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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-----
+ 

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
+ 

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

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--
+----------------------------------

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
+ 

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

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
+ 

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

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
+ 

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-----------------

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------------
+ 

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
+ 

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
+ 

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-

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
+ 

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

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--------------------------------

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
+ 

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------
+ 

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

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-------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------

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
+ 

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
+ 

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
+ 

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

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
+ 

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

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
+ 

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

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
+ 

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
+ 

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
+ 

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
+ 

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
+ 

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
+ 

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--
+ 

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
+ 

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
+ 

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
+ 

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
+ 

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
+ 

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
+ 

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------------

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
+ 

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---
+ 

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

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
+ 

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
+ 

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
+ 

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
+