQDPRARLLEKLAKVNVCMLTTAEQDGTLVTRPMGLQQAEDGGTLWFLTRATSDVAAD +APQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNPATEAFFGEGSSPEDPQIVLVRV +DVDTAQFWESPGAVATAVELVKAKVTGGTAEPGDSETVRF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001654.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001654.fa new file mode 100644 index 0000000000000000000000000000000000000000..58a7a702d1c14e1ede10d4ad9725cdd39faa2e18 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001654.fa @@ -0,0 +1,45 @@ +>PROKKA_02115 +MSDYQPRRPGSKPTPNRQRDRAGKPALGRPERGLIDESEARQLAEDRERMRRAGVGHQLS +APKRREAATAERPQVMPKTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLKERQEKA +KEIGLPAFRAKQLSVHYFEHYTTDPEQMTDLPKDKREAIAEAFFPPLLTEVRRMETDRGD +TIKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTAEIVE +QIVLANQVIAQGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPSPEG +LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID +AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW +TASEKDVTREFVDRLNAAGIPTTLRDTRGKEIDGACGQLAAEDVD +>PROKKA_01823 +MSDYQPRRPGSKSTPNRQRDRAGKPALGRPERGLIDESEARQLAEDRERMRRAGVGHQLS +APKRREAATAERPQVMPKTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLKERQEKA +KEIGLPAFRAKQLSVHYFEHYTTDPEQMTDLPKDKREAIAEAFFPPLLTEVRRMETDRGD +TVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTAEIVE +QIVLANQVIAQGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPSPEG +LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID +AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW +TASEKDVTREFVDRLNAAGIPTTLRDTRGKEIDGACGQLAAEDVD +>PROKKA_00665 +MSDYQPRRPGSNPAPARRTDRAGKPALGRPKRGLIDESEARQLAEDRERMRRAGVGHQLS +APKRREAATAERPQVMPQTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLAERQAKA +KEIGLPAFRAKQLSVHYFERYTTDPEQMTDLPKDKREVIAEAFFPPLLTEVRRMETDRGD +TVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTAEIVE +QIVRANQVIAEGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPAPEG +LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID +AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW +TASEKDVTREFVERLNAAGIPTTLRDTRGKEIDGACGQLAAGDEDA +>PROKKA_00581 +MEGMSDYTPRRPGSKPTPARQKDRAGKPALGRPRRGMIDEPEARQLAEDRERMHRAGVGH +QLSAPPRRAAEVDADRPQVMPKTEGWQQPMGPDGRPQLQFKQPRVSQPPQHLADMTLAER +QAKAKEIGLPAFRAKQLSVHYFEHFTTDPEQMTDLPKGKREEIAEAFFPPLLTEVRRLTT +DRGDTVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTA +EIVEQIVRANQVIAEGGLGGTRRDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDP +APEGLGMSARHVTLSTVGLVPAIKKLAQEGVPLTFALSLHAPDDELRDELIPVNARWKAD +EAIDAAYEYFLATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTP +GSIWTASEKDVTREFVDRLNAAGIPATLRDTRGKEIDGACGQLAADDEDVAARA +>PROKKA_02053 +MSDYQPRRTGSKPTPNRQRDRAGKPALGRPERGLIDESEARQLAEDRERMRRAGVGHQLS +APKRREAATAERPQVMPKTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLKERQEKA +KEIGLPAFRAKQLSVHYFEHYTTDPEQMTDLPKDKREAIAEAFFPPLLTEVRRMETDRGD +TVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSPAEIVE +QIVLANQVIAQGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPSPEG +LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID +AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW +TASEKDVTREFVDRLNAAGIPTTLRDTRGKEIDGACGQLAAEDVD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001655.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001655.fa new file mode 100644 index 0000000000000000000000000000000000000000..393d0c178cc937d8fa80fad56fa3d0a011c6852a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001655.fa @@ -0,0 +1,15 @@ +>PROKKA_02117 +MSINTTSHHLPTAPSPLMQRHVLQRVEETLLRRFEGTVTAETVRSVVREVVADLKRGARI +TTFLPALAEREATRRLQAATPAHEAMAVAA +>PROKKA_01825 +MSINTTSHHLPTAPSPLMQRHVLQRVEETLLRRFEGTVTAETVRSVVREVVADLKRGARI +TTFLPALAEREATRRLQATTPAHEAMAVAA +>PROKKA_00663 +MSINTVHHLPAAPSPLMQRHVLKRVEETLARRFEGVATAEAVRATVREVASELKRSARMT +MFLPALTEREAARRLQAGAPAHEPLAAAA +>PROKKA_00580 +MTATLTTQHHMPVHPDTTMQQRVLERIAGTLIRRFDGSVPAADVRTTVAEVTAELEAEAR +LTTYLPALTEREALNRLEAMAAAPAHMTITHARHAA +>PROKKA_02055 +MVRQPKEVLTVSINTTSHHLPTAPSPLMQRHVLQRVEETLLRRFEGTVTAETVRSVVREV +VADLKRGARITTFLPALAEREATRRLQAATPAHEAMAVAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001656.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001656.fa new file mode 100644 index 0000000000000000000000000000000000000000..80672ee4cf46cbc9b02eb16119bb1ca10cedb7d1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001656.fa @@ -0,0 +1,40 @@ +>PROKKA_02118 +MSVRSLLPDLGTSATGTPEAAVPPFARAVLWAHGDDAWRGEGGWTVLLDGPDRLRRLSAL +WQAAVAGRPDPTAPLRGWISSTFADDSPEPAVLRIPADLRRATPSGVRDVAQHVDADALA +AAVAADRGARLLADGEVPLPADVADLAWDDAGYAAGVRELLTRMADSGGELAKVVISRTM +TVPADDADLWRAIGELRREYPQTWVFAVGGLLGATPEVLATRHAGLVGSRVLAGSMPRGA +DEEEDAALRERLASDPRLAEEHRWAARSVLDALAPVVDLADDDPAPTVLTLPNVHHLATS +VRGRLRDGRGTVLDVVAALHPTAAVGGTPTPDAVRVIAEVEPVDRGRYAGPVGWLDQDGD +GEIALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKFLPMRRALGVAED +>PROKKA_01826 +MGAMSVRSLLPDLGAPATGAPEAAVPPFARAVLWAHGDDAWRGEGGWTVLLDGTDRLRRL +SALWQTAVAGRPDPTAPLRGWISSTFADDSPEPAVLRIPADLRRATPSGVRDVAQHVDAD +ALAAAVAADRGARLLADGAVPLPAGVADRAWDDAGYAAGVRELLTRMADSGGELAKVVIS +RTMTVPADDADLWRAIGELRREYPQTWVFAVGGLLGATPEVLATRHAGLVGSRVLAGSMP +RGADEEEDAALRERLASDPRLAEEHRWAARSVLDALAPVVDLADDDPAPTVLTLPNVHHL +ATSVRGRLRDGRGTVLDVVAALHPTAAVGGTPTPDAVRVIAEVEPVDRGRYAGPVGWLDQ +DGDGEIALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKFLPMRRALGVAED +>PROKKA_00662 +MSVPTLLPELGTAAAEAAVPPFARAVLWAHGDAAWRGDDGWTVLVDGPDRLRRLSALWQA +AVAGREDPAAPVRGWVSAPFSDDSVEPAVLRVPARLRRSTASGIRETPQHVDAAALADAV +AADGGGRLLPDGEVPLPADTSESAWDDAGYAAGVRELLARMAASDGALAKVVISRTLTVP +ADDADLWRAIRALRREYPQTWVFAVGGLLGATPEILATRHAGLVGSRVLAGSLPRGEDEA +EDAALRARLATDPRLGEEHRWAARSVLDALAPVVDLADPDPAPTVLTLPNVHHLATSVRG +RLRDGRGTVLDVVAALHPTAAVGGTPTPEAVRVISEVEPVDRGRYAGPVGWLDQDGDGEI +ALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKLLPMRRALGIDLD +>PROKKA_00579 +MPPVPSVAVAALAARALSPSGSAAGRVPAFARAVVWAREDTVRVGVGGHTVLLDGPDRLR +RLSALWRAAVAARPEPASPALAWVSSAFDDASPVPSVLRVPARVLQAGPDGVVEVPVAMP +REALAAAVAACPGARLTEAGEVPLPADDPALAWDDAGYAAGVEEVVARMEASAGALSKVV +VSRTETVPAGEDRLWAAVDALRAEYPQTWTFAVGGLVGATPEMLATRRDGVVASRVLAGS +LPRGVDEGDDARLRARLAADPRLLREHHWAARSVLDALAPVVELEDAHPAPFVLTLPNVH +HLATDVRGRLRPGEGAVLDVVAALHPTAAVGGTPTAEALEVIRAVEPVDRGRYAGPVGWL +DQDGDGEIALALRCGQQVPGGVRLQAGGGIVPGAAAEEEVVEVGVKLLPMRRALGVA +>PROKKA_02056 +MGAMSVRSLLPDLGTPATGTPEAAVPPFARTVLWAHGDDAWRGEGGWTVLLDGTGRLRRL +SALWQAAVAGRPDPTAPLRGWISSTFADDSPEPAVLRIPADLRRATPSGVRDVAQHMDAD +ALAAAVAADRGARLLADGAVPLPADVADRAWDDAGYAAGVRELLTRMADSDGELAKVVIS +RTMTVPADDADLWRAIGALRREYPQTWVFAVGGLLGATPEVLATRHAGLVGSRVLAGSMP +RGADEEEDAALRDRLASDPRLAEEHRWAARSVLDALAPVVDLADDDPAPTVLTLPNVHHL +ATSVRGRLRDGRGTVLDVVAALHPTAAVGGTPTPDAVRVIAEVEPVDRGRYAGPVGWLDQ +DGDGEIALALRCGQQVPGGVRLQAGGGMVPGAVPEEEVTEIRAKFLPMRRALGVAED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001658.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001658.fa new file mode 100644 index 0000000000000000000000000000000000000000..4297fcdeae47a9d8c406bedf1d63842cf6df2ba2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001658.fa @@ -0,0 +1,18 @@ +>PROKKA_02120 +MSTDSTTTAPAAASPLPSAAADACDGHRPPHEVHRDKAKHLARLRRIEGQVRGLHRMVDE +DVYCIDVLTQVAAVTKALQSLSLNLTSEHLRHCVAEAAVQAEAEGRTELIDEKVAEATAA +LGRLLR +>PROKKA_01828 +MSTDSTTTAPAAASPLPSAAADACDGHRPPHEVHRDKAKHLARLRRIEGQVRGLHRMVDE +DVYCIDVLTQVAAVTKALQSLSLNLTSEHLRHCVAEAAVQAEAEGRTELIDEKVAEATAA +LGRLLR +>PROKKA_00660 +MSTLPTTTDAHDGADPCAGAHPPHAAHRDKDAHLTRLRRIEGQVRGIHRMVDEDVYCIDI +LTQVAAVTKALQAMSLNLTSEHLRHCVAEAAVEAEASGRTELIDEKVAEATAAIGRLLR +>PROKKA_00577 +MEHDRHAGPGYSPQREAYLKRLKRIEGQVRGIHRMVEEDVYCIDVLTQVAAATKALHAVS +LGLVEDHLRHCVAEAAVQAEAEGRTELIDEKVAEATAALGRLLR +>PROKKA_02058 +MSTDSTTTAPAAASPLPSAAADACDGHRPPHEVHRDKAKHLARLRRIEGQVRGLHRMVDE +DVYCIDVLTQVAAVTKALQSLSLNLTSEHLRHCVAEAAVQAEAEGRTELIDEKVAEATAA +LGRLLR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001661.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001661.fa new file mode 100644 index 0000000000000000000000000000000000000000..82bedbfcb7f796236ad36d451844f659c765fbb0 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001661.fa @@ -0,0 +1,14 @@ +>PROKKA_02125 +MSAGQGATTAGPVIESVELHVAAGAEAAFEAAVAEAEPLFRDGGATSFALSRQVEDPARY +RLLIGWRTLEDHTVAFRESDSFLAWRALVTPHLAQLPAATHWSAV +>PROKKA_01833 +MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAEPLFRDKGATSFALSRQVEDPARY +RLLIGWRTLEDHTVAFRESDAFLAWRALVTPHLAQPPAATHWSAV +>PROKKA_00655 +MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAAELFRGARATSFALTRQVEDPARY +RLLIGWRTLEDHTVGFRESEAFGQWRALVTPHLAQPPAATHWESVAAAF +>PROKKA_00572 +MEDPARYRLLIGWRTLEDHTVGFRESDAFLAWRALVTPHLAQPPAATHWSAV +>PROKKA_02063 +MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAEPLFRDGGATSFALSRQVEDPAHY +RLLIGWRTLEDHTVAFRESDAFLAWRALVTPHLAQPPAATHWSAV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001662.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001662.fa new file mode 100644 index 0000000000000000000000000000000000000000..38ea0b9ac205ceafff68df89332656ed782b6b38 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001662.fa @@ -0,0 +1,20 @@ +>PROKKA_02126 +MTETPQSSSGQSRDEILARLEEIYANDPAVREHGVTLGEVAEGRVVLHRDVTADMVNSHE +ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPARLGAHLVATARQSVEFGRDRM +IEVGIEADGQLAAWFTGHSTSPRVHA +>PROKKA_01834 +MTETPQSSSGQSRDEILARLEEIYANDPAVREHGVTLGEVAEGRVVLHRDVTADMVNSHE +ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPARLGAHLVATARQSVEFGRDRM +IEVGIEADGQLVAWFTGHSTSPRVHA +>PROKKA_00654 +MTETPQSSSGQSRDEILARLEEIYANDPAVREHGVTLGEVAEGRVVLHRDVTADMVNSHG +ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPARLGAHLVATARQSVEFGRDRM +IEVGIEADGQLVAWFTGHSTSPRVHA +>PROKKA_00570 +MTDTPQSSSGQSRDEILARLEEIYANDPAVREHDVTLGEVAEGRVVLHRDVTAGMVNSHE +ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPAKLGAHLVATARQSVEFGRDRM +IEVGIEADGQLVAWFTGHSTSPRVHA +>PROKKA_02064 +MTETPQSSSGQSRDEILARLEEIYANDPAVREHGVTLGEVAEGRVVLHRDVTADMVNSHE +ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPARLGAHLVATARQSVEFGRDRM +IEVGIEADGQLVAWFTGHSTSPRARA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001665.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001665.fa new file mode 100644 index 0000000000000000000000000000000000000000..0bf834ebdf00a88ac9ddbe8562b37d7f245d901f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001665.fa @@ -0,0 +1,50 @@ +>PROKKA_02129 +MTVYAFPGTEGAKVEFKSRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID +AALDAAWKAAPAWGATSPAERALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADVP +LAIDHFRYFAGAIRAQEGRLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL +AAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT +GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMANDDAYWDKAQEGFTLFALNQGE +VCTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIG +RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA +MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE +NHLMMLDHYQQTKNLLVSYSEDKLGFF +>PROKKA_01837 +MTVYAFPGTEGAKVEFKSRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID +VALDAAWKAAPAWGATSAAERALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADVP +LAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL +AAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT +GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMAADDAYWDKAQEGFTLFALNQGE +VCTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIG +RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA +MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE +NHLMMLDHYQQTKNLLVSYSEDKLGFF +>PROKKA_00651 +MTVYAFPGTEGAKVEFKPRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID +VALDAAWKAAPAWGATSAAERALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADVP +LAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL +AAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT +GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMANDDAYWDKAQEGFTLFALNQGE +VCTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKIISYLDIG +RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA +MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE +NHLMMLDHYQQTKNLLVSYSEDKLGFF +>PROKKA_00567 +MTVYAFPGTEGAKVEFKPRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID +VALDAAWKAAPAWGATSAAERALVLHRIADRMEENLEMLAVAETWDNGKAIRETLNADLP +LAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL +AAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT +GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMANDDAYWDKAQEGFTLFALNQGE +ICTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIG +RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA +MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE +NHLMMLDHYQQTKNLLVSYSEDKLGFF +>PROKKA_02067 +MTVYAFPGTEGAKVEFKSRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID +VALDAAWKAAPAWGATSAAERALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADLP +LAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL +AAGNAVVIKPAEQTPASVMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT +GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMAADDAYWDKAQEGFTLFALNQGE +VCTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIG +RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA +MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE +NHLMMLDHYQQTKNLLVSYSEDKLGFF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001666.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001666.fa new file mode 100644 index 0000000000000000000000000000000000000000..6ed25bc91bb22ff991a7ca948c63bb08b6e85108 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001666.fa @@ -0,0 +1,48 @@ +>PROKKA_02130 +MSSTLATGAYRRAVDRAHESLDSVRLSLAPSSSTAPTGADQGLRAALQGLRREVRESWLR +SLGALTPAGSALDAGASAAAPAVPGQTDPATLADDDLAAARREQRLAVALPVVRRMLIQP +AAEAGMLAAIGNARGHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAP +TQVSRGEHLSPRVHPWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLLSTVDAVH +AAWRDLPAPSRGRPRGTVPTPGPSAPPSASPGPSPAGAPHRHDEAAGLLRVTGHLPPTLD +GVELTGRHAEILTLLAWHGPGLTGAELEVALYPEETAGPRSAPGDAPARAISLRAEVHRL +RRALRDVGAPVELLSRPYRLVGEVHADLLCAREALRAGDLDRALHAAVGPVLPRSASPGV +ASIRAELGEALREAVAQDADVDQLWAYLGRPEARDDVELWGAALRLLPTDSPRRALAVAT +LERIERDLA +>PROKKA_01838 +MSSTLATGAYRRAVDRAHESLAAVRLSLAPSSPTAPAGADQGLRAALQGLRREVRESWLR +SLGALTPAVPGQTDPATLSDDDLAAARRDQRLAVALPVVRRMLIHPAAEAGMLAAIGNAR +GHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAPTQVSRGEHLSPRVH +PWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQATVDAVHAAWRDLPAPSRGRP +RGTAPTPGPSAPPSASPGPSPAAAPHRHDAAAGLLRVTGHLPPTLDGVELTGRHAEILTL +LAWHGPGLTGAELEVALYPEETAGPRPAPGDSPARAISLRAEVHRLRRALRDVGAPVALL +SRPYRLVGEVHADLLCAREALRAGDLDRALHAAAGPVLPRSTSPGVASIRAELGEALREA +VAQDADVDQLWAYLGRPEARDDVELWGAALRLLPTDSPRRALAVATLERIERDLA +>PROKKA_00650 +MSSTLATGAYRRAVDRAHESLDSVRLSLAPSSPTAPTGADQGLRTALQGLRREVRESWLR +SLGALTPAGSALDAEAAATAPAVPGQTDPATLADDDLAAARREQRLAVALPVVRRMLIHP +AAEAGMLAAIGNARGHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAP +TQVSRGEHLSPRVHPWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQATVDAVH +AAWRDLPAPSRGRPRGTVPTPGPSAPPSASPGPSPAAAPHRHDAAAGLLRVTGHLPPTLD +GVELTGRHAEILTLLAWHGPGLTGAELEVALYPEETAGPRSAPSDAPARAISLRAEVHRL +RRALQDAGAPVELLSRPYRLVGEVHADLLCAREALRAGDLDRALHAAAGPVLPRSVSPGV +ASIRAELGEALREAVAQDADVEQLWAYLGRPEARDDVELWGVALRLLPADSPRRALAVAT +LERIERDLA +>PROKKA_00566 +MSSTLATGAYRRAVDRAHESLAAVRLSLAPSSPTAPTGADQGLRAALQGLRREVRESWLR +SLGVLTPAGSALDAGASATAPAVPGQTDPATLSDDDLAAARREQRLAVALPVVRRMLIQP +AAEAGMLAAIGNARGHLLWVEGDRTAVRHAEALGFVAGADWSEASMGTSAPGIVLATGAP +TQVSRGEHLSPRVHPWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQTTVDAVH +AAWRDLPAPSRGRSRGTVPTPGPSAPPSVSPGPSPAAAPHRHDAAAGLLRVTGHLPPTLD +GVELTGRHAEILTLLAWHGPGLTGAELEVALYPEETVGPRSAPGDAPARAISLRAEVHRL +RRALRDVGARVELLSRPYRLVGAVHADLLCAREALRAGDLDRALHAAAGPVLPRSASPGV +ASIRAELGEALREAVAQDADVEQLWAYLGRPEARDDVELWGAALRLLPADSPRRALAVAT +LERIERDLT +>PROKKA_02068 +MSSTLATSAYRRAVDRAHESLAAVRLSLAPSSPTAPAGADQGLRAALQGLRREVRESWLR +SLGALTPAVPGQTDPATLSDDDLAAARRDQRLAVALPVVRRMLIHPAAEAGMLAAIGNAR +GHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAPTQVSRGEHLSPRVH +PWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQATVDAVHAAWRDLPAPSRGRP +RGTAPTPGPSAPPSASPGPSPAAAPHRHDAAAGLLRVTGHLPPTLDGVELTGRHAEILTL +LAWHGPGLTGAELEVALYPEETAGPRPAPGDSPARAISLRAEVHRLRRALRDVGAPVALL +SRPYRLVGEVHADLLCAREALRAGDLDRALHAAAGPVLPRSASPGVASIRAELGEALREA +VAQDADVEQLWAYLGRPEARDDVELWGAALRLLPADSPRRALAVATLERIERDLA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001670.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001670.fa new file mode 100644 index 0000000000000000000000000000000000000000..76948d025751ffeafae7587107c8da3705f3be03 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001670.fa @@ -0,0 +1,30 @@ +>PROKKA_02134 +MLSAPTLTRLASLAAFLNTAPGLRGGQPADERFTAATQLPSLVPELQEDEVRLRLAAAAA +VRGRELRGRLAEVWALAAVDEAAAVERVNALLAAAGPLRLTAGGDVVGLAPAQVPADAVE +RLAAMAALALAETAMDGELVRLRVCEGEDCENALVDASRNRSKRFCDEANCANRTHVRSY +RARLAEAAEAAPATDPAGPEEAEAPEAVADEAAPADKPRQETEKEKKERKKAEKKAEKKA +RKKAEKKARKKKSDKKKD +>PROKKA_01842 +MLSAPTLSRLASLAAFLNTAPGLRGGQPADERFTAATQLPSLVPELQEDEVRLRLAAAAA +VRGRELRGRLAEVWALAAGDEAAAVERVNALLAAAGPLRLTAGGDVVGLAPAQVPADAVE +RLAAMAALALAETAMDGELTRLRVCEGEDCENALVDASRNRSKRFCDEANCANRTHVRSY +RARLAEAAESAPAADPAGPEEAEAPEAVVDSEAAADEPRRETKKEKKERRKAEKKARKKA +EKKAGKKKSDKKKD +>PROKKA_00638 +MLSPRTLARLSSVAAFLNTAPGPRGGQEAPERFTAATQLPALVPELQEGEVRLRLAAAAA +VRARELRERLTRVWALAATDESAAVERVNELLAEAGPLRLTAGGDVVGLAPAQVPADAVE +RLAAMATLALAETAMDGELARLRVCEGEDCENALVDGSRNRSKRFCDEANCANRTHVRSY +RARLAEAAEAAPATDPAGPEEAEGTEAVVDEAAPADEPLQETEKEKKERRKAQKKARKKA +EKKAGKKKSDKKKSDKKKD +>PROKKA_00561 +MLSPHTLARLASISAFLNTAPGVRGGQEAEERLTAGTQLPALVPELQEGESRLRVAAAAR +TRAHELRARLTELWAAADAEDVPAAVAAVNELLAETGPLRLEVSDGSADLAPAQVPADAV +ERLTAMAALALTEAALEGELTRLRVCAGEDCENTLVDASRNRSKRFCDAANCANRTHVRS +YRARLAEAEDTQADVEAADAAPLPEVAPEADPQDATDLEAIEAAEGVESAVQEPVKKDST +KDKKSKSEKKARRAAKKKAEKESEAAAEGKKGKREKSKKSEKHKKKAAKD +>PROKKA_02072 +MLSAPTLSRLASLAAFLNTAPGLRGGQPADERFTAATQLPSLVPELQEDEVRLRLAAAAA +GRGRELRGRLAEVWALAAVDEAAAVERVNALLAAAGPLRLTAGGDVVGLAPAQVPADAVE +RLAAMAALALAETAMDGELTRLRVCEGEDCENALVDASRNRSKRFCDEANCANRTHVRSY +RARLAEAAESAPAADPAGPEEAEAPEAVVDSEAAADEPRRETKKEKKERRKAEKKARKKA +EKKAGKKKSDKKKD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001673.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001673.fa new file mode 100644 index 0000000000000000000000000000000000000000..d72fbd213076bfb2629ffdbcb449f97f04f1ab2a --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001673.fa @@ -0,0 +1,45 @@ +>PROKKA_02138 +MAGPSGSTAAPAPQDARALTRRILALAVPAFGALIAEPLFLLADTAIIGHLGTAQLAGVG +IGTTILHTLTGLMIFLAYATTPAVARLIGAGNLAAAMDRGRDGIWLGLLLGAVLAVLGWL +AAPALTAALGATGEVQAHAVAYLRWSMPGLPALLAVLAATGVLRGLQDTVTPLVVAGVGF +GANIGLNVALVYGLGWGVAGSAVGTSVVQWAMLVTYLFVLAPRFRRSGTAWAPRASGMRA +TAQVGSWLLLRTASLRAAILITVMAAAGAGDLTLAAHQLVFTLFSTLAFALDALAIAAQA +LIGAELGAARPDAARRLTRTMVRWGLGFGVVTGAVLALAAPVLPGLFTTDPTVQAAATVG +LWVLAAGQPVAGYVFVLDGVLIGAGDARYLALAGLVNLVVYAPALWVLAQLATGGFGWTA +AWPGPNAAVPDAGVQLGLLWLGFAGVYMGMRALTLGWRARRDDWMRLGVV +>PROKKA_01846 +MAGPSGSTAAPAPQDARALTRRILALAVPAFGALIAEPLFLLADTAIIGHLGTAQLAGVG +IGTTILHTLTGLMIFLAYATTPAVARLIGAGNPAAAMDRGRDGIWLGLLLGAVLAVLGWL +AAPALTAALGATGEVQAHAVAYLRWSMPGLPALLAVLAATGVLRGLQDTVTPLVVAGVGF +GANIGLNVALVYGLGWGVAGSAVGTSVVQWAMLVTYLFVLAPRFRRSGTVWAPRASGMRA +TAQVGSWLLLRTASLRAAILITVMAAAGAGDLTLAAHQLVFTLFSTLAFALDALAIAAQA +LIGAELGAARPDAARRLTRTMVRWGLGFGVVTGAVLALAAPVLPGLFTTDPTVQAAATVG +LWVLAAGQPVAGYVFVLDGVLIGAGDARYLALAGLVNLVVYAPALWVLAQLATGGFGWTA +AWPGPNAAVPDAGVQLGLLWLGFAGVYMGMRALTLGWRARRDDWMRLGVG +>PROKKA_00634 +MAEPQGSTAAPAPQDGRALTRRILALAVPAFGALLAEPLFLLADTAIVGRLGTPELAGVG +IGTTVLHTATGLMIFLAYATTPAVARLIGAGDHAAAMDRGRDGVWLGLLLGAALAVLGWI +AAPWLTGALGATGEVQEHAVAYLRWSMPGIPALLAVLAATGVLRGLQDTVTPLVVAGAGF +AVNIGLNFALVYGAGLGVAGSAIGTSAVQWGMLLTYLAVLAPRFRRAGTSLAPRASGMRA +TAQVGSWLLLRTASLRAAILITVMAAAGAGDMTLAAHQLVFTLFSTLAFALDALAIAAQA +LIGAELGASRPATARRLTDVMVRWGLGFGVVTGGLLALAAPWLPALFTTDPQVQAAATVG +LWVLAAGQPIAGYVFVLDGVLIGAGDARYLALAGLVNLAVYAPVLWVLAQVAAGGLGWTV +DWSDPAAHVPDAGEQLGLLWLGFAGVYMGMRALTLGWRARRDDWMRVGAH +>PROKKA_00558 +MPSRPPHDDAAPAPEDRRALARQVLGLAVPAFGALIAEPLFLLADTAIVGHLGTAQLAGV +GVGTTVLHTVTGLLVFLAYATTPAVARMVGAGNPAGALDRGRDGMWLGLMLGFVLGAAGW +LAAPWLTGALGAAGEVHSHATEYLRWSMPGLPALLAVLAATGVLRGLQDTVTPLVVAGGG +FAVNIGLNWALVYGAGLGVAGSAIGTAAVQWAMLAVYLAVLAPRFRAAGTRPGPRADGLR +ATAQVGSWLMLRTASLRAAILITVAAATGLGDVTLAAHQLVFTLYSTLAFALDALAIAAQ +ALIGAELGASRPRTARRLTDLMVRWGLGFGVVTGAGLAAAAWALPPLFTPDPGVHAAATA +GLLVLALSQPVAGYVFVLDGVLIGAGDARYLALAGVVNLAVYAPVLWGLARLAAGGADAG +AQVALLWLGFAGVYLGMRAATLGLRARRDAWMRLG +>PROKKA_02076 +MAGPSGSTAAPAPQDARALTRRILALAVPAFGALIAEPLFLLADTAIIGHLGTAQLAGVG +IGTTILHTLTGLMIFLAYATTPAVARLIGAGNPAAAMDRGRDGIWLGLLLGAVLAVLGWL +AAPALTAALGATGEVQAHAVAYLRWSMPGLPALLAVLAATGVLRGLQDTVTPLVVAGVGF +GANIGLNVALVYGLGWGVAGSAVGTSVVQWAMLVTYLFVLAPRFRRSGTVWAPRASGMRA +TAQVGSWLLLRTASLRAAILITVMAAAGAGDLTLAAHQLVFTLFSTLAFALDALAIAAQA +LIGAELGAARPDAARRLTRTMVRWGLGFGVVTGAVLALAAPVLPGLFTTDPTVQAAATVG +LWVLAAGQPVAGYVFVLDGVLIGAGDARYLALAGLVNLVVYAPALWVLAQLATGGFGWTA +AWPGPNAAVPDAGVQLGLLWLGFAGVYMGMRALTLGWRARRDDWMRLGVG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001674.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001674.fa new file mode 100644 index 0000000000000000000000000000000000000000..51370655a88204d44b70d0eb5945419caccc1077 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001674.fa @@ -0,0 +1,34 @@ +>PROKKA_02139 +MSVPPSGPPAGPPAGWPPSGRPSARRAAVAPSLHGHPGAPGGVPAGWPGRRPAARPAPDW +TPGRFHWGDAVVVLVYVALMVLGLGLWLAVSLGLVPGDLEAFDLVRDGFTVNIVSYAILV +VLVLAVAWRPLVTSLRVFRTGTWWKLLLLPATWLACIVVNVIVLSLIGEAQTSANQAALE +EMTTQAPPVLMILMTVVAAPLVEEYLFRHLLIGKLSRWINVWVCAVVSVLAFTLLHFLGT +GGDFRLVETVPYLTLAVAITVSYILMGRSFGYAVLLHMVNNGIAIAMLYLVAPLLPDTLP +GPTAPTTALAPLLALLG +>PROKKA_01847 +MSVPPSGPPAGPPAGWPPSGRPSARRAAVAPSLHGHPGAPGGVPAGWPGRRPAARPAPDW +TPGRFHWGDAVVVLVYVALMVLGLGLWLAVSLGLVPGDLEAFDLVRDGFTVNIVSYAILV +VLVLAVAWRPLVTSLRVFRTGTWWKLLLLPATWLACIVVNVIVLSLIGEAQTSANQAALE +EMTTQAPPVLMILMTVVAAPLVEEYLFRHLLIGKLSRWINVWVCAVVSVLAFTLLHFLGT +GGDFRLVETVPYLTLAVAITVSYILMGRSFGYAVLLHMVNNGIAIAMLYLVAPLLPDTLP +GPTAPTTALAPLLALLG +>PROKKA_00633 +MPAGWPGRTPGPRTAPDWEPGRFHWGDAVVVLAYAGLMLFGLGLPLAMLLGLVPGDLAAF +DLVRDGFTVNMVSYAILTALVLIVAWRPLVTSLRVFRTGTWWKILLLPAVWFTCILVNVL +VLSLIGEAQTSANQAALEEMSAQAPPVLMILMTVVGAPLVEEYLFRHLLVGKLSRWVNVW +VCAVVSMLAFTLLHFLGTGGQFDLVETVPYLTLAIAITVTYILMGRSFGYAVLLHMVNNG +IAIAMLYLVAPLLPDVLPEPTAPAAALSPLLALLG +>PROKKA_00557 +MSVPPPGPHDAGALPPPGSTAPTSAAGEAPEGWPPAGWPGRASAGGAPQGWPPSGWPGRT +ASARTAPSWEPGRLHWGDAAVVVLYVLMMVVGLGYLLAVLLGLAPRDPAAMDVMDGFRVN +LVSYAVLVVAVLAVSWRPLVASLRVFATHTWLKILLLPALWLVTVLVNALLLSLIGQAQT +SANQAALEEMTTQAPALGMVLMTVVGAPIVEEYLFRHLLVGKLSRWINVWVCAAISVAAF +TLLHFLGTGGDFQWVETVPYLTLAVTITVTYVLIGRSFGYAVLLHMVNNGIAIAMLYLVA +PLLPSAPAPVGPGALLSPLLALLG +>PROKKA_02077 +MSVPPSGPPAGPPAGWPPSGRPSARRAAVAPSLHGHPGAPGGVPAGWPGRRPAARPAPDW +TPGRFHWGDAVVVLVYVALMVLGLGLWLAVSLGLVPGDLEAFDLVRDGFTVNIVSYAILV +VLVLAVAWRPLVTSLRVFRTGTWWKLLLLPATWLACIVVNVIVLSLIGEAQTSANQAALE +EMTTQAPPVLMILMTVVAAPLVEEYLFRHLLIGKLSRWINVWVCAVVSVLAFTLLHFLGT +GGDFRLVETVPYLTLAVAITVSYILMGRSFGYAVLLHMVNNGIAIAMLYLVAPLLPDTLP +GPTAPTTALAPLLALLG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001675.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001675.fa new file mode 100644 index 0000000000000000000000000000000000000000..c91c7731a3ee0f0ea0b82b44020ab94b5810c93d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001675.fa @@ -0,0 +1,20 @@ +>PROKKA_02140 +MALFSQPVFINLPTTDTERIREFWTTLGATAMDDYSDEHSVCIELTESTYAMYLSPGYYT +DFIGNREIADCLTTNSALMALTVGDAAAVDALADRAIELGAAEVPLPEDLREEMADSGMH +SREIVDPDGHQWEFVTA +>PROKKA_01848 +MALFSQPVFINLPTTDTERIREFWTTLGATAMDDYSDEHSVCIELTESTYAMYLSPGYYT +DFIGNREIADCLTTNSALMALTVGDAAAVDALADRAIELGAAEVPLPEDLREEMADSGMH +SREIVDPDGHQWEFVTA +>PROKKA_00632 +MALFSQPVFINLPTTDTERIREFWTSLGAQAIEDFSDENSVCIELTESTFAMYLSPGYYT +DFIGDREIADCMTTNSALMALTVGDAAAVDALADRAIEAGAAEVPLPVDLREEMVDSGMH +SREIVDPDGHQWEFVTA +>PROKKA_00556 +MRTRWSTVLVMALFSQPVYINLPSTDTERIREFWTSMGADIDEDFSDENSVCVQLTESTF +AMYLSPGFYTDFIGDREIADCLTTNSVLLQLTAPDRGAVDALVRAAVEAGGSEVPLPDEL +QEDMTATGVHSRQVVDPDGHQWEFMAA +>PROKKA_02078 +MALFSQPVFINLPTTDTERIREFWTTLGATAMDDYSDEHSVCIELTESTYAMYLSPGYYT +DFIGNREIADCLTTNSALMALTVGDAAAVDALADRAIELGAAEVPLPEDLREEMADSGMH +SREIVDPDGHQWEFITA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001676.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001676.fa new file mode 100644 index 0000000000000000000000000000000000000000..9d6640d333b6afb58cd8577b2bc6ca5a1c034319 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001676.fa @@ -0,0 +1,50 @@ +>PROKKA_02141 +MPAPAATTTTTPPATPRERQSVLRTLRTPRWLGTEVLAAVVVALALIPEAIAFSIIAGVD +PRVGLFASFTMAVTTAIVGGRPAMISAATGAVALVVAPLSHAYGVGHLLAAIILGGVIQI +LLGVFGVARLMRFVPRSVMVGFVNALAILVFTSQLPELIGVPWLVYPLTALALAIVVLLP +RLTTAVPATLVAVVVVTALVMAAGLAVPRVGDRGALPDALPVLGLPDVPLTWETLRLILP +FSVGIAFVGLLESLLTAKLVDDITDTRSDKTRESWGQGVANVVSGLFGGMGGCAVVGQTM +MNVKANGARTRISTFLAGVFLLVLVVAFGGFVAQIPMAALVGVMMFVAAATFDWHSVRPA +TLRAMPRSETAVMVVTVAATVLTHNLAIGVGVGVLAALVLFAQRVSRLVTVVREVHDDGD +AVTYRVHGALFFASSNDLYSQFEYALDPPRVVIDMSAAHVWDASTVAALDSVLTKYARHG +IHAEVTGLNEASAAMHARLTGRLGA +>PROKKA_01849 +MPALPAAPPPALTPLQRQSVLRTLRSPRLLGTEVLAAVVVALALIPEAIAFSIIAGVDPR +VGLFASFTMAVTTAIVGGRPAMISAATGAVALVVAPLSHAYGVGHLLAAIILGGVIQILL +GVFGVARLMRFVPRSVMVGFVNALAILVFTSQLPELIGVPWLVYPLTALALAIVVLLPRL +TTAVPATLVAVVVVTALVMAAGLAVPRVGDRGALPDALPVLGLPDVPLTWETLRLILPFS +VGIAFVGLLESLLTAKLVDDITDTRSDKTRESWGQGVANVVSGLFGGMGGCAVVGQTMMN +VKANGARTRISTFLAGVFLLVLVVAFGGFVAQIPMAALVGVMMFVAAATFDWHSVRPATL +RAMPRSETAVMVVTVAATVLTHNLAIGVGVGVLAALVLFAQRVSRLVTVVREVHDDGDAV +TYRVHGALFFASSNDLYSQFEYALDPPRVVIDMSAAHVWDASTVAALDSVLTKYARHGIH +AEVTGLNEASAAMHARLTGRLGA +>PROKKA_00716 +MTPASTASARVAAPPNSREPSPEQLQSVRLTLRSPGRLKTEVLAGLVVALALIPEAIAFA +LIAGVDPQVGLFAAATMAMTIAFVGGRPAMVSAATAATALVVAPLVASHGLDHLIAAVIL +AGGLQVVLGLLGVAKLMRFVPRSVMVGFVNALAILIFTSQLPDLMGVPWLVYPLTALGLA +IILLLPRVTTAVPAPLVAIVVVTVIVLLAGADVPTVGDKGRLPDSLPALLVPDVPFTLET +LQLLFPYALGMAVVGLLESLMTAKLVDDITDTRSSKTRESWGQGVANVVSGLFGGMGGCA +MVGQTMINVKASGARTRISTFMAGVFVLILSVTLGDVVALVPMAALVAVMIFVSLATFDW +HSIRPSTLAFMPKSETAVMLVTVAATVLTHNLAIGVGLGVLAAMVMFAQRVSHLATVTRT +LEGQGRDAVARYRVQGELFFASSNDLYTQFDYAGDPARVVIDFSQAHLWDASTIAALDAV +EEKYRRHGATVEITGLNVASRAMRARMSGRLGGGH +>PROKKA_00554 +MPASPAAPPPALTPLQRQSVLRTLRTPRWLGTEVLAAVVVALALIPEAIAFSIIAGVDPR +VGLFASFTMAVTTAVVGGRPAMISAATGAVALVVAPLSHAHGLDHLIAAIILGGLIQVAL +GLLGVARLIRFIPRSVMVGFVNALAILVFTSQLPELIGVPWLVYPLTALALGIVLLLPRL +TTAVPSTLVAIVVVTALVMAAGWSVPRVGDRGELPDALPGLFVPDVPLTWETLRLILPFS +VGMAVVGLLESLLTAKLVDDVTDTRSDKTRESWGQGVANIVSGLFGGMGGCAVVGQTMMN +VKANGARTRISTFLAGVLLLVLVVALGDLVGQIPMAALVGVMVFVAGAAFDWHSVRPATL +RAMPRSETAVMLLTVLATVVTHNLAIGVGVGVLTAMVLFAQRVSRLARVERVVTDDNGGT +AVYRVHGELFFASSNDLYSQFEYALDPPRVVIDLSAAHVWDASTVAALDAVVTKYAQHGI +AAEVTGLNEASAAMHARLTGRTGA +>PROKKA_02079 +MPALPAAPPPALTPPATPRERQSVLRTLRTPRWLGTEVLAAVVVALALIPEAIAFSIIAG +VDPRVGLFASFTMAVTTAIVGGRPAMISAATGAVALVVAPLSHAYGVGHLLAAIILGGVI +QILLGVLGVARLMRFVPRSVMVGFVNALAILVFTSQLPELIGVPWLVYPLTALALVIVVL +LPRLTTAVPATLVAVVVVTSLVMAAGLTVPRVGDRGALPDALPALGLPDVPLTWETLWLI +LPFSIGMAFVGLLESLLTAKLVDDITDTRSDKTRESWGQGVANVVSGLFGGMGGCAVVGQ +TMMNVKANGARTRISTFLAGVFLLVLVVAFGGFVAQIPMAALVGVMMFVAAATFDWHSVR +PATLRAMPRSETAVMVVTVAATVLTHNLAIGVGVGVLAALVLFAQRVSRLVTVVREVHDD +GDAVTYRVHGALFFASSNDLYSQFEYALDPPRVVIDMSAAHVWDASTVAALDSVLTKYAR +HGIHAEVTGLNEASAAMHARLTGRLGA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001677.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001677.fa new file mode 100644 index 0000000000000000000000000000000000000000..b8af0af8c2dfe7f6a0f742686aba75ae6c525348 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001677.fa @@ -0,0 +1,40 @@ +>PROKKA_02143 +MNLRTLLREALTAARTAPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPAARV +LTVTDSGGTGFLTGATVATLAGLDSAEAALARDMPVDTVNAAIGAGGTRVAVTHVVGTVD +RGVELTRGRLPGPGEVVVPEAKLAELGLAQPSGALESGDGRQWAVVGAFEALTPFEDLAD +YAIAVPAAPASLVVQQVRVLAPDTAGTRAMQDSALAVIDPDPRSSQVQTARALAAGNATI +TGELAGLGRSLLLLILGAGAFFVAIVVLADVLIRRRDLGRRRTLGIGRADLVLLVAVRTA +APAVLGAVVGAGTGYAVVVGQGGALGLDFVAGVAVLAALTAVVASLLPAAFAAFRDPVRV +MRTA +>PROKKA_01850 +MNLRTLLREAVTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPGARV +LTVTDTGGTGFLTGATAATLAGLDTAEAALARDSPMDAVNTGIGRGGARVAVTNVVGTLD +RGIVLTRGRLPAPGEVVVPEAKLAELGLAQPSGAIEATDGGQWAVVGAFQAQDPFQDLDG +YALTVPAAPDALVMQQVRVLAADTAGTRAMQEAALAVIDPDPRASSIQTARALSAGNQVI +TGELAGLGRSLLLLILGAGAFFVSIVVLADVLIRRRDLGRRRTLGIGRGDLILLVAVRTA +VPALLGAVLGSGAGYAVVAGQGGTLGVDFVAAVAVLAALTALLASLAPAAFAAFRDPVRV +MRTA +>PROKKA_00629 +MNLRTLLREALTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPAARV +LTVTDSGGTGFLTGATVTTLAGLDAAEAALARDMPVDTVNAAIGAGGTRVAVTHVVGTLD +RGVELTRGRLPGPGEVVVPEAKLAELGLAQPSGALESGDGRQWAVVGAFEARTPFEDLDG +YALAVPATPASLVVQQVRVLALDTAGTRAMQDSALAVIDPDPRSSQVQPARALAAGNETI +TGELAGLGRSLLLLILGAGAFFVAIVVLADVLIRRRDLGRRRTLGIGRADLVLLVAVRTA +APAMRGAAVGAGAGHGLVLAQGSALGSAFVVGAAVLAVLTAVVASLLPAAFAAFRDPVRV +MRTA +>PROKKA_00553 +MNLRTLLREAVTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPGARV +LTVTDTGGTGFLTGATAATLAGLDTAEAALARDSPMDAVNTWIGRGGARVAVTNVVGTLD +RGIELTRGRLPAPGEVVVPEAKLAELGLAQPSGAIEATDGRQWAVVGAFQAQDPFQDLDG +YALTVPAAPDALVMQQVRVLAADTAGTRAMQEAALAVIDPDPRASSIQTARALSAGNQVI +TGELAGLGRSLLLLILGAGAFFVSIVVLADVLIRRRDLGRRRTLGIGRGDLILLVAVRTA +VPALLGAVLGSGAGYAVVAGQGGTLGVDFVAAVAVLAALTALLASLAPAAFAAFRDPVRV +MRTA +>PROKKA_02080 +MNLRTLLREAVTAARTSPVPSALVLLVVAAMCFAAVATVGRQAATEAAVAAELSGPGARV +LTVTDTGGTGFLTGATAATLAGLDTAEAALARDSPMDAVNTGIGRGGARVAVTNVVGTLD +RGIVLTRGRLPAPGEVVVPEAKLAELGLAQPSGAIEATDGRQWAVVGAFQAQDPFQDLDG +YALTVPAAPDALVMQQVRVLAADTAGTRAMQEAALAVIDPDPRASSIQTARALSAGNQVI +TGELAGLGRSLLLLILGAGAFFVSIVVLADVLIRRRDLGRRRTLGIGRGDLILLVAVRTA +VPALLGAVLGSGAGYAVVAGQGGTLGVDFVAAVAVLAALTALLASLAPAAFAAFRDPVRV +MRTA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001678.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001678.fa new file mode 100644 index 0000000000000000000000000000000000000000..6856f9360817e54c657c46771971058364bf8261 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001678.fa @@ -0,0 +1,25 @@ +>PROKKA_02144 +MNAELSVADLRFAYTRGAEELFDGLTHRFTPGAVTALTGPSGRGKSTLLYVLGLMLTPSA +GVVRLGDVDASALPDRRRARLRATSVGFVFQDAELDPSRPILDSVVEPGLYAGLSRRELE +GRARILLERFGLGHRAEHRPGQVSGGQAQRVAVCRALVNTPAVVLADEPTGNLDPDNASL +VLDALAEAAGEGRTVVVATHDPAVVARADEVVRL +>PROKKA_01851 +MTGPATPGTPAAPVVPAALAVEDLRFAYTRAAEELFDGLTHAFTPGAVTALTGPSGRGKS +TLLYVLGLMLTPTSGVVRLGDVDASTRPDRERSRLRATSVGFVFQDSELDPSRPILDSVV +EPGLYAGLERQTLEDRARALLERFGLAHRADHRPGQVSGGQAQRVAVCRALVNAPAVVLA +DEPTGNLDPDNAGLVMDALADAAAEGRTVVVATHDPAVVARADEVVRL +>PROKKA_00628 +MNAELSVADLRFAYTRGAEELFDGLTHRFTPGAVTALTGPSGRGKSTLLYVLGLMLTPSA +GVVRLGDVEASALPDRRRARLRATSVGFVFQDAELDPSRPILDSVVEPGLYAGLERRVLE +ERARALLERFGLGHRAEHRPGQVSGGQAQRVAVCRALVNTPAVVLADEPTGNLDPDNASL +VLDALAETAAEGRTVVVATHDPAVVARADEVVRL +>PROKKA_00552 +MTGPATPGTPAAPGTPAALAVEDLRFAYTRAAEELFDGLTHAFTPGGVTALTGPSGRGKS +TLLYVLGLMLTPTSGVVRLGDVDASTRPDRERSRLRATSVGFVFQDSELDPSRPILDSVV +EPGLYAGLERQTLEDRARALLERFGLAHRADHRPGQVSGGQAQRVAVCRALVNAPAVVLA +DEPTGNLDPDNAGLVMDALADAAAEGRTVVVATHDPAVVARADEVVRL +>PROKKA_02081 +MTGPATPGTPAAPVVPAALAVEDLRFAYTRAAEELFDGLTHAFTPGAVTALTGPSGRGKS +TLLYVLGLMLTPTSGVVRLGDVDASTRPDRERSRLRATSVGFVFQDSELDPSRPILDSVV +EPGLYAGLERQTLEDRARALLERFGLAHRADHRPGQVSGGQAQRVAVCRALVNAPVVVLA +DEPTGNLDPDNAGLVMDALADAAAEGRTVVVATHDPAVVARADEVVRL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001680.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001680.fa new file mode 100644 index 0000000000000000000000000000000000000000..1bd5b6faf1f8b10457aca0900b1a864affee7fc4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001680.fa @@ -0,0 +1,29 @@ +>PROKKA_02146 +MVGLVGALLLAGCASGADAGASAHAETGSTPSKVWDAATWKPTEVIEPVLATEPEKEAAY +REQMDRLAESGGTPEILQVQRKDWSTTPLESDQKVASCMRADGFPVEVSPTGGLRYSTPP +AAQARAWALAMNTCIAQHPVDPSYTQDWSEPQLRLVYDYWDQYLIPCLEAQGFTVDTSTR +PSKESFVTAFFTPGRHDWWPLQATMRGVPEERQTQVVQTCPELPPQDVFWGTSG +>PROKKA_01853 +MTSLRIPATAALVAAVALTLTGCVGRESAGLGGSSTVAAPPTATAEKTWDASQWVPTERI +EPLLTTEAEKERAYREQVARHAQGAGMPAPPQVERSGWYATSLESDRMVSTCLAEAGWPN +SVGPTGGIQIDTPPESQRSAFEAAYVTCYAQHPVDPSYTQDWTDPQLRLVYDYWDQYLIP +CLEAYGYTVDTSARPSKEAFVSAFYTPGRHQWWPFADSMRGVSAERQAEVAQTCPELPPQ +DVFWGSSG +>PROKKA_00626 +MKTKFAAVTAAAVTAVLTLSGCATTAPSTSAAATGSPTEKVWDPETWTPTEKIERRMTEA +DERERWYESQLARNAAFLGIRNPPAVTRRGWATSRQEQARWSAQCMTERGVPATYNEVMV +GVTYDTPPPSQEAAVKLVSWTCDALFPIDPSLDQEFSDAQLRLLYDYWDQYAIPCLEDHG +ITVDTSQRPSKETWLAAFNTPERISWWPVQDSIMGLTDARSAEVSEACPVQPPDSMLFGY +SE +>PROKKA_00550 +MTSLRIPATAALVAAVALTLTGCVGRESAGLGGSSTVAAPPTATAEKTWDASQWVPTERI +EPLLTTEAEKEAAQREQVERMAREAGTPELLQVRRMDWSSTTLESSQKIGECMAAAGFPV +EVTPTGGLRYPTPPESQKRAWNLAENTCAVKHPVDPAYAHDWTEPQLRLVYDYWDQYLIP +CLEAQGLHVDTSSRPSKESFVTSFFTQDRHDWWPFSTTMVGVSEERKAHIAQTCPELPPP +DVFWGTAP +>PROKKA_02083 +MTSLRIPATAALVAAVALTLTGCVGRESAGLGGSSTVAAPPTATAEKTWDASQWVPTERI +EPLLTTEAEKERAYREQVARHAQGAGMPAPPQVERSGWYATSLESDRMVSTCLAEAGWPN +SVGPTGGIQIDTPPESQRSAFEAAYVTCYAQHPVDPSYTQDWTDPQLRLVYDYWDQYLIP +CLEAYGYTVDTSARPSKEAFVSAFYTPGRHQWWPFADSMRGVSAERQAEVAQTCPELPPQ +DVFWGSSG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001681.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001681.fa new file mode 100644 index 0000000000000000000000000000000000000000..c7458080c6bb7056cec7c0a467924c01b86dd0b8 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001681.fa @@ -0,0 +1,65 @@ +>PROKKA_02147 +MSEHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLVVVALMVLV +AVVLNVWAPHVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTP +GEGIDFTELGRLILIVLGMYLVAQTFMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSY +FDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMMFWLSWQLALIALIAL +PVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNE +ELYEAAFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN +QPLGQIAGMSNMLISGVASAERIFELLDEPEETPDGTPARTPARTFVRETAPSEGTFVRE +TAPSAASGPDVVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNLVAEPGQTVAIVGPTGA +GKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRSELRAATGMVLQDAVLFGGTIRENIRYG +RLDATDEEVVAAAKATYVDRFVHTLPEGYDTVIEHDASNVSAGERQLITIARAFLAQPSL +LILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVMEHGDIVEQGS +HAELLAAKGAYHRLYMSQFKGGEDDDGAASRDDAR +>PROKKA_01855 +MSEHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLVVVALMVLV +AVVLNVWAPHVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTP +GEGIDFTELGRLILIVLGMYLVAQTFMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSY +FDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMMFWLSWQLALIALVAL +PVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNE +ELYEAAFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN +QPLGQIAGMSNMLISGVASAERIFELLDEPEETPDGTPARTPDGTFVWETAPSESAFVRE +TAPSAIPGPDGVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNFVAEPGQTVAIVGPTGA +GKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRGELRAATGMVLQDAVLFGGTIRENIRYG +RLDATDEEVVAAAKATYVDRFVHTLPDGYDTVIEQDAANVSAGERQLITIARAFLAQPSL +LILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVMEDGDIVEQGS +HDQLLAARGAYFRLYRSQFQGGEQAEEQDDDGAPAAREDAR +>PROKKA_00622 +MSGTEKHGSTAAPQGEVGELTDAEIAAFQEAGVTDEWGEGPPRKAKAFWPSAMRLLGLFA +PERTGLILVSLMVLVAVVLNVWAPHVLGQAMDVIFGGLISRDMPAGLTREQVIEGLRGQG +QGQAADMLSGMAFVPGQGIDFAELARLILIVLGMYVVAQLFMWLQGRVLNDLVMRIVFRL +REDIEAKLNRLPLSYFDTRQRGDLLSRTTNDVDNVQQAMQQAFATLVYSVLTIIGIVGMM +FWLSWQLALIALIALPVAGVMVGVIGSKSQKLFTAQWRETGRLNGHIEESFTGHELVTVF +GRQADMAERFDERNEAMYEASFKAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMT +LGAVTAFIQYSREFNQPLGQVAGMSNMLISGVASAERIFELLDEDEQDSDAEVARRASDD +DVAEPADASVRETGASADDDVAHLPQPVAGRVEFEHVRFSYTEAKPLITDLNLVAEPGQT +IAIVGPTGAGKTTLVNLIMRFYEVDGGRILVDGVDTRTVSREELRSHTGMVLQDAVLFGG +TIRENIRYGRQDATDEEVVAAAKATFVDRFVHTLPEGYDTVIEQDASNVSAGERQLITIA +RAFLAQPSLLILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVME +HGDIVEQGNHAELLAARGAYHRLYMSQFKGGEDDGGGAASGEDAR +>PROKKA_00547 +MSEQLTDQEIVELQESGATDEWGGGPGRKAKAFWPSAKRLLGLFRTEKAGLALVAAMVLV +AVVFNVWAPHVLGRAMDVLFGGVISKGMPAGVSREQVIEGLRGQGQGQAADMLSGMDFTP +GQGIDFDALARLILTVLGMYVVAQGFMWLQGRVLNDVVMRIVFRLREQIEAKLNRLPLSH +FDTRQRGDLLSRATNDVDNVQQAMQQAFATLVYSVLTIFGIVGMMFWLSWELALIALIAL +PVAGVVVGVVGKKSQALFTAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAERFDERND +AMYEASFKAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN +QPLGQVAGMSNMLISGVASAERIFELLDEPEEEPDDVVAARADDDVAHLPQPVAGRVEFE +HVRFSYTEAKPLITDLNLVAEPGQTIAIVGPTGAGKTTLVNLIMRFYEVDGGRILLDGVD +TRRVPRQELRAATGMVLQDAVLFGGTIRENIRYGRLEATDEEVLAAAKATYVDRFVHTLP +DGYDTVIEQDASNISAGERQLITIARAFLAQPSLLILDEATSSVDTRTEVLVQQAMAALR +NDRTSFVIAHRLSTIRDADVILVMEHGDIVEQGSHEELLAARGAYHRLYTSQFRGGEDEH +HDDGAPASR +>PROKKA_02085 +MSEHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLAVVAVMVLV +AVVFNVWAPRVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTP +GEGIDFTELGRLILIVLGMYLVAQTFMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSY +FDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMMFWLSWQLALIALVAL +PVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNE +ELYEAAFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN +QPLGQIAGMSNMLISGVASAERIFELLDEPEETPDGTPARTPDGTFVWETAPSESAFVRE +TAPSAIPGPDGVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNFVAEPGQTVAIVGPTGA +GKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRGELRAATGMVLQDAVLFGGTIRENIRYG +RLDATDEEVVAAAKATYVDRFVHTLPDGYDTVIEQDAANVSAGERQLITIARAFLAQPSL +LILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVMEDGDIVEQGS +HDQLLAARGAYFRLYRSQFQGGEQAEEQDDDGAPAAREDAR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001683.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001683.fa new file mode 100644 index 0000000000000000000000000000000000000000..213f0a09eba7fa0793410ff6520882c440159edf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001683.fa @@ -0,0 +1,43 @@ +>PROKKA_02149 +MRRPSLPSLSRLPVRRLLRGAAVAAGVGLVGLPLTVAAGLTGVDMVKRGGRVRRPAPNPG +VFDAHVEGSELRIFTSGEDLYKEMIAAIDGAQRIIKFETFIWKGDPTGQRFMDAFNRAAA +RGVEVYVSYDGFGNLVVPPRFYRQLDPRIHVFRLPAFARPIWRGVVRHSGFNHSKIMVVD +DEVGFAGGFNIGDDYARLWRDTHVRERGPAVWALGQSISIKWNAHHRAGEQMSWRPPDTW +DPRVTVAANQPPLLVYPIRLSYLDAIQRAQHRILINTPYFIPDQQVLEALLHAARRGVDV +QVMVPEDSNHIVADWASRGFFGKMLEAGITILLYRASMIHAKTATVDGIWSTVGSANVDR +LSLGFNYESNVVVVDRDFAARMEEIFALDAQRAVRIDTPRWEDRHGLARVVEALLVPLRP +LL +>PROKKA_01862 +MAAGVGLVGLPLTVAAGLTGVDMVKRGGRVRRPAPNPGVFDAHVEGSELRIFTSGEDLYK +EMIAAIDGAQRIIKFETFIWKGDPTGQRFMDAFNRAAARGVEVYVSYDGFGNLVVPPRFY +RQLDPRIHVFRLPAFARPIWRGVVRHSGFNHSKIMVVDDEVGFAGGFNIGDDYARLWRDT +HVRERGPAVWALGQSISIKWNAHHRAGEQMSWRPPDTWDPRVTVAANQPPLLVYPIRLSY +LDAIQRAQHRILINTPYFIPDQQVLEALLHAARRGVDVQVMVPEDSNHIVADWASRGFFG +KMLEAGITILLYRASMIHAKTATVDGIWSTVGSANVDRLSLGFNYESNVVVVDRDFAARM +EEIFALDAQRAVRIDTPRWEDRHGLARVVEALLVPLRPLL +>PROKKA_00613 +MSPLPASPLHRIPVRRIVRGAALAAGTGLVGVPMAVAAGLTGVDMVKRRGRRRRPAHNPG +VFDAPVKDCHLRIFTSGEDLYEEMLAAIDSAERIVKFETYIWKADPTGQRFIEAFNRAAA +RGVEVYVSYDGFGNLVVPRAFYRQLDPRIRVFRLPAFARPFWRGPVRNTGFNHSKIMVVD +DEIGFVGGFNIGDDYATFWRDTHVCERGPAVWALDQSISIKWNAHHREGEQMSWRPPESW +DPRVTVSANQPPLLVYPIRLTYLEAIQRAQHRILINTPYFIPDQQVLQALLHAARRGVDV +QVMVPRDSNHIVADWASRGFYAGMLEAGITILLYEASMIHAKTATVDGIWSTVGTANIDR +LSLGFNYESNVVVVDRDFAARMEEIFAIDAEQSERVESPRWQDRHGVARMVERLLVPLRP +LL +>PROKKA_00537 +MGYALRRAAVAGTTAFVGVPLATAVAVSAYDAFKHRGRKLRPAERPGTFQAQVGPDALTI +YTAGDDVYDAMIQAIDDARETVKFETFIWKDDATGQRFVDALNRAAARGVQVWASYDGFG +NLLIPPSFYRQFDPRVRVFRLPAFARPLWRGVVRYSGFNHSKILTVDGRVGFVGGYNVGD +LYAAHWRDTHLRVEGPAVWGLEHSLSVLWNEGYTDMAEMPWTRPEEWEERTVVAANLPTQ +LVYPIRNTYLNAIARAQDHIYISTPYFVPDRQVLDALKEAARRGVDVQVLVPKDSNHVVA +DWVSRGFYSEMLDAGITILLYAAGMIHAKTATIDGRWATVGTANIDRLSLSFNYETNVSV +VDRDFAARMEDVFRADAARSERIQSPRWKDRHGLARVVEKLLVPLRPLM +>PROKKA_02092 +MHRPPLPSLSRLPVRRLLRGAAVAAGVGLVGLPLTVAAGLTGVDMVKRRGRVRRPAPNPG +VFDAHVKGSELRIFTSGEDLYEEMIAAIDGAQRIIKFETFIWKGDPTGQRFMDAFNRAAA +RGVEVYVSYDGFGNLVVPPRFYRQLDPRIHVFRLPAFARPIWRGVVRHSGFNHSKIMVVD +DEVGFAGGFNIGDDYARLWRDTHVRERGPAVWALGQSISIKWNAHHRAGEQMSWRPPDTW +DPRVTVAANQPPLLVYPIRLSYLDAIQRAQHRILINTPYFIPDQQVLEALLHAARRGVDV +QVMVPEDSNHIVADWASRGFFGKMLEAGITILLYRASMIHAKTATVDGIWSTVGSANVDR +LSLGFNYESNVVVVDRDFAARMEEIFALDAQRAVRIDTPRWEDRHGLARVVEALLVPLRP +LL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001684.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001684.fa new file mode 100644 index 0000000000000000000000000000000000000000..c94e53aed09ba4f2c02bbc1a63947783bf1dd641 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001684.fa @@ -0,0 +1,35 @@ +>PROKKA_02150 +MRPPGALALEFRADSFDHPTGLVDAGTVISWIEKAGYAVAASWAGTFVRARYMGHTQFRH +PVPVDRRAVVQARVVHTDGAEVHVQTRLLLPEIRDDDGDPVVATSSLVVYAAEEGGVPVT +VPVWEPSTPGQIERDEQARRSTVARRAVERGMARLPFPAPGEAPEEMSTLAFLAPNAEAT +VGGTINAGAILRWVDEAAAVCAARWTGHESVVAVFGGGVRFVRNIHVGDLVRVEALLVNT +TERSMHVALRVYASRRTGAESRLVAHSIAVMVDVSAEDQAQRVRQYIPESESARRLQETA +IELVRMRSEVSAAWTEMRRSTDPR +>PROKKA_01863 +MRPPGALALEFRADSFDHPTGLVDAGTVISWIEKAGYAVAASWAGTFVRARYMGHTQFRH +PVPVDRRAVVQARVVHTDGAEVHVQTRLLLPEIRDDDGDPVVATSSLVVYAAEEGGVPVT +VPVWEPSTPGQIERDEQARRSTVARRAVERGMARLPFPAPGEAPEEMSTLAFLAPNAEAT +VGGTINAGAILRWVDEAAAVCAARWTGHESVVAVFGGGVRFVRNIHVGDLVRVEALLVNT +TERSMHVALRVYASRRTGAESRLVAHSIAVMVDVSAEDQAQRVRQYIPESESARRLQETA +IELVRMRSEVSAAWTEMRRSTDPR +>PROKKA_00612 +MKPAGALALEFRADSFDHPGGLVDAGTVISWIEKAGYAVAASWAGTFVRARYMGHTQFRH +SVPVDHRAVVQARVVHTDGADVHVQTRLLLPEVKDESGDPVVATSSLVVYSAEEDGARVT +VPAWVPSTPGQIERDEQASRSTVARRAVERGMARLPFPSPGQAPEEMSTLAFLAPASEAT +VGGTMNAGAILRWLDEAAAVCAARWTGHESVVAVFGGGVRFVRNILVGDLVRVDALLVNT +TERSMQVALRVYAGRPTGVQPRLVAHSIAVMVDVSAEDKAQPVRQYVPESEGARSLQEAA +VQLVRLRSEVGAAWTETRRSPESR +>PROKKA_00536 +MMRSGALSLDFRADSFDHPSGLVDAGTAIGWIDKVGYAVAASWSGTYVRARYMGTMQFRH +PVPVDMRVTVQGRVVRTHGAAVHVQLRLLLPEVLDDDGRPVVSTSTLSVYYAEEDGQMLQ +VPEWTPSTPDQIERDERARVSSVERRGIEQVMARLPFPEPGQEHEEMTTLAFIAPMAEAS +VGGTVAAGAVMRWLDEAAGVCAARWTGHENVVAVFAGGVRFVRPVKVGDLVRVDALLVHT +SERSMHVALRVHAGPRHQRDHRLVAHSIAVMVDVTREGRAESVRPYAPGSPAAHRLEESA +VELVRLRSEAGAVWSDPS +>PROKKA_02093 +MRPPGALALEFRADSFDHPTGLVDAGTVVSWIEKAGYAVAASWAGTFVRARYMGHTQFRH +PVPVDRRAVVQARVVHTDGAEVHVQTRLLLPEIRDDDGDPVVATSSLVVYAAEEDGVPVT +VPAWEPSTPGQIERDEQARRSTVARRAVERGMARLPFPAPGEAPEEMSTLAFLAPNAEAT +VGGTINAGAILRWVDEAAAVCAARWTGHESVVAVFGGGVRFVRNIHVGDLVRVEALLVNT +TERSMHVALRVYASRRTGAESRLVAHSIAVMVDVSAEGQAQPVRQYVPESESARRLQETA +IELVRMRSEVSAAWTETRRSTDPR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001685.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001685.fa new file mode 100644 index 0000000000000000000000000000000000000000..dcecda151b5e822975c14fc901e4104dd2bc2f2f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001685.fa @@ -0,0 +1,25 @@ +>PROKKA_02151 +MTAFDRFPLPAEPQTPHDRLRRRTEAAVAERGEAAVAGLAVRLMTGAATPDDVTSGAARA +LTGDDGDLSPAATGALALMHAWHRSALPALTGALTAPEADVRSAAHLVLASRAGSLRRDA +AVDRTLVDAVRAGCADPDPEVRASAASALGALARPEDLESALPVLTGMVMDVDADLAAAA +ELALEQLAIRLDRPGLRVSLEG +>PROKKA_01864 +MTAFDRLPLPAEPQTPHDRLRRRTEAAVAERGEAAVAGLAVRLMTGAATPDDVTSGAARA +LTGDDGDLSPAATGALALMHAWHRSALPALTGALTAPEADVRSAAHLVLASRAGSLRRDA +AVDRTLVDAVRAGCADPDPEVRASAASALGALARPEDLESALPVLTGMVMDVDADLAAAA +ELALEQLAIRLDRPGLRVSLEG +>PROKKA_00611 +MTAFDRLPLPAEPQTPHDRLRRRVAAAVAERGEAAVAGLAVRLLTGSVTPADVTSGAARA +LTGDDGDLTAGATGALALGHAWHRSALPALTSALSAPEPDVRSAAHLVLAARAGSLRADV +AVDRALVDAVRAGCADPDPQVRASAASALGALAGPQDLEAALPVLTGMVMDVDADLATAA +ELALDHLAERLDRPDLRVGAEG +>PROKKA_00535 +MTSRDLPLPVEPQTPHTRLARRVEAAVSARGEAAVAGLAVRLLTGAPTPEDVTSGAARDL +IGDDGELTPGATGALALGVVWHRGAAGALAAALDAPEPEVRAAALLVLAARADRLRADAQ +AGRALVEAVTARASDADPQVREAAASALGALARAEDLSAVEPVLSALVMDVDPELATAAE +LALAHLAARLDRPELDPTPQA +>PROKKA_02094 +MTAFDRLPLPAEPQTPHDRLRRRTEAAVAERGEAAVAGLAVRLMTGAATPEDVTSGAARA +LTGDDGDLSPAATGALALMHAWHRSALPALTGALTAPEADVRSAAHLVIASRAGSLRRDA +AVDRALVDAVRAGCADPDPEVRASAASALGALARPEDLESALPVLTGMVMDVDADLAAAA +ELALEQLAIRLDRPGLRVSLEG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001686.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001686.fa new file mode 100644 index 0000000000000000000000000000000000000000..6ffb8342852e44a39ce56a76cdc20f4686b81491 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001686.fa @@ -0,0 +1,41 @@ +>PROKKA_02152 +MQCPHFDVGECRSCPLMGVPYARQLADKQAAVLAALADALDADTVVAEPFASAEAGFRNK +AKLVVTGSAAAPRLGILDPRQHPRHHDGAGVDLRDCGLYEAGMEGVFEACAAAVTAAGLE +PYDVAARTGELKNVIVTLSPDREAMVRFVLRSADRLDALRAAVPGLLDDLAARGTPAAVV +SANLLPEHVALPEGDEEIVLAGGPTLRMELNGIGLRLRPQGFFQTNTAVTEGLYATAAAW +VAEGGVPASAWDLYCGVGGFAFHLARAGVRDVWGMESSAEAVAAARETAAELGLADRARF +SAGDATSALSFEKRRAPEALSFEKRRSRPDAVVVNPPRRGIGAELADALEDSGAPTVLYS +SCNPTTLAQDLARMPSYRVARVQLFDMFPQTLHAEVLTLLTRR +>PROKKA_01865 +MQCPHFDVGECRSCPLMGVPYARQLADKQAAVLAALADAVDADTVVAEPFASAEAGFRNK +AKLVVTGSAAAPRLGILDPRQHPRHHDGAGVDLRDCGLYEAGMEGVFDACAAAVTAAGLE +PYDVAARTGELKNVIVTLSPDREAMVRFVLRSADRLDALRAAVPGLLDDLAARGTPAAVV +SANLLPEHVALPEGDEEIVLAGGPTLRMELNGIGLRLRPQGFFQTNTAVTEGLYATAAAW +VAEGGVPASAWDLYCGVGGFAFHLARAGVRDVWGMESSAEAVAAARETAAELGLADRARF +SDGDATSALSFEKRRAPEALSSKKRRPRPDAVVVNPPRRGIGAELADALEDSGVPTVLYS +SCNPATLAQDLARMPSYRVARVQVFDMFPQTRHAEVLTLLTRR +>PROKKA_00610 +MQCHHYDAGRCRSCALMGVPYGVQLTDKDAAVCARLDAAVPAEAWLPPQASAESGFRNKA +KLVATGTAAAPRLGILDPEQHPRHHDGTGHDLRDCGLYEDGMEAAFHAIAETIPAAGLEP +YDVAARTGELKSVIVTLSPDRELMVRFVLRSAARLDALRAAVPGLRSALAGLGTPAAVVT +ANLHPEHVALPEGPDEVHLAGDPTLRMELNGIGLRLRPQGFFQTNTDVTRRLYATAAAWL +AEAAAADGTPVHSAWDLYCGVGGFAFHLARPVAEGGAGVAEVWGLETSEDAVAAARDTAA +ELGLAGAVRFTAGDATRALSPGRREPSEALSSGKREAWDALSSGSREPSDAGAHPDDDAA +PAAMPDAVVVNPPRRGIGPELAARLQDSGVPHVLYSSCNAASLAKDLAAMPAYRARRAQV +FDMFPQTGHAETLVLLSRA +>PROKKA_00534 +MQCPHFDAGECRSCALMGVPYGAQLADKDAAVRARLAEATDARTRWEAPAASAESGFRNK +AKLVVTGTAAAPRLGILDPRQHPRHHDGTGVDLRDCGLYEDGMEAAFHAIAGAVTAAGLE +PYDVAARTGELKNVIVTRSPDRELMVRFVLRSADRLEALRPEVPALREALAALGTPAAVV +TANLHPEHVALPEGPEEVHLAGDATLRMELNGIGLRLRPQGFFQTNTDITQRLYATAAAW +LAEAAAEGGTPVERAWDLYCGVGGFAFHLARPVAEGGAGVAEAWGLEVSAEAIEAAREAA +AELGVAERVRFTAGDATTALAAPGGTRPDAVVVNPPRRGIGAELAGRFEESGVPFVLYSS +CNAATLATDLTAMPSYRVARAQVFDMFPQTGHAETLVLLARR +>PROKKA_02095 +MQCPHFDVGECRSCPLMGVPYARQLADKQAAVLAALADAVDADTVVAEPFASAEAGFRNK +AKLVVTGSAAAPRLGILDPRQHPRHHDGAGVDLRDCGLYEAGMEGVFDACAAAVTAAGLE +PYDVAARTGELKNVIVTLSPDREAMVRFVLRSADRLDALRAAVPGLLDDLAARGTPAAVV +SANLLPEHVALPEGDEEIVLAGGPTLTMRLNGVGLRLRPQGFFQTNTAVTEGLYATAAAW +VAEAGLPAAAWDLYCGVGGFAFHLARAGVRDVWGMESSAEAVAAARETAAELGLADRARF +SAGDATSALSFEKRRAPEALSSKKRRPRPDAVVVNPPRRGIGAELADALEDSGVPTVLYS +SCNPATLAQDLARMPSYRVARVQVFDMFPQTRHAEVLTLLTRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001688.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001688.fa new file mode 100644 index 0000000000000000000000000000000000000000..4a4b5828cbb86c4cc54de7c325674e36f49dd005 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001688.fa @@ -0,0 +1,50 @@ +>PROKKA_02157 +MEVLLALSPILLTLVLLLTRLPAWVAPAAGTAVAVLLALTAFGVAPGDLGGAIGAGVPTL +LEILAIIAGGITLSRVMEYSGGHARLAAWLSAGNGPTIATALLMVHGVIPFLETVTGFGV +SLIVGVPLLLGLGYTAFRSALISVLALTIGPWGSMAPGTLMGARLFGLDFREIGVTAAVF +NLPACLVAGVATVLLLRGARGMRVDVGPARTLPWLGVAVLSGVAQWALILGANLVVGTAP +AGAVATFVLTVAWLLVIRGGRLLPGPGRDVVPYLTLMAGTVLGTTVKGAFGLEGAAALVG +TPALWAFVAVGVGVQLLHLDAAARRRVPREAGKLWVGTAIPNALYVAFGLILSAGGVSQA +LAGALSGMGESYLVAMPFLGAFAGFITASNTGAMALIGPLQMDTGAALGVPPPWSNGLHN +AAAGWGIVAGPARIQVAHGMAAGAQSPHMPGWAVTRRNLFVVLLPAMLAGILGMAVMGWF +LLPR +>PROKKA_01870 +MEVLLALSPILLTLVLLLTRLPAWVAPAAGTAVAVLLALTVFGVAPGDLGGAVGAGVPTL +LEILAIIAGGITLSRVMEYSGGHARLAAWLSAGNGPTIATALLMVHGVIPFLETVTGFGV +SLIVGVPLLLGLGYTAFRSALISVLALTIGPWGSMAPGTLMGARLFGLDFREIGVTAAVF +NLPACLVAGVATVLLLRGARGMRVDVGPARTLPWLGVAVLSGVAQWALILGANLVVGTAP +AGAVATFVLTVAWLLVIRGGRLLPGPGRDVVPYLTLMAGTVLGTTVKGAFGLEGAAALVG +TPALWAFVAVGVGVQLLHLDAAARRRVPREAGKLWVGTAIPNALYVAFGLILSAGGVSQA +LAGALSGMGESYLVAMPFLGAFAGFITASNTGAMALIGPLQMDTGAALGVPPPWSNGLHN +AAAGWGIVAGPARIQVAHGMAAGAQSPQMPGWAVTRRNLFVVLLPAMLAGILGMAVMGWF +LLPR +>PROKKA_00601 +MQVLLALTPILLTLALLLTRLPAWVAPAAGGVLAAALAPTVFGVDPGVLAAEVGRGVPTV +VEILAIIAGGITLSRVMEHSGAHARLALWLSAGNGPTLATALLMVHGIIPFLETVTGFGV +SLIVGVPLLLGLGFTAFRSALLAVLALTIGPWGSMAPGTLMGARLYDLDFQAVGVTAALF +NLPASLVAGAATVLLLRGAQGMRGDGEPARTVPWLAVGLLSGAAQWALILGANLSVGTAP +AGAVGTFVLTVAWLLVIRRGRLTPGPGRDVVPYVTLMAGTVFGTTVEDALGLTGVLSVVG +TPALWSFVAVGAGVALLGLGPHARRTVPGEAARLWVGTAIPNALYVAFGLTLSAGGVSQA +LAGALSGMGPAYLAAIPVIGAFSGFVTASNTGAMALMGPLQMDTGAALGVPPTWTNGLHN +AAAGWGIIAGPARIQVAHAMAVGAQTPEMPGWAVSRRALLAVLLPAMVVGIALMSLLGLA +VLPRV +>PROKKA_00523 +MQVLLALAPILLTLGLLMTRLPAWAAPAAGSVAAVVLGLTVFGVDPAVLGAAVGHGVPTV +LEILAIIAGGITLSRVMEHSGAHARLGGWLSAGNGPTLATALLMVHGVIPFLETVTGFGV +SLVVGVPLLLGLGFTAYRAALLSVLSLTIGVWGSMAPGTLMGARLAGLDVQEVGVTAAVF +NLPASLVAGVATVLAVRGARGLRDDSAPARLAPWLGVALASGTAQWALILGANLLVGTAP +AGAVATFALTLAWLLVIRRGRLTPGPGRDVVPYVTLMAGTVLGTTAEDALGLTGPLSVVG +TPALWSFVAVGVGLRLLDLDAAARRTVPRESLRLWRGTAVPNALYVAFGLVLSAGGASPA +LAGALSGLGESYLAAMPFIGAFAGFVTASNTGAMALVGPLQMDTGAALGVPPAWSNGLHN +AAAGWGIIAGPARIQVAHGMAAPAQTPDMPGRAVSPRGLVAALLPASLAGVAGMSLMGWL +LLPR +>PROKKA_02100 +MEVLLALSPILLTLVLLLTRLPAWVAPAAGTAVAVLLALTAFGVAPGDLGGAIGAGVPTL +LEILAIIAGGITLSRVMEYSGGHARLAAWLSAGNGPTIATALLMVHGVIPFLETVTGFGV +SLIVGVPLLLGLGYTAFRSALISVLALTIGPWGSMAPGTLMGARLFGLDFREIGVTAAVF +NLPACLVAGVATVLLLRGARGMRVDVGPARTLPWLGVAVLSGVAQWALILGANLVVGTAP +AGAVATFVLTVAWLLVIRGGRLLPGPGRDVVPYLTLMAGTVLGTTVKGAFGLEGAAALVG +TPALWAFVAVGVGVQLLHLDAAARRRVPREAGKLWVGTAIPNALYVAFGLILSAGGVSQA +LAGALSGMGESYLVAMPFLGAFAGFITASNTGAMALIGPLQMDTGAALGVPPPWSNGLHN +AAAGWGIVAGPARIQVAHGMAAGAQSPQMPGWAVTRRNLFVVLLPAMLAGILGMAVMGWF +LLPR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001689.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001689.fa new file mode 100644 index 0000000000000000000000000000000000000000..497d185a3a010c11f43398c8aab294004496a974 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001689.fa @@ -0,0 +1,40 @@ +>PROKKA_02158 +MTQPSHPDDVTRARLIPPVPVAVAPMAGGPSTPELVAAVVGAGGGGFLAGGMRTAAQMRA +QVDALRALLGAERPDRWGVNLFVPDAVNTAIPAAARTEAARSARAAAVAAYRAGLTADGA +ADLPAVADVVPDPDAERADFEAMLVAAEEQAWPLVSFTFGLPAADVFARLAAAGVPAGAT +VTDAAEARAALEHGAAFLVVQGHRAGGHRGTSDPAAEPTRAELPTVLAAVRDVVGTGAAS +AAPVVAAGGVGTAEDVRALLTAGADAVSAGTAFLLTPEAGTSAAHRAAVAACAAGTRFSA +DDGRARTALTRAYTGRWARSLATAFMAEHPDAPAAYPEVNVLTKGLRAAAAAVGDLERVH +LWAGTEAHRVREAPAADVLASLTP +>PROKKA_01871 +MTQPSHPDDVTRARLIPPVPVAVAPMAGGPSTPELVAAVVGAGGGGFLAGGMRTAAQMRA +QVDALRALLGAEGPDRWGVNLFVPDAVNTAIPDAARTEAARSARAAAVAAYRADLTADGA +ADLPTAADVVPDPDAERADFDALLTAAEEQAWPLVSFTFGLPAADVFARLAAAGIPAGAT +VTDATEARAALEHGAAFLVVQGHRAGGHRGTSDPAAEPPRAELPAVLPAVRDVVGTGATS +AVPVVAAGGVGTAEDVRALLTAGADAVSAGTAFLLTPEAGTSAAHRAAVAACAAGTRFSA +DDGRARTGLTRAYTGRWARSLATAFMAEHPDAPAAYPEVNVLTKGLRAAAAAAGDLERVH +LWAGTEAHRVREAPAVDVLASLTP +>PROKKA_00600 +MSAAQLPDDVVRARLIPPARVLAAPMAGGPSTPELVAAVVRAGGSGFLAGGMRTAAQVRE +QVDALRGLLGGGDGSVDGSDAARRWGVNLFVPDAVNTAIPAADRTERARAERRAAVAAYR +ERLAAEGERAAGGAAAEGAGGAPTLPSPDDVTPDPARERAEFAAMLTAAEEQAWPLVSFT +FGLPEPAVFARLAAAGIPAGVTVTDADEARSARAHGAAFLVVQGHRAGGHRGTLDPAADP +VERELPSVLAQVRAVVGTRVPVVAAGGVGAAAHVRSLLAAGADAVAAGTAFLLAAEAGTS +VAHRAGIRRCAAGEGFVGPDGAARTVLTRAYTGRWARTLATDFAAAHPDAPAAYPELNAL +TTGLRAAAATAGDLERVHLWAGTQAHTAREAGAADVVAGLTP +>PROKKA_00522 +MSSTTVPSVPAPVPAPLDPPVPVLAAPMAGGPSTPELAAAVIRAGGGAFLAGGMRSAAQV +REQVDGLRALLTAPEEAGRFGVNLFVPDAVNTAVAASARGGAARIARAQAVASYRERLAP +LAADLGAELPSVLTVTPDPDAERAAFEDMLAAAEEQSWPAVSFTFGLPAPDVFARLDAAG +IPAGVTVTSPAEAMAAVASGARFLVVQGPKAGGHRATLDPQGRPGITDLRTLVFAVRHAL +GPAAVPLVAAGGITDGAQVRPLLEAGAVAVAAGTAFLLTPEAGTSAAHRTALRQASAGVA +FAHPDDGAASTALTRAYTGRWARGLVTPFMDEHHDAPAAYPEVNGLTGPLRRAAAEEGDL +EHVHLWAGTGAHRVEEVGAAEVLASLAPRAEP +>PROKKA_02101 +MTQPSHPDDVTRARLIPPVPVAVAPMAGGPSTPELVAAVVGAGGGGFLAGGMRTAAQMRA +QVDALRALLGAEGPDRWGVNLFVPDAVNTAIPDAARTEAARSARTAAVAAYRAGLTADGA +AGLPTAADVVPDPDAERADFDALLTAAEEQAWPLVSFTFGLPAADVFARLAAAGIPAGAT +VTDATEARAALDHGAAFLVVQGHRAGGHRGTSDPAAEPTRAEMPTVLAAVRDVVGTGAAS +AAPVVAAGGVGTAEDVRALLTAGADAVSAGTAFLLTPEAGTSAAHRAAVAACAAGTRFSA +DDGRARTGLTRAYTGRWARSLATAFMAEHPDAPAAYPEVNVLTKGLRAAAAAAGDLERVH +LWAGTEAHRVREAPAADVLASLAP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001690.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001690.fa new file mode 100644 index 0000000000000000000000000000000000000000..7e568eebc13ceaa9abf382aa2f59c2086ce71866 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001690.fa @@ -0,0 +1,46 @@ +>PROKKA_02159 +MNPLRRLDQWTRLHPVRTDVMAAAALFTVLVALPWIALGPMVAPDPQGRQTAVSLLAGAG +MVLPWAVRRVRPVASAAVVTAAAVLHLLAGPEFSLSLLMVPLTVYNLAANAPRSVSVAGL +LLGLVGGVANGVKVWLFPAQFVTPDGLTVRSPAEPLAMVIMAIGCGLMVLTAWAFGDVVR +NRRLTVRALEDRAHRLEVQSRQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYA +AAAKPALAVTALETIGQTGRSALADMRQLLGVLRETGETVAGVPGVTDDDARRPAADVVA +SPDGRGTRLPPGRRPQPRLADLPALVETMRLSGLEVSLLETGTPRRTLPAGGELAAYRIV +QEALTNTLRHGGPDADAFVTLAWTAHGLDLQIDDDGCGAAADPATRGSGQGLRGAAERTA +LFGGTLETGPRVGAGYRVSAHLPYSAV +>PROKKA_01872 +MNPLRRLDQWTRLHPVRTDVMAAAALFTVLVALPWIALGPMVAPDPQGRQTAVSLLAGAG +MVLPWAVRRVRPVASAAVVTAAAVLHLLAGPEFSMSLLMVPLTVYNLAANAPRSISVAGL +LLGLVGGVANGVKVWLFPAQFVTPDGLTVRSPAEPLAMVIMAIGCGLMVLTAWAFGDVVR +NRRLTVRALEDRAHRLEVQSRQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYA +AAAKPALAVTALETIGQTGRSALADMRQLLGVLRETGETVAGVPGVTDDDARRPAADVVA +SPDGRGTRLPPGRRPQPRLADLPALVETMRLSGLEVSLLETGTPRRTLPAGGELAAYRIV +QEALTNTLRHGGPDADAFVTLAWTAHGLDLQIDDDGCGAAADPATRGSGQGLRGAAERTA +LFGGTLETGPRVGAGYRVSAHLPYSAV +>PROKKA_00599 +MNPLHRIDQWMRAHPVRTDVLVSVLLFAVLGLTPWVMLGSLAGPTPGSIVASILIALALI +APWAFRRVRPVASAAAVAAAAVAHLVAGPEFSLALVLVPMTVYNLAANAPRWASFTGLVA +ALLGGVANGIRVGLFPDPAMRPDGVYEPVDPSLEALLVMVFGCAAVVLTAWAFGDVVRHR +RLAVRALEDRNRRLETMALQERRLAASDERNHIAREMHDIVAHSLQVIISQADGARYAAA +AKPELAVATLDTIGLTGRAALADMRQLLGVLRETGETVAGVPGVAPDDGAPGPAAGASDE +GAAGAADEGAAGAADEGAAGAGTAGAGTTPGAGRTRLPADVASRDGRGARQPPGHRPQPT +LADVPALIETMRLSGLEVSLLETGAPRRPLPPGGELAAYRIVQEALTNTLRHGGPQASAF +LTLAWTGRGLDVQSDDDGRGADADPGTRGSGHGLRGVAERVALFGGTVETGPRAGAGYRV +SAHLPYSAV +>PROKKA_00521 +MNPLRRLDVLLRRHPVRTDVTAAVLLTLVLVLAPLVMLGGGVGSPAAWQTAGTVVAGLLM +TGAWGLRRVRPVAAAGVTVAGALLHLAVGPEFTIALAMVPATVYNLAAIGPRWASLAGLA +TGLAGGLANGLKVWLFPPRFTTPDGVQVQSPAEPVAMVVMAVLCGMAVLTAWAFGDVVRN +RRLAVQALEDRARRLETQALQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYAA +AAKPELAVETLETIGQTGRSALADMRQLLGVLRGPAEPTGGPDRARRDPAAPDGHRAPPG +LADLPALFQTLRLSGLEISLLEQGSPRRDLPAGGELTAYRTVQEALTNTLRHGGEGAHAF +LTLRWTARGLEIQADDDGRSQADAETTGSGQGLRGIAERVALFGGTMEAGPRVGAGWRVW +AELPYADV +>PROKKA_02103 +MNPLRRLDQWTRLHPVRTDVMAAAALFTVLVALPWIALGPMVAPDPQGRQTAVSLLAGAG +MVLPWAVRRVRPVASAAVVTAAAVLHLLAGPEFSLSLLMVPLTVCNLAANAPRSVSVAGL +LLGLVGGVANGVKVWLFPAQFVTPDGLTVRSPAEPLAMVIMAIGCGLVVLTAWAFGDVVR +NRRLTVRALEDRAHRLEVQSRQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYA +AAAKPALAVTALETIGQTGRSALADMRQLPGVLRETGETVAGVPGVTDDDTRRPADPAPD +RADPTGTRPDVVAAPDGRGARLPPGRRPQPRLADLPALVETMRLSGLEVSLLETDTPRRA +LPAGGELAAYRIVQEALTNTLRHGGPDADAFVTLAWTARGLDLQIDDDGRGAAADPATRG +SGQGLRGAAERTALFGGTLETGPRVGTGYRVSAHLPYSAV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001691.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001691.fa new file mode 100644 index 0000000000000000000000000000000000000000..1e7ded723227736df473ab4c550fabccdc91fdff --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001691.fa @@ -0,0 +1,14 @@ +>PROKKA_02161 +MTGSILDHPAPTTSRASDPAAERAQRDSECVAFFVALVTAAVVMLGLSLFTGVEGLLRLA +LTAGAGLLAGAVAWATARPVLEDDAPGD +>PROKKA_01874 +MTGSILDHPTPTTSRASDPAAEQAQRDSECVAFFVALVTAAVVMLGLSLFTGVEGLLRLA +LTAGAGLLAGAVAWATARPVLEDDAPGD +>PROKKA_00596 +MTAAVVILGLSLFTQVEGLPRLLVTAASGLLAGAVTWSVTQPVLEDEVLHG +>PROKKA_00519 +MSAAPAPSPAAPAVPPVTAVPPAAREPEGTSPSDRERERGDAECLAFFLALVTAALVMAG +LALATDLGPLLRVLLSLGASGLAGALTLAFTRPSLED +>PROKKA_02105 +MTGSILDHPAPTTSRASDPAAERAQRDSECVAFFVALVTAAVVMLGLSLFTGVEGLLRLA +LTAGAGLLAGAVAWATARPVLEDDAPGD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001692.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001692.fa new file mode 100644 index 0000000000000000000000000000000000000000..7177cef96265090eb3798b2d53263bd34445f2dc --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001692.fa @@ -0,0 +1,30 @@ +>PROKKA_02163 +MDTSSPAHPFSPTTPGPVAPGPGTPSSSATTTTAPAVCARGLTRAYGRGDAQVHALRGVD +VDFASGAFTAIMGPSGSGKSTLLHCLAGLDARTSGSVRIGGTEITGLDDTALTRLRRDRV +GFVFQAFNLVPTLTAEQNIVLPLELAGRTPDRAWLDEITRALGLADRLGHRPHELSGGQQ +QRVAVARALLTRPDVVFGDEPTGNLDTATSAEVLGLLRRSAREMGQTVIMVTHDPVAASA +ADRVVLLADGRLAGELVDPTVESVTAALTALSAPAEGGVR +>PROKKA_01877 +MDTSSPAHPFSPTTPGPVAPGPGTPSSSATTTTAPAVCARGLTRAYGRGDAQVHALRGVD +VDFASGAFTAIMGPSGSGKSTLMHCLAGLDAPTSGSVRIGGTEITGLDDTALTRLRRDRV +GFVFQAFNLVPTLTAEQNIVLPLELAGRTPDRAWLDEITRTLGLADRLGHRPHELSGGQQ +QRVAVARALLTRPDVVFGDEPTGNLDTATSAEVLGLLRRSAREMGQTVIMVTHDPVAASA +ADRVVLLADGRLAGELVDPTVESVTAALTALSAPAEGGVR +>PROKKA_00594 +MSTTADSHSAHSTPPGAGASGPGMPSSSTTTTTAPAASARALTKTYGRGDAEVHALRGVD +VDFAAGAFTAIMGPSGSGKSTLMHCLAGLDTPTSGSVVLGGTEITGLGDTALTRLRRDRV +GFVFQAFNLVPTLTAEQNIVLPLELAGRKPDRAWLDEITATLGLTDRLKHRPHELSGGQQ +QRVAVARALLTRPDVVFGDEPTGNLDSATSAEVLGLLRRSAREMGQTVIMVTHDPVAASA +ADRVVLLADGRLAGELLDPTVESVTNALAALSAPGAADAAGTFDAPADGGR +>PROKKA_00517 +MDITSPRSAAHDAGAHALATPLAHAAAPPAPAVSARGLTKTYGRGDAAVHALRGVDVDVE +TGRFTAIMGPSGSGKSTLMHCLAGLDTPDAGVVTLGDTVITGLSDAALTRVRRDRVGFVF +QAFNLVPTLTAEQNIVLPMELAGRTPDRAWLAEIVDRLGLSDRLAHRPHELSGGQQQRVA +VARALLTRPDVVFGDEPTGNLDSATGAQVLDLLRRATRETGQTVIMVTHDPVAAAAADRV +VLLADGALAGELHAPTAERVAEALTALQQGRPLPQGRPLPQDGGR +>PROKKA_02108 +MDTSSPAHPFSPTTPGPVAPGPGTPSSSATTTTAPAVCARGLTRAYGRGDAQVHALRGVD +VDFASGAFTAIMGPSGSGKSTLMHCLAGLDAPTSGSVRIGGTEITGLDDTALTRLRRDRV +GFVFQAFNLVPTLTAEQNIVLPLELAGRTPDRAWLDEITRTLGLADRLGHRPHELSGGQQ +QRVAVARALLTRPDVVFGDEPTGNLDTATSAEVLGLLRRSAREMGQTVIMVTHDPVAASA +ADRVVLLADGRLAGELVDPTVESVTAALTALSAPAEGGVR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001694.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001694.fa new file mode 100644 index 0000000000000000000000000000000000000000..ab8746dbcbf28327486545c79849922bb88be258 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001694.fa @@ -0,0 +1,60 @@ +>PROKKA_02167 +MTSLLRILRFAPQLNRLYLGIAVSSVLAAVLALATPFLIGAATDRIVAAVAGETDVAEAV +TAVTWLAVAFLAVEVATTLVVSVGGYWGDVMAARMRTILSTRYFEQLLHLPQRYFDTAIT +GRVVNRLNRTINELTQFLQFFANNAFTMLITTAAVLVITAFYWWPLAILLAVVFPVYMWL +TARTSTKWQVWEGEKNTEVDIASGRFAEVVSQMSVVRAYNRQDHELSGFRDRFLRTVGIT +RQQSRFWHGMDAGRRLALNVAFGAMYLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSM +SFLVDSAQRAVAGSKDYFEVLAEERERAGGAALAVAGASAESAGADAPRVPAEPRADVVP +GAPDVPADVPAVRFDEVSFAYDADASRPVLDRVSFDIPRGARVALVGESGGGKSTIAHLL +LGLYPVTSGRIEVFGQDVAGLDLAVLRGRIATVFQEPSLFSGTVRENIAYADPDASDERV +RAAAEAAYAHRFVEAFDDGYEQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEATSA +LDTKSERLVQAALEELMVGRSSLIVAHRLSTIASVDRIVTLRGGQVQEIGTPAELAESGG +IYAQLLELQRAGTQEARKMLKEYGLSG +>PROKKA_01881 +MTSLLRILRFAPQLHRLYLGIAVSSVLAAVLALATPFLIGAATDRIVAAVAGETDVAEAV +TAVTWLAVAFLAVEVATTLVVSVGGYWGDVMAARMRTILSTRYFEQLLHLPQRYFDTAIT +GRVVNRLNRTINEITQFLQFFANNAFTMLVTTAAMLVITAFYWWPLAILLAVVFPVYMWL +TARTSAKWQVWEGEKNTEVDVASGRFAEVVSQMSVVRAYNRQDHELTGFRDRFLRTVEIT +RQQSRFWHGMDAGRRLALNVAFGAMYLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSM +SFLVDSAQRAVAGSKDYFEVLAEERERAGGAALAAASASAESAGADAPRVPAEPRADVVP +GAPDVPADVPAVRFDEVSFAYDADASRPVLDRVSFDIPRGARVALVGESGGGKSTIAHLL +LGLYPVTSGRIEVFGQDVAGLDLAVLRGRIATVFQEPSLFSGTVRENIAYADPDASDERV +RAAAEAAYAHRFVEAFDDGYEQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEATSA +LDTKSERLVQAALEELMVGRSSLIVAHRLSTIASVDRIVTLRGGQVQEIGTPAELAESGG +IYAQLLELQRAGTQEARKMLKEYGLSG +>PROKKA_00585 +MLAAVLTLATPFLIGAATDRIVAAIAGETTVEDAVVAVTWLAVAFLAVEVTTTLVVSVGG +YWGDVMAARMRTILSTRYFDQLLHLPQRYFDTAITGRVTNRLNRTINELTQFLQFFANNA +FTMLITTTAVLVITAFYWWPLAILLAIVFPVYMWLTAKTSAKWQVWEGEKNIEVDMASGR +FAEVVSQMSVVRAYNRQDHELAGFRERFTRTVGITRKQSRFWHGMDAWRRLALNVVFGAM +YLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSMSFLVDSAQRAVAGSRDYFEVLAEER +ERAGGAGPQGRGAAAVAAGQPRADDDGGTDVRWGGAAPSRPAQPRADVVPGDGTGGMPAG +PSADVVPAVRFDEVSFAYDPDASRPVLDRVSFEIPQGQRVALVGESGGGKSTIAHLLMGL +YPVTGGRIEVFGQDVAELDLAELRERIAAVFQEPSLFSGTVRENIAYADPAASDERVRAA +AEAAYAHRFVEAFDDGYEQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEATSALDT +KSERLVQGALEELMVGRSSLIVAHRLSTIASVDRIVTLRGGRVQEVGTPAELAESGGIYA +QLLRLQKAGTKEARKMLKEYGLSG +>PROKKA_00512 +MRALLRILRFAPQLNPLYLGIAVCSVLAAALSLATPFLIGAATNRIVDAIAGRSTLDDAV +AAVTWLALAFLAVEVATTAVVSVGGYWGDVMAARMRAALSGRYYDHLLHLPQRYFDTAIT +GRIVNRLNRSITELTQFLQFFSNNAFTMLITTAAVLVITAFYWWPLAVLLAVVFPVYMWL +TAKTSAKWQGWEGEKNTEVDIASGRFAETVAQMNVVRAYNRQDHELAGFTERFRRTVGIT +RKQSRFWHGMDAGRRLALNLVFGVMYLIVFVRTARGLFSVGDMVILLQLMNMARQPIFSM +SYLVDSAQRAVAGSKDYFGVLAEERERSGGAALPAGLGSAEAPTTTTATGVVVRDRAEAP +TGAPVRAGADVPAVRFADVTFAYDPEAERPVLDGVTFDIPQGAKVALVGESGGGKSTLAH +LLMGLYPVGSGRVEVFGRDVAGLDLAVLRGQVAAVFQEPFLFSGTIRENIAYADPDASGE +RVRAAAKAAFADGFVEEFEHGCEQLIGERGLRLSGGQKQRIAVARAVLKDAPVLVLDEAT +SALDTKSERLVQSALDDLMVGRSSLIVAHRLSTIASVDRIVTLRGGRVQEVGTPAELAQS +GGIYAQLLRLQKAGTKEARKLLKEYGLSG +>PROKKA_02112 +MTSLLRILRFAPQLHRLYLGIAVSSVLAAVLALATPFLIGAATDRIVAAIAGETGVAEAV +TAVTWLAVAFLAVEVATTLVVSVGGYWGDVMAARMRTILSTRYFEQLLHLPQRYFDTAIT +GRVVNRLNRTINELTQFLQFFANNAFTMLITTAAVLVITAFYWWPLAVLLAVVFPVYMWL +TARTSAKWQVWEGEKNTEVDIASGRFAEVVSQMGVVRAYNRQEQELSGFRDRFLRTVGIT +RQQSRFWHGMDAGRRLALNAAFGAMYLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSM +SFLVDSAQRAVAGSKDYFEVLAEERERAGGAVLAVASADAPRVPAEPRADVVAGAPDVPA +DVPAVRFDEVSFAYDADASRPVLDRVSFDIPRGAKVALVGESGGGKSTIAHLLLGLYPVT +SGRIEVFGQDIAGLDLAALRGRIATVFQEPSLFSGTVRENIAYADADASDERVRAAAQAA +YAHRFVAAFDDGYDQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEATSALDTKSER +LVQAALDELMVGRSSLIVAHRLSTIASVDRIVTLRAGRVEEVGSPAELAESGGIYAQLLE +LQRAGTQEARKMLKEYGLSG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001695.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001695.fa new file mode 100644 index 0000000000000000000000000000000000000000..ac4ba4bcd229c38926b351541f5f5c2f01cb3803 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001695.fa @@ -0,0 +1,31 @@ +>PROKKA_02169 +MARTWDGSYPRSVTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLTVCFVADVA +LLVLGAGGVGVVAERWPWLVPALTVAGVVYLLGFAAGALRSAWRGDRTLSTAAADVEGTG +HGPDRIDLAVLTGELPLIDPVTGRLAEREPAGAGVGHHDDGAPGFGAPSGGGSVTVRQRV +QPRRVALDRPQTPLPRIILLALSVSLVNPHAILDTVVMMGTFAQTFGAAKWAYVGGAVAA +SLVWFTALGWGGTKLAPSMDSARTWRIVDAVVGVLMLGIAVKVGLTLL +>PROKKA_01883 +MARTWGDSYPRSVTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLTVCFVADVA +LLVLGAGGVGVVAERWPWLVPALTVAGVVYLLAFAVGALRSAWRGDRTLTTAAADAAGTG +HGPDRIDLAVLTGELPLIDPATGRLAEREPAGAGVGQHDDGAPGVGAPSGGGSVAARQRV +QPRRVALDRPQTPLPRIILLALSVSLVNPHAILDTVVMMGTFAQTFGAAKWTYVGGAVAA +SLVWFTALGWGGTKLAPSMDSARTWRIVDAVVGVLMLGIAVKVGLTLL +>PROKKA_00583 +MTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLIVCFLGDVALLALGAAGIGVV +AERWPWLVTALTVAGVVYLVWFAAGALRSAVRGQRTLAAAAEAEGPAVGLTDGEIAALTG +ELPLIDPATGRLSADFTGRTAEGRAVPVGAGVGMGRGHDPLGDESRTVGGIPVGNPRLCG +TRPGERGADGRSGGVAVKQRVQPRRVVLSAPQTPLPRIVLLALSVSFLNPHAVLDTVVMM +GTFAQTYGPGKWVYVGGAVAASLVWFTALGWGGTRLAPYMNTPRTWRIVDAAVGVLMLVI +AAKVGLTLL +>PROKKA_00509 +MTVFSAGFLTYLALIVAIGAQTLFLLRQVVRGDRAWTAIGVCFLSDIVLLLAGAAGVGAA +AERAPWLVPALTVAGVAYLVWFGVSALRSAHRGDRTLAGAAAEVEDDAWAPTAEEVAAMT +GSLPVVAAGPDAGADAATAPAGTGGGVALRTRPVSTTAPASAAPRPALTPLPRLVLLCLS +VSLLNPHAILDAVVMMGTFAQGYGADKWLYVAGAVASSALWFLVLGWGGAKLAPLMNTPR +TWRIVDGAVGVVVLGIAGKVALTLF +>PROKKA_02114 +MARTWDGSYPRSVTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLTVCFVADVA +LLVLGVGGVGVVAERWPWLVPALTVAGVVYLLAFAVGALRSAWRGDRTLTTAAADGAGTG +HGPDRIDLAVLTGELPLIDPATGRLADREPAGAGVGRHDDGAPGVGAPSGGGSVAVRQRV +QPRRVALDRPQTPLPRIILLALSVSLVNPHAILDTVVMMGTFAQTFGAAKWVYVGGAVAA +SLVWFTALGWGGTKLAPSMDSARTWRIVDAVVGVLMLGIAVKVGLTLL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001696.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001696.fa new file mode 100644 index 0000000000000000000000000000000000000000..de851d3b6bdf87ae228c799e3d127a862752efd1 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001696.fa @@ -0,0 +1,33 @@ +>PROKKA_02170 +MATPTLDRMNSDHLRALVAAVDHGTFDAAADSLRISGSAFSQRIKALERQVGQVLLARTV +PVRPTAAGERMLRLARQTLALEDETLAALGRGDGGRVPLRVALNADSLDTWWEPVLREAA +TWDDVVLQMQSEDQEHTAVLLRDGAVVAAVTDDPTPVAGCTSTPLGTMRYHAVCASFLLE +LHRDARGRVDFGSLPIVDYGPRDGLQHTVLRRVTRGRPVADPPTHLVPSVHAYLRAVELG +LGWGMLPSVQIPPGVLEGRHPDLETIPALGAADVHLHWQRWTAGTAALDRLTDAVLRAAP +SAGDTAD +>PROKKA_01884 +MATPTLDRMNSDHLRALVAAVDHGTFDAAADSLRISGSAFSQRIKALERQVGQVLLARTV +PVRPTAAGERMLRLARQTLVLEDETLAALGRGDGGRVPLRVALNADSLDTWWEPVLREAA +TWDDVVLQMQSEDQEHTAVLLRDGAVVAAVTDDPTPVAGCTSTPLGTMRYHAVCASFLLE +LHRDARGRVDFGTLPIVDYGPRDGLQHTVLRRVTRGRPVADPPTHLVPSVHAYLRAVELG +LGWGMLPSVQIPPGVLEGRHPDLEPIPALGAADVHLHWQRWTAGTAALDRLTDAVLRAAP +SAGDTAD +>PROKKA_00582 +MNSDHLRALVSAVDHGTFDAAADALRISGSAFSQRVKALERQVGQVLLARTVPVRPTPAG +ERMLRLARHTLALEEEALASLGRGDGGRVPVRVAINADSLDTWWELVLREAATWDDVVLQ +LRTEDQEHTAALLRDGTVVAAVTDDPTPVSGCTSTPLGTMRYHAVCASFLLEMHRDERGR +LDLATLPRVDYGLRDGLQRTVLRRAARGRAAFDPPHHLVPSVQSYLRAVELGLGWGMLPS +AQLPPGVLEGRHPDLEPVPSLGTVDLTLHWQRWSAGTAALDRLTDAVLRAAPSVADAAD +>PROKKA_00508 +MNSDHLRALAAAVDEGTFDAAAAWLGISGSALSQRIKALEGQTGQVLLTRTVPVRPTEAG +ERMLRLARQTLPLEEEALAALGRGTGRRAPLRVGVNADSLETWWTPVLREAATWDDVVLH +LHAEDQGHTPELLRQGTVVAVVTDDPTPVTGCTVTRIGTMRYHAVAASFLLDLHRDAHGR +VDVATMPVVDYGPRDGLQRTMLERAARGRVSVPRPPHHLVPSVGAYASAVGMGLGWGMLP +TGQVPPELAAGSHPDLELVPELGTAEVPLYWQRWSAGTPALDRLTAAVTAAAPAG +>PROKKA_02115 +MTTPTLDRMNSDHLRALVAAVDHGTFDAAADSLRISGSAFSQRIKALERQVGQVLLARTV +PVRPTAAGERLLRLARQTLALEDEALAALGRGDGGRVPLRVALNADSLDTWWEPVLREAA +TWDDVVLQMQSEDQEHTAVLLRDGAVVAAVTDDPTPVAGCTSTPLGTMRYHAVCASFLLE +LHRDARGRVDFGSLPIVDYGPRDGLQHTVLRRVTRGRPVADPPTHLVPSVHAYLRAVELG +LGWGMLPSVQIPPGVLEGRHPDLEPIPALGAADVHLHWQRWTAGTAALDRLTDAVLRAAP +SAGDTAD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001699.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001699.fa new file mode 100644 index 0000000000000000000000000000000000000000..2425674b5fa18fbfe8460eba37886399b647ff18 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001699.fa @@ -0,0 +1,35 @@ +>PROKKA_02176 +MPSTALASPARVRAGVLMGALPAALLLAALVAGVALGARTVPATTALDTLGAILTGHPVP +EGIEAAAVASRVPRVVTGALVGAALAVAGAALQGATRNPLGDPGLLGLSAGAGLAVAAGM +ALGVAGSTFGVLALAAVGTLVAAALGYAVAAAATRSGRTPGAPSPMALVLAGAALTAGAT +AGTTALLVLSPTVQDRLRFWAVGTVARADLGEALALAPVIAVGLLAAVAVAPGLDALALG +DDLAHGLGGRPERVRAVLLGAVVLLTAAAVALAGPVGFVGLLVPHALRRLRPPSTRALMV +GCALWGAVLVILADLAGRLVVAPGEIHLGVTTVLLGVPVLLALLRRPGVAA +>PROKKA_01890 +MPSTALASPARVRAGVLMGALPAALLLAALVAGVALGARTVPATTALDTLGAVLTGHPVP +EGIEAAAVASRVPRVVTGALVGAALAVAGAALQGATRNPLGDPGLLGLSAGAGLAVAAGM +ALGVAGSTFGVLALAAVGTLVAAALGYAVAAAATRRGRTTPGAPSPMALVLAGAAITAGA +TAGTTALLVLSPTVQDRLRFWAVGTVARADLGEALALAPVIAVGLLAAVAVAPGLDALAL +GDDLAHGLGGRPERVRAVLLGAVVLLTAAAVALAGPVGFVGLLVPHALRRLRPPSTRALM +AGCALWGAVLVILADLAGRLVVAPGEIHLGVTTVLLGVPVLLALLRRPGVAA +>PROKKA_00576 +MPRALLLIAPAVLAVLAALASLALGARPVPVDAAVGALTEAALHGPAAVTGMDGAAVLSR +VPRTLAAILVGAGLAVAGAALQGATRNPLGDPGLLGLTAGAVLAFALGIALGVAGSLPAV +MALAILGTLAAAALVTAVAAGAARVSGVPGPPSPLSLVLAGAATTAGATAVTSALVVLHP +AVRDRLRLWTVGSVARADLGDALWLAPVVLAAVAAVVVLGPGMDALALGTDLAHGLGARP +ERVRALLLAAAVVLTAAAVALAGTVGFLGLVIPHAVRRLRPPDARTLVLACALWGAVLVL +VADTLGRLVIAPAEVHLGVTTAVLGVPVLLALLRRRGVAA +>PROKKA_00503 +MPSSPTRGALLFGLLPLALLLTAGLAALALGARPVPLTTTATTLQAMLAGEGVPAGVDAA +AVASRVPRTLTAALVGAALAVAGAALQGATRNPLGDPGLLGLSAGASLATAIGLALGVSG +STFWVLALAAAGTLAAALLVYAVAAAASRGAGAGGAPTPIGLVLAGAAVTAGAGAVTTAL +LVLSPVVRDRFRFWAVGTVARADLGEAALLTPVIGLGIVLALAAARGLDALALGDDLAHG +LGARPGRTRALLLAAVVLLTAAAVALAGPVGFVGLVVPHALRRLRPGGTRTLLIGSALWG +AVLLVAADLLGRLVIAPAEIHLGVTTVLLGVPVLLVLLRRTGLGS +>PROKKA_02121 +MPSTALASPARVRAGVLMGALPAALLLAALVAGVALGARTVPATTALDTLGAVLTGHPVP +EGIEAAAVASRVPRVVTGALVGAALAVAGAALQGATRNPLGDPGLLGLSAGAGLAVAAGM +ALGVAGSTFGVLALAAVGTLVAAALGYAVAAAATRRGRTPGAPSPMALVLAGAAITAGAT +AGTTALLVLSPTVQDRLRFWAVGTVARADLGEALALAPVIAVGLLAAVAVAPGLDALALG +DDLAHGLGGRPERVRAVLLGAVVLLTAAAVALAGPVGFVGLLVPHALRRLRPPSTRALMV +GCALWGAVLVILADLAGRLVVAPGEIHLGVTTVLLGVPVLLALLRRPGVAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001700.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001700.fa new file mode 100644 index 0000000000000000000000000000000000000000..51ea37aa70d783a62cf9c7de06c7c3d569cce61b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001700.fa @@ -0,0 +1,36 @@ +>PROKKA_02177 +MSLQCTAPDDVVARLRRADRRRLGGACAGLAVAVLVLALLRVVWGTYQVTVPDLVRILGG +ETIPGASFIVLEEKLPRAVAAVLTGAALGAAGALYRRTLRNPLASPDILGVTQGAAAAVV +LGMLATAGQTGGGSDLMRAATALIGGLAAVVAVFATARSVGGERFVVAGIAVAAAGQAVV +AGAMLSLAQHDLQSATVWIAGSLNGVTWGRIALLAGVLVVALPLAGVLHARLAPADVGPD +LAHALGARPRPTSAAALGLGAVLAAVATAVVGPLAFVALLATPVARGLTRGLPSLPAAAL +TGAALVLLADLVAGEAVPLLTGAALPTGVLTGAAGAPLMLWLLLCQGRTPGGVRSA +>PROKKA_01891 +MNLQHTAPDDVVARLRRSDRRRLGRACAGLAVAVLVLALLRVVWGTYQVTVPDLVRILGG +ETIPGASFIVLEEKLPRAVAAVLTGAALGAAGALYRRTLRNPLASPDILGVTQGAAAAVV +LGMLATAGQTGGGSDLMRAATALIGGLVAVAAVFATARSVGGERFVVAGIAVAAAGQAVV +AGAMLSLAQHDLQSATVWIAGSLNGVTWGRIALLAGVLAAALPLAGALHTQLAPADVGPD +LAHALGARARPTSAAALGLGAVLAAVATAVVGPLAFVALLATPVARGLTRGLPSLPAAAL +TGAALVLLADLVAGEAVPLLTGAALPTGVLTGAAGAPLMLWLLLRQGRTPGGVRPA +>PROKKA_00575 +MSGRGSATLEHAVARVRAARRRDARRVGTALAVLTAAVLALVLLRLTWGAYMVAVPDLVR +ILTGTTIPGASFIVTEEKLPRAAAAVLAGAALGAAGALYRRGLGNPLASPDVLGVTSGAA +AGAVLWQAAATGTGGTTDAARAAAALAGGLIAALAVLLAARGTGGERFVVAGIAVAAGAQ +AVVAGTMVTLAEHDLQAAALWVSGSLTGVTWGRIGLLAAAVALALPLAAWLHGRLEPADT +GEDLAHALGARPRRTRPAALLLGAVLAAAATAAVGPLAFVALLATPLARGLAGGRPSLAA +AALAGAVLVLAADLLAAEAVALLADGTRLPTGVLTGAAGAPLMMTLLIRAGRRGERTA +>PROKKA_00502 +MSARRETTTPGRRDAAPGGDAPETVRALRRADARRVAGVVLGLAVLTAGLMLLRVTWGTY +QVTVPDLVRILGGERIAGASFIVWEEKLPRAVAATLTGAALGAAGALYRRTLRNPLASPD +VLGTTAGAAAGVVLTLTASAGQAGGSSDLARAGAALLGALAAGAAVLLAARSVGGQRFVV +AGVGVAAAGQAIVSGAMLSLSEHDLASATRWIAGSLNGVTWGRIGLLAAVLALALPAAGW +LHRRLAPADVGDDLAHALGARPRTTAALALTVGAVLAAAATATVGPLSFVALLATPLALG +LTRGRPSLPAAALTGAGIVLLADVLGTEALGLIADGAALPTGVLTGAAGAPLMLALLLRA +GRSSEGTR +>PROKKA_02122 +MSVQRTASDDVVARLRRSDRRRLGGACTGLAVAVLVLALLRVVWGTYQVTVPDLVRILAG +ETIPGASFIVLEEKLPRAVAAVLTGAALGAAGALYRRTLRNPLASPDILGVTQGAAATVV +LGMLATAGQTGGGSDLMRAATALIGGLVAVAAVFATARSVGGERFVVAGIAVAAAGQAVV +AGAMLSLAQHDLQSATVWIAGSLNGVTWGRIALLAGVLAAALPLAGALHTQLAPADVGPD +LAHALGARARPTSAAALGLGAVLAAVATAVVGPLAFVALLATPVARGLTRGLPSLPAAAL +TGAALVLLADLVAGEAVPLLTGAALPTGVLTGAAGAPLMLWLLLRQGRTPGGVRPA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001701.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001701.fa new file mode 100644 index 0000000000000000000000000000000000000000..69804e174656aaf811fb00f94db632af3a9825ea --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001701.fa @@ -0,0 +1,32 @@ +>PROKKA_02178 +MTAPPLTVPSPAAPRAGAADDVAIRLRGLTLGYGPASAPPIVADLDLDVPAGRVTAIIGA +NGCGKSTLLRGLTRQLAPRAGSIEVLGRDAARVSARDYARTVALLPQHPVAPEGMTVAQL +VARGRHPHRGLLGGRAAGDDAAIASALERTDLVELADREAGTLSGGQRQRAWLALVLAQQ +TPVVLLDEPTSYLDLSHQVEVLDLVRALPDPRGGGRATVVAVLHELNLAARSADHIVAMA +AGRVVAQGTPGEVIVPEVLAEVFGLDADVVADPLLGHPVVLPRGDGDRR +>PROKKA_01892 +MTAPPLTVPSPAAPRAGAADDVAIRLRGLTLGYGPASAPPIVEDLDLDVPAGRVTAIIGA +NGCGKSTLLRGLTRQLAPRAGSIEVLGRDAARVSARDYARTVALLPQHPVAPEGMTVAQL +VARGRHPHRGLLGGRAAGDDAAIASALERTDLVELADREAGTLSGGQRQRAWLALVLAQQ +TPVVLLDEPTSYLDLSHQVEVLDLVRALPDPRGGGRATVVAVLHELNLAARSADHIVAMA +AGRVVAQGTPGEVIVPEVLAEVFGLDADVVADPLLGHPVVLPRGDGDRR +>PROKKA_00574 +MTPPHPAAAPAERPGADPATGPAQDPALRLRGVRLGYGRPDTPDTVGPVDLDVPAGRVTA +LIGANGCGKSTLLRGLTRQLPLRGGSAEVLGRDLGAYSAREYARTVALLPQHPVAPEGMT +VAQLVQRGRHPHRGLFGTTGADDDAAVARALRHTDLEKLADREVAELSGGQRQRAWLALV +LAQRTPVLLLDEPTSYLDLAHQVEVLDLVRGLTRPDGDEEPVTVVAVLHELSLAARVADR +LVALRDGRVAAAGTPAEVLTPAVLAEVFDLDADVRPDPLLGHPVVLPRGAADRGAPLPSP +TTQETR +>PROKKA_00501 +MTSSPPTPAAPSTAPAPALRLRGVELSYGPASAPPTVGPVDLDVPAGQVTAVIGANGCGK +STLLRGLTRQLPLRAGTVDVLGRDAAGMSARDYARTVALLPQQPVTPEGLTVAQLVERGR +HPWRGLLGGRAAGDDAAVAAALARTGLVDLAARDAATLSGGQRQRAWLALVLAQQTPVVL +LDEPTSYLDLAHQVEVLDLVRTLPDPRAVGARTVEAAGGVVGGGAGTEAGPPPRATVVAV +LHELSLAARAADHVVAMAGGRVVATGTPAEVIVPEVLAEVFGLDADVVPDPLLGHPVVLP +RGRGDRA +>PROKKA_02123 +MTAPPLTVPSPAAPRAGAADDVAIRLRGLTLGYGPASAPPIVEDLDLDVPAGRVTAIIGA +NGCGKSTLLRGLTRQLAPRAGSIEVLGRDAARVSARDYARTVALLPQHPVAPEGMTVAQL +VARGRHPHRGLLGGRAAGDDAAIASALERTGLVELAEREAGTLSGGQRQRAWLALVLAQQ +TPVVLLDEPTSYLDLSHQVEVLDLVRALPDPRGGGRATVVAVLHELNLAARSADHIVAMA +AGRVVAQGTPGEVIAPEVLAEVFGLDADVVADPLLGHPVVLPRGDGDRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001707.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001707.fa new file mode 100644 index 0000000000000000000000000000000000000000..8144f732a51c2abc5b3c52135751d66aef9a00a2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001707.fa @@ -0,0 +1,20 @@ +>PROKKA_02185 +MTQPTTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLAEEARVRALAAWATTT +ASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRCVLCDAV +FVQVDPAAGRPVAVSDEERAAFERVLIPAED +>PROKKA_01899 +MTQPTTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLAEEARVRALAAWATTT +ASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRCVLCDAV +FVQVDPAAGRPVAVSDEERAAFERVLIPAED +>PROKKA_00565 +MNGQDGGQGRTTTDGATGREAPVPFETEIQVRWSDEDRYGHVNNARLLTLTEEARVRATR +AWSGVTPGRDVHRVVRAMEVQYEAPVVYGPELTAKVWIARIGTSSYTLRHELWQDGRRCV +LCDAVFVHVDPETGRSVALAEDERVTLERVLIPAEADAT +>PROKKA_00490 +MSDSQPRPYEGVLDLRWSDMDLYGHVNNVRILTLTEEARVRALKAWDEGDVGRDVMRVVR +AMTTEYERPVEYGPELTAKVWVRALGRTSYTLHHELWQEGVRCVTCDAVMVHLDPETGAP +LPHDDARRARLQAVLVPAEG +>PROKKA_02130 +MTQPTTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLTEEARVRALAAWATTT +ASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRCVLCDAV +FVQVDPAAGRPVAVSDEERAAFERVLIPAED diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001708.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001708.fa new file mode 100644 index 0000000000000000000000000000000000000000..a0c5bfac0290ae97e19f4374dc252c9174717492 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001708.fa @@ -0,0 +1,30 @@ +>PROKKA_02186 +MEQDPSPDAPAPSADVEALRGTPVSELTQLTPAASGALERLRRDVERFDLEYRSALLQVE +ARLEVLRDEFTHLHDYNPIEHIVTRVKSPESILRKASARGLSLDLDALRTNVTDIAGARV +IVSFARDVYRVFRQFTQQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPIHLSTGTIPVTV +EMQFRTSAMDFWATLEHKINYKFDGGVPPDIATELVAAARVAADLDTRMERLHDQVQETD +RDDDAAAAWEDDGGPAFEDEPTVEPGEARPGDAPGASTA +>PROKKA_01900 +MEQDPSPDAPAPSADVEALRGTPVSELTQLTPAASGALERLRRDVERFDLEYRSALLQVE +ARLEVLRDEFTHLHDYNPIEHIVTRVKSPESILRKASARGLSLDLDALRTNVTDIAGARV +IVSFARDVYRVFRQFTQQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPIHLSTGTIPVTV +EMQFRTSAMDFWATLEHKINYKFDGGVPPDIATELVAAARVAADLDTRMERLHDQVQETD +RDDDAAAAWEDDGGPVFEDEPAAGPGEARPGDDAPGASTV +>PROKKA_00563 +MEQDRDPEESSQSTAIETLRGTPVSELTHLPPAMAGALDRLRRDVERFDLEYRSALLQVE +ARLEVLRDEFTHLHDYNPIEHIVTRVKTPESILRKAASRGLSMDLDALRSNVTDIAGARV +IVSFARDVYEVFRLFTRQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPVHLSTGSIPVTV +EMQFRTSAMDFWATLEHKINYKFDGAVPPDITTELIAAARVAADLDTRMERLSDQVRQTD +KDDDAAASWEDDGGPAFEDEGDDDGPDGDAPGTSTG +>PROKKA_00489 +MPRDVDHPPPADDPAPVERPAPGGRGVTSASTALEALRATPLTDLTQLPGEVADALASLR +TDFERFDLEYRSALLQVETRLETLQDEFTHLHEYNPIEHIATRVKSPESLLRKAASRGLS +LDLDALRSGVTDIAGARVIVSFTEDVYRVFRQFTSQPDIRVLEVEDYIRDPKPSGYRSLH +CLVQVPVHLTTGTVPVTVELQFRTIAMDFWASLEHKINYKFAGHVPPAITTELAAAARVA +HDLDARMERLHQAVHDAGAGPDEHDDEDDWVGHA +>PROKKA_02131 +MEQDPSPDAPAPSADVEALRGTPVSELTQLTPAASGALERLRRDVERFDLEYRSALLQVE +ARLEVLRDEFTHLHDYNPIEHIVTRVKSPESILRKASARGLSLDLDALRTNVTDIAGARV +IVSFARDVYRVFRQFTQQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPIHLSTGTIQVTV +EMQFRTSAMDFWATLEHKINYKFDGGVPPDIATELVAAARVAADLDTRMERLHDQVQETD +RDDDAAAAWEDDGGPAFEDEPAAGPDGTDPGEARPGDDAPGASTV diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001709.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001709.fa new file mode 100644 index 0000000000000000000000000000000000000000..6802491a3a401d4c9b547737108f29714e1f1f6e --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001709.fa @@ -0,0 +1,25 @@ +>PROKKA_02189 +MSIPATEVEARWNAAAEPFTAVVREVRDWDAATPCEGWDALDLLDHVIAGQRDFAARQGR +EVPLFDGSRQQLATQWAKHAAAMSALAGDEEFIMRPMKTALGEMPVGEALIRFHAFDVIV +HRWDLARSQGVDARFTDAEIDCVEESLELFGDAAYTPGILGEPVPVADDADRQTRLLGRL +GRRG +>PROKKA_01903 +MSIPATEVEARWNAAAEPFTAVVREVRDWDAATPCEGWDALDLLDHVIAGQRDFAARQGR +EVPLFDGSRQQLATQWAKHAAAMSALAGDEEFIMRPMKTALGEMPVGEALIRFHAFDVIV +HRWDLARSQGVDARFTDAEIDCVEESLELFGDAAYTPGILGEPVPVADDADRQTRLLGRL +GRRG +>PROKKA_00557 +MSIPATEVEARWNEASEPFTAVVRAVRDWDAATPCEGWDALDLLDHVVGAERDFAARQGR +EVPLFDGSRQQTANQWTKHSAALSALAGDEEFIMKPMHTALGEMTVGEAMIRFHAFDLIV +HRWDLARSQGVDERFTDAEMDCIEESLDLFGDAAYTPGILAQPVPVADDADRQARLLGRL +GRRA +>PROKKA_00484 +MSTQTDVEQYWMDCVEPFTDVVRAVEDWDASTPCKGWSAQDLLDHVVVAERDFAARQGRE +IPVFDGSRNELWTQWVKHASAVTALAGDETFIMQSLHTATGDMTVGEALLHFHGFDLLVH +RWDLARSQGRDEQWTDEEMDRIERALDSFGEQAYQPGILADPVPVADDAPRQVRLLGRLG +RRA +>PROKKA_02134 +MSIPATEVEARWNAAAEPFTAVVREVRDWDAATPCEGWDALDLLDHVIAGQRDFAARQGR +EVPLFDGSRQQLATQWAKHAAALSALAGDEEFIMRPMKTALGEMPVGEALIRFHAFDVIV +HRWDLARSQGVDARFTDAEIDCVEESLELFGDAAYTPGILGEPVPVADDADRQTRLLGRL +GRRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001712.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001712.fa new file mode 100644 index 0000000000000000000000000000000000000000..cf91be46d75e693142fdd06673ba21ada87a0e88 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001712.fa @@ -0,0 +1,75 @@ +>PROKKA_02195 +MLFRYELRRFRRGLPLLALLFIFLVPAIYGALYLSANWDPYGAMDRLPVAIVNEDEPVQR +GDTTLRTGADMTERLKDDRAFDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGG +GTPQQAQITLRRDDANGFVIGSVTNASQAKVEAAVNRSAIEAYFEAVFSSLGELRSGMVD +AADGAAQLADGTASAEDGASRLEDGIVQAHDGSGKLAEGAGQLATGAGDLADGAAQADDG +AQRLAEGAASAQDGAGRLADGLDQAREGSQALADGAGQLAENAPALRQGATDLSDGLAQL +QTGSAELTDGATQVADGTQQLYDTVVPGLDQVIERQDAVAADVAAVDEDVQRVAEVAGTA +EDGAGARIADAQTALAALAEEDPTLAESEQYAALQEALTGADERVTAVAGRAEEAAATSA +AANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF +ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGA +GQLESGATELDGGLAQLQDGAGELRAGLGTLDDGAHELASGLSDGADRVPALTEDERDEA +ALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIAAFNIMRPISGRLLAGRRNPV +AIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL +GTPGSALLLVLLVLQLASTGGTYPAEVLPGFFQALHPFMPMSYSIEAFRNAISGGPDQRF +WVPVVVLMGIGAAALALDVLVVRRRRRFRMKDLHPALQA +>PROKKA_01908 +MLFRYELRRFRRGLPLLALLFIFLVPAIYGALYLSANWDPYGAMDRLPVAIVNEDEPVQR +GDTTLRTGADMTERLKDDRAFDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGG +GTPRQAQITLRRDDANGFVIGSVTNASQAKVEAAVNRSAIEAYFEAVFSSLGELRSGMVD +AADGAAQLADGTASAEDGASQLEDGIVQAHDGSGKLAEGAGQLATGAGDLADGAAQADDG +AQRLAEGAASAQDGAGRLADGLDQARGGSQALADGAGQLAENAPALRQGATDLSDGLAQL +QTGSAELTDGATQVADGTQQLYDTVIPGLDQVIERQDAVAADVAAVDEDVQRVAEVAGTA +EDGAGARIADAQAALAELAEEDPTLAESEQYAALQEALTGADERVTAVAGRAEEAAATSA +AANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF +ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGA +GQLESGATELDGGLAQLQDGAGELRAGLGTLDDGAHELASGLSDGVDRVPALTEDERDEA +ALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIAAFNIMRPISGRLLAGRRNPV +AIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL +GTPGSALLLVLLVLQLASTGGTYPAEVLPGFFQALHPFMPMSYSIEAFRNAISGGPDQRF +WVPVVVLMGIGAAALALDVLVVRRRRRFRMKDLHPALQA +>PROKKA_00549 +MLFRYELRRFRRGLPLLALLFILLVPAIYGALYLSANWDPYGAMNRLPVAIVNEDEPVQR +GDTTLRTGADMTARLKEDHAFDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGG +GTPQQAQITLRRDDANGFVIGSVTASSQAKVEAAVNRSAIEAYFEAVFSSLGELRSGMVD +AADGAAQLADGSASAVDGASQLEDGIVQAHDGSGRLAEGAGQLATGAGDLADGAAQADDG +AQRLAEGATSAQDGAGRLADGLDQAREGSQALADGAGQLAENAPALRQGATDLSDGLAQL +QTGSAELTDGATQVADGTQQLYDTVVPGLDRVIERQDAVAADVAAVDEDVQRVAEVAGTA +GDGAGARIADAQAALAALAEEDPTLAESEQYAALQEALTGADERVTAVAGRAEEAAATSA +AANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF +ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGA +GQLESGATELDDGLAQLQDGAGELHTGLRTLDDGAHELASGLSDGVDRVPALTEDQRDEA +ALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIAAFNIMRPISGRLLAGHRNPV +AIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL +GTPGSALLLVLLILQLASTGGTYPAEVLPGFFRALHPFMPMSYSIEAFRNAISGGLDQHF +WVPVVVLMGVGAAALALDVLVVRRRRRFRMKDLHPALQA +>PROKKA_00478 +MLFRYELRRFRGVLPTIALLFIVLVPTIYGALYLSANWDPYGNLSSLPVAIVNEDRPVES +DGKTLTTGADITEELVDQHTFDWHETTRDDAEAGLRDGRYYLVMEIPEGLSADLVSANTS +DPQQAHITLRRNDANGFVIGSVTSSSQSKIENAVDKAAVEAYFKAVFENLATIRQGMADA +RDGAGRLADGAGQADDGAAQLADGIVQAHDGSGQLAQGASDAQDGAGQLADGAGQLKDGA +DQLAAGATSAKDGAVQLQTGIGQAREGSQKLADGAGQIAAKVPDLRDGATALSNGLTQLD +TGSADLADGAHQVADGTQQLYDTVIPGLDAVIERQDKVASDVATVNQDVQTLNDAVATAG +SGAGGDIDTASEQLQALAESNPDIAVAPEYAALQQSLTDAKEKAGSATSTAQDVADRSAA +VNSRVQGFVSEDVAGNAKADITKLNDGAHAVAEGADTLHAGIGQANTGAQALADGVGRFA +DALDQLAAGATALDDGLAQLEDGSGRLVDGLGKLETGAGDLADGAGRLDQGAGELQTGLG +KLSDGATSLDSGLAQLETGSGDLKTGLDSLSDGATQLHDGLASGTDKIPALSEDAADEAA +LVMSRPVQVDMDVLNPAGVYGRGVAPLFFSIALWVFGIAAFNVMRPVNGRLLAGRRNPLL +LALSAWLPVGLLSVVGSLVMLAATVPLGIDPVHPWHLVGLVVFTALAFSLFAHLVMTALG +TPGSAVLLVTLILQLGSAGGTYPADVLPPFFRWVSPLMPMTHSINAIRYALSGGQPAQFW +GAVAFLAVFGAACLFLDMAVVRRRQRFRMKDLHPALEK +>PROKKA_02139 +MLFRYELRRFRRGLPLLALLFIFLVPAIYGALYLSANWDPYGAMDRLPVAIVNEDEPVQR +GDTTLRTGADMTERLKDDRAFDWRETTREEAEEGLREGRYYLVLEIPAELSRDLVSPEGG +GTPQQAQITLRRDDANGFVIGSVTNASQAKVEAAVNRSAIEAYFEAVFSSLGELRSGMVD +AADGAAQLADGTASAKDGASQLEDGIVQAHDGSGKLAEGAGQLATGAGDLADGAAQADDG +AQRLAEGAASAQDGAGRLADGLDQARGGSQALADGAGQLAENAPALRQGATDLSDGLAQL +QTGSAELTDGATQVADGTQQLYDTVVPGLDQVIERQDAVAADVAAVDEDVQRVAEVAGTA +EDGAGARIADAQAALAALAEEDPTLAESEQYAALQEALTGADERVTAVAGRAEEAAATSA +AANERVQGFVEDDVAASAKADLTDLNDGAHAVAAGAEKLQGGIGEAKDGADSLADGAGKF +ADGLEQLGSGATELDGGLAQLQDGAGELQSGLGELTDGATTLAEGNAALHDGALTLQDGA +GQLESGATELDDGLAQLQDGAGELHTGLGTLDDGAHELASGLSDGVDRVPALTEDERDEA +ALVMSRPVEAVMQVDNSAEVYGRGMAPMFFSIALWVFGIAAFNIMRPISGRLLAGRRNPV +AIALAAWLPVGIVAVGGGLLMLAATLPLGLAPVHPVRAVALTVLVAVVFSLIAHLVQTAL +GTPGSALLLVLLILQLASTGGTYPAEVLPGFFQALHPFMPMSYSIEAFRNAISGGLDQRF +WVPVVVLMGIGAAALALDVLVVRRRRRFRMKDLHPALQA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001713.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001713.fa new file mode 100644 index 0000000000000000000000000000000000000000..28831d2c4686e4c1a97c42ff81a012856053a22d --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001713.fa @@ -0,0 +1,30 @@ +>PROKKA_02196 +MSSTPTDADHHGPGPAPVPAHLDDLPPATLVARGLTLRGGRGPVFGPLDLVLPPQTHLAV +LGTQGSGRSALLLALTGRLQGVRGELVLTGGPVDVALDGPERPAARAYRPPIDAARHPHA +LRARTAVAHTTDVVELEPALTAAEVVDERCLADGVRRRAGRARFALLADAVRLSVAPEAV +VGELPAPERALLAAVVACLRPARLVTFDDVDATLTIDELVALHAALDVLKDHGHPFAVSA +VASAPVPRDAVVLTLPPVREN +>PROKKA_01909 +MSSTPTDADHHGPGPAPDPAHLDDLPPATLVARGLTLRGSRGPVFGSLDLVLPPQTHLAV +LGTQGSGRSALLLALTGRLQGVRGELVLTGGPVDVALDGPERPAARAYRPPIDAARHPHA +LRARTAVAHTTDVVELEPALTAAEVVDERCLTDGVRRRAGRARFALLADAVRLTVAPEAV +VRELSAPDRALLAAVVACLRPARLVTFDDVDATLTIDELVALHAALDVLKDHGHPFAVSA +VASAPVPRDAVVLTLPPVREN +>PROKKA_00548 +MSSTPTDADHHGPGPVSVPAHLDDLPPATLVARGLTLRGGRGPVFGPLDLVLPPQTHLAV +LGTQGSGRSALLLALTGRLRGVRGELVLTGGPVDVALDGPERPAARAYRPLIDATRHPYA +LRARTAIAHTTDVVELEPALTAAEVVDERCLADGVRRRAGRARFALLADAVRLTVAPEAV +VGELSAPDRALLAAVVACLRPARLVTFDDVDATLTLDELVALHAALDVLKDHGHPFAVSA +VASAPVPRDAVVLTLPPVREN +>PROKKA_00479 +MTEDQTPAPIETDDVVAERAPEPAPGGSHQVGRALTARGLTLRSIRGTVFGPVDVDLPPG +VPGAVLGTQGSGRSALLLALVGRLQGVGGELTLGDMDGIRHPHRLRRATTVARITDYVEL +EPLLTIRECIDEHCLAEGISRRTGRKRFARLEAAVGFHPDHGDQVSSLPVEDRTILTCML +ACLRPADVIVYDDIDSSLTRPQLEHVYRVLETLGRLGHRFVVSALTSAPVPRGAVVVELP +TPGHDDLPAALPTRPSLED +>PROKKA_02140 +MSSTPTDADHHGPGPAPVPAHLDDLPPATLVARGLTLRGGRGPVFGPLDLVLPPQTHLAV +LGTQGSGRSALLLALTGRLQGVRGELVLTGGPVDVALDGPERPAARAYRPPIDAARHPHA +LRARTAVAHTTDVVELEPALTAAEVVDERCLADGVRRRAGRARFALLADAVRLSVAPEAV +VGELPAPERALLAAVVACLRPARLVTFDDVDATLTIDELVALHAALDVLKDHGHPFAVSA +VASAPVPRDAVVLTLPPVREN diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001718.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001718.fa new file mode 100644 index 0000000000000000000000000000000000000000..b6bfce40f28fa51685e72d41b37c596f22a14b45 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001718.fa @@ -0,0 +1,27 @@ +>PROKKA_02202 +MPPAPTARLRFREMADADLDHLAGLLADPVVMRFYPAPRTRAEAAAWIAGNRRRYAQDGH +GLWIIETHDDGGPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACRDHAR +DVLGHHELVAIIHPENTASRRVAERIGMTVVGEDRTGAPEARAALGLEARTVLGMRLRPG +A +>PROKKA_01915 +MPPAPTARLRFREMADADLDHLAGLLADPVVMRFYPAPRTRAEAAAWIAGNRRRYAQDGH +GLWIIETHDDGGPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACRDHAR +DVLGHHELVAIIHPENTASRRVAERIGMTVVGEDRTGAPEARAALGLEARTVLGMRLRPG +A +>PROKKA_00541 +MLPAPTARLRFREMTEADLDAMAALLGDPAVMRFYPAPRTREQAAEWIAGNRRRYAQDGH +GLWVIETLPEHSDDGEPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACR +DHARDALGHHELVAIIHPENSVSRRVAEKIGLREAEQDFTGAAEARETMGLASRTVMAMR +F +>PROKKA_00472 +MTQPIPRHPDPGNTGTDALDDVVREHMLLLRRAVHGLGAYRRPEALDRSAVLLLARLEAQ +GPMTMAELAAAFGLDVSTLQRQIGAAQRAGFVERFRDPAGGQARLHRATDAGRAALEGEL +AARRAAVAEVTRSWPAPDVAALARLLRRFNEGSEELREQPWPRERPEAPGAAAVPAGTAR +LRFREMTEADLDVLVGLLGDPEVMEFYPAPKTRAEVADWIAWNRRSYAEHGHGLWIVETH +AGAFVGECGLTWQRVNGERRLEVGYHVAPVLQGRGYATEAAAACRDHARDVLGAPELVAI +VHPENTASRRVAEKIGMEVLEEDRTGVDASYLEAIGAEARTVLGMRLA +>PROKKA_02146 +MPPAPTARLRFREMADADLDHLAGLLADPVVMRFYPAPRTRAEAAAWIAGNRRRYAQDGH +GLWIIETHDDGGPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACRDHAR +DVLGHHELVAIIHPENTASRRVAERIGMTVVGEDRTGAPEARAALGLEARTVLGMRLRPG +A diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001719.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001719.fa new file mode 100644 index 0000000000000000000000000000000000000000..ef7936091e8a0893720628c8c5216971427a5dcf --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001719.fa @@ -0,0 +1,37 @@ +>PROKKA_02206 +MSVTQTTPAPDWRPPWQSLPDDLAERLAPAIPGIMERIIETVPDQIPAYAAARDGHYGKN +LTAGVTTALEQLMSLPGTTRPALNSESRVLMARLGAGEFREGRSMDALLGAYRTSARIVF +RELSAECARLGLEMSVVIELGESIWAYIDELSSVSAQAYAEAQSAQAGVLELHRAALATA +LVRGGTEEKEVQRLAALADWRLPRRLAVVVLPADAGVAVRERLGRAGLVVERDSEVVAVI +DATPSQGRRERMLRLLAGTAAVVGPAVDWPLVPHSYRVARTLAVQEAAGRTAEPAQGEDD +DGAPSPILAADHLARVVLGAEPRVVTQLAERVLAPLDEVSEAKRAVLEETLLAWLTHWGQ +RAPIAAELGVHPQTVGYRVGRLRELFGEALEDPDARFDLEIVLRARRDGVG +>PROKKA_01919 +MSVTQTTPAPDWRPPWQSLPDDLAERLAPAIPGIMERIIETVPDQIPAYAAARDGHYGKN +LTAGVTTALEQLMSLPGTTRPALNSESRVLMARLGAGEFREGRSMDALLGAYRTSARIVF +RELSAECARLGLEMSVVIELGESIWAYIDELSSVSAQAYAEAQSAQAGVLELHRAALATA +LVRGGTEEKEVQRLAALADWRLPRRLAVVVLPADAGVAVRERLGRAGLVVERDSEVVAVI +DATPSQGRRERMLRLLAGTAAVVGPAVDWPLVPHSYRVARTLAVQEAAGRTAEPAQGEDD +DGAPSPILAADHLARVVLGAEPRVVTQLAERVLAPLDEVSEAKRAVLEETLLAWLTHWGQ +RAPIAAELGVHPQTVGYRVGRLRELFGEALEDPDARFDLEIVLRARRDGVG +>PROKKA_00539 +MTSPRPESDWRPPWQDLPADLPGRLAHALPGIMERIIQTVPDQIPAYAAARDGRYGKNLT +LGVTTALEQLMSLPGTSRPALSAQSRELMARLGAGEFREGRSMDALLGAYRTSARIVFRD +LSAECARLGMDMSVVIELGESIWAYIDELSAVSAQAYAEAQSAQAGVRELHRTALAAALV +RGGAEEKEVERLAALADWRVPARLAVVALPPDAGQAVRARLGRGGLVVERDSEVVAVVGA +DAPARRRRLLRILAGTAAVVGPAVEWPLAPHSYRVARTLAGQEAARRAAEQRAAARPEGD +GSAADGPGAEEAVGFEPVGGADPAPGTPILAEEHLARVVLGAEPRVVAELAERVLAPLAE +LTDAKRAVLEQTLLSWLVHWGQRAPIAAELSVHPQTVGYRVARLRELFGDALEDPDARFD +LELVLRARAGGMAA +>PROKKA_00469 +MVLSAPPRSPVVTRRLLAALQGTGAVVGPEVDALEVARSLHVARAVLARRDALSGVAPGA +AVLAEEHLADVVLGAEPEALRRLSERVLAPLDGLSDAKRATLEATLAAWLAHRGARGPMA +AELNVHPQTVGYRVGRLRELFGGALDDADARFDLELALRSRRGQG +>PROKKA_02150 +MSVTQTTPAPDWRPPWQSLPDDLAERLAPAIPGIMERIIETVPDQIPAYAAARDGHYGKN +LTAGVTTALEQLMSLPGTTRPALNSESRVLMARLGAGEFREGRSMDALLGAYRTSARIVF +RELSAECARLGLEMSVVIELGESIWAYIDELSSVSAQAYAEAQSAQAGVLELHRAALATA +LVRGGTEEKEVQRLAALADWRLPRRLAVVVLPADAGVAVRERLGRAGLVVERDSEVVAVI +DATPSQGRRERMLRLLAGTAAVVGPAVDWPLVPHSYRVARTLAVQEAAGRTAEPAQGEDD +DGAPSPILAADHLARVVLGAEPRVVTQLAERVLAPLDEVSEAKRAVLEETLLAWLTHWGQ +RAPIAAELGVHPQTVGYRVGRLRELFGEALEDPDARFDLEIVLRARRDGVG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001720.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001720.fa new file mode 100644 index 0000000000000000000000000000000000000000..0986141a40e2ec844434823258a77122457bfc59 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001720.fa @@ -0,0 +1,40 @@ +>PROKKA_02208 +MTQTPTAPDRTGATAPDDLALAIPGTTVRGRAARVLPQDRPDTTSWAPRTAESRAAATTP +GLPGVVGSPAVRPPGAAHLTDAQVAELGRELDAIRDDVLARRGTSDAAYIRRVIRWQRRL +ELGGRALLLNARHPAAFVAGTAMLTVAKIVENMEIGHNVLHGQWDWMRDPDIHSTTWEWD +FVTPSRAWQNTHNDLHHRWTNVVGKDRDVGYNVLRMDESEPWRPRHLLNPVINAGLAPIF +EWGIALYDLELDRVQSGEKSREELMTDLRSVGVKAARQFAKDYVATPAVAEVLTGSGKAA +LVGTLLANGLRNIWAHAVIFCGHFPEGAETFSEEMVDGETRGDWYVRQMIGSANISGSKL +MHFMTGNLSHQVEHHLFPDLPSSRYAEVAPRVREICARYGLPYTTGPLLRQVGSAWKKVF +RLALP +>PROKKA_01921 +MTQTPTTPSRTGATAPDDLALAIPGTTVRGRAARVLPQDRPDTTSWAPHTAESRAATSRS +TAAATTPGLPGVVGSPAVRPPGAAHLTDAQVAELGRELDAIRDDVLARRGTSDAAYIRRV +IRWQRRLELGGRALLLNARHPAAFVAGTAMLTVAKIVENMEIGHNVLHGQWDWMRDPDIH +STTWEWDFVTPSRAWQNTHNDLHHRWTNVVGKDRDVGYNVLRMDESEPWQPRHLLNPVIN +AGLAPIFEWGIALYDLELDRVQSGEKSREELMTDLRSVGVKAARQFAKDYVATPAVAEVL +TGSGKATLAGTLLANGLRNIWAHSVIFCGHFPEGAETFSEEMVDGETRGDWYVRQMIGSA +NISGSKLMHFMTGNLSHQVEHHLFPDLPSSRYAEVAPQVREICARYGLPYTTGPLLRQVG +SAWKKVFRLALP +>PROKKA_00537 +MTQTLPATERTGATAPDDLSLAIPGTTVRGRTARVLPEDRPDTTSWAPQTADAGTDAAAP +AASETPEAPTADAATRPAANAKPGLLGVVGSPAVRPPGAAHLTDEQVAELGRELDAIRDD +VLSRRGASDAAYIRRVIRLQRWLEIGGRAALLNARHPAAFVAGTTMLTVAKIVENMEIGH +NVLHGQWDWMRDPDIHSTTWEWDFVTPSRAWQNTHNDLHHRWTNVIGKDRDVGYNVLRMD +ESEPWRPRHLLNPVINAGLAPIFEWGIALYDLELDRVHAGEKSRKELMTDLRSVGVKASR +QFAKDYVATPAVAEFLTGSGKAALVAGLLANGLRNIWAHSVIFCGHFPEGAETFSEEMVD +GETRGDWYVRQMIGSANISGSKLMHFMTGNLSHQVEHHLFPDLPSNRYAEVAPKVREICA +RYGLPYTTGPLLKQVGSAWKKVFRLALP +>PROKKA_00468 +MIRSATAGKIIENMEIGHNVLHGQWDWMRDPDIHSTTWEWDFVTPSSAWQHTHNDAHHRW +TNVTGLDEDLGYNVLRMDEAEPWEPRHLLNPVINAILAPFFEWGIAIYDLELAKVRAGEK +PVADLRRDLASVAVKAVRQLAKDSLATPIAAELVSRSGSAWRKVFRLALP +>PROKKA_02152 +MTQTPTTPSRTGATAPDDLALAIPGTTVRGRAARVLPQDRPDTTSWAPHTAESRAATSRS +TAAATTPGLPGVVGSPAVRPPGAAHLTDAQVAELGRELDAIRDDVLARRGTSDAAYIRRV +IRWQRRLELGGRALLLNARHPAAFVAGTAMLTVAKIVENMEIGHNVLHGQWDWMRDPDIH +STTWEWDFVTPSRAWQNTHNDLHHRWTNVVGKDRDVGYNVLRMDESEPWQPRHLLNPVIN +AGLAPIFEWGIALYDLELDRVQSGEKSREELMTDLRSVGVKAARQFAKDYVATPAVAEVL +TGSGKATLAGTLLANGLRNIWAHSVIFCGHFPEGAETFSEEMVDGETRGDWYVRQMIGSA +NISGSKLMHFMTGNLSHQVEHHLFPDLPSSRYAEVAPQVREICARYGLPYTTGPLLRQVG +SAWKKVFRLALP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001721.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001721.fa new file mode 100644 index 0000000000000000000000000000000000000000..4538f7f4c71c5cc97eb01d663e8d3ed7f364c0c9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001721.fa @@ -0,0 +1,30 @@ +>PROKKA_02216 +MPAQPSPSGHTVHLSTSGVDARITPDEFGGFVLEIGGAVQSHVDLADPARIRYEYLRRMA +HVLDAASPAGAPVRVLHLGAGALTLPRYLQATRPGSEQTVVDLDRELVSFVLAELPLPAG +TDLVSVVADARLAAVDLALDGERFDAVVLDIGTGEEGAEHLRGAVFYGELLELLTAGGVL +LVNIGDDAGLRFLGAELGALEEAAAEAGVPGPWTLADQGMLERLDWGNVVLAAGAPLGEA +GCTERLAAAGPHPAAVLDPAESAALADRIRRA +>PROKKA_01929 +MPAQPSPSGHTVHLSTSGVDARIAPDEFGGFVLEIGGAVQSHVDLADPARIRYEYLRRMA +HVLDAASPTGAPVRVLHLGAGALTLPRYLQATRPGSEQTVVDLDRELVSFVLAELPLPAG +TDLVSVVADARLAAVDLALDGERFDAVVLDIGTGEEGAEHLRGAVFYGELLELLTAGGVL +LVNIGDDAGLHFLGAELGALEEAAAEAGVPGPWTLADQGMLERLDWGNVVLAAGAPLGEA +GCTERLAAAGPHPAAVLDPAESAALAARIRRA +>PROKKA_00525 +MRAHPSPTGRTVHLSATGEDARILADELGGSVLEIGGAVQSHVDPADPTALRYEYLRRMA +NVLDGVAPAGAPLRVLHLGAGALTLPRYVQATRPGSEQTAVDLDRELVSFVLAELPLPAG +TDLVSVVADARLAAVDLLMDGERFDAVVLDIGTGEDGAAHLTGAEFYGELLGLLTAAGVL +LVNIGDDDGLRFLGAQLRHMEAACAEAGVPGPWTLASAAMLERLELGNAVLAAGPALRGD +GAAAGGDAGPEEDGGPLTPAALLARGPHPGAVLDEAASADLARRVAGR +>PROKKA_00467 +MPTQPQDDASSPAPSPTARTVHLAASGVDARILPDPHAGGWMLEVGGAVQSHVDLADPTQ +VRYEYLRRIANVLDALAPAGEPLRVLHLGGGALTLPRYVAATRPGSVQTVVDLDRELMGL +VLEELPLPADADVYVVVADARAVVDDLLDPLEGESQAGAWDAVVLDIDTDAGAVAHLTGA +AFHAELLELLAPGGVLCVNIGDDDGLAYLATQLTALEAACADAAEGAGVPGPWTLGPNSV +LERRELGNAVLVAGPGLAGMDAAALHAAGPHPAVVLDAHESAALAERITAAP +>PROKKA_02155 +MPAQPSPSGRTVHLSTSGVDARIAPDEFGGFVLEIGGAVQSHVDLADPARIRYEYLRRMA +HVLDGVAPAGAPVRVLHLGAGALTLPRYLQATRPGSEQTVVDLDRELVSFVLAELPLPAG +TDLVSVVADARLAAVDLAMDGERFDAVVLDIGTGEEGAEHLRGAVFYGELLELLTAGGVL +LVNIGDDAGLRFLGAELGALEKAAAEAGVPGPWTLADQGMLERLDWGNVVLAAGAPLREA +GCTERLAAAGPHPAAVLDPAESAALAARIRRA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001722.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001722.fa new file mode 100644 index 0000000000000000000000000000000000000000..3d0dee4895531442ed924a8eccb3c7b7c71725d9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001722.fa @@ -0,0 +1,35 @@ +>PROKKA_02219 +MPPEPSAPSGERGPARPHPADVAARPDAPSPRATALLFALAVAAGSVMPLQGRINSRLAH +LTGDPVLAALCSFAAGLVVMVLVSVLTPRGRRGLARIRPALAAGSVRPWYAVAGVIGGLL +VLTQSATIGPLGVAVFTVAVVTGQVVGGMVVDRLGLSPAGVQRLTPRRLTGAALALAAVA +LVVWPSLGEAGGGPGWALLALLPLLAGLATAGQQVFNARQTTAYGTAIPATLVNFTAGVL +FLGIVWGGIALASGHGLPALPHDWRLYLGGPLGCVFIGVGAMVVPRLGVFAATLGLVSGN +LLGSLVVDLVAPTDGSTVTTTTVLGTLGALAAVALASWPARRR +>PROKKA_01932 +MPPESSVPSAERGPSRPRPAAVAARPEAPSPRATALLFALAVAAGSVMPLQGRINSRLAH +LTGDPVLAALCSFAAGLAVMVLVSVLTPRGRRGLARIRPALAAGSVRPWYAVAGMIGGLL +VLTQSATIGPLGVAVFTVAVVTGQVVGGMVVDRLGLSPAGVQRLTPRRLTGAALALAAVA +LVVWPSLGEAGGGPGWALLALLPLLAGLATAGQQVFNARQTTAYGTAIPATLVNFTAGVL +FLGIVWGGIALASGHGLPALPHDWRLYLGGPLGCVFIGVGAMVVPRLGVFAATLGLVSGN +LLGSLVVDLVAPTDGSTVTTTTVLGTLGALAAVALASWPARRR +>PROKKA_00527 +MSARAARAARAGEGRQGSDAPAGADARPGAAGSALLFAMAIVAGSTIPVQARLNSALAER +SGDPTLAAVASFAAGLVLVAAVTVLTPAGRRGLRAVRPALAAGRVRWWYLLAGTIGGAMV +FSQATTVGLIGVAVFTVAVVTGQLIGGMVVDRLGLTPAGVRRMTPRRLAGAALALACVVL +VVAPQLGARGDGGPPLWLLVALAPLAVGLATSIQQTLNARQAAAYGSVLPVTTVNFVAGT +GILALVHLGGRLGGGVGGTLPGDWWLYLGGPMGVVFIAFSAYLVPRVGAFLTMLGLVSGK +LLGSLAVDALAPVGEVAASPWTVVGTLGALAAVVLASGAARPARKG +>PROKKA_00465 +MPASSPALTPAPRSGATTALLFLLALVAGLAMPVQGRVNSALSLAVGSPALAACASFATG +LAVLVLATLLLPSGRRGAARIPAAVRNGDVRWWQLLAGTIGAAFVLTQAWTIPLIGVAVF +TVAVVTGQMLGGMLWDRLGWTPAGVQRISRRRLFGALLAFCAVTAVVWPRLQESGSPGAW +LALAVLPLAAGVATSGQQAMNGHQTAHFGTPLPPTLVNFAAGTAVLAAATAVAAGTGAGM +GPLPAAWWMYLGGPLGTVFVGLGAFLIPRVGAFLTTLGMVAGQLVGSLLLDVVAPAPGAQ +VTWLTVVGTLGALAAMVVASSPQVPAGLRASRRRARRG +>PROKKA_02158 +MPPEPSAPSGERGPARPHPADVAARPDAPSPRATALLFALAVAAGSVMPLQGRINSRLAH +LTGDPVLAALCSFAAGLVVMVLVSVLTPRGRRGLARIRPALAAGSVRPWYAVAGVIGGLL +VLTQSATIGPLGVAVFTVAVVTGQVVGGMVVDRLGLSPAGVQRLTPRRLTGAALALAAVA +LVVWPSLGEVGGGPGWALLALLPLLAGLATAGQQVFNARQTTAYGTAIPATLVNFTAGVL +FLGIVWGGIALASGHGMPALPHDWRLYLGGPLGCVFIGVGAMVVPRLGVFAATLGLVSGN +LLGSLVVDLVAPTDGSTVTTTTVLGTLGALAAVTLASWPARRR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001723.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001723.fa new file mode 100644 index 0000000000000000000000000000000000000000..2f49de14bcb275cce1ce349642c5e7cb5d148a2f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001723.fa @@ -0,0 +1,25 @@ +>PROKKA_02220 +MKHEIVLTRGDLTLRPLTPDDGPALRELVDAAMWAGNSAPLPVDGAAMSAHLAELSEREG +TFAFAVEQGGELVGRTSLYDLVPGLRVEVGHTVYARRVWGTSVNPGCKLLLFGHAFEEWA +LERVALRCDHRNARSHAAIARLGATFEGTLRRFRPAADGTIADVDYFSVVREEWPAVRGG +LEARLAA +>PROKKA_01933 +MKHEIVLTRGDLTLRPLSPTDGPALRELVDAAMWAGNSAPLPVDGAAMSAHLAELIEREG +AFAFAVEQGGELVGRTSLYDLVPGLRVEVGHTVYARRVWGTSVNPGCKLLLFGHAFEEWA +LERVALRCDHRNARSHAAIARLGATFEGTLRRFRPAADGTIADVDYFSVVREEWPAVRAG +LEARLTA +>PROKKA_00515 +MSHDLHLTHGPIRLRPLTPDDAPRLRAIVDEASWAGMSTPLPETDAAMAEHLRELMGRPG +LQAFAVERDGEFVGRTALYDPVPTVRVDVGHTVYARPVWGTEVNPACKLLLLGHAFEELG +VARVGLRCDHRNTRSHRAILRLGATFEGTLRAFRRAADGTVADADHFSVTAPEWPAVRAG +LETRLGA +>PROKKA_00462 +MPAAQLPADLLLEHGAVRLRPLTLDDAPRLRALVDAGSWAGMSSPLPTSDEAMAAHLAQL +MAREDLTAFAVERDGEFVGRTAYYEHVPGVRVDVGHTIYAREVWGTEVNPACKLLLLRHA +FEALGVERVGLRCDHRNTRSHRAILRLGATFEGTLRAFRPAADGTVADVDYFSVLAAEWP +AVRAGLEARLAGSAPAD +>PROKKA_02159 +MKHEIVLTRGDLTLRPLSPTDGPALRELVDAVMWAGNSTPLPVDGAAMSAHLAELIEREG +TFAFAVEQGGELVGRTSLYDLVPGLRVEVGHTVYARRVWGTSVNPGCKLLLFGHAFEEWA +LERVALRCDHRNARSHAAIARLGATFEGTLRRFRPAADGTIADVDYFSVVREEWPAVRAG +LEARLAA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001724.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001724.fa new file mode 100644 index 0000000000000000000000000000000000000000..1b2c1b6ab00aa6a1ddf2b7dcb817c97d7b3b98c9 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001724.fa @@ -0,0 +1,55 @@ +>PROKKA_02239 +MQLDLIVENARLITGDPARPSASRLGVWRGVVVGVDEELDGLAARERLDARGRTVLAGFN +DAHAHSVWFGQSRLDVDLEGARTAEEVHRRVRARAAELDPGAWVTCTGFDPGHLTGPQPD +RDGLDAAASGRPVLIRHNTGHAVTVSGAVLVLAGVGEQVLQQPEGGRILTDAEGRPTGLL +EETAMSLVTRLLQSESHEHIGACLARASQGYAAEGITSVTDAGVAGGWIGHSPLEFGAYQ +RARDAGLLRTRFQTMVTLDALHSVDGHPDDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDG +SMLGQTAAMTEDYCGHGHGRGYLQQDAGEMRRACLGAAAAGWALALHAIGDAALDFALDV +IAEARGRFGRPVMPHRVEHGGVVRDDQVARMAELEVVMATQPNFISAFGGSVRERIGPER +AALSYPAGRLLRAGLVLPGSSDRPVAGGRPLEVIQDFVLRRTETGEQYGPDAERLTVAEA +LHAYTVGSAEATGWGGRKGRLVAGQLADFTVLSEDPRVVPSDQIAAIDVVATAVGGEFVH +GGL +>PROKKA_01941 +MQLDLIVENARLITGDPARPSASRLGVWRGVVVGVDEELDGLTARERLDARGRTVLAGFN +DAHAHSVWFGQSRLDVDLEGARTAEEVHRRVRARAAELGPGAWVTCTGFDPGHLTGPQPD +RDSLDAAASGRPVLIRHNTGHAVTVSGAVLVLAGVGEQVLQQPEGGRILTDAAGRPTGLL +EETAMSLVTRLLQPESHEHIGACLARASQEYAAEGITSVTDAGVAGGWIGHSPLEFGAYQ +RARDAGLLRTRFQTMVTLDALRPVDGHPDDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDG +SMLGQTAAMTEDYCGHGHGRGYLQQDAGEMRRACLGAAAAGWALALHAIGDAALDFALDV +IAEARGRFGRPVMPHRVEHGGVVRDDQVARMAELEVVMATQPNFISAFGGSVRERIGPER +AALSYPAGRLLRAGLVLPGSSDRPVAGGRPLEVIQDFVLRRTETGEQYGPDAERLTVAEA +LHAYTVGSAEATGWGGRKGRLVAGQLADFTVLSEDPRAVPSDQIAAIDVVATAVGGEFVH +GGL +>PROKKA_00506 +MQLDLIVENAHLLTGDPARPEATRLGVWRGAVVGVDEELDGLGARERLDARGRTVLAGFN +DAHAHSVWFGQSRLDVDLEGAHTAQEVYDRIRARAAELTPGAWVTCTGFDPGHLTGPQPD +RDGLDAAAAGRPVLIRHNTGHAFTVSGAVLFLAGVGEQVMQQPEGGRIITDAADRPTGLL +EETAMNLVTRLLQPESHEHIGACLARASQEYAAEGITSVTDAGIAGGWIGHSPLEFGAYQ +RARDAGLLRTRFQAMVTLDALRPVDGHADDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDG +SMLGQTAAMTADYCGHGHGRGYLQQDAGEMRRECLGAAAAGWSLALHAIGDAALDFALDV +IAEARARFGRPVMPHRVEHGGVVRDDQVARLAELEVVMATQPNFISAFGGSVRERIGPER +AALSYPAGRLLRAGLVLPGSSDRPVAGGRPLDVIQDFVLRRTETGEQYGPDLERLTVAQA +LQAYTVGSAEATGWGGRKGRLVAGQLADFTVLSADPRAVPSEEIAAIDVVATAVGGEFVH +GGL +>PROKKA_00442 +MQLDLIVENARLITGDPARPSASRLGVWRGVVVGVDEELDGLAAGERLDARGRTVLAGFN +DAHAHSVWFGQSRLDVDLEGARTAEEVHRRVRARAAELDPGAWVTCTGFDPGHLTGPQPD +RDSLDAAASGRPVLIRHNTGHAVTVSGAVLVLAGVGEQVLQQPEGGRILTDAAGRPTGLL +EETAMSLATRLLQPESHEHIGACLARASQEYAAEGITSVTDAGVAGGWIGHSPLEFGAYQ +RARDAGLLRTRFQTMVTLDALRPVDGHPDDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDG +SMLGQTAAMTEDYCGHGHGRGYLQQDAGEMRRACLGAAAAGWALALHAIGDAALDFALDV +IAEARGRFGRPVMPHRVEHGGVVRDDQVARMAELEVVMATQPNFISAFGGSVRERIGPER +AALSYPAGRLLRAGLVLPGSSDRPVAGGRPLEVIQDFVLRRTETGEQYGPDAERLTVAEA +LHAYTVGSAEATGWGGRKGRLAAGQLADFTVLSEDPRAVPSDQIAAIDVVATAVGGEFVH +GGL +>PROKKA_02171 +MQLDLIVENARLITGDPARPSASRLGVWRGVVVGVDEQLDGLATRERLDARGRTVLAGFN +DAHAHSVWFGQSRLDVDLEGARTAEEVHRRVRARAAELDPGAWVTCTGFDPGHLTGPQPD +RDSLDAAASGRPVLIRHNTGHAVTVSGAVLVLAGVGEQVLQQPEGGRILTDAAGRPTGLL +EETAMSLVTRLLQPESHEHIGACLARASQEYAAEGITSVTDAGVAGGWIGHSPLEFGAYQ +RARDAGLLRTRFQTMVTLDALHPVDGHPDDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDG +SMLGQTAAMTEDYCGHGHGRGYLQQDAGEMRRACLGAAAAGWALALHAIGDAALDFALDV +IAEARGRFGRPVMPHRVEHGGVVRDDQVARMAELEVVMATQPNFISAFGGSVRERIGPER +AVLSYPAGRLLRAGLVLPGSSDRPVAGGRPLEVIQDFVLRRTETGEQYGPDAERLTVAEA +LHAYTVGSAEATGWGGRKGRLVAGQLADFTVLSEDPRAVPSDQIAAIDVVATAVGGEFVH +GGL diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001729.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001729.fa new file mode 100644 index 0000000000000000000000000000000000000000..37f271b42af8b88dd05225f2b8d68efb2b858199 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001729.fa @@ -0,0 +1,50 @@ +>PROKKA_02247 +MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLTDMVGQLARGGSSSAGISSF +QSFAMALGGRIGVGNIAGVAAAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVR +GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQIQANAVTAATTEAWGWDPLW +VGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQVPAMFGLIFSS +ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVD +TLFVCTMTGLMILATNSFNVLGPDGESLLAEHVPGVEEGPAWVQIAIDEALPAFGPSFVA +IAVFLFSFTTLLSFAFYAETNVAYLIPNKTAQRAVIAIARLLLAGSMVFGSVQTSAFVWS +LADFGVGLYTWVNIVALILLSPVAIRLFKDYDRQRRAGQDPVLDPAAIGVRNARLWEQIH +AAYQQTGDLDRAMEHVADTAPDTRAITVVPRREG +>PROKKA_01949 +MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLRDMVGQLVRGGSSSAGISSF +QSFAMALGGRIGVGNIAGVAAAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVR +GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQIQANAVTAATTEAWGWDPLW +VGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQVPAMFGLIFSS +ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVD +TLFVCTMTGLMILATNSFNVLGTGEGPPIVEHLPGVEEGPAWVQIGIDVVLPSFGPSFVA +VAVFLFAFTTLLSFAFYAETNLAYLIPNKKAQRICIAAARLLLAASMVIGSVQTSAFVWS +LADFGVGLYTWVNILALVLLSPVAIRLLKDYDRQRRAGQDPVLDPAAIGVRNAHLWEQIH +AAYQQTGDLDRAMEHVADTAPDTRAITVVPRREG +>PROKKA_00499 +MEQFLAGANAIMWSLPMVFGLLALGLYFTIRMGAPQLRRIPDMIGQLVRGGSSSAGISSF +QAFAMALGGRIGVGNIAGVATAISLGGPGALFWMWVTALLGAPVALAESSLAQLYKHKVR +GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVITGPQIQANAVTAATTQAWGWDPLW +VGLAMAVLFCVIVFGGMHRLGRTVGLVVPFMAAAYIIVGVVVVALMWQQVPAMFGLIFTS +AFAADSLYAGMLGAAISWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAFVD +TLFVCTVTGLMILSTNSFNVLGPDEETVLVEHVPGIEAGPAWVQTAIDSVIPAFGPAFVA +VAVFLFSFTTLLSFAFYAETNLAYLIPNKSVQRACIAVARLGLAASMVFGAVQTSTLVWS +FADFGVGLYTWVNILALVLLSPVAIRLMKDYDRQRRAGQDPVLDPRAIGVRNATLWEQIH +DEYERTGDVTAALDHVADTAPDTRAISVVRSHGERGQG +>PROKKA_00437 +MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLKDMVGQLVRGGSSSAGISSF +QSFAMALGGRIGVGNIAGVAAAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVR +GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQIQANAVTAATTEAWGWDPLW +VGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQVPAMFGLIFSS +ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVD +TLFVCTMTGLMILATNSFNVLGPDGESLLAENVPGVEEGPAWVQIAIDAALPAFGPSFVA +IAVFLFSFTTLLSFAFYAETNVAYLIPNKTAQRAVIAIARLLLAGSMVFGSVQSSALVWA +FADFGVGLYTWVNIVALILLSPVAIRLFKDYDRQRRAGQDPVLDPAAIGVRNARLWEQIH +AAYQQTGDLDRAMEHVADTAPDTRAITVVRGGPERGEG +>PROKKA_02179 +MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLTDMVGQLARGGSSSAGISSF +QSFAMALGGRIGVGNIAGVAAAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVR +GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQIQANAVTAATTEAWGWDPLW +VGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQIPAMFGLIFSS +ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVD +TLFVCTMTGLMILATNSFNVLGPDEESLLAEHVPGVEEGPAWVQIAIDEALPAFGPSFVA +IAVFLFSFTTLLSFAFYAETNVAYLIPNKTAQRAVIAIARLLLAGSMVFGSVQTSAFVWS +LADFGVGLYTWVNIVALILLSPVAIRLLKDYDRQRRAGQEPVLDPHAIGVRNARLWEQIH +AAYQQTGDLDRAMEHVADTAPDTRAITVVPRREG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001730.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001730.fa new file mode 100644 index 0000000000000000000000000000000000000000..48d6b104e5ce5be40002b2e70b4566783db56daa --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001730.fa @@ -0,0 +1,29 @@ +>PROKKA_02254 +MMGPSHAATGAAAWLALTHWQSPIAVLHLPAELQLLGAVTTAGAAMISDWDHPRATVVHA +LPPLTEWLSRGIRHVAGGHRRGTHSLVGVAAFTAIATAAASIQVPIAGHVYTPGQGVIAA +FLAAVAAKALRLLPNRGWRAAWALGILVAVSATVLSDGLWWIPASVAVGVSVHILGDALT +NNGVALLWPLSPEPPARLWWWQSSGRFRLPLLGRTGSWREWALVSVVTAFTVVRAVRLVP +LAARGVAALF +>PROKKA_01954 +MMGPSHAATGAAAWLALTHWQSPIAALHLPAELQLLGAVTTAGAAMISDWDHPRATVVHA +LPPLTEWLSRGIRHVAGGHRRGTHSLVGIAAFTAVATAAASIQVPIAGHVYTPGQGVIAA +FLAAVAAKALRLLPNRGWRAAWALGILVAVSATVLSDGLWWIPASVAVGVSVHILGDALT +NNGVALLWPLSPEPPTRLWWWQSSGRFRLPLLGRTGSWREWALVSVVTAFTVVRAVRLIP +LAARGVAALF +>PROKKA_00477 +MGPSHAATGAAAWLALTHWQSPIAVLHLPAELQLLGAVTTAGAAMISDWDHPRATVVHAL +PPLTEWMSRGIRHVAGGHRRGTHSLVGIAAFTAIATAAASIQVPIAGHVYTPGQGVIAAF +LAAVAAKALRLLPNRGWRAAWALGILVAGAATVLSDGLWWIPASVAVGVSVHILGDALTN +NGVALLWPLSPEPPARLWWWQSSGRFRLPLLGRTGSWREWAFVSVVTAFTVVRAVRLVPL +AARGVAGLLGAGAPS +>PROKKA_00432 +MSTPPAALALFLPRGPPAGPRGCGDAAWLALTHGQSPVGVRHLPAELQLLGAVTTAGAAM +ISDWDYPRATAIATAAASIHVPIAGHVYTPGQGVIAAFVAAVAAKALRLLPNRGWRAAWP +LGILVAVSATVFSDGLRWIPVSVAVGVSVHILGDALTNNGVALLWPLSPEPPARLWWWQS +SGRFRLPLLGRTGSWREWALVSVVTAFTVVRAVRLVPLAARGAALF +>PROKKA_02185 +MMGPSHAATGAAAWLALTHWQSPIAVLHLPAELQLLGAVTTAGAAMISDWDHPRATVVHA +LPPLTEWLSRGIRHVAGGHRRGTHSLVGIAAFTAIATAAASIQVPIAGHVYTPGQGVIAA +FLAAVAAKALRLLPNRGWRAAWALGILVAVSATVLSDGLWWIPASVAVGVSVHILGDALT +NNGVALLWPLSPEPPARLWWWQSSGRFRLPLLGRTGSWREWALVSVVTAFTVVRAVRLLP +LAARGVAALF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001731.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001731.fa new file mode 100644 index 0000000000000000000000000000000000000000..893cca3d70dea201be1bb42d2d3d75d8836bfda5 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001731.fa @@ -0,0 +1,30 @@ +>PROKKA_02255 +MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLSRRLWLAARQTALLTPVLVTIVLVAA +FLALTGIDYETYMNGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTVGSLTAM +VSAVLIVRAMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP +WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL +AMTG +>PROKKA_01955 +MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLSRRLWLAARQTALLTPVLVTIVLVAA +FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTVGSLTAM +VSAVLIVRAMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP +WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL +AMTG +>PROKKA_00476 +MNGAELADSLAEAWDALLHTPLFGIALTLAVAVLARRLWLAARQTALLTPVLVTIVLVAA +FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPIAVGVTVGSLTAM +VSAVLIVRLMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVFAP +WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL +AMTG +>PROKKA_00431 +MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLARRLWLAARQTALLTPVLVTIVLVAA +FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTAGSLTAM +VSAVLIVRVMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP +WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL +AMTG +>PROKKA_02186 +MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLSRRLWLAARQTALLTPVLVTIVLVAA +FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTVGSLTAM +VSAVLIVRAMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP +WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL +AMTG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001732.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001732.fa new file mode 100644 index 0000000000000000000000000000000000000000..68ca3dea7c377eca7c85b24316c6ba23082a743b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001732.fa @@ -0,0 +1,17 @@ +>PROKKA_02256 +MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTASHHLLQ +HLPLLFVPAGVGVVAVLGLIEEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTDKEDAQ +>PROKKA_01956 +MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTASHHLLQ +HLPLLFVPAGVGVVAVLGLIEEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTDKEDAQ +>PROKKA_00475 +MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTTSHHLLQ +HLPLLFVPAGVGVVAVLGLIGEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTNKKENA +Q +>PROKKA_00430 +MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVITASHQLLQ +HLPLLFVPAGVGVVAVLGLIQEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTNKKEDA +Q +>PROKKA_02187 +MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTASHHLLQ +HLPLLFVPAGVGVVAVLGLIEEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTDKEDAQ diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001733.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001733.fa new file mode 100644 index 0000000000000000000000000000000000000000..ad89074ad0fda0e2254155e7f11cdc7d31dc1067 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001733.fa @@ -0,0 +1,30 @@ +>PROKKA_02257 +MHPITLARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTEAGISRT +PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP +LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH +AATGGSVDAARRLLDGHAEICAQLAAGRAADAQRALQAHLDAAGSGVVPGLPPVGPSEAG +EPR +>PROKKA_01957 +MHPITLARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTEAGISRT +PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP +LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH +AATGGSVDAARRLLDGHAEICAQLAAGRAADAQRALQAHLDAAGSGVVPGLPPVGPSEAG +EPR +>PROKKA_00474 +MHLIILARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVRLSTEAGISRT +PAREALLQLESWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP +LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH +AATGGSVDAARRLLDGHAEICAQLAAGCAADAQRALQAHLDAAGTGVVVPGLPTVSQPEA +GEPR +>PROKKA_00429 +MHLIILARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTDAGISRT +PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP +LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIAMCGNAAFDEIMGTFAPRLARLIH +AATGGSVDAARRLLDGHVQICAQLAAGRAADAQRALQAHLDAAGAGVVVPGLLPVGSSEA +GEPR +>PROKKA_02188 +MHPITLARMTPLSDPLWGSRATAAGRLAHDVAWRIVRGEIAAGEMLTEVQLSTEAGISRT +PAREALLQLERWGLVRLLPKKGAAVQALTPQSVADLTALRGLLESTALATVAARPDAVGP +LVATLTANLEQQRAALDAGDLAAFSALDVRFHRDVIATCGNAAFDEVVRTFAPRLARLIH +AATGGSVDAARRLLDGHAEICAQLAAGRAADAQRALQAHLDAAGSGVVPGLPPVGPSEAG +EPR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001734.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001734.fa new file mode 100644 index 0000000000000000000000000000000000000000..c02ce2c33e621d4024be4e28956bdd30c6ccd633 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001734.fa @@ -0,0 +1,55 @@ +>PROKKA_02268 +MPTLRTVPLSAATREDHLARLRATSPEAPLDILVVGGGSTGVGAAFDAATRGLDVGIVEA +RDWASGTSSRSSRLMHGGLRYLEMLDVKLVYEALRERDLLLTQTAPHLVRPLRFVFPFFH +KVIDRGFIGAGVTMYDAMQSLGRRRAMGAHRHLSRRSMAATFPSLDDEKIVGAVEYADAQ +FDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGDDGRVQGVRVREETSGEEFDVHARAVI +LAGGVWTQEQQELAGADGGLEVLASKGAHITVPRDRIRADAATGVITKTEKSVLFLIPWD +EYWVIGTTDTPWAEDVAHPATTADDIDYILEHANAVLKEDLTRDDVVATYAGLRPLLQPV +TGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTYRAMAEDVVDFVVRETHPTRPSLTERI +PVLGGLGYSEIEAEADRIAADYGLDEARVDRLLFRYGTVLRHVLDLIDADPSLSVPLAEA +PRYLRAEIVYAARAEGVVHLDDVIERRTRLSTEVRDRGVAAAEEIASLVAPELGWDEERI +AGEIRAYKNLVAARLRGETAHDDVTAAAALAAADADAAPTP +>PROKKA_01961 +MPTLRTVSLSAATREDHLARLRATSPEAPLDILIVGGGSTGVGAAFDAATRGLDVGIVEA +RDWASGTSSRSSRLMHGGLRYLEMLDVKLVYEALRERDLLLTQTAPHLVRPLRFVFPFFH +KVIDRGFIGAGVTMYDAMQSLGRRRAMGAHRHLSRRSMAATFPSLDDEKIVGAVEYADAQ +FDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGDDGRVQGVRVREETSGEEFDVHARAVI +LAGGVWTQEQQELAGADGGLEVLASKGAHITVPRDRIRADAATGVITKTEKSVLFLIPWD +EYWVIGTTDTPWAEDVAHPATTADDIDYILEHANAVLKEDLTRDDVIATYAGLRPLLQPV +TGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTYRAMAEDVVDFVVRETHPTRPSLTEHI +PVLGGLGYSEIEAEADRIAADYGLDEARVDRLLFRYGTVLRHVLDLIDGDPSLSVPLAEA +PRYLRAEIVYAARAEGVVHLDDVIERRTRLSTEVRDRGVAAAEEIASLVAPELGWDEERI +AGEIRAYKNLVAARLRGETAHDDVTAAAALAAADAAPVHGKEPVHGHDLPA +>PROKKA_00462 +MGGGSTGVGAAFDAATRGLDVGIVEARDWASGTSSRSSRLMHGGLRYLEMLDVKLVYEAL +RERDLLLTQTAPHLVRPLRFVFPFFHKVIDRGFIGAGVTMYDAMQSLGRRRAMSAHRHLS +RRSMAATFPSLDDEKIVGAVEYADAQFDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGD +DGRVQGVRVREETSGEEFDVHARAVILAGGVWTQEQQELAEADGGLEVLASKGAHITVPR +DRIRADAATGVITKTEKSVLFLIPWDEYWVIGTTDTPWAEDVAHPAATADDIDYILEHAN +AVLKEDLTRDDVIATYAGLRPLLQPVTGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTY +RAMAEDVVDFVVRETHPTRPSLTERIPVLGGLGYSEIEAEADRIAADYGLDEARVDRLLF +RYGTVLRHVLDLIDADPSLSVPLAEAPRYLRAEIVHAARAEGVVHLDDVIERRTRLSTEV +RDRGVAAAEEIASLVAPELGWDEERIAGEIRAYKSLVAARLRGETAHDDVTAAAALAAAD +AASTH +>PROKKA_00493 +MPTLRTVELSPATRADHLARLRAADADHPLDVLVVGGGSAGVGAAFDAATRGLDVGIVDA +GDWAGGTSSRSSRLMHGGLRYLEMLDVKLVYEALRERDLLLTRTAPHVVRPLRFVFPLEH +ARDRGWIGAGVGVYDAMQSVGRRRAVGGHRHLGRKALAETFPGLDPEAAVGAVEYADAQF +DDARLALLLVRSAVDLGAAALNHAPVVGYLKDGAGAVVGARVRESLTGEELQVHARAVIL +AGGVWTQEQQELAGVDGGLEVLASKGVHVTVPRERIAAEPGVGVITRTEKSVLFVIPSDE +HWIIGTTDTPWRQDVDHPAATAADVDYVLEHANAVLSEDLTRADVVAVYAGLRPLLQPAA +GADDASTKVSREHTVTELAPGLTAVAGGKWTTYRAMAEDTVDFAVRDLFPTRPSLTAHTP +VLGGLGYAEIAARAAEIAAERGFDAARVDRLLRRYGTLLPHVLALVDADPALGEPLPGGE +AYLRAEVVYAARAEGAVHLDDVLERRLRLSTEVPDRGADAASEAAALVADVLGWDAARRD +AEVAAYRALVAARRRAEGLDDDAAAAAELAAAGERAGVVPVTSRETVTPEEKGGAR +>PROKKA_02200 +MPTLRTVSLSAATREDHLARLRATSPEAPLDILIVGGGSTGVGAAFDAATRGLDVGIVEA +RDWASGTSSRSSRLMHGGLRYLEMLDVKLVYEALRERDLLLTQTAPHLVRPLRFVFPFFH +KVIDRGFIGAGVTMYDAMQSLGRRRAMGAHRHLSRRSMAATFPSLDDEKIVGAVEYADAQ +FDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGDDGRVQGVRVREETSGEEFDVHARAVI +LAGGVWTQEQQELAEADGGLEVLASKGAHITVPRDRIRADAATGVITKTEKSVLFLIPWD +EYWVIGTTDTPWAEDVAHPATTADDIDYILEHANAVLKEDLTRDDVVATYAGLRPLLQPV +TGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTYRAMAEDVVDFVVRETHPTRPSLTEHI +PVLGGLGYSEIEAEADRIAADYGLDEARVDRLLFRYGTVLRHVLDLIDADPSLSVPLAEA +PRYLRAEIVYAARAEGVVHLDDVIERRTRLSTEVRDRGVAAAEEIASLVAPELGWDEERI +ADEIRAYKNLVAARLRGETAHDDVTAAAALAAADAAPTP diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001737.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001737.fa new file mode 100644 index 0000000000000000000000000000000000000000..4b32d2ce4f50b07567f8f0b6d9da1eafe9c06b45 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001737.fa @@ -0,0 +1,40 @@ +>PROKKA_02285 +MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA +VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV +RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV +EESKGTDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM +GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR +LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTCVFPNPADTKVLEEGD +RLLCFGKTENMRALIPARARRPKRVRRLPATPILASVAEEAPAPEAPADDA +>PROKKA_01976 +MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA +VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV +RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV +EESKGTDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM +GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR +LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTSVFPNPADTKVLEEGD +RLLCFGKTENMRALIPARARRPKRVRKLPATPILASVAEEAPAPEAPADDA +>PROKKA_00452 +MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA +ILPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV +RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV +EESKGKDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM +GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR +LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTSVFPNPADTKVLEEGD +RLLCFGKTENMRALIPARARRPKRVRKLPATPILASVAEEAPAPEAPADDA +>PROKKA_00405 +MKLAILSRSLRAYSTQRLKSAALDRGHDVKVLDTLRFGIDLAGDEPDMMFRGKPLSSYDA +VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRASQILSRHGIAQPATVFV +RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV +EESKGKDVRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVEQVELSEEYAETAVRAAHIM +GLRVAGVDMLEGEDGPLVMEVNSSPGLEGIERATTLDVAGAIVDYIADQAGFPEVDVRQR +LAVSTGYGVAEIAVLAGSDMAGQSIEDSGLLEKDLQVLTLHRGASVFPNPADSKVLEEGD +RLLCFGKTENMRALIPARSQRPKRVKKLPKNPIIEAPPAEPAVRPDAESGES +>PROKKA_02224 +MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA +VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV +RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV +EESKGTDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM +GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR +LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTSVFPNPADTKVLEEGD +RLLCFGKTENMRALIPARARRPKRVRKLPATPILASVAEEAPAPEAPADDA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001741.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001741.fa new file mode 100644 index 0000000000000000000000000000000000000000..5839abf10a123cade7cbbce31ce76628c5977f95 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001741.fa @@ -0,0 +1,15 @@ +>PROKKA_02290 +MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ +AVKNAREVALLPYAGAGRG +>PROKKA_01982 +MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ +AVKNAREVALLPYAGAGRG +>PROKKA_00448 +MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ +AVKNAREVALLPYAGAGRG +>PROKKA_00400 +MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ +AIKNAREVALLPYAGAGRG +>PROKKA_02230 +MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ +AVKNAREVALLPYAGAGRG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001742.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001742.fa new file mode 100644 index 0000000000000000000000000000000000000000..75fce4a72a072afc86e9fa4ef28fc234cb1a33b2 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001742.fa @@ -0,0 +1,25 @@ +>PROKKA_02291 +MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW +REAAENVAESLTKGMRVIVQGRLRARSYDDRDGNRRTSWELDVDEVGPALRFATAKVTRA +QRGGGGGGGFGGGQQGGGFGGAPAGGGFGGNSDGGFGGAQQGGGWGGQQQGGGQAAPQDP +WSGGGGGGWDTPSSNEPPF +>PROKKA_01983 +MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW +REAAENVAESLTKGMRVIVQGRLRARSYDDRDGNRRTSWELDVDEVGPALRFATAKVTRA +QRGGGGGGGFGGGQQGGGFGGAPAGGGFGGNNDGGFGGAQQGGGWGGQQQGGGQAAPQDP +WSGGGGGGWDTPSSNEPPF +>PROKKA_00447 +MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW +REAAENVAESLTKGMRVIVQGRLKARSYDDRDGNRRTSWELDVDEVGPALKFATAKVTRA +QRSGGGGGGGFGGGQQGGGFGGAPAGGGFGGNNDGGFGGAPQGGGWGGQQQGGGQAAPQD +PWSGGGGGGGWDTPSSNEPPF +>PROKKA_00399 +MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDEEALFVRCSVW +REAAENVAESLTKGMRVIVQGRLKANSYQDREGNKRTSWELQVDEVGPALKFATAKVTRS +QRGGGGGGGFGGGQQGGGFGGSPQGGGGFGGGQQQSGGWGQPSGGGQSAPAQDPWSGSGG +GGWDTPSNGEPPF +>PROKKA_02231 +MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW +REAAENVAESLTKGMRVIVQGRLRARSYDDRDGNRRTSWELDVDEVGPALRFATAKVTRA +QRGGGGGGGFGGGQQGGGVGGAPAGGGFGGNNDGGFGGAQQGGGWGGQQQGGGQAAPQDP +WSGGGGGGWDTPSSNEPPF diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001743.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001743.fa new file mode 100644 index 0000000000000000000000000000000000000000..ab7d539fcf0a5bb5343a151724cdcff970a43a9b --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001743.fa @@ -0,0 +1,15 @@ +>PROKKA_02292 +MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVDNIDVWGRRKTAYEIQKKSEAIY +VVVNFQSEPAATQELDRLLNLNETILRTKIIRPEEQKITAE +>PROKKA_01984 +MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVDNIDVWGRRKTAYEIQKKSEAIY +VVVNFQSEPAATQELDRLLNLNETILRTKIIRPEEQKITAE +>PROKKA_00446 +MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVDKVDVWGRRKTAYEIQKKSEAIY +VVVDFQSEPAATQELDRLLNLNETILRTKIIRPEEQKITAE +>PROKKA_00398 +MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVEKIDVWGRRKTAYEIQKKSEAIY +VVVDFTAEPAATQELDRVLNLNETILRTKIIRPEEQKISAE +>PROKKA_02232 +MRAYELMVLIDPEVDERTVEPTLKKYLEVVTNAGGTVDNIDVWGRRKTAYEIQKKSEAIY +VVVNFQSEPAATQELDRLLNLNETILRTKIIRPEEQKITAE diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001745.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001745.fa new file mode 100644 index 0000000000000000000000000000000000000000..4b5d846a65c4aeb2c8456e980085a5aac98ac3ff --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001745.fa @@ -0,0 +1,16 @@ +>PROKKA_02294 +MDIMIAVAVGVFLLVAWTVGGWAIVRMGFTRDGDAARTPAHDDGAARPAHPGAAADPATD +PHVIWREQMKAATAASGAPCVCPPPPREGGAAEAGTSAPPSSPDCPIHRWDYA +>PROKKA_01987 +MDIMIAVAVGVFLLVAWTVGGWAIVRLGFTRDGDAARAPAHDDGAARPAHRGPAADPATD +PHVIWREQMKAATAASGAQCVCPPPREGGAAEAGTSAPPSSPDCPIHRWDYA +>PROKKA_00442 +MEIMIVVAVGVFLMVAWTVGGWVIVRMGFTRDSDAASRAGSQDDDGTRPVPDGPVPVDPA +SDPNAIWREQMKAATAASGAACTCPRRPVGTPSESPAGSGEQGAAVDSAVDRALDPAADH +AAVDPSPDCPIHRWDYA +>PROKKA_00395 +MPNEVLLVAGVGAALFVLWAVGGWLIVRMGFTRDRDRLPDGPGHASALPDGDGAPSPGRL +PADPAQDPHAAWREQMKAATVASGARCTCEDGAVPDPDCPVHRWDYA +>PROKKA_02235 +MDIMIAVAVGVFLLVAWTVGGWAIVRMGFTRDGDAARTPAHDAHDDGAARPAHPGAAADP +ATDPHVIWREQMKAATAASGAQCVCPPPREGGAAEAGTSTPPSSPDCPIHRWDYA diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001747.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001747.fa new file mode 100644 index 0000000000000000000000000000000000000000..d68b8b2552ed1a244db30d74ae1ea8116aff7a8c --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001747.fa @@ -0,0 +1,40 @@ +>PROKKA_02296 +MATNPIRVAIAGVGNCATSLIQGVEYYREAKATDTVPGLMHVQFGDYHVSDLEFVAAFDV +DAKKVGLDLSEAITASENNTIKIADVPHADVTVQRGPTLDGLGKYYAETIEESDVEPVDV +AQALRDAKVDVLVCYLPVGSQRATEHYAQAAIDAGVAFVNALPVFIAGTPEWAEKFTAAG +VPIVGDDIKSQIGATITHRVMAKLFQDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI +SKTQAVTSNTSAQLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD +SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHNDDAAHELVEAFIRGDIE +R +>PROKKA_01989 +MATNPIRVAIAGVGNCATSLIQGVEYYREAKATDTVPGLMHVQFGVYHVSDLEFVAAFDV +DAKKVGLDLSEAITASENNTIKIADVPHADVTVQRGPTLDGLGKYYAETIEESEAEPVDV +AQALRDAEVDVLVCYLPVGSQRATEHYAQAAIDAGVAFVNALPVFIAGTPEWAEKFTAAG +VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI +SKTQAVTSNTSAQLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD +SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHNDDAAHELVEAFIRGDIE +R +>PROKKA_00440 +MATTPIRVAIAGVGNCATSLIQGVEYYRDAKATDTVPGLMHVQFGDYHVSDLQFVAAFDV +DAKKVGLDLSEAILASENNTIKLADVPHADVTVQRGPTLDGLGKYYAETIEESDAEPVDV +AQALRDAQVDVLVCYLPVGSQLATEHYAQTAIDAGVAFVNALPVFIAGTPEWADKFTAAG +VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI +SKTQAVTSNTSAKLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD +SPNSAGVIIDAVRAAKIALDRGTGGPILSASSYFMKSPPVQHNDDEARELVEAFIRGDIE +R +>PROKKA_00393 +MAENPIRVAIAGVGNCATSLIQGVEYYKDAQASDTVPGLMHVQFGDYHVSDLEFVAAFDV +DAKKVGLDLSEAILASENNTIKISDVPATGVTVQRGPTLDGLGKYYRETIEESSAEPVDV +VQALKDAKVDVLVSYLPVGSEEADKFYAQCAIDAKVAFVNALPVFIAGTQEWADKFTEAG +VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI +SKTQAVTSNTSAELAEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD +SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHADDEAHELVEAFIRGDIE +R +>PROKKA_02237 +MATNPIRVAIAGVGNCATSLIQGVEYYREAKATDTVPGLMHVQFGDYHVSDLEFVAAFDV +DAKKVGLDLSEAITASENNTIKIADVPHADVTVQRGPTLDGLGKYYAETIEESEAEPVDV +AQALRDAKVDVLVCYLPVGSQRATEHYAQAAIDAGVAFVNALPVFIAGTPEWAEKFTAAG +VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI +SKTQAVTSNTSAQLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD +SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHNDDAAHELVEAFIRGDIE +R diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001748.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001748.fa new file mode 100644 index 0000000000000000000000000000000000000000..dc0c4f8da08749916599ce1fa6a3d911de80fd0f --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001748.fa @@ -0,0 +1,50 @@ +>PROKKA_02299 +MDLTTATHALPPGFPADATLPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRPSPDLDFT +TDADPDASEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG +DSLEDDLLRRDFTVNAMALRLPALELVDPFGGMRDLHAGVLRTPGTPEDSFSDDPLRMMR +AARFASQLGFAVAPEVEQAMTAMAERITIISAERVREELVKLVCGAHPRAGLDLLVRTGL +ADHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEGEYAPSTPDPVLRLAALLHDV +GKPATRRFEKGGAVTFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGDA +GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIAEITEAEEL +AAVRPDLDGQQIMALLGIRPGPVVGRAYTHLLEWRLDEGPHEPAEAEAELRRWWAEQPEA +QQD +>PROKKA_01992 +MDLTTATHALPPGFPADATLPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRTSPDLDFT +TDADPDASEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG +DSLEDDLLRRDFTVNAMALRLPALELVDPFGGMRDLHAGVLRTPGTPEDSFSDDPLRMMR +AARFASQLGFAVAPEVEEAMAAMAERITIISAERVREELVKLVCGAHPRAGLDLLVRTGL +ADHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEGEYAPSTPDPVLRLAALLHDV +GKPATRRFEKGGAVTFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGDA +GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIAEIAEAEEL +AAVRPDLDGQQIMALLGIRPGPVVGRAYNHLLEWRLDEGPHEQAEAEAELRRWWAEQPEA +QQD +>PROKKA_00437 +MDLTTATLALPAGFPADAALPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRVSGDLDFT +TDAGPDAAEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG +DSLEEDLLRRDFTVNAMALRLPGLELVDPYGGVQDLAAGVLRTPGAPEDSFSDDPLRMLR +AARFASQLGFTVADEVEAAMTAMAERIGIISAERVREELVKLVCGAHPRRGLDLLVRTGL +AEHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEAEYSPSAPDPVLRLAALLHDV +GKPATRRFEKGGAVSFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGEA +GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNKRKAERLAHAYDDLERRIAEIAEQEEL +AAVRPDLDGEQIMALLGIRPGPVVGRAYRHLLEWRLDEGPHEPAEAEAELRRWWAEQPEA +AEG +>PROKKA_00390 +MEPRTDTRPLPAGFPADAALPAVVVELGRRFEAAGHELSLVGGPVRDLLLGRPVVDLDFT +TDADPDATERIGAGWAEAAWDVGRHFGTIGFQKGGWQLEVTTYRAEQYDPTSRKPQVAFG +DSLEDDLLRRDFTVNAMALRLPAMELVDPHGGVRDLAAGVLRTPGAPEDSFSDDPLRMMR +AARFASQLGFGVADEVEAAMTDMAERIGIISAERVRDELVKLVRGDRPRAGLDLLVRTGL +AQIVLPELPALQLETDEHHRHKDVYAHSLQVLEQAMGEEERYSPERPDVVLRLAALLHDV +GKPATRRFEPSGAVSFRHHENVGAKLVRRRLKALRFDNDTIKAVARLVELHMRFYGYGEA +GWTDSAVRRYVHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIEEISAAEEL +AAVRPDLDGQQIMALLGIRPGPVVGRAYAHLLEWRLDEGPHEQAAAEAELRRWWAEQPEA +AGASSGGGARD +>PROKKA_02240 +MDLTTATHALPPGFPADATLPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRPSPDLDFT +TDADPDASEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG +DSLEDDLLRRDFTVNAMALRLPALELVDPFGGMRDLHAGVLRTPGTPEDSFSDDPLRMMR +AARFASQLGFAVAPEVEQAMTAMAERITIISAERVREELVKLVCGAHPRAGLDLLVRTGL +ADHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEGEYAPSTPDPVLRLAALLHDV +GKPATRRFEKGGAVTFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGDA +GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIAEIAEAEEL +AAVRPDLDGQQIMALLGIRPGPVVGRAYTHLLEWRLDEGPHEPAEAEAELRRWWAEQPEA +QQD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001749.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001749.fa new file mode 100644 index 0000000000000000000000000000000000000000..88da44b30f31cbdc886c217b965c04407ac16388 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001749.fa @@ -0,0 +1,60 @@ +>PROKKA_02301 +MDPADETPEGERRAGRSTAIMASGTLLSRVLGLVRATLVTVAIGLSADMADIFEIANSLP +NVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGTLVMLAGTVVVMLAAAPLM +TALTRGWSPEKLEMATVFALWCLPQVFFYGMYALVGQVLNANGRFGAYMWAPVLNNVVAI +GAIVLYLGMFGAYRAGDDLAGWTSAQTVVLAGGHTLGVVLQAVILFLPLRGLGLGLRPRF +GWKGIGLRDTGRIAGYTLITMVATNVVLLLCQRYVTSATEARDRGELRIPGTETWSAEMA +QAAIPGVAAYNMAMLMAVLPHSVFVLSLATVLFNRLARAMGRQDMSAVRRTTAQGLRAFT +VPLMFCLAGVVVLAGPLGRVFGSTAETAMVAGVAVGSVLLALALSIPFRSGSFYLLRVFY +AAEDAKVPMVVQVSGSLLMLLLSWAGAMLLPLWSMALWVAVASSVSYVYQFVLTHVLTVR +RFGDYGLASVLRAHVQTGLAALAAAAAGAVVVWLLGGYTGGFAWNSIGTALLTCAVAAVA +MGPVYLMVLRAMRFPELDDALRPLVARVPALGRLLRVG +>PROKKA_01994 +MDPADETPEGERRAGRSTAIMASGTLLSRVLGLVRATLVTVAIGLSADMADIFEIANSLP +NVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGTLVMLAGTVVVMLAAAPLM +TALTRGWSPEKLEMATVFALWCLPQVFFYGMYALVGQVLNANGRFGAYMWAPVLNNVVAI +GAIVLYLGMFGAYRAGDDLAGWTSAQTVVLAGGHTLGVVLQAVILFLPLRGLGLGLRPRF +GWKGIGLRDTGRIAGYTLITMVATNVVLLLCQRYVTSATEARDRGELRIPGTETWSAEMA +QAAIPGVAAYNMAMLMAVLPHSVFVLSLATVLFNRLARAMGRQDMSAVRRTTAQGLRAFT +VPLMFCLAGVVVLAGPLGRVFGSTAETAMVAGVAVGSVLLALALSIPFRSGSFYLLRVFY +AAEDAKVPMVVQVSGSLLMLLLSWAGAMLLPLWSMALWVAVASSVSYVYQFVLTHVLTVR +RFGDYGLASVLRAHVQTGLAALAAAAAGVVVVWLLGGYTGGFAWNSIGTALLTCAVAAVA +MGPVYLMVLRAMRFPELDDALRPLVARVPALGRLLRVG +>PROKKA_00436 +MASPDPSAHRGAPLPSALGAWHRRPQPPARPEPAPAPGPRPAASGLPTVEEVSAGGVVVR +EHDGGLEVAIIARYNRGGRLEWCLPKGHPEGVEDHRQAAVREVEEETGIAGDILEPLGAI +DYWFTVSRHRVHKTVHHFLLRATGGELTTENDPDHEAVDVAWVRLEDVARRLSFANERRI +VDLARQVVDRHFPRAPPGAPAPDPPPRTRGSSDHDWVTLEQQPLPAPRAGTPPAPAVADE +EPTTADPAPATDPEAPAREDRPDETPEGERRAGRSTAIMASGTLISRVLGLVRAMLVTVA +IGLSTDMADIFEIANSLPNVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGT +LVMLGGTLVVMAVAAPLMTALTRGWSPEKLEMATVFALWCLPQVFFYGMYALVGQVLNAN +GRFGAYMWAPVLNNVVAIAAIGLYLAMFGAYRAGEDVAGWTSTQTLVLAGGHTLGVILQA +VILFLPLRGLGLGMRPRFGWKGIGLRETGRIAGYTLVTMMVTNVVLLLCQRYVTSATEAR +DRGELRIPGTEAWSTEMAQAAIPGVAAYNMAMLIAVLPHSVFVLSLATVLFNRLARAMTR +QDMPAVRRTTAQGLRAFTVPLMFSLAGIVVLAGPLGRVFGSTAETSMVAGIAVGAVLLAL +ALSIPFRSGSFYLLRVFYAAEDAKVPMVVQVSSSLLMLLLSWAGAMLLPLWSMALWVAIA +SSVSYVYQFALTHVLTVRRFGDYGFASVLRAHGQTGLAALAAAAAGAVVVWLLGGYTGGF +AWETIVTALITCAVAAAVMAPVYVVTLKLLRFPELDDALRPVVSRVPALGRLLRVG +>PROKKA_00388 +MSSRTAPRRALPADDAPRPKEVEDVVLPASDPEAPAQAQEEVPEGERRAGRSTAIMAAGT +MISRVLGFVRAALLTIAIGTTVGTVADIFEVANSLPNVIYLLLVGGVFNVVLVPQLIKHA +KDADRGADYTSRLMTLAVLVMLAATVLVTAAAAPLMAALTRGWSPEMLQLGTVFALWCLP +QMFFYGMYALVGQILNANGRFGAYMWAPVLNNVVAIAAIGLYLVMFGRYSGGDLLGRWTP +EQTLVLAGGHTLGVILQALILFLPLRGLGLGLRPRFGWRGMGLRHTGRIAGYTLFTMAAS +NIVLLLSHRYINGASAAREDPSVRVPGTEGWDPAMADALIPGLTAYNQAMLISVLPHSVF +VLSLATVLFNKLARSMAAGDHAAVRETTARGLRTFAAPIMFSLAGVVVLAGPLGRLFGST +AESAQVTGMAVGAVILLMSLSMPFRSGSFYLLRVFYAAESARIPMVVQVTTSLLTLAVTA +AGAYLLPLWAITYWAALASVVSHAFQFFFAHVLAVRRFGDYGFTHVLAAYATTGAAGVVA +GAAGAVVAWLLGAYSGGWAWGSILSALVTCAVVGLVMAPVYVVALRVLRFPELASAAAPL +ARRVPALGRLLGAR +>PROKKA_02242 +MDPADETPEGERRAGRSTAIMASGTLLSRVLGLVRATLVTVAIGLSADMADIFEIANSLP +NVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGTLVMLAGTVVVMLAAAPLM +TALTRGWSPEKLEMATVFALWCLPQVFFYGMYALVGQVLNANGRFGAYMWAPVLNNVVAI +GAIVLYLGMFGAYRAGDDLAGWTTAQTVVLAGGHTLGVVLQAVILFLPLRGLGLGLRPRF +GWKGIGLRDTGRIAGYTLVTMVATNVVLLLCQRYVTSATEARDRGELRIPGTETWSAEMA +QAAIPGVAAYNMAMLMAVLPHSVFVLSLATVLFNRLARAMGRQDMSAVRRTTAQGLRAFT +VPLMFCLAGVVVLAGPLGRVFGSTAETAMVAGIAVGSVLLALALSIPFRSGSFYLLRVFY +AAEDAKVPMVVQVSGSLLMLLLSWAGAMLLPLWSMALWVAFASSVSYVYQFVLTHVLTVR +RFGDYGLASVLRAHVQTGLAALAAAAAGAVVVWLLGGYTGGFAWNSIGTALLTCAAAAVA +MGPVYLVVLRAMRFPELDDALRPLVARVPALGRLLRVG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001750.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001750.fa new file mode 100644 index 0000000000000000000000000000000000000000..077b07f5a3b5925cecbfed3f168e9612e1b1e9c4 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001750.fa @@ -0,0 +1,61 @@ +>PROKKA_02302 +MPQPIAVGAVLGGRYRITQHVVTSADQDMVFLGTDQVLNRRVTVLVASRENATQVASSAR +ELATGERTDDVQVLDLGLSEGRTYLIAGGDPDPDVLLGLAYPQELYVEPFQTDSLGSELF +GESRTGDPHAYDDDEAYYTDLDRRLRADEDEAQRRPGFLNRLSERLAERVRPSDGTAAKA +AAGASALAAADAATRKQQEERERAEREAAERAERERKEAAERAERERKEAAERAERERKE +AEEKARAEREAAERAERERKEAAERAERERREAEERAEEERRAEAERARRQAEQEAEERA +AREREAEQARLAAEREEAERRELERRAEARRRAEEERAREAAEREAEKRAAQEREAAERE +AQAGTAALPAVAAGAAAAQAPDADADGATPPTEPVESVAAEKTDPPEPVAPDTEAIPVRR +QRPVPRRAIVAESAPTAHEESRGTAAPVAAGAGVATAAGAAAAGSTAAAAAPDAQAAPAT +TGGGDGATVADPGDGHGRTRGGGPLALLLVLGLLAALVVGGVLLAQNLRGGPAPQAASSE +SESASSESASDTPSPSESTSPSPTPSSESAAAAPQPVQALRSVPDLPEHEAEHDADLSNL +IDGDPTTVWRTFAYARPNFGGYVESMNLVVQLEERTEVNEVTLQSTGATGGAWFAYIADS +PEGANAKEIGNGTFDQDTVSIPVPFEGTEAEAEYVIVSLTSLPQLEGTTSDLPFGLRLGE +IAVR +>PROKKA_01995 +MPQPIAVGAVLGGRYRITQHVVTSADQDMVFLGTDQVLNRRVTVLVASRENATQVASSAR +ELATGERNDDVQVLDLGLSEGRTYLIAGGDPDPDVLLGLAYPQELYVEPFQTDSLGSELF +GESRTGDPHAYDDDEAYYTDLDRRLRADEDEAQRRPGFLNRLSERLAERVRPSDGTAAKA +AAGASALAAADAATRKQQEERERAEREAAERAERERKEAEEKARAEREAAERAERERKEA +AERAERERREAEERAEEERRAEAERARRQAEQEAEERAAREREAEQARLAAEREEAERRE +LERRAEARRRAEEERAREAERREAEKREAQEREAAEREAQEREAAEREAQAGTAALPAVA +AGAAAAQATDADADGATPPTEPVEPVESVAAEKTDPPEPVAPDTEAIPVRRQRPVPRRAI +VAESAPPVHEESRSTAAPVAAGTATGATAAAAGSTSAAAAPDALAAPATTGGDDGATVAD +PGDGNGRTRGGGPLALLLVLGLLAALVVGGVLLAQNLRGGPAPQAAAASSESASSESASD +TPSPSESTSPSPTPTSESAAAAPQPVQALRSVPDLPEHEAEHDADLSNLIDGDPTTVWRT +FAYARPNFGGYVESMNLVVQLEERTEVNEVTLQSTGATGGAWFAYIADSPEGANAKEIGN +GTFDQDTVSIPVPFEGTEAEAEYVIVSLTSLPQLEGTTSDLPFGLRLGEIAVR +>PROKKA_00435 +MAPGAAETDTVETRADEPAAAEPESTATAPAEDVDPEPTAPAPVVPASTAPDSAPDTEAI +PVRRQRPVPRRAMVVEPTTPDADRSPDAQRSRGAGAPLAAAGAGAVAAAGATAASAAAAG +AAPSATSAPSTASAAPEATAAGTSPADGDGGAPVDPDQGGSRRGGWPLALLLLAVLVGAL +VLGGVLLAQNLRGAPHRAGRPARLPHRDRRGARTRRQPPPTQSDEASPTEASPTESSPAA +STSASPTESETAAAAPQPARALRMVPDLPAHESEHDGELPNLIDGDPSTAWRTFAYARPN +FGGYVESMNLVVELEDRAEVNEVTLQSTGATGGAWFAYIADSPEGENAREIGNGTFDQDS +VTVPVPFDGAEAEAEYVIVSLTSLPRLDGTTPDLPFGLRLGEIGVR +>PROKKA_00387 +MPQPLAVGSVLGGRYRITDHVVTSADQNMVFQGADQVLNRRVTVLVASPENATQVAASAR +ELATGERQDDVQVLDLGLSEGRTYLIAGGNPDPDVLLGLAYAQELYVEPFQTDSLGSEIF +GESRTEQAHEYDDDDAYYADLDRRLRADQKQSQRRPGFLNRISEKLNERVRPADGTAAKA +AAGASALAAADAATKAQLAEQERAEREAREAQERAEREEAQEAERREREAQERAERERLE +RAAAAQAEKDRAAREAAEAEAAARREREAQRHAEAETRRREEEAAAAAALAAAAPAADAD +PADAPTQAVPVTEPASTPEAVPAPVRRPRPAPRRALPAVASAAAVAASVSAEEGASAAEA +APAESVAPEAVPTATATSSAAIAVAEAEPAVTEHREEAHAAPVAGGAGAGAPAAGATAAP +ARSTSGKGWLMVLGLLALLALAGLAGLFLLGQNTRSVEPAPSASASSAAPSTAQASSAPP +AASSSAAPTASSSAAPSTEPAPSTSAAAPAPTAAPQAVAVTRQVPEMPELEAPNDATLAN +LIDGDPNTAWQSYTYARPNFGGYVGSMNLVVQLQERTTISEVQLENRGATGGKWIAYVAN +TAQGGEGDARVIGQGTFDEDSITIPVDIAENQGQYVILSITGLPQLEGAGQRPYGLQLTE +IGVR +>PROKKA_02243 +MPQPIAVGAVLGGRYRITQHVVTSADQDMVFLGTDQVLNRRVTVLVASRENATQVASSAR +ELATGERTDDVQVLDLGLSEGRTYLIAGGDPDPDVLLGLAYPQELYVEPFQTDSLGSELF +GESRTQDPHAYDDDEAYYTDLDRRLRADEDEAQRRPGFLNRLSERLAERVRPSDGTAAKA +AAGASALAAADAATRKQQEERERAEREAAERAERERKEAEERARAEREAAERAERERKEA +AERAERERREAEERAEEERRAEAERARRQAEQEAEDRAAREREAEQARLAAEREEAERRE +LERRTEARRRAEEERAREAERREAEKRAAQEREAAEREAEKREAQAGTAALPAVAAGAAA +AQTTDADADGATPPVEPVEPVEPVAAEKTDAPEPVAPDTEAIPVRRQRPVPRRAIVAESA +PPVHEESRSTAAPVAAGAATGATAAAAGSTSAAAAPDALAAPATTEGDDGATVADPGDGN +GRTRGGGPLALLLVLGLLAALVVGGVLLAQNLRGGPAPQAAAASSESESASSESASDTPS +PSESTSPSPTPTSESAAAAPQPVQALRSVPDLPEHEAEHDADLSNLIDGDPTTVWRTFAY +ARPNFGGYVESMNLVVQLEERTEVNEVTLQSTGATGGAWFAYIADSPEGANAQEIGNGTF +DQDTVSIPVPFEGTEAEAEYVIVSLTSLPQLEGTTSDLPFGLRLGEIAVR diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001751.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001751.fa new file mode 100644 index 0000000000000000000000000000000000000000..7880d914cb74795b7f2e5eee4245f3da709b6004 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001751.fa @@ -0,0 +1,15 @@ +>PROKKA_02304 +MSTITVTDADFDQKVLQSELPVLVDFWAEWCGPCRMLGPVLEDMAVEHEGKAVIAKLNVD +ENPAIAARYGVTSIPLVVGFQNGEKVAESVGAKPKAALEKEFSALLG +>PROKKA_01997 +MSTITVTDADFDQKVLQSELPVLVDFWAEWCGPCRMLGPVLEDMAVEHEGKAVIAKLNVD +ENPAIAARYGVTSIPLVVGFQNGEKVAESVGAKPKAALEKEFSALLG +>PROKKA_00433 +MSTINVTDTDFDQKVLQSELPVLVDFWAEWCGPCRMLGPVLDEMAVEHEGKAVIAKLNVD +ENPATAARFGVTSIPLVLGFQGGEKVAESVGAKPKAALEKEFSALLG +>PROKKA_00385 +MSTINVTDADFQAKVLDSELPVLVDFWAEWCGPCRMLGPVLDELAAEHEGEVLVAKLNVD +ENPASAARYGVTSIPLVLGFQGGEKVAESVGAKPKAQLEKEFAALLG +>PROKKA_02245 +MSTITVTDADFDQKVLQSELPVLVDFWAEWCGPCRMLGPVLEDMAVEHEGKAVIAKLNVD +ENPAIAARYGVTSIPLVVGFQNGEKVAESVGAKPKAALEKEFSALLG diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001753.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001753.fa new file mode 100644 index 0000000000000000000000000000000000000000..1214dc1af9cfb2ced29eb6d436dba4dc99904782 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001753.fa @@ -0,0 +1,29 @@ +>PROKKA_02307 +MTERGSAYERRPGLDPQDRGDRPAPVGQPAPPLTDALRPAAVELFGEALPRAEAYVAHLA +DTGIEWGLIGPREAPRLWERHVLNCAVVEELLPQGALVADVGSGAGLPGLCLALARPDCQ +FLLIEPLERRVEWLDMVVADLGLENVDVIRGRAEQVSGNLDVDVVAARAVSALKTLVPLT +MPMLQGAGELLAIKGRSAADEIAAARKVLRKYGGAEPEILTVGEGLLPETTTVVRVSARP +R +>PROKKA_02000 +MTEQGSAYERRPGLDPRDRGDRPAPVGQPAPPLTDALRPAAVELFGEALPRAEAYVAHLA +DTGIEWGLIGPREAPRLWERHVLNCAVVEELLPQGALVADVGSGAGLPGLCLALARPDCQ +FLLIEPLERRVEWLDMVVADLGLENVDVIRGRAEQVSGNLDVDVVTARAVSALKTLVPLT +MPMLQGAGELLAIKGRSAADEIAAARKVLRKYGGAEPEILTVGEGLLPETTTVVRVSARP +R +>PROKKA_00429 +MPEQASPYERRPGLDPKERGDRPAPVGQPAPPLIDALRPAAVELFGEDLPRAERYVAHLA +DTGIEWGLIGPREAPRLWERHVLNCAVVEELIPEGALVADVGSGAGLPGLCLALARPDCR +FLLIEPLERRVEWLDMVVEDLGLENVDVIRGRAEQVSGNLDVDVVTARAVSALKTLVPLT +MPMLQGDGQLLAIKGRAAADEIAAARKVLRKYGGDEPEILTVGEGLLPETTTVVRVSARA +R +>PROKKA_00382 +MSAPQLTAELRPAAEDLFGEALPLAERYVDHLATTGIEWGLLGPREVPRLWGRHVLNCAV +VARLLPEGSLVADVGSGAGLPGLCLALARPDCRFTLIEPLERRVAWLEMVIADLGLTNVE +VVRGRSEQVADEIQVDIVTARAVSALKTLLPLTMPLLRSSGHLLAIKGRSAAEEITAAQK +PLRKYGGGDPEIVTVGEGLLPEPTTVVRVPARRAR +>PROKKA_02248 +MTERGSAYERRPGLDPRDRGDRPAPVGQPAPPLTDALRPAAVELFGEALPRAEAYVAHLA +DTGIEWGLIGPREAPRLWERHVLNCAVVEELLPQGALVADVGSGAGLPGLCLALARPDCQ +FLLIEPLERRVEWLDMVVADLGLENVDVIRGRAEQVSGNLDVDVVTARAVSALKTLVPLT +MPMLQGAGELLAIKGRSAADEIAAARKVLRKYGGAEPEILTVGEGLLPETTTVVRVSARP +R diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001754.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001754.fa new file mode 100644 index 0000000000000000000000000000000000000000..57ce0bb2323a8eefe455c5a42d965b0c4c6da853 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001754.fa @@ -0,0 +1,25 @@ +>PROKKA_02308 +MSAENVTPAPEAEDAVVETPAGQGSRVAEQDGAAVSEAVRRLEEEGDVAADYVEELLDIA +DLDGDIDIEVRDGRTYVSVVSEDHDERLDGLVGPDGRTLEALQELVRLAVLAATGHRSRL +ILDVCGHRERRNVALRTAAQAAVERVRVGEGPVHLEPMGAYERKIVHDVVADAGLTSESE +GEGARRHVVISADD +>PROKKA_02001 +MSAENVTPASEAEDAVVETPVGQGSRVAEQDGAAVSEAVRRLEEEGDVAADYVEELLDIA +DLDGDIDIEVRDGRTYVSVVSEDHDERLDGLVGPDGRTLEALQELVRLAVLAATGHRSRL +ILDVCGHRERRNVALRTAAQAAVERVRAGEGPVHLEPMGAYERKIVHDVVADAGLTSESE +GEGARRHVVISADD +>PROKKA_00428 +MSAENVNPAAEAEDAVVETTPAPDAPQAPAAEERTGSDAAVAAGEGAESSAAESASDGVR +RLEEEGDVAADYVEELLDIADLDGDIDIEVRDGRTYVSVVSEDHDERLNALVGRDGKTLE +ALQELVRLAVLAATGHRSRLILDICGHRERRDADLRETAQDAVERVRAGEGPVHLSPMGA +YERKIVHDVVADAGLASASEGEGARRHVVISADA +>PROKKA_00381 +MTAEHEGPLADAAEDSPAVEAPVEATAPDAAVDEQAEAVRRLEEEGDVAADYVEELLDIA +DLDGDIDIEVRDGRTYVSVVPGEDDEDDRLADLVGPDGKALEALQELVRLAVLTATGHRS +RLILDIAGHRRRRDAELRTLAGEAVERVRSGAGEVHLDPMGAYERKIVHDVVAEAGLASE +SEGEGPRRHVVISG +>PROKKA_02249 +MSAENVTPAPEAEDAVVETPAGQGSRVAEQDDAAVSEAVRRLEQEGDVAADYVEELLDIA +DLDGDIDIEVRDGRTYVSVVSEDHDERLDGLVGPDGRTLEALQELVRLAVLAATGHRSRL +ILDVCGHRERRNVALRTAAQAAVERVRAGEGPVHLEPMGAYERKIVHDVVADAGLTSESE +GEGARRHVVISADD diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001757.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001757.fa new file mode 100644 index 0000000000000000000000000000000000000000..aedce19802f92ee55ab54ea7be25b9b26bbe91d7 --- /dev/null +++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Single_Copy_Orthologue_Sequences/OG0001757.fa @@ -0,0 +1,20 @@ +>PROKKA_02311 +MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDQTRSTPPSAPRPRAGFVVSKAV +GNAVTRNRVRRRLRAVVADQMRTAPLRELPVLVQVRALPAAAEADFALLRRETVGALGKA +LKPHLPAASEHA +>PROKKA_02004 +MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDQTRSTSPSAPRPRAGFVVSKAV +GNAVTRNRVKRRLRAVVADQMRLPPLRDLPVLVQVRALPAAAEADYALLRRETVGALGKA +LKPHLPAASEHA +>PROKKA_00425 +MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDHTRSTSPSVPRPRAGFVVSKAV +GNAVTRNRVKRRLRAVVAEQMRAAPLRELPVLVQVRALPPAAEADHALLRRETVGALAKA +LRPHLPAVPRDEA +>PROKKA_00378 +MLPRDRRVRTPEEFRRIRRTGSRAGRSTVVVSVAADTDPARPGATSQPRRPRAGFVVSKA +VGNSVVRHRVTRRLRALLRAELDSPALRDRALLIQVKALPAAVDADHATLRRDVHGALGA +AVRKLDQADRSR +>PROKKA_02252 +MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDQTRSTSPSAPRPRAGFVVSKAV +GNAVTRNRVKRRLRAVVADQMRLPPLRDLPVLVQVRALPAAAEADYALLRRETVGALGKA +LKPHLPAASEHA