diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000011.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000011.fa
new file mode 100644
index 0000000000000000000000000000000000000000..32e807ddec7a7d12e37b2619b6f3c0ab82b31149
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000011.fa
@@ -0,0 +1,39 @@
+>0_584
+MLTIATRLDVMNRLGRAMADPTRSRILLNLLEGPGYPAELAQALGLTRSNVSNHLACLRD
+CGIVAAEHQGRRTRYAIVDAHLARALSALLEVTLAVDASAPCLDPGCPVPGCCDTGQVAS
+>0_591
+MMTIASRLDVMNRLGRALADPTRSRIILTLLDHPAYPAELARDLDLTRPNVSNHLACLRD
+CGIVVSEPEGRRTRYEIADSHLAQALTALVDATLAVDEDAPCIDPACSLPGCDAAGEGA
+>0_2013
+MADPTRSRILMTLLERPAYPAELARDLGLTRSNVSNHLACLRDCGIAVAVAEGRQTRYEI
+ADAHLARALTALVEVTLAVDESAPCIDPACSLPGCDAAGEGA
+>1_323
+MMTIASRLDVMNRLGRALADPTRSRIILTLLDHPAYPAELARDLDLTRPNVSNHLACLRD
+CGIVVSEPEGRRTRYEIADSHLAQALTALVDATLAVDEDAPCIDPACSLPGCDAAGEGA
+>1_334
+MQMCRYQQREPHTRGQQVLYAQRMLTIASRLDVMNRLGRAMADPTRSRILMTLLEGPSYP
+AVLARDLGRV
+>1_753
+MQMCRYQQREPHTRGQQVLYAQRMLTIASRLDVMNRLGRAMADPTRSRILMTLLEGPSYP
+AVLARDLGHV
+>1_1719
+MLTIATRLDVMNRLGRAMADPTRSRILLSLLEGPGYPAELAQALGLSRSNVSNHLACLRD
+CGIVAVEHQGRRTRYAIVDAHLARALSSLLEVTLAVDASAPCLDPGCPVPRCCDTAEVAS
+>1_1729
+MMTIASRLDVMNRLGRALADPTRSRIILTLLDHPAYPAELARDLDLTRPNVSNHLACLRD
+CGIVVSEPEGRRTRYEIADSHLAQALTALVDATLAVDEDAPCIDPACSLPGCDAAGEGA
+>2_701
+MLTITSRLEVMNRLGRAMADPTRSRIILTLLDHPAYPAELARDLDLTRPNVSNHLACLRD
+CGIVVSEPEGRRTRYEIADSHLAQALTALVDATLAVDEDAPCIDPACSLPGCDAAGEGA
+>2_709
+MLTIASRLDVMNRLGRAMADPTRSRILMTLLEGPSYPAVLARDLGLTRSNVSNHLTCLRD
+CGIVVAEPEGRQTRYEIADPHLGAAMTALVEVTLAVDENAPCVDATCTVPGCCPSGTVA
+>2_2314
+MLTVASRLDVMNRLGRAMADPTRSRILMTLLDGPSYPAVLSRELELTRSNVSNHLTCLRD
+CGIVVAEPEGRQTRYEIADPHLAAALTALVDVTLAVDEHAPCVDSSCTVPGCCGTGAGE
+>4_1942
+MADPTRSRILMTLLERPAYPAELARDLGLTRSNVSNHLACLRDCGIAVAVAEGRQTRYEI
+ADAHLARALTALVEVTLAVDESAPCLDPACSVPGCCEKGVGA
+>4_1945
+MSTTTLTHVSALSRLGHALSDDTRTRILLALRDGPARPSALAGELGVSKQVMSNQLACLR
+GCGLVTTTAEGRNVWYALADPRLGQTLGELLELTLTIDPDCCSAAGCTCA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000018.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000018.fa
new file mode 100644
index 0000000000000000000000000000000000000000..738bb0488ee438ffc46d44851ed3cc648fe53924
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000018.fa
@@ -0,0 +1,57 @@
+>0_1505
+MPRVVTPLPPDQPAVLLATDLARLGLPPDRARRSDLERVGQGFHRQRARPGTGWADLGLP
+EPGHGFSPDHLAALLRRRPDAVLSHETAAHLHALPMPTRAWRRRDPATGELEADPPVHLT
+VARGTRRVRRAGLMDHRRPLAPEFVTLVHGLRVTTVDRTWLDLCSLTPPWTFEDLVAAGD
+HAVRHPWTPAGRTDPATTIAALRSALHASGRFHGRPAAREALDSVRVGADSPPETRLRLA
+LVAGGLPEPELQAALEPGDPVSPVADLAYRHVRLALQYDGAGHRTREQQARDARRDRYGQ
+ARGWTTLRVTWADGREDFRGVVAVVRRRLGPSAST
+>0_1604
+MPFAPDLPLVPVFTTRDVLERGLPPSRVRRSDVLRLARGIHRRRDMPLRTWESAGLPPPH
+HGVGLDLLTALLRSRPDAVLSHETAAHLHGLPLPPGGATRRAAVEITLHRGTARARIPGV
+MEHRRPLPAGHVTSVLGLRVTTPERTWLDLCSIGHPWDEASLVSAGDHLVRHPWSPRGRR
+PPITTVTALHEAMRPLGRFVGRPRATAALERVRVGADSPQETRLRLALVEAGLGEPALQH
+VFDPGRRDAPEADLWFEDCRLVLQYDGEVHRSAEQHARDARRDQYYAERGQMTLHVTGRD
+VGEGYARVIEAVLRRRAQVSNGWDA
+>0_1786
+MPRRPAPLPPALAGRVFTRREALDRLSLSSDRLRSLDLRQVTHGAHRAVVDVPGSWAALG
+YPRPVAALPPEEAAVVVALTRGVASHLTAARLHGLVLPWWAEEDMRVHVSRPHRTGRTGR
+AGVACHGRTVPAEDRVEVHGVPVTSLERTWVDLCSLLRPDQVADAVVAGDALVNRPWVDG
+SRLPPRTTASRLSAALERAGRFKGVRVARAALALIRVGADSPPETRLRLALLDAGLPEPR
+LQAQLVSPAGERTDADMVVERSRVALHYDGGHHRTPEQQRRDARRDRLWQEAGHLSITVM
+GADLAEDFRTVVAAVVRHDRAARATSTISAPAPAAGLSNVKSGEWALSNVG
+>1_1225
+MPRVVTPLPPDQPAVLLATDLARLGLPPDRARRSDLERVGQGFHRQRAHPGTGWADLGLP
+EPGHGFSPDHLAALLRRRPDAVLSHETAAHLHGLPMPARAWRRRDPATGELDVDPPVHLT
+VARGTRRVRRAGLMDHRRPLAPEFVTHVHGLRVTTVDRTWLDLCSLTPPWTFEDLVAAGD
+HAVRHPWTPAGRTDPATTIAALRSALHASGRFHGRPAAREALDSVRVGADSPPETRLRLA
+LVAGGLPEPGLQAALEPEDPFSPVADVAYRHVRLALQYDGAGHRTREQQARDARRDRYGQ
+ARGWTTLRVTWADGREDFRGVVAVVRRRLGHSAST
+>1_1319
+MSFAPDLPLVPVFTTRDVLERGLPPSRVRRSDVLRLARGIHRRRDMPLRTWESAGLPPPH
+HGVGLDLLTALLRSRPDAVLSHETAAHLHGLPLPPGGATRRAAVEITLHRGTARARIPGV
+MEHRRPLPAGHVTSVLGLRVTTPERTWLDLCSIGHPWDEASLVSAGDHLVRHPWSPRGRR
+PPITTVTALHEAMRPLGRFVGRPRATAALERVRVGADSPQETRLRLALVEAGLGEPTLQH
+VFDPGRRDAPEADLWFEDCRLVLQYDGEVHRSAEQHARDARRDQYYAERGQMTLHVTSRD
+VGEGYARVIEAVLRRRAQVSNGWDA
+>2_1211
+MRVHRRTVPVEHRSVVHGLTVTSPERTWADLCAVRPRWDEADLVAAGDHLVRHPWAGGGR
+LPPRTTVERLAEVLEALAPFHGVGRARAALGRVRVGADSAMETHARLALIDAGLGEPLLQ
+HKVAPDDPALAESDLYFADLRVALEYDGEHHLGRQQQARDARRDRRLLSYGVTPMRITAA
+DHAEGYRSVIAQLQQRRRAHDSPSEETARGES
+>3_1123
+MLERVRVGADSAVVSLARLALVDAGLGEPLLQHRLDPWDPDCPETHMFSPELAVALEYDG
+GGHLTPAQQARDARRDRRLPARGVTPLRNTAEDHAEGYRRLIAQLQDRRRGR
+>4_1432
+MPRVVTPLPPDQPAVLLATDLARLGLPPDRARRSDLERVGQGFHRQRAHPGTGWADLGLP
+EPGHGFSPDHLAALLRRRPDAVLSHETAAHLHGLPMPARAWRRRDPATGELDVDPPVHLT
+VARGTRRVRRAGLMDHRRPLAPEFVTHVHGLRITTVDRTWLDLCSLTPPWTFEDLVAAGD
+HAVRHPWTPAGRTDPATTIAALRWALHASGRFHGRPAAREALDSVRVGADSPPETRLRLA
+LVAGGLPEPELQAALEPGDPFSPVADLAYRHVRLALQYDGAGHRTREQQARDARRDRYGQ
+ARGWTTLRVTWADGREDFRGVVAVVRRRLSPSAST
+>4_1534
+MSFAPDLPLVPVFTTRDVLERGLPPSRVRRSDVLRLARGIHRRRDMPLRTWESAELPPPH
+HGVGLDLLTALLRSRPDAVLSHETAAHLHGLPLPPGGATRRAAVEITLHRGTARARIPGV
+MEHRRPLPAGHVTSVLGLRVTTPERTWLDLCSIGHPWDEASLVSAGDHLVRHPWSPRGRR
+PPITTVTALHEAMRPLGRFVGRPRATAALERVRVGADSPQETRLRLALVEAGLGEPTLQH
+VFDPGRRDAPEADLWFEDCRLVLQYDGEVHRSAEQHARDARRDQYYAERGQMTLHVTSRD
+VGEGYARVIEAVLRRRAQVSNGWDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000030.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000030.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d2d44f3605bc396401b43d74c981800fdc938c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000030.fa
@@ -0,0 +1,68 @@
+>0_161
+MTVGAGLLLITLDNSILYTALPTLTADLGASGSSTLWIINAYPLVMAGLLLGAGTLGDRI
+GHRRMFVVGLWIFGAASLAAALSPNPAFLIGARALLAVGAAAMMPATLALIRLAFNDPRE
+RNIAIAIWGSLSIAGAALGPILGGALLERFWWGSVFLINVPVVVIALVATAIIAPHNDPD
+PSKKWDLVSSLYAMVGLVGTVLVIKELAHIPQNWVLIAGALASAVIGFVLFVRRQGRLEE
+PLIEFSIFRNRAFAGGSLAAFFAMFTIAGAQLATTQRFQLVEGFTPLQAGLLVAASALGA
+LPSGVLGAAILHIVGLRIIISGSLAIAALGLALAVLASANGSLPLLVVSFIVTGFGLGGT
+FAVASAAIMGNAPPRKAGMAASIEEVSYEMGSLSAVALLGSLLTFVYATVVRLPDGTPAA
+AGESIADALGIADGDLDVIAAATSAYDTAYLVTMIVLAVMLASGAALTNRLLRAYGRGSE
+AMEYAENH
+>1_344
+MTVGAGLLLITLDNSILYTALPTLTADLGASGSSTLWIINAYPLVMAGLLLGAGTLGDRI
+GHRRMFVVGLWIFGAASLAAAFSPNPAFLIGARALLAVGAAAMMPATLALIRLAFDDPRE
+RNIAIAIWGSLSIAGAALGPILGGALLERFWWGSVFLINVPVVAIALVATAIIAPHNHPD
+PSKKWDLVSSLYAMVGLVGTVLVIKELAHIPQNWVLIAGALASAVIGFVLFVRRQGRLEE
+PLIEFSIFRNRAFAGGSLAAFFAMFTIAGAQLATTQRFQLVEGFTPLQAGLLVAAIALGA
+LPSGVLGAAILHIVGLRIIISGSLAIAALGLALAVLASANGSLPLLVVSFIVTGFGLGGT
+FAVASAAIMGNAPPRKAGMAASIEEVSYEMGSLSAVALLGSLLTFVYATVVRLPDGTPAA
+AGESIADALGIADGDLDVIAAATSAYDTAYLVTMIVLAVMLASGAALTNRLLRAYGRGSE
+AMEYAENH
+>2_161
+MSALRRWSALAVLVLPVLLISIDMSVLGIAVPALSADLDPTSGQLLWIIDLYSFLLAGLL
+IFMGSLGDRIGRRRILLIGAPLFGAASLAAAFASSAEMLIAARALLGVGGATLMPSTLGL
+IRTIFPDRAERRTAIAVWAMAFSGGAALGPVVGGILLERFWWGSVFLMNVPVMAVFLLVA
+PFLLPESRDPSPGPFDPLSSVLSIAGIVGLVYALKTAAKSPDWTALAGLVVGATALAWFI
+ARQRRLAHPMIDVALFRNVAFTSAVSVNVISVFAFMGLMFFLPQFLMLVQGMGPAEAGLW
+MLPLAAAAVVGTLLAPLLARVVAVRTVILTGLALVIAGFAVGTRLDGAAPLVAFVLLSCL
+FGVGVGLAETLTNDVILTAAPPERAGAAAAISETGYEFGGAMGTAVLGTVGMAVYAARVQ
+EAAGLPGLGPADAEAAAQTLAAAHRIGEGLPDGGARLVEVANGAFTAGMDLVAGIGIGVA
+AVTLLLAWRGLRSEARVERPVED
+>2_181
+MVILNETIMSVALPRLMAEFTVTAATAQWLTTGFMLTMAVVIPFTGWLLNRMSLRAVFIL
+AMGTFTAGTAIAGLAPTFGLLLTGRVVQAVGTAIMMPLLMTTVLNVVPLSRRGRVMGLIS
+IVISVAPASGPAVGGVILEHLSWRWLFFTVLPIAAIALAAGAAWVRNVTEPRPVRLDVLS
+GVLSAVGFASLIFGLSSIGEAAAGNAAMPPWIPVAVGVLALALFAVRQLRLKDDALLDLR
+TLSRPTFTVALAVMLTSMLALFGTIVLLPIYLQEVLGWTTQQSGLALLPGGMVMALLGYV
+VGHLYDRVGAPPLIVPGAVLGAAGLWGYTFLSEDSSAFMVVGLHVLISTGLSMLFSPLMT
+TALSALPRSLYAHGSALVSTLQQVAGAAGTALFITLLTVGTASSVAGGLGEVASLMDGVH
+LAFLSGALVFTVNVVAVWFVKRPAPNPL
+>2_2167
+MLSGTSTTSRGTGPAPVRAWLVLCAMSMLQFFIAVDVTVVNIALPSIGADLGVAGHSLTW
+VVVGYTITGGGLLMLGGRIGDLLGRRRTLLVGTSVFGAASLLAGLAPSFPVLVAARLLQG
+AGEAVALPAAMATIVLLFPEGPRRSRALSVWAAVASCGLVLGFALSGIITAHLGWRWVFL
+VSVPFILVVIVTALLLVPADRPASGGRVRLDLPGSLLLTACPLLFVYAAVEAGEPATGLW
+VSGVALLCAVLAAAGFVRVESRSPNPLVPLTFFADRARLRANLTTMLLSGALSTSFLLFT
+FYLQDRLGIGPLGAGLTMLPLAVALIVASVLVPRLLGRWGARACVLVGLGAAAGAMGVVA
+LVAVLGSGATWLLPAMLLIAAGMGFGLVGLQYIAVSGTTEEDAGIASGVQRASDQLGGAA
+GVAVYVGLGFAPALHADAGDPFVVAAVLAVVGLVVGAVVISRSPSTAAGQPQAG
+>2_2283
+MTVGAGLLLITLDNSILYTALPTLTADLGASGSSTLWIINAYPLVMAGLLLGAGTLGDRI
+GHRRMFVVGLWIFGAASLAAAFSPSPAFLIGARALLAVGAAAMMPATLALIRLAFDDPRE
+RNIAIAIWGSLSIAGAALGPILGGALLERFWWGSVFLINVPVVVIALVATAVIAPHNDPD
+PSKKWDLVSSLYAMVGLVGTVLVIKELAHIPQNWVLIAGALASAVIGFVLFVRRQGRLEE
+PLIEFSIFRNRAFAGGSLAAFFAMFTIAGAQLATTQRFQLVEGFTPLQAGLLVAAIALGA
+LPSGVLGAAILHIVGLRIIISGSLAIAALGLALAVLASANGSLPLLVVSFIVTGFGLGGT
+FAVASAAIMGNAPPRKAGMAASIEEVSYEMGSLSAVALLGSLLTFVYATVVRLPDGTPAA
+AGESIADALGIADGDLDVIAAATSAYDTAYLVTMIVLAVMLASGAALTNRLLRAYGRGSE
+AMEYAENH
+>4_1950
+MTVGAGLLLITLDNSILYTALPTLTADLGASGSSTLWIINAYPLVMAGLLLGAGTLGDRI
+GHRRMFVVGLWIFGAASLAAAFSPNPAFLIGARALLAVGAAAMMPATLALIRLAFDDPRE
+RNIAIAIWGSLSIAGAALGPILGGALLERFWWGSVFLINVPVVAIALVATAIIAPHNHPD
+PSKKWDLVSSLYAMVGLVGTVLVIKELAHIPQNWVLIAGALASAVIGFVLFVRRQGRLEE
+PLIEFSIFRNRAFAGGSLAAFFAMFTIAGAQLATTQRFQLVEGFTPLQAGLLVAATALGA
+LPSGVLGAAILHIVGLRIIISGSLAIAALGLALAVLASANGSLPLLVVSFIVTGFGLGGT
+FAVASAAIMGNAPPRKAGMAASIEEVSYEMGSLSAVALLGSLLTFVYATVVRLPDGTPAA
+AGESIADALGIADGDLDVIAAATSAYDTAYLVTMIVLAVMLASGAALTNRLLRAYGRGSE
+AMEYAENH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000033.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000033.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e53c10c21dfc3cb12e8dca219d5ec63f0db67596
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000033.fa
@@ -0,0 +1,58 @@
+>0_251
+MPDSSPSTPSVRSGAPSRARRSSAWRQARSLRWRAFWAAAPLSRVYLAFGSAFLLASTAS
+DIGLFGPGHGAIPVLDGIAIASATSAFLAQWWRSTVGFALLLPGAVATVVGGSEVLFAVV
+APVVLGAVAATARSWGFVVTAAVLALTWGVAQPFAVGQSNATWFILLLMSMGLGGGLFIR
+ESLARRERDRRRVFEAEERARLAAEAERRSLARDLHDVVAHNLTIISMQARTARYLGAPE
+AAQGVLDVVGDSAKDALRDLRRMLSILQEDGIVDPSGEPGAAGGADGATSADPVLSVAQL
+AEELRSLGMTVETDVRCDQNAMPISVRSTLHRVLQEATTNVAKHAGEGARVCIELRDAGP
+DVVLEVENTVTERSGPPQWNSSGVGLNSMRDRVATFGGTIEAGPGGWGWRVRAVLPRSV
+>1_2215
+MPDSSPSTPSVRSGAPSRARRSSAWRQARSLRWRAFWAAAPLSRVYLAFGSAFLLASTAS
+DLGLIGPGLGAIPVLDGIAIASATSAFLAQWWRSTVGFALLLPGAVATAAGGSEVLFAVV
+APVVLGAVAATARSWWFVVTAAVLALTWGVAQPFAVGQSNATWFILLLMSMGLGGGLFIR
+ESLARRERDRRRVFEAEERARLAAEAERRSLARDLHDVVAHNLTIISMQARTARYLGAPE
+AAQGVLDVVGDSAKDALRDLRRMLSILQEDGIVDPSGEPGAAGGADGATSADPVLSVAQL
+AEELRSLGMTVETDVRCDQNAMPISVRSTLHRVLQEATTNVAKHAGEGARVCIELRDAGP
+DVVLEVENTVTERSGPPQWNSSGVGLNSMRDRVATFGGTIEAGPGGWGWRVRAVLPRSV
+>2_100
+MPESTAVRSRLLSGAPRRARRSSSPDEESLGPAGRWRAFWAAGPLSRVYLVAGSVLLLVS
+AASDLGLIGGGAFATAPLDVAVIVSTTAAFLAQWWRSTVGFALLVPAGAATIAGGTEALV
+TLVTAAMLAAVTVTARSWAFVVAAATLALAWGVVRPVASGRPSEAWFVLALMTAALGVGL
+FIRESVARRERDRRRILEAEERARLAAERERRSLARDLHDVVAHNLTIISMQARTAQYLG
+TPEAAQSVLAVVGDSAKDALVDLRRMLAILQEDGIVDPAGEPGAAGGADGATSADLALTA
+GRMAAELRSLGMSVEQDLRFDPEAVPMSVRSALHRVLQEATTNAAKHAGTGAEVRIMVAE
+QGRDVVLEVENSVAAPQRSMRWNSSGVGLQSMRDRVATFGGTLEAGPGGRGWLVRAAIPR
+APEGA
+>2_572
+MAGVELAYLSDFISEMPWRHGVGWVALGAAVLALPLAWRRRFPVTVMLTISVLYIALASW
+VGIELYASQVVLFLGFYSVGAWCPDRRRALWSRTAVAAAMAVWLGWVTVDGFTDPEVGER
+GVNAYAAVAAIQFLVNLAYFSGAWIFGDRAWREAIRRQRLEAAHAEIRAQQARIAAQEVS
+LERLRIARELHDVVAHHVTAMGVQAGAARLTLDRDPEAAAGHLRGIESSAREAVAELKTM
+VHTLRDADAAPDSLPRLADLEDLVAQAVRLGTDARLTRVGPEPRLGAPAELALYRVAQEG
+LTNARRHAGPRAAVEVRLRTEPERVELEVSDDGRARPDAEAGSERSPGGAGGAVPAGTGL
+GLVGMAERMASVGGTVRCGPKPGGGWLVRASVPTLPEPGEDAAWDAPDEPAPAPDETVQP
+ETMPDPTTEATR
+>3_68
+MSRARLGSTLRSLLDPVSPPAGGRVRFWDAAPANRVYLVVGSVFSVASTTSDVMIELGRG
+GGDTRADIAFMVLACLAFLAQWWRTTVAYAVVLLLMAASLVGGDAVSVVLVLPFVLGTVV
+ATAQSGRYLLAAGATALAWVVAVSLVGSGKVDGVAWLTLLLVVVGLGVGASIRAAKLQRV
+QDGRRIAEAERLAREAAERERRILARDLHDIVAHNLTIIAMQANAAQYLGTPEAAQQVVR
+VVGESARDALTDLRRMLSILQEDGVVEPAPTPGTPETDDAATVAQLGPGAERLAEELRLA
+GVDAAVRVELGEVGLNLGVRAALYRVMQESVTNVAKHAGPGQACEISIEARGGEVVLEVV
+NTLPEDGPRSVVGNSSRVGLTSMRDRIEAFGGRLEVGPCGGDRWRVRAAVPRPEA
+>3_507
+MVGGLLLVWETADLALGAAGRPGGGLLDSADALFSLGTGVTLVLALAGARALMGCYTLLV
+LSALASGFYALPVVTVGLAMGFAALYLSRTPLVVFSCTLLATTVLTAALRPDHLDVLPLM
+LVPALAGTAVGLLLRRESVSLERARRRNLELVEARDRATADIRRSLARDLHDVVAQDLAV
+LAMQTQAIRVAPDRAAQQRMADAVADVARQAHANLRGLLQVLYAGTDVDARRGTGTPDAL
+DTALVTSSAQAARDAAARLRAHGFDVDLQVQEQDGVRAPRHVDATVHRIAHEAVTNVVKH
+APAGGACQVLFTLSPGQVRLRVLSELSPAQHPGRPRDAPQPDGSFGVLNIRERAGLLGGR
+ADVGPREGRWHVDVRIPFGVPA
+>4_249
+MPDSSPSTPSVRSGAPSRARRSSAWRQARSLRWRAFWAAAPLSRVYLAFGSAFLLASTAS
+DIGLFGPGHGVIPVLDGIAIASVTSAFLAQWWRSTVGFALLLPGAVATVVGGSEVLFAVV
+APVVLGAVAATARSWGFVVTAAVLALTWGVAQPFAVGQSNATWFILLLMSMGLGGGLFIR
+ESLARRERDRRRVFEAEERARLAAEAERRSLARDLHDVVAHNLTIISMQARTARYLGAPE
+AAQGVLDVVGDSAKDALRDLRRMLSILQEDGIVDPSGEPGAAGGADGATSADPVLSVAQL
+AEELRSLGMTVETDVRCDQNAMPISVRSTLHRVLQEATTNVAKHAGEGARVCIELRDAGP
+DVVLEVENTVTERSGPPQWNSSGVGLNSMRDRVATFGGTIEAGPGGWGWRVRAVLPRSV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000037.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000037.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dcc3a302fd90a8d9bd049f57a27333f609c0df46
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000037.fa
@@ -0,0 +1,33 @@
+>0_722
+MAARGETTADRRGGRGTDRRPGTAGAVALGGAAGVLCGAGVMNAVTALAGAPNFRGTFGA
+AFGAVDVLVQALPLFVVNVLGSFLLGLLWAASRRRGPDWRPRLVAGLGTGFLGAFTTISS
+AVALVLWPVRLGAAVSGAGGVLAAAVAVLLVLALMAALSTAAAMLGLRAGGAPGSRVVGT
+DRSEEDA
+>1_461
+MAARGEPTADRRGGRGTDRRPGTAGAVALGGAAGVLCGAGVMNAVTALAGAPNFRGTFGA
+AFGAVDVLVQALPLFVVNVLGSFLLGLLWAASRRRGPDWRPRLVAGLGTGFLGAFTTISS
+AVALVLWPVRLGAAVSGAGGVLTAAASVLLVLALMAALSTAAAVLGLRAGGAPGSRVVGA
+DRSAEDA
+>2_2132
+MRAPGVRGAVALGGAAGVVAGSTAMELVGVGGLLALAGRDGGVGLGPVAALAFAALPLAV
+VNVLGSFLLGLLLARSRHAGLDRRPALVAGLGTGFLGSFTTIATAAAVFLLTPLEAGWSA
+IAASSGVGGFLSATAGLLLPPLALLALLAALSTAAAVLGLRLGGAPARGADAEARVDGVA
+SDGTAADGAPA
+>3_668
+MNAALIVVVALGGGAGAAGRFLLDGLINTGREFRLPVGTLTINITGSLLLGIIVGAATHL
+GAVPVAVLGTGVMGGYTTFSTASFETVRLARSGRITAAAINGLGMLVVSVAAATAGILLG
+GTL
+>3_669
+MTTRTDTPMPDDQLPPDPDVDVSDPATTMRPVHLRWRYVGLVAVGGAGGTALRDVISSVL
+PADGGVSWSIFWINITGALALGVLLEALAHRGPDAGRRRVLRLLLGTGVLGGFTTYSTLA
+ESTAALFLDGHGLAGTGYALLTVLSGAIATACGLVVAGWFRPRTEEA
+>3_2026
+MADARPAAGGAAARRTLPWVALGGAAGALASLGAGALIAQAMGPGDPSISGPLGTASATL
+ASVAAVNVLGSFLLGLLRGASGRPGARWDPRLVAALGTGFLGAFTTFGTVAATLALPVMM
+TAGLAATGDTWWILLAVVVVGLLIAVAVLAALSTAAAALGLHLGGRGAGSGSAGRPDGAA
+A
+>4_686
+MAARGETTADRRGGRGTDRRPGTAGAVALGGAAGVLCGAGVMNAVTALAGAPNFRGTFGA
+AFGAVDVLVQALPLFVVNVLGSFLLGLLWAASRCRGPDWRPRLVAGLGTGFLGAFTTISS
+AVALVLWPVRLGAAASGAGGVLAAAVAVLLVLALMAALSTAAAVLGLRAGGAPGSRAVGT
+DRSAEDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000038.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000038.fa
new file mode 100644
index 0000000000000000000000000000000000000000..076463b5a86cc75ddf726c2a247c23e0bc106f76
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000038.fa
@@ -0,0 +1,74 @@
+>0_806
+MGWEHEDPRFDARATGFANEPHRFGYIVEIDP
+>0_807
+MGRFKHEGANVIVADDGHVVAYMGDDERFDYLYKFVSKDIYRKNDRRHNMTLLNEGDLYV
+ARFSGTSDGEIDGSGRVPADGTFDGSGRWIPLVQGGRSTVEGMAVDQVLVFTRLAADRVG
+ATKMDRCEDVEPSPGSGKIYVACTNNSQRGVDGQATADEANPRTENRDGHIVEITEHRGD
+HTSTRFTWDLLMLCGDPSQGDATYFGGFPVDQVSPISCPDNLAFDTDGNLWISTDGAPDG
+IGYNDGLFKVAVEGRNRGQVAQFLSVPRDAETCGPVIHDDEAMVFVAVQHPGEEGSYTDI
+RSAFPDYVPSEARPGDGEVRGPRPSIVQVYRT
+>0_1720
+MLKRLLPMAGHTRGNRSAVTCELKCGNACAHPVPNTSANPTFQQIAETAISRRSALVGGT
+GLAAAVVIGSQVAQAPEALADNGRRPTGGGKLPFEPIAPVTRTVDTMTVPEGYDWGTVIR
+WGDPLFADSPEFDIEHQTGASQAAQFGYNNDYLNIITDGGNDRSGYLVSNHEYTNENIMF
+SPEYIASNFEDVVNVGLQAHGLSIVELKCAKRGAQWEYVRGGRRNRRITGTTEFEVRGPA
+AGHALLTTVEDPTGTRVLGTLNNCAGGTTPWGTVLSGEENFNQYFKGRGTAEEKRYGIST
+SATRRGWEKVHDRFDLTKPGYENEANRFGWVVEIDPEDPTSTPVKHTLLGRFKHEAGTAV
+ISPSGHAVVYSGDDERHDYLYKFVSAEKVREGDKKHNMRLMDKGTLYVAKFSGDSPAAQI
+DGRGTLPSDGAFDGSGEWIALADEKTSFVPGMSLAEVLVYTRLAADKMGATKMDRPEDVE
+TNPVTGKVYAALTNNTKRTAVDEANPVIGNRDGHVIEITERGGDHTSTTFTWVILLLAGD
+PAVSSSAYFAGYPKEKVSPISCPDNLAFDSEGNLWISTDGQPGTIGYADALHKVTLDGAE
+RGRVQQFLAVPRDAETCGPVIHDRDNSVFVNVQHPGEDGTWGAHTSYFPDFLSPTGPVQV
+GDKVAAPRPSVVQVFNATGNNGVGKGAGKEKGNKGKGNGNGNGKGNGNGKGPKG
+>1_1437
+MLKRLLPMAGHTRGNRSAVTCELKCGNACAHPVPNTSANPTFQQIAETAISRRSALVGGT
+GLAAAVVIGSQVAQAPEALADNGRRPTGGGKLPFEPIAPVSRTVDTMTVPEGYDWGTVIR
+WGDPLFADSPEFDIEHQTGASQAAQFGYNNDYLNIITDGGNDRSGYLVSNHEYTNENIMF
+SPEYIASNFEDVVNVGLQAHGLSIVDLKRAKRGAPWEYVRGGRRNRRITGTTEFEVRGPA
+AGHALLKTVEDPTGTRVLGTLNNCAGGTTPWGTVLSGEENFNQYFKGRGTAEEKRYGISA
+AATSRGWEKVHDRFDLTKPGYENEANRFGWVVEIDPEDPTSTPVKHTLLGRFKHEAGTAV
+ISPSGHAVVYSGDDERHDYLYKFVSAEKVREGDKKHNMRLMDKGTLYVAKFSGDSPAAQI
+DGRGTLPSDGAFDGSGEWIALADEKTSFVPGMSLAEVLVYTRLAADKMGATKMDRPEDVE
+TNPVTGKVYAALTNNTKRTAVDEANPVIGNRDGHVIEITERGGDHTSTTFTWVILLLAGD
+PAVSSSAYFAGYPKEKVSPISCPDNLAFDSEGNLWISTDGQPGTIGYADALHKVTLDGAE
+RGRVQQFLAVPRDAETCGPVIHDRDNSVFVNVQHPGEDGTWGAHTSSFPDFLSPTGPVQV
+GDKVAAPRPCVVQVFNATGNNGIGKGAGKEKGNKGKGNGNGNGKGNGKGNGNGKGPKG
+>2_1078
+MLKRLLPMAGHTRGNRSAVTCALKCGNACSHPMPNTSANTTFQEIAETAISRRAALGVGG
+GLAAAVVIGAQVAQAPEALADNGAAPRGGGKLDYRAIAPVPRTVDTVTVPEGYDWGTVIR
+WGDPLFADSEEFDILHQTGASQAGQFGYNNDYLNIISDGGNDRSGYLVSNHEYTNEYIMF
+PPAYIASNFTDVVDAAIEAHGLSIVDLKRAKQGAKWEYVRGGRRNRRITGTTPFTVTGPA
+AGHALLKTVEDPTGTRVLGTLNNCAGGTTPWGTVLSGEENFNQYFKGRGTAEEKRYGIGT
+GTTERRWEEVHDRFDLTAPGYENEANRFGWIVEIDPEDPASTPVKRTLLGRFKHEAGTAV
+VAPSGQAVVYSGDDERHDYLYKFVSAEKVVEGDKKHNMTLLDEGTLYVARFTGDSPASEI
+DGRGTLPSDGEFDGSGEWIALTTDKKSFVPGMSVAEVLVYTRLAADKMGATKMDRPEDVE
+TNPVNGKVYMALTNNTRRTAVDEANPVVGNRDGHVIELTERGGDHASTRFDWVILLLAGD
+PAVSSSVYFSGFPQEKVSPISCPDNVAFDSAGNLWISTDGQPGAIGFGDALHKVTLDGPE
+RGRVEQFLSVPRDAETCGPVVHDRDNSVFVNVQHPGENGMWGAQTSYFPDYLDPAGPVQV
+GDKVAAPRPSVVQVFDVTGNNGVGKGSGKDKGGKGKGNKGGKGKGPKA
+>3_1003
+MLKRLLPMAGHTRGNRSAVTCELKCGNACSHPIPNTSANETFHSVAERAISRRAALGVGG
+GLAAAVVIGANVAHAPEALADNGLRPAGGGKLDFTAIQPVQRTVDTMTVPEGYDWGTIIR
+WGDPLFADSEEFDIEHQTGASAAGQFGYNNDYLNIISDGGNHRRGYLVSNHEYTNENIMF
+SPEYIASNPEDVVNAGIESHGLSVVELERRKAGAKWEYVRGGRRNRRITGTTPFRVTGPA
+AGHDLLKTVEDPTGTRVLGTLNNCSGGTTPWGTVLSGEENFNQYFKGRGTAEEKRYGIST
+SATQRGWERFHDRFDLTKAGYENEAHRFGWVVEIDPEDPTSTPVKHTLLGRFKHEAGTAI
+ISESGHAVVYSGDDERHDYLYKFVSSKKVIEGNKKHNMTLMDEGTLYVAKFTGDSPASEI
+DGKGTLPSDGAFDGSGEWIALASHKKSYVPGMSLAEVLVFTRIAADKMGATKMDRPEDVE
+TNPVNGKVYAALTNNTKRTAVDETNPVIGNRDGHVLEITEKCGDHTSTSFNWVILLLAGD
+PKVSSSAYFAGYPKELVSPISCPDNVAFDSEGNLWISTDGQPGTIGYADALHKVTLDGPE
+RGRVQQFLAVPRDAETCGPVIHDRDNSVFVNVQHPGEDGNWGAHTSYFPDFLSPNGPVQV
+GDKVAAPRPSVVQVFNATGNNGIGKGSGNKKGNHGKGRGNSAFGHAQGHGPKK
+>4_1649
+MLKRLLPMAGHTRGNRSAVTCELKCGNACAHPVPNTSANPTFQQIAETAISRRSALVGGT
+GLAAAVVIGSQVAQAPEALADNGRRPTGGGKLPFEPIAPVTRTVDTMTVPEGYDWGTVIR
+WGDPLFADSPEFDIEHQTGASQAAQFGYNNDYLNIITDGGNDRSGYLVSNHEYTNENIMF
+SPEYIASNFEDVVNVGLQAHGLSIVELKRAKRGAPWEYVRGGRRNRRITGTTEFEVRGPA
+AGHALLTTVEDPTGTRVLGTLNNCAGGTTPWGTVLSGEENFNQYFKGRGTAEEKRYGIST
+SATRRGWEKVHDRFDLTKPGYENEANRFGWVVEIDPEDPTSTPVKHTLLGRFKHEAGTAV
+ISPSGHAVVYSGDDERHDYLYKFVSAEKVRDGDKKHNMRLMDKGTLYVARFSGDSPAAQI
+DGKGTLPSDGAFDGSGEWIALADEKTSFVPGMSLAEVLVYTRLAADKMGATKMDRPEDVE
+TNPVTGKVYAALTNNTKRTAVDEANPVIGNRDGHVIEITERGGDHTSTTFTWVILLLAGD
+PAVSSSAYFAGYPKEKVSPISCPDNLAFDSEGNLWISTDGQPGTIGYADALHKVTLDGAE
+RGRVQQFLAVPRDAETCGPVIHDRDNSVFVNVQHPGEDGTWGAHTSYFPDFLSPTGPVQV
+GDKVAAPRPCVVQVFNATGNNGIGKGAGKEKGNKGKGNGNGNGKGNGKGNGNGKGPKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000041.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000041.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3625fa294816c4b702f2f85749f6311db2c98060
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000041.fa
@@ -0,0 +1,48 @@
+>0_1134
+MSSFETPQPPTARRRRRLLPLLSLGAAGLMLATACATGDDGADQPHSDTASASTSAAPER
+AAVGEGQGEPDALTGVTFTEGDGGAPTVEIDGEIDTDQPTTRVLTAGEGEQVQEGDVLKM
+SIAVVDPASGEVVAENFSGEPEAVPVDDQLKSMNPEIHEMLVGSGAGTIVAAYSPEYDVS
+VPQTESASPSASPSTQTQPAQLFVYKIDAILPKQAEGEEVTERDERLPDVTVDEQSGRPS
+IAKPDGEAPQELVVQPLIEGEGHEVGADDTVTVQYEGVTWSDGEVFDSSWETGQAITFSL
+NRVIEGWKEGLAGQKVGSRVLLSIPAEKAYGEQGSPPDIGENEPLLFVVDILDAQASATP
+SAN
+>1_862
+MSSFETPQPPTARRRRRLLPLLSLGAAGLMLATACATGDDGADQPHSDTASASTSAAPER
+AAVGEGQGEPDALTGVTFTEGDGGAPTVEIDGEIDTDQPTTRVLTAGEGEQVQEGDVLKM
+SIAVVDPASGEVVAENFSGEPEAVPVDDQLKSMNPEIHEMLVGSGAGTIVAAYSPEYDVP
+VPQTESASPSASPSTQTQPAQLFVYKIDAILPKQAEGEEVTERDERLPDVTVDEQSGRPS
+IAKPDGEAPQELVVQSLIEGEGREVGADDTVTVQYEGVTWSDGEVFDSSWETGQAITFSL
+NQVIEGWKEGLAGQKVGSRVLLSIPAEKAYGEQGSPPAIGENEPLLFVVDILDAQAPATE
+SAN
+>2_1677
+MTDGTPEIGDAEGEAPSEMVVQPLIRGEGPEVGPDDSVTVNYVGETWSEGTRFDSSWERG
+APISFSLNQVIPGWKEGLAGQPVGSRVLLSIPAEKAYGEQGSPPDIGPNEPLLFVVDILD
+AQAPSTPPTN
+>2_1678
+MSSFQTPETTTPRRRRRLLPLVSLGVAGLFLATACASGQDDTPEPQEDAASASQSAAPER
+AAVGEGQGEPDALEGLSFSEGEDGAPSVEVDGELATDQPTTRVLTAGEGDQVKEGDVLKM
+SIAVVDPASGDVLAENFTGDPESVPVDQQLKSMNPEMHDLLVRNGVGSVVAAYSPEREVP
+APPADGASPSASPPPRPSPPSSSCTRSSRSCPRRPRARRSPSATSGCPRSP
+>3_300
+MRPLLPLALTVLMLSAGLTGCAPSSPLDSVQVEEVTGQAQGRSVKFQTPVAVEEVSIRQL
+RAGTGAELDAGDAIVLKMDLFKGSDGTPIEAPFAGGPGQVIALDDQFKAQVPELHEALLQ
+AQEGTMLAYSSPQTAGAAGDESTAVEIYEVAQKIPTTIEGKTSPVPDGLPPITEDETGAP
+VVGPPQGQVPDELVAEYLIQGGGEPVQAGDTVIVHHLGMRWADAQVFDSSYQRGAPARFV
+LDNVIKGWQKGLIGKRTGSRVVLSVPVDQAYGTEAELGDNAPFPAGDLLFVIDILTTQPT
+PPVPTP
+>3_1575
+MNRAPSSAAAPRRRRPRTALSLSLAGLLLATACGAGESSDGSSSPASASSSAAAQGSEAT
+SSSAAPVEYGDPAALDGLTFTVGADGTPSATVGKAIESDKAVVKTLTKGTGATPKAGDVL
+RLSTALLDPATGKVLNENFTTQPEMVAVGSDPASMNPYVHKAVYGAPVGSDVAVYLPAPS
+SSASAPSGTEAAPAQLAVFRVQGVAEQLPQADERLPKVSVDPATGRPSIEKPTGSAPEEL
+VVEPLIQGEGPEVEDTDTVAVQYQGVTWSDGSTFDSSYERGTPATFSLDQVIAGWKEGLA
+GQKVGSRVLISVPSEKAYGAEGTPDGSIGKDEDLLFVVDILAAQPAAASSPAAPSGSTAP
+SGSSSASPSN
+>4_1084
+MSSFETPQPPTARRRRRLLPLLSLGAAGLMLATACATGDDGADQPHSDTASASTSAAPER
+AAVGEGQGEPDALTGVTFTEGDGGAPTVEIDGEIDTDQPTTRVLTAGEGEQVQEGDVLKM
+SIAVVDPASGEVVAENFSGEPEAVPVDDQLKSMNPEIHEMLVGNGAGTIVAAYSPEYDVS
+VPQTESASPSASPSTQTQPAQLFVYKIDAILPKQAEGEEVTERDERLPDVTVDEESGRPS
+IAKPDGEAPQELVVQPLIEGEGREVGADDTVTVQYEGVTWSDGEVFDSSWETGQAITFSL
+NQVIEGWKEGLAGQKVGSRVLLSIPAEKAYGEQGSPPDIGENEPLLFVVDILDAQASATP
+SAN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000054.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000054.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da9fb9eddcb8c05c13066836a2cf112e3f5ae358
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000054.fa
@@ -0,0 +1,63 @@
+>0_2192
+MTLTLSARLERTAAEHPHSTALILGENRMTYAELQDQSQRLAGLMRQEGIGPGDRVALMV
+PNIPAFPVVFFAALQLGAVVVPMNPLFKRREIECYLEDSGASMLWSVPSEEAVEGARERG
+VPLRTLGEDGLAPHLAESPGPVTETVERDLEDDAVILYTSGTTGRPKGAQLTHRNMGTNA
+DTVAETLIQLQHGETVLGCLPLFHVFGLTCALMAPVTIGASLALIPRFDPAVAAQTVREH
+AVDVFIGVPTMYGAVLAAAKDHPEDLASLRLGVSGGSAMPVELLRRFEATFDCEILEGYG
+LSETSPVACFNHPGEEHHPGSIGRAVRGCEMQLVTPDGAVVPEGDEETLGEVWIRGENVM
+KGYWGKPEATAQAITEDGWFRSGDLARRDAAGNYYIVDRTKDMILRGGLNVYPREIEEVL
+YEHPAVAEAAVVGVPHPELGQEVAAHVVLAPGAHATEEELIQHVKSQVAPYKYPRTVTVR
+DGLPKTATGKILKRELTPAE
+>0_2214
+MGWRFLRGPLNLDPGDVENLDEVRLRGGMNVYPQEIEEVLYEHPALAEAAVVGVPHPELG
+EEVAAYVTLAPGATATEEELVAHVKSQVAPYKYPRSVVAMDGLPKTATGKILKRELKAAR
+>1_1902
+MTLTLPARLERTAAEHPNSTALILGENRMTYAELHDQSQRLAGLMRQEGIGPGDRVALMV
+PNIPAFPVVFFAALQLGAVVVPMNPLFKRREIEYYLEDSGASMLWSVPSEEAVEGARERG
+VPLRTLGEDGLAPHLAESPGPVTETVERDLEDDAVILYTSGTTGRPKGAQLTHRNMGTNA
+DTVAETLIQLQHGETVLGCLPLFHVFGLTCALMAPVTMGASLALIPRFDPAVAAQTVREH
+AVDVFIGVPTMYGAVLAAAKDHPEDLASLRLGVSGGSAMPVELLRRFEATFDCEILEGYG
+LSETSPVACFNHPGEEHHPGSIGRAVRGCEMQLVTPDGAVVPEGDEETLGEVWIRGENVM
+KGYWGKPEATAQAITEDGWFRSGDLARRDAAGNYYIVDRTKDMILRGGLNVYPREIEEVL
+YEHPAVAEAAVVGVPHPELGQEVAAHVVLAPGAHATEEELIQHVKSQVAPYKYPRTVTVR
+DGLPKTATGKILKRELTPAE
+>2_470
+MTLTLPARLERTAAEHPNSTALILGENRMTYAELQDQSQRLAGLMRQEGIGPGDRVALMV
+PNIPAFPVVFFAALQLGAVVVPMNPLFKRRQIEYYPEDSGASMLWSVPSEDAVEGARERG
+VPLRTLGEDGLAPHLAESPGPVTETVERDLEDDAVILYTSGTTGRPKGAQLTHRNMGTNA
+DTAAETLIQLQHGETVLGCLPLFHVFGLTCALMAPVTTGASLALIPRFDPAVAAQTVRGC
+AVDVFIGVPTMYGAVLAAAKDHPEDLASLRLGVSGGSAMPVELLRRFEATFHCEILEGYG
+LSETSPVACFNHPGEEHQPGSIGRAVRGCELQLVTPDGAVVPEGDEETLGEVWIRGENVM
+KGYWGKPEATAQAITEDGWFRSGDLARRDAAGNYSIVDRTKDMILRGGLNVYPREIEEVL
+YEHPAVAEAAVVGVPHPELGQEVAAHVVLAPGAHATEEELIQHVKSQVAPYKYPRTVSVR
+DGLPKTATGKILKRELTPAE
+>2_475
+MPDVVVPILLERTAAAEPDRTALILGEERLTYAELQDQVHRIAGLLRSQGLGPGDRMAIM
+LPNVLAFPVLFFGALQVGAVVVPMNPLFKTREIQYYLEDSGAVMLWGVPSEEAEAATQAV
+GVPFHALGADGLAPHLTASPGPVTEAAERDPQDDAVILYTSGTTGRPKGAQLTHRNLTSN
+ANTVVETLIHLKAGETILGCLPLFHVFGLTCSMLTCVSVGATLSLIPRFDPTQAIETIRR
+DAVDVFIGVPTMYGAILTVGAEDPSALASLRVAVSGGSSMPVEVLRRFESTFGCQILEGY
+GLSETSPAACFNHPDTDRQPGSIGTPIRGVELRLVTPGGEEVPEGDAETIGEVCIRGENI
+MKGYWGRPDATAEAIDDDGWFHSGDLGRRDAAGNYYIVDRTKDMILRGGLNVYPREIEEV
+LYEHPAVAEAAVVGVPHPELGEDVAAYVVLAPGAEATEAELIAHVKDRVAPYKYPRTVHL
+MDGLPKTATGKILKRELGTAG
+>3_417
+MTLTLPARLERTAAEHPNSTALILGENRMTYAELQDQSQRLAGLMRQEGIGPGDRVALMV
+PNIPAFPVVFFAALQLGAVVVPMNPLFKRREIEYYLEDSGASMLWSVPSEEAVEGARERG
+VPLRTLGEDGLAPHLAESPGPVTETVERDLEDDAVILYTSGTTGRPKGAQLTHRNMGTNA
+DTAAETLIQLQHGETVLGCLPLFHVFGLTCALMAPVTTGASLALIPRFDPAVAAQTVREC
+AVDVFIGVPTMYGAVLAAAKDHPEDLASLRLGVSGGSALPVELLRRFEATFDCEILEGYG
+LSETSPVACFNHPGEEHQPGSIGRAVRGCEMQLVTPDGAVVPEDDEETLGEVWIRGENVM
+KGYWGKPEATAQAITEDGWFRSGDIARRDAAGNYYIVDRTKDMILRGGLNVYPREIEEVL
+YEHPAVAEAAVVGVPHPELGQEVAAHVVLAPGAHATEEELIQHVKSQVAPYKYPRTVRVR
+DGLPKTATGKILKRELTPAE
+>4_2124
+MTLTLPARLERTAAEHPNSTALILGENRMTYAELQDQSQRLAGLMRQEGIGPGDRVALMV
+PNIPAFPVVFFAALQLGAVVVPMNPLFKRREIEYYLEDSGASMLWSVPSEEAVEGAREHG
+VPLRTLGEDGLAPHLAASPGPVTETVERDLEDDAVILYTSGTTGRPKGAQLTHRNMGTNA
+DTAAETLIQLQHGETVLGCLPLFHVFGLTCALMAPVTTGASLALIPRFDPAVAAQTVREC
+AVDVFIGVPTMYGAVLAAAKDHPEDLASLRLGVSGGSALPVELLRRFEATFDCEILEGYG
+LSETSPVACFNHPGEEHQPGSIGRAVRGCEMQLVTPDGAVVPEGDEETLGEVWIRGENVM
+KGYWGKPEATAQAITEDGWFRSGDLARRDAAGNYYIVDRTKDMILRGGLNVYPREIEEVL
+YEHPAVAEAAVVGVPHPELGQEVAAHVVLAPGAHATEEELIQHVKSQVAPYKYPRTVTVR
+DGLPKTATGKILKRELTPAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000057.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000057.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1dc346edc7d4775c9c81766b87ebb6995bfcd8d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000057.fa
@@ -0,0 +1,61 @@
+>0_33
+MLDEVLAQLRSTGSETALIEVKSAAGGCPRSVRETLSAFANARGGVVVLGLDDSTFEPTG
+ADAPALRDALAGMAADDMTPPVRGVISIENAEGGHQVVVMEVPEFAPDQKPCYITAAGRY
+QGSYTRSDEGDRRLTAYEIDRLIEGQGQPQHDREPVHGATADDLRPDLVEALTGRLRTVQ
+PRAFGSLTDQECLRRANVLVDADGVLVPTLAGLLACGEYPQGFFPQLSISVVVLPGTTFG
+DTGPHGERFVDNRTCEGPLVDMIADARDVLVRHMSRASVIDGTGRADRLEYPLEVIRELL
+VNAVMHRDYSAGARGTQVQVELYPDRLVVRSPGGFFGPVDPSSFGEPDVSSSRNSVLARL
+LSDLPGSDGRMIAENRGSGIPTVLKVLEAAGMVPPEFHSTLTRVEVDVAHDSLLTAETHE
+WIQGLGQDGLTQWQIQALALARSGRTVRNQTLQGWGAHQADATRELSDLVRRGLTVKLGD
+RRGARYTLNPDYVPPAAETGAGGLSERQQAILRALADGPMKATEVGDAVGTSYRTAMNAL
+NDLIEAGLVEPTAPPRSRRRRYRLTPQEETA
+>0_544
+MDVIQLDQTQLMALLSRAEGHFLDYKRTDVAPGKLTRSLAAFCNSDGGDIYVGIAETDGT
+QSWQGAADPEEFNGHLQAFEEVSPFGADWNAEFITAQNESGYVLRINALKSRQVRSDSSG
+KVYKRVGAQNVPVDSEEGLQTLRRLKGLESFEEETLNVDMEEVTNSTHIIKFLVNDPSPT
+DPELYLKRQQLIRGGKPTVASALLFAELPQAMLPKRCGIKIYRYTSSVAHRDQLYSDPVT
+VEGYLYGQIYEAVDQTIDIINQAQFLDVDGLRQVRYPRETLHEVITNAVLHRDYSIQDDI
+HVRIFENRVEVQSPGRLPGHITLKNILEERLSRNGHLVRNINRFVDPPNKDVGEGLNTAF
+ESMRKFNLKEPIIEELENSVMVTIRHQSLASPEQQIMEYLAEHSQIRNQEARNLVGIESE
+SKMKKILQGLVGTGEIEHVPGTAKRGYAYRARAEAAAQEGNR
+>0_2213
+MNWSSDDLTATLDALRARRGDTTSVEVKRATGGVPSMPETLCAFANMPDGGTVVCGVDEA
+HGEFRVVGVPDVAVLEAGLVAQAREAVTPSPTLLPQVFRLEGKDVLVAHVVPLRLTDRPA
+TVRGQAYLRQSDGDYVMHAHELRMVEVAKLHADERVDYDVKPVTGMSEEDLVPELVTDYV
+AAVRERDRRLRDRTHQEILRQTNVLTAAGEPTLAGLYALGDYPQGRYPGLTVTAAVQVRG
+GEGQARSRNLTDFTGPVPVLLDEVMAWVRQNLGTEHVYRPDGQLERRPELPLAAVRELLG
+NALVHRDLGPDTLGAGKAIQVRLTDRALFIQSPGGLRGVSLTQLESDEHAQAAVNQRLYQ
+IAKKLTTPDGASVIEGEGGGIHEVFRSARQWGLGRPQLIDTGVQFKALLWRPRPEGARPS
+RREPAVEVARTPPVEEVPDVKADAPSSAVPPSSAPTRHEGRVLGALAAGEAVGIRDLEEA
+TMLTARQIRYALRQPLLDGLVEMTGGQGHKDTRYRLVSARGAGD
+>2_446
+MANTPGSGALIVGVSKTAELIGTALDREWLRFRLYELTGRALTVDVQEVQVQGARLLVLY
+PPAAVEPIRVEGRIRWRVDDHCAEVDASTWFTRQMYRRQYDWSAETSNVPAGEARPAAVD
+IARAFLYDSGDERGEELAEAETPQLLRRLNVVAEGGMLTNAGVLAFVGRPEPALDYTHHE
+VAGADSSIRVHRGGRSLLEELADVLQAFEARNTVRHVQSGLTIGQLRDIPRLAAREALVN
+GLAHREWGDPGATRVEHIGRTLRVTSPGGFFGGVDPSNIITHPSVSRNPALTQLLADLRV
+AERQGIGVDRMVREMVRVGHPQPGIEEVAGPYVRTTLVGETLDEPWMAWLSQVQPRPLTR
+DVSAVLILRHLVDRVWIDEMTAAALTQVSRAESRSMLERLHTATVGGGTILEAVSGVPDA
+VPQAWRLGEAAAQLLAALDQETGIQRTVPDRRALAADYARARGRISTTELASLVGGHASN
+MGAPLRALETEGFLEPSNASRRGRGFFYRWVGDEPA
+>3_410
+MDLGPLLAAGETLDVEFKRRLGKDDLYQAVVCMANGIGGRILVGVDDDGTVVGTTADHGG
+AVDADLLAGRIQNGIEPPLSVDVEVVPWEGKDVAVITVPQAKSSFVGTRKGLFVKRVVGP
+DGRPACMPMTPMDVLRAGFDGVGLDYARAEARGAEWGHLDPTEFDRFRRLAGQSAGDSGL
+AELTDAELLRTLDLLTPDGGISLGAVLVFGTSEALRRWAPTAEVLFQDSRPHGVEANEDL
+LLPLLNAFEEIETRLALRNSITPVEVGLVRVDVPLLAESVRRESIANALVHRDYAEAGPI
+QVTLTGSTFSVASPGGFPRDVSPANILNRSAPRSPALANVFKRAGLVERRGKGVQDMFAS
+QLRAGRGAPDYSRSTHRSVIVDIPLGDEDRELLIFLARRQNEGQRALTLTELRVVHEIKH
+GGPAGAAEAAERLRLPVADVRAAATALVEAGVLESRGNGRAQRYMLTARFYELAEDRAAY
+LRLRPVDRIQQRRLIADYIREYGSITRGKAAELCQIAPTAARAVLKGMTEEGLLELRGER
+RAAHYVLPDS
+>4_2148
+MRRGDTTNVEVKRAAGGVPQLAETLCAFANMPEGGTIILGVDEARGAFNVTGVADVALLE
+AGVAAQAREGVTPSPQIIPQTLQLDERQVLLIHVVPLRTADKPATVQGVAYLRQSDGDYR
+MHEHELRMLEVAKLHADERVDYELKVATGLGEQDLVSSLVDEYVAAVRRKNRRLRDRTSE
+EILRQTSVLTSSGEPTLAGLYALGDFPQGRFPGLTVTAAVQLPGGEGQPRNRNLEDFVGP
+LPDLLRDLMAWVSDNIDTVRRYRRDGHMEEVAELPLTAVRELLANALVHRDLGPSTLGMG
+KGVQVRLTPRNLFIQNPGGLQGLSLTQLQSDDHAQAAVNQRLYQFAKKLTTSDGASLIEG
+EGGGIREVFRAAERQGLPRPQLIDTGVQFKAILWRAADRNARAGVEDAKGASAVETAVPR
+AVPASASPTRHEHAVLAALVRMPDGATLRALTSVTGLTDRQVRYALRLPLDEGIVVMDGG
+QGNRQTAYRLMSDSRRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000059.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000059.fa
new file mode 100644
index 0000000000000000000000000000000000000000..452b65ae51b8094596f0f1c8a32951f3b4d39033
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000059.fa
@@ -0,0 +1,38 @@
+>0_49
+MRADLTLIPTSRVPGCGSGHPTARPRYGDPVRPTSPRPAPAYLTDSVPARRGHPLGFAHR
+GAAVDRENSLAAFVDAHAAGFTYLELDVRTTADGELLVFHDDTLDRVSTGRGRLRDHTWE
+RLADVTVGGEPLLRFTELLTALPEARLNVDLKDRASAPALARILAEHGAWDRVLVASFHD
+SRRRLFRRALARLGHPERAYGPERVATSGGAAAIAALVTLGPLGLTRWLRRCALDVDCVQ
+VPVRHGRVPVATADFVRRCHAAGLPVHVWVVDEPAEIERLLDLGVDGVMTDRADVLAEVY
+ARRGFWPQR
+>1_2013
+MRPTSPRPAPAYLTDSVPARRGHPLGFAHRGAAVDRENSLAAFADAHAAGFTYLELDVRT
+TADGELVVFHDETLDRVSTGRGRLRDHTWERLADVTVGGEPLLRFTELLTALPEARLNVD
+LKDRASAPALARILAEHGAWDRVLVASFHDSRRRLFRRALARLGHPERAYGPERVATSGG
+AAAIAALVTLGPLGLTRWLRRCALDVDCVQVPVRHGRVPVATADFVRRCHAAGLPVHVWV
+VDEPAEIERLLDLGVDGVMTDRADVLAEVYDRRGFWPQR
+>2_331
+MTRRPPSSRHRPAPAYLADSAPGREGWPLGFAHRGADVGRENSLAAFQAAHDAGFAYLEL
+DVRTTSDGELVVFHDETLERVTTGRGRLQEHTWHGLTEVHVGGEPLLRFADLLAALPEAR
+LNVDLKDRAAAPAMARLLAEHEAWERVLVASFHDSRRRAFRRALAALGHEDRAFGPGRVA
+TSGGVAAIAALVALGPVGLTRWLARHALDIDCVQVPVRHGRVRVVTADFVRRCHAAGLPV
+HVWVIDEPDEMHRLLDLGVDGIMTDRADVLADVFTTRGIWPQR
+>3_270
+MEDSSGSLAASSIRPPSSGPSSTPPPARPAPAYLADSAPGREGWPLGFAHRGADVGRENS
+LAAFQAAHDAGFAYLELDVRTTSDGELVVFHDETLERVTTGRGRLQEHTWHGLTEVHVGG
+EPLLRFADLLAALPEARLNVDLKDRAAAPAMARLLAEHEAWERVLVASFHDSRRRAFRRA
+PAALGHEDRAFGPGRVATPGGAAAIAALVALGPVGLTRWLARHALDVDCVQVPVRHGRVR
+VVTADFVRRCHAAGLPVHVWVIDEPDEMHRLLALGVDGIMTDRADVLADVFTTRGIWPQH
+>3_279
+MRIRAATTSPALRPAPAYLAASAPARRGWAVGFAHRGAGNERENTLAAFTAAWEAGFRYL
+ELDVRTTSDGVLVVFHDATLDRVSTAAGDFSALAWADFAAHTVGGEPFLRFADLLAALPE
+ARFNVDLKDADAAPAMAALLAEHDAWDRVLVASFHDSRRRAFRRAVAALGHPERAHGPER
+VATSGGAAAIAALVLLGPLGLTGWLRRHALDIDCVQVPLHQGRVPVVTADFVRRCHAAGL
+PVHVWVVDDPAEMERLLDLGVDGIMTDRADVLAEVFTRRGIWPQR
+>4_44
+MRADLTLIPTSRVPGCGSGHSAVRPRYGDPVRPTSPRPAPAYLTDSVPARRGHPLGFAHR
+GAAVDRENSLAAFVDAHAAGFTYLELDVRTTADGELVVFHDETLDRVSTGRGRLRDHTWE
+RLADVTVGGEPLLRFTELLTALPEARLNVDLKDRASAPALARILAEHGAWDRVLVASFHD
+SQRRLFRRALARLGHPERAYGPERVATSGGAAAIAALVTLGPLGLTRWLRRYALDVDCVQ
+VPVRHGRVPVATADFVRRCHAAGLPVHVWVVDEPAEIERLLDLGVDGIMTDRADVLAEVY
+ARRGLWPQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000064.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000064.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f9a12c450a92ead7ab1dc8f1c4a488ececbba12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000064.fa
@@ -0,0 +1,61 @@
+>0_114
+MLLKLIEPTSGEISFEGRDVLALKGEGLKDFRQRVQAVFQDPFSSLNPSFTVGRIIEEPL
+QTYRRGNATQRRARVLELMDQVALPSHFHRRYPAELSGGQRQRVAIARALALNPELIVCD
+EPVSALDVLVQDQILTLLRRLQDELGLRSYLFISHDLAVVRLISDYVCVMKDGRVVEAAS
+SEEVFTNPRHPYTRRLLASIPGNELGIAVEADGTHV
+>1_2081
+MDPKHDDGAPGPGAAPAVPAAGAPLLEIRDLDVEFTTQQGTVQAVEGASLTLPAGGTLAI
+VGESGSGKSTTAMAAIGLLPGNGRVTAGSVRFAGEELVGLPESRMRRIRGRRIGLVPQDP
+MSNLNPVTRVGQQIGETLLTHGMATKKDVGAAVVEVMERAGIPEPARRAKQYPHELSGGL
+RQRVLIAIGLACRPQLLIADEPTSALDVTVQQVILDQIGEMTRELGSSVLLITHDLGLAA
+ERAQQLVVMHRGRVVESGDARAILEDPQHAYTRSLVAAAPSVAAARLLPEAFDPAPVALA
+EDDTAALTTVALAKQDLTPLVEIRDLTKVYPVRGHEDFIAVKDVSLKIPRGKTVSIVGES
+GSGKTTTARMLLKLIEPTSGEITFEGRDVLALKGEGLKDFRQRVQAVFQDPFSSLNPSFT
+VGRIIEEPLQTYRRGNATQRRARVLELMDQVALPSHFHRRYPAELSGGQRQRVAIARALA
+LNPELIVCDEPVSALDVLVQDQILTLLRRLQDELGLSYLFISHDLAVVRLISDYVCVMKD
+GEVVEAASSEEVFTNPRHPYTRRLLASIPGNELGIAVEADGTHV
+>2_79
+MTAALTTRENTAPAAEPAGARIPVAELRNLRVGFDDGAGGTRAVVHGVDLRIEPGQCVAI
+VGESGSGKSVTARTLVGLTGAGSRVSADLARLGEDDVLALDERAWRRRRGVRVGYILQDA
+LVSLDPLRTVGAEIGDVLRLHGVSDRGERRRRAADLLAEVGVPEPQVRLDQRPGELSGGL
+RQRALIASAVALQPELVIADEPTTALDVSVQVQVLELLSRLKSSGTAVLLISHDFAVVSR
+LADHVLVMEGGRIVESGPVRRILDAPEHPYTRRLLAAIPSGDTRGQRLSPEPRAVVTHAP
+LVAAPTAQGGPTLAARGLTKRYRGPDGRDRTVVDDVSFDVFAGQTLGIVGESGSGKSTTA
+AMALGLVQPDAGTVELDGRPWSGVSARARRARRRQVAVVYQDPLSSFDPRWNGERILADA
+AGAGVPPWASPARRRAARDDARARAVDLARLVGLDPRHLTRSPARLSGGQRQRLAITRAL
+AVQPRVLVLDEAVSALDVSVQAQVLDLLGDLKEGLGLTSLFISHDLGVIHHVSDRILVMK
+DGRAVEQGDADQVFHAPRHEYTRGLLASLEQLSIR
+>2_252
+MDPKHDDGALGAGSHAAAPEAAPTAGTDPAGVGSAEMPAPGAPLLEIRDLDVEFRTQQGT
+VKAVEGASLTLPAGGTLAIVGESGSGKSTTAMAAIGLLPGNGRVTGGSVKFAGEELVGLS
+DAKMRRIRGRRIGLVPQDPMSNLNPVTRVGQQIGETLLTHGLATKKDVGAKVVEVMERAG
+IPEPARRAKQYPHELSGGLRQRVLIAIGLACRPQLLIADEPTSALDVTVQQVILDQIDEM
+TRELGSSVLLITHDLGLAADRAQQLVVMHRGRVVESGDARAILEDPQHAYTRSLVAAAPS
+VAAARLLPEAFDPAPSALKEDDTAALSTVALAKKDLTPLVEIRDLTKVYPVRGHDDFTAA
+KDVSLKIPRGKTVSIVGESGSGKTTTARMLLKLIEPTSGEITFEGKDVLGMKGEDLKDFR
+QRVQAVFQDPFSSLNPSFTVGRIIEEPLQTYKRGNAKERRARVLELMEQVALPSHFHRRY
+PAELSGGQRQRVAIARALALNPELIVCDEPVSALDVLVQDQILTLLRRLQDELGLSYLFI
+SHDLAVVRLISDYVCVMKDGEVVEAASSEEVFTNPRHPYTRRLLASIPGNELGIAVEADG
+EHV
+>3_127
+MSIPKSPTSTLPSAVAPAPALSVHGLDVDYAGRHGQAPALRDVRLEVPAGGTLAVVGESG
+SGKSTLARVLLGLSAANARIRSGRIHVAGQTVDAADTDALARLRGRCIGFVPQDPVTGLN
+PVRTIGEQVVAAVRTHTRLRVDDAYGRAEALLAEAGVDRPGHRLGQFPHELSGGLRQRVL
+IALALAGDPEVIVADEPTSALDATVQQQVLDRLGLLQERTGAALVLITHDLAVAAGRAER
+IVVMRQGRIVEAGPAEQIAQSPQDSFTRRLVAASPGRRPTARVLAAPDVEAGPGADPAPV
+VRVRGLRHEYPGVHGSAPHVAVDGVDLDIRAGETLALIGESGSGKTTTGRLVLGLETVRE
+GSVQIRGVETAGVGGRAWRRARRHLQTVHQNPFASLDPRQTVERIVAEPLRAFSVGSRTE
+RRDRVTELLERVSLPAATASRRPGELSGGQRQRVAIARALALDPDVLVCDEPTSALDVSV
+QAQVLELLARLQDEQGLACLFITHDLRVVWDIAHRVAVMRDGRILETAATERLFRAPEHP
+YTAELLAAAGVTAPLTGTQTSAGTMTPAGARALVGRP
+>4_122
+MDPKHDDGAPGPGAAPAVPAAGAPLLEIRDLDVEFTTQQGTVQAVEGASLTLPAGGTLAI
+VGESGSGKSTTAMAAIGLLPGNGRVTAGSVRFAGEELVGLPESRMRRIRGRRIGLVPQDP
+MSNLNPVTRVGQQIGETLLTHGMATKKDVGAAVVEVMERAGIPEPARRAKQYPHELSGGL
+RQRVLIAIGLACRPQLLIADEPTSALDVTVQQVILDQIGEMTRELGSSVLLITHDLGLAA
+ERAQQLVVMHRGRVVESGDARAILEDPQHAYTRSLVAAAPSVAAARLLPEAFDPAPVALA
+EDDTAALTTVALAKQDLTPLVEIRDLTKVYPVRGHEDFIAVKDVSLKIPRGKTVSIVGES
+GSGKTTTARMLLKLIEPTSGEITFEGRDVLALKGEGLKDFRQRVQAVFQDPFSSLNPSFT
+VGRIIEEPLQTYRRGNATQRRARVLELMDQVALPSHFHRRYPAELSGGQRQRVAIARALA
+LNPELIVCDEPVSALDVLVQDQILTLLRRLQDELGLSYLFISHDLAVVRLISDYVCVMKD
+GEVVEAASSEEVFTNPRHPYTRRLLASIPGNELGIAVEADGTHV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000065.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000065.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f1df186ee1b0daf12a8a64c2a9e3b6a3b9a0dc28
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000065.fa
@@ -0,0 +1,33 @@
+>0_167
+MTPPAALLLDLDGTLLDHGRAARIALGQAMQEAGLTDADHSSALLLWGELERIHFQEYLD
+GQTTFEEQRVRRVRAFLAHYGRTRLDRTSALAWFDTYRTAYERAWS
+>0_824
+MSRDASTTPAGGSAGAPAPPAWDAVLFDLDDTLLDLRSAQHAAFDATVRRQWAGAADVDP
+AVLAEATDAFASDAGGHYGRYVAGELTFEEQRLARVADALRALGVPEDAATPLDGLWTTD
+YEEVVRGHWALFPATADVLAEVRGTGRGVGIVTNNVEAYQRGKADALGLEWVEVLIGSDT
+AGAPKPDPAPFLAGCSRLGTDPGRTLMVGDSLRHDVEGARSAGLVPVWMSPDAPAHGGAE
+EPLWDEEHACWRMRAIGGLRTWLAA
+>1_555
+MSRGASTTPADGSAGAPAPPAWDAVLFDLDDTLLDLRSAQHAAFDATVRRQWAGAADVDP
+AVLAEATEAFASDAGGHFGRYVAGELTFEEQRLARVADALRALGVPEDAATPLDGLWTTD
+YEEVVRGHWALFPATADVLAEVRGTGRGVGIVTNNVEAYQRGKADALGLEWVEVLIGSDT
+AGAPKPDPAPFLAGCSRLGTDPGRTLMVGDSLRHDVEGARSAGLVPVWMSPDAPAHGGAE
+EPLWDEEHACWRMRAIGGLQTWLAA
+>2_2034
+MSGAPATGQATTTAAGGSPSSPAPAPPEWDAVLFDLDDTLLDLRAAQHAAFDATVRRQWA
+GAADVDPARMAEATEAFASDAAGHYERYVAGELTFEQQRLARAADALRALGAPEESATPL
+EALWTADYEDVVRGHWALFPATAEVLAQVRSSGRGVGIVTNNVEAYQRAKADALGLEWVD
+VLIGSDTAGAPKPDPAPFLAGCARLGAEPGRTLMVGDSLTHDVAGARAAGLVPVWMSPAA
+PARGAAEDPVWDPERGCWRLRAIGGLRAWLRR
+>3_1928
+MIRTPGTPSAPVVDGVLFDLDDTLLDLRGAQLPAFAETVRAQWPDAPPAEAGVFVRAADH
+FAADRSGHYQRYIAGELDFAGQRLARARDALAVLGAPGAVAEPDPALWTDEYEVRVRAHW
+ALFDDVVPTLATLRSSGVALGIVTNNVEAYQRAKADALGLEAITVLVGSDSAGAPKPDPA
+PFLEACRRMGTTPGRTACVGDSLSHDVRGARAAGLVPVWLRRGAGAADGGGEGRWDAAEG
+AWTIGGLGALAAWFPGSGADLASGREVL
+>4_783
+MSRGASTTPADGSAGAPAPPAWDAVLFDLDDTLLDLRSAQHAAFDATVRRQWAGAADVDP
+AVLAEATEAFASDAGGHFGRYVAGELTFEEQRLARVADALRALGVPEDAATPLDGLWTTD
+YEEVVRGHWALFPATADVLAEVRGTGRGVGIVTNNVEAYQRGKADALGLEWVEVLIGSDT
+AGAPKPDPAPFLAGCSRLGTDPGRTLMVGDSLRHDVEGARSAGLVPVWMSPDAPAHGGAE
+EPLWDEEHACWRMRAIGGLQTWLAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000071.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000071.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bbe01ee2dfb764db6630e11f552dab7bd1765185
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000071.fa
@@ -0,0 +1,54 @@
+>0_227
+MALSVLDLFSIGIGPSSSHTVGPMRAARRFTDSMGQHGVLERTARVHAELFGSLAATGVG
+HGSDTAVLLGLAGQDPETIDPDACTGLVAEIVTGGRLPLDGRHEIAFDRQADLTLHMRES
+LPGHPNGMRLTAYDDAGEQLHTRDYYSVGGGFVVTSDELEAELDATKDVNRTDDGDTGEP
+YPFSTGAELAARCREAGLSIAELMLANEATRHDLDELRTQLLAIWAVMEECVHNGVTRTE
+PILPGGLQVRRRAPALREHLLQTTDRTDPMWAMEWVNLFALAVNEENASGGRIVTAPTNG
+AAGIIPAVMLYYMRFVLPEGATQQERDDKVVEFLLTAAAIGILYKRNASISGAEVGCQGE
+VGSACSMAAGALCAVLGGTVDQVENAAEIGIEHNLGLTCDPVGGLVQVPCIERNAIASVK
+AINAARLALLGDGSHRVTLDQAITTMRDTGADMKSKYKETSRGGLAVNVIEC
+>1_90
+MALSVVDLFSVGIGPSSSHTVGPMRAGRRFALGLVERGLVDATERIHVQLFGSLSATGHG
+HGSDRAVLLGLEGEDPETVDTDRANARVESMKAERRLALAAGAEQGGKDLDFDPDADLVM
+HRRRSLPYHPNGMSFTAYDGSGEVVVERVYYSVGGGFVVDDEAAGADRVVEDATEPPLPF
+SSGRELLNHCDREGISIPELMRRNEEAFRPWEAARAALLNTWRVMQECVEAGCEATGTLP
+GGLKVPRRAALLKEQLEVSAPRDGSAPPRDGGAPDALGAMEWVNLYALAVNEQNASGGRI
+VTAPTNGAAGIIPAVLHYWRDFLAREMTAEHIEDGVVDFLLTAAAIGILIKENASISGAE
+MGCQGEVGSACSMAAAGLCQLLGGTPQQVENAAEVGIEHNLGLTCDPVGGLVQIPCIERN
+AIASVKAINAARLCRRGDGRHTVSLDQAIKTMRETGQDMKVKYKETSRGGLAVNVIEC
+>1_2191
+MALSVLDLFSIGIGPSSSHTVGPMRAARRFTDSMGQHGVLERTARVHAELFGSLAATGVG
+HGSDTAVLLGLAGQDPETIDPDACTGLVEEIVTGGRLPLDGRHEIAFDRQGDLTLHMRES
+LPGHPNGMRLTAYDDAGEQLHTRDYYSVGGGFVVTSDELEAELDATKDVNRTDDGDTGEP
+YPFSTGAELAARCHEAGLSIAELMLANEATRHDLDELRTRLLAIWAVMEECVHNGVSRTE
+PILPGGLQVRRRAPALREHLLQTTDRTDPMWAMEWVNLFALAVNEENASGGRIVTAPTNG
+AAGIIPAVMLYYMRFVLPEGATQQERDDKVVEFLLTAAAIGILYKRNASISGAEVGCQGE
+VGSACSMAAGALCAVLGGTVDQVENAAEIGIEHNLGLTCDPVGGLVQVPCIERNAIASVK
+AINAARLALLGDGSHRVTLDQAIKTMRDTGADMKSKYKETSRGGLAVNVIEC
+>2_126
+MALSVLDLFSIGIGPSSSHTVGPMRAARRFTQSMDQHGVLERTARVEAELFGSLAATGIG
+HGSDTAVLLGLAGQDPETIDPDACVGLVDEILQGGRMPLDGRHEIAFDRQKDMTLHMRRT
+LPGHPNGMRLTAFDADGEQLHTRDYYSVGGGFVVTSDELEAELDESRDVSRHDDGEGGEP
+YPFATGAELAGRCRTNGLSIAELMLANEATRHDLGELRTQLLAIWDVMQECVHNGVTRTE
+PILPGGLKVRRRAPALRAHLLETTDRTDPMWAMEWVNLFALAVNEENASGGRIVTAPTNG
+AAGIIPAVLHYYMRFVLPQDATQQERDDKVVEFLLTAAAIGILYKRNASISGAEVGCQGE
+VGSACSMAAGALCAVLGGTVDQVENAAEIGIEHNLGLTCDPVGGLVQVPCIERNAIASVK
+AINAARLALLGDGSHRVTLDQAIKTMRDTGADMKSKYKETSRGGLAVNVIEC
+>3_91
+MALSILDLFSIGIGPSSSHTVGPMRAARRFTYALERDGLVERTARVKGELFGSLSATGVG
+HGSDMAVILGLCGNDPETIDPEAAAPQVQACVEGGTLPLDGTHEIPFDRPKDLVLHMRRS
+LPGHPNGMRLTAFDADGAELLTRDYYSVGGGFVVTGEELEAELDETRDVSRHGEEPEPHP
+FSTGADLIAQCEIHGLSIADVVRANEAARGDLADVEAKVLEIWDVMQECVAHGIHRTEPI
+LPGGLKVKRRAPGLHAQLLEKGTDGAEKDPMWAMEWVNLFALAVNEENASFGRIVTAPTN
+GAAGIIPAVLHYYDRFVLPPGTPAEERRAKILDFLFTAAAIGILFKRNASISGAEVGCQG
+EVGSACSMAAGALCAVLGGTPLQVENAAEIGIEHNLGLTCDPVGGLVQVPCIERNAIASV
+KAINAARLALVGDGDHRVTLDQAIQTMRETGADMKSKYKETSRGGLAVNVIEC
+>4_228
+MALSVLDLFSIGIGPSSSHTVGPMRAARRFTDSMGQHGVLERTARVHAELFGSLAATGVG
+HGSDTAVLLGLAGQDPETIDPDACTGLVEEIVTGGRLPLDGRHEIAFDRQGDLTLHMRES
+LPGHPNGMRLTAYDDAGEQLHTRDYYSVGGGFVVTSDELEAELDATKDVNRTDDGDTGEP
+YPFSTGAELAARCHEAGLSIAELMLANEATRHDLDELRTRLLAIWAVMEECVHNGVTRTE
+PILPGGLQVRRRAPALREHLLQTTDRTDPMWAMEWVNLFALAVNEENASGGRIVTAPTNG
+AAGIIPAVMLYYMRFVLPKGATQQERDDKVVEFLLTAAAIGILYKRNASISGAEVGCQGE
+VGSACSMAAGALCAVLGGTVDQVENAAEIGIEHNLGLTCDPVGGLVQVPCIERNAIASVK
+AINAARLALLGDGSHRVTLDQAIKTMRDTGADMKSKYKETSRGGLAVNVIEC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000087.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000087.fa
new file mode 100644
index 0000000000000000000000000000000000000000..62cdc1283b5aab82aded8c76424ee305cf10619b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000087.fa
@@ -0,0 +1,60 @@
+>0_467
+MTVTAEREKALLESVPTGLLIDGEWRDASSGKTFDVKDPATGKVIASLQDANSDDAMAAF
+DAACAAQADWARTPAKERADILRRAYDLINERAEDFALLMTLEMGKPLAEARGEVTYGNG
+FLRWFSEEAGRHYGRTLTVPEGTLRMQVHHRPVGPCLLITPWNFPLAMATRKVGPAVAAG
+CTMVLKAAKLTPLTTQLFAQVMQEAGLPKGVLNVVAGSSASSISSPILQDRRLRKVSFTG
+STPVGVRLMKDAADNVLRTSMELGGNAPLIVFEDADLDAAVEGAFAAKMRNMGEACTAAN
+RFLVHEDVAEEFTQKFVAKLEALKPLRGTDPESTLGPIVDEGARDDIDQLVQDAVAAGGE
+VLTGGHKIEGDGYFYAPTAIKVEKGNPILQQEIFGPVAPIVTFSSEEEAIEMANDTEYGL
+ASYVFTKDQARMYRVAESIEFGLMGYNVGVISNPAAPFGGVKQSGLGREGGAEGIEEYTS
+VQYIGIADPWAATKA
+>1_197
+MTVTAEREKALLESVPTGLLIDGEWRDASSGKTFDVKDPATGKVIASLQDANSDDAMAAF
+DAACAAQADWARTPAKERADILRRAYDLINERAEDFALLMTLEMGKPLAEARGEVTYGNG
+FLRWFSEEAGRHYGRTLTVPEGTLRMQVHHRPVGPCLLITPWNFPLAMATRKVGPAVAAG
+CTMVLKAAKLTPLTTQLFAQVMQEAGLPKGVLNVVAGSSASSISSPILQDRRLRKVSFTG
+STPVGVRLMKDAADNVLRTSMELGGNAPLIVFEDADLDAAVEGAFAAKMRNMGEACTAAN
+RFLVHEDVAEEFTQKFVAKLEALKPLRGTDPESTLGPIVDEGARDDIDQLVQDAVAAGGE
+VLTGGHKIEGDGYFYAPTAIKVEKGNPILQQEIFGPVAPIVTFSSEEEAIEMANDTEYGL
+ASYVFTKDQARMYRVAESIEFGLMGYNVGVISNPAAPFGGVKQSGLGREGGAEGIEEYTS
+VQYIGIADPWAATKA
+>2_2404
+MTVTAEREKALLESVPTGLLIDGEWRDASSGKTFDVKDPATGKVIASLQDANSDDAMAAF
+DAACAAQADWARTPAKERADILRRAYDLINERAEDFALLMTLEMGKPLAEARGEVTYGNG
+FLRWFSEEAGRHYGRTLTVPEGTLRMQVHHRPVGPCLLITPWNFPLAMATRKVGPAVAAG
+CTMVIKAAKLTPLTTQLFAQVMQEAGLPKGVLNVVAGSSASSISSPILQDRRLRKVSFTG
+STPVGVRLMKDAADNVLRTSMELGGNAPLIVFEDADLDAAVEGAFAAKMRNMGEACTAAN
+RFLVHEDVAEEFTQKFVAKLEALKPLRGTDPESTLGPIVDEGARDDIDQLVQDAVAAGGE
+VLTGGHKIEGDGYFYAPTAIKVEKGNPILQQEIFGPVAPIVTFSSEEEAIEMANDTEYGL
+ASYVFTKDQARMYRVAESIEFGLMGYNVGVISNPAAPFGGVKQSGLGREGGAEGIEEYTT
+VQYIGIADPWAAVKA
+>3_2287
+MTVTAEREKALLESVPTGLLIDGEWRDASSGKTFDVKDPATGKVIASLQDANSDDAMAAF
+EAAVAAQADWARTPAQERADILRRAYDLINERAEDFALLMTLEMGKPLAEARGEVVYGNG
+FLRWFSEEATRHYGRTMIMPDGKLRMQVHHKPVGPSLLITPWNFPLAMATRKVGPAVAAG
+CTMVLKAAKLTPLTTQLFAQVMLEAGLPKGVLNVVSGSSASAISGPILEDPRLRKVSFTG
+STPVGVRLMQDAAKNVLRSSMELGGNAPLIVFEDADMDKAVDGAFAAKLRNMGEACTAAN
+RFLVHESVAEEFTRRFVERLEALKPLRGTDPESTLGPIVDEGARDDIHALIEEAVAAGGE
+ILTGGHKIEGDGYFYAPTALKVGKDNPILKKEIFGPVAPIVTFSTEEEAIQMANDTEYGL
+ASYVFTEDNARMHRVTEQIDFGIVGYNVGVVSNPAAPFGGVKQSGLGREGGAEGIAEYTT
+VQYIGIEDPFAGR
+>4_466
+MTVTAEREKALLESVPTGLLIDGEWRDASSGKTFDVKDPATGKVIASLQDANSDDAMAAF
+DAACAAQADWARTPAKERADILRRAYDLINERAEDFALLMTLEMGKPLAEARGEVTYGNG
+FLRWFSEEAGRHYGRTLTVPEGTLRMQVHHRPVGPCLLITPWNFPLAMATRKVGPAVAAG
+CTMVLKAAKLTPLTTQLFAQVMQEAGLPKGVLNVVAGSSASSISSPILQDRRLRKVSFTG
+STPVGVRLMKDAADNVLRTSMELGGNAPLIVFEDADLDAAVEGAFAAKMRNMGEACTAAN
+RFLVHEDVAEEFTQKFVAKLEALKPLRGTDPESTLGPIVDEGARDDIDQLVQDAVAAGGE
+VLTGGHKIEGDGYFYAPTAIKVEKGNPILQQEIFGPVAPIVTFSSEEEAIEMANDTEYGL
+ASYVFTKDQARMYRVAESIEFGLMGYNVGVISNPAAPFGGVKQSGLGREGGAEGIEEYTS
+VQYIGIADPWAAAKA
+>4_1499
+MTPTPDPTATQYIDGAWVPSSDGGTRTIHCPADGSEVGVVAEGTREDALAAIAAARRAFD
+SGEWSSTPAAERGDLLIRLADHILEHRDEFARAEALDTGKRLVEAEGDMADIAACFRYFG
+KIADQNPGRLVDAGDPTVLSRVVTEPVGVCGMITPWNFPLLQAAWKIAPALAAGCTFVLK
+PAEQTPHTAILTMRALESLGLPAGVANLVLGPGATVGEPLSSHPDVDLVSFTGGLATGKT
+IAQAAAGTVKKVALELGGKNPNVIFPDAHYEAALDNALNAAFTDSGLVCSAGTRLIVHES
+IAERFVDDLVERAGHIVMGGPFDEHAETGPLISAAHRDKVTDYVRRGVEAGARLRVGGHW
+GGEEHKDGFFYAPTVLDRCDRDNPAVIEEGFGPVITVETFSTEAEAIEIANHTEYGLAGA
+VWSSDAGTCQRVSRALRHGTVWINDYHPYLPQAEWGGFKASGIGRELGPTGLGEYVEHKH
+IYQNTEPAVTGWFADRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000102.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000102.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7e9779bfccace00230b7b1f14124aca91dca8ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000102.fa
@@ -0,0 +1,37 @@
+>0_630
+MTSAVSTSPAPPRGGRDLKSAVLVGVGLLATALVGLFWLDWLLVLLVVALLVGAVSEIAT
+AVRGIGLDVPRPPLWVAAAVLPLTAWRWGVPALFIALVACLALVAVWTALTRRRPAGQFM
+LAGVFIVLWAPFLLSFAAALLDEPLGHRMVAVLLLMVVSNDTFGYIVGYRFGRTPIAPRI
+SPKKSWEGLAGSLAGSVLVGVVAVPLLVGQPWWVGAVLGVTTVAAATSGDFSESMVKREL
+GIKDMSSALPGHGGVMDRLDSLVFAAPVAYTVLALPLT
+>1_376
+MTSAVSTSPAPPRGGRDLKSAVLVGVGLLATALVGLFWLDWLLVLLVVALLVGAVSEIAT
+AVRGIGLDVPRPPLWVAAAVLPLTAWRWGVPALFIALVACLALVAVWTALTRRRPAGQFM
+LAGVFIVLWAPFLLSFAAALLDEPLGHRMVAILLLMVVSNDTFGYIVGYRFGRTPIAPRI
+SPKKSWEGLAGSLAGSVLVGVVAVPLLVGQPWWVGAVLGVTTVAAATSGDFSESMVKREL
+GIKDMSSALPGHGGVMDRLDSLVFAAPVAYTVLALPLT
+>2_152
+MVGLLGPTAGGLLLGVVGVLAAASVIAAVLRARMGARNPELIGNLVQRIGAWWAMVAVLA
+AVLALGETATLLLFLVLTWLSLREFLTISPTGRADHRTLVWLFFVVTPLHYWFVWEHWYG
+MFSVFIPVYAFLFLPVRAALAGRTEGFLRRAAAVQWAAMVCVYAVSHIPAVLQLPVAMEH
+GRHMAEGSAPGSGDEAGALLLLFLLLVVQGSDVFQYVWGKTLGRRPIAPSVSPNKTWEGF
+VGGVLTATALGAALSFLTPFPWWVAALFAFVSCLLGFGGGLVMSAIKRDRGIKDFGSLIP
+GHGGIMDRIDSLVFAAPVFFHLVRFFYA
+>2_2257
+MTTAVSTPAPPRGGRDLKSAVLVGVGLLVLALVGLVWLDWLLVLLVVALLVGAVTEVATA
+VRGIGLQVPRPPLWAAAVALPVSAWLWGVPALFVALAACLALLAVWTALTRHRPTGQFML
+AGVFIVLWAPFLLSFAVAMLDQPRGNLLVAITLLMVVSNDTFGYIVGYRFGRTPIAPRIS
+PKKSWEGLAGSLAGSALVGVVTVPLFVGQPWWVGAILAVTTVAAATSGDFSESMVKRELG
+IKDMSSALPGHGGVMDRLDSLVFAAPVAYTVLALPLT
+>3_2113
+MTPDATAPSPPRGGRDLRSAVLVGVGLLGTALVGLVWLPWLLVLLVVSLLVGAVNEVAVA
+IRQIGLDVPRPPLWVGATVMPLAAWTGGIPALFLALMASLVLMFAWTAVTRRRPTGQFML
+AGTFVLLWAPFLLSFAAALLDQPAGHMMVVCLVLMVVSNDTFGYMVGYRWGRTPIAPRIS
+PKKSWEGALGSLAGSVAVGSVLVPVLVGHPWWAGALLGALTVGAATAGDFSESMVKRELG
+IKDMSSALPGHGGIMDRLDSLVFAAPVAYAVLALPLS
+>4_600
+MTSAVSTSPAPPRGGRDLKSAVLVGVGLLATALVGLFWLDWLLVLLVVALLVGAVSEIAT
+VVRGIGLDVPRPPLWVAAAVLPLTAWRWGVPALFIALVACLALVAVWTALTRRRPAGQFM
+LAGVFIVLWAPFLLSFAAALLDEPLGHRMVAVLLLMVVSNDTFGYIVGYRFGRTPIAPRI
+SPKKSWEGLAGSLAGSVLVGVVAVPLLVGQPWWVGAVLGVTTVAAATSGDFSESMVKREL
+GIKDMSSALPGHGGVMDRLDSLVFAAPVAYTVLALPLT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000123.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000123.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2df902ed64452c2670f451743f9098dcc8ab4a73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000123.fa
@@ -0,0 +1,56 @@
+>0_1224
+MSAESSPLSAAAVDPEERRLEAALRPKHLDEFVGQMRVREQLDLMLASARLRDRAADHVL
+LSGPPGLGKTTLAMIVAAEMNAPLRLSSGPAIQHAGDLAAILSSLTEGEVLFLDEIHRMS
+RPAEEMLYMAMEDFRVDIVVGKGAGATSIPLELPPFTLVGATTRAGLLPGPLRDRFGFTG
+HLDFYTEVELERVLRRSALLLDMRLATEGYRQIARRSRGTPRIANRLLRRVRDWALVKGL
+AEVGAHDAAAALDMYEVDGRGLDRLDRSVLTALCTTFGGGPVGLSTLATAVGEEAETVET
+VAEPFLIREGMVARTPRGRVALPGAWEHLGLAAPEATPGP
+>1_952
+MSAESSPLSAAAVDPEERRLEAALRPKHLDEFVGQMRVREQLDLMLASARLRDRAADHVL
+LSGPPGLGKTTLAMIVAAEMNAPLRLSSGPAIQHAGDLAAILSSLTEGEVLFLDEIHRMS
+RPAEEMLYMAMEDFRVDIVVGKGAGATSIPLELPPFTLVGATTRAGLLPGPLRDRFGFTG
+HLDFYTEVELERVLRRSALLLDMRLATEGYRQIARRSRGTPRIANRLLRRVRDWALVKGL
+AEVGAHDAAAALDMYEVDGRGLDRLDRSVLTALCTTFGGGPVGLSTLATAVGEEAETVET
+VAEPFLIREGMVARTPRGRVALPGAWEHLGLAAPEATPGP
+>2_1585
+MSAEPSPLSGLAADPEERRLEAALRPKHLDEFVGQRRVREQLDLMLASARLRDRAADHVL
+LSGPPGLGKTTLAMIVAAEMNAPLRLSSGPAIQHAGDLAAILSSLTEGEVLFLDEIHRMS
+RPAEEMLYMAMEDFRVDIVVGKGAGATSIPLELPPFTLVGATTRAGLLPGPLRDRFGFTG
+HLDFYAEAELERVLRRSALLLDVRLASDGYRQIATRSRGTPRIANRLLRRVRDWALVKGV
+EQVEADHAAAALDMYDVDARGLDRLDRSVLTALCTTFGGGPVGLTTLATAVGEEAETVET
+VAEPFLIREGMVARTPRGRIALPGAWDHLGLASPEAGSGA
+>3_1480
+MSERPVTAFEADAEERRLEAALRPKHLDEFVGQARVREQLDLMLASARLRDRAADHVLLS
+GPPGLGKTTLAMIVAQEMNAPLRLSSGPAIQNAGDLAAILSSLTEGEVLFLDEIHRMSRP
+AEEMLYMAMEDFRVDIVVGKGAGATSIPLELPPFTLVGATTRAGLLPGPLRDRFGFTGHL
+EFYAIEELERVLRRSSALLDMRVETDGYRQIASRSRGTPRIANRLLRRVRDWALVKGLDT
+VDAEAASAALTMYEVDARGLDRLDRSVLTALCTTFGGGPVGLTTLATAVGEEAETVETVA
+EPFLIREGMMARTPRGRVALPGAWDHLGMTPPEAPLG
+>4_1181
+MSAESSPLSAAAVDPEERRLEAALRPKHLDEFVGQMRVREQLDLMLASARLRDRAADHVL
+LSGPPGLGKTTLAMIVAAEMNAPLRLSSGPAIQHAGDLAAILSSLTEGEVLFLDEIHRMS
+RPAEEMLYMAMEDFRVDIVVGKGAGATSIPLELPPFTLVGATTRAGLLPGPLRDRFGFTG
+HLDFYTEVELERVLRRSALLLDMRLATEGYRQIARRSRGTPRIANRLLRRVRDWALVKGL
+AEVGAHDAAAALDMYEVDGRGLDRLDRSVLTALCTTFGGGPVGLSTLATAVGEEAETVET
+VAEPFLIREGMVARTPRGRVALPGAWEHLGLAAPEATPGP
+>4_1823
+MSILRVHDGLFGLTFQQALDKASPGATIALTPGTYAEFESIPVGNLRIIGAGSRPEDVIL
+VTQLDVHGQISVENLTLQAPHFHNAVRLHGPTASAVFLYTAIQPEPTGQFPAVYSEGGAV
+TVRRSTLDQGPGGCALYVEGQGTATFEDSTTGTVNAVASTVTTVDSTHGAFHLSAASKVH
+ARGTLCLAPAEGMRGLVLTAFSVLKAERLTTDITYLELSLEDSALDVAEVSTSSDVDVHV
+MTSGGSHVQIPPDTVRVTDIDRQKAEQEVAERRQREEAAARRRAEEAAAEAAATGEAARQ
+AAAEAQAEARRQEEAKPRAVMWTAAQGADFTTVQDQLRPGDTLVLEEGDFHLPDPAIMLN
+CHIRGTGRADRIRLHGAVGIPNGATVRLENMLLVTPSTGNAVNVHAGGNATLTGVLVDPT
+KAEVFSPLCSSGGRLTLNEVRVVSEPTSYLADVLGTQGGVIVAEDSTFGIVRLESSARAT
+LTDCTANQLYVLGSGEALSLGTLRIPPTTPHLRALAVEEGGRGTIADLCVEEPCEVFVAG
+SLQIAHVSSAPHALHLITTDTALHSIPEDAIATAEEPSQTATADATLVEHPGENSTGDRE
+PSAGRGHDGADLADTNCDPMAQLSALTGLADVKNQVQTFIAEVRFAEARRQRGFAVRRQT
+LHSQFLGNPGTGKTTVARLLGRALHQAGVLSSDVFVEVTREDLVSEHIGGTGPKTRRILE
+SALGGILFIDEAYTLAEGGPQDFGREAIATLLAFMENHRDEFMVILAGYPEQMHAFFKAN
+PGLRSRVPLRFDFEDYSTAELVQMGLAALADDGFTVDPDAYRRTVAEAHRSSGDRSNGRW
+VRNLNDRLVRHMAHRVMAESGAAEDMVGVEDERLTQVDPADLHALLGRSTEDDTGVDHLL
+VELDEMVGLETVKAWVRGLVAQAEADERLRDAGVDLPRPTYHMVFAGSPGTGKTTVARLV
+GKLFHRLGILSTPQVVEASRERMVGRYIGHTEERTGLLLDEARGGVLFVDEAYQLDMPDS
+SNDFGKVAVETLITRLEDDRHSFIAIFAGYTDRMAQFLSLNPGLASRVPHNIEFPDYSPD
+DIAEIVVRTLRRTWSFDETVLRSAVAQGYAALPPESRANARQARNYADAISQAHKTWITE
+SSTDGDDIRHIRDATIIGVLAAEPTGQDQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000128.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000128.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d70eb1d3518221ffbf56d2b2575ae13e8465d85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000128.fa
@@ -0,0 +1,144 @@
+>0_1388
+MSLSSAAPTPPSVPLDPAGAPHRPQLPGSERTPPARTLVELFDATAREHPDATALDDGVE
+PLTYAELRERVDETARHLWAAGVRAGDRVGVRIASGTAALYVSILGVLAAGAAYVPVDAD
+DPEERARLVFGEAKVAGVLTDERVYAPHPEHTADPAAEARAPGLEDDAWIIFTSGSTGTP
+KGVAVSHRSAAAFVDAEARIFLADDPLAPGDRVLAGLSVAFDASCEEMWLAWRHGACLVP
+APRSLVRSGMDLGPWLAERRITAVSTVPTLAAMWPTEAMDNVRLLIFGGEACPPELAARL
+AEDGREVWNTYGPTEATVVACAAPLTGLGPVRIGLPLDGWDLAVVDPQTTLPVAEGETGE
+LIIGGVGLARYLDPAKDAEKYAPMPSLGWERAYRSGDLVVFEPEGLLFVGRADDQVKLGG
+RRIELGEVDAALQALPGVHGGAAAVQTTPAGHQILVGYLVPADPEAELDLHMAREHLAAE
+LPAALVPRLAVVDSLPTKTSGKVDRHALPWPLPGAEVDEDAPPPDEDTADGWVLRQWADV
+LGAPPKDADTDFFEAGGGSLAAAQLVARLRLRHPAVTVQDVYRNPTAGALVAAVVGDDGP
+RGIEVHDRHVDRTRHRTQWVQTLVGLPVFVLPALRLGVWTGLALNLLTLSGLAPGLPTVP
+WWVLIVAGLLVVTVPGRMLLTAATARLLLRGVSPGSYPRGGRVHLRLWLAQQISDLVDPY
+SLAGATWVPAYARLLGNRIGKDVDMHTVPPVTGMLTVEEGAAIEPEVDLSGYWVDGDVVR
+LGEVRIGADAVVGARSTLLPGAQVGAGAHVEAGSTVAGRVRGGQRHAGSPAVKVGKVKSR
+GPAEAPRETPGWRLMATVLSTLISLLPLVSAAAAAAVAAWSLTWWPPAPEAGPLAAVGTT
+AARLLAASPLVAGVWFLTQMLLVLVTVRLLALGITEGHHPVRSRVGWQVWATERVLDAAR
+DQLFPIYASRFTPTWLRLLGAEVGRGVEASTVVLLPCMTRVGDGAFLADDTMVSSYSLDG
+GWMHVAPAKVGKRSFVGNSGMVPGGRTLRRDSLVAVLSTTPAKTKAGTSWMGSPPVRLRR
+NEVTADAALTYDPPARLKAARTAWELLRAIPVWLHVALSLAVGATLAALIAVGTWALAFV
+LGGVVLLAAGAVAASLTVLAKRVFVGRIRAGEHPLWSSFIWRNEVADTFTEFLAAPWFSR
+AAAGTPALVWFLRAMGARIGHGAWVESYWLPEADLVELGDGATVNRGCVVQTHLFHDRVM
+SLDAVVLEDGATLGPHSVVLPAARLGRGTTVGAGSLVMRGEELPAGTWWLGNPVSPWRRP
+DGDPAAAATPSREEA
+>1_1129
+MSLSSAAPTPPSVPLDPAGAPHRPQLPGSERTPPARTLVELFDATAREHPDATALDDGVE
+PLTYAELRERVDETARHLWAAGVRAGDRVGVRIASGTAALYVSILGVLAAGAAYVPVDAD
+DPEERARLVFGEAKVAGVLTDERVYAPHPEHTADPAAEARAPGLEDDAWIIFTSGSTGTP
+KGVAVSHRSAAAFVDAEARIFLADDPLAPGDRVLAGLSVAFDASCEEMWLAWRHGACLVP
+APRSLVRSGMDLGPWLAERRITAVSTVPTLAAMWPTEAMDNVRLLIFGGEACPPELAARL
+AEDGREVWNTYGPTEATVVACAAPLTGLGPVRIGLPLDGWDLAVVDPQTTLPVAEGETGE
+LIIGGVGLARYLDPAKDAEKYAPMPSLGWERAYRSGDLVVFEPEGLLFVGRADDQVKLGG
+RRIELGEVDAALQALPGVHGGAAAVQTTPAGHQILVGYLVPADPEAELDLHMAREHLAAE
+LPAALVPRLAVVDSLPTKTSGKVDRHALPWPLPGAEVDEDAPQPNEDTADGWVLRQWADV
+LGAPPKDADTDFFEAGGGSLAAAQLVARLRLRHPAVTVQDVYRNPTAGALVAAVVGDDGP
+RGIEVHDRHVDRTRHRTQWVQTLVGLPVFVLPALRLGVWTGLALNLLTLSGLAPGLPTVP
+WWVLIVAGLLVVTVPGRMLLTAATARLLLRGVSPGSYPRGGRVHLRLWLAQQISDLVDPY
+SLAGATWVPAYARLLGNRIGKDVDMHTVPPVTGMLTVEEGAAIEPEVDLSGYWVDGDVVR
+LGEVRIGADAVVGARSTLLPGAQVGAGAHVEAGSTVAGRVRGGQRHAGSPAVKVGKVKSR
+GPAEAPRETPGWRLMATVLSTLISLLPLVSAAAAAAVAAWSLTWWPPAPEAGPLAAVGTT
+AARLLAASPLVAGVWFLTQMLLVLVTVRLLALGITEGHHPVRSRVGWQVWATERVLDAAR
+DQLFPIYASRFTPTWLRLLGAEVGRGVEASTVVLLPCMTRVGDGAFLADDTMVSSYSLDG
+GWMHVAPAKVGKRSFVGNSGMVPGGRTLRRDSLVAVLSTTPAKTKAGTSWMGSPPVRLRR
+NEVTADAALTYDPPARLKAARTAWELLRAIPVWLHVALSLAVGATLAALIAVGTWALAFV
+LGGVVLLAAGAVAASLTVLAKRVFVGRIRAGEHPLWSSFIWRNEVADTFTEFLAAPWFSR
+AAAGTPALVWFLRAMGARIGHGAWVESYWLPEADLVELGDGATVNRGCVVQTHLFHDRVM
+SLDAVVLEDGATLGPHSVVLPAARLGRGTTVGAGSLVMRGEELPAGTWWLGNPVSPWRRP
+DGDPAAAATPSREEA
+>2_1432
+MSHPSVAPVPPPDPVDPADDAAAVHPPQLPGALRTPPARTLVELFDATAREHPDAPALDD
+GVEPLTYAELQARVDETARHLWAAGVRTGDRVGVRIASGTAALYVSILGVLAAGAAYVPV
+DADDPEERARLVFGEARVAGVLTDERVYAPAAVHAPRPDAEDRAPGLEDDAWIIFTSGST
+GTPKGVAVSHRSAAAFVDAEARIFLSEDPLAPGDRVLAGLSVAFDASCEEMWLAWRHGAC
+LVPAPRSLVRSGMDLGPWLAERRITAVSTVPTLAAMWPTEALDNVRLLIFGGEACPPELA
+ARLAEDGREVWNTYGPTEATVVACAAPLTGVGPVRIGLPLDGWDLAVVDPATGVPVAEGA
+TGELIIGGVGLARYLDPVKDAEKYAPMPTLGWERAYRSGDLVVFEPEGLLFVGRADDQVK
+LGGRRIELGEVDAALQALPGVHGGAAAVQTTPAGHQILVGYLVSADPEADLDLHLARERL
+AEELPAALVPRLALMDALPTKTSGKVDRHALPWPLPGAEPDDEAPQPDEASPHGWVLRQW
+ADVLGAPPSGPDADFFEAGGGSLAAAQLVARLRLRHPAVTVQDVYRSPTASALAAAVVGE
+DGGAGGIEVHDRHVASTRHRTQWAQTLVGLPVFVLPALRLGVWTGLALNLLALTGLAPGL
+PTVPWWVLAVAGLLVVTVPGRMLVTALAARLLLRGVEPGSHPRGGRVHLRLWLAQQITDV
+VDPYSLAGAMWVPAYARLLGNRIGADVDLHSVPPVTGLLTVGEGASIEPEVDLSGYWVDG
+DVVRIGEVRIGAGAVVGARSTLLPGARVGAGAHVEAGSTVAGRLRGGQRHAGSPAAKVGK
+VRADGPNVAPPRATGWRAVSTVLSTLVALLGLVAAGAAAAVGAWSLTWWPPADPTGPAAA
+VGVTALRLLAASPLIAAVWFGAQMLLVLGAVRLLSVGITEGHHPVRSRVGWQIWATERIL
+DAARDHLFPLYASRFTPVWLRLLGAEVGRGVEASTVVLLPGMTRVGDGAFLADDTMVSSY
+SLEGGWMHVAPAKVGKRAFVGNSGMVPAGRTLRRDSLVAVLSTTPAKTKAGTSWMGSPPV
+RLRRTEVAADASVTYAPTARLKAARTGWELLRAIPVWLHVALTIATGAALAALTAVGTWA
+LAAVLGGAVLLAAGAAAASLTVLAKKAFVGRVRPGEHPLWSSFIWRNEVADTFTEFLAAP
+WFARAAAGTPALVWFLRAMGARIGRGAWVESYWLPEADLVTLGDGATVNRGCVVQTHLFH
+DRVMSLDEVVLADGATLGPNSVVLPAARLGRGTTVGAGSLVMRGEELPAGTWWLGNPVSP
+WRRPDGVPDPSPAPSREAA
+>3_1340
+MTAPHPSTPRSAPHDAGTPHAPQLPGTDRTPPPRTLIDILDATAREHPEAPALDDSTAQL
+GYAELLDRVLESARFLQAHGIGAGDRVGVRIPSGTAALYVSILAVMAVGAAYVPVDADDP
+EERARLVFGEARVAGVLTGERALDDRAAAERAEAPEARAPRLEDDAWIIFTSGSTGTPKG
+VAVSHRSAAAFVDAEARIFLTADPLGPGDRVLAGLSVAFDASCEEMWLAWRHGACLVPAP
+RALVRSGMDLGPWLAERRITAVSTVPTLAAMWPTAALANVRLLIFGGEACPPDLAARLAV
+PGREVWNTYGPTEATVVACAAPLAGEGPVRIGLPLDGWDLAVVDPASGVPVAEGETGELI
+IGGVGLARYLDPAKDAEKYAPMETLGWDRAYRSGDLVLYDPAGLLFLGRADDQVKVGGRR
+IELGEVDAALQNLPGVQGGAAAVRTTPAGNQLLVGYLKPTGPLEGFDLDAAHARLAEELP
+AAIVPRLALVDSLPTKTSGKVDRNALPWPLPGTAATDDADTPDESTPDGWVLAQWAAVLG
+AAPADGSTDFFSAGGGSLAAAQLVARLRERHPGVTVQDVYRHPTADELVSAVLGEGAEGI
+EVHERNVDTTRRRTQWAQTLVGLPAFILPALRLGTWTGVAVNLLAATGLVPGLPTVPWWI
+LALVGLFVVTAPGRMLVAGLTARALLHGVGPGAHPRGGRVHLRLWLAQQVTDLVDPYSLA
+GAGWIPAYGRLLGNRIARDADLHALPPVTGLLTVGEGASIEPEVDLSGYWVDGDVLRVGT
+VEVGAGAVVGSRSTLLPGAKVGAGAHVEAGSTVAGRLRGHQRHGGSPAVKLGKVKRGSAP
+AETAPDAAGWRVLSTLSSTAVALLPLAAVAAAAAVGAWSLTWWPPAAADASPLQAVGTAA
+ARLLAASPLIAAVWFGVQMLLVLVAVRVLAIGITPGHHPVRSRVGWQIWATERLLDAARD
+QLFPIYASRFTPTWLRWLGARVGKDVEASTVVLLPTMTQVGDGAFLADDTMVSSYTLEDG
+WMHVAPAKVGKRSFVGNSGMVPGGRTLRRDSLVAVLSTTPAKTKAGTSWMGSPPVRLRRT
+EVEADASLTYAPPARLKAARTGWELLRAIPVWLHVALTIAVGAALAALAAVGTWWLAALL
+GGAVLLAAGAVAAVVTVLAKRAFVGRVRAGEHPLWSSFIWRNEVADTFTEFLAAPWFSRA
+AAGTPAMVWFLRGMGARIGRGAWVESYWLPEADLVTLGDGATVNRGCVVQTHLFHDRVMA
+LDEVVLADGATLGPNSVVLPAARLGEGTTVGAGSLVMRGEELPGGTWWLGNPVAPWRRPG
+KTPTAHQRAAAATGALPVIPDPTSAGGIR
+>3_2386
+MTTQQFHPARAPAAATSAVESEDRALYPVEPPPAPRTLVDILKATAAAHPDAVALEGHGP
+GGSAALNYMQLLARAEQVAARLREAGIGPGDRVGLRVPSGTTDLYVALVAILLSGAAYVP
+VDWDDPASRAETVFGEAAVACVIGEGMAITPVDGVAPLRRTGAPGLEDDAWIIFTSGTTG
+LPKGVAITHRNAAALVDAEARMYLQDDPLGPGDRVMAGLAVSFDASCEEMWLAWRHGAAL
+IAAPREVVRSGPDLGAWIAQKRLTAISTVPTLAALWPDDSLVGIRLLIFGGEACPPELVA
+RLATQDRELWNTYGPTEATVIASGAILRPGQEVRIGLPVPGWKLAVVDPEGRPVRWGEAG
+ELVIGGVGLGRYLDPEKDAEKYAPLAALGWDRCYRTGDMVVAEPEGLVFAGRIDDQVKIS
+GKRIELGEVDAHLTAMPGVRAGAAAVQLTDSGTAVLVGYLMPEKGVELDLPRIRELMGER
+LPGGVVPTLAVVDELPMKSSGKVDRTALPWPLPFDAGEAPPLPEDLRWLAERWTAVLGPA
+PLTPESDFFALGGSSVAVAHLVTALREHHPQLEFPQVYANPTLAGMADLLAGMADSGPRV
+ERRQPAAMPRFTGPAQIAWVTALTGVAGLRYVAGATVAIWALGQFFGAGWVVTPPVLPTL
+IAWAVLFSVPGRLYGTALVVRVLNAGLRPGRYRRGGLTHLRVWAADRAIATARLEYLLGG
+PAASHVHRVFGTRVGSGAHLDHMPSATGLVRIGHGVSVGAEADLHGHWVEAGTFVLGEIV
+VGDHARIGARSIVLPGVRVGSWAEIQAGSRVASSVPAHEYWGGSPLRRLGEAGVTWPSED
+PRAARGVRAWPVALAAAGQMFTLAVLALLPMVALLPWVVLVLSPLRGATDFRDVLPVMAL
+WVPVVVVLAVPTWFLLVSAFVRLLAPLVKPGFYPVHSLQAWAAWSIQNVMRRTLIGTYPV
+YASSATPWLMRLMGARIGRNVEISTVEAIPHLTVVEDGAFLADHSMAAVPRVGRGWVHIG
+STVIGRGSFVGNSAIVGPDRDLPDDALVAVLGVSPHRPAPGTSWLGRSPTAIPRVKVAAD
+AAATFAPPRRLKAARWAVELCRFVPAFIVGWLDIAVVYFLATVYMGASGQGSDPLRGVVV
+ATVASLPAAVAAALIASAMPVLFKWALVGEFVPQDRPLFSSFVWRNELMDAFVEVLAVPS
+LIRIGLGSPVLTMWARWMGVEIGRNAWVESWWLPETDLVSIADNATVNRGTVLQTHLFHD
+RVMTMQPVRLDEGATLGPNSFMLPGSSLGPCATVRPGSLVLREDAVPGHSDWSGNPIRAV
+QDAPAAAATGDTATRARARADHLDADERPQTGPIPVVATSTPAREEPTS
+>4_1337
+MSLSSAAPTPPSVPLDPAGAPHRPQLPGSERTPPARTLVELFDATAREHPDATALDDGVE
+PLTYAELRERVDETARHLWAAGVRAGDRVGVRIASGTAALYVSILGVLAAGAAYVPVDAD
+DPEERARLVFGEAKVAGVLTDERVYAPHPEHTADPAAEARAPGLEDDAWIIFTSGSTGTP
+KGVAVSHRSAAAFVDAEARIFLADDPLAPGDRVLAGLSVAFDASCEEMWLAWRHGACLVP
+APRSLVRSGMDLGPWLAERRITAVSTVPTLAAMWPTEAMDNVRLLIFGGEACPPELAARL
+AEDGREVWNTYGPTEATVVACAAPLTGLGPVRIGLPLDGWDLAVVDPQTTLPVAEGETGE
+LIIGGVGLARYLDPAKDAEKYAPMPSLGWERAYRSGDLVVFEPEGLLFVGRADDQVKLGG
+RRIELGEVDAALQALPGVHGGAAAVQTTPAGHQILVGYLVPADPEAELDLHMAREHLAAE
+LPAALVPRLAVVDSLPTKTSGKVDRHALPWPLPGAEVDEDAPQPNEDTADGWVLRQWADV
+LGAPPKDADTDFFEAGGGSLAAAQLVARLRLRHPAVTVQDVYRNPTAGALVAAVVGDDGP
+RGIEVHDRHVDRTRHRTQWVQTLVGLPVFVLPALRLGVWTGLALNLLTLSGLAPGLPTVP
+WWVLIVAGLLVVTVPGRMLLTAATARLLLRGVSPGSYPRGGRVHLRLWLAQQISDLVDPY
+SLAGATWVPAYARLLGNRIGKDVDMHTVPPVTGMLTVEEGAAIEPEVDLSGYWVDGDVVR
+LGEVRIGADAVVGARSTLLPGAQVGAGAHVEAGSTVAGRVRGGQRHAGSPAVKVGKVKSR
+GPAEAPRETPGWRLMATVLSTLISLLPLVSAAAAAAVAAWSLTWWPPAPEAGPLAAVGTT
+AARLLAASPLVAGVWFLTQMLLVLVTVRLLALGITEGHHPVRSRVGWQVWATERVLDAAR
+DQLFPIYASRFTPTWLRLLGAEVGRGVEASTVVLLPCMTRVGDGAFLADDTMVSSYSLDG
+GWMHVAPAKVGKRSFVGNSGMVPGGRTLRRDSLVAVLSTTPAKTKAGTSWMGSPPVRLRR
+NEVTADAALTYDPPARLKAARTAWELLRAIPVWLHVALSLAVGATLAALIAVGTWALAFV
+LGGVVLLAAGAVAASLTVLAKRVFVGRIRAGEHPLWSSFIWRNEVADTFTEFLAAPWFSR
+AAAGTPALVWFLRAMGARIGHGAWVESYWLPEADLVELGDGATVNRGCVVQTHLFHDRVM
+SLDAVVLEDGATLGPHSVVLPAARLGRGTTVGAGSLVMRGEELPAGTWWLGNPVSPWRRP
+DGDPAAAATPSREEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000142.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000142.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f7e27c904c3dc90d732603f710a62bd94ae4c7a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000142.fa
@@ -0,0 +1,42 @@
+>0_1627
+MRVLVTGGAGYLGSHTVLTLLEAGHDVLVLDSLVTATTTSLERVAELAETRLGGSRLRLH
+VADIRRPEDYRGALADFGPAALVHFAGLKSPTESMTRPAAYYDVNVGGTAAVAEAALAAG
+ARTVLFSSSATVYGDRAPVPVAEDAATDPVSPYGHSKLMAEQVLRDVCATVDGGGLAMLR
+YFNPVGAHPSGRLGEDPSGVPANLMPFVARVASGAYPELRVFGADFDTRDGSAVRDFIHV
+MDLAEAHVAGLEWLAARVAAGGGTTTRVWNIGRGEGVTVFEMVRAFEAVTGGRIPYRVVE
+RRPGDIAESCAAVDAIGAEVGWHARRDVTAMVRDLWAWQEANPAGFSPRTE
+>1_1341
+MRVLVTGGAGYLGSHTVLTLLEAGHDVLVLDSLVTATTTSLERVAELAGTRLGGSRLRLH
+VADIRRPEDYRGALADFGPAALVHFAGLKSPTESMTRPAAYYDVNVGGTAAVAEAALAAG
+VRTVLFSSSATVYGDRAPVPVAEDAATDPVSPYGHSKLMAEQVLRDVCATVDGGGLAMLR
+YFNPVGAHPSGRLGEDPSGVPANLMPFVARVASGAYPELRVFGADFDTRDGSAVRDFIHV
+MDLAEAHVAGLEWLAARVATGGGTTTRVWNIGRGEGVTVFEMVRAFEAVTGGRIPYRVVE
+RRPGDIAESCAAVDAIGAEVGWHARRDVTAMVRDLWAWQEANPAGFSSRAE
+>2_1172
+MPMRVLVTGGAGYLGSHTVVVLLEAGHDVLVLDSLVAGSTAPLERAAELAGVALGGRRLD
+LVVADIRCPADYRAALEAFAPEAMVHFAGLKSPAESLSRPADYYDVNVGGTAAVAAAALA
+AGARTVLFSSSATVYGDRAPVPVDETAPTDPVSPYGRSKLMAEQVLRDVCATTDGVGLAM
+LRYFNPVGAHPSGRLGEDPRGVPANLMPFVARVATGAYPELQVFGADFPTRDGSAVRDFI
+HVMDLAEAHLAALAWLAARRGDGAEPTTRVWNIGRGEGVTVFEMVRAFEEVTGARIPCRV
+TARRAGDIAESCAAVDAVGAEVGWRARRDVTAMVRDLWAWQRAHPHGFGTGAA
+>2_1184
+MRVLVTGGAGFLGSHTVSVLLDAGHDVLVLDSLVSSTTVPLERIADLAGVTFGGSRLRFH
+RADVREPTSYREAVVAFGPDAVVHFAGLKSPTESLADPASYYTVNVAGTAAVAEVAGGAG
+VRAFLFSSSATVYGDEAPVPVGEDAAVAPVTPYGHSKLMAEQVLRHMHEAGRHMGVAVLR
+YFNPVGAHPSGRLGEDPQGVPANLMPFVARVAGGRYEQLNVFGADFATRDGSAVRDFIHV
+MDLAEAHVATLEWMVAQPGDEVGVRVWNIGRGEGVTVFEMIQAFERVTGRPVPFQVVGRR
+PGDIAASCASVDAIAATVGWRASRDTDAMVRDLWAWQQANPSGYAGDAP
+>3_1102
+MRALVTGGAGYLGSHTVTTLLDAGHDVLVLDSLAGAGRAGLERAAEVCGVGLGGARLRLV
+VADIRRPEDWADEVVAWAPDTVVHFAGLKSPTESMASPAEYYSVNVGGTAHVAEAAVRAG
+ARTLLFSSSATVYGDRAPVPVAESAPIDPVSPYGRSKAMAEQVLTDVHAASPGLSVASLR
+YFNPVGAHPSGRMGEDPQGTPANLMPFVSRVASGAYPELTVFGADFATRDGSAVRDFIHV
+MDLAEAHVAALEWMAARPSEEAGVRVWNIGRGEGVTVFEMVRAFEEVTGRPVPFTVGGRR
+AGDIAESCADVGAVARDVGWRARRDVREMVRDLWAWQQAEQEGDGGP
+>4_1556
+MRVLVTGGAGYLGSHTVLTLLEAGHDVLVLDSLVTATTTSLERVAELAGTRLGGSRLRLH
+VADIRRPEDYRGALADFGPAALVHFAGLKSPTESMTRPAAYYDVNVGGTAAVAEAALAAG
+ARTVLFSSSATVYGDRAPVPVAEDAATDPVSPYGHSKLMAEQVLRDVCATVDGGGLAMLR
+YFNPVGAHPSGRLGEDPSGVPANLMPFVARVASGVYPELRVFGADFDTRDGSAVRDFIHV
+MDLAEAHVAGLEWLAARVATGGGTTTRVWNIGRGEGVTVFEMVRAFEAVTGGRIPYRVVE
+RRPGDIAESCAAVDAIGAEVGWHARRDVTAMVRDLWAWQEANPAGFSSRTE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000150.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000150.fa
new file mode 100644
index 0000000000000000000000000000000000000000..65ef6864cddf494d23d048e435b2ca13c6b80572
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000150.fa
@@ -0,0 +1,35 @@
+>0_1793
+MTTLTAPQADLDALRTPAAAAAHRVAGERPAAAADATPALSVRDLVLEYPDGERGVLRAL
+DEVSLDLLPGTFTAMVGPSGSGKSSLLAVAAGLVTPTSGSVSVAGREMAGLSRKERTALR
+GQEIGVIFQQPNLIPSLTAAEQLELTVHLDRDATRADRRAAKARAMELLERVDLADQAGK
+RPHQLSGGQRQRVNIVRALMASPTLLLVDEPTSALDRERSAAVVDLLGTLTREEQVATLM
+VTHDHEFLSVTDRTLTMVDGRLSAE
+>1_1500
+MTALTAPQADLDALRTPAAAAAHRVAAERPATAADATPALSVRDLVLEYPDGERGVLRAL
+DEVSLDLLPGTFTAMVGPSGSGKSSLLAVAAGLVTPTSGSVSVAGREMAGLSRKERTALR
+GQEIGMIFQQPNLIPSLTAAEQLELTVHLDRDATRADRKAARARALELLERVDLADQARK
+RPHQLSGGQRQRVNIVRALMASPTLLLVDEPTSALDRERSAAVVDLLGTLTREEQVATLM
+VTHDHEFLSATDRTLTMVDGRLHAE
+>2_995
+MTTTLASQTDLDPMRTPAAAAAHRIAPGTAAPDGSGGTPALSVRDLVLEYPDGERGVLRA
+LDEVSLDLHAGTFTALVGPSGSGKSSLLAVAAGLVPPTSGTVTVAGRELTGLSRTERTGL
+RGREIGVIFQQPNLIPSLTAAEQLELSVHLDRDATRTDRKAARDRAMALLERVDLADQAG
+KRPHQLSGGQRQRVNIVRALMASPALLLVDEPTSALDRERSAAVVDLLGALTRDEGTATL
+MVTHDHEFLAATDRTLTMVDGRLTD
+>2_1037
+MSTTTPVIQLSSVTKTYQRRDLYTDASVTVIPGRAHAIVGPNGSGKSVMMRLMCGFLLPS
+SGSVTIDPRYLDGRRTFPDKFGVVIDKPGMLPHLTGLENLRRLAEIQKKIGDERIREVMQ
+SFGLDPDARQRVHQYSLGMKQKLNLCQAVMEDPEVLVLDEPFNALDADSADALRGRLASF
+VADGGTLVFTSHDSRDVEQLADSVIRLENGRVTQEDASPRT
+>3_938
+MTISTHTPDLSAYRSPAAARVTAHDAAPAAPDAAPVLSVRDLVLEYPDGEGRTLRALDGV
+SLDLTPGTFTAMIGPSGSGKSSLLAVAAGLIAPTSGSVTVAGTELTGLSRAARTRLRGDR
+IGVVFQQPNLLPSLTAREQLELVVRLDPKSTRADRTAAAARAQELLERVDLGRRADQRPH
+QLSGGQRQRVNIVRALMGTGSGAPALLLVDEPTSALDRERSAAVVELLGELTRQEGVATL
+MVTHDHEFLGATDRVLTMVDGRLAA
+>4_1714
+MTTLTAPQADLDALRTPAAAAAHRVAGERPAAAADATPALSVRDLVLEYPDGERGVLRAL
+DEVSLDLLPGTFTAMVGPSGSGKSSLLAVAAGLVTPTSGCVSVAGREMAGLSRKERTALR
+GQEIGMIFQQPNLIPSLTAAEQLELTVHLDRDATRADRRAAKARALELLERVDLADQAGK
+RPHQLSGGQRQRVNIVRALMASPTLLLVDEPTSALDRERSAAVVDLLGTLTREEQVATLM
+VTHDHEFLSATDRTLTMVDGRLSAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000153.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000153.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a728a643bd84af0d535cecaf8b6038ddd425ef69
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000153.fa
@@ -0,0 +1,49 @@
+>0_1914
+MPPSQDAASLTQLGVIGVILLVVLFYGGTMIMSVAISKKKENADAYMTAGNQIGFGVSAA
+SMTATWIWAASMYASVTAGYTYGVSGPLHYGL
+>0_1915
+MILFIYPFGRRIRAVAPRAHTLAEVMYARHGRSSQLMLAGSNVLGSVISLTSNFIAGGAL
+ISLLSPLSFGAGILIVAAGVLLYTLWSGFRASVLTDFAQVMAMLGATVIIIPAVFFAAGG
+PDMFQAGVEAGHVTAQQQSFFSSDAFMNQGAPYIAAVLAYAIGNQTIAQRLFAVREDLIK
+PTFITATLGYGGTVIGVGMLGVMALYLGVEPLDGDVNNLLPQMVADHLPLALVALAFLMI
+IGSLSSTADSDLSALSSIVMTDVYGQSVGRKNADPKTMLLIGRITMIVATAAALYFATAK
+FDILDLLVFVGALWGCLVFPVIASFYWGRITNVAFTVSVLAALTVFLPVRFEWIPIEGAW
+AFVVETLAILGVGVVLCIMCFGFFGLRPAVVVGAIASVVMLFLGYGFLRDYATLTGSLVA
+YAVSFLVCWGLSVRSGQDFDFDRIARVTGDFDPATEDLPQVERASAPVS
+>1_1619
+MPPSQDAASLTQLGVIGVILLVALFYGGTMIMSVAISKKKENADAYMTAGNQIGFGVSAA
+SMTATWIWAASMYASVTAGYTYGVSGPLHYGLWGALMILFIYPFGRRIRAVAPRAHTLAE
+VMYARHGRSSQLMLAGSNVLGSVISLTSNFIAGGALISLLSPLSFGAGILIVAAGVLLYT
+LWSGFRASVLTDFAQVMAMLGATVIIIPAVFFAAGGPGMFQAGVEAGHVTAQQQSFFSSE
+AFMNQGAPYIAAVLAYAIGNQTIAQRLFAVREDLIKPTFITATLGYGGTVIGVGMLGVMA
+LYLGVEPLDGDVNNLLPQMVADHLPLALVALAFLMIIGSLSSTADSDLSALSSIVMTDVY
+GQSVGRQNADPKTMLLIGRITMIVATAAALYFATAKFDILDLLVFVGALWGCLVFPVIAS
+FYWGRITNVAFTASVLAALAVFLPVRFEWIPLEGAWAFVVETLAILGVGVVLGIMCFGFF
+GLRPAVVVGAIASVVMLFLGYGFLRDYATLTGSLVAYAVSFLVCWGLSVRSGQDFDFDRI
+ARVTGDFDPATEDLPQVERASASVS
+>2_863
+MPPSQDGAELVQLGVIGVIVLVVFFYGGTMLMSLAISRRKENADAYMTAGNKIGFGVSAA
+SMTATWIWASSMYASVTAGYTYGVSGPIHYGLWGALMILFIYPFGRRIRKVAPRAHTLAE
+VMYARHGRSSQLMLAGSNVLGSVISLTSNFIAGGALIAILSPLSFGAGILIVAAGVLLYT
+LWSGFRASVLTDFAQVMAMLGATVVIIPAVFFAAGGPGMFEAGVQAGNVTAQQQDFFSSE
+AFMNQGAPYIAAVLAYAIGNQTIAQRLFAVREDLIKPTFITATVGYGGTVIGVGMIGVMA
+LYLGVQPLDGDVNNLLPQMVSSYLPLLVVALAFLMIIGSLSSTADSDLSALSSIVMTDVY
+GQSVGRENANPKTMLLIGRVTMIVATAAALYFATARFNILDLLVFVGALWGCLVFPVIAS
+FYWRKVTNAAFTVGVLAALAVFLPVRFEWIPLTGAWALVVEALAILGVGVVLGIMAFGFF
+GLRAAVVVGALATAATAFVGFGFLRDYATLSGSLVAYAVSFLVCWGMSVRSGQDFDFDRI
+ARVTGDFDPATDDAADRPVAQPAGARAS
+>3_799
+MSVLAALAVFLPVRFEWFPLEGAWAFVVETLAILGVGVALGIMCFGFFGLRPAVVVGAIA
+SVVMLFLGYGFLRDYATLTGSLVDYAVSFLVCWGLPVRSGQDFDFDQIARVTGDFDPATE
+DLPQVERVAASVS
+>4_1841
+MPPSQDAASLTQLGVIGVILLVALFYGGTMIMSVAISKKKENADAYMTAGNRIGFGVSAA
+SMTATWIWAASMYASVTAGYTYGVSGPLHYGLWGALMILFIYPFGRRIRAVAPRAHTLAE
+VMYARHGRSSQLMLAGSNVLGSVISLTSNFIAGGALISLLSPLSFGAGILIVAAGVLLYT
+LWSGFRASVLTDFAQVMAMLGATVIIIPAVFFAAGGPDMFQTGVEAGHVTAQQQSFFSSD
+AFMNQGAPYIAAVLAYAIGNQTIAQRLFAVREDLIKPTFITATLGYGGTVIGVGMLGVMA
+LYLGVEPLDGDVNNLLPQMVADHLPLALVALAFLMIIGSLSSTADSDLSALSSIVMTDVY
+GQSVGRQNADPKTMLLIGRITMIVATAAALYFATAKFDILDLLVFVGALWGCLVFPVIAS
+FYWGRITNVAFTASVLAALAVFLPVRFEWIPIEGAWAFVVETLAILGVGVVLGIMCFGFF
+GLRPAVVVGAIASVVMLFLGYGFLRDYATLTGSLVAYAVSFLVCWGLSVRSGQDFDFDRI
+ARVTGDFDPATEDLPQVERASAPAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000166.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000166.fa
new file mode 100644
index 0000000000000000000000000000000000000000..454da8fee87edcd5d6f9bf64d226d9915d91fc0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000166.fa
@@ -0,0 +1,25 @@
+>0_2107
+MSPSPSDSARTPTVTAGEVIRVSAVVLARPDRRVLTVRKAGTAMFMFPGGKHLPGEAPVD
+TAVREVAEETGLRLRPDELTRLGAWDTAAANEPGAALHSEVFALWRPVARHEVPEPTDEI
+VALHWMDPAAPAAPGGHGVAPLLHPVLAAVAATPPF
+>1_1832
+MSPSPSDSSRTPTVAAGEVIRVSAVVLARPDRRVLTVRKAGTAMFMFPGGKHVPGEAPVD
+TAVREVAEETGLRLRPDELTRLGAWDTAAANEPGAALHSEVFALWRPVARHEVPEPTDEI
+VELHWMDPAAPAAPGGHGVAPLLHPVLAAVAAAPPF
+>2_566
+MSPSPSGSVPSSSSVSAESRGMGAAAPGQAAVPGETGAAAAVETIRVSAVVLARPDRRVL
+TVRKAGTTMFMFPGGKHLPGEDPLDTAVREVAEETGLRLRPDELTRLGAWDTDAANEPGA
+ALHSEVFALWRPVARHETPAPTDEIVELHWMDPAAPAAPAGHQVAPLLVAVLAAVAKNPP
+F
+>3_493
+MTAPAARSDEPAEIRVSAVVIARPDRRVLTVRKAGTAVFMFPGGKHEPGETPLETAVRET
+REETGLRIRPDELVHLGAWDTPAANEPGMALHSEVFALWRPMARHEVPAADDEIAELHWM
+DPAAPAAPAGAGVAPLLLPVLARVAAQPLF
+>3_1863
+MAAPDFVLSLREHVGHAPLWLSGVKAVALRAGDREVLLVRRADDGRWTLPAGILEPGEEP
+ADAAVREVAEETGVRCAPRRLAGVGTTAGAVYPNGDRARYLDVVLVLDETGGHAHVADDE
+NLEVGWFSVDGLSDLPPLHARALSWALEDGPARFVAGGDVLP
+>4_2053
+MSPSPSDSARTPTVAGGEVIRVSAVVLARPDRRVLTVRKAGTAMFMFPGGKHLPGEAAVD
+TAVREVAEETGLRLRPDELTRLGAWDTAAANEPGAALHSEVFALWRPVARHEVPEPTDEI
+VELHWMDPAAPAAPGGHGVAPLLHPVLAAVAAAPPF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000167.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000167.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab70050978632af21c74ef9659d0235507d86ea4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000167.fa
@@ -0,0 +1,66 @@
+>0_2123
+MDFSAPLDPTPAAPPAADAPPADVVARLQAELPGRVDVSAAALEAARADRSGHRSPAAPL
+AVVRARTVEDVQAACRIAHGTRTPLVTRGAGTGLAGGAVAGAGEIVLDMTAMDRILEVSP
+ADRVAVVEPGILNGALNAALAEHGLWWAPDPASKDISTVGGNIAMNAGGLLCAKYGVTRE
+AVLGLDVVLADGTLLRLGHRTVKGVTGYDLVALMIGSEGTLGVIVGATLALRPAVRGVPV
+TLGGFFPDVVAGAAAAEAITGAGHVPALMELMDEATLAAVRAHAGPERGAALPESGAFLL
+VQADGAGAEADGEAMAALMRTHGGDVTVTVDPAEGEALMALRRTAFPALERLGTPLVEDV
+AVPRSRMAEMFARIREIEARTGVAIPTTAHAGDGNLHPILLFGAAAQVGGAAEDAASIPA
+DVWEAAGELFRAGLELGGTLTGEHGVGLLKRAFLRDELGDAQHDLQQRIKAVFDPHGILN
+PGKVFTP
+>1_1848
+MDFSAPLAPAAPLAPAPAADAPPADVVARLQAELPGRVDVSAAALQAARADRSGHRSPAA
+PRAVVRARTVEDVQAACRIAHGTRTPLVTRGAGTGLAGGAVAGAGEIVLDMTAMDRILEV
+SPADRVAVVEPGILNGALNAALAEHGLWWAPDPASKDISTVGGNIAMNAGGLLCAKYGVT
+REAVLGLDVVLADGTLLRLGHRTVKGVTGYDLVALMIGSEGTLGVIVGATLALRPAVRGV
+PVTLGGFFPDVVAGAAAAEAITGAGHVPALMELMDEATLAAVRAHAGPERGAALPESGAF
+LLVQADGAGAEADGEAMAALMRAHGGDVTVTVDPAEGEALMALRRTAFPALERLGTPLVE
+DVAVPRSRMAEMFARIREIEARTGVAIPTTAHAGDGNLHPILLFGAAAQVGGAAEDAASI
+PADVWEAAGELFRAGLELGGTLTGEHGVGLLKRAFLRDELGDAQHDLQQRIKAVFDPHGI
+LNPGKVFTP
+>2_548
+MDSPASPGAPHPETTRPADVVARLQAALPGRVDVSPPPSRPPARDRSGHRSPAVPLAVVH
+AASVADVQAVCRLAHETRTPLVTRGAGTGLAGGAVAGAGEVVLDVMGMDRILEVSPADRV
+AVVEPGILNGALNAALAEHGLWWAPDPASKDISTVGGNIAMNAGGLLCAKYGVTREAVLG
+LDVVLADGTLMRLGHRTVKGVTGYDLTALMIGSEGTLGVIVGATLSLRPAVRGTQVTLGG
+FFPDVVAGAAAAEAVTGAGHVPALMELMDEVTLAAVRADAGPERGAALPESGAFLLVQAD
+GAGAEEDGAAMADLMRAHGGDVTVTADHAEGEALMALRRTAFPALERLGTPLVEDVAVPR
+SRMAEMFARIRDIEARTGIPIPTTAHAGDGNLHPILLFGAAAQVGGAAEDATSIPADVWE
+AAGELFRAGLELGGTLTGEHGVGLLKRAFLRDELGDAQHALQAKIKAVFDPHGILNPGKV
+FTP
+>3_474
+MTCIISVSPDDVLHRLRAALGDAVVTDPAALEPLRADRSGHRSPGAPLAAVRARTVEDVQ
+AACRIAHATGTPLVTRGAGTGLAGGAVAGPGQVVLDLSGMDRILEVAPEDRVAVVEPGVL
+NGALNRALEPHGLWWAPDPASKEISTVGGNIAMNAGGLLCAKYGVTREAVLGLAVVLADG
+TLMRLGHRTVKGVTGYDLTALMIGSEGTLGVIVEATLALRPLPEGAVHTLGAFFPDVAVG
+ARAAAAITGAGHVPAIMELMDEATLAAVRAHVSADDAARLPETGAFLLVQADGPGADEQA
+AAMAELIRSAGGEVTVTADPAEADRLVSLRRTAFPALEALGTPLVEDVAVPRSRMPEMFA
+RIREIEAETGLRIPTSAHAGDGNLHPVVLFGEPSRVGGEDGAQEAIPAEVWAAAGMLFRA
+GLELGGTLTGEHGVGLLKRAFLKEELGEAQHGLQERIKAVFDPRGILNPGIVFTP
+>4_158
+MLRSLEDVLTKPGQVSGRALDRHAAAADASHFLLVPEAVVTPTDAAEVGALMRASAAQGV
+SLTFRSGGTSLSGQAVTDSVLVDVRKNFRDIEVLDEGARVRVRPGATVRQVNARLARHGR
+RLGPDPASEAACTIGGVVANNSSGMNCGITENTYQTLESMTLVLPSGTVIDTAAPDADGI
+LRHHEPHLYRGLAQLADRVRSDSASVATVRRQFSMKNTMGYGLNALLDFDTPAQILAHLA
+IGSEGTLGFVAEAVFRTVVRPTHSATALLVFEELQAANEALPALVDSRAATVELLDATSL
+RVGQRLTGTPPIVRDLRVQDHAALLVEYSATTAEQLEELRQHGEALTGRIGLSQPAGFTT
+DADARAALWHLRKGLYASVAGARPQGTTALLEDIVVPVLALGRTCTALTQLFDRYDYRDS
+VIFGHAKDGNVHFMLTDDFADPARLQRYSDFTEDMVDLVLGEGGSLKAEHGTGRVMAPYV
+RRQYGDELYGVMREIKQLCDPGGVLNPGVLLNDDPQAHLRHIKAEPSVAEEVDRCVSCGY
+CEPVCPSRDLTLTPRQRIVTLRAIRSARLAGDEALAQSLEEDYDYAAVQTCAVDGMCQTA
+CPVEINTGDLVKRLRRQETGAVAQAGWNLAAQHWGTASIVAGRALDLAAKLPAAATITAN
+QLVRRIAGADSVPLYSPELPRGGGRRRRPAPVGEPVAVYFPACVSAMFGPAQPGTGAPGA
+AGVQDSVLALAQRAGVELLVPSDIDALCCGTPWSSKGKHTGQETITGRTIAALRRDSDHG
+RLPIVCDASSCTEGLRHALEVEVPPAGQQPLRILDAVEFTAEHLLPRLPEPRRIPSLTLH
+PTCSSTRMGLNPALARVAEAIAEDVQIPDDWGCCAFAGDRGLLHPELTASATARQAEQVQ
+AIDASAHASCNRTCELGMSRATGYPYSHVLELLNQSTIAGG
+>4_2069
+MDSSAPLDPTRAAPPAADAPPADVVARLQAELPGRVDVSAAALEAARADRSGHRSPAAPL
+AVVRARTVEDVQAACRIAHGTRTPLVTRGAGTGLAGGAVAGAGEIVLDMTAMDRILEVSP
+ADRVAVVEPGILNGALNAALAEHGLWWAPDPASKDISTVGGNIAMNAGGLLCAKYGVTRE
+AVLGLDVVLADGTLLRLGHRTVKGVTGYDLVALMIGSEGTLGVIVGATLALRPAVRGVPV
+TLGGFFPDVVAGAAAAEAITGAGHVPALMELMDEATLAAVRAHAGPERGAALPESGAFLL
+VQADGAGAEADGEAMAALMRTHGGDVTVTVDPAEGEALMALRRTAFPALERLGTPLVEDV
+AVPRSRMAEMFARIREIEARTGVAIPTTAHAGDGNLHPILLFGAAAQVGGAAEDAASIPA
+DVWEAAGELFRAGLELGGTLTGEHGVGLLKRAFLRDELGDAQHDLQQRIKAVFDPHGILN
+PGKVFTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000170.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000170.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f21b4d9b3511fe65be88fefba82f25d941335cb8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000170.fa
@@ -0,0 +1,42 @@
+>0_2242
+MAPTAQDQSVHNVVIVGSGPAGYTAAIYTARAELSPVLVAGAVTAGGELMNTTEVENFPG
+FPEGVQGPELMANLEAQARRFNTEVVYDDVVQADLTSNPKVLTLGDGTQLRTHAVILTTG
+SAYRKLGVPGEERLSGHGVSWCATCDGFFFREQEIAVVGGGDSAMEEALFLTKFASKVTV
+LVRKDELRASKVMAHRAMENEKIEFRWNTEVTEVTGDDKVNTLRLRDTRTGEASTLDVTG
+LFVAIGQDPRTDLVQGQVELTEHGTIRIDHPSSRTSQPGVFAAGDVTDHTYRQAVTAAGS
+GCVAAQDVEHYLATVADVEEAAPAGPESDANPA
+>1_1946
+MAPTAQDPSVHNVVIVGSGPAGYTAAIYTARADLSPVLVAGAVTAGGELMNTTEVENFPG
+FPEGVQGPELMANLEAQARRFDTEVVYDDVVQADLTSNPKVLTLGDGTQLRTHAVILTTG
+SAYRKLGVPGEERLSGHGVSWCATCDGFFFREQEIAVVGGGDSAMEEALFLTKFASKVTV
+LVRKDELRASKVMAHRAMENEKIEFRWNTEVTEVTGDDKVNTLRLRDTRTGEASTLDVTG
+LFVAIGQDPRTDLVQGQVELTEHGTIRIDHPSSRTSQPGVFAAGDVTDHTYRQAVTAAGS
+GCVAAQDVEHYLATVADVEEAAPAGPESDANPA
+>2_416
+MAPTAQDQSVHNVVIVGSGPAGYTAAIYTARAHLQPVLVAGSVTAGGELMNTTEVENFPG
+FPEGIQGPELMANLEAQARRFDTEVLYEDVVKADLTASPKVLTLGDGTELRAHAVILTTG
+SAYRKLGVEGEERLSGHGVSWCATCDGFFFREQEIAVVGGGDSAMEEALFLTKFASKVTV
+LVRKDELRASKVMARRALENEKIEFRWNTEVAEVIGGEKVQTLRLRDTQTGEESTLDVTG
+LFVAIGQDPRTDLVQGQLELTEHGTIRIEHPSSRTSLPGVFAAGDVTDHTYRQAITAAGS
+GCVAAQDVEHYLATVADVEEAAPAGPDSDANPA
+>2_721
+MSTTSTDTTSTEQATDQLIIIGSGPAGYTAAIYAARAGLAPRVIAGSVTHGGALMNTTEV
+ENFPGFPGGIQGPELMAGLAEQAARFGAVIEYDDADTVQLKQHLKEVTTLAGKTYRAPAV
+IVATGSAYRELGLPEEKKLSGHGVSWCATCDGFFFREQDIIVVGGGDSAMEEALFLTRFA
+KSVTVVVRRDALRASKIMAARAKDNEKIRFAYNSAVTAIHGTDKVTGVTLADTITGDTRE
+VAATGVFVAIGHLPRTELVAGQLDLDDEGYIVVDARTTHTNLSGVFACGDAVDHRYRQAI
+TAAGTGCAAALDAERYLAALHDAYSIATALVEEPTHG
+>3_369
+MTTAEQDQQVRNVAIIGSGPAGYTAAIYTARANLSPVLLAGSVTAGGELMNTTEVENFPG
+FPEGIQGPELMANLEAQARRFDTEVVYDDVVQADLTSDPKVLTLGDGSQIRAHAVIMTTG
+SAYRELGVEGEKRLSGHGVSWCATCDGFFFREQEIAVAGGGDSAMEEALFLTKFASKVHV
+LVRRGELRASKIMAQRALEEPKIEFHWNTEVAEVQGDDKLSTLTLRDTVTGEESSLEVTG
+LFVAIGHDPRTDLVKGQLELTEHGTIRIDHPSSRTSVPGVFAAGDVTDHTYRQAITAAGS
+GCVAAQDVEHYLATVADVAEAAPAAPDSDSVA
+>4_2184
+MAPTAQDQSVHNVVIVGSGPAGYTAAIYTARADLSPVLVAGAVTAGGELMNTTEVENFPG
+FPEGVQGPELMANLEAQARRFNTEVVYDDVVQADLTSNPKVLTLGDGTQLRTHAVILTTG
+SAYRKLGVPGEERLSGHGVSWCATCDGFFFREQEIAVVGGGDSAMEEALFLTKFASKVTV
+LVRKDELRASKVMAHRAMENEKIEFRWNTEVTEVTGDDKVNTLRLRDTRTGEASTLDVTG
+LFVAIGQDPRTDLVQGQVELTEHGTIRIDHPSSRTSQPGVFAAGDVTDHTYRQAITAAGS
+GCVAAQDVEHYLATVADVEEAAPAGPESDAVPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000174.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000174.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff2cf5a99802a80ccc57bdeaa6e40e155592f0f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000174.fa
@@ -0,0 +1,50 @@
+>0_0
+MVADQAVLSSWRSVVGSLEDDARVSARLMGFVYLAQPQGLIGNTLLLAVPNETTRETLQG
+TQVADALTDALTQEFREEILLAISIDANLQPPRTPSSEARRSSLAGGPSGAAAPDVELPP
+AATAATSRRAVAEELPGFRIEPPADVVPAANAAPNGNGKPTPAPPSTSAETSRLNDRYHF
+ETFVIGSSNRFAHAAANAVAEAPAKAYNPLFIYGESGLGKTHLLHAIGHYARRLYPGLRV
+RYVNSEEFTNDFINSIRHDEGASFKQVYRNVDILLIDDIQFLADKEATVEEFFHTFNTLY
+NNNKQVVITSDLPPKQLSGFEDRLRSRFEWGLITDIQPPDLETRIAILRKKAEAEGLVAP
+PEALEYIASRISTNIRELEGALIRVTAFASLNRQTVDIELAEHVLKDLITDETAHEITPE
+LILHATGEYFNLTLEELTSKSRTRTLVTARQIAMYLLRELTEMSLPKIGQVLGGRDHTTV
+IHADRKIRELMAERRTIYNQVTELTNEIKRKQRGA
+>1_1956
+MVADQAVLSSWRSVVGSLEDDARVSARLMGFVYLAQPQGLIGNTLLLAVPNETTRETLQG
+TQVADALTDALTKEFREEILLAISIDANLQPPRTPSSEARRSSLAGGPSGAAAPDVELPP
+AATAATSRRAVAEELPGFRIEPPADVAPAATAAPNGNGNGKPTPAPPSTSAETSRLNDRY
+HFETFVIGSSNRFAHAAANAVAEAPAKAYNPLFIYGESGLGKTHLLHAIGHYARRLYPGL
+RVRYVNSEEFTNDFINSIRHDEGASFKQVYRNVDILLIDDIQFLADKEATVEEFFHTFNT
+LYNNNKQVVITSDLPPKQLSGFEDRLRSRFEWGLITDIQPPDLETRIAILRKKAEAEGLV
+APPEALEYIASRISTNIRELEGALIRVTAFASLNRQTVDIELAEHVLKDLITDETAHEIT
+PELILHATGEYFNLTLEELTSKSRTRTLVTARQIAMYLLRELTEMSLPKIGQVLGGRDHT
+TVIHADRKIRELMAERRTIYNQVTELTNEIKRKQRGA
+>2_405
+MVADQAVLSSWRSVVGALEDDARVSARLMGFVYLAQPQGLIGNTLLLAVPNETTRETLQG
+AQVAEALTDALTAEFREEILLAISIDANLQPPRAPEPEARRSALAGEPVTPAAPAAPGPE
+QSAGTGEPSRRAVAEELPGFRTEPPADVVPPEAAGAQAGKPTPAPPSTSAETSRLNDRYH
+FETFVIGSSNRFAHAAANAVAEAPAKAYNPLFIYGESGLGKTHLLHAIGHYARRLYPGLR
+VRYVNSEEFTNDFINSIRHDEGASFKQLYRNVDILLIDDIQFLADKEATVEEFFHTFNTL
+YNNNKQVVITSDLPPKQLSGFEDRLRSRFEWGLITDIQPPDLETRIAILRKKAEAEGLVA
+PPEALEYIASRISTNIRELEGALIRVTAFASLNRQSVDIELAEHVLKDLITDETAHEITP
+ELILHATGEYFNLTLEELTSKSRTRTLVTARQIAMYLLRELTEMSLPKIGQVLGGRDHTT
+VIHADRKIRELMAERRTIYNQVTELTNEIKRKQRGA
+>3_359
+MAADQELLDRWREVVTALDDDPRVSARLMGFVYLAQPQGLIGNTLLLAVPNETTRETLQG
+AQVADALTDALTAVFREEILLAISIDSSLQPPRTPSADDRRAEELPDLAAARAETSPAPA
+PAAGMHRGVAEELPGMPAPREEPAPSRAAAPAAGAPTPAPPSTSSETSRLNDRYHFDTFV
+IGSSNRFAHAAANAVAEAPAKAYNPLFIYGESGLGKTHLLHAIGHYARRLYPGLRVRYVN
+SEEFTNDFINSIRHDEGASFKAVYRNVDILLIDDIQFLADKEATVEEFFHTFNTLYNNNK
+QVVITSDLPPKQLSGFEDRLRSRFEWGLITDIQPPDLETRIAILRKKAEAEGLVAPPEAL
+EYIASRISTNIRELEGALIRVTAFASLNRQPVDIELAEQVLKDLITDDATQEITPELIVH
+TTAEYFNLTIDELTSKSRTRTLVTARQIAMYLLRELTEMSLPKIGQELGGRDHTTVMHAD
+RKIRELMAERRTIFNQVTELTNEIKRKQRGA
+>4_0
+MVADQAVLSSWRSVVGSLEDDARVSARLMGFVYLAQPQGLIGNTLLLAVPNETTRETLQG
+TQVADALTDALTKEFREEILLAISIDANLQPPRTPSSEARRSSLAGGPAAAAVPDVELPP
+AATAATSRRAVAEELPGFRIEPPADVAPAATAAPSGNGKPTPAPPSTSAETSRLNDRYHF
+ETFVIGSSNRFAHAAANAVAEAPAKAYNPLFIYGESGLGKTHLLHAIGHYARRLYPGLRV
+RYVNSEEFTNDFINSIRHDEGASFKQVYRNVDILLIDDIQFLADKEATVEEFFHTFNTLY
+NNNKQVVITSDLPPKQLSGFEDRLRSRFEWGLITDIQPPDLETRIAILRKKAEAEGLVAP
+PEALEYIASRISTNIRELEGALIRVTAFASLNRQTVDIELAEHVLKDLITDETAHEITPE
+LILHATGEYFNLTLEELTSKSRTRTLVTARQIAMYLLRELTEMSLPKIGQVLGGRDHTTV
+IHADRKIRELMAERRTIYNQVTELTNEIKRKQRGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000191.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000191.fa
new file mode 100644
index 0000000000000000000000000000000000000000..65ae73f08a094d4b8c764219b16c3d60f8b8e679
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000191.fa
@@ -0,0 +1,46 @@
+>0_19
+MTEVISPARPRRNIELVLLLAALTIALGADLLGMIGTDAPLDSTAWVPLGIFGAATLVLH
+VVLRLRAPYADPFMLPITALLNGLGLAMIHRLSQDAAMANPTSQLVWSVLAVLVASALVF
+LVRDHRVLRRWPYLFLAASGVLLLLPLVPGLGLSMYGARIWIDVGFGTFQPGEIAKITLA
+IFFAGYLSANRDLILLAGRRVGPVTFPRARDLGPLLAGWLLALGVLVFQRDLGSALLFFG
+MFMAMLYIATSRASWILLGLGLIAFGAALAFLFMPHVTARFEIWLRAFDPEIYHRDFGGS
+YQVVQGLFAMASGGLMGTGLGAGNPTQVPLSFSDMILTAIGEELGFVGLAAVLVLYLLLV
+TRMMRAALGVRDAFGKVLASGLAFTMAWQVFVVMGGVTLVLPLTGLTTPFLAAGGSSLLA
+NWIIVGLVLRISNAARRPVVVDGMVNASGPGAGHLDPGTALPAAAVPPGGGEER
+>1_1988
+MTEVISPARPRRNIELVLLLAALAIALGADLLGMIGTDAPLDSTAWVPLGVFGAATLVLH
+VVLRLRAPYADPFMLPITALLNGLGLAMIHRLSQDAAMANPTSQLVWSVLAVLVASALVF
+LVRDHRVLRRWPYLFLAASGVLLLLPLVPGLGLSMYGARIWIDVGFGTFQPGEIAKITLA
+IFFAGYLSANRDLILLAGRRVGPVTFPRARDLGPLLAGWLLALGVLVFQRDLGSALLFFG
+MFMAMLYIATSRASWILLGLGLIAFGAALAFLFMPHVTARFEIWLRAFDPEIYHRDFGGS
+YQVVQGLFAMASGGLMGTGLGAGNPTQVPLSFSDMILTAIGEELGFVGLAAVLVLYLLLV
+TRMMRAALGVRDAFGKVLASGLAFTMAWQVFVVMGGVTLVLPLTGLTTPFLAAGGSSLLA
+NWIIVGLVLRISNAARRPVVVDGMVNASGPGAGHLDPGTALPAAAVPPGGGEER
+>2_358
+MTEVISPARPRRNIELVLLLAALAIALGADLLGTIGTDAALDSTAWVPLGIFGAATLVLH
+VVLRLRAPYADPFMLPITALLNGLGLAMIHRLSQDAAMANPTSQLVWSVLAIVVASALLF
+LVRDHRVLRRWPYLFLAASGVLLLLPLVPGLGLSMYGARIWIDVGFGTFQPGEIAKITLA
+IFFAGYLSANRDLILLAGRRVGPVTFPRARDLGPLLAGWLLALGVLVFQRDLGSALLFFG
+MFMAMLYIATSRASWILLGLGLIAFGAALAFLFMPHVTARFEIWLRAFDPEIYHRNFGGS
+YQVVQGLFAMASGGLMGTGLGAGNPTQVPLSFSDMILTAIGEELGFVGLAAVLVLYFLLV
+TRMMRAALGVRDGFGKVLASGLAFTMAWQVFVVMGGVTLVLPLTGLTTPFLAAGGSSLLA
+NWIIVGLVLRISNAARRPVVVDGMVNASGPGAGHLDPGTALPAAAVPMRGGEAR
+>3_341
+MTEVISPPRPRRATELMLLLGAVALTLGADLLGTYTTTGALESTAWVPLTVFGCASLVLH
+AVLRLRARYADPFILPIATLLNGLGIAMIHRLSADTAAARPTSQLAWSVLAVLVAAALVF
+LVRDHRMLRRWPYVFLAVSGVLLLLPLVPGLGLSANGARIWINVGVGTFQPGEIAKITLA
+IFFAGYLSTNRDLILLAGRRVGPMTFPRMRDLGPLLVAWAVAMGVLVFQRDLGSALLFFG
+MFMAMLYIATSRASWVLLGLSLVAVGAAVAFLFLPHVTARFEIWLNAFDPEIYRRDFGGS
+YQVVQGLFAMASGGLLGTGLGGGNPTQVPLSFSDMILAAIGEELGLVGLSAVLVLYLLLV
+TRMARAALGVRDAFGKVLAAGLAFTMAWQVFVVMGGVTLVLPLTGLTTPFLAAGGSSLLA
+NWIILGLVLRISHAARRPAVVDGMVNASGPGAGHLDPGAALPEPAQRPGPWRAAAPAGGE
+AR
+>4_19
+MTEVISPARPRRNIELVLLLAALAIALGADLLGMIGTDAPLDSTAWVPLGIFGAATLVLH
+VVLRLRAPYADPFMLPITALLNGLGLAMIHRLSQDAAMANPTSQLAWSVLAIVVASALVF
+LVRDHRVLRRWPYLFLAASGVLLLLPLVPGLGLSMYGARIWIDVGFGTFQPGEIAKITLA
+IFFAGYLSANRDLILLAGRRVGPVTFPRARDLGPLLAGWLLALGVLVFQRDLGSALLFFG
+MFMAMLYIATSRASWILLGLGLIAFGAALAFLFMPHVTARFEIWLRAFDPEIYHRDFGGS
+YQVVQGLFAMASGGLMGTGLGAGNPTQVPLSFSDMILTAIGEELGFVGLAAVLVLYLLLV
+TRMMRAALGVRDAFGKVLASGLAFTMAWQVFVVMGGVTLVLPLTGLTTPFLAAGGSSLLA
+NWIIVGLVLRISNAARRPVVVDGMVNASGPGAGHLDPGTALPAAAVPPGGGEER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000192.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000192.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5974f7ea4bb1000daeeee887f30da96200360c17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000192.fa
@@ -0,0 +1,54 @@
+>0_20
+MTLVLRYAARSDVGRVRAKNDDSAYVGRHLVVLADGMGGHVGGDVASASTVLDLAPLDAV
+GYEDPATVLPDEIQNANLILNELVHANPKLAGMGTTCTAALLAGTTLHIAHIGDSRAYRL
+ANGEFSQVTTDHTFVQKLVDEGRLEAGEAPFHPNKNVLMRVLGDVDASPELDVFEVPVAP
+GERWLFCSDGLTDVVSPEKIHEVLRDSEALNQAVDTLVDLTLKGGAPDNVTVVAFEIAEG
+TAEELAPVPDVHLSEQALAAAHPPEVGPVSGLLLREDLDARPHLLVGAASNAVRTDRIPV
+VTRSSTRRRAAALLGETPVPENRPRRTAAVLTDGPDPDVAARPDPSAPPAAPRGTAAAVG
+SSSAATPAATAADQPSDEAAEASATAPTPAPATSGPAGGPEDGAARRRRGKDDRPVQYRR
+GWFIPVFTTLLALTLAAVAVWGYLWTQTQYYVGANDGRIAVFKGVSQRLGPLELSHVDRQ
+TDLPVDALPAYARDRVNAGMPARDVDHAEQIVAELRDSLHPNAPAPAGEPSERARPSTTP
+SSSSARPSDASGSTAPTSPASSPSATGGEAP
+>1_1989
+MTLVLRYAARSDVGRVRAKNDDSAYVGRHLVVLADGMGGHVGGDVASASTVLDLAPLDAV
+GYEDPATVLPDEIQNANLILNELVHANPKLAGMGTTCTAGLLAGTTLHIAHIGDSRAYRL
+ADGEFSQVTTDHTFVQKLVDEGRLEAGEAPFHPNKNVLMRVLGDVDASPELDVFEVPVAP
+GERWLFCSDGLTDVVPPEKIHEVLRDSEALNQAVDTLVDLTLKGGAPDNVTVVAFEIAEG
+TAEELAPVPDVHLSEQALAAAHPPEVGPVSGLLLREDLDARPHLLVGAASNAVKTDRIPV
+VTRSSTRRRAAALLGETPVPENRPRRTAAVLTDGPDPAAAPRPDASVPPAAPSGTAAAAG
+SSSAATPAATAADHPSDEAAEPMTTAPTPAPATAGPAGGPEDGAARRRRGKDDRPVQYRR
+GWFIPVFTTLLALTLAAVAVWGYLWTQTQYYVGANDGRIAVFKGVSQRLGPLELSHVDRQ
+TDLPVDALPAYARDRVNAGMPARDVDHAEQIVAELRDSLHPNAPAPAGEPSERARPSTTP
+SSSSARPSDASGSTAPTSPASSPSATGGEAP
+>2_357
+MTLVLRYAARSDVGRVRAKNDDSAYVGRHLVVLADGMGGHVGGDVASASTVLDLAPLDAV
+GYEDPATVLPDEIQNANLILNELVHANPKLAGMGTTCTAGLLAGTTLHMAHIGDSRAYRL
+ADGEFSQVTTDHTFVQKLVDEGRLEAGEAPFHPNKNVLMRVLGDVDASPELDVFEVPVAP
+GERWLFCSDGLTDVVSSEKIHEVLRDSEALNQAVDTLVDLTLKGGAPDNVTVVAFEIAEG
+TAEEMAPVPDVHLTEQALAAAHPPEVGPVSGLLLREDLDARPHLLVGAASNAVKTDRIPV
+VTRSSTRRRAAALLGETPVPENRPRRTAAVLTDGPDRDAAPRPDASAPPAAPSGTAAAAG
+SSSAAAPTATVADHPSDEAAEVSTRAATPAPATAGPAGGSQDGAARRRRGKDDRPVQYRR
+GWFIPVFTTLLALTLAAVAVWGYLWTQTQYYVGANDGRIAVFKGVSQRLGPLELSHVDRQ
+TDLPVDALPVYARDRVNAGMAARDVDHAEQIVAELRDSLHPDAPAPAGEPSERAQPSTTP
+SSSSARPSDASGSAAPTSPTASPSATGGEAP
+>3_340
+MTLVLHHAARTDVGRVRSKNDDSAYAGRHLAVLADGMGGHVGGDVASASTVLDLAHLDDV
+GYEDPATVLPDEIQNANLVLTSLVHANPKLAGMGTTCTAGLLAGEVLHMAHIGDSRAYRL
+KDGEFTQVTRDHTFVQKLVDEGRLEAAEAQFHPNKNVLMRVLGDVDASPELDVFEVPVAP
+GERWLLCSDGLTDVLSVERIRELIEPPATLAEAADALVAHTLRGGAPDNVTVVVFDVAEG
+SPEELEPAGEVHLSDEALAAAHPADRGPVSGRLLAEELDARPHELVGAADAAVHSDRIPV
+VTRSATRRRAGVLLGESPVPENRPRRTAAHLTAPNASDVDDAPAAPLTAAASPIETPAPA
+DAATETPAVDAPAPAPGPEVDPADADAAPAPAADPAPAHAVETGRTSRRRRRDRPVEYRR
+GWFIPVFTALLALILVVVAVWSYLWTQTQYYVGEDAGSVAVFQGVPQQLGPLELSHLDHT
+TDIPLDRLPAYAQERVGRGMAATDRAHADQIVEELRTVSDTAAKGGGTP
+>4_20
+MTLVLRYAARSDVGRVRAKNDDSAYVGRHLAVLADGMGGHVGGDVASASTVLDLAPLDAV
+GYEDPATVLPDEIQNANLILNELVHANPKLAGMGTTCTAGLLAGTTLYMAHIGDSRAYRL
+VDGEFCQVTTDHTFVQKLVDEGRLEAGEAPFHPNKNVLMRVLGDVDASPELDVFEVPVAP
+GERWLFCSDGLTDVVSPEKIHEVLRDSEALNQAVDTLVDLTLKGGAPDNVTVVAFEIAEG
+SAEELAPVPDVHLSEQALAAAHPPEVGPVSGLLLREDLDARPHLLVGAASNAVKTDRIPV
+VTRSSTRRRAAALLGETPVPENRPRRTAAVLTDGPGPAADAAPRPDASAPPAAPSGTAAA
+AGSSAAATPAATAADRPSDEAAEASTTAATPSPVTSGPAGGSEDGAARRRRGKDDRPVQY
+RRGWFIPVFTTLLALTLAAVAVWGYLWTQTQYYVGANDGRIAVFKGVSQRLGPLELSHVD
+RQTDLPVDALPAYARDRVNAGMAARDVDHAEQIVGELRDSLHPDAPAPAGEPSERARPST
+TPSSSSARPSDASGSAAPTSPASSPSATGGEAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000198.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000198.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a0451e96a652ec2846a1e886b114e40ea6c907a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000198.fa
@@ -0,0 +1,29 @@
+>0_35
+MMASKTPHQNVTFDLPTKDAGQDGDRTGHGYLALPASGKGPGVIVIQEWWGLVDHIKDVC
+DRLADLGFVALAPDLYGGWIAHDGDEAGEMMQNLPAEEGARQLAGAVDWLLARDEVTSQT
+VGAIGFCMGGGFVLALAAQQGDKVSAAVPFYGVGQGVPGDFSGVTAAVQGHYAEQDDSFP
+VEDARRQEQQIREESGADVEYFYYDAPHAFHNDENPQGNYRPEAAALAWDRAVSFLKEKV
+R
+>1_1999
+MMASKTPHQNVTFDLPTKDAGQDGDRTGHGYLALPASGKGPGVIVIQEWWGLVDHIKDVC
+DRLADLGFVALAPDLYGGWIAHDGDEAGEMMQNLPAEEGARQLAGAVDWLLARDEVTSQT
+VGAIGFCMGGGFVLALAAQQGDKVSAAVPFYGVGQGVTGDFSGVTAAVQGHYAEQDDSFP
+VEDARRQEQQIREESGADVEYFYYDAPHAFHNDENPQGNYRPEAAALAWDRAVSFLKEKV
+R
+>2_346
+MMASKTPHQNTTFDLPSKDASHDGDQVGHGYLALPESGSGPAVIVIQEWWGLVDHIKDVC
+DRLAAEGFVALAPDLYGGWIAHDGDEAGEMMQKLPAEEGARQLAGAVDWLLAREEVTSTT
+VGAIGFCMGGGFVLALAAQQGEKVSAAVPFYGVGQGVPGDFAGVKAAIQGHYGEQDSMFS
+VEDAKKQEQQIRDESGAEVEYFYYDAPHAFHNDDDPQGNYRPEAAALAWGRAVAFLKEKV
+R
+>3_288
+MMASKTPHQNVSFPLPTKDAAHGDQTGHGYLALPAAGKGPAVIVIQEWWGLVDHIKDVCD
+RLAEEGFVALAPDLFGGWIAHDGDEAGEMMQNLPAEEGARQLAGAVDWLLARDEVTSSRV
+EAIGFCMGGGFVLALAAQQGDKVSAAVPFYGVGQGVPGSFEGVTAAIQGHYAEQDDFFPV
+EDAKKQERQIREESGAEVEYFYYDAPHAFHNDENPQGNYRPEAAQLAWDRAVSFLKEKVR
+>4_30
+MMASKTPHQNVTFDLPTKDAGQDGDRTGHGYLALPASGKGPGVIVIQEWWGLVDHIKDVC
+DRLADLGFVALAPDLYGGWIAHDGDEAGEMMQNLPAEEGARQLAGAVDWLLARDEVTSQT
+VGAIGFCMGGGFVLALAAQQGDKVSAAVPFYGVGQGVPGDFSGVTAAVQGHYAEQDDSFP
+VEDAREQAQQIREESGADVEYFYYDAPHAFHNDENPQGNYRPEAAALAWDRAVSFLKEKV
+R
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000207.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000207.fa
new file mode 100644
index 0000000000000000000000000000000000000000..deb0d3f9bfd7cf662c5ef8dd5a5a34c0144c38b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000207.fa
@@ -0,0 +1,50 @@
+>0_50
+MSTQPPGLTTDAPDTPDDDPVREPLPTEALPIAPAGPRPEEPRAAVERLRAAARSRAAHP
+RAVRVRQLKGLKRMLTEHADRFVAALGTDLGKPATEALITEIVSVRSEVDHALLHLTDWM
+EPRPVKLPLALRPASAEVRPRPKGLVLVIGAWNYPVQLALAPVVGALAAGNTVVLSPSEK
+APATAAALRELVPQYLDSALVSVVAGGKECNTALLAEPWDHILYTGGERVGRIVYEAAAK
+TLSPVTLELGGKSPAVVTPSRNTGAMARRIAWAKFTNAGQTCVAPDYVLAVGEAALRQVT
+AELPAALREFYGDDPRASKDYGRLISAEHAERLREMLQADLDAGAELLVGGDVDVAGRYM
+APTVVTGVKPDGALMQEELFGPILPVLTVDTFQDALDFIAERPHPLAAYLFTDRPSYHRA
+FDDQVQAGGLGYDVGLLHAGIATLPFGGIGASGMGAYHGIHGFETFSHLRPSITKSDQVD
+TLKTAYPPYGRMKRALLPKML
+>1_2014
+MSTQPPGLTTDSSDTPDDDPVREPLPTEALPIAPAGPRPEEPRAAVERLRAAARSRAAHP
+RAVRVRQLKGLKRMLTEHADRFVAALGTDLGKPATEALITEIVSVRSEVDHALLHLTDWM
+EPRPVKLPLALRPASAEVRPRPKGLVLVIGAWNYPVQLALAPVVGALAAGNTVVLSPSEK
+APATAAALRELVPQYLDSALVSVVAGGKECNTELLAEPWDHILYTGGERVGRIVYEAAAK
+TLSPVTLELGGKSPAVVTPSRNTGAMARRIAWAKFTNAGQTCVAPDYVLAVGEAALRQVT
+AELPAALREFYGDDPRASRDYGRLISAEHAERLREMLQADLDAGAELLVGGDVDVAGRYM
+APTVVTGVTPDGALMQEELFGPILPVLTVDTFQDALDFIAERPHPLAAYLFTDRPSYHRA
+FDDQVQAGGLGYDVGLLHAGIATLPFGGIGASGMGAYHGIHGFETFSHLRPSITKSDQVD
+TLKTAYPPYGRMKRALLPKML
+>2_329
+MSTQHPGIATDSPVSSDDDLRPGLDAAPVGPAGEDGDDPVREPLPTEALPLAPAGPRPED
+PRAAVVRLRAAARSRAAHPRAVRVRQLKGLKRLLTEGQDRLVAALGQDLGKPATEALMTE
+VVSVRSEVDHALLHLTDWMEPRPAKLPLALRPASAEVRPRPKGLVLIIGAWNYPVQLTLA
+PLVGALAAGNAVVVSPSEKAPATAAALRELVAEHLDSALVSVVEGGKDCNTALLAEPWDH
+ILYTGGERVGRIVYEAAAKTLSPVTLELGGKSPAVVTPSRNTGAMARRIAWAKFTNAGQT
+CVAPDYVLAVGDVAHRQVVEELPGALREFYGADPRASKDYGRLVSAEHAERLRDLLREDL
+DAGAVVLVGGDVDVAGRYMAPTVVTGVRPDGALMREEIFGPILPVLRVDTFQEALDFIAE
+RPHPLAAYLFTDRPSYHRAFDDQVQAGGLGYDVGLLHAGIATLPFGGVGASGIGAYHGVH
+GFETFSHLRASITKSDQVDTLKTAYPPYGWVKRTMIPKML
+>3_268
+MSTQPPGLTTDSPDSPADDPVREPLPTEALPIAPAGPRPEEPRAAVERLRAAARSRAAHP
+RAVRVRQLKGLKRMLTEHADRFVAALGTDLGKPSTEALITEIVSVRSEVDHALLHLTDWM
+EPRPVKLPLALRPASAEVRPRPKGLVLVIGAWNYPVQLALAPVVGALAAGNTVVLSPSEK
+APATAAALRELVPQYLDSALVSVVAGGKDCNTELLAEPWDHILYTGGERVGRIVYEAAAK
+TLSPVTLELGGKSPAVVTPSRNTGAMARRITWAKFTNAGQTCVAPDYVLAVGEAALRQMT
+AELPAALREFYGDDPRASRDYGRLISAEHAERLREMLQADLDAGAELFVGGDVDVAGRYM
+APTVVTGVKPDGALMQEELFGPILPVLTVDTFQDALDFIAERPHPLAAYLFTDRPSYHRA
+FDDQVQAGGLGYDVGLLHAGIATLPFGGIGASGMGAYHGIHGFETFSHLRPSIAKSDQVD
+TLKTAYPPYGRMKRALLPKML
+>4_45
+MSTQPPGLTTDSPDSPADDPVREPLPTEALPIAPAGPRPEEPRAAVERLRAAARSRAAHP
+RAVRVRQLKGLKRMLTEHADRFVAALGTDLGKPATEALITEIVSVRSEVDHALLHLTDWM
+EPRPVKLPLALRPASAEVRPRPKGLVLVIGAWNYPVQLALAPVVGALAAGNTVVLSPSEK
+APATAAALRELVPQYLDSALVSVVAGGKECNTALLAEPWDHILYTGGERVGRIVYEAAAK
+TLSPVTLELGGKSPAVVTPSRNTGAMARRIAWAKFTNAGQTCVAPDYVLAVGEAALRQVT
+AEIPAALREFYGDDPRASKDYGRLISAEHAERLREMLQTDLDAGAELLVGGDVDVAGRYM
+APTVVTGVRPDGALMQEELFGPILPVLTVDTFQDALDFIAERPHPLAAYLFTDRPSYHRA
+FDDQVQAGGLGYDVGLLHAGIATLPFGGIGASGMGVYHGIHGFETFSHLRPSITKSDQVD
+TLKTAYPPYGRMKRALLPKML
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000210.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000210.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa8117828ee472ee5fb81ef74a94606d68ac1394
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000210.fa
@@ -0,0 +1,40 @@
+>0_53
+MAQPEPVRLVPGGAVDRPAEQALLAAAAACDGDVDAMVELLRAASGAPSGEDAAPLDLPL
+TGAGRTREQWELLASVAAQDLSAARVLEPHLDALSILSQAGVPAPAGLLGVYASESGGRT
+PALRPAPDGPDTAWLLDGEKPWCSLADRCAAAVVTGREADGTRRAVLVDLSHPGVAETDS
+AWPALGLAPIRTVGLAFDAVPGSAVGGAEWYLRRPGFAWGGIGVAAVWFGGAVGIARTLR
+NATAARAAAEAEGRGPGPDQIGQAALGRVDRLLHAMAALLARAADDVDAGRLDHGRGMVE
+ADRIRGTVAQLCTEVMDVVGQATGPGPLTGSAAHARAVADLQVYLRQHHGHRDDARLGAA
+LLTGETDGGWTW
+>1_2017
+MAQPEPVRLVPGGAVDRPAEQALLAAAAACDGDVDAMVELLRAASGAASGEDAAPLDLPL
+TGAGRTREQWELLASVAAQDLSAARVLEPHLDALSILSQAGVPAPAGLLGVYASESGGRT
+PALRPAPDGPDTAWLLDGEKPWCSLAGRCAAAVVTGREADGTRRAVLVDLSHPGVAETDS
+AWPALGLAPIRTVGLAFDAVPGIAVGGAEWYLRRPGFAWGGIGVAAVWFGGAVGIARTLR
+NATAARAAAEAEGRGPGPDQIGQAALGRVDRLLHAMAALLARAADDVDAGRLDHGRGMVE
+ADRIRGTVAQLCTEVMDVVGQATGPGPLTGSAAHARAVADLQVYLRQHHGHRDDARLGAA
+LLTGETDGGWTW
+>2_323
+MAQPEPVRLAPPGRTAEPDAARPAERALLAAASACDGDVAPMLALLGAGRAPDTEASAPD
+AAAPLELPLTGEGRTRQQWELLASVAAQDLSAARVLEPHLDALSILSQASVPAPAGLLGV
+YASESGGRTPRLTPAPHDDDAGSASDGRPDAGPDAWLLDGEKPWCSLADECAAAVITGRE
+ADGTRRAVLVDLDHPGVAETSSAWPALGLAPIRTVGLGFDAVPGTAVGGPEWYLRRPGFA
+WGGIGVAAVWFGGAVGIARTLRDATRSRAAAEAEGRGPGPDQVAQAALGRVDRLLHAMAA
+LLARAAEDVDAGRLDHGRGMVEADRIRGTVAQLCTEVVDVVGQATGPGPLTGSAAHARAV
+ADLQVYLRQHHAHRDDARLGRALLDGDADGGWTW
+>3_264
+MSETPWVHLPGAEGDGRPAAPTEAEAALLAAARDGEDGEAGIEPILALLSGDDAAASLDL
+PLTGAGRTRRQWELLASVGAVSLPAARVLEPHLDALSILDQAGVPAPRGVLGVYASESGG
+VSPSARPAPGAAVGDEDAVWRLDGDKPWCSLADRCTAAVVTARQEDGLRRAFLVDLGEPG
+MEVADPRWPSLGLAPITTVGLRFADVPAVPVGGPEWYLRRPGFAWGGIGVAAVWFGGAVH
+VARTLRTSLERRTAAASDGSGPGPDQVGLAALGRVDRHLHAMASLLGRAADDVDAGRLDH
+AHGLVEADRIRGTVAQLCTEVLDVVGQATGPGPLTGDAAHARAVADLQVYLRQHHGPRDD
+ARLAESLLAADPAERAELQPW
+>4_48
+MAQPEPVRLVPGGAVDRPAEQALLAAAAACDGDVDAMVELLRAASGAASGEDAAPLDLPL
+TGAGRTREQWELLASVAAQDLSAARVLEPHLDALSILSQAGVPAPAGLLGVYASESGGRT
+PALRPVPDGPDTAWLLDGEKPWCSLADRCAAAVVTGREADGTRRAVLVDLSHPGVAETDS
+AWPALGLAPIRTVGLAFDAVPGSAVGGAEWYLRRPGFAWGGIGVAAVWFGGAVGIARTLR
+NATAARAAAEAEGRGPGPDQIGQAALGRVDRLLHAMAALLARAADDVDAGRLDHGRGMVE
+ADRIRGTVAQLCTEVMDVVGQATGPGPLTGSAAHARAVADLQVYLRQHHGHRDDARLGAA
+LLTGETDGGWTW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000212.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000212.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eeae34463e6c0c19cf13b70755c01c6bde24221e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000212.fa
@@ -0,0 +1,49 @@
+>0_56
+MTLPTPVRLGRMQTSDAAPAADDDRTPSAPGPARLLDRSAVRLREDLAAGELSAREVTEA
+ALAAAQTHADLGAFALLDAEGARARAAELDAAHPRVAPRAVPGPRTSPAPDDDGAPASLH
+GLPLAYKDLIDVRGMPTRFGSALLADAPPAAQDDPLALRLRAAGTVTLGKTTVPEFGLDS
+YSENLVTAPARNPLDPTRTAGGSSGGAAAAVAAGILPFAPGSDGGGSIRIPAAACGLVGL
+KPGRGELPMDEHADTVRNLTVSGPLAHTVEDAALLYDVLLSPEGLPGRVLPDLRRTVETA
+RAGGAVDARRIGVTTASPFASDLEISLARPAVTALTKAAAALDAGGHAVEDLSPYYGEDY
+HRDFRTVWTAGLLRAPLPEDAEAHVGAVAAHFLRTARAAGRAELDDAAHRLEEWARGVRA
+QFAAVDVVMTPVLATAPPPVGHFLAMEPEANYEAQCAFTPYTSMVNVLGLPAVAVPVLRD
+ERGLNWSVQLIGRPGTSAPLLALAAHLELLLAG
+>1_2020
+MTRATPVRLGRMQTSDAAPAADDDDRTPSAPGPARLLDRSAVRLREDLAAGELSAREVTE
+AALAAAQAHADLGAFALLDAEGARTRAAELDAAHPRVAPRAVPGPHTSPAPDDDGAPASL
+HGLPLAYKDLIDVRGMPTRFGSALLADAPPAAQDDPLALRLRGAGTVTLGKTTVPEFGLD
+SYSENLVTAPARNPLDPTRTAGGSSGGAAAAVAAGILPFAPGSDGGGSIRIPAAACGLVG
+LKPGRGELPMDEHADTVRNLTVSGPLAHTVEDAALLYDVMLTPEGLPGRVLSDLRRTVET
+ARAGDAVDVRRIGVTTASPFASDLEISLARPAVTALTKAAAALDAGGHAVEDLSPYYGED
+YHRDFRTVWTAGLLRAPLPEDAEAHVGAVAAHFLRTARAAGRAELDDAAHRLEEWAHGVR
+AQFAAVDVVMTPVLATAPPPVGHFLAMEPEANYEAQCAFTPYTSMVNVLGLPAVAVPVLR
+DERGLNWSVQLIGRPGTSAPLLALAAHLELLLAG
+>2_320
+MQLRDALAAGELSAREVTQAALDAAERHAGLGAFTLLDPEGALARADELDDDGARASLHG
+LPLAYKDLTDVRGLPTRHGSALLAGAPAAEEDAPLVRRLVGAGTVTLGKTTVPEFGLDSY
+SENLVSAPARNPLDPARTPGGSSGGSAAAVAAGILPFAPGSDGGGSIRIPAAACGLVGFK
+PGRGELPVDEPADTVRNLTVSGPLAHTVEDAALLYDELLTPEGLPGRVLADLRRTVETAR
+AGGAVEGRRIGVTTASPFAPDVPITLARPAVTALTKAAAALSAGGHAVQDLHPAYGEEYH
+RDFRTVWTSGLLRAPLPEDAEERVGAIAAHFLRTARSAGRQEIDDAVRRLEAWARGVRGQ
+FAAVDVVMTPVLAAAPPPVGHFLAMEPEDNYAAQCAFTPYTSMVNVLGLPAASVPVLRDE
+RGLSWSVQLIGRPGTSGALLALAAHLELLLAG
+>3_262
+MAVSEPLSPSDQPTSPTPAPDAPARLLGRTALALRDALAAGELSAAEVTEASLAAAHAHA
+GLGAFVLLDEDGARVRAAALDARPDDAAGASLRGLPLAFKDLTDVAGLPTRMGSAVLAQA
+PAAAEDDPLTTRLRAAGTVLLGKTTVPEFGLDAYSENPVDPPARNPLDPSRTPGGSSGGS
+AAAVAAGILPFAPGSDGGGSVRIPAAACGLVGLKPGRGTVPTDPGEDAVTNLTVSGPLAH
+TVEDAALLFDVMTSPEGLEGRTGPDLRRFLDARAAGEPVAPVRIGVSTASPFSPDLEITL
+ARPALSALARSGAALAAGGHAVDEFVPHYGERYHRDFRTAWTSGLLKAPLPDGAEALVGP
+VAASFLASARAAGPEQIATAIGRLEAWAADVRGQFAAVDVVMTPVLAFAPPAIGHFLALD
+PEENYAEQCRFTPYTSMVNVLGLPAVAVPVLRDEAGLSWSVQLVGRPGAEGRLLELAGHL
+RLLLAG
+>4_51
+MTLPTPVRLGRMQTSDAAPAADDDRTPSAPGPARLLDRSAVRLREDLAAGELSAREVTEA
+ALAAAQTHADLGAFALLDAEGARTRAAELDAAHPRVAPRAAPGPHTSPAPDDDGAPASLH
+GLPLAYKDLIDVRGMPTRFGSALLADAPPAAQDDPLALRLRAAGTVTLGKTTVPEFGLDS
+YSENLVTAPARNPLDPARTAGGSSGGAAAAVAAGILPFAPGSDGGGSIRIPAAACGLVGL
+KPGRGELPMDEHADTVRNLTVSGPLAHTVEDAALLYDVLLSPEGLPGRVLPDLRRTVETA
+RAGGAVDARRIGVTTASPFASDLEISLARPAVTALTKAAAALDAGGHAVEDLSPYYGEDY
+HRDFRTVWTAGLLRAPLPEDAEAHVGAVAAHFLRTARAAGRAELDDAAHRLEEWARGVRA
+QFAAVDVVMTPVLATAPPPVGHFLAMEPEANYEAQCAFTPYTSMVNVLGLPAVAVPVLRD
+ERGLNWSVQLIGRPGTSAPLLALAAHLELLLAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000217.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000217.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7ab490e8673d0f86788b34f1f9b20a833d84137
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000217.fa
@@ -0,0 +1,25 @@
+>0_63
+MFVLTINQRDTLDAGDRVDTFLRALQDVPGLDDAVVLPFQRAVGDELIGAVEDPRVAVDV
+ALRALRQRRWNVGVGVGTVTHADGAAGAPASGDLHDAGGPGLAAARRAVEAAAVSTARIP
+LAVRGRDEEAAAEAEAVLRLVGQLVWSRTDAEWAVLDLLVPGVRGQQKPAAAALGITAQA
+VSQAVQRSYWNEEHACRPAAARLLTLAGG
+>1_2027
+MFVLTINQRDTLDAGDRVDTFLRALQDVPGLDDAVVLPFQRAVGDELIGAVEDPRVAVDV
+ALRALRQRRWNVGVGVGTVTHADGAAGAPASGDLHDAGGPGLAAARRAVEAAAVSTARIP
+LAVRGRDEEAAAEAEAVLRLVGQLVWSRTDAEWAVLDLLVPGVRGQQKPAAAALGITAQA
+VSQAVQRSYWNEEHACRPAAARLLTLAGG
+>2_312
+MLVLTINQRDTLDAGDRVDAFLRSLGDAPGLAGAVALPFQRAVGDELIGAVTDPAAAVEV
+ALRALRERRWNVGIGVGALRGADGTEGAPSSGSLDDAAGPALAHARRAVEAAAVSTARIP
+LAVRGADAQASAEAEAVLRLVGQLVWSRTDAEWAVLDLLVPGVRGQQKPAADALGITAQA
+VSQAVQRAYWNEEHACRPAASRLLALAEEG
+>3_253
+MFVLTLNQRDTPDAGDRVDALLRELTDAAAAVPGLRSPALPFQRSVGDELVGVLEDPHAA
+VDVALRALRQRRWNVGIGVGTVCHADGSAGIPASGDLHHAGGPGLAAARRAVEAAALSTA
+RIPLAVRGRDAEAAAEAEAVLKLIGQLVWTRTAAEWSVLDLLVPGVRGQQKPAAQALGIT
+TQAVSQAVQRSFWNEEHACRPAAARLLALAAG
+>4_57
+MFVLTINQRDTLDAGDRVDTFLRALQDVPGLGDAVVLPFQRAVGDELIGAVEDPRVAVDV
+ALRALRQRRWNVGVGVGTVTHADGAAGAPASGDLHDAGGPGLAAARRAVEAAAVSTARIP
+LAVRGRDEEAAAEAEAVLRLVGQLVWSRTDAEWAVLDLLVPGVRGQQKPAAAALGITAQA
+VSQAVQRSYWNEEHACRPAAARLLTLAGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000219.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000219.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f910e9f409cc1e668ba2e0d666f1a8a7e3464f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000219.fa
@@ -0,0 +1,40 @@
+>0_66
+MSDDHATDRPRTAADAEPGAPAEPGPAVAHPVDWAFAARTARSLAAAGPRFTPREATREA
+EGLRAAAEAAVPHVHRLTGLEAARDLRDSQVLVVDRPTWSRAATQSFATLLDPTFAHLRD
+TRPREHAATTRVTRHATALEMGGILAWMSGKILGQYDPFIALPGPGGTAAGPAGGRLLLV
+APNVAQVRAEINVDPADFRLWVCLHEQTHRVQFAAAPWLREHLRGEITALTVGLFDKAES
+LPERLRTALAAANPLGREADAGRTGTRDGHDAQDAVAARPAPGLLGAIQDEEDRERLSRL
+TAVMSLLEGHANVVMDGVDSSVVSSVKTIRRRFDERGDRRSPLDRMLRRLLGMDAKMAQY
+RDGQRFVAAAVAELGMAGFNVVWDAPELLPSEAELHAPETWVARIRAQA
+>1_2030
+MSDDHATDRPRAAADAEPGAPAEPGPAVAHPVDWAFAARTARSLAAAGPRFTPREATREA
+EGLRAAAEAAVPHVHRLTGLEAARDLRDSQVLVVDRPTWSRAATQSFATLLDPTFAHLRD
+TRPREHAAATTRVTRHATALEMGGILAWMSGRILGQYDPFIALPGPGGTAGGPAGGRLLL
+VAPNVAQVRAEINVDPADFRLWVCLHEQTHRVQFAAAPWLREHLRAEITALTVGLFDKAE
+SLPERLRTALAAANPLGREADAGRTGARDGHDAQDAAPARPTPGLLGAIQDEEDRERLSR
+LTAVMSLLEGHANVVMDGVDSSVVSSVKTIRRRFDERGDRRSPLDRMLRRVLGMDAKMAQ
+YRDGQRFVAAAVAQLGMAGFNVVWDAPELLPSEAELHAPETWVARIRAQA
+>2_307
+MDTAPADRVPQPVDWAFAARTAAALAPAGPRFTAREAAREAAGLRAAAEASVPHVHRLTG
+LAAAEDLRDSQVLVVDRPTWSASATQSFATMLEPTFAHLQATRPQEYQAALTPVARHATA
+LEMGGILAWLSGKVLGQYDPFAGPSGGRLLLNAPSVAQVRTEINVDPEDFRLWVCLHEQT
+HRVQFAAAPWLRGHLQEQITALASGLFDKAESLPERLRSALAAANPLGRGSGAGAASTGP
+ASGPDDGRPGPAQAGGDVVPARGAGLLGALQDEEDRARLSHVTAVMSLLEGHANVVMDGV
+DADVVSSVKTIRRRFEDRADRRSPLDRMLRRLLGMDAKMAQYRDGQRFVSAAVAELGMDG
+FNVVWDAPELLPTEDELHRPERWTARVRAQA
+>3_250
+MTADQPVPSPAHPVDWDAAARAAGSLAAAGPRIGTREARREAEGLRAAAAASVAHVHRLT
+GLAAAEDLRDSQVLVVDRPTWSLANTQSFAGLLEPSFAHLRATRPQEYALTTAPLTRRAA
+ALEMGGILAWLSSKVLGQYDPFSALPGPDGVPAGPAGGRLLLVAPNVAQVRREIHVDPAD
+FRLWVCLHEQTHRVQFAAAPWLRGHLQGEITALTGGLFDKAESLPERLRSALAAANPLGA
+STSPGAGRAGQDDGAAGPGGRPALGLLGAIQDEEDRARLSRLTAVMSLLEGHANVVMDAV
+DSSVVSSVKTIRRRFDARGDRRSGLDRLLRRLLGMDAKMAQYRDGQRFVDAAVAELGRDG
+FNVVWDAPELLPSEEEIHAPDRWVARIRAQA
+>4_60
+MSDDHATDRPRTAADAEPGAPAEPGPAVAHPVDWAFAARTARSLAAAGPRFTPREATREA
+EGLRAAAEAAVPHVHRLTGLEAARDLRDSQVLVVDRPTWSRAATQSFATLLDPTFAHLRD
+TRPREHAAATTRVTRHATALEMGGILAWMSGRILGQYDPFIALPGPGGTAAGPAGGRLLL
+VAPNVAQVRAEINVEPADFRLWVCLHEQTHRVQFAAAPWLREHLRAEITALTVGLFDKAE
+SLPERLRTALAAANPLGREADAGRIGTRDGHDAQDAAAARPAPGLLGAIQDEEDRERLSR
+LTAVMSLLEGHANVVMDGVDSSVVSSVKTIRRRFDERGDRRSPLDRMLRRLLGMDAKMAQ
+YRDGQRFVAAAVAELGMAGFNVVWDAPELLPSEAELHAPETWGARIRAQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000230.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000230.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb7a6882c82812458a69c48b5b164a991cf05db7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000230.fa
@@ -0,0 +1,20 @@
+>0_80
+MTDQPEMSPLTEPEREWVRVRRDFAAQEGVDHLDLDAVAAYYDAVLARSQAEADELDPEE
+LAVLLDVVAVLLGEHLGARHGMQWVTVADEEGPALALRDTLSDAVVFPQPVVGQSWNDQA
+TGEWMGGYVDWLGEQLQQIRADAGTLPGA
+>1_2044
+MTDQPEMSPLTEPEREWVRVRRDFAAQEGVDHLDLDAVAAYYDAVLARSQAEAEELDPEE
+LAVLLDVVAVLLGEHLGARHGMQWVTVADEEGPALALRDTLSDAVVFPQPVVGQSWNHQA
+TGEWMGEYVDWLGEQLQQIRADAGTRPGA
+>2_292
+MTEQPEMHPLSEPEQEWVRVRREFAAQEGVDHLDLDAVAAYYDGVLARSVSEAEALDPDE
+LAVLLDVVAVLLGEHLGARHGMQWVTVSDDEGPALALRDTLSDAVVFPQPAVGQAWNEQV
+TGAWLGEYVDWLGEQLQGIRAGDRPDGVAQQG
+>3_237
+MSEQQIRPLTAAEQEWVAVRRDFAAQEGTGHLDLDAVDAYHGRLLARSRSEDVDPDELGV
+LLDVVAVLLGEHLGARHGLAWVAVTEGDATDLGLRDPLSDAVVFPQSVVAQHWNDGDAHW
+IPGYVDWLGAQLAPLREERRAAEG
+>4_75
+MTDQPEMSPLTEPEREWVRVRRDFAAQEGVDHLDLDAVAAYYDAVLARSQAEAEELDPEE
+LAVLLDVVAVLLGEHLGARHGMQWVTVADEEGPALALRDTLSDAVVFPQPVVGQSWNHQA
+TGEWMGEYVDWLGEQLQQIRADAGTRPGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000234.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000234.fa
new file mode 100644
index 0000000000000000000000000000000000000000..11ec6ce5ddb3f9d10ddec46f85a9b0234dce352c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000234.fa
@@ -0,0 +1,25 @@
+>0_85
+MTTSNNPDEIRADIERTRRELGQDVDALAEKVSPTKAVSRQTNRIKDGFIHAKENIMGSP
+EQHRHEPSLGDRAHAVVDDARASAYDAAGQAQDRLGDAGDRVSEWADDAQHALHQAPAQL
+RGRTAGNPLAAGLIAFGAGLLLSSLIPASRAEQRAAEGLKDQAAPLVDEAKQAAQQLRED
+LEPAAREAAGSVKESAAEAASHLKEQGTDTAQGLKAESQDAARQVKDTAKDA
+>1_2049
+MTTSNNPDEIRADIERTRRELGQDVDALAEKVSPTKAVSRQTNRIKDGFIHAKENIMGSP
+EQHRHEPSLGDRAHGVIDDARASAYDAAGQAQDRLGDAGDRVSEWADDAQHALHQAPAQL
+RGRTAGNPLAAGLIAFGAGLLLSSLIPASRAEQRAAEGLKDQAAPLVDEAKQAAQQLRED
+LEPAAREAAGSVKESAAEAASHLKEQGTDTAQGLKAESQDAARQVKDTAKDA
+>2_287
+MTTSNNPDEIRAEIERTRHQLGQDVDALAEKVSPTKAVSRQTNRMKDGLLSVKENIMGSP
+EDHGRQPSMGDRAHAAADDARASMHGAADQARDAMGHASDRVSGWADDAQHAVQQAPAQL
+RGRTAGNPLAAGLIAFGAGLLVSSLIPASRVEQRAAEGLKEQAAPLVDEAKQVAQQLRED
+LEPVARDAAQSVKESATEAVDHVKADGADKAQDLKAESQDAARQVKGAAQDG
+>3_233
+MTTSSNPDEIRAEIERTRHALGQDVDALAEKVSPTKAVSRQTNRVKDGFITVKENIMGTP
+EHHEGPGAVDRARFAAQDAAGQVQGTAHDVADQARGYAQQAGEAASQWVDDAQHAVQQAP
+AQVRGRTAGNPLAAGLIALGAGWLIGSLIPASPVEKRAAERVKDQAAPLLESAKQEAAQV
+AQDVREQVEPEVRDAAASLKDSAAESVQSLKSEGAEKAQDLKGSSQDAAQQVKHAAKHA
+>4_80
+MTTSNNPDEIRADIERTRRELGQDVDALAEKVSPTKAVSRQTNRIKDGFIHAKENIMGSP
+EQHRHEPSLGDRAHGVIDDARASAYDAAGQAQDRLGDAGDRVSEWADDAQLALQQAPAQL
+RGRTAGNPLAAGLIAFGAGLLLSSLIPASRVEQRAAEGLKEQAAPLVDEAKQAAQQLRED
+LEPAAREAAGSVKESAAEAASHLKEQGTDTAQDLKAESQDAARQVKDTAKDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000236.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000236.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9086349f23c8054c1ee32b13b42e027bbef39b6a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000236.fa
@@ -0,0 +1,25 @@
+>0_87
+MTPERLAAAFDGPSPALAATLLGCRLTVVAPDGAVTVRLTETEAYGNAGADPGAHSFRGR
+TERNAALFGPPRRTYVYLNYGIHRCLNLVGHPEGEAGGVLLRAAEVLAGGDLAVARRGRD
+TGPKLLSGPGNLGQGLGITLEMGHAPVEIVAAPPEVADDGGTSARLAAPAAPARFLLAPP
+APRDPAEPPIEVVTGPRVGVSGEGGSVRFPWRFSVAGHRSVSAFRRGRNVPD
+>1_2051
+MTPERLAAAFDGPSPALAATLLGCRLTVVAPDGAVTVRLTETEAYGNAGADPGAHSFRGR
+TERNAALFGPPRRTYVYLNYGIHRCLNLVGHPEGEAGGVLLRAAEVLAGGDLAVARRGRD
+TGPKLLSGPGNLGQGLGITLEMGHAPVEIVAAPPEVADDGGTPARLAAPAAPARFLLAPP
+APRDPAAPPIEVVTGPRVGVSGEGGSVRFPWRFSVAGHRSVSAFRRGRNVPD
+>2_285
+MTPERLAAAFDGPSPALAATLLGCRLTVVAPDGAVTVRLTETEAYGDAGADPGAHSFRGR
+TERNAALFGPPRRTYVYLNYGIHRCLNLVGHPEGEAGGVLLRAAEVLAGGDLAVARRGRD
+TGLKLLSGPGNLGQGLGITLEMGHAPVEIVAAPPEVADDGGTPARLAAPARFLLAPPASR
+DPAEPPIEVVTGPRVGVSGEGGSVRFPWRFNVAGHRSVSAFRRGRNVPD
+>3_231
+MTPERLAAAFDGPTPALAATLLGCRLTVVAPDGAVTVRLTETEAYGNAGADPGAHSFRGR
+TERNAALFGPPRRTYVYLNYGIHRCLNLVGHPEGEAGGVLLRAAEVLAGGDLAVARRGRD
+TGLKLLSGPGNLGQGLGITLQMGHVPVEIVAAPPEVADDGGTPARLAAPARFLLAPPASR
+DPAEPPIEVVTGPRVGVSGEGGSVRFPWRFSVAGHRSVSAFRRGRNVPD
+>4_82
+MTPERLAAAFDGPSPALAATLLGCRLTVVAPDGAVTVRLTETEAYGNAGADPGAHSFRGR
+TERNAALFGPPRRTYVYLNYGIHRCLNLVGHPEGEAGGVLLRAAEVLAGGDLAVARRGRD
+TGPKLLSGPGNLGQGLGITLEMGHAPVEIVAAPPEVADDGGTSARLAAPAAPARFLLAPP
+APRDPAEPPIEVVTGPRVGVSGEGGSVRFPWRFSVAGHRSVSAFRRGRNVPD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000242.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000242.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a35d77ccafac5c9e042bdbdcb0109f44d9767afc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000242.fa
@@ -0,0 +1,50 @@
+>0_93
+MTTQNSASAAVDHHDQQAVRAAKREQLLASGREAYPVQVPRTHALAEVRERFDGHEPDWT
+SGETVSVTGRVVFLRNTGKLCFATLQESGADGEAVRLQVMVSLAAVGEESLAEWKKVVDL
+GDFLSVTGEVIVSRRGELSIMASAWEMASKALRPLPVLHADLNEETRVRQRYADLIVREE
+ARRMVYTRAKVTSAVRRTLEGHGYVEVETPMLQLVHGGALARPFETHLNAFDQPMTLRIA
+TELYLKRAVVGGIDRVFEIGRVFRNEGVDSTHSPEFTTLESYEAWADMHVMAERMQEIIL
+NAADAVGAGRRLETAKGVIDLDGEWAWVAVYPGLSEAVGREITPETDAETLRAIAAEHEV
+KVDPAWDAEKLVIELFGEIVEPTLMNPTFVYDYPPAAQPLARPHRSDDRVIEAWDLIIGG
+MERGTAFSELIDPVIQRERLTAQSAMAAAGDDEAMQLDEDFLRALEYGAPPMGGIGLGID
+RLVMLFTDAGIRETILFPLLKPEA
+>1_2057
+MTTQNSASAAVDHHDQQAVRAAKREQLLASGREAYPVQVPRTHALAEVRERFDGHEPDWT
+SGETVSVTGRVVFLRNTGKLCFATLQESGADGEAVRLQVMVSLAAVGEESLAEWKKVVDL
+GDFLSVTGEVIVSRRGELSIMASAWEMASKALRPLPVLHADLNEETRVRQRYADLIVRDE
+ARRMVYTRAKVTSAVRRTLEGHGYVEVETPMLQLVHGGALARPFETHLNAFDQPMTLRIA
+TELYLKRAVVGGIDRVFEIGRVFRNEGVDSTHSPEFTTLESYEAWADMHVMAERMQEIIL
+NAADAVGAGRRLETAKGVIDLDGEWAWVAVYPGLSEAVGREITPDTDAGTLRAIAAEHEV
+KVDPAWDAEKLVIELFGEIVEPTLMNPTFVYDYPPAAQPLARPHRSDDRVIEAWDLIIGG
+MERGTAFSELIDPVIQRERLTAQSAMAAAGDDEAMQLDEDFLRALEYGAPPMGGIGLGID
+RLVMLFTDAGIRETILFPLLKPEA
+>2_279
+MTSQNSANPQTSAVDHHDQQAVRAAKREQLLAAGREAYPVQVPRTHTLTEVREQFDGHEP
+DWASGETVSVTGRVVFLRNTGKLCFATLQESGVDGEAVRLQVMVSLAAVGEDSLAQWKKA
+VDLGDFLSVTGEVIVSRRGELSIMASAWEMASKALRPLPVLHADLNEETRVRQRYADLIV
+RDEARRMVYTRAKVTSAVRRTLEGHGYVEVETPMLQLIHGGALARPFETHLNAFDQPMTL
+RIATELYLKRAVVGGIDRVYEIGRVFRNEGVDSTHSPEFTTLESYEAWADMHVMAERMQE
+IILAAADAVGAGRRIETDRGVIDLDGEWAWVSVYPGLSEAVGREITPDTDAETLRAIAAE
+HEVKVDPAWDAQKLVIELFGEIVEPTLMNPTFVHDYPPAAQPLARPHREDGRVIEAWDLI
+IGGMERGTAFSELIDPVIQRERLTAQSAMAAAGDDEAMQLDEDFLRALEYGAPPMGGIGL
+GIDRLVMLFTDAGIRETILFPLLKPEA
+>3_225
+MTPENPAPAAVDHHDQQAVRAAKREQLLTSGRQAYPVQVPRTHSLAAVRAKFDGKHEAGW
+EEGPEVSVTGRVVFLRNTGKLCFATLQESGAAGEAVRLQVMVSLAEVGEESLGEWKKSVD
+LGDFLSVTGRVIVSRRGELSIQAAAWEMASKALRPLPVLHADLNEETRVRQRYTDLIVRD
+EAREMVYKRAKITSAVRRTLESHGYVEVETPILQLVHGGAQARPFETHLNAFDQDMTLRI
+ATELYLKRAVVGGIERVYELGRVFRNEGVDSTHSPEFTTLESYEAWADMHVMADRIKEII
+LNAADAIGAGRRIETSRGVIDLDGEWAWVSVYPGLSEAVGREVTPDTDAETLRAIAAEHD
+VKVDPKWDAQKLVIELFGEIVEPTLMNPTFVYDYPPAAQPLARPNRDDDRVIEAWDLIIG
+GMERGTAFSELIDPVIQRERLTEQSLKAADGDDEAMQLDEDFLRALEYGAPPMGGIGLGI
+DRLVMLFTDAGIRETILFPLLKPEA
+>4_88
+MTTQNSASAAVDHHDQQAVRAAKREQLLASGREAYPVQVPRTHALAEVRERFDGHEPDWA
+SGETVSVTGRVVFLRNTGKLCFATLQESGADGEAVRLQVMVSLAAVGEESLADWKKVVDL
+GDFLSVTGEVIVSRRGELSIMASAWEMASKALRPLPVLHADLNEETRVRQRYADLIVREE
+ARRMVYTRAKVTSAVRRTLEGHGYVEVETPMLQLVHGGALARPFETHLNAFDQPMTLRIA
+TELYLKRAVVGGIDRVFEIGRVFRNEGVDSTHSPEFTTLESYEAWADMHVMAERMQEIIL
+NAADAVGAGRRLETAKGVIDLDGEWAWVAVYPGLSEAVGREITPETDAETLRAIAAEHEV
+KVDPAWDAEKLVIELFGEIVEPTLMNPTFVYDYPPAAQPLARPHRSEDRVIEAWDLIIGG
+MERGTAFSELIDPVIQRERLTAQSAMAAAGDDEAMQLDEDFLRALEYGAPPMGGIGLGID
+RLVMLFTDAGIRETILFPLLKPEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000253.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000253.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c5594a349fbf828665bc82e378863687833a547
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000253.fa
@@ -0,0 +1,30 @@
+>0_106
+MSKRIQAIDVDVFYGKFKAVEGVNIDIAPRSVTAFIGPSGCGKTTFLRSINRMHEVLPGA
+TVDGQLLLDGEDIYGPGVDPVRVRSQIGMVFQRPNPFPTMSIRDNVLAGYKLNGTRLNKS
+RADELVEKSLRGANLWNEVKDRLDKPGSGLSGGQQQRLCIARSIAVQPDVILMDEPCSAL
+DPISTLAVEDLINELKEEYTVIIVTHNMQQAARVADKTAFFNIQGVGKPGKLIEYDDTNV
+IFNNPSSQQTEDYVSGRFG
+>1_2070
+MSKRIQAIDVDVFYGKFKAVEGVNIDIAPRSVTAFIGPSGCGKTTFLRSINRMHEVLPGA
+TVDGQLLLDGEDIYGPGVDPVRVRSQIGMVFQRPNPFPTMSIRDNVLAGYKLNGTRLNKS
+RADELVEKSLRGANLWNEVKDRLDKPGSGLSGGQQQRLCIARSIAVQPDVILMDEPCSAL
+DPISTLAVEDLINELKEEYTVIIVTHNMQQAARVADKTAFFNIQGVGKPGKLIEYDDTNV
+IFNNPSSQQTEDYVSGRFG
+>2_265
+MSKRIQAKDVDVYYGKFKAVEGVNIDIAPRTVTAFIGPSGCGKTTFLRAINRMHEVLPGA
+HVEGQLLLDGEDVYGPGVDPVTVRSQIGMVFQRPNPFPTMSIRDNVLAGYKLNGTRLSRS
+RADEIVEKSLRGANLWNEVKDRLDKPGSGLSGGQQQRLCIARSVAVSPDVILMDEPCSAL
+DPISTLAVEDLINELKEQYTVIIVTHNMQQAARVADKTAFFNIQGIGQPGKLIEFDDTNV
+IFNNPSNQQTEDYVSGRFG
+>3_207
+MSKRIQAKDVDVYYGKFKAVEGVSIDIAPRTVTAFIGPSGCGKTTFLRAINRMHEVLPGA
+HVEGQLLLDGEDVYGPGVDPVTVRSQIGMVFQRPNPFPTMSIRDNVLAGYKLNGTRLTKS
+RADEIVEKSLRGANLWNEVKDRLDKPGSGLSGGQQQRLCIARSVAVEPDVILMDEPCSAL
+DPISTLAVEDLINELKEDYTVIIVTHNMQQAARVADKTAFFNIQGIGQPGKLIEYAETNT
+IFNNPSNQQTEDYVSGRFG
+>4_101
+MSKRIQAVDVDVFYGKFKAVEGVNIDIAPRSVTAFIGPSGCGKTTFLRSINRMHEVLPGA
+TVDGQLLLDGEDIYGPGVDPVRVRSQIGMVFQRPNPFPTMSIRDNVLAGYKLNGTRLNKS
+RADELVEKSLRGANLWNEVKDRLDKPGSGLSGGQQQRLCIARSIAVQPDVILMDEPCSAL
+DPISTLAVEDLINELKEEYTVIIVTHNMQQAARVADKTAFFNIQGVGKPGKLIEYDDTDV
+IFNNPSSQQTEDYVSGRFG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000254.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000254.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9cacc89443b2efea6e53355a96da6814618214fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000254.fa
@@ -0,0 +1,35 @@
+>0_107
+MTAGLAVVLVLLCAVGALMGFRDAPNAAALPVRYRALTPRGALLLTGAVNTVGALLGIGL
+ITLSVHYFTSPAVRSEIGPLAVGVSCAVTLVWGLLLWWRRLPGSSTHALISALAGSHLAV
+RLSLHIDVAHTIFDLVRAEVLLSLLLSPLIAWALARLLTAPAMRLATRGTTVNVQHRARV
+ALGISASAMAMGHGLQAGQRMGVLWAAVLVGSGSVLAPDALTAEFVGGAFLFALAVGLGT
+LGGAWRIAWTLTERLVRLDPLRASVAAVIPAGLLFVGSLVFHLPLSSTHTATAAIVGAGQ
+TQTYASVRWPTVLRVVGWWLLTPVACALLGLLGTLALLPLA
+>1_2071
+MTAGLAVVLVLLCAVGALMGFRDAPNAAALPVRYRALTPRGALLLTGAVNTVGALLGIGL
+ITLSVHYFTSPAVRSEIGPLAVGVSCAVTLVWGLLLWWRRLPGSSTHALISALAGSHLAV
+RLRLHIDVAHTIFDLVRAEVLLSLLLSPLIAWALARLLTAPAMRLATRGTTVNVQHRARV
+ALGISASAMAMGHGLQAGQRMGVLWAAVLVGSGSVLAPDALTAEFVGGAFLFALAVGLGT
+LGGAWRIAWTLTERLVRLDPLRASVAAVIPAGLLFVGSLVFHLPLSSTHTATAAIVGAGQ
+TQTYASVRWPTVLRVVGWWLLTPVACALLGLLGTLALLPLA
+>2_264
+MTPGLAVVALLLCALAAMMGFRDAPNAVALPVRFRALTPRLALVMTALINAVGALLGIGL
+ITLSVHYFTSPAVRGDVGPLAVGVTAVVAVLWGLLLWWRRLPGSTTHAVLSALAGAHLAV
+QLSLHDDLAGSILESVRVEVVLSLLLSPVIAWGLARLLTGPVVQVATTGTTVNVQRRARI
+ALAVSAGAMAMGHGLQAGQRVGVLWAAVLVGSGAALSPDALTAEFVVGSVLFALAIALGT
+LGGAWRIAWTLTERLVRLDPLRASVAAVVPAGLLFVGSLVLHLPLSSTHTATAAIVGAGQ
+TQTYASVRWPTVLRVGGWWLLTPVVCAALGLLGTLALLPLA
+>3_206
+MTAPLLVPVLVLLLAVGGLMGFRDAPNAVALAVRFRALTPRVALILSALLNAVGVLLGAL
+MLTLGLPLMVAGGTARPEVLALVGVAAAVTLGWGVLAWRFRAPTSTTHALLASLAAAHVA
+SVSALGSGLDPAFENGARWEVAASLLLSPVLAWGLARLTARPVLRLATTGTTVNVQHRAR
+IALAVSTGLIALGHGVQAALRLLPLAVLVATAAVGTGLPPGTELSAAFVAAAAVGIGTLG
+GAWGIAWTLTERLVILDPLRAAVAAVVPAVLLFAGTMLLHLPLSSTHTGVAGIVGAGQTQ
+SYASVRWGAVARVAVWWVATPLVCGSLAFAAGAVLLPLLG
+>4_102
+MTAGLAVVLVLLCAVGALMGFRDAPNAAALPVRYRALTPRGALLLTGAVNTVGALLGIGL
+ITLSVHYFTSPAVRSEIGPLAVGVSCAVTLVWGLLLWWRRLPGSSTHALISALAGSHLAV
+RLSLHIDVAHTIFDLVRAEVLLSLLLSPLIAWALARLLTAPATRLATRGTTVNVQHRARV
+ALGISASAMAMGHGLQAGQRMGVLWAAVLVGSGSVLAPDALTAEFVGGAFLFALAVGLGT
+LGGAWRIAWTLTERLVRLDPLRASVAAVIPAGLLFVGSLVFHLPLSSTHTATAAIVGAGQ
+TQTYASVRWPTVLRVVGWWLLTPVACALLGLLGTLALLPLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000264.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000264.fa
new file mode 100644
index 0000000000000000000000000000000000000000..57ec3d34c393d8242cadb800a51ec3219b9825ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000264.fa
@@ -0,0 +1,35 @@
+>0_121
+MSAQTQPAATRREDAPLGVLVGVDGSDQSVSAARWAQREAGLRGEPLTLVTAYSIPAYWG
+YGADASGAVLDDSRLREGVQALLEEVAGKLDADGVRPELRVEIGDAAGVLVELSAEASLL
+VSGARGRGGFMGRLLGSVAAALPGHAHCPVAIIPAGVEASRAGDRTAVVVGVDGSEQGRA
+AALEAAEEARLRQAPLKLVCAVPPLGANAAWLAVSLDEEARERELRERLEAGAAWISSEF
+PGLEVLTELVDGTPVDVLVDQTATARLTVVGTRGLGGFAGAIVGSTSRGVADHAKGPVLV
+VPFREDVRLGRRASFGPVQDQSGS
+>1_2086
+MSAQTQPAATRREDAPLGVLVGVDGSDQSVSAARWAQREAGLRGEPLTLVTAYSIPAYWG
+YGADAGGAVLDDSRLREGVQALLEEVAGKLDADGVRPELRVEIGDAAGVLVELSAEASLL
+VSGARGRGGFMGRLLGSVAAALPGHAHCPVAIIPAGVEASRAGDRTAVVVGVDGSEQGRA
+AALEAAEEARLRQAPLKLVCAVPPLGANAAWLAVSLDEEARERELRERLDAGAAWISSEF
+PGLEVLTELVDGTPVDVLVDQSATACLTVVGTRGLGGFAGAIVGSTSRGVADHAKGPVLV
+VPFREDVRLSRRASFGPVQDQPES
+>2_246
+MSAQTQPAAPREDAPLGVLVGVDGSEQSVSAARWAQREAGLRGEPLTLVTAYSIPAYWGY
+GADAGGTVLDDSRLREGVQVLLDEVAAKLDADGVRPELRVEVGDAAGVLVDLSKAASLLV
+SGGRGRGGFIGRLLGSVASALPGHAHCPVAIIPAGVEASRAADGAAVVAGVDGSEQGRAA
+ALVAAEEARIRQAPLKLVCALPPVGGNAAWLGVTLDEAAREQELRERLDAGAAWIASEFP
+GLEVVTELVDGTPVDVMREQTATARLTVVGTRGLGGFTGALVGSTSRGVTDHAKGPVMVV
+PFRKDARLGTRTKFGPVADQD
+>3_180
+MSAETTPSTLPAEAPLGVLVGVDGSDQSISAARWAQREAGLRNLPLTLATAYTVPAFWGY
+AADGAGLLTDDGRLHAGVEALLREVAGKLDPAGVAPELRVEVGDAAGVLIDLSAQAELLV
+SGSRGRGGFIGRLLGSVSSALPGHAHCPVAIIPAGVEASRADSGAPVVVGVDGSEQGRAA
+ALVAAEEAQARKAPLHLISALPPISPNAAWLAVSLDEEAREQELRERLEDGARWLASEFP
+GLEVTSELASGVPVDVMVEQTATARLTVLGTRGLGGFSGALMGSTSAGVANHAKGPVMVV
+PFREDVRLGRRAEFGAVVDQDDPRV
+>4_129
+MSAQTQPAATRREDAPLGVLVGVDGSDQSVSAARWAQREAGLRGEPLTLVTAYSIPAYWG
+YGADAGGAVLDDSRLREGVQALLEEVAGKLDADGVRPELRVEIGDAAGVLVELSAEASLL
+VSGARGRGGFMGRLLGSVAAALPGHAHCPVAIIPAGVEASRAGDRTAVVVGVDGSEQGRA
+AALEAAEEARLRQAPLKLVCAVPPLGANAAWLAVSLDEEARERELRERLDAGAAWISSEF
+PGLEVLTELVDGTPVDVLVDQSATACLTVVGTRGLGGFAGAIVGSTSRGVADHAKGPVLV
+VPFREDVRLGRRASFGPVQDQPES
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000265.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000265.fa
new file mode 100644
index 0000000000000000000000000000000000000000..223807eef9811c50f1af3609f46876391bbea6e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000265.fa
@@ -0,0 +1,19 @@
+>0_122
+MDHRPSPEQPAATWMSEQEFDDAVSAALTRIPDELARLLTNVVVVVEDEYEPQRWEDPAT
+ELFGLYEGVPLTERAEFAWQMPDRIVVFRGPLTRHCTSRAELEDEITVTVMHEVGHFFGI
+SEERLHELGWG
+>1_2087
+MDHRPSPDQPAATWMSEQEFDDAVSAALARIPDELARLLTNVVVVVEDEYEPQRWEDPAT
+ELFGLYEGVPLTERAEFAWQMPDRIVVFRGPLTRHCTSRAELEDEITVTVMHEVGHFFGI
+SEERLHELGWG
+>2_245
+MSEQEFDDAVSAALTRIPDELARLLTNVVVVVEDEYEPQRWENPDTELFGLYEGVPLTER
+AEMPWQMPDRIVVFRGPLTRHCTSRAELEHEITVTVMHEVGHFFGIDEERLHELGWG
+>3_179
+METWMSEEEFDAAVDAALLRIPDELARLLTNVVVIVEDEYEPQRWEDPDTELFGVFEGFS
+LAERAEAAWQLPDRIVIFRGPLTRHCRSRAELEHEITVTVMHEVGHFFGISEERLHELGW
+G
+>4_130
+MDHRPSPEQPAATWMSEQEFDDAVSAALTRIPDELARLLTNVVVVVEDEYEPQRWEDPAT
+ELFGLYEGVPLTERAELAWQMPDRIVVFRGPLTRHCTSRAELEDEITVTVMHEVGHFFGI
+SEERLHELGWG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000271.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000271.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d0d685449a63c59caaebf44162a4c8b151950485
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000271.fa
@@ -0,0 +1,33 @@
+>0_130
+MRELQQRIIAQQGVLPEIDPAAEVERRVAFLADYLAATGASGFVLGISGGVDSTVGGRLA
+QLAVERRRAQLGVTDAVALGGPDTTPPGEAGVGADVVPSRENPRFTAVRLPYKVQHDEAD
+ARAAMDFVGADQDVTLNIAEAVQGLAAAFAEAVGEPISDYNQGNVKARIRMTAQYAVAGA
+HGQLVIGTDHAAEAVTGFYTKFGDGGADVLPLAGLNKRQVRALGRELGAPEPLWNKVPTA
+DLLDGTPGQTDEAELGMTYEDIDDYLEGKDVPTEVAEKLEGIWLRSRHKRTTPVTIHDDW
+WR
+>1_2095
+MRELQQRIIAQQGVLPEIDPAAEVERRVAFLADYLAATGASGFVLGISGGVDSTVGGRLA
+QLAVERRRAQLGVPDAVALGGPGTTPPGEAGVGADVVPSRENPRFTAVRLPYKVQHDEAD
+ARAAMDFVGADQDVTLNIAEAVQGLAAAFAEAVGEPISDYNQGNVKARIRMTAQYAVAGA
+HGQLVIGTDQAAEAITGFYTKFGDGGADVLPLAGLNKRQVRALGRELGAPEPLWNKVPTA
+DLLDGTPGQTDEAELGMTYEDIDDYLEGKDVPTEVAEKLEGIWLRSRHKRTTPVTIHDDW
+WR
+>2_236
+MRELQQQIIAEQGVRPQIDPAQEIERRVEFLVDYLEATGAAGFVLGISGGVDSTVGGRLA
+QLAVERRRARLGAPDAVALGGPEAPRGAPAADEAPSPQRPQFTAVRLPYRQQKDEADARA
+AMDFVDADREITLDIAAGVEGIASAFVEATGDEIADFDKGNVKARMRMVAQYALAGAHRQ
+LVIGTDHAAEAVTGFYTKFGDGGADVLPLSGLNKRQVRALGRELGAPEHLWNKVPTADLL
+DGNPGRTDEDELGMTYEHIDDYLEGGDIPEEAAEKLEGIWLRSRHKRTMPVTVHDDWWR
+>3_170
+MPEPYAGAMRELQQQIIAEMGVRPEVDPAAEVEARVRFLVDYLEATGASGFVLGISGGVD
+STTAGRLAQLAVERRRAELGTEAGDDAAPSRENPRFTAVRLPYRVQADEADATAAMDFVG
+ADGRVTLNIAEAVAGMASAFQEATGEPISDYNQGNVKARMRMVAQYAIAGAHGQLVIGTD
+HAAESITGFFTKFGDGGADVLPLAGLDKRQVRAVAKELGAPEHLWAKVPTADLLDGSPGR
+ADEDELGLSYEHIDDYLEGREIPEEAAEKLEGVWRRSRHKRTTPVTIHDDWWR
+>4_138
+MRELQQRIIAQQGVLPEIDPAAEVERRVAFLVDYLAATGASGFVLGISGGVDSTVGGRLA
+QLAVERRRAQLGVTDAVALGGPGTTPPGEAGVGADVVPSRENPRFTAVRLPYKVQHDEAD
+ARAALDFVGADQDVTLNIAEAVQGLAAAFAEAVGEPISDYNQGNVKARIRMTAQYAVAGA
+HGQLVIGTDQAAEAITGFYTKFGDGGADVLPLAGLNKRQVRALGRELGAPEPLWNKVPTA
+DLLDGTPGQTDEAELGMTYEDIDDYLEGKDVPTEVAEKLEGIWLRSRHKRTTPVTIHDDW
+WR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000286.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000286.fa
new file mode 100644
index 0000000000000000000000000000000000000000..22503423b1ac97e9bdb0ea7cfb63d76dd96141af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000286.fa
@@ -0,0 +1,24 @@
+>0_160
+MMVRESKKTMILDAAIQVIEEDGITAVTFDSVAAAAGITRAGIIYHFPSRDDLIAAIHQR
+LADRWERQLEIACGKPTAEATSMERLTAYILTCSTAASRAEFQMILDSQHTQHMAIWEDL
+IDRWTGRSERDEAERDQMTSLALLAADGLWVNDLIGSRPISQDHRSETAKQIIALLQNDV
+HESEAKPNG
+>1_343
+MMVRESKKTMILDAAIQVIEEDGITAVTFDSVAAAAGITRAGIIYHFPSRDDLIAAIHQR
+LADRWERQLEIACGKPTAEATPMERLTAYILTCSTAASRAEFQLILDSQHTQHKAIWEDL
+IDRWTGRSERDEAERDQMTSLALLAADGLWVNDLIGSRPISQDHRSETAKQIIALLQNDV
+HESEAKPNG
+>2_2282
+MMVRESKKTMILDAAIQVIEEDGITAVTFDSVAAAAGITRAGIIYHFPSRDDLIAAIHQR
+LADRWERQLEIACGKPTAEATPMERLTAYILTCSTAASRAEFQMILDSQHTQHKAIWEDL
+IDRWTGRSERDEAERDQMTSLALLAADGLWVNDLIGSRPISQDHRSETAKQIIALLQNDV
+HESEAKPNG
+>3_659
+MAKTTEQLLDDAIAVLRRGGVVTIDSVASEAGMSKAGVVHHFSSKEALMVGVVNRVMDLW
+EGQLAATIGEVTDPVERLRAYVDFEVLSDFDGGDLALLADVKLRDTLAAQWRERLRPWFG
+EDAPGDAGQKAALQSARLIADGAWTDQALGLLSMTGEQRALVRGIAQRLIDEGVQK
+>4_1951
+MMVRESKKTMILDAAIQVIEEDGITAVTFDSVAAAAGITRAGIIYHFPSRDDLIAAIHQR
+LADRWERQLEIACGKPTAEATPMERLTAYILTCSTAASRAEFQMILDSQDTQHKAIWEDL
+IDRWTGRSERDEAERDQMTSLALLAADGLWVNDLIGSRPISQDHRSETAKQIIALLQNDV
+HESEAKPNG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000304.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000304.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c238c24163a226960a27ba83bfdc8e6462cdfbef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000304.fa
@@ -0,0 +1,40 @@
+>0_195
+MTTYATLAARYADAFDSVAHGERAREAGRHLPFAALGELQAAGFGKVGVPEDAGGEGGGS
+ETVLRLLMDLAARDVNTAHVWRSHLVFIATAMDQAPARRERWLRHIVDGDWAGSALAERA
+GGAAPGRAATLASRDEGGTWVVRGQKYYATGSAFATWTAATVGIEGADLVSRRNSKRAGG
+AVREPDRAVAVVRVRQPRVGIKDDWDGFGQRLTATGSVVLDDAAAEELLEVPRQDGPVPV
+LMEATLLALQAGIGRAALTEGTQLLRQRRRTFNTGTAALPKDDPQLLEIMGQLAGRQAAA
+ELMVREIGRLLDEGQDGADGAGPAEADVVAASAEAMAAAYRAQAVVPEAVLEVCTRIFDT
+LGASATSATLRLDRHWRNARTLATHDPAAFKVRMAGDWLVNGTPPTAYTSAGEVPEGD
+>1_2141
+MTTYATLAARYADAFDSVAHGERAREAGRHLPFAALAELQAAGFGKVGVPEDAGGEGGGS
+ETVLRLLMDLAARDVNTAHVWRSHLVFIATAMDQAPARRERWLRHIVDGDWAGSALAERA
+GGAAPGRAATLASRDEGGTWVVRGQKYYATGSAFATWTAATVGIEGADLVSRRNSKRAGG
+AVREPDRAVAVVRVRQPRVGIKDDWDGFGQRLTATGSVVLDDAAAEELLEVPRQDGPVPV
+LMEATLLALQAGIGRAALTEGTQLLRQRRRTFNTGTAALPKDDPQLLEIMGQLAGRQAAA
+ELMVREIGRLLDEGQDGADGAGPAEADVVAASAEAMAAAYRAQAVVPEAVLEVCTRIFDT
+LGASATSATLRLDRHWRNARTLATHDPAAFKVRMAGDWLVNGTPPTAYTSAGEVPEGD
+>2_178
+MTSYADLAARFADAFDAVGHGERAREAGRHLPFAVQRGLQEAGFGRVSVPEVAGGDGASH
+ETALRLLMDLAARDVNTAHLWRSHLVFVATVLDQVPAAAEPWLERVVAGDWAGSALAERG
+TAAPGRAATMAERDEGGTWVVTGEKYYATGSAFATWTIATVGVDGDGLVSRRNSKRAGGV
+VREPGRAVAVVRVRQPRVRVKDDWDGFGQRLTATGSVVLDGAAAEALLEVPRREGPVPVL
+QEASLLALQVGVGRAALAEGVELLRARRRTFNTGTEALPAQDPQLLEIMGRLAGQLAAAE
+ALVRQVGGLMDEAEERGTAGDDDGAARLMEEAMVAAYRAQAVVPDAVLGVCTGIFDTLGA
+SATSAALQLDRHWRNARTLATHDPAAFKVRMAGDHLVNGTPPTAYTSAGVVDDD
+>3_133
+MTTYATLAARYADAFDSVAHGERAREAGRHLPFAALGELQAAGFGKVGVPVDAGGEGGGS
+ETVLRLLMDLAARDVNTAHVWRSHLVFIATAMDQAPARRDRWLRHIVAGDWAGSALAERA
+GGAAPGRAATLASRDEGGTWVVRGQKYYATGSAFATWTAATVGIEGADLVSRRNSKRAGG
+AVREPDRAVAVVRVRQPRVGIKDDWDGFGQRLTATGSVVLDDAAAEELLEVPRQDGPVPV
+LMEATLLALQAGIGRAALTEGTQLLRKRRRTFNTGTAALPKDDPQLLEIMGQLAGRQAAA
+ELMVREIGRLLDEGEDGADGAGLAEADVVAASAEAMAAAYRAQAVVPEAVLEVCTRIFDT
+LGASATSATLRLDRHWRNARTLATHDPAAFKVRMAGDWLVNGTPPTAYTSAGDAQD
+>4_197
+MTTYATLAARYADAFDSVAHGERAREAGRHLPFAALGELQAAGFGKVGVPVDAGGEGGGS
+ETVLRLLMDLAARDVNTAHVWRSHLVFIATAMDQAPARRERWLRHIVDGDWAGSALAERA
+GGAAPGRAATLASRDEGGTWVVRGQKYYATGSAFATWTAATVGIEGADLVSRRNSKRAGG
+AVREPDRAVAVVRVRQPRVGIKDDWDGFGQRLTATGSVVLDDAAAEELLEVPRQDGPVPV
+LMEATLLALQAGIGRAALTEGTQLLRQRRRTFNTGTAALPKDDPQLLEIMGQLAGRQAAA
+ELMVREIGRLLDEGEDGADGAGPAEADVVAASAEAMAAAYRAQAVVPEAVLEVCTRIFDT
+LGASATSATLRLDRHWRNARTLATHDPAAYKVRMAGDWLVNGTPPTAYTSAGEVPEGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000313.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000313.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d70f307b689caa5f457b15aa1e93770e6ba13f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000313.fa
@@ -0,0 +1,10 @@
+>0_207
+MDRELRTPPELEGVDWHDDAPRRPRPIVTLVAWIAILGLVLSVGAGIFSAF
+>1_2151
+MDRELRTPPELEGVDWHDDAPRRPRPIVTLVAWIAILGLVLSVGAGIFSAF
+>2_156
+MDRSNEIPPELQGLDWGEDDAPRRRRPLITLVAWLCIIGLVLGVAAGLFSIL
+>3_109
+MADLPPELEFAEFDDDPRPSAPSPWVRVLAVVVLLGLVGSLAAGLFGGI
+>4_207
+MDRELRTPPELEGVDWHDGAPRRPRPIVTLVAWIAILGLVLSVGAGIFSAF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000326.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000326.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5aceba32e6633e24cffca2f6b663f358e66d9a69
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000326.fa
@@ -0,0 +1,40 @@
+>0_226
+MAIHPVDATLEAAKIDPDQRAERLKGVKLDGAGWKYALTRALKEFGNDGGTDLAAKLTYY
+LVLSLAPSLLAVFSILSLVLASNRGAIDDLLGELTGLVPSDYQPLVTNLVTTMSDSAGSG
+GGIIALIIGIATALWSASAYVKAFNRSANTVYGYEEGRGLVKLTLTNLLTTLILIVGIVV
+VLLSLALNRSLVDGFLQPIAGPLGMTGVVNFLSDTFLPVWAWAKWPVVVVILLVLIATLY
+YTTPNVQKPRFHLFGPGNIVALVGMVLAAVALSVYFTQFAGYSAYGAIGTVMALLFALWI
+FNIVLLLGLEVDAEVERARQLEAGLPAEARVQLPPKDVAGVEKRAEKQTAVEERGYELRA
+VHEGR
+>1_2190
+MAIHPVDATLEAAKIDPDQRAERLKGVKLDGAGWKYALTRALKEFGNDGGTDLAAKLTYY
+LVLSLAPSLLAVFSILSLVLASNRGAIDDLLGQLTGLVPSDYQALVTNLVTTMSDSAASG
+GGIIALVIGIATALWSASAYVKAFNRSANTVYGYEEGRGLVKLTLTNLLTTLILIVGIVV
+VLISLALNRSLVDGFLQPIAGPLGMTGVVNFLSDTFLPVWAWVKWPVVVLILLLLIATLY
+YTTPNVQKPRFHLFGPGNIVALVGMVLAAVALSVYFTQFAGYSAYGAIGTIMALLFALWI
+FNIVLLLGLEVDAEVERARQLEAGLPAEARVQLPPKDVAGVEKRAEKQTAVEERGYELRA
+VHEGR
+>2_127
+MAIHPVDATLQAAKIDPEERTERLQGVKLDGAGWKYALGRAFKEFGKDGGTDLAAKLTYF
+MVLSLAPSLLAVFSILSLVLASNRGAIDDLMAQMTGLVPGEYQPLVTDLVTTMSESASGG
+GGIVALVVGILTALWSASAYVKAFNRSVNTVYGYEEGRGFVKLTLSNLLTTLIMIVGIVV
+VLISLALNRSLVDGFLAPIAGPLGMTGAVNFLSDTFLPIWAWVKWPVVVVILLLLIATLY
+YTTPNVRKPSFNLFGPGNVFALVGMVLAAVGLSVYFTQFAGYSAYGAIGTIMALLFALWI
+FNIVLLLGVEIDAEVERAKQLVAGLPAEEAVRLPPKDASALEKRVEKQTALQERGYELRA
+THEDR
+>3_92
+MAIHPVDATLEAARIDPEERTRRLKGVKLDGAGWKYAFTRALKEFGNDGGTDLAAKLTYF
+MVLSLAPALLAVFSILTLVLSSNRSAVDDVVRQLTELVPADYQGVVGDVVDNLLGQAGGG
+VLALIIGILTALWSASAYVKAFSRASNQVYNYSEGRGFVKLTLTNLVTTVVMLVGIVLVL
+ISLALNRSLVDGFLAPIAGPLGMTDAVNFLSDTFLPIWAWLKWPVVVALLLVLIATLYYF
+APNVKKPSFHMFGPGNIFALVGMALAAVALYFYFTTLAGYSAYGAIGGVMALLFALWIFN
+IVLLLGLEIDTEVERAKQLTAGMPAEDAVKLPPKDVSALEKKVEKQEELEEKGYELRALH
+DDGSDSDSDEGKGVSRAPRHAAGSHGA
+>4_227
+MAIHPVDATLEAAKIDPDQRAERLKGVKLDGAGWKYALTRALKEFGNDGGTDLAAKLTYY
+LVLSLAPSLLAVFSILSLVLASNRGAIDDLLGQLTGLVPSDYQALVTNLVTTMSDSAASG
+GGIIALVIGIATALWSASAYVKAFNRSANTVYGYEEGRGLVKLTLTNLLTTLILIVGIVV
+VLISLALNRSLVDGFLQPIAGPLGMTGVVNFLSDTFLPVWAWVKWPVVVLILLVLIATLY
+YTTPNVQKPRFHLFGPGNIVALVGMVLAAVALSVYFTQFAGYSAYGAIGTIMALLFALWI
+FNIVLLLGLEVDAEVERARQLEAGLPAEARVQLPPKDVAGVEKRVEKQTTLEERGYELRA
+VHEGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000334.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000334.fa
new file mode 100644
index 0000000000000000000000000000000000000000..04db9b25d868322592c4b8acdada531065bb04a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000334.fa
@@ -0,0 +1,30 @@
+>0_239
+MDLSNQSAIVTGGASGLGHATARRLADAGAAVVVVDLPDRERETVRADAVAALGPRARFV
+TGDVTAEDTAREAVAAALEAGPLRVLVNCAGVATPGKLVGRDGPLSAEVLSRVLAINTVG
+TVAMMAQAAAAMKAQEPLGEDRGVIVNTASVAAYDGQIGQIAYSASKGAVVALTLPAARE
+LASSQIRVVTIAPGLMETPMMAGLPEAAREALSTKTPHPARLGRPEDHALLVEQIVSNPF
+LNGEVIRLDGAVRLEPR
+>1_2202
+MDLSNQSAIVTGGASGLGHATARRLADAGAAVVVVDLPDREGETVRADAVAALGPRARFV
+TGDVTAEDTAREAVAAALEAGPLRVLVNCAGVATPGKLVGRDGPLSAEVLSRVLAINTVG
+TVSMMAQAAAAMKAQEPLGEDRGVIVNTASVAAYDGQIGQIAYSASKGAVVSLTLPAARE
+LASSQIRVVTIAPGLMETPMMAGLPEAAREALSTKTPHPARLGRPEDYALLVEQIVSNPF
+LNGEVIRLDGAVRLEPR
+>2_113
+MDLSNQSAIVTGGASGLGHATARRLAEAGAAVVVVDLPDREGETLRADAVAALGPRARLV
+TGDVTAEATAEEAVAAALEAGPLRVLVNCAGVATPGKLVGRGGPLSAEVLTRVLAINTVG
+TVNFMSRAAAAMQGQEPQGEDRGVIVNTASVAAYDGQIGQIAYAASKGAVVSLTLPAARE
+LAASQIRVVTIAPGLMETPMMAGLPEAAREALATKTPHPARLGRPEDYALLVEQIVANPF
+LNGEVIRLDGAVRLEPK
+>3_81
+MARRESLDLQGASAIVTGGASGLGHATARRLAAAGAAVVVVDLPDREGESLRADAVASLG
+ERARFITGDVTAEATAEQAVAAALEAGPLRVLVNCAGVATPGKLVGRDGPLAAEALSRVL
+AINVVGTVTMMARAAAVMKDQELWGEDRGVIVNTASVAAFDGQIGQIAYSASKGAVAALT
+LPAARELAASQVRVVTIAPGLMETPMMAGLPEAAREALSTKTPHPARLGAPDDYALLVEQ
+IVSNPFLNGETIRLDGAVRLEPR
+>4_239
+MDLSNQSAIVTGGASGLGHATARRLADAGAAVVVVDLPDREGETVRADAVAALGPRARFV
+TGDVTAEDTAREAVAAALEAGPLRVLVNCAGVATPGKLVGRDGPLSAEVLSRVLAINTVG
+TVSMMAQAAAAMKAQEPLGEDRGVIVNTASVAAYDGQIGQIAYSASKGAVVALTLPAARE
+LASSQIRVVTIAPGLMETPMMAGLPEAAREALSTKTPHPARLGRPEDYALLVEQIVSNPF
+LNGEVIRLDGAVRLEPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000335.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000335.fa
new file mode 100644
index 0000000000000000000000000000000000000000..021e709f0a83c77f3a887a7e2db89c41e1bf006e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000335.fa
@@ -0,0 +1,24 @@
+>0_240
+MKKPPLAQDPIREAARNWERHGWGDVARPMAAITSIMRAQQILLGRAQAALKPYGLTFAR
+YELLALLNFSRENRMRMSKASALLQVHPTSVTNAVDRLEAAGLVERTPHESDRRALVLAL
+TDEGRRVAVAATETLNAEVFGRSGFGPADVDTLIDVLGRFRAEAGDFQVDGPDAGAPATA
+EHTSS
+>1_2203
+MKKPPLAQDPIREAARNWERHGWGDVARPMAAITSIMRAQQILLGRAQAALKPYGLTFAR
+YELLALLNFSREKRMRMSKASALLQVHPTSVTNAVDRLEAAGLVERTPHESDRRALVLAL
+TDEGRRVAVAATETLNAEVFGRSGFDPADVDTLIDVLGRFRAEAGDFEADGPDAGAPATA
+EHTSS
+>2_112
+MKNAPLPQDPIREAARNWERHGWGDVARPMAAVTSIMRAQQILLGRTQAALKPFGLTFAR
+YELLALLNFSREKRMRMSKASALLQVHPTSVTNAVDRLESAGLVERTPHESDRRALVLAL
+TDEGRRVAVAATETLNEEVFGRTGFDEADVDALIDVFGRFRAGAGDFEADGADTTTERPS
+A
+>3_80
+MSTRDPLPQDPIREAARNWEHHGWGEVAAPMAAVTAIMRTQAILLARTQAVLKPFGLTFA
+RYELLALLNFSRERRQLMSKAGALLQVHPTSVTNAVDRLEAAGLVERQPHETDRRALLLA
+LTDEGRRVADAATEALNAEVFGATGFTDDDVAALNEILGRFRAGSGDFEA
+>4_240
+MKKPPLAQDPIREAARNWERHGWGDVARPMAAITSIMRAQQILLGRAQAALKPYGLTFAR
+YELLALLNFSREKRMRMSKASALLQVHPTSVTNAVDRLEAAGLVERTPHESDRRALVLAL
+TDEGRRVAVAATETLNAEVFGRSGFDPADVDTLIDVLGRFRAEAGDFEADGPDAGAPATA
+EHTSS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000337.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000337.fa
new file mode 100644
index 0000000000000000000000000000000000000000..59304c51d91498df44f766c3a1c4a248c33d506c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000337.fa
@@ -0,0 +1,90 @@
+>0_246
+MTSPQTTESTTALPHERVEPKDTASAPFVARHIGPRPADVEHMLQTLGYDSLEALVDTAV
+PAGIRQPKPLELPAPLTESAVLEQLREIAGRNVMKTQMIGQGFSDTVTPGVILRKVLENP
+AWYTAYTPYQPEISQGRLEALLNYQTMVQDLTGLDIANASLLDEASAAAEAVLLMHRANR
+RRTDGVTLLDADLFPQTLSVVRLRAEAVGIDVRVADLSAGIPEDVRAEVEEKGLCGVVLQ
+QPGDSGRIHDHAAVIAQAKEAGALVTVAADILSLALITPPGEQGADIAVGSTQRFGVPLF
+FGGPHAAYMAVKEGLQRSMPGRLVGVSHDDAGKPAYRLALQTREQHIRREKATSNICTAQ
+ALLAIVASMYAVYHGPQGIARIARHAHAQAVRLAEALRAGGVEVAEEHFFDTITVRVPGR
+AEQVLQAAEENGVNLRLVDADTLRIAADETTVDADLVAVLTAFGLDAGSLPASAHEGAVA
+TPAVPESLRRSSAFMMHPVFNTHHSETKMLRYLRRLSGYDLALDRTMIPLGSCTMKLNAT
+AEMEAISWPEFCSIHPFAPDHQTEGWRFLIADLEAKLAEITGYAGVSVAPNAGSQGEFAG
+LWAIRQYHLARGEGERDICLIPASAHGTNAASAVLAGLKVVVVATADDGTIDAADLDAKI
+AANEGRIAAIMITYPSTHGVYDADVKEVCATVHAAGGQVYIDGANLNALVGLAQPGEFGG
+DVSHLNLHKTFCIPHGGGGPGVGPVAVGEHLVPYLPSREALMTAAPHGSAGVLPISWAYI
+HLMGAEGLRSATAHALLGANYISRRLAPLYPTLYTGNDGLVAHECILDLRELTARTGVTA
+EDVCKRLIDYGFHAPTLAFPVAGTLMVEPTESEDLEEIERFIEAMEAIHAEITAVTPETV
+ADSVLRRAPHTLNVLMADEWDRPYSRAQAGTPVPSLRLDKYLPPVGRIDGAYGDRNLVCS
+CPPPEAFEGAVADTADED
+>1_2211
+MTSPQTTESTTALPHERVEPKDTASAPFVARHIGPRPADVEHMLQTLGYDSLEALVDTAV
+PAGIRQPKPLELPAPLTESAVLEQLREIAGRNVMKTQMIGQGFSDTVTPGVILRKVLENP
+AWYTAYTPYQPEISQGRLEALLNYQTMVQDLTGLDIANASLLDEASAAAEAVLLMHRANR
+RRTDGVTLLDADLFPQTLSVVRLRAEAVGIDVRVADLSAGIPEDVRAEVEEKGLCGVVLQ
+QPGDSGRIHDHAAVIAQAKEAGALVTVAADILSLALITPPGEQGADIAVGSTQRFGVPLF
+FGGPHAAYMAVKEGLQRSMPGRLVGVSHDDAGKPAYRLALQTREQHIRREKATSNICTAQ
+ALLAIVASMYAVYHGPQGIARIARHAHAQAVRLAEALRAGGVEVAEEHFFDTITVRVPGR
+AEQVLQAAEENGVNLRLVDADTLRIAADETTVDADLVAVLTAFGLDAGSLPASAHEGAVA
+TPAVPESLRRSSAFMTHPVFNTHHSETKMLRYLRRLSGYDLALDRTMIPLGSCTMKLNAT
+AEMEAISWPEFCSIHPFAPDHQTEGWRFLIADLEAKLAEITGYAGVSVAPNAGSQGEFAG
+LWAIRQYHLARGEGERDICLIPASAHGTNAASAVLAGLKVVVVATADDGTIDAADLDAKI
+AANEGRIAAIMITYPSTHGVYDADVKEVCATVHAAGGQVYIDGANLNALVGLAQPGEFGG
+DVSHLNLHKTFCIPHGGGGPGVGPVAVGEHLVPYLPSREALMTAAPHGSAGVLPISWAYI
+HLMGAEGLRSATAHALLGANYISRRLAPLYPTLYTGNDGLVAHECILDLRELTARTGVTA
+EDVCKRLIDYGFHAPTLAFPVAGTLMVEPTESEDLEEIERFIEAMEAIHAEITAVTPETV
+ADSVLRRAPHTLNVLMADEWDRPYSRAQAGTPVPSLRLDKYLPPVGRIDGAYGDRNLVCS
+CPPPEAFEDAVADTADED
+>2_105
+MTSPQTTESTTALPHERVEPKDTASAPFVARHIGPRPADVEHMLQTLGYDSLEALVDTAV
+PAGIRQPKPLELPAPLTESAVLEQLREIAGRNVMKTQMIGQGFSDTVTPGVILRKVLENP
+AWYTAYTPYQPEISQGRLEALLNYQTMVQDLTGLDIANASLLDEASAAAEAVLLMHRANR
+RRTDGVTLLDADLFPQTLSVVRLRAEAVGIDVRVADLSAGIPEDVRAEVEEKGLCGVVLQ
+QPGDSGRIHDHAAVIAQAKEAGALVTVAADILSLALITPPGEQGADIAVGSTQRFGVPLF
+FGGPHAAYMAVKEGLQRSMPGRLVGVSHDDAGKPAYRLALQTREQHIRREKATSNICTAQ
+ALLAIVASMYAVYHGPQGIARIARHAHAQAVRLAEALRAGGVEVAEEHFFDTLTVRVPGR
+AEQVLQAAEENGVNLRLVDADTLRIAADETTVDADLVAVLTAFGLDAGALPASAHEGAVA
+TPAVPEALRRSSAFMTHPVFNTHHSETQMLRYLRRLSGYDLALDRTMIPLGSCTMKLNAT
+AEMEAISWPEFCSIHPFAPDHQTEGWRFLIADLEAKLAEITGYAGVSVAPNAGSQGEFAG
+LWAIRQYHLARGEGERDICLIPASAHGTNAASAVLAGLKVVVVATADDGTIDAADLDAKI
+AANEGRIAAIMITYPSTHGVYDADVKEVCATVHAAGGQVYIDGANLNALVGLAQPGGFGG
+DVSHLNLHKTFCIPHGGGGPGVGPVAVGEHLVPYLPSREALMTAAPHGSAGVLPISWAYI
+HLMGAEGLRSATEHALLGANYISRRLAPLYPTLYTGNDGLVAHECILDLRELTARTGVTA
+EDVCKRLIDYGFHAPTLAFPVAGTLMVEPTESEDLQEIERFIEAMEAIHAEITAVTPETV
+ADSVLRRAPHTLNVLMADEWDRPYSRAQAGTPVPSLRLDKYLPPVGRIDGAYGDRNLVCS
+CPPPEAFEDAVADTADED
+>3_73
+MTSPLTPTEPRDTASAPFVARHIGPRGEDVRHMLQTLGLGSVDELVDTAVPSVIRQSAPL
+DLPAPLTEAAALEQLREIAGRNVVKTQMIGQGFYDTVTPGVILRKVLENPAWYTAYTPYQ
+PEISQGRLEALLNYQQMVEDLTALPIANASLLDEASAAAEAVLLMHRANRKKADGITLLD
+ADLFPQTLTVAQMRAEAVGLEVRVADLSAGIPEDVRAEVEEKGLCGVVLQQPGDSGRLHD
+HSAVIAQAKEAGALITVAADILSLALITPPGEQGADIAIGSTQRFGVPLFFGGPHAAYLA
+VREGLQRSMPGRLVGVSHDDAGKPAYRLALQTREQHIRREKATSNICTAQALLAITASMY
+AVYHGPAGITAIARHAHAQAHRLAIALAGAGVEVAHAEYFDTLTLNVPGRAEEVVRAAEE
+AGVNLRLVDADIVRVACDETTVDEDLAAVLTAFGADPASLPAAPHEGAVQTPAVPEAQRR
+TSAFMTHPVFNTHRSETQMLRYITRLANRDLALDRTMIPLGSCTMKLNATTEMEAISWPE
+FCAIHPFAPDHQTEGWRFLISDLEERLAEITGYAGVSVAPNAGSQGEFAGLWAIRQYHLA
+HGDGERDVCLIPASAHGTNAASAVLAGLRVVVVATADDGTIDSADLDAKIAAHEGRVAAI
+MITYPSTHGVFDGDVTEVCDKVHAAGGQVYIDGANLNALVGLARPGAFGGDVSHLNLHKT
+FCIPHGGGGPGVGPVAVGEHLVPFLPSAERLVTAAPHGSAGVLPISWAYIAMMGGEGLKD
+ATEQALLNANYISRRLADHYPTLYTGEGGLVAHECILDLRELTAQTGVTAEDVCKRLIDY
+GFHAPTLAFPVAGTLMVEPTESEDLAELDRFIDAMISIHAEITATTPETVEQSVLRRAPH
+TLGATTGEDWDRPYTRAQALYPLPSLVDDKYLPPVGRIDGAYGDRNLVCSCPPPEAFEEA
+AASPESTEPVSAADTASTSH
+>4_245
+MTSPQTTESTTALPHERVEPKDTASAPFVARHIGPRPADVEHMLQTLGYDSLEALVDTAV
+PAGIRQPKPLELPAPLTESAVLEQLREIAGRNVMKTQMIGQGFSDTVTPGVILRKVLENP
+AWYTAYTPYQPEISQGRLEALLNYQTMVQDLTGLDIANASLLDEASAAAEAVLLMHRANR
+RRTDGVTLLDADLFPQTLSVVRLRAEAVGIDVRVADLSAGIPQDVRAEVEEKGLCGVVLQ
+QPGDSGRIHDHAAVIAQAKEAGALVTVAADILSLALITPPGEQGADIAVGSTQRFGVPLF
+FGGPHAAYMAVKEGLQRSMPGRLVGVSHDDAGKPAYRLALQTREQHIRREKATSNICTAQ
+ALLAIVASMYAVYHGPQGIARIARHAHAQAVRLAEALRAGGVEVAEEHFFDTITVRVPGR
+AEQVLKAAEENGVNLRLVDADTLRIAADETTVDADLVAVLTAFGLDAGSLPASAHEGAVA
+TPAVPEALRRSSAFMTHPVFNTHHSETKMLRYLRRLSGYDLALDRTMIPLGSCTMKLNAT
+AEMEAISWPEFCSIHPFAPDHQTEGWRFLIEDLEAKLAEITGYAGVSVAPNAGSQGEFAG
+LWAIRQYHLARGEGERDICLIPASAHGTNAASAVLAGLKVVVVATADDGTIDAADLDAKI
+AANEGRIAAIMITYPSTHGVYDADVKEVCATVHAAGGQVYIDGANLNALVGLAQPGEFGG
+DVSHLNLHKTFCIPHGGGGPGVGPVAVGEHLVPYLPSREALMTAAPHGSAGVLPISWAYI
+HLMGAEGLRSATAHALLGANYISRRLAPLYPTLYTGNDGLVAHECILDLRELTARTGVTA
+EDVCKRLIDYGFHAPTLAFPVAGTLMVEPTESEDLEEIERFIEAMEAIHAEITAVTPETV
+ADSVLRRAPHTLNVLMADEWDRPYSRAQAGTPVPSLRLDKYLPPVGRIDGAYGDRNLVCS
+CPPPEAFEGAVADTADED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000348.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000348.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89a2850740a7a07060384175ec7048dc7e8664f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000348.fa
@@ -0,0 +1,30 @@
+>0_260
+MVAPPPHHDAAPSPVFPVAAGLQAGLTASQLRGPRFDAPHHGLRHTAGGQPSLADVVRAL
+QRTNPGTAATHATAARLWGMWLPRQWERGPIHLARTRAEGGAPRRSGVVGHELHPQDPVL
+VRARVRITTPAATWAALAQLGLPLADVVAAGDSLLQRADGPAGRRRPGDHPRCTVRDLEA
+EVLRVRGRRGTRTLRAALPLLRDGADSRAETLLRLALADAGVPEPEVNPLLMLSDGSTVR
+PDLVWREAHVCVQYEGDHHRTDPRQWRRDIERDRRMQAEGWIVLRVTASVFTRRGLDALL
+RDLAAHLRLPLPA
+>1_2224
+MVAPPPHHDAAPSPVFSVAAGLQAGLTASQLRGPRFDAPHHGLRHTAGGQPSLADVVRAL
+QRTNPGTAATHATAARLWGMWLPRQWERGPIHLARTRAEGGAPRRSGVVGHELHPQDPVL
+VRARVRITTPAATWAALAQLGLPLADVVAAGDSLLQRADGPAGRRRPGDHPRCTVRDLEA
+EVLRVRGRRGTRTLRAALPLLRDGADSRAETLLRLALTDAGVPGPEVNPLLLLSDGSTVR
+PDLVWREAHVCVQYEGDHHRTDPRQWRRDIERDRRMQAEGWIVLRVTASVFTRRGLDALL
+RDLAAHLRLPLPA
+>2_426
+MWLPAEAEQRVHLSRVRPGAQPRIAGVAGHRIRIDPVTGLTVLGVGDKAYTVTTPERTWT
+DLASMGLTREDLIVAGDALLHRRDGPGGEVAAGRQHPLSSLADLGVAVAEARGVTGWRLL
+GEALPHLRERSDSPQETRLRVRLVGAGFPEPQVNPEVPLVWDAWGRILRSTPVDLYFAAA
+KVALQFEGEHHFSRARQYRRDMRRDEELRDVGVETVRVDSAVFGAGEWARFMARLQRLLT
+TRGGA
+>3_380
+MDGPRDLVWREARVAIEYEGAHHFEDADQYRRDMRRDEELRALGWVVLRVDRDVWTPQGW
+EVFLGRLGAALARWSC
+>4_258
+MVAPPPHHDAAPSPVFPVAAGLQAGLTASQLRGPRFDAPHHGLRHTAGGQPSLADVVRAL
+QRTNPGTAATHATAARLWGMWLPRQWERGPIHLARTRAEGGAPRRSGVVGHELHPQDPVL
+VRARVRITTPAATWAALAQLGLPLADVVAAGDSLLQRADGPAGRRRPGDHPRCTVRDLEA
+EVLRVRGRRGTRTLRAALPLLRDGADSRAETLLRLALADAGVPEPEVNPLLMLSDGSTVR
+PDLVWREAHVCVQYEGDHHRTDPRQWRRDIERDRRMQAEGWIVLRVTASVFTRRGLDALL
+RDLAAHLRLPLPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000352.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000352.fa
new file mode 100644
index 0000000000000000000000000000000000000000..441dbbe10d72276b423a52c07fdf32522cfea81e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000352.fa
@@ -0,0 +1,20 @@
+>0_269
+MSVRTPDPNPGWLSDEDLYEARRRLPMVYVEAIPVRLDSLGYVTEIGLLYVADETGTFQR
+TFVSGRVQYRETIRAALMRHLEKDLGPLAFPQLPPSVVPCTVAEYFPAPSETGLTDDRQH
+AVALVYVVPVTGECQPRQNALELTWLTPEEALGEDIQAEFIGGRGDLVRQALAHVGWGR
+>1_2235
+MSVRTPDPNPGWLSDEDLYEARRRLPMVYVEAIPVRLDSLGYVTEIGLLYVADETGTFQR
+TFVSGRVQYRETIRAALMRHLEKDLGPLAFPQLPPSVVPCTVAEYFPAPSETGLTDDRQH
+AVALVYVVPVTGECQPRQNALELTWLTPEEALGEDIQAEFIGGRGDLVRQALAHVGWGR
+>2_66
+MSVRTPDPNPGWLSDEDLYEARRRLPMVYVEAIPVRLDSLGYVTEIGLLYVADETGTFQR
+TFVSGRVQYRETIRAALMRHLEKDLGPLAFPQLPPSVVPCTVAEYFPAPSETGLTDDRQH
+AVALVYVVPVTGECQPRQNALELTWLTPEEALGQDIQAEFIGGRGDLVRQALAHVGWGR
+>3_51
+MSVRTPDPNPGWLNEEDLYEARRRLPMVYVEAIPVRVDALGYVSEIGLLYVADEEGQFQR
+TFVSGRVMYRETIRGALMRHLEKDLGPLAFPQLPPSLVPCAVAEYFPAPSETGLTDDRQH
+AVSLVYVVPVSGECSPRQDALELTWLTPQEALGEDVQAEFIGGRGNLVRQALAHVGWGR
+>4_268
+MSVRTPDPNPGWLSDEDLYEARRRLPMVYVEAIPVRLDSLGYVTEIGLLYVADETGTFQR
+TFVSGRVQYRETIRAALMRHLEKDLGPLAFPQLPPSVVPCTVAEYFPAPSETGLTDDRQH
+AVALVYVVPVTGECQPRQNALELTWLTPEEALGEDIQAEFIGGRGDLVRQALAHVGWGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000358.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000358.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9541a5c43c018d2e81c145fb6c3068d1697617c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000358.fa
@@ -0,0 +1,40 @@
+>0_280
+MTSTARSPRVSRRAALGLGVGALAVGGVAVVTDLAGAPAGPLGANATALYGMRSSTGHTY
+ATLPGRAGRIDVYRPPGQGPFPVLVWNAGSGWRSDRGYSDGVDVARGLVPHGYAVAAFSV
+RSSKQGTFPAQVEDATAAVRWVRRNAPGLQLDAGRVAVAGSSSGGWNALMAGLTGGQDLD
+REQVPLPGREVPDGGHAIPEEDRVQAIVDFFGPTDFLTMNRQMLPGACADYNRANRLKHC
+HLDDRSTKSDMLGVPVLASGGLTRLASPIAHVRPDSPPLLVVHGRKDVTVPWGQSLELYR
+AAETAGLRTAFYSVAEGSHDLGMMTAKTRSAEVLRNGVPASAVHATISWSAVASFLDAVL
+PR
+>1_2253
+MTSTARSPRVSRRAALGLGVGALAVGGVAVVTDLAGAPAGPLGANATALYGMRSSTGHTY
+AALPGRAGRIDVYRPPGQGPFPVLVWNAGSGWRSDRGYSDGVDVARGLVPHGYAVAAFSV
+RSSKQGTFPAQVEDATAAVRWVRRNAPGLQLDAGRVAVAGSSSGGWNALMAGLTGGQDLD
+REQVPLPGREVPDGGHAIPEEDRVHAIVDFFGPTDFLRMNRQMLPGACADYNRANRLEHC
+HLDDHSTKADMLGVPVLASGGLTRLASPIAHVRPDSPPLLVVHGRKDVTVPWGQSLELYR
+AAEAAGLRTAFYSVAEGGHDLGMMTAKTRSAEVLRTGVPASAVHASISWSAVASFLDAVL
+PR
+>2_56
+MATSGRRGRLTRRAVLGLGAGALALGGGAAVANLAGVPPAPVGPDVNALFGMRSSTGHRY
+ADLPGRAGRVDVYRPQGPGPFPVVVWNAGSGWRDDRGYHDGQTVARGLVPHGYAVAAFSV
+RSSKQGRFPAQVEDATAAVRWVRAHAVELDLDASRLTVAGTSSGGWNALMAGLTGGRDLD
+RAHVPPPGREVPPGGHAIPEEDRVQAILDFFAPTDFLAMNAQMPPGACADYNRQRRLEHC
+HLDDHSTKSAMLGVPVLASYGLTRLASPIAHVRPDSPPMMIVHGLKDPTVPWRQSLELYE
+AAEAAGVRAAFYSVADAGHDLGMMGGGWGSAEVLRSGVPLSAVHATISWAAVAAFLDTVL
+PG
+>3_35
+MGGDTSTARAPRVRRRTLLGLGLGALAVGGTATALGHGSPVDSPALRQTMGALFGTTVIS
+GIVYADLPGAAGRMDLYLPEGEGPFPVLAWNAGSGWRSDRGFQGGDAVARGLVPAGHAVA
+AFSVRSAREDAFPAQVLDATAAVRHLRENAGELRVDPGRIAVGGNSSGGWNALMAGLTGG
+RDLDRSAVPAPGDEVPEGGHAIPEEDRVQAIVDCFAPVDFLQMNVQMPRGACEEYDRRNH
+TRHCHLDDASTKSRMLGAPVMARPELARLANPAVHVTPAAPPTLIVHGRADREVPYVQSR
+GLYQAYVGAGVPVAMYSVEGAGHDLQMMARRVGRTDVVRSGLPRQAVHGSISWSAVAAFL
+DVAMPRPRR
+>4_286
+MTSTARSPRVSRRAALGLGVGALAVGGVAVVTDLAGAPAGPLGANATALYGMRSSTGHTY
+AALPGRAGRIDVYRPPGQGPFPVLVWNAGSGWRSDRGYSDGVDVARGLVPHGYAVAAFSV
+RSSKQGTFPAQVEDATAAVRWVRRNAPGLQLDAGRVAVAGSSSGGWNALMAGLTGGQDLD
+REQVPLPGREVPDGGHAIPEEDRVHAIVDFFGPTDFLRMNRQMLPGACADYNRANRLEHC
+HLDDHSTKADMLGVPVLASGGLTRLASPIAHVRPDSPPLLVVHGRKDVTVPWGQSLELYR
+AAEAAGLRTAFYSVAEGGHDLGMMTAKTRSAEVLRTGVPASAVHASISWSAVASFLDAVL
+PR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000363.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000363.fa
new file mode 100644
index 0000000000000000000000000000000000000000..726db5782e7efd82505627ebee16b5de5158bd3e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000363.fa
@@ -0,0 +1,60 @@
+>0_285
+MADNATTSFADRALADAPTDYAQLREWVAQIAELTQPDSVQWVDGSEEERDRLADELVAA
+GTLTRLAEDKFPNSFAAFSDPADVARVEDRTFICSEKEEDAGFTNNWMDPAKMHGILDDA
+FTGAMRGRTMYVIPFVMGHLDAEDPKYGVEITDSAYVVLSMRIMARIGQDVLDKMSREQA
+FYVPAVHSVGAPLEPGEQDVPWPCNETKWIVHFPEERSIWSFGSGYGGNALLGKKCYALR
+IASVMARDEAWLAEHMLILKLTNPEGRSYHITGAFPSACGKTNLALIDPTIEGWKAETLG
+DDITWIRAGKDGEFRVINPETGYFGVAPGTGWSTNPNAMRAISKGNSIFTNVALTDDGGV
+WWEGMTDEVPEHLTDWRGNDWTPEFGTPAAHPNSRFCTPIEQTDMLADEYRDPRGVKLDA
+ILFGGRRKTTVPLVTEAFDWEDGILKGATLSSETTAAAAGAVGVVRRDPMAMLPFLGYDA
+GDYLAHWVRESGKADPEKLPRIYLVNWFRRNRDGGFAWPGFGENSRVLKWVVERLEGKAE
+AEETPIGLVPAAGSLDLSGIEVSAEDLEDALKVDAAEWAEENELIEQWLGRFGESLPAVV
+RERFEAQKARFAQA
+>1_2
+MADNATTSFADRALADAPTDYAQLREWVAQIAELTQPDSVQWVDGSEEERDRLADELVAA
+GTLTRLAEDKFPHSFAAFSDPADVARVEDRTFICSEKEEDAGFTNNWMDPAKMHGILDDA
+FTGAMRGRTMYVIPFVMGHLDAEDPKYGVEITDSAYVVLSMRIMARIGQDVLDKMSREQA
+FYVPAVHSVGAPLEPGEQDVPWPCNETKWIVHFPEERSIWSFGSGYGGNALLGKKCYALR
+IASVMARDEAWLAEHMLILKLTNPEGRSYHITGAFPSACGKTNLALIDPTIEGWKAETLG
+DDITWIRAGKDGEFRVINPETGYFGVAPGTGWSTNPNAMRAISKGNSIFTNVALTDDGGV
+WWEGMTDEVPEHLTDWRGNDWTPESGTPAAHPNSRFCTPIEQTDMLADEYRDPRGVKLDA
+ILFGGRRKTTVPLVTEAFDWEDGILKGATLSSETTAAAAGAVGVVRRDPMAMLPFLGYDA
+GDYLAHWVRESGKADPEKLPRIYLVNWFRRNRDGGFAWPGFGENSRVLKWVVERLEGKAE
+AEETPIGLVPAAGSLDLSGLEVSAEDLEDALKVDAAEWAEENELIEEWLGRFGESLPQAI
+RDRFEAQKQRFAQA
+>2_51
+MADNATTSFADRALQDAPTDYAQLREWVAQVAELTQPDAVQWVDGSEEEYARLADELVAA
+GTLTRLAEDKFPNSFAAFSDPADVARVEDRTFICSEKEEDAGFTNNWMDPEKMHGILDDV
+FAGSMRGRTMYVIPFVMGHLDAEDPKYGVELTDSAYVVLSMRIMARIGQDVLDKMSREQA
+FYVPAVHSVGAPLEPGQEDVPWPCNSTKWIVHFPEERSIWSFGSGYGGNALLGKKCYALR
+IASVMARDEAWLAEHMLILKLTSPEGRSYHITGAFPSACGKTNLALIDPTIEGWKAETLG
+DDITWIRAGKDGEFRVINPETGYFGVAPGTGWSTNPNAMRAIAKGNSIFTNVALTDDGGV
+WWEGMTDEVPEHLTDWRGNDWTPASETPAAHPNSRFCTPIEQTDMLADEYRDPKGVKLDA
+ILFGGRRKTTVPLVTESFDWEDGILKAATLSSETTAAAAGAVGVVRRDPMAMLPFLGYDA
+GDYLAHWVEESGKADPEKLPRIYLVNWFRRNRDGGFAWPGFGENSRVLKWVVERLEGRAD
+AVETPIGHVPSPEALDLTGIDVSAEDLEDALKVDAEEWAKENELIEEWLGRFGESLPAMV
+RERFEAQKERFARA
+>3_29
+MADNATTSFTELATKDAPTDYAQLREWVAGIAELTQPDAVHWVDGSQEEYDRLAAELVAA
+GTLTKLNEKKLPNSYAAFSDPADVARVEDRTFICSEKEEDAGFTNNWMDPKEMHGILDDA
+FAGSMRGRTMYVIPFVMGHLDAEDPKYGVEITDSAYVVLSMRIMARIGQDVLDKMSREQA
+FYVPAVHSVGAPLEPGEQDVPWPCNETKWIVHFPEERSIWSFGSGYGGNALLGKKCYALR
+IASVMARDEAWLAEHMLILKLTNPEGRSYHITGAFPSACGKTNLALIDPTIEGWKAETLG
+DDITWIRAGKDGEFRVINPETGYFGVAPGTGWSTNPNAMRAISKGNSIFTNVALTDDGGV
+WWEGMTDEVPEHLTDWRGNDWTPESGTPAAHPNSRFCTPIEQTDMLADEYRDPRGVKLDA
+ILFGGRRKTTVPLVTEAFDWEDGILKGATLSSETTAAAAGAVGVVRRDPMAMLPFLGYDA
+GDYLAHWVKESGKADPEKLPRIYLVNWFRRNRDGGFAWPGFGENSRVLKWVVERLEGKAG
+AEETPIGLVPAAGSLDLSGIEVSAEDLEDALKVDAAEWAEENELIEEWLGRFGESLPQAI
+RDRFEAQKARFAQA
+>4_292
+MADNATTSFADRALADAPTDYAQLREWVAQIAELTQPDSVQWVDGSEEERDRLADELVAA
+GTLTRLAEDKFPNSFAAFSDPADVARVEDRTFICSEKEEDAGFTNNWMDPAKMHGILDDA
+FTGAMRGRTMYVIPFVMGHLDAEDPKYGVEITDSAYVVLSMRIMARIGQDVLDKMSREQA
+FYVPAVHSVGAPLEPGEQDVPWPCNETKWIVHFPEERSIWSFGSGYGGNALLGKKCYALR
+IASVMARDEAWLAEHMLILKLTNPEGRSYHITGAFPSACGKTNLALIDPTIEGWKAETLG
+DDITWIRAGKDGEFRVINPETGYFGVAPGTGWSTNPNAMRAISKGNSIFTNVALTDDGGV
+WWEGMTDEVPEHLTDWRGNDWTPESGTPAAHPNSRFCTPIEQTDMLADEYRDPRGVKLDA
+ILFGGRRKTTVPLVTEAFDWEDGILKGATLSSETTAAAAGAVGVVRRDPMAMLPFLGYDA
+GDYLAHWVRESGKADPEKLPRIYLVNWFRRNRDGGFAWPGFGENSRVLKWVVERLEGKAE
+AEETPIGLVPAAGSLDLSGLEVSAEDLEDALKVDAAEWAEENELIEEWLGRFGESLPQAI
+RDRFEAQKQRFAQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000376.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000376.fa
new file mode 100644
index 0000000000000000000000000000000000000000..484dcdb78e82600c89dfcdd48953338589445465
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000376.fa
@@ -0,0 +1,26 @@
+>0_301
+MSTQTEHRGLFVAVEGPDGSGKSTQARALTEVLRAAGHEVVLTREPGGSDLGETLRELLL
+DPEHAPVDPRTEALLFAAARSAHAVRTLRPALARGALVVTDRYVDSSVAYQGAARGLGEA
+RIAALNEWATDGLVPDLTVLIDVDAATAADRRERRAAGGEGAPDRMERETADRHEALRAA
+FLARAAAAPERYLVLDGALPPQELTARALARVTAEAADR
+>1_25
+MSTQTEHRGLFVAVEGPDGSGKSTQARALTEALRAAGHEVVLTREPGGSDLGETLRELLL
+DPGHAPVDPRTEALLFAAARSAHAVRTLRPALARGAVVVTDRYVDSSVAYQGAARGLGEA
+RIAALNEWATDGLVPDLTVLIDVDAATAADRRDRRAAEGEGTPDRMERETADRHEALRAA
+FLARAAAAPERYLVLDGALPPQELTARALARVTAQAADR
+>2_18
+MSTETEHRGLFVAVEGPDGSGKSTQARALVAALRAAGREAVLTREPGGSDLGETLRGLLL
+DPAHAPVDPRTEALLFAAARAAHAVRTLRPALARGAVVVTDRYVDSSVAYQGAVRGLGEE
+WIARLNDWATDSLVPDLTVLIDVDAATAAARRTGRDGDGADRMEQETADQHEALRAAFLA
+RAAAAPERYLVLDGALDPEELTARALARVTAEADAR
+>3_14
+MSTPSPRPAPHPAPTPAADPADSPAAAAQGMPGRGLFVAFEGADGTGKSTQARAVAQALR
+DAGREVVLTREPGGSDLGEAVRALLLDPAHAPVDARTEALLFAAARAAHVARTVRPALAA
+GTVVLTDRYVDSSVAYQGEVRGLGAERVAELNDWATEGLVPDLTVLLDADAATAEARRAA
+RHAGGGDAPDRMEQETAQAHGTLRAAFRARAAAAPHRYLVLDAAGAPEELTAAIAARVLT
+AAADAARDGTGA
+>4_308
+MSTQTEHRGLFVAVEGPDGSGKSTQARALTEALRAAGHEVVLTREPGGSDLGETLRELLL
+DPGHAPVDPRTEALLFAAARSAHAVRTLRPALARGAVVVTDRYVDSSVAYQGAARGLGEA
+RIAALNEWATDGLVPDLTVLIDVDAATAADRRDRRAAGGEGSPDRMERETADRHEALRAA
+FLARAAAAPERYLVLDGALPPQELTARALARVTAQAADR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000380.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000380.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54ed4fe90a9d150951def436d2f92bf1f2ebfc53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000380.fa
@@ -0,0 +1,40 @@
+>0_306
+MDPVIIGLLCGAVGLFTGVASMLAFRASERSRTVDLTVGEPTLAPGAAEVLSVVGRAYAV
+VDDVDGVVRANPAAYALGLVRGHSLVQDQLRELTRTVRADGVIVERRMELPRGPLGQSSL
+VVELRVAPLDEEYILILADDRTDVTRTEAMRHDFVVNVSHELKTPVGAISLLSEAIGDAA
+EDEEAVRRFAARLGVESRRLSALVQDIIEFSRLQAKDVVQDGGPVDLNAVVADAVDRLRL
+TAEDRGIALRVGGRVDAVVHGDQDQLMTAVRNLVDNAVRYSPEGTTVGIGLSSVDGLAQV
+TVTDQGIGISPEEQERVFERFYRVDAARSRQTGGTGLGLSIVKHVVINHGGEVTLWSQPG
+RGSTFTIRLPEWGDGVAVDGAPGAAHVTERRGHRVTASAAPPTRKETSA
+>1_30
+MDPVIIGLLCGAVGLFTGVASMLAFRASERSRTVDLTVGEPTLAPGAAEVLSVVGRAYAV
+VDDVDGVVRANPAAYALGLVRGHSLVQDQLRELTRTVRADGVIVERRMELPRGPLGQSSL
+VVELRVAPLDEEYILILADDRTDVTRTEAMRHDFVVNVSHELKTPVGAISLLSEAIGDAA
+EDEEAVRRFAARLGVESRRLSALVQDIIEFSRLQAKDVVQDGGPVDLNAVVADAVDRLRL
+TAEDRGIALRVGGRVDAVVHGDQDQLMTAVRNLVDNAVRYSPEGTTVGIGLSSVDGLAQV
+TVTDQGIGISPEEQERVFERFYRVDAARSRQTGGTGLGLSIVKHVVINHGGEVTLWSQPG
+RGSTFTIRLPEWGDGVAVDGAPGAAHVTERRGHRVTASAAPPTRKETSA
+>2_13
+MDPVIIGLLCGAVGLFIGVASMLAFRASERSRTVDLAVGEPTLAPGAAEVLAVVGRAYAV
+VDDVDGVVRANPSAYALGLVRGHSLVQQQVKDLTRSVRAEGVIVERRLELPRGPLGQSSL
+VVELRVAPLDEEYILILADDRTDVTRTEAMRHDFVVNVSHELKTPVGAISLLAEAIGDAA
+EDEEAVRRFASRLGIESRRLTALVQDIIEFSRLQAKDVVQDGRAVDLNAVVADAVDRLRL
+TAEDRGITLRVGGRVDAVVHGDADQLMTAVRNLVDNAVRYSPEGTTVGIGLSSADGLAQV
+TVTDQGIGISPEEQERVFERFYRVDSARSRQTGGTGLGLSIVKHVVINHGGEVSLWSQPG
+RGSTFTIRLPEWEDDGAAVDGPPAASHVTERRGHRVTASAASPPRKESSA
+>3_9
+MDPVIIGLLCGAVGLLIGVASMLAFRASERSRTVDLSVEEPTLSPGAAEVLSVIGRSYIV
+VDAVDGVVRANPSAYAMGLVRGHTLVPDALRELTGAVRADGVVRERQVDLPRDPRHQSSL
+VVELRVAPLDDEYILVLAEDRTGAMRTEAMRHDFVVNVSHELKTPVGAISLLSEAIADAA
+DDDDAVRRFARRLGVESTRLTALVQDIIEFSRLQAKDVVREGRSVDLNLVVAEAVDRVRL
+TAEARGISIRAGGHVDTVVHGDPDQLMTAVRNLVDNAVRYSPDGTTVGVGLTSKDGLAQI
+TVTDQGIGISPEEQERVFERFYRVDAARSRQTGGTGLGLSIVKHVVINHGGEVTLWSQPG
+RGSTFTIRLPEWAQAPQTPDAGAPATVATLPERRGHRVAAAAAPARKEHSA
+>4_313
+MDPVIIGLLCGAVGLFTGVASMLAFRASERSRTVDLTVGEPTLAPGAAEVLSVVGRAYAV
+VDDVDGVVRANPAAYALGLVRGHSLVQDQLRELTRTVRADGVIVERRMELPRGPLGQSSL
+VVELRVAPLDEEYILILADDRTDVTRTEAMRHDFVVNVSHELKTPVGAISLLSEAIGDAA
+EDEEAVRRFAARLGVESRRLSALVQDIIEFSRLQAKDVVQDGGPVDLNAVVADAVDRLRL
+TAEDRGIALRVGGRVDAVVHGDQDQLMTAVRNLVDNAVRYSPEGTTVGIGLSSVDGLAQV
+TVTDQGIGISPEEQERVFERFYRVDAARSRQTGGTGLGLSIVKHVVINHGGEVTLWSQPG
+RGSTFTIRLPEWGDSVAVDGAPGAAHVTERRGHRVTASAAPPTRKETSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000381.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000381.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9f4ccc266656b3e6037b4563ea3aa6cd8f13f80a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000381.fa
@@ -0,0 +1,25 @@
+>0_307
+MSRILIVEDEESFSDPLSYLLEKEGFEVTVAADGNEALSVFERDSADLILLDLMLPGMSG
+TEVCRQVRQRSNVPVIMLTAKDSEIDKVVGLELGADDYVTKPYSSRELVARVRAVLRRQG
+EQEEPMSATISAGPVRMDVERHVVSVDGEQVSLPLKEFELLEMLLRNAGRVLTRGQLIDR
+VWGSDYVGDTKTLDVHVKRLRSKIEPDPSSPRYLVTVRGLGYKFEA
+>1_31
+MSRILIVEDEESFSDPLSYLLEKEGFEVTVAADGNEALSVFERDSADLILLDLMLPGMSG
+TEVCRQVRQRSNVPVIMLTAKDSEIDKVVGLELGADDYVTKPYSSRELVARVRAVLRRQG
+EQEEPMSATISAGPVRMDVERHVVSVDGEQVSLPLKEFELLEMLLRNAGRVLTRGQLIDR
+VWGSDYVGDTKTLDVHVKRLRSKIEPDPSSPRYLVTVRGLGYKFEA
+>2_12
+MSRILIVEDEESFSDPLSYLLEKEGFEVAVAADGNEALGVFERDGADLILLDLMLPGMSG
+TEVCRQVRQRSNVPVIMLTAKDSEIDKVVGLELGADDYVTKPYSSRELVARVRAVLRRQG
+EPEELVSATLGAGPVRMDVERHVVSVDGEQVSLPLKEFELLEMLLRNAGRVLTRGQLIDR
+VWGSDYVGDTKTLDVHVKRLRSKIEPDPSSPRHLVTVRGLGYKFEA
+>3_8
+MSRILIVEDEESFSDPLSYLLNKEGFEVAVAADGNDALEEFERGGADLILLDLMLPGMSG
+TEVCRQIRQRSHVPIIMLTAKDSEIDKVVGLELGADDYITKPYSSRELVARVRAVLRRGG
+EPEELVTSTVSAGPVRMDVERHVVAVDGEPVNLPLKEFELLEMLLRNAGRVLTRGQLIDR
+VWGSDYVGDTKTLDVHVKRLRAKIEPDPSSPRHLVTVRGLGYKFES
+>4_314
+MSRILIVEDEESFSDPLSYLLEKEGFEVTVAADGNEALSVFERDSADLILLDLMLPGMSG
+TEVCRQVRQRSNVPVIMLTAKDSEIDKVVGLELGADDYVTKPYSSRELVARVRAVLRRQG
+EQEEPMSATISAGPVRMDVERHVVSVDGEQVSLPLKEFELLEMLLRNAGRVLTRGQLIDR
+VWGSDYVGDTKTLDVHVKRLRSKIEPDPSSPRYLVTVRGLGYKFEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000383.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000383.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ed316a9e81a0443a58e5fd6fcccb8ef73f9c3a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000383.fa
@@ -0,0 +1,21 @@
+>0_309
+MVFEVGETVVYPHHGAARIEEIKMRTIKGEEKMYLKLKVAQGDLTIEVPAENVDLVGVRD
+VVDAEGLEHVMEVLRAEHVEEPTNWSRRYKANLEKLASGDVNKVAEVVRDLWRRDQDRGL
+SAGEKRMLAKARQVLVSELALAKKVTEEEAEGRLDKVLEG
+>1_33
+MVFEVGETVVYPHHGAARIEEIKMRTIKGEEKMYLKLKVAQGDLTIEVPAENVDLVGVRD
+VVDAEGLEHVMEVLRAEHVEEPTNWSRRYKANLEKLASGDVNKVAEVVRDLWRRDQDRGL
+SAGEKRMLAKARQVLVSELALAKKVTEEEAEGRLDKVLEG
+>2_10
+MVFEVGETVVYPHHGAARIEEIKMRTIKGEEKMYLKLKVAQGDLTIEVPAENVDLVGVRD
+VVDSEGLEEVVEVLQAEQVEEPTNWSRRYKANLEKLASGDVKKVAEVVRDLWRRDQDRGL
+SAGEKRMLSKARQVLVSELALAKKVTEEEAEGMLDQVLEG
+>3_6
+MPDTRGVFRVSVVESTDRKGAFHMVFEVGETVVYPHHGAARIEEIKTRTIKGEEKMYLKL
+KVAQGDLTIEVPAENVDLVGVRDVVDDKGLEHVVEVLQAEHVEEPTNWSRRYKANLEKLA
+SGDVNKVSEVVRDLWRRDHDRGLSAGEKRMLSKARQVLVSELALAKKVSEEEAEGMLDKV
+LEG
+>4_316
+MVFEVGETVVYPHHGAARIEEIKMRTIKGEEKMYLKLKVAQGDLTIEVPAENVDLVGVRD
+VVDAEGLEHVMEVLRAEHVEEPTNWSRRYKANLEKLASGDVNKVAEVVRDLWRRDQDRGL
+SAGEKRMLSKARQVLVSELALAKKVTEEEAEGRLDKVLEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000427.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000427.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0fa1640d3ee51d84ce9870db50733ccb5fe0ce9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000427.fa
@@ -0,0 +1,35 @@
+>0_364
+MLEIPRVEDNGRLGPVNSALVPRYGGTPTYALLPRLDEAAAAGVAPEIKVVGVPFDAGVS
+YRPGARFGSGHVRQSSRLLRPYNPATDTSPFAQAQVVDAGDMAVNPFDIGEAIEAIQQDA
+MDLTEDGSSLMTIGGDHTIALPLLRAASARAGEPVALLHFDAHLDTWDTYFGAEYTHGTP
+FRRAVEEGILDTEAISHVGTRGPLYGKKDLDDDHRMGFGIVTSSDVFRQGVDEIVDQLRQ
+RIGGRPLYISVDIDVLDPAHAPGTGTPEAGGITSRELLEILRGLRGLDIVGADLVEVAPA
+YDHAELTGVAASHVAYDLISLMADRRATRAAAGEESAR
+>1_97
+MLEIPRVEDNGRLGPVNSALVPRYGGTPTYALLPRLDEAAAAGVAPEIKVVGVPFDAGVS
+YRPGARFGSGHVRQSSRLLRPYNPATDTSPFAQAQVVDAGDMAVNPFDIGEAIEAIQQDA
+MDLTEDGSSLMTIGGDHTIALPLLRAASARAGEPVALLHFDAHLDTWDTYFGAEYTHGTP
+FRRAVEEGILDTEAISHVGTRGPLYGKKDLDDDHRMGFGIVTSSDVFRQGVDEIVDQLRQ
+RIGGRPLYISVDIDVLDPAHAPGTGTPEAGGITSRELLEILRGLRGLDIVGADLVEVAPA
+YDHAELTGVAASHVAYDLISLMADRRATRAAAGEESAR
+>2_2514
+MLEIPRVEDNGRLGPVNSALVPRYGGAPTYALLPRLDEAAAAGVAPEIKVVGVPFDAGVS
+YRPGARFGSGHVRQSSRLLRPYNPATDTSPFAQSQVVDAGDMAVNPFNIGEAIEAIQQDA
+MDLTEDGASLMTIGGDHTIALPLLRAASARAGEPVALLHFDAHLDTWDTYFAAEYTHGTP
+FRRAVEEGILDTEAISHVGTRGPLYGKKDLDDDHRMGFGIVTSSDVFRKGVDEIVDQLRQ
+RIGDRPLYISVDIDVLDPAHAPGTGTPEAGGITSRELLEILRGLRGLDIVGADLVEVAPA
+YDHAELTGVAASHVAYDLITLMADRRASRAAAGEEQGR
+>3_1718
+MLEIPRVEDNGRLGPVNSALVPRYGGAPTYALLPRLDEAAAAGVAPEIKVVGVPFDAGVS
+YRPGARFGSGHVRQSSRLLRPYNPATETSPFAQAQVVDTGDMAVNPFHIGEALESIQQDA
+MDLTEDGASLMTIGGDHTIALPLLRAASARAGEPVALLHFDAHLDTWDTYFGAAYTHGTP
+FRRAVEEGILDTEAISHVGTRGPLYGKKDLDDDHRMGFGIVTSSDVFRKGVDEIVDQLRQ
+RIGGRPLYISVDIDVLDPAHAPGTGTPEAGGLTSRELLEILRGLRGLDIVGADLVEVAPA
+YDHAELTGVAASHVAYDLISLMADRRATRAAAEGGVDA
+>4_370
+MLEIPRVEDNGRLGPVNSALVPRYGGAPTYALLPRLDEAAAAGVAPEIKVVGVPFDAGVS
+YRPGARFGSGHVRQSSRLLRPYNPATDTSPFAQAQVVDAGDMAVNPFDIGEAIEAIQQDA
+MDLTEDGSSLMTIGGDHTIALPLLRAASARAGEPVALLHFDAHLDTWDTYFGAEYTHGTP
+FRRAVEEGILDTEAISHVGTRGPLYGKKDLDDDHRMGFGIVTSSDVFRQGVDEIVDQLRQ
+RIGGRPLYISVDIDVLDPAHAPGTGTPEAGGITSRELLEILRGLRGLDIVGADLVEVAPA
+YDQAELTGVAASHVAYDLISLMADRRATRAAAGEEPGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000433.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000433.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b1226f10c93c9f8c93f02f2163c0b1ec42a05f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000433.fa
@@ -0,0 +1,45 @@
+>0_373
+MNESLETLRDEVFARNPGEAEFHQAVSEVFEALGPVVQRHPQYVEAGVMHRLCEPERQII
+FRVPWIDDAGVVQVNRGFRVEFNSALGPYKGGLRFHPSVYLGIVKFLGFEQIFKNSLTGM
+PIGGGKGGSDFDPAGKSDREIMRFCQSFMTELHRHIGEHTDVPAGDIGVGAREIGYMFGQ
+YKRLTNRFEAGALTGKGLTWGGSLVRTEATGYGAVMFVDSMLRTRGESMDGQQVLISGSG
+NVAIYAAEKAAALGATVLTASDSSGYIVDPDGLDLDLLKQIKEVERARISEYAERRGGRS
+RYVTGGSVWDVEGTVALPCATQNELDESAARTLLKNGVKAVAEGANMPCTEAAAHLFVDS
+GTLFGPGKAANAGGVATSALEMQQNASRDSWSFDYTHDRLEQIMRDIHDRCVETAEEYGT
+PGNYVAGANIAGFIKVADAMIAQGVV
+>1_106
+MNESLETLRDEVFARNPGEAEFHQAVSEVFEALGPVVQRHPQYVEAGVMHRLCEPERQII
+FRVPWIDDAGVVQVNRGFRVEFNSALGPYKGGLRFHPSVYLGIVKFLGFEQIFKNSLTGM
+PIGGGKGGSDFDPAGKSDREIMRFCQSFMTELHRHIGEHTDVPAGDIGVGAREIGYMFGQ
+YKRLTNRFEAGALTGKGLTWGGSLVRTEATGYGAVMFVDSMLRTRGESMDGQQVLISGSG
+NVAIYAAEKAAALGATVLTASDSSGYIVDPDGLDLDLLKQIKEVERARISEYAERRGGRS
+RYVTGGSVWDVEGTVALPCATQNELDESAARTLLKNGVKAVAEGANMPCTEAAAHLFVDS
+GTLFGPGKAANAGGVATSALEMQQNASRDSWSFDYTHDRLEQIMRDIHDRCVETAEEYGT
+PGNYVAGANIAGFIKVADAMIAQGVV
+>2_2506
+MNHALETLRDEVFARNPGEAEFHQAVSEVFEALDPVMERHPQYVEAGVLHRLCEPERQII
+FRVPWIDDNGVVQVNRGFRVEFNSALGPYKGGLRFHPSVYLGIIKFLGFEQIFKNSLTGM
+PIGGGKGGSDFDPAGKSDREIMRFCQSFMTELHRHIGEHTDVPAGDIGVGGREIGYMFGQ
+YKRLTNRFEAGVLTGKGLTWGGSLVRTEATGYGAVMFADSMLKTRGESMDGQQVLISGSG
+NVAIYAAEKAASLGATVLTASDSAGYIVDPDGLDLDLLKQIKEVERARISEYVERKGGRA
+RYVAGGSVWDVEGTVALPCATQNELDESAAKTLLGNGVKAVAEGANMPCTEAATRLFLHA
+KTLFGPGKAANAGGVATSALEMQQNASRDSWNFEYTHDRLEAIMRDIHDRCVETAEEYGT
+PGNYVAGANIAGFIKVADAMIAQGVV
+>3_2378
+MHQVLQTLRDEVFARNPGEAEFHQAVSEVFEALDPVVERHPHYVDAGVLHRLCEPERQII
+FRVPWIDDAGVVQVNRGFRVEFNSALGPYKGGLRFHPSVYLGIIKFLGFEQIFKNSLTGM
+PIGGGKGGSDFDPAGKSDREIMRFCQSFMTELHRHIGEHTDVPAGDIGVGGREIGYMFGQ
+YKRLTNRFESGVLTGKGLTWGGSLVRTEATGYGAVMFADSMLRTRGESMDGQKVLISGSG
+NVAIYAAEKAAQLGATVLTASDSAGYIVDPDGVDVELLKQIKEVERARISEYAERKGGKV
+RYVAGGSVWDVEGTVALPCATQNELDESAAKTLLQNGVKAVAEGANMPSTEAATHLFLDA
+GTLFGPGKAANAGGVATSALEMQQNASRDSWDFDYTHDRLERIMRDIHDRCVETAEEYGT
+PGNYVAGANIAGFIKVADAMIAQGVV
+>4_379
+MNESLETLRDEVFARNPGEAEFHQAVSEVFEALGPVVQRHPQYVEAGVMHRLCEPERQII
+FRVPWIDDAGVVQVNRGFRVEFNSALGPYKGGLRFHPSVYLGIVKFLGFEQIFKNSLTGM
+PIGGGKGGSDFDPAGKSDREIMRFCQSFMTELHRHIGEHTDVPAGDIGVGAREIGYMFGQ
+YKRLTNRFEAGALTGKGLTWGGSLVRTEATGYGAVMFVDSMLRTRGESMDGQQVLISGSG
+NVAIYAAEKAAALGATVLTASDSSGYIVDPDGLDLDLLKQIKEVERARISEYAERRGGRS
+RYVTGGSVWDVEGTVALPCATQNELDESAARTLLKNGVKAVAEGANMPCTEAAAHLFVDS
+GTLFGPGKAANAGGVATSALEMQQNASRDSWSFDYTHDRLEQIMRDIHDRCVETAEEYGT
+PGNYVAGANIAGFIKVADAMIAQGVV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000437.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000437.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7526e3a29b148a48fa55bfa8e4df1a1af1db8164
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000437.fa
@@ -0,0 +1,25 @@
+>0_378
+MRIVALVSGSGTNLQAVLDAVASGALDMEIAAVGADVADAGGLERARAHGIETFVVSPKD
+HADRRAWDEALADAVAAYAPDWVVCSGFMRILGAPLLERFDGRILNTHPALLPSFPGAHG
+VRDALAHGVKVTGCTVHVVDAGVDTGPILAQAAVPVLDTDTEAELHERIKVQERALLLRV
+LGELSRR
+>1_111
+MRIVALVSGSGTNLQAVLDAVASGALDMEIAAVGADVADAGGLERARAHGIETFVVSPKD
+HADRRAWDEALADAVAAYAPDWVVCSGFMRILGAPLLERFDGRILNTHPALLPSFPGAHG
+VRDALAHGVKVTGCTVHVVDAGVDTGPILAQAAVPVLDTDTEAELHERIKVQERALLLRV
+LGELSRR
+>2_2502
+MRIVALVSGSGTNLQAVLDAVASGALDVEIAAVGADVADAGGLERARAHGIETFVVSPRD
+HADRHAWDVALADAVAAHEPDWVLCSGFMRILGAPLLERFEGRILNTHPALLPSFPGAHG
+VRDALAHGVKVSGCTVHVVDAGVDTGPILAQAAVPVLDTDTESELHERIKVQERALLLRV
+LGELSRR
+>3_2373
+MRILALVSGSGTNLQAVLDAVASGALPLEVAAVGSDVPGVQGLARAEAAGIPTFTVAPAD
+HPDRAAWNVALAEAVAAYEPDWVVCSGFMRILGAPLLEAFPGRIVNTHPALLPSFPGAHG
+VRDALAYGVKVTGCTVHLVDAGVDTGPILAQAAVPVLDTDTEEVLHERIKVQERVLLLRV
+LGELAAGRSPRQA
+>4_384
+MRIVALVSGSGTNLQAVLDAVASGALDVEIAAVGADVADAGGLERARAHGIETFVVSPKD
+HADRRAWDEALADAVAAYAPDWVVCSGFMRILGAPLLERFEGRILNTHPALLPSFPGAHG
+VRDALAHGVKVTGCTVHVVDAGVDTGPILAQAAVPVLDTDTEAELHERIKVQERALLLRV
+LGELSRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000440.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000440.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ecc102c191bed71e22f2452f80adfc44d13568ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000440.fa
@@ -0,0 +1,70 @@
+>0_382
+MSKIIYTLTDEAPMLATASLLPIVRAYAGTAGVELETRDISLAGRILAAFKDVLPEDQRT
+ADALAELGELVKSPEANVIKLPNISASVPQLRAAIKELQADGYALPEYPDEPKTDEEKDA
+KARYDSVKGSAVNPVLREGNSDRRAPKAVKAYAKRFPHSMGEWTPDSKTAVATMGADDFR
+ANEQSVTLPAADVLTIEFTGEDGKTTVLKEGLKVLKGEVVDGTFMSAKALDAFLAEQVKR
+AKEEGILFSAHLKATMMKVSDPVIFGHVVKAYFSELFEKYGEQLAAAGLSANNGLAAIEG
+GLDKLDAETAEGVRAAIAAAYENGPDVAMVNSAKGITNLHVPSDVIVDASMPAMIRTSGR
+MWNKDDQTQDTLAVIPDSSYAGVYQAVIDDCKANGAYDPTTMGTVPNVGLMAQKAEEYGS
+HDKTFIMDAAGTVAVKNSAGETLLSHDVEAGDIWRACQTKDVPVRDWVKLAVTRARASQT
+PAVFWLDETRAHDRELIKKVEEYLKEHDTEDLDIRILSPVEAAKLSVERIRRGEDTISVT
+GNVLRDYNTDLFPILELGTSAKMLSVVPLLNGGGLFETGAGGSAPKHVQQLVEENHLRWD
+SLGEFLALAVSFEHEAVANENHRARVLADTLDAATGTLLIEGKSPKRKVGELDNRGSHFY
+LALYWARELAKQTEDAELAAAAKPVAEELEAQEETILGELNGVQGSPVDLGGYYWPELEK
+VTSVMRPSATLNAIVDKLSV
+>1_114
+MSKIIYTLTDEAPMLATASLLPIVRAYAGTAGVELETRDISLAGRILAAFKDVLPEEQRT
+ADALAELGELVKTPEANVIKLPNISASVPQLRAAIKELQAHGYALPEYPDEPKTDAEKDA
+KARYDSVKGSAVNPVLREGNSDRRAPKAVKAYAKRFPHSMGEWTPDSKTAVATMGADDFR
+ANEQSVTLPAADVLTIEFTGEDGKTTVLKEGLKVLKGEVVDGTFMSAKALDAFLAEQVKR
+AKEEGILFSAHLKATMMKVSDPVIFGHVVKAYFSELFEKYGEQLAAAGLSANNGLAAIEG
+GLDKLDAETAEGVRAAIAAAYENGPDVAMVNSAKGITNLHVPSDVIVDASMPAMIRTSGR
+MWNKDDQTQDTLAVIPDSSYAGVYQAVIDDCKANGAYDPTTMGTVPNVGLMAQKAEEYGS
+HDKTFIMDAAGTVAVKNSAGETLLSHEVEAGDIWRACQTKDVPVRDWVKLAVTRARASQT
+PAVFWLDETRAHDRELIKKVEEYLKEHDTEGLDLRILSPVEATKLSVERIRRGEDTISVT
+GNVLRDYNTDLFPILELGTSAKMLSIVPLLNGGGLFETGAGGSAPKHVQQLLEENHLRWD
+SLGEFLALAVSFEHEAVANENHRAQVLADTLDAATGTLLIEGKSPKRKVGELDNRGSHFY
+LALYWARELAKQTEDAELAAAAKPIAEELEAQEETILAELNGVQGSPVDLGGYYAPEMEK
+VTSVMRPSATLNAIVDKLSV
+>2_2497
+MSKIIYTLTDEAPMLATASLLPIVRAYAGTAGVELETRDISLAGRILAAFRDVLPEDQRT
+ADALAELGELVKSPEANVIKLPNISASVPQLRAAIKELQEDGYALPEYPDEPKTDEEKDA
+KARYDSVKGSAVNPVLREGNSDRRAPKAVKNYAKMFPHSMGEWTPDSKTAVATMGADDFR
+SNEKSVTMPADDTLTIEFTGEDGKTTVLKEGLKVLAGEVVDGTFMSAKALDAFLAEQVKR
+AKEEGILFSAHLKATMMKVSDPVIFGHVVKAYFSELFEKYGEQLEAAGLNPNNGLAAIEG
+GLDKLDAETAEGVKKAIAAAYEEGPDVAMVNSAKGITNLHVPSDVIVDASMPAMIRTSGR
+MWNKDDQTQDTLAVIPDSSYAGIYQAVIEDCKKHGAYDPTTMGTVPNVGLMAQKAEEYGS
+HDKTFILESAGTVAVKNAAGETLISHDVEAGDIWRACQTKDVPVRDWVKLAVTRARASQT
+PAVFWLDETRAHDRELIAKVEEYLKEHDTEGLDLRILSPVEAAKLSVERIRRGEDTISVT
+GNVLRDYNTDLFPILELGTSAKMLSVVPLLNGGGLFETGAGGSAPKHVQQLVEENHLRWD
+SLGEFLALAVSFEHEAVANENHRAQVLADTLDAATGTLLIEGKSPQRKVGELDNRGSHFY
+LALYWARELAKQTEDAELVAAAKPVAEELEAQEETILAELNGVQGSPVDLGGYYWPELEK
+VTSVMRPSATLNAIVDKLSV
+>3_2366
+MSKIIYTLTDEAPMLATASLLPIVRAYAGTAGVELETRDISLAGRILAAFNDLLPEEQRV
+NDALAELGELVKTPEANVIKLPNISASVPQLRAAIKELQADGYALPEYVDDPQTDKEKDA
+RKRYDSVKGSAVNPVLREGNSDRRAPKAVKNYAKKFPHSMGAWTADSKTAVATMGQDDFR
+SNEKSVTMPKDDVLSIEFTGQDGTTKILKEGLKVLEGEVVDGTFMSAKALDAFLAEQVTR
+AKEEGVLFSAHLKATMMKVSDPVIFGHVVKAYFADLFAQYGEQLAAAGLDPNNGLAAIEA
+GLDKLDAETAEGVRKAIADAYQNGPDVAMVNSDKGITNLHVPSDVIVDASMPAMIRTSGH
+MWDKDGAERDTLAVIPDSSYAGIYQVVIDDCKANGAYDPTTMGTVPNVGLMAQKAEEYGS
+HDKTFVMEADGTVEVKDSAGEVLFSHEVEAEDIWRACQTKDVPVQDWVKLAVTRARASQT
+PAVFWLDETRAHDRELIKKVEQYLQGHDTEGLDLRIMSPVEATKFTVERMRRGEDTITVT
+GNVLRDYNTDLFPILELGTSAKMLSIVPLINGGGLFETGAGGSAPKHVQQLVGENHLRWD
+SLGEFLALAVSFEHEAAHNGNHRAQVLADTLDAATGILLIEGKSPERKAGQLDNRGSHFY
+LALYWAQELAKQTADAELAAAAKPVAEELEAQEETILAELNGVQGSPVDLGGYYAPSMDK
+VSEVMRPSATLNGIIATLGA
+>4_388
+MSKIIYTLTDEAPMLATASLLPIVRAYAGTAGVELETRDISLAGRILAAFKDVLPEEQRT
+ADALAELGELVKSPEANVIKLPNISASVPQLRAAIKELQADGYALPEYPDEPKTDEEKDA
+KARYDSVKGSAVNPVLREGNSDRRAPKAVKAYAKRFPHSMGEWTPDSKTAVATMGADDFR
+ANEQSVTLPAADVLTIEFTDEDGETTVLKEGLKVLKGEVVDGTFMSAKALDAFLAEQVKR
+AKEEGILFSAHLKATMMKVSDPVIFGHVVKAYFSELFEKYGEQLAAAGLSANNGLAAIEG
+GLDKLDAETAEGVRAAIAAAYENGPDVAMVNSAKGITNLHVPSDVIVDASMPAMIRNSGR
+MWNKHDQTQDTLAVIPDSSYAGVFQAVIDDCKANGAYDPTTMGTVPNVGLMAQKAEEYGS
+HDKTFIMDAAGTVAVKNSAGETLLSHDVEAGDIWRACQTKDVPVRDWVKLAVTRARASQT
+PAVFWLDETRAHDRELIKKVEEYLKEHDTEDLDIRILSPVEAAKLSVERIRRGEDTISVT
+GNVLRDYNTDLFPILELGTSAKMLSVVPLLNGGGLFETGAGGSAPKHVQQLVEENHLRWD
+SLGEFLALAVSFEHEAVANENHRARVLADTLDAATGTLLIEGKSPKRKVGELDNRGSHFY
+LALYWARELAKQTEDAELAAAAKPIAEELGAQEETILAELNGVQGSPVDLGGYYWPELEK
+VTSVMRPSATLNAIVDKLSV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000446.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000446.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3dfd9526fabb903bb9aaee08c135a1ddc53db2c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000446.fa
@@ -0,0 +1,32 @@
+>0_392
+MSTAASAPAPEGRAPEGRAPHRRGTGKATALWWILTVVIGVWCLFPLFSIFATSFKTPAD
+LANGKLLPTQWSTVNYEEIFVGGSRELFLTALRNSIGITVIATIIAVILATLCAYAIARL
+DFPGKRLVLTVSLMVSMFPVISLVTPLFNMWRTLGLYDTWVGLIIPYLSLTLPISIWTLA
+AFFRQIPWELDQAAQVDGATPLEAFRKVIVPLAAPGVFTTAIIAFFIAWNDFVFGISLTS
+TETARTVPAALAFFTGASQFESPTGAISAAAIIVTIPIVILVLAFQRQIVAGLTNGAVKG
+>1_121
+MSTAASAPAPEGRAPEGRAPHRRGTGKATALWWILTVVIGVWCLFPLFSIFATSFKTPAD
+LANGKLLPTQWSTVNYEEIFVGGSRELFLTALRNSIGITVIATIIAVILATLCAYAIARL
+DFPGKRIVLTVSLMVSMFPVISLVTPLFNMWRTLGLYDTWVGLIIPYLSLTLPISIWTLA
+AFFRQIPWELDQAAQVDGATPLEAFRKVIVPLAAPGVFTTAIIAFFIAWNDFVFGISLTS
+TETARTVPAALAFFTGASQFESPTGAISAAAIIVTIPIVILVLAFQRQIVAGLTNGAVKG
+>2_2490
+MSTAVSAPAPEGRAPEGRGPEGRAPRRRGTGKATALWWILTVVIGVWCLFPLFSIFATSF
+KTPADLANGKLLPTQWSTVNYEEIFVGGSRELFLTALRNSIGITVIATIIAVILATLCAY
+AIARLDFPGKRLVLTVSLMVSMFPVISLVTPLFNMWRTLGLYDTWIGLIIPYLSLTLPIS
+IWTLAAFFRQIPWELDQAAQVDGATPLEAFRKVIVPLAAPGVFTTAIIAFFIAWNDFVFG
+ISLTSTETARTVPAALAFFTGASQFESPTGAISAAAIIVTIPIVILVLAFQRQIVAGLTN
+GAVKG
+>3_2358
+MSTGNPIPAPQEPVTTRPDGAAERTEAGTAVGDRGVAPTTTRRTRKGSSSWIWWLLAVLI
+GVWCLFPLFSIFATSFKTPADLSNGKLLPTQWSTVNYEEIFVGGSRELFLTALRNSIGIT
+VIATLIAVVLATLCAYAIARLDFPGKRIVLTVSLMVSMFPVISLVTPLFNVWRTLGLYDT
+WLGLIIPYLSLTLPISIWTLAAFFRQIPWELDQAAQVDGATPLQAFRKVIVPLAAPGVFT
+TAIIAFFIAWNDFVFGISLTSTEAARTVPAALAFFTGASQFESPTGAISAAAIVVTIPIV
+ILVLLFQRQIVAGLTNGAVKG
+>4_395
+MSTAASAPAPEGRAPEGRAPHRRGTGKATALWWILTVVIGVWCLFPLFSIFATSFKTPAD
+LANGKLLPTQWSTVNYEEIFVGGSRELFLTALRNSIGITVIATIIAVILATLCAYAIARL
+DFPGKRIVLTVSLMVSMFPVISLVTPLFNMWRTLGLYDTWVGLIIPYLSLTLPISIWTLA
+AFFRQIPWELDQAAQVDGATPLEAFRKVIVPLAAPGVFTTAIIAFFIAWNDFVFGISLTS
+TETARTVPAALAFFTGASQFESPTGAISAAAIIVTIPIVILVLAFQRQIVAGLTNGAVKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000449.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000449.fa
new file mode 100644
index 0000000000000000000000000000000000000000..554b73144966d2a1707fcc59309b454c23bde04b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000449.fa
@@ -0,0 +1,34 @@
+>0_396
+MDTAALSPSPSPASGAEHAHVLTLACTNRKGIVHAVTGALLGVEADITESQQYGSPDTGD
+FFMRVEFMTPAVREDIEQALAPVREEFGMRMGLWDAAHRMRTLVMCSKDGHTLNDLLFQQ
+RAGTLPIEIPVVVSNHLDLQPLASFYGVPFIHVPVSKDPSSRDSKEAAEDRLRDLIAQFD
+IELVVLARYMQILSDELCRDLAGMAINIHHSFLPSFKGARPYHQAHERGVKLIGATAHYV
+TADLDEGPIIAQSVQPVTHAQTAADFVARGRDVEGSTLAQAVRWHAQHRVLTDGRRTVVF
+S
+>1_126
+MDTAALSPSPSPASGAEHARVLTLACTNRKGIVHAVTGALLGVEADITESQQYDSPDTGD
+FFMRVEFVTPATREDIEQALAPVREEFGMRMGLWDAAQRMRTLVMCSKDGHTLNDLLFQQ
+RAGTLPIEIPVVVSNHLDLQPLASFYGVPFIHVPVSKDPSSRDSKEAAEDRLRDLIAQFD
+IELVVLARYMQILSDELCRDLAGMAINIHHSFLPSFKGARPYHQAHERGVKLIGATAHYV
+TADLDEGPIIAQSVQPVTHAQTAADFVARGRDVEGSTLAQAVRWHAQHRVLADGRRTVVF
+S
+>2_2487
+MDTATLSPSPTPASGAEHAHVLTLACTNRMGIVHAVSGALLQVGADITESQQYDSPESGD
+FFMRVEFVTPARREEVAAALEPVREEFGMRMGLWDAGHRMRTLVMCSKDGHTLNDLLFQQ
+RAGTLPIEIPVVVSNHLELQSLASFYGVPFIHVPVSADPESRDSKAAAEDRLRGLIAEYD
+IELVVLARYMQILSDELCRDLAGMAINIHHSFLPSFKGARPYHQAHERGVKLIGATAHYV
+TADLDEGPIIAQSVQPVTHAQTAADFVARGRDVEGSTLVQAVRWHAQHRVLADGRRTVVF
+S
+>3_2355
+MDSTPAAPSEASARHRIVLTLSCPDRPGIVHAVTGALLEADANITESQQYDSPDTGTFFM
+RVAVDAAATREEVEAAVRPVADRFGMHLQVWDADTPLRALVMCSKDGRTLNDLLFQQRTG
+SLPVQIPVVVSNHLDLQPLASFYGVPFIHVPLSTDPASRNSKAAAEDRLRELIREYEIDV
+VVLARYMQILSDELCRDLEGMAINIHHSFLPSFKGARPYHQAHERGVKIIGATAHYVTAD
+LDEGPIIAQSVHPVTHAQTAEDFVERGRDVEGATLVQAVRWHAEHRVLLDGHRTVVFS
+>4_399
+MDTAALSLSPSPASGAEHAHVLTLACTNRKGIVHAVTGALLGVEADITESQQYGSPDTGD
+FFMRVEFMTPAVREDIEQALAPVREEFGMRMGLWDAAHRMRTLVMCSKDGHTLNDLLFQQ
+RAGTLPIEIPVVVSNHLDLQPLASFYGVPFIHVPVSKDPSSRDSKEAAEDRLRDLIAQFD
+IELVVLARYMQILSDELCRDLAGMAINIHHSFLPSFKGARPYHQAHERGVKLIGATAHYV
+TADLDEGPIIAQSVQPVTHAQTAADFVARGRDVEGSTLAQAVRWHAQHRVLTDGRRTVVF
+S
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000464.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000464.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5ae987c81bb66766ff22caed1311a206eff2032b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000464.fa
@@ -0,0 +1,20 @@
+>0_414
+MSTTAETTIAAPRSRRLDPKYTRDGGGRGNFEMLAWLFMRISGVFLVVLIAVHLTTNLLV
+GDGIHAIDFGFVAGKWAHPLWQFWDLALLWLAMLHGANGVRTIINDYTRRGSARFWLTMI
+LYIATAVIIILGTLVIFTFDPCMVDASGALLEGSPAFCG
+>1_144
+MSTTAETTIAAPRSRRLDPKYTRDGGGRGNFEMLAWLFMRISGVFLVVLIAVHLTTNLLV
+GDGIHAIDFGFVAGKWAHPLWQFWDLALLWLAMLHGANGVRTIINDYTRRGSARFWLTMI
+LYIATAVIIILGTLVIFTFDPCMVDASGALLEGSPAFCG
+>2_2466
+MSTTAETTIAAPRTGRIDPKYTRDKGGRGNFEMLAWLFMRVSGVILVLLIAVHLTSNLLM
+GDGIQGIDFGFVAGKWAHPLWQFWDLALLWLAMLHGANGVRTIINDYTERGTARFWLTMI
+LYIATAVIITLGTLVIFTFDPCMVDASGALLEGSPAFCG
+>3_2337
+MSTTAETPLAAPRTGRLDSKYVRGESGKGNFEMLAWLFMRVSGVFLVVLVFAHIFANLMV
+GDGISGLDFGFVAGKWANPLWQLWDLALLWLAMLHGANGVRTIINDYAERDGVRFWLSMI
+LYVATAVIIVLGSLVIFTFDPCMVDASGALLEGSPAICR
+>4_417
+MSTTAETTIAAPRSRRLDPKYTRDGGGRGNFEMLAWLFMRISGVFLVVLIAVHLTTNLLV
+GDGIHAIDFGFVAGKWAHPLWQFWDLALLWLAMLHGANGVRTIINDYTRRGSARFWLTMI
+LYIATAVIIILGTLVIFTFDPCMVDASGALLEGSPAFCG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000480.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000480.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc3a1882eeff771d35e508cd34a4e0c17321c824
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000480.fa
@@ -0,0 +1,30 @@
+>0_434
+MANPVMNSQNFQQQMQGGGQAQPGWYQGGQQSAQSPYGQQQSPYGQAQAFGAGQAAQQYA
+HQQSMEDAFRAPSAGPEQTGRMTYNDVVGKTGLMLVLVVVAGAVGWFSPGLMIIGAIAGL
+VLGLVNSFKREPSPVLIMLYALAEGLFLGGISAVFEAAYPGIVVQAVLGTFSVFAVMLAL
+YTSGKFRPTPRMTKIVMTAMLGYLVFMLINLVLTWTGIANLRTGGLGLIIGAIAVLLAAY
+SLTMDFEMAAVGVKNGAPQKYSWSVAFGLTVTLIWLYVEILRIVAILRGND
+>1_161
+MANPVMNSQNFQQQMQGGGQAQPGWYQGGQQSAQSPYGQQQSPYGQAQAFGAGQAAQQYA
+HQQSMEDAFRAPSAGPEQTGRMTFNDVVGKTGLMLVLVVVAGAVGWFSPGLMIIGAIAGL
+VLGLVNAFKREPSPVLIMAYAVAQGLFLGGISAFFEGAYPGIVVQAVLGTFSVFAVMLAL
+YTSGKFRPTPRMTKIVMGAMIGYLVFMLVNLVLTWTGIGNMREGGLGLIIGAIAVLLAAY
+SLTMDFEMAAVGVKNGAPQKYSWSVAFGLTVTLIWLYIEILRIVAILRGND
+>2_2436
+MANPVMNSQNFQQQMQGGGQAQPGWYQGGTQSAQSPYGQQQSPYGQAQAFGAGQAAQQYA
+HQQSMEDAFRAPSAGPEQTGRMTFNDVVGKTGLMLVLVVVAGAVGWFSPGLMIIGAIAGL
+VLGLVNAFKREPSPVLIMAYAVAQGLFLGGISAFFEGAYPGIVVQAVLGTFSVFAVMLAL
+YTSGKFRPTPRMTKIVMGAMIGYLVFMLVNMVLTWTGIGNMREGGLGLIIGAIAVLLAAY
+SLTMDFEMAAVGVKNGAPQKYSWSVAFGLTVTLIWLYIEILRIVAILRGND
+>3_2320
+MANPVMNSNNFQQQMHAGQQQPGWYQNAAPQAPSGQQQSPYGQSQAYGAQQAAQQAAFQQ
+NMEQAFRAPAAGAAETGRMTYNDIVGKTALMLTLVVIGGAIGWTMPALMLIGAIVGLVLG
+LVNSFKREPSPVLIMGYALAEGLFLGGISASFEAAYGGIVLQAVLGTVSVFAVMLALYTS
+GKFRPTPRMTKIVMAAMIGYMLFMLLNLVLTFTGIANLRLGAMGLIVGAVAVLLAAYSLT
+MDFEMGAQGVKNGVPQKYSWTVAFGLTVTLIWLYVEILRILSILRSDD
+>4_434
+MANPVMNSQNFQQQMQGGGQAQPGWYQGGQQSAQSPYGQQQSPYGQAQAFGAGQAAQQYA
+HQQSMEDAFRAPSAGPEQTGRMTFNDVVGKTGLMLVLVVVAGAVGWFSPGLMIIGAIAGL
+VLGLVNAFKREPSPVLIMAYAVAQGLFLGGISAFFEGAYPGIVVQAVLGTFSVFAVMLAL
+YTSGKFRPTPRMTKIVMGAMIGYLVFMLVNLVLTWTGIGNMREGGLGLIIGAIAVLLAAY
+SLTMDFEMAAVGVKNGAPQKYSWSVAFGLTVTLIWLYIEILRIVAILRGND
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000486.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000486.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8241f3b094678430b62bec0e1182b28f49b539a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000486.fa
@@ -0,0 +1,20 @@
+>0_440
+MSHHAPAVRAQDPTLANRYGTDHTRPGRRRLWAGLGGLGLVVAVLLSVWIGLNMSVGAIE
+YKDVGFTIEDDGHATVTFQASVPEGVQAECDVLVTDSHAAPVGFRTVRLETLPADRRDSP
+SDAQQRYTVDVRTVVRGDSGVVETCRKV
+>1_167
+MSHHAPAVRAQDPTLANRYGTDHTRPGRRRLWAGLGGLGLVVAVLLSVWIGLNMSVGAIE
+YKDVGFTIEDDGHATVTFQASVPEGVQAECDVLVTDSHAAPVGFRTVRLETLPADRRDSP
+SDAQQRYTVDVRTVVRGDSGVVETCRKV
+>2_2430
+MSHHAHAVHAQDPTLANRYGTDQDRPSRRRLWVGLGVLGLLGAVLLAVWLGLNLSVGNIE
+YKDVGYTIEDDGNATVTFQVLVPEGVQAECDVLVMDSHAAPVGFRTVRLVSVPQDQRDTP
+SDAQQVYTVDVRTVVRGDSGVVEACRKL
+>3_2314
+MSSTPAPAASAPETTLATRYGVGQRRDRRRLWTVLGAVALVLAVATAVAVALGNSVGRVE
+AEDVGYRIDDAAHAAVTFQVTLPRGVEAAACDLKVMDARYAPVGFHTVRVSAGPDHPAGE
+TVTYTADVRTVGRGVTGVVEGCRPA
+>4_440
+MSHHAPAVRAQDPTLANRYGTNHTRPGRRRLWAGLGGLGLVVAVLLSVWIGLNMSVGAIE
+YKDVGFTIEDDGHATVTFQASVPEGVQAECDVLVTDSHAAPVGFRTVRLETLPADRRDSP
+SDAQQRYTVDVRTVVRGDSGIVETCRKV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000491.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000491.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f10b2cbafa89750b561371c9c3d867b80c1efbe8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000491.fa
@@ -0,0 +1,49 @@
+>0_446
+MVAELVEHAQTRQEPSSRPGQARAEAGAAEATGLRTYVVDTSVLLSDPRALLHFAEHEVV
+LPLVVVSELEAKRADPDLGYDARTALRLLDDLRGRHGALDQPVPITPEGGTLRIELNHVS
+VDVLPLGIRGTDNDSRILAVAKALADEGAMVTVVSKDLPMRVKAAAMGLAADEYRHELVR
+DSGWRGTVSLSVAQERLDALYDDGEVDLAGVPLGTLTGTGVETGPEEAPAEADRLPVNTG
+LVLTAPRGSALARVGEGGRACLVRGDRDVFGLHGRSAEQRLAIELLTDPSVGIVSLGGRA
+GTGKSALALCAGLDAVMERREHRRVVVFRPLYAVGGQDLGYLPGSEGDKMGPWAQAVFDT
+LGALVSPSVVDEVVDRGMLEILPLTHIRGRSLHDAWVIVDEAQSLERNVLLTVLSRMGRN
+SKVVLTHDVAQRDNLRVGRHDGIAAVVERLKGHPLFGHVTLTRSERSPIAALVTDLLEEG
+RA
+>1_173
+MVAELVEHAQTRQEPSSRPGQARAEAGAAEATGLRTYVVDTSVLLSDPRALLHFAEHEVV
+LPLVVVSELEAKRADPDLGYYARTALRLLDDLRGRHGALDQPVPITPEGGTLRIELNHVS
+VDVLPLGIRGTDNDSRILAVAKALADEGATVTVVSKDLPMRVKAAAMGLAADEYRHELVR
+DSGWRGTVSLSVAQERLDALYDDGEVDLAGVPLGTLTGTGVETGPGEAPAEADRLPVNTG
+LVLTAPRGSALARVGEGGRACLVRGDRDVFGLHGRSAEQRLAIELLTDPSVGIVSLGGRA
+GTGKSALALCAGLDAVMERREHRRVVVFRPLYAVGGQDLGYLPGSEGDKMGPWAQAVFDT
+LGALVSPSVVDEVVDRGMLEILPLTHIRGRSLHDAWVIVDEAQSLERNVLLTVLSRMGRN
+SKVVLTHDVAQRDNLRVGRHDGIAAVVERLKGHPLFGHVTLTRSERSPIAALVTDLLEEG
+RA
+>2_2425
+MVAERVEHGRALTGTTEARPDAAGAAGHAAAARTGAADAVVAPDARETGLRTYVVDTSVL
+LSDPRAVLRFAEHEVILPLVVVSELEAKRADPDLGYFARTALRLLDDLRGRHGALDRAVP
+ISPEGGTLRVELNHVSTDVLPLGIRGTDNDSRILAVAKAFADEGRDVTVVSKDLPMRVKA
+AAMGLSADEYRHELVRDSGWRGTVTLTVEQELLDALYDDGEASLAGVPVDGTDGVGAGVE
+ADGTGAGGSGVDRTGAEGPGAAVLPVNTGLVLLAPRGSALARVAEGGRALLVRGDQDVFG
+LHGRSAEQRLAIDLLTDPAVGIVSLGGRAGTGKSALALCAGLDAVMERREHRKVVVFRPL
+YAVGGQELGYLPGSEGEKMGPWAQAVFDTLGALVSPSVIDEVVDRGMLEVLPLTHIRGRS
+LHDAWVIVDEAQSLERNVLLTVLSRMGRNSKVVLTHDVAQRDNLRVGRHDGIAAVVERLK
+GHPLFGHVTLTRSERSPIAALVTEMLEDGRG
+>3_2308
+MTLQADGTGRHGRGTGETGAEVREGAASDGRRSYVVDTSVLLSDPRALVRFAEHEVVLPL
+VVVSELEGKRQDPDLGHAARHALRLLEDLRVRHGSLEDAVPFTAQGGTLRVELNHVSTDV
+LPFGIRGTDNDSRILAVAKALADEGRDVTLVSKDLPMRVKAAAMGLAADEYRHELVRDSG
+WRGAVSLRVDEDRLDSLYDDGRMGLHGIPLDEVAGSGVDAVPGEPAPTAVDLPVNTGLSL
+TSPRAAGLARVREGGVATLVRGDADVFGLHGRSAAQRLAIDLLTDPSVGIVSLGGRAGTG
+KSALALCAGLEAVMERREHRRVVVFRPLYAVGGQDLGYLPGTEGEKMGPWAQAVFDTLSA
+IVSPSVIDEVVDRGMLEVLPLTHIRGRSLHDSWVIVDEAQSLERNVLLTVLSRMGRDSKV
+VLTHDVAQRDNLRVGRHDGIAAVVETLKGHPLFGHVTLTRSERSPIAALVTELLEEGED
+>4_446
+MVAELVEHAQTRQEPSSRPGQARAEAGPAEATGLRTYVVDTSVLLSDPRALLHFAEHEVV
+LPLVVVSELEAKRADPDLGYYARTALRLLDDLRGRHGALDQPVPITPEGGTLRIELNHVS
+VDVLPLGIRGTDNDSRILAVAKALADEGATVTVVSKDLPMRVKAAAMGLAADEYRHELVR
+DSGWRGTVSLSVAQERLDALYDDGEVDLAGVPLGTLTGTGVETGPEEAPAEADRLPVNTG
+LVLTAPRGSALARVGEGGRACLVRGDRDVFGLHGRSAEQRLAIELLTDPSVGIVSLGGRA
+GTGKSALALCAGLDAVMERREHRRVVVFRPLYAVGGQDLGYLPGSEGDKMGPWAQAVFDT
+LGALVSPSVVDEVVDRGMLEILPLTHIRGRSLHDAWVIVDEAQSLERNVLLTVLSRMGRN
+SKVVLTHDVAQRDNLRVGRHDGIAAVVERLKGHPLFGHVTLTRSERSPIAALVTDLLEEG
+RA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000508.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000508.fa
new file mode 100644
index 0000000000000000000000000000000000000000..db8f6dc02ca108ccd5117ee0a4f5ef7f37bbe13c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000508.fa
@@ -0,0 +1,51 @@
+>0_464
+MEPVPATALAPRPAAVAADDGPFGVAALRARLGVSAAPLTRWHWILPLLVTVIAGVLRFT
+NLAHPDQLIFDETYYPKDAYSLLESGYERRWGEDVNDAFARGEAEPLEGAAYVVHPPLGK
+WLIGLGMLAFGPDNGVGWRFSAAVAGTLSVLLVALATQHLLRSVSLGAVAGLLLAVEGHH
+LVMSRIGLLDIFLSFFVLAAFAALLADRVHGRRLLAERLAHDVARRGRDALASGPWLGWR
+PWRLLAGVLLGAGCAVKLSGLAFMAAFGLLTVLWDMSARRTAGVRRWAWAGVEKDGLYAF
+VAVVGGGLVAYLASWTGWFVTEGGYYRDWHRDNPPEGVLAGLVPGPLRSLWHYHVESTTF
+HQGLTSPHDYAANPWTWPFMGRPVSYYYEGAEPGEGICPADAAGACSAAITDIANPFVWW
+TGLAAVLVCVWLLVRHRDWRAGALLGAYAAGQLVWSLWPERTMFFFYTIAYEPFLVMMIA
+LALSLLLRPGRRPGPRWGSALVLAYVTIAVAVSLFFLPVWIGDVIPYDQWRWRMWFSSWI
+>1_192
+MEPVPATALAPRPAAVAVDDGPFGVAALRARLGVSAAPLTRWHWILPLLVTVIAGVLRFT
+NLAHPDQLIFDETYYPKDAYSLLESGYERRWDEDVNDAFARGEAEPLEGAAYVVHPPLGK
+WLIGLGMLAFGPDNGVGWRFSAAVAGTLSVLLVALATQHLLRSVSLGAVAGLLLAVEGHH
+LVMSRIGLLDIFLSFFVLAAFAALLADRAHGRRLLAERLAHDVARRGRDALASGPWLGWR
+PWRLLAGVLLGAGCAVKLSGLAFMAAFGLLTVLWDMSARRTAGVRRWAWAGIEKDGLYAF
+VAVVGGGLVAYLASWTGWFVTEGGYYRDWHRDNPPEGLLAGLVPGPLRSLWHYHVESTTF
+HQGLTSPHDYAANPWTWPFMGRPVSYYYEGAEPGEGICPPDAAGACSAAITDIANPFVWW
+TGLAAVLVCVWLLVRHRDWRAGALLGAYAAGQLVWFLWPERTMFFFYTIAYEPFLVMMIA
+LALSLLLRPGRRPGPRWGSALVLAYVTIAVAVSLFFLPVWIGDVIPYDQWRWRMWFSSWI
+>2_2407
+MEPVPATALAPRPAAVAVDGAPFGVAALRARLGVSAAPLTRWHWILPLLVTALAGVLRFT
+NLAHPDQLIFDETYYPKDAYSLLQSGYERRWEEDVNDAFVRGEAEPLESAAYVVHPPLGK
+WLIGLGMLAFGTDNGVGWRFSSAVAGTLSVLLVALVAQHLLRSVSLGAVAGLLLAVEGHH
+LVMSRIGLLDIFLSFFVLAAFAALLADRAHGRQLLARRLAHDVARRGHAALATGPWLGWR
+PWRLLAGVLLGAGCAVKLSGLAFMAAFGLLTVLWDMAARRDAGVRDWARAGVVKDGLLAF
+VAVVGGGLVAYLASWTGWFATEGGYYRMWHRDNPPEGPLAGLVPGPLRSLWHYHVESTTF
+HEGLTSPHDYAASPWTWPFMGRPVSYYYRGGEPGQEVCPADAPSACSAAITDIANPLLWW
+TGLIAVLVCLWLLIRHRDWRAGALLGAYLAGQVVWFLWPERTMFFFYTVAYEPFLILMIV
+LALSLLLRPGRRPGPRWGSALVLAYAAAVVGVSLFFLPVWIGDVIPYDQWRWRMWFNSWI
+>3_2289
+MACVPASSLTRRPAHALPAPADDAAAHPFGAAALRARLGVQAAVLTRWHWIVPLAVTVLA
+GVIRFTNLAFPDKLIFDETYYPKDAYSLILSGYERRWAPDVDAAFAQGTAQPLDEPAYVV
+HPPLGKWLIALGMLAFGPDNGVGWRFSAAVAGTLSVLLVTLVAQRLFRSVSLGALAGLLL
+AVEGHHIVMSRIGLLDIFLSFFMIAAFAALLADRDHGRRLLASRLAEQVAAHDAGTRRGD
+PLAFGPRLGWRPWRILAGALLGAGCAVKLSGLAFMAVFGILTVLWDMEARRTAGIRHWLR
+AGVVRDGLPAFAAVVGAGLAVWLASWTGWFASEGGYYRRWAQDNPPEGPLSALLPGPLRS
+LIHYQLEAFTFHEGLTSPHDYGSSPWTWPFMGRPVSYFYEGGKPGENGCPSTAADACSSA
+ITDIANPFIWWTGLIAVLVCLAVLVRHRDWRAGALLGAYVAGQVVWFRWPERTMFFFYTV
+AYEPFLILMIVLALSLLLRRGHRPGPRWGAVLVAAYLLVAVGVSLFFLPVWIGERIPYPQ
+WSWRMWFSTWI
+>4_464
+MEPVPATALASRPAAVAVDDGPFGVAALRARLGVSAAPLTRWHWILPLLVTAIGGVLRFT
+NLAHPDQLIFDETYYPKDAYSLLESGYERRWDEDVNDAFARGEAEPLEGAAYVVHPPLGK
+WLIGLGMLAFGPDNGVGWRFSAAVAGTLSVLLVALATQHLLRSVSLGAAAGLLLAVEGHH
+LVMSRIGLLDIFLSFFVLAAFAALLADRVHGRRLLAERLAHDVARLGRDALASGPWLGWR
+PWRLLAGVLLGAGCAVKLSGLAFMAAFGLLTVLWDMSARRTAGVWHWAWAGVEKDGLYAF
+VAVVGGGLVAYLASWTGWFVTEGGYYRDWHRDNPPEGLLAGLVPGPLRSLWHYHVESTTF
+HQGLTSPHDYAANPWTWPFMGRPVSYYYEGAEPGEGICPADAAGACSSAITDIANPFVWW
+TGLAAVLVCVWLLVRHRDWRAGALLSAYVAGQLVWFLWPERTMFFFYTIAYEPFFVMMIA
+LALSLLLRPGRRPGPRWGSALVLAYVTIAVAVSLFFLPVWIGDVIPYDQWRWRMWFSSWI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000511.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000511.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3e286bcb89dab1f91d401b30f77206fefd9b1f53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000511.fa
@@ -0,0 +1,60 @@
+>0_469
+MLTRLLKARLPEGTQYLVDRPMRIRLVFVVLGSVLVAGLEMVALASILPLVSLLTSGELG
+SPALEGLLARFGAVTVPEQTVAFAVVIVLAFLLKAILVLAFRWWTMGFTNQNLIRTSATL
+LRYYLRADYGLHLTRTVGTLVNNVTGTSSMAYTGVVNASVTFLTEAVTLVAVTVVVGVAM
+PLTGLGMALYFLAVAWVIKTVIRRPASRLGWTLVTAGERANTAALQGLENYKDVKIRGND
+SAFMEEYRAARMESAEATRLKMILTMMPRYVLEVAFVAAIAALVAVAFIQGRGGEAFGSL
+ALLAMAGFRVLPSMAALMATTNEIRTSWPAFERTTAELAAAQPVLHAADRPYERITFEES
+IEVRDASFTYPGKAEPVLRDIDLRIPFGSSYAFVGGSGAGKTTLVDLVIGFHHAQRGGVY
+VDGVELEANPRGWWDNVAFVPQSVTVVNGTVLHNVLLDVEAAQTADRAEVERVLREAQLG
+QWLDELPDGLDTVIGEGAVGVSGGQRQRLGIARALFRRPRLLVLDEATSALDNLTERRVT
+EVIESLRGRITVIVVAHRLSTVKRCDQIVLMDQGRIIGQGTFAGLQETSPEFRELVRLGD
+LST
+>1_199
+MLTRLLKARLPEGTQYLVDRPMRIRLVFVVLGSVLVAGLEMVALASIIPLVSLLTSGELG
+SPALEGLLARFGAVTVPEQTVAFAVVIVVAFLLKAILVLAFRWWTMGFTNQNLIRTSATL
+LRYYLRADYGLHLTRTVGTLVNNVTGTSSMAYTGVVNASVTFLTEAVTLVAVAVVVGVAM
+PLTGLGMALYFLAVAWVIKTVIRRPASRLGWTLVTTGERANTAALQGLENYKDVKIRGND
+SAFMEEYRAARMESAEAMRLKMILTMMPRYVLEVAFVAAIAALVAVAFIQGRGGEAFGSL
+ALLAMAGFRVLPSMAALMATTNEIRTSWPAFERTTAELAAAQPVLHAADRPYERITFEEA
+IEVRDASFTYPGKAEPVLRDIDLRIPFGSSYAFVGGSGAGKTTLVDLVIGFHHAQRGGVY
+VDGVELEANPRGWWDNVAFVPQSVTVVNGTVLHNVLLDVEAAQTADRAEVERVLREAQLG
+QWLDELPDGLDTVIGEGAVGVSGGQRQRLGIARALFRRPRLLVLDEATSALDNLTERRVT
+EVIESLRGRITVIVVAHRLSTVKRCDQIVLMDHGRIIGQGTFAGLQETSPEFRELVRLGD
+LST
+>2_2402
+MLTRLLKARLPEGTQYLVDRPMRIRLVFVVLGSVLVAGLEMVALASILPLVSLLTSGELG
+SPALEGLLARFGAVTVPEQTVAFAVVIVLAFLLKAILVLAFRWWTMGFTNQNLIRTSATL
+LRYYLRADYGLHLTRTVGTLVNNVTGTSSMAYTGVVNASVTFLTEAVTLVAVAVVVGVSM
+PLTGLGMALYFLAVAWVIKAVIRRPASRLGWTLVTTGERANTAALQGLENYKDVKIRGND
+SAFMEEYRAARAESAEATRLKMILTMMPRYVLEVAFVAAIAALVAVAFVQGRGGEAFGSL
+ALLAMAGFRVLPSMAALMATTNEIRASWPAFERTTAELADAQPVLDAADRPYERLEFARE
+IEVRGASYTYPGSDEPVLRDIDLTIPFGTSYAFVGGSGAGKTTLIDLLIGFHHAQDGAVL
+VDGVELEANPRGWWDNVAFVPQSVTVVNGSVLHNVVLDLEAAETADRAAVEQVLRDAQLG
+EWLDALPEGLDTVIGEGAVGVSGGQRQRLGIARALFRRPRLLVLDEATSALDNLTERRVT
+EVIESLKGRITVLVVAHRLSTVKHCDQIVLMDQGRIIGQGTFRGLQETSPEFQELVRLGD
+LSA
+>3_2285
+MVTRLLKSRLPEGTQYLVDRPMRIRLGFVVLGSILVALLEMAALASILPLVNLLTTGSPG
+APVITELLASVGAVSVAEQTVAFAGVIVVAYLLKAVLVLSFRWWTMGFTNKNLIQTSAKL
+LRYYLRADYGLHLTRTVGTLVNNVTGTSSMAYTGVVNASVTLLTEAVTLLAVGIVVGVTM
+PLTALGMGAYFLVVTLIIRHVIRKPASQLGWTLVVTGERANTAALQGLENYKDVKVRGND
+SAFMDEYVDARRENAEAIRLKMILTMMPRYVLEVAFVAAIAGLVAVAFASGRGDQAFGSL
+ALLAMAGFRLLPSIASVMATSNEIRASWPAFERTVAELKDAQPVLDAADRPYDRLPFERS
+LEARNASFTYPGKDEPVLKGIDLSIPFGASYAFVGGSGAGKTTLVDLLIGFHHAQQGGVY
+VDGVELQADPRGWWDNVAFVPQSVTVVNGSVLHNVVLDIEAARTADRTEVERVLRDAQMG
+DWLDALPDGLDTVVGEGAVGVSGGQRQRLGIARALYRRPRLLVLDEATSALDNVTERKVT
+DVIESLKGRITVIVVAHRLSTVKHCDQVVLMDEGRILDQGTFAGLQETSPEFQELVRLGD
+LSS
+>4_468
+MLTRLLKARLPEGTQYLVDRPMRIRLVFVVLGSVLVAGLEMVALASILPLVSLLTSGELD
+SPALEGLLARFGAVTVPEQTVAFAVVIVLAFLLKAILVLAFRWWTMGFTNQNLIRTSATL
+LRYYLRADYGLHLTRTVGTLVNNVTGTSSMAYTGVVNASVTFLTEAVTLVAVAVVVGVAM
+PLTGLGMALYFLAVAWVIKTVIRRPASRLGWTLVTAGERANTAALQGLENYKDVKIRGND
+SAFMEEYRAARMESAEATRLKMILTMMPRYVLEVAFVAAIAALVAVAFIQGRGGEAFGSL
+ALLAMAGFRVLPSMAALMATTNEIRTSWPAFERTTAELAAAQPVLHAADRPYERVTFEEA
+IEVRDASFTYPGKAEPVLRDIDLRIPFGSSYAFVGGSGAGKTTLVDLVIGFHHAQRGGVY
+VDGVELEANPRGWWDNVAFVPQSVTVVNGTVLHNVLLDVEAAQTADRAEVERVLREAQLG
+QWLDELPDGLDTVIGEGAVGVSGGQRQRLGIARALFRRPRLLVLDEATSALDNLTERRVT
+EVIESLRGRITVIVVAHRLSTVKRCDQIVLMDQGRIIGQGTFAGLQETSPEFRELVRLGD
+LST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000528.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000528.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a29c64db0144d9d7752c30ee6bed12d8090f673b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000528.fa
@@ -0,0 +1,45 @@
+>0_499
+MRITETAIPGLLVLDLDVHGDNRGWFKENWQREKIRALAAEHPRLAALAPVQNNISFNDA
+VGTTRGIHAEPWDKYVAVAHGRIFGAWVDLREGPSFGAVATVELGPEKAVFVPRGVGNSY
+QTLEPDTAYTYLVNDHWSADAQGRYTFLNLADPTAAIAWPIPLEDAELSDKDRAHPMLAD
+VTPMPSAPILVLGAGGQLGRALVARAEAAGIPVEAHGRDTWDMTDPASWPREHFRGLRAV
+VNASAMTAVDAAETPEGRAQAWAVNAAAVAELARRCTKAGVPLAHVSTDYVFDGALPVGQ
+EHPVDHPLAPLGVYGQSKAAGEAAVRTVPRHWIVRTSWVIGEGKNFVATMASLAERGIDP
+AVVADQHGRLTFADDLADALLHLVTTDAPTGTFHMTNSGDVVTWHDVARWVFEDTGHDAA
+RVSATTTAAYLAGKEGVAPRPTNSALDLGPLAAVGYTAPDQRERLRDHLTEFKAGTC
+>1_230
+MRITETAIPGLLVLDLDVHGDNRGWFKENWQREKIRALAAGHPRLASLAPVQNNISFNDA
+VGTTRGIHAEPWDKYVAVAHGRIFGAWVDLREGPSFGAVATVELGPEKAVFVPRGVGNSY
+QTLEPDTAYTYLVNDHWSADAQGQYTFLNLADPTAAIAWPIPLEDAELSDKDRAHPMLAD
+VTPMPPAPILVLGAGGQLGRALVVRAEAAGIPVEAHGRDTWDMTDPASWPREHFRGLRAV
+VNASAMTAVDAAETPEGRAQAWAVNATAVAELARRCTEAGVPLAHVSTDYVFDGTLPVGQ
+EHPVDHPLAPLGVYGQSKAAGEAAVRTVPRHWIVRTSWVIGEGKNFVATMASLAERGIDP
+AVVADQHGRLTFADDLADALLHLVTTDAPTGTFHMTNSGDVVTWHDVARWVFEDTGHDAG
+HVSATTTAAYLAGKEGVAPRPTNSALDLGPLAAVGYTAPDQRERLRTYLRR
+>2_2374
+MKITETAIPGLLVIDLDVHGDNRGWFKENWQREKIRALAAEHPRLATLAPVQNNISFNDA
+VGTTRGIHAEPWDKYVAVAHGRIFGAWVDLREGPSFGAVATVELGPEKAVFVPRGVGNSY
+QTLEPDTAYTYLVNDHWSADAQSQYTFLNLADPTAAIAWPIPLEEAELSDKDRAHPMLAD
+VTPMPPAPILVLGAGGQLGRALVARAEAAGIPVEAHDRTTWDLEDPDSWPREHFRGLRAV
+VNASAMTAVDAAETPEGRAQAWAVNATAVAELARRCAEAGVPLAHVSTDYVFDGTLPVGQ
+EHPVDHPLAPLGVYGQSKAAGEAAVRTVPRHWIVRTSWVIGEGRNFVATMASLAERGIDP
+AVVDDQHGRLTFADDLADALLHLVTTDAPTGTFHMTNSGDVVTWHDVARWVFEDTGHDAA
+RVSATTTAAYTAGKEGVAPRPTNSALDLGPLAVVGYTAPDQRGRLRDHLSELTGDAR
+>3_2256
+MKITETAIPGLLVLDLDVHGDNRGWFKENWQREKIRALAAEHPRLASLAPVQNNISFNDA
+VGTTRGIHAEPWDKYVAVAHGRIFGAWVDLREGPSFGAVATVELGPEKAVFVPRGVGNSY
+QTLEPDTAYTYLVNDHWSADAQGQYTFLNLADPTAAIAWPIPLEDAELSDKDRAHPMLAD
+VTPMPPAPILVLGAGGQLGRALVARAEAAGIPVEAHGRDTWDMTDPASWPREHFRGLRAV
+VNASAMTAVDAAETPEGRAQAWAVNATAVAELARRCTEAGVPLAQVSTDYVFDGTLPVGQ
+EHPVDHPLAPLGVYGQSKAAGEAAVRTVPRHWIVRTSWVIGEGKNFVATMASLAERGIDP
+AVVADQHGRLTFADDLADALLHLVTTDAPTGTFHMTNSGDVVTWHDVARWVFEDTGHDAA
+RVSAATTAEYMAGKEGAAPRPTNSALDLGPLAAVGYTAPDQRERLRDHLSEAAGGTR
+>4_499
+MRITETAIPGLLVLDLDVHGDNRGWFKENWQREKIRALAAEHPRLASLAPVQNNISFNDA
+VGTTRGIHAEPWDKYVAVAHGRIFGAWVDLREGPSFGAVATVELGPEKAVFVPRGVGNSY
+QTLEPDTAYTYLVNDHWSADAQGQYTFLNLADPTAAIAWPIALEDAELSDKDRAHPMLDD
+VVPMPPAPILVLGAGGQLGRALVARAEAAGIPVEAHGRDTWDMADPASWPREHFRGLRAV
+VNASAMTAVDTAETTEGRAQAWAVNATAVAELARRCTEAGVPLAHVSTDYVFDGALPVGQ
+EHPVDHPLAPLGVYGQSKAAGEAAVRTVPRHWIVRTSWVIGEGKNFVATMASLAERGIDP
+AVVADQHGRLTFADDLADALLHLVTTDAPTGTFHMTNSGDVVTWHDVARWVFEDTGHDAA
+RVSATTTAAYLAGKEGVAPRPTNSALDLGPLAAVGYTAPDQRERLRDHLTEFKAGTC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000530.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000530.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa4f1b2c43ce4711c1c106dc2cf1d05357bad6ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000530.fa
@@ -0,0 +1,25 @@
+>0_504
+MTTGTTLIVGLGNPGPEYERTRHNVGQMVADELASRMGVGFTRHRAGAVVATGRLGIGGP
+RVVLAKSTGYMNVSGRPVSALAAFYGIGPEDLVVVHDELDIPFDTLRLKRGGGEGGHNGL
+KSITASLGTKDYARVRVGIGRPPGRMDVADFVLRPFTKPEQDALPLHVDRAADAVEKLVT
+DGLEPAQQAFH
+>1_234
+MTTGTTLIVGLGNPGPEYERTRHNVGQMVADELASRMGVGFTRHRAGAVVATGRLGIGGP
+RVVLAKSTGYMNVSGRPVSALASFYGIGPEDLVVVHDELDIPFDTLRLKRGGGEGGHNGL
+KSITASLGTKDYARVRVGIGRPPGRMDVADFVLRPFTKPEQDVLPLHVDRAADAVEKLVT
+DGLAPAQQAFH
+>2_2371
+MSAGTTLIVGLGNPGPEYERTRHNVGQMVADELASRMGAGFTRHRAGAVVATGRLGIGGP
+RVVLAKSTGYMNVSGRPVSALASFYGVGPEDLVVVHDELDIPFDALRLKRGGGEGGHNGL
+KSITASLGTKDYARVRVGIGRPPGRMDVADFVLRSFSKPEQDALPLHVDRAADAVEKLVT
+DGLEAAQQAFH
+>3_2253
+MTGTTLIVGLGNPGPEYERTRHNVGHMVAGELASRMGVGFTRHKAGAVVATGRLGIGGPR
+VVLAMSTGYMNTSGRPVSALTNFYDVAPEDLVVVHDELDIPFETLRLKRGGGEGGHNGLK
+SITASLGTKDYHRVRVGIGRPPGRMDVADFVLKPFTKQEQELLPLHVDRAADAVEKLVTD
+GLEAAQQAFNS
+>4_504
+MTTGTTLIVGLGNPGPEYERTRHNVGQMVADELASRMGVGFTRHRAGAVVATGRLGIGGP
+RVVLAKSTGYMNVSGRPVSALASFYGIGSEDLVVVHDELDIPFDTLRLKRGGGEGGHNGL
+KSITASLGTKDYARVRVGIGRPPGRMDVADFVLRPFTKPEQDVLPLHVDRAADAVEKLVT
+DGLEAAQQAFH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000532.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000532.fa
new file mode 100644
index 0000000000000000000000000000000000000000..84ed029e663f56f11702ff117423f9117acfa1ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000532.fa
@@ -0,0 +1,37 @@
+>0_507
+MSALWAVALIMLLSGTAKLRSGEDVQATFTRLRVPRPFAAPALARAFPWLELLLAAALLQ
+PFTPLRPVVGLAAVALFAAFLALVVRAQDDGVSCGCFGEASAAPISRTTVVRNVVFLVLA
+VLALVEGIVSLAVHGAGLAWQPLTAFGAGAWAWALLVTVLLTTAAFLAGRESVPAAPDAA
+PATPEAPATPEAPDAADPVGEAEPERRPFPDAVVVADGEYTGLHRLVQDGAVVALRLSTG
+CGSCARVIERLDEFKDALGPVRLRVLMPQRAPGADGAIRSGAVDASLVLADPDGAASQAI
+GLHSFPTAVLLGTDRLTAGGPVGGADDVLAFLEEIREIMTTELPAATDGSTATPEVRA
+>1_237
+MSALWAVALIMLLSGTAKLRSGEDVQATFTRLRVPRPFAAPGLARAFPWLELLLAAALLQ
+PFTLLRPVVGLVAVVLFAAFLALVVRAQDDGVSCGCFGEASAAPISRTTVVRNVVFLALA
+VLALAEGIVSLAVHGAGLAWQPLTAFGAGAWAWALLVSVLLATAAFLAGRESVPAAPDAV
+PAMPTPEAPAAVDPAAVDPADGDPADAAEPERHPFPDAVVVADGEYTGLHRLVADGAVVA
+LRLSTGCGSCARVIERLDEFTDALGPVRLRVLMPQRAPGAEGAIHSGAVDASLVLADPAG
+AASQALGLYSFPTAVLLGTDRLTAGGPVGGADDVLAFLEEIREIMTTELPAATDGSTATP
+EVRA
+>2_2369
+MPALWAVALILLLSGTAKLRSGEDVQATFTRLRVPRPFAAPALARAFPWLELLLAAALLQ
+PFTQLRPVVGLVAVALFAAFLALVVRAKGDGVSCGCFGEASAAPISRTTVVRNVVFLVLA
+VLALAEGIVSLAVHGGGLAWQPLTAFGAGAWAWALLVSVLLATAAFLAGRESVPAAPDAA
+PAASTPEAPAAVDPADGAEPERHPFPDALVIEDGRYTGLHALASRGAVVALRLSAGCGSC
+SRVIARLDEFRASLGPVRLRVLMPQHEAGATPSASTGAIPEDLVVDDPNGAAARGLGLTS
+YPMAVLLGTDLLTAGGPVGGADDVLAFLEEIRDIMAAEAPAAPAAPARSPASDTPTPEVR
+A
+>3_2250
+MSALWAVALIMLFSGAAKLRSREDVGAVFTRLKVPAPWNDARLARAFPWLELLLALALVQ
+PFTVLRPLVGLAAVALFVAFLVLVVRATGDGVSCGCFGEASAAPITGQTVVRNVLFLLLA
+VMALFEGVASLAVHGIATEWLPLTAFGEDVTAWTVVVTLLLAAAAVLVGRESVPAAASAV
+PVPAAGVPGSAAPAPAEGQGDEPERRPFPVAAVQQGGAFVTLHQLVIPGAVVALRLSVGC
+GSCSAVIARLPELVERLGPIRVRVLMPQTVPGGELRHGTIPAELVLEDPAGAAAGGLGLT
+GFPSAVLLGADGMTAGGPVFGADEVIAFLEEIGEIVATELPAAAEGSHRP
+>4_507
+MSALWAVALIMLLSGTAKLRSGEDVQATFTRLRVPRPFAAPGLARAFPWLELLLAAALLQ
+PFTLLRPVVGLVAVALFAAFLALVVRAQDDGVSCGCFGDASAAPISRTTVVRNVVFLALA
+VLALAEGIVSLAVHGAGLAWQPLTAFGAGAWAWALLVSVLLATAAFLAGRESVPAAPDAV
+PATPTPEAPAVADPADGAEPERHPFPDAVVVADGEYTGLHRLVQDGAVVALRLSTGCGSC
+ARVIERLDEFKDALGPVRLRVLLPQYAPGAEGAIRSGAVDASLVLADPAGAASQALGLHS
+FPTAVLLGTDRLTAGGPVGGADDVLAFLEEIREIMTTELPAAMDGSTATPEFRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000533.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000533.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b695b46e380d00eeecb4ac51fb70a976a63824f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000533.fa
@@ -0,0 +1,110 @@
+>0_508
+MSAPETTPVLAPLLPRLRAERALEAAAASASRPLEARGVELEIGLPDGARAPLLTVLAEA
+LAEGHGERAAVLVVTATTREAEDLVTDLAAWAPAGAAALFPSWETLPHERLSPRSDTVGA
+RLAVLRRLAHPEEHAEGPLRIVVAPVRAVLQPLVAGLGELSPVTLRTGEERDFDGVVAAL
+ADAAYSRVDMVSRRGEFAVRGGLIDVFPPTEDYPVRIEFFGDEVEQMRWFSVADQRSLED
+TTEDGSGHPSELYAPPCRELLITDHVRRRAKELIPAMPAAADMLDRIAEGVAVEGMESLS
+PLLAEAMTSLPRMLPTGSLTVLVEPERLRGRADDLLATNEEFLQAAWAGAAQGAVAPVDV
+AEADQSAAGGFLTVAELRAAALEQDQGFWSVTALVSDAELLPDAATLRATLGVPQTFSGD
+IEAMVAHTRVRLAEGWHAVVLTDGPGSARRLAELNAEAGLTASVVDGPLPADLAPGRVSI
+ATAPVGSGFTIPDAQIALITEHDLFGRHRTAGTRAPGARLARKRRNAVDPLTLQPGGHVV
+HSQHGIARFVELQRRKVTGGPRTAPGAEESYREYLVLEYAPSKRGAPGDRLFVPTDQLDL
+ISTYVGGETPSLSKMGGSDWAQTKSKAKRATREIAGELIRLYSARMASRGHAFAPDTPWQ
+GELEEAFPFIETPDQLTTIEDVKKDMEAAVPMDRLVSGDVGFGKTEVAVRAAFKAVQDGK
+QVAVLVPTTLLARQHHQTFSDRFAGFPVKVAALSRFQTAKESKEVIEGLAHGEVDVVIGT
+HRLLSDQVQFKDLGLVIVDEEQRFGVEHKEALKKMRTNVDVLAMSATPIPRTLEMSLTGI
+RETSTLATAPEERHPVLTSVGPYSDQQVTAAIRRELMREGQVFYVHNRVTTIDKVAKRIA
+ELVPEARIAVAHGKMSEARLEQIMVDFWERKFDVLVSTTIIETGLDIANANTLIVEDAHR
+YGLSQLHQLRGRVGRGRERAYAYFLYDPQKPLGEVALERLKAVATHNELGAGMQLAMKDL
+EIRGAGNLLGGEQSGHIAGVGFDLYLRMVGEAVADFKGEEDTAPAEVKVELPVNAHLPHD
+YVPGERLRLEMYRNLAQAADDAAVDAVVEELKDRYGPLPEPVEALVAVARFRNRARAAGV
+TEVMLLGQNVKFGPAADLPESRQMRLTRMYKGAQVKPALNGVLIPRPKTKPVMGQDLVDV
+PLLEWAQQVVDAIFAPEG
+>1_238
+MSAPETTPVLAPLLPRLRAERALEAAAASAARPLESRGVELEIGLPDGARAPLLTVLAEA
+LAEGHGERAAVLVVTATTREAEDLVTDLAAWAPAGTAALFPSWETLPHERLSPRSDTVGA
+RLAVLRRLAHPEEHAEGPLRVVVAPVRAVLQPLVAGLGELSPVTLRTGEERDFDGVVAAL
+ADAAYSRVDMVSRRGEFAVRGGLIDVFPPTEDYPVRIEFFGDEVEQMRWFSVADQRSLED
+TTEDGSGHPSELYAPPCRELLITDHVRRRAKELIPAMPAAADMLDRIAEGVAVEGMESLS
+PLLAEAMTSLPRMLPAGSLTVLVEPERLRGRADDLLATNEEFLQAAWAGAAQGAVAPVDV
+AGADQSAAGGFLTVAELRAAALEQDQGFWSVTALVSDDELLPDAATLRATLGVAQTFSGD
+IEAMVAHTRVRLAEGWHAVVLTDGPGSARRLAELTTEAGLTAAVVDGPLPADLAPGRVSI
+ATAPVGSGFTIPDAQIALITEHDLFGRHRTAGTRAPGARLARKRRNAVDPLTLQPGDHVV
+HSQHGIARFVELQRRKVTGGPRTAPGAEESYREYLVLEYAPSKRGAPGDRLFVPTDQLDL
+ISTYVGGETPSLSKMGGSDWAQTKSKAKRATREIAGELIRLYSARMASRGHAFAPDTPWQ
+GELEEAFPFIETPDQLTTIEDVKKDMEAAVPMDRLVSGDVGFGKTEVAVRAAFKAVQDGK
+QVAVLVPTTLLARQHHQTFSDRFAGFPVKVAALSRFQTAKESKEVVEGLAHGEVDVVIGT
+HRLLSDQVQFKDLGLVIVDEEQRFGVEHKEALKKMRTNVDVLAMSATPIPRTLEMSLTGI
+RETSTLATAPEERHPVLTSVGPYSDQQVTAAIRRELMREGQVFYVHNRVTTIDKVAKRIA
+ELVPEARIAVAHGKMSEARLEQIMVDFWERKFDVLVSTTIIETGLDIANANTLIVEDAHR
+YGLSQLHQLRGRVGRGRERAYAYFLYDPQKPLGEVALERLKAVATHNELGAGMQLAMKDL
+EIRGAGNLLGGEQSGHIAGVGFDLYLRMVGEAVADFKGEEDTAPAEVKVELPVNAHLPHD
+YVPGERLRLEMYRNLAQAADDAAVDAVVEELKDRYGPLPEPVEALVAVARFRNRARAAGV
+TEVMLLGQNVKFGPAADLPESRQMRLTRMYKGAQVKPALNGVLIPRPKTKPVMGQDLVDV
+PLLEWAQQVVDAIFAPEG
+>2_2368
+MPPRPPPVVAPLLPRLRAERAIEAAAASAARPLEARGVELEIGLPDGARAPLLTVLAEAL
+AEGHGERAAVLVVTATTREAEDLVTDLAAWAPAGAAALFPSWETLPHERLSPRSDTVGAR
+LAVLRRLAHPEEHAQGPLRIVVAPVRAVLQPLVAGLGELSPVTLRTGEERDFDGVVAALA
+DAAYSRVDMVSRRGEFAVRGGLIDVFPPTEDHPVRIEFFGDEVEQMRWFSVADQRSLEDT
+TEDGSGHPTELYAPPCRELLITDHVRRRAKELIPAMPAAADMLDRIAEGVAVEGMESLSP
+LLAEAMTSLPRMLPTGSLTVLVEPERLRGRADDLLATNEEFLQAAWAGAAQGAVAPVDIA
+GADQSAAGGFLTVAELRAAALEQDQGFWSVTALAPDDELLPDAATLRSTLGVPRTFAGDM
+EAMVEHTRTRLAEGWHAVILTDGPGSARRLAELHADAGLTASVADGPVPAEPAPGRVTIA
+TAAVGAGFTVPDERLAVITEHDLFGRHRTAGTRAPGARLARKRRNAVDPLALQPGDHVVH
+AQHGIARFVELQRRKVTGGPRTAPGAEESYREYLVLEYAPSKRGAPGDRLFVPTDQLDLV
+SSYVGGEAPSLSKMGGSDWAQTKSKAKRATREIAGELIRLYSARMASRGHAFAPDTPWQS
+ELEEAFPFIETPDQLTTIEDVKKDMEAAVPMDRLVSGDVGFGKTEVAVRAAFKAVQDGKQ
+VAVLVPTTLLARQHHQTFSDRFAGFPVKVAALSRFQTAKESKEVVEGLAHGEVDVVIGTH
+RLLSDQVQFKDLGLVIVDEEQRFGVEHKEALKKMRTNVDVLAMSATPIPRTLEMSLTGIR
+ETSTLATAPEERHPVLTSVGPYSDQQVTAAIRRELMREGQVFYVHNRVTTIDKVARRIAE
+LVPEARIAVAHGKMGEARLEQIMVDFWERRFDVLVSTTIIETGLDIANANTLIVEDAHRY
+GLSQLHQLRGRVGRGRERAYAYFLYDAQKPLGEVALERLKAVATHNELGAGMQLAMKDLE
+IRGAGNLLGGEQSGHIAGVGFDLYLRMVGEAVADFKGEEDTAPAEVKVELPVNAHLPHDY
+VPGERLRLEMYRNLAQAADDAAVDAVVEELKDRYGPLPDPVEALVAVARFRNHARAAGIT
+EVMLLGQNVKFGPAADLPESRQMRLARMYKGSQVKPALNGVLIPRPKTKPVMGQDLVDVP
+LLEWAQQVIDAIFAPEG
+>3_2249
+MSPADVTAPVPVLAPLLPVLAREPAFEAAAASAARALPARGQELEIGLPDGARAPLFAHL
+ADALAAGHGADAVLLVVTATAREAEDLIGDLAAWADPASVALFPSWETLPHERLSPRSDT
+VGARLDVLRRLAHPGEDGRPPLRVVVAPVRSVIQPLVRGLGELAPVHLRVGQERDFDAVV
+QDLADAAYARVDMVSRRGEFAVRGGLIDVFPPTADHPVRVEFFGDEVEQMRWFSVADQRS
+LQDTSEDGSGHPTELHAPPCRELLVTPSVQERARALMARLPGAADMLERIAEGQAVEGME
+SLSPLLADGMTSLVHLLPEGSLTLLVEPERIRSRADDLLATNEEFLAAAWAGAAQGAQAP
+VDLGADQSAAGGFLTLAELREAVLEERQGHWSTTALSPDAELLPDASALRSSLGVPTTFG
+ADMEAMVRFTRERLADGWSVVLLTDGPGSARRLAELHADAGLTASVLDGPVDPAPAPGRV
+RVATAAVGTGFTDPETKLAVVTEQDLFGRHRTAGTRAAGGKLARRRRNAVDPLALQPGDF
+VVHSQHGIARFVELQRRPVTGGARKRPGEEESYREYLVLEYAPSKRGAPGDRLFVPTDQL
+DLISQYVGGEAPALSKMGGSDWAQTKSKAKRATREIAGELIRLYSARMATRGHSFAPDTP
+WQAELEEAFPYIETPDQLTTIEEVKKDMESPVPMDRLVSGDVGFGKTEVAVRAAFKAVQD
+GKQVAVLVPTTLLARQHHQTFTDRFAGFPVTVAALSRFQTAKESKEVVEGLAAGEVDVVV
+GTHRLLSKEVQFKDLGLVIVDEEQRFGVEHKEALKKMRTNVDVLAMSATPIPRTLEMSLT
+GIRETSTLATAPEERHPVLTSVGPYTDQQVIAAIRRELMREGQVFYVHNRVTTIDKVASR
+LAQLVPEARIAVAHGKMSESRLEQIMVDFWEKRFDVLVSTTIIETGLDIANANTLIVEDA
+HRYGLSQLHQLRGRVGRGRDRAYAYFLYDAQKPLGEVAMERLKAVAQHNELGAGLQLAMK
+DLEIRGAGNLLGGEQSGHIAGVGFDLYLRMVGEAVADFKGEEDTAPAEVKVELPVNAHLP
+HDYVPGERLRLEMYRSLATAVDDAAVDAVVEEMKDRYGPLPEPVQALVAVARFRNRAREA
+GVTEVMLLGQNVKFGPAADLPESRQLRAQRMYKGAQLKPALNALLIPRPKTKPVMGQDLV
+DAPLLEWADQVVQAIFAPEPVSAG
+>4_508
+MSAPVLAPLLPRLRAERAIEAAAASASRPLEARGVELEIGLPDGARAPLLTVLAEALAEG
+HGERAAVLVVTATTREAEDLVTDLAAWAPAGAAALFPSWETLPHERLSPRSDTVGARLAV
+LRRLAHPEEHAEGPLRIVVAPVRAVLQPLVAGLGELSPVTLRTGEERDFDGVVAALADAA
+YSRVDMVSRRGEFAVRGGLIDVFPPTEDYPVRIEFFGDEVEQMRWFSVADQRSLEDTTED
+GSGHPSELYAPPCRELLITDHVRRRAKELIPAMPAAADMLDRIAEGVAVEGMESLSPLLA
+EAMTSLPRMLPTGSLTVLVEPERLRGRADDLLATNEEFLQAAWAGAAQGAVAPVDVAGAD
+QSAAGGFLTVAELRAAALEQDQGFWSVTALVSDAELLPDAATLRATLGVAQTFSGDIEAM
+VAHTRVRLAEGWHAVVLTDGPGSARRLAELNAEAGLTASVVDGPLPADLAPGRVSIATAP
+VGSGFTIPDAQIALITEHDLFGRHRTAGTRAPGARLARKRRNAVDPLTLQPGDHVVHSQH
+GIARFVELQRRKVTGGPRTAPGAEESYREYLVLEYAPSKRGAPGDRLFVPTDQLDLISTY
+VGGETPSLSKMGGSDWAQTKSKAKRATREIAGELIRLYSARMASRGHAFAPDTPWQGELE
+EAFPFIETPDQLTTIEDVKKDMEAAVPMDRLVSGDVGFGKTEVAVRAAFKAVQDGKQVAV
+LVPTTLLARQHHQTFSDRFAGFPVKVAALSRFQTAKESKEVVEGLAHGEVDVVIGTHRLL
+SDQVQFKDLGLVIVDEEQRFGVEHKEALKKMRTNVDVLAMSATPIPRTLEMSLTGIRETS
+TLATAPEERHPVLTSVGPYSDQQVIAAIRRELMREGQVFYVHNRVTTIDKVAKRIAELVP
+EARIAVAHGKMSEARLEQIMVDFWERKFDVLVSTTIIETGLDIANANTLIVEDAHRYGLS
+QLHQLRGRVGRGRERAYAYFLYDPQKPLGEVALERLKAVATHNELGAGMQLAMKDLEIRG
+AGNLLGGEQSGHIAGVGFDLYLRMVGEAVADFKGEEDTAPAEVKVELPVNAHLPHDYVPG
+ERLRLEMYRNLAQAADDAAVDAVVEELKDRYGPLPEPVEALVAVARFRNRARAAGVTEVM
+LLGQNVKFGPAADLPESRQMRLTRMYKGAQVKPALNGVLIPRPKTKPVMGQDLVDVPLLE
+WAQQVVDAIFAPEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000536.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000536.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07b4ec3818b4612a695218098dcbbf4c2ac1a962
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000536.fa
@@ -0,0 +1,32 @@
+>0_511
+MSRDHRPPIRNPFLPPTPEEPEVPARDGGHPAGDGGDADAPAASTAREDRLAEFRLGPAF
+RPHPADRVPGPVPSARVLVVCTGNICRSAYVEYALQAQLNALLGDRGRAEVTSAGTEPNQ
+ALTVPGPLLDRAPSRRVRAALTQHRPQQLTGRSLAGQDLVLTATDDHLDEVLREDPAAVR
+RTFTILGMGTLLRDHGEELAAAVPPGAGVTALVTALAALRSRLIAHGERPDADLPDPFRG
+PAEGYAAMAQTAQPIVELLAWEIARALDGDLVEEEPTGA
+>1_244
+MSRDHRPPIRNPFLPPTPEEPEVPARDGGHPAGDGGDADAPAASTAREDRLAEFRLGPAF
+RPHPADPATPRQRATPTERTVAPAPVRAAEPASPASPAGRVPGPLPSARVLVVCTGNICR
+SAYVEYALQAQLNALLGDRGRAVVTSAGTEPNQALTVPGPLLDLAPSRRVRAALTQHRPQ
+QLTGRSLADQDLVLTATDDHLDEVLREDPAAVRRTFTILGMGTLLRDHGEELAAAVPPGA
+GVTALVTALAELRSRLIAQGERPDADLPDPFRGPAEGYAAMAQTAQPIVELLAWEIARAL
+DGDLVEEEPTGA
+>2_2362
+MSQDRRAPIRNPFLEPGASVPGAPPRRADADPEDRLAEFRLGPAFGGRPAQPRRPQGFGG
+RTAPGEGTTTTPRPDGTAAAEPADTAAEPVDTAAEPAANPKTARPAESAEAADAPAPAPA
+PLPTVRVLAVCTGNICRSAYVQHTLQAQLNALLGDRGRAEVTSAGTEPNQALTVPEPLRE
+LSPSRRVRAALTEHRPQQLTAASLWGQDLVITAADDHLEEVLREDPGAVRRTFTVRGIGT
+LLGEHGEEIAAAVPPGAGLAALVDAMADLRVRLIGRGEEPDADLPDPFRGPAEGYAQMVE
+TARPIVELLAWEIARALDGDLVEDDEPTRV
+>3_2243
+MSWFERPALRSPFAAAPGMDAPADDGAGGPLRILTVCTGNICRSAWAHHVLQARLDAALG
+ADVVEVSSAGTGPNQALAVPEELLTLAPDAGVRAALAAHRPRRLTARVLAGQDLVLTATE
+AHRDAVVREAPAALRRSATLLDAGALLADPDAVAPGGGGRALVAALEAARREGRGLDAGR
+RGLFPAGRRAADLADPFRGPAEGYTEMTRALEPALAAVEAAVVRAVEPAR
+>4_514
+MSRDHRPPIRNPFLPPTPEEPEVPTRDGGHPAGDGGDAGAPAAATAREDRLAEFRLGPAF
+LPHPADPAAPRQHATPAERAVAPATAAAAEPASPAAPADRVPGPLPSARVLVVCTGNICR
+SAYVEYALQAQLNALLGDRGRAVVTSAGTEPNQALTVPGPLLDLAPSRRVRAALTQHRPQ
+QLTGRSLADQDLVLTATDDHLDEVLREDPAAVRRTFTILGMGTLLRDHGEELAAAVPPGA
+GVTALVTALAELRSRLIAQGERPDADLPDPFRGPAEGYAAMAQTAQPIVELLAWEIARAL
+DGDLVEEEPTGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000539.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000539.fa
new file mode 100644
index 0000000000000000000000000000000000000000..041408c6b0a46932983e0e9de3fac51c8f523b0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000539.fa
@@ -0,0 +1,55 @@
+>0_515
+MPAHPPHDDVAALPEDVLARAERWAAEDPDPAHRDTLRAELDAAAGVGPEAAAARAALAA
+RFAGPLVFGTAGLRAEEGPGESRMNRLVVRRTAAGLAAHLWDGVGRDAAPPLAVVGYDAR
+RGSAAFAADTAAVLTAAGVQTVLLPDPLPTPVLAFAVRHLSADAGVMVTASHNPPADNGY
+KVYLGGRLTDEAGRGAQIVSPADAEIAARIDHAAWAADIPLADDGWTVAGPDLLEAYRAA
+ALGVLDDDRHGHRDLRVVYTPLHGVGGAVVPGLLEDAGFGPVHVVAEQAAPDPAFPTVAF
+PNPEEPGAMDLALALAAEVDADLVIANDPDADRLALAAPVTDADGARTWRMLSGDAVGTL
+LGAHAMPALHAAGRSAANSVVSSPQLAALAEANGVRHHVTLTGFKWISRAPDLGFGYEEA
+LGYCVDPDMVRDKDGITAALMAAELAAALTAQGRGLMDALADVDAVTGAMPSAQVSVRVA
+DLSLIARTMTALRQQAPATLAGEPVTVRRDLAAGGDGLPPTDALLFATDSGTRVLVRPSG
+TEPKLKCYLGTRDADPAAAAERLEALRAEVTALVGG
+>1_248
+MPAHPPHDDVAALPEDVLARAERWAAEDPDPAHRDTLRAELDAAAGVGPEAAAARAVLAA
+RFAGPLAFGTAGLRAEEGPGESRMNRLVVRRTAAGLAAHLWDGVGRDAAPPLAVVGYDAR
+RGSAAFAADTAAVLTAAGVQTVLLPDPLPTPVLAFAVRHLSADAGVMVTASHNPPADNGY
+KVYLGGRLTDEAGRGAQIVSPADAQIAARIDHAAWAADIPLADDGWTVAGPDLLEAYRAA
+ALGVLDDDRHGHRDLRVVYTPLHGVGGAVVPGLLEDAGFGPVHVVAEQAAPDPAFPTVAF
+PNPEEPGAMDLALALAAEVDADLVIANDPDADRLALAAPVTDAHGVRTWRMLSGDAVGTL
+LGAHAMPALHAAGRSAANSVVSSPQLAALAEANGVRHHVTLTGFKWISRAPDLGFGYEEA
+LGYCVDPDMVRDKDGITAALMAAELAAALTAQGRGLMDALADVDAVTGAMPSAQVSVRVA
+DLSLIARTMTALRQQAPATLAGEPVTVRRDLAAGGDGLPPTDALLFATDSGTRVLVRPSG
+TEPKLKCYLGTRDADPAAAAERLEALRAEVTALVGG
+>2_2358
+MSGPEHLPPTADDDAVPASEARALALAERWSVEDPDPMHREALRAELDAAAGSGPEAEAA
+RASLASRFSGPLAFGTAGLRAEEGPGESRMNRLVVRRTAAGLARHLWEDVGEDAAAPLAV
+VGYDARRGSLGFAQDTAAVLTAAGVQVVLLPDALPTPVLAFAVRHLSADAGVMVTASHNP
+PADNGYKVYLGGRMTDEAGRGAQIVSPADVAIAELIDHEAWTADIPLAEDGWTVAGDELL
+EAYREAALAVLDEDRHPDRALRIVYTPLHGVGGAVLPGLLDEAGFGPVHVVPEQAEPDPA
+FPTVAFPNPEEPGAMDLALALAAEVDADLVIANDPDADRLALAAPFPGPDGTRVWRMLSG
+DAVGTLLGAHLLPALAAAERSVANSVVSSPQLAALAEAQSVAHHVTLTGFKWISRAPRLG
+FGYEEALGYCVDPDMVRDKDGITAALVAAELVAGLAARGCTVADALADVDAVTGSMPSGQ
+VSVRVADLSVIPRTMAALRAQGPATLAGEPVTVRRDLAEGGAGLPSTDALLFATASGTRV
+LVRPSGTEPKLKCYLGARDADPAVAAERLEALRAEVAALVGG
+>3_2240
+MRALDPRVRELAERWSVEDPEPMHRAVLMDELAAADGDDPAAEAARASLASRFSGPLAFG
+TAGLRAEEGPGESRMNRLVVRRTAAGLGRHLWNELGPDQPAPLVAVGYDARRGSADFAAD
+TAAVLTAAGAQVVLLPRALPTPVLAFAVRHLHADAGVMVTASHNPPADNGYKVYLGGRMT
+DEAGRGAQIVSPADVQIAAQIDHDAWTADIPLAAEGWEVAGEDLLEAYRAAALGVLDPGG
+HPGRDLRIVYTPLHGVGGAVLPDLLAEAGFADVHVVPEQAAPDPAFPTVAFPNPEEPGAM
+DLALALAAEVGADLVIANDPDADRLALAVPAGDGAAPSWRMLSGDAVGTLLGAHLLPRLA
+AQGRSAANSVVSAPQLAALAAAAGVEHHVTLTGFKWISRAPRLGYGYEEALGYCVAPDMV
+RDKDGMTAALVAAELAASLKAAGRTLDDARADADAVTGSMPSGQVSVRVQDLRIIADTMA
+ALRARPPAALAGDPVTVERDLAAGSADLPATDALLFATDAGTRVLVRPSGTEPKLKCYLG
+TQDADPTAAAARLDRLREEVAALVAG
+>4_518
+MPAHPPHDDVAALPEDVLARAERWAAEDPDPAHRDTLRAELDAAAGVGPEAAAARAVLAA
+RFAGPLAFGTAGLRAEEGPGESRMNRLVVRRTAAGLAAHLWDGVGRDAAPPLAVVGYDAR
+RGSAAFAADTAAVLTAAGVQTVLLPDPLPTPVLAFAVRHLSADAGVMVTASHNPPADNGY
+KVYLGGRLTDEAGRGAQIVSPADAEIAARIDHAAWAADIPLADDGWTVAGPDLLEAYRAA
+ALGVLDDDRHGHRDLRVVYTPLHGVGGAVVPGLLEDAGFGPVHVVAEQAAPDPAFPTVAF
+PNPEEPGAMDLALALAAEVDADLVIANDPDADRLALAAPVTDADGVRTWRMLSGDAVGTL
+LGAHAMPALHAAGRSAANSVVSSPQLAALAEANGVRHHVTLTGFKWISRAPDLGFGYEEA
+LGYCVDPDMVRDKDGITAALMAAELAAALTAQGRGLMDALADVDAVTGAMPSAQVSVRVA
+DLSLIARTMTALRQQAPATLAGEPVTVRRDLAAGGDGLPPTDALLFATDSGTRVLVRPSG
+TEPKLKCYLGTRDADPAAAAERLEALRAEVTALVGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000548.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000548.fa
new file mode 100644
index 0000000000000000000000000000000000000000..15a4b3186a3d43012b7db1391e9ec5368408226b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000548.fa
@@ -0,0 +1,40 @@
+>0_526
+MSRPETPDTAPLPIVPPAEDETARDVEERSAEPAGWTSAMRTLDAGLVVGPRAYTSREVA
+QRLGVSMASARKIWRALGYPTSPEGHKAFTEADIEAFESVLTLVRSGTLNEDTAISLARS
+IGQMTDRMVVWQIEALVEDKIASEGLTDPEARRAVVDMLPDMVGPLEKSMRIVYRRQLNR
+AVQRLTVRVEAGLAASAEGRDGSESDAPLPLARAVGFADMVSYTTLSRTMDDRTLARMVL
+RFESLAAETISAGGGWLVKTIGDEVMFNAETPEAGAAIALSLAETIAADEELPSARVALT
+WGRVLSRMGDIYGPTVNLAARLTSLADPGTVLVDAMTAAALSRDERFVLVPQPPRIVRGF
+GEVRPSLLLDGSAQTLLAD
+>1_260
+MSRPETPDTAPLPIVPPAEDETARDVEERSAQPAGWTSAMRTLDAGLVVGPRAYTSREVA
+QRLGVSMASARKIWRALGYPTSPEGHKAFTEADIEAFESVLTLVRSGTLNEDTAISLARS
+IGQMTDRMVVWQIEALVEDKIASEDLTDPEARRAVVDMLPDMVGPLEKAMRIVYRRQLNR
+AVQRLTVRVEAGLAASAQGRDGSESDAPLPLARAVGFADMVSYTTLSRTMDDRTLARMVL
+RFESLAAETISAGGGWLVKTIGDEVMFNAETPEAGAAIALSLAETIAADEELPSARVALT
+WGRVLSRMGDIYGPTVNLAARLTSLADPGTVLVDAMTAAALSRDERFVLVPQPPRIVRGF
+GEVRPSLLLDGSAQTLLAD
+>2_2344
+MSRAETPETAPLPIIAPDGSGPAEAPRRKDPHDERRADRHEDRRGEAAADRLEEVDAPPP
+GAGWTTAMRTLDAGLVVGPRAYTAREVAQRMGVSTASARKIWRALGYPTSPEGHKAFTEA
+DVEAFESVLELVRSGALNEDAAISLARSIGQMTDRMVVWQIEALVEDKIVSEGLTDPEAR
+RAAVDLLPEIVTPLERAMQIVYRRQLNRAVKRLTVRVEAGLAASEEGRDGSESDSPLPLA
+RAVGFADMVSYTTLSRTMDDRTLARMVQRFETLSAEIISAGGGWLVKTIGDEVMFNAETP
+ETGAAIALALAEAIAADDELPSARVALTWGRVLSRMGDIYGPTVNLAARLTSLADPGTVL
+VDAMTAAALSRDERFVLVPQPPRIVRGVGEVRPSLLLNGSAQTLLAD
+>3_2228
+MTRDTHHDAVPETAPLPVQAPAGAADPAVGRRESDALHHGWTSAIRTLDAGLLDRPRSYS
+RREAAQRLGISSVSARKIWRALGYPTVKDEEKVFSAEDIDAFEQVLSLVRDGMLNEDTAI
+SLARSVGQMTDRMVVWQIEALVEDQIAAEGKTDPEARRAAVEMLPGLVEPLEKVMRIVYR
+RQLTNAVQRLTVRVEAGLAASERGRDGSEDDAPLPLARAVGFADMVSYTTLSRTMGERTL
+ARTVQRFESKAAEIIAAGGGWLVKTIGDEVLFNAETPEAGATIALALAEAMADDDQLPAA
+RVSLAWGRVLSRLGDIYGPTVNLASRLTSLADPGTVLVDAMTAAALSRDERFVLVPQPPR
+IVRGFGEVRPSLLMNGAAQPLIAD
+>4_529
+MSRPETPDTAPLPIVPSAEDETARDVEERSAQPAGWTSAMRTLDAGLVVGPRAYTSREVA
+RRLGVSMGSARKIWRALGYPTSPEGHKAFTEADIEAFESVLTLVRSGTLNEDTAISLARS
+IGQMTDRMVVWQIEALVEDKIASEDLTDPEARRAVVDMLPDMVGPLEKAMRIVYRRQLNR
+AVQRLTVRVEAGLAASAQGRDGSESDAPLPLARAVGFADMVSYTTLSRTMDDRTLARMVL
+RFESLAAETISAGGGWLVKTIGDEVMFNAETPEAGAAIALSLAETIAADEELPSARVALT
+WGRVLSRMGDIYGPTVNLAARLTSLADPGTVLVDAMTAAALSRDERFVLVPQPPRIVRGF
+GEVRPSLLLDGSAQTLLAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000556.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000556.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d7850bacc59a9bbef25e94c9545004755d61fb4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000556.fa
@@ -0,0 +1,31 @@
+>0_535
+MPATPRTSRTPAVRPAPALPAPSARTVRWEIAIVLGLSLGKSAVYAIVQLIDKATQAPLG
+EQTTVLNPALADRWAFDLTYQLLGIGFALVPVALVLHLMHLRGRNPFRVLGLDLRRPGRD
+LAWGLGLFAAIGLGTLGVYAAGRALGITTAIVGSALGESWYQVPVLLLSALRHGLLEEVI
+VGAWLVDRLGYLQRLRAAGLARDPAPAVPSSWVSAEGLYLPTRAAVVVLALALLRGAYHL
+YQGIGPGVGNALMGVVFALVFLRVRRVMPLVIAHTLLDAVGFVGYPLLARAGLLG
+>1_269
+MPATPRTSRTPAGPAVRPAPALPAPSARTVRWEIAIVLGLSLGKSAVYAIVQLIDKATQA
+PLGEQTTVLNPALADRWAFDLTYQLLGIGFALVPVALVLHLMHLRGRNPFRVLGLDLRRP
+GRDLAWGLGLFAAIGLGTLGVYAAGRALGITTAIVGSALGESWYQVPVLLLSALRHGLLE
+EVIVGAWLVDRLGYLQRLRAAGLAHDPAPAVPSSWVSAEGLYLPTRAAVVVFALALLRGA
+YHLYQGIGPGVGNALMGVVFALVFLRVRRVMPLVIAHTLLDAVGFVGYPLLARAGLLG
+>2_2332
+MSLPVPPALASPVPTALPAPSARTVRWEIAIVLGLSLGRSAVYAVVQLIDKATQAPLGDQ
+TTVLNPTVDDRWAFDLTYQLLGIAFALVPVLLVLHLMHLRGRNPFRTLGLDLRRPGRDLA
+WGVGLFAVIGLGTLGVYAAGRALGLTTAIVANAMDESWYQIPVLLLSALRHSLLEEVIVG
+AWLVDRIGYLQRLKAAGLDRDPVPAVPAAPARRTGAPSSSWTTPEGLFLPTCVATALLAL
+ALLRGAYHLYQGVGPGIGNALMGVVFVLVFLRVRRVMPLVVAHFLLNAVGFVGYPLLARA
+GLLG
+>3_2215
+MTATARPEHAAGRRGPGAPALPAPSARTVRWEIAIVLGLSLGRSAVYAVVQLIDQATRAP
+LGDQTTVLNPTVADRWAFDLTYQLLGIAFSLVPVLLVLHLLWLRGRHPFRVLGLDLRRPG
+RDLAWGLGLFTVIGVGTLGVYAAGRALGITTAIVANAMDESWYQVPVLLLSAARHALLEE
+VIVGAWLIDRLGYLQRLREAGLGASSSWAGTEGLFLPLRTWPVVLSLALLRGAYHLYQGV
+GPGIGNALMGAVFVLVFLRVRRVMPLVLAHFLLDAVGFVGYPLLARAGLLG
+>4_538
+MPATPRTSRTPAVRPAPALPAPSARTVRWEIAIVLGLSLGKSAVYAIVQLIDKATQAPLG
+EQTTVLNPALADRWAFDLTYQLLGIGFSLVPVALVLHLMHLRGRDPFRVLGLDLRRPGRD
+VAWGLGLFAAIGLGTLGVYAAGRALGITTAIVGSALGESWYQVPVLLLSALRHGLLEEVI
+VGAWLVDRLGYLQRLRAAGLARDPAPAVPSSWVSAEGLYLPTRVAVVVLALALLRGAYHL
+YQGIGPGVGNALMGVVFALVFLRVRRVMPLVIAHALLDAVGFVGYPLLARAGLLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000557.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000557.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2964ed4aedab911c8b9487b551648165780124a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000557.fa
@@ -0,0 +1,25 @@
+>0_536
+MDHVSYAAGPEGLDATVARIAETLGIERIKGGVHPRFGTQNALFPMAGRQYLEVVEALDH
+PASLSAPFGQLVRARTEQGGGWMSWAVATTDIGRFERRLGREAVPGNRRFPDGRELSWRQ
+IGVKGTLADPQLPFILRWADGQEDMHPSQAAEPQATIERLNIAGSPERLAEWLGDDEDGQ
+VQDVNIEYVAPSGTPGIVSVTFRTPKGEVTL
+>1_270
+MDHVSYAAGPEGLDATVARIAETLGIERIKGGVHPRFGTQNALFPMTEGQYLEVVEALDH
+PASLSAPFGQLVRARTEQGGGWMSWAVATTDIGRFERRLGREAVPGNRRFPDGRELSWRQ
+IGVKGTLADPQLPFILRWADGQEDMHPSQAAEPQATIERLNIAGSPERLAEWLGDDEDGQ
+VQDVNIEYVAPSGTPGIVSVTFRTPKGEVTL
+>2_2331
+MDHVSYAAGPEGLDATVARIAEALGVERIKGGIHPRFGTQNALFPMAGGQYLEVVEALDH
+PASLSAPFGQLVRSRSEQGGGWMSWAVSTTDIGRFERRLGREAVPGNRRFPDGRELSWRQ
+IGIKGTIADPQLPFIMRWADGQEDMHPSQAAEAQASIERLSIAGSPDRLAEWLGGEGEDA
+HVEDLNVEYVAPSGTPGIVSVTFRTPRGDVTL
+>3_2214
+MNTCRMDHVSYAAGPEGLDATVARIAERLGVERVKGGIHPRFGTQNALFPMTGNQYLEVV
+EALDHPASLSAPFGQLVRTRSEQGGGWMSWAVTTNDIGRFERRLGREAVPGNRRFPDGRE
+LSWRQIGVKGTLADPQLPFILRWADGQEDMHPSQAAPAQASIARLSIAGSPDRLREWLGG
+TEDDEVADVSVDYVAPSGTPGIVSVTFSTPKGEVTL
+>4_539
+MDHVSYAAGPEGLDATVARIAETLGIERIKGGVHPRFGTQNALFPMTEGQYLEVVEALDH
+PASLSAPFGQLVRARTEQGGGWMSWAVATPDIGRFERRLGREAVPGNRRFPDGRELSWRQ
+IGIKGTLADPQLPYILRWADGQEDMHPSQAAEPQATIEHLNIAGSPERLAEWLGGEDEDG
+QVQDVNIEYVAPSGTPGIVSVTFRTPKGEITL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000560.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000560.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a3024b7e3fa0d379381b800696085d48a3f496e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000560.fa
@@ -0,0 +1,31 @@
+>0_539
+MGNPSSSQPPHASDATPVDDPAAHPWRRYVAIGDSFSEGIGDPDPDRPGYHRGWADRLAE
+ELSRLTPPGEDLAYANLAVRGKLLDQIAEDQVEPAIALRPDLISVCAGGNDILRGADPDE
+IAARLDAVVERLASAGATVLLFNATDVKGTPVIGRIRGTVAIYNENVRTIALRHDALVPD
+MWSLKDLARREMWAEDRLHFSALGHHTIAAMVLDTLGVEHGLEHLRLSPPAPRTWRAARA
+SDAAWVRTHLAPWVVRRLRGVSSGDGVTAKRPVPEPLFGAPMPQGSDHTEPLDIVEP
+>1_273
+MGNPSSSQPPHASDATPVDDPAAHPWRRYVAIGDSFSEGIGDPDPDRPGYHRGWADRLAE
+ELSRLTPPGEDLAYANLAVRGKLLDQIAEDQVEPALALRPDLISVCAGGNDILRGADPDE
+IAVRLDAVVERLASDGATVLLFNATDVKGTPVIGRIRGTVAIYNENVRTIALRHDALVPD
+MWSLKDLARREMWAEDRLHFSALGHHTIAAMVLDTLGVEHGLEHLRLSPPAPRTWREARA
+SDAAWVRTHLAPWVARRIRGVSSGDGVTAKRPVPEPLFGAPMPQGSDHTESLNVVEP
+>2_2328
+MRAESPDGDDFPSESTGGGGRGRRGRLTDDGGASRLLLVSNQQESAPQHPAAAEAEPPAD
+VVTRAETAAHPWRRYVAIGDSFTEGIGDPDPDRPGYHRGWADRAAEELARRTPDGEDLAY
+ANLAVRGKLLDQIAADQVEPALALRPDLISVCAGGNDILRRADPDDVAVRLDAVVERLSA
+NGATVLLFNATDTKDTPVLGRIRGTVAIYNENVRTVALRHDALVADMWSLKELARREMWA
+EDRLHFSATGHHTIAAMVLDTLAVPHGLEPLRPEPAAPRTWRQARASDAAWARTHLAPWV
+VRRIRGVSSGDGVSAKRPVPAPLFGAEMPHGSDPTEPLDVVAR
+>3_2211
+METMSPLTNTADSEPPHAEGHASAEPAHPWRRYVAVGDSFTEGIGDPDPERPGYHRGWAD
+HLAEELARLTPAGEEFSYASLAVRGKLMDQIRADQIDPAVELAPDLVSICAGGNDILRRA
+DPDETALHLDDAVGRLAETGATVLLFNVPDIKETPVLARIRGRVAIYNENIRTVAARHHA
+VVADMWSLKDLARPEMWAPDRLHFSPVGHHTIAAMALDTLGVEHELEPLSPKRAAPRTWR
+EARVDDARWARTHLVPWVGRRLRGVSSGDGMQPKRPLPAPLFGADMPHGSDYTEHAAD
+>4_542
+MGNPSSSQPPHASDATPVDDPAAHPWRRYVAIGDSFSEGIGDPDPERPGYHRGWADRLAE
+ELSRLTPPGEDLAYANLAVRGKLLDQIAEDQVEPALALRPDLISVCAGGNDILRGADPDE
+IAVRLDAVVERLASDGATVLLFNATDVKGTPVIGRIRGTVAIYNENVRTIALRHDALVPD
+MWSLKDLARREMWAEDRLHFSALGHHTIAAMVLDTLGVEHGLEHLRLSPPAPRTWREARA
+SDAAWVRTHLAPWVVRRLRGVSSGDGVTAKRPVPEPLFGAPMPQGSDHTEPLDVVEP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000564.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000564.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a15d45d5fac4af3dfa1cf0ea91c3c71d642ef3a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000564.fa
@@ -0,0 +1,38 @@
+>0_543
+MDLPAGVTLRPWAEGDDLRLLEVWGDPADVQQHQDRAMLAPDADTPWRHTLVAEDDGVPV
+GAGTVVAQALHPRRLWLYLEVAPTARRRGIGSALLGALRDAVEQAHAAGQVTTTHLKTRF
+AVASRVAVATGRSADAAEATAPAAGEEAGEAHAAQVAGTEAFLVAAAFSPVQRSRRVAVA
+PGSIALPPLRDEDHPEGAVLEDAATGSVELTRAVAAFYDAVHGWDPAQMSVGAAQQLILG
+PATGASGAVVLRDAPREEGGAVQAFAVSYTAERQDAPADVFLGWDPELPLDQAQLAAGQL
+LAMLVAQHPVQVEVDEAMTALEPILDGLIAQRAAATLVDTRIWATDPA
+>1_277
+MTGAAGAAGHDDGGALFDSAAVAGGEIVLRPWRPGDDLALLEVWGDPANAQQHQDRAMLA
+EDAERPWRRALVAEAAGVPVAAGVVYASSVHPRRLWLYVETAAAERRRGIGRALVAALRG
+LAAEAHAAGAIPTTALKARFAKDALVPGVSGADPQTDAEGPAGQPPVDTEAVRSQTAALA
+AGTEAFLVAEGFTPVQRSRRVAIAPGAIGLPDVRGEEHPDGVVLEEASTGSVELTQAVTA
+FYDAVHAWDPSTLSVGAAQQLLLGPATGAAGAVVLRDAPKAEGGRIRAFAVSYTPERQDA
+PADVLVGWDPELGEEDALQAVADLLALLVAQYPVQIEVDEAMAPLERIVDGLIGGNAART
+LVDTYVFVDDAPGA
+>2_2324
+MSGAYDDDAGALFDSAAVSGGEVVLRPWRAGDDLALLQVWGDPANVQQHQDRAMLAEDAE
+RPWRRALVAEDAGVPVAAGVVYASSLHPQRLWLYVETAAPERRRGIGRALVAALRGLAAE
+AHAAGTVPTAALKARFAKDALVPGTAVEEGVDTEAVRAQTAALAAGTEAFLAAEGFTPVQ
+RSRRVAVAPGAIGLPDVRDEDRPDGVVLEEASTGSVELTQAVAAFYDAVHAWDPSTMSVG
+AAQQLLLGPATGASGAVVLRDAPKAEGGRIRAFAVSYTPERQEAPADVLVGWDPELSEED
+ALQSVADLLALLVAQHPVQVEVDEAMAPLERIVDGLIGGNAARTLVDTYVFVDDAA
+>3_2207
+MSPRHDDDAPALTAAVSGGEVVLRPWAEGDDLRLLEVWGDPADVQQHQDRAMLAADADSP
+WRRTLVAEEDGVPVGAAVAFAQPLHPGRLWVYGEVARTVRGRGVGRALLEALRGLVAAAH
+EAGAVPTTELKARFAVASRVPVGGGEVVEAAPGEAPEAGAAGAEAHAAQVAATERFLVAA
+GFTPVQRSRRIAVAPGVIALPALRDEEHPEGRVLEEISTGSVELTRAVAAFYDAAHAWDP
+SQMSVGAAQQLILGPQTGAAGAVVLRDAPREEGGTIQAFAVSYTAERQDAPADVLLGWDP
+SLGLEEAQLAVGDLLALLVAQHPVQVEADEAMTALEPILDALLAKRAAGTLVDTRVWATD
+PS
+>4_546
+MTGAAGAAGHDDGGALFDSAAVGGGEIVLRPWRPGDDLALLEVWGDPANAQQHQDRAMLA
+EDAERPWRRALVAEAAGVPVAAGVVYASSVHPRRLWLYVETAAAERRRGIGRALVAALRG
+LAAEAHAAGAIPTTALKARFAKDALVPGVTGADPQTEADGATGRPPVDTDAVRSQTAALA
+AGTEAFLVAEGFTPVQRSRRVAIAPGAIGLPDVRGEEHPDGVVLEEASTGSVELTQAVTA
+FYDAVHAWDPSTLSVGAAQQLLLGPATGAAGAVVLRDAPKAEGGRIRAFAVSYTPERQDA
+PADVLVGWDPELGEKDALQAVADLLALLVAQYPVQIEVDEAMAPLERIVDGLIGGNAART
+LVDTYVFVDDATGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000565.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000565.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7440100af1c5feda036f25ec11ab256cd099e75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000565.fa
@@ -0,0 +1,33 @@
+>0_548
+MTRKHLGFLNFGHWIHRPGAEPDARQALDDVVAMAVAAEDAGLDGAWLRVHHFQRMFSSP
+FPILAAMAARTERISLGTGVIDLRYENPLYMAEAAATTDLISGGRLELGVSRGSPEAALD
+GQAQFGYALDEGQTWADVTRERGRRFLSAVRGEGIATPDLTSGWAHSSQPLRIEPHSPGL
+ADRIWWGSGSVGSVAGAATDGYNMLSSTLLLQDDGRPFHVQQADQIARYREAFAAAGHAG
+PGRTAVTRSAFVIQDREDELYFGRERASRDSSGMLEGGAARSGPTYAGSAEEVAEKLAAD
+DAVAAADWVLFANPNQLGVEYNAKIFAGWAEVWRLLGWDA
+>1_281
+MRYENPLYMAEAAATTDLISGGRLELGVSRGSPEAALDGQAQFGYALDEGQTWADVTRER
+GRRFLSAVRGEGIATPDLTSGWAHSSQPLRIGPHSPGLADRIWWGSGSTPSAVEAGRDGY
+NMLSSTLLLQDDGRPFHVQQADQIARYREAFAAAGHTGPGRTAVTRSAFVIQDREDELYF
+GRERASRDSSGMLEGGAARSGPTYAGSAEEVAEKLAADDAVAAADWVLFANPNQLGVEYN
+AKIFAGWAEVWRLLGWDA
+>2_2321
+MNECCNRDIRYENPLYMAEAAATADLLAGGRLELGVSRGSPEAAKDGQAQFGYELADGQT
+WAGVTRKRGRRFLAAVRGEGIATPDLASGWAHSSAPLRIEPHSPGLADRIWWGSGSAGSA
+VEAAKDGYDMLSSTLLLQDDGRPFHVQQADQIAGYLEAYEAAGHAGTGRTAVTRSAFVIQ
+DHEDELYFGRDRNSRESAGMLDGGRARSGPTYAGSAEEVAEKLAADDAVQAADWVLFANP
+NQLGPEYNAKIFAGWAEVWRLLGWDR
+>3_2200
+MTTKNLGFLNFGHWIHRPRVGRRPVEPDAKQAIDDVVQMAVDAEAAGLDGAWIRIHHFQR
+MFSSPFPILTAMAAHTERIHLGTGVIDLRYENPLYMAEAAATTDLLAGGRLELGVSRGSP
+EAARDGQAQFGYELADGQTWSDVARERGRRLLAGVRGEGIATPDLSSGWAHSSAPLRIEP
+HSPGLADRIWWGSGTVGSAVEAAKDGYGMLSSTLLLQDDGRPFHVQQADQIARYLEAYEA
+GGHTTPARTAVTRSAFVIQDHEDELYFGRDRHSRDSSGHLDGGAARSGPTYAGSAEEVAE
+LLAADDAVQAADWVLFANPNQLGAEYNAKLFAGWAEVWRLLGWDS
+>4_549
+MTRKHLGFLNFGHWIHRPGTAPDARQALDDVVAMAVAAEDAGLDGAWLRVHHFQRMFSSP
+FPILAAMAARTERISLGTGVIDLRYENPLYMAEAAATTDLLSGGRLELGVSRGSPEAALD
+GQAQFGYALAEGQTWADVTRERGRRFLSAVRGEGIATPDLTSGWAHSSQPLRIEPHSPGL
+ADRIWWGSGSVGSVAGAAADGYNMLSSTLLLQDDGRPFHVQQADQIARYREAFAAAGHAG
+PGRTAVTRSAFVIQDREDELYFGRERASRDSSGMLEGGAARSGPTYAGSAEEVAEKLAAD
+DAVAAADWVLFANPNQLGVEYNAKIFAGWAEVWRLLGWDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000589.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000589.fa
new file mode 100644
index 0000000000000000000000000000000000000000..112b8f2ce9da1f73b6bace6c42ed34f8e3a4fbc5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000589.fa
@@ -0,0 +1,25 @@
+>0_631
+MTPRTTPDAEPVFELVEQDEIGYETTHVDAFMARAREARDGGAPLTAEEVRQARFATVNG
+GYATDEVDDELDRLEEELAAAERQAFVAERGDEDWAADLEERVAELVARADRAPAERFRR
+PSRADAVSYDVDQVDALVDRLRVTLAGAEDSTDPGAEGGLTADDVRRASFGEAEGAAGYE
+EGQVDAYLDAAVDVLLRRA
+>1_377
+MTPRTTPDAEPVFELVEQDEIGYETTHVDAFMARAREARDGGAPLTAEEVRQARFATVNG
+GYATDEVDDELDRLEEELAAAERQAFVAERGDEDWAADLEERVAELVARADRAPAERFRR
+PSRADAVSYDVDQVDALVDRLRVTLAGAEDSTDPGAEGGLTADDVRRASFGEAEGAAGYE
+EGQVDAYLDAAVDVLLRRA
+>2_2256
+MTTRRPQDAEPPFELVEQDEIGYETSHVDAFLARAREAREGGAPLTADEVRQARFATVNG
+GYATDEVDDELDRLEGELAAAEREAFVSERGDEDWSADLEERVAELVARADRAPAERFRR
+PSREDATSYDVDAVDALVDRLRVTLAGAEGAAAPDARGGLTADDVRRASFGEAEGDRGYE
+EGQVDAYLDAAVDVLLRRA
+>3_2112
+MTPTSPEARADFEHVGPDEIGYEPAHVDAFLERARRAEAGEGDLTAEDVRQARFATVNGG
+YAADQVDDELDRLEEVLMGREREDAVGDGAWDRELAERSQELLGRADRAPAERFRRPSAD
+DAQSYDVDDVDALVDRLRATLTDGSDELTADDVRRAGFASAQGGDGYDEAQVDAYLDAAV
+DVLLRRG
+>4_601
+MTPRTTPDTEPVFELVEQDEIGYETTHVDAFMARAREARDGGAPLTAEEVRQARFATVNG
+GYATDEVDDELDRLEEELAAAERQAFVAERGDEDWAADLEERVAELVARADRAPAERFRR
+PSRADAVSYDVDQVDALVDRLRVTLAGAEGSTDPDAEGGLTADDVRRASFGEAEGAAGYE
+EGQVDAYLDAAVDVLLRRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000599.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000599.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fe2d0eb454815cb41a197471737e6cf27aa6b19b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000599.fa
@@ -0,0 +1,45 @@
+>0_645
+MTVVEILWYVAGVLAVALGLAVSIALHEIGHLVPAKLFGVRVTQYMIGFGPTLVSWRRGE
+TEYGFKAVPLGGYVAMIGMLPPPRPGQTPRAASTGFVQQLGRMADDARAQAAEEVRPGDE
+HRRFLALPVWKRVVIMLGGPFMNLLIALGATALLVTTVGTSQPSTTVAEVYRCVVTMQEQ
+QARAASGGTEDCRPGDPAAPAHEAGLRPGDTVLAFDGRPVSDWDALSAAIRDRAGQPTRI
+EWERDGERMSATLTPRLTERPVTDALGRPERAPDGTVATHEVGFIGMGAQLETVRGTPLD
+AGPLVAQQVRGVVDVVLVLPQRLWDTAVAVVTPAERDPDGPMSVVGVGRIAGEAAALEEA
+TLTDKAALLLSLLAGVNVALMVFNLIPLLPLDGGHVAGALWEAVRRGWARITGRPDPGPF
+DLARMLPLTYAVGAAMLLMGVILIVADIVEPVRLF
+>1_391
+MTVVEILWYVAGVLAVALGLAVSIALHEIGHLVPAKLFGVRVTQYMIGFGPTLVSWRRGE
+TEYGFKAVPLGGYVAMIGMLPPPRPGQTPRAASTGFVQQLGRMADDARAQAAEEVRPGDE
+HRRFLALPVWKRVVIMLGGPFMNLLIALGATALLVTTVGTSQPSTTVAEVYRCVVTMQEQ
+QARAASGGTEDCRPGDPAAPAHEAGLRPGDTVLAFDGRPVSDWDALSAAIRDRAGQPTRI
+EWERDGERMSATLTPRLTERPVTDALGRPERAPDGTVATHEVGFIGMGAQLETVRGTPLD
+AGPLVAQQVRGVVDVVLVLPQRLWDTAVAVVTPAERDPDGPMSVVGVGRIAGEAAALEEA
+TLTDKAALLLSLLAGVNVALMVFNLIPLLPLDGGHVAGALWEAVRRGWARITGRPDPGPF
+DLARMLPLTYAVGAAMLLMGVILIVADIVEPVRLF
+>2_2241
+MSAVEVLWYVLGVVAVALGLAVSIALHEVGHLMPAKLFGVRVTQYMIGFGPTIASWRRGE
+TEYGFKAVPLGGYVAMVGMLPPPRPGQEPRTASTGFVQQLGRMADDARTQAAAELTAADE
+GRQFIQLPVWKRVVIMLGGPFMNLLIALGVTALLVTTVGTSQPSTTAAEVYRCVVTTDEQ
+QARAAEGGGQDCRPGDPVAPAHEAGLRPGDTVTSFDGRPVDDWDALSGLIRERAGQPTAI
+EWERDGEPHSATITPRLTQRPVTDAVGRPERAPDGTALTEEVGFIGMGSQIETVQQSPLA
+AGPVVAQQVRGVVDVVLVLPQRLWDTAVAVVTPAERDPDGPMSVVGVGRIAGEAAALQEA
+ELADKAALLLSLVAGVNVALMVFNLIPLLPLDGGHVAGALWEALRRGWARLRGRPDPGPF
+DLARMLPLTYAVAGLMLVMGVVLIVADIVEPIRLF
+>3_2102
+MSAVEALWFVGGVVVVALGLALSIALHEVGHLVPAKLFGVRVTQYMVGFGPTVASWRRGE
+TEYGIKAFPLGGYVAMVGMLPPPKGGTVARTGSTGFRARAGRMADDARAQAAEEITAADE
+GRQFIQLPVWKRVVIMLGGPFVNLLIALALTAVLVSTLGVARPSTTADEVFQCVVSQSEQ
+QSRAADGGAAQDCRPGDPAAPAYEAGLRPGDRVVSFDGRDVGSWAELSTAIRARAGQATA
+IAWERDGTRTESTLTPLLTERPVTDALGVPERGADGGVKTEPVGFIGLASRQETVTLAPW
+EAVPLVGRQAQGVVGVILALPQRLWDTAVAVVTPAPRDPNGPMSVVGVGRIAGEAAALDT
+ASPADKAALLLSLVAGVNVALLVFNLIPLLPLDGGHVAGALWEGLRRGWARLRGRPDPGP
+FDLAVMMPLTYVVGAAMLAMGVLLIVADIVKPVQLF
+>4_615
+MTVVEILWYVAGVLAVALGLAVSIALHEIGHLVPAKLFGVRVTQYMIGFGPTLVSWRRGE
+TEYGFKAVPLGGYVAMIGMLPPPRPGQTPRAASTGFVQQLGRMADDARAQAAEEVRPGDE
+HRRFLALPVWKRVVIMLGGPFMNLLIALGATALLVTTVGTSQPSTTVAEVYRCVVTMQEQ
+QARAASGGTEDCRPGDPAAPAHEAGLRPGDTVLAFDGRPVSDWDALSAAIRDRAGQPTRI
+EWERDGERMSATLTPRLTERPVTDALGRPERAPDGTVATHEVGFIGMGAQLETVRGTPLD
+AGPLVAQQVRGVVDVVLVLPQRLWDTAVAVVTPAERDPDGPMSVVGVGRIAGEAAALEEA
+TLTDKAALLLSLLAGVNVALMVFNLIPLLPLDGGHVAGALWEAVRRGWARITGRPDPGPF
+DLARMLPLTYAVGAAMLLMGVILIVADIVEPVRLF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000600.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000600.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3286b49a504c061d3a55013c281e64a2cb160db9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000600.fa
@@ -0,0 +1,40 @@
+>0_646
+MPVSLGMPSAPPPVLAPRRTTRQIQVGSVGVGSQHPVSVQSMTTTKTHDIGATLQQIAEL
+TAAGCDIVRVACPTDKDAEALKVIAQQSTIPVIADIHFQPKYVFAAIEAGCGAVRVNPGN
+IKKFDDKVKEIAQAASDHGTSLRIGVNAGSLDPRLLQKYGKATPEALVESAVWEASLFEE
+HGFKDFKISVKHNDPVIIARAYELLAEQGDWPLHLGVTEAGPAFQGTIKSATAFGYLLGQ
+GIGDTIRVSLSAPPVEEVKVGLQILQSLNLRERKLEIVSCPSCGRAQVDVYTLAEQVTEG
+LQDLEVPLRVAVMGCVVNGPGEAREADLGVASGNGKGQIFVKGEVIRTVPEDQIVETLIE
+EANRIAGEMDLGEDGGDQAAAGAPVVSVH
+>1_392
+MPVSLGMPSAPPPVLAPRRTTRQIQVGSVGVGSQHPVSVQSMTTTKTHDIGATLQQIAEL
+TAAGCDIVRVACPTDKDAEALKVIAQQSTIPVIADIHFQPKYVFAAIEAGCGAVRVNPGN
+IKKFDDKVKEIAQAASDHGTSLRIGVNAGSLDPRLLQKYGKATPEALVESAVWEASLFEE
+HGFKDFKISVKHNDPVIMARAYELLAEQGDWPLHLGVTEAGPAFQGTIKSATAFGYLLGQ
+GIGDTIRVSLSAPPVEEVKVGLQILQSLNLRERKLEIVSCPSCGRAQVDVYTLAEQVTEG
+LQDLEVPLRVAVMGCVVNGPGEAREADLGVASGNGKGQIFVKGEVIRTVPEDQIVETLIE
+EANRIAGEMDLGEDGGDQAAAGAPVVSVH
+>2_2240
+MPVSLGMPSAPPPVLAPRRATRQIRVGSVGVGSQHQVSVQSMTTTKTHDIGATLQQIAEL
+TAAGCDIVRVACPTDKDAEALKVIAQQSTIPVIADIHFQPKYVFAAIEAGCGAVRVNPGN
+IKKFDDKVKEIAQAAAEHGTSIRIGVNAGSLDPRLLKKHGKATPEALVESAVWEASLFEE
+HGFKDFKISVKHNDPVIMARAYELLAEQGDWPLHLGVTEAGPAFQGTIKSATAFGYLLGK
+GIGDTIRVSLSAPPVEEVKVGLQILQSLNLRERKLEIVSCPSCGRAQVDVYTLAEEVTEG
+LKDLEVPLRVAVMGCVVNGPGEAREADLGVASGNGKGQIFVKGEVIRTVPEDQIVDTLIE
+EANRIAAEMGVGEESGDQAAAGAPVVSVH
+>3_2101
+MPVSLGMPSAPPPVLAPRRRTRQIQVGRVGVGSEHPVSVQSMTTTKTHDIGATLQQIAEL
+TAAGCDIVRVACPTDKDADALKVIAQQSTIPVIADIHFQPKYVFAAIEAGCGAVRVNPGN
+IKKFDDKVKEIAQAATEHGTSLRIGVNAGSLDPRLLQKHGKATPEALVESAVWEASLFEE
+HGFKDFKISVKHNDPVIMARAYELLAEQGDWPLHLGVTEAGPAFQGTIKSATAFGYLLGK
+GIGDTIRVSLSAPPVEEVKVGLQILQSLNLRERKLEIVSCPSCGRAQVDVYTLAEQVTEG
+LKDVTVPLRVAVMGCVVNGPGEAREADLGVASGNGKGQIFVKGEVIRTVPEDQIVDTLIE
+EARRIAAEMGHEDGEGEAAPAGAPSVTVH
+>4_616
+MPVSLGMPSAPPPVLAPRRTTRQIQVGSVGVGSQHPVSVQSMTTTKTHDIGATLQQIAEL
+TAAGCDIVRVACPTDKDAEALKVIAQQSTIPVIADIHFQPKYVFAAIEAGCGAVRVNPGN
+IKKFDDKVKEIAQAASDHGTSLRIGVNAGSLDPRLLQKYGKATPEALVESAVWEASLFEE
+HGFKDFKISVKHNDPVIMARAYELLAEQGDWPLHLGVTEAGPAFQGTIKSATAFGYLLGQ
+GIGDTIRVSLSAPPVEEVKVGLQILQSLNLRERKLEIVSCPSCGRAQVDVYTLAEQVTEG
+LQDLEVPLRVAVMGCVVNGPGEAREADLGVASGNGKGQIFVKGEVIRTVPEDQIVETLIE
+EANRIAGEMDLGEDGGDQAAAGAPVVSVH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000605.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000605.fa
new file mode 100644
index 0000000000000000000000000000000000000000..afadb1bc6b69ba35a069e00da86c868f3108d9e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000605.fa
@@ -0,0 +1,35 @@
+>0_651
+MSALRMLEAEREIPMDRLIPTIEQALLMAYHRTPGALKRARVEIDRATGHVTVWATELDE
+DDTPIGEFDDTPNGFGRVAASTARQVMIQRMREEDDDKVLGEFKDKEGELVSGVIQQGLN
+RHMVQVNLGTLEAVLPPPEQVPGEDYAHGRRIRAYVVSATRGAKGPSVTVSRSHPGLVRK
+LFELEVPEIADGSVEITALAREAGHRTKMAVRATRPGVNAKGASIGEMGSRVRAVMTELN
+DEKIDIVDHVDDPAAMIANALSPATTVSVEILDADQHSARAVVPEYQLSLAIGKEGQNAR
+LAAKLTGWRIDIVGDGVTTSAPGR
+>1_397
+MSALRMLEAEREIPMDRLIPTIEQALLMAYHRTPGALKRARVEIDRATGHVTVWATELDE
+DDTPIGEFDDTPNGFGRVAASTARQVMIQRMREEDDDKVLGEFKDKEGELVSGVIQQGLN
+RHMVQVNLGTLEAVLPPPEQVPGEDYAHGRRIRAYVVSATRGAKGPSVTVSRSHPGLVRK
+LFELEVPEIADGSVEITALAREAGHRTKMAVRATRPGVNAKGASIGEMGSRVRAVMTELN
+DEKIDIVDHVDDPAAMIANALSPATTVSVEILDADQHSARAVVPEYQLSLAIGKEGQNAR
+LAAKLTGWRIDIVGDGVTTSAPGR
+>2_2235
+MSALRMLEAEREIPMDRLIPTIEQALLMAYHRTPGALKRARVEIDRVSGHVTVWATELDE
+DGTPIGEFDDTPNGFGRVAASTARQVMIQRMREEDDDKVLGEFKDKEGELVSGLIQQGVN
+RHMIQVNLGTLEAVLPPPEQVPGEDYSHGRRLRAYVVSATRGNKGPSVTVSRSHPGLVRK
+LFELEVPEIADGSVEITALAREAGHRTKMAVRATRPGVNAKGASIGEMGSRVRAVMTELN
+DEKIDIVEHAEDPAQMIANALSPAKTVSVEVLDADQHSARAVVPEHQLSLAIGKEGQNAR
+LAAKLTGWRIDIVGDGSDASAPAR
+>3_2096
+MSALRMLVAERDIPLDRLVPAIEQALLIAYHRTPGAIKGSRVELDRSTGHVTVWAPEVED
+DGTCVGEFDDTPNGFGRIAASTARQVIFQRLRDADDAKVLGEFKDREGELVSGVIQQGSH
+RHMVQVDLGSLEAVLPPPEQVPGEDYRHGRRIRAVIVSATRGPKGPSVTLSRSHPNLVRR
+LFALEVPEIADGTVEITALAREAGHRTKMAVKATRPGVNPKGAAIGEMGSRVRAVMTELG
+GEKIDIVEHADDPAEMIKHALSPAQALSVEILDADQHSARAVVPQHQLSLAIGKEGQNAR
+LAARLTGWRIDIVGDAAQQPGADAAQQPGADAASEMAPATEAGAEA
+>4_621
+MSALRMLEAEREIPMDRLIPTIEQALLMAYHRTPGALKRARVEIDRATGHVTVWATELDE
+DDTPIGEFDDTPNGFGRVAASTARQVMIQRMREEDDDKVLGEFKDKEGELVSGVIQQGLN
+RHMVQVNLGTLEAVLPPPEQVPGEDYAHGRRIRAYVVSATRGAKGPSVTVSRSHPGLVRK
+LFELEVPEIADGSVEITALAREAGHRTKMAVRATRPGVNAKGASIGEMGSRVRAVMTELN
+DEKIDIVDHVDDPAAMIANALSPATTVSVEILDADQHSARAVVPEYQLSLAIGKEGQNAR
+LAAKLTGWRIDIVGDGVTTSAPGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000613.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000613.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a91bb25f09a2760a806e9bc1d68164d24273f77
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000613.fa
@@ -0,0 +1,34 @@
+>0_660
+MSTPPVPHSPAPSSFPLRPPAPPLDLPLIGHGYPALLRTPRARWWNPLASFGLVLAGLVG
+LLVLGGVLGALALIATSGPALLGAADPTDVTDLDLYSAPMVLLNNLLLAALIGVALLAVA
+LGHPVAARFVHSVEGRVRWRWLARCVVVLTPLFLAYVLGAWALDGAPTAPRAQDWVWLLV
+MAFVLTPFQAAGEEYLFRGWLLLAVGTWIRRPVVAAAVTAVLSAATFSLAHGSLDPWILL
+DLAAFAVAAVLLTWRTGGLEAAVALHVVNNVVIIAVGTLVGTVEDSYVGAETAGSPAATL
+LSVAVVAVATALLLWQARRAGIARTVPVTVGARP
+>1_406
+MSTPPVPHSPAPSSFPLRPPAPPLDLPLIGHGYPALLRTPRARWWNPLASFGLVLAGLVG
+LLVLGGVLGALALIATSGPALLGAADPTDVTDLDLYSAPMVLLNNLLLAALIGVALLAVA
+LGHPVAARFVHSVEGRVRWRWLARCVVVLTPLFLAYVLGTWALDGAPTAPRAQDWVWLLV
+MAFVLTPFQAAGEEYLFRGWLLLAVGTWVRRPVVAVAVTAMLSAAAFSLAHGSLDPWILL
+DLAAFAVAAVLLTWRTGGLEAAVALHVVNNVVIIAVGTLVGTVEDSYVGAETAGSPAATL
+LSVAVVAVATALLLWQARRAGIARTVPVTVGARP
+>2_2221
+MTTASPPPPPPRGRLAPAAAPTPPGRRLDLPIIGAEYPQLLRTPRSRWWHPLLSAGLVLG
+SVLVLLAVLTLPMMLALVSEVGWDVFASADPADLARVEEALFSAPMMLLNNLMLAAFIGI
+AVLAVAVCHPVAARFVHSVQGRIRWRWLLRAHLVLLPLFLVYVLGTWALDGAPTAPRAED
+WVWLVVMAFLLTPLQAAGEEYLFRGWLLLAIGSWFRRPLPAIVLAAAVSAVTFSLAHGSF
+DPWILLDLSVFAVAAVLLTWRTGGLEAAVALHVVNNVVVIVFGTLAGTVNESFVDVETTG
+SPLATLVSAAVIALSTALLLWQARRAGIARTVPVSVGARP
+>3_2087
+MRTPRARWWNPLASFGMVLLGVGVLTVLLTVPMALVLFQQLDPGELWSAEGPSEASLELA
+LFSAPMVLLNNLLLAALTGVALLAVLVAHPVKARFLHSVEGRVRWRWLLRAHLVLLPLFL
+VYVLGTWALDGARVAPRPEDWGWLLAMALLVTPFQAAGEEYLFRGWTMLALGTWIRRPGV
+AVAVTAAVSAVAFALAHGSLNPWILLDLGVFAVAAVLLTWRTGGLEAAVALHVVNNVVIL
+AFGTVTGLATESYVTASTQGDPLATLVSAAVTALATVLLLWQAKRAGVARTVPSAVGARP
+>4_630
+MSTPPVPHSPAPSSFPLRPPAPPLDLPLIGHGYPALLRTPRARWWNPLASFGLVLAGLVG
+LLVLGGVLGALALIATSGPALLGAADPTDVTDLDLYSAPMVLLNNLLLAALIGVALLAVA
+LGHPVAARFVHSVEGRVRWRWLARCVVVLTPLFLAYVLGAWALDGAPTAPRAQDWVWLLV
+MAFVLTPFQAAGEEYLFRGWLLLAVGTWIRRPVVAAAVTAVLSAATFSLAHGSLDPWILL
+DLAAFAVAAVLLTWRTGGLEAAVALHVVNNVVIIAVGTLVGTVEDSYVGAETAGSPAATL
+LSVAVVAVATALLLWQARRAGIARTVPVTVGARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000619.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000619.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3ec20391b18cb709493ee5ee563c506ced46855
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000619.fa
@@ -0,0 +1,35 @@
+>0_667
+MSAVRSAVIPSELLFGTVVPAMVTPMTDEGAVDLEAAAALAEHLVDRGADGLVVTGTTGE
+TSTLTDDENVAMFRTVVEAVGDRARVVAGTGTNDTAHTLELSRRAAETGVDGLLLVTPYY
+NKPNQAGIRAHFETVADGVDLPIMLYDIPGRSVMPIEPETLIALAQHPNIRALKDAKGDL
+QSTTTVLAHTDLDLYSGDDGATLPLMALGAVGVVSVAAHAAPELYRQLVDAVHAGDLAGA
+RDHHFALDPVQRGIMTHVQGAVAAKAVLAAQGVIPSAAVRLPLVQATRDELSVIRADLAE
+AGITF
+>1_413
+MSAVRSAVIPSELLFGTVVPAMVTPMTDEGAVDLEAAAALAEHLVDRGADGLVVTGTTGE
+TSTLTDDENVAMFRTVVEAVGDRARVVAGTGTNDTAHTLELSRRAAETGVDGLLLVTPYY
+NKPNQAGIRAHFETVADGVDLPIMLYDIPGRSVMPIEPETLIALAQHPNIRALKDAKGDL
+QSTTTVLAHTDLDLYSGDDGATLPLMALGAVGVVSVAAHAAPELYRQLVDAVHAGDLAGS
+RDHHFALDPVQRGIMTHVQGAVAAKAVLAAQGVIPSAAVRLPLVQATPDELSVIRADLAE
+AGITF
+>2_2211
+MSAVRSASAPSELLFGTVVPAMVTPMTDEGAVDLEAAAALAEHLVDGGADGLVVTGTTGE
+TSTLTDEENLAMFRTVVEAVGDRAKVVAGTGTNDTAHTLELSRRAKETGVDGLLLVTPYY
+NKPNQAGIRAHFEAVADGVDLPIMLYDIPGRSVMPIEPETLIALAQHPNIRALKDAKGDL
+QSTTTVLAHSDLDLYSGDDGATLPLMALGAVGVVSVAAHVAPGLYRKLVDAVHAGDLAAA
+REHHFALDPVQRGIMTHVQGAVAAKAVLAAQGVIPSAAVRLPLVQASADELSDIRADLAE
+AGITF
+>3_2080
+MTDARRTVNPSELPFGTVVPAMVTPMDQDGAVDLQAAAVLATHLVDQGADALVITGTTGE
+TSTLTDEENLAMFRTVVEAVGERARVIAGTGTNDTHHSLELSRRAAEIGVHGLLLVTPYY
+NKPNQAGIRRHFETIADGVDLPIMLYDIPGRSVMPIQPETLVALAAHPNITALKDAKGDL
+QSTTTVLAHTDLHVYSGDDGATLPLMAMGAVGVVSVAAHVAVPGYRALVDAVHAGDLRAA
+RDAHFALDPVQRGIMSHVQGAVAAKTVLAGQGIIPTAAVRLPLVAADDAELAAIRADLAE
+AGISF
+>4_637
+MSAVRSAVIPSELLFGTVVPAMVTPMTDEGAVDLEAAAVLAEHLVDRGADGLVVTGTTGE
+TSTLTDDENVAMFRTVVEAVGDRARVVAGTGTNDTAHTLELSRRAAETGVDGLLLVTPYY
+NKPNQAGIRAHFEAVADGVDLPIMLYDIPGRSVMPIEPETIIALAQHPNIRALKDAKGDL
+QSTTTVLAHTDLDLYSGDDGATLPLMALGAVGVVSVAAHAAPELYRQLVDAVHAGDLAGA
+RDHHFALDPVQRGIMTHVQGAVAAKAVLAAQGVIPSAAVRLPLVQATPDELSVIRADLAE
+AGITF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000621.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000621.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d534a65a8848e33dbe05f3073527669389f4ede1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000621.fa
@@ -0,0 +1,89 @@
+>0_669
+MPAVSAVRGSLVGMATRTSPTRSSSSSATSRSGSAGRRGSGRKGSTATVPEADRPAAPLR
+ALHTLWMGLATPVGAGFRKLGPDVRIDREERRDGTGLVLLLLAALIAAVEWWGLRGTAVG
+RVVHGVVGGTVGWFALLVPIALLVVAVRCFRHATDHRANGRIIIGLLMATVAGSGIAHLV
+GGVPSAADAFEDMLGAGGMVGYLATAPLASLLTPVPVWVLMILLAFFSVLVLTATPVGSI
+PQRIAGGYDWLTGQDPEGASEQRAARRAERRRAREERREAEDLAAPLSVDAETGRTHPDH
+DQSYLDGPAAGAHAAGASRPGLFARLFGGRRAREEQAADAAPEHTASTAYDSPVIHEAEV
+GSHAAPEAETTQVLPRPAPRRAARGEQGVFDSEQAAADARDAGRDASDDFDPWVDEDDAP
+EDADAEPQPPAGVRRPTAADRALEQVREHARAQREAAAPAAAAPEEDAGEDTPFALDDAP
+RQGSGAAAPSSSSAVPASTPAPVPPVTAEPARGTQSELGGDVSYTLPQSALLPAGPQPKE
+RSEANDRVVAALTTTFTEFKVDAQVTGFSRGPTVTRYEVEVAPGTKVEKVTALEKNIAYA
+VASSDVRILSPIPGKRAIGIEIPNTDKEVVALGDVLRSQAAQRTDHPMVMGVGKDVEGGY
+VVANLAKMPHMLVAGATGAGKSSFVNSMITSILMRSTPDEVRMVMVDPKRVELTAYEGVP
+HLVTPIITSPKKAAEALQWVVKEMDTRYDDLAAFGYKHVDDFNKAVRAGQVKLPPDSKRV
+LRPYPYLLVIVDELADLMMVAPRDVEDAIVRITQLARAAGIHLVLATQRPSVDVVTGLIK
+ANVPSRMAFATSSVTDSRVVLDQPGAEKLLGQGDALFLPMGKSKPMRVQGAWVNESEIHA
+VVEHVKSQMQVQYRADVIPEKTEKVIDEDIGDDLDLLLQAVELVVTTQFGSTSMLQRKLR
+VGFAKAGRLMDLMESRGVVGPSEGSKARDVLVKPDDLADVLATISGDTPPSATSGDGDAS
+AGTGDGDASASAAPRDLVQEDLDSRPAAVDWNDEDDDEGSEDAWQLTGR
+>1_415
+MATRTSPTRSSSSSATSRSGSAGRRGSGRKGSTATVPEADLPAAPLRALHTLWMGLATPV
+GAGFRKLGPDVRIDREERRDGTGLLLLLLAALIAAVEWWGLRGTAIGRVVHGVVGGTVGW
+FALLVPIALLVVAVRCFRHATDHRANGRIIIGLLMATVAGSGIAHLVGGVPSAAEAFEDM
+LGAGGMVGYLATAPLASLLTPVPVWVLMILLAFFSVLVLTATPVGSIPQRLAGGYDWLTG
+QDPEGASERRAARRDERRRAREVRREAEDLATPLSVDAETGRTHPDHDQSYLDGPAAGAH
+AAGASRPGLLARLFGGRRAREDQAADAAPEHTAGTAYDSPVIHEAEAGSHAAPEAETTQV
+LPRPAPRRAARGEQDVFDAERAAANARDADQDASDDFDPWVDEDDAPEDADAEPQPPAGV
+RRPTAADRALEQVREHARAQREAAAPAAASLEEDAGEDTPFALDDAPGQGSGTAASSSAV
+PASTPAPVPPVTAEPARGTQSPLGGDVSYTLPQSALLPAGPQPKERSEANDRVVAALTTT
+FTEFKVDAQVTGFSRGPTVTRYEVEVAPGTKVEKVTALEKNIAYAVASSDVRILSPIPGK
+RAIGIEIPNTDKEVVALGDVLRSQAAQRTDHPMVMGVGKDVEGGYVVANLAKMPHMLVAG
+ATGAGKSSFVNSMITSILMRSTPDEVRMVMVDPKRVELTAYEGVPHLVTPIITSPKKAAE
+ALQWVVKEMDTRYDDLAAFGYKHVDDFNKAVRAGQVKLPPDSKRVLRPYPYLLVIVDELA
+DLMMVAPRDVEDAIVRITQLARAAGIHLVLATQRPSVDVVTGLIKANVPSRMAFATSSVT
+DSRVVLDQPGAEKLLGQGDALFLPMGKSKPMRVQGAWVNESEIHAVVEHVKSQMQVQYRA
+DVIPEKTEKVIDEDIGDDLDLLLQAVELVVTTQFGSTSMLQRKLRVGFAKAGRLMDLMES
+RGVVGPSEGSKARDVLVKPDDLADVLATISGDTPPSATSGDGDASASAGPRDLVQEDLDS
+RPAAVDWNDEDDDEGSEDAWQLTGR
+>2_2209
+MVLPRPTRRRPARGAQGVFDAERADDPAGSRDADRDASDDFDPWVDEEDAPEDADAEPTP
+PAGVRRPTAADRALEQVREHARAQREAAAAAEEPAEDADVDLEVEEPGRAAGPAAPSSPA
+AAVPSSTPEPVPPVTAEPARGTQSELGGDVSYTLPQSALLPAGPQPKERSEANDRVVAAL
+TTTFTEFKVDAQVTGFSRGPTVTRYEVEVAPGTKVEKVTALEKNIAYAVASSDVRILSPI
+PGKRAIGIEIPNTDKEVVALGDVLRSQAAQRTDHPMVMGVGKDVEGGYVVANLAKMPHML
+VAGATGAGKSSFVNSMITSILMRSTPDEVRMVMVDPKRVELTAYEGVPHLVTPIITSPKK
+AAEALQWVVKEMDTRYDDLAAFGYKHVDDFNKAVRAGQVKLPPDSKRVLRPYPYLLVIVD
+ELADLMMVAPRDVEDAIVRITQLARAAGIHLVLATQRPSVDVVTGLIKANVPSRMAFATS
+SVTDSRVVLDQPGAEKLLGQGDALFLPMGKSKPMRVQGAWVNESEIHAVVEHVKSQMQVQ
+YREDVVPEKTEKVIDEDIGEDLDLLLQAVELVVTTQFGSTSMLQRKLRVGFAKAGRLMDL
+MESRGVVGPSEGSKARDVLVKPDDLADVLATISGDAPPSGGSGEGGAPAAAPAAPASAGP
+RDLVQEDLDARPAAQSWDDEDDDEGSEDAWQLTGR
+>3_2079
+MATRTSPARSSSSSAKSRSGSSRPAKGSSGKGASAASPDLDRQPAFARAVRTGWMALATP
+VGAAVRKAGPDVRIARDDRRDGTGLLLVLVALLVAAVEWWGLRETAVGGVVHDVVGGTVG
+WFAFLLPVVLGVVAVRCFRHPLDHRANGRIVIGLLLATVAGSGIAHLVGGLPSAAESFAD
+VLHAGGIVGYLATVPLASLLTAVPVWALMVALAVFSLLVITATPLGSIGSRLRGAYAWLT
+GQDAEDAEARREQRRAERADRREAGEHRGEQTTADLFGDDRPGGRTHPDHDQSYLDAHGS
+SAAPAPARRPGLLARLFGRGHEEPAPAGRVSAPRAYESAVVEEAPAASRAASGSHAADEA
+PAAAVEPARPARRRNAAPRRAAATEVFDAEAPRGRRSAPPADDDFDPWVDEDSADDLDRA
+DDADTGALEVVPPAGVKRPTAADRALEQVREHARSQREATVEEAEKAEEHDDEAWDEHET
+LVLPTAAASAPAPAPAAVVPSVSRPEPVPEVTPEPARPSRPPQDGGHPYELPQSALLPAG
+PQPKERTESNDRVVQALTTTFTEFKVDAQVTGFSRGPTVTRYEVEVAPGTKVEKVTALEK
+NIAYAVASSEVRILSPIPGKRAIGIEIPNTDKEVVALGDVLRSQAAQRNDHPMIMGVGKD
+VEGGYVVANLAKMPHMLVAGATGAGKSSFVNSMIVSILMRSTPDEVRMVMVDPKRVELTA
+YEGVPHLVTPIITSPKKAAEALQWVVKEMDTRYDDLAAFGFKHVDDFNRAVRAGEVKLPP
+DSKRVLRPYPYLLVIVDELADLMMVAPRDVEDAIVRITQLARAAGIHLVLATQRPSVDVV
+TGLIKANVPSRMAFATSSVTDSRVVLDQPGAEKLLGQGDALFLPMGKSKPMRVQGAWVNE
+SEIHAVVEHVKAQMQVQYREDVVPEKSEKVIDEDIGDDLDLLLQAVELVVTTQFGSTSML
+QRKLRVGFAKAGRLMDLMESRGVVGPSEGSKARDVLVKPDDLADVLATINGDTPPSRPAA
+PASAAAPAPAPAAATEAAPDRWASADLVGDDLDSRPAATSWDGEDDDEGSEDAWQLTGR
+>4_639
+MATRTSPTRSSSSSSATSRSGSAGRRGSGRKGSTATVPEADRPAAPLRALHTLWMGLATP
+VGAGFRKLGPDVRIDREERRDGTGLVLLLLAALIAAVEWWGLRGTAVGRVVHGVVGGTVG
+WFALLVPIALLVVAVRCFRHATDHRANGRIIIGLLMATVAGSGIAHLVGGVPSAADAFED
+MLSAGGMVGYLATAPLASLLTPVPVWVLMILLAFFSVLVLTATPVGSIPQRIAGGYDWLT
+GQDPEGASEQRAARRAERRRAREERREAEDLATPLSVDAETGRTHPDHDQSYLDGPAAGA
+HAAGASRPGLFARLFGGRRAREEQAADAAPEHTASTAYDSPVIHEAEAGSHAAPEAETTQ
+VLPRPAPRRAARGEQGVFDAEQAAADARDAGRDASDDFDPWVDEDDAPEDADAEPQPPAG
+VRRPTAADRALEQVREHARAQRESAAPAAARQEGDAGEDTPFALDDAPGQGSGAAAPSSS
+SAVPASTPAPVPPVTAEPARGTQSELGGDVSYTLPQSALLPAGPQPKERSEANDRVVAAL
+TTTFTEFKVDAQVTGFSRGPTVTRYEVEVAPGTKVEKVTALEKNIAYAVASSDVRILSPI
+PGKRAIGIEIPNTDKEVVALGDVLRSQAAQRTDHPMVMGVGKDVEGGYVVANLAKMPHML
+VAGATGAGKSSFVNSMITSILMRSTPDEVRMVMVDPKRVELTAYEGVPHLVTPIITSPKK
+AAEALQWVVKEMDTRYDDLAAFGYKHVDDFNKAVRAGQVKLPPDSKRVLRPYPYLLVIVD
+ELADLMMVAPRDVEDAIVRITQLARAAGIHLVLATQRPSVDVVTGLIKANVPSRMAFATS
+SVTDSRVVLDQPGAEKLLGQGDALFLPMGKSKPMRVQGAWVNESEIHAVVEHVKSQMQVQ
+YREDVIPEKTEKVIDEDIGDDLDLLLQAVELVVTTQFGSTSMLQRKLRVGFAKAGRLMDL
+MESRGVVGPSEGSKARDVLVKPDDLADVLATISGDTPPSAASGDGDASASAAPRDLVQED
+LDSCPAAVDWNDEDDDEGSEDAWQLTGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000643.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000643.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d49acbcf38a4270e28182062a68a41c3c764a39e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000643.fa
@@ -0,0 +1,40 @@
+>0_698
+MRTRTLTGVATAALGAVVVAGAGPALAQTTLTQGSAITAPAGACSLTIVDDATAYTAAHC
+GAGQWQIGSTVRDVDGTAIGTVSALPGDSGVDAVRVALADDVDVVGDWSTRPASSIGVGE
+TVYTHGSSVPLGAPNTVSHTQTFEAATVCDDAYADQVALDTASTYAGDSGGAVYDAQQRV
+VGVISGIAPVTFDAEGNVVGCDAQAMSSIMVPVESLDALDASAAPAAETAAAAETAPAAE
+TAPAIADVAGPVADEDLPTGGEPAVDESELTEFTPAEEEAIAAELKARAEAAAEEEAAEA
+APAAEAPVAEAAAPGVTDVVAAPAEGVAYGTQVVAQTDQGGFASVTVTAYDADGTVLGQD
+GLDLTGEYRAWLPVPAEVPAGGSVVVTVVDAAGAATDATVTLGGQLVG
+>1_438
+MRTRTLTGVATAALGAVVVAGAGPALAQTTLTQGSAITAPAGACSLTIVDDATAYTAAHC
+GAGQWQIGSTVRDVDGTAIGTVSALPGDSGVDAVRVALADDVDVVGDWSTRPASSIGVGE
+TVYTHGSSVPLGAPNTVSHTQTFEAATVCDDAYADQVALDTASTYAGDSGGAVYDAQQRV
+VGVISGIAPVTFDAEGNVVGCDAQAMSSIMVPVESLDALDASAAPAAETAAAAETAPAAE
+TAPAIADVAGPVADEDLPTGGEPAVDESELTEFTPAEEEAIAAELKARAEAAAEEEAAEA
+APAAEAPVAEAAAPGVTDVVAAPAEGVAYGTQVVAQTDQGGFASVTVTAYDADGTVLGQD
+GLDLTGEYRAWLPVPAEVPAGGSVVVTVVDAAGAATDATVTLGGQLVG
+>2_2184
+MRTRTLTGVATAALGAVVVAGAGPALAQTVITQGSALSAPAGACSLTIVDDATAYTAAHC
+GAGQWEVGSPVLDAEGVQIGTVSGLPGTSGVDVVRVALAEDVEVVGEWSTRPAASVEVGE
+TVFTHGSSVPLGAPNSLSHTQTFDAATVCDDAYSDQMALDVASTYPGDSGGAVYDAQQRV
+VGVISGVAPVTFDEEGNVVGCDAQSLSSIMVPVESLDAVGQETAAPAAVEPAAAEAPATE
+VTETPAIADVAGPVADEDLPTGGEPAVDESELTEFTPAEEEAIRAELIERAEAEAAAEAP
+AEQPAAEAPVAEAVVAGTEDVVAAPAEGVAYGTQVMAETSQGGFASVTVTAYDADGTVLG
+VDGLDLTGEYRAWMPVPAEVPAGGSVVVTVVDAAGDATDTQVTLGGQLIG
+>3_2055
+MKKTTLTGATTAALGAVVVAGAGSALAATPLTQGAALSVPAGECSITLVSDTTAFTAAHC
+GAGQWTVGSAVHAADGARIGSVSALPGSTGVDVVKIALDEDVDVVGDWSTRPAASVKPGE
+TVYTQGSSVPLGSPNSISDPETYDIAETCGDVYTDQVSLDAATTRPGDSGGAVYDAKQRV
+VGVVSGLAPVSFDEEGRAVGCDAASLSTIMVPAESLKAVAAAPAKATAPAPTVGKHGVIL
+KAPTAPAAKAPAAEKKAPAAKAPAAEKKAAPAPTLGKHGVSAETATAGTTTLKVAPEDGI
+DFRTRVQATTKTGGFSYMAVTAYDAAGKQIGHLHLHSDGQPMTWINTPAQVPAGGHIEVQ
+LKDAAGQPTDATVTLGGVPVN
+>4_662
+MRTRTLTGVATAALGAVVVAGAGPALAQTTLTQGSAITAPAGACSLTIVDDATAYTAAHC
+GAGQWQIGSTVRDVDGTAIGTVSALPGDSGVDAVRVALADDVDVVGDWSTRPASSIGVGE
+TVYTHGSSVPLGAPNTVSHTQTFEAATVCDDAYADQVALDTASTYAGDSGGAVYDAQQRV
+VGVISGIAPVTFDAEGNVVGCDAQAMSSIMVPVESLDALDASAAPAAETAAAAETAPAAE
+TAPAIADVAGPVADEDLPTGGEPAVDESELTEFTPAEEEAIAAELKARAEAAAEEEAAEA
+APAAEAPVAEAAAPGVTDVVAAPAEGVAYGTQVVAQTDQGGFASVTVTAYDADGTVLGQD
+GLDLTGEYRAWLPVPAEVPAGGSVVVTVVDAAGAATDATVTLGGQLVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000645.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000645.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c36f530964d9a60546dbf0cd57618561fe00f304
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000645.fa
@@ -0,0 +1,25 @@
+>0_700
+MTTPGAPDASAPFTPQARHLAVVSGGSGDPSQTRMLAERMAESASAALSEHGVVPQIHLI
+TLRELAVDIAQALVTFAISPALRAALDEVAQADAVIAVSPTYKASYSGLFKSFWDLAEPT
+SVVGVPVLLGATGGTARHSLMIDTAMRPLFAYLKARIVPTAVFAASDDWGEAAGVQASMR
+TDPLQSRIRAAGRDLAEITLSRPPRARAAAPADIDLEVTPFEQLLNPGP
+>1_440
+MTTPGAPDASAPFTPQARHLAVVSGGSGDPSQTRMLAERMAESASAALSEHGVVPQIHLI
+TLRELAVDIAQALVTFAISPALRAALDEVAQADAVIAVSPTYKASYSGLFKSFWDLAEPT
+SVVGVPVLLGATGGTARHSLMIDTAMRPLFAYLKARIVPTAVFAASDDWGEAAGVQASMR
+TDPLQSRIRAAGRDLAEITLSRPPRARAAAPADIDLEVTPFEQLLNPGP
+>2_2182
+MIGQGAFEATDPLMPQARHVAVVSGGSGDPSQTRMLAERMAEAASAALSEHGVVPEIHLI
+TLRELATDIAQAMVTFAVSPALRAALDEVQQADAVIAVSPTFKASYSGLFKSFWDLVDDE
+SLIGVPVLLGATGGTVRHSLMIDTALRPLFAYLKSRIVPTAVFAASDDWGEADGAQASTR
+TDPLRSRIRSAGRDLAEILLNRPPRARAAAPETLDLEVTPFEQLLNPDA
+>3_2053
+MSTSAFESTDPFTPGARHIAVVSGGIGDPSQTRKLADRLARASADALSAAGVVPEIHVVS
+LRELATDLGAGMVTTARSPALLDAVAQVEHADAVIAVSPTFKASYSGLFKSFVDLIDDEA
+LVGVPVLLGATGGTARHSLMIDQAMRPLFAYLKARIVPTAVFAASDDWGRADGQNDSTRT
+TPLDARIRAAGEDLAEVLRHRPARVRPAADATDDDLEVIPFDQLLHPGR
+>4_664
+MTTPGAPDASAPFTPQARHLAVVSGGSGDPSQTRMLAERMAESASAALSEHGVVPQIHLI
+TLRELAVDIAQALVTFAISPALRAALDEVAQADAVIAVSPTYKASYSGLFKSFWDLAEPT
+SVVGVPVLLGATGGTARHSLMIDTAMRPLFAYLKARIVPTAVFAASDDWGEAAGVQASMR
+TDPLQSRIRAAGRDLAEITLSRPPRARAAAPADIDLEVTPFEQLLNPGP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000646.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000646.fa
new file mode 100644
index 0000000000000000000000000000000000000000..854926725fa0f85fb093a759acf3e9dc3989913b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000646.fa
@@ -0,0 +1,40 @@
+>0_701
+MQFGVFTIGDITADPTNGTAPTEHQRIKDTVKIARHAEQAGFEVFATGQHHNPPFVAPGN
+PPTLLAYLAAQTETLQLSTATTLITTMDPVRLAEDYAYLQHLADGRVDLTMGRGNTGPVY
+PWFGKDIRQGIQLAVENYNLLYRLWHEETVDWSGNHRTPLQDFTLTPQPLDGVAPFVWHG
+SIRSPEIAEQAAYYGDGYFHNNIFWNKEHVIQMVRLYRQRYEYYGHGKAHQAYVALGGQA
+YMAKNSQDAVAEFRPYFDNAPVYGHGPSLEDFSRMTPLTVGSPQQVIERTLTFRDWVGDY
+QRQMFLIDHAGLPTDTVLRQIDLFGEEVLPVLRKEFDALKPDDVPAAPTHEFLVARARRG
+EAPVPGGKEGSQAQLDRAAAAEQRATADAAKGGAAQ
+>1_441
+MQFGVFTIGDITADPTNGTAPTEHQRIKDTVKIARHAEQAGFEVFATGQHHNPPFVAPGN
+PPTLLAYLAAQTETLQLSTATTLITTMDPVRLAEDYAYLQHLADGRVDLTMGRGNTGPVY
+PWFGKDIRQGIQLAVENYNLLYRLWHEETVDWSGNHRTPLQDFTLTPQPLDGVAPFVWHG
+SIRSPEIAEQAAYYGDGYFHNNIFWNKEHVIQMVRLYRQRYEYYGHGKAHQAYVALGGQA
+YMAKNSQDAVAEFRPYFDNAPVYGHGPSLEDFSRMTPLTVGSPQQVIERTLTFRDWVGDY
+QRQMFLIDHAGLPTDTVLRQIDLFGEEVLPVLRKEFDALKPDDVPAAPTHEFLVARARRG
+EAPVPGGKEGSQAQLDRAAAAEQRATADAAKGGAAQ
+>2_2181
+MQFGVFTIGDVTQDPTTGTTPTEHQRIKDTVRIAQHAAQAGFEVFATGQHHNPPFVAPGN
+PPTLLAYLAAMTTDLQLSTATTLITTMDPVRLAEDYSYLQHLADGRVDLTMGRGNTGPVY
+PWFGKDIRQGIPLAVENYNLLYRLWHEETVDWSGKFRSPLQNFTLTPQPLDGVAPFVWHG
+SIRSAEIAEQAAYYGDGFFYNNIFWNKEHVIQMVRLYRQRYEYYGHGKAHQAYVALGGQA
+YMAKNSQDAVKEFRPYFDNAPVYGHGPSLEQFSSMTPLTVGSPQQVIERTLGFRDWVGDY
+QRQMFLIDHAGLPTDTVLKQIDIFGEEVLPVLRKEFAALKPDDVPEAPTHEFLVERARRG
+EAPVPGGKEGSQAQIDRAAAAEKRAAAKAGEGA
+>3_2052
+MQLGIFTIGDITADPTTGTTPTEHQRIKDTVTIARHAEQAGFDVFATGQHHNPPFVAPGN
+PPTLLSHLAAVTETMTLSTATTLITTMDPVRLAEDYSYLQHLADGRVDLTLGRGNTGPVY
+PWFGKDIRQGVNLAVENYNLLYRLWHEETVDWSGQFRTPLQDFTLTPQPLDGVAPFVWHG
+SIRSPEIAEQAAYYGDGFFHNNIFWNKEHIIRMVRLYRQRFEHYGHGKAHQAYVGLGGQA
+YMAKNSQDAVKEFRPYFDNAPVYGHGPSLEDFTSMTPLTVGSPQQVIERTLSFRDWVGDY
+QRQMFLIDHAGLPTDTVLKQIDLFGEEVLPVLREEFAALKPDDVPEAPTHEFLVERARRG
+EAPVPGGREGSPAHAAREAARAKQAEQQKKKEDAR
+>4_665
+MQFGVFTIGDITADPTNGTAPTEHQRIKDTVKIARHAEQAGFEVFATGQHHNPPFVAPGN
+PPTLLAYLAAQTETLQLSTATTLITTMDPVRLAEDYAYLQHLADGRVDLTMGRGNTGPVY
+PWFGKDIRQGIQLAVENYNLLYRLWHEETVDWSGNHRTPLQDFTLTPQPLDGVAPFVWHG
+SIRSPEIAEQAAYYGDGYFHNNIFWNKEHVIQMVRLYRQRYEYYGHGKAHQAYVALGGQA
+YMAKNSQDAVAEFRPYFDNAPVYGHGPSLEDFSRMTPLTVGSPQQVIERTLTFRDWVGDY
+QRQMFLIDHAGLPTDTVLRQIDLFGEEVLPVLRKEFDALKPDDVPAAPTHEFLVARARRG
+EAPVPGGKEGSQAQLDRAAAAEQRATADAAKGGAAQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000652.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000652.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bbdeac9a722197e0ae28e7f9fa001ce181c9f65e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000652.fa
@@ -0,0 +1,34 @@
+>0_708
+MTSALIWAALLGLTLGAGLLLILVTQPVGWRPSLEQRVEPQLRHHIPASRLLEEERAGAS
+PWGTWGRILDPVVQAGVGWVQRISPGGAALDRKLAAAGLAVTSTDFRAQQVLSGAAGAAV
+AAVLALSLTVTGRVPVITGVALVIAGGMAGFLLREQLLSLRVRRRREAILSEFPSVAELF
+ALSVGAGESAAGALERIAGTARGELAGEFRTTLADMRAGASLSAALKAMGRRVQLAPVER
+FIGGVLIALDRGTPLADVLRAQAQDVREMGRRELMEAAGRKEIQMMVPLVFGILPLTVIF
+AVFPGISLMRLGF
+>1_448
+MTSALIWAALLGLTLGAGLLLILVTQPVGWRPSLEQRVEPQLRHHIPASRLLEEERAGAS
+PWGTWGRILDPVVQAGVGWVQRISPGGAALDRKLAAAGLAVTSTDFRAQQVLSAAAGAAV
+AAVLALSLTVTGRVPVITGVALVIAGGMAGFLLREQLLSLRVRRRREAILSEFPSVAELF
+ALSVGAGESAAGALERIAGTARGELAGEFRTTLADMRAGASLSAALKAMGRRVQLAPVER
+FIGGVLIALDRGTPLADVLRAQAQDVREMGRRELMEAAGRKEIQMMVPLVFGILPLTVIF
+AVFPGISLMRLGF
+>2_2169
+MSASLLWAALLGLTLGAGLLLIAVAQPLGWRPTLEQRVEPQLRHHTPASRLLEDEEAGAS
+PWGAWGRILDPVLRAGVGWLHRLSPAGETLERKLAAAGMTVSAADFRAQQVLSAAAGAGI
+ATAFSVALALAGRIPVVTGVGFVIVGGMAGYLLRDQLLSLRVQRRRAAILTEFPSVAELF
+ALSVGAGESAAGALERIATTARGELAGEFRATLAEMRAGSSLSAALKSMGRRVQLAPVER
+FIGGILIALDRGTPLADVLRAQAQDVREMGRRELMEAAGRKEIQMMVPIVTR
+>3_2044
+MSGGLLWGIALGLVMAAGVWLIVTAQPWGWRPSLEERIEPQLRHHVPASRLLADGRATST
+PWGTWGRLLGPSLAGATRGLQRLSPAGESLTLKLQAAGSELSVMDFRAQQVLCAVIATAA
+GTVLSVLLTLAGAVPVVSGVALVVAAGLSGYVLRDQMLTWAVARRRTAILTEFPSVAELF
+ALSVGAGESATGAMERIVRSARGEMAGEFDRTLADVRAGASLSSALKAMGRRVQLEPVER
+FIGGILIALDRGTPLADVLRAQAQDVRELGRRELMESAGRKEIQMMVPLVFGILPLTVVF
+AIFPGLALLRLSF
+>4_672
+MTSALIWAALLGLTLGAGLLLILVTQPVGWRPSLEQRVEPQLRHHIPASRLLEEERAGAS
+PWGAWGRILDPVVQAGVGWVQRISPGGVALDRKLAAAGLAVTSADFRAQQVLSAAAGAAV
+AAVLALSLTVTGRVPVITGVALVIAGGMAGFLLRDQLLSLRARRRREAILSEFPSVAELF
+ALSVGAGESAAGALERIAGTARGELAGEFRVTLADMRAGASLSAALKAMGRRVQLAPVER
+FIGGVLIALDRGTPLADVLRAQAQDVREMGRRELMEAAGRKEIQMMVPLVFGILPLTVIF
+AVFPGISLMRLGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000655.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000655.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f4ee070342bb42b73ea9ff8ef2290f6d20f9c21f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000655.fa
@@ -0,0 +1,20 @@
+>0_711
+MRSVNDVRDERGAATVEFLGLTLVLLIPVVYLMIYVSQVQAAAFASVAAADQAVKAVVAE
+ADHPSAGAAHATVELTLADYGVGAGQYDLTVGCDQGGCGTLEPGEVVAVRVDVGVPVPLT
+PAAWSLTPVTVGSDARQTVPRF
+>1_451
+MRSVNDVRDERGAATVEFLGLTLVLLIPVVYLMIYVSQVQAAAFASVAAADQAVKAVVAE
+ADHPSAGAAHATVELTLADYGVGAGQYDLTVGCDQGGCGTLEPGEVVAVRVDVGVPVPLT
+PAAWSLTPVTVGSDARQTVPRF
+>2_2143
+MPIASDVRDERGSATVEFLGLTLVLLIPVVYLMIYVSQVQAAAFASVAAADQAAKVVVSG
+TEGRSAAQAHAAVRLTLADFGIDYGAYELDLGCSAGDCVSLDPGEVVQARVDVEVPIPLT
+PADWSLAPVTVGSDARQAVPRF
+>3_2041
+MPSATDARHGPTHAPWRGTDLADDVGSATVEFLGLSLILLIPLAYLMLFVSQVQAAAFGA
+LASADQAARVMVSGEGGNPGQAEGTIPLTLADYGFDAADAEWSVACDVGGCGTLEPGEVV
+DVTVAISLDPPLLPDGWVSVDIATVDSHSRARMPRF
+>4_675
+MRSVNDVRDERGAATVEFLGLTLVLLIPVVYLMIYVSQVQAAAFASVAAADQAVKAVVAE
+ADHPSAGAAHATLELTLADYGVGAGQYDLTVGCDQGGCGTLEPGEVVAVRVDVAVPVPLT
+PAAWSMTPVTVGSDARQTVPRF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000659.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000659.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40b2a30d408899511d7db0bc4a0cec0760b803ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000659.fa
@@ -0,0 +1,40 @@
+>0_716
+MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALERAGVAPEDVDMV
+YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLIRLGEADVVV
+AGGQESMTNAPHLLPGARKGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA
+RAEQDEVAAASHQRAARAQSEGVFEGEIAPVEVPQRKGDPLVVSQDEGVRPDTTAESLGA
+LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAFAEEKGLTILATVGAPGQTAGPDSSQLH
+SQPSDAINAAVRKQGWDVADLDFIEINEAFGAVAVQSLRDLDYPHEKTNIHGGAIALGHP
+IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR
+>1_456
+MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALERAGVAPEDVDMV
+YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLIRLGEADVVV
+AGGQESMTNAPHLLPGARKGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA
+RAEQDEVAAASHQRAARAQSEGVFEGEIAPVEVPQRKGDPLVVSQDEGVRPDTTAESLGA
+LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAFAEEKGLTILATVGAPGQTAGPDSSQLH
+SQPSDAINAAMRKQGWDVADLDFIEINEAFGAVAVQSLRDLDYPHEKTNIHGGAIALGHP
+IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR
+>2_2137
+MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALECAGVAPEDVDMV
+YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLVRLGEADVVV
+AGGQESMTNAPHLLPGARKGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA
+RAEQDEVAAASHQRAARAQSEGVFEGEIAPVEVPQRKGDPLVVSQDEGVRPDTTAESLGA
+LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAYAEEKGLTILATVGALGQTAGPDSSQLH
+SQPSDAINAAMRKQGWDVADLDFIEINEAFGAVAVQSLRDLDYPHEKTNIHGGAIALGHP
+IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR
+>3_2034
+MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALERAGVAPEDVDMV
+YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLIRLGEADVVV
+AGGQESMTNAPHLLPGARKGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA
+RAEQDEVAAASHQRAARAQSQGVFEGEIAPVEVPQRKGDPLVVSQDEGVRPDTTAESLGS
+LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAFAEEKGLTVLATVGAPGQTAGPDSSQLH
+SQPSDAINAAVRKQGWDVADLDFIEINEAFGAVAVQSLRDLGYPHEKTNIHGGAIALGHP
+IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR
+>4_681
+MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALERAGVAPEDVDMV
+YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLIRLGEADVVV
+AGGQESMTNAPHLLPGARTGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA
+RAEQDEVAAASHQRAARAQSEGVFEGEIAPVEIPQRKGDPLVVSQDEGVRPDTTAESLGA
+LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAFAEEKGLTILATVGAPGQTAGPDSSQLH
+SQPSDAINAAVRKQGWDVADLDFIEINEAFGAVAVQSLRDLGYPHEKTNIHGGAIALGHP
+IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000679.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000679.fa
new file mode 100644
index 0000000000000000000000000000000000000000..02421a8cd4486e597aab71c57e3e7cd4539279a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000679.fa
@@ -0,0 +1,53 @@
+>0_740
+MDTNTVFLLAAIGLYFLAMIAIGLYASRKNTDLDDYMLAGRDMKPSVAALSAGASDMSGW
+LLMGLPGAIYAAGLVEGWMAVGLTVGAWVNWRVVAPRLRSYTEVAGNSITIPSFLENRFK
+DRTHILRIVAGLIILVFFTFYVSSGMVAGGKFVESTFGPESFYAQGISINYLTGMLVVAG
+ITVLYTLFGGFLGASLTDVAQGVLMFLSLLAVPIVVILTMGGWDAVVEGIRAADAAGGGV
+NHFSMFENATLIGVLSSLAWGLGYFGQPHIIVRFMALRTPHDAAVARRVGIGWMALSVFG
+AVMVALVGIAYFQANPGTTLEDPETVFLVLASIMFHPFVAGLVLAAVLAAIMSTLSSQLI
+VCSSALVEDLYMLRGRTGSPTFTLWLGRIGVLVVALVAGLLALDPDSSVLELVSFAWAGF
+GAAFGPVILLALYWPRFTSWGAMAAMVTGAAVAWVWSEASAETWEWFGLYELLPGFVAAF
+VVGVVVSLVTQRSRRVQRRIDAEFTGAIDIVAGREPDPDVAPAAMTRDAAGGSTAAAADP
+RAQA
+>1_479
+MDTNTVFLLAAIGLYFLAMIAIGLYASRKNTDLDDYMLAGRDMKPSVAALSAGASDMSGW
+LLMGLPGAIYAAGLVEGWMAVGLTVGAWVNWRVVAPRLRSYTEVAGNSITIPSFLENRFK
+DRTHILRIVAGLIILVFFTFYVSSGMVAGGKFVESTFGPDSFYAQGISINYLTGMLVVAG
+ITVLYTLFGGFLGASLTDVAQGILMFLSLLAVPIVVILTMGGWDAVVEGIRAADAAGGGV
+NHFSMFENATLIGVLSSLAWGLGYFGQPHIIVRFMALRTPHDAAVARRVGIGWMALSVFG
+AVMVALVGIAYFQANPGTTLEDPETVFLVLASIMFHPFVAGLVLAAVLAAIMSTLSSQLI
+VCSSALVEDLYMLRGRTGSSTFTLWLGRIGVLVVALVAGLLALNPDSSVLELVSFAWAGF
+GAAFGPVILLALYWPRFTSWGAMAAMVTGAAVAWAWSEASAETWEWFGLYELLPGFVAAL
+VVGVVVSLVTQRSRRVQRRIDAEFTGAIDIVAGREPHPDVAPAAMTRDAAGGSTAAAADP
+RAQA
+>2_2113
+MDQNTFFLILAIGLYFAAMIAIGLWASRKNTDLDDYMLAGRDMKPGVAALSAGASDMSGW
+LLMGLPGAVYAAGLVEAWMAIGLTVGAWINWKVVAPRLRAYTQVAGNSITIPSFLENRFQ
+DRTHILRIVSGLIILVFFTFYVSSGMVAGGKFVESTFGPESLYAQGVSVNYLTGMLVVAG
+ITVLYTLFGGFLGASLTDVAQGTIMFLALIAVPIATIVAMGGWGAMVEGLRAADAASAAA
+GEAVDHLSLFHNATLIGVLSSLAWGLGYFGQPHIIVRFMALRTVQDASTARRIGIGWMAL
+SVFGAVMVALVGIAYFQANPGTTLADPETVFLVLASILFHPFIAGLVLAAVLAAIMSTLS
+SQLIVCSSALVEDLYKLTGRQGSPRAMVWLGRIGVLVVAVVAGLLALDPESSVLELVSFA
+WAGFGAAFGPVILLALYWQRFTSWGAMAAVVTGALVAWLWSEASAETWEWFGLYELLPGF
+IAALVVGVVVSLLTQRSRPVQTRIEREFTGAVDVVAGRAAPTA
+>3_2008
+MDSNTAFLLAAIGLYFVAMIAIGLYAARRNNDLDDYMLAGRDMKPGVAALSAGASDMSGW
+LLMGLPGAVYASGLIEGWMAIGLIVGAWVNWKVVAPRLRSYTEVAGDSITIPTFLENRFK
+DHTHILRIVAGLIILVFFTFYVSSGMVAGGKFVESTFGPDSIYAQGVSVNYLTGMVVVAG
+ITVLYTLFGGFLGASLTDVAQGVLMFLALLVVPVAVIATMGGWDQVLEGIRAADAAVGPE
+ADRFSLFQNATRIGVLSSLAWGLGYFGQPHIIVRFMALRTPQDAAAARRIGIGWMVLSVF
+GAVMVGLVGLAYFQANPGTELNDPETVFLVLASILFHPFVAGLVLAAVLAAIMSTLSSQL
+IVCSSALVEDLYMLRGRRGSPRTMVWLGRIGVLVVALIAGLLALNPDASVLELVSFAWAG
+FGAAFGPVILLALYWERFTSWGAMAAMVVGAAVAWFWSTASADTWDWFGLYELLPGFVAA
+LAAGVVVSRLTRRPDHVQEHISGEFTGAADIVAGREPTALTGSTGAVGGSTAAPRA
+>4_704
+MDTNTVFLLAAIGLYFLAMIAIGLYASRKNTDLDDYMLAGRDMKPSVAALSAGASDMSGW
+LLMGLPGAIYAAGLVEGWMAVGLTVGAWVNWRVVAPRLRSYTEVAGNSITIPSFLENRFK
+DRTHILRIVAGLIILVFFTFYVSSGMVAGGKFVESTFGPDSFYAQGISINYLTGMLVVAG
+ITVLYTLFGGFLGASLTDVAQGILMFLSLLAVPIVVILTMGGWDAVVEGIRAADAAGGGV
+NHFSMFENATLIGVLSSLAWGLGYFGQPHIIVRFMALRTPHDAAVARRVGIGWMALSVFG
+AVMVALVGIAYFQANPGTTLEDPETVFLVLASIMFHPFVAGLVLAAVLAAIMSTLSSQLI
+VCSSALVEDLYMLRGRTGSPTFTLWLGRIGVLVVALVAGLLALNPDSSVLELVSFAWAGF
+GAAFGPVILLALYWPRFTSWGAMAAMVTGAAVAWVWSEASAETWEWFGLYELLPGFVAAF
+VVGVVVSLVTQRSRRVQRRIDAEFTGAIDIVAGREPDPDVAPAAMTRDAAGGSTASAADP
+RAQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000704.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000704.fa
new file mode 100644
index 0000000000000000000000000000000000000000..791da2b4c1673af54f9eeec79d4f189d5a5e8199
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000704.fa
@@ -0,0 +1,30 @@
+>0_768
+MGAQIRVYRQKIASTSSMKKIFKAMELIATSRITKARERVSASLPYANAITRAVSAVSSQ
+HDIDHVLTTEPENPTRAAVLIMSSDRGLAGAYSANVLRKAEQLLTRLGEEGKDVDVYVVG
+RKAQTYFDFRGRGYKQLWTGQTDAPVAERAAEIGEVLVDAFLTDTADGGVDEIHVVFTEF
+VSLVKQNPHVVRLLPLEVVEEEAATAEDVLPLYEYEPDAEEVLDALLPKYIESRIFNAML
+QSAASELANRQRAMKSAGDNATSLIKDYTLLMNNARQAEITQELTELIAGADALNNS
+>1_508
+MGAQIRVYRQKIASTSSMKKIFKAMELIATSRITKARERVSASLPYANAITRAVSAVSSQ
+HDIDHVLTTEPENPTRAAVLIMSSDRGLAGAYSANVLRKAEQLLTRLGEEGKDVDVYVVG
+RKAQTYFDFRGRGYKQLWTGQTDAPVAERAAEIGEVLVDAFLTDTADGGVDEIHVVFTEF
+VSLVKQNPHVVRLLPLEVVEEEAATAEDVLPLYEYEPDAEEVLDALLPKYIESRIFNAML
+QSAASELANRQRAMKSAGDNATSLIKDYTLLMNNARQAEITQELTELIAGADALNNS
+>2_2087
+MGAQIRVYRQKIASTSSMKKIFKAMELIATSRITKARERVNASLPYANAITRAVSAVSSQ
+HDIDHVLTTEPENPTRAAVLILSSDRGLAGAYSANVLRKAEQLLTRLGEEGKDVDVYVVG
+RKAQTYFDFRGREYKQLWTGQTDAPAAERASEIGETLVDAFLTDTAAGGVDEIHIVFTEF
+VSLVKQNPHVVRLLPLEVVEEEVAAPEDVLPLYEYEPDAEEVLDALLPKYIESRIFNAML
+QSAASELANRQRAMKSAGDNASGLIKDYTLLMNNARQAEITQELTELIAGADALNNS
+>3_1979
+MGAQIRVYRQKIASTTSMKKIFKAMELIATSRITKARERVNQSLPYANAITRAVTAVSSQ
+HDIDHVLTTEPENPTRAAVLIMSSDRGLAGAYSANVLRKAEQLLTALHEEGKDVDVYVVG
+RKAQTYFDFRGREYKQLWTGQTDAPKAERAQEIGTILVESFLTDTAAGGVDEIHVVFTEF
+VSLVKQNPHVIRLLPLEVVEQDVVSPEEVLPLYEFEPDADEVLDALLPKYIESRIFNAML
+QSAASELANRQRAMKSAGDNASSLIKEFTLRMNNARQAEITQELTELIAGADALNNS
+>4_735
+MGAQIRVYRQKIASTSSMKKIFKAMELIATSRITKARERVSASLPYANAITRAVSAVSSQ
+HDIDHVLTTEPENPTRAAVLIMSSDRGLAGAYSANVLRKAEQLLTRLGEEGKDVDVYVVG
+RKAQTYFDFRGRGYKKLWTGQTDAPVAERAAEIGEVLVDAFLTDTADGGVDEIHVVFTEF
+VSLVKQNPHVVRLLPLEVVEEEAATAEDVLPLYEYEPDAEEVLDALLPKYIESRIFNAML
+QSAASELANRQRAMKSAGDNATSLIKDYTLLMNNARQAEITQELTELIAGADALNNS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000705.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000705.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c5dd59c650629ce3d74c527150e903521f458990
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000705.fa
@@ -0,0 +1,50 @@
+>0_769
+MTATITDQGTGTPTGGATGRVSRVIGPVIDAEFPANAMPEIYNALTTEIDLNGQRRTVTF
+EVAQHLGDNMVRAISLQSTDGLVRGTDVVDTGAPISVPVGDAVKGHIFNVLGETLDMPTS
+QLQAEDRWPIHRPAPNFASLEGSTEMLETGIKVIDLLTPYIKGGKIGLFGGAGVGKTVLI
+QEMITRVARNFGGTSVFAGVGERTREGNDLWVEMDEADVLKDTALVFGQMDEPPGTRLRV
+ALSALTMAEYFRDVQNQDVLLFIDNIFRFSQAGSEVSTLLGRMPSAVGYQPNLADEMGVL
+QERITSTRGHSITSMQAVYVPADDYTDPAPANVFAHLDATTNLTRDLASRGLYPAVDPLA
+STSRILDPQYVGQEHYDVAIRVKQILQKNKELQDIIAILGVDELSEEDKITVGRARKIEQ
+FLSQNTYTAKQFTGVEGSTVPVKDTVEGFKAIADGDLDHVAEQAFYNVGGLDDVEREWAK
+IQAEG
+>1_509
+MTATITDQGTGTPTGGATGRVSRVIGPVIDAEFPANAMPEIYNALTTEIDLNGQRRTVTF
+EVAQHLGDNMVRAISLQSTDGLVRGTDVVDTGAPISVPVGDAVKGHIFNVLGETLDMPAS
+QLQAEDRWPIHRPAPNFASLEGSTEMLETGIKVIDLLTPYIKGGKIGLFGGAGVGKTVLI
+QEMITRVARNFGGTSVFAGVGERTREGNDLWVEMEEADVLKDTALVFGQMDEPPGTRLRV
+ALSALTMAEYFRDVQNQDVLLFIDNIFRFSQAGSEVSTLLGRMPSAVGYQPNLADEMGVL
+QERITSTRGHSITSMQAVYVPADDYTDPAPANVFAHLDATTNLTRDLASRGLYPAVDPLA
+STSRILDPQYVGQDHYDVAIRVKQILQKNKELQDIIAILGVDELSEEDKITVGRARKIEQ
+FLSQNTYTAKQFTGVEGSTVPVKDTVEGFKAIADGDLDHVAEQAFYNVGGLDDVEREWAK
+IQAEG
+>2_2086
+MTATITDQGTGTPTGGATGRVSRVIGPVIDAEFPANAMPEIYNALTTEIDLNGQRRTVTF
+EVAQHLGDNMVRAISLQSTDGLVRGTDVVDTGAPISVPVGDAVKGHIFNVLGETLDVETS
+SLNFEERWPIHRAAPNFASLEGSTEMLETGIKVIDLLTPYIKGGKIGLFGGAGVGKTVLI
+QEMITRVARNFGGTSVFAGVGERTREGNDLWVEMDEADVLKDTALVFGQMDEPPGTRLRV
+ALSALTMAEYFRDVQNQDVLLFIDNIFRFSQAGSEVSTLLGRMPSAVGYQPNLADEMGVL
+QERITSTRGHSITSMQAVYVPADDYTDPAPANVFAHLDATTNLTRDLASRGLYPAVDPLA
+STSRILDPQYVGQDHYDTAIRVKQILQKNKELQDIIAILGVDELGEEDKITVARARKIEQ
+FLSQNTYTAKQFTGVEGSTVPIKDTVEGFKAIADGDLDHIAEQAFYNVGGLDDVEREWAK
+IQAEG
+>3_1978
+MTATFTDQGTGTPTAGATGRVARVIGPVIDAEFPANAMPEIYNALTATVELAGQTRVVTF
+EVAQHLGDNMVRAISLQSTDGLVRGADVQDTGAPISVPVGDAVKGHLFNVLGETLDMPIS
+ELDVQERWPIHRPAPSFAALEGSTEMLETGIKVIDLLTPYIKGGKIGLFGGAGVGKTVLI
+QEMITRVARNFGGTSVFAGVGERTREGNDLWVEMDEADVLKDTALVFGQMDEPPGTRLRV
+ALSALTMAEYFRDVQNQDVLLFIDNIFRFSQAGSEVSTLLGRMPSAVGYQPNLADEMGVL
+QERITSTRGHSITSMQAVYVPADDYTDPAPANVFAHLDATTNLTRDLASRGLYPAVDPLA
+STSRILDPQYVGQEHYDVATRVKQILQKNKELQDIIAILGVDELSEEDKITVSRARKMEQ
+FLSQNTYTAKQFTGVEGSTVPIKDTVEGFKAIADGDLDHVAEQAFYNVGGLDDVEREWAK
+IQAEG
+>4_736
+MTATITDQGTGTPTGGATGRVSRVIGPVIDAEFPANAMPEIYNALTTEIDFNGQRRTVTF
+EVAQHLGDNMVRAISLQSTDGLVRGTDVVDTGAPISVPVGDAVKGHIFNVLGETLDMPTS
+QLQAEDRWPIHRPAPNFASLEGSTEMLETGIKVIDLLTPYIKGGKIGLFGGAGVGKTVLI
+QEMITRVARNFGGTSVFAGVGERTREGNDLWVEMDEADVLKDTALVFGQMDEPPGTRLRV
+ALSALTMAEYFRDVQNQDVLLFIDNIFRFSQAGSEVSTLLGRMPSAVGYQPNLADEMGVL
+QERITSTRGHSITSMQAVYVPADDYTDPAPANVFAHLDATTNLTRDLASRGLYPAVDPLA
+STSRILDPQYVGQDHYDVAIRVKQILQKNKELQDIIAILGVDELSEEDKITVGRARKIEQ
+FLSQNTYTAKQFTGVEGSTVPVKDTVEGFKAIADGDLDHVAEQAFYNVGGLDDVEREWAK
+IQAEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000709.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000709.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e2635568e007c33a5fcb678bc0dc77275ed2f821
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000709.fa
@@ -0,0 +1,16 @@
+>0_773
+MPRSNRPRRSSAPRRSERGASGASRRSRPSPGRSDPLQELLGLDAGYSRQSGSDGGWHVR
+QIPAWRAVKDYTCPGCGRVIRQGQAHLVAWRADWIMGDEDAGEDRRHWHPVCWRTRPSR
+>1_513
+MPRSNRPRRSSAPRRSERGASGVSRRSRPSPGRSDPLEELLGLDAGYSRQSGSDGGWHVR
+QIPAWRAVKDYMCPGCGRVIRQGQAHLVAWRADWIMGDEDAGADRRHWHPVCWRTRPGR
+>2_2081
+MADPLKELLGLDPGYSHQSGGDGGWHVRQIPSWRAVKDYTCPGCGRVIRQGQAHLVAWRS
+DWIMGDEDAGADRRHWHPVCWRTRVGR
+>3_1973
+MVTMPRSNRPRRSAAPRRGEGAAGGASRRSRPGPGRADPLEELLGMDPGYSHQSGSDGGW
+HVRDIPSWRAVKDYTCPGCGRTIRQGQAHLVAWRSDWIMGDEDAGADRRHWHPTCWRTRA
+SR
+>4_740
+MPRSNRPRRSSAPRRSERGASGASRRSRPSPGRADPLEELLGLDAGYSRQSGSDGGWHVR
+QIPAWRAVKDYTCPGCGQVIRQGQAHLVAWRADWIMGDEDAGADRRHWHPVCWRTRPGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000713.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000713.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b6c3ace6f662d61529eedfe5e70996df62edeb11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000713.fa
@@ -0,0 +1,50 @@
+>0_777
+MALTLVRLRWTLTLNQWRRSPFTLVVSVLGALYVLGMAAVAVTLLVTGLPALPDEARGAT
+TVLVAAVVVLAWLVIPPFVTGVDATLDPHSFVLFPVPARTLIAGLVLSAFTTPAGLATLA
+VLVGLGASWWDRPAALAAGLAGGALTAVTAVAIGSGLAGLLAAYASRRRVRDVVSVLLFI
+PLMLGGVALSRAVASFEDFLAIAPQVARGAAWTPFGAGPAAAWAAAEGRGAAAALHLAVA
+AAWCLAALALWHLAVRRTVEPVAVGGGGSRRVGAGADPTPLRWLGRPATGPRTAIAARAQ
+RYWLADPRYAAGLIIIPLMAVVLWFTGGLASGGGLGPGLLLILGPMTAWSLAYSISADIA
+YDHTAFHLHVVSGVRGVDDRWGRVLGLAGWGVPMILLVTTATVAAAGDWSLLAPMLGLAL
+GLFGTTAGLSAFLSARFVYPVPKPGDSPFKTPQGAAMRTMLVQGASMLVSLALAVPFLVP
+FIVRLATGAAVWGWVTVALGFAWGAVALWLGVRLGARWYDRAQAETYQAVAAF
+>1_517
+MALTLVRLRWTLTLNQWRRSPFTLVMSVLGALYVLGMAAVAVTLLVTGLPALPDEARGAT
+TVLAAAVVVLAWLVIPPFVTGVDATLDPHSFVLFPVPARTLIAGLVLSAFTTPVGLATLA
+VLVGLGASWWDRPAALAAGLAGGALTAVTAVAIGSGLAGLLAAYASRRRVRDVVSVLLFI
+PLMLGGVALSQAIASFEDFLAIAPQVARGAAWTPFGAGPAAAWAAAEGRGAAVALHLAVA
+AAWCLAALALWHLAVRRTVEPVAVGGGRSRRVAAGADPMPLRWLGRRATGPRTAIAARAQ
+RYWLADPRYAAGLIIIPLMAVLLWFTGGMAAEGGPGLGLLLILGPITAWSLAYSISADIA
+YDHTAFHLQVVSGVRGVDDRWGRVLGLAGWGVPMILLVTTATVAAAGDWSLLAPMLGLAL
+GLFGTTAGLSAFVSARFVYPVPKPGDSPFATPQGAAMRTMLVQGAAMLVSLALAVPFLVP
+FVVRLVTGAAVWGWVTVALGLAWGAVALWLGVRLGARWYDRAQAETYQAVAAF
+>2_2077
+MALTLVRLRWALTLNQWRRSTFTLVLAVLGALYVLGLAVFVVVMLVTFLPDAWVVDRGTV
+TVIVASALALGWLLIPPFITGVDATLDPHSFVLFPVRARTLIAGLTLSAFTTPSGLATLI
+VMLGTGLSWWDIPAALAAALVGGALTAVTAVASGYGLAGLMAAYAGRRRVREVLSIALLI
+PVMLSGVIVAQTLDSLGDLFDVAPRVAAVAAWTPFGAGPAAAWAVAEGQGLRAAAHLLVA
+AAWCLAALALWHLAVRRTVEPVAVGGGSAREAGRADGAPLRWLGRPATGPRTAIAARAQR
+YWLRDPRYAAGLVMIPVLAAVLWFASTAGGDAGPGLGMLTMLGPVSAWALAYSISADIAY
+DHTAFHLHVVSGVRGADDRWGRVMGLAGWGVPALVVLTVATTAAADRWDLLPALLGLTLG
+LFGVTAAMSAFVSARFVYPVPKPGESPFKTPQGATMRIMLVQGAAMLVVVPLAVPVVVPF
+VVALVTQSAVWGWATLAVGLAWGAVALWLGVRMGAAWYDRAQAETYQAVAAF
+>3_1969
+MALTLTRLRWALTLNGWRRSTLTLVLSVLGALYFFGMAAMAVAALVVGLPEAELPVRGAV
+TVLVAAVVVLLWTILPPLVTGVDATLDPSSFVLFPVPARTLVAGLLLSTFTTPIGALTLL
+GLLGVAASWWDTPAALAAAAVGAVLSAVTAVCLGYGVTGLMSSFTGRRRVREAISLLVLI
+PLMLGGVALSRVMQSIDDLLWLGPVLANAAVWTPFGAGLGAGWAAAEGRWGLAGLRLLVA
+LAWAVAAAALWMLAIRRTVEPAAVGSTDSAAPRGDRATDLRWLGRPATSARTAIAARAQL
+YWFKDPRYMASLVTVPLMFVLLWFMGTSGPEGATAILLAAGPVTAWALGYSLSADIAYDH
+TAFHLHVLAGVKGIDDRLGRVMGLLGWALPVVAGVTLATVAMHGDWSVLPAILGVSLGVL
+GACLGLSALVSARWVYPVPKPGDSPLKTPQGAAMRIMLVQGTSLLVTLVLLVPMAVPFVV
+LLVTGAAVWSWVTLAVGLAWGALALWLGVRAGAAWYDRAQAETLQAVQSW
+>4_744
+MALTLVRLRWTLTLNQWRRSPFTLVMSVLGALYVLGMAAVAVTLLVTGLPALPDEARGAT
+TVLAAAVVVLAWLVIPPFVTGVDATLDPHSFVLFPVPARTLIAGLVLSAFTTPVGLATLA
+VLVGLGASWWDRPAALAVGLVGGALTAVTAVAIGSGLAGLLAAYASRRRVRDVVSVLLFI
+PLMLGGLALSRAIASFEDFLAIAPQIARGAAWTPFGAGPAAAWAVAEGRGAAVALHLAVA
+AAWCLAALALWHLAVRRTVEPVAVGGGRSRRVAAGADPTPLRWLGRPATGPRTAIAARAQ
+RYWLADPRYAAGLIIIPLMAVLLWFTGGMAGEGGPGLGLLLVLGPITAWSLAYSISADIA
+YDHTAFHLHVVSGVRGVDDRWGRVLGLAGWGVPMILLVTTATVAAAGDWSLLAPMLGLAL
+GLFGTTAGLSAFVSARFVYPVPKPGDSPFATPQGAAMRTMLVQGAAMLVSLALAVPFLVP
+FVVRLVTGAAVWGWITVALGLAWGAVALWLGVRLGARWYDRAQAETYQAVAAF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000715.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000715.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed7bcb3a0128d911889c360787460a8ac0429591
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000715.fa
@@ -0,0 +1,60 @@
+>0_779
+MADGRSLTSGTPDGSVQHDLFHIGEDLPPAMPERAAWGTAPKLRQWQQEALERYLQTAPQ
+DFLTVATPGAGKTTFALRVAKILLDSGVVQRLTVVAPTDHLKRQWADNAARVGIAIDPNF
+KNADGRHGAEYRGVALTYAQVANKPVLHRNRTEAAKTLVILDEIHHGGDALSWGEGIREA
+FEPATRRLSLTGTPFRSDTASIPFVRYELGADGIERSKADYTYGYGPALRDHVVRPVIFM
+AYSGQMRWKTSTGEVMEAQLGEAATKDITASAWRTALDPAGEWIPSVLRAADRRLSEVRR
+NVPDAGGLVIASDHQDARAYAAQLEALTGQRPAVILSDDKGASDRIEEFAASDERWMVAV
+RMVSEGVDVPRLCVGVYATSTSTPLFFAQAVGRFVRSRRRGETASVFLPSVPALMLLANE
+MELERDHALDRKEGAVEVEDLEDAPEEDLIAEANRAESGSDALTREKFEALESRASFDKV
+LFDGGEFGLGGAVGSEEEQDFLGIPGLLDAEQVSALLRQRQAEQIQRRPRAQAAEPADVV
+DHRRMKELRSELSKTVSAWATRSGQPHGVIHNRLREISGGPAVAQASREQLEKRLSTLRG
+WFVGRT
+>1_519
+MADGRSLTSGTPDGSVQHDLFHIGEDLPPAMPERAAWGTAPKLRQWQQEALERYLQTAPQ
+DFLAVATPGAGKTTFALRVAKILLDSGVVQRLTVVAPTDHLKRQWADNAARVGIAIDPNF
+KNADGRHGAEYRGVALTYAQVANKPVLHRNRTEAAKTLVILDEIHHGGDALSWGEGIREA
+FEPATRRLSLTGTPFRSDTASIPFVRYELGQDGIERSKADYTYGYGPALRDHVVRPVIFM
+AYSGQMRWKTSTGEVMEAQLGEAATKDITASAWRTALDPAGEWIPSVLRAADRRLTEVRR
+NVPDAGGLVIATDHQDARAYAAQLEALTGQRPAVILSDDKGASDRIEEFAASDERWMVAV
+RMVSEGVDVPRLCVGVYATSTSTPLFFAQAVGRFVRSRRRGETASVFLPSVPALMLLANE
+MELERDHALDRKEGAVEVEDLEDAPEEDLIAEANRAESGSDALTREKFEALESRASFDKV
+LFDGGEFGLGGAVGSEEEQDFLGIPGLLDAEQVSALLRQRQAEQIQRRPRAQAAEPADVV
+DHRRMKELRSELSKTVSAWAARSGQPHGVIHNRLREISGGPAVAQASREQLEKRLSTLRG
+WFVGRT
+>2_2075
+MAERRSSASGTPDGAVQHDLFHIGEDLPPAMPERAAWGTAPKLRQWQQEALEKYLETGPQ
+DFLAVATPGAGKTTFALRVAKILLDSGVVQRLTVVAPTDHLKRQWADNAARVGIAIDPNF
+KNADGRHGSEYRGVALTYAQVANKPVLHRNRTEAAKTLVILDEIHHGGDALSWGDGIREA
+FEPAARRLALTGTPFRSDTSTIPFVEYVDGPDGLSRSKADYTYGYGPALRDHVVRPVLFM
+AYSGQMRWKTSTGEVMEAQLGEAATKDITASAWRTALDPKGEWIPAVLRAADRRLSEVRR
+GVPDAGGLVIATDHEDARAYAAQLEALTGQRPALILSDDKGASDRIEEFAASDERWMVAV
+RMVSEGVDVPRLCVGVYATSTSTPLFFAQAVGRFVRSRRRGEVASVFLPSVPQLMLLANE
+MELERDHALDRREGGVDVEDLEDAPEEDLLAQANREESGSDALLRGKFEAMESRASFDKV
+LFDGGEFGLGGAVGSEEEQDFLGIPGLLDAEQVSALLRQRQAEQVQRRPKAPAKEPADVV
+DHRRMKELRSELSKTVSAWSARSGTPHGVIHNRLREVSGGPAVAQASRDQLEKRLSTLRG
+WFVGRT
+>3_1967
+MAEGRSETSGAPTPDGIQPDLFHVGEDLPPALPERAAWGTAPKLRQWQQEALEKYLREAP
+QDFLAVATPGAGKTTFALRVAKILMDSGVVQRLTVVAPTDHLKRQWADNAARVGLAIDPN
+FKNADGRHGPEYRGVALTYAQVANKPVLHRNRTEAARTLVILDEIHHGGDARSWGEGIRE
+AFEPASRRLSLTGTPFRSDDAYIPFVRYERGEDGFERSRADYTYGYGPALRDHVVRPVIF
+LAYSGQMRWKTSTGEVMEAQLGEAATKDITASAWRTALDPAGEWIPSVLRAADRRLTEIR
+RGIPDAGGLVIASDHEDARAYAAQLQAVTGQAPAVILSDDKGASDRIEEFAASDERWMVA
+VRMVSEGVDVPRLCVGVYATSTSTPLFFAQAVGRFVRSRRRGEVASVFLPSVPQLMLLAN
+EMELERDHALDRREGAVTVEELEDLSQAPEEDLIAEANRAERGSETLTRASFEALESRAS
+FDKVLFDGGEFGLGGDVGSEEELDFLGIPGLLDAEQVSELLRQRQNEQIRRKPAAAPKES
+RDVVDHRRMKELRAELSTTVSAWSARSGQPHGVIHNRLREISGGPAVAQASREQLEKRLE
+TLRGWFVGRR
+>4_746
+MADGRSLTSGTPDGSVQHDLFHIGEDLPPAMPERAAWGTAPKLRQWQQEALERYLQTAPQ
+DFLAVATPGAGKTTFALRVAKILMDSGVVQRLTVVAPTDHLKRQWADNAARVGIAIDPNF
+KNADGRHGAEYRGVALTYAQVANKPVLHRNRTEAAKTLVILDEIHHGGDALSWGEGIREA
+FEPATRRLSLTGTPFRSDTASIPFVRYELGQDGIERSKADYTYGYGPALRDHVVRPVIFM
+AYSGQMRWKTSTGEVMEAQLGEAATKDITASAWRTALDPAGEWIPSVLRAADRRLSEVRR
+NVPDAGGLVIATDHQDARAYAAQLEALTGQRPAVILSDDKGASDRIEEFAASDERWMVAV
+RMVSEGVDVPRLCVGVYATSTSTPLFFAQAVGRFVRSRRRGETASVFLPSVPALMLLANE
+MELERDHALDRKEGAVDVEDLEDAPEEDLIAEANRAESGSDALTREKFEALESRASFDKV
+LFDGGEFGLGGAVGSEEEQDFLGIPGLLDAEQVSALLRQRQAEQIQRRPRAQAVEPADVV
+DHRRMKELRAELSKTVSAWAARSGQPHGVIHNRLREISGGPAVAQASREQLEKRLSTLRG
+WFVGRT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000723.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000723.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e539bdcb250a925bc78986927141a8783459a918
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000723.fa
@@ -0,0 +1,25 @@
+>0_788
+MSAPASSSAGLPEGARVVLATHNAGKVRELRQLLAGAVPGLEVETAVVDAGAVGAPDVVE
+DGVTFAQNALKKARAVAAHTGLIAVADDSGLAVDVLHGAPGIFSARWAGRHGDDRANLEL
+LLAQLADVPDEHRGAQFVCAAALAVPSGPDAAGARAIHVEHVEHGRLPGTLLREPVGDGG
+FGYDPILRPEGRDVSTAQLSPEDKNAISHRGHAFRALLPYLVDALDARP
+>1_529
+MSAPASSSAGLPEGARVVLATHNAGKVRELRQLLAGAVPGLDVEAAVVDAGAVGAPDVVE
+DGVTFAQNALKKARAVAAHTGLIAVADDSGLAVDVLHGAPGIFSARWAGRHGDDRANLEL
+LLAQLADVPDEHRGAQFVCAAALAVPSGPDAAGARAIHVEHVEHGRLPGTLLREPVGDGG
+FGYDPILRPEGRDVSTAQLSPEDKNAISHRGHAFRALLPYLVDALDARP
+>2_2066
+MSGAATGVPEGARVVLATHNAGKVRELRQLLEGAVPGLDASVAVVDAGAVGAPDIVEDGV
+TFAQNALKKARAVAAHTGLIAVADDSGLAVDVLHGAPGIFSARWAGRHGDDRANLELLLA
+QLADVPDAHRGAEFVCAAALAVPSSADARGTHAIHVEHVEHGRLRGTLLRAPVGDGGFGY
+DPILRPDGRDESTAQLSAADKNAISHRGHAFRALLPYLVDALDARA
+>3_1956
+MSTPTAPVAPAGARVVLATHNAGKVRELRSLLAEALPALDVETAVVDAGAVGAPDVVEDG
+VTFEQNALKKARAVAAHTGLIAVADDSGLAVDVLGGAPGIFSARWAGRHGDDKANLELLL
+AQLGDVPDEHRGAAFVCAAALATPRGGDHVELGRMPGMLLREPVGDGGFGYDPILRPAGE
+DRSTAQLSSAEKNAISHRGQAFRALLPHLVAALSADS
+>4_757
+MSAPASSSAGLPEGARIVLATHNAGKVRELRQLLAGAVPGLDVEAAVVDAGAVGAPDVVE
+DGVTFAQNALKKARAVAAHTGLIAVADDSGLAVDVLHGAPGIFSARWAGRHGDDRANLEL
+LLAQLADVPDEHRGAQFVCAAALAVPSGPDAAGARAIHVEHVEHGRLPGTLLREPVGDGG
+FGYDPILRPEGRDVSTAQLSPEDKNAISHRGHAFRALLPYLVDALDARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000730.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000730.fa
new file mode 100644
index 0000000000000000000000000000000000000000..924c11234c6db5a19f8a7de42302817030a32c71
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000730.fa
@@ -0,0 +1,55 @@
+>0_795
+MQPTRRAFLGGGLGLLGLGVAGCTTSPAAPSSAAPSSSGPGRLLVVGAPARALTRDPARA
+LDVESFRLIRQVFETLLGVDADTGAPTPRLAERHEESDGGRLHTFHLVSGVVFDDGEPCD
+AAAVVANIERWAAAPAPVDGTVSPPSSFVSAFGGYAGDADSAFAGVEAHGELEVRLRLHS
+PRRHLAAALASPAFAISSPASWDRTVDVDGSEVTTPAGTGPYRWADAAETAELTRAHPGA
+SGATFLVPSARHRGSDPAAHPVAVQAWGRASVRLRELRRGTADVIDVVAPGQLRPLVEAG
+TQVLPRDPLGVLYVGMNLDHPLVHAQYLRQAIAYAVDRPRIAGSDVFLEGTRLAHDLVPP
+SLGVGDEEARRYDVNPGRAREFLGLAGYDGEPLEFLYPAGTARPSLPEPERVYAMVARDL
+GAVGMHIVPVPVPEDQDYLHAVVSRPTRALHLMGRTGDYRDPHAFLEPFARSGRAETGYR
+NPRVVEDVDAAAAETDDDTRRALFRRVVRAMALDLPALPLVYPISALATGPRVASYPTSP
+QLDEPFSRVRLTEG
+>1_536
+MQPTRRAFLGGGLGLLGLGVAGCTTSPAAPSSAAPSSSGPGRLLVVGAPARALTRDPARA
+LDVESFRLIRQVFETLLGVDADTGAPTPRLAERHEESDGGRLHTFHLVSGVVFDDGEPCD
+AAAVVANIERWAAAPAPVDGTVSPPSSFVSAFGGYAGDADSAFAGVEAHGELEVRLRLHS
+PRRHLAAALASPAFAISSPASWDRTVDVDGSEVTTPAGTGPYRWADAAETAELTRAHPGA
+SGATFLVPSARHRGSDPAAHPVAVQAWGRASVRLRELRRGTADVIDVVAPGQLRPLVEAG
+TQVLPRDPLGVLYVGMNLDHPLVHAQYLRQAIAYAVDRPRIAGSDVFLEGTRLAHDLVPP
+SLGVGDEEARRYDVNPGRAREFLGLAGYDGEPLEFLYPAGTARPSLPEPERVYAMVARDL
+GAVGMHIVPVPVPEDQDYLHAVVSRPTRALHLMGRTGDYRDPHAFLEPFARSGRAETGYR
+NPRVVEDVDAAAAETDDDTRRALFRRVVRAMALDLPALPLVYPISALATGPRVASYPTSP
+QLDEPFSRVRLTEG
+>2_2059
+MQPSRRALLGAGLGALGLGLGGCAGTPTPAPSASGTAPATPSGPSRLLVVGAPGRPFTRD
+SARAWDSESFRIIRQVLETLLGVDPDTGAPTPRLAERHEVSADGRVHAFHLVPGLVFDDG
+EPCDADAVVANIRRWAQAPAPVEGSVPMPSSFVSAFGGHEGEEGSVYAGVEARGAHEVRL
+RLTSPLRHLAAALSSPAFAISSPASWERTVPVDGVETVTPAGTGPYRWATEAEVAELSRD
+QPDGADVAYLVPSASHRGEEPAVRPVVVHPWGRATTRLRELRRGTADVIDVVAPGQLRPL
+VEAGTQVLPRDPLAVLYVGMNLDHPRIRSQYLRQAIAYAVDRPRIAASDVFLEGTRLAHD
+LVPPALGVGDEEARRYDVNPAQARRLVELSGYDGEELEFLYPAGTSSPSLPEPERVYAMV
+AQDLGAIGLHITPVPVPADHDYLRAVVSRPTRALHLMGRNGAYRDPHAFLEPFARSWRAE
+TGYRNPRVIQDVDAAASEQDDEARRGLFRRVVRAMALDLPALPLVYPISALATGPRVASY
+PTSPQLDEPFARVRLTEG
+>3_1949
+MDASRRSVLSLGLAGLGLGLSACGAGRATPASSSSSAASAPAVRPLVLGAPGRPLTRTPA
+LAWDTESLRLIAQVLEPLLGVDQDTGAPTPLLAEHRESEDGLTHTFVLTPDLRFSDGVAC
+DADAVVANLRRWSEGEPAEAVAMPSPFVAAFGGLAGEDSTAFRDATAADARTVRLRLRRR
+LRHLPAALASPRFAISSPASWKRTQDVDGAPVATPAGTGPHRWADPTESVEVLEPLGGTG
+PATVLVPNEHARAGLPTPPTAVVHSWGRASTRLRELRRGNADVIDVVAPGQLRPLVEAGT
+QVLPRDPFSVLYLGMNLDHPLLHSLYLRQAVAYAVDRPRLASSDVFLQGTALAHDLVPPA
+LGVAVEDGPRYDVDPARARRLLELAGYRGEPLEFLYPSGHAWPSLPEPERVFAMVSSDLG
+VVGLRVVPVPVPADQDYRRAVLGRRGRALHLMGRDGHYRDPHAFLEPFARSARTETGYVN
+AALTADVDAAASETDDERRRELHRRAGRTLLLDLPALPLVHPISALATGPRVASYPTSPQ
+LDEPLAQVRLADS
+>4_764
+MQPTRRAFLGGGLGLLGLGVAGCTTSPAVPSSAAPSSSGPGRLLVVGAPARALTRDPARA
+LDVESFRLIRQVFETLLGVDADTGAPTPRLAERHEESDGGRLHTFHLVSGVVFDDGEPCD
+AAAVVANIERWASAPAPVDGTVAPPSSFVSAFGGYAGDADSAFAGVEARGELEVRLRLHS
+PRRHLAAALASPAFAISSPASWDRTVDVDGSEVTTPAGTGPYRWADAAETAELTRAHPGA
+SGATILVPSARHRGSDPAAYPVAVQAWGRASVRLRELRRGSADVIDVVAPGQLRPLVEAG
+TQVLPRDPLGVLYVGMNLDHPRVRSQYLRQAIAYAVDRPRIAGSDVFLEGTRLAHDLVPP
+SLGVGDEEARRYDVNPGRAREFLHLAGYDGEPLEFLYPAGTARPSLPEPERVYAMVARDL
+GAVGMHIVPVPVPEDQDYLHAVVSRPTRALHLMGRTGDYRDPHAFLEPFARSGRAETGYR
+NPRVVEDVDAAAAETDDDARRALFRRVVRAMALDLPALPLVYPISALATGPRVASYPTSP
+QLDEPFSRVRLTEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000740.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000740.fa
new file mode 100644
index 0000000000000000000000000000000000000000..82547f4d950df12faaec318d58290009e5248f65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000740.fa
@@ -0,0 +1,36 @@
+>0_818
+MTETTRSSADPLDIAVIGGDGIGPEVTDQAAAVLQAALRAEGRPEARLTPYPLGAEHWLE
+TGEALTDEVLESLRRHDAILFGAVGAAPGDERIPSGLIERGMLLKLRFALDHGVNLRPAT
+LLPGAVSPLAAPGEIDFTVVREGTEGPYVGNGGAIRVDTPHEIATEVSVNTAFGVRRVVE
+DAFRRADAGERKRLTLVHKHNVLVHAGHLWRRTVESVGADFPAVTWDYMHVDAAMIFLAT
+DPARFDVIVTDNLFGDIITDLAAAVTGGIGLAASGNINVEGTAPSMFEPVHGSAPDIAGQ
+GIADPVAAILSAALLLEHVGETGAAARVRTAVWAHLKDRVDGARGTTAEVGADVAARV
+>1_549
+MTETTRSSADPLDIAVIGGDGIGPEVTDQAAAVLQAALRAEGRPEARLTPYPLGAEHWLE
+TGEALTDEVLESLRRHDAILFGAVGAAPGDERIPSGLIERGMLLKLRFALDHGVNLRPAT
+LLPGAVSPLAAPGEIDFTVVREGTEGPYVGNGGAIRVDTPHEIATEVSVNTAFGVRRVVE
+DAFRRADAGERKRLTLVHKHNVLVHAGHLWRRTVESVAADFPAVTWDYMHVDAAMIFLAT
+DPARFDVIVTDNLFGDIITDLAAAVTGGIGLAASGNINVEGTAPSMFEPVHGSAPDIAGQ
+GIADPVAAILSAALLLEHVGETGAAARVRTAVWAHLKDRVDGARGTTAEVGADVVARV
+>2_2041
+MTESTRPSADPLDIAVIGGDGIGPEVTEQAAAVLQAALGAEGRPEARLTPYPLGAEHWLR
+TGEALPDETLEALRGHDAILFGAVGAAPGDERIPSGLIERGMLLRLRFELDHGVNLRPAA
+LLPGAVSPLAEPGTIDFTVVREGTEGPYVGNGGAIRTGTPHEIATEVSVNTAHGVRRVVE
+DAFARAAAGERKRLTLVHKHNVLVHAGHLWRRTVEAVAADFPEVSWDYMHVDAATIFLTT
+DPARFDVIVTDNLFGDILTDLAAAVTGGIGLAASGNINVEGTAPSMFEPVHGSAPDIAGQ
+GVADPVAAILSAALLLEHVGETGAAQRVRTAVWAHLKDRVDGARGSTAEVGADVAARV
+>3_1940
+MTESTRTSAAPLDIAVIGGDGIGPEVTDQAVAVLEAALAAEGRPAPRLTPYALGAEHWLA
+TGEALTDETLEALRGHEAILFGAVGAAPGDQRIPSGLIERGILLRLRFELDHGVNLRPSR
+LYPGTTSPLAEPGEIAFTVVREGTEGPYVGNGGAIRTGTEHEIATEVSVNTAHGVRRVVR
+DAFRRASATERRRLTLVHKHNVLVHAGHLWRRTVEEVAAEFPEVAHDYMHVDAATIVMTT
+DPARFDVIVTDNLFGDILTDLAGAVTGGIGLAASANINVERTAPSMFEPVHGSAPDIAGQ
+GIADPVAAILSAGLLLEHVGERAAADRIDRAVWAHLAERGPQRGSTAEVGVDVVRRVRES
+SAA
+>4_777
+MTETTRSSADPLDIAVIGGDGIGPEVTDQAAAVLQAALRAEGRPEARLTPYPLGAEHWLE
+TGEALTDEVLESLRRHDAILFGAVGAAPGDERIPSGLIERGMLLKLRFALDHGVNLRPAT
+LLPGAVSPLAAPGEIDFTVVREGTEGPYVGNGGAIRVDTPHEIATEVSVNTAFGVRRVVE
+DAFRRADAGERKRLTLVHKHNVLVHAGHLWRRTVESVAADFPAVTWDYMHVDAAMIFLAT
+DPARFDVIVTDNLFGDIITDLAAAVTGGIGLAASGNINVEGTAPSMFEPVHGSAPDIAGQ
+GIADPVAAILSAALLLEHVGETGAAARVRTAVWAHLKDRVDGARGTTAEVGADVVARV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000752.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000752.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1e919ed3a7b33b31c32ac466813d53982edfc34d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000752.fa
@@ -0,0 +1,45 @@
+>0_832
+MAKLLTIHGGKPLTGEVTVRGAKNLVPKAMVAALLGNSPSVLRNIPEIKDVDVVSSLLEI
+HGVSVEWDKETGRITMDPAGVKSALTAEIDAHAGDSRIPILFCGPLMHAIGEAFIPDLGG
+CKIGDRPIDYHLAVLRNFGAVVDKRPGGISISAPKGLHGAKLELPYPSVGATEQVLLTAV
+KAEGITELKGAAVEPEIHDLIAVLQKMGAIITVQTDRTIRIEGVSEMRGYNHIALPDRNE
+SASWASAALATRGDIYVRGAEQRDLTAFLNTYRKIGGEFDVVDDGIRFWHAGGDLNPLVL
+ETDVHPGFMTDWQQPLVVALTQAKGVSIVHETVYENRFGFTDALVRMGASIQLHRECLGS
+VPCRFGQRNFLHSAVISGPTPLHGVEFDIPDLRGGFSHLIAALTAEGTSTATGLEIINRG
+YEHFMAKLEGLGADVELTERDR
+>1_563
+MAKLLTIHGGKPLTGEVTVRGAKNLVPKAMVAALLGNSPSVLRNIPEIKDVDVVSSLLEI
+HGVSVEWDKETGRITMDPAGVKSALTAEIDAHAGDSRIPILFCGPLMHAIGEAFIPDLGG
+CKIGDRPIDYHLAVLRNFGAVVDKRPGGISISAPKGLHGAKLELPYPSVGATEQVLLTAV
+KAEGITELKGAAVEPEIHDLIAVLQKMGAIITVQTDRTIRIEGVSEMRGYNHIALPDRNE
+SASWASAALATRGDIYVRGAEQRDLTAFLNTYRKIGGEFDVVDDGIRFWHAGGDLNPLVL
+ETDVHPGFMTDWQQPLVVALTQAKGVSIVHETVYENRFGFTDALVRMGASIQLHRECLGS
+VPCRFGQRNFLHSAVISGPKPLHGVEFDIPDLRGGFSHLIAALTAEGTSTATGLEIINRG
+YEHFMAKLEGLGADVELTERDR
+>2_2027
+MAKLLTIHGGKPLTGEVTVRGAKNLVPKAMVAALLGNTPSVLRSIPEIKDVDVVSSLLEI
+HGVSVEWDKESGRITMDPAGVKSALTAEIDAHAGDSRIPILFCGPLMHAIGEAFIPDLGG
+CKIGDRPIDYHLAVLRNFGAVVDKRPGGISISAPKGLHGAKLELPYPSVGATEQVLLTAV
+KAEGITELKGAAVEPEIHDLIAVLQKMGAIITVQTDRTIRIEGVTEMRGYNHEALPDRNE
+SASWASAALATGGDIFVRGASQRDLTAFLNTYRKIGGEFDVVDDGIRFWHAGGDLNPLVL
+ETDVHPGFMTDWQQPLVVALTQAKGVSIVHETVYENRFGFTDALVRMGASIQLHRECLGS
+VPCRFGQRNFLHSAVISGPTPLHGVEIDIPDLRGGFSHLIAALAAEGTSTATGLEIINRG
+YEHFMDKLQGLGADVELSDRTR
+>3_1920
+MAKLLTIHGGKPLQGEVTVRGAKNLVPKAMVAALLGTGPSVLRSIPEIKDVDVVSSLLEI
+HGVTVDWDKESGTITMDPAGVKSALTAEIDAHAGDSRIPILFCGPLMHAIGEAFIPDLGG
+CKIGDRPIDYHLAVLRNFGAVVDKRPGGISISAPKGLHGAKLELPYPSVGATEQVLLTAV
+KAEGITELKGAAVEPEIHDLIHVLQKMGAIITVQTDRTIRIEGVPELRGYNHVAIPDRNE
+SASWASAALATKGDIFVRGASQRDLTAFLNTYRKIGGEFEVTDEGIRFWHGGGELNPLVL
+ETDVHPGFMTDWQQPLVVALTQATGVSIVHETVYENRFGFTDALVRMGASIQLHRECLGS
+VPCRFGQRNFLHSAVISGPTPLHGVDFDVPDLRGGFSHLIAALAAEGTSHATGLEIINRG
+YEHFMAKLQGLGADVELSERPR
+>4_791
+MAKLLTIHGGKPLTGEVTVRGAKNLVPKAMVAALLGNSPSVLRNIPEIKDVDVVSSLLEI
+HGVSVEWDKETGRITMDPAGVKSALTAEIDAHAGDSRIPILFCGPLMHAIGEAFIPDLGG
+CKIGDRPIDYHLAVLRNFGAVVDKRPGGISISAPKGLHGAKLELPYPSVGATEQVLLTAV
+KAEGITELKGAAVEPEIHDLIAVLQKMGAIITVQTDRTIRIEGVSEMRGYNHIALPDRNE
+SASWASAALATRGDIYVRGAEQRDLTAFLNTYRKIGGEFDVVDDGIRFWHAGGDLNPLVL
+ETDVHPGFMTDWQQPLVVALTQAKGVSIVHETVYENRFGFTDALVRMGASIQLHRECLGS
+VPCRFGQRNFLHSAVISGPTPLHGVEFDIPDLRGGFSHLIAALTAEGTSTATGLEIINRG
+YEHFMAKLEGLGADVEPTERDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000761.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000761.fa
new file mode 100644
index 0000000000000000000000000000000000000000..42390d4882fd9f4de992c2726e1f13a335ce3872
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000761.fa
@@ -0,0 +1,41 @@
+>0_841
+MDGTQPTPGAAPHDVDVDAPWRRTAAAAGLLGDAGPVPTVFETMTGLAVEHGAVNLGQGF
+PDADGPDALLRLAADAVLAGPNQYAPGTGDPALRQAVAEHRRRHWGVTEDPATQVMITTG
+ATEGIAATVLAFVRPGDEVVTVEPFYDSHAATIALAGARHVSVPVEAPDFLPDPARVAAA
+MTDRTRLLIVNTPHNPTGAVYPRELLEELVALCRSRGVLILSDEVYDHLVYEGEHVSLRS
+VAGAEDIALTVSSAGKAFAVTGWKVGWLTGPAELVGAARAVKQFLTYSSGPAFQRALGAY
+LPTDGAERHLAGQRERYRDARDRLVAGLREAGLDPVVPAAGYFVVVDLAPWGVTDAAEAA
+VRWTREAGVTGIPVGALCRPDGGHLRSWLRLAFCKSPDAIDEAMRRLAEAAPRLRAA
+>1_572
+MDGTQPTPGSARHDVDVDAPWRRTAAAAGLLGDTGPVPTVFETMTGLAVEHGAVNLGQGF
+PDADGPDALLRLAADAVLAGPNQYAPGTGDPVLRQAVAEHRRRHWGVTEDPATQAMITTG
+ATEGIASTVLAFVRPGDEVITVEPFYDSHAATIALAGGRHVSVPVEAPDFLPDPARVADA
+ITDRTRLLIVNTPHNPTGAVYPRELLEELVALCRSRGVLMLSDEVYDHLVYEGEHVSLRS
+VAGAEDIALTVSSAGKAFAVTGWKVGWLTGPAELVGAARAVKQFLTYSSGPAFQRALGAY
+LPTDDAERHLAGQRERYRDARDRLVAGLREAGLDPVVPAAGYFVVVDLAPWGVTDAAEAA
+VQWTREAGVTGIPVGALCRPDGGHLRSWLRLAFCKSPDAIDEAMRRLAEAAPRLRAP
+>2_2018
+MNADASDRTRPPRTGPAPAPATGPAPADVAGTAFVAGPWRRTAAAAGLLDDGAPVPTVFE
+TMTGLAVEHGAVNLGQGFPDADGPDALLRLAAEAVLAGPNQYAPGTGDPVLRQAVAEHRR
+RHWGVTEDPATQVMITTGATEGIAATVLAFVRPGDEVITVEPFYDSHAATIALAGGRHVS
+VPVEAPDFLPDPARVADAITDRTRLLIVNTPHNPTGAVYPRELLEELVTLCRSRGVLILS
+DEVYDHLVYEGEHVSLRSVAGAEDIALTVSSAGKAFAVTGWKVGWLTGPAELVGAARAVK
+QFLTYSSGPAFQRALGAYLPTEDAKRHLAGQRERYRDARDRLVAGLRAADLDPVVPAAGY
+FVVVDLAPWGVTDAAEAAVRWTREAGVTGIPVGALCRPDGGHLRSWLRLAFCKSPDAIDE
+AMRRLAAAAPALDGRRPRP
+>3_1911
+MSHDSPSPTDAAAAPSDVRLAGPWRAASAAAGVLRDGAPVPTVFETMTALAVEHGAVNLG
+QGFPDADGPPELLALAAEAVTTGPNQYAPGTGRADLRAAVAAHRARHWGVAEDPDTQVLA
+TTGATEAIAATVLALVRPGDEVITVEPFYDSHAAVVALAGGRHVTVPVHAPDFLPDPARI
+AAAITPRTRLLIVNTPHNPTGAVYPRALLEELVALCRARDVLMLSDEVYDHLVHEGRHVT
+LRAIPGAERIALTASSAGKSLAVTGWKVGWLTGPADLVAAVRGVKQFLSYSSGPAFQQAV
+AAFLPRADDFLAGQLARHRRSRDLLVSGLRDIGLDPVVPAAGYFTVVDLAPWGVRDAAAA
+ARTWTERAGVAGIPVSALCRPDGDHLRSWLRLTFCKSEDTVAEAVARLTRHAADLRAG
+>4_800
+MDGTQPTPRSAPHDVDVDAPWRRTAAAAGLLGDAGPVPTVFETMTGLAVEHGAVNLGQGF
+PDADGPDALLRLAADAVLAGPNQYAPGTGDPALRRAVAEHRRRHWGVTEDPATQVMITTG
+ATEGIAATVLAFVRPGDEVVTVEPFYDSHAATIALAGGRHVSVPVEAPDFLPDPARVAAA
+MTDRTRLLIVNTPHNPTGAVYPRELLEELVALCRSRGVLILADEVYDHLVYEGEHVGLRS
+VAGAEDIALTVSSAGKAFAVTGWKVGWLTGPAELVGAARAVKQFLTYSSGPAFQRALGAY
+LPTDDAERHLAGQRERYRDARDRLVAGLREAGLDPVVPAAGYFVVVDLAPWGVTDAAEAA
+VQWTREAGVTGIPVGALCRPDGGHLRSWLRLAFCKSPDAIDEAMRRLAEAAPRLRAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000767.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000767.fa
new file mode 100644
index 0000000000000000000000000000000000000000..97976d8c5ac25d22ea8370f1aa003fd466c4a496
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000767.fa
@@ -0,0 +1,34 @@
+>0_847
+MPELPEAEVVRRGLARWATDAVAAELEVLDPRSLRRSPGGADALRERLRGARLAEPARRG
+KFLWLPLAEGDDAVVVHLGMSGQILVDEPGAADQRHLRLRLPVTAVDGSARELRFVDQRI
+FGGWWLDALRPDDAAGGERIPTTAAHIALDPLHPLFDPAAVHARLARRRSTLKRALLDQS
+LVSGIGNIYADEALWGARLHPERPTERMRRADTLRLLAAVQDVMRRALEVGGTSFDALYV
+NVDGRSGYFARSLAAYGRTGQPCRRCAAEGVDSRIVREPFMNRASHLCPRCQPRPRRRRA
+AAADA
+>1_578
+MPELPEAEVVRRGLARWATDAVAAELEVLDPRSLRRSPGGADALRERLRGAQLAEPARRG
+KFLWLPLAEGDDAVVVHLGMSGQILVDEPGAADQRHLRLRLPVTAADGSARELRFVDQRI
+FGGWWLDALRPDDAAGGERIPTTAAHIALDPLHPLFDPAAVHARLARRRSTLKRALLDQS
+LVSGIGNIYADEALWGARLHPERPTERMRRADTLRLMAAVQDVMRRALEVGGTSFDALYV
+NVDGRSGYFARSLAAYGRTGQPCRRCAAEGIDSRIVREPFMNRASHLCPRCQPRPRRRRA
+VAADA
+>2_2012
+MPELPEAEVVRRGLARWATDAVAGALQVHDPRSLRRSPGGAEALRARLEGARLAEPARRG
+KFLWLPLADADEAVVVHLGMSGQILVDEPGAPDQRHLRLRLPVTAADGAARELRFVDQRI
+FGGWWLDALHPDFAAGGEPIPATAAHIALDPLHPLFDADAVHARLARRRSTLKRALLDQS
+LVSGIGNIYADEALWGARLHPERPTERMRRADTRRLMAAVQDVMRRALAVGGTSFDALYV
+NVDGRSGYFARSLDAYGRTGQPCRRCAAEGVESRIVREPFMNRASHRCPRCQPTPRRRRT
+ATPADGPARP
+>3_1905
+MPELPEAEVVRRGMARWASGARAADLDVLDARSVRRSPGGAEALRERLSGAVLAEPARRG
+KFLWLPLEDADDAVVVHLGMSGQVRVDEPGAPDQRHLRLRLPITAADGSDRELRFVDQRL
+FGGWWLDPVVVGPETGDAVPASAAHIALDPLHPDFDPDAVHRRLVRRRSTLKRSLLDQTL
+VSGIGNIYADEALWAARLHPERPTQRMARAQTRAVLAAVQDVMRRALAVGGTSFDALYVN
+VDGRSGYFARSLEAYGRTGQPCRRCTAEGRRTLIVREPFMGRASHRCPVCQPVPRRSPSR
+>4_806
+MPELPEAEVVRRGLARWATDAVAAELEVLDPRSLRRSPGGADALRERLRGARLAEPARRG
+KFLWLPLAEGDDAVVVHLGMSGQILVDGPGAADQRHLRLRLPVTAADGSARELRFVDQRI
+FGGWWLDALRPDDAAGGERIPTTAAHIALDPLHPLFDPVAVHARLARRRSTLKRALLDQS
+LVSGIGNIYADEALWGARLHPERPTERMRRADTLRLLAAVQDVMRRALEVGGTSFDALYV
+NVDGRSGYFARSLAAYGRTGQPCRRCAAEGVDSRIVREPFMNRASHLCPRCQPRPRRRRA
+AVADA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000777.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000777.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fbee7701af14ede915f0644b905bb767698ae631
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000777.fa
@@ -0,0 +1,50 @@
+>0_871
+MFNSLSDRLTATFRSLKGKGRLSEADIDATAREIRRALLDADVAVPVVRQFIAQIKERAL
+SAEVAQALNPGQQVVKIVNEELVGILGGETRRIQHAKTGTTVIMLVGLQGAGKTTLAGKL
+AHLLKSQGHTPLLVACDLQRPNAVKQLQVGGERAGVPVYAPHPGVSSEFEAATGDPVQVA
+RDGVAEANTKYHDVVIIDTAGRLGVDAELMQQAADIRAAVDPDEVLFVIDAMIGQDAVAT
+AQAFNEGVGFTGVVLTKLDGDARGGAALSVRHVTGKPIMFASTGEGLKDFEVFHPDRMAS
+RILDMGDVLSLIEQAEQNWDRTEAEKMARKFADQEDFTLDDFLAQMQQLKKMGSLKKMLM
+MMPGAQGMRQQLEQFDESSIGRVEAIIHSMTPHERVAPKIINGSRRARIARGSGVSVSEV
+NGLLERFAEAQKMMKRMAAGGGIPGMPGTPGGASRKGKGKGKNAKRDRVKSGNPAKAAAE
+RKAIEERRARAAQAQAGAVFGRDGAGMDGFDPSTLNLPAGFEKYLKDR
+>1_599
+MFNSLSDRLTATFRSLKGKGRLSEADIDATAREIRRALLDADVAVPVVRQFIAQIKERAL
+GAEVAQALNPGQQVVKIVNEELVGILGGETRRIQHAKTGTTVIMLVGLQGAGKTTLAGKL
+AHLLKSQGHTPLLVACDLQRPNAVKQLQVGGERAGVPVYAPHPGVSSEFEAATGDPVQVA
+RDGVAEANTKYHDVVIIDTAGRLGVDAELMQQAADIRAAVDPDEVLFVIDAMIGQDAVAT
+AQAFNEGVGFTGVVLTKLDGDARGGAALSVRHVTGKPIMFASTGEGLKDFEVFHPDRMAS
+RILDMGDVLSLIEQAEQNWDRTEAEKMARKFADQEDFTLDDFLAQMQQLKKMGSLKKMLM
+MMPGAQGMRQQLEQFDESSIGRVEAIIHSMTPHERVAPKIINGSRRARIARGSGVSVSEV
+NGLLERFAEAQKMMKRMAAGGGIPGVPGMPGGASRKAKGKGKNAKRDRVKSGNPAKAAAE
+RKAIEERRARAAQAQAGAVFGRDGAGMDGFDPSTLNLPAGFEKYLKDR
+>2_1995
+MFNSLSDRLTATFRSLKGKGRLTEADIDATAREIRRALLDADVAVPVVRQFIAQIKERAL
+GEEVAQALNPGQQVVKIVNEELVGILGGETRRIRHAKTGTTVIMLVGLQGAGKTTLAGKL
+AHLLKAQGHTPLLVACDLQRPNAVKQLQVGGERAGVPVFAPHPGVSSEFEAATGDPVQVA
+RDGVAEANAKYHDVVIIDTAGRLGVDAELMQQAADVRAAVEPDEVLFVIDAMIGQDAVAT
+AQAFNEGVGFTGVVLTKLDGDARGGAALSVRHVTGKPIMFASTGEGLKDFEVFHPDRMAS
+RILDMGDVLSLIEQAEQNWDRSEAEKMAKKFADQEDFTLDDFLNQMQQLKKMGSLKKMLM
+MMPGAQGMRQQLEQFDESSIGRVEAVIHSMTPHERVAPKIINGSRRARIAKGSGVSVSEV
+NGLLERFAEAQKMMKRMAAGGGMPGMPGAPGGVSRKAKGKNAKRNKVKSGNPAKAAAERK
+ALEERQARAAQAQAGAVFGRDGGAGMDGFDPSSLNLPAGFEKYLKDR
+>3_1892
+MFTSLSDRLTATFRNLKGKGRLTEADIDATAREIRRALLDADVAVPVVRQFIAQIKERAL
+GEEVSQALNPGQQVVKIVNEELVAILGGETRRIQHAKTGTTVIMLVGLQGAGKTTLAGKL
+AHLLKSQGHTPLLVACDLQRPNAVKQLQVNGERAGVPVFAPHPGVSSEFEAATGDPVQVA
+RAGIDEANTKYHDVVIIDTAGRLGVDAELMQQAADIRAAVQPDEVLFVIDAMIGQDAVAT
+AQAFNEGVGFTGVVLTKLDGDARGGAALSVRHVTGKPIMFASTGEGLKDFEVFHPDRMAS
+RILDMGDVLSLIEQAEQNWDRAEAEKMAKKFADQEDFTFDDFLTQMQQLKKMGSMKKLLG
+MMPGAQGMRQQLEQFDESSIGRVEAIIHSMTPHERVAPKIINGSRRARIAKGSGVQVTEV
+NALLERFAEAQKMMKKLAGGGVPGMPGMGPGPGRKSKGRNAKKTKVKSGNPAKAAAERRA
+LEERRSRPAAGGVFGQGGTMPDMTDFDPSQLNLPAGFEKYLKDR
+>4_819
+MFNSLSDRLTATFRSLKGKGRLSEADIDATAREIRRALLDADVAVPVVRQFIAQIKERAL
+GAEVAQALNPGQQVVKIVNEELVGILGGETRRIQHAKTGTTVIMLVGLQGAGKTTLAGKL
+AHLLKSQGHTPLLVACDLQRPNAVKQLQVGGERAGVPVYAPHPGVSSEFEAATGDPVQVA
+RDGVAEANTKYHDVVIIDTAGRLGVDAELMQQAADIRAAVDPDEVLFVIDAMIGQDAVAT
+AQAFNEGVGFTGVVLTKLDGDARGGAALSVRHVTGKPIMFASTGEGLKDFEVFHPDRMAS
+RILDMGDVLSLIEQAEQNWDRSEAEKMARKFADQEDFTLDDFLAQMQQLKKMGSLKKMLM
+MMPGAQGMRQQLEQFDESSIGRVEAIIHSMTPHERVAPKIINGSRRARIARGSGVSVSEV
+NGLLERFAEAQKMMKRMAAGGGIPGMPGMPGGASRKAKGKGKNAKRDRVKSGNPAKAAAE
+RKAIEERRARAAQAQAGAVFGRDGAGMDGFDPSTLNLPAGFEKYLKDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000779.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000779.fa
new file mode 100644
index 0000000000000000000000000000000000000000..73d13c81782586bb8f5ae587db309aa9fb8e5d60
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000779.fa
@@ -0,0 +1,15 @@
+>0_873
+MLTEALEHLVRGIVDTPEAVRVDARSQRRGDMLEVRVAPEDLGRVIGRQGRTATALRTVL
+DGLAGHPVRVDVVETDRRS
+>1_601
+MLTEALEHLVRGIVDTPEAVRVDARSQRRGDMLEVRVAPEDLGRVIGRQGRTATALRTVL
+DGLAGHPVRVDVVETDRRS
+>2_1993
+MLTEALEHLVRGIVDTPEAVRVDARSQRRGDMLEVRVAPEDLGRVIGRQGRTATALRTVL
+DGLAGHPVRVDVVETDRRR
+>3_1890
+MLAEALEHLVRGIVDTPDAVRVASRPQRRGEMLEVRVAPEDLGRVIGRQGRTATALRTVL
+DGLAGHPVRVDVVETDRAR
+>4_821
+MLTEALEHLVRGIVDTPEAVRVDARSQRRGDMLEVRVAPEDLGRVIGRQGRTATALRTVL
+DGLAGHPVRVDVVETDRRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000797.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000797.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3207fbec086bf406068985e328735dc7b367de51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000797.fa
@@ -0,0 +1,85 @@
+>0_891
+MSAAEESSQIRSGLTDQLPDKDPQETSEWIESLDGLIEERGTERAQYIMRSLMQRASAQS
+VALPYVTTTDYVNTIPADQEPEYPGDEELERRYRNYLRWNAMALVQRAQRDGVGVGGHIS
+SYAGQATLYEVGLNHFFRGQDHPGGGDHIFFQGHSSPGNYARAFLEGRLTEEDLDGFRQE
+KSRQGHGLPSYPHPRMMPHFWQYPTVSMGLGPMNAIFQAQTNRYLHNNGIKDTSDQHVWA
+FLGDGEMDEPESRGQLHIAANDKLDNLTFVINCNLQRLDGPVRGNGKIVQELESYFRGAG
+WNVIKVLWGREWDPLLEADDEGELVRIMNETLDGDYQTYKAESGGFVRDHFFGRSSVTKE
+MVADMTDDEIWGLKRGGHDYKKVYAAYKAAMEHKGQPTVILAHTIKGYGLGKSFEGRNAT
+HQMKKLTVDDLKVFRDRHRIPISDEQIEKDPYNIPYYHPGADAPEITYMMERRKELGGFV
+PERRSDYHAIPLPPESAYKQARKGSGKQQAATTMAFVRLLKDLMRDKNMGPRFVPIIPDE
+ARTFGMDSFFPTAKIYNPKGQNYLSVDRDLFLSYKESPQGKIYHVGINEDGATAAFNAIG
+TAYSTHGEPMIPVYIFYSMFGFQRTADNIWAAGDQLARGFMIGATAGRTTLAGEGTQHMD
+GHSPVLASTNPAVKHYDPAYSYEIAHIVRQGLEDMYGDHDRGDDVRNVIYYLTVYNEPIT
+HIEEPEGLDVEGLLKGIYRLSEGQGDGPKVQLLGSGVSVPWALDAQRILSEEWGVNASVW
+SVTSYNELYRDAVAAEKDALKDPSATPRVPYVTQALQGAEGPIVATSDYSTSWTNQIRPF
+VPNRFSALGADEFGFADTRAAARRYFLIDTHSMVVRALQLLEEEGEVERGTAAKAHEKYR
+LDDVNAGTTGIAGGDA
+>1_619
+MSAAEESSQIRSGLTDQLPDKDPQETSEWIESLDGLIEERGTERAQYIMRSLMQRASAQS
+VALPYVTTTDYVNTIPADQEPEYPGDEELERRYRNYLRWNAMALVQRAQRDAVGVGGHIS
+SYAGQATLYEVGLNHFFRGQDHPGGGDHIFFQGHSSPGNYARAFLEGRLTEQDLDGFRQE
+KSRQGHALPSYPHPRMMPHFWQYPTVSMGLGPMNAIFQAQTNRYLHNNGIKDTSDQHVWA
+FLGDGEMDEPESRGQLHVAANDKLDNLTFVINCNLQRLDGPVRGNGKIVQELESYFRGAG
+WNVIKVLWGREWDPLLEADDEGELVRIMNETLDGDYQTYKAESGGFVRDHFFGRSSVTKE
+MVADMTDDEIWGLKRGGHDYKKVYAAYKAAMEHKGQPTVILAHTIKGYGLGKSFEGRNAT
+HQMKKLTVDDLKVFRDRHRIPISDEQIEKDPYNIPYYHPGADAPEITYMMERRKELGGFV
+PERRSDYHAIPLPPESAYKQARKGSGKQQAATTMAFVRLLKDLMRDKNMGPRFVPIIPDE
+ARTFGMDSFFPTAKIYNPKGQNYLSVDRDLFLSYKESPQGKIYHVGINEDGATAAFNAIG
+TAYSTHGEPMIPVYIFYSMFGFQRTADNIWAAGDQLARGFMIGATAGRTTLAGEGTQHMD
+GHSPVLASTNPAVKHYDPAYSYEIAHIVRQGLEDMYGDHDRGDDVRNVIYYLTVYNEPIT
+HIEEPEGLDVEGLLKGIYRLSEGQGDGPKVQLLGSGVSVPWALDAQRILSEEWGVNASVW
+SVTSYNELYRDAVAAEKDALKDPSASPRVPYVTQALQGAEGPIVATSDYSTSWTNQIRPF
+VPNRFSALGADEFGFADTRAAARRYFLIDTHSMVVRALQLLEEEGEVERGTAAKAHEKYR
+LDDVNAGTTGIAGGDA
+>2_1974
+MSAAEESSQILSGLTQQFPDKDPQETAEWIESLDGLIEERGTERAQFIMRSLLQRAGAKS
+VGVPMVTTTDYVNTIPADQEPEYPGDEELERRYRNYLRWNAAAIVQRAQKEGIGVGGHIS
+SYAGQATLYEVGLNHFFRGQDHPGGGDHIFFQGHSSPGNYARAFLEGRLTEEDLDGFRQE
+KSRQGHALSSYPHPRMMPDFWQFPTVSMGLGPMNAIFQAQTNRYLHNHGIKDTSDQHVWA
+FLGDGEMDEPESRGQLHVAANDKLDNLTFVINCNLQRLDGPVRGNGKIVQELESYFRGAG
+WNVIKVLWGREWDPLLEADDEGELVRIMNETLDGDYQTYKAESGGFVRDHFFGRSSATKE
+MVADMSDEEIWGLKRGGHDYRKVYAAYKSAMEHKGQPTVILAHTIKGYGLGKSFEGRNAT
+HQMKKMTVEDIKVFRDRHRIPVTDEQIERDPYDIPYYHPGKDAPEIKYLMERRKELGGFV
+PERRAKHHSIPVPPEAAYKQARKGSGKQQAATTMAFVRLLKDLMRDKNMGSRIVPIIPDE
+ARTFGMDSFFPTAKIYNPKGQNYLSVDRDLFLSYKESPQGKIYHVGINEDGATAAFNAVG
+TAYSTHGEPMIPVYIFYSMFGFQRTADNIWAAGDQLARGFMIGATAGRTTLAGEGTQHMD
+GHSPVIAGTNPAVKHYDPAYSYEIAHIVRQGFEDMYGEHDRGEDVRNVIYYLTVYNEPIH
+HIDEPEDLDVEGLLKGIYRLSEGQGDGPKVQLMGSGVSLPWAVEAQGILAEEWGVNASVW
+SVTSYNELYRDAVAAEKDALKDPSAAPRVPYVTQKLEGAEGPVVATSDFATSWTNQIRPF
+IPNRFAALGADEFGFADTRSAARRYFLIDSHSMVVRALQLLEEEGSVEKGTAAKAHEKYR
+LDDVNAGTTGNAGGDA
+>3_1872
+MSAAEESSQIVSGLTSQRPDKDPQETAEWIESFDGLVDERGTERAEYIMRSLMQRAGAKS
+VALPHVTTTDYVNTIPADQEPEYPGDEELERRYRNYLRWNAMALVQRAQRDAVGVGGHIS
+SYAGQATLYEVGLNHFFRGQDHPGGGDHIFFQGHSSPGNYARAFLEGRLTEEDLDGFRQE
+KSRQGHALPSYPHPRMMPHFWQYPTVSMGLGPMNAIFQAQTNRYLHNNGIKDTSDQHVWA
+FLGDGEMDEPESRGQLHVAANDKLDNLTFVVNCNLQRLDGPVRGNGKIVQELESYFRGAG
+WNVIKVLWGREWDPLLEADDEGELVRIMNETLDGDYQTYKAESGGFVREHFFGRSSVTKE
+MVADMTDDEIWGLKRGGHDYKKVYAAYKAAMEHKGQPTVILAHTIKGYGLGKSFEGRNAT
+HQMKKLTVDDLKVFRDRHRIPISDEQIEKDPYNIPYYHPGADAPEITYMMERRKELGGFV
+PERRSTYHQIPLPPESVYKQARKGSGKQQAATTMAFVRLLKDLMRDKNMGPRFVPIIPDE
+ARTFGMDSFFPTAKIYNPKGQNYLSVDRDLFLSYKESPQGKIYHVGINEDGATAAFNAIG
+TAYSTHGEPMIPVYIFYSMFGFQRTADNIWAAGDQLARGFMIGATAGRTTLAGEGTQHMD
+GHSPVLASTNPAVKHYDPAYSYEIAHIVRQGLEDMYGDHEDGDARRNVIYYLTVYNEPIT
+HIEEPEGLDVEGLLKGIYRLSEGQGDGPKVQLLGSGVSVPWALDAQRILSEEWGVNASVW
+SVTSYNELYRDAVAAEKDALKDPSATPRVPYVTQALQGAEGPIVATSDYSTSWTNQIRPF
+VPNRFSALGADEFGFADTRAAARRYFLIDTHSMVVRALQLLEEEGGVERGTAAKAHEKYR
+LDDVTAGTTGIAGGDA
+>4_839
+MSAAEESSQIRSGLTDQLPDKDPQETSEWIESLDGLIEERGTERAQYIMRSLMQRASAQS
+VALPYVTTTDYVNTIPADQEPEYPGDEELERRYRNYLRWNAMALVQRAQRDAVGVGGHIS
+SYAGQATLYEVGLNHFFRGQDHPGGGDHIFFQGHSSPGNYARAFLEGRLTEQDLDGFRQE
+KSRQGHALPSYPHPRMMPHFWQYPTVSMGLGPMNAIFQAQTNRYLHNNGIKDTSDQHVWA
+FLGDGEMDEPESRGQLHVAANDKLDNLTFVINCNLQRLDGPVRGNGKIVQELESYFRGAG
+WNVIKVLWGREWDPLLEADDEGELVRIMNETLDGDYQTYKAESGGFVRDHFFGRSSVTKE
+MVADMTDDEIWGLKRGGHDYKKVYAAYKAAMEHKGQPTVILAHTIKGYGLGKSFEGRNAT
+HQMKKLTVDDLKVFRDRHRIPISDEQIEKDPYNIPYYHPGADAPEITYMMERRKELGGFV
+PERRSDYHAIPLPPESAYKQARKGSGKQQAATTMAFVRLLKDLMRDKNMGPRFVPIIPDE
+ARTFGMDSFFPTAKIYNPKGQNYLSVDRDLFLSYKESPQGKIYHVGINEDGATAAFNAIG
+TAYSTHGEPMIPVYIFYSMFGFQRTADNIWAAGDQLARGFMIGATAGRTTLAGEGTQHMD
+GHSPVLASTNPAVKHYDPAYSYEIAHIVRQGLEDMYGDHDRGDDVRNVIYYLTVYNEPIT
+HIEEPEGLDVEGLLKGIYRLSEGQGDGPKVQLLGSGVSVPWALDAQRILSEEWGVNASVW
+SVTSYNELYRDAVAAEKDALKDPSATPRVPYVTQALQGAEGPIVATSDYSTSWTNQIRPF
+VPNRFSALGADEFGFADTRAAARRYFLIDTHSMVVRALQLLEEEGEVERGTAAKAHEKYR
+LDDVNAGTTGIAGGDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000805.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000805.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9e02a56d7105b055fcffb51e19db6e0925944ca3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000805.fa
@@ -0,0 +1,50 @@
+>0_899
+MTEQTTTVPVGAADIGVTGLAVMGANLARNFARHGYTVALHNRSRARTDQLVAEHGDEGA
+FVATETLAELVQSLAVPRRVLIMVKAGAPVDAVIDQLVPLLDEGDIVIDAGNSHFEDTRR
+REAALAEKGLHFVGVGVSGGEEGALHGPAIMPGGPEKSYEALGPMLEKIAAQFEGEPCCA
+WVGTDGAGHYVKMVHNGIEYADMQVIGEAYDLLRRVGGLEPAEQAEVFTAWNQTDLASYL
+IEITAEVLAQVDAATGRPLVDVIVDEAGQKGTGRWTAISGLDVGSPVAAIAESVFARSLS
+SQRAVREVARETLAAGVDEEAQRAPQDTDAFVEDVRQALFASKLVAYAQGMDMLAAAAEE
+YGWSLDLGTIASLWRDGCIIRADLLDVIMQAFGGRDTSRHPAPGTRAPGQPLNLLFAPEF
+AQAIAEALPAWRRVVGTAVAAGVPVPVFSSALAYYDGLRADRLPAALVQGQRDYFGAHTY
+LRVDREGSFHTLWSGDRTEVDGEGVPVVMPQPTEGDPTQD
+>1_627
+MTEQTTTVPVGAADIGVTGLAVMGANLARNFARHGYTVALHNRSRARTDQLVAEHGDEGA
+FVATETLAELVQSLAVPRRVLIMVKAGAPVDAVIDQLVPLLDEGDIVIDAGNSHFEDTRR
+REAALAEKGLHFVGVGVSGGEEGALHGPAIMPGGPEKSYEALGPMLEKISAQFEGEPCCA
+WVGTDGAGHYVKMVHNGIEYADMQVIGEAYDLLRRVGGLEPAEQAEVFTAWNQTDLASYL
+IEITAEVLAQVDAATGRPLVDVIVDEAGQKGTGRWTAISGLDVGSPVAAIAESVFARSLS
+SQRAVRQVARETLAAGVDEEAQRAPQDTDTFVEDVRQALFASKLVAYAQGMDMLAAAAEE
+YGWSLDLGTIASLWRDGCIIRADLLDVIMQAFGGRDTSRHPAPGTRAPGQPLNLLFAPEF
+AQAIAEALPAWRRVVGTAVAAGVPVPVFSSALAYYDGLRADRLPAALVQGQRDFFGAHTY
+LRVDREGSFHTLWSGDRTEVDGEGVPVVMPQPTEGDPTQD
+>2_1965
+MTEQTTTVPVGAADIGVTGLAVMGANLARNFARHGYTVALHNRSHGRTDQFVAEHGDEGA
+FVATETLAELVQSLAVPRRVLIMVKAGAPVDAVIDQLVPLLDEGDIVIDAGNSHYEDTRR
+REAALAEKGLHFVGVGVSGGEEGALHGPAIMPGGPEKSYEALGPMLEKISAQFEGEPCCA
+WVGTDGAGHYVKMVHNGIEYADMQVIGEAYDLLRRVGGLEPAEQAEVFTAWNQTDLASYL
+IEITAEVLAQVDAATGRPLVDVIVDEAGQKGTGRWTAISGLDVGSPVAAIAESVFARSLS
+SQREVRAAAREVLQAGVDEAAVPAVTDTDAFVEDVRQALFASKLVAYAQGMDMLAAAAEE
+YGWSLDLGTIASLWRDGCIIRADLLDVIMKAFGGRDTARHPEPGTRAEGQPLNLLFAPEF
+AQAIAEALPAWRRVVGTAVAAGVPVPVFSSALAYYDGLRADRLPAALVQGQRDYFGAHTY
+LRVDREGSFHTLWSGDRTEVDGEGVPVVMPQPAEGDPTQD
+>3_1860
+MTETSTVRGTADIGVTGLAVMGANLARNFARHGYTVALHNRSRAKTDALVAEHGHEGSFV
+ATETLEELVGSLASPRRVLIMVKAGAPVDAVIDQLVPLLDEGDIVIDAGNSHYEDTRRRE
+AALAEKGLHFVGVGVSGGEEGALNGPAIMPGGPEESYAALGPLLEDIAASYDGEPCCAWI
+GTDGAGHYVKMVHNGIEYADMEVIGEAFDLLRRVAGIEPAEQAQVFDAWNQTELASYLIE
+ITAEVLQQVDAATGAPLVDVIVDEAGQKGTGRWTAISGLDVGSPVAAIAESVFARSLSAQ
+TEVRATAREVLAAGVESAPAVSPQDRDAFVEDVRQALFASKLVAYAQGLDMLSAAAIEYG
+WALDLGTIASLWRDGCIIRADLLDVIMKAFGGRDTSRHPEPGTRAEGQPLNLLFAPEFAQ
+AMAEALPAWRRVVGAAVAAGVPVPVFSSALAYYDGLRADRLPAALIQGQRDFFGAHTYRR
+TDRDGSFHTLWSGDRTEVDGDGAPVVMPQPAEGDPTDETAR
+>4_848
+MTEQTTTVPVGAADIGVTGLAVMGANLARNFARHGYTVALHNRSRARTDQLVAEHGDEGA
+FVATETLAELVQSLAVPRRVLIMVKAGAPVDAVIDQLVPLLEEGDIVIDAGNSHYEDTRR
+REAALAEKGLHFVGVGVSGGEEGALHGPAIMPGGPEKSYEALGPMLEKISAQFEGEPCCA
+WVGTDGAGHYVKMVHNGIEYADMQVIGEAYDLLRRVGGLEPAEQAEVFTAWNQTDLASYL
+IEITAEVLAQVDAATGRPLVDVIVDEAGQKGTGRWTAISGLDVGSPVAAIAESVFARSLS
+SQRAVREVARETLAAGIDEDAQRVPQDTDAFVEDVRQALFASKLVAYAQGMDMLAAAAEE
+YGWSLDLGTIASLWRDGCIIRADLLDVIMQAFGGRDTSRHPAPGTRAPGQPLNLLFAPEF
+AQAIAEALPAWRRVVGTAVASGVPVPVFSSALAYYDGLRADRLPAALVQGQRDYFGAHTY
+LRVDREGSFHTLWSGDRTEVDGEGVPVVMPQPTEGDPTQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000811.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000811.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7ceb47a9ed3255888acccd93d296c35f96b7bca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000811.fa
@@ -0,0 +1,32 @@
+>0_905
+MSGRVLQVEADGGSRGNPGVAGYGALVRDPATGEILRTDAAPLGKASNNVAEYSGLVAGL
+RMARDLDPEARVHVLMDSKLVVEQMSGRWKIKHDDMRRLAAEARSVLPPERVSYEWIPRN
+RNKDADRLSNEAMDAGARGEQWDAGASEVPVAAPAKASTTSASAVAESGLEADADVRAVE
+ADGPDAVASPEDATPAPAPTGRLHHVEIWVADLAAAEASLGWLFGELGYVPGEGWAEGRT
+YQGAGEYLVLEAGPDVAAGAHERTRPGLNHLAFRAGSRARVDELTAAARDRGFRLLFEDR
+HPHAGGPDHYAAYLETADGFEVELVAVED
+>1_633
+MSGRVLQVEADGGSRGNPGVAGYGALVRDPATGEILRTDAAPLGKASNNVAEYSGLVAGL
+RMARDLDPEARVHVLMDSKLVVEQMSGRWKIKHDDMRRLAAEARAVLPPERVSYEWIPRN
+RNKDADRLSNEAMDAGARGGQWDAGASEVPVAAPAEASTTSTSAVAESGLDADADVRAVE
+ADGPDAVASPEDATPGPAPTGRLHHVEIWVADLAAAEASLGWLFGELGYVPGEGWAEGRT
+YQGAGEYLVLEAGPDVAAGAHERTRPGLNHLAFRAGSRSRVDELTAAARGRGFRLLFEDR
+HPHAGGADHYAAYLETADGFEVELVAVED
+>2_1958
+MLEADADARAVEAEAPDAVGQDAAAPQAPTPTGRLHHVEVWVADLAAAEAGLGWLLGELG
+YVLGEGWAEGRTYQGAGEYIVLESGPDVVGGAHERTRPGLNHLAFRAGTRARVDELTAAA
+RERGFRLLFADRHPHAGGADHYAAYLEAPDGFEVELVAVED
+>3_1854
+MAERTLQVEADGGSRGNPGVAGYGALVRDPATGDVLMTDAAPLGKASNNVAEYSGLIAGL
+EMAKTLDPDARVHVKMDSKLVVEQMSGRWKIKHEDMRRLAQQARAVLPPSRVTYEWIPRA
+QNKDADQLSNEAMDAGARGGRWDAGASKVPVTAPSAPTSAGAPAAEPDKEPLEEPPVPEE
+RTRPRPVGRLHHVEIWAADLDAAVESLGWLFEQVGYAPGDAWAEGRVYRGAGDYLVLESG
+RDVAPGGHDRLRPGLNHLAFRAGTRADVDRIAAQAADHGFTLLFEDRHPFAGGRDHYAAY
+LETADGFEVELVADPA
+>4_854
+MSGRVLQVEADGGSRGNPGVAGYGALVRDPATGEILRTDAAPLGKASNNVAEYSGLVAGL
+RMARDLDPEARVHVLMDSKLVVEQMSGRWKIKHEDMRRLAAEARSVLPPERVSYEWIPRN
+RNKDADRLSNEAMDAGARGEQWDAGASEVPVAAPAAAGSTAAEASTTSASAVAESCLDAD
+ADVRAVEADGPEAVASPGDATPAPAPTGRLHHVEIWVADLAAAEASLGWLFGELGYVPGE
+GWAEGRTYQGAGEYLVLEAGPDVAAGAHERTRPGLNHLAFRAGSRARVDELTAAARDRGF
+RLLFEDRHPHAGGPDHYAAYLETADGFEVELVAVED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000814.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000814.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dca16eeb73c4b28ec0b2195bafc50f50f143bda8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000814.fa
@@ -0,0 +1,50 @@
+>0_908
+MADTASTQTPEWNTQQKLAEKMVPLLGTLYREHNVVTSIYGRSLVNRGVIDIIKAHRYAR
+RVQEAPLSVESTYPLVEAMAAMDLGAATIDLAELAAKHKASGQDVQAFLDAELAEVKGKA
+GEGLGETQDVVLYGFGRIGRLLARILLDHAGGGSKLRLRAVVVRKNSEDDLIKRASLLRR
+DSIHGPFDGTIVVDEDRDVITANGTEIQVIYSNDPTTVDYTSYGIKDALVVDNTGRWRDD
+EGLSQHLQAKGAAKVLLTAPGKGEMKNIVFGVNSDDITPQDTIVSAASCTTNGITPVLKV
+IQDDYGIDHGHVETVHAYTNDQNLVDNFHKGARRGRAAGMNMVLTETGAAKAVAKALPEL
+KGKLSGNAIRVPTPDVSMAILNLELTTPTSVEELNARLKQESLTGPLRGQVGYVDSPEVV
+STDFVGSDRAGVVDGLATLVNNDGKNAILYVWYDNEYGYSHQVIRVVEKMAGQQVPAFPQ
+A
+>1_636
+MADTASTQTPEWNTQQKLAEKMVPLLGTLYREHNVVTSIYGRSLVNRGVIDIIKAHRYAR
+RVQQAPLSVESTYPLVEAMAAMDLGAATIDLAELAAKQKASGQDVQAFLDAELAEVKGKA
+GEGLGETQDVVLYGFGRIGRLLARILLDHAGGGSKLRLRAVVVRKNSEDDLIKRASLLRR
+DSIHGPFDGTIVVDEDRDVITANGTEIQVIYSNDPTTVDYTSYGIKDALVVDNTGRWRDD
+EGLSQHLQAKGAAKVLLTAPGKGEMKNIVYGVNSDDITPQDTIISAASCTTNGITPVLKV
+IQDDYGIDHGHVETVHAYTNDQNLVDNFHKGARRGRAAGMNMVLTETGAAKAVAKALPEL
+KGKLSGNAIRVPTPDVSMAILNLELTKPTSVGELNARLKQESLTGPLRGQVGYVDSPEVV
+STDFVGSDRAGVVDGLATLVNNDGKNAILYVWYDNEYGYSHQVIRVVEKMAGQQVPAFPQ
+A
+>2_1954
+MADTASTQTPEWNTQQELAERMVPLLGSLYRENNVVTSIYGRSLVNRGVIDIIKAHRYAR
+RVQDAPLSVAATYPLVEAMAAMDLGAANVDLAELAARHKESGQEVQAFLDAELAEVKGKG
+GEGLGEPQDVVLYGFGRIGRLLARILLDHAGGGSKLRLRAVVVRKNSEDDLVKRASLLRR
+DSIHGPFDGTIVVDEDRNVITANGTEIQVIYSNDPTTVDYTAHGIKDALVIDNTGRWRDD
+EGLSQHLQAKGVKKVLLTAPGKGEMKNIVFGVNSDDITPEDTIVSAASCTTNGITPVLKV
+IQDDYGIDHGHVETVHAYTNDQNLTDNFHKGSRRGRSAGLNMVLTETGAAKAVAKALPEL
+KGKLSGNAIRVPTPDVSMAILNLELNKATSVEELNARLKQESLTGVLRGQVGYVDSPEVV
+STDFVGSDRAGVVDGLATLVNNEGKNAILYVWYDNEYGYSHQVVRVVSGPRPGRDQAPSA
+RPWSASGPCCSIASASSSSSCPKGSSSVPGSQVTPGTFMRSARCARFQRRCHLPSRRLT
+>3_1851
+MADTASTQTPEWNTQQKLAEKMVPLLGTLYREHNVVTSIYGRSLVNRGVIDIIKAHRYAR
+RVQEAPLSVEATFPLVEAMAGMDLGAANIDLAELAAKQQASGQDVQAFLDAELADVTGKS
+GEGLGETQDVVLYGFGRIGRLLARILLDHAGGGSKLRLRAVVVRKNSEDDLIKRASLLRR
+DSIHGPFDGTIVVDEDRNVITANGTEIQVIYSNDPTTVDYTSYGIKDALVVDNTGRWRDV
+EGLSQHLQAKGATKVLLTAPGKGDMKNIVFGVNSDDILDEDTIVSAASCTTNGITPVLKV
+IQDEYGVQHGHVETVHAYTNDQNLVDNFHKGARRGRAAGMNMVITETGAAKAVAKALPEL
+KGKLSGNAIRVPTPDVSMAIINIALEKPTSVEEINARLKQESLTGDLRGQIGYVDSPEVV
+STDFVGSDRAGVVDGLATIVNNEGKNAILYVWYDNEYGYSHQVVRVVEKMAGQQVPSFPK
+A
+>4_857
+MADTASTQTPEWNTQQNLAEKMVPLLGTLYREHNVVTSIYGRSLVNRGVIDIIKAHRYAR
+RVQEAPLSVESTYPLVEAMAAMDLGAATVDLAELAAKQKASGQDVQAFLDAELAEVKGKA
+GEGLGETQDVVLYGFGRIGRLLARILLDHAGGGSKLRLRAVVVRKNSEDDLIKRASLLRR
+DSIHGPFDGTIVVDEDRDVIIANGTEIQVIYSNDPTTVDYTSYGIKDALVVDNTGRWRDD
+EGLSQHLQAKGAAKVLLTAPGKGEMKNIVFGVNSDDITPEDTIVSAASCTTNGITPVLKV
+IQDDYGIDHGHVETVHAYTNDQNLVDNFHKGARRGRAAGMNMVLTETGAAKAVAKALPEL
+KGKLSGNAIRVPTPDVSMAILNLELNTPTSVEELNARLKQESLTGPLRGQVGYVDSPEVV
+STDFVGSDRAGVVDGLATLVNNDGKNAILYVWYDNEYGYSHQVIRVVEKMAGQQVPAFPQ
+A
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000818.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000818.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ddabe374a605b783fa0c51eb7c0fc92eae3346e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000818.fa
@@ -0,0 +1,55 @@
+>0_922
+MSVSTPRPSGSTAHRPEYVGVGGLRADPQVAGADWWPILVGTLGSLLLVVGSYSVGWLAS
+ASPINRWQWLIPWRTQETGVLAGAALLTLGCWVMFWAWLRLGQTIRPFGRGALRTVNLAT
+VLWCLPQVVALPIFSRDIFAYVGQGRLMEAGQDPYVDTISSLSNWFQLGADATWADSETP
+YGPIFLWIEQAVVAISGDMNPDLAIFLFRLVAVAGVALIMVFVPLLARRMGVNDAWAQWI
+SVANPLFTISFVASGHNDALMVGLALAGTWCALRAGHPLRPQRPGQSVAWGVAGVVLVTL
+SLGIKPITLVLLPFIGLLWAGPTARWPRRFAFWALTAGISFGLMALVGVLNGFGFGWVAV
+MVGTGTGTVPWGPIGMLSLITVGASELLGQGADVQAVEGVYKTAGRVLSVLIVLALMFLG
+RQDRVMTRMTWAFTALVILSPIIQPWYLLWLLPFFAVIGIRDNWQIKWVVFTVGYFLAFG
+ASDQLFTWQFLDIADQVKAVSLIVSAVCLLWILVVDRRTSRFVKDHWHVRPAVRAGLARL
+RGAPRPVEPGE
+>1_644
+MSVSTPRPSGSTAHRPEYVGVGGLRADPQVAGADWWPILVGTLGSLLLVVGSYSVGWLAS
+ASPINRWQWLIPWRTQETGVLAGTVLLTLGCWVMFWAWLRLGQTIRPFGRGALRTVNLAT
+VLWCLPQVVALPIFSRDIFAYVGQGRLMVAGQDPYVDTISSLSNWFQLGADATWADSETP
+YGPIFLWIEQAVVAISGDMNPDLAIFLFRLVAVAGVALIMVFVPLLARRLGVNDAWAQWI
+SAANPLFTISFVASGHNDALMVGLALAGTWCALRAGHPLRPQRPGQSVAWGVAGVVLVTL
+SLGIKPITLVLLPFIGLLWAGPTARWPRRFAFWALTAGISFGLMALVGVLNGFGFGWVAV
+MVGTGTGTVPWGPIGMLSLITVGASELLGQGADVQAVEGVYKTAGRVLSVLIVLALMFLG
+RQDRVMTRMTWAFTALVILSPIIQPWYLLWLLPFFAVIGIRDNWQIKWVVFTVGYFLAFG
+ASDQLFTWQFLDIADQVKAVSLIVSAVCLLWILVVDRRTSRFVKDHWHVRPAVRAGLARL
+RGAPRPVEPGE
+>2_1889
+MSVTTPRPSGSTAGRPAHIGVGGLRADPKVAGGNTWPILVGTLGSLLLVAGSFSVGWLAS
+ASPINRWQWLIPWRTQETGVIVGTILLTLGCWVMFWAWLRLGQTVRPFGRGSLRTVNLAT
+ALWCLPQVFALPIFSRDIFAYVGQGRLMVAGQDPYEDTISSLSNWFQLGADATWADSETP
+YGPIFLWIEQAVVAVSGDMNPDLAIFLFRLVAVAGVVLIMVFVPLLARRLRVNGAWAQWV
+SAANPLFTISFVASGHNDALMVGLALAGTWCALRAGHPLRPQSAARSAAWGVAGVVLVTL
+SLGIKPITLVLLPFIGLLWAGPTAGWIRRFVLWFLTAGISFGIMAVVGALNGFGFGWVAV
+MVGTGTGTVPWGPIGILSLLTVGISELVGQGADQQAVEGVYKTAGRVLSVLIVLALMFLG
+RQDRVLTRMTWAFTALVILSPIIQPWYLLWLLPFFAVIGIRDDWQIKWVVFTVGYFLAFG
+ASDQLFTWQFLAIADQVKAISLIVSAVCLAWILVVDRRTSRFVKDHWHVRPAVRAGLARL
+RRAPRTPEPGE
+>3_1840
+MGVPAAGPSGSTAFRPEYIGVGGLRADPQVAGRPLWPILVGLLGSLMLVAGSFSVGWLAS
+ASPINRWQWLIPWRTQESGVMTGTVLLTLGCWVMFWAWLRLGQTVRPFGPGALRTVNVAT
+ALWCLPMVFALPIFSRDIFAYVGQGRLMVNGQDPYTDAISSLNNWFQLGADATWAGSETP
+YGPVFLWIEEVVVRISGDMNPDLAIFLFRLVAVVGVVLTMVFVPLLARRLSVNGAWAQWV
+SAANPLFTVSFVASGHNDALMVGLALAGTWCALRAGHPRGGQSTASHVGWGVAAVVLVTA
+SLGVKPITLVLLPFIGLLWAGPRAGWSRKFVYWAVTGGLSLALMVLVGRLNGFGFGWLEV
+MAGTGSGTSPWAPVGMMSIATRVLMEVLQLGPDLQAIEGFYKSVCRLLSVLIVLALMFLG
+RQDRVFTRMTWAFTTLVVLSPIVQPWYLLWLLPFFAVIGLRDNWQIKWVVFTVGYFLAFG
+AMDQLFTWQFLDIAEEVRAASLLVSGVSLVWILAVDRKTSRFIKDHWHVRPALREGVRRL
+RRRPTGGAAAPHTRPHPVERLGESGSEDAAARGAR
+>4_868
+MSVSTPRPSGSTAHRPEYVGVGGLRADPQVAGADWWPILVGTLGSLLLVVGSYSVGWLAS
+ASPINRWQWLIPWRTQETGVLAGTALLTLGCWVMFWAWLRLGQTIRPFGRGALRTVNLAT
+VLWCLPQVVALPIFSRDIFAYVGQGRLMEAGQDPYVDTISSLSNWFQLGADATWADSETP
+YGPIFLWIEQAVVAISGDMNPDLAIFLFRLVAVAGVALIMVFVPLLARRLGVNGARAQWI
+SAANPLFTISFVASGHNDALMVGLALAGTWCALRAGHPLRPQRPGQSVAWGVAGVVLVTL
+SLGIKPITLVLLPFIGLLWAGPTARWPRRFAFWALTAGISFGLMALVGVLNGFGFGWVAV
+MVGTGTGTVPWGPIGMLSLITVGASELLGQGADVQAVEGVYKTAGRALSVLIVLALMFLG
+RQDRVMTRMTWAFTALVILSPIIQPWYLLWLLPFFAVIGIRDNWQIKWVVFTVGYFLAFG
+ASDQLFTWQFLNIADQVKAVSLIVSAVCLLWILVVDRRTSRFVKDHWHVRPAVRAGLARL
+RGAPRPVEPGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000826.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000826.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ccb69760e039af7eff030ec82725c543980a6dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000826.fa
@@ -0,0 +1,34 @@
+>0_935
+MPEGHSVHRLARQFTDVFGGRRIRATSPQGRFAEGAALLDGQVLKRARAHGKHFFADVSG
+GHVLHVHLGMYGAWTFGGDQDFAAASSIGAPRRIGEREVHDDGAPAAEPARDADGWVQPP
+PPAATVRLRLRAEHGWADLIGASRCRALTPAEAADVVAGLGPDPLSDDDPAPFYDLARRT
+RRPIGVVLMDQAAVSGIGNIFRAEALFRVGIDPWRPARDVSASELESLWADNAALMREGV
+RLGRIVTTRPEHRPGIPAEAAWPEHASYVYQRQGLACLVCGRETIVVEEMAARKLYRCLT
+CQS
+>1_657
+MPEGHSVHRLARQFTDVFGGRRIRATSPQGRFAEGAALLDGQVLKRARAHGKHFFADVSG
+GHVLHVHLGMYGAWTFGGDQDFAAASSIGAPRRIGEREVHDDGAPAAEPARDADGWVQPP
+PPASTVRLRLRAEHGWADLIGANRCRALTRAEAADVVAGLGPDPLNDDDPAPFYDLARRT
+RRPIGVVLMDQGAVSGIGNIFRAEALFRAGIDPWRPAREVSAPDLAFLWADNAALMREGV
+RLGRIVTTRPEHRPGIPAEAAWPEHANYVYQRQGLACLVCGRETIVVEEMAARKLYRCLT
+CQS
+>2_1878
+MPEGHSIHRLARQFTDVFGGWPIRASSPQGRFAEGAARMDGQVLEAARAHGKHFFADLAD
+GHVLNVHLGMYGAWSFGGDERFDAASSIGAPRRIGEREVHADGAAAAEPDRDDDGWVLPP
+PPVPTVRLRVRAEHGWADLIGASTCRLLTPAEAGDVVAKLGPDPLNDDDPAPFLDLAGRT
+RRPIGAVLMDQAAVGGIGNIFRAEALFRAGLDPWRPSNAVPREVLRRLWSDNAELMREGV
+RLGRIVTTRPEHRPGVPAEQAWPEHANYVYQRQGSPCLVCGQDAIVVEGMAARKLYRCTV
+CQR
+>3_1825
+MPEGHSIHRLARQVQDVFGGQALAASSPQGRFADGAALLDGRVLERAWAHGKHFFADIEG
+GLTLNVHLGMYGAMTFGGDEAFAAASSIGAPRRIGETEDHGALAAAEPPPARPTVRLRLR
+SAHGWADLIGAGTCRVLTPQELAEVTSKLGPDPLNDDDPAAFVARAARTGRPVGVVLMDQ
+SMVGGIGNIYRAEVLFRAGLDPWTPARDVGADVLAALYADAQALMRDGVRLGRIVTTAPE
+HRPGVAAEDAWPEHANYVYRRQGMPCRVCGQDAIVREEMAARNLFRCTDCQR
+>4_878
+MPEGHSVHRLARQFTDVFGGRRIRATSPQGRFAEGAALLDGQVLKRARAHGKHFFADVSG
+GHVLHVHLGMYGAWTFGGDQDFAAASSIGAPRRIGEREVHDDGAPAAEPARDADGWVQPP
+PPAATVRLRLRAEHGWADLIGASRCRALTPAEAADVVAGLGPDPLSDDDPAPFYDLARRT
+RRPIGVVLMDQAAVSGIGNIFRAEALFRAGIDPWRPAREVSASDLAFLWADNAALMREGV
+RLGRIVTTRPEHRPGIPAESAWPEHANYVYQRQGLACLVCGRETIVVEEMAARKLYRCLT
+CQS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000841.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000841.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f9838cd4f446fcfa344e4dc16b68879156ecea6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000841.fa
@@ -0,0 +1,30 @@
+>0_950
+MTVVMEDVGKSFGGPTPVLEDVSVRIEPGEFVCLLGASGCGKSTLLNLVARLEAPTAGVV
+KTPREGAAFMFQDAALFPWLTARGNIELALRFAGVAAGERRERAGELLRLVHLDDAADLR
+PHQLSGGMRQRVALARALAQDRPLLLMDEPFAALDAITRDLLHGELERVWRQTGRTVVFV
+THNVAEAVRLGQRVLLLSSRPGRVVAEWDVPAAARHDAPAAAALTAAITARLGQEIRRHA
+H
+>1_673
+MTVVMEDVGKSFGGPTPVLEDVSVRIEPGEFVCLLGASGCGKSTLLNIIARLEAPTAGVV
+KTPREGAAFMFQDAALFPWLTARGNIELALRFAGVAAGERRERAGELLRLVHLDDAADLR
+PHQLSGGMRQRVALARALAQDRPLLLMDEPFAALDAITRDLLHGELERVWRQTGRTVVFV
+THNVAEAVRLGQRVLLLSSRPGRVVAEWDVPAAARHDAPAAAALTAAITARLGQEIRRHA
+H
+>2_1862
+MTVVMEDVGKSFGGPTPVLEDVSVRIEPGEFVCLLGASGCGKSTLLNLIARLEAPTAGVV
+KAPRQGAAFMFQDAALFPWLTARGNIELALRFAGVPAAERRGRAGELLRLVHLGDAADLR
+PHQLSGGMRQRVALARALAQDRPLLLMDEPFGALDAITRDLLHVELERVWRQTGRTVVFV
+THNVAEAVRLGQRVLLLSSRPGRVVAEWDVPAAARHDAPAAAALTAAITARLGQEIRRHA
+H
+>3_1808
+MTVVMEDVGKSFGGPTPVLEDVSVRIEPGEFVCLLGASGCGKSTLLNLIARLEAPTAGVV
+KTPREGAAFMFQDAALFPWLTARGNIELALRFAGVPAAGRRERAGELLRLVHLGDAADLR
+PHQLSGGMRQRVALARALAQDRPLLLMDEPFAALDAITRDLLHVELERVWRQTGRTVVFV
+THNVAEAVRLGQRVLLLSSRPGRVVAEWDVPAAAHHDAPAAAALTAAITARLGQEIRRHA
+H
+>4_893
+MTVVMEDVGKSFGGPTPVLEDVSVRIEPGEFVCLLGASGCGKSTLLNLVARLEAPTAGVV
+KTPREGAAFMFQDAALFPWLTARGNIELALRFAGVAAGERRERAGELLRLVHLDDAADLR
+PHQLSGGMRQRVALARALAQDRPLLLMDEPFAALDAITRDLLHGELERVWRQTGRTVVFV
+THNVAEAVRLGQRVLLLSSRPGRVVAEWDVPAAARHDAPAAAALTAAITARLGQEIRRHA
+H
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000843.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000843.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9961ad7cd698eaea94dbe4af39871a14449ae6f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000843.fa
@@ -0,0 +1,45 @@
+>0_952
+MTASDLYPTSLRLLGRPVLIVGGGRVAGRRVGALLDAGALVSVVAPEPGEEVERLAAAGL
+LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVV
+RAGDVTVAVNAGGDPRRARALKDAIALALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL
+ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA
+RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSAVSVPAAAGIPVTHRGVA
+TGFTLVTGHEELAEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD
+QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGAPAAGIPAPISTLNPTSEGA
+RA
+>1_675
+MTASDLYPTSLRLLGRPVLMVGGGRVAGRRMGALLDAGALVTVVAPEPGEEVERLAAAGL
+LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVV
+RAGDVTVAVNAGGDPRRARALKDAITLALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL
+ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA
+RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSAVSVPAAAGIPVTHRGVA
+TGFTLVTGHEELSEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD
+QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGAPAAGVPAPISTLNSTSEGA
+RA
+>2_1860
+MTASDLYPTSLRLLGRPVLMVGGGRVAGRRVGALLDAGALVTVVAPEPGEEVERLAAAGL
+LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVV
+RAGDVTVAVNAGGDPRRARALKDAITLALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL
+ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA
+RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSAVSVPAAAGIPVTHRGVA
+TGFTLVTGHEELSEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD
+QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGARAAGVPAPILTLNPTSEGA
+RA
+>3_1806
+MTASDLYPTSLCLLGRPVLIVGGGRVAGRRVGALLDAGALVTVVAPEPGEEVERLAAAGL
+LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVA
+RAGDVTVAVNAGGDPRRARALKDAITLALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL
+ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA
+RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSAVSVPAAAGIPVTHRGVA
+TGFTLVTGHEELAEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD
+QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGAPAAGVPAPISTLNPTSEGA
+RA
+>4_895
+MTTSDLYPTSLRLLGRPVLVVGGGRVAGRRMGALLDAGALVTVVAPKPGEEVERLAAAGL
+LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVV
+RAGDVTVAVNAGGDPRRARALKDAITLALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL
+ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA
+RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSVVSVPAAAGIPVTHRGVA
+TGFTLVTGHEELSEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD
+QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGAPAAGIPAPILTLNPTSEGA
+RA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000844.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000844.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3d66a9d496354c091f898d8392439cc04e58b5c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000844.fa
@@ -0,0 +1,100 @@
+>0_955
+MYPLASSAPDGRTPASPRFPEIERRILAYWDEDGTFQASIDQRPTRNEDGSQNEFVFYDG
+PPFANGLPHYGHLLTGYVKDLVARYQTQQGRRVERRFGWDTHGLPAELEAMKQLGMTDKS
+EIEAMGIDTFNDACRSSVLKYTDQWQDYVTRQARWVDFENDYKTLTPDFMESVIWAFSEL
+HRKGLTYRGFRVLPYCWNDETPLSNHELRMDDDVYKMRQDPSVTVTFPITGLPADPALVP
+DGGADAALAAHLAGVHVLAWTTTPWTLPTNAALAVGPQIQYAVVPAGPEGATADGDRFLL
+AVDLVGAHARELGYADADAARAAVTETIPGARLGGLAYAPLFTDVFDAHRGETFTVNGRD
+LGVEGAHRILVDDYVSTEDGTGVVHQAPAYGEDDQRVCEANGIPVMLSVDSGARFLPLFA
+REDVGRGDLREIAGVQVFEANRTIIRALRALGRVAREASYEHSYPHCWRCRTPLIYRAVT
+SWYVKVTQIKERMLELNEEITWIPGNVKHGQFGTWVANARDWSISRNRYWGSPIPVWESD
+HPDFPRQEVYGSLAEIEEAFGRLPRNAEGEVDLHRPWVDDLTRPHPDPEAAAAGAVMRRV
+EDVLDVWFDSGSMPYAQVHYPFERADWFPTHNPADFIVEYIGQTRGWFYTMHILATALFD
+RPAFSHVISHGIVLGSDGQKMSKSLRNYPDVTEVLDRDGADAMRWFLMASPILRGGNLIV
+TEEGIREGVRQVLLPAWNAYHFFTLYANTAHDGGARPEGYRAQERHTAEDPLDQYILAAA
+GRMLREVKAGLDAYEVSDATDALRGFMDTLTNWYIRRSRERFFDEDTVAFDVLYTVLEAF
+TRAAAPLMPLIAEEIWRGLTGGRSVHLTDYPDADLFPHGPEADSLVARMDAVRRISSAGS
+ALRKGAGRRVRLPLPRLSVVVPDAAGLEGTYARIVADELNLKDVELTELSEEAIARYGIG
+TELKLNFRELGKAFGRQVPLVKQAVDAGAYEETAEGLAVTLADGETVTLAPALYELRTVS
+TGAPEGTAVGVLPGTAGFLVLDTEVSAELAAEGTARDVVRAVQAARKDAGLDVSDRVRTR
+IEGPTAVVAALEAHRGLVAEETLTVDLELVDSGAADPRKDPADDAMKTVAVSVAKADA
+>1_678
+MYPLASSAPDGRTPASPRFPEIERRILAYWDEDGTFQASIDQRPAFNEDGSQNEFVFYDG
+PPFANGLPHYGHLLTGYVKDLVARYQTQQGRRVERRFGWDTHGLPAELEAMKQLGMTDKS
+EIEAMGIDKFNDACRSSVLKYTDQWQDYVTRQARWVDFENDYKTLTPDFMESVIWAFSEL
+HRKGLTYRGFRVLPYCWNDETPLSNHELRMDDDVYKMRQDPSVTVTFPITGLPADPALVP
+DGGADAALAAHLAGVHVLAWTTTPWTLPTNAALAVGPQIQYAVVPAGPEGATADGDRFLL
+AVDLVGAHARELGYADADAARAAVTETIPGARLGGLAYAPLFTDVFDAHRGETFTVNGRD
+LGVEGAHRILVDDYVSTEDGTGVVHQAPAYGEDDQRVCEANGIPVLLSVDSGARFLPLFA
+REDVGRGDLREIAGVQVFEANRTIIRALRALGRVAREASYEHSYPHCWRCRTPLIYRAVT
+SWYVKVTQIKERMLELNEEITWIPGNVKHGQFGTWVANARDWSISRNRYWGSPIPVWESD
+HPDFPRQEVYGSLAEIEEAFGRLPRNAQGEVDLHRPWVDDLTRPHPDPEAAAAGAVMRRV
+EDVLDVWFDSGSMPYAQVHYPFERADWFPTHNPADFIVEYIGQTRGWFYTMHILATALFD
+RPAFSHVISHGIVLGSDGQKMSKSLRNYPDVTEVLDRDGADAMRWFLMASPILRGGNLIV
+TEEGIREGVRQVLLPAWNAYHFFTLYANTAHDGGARPEGYRAQERHTAEDPLDQYILAAT
+GRMLREVKTGLDAYEVSDATDALRGFMDTLTNWYIRRSRERFFDEDTVAFDVLYTVLEAF
+TRAAAPLMPLIAEEIWRGLTGGRSVHLTDYPDADLFPHGPEADSLVARMDAVRRISSAGS
+ALRKGAGRRVRLPLPRLSVVVPDAAGLEGTYARIVADELNLKDVELTELSEEAIARYGIG
+TELKLNFRELGKAFGRQVPLVKQAVDAGAYEETAEGLAVTLADGETVTLAPALYELRTVS
+TGAPEGTTVGVLPGTAGFLVLDTEVSAELAAEGTARDVVRAVQAARKDAGLDVSDRVRTR
+IEGPTAVVAALEAHRGLVAEETLTVDLELVDSGAADPRKDPADDAMKTVAVTVAKADA
+>2_1857
+MYPLASSAPDGRTPASPRFPEIERRILAYWDEDGTFQASIDQRPALNEDGSQNEFVFYDG
+PPFANGLPHYGHLLTGYVKDLVARYQTQQGRRVERRFGWDTHGLPAELEAMKQLGMTDKS
+EIEAMGIDTFNDACRSSVLKYTDQWQDYVTRQARWVDFENDYKTLTPDFMESVIWAFSEL
+HRKGLTYRGFRVLPYCWNDETPLSNHELRMDDDVYKMRQDPSVTVTFPITGLPADPALVP
+DGGADAALAAHLAGVHVLAWTTTPWTLPTNAALAVGPQIQYAVVPAGPEGATADGDRFLL
+AVDLVGAHATELGYADADAARAAVTETIPGARLGGLAYEPLFTDVFDAHADETFTVNGRD
+LGVEGAHRILVDDYVSTEDGTGVVHQAPAYGEDDQRVCEANGIPVLLSVDSGARFLPLFA
+REDVGRGDLREIAGVQVFEANRTIVRALRGLGRVAREASYEHSYPHCWRCRTPLIYRAVT
+SWYVKVTQVKERMLELNEEITWIPGNVKHGQFGTWVANARDWSISRNRYWGSPIPVWESD
+HPDYPLQEVYGSLAEIEEAFGRLPRNAEGEVDLHRPWVDDLTRPHPDPEAAAAGAVMRRV
+EDVLDVWFDSGSMPYAQVHYPFERADWFPTHNPADFIVEYIGQTRGWFYTMHILATALFD
+RPAFSNVISHGIVLGSDGQKMSKSLRNYPDVTEVLDRDGADAMRWFLMASPILRGGNLVV
+TEEGIREGVRQVLLPAWNAYHFFTLYANTAHDGGARPDGYRAQERHTAEDPLDQYILAAT
+GRMLREVKTGLDAYEVSDATDALRGFMDTLTNWYIRRSRQRFFDEDTAAMDVLYTALEAF
+ARAAAPLMPLVAEEIWRGLTGGRSVHLTDYPDADLFPHGPEADSLVARMDAVRRISSAGS
+ALRKGAGRRVRLPLPRLSVVVPDAEGLEGTYARIVADELNLKDVSLTELSDEAIARYGIG
+TELKLNFRELGKVYGKQVPLVKKAVDAGSYEETADGLAVTLADGATVTLDPALYELRTVS
+TGAPEGTAVGVLPGAAGFLVLDTEVSAELAAEGTARDVVRAVQAARKDAGLDVSDRVRTR
+IDGPAAVVAALEAHRDLVAEETLTVELELVDSGEADPRKDPADDAMKTVAVTVAKADA
+>3_1803
+MYPLASTDPAGATPASPLLPEIEQRILRYWDEDGTFQASIDARPAVNEDGSQNEFVFYDG
+PPFANGLPHYGHLLTGYVKDLVARYQTQQGRRVERRFGWDTHGLPAELEAMKQLGMTDKS
+EIEAMGIDRFNDACRSSVLKYTEEWRRYVTRQARWVDFDNDYKTLTPDFMESVIWAFSEL
+HRKGLTYRGFRVLPYCWHDETPLSNHELRMDDDVYKMRQDPSVTVSFPILGLPDDAALVP
+AGGADAALADELAGVHVLAWTTTPWTLPTNAALAVGPEIEYAVVPAGPEGATVAAAERFL
+LAVDLVGAHAKELGYADADAARAAVERTVLGARLGGLRYEPLFTDVFEAHAGETFPVGAR
+TLTLDGVHRILVDDYVSTDDGTGVVHQAPAYGEDDQRVCEANGIPVLLSVDEGARFLPLF
+AREGQGRGDLKDIAGVQVFEANRTIIRALRALGRIAREASYEHSYPHCWRCRTPLIYRAI
+TSWYVSVTKVKDRMLELNEDITWIPGNVKHGQFGTWVANARDWSISRNRYWGSPIPVWES
+DHPDYPLQEVYGSLAELEEAFGRLPRNADGEVDLHRPWIDDLTRPHPDPEAAAAGATMRR
+VEDVLDVWFDSGSMPYAQVHYPFERADWFPTHNPADFIVEYIGQTRGWFYTMHILATALF
+DRPAFSHVISHGIVLGSDGQKMSKSLRNYPDVTEVLDRDGSDAMRWFLMASPILRGGNLI
+VTEEGIREATRQVILPLWNAWHFFTLYANTAHDGGARPEGYRASERHTAEDPLDQYVLAA
+CGTMLRQVKAALDAYEVSDAADALRAFMDTLTNWYIRRSRERFFAEDTAAMDVLSTVLEA
+FTRAAAPLLPLVAEEIWRGLTGGRSVHLTDYPDADLFPHGPEADALVARMDLVRSITSAG
+SALRKGAKRRVRLPLAAMSVVVPDAAALEGTFTRIVADELNLKEVRLTELSEEAISRYGI
+GTELKLNFRELGKHFGRQVPLIKKAVDAGAYAEGEQGLDVTLADGAVVTLAPELYELRTV
+STGAPEGTAVGVLPGGGFLVLETAVSAELAAEGVARDVIRAVQAARKDAGLDVADRVRTR
+IEGPAPVVAALESHRDLVAQETLTVELDLVDSGAADPRRDPADDAMKTVAVAVAKAQA
+>4_898
+MYPLASSAPDGRTPASPRFPEIERRILAYWDEDGTFQASIDQRPTRNEDGSQNEFVFYDG
+PPFANGLPHYGHLLTGYVKDLVARYQTQQGRRVERRFGWDTHGLPAELEAMKQLGMTDKS
+EIEAMGIDTFNDACRSSVLKYTDQWQDYVTRQARWVDFENDYKTLTPDFMESVIWAFSEL
+HRKGLTYRGFRVLPYCWNDETPLSNHELRMDDDVYKMRQDPSVTVTFPITGLPADPALVP
+DGGADAALAAHLAGVHVLAWTTTPWTLPTNAALAVGPQIQYAVVPAGPEGATADGDRFLL
+AVDLVGAHARELGYADADAARAAVTETIPGARLGGLAYAPLFTDVFDAHRGETFTVNGRD
+LGVEGAHRILVDDYVSTEDGTGVVHQAPAYGEDDQRVCEANGIPVLLSVDSGARFLPLFA
+REDVGRGDLREIAGVQVFEANRTIIRALRALGRVAREASYEHSYPHCWRCRTPLIYRAVT
+SWYVKVTQIKERMLELNEEITWIPGNVKHGQFGTWVANARDWSISRNRYWGSPIPVWESD
+HPDFPRQEVYGSLAEIEEAFGRLPRNAQGEVDLHRPWVDDLTRPHPDPEAAAAGAVMRRV
+EDVLDVWFDSGSMPYAQVHYPFERADWFPTHNPADFIVEYIGQTRGWFYTMHILATALFD
+RPAFSHVISHGIVLGSDGQKMSKSLRNYPDVTEVLDRDGADAMRWFLMASPILRGGNLIV
+TEEGIREGVRQVLLPAWNAYHFFTLYANTAHDGGARPDGYRAQERHTAEDPLDQYILAAT
+GRMLREVKTGLDAYEVSDATDALRGFMDTLTNWYIRRSRERFFDEDTVAFDVLYTVLEAF
+TRAAAPLMPLIAEEIWRGLTGGRSVHLTDYPDADLFPHGPEADSLVARMDAVRRISSAGS
+ALRKGAGRRVRLPLPGLSVVVPDAAGLEGTYARIVADELNLKDVELTELSEEAIARYGIG
+TELKLNFRELGKAFGRQVPLVKQAVDAGAYEETAEGLAVTLADGETVTLAPALYELRTVS
+TGAPEGTTVGVLPGTAGFLVLDTQVTAELAAEGTARDVVRAVQAARKDAGLDVSDRVRTR
+IEGPTAVVAALEAHRGLVAEETLTVDLELVDSGAADPRKDPADDAMKTVAVTVAKADA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000857.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000857.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e321d589bfdeb9c0d1a7b07c9a8354384b52a0c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000857.fa
@@ -0,0 +1,24 @@
+>0_969
+MRLILLRHGETDWNVLDRYQGHTDIELNAEGERQARRAAGGPVGDLVEDAEELVAVCSPL
+ARARRTAEIVLEARVGAASVAVDPELMELAGGEWEGLELSAIAERWPDEHRLWRAEPALD
+AGPVGGETLRGGGERALRALRGHVPPHWADTPRDGGAHTLLVVAHGALIRAATGLLLRHE
+GEAFAAMERIGNARAAVLQGAFTADTGAEGWGDWTLEGYGI
+>1_692
+MRLILLRHGETDWNVLDRYQGHTDIELNAEGERQARRAAGGPVGDLVEDAEELVAVCSPL
+ARARRTAEIVLEARVGAASVAVDPELMELAGGEWEGLELSAIAERWPDEHRLWRAEPALD
+AGPVGGETLRGGGERALRALRGHVPPHWADTPRDGGAHTLLVVAHGALIRAATGLLLRHE
+GEAFAAMERIGNARAAVLQGAFTADTGAEGWGDWTLEGYGI
+>2_1844
+MRLILLRHGETDWNAGDRYQGRTDVELNAVGERQARRAAVGPVGDLLEEAAELVAVASPL
+ARARRTAEILLEARVGAADLALDEQLMELHGGDWEGLGLTAIAQRWPEEHRSWRAVPALD
+AGPVGGETLRAAGERALGALRGRVPQHWAVYAAAL
+>3_1770
+MRLVLLRHGETDWNALDRYQGRTDVPLNALGERQAAAAAAGPVGELLRSAEDLVAVSSPL
+IRARRTAEIVLEDAVGAVELAVDSRLVELGGGEWEGLDFTEIGARWPHEHHAWRTVPDLD
+GGPVGGEVLRAGGERVLAAAAAHVPEDWSTPRPARVPDARTLLIVAHGAVIRAAAGLALA
+LEGADFAHLARVSNARAVILDGTFAGEGPGAWSLLGYDV
+>4_912
+MRLILLRHGETDWNALDRYQGHTDIELNAEGERQARRAAGGPVGDLLEDAEELVAVCSPL
+ARARRTAEIVLQARVGAASVAVDPELMELAGGEWEGLELSAIAERWPDEHRLWRAVPALD
+AGPVGGETLRGGGERALRALRGHVPPHWADTPRDGGAHTLLAVAHGALIRAATGLLLRHE
+GEAFAAMERIGNARAAVLQGAFAPATEGWGDWTLEGYGI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000858.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000858.fa
new file mode 100644
index 0000000000000000000000000000000000000000..21ad43855b0fe37643d948cd9f947a83d473e835
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000858.fa
@@ -0,0 +1,49 @@
+>0_973
+MTTAPATAGRERRTSDVVVIGAGPAGLMAARTAKAQGLSVTVLEARRRVGGRTWNGLVEG
+ADGKDHFIEIGGQWISPDQTRLISLVEELGLPTFSRFRDGRNVYVDPRGERHVYDGLDFP
+VAEKTDREMDRLIAKIDELTAEIDAAAPWEHPRAAELDKISFRHWLEQQSDDPEAIDNVS
+IYIASGMLTKPSHTFSLLQALLMSASAGSFRNLVDEDFILDKRVEGGMQSVSLAMAAELG
+DDVVLGQPVRTLRWAEPDPSTADEKNGVAADVRNGVAHDGAAGDVVALTDDYEVHARYAV
+LAVPPNLYSRISFEPPMPREQQIAHQHISMGLVIKVHAVYETPFWREEGLSGTCFGGGRL
+VQEIYDNTNRGENLAGGAPGKEDPHGTLVGFVSDVYAEQMWALPEEERKAAILGAMAEYL
+GPRTLEPIAFFLSDMAAEEWTRGAYATSYDLGGLSRWGHLQNRPTGPIHYACSDIAAEGY
+QHVDGAIRMGEAAALAIAEREATDAGQPTG
+>1_696
+MTTAPATAGRERRTSDVVVIGAGPAGLMAARTAKAQGLSVTVLEARRRVGGRTWNGLVEG
+ADGKDHFIEIGGQWISPDQTRLISLVEELGLPTFSRFRDGRNVYVDPRGERHVYDGLDFP
+VAEKTDREMDRLIAKIDELTAEIDAAAPWEHPRAAELDKISFRHWLEQQSDDPEAIDNVS
+IYIASGMLTKPSHTFSLLQALLMSASAGSFRNLVDEDFILDKRVEGGMQSVSLAMAAELG
+DDVVLGQPVRTLRWAEPDPSTADEKNGVAADVRNGVAHDGAAGDVVALTDDYEVHARYAV
+LAVPPNLYSRISFEPPMPREQQIAHQHISMGLVIKVHAVYETPFWREEGLSGTCFGGGRL
+VQEIYDNTNRGENPAGGAPGEEDPHGTLVGFVSDVYAEQMWALPEEERKAAILGAMAEYL
+GPRTLEPIAFFLSDMAAEEWTRGAYATSYDLGGLSRWGHLQNRPTGPIHYACSDIAAEGY
+QHVDGAIRMGEAAALAIAEREATDAGQPTG
+>2_1838
+MTTAPATAGRERRTSDVVVIGAGPAGLMAARTAKAQGLSVTVLEARRRVGGRTWNGLVEG
+ADGKDHFIEIGGQWISPDQTRLISLVEELGLPTFSRFRDGRNVYVDPRGERHVYDGLDFP
+VAEKTDREMDRLIGNIDELTAEIDAAAPWEHPRAAELDTISFRHWLEQESDDPEAIDNVS
+IYIASGMLTKPSHTFSMLQALLMAASAGSFRNLVDEDFILDQRVEGGMQSVSLAMAAELG
+DDVVLGQPVRTLRWTEPDPSTADEKNGVAADVRNGVAHDGDAGDVVALTDDYEVHARYAV
+LAVPPNLYSRISFEPPMPREQQIAHQHISMGLVIKVHAVYETPFWREEGLSGTCFGGGRL
+VQEIYDNTNRGENLAGGAPGEEDPHGTLVGFVSDVYAEQMWALPEEERKAAILGAMAEYL
+GPRTLEPIAFFLSDMAAEEWTRGAYATSYDLGGLSRWGHLQNRPTGPIHYACSDIAAEGY
+QHVDGAIRMGEAAALAIAEREATDAGQPTG
+>3_1206
+METPSDVIVVGAGLAGLVAARTLAEAGLSVRVLEREAEVGGRQRTRTVDGFVLDRGFQLV
+NPAYPELPRHADVDALGLRPFGAGVRVRTRRGLALLADPRREPRLAARTLRDGVRHGLLD
+ARELAALSRWAAPALAAPRVAKHRMDAPLIEAWDRAGVRGPLRDAVLEPFLRGVLADPDL
+TTSSRFTELLVRMFVLGTPGVPARGVAALPEQLAARVRAAGTRVTTGASVTAVRPAADGV
+VVDVAGGAPLHARAAVLAVGPEAFTGLLPEAATDRLPVPSRGLTTWWFRAPSAPARERFL
+AVDGTGSGPLVHTAVMTAAAPGLSPDGTPLVEATALLDPSAPAVTDAQARAHAARIWGVD
+ASDWDLLARDDVPHALPVQAAPLRLRAEARVAERVYAAGDHRDTASIQGALVSGRRVAER
+LLHELPR
+>4_916
+MTTAPATAGRERRTSDVVVIGAGPAGLMAARTAKAQGLSVTVLEARRRVGGRTWNGLVEG
+ADGKDHFIEIGGQWISPDQTRLISLVEELGLPTFSRFRDGRNVYVDPRGERHVYDGLDFP
+VAEKTDREMDRLIAKIDELTAEIDAAAPWEHPRAAELDKISFRHWLEQQSDDPEAIDNVS
+IYIASGMLTKPSHTFSLLQALLMSASAGSFRNLVDEDFILDKRVEGGMQSVSLAMAAELG
+DDVVLGQPVRTLRWAEPDPSTADEKNGVAADVRNGVAHDGAAGDVVALTDDYEVHARYAV
+LAVPPNLYSRISFEPPMPREQQIAHQHISMGLVIKVHAVYETPFWREEGLSGTCFGGGRL
+VQEIYDNTNRGENLAGGAPGKEDPHGTLVGFVSDVYAEQMWALPEEERKAAILGAMAEYL
+GPRTLEPIAFFLSDMAAEEWTRGAYATSYDLGGLSRWGHLQNRPTGPIHYACSDIAAEGY
+QHVDGAIRMGEAAALAIAEREATDAGQPTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000875.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000875.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e9bd05cf376b8c872df850eb9d73bd361144eaf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000875.fa
@@ -0,0 +1,30 @@
+>0_998
+MCGRYVMARATSDLVALGDAEANEDLVLRQSWNVAPTAEVPILVAHADDVGAGGTRGGDG
+GAGVTRRIHVARWGLVPPWAKELSVGSRAFNARSETVASKPTFRAAVRARRCAVPVEGYY
+EWKTPEPGAKGPDGRIAKKQPYYVHPAGAGDGEGPVIWFAGLYEWWQDPEAKAAGEDAWV
+LSTTILTMAAPDADDDDPVLAALGQLHDRLPVPMDAETMDRWLAPDTLGSAEEADALVGQ
+VCAGAYDVAAGWSLRPVGSAVGNVRNNGPELIQEMREQQGTLL
+>1_720
+MCGRYVMARATSDLVALGDAEANEDLVLRQSWNVAPTAEVPILVAHADDVGAGGARGGDG
+GAGVTRRIHVARWGLVPPWAKELSVGSRAFNARSETVASKPTFRAAVRARRCAVPVEGYY
+EWKAPEPGAKGPDGRAAKKQSYYVHPAGAGDGEGPVIWFAGLYEWWQDPEAKAAGEDAWV
+LSTTILTMAAPDADDDDPVLAALGQLHDRLPVPMDAETMDRWLAPDTLGSAEEADALVGQ
+VCAGAYDVAAGWSLRPVGSAVGNVRNNGPELIQEMREQQGTLL
+>2_1810
+MCGRYVMARAAGDLVALGGGELPDERLELRRSWNVAPTSDVPILLEREADGAVRRELHVA
+RWGLVPSWAKELAVGSRAFNARSETVASKPTFRAAVRARRCAVPVEGYYEWKAPAPGAKG
+PDGKAAKKQPYYVHPAGAGDGEGPVIWFAGLYEWWQDPEAEAAGRDPWVLSTTILTMAAP
+DADDEDEVLGSLGDLHDRLPVPLDAETMDAWLTPGRLGSAEEADALVGQVCAGAYDVAAG
+WVLRPVGTAVGNVRNDGPELIQAEEPAQGTLL
+>3_1699
+MARAAGDLVALGGGLLPEEGLELRPNWNVAPTADVPILLEREDAGVVRRELHVARWGLVP
+TWAKELSVGSRAFNARSETVTSKPTFRSAVRARRCAVPVEGYYEWKAPEPGSTGPDGKAA
+VKQPFYVHPAGGGDGEGPVIWFAGLYEWWKDAGAEARGDDPWVLSTTILTMPSPADDEPG
+VLGELADLHDRLPMPMGPAAMDSWLSPDKLGSADEAAALVDEMTAQAYDVARGWELRPVG
+RAVGNVRNNGPELIAPPAEVQDALL
+>4_940
+MCGRYVMARATSDLVALGDAETNEELVLRQSWNVAPTAEVPILVAHADDVGAGVTRRIHV
+ARWGLVPPWAKELSVGSRAFNARSETVASKPTFRAAVRARRCAVPVEGYYEWKTPEPGAK
+GPDGRAAKKQPYYVHPAGAGDGEGPVIWFAGLYEWWQDPEAKAAGEDAWVLSTTILTMAA
+PDADDDDPVLAALGQLHDRLPVPMDAETMDRWLAPDTLGSAEEADALVGQVCAGAYDVAA
+GWSLRPVGSAVGNVRNNGPELIQEMREQQGTLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000877.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000877.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb3035f62785910981fe7a0bf7dd81a0af998cb8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000877.fa
@@ -0,0 +1,15 @@
+>0_1003
+MGVLTQSVAVECGADGTPQGLRWNGRDYVLAERPVRWFERRRWWAEEVRAEKGRGAGLVD
+HEMWRLQVRLARAGAAPLQTLDVAHHLDSGRWRLVRVHEHAQDLRRSA
+>1_725
+MGVLTQSVAVECGADGTPQGLRWNGRDYVLAERPMRWFERRRWWAEEVRAEKGRGAGLVD
+HEMWRLQVRLARAGAAPLQTLDVAHHLDSGRWRLVRVHEHAQDLRRSA
+>2_1809
+MGVLTQSVAVERAADGTPQGLRWNGRDYVLAEPPVRWFERRRWWAEEVRAEKGRGAGLVD
+HEIWRLQVRLARAGSAPVQTVDVAHHLDSGRWRLVRVHEQARDLRRSA
+>3_1695
+MGTFTQSVAVERDRQGAPARLHWEGREYVLAERPLRWFERRRWWAEEARAEKGRGPGLVD
+HEIWRLQVRLARAGNAPVRTVDLAHHLDSGRWRLVRVHAPAQERTLSRTA
+>4_944
+MGVLTQSVAVECGADGTPQGLRWNGRDYVLAERPVRWFERRRWWAEEVRAKKGRGAGLVD
+HEMWRLQVRLARAGAAPLQTLDVAHHLDSGRWRLVRVHEHAQDLRRSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000883.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000883.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8eb6093210fcaa0e72e52ae85c6564b09875b92b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000883.fa
@@ -0,0 +1,20 @@
+>0_1009
+MTENHAVPAALAEIIDDFAGVPDPEKLELLLEFSDELPALPERYDGHEAEMEQVVECQTP
+LFLAVELEGEPGPQAPVRLFITAPPEAPTTRGFASVLTQGLDGLSALEVVDVPEDIPTRL
+GLAKALTPLRLRGMSAMLGRIKRNVREQAGIA
+>1_731
+MTENHAVPAALAEIIDDFAGVPDPEKLELLLEFSDELPALPERYDGHEAEMEQVVECQTP
+LFLAVELEGEPGPQAPVRLFITAPPEAPTTRGFASVLTQGLDGLSALEVVDVPEDIPTRL
+GLAKALTPLRLRGMSAMLGRIKRNVREQAGIA
+>2_1800
+MTQNHAVPAALAEIVDDFAGVPDAEKLELLLEFADELPALPERYDGHEAEMEQVVECQSP
+LFLAVELEGEDEPGPESVVRLFITAPPEAPTTRGFASVLSQGLDGLTARQIVDVPEDIPS
+RLGLAKALTPLRLRGMSAMLGRIKRNVREQTGVA
+>3_1689
+MTDTAVPANLAEIVDDFAGVPDPQKLELLLEFSDELPALPERYAGHEDEMEQVVECQSPL
+FLAVELEDGATGDDAVVRLFISSPPEAPTTRGFASVLTQGLDGCTARQVLAVPEDIPSRL
+GLQKALTPLRLRGMSAMLGRIKRNVREQAGIA
+>4_950
+MTENHAVPAALAEIIDDFAGVPDPEKLELLLEFSDELPALPERYDGHEAEMEQVVECQTP
+LFLAVELEGEPGPQAPVRLFITAPPEAPTTRGFASVLTQGLDGLSALEVLDVPEDIPTRL
+GLAKALTPLRLRGMSAMLGRIKRNVREQAGIA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000888.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000888.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4aa8bbca78f86e2da975160a4fb46a13e8cf1627
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000888.fa
@@ -0,0 +1,40 @@
+>0_1014
+MTAPTPLRVLYAGTPETAVPVLRALLDSPHEVVGVLTRPDAPVGRRRVLTPSPVAVVAEE
+ARLPVLKADRLRGPEGADALQAIRALEADVAVVVAYGALVPAEALQTPRHGWLNLHFSAL
+PAYRGAAPVQRAVMAGETEIAADVFQLEEGLDTGPVFARLTRPVAADETAGTVLTDLAER
+GGPLVIDVLDRLADGTATATPQRGEPTHAPKLTAADGLVDPARPAAEVAARINGVTPEPG
+AWGWLTADDGAAPARFKLDGVAPVRAGDDGWPSVLDAAVPGQILVAAKAAWLRTAGGAVR
+LSRVQPAGRKLMPAADWARGAAAGAALLAGEALAHHEEQARRDAAARAAARQAARNATEQ
+DEEARA
+>1_742
+MTAPTPLRVLYAGTPETAVPVLRALLDSPHEVVGVLTRPDAPVGRRRVLTPSPVAVVAEE
+ARLPVLKADRLRGPEGADALQAIRALEADVAVVVAYGALVPAEALQTPRHGWLNLHFSAL
+PAYRGAAPVQRAVMAGETEIAADVFQLEEGLDTGPVFARLTRPVAADETAGAVLTDLAER
+GGPLVIDVLDRLADGTATATPQRGEPTHAPKLTAADGLVDPARPAAEVAARINGVTPEPG
+AWGWLTADDGAAPARFKIDGVAPVRPGDDGWPTALDAAAPGQILVAAKAAWLRTTDGAVR
+LSRVQPAGRKLMPAADWARGAAPGAALLAGEALAHHEDQARQEAAARAAARQAARNATAQ
+DEEARA
+>2_1795
+MTATTPLRVLYAGTPETAVPVLRALLDSPHEVVGVLTRPDAPIGRRRVLTPSPVAVVAEE
+AGVPVVKADRLRGPAGEPALEAVRALEPDVAVVVAYGALVPAEALALPRHGWLNLHFSAL
+PAYRGAAPVQRAVMAGEPEIAADVFQLEEGLDTGPVHARLTRAVAPDETAGQILADLAER
+GGPLVLELLGRIADGTAAPRPQEGEPSHAPKLTAADGLVDPARPAAEVAARINGVTPEPG
+AWGWLTVGEGGEPARFKLDGVAPATPADADWPADLDAAPPGALRTAGRAAWLRTADGAVR
+LGRVQPAGKKLMPAADWARGAADGAALLAGEALAAHTARLGQEAAARAARREAARETEAH
+A
+>3_1684
+MSIPETALSPDAGSAPARSLRVLFAGTPEAAVPVLRALVGSAHEVAGVLTRTDAPVGRKR
+VLTPSAVARAAAESAPDVPVLKADRLRGPEAAEVLEAIRALEADVAVVVAYGALVPAEAL
+TIPAHGWLNLHFSHLPAYRGAAPVQRALMDGVERTGADVFQLEEGLDTGPVFARIGRDVA
+PEDTAGDLLAALAEDGGPLVLEVLDALAAGEARSVPQTGEPTHAPKLTAADGLVDAAAGT
+REVAARINGTTPEPGAWGWLVPAGEADAAPARLKLGGVVPTHPGEDGWPEAAEAAAPGAI
+VAAGGTAWLRTAGGAVRLDQVQPAGKKPMSAADWARGLTAPVRLLAGDELAAHLAALDAE
+AARRAAQQAAARAAQAGEGA
+>4_961
+MTAPTPLRVLYAGTPETAVPVLRALLDSPHEVVGVLTRPDAPVGRRRVLTPSPVAVVAEE
+AGLPVLKADRLRGPEGADALQAIRVLEADVAVVVAYGALVPVEALQIPRHGWLNLHFSAL
+PAYRGAAPVQRAVMAGETEIAADVFQLEEGLDTGPVFARLTRPVAADETAGAVLTDLAER
+GGPLVIDVLDRLADGTATATPQRGEPTHAPKLTAADGLVDPARPAAEVAARINGVTPEPG
+AWGWLTADDGAAPARFKLDGVAPVSAGDDGWPSALDAAAPGQILVAAKAAWLRTAGGAVR
+LSRVQPAGRKLMPAADWARGAAAGAALLAGEALAHHEEQARREAAARAAAREAARNATAQ
+DEEARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000889.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000889.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8dc9665ad48e89fdd0e8aaa4d7e1d15a2d6ac0ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000889.fa
@@ -0,0 +1,55 @@
+>0_1015
+MSREGQAGQGRGERGARGERGRAPRPDPQDRRDAQGRTRNRGRSGAGRKYSAQAPSQRSR
+TADPARRVAFGVVRSVHAEDAYANLVLPARIRQARLDRRDAGFATELAYGTLRGLGLYDA
+ILTRCVDRPLEQIDPPVLDALRLGAHQLLGMRVPAHAALDATVSLVRAEIGAGASGFVNA
+VLRRVAERPLEEWLADVAPADGGDAALAVRASHPVWIVRALRQALAAHRGTRHIADRDAE
+LAALLEADNAPPVVNLVALPVAGGAEALAAALDDGAEPGPLAPDSALHSGGDAGRLPGVR
+EGVLRVQDAGSQLTARALAQAPVPAAEGRAERWLDLCAGPGGKAALLAALAAERGATLVA
+NEVAPHRADLVRQALAAVPADAWTVRTGDGRTIADAPEAAPAFDRVLVDAPCTGLGALRR
+RPESRWRRTPADLAELTGLQAELLDAAVSVLAPGGVLAYVTCSPHVAETVVQVQDLVRRH
+PELELLDARTALDTVALDDLRLDEAEPAGAPKPGDVVARTAQLWPHRHGTDAMFLALLRA
+PGA
+>1_743
+MSRERQPGQGRGERGARGERGRAPRPDAQDRRDAQGRTRNRGRSGAGRKYSAQAPSQRSR
+TADPARRVAFGVVRSVHAEDAYANLVLPARIRQARLDRRDAGFATELAYGTLRGLGLYDA
+ILTRCVDRPLEKIDPPVLDALRLGAHQLLGMRVPAHAALDATVSLVRAEIGAGASGFVNA
+VLRRVAERPLEEWLADVAPADGGDAALAVRASHPVWIVRALRQALAAHRGTRHTADRDAE
+LAALLEADNAPPVVNLVALPVAGGAEALAAALDDGAEPGPLAPDSALHSGGDAGRLPGVR
+EGVLRVQDAGSQLTARALAQAPVPAAEGRAERWLDLCAGPGGKAALLAALAAERGATLVA
+NEVAPHRADLVRQALAAVPAGAWTVRTGDGRTIADAPEAAPAFDRVLVDAPCTGLGALRR
+RPESRWRRTPADLAELTGLQAELLDAAVAVLAPGGVLAYVTCSPHVAETVVQVQDLVRRH
+PELELLDARTALDAVALDDLRLDEAEPAGAPEPGDVVARTAQLWPHRHGTDAMFLALLRA
+PGA
+>2_1794
+MSGEGQGRQGRGRGGSGGGSRGGAGGGSRGGSRNGSGGGPRGGSHGGPRGGSGGARRESG
+GEERRDAQGRTRSRGRSGAGRRYSAQAPAQRSRTADPARRVAFEVIRAVHAEDAYANLVL
+PGRIRQARLDRRDAGFATELAYGTLRGIGLYDAVLARCVDRPLEKIDPPVLDALRLGAHQ
+LLAMRVPAHAALDATVALVRAEIGAGPSGFVNAVLRRVAERPLEDWLADVAPAEGGDAAL
+AVRASHPVWIVRALRQALAAHRGTRHVADRDAELGALLEADNASPVVNLVALPVPGGREG
+LSAALEDGAEPGPLAPDSALHAGGDAGRLTGVREGVLRVQDAGSQLTARALAAAPAAAAE
+GRPERWLDLCAGPGGKAALLAALAAERGATLVANEVAEHRAELVRQALGAVPAAAWTVRA
+GDGRAIADAPEAAGGFDRVLVDAPCTGLGALRRRPESRWRRTPADLAELTGLQSELLDAA
+AAVLAPGGVLAYVTCSPHVAETTVQVQDLLRRRPELELLDAGAVLSEVALGDLRLDEGEP
+GGDEAAGAAAPDDVAARTAQLWPHRHGTDAMFLALLRAPSDTPESPERTRG
+>3_1683
+MSAGQDGSTGRGAGQGGRGRGGAEGRQGPGGRQGAGGQDRRDAQGRQLNRGASGTGRHRT
+TLAPKERARRADPARRVAFEVVRAVHAEDAYANLVLPARIRQGRLDRRDAGFATELTYGT
+LREQGLYDAVLARCVDRALDALDAPVLDALRLGAHQLLGMRVPAHAALDATVALVRAEVG
+AGPAGFVNAVLRRVSERPREDWLAEVAPADGGDTARAVRHSHPAWIVRALRQALAGHPGT
+ADVEDRDAELEALLVADNAAPVVNLVGLPVPGGREALASALGDGAEPHPLTPDAALHAGG
+DAGRLPGVREGVLRVQDAGSQLTARALAAVPAASGRDAGGRKAERWLDLCAGPGGKAALL
+AALASERGATVLANEVAPHRADLVRSALAGVPASAWEVRTGDGRTIAEDAPAGGFDRILV
+DAPCTGLGALRRRPESRWRRTPADLAELTGLQAELLDAAVGVLAPGGVLAYVTCSPHVAE
+TLVQVQDLLRRHPVLEQLDAPAALQDVAVADLGLAAPEDADPVLARTAQLWPHRHGTDAM
+FLALFRAPVA
+>4_962
+MSRERQPGQGRGERGARGERGRAPRPDPQDRRDAQGRTRNRGRSGAGRKYSAQAPSQRSR
+TADPARRVAFGVVRSVHAEDAYANLVLPARIRQARLDRRDAGFATELAYGTLRGLGLYDA
+ILTRCVDRPLEKIDPPVLDALRLGAHQLLGMRVPAHAALDATVSLVRAEIGAGASGFVNA
+VLRRVAERPLEEWLADVAPADGGDAALAVRASHPVWIVRALRQALAAHRGTRHIADRDAE
+LAALLEADNAPPVVNLVALPVAGGAEALAAALDDGAEPGPLAPDSALHSGGDAGRLPGVR
+EGVLRVQDAGSQLTARALAQAPVPAAEGRAERWLDLCAGPGGKAALLAALAAERGATLVA
+NEVAPHRADLVRQALAAVPADAWTVRAGDGRTIADAPEAAPAFDRVLVDAPCTGLGALRR
+RPESRWRRTPADLAELTGLQAELLDAAVAVLAPGGVLAYVTCSPHVAETVVQVQDLVRRH
+PELELLDARTALDAVALDDLRLDEAEPAGAPKPGDVVARTAQLWPHRHGTDAMFLALLRA
+PGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000904.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000904.fa
new file mode 100644
index 0000000000000000000000000000000000000000..61bf9d8befdf1f0d65d1280ff4fd9f91d2411381
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000904.fa
@@ -0,0 +1,35 @@
+>0_1043
+MTALASLASPAALAPLAAFPAPGWDGFQLGPVKIHAYALCIILGIVLALWLAERRWRARG
+GPEDRVLDIALWAIPFGFVGGRLYHVFSSPDRYFGPGFDGTGDPIQILYVWNGGLGIWGA
+IALGAVGAWIACRRYGLRLTAFGDVVAPGILLAQAIGRWGNWFNQELFGGPTTLPWGLEV
+DPASPNFPAGYAPDTLFHPTFLYECLWNLAGVALLLLVDRALHLRHGLMLWSYVAWYTAG
+RTWIEMLRIDDAEMVTLFGVTQRLNVWTSLLVFVIALAFIVGILLRHRGAAAGPHAHQSV
+WRAGHAPEGDDGVAVAAGRSGSHAVGAAEDDAVRR
+>1_771
+MTAALAPLAAFPAPGWDGFQLGPVKIHAYALCIILGIVLALWLAERRWRARGGPEDRVLD
+IALWAIPFGFVGGRLYHVFSSPDRYFGPGFDGTGDPIQILYVWNGGLGIWGAIALGAVGA
+WIACRRYGLRLTAFGDVVAPGILLAQAIGRWGNWFNQELFGGPTTLPWGLEVDPASPNFP
+AGYAPDTLFHPTFLYECLWNLAGVALLLLVDRALHLRHGLMLWSYVAWYTAGRTWIEMLR
+IDDAEMVTLFGVTQRLNVWTSLLVFVIALAFIVGILLRHRGAAAGPHAHQSVWRAGHAPE
+GDDGAAVAAGRSGSHAVGAAEDDAVRR
+>2_1776
+MKIYAYALSIILGIVLALWLAERRWKARGGPEGRVLDVALWAIPFGFVGGRLYHVFSSPD
+RYFGPGFDGTGDPVQILHVWNGGLGIWGAIALGAVGAWIACRRYGLRLSAFGDVVAPGIL
+LAQAVGRWGNWFNQELFGRPTTAPWGLRVDADHPNFPDGVAPDTLFHPTFLYESLWCLLG
+VAVLLLADRRWRLRRGAMVWAYVAWYTAGRVWIETLRIDDAELVTLFGLTQRLNVWTSIV
+MLLLALVMLAVILVKHGPAAAGPRSDDSVWLPGRGPALEAGAGAPVDAAVAGQGPDDGAG
+STAAGVREDR
+>3_1664
+MGSGALTPLAAFPAPVWDGFELGPMKIHAYALCIIAGIVVALWLSGRRWADRGGPEGRVL
+DIALWAIPFGFVGGRLYHVFSSPDLYFGPGYDGTGDPIKILYVWNGGLGIWGAIALGAVG
+AWIACRRYGLRLTAFADVVAPGVLLAQAIGRWGNWFNQELFGGPTTLPWGLTVDPASPNF
+PAQYAPGTLFHPTFLYESLWNLLGVAVLLLVDRRLHLRHGAMLWSYVAWYTAGRTWIEMM
+RIDDAELVTLFGVTQRLNVWTSLLMFAIALAFLIGILLRHRGAAAGPHARQSVWRDGHGP
+VGEDVEGAGPAAAPAVRTTQGGSGSHAWDDVGA
+>4_992
+MTAALAPLAAFPAPGWDGFQLGPVKIHAYALCIILGIVLALWLAERRWRARGGPEDRVLD
+IALWAIPFGFVGGRLYHVFSSPDRYFGPGFDGTGDPIQILYVWNGGLGIWGAIALGAVGA
+WIACRRYGLRLTAFGDVVAPGILLAQAIGRWGNWFNQELFGGPTTLPWGLEVDPASPNFP
+AGYAPDTLFHPTFLYECLWNLAGVALLLLVDRALHLRHGLMLWSYVAWYTAGRTWIEMLR
+IDDAEMVTLFGVTQRLNVWTSLLVFVIALAFIVGILLRHRGAAAGPHAHQSVWRAGHAPE
+GDDGAAVAAGRSGSHAVGAAEDDAVRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000931.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000931.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1472d9cd099339fa72bf541368d8d86f3417e0cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000931.fa
@@ -0,0 +1,35 @@
+>0_1076
+MALTMTLKEELARVPVAATPERRAETAAMLRFAGGLHLVAGRVVVEVELDHGASARRLRA
+AITELYGLAPEIVVVSGGNLRRGQRYVLRVVRGGEDLARQTGLIDQRGRPVRGLAPVLVS
+GTTAATAAVWRGALLAHGSLTEPGRSAALEVTTPGPEAALALVGAARRLRVAAKAREVRQ
+SDRVVVRDGEAIATLLAAVGAEQTATLWRERRERKEVRATANRLANFDDANLRRSAQAAV
+TAGAKVERALEILGDEVPDHLRYAGRLRLEHKQASLDELGRLADPPMTKDAVAGRIRRLL
+AMADKRAAERGIPGTDAASEG
+>1_804
+MALTMTLKEELARVPVAATPERRAETAAMLRFAGGLHLVAGRVVVEAELDHGASVRRLRA
+AITELYGLAPEIVVVSGGNLRRGQRYVLRVVRGGEDLARQTGLIDQRGRPVRGLAPVLVS
+GTTAATAAVWRGALLAHGSLTEPGRSAALEVTTPGPEAALALVGAARRLRVAAKAREVRQ
+SDRVVVRDGEAIATLLAAVGAEQTATLWRERRERKEVRATANRLANFDDANLRRSAQAAV
+TAGAKVERALEILGDEVPDHLRYAGRLRLEHKQASLDELGRLADPPMTKDAVAGRIRRLL
+AMADKRAAERGIPGTDAASEG
+>2_1740
+MALTMTLKEELARVPVAATPERRAETAAMLRFAGGLHLVSGRVVVEAELDHGASARRLRA
+SITELYGLATEIVVVSGGNLRRGQRYVIRVVRGGEDLARRTGLIDQRGRPVRGLASALVT
+GTTADTAAVWRGALLAHGSLTEPGRSAALEVTTPGPEAALALVGAARRLDVAAKAREVRQ
+ADRVVVRDGEAIATLLTAVGAEQTAALWRERRERKEVRATANRLANFDDANLRRSAQAAV
+AAGAKVERALEILGDEVPEHLRYAGRLRLEHKQASLDELGRLADPPMTKDAVAGRIRRLL
+AMADKRAAERGVPGTDTPAED
+>3_1632
+MALTMTLKEELARVPVGAVPERRAETATMLRFAGGLHLVSGRVVIEAELDHGASARRLRA
+AITELYGHATEIVVISGGNLRRGQRYVIRVVRGGEDLARQTGLLDLRGRPVRGLPPALVQ
+GSAADTAAVWRGALLAHGSLTEPGRSSCLEVTTPGPEAALALVGAARRLGVAAKAREVRQ
+ADRVVVRDGEAIAALLTAVGADQTAALWQERRERKEVRATANRLANFDDANLRRSAQAAV
+AAGARVERALEILGDDVPDHLGYAGRLRLEHKQASLDELGRLADPPMTKDAVAGRIRRLL
+SMADKRAAAEGIPGTAVDGA
+>4_1026
+MALTMTLKEELARVPVAATPERRAETAAMLRFAGGLHLVAGRVVVEVELDHGASARRLRA
+AITELYGLAPEIVVVSGGNLRRGQRYVLRVVRGGEDLARQTGLIDQRGRPVRGLAPVLVS
+GTTAATAAVWRGALLAHGSLTEPGRSAALEVTTPGPEAALALVGAARRLRVAAKAREVRQ
+SDRVVVRDGEAIATLLAAVGAEQTATLWRERRERKEVRATANRLANFDDANLRRSAQAAV
+TAGAKVERALEILGDEVPDHLRYAGRLRLEHKQASLDELGRLADPPMTKDAVAGRIRRLL
+AMADKRAAERGIPGTDAASEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000933.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000933.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8bb170bd5dab17f7d4c5190de36ce38e89e3a121
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000933.fa
@@ -0,0 +1,35 @@
+>0_1078
+MTKIAINGYGRIGRNIVRVLRDRGHENLELVAVNDLADPEDLFWLTQYDTILGRYPGELE
+RTEKGFRIDGRDVAFFQEADPTKLPWGELGVDLVIECTGIFTTGPKAQAHLDAGAKKVLI
+SAPAKEVDGTFVMGVNEHTYDAESMHIVSNASCTTNCLAPMAKVLNDEFGIVDGIMTTIH
+AYTGDQNLHDNVHKKDRRRARAAAQNMVPTSTGAAKAIGEVIPELKGKLDGFAMRVPTIT
+GSATDLTVELTRHVEVEEINAAFKKAAESGPLQGRLVYSEDPIVSSDIITSPAACTFDAP
+LTKSIGQTVKIIGWYDNEYGYTSQLMDFADLIGSKL
+>1_806
+MTKIAINGYGRIGRNIVRVLRDRGHEGLELVAVNDLADPEDLFWLTKYDTILGRYPGELE
+RTEKGFRIDGRDVAFFQEADPTKLPWGELGVDLVIECTGIFTTGPKAQAHLDAGAKKVLI
+SAPAKEVDGTFVMGVNEHTYDAETMHIVSNASCTTNCLAPMAKVLNDEFGIVDGIMTTIH
+AYTGDQNLHDNVHKKDRRRARAAAQNMVPTSTGAAKAIGEVIPELKGKLDGFAMRVPTIT
+GSATDLTVELTRHVEVEEINAAFKKAAESGPLQGRLVYSEDPIVSSDIITSPAACTFDAP
+LTKSIGQTVKIIGWYDNEYGYTSQLMDFADLIGSKL
+>2_1738
+MTKIAINGYGRIGRNIVRVLRDRGYENLELVAVNDLADNEDLFWLTQYDTILGRYPGELE
+LTETGFRIDGRDVAFFSEPDPAKLPWGELGVDIVIECTGFFTTGPKAKAHLDAGAKKVLL
+SAPGKEVDGTFVMGVNEKNYDSATMDIVSNASCTTNCLAPMAKILNDEFGIVDGIMTTIH
+AYTGDQNLHDSVHKKDRRRARAAAQNMVPTDTGAAKAIGEVIPELKGKLDGFAMRVPTIT
+GSATDLTVELTRHVEVEEINAAFKKAAESGPLQGRLVYSEDPIVSSDIITSPAACTFDAP
+LTKSIGQTVKIIGWYDNEYGYTSQLVDFADLIGSKL
+>3_1630
+MTKIAINGYGRIGRNAVRVLLEQGHDDLELVAVNDLAATEDLFWLTKYDTILGRFPGELE
+LTDKGFSINGKDVAFFAETDPANLPWGELGVDIVVECTGRFTTGPAAKAHLDAGAKKVLL
+SAPGKEVDGTFVMGVNEGDYDSSTMHIVSNASCTTNCLAPMVKVLNDEFGIVDGIMTTIH
+AYTGDQNLHDNVHKKDRRRARAAAQNMVPTSTGAAKAIGEVIPELKGKLDGFAMRVPTIT
+GSATDLTVELTRHVEAEEVNEAFRRAAESGPLVGRLVYSTDPIVSSDIVTAPAACTFDAP
+LTKSIGQTVKVIGWYDNEYGYTCQLMDMASHMASKL
+>4_1028
+MTKIAINGYGRIGRNIVRVLRDRGHENLELVAVNDLADPEDLFWLTQYDTILGRYPGELE
+RTEKGFRIDGRDVAFFQEADPTKLPWGELGVDLVIECTGIFTTGPKAQAHLDAGAKKVLI
+SAPAKEVDGTFVMGVNEHTYDAETMHIVSNASCTTNCLAPMAKVLNDEFGIVDGIMTTIH
+AYTGDQNLHDNVHKKDRRRARAAAQNMVPTSTGAAKAIGEVIPELKGKLDGFAMRVPTIT
+GSATDLTVELTRHVEVEEINAAFKKAAESGPLQGRLVYSEDPIVSSDIITSPAACTFDAP
+LTKSIGQTVKIIGWYDNEYGYTSQLMDFADLIGSKL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000940.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000940.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b7e88863c4ba0ffdfdda54214cbec8a95cadc9b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000940.fa
@@ -0,0 +1,40 @@
+>0_1085
+MSTPQNPNTAALAQAGVSIWLDDLSRTRLDEGTLEELIATRSVTGVTTNPSIFAVALADA
+GAYQGQLRDLAAAGASVDEAVVALTTEDVRRAADVLAPVHERTGGADGFVSLEVDPRLAR
+DAAGTVAQARELAAAVDRPNLMVKIPATVEGLSAIADVLGAGISVNVTLIFSLPRYRRVL
+NAWLTGLEKARANGHDVRRLHSVASFFVSRVDTEVDARLRAIGTPEAEALTGRAAVANAR
+LAYRAFEQALDSERWRLLEAAGAPVQRPLWASTGVKDPALPDTLYVTELVAPHTVTTLPE
+KTLEAVADHGVIAADTVTGAYAEADALLDAVGAAGVSYQDVVDVLETEGLEKFEAAWDEL
+LGSVRSGLDAHR
+>1_813
+MSTPQNPNTAALAQAGVSIWLDDLSRTRLDEGTLEELIATRSVTGVTTNPSIFAVALADA
+GAYQGQLRDLAAAGASVDEAVVALTTEDVRRAADVLAPVHERTGGADGFVSLEVDPRLAR
+DAAGTVAQARELAAAVDRPNLMVKIPATVEGLSAIADVLGAGISVNVTLIFSLPRYRRVL
+NAWLTGLEKARANGHDVRRLHSVASFFVSRVDTEVDARLRAIGTPEAEALTGRAAVANAR
+LAYRAFEQALDSERWRLLEAAGAPVQRPLWASTGVKDPALPDTLYVTELVAPHTVTTLPE
+KTLEAVADHGVIAADTVTGAYAEADALLDAVGAAGVSYQDVVDVLETEGLEKFEAAWDEL
+LGSVRSGLDAHR
+>2_1730
+MSTQQNPNTAALAEAGVSIWLDDLSRKRLDEGTLEELMATRSVTGVTTNPSIFAVALADA
+GSYEGQLRELAAAGADVDEAVTALTTQDVRRAADVLAPVHERTGGADGFVSLEVDPRLAR
+DAEGTARQAQELAAAVDRPNLMVKIPATVEGLAAITDVLAEGISVNVTLIFSLPRYRQVL
+NAWLAGLEKARENGHDLSRIHSVASFFVSRVDTEVDARLRALGTPEAEALTGQAALANAR
+LAYRAFEQALDSERWRLLEAAGAPVQRPLWASTGVKDPALPDTLYVTGLVAPRTVTTLPE
+QTLEAVADHGEVAGDTVTGGYAEADALLDAVGAAGVSYQDVVDVLETEGLQKFESAWEEL
+LGSVRDGLAAHR
+>3_1623
+MTTETTPATAALAAAGVSLWLDDLSRTRLNEGSLERLIATRNVTGVTTNPSIFAAALKDA
+GAYEAQLAELAAAGADVDAAVTALTTTDVRRACDLLAPVHQETGGRDGYVSIEVDPRLAR
+DTAGTVAQARELVALVDRPNLMVKIPATVEGLPAITEVLGAGISVNVTLIFSLPRYREVL
+NAWLSGLELARANGHDVSRIHSVASFFVSRVDTDVDAQLRALAEQGRPEAGELTGRAGLA
+NARLAYRAFEQMKDTERWSLLEAAGAPVQRPLWASTGVKDPALADTLYVTALVAPDTVNT
+MPEKTLEAYADHGELTAEPVVGGYAQADADLDAIGELGISYTELVDRLETEGLQKFEAAW
+DELLASVRAGLAAHR
+>4_1035
+MSTPQNPNTAALAQAGVSIWLDDLSRTRLDEGTLEELIATRSVTGVTTNPSIFAVALADA
+GAYQGQLRELAAAGASVDEAVVALTTEDVRRAADVLAPVHERTGGADGFVSLEVDPRLAR
+DAAGTVAQARELAAAVDRPNLMVKIPATVEGLSAIADVLGAGISVNVTLIFSLPRYRRVL
+NAWLTGLEKARANGHDVRRLHSVASFFVSRVDTEVDARLRAIGTPEAEALTGRAAVANAR
+LAYRAFEQALDSERWRLLEAAGAPVQRPLWASTGVKDPALPDTLYVTELVAPHTVTTLPE
+KTLEAVADHGVIAADTVTGAYAEADALLDAVGAAGVSYQDVVDVLETEGLEKFEAAWDEL
+LGSVRSGLDAHR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000949.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000949.fa
new file mode 100644
index 0000000000000000000000000000000000000000..786bbacfd1a7c4c3c306aeb3ab137de6031ad526
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000949.fa
@@ -0,0 +1,30 @@
+>0_1094
+MATLQITDLHVQIATENGPKEILKGLSLTIETGETHAIMGPNGSGKSTLASTIAGHPRYE
+VTSGSITLDGEDVLEMGVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTALDGEAPSLR
+TWTKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV
+DALRIVSEGVNRAQAQNEMGTLLITHYTRILNYIKPDHVHVLVDGRVAESGGPELAEQLE
+AEGYARFEKAAAGA
+>1_822
+MATLQITDLHVQIETENGPKEILKGLSLTIETGETHAIMGPNGSGKSTLASTIAGHPRYE
+VTSGSITLDGEDVLEMSVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTALDGQAPSLR
+TWTKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV
+DALRIVSEGVNRAQAQNEMGTLLITHYTRILNYIKPDHVHVLVDGRVAESGGPELAEQLE
+AEGYARFEKAAAGA
+>2_1721
+MATLQITDLHVQIETENGPKEILKGLSLTIETGQTHAIMGPNGSGKSTLASTIAGHPRYE
+VTSGSITLDGEDVLEMGVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTALDGEAPSLR
+TWTKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV
+DALRIVSEGVNRAAEQNEMGTLLITHYTRILNYIKPDHVHVLVDGRVAESGGPELAAQLE
+AEGYARFEKAAAGV
+>3_1614
+MATLQITDLHVQIETENGPKEILKGLSLTINTGETHAIMGPNGSGKSTLASTIAGHPRYE
+VTSGSITLDGEDVLEMSVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTAIDGEAPSLR
+TWSKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV
+DALRIVSEGVNRAAEANEMGTLLITHYTRILNYIKPQHVHVLVDGRVAESGGPELAARLE
+SEGYARFEKAAAEA
+>4_1044
+MATLQITDLHVQIATENGPKEILKGLSLTIETGETHAIMGPNGSGKSTLASTIAGHPRYE
+VTSGSITLDGEDVLEMGVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTALDGQAPSLR
+TWTKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV
+DALRIVSEGVNRAQAQNEMGTLLITHYTRILNYIKPDHVHVLVDGRVAESGGPELAEQLE
+AEGYARFEKAAAGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000959.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000959.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a66e78d3dc20c20f480226217f16a8e12307c0b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000959.fa
@@ -0,0 +1,15 @@
+>0_1107
+MKSEIHPDYRYVIFNDLASGEKILTRTTANSDKTAEWTDGNTYPVIDVEISAASHPFYTG
+KQRIMDTAGRVERFNARFKGFGGKK
+>1_835
+MKSEIHPDYRYVIFNDLASGEKILTRTTANSDKTAEWTDGNTYPVIDVEISAASHPFYTG
+KQRIMDTAGRVERFNARFKGFGGKK
+>2_1707
+MKSEIHPDYRYVIFNDLASGEKILTRTTANSEKTAEWTDGNTYPVIDVEISAASHPFYTG
+KQRIMDTAGRVERFNARFKGFGGSK
+>3_1601
+MKSEIHPDYRYVIFNDLASGEKILTRTTATSEKTAEWTDGNTYPVIDVEISAASHPFYTG
+KQRIMDTAGRVERFNARFKGFGGKK
+>4_1057
+MKSEIHPDYRYVIFNDLASGEKILTRTTANSDKTAEWTDGNTYPVIDVEISAASHPFYTG
+KQRIMDTAGRVERFNARFKGFGGKK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000960.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000960.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4965d833259a88977c7106b69f5413a30ce91947
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000960.fa
@@ -0,0 +1,35 @@
+>0_1108
+MTTLHGEYKVIGGKLVAADLSLADGRIATASINGDFYLEPDEALEDLNAAVAGLSADAEH
+RVIREAVERGLRPEAELFGVDAFAVASAVRRALGKATTWGDHEWEVIGPEPMPIALTVAL
+DEVLTRQVAEGRRKPTMRLWQWNEPAVVIGAFQSLANEVDPEGARRHGINVVRRISGGGA
+MFMEADNCVTYSMHVPSSLVDGLETAESYPFLDEWTMDALSRLGVHAFYQPLNDIATDQG
+KIGGAAQKRVGTAGLLHHVTMSYDIDADKMLEVLRIGREKLRGKGVTSAKKRVDPLRRQT
+GVSRAEIWETMMTTFEERYGARRVELDEATREEAEQLARTKFATPEWTARVP
+>1_836
+MTTLHGEYKVIGGKLVAADLSLADGRIATASINGDFYLEPDEALEDLNAAVAGLSADAEH
+RVIREAVERGLRPEAELFGVDAFAVASAVRRALGKATTWGDHEWEVIGPEPMPIALTVAL
+DEVLTRQVAEGRRKPTMRLWQWNEPAVVIGAFQSLANEVDPEGARRHGINVVRRISGGGA
+MFMEADNCVTYSMHVPSSLVDGLETAESYPFLDEWTMDALSRLGVHAFYQPLNDIATDQG
+KIGGAAQKRVGTAGLLHHVTMSYDIDADKMLEVLRIGREKLRGKGVTSAKKRVDPLRRQT
+GVSRAEIWETMMTTFEERYGARRVELDEATREEAEQLARTKFATPEWTARVP
+>2_1705
+MTTHHGEYKVIGGKLVAADLTIDDGRIAAASINGDFFLEPDEALEDLNAAVTGLSADAEH
+RVIQAAVEAGLREDAELFGVDAHAIATAVRRALGKATTWEDHEWEIIPPEPLPIALTVAL
+DEVLTRQVAEGRRRPTMRLWQWNEPAVVIGAFQSLANEVDPEGASRHGINVVRRISGGGA
+MFMEADNCVTYSLHVPRSLVDGLETAESYPFLDEWTMDALSRLGVQAFYQPLNDIATDQG
+KIGGAAQKRVGQDGLLHHVTMSYDIDADKMLEVLRIGREKLKGKGVASAKKRVDPLRRQT
+GVARPEIWETMMATFEERYGARRVELDDATRAEAEELARTKFGTQEWTARVP
+>3_1600
+MSTQTTHHGEFKVLGGKLVAADLEVQDGVIVRASVNGDFFLEPDDALEDINAALTGLPAD
+TEHHVLAERVRAGLRPEARLFGFDAEAVATAVRRAVGLATTWESHRWEILPPEPLPIEMN
+TALDQILTEDVAAGRRNPVMRLWQWTEPAVVIGAFQSLANEVDPDGVTRHGIHVVRRVSG
+GGAMFMEADNCVTFALSAPASLVDGIDTAESYPFLDEWVMEALRELGVQAFYQPLNDIAT
+DQGKIGGAAQKRFGATGLLHHVTMSYDIDADKMTEVLRIGREKLRGKGVASAKKRVDPLR
+RQTGVPREQIWETMMAVFERRYGARRVELDADTRARAEELARTKFSSPEWTARVP
+>4_1058
+MTTLHGEYKVIGGKLVAADLSLADGRIATASINGDFYLEPDEALEDLNAAVAGLSADAEH
+RVIREAVERGLRPEAELFGVDAFAVASAVRRALGKATTWGDHEWEVIGPEPMPIALTVAL
+DEVLTRQVAEGRRKPTMRLWQWNEPAVVIGAFQSLANEVDPEGARRHGINVVRRISGGGA
+MFMEADNCVTYSMHVPSSLVDGLETAESYPFLDEWTMDALSRLGVHAFYQPLNDIATDQG
+KIGGAAQKRVGTAGLLHHVTMSYDIDADKMLEVLRIGREKLRGKGVTSAKKRVDPLRRQT
+GVSRAEIWETMMTTFEERYGARRVELDEATREEAEQLARTKFATPEWTARVP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000961.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000961.fa
new file mode 100644
index 0000000000000000000000000000000000000000..790a8ed31dfc62bea4996ea15f72a5c13f19a82a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000961.fa
@@ -0,0 +1,80 @@
+>0_1110
+MTDTTPDLDATNVTRAEAADRSRLLTVQDYVVDVDLSDARDAAADTYPVRTVIRFACAEP
+GAQTHLDWIHGGVESVALNGTALDVAEVVGEARVLLPDLAAQNVVELVGRSVYSRSGEGL
+HRFTDPADGEVYLYTQYEPADARRVFPDFEQPDLKAAFTFSLTGPEDWVLASNRPEVSRT
+PTGDGVVRVEFAPTLPQSTYITTLLAGPYAQWEDAWDGHPASGAQAVPLRLFTRRTMADA
+FDPEAVFDVTKRGLTFFHDLFGVAYPWGKYDQAFVPEYNLGAMENPGLVTFTEDFVFTSR
+ATAVQYEGRANVILHEMAHMWFGDLVTMHWWDDLWLKESFADYMGALGVDEATDFRTAWV
+TFASRRKAWAYVQDQMPTTHPIVADIVDLEAARQNFDGITYAKGASVLKQLAAYVGRDAF
+LDAAHRYFAAHAWGNASLADFMAVLEAASGRDMRAWADAWLHTSGVPRLRVDVDGDAPVL
+RQEGADPVTGGPILRPHVLKVGVFTPGQDGVLRRTAQVTADVPGGAEGAAVPLPDLEVPG
+GVRLVLPNDEDLTYAAVALDAGSLRAALTHPIADPLAEATVWAALWSMTRDGELPVARFL
+DAVATLSARIATVGVHAQVLAQAAAAVGQYARAEDRDALRSRLGEVLAEQTRTLEAGSDR
+QRTAARTWATLARADVGMAAALEAALLGEDAAAFAPGLAVDAELRWLVLQALAATGRADQ
+DRLDAELEAGRTAQTVTWHRLAAAARPEAEVKAAAWEAVMSGRTTTGTELSNDLLSATAA
+GFAAGGVELLAPYESGFWPRLTSVWASRSNGLASRAIGGLFPGRQDAVAGGADAQESHPT
+LAAAQRWLDEHPDAPGALRRLVVEHTDALRRSLRVQAVQPAG
+>1_838
+MTDTTPDLDATNVTRAEAADRSRLLTVQDYVVDVDLSDARDAAADTYPVRTVIRFACAEP
+GAQTHLDWIHGGVESVTLNGTALDVAEVVGEARVLLPDLAAQNVVELVGRSVYSRSGEGL
+HRFTDPADGEVYLYTQYEPADARRVFPDFEQPDLKAAFTFSLTGPEDWVLASNRPEVSRT
+PTGDGVVRVEFAPTLPQSTYITTLLAGPYAQWEDAWDGHPASGAQAVPLRLFTRRTMADA
+FDPEAVFDVTKRGLTFFHDLFGVAYPWGKYDQAFVPEYNLGAMENPGLVTFTEDFVFTSR
+ATAVQYEGRANVILHEMAHMWFGDLVTMHWWDDLWLKESFADYMGALGVDEATDFRTAWV
+TFASRRKAWAYVQDQMPTTHPIVADIVDLEAARQNFDGITYAKGASVLKQLAAYVGRDAF
+LDAAHRYFAAHAWGNASLADFMAVLEAASGRDMRAWADAWLHTSGVPRLRVDVDGDAPVL
+RQEGADPVTGGPILRPHVLKVGVFTPGQDGVLRRTAQVTADVPGGAEGAAVPLPDLEVPG
+GVRLVLPNDEDLTYAAVALDAGSLRAALTHPIADPLAEATVWAALWSMTRDGELPVARFL
+DAVATLSARIATVGVHAQVLAQAAAAVGQYARAEDRDALRSRLGEVLAEQTRTLEAGSDR
+QRTAARTWATLARADVGMAAALEAALLGEDAAAFAPGLAVDAELRWLVLQALAATGRADQ
+DRLDAELEAGRTAQTVTWHRLAAAARPEAEVKAAAWEAVMSGRTTTGTELSNDLLSATAA
+GFAAGGVELLAPYESGFWPRLTSVWASRSNGLASRAIGGLFPGRQDAVAGGADAQESHPT
+LAAAQRWLDEHPDAPGALRRLVVEHTDALRRSLRVQAVQPAG
+>2_1702
+MPRPHAAVDLDATNVTRAEAAERSRLLTVSAYEVHVDVSGARDEAAETYPVEATLRFVCA
+EPGAAAHVDWIHAGVDAVVLNGRELEPADVVGDARILLPELAAENELVLRGRSRYSRSGE
+GLHRFTDPADGQVYLYTQYEPADARRVFPDFEQPDLKAAFTFALTGPADWVLASNRPEAS
+RTEVRPGVVRVDFEPTLPQSTYITTLLAGPYASWEDRWDGHAGTDAPAVPLRLFTRQTMA
+EAFDPEAVFDVTRRGLDLFHELFGVPYEWGKYDQAFVPEYNLGAMENPGLVTFTEDFVFT
+SRATAAQYEGRANVILHEMAHMWFGDLVTMRWWDDLWLKESFADFMGTLGVDEATDFETA
+WVTFASRRKAWAYVQDQMPTTHPIVADIVDLEAARQNFDGITYAKGASVLKQLAAYVGRD
+AFLDAARRYFRAHAWGNAELTDFMAALEAASGRDMGAWADAWLHTSGVPRLRVEAGDDGA
+SMLHQEGADPVTGRPVLRPHALKVGVFTPDEAGVLRRTAQVAADVPGGADGAAVVLEGLT
+VPAGVRLVLPNDEDLTYAALALDEASLQAALTHPIADPLAEATVWAALWSMTRDGELSAA
+RFLEAVERLSAGIETVGVHTQVLAQAAAAVSQFAAAADRPSLRARLAETLAEQVRTLEAG
+SDRQRTAARTWALVARADADLARPLAAALLGGTGAGAADGEAGEDAPGLAVDAEIRWLVL
+QALAATGQADEARLDAELAAGRTAQTVTWHRLATAARPEPAVKAAAWEAVMAGRTADGVE
+LSNDLLSATAAGFAAGDVELLAEHEAGFWPRLEQVWASRSNGLASRAIGGLFPGHQDAVA
+GDAGAQESHPTLASAQRWLDEHPDAPGALRRLVVEHTDHLRRSLRVQAAQPTA
+>3_1599
+MTDSPTLTRDEARARARLITVHDYDVHVDVSGAADASAAAYPVTATIRFDCAEPGAETWL
+DWISASVESVELNGEALDPAVVASRSRVRLPDLAAQNTVTLRGTSLYSRSGEGLHRFVDP
+ADGRTYLYTQYEPADARRVFPDFEQPDLKASFTFRLTGPADWVLASNGAEVGREDAGEGA
+VTVAFAPTRRLSTYITALVAGPYAVVEDRWDGHAATGAEPLPLRVMCRRALAEHLDADEL
+FRITKAGLDFFHDLFGIPYEWGAYDQAFVPEYNLGAMENPGLVTFTEHYIHDTAPTRGQL
+EGRATTVLHEMAHMWFGDLVTMRWWDDLWLKESFADYMGTLAADEAAGFDESWTTFASRR
+KAWAYVQDAYPTTHPIVADIVDLEAARQNFDGITYAKGASVLKQLAAFVGRDAFMEAARV
+YFHRHAWGNAELDDFLAVLGAASGRDMSAWADAWLRTAGVPALAVEVDGDGAPVLVQSGV
+DPRTGEPIRRPHVLRVGVFTPDADGALTRTAQVDADIAAGAERTTLPGLAVPDGPRLILP
+NDEDLTYAAVALDEASLDAVLTRPVADPLAQATVWAALWSMVREGTLPAARFVGAVQELS
+ASVAGVAVYTQVVSQAAAAVELYATAAQRGALRAGLGEHLLSALRSLEAGGDRQRAAVRT
+LAVLARGDADLARRLETAVLEDAETGAPGLAVDAEIRWLVLQALAATGSADRARLDAALA
+EERTAKTVVAHRLAVQAIPDPAVKRAAWDAVLAGEDAEGQALSNDLLSATASGFAAGGHD
+LVDPFEPGFWGELEGLWSSRSNGLASRAISGLFPLHQDALPGDAAAQEAHPVLARAQAWL
+DEHTAAPGALRRLVVEQTDALRRSLRVQAAQPTP
+>4_1060
+MTDTTPDLDATNVTRAEAADRSRLLTVQDYVVDVDLSDARDAAADTYPVRTVIRFACAEP
+GAQTHLDWIHGGVESVTLNGTALDVAEVVGEARVLLPDLAAQNVVELVGRSVYSRSGEGL
+HRFTDPADGEVYLYTQYEPADARRVFPDFEQPDLKAAFTFSLTGPEDWVLASNRPEVSRT
+PTGDGVVRVEFAPTLPQSTYITTLLAGPYAQWEDAWDGHPASGAQAVPLRLFTRRTMADA
+FDPEAVFDVTKRGLTFFHDLFGVAYPWGKYDQAFVPEYNLGAMENPGLVTFTEDFVFTSR
+ATAVQYEGRANVILHEMAHMWFGDLVTMHWWDDLWLKESFADYMGALGVDEATDFRTAWV
+TFASRRKAWAYVQDQMPTTHPIVADIVDLEAARQNFDGITYAKGASVLKQLAAYVGRDAF
+LDAAHRYFAAHAWGNASLADFMAVLEAASGRDMRAWADAWLHTSGVPRLRVDVDGDAPVL
+RQEGADPVTGGPILRPHVLKVGVFTPGQDGVLRRTAQVTADVPGGAEGAAVPLPDLEVPG
+GVRLVLPNDEDLTYAAVALDAGSLRAALTHPIADPLAEATVWAALWSMTRDGELPVARFL
+DAVATLSARIATVGVHAQVLAQAAAAVGQYARAEDRDALRSRLGEVLAEQTRTLEAGSDR
+QRTAARTWATLARADVGMAAALEAALLGEDAAAFAPGLAVDAELRWLVLQALAATGRADQ
+DRLDAELEAGRTAQTVTWHRLAAAARPEAEVKAAAWEAVMSGRTTTGTELSNDLLSATAA
+GFAAGGVELLAPYESGFWPRLTSVWASRSNGLASRAIGGLFPGRQDAVAGGADAQESHPT
+LAAAQRWLDEHPDAPGALRRLVVEHTDALRRSLRVQAVQPAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000962.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000962.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eafa1aff9d39b67f70567420adf338f25d772f12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000962.fa
@@ -0,0 +1,40 @@
+>0_1111
+MVQKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGTYRLIDFALSNLVNSRYREIVVLTQ
+YKSHSLDRHISETWRMSTLLNNYVASVPAQQRRGKDWFTGSANAIYQSMNLIHDARPDIV
+VVIGADHVYHMDFQQMVDQHIASGAKATVAAVRQPLELASSFGVIETDPQDRTRISAFVE
+KPETTPGLPDDPTQFLASMGNYVFDTDALVAALNQDEENPESNNDMGGDIIPLFVERGEA
+GVYDFTANEVPGGTAGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNREWPLYTRQSVSP
+PAKLVRSSTRRPGSANDSILSQGVVISGGTVAQSVLSTDVRVHNEAWVEQSVLLDSVVIG
+EGAHVRNAILDKNVVVPPGARIGFDRAEDEANGYTVTESGLTVLSKGQPVPTPH
+>1_839
+MVQKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGTYRLIDFALSNLVNSRYREIVVLTQ
+YKSHSLDRHISETWRMSTLLNNYVASVPAQQRRGKDWFTGSANAIYQSMNLIHDARPDIV
+VVIGADHVYHMDFQQMVDQHIASGAKATVAAVRQPLELASSFGVIETDPQDRTRISAFVE
+KPETTPGLPDDPTQFLASMGNYVFDTDALVAALNQDEENPESNNDMGGDIIPLFVERGEA
+GVYDFTANEVPGGTAGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNREWPLYTRQSVSP
+PAKLVRSSTRRPGSANDSILSQGVVISGGTVAQSVLSTDVRVHNEAWVEQSVLLDSVVIG
+EGAHVRNAILDKNVVVPPGARIGFDRAEDEANGYTVTESGLTVLSKGQPVPTPH
+>2_1701
+MVQKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGTYRLIDFALSNLVNSRYREIVVLTQ
+YKSHSLDRHISETWRMSTLLNNYVASVPAQQRRGKDWFTGSANAIYQSMNLIHDARPDIV
+VVIGADHVYHMDFQQMVDQHIASGAKATVAAVRQPLELASSFGVIETDPQDRTRISAFVE
+KPQTTPGLPDDPTLFLASMGNYVFDTDALVAALNQDEENPESNNDMGGDIIPLFVERGEA
+GVYDFTANEVPGGTAGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNRDWPLYTRQSVSP
+PAKLVRSSTRRPGSANDSILSQGVVISGGTVAQSVLSTDVRVANEAWVEQSVLLDSVVIG
+EGAHVRNAILDKNVVVPPGARIGFDRAEDEANGYTVTDSGLTVLAKDQSVPKPH
+>3_1598
+MVEKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGEYRLIDFALSNLVNSRFREIVVLTQ
+YKSHSLDRHISETWRMSTMLNNYVATVPAQQRRGKDWFTGSANAIYQSMNLISDARPDIV
+VVIGADHVYHMDFQQMVDHHVASGAKATVAAVRQPLELADQFGVIETDATDPGRITAFVE
+KPATTPGLADDPAQFLASMGNYVFDTDALVEALNADDANPESNNDMGGDIVPYFVGRGEA
+GVYDFTTNEVPGGTPGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNRAWPLYTRQSVSP
+PAKLVRSASRRPGTAGDSILAQGVVISGGTVAQSVLSTDVRVGNEAWVEQSVLLDSVTVG
+EGAHVRNAIIDKNVVIPAGARIGFDRAEDEANGYTVTDSGLTVLSKNQRVPDPR
+>4_1061
+MVQKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGTYRLIDFALSNLVNSRYREIVVLTQ
+YKSHSLDRHISETWRMSTLLNNYVASVPAQQRRGKDWFTGSANAIYQSMNLIHDARPDIV
+VVIGADHVYHMDFQQMVDQHIASGAKATVAAVRQPLELASSFGVIETDPQDRTRISAFVE
+KPETTPGLPDDPTQFLASMGNYVFDTDALVAALNQDEENPESNNDMGGDIIPLFVERGEA
+GVYDFTANEVPGGTAGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNREWPLYTRQSVSP
+PAKLVRSSTRRPGSANDSILSQGVVISGGTVAQSVLSTDVRVHNEAWVEQSVLLDSVVIG
+EGAHVRNAILDKNVVVPPGARIGFDRAEDEANGYTVTESGLTVLSKGQPVPTPH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000970.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000970.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9e0eb15163175df169ff764e60b04930aa3d81ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000970.fa
@@ -0,0 +1,15 @@
+>0_1120
+MREQLMSSTLDAISRGQKWEYLVMTVAAHESLADARRRLVEHAEYGQWELQRSVHYRDGA
+RRYWMRRRVMRVASTLQTL
+>1_848
+MREQLMSSTLDAISRGQKWEYLVMTVAAHESLADARRRLVEHAEYGQWELQRSVHYRDGA
+RRYWMRRRVMRVASTLQTL
+>2_1692
+MREQLMSSTLDSIARGQKWEYLVITVSPDESLGDARRRLVEHAEYGRWELQRSVHFRGGA
+RRYWLRRRVVRVASTLASA
+>3_1589
+MDGMREQLMSSTLDSIARGEKWEYLVITVAPHESLADARRRLVDHAEYGQWELQRSVHYR
+GGTRRHWMRRRVIRVRSTLQS
+>4_1070
+MREQLMSSTLDAISRGQKWEYLVMTVAAHESLADARRRLVEHAEYGQWELQRSVHYRDGA
+RRYWMRRRVMRVASTLQTV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000971.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000971.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c22c6e0df1c9ce22b149e284e92827a31023f932
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000971.fa
@@ -0,0 +1,15 @@
+>0_1121
+MSSDARMALEALTTALNEHLVAAQNKRGEDDPAVEAAFFAVADAFEAYEDALYADTEEVT
+PLDLFDDEDDDD
+>1_849
+MSSDARMALEALTTALNEHLVAAQNKRGEDDPAVEAAFFAVADAFEAYEDALYADTEEVT
+PLDLFDDEDDDD
+>2_1691
+MSSDARMALEALTTALNEHLVAAQNKRGEDDPAVEAAFFAVADAFEAYEDALYADTEEVT
+PLEVFDDEEDDEA
+>3_1588
+MSSDARVALEALTSALNEHLVAAQNRRGEDDPAVEAAFFAVADAFDAYEEALYAETEEVT
+PLELFDDEDDLDEED
+>4_1071
+MSSDARMALEALTTALNEHLVAAQNKRGEDDPAVEAAFFAVADAFEAYEDALYADTEEVT
+PLDLFDDEDDDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000975.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000975.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de672f5ec7d3937e7a755c63c6c8a537d9d5730c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000975.fa
@@ -0,0 +1,28 @@
+>0_1125
+MSRHPAPAPDDRARRLPRAVLWDMDGTLVDTEPLWNAVQRRLVVEHGGTWSEDLAASLVG
+RPLDEGARRLQEAGLDLPVQRIIDLTMHEVVQGVVSGVPWRPGARELLVALAEAGVPGAL
+VTMSHAPLARALAERAPAGTLDVVVSGDMVSRGKPDPEAYRLGLQLLAERTPGLTAADCV
+AVEDSPVGVGAAMAAGLPTVGVPSVLPLPAGLATVEWTTLAGRTPADLAAVRQIAAARGP
+GGDGAE
+>1_853
+MPRHPAPAPDDRARRLPRAVLWDMDGTLVDTEPLWNAVQRRLVAEHGGTWSDDLAASLVG
+RPLDEGARRLQEAGLDLPVQRIIDLTMDEVVQGVVRGVPWRPGARELLVALAEAGVPGAL
+VTMSHAPLARALAERAPAGTLDVVVSGDMVSRGKPDPEAYRLGLQLLAERTPGLTAADCV
+AVEDSPVGVGAAMAAGLPTVGVPSVLPLPAGLATVEWTTLAGRTPADLAAVRRIAAARGP
+GADGAG
+>2_1687
+MDGTLADTEPLWNASQRRLLAEHGGVWSEALADSLVGRPLDEGARRLQAAGLDLPVDEII
+ERTMGAVTRGVADRVPWRPGARELLAALAEAGVPGALVTMSHAPLARALAERAPAAALDV
+VVSGDLVARGKPDPEAYLLALDLLAARHPGLDAAGCVAVEDSPVGVAAAVAAGLPTVGVP
+SVLPLPAGAATVEWDTLAGRAPADLAAVRDVAAGRAEDAPAPAGPGGRA
+>3_1584
+MPRTPAAPAPVLPAALLWDMDGTLVDTEPLWNAVQRRLVEEHGGTWSDGLAASLVGRPLD
+EGARSLRAAGLRMEVPEIIEATMAEVARGVEAATPWRPGALELLTAQAEAGVPGALVTMS
+HAPLARVLAERAPAGALRVVVTGDRVSRGKPDPEAYLLALEELSAHVPGLRAEDCVAVED
+SPVGVAAAVAAGLPTVGVPSVLPLPEGAATVQWGTLAGRGLADLAAVRPGAAG
+>4_1075
+MPRHPAPAPDDRARRLPRAVLWDMDGTLVDTEPLWNAVQRRLVVEHGGTWSEDLAASLVG
+HPLDEGARRLQEAGLDLPVQRIIDLTMDEVVQGVVGGVPWRPGARELLVALAEAGVPGAL
+VTMSHAPLARALAERAPAGTLDVVVSGDMVSRGKPDPEAYQLGLQLLAERTPGLTAADCV
+AVEDSPVGVGAAVAAGLPTVGVPSVLPLPAGLATVEWTTLAGRTPADLAAVRRIAAARRP
+GADEPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000976.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000976.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5386f4f44b6e06db9f62fb503a6ba8c915f5390d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000976.fa
@@ -0,0 +1,40 @@
+>0_1126
+MSGPASVRLGTIAGAPVRLSWSWLLIAAAITLAFGPQIQRALPSLGGGAYGVALGYAVLL
+ALSVLVHEAAHALTGRAFGQRTEEIALTLWGGHTQFRSPSARPLDTVLTAMAGPAANLVL
+AGLAHLAARAVAGPSVPALLLEVTVWANLLLAAFNALPGTPLDGGRMVESAVWAATGSRA
+RGVEAAGWAGRVVAVGVLAAVLGPPILAGRAPDLFVVVLAAWVALTLWRGADDAVRHGRW
+SRRLETLRLEQVEAPAVALPEHLSVAEALAQADDGRRAVVAVDGAGRPRGVLDLAAAAGL
+TPERRTTTALAAVAVALAPGAVLVRDDVPAAGPDLAARLADPQTPVWVLTDAHGLVRSVV
+PRETILAAVDATRRP
+>1_854
+MSGPASVRLGTIAGAPVRLSWSWLLIAAVITLAFGPQIQRALPLIGGGAYGVALGYAVLL
+ALSVLVHEAAHALTGRAFGQRTEEIALTLWGGHTQFRSPSARPLDTVLTAMAGPAANLVL
+AGLAHLAARAVAGPSVLALLLEVTVWANLLLAAFNALPGTPLDGGRMVESAVWAATGSRA
+RGVEAAGWAGRVVAVGVLAAVFGPPTLAGRAPDLFVVVLAAWVALTLWRGADDAVRHGRW
+SRRLETLRLEQVEAPAIALPEHLCVAEALAQADGGRRAVVAVDGAGRPRGVLDHTAAAGL
+TPARRTTTALAAVAVALAPEAVLVRDDVPAAGPDLASRLADPQTPVWVLTDAHGLVRSVV
+PRETILAAVDATRRP
+>2_1686
+MSGAAARRIGSLRLGSVAGAPVLLSWTWLLIAVAIVLALGPQIRRALPELGAGAYGVALG
+YAVLLALSVLVHEVAHALAGRAAGQRAEEIALTLWGGHTQFRGAHAGPLGTVLTAMAGPA
+ANLALAGLAHLAARAVDGPSVAALLLDVSVWANLLLAAFNALPGAPLDGGRMVESAVWAA
+TGSRDRGVEASGWAGRVIAAGIVAAALLAPLLQGRTPDVLFTALLIWAALTLWRGAGDAV
+ARGRWGRRLAGLRLADLELAAVAVPEHLSVAEALAHADGGRRAAVAVDGAGLPRGVLDRT
+AVGRLDAAARAGTPVAAAAVALAPQAVLEREALPEAGPELAAVLADPETPVWVLTDVRGL
+VRSVVTRERILAAVHATRRP
+>3_1583
+MSGPRALTLGRIAGAPVRLSPAWVAVAGAVVLLFGPQVARALPGLGGAAWLVALGYAALL
+ALSVLVHEAAHAVAGRAFGQRPQEIVLTLWGGHTQFAAPQATPVGTVVTALAGPAANVVL
+AGLAWALGAAADARGVPGLLVDATVWANLLLAGFNALPGAPLDGGRMVESAVWAATGSRD
+RGVAAAGWTGRLIAAALVIGWVAVPLVRGERPGLVVSLLLVWVAVTLWRGASESVERGRW
+GRRLAGVRLADLAIPALAVPVDADASAVLAGVPAGLAVVAVDEAGRPVGVLDRAALDGAA
+ASARVPVAAACRAVAPHAVLAADSLPPSGGALVASLATAAESAADPRPGVPGLDSTPVWV
+LTDGHGAVRSVLPRERILTALATASRPDPEEPRP
+>4_1076
+MSGPASVRLGTIAGAPVRLSWSWLLIAAVITLAFGPQIQRALPSLDGGAYGVALGYAVLL
+ALSVLVHEAAHALTGRAFGQRTEEIALTLWGGHTQFRSPSARPLDTVLTAMAGPAANLVL
+AGLAHLAARAVPGPSVPALLLEVTVWANLLLAAFNALPGTPLDGGRMVESAVWAATGSRA
+RGVEAAGWAGRVVAVGVLAAVFGPPTLAGRAPDLFVVVLAAWVALTLWRGADDAVRHGRW
+SRRLETLRLEQVEAPAIALPEHLCVAEALAQADGGRRAVVAVDGAGRPRGVLDHTAAAGL
+TPARRTTTALAAVAVALAPEAVLVRDDVPAAGPDLASRLADPQTPVWVLTDAHGLVRSVV
+PRETILAAVDATRRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000979.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000979.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a9f476b69e55029facfcd16519181aabc3b2ade4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000979.fa
@@ -0,0 +1,55 @@
+>0_1129
+MSAFGRGAADGFARAAAVDVGPTPAFEGQRRLFHGAAVPPNGRDAAGWGVHRVMGTETEF
+GIHAPANPGAHHSVLSVELVNAYADLVTRSGSAVAGTEWDYTGESPLVDARGWRLPRSAA
+HPSQLTDEALVGPDGEPVHLLLSTVLANGARWYVDHAHPEYSSPETTTPRDAMVWDAAGD
+LVAQAAAEHIGQAEGAPEVLVYKNNVDGKGQSYGAHENYLVARSLDFEELTAVLLPFFAA
+RQVLVGAGRVGLGPAGERPGFQLSQRADYFEEPVGLETTIHRPIVNTRDEPHARPEAYRR
+LHVIIGDATLSQHATWLRMGMTALVLAMAEAGTAPRLTLDDPVAALQTISHDPGLRATVP
+LLERTADGPVRRHWTGLQILRSYLDAARAHCAAFGVTDPQTREVLEAWAIDLDDATADPL
+SLSDRADWAAKLRVLEGLRARTGADWTDPRLAMVDLQYADLRPARSLHRRLVAAGALRTL
+ADEAEIRAAVATPPRATRAWTRGNLVGRHGDRVAGAAWETLLLRGAGERVHRLHLAEPLV
+GAAVDLPGWWEDAAAPRPDDEALVATLAPLFGARA
+>1_857
+MSAFGRGAADGFARVAAVDVGPTPAFEGQRRLFHGAAVPPNGRDAAGWGVHRVMGTETEF
+GIHAPANPGAHHSVLSVELVNAYADLVTRSGSAVAGTEWDYTGESPLVDARGWRLPRSAA
+HPSQLTDEALVGPDGEPVHLLLSTVLANGARWYVDHAHPEYSSPETTTPRDAMVWDAAGD
+LVAQAAAEHIGQAEGAPEVLVYKNNVDGKGQSYGAHENYLVARSLDFEELTAVLLPFFAA
+RQVLVGAGRVGLGPAGERPGFQLSQRADYFEEPVGLETTIHRPIVNTRDEPHARPEAYRR
+LHVIIGDATLSQHATWLRMGMTALVLAMAEAGTAPRLTLDDPVAALQTISHDPGLRATVP
+LLERTADGPVRRHWTGLQILRSYLDAARAHCAAFGVTDPQTREVLEAWAIDLDDATADPL
+SLSDRADWAAKLRVLEGLRARTGADWTDPRLAMVDLQYADLRPARSLHRRLVAAGALRTL
+ADEAEIRAAVATPPRATRAWTRGNLVGRHGDRVAGAAWETLLLRGAGERVHRLHLAEPLV
+GAAVDLPGWWEDAAAPRPDDEALVATLPPLFGARA
+>2_1683
+MSAFGRGTADGFARAVAVDVGPTPAFEGQRRLFHGAAVPPNGRDAAGWGVHRVMGTETEF
+GIHAPANPGAHHSVLSVELVNAYADLVTRSGSAVAGTEWDYTGESPLVDARGWRLPRSAA
+HPSQLTDEALVGPDGEPVHLLLSTVLANGARWYVDHAHPEYSSPETTTPRDAMVWDAAGD
+LVAQAAAEHIGQAEGAPEVLVYKNNVDGKGQSYGAHENYLVARSLDFDELTAVLLPFFAA
+RQVLVGAGRVGLGPAGERPGFQLSQRADYFEEPVGLETTIHRPIVNTRDEPHARPEAYRR
+LHVIIGDATLSQHATWLRMGMTALVLALAEAGTAPRLVLDDPVAALQTISHDPGLRATVP
+LLEHTADGPVRRHWTGLQILRSYLDAAHAHCAAFGVTDPQTREVLEAWAIDLDDATADPL
+SLSDRADWAAKLRVLEGLRARAGADWTDPRLAMVDLQYADLRPARSLHRRLVAAGALRTL
+ADEAEIRAAVATPPRATRAWTRGNLVGRHGDRVAGAAWETLLLRGAGERVHRLHLAEPLV
+GAAVDLPGWWEDAAAPRPDDEALVATLPPLFGARA
+>3_1580
+MPGGIGGAPEAVAGTPAFAGQRRLFPADLTAPPGGRDAAGWGVHRVMGTESEFGIHAPAN
+PGAHHSVLSVELVNSYADLITHSGGAVAGTEWDYAGESPLVDARGWRMPRSAAHPSQLTD
+QALVGPDGEPVHLLLSTVLPNGARWYVDHAHPEYSSPEVASPREAVVWDAAGDRVAQAAA
+EHIAAAEGAPEVLVYKNNTDGKGQSYGSHENYLVARALPFDELAEVLLPFFAARQVLVGA
+GRVGVGLRGERPGFQLSQRADFFEEQVGLETTIRRPIVNTRDEPHARGDAYRRLHVIIGD
+ANLSQHATWLRMGMTALVLALAEAGTAPRIVLDDPVAALQTISHDPTLRAAVPGRERGAD
+GVWTRREWTGLQILGAYLDAAREHCARCGVDDAETAAVLDAWGTDLADAAADPLALADRA
+DWAAKLRVLEGLRARGGLDWSDPRLAMVDLQYADLRPAKSLHRRLVAAGAMRVLVEDAEV
+EAAVVAPPRSTRAWTRGNLVRHHARQVSGAAWDSVLVRAAEEAPLHRLRLEEPLVGAAED
+LPGWWDDTPGSAAPAPEPNELVTRLGELLRR
+>4_1079
+MSAFGRGAADGFARAVDVGPTPAFEGQRRLFHGAAVPPNGRDAAGWGVHRVMGTETEFGI
+HAPANPGAHHSVLSVELVNAYADLATRSGSAVAGTEWDYTGESPLVDARGWRLPRSAAHP
+SQLTDEALVGPDGEPVHLLLSTVLANGARWYVDHAHPEYSSPETTTPRDAMVWDAAGDLV
+AQAAAEHIGQAEGAPEVLVYKNNVDGKGQSYGAHENYLVARSLDFEELTAVLLPFFAARQ
+VLVGAGRVGLGPAGERPGFQLSQRADYFEEPVGLETTIHRPIVNTRDEPHARPEAYRRLH
+VIIGDATLSQHATWLRMGMTALVLAMAEAGTAPRLTLDDPVAALQTISHDPGLRATVPLL
+ERTADGPVRRHWTGLQILRSYLDAARAHCAAFGAADPQTREVLDAWAVDLDDATADPLSL
+SDRADWAAKLRVLEGLRARTGADWTDPRLAMVDLQYADLRPARSLHRRLVAAGALRTLAD
+EAEIRAAVATPPRATRAWTRGNLVGRHGDRVAGAAWETLLLRGAGERVHRLHLAEPLVGA
+AVDLPGWWEDAAAPRPDDEALVATLAPLFGARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000981.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000981.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c776972edb9ca940627094d95cac18e39e5b1d3a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000981.fa
@@ -0,0 +1,20 @@
+>0_1131
+MRLWTLHPRHLDRQGLTGAWREALLAQAVLAGRTRGYRDHPQLLRFREHPDPSGAIGAFL
+SGLEAEATARGYRFDHSRIDRPCPAPDGAVRIPPAGLAPIPATTGQRDLEWRHLCAKLAA
+RSPAWLERWSDTPVPDVHPLFTIVPGPVASWERA
+>1_859
+MRLWTLHPRHLDRQGLTGAWREALLAQAVLAGRTRGYRDHPQLLRFREHPDPSGAIGAFL
+SGLEAEATARGYRFDHSRIDRPCPAPDGAVRIPPAGLAPIPATTGQRDLEWRHLCAKLAA
+RSPAWLERWSDTPVPDVHPLFTIVPGPVASWERA
+>2_1681
+MRLWTLHPRHLDRQGLTGAWREALLAQAVLAGRTRGYRDHPQLLRFREHPDPSGAVGAFL
+SGLEAEATARGYRFDHSRIDRPCPAPDGAVRIPTVGLAPIPATTGQRDLEWRHLCAKLAA
+RSPAWLERWADTPVPDVHPLFTIVPGPVASWERA
+>3_1578
+MRLWTLHPRHLDRQGLTGGWREALLAQAVLARRTKGYRDHPQLERFRGHGDPAAAIGAFL
+SGIALEASARGYRFDVSKIDRPLLPADGAGELVLPFRIAPIEVTTGQVAHEWGHLRAKLA
+ARSPGWLERWADVQTPDVHPLFEVVDGPIASWERP
+>4_1081
+MRLWTLHPRHLDRQGLTGAWREALLAQAVLAGRTRGYRDHPQLLRFREHPDPSGAVGAFL
+SGLEAEATARGYRFDHSRIDRPCPAPDGAVRIPPAGLAPIPATTGQRDLEWRHLCAKLAA
+RSPAWLEQWSDTPVPDVHPLFTIVPGPVASWERA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000994.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000994.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e6766ebc3a010eb216f2512f27d903b8ddf381a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000994.fa
@@ -0,0 +1,65 @@
+>0_1145
+MTSSPVAVSPLLQPITLGPLTLPNRVVMASMHMGLEDRHDDLPQLAAFYAERARGGVGLI
+VTGGLGVVPEGTVTLGGGMLASEEDARAHRVVTDAVHAAGGRILAQLLHAGRYAPSPDLV
+SASAVRAPISRHTPREMTAADIERTVNAFARAATLALEAGYDGVEIMASEGYLLNQFLAP
+ATNRRADEYGGDAERRRRFPVAVVAAVREALGERGVLSVRTSAADLVPDGQTRAEIADTA
+RAFEAAGADVLMTGIGWHESRVPTIVTSVPRAAFLAASADLTAAVDIPVIASNRLTTPAE
+AEEALTSGAAALVGLARPLLADPDWMAAIGDPRARTLTPCIACNQACLDHVFTGAKVSCL
+MNPRAGRETEPEYAAPVPVALGRRRRIAVVGAGPAGLTAAERAARFGHEVTLFDRHAEPG
+GQFRLARRIPGKEEFGPALEHLAARAAASGVTLVTGEEVSAQTLLTDDGRPGYDEVLLTT
+GVRPRPVALPGTGEPGAPAVHAYDDVVLGHVDVGPRVAVIGAGGVGVDVAEALAAGTERP
+DGTPETQEHWRARWGVALTSQTPGQLAKPAAADPGREVHLLQRSPGPIGVRLRPTTGWVH
+RAELRRHGVHLHSGVTYEGLGPDGLRVTAPSPEDPEARVALTLDVTDVVVCAGQESETDL
+VEDLVAAGYAPEAVRLIGGAAEARELDAYRAMDHAVRAVQG
+>1_873
+MTSSPVAVSPLLQPITLGPLTLPNRVVMASMHMGLEDRHDDLPQLAAFYAERARGGVGLI
+VTGGLGVVPEGTVTLGGGMLASEEDARAHRVVTDAVHAAGGRILAQLLHAGRYAPSPDLV
+SASAVRAPISRHTPREMTAADIERTVNAFARAATLALEAGYDGVEIMASEGYLLNQFLAP
+ATNRRADEYGGDAERRRRFPAAVVAAVREALGERGVLSVRTSAADLVPDGQTRAEIADTA
+RAFEAAGADVLMTGIGWHESRVPTIVTSVPRAAFLAASADLTAAVDIPVIASNRLTTPAE
+AEEALTSGAAALVGLARPLLADPEWMAAISDPRARTLTPCIACNQACLDHVFTGAKVSCL
+MNPRAGRETEPEYAAPVPVALARRRRIAVVGAGPAGLTAAERAARFGHEVTLFDRHAEPG
+GQFRLARRIPGKEEFGPALEHLAARAAASGVTLVTGEEVSAQTLLTDDGRPGYDEVLLTT
+GVRPRPVALPGAGEPGAPAVHAYDDVVLGHVDVGPRVAVIGAGGVGVDVAEALAAGTERP
+DGTPETQEHWRARWGVALTAETPGQLAKPAAAHPGREVHLLQRSPGPIGVRLRPTTGWVH
+RAELRRHGVHLHSGVTYEGLGPDGLRVTAPSPEDPETRVPLTLDVTDVVVCAGQESETDL
+VEDLVAAGYAPEAVRLIGGAAEARELDAYRAMDHAVRAVQG
+>2_1666
+MTVAPAITSPLLEPITLGPLTLPNRVVMASMHLGLEDRHEDLPRLAAFYAERARSGVGLI
+VTGGVGVVPEGTVAPGGGLLATAEDARAHRVVTDAVHAEGGRILVQLLHTGRYARGEDLV
+CASAVRAPISAHTPREMDEADLERTVAAFARAAALALEAGYDGVEVMASEGYLLNAFLAP
+VTNRRQDAYGGSAQARRRFPVRVVEAVRAALGERGVLSVRTSAADLVPGGQTREEVADTA
+RAFEAAGADVLMTGIGWHESRVPTIVTSVPRATFLPATAALSAAVDIPVIAANRLTTPAE
+AEEAIASGAAALVGLARPLLADPDWMAGIGVDDAAALTPCIACNQACLDHVYTGAPVSCL
+MNPRAGRETDPAYARPVPVAIGRRRRVAVVGAGPAGLTAAERAARFGHEVTLFDRHDEPG
+GQFRLARRIPGKEEFGPALEHLAARARASGVTVLTGEEVTVQTLLTPEGGPAFDEVLLTT
+GVRPRRIALPGAGEPGAPAVHAYDDVVLGHAQLGPRVAVIGAGGVGVDVAEALTAGAHRP
+DGTPESAEQWRARWGVALDSPTPGQLGEPTGEPPAREVHLLQRSPEPIGARLRPTTGWVH
+RAELRRHGVRLHSGVAYEGLSAAGLHVTVPDPERPEERTPLTLDVTDVVVCAGQESEDGL
+AGDLVAAGYPAEAVRLVGGAAEARELDAYRAMDHAVRAIQG
+>3_1564
+MTHMTDAPASHRLLEPLTVRRTVLRNRVVMGSMHLGLEDSHADLPALAAFYAERAAGGVG
+LIVTGGVGVTPEGAVSPGGGLLADAADAAAHRTLTDAVHAEGGRILVQLLHAGRYARGAD
+LVSASATRAPISRHTAHALTEAEVEELVAAYARSARLALEAGYDGVEVMASEGYLLNQFL
+APSTNLREDRYGGSAENRRRFPVAVVAAVREALGETGLLSVRTSLTDLVPGGQTSAEALD
+TARAFEAAGADLIMTGIGWHESRVPTVVTSVPRAAWAEASARVRAAVGIPVIAANRLTTP
+DDAEALLRGGAADLVAVARPLLADPDWVRTVGRAGAEHLTPCIACNQACLDHVMAGRPVS
+CLMNPRAGRETDPRYARPVPVEIGRRRRVAVVGAGPAGLTAAHRAAGFGHDVTLFEATEE
+VGGQFRLARRIPGKEEFEPALRHLEARAVAAGVHLRRETRVTPRTLLTEDGRPAFDRVII
+ATGVRPRDVDLPGVGEPGAPAVHRYDDVVAGRVRCGAAVAVIGAGGVGVDVAELLASPEG
+GAALGEPEPLEHWRARWGVADDDPTAPGGLTRPEPAERARRVFLLQRSPEPVGSRLRPTT
+GWVHRLELRALGVEMLSGVSYERVDRDGLHVTAPAVGGDGDPGRRRLVLPVTDVVVCAGQ
+ESEDGLAGDLLAAGWDPEAVTVIGGARVAAEVDAYRAMDDAVLAVQD
+>4_1095
+MTSSPVAVSPLLQPITLGPLTLPNRVVMASMHMGLEDRHDDLPQLAAFYAERARGGVGLI
+VTGGLGVVPEGTVTLGGGMLASEEDARAHRVVTDAVHAAGGRILAQLLHAGRYAPSADLV
+SASAVRAPISRHTPREMTAADIERTVNAFARAATLALEAGYDGVEIMASEGYLLNQFLAP
+ATNRRADEYGGDAERRRRFPAAVVAAVREALGERGVLSVRTSAADLVPDGQTRAEIADTA
+RAFEAAGADVLMTGIGWHESRVPTIVTSVPRAAFLAASADLTAAVDIPVIASNRLTTPAE
+AEEALTSGAAALVGLARPLLADPEWMAAISDPRARTLTPCIACNQACLDHVFTGAKVSCL
+MNPRAGRETEPEYAAPVPVALGRRRRIAVVGAGPAGLTAAERAARFGHEVTLFDRHAEPG
+GQFRLARRIPGKEEFGPALEHLAARAAASGVTLVTGEEVSAQTLLTDDGRPGYDEVLLTT
+GVRPRPVDLPGTGEPGAPAVHAYDDVVLGHVDVGPRVAVIGAGGVGVDVAEALAAGTERP
+DGTPETQEHWRARWGVALTSQTPGQLAKPAAADPGREVHLLQRSPGPIGVRLRPTTGWVH
+RAELRRHGVHLHSGVTYEGLGPDGLRVTAPSPEDPEARVALTLDVTDVVVCAGQESETDL
+VEDLVAAGYAPEAVRLIGGAAEARELDAYRAMDHAVRAVQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001009.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001009.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d188413651fe0ea61b90f79b64b1a7ea8eddbdfc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001009.fa
@@ -0,0 +1,24 @@
+>0_1161
+MFKRDKTPETAPAPSTHGSSAAPAEGAAVAEAGPRDRSQGKKGPTPRRRDQEAARRRTLV
+PEDRKAARKAERQAMAQERMRQRAALETGDERGLPARDKGPQKRWVRDYVDARTGIGEWL
+MPVVFAYVLLMFIPGREAQLILMISLYVLVALVLIESFLVSRHIKKGLTERFGTPEPGTG
+FYGIMRALQFRRLRLPKPQVKRGEYPA
+>1_889
+MFKRDKTPETAPAPSTHGSSAAPAEGAVSGAAPRDRSQGKKGPTPRRRDQEAARRRTLVP
+EDRKAARKAERQAMAQERMRQRAALETGDERGLPARDKGPQKRWVRDYVDARTGIGEWLM
+PVVFAYVVLMFIPGREAQLILMISLYALVALVLIESFLVSRHIKKGLTERFGTPEPGTGF
+YGIMRALQFRRMRLPKPQVKRGEYPA
+>2_1649
+MVPEDRKAARKAAREAAAQDRMRQRVALETGDERGLPLRDRGPQKRWVRDYVDARTGIGE
+WLMPVVFAYVLLMFLPGREVQLFLMISLYALVALVVIESLIVARRIKKGLTERFGEPESG
+TGFYGVMRALQFRRLRLPKPQVKRGQFPA
+>3_1546
+MLNRRKKTENDAPASHGSTALGAGNTPAAQPAPRDRSQGKTGPTPRRRDQEAARRRTLVP
+EDRKAARKAERDAATAERMRQRQALETGDERNLPARDKGPQKRYVRDYIDARTGLGEWLM
+PIVLVYVIAMFIPGTRAQVILMVTLYVIVGLVIAESFYISAQIKKRLTATFGTPEPGSRF
+YGVMRALQFRRLRLPKPQVRRGEFPA
+>4_1118
+MFKRDKTPETAPAPSTHGSSAAPAEGAAVAEAGPRDRSQGKKGPTPRRRDQEAARRRTLV
+PEDRKAARKAERQAMAQERMRQRAALETGDERGLPARDKGPQKRWVRDYVDARTGIGEWL
+MPVVFAYVLLMFIPGREAQLILMISLYVLVALVLIESFLVSRHIKKGLTERFGTPEPGTG
+FYGIMRALQFRRLRLPKPQVKRGEYPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001011.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001011.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a35e402c8816bb7f9e3f2b4ea4cb5a54164f3b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001011.fa
@@ -0,0 +1,39 @@
+>0_1163
+MARDPIQPPPPDPSAPHGAPAGGPTEEDTRPFLDDPPGLGWVPDGLPGFERCTLGLDTDE
+QGQNLVTVVRPRTDAPRDPARRPILSVHGWSDYFYNAPLAHAFEAAGYAFHAVDLRHYGR
+SLRAGQTPGWTDDLTRYDADLEAAFETIAQDHPLPPILMGHSTGGLIAALWADRNPGRLA
+ALVLNSPWLEMQGSAGVRLLAKSIVGPVSAMKPYATLTLPRIDHYWRTLSDQAEGEWDLH
+PLWRPPHAFEVPAAWLSAVLSGHRAVAGRLHVSVPILVLVSARGHRGTSYGEAMLTSDIV
+LDPDAMARRSLRLGDRVTVHRLPDALHDVFASPASVREAAGAATLTWLGAYAPPSATEAE
+SGAPDDGAG
+>1_891
+MARDPLQPPPPDPSAPHGAPAGGPTEEDTRPFLDDPPGLGWVPDGLPGFERCTLGLDTDE
+QGQNLVTVVRPRTDAARDPARRPILSVHGWSDYFYNAPLAHAFEAAGYAFHAVDLRHYGR
+SLRTGQTPGWTDDLARYDADLEAAFETIAQDHPLPPILMGHSTGGLIAALWADRNPGRLA
+ALVLNSPWLEMQGSAGVRLLAKSIVGPVSAMKPYAMLTLPRIDHYWRTLSDQAEGEWDLH
+PLWRPPHAFEVPAAWLSAVLSGHRAVAGRLDVTVPILVLVSARGHRGTSYAEAMLTSDIV
+LDPDAMARRSLRLGDRVTVHRLPDALHDVFASPASVREAAGAATLTWLGAYAPPSASEAG
+APDDGAG
+>2_1647
+MSIKPAEQPIPADESEPSRPPEGGPTDEDTRPLLDDPPGLGWVEDGMAGFERLTLGLDTD
+EQGQNLVTVVRPQATGPRDRTRRAILSVHGWSDYFYNAPLARAFEEAGYAFHAVDLRHYG
+RSLREGQTPGWTDDLARYDADLEAALATIAEDHPLPPVLMGHSTGGLIASLWAHRNPGRI
+SALVLNSPWLEMQGSAGVRLLAKTIVDPVSALKPYAMLTLPRIDYYWRTLSDQAEGEWDL
+HPLWRPTHAFEVPAAWLSAVLKGHRTVARRLQVSAPILVLVSARGHRGTSYDEAMLASDI
+VLDPDAMARRSLRLGDRVTVHRLPDALHDVFASPASVREAAGAATLTWLGAYAPPSASEA
+ESGAPDDGAG
+>3_1544
+MTLFPHVRGPWPRHGLGLPADDAAAPPTPVDPEAGWTPDVLDGFERRSLALNADRQGRNV
+VTVVRRRAASRHRDPCRRPFVAVHGWSDYFYNTPLAEAVESAGYAFHAVDLRHHGRSLRP
+GQTPGFVDRLDRHHEDLDAALALIAEDHPATPVVEAHSTGGLTTALWAADRPEAASALVL
+NSPWLQTHGGPLARAVAAPAVRRIARRDPYEILPLPRVDHYWRSLSAEADGEWDLEPAWR
+DRWAFAVPAGWLAAVLDGHTTVARGLDLPVPVLVLVSDRGGLPLATRRRAASSDVILSPR
+AQARAARRLGPGVVVHRCPGALHDVFASAPPVRRAALDATLSWLAETAPPRIAG
+>4_1120
+MARDPIQPPPPDPSAPHGAPAGGPTEEDTRPFLDDPPGLGWVPDGLPGFERCTLGLDTDE
+QGQNLVTVVRPRTDAPRDPARRPILSVHGWSDYFYNAPLAHAFEAAGYAFHAVDLRHYGR
+SLRTGQTPGWTDDLTRYDADLEAAFETIAQDHPLPPILMGHSTGGLIAALWADRNPGRLA
+ALVLNSPWLEMQGSAGVRLLAKSIVGPVSAMKPYAVLTLPRIDHYWRTLSDQAEGEWDLH
+PLWRPPHAFEVPAAWLSAVLSGHRAVAGRLDVSVPILVLVSARGHRGTSYAEAMLTSDIV
+LDPDAMARRSLRLGDRVTVHRLPDALHDVFASPASVREAAGAATLTWLGAYAPPSATEAE
+SGAPDDGAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001015.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001015.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51caec4ea0c34692f71883e9f72901282f71bd30
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001015.fa
@@ -0,0 +1,45 @@
+>0_1168
+MLTPAVLFALFLVFLGLTWTLSLAESAFSYLSRRDAEDIVRERPGSKVLEIARERESHLG
+ALRVWRFVAEALSAVCLTAAADAVVDDTWLAVAIAAVVLVGVAALLGVWSPRPIGSRNEA
+AVARRLGGLVWVLRRALGPLAARLDRDRRRREVEPEDEDDFQERHLREFVARAHDADVLA
+DSEAELIQSVFSMNDTIVRSVMVPRTDVVTIDADHTLGQAMALFLRSGNSRIPVIGEDAD
+DIRGMLHLKDVTRALHHDGAATDTPVTEVMRDVRFVPESKSVATLLQELQRESTHVAVVV
+DEYGGTAGLVTLEDLIEEIVGEIYDEDDQPDRPEVEFVAPGVYSVDARMGIHDFREEFEL
+PEEDEDDDVDTVGGLLAKELGRVPIQGSRVVVQGIELVADTLEPRRNRVARLRVSETPDR
+PVRLRRREEQAHGAAPADPVA
+>1_896
+MLTPAVLFALFLVFLGLTWTLSLAESAFSYLSRRDAEDIVREQPGSKVLEIARERESHLG
+ALRVWRFVAEALSAVCLTAAADAVVDDTWLAVAIAAVVLVGVAALLGVWSPRPIGSRNEA
+AVARRLGGLVWVLRRALGPLAARLDRDRRRREVEPEDEDDFQERHLREFVARAHDADVLA
+DSEAELIQSVFSMNDTIVRSVMVPRTDVVTIDADHTLGQAMALFLRSGNSRIPVIGDDAD
+DIRGMLHLKDVTRALHHDGAATDTPVTEVMRDVRFVPESKSVATLLQELQRESTHVAVVV
+DEYGGTAGLVTLEDLIEEIVGEIYDEDDRPDRPEVEFVAPGVYSVDARMGIHDFREEFEL
+PEEDEDDDVDTVGGLLAKELGRVPIQGSRVVVQGIELVADTLEPRRNRVARLRVSETPDR
+PVRLRRREEQAHGAEPADPVA
+>2_1643
+MLTPAVLFALFLVFLALVWTLSLAESAFTYLSRRDAEDIVRRRPGSRVLDVTAERDSHLG
+ALRVWRFVAEALSAVCLTAAADAVVDNTWFAVLIAAAVLVGVAALLGVWSPRPFGSRNEA
+AVARRLGGLVWGLRRALGPLADRLGRDRRRREDELEEEDDFQERHLREVVARAHDADVLA
+DSEAELIQSVFSMNDTIVRSVMVPRTDVVTIDADHTLGQAMALFLRSGNSRIPVIGEDAD
+DIRGMLHLKDVTRALHQDGAAQSGPVTAAMRDVRFVPESKSVAALLQELQRESTHVAVVV
+DEYGGTAGLVTLEDLIEEIVGEIYDEDDLPDRAEVEMIEPGVYSVDARMGLHHFREEFEL
+PEEEDEDDDVDTVGGLLAKELGRVPIQGSRVVVQGLELLADTLEPRRNRVARLRVSETPD
+RPARLRRRDEEPHGSSAAETAA
+>3_1539
+MATAVSLVLLFLACLACTWVLALAESAFTYLPRKDAEDVARTRPGSRILDVTADLDGHLG
+ALRVWRFLSEAFAAMFLTAGLHALTDSVWAALAVTAVLLVGTAAVLGVWSPRPIGSRNEA
+AVAARTAGLVHGLKQALGPVGDRLGRDRRRTEAEAADEDDFHERHLREVVARAHDAEVLE
+DSEAELIASVFSMGDTLVRSVMVPRTDVVTIDADHTLGQALDLFLRSGCSRVPVIGEDSD
+DVRGMLYLKDAVRALHHEGHASQDAVTAVMREVRFVPESKPVSVLLEELQRESTHVAIVV
+DEYGGTAGLVTLEDLIEEIVGEIWDEDDRPDRPEIEELAPGVYSVDARMGIGDFREEFEL
+PEDEDEDDDVDTVGGLLAKELGRVPIRGSRVVVHGLELTADTLEPRRNRVARLKVVETED
+RPARLRRQHDPTDPD
+>4_1125
+MLTPAVLFALFLVFLGLTWTLSLAESAFSYLSRRDAEDIVRERPGSKVLEIARERESHLG
+ALRVWRFVAEALSAVCLTAAADAVVDDTWLAVAIAAVVLVGVAALLGVWSPRPIGSRNEA
+AVARRLGGLVWVLRRALGPLAARLDRDRRRREVEPEDEDDFQERHLREFVARAHDADVLA
+DSEAELIQSVFSMNDTIVRSVMVPRTDVVTIDADHTLGQAMALFLRSGNSRIPVIGEDAD
+DIRGMLHLKDVTRALHHDGAATDTPVTEVMRDVRFVPESKSVATLLQELQRESTHVAVVV
+DEYGGTAGLVTLEDLIEEIVGEIYDEDDQPDRPEVEFVAPGVYSVDARMGIHDFREEFEL
+PEEDEDDDVDTVGGLLAKELGRVPIQGSRVVVQGIELVADTLEPRRNRVARLRVSETPDR
+PVRLRRREEQAHGAAPADPVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001024.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001024.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c30e8c4419b65d23e2faf7e4d88cdaf945d49387
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001024.fa
@@ -0,0 +1,25 @@
+>0_1178
+MAFDLHRALSLGRRTARLIGALRDDARPRRAASEAGRRAGDRSGPSPFPGPPGPPGPAWD
+PTEPTDSWPMPGPGQERRPRRQDAGRHVSLPDFTGTVRVEYAPVPGPTAGPGEVVWTWVP
+YEEMDGRGKDRPVLLIGRDGAHLLGLMLTSRDRNNALARDEDYVDVGAGAWDRSGRASEV
+KLDRVVRVDPAAVRREGGVLDRAAFDRVTAALARARRRGR
+>1_906
+MAFDLHRALSLGRRTARLIGALRDDARPRRAASEAGRRAGERSGPSPFPGPPGPPGPAWD
+PTEPTDSWPMPGPGQERRPRRQDTDRHVSLPDFTGTVRVEYAPAPGPTAGPGEVVWTWVP
+YEEMDGRGKDRPVLLIGRDGALLLGLMLTSRDRNNALTRDEDYVDVGAGAWDRSGRASEV
+KLDRVVRVDPAAVRREGGVLDRAAFDRVTAALARARRRVR
+>2_1633
+MAFDLNRALALGRRAIRLIGSLRDDDARRSWTGDAAGRGSGAAPFPGPPGPAGRAWDPKE
+PTDSWPFPDRGHDGRPRGGQDRTRPASGATDPQGRALLADFTGMGRVEYAPVPGPAAGPG
+EVVWTWVPYEEMDGRGKDRPVLLVGRDGDLLLGLMLTSRDRNNARVRDEDYVDVGSGPWD
+RAGRPSEAKLDRVLRVDPAAVRREGGVLDPAAFERVGDALARAQGWRR
+>3_1530
+MAFDFQRALTLGRTALRLVEQVRSMSGAGTTRGAAPSSPASRAGRRRRADAEETRGARSG
+GAGSDHALLPDFTGRARVEYAPVPGATPDPGEVVWTWVPFEEMDGRGKDRPVLLVGRDGD
+LLLALMLTSKDHTNAARRDADYVDVGTGPWDRGGRASEAKLDRILRVDPAAVRREGGVLE
+RSRFDAVAEALARAQGWDR
+>4_1136
+MAFDLHRALSLGRRTARLIGALRDDARPRRAASEAGRRAGDRSGPSPFPGPPGPPGPAWD
+PTEPTDSWPMPGPGQERRPRRQDTGRHASLPDFTGTVRVEYAPVPGPTAGPGEVVWTWVP
+YEEMDGRGKDRPVLLIGRDGAHLLGLMLTSRDRNNARARDEDYVDVGAGAWDRSGRASEA
+KLDRVVRVDPAAVRREGGVLDRAAFDRVTAALARARRRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001033.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001033.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a98f5c97895d67aa03e72a453c24408a7964c90
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001033.fa
@@ -0,0 +1,65 @@
+>0_1187
+MPHLDREFDYLVPVALDARAVPGSRVSVRFGGRAMTGWLVSREQEPATGAQLTELTGVLT
+VIPPLTEEVLATARAVARRQAGVVTDVLRAAVPPRVAQVEKAALAEDAEAAADHPVTLTG
+TDAERPEPPAAEEGLVPTVWESLEGGTAFVSAVLAGDAARAAAVVPSRLFEWDEAGALAA
+LARTVAASDGGVLLLVPDHRDLDRLCAALDEHVGEDAYARIGSEDGNTPRYRAHLAALRG
+TRRIVAGTRAAVWSPVRDLRLVVLWDDGDDAWAEPRAPYFHAREVVLERARATGAALLFA
+GPSRSVPVQRLVESGWLLHLGPSRAAQRELGPRVVSTADAWETARDPFAQRARLPQAAWA
+AARAALLGPRPGPVLVQVARAGFIPALVCERCRTPARCRVCAGPLGFRDARAARHGEVAC
+RWCGTRERGFRCTECGGTTLRAGARGVDRTAEELGRAFPRVPVHASSAQHMLGSVPPGPS
+LVVATVGAEPVTPDGYAAALLLDGDSQLQREGLDVPGRVLARWLAAACLVRPASDGGVVV
+VTADASEAVNALVRRDPDGFAARQVAERRELHLPPAGRLAEVSGDAAAVAEYLELVEAAR
+RERPDEDIHEDPHSAPLDGGPARLPWIGPVPDPADETRSRALLIFPYAAAEATVGALRAA
+RSAASARRETAPVRVRLDPAGVL
+>1_915
+MPHLDREFDYLVPVALDDRAVPGSRVSVRFGGRAMTGWLVSREQEPATGAQLTELTGVLT
+VIPPLTEEVLATARAVARRQAGVVTDVLRAAVPPRVAQVEKAALAEDAETAADHPVTLTG
+TDAERPEPPAAEEGLVPTVWESLEGGTAFVSAVLAGDAARAAAVVPSRLFEWDEAGALAA
+LARTVAASDGGVLLLVPDHRDLDRLCAALDEHVGEDAYARIGSEDGNTPRYRAHLAALRG
+TRRIVAGTRAAVWSPVRDLRLVVLWDDGDDAWAEPRAPYFHAREVVLERARATGAALLFA
+GPSRSVPVQRLVESGWLLHLGPSRATQRELGPRVVSTADAWETARDPFAQRARLPQAAWA
+AARAALLGPRPGPVLVQVARAGFIPALVCERCRTPARCRVCAGPLGFRDARAARHGEVAC
+RWCGTRERGFRCTECGGTTLRAGARGVDRTAEELGRAFPRVPVHASSAQHMLGSVPPGPS
+LVVATVGAEPVTPDGYAAALLLDGDSQLQREGLDVPGRVLARWLAAACLVRPASDGGVVV
+VTADAGEAVNALVRRDPDGFAARQVAERRELHLPPAGRLAEVTGEAAAVAEYLELVEAAR
+RERPDEDVHEDPHSAPLDGGPARLPWIGPVPDPADEIRSRALLIFPYAAAEATVGALRAA
+RSAASARRETAPVRVRLDPAGVL
+>2_1624
+MARVLLDSPVPHLDREFDYLIPVTLDERARPGSRVAVRFGGRPMTGWLVSREDEPATGAQ
+LTELTAVLTSVPPLTEEVLASARAVARRQAGVVTDVLRAAVPPRVAQVEKAALAEDAGAA
+ADHPVALAVEEAPEGEPVGAGDGIAPTVWESLEGGRAFVAAVLAGDGPRAAAVVPSRLLE
+WDEAAAMAHLARAVAAGGGGVLLLVPDHRDLDRLCAALDDAVGEEAYARIGSEDGNTPRY
+RAHLAALRGTRRIVAGTRAAAWAPVRDLRLTVLWDDGDDAWAEPRAPYFHAREVVLERTR
+RTGSALLFAGPSRSVPVQRLVESGWLLHLGPSRAAQREIGPRIVSTADAWETARDPFAQR
+ARLPQAAWGAARAALLGERPGPVLVQVARAGFIPALVCDRCRTPARCRRCAGPLGFRDAR
+AARLGEVACRWCGTRERGFRCTECGAGALRAGARGVDRTAEELGRAFPRIPVHSSSAQHR
+LGTIPPGPSLVVATVGAEPVAEDGYAAALLLDGDAQLQREGLDVPGRVLARWLAAACLVR
+PAADGGVVVVTADAGEAVNALVRRDPDGFAAHQVAERRELHLPPAGRLAEVTGEASAVRE
+YLDLVEAARRERPEEDVHEDPHSAPLDGGPARLPWIGPVPDAADETRSRALLLFPYAAAD
+ATVAALRAARSAASARRETSPVRVRLDPAGVL
+>3_1521
+MARVLLDSPVPHLDREFDYLVPPALDERAVPGSRVSVRFGGRETTGWLVERVAAPATHAR
+LTELAGVLTAVPPLTEHVLAVARAVAARQAGVVSDVLRSAVPPRVVSVEKEVLAELASGP
+EVDHPVQGVVADPHARLVWEELTGGTAFVASAVAGDPVRAAAVVPSRVGDWDESSALAAL
+ATAVSRAGGGVLLLVPDHRDLDRLSAALAREVGEDGFVRVGSEDGNTPRYRAHLRALTGL
+ARVVAGTRAAAWAPVQDLRLVVVWDDGDDAHAEPRAPYFHVREVALERARQSGSALLFAG
+PSRSVPVQRLVEHGWLLEVSADRASQRAASPRIVASADSWESARDPFARRARLPHAAWAA
+AGEALSGPTPGPVLVQVARAGFIPAVVCGRCRTPARCRVCAGPLAFRDRRSAERGELACR
+WCGTRERDFHCAECGFTGLRAGVRGVDRTAEELGRAFPQVPVHSSSADHRLGEVGEGPAL
+VVATVGAEPHARGGYAAALLLDGDAQLQREGLDVPVRVLTRWLAAASLVRPAAEGGTVVV
+TAEHDAAVGALVRRDPQGFAGHLLAERRELHLPPAGRLAEVTGEAGAVAEYLALVEAARR
+ERRRVGPDADPSLDLDVEARPGDATPLPWIGPVPDVADESRSRALLLFPWAASAATVDAL
+RVARSAASARRERSAVRVRLDPPGVL
+>4_1145
+MPERAEGWPERPIARVLLDSPVPHLDREFDYLVPVALDARAVPGSRVSVRFGGRAMTGWL
+VSREQEPATGAQLTELTGVLTAIPPLTEEVLATARAVARRQAGVVTDVLRAAVPPRVAQV
+EKAALAEDAEAAADHPVTLTGTDAERPEPPAAEEGLVPTVWESLEGGTAFVSAVLAGDAA
+RAAALVPSRLFEWDEAGALAALARTVAASGGGVLLLVPDHRDLDRLCAALDEHVGEDAYA
+RIGSEDGNTPRYRVHLAALRGTRRIVAGTRAAVWSPVRDLRLVVLWDDGDDAWAEPRAPY
+FHAREVVLERARATGAALLFAGPSRSVPVQRLVESGWLLHLGPSRAAQRELGPRVVSTAD
+AWETARDPFARRARLPQAAWAAARAALLGPRPGPVLVQVARAGFIPALVCERCRTPARCR
+VCAGPLGFRDARAARHGEVACRWCGTRERGFRCTECGGTTLRAGARGVDRTAEELGRAFP
+RVPVHASSAQHMLGSVPPGPSLVVATVGAEPVTPDGYAAALLLDGDSQLQREGLDVPGRV
+LARWLAAACLVRPASDGGVVVVTADAGEAVNALVRRDPDGFAARQVAERRELHLPPAGRL
+AEVTGEAPAVAEYLELVEAARRERPDEDVHEDPHSAPLDGGPARLPWIGPVPDPADETRS
+RALLIFPYAAAEATVGALRAARSAASARRETAPVRVRLDPAGVL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001038.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001038.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c2b31174878f428e63abd91be3b14b26bd53707
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001038.fa
@@ -0,0 +1,15 @@
+>0_1192
+MALRQLSVQERAEARRKALQARQARAELKAAFAAGEVGLADIFARADADDAVARLRTVDL
+LLALPGVGEVRAREAMAGCGISPRRRLGGLGRRQREALIAYIGR
+>1_920
+MALRQLSVQERAEARRKALQARQARAELKAAFAAGAVGLADVFARADTEDAVARLRTVDL
+LLALPGVGEVRARETMAGCGISPRRRLGGLGRRQREALIAYIGR
+>2_1619
+MALRQLSVEERAEARSKALAARQERAALKADFAAGQVSLAEVFSRADAEDAIGRLRTVDL
+LQALPGVGEVRAREAMAGCGISPRRRLRGLGRRQREALIAYIGR
+>3_1516
+MALRQLSVEERAEARAKALRARQERATLKTSFANRDLSLQEVFARADVDPAIGRLRTVDL
+LQAMPGVGEVRASAVMEACEISPARRLKGLGRRQREALIAYIGR
+>4_1150
+MALRQLSVQERAEARRKALQARQARAELKAAFAAGEVGLADIFARADADDAVARLRTVDL
+LLALPGVGEVRAREAMAGCGISPRRRLGGLGRRQREALIAYIGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001055.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001055.fa
new file mode 100644
index 0000000000000000000000000000000000000000..69975b90537fdf1f496614f145710df08f8152dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001055.fa
@@ -0,0 +1,23 @@
+>0_1210
+MTQSTPQQSTPQHTAAQQPAPYGRPGAGGPALPQADYRILRSVPAYAEAQALVDQLSDAG
+FPVERVRIVGTGLRSVEQVLGRMTTGKAAVRGGLQGLWFGLLLGLLFSIFAPGFGFLWIL
+LISLGLGALWGAVFGAIGHAATGGRRDFTSLQTMEAESYDVLVEASHLDQAGQLLGADPG
+TAATPRA
+>1_938
+MTQSTPQQSTPQHTAAQQPAPYGRPGAGGPALPQADYRILRSVPAYAEAQALVDQLSDAG
+FPVERVRIVGTGLRSVEQVLGRMTTGKAAVRGGLQGLWFGLLLGLLFSIFAPGFGFLWIL
+LISLGLGALWGAVFGAIGHAATGGRRDFTSLQTMEAESYDVLVEASHLDQAGQLLGADPG
+TAATPRA
+>2_1599
+MSQHQPYAQDPRSTVPATTADAAYAGGPLGAADHRVLESVPDYARAQAIVDQLSDAGFPV
+EHVRIVGTGLRTVEQVLGRMTTGKAAGRGAVQGLWFGLLLGLLFSIFSPGFGFLWILLIS
+LGLGALWGAVFGAIGHAATRGRRDFSSLQTMDAASYEVQVEAAHLDRARQTLGAGPAAPR
+A
+>3_1497
+MSASAAHYAVLSTVPDYAHAQSTVDRLSDSGFPVEHVRVAGTGLRSVEQVTGRLTTGAVG
+VC
+>4_1167
+MTQSTPQQSTPQHTAAQQPAPYGRPGAGGPALPQADYRILRSVPAYAEAQALVDQLSDAG
+FPVERVRIVGTGLRSVEQVLGRMTTGKAAVRGGLQGLWFGLLLGLLFSIFAPGFGFLWIL
+LISLGLGALWGAVFGAIGHAATGGRRDFTSLQTMEAESYDVLVEASHLDQAGQLLGADPG
+TAATPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001065.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001065.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88466730d6625b382f09ec49b5a8cdd8a76e0e0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001065.fa
@@ -0,0 +1,70 @@
+>0_1220
+MSEQDPTPVPVRPRGRIARLTGRHATEYSPLLEPLMRTVRQRATKTELADIVRAFEVARA
+AHEGQMRRSGDPYITHPVAVATILAEIGVTGPTLLAALLHDTVEDTDYSLERLRADFGSD
+VALLVDGVTKLDKVTYGAAAQAETVRKMVIAMAQDVNVLLIKLADRLHNARTWRYVSPES
+SARKAQETLDIYAPLAHRLGMNTVKWELEDLSFAALKPKMYAEIVRLVGERNPEREKHIA
+ALRTVIEDHLREHRIRATVTGRPKHYYSIYQKMVTRGKDFDDIHDLTGIRVLVDSVRDCY
+AVLGAIHARWNPVPGRFKDYIAVPKLNMYRSLHTTVMVPGGKPVEIQIRTQEMHRQAEYG
+VAAHWRYKAQAAGQAPVQATPAWLRSVMDWQADTRDPDEFLASLRTQIGADEVYVFTPKG
+EIRTLPAGSTPVDFAYAIHTDVGHRTIGARVNGKLVPLSTPLSHGDTVEVFTSRAEDAGP
+SRDWLGFVVSPRARSKIRHHFATQRRGEQADRGRESLTRQLRKAGMTVQHVLGGEELVQL
+ATDLGYADLDGLFVALGDGHVSAQSVQERVAERLAPPTPTQAEPEGELTVGEVDLQELVP
+AQARRAPARATNDAGVLVDGDGGVMAKLARCCNPVPPDAIDGFVTRGSGVSVHRVDCPNL
+ATLLAQEPERHTPVSWAPSRDTVYLVEIQIEALDRKSLLSDVTRVLSENHVNILSASVNT
+TRDRVAMSRFVFEMGDPRFLGHVIDAVRRIDGVFDVHRT
+>1_948
+MSEQDPTPAPARPAPARPAPVRPRSRIARLTGRHATEYSPLLEPLMRTVRQRATKTELAE
+IVRAFEVARAAHEGQMRRSGDPYITHPVAVATILAEIGVTGPTLLAALLHDTVEDTDYSL
+ERLRADFGSEVALLVDGVTKLDKVTYGAAAQAETVRKMVIAMAQDVNVLLIKLADRLHNA
+RTWRYVSPESSARKAQETLDIYAPLAHRLGMNTVKWELEDLSFAALKPKMYAEIVRLVGE
+RNPEREKHIAALRTVIEEHLREHRIRATVTGRPKHYYSIYQKMVTRGKDFDDIHDLTGIR
+VLVDSVRDCYAVLGVIHARWNPVPGRFKDYIAVPKLNMYRSLHTTVMVPGGKPVEIQIRT
+QEMHRQAEYGVAAHWRYKAQVAGQAPVQATPAWLRSVMDWQADTRDPDEFLASLRTQIGA
+DEVYVFTPKGEIRTLPAGSTPVDFAYAIHTDVGHRTIGARVNDKLVPLSTPLSHGDTVEV
+FTSRAEDAGPSRDWLGFVVSPRARSKIRHHFATQRRDEQADRGRESLTRQLRKAGMAVQQ
+VLGGEELVQVATDLGYADLDGLFVALGDGHVSAQSVQERVAERLAPPTSTQAEPEGELTV
+GEVDLQELVPAQSRRAPARATNDAGVLVDGDGGVMAKLARCCNPVPPDAIDGFVTRGSGV
+SVHRVDCPNLATLLAQEPERRTPVSWAPSRDTVYLVEIQIEALDRKSLLSDVTRVLSENH
+VNILSASVNTTRDRVAMSRFVFEMGDPRFLGHVIDAVRRIDGVFDVHRT
+>2_1589
+MSEHDPTHAPARVAAVRPRGRIARLTGRHATEYSPLLEPLMRTVRQRATKAELADLIRAF
+EVARAAHEGQMRRSGDPYITHPVAVATILAEIGVSGPTLLAALLHDTVEDTDYSLERLRA
+DFGPEVALLVDGVTKLDKVTYGAAAQAETVRKMVIAMAQDVNVLLIKLADRLHNARTWRY
+VSPESSARKAQETLDIYAPLAHRLGMNTVKWELEDLSFAALKPKMYAEIVRLVGERNPER
+EKHIAALRTVIEDHLREHRIRAEVTGRPKHYYSIYQKMVMRGKDFDEIHDLTGIRVLVDS
+VRDCYAVLGVIHARWNPVPGRFKDYIAVPKLNMYRSLHTTVMGPGGRPVEIQIRTHEMHR
+QAEYGVAAHWRYKAQAAAESSSSSSGTPAWLRSVMDWQKDTRDPDEFLDSLRTQIGADEV
+YVFTPSGEIRSLPAGSTPVDFAYAIHTDVGHRTIGAKVNGKLVPLSTPLNHGDTVEAFTS
+RAEDAGPSRDWLGFVVSPRARSKIRHHFATQRRDEQAERGRESLTRQLRRAGLAVQSVLG
+GEELAQVASDMGYADLDGLLVALGDGHVSAQAVQERVSERLAPPPPARTEPQGELTVGEV
+DLAELVPAQARRTPARATNDAGVLVDGDGGVMAKLARCCNPLPPDAIDGFVTRGSGVSVH
+RLDCPNLATLLEQEPERRTPVGWAPSRHTVYLVEIQVEALDRKSLLSDVTRVLSENHVNI
+LSASVNTTRDRVAMSRFVFEMGDPRFLGHVIAAVRRIDGVFDVHRT
+>3_1484
+MTEQDRRPAAPPRRGRIARLTGRRATEYSPLLEPLMRTVRQSATHAEQEDIVRAFEVAER
+AHRGQMRRSGDPYITHPVAVATILAELGVTGPTLLAALLHDTVEDTDYSLEQLTADFGPQ
+VALLVDGVTKLDKVTYGAAAQAETVRKMVIAMAQDVNVLLIKLADRLHNARTWRYVSPES
+SAKKARETLDIYAPLAHRLGMNTVKWELEDLSFAALQPKVYAEIVRLVGERNPEREKQLA
+ALRGVLEEQLREQRVRATVTGRPKHYYSVYQKMVTQKKDFAQIYDLTGIRVLVDSVQDCY
+AVLGVVHARWNPVPGRFKDYIAVPKLNMYRSLHTTVMGPEGKPVEIQIRTWEMHRQAEYG
+VAAHWRYKAGARGELEAGRSQQTPGWLRSVMDWQEDTRDPDEFLAALRTQIGADEVYVFT
+PKGEIRSLPADSTPVDFAYAIHTDVGHRTVGARVNGRLVPLSTVLRHGDTVEVFTSKAED
+AGPSRDWLNFVVSPRAKSKIRHHFATRRRDEQIERGREAFTRQLRKAGLSVQRVLGGEDL
+GVVAGELGYHDPDTLFAAMADGHVSPQAVTERLEARLAPPPAPTAPDAELRVGEVDLAGL
+VPEKARRAPTRSTNEAGVLVNGDGGVLAKLARCCNPVPPDEVVGFVTRGSGVSVHRGDCR
+NLATMLENEPERRVDVAWAPSRDAVYLVEIQVQALDRTSLLSDVTRVLSENHVNILSASV
+NTTRDRVAMSRFVFEMGDPKFLEHVVNAVRRIDGVFDVRRT
+>4_1177
+MSEQDPTPAPARPAPARPAPVRPRSRIARLTGRHATEYSPLLEPLMRTVRQRATKTELAE
+IVRAFEVARAAHEGQMRRSGDPYITHPVAVATILAEIGVTGPTLLAALLHDTVEDTDYSL
+ERLRADFGSEVALLVDGVTKLDKVTYGAAAQAETVRKMVIAMAQDVNVLLIKLADRLHNA
+RTWRYVSPESSARKAQETLDIYAPLAHRLGMNTVKWELEDLSFAALKPKMYAEIVRLVGE
+RNPEREKHIAALRTVIEEHLREHRIRATVTGRPKHYYSIYQKMVTRGKDFDDIHDLTGIR
+VLVDSVRDCYAVLGVIHARWNPVPGRFKDYIAVPKLNMYRSLHTTVMVPGGKPVEIQIRT
+QEMHRQAEYGVAAHWRYKAQVAGQAPVQATPAWLRSVMDWQADTRDPDEFLASLRTQIGA
+DEVYVFTPKGEIRTLPAGSTPVDFAYAIHTDVGHRTIGARVNDKLVPLSTPLSHGDTVEV
+FTSRAEDAGPSRDWLGFVVSPRARSKIRHHFATQRRDEQADRGRESLTRQLRKAGMAVQQ
+VLGGEELVQVATDLGYADLDGLFVALGDGHVSAQSVQERVAERLAPPTSTQAEPEGELTV
+GEVDLQELVPAQSRRAPARATNDAGVLVDGDGGVMAKLARCCNPVPPDAIDGFVTRGSGV
+SVHRVDCPNLATLLAQEPERRTPVSWAPSRDTVYLVEIQIEALDRKSLLSDVTRVLSENH
+VNILSASVNTTRDRVAMSRFVFEMGDPRFLGHVIDAVRRIDGVFDVHRT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001070.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001070.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed2c99193b47ddba77e329c38a80fc43e1f01d49
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001070.fa
@@ -0,0 +1,25 @@
+>0_1226
+MDPGLTRCGIAVVDVDARRRAALVHVEVTGTPPTAPLDQRLLRIDEAVSAVLAAHRPDRA
+AVERMFANTNTPTVLGTAQAAGVAIAAAARAGVPVGLHTPSEVKAAVTGHGDAGKEQVTT
+MVTRILRLDAPPRPADAADALALAIAHGWRGTALGAAAGQTGLDTADLASRAGRSQFAAK
+APARARQRGQLTAAQRAWLDAERSAGGGRRR
+>1_954
+MDPGLTRCGIAVVDVDARRRAALVHVEVTGTPPTAPLDQRLLRIDEAVSAVLAAHRPDRA
+AVERMFANTNTPTVLGTAQAAGVAIAAAARAGVPVGLHTPSEVKAAVTGHGDAGKEQVTT
+MVTRILRLDAPPRPADAADALALAIAHGWRGTALGAAAGQTGLDTADLASRAGRSQFAAK
+APARARPRGQLTAAQRAWLDAERSAGGGRRR
+>2_1583
+MVDVDARRRAALVHVEVAGTPPTASLDQRLLRIDEAVSAVLTAHAPDRAAVERMFANTNT
+PTVLGTAQAAGVAIAAAARAGIPVGLHTPSEVKAAVTGYGDAGKEQVTTMITRILGLDAP
+PRPADAADALALAIAHGWRGTALGAAAGQTGLDTSDLASRAGRSQFAAGTRSRGGRRGEL
+TAAQRAWLDAERSAGGGCR
+>3_1478
+MTDRPAGVVRVLGVDPGLTRCGIAVVDVDARRRAELVHVEVAGTAPEESLDARLLCIDRA
+VSAVLVRFRPERAAVERMFANNNTPTVLGTAQAAGVAIAAAARAGVPVGLHTPSEVKAAV
+TGNGDAGKEQVTTMVTRILRLDAPPRPADAADALALAIAHAWRGTALGRAAGHTGLDTSG
+LASRTGASRGAAGARVRRAPKAALTPAQQAWLAAERSAGARPGRRSAG
+>4_1183
+MDPGLTRCGIAVVDVDARRRAALVHVEVTGTPPTAPLDQRLLRIDEAVSAVLAAHRPDRA
+AVERMFANTNTPTVLGTAQAAGVAIAAAARAGVPVGLHTPSEVKAAVTGHGDAGKEQVTT
+MVTRILRLDAPPRPADAADALALAIAHGWRGTALGAAAGQTGLDTADLASRAGRSQFAAK
+APARARPRGQLTAAQRAWLDAERSAGGGRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001071.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001071.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9bcf8fae4ee170b638610d5924757409d7d1b8c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001071.fa
@@ -0,0 +1,30 @@
+>0_1227
+MAGHSKWATTKHKKAVIDARRAKAFAKYIKNIEVAARAGGPDVAGNPALDLAVSKAKKAS
+VPNDNIDRAVKRGAGLTGEVIDYAEIMYEVRGPQGSALLVECLTDNKNRAAADVRAAVTR
+NGGTMADSGSVSFLFERKGLVRLPAEGNTEDGLLEAVLEGGADAEEVVVSGDSFEILSDP
+SDLQSVAKALDEAGVEYESDELEFVPTMKVDLDASGARTFLKLADALEDLDDVQNVFSNV
+DIAPEVLAELDED
+>1_955
+MAGHSKWATTKHKKAVIDARRAKAFAKYIKNIEVAARAGGPDVAGNPALDLAVSKAKKAS
+VPNDNIDRAVKRGAGLTGEVIDYAEIMYEVRGPQGSALLVECLTDNKNRAAADVRAAVTR
+NGGTMADSGSVSFLFERKGLVRLPAEGNTEDGLLEAVLEGGADAEEVVVSGDSFEILSDP
+SDLQSVAKALDEAGVEYESDELEFVPTMKVDLDASGARTFLKLADALEDLDDVQNVFSNV
+DIAPEVLAELDED
+>2_1582
+MAGHSKWATTKHKKAVIDARRAKAFAKYIKNIEVAARAGGADLAGNPALDLAVSKAKKAS
+VPNDNIDRAVKRGAGLTGEVVDYAEIMYEVRGPQGSAVLVECLTDNKNRAAAEVRTAVTR
+NGGTMADSGSVSFLFTRQGVVRLPAEGRTEDELLEAVIEAGAEEVVLSGDEFEILSDPSD
+LRAVAEALDAAGIDYESDETEFVPTMKVELEDAKGAGTFLKLADALEELDDVQNVYSNVD
+ISPEVLAELDQD
+>3_1477
+MSGHSKWATTKHKKAVIDQRRAKAFAKYIKGIEVAARAGGADLSGNPALDLAVSKAKKNS
+VPNDNIDRAIKRGAGLTGEVIDYTEIMYEVRGPQGSALLVECLTDNKNRAAADVRAAVTR
+NGGTMADSGSVSFLFHRKGVVRLPAAGNTEDSLLEAVLEGGADAEEVVLSGDDFEIVSEP
+GDLRAVAEALDAAGIDYETDEMEHLPTMKVELDAKGARTFLKLADALEDLDDVQNVFSNV
+DIAPEVMDELEQD
+>4_1184
+MAGHSKWATTKHKKAVIDARRAKAFAKYIKNIEVAARAGGPDVAGNPALDLAVSKAKKAS
+VPNDNIDRAVKRGAGLTGEVIDYAEIMYEVRGPQGSALLVECLTDNKNRAAADVRAAVTR
+NGGTMADSGSVSFLFERKGLVRLPAEGNTEDGLLEAVLEGGADAEEVVVSGDSFEILSDP
+SDLQSVAKALDEAGVEYESDELEFVPTMKVDLDASGARTFLKLADALEDLDDVQNVFSNV
+DIAPEVLAELDED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001082.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001082.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8231dc01bd882aa9e6f879e55a508d94613da319
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001082.fa
@@ -0,0 +1,65 @@
+>0_1239
+MEHLPPTSPGAPLLPQIARPADLSALTEDQLTALAAEIRAYLIAHVSKTGGHLGPNLGVV
+ELTLAVHRVFESPKDAVIFDTGHQSYVHKLLTGRQDFTTLRQEGGLSGYGDRTESEHDVV
+ESSHASSSLSWADGIARAWAQTGQGDRTVVAVIGDGALTGGMAWEAVNNIAAGRDRRVVI
+VVNDNGRSYAPTVGGVAEHLGGLRRGVLDKVRTHHRYEQTLDYLKRRLQEAGLAGELVYR
+PLHAAKKGLKDLWAPQGLFEDLGMKYIGPVDGHDLTAMEEALEDARAYGGPVIVHAMTEK
+GHGYAPAVAHEADQFHAIGVIDPSTGEPITSSTAQSWTSVFGEEMVAIADERPDVVAITA
+AMQNPVGLAPMALAHPDRVFDVGIAEQHAVTSAAGMAFGGLHPVVAVYATFLNRAYDQVL
+MDVGLHRAGVTFVLDRAGVTGPDGPSHHGMWDLALLQSVPGLRISAPRDADTLREELREA
+VAVEDAPTVVRFAKGSVGESVRALERLSDGTDVLARRGEAGGRDGAERDVLIVAVGAMAE
+LGLDVAERLERHGISATVIDPRWVLPVARSVIDTAARHRIVVCLEDGVRAGGVGSRIRQE
+MRAAGVDTALNEVGLPVEFLAHGSREQVLARVGLTAQRITQDTVAQVLGAKVPYARPVPE
+DAAAPHHQEQA
+>1_967
+MEHLPPTSPGAPLLPQIARPADLSALTEDQLTALAAEIRAYLIAHVSKTGGHLGPNLGVV
+ELTLAVHRVFESPKDAVIFDTGHQSYVHKLLTGRQDFTTLRQEGGLSGYGDRTESEHDVV
+ESSHASSSLSWADGIARAWAQTGQGDRTVVAVIGDGALTGGMAWEAVNNIAAGRDRRVVI
+VVNDNGRSYAPTVGGVAEHLGGLRRGVLDKVRTHHRYEQTLDYLKRRLQEAGLAGELVYR
+PLHAAKKGLKDLWAPQGLFEDLGMKYIGPVDGHDLTAMEEALEDARAYGGPVIVHAMTEK
+GHGYAPAVAHEADQFHAIGVIDPSTGEPITSSTAQSWTSVFGEEMVAIADERPDVVAITA
+AMQNPVGLAPMALAHPDRVFDVGIAEQHAVTSAAGMAFGGLHPVVAVYATFLNRAYDQVL
+MDVGLHRAGVTFVLDRAGVTGPDGPSHHGMWDLALLQSVPGLRISAPRDADTLREELREA
+VAVEDAPTVVRFAKGSVGEPVRALERLSDGTDVLARRGEAGGRDGAERDVLIVAVGAMAE
+LGLDVAERLERHGISATVIDPRWVLPVARSVIDTAARHRIVVCLEDGVRAGGVGSRIRQE
+MRAAGVDTALNEVGLPVEFLAHGSREQVLARVGLTAQRITQDTVAQVLGAKVPYARPVPE
+DAAAPHHQEQA
+>2_1568
+MEHLPPTSPGAPLLPQIASPADLADVSEEQLTALAAEIRDYLIAHVSKTGGHLGPNLGVV
+ELTLAVHRVFESPKDAVLFDTGHQSYVHKLLTGRQDFTTLRQEGGLSGYGDRAESEHDVV
+ESSHASSSLSWADGIARAWHQTGQGDRTVVAVIGDGALTGGMAWEAVNNIAAGRDRRVVI
+VVNDNGRSYAPTVGGIADHLDGLRRGVLDKVRTHHRYEQTLDFLKRRLQEAGTAGEMVYR
+PLHAAKKGLKDLWAPQGLFEDLGMKYIGPVDGHDLGELEEALEDAKAYGGPVIVHALTEK
+GHGYAPARAHEDDQFHAIGVIDPSTGEPVTSSTAQSWTSVFGEEMLAIAEERPDVVAITA
+AMRNPVGLAPMALAHPDRVFDVGIAEQHAVASAAGMAFGGLHPVVAVYATFLNRAYDQVL
+MDVGLHRAGVTFVLDRAGVTGPDGPSHHGMWDLALLQSVPGLRIAAPRDAETLREELREA
+VAVEDAPTVVRFAKGSVGEPVRAIERLADGTDVLARRGEAGARDGAERDVLIVAVGALAE
+LGLDVAERLERHGISSTVVDPRWVLPVAESVIEAAARHRIVVCLEDGVRAGGVGSRIRQE
+MRAAGVDTALNEVGLPVEFLAHGSREQVLARVGLTAQRVTQDTVAQVLGAKVPYARPVPQ
+DEAARHPQEHA
+>3_1464
+MSDTSRAPLGAPLLPGIHSPEDLALLSDAQLRALAAEIRAFLIQHVSQTGGHLGPNLGVV
+ELTLAIHRVFDSPRDAVVFDTGHQSYVHKLLTGRQDFSRLRQQGGLSGYGDRAESEHDVV
+ESSHASSSLSWADGISRAWKQTGQGDRTVVAVIGDGALTGGMAWEAVNNIAADRDRRVVI
+VVNDNGRSYAPTVGGIADHLGGLRRGVLDKVRMHHRYEQTLDYLKRRLQEAGTAGEMVYR
+PLHAAKKGLKDLWAPQGLFEDLGMKYIGPVDGHDEHALEEALEDAKAYGGPVIVHAMTEK
+GHGYGPATSHEDDMFHAIGRIDPETGRPISSPTAQSWTSVFGEEILDIARERPDVVAITA
+AMQNPVGLGPMAAEFPDRVFDVGIAEQHAVTSAAGMAFGGLHPVVAVYATFLNRAFDQVL
+MDVGLHRAGVTFVLDRAGVTGPDGPSHHGMWDLALLQSVPGLRIAAPRDADTLREELREA
+VAVDDAPTVLRFAKGSVGEPVRALERLSDGTDVLARLGAPTGADGAERDVLIVAVGSFAE
+LGLDVARRLGQHGITATVVDPRWVLPVARSVIELAGRHRIVVCLEDGVRAGGVGSRIRQE
+MRAAGVDTALNEVGLPVEFLAHATRDQVLERVGLTAQRITQDTVAQVLGAKVPYARALPR
+DAEHPEASAHPAGAPTTSAQAARPEEQA
+>4_1196
+MEHLPPTSPGAPLLPQIARPADLSALTEDQLTALAAEIRAYLIAHVSKTGGHLGPNLGVV
+ELTLAVHRVFESPKDAVIFDTGHQSYVHKLLTGRQDFTTLRQEGGLSGYGDRTESEHDVV
+ESSHASSSLSWADGIARAWAQTGQGDRTVVAVIGDGALTGGMAWEAVNNIAAGRDRRVVI
+VVNDNGRSYAPTVGGVAEHLGGLRRGVLDKVRTHHRYEQTLDYLKRRLQEAGLAGELVYR
+PLHAAKKGLKDLWAPQGLFEDLGMKYIGPVDGHDLIAMEEALEDARAYGGPVIVHAMTEK
+GHGYPPAVAHEADQFHAIGVIDPSTGEPITSSTAQSWTSVFGEEMVAIADERPDVVAITA
+AMQNPVGLAPMALAHPDRVFDVGIAEQHAVTSAAGMAFGGLHPVVAVYATFLNRAYDQVL
+MDVGLHRAGVTFVLDRAGVTGPDGPSHHGMWDLALLQSVPGLRISAPRDADTLREELREA
+VAVEDAPTVVRFAKGSVGEPVRALERLSDGTDVLARRGEAGGRDGAERDVLIVAVGAMAE
+LGLDVAERLERHGISATVIDPRWVLPVARSVIDTAARHRIVVCLEDGVRAGGVGSRIRQE
+MRAAGVDTALNEVGLPVEFLAHGSREQVLARVGLTAQRITQDTVAQVLGAKVPYARPVPE
+DAAAPHHQEQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001093.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001093.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf798e9322a0fff32a4d5b923b5639616da139c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001093.fa
@@ -0,0 +1,15 @@
+>0_1257
+MATDYDAPRKNEEELSQNSIEELKARRTDTQSAVVDEDEAEAAEGFELPGADLSGEELMV
+RVLPAQSDEFTCASCFLVRHRSQAAREKNGLIYCTDCEG
+>1_989
+MATDYDAPRKNEEELSQNSIEELKARRTDTQSAVVDEDEAEAAEGFELPGADLSGEELMV
+RVLPAQSDEFTCASCFLVRHRSQAAREKNGLIYCTDCEG
+>2_1557
+MATDYDAPRKNEEELSQNSIEELKARRTDTQSAVVDEDETEAAEGFELPGADLSGEELMV
+RVLPAQSDEFTCASCFLVRHRSQAAREKNGMTYCTDCEG
+>3_1453
+MATDYDAPRKNEEELSQNSIEELKARRTDTQSAVVDEDETEAAEGFELPGADLSGEELMV
+RVLPAQSDEFTCASCFLVRHRSQAAREEGGLVYCTDCEG
+>4_1214
+MATDYDAPRKNEEELSQNSIEELKARRTDTQSAVVDEDEAEAAEGFELPGADLSGEELMV
+RVLPAQSDEFTCASCFLVRHRSQAAREKNGLIYCTDCEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001101.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001101.fa
new file mode 100644
index 0000000000000000000000000000000000000000..23516f41d56f4c22dd3207c88c71c62ad9bc7c51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001101.fa
@@ -0,0 +1,35 @@
+>0_1268
+MTNVSGNASYEYSRAALLAVTEVEAPLEVTSDDLDERLADVLRRLKLPPHLLQRVAGVRA
+RRNWDASQDFQEAAAQAGTAALAAAGIGPERVGLLINTSVTRATLEPSVAVRIHHMMGLP
+TSATNFDITNACLGFVNGLMLASTLVDAGQVDYAVVVASEDASKVQDATVENLHASTTNR
+GNFMEQFASLTLGCGAAAAVVGSIEDHPDAHRIVRGITRAGTDHHDLCVGDHRGMYTDST
+ALLNDGLELVMDAWNDTPAEWAWKDADRFITHQVSQLHTNAISESAGLPLDRIPTTFPVL
+GNVGPASLPITLVREMDELSAGDTVVCLGVGSGLNTAMLEIQW
+>1_998
+MTNVSGNASYEYSRAALLAVTEVEAPVEVTSQDLDDQLAEVLTRLRLPGSLLERVAGVRS
+RRNWDETEDFQEAAARAGVAALEQAGVPRERVGLLVNTSVTRATLEPSVAVRIHHLMGLP
+TSATNFDITNACLGFVNGLMLASTLVDAGQIDYAVVVAAEDASKVQAATVANLHAETTHR
+GNFMEQFASLTLGSGAAAAVVGRIEDHPDAHRIVRGITRAGTDHHGLCVGDHHGMYTDST
+ALLKDGLELVMDAWHDVPAEWAWPQADRFITHQVSQMHTDAIAESAHLDPARIPTTFPTL
+GNVGPASLPITLVREMDALEDGDTVVCLGVGSGLNTAMLEIEW
+>2_1546
+MTNVSGNASYEYSRAALLAVTEVEAPLEVTSDDLDERLADVLRRLKLPPHLLQRVAGVRA
+RRNWDASQDFQEAAAQAGTAALAAAGIGPERVGLLINTSVTRATLEPSVAVRIHHMMGLP
+TSATNFDITNACLGFVNGLMMASTLVDAGQVDYAVVVASEDASKVQDATVENLHASTTNR
+GNFMEQFASLTLGCGAAAAVVGSIEDHPDAHRIVRGITRAGTDHHDLCVGDHRGMYTDST
+ALLNDGLELVMDAWNDTPAEWAWKDADRFITHQVSQLHTNAISESAGLPLDRIPTTFPVL
+GNVGPASLPITLVREMDELSAGDTVVCLGVGSGLNTAMLEIQW
+>3_1442
+MVQVPHVSGNASFEFSRAALLSVTEVQAPLEVTSDDLDEQLADVLTRLRLPRHLLERVAG
+VKVRRAWDAQKDFQQAAAEAGTAALAAAGVAPGQVGLLVNTSVTRATLEPSVAVRIHDLM
+GLPTSATNFDITNACLGFVNGLMLASTMVDAGQIDYAVVVAAEDASKVQASTVANLHAET
+TVRGNFMEQFASLTLGSGAAAAVVGRTDEHPDAHRILRGITRAGTDHHQLCVGDHNGMFT
+DSNALLKDGLELVMDAWHDVPAEWGWDHAARYVTHQVSQMHTDAISESAGIPLEKLPTTF
+PVLGNVGPASLPITLVREQDSLRRGDAVVCLGVGSGLNTAMLEIQW
+>4_1223
+MTNVSGNASYEYSRAALLAVTEVEAPVEVTSQDLDDQLAEVLTRLRLPGSLLERVAGVRS
+RRNWDETEDFQEAAARAGVAALEQAGVPRERVGLLVNTSVTRATLEPSVAVRIHHLMGLP
+TSATNFDITNACLGFVNGLMLASTLVDAGQIDYAVVVAAEDASKVQAATVANLHAETTHR
+GNFMEQFASLTLGSGAAAAVVGRIEDHPDAHRIVRGITRAGTDHHGLCVGDHHGMYTDST
+ALLKDGLELVMDAWHDVPAEWAWPEADRFITHQVSQMHTDAIAESAHLDPARIPTTFPTL
+GNVGPASLPITLVREMDALEDGDTVVCLGVGSGLNTAMLEIEW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001102.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001102.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f0c3dff12f0def4752d4640f0b72cab35ff1e22
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001102.fa
@@ -0,0 +1,89 @@
+>0_1269
+MPQIPAAPAVLPPADRLPGWDPAWSRLVEIRSAADPEGTVRTLHVADTGPVLAAAGAEIV
+GTIVAVHGNPTWSWLWRSLLAETVRRARRGMAAWRVVAPDQLDMGFSERLAHTGSPSASS
+MGRADDTYRTLGGRIADLDALLAALGLRDLAATGHPLITLGHDWGGVVSLGWAARHPELV
+AGVATLNTAVHQPEGAPIPAPLQAALAGPVLPASTVTTDAFLSVTTSLATPALDRETRAA
+YHLPYDTAARRGGVGGFVADIPADPGHGSHPELQRVGEDLAALGRTDVPALILWGADDPV
+FLDRYLDDLRDRLPHARVHRYEGAGHLLVDDRDITAPLLQWAQLLRAGQLSDPASGLPGP
+VPHATADPGLEVDLGEEPGAREPGMVRLWDHLRDWGAPGSDHREYTALVDMAGAQAGRSL
+VGTARRPVAVTWGELQEMVSAIATGLWAAGMRPGDRVAMLVPPGRDLSAALYAVLRVGAV
+AVVADQGLGVKGMTRAMKSARPRWIIGRTPGLTLARAQSWPGTRISVTEPGAAQRRLLDV
+SDSLYAMVDRHRDPATGDAVDEHGTVLPEPALDADAAVLFTSGSTGPAKGVVYTHERLGR
+LVAMISRTLGIRPGGSLLAGFAPFALLGPALGAASVSPDMDVTKPATLTARSLADAAIAG
+QSTVLFASPAALANVVATADGLDAARRDALDAVRLVLSAGAPVHPQLMRQVRDLMPNAEV
+HTPWGMTEGLLLTDIDGETVQRLRGADDEGVCVGTALPTVSLAIAPLLEDGTAEDLILDP
+AQGHGVLGEIVVSAPHLKDRYDALWHTDQQSKRDGLWRRDGRVWHRTADIGHFDAEGRVW
+LEGRLQHVITTPEGPLGPGGPEKTVDALGPVRRSAVVGVGPRGTQAVVVVVEAAVPATRP
+ARRAGQHRDGRPKQGLAPTALASAVRAALEPLPVAAVLVADEIPTDIRHNSKIDRARVAR
+WAEGVLAGGRAGAL
+>1_999
+MPQIPAAPAALPPADRLPGWDPAWSRLVEIRSAADPEGTVRTLHVADTGPVLAAAGAEIV
+GTIVAVHGNPTWSWLWRSLLAETVRRARRGMAAWRVVAPDQLDMGFSERLAHAGYPSAAS
+MGRAGDTYRTLGGRIADLDALLAALGLRDLAATGHPLITLGHDWGGVVSLGWAARHPELV
+AGVATLNTAVHQPEGAPIPAPLQAALAGPVLPASTVTTDAFLSVTTSLATPALDRETRAA
+YHLPYDAAARRGGVGGFVADIPADPGHGSHPELQRVGEDLASLGRTDVPALILWGADDPV
+FLDRYLDDLRDRLPRARVHRYEQAGHLLVDDRDITAPLLQWAQLLRGGQLSDPASGLPGP
+VPHATTDAAADPGLEVDLGEEPGARDPGVVRLWDHLRDWGAPGSDHREYTALVDMAGAQA
+GRSLVGTARRPVAVTWGELQEMVSAIATGLWAAGMRPGDRVAMLVPPGRDLSAALYAVLR
+VGAVAVVADQGLGVKGMTRAMKSARPRWIIGRTPGLTLARAQSWPGTRISVTEPGAAQRR
+LLDVSDSLYAMVDRHRDPAAGDAVDEHGTVLPEPALDADAAVLFTSGSTGPAKGVVYTHE
+RLGRLVALISRTLGIRPGGSLLAGFAPFALLGPALGAASVSPDMDVTQPATLTAQKLADA
+AIAGQSSVLFASPAALANVVATADGLDAPQREALDAVRLVLSAGAPVHPQLMRQVSDLMP
+NARVHTPWGMTEGLLLTDIDGDEVQRLRTADDAGVCVGSALPTVSLAIAPLLEDGSADDV
+ILDPARGHGVLGEIVVSAPHLKDRYDALWHTDQQSKRDGLWRRDGRVWHRTADVGHFDAE
+GRVWLEGRLQHVITTPEGPVGPGGPEKTVDALGPVRRSAVVGVGPRGTQAVVVVVEAAVP
+ATRPARRPGHHRDGRPKQGLAPTALASAVRAALEPLPVAAVLVADEIPTDIRHNSKIDRA
+RVADWAEAVLAGGKAGAL
+>2_1545
+MEIRSAADPEGTVRTLHVADTGPVLAAAGAEIVGTIVAVHGNPTWSWLWRSLLAETVRRA
+RRGMAAWRVVAPDQLDMGFSERLAHPGHPAAASMGRDGDTYRSLGARIEDLDALLETLGL
+RDLAATGHPLITLGHDWGGVVSLGWAGRNPELVDGVATLNSAVHHPEGAPIPAPLQAALA
+GPVLPASTVLTDAFVSVTTSLAKPALASDVRAAYHLPYETADRRGGVGGFVADIPAEPSH
+GSHAELRRVWEGVSALGRAGTPALILWGADDPVFLDRYLDDLRDRLPQARVHRYEEAGHL
+LVDDRDVTAPLLQWAQLLRAGQLDDPGSGLPGPVPHAPAASPADEDGLHVDLGEHAAPAG
+DDVARLWDHLRDWGAPGSEHREYTALVDMAGAQTGRSLVGGARRPVAVSWGELQETVSAI
+ATGLWAAGMRPGDRVAMLVPPGRDLSAALYAVLRVGGVAVVADQGLGIAGMTRAMKSARP
+RWIIGRTPGLTLARAQSWPGARISVTEPGAAQKRLLDVSDSIYAMIERHRDPAVGEPVDE
+HGSPLPEPALAADAAVLFTSGSTGPAKGVVYTHERLGRLVAMISRTLGIRPGGSLLAGFA
+PFALLGPALGAASVSPDMDVTKPATLTARSLADAAIAGQSTVLFASPAALANVVASADGL
+DAARRDALDAVRLVLSAGAPVHPQLMRQVRDLMPNAEVHTPWGMTEGLLLTDIDGETVQR
+LRGADDEGVCVGTALPTVSLAIAPLLEDGTAEDLILDPAQGHGVLGEIVVSAPHLKDRYD
+ALWHTDQQSKRDGLWRRDGRVWHRTADIGHFDAEGRVWLEGRLQHVITTPEGPLGPGGPE
+KTVDALGPVRRSAVVGVGPRGTQAVVVVVEAAVPATRPARRAGQHRDGRPKQGLAPTALA
+SAVRAALEPLPVAAVLVADEIPTDIRHNSKIDRARVARWAEGVLAGGRAGAL
+>3_1441
+MPRIPAAPAALPPFDQLPGWDPDWSRLVTIRSAADLPGVERTLHVADNGPQLAALGAELA
+GTILAVHGNPTWSYLWRALLAETTRRARRGQQAWRVVAPDQLDMGYSERLEHPASPTPSE
+MGRARSTYRSLGDRLDDLDALTAALGLTDLAATGHPLITLGHDWGGVVSLGWAGRHRDVV
+AGVSTLNTAVHQPPQAKIPAPLQAALAGPVLPASTVSTDAFIAVTTSLAKPSLAPEVRAA
+YHLPYPSAERRGGVGGFVADIPVDASHGSHAALEEVSSGVSALGAQGTPALIQWGADDPV
+FLDRYLDDLRDRLPAARVHRYEEAGHLLIDDRDVVTPLLTWAQLLTAGLLADPASGLPGP
+RPHADDAAPRTSALPLLPEASRGVHVDIADHASEAGSPAGLPRLWDRLEDWGAPDSPMRE
+YTALVDMAGAETSRALFGGARRPVAVSWGEFQETVSAIATGLWEAGMRPGDRVSMLVPPG
+RDLSAALYAVLRVGAVAVVADQGLGVSGMTRAMKSARPRWVIGKTAGLTLARAQNWPGTR
+LSVSTLAAPQRALLDVSDSLYAMVDRHRAPELGVPRDAAGAPLPVPELGADAAVLFTSGS
+TGPAKGVVYTHERLGHLVRLIARTLDIRPGASLLAGFAPFALLGPALGAASVSPVMDVTK
+PATLTAAALADAAIAGQSSVLFASPAALANVVATAGDLSGEQRTALRQVRQVLSAGAPVH
+PALLRQVSALMPEAEVNTPYGMTEGLLLANIDGETIHALRRADDAGVCVGSPLPTVEFRI
+APLAEDGTPEEVTLDPAAGHGVLGEFVVSAPHLKDRYDALWFTDHQSKRDGLIRRDGRVW
+HRTADVGHFDAEGRVWIEGRAQHVLTTPDRPLAPGGPEGVVDALGPVARSAVVGVGPAGT
+QAVVVVVEAAVPAARPPRRAGHHRDGRPKQGLAPTALAASVRSALEPLPVAAVLVADHIP
+TDIRHNSKIDRPRVARWAEGVLAGGTVDGL
+>4_1224
+MPQIPAAPAALPPADRLPGWDPAWSRLVEIRSAADPEGTVRTLHVADTGPVLAAAGAEIV
+GTIVALHGNPTWSWLWRSLLAETVRRARRGMAAWRVVAPDQLDMGFSERLAHAGSPSAAS
+MGRAGDTYRTLGGRIADLDALLAALGLRDLAATGHPLITLGHDWGGVVSLGWAARHPELV
+AGVATLNTAVHQPEGAPIPAPLQAALAGPVLPASTVTTDAFLSVTTSLATPALDRETRAA
+YHLPYDTAARRGGVGGFVADIPADPGHGSHPELQRVGEDLAALGRTDVPALILWGADDPV
+FLDRYLDDLRDRLPHARVHRYEQAGHLLVDDRDITAPLLQWAQLLRGGQLSDPASGLPGP
+VPHATADAAADPGLEVDLGEEPGAREPGVVRLWDHLRDWGAPGSDHREYTALVDMAGAQA
+GRSLVGTARRPVAVTWGELQEMVSAIATGLWAAGMRPGDRVAMLVPPGRDLSAALYAVLR
+VGAVAVVADQGLGVKGMTRAMKSARPRWIIGRTPGLTLARAQSWPGTRISVTEPGAAQRR
+LLDVSDSLYAMVDRHRDPAAGDAVDEHGTVLPEPALDADAAVLFTSGSTGPAKGVVYTHE
+RLGRLVALISRTLGIRPGGSLLAGFAPFALLGPALGAASVSPDMDVTQPATLTAQKLADA
+AIAGQSSVLFASPAALANVVATADGLDAPRREALDAVRLVLSAGAPVHPQLMRQVSDLMP
+NARVHTPWGMTEGLLLTDIDGAEVQRLRAADDEGVCVGSALPTVSLAIAPLLEDGSAEDV
+ILDPARGHGVLGEIVVSAPHLKDRYDALWHTDQQSKRDGLWRRDGRVWHRTADVGHFDAE
+GRVWLEGRLQHVITTPEGPVGPGGPEKTVDALGPVRRSAVVGVGPRGTQAVVVVVEAAVP
+ATRPARRPGHHRDGRPKQGLAPTALASAVRAALEPLPVAAVLVADEIPTDIRHNSKIDRA
+RVADWAEAVLAGGKVGAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001109.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001109.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bbac7c29cfa8cd17f5dc0cc6d40437e29a758799
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001109.fa
@@ -0,0 +1,50 @@
+>0_1276
+MITLDRPTLTARALEDLTASALVVGVGTGPDGPVLLTDALPAEAATALEASFELLGVRGA
+ADEVHRLPGLGGVPVPLLVLAGVGGLDDDGEAADESLRRAAGAAVRSLAGTDAVALALPA
+DTPARLAAVAEGAVLGAYAFTAQKSERARAETDTSRPVREVEVVTPLAAADADPVLRRAA
+VVGDAVCAVRDLVNTAPSHLYPATFADAVAEDLADSSVSVDVWDEDRLRAEGFGGILAIG
+QGSSRPPRLVRIEHAPADAAAHIALVGKGITFDTGGISLKPAASMMTMKSDMAGAATVFA
+VVRAAAALDVPVKVTGWLALAENMPSGTAIRPSDVITMYGGKTVEVMNTDAEGRVVMADA
+LVAATDERPDAVLDVATLTGAQLVALGVRHTGVMGDDALRDEVVAAADAAGELAWGMPLP
+EQLRASLTSRVADISNMGDRFGGMMTAATFLREFVDAGRSEGDAAARTPWAHLDIAGPSF
+NESAAYGYTPQDATGVMVRTLVGLIEGRAR
+>1_1006
+MITLDRPTLTARALEDLTASALVVGVGTGPDGPVLLTDALPAEAATALEASFELLGVRGA
+EDEVHRLPGLGGVPVPLLVLAGVGGLDDDGEASDESLRRAAGAAVRSLAGTDAVALALPA
+DTPARLAAVAEGAVLGAYAFTAQKSERARAEADSSRPVRELEVVTPLAAADADPVLRRAA
+VVGDAVCAVRDLVNTAPSHLYPATFADAVAEDLADSSVSVDVWDEDRLRAEGFGGILAIG
+QGSSRPPRLVRIEHAPADAAAHIALVGKGITFDTGGISLKPAASMMTMKSDMAGAATVFA
+VVRAAAALDVPVKVTGWLALAENMPSGTAIRPSDVITMYGGKTVEVMNTDAEGRVVMADA
+LVAATDERPDAVLDVATLTGAQLVALGVRHTGVMGDDALRDEVVAAADAAGELAWGMPLP
+EQLRASLNSRVADISNMGDRFGGMMTAATFLREFVDAGRPQDDDAARTPWAHLDIAGPSF
+NESAAYGYTPQDATGVMVRTLVGLIEGRAR
+>2_1537
+MITLDRPTLTARTLEDVSASALVVGVGTGPDGPVLLTDALDAPAASALEASFDLLGVRGA
+QDEVHRLPGLGGSPVPMLVLVGVGPLDDDGEVSDEALRRAAGAAVRSLAGTDAVALALPA
+DTAQRLSAVAEGASMGAYAFTALKSEKAREEAEKSRPVRGLEFVTALGAEEAEAALRRAA
+VLGDAVCAVRDLVNTAPSHLYPGTFADAVAQDLSGSSVSVDVWDEERLTAEGFGGILAIG
+QGSSRPPRLVRIEHAPAEAKAHIALVGKGITFDTGGISLKPAASMMTMKSDMAGAATVFA
+VVRAAAALDVPVKVTGWLALAENMPSDTAIRPSDVVTMYGGKTVEIMNTDAEGRVVMADA
+LVAATDERPDAVLDVATLTGAQMVALGTRYTGVMGDDALRTEVVEAADRVGELAWAIPIP
+ENQRASLNSRVADISNMGDRFGGMMTAAAFLREFVDAGRTGEEDAPRTPWAHLDIAGPSF
+NESAAHGYTPQDATGVMVRTLMGLIEGRGR
+>3_1433
+MISQERPTLIARSLAEVTAPAVVVGVGAGPDGPLLLTDALPDEAAVALESSLELLEVKGR
+PDEVHRLPGLSGSRWPLLVLVGLGDLDQDGGADDEALRQASGAAVRSLAGTESVALALPA
+DTPSRLAAVAEGAALGAYAFTAFTSAGDTPGRAPVSTVELVTPLPASASEPVLRRAAVIG
+DAVCAVRDLVNTPPSHLYPASFADAVVGDLEGTDVDVRVWDEAQLAAEGFGGIVGIGQGS
+SRPPRLVRVEHAPAGARAHVALVGKGITFDTGGISLKPPASMMTMKSDMAGAATVFAVVR
+AAAALEIPVRVTGWLAMAENMPSDTALRPSDVLTMHGGKTVEVMNTDAEGRVVMADALVA
+ATDERPDAVLDVATLTGAQLVALGVRHTGVMGDEALRNEVVAAAGAAGELAWPMPIPEQL
+RPSLDSRVADISNMGERFGGMMTAAAFLREFVDAGRPAAERAESPTPWAHLDIAGPSFNE
+SAAYGYTPRDATGTMVRTLVGLIAGRAG
+>4_1231
+MITLDRPTLTARALEDLTASALVVGVGTGPDGPVLLTDALPAEAATALEASFELLGVRGA
+EDEVHRLPGLGGVPVPLLVLAGVGGLDDDGEAADESLRRAAGAAVRSLAGTDAVALALPA
+DTPARLAAVAEGAVLGAYAFTAQKSERARAEADTSRPVRELEVVTPLAAADADPVLRRAA
+VVGDAVCAVRDLVNTAPSHLYPATFADAVAEDLADSSVSVDVWDEDRLRAEGFGGILAIG
+QGSSRPPRLVRIEHAPADAAAHIALVGKGITFDTGGISLKPAASMMTMKSDMAGAATVFA
+VVRAAAALDVPVKVTGWLALAENMPSGTAIRPSDVITMYGGKTVEVMNTDAEGRVVMADA
+LVAATDERPDAVLDVATLTGAQLVALGVRHTGVMGDDALRDEVVAAADAAGELAWGMPLP
+EQLRASLNSRVADISNMGDRFGGMMTAATFLCEFVDAGRPEGDAAARTPWAHLDIAGPSF
+NESAAYGYTPQDATGVMVRTLLGLIEGRAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001127.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001127.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8cffd916fa8ab00254fb12409ef274c9f5b0392d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001127.fa
@@ -0,0 +1,21 @@
+>0_1297
+MLTALIVAVLAYALDQLTKYAVESTMQLGDSVAVIPGVLRWHYILNPGAAFSIGEDHTWV
+FTIIQAVVAVAALVGIARVRSTPWALALGGLAGGVLGNLTDRLFRPPAFGRGHVVDMISV
+PHFAIFNVADSFIVCSVIGVALLVMTGRRLDGTREA
+>1_1026
+MLTALVVAVLAYALDQLTKYAVESTMQLGDSVAVIPGVLRWHYILNPGAAFSIGEDHTWV
+FTVIQAVVAVAALVGIARVRSTPWALALGGLAGGVLGNLTDRLFRPPAFGRGHVVDMISV
+PHFAIFNVADSFIVCSVIGVALLVMTGRRLDGTREA
+>2_1517
+MSAAVEAPAPAAGPGARRRAVLAALLVAVLAYALDQLTKLWVETTMELGDSVTVVPGLLR
+WHYILNPGAAFSIGEDHTWVFTVIQAVVAVAAVVGIVRARSLPWALALGGLAGGVLGNLT
+DRLFRPPSFGQGHVVDMISVPRFAVFNVADSFIVCSILAIAFLVMTGRRLDGTREA
+>3_1413
+MSPAAPQDALTDHRDAPARPGRGVVGAALGVATLAYALDQGTKLLVERTMELGESIVVIP
+GLLRWHYILNPGAAFSIGTDVTWLFTLIQAVVAVVALVALLRSRSRAWSVALGGLLGGVM
+GNLTDRLFRPPSFGQGHVVDMVSVPNFAIFNVADSFIVCSILTLCLLLMSGRRLDGTRES
+DAAAEA
+>4_1251
+MLTALIVAVLAYALDQLTKYAVESTMQLGDSVAVIPGVLRWHYILNPGAAFSIGEDHTWV
+FTVIQAAVAVAALVGIARVRSMPWALALGGLAGGVLGNLTDRLFRPPAFGRGHVVDMISV
+PHFAIFNVADSFIVCSVIGVALLVMTGRRLDGTREA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001135.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001135.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c94ff595576ddcfd6b14cf8cffe4601a777e6c1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001135.fa
@@ -0,0 +1,50 @@
+>0_1305
+MSRDESTRPAAEGRFADLGRVHLLGIGGVGVSGVARILQEQGVAVSGSDAKDLPVMRELA
+AGGARITVGYDAAHLGRDVTTVIASSIAGPGNPEHDAAVARGLRVLHRSEGLALAMRGHR
+VLAVAGTHGKTTTSSMAAMAFSDAGWDPTFAVGAAVAGLGTNARAGRGEWFIAEADESDG
+TLVNYPSTIGIVTTVEADHLDHYGTEEAVHQVFRDFAGGLPAAAQGGVLVACLDDAGAAD
+LAAWAREHAAADVVTYGSAPRDGVAPDLLVTDLAVEPGETGVGQRATFRMAGGPERTLHL
+QVPGRHNALNAAAVVLAAVRAGMAFEAAVRGVEAFRGTARRFEFRGAARGVRVFDDYAHH
+PTEVAAAVSAGRAVAGDARVHVLFQPHLFSRTRDFAAEFAAALSGADAVRVLPVYAAREE
+PMPGVDSSLIASRLTTGAAEDRVVAEDRAEAVRSLAAGATAGDVVLTMGAGDVTALGADL
+LAELGRDAAPGVAHP
+>1_1034
+MSRDESTRPAAEGRFADLGRVHLLGIGGVGVSGVARILQEQGVAVSGSDAKDLPVMRELA
+AGGARITVGYDAAHLGRDVTTVIASSIAGPGNPEHDAAVARGLRVLHRSEGLALAMRGHR
+VLAVAGTHGKTTTSSMAAMAFSDAGWDPTFAVGAAVAGLGTNARAGQGEWFIAEADESDG
+TLVNYPSTIGIVTTVEADHLDHYGTEEAVHQVFRDFAGGLPAAAQGGVLVACLDDAGAAD
+LAAWAREHAAADVVTYGSAPRDGVAPDLLVTDLAVEPGETGVGQRATFRMAGGPERTLHL
+QVPGRHNALNAAAVVLAAVRAGMAFEAAVRGVEAFRGTARRFEFRGAARGVRVFDDYAHH
+PTEVAAAVSAGRAVAGDARVHVLFQPHLFSRTRDFAAEFAAALSGADAVRVLPVYAAREE
+PMPGVDSSLIASRLTTGAAEDRVVAEDRAEAVRSLAAGATAGDVVLTMGAGDVTALGPDL
+LAELGRDAAPGVAHP
+>2_1509
+MSRDESTRPVAEGRFDELGRVHLLGIGGVGVSGVARILQDQGVAVSGSDAKDLPVMRELA
+AAGARITVGYDAAHLGEDVTTVIASSIAGPGNPEHDAAVARGLRVLHRSEGLALAMRGHR
+VLAVAGTHGKTTTSSMAAMAFASAGWDPTFAVGAAVAGLGTNARAGQGEWFIAEADESDG
+TLVNYPTTIAVVTTVEADHLDHYGTEEAVHQVFRDFAAGLPDAASGGVLVACLDDDGAAG
+LAAWAREHAAARVLTYGTGPRDGVAPDLLVADLAVEPGESGVGQRATLRLASGPEATLHL
+QVPGRHNALNAAAVALAAVQAGMGFEDAVRGLEAFRGTARRFEFRGAGRGVKVFDDYAHH
+PTEVTAAVSAGRAVAGDGRVHVLFQPHLFSRTREFAAEFAAALSAADVVRVLPVYAAREE
+PMEGVDSSLIAGRLTTAADADRAVAEDRAVAVRELAAGAESGDVILTMGAGDVTALGADL
+VAALGPDAAPGAAGR
+>3_1405
+MTTQQTPEGRARRERVAALGRVHLLGIGGVGVSGVARILQDQGVAISGSDAKDLPVMHDL
+AAGGARITVGYDAAHVGDDVTTVIASSIAGPGNPEHDAAVARGLRVLHRSEGLALAMEGH
+RVLAVAGTHGKTTTSSMAAMAFTDAGWDPTFAVGAAVAGLGTNARAGAGEWFVAEADESD
+GTLVNYPTTIAVVTTVEADHLDHYGTEEAVHEVFRVFAGQLPAAEDGGALVACLDDEGAA
+GLAAWAHEHARAAVVTYGTGPRDGVEPDLLVDGVTVEPGESGVGQRARFTLADGTSAEVR
+LQVPGRHNALNAAAVALAAVRAGMSLREAVHGLEQFRGTARRFEFRGAERGVRVFDDYAH
+HPTEVVAAVSAARAVAGEGRVHVLFQPHLFSRTRDFAAEFAAALSGADRVRVLPVYAARE
+EPMEGVDATLITRALTTPDPADRTVAVDRAAAVRELAAGAREGDVILTMGAGDVTALGPD
+LVAALAADPSVDA
+>4_1259
+MSRDESTRPAAEGRFADLGRVHLLGIGGVGVSGVARILQEQGVAVSGSDAKDLPVMRELA
+AGGARITVGYDAAHLGRDVTTVIASSIAGPGNPEHDAAVARGLRVLHRSEGLALAMRGHR
+VLAVAGTHGKTTTSSMAAMAFSDAGWDPTFAVGAAVAGLGTNARAGQGEWFIAEADESDG
+TLVNYPSTVGIVTTVEADHLDHYGTEEAVHQVFRDFAGGLPAAAQGGVLVACLDDAGAAD
+LAAWAREHAAADVVTYGSAPRDGVAPDLLVTDLAVEPGETGVGQRATFRMADGPERTLHL
+QVPGRHNALNAAAVVLAAVRAGMAFEAAVRGVEAFRGTARRFEFRGAARGVRVFDDYAHH
+PTEVAAAVSAGRAVAGDARVHVLFQPHLFSRTRDFAAEFAAALSGADAVRVLPVYAAREE
+PMHGVDSSLIASRLTTGAAEDRVVAEDRAEAVRSLAAGATAGDVVLTMGAGDVTALGPDL
+LAELGRDAAPGVAHP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001138.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001138.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d277e75d89d286e27c98b735ceccbe1def643621
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001138.fa
@@ -0,0 +1,50 @@
+>0_1308
+MTGPASDAAPAPVRRPRADTARTADLTSWDAPGWAGLRVVVTGLGLTGFSVADTLAELGA
+AVVVVEGDDGPENRARAETLRIVGVREVLLDRAATQALPEVDGAAADLVVTSPGWRPDQP
+LLMAAHAAGLPIWSDVELAWRLRERAGRKTADWVCLTGTNGKTTTVTMVEAILRADGRRA
+VACGNVGTPVLDAIRDPQGFDVLALELSSFQLHWTHGLAPASSAVLNLAEDHVDWHGSME
+EYAAAKGKVYANTRVACVFNEQDPLTRTLVERADVQEGCRAIGFTTDTPGLSDIGVVDGI
+LVDRAFLDNRRHEAIALAERADLGPVAPRHTVANAAAAAALTRAVGVSPAAVAEGLRSYD
+RGEHRIQLVATSRDVMWVNDSKATNPHAADASLAAFSSVVWLAGGLPKGVTYHELVAAHA
+HRLRAVVLLGRDTSALRAALAAHAPEVPVHAPLAAADGTGPADGAAVMAEAVRVADGLAR
+PGDIVLMAPAAASMDQFRSYAARGDAFIEAVAGLMREHGWDVHDDAAPDAD
+>1_1037
+MTGPASAAAPAPVRRPRADTARTADLTSWDAPGWAGLRVVVTGLGVTGFSVADTLAELGA
+AVVVVDGDDGPENRARAETLRIVGVREVLLDRAATQVLPEVDGAAADLVVTSPGWRPDQP
+LLMAAHAAGLPIWSDVELAWRLRERAGRKTADWVCLTGTNGKTTTVTMVEAILRADGRRA
+VACGNVGTPVLDAIRDPQGFDVLALELSSFQLHWTHGLAPASSAVLNLAEDHVDWHGSME
+EYAAAKGKVYANTRVACVFNEQDPVTRTLVERADVQEGCRAIGFTTDTPGLSDIGVVDGI
+LVDRAFLDNRRHEAIALAERADLGPVAPRHTMANAAAAAALTRAVGVSPAAVAEGLRSYD
+RGEHRIQLVATSRDIMWVNDSKATNPHAADASLAAFSSVVWLAGGLPKGVTYHELVAAHA
+HRLRAVVLLGRDTSALRAALAAHAPDVPVHAPLAAADGTGPADGAAVMAEAVRVADGLAR
+PGDTVLMAPAAASMDQFRSYAARGDAFIEAVAGLMREHGWDVHDDAAPDTD
+>2_1506
+MSASENTALVPVRRPLADTGRTAALTSWDAEGWAGLRVVVAGLGVTGFSVADTLAELGAV
+VVVVDGNDGPENQARAETLRIVGVHEVLLDAEATQSLPEVDGAPAELVVTSPGWRPDQPL
+LMAAHAAGLPIWSDVELAWRVRERAGRPTADWVCLTGTNGKTTTVTMVEAILRADGRRAI
+ACGNVGTPVLDAIRDPEGYDVLALELSSFQLHWTHRVAPASSAVLNLAEDHVDWHGSMEE
+YAAAKGKVYENTRVACVFNEHDPVTRTLVERADVQDGCRAVGFTTDTPGLSDVGVVDGIL
+VDRAFTENRRHEAIALAERTDLGPVAPRHTMANAAAAAALTRAVGVAPAAVAEGLRSYDR
+GEHRIQLVATSRDVMWVNDSKATNPHAADASLAAFTSVVWIAGGLPKGVTYEELVGAHAH
+RLRAVVLLGTDASALRSALAAHAPDVPVHAPLADADGTGPADGAAVMAEAVRVADGLARP
+GDTVLMAPAAASMDQFRSYAQRGEAFIDAVAALMREHGWDTDAGTAAP
+>3_1402
+MSAPVMRPHADTDRTRGLRTWDDAGWAGLRVVVTGLGVSGFSAADTLAELGARVVVVDGR
+DSPENRAKADTLRIVGVADVLLSEDATHSLPEVDGERPDLVVTSPGWRPDQPLLMAAHEA
+GLPIWSDVELAWRLRERAGRRTADWVCLTGTNGKTTTVTMVEAILRADGRRALACGNVGT
+PVLDAVRDPEGFDTLAVELSSFQLHWTHSIVPASSAVLNLAEDHVDWHGSMEEYAAAKGK
+VYERTTVACVFNEADALTRTLVERADVAEGCRAVGFTTDTPGLSDVGVVDGIIVDRAFLE
+NRRHEAIALAERSDLGAVAPRHTVANACAAAALTRAVGVSPEAVAEGLRSYDRGEHRIQL
+VATSRDVMWVNDSKATNPHAADASLAAFSSVVWIAGGLPKGVTYDELVSAHAGRLREVIL
+LGTDTSELRRALAAHAPEVPVHAPLADADGHGSPDGRAVMAEAVRLADAHACPGDTVLMA
+PAAASMDQFRSYAERGDAFIAAVAELMREHGWDVDSEADAPA
+>4_1262
+MTGPASDAAPAPVRRPRADTARTADLTSWDAPGWAGLRVVVTGLGLTGFSVADTLAELGA
+AVVVVDGDDGPENRARAETLRIVGVREVLLDRAATQVLPEVDGAAADLVVTSPGWRPDQP
+LLMAAHAAGLPIWSDVELAWRLRERAGRKTADWVCLTGTNGKTTTVTMVEAILRADGRRA
+VACGNVGTPVLDAIRDPEGFDVLALELSSFQLHWTHGLAPASSAVLNLAEDHVDWHGSME
+EYAAAKGKVYANTRVACVFNEQDPLTRTLVERADVQEGCRAIGFTTDTPGLSDIGVVDGI
+LVDRAFLDNRRHEAIALAERADLGPVAPRHTMANAAAAAALTRAVGVSPAAVAEGLRSYD
+RGEHRIQLVATSRDIMWVNDSKATNPHAADASLAAFSSVVWLAGGLPKGVTYHELVAAHA
+HRLRAVVLLGRDTSALRAALAAHAPDVPVHAPLAAADGTGPADGAAVMTEAVRVADGLAR
+PGDTVLMAPAAASMDQFRSYAARGDAFIEAVAGLMREHGWDVHDDAAPDTD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001153.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001153.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09116f3561ab208d16590178ec5307034c3d92dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001153.fa
@@ -0,0 +1,60 @@
+>0_1325
+MHEISEPYHHPRLSPEANITDFLERQATERPDHGLFAVPDAQDQWTDVSARDARERVRAL
+AKGLIAAGIQPGETVGLLASTRLEWTLVDFAIWYAGAVTVPVYETSSVSQVSWIIEDSDV
+RAVVTGNEDLAKTVRDAVQREGLPELIGLWTMDPADGAPGSGLEALVALGADVTDEELET
+RRSSAGLADLATIIYTSGTTGRPKGCELTHENFAELVNQTLSSSLGDVVREDTSTVLFIP
+LAHVFARFVSVLTVAAGARCGHVSDIKRLSVSLQTFQPSFVLAVPRVFEKIYNAALLNAQ
+SGGKEKIFRRGADVAIRWSRALDSGQMTAPLRLQRAFYSALVYRRIRTAMGGRLAYAVSG
+GGPLSTDLAHFFRGVGVTILEGYGLTETTAPITVGRPDRLKIGTVGHPLGGNQVRIAEDG
+EILTRGTSLMRGYHNRPEANEEAFEDGWFRTGDLGALDDDGFLTITGRKKELLVTAGGKN
+VAPAMLEDAIRSDALVSQVMVVGDGKPFIAAIVTLDTDTLPAWLAANGLPKDLDVAAAAR
+EDAVRRHIQEAVDKANSLVSRAEGIREFRILDRDFSLEEGHVTPSLKMRRSAIMKDFAAQ
+IADIYGEPAPQN
+>1_1054
+MHEISEPYHPRLSPEANITDFLERQATERPDHGLFAVPDAQDQWTDVSARDARERVRALA
+KGLIAAGIQPGETVGLLASTRLEWTLVDFAIWYAGAVTVPVYETSSVSQVSWIIEDSHVR
+AVVTGNENLAKTVRDAVQREGLPELIGLWTMDPADGAPGSGLEALVALGTDVTDEELETR
+RSSAGLADLATIIYTSGTTGRPKGCELTHENFAELVNQTLSSSLGDVVRQDTSTVLFIPL
+AHVFARFVSVLTVAAGARCGHVSDIKRLSVSLQTFQPSFVLAVPRVFEKIYNAALLNAQS
+GGKEKIFRRGADVAIRWSRALDSGQMTAPLRLQRAFYSALVYRRIRTAMGGRLAYAVSGG
+GPLSTDLAHFFRGVGVTILEGYGLTETTAPITVGRPDRLKIGTVGHPLGGNQVRIAEDGE
+ILTRGTSLMRGYHNRPEANEEAFEDGWFRTGDLGALDDDGFLTITGRKKELLVTAGGKNV
+APAMLEDAIRSDALVSQVMVVGDGKPFIAAIVTLDTDTLPAWLAANGLPKDLDVAAAARE
+DAVRRHIQEAVDKANSLVSRAEGIREFRILDRDFSLEEGHVTPSLKMRRSAIMKDFAAQI
+ADIYGEPAPHN
+>2_1489
+MREISEPYHPRLSPESNITDFLERQAEERPDHGLFAVADEQDQWTDVSARDARERVRALA
+KGLIAAGVGAGDRVGLIAATRLEWTLVDFAIWYAGAVTVPIYETSSATQVAWIVEDADVC
+AVVAGDESLVKTVRDAVHREHLPELRGVWVMDVAGGEPGSGLDELAALGADVSDEDLEAR
+RSAANLEDLATIIYTSGTTGRPKGCELTHENFAELVNQTLSSSLGEVVRPDTSTVLFIPL
+AHVFARFVSVLTVAAGARCGHVTDLKRLSNSLQTFQPSFVLAVPRVFEKIYNAALLNAQS
+GGKDKIFRRGADVAVRWSRALDSGKMTAPLRLQRAFYSALIYRRIRAAMGGRLEYAVSGG
+GPLSPDLAHFFRGVGLTILEGYGLTETTAPITVGRPGRLKIGTVGLPLGGNAVRIAEDGE
+ILTRGTSLMRGYHDRPEANEEAFEDGWFRTGDLGSLDEDGFLTITGRKKELIVTAGGKNV
+APAMLEDAIRSDALISQVMVVGDAKPFIAAIVTLDADTLPSWLAAHGLPKDLDVAAAAKE
+ERVRRHVQEIVDKASSAVSRAEGIREFRILDRDFSMEEGHMTPSLKMKRAVIMQDFAAEI
+ADIYGEAPAQG
+>3_1384
+MRQISEPYLPRLSPDAAITDFLRDQAVQHPERALFAVPREDGSWDDVTAAEAWDRVRALA
+RGLVAAGVGPGDRVAIVSATRLEWTLADFAIWTAGAVTVPVYETSSASQIAWIFEDAGVG
+AAIADTPARAKSVSDAVHREGLPELKGLWVMDEDGGAPGAGLDRLTDAGADVPADELDAR
+REGVTLESLATIIYTSGTTGRPKGCELTHGNFAELVNQTLRSSLGEVVDEGASTLLFIPL
+AHVFARFVSVLTVAAGARCGHVPDLSRLATSMDTYHPTFLLAVPRVFEKIYNASLLKAQA
+GGKEKIFRRGADVAVRWSRALEEGRMTAPLRLQRAFYSALLYRRIREAMGGHLKYAVSGG
+GPLSPDLAHFFRGVGVTILEGYGLTETTAPITVGRPGKLKIGRVGQPLGGNEVRIDDDGE
+ILTRGTSLFRGYRNRPEANAEAFTEDGWFRTGDLGELDDDGFLKITGRKKEIIVTAGGKN
+VAPAQLEDAIRSDALVSQVMVVGEAKPFVAAIVTLDADTLPSWASAHGLDPQISMAEAAR
+EPQVIAHVQKAVDRANDTVSRAEGIREFRILDRDFSADEGHMTPSLKMRRTAILKDFQPV
+LDEIYGAGPARG
+>4_1279
+MHEISEPYHHPRLSPEANITDFLERQATERPDHGLFAVPDAQDQWTDVSARDARERVRAL
+AKGLIAAGIQPGETVGLLASTRLEWTLVDFAIWYAGAVTVPVYETSSVSQVSWIIEDSHV
+RAVVTGNENLAKTVRDAVQREGLPELIGLWTMDPADGAPGSGLEALVALGTDVTDEELET
+RRSSAGLADLATIIYTSGTTGRPKGCELTHENFAELVNQTLSSSLGDVVRQDTSTVLFIP
+LAHVFARFVSVLTVAAGARCGHVSDIKRLSVSLQTFQPSFVLAVPRVFEKIYNAALLNAQ
+SGGKEKIFRRGADVAIRWSRALDSGQMTAPLRLQRAFYSALIYRRIRTAMGGRLAYAVSG
+GGPLSTDLAHFFRGVGVTILEGYGLTETTAPITVGRPDRLKIGTVGHPLGGNQVRIAEDG
+EILTRGTSLMRGYHNRPEANEEAFEDGWFRTGDLGALDDDGFLTITGRKKELLVTAGGKN
+VAPAMLEDAIRSDALVSQVMVVGDGKPFIAAIVTLDTDTLPAWLAANGLPKDLDVAAAAR
+EDAVRRHIQEAVDKANSLVSRAEGIREFRILDRDFSLEEGHVTPSLKMRRSAIMKDFAAQ
+IADIYGEPAPHN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001155.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001155.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb33b82a3246a7cd5d860b2df0b35a293c9435db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001155.fa
@@ -0,0 +1,105 @@
+>0_1327
+MTAPVENFTPPEDAAGSTGAGAVFSKVLVANRGEIAVRAFRACYELGARTVAVFPYEDRN
+SIHRQKADEAYRIGEEGHPVRAYLDVDEIIRVAKDAGADAIYPGYGFLSENAGLARAAAE
+NGITFVGPPADVLELTGNKVEALRAAKRAGIPTLASSDPSADVEWLLEQAEEIGFPIFVK
+AVAGGGGRGMRRVERREDLRGSLEAAMREADTAFGDPTVFLEQAVLRPRHIEVQILADGE
+GNVVHLFERDCSLQRRHQKVIEMAPAPNLDEEIRQALHRDAVAFAKEMGYVNAGTVEFLV
+DTAGERAGQHVFIEMNPRIQVEHTVTEEVTDVDLVSAQLRIAAGATLPELGITQDALQVR
+GFAIQCRITTEDPANGFRPDTGTITAYRSAGGSGVRLDGGTIYAGAEISPHFDSMLVKLT
+CRGRDYATAVRRVRRALAEFRVRGVATNIPFLMNVMDDPQFLSGDVATDFIDKHPELATV
+NRSQDRGSKALQYLVDVTVNQPHGPRVEGIDPRDRLPEHPGDKHQEPDRSPFDGPSRNED
+AVPPHGWRQVLLEQGPEGFARTLREQTALAVTDTTFRDAHQSLLATRVRTRDLLAAAPAV
+AHTLPGLLSVEAWGGATYDVALRFLHEDPWQRLELLRAELPNIPIQMLLRGRNTVGYTPY
+PTEVTDAFVAEAAASGVDVFRIFDALNDVEQITPAIEAVRATGTAVAEAALCYTGNMTDP
+KETLYTLDYYLGLARRMVDAGAHVLAIKDMAGLLRPAAARELVTALRAEFDLPVHLHTHD
+TAGGQLATLLAAAEAGVDAVDAATASMAGTTSQVPLSALVAALEHTERDTGLGLEAATAM
+EPYWESVRSAYAPFEAGLPAPTGRVYHHEIPGGQLSNLRTQAIALGLGERFEAIESMYAA
+ADDLLGHLVKVTPSSKVVGDLALQLVGSGVDPKEFAERPQEFDIPDSVIGFLRGELGDPP
+GGWPEPFRTKALQGRREGAGMVEISAEDSSALGEAGQTRRGVLNRLLFPGPTKEFEAHRE
+EFGDTVTLHTRDFLYGLVPGREHVISLGRGVRLLATLMSVSEPDEKGMRTVMVTLNGQLR
+QMTVRDRSIESTVRTAEKADPGTPGHVAAPFAGSVTVQVAEGDAVEVGQAVATIEAMKME
+AAITAQVAGTVRRVVTEGITPVNGGDLLLVIE
+>1_1056
+MTAPVENFTPPEDAAGSTGAGAVFSKVLVANRGEIAVRAFRACYELGARTVAVFPYEDRN
+SIHRQKADEAYRIGEEGHPVRAYLDVDEIIRVAKDAGADAIYPGYGFLSENAGLARAAAE
+NGITFVGPPADVLELTGNKVEALRAAKRAGIPTLASSDPSADVEWLLEQAEEIGFPIFVK
+AVAGGGGRGMRRVERREDLRGSLEAAMREADTAFGDPTVFLEQAVLRPRHIEVQILADGE
+GNVVHLFERDCSLQRRHQKVIEMAPAPNLDEEIRQALHRDAVAFAKEMGYVNAGTVEFLV
+DTAGERAGQHVFIEMNPRIQVEHTVTEEVTDVDLVGAQLRIAAGATLPELGITQDALQVR
+GFAIQCRITTEDPANGFRPDIGTITAYRSAGGSGVRLDGGTIYAGAEISPHFDSMLVKLT
+CRGRDYATAVRRVRRALAEFRVRGVATNIPFLMNVMDDPQFVSGDVATDFIDKHPELATV
+NRSQDRGSKALQYLVDVTVNQPHGPRIEGIDPRDRLPEHPGDKHQEPDRSPFDGPSRNED
+AAPPHGWRQVLLEQGPEGFARTLREQTALAVTDTTFRDAHQSLLATRVRTRDLLAAAPAV
+AHTLPGLLSVEAWGGATYDVALRFLHEDPWQRLELLRAELPNIPIQMLLRGRNTVGYTPY
+PTEVTDAFVAEAAASGVDVFRIFDALNDVEQITPAIEAVRATGTAVAEAALCYTGNMTDP
+KETLYTLDYYLGLARRMVDAGAHVLAIKDMAGLLRPAAARELVTALRAEFDLPVHLHTHD
+TAGGQLATLLAAAEAGVDAVDAATASMAGTTSQVPLSALVAALEHTERDTGLGLEAATAM
+EPYWESVRSAYAPFEAGLPAPTGRVYHHEIPGGQLSNLRTQAIALGLGERFEAIESMYAA
+ADDLLGHLVKVTPSSKVVGDLALQLVGSGVDPKEFAERPQEFDIPDSVIGFLRGELGDPP
+GGWPEPFRTKALQGRREGAGMVEISAEDSTALAEAGQTRRAVLNRLLFPGPTKEFEAHRE
+EFGDTVTLHTRDFLYGLVPGREHVISLGRGVRLLATLMSVSEPDEKGMRTVMVTLNGQLR
+QMTVRDRSIESTVRTAEKADPGTPGHVAAPFAGSVTVQVAEGDAVEVGQAVATIEAMKME
+ATITAQAAGTVRRVVTEGVTPVNGGDLLLVIE
+>2_1487
+MTAPVENFTPPEDAAGSTGAGAVFSKVLVANRGEIAVRAFRACYELGARTVAVFPYEDRN
+SIHRQKADEAYRIGEEGHPVRAYLDVDEIIRVAKDAGADAIYPGYGFLSENAGLARAAAE
+NGITFVGPPADVLELTGNKVEALRAAKRAGIPTLASSDPSADVEWLLEQAEEIGFPIFVK
+AVAGGGGRGMRRVERREDLRGSLEAAMREADTAFGDPTVFLEQAVLRPRHIEVQILADGE
+GNVVHLFERDCSLQRRHQKVIEMAPAPNLDEEIRQALHRDAVAFAKEMGYVNAGTVEFLV
+DTAGERAGQHVFIEMNPRIQVEHTVTEEVTDVDLVGAQLRIAAGATLPELGITQDALQVR
+GFAIQCRITTEDPANGFRPDTGTITAYRSAGGSGVRLDGGTIYAGAEISPHFDSMLVKLT
+CRGRDYATAVRRVRRALAEFRVRGVATNIPFLMNVMDDPQFVSGDVATDFIDKHPELATV
+NRSQDRGSKALQYLVDVTVNQPHGPRVEGIDPRDRLPEHPGDKHQEPDRSPFDGPSRNED
+AVPPHGWRQVLLEQGPEGFARTLREQTALAVTDTTFRDAHQSLLATRVRTRDLLAAAPAV
+AHTLPGLLSVEAWGGATYDVALRFLHEDPWQRLELLRAELPNIPIQMLLRGRNTVGYTPY
+PTEVTDAFVAEAAASGVDVFRIFDALNDVSQITPAIEAVRATGTAVAEAALCYTGNMTDP
+AEKLYTLDYYLGLARQMVDAGAHVLAIKDMAGLLRPAAARELVTALRAEFELPVHLHTHD
+TAGGQLATLLAAAEAGVDAVDAATASMAGTTSQVPLSALVAALEHTERDTGLGLEAATAM
+EPYWESVRAAYAPFEAGLPAPTGRVYHHEIPGGQLSNLRTQAIALGLGERFEAIESMYAA
+ADDLLGHLVKVTPSSKVVGDLALQLVGSGVDPKQFAERPQEFDIPDSVIGFLRGELGDPP
+GGWPEPFRTKALQGRREGAGMVEISAEDSTALGEAGQTRRAVLNRLLFPGPTKEFEAHRE
+EFGDTVTLHTRDFLYGLVPGREHVISLGRGVRLLATLMSVSEPDEKGMRTVMVTLNGQLR
+QMTVRDRSIESTVRTAEKADPGTPGHVAAPFAGSVTVQVAEGDAVEVGQPVATIEAMKME
+AAITAQVAGTVRRVVTEGVTPVNGGDLLLVIE
+>3_1382
+MSLPLDPDTTRNGAGRPAHAAAPAFSKVLVANRGEIAVRAFRACHELGARTVAVFPHEDR
+NSIHRQKADEAYRIGQEGHPVRAYLDVDEILRVAKDVGADAIYPGYGFLSENAGLARAAA
+EAGITFVGPPADVLELTGNKVEALRAAKRAGIPTLKSSDPSSDVEWLLGQAEEIGFPIFV
+KAVAGGGGRGMRRVERPEDLKDSLEAAMREADTAFGDPTVFLEQAVLRPRHIEVQVLADA
+EGNVVHLFERDCSLQRRHQKVIEMAPAPHLDEEIRQALHRDAVAFAKEMGYVNAGTVEFL
+VDTAGERAGQHVFIEMNPRIQVEHTVTEEVTDVDLVAAQLRIAAGATLEELGIRQEDLHV
+RGFAIQCRITTEDPANGFRPDTGTITAYRSAGGSGVRLDGGTIYAGAEISPHFDSMLVKL
+TCRGRDYETAVRRVRRALAEFRVRGVTTNIPFLMNVMDDPQFVAGDVATDFIDKHPELAM
+VNRSQDRGSKALQYLADVTVNKPHGERVDGIDPRDRLPGHPSDKRHEPDRSPFDGPSRNP
+GAVPPAGWRQVLAEQGPEGFARTLREQTALAVTDTTFRDAHQSLLATRVRTRDLLAAAPA
+VAHTLPGLLSVEAWGGATYDVALRFLHEDPWQRLELLRAELPNIPIQMLLRGRNTVGYTP
+YPTEVTDAFVQEAAATGVDVFRIFDALNDVEQIIPAIAAVRATGTAVAEAALCYTGNMTD
+PAEELYTLEYYLGLARRMVDAGAHVLAIKDMAGLLRPAAAKELVGALRAEFDLPVHLHTH
+DTAGGQLATLLAASEAGVDAVDVAVASMAGTTSQAPMSALVAALEHTERDTGLTLEAAAA
+MEPYWESVRAIYAPFEAGLKAPTGRVYQHEIPGGQLSNLRTQAIALGLGERFEQVEAMYA
+AADDILGHLVKVTPSSKVVGDLALQLVGGGVDPDQFRERPEDFDIPDSVVGFLRGELGDP
+PGGWPEPFRTRALKGRREGSGMVQVSEEDAAALAEAGQGRRDVLNRLLFPGPTKEYEAHR
+EEFGDISTLHTRDFLYGLVPGREHVVSLGRGVRLIATLQSVSEPDEKGMRTAMLTLNGQL
+RQIQVRDRSVESSVRQAEKADAAVPGQVPAPFAGSVTVQAAVGDVVEQGAPVATIEAMKM
+EAAITAPVSGTVTRVVTQGVTPVQGGDLLLVIE
+>4_1281
+MTAPVENFTPPEDAAGSTGAGAVFSKVLVANRGEIAVRAFRACYELGARTVAVFPYEDRN
+SIHRQKADEAYRIGEEGHPVRAYLDVDEIIRVAKDAGADAIYPGYGFLSENAGLARAAAE
+NGITFVGPPADVLELTGNKVEALRAAKRAGIPTLASSDPSADVEWLLEQAEEIGFPIFVK
+AVAGGGGRGMRRVERREDLRGSLQAAMREADTAFGDPTVFLEQAVLRPRHIEVQILADGE
+GNVVHLFERDCSLQRRHQKVIEMAPAPNLDEEIRQALHRDAVAFAKEMGYVNAGTVEFLV
+DTAGERAGQHVFIEMNPRIQVEHTVTEEVTDVDLVGAQLRIAAGATLPELGITQDALQVR
+GFAIQCRITTEDPANGFRPDTGTITAYRSAGGSGVRLDGGTIYAGAEISPHFDSMLVKLT
+CRGRDYAMAVRRVRRALAEFRVRGVATNIPFLMNVMDDPQFVSGDAATDFIDKHPELATV
+NRSQDRGSKALQYLVDVTVNQPHGPRIEGIDPRDRLPEHPGDKHQEPDRSPFDGPSRNED
+AAPPHGWRQVLLEQGPEGFARTLREQTALAVTDTTFRDAHQSLLATRVRTRDLLAAAPAV
+AHTLPGLLSVEAWGGATYDVALRFLHEDPWQRLELLRAELPNIPIQMLLRGRNTVGYTPY
+PTEVTDAFVAEAAASGVDVFRIFDALNDVEQITPAIEAVRATGTAVAEAALCYTGSMTDP
+KETLYTLDYYLGLARRMVDAGAHVLAIKDMAGLLRPAAARELVTALRAEFDLPVHLHTHD
+TAGGQLATLLAAAEAGVDAVDAATASMAGTTSQVPLSALVAALEHTERDTGLGLEAATAM
+EPYWESVRSAYAPFEAGLPAPTGRVYHHEIPGGQLSNLRTQAIALGLGERFEAIESMYAA
+ADDLLGHLVKVTPSSKVVGDLALQLVGSGVDPKEFAERPQEFDIPDSVIGFLRGELGDPP
+GGWPEPFRTKALQGRREGAGMVEISAEDSSALAEAGQTRRAVLNRLLFPGPTKEFEAHRE
+EFGDTVTLHTRDFLYGLVPGREHVISLGRGVRLLATLMSVSEPDEKGMRTVMVTLNGQLR
+QMTVRDRSIESTVRTAEKADPGTPGHVAAPFAGSVTVQVAEGDAVEVGQAVATIEAMKME
+ATITAQAAGTVRRVVTEGVTPVNGGDLLLVIE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001161.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001161.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5289a137af5ab0a5e070bf3c4ebe6acc3cf033c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001161.fa
@@ -0,0 +1,50 @@
+>0_1333
+MENPQNPLAGRVPDVEPSARVAASTATRPDDATPDWRGRPFLGQPGPLANLFSVELWERF
+SFYGMQAMLVYYMSWTAAEGGLGIDPAVATGIVGAYGGMVYVFCILGGWVADRLLGSERT
+MFVSAVGIMLGHIALALVPGVPGLTLGLVLVAVGSGGLKANATNLVGSLYSREDPKRDAG
+FSIFYMGVNIGALFGPLLTGLARDTMGFHVGFGLAAAGMAIGLTQYALTRKNLPTDVHRV
+PDPLPRSQYGRWGLIGLGMVAVVVALFLTDVITLDNLSDAVVVLAAVAAIAIFAVLLTST
+KVSEEERSRVKAFIPLFIGTSVFFALFQQQFTVIALYSEHRLDRNLFGWLMPMEWVNSIN
+PIFIIVFAPVFAALWTKLGTRQPATPVKFGIGIVLIGIAFLLFIPVADVAAVPLLWLTLI
+LFVCTMGELLVSPVGLSLATKVAPRSFPVMMVSLYNLSVALGTALAGSLAGSYSEQNEVG
+YFGTIGAVTLGVGLIVLAIAKPVRRGMRGVL
+>1_1062
+MENPQNPLAGRVPDVEPSARVAASTATRPDDATPDWRGRPFLGQPGPLANLFSVELWERF
+SFYGMQAMLVYYMSWTAAEGGLGIDPAVATGIVGAYGGMVYVFCILGGWVADRLLGSERT
+MFVSAVGIMLGHIALALVPGVPGLTLGLVLVAVGSGGLKANATNLVGSLYSREDPKRDAG
+FSIFYMGVNIGALFGPLLTGLARDTMGFHVGFGLAAAGMAIGLAQYALTRKNLPTDVHRV
+PDPLPRSQYGRWGLIGLGMVAVVVALFLTGVVTLGNLSDAVVVLAAVAAIAIFAVLLTST
+KVTEEERSRVKAFIPLFIGTSVFFALFQQQFTVIALYSENRLDRNLFGWLMPMEWVNSIN
+PIFIIVFAPVFAALWTKLGTRQPATPVKFGIGIVLIGIAFLLFIPVADVVAVPLLWLTLI
+LFVCTMGELLVSPVGLSLATKVAPRSYPVMMVSLYNLSVALGTALAGSLAGSYSEENEVG
+YFGVIGAVTLGVGLLVLAIAKPVRRGMRGVL
+>2_1481
+MHTPQNPPTGHEPAVEPSARVAAPTAAAPDPAAAPDWHGRPFLGQPGPLANLFSVEMWER
+FSFYGMQAMLVYYMSWTLAEGGLGIDVAVATGIVGAYGGMVYVFCILGGWIADRLLGSER
+TMFYSAVTIMLGHIALALVPGIPGLALGLILVAVGSGGLKANAANLVGALYSQQDPKRDA
+GFSIFYMGVNIGALFGPLLTGLARDSWGFHFGFGLAAVGMAIGLVQYALTRKNLPSDVHR
+IPNPLPRSQYGRWVLIALAAVAVGVVLFLTGIVTVANLADAVVVLAAVAAIGIFAVLLTS
+KKVTEEERSRVKAFIPLFIGTAVFFALFQQQFTVIALYSENRLDRNLFGWEMPMEWVNSI
+NPIFIIAFAPVFAALWTKLGPRQPGTPVKFGIGIVLIGLAFLLFIPVADVLAVPLLWLAL
+ILFVCTMGELLVSPVGLSLSTKVAPRSFPVMMVSLYNLSVALGTALAGSLAGSYSEENEV
+GYFGVIGAVTVGVGLLMLAIAKPVRRGMRGVL
+>3_1376
+MTHSPDSGASVAPDADLGAAQAPAPDWHGRRFFGQPGPLANLFSVEMWERFSYYGMQAML
+VYYMSWTAERGGLGIDEATATGIVGAYGGMVYVFCILGGWIADRLLGSERTMFFSAVGIM
+LGHIALALVPGVPGLILGLVLVAVGSGGLKANAANLVGSLYAKGDQARDAGFSIFYMGVN
+LGGLVGPLLTGWARQTWGFHVGFGLAAVGMAIGLTQYALTRKNLPSTVHGVPDPLPRSQY
+GRWALIGLAGLAVVAVLLLTGVVNVGNLADAVVVLAALAAIAIFAVLLTSSKVSAEERSR
+VKAFIPLFIGTAVFFALFQQQFTVVALYSENRLDRTLFGTEIPMEWVSSINPIFIIAFAP
+VFAALWTRLGDRQPSTPVKFALGILLIGAAFLLFIPASGFLAVPLLWLTLILFVMTMGEL
+MISPVGLSLSTKVAPAAFPVLMVALYNLSVALGTALAGSLAGSYTAENEAGYFGVIGGVT
+IAVGVVMLLLAPAVRRGMRGVR
+>4_1287
+MENPQNPLAGRVPDVEPSARVAASTATRPDDATPDWRGRPFLGQPGPLANLFSVELWERF
+SFYGMQAMLVYYMSWTAAEGGLGIDPAVATGIVGAYGGMVYVFCILGGWVADRLLGSERT
+MFVSAVGIMLGHIALALVPGVPGLTLGLVLVAVGSGGLKANATNLVGSLYSREDPKRDAG
+FSIFYMGVNIGALFGPLLTGLARDTMGFHVGFGLAAAGMAIGLTQYALTRKNLPTDVHRV
+PDPLPRSQYGRWGLIGLGMVAVVVALFLTDVITLDNLSDAVVVLAAVAAIAIFAVLLTST
+KVSEEERSRVKAFIPLFIGTSVFFALFQQQFTVIALYSEHRLDRNLFGWLMPMEWVNSIN
+PIFIIVFAPVFAALWTKLGTRQPATPVKFGIGIVLIGIAFLLFIPVADVAAVPLLWLTLI
+LFVCTMGELLVSPVGLSLATKVAPRSFPVMMVSLYNLSVALGTALAGSLAGSYSEQNEVG
+YFGTIGAVTLGVGLIVLAIAKPVRRGMRGVL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001162.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001162.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7dbc98d13a8c7a91ab3456b7d86ae62c6c383b87
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001162.fa
@@ -0,0 +1,22 @@
+>0_1354
+MSLIRRRPAALSLATLAALALAASGCAVDDGETRAALQSAEDRLAQAEDRISELEADASD
+RVDLGQLRQEAEDALEEADQRAAEVVEDLTRSLPSGSDIVDVEALREDGKVVIEYGQSLL
+EADPQVLEDTMREAADRARDAIPDLEDVEFRVGDRTFTY
+>1_1093
+MSLIRRRPAALSLATLAALALAASGCAVDDGATRAALQSAEDRLAQAEDRISELEADASD
+RVDLGQLRQEAEGALEEADQRAAEVVEDLTRSLPSGSDIVDVEALREDGKVVIEYGQSLL
+EADPQVLEDTMREAADRARDAIPDLEDVEFRVGDRTFTF
+>2_1463
+MTTLRPRRPAVLSLAALAALSLALSGCGVDEGDAQAALESAEDRLAQAEDRISELEADAS
+NRVDLGELQRQAEGALDGADQRVGELLEDLRGRAEPLREITEQDLRDLELPRIEGLDLEA
+EAAVEDLMKSLPSGPDMADVEALREDGRVIVEYAESALEADPQVLEDTMREVAEQARNAI
+PDLKDVEFRVGDQSFRF
+>3_1375
+MVVPGWPASLALMTTTPRASRASRPAAALLTLAGAALALTGCAAGPDQETADALASADER
+IASAEAEIADLKDRMDRVPDTAAMQSQASEAVSSAVAQATGAAGSLGADAARRAQEAVDG
+VSGLPDAEAVQQVEDGGRVIVEYAQDALPKDPAELQARLDEAADAVRRQVPDSAGVEFKV
+GDQTFTF
+>4_1303
+MSLIRRRPAALSLATLAALALAASGCAVDDGATRAALQSAEDRLAQAEDRISELEADASD
+RVDLGQLRQEAEGALEEADQRAAEVVEDLTRSLPSGSDIVDVEALREDGKVVIEYGQSLL
+EADPQVLEDTMREAADRARDAIPDLEDVEFRVGDRTFTF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001183.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001183.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92b0860abd2264606e3204aface90ff07747c697
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001183.fa
@@ -0,0 +1,20 @@
+>0_1381
+MAAPTTKIARQAAIREILATRGIRSQAELSDALGDRGLSVTQGTLSRDLVDLGAVRTRGP
+AGMVYALPAEGDDGAVPGRGSDAQLNRLASMARELLVSAEPTANLVVLRTPPGAAQFLAS
+VIDQARVEHVMGTIAGDDTILLITTGTTSAPAVAAHLLGLAG
+>1_1122
+MAAPTTKIARQAAIREILATRGIRSQAELSDALGDRGLSVTQGTLSRDLVDLGAVRTRGP
+AGMVYALPAEGDDGAVPGRGSDAQLNRLASMARELLVSAEPTANLVVLRTPPGAAQFLAS
+VIDQARVEHVMGTIAGDDTILLITTGTTSAPAVAAHLLGLAG
+>2_1439
+MAVPTTKTARQAAIREILATRGIRSQAELSDALGDRGLSVTQGTLSRDLVDLGAVRTRGP
+GGMVYALPAEGDDGALPGRGSDAQLSRLSSMARELLISAEPTENLVVLHTPPGAAQFLAS
+VIDQARVENVMGTIAGDDTILLITTGVSAAPVVAAHLLGLAG
+>3_1347
+MATPATKTARQAAIRDVLQTRAIRSQAELSDALAERGLSVTQGTLSRDLVDLGAVRLRGA
+EGMVYAVPADGEEAVAGRSAESQTGRLASMARELLLSAEPTENLVVLRTPPGAAQFLASV
+VDQARVEGIVGTIAGDDTVLLITAGTREAPAVAARLLGMAG
+>4_1330
+MAAPTTKIARQAAIREILATRGIRSQAELSDALGDRGLSVTQGTLSRDLVDLGAVRTRGP
+AGMVYALPAEGDDGAVPGRGSDAQLNRLASMARELLVSAEPTANLVVLRTPPGAAQFLAS
+VIDQARVEHVMGTIAGDDTILLITTGTTSAPAVAAHLLGLAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001186.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001186.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88763b48442b1745b2132848580862bb7dedcb83
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001186.fa
@@ -0,0 +1,35 @@
+>0_1384
+MTPHTDPATAAAPVLSTADRLDRAESKAEVLVEALPWIRRFAGTVMVVKYGGNAMVSEEL
+RRAFAEDIVFLHHVGVHPVVVHGGGPQINAMLDRLGIASEFRGGLRVTTEEAMDVVRMVL
+TGQVGRELVGLVNSHGPYAVGFSGEDAGLLRARRTGAVVDGQEVDLGLVGEVTGVDPTAI
+LDVIESGRIPVVSSVAPEINDDGEPTGQVLNVNADTAAAALAAALGAAKLVLLTDVEGLY
+ADWPDRDSLISSLTAAQLRALLPSLASGMIPKMAACLAAVDAGVQRAHVVDGRRPHSMLL
+EVFTSAGVGTQVVPDAEPTAPTTPEEDA
+>1_1125
+MSPHTDPATAAAPVLSTADRLDRAESKAEVLVEALPWIRRFAGTVMVVKYGGNAMVSEEL
+RRAFAEDIVFLHHVGVHPVVVHGGGPQINAMLDRLGIASEFRGGLRVTTEEAMDVVRMVL
+TGQVGRELVGLVNSHGPYAVGFSGEDAGLLRARRTGAVVDGQEVDLGLVGEVTGVDPTAI
+LDVIESGRIPVVSSVAPEINDDGEPTGQVLNVNADTAAAALAAALGAAKLVLLTDVEGLY
+ADWPDRDSLISSLTAAQLRALLPSLASGMIPKMAACLAAVDAGVQRAHVVDGRRPHSMLL
+EVFTSAGVGTQVVPDAEPTAPTTPEEDA
+>2_1436
+MSQSSSRQPDPVTTAAAPVLSAADRLDRAESKAEVLIEALPWIQRFAGSVMVIKYGGNAM
+VSDELRRAFAEDVVFLHHVGVHPVVVHGGGPQINAMLDRLGIESEFRGGLRVTTEEAMDV
+VRMVLTGQVGRELVGLVNSHGPYAVGFSGEDAGLLRARRTGAVVDGQEVDLGLVGEVTGV
+DPTAILDVVRSGRIPVVSSVAPEIDEHGEPTGQVLNVNADTAAAALASALGAAKLVLLTD
+VEGLYADWPDRESLISSLTAGQLRALLPSLASGMIPKMAACLAAVDAGVQRAHVVDGRRP
+HSMLLEVFTSAGVGTPVVPDADTAGRPAPTTVQEDA
+>3_1344
+MTGQPAPADPTTPSVPVLSTAQRLERAASKAEVLVEALPWVQRFAGATMVIKYGGNAMVS
+DELRRAFAEDVVFLHHVGVHPVVVHGGGPQINAMLERLGIESEFRGGLRVTTPEAMEVVR
+MVLTGQVGRELVGLINSHGAYAVGSSGEDAGLFRARRTGAVVDGETVDLGLVGEVTAVNP
+EAIRDVIDAGRIPVVSSVAPEIGDDGEPTGEVLNVNADTAAAALAAGLGAAKLVLLTDVE
+GLYADWPDRDSLISSLTASQLRGLLPGLQSGMIPKMAACLHAVDSGVHRAHVVDGRRPHS
+MLLEVFTSDGVGTQVVPDPTPATRPASAPTTATAQEDA
+>4_1333
+MSPHTDPATAAAPVLSTADRLDRAESKAEVLVEALPWIRRFAGTVMVVKYGGNAMVSEEL
+RRAFAEDIVFLHHVGVHPVVVHGGGPQINAMLDRLGIASEFRGGLRVTTEEAMDVVRMVL
+TGQVGRELVGLVNSHGPYAVGFSGEDAGLLRARRTGAVVDGQEVDLGLVGEVTGVDPTAI
+LDVIESGRIPVVSSVAPEIDDDGQPTGQVLNVNADTAAAALAAALGAAKLVLLTDVEGLY
+ADWPDRDSLISSLTAAQLRALLPSLASGMIPKMAACLAAVDAGVQRAHVVDGRRPHSMLL
+EVFTSAGVGTQVVPDAEPTAPTTPEEDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001193.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001193.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3c4619dd78963eeddd17d98ae8e83886f6e2101
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001193.fa
@@ -0,0 +1,35 @@
+>0_1392
+MTPSPETGAEPTAPVAEISPVDAEAVEAAVQAALAAYEAAADLDELKAARLAHTGDRAPL
+TLANKAIGALPKERKAEAGKLMGAARGRLGKALAARTEVLEAEQAARILREETVDVTTAV
+RRRRVGARHPLSLTMDRVSEIFVGMGWEIAEGPELESEWFNFDSLNFAPDHPAREMQDTF
+FVDPAEAHLLLRTHTSPVQMRSLLERGAPTYVLCPGRTFRTDELDATHTPVFHQFEGLAV
+DKGLTMAHLRGTLEYFARQMFGAEAAIRLRPNFFPFTEPSAELDIWHPGAKGGPRWIEWG
+GCGMVHPNVLRAAGLDPEEYSGFAFGMGVERTLMFRNEVPDMHDMIEGDVRFSQHFGMEV
+>1_1133
+MTPSPETGAEPTAPVAEISPVDAEAVEAAVQAALAAYEAAADLDELKAARLAHTGDRAPL
+TLANKAIGALPKERKAEAGKLMGAARGRLGKALAARTEVLEAEQAARILREETVDVTTAV
+RRRRVGARHPLSLTMDRVSEIFVGMGWEIAEGPELESEWFNFDSLNFAPDHPAREMQDTF
+FVAPAEAHLLLRTHTSPVQMRSLLERGAPTYVLCPGRTFRTDELDATHTPVFHQFEGLAV
+DKGLTMAHLRGTLEYFARQMFGAEAAIRLRPNFFPFTEPSAELDIWHPGAKGGPRWIEWG
+GCGMVHPNVLRAAGLDPEEYSGFAFGMGVERTLMFRNEVPDMHDMIEGDVRFSQHFGMEV
+>2_1428
+MTPSPETGAEPTAPAAEISPVDAAAVDAAVQAALAAFDAATDLDELKAARLAHTGDRAPL
+TLANKGIGALPKERKAEAGKLMGDARGRLNKALAARTEVLEAEQAERILREETVDVTAAV
+RRRRVGARHPLSLTMDRVSEIFVGMGWEIAEGPELESEWFNFDSLNFAPDHPAREMQDTF
+FVEPSEAHLLLRTHTSPVQMRSLLERGAPTYVLCPGRTFRTDELDATHTPVFHQFEGLAV
+DRGLTMAHLRGTLEYFARQMFGEEAAIRLRPNFFPFTEPSAELDIWHPGAKGGPRWIEWG
+GCGMVHPNVLRAAGLDPEEFSGFAFGMGVERTLMFRNEVPDMRDMIEGDVRFSQHFGMEV
+>3_1336
+MTSSPETGASEDAPQLSPVDGPAVDAAVAEALAAFEAAADLEELKAARLAHQGDRAPLTL
+ANKAIGTLPKEQKAEAGKTMGAARSRIGKALAARTEVLEAEHAARMLAEETVDVTAAAAR
+RLPGARHPLSLLQERVSDIFVGMGWEIAEGPELEHDWFNFNALNFPPDHPAREMQDTFFV
+EPLESNLLLRTHTSPVQVRSMLERGAPVYVLCPGRTFRTDELDATHTPVFHQFEGLAVDR
+GLTMADLRGTLEYFARQMFGPEAEIRLRPNFFPFTEPSAEMDIWHPQAKGGPRWIEWGGC
+GMVHPNVLRSAGIDPEEFSGFAFGMGIERTLMFRNEVPDMRDMIEGDVRFSQHFGMEL
+>4_1341
+MTPSPETGAEPTAPVAEISPVDAEAVEAAVQAALAAYEAAADLDELKAARLAHTGDRAPL
+TLANKAIGALPKERKAEAGKLMGAARGRLGKALAARTEVLEAERAARILREETVDVTTAV
+RRRRVGARHPLSLTMDRVSEIFVGMGWEIAEGPELESEWFNFDSLNFAPDHPAREMQDTF
+FVAPAEAHLLLRTHTSPVQMRSLLERGAPTYVLCPGRTFRTDELDATHTPVFHQFEGLAV
+DKGLTMAHLRGTLEYFARQMFGAEAAIRLRPNFFPFTEPSAELDIWHPGAKGGPRWIEWG
+GCGMVHPNVLRAAGLDPEEYSGFAFGMGVERTLMFRNEVPDMHDMIEGDVRFSQHFGMEV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001224.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001224.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c4b23d74c937554e9ba5dc79a1b4a5b229092bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001224.fa
@@ -0,0 +1,24 @@
+>0_1429
+MPDSPTPPRPNPHEGADRAPAPGTPGFRILLLTPEIPGNTGNAIRLAALTGAELHLVEPL
+GFGFEDAHLRRAGLDYHDLAVVTVHPDLDAALAALAPARVLAFTARGSVRHDRVAYRPGD
+VLLFGRESTGLPEEVLTDPRVTETVCLPMQPARRSLNLANAVSIAVYEAWRQHDFAGSAA
+RPDSLD
+>1_1170
+MPDSPAPPRPNPHEGADRAPAPGTPGFRILLLTPEIPGNTGNAIRLAALTGAELHLVEPL
+GFGFEDAHLRRAGLDYHDLAVVTVHPDLDAALAALAPARVLAFTARGSVRHDRVAYRPGD
+VLLFGRESTGLPEEVLADPRVTETVCLPMQPARRSLNLANAVSIAVYEAWRQHDFAGSAV
+RPDSLD
+>2_1395
+MEPLGFGFEDAHLRRAGLDYHDLAVVTVHPDLDAALAALAPARVLAFTARGRVRHDRVDY
+RPGDVLLFGRESTGLPEEVVADPRVAETVALPMQPSRRSLNLANAVSIAVYEAWRQHGFA
+GAASETDSLD
+>3_1295
+MPQTPPDPSPAAPPPAARNPHLDAERAPAPGTPGFRILFHTPEIPGNTGNAIRLAAITGA
+ELHLVEPLGFDFSDAHLRRAGLDYHDLAVMTVHPDLDTALAALAPARVFAFSARGRVRHD
+RVAYEAGDVLLFGRESTGLPEDVLSDPRVTDTVSLPMQPSRRSLNLANAASIAVYEAWRQ
+HGFAGAGSPAADSLH
+>4_1378
+MPDSPTPPRPNPHEGADRAPAPGTPGFRILLLTPEIPGNTGNAIRLAALTGAELHLVEPL
+GFGFEDAHLRRAGLDYHDLAVVTVHPDLDAALAALAPARVLAFTARGSVRHDRVAYRPGD
+VLLFGRESTGLPEEVLTDPRVTETVCLPMQPARRSLNLANAVSIAVYEAWRQHDFAGSAA
+RPDSLD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001237.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001237.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d8facaa314330be66eb9366e577d74ba324686f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001237.fa
@@ -0,0 +1,39 @@
+>0_1465
+MDRQPLRLAALAAAAVPGLAPVSVEASPDDPADFSTAVVVDGEGQRWRVRSPRTPEAGIR
+LETELQVLAGLTPAVRAGLPFRTPSVAGAVRLEGLRTFVYQDMPGRPVTLDELARLGEPA
+VQDVGRVLAAIHTLPSDVVDHADLPSYTAEQIRQRHLHALDQAATSGRVPPLLLRRWEEA
+MEEEALWRFTPVPVHGDLHEDNLLLERGRVVGVTGWTDLHVGDPAGDVAWLAAATDPDLA
+DRVLDAYAARRADAGAADDGDAHLMRRAALLAEFALSQWLTRGLDRHDEGMVAEAEAMLA
+ELEGDVRAAQEAAARQAEADAAADAAEDARDAAEDAREAAAVRSADPETGSLPAVEVVRP
+INGGPGRP
+>1_1184
+MDRQPLRLAALAAAAVPGLAPVSVEASPDDPADFSTAVVVDGEGQRWRVRSPRTPEAGIR
+LETELQVLAGLTPAVRAGLPFRTPSVAGAVRLEGLRTFVYQDMPGRPVTLDELARLGEPA
+VQDVGRVLAAIHTLPSDVVDHADLPSYTAEQIRQRHLHALDQAATSGRVPPLLLRRWEEA
+MEEEALWRFTPVPVHGDLHEDNLLLERGRVVGVTGWTDLHVGDPAGDVAWLAAATDPDLA
+DRVLDAYAARRADAGAADDGDAHLMRRAALLAEFALAQWLTRVLDRHDEAMVAEAEAMLA
+ELAGDVRAAQEAAARQAEADAAADAAEDARDAAEDAREAAAARTADPETGPLPAAEVVRP
+INGGPGRP
+>2_1381
+MEASPDDPADFSTAVVVDGEGQRWRVRSPRTPEAGIRLETELQVLAGLTPAVRAALPFRT
+PSVAGAVRLEGLRTFVYQDMPGRPVSLDELARLGEPAVQDVGRVLAAIHTLPDDVVDQAD
+LPSYSAEEIRQRHLHALDQAATSGRVPPLLLRRWEEAMEEEALWRFTPVPVHGDLHEDNL
+LLERGRVVGVTGWTDLHRGDPAADVAWLAAAEDPDLADRVLDAYESRRAAAGAADDGDTH
+LMRRAALLAEFALAQWLARGLDRHDAAMVTEAEAMLAELAADVRAAQEAEDRQDREQAAA
+DAAEDADAAADARDDAQRHAAVQEGSPPGGAEPGGASGRRRVTDA
+>3_1281
+MHRQPLRLAALAAAAVPGLTPVSVEPSPDDSPDVAAALVVDDAGQRWLVRSPRSAEAGIR
+LETELQVLAGFDPHLRAGLPFRVPSVAGAVRIDGLRTFVYQALPGEPATLEQIGGLGDAA
+VQDLGRILAALHTLPLTVVEQADLPVYTADHVRERHLTELDRAAATGQVPPRLLRRWEET
+LEEADLWDFSPVPVHGDLHEDGLLVSRGRVVGVSGWTDLHVGDPAEDFAWLAAAEDPALP
+ERVLAAYAERLDSEGAAAPDAHLLRRGALLAEFALARWLLRGVDRHDAETTADARALLTE
+LAEAVGVAEATAPQAAPTADNVVGLHAAHDDRAPDWDEDDADGVVDVSDDDGRAGGTVSV
+LRPVD
+>4_1392
+MDRQPLRLAALAAAAVPGLAPVSAEASPDDPADFSTAVVVDGEGQRWRVRSPRTPEAGIR
+LETELQVLAGLTPAVRAGLPFRTPSVAGAVRLEGLRTFVYQDMPGRPVTLDELARLGEPA
+VQDVGRVLAAIHTLPSDVVDHADLPSYTAEQIRQRHLHALDQAATSGRVPPLLLRRWEEA
+MEEEALWRFTPVPVHGDLHEDNLLLERGRVVGVTGWTDLHVGDPAGDVAWLAAATDPDLA
+DRVLDAYAARRADAGAADDGDAHLMRRAALLAEFALAQWLTRGLDRHDAGMVAEAEAMLA
+ELEGDVRAAQEAAARQAEADAAADAAEDARDAAEDAREAAAARTADPETGPLPAVEVVRP
+INGGPGRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001250.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001250.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aec34eeeaab623fd2ecaaa0ab3f2f6e95da1a37f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001250.fa
@@ -0,0 +1,25 @@
+>0_1478
+MTKDSTTTPAEAGKDWFTTYTVFARPQGEPGWLGLEGRDAKKAAKEFDEAVARVAQTGVT
+VRGVYDVSGMREAGDVMVWMYGQVPEDLQAAIRELRRTRLLEGTTMVLSAMGADRMAEFN
+KDHVPAFAMGRKALKWLCFYPFVRSYDWYLLDPKERARMLREHGQLGQDFPQVWANTTSA
+FGLNDWEWLLGLEADELTDLVDMMRHLRNNETRLHVRSEVPFYTGRRLETAEIAEVLA
+>1_1198
+MTKDSTTTPAEAGKDWFTTYTVFARPQGEPGWLGLEGRDAKKAAKEFDEAVARVAQTGVT
+VRGVYDVSGMREAGDVMVWMYGQVPEDLQAAIRELRRTRLLEGTTMVLSAMGADRMAEFN
+KDHVPAFAMGRKALKWLCFYPFVRSYDWYLLDPKERARMLREHGQLGQDFPQVWANTTSA
+FGLNDWEWLLGLEADELTDLVDMMRHLRNNETRLHVRSEVPFYTGRRLETAEIAEVLA
+>2_1368
+MTKDTATTPAEAGKDWFTTYTVFARPQGQPGWLGLEGRDAKKAVQEFDALVADLAKAGVT
+VRGVYDVSGMREAGDVMVWMYGQVPEDLQAAIRRLRRTRLLERTTMVLSAMGADRLAEFN
+KDHIPAFAMGRKALPWLCFYPFVRSYDWYLMEPKERARMLREHGQLGQEFPQVWANTTSA
+FGLNDWEWLLGLEAPELKDLVDMMRHLRNNETRLYVRAEVPFYTGRRVETADLLEVLA
+>3_1260
+MSNTAAQPGQDWFTTYTVFARPQGEPGWLGLDGREAKKAVKEFDGVVKSLATRGVTVRGV
+YDVSGMRAEGDVMVWMYAHAPEDLQAAIRDLRRTRLLDGTNMVLSAMGADRMAEFNKDHI
+PAFAMGRKPLDWLCFYPFVRSYDWYTLDPKERARMLREHGKLGQDFPQVWANTTSAFALN
+DWEWLLGLEAPKLNDLVDMMRHLRDNETRHYVREEVPFYTGRRLETSELPEVLA
+>4_1405
+MTKDSTTTPAEAGKDWFTTYTVFARPQGEPGWLGLEGRDAKKAAKEFDEAVARVAQTGVT
+VRGVYDVSGMREAGDVMVWMYGQVPEDLQAAIRELRRTRLLEGTTMVLSAMGADRMAEFN
+KDHVPAFAMGRKALKWLCFYPFVRSYDWYLLDPKERARMLREHGQLGQDFPQVWANTTSA
+FGLNDWEWLLGLEADELTDLVDMMRHLRNNETRLHVRSEVPFYTGRRLETAEIAEVLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001260.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001260.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c582fc636c63be6b53305f969473f7c5fa3956aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001260.fa
@@ -0,0 +1,30 @@
+>0_1489
+MSIMMPNPQPGAEQGLPRGELLATYATYAQAREQVDRLAATDFPVSAVSIVGKDLRVVER
+VRGRLNYAQVALSAGVRGVFFGGLIGVFLYLLAPEAGPGQILTSMLLGLAVWLIFGVIGF
+AMRRGQHGFASSQAVVPTAFDLVVAFDHAARARQELGLGGAAAPTPPAASQPAPAPAAEA
+EDGSVQATPAPAPSSGGSHAAPAPGGPEAPARPAPEADPAPTGLDRSYGVTLPPEEVAKL
+IEARGGHPPRPQDEPRG
+>1_1209
+MSFMMSNPQPGAEQGLPRGELLATYATYAQAREQVDRLAATDFPVSAVSIVGKDLRVVER
+VRGRLNYAQVALSAGVRGVFFGGLIGVFLYLLAPEAGPGQILTSMLLGLAVWLIFGVIGF
+AMRRGQHGFASSQAVVPTAFDLVVAFDHAARARQELGLGGAAAPTPQPAPQPAPAPAAEE
+AGGGSVQATPAAAPSSGGSHAAPAPGGPEASARPTPEADTAPTGLDRSYGVTLPPEEVAK
+LIEARGGHPPRPQDEPRG
+>2_1357
+MSFMMSSPPPGADRGLPRGELLATYASYADAREQVDRLAATDFPVSAVSIVGKDLRVVER
+VRGRLNYAQVALSAGVRGVFFGGLIGVFLFLLTPEGGAGQILTSMLLGLAVWLIFGVIGF
+GMRKGRHGFASSQAVVPTGYDLVVAFEHAARARTELGLGGAAATAAAAVSTSPATPAPAA
+PQAGPNQNGAGQVDAPRPDAPQADAQHAPQAGAPSSGGSHAAPDADAQPAGAEAAPAAGA
+VPTGLDRSYGVTLPPEEVAKLIQARGGQASRPQEDPRD
+>3_1249
+MMMSGPAAGGLPQGELLATYSTYEQAREQVDRLAEADFPVTALSIVGKDLRVVERVRGRL
+NYGRVALGAAVQGALFGAMIGAFLLLLDSSAGGMQIVTSALLGVAVWVIFGVVGFASRKG
+RHGFASTQALVPGGYDLVVAFEHAGRARQELGLGARGAATPAPAPMPVQESAPAPAPAPA
+PSGSAVSGPSGSHAAPASSAEPAPAHVDGPAQDPAAPAGLDRSYGVTLPPEEVARLIEAR
+GGRPRQDPQAPQGQPHPWDRPQS
+>4_1416
+MSIMMPNPQPGAEQGLPRGELLATYATYAQARDQVDRLAATDFPVSAVSIVGKDLRVVER
+VRGRLNYAQVALSAGVRGVFFGGLIGVFLYLLAPEAGPGQILTSMLLGLAVWLIFGVIGF
+AMRRGQHGFASSQAVVPTAFDLVVAFDHAARARQELGLGGAAAPTPPAASQPAPAPAAEA
+EDGSVQATPAPAPSSGGSHAAPAPGGPEAPARPAPEADPAPTGLDRSYGVTLPPEEVAKL
+IEARGGHPPRPQDEPRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001281.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001281.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9084de023af0969276698bd6884e87f9d64365c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001281.fa
@@ -0,0 +1,50 @@
+>0_1513
+MLKFILKRLGSSLLVLFGASILLFFLVAHSGDPLQDLRESQNPNRETLIAARTAFMGLDQ
+PWYARYWDWLQGIGGCVTGQCDLGLSRNGQSVADLLSNAAASTLRLVVLATVLAIIIGIA
+IGIVTAIRQYSGLDYVVTFLIFLFFSLPVFWAAVLLKEYMGIRFNDWIRSPELNWPLLIG
+VAVLAGLVLQAVMAGDLRRRAFTFGATAAFILLAGWVLFAVDFWRHPQMGPVVQLVIGLA
+AAVGATAVISGLRNRSVLKAALVTVAIGLVAYYATYGLLWRTPSALLLAGLGVILVLVAI
+LVGRLLGGFSKGSAVSASLVTALIMGVAIVAEHLMNYWPTFLKVKPRPISTIGSGTPNLD
+AHFWVVFLDRGAQLLLPTILLTIISVATYSRYTRSSMLEVSRQDYIRTARAKGLPERQVI
+LKHAFRNSLIPITTIMAFDFAGLIGGAVITEQVFGWKGMGELFATGLRDVDPMPVMAFFL
+VTGTAAVLMNLVADVLYAVLDPRIRV
+>1_1233
+MLKFILKRLGSSLLVLFGASILLFFLVAHSGDPLQDLRESQNPNRETLIAARTAFMGLDQ
+PWYARYWDWLQGIGGCVTGQCDLGLSRNGQSVADLLSNAAASTLRLVVLATVLAIIIGIA
+IGIVTAIRQYSGLDYVVTFLIFLFFSLPVFWAAVLLKEYMGIRFNDWIRSPELNWPLLIG
+VAVLAGLVLQAVMAGDLRRRAFTFGATAAFILLAGWVLFAVDFWRHPQMGPVVQLVIGLA
+AAVGATAVISGLRNRSVLKAALVTVAIGLVAYYATYGLLWRTPSALLLAGLGVILVLVAI
+LVGRLLGGFSKGSAVSASLVTALIMGVAIVAEHLMNYWPTFLKVKPRPISTIGSGTPNLD
+AHFWVVFLDRGAQLLLPTILLTIISVATYSRYTRSSMLEVSRQDYIRTARAKGLPERQVI
+LKHAFRNSLIPITTIMAFDFAGLIGGAVITEQVFGWKGMGELFATGLRDVDPMPVMAFFL
+VTGTAAVLMNLVADVLYAVLDPRIRV
+>2_1334
+MLKFILKRLGSSLLVLFGASILLFFLVAHSGDPLQDLRESQNPNRETLIAARTEFMGLDQ
+PWYARYWDWLQGIGGCVTGQCDLGLSRNGQSVGDLLSSAAASTLRLVVLATVLAIIIGIA
+IGIVTAIRQYSGLDYVVTFLIFLFFSLPVFWAAVLLKEYMGIRFNDWIRSPELNWPLLIG
+VAVLAGLVLQAVMAGDLRRRAFTFGATAAFILLAGWVLFAVDFWRHPQMGPVVQLVIGLA
+AAVGATAVISGLRNRSVLKAALVTVAIGLVAYYATYGLLWRTPSALLLAGLGVILVLVAI
+LVGRLLGGFSKGSAVSASLVTALIMGVAIVAEHLMNYWPTFLKVKPRPISTIGSGTPNLD
+AHFWVVFLDRGAQLLLPTILLTIISVATYSRYTRSSMLEVSRQDYIRTARAKGLSERQVI
+LKHAFRNSLIPITTIMAFDFAGLIGGAVITEQVFGWKGMGELFATGLRDVDPMPVMAFFL
+VTGTAAVLMNLVADVLYAVLDPRIRV
+>3_1226
+MLKFILRRLGSSALVLFGASILLYVLTVNSGDPLKDLRESQASNREQLMQARIDYMGLDD
+PWYERYWNWLTGVVKYLIGAGTLGTDRSGVQVESLLGNAAASTLRLVVLATVLAIVIGVA
+IGIITAIRQYSGLDYAVTFLIFLFFSLPVFWAAVLLKEYLAIGFNNWIARPTMDWPLVIG
+LAVVLGLALQAAMGGRLVRRLLTFAATVAVIVLGGYLLFALDMWRNPRMGPLVQLLIGLA
+VAVGGTALVAGLKNRSVLKAALATVAVGVVAYYATYGVLMQSPSGWLIAGLGVIAVLVGV
+LAGRLLGGFSKGSAVSVSVVTALVMGLSILAEHMMNYWPQLLKAKPRPIATIGAETPNLT
+GHFWVLFLDKGTQLLLPTVLLTIISVATYSRYTRSSMLEVSRQDYIRTARAKGLGERQVI
+LKHAFRNSLIPITTIMAFDFAGLIGGAVITESVFGWKGMGELFRTGLDQVDPAPVMAFFL
+VTGTAAVLMNLVADILYAVLDPRIRV
+>4_1440
+MLKFILKRLGSSLLVLFGASILLFFLVAHSGDPLQDLRESQNPNRETLIAARTEFMGLDQ
+PWYARYWDWLQGIGGCVTGQCDLGLSRNGQSVGDLLSNAAASTLRLVVLATVLAIIIGIA
+IGIITAIRQYSGLDYVVTFLIFLFFSLPVFWAAVLLKEYMGIRFNDWIRSPELNWPLLIG
+VAVLAGLVLQAVMAGDLRRRAFTFGATAAFILLAGWVLFAVDFWRHPQMGPVVQLVIGLA
+AAVGATAVISGLRNRSVLKAALVTAAIGLVAYYATYGLLWRTPSALLLAGLGVILVLVAI
+LVGRLLGGFSKGSAVSASLVTALIMGVAIVAEHLMNYWPTFLKVKPRPISTIGSGTPNLD
+AHFWVVFLDRGAQLLLPTILLTIISVATYSRYTRSSMLEVSRQDYIRTARAKGLPERQVI
+LKHAFRNSLIPITTIMAFDFAGLIGGAVITEQVFGWKGMGELFATGLRDVDPMPVMAFFL
+VTGTAAVLMNLVADVLYAVLDPRIRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001297.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001297.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fe5c2f21f3149de63eec9c5bac5deff3260a7d21
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001297.fa
@@ -0,0 +1,55 @@
+>0_1540
+MALHLQRYREIAHVMARNGLMATAVQAGLSRWLPLEEGEPHLGIDAEARPELFVRTFEEL
+GVTFVKLGQLISARPDVFPEAYCAAFARLTDSTSAVPFEAVARTVEEDLGADVDTLFAWF
+DRAPLATASIGQAHRARLHDGRAVVVKVRKPGVVEQVQADLEILRTLAATWSRASRTFAD
+LDVPAMVDEFDRSLRAELDYVVEARACEEIAAGFRDTPGVRFPWIEWDLTTSRVLTMQEL
+SGLRVDDLAGLDAAGIDREELAYRAADVLLAMVFEHGVFHADPHPGNLFIEPDGTVGFID
+FGSVGRISPSLRRRFAGLAMALARQDTDGLVRALLDIAPPRGPVDRRRLRLEVARIVGRL
+EGRELEDIRVAQLISEIFALVRRHRLSLPPELVQLLRMLIIVDGIGRRLHPGFDYTRVLD
+PFALRLVGEHLDPRRVAGRIGRATIAAAELGIDLPEYARKVMERIDDGGIDVTVRASELE
+PLVTRLERTGDRVVAAMVVAAMITGGTNVLVAYKDRLGRFAGPVVAAGGAALTGGSAYLA
+WISRPRRRPR
+>1_1262
+MALHLQRYREIAHVMARNGLRATAVQAGLSRWLPLEEGEPHLGIDAEARPELFVRTFEEL
+GVTFVKLGQLISARPDLFPEAYCAAFARLTDSTTAVPFEAVARTVEEDLGADVDTLFAWF
+DRAPLATASIGQAHRARLHDGRAVVVKVRKPGVVEQAQADLEILRTLAATWSRASRTFAD
+LDVPAMVDEFDRSLRAELDYVVEARACEEIAAGFRDTPGVRFPWIEWDLTTSRVLTMQEL
+SGLRVDDLAGLDAAGIDREELAYRAADVLLAMVFEHGVFHADPHPGNLFIEPDGTVGFID
+FGSVGRISPSLRRRFAGLAMALARQDTDGLVRALLDIAPPRGPVDRRRLRLEVARIVGRL
+EGRELEDIRVAQLVSEIFALVRRHRLSLPPELVQLLRMLIIVDGIGRRLHPGFDYTRVLD
+PFALRLVGEHLDPRRVAGRIGRATIAAAELGIDLPEYARKVMERIDDGGIDVTVRASELE
+PLVTRLERTGDRVVAAMVVAAMITGGTNVLVAYKDRLGRFAGPVVAAGGAALTGGSAYLA
+WISRPRRRPR
+>2_1302
+MPSRLHRSREIALILGRNGLQATALAAGLGRWLPAADARTARDAVLRPDMLVDVFEQLGT
+TFVKLGQLISARPDMFPESICTAFARLTDDTTPVPFEAMAATVLEDFGASVDELYAWFDP
+VPLATASIGQAHRARLHDGRDVVVKIRKPGVVEQVRTDLEILRTVASRLSRASRALQDMD
+VVSLVDEFDRALRAELDYLVEARACEQIAENLRDVPGVRVPWVDWATTSSRVLTMEEITG
+FRVDDLASLDAAGIDRADLAYRAAEVLMGMVFEDGLFHADPHPGNVFIEADGGIGFIDFG
+SVGRISSGMRRRFARMAMALVRQDPDGLVRALVAIAPPRGDLDRRALRLEVSRITGRLEG
+RDLADIRVDQLVGQIFGIVRRHRLALPPELVQLFRMLIIVDGLGKRLHPGFDYTRVLNPF
+AVRVAGEELDPRRVAGRIGQAGLAAAELGLDLPEYARKVIDHLEDGGLDVTLRTGELEPL
+VARMERTGDRVVAALVVAAMITGGTNVLVAYKDRLGRFAGPVVAAGGAALTGGSAYLAWT
+GRPRRMRRRPRG
+>3_1191
+MALHLQRYREIAHVMARNGLDATARLAGLGRWLAPQDPTARRPLDAEARPELLVRTFEEL
+GTTFVKLGQLISTRPDLFPESYCTAFARLTDRATPVPYAAIARTVEEDFGAPVDELFAEF
+DRTPLATASVGQVHGAVLHDGRDVVVKVRKPGVVEAVTADLEILRTLTGRLVRASRTLAD
+MDVAGMVDQFDRSLRAELDFVVEARACEEIAAGFTGTPGVRFPWIAWELTSARVLTMERM
+AGMRVDDLPALEAAGIDREELAYRAADVLMRMVFQHGVFHADPHAGNVFIEPDGTIGFID
+FGSVGRIGPGVRERISGLAMALARQDVDGLVRALLEIAPPRGPVDRRRLRSEVGRIVARV
+DGRDLQDIKVPQLVSEVFAIVRRHRLSLPPELVQVFRMVLIVDGLGRRLDPGFDYTRVLD
+PFVRRMVMDQLDPRRLARRLRRATITTADIGLELPQYLRTLMERIEDGGIDVNVRTSELE
+PLVARVERTGDRVVAALVVAAMITGGTNVLVAYKDRLGPFAGPLVAAGGAALTSGSAYLA
+WISRPRRAPRR
+>4_1467
+MALHLQRYREIAHVMARNGLMATAVQAGLSRWLPLEEGEPHLGIDAEARPELFVRTFEEL
+GVTFVKLGQLISARPDVFPEAYCAAFARLTDSTSAVPFEAVARTVEEDLGADVDTLFAWF
+DRAPLATASIGQAHRARLHDGRAVVVKVRKPGVVEQVQADLEILRTLAATWSRASRTFAD
+LDVPAMVDEFDRSLRAELDYVVEARACEEIAAGFRDTPGVRFPWIEWDLTTSRVLTMQEL
+SGLRVDDLAGLDAAGIDREELAYRAADVLLAMVFEHGVFHADPHPGNLFIEPDGTVGFID
+FGSVGRISPSLRRRFAGLAMALARQDTDGLVRALLDIAPPRGPVDRRRLRLEVARIVGRL
+EGRELEDIRVAQLISEIFALVRRHRLSLPPELVQLLRMLIIVDGIGRRLHPGFDYTRVLD
+PFALRLVGEHLDPRRVAGRIGRATIAAAELGIDLPEYARKVMERIDDGGIDVTVRASELE
+PLVTRLERTGDRVVAAMVVAAMITGGTNVLVAYKDRLGRFAGPVVAAGGAALTGGSAYLA
+WISRPRRRPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001300.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001300.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d2075e53b9c38e89ef76201dafe9aa2d8726875
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001300.fa
@@ -0,0 +1,18 @@
+>0_1544
+MTKHRQPVPLSQTAARLGLGGFMTAAGLSHLTVARREFRAQVPSWVPLPADLVVLGSGVA
+EIGLGAALLALPGQRRLTGTALAAFYTAIYPGNIGQYAERKDGFGLDTDGRRLARLFGQP
+ALIAAALWAAGIPEREQGGRG
+>1_1266
+MTKHRQPVPLSQTAARLGLGGFMTAAGLSHLTVARREFRAQVPSWVPLPADLVVLGSGVA
+EIGLGAALLALPGQRRLTGTALAAFYTAIYPGNIGQYAERKDGFGLDTDGRRLARLFGQP
+ALIAAALWAAGIPEREQGGRG
+>2_1270
+MTKRRQSVPLSQTAARLGLGAALWAAGIPEREHGGRG
+>3_1180
+MTKRRQSVPLSQTAARLGLGGFMTAAGLSHLTVARREFRAQVPSWVPLPADLVVLGSGVA
+EIGLGAALLALPGQRRRTGTALAAFYTAIYPGNIGQYAERKDGFGLDTDGRRLARLFGQP
+ALIAAALWAAGIPEREHGGRG
+>4_1471
+MTKRRQSAPLSQTAARLGLGGFMTAAGLSHLTVARREFRAQVPSWVPLPADLVVLGSGVA
+EIGLGAALLALPGQRRLTGTALAAFYTAIYPGNIGQYAERKDGFGLDTDGRRLARLFGQP
+ALIAAALWAAGIPEREQGGRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001314.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001314.fa
new file mode 100644
index 0000000000000000000000000000000000000000..14c2b0357a081246633725212346f64dde1ef5c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001314.fa
@@ -0,0 +1,40 @@
+>0_1578
+MEGMSAPSVSARPSAVGLGMPQVPRVRRSREEVEAAAPVSGEKRVLLAAPRGYCAGVDRA
+VVAVEKALEHHGAPVYVRKEIVHNRHVVDTLTERGVVFVDELDEVPEGALTVFSAHGVSP
+AVVEEAAQRNLRTIDATCPLVTKVHREAVRFAKQDKRILLIGHDGHEEVEGTFGEAPEHT
+TVINDVAEARTVQVEDPDNLIWLSQTTLSVDETLEIVSVLRERFPNLQDPPSDDICYATS
+NRQAAIKSISPECDLVIIVGSANSSNSVRLKEVAAEYGASRAERVDFANQVDESWFEGVA
+TVGLSSGASVPEVLVQEVLALLAEYGYGQVDEVVTAEEDIIFSLPKELRAEMKRVGDDGR
+ALGGRRRAAEA
+>1_1293
+MEGMSAPSVSARPSAVGLGMPQVPRVRRSREEVEAAAPVSGEKRVLLAAPRGYCAGVDRA
+VVAVEKALEHHGAPVYVRKEIVHNRHVVDTLTERGVVFVDELDEVPEGALTVFSAHGVSP
+AVVEEAAQRNLRTIDATCPLVTKVHREAVRFAKQDKQILLIGHEGHEEVEGTFGEAPEHT
+TVINDVAEAQTIQVEDPDNLIWLSQTTLSVDETLEIVSVLRERFPNLQDPPSDDICYATS
+NRQAAIKSISPECDLVIIVGSANSSNSVRLKEVAAEYGASRAERVDFTNQVDESWFEGVA
+TVGLSSGASVPEVLVQEVLALLAEYGYGQVDEVVTAEEDIIFSLPKELRAELKRVGDESR
+SLGGRRRDAEA
+>2_1238
+MGGMSAPSVSARPSAVGLGMPQVPRVRRTREDVEAAAPVSGDKRVLLAAPRGYCAGVDRA
+VVAVEKALEHHGAPVYVRKEIVHNRHVVDTLTERGVVFVEELDEIPEGALTVFSAHGVSP
+AVVQDAERRSLRTIDATCPLVTKVHREAVRFAKQDKQILLIGHEGHEEVEGTYGEAPEHT
+TVINDVAEARAVQVADPDNLIWLSQTTLSVDETLEIVAVLRERFPNLQDPPSDDICYATS
+NRQAAIKSISPECDLVIIVGSANSSNSVRLKEVAAEYGASRAERVDFASQVDESWFEGVS
+TVGLSSGASVPEVLIQDVLALLAEYGYGQVDEVVTAEEDIMFSLPKELRAELKRVGDDSR
+GLGGRRQTEG
+>3_1148
+MDGMSVPTASAPSTVGLGMPQVPRTRRSREEVEAAAPVAGDKRVLLAAPRGYCAGVDRAV
+VAVEKALEHHGAPVYVRKEIVHNRHVVDTLTERGAVFVQELDEVPAGALTVFSAHGVSPA
+VVAEAAERDLQTIDATCPLVTKVHREAVRFARQDKRILLIGHTGHEEVEGTYGEAPEHTT
+VINDVEEARTVQVDDPDNLIWLSQTTLSVDETLEIVAVLRERFPNLQDPPSDDICYATSN
+RQAAIKRISPQCDLVIIVGSANSSNSVRLKEVALEYGAARAERVDFASQVDESWFEGVAT
+VGLSSGASVPEVLVQDVLALLADYGYGQVEEVVTAEEDIIFSLPKELRAQLKQAGDEERS
+LGGRRRPAE
+>4_1507
+MSAPSVSARPSAVGLGMPQVPRVRRSREEVEAAAPVSGEKRVLLAAPRGYCAGVDRAVVA
+VEKALEHHGAPVYVRKEIVHNRHVVDTLTERGVVFVDELDEVPEGALTVFSAHGVSPAVV
+EEAAQRNLRTIDATCPLVTKVHREAVRFAKQDKQILLIGHEGHEEVEGTFGEAPEHTTVI
+NDVAEAQTIQVEDPDNLIWLSQTTLSVDETLEIVSVLRERFPNLQDPPSDDICYATSNRQ
+AAIKSISPECDLVIIVGSANSSNSVRLKEVAAEYGASRAERVDFANQVDESWFEGVATVG
+LSSGASVPEVLVQEVLALLAEYGYGQVDEVVTAEEDIIFSLPKELRAEMKRVGDDGRALG
+GRRRDAEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001315.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001315.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a263d3d0ec45f2846138f66316236e1e217660bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001315.fa
@@ -0,0 +1,38 @@
+>0_1579
+MRTTLSLLVAALAGLLAVLATAGALVDEATHRPELLRGVTEQVAVDPEVRAAVPGVIDDV
+VHDAVPEQVPDPLAQAAEDLLRPLAQRVADDPQVVQGWSDTADEARRAWLAQLEDPQGAD
+EPGSGADVTIPFGPVAQSGITAALGDIERDLREDRFDLPGQALLETIAGADVGDWAADTL
+LAPLYDRAADLRDSTALRMDARIDALAGTDRATVHRWVDASAHWRWAAAASVLALVGALL
+LAPRGRRGLAVAVAGAVALAGGLIGGARLGPDAVHLTAPEGASPGVAAFVQQMEEAARPA
+FAAAVAPYPQTLTTLGWIVLAAGLLLALAELWVARRGRVRAARADGPPAVGRSHTAADVT
+SR
+>1_1294
+MRTTLSFLVAALAGLLAVLATAGALVDEATHRPELLRGVTEQVAVDPEVRAAVPGVIDDV
+VHDAVPEQVPGPLAQVAEDLLRPLAQRVADDPQVVQGWSDTADEARRAWLAQLEDPQGAD
+EPGSGADVTIPFGPVAQSGITAALGDIERDLREDRFDLPGQALLETIAGADVGDWAADTL
+LAPLYDRAAELRDSTALRMDARIDALAGTDRATVHRWVDASAHWRWAAAASVLALVGALL
+LAPRGRRGLAVAVAGAVALAGGLIGGARLGPDAVHLTAPEGASPGVAAFVQQMEEAARPA
+FAAAVAPYPQTLTTLGWIVLAAGLLLALAELWVARRGRVRAARADGPPAVGRSHTAADVT
+SR
+>2_1237
+MRQLTAVLLALVAGVLAVLATAGALVDEAAHRPALVRQAAEQVASDDDVRAAIPGAVADA
+VGDAVPEGVPGPLRGLAQDLVRPMAESAAQDEGVVRGWSDTADEARRAWLHDLREASDAT
+GPVPGGDFTIPFGPVAQSGVAAALGDLETDLREDRLNLPGQQLVERLLGVDFGDWAVDTL
+VGPLHERAAELRDRTDLTMTVTVDALRDVDRSEVARWVSASVHWRWAAGGAVVLLAAAVL
+IAPLRWRGVAVLLSAATALVGGYLLANATRAEAFAVAAPEGAPAGIARLVERVEQALRPA
+VDAALAPYADGLTTAGWIALAVGAALLVAELVLSAARAGRTTPPRARGGSRAAADPASR
+>3_1147
+MRSLLSLLSAVLAALLAVLATAGALVDRTAHQPDTVRQVAERIAADDAVRAAVPRAVTDS
+IEGAVPESVPAPLTQLAQDIVRPIAEDVAKDPDVATGFADTADEARRAWLMDLERARDGG
+EHAPGGEFRIPFGPVAQSGVASAVGDLETRLRSDQLNLPGQSIVEAIVGVDVGTWAADTL
+VKPLYDRAAELRDSTDLTMTVRVDALAGTDRATVARWVDASAHWRWAAGGSVLALVASLL
+LARRGRRGLALAVAGVTVLLAVLLASSAVDSSRWSLAAPDGATGGVAALARAAEAAFRPA
+VADVLAPWLGGLTTWGTVALLAGLVLMAIEVLAGPVRRRLARTRPSGTGSHTGR
+>4_1508
+MRTTLSFLVAALAGLLAVLATAGALVDEATHRPELLRGVTEQVAVDPEVRAAVPGVIDDV
+VHDAIPEQVPGPLAQTAEDLLRPLAQRVADDPQVVQGWSDTADEARRAWLAQLEDPQGAD
+EPGSGADVTIPFGPVAQSGITAALGDIERDLREDRFDLPGQALLETIVGADVGDWAADTL
+LAPLYDRAAELRDSTALRMDARIDALDGTDRATVHRWVDASAHWRWAAAASVLALVGALL
+LAPRRRRGPAVAVAGAVALVGGLIGGARLGPDAVHLTAPEGASPGVAAFVQQMEEAAGPA
+FAAAVAPYPQTLTTLGWIVLAAGLLLALAELWVARRGRVRAARVDGPPAVGRSHTAADVT
+SR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001319.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001319.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07545b22c1516fc7b3c0daa6bd2c3a56dc3aac37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001319.fa
@@ -0,0 +1,40 @@
+>0_1584
+MPTPHPRQIRQSAKLLNVRYDVRGPILEEAQRMEAAGHRIMKLNIGNPAPFGFEAPDAVL
+AAMHQHLPHAQGYSDSKGIYSARTAVSQYYESRGIRDIGVDDVFIGNGVSEMITMVLQAL
+VDDGDEILVPSPDYPLWTGATTLAGGRAVHYRCVEEEGWEPDLEHIESLVTERTKGIVLI
+NPNNPTGAVYSRAVLQGIVDVARRHNLVLMADEIYEKITYDGARHINAAGLSDDVLTLTF
+SGLSKAYRVAGYRSGWVAVSGPKHRAADFLEGLTLLANMRMCANVPAQHAIQVALGGYQS
+INDLVLPGGRLLEQRNLAQDRLNAIPGVSVQPAHGALYLFPRLDPEVYAIDDDEAFVIEL
+LRAKKILVSHGGAFNYPHSDHFRLVTLPSVKDLDVALDRLEDFLEDWRERHG
+>1_1299
+MPTPHPRQIRQSAKLLNVRYDVRGPILEEAQRMEAAGHRIMKLNIGNPAPFGFEAPDAVL
+AAMHQHLPHAQGYSDSKGIYSARTAVSQYYESRGIRDIGVDDVFIGNGVSEMITMVLQAL
+VDDGDEILVPSPDYPLWTGATTLAGGRAVHYRCVEEEGWEPDLEHIESLVTERTKGIVLI
+NPNNPTGAVYSRAVLQGIVDVARRHNLVLMADEIYEKITYDGARHINAAGLSDDVLTLTF
+SGLSKAYRVAGYRSGWVAVSGPKHRAADFLEGLTLLANMRMCANVPAQHAIQVALGGYQS
+INDLVLPGGRLLEQRNLAQDRLNAIPGVSVQPAHGALYLFPRLDPEVYAIDDDEAFVIEL
+LRAKKILVSHGGAFNYPHSDHFRLVTLPSVKDLDVALDRLEDFLEDWRERHG
+>2_1232
+MPTPRPRQIRQSAKLLNVRYDVRGPILEEAQRMEAAGHRIMKLNIGNPAPFGFEAPDAIL
+QAMYRHLPHAQGYSDSQGIYSARTAVSQYYESRGIRDIGVEDVFIGNGVSEMISMVLQAL
+VDDGDEILVPSPDYPLWTGATTLAGGRAVHYRCVEEEGWAPDLEHIESLVTERTKGIVLI
+NPNNPTGAVYSRQILQGIIDVARRHGLVLMADEIYEKITYDGARHINAAGLSDDVLTLTF
+SGLSKAYRVAGFRSGWVAVSGPKHRARDFLEGLTLLANMRMCANVPAQHAIQVALGGYQS
+IDDLVLPGGRLLEQRNLAQKRLNDIPGVSVQPAQGALYLFPRLDPEVYAIEDDQEFVIDL
+LRAKKILVSHGGAFNYPHTDHFRLVTLPSVEDLDVALDRLEDFLEDWRERRG
+>3_1142
+MAPSTPREFRQSSKLLNVRYDVRGPILEEAQRMEAAGHRIMKLNIGNPAPFGFEAPDAIL
+QAMYQHLPHAQGYSDSKGIYSARTAVSQYYESRGIRDISVDDVFIGNGVSEMITMVLQAL
+VDDGDEILVPSPDYPLWTGATTLSGGRAVHYRCVEEEGWAPDLEHLESLITERTKGLVII
+NPNNPTGAVYSREVLNGVVDIARRHNLVLLADEIYEKITYDGARHINAAGLSDDVLTLTF
+SGLSKAYRVAGYRSGWVAVSGPKHRAKDFLEGLTLLSNMRMCANVPAQHAIQVALGGYQS
+IEDLILPGGRLLEQRNLAQKRLNDIPGVSVQPAHGALYLFPRLDPEVYAIDDDEKFVIEL
+LQAKKILVSHGGAFNYPQPDHFRLVTLPSVKDLDIALDRLEDFLEDWRERRG
+>4_1513
+MGGMPTPHPRQIRQSAKLLNVRYDVRGPILEEAQRMEAAGHRIMKLNIGNPAPFGFEAPD
+AVLAAMHQHLPHAQGYSDSKGIYSARTAVSQYYESRGIRDIGVDDVFIGNGVSEMITMVL
+QALVDDGDEILVPSPDYPLWTGATTLAGGRAVHYRCVEEEGWEPDLEHIESLVTERTKGI
+VLINPNNPTGAVYSRAVLQGIVDVARRHNLVLMADEIYEKITYDGARHINAAGLSDDVLT
+LTFSGLSKAYRVAGYRSGWVAVSGPKHRAADFLEGLTLLANMRMCANVPAQHAIQVALGG
+YQSINDLVLPGGRLLEQRNLAQDRLNAIPGVSVQPAHGALYLFPRLDPEVYAIDDDEAFV
+IELLRAKKILVSHGGAFNYPHSDHFRLVTLPSVKDLDVALDRLEDFLEDWRERHG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001333.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001333.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c35680090a59fb311ff44724f33e7bce5c0a3d75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001333.fa
@@ -0,0 +1,40 @@
+>0_1598
+MTNQIEIGRGKRGRRAFSLDDVSVVPARRTRDPQDVSLTWRIDAYTFDMPVIGAPMDSVM
+SPEAAIAMGRLGGLGVLNLEGLWTRHEDPRPLLEEIAALQAGPAGTEATRKLQEAYAAPI
+RPDLITERLAQIREAGVVVAGSLTPQNTQEFYRTVVAAGVDLFVIRGTTVSAEHVSSTQE
+PLDLKQFIYELDVPVIVGGAAGYTPALHLMRTGAAGVLVGFGGGASTTTRRAMGIRVPMA
+TAISDIAEARRDYMDESGGRYVHVIADGGVSTSGEIVKAIAMGADAVVLGAALARATDAP
+GGGWHWGLEAAHPELPRGHRTQVGQVAPLEEVLWGPGRHADGTSNLMGGLKRAMATCGYT
+ELKDFQKVEVLVTPTQTV
+>1_1313
+MTNQIEIGRGKRGRRAFSLDDVSVVPARRTRDPQDVSLTWRIDAYTFDMPVIGAPMDSVM
+SPETAIAMGRLGGLGVLNLEGLWTRHEDPRPLLEEIAALEAGPAGTEATRMLQEAYAAPI
+RPDLITERLAQIREAGVVVAGSLTPQNTQEFYRTVVAAGVDLFVIRGTTVSAEHVSSTQE
+PLDLKQFIYELDVPVIVGGAAGYTPALHLMRTGAAGVLVGFGGGASTTTRRAMGIRVPMA
+TAISDIAEARRDYMDESGGRYVHVIADGGVSTSGEIVKAIAMGADAVVLGAALARATDAP
+GGGWHWGLEAVHPELPRGHRTHVGQVAPLEEVLWGPGRHADGTSNLMGGLKRAMATCGYT
+ELKDFQKVEVLVTPTQTV
+>2_1216
+MTNQIEIGRGKRGRRAFSLDDVSVVPARRTRDPKDVSLTWRIDAYTFEMPVIGAPMDSVM
+SPETAIALGRLGGLGVLNLEGLWTRHEDPRPLLEEIAALEAGPDGTEATRRLQEAYAAPI
+RAELITERLAQIREAGVVVAGSLTPQNTQEFYKTVLAAGVDLFVIRGTTVSAEHVSSSHE
+PLDLKQFIYELDVPVIVGGAAGYTPALHLMRTGAAGVLVGFGGGSSTTTRRAMGIRVPMA
+TAIADIAEARRDYMDESGGRYVHVIADGGVSTSGEIVKALAMGADAVVLGAALARATDAP
+GGGWHWGLEAAHPELPRGHRTHVGQVAPLEEVLWGPGHHADGTSNLMGGLKRAMATSGYT
+ELKEFQKVEVLVTPTQTV
+>3_1128
+MTNQIEIGRGKRGRQAFSFDDVSVVPSRRTRDPKDVNLSWRIDAYTFDMPVMGAPMDSVM
+SPETAIALGRLGGLGVLNLEGLWTRHEDPEPLLEEIAAMEAEAGSPEVTRRLQEIYSAPI
+RADLITERLAQIRESGVVVAGSLTPQNTQQFSQTVLAAGVDLFVIRGTTVSAEHVSSTHE
+PLDLKQFIYELDVPVIVGGAAGYTPALHLMRTGAAGVLVGFGGGASTTTRRAMGIRVPMA
+TAIADIAEARRDYMDESGGRYVHVIADGGVGTSGEIVKAIAMGADAVTLGTALARATEAP
+GRGWHWGLEAAHPELPRGHRTRVGQVAPLEEVLWGPGHTTDGTSNLMGALKRAMATSGYT
+ELKDFQKVEVLVTGARTH
+>4_1528
+MTNQIEIGRGKRGRRAFSLDDVSVVPARRTRDPQDVSLTWRIDAYTFDMPVIGAPMDSVM
+SPETAIAMGRLGGLGVLNLEGLWTRHEDPRPLLEEIAALEAGPAGTEATRKLQEAYAAPI
+RPDLITERLEQIREAGVVVAGSLTPQNTQEFYRTVVAAGVDLFVIRGTTVSAEHVSSTQE
+PLDLKQFIYELDVPVIVGGAAGYTPALHLMRTGAAGVLVGFGGGASTTTRRAMGIRVPMA
+TAISDIAEARRDYMDESGGRYVHVIADGGVSTSGEIVKAIAMGADAVVLGAALARATDAP
+GGGWHWGLEAAHPELPRGHRTHVGQVAPLEEVLWGPGRHADGTSNLMGGLKRAMATCGYT
+ELKDFQKVEVLVTPTQTV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001338.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001338.fa
new file mode 100644
index 0000000000000000000000000000000000000000..13f6af0a8cd1cfd99ab049a17bb47a282ce64389
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001338.fa
@@ -0,0 +1,39 @@
+>0_1606
+MAEPLATAPGRLPAPLGGATAAGPVDADAPRRSGAFVTAAERRRYAVVVAVLAAVAVLST
+AGILLWGNEAEPGSRAFWMIARMRVESLGVIGIVALCHSFATVTFHTVTGNRIITPSIMG
+FEALYTAVSTVAVYVLGAAGVAVLTGVGPFLAQAALMVALTTALYSWLLSRPYGSVHLML
+LVGVVLGGGLAALSTFMQRLLDPNSFDLLSARLFGNISNARTEYVAIAAPIAVVVCALLW
+LRSRRLNTVALGADAATNLGLHHRRELMVTLLLVSVLMAMTTALVGPMTFLGFLVATLAY
+SLVDTHDHRFILPVAALAGYAVLTSAYFVLRHVFYAGGAVTVVIELIGGITFLVVVMRKG
+RL
+>1_1321
+MAEPLATAPGRIPAPPGGATAAGPVEADAPRRSGAFVTAADRRRYAVVVAVLAAVAVLST
+AGILLWGNEAEPGSRAFWMIARMRVESLGVIGIVALCHSFATVTFHTVTGNRIITPSIMG
+FEALYTAVSTVAVYVLGAAGVAVLTGVGPFLAQAALMVALATALYSWLLSRPYGSVHLML
+LVGVVLGGGLAALSTFMQRLLDPNSFDLLSARLFGNISNARTEYVAIAAPIAVVVCALLW
+LRSRRLNTVALGADAATNLGLHHRRELMVTLLLVSVLMAMTTALVGPMTFLGFLVATLAY
+SLVDTHDHRFILPVAALAGYAVLTSAYFVLRHVFYAGGAVTVVIELIGGITFLVVVMRKG
+RL
+>2_1209
+MVAVLAVVAVLSTAGILLWGNEAEPGSRAFWMIAGMRLDSLGVIAIVALCHSFATVSFHT
+VTGNRIITPSIMGFEALYTAVQTGAVYVLGAAGIGVVTGTGPFLAQAALMVVLATVLYSW
+LLSRPYGSIHLMLLVGVVLGGGLAALSTFMQRLLDPNSFDVLSARLFGNISNARSEYVAI
+AAPIVVVVCLVLWLRSRRMNVLALGADSATNLGLHHRRELMVTLLLVSVLMAMTTALVGP
+MTFLGFLVATLAYSLVDTHDHRMVLPVAALGAYAVLTLAYFVLRHVFYAGGAVTVIIELV
+GGITFLIVVMRKGRL
+>3_1121
+MAEPLATAPGRIPAPSGGATAAGPVDADAPRRSGAFVTAADRRRYALVVAVLAAVAVLST
+AGILLWGNEAEPGSRAFWMIARMRVESLGVIGIVALCHSFATVSFHTVTGNRIITPSIMG
+FEALYTAVSTAAVYVLGAAGVAVLTGVGPFLAQAALMVALATALYSWLLSRPYGSVHLML
+LVGVVLGGGLAALSTFMQRLLDPNSFDLLSARLFGNISNARTEYVAIAAPIAVVVCALLW
+LRSRRLNTVALGADAATNLGLHHRRELMVTLLLVSVLMAMTTALVGPMTFLGFLVATLAY
+SLVDTHDHRFILPVAALAGYAVLTSAYFVLRHVFYAGGAVTVVIELIGGITFLIVVMRKG
+RL
+>4_1536
+MVEPLATAPGRIPAPPGGATAAGPVDADAPRRSGAFVTAADRRRYAVVVAVLAVVAVLST
+AGVLLWGNEAEPGSRAFWMIARMRVESLGVIGIVALCHSFATVSFHTVTGNRIITPSIMG
+FEALYTAVSTAAVYVLGAAGVAVLTGVGPFLAQAALMVALATALYSWLLSRPYGSVHLML
+LVGVVLGGGLAALSTFMQRLLDPNSFDLLSARLFGNISNARTEYVAIAAPIAVVVCALLW
+LRSRRLNTVALGADAATNLGLHHRRELMVTLLLVSVLMAMTTALVGPMTFLGFLVATLAY
+SLVDTHDHRFILPVAALAGYAVLTSAYFVLRHVFYAGGAVTVVIELIGGITFLVVVMRKG
+RL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001344.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001344.fa
new file mode 100644
index 0000000000000000000000000000000000000000..acb12499502ffc9fa8457d0bf592897e67d06345
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001344.fa
@@ -0,0 +1,35 @@
+>0_1612
+MRIVVLGATGNVGTAVLHRLQAADEVSSIVGVSRRGPDRAGAPYDGVEWHRLDVAEPTAA
+GRLHDIVAGADAVVDLVWVIRPNRDRDHLRAVNVAGNERVFRAVAEAGVPHLVYASSVGA
+YGPGPKGRAVAESHPTTGVPTSHYAAQKAEVESILDRVQAEHPEMLVTRLRPGLIFQSAA
+GPEIKDYFLGDLVPARLVARLRAPVLPFPRGLRFQALTAQDVADAYWRVIAHRAGGAFNV
+AAEPVLDAHTMGTVLGARRILELPVGLFRAAAALTYRARLQPTDPGWVDMAAAVPIMDTT
+ALRAATGWSETTDAREAVRLVLDHLDGAEGLGNAGHRSHSPTE
+>1_1327
+MRIVVLGATGNVGTAVLHRLQAAAEVSSIVGVSRRGPDRAGAPYDGVEWHRLDVAEPTAA
+GRLREIVAGADAVVDLVWVIRPNRDRDHLRAVNVAGNERVFRAVAEAGVPHLVYASSVGA
+YGPGPKGRAVPESHPTTGVPTSHYAAQKAEVESILDRVQAEHPELLVTRLRPGLIFQSAA
+GPEIKDYFLGDLVPARLVARLRTPVLPFPRGLRFQALTAQDVADAYWRVIVHRAGGAFNV
+AADPVLDAHTMGTVLGARRILELPVGLFRAAAALSYRARLQPTDPGWVDMAAAVPIMDTT
+ALRAATGWSETTDAREAVRLVLDHLDGAEGLGNAGHRSHSPTE
+>2_1203
+MRIVVLGATGNVGTALLERLHAADEVTSIVGVSRRGPDRAGAPYDGVEWHRLDVAEPTAA
+GRLSEIVAGADAVVDLVWVIRPNRDRDHLRAVNVAGNERVFRAVAEARVPHLVYASSVGA
+YGPGPKGRAVPESHPATGVPTSHYAAQKAEVESILDRVQAEHPEMLVTRLRPGLIFQAGA
+GPEIKDYFLGDLVPARLVARLRAPVLPFPRGLRFQALTAQDMADAYWRVIAHRAGGAFNV
+AAEPVLDAHTMGTVLGARRILELPVGLFRAAASLTYRARLQPTDPGWVDMAAAVPIMDTT
+ALRAATGWSETTDAREAVRLVLDHLDGAEGLGNAGHRSHSPTE
+>3_1115
+MRIVVLGATGNVGTALLERLHRAPEATELVGVSRRGPDRAGAPYDGVEWHRMDIADAASA
+PRLTEVLRGADAVVDLVWVIRPNRDRAHLRAVNVDGNERVFRAAAAAGVPHLVYASSVGA
+YGPGPKDVRVDESHPTTGVPTSHYAAQKAEVETILDRVAAEHPRMLVSRLRPGLIFQSGA
+GPEIKDYFLGDLVPARLAARLRTPVLPFPTGLRFQALTAQDVAEAYWQVVAHRAGGAFNV
+AAEPVLDAHTMGTVLGARRILELPVAVFRAAAAVSYRARLQPTDPGWVDMAAAVPVMDTS
+ALRRATDWRPRTDARDAVRLVLDHLDGREGLGNAGHRSHSPLE
+>4_1542
+MRIVVLGATGNVGTAVLHRLQAADEVSSIVGVSRRGPDRAGAPYDGVEWHRLDVAEPTAA
+GRLREIVAGADAVVDLVWVIRPNRDRDHLRAVNVVGNERVFRAVAEAGVPHLVYASSVGA
+YGPGPKGRAVAESHPTTGVPTSHYAAQKAEVESILDRVQAEHPELLVTRLRPGLIFQSAA
+GPEIKDYFLGDLVPARLVARLRTPVLPFPRGLRFQALTAQDVADAYWRVIAHRAGGAFNV
+AADPVLDAHTMGTVLGARRILELPVGLFRAAAALSYRARLQPTDPGWVDMAAAVPIMDTT
+ALRAATGWSETTDAREAVRLVLDHLDGAEGLGNAGHRSHSPTE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001376.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001376.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a6ca89206b6be7d77d2f25f8925a4d541cebafac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001376.fa
@@ -0,0 +1,30 @@
+>0_1649
+MTENINQKDTQVTESTETTVSETGSGSASQTTERATGGRGGRDGGRGGRDGDRRGGRRDD
+RNRRGAQDDEKDQFLERVVGINRVSKVVKGGRRFSFTALVVVGDGDGTVGVGYGKAKEVP
+AAIQKAVEEAKKSFFRVPRVGSTIPHLVQGEDAAGVVLLRPASPGTGVIAGGPVRAVLEC
+AGIHDVLSKSMGSVNAINIVRGTVDALKKLEEPQAVAARRGKALDEIAPHAMLRTMENDR
+AQKSAKAGA
+>1_1366
+MTENINQKDTQVTESTETTVSETGSGSASQTTERATGGRGGRDGGRGGRDGDRRGGRRDD
+RNRRGAQDDEKDQFLERVVGINRVSKVVKGGRRFSFTALVVVGDGDGTVGVGYGKAKEVP
+AAIQKAVEEAKKSFFRVPRVGSTIPHLVQGEDAAGVVLLRPASPGTGVIAGGPVRAVLEC
+AGIHDVLSKSMGSVNAINIVRGTVDALKKLEEPQAVAARRGKALDEIAPHAMLRTMENDR
+AQKSAKAGA
+>2_1150
+MTENNNQKDTQVTESTETTVSETASGSSSQTTERSAGGRGGRDGGRGGRDGDRRGGRRDD
+RNRRGAQDDEKDQFLERVVAINRVSKVVKGGRRFSFTALVVVGDGDGTVGVGYGKAKEVP
+AAIQKAVEEAKKSFFRVPRVGSTIPHLVQGEDAAGVVLLRPASPGTGVIAGGPVRAVLEC
+AGIHDVLSKSMGSVNAINIVRGTVDALKKLEEPQAVAARRGKALDEIAPHAMLRTMENDR
+AQKSAKAGA
+>3_1081
+MTETNDQKDTQVSETTETTVSETSAGSAGQSTERSGGRGGRDGGRGGRDGDRRGGRRDDR
+NRRGAQEDEKDAFLERVVAINRVSKVVKGGRRFSFTALVVVGDGDGTVGVGYGKAKEVPA
+AIQKAVEEAKKSFFRVPRVGSTIPHLVQGEDAAGVVLLRPASPGTGVIAGGPVRAVLECA
+GIHDVLSKSMGSANAINIVRGTVDALKRLEEPQAVAARRGKALDEVAPHAMLRTMENDRA
+SKGAQKAGV
+>4_1578
+MTENINQKDTQVTESTETTVSETGSGSASQTTERATGGRGGRDGGRGGRDGDRRGGRRDD
+RNRRGAQDDEKDQFLERVVGINRVSKVVKGGRRFSFTALVVVGDGDGTVGVGYGKAKEVP
+AAIQKAVEEAKKSFFRVPRVGSTIPHLVQGEDAAGVVLLRPASPGTGVIAGGPVRAVLEC
+AGIHDVLSKSMGSVNAINIVRGTVDALKKLEEPQAVAARRGKALDEIAPHAMLRTMENDR
+AQKSAKAGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001379.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001379.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aadbaecd0637156d4c958857e3ef55c12a2fa39a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001379.fa
@@ -0,0 +1,20 @@
+>0_1652
+MTMTDPVADMLTRLRNANSAYHDTVSMPSSKLKTRVAEILKAEGYIQDWREEEAEVGKKL
+TIDLKFGPQRERAIAGLRRISKPGLRVYAKSTNLPHVLGGLGIAILSTSSGLLTNQQAAK
+KGVGGEVLAYVW
+>1_1369
+MTMTDPVADMLTRLRNANSAYHDTVSMPSSKLKTRVAEILKAEGYIQDWREEEAEVGKKL
+TIDLKFGPQRERAIAGLRRISKPGLRVYAKSTNLPHVLGGLGIAILSTSSGLLTNQQAAK
+KGVGGEVLAYVW
+>2_1147
+MTMTDPVADMLTRLRNANSAYHDTVSMPSSKLKTRVAEILKSEGYIQDWREEEAEVGKKL
+TIDLKFGPQRERAIAGLRRISKPGLRVYAKSTNLPHVLGGLGIAILSTSSGLLTNQQAAK
+KGVGGEVLAYVW
+>3_1078
+MTMTDPVADMLTRLRNANSAYHDTVSMPSSKLKVRVAEILKAEGYIQDWREEEAEVGKKL
+TIDLKFGPQRERAIAGLRRISKPGLRVYAKSTNLPHVLGGLGIAILSTSSGLLTDRQASQ
+KGVGGEVLAYVW
+>4_1581
+MTMTDPVADMLTRLRNANSAYHDTVSMPSSKLKTRVAEILKAEGYIQDWREEEAEVGKKL
+TIDLKFGPQRERAIAGLRRISKPGLRVYAKSTNLPHVLGGLGIAILSTSSGLLTNQQAAK
+KGVGGEVLAYVW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001384.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001384.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d0551fd163b4233c6c2a5d2f1ce28d2cc6e82d09
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001384.fa
@@ -0,0 +1,15 @@
+>0_1657
+MAIGTKDLNVESLDGMDNARLLEALKSSKEELFNLRFQAATGQLDNASRLKAVKRDIARI
+YTILRERELGIRGDVAAEAQAEKNEEAAK
+>1_1374
+MAIGTKDLNVESLDGMDNARLLEALKSSKEELFNLRFQAATGQLDNASRLKAVKRDIARI
+YTILRERELGIRGDVAAEAQAEKNEEAAK
+>2_1142
+MAIGTKDLNVESLDGMDNARLLEALKSSKEELFNLRFQAATGQLDNSSRLKAVKRDIARI
+YTILRERELGIRGDVAAEAQADNNEEAAK
+>3_1073
+MAIGTKDLNVESLDGMDNARLLEALKSSKEELFNLRFQAATGQLEDSSRLKAVKRDIARI
+YTILRERELGIRGDVETAGAEKNEEAAK
+>4_1586
+MAIGTKDLNVESLDGMDNARLLEALKSSKEELFNLRFQAATGQLDNASRLKAVKRDIARI
+YTILRERELGIRGDVAAEAQAEKNEEAAK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001394.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001394.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca089538f10d3a809dec684ff6d0812b725f6729
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001394.fa
@@ -0,0 +1,20 @@
+>0_1667
+MSLPSPRRLFAVTAMAEMFTWAGLLIAMGLKYGGVTERVVPIAGGVHGFVFLCYLVVTVA
+VWIDGRWPVARGLLGLGSTIVPFMTVPFERAQRRRGEPASRWQVVDRAPGERRPLERLLV
+VVLRHPVVSALLAVAVVAVVFTLLLNAGPPTEWGR
+>1_1384
+MSLPGPRRLFAVTAMAEMFTWAGLLIAMGLKYGGVTERVVPIAGGVHGFVFLCYLVVTVA
+VWIDGRWPVARGLLGLGSTIVPFMTVPFERAQRRRGEPASRWQVVDRAPGERGPLERLLV
+VVLRHPVVSALLAVAVVAVVFTLLLNAGPPTEWGR
+>2_1132
+MSLPSPRSLFRVTAAAEMVTWAGLLTAMALKYTGVTDAVMPIAGGIHGFVFLCYFVVTVA
+VWIDGRWPAARGLLGLGSAVVPFMTVPFERAQLRRGEPARHWRVLEGEPGERTGAQRVLA
+AVLGRPLVSALVALIAVVVVFTLLLNAGPPTEWGR
+>3_1063
+MRVPGPRSLYRATAVAEMATWTLLLLAMALKYGGVTAALMPAAGGVHGFVFLCYAAVVVA
+VWIDGRWGVGRGLLALGSAVVPYMTVPMERALLRRGEPAPRWRVLEEAGRTSATDRLLRT
+VLRRPRVSALAVLVAVVVVFSLLLRAGPPTEWFSR
+>4_1596
+MSLPSPRRLFAVTAMAEMFTWAGLLIAMGLKYGGVTERVVPIAGGVHGFVFLCYLVVTVA
+VWIDGRWPVARGLLGLGSTIVPFMTVPFERAQRRRGEPASRWQVVDRAPGERRPLERLLV
+VVLRHPVVSALLAVAVVAVVFTLLLNAGPPTEWGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001413.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001413.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fc4613b92255ec17644b21b36054b1ade0db961b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001413.fa
@@ -0,0 +1,30 @@
+>0_1686
+MRPDHPAVGVLALGLARRLGLPDTALLPDDAPAAGAEPRRIEVARQGVAEAEVLALPWAT
+VVAGPAWFTRACRGVPAEALGVESALLRTAVRAAAGEAVRSRGEFTLYAAEEPPPVDPSR
+TVAVSDDPAHVHAVVAQAPADDVAEAGVPSWESSVALVPDDGAGRAIEAAVAAAGHRVTG
+GVLASLGTLTPPRLRGRGLGRYAVAVAMDRAALEGLLPFAEVPAGHTAAHHVAIAVGLEA
+AGTRTVLALD
+>1_1403
+MRPDHPAVGVLALGLARRLGLPDTALLPGDAPAAGAEPRRIEVARQDVAEAEVLALPWAT
+VVAGPAWFTRACRGVPAEALGVESALLRTAVRAAAGEAVRSRGEFTLYAAEEPPPVDPSR
+TVAVSDDPAHVHAVVAQAPADDVAEAGVPSWESSVALVPDDGAGRAIEAAVAAAGHRVTG
+GVLASLGTLTPPRLRGRGLGRYAVAVAMDRAALEGLLPFAEVPAGHTAAHHVAIAVGLEA
+AGTRTVLALD
+>2_1112
+MSGAPSFAGVLALGLARRLGLPDTALLPDDDGATKPRRLEAVREDAAEAEVLALPWATVV
+AGPAWFAAACRNVPAEVLGVESALLRTAAGAAPGAGSGGGAAVRSRGEFTLYAAEEPPVL
+EPSRSVAVSEDPAHALAVAAQAPADDLAEAAAQAWTSSASLVPDDGAGHGLEAPVAAAGH
+RVSGGILAELGVLTVPRLRGHGLGRYAAAVAMDRATLEGLLPVAHLRAGHTAAHHVAIAV
+GLEPVGSRTVLALG
+>3_1042
+MTAAEPLPEHVRELVALAWGRALGVPDDVAALARATGRRVALPRPAGPETDILLLEAAGL
+EVLAGPEPLLAAAADRATEELALESTLLRLASGWGPRSRGEHTLLHLDEPPEVAPSGRVA
+VSDDPADAAALARECPADDARAAGLDELHALRTLVPDDGAGRATGTPLAAAGHATRAGLL
+ADVRVLVRPELRGRGLGAYAAAVAAGAAWDEGLVPQARVPAAQDGALRLALGVGFVPTGR
+LTRVELTRAG
+>4_1615
+MRPDHPAVGVLALGLARRLGLPDTALLPGDAPAAGAEPRRIEVARQGVAEAEVLALPWAT
+VVAGPAWFTRACRGVPAEALGVESALLRTAVRAAAGEAVRSRGEFTLYAAEEPPPVDPSR
+TVAVSDDPAHVHAVVAQAPADDVAEAGVPSWESSVALVPDDGAGRAIEAAVAAAGHRVTG
+GVLASLGTLTPPRLRGRGLGRYAVAVAMDRAALEGLLPFAEVPAGHTAAHHVAIAVGLEA
+AGTRTVLALD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001414.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001414.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef4253c3d64a5200bf1a0ccc0a8d56da7832e225
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001414.fa
@@ -0,0 +1,40 @@
+>0_1687
+MTTSRSPLLDLAVAEPQGPAGGAVEGRGPDAGVAAHYGRPLPEQRALARGRALVDLSHRA
+VLSVSGPDRLSWLHTLGTQHVETLPPGTSTEILFLDVQGRIEHAAHLLEDGTAAWLVTDR
+EDGPGLAAWLTSMRFSHDVTLRDHTGAVAVVGATAPVPGWEDRTVWLDPWPRVGAGGWAY
+TADPDPATHPGADWSWREYLVTRADLEATVRALGTGVLAGWSLAGTTAAEALRIEAGRPR
+RALDVDDRAIPHELDLLRTAVHLEKGCYRGQETVARVHNLGRPPRRLTRLLLDGSGHALP
+EHGAPVILRPAEDTPEARAAARPVGTVTAAAQHHEAGAVALALLKRTVPVDAELLVREDA
+PGEDGVAEGGWIAASQEPLVSPDAGQVVGRPRGVGRLR
+>1_1404
+MTTSRSPLLDLAVAEPQGPAGGAVEGRGPDAGVAAHYGRPLPEQRALARGRALVDLSHRA
+VLSVSGPDRLSWLHTLGTQHVETLPPGTSTEILFLDVQGRIEHAAHLLEDGTAAWLVTDR
+EDGPGLAAWLTSMRFSHDVTLRDHTGAVAVVGATAPVPGWEDRTVWLDPWPRVGAGGWAY
+TADPDPATHPGADWSWREYLVTRADLEATVRALGTGVLAGWSLAGTTAAEALRIEAGRPR
+RALDVDDRAIPHELDLLRTAVHLEKGCYRGQETVARVHNLGRPPRRLTRLLLDGSGHALP
+EHGAPVILRPAEDTPEARAAARPVGTVTAAAQHHEAGAVALALLKRTVPVDAELLVREDA
+PGEDGVAEGGWIAASQEPLVSPDAGQVVGRPRGVGRLR
+>2_1111
+MTGAEPAQRSPLLDLASAEPHGPAGGAVEGVGPDAGVAAHYGRPLPEQRALARGRALVDL
+SHRAVLSVSGPDRLTWLHTLGTQHVADLPAGTSTEILFLDAQGRIEHAAHLLEDGTAAWL
+VTDREDGPGLAAWLASMRFSHQVTLRDHTGAVAVVGSTAPVPGWEDRTVWVDPWPHVGVG
+GWAYTADPRPESHPGADWSWREHLVTRADLEATVRTLGTGPLEGWSLAGTTAAEALRIEA
+GRPRMATDVDERALPHELDLLRTAVHLEKGCYRGQETVARVHNLGRPPRRLTRLMLDGSV
+HALPPHGAPVILRPAEDTPQARAAARPVGAVTSSAQHHEAGAVALALLKRSVPVDAELLV
+CEDLPGDAEAGDAADAAETGWIAAAQEPLVSPAAGQVVGRPRGVGRLR
+>3_1041
+MTEPRPEPAPAVRAARRSPLLAPPPAAPGGPAEGAVEGVGQDAGVAAHYGRPLVEQRALA
+RGRALVDLSQKTVVSVSGPDRLSWLHTLSTQHLKDRPAGTSTEALFLDANGRIEIAVHLL
+EDGAAAWLIADPAHADVLVTWLRSMVFSHRVTLRDHTGVVAVVGAMAPVPGWEDRTVWLD
+PWPRVDVGGWPYSPDPDPAAHPGAGWSWREYLVTRGDLVATVDRLGTGELEGWSLAGALA
+AEALRIEAGRPRPAVDADARAIPHELDILRTAVHLEKGCYRGQETVARVYNLGRPPRRLT
+QLLLDGSSHALPAAGAAVILRPEPDTADARAAARPVGTVTSAVQHHEAGAVALAVLKRAV
+PVAAELLVREEAAGGGEPEWIAASQQALVSPDAGQVVGRPAGLSRRA
+>4_1616
+MTTSRSPLLDLAVAEPQGPAGGAVEGRGPDAGVAAHYGRPLPEQRALARGRALVDLSHRA
+VLSVSGPDRLSWLHTLGTQHVETLPPGTSTEILFLDVQGRIEHAAHLLEDGTAAWLVTDR
+EDGPGLAAWLTSMRFSHDVTLRDHTGAVAVVGATAPVPGWEDRTVWLDPWPRVGAGGWAY
+TADPDPATHPGADWSWREYLITRADLEATVRALGTGVLAGWSLAGTTAAEALRIEAGRPR
+RALDVDDRAIPHELDLLRTAVHLEKGCYRGQETVARVHNLGRPPRRLTRLLLDGSVHALP
+EHGAPVILRPAEDTPEARAAARPVGTVTAAAQHHEAGAVALALLKRTVPVDAELLVREDA
+PGEDGAAEGGWIAASQEPLVSPDAGQVVGRPRGVGRLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001421.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001421.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4116490f47b7d3fb929ecf7868e24116214694e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001421.fa
@@ -0,0 +1,30 @@
+>0_1694
+MGRVSIPTPYEDLLADVMAHGAVKTDRTGTGTRSVFGRQLRFDLAESFPLITTKRVHFKS
+VALELLWFLRGDSNVRWLQERGVRIWNEWADEDGELGPVYGVQWRSWPTPDGGHIDQIAK
+VVEQIRTNPDSRRHIVTAWNPAEVDEMALPPCHALFQFYVSPGQDGAPGRLSCQLYQRSA
+DLFLGVPFNIASYALLTVMVAQQTGLTPGEFVWTGGDVHIYANHEEQVREQLSREPYPYP
+RLRLRRTPASIFDYDYEDFEVLDYRHHPTITAPIAV
+>1_1411
+MGRVSIPTPYEDLLADVMAHGAVKTDRTGTGTRSVFGRQLRFDLAESFPLITTKRVHFKS
+VALELLWFLRGDSNVRWLQERGVRIWNEWADEDGELGPVYGVQWRSWPTPDGGHIDQIAK
+VVEQIRTNPDSRRHIVTAWNPAEVDEMALPPCHALFQFYVSPGQDGAPGRLSCQLYQRSA
+DLFLGVPFNIASYALLTVMVAQQTGLTPGEFVWTGGDVHIYANHEEQVREQLSREPYPYP
+RLRLRRTPASIFDYDYEDFEVLDYRHHPTITAPIAV
+>2_1104
+MSIPTPYEDLLADVMANGAVKSDRTGTGTRSVFGRQMRFDLSRSFPLITTKRVHFKSVAL
+ELLWFLRGDSNVRWLQERGVRIWNEWADEDGELGPVYGVQWRSWPTPDGGHIDQIAKVVE
+QIRTNPDSRRHIVTAWNPAEVDEMALPPCHALFQFYVSPGQDGAPGRLSCQLYQRSADLF
+LGVPFNIASYALLTVIVAQQTGLAPGEFVWTGGDVHIYANHEEQVREQLSREPYPYPRLW
+LRRTPASIFDYDYEDFEVLDYRHHPTITAPIAV
+>3_1030
+MSIPTPYEDLLADVLAHGAVKADRTGTGTRSVFGRQLRFDLAESFPLITTKRVHFKSVAL
+ELLWFLRGDSNVRWLQERGVTIWDEWADEGGELGPVYGVQWRSWPTPDGGSIDQIAKVVE
+QIRTSPDSRRHLVTAWNPAEVDEMALPPCHAMFQFYVAPDVDGAPGVLSCQLYQRSADLF
+LGVPFNIASYALLTLMVAQQTGLTPGEFVWTGGDCHIYANHEEQVREQLSREPYPYPTLR
+IRRTPESIFDYEYDDFELVDYRHHPAIKAPVAV
+>4_1623
+MGRVSIPTPYEDLLADVMAHGAVKTDRTGTGTRSVFGRQLRFDLAESFPLITTKRVHFKS
+VALELLWFLRGDSNVRWLQERGVRIWNEWADEDGELGPVYGVQWRSWPTPDGGHIDQIAK
+VVEQIRTNPDSRRHIVTAWNPAEVDEMALPPCHALFQFYVSPGQDGAPGRLSCQLYQRSA
+DLFLGVPFNIASYALLTVMVAQQTGLTPGEFVWTGGDVHIYANHEEQVREQLSREPYPYP
+RLRLRRTPASIFDYDYEDFEVLDYRHHPTITAPIAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001437.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001437.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad176e89214d8f8cfd49da8352f4fba6ffde7e91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001437.fa
@@ -0,0 +1,20 @@
+>0_1711
+MLYLIDPRGAVWSADTTIGRARARARVDGRPVDDLKFAKAAMLLTFDDHVDLALRHGVAA
+PRGLLLDHGFVAQVLAPANLKAQRANQDAIAEQLAVVERRTEDVGSLRSHRHAAAYEGAD
+QSLERRIKKAEEAARETLQAAPDEDLVRHWTRLGGAVPATLQAGRDR
+>1_1428
+MLYLIDPRGAVWSADTTIGRARARARVDGRPVDDLKFTKAAMLLTFEDHVDLALRHGIAA
+PRGLLLDHGFVAQVLAPANLKAQRANQDAIAEQLAVVERRTEDVGSLRSHRHAAAYEGAD
+QDLERRIKKAEEAARETLQAAPDEDLVRHWTRLGGAVPATLQADRDR
+>2_1087
+MLYLIDPRGAVWSADATIGQARARARVDGRPIDDLKFARAAMLLTLDDYVDLALRHGVEA
+PRGILLDHGFVAQALAPANLKAQRANQDAMAEQLLPVERRTEDAGSLRGHRHDAAYEGAH
+QDLDRRIKKAEETARETLQKTPDEDLIRHWRRLGGDVPATIEADRKD
+>3_1014
+MLYLIDPRGAVWQSDVTLGRALARQKVDGRPVDDVPLKKAVLPIDEADVLDLGLRHGVAA
+PRGILLDGGWVTQVLQPSQLKRQRANQDATADQLEPVELRTETDSLRSSRHAAVVEGAHR
+DLDTRIEKAEKAAREALQAAPRRELVTHWRGMGGGLPATIQADLADAD
+>4_1640
+MLYLIDPRGAVWSADTTIGRARARARVDGRPVDDLKFTKAAMLLTFEDHVDLALRHGIAA
+PRGLLLDHGFVAQVLAPANLKAQRANQDAIAEQLAVVERRTEDVGSLRSHRHAAAYEGAD
+QDLERRIKKAEEAARETLQAAPDEDLVRHWTRLGGAVPATLQADRDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001441.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001441.fa
new file mode 100644
index 0000000000000000000000000000000000000000..68db6e965f2f5ad3c77ef452c97cc58d996f6f66
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001441.fa
@@ -0,0 +1,20 @@
+>0_1716
+MTAPAPVSHAPDDYVCPFCGLVASDVSDPGNRCELGDTVYQDEDLLVLIAVDGFGDHEGH
+AMVCPAEHYENLYDLPPRVLQRIALMAQQVALAMKRAWAPDGVSTRQHNEPAGNQHVWHY
+HLHVFPRFEGDMLYRQLRHPVAPEVRAGKARELAAALDPAPTRLD
+>1_1433
+MTAPAPVSHAPDGYVCPFCGLVAGDVSDPGNRCELGDTVYQDEDLIVLIAVDGFGDHEGH
+AMVCPAEHYENLYDLPPRVLQRIALMAQQVALAMKRAWAPDGVSTRQHNEPAGNQHVWHY
+HLHVFPRFEGDMLYRQLRHPVAPEVRAGKARELAAALDPAPTRLD
+>2_1082
+MSGPRLRSHAPEGYVCPFCGLVAGDVSDPGNRCELADTVYQDEDLLVLIAVDGFGDHEGH
+AMVCPAGHYENLYELPPRVLQRIALMAREVALAMKRAWSPDGVSTRQHNEPAGNQHVWHY
+HLHVFPRFEGDLLYRQLRHPVSPEVRALKARELAAELDPAPTFLD
+>3_1008
+MSAQPLSHAPEGYVCPFCGLVAGDVSDPGNRCELEDTVYQDEDVLVLIAVDGFGEHDGHA
+MVCPSGHYENLYDLPPRVLQRIALMAQQVALAMKRAWGPDGVSTRQHNEPAGNQHVWHYH
+LHVFPRYEDDLLYRQLRHPVAPEVRAARARELAAALDPAPTLLD
+>4_1645
+MTAPAPVSHAPDGYVCPFCGLVAGDVSDPGNRCELGDTVYQDEDLLVLIAVDGFGDHEGH
+AMVCPAEHYENLYDLPPRVLQRIALMAQQVALAMKRAWAPEGVSTRQHNEPAGNQHVWHY
+HLHVFPRFEGDMLYRQLRHPVAPEVRALKARELAAALDPVPTRLD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001442.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001442.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7bde2bf4402662328127aace0f7e6761ddb80765
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001442.fa
@@ -0,0 +1,36 @@
+>0_1717
+MTTADPGFALPSGFEPLAEHGRVLEVVLTALEQVEEQLDTALGFDDLFSDTAAHHLLAAG
+GKRVRPVLTVLASLLGDPALASGEVADVDAPARQAAVVMELTHLATLYHDDVMDEAPVRR
+GAPAAHRLWGNSAAILAGDLIFARASQLMAELGPRPVQIQADTFERLVQGQLWETRGPAE
+GADPIEHYYAVLSGKTGSLIAAAGMLGALLGGADEAAVQVMRAYGEKVGLAFQLADDLID
+LTGDAERIGKVPGTDLRERVPTLTTLLLARAAQGEGPEAEDARRVRALVDGPLDTDEQLA
+AAVAALTGHPAIDEAWAITRGWAEQAKQALDPLPDSAVKAALEAFADYVVGRSA
+>1_1434
+MTTADPGFALPSGFEPLAEHGRVLEVVLTALEQVEEQLDSALGFDDLFSDTAAHHLLAAG
+GKRVRPVLTVLASLLGDPALASGEVADVDAPARQAAVVMELTHLATLYHDDVMDEAPVRR
+GAPAAHRLWGNSAAILAGDLIFARASQLMAELGPRPVQIQADTFERLVQGQLWETRGPAE
+GADPIEHYYAVLSGKTGSLIAAAGMLGALLGGADEAAVQVMRAYGEKVGLAFQLADDLID
+LTGNAERIGKVPGTDLRERVPTLTTLLLARAAQGEGPEAEDARRVRALVDGPLDTDEQLA
+AAVAALTGHPAIDEAWAITRGWAEQAKQALDPLPDSAVKAALEAFADYVVGRSA
+>2_1081
+MSTADPGFALPSGFEPLAEHGRVLEVVLTGLEQVEEQLDRAVSFEDPFSDTAAHHLLAAG
+GKRVRPVLTVLASLLGDPALASGEVADVNAQVRQAAVVMELTHLATLYHDDVMDEAPVRR
+GAPAAHRLWGNSAAILAGDLIFARASQLMSELGMRPVRVQADTFERLVQGQLWETQGPAE
+GADPVEHYYRVLAGKTGSLIAAAGMLGALLGGADEEAVQVMSAYGEKVGLAFQLADDLID
+LTGTAEQIGKTPGTDLRERVPTLTTLLLDRAAAGEGPDAQEARRVRALVDGPLDTDEQLA
+AAVAALTAHPAIDEAWAVTRAWVDDAKQALAPLPDSVVKTSLEGFADYVVERSAWPGARP
+RAVHRRAAVRAPLGGADLSPGRSGPGRARRRAPGP
+>3_1006
+MTTSAAGFALPSGFDPLAEHGRVLEAVLTALERVEEQLTASLEFDDVFSQTATRHLASAG
+GKRVRPVLTVLASLLGDAGLAEGQVGEVGPETRQAAVVMELTHLATLYHDDVMDEAPVRR
+GAPAAHRLWGNSQAILAGDLIFARASQLMAELGPRPVRIQAETFERLVQGQLWETRGPDE
+GQDLLEHYYRVLRGKTGSLIAAAGVLGAYLGGADETAVQVMADYGEKVGLAFQLADDLID
+LTSSAEELGKTPGTDLREHVPTLSTILVARAAAGEGPEADDARRVLALVDGPLDTDEQLA
+AAVAALTAHPAFAEAGALTRRWAEEAKAALAPLPESVVTEALAAFADYVVSRAS
+>4_1646
+MTTADPGFALPSGFEPLAEHGRVLEVVLTALEQVEEQLDTALGFDDLFSDTAAHHLMAAG
+GKRVRPVLTVLASLLGDPALASGEVADVDAPARQAAVVMELTHLATLYHDDVMDEAPVRR
+GAPAAHRLWGNSAAILAGDLIFARASQLMAELGPRPVQIQADTFERLVQGQLWETRGPAE
+GADPIEHYYAVLSGKTGSLIAAAGMLGALLGGADEAAVQVMRAYGEKVGLAFQLADDLID
+LTGDAERIGKVPGTDLRERVPTLTTLLLARAAQGEGPEAEDARRVRALVDGPLDTDEQLA
+AAVAALTGHPAIDEAWAITRDWAEQAKQALAPLPDSAVKTALEAFADYVVGRSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001459.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001459.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a461d0179e9f47a8ee7ae7b92e4ee4d05fb86cc3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001459.fa
@@ -0,0 +1,29 @@
+>0_1751
+MSGTSPTDPHGSQNPYGTDPYGAAPQGPTPGSPDPAGASPYGQNPYGAPPAAPYGAPGQA
+GMPQAPSPHGPAGWQSPGPVELPPRPRSLTAAFWLIVSGGLLLLATTLLAAFAITQPEGQ
+VAIQQELDRSVEQMNLPADQAEQMRTMMDGMLPALATTAAVFGVLAFLVYLWVAFAIRGG
+SRAARIVGTVLASLSVLVLVSNAVMGAFSPLDLVWVGLGVAGIVLAYRPDATEYMRLKTW
+QRFARR
+>1_1459
+MSGTSPTDPHGSQNPYGTDPYGAAPQGPTPGSPGPAGASPYGQNPYGAPPAAPYGAPGQA
+GMPQAPSPHGPAGWQSPGPVELPPRPRSLTAAFWLIVSGGLLLLATTLLAAFALTQPEGQ
+AAIQQELDRSVEQMDLPADQAEQMRAMMDGMLPALATTAAVFGVVAFLVYLWVAFAIRGG
+SRAARIVGTVLAALSVLVLVSNAVMGAFSPLDLVWVGLGVAGIVLAYRPDATEYMRLKAW
+QRFARR
+>2_1043
+MSGTSPTDPQRGQNPYGQEAPGPSPYGENPYGAHPYGQAPYGQGGPAQGQPGQGHPNPGH
+PAPSYADQGYPAQGGWPGQQAPGPLTAPRRPGAITASFWLILAGGLVLLASTLLAAFAMT
+LPESRAMLEQQMRETYEQMGLPADQLAQMEQMTDQLLPVMSVVAAAFGVVAFLVYLLIAL
+KIRKGSRAARTVGTVLAALSVLMIVTNLMMGAFNPFDLLWVGLGVAGIVMAFRPEASEYM
+RLKAWERAGTR
+>3_979
+MSGTENSNPYGRPAGQSGPQWPDAAAQAPYGQAPDASAQAPYGAPPQGWGAPQQWGGQPG
+WPAAAPVPARRPGPINAAFWLIVSAGVVFLASTVLSALVATSDAGRRELEAAMTKVWGDY
+GMTPEQIREYQDMLPPMMPVMAGVMVAVGVLALLVYLLIASKIRGGSRAARTVGTVLAVL
+SVLMVLAPLASGQFSPLDLLWCLLGVAGIATAYRKEATEFMRLRAWERAARR
+>4_1673
+MSGTSPTDPHGSQNPYGADPYGAVPQGSTPGSPDPAGASPYGQNPYGAPPATPYGAPGQA
+GMPQAPSPHGPAGWQSPGPVELPPRPRSLTAAFWLIVSGGLLLLATTLLAAFALTQPEGQ
+AAIQQELDRSVEQMDLPADQAEQMRAMMDGMLPALATTAAVFGVLAFLVYLWVAFAIRGG
+SRAARIVGTVLAALSVLVLVSNAVMGAFSPLDLVWVGLGVAGIVLAYRPDATEYMRLKAW
+QRFARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001463.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001463.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f89939dfdb9dc3c5f6fd7dd743d2ae236c5d7e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001463.fa
@@ -0,0 +1,48 @@
+>0_1755
+MAGPRPTPHARRHGGVRRPGGLPRPGQASTLESSTDLRTVLRRSGRAVSSVVGGSPARAA
+LSAFALMALVFTGLLALPWAAADGHATPLHDAMFTAVSAFSVTGLTTVNTAAHWSPAGQV
+IILVAIQIGGLGILSIASLLTLAVSRHLGLRSKLATQQAGMTSGSLGEVGQLLRVVVVTV
+LTAEAALALVLVPRFAAISGSWLTGLWHGVFYSVSAFNNAGFTLHVDGLPEIMHDPVIIT
+VLGVGVFLGALGFPVVMVLLEKGWRFREWNLHTKLTVEVTLALLVLGAVALFFFEAGNPA
+TQAGMGFWQRVGHSLFGSVMTRSGGFAIDDTNAHRPESLLLMDALMFVGGGSASTAGGIK
+VTTLAIMFLAIVAEARGDREVTAHGRTIAPESLRVAIAVLALGATLVLVATLALVHITDE
+SLQRPLFEVISAFGTCGLSVGVSAESPPAGKYVLTAMMFAGRVGTITFAAALALRQRRVL
+YRYPVERPVIG
+>1_1463
+MAGPRPTPHARRHGGVRRPGGLPRPGQASTLESSTDLRTVLRRSGRAVSSVVGGSPARAA
+LSAFALMALVFTGLLALPWAAADGHATPLHDAMFTAVSAFSVTGLTTVNTAVHWSPAGQV
+IILVAIQIGGLGILSMASLLTLAVSRHLGLRSKLATQQAGMTSGSLGEVGQLLRVVVLTV
+LTAEAALALFLVPRFAAISGSWLTGLWHGVFYSVSAFNNAGFSLHVDGLPEIMHDPVIIT
+VLGVGVFFGALGFPVVMVLLEKGWRFRQWNLHTKLTVEVTLALLVLGAVALFFFEAGNPA
+TQAGMGFWQRVGHSLFGSVMTRSGGFAIDDTNAHRPESLLLMDALMFVGGGSASTAGGIK
+VTTLAIMFLAIVAEARGDREVTAHGRTIAPESLRVAIAVLALGATLVLVATLALVHITDE
+SLQRPLFEVISAFGTCGLSVGVSAESPPAGKYVLTAMMFAGRVGTITFAAALALRQRRVL
+YRYPVERPVIG
+>2_1039
+MSTLESSSELRTALRRSSRAVSSVVSGSPARAALSAFLLVSLVFTALLSLPWASADGRPT
+ALHDAMFTAVSAVSVTGLTTLNTAEHWSVAGQVIILVAIQIGGLGILSMASLLTLAVSRH
+LGLRSKLATQEAGMTTGNVGEVGRLLRVVVVTVLTCEAALAVFLVPRFAAESGSWLTGLW
+HGVFYSVSAFNNAGFSLHVDGLSAVAHDPVILTVIAVGVFAGALGFPVVMVLLDKGWRYR
+AWNLHTKLTVEVTLALLVLGAVLLFFFEAGNPGTNGDLGVVERIWRSLFGSVMTRSGGFA
+IDDTNAHRPESLLLMDALMFVGGGSASTAGGIKVTTLAVMFLAILAEARGDREVTAHGRT
+IAPETLRVAISVLALGATLVLVATLALVNIMDESLQRPLFEVISAFATCGLSVGVSAEAP
+PAGKYLLAAMMFAGRVGTITFAAALALRQRRVLYRYPVERPILG
+>3_975
+MPSGALSPARRVVTAVTGVVAGSPARAALSAFALGALLFTGLLMLPAAATDGRVTPLHDA
+MFTAVSAFSVTGLTTLDTAEHWTPLGQVILLAAMQIGGLGILSMASLLTLAVSRHLGLRT
+KLATQESGMTTGNMGEVGHLLKVVVLTVLTCEGALAVILVPRFAALSDSWATGLWQGVFY
+SVSAFNNAGFTIHEGGTAAFMHDPVILTVIAVGVFAGALGFPVVMVLVDKGWRFRSWNLH
+TKLTVEVTLVLLVVGAVALFFFEAGNPATHGDMVVGQRIGHSFFGSVMTRSGGFAIDDTN
+SHRPESLLLMDALMFVGGGSASTAGGIKVTTLAVMFLAIVAEARGDKEVTVHGRTIAPET
+LRVAISVLALGATLVLLATLALVSIVDQPLQRPLFEVVSAFGTCGLSVGVSAEAPPAGKY
+LLTAMMFAGRVGTITFAAALALRQRRVLYRYPVERPILG
+>4_1677
+MAGPRPTPHARRHGGVRRPGGLPRPGQASTLESSTDLRTALRRSGRAVSSVVGGSPARAA
+LSAFALMALVFTGLLALPWAAADGHATPLHDAMFTAVSAFSVTGLTTVNTAEHWSPAGQV
+VILVAIQIGGLGILSMASLLTLAVSRHLGLRSKLATQQAGMTSGSLGEVGQLLRVVVVTV
+LTAEAALALVLVPRFAAISGSWLTGLWHGVFYSVSAFNNAGFTLHVDGLPEIMHDPVVIT
+VLGVGVFLGALGFPVVMVLLEKGWRFREWNLHTKLTVEVTLALLVLGAVALFFFEAGNPA
+TQAGMGFWQRVGHSLFGSVMTRSGGFAIDDTNAHQPESLLLMDALMFVGGGSASTAGGIK
+VTTLAIMFLAIVAEARGDREVTAHGRTIAPESLRVAIAVLALGATLVLVATLALVHITDE
+SLQRPLFEVISAFGTCGLSVGVSAESPPAGKYVLTAMMFAGRVGTITFAAALALRQRRVL
+YRYPVERPVIG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001471.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001471.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a2b3e29305305e6b3444eeb1c954dc7a66d350e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001471.fa
@@ -0,0 +1,30 @@
+>0_1763
+MRDGRGLARTGLTPYPSDMTEHLDPALVDIWFAAWSRSRGYRTSQEAGRRAALRTPRPAH
+MIPGGSGRATVDVPATWEHVVVNPSRAELEDLREAVRDQEQILLTVFGDAGEDPKAMGLK
+AQAEPERFMTMDMDPELQDVEPPLLPEGYEARVDQPMEGSRRLRILAVGASTAPEGEEEL
+AALGWVTEEDGTAVYDRIWTSPNHRRRGLGSLVMRYLTSEVMSEGEISRGLLVASPDGQK
+LYRHLAWTDLGPVSIWGRGLAEDNPTAEHTGTMGA
+>1_1471
+MTEHLDPALVDIWFAAWSRSRGYRTSQEAGRRAALRTPRPACMIPGGSGRATVDVPATWE
+HVVVNPSRGELEDLREAVRDQEQILLTVFGDAGEDPKAMGLKAQAEPERFMTMDMDPELQ
+DVEPPLLPEGYEARVDQPMEGSRRLRILAVGASTVPEGEEELAALGWVTEEGGTAVYDRI
+WTSPNHRRRGLGSLVMRYLTSEVMSEGEISRGLLVASPDGQKLYRHLAWTDLGPVSIWGR
+GLAEDNPAAEHTGTMGA
+>2_1026
+MSEHLDTALVDTWFAAWSRSRGYRTSPEAGRRAALRTRRPARMIPGGSGRATVDVPATWE
+YVVVDPTREQLEELREALRDEEQILLTVFGDAGADPKAMGLTPQAEPERFMSMDMDPEVQ
+DVEPPLLPDGYEARVDQPMEGSVRVRIMAVGASTAPEGEEELAALGWVTREDGTAVYDRI
+WTSPNHRRRGLGSLVMRYLTSEVMSDGEISLGLLVASPDGRKLYEHLAWTDLGPVSIWGR
+GLAADTPTAEHTGTMGA
+>3_966
+MTQSIDDTLVGTWFAAWSRSRGYETRIEDGMRSALRKKRSAQRIPGGAGRAAMDIPTTWE
+HVLVSPDADALAPALASLEEQPDRLVTVFGETDQDLTSAGLHSAVLPERFMSMELDREVQ
+DVEPPLLPEGYEAHVDEPRPGSRRVRFYAAGALSGVPEGEEELAALGWVTFEGETAVFDR
+IWTSPDHRRRGLGSLVMRHLTSEALGADDELERGLLVASPDGQKLYGHLGWTDLGPVRIW
+TRADGEAPGAEHTGTMAR
+>4_1685
+MRDGRGLARTGLTPYPSDMTEHLDPALVDIWFAAWSRSRGYRTSQEAGRRAALRTPRPAH
+MIPGGSGRATVDVPATWEHVVVNPSRAELEDLREAVRDQEQILLTVFGDAGEDPKAMGLK
+AQAEPERFMTMDMDPELQDVEPPLLPEGYEARVDQPMEGSRRLRILAVGASTAPEGEEEL
+AALGWVTEEDGTAVYDRIWTSPNHRRRGLGSLVMRYLTSEVMSEGEISRGLLVASPDGQK
+LYRHLAWTDLGPVSIWGRGLAEDNPTAEHTGTMGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001481.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001481.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c04e4273b7d478de4e650c92402a7c76e51862f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001481.fa
@@ -0,0 +1,20 @@
+>0_1774
+MAFSTRSTGETMRATGPSAAAPSAAPVAGGAAGVVSTSLPVVAVDGSLPTPPYRQIVDAV
+LAGVTSGSLARGDRLPPVRALAAELGVAPGTVARAYKELEAHGTIRTRGRAGTFVAASAD
+ARADAAHQAVRRCLDTLLERLGYTPDEAVELVRRDAAARA
+>1_1482
+MAVSTRSTGETMRAPGPSAAAPSAAPVAGGAAGVVSASLPVVAVDGSLSAPPYRQIVDAV
+LAGVASGSLARGDRLPPVRALAAELGVAPGTVARAYKELEAHGTIRTRGRAGTFVAASAD
+ARADAAHQAVRRCLDTLLERLGYTPDEAVELVRRDAAARA
+>2_1014
+MTATPSGAAPSPASAEGGAARVVSASLPVVAVDAALSAPPYRQITDAVLAGVASGCLARG
+DRLPPVRALASELGVAPGTVARAYKELEARGTILTRGRAGTFVAASADARADAAHQAVRR
+CLDTLLDRLGYTADEAVELVRRDAAARA
+>3_1032
+MNGVEPTLELDLRSPVPPFEQIRAGISAFVDAGVLAPGDRLPSVRALAADLGVAPNTVVR
+AYRELESAGVVRTARGKGTVVADRPRGALTADDDGTARTLEAAVHSALAAGWDRERVQRV
+VEAALVSPPAPVDRKDTP
+>4_1696
+MAVSTRGTGESMRLPGPFAAAPVADGAAGVVSASLPVVAVDASLPAPPYRQIVDAVLAGV
+ASGSLARGDRLPPVRVLAAELGVAPGTVARAYKELEAHGTIRTRGRAGTFVAASADARAD
+AAHQAVRRCLDTLLERLGYTPDEAVELVRRDAAARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001482.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001482.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6d22922180d9574bb677bd18511463aeb2e17c49
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001482.fa
@@ -0,0 +1,14 @@
+>0_1775
+MSTAAIVMMSLAILLVWGGLAVSAIHLLRHPDDSSGDLAIEDDLAPAVWEREDGLLDAQH
+R
+>1_1483
+MSTAAIVMMSLAILLVWGGLAVSAIHLLRHPDDSSGDLAIEDELAPAVWEREDGRLDAQH
+R
+>2_1013
+MSTAAIVMMSLAILLVWGGLALSAVHLLRHPDDSSGDLALGDRLAPAAWEREDELGREDV
+RLGARRG
+>3_955
+MHTPALIMMVIAMLTVWGGLVLSAVHLLKHPDETSGTLADAVDVDHTL
+>4_1697
+MSTAAIVMMSLAILLVWGGLAVSAIHLLRHPDDSSGDLAIEDELAPAVREREDGRLDARH
+R
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001484.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001484.fa
new file mode 100644
index 0000000000000000000000000000000000000000..871693d0ff5a9bb6c9e788383fb2a34d2d2a0599
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001484.fa
@@ -0,0 +1,26 @@
+>0_1778
+MDLEVLRKAPLFTNLDDEVFAILTSELTEVELSRGASAFHEGDQGDQLYVIMSGKIKLGR
+TASDGRENLVAVLGPGEIFGEMALFNPAPRNATATAVSATRLAGLRHENLRRAIASSPDV
+SVQLLQALAQRLSKTNESLADLVFSDVPGRVAKALLDLADRFGRPAADGLLVAHDLTQEE
+LAQLVGASRETVNKALAEFVQRGWIRLENRAVVILDLQRLRQRSR
+>1_1486
+MDLEVLRKAPLFTNLDDEVFAILTSELTEVELSRGASAFHEGDQGDQLYVIMSGKIKLGR
+TASDGRENLVAVLGPGEIFGEMALFNPAPRNATATAVSATRLAGLRHENLRRAIASSPDV
+SVQLLQALAQRLSKTNESLADLVFSDVPGRVAKALLDLADRFGRPAADGLLVAHDLTQEE
+LAQLVGASRETVNKALAEFVQRGWIRLENRAVVILDLQRLRQRSR
+>2_1010
+MDLEVLRKAPLFTNLDDEVFAILTSELTEVELSRGASAFHEGDQGDQLYVIMSGKIKLGR
+TASDGRENLVAVLGPGEIFGEMALFNPAPRSATATAVSATRLAGLRHENLRRAIGSSPDV
+SVQLLQALAQRLSKTNESLADLVFSDVPGRVAKALLDLADRFGRPAADGLLVAHDLTQEE
+LAQLVGASRETVNKALAEFVQRGWIRLENRAVVILDLQRLRQRSR
+>3_952
+MGHNGTDIPGAPRPRLAVSQKGRARMDLEVLRKAPLFTNLDDEVFSILTSELTEVELSRG
+ASAFHEGDQGDQLYVIMSGKIKLGRTASDGRENLVAVLGPGEIFGEMALFNPAPRSATAT
+AVSAARLAGLRHENLRRAIASSPDVSLQLLQALAQRLSKTNESLADLVFSDVPGRVAKAL
+LDLADRFGRPAADGLLVAHDLTQEELAQLVGASRETVNKALAEFVQRGWIRLENRAVVIL
+DLQRLRQRSR
+>4_1700
+MDLEVLRKAPLFTNLDDEVFAILTSELTEVELSRGASAFHEGDQGDQLYVIMSGKIKLGR
+TASDGRENLVAVLGPGEIFGEMALFNPAPRNATATAVSATRLAGLRHENLRRAIASSPDV
+SVQLLQALAQRLSKTNESLADLVFSDVPGRVAKALLDLADRFGRPAADGLLVAHDLTQEE
+LAQLVGASRETVNKALAEFVQRGWIRLENRAVVILDLQRLRQRSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001488.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001488.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f4c8d5047f9e75240e5bf9188632c4b1c524b43d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001488.fa
@@ -0,0 +1,70 @@
+>0_1782
+MASRTTRFPAPSSALGRLLAFVGLSAVAGLLVAALLLPVAGLAGVAAASGREMLDELPDE
+LPTEPVSVPSRILSEDGEEIAVFYEENRTPVPLDEISEHMQHAIVAIEDERFYDHDGVDA
+RGLIRATVNNATSDSTQGASTLTQQFVNNMLVNVQQIRGDSRLTLSGSKNIADKVKEIKL
+AVAVEKQMSKDEILEGYLNIVLFSGRAYGVEAASQYVFGKSAADLESWEAATLAGMVQSP
+TRFNPARNPEEATERRNLVLNAMKDNGYLSQEEYDHAVAQPMEVVMESRPSGCLYAKFGT
+YFCDYVERQILADPTFGPDVQSRQALLDRGGLTIRTTIDSTLQKETEKNLRASVPNNESL
+GAGHALTSVEAGTGNIRTMAQNTEYAIQDELGHTSLNFNVDKQWGGGQGFQAGSTLKPFV
+ALTWLRNGNRLVDSVDASRNVYPTGTRFAASCRPGGYTTIGGTWQFKNVIPGMLRQVRVD
+EGLFWSVNTPTVATAYQLDLCDITSLTTQLGITRALDSSPLQPDDPSFLLGKDSVAPLSL
+AGAYAAIAANGLYCEPRAILEVTDTVGNQYDVADPQCDQVIDPDHVRELMPVLRHIAGFN
+IAEEGAGYEFGGKTGTNDNVSSTWFVGFTSELATAVWTGRYNNLKSMTGETVNGEVRNPF
+YSTSINGPSWLEYNQLAKEKFPPGELPEWDGPQSEDPGEAGEHPDGRQFHIDDLDRGGPL
+PEAVPGF
+>1_1490
+MASRTTRFPAPSSAPGRLLAFVGLSALAGLLVAALLLPVAGLAGVAAASGREMLDELPDE
+LPAEPVSVPSRILSEDGEEIAVFYEENRTPVPLDKISKHMQHAIVAIEDERFYDHDGVDA
+RGLIRATVNNATSDSTQGASTLTQQFVNNMLVNVQQIRGDSRLTLSGSKNIADKVKEIKL
+AVAVEKQMSKDEILEGYLNIVLFSGRAYGVEAASQYVFGKSAADLESWEAATLAGMVQSP
+TRFNPARNPEEATERRNLVLNAMKDNGYLSQEEYDHAVAQPMEVVMESRPSGCLYAKFGT
+YFCDYVERQILADPTFGPDVQSRQALLDRGGLTIRTTIDSTLQKETEKNLRASVPNNESL
+GAGHALTSVEAGTGNIRTMAQNTEYAIQDELGHTSLNFNVDKQWGGGQGFQAGSTLKPFV
+ALTWLRNGNRLVDSVDASRNVYPTGTRFAASCRPGGYTTIGGTWQFKNVIPGMLRQVRVD
+EGLFWSVNTPTVATAYQLDLCDITSLTTQLGITRALDSSPLQPDDPSFLLGKDSVAPLSL
+AGAYAAIAANGLYCEPRAILEVTDTVGNQYDVADPQCDQVIDPDHVRELMPVLRHIAGFN
+IAEEGAGYEFGGKTGTNDNVSSTWFVGFTSKLATAVWTGRYNNLKSMTGETVNGEVRNPF
+YSTSINGPSWLEYNQLAKEKFPPGELPEWDGPQSEDPGEAGEHPDGRQFHIDDLDRGGPL
+PEAVPGF
+>2_1006
+MASRTSRRLPEPSSALGRLLAFLGLSALAGLLVAALLLPLAGLTGVAAASGREMLDELPD
+ELPAEPVSVPSRMISEDGEEIAVFYEEDRIPVPLDQISEHMRNAIVAVEDERFYEHDGVD
+ARGLIRATVNNATSDSTQGASTLTQQFVNNMLVNVQQIRGDSRLTLSGTKNVSDKVKEIK
+LAVAVEEQMTKDEILEGYLNIVLFSGRAYGVEAASRYVFGKSAAELESWEAATLAGMVQS
+PTRFNPARNPEEATERRNLVLGAMKKNGYLTEEEHAEAVAQPMEVVMESRPSGCLYSKFG
+SYFCDYVERQILADPAFGPDPQSRQALLDRGGLTIRTTIDSELQKAAEENLRKSVPNNES
+LGAGHALTSVQAGTGNIVTMAQNTEYAIQDELGHTSLNFNVDREWGGGQGFQAGSTLKPF
+VALTWLRNGNRMVDSVDASRNVYPTGTRFEASCRPGGYTTIGGTWQFKNVIPGMLRQVRV
+DEGLFWSVNTPTVATAYQMDLCDITSLTTQLGITRALDSSPLQPDDPSFLLGKDSIAPLS
+LAGAYAAIAADGLYCEPRAILEVTDTVGNQYDVAGPQCDQVVDPKHIAELMPVLRHIGAF
+NIAEEGAGYEFGGKTGTNDNVSSTWFTGFTTELATAVWTGRYNNMKSMTGETVNGEVRNP
+FYSTSINGPSWLEYNQLAKEKYPPGELPDWDGPQSEDPGAEGEHPDGTAFRIDDLDRGGP
+QPQAVPGN
+>3_948
+MASRSSRLPARSSALGRLLSFLGLSALAGLLVAGLMMPAAGATGIVFASGRDMLDELPDQ
+LPAEPVSMPSKIYSADGELIATFFQENRQPVPLDQISPYMRNAIVAIEDERFYQHDGVDA
+KGLVRAMVNNVSSSSTQGASTLTQQFVNNMLINSQQVRGDSRLTLSGTKQASDKVKEIKL
+AVAVEKQMSKDQILEGYLNLVLFQGRAYGIEAASQYVFGKPAKDLELWEAATLAGMVQSP
+TRFNPARNPEGTTARRNTVLKAMLKNGYISQEEHDHAVAQPLTYTMKGQSTGCLSAAFGA
+YFCDYVERQILADPTFGPDTASRQALLDRGGLTIRTTIDSNLQKKAEELTRRVIPNNESL
+GAGHSLISLRPGSGDIVTMAQNTEYSIQDELGKTTLNLNVDAKWGGGTGFAAGSTFKPFI
+GLTWLRNGGKLIDSVDGSKDRYPPDARFQASCLPGGYTTAGGGTQGWQLNNVIDGMKKRD
+RIDEGIFWSVNTPTVALAYQMDLCDIVNTLTQVGIVTARDGAPLSPAEPSFVLGKDDVSP
+MTMAGAYATLAANGKYCKPRAITEVTDTTGNQYTVPAPECRQVLDPAQVAEVTPLLRHIA
+AHNIAPDGTGYEFAGKTGTNNNMSSTWFIGYTTELATAVWAGRYTSQKTMRGETINGVVQ
+KEFYGATVNGGTWLEWNDMAKRTFVPGELPEFDGPQSEDPALEGDHPDGRFYRPEDIDRN
+GGTPTSSLGPAAGETAFSSAENAAKFESGVLTR
+>4_1704
+MASRTTRFPAPSSALGRLLAFVGLSAVAGLLVAALLLPVAGLAGVAAASGREMLDELPDE
+LPTEPVSVPSRILSEDGEEIAVFYEENRTPVPLDEISEHMQHAIVAIEDERFYDHDGVDA
+RGLIRAAVNNATSDSTQGASTLTQQFVNNMLVNVQQIRGDSRLTLSGSKNIADKVKEIKL
+AVAVEEQMSKDEILEGYLNIVLFSGRAYGVEAASQYVFGKSAADLESWEAATLAGMVQSP
+TRFNPARNPEEATERRNLVLNAMKDNGYLSQEEYDHAVAQPMEVVMESRPSGCLYAKFGA
+YFCDYVERQILADPTFGPDVQSRQALLDRGGLTIRTTIDSTLQKETEKNLRASVPNNESL
+GAGHALTSVEAGTGNIRTMAQNTEYAIQDELGHTSLNFNVDKQWGGGQGFQAGSTLKPFV
+ALTWLRNGNRLVDSVDASRNVYPTGTRFAASCRPGGYTTIGGTWQFKNVIPNMLRQVRVD
+EGLFWSVNTPTVATAYQLDLCDITSLTTQLGITRALDSSPLQPDDPSFLLGKDSVAPLSL
+AGAYAAIAANGLYCEPRAILEVTDTAGNQYDVADPQCDQVIDPDHVRELMPVLRHIGGFN
+IAEEGAGYEFGGKTGTNDNVSSTWFVGFTSKLATAVWTGRYNNLKSMTGETVNGEVRNPF
+YSTSINGPSWLEYNQLAKEKFPPGELPEWDGPQSEDPGEAGEHPDGRQFTIDDLDRGGPQ
+PQAVPGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001495.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001495.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cdbce6eda3af8e97fe3a909c392a27c3d93d5d10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001495.fa
@@ -0,0 +1,40 @@
+>0_1792
+MFLALRDLRFATGRFALMGSVVALISLLLVMLSGLTAGLGGQNTAAIDRLGEQGVQRLVF
+GGAAGQEPTASFTQSEFTVAQRDAWAATDGVASVEPLGVSQGRAIGLEHPVDTDPQGRAD
+VSGEPTTGVATTAFIGLTPGGSDAPAGVELGQIVLSQDVADSLHAQAGDAVAVSGFVYTV
+ADVVPTEYYSHSPVTWLALEDWNAISHTADDAVLGTAGLVRFDAGADVDAVAAAGDDAAG
+TVAETVKGSYAALPSYRSENGSLMTMQGFLYGISALVVIAFLSIWTVQRTRDIAVLKALG
+GSNGWVLKDSLAQAAFVLVGGVAVGTGLAAVIGAFAGRAVPFELSWATTAVPAAGVLVLG
+MLAAVIAVYRVTRIDPLVALGGN
+>1_1499
+MFLALRDLRFATGRFALMGSVVALISLLLVMLSGLTAGLGGQNTAAIDRLGEQGVQRLVF
+DGAAGQEPTASFTQSEFTVAQRDAWAATDGVASVEPLGVSQGRAIGLEHPVDTDPPGRAD
+VSGEPTTGVATTAFIGLTPGGSDAPAGVEPGQIVLSQDVADSLHAQEGDAVAVSGFVYTV
+ADVVPTEYYSHSPVTWLALEDWNAISHTADDAVLGTAGLVRFDADTDVDAVAAAGDDAAG
+TVAETVKGSYAALPSYRSENGSLMTMQGFLYGISALVVIAFLSIWTVQRTRDIAVLKALG
+GSNGWVLKDSLAQAAFVLVGGVAVGTGLAAAIGAFAGRAVPFELSWATTAVPAAGVLVLG
+MLAAVVAVFRVTRIDPLVALGGN
+>2_996
+MFLALRDLRFATGRFALMGSVVALISLLLVMLSGLTAGLGGQNTAALDRLEEQGVQRLVF
+GGAAGQEATASFTQSKFTAEQRDAWAATDGVASVEPLGVSQGRAVGLAHGVETDEAGRAD
+VADVPTTGVASTAFLGLVPGGADAPAALAPGEVVLSSDVADSLGAQAGDAVAVSGFVFTV
+AEVVPNEFYSHSPVTWLALEDWRAISHTADDAVLGTAGLVRFAAGADPDAVAAAGDAAAG
+TVSETVRGSYAALPSYRSENGSLMTMQGFLYGISALVVIAFLSIWTVQRTRDIAVLKALG
+GTDGWVLKDALTQAAFVLLGGVLVGTALAAGIGVLAARGVPFELSWATTLVPAAGILVLG
+MLAAVAAVFRVTRIDPLVALGGN
+>3_939
+MFLALRDLRFATGRFSLMGAVVALITVLLVMLSGLTAGLGHQNTAALDDLGARGTDRIVF
+GGTAGQDPTASFTSSEVTAAQLDSWCAADGVARVEPVGVAQGRLTGVAGHVDTDAAGRPA
+ETPEVAGVGSASFVGLDPAAPQAPAGLEDGELVLSQALAEALEVEEGGQVESSGRVYTVA
+SVAADSWYSHTPVAWTTLTDWRALSHTEDADVAGTAGLVTLVDGADADAVASAADDAAHT
+VATDVKGAYAALPAYSSEHGSLTMMQGFLYGISALVVVAFLSIWTIQRTREIAVLKALGA
+STGWVLRDSLLQGGIVLAVGVGLGTALAAGAGWFAAQAVPFVLSPATTVLPALGVLALGL
+AGSALAVARVTRIDPLIALGGN
+>4_1713
+MFLALRDLRFATGRFALMGSVVALISLLLVMLSGLTAGLGGQNTAAIDRLGEQGVQRLVF
+GGAAGQEPTASFTQSEFSVAQRDAWAATDGVASVEPLGVSQGRAIGLEHPVDTDPQGRAD
+VSGEPTTGVATTTFIGLTPGGSDAPAGVEPGQIVLSQDVADSLHAQEGDAVAVSGFVYTV
+ADVVPTEYYSHSPVTWLALEDWNAISHTADDAVLGTAGLVRFDAGADVDAVAAAGDDAAG
+TVAETVKGSYAALPSYRSENGSLMTMQGFLYGISALVVIAFLSIWTVQRTRDIAVLKALG
+GSNGWVLKDSLAQAAFVLVGGVAVGTGLAAVVGAFAGRAVPFELSWATTAVPAAGVLVLG
+MLAAVVAVYRVTRIDPLVALGGN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001509.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001509.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa9a77f007c29b5e6b0bce00a7cf93e68c27ea82
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001509.fa
@@ -0,0 +1,30 @@
+>0_1807
+MSTQAPVSPAPAMKPGRARRRRRLSLIIQAAVFVLALVVLAVLIDWGALAENVLNFPAVA
+PMFPNVILVGLGNTLFYTVTSFVVGLLGGIVLALMRLSSFGPYRWLATAYVEFFRGVPAL
+LVFLAFGYGVPFAFGVSWPIPVVVMVALGMVSAAYIAETLRAGLQAVPRGQMEAARSLGM
+PTWRAMVTIVIPQAFRIVLPPLTNEVILLTKDSSLVYVLGLAAHEYELTKFGRDGISALD
+AGMTPILVAGLFYLVITVPLSLLARRFETRSTKKGH
+>1_1514
+MSTQAPVSPAPAMKPGRARRRRRLSLIIQAAVFVLALVVLAVLIDWGALAENVLNFPAVA
+PMFPNVILVGLGNTLFYTVTSFVVGLLGGIVLALMRLSSFGPYRWLATAYVEFFRGVPAL
+LVFLAFGYGVPFAFGVSWPIPVVVMVALGMVSAAYIAETLRAGLQAVPRGQMEAARSLGM
+PTWRAMVTIVIPQAFRIVLPPLTNEVILLTKDSSLVYVLGLAAHEYELTKFGRDGISALD
+AGMTPILVAGLFYLVITVPLSLLARRFEARSTKKGH
+>2_973
+MFVLAIVVLALLIDWGTIGENVLNFPAVAPLFPNIILVGLGNTLFYTATSFVVGLLGGIA
+LALMRMSAFAPYRWLATAYVEFFRGVPALLVFLAFGYGVPFAFGVSWPIPVVVMTALGMV
+AAAYIAETLRAGLQAFPPGQMEAARSLGMPAWQAMITIVIPQAFRIVLPPLTNEVILLTK
+DSSLVYVLGLAAHEYELTKFGRDGISALDAGMTPILVAGLFYLVITVPLSLLARRFEARS
+TKKGH
+>3_912
+MSTQASPAPRTAAAPSRAGRRRTLSVAVQAAVFVLAIVVVALLADWQAIAENVLNFSAAG
+PMFPNVILVGLGNTIFYTVTAFVVGLLGGMLLALMRMSSFAPYRWLATAYVEFFRGIPAL
+LVFLAFGYGVPFAFGVSWPIPVVVMIALGMVSAAYIAETLRAGLQAVPKGQMEAARSLGM
+PHWRAMLTIVIPQAFRVVLPPLTNEVILLTKDSSLVYVLGLAAHEYELTKFGRDGIAALD
+AGMTPILVAGLCYLVITIPLSLLARRFEARSSRKAH
+>4_1728
+MSTQAPVSPAPAMKPGRARRRRRLSLIIQAAVFVLALVVLAVLIDWGTLTENVLNFPAVA
+PMFPNVILVGLGNTLFYTVTSFVVGLLGGIVLALMRLSSFGPYRWLATAYVEFFRGVPAL
+LVFLAFGYGVPFAFGVSWPIPVVVMVALGMVSAAYIAETLRAGLQAVPRGQMEAARSLGM
+PTWRAMVTIVIPQAFRIVLPPLTNEVILLTKDSSLVYVLGLAAHEYELTKFGRDGISALD
+AGMTPILVAGLFYLVITVPLSLLARRFETRSTKKGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001541.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001541.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5a98c1f4720d341479d729711cb4295a24810b6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001541.fa
@@ -0,0 +1,15 @@
+>0_1847
+MAMNRKELVAAVAERSGNTQAAVSDVLDALFEVFTAQVKKGEKVSIPGWLAVERTERKER
+TGRNPRTGEEITIPAGHSVKVTAGSKLKAAASE
+>1_1554
+MAMNRKELVAAVAERSGNTQAAVSDVLDALFEVFTAQVKKGEKVSIPGWLAVERTERKER
+TGRNPRTGEEITIPAGHSVKVTAGSKLKAAASE
+>2_931
+MAMNRKELVAAVAERSGNTQAAVSDVLDALFEVFTAQVKKGEKVSIPGWMAVERTERKER
+TGRNPRTGEEITIPAGYSVKVTAGSKLKAAASE
+>3_872
+MAMNRKELVAAVAERSGNTQAAVSDVLDALFEAFTAQVKKGEKVSIPGWLAVERTERKER
+TGRNPRTGEEITIPAGYSVKVTAGSKLKAAASE
+>4_1768
+MNRKELVAAVAERSGNTQAAVSDVLDALFEVFTAQVKKGEKVSIPGWLAVERTERKERTG
+RNPRTGEEITIPAGHSVKVTAGSKLKAAASE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001544.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001544.fa
new file mode 100644
index 0000000000000000000000000000000000000000..293efe8a34de115db9e5a7cae7100139c1918e59
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001544.fa
@@ -0,0 +1,15 @@
+>0_1850
+MAAHCQVTGAGPGFGHSISHSHRRTKRRFDPNIQKKTYWVPSLRRNVTLTLSAKGIKTID
+VRGIDAVVADLIAKGVKL
+>1_1557
+MAAHCQVTGAGPGFGHSISHSHRRTKRRFDPNIQKKTYWVPSLRRNVMLTLSAKGIKTID
+VRGIDAVVADLIAKGVKL
+>2_928
+MAAHCQVTGAGPGFGHSISHSHRRTKRRFDPNIQKKTYWVPSLRRNVTLTLSAKGIKTID
+VRGIDAVVADLIAKGVKL
+>3_869
+MAAHCQVTGAGPGFGHSISHSHRRNKRRFDPNIQKKTYWVPSLRRNVTLTLSAKGIKTID
+VRGIDAVVADLISKGVKL
+>4_1771
+MAAHCQVTGAGPGFGHSISHSHRRTKRRFDPNIQKKTYWVPSLRRNVTLTLSAKGIKTID
+VRGIDAVVADLIAKGVKL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001548.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001548.fa
new file mode 100644
index 0000000000000000000000000000000000000000..49a93363c3f04fb5be5624f5ace3b762f7474e3f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001548.fa
@@ -0,0 +1,20 @@
+>0_1860
+MTILVGYAPSKAADAALDTALDIARSTGEHVVVVNAGPGGEHRTKSLVTEEQQRGVQARL
+DASGVTAEFRQYARGRSTVEEMKDVAAELDPSIVVIGVRRRGGFGRFVMGSVSDELLQEI
+DQPVLCVKEYRQYGDHTPEAVSHVAETDPAAHGLPASEPMAERRRLTPVDSGDPTLER
+>1_1567
+MTILVGYAPSKAADAALDTALDIARSTGEHVVVVNAGPGGEHRTKSLVTEEQQRGVQARL
+DASGVTAEFRQYARGRSTVEEMKDVAAELGPSIVVIGVRRRGGFGRFVMGSVSDELLQEI
+DQPVLCVKEYRQYGDHTPEAVSHVAETDPAAHGLPASEPMAERRRLTPVDSGDPTLER
+>2_920
+MTILVGYAPSTSADAALDTALDIARSTGERVVVVNAGPGGEHRTKSLVTEEQQRGVQARL
+DASGVDAEFRQYARGRSTVQEMKDVAAELDPSIVVIGVRRRGGFGRFVMGSVSDELLQEI
+DQPVLCVKEYTQYGDRTPEAVSHVAETDPATRGLPASEPMLEQHPLTPVKDQDPTRRG
+>3_856
+MTILVAYKPSETAKAALSTALDVARQTGEHVVVVNAGPGGEHRSPSLVTEAQQQEVQRLL
+DDSGVSAEFRQYARGRSTADELKSVADELDPSIVVVGLRRRGGFGRFVMGSVSDELLQVI
+DQPVLAVKEYRGRTPDAVSSVAETDPATHGMPSAEPGHAPRPFTGEHAADDGR
+>4_1781
+MTILVGYAPSKSADAALDTALDIARSTGEHVVVVNAGPGGEHRTKSLVTEEQQRGVQARL
+DASGVTAEFRQYARGRSTVEEMKDVAAELDPSIVVIGVRRRGGFGRFVMGSVSDELLQEI
+DQPVLCVKEYRQYGDHTPEAVSHVAETDPATHGLPASEPMAERRRLTPVDPGDPTLER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001554.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001554.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a1ff1ce868110032cd49512dfaf978d9ce140a29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001554.fa
@@ -0,0 +1,42 @@
+>0_1868
+MTLPAPAARRPSAALLWVLLAAMGAGPLFTYGVSASSTVVMERLDVTSGQLGTVMTVVFA
+AAAVTSLGLGRAADRLSARAQLSIIFGGTAAALVLGAVAPSLPVLYAAAAVAGVTQAISN
+PTTNRIIRTVVPPERRIGWVGVKQSGVQAAQLVGGLFFPAASLALGWTGAALGAAVLIGA
+LWVLALVAAPPLPGAPPSATGPAGGRRRRDTSPLPATVWFSAAIAFLTGLGMQATNTYLP
+LFAVETLGMTLVAGGAAAAVSGVVGVLSRIGWSRRMSSGDRPTTLLTVICLGAVAGVVVF
+LAADLLDLPALLWVGAAVHGLTVLGANVVVNAGLLSEVPAERLGRATGANSMGMYAGFAL
+GPLLMGVLRDVTGDYRAGFAVVALGYLLALGVVLLLRRHVGRRGAA
+>1_1575
+MTLPAPAARRPSAALLWVLLAAMGAGPLFNYGVSASSTVVMERLDVTSGQLGTVMTVVFA
+AAAVTSLGLGRAADRLSARAQLSIIFGGTAAALVLGAVAPSLPVLYAAAAVAGVTQAISN
+PTTNRIIRTVVPPERRIGWVGVKQSGVQAAQLVGGLFFPAASLALGWTGAALGAAVLIGA
+LWVLALVAAPPLPGAPPPATGPVGGRRRRDTSPLPATVWFFAAIAFLTGLGMQATNTYLP
+LFAVETLGMTLVAGGAAAAVSGVVGVLSRIGWSRRMSSGDRPTTLLAVICLGAVAGVAVF
+LAADLLDLPALLWVGAAVHGLTVLGANVVINAGLLSEVPAERLGRATGANSMGMYAGFAL
+GPLLMGVLRDVTGDYRAGFAVVALGYLLALGVVLLLRRHVGRRGAA
+>2_911
+MTPPSSAPAAARSGPSTALLWVLLAAMGAGPLFNYGISASSTVIIERLGVTSGQLGTVMT
+AVFAAAAVTSLGLGRAADRLSSRAQMSIIFGGTAVALVMGAFAPSLPVLYAAAAVAGVTQ
+AISNPTTNRIIRTVVPPERRIGWIGVKQSGVQAAQLFGGLFFPAASLALGWTGAALVVAV
+LACVLWGFALWAAPPLPGTAPTADPDAGRASAPDVDRASAPDAGPAAARARRRDGRRRRG
+TTALPASVWFFAAIAFLTGLGMQATNMYLPLFAVESLDLTLVAGGAAAAVSGVIGVFSRI
+WWSRRMAVGARPTTLLAAICLGALAGVVVLLAADLAHLPALLWVGAAVHGLTVLGANVVT
+NAGLMSEVPAESLGRASGANAMGMYAGFALGPLVMGVLRDLTGDYRAGFAAVGLGYILAF
+LVVLLLRRHVGRRAADPRAEAA
+>3_844
+MGDAGAGRRLTGSSGGPAAPGGPTLGAVTASPPSRPADRAPGTLLLWTLLAAMGAGPVFN
+YAVSTSSTVIIERLGVTSGQLGTVMTVVFAAAAVTSVGLGRAADRLSSRTQMAIIFFGSA
+LALAVGGFAGSLWALYGAAVLAGVTQTISNPTTNRIIRTSVPAERRIGWIGVKQSGVQAS
+QLFAGLFFPVAALGLGWTGASLVAAALVGLLGVVALRAAPPLPGAPAAPPTTTPDAGRPR
+AGRARAPLPATVWFFAGIAFLTGFGMQATNMYLPLFAVESLDQTLVIGGAAAATSGVIGV
+FSRIWWSRRMAAGHRPTTLLAGIALGAVVGVVVFLGADLLHAPALLWVGAAVHGLTVLGT
+NVVTNAGLMDAVPAHHLGRASGVNAMGMYAGFACGPLVMGLMRDLTGDFRAGFLAVGVFY
+LLALAVVGLLRRHTDRQGAPRAA
+>4_1788
+MTPPAPAARRPSAALLWVLLAAMGAGPLFNYGVSASSTVVMERLDVTSGQLGTVMTVVFA
+AAAVTSLGLGRAADRLSARAQLSIIFGGTAAALVLGAAAPSLPVLYAAAAVAGVTQAISN
+PTTNRIIRTVVPPERRIGWVGVKQSGVQAAQLVGGLFFPAASLALGWTGAALGAAVLIGA
+LWVLALVAAPPLPGAPPPATGPVGGRRRRDTSPLPATVWFFAAIAFLTGLGMQATNTYLP
+LFAVETLGMTLVAGGAAAAVSGVVGVLSRIGWSRRMSSGDRPTTLLTVICLGAVAGVVVF
+LAADLLDLPVLLWVGAAVHGLTVLGANVVINAGLLSEVPAERLGRATGANSMGMYAGFAL
+GPLLMGVLRDVTGDYRAGFAVVAAGYLLALGVVLLLRRHVGRRGAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001566.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001566.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed5cfbd299e356e3db90d03bdfd9532f1c4117a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001566.fa
@@ -0,0 +1,50 @@
+>0_1883
+MPDQITHPTDAAAHPSPAPEDTIGRVFARAVARSPQAVALRFEDRDWTYTQLRDGAHRVA
+RRLQDTGLPAGTRVAAYATNSDAYALLFLACVTAGYVHVPVNFALKGGELAHALEDSGAE
+LLVADAGMLERVDQVRAEGRASALRHVWTMLPAGHAEPSVLETARDETLDAAAPEAEVSA
+TDLAQLLYTSGTTSTPKGAMMSHRALVAEYLSSMIALDFTAEDRPLVAMPLYHSAAMHVF
+LLPYLSLGATVRLLAAPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLRK
+AQYGASIMPVTVLQRLRQSQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHV
+EARVMTADGAPAAPGEPGEIQYRSPQLLSGYWNRPDATADAFTDDGWFRSGDQVTQDAAG
+YIQVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVVGLPDERWIEAVTAVVVLKEG
+AELTAETVRAHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR
+>1_1590
+MPDQITHPTDAGHLSPAPEDTIGRVFARAVARSPQAVALRFEDRDWTYAQLRDGAHRVAR
+RLQDTGLPAGTRVAAYATNSDAYALLFLACVTAGYVHVPVNFALKGGELAHALEDSGAEL
+LVADAGMLERVDQVRAEGRASALRHVWTMLPAGHAEPSVLETAQDETLDAAAPEAEVSAT
+DLAQLLYTSGTTSTPKGAMMSHRALVAEYLSSIIALDFTAEDRPLVAMPLYHSAAMHVFL
+LPYLSLGATVRLLAAPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLHKA
+QYGASIMPVTVLQRLRQSQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHVE
+ARVMTADGAPAAPGEPGEIQYRSPQLLSGYWNRPDATADAFTDDGWFRSGDQVTQDAAGY
+IQVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVIGLPDERWIEAVTAVVVLKEGA
+ELTAETVRTHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR
+>2_893
+MTEQTSPAAPTADSPSPEDTIGRLFTRAAARHPETVALRFEDRDWTYAQLLDGVHRVARR
+LLATGLPRGTRVAAYGANSDAYAVLFLACVTAGYVHVPVNFALKGGELAHALEDSGAEVL
+VADAGMLERVEQVRADGGGAGLRHVWTMLPAGHAEPSLLETARDEAADATAPDVPVTATD
+LAQLLYTSGTTSTPKGAMMSHRALITEYLSSIIALDFTAEDRPLVAMPLYHSAAMHVFLL
+PYLSLGATVRLLATPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLRKAQ
+YGASIMPVTVLQRLRQSQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHVEA
+RVMTADGAPAAPGEPGEIQYRSPQLLSGYWNRPDATADAFTDDGWFRSGDQVTQDAAGYI
+QVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVIGLPDERWIEAVTAVVVLKEGAE
+LTAETVRTHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR
+>3_832
+MPDQITHPTDAAAHLSPAPEDTIGRVFARAVARSPQAVALRFEDRDWTYAQLRDGAHRVA
+RRLQGTGLPAGTRVAAYATNSDAYALLFLACVTAGYVHVPVNFALKGGELAHALEDSGTE
+LLVADAGMLERVDQVRAEGRASALRHVWTMLPAGHAEPSVLETAQDEALDAAAPEAEVSA
+TDLAQLLYTSGTTSTPKGAMMSHRALVAEYLSSIIALDFTAEDRPLVAMPLYHSAAMHVF
+LLPYLSLGATVRLLAAPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLRK
+AQYGASIMPVTVLQRLRQSQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHV
+EARVMTADGVPAAPGMPGEIQYRSPQLLSGYWNRPDATADAFTDDGWFRSGDQVTQDAAG
+YIQVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVIGLPDERWIEAVTAVVVLKEG
+AELTAETVRTHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR
+>4_1803
+MPDQITHPTDAGHLSPAPEDTIGRVFARAVARSPQAVALRFEDRDWTYAQLRDGAHRVAR
+RLQDTGLPAGTRVAAYATNSDAYALLFLACVTAGYVHVPVNFALKGGELAHALEDSGAEL
+LVADAGMLERVDQVRAEGRASALRHVWTMLPAGHAEPSVLQTAQDETLDAAAPEAEVSAT
+DLAQLLYTSGTTSTPKGAMMSHRALVAEYLSSIIALDFTAEDRPLVAMPLYHSAAMHVFL
+LPYLSLGATVRLLAAPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLHKA
+QYGASIMPVTVLQRLRQSQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHVE
+ARVMTADGAPAAPGEPGEIQYRSPQLLSGYWNRPDATADAFTDDGWFRSGDQVTQDAAGY
+IQVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVIGLPDERWIEAVTAVVVLKEGA
+ELTAETVRAHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001578.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001578.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1f57b686495d9d0ea6ef0cbcf830da646ef6e1be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001578.fa
@@ -0,0 +1,20 @@
+>0_1913
+MTVPPGSPAAPSAPASRRRRRALAAALAVAVVVQLVVLYLPGEQVPQAGFAAPGLDKAIH
+VAVFALPAFLAVGRGRSAWWALPFAVHAPVSELVQHAWVPLRTGDPVDVVADLAGVVLGV
+VAARSRRIGGSGASGV
+>1_1618
+MTVPSGSPAAPSAPASPRRRRALAAALAVAVAVQLVVLYLPGEQVPEAGFTVPGLDKAIH
+VAVFALPAFLAVGRGRSAWWALPFAVHAPVSELVQHAWVPLRTGDPVDVVADLAGVVLGV
+VAARSRRIGGSGASGV
+>2_865
+MGDARPRVPVCPSSRRRRRALAALLAVVVVVHLVVLYLPGSDVPQTGFEVPGLDKTIHVL
+AFAAPTWAAVRLGSSWWWALPFAVHAPVSEAVQHAWVPLRTGDAWDMVADLAGVVLGAAL
+AWRAVRREVEAPGEVGEVGEAGRGDRIGGSGRPGV
+>3_808
+MPARSSAPAAPPPSAARRRTLALLLVIALAAHLVVLYLPGDDVPAVGFEVPGMDKAIHVA
+TFGVPALLGVLLARRVWPAAVLAVHAPLSEVLQAVQGLGRTGDPADAVADLAGVALGLLA
+ARAALRRGPTGRPIGAAPGRGV
+>4_1840
+MTVPSGSPAAPSAPASRRRRRAVAAALVVAVVVQLVVLYLPGEQVPEAGFAVPGLDKAIH
+VAVFALPAFLAVGRGRSAWWALPFAVHAPVSELVQHAWVPLRTGDPVDVVADLAGVVLGV
+LAARSRRIGGSGASGV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001585.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001585.fa
new file mode 100644
index 0000000000000000000000000000000000000000..902fc9ca91f7c045cd9b7d8186ad839f5090b0a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001585.fa
@@ -0,0 +1,35 @@
+>0_1925
+MSDERARSFSASTASAADDGARGTGTTRVKRGLADMMKGGVIMDVVNAEQARIAEDAGAV
+AVMALERVPADIRAQGGVARMSDPDLIDGIVEAVSIPVMAKARIGHFVEAQVLQALKVDF
+IDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITEGAAMIRSKGEAGTGDVSEA
+VKHIRTIRKEIAQLQGLAQDELYVAAKELQAPYELVREVAETGALPVVMFTAGGVATPAD
+AALMMQMGADGVFVGSGIFKSGNPAERARAIVKATAQFDDPMAVAEASRGLGEAMVGINV
+GDLPAPHRLAERGW
+>1_1630
+MSDERARNFSASTASAADDGARGTGTTRVKRGLADMMKGGVIMDVVNAEQARIAEDAGAV
+AVMALERVPADIRAQGGVARMSDPDLIDGIVEAVSIPVMAKARIGHFVEAQVLQALKVDF
+IDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITEGAAMIRSKGEAGTGDVSEA
+VKHIRTIRKEIAQLQGLAQDELYVAAKELQAPYELVREVAETGTLPVVMFTAGGVATPAD
+AALMMQMGADGVFVGSGIFKSGNPAERARAIVKATAQFDDPMAVAEASRGLGEAMVGINV
+GDLPAPHRLAERGW
+>2_852
+MSDERARSFSASTASAADDGARGTGTTRVKRGLADMMKGGVIMDVVNAEQARIAEDAGAV
+AVMALERVPADIRAQGGVARMSDPDLIDGIVEAVSIPVMAKARIGHFVEAQVLQALKVDF
+IDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITEGAAMIRSKGEAGTGDVSEA
+VKHIRTIRKEIAQLQGLAQDELYVAAKELQAPYELVREVAETGALPVVMFTAGGVATPAD
+AALMMQMGADGVFVGSGIFKSGNPAERARAIVKATAQFDDPMAVAEASRGLGEAMVGINV
+GDLPAPHRLAERGW
+>3_789
+MSDDRAQSFSASTGAAADDGARGTGTTRVKRGLADMLKGGVIMDVVTPEQARIAEDAGAV
+AVMALERVPADIRAQGGVARMSDPDLIDGIVEAVSIPVMAKARIGHFVEAQVLQALKVDF
+IDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITEGAAMIRSKGEAGTGDVSEA
+VKHIRTIRKEIAQLQGLAQDELYVAAKELQAPYELVCEVAETGALPVVMFTAGGVATPAD
+AALMMQMGADGVFVGSGIFKSGNPAERARAIVKATAQFDDPMAVAEASRGLGEAMVGINV
+GDLPAPHRLAERGW
+>4_1852
+MSDERARSFSASTASAADDGARGTGTTRVKRGLADMMKGGVIMDVVNAEQARIAEDAGAV
+AVMALERVPADIRAQGGVARMSDPDLIDGIVEAVSIPVMAKARIGHFVEAQVLQALKVDF
+IDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITEGAAMIRSKGEAGTGDVSEA
+VKHIRTIRKEIAQLQGLAQDELYVAAKELRAPYELVREVAETGTLPVVMFTAGGVATPAD
+AALMMQMGADGVFVGSGIFKSGNPAERARAIVKATAQFDDPMAVAEASRGLGEAMVGINV
+GDLPAPHRLAERGW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001590.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001590.fa
new file mode 100644
index 0000000000000000000000000000000000000000..406212ef9875c150ee97f89a6d03de21651183ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001590.fa
@@ -0,0 +1,25 @@
+>0_1931
+MRRTDIGTVGLAGAPVSKADRAYQAILEGIRDQRHEPGDRLVLSQIAAELGMSVVPVREA
+IRRLQSEKLVAYERNVGATVVGIDPVEYRHTMETLALVEGFSTAQCAPHVTGEDLAAARE
+VNATMRAMTESETAWDPMAFTELNRRFHSILFEHHQNEHVHDLVHRGWNRLAALRSSTFA
+YVPGRAVASVDEHEHLLRLIEDGARFEEIEAAARAHRLNTLHAYLEHSAEPSA
+>1_1636
+MRRTDIGTVGLAGAPVSKADRAYQAILEGIRDQRHEPGDRLVLSQIAAELGMSVVPVREA
+IRRLQSEKLVAYERNVGATVVGIDPVEYRHTMETLALVEGFSTAQCAPHVTAEDLAAARE
+VNATMRAMTESETAWDPVTFTELNRRFHSILFEHHQNEHVHDLVHRGWNRLAALRSSTFA
+YVPGRAVASVDEHEHLLRLIEDGARFEEIEAAARAHRLNTLRAYLEHSAEPSA
+>2_846
+MSRTDIGTVGLAGTPVSKADRAYQAILEGIRDQRHEPGDRLVLSQIAAELGMSVVPVREA
+IRRLQSENLVAYERNVGATVVGIDPVEYRHTMETLALVEGFSTAQCAPHVTAEDLSAARE
+VNATMRAMTASEKAWDPVAFTELNRRFHSILFEHHQNEHVHDLVHRGWTRLAALRSSTFA
+YVPGRAVASVDEHEHLLRLIEDGARFEEIEAAARAHRLNTLHAYLAHQGELS
+>3_785
+MRRTDIGTLGLAGTPVSKADRAYQAILEGIRDQRHEPGDRLVLSQIAAELGMSVVPVREA
+IRRLQSENLVAYERNVGATVVGIDPVEYRHTMETLALVEGFSTAQCAPHVTAEDLAAARD
+VNAAMRAMTASEKAWDPVAFTELNRRFHSILFEHHQNEHVHDLVHRGWNRLAALRSSTFA
+YVPGRAVASVDEHEHLLRLIEDGARFEEIEAAARAHRLNTLHAYLEHSAEPSA
+>4_1858
+MRRTDIGTVGLAGAPVSKADRAYQAILEGIRDQRHEPGDRLVLSQIAAELGMSVVPVREA
+IRRLQSEKLVAYERNVGATVVGIDPVEYRHTMETLALVEGFSTAQCAPHVTAEDLAAARE
+VNATMRAMTESERAWDPVAFTELNRRFHSILFEHHQNEHVHDLVHRGWNRLAALRSSTFA
+YVPGRAVASVDEHEHLLRLIEDGARFEEIEAAARAHRLNTLHAYLEHGAEPSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001598.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001598.fa
new file mode 100644
index 0000000000000000000000000000000000000000..19b73ce3c2e1348a77ebf57125300a9fb7610d54
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001598.fa
@@ -0,0 +1,30 @@
+>0_1943
+MAEHDGGPVREGAPSQTLSRALTLLEAVVEAPEPPTIADLADGLGVHRSVAYRMLRTFET
+HGLLRRDGLGRVHAAPGLAVLARRVEQDLRAAAMPHLTAVSTDLGMTAFLVVWDGAHCLT
+LATAEPPSGNLVTQRPGTRHPLGVGAPGMAIAVALTGQEWARLPGEAAPERPELDDVRER
+GWAVSSDEVITGVSSVAVPLRVPGQLPAALAVVYATRPEDPARLGDRLGEAARAVAVAFG
+AA
+>1_1664
+MAEHDGGPVREGAPSQTLSRALTLLETVVEAPEPPTIADLADGLGVHRSVAYRMLRTFEA
+HGLLRRDGLGRVHAAPGLAVLARRVEQDLRAAAMPHLTAVSTDLGMTAFLVVWDGAHCLT
+LATAEPPSGNLVTQRPGTRHPLGVGAPGMAIAVALTGQEWARLPGEAPPERPELDDVRER
+GWAVSSDEVITGVSSVAVPLRVPGQLPAALAVVYATRPEDPARLGDRLGEAARAVAVAFG
+AA
+>2_819
+MAEDDGGPAPAREGAPSQTLSRALALLEAVVEAAEPPTIAELADGLGVHRSVAYRVLRTF
+EAHGLLRRDPLGRVHSAPGLAVLARRVEQDLRTAAMPHLSAVSADLGMTAFLVVGDGSTC
+LTLATVEPPRGNLVTQRPGTRHPLGIGAPGMAVALALPEQEWEQRRGDAAPERPELGEAR
+ERGWAVSRDEVITGVSSVAVPLSVPGQLPAALAVVYATRPEDPERLGGRLKEAAQAVAAS
+LGAA
+>3_757
+MDPHDDSVPAVSAPPPSAPGVRPGAPSQTLSRALTMLELVADRPTPPSIAELADDLGVHR
+SVAYRMLRTFEVHGLLRRDAAGLVHGAPGLVTLAGGVEQDLRAAAVTELSRVSDALAMTA
+FLVVWDGRDCLTLATVEPPRGNLVTQRPGTRHPLGVGAPGIAIASVLPAEGQDRPAVREA
+RARGWAASRDEVITGVGSVAAPVPAAAGMPAALAVVFTSPAVDEEAVGAELAAAARRLGA
+VLGEG
+>4_1882
+MAEHDGGPVREGAPSQTLSRALTLLETVVEAPEPPTIADLADGLGVHRSVAYRVLRTFET
+HGLLRRDGLGRVHAAPGLAVLARRVEQDLRAAAMPHLTAVSTDLGMTAFLVVWDGAHCLT
+LATAEPPSGNLVTQRPGTRHPLGIGAPGMAIAVALTGQEWARLPGEAPPERPELDDVRER
+GWAVSSDEVITGVSSVAVPLRVPGQLPAALAVVYATRPEDPARLGDRLGEAARAVAVAFG
+AA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001601.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001601.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3dd910af6273716c18d1c96eb36db59586493382
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001601.fa
@@ -0,0 +1,35 @@
+>0_1947
+MTQTSSPQHLASVPSPEDAAGQENFDRLIAEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE
+IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDELNEQLLSGRA
+KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRASYGPYGRAMVRICKEESFHQRQG
+WEILYELSHGTPEQKQMAQDAVNRFYGPALQMFGPTDEDSPNSRQSMAWKVKRFSNDDLR
+QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDEFMSVIKGDGPMNTQRMARR
+IQAHEDGAWVREAAAAYARRQAEQNAPAETHLIGA
+>1_1668
+MTQTSSPQHLASVPSPEDAAGQENFDRLIAEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE
+IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDELNEQLLSGRA
+KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRASYGPYGRAMVRICKEESFHQRQG
+WEILYELSHGTPEQKQMAQDAVNRFYGPALQMFGPPDEDSPNSRQSMAWKVKRFSNDDLR
+QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDEFMSVIKGDGPMNTQRMARR
+IQAHEDGAWVREAAAAYARRQAEQNAPAETHLIGA
+>2_815
+MTQTSSTTRLASVPSPEDAAGQENFDRLIAEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE
+IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDVLNDQLLEGKA
+KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRSSYGPYGRAMVRICKEESFHQRQG
+WEILYELSHGTPEQKQMAQDAVDRFYGPALQMFGPPDEDSPNSKQSMAWKVKRFSNDELR
+QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDELMSVIKGNGPMNTQRLARR
+IQAHEDGAWVRDAAAAYARRQAEQHAPAETHLIGA
+>3_753
+MTQTSSSPHLASVPSPDDAAGQENFDRLIQEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE
+IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDELNEQLLSGRA
+KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRASYGPYGRAMVRICKEESFHQRQG
+WEILYELSHGTPEQKQMAQDAVNRFYGPALQMFGPPDEDSPNSQQSMAWKVKRFSNDELR
+QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDEFMSVIKGNGPMNTQRLARR
+VQAHEDGAWVREAAAAYARRQAEQHVPADTQLIGA
+>4_1886
+MTQTSSPQHLASVPSPEDAAGQENFDRLIAEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE
+IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDELNAQLLSGRA
+KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRASYGPYGRAMVRICKEESFHQRQG
+WEILYELSHGTPEQKQMAQDAVDRFYGPALQMFGPPDEDSPNSRQSMAWKVKRFSNDDLR
+QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDEFMSVIKGDGPMNTQRMARR
+IQAHEEGAWVREAAAAYARRQAEQNAPAETHLIGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001602.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001602.fa
new file mode 100644
index 0000000000000000000000000000000000000000..10dd29bb354c9e3a38ba575d962f58781e6d3b7a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001602.fa
@@ -0,0 +1,15 @@
+>0_1948
+MSETTAASHAWPLWEVFVRANRGLSHVHAGSLHAPDATLALRNARDLYTRRNEGTSVWVV
+PAEAIAASDPDSKGGFFESAQGKSYRHATYYQQSEGVPHL
+>1_1669
+MSETTAASHAWPLWEVFVRANRGLSHVHAGSLHAPDATLALRNARDLYTRRNEGTSVWVV
+PAEAIAASDPDSKGGFFESAQGKSYRHATYYQQSEGVPHL
+>2_814
+MGENTAASNAWPLWEVFVRANRGLSHVHAGSLHAPDASLALRNARDLYTRRNEGTSVWVV
+PAEAIAASDPDSKGGFFESPQGKSYRHATYYQQSEGVPHL
+>3_752
+MTENTAPSNEWPLWEVFVRANRGLSHVHAGSLHAPDATMALRNARDLYTRRNEGTSVWVV
+PADAVAASDPDSKGGFFESPQGKSYRHATYYQKSEGVPHL
+>4_1887
+MSETTAASHAWPLWEVFVRANRGLSHVHAGSLHAPDATLALRNARDLYTRRNEGTSVWVV
+PAEAIAASDPDSKGGFFESAQGKSYRHATYYQQSEGVPHL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001603.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001603.fa
new file mode 100644
index 0000000000000000000000000000000000000000..18a3f6c5bb77b9ba8726514b00ab9169dc429a38
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001603.fa
@@ -0,0 +1,30 @@
+>0_1949
+MSFATNDSATRHSAGVAITAEEIAAGEQKANDDVARYALALGDDALMLGQRLSWWISRAP
+EIEEDIALGNIALDLVGHARFLLSYAGTAWGKTEDELAYFRDEEEFRSVRLVEAENGDFA
+KTIARQLYYSFYSYELYTRLRESTDPTLAAIADKALKEVLYHQDHAALWLQRLGLGTEES
+KRRMQRGLDELWPYVAELFHDDDVVRALAEQGVAVLPSSLEEPTMTRIRAAIEEACLTVP
+TTGTARGGDRSGAMSEYRGYILAEMQSLARRHPGATW
+>1_1670
+MSFATNDSATRHSAGVAITAEEIAAGEQKASDDVARYALALGDDALMLGQRLSWWISRAP
+ELEEDIALGNIALDLVGHARFLLSYAGTAWGKTEDELAYFRDEEEFRSVRLVEAENGDFA
+KTIARQLYYSFYSYELYTRLRESTDSTLAAIADKALKEVLYHQDHAALWLQRLGLGTEES
+KRRMQRGLDELWPYVAELFHDDDVVRALAEQGVAVLPSSLEEPTMTRIRAAIEEAGLTVP
+TTGTARGGDRSGAMSEYRGYILAEMQSLARRHPGATW
+>2_813
+MSFATNDSATKHSAGVAITAEEIASGEQKASEETARYALYLGDDALMLGQRLSWWISRTP
+ELEEDIALGNIALDLVGHARFLLSYAGTAWGQSEDELAYFRDEEEFRSVRLVEAENGDFA
+KTIARQLYYSFYAFELYTRLKESTDATLAAIADKALKEVLYHQDHAALWLNRLGLGTDES
+KFRMQRGLDELWPYLPELFHDDETTRPLAEQGIAVLPSSLEEPTMTRIREAIEAAGLEVP
+TTGTARGGDRSGAMSEYRGYILAEMQSLARRHPGASW
+>3_751
+MSFATNDSATRHSAGVANTAEEIASGGQKASDEVARYAVYLGDDALMLGQRLSWWISRAP
+ELEEDIALGNIALDLVGHARFLLSYAGTAWDKSEDDLAYFRDEEEFRSTRLVEAENGDFG
+KTIARQLYYSVYAHGLYTRLKDSKDATLAAIADKALKEVEYHLDHAEQWVNRLGLGTEES
+NARLQRGLDELWPYLPELFHDDELTRSLAEQGIAVLPSSLEESTMARIRAAIEGADLKVP
+ETGAARGGDRSGQMSEYRGYILAEMQSLARRHPGASW
+>4_1888
+MSFATNDSATRHSAGVAITAEEIAAGEQKASDDVARYALALGDDALMLGQRLSWWISRAP
+ELEEDIALGNIALDLVGHARFLLSYAGTAWGKTEDELAYFRDEEEFRSVRLVEAENGDFA
+KTIARQLYYSFYSYELYTRLRESADPTLAAIADKALKEVLYHQDHAALWLQRLGLGTEES
+KRRMQRGLDELWPYVAELFHDDDVVRALAEQGVAVLPSSLEEPTMTRIRAAIEEAGLTVP
+TTGTARGGDRSGAMSEYRGYILAEMQSLARRHPGATW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001604.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001604.fa
new file mode 100644
index 0000000000000000000000000000000000000000..97420f0c77d002cf38b92194c05989db10ae4f03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001604.fa
@@ -0,0 +1,20 @@
+>0_1950
+MTTASELRPADPAGARVWDAASTVHDPEIPVLSIADLGILREARVEGERAVVVITPTYSG
+CPAMDTITTDVARALGRAGFPDAEVRLVLQPAWTTDWMTDEGKAKLNEYGIAPPVARTTD
+GPVRIGMAVKCPRCHSLNTREITRFGSTSCKALYTCRECLEPFDYFKVH
+>1_1671
+MTTASELRPADPADARVWDAASTVHDPEIPVLSIADLGILREARAEGERAVVVITPTYSG
+CPAMDTITTDVTRALERAGFPDAEVRLALQPAWTTDWMTDEGKAKLNEYGIAPPVARTTD
+GPVMIGMAVKCPRCHSLNTREITRFGSTSCKALYTCRECLEPFDYFKVH
+>2_812
+MTTASELRPADPADARVWDAASTVHDPEIPVLSIADLGILREARAEGEKAVVVITPTYSG
+CPAMDTITTDVSRALERSGFEESEVRLVLQPAWTTDWMTDEGKAKLAEYGIAPPSARTTD
+GPVMIGMAVKCPRCHSLNTREITRFGSTSCKALYTCRECLEPFDYFKVH
+>3_750
+MTTAAELRPSDPAAAQVWDAAATVHDPEIPVLSIADLGILRDVQVEDGRAVVVITPTYSG
+CPAMGTITADVTTALGRAGYPDAEVRTVLQPAWTTDWMTDEGKAKLAEYGIAPPSARTDE
+GPVRVGLAVKCPRCHSLNTREITRFGSTSCKALYTCQECLEPFDYFKVH
+>4_1889
+MTTASELRPADPADARVWDAASTVHDPEIPVLSIADLGILREARVEGERAVVVITPTYSG
+CPAMDTITTDVTRALERAGFPDAEVRLVLQPAWTTDWMTDEGKAKLNEYGIAPPVARATD
+GPIRIGMAVKCPRCHSLNTREITRFGSTSCKALYTCRECLEPFDYFKVH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001612.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001612.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4fc0d22e7b2c616881bb592f0baf46ae3e4823a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001612.fa
@@ -0,0 +1,35 @@
+>0_1961
+MRCGLDGLLRDPTVFSTPAAREAGVSAARLRRGDVVSLGWGLWGRRGIEPDPMDHVRALQ
+DLHPEGVFSHVTAARVLGLWLTGPLAADRSVHVATPRGHGTASSRAGVRSHRLRADAPVR
+IVDGVRVTAPGWIFVDLAAQAGPLEHLVALGDSMVRTAPTEARRRRLPPGVTDVAELRAA
+VEERGRVRGIRAAREALELVRPGADSPQESRLRVRLVLDGVPEPAVNPCIRLATGQRLRV
+DLVWADAKVAVEYDGDQHRTDRRQWREDRERDAALRAEGWEVIRVTADVFRPGHWELFVR
+QLRGLVAARTPPGRVPPSWI
+>1_1681
+MRCGLDGLLRAPTVFSTPAARETGVSAARLRRGDVVSLGWGLWGLRGVEPDPMDHLRALQ
+DLHPEGVFSHVTAARVLGLWLTGPLAADRSVHVATPRGHGTASSRAGVRSHRLRADAPVR
+IVDGVRVTAPGWIFVDLAAQAGPLDHLVALGDSMVRTAPTEARRRRLPPGVTDVAELRAA
+VEERGRVRGIRAAREALELVRPGADSPQESRLRARLVLDGVPEPAVNPCIRLATGQRLRV
+DLVWAEAKVAVEYDGDQHRTDRRQWREDRERDAALRAEGWEVIRVTADVFRPGHWELFVR
+QLRGLVAARTPPGRVPPSWI
+>2_779
+MRCGLDETEREPTVFSTNAAQEAGVPPGRLRRSDLEPWGRGLWRVRDAVPDVMDHLRALQ
+DLHPEGVFTHVTAARVLGLWLTGPLARDPAIHLGAPRHHGTGSRREGVRSHRLYGDVPVR
+IVDGVRVTATGWTFVDLAAAAATVETLVALGDSAVRSAPTERRRRDLPPGVTSLEELRGA
+VAERPRVKGIRLARDAVDLVRPGADSPQESRLRVGLVLDGVPEPQVNPRIVLSTGQWLRV
+DLAWPAARLVVEYDGDQHRTEQRQWREDRSRDAGLRADGWEVLRVTADVFRPAEWELFVR
+RVRARLGRDAAGRAAAG
+>3_740
+MPRSPAPLPPMRCGLDGLLRAPTVFSTPAAREAGVSAARLRRGDVVSLGWGLWGRRGVEP
+DPLDHVRALQDLHPEGVFNHVTAARVLGLWLTGPLAADRSVHIATPRGHGTASSRAGIRS
+HRLRADAPVRIVDGVRVTAPGWTFVDLAAQAGPLEHLVALGDSMVRTAPTEARRRRLPPG
+VTDVAELRAAVEERGRVRGIRAAREALELVRPGVDSPPESRLRVRLVLDGVPEPAVNPCI
+RLATGQRLRVDLVWAEAKVAVEYDGDQHRTDRRQWREDRERDAALRAEGWEVIRVTADVF
+RPGHWELFVRQLRGLVAARTKPGRVPPSWI
+>4_1899
+MRCGLDGLLRAPTVFSTPAAREAGVSAARLRRGDVVSLGWGLWGRRGVEPDPMDHVRALQ
+DLHPEGVFSHVTAARVLGLWLTGPLAADRSVHIATPRGHGTASSRAGIRSHRLRADAPVR
+IVDGVRVTAPGWTFVDLAAHAGPLEHLVALGDSMVRTAPTEARRRRLPPGVTDMAELRAA
+VEERGRVRGIRAAREALELVRPGADSPQESRLRVRLVLDGVPEPAVNPCIRLATGQRLRV
+DLVWADAKVAVEYDGDQHRTDRRQWREDRERDAALRAEGWEVIRVTADVFRPGHWELFVR
+QLRGLVAARTPPGRVPPSWI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001616.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001616.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bda431b356c56a41d4ff1fe87ee784919ca64f23
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001616.fa
@@ -0,0 +1,25 @@
+>0_1965
+MPQSSPTPRRGRPGYDRQTLLAECVELFNRHGYEATSMGMLATHLGISKSAIYHHVESKE
+AILDHAVTEALDALEACLDDVVASGVDAGAQVEAAIRGTLGVLAEKQPEVTLLLRLRGNS
+AVEVAAVERRREITRRFGDLLEAAQAAGAVRSDVTPRNLARLALGMINSIVDWYRPDRGV
+PGQEGPGQMIDAVTGVVLGGLRG
+>1_1685
+MPQSSPTPRRGRPGYDRQTLLAECVELFNRHGYEATSMGMLAAHLGISKSAIYHHVESKE
+AILDHAVTEALDALEACLDDVVASGADAGAQVEAAIRGTLGVLAEKQPEVTLLLRLRGNS
+AVEVAAVERRREITRRFGDLLEAAQAAGAVRSDVTPRNLARLALGMINSIVDWYRPDRGV
+PGQQGPDQMIDAVTGVVLGGLRG
+>2_775
+MPHSSTAPRRGRPGYDRQTLLTVCVDVFNRHGYEATSMGMLAQHLGISKSAIYHHVESKE
+AILEQALDDALDALEASLDGVMADFAGPGEQVEAAVRGTLRVLVEKMPEVTLLLRLRGNS
+AVELAAMERRRAITRRLGEMIAAAQEAGAVRGDITPRNLARLALGMINSIVDWYRPESDS
+PGHKSVTEMVDAVTRVVLGGLRG
+>3_736
+MPQSSPTPRRGRPGYDRQTLLAECVELFNRHGYEATSMGMLATHLGISKSAIYHHVESKE
+AILDHAVTEALDALEACLDDVVASGADAGAQVEAAIRGTLGVLAEKQPEVTLLLRLRGNS
+AVEVAAVERRREITRRLGDLLESAQAAGAVRSDVTPRNLARLALGMINSIVDWYRPDGAD
+PGHKSVEEMVAAVTGVVMGGLRG
+>4_1903
+MPQSSPTPRRGRPGYDRQTLLAECVELFNRHGYEATSMGMLAAHLGISKSAIYHHVESKE
+AILDHAVTEALDALEACLDDVVASGADAGAQVEAAIRGTLGVLAEKQPEVTLLLRLRGNS
+AVEVAAVERRREITRRFGDLLEAAQAAGAVRSDVTPRNLARLALGMINSIVDWYRPDRGV
+PGQQGPDQMIDAVTGVVLGGLRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001620.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001620.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c687b3e6bbf3eb395616d5044f45e5b7f0a10f86
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001620.fa
@@ -0,0 +1,49 @@
+>0_1973
+MGAMTSQPAPASTAHRRPLAEAGIALGPLDGRYRAAVEPLVEHLSEAALNRNRIHVEVEW
+FIHLAEHRVLPGLEPLTAEQQAGLRAIVTDFDAESVAELAATEKVTVHDVKAVEYFIADR
+LEGLGLGRLKPLVHFACTSEDINNLAYAVGVRDAVEQVWLPAARAAVATVSAMAAEAAET
+PMLSRTHGQPATPTTLGKEMAVFVHRLTRQTRRIAGQEYLGKINGATGTYAAHLAAAPDA
+DWPALSRSFVEHLGLTWNPLTTQIESHDWQAELYADVARFNRILHGFCVDVWSYISIGYF
+AQIPVAGATGSSTMPHKVNPIRFENAEANLELSCALLDSLGATLVESRWQRDLTDSTSQR
+NIGVALGHSVLALTNVTKGMGQLQVADPVLAEDLDTNWEVLGEAVQTVMRAEAIAGVEGM
+DNPYERLKELTRGHRVDGARMREFVQGLGLSEGAQARLLELTPAGYTGVASELAKEFGPA
+QD
+>1_1691
+MTSQPAPASTAHRRPLAEAGIALGPLDGRYRAAVEPLVEHLSEAALNRNRIHVEVEWFIH
+LAEHRVLPGLEPLTAEQQAGLRAIVTDFDAESVAELAATEKVTVHDVKAVEYFIADRLEG
+LGLGRLKPLVHFACTSEDINNLAYAVGVRDAVEQVWLPAARAAVATVSAMAAEAAETPML
+SRTHGQPATPTTLGKEMAVFVHRLTRQTRRIAGQEYLGKINGATGTYAAHLAAAPDADWP
+ALSRSFVEHLGLTWNPLTTQIESHDWQAELYADVARFNRILHGFCVDVWSYISIGYFAQI
+PVAGATGSSTMPHKVNPIRFENAEANLELSCALLDSLGATLVESRWQRDLTDSTSQRNIG
+VALGHSVLALTNVTKGMGQLQVADPVLAEDLDTNWEVLGEAVQTVMRAEAIAGVEGMDNP
+YERLKELTRGHRVDGARMREFVQGLGLSEGAQARLLELTPAGYTGVASELAKEFGPAQD
+>2_765
+MTTQPAGPSPASTDHRRSLADSGAALGPLDGRYRAAVAPLVEHLSEAALNRNRIHVEVEW
+FIHLAEHAVLPGLTPLTDEQKAGLRAIVTDFDADSVAELAATEKVTVHDVKAVEYFIADR
+LEGLGLGRLKPLVHFACTSEDINNLAYAVGVRDAVEQVWLPAARAAVATVSAMAAEAAET
+PMLSRTHGQPATPTTLGKEMAVFVHRLTRQTRRIAAQEYLGKINGATGTYAAHLAAAPDA
+DWPALSRSFVEHLGLTWNPLTTQIESHDWQAELYADVARFNRILHGFCVDVWSYISIGYF
+TQIPVAGATGSSTMPHKVNPIRFENAEANLELSCALLDSLGATLVESRWQRDLTDSTSQR
+NIGVALGHSVLALTNVTKGMGQLQVAEPVLAEDLDTNWEVLGEAIQTVMRAEAIAGVPGM
+DNPYERLKELTRGHRVDGERMREFVRGLGLSDGAQARLLELTPAGYTGVAADLAREFGPA
+QG
+>3_731
+MGAMTSQPAPASTAHRRSLAEAGIALGPLDGRYRAAVEPLVEHLSEAALNRNRIHVEVEW
+FIHLAEHRVLPGLEPLTAEQQAGLRAIVTDFDAESVSELAATEKVTVHDVKAVEYFIADR
+LEGLGLGRLKPLVHFACTSEDINNLAYAVGVRDAVEQVWLPAARAAVATVSAMAAEAAET
+PMLSRTHGQPATPTTLGKEMAVFVHRLTRQTRRIAGQEYLGKINGATGTYAAHLAAAPDA
+DWPALSRSFVEHLGLTWNPLTTQIESHDWQAELYADVARFNRILHGFCVDVWSYISIGYF
+AQIPVAGATGSSTMPHKVNPIRFENAEANLELSCALLDSLGATLVESRWQRDLTDSTSQR
+NIGVALGHSVLALTNVTKGMGQLQVAEPVLAEDLDTNWEVLGEAVQTVMRAEAIAGVEGM
+DNPYERLKELTRGHRVDGARMREFVQGLGLSEGAQARLLELTPAGYTGVASELAKEFGPA
+SAQG
+>4_1909
+MGAMTSQPAPASTAHRRSLAEAGIALGPLDGRYRAAVEPLVEHLSEAALNRNRIHVEVEW
+FIHLAEHRVLPGLEPLTAEQQAGLRAIVTDFDAESVAELAATEKVTVHDVKAVEYFIADR
+LEGLGLGRLKPLVHFACTSEDINNLAYAVGVRDAVEQVWLPAARAAVATVSAMAAEAAET
+PMLSRTHGQPATPTTLGKEMAVFVHRLTRQTRRIAGQEYLGKINGATGTYAAHLAAAPDA
+DWPALSRSFVEHLGLTWNPLTTQIESHDWQAELYADVARFNRILHGFCVDVWSYISIGYF
+AQIPVAGATGSSTMPHKVNPIRFENAEANLELSCALLDSLGATLVESRWQRDLTDSTSQR
+NIGVALGHSVLALTNVTKGMGQLQVAAPVLAEDLDTNWEVLGEAVQTVMRAEAIAGVEGM
+DNPYERLKELTRGHRVDGARMREFVQGLGLSEAAQARLLELTPAGYTGVAAELAKEFGPA
+QG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001621.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001621.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc37960287d120957f3f3d864b581f47f7d0a9de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001621.fa
@@ -0,0 +1,30 @@
+>0_1974
+MLLPLLPVWLLSAAPKDPAELERDVPEPIDAHGELADAVTAAITAVDLVGVFFFAISGAV
+LAVRKGYDIVGSLLLALMVGTGGGVVRDLVVGRDVPAAFDNPWYLILPAVASLAVFLRIF
+DGERGHHAVMAFDAIGLAVYCVVGTRIALLAGLSPVAAAVLGLVTAVGGGILRDVVAGEP
+PAVFGGRGWYALPAILGAGTTAALGQAEVLNPLTSAAVMVLVLVLRVVSLRREWLAPGAE
+ISGETQRQRMDPHDEPPVPDIRDRKGRDGPPAAPGEDGPPANEETPGADEDVTPRGTPG
+>1_1692
+MLLPLLPVWLLSAAPKDPAELERDVPEPIDAHGELADAVTAAITAVDLVGVFFFAISGAV
+LAVRKGYDIVGSLLLALMVGTGGGVVRDLVVGRDVPAAFDNPWYLILPAVASLAVFLRIF
+DGERGHHAVMAFDAIGLAVYCVVGTRIALLAGLSPVAAAVLGLVTAVGGGILRDVVAGEP
+PAVFGGRGWYALPAILGAGTTAALGQAEVLNPLTSAAVMVLVLVLRVVSLRREWLAPGAE
+ISGETQRQRMDPHDEPPVPDIRDRKGRDGPPAAPGEDGPPANEETPGADEDVTPRGTPG
+>2_763
+MLLPSLPVWLLSATPKDPAELERDVPEPIDAHGELADAITAAITAVDLVGVFFFAISGAV
+LAVRKGYDIVGSLLLALMVGTGGGVVRDLVVGRDVPAAFDNPWYLILPAVASLAVFLRIF
+DGERGHHAVMAFDAIGLAVYCVVGTRIALLAGLSPVAAAVLGLVTAVGGGILRDVVAGEP
+PAVFGGRGWYALPAILGAGTTAALGQAELLGPLTSAAVMVLVLVLRVVSMRREWLAPGAE
+ISGETQRQRMDPHDEPPVPDIRDRKGRDGPPADPGEDGPPANEETPGAGEGVPPGTPG
+>3_730
+MLLPLLPVWLLSAAPKDPAELERDVPEPIDAHGELADAITAAITAVDLVGVFFFAISGAV
+LAVRKGYDIVGSLLLALMVGTGGGVVRDLVVGRDVPAAFDNPWYLILPAVASLAVFLRIF
+DGERGHHAVMAFDAVGLAVYCVVGTRIALLAGLSPVAAAVLGLVTAVGGGILRDVVAGEP
+PAVFGGRGWYALPAILGAGTTAALGQAELLGPLTSAAVMVLVLVLRVVSLRREWLAPGAE
+ISGETQRQRLDPHDEPPVPDIRDRKGKDGPPADPGEDGPPATEETPGADEGVPPGTPG
+>4_1910
+MLLPSLTVWLLSATPKDPAELERDVPEPIDAHGELAEAITAAITAVDLVGVFFFAISGAV
+LAVRKGYDIVGSLLLALMVGTGGGVVRDLVVGRDVPAAFDNPWYLILPAVASLAVFLRIF
+DGERGHHAVMAFDAVGLAVYCVVGTRIALLAGLSPVAAAVLGLVTAVGGGILRDVVAGEP
+PAVFGGRGWYALPAILGAGTTAALGQAEVLNPLTSAAVMVLVLVLRVVSLRREWLAPGAE
+ISGETQRQRMDPHDEPPVPDIRDRKGRDGPPAAPGEDGPPANEETPGADEDVTPRGTPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001623.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001623.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e12958f6864e41cff1adb1c1b4d3201f1133dca8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001623.fa
@@ -0,0 +1,50 @@
+>0_1979
+MTGTHETARPASTTTEAAASGPLHRVGFDRAKYIELQSQHIQERRRQIGGKLYLEMGGKL
+FDDLHASRVLPGFTPDNKIAMLDRIKDETEILVCFNAKDLERNKVRADLGITYEDDVLRL
+VDVFRERGFLVEHVVVTQLEDANHRALAFLEKLERLGLKVARHRVIPGYPHAMSTIVSEQ
+GFGANEWSETTRDLVVVTAPGPGSGKLATCLSQVYNDRQRGIPAGYAKFETFPIWNLPLE
+HPVNAAYEAATVDLDDINLIDPFHLAEYGERVTSYNRDVEVFPLLSALLEKVTGTTPYKS
+PTDMGVNMAGAAIVDDEVCQEAAKQEIIRRYYKAQVNEALEGADDTESERVALVMSKLGL
+SSEDRPVVGAAQLVAERTGEPGAAVQLADGTLVTGKTSELLGCSAAVLLNALKVLAGIED
+DVHLLSPASIEPIQTLKTVHLGSKNPRLHTDEVLIALSVSAATDANARAAVEQLASLEGC
+DVHTTTILGSVDEGIFRSLGMLVTSEPKFQKKGLYRKR
+>1_1694
+MTGTHETARPASTTTEAAASGPLHRVGFDRAKYIELQSQHIQERRRQIGGKLYLEMGGKL
+FDDLHASRVLPGFTPDNKIAMLDRIKDETEILVCFNAKDLGRNKVRADLGITYEDDVLRL
+VDVFRERGFLVEHVVVTQLEDANHRALAFLEKLERLGLKVARHRVIPGYPHAMSTIVSEQ
+GFGANEWSETTRDLVVVTAPGPGSGKLATCLSQVYNDRQRGIPAGYAKFETFPIWNLPLE
+HPVNAAYEAATVDLDDINLIDPFHLAEYGERVTSYNRDVEVFPLLSALLEKVTGTTPYKS
+PTDMGVNMAGAAIVDDEVCQEAAKQEIIRRYYKAQVNEALEGADDTESERVALVMSKLGL
+SSEDRPVVGAAQLVAERTGEPGAAVQLADGTLVTGKTSELLGCSAAVLLNALKVLAGIED
+DVHLLSPASIEPIQTLKTVHLGSKNPRLHTDEVLIALSVSAATDENAKAAVEQLASLEGC
+DVHTTTILGSVDEGIFRSLGMLVTSEPKFQKKGLYRKR
+>2_760
+MTGTHETALPASTTDGRAASAPLRRIGFDRAKYIDLQSQHIQERRREIGGKLYLEMGGKL
+FDDLHASRVLPGFTPDNKIAMLERIKDETEILVCFNAKDLERNKVRADLGITYEDDVLRL
+VDVFRERGFLVEHVVVTQLEDANHRALAFLEKLERLGLKVARHRVIPGYPHATARIVSEE
+GFGRNEWSQTTRDLVVVTAPGPGSGKLATCLSQVYHDHQRDIPSSYAKFETFPIWDLPLE
+HPVNVAYEAATADLDDINLIDPFHLAAHGEQVTSYNRDVEVFPLLAALLEKLTGTSPYRS
+PTEMGVNMAGAAIVDDEACREAARQEIIRRWYKAAVEEAANGESDEVSERIALIMSRLGL
+TSEDRPVVGASLLVAERTGEPGAAVQLADGTLVTGKTSALLGCSAAMLLNALKVLAGLSD
+EVHLLTPESIEPIQTLKTVHLGSTNPRLHTDEVLIALSVSAATDPNAKAAVEQLASLAGC
+DVHTTTILGSVDEGIFRSLGMLVTSEPKFQKKGLYRKR
+>3_728
+MTGTADMAPQKISRPLGFDREQYIALQSQHIQERRRQLGGKLYLEMGGKLFDDLHASRVL
+PGFTPDNKIAMLDRIKDETEILVCFNAKDLERNKVRADLGITYEEDVLRLVDVFRERGFL
+VEHVVVTQLEDSNHLALAFIEKLGRLGLKVARHRVIPGYPHAMATIVSEQGFGANEWSET
+TRDLVVVTAPGPGSGKLATCLSQVYNDRQRGIPAGYAKFETFPIWNLPLEHPVNAAYEAA
+TVDLDDINLIDPFHLAEYGEKVTSYNRDVEVFPLLSALLEKVTGTTPYKSPTDMGVNMAG
+AAIVDDAVCRAAAEQEIIRRYYKAQVNEALEGADDTESERAALVMSKLGLSSEDRPVVGA
+AQLVAERTGEPGAALELADGTIVTGKTSELLGCSAAMVLNALKVLAGIDDDAHLLSPASI
+EPIQTLKTQHLGSKNPRLHTDEVLIALSVSAATDENAKAAVEQLASLEGCDVHTTTILGS
+VDEGIFRSLGMLVTSEPVFQKKGLYRKR
+>4_1912
+MTGTHETARPASTTTEAAASGPLHRVGFDRAKYIELQSQHIQERRRQIGGKLYLEMGGKL
+FDDLHASRVLPGFTPDNKIAMLDRIKDETEILVCFNAKDLGRNKVRADLGITYEDDVLRL
+VDVFRERGFLVEHVVVTQLEDANHRALAFLEKLERLGLKVARHRVIPGYPHAMSTIVSEQ
+GFGANEWSETTRDLVVVTAPGPGSGKLATCLSQVYNDRQRGIPAGYAKFETFPIWNLPLE
+HPVNAAYEAATVDLDDINLIDPFHLAEYGERVTSYNRDVEVFPLLSALLEKVTGTTPYKS
+PTDMGVNMAGAAIVDDEVCQEAAKQEIIRRYYKAQVNEALEGADDTESERVALVMSKLGL
+SSEDRPVVGAAQLVAERTGEPGAAVQLADGTLVTGKTSELLGCSAAVLLNALKVLAGIED
+DVHLLSPASIEPIQTLKTVHLGSKNPRLHTDEVLIALSVSAATDENAKAAVEQLASLEGC
+DVHTTTILGSVDEGIFRSLGMLVTSEPKFQKKGLYRKR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001627.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001627.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1174e7af295b0497810c62a98e4a92a40797dadc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001627.fa
@@ -0,0 +1,21 @@
+>0_1994
+MDSTLFTRSADRAAHNDVNFRTRKWVKPEDLNANNTLFGGSLLRWVDEEAAIYATLQLGN
+PRCVTKLISEINFLASAKQGDMIEMGLRATEFGRTSLTMRAKVRNIVTGEMILTIDKIVF
+VSLGEDGKPVPHGFTEITYDRDRLPLDNPL
+>1_1711
+MDSTLFTRSADRAAHDDVNFRTRKWVKPEDLNANNTLFGGSLLRWVDEEAAIYATLQLGN
+PRCVTKLISEINFLASAKQGDMIEMGLRATEFGRTSLTMRAKVRNIVTGEMILTIDKIVF
+VSLGEDGKPVPHGFTEITYDRDRLPLDNPL
+>2_693
+MDTSTAPGADHGRAADDISYRTRKWVKPEDLNANGTLFGGSLLRWIDEEAAIYAIIQLGN
+PRSVTKLISEINFRSSARQGDMIEMGLRAVEFGRTSLTMRAKVRNIISGEVILTIEKIVF
+VSLDEDGNPVPHGYTDITFDRDRLPQDTAR
+>3_708
+MATHHAPNLTAHEDDDVSYRTRKWVKPEDLNANGTLFGGSLLRWIDEEAAIYSIIQLGNP
+RSVTKLISEIEFSASARQGDMIEMGLRAVKFGRTSLTMRAKVRNIVTGEVILTIDKIVFV
+SLDEEGRPQPHGYTDITYDRDRLPLDTSR
+>4_1929
+MPAATVKPSTGTSRQVASGVAGSGWGRMVIGRVPPVWSVADPSGDPTARSSTSPHRAPSL
+VPASASLYRGAMDSTLFTRSADRAAHDDVNFRTRKWVKPEDLNANNTLFGGSLLRWVDEE
+AAIYATLQLGNPRCVTKLISEINFLASAKQGDMIEMGLRATEFGRTSLTMRAKVRNIVTG
+EMILTIDKIVFVSLGEDGKPVPHGFTEITYDRDRLPLDNPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001640.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001640.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1212a5b56045f5aca621b1252ecebd60acb0715f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001640.fa
@@ -0,0 +1,28 @@
+>0_2027
+MCVRLPDMTQSTPGGPATDLPDFRPSGNQGVDPALYEIENAAMDREGALWAALQEAAPWT
+GRTLLDLGAGTGFWLPRYADAAETIAVEPDARLLGAARARPGGARVLYGSAEQIPLPEAS
+VDVVHARFAYFFPHPRWDVRPGLDEVTRVLRPGGALVVIDNDTERGQFAELLRASTNAAA
+QGQDTYAREWWAGIGAETREVMSSWTFDSRADLEAVLRLEFERGVADAWLAEHPAATSLS
+YGYLLHVWR
+>1_1743
+MCVRLPDMTQSTPGGPATDLPDFRPSGNQGVDPALYEIENAAMDREGALWAALQEAAPWT
+GRTLLDLGAGTGFWLPRYADAAETIAVEPDARLLGAARARPGGARVLYGSAEQIPLPEAS
+VDVVHARFAYFFPHPRWDVRPGLDEVTRVLRPGGALVVIDNDTERGQFAELLRASTNAAA
+QGQDTYAREWWAGIGAETREVMSSWTFDSRADLEAVLRLEFERGVADAWLAEHPAATSLS
+YGYLLHVWR
+>2_568
+MTATPELPDFVPASNQGGDPAVYEVENAALDREGTLWAALQEAAPWAGRTLLDLGAGTGF
+WLPRYADAAEVIAVEPDTRLLDAARARPGGARVRRGSAERIPLAEASVDVVHARFAYFFP
+HPQWDVRPGLEEVARVLRPDGALVVIDNDTERGEFAELLVRSDAAADQGQDTYARRWWAD
+VGAETREVMSSWTFDTRADLEAVLRLEFPAELAEEWLAAHPEATSLTYGYLLHVWRPRG
+>2_677
+MELPDFRPSGNQGVDPALYEIENAAMDREGALWAALQEAAPWAGRTLLDLGAGTGFWLPR
+YADAAETIAVEPDARLLGAARARPGGARVLYGSAEQIPLPEASVDVVHARFAYFFPHPHW
+DVRPGLDEVTRVLRPGGALVVIDNDTERGQFAELLRASTNAAAQGQDTYAREWWAGVGAE
+TREVMSSWTFDSRADLEAVLRLEFERGVADAWLAEHPAATSLSYGYLFHVWR
+>4_1967
+MEGGCVRLPGMTQSTPGGPATGLPDFRPSGNQGVDPALYEIENAAMDREGALWAALQEAA
+PWAGRTLLDLGAGTGFWLPRYADAAETIAVEPDVRLLGAARARPGGARVLYGSAEQIPLP
+EASVDVVHARFAYFFPHPRWDVRPGLDEVTRVLRPGGALVVIDNDTERGQFAELLRASTN
+AAAQGQDTYAREWWAGVGAETREVMSSWTFDSRADLEAVLRLEFERGVADAWLAEHPAAT
+SLSYGYLLHVWR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001644.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001644.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24fac21ffa2d6b32bd004a518182eb78fdf55341
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001644.fa
@@ -0,0 +1,16 @@
+>0_2041
+MTFLDLVLVFVGFALAVLVGAALVGRVRGEHLRAVAATLVALWALTAVFDNVMIAAGLFD
+YGHELLVGAYVGQAPVEDFAYPLGSALLLPALWLLLTSRGRAGRRGRRPGRRPHPGDR
+>1_1759
+MTFLDLVLVFVGFALAVLVGAALVGRVRGEHLRAVAATLVALWALTAVFDNVMIAAGLFD
+YGHELLVGAYVGQAPVEDFAYPLGSALLLPALWLLLTSRGRAGRRGRRPGRRPHPGDR
+>2_659
+MTFLDLILVFVGLAAAVLAAVALTGRVRARHAAAIAVAIAALAVLTAVFDNVMIAAGLFD
+YGHDLLSGIYVGLAPIEDFAYPVGSALLLPAVWLLMTGRRRRGGERSPDGGAEPTGDGSS
+TADAGR
+>3_575
+MTYLTISLPFLAVAAAVLLASALTGRLDRRRRLGLVLAVALLVVLTAVFDSVIIGLGIVD
+YTQANINGARIGLAPVEDFLYPLAGVALLGGLWTLVRGGTR
+>4_1982
+MTFLDLVLVFVGFALAVLVGAALVGRVRGEHLRAVTATLVALWALTAVFDNVMIAAGLFD
+YGHELLVGAYVGQAPVEDFAYPLGSALLLPALWLLLTSRGRAGRRGRRPGRRPHPGDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001647.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001647.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9dc1ecd6895ba4cddc0c0f1b045ffcc6ff777b50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001647.fa
@@ -0,0 +1,55 @@
+>0_2044
+MSARDTALGPRTVVVGGGFAGLATAGLLARDGHRVTLLERGAVLGGRAGRWSEAGFTFDT
+GPSWYLMPEVIDRWFRLMGTSAAERLDLRRLDPGYRVYFEGHLHEPPVDVRTGHAETLFE
+SLEPGAGRRLRAYLDSASRIYGLAKEHFLYTDFRRPAALAHPDVLRALPALGPQLLGGLR
+SHVAARFQDPRLRQILGYPAVFLGTSPDRAPAMYHLMSHLDLADGVQYPLGGFAALVDAM
+AEVVREAGVEIRTGVEATAVEVVDRPAPAGRLGRLAARLPRPGAARGDEGRRRRPGRVTG
+VAWRSDDGAAGRLDADVVVAAADLHHVQTRLLPPGRRVAESTWDRRDPGPSGVLVCVGVR
+GSLPQLAHHTLLFTADWEDNFGRIERGEDLAADTSIYVSRTSATDPGVAPEGDENLFILV
+PAPAEPGWGRGGIRVRDGQGWRVDRAGDAQVEAVADRALDQLARWAGIPDLAERIVVRRT
+YGPGDFAADVHAWRGSLLGPGHTLAQSAMFRPSVRDADVAGLMYAGSSVRPGIGVPMCLI
+SAEVVRDELRHDARRVRPAGPGGSGT
+>1_1762
+MSARDTALGPRTVVVGGGFAGLATAGLLARDGHRVTLLERGAVLGGRAGRWSEAGFTFDT
+GPSWYLMPEVIDRWFRLMGTSAAERLDLRRLDPGYRVYFEGHLHEPPVDVRTGHAETLFE
+SLEPGAGRRLRAYLDSASRIYGLAKEHFLYTDFRRPAALAHPDVLRALPALGPQLLGGLR
+SHVAARFQDPRLRQILGYPAVFLGTSPDRAPAMYHLMSHLDLADGVQYPLGGFAALVDAM
+AEVVREAGVEIRTGVEATAVEVVDRPAPAGRLGRLAARLPRPGAARGDEGRRRRPGRVTG
+VAWRSDDGAAGRLDADVVVAAADLHHVQTRLLPPGRRVAESTWDRRDPGPSGVLVCVGVR
+GSLPQLAHHTLLFTADWEDNFGRIERGEDLAADTSIYVSRTSATDPGVAPEGDENLFILV
+PAPAEPGWGRGGIRVRDGQGWRVDRAGDAQVEAVADRALDQLARWAGIPDLAERIVVRRT
+YGPGDFAADVHAWRGSLLGPGHTLAQSAMFRPSVRDADVAGLMYAGSSVRPGIGVPMCLI
+SAEVVRDELRHDARRVRPAGPGGSGT
+>2_656
+MSAAPNVASGAAAHDDGPRAVVIGGGFAGLATAGLLARDGHRVTLLERNDGLGGRSGRWS
+AEGFAFDTGPSWYLMPEVIDRWFRLMGASAAERLDLRRLDPGYRVYFEDHLDAPPVDVRT
+GHAEELVESLEPGAGERLRAYLDSAGRVYELAKEHFLYTDFRRPADLARPAVLRALPSLG
+PQLLGGLRAHVAARFRDPRIRQILGYPAVFLGTSPDRAPAMYHLMSHLDLRDGVQYPIGG
+FAALVDAMADLVREAGVEVVTGAEATRIEVEDAERRRRRRGRVTGVVVRQDGTERRLSAD
+VVVAAADLHHVQTALLPPAQRVAESAWDRRDPGPSGVLVCVGVRGALPQLAHHTLLFTAD
+WEDNFGRIERGEDLAADTSLYVSRTSATDPGVAPDGDESLFVLVPAPAEPGWGRGGIRVR
+EGDGWRVEREGDAQVEAVADRALDQLARWAGIEDLHERIVVRRTIGPGDFAADVHAWRGS
+MLGPGHTLAQSAMFRPSVRDADVAGLLYAGSSVRPGIGVPMCLISAEVVREELRHAARRD
+ALRAQRRGRSQDDDDGARRGRVAAS
+>3_573
+MTPTTPAARPAAAPSGSRRVVVIGGGFAGLATAGLLAQDGHRVTLLEKNPVLGGRSGRWS
+AEGFTFDTGPSWYLMPEVIDRWFRLMGTSADEALDLRALSPAYRVYFQEHAADDAAAPGD
+GSTPGARAPLDVVSGREESLALAEELEPGAGGRLAAYLDSAERIYALAKRRFLYTDFQDL
+TELLRPDVLRALPALAPQLLGDLRGFVARRFEDGRLRRVLGYPAVFLGTSPGKAPAMYHL
+MSHLDLADGVQYPIGGFAALVDAMAELVRAAGVEIVTAAEVTAVDVVSDPRPRGRLPRLL
+DGAPRPWEPRTPAGGRRRSGHVRGVSWRDAEGGSHRLDADAVVAAADLHHVQTALLPGDQ
+RVAERTWDRRDPGPSAVLVCVGVRGRLPELLHHTLLFTEDWDENFRRIDEGEDLQEETSL
+YVSMTSATDPGVAPEGDESLFLLVPAPAVPEWGRGGVRTPEEDRAGDAQVETVADRALAQ
+LARWAGVPDLGERIVVRRTWGPADFTADVHAWRGSLLGPGHVLRQSALFRPPVRDPRVAG
+LVYAGSSVRPGIGVPMCLISAELARDAVSGVRPGGAAPGAPAMAGR
+>4_1985
+MSARDTALGPRTVVVGGGFAGLATAGLLARDGHRVTLLERGAVLGGRAGRWSEAGFTFDT
+GPSWYLMPEVIDRWFRLMGTSAAERLDLRRLDPGYRVYFEGHLHEPPVDVRTGHAETLFE
+SLEPGAGRRLRAYLDSASRIYGLAKEHFLYTDFRRPAALAHPDVLRALPALGPQLLGGLR
+SHVAARFQDPRLRQILGYPAVFLGTSPDRAPAMYHLMSHLDLADGVQYPLGGFAALVDAM
+AEVVREAGVEIRTGVEATAVEVVDRPAPAGRLGRLAARLPRPGAARGDEGRRRRPGRVTG
+VAWRSDDGAAGRLDADVVVAAADLHHVQTRLLPPGRRVAESTWDRRDPGPSGVLVCVGVR
+GSLPQLAHHTLLFTADWEDNFGRIERGEDLAADTSIYVSRTSATDPGVAPEGDENLFILV
+PAPAEPGWGRGGIRVRDGQGWRVDRAGDAQVEAVADRALDQLARWAGIPDLAERIVVRRT
+YGPGDFAADVHAWRGSLLGPGHTLAQSAMFRPSVRDADVAGLMYAGSSVRPGIGVPMCLI
+SAEVVRDELRHDARRARPAGPGGSGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001663.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001663.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2bd1e6c423181ad251a4b741ebf18d3bd519624f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001663.fa
@@ -0,0 +1,32 @@
+>0_2066
+MTQTTSTPARLRARDGFVLAARHFAPTTAPQARPAGAVVIAPATGVKATYYRRYAEFLAG
+HGFHAVTFDYRGVGESREPFAVARQARWADWGALDADAVLGWARTHLPGPLLTVGHSYGG
+FGIGLADEARHVARHVAVGGQHAHWRDYRARPGRARMWARWHAAMPVVTLARGHLPGRRL
+GWLEDLPRGVALDWARSRRDFTASARTAAGRDELRRRLAAFTADALIVAPVDDDFGTEAA
+LDRADAYSPGRRTVRWRVRPEELGVAEIGHFGLFHARFAPTFWPATLEWLRDGVAPDAAR
+>1_1785
+MTQTTSTPVRLRARDGFVLAARHFAPTTTTPPARPAGAVVIASATGVKATYYRRYAEFLA
+GHGFHAVTFDYRGVGESREPFAVARRARWADWGALDADAVLGWARTRLPGPLLTVGHSYG
+GFGIGLADEARHVARHVAVGGQHAHWRDYRARPGRARMWARWHAAMPAITLARGHFPGRR
+LGWLEDLPRGVALDWARSRRDFTASARTTAGRDELRRRLAAFTADALIVAPVDDDFGTDA
+ALDRADAYSPGRRTVRWRVRPEELGVAEIGHFGLFHARFAPAFWPATLEWLRDGVAPAAA
+R
+>2_635
+MTQTTSTPVRLRAPDGFVLAARHFTPTTTTPPASPAGTVVIASATGVKATYYRRYAEFLA
+GHGFHAVTFDYRGVGESREPFAVARRARWADWGVLDADAVLGWARTHLPGPLLTVGHSYG
+GFGIGLADEARHVARHVAVGGQHAHWRDYRARPGRVRMWARWHAAMPAITLARGHFPGRR
+LGWLEDLPRGVALDWARSRRDFTASARTAAGRDELRRRLAAFTADALIVAPVDDDFGTDA
+ALDRADSYSPGRRTVRWRVRPEELGVAEIGHFGLFHARFAPTFWPATLEWLRDGVVPAAA
+R
+>3_552
+MTQTTSTLVRLRARDGFVLAARHFAPTTTPPARPAGAVVIAPATGVKATYYRRYAEFLAG
+HGFHAVTFDYRGVGESRAPFAVARRARWADWGALDADAVLGWARTHLPGPLLTVGHSYGG
+FGIGLADEARHVARHVAVGGQHAHWRDYRARPGRARMWARWHALMPMVTLARGHFPGRRL
+GWLEDLPRGVALDWARSRRDFTASARTVAGRDELRRRLAAFTADALIVAPVDDDFGTDAA
+LDRADSYSPGRRTVRWRVRPEELGVGEIGHFGLFHARFASTFWPATLEWLRDGVAPAGAR
+>4_2005
+MTQTTSTPARLRARDGFVLAARHFAPTTAPQARPAGAVVIAPATGVKATYYRRYAEFLAG
+HGFHAVTFDYRGVGESREPFAVARQARWADWGALDADAVLGWARTHLPGPLLTVGHSYGG
+FGIGLADEARHVARHVAVGGQHAHWRDYRARPGRVRMWARWHAAMPAITLARGHFPGRRL
+GWLEDLPRGVALDWARSRRDFTASARTAAGRDELRRRLAAFTADALIVAPVDDDFGTDAA
+LDRADAYSPGRRTVRWRVRPEELGVTEIGHFGLLHARFAPTFWPATLEWLRDGVAPDAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001667.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001667.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c07b2d56aaa815ac50b1c5a6fa1de7b6ef9e81db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001667.fa
@@ -0,0 +1,20 @@
+>0_2070
+MTVPSSSAEHAPALEARPEMPGETVSRVAMTPAALELIRRLLPIHGPLMFHQSGGCCDGS
+APMCYPAGDFTTGAADVLLGTFALPAEGDQAAVEIPFWMSAAQFEYWKHTHLTLDVVDGR
+GSGFSVEAPEGKRFLIRSRLMAGSG
+>1_1789
+MTVPSSSAEHAPALEARPEMPGETLSRVAMTSAALELIRRLLPIHGPLMFHQSGGCCDGS
+APMCYPAGDFTTGAADVLLGTFALPAEGDQAAVEIPFWMSAAQFEYWKHTHLTLDVVDGR
+GSGFSVEAPEGKRFLIRSRLMAGSG
+>2_631
+MTVPSSSAEHAPALEARPELPGETVSRVAMTPAALELIRRLLPIHGPLMFHQSGGCCDGS
+APMCYPAGDFTTGAADVLLGTFALPAEGDQDAVEIPFWMSAAQFEYWKHTHLTLDVVDGR
+GSGFSVEAPEGKRFLIRSRLMAGSG
+>3_548
+MTVSSSSAEHAPALEARPELPGETVSRVAMTPAALALIRRLLPIHGPLMFHQSGGCCDGS
+APMCYPAGDFTTGAADVRLGTFVVPAEGDQAAVEIPFWMSAAQFEYWKHTHLTLDVVDGR
+GSGFSVEAPEGKRFLIRSRLMAGSG
+>4_2009
+MTVPSSSAEHALDARPELPGETVSRVAMTPAALELIRRLLPIHGPLMFHQSGGCCDGSAP
+MCYPAGDFTTGAADVLLGTFALPAEGDQAAVEIPFWMSAAQFEYWKHTHLTLDVVDGRGS
+GFSVEAPEGKRFLIRSRLMAGSG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001669.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001669.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8910c4022a4152565ee49d097c54245b65b67fa0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001669.fa
@@ -0,0 +1,55 @@
+>0_2072
+MSQTSQATGRLSAGHVIVKTLESHGVKRVYSVPGESYLDVLDGLHDSGIENVVCRHEGGA
+TYMAEADGKMNVVPGVAMVTRGPGAANAHVGLHTAWQDSTALVLFVGLIPFEHRDREAFQ
+EFDPHAWFGTGAKRVMVLDHPERASEIVAEAMFAASSGRPGPVVVGLPEDVIREEIDAHL
+HPQIPVASGGMTVGDWKSLHAALKESRKPLFITGGNDWTDEGAQTLTTWLEEHKIPAAAE
+WRTEGTVPFSSPSYVGPIGYGRPKPTYDMLEETDLIVFVGTVPGDVVTNGFTIRQNWDKK
+NFLVTIDPSLRGRSGPVSHQIVAKPDGFIRDLVRMELEVKPEWEEWTSRMRGEQEKFAAL
+PPAEPSEGQAKMATLMANLVPKLPKDSMISLGAGEHTNWAHRYFPTEGYRSMISARNGSM
+GYSVPGAVAASLNFPDRTVVTIAGDGEFLMNGQELATAAQYGATPLVIVMDNQEYGTIRT
+HQERQYPGRVSGTQLKNPDFAAMAQAFGGFGVRVERDADVPAAVDAALKAVQEEGRFALI
+HLIVEQRVKAY
+>1_1791
+MSQTSQATGRLSAGHVIVKTLESHGVKRVYSVPGESYLDVLDGLYDSGIENVVCRHEGGA
+TYMAEADGKMNVVPGVAMVTRGPGAANAHVGLHTAWQDSTALVLFVGLIPFEHRDREAFQ
+EFDPHAWFGTGAKRVMVLDHPERASEIVAEAMFAASSGRPGPVVVGLPEDVIRQEIDAHL
+HPQIPVAPGGMTVEDWKSLHAALKESRKPLFITGGNDWTDEGAQTLTTWLEEHKIPAAAE
+WRTEGTVPFSSPSYVGPIGYGRPKPTYDMLEETDLIVFVGTVPGDVVTNGFTIRQNWDKK
+NFLVTIDPSLRGRSGPVSHQIVAKPDVFIRDLVRMELEVKPEWEEWTSRMRGEQEKFAAL
+PPAEPSEGQAKMATLMANLVPKLPKDSMISLGAGEHTNWAHRYFPTEGYRAMISARNGSM
+GYSVPGAVAASLNFPDRTVVTIAGDGEFLMNGQELATAAQYGAKPLVIVMDNQEYGTIRT
+HQEREYPERVSGTQLKNPDFAAMAQAFGGFGVRVERDADVPAAVDAALKAVQEEGRFALI
+HLIVEQRVKAY
+>2_629
+MSQTTEAGGRLSAGHVIVKTLESHGVRRIYSVPGESYLDVLDGLHDSQIENVVCRHEGGA
+TYMAEADGKMNEVPGIAMVTRGPGAANAHVGLHTAWQDSTALVLFVGLIPFEHREKEAFQ
+EFDPHAWFGTGAKRVMVLDHADRASEIVAEAMFAATSGRPGPVVVGLPEDVIREQIDATL
+HPVIPVATGGMTVEDWKSLHSALKESKKPLFITGGNDWTDEGAQQLTQWLEGHKIPAAAE
+WRTEGTVPFSSPSYVGPIGYGRPKPTYDLLEETDLIVFIGTVPGDVVTNGFKIRQNWDKK
+NFLVTIDPSLRGRSGPVSHQIVAKPDVFVRDLVRMDLDVKPEWEEWTSRMRGEQETFAAL
+PPAEPSEGQAKMATLMANLMPKLPKDSMISLGAGEHTNWAHRYFPTEGYRAMISARNGSM
+GYSVPGAVAASLNFPDRTVVTIAGDGEFLMNGQELATAAQYGATPLVIVMDNQEYGTIRT
+HQEREYPERVSGTQLKNPDFAGMAEAFGGLGIRVEKDADVPAAVDAALKAVQEEGRFALI
+HLIVEQRVKAY
+>3_546
+MSQNSEAPGRLSAGHLIVKTLESHGVRRVYSVPGESYLDVLDGLHDSAQIENVVCRHEGG
+ATYMAEADGKMNEVPGIAMVTRGPGAANAHVGLHTAWQDSTAMVLFVGLIPFEHRDREAF
+QEFDPHAWFDSGAKRVMVLDHPERASEIVAEAMFAAASGRPGPVVVGLPEDIIRVEVDAH
+LHPQIPVAPGGMTVEDWKSLHAALKESQKPLFITGGNDWTDAGAEALTSWLEDHKIPAAA
+EWRCEGTVPFSSPSYVGPIGYGRPDFTQHLLEETDLIVFVGTVPGDVVTDGFTIRQNWDK
+KNFLVTIDPSLRGRSGPVSHQIVAKPDVFVRDLVRMDLAVKPEWEAWTSRLRGQQEEFAA
+LPAAEPGDGQAKMATLMATLMPKLPKDSMISLGAGEHTNWAHRYFPTEGYRAMISARNGS
+MGYSVPGAVAASLNFPDRTVVTIAGDGEFLMNGQELATAAQYGATPLVIVMDNQEYGTIR
+THQEREYPERVSGTQLKNPDFAAMAEAFGGFGVRVEQDADVPAAVDAALKAVQEEGRFAL
+IHLIVEQRVKAY
+>4_2011
+MSQTSQATGRLSAGHVIVKTLESHGVKRVYSVPGESYLDVLDGLHDSGIENVVCRHEGGA
+TYMAEADGKMNVVPGVAMVTRGPGAANAHVGLHTAWQDSTALVLFVGLIPFEHRDREAFQ
+EFDPHAWFGTGAKRVMVLDHPERASEIVAEAMFAASSGRPGPVVVGLPEDVIREEIDAHL
+HPQIPVAPGGMTVEDWKSLHAALKESRKPLFITGGNDWTDEGAQTLTTWLEEHKIPAAAE
+WRTEGTVPFSSPSYVGPIGYGRPKPTYDMLEETDLIVFVGTVPGDAVTNGFTIRQNWDKK
+NFLVTIDPSLRGRSGPVSHQIVAKPDGFIRDLVRMELEVKPEWEEWTSRMRGEQEKFAAL
+PPAEPSEGQAKMATLMANLVPKLPKDSMISLGAGEHTNWAHRYFPTEGYRSMISARNGSM
+GYSVPGAVAASLNFPDRTVVTIAGDGEFLMNGQELATAAQYGATPLVIVMDNQEYGTIRT
+HQERQYPGRVSGTQLKNPDFAAMAQAFGGFGVRVERDADVPAAVDAALKAVQEEGRFALI
+HLIVEQRVKAY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001672.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001672.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f4fe78d8c3fc004a896ee343edcdc2d8acfc433
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001672.fa
@@ -0,0 +1,25 @@
+>0_2076
+MQTPLEISSVVFKPILIRAVVALAFGLTTVFVAEPGLTWMKVMFALYLAFSGSAMWEYLR
+RDPVPVAMRSPLSLAAAAWMLGVIVLLFLGSPAAVGVAAGAALVLGGVAELVAWARHRRE
+FIPARDQLWTGLVGLLSGGGVVVAALQGFGPHALLGIAGGGAILIGVLLMVSGLGFHHEV
+RRDRGTARGL
+>1_1795
+MQTPLEISSVVFKPILIRAVVALAFGLTTVFVAEPGLTWMKVMFALYLAFSGSAMWEYLR
+RDPVPVAMRSPLSLAAAAWMLGVIVLLFLGSPAAVGVAAGAALVLGGVAELVAWARHRRE
+FIPARDQLWTGLVGLLSGGGVVVAALQGFGPHALLGIAGGGAILIGVLLMVSGLGFHHEV
+RRDRGTARGL
+>2_617
+MQTPLEISSVVFKPILIRAVVALAFGLTTVFVAAPGLTWMKVSLALYLAFSGSAMWEYLR
+REPVPVAMRSPLSMAAAASMLGVIVLLFLGTPAGVGLAAAAALVLGGAAELVAWARHRRE
+FIPARDQLWTGLVGLLSGLGVAFGALQGFGPHALLGIAGGGAIIIGVLLLVSGLGFHHEV
+RRDRGTAKGL
+>3_542
+MTSPQTPLEISSEVFKPVLIRAGVALIFGLTTVFVQNPGLTWMKVAFALYLVFSGSALWE
+YLRRDPVPVGMRSPLSLAAAAWMLGTVVLVIMGSPAAVGIVVGLALLAGGAAELTAWARF
+RREFIPARDQLWTGLVGALSGLGVLVGAVQGFGPHALLGIAGGGAIIVGVLMLISGLGFH
+HEVRRDRGTAKGL
+>4_2015
+MQTPLEISSVVFKPILIRAVVALAFGLTTVFVAEPGLTWMKVMFALYLAFSGSAMWEYLR
+RDPVPVAMRSPLSLAAAAWMLGVIVLLFLGSPAAVGVAAGAALVLGGVAELVAWARHRRE
+FIPARDQLWTGLVGLLSGGGVVVAALQGFGPHALLGIAGGGAILIGVLLMVSGLGFHHEV
+RRDRGTARGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001682.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001682.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1f9146844ed0b22ca5cf0d60d18625ad8b7e67be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001682.fa
@@ -0,0 +1,55 @@
+>0_2087
+MLWTLLRRHGRRYRGDVAAVVVLQLISTLAMLYLPSLNARIIDEGVARGDTARIWDIGLV
+MLGVALVQVVAAIAAVWFGAKASMGVGRDLRRAVYTRVDAFSAEELGRFGAATLITRGTN
+DVNQVQMLTLMALNFMVAVPIMAVGGIVMAIREDPGLSWLVWVSVPVLLVIVAWIVARLM
+PLFQQMQDNIDDVNGVLREQIQGIRVVRAFVRERHETRRFTDANAALTETSVRIGRLFVL
+LGPVITMILHLATAAVLWFGGQRVDAGLVQVGALTAFMQYLLQILMAVMMGTFMMMMLPR
+AVISARRIGEVLDTVPTLGEPVRPVTPERRDGAVELRHVTFQYPGAEAPVLDDVSFAVAP
+GTTTAIIGSTGSGKSTLISLLPRLYDATSGEVLVDGVPVTDLARAELTEAVALVPQKPYL
+FSGTVRENMQFGAPDASDERIWAALETAQAADFVRARTTGKGEAAASGLDSRLSQGGTDV
+SGGQRQRLSIARALVAEPRILVFDDSFSALDVTTDARLRAALDRAAAGVTRIVVAQRVAT
+ITDADQIIVLDEGRVVGRGTHAELLADNQTYREIVDSQLTAEDVA
+>1_1806
+MLWTLLRRHGRRYRGAVAAVVVLQLISTLAMLYLPSLNARIIDEGVARGDTARIWDIGLV
+MLGVALVQVVAAIAAVWFGAKASMGVGRDLRRAVYTRVDAFSAEELGRFGAATLITRGTN
+DVNQVQMLTLMALNFMVAVPIMAVGGIIMAIREDPGLSWLVWVSVPVLLVIVAWIVARLM
+PLFQRMQDNIDDVNGVMREQIQGIRVVRAFVRERHETRRFTDANAALTETSVRIGRLFVL
+LGPVITMILHLATAAVLWFGGERVDAGLVQVGALTAFMQYLLQILMAVMMGTFMMMMLPR
+AVISARRIGEVLDTVPTLAEPVRPVTPARRDGAVELRHVTFQYPGAEAPVLDDVSFAVAP
+GTTTAIIGSTGSGKSTLISLLPRLYDATSGEVLVDGVPVTDLARAELTEAVALVPQKPYL
+FSGTVRENMQFGAPDASDERIWAALETAQAADFVRARTTGKAETAASGLDSRLSQGGTDV
+SGGQRQRLSIARALVAEPRILVFDDSFSALDVTTDARLRAALDRAAAGVTRIVVAQRVAT
+ITDADQIIVLDEGRVVGRGTHAELLADNQTYREIVDSQLTAEDVA
+>2_603
+MLWTLLRRPRRPDLGAVTAVVVLQLISTLAMLYLPSLNARIIDEGVARGDTDRIWDLGLV
+MLGVALVQVVAAIVAVWFGAKVAMGIGRDLRRAVYTRVDGFSAEELGRFGAPTLITRGTN
+DVNQVQMVTLMGLNFMVAVPIMAIGGIIMAVREDPGLSWLVWVSVPVLLVIVAWIVAKLM
+PLFQRMQDDIDRVNGVMREQVMGIRVVRAFVREPHESARFSGANAALTRTSVLIGRLFVL
+LGPVITMILHLATAAVLWFGGHRVADGLVEVGALTAFMQYLLQILMAVMMGTFMMMMLPR
+AVVSAGRIGEVLDTVPTLAEPVNPVTPADPRGAVELRDVTFAYPGAEAPVLDGVSFTVAP
+GSTTAIIGATGSGKSTLVNLIPRLYDATSGQVLIDGVPVTELARAELTRAVALVPQKPYL
+FSGTVAENMRFGAPEATEEEIWAALETAQAAGFVRERTTGEGETAAGGLDSRLSQGGTDV
+SGGQRQRLSIARALVARPRILLFDDSFSALDVATDARLRGALDATAAGTTRIVVAQRVAT
+ITEADQIIVLDEGRVVGRGTHAELLAGNETYKAIVDSQVREEELA
+>3_529
+MLWTLLRRHLNPYAGAVTAVIVLQLVSTLAMLYLPSLNARIIDEGVARGDTARIWDLGLV
+MLGVAAVQVVAAISAVWFGAKASMGVGRDLRRAVYTRVDGFSAEELGRFGAATLITRGTN
+DVNQVQMLTLMALNFMVAVPIMAVGGIVMAVREDAGLSWLVWVSVPLLLVIVGFIVSRLM
+PLFQRMQDDIDAVNGVMREQVMGIRVVRAFVRQDHEAARFTDANQALTDTSVRIGRLFVL
+LGPVITMVLHLATAAVLWFGGHRVDQGLVQIGSLTAFMQYLLQILMAVMMGTFMMMMLPR
+AVISARRIGEVLDTAPTLGEPVHPVTPERREGRVELRDVTFAYPGAEAPVLDGVSFTAEP
+GTTTAIIGATGSGKSTLVNLIPRLYDATSGQVLVDGVPVTDLARAELTDAVAIVPQKPYL
+FSGTVRDNMRFGAPEATDEQIWAALETAQAADFVRERTTGEGETAASGLDSSLSQGGTDV
+SGGQRQRLSIARALVADPRILLFDDSFSALDVTTDATLRAALDASAAQTTRVVVAQRVAT
+ITDADQIVVLEAGRVVGRGTHAELLAGNETYRQIVDSQVREEELA
+>4_2026
+MLWTLLRRHGRRYRGAVAAVVVLQLISTLAMLYLPSLNARIIDEGVARGDTARIWDIGLV
+MLGVALVQVVAAIAAVWFGAKASMGVGRDLRRAVYTRVDAFSAEELGRFGAATLITRGTN
+DVNQVQMLTLMALNFMVAVPIMAVGGIIMAIREDPGLSWLVWVSVPVLLVIVAWIVAGLM
+PLFQRMQDNIDDVNGVMREQIQGIRVVRAFVRERHEARRFTDANAALTETSVRIGRLFVL
+LGPVITMILHLATAAVLWFGGQRVDAGLVQVGALTAFMQYLLQILMAVMMGTFMMMMLPR
+AVISARRIGEVLDTVPTLGEPARPVSPARRDGAVELRHVTFQYPGAEAPVLDDVSFAVAP
+GTTTAIIGSTGSGKSTLISLLPRLYDATSGEVLVDGVPVTDLARAELTEAVALVPQKPYL
+FSGTVRENMQFGAPDASDERIWAALETAQAADFVRARTTGKGEAAASGLDSRLSQGGTDV
+SGGQRQRLSIARALVAEPRVLVFDDSFSALDVTTDARLRAALDRAAAGVTRIVVAQRVAT
+ITDADQIIVLDEGRVVGRGTHAELLADNQTYREIVDSQLTAEDVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001687.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001687.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5eef8309a10bf63f41176162ea648215b6cbe848
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001687.fa
@@ -0,0 +1,100 @@
+>0_2093
+MSQTLTPAAPQDLNARRHRLRRYRAVIFDMDGVITDTAGVHAQAWKELFDGALPAVGALP
+ANAAVVAADPDVLRPFDAAADYLHHVDGRPREDGVRTFFASRGLRVPEADAPEADAAPEL
+TVLALAERKQGYFEQVLERDGVRVFPEAQDLLERLRAKGVPVALVTSSKNSRAVLTAGGV
+LDFFPVIVDGNTAVERGLPGKPDPAMFWEAARELGVDVADAMVLEDAVSGVKAAADGRFG
+LVIGVDREPELGKGRLKAAGAHLVVQDYGTLHLEDRTTTPFDPAWVLRWDHFDPASEGTR
+EVLSTLANGYWGTRGAVPGTRISSVHYPGTYMAGVFNRLTSMVQGRVVETEHMVNIQDWT
+PLVVTPRHGRPLLPGEENLVEYGQEMDLRRGVLSRTMTFEDEQGRRTTVHTRQFTSLANR
+HLAAIELTVVAENWSGDLTVRSKIEGRVANLNVSDDRTLANQHLEPVQAREIDGETVLLE
+TATNQSGIHVAVATRTRQVAPVGHHEPIRRPVDGSDLVVGQDILLHVDEGVPLVLEKVAA
+VATSHDHASASVWESAVKDAQRAQNFRNLLTLHEQRWGTNWDRFSVRIDLAEPYRHHRRS
+TAAETGGEYAPPVVAAGHSAPVGSAVPMGKDGASLRQQLALNLHTFHVLQTAYGRRRDLD
+ASVGARGLHGEGYRGHIFWDEIYVYPMLTLRRPEITRGLLMYRYRRLNEARANAQAAGWA
+GAMYPWQSGADGSEETPTELWNPRSRMWMPDNSHNQRHVSLDIAYSVLRYIEITKDTSFI
+SDYGAEMLVEISRFFMSMTLHNAVTDRYEIHGVMGPDEFHDGYPETPGSGLRNNAYTNVL
+TSWVLAETARLVRWLDTIDDGLPELMEISEEEIERWEEVSTRLTVPFFEEGEEAGILAQF
+EGYQDLLEFDWEAYRAKYGNIGRMDLILQAEGDATNRYKLSKQADTLMLGYLFSSEELDR
+ILRRMGYELPQEAFERMVTYYEARSTHGSTLSRLVHAWVAARTDPDRSWDLFTEALESDL
+SDTQGGTTKEGIHLGLMAGTVDTVIRCYAGLETRDDVVRLHPRMPAQLPGARFTIRFRQQ
+PVVIHMTQREVTVAAGEGMWHDVPMIIAGREHTLSPGEKLTVPLD
+>1_1817
+MSQTLTPAAPQDLNARRHRLRRYRAVIFDMDGVITDTAGVHAQAWKELFDGALPAVGALP
+ANAAVVAADPDVLRPFDAAADYLHHVDGRPREDGVRTFFASRGLRVPEADAPEADAAPEL
+TVLALAERKQGYFEQVLERDGVRVFPEAQDLLERLRAKGVPVALVTSSKNSRAVLTAGGV
+LDFFPVIVDGNTAVERGLPGKPDPAMFWEAARELGVDVADAMVLEDAVSGVKAASDGRFG
+LVIGVDREPELGKGRLKAAGAHLVVQDYGTLHLEDRTTTPFDPAWVLRWDRFDPASEGTR
+EVLCTLANGYWGTRGAVPGTHISSVHYPGTYMAGVFNRLTSMVQGRVVETEHMVNIQDWT
+PLVVTPRHGRPLLPGEENLVEYGQEMDLRRGVLSRTMTFEDEQGRRTTVHTRQFTSLANR
+HLAAIELTVVAENWSGDLTVRSKIEGRVANLNVSDDRTLANQHLEPVQAREIDGETVLLE
+TATNQSGIHVAVATRTRQVAPVGHHEPIRRPVDGSDLVVGQDILLHVDEGVPLVLEKIAA
+VATSHDHANASVWESAVKDVQRAQNFRNLLTLHEQRWGTNWDRFSVRIDLAEPYRHQRRS
+TAAEAGGEYAPPVVDAGHSAPVGSAVPMGKDGASLRQQLALNLHTFHVLQTAYGRRRDLD
+ASVGARGLHGEGYRGHIFWDEIYVYPMLTLRRPEITRGLLMYRYRRLNEARANAQAEGWA
+GAMYPWQSGADGSEETPTELWNPRSRMWMPDNSHNQRHVSLDIAYSVLRYIEITKDTSFI
+SDYGAEMLVEISRFFMSMTLHNAVTDRYEIHGVMGPDEFHDGYPETPGSGLRNNAYTNVL
+TSWVLAETARLVRWLDTIDDGLPELMEISEEEIERWEEVSTRLTVPFFEEGEEAGILAQF
+EGYQDLLEFDWEAYRAKYGNIGRMDLILQAEGDATNRYKLSKQADTLMLGYLFSAEELDR
+ILRRMGYELPEEAFERMVTYYEARSTHGSTLSRLVHAWVSARTDPDRSWDLFTEALESDL
+SDTQGGTTKEGIHLGLMAGTVDTVIRCYAGLETRDDVVRLHPRMPAQLPGARFTIRFRQQ
+PVVIQMTQREVTVAAGEGMWHDVPMIIAGREHTLSPGEKLTVPLG
+>2_591
+MDGVVTDTAGVHAQAWKELFDEALPAVGALPANAAAVAADPEALRPFDAAADYLHHVDGR
+PREDGVRTFFHSRGLRVPEADSPEAATTPQLTVLALAERKQGYFEQVLARDGVRVFPEAQ
+DLLEKLRAKGVPVALVTSSKNSRAVLGAGGVLDFFPVIVDGHTAIERGLPGKPDPAMFWE
+AARELGVDVADAMVLEDAVSGVKAAADGRFGLVIGVDREPDLGKGRLKGAGAHLVVQDYG
+TLCLEQRTTTPFDPAWVLRWDEFDPASEGTREVLCTLANGYWGTRGAVPGTRISDVHYPG
+TYMAGVFNRLTSMVQGRAVDTEHMVNIQDWTPLVVTPRGGRPLLPGEETLVDFSQEMDLR
+RGVLSRTMAFEDEQGRRTSLHTRQFTSLANRHLAAIELTVVAENWTGELTVRSTIEGRVA
+NLNVSDDRTLANQHLEPSQAREIDGETVLLETTTSQSRIDIAVATRTRQMAPVGHHEPIR
+RPVDGSDLRVGQDIRLHVEEGVPLVIEKIAAVATSHDHAQASVWESAVKDVQRANNFRNL
+LTLHEQRWGTNWDRFSVRIDIAEPYRHQRRSAAAAEGAEYAPPVVDAGRSASVGSAVPMG
+KDGASLRQQLALNLHTFHVLQTAYGRRRDLDASVGARGLHGEGYRGHIFWDEIYVYPMLT
+LRRPEITRGILMYRYRRLNEARANAQAEGWAGAMYPWQSGADGSEETPTELWNPRSRMWM
+PDNSHNQRHVSLDIAYSVLRYIEITKDTSFISDYGAEMLVEVSRFFMSMALHNADTDRYE
+IHGVMGPDEFHDGYPETPGSGLRNNAYTNVLTSWVLSETARLVRWLDTLDDGLPEIMEIT
+EEEIERWEDVSARLTVPFFEDGEEAGILAQFEGYQDLKEFDWEAYRAKYGNIGRMDLILQ
+AEGDATNRYKLSKQADTLMLGYLFSAEELDGILRRMGYELPQEAFERMVTYYEARSTHGS
+TLSRLVHAWVAARTDPDRSWDLFTEALESDLSDTQGGTTREGIHLGLMAGTVDTVIRCYA
+GLETREDVVRVDPRMPSQLPGASFTIRFRQQPVQIHMRRSEVTVRAGSGMWHDVPMIIAG
+QEHTLSPGAEITVPLG
+>3_516
+MTQTLTPVDQQDRNARRHRLRRYRAVIFDMDGVITDTAGVHAAAWKELFDQALPAVGALD
+ANRAAVAADPGVLRPFDPEADYLHHVDGRPREDGVRAFFASRGLTVPEVDDADAPVDLTV
+LALAERKQGFFEKVLERDGVRVFPEATDLLEKLRDKGVPVALVTSSKNSRAVLTAGGVLD
+YFPVIVDGHTAIERGLPGKPDPAMFWEAARELGVDVADAMVLEDAVSGVKAAADGRFGLV
+IGVDREHGEGGKPRLKDAGAHIVVKDYGTLRLADRTTAPFDAAWVLRWDHFDPATEGTRE
+VLCTLANGYWGTRGSIPGTRISDVHYPGTYLAGVFNRLTSMVQGRQVETEHMVNMQDWTP
+LQVIPAGGRPLIPGEETLLDYHQEMDLRRGVLSRSMRFEDAQGRITTLHTRQFQSLADRH
+LGAIELTVEAENWSGDLVVRTLVDGRVANLNVSDDRTLANQHLEPVAAREVDGETLLLET
+VTSQSRVHVAVAARTRQMAPKGHHQPIRRPVEGSDLMVGQDIHLHVEQDVPLVLEKVAAV
+ANTHDHALASVDASAIKKVQRAQNFRNLLTLHEQRWGMNWDRFSVRIDLAEEHRNQRRST
+AVLAEGEEFEAPVFEAGRSASVGSAATMGKDGASLRQQLALNLHTYHVLQTAFGKRRDLD
+ASVGARGLHGEGYRGHIFWDEIFVYPMLTLRRPEITRGILMYRYRRLNEARANAQAEGWA
+GAMYPWQSGSDGREETPAELWNPRSHMWMPDNSHNQRHVSLDIAYSVLRYIEITKDASFI
+SDYAAEMLVEISRFFTSMTLHNAETGRYEIHGVMGPDEFHDGYPETPGSGLRNNAYTNVL
+TSWVLSETARLLRWLDTLDDGLPEVMEVTEEEIARWEEIAAKLTVPFFTEGPEAGILAQF
+EGYQDLLEFDWEGYRAKYGNIGRMDLILQSEGDATNRYKLSKQADTLMLPYLFSGAELEQ
+ILGRMGYELHQEALERTVEYYEARSTHGSTLSRLVHAWVAARTDPDRSWDLFTEALESDL
+SDTQGGTTREGIHLGLMAGTVDTVIRCYSGLETRDDVVRLDPRLPRQLPGARFTIRYHQQ
+PVVIHMTQRDVTVTAGEGMWHEVPMVIAGREHTLEPGGEVTVALG
+>4_2037
+MSQTLTPAAPQDLNARRHRLRRYRAVIFDMDGVITDTAGVHAQAWKELFDGALPAVGALP
+ANAAVVAADPDVLRPFDAAADYLHHVDGRPREDGVRTFFASRGLRVPEADAPEADAAPEL
+TVLALAERKQGYFEQVLERDGVRVFPEAQDLLERLRAKGVPVALVTSSKNSRAVLTAGGV
+LDFFPVIVDGNTALERGLPGKPDPAMFWEAARELGVDVADAMVLEDAVSGVKAAADGRFG
+LVIGVDREPELGKGRLKAAGAHLVVQDYGTLHLEDRTTTPFDPAWVLRWDRFDPASEGTR
+EVLCTLANGYWGTRGAVPGTHISSVHYPGTYMAGVFNRLTSMVQGRVVETEHMVNIQDWT
+PLVVTPRHGRPLLPGEENLVEYGQEMDLRRGVLSRTMTFEDEQGRRTTVHTRQFTSLANR
+HLAAIELTVVAENWSGDLTVRSKIEGRVANLNVSDDRTLANQHLEPVQAREIDGETVLLE
+TATNQSGIHVAMATRTRQVAPVGHHEPIRRPVDGSDLVVGQDILLHVDEGVPLVLEKIAA
+VATSHDHANASVWESAVKDVQRAQNFRNLLTLHEQRWGTNWDRFSVRIDLAEPYRHQRRS
+TAAEAGGEYAPPVVDAGHSAPVGSAVPMGKDGASLRQQLALNLHTFHVLQTAYGRRRDLD
+ASVGARGLHGEGYRGHIFWDEIYVYPMLTLRRPEITRGLLMYRYRRLNEARANAQAAGWA
+GAMYPWQSGADGSEETPTELWNPRSRMWMPDNSHNQRHVSLDIAYSVLRYIEITKDTSFI
+SDYGAEMLVEISRFFMSMTLHNAVTDRYEIHGVMGPDEFHDGYPETPGSGLRNNAYTNVL
+TSWVLAETARLVRWLDTIDDGLPELMEISEEEIERWEEVSTRLTVPFFEEGEEAGILAQF
+EGYQDLLEFDWEAYRAKYGNIGRMDLILQAEGDATNRYKLSKQADTLMLGYLFSAEELDR
+ILRRMGYELPQEAFERMVTYYEARSTHGSTLSRLVHAWVAARTDPDRSWDLFTEALESDL
+SDTQGGTTKEGIHLGLMAGTVDTVIRCYAGLETRDDVVRLHPRMPAQLPGARFTIRFRQQ
+PVVIHMTQREVTVAAGEGMWHDVPMIIAGREHTLSPGDKLTVPLD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001702.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001702.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf58d996e25745a96ca2f9915ae7575119c33245
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001702.fa
@@ -0,0 +1,36 @@
+>0_2118
+MSADGMIVAHTRVVSVEQPCRGFRRIVLAGPDLEAASGDLLGLLPPGVADLHALYRGARP
+RRDAYVKLLIPPPGGTSADPDLSAGFRAGFLAIPEEERGWMRTYTVRSAGLVRLDGRQVP
+SLTVDVVLHGDPDDPADPHQGPGLRWARAVQAGDAVNVLVPSAEAPAWSGWRQTGAHRVL
+AVGDETAVPALVSVAEELADPFGGFDGEADLVLELPHDGQAADLIAERLAVPEPWDWRAV
+TELTDRGRVRLHVGRRAPGAPSGSWAHARLAALLGVDPDDAGGPVAPPAASVEREWTVAA
+LEADERPEAYVFLAGESAMVRALRRLSVGPGGVPKKHVSFMGYWREGQAES
+>1_1843
+MSADGMIVAHTRVVSVEQPCRGLRRIVLAGPDLEAASGDLLGLLPPGVADLHALYRGARP
+RRDAYVKLLIPPPGGTSADPDLSAGFRAGFLAIPEEERGWMRTYTVRSAGLVRLDGRQVP
+SLTVDVVLHGDPDDPADPHQGPGLRWARAVQAGDAVNVLVPSAEAPAWSGWRQTGAHRVL
+AVGDETAVPALVSVAEELADPFGGFDGEADLVLELPHDGQAADLIAERLAVPEPWDWRAV
+TELTDRGRVRLHVGRRAPGAPSGSWAHARLAALLGVDPDDAGGPVAPPAASVEREWTVAA
+LEADERPEAYVFLAGESAMVRALRRLSVGPGGVPKKHVSFMGYWRQGQAES
+>2_555
+MSEGMFVAHTRVVSVEQPCRGFRRIVLAGPDLERASPDLMGLLPPGTADLHALYRGSRPR
+RDAYVKVLIPPPGGVSADPDLSAGFRAGFLAIPEAERGWMRTYTVRSAGPVRLDGRPVPS
+LTVDVVLHGDADDPADPHQGPGLRWARAVQAGDAVNVLVPSAEAPAWSAWRQTGARRVLA
+VGDETAVPALVSVAEELADPFGGFDGVADLVLELPHDGQVADLIAERLAVPEPWDWRQVT
+ELADRGRVRLHVGRRAPGAPSGSWAHARLAALLGVDPDDAGGPVAPPAASADREWSVAAL
+AEDERPEAYVFLAGESAMVRALRRLTVGPGGVPKAHVSFMGYWRQGQAES
+>3_483
+MSTEAMFVAHTRVVSTSQPCRGFRRIVLAGEDLEHASADLLGTLPPGVPDLHAIYRGSRP
+RRDAYVKVLVPPPGGVSADPDLSAGFRAGFTAVPEDERGWMRTYTVRSAGRTRVDGREVP
+ALTIDVVLHGDPDDAADPHQGPGLRWARTVAAGESVNVLVPTGEAPAWAGWRDTGARRVL
+AVGDATAAPALLSVAEELADPFGGFDGEADLVLELPADAELADLIAERLAVPEPWDESRP
+LDVAEHGRVRLHVGRTAPGRPVGAWAQARLGALLGLSGTARAGVVGVDGVVEAPPAEGAA
+REWTLADLEPVTGVDRPDTYVFLAGESGMVRALRRLAVDGGDIPKKNVSFMGYWRQGQAE
+S
+>4_2064
+MSADGMFVAHTRVVSVEQPCRGFRRIVLAGPDLEAASRDLLGLLPPGVADLHALYRGARP
+RRDAYVKLLIPPPGGTSADPDLSAGFRAGFLAIPEEERGWMRTYTVRSAGLVRLDGRQVP
+SLTVDVVLHGDPDDPADPHQGPGLRWARAVQAGDAVNVLVPSAEAPAWSGWRQTGAHRVL
+AVGDETAVPALVSVAEELADPFGGFDGEADLVLELPHDGQAADLIAERLAVPEPWDWRAV
+TELADRGRVRLHVGRRAPGAPSGSWAHARLAALLGVDPDDAGGPVAPPAASVEREWTVAA
+LEADERPEAYVFLAGESAMVRALRRLSVGPGGVPKKHVSFMGYWREGQAES
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001725.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001725.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3e9ef78b1ec120a70f7a00a680da16da0032ec57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001725.fa
@@ -0,0 +1,40 @@
+>0_2179
+MSAAPPPPAFGTVLHHRAHGMAPGESISPPLVHASAFHLPGADPDGAPTAPGADVPFQYA
+RWATPTWSALEAALGALEDADVAVVPSGMAAIAAVLLPLLHPGDRALLPADGYGPTRALA
+AEHLTPRGVHVDLVATQGLAHADLSGYDLVLVETPSNPGLRVADLADVAARAHANGRRDG
+AGALVVVDNTLLTPLGQRPLELGADVVVASDTKAVNGHTDALGGHVASRDPQVMARVRGW
+RTLAGGILGTHEAWLIHRGLETLEVRFARMCASAQAVAELAAGHPAVRAVVYPGLADHPD
+AEVVARQMTAAGGLVGLRFADAAAAERFIAAAQYVVPQTSFGGTHTAAERRARWGDDVPD
+GFVRLSVGVEPTAELLADLERAMTAAGGGPTA
+>1_1892
+MSAAPPPPAFGTVLHHRAHGMAPGESISPPLVHASAFHLPGADPDGAPTAPGADVPFQYA
+RWATPTWSALEAALGALEDADVAVVPSGMAAIAAVLLPLLHPGDRALLPADGYGATRALA
+AEHLTPRGVHVDLVATQGLAHADLSGYDLVLVETPSNPGLRVADLADVAARAHANGRRDG
+AGALVVVDNTLLTPLGQRPLELGADVVVASDTKAVNGHTDALGGHVASRDPQVMARVRGW
+RTLAGGILGTHEAWLIHRGLETLEVRFARMCASAQAVAELAAGHPAVRAVVYPGLADHPD
+AEVVARQMTAAGGLVGLRFADAAAAERFIAAAQYVVPQTSFGGTHTAAERRARWGDDVPD
+GFVRLSVGVEPTAELLADLERAMTAAGGGPTA
+>2_487
+MPDSAARHSAARHDVPAPPPFGPVLHHRAHGMAPGDAISPPLVHASAFHLPGAGPDGAPA
+EPAAQGGFQYARWGTPTWAALEAALGVLEDADVAVVPSGMAAIASVLLSHLRPGDRALLP
+SDGYGATRALAAEHLSPIGVHVDLVPTPALASADLSAYDLVFVETPSNPGLRVADLADVA
+ARAHANGRRGGAGALVVVDNTSLTPLGQRPLDLGADVVVASDTKALNGHSDALGGHVASR
+DADVLARVRGWRTLTGAILGTHEAWLIHRGLETLEVRFARMCASALAVAELAAGHSAVRA
+VAYPGLPDHPDAEVVARQTTAAGSVVGLEFADAAAAERFLAAARLVVPQTSFGGTHTSAE
+RRARWGDDVPAGFVRLSVGVEPTAELLADVERALEAAG
+>3_424
+MASPQPPAFGPVLHHRAHGMAPGDAISPPLVHASAFHLPGAGPDGAPVAPGADVAFQYAR
+WGTPTWAALEAALGVLEDADVAVVPSGMAAIAAALLPVLRPGGRALLPSDGYGATRALAA
+EHLVPAGVHVDFVSTPGLADAGFSAYDLVFVETPSNPGLRVADLADVAARAHANGRRDGK
+GALVVVDNTSLTPLGQRPLDLGADVVVASDTKALNGHTDALGGHVASRDPELMTRVRGWR
+TLAGGILGTHEAWLIHRGLETLEVRFARMCASALAVAELAAGHPAVRAVAYPGLPDHPDA
+AIVARQMTAAGGVVGLEFADAAAAERFIGAAAYVVAQTSFGGTHTAAERRARWGDDVPAG
+FVRLSVGVEPTAELLTDLARALDAAAGPA
+>4_2112
+MSAAPPPPAFGTVLHHRAHGMAPGESISPPLVHASAFHLPGADPDGAPTAPGADVPFQYA
+RWATPTWSALEAALGALEDADVAVVPSGMAAIAAVLLPLLHPGDRALLPADGYGPTRALA
+AEHLTPRGVHVDLVATQGLAHADLSGYDLVLVETPSNPGLRVADLADVAARAHANGRRDG
+AGALVVVDNTLLTPLGQRPLELGADVVVASDTKAVNGHTDALGGHVASRDPQVMARVRGW
+RTLAGGILGTHEAWLIHRGLETLEVRFARMCASAQAVAELAAGHPAVRAVVYPGLADHPD
+AEVVARQMTAAGGLVGLRFADAAAAERFIAAAQYVVPQTSFGGTHTAAERRARWGDDVPD
+GFVRLSVGVEPTAELLADLERAMTAAGGGPTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001728.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001728.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e72b57be6604efa8151ede049423f6858fb77c95
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001728.fa
@@ -0,0 +1,21 @@
+>0_2184
+MTPRSLAGLALTVAALMSAFVLMAPTAPGLFVGVLTVGTFGFGPFYGEPSRQLVDRPWRR
+DTRWRDLARRVRTDWLSRQLGAVGWNAAISRRITGRADLRRIRTAAVGSLVSHAASAGLH
+AVAGVALAAVGHPVWGVVAVALGLVVHAWPALLQVSVLGRIDGLQTQIRGDQLLW
+>1_1897
+MTPRSLAGLALTVAALMSAFVLMAPTAPGLFVGVLTVGTFGFGPFYGEPSRQLVDRPWRR
+DTRWRDLARRVRTDWLSRQLGAVGWNAAISRRITGRADLRRIRTAAVGSLVSHAASAGLH
+AVAGVALAAVGHPVWGVVAVALGLVVHAWPALLQVSVLGRIDGLQTQIRGDQLLW
+>2_482
+MTPRSLAGLALAVAALAAAFALMAPTAPGLFVGVLTAGTLGFGPFYGEPTRHLVDRPWRR
+DRRWHELARRVRTDWLSRQLGAAGWNAAIRRRITGRADLRRIRTAAVGSLVSHAASVGLH
+GIAALALAVVGHPGWGLLAVLLGLVVHAWPALLQVAVLGRIDGLQAQLRGDRLLW
+>3_494
+MRIPAVCAAVAVVTLLAWGFRQVVPASPGAYVAVLTAATVGFGPFYGVPTRAVVDLPWRR
+LRRLRALAARAHTWWLARQLRVAGSDARIRRRIRSRADVLAFRREAVGRLLNHGLSAVLH
+AAAGVALAAAGHPLWGVVAVVAGLLVHGWPGLLQVGVLGRVDELQATVQARRGVGGAASA
+GR
+>4_2117
+MTPRSLAGLALTVAALMSAFVLMAPTAPGLFVGVLTVGTFGFGPFYGEPSRQLVDRPWRR
+DTRWRDLARRVRTDWLSRQLGAVGWNAAISRRITGRADLRRIRTAAVGSLVSHAASAGLH
+AVAGVALAAVGHPVWGVVAVALGLVVHAWPALLQVSVLGRIDGLQTQIRGDQLLW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001746.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001746.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7515168744348b2e69eb6c0eb89972447f147b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001746.fa
@@ -0,0 +1,51 @@
+>0_2234
+MRPAPAHAATPSEPPTHAADGAPSDAVTAPGAPAGRSADSAPSGTLPAPGERGGRFQLAG
+GLAANGPGRGTGSWAGPVALTGLLVALAAVVTVLQKSPCLLHGWGAPDVYYAGCYSDWAA
+LYGGRGFAADPWAPFRAGSTFEYPVLMSVVGSVAAWITQALPFSPEQGTVVFWLVNLGFV
+VVLWAVVAVLTVRMAGRRWTDGLMVAVAPGIVLAGTINWDLWAVALLACGMYAWSRGRSL
+TAGVLFGLGAAMKLYPLLILGPLLILAVRSRRWRPFLLAAGGTVAAWAAVNVPLMAVNFQ
+AWSVFFTFSGERGPGLSSVWHAWDVTAAQAGWAFVPEDSLTLLAYGTFAVCCLGIFVLGV
+RVRHTPRLAQLTFLVVAAFVLTNKVYSPQFVVWLIPLLALALPRWRDFWVWQTVEALHFF
+AVWMYLAKGVAETPPQHSMDDSVYVAAILAHILAVLWLCGRVVWEMLHPAEDLVKRDHGG
+HPDADPLAGAYAGPARGRSGRPAAVQA
+>1_1938
+MRPAPAHAATPSEPPTHAADGAPCDAVADPGAPAGRSADSAPSGALPAPGERGGRFQLAG
+GLAANGPGRGTGSWAGPVALTGLLVALAAVVTVLQKSPCLLHGWGAPDVYYAGCYSDWAA
+LYGGRGFAADPWAPFRAGSTFEYPVLMSVVGSVAAWITQALPFSPEQGTVVFWLVNLGFV
+VVLWAVVAVLTVRMAGRRWTDGLMVAVAPGIVLAGTINWDLWAVALLACGMYAWSRGRSL
+TAGVLFGLGAAMKLYPLLILGPLLILAVRSRRWRPFLLAAGGTVAAWAAVNVPLMAVNFQ
+AWSVFFTFSGERGPGLSSVWHAWDVTAAQAGWAFVPEDSLTLLAYGTFAVCCLGIFVLGV
+RVRHTPRLAQLTFLVVAAFVLTNKVYSPQFVVWLIPLLALALPRWRDFWVWQTVEALHFF
+AVWMYLAKGVAETPPQHSMDDSVYVAAILAHMLAVLWLCGRVVWEMLHPAEDLVKRDHGG
+HPDADPLAGAYAGPARGRSGRPAAVQA
+>2_423
+MRPAPAHAATPSEPPTHAVDGPSWAGPDGRAEAGGSAVSAPPSRGPAAVPAPVPAPGDRG
+GRFQLPGGLAANRFTLGGRGGTGSWASPAALAGVLVALAAVVTVLQKAPCLLHGWGAPNV
+YYAGCYSDWAALYGGRGFAADPWAPFQAGSTFEYPVLMSLVGSVGAQLTQWLPFGAEHGT
+LVFWLVNLLFVVGLWAAVAVLTVRMAGRRWSDGLMVAVAPGVILAGTINWDLWAVALLAL
+GMYAWARERPLAAGVLIGLGAAMKIYPLLILGPLLILAVRSRRWRPFLLAAGGAVAAWAA
+VNVPLMVANFEAWSVFFTFSGERGPGLSSVWHAWDVTAAQAGWAFVPEDSLTLLAYGAFA
+VCCLGIFVLGVRVRHTPRLAQLTFLVVAAFVLTNKVYSPQFVIWLIPLVALALPRWRDFW
+AWQTVEALHFFAVWMYLAKGASGSMPQHSMDDSVYVAAILAHMLAVLWLCGRVVWEMLHP
+EDDLVRRDHTDLPGGDPLAGAYRSAQA
+>3_377
+MSSSPAPGAAPDDPPAPAPQARPDVPVGAHRAPRHALTTPPPGSAEGAPSAGSGAVESDE
+ATPEGEVDPRVVPAPGDRGGRFAIPGGLAANGRGRGTGAWAGPVALTALLVALGAIATVL
+QKSPCLLHGWGAPNVYYAGCYSDWAALYGGRGFAADPWAPFQAGSTFEYPVLMSLVASVG
+AQLTQWLPFPASVGTVVFWCVNLLFVVGLWAATAVLTVRTAGRRWTDGLMVAVAPGIILA
+GTVNWDLWAVALMAWGMWVWLRGRPGWAGVLFGLGAATKLYPLLILGPLLILAVRSRRFG
+PFLKATGGAVAAWLAVNLPLMLTHFESWKVFFTFSAERGPGLSSVWHAWDVVAAQAGWAA
+VPDERLGMYAYGAFAVCCLGIFVLGVVAKRPPRLAQLTFLVVAAFVLTNKVYSPQFVIWL
+IPLMALALPRWKDFWVWQTVEALHFFAVWMYLAKGASGSMPQHSMDDSVYVAAILAHMLA
+VLWLCARVVLEILDPDDDLVRGPGGDPARDPEDPSAGPADPGMTGVRPVREAVAAGVGAA
+SAQA
+>4_2176
+MRPAPAHAATPSEPPTHAADGAPCDAVADPGAPAGRSADSAPSGTLPAPGERGGRFQLAG
+GLAANGPGRGTGSWAGPAALTGLLVALAAVVTVLQKSPCLLHGWGAPDVYYAGCYSDWAA
+LYGGRGFAADPWAPFRAGSTFEYPVLMSVVGSVAAWITQALPFSPEQGTVVFWLVNLGFV
+VVLWAVVAVLTVRMAGRRWTDGLMVAVAPGIVLAGTINWDLWAVALLACGMYAWSRGRSL
+TAGMLFGLGAAMKLYPLLILGPLLILAVRSRRWRPFLLAAGGTVAAWAAVNVPLMAVNFQ
+AWSVFFTFSGERGPGLSSVWHAWDVTAAQAGWAFVPEDSLTLLAYGTFAVCCLGIFVLGV
+RVRHTPRLAQLTFLVVAAFVLTNKVYSPQFVVWLIPLLALALPRWRDFWVWQTVEALHFF
+AVWMYLAKGVAETPPQHSMDDSVYVAAILAHMLAVLWLCGRVVWEMLHPAEDLVKRDHGG
+HPDTDPLAGAYAGPARGRSGRPAAVQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001777.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001777.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d17941f8822505ccfa939f57d20f1367878b1527
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001777.fa
@@ -0,0 +1,15 @@
+>0_79
+MRIMTVCLGNICRSPAAEAVLNRKLAEAGLHDVEVTSAGTSDEHVGARPHHLTREVGGEL
+GYEFPTVGVQLSADLVDEADLILVMDEANLADARRLATTDEQRDRIHLMGEFASDADSAG
+VREVPDPYGYPRPQFEEMYRQIEDAADGVVAAIRDGRL
+>1_2043
+MRIMTVCLGNICRSPAAEAVLNRKLAEAGLDDVEVTSAGTSDEHVGARPHHLTREVGGEL
+GYEFPTVGVQLSADLVDDADLILVMDEANLADARRLATTDEQRDRIHLMGEFASDADRAG
+VREVPDPYGYPRPQFEEMYRQIEDAADGVVAAIRDGRL
+>2_294
+MTVCLGNICRSPAAEAVLHRKLAEAGLADEVTVTSAGTADYHVGDRPHELTRAVGGELGY
+AFESVGVHLAAGHLDEADLVLVMDESNLADVRALAATDEQRAKVRMMGEFASDADTAGVL
+EVPDPYGHPRAQFEDMYRQLEDAADGVVAAIRDGRL
+>4_73
+MGVQLSAELVDDADLILVMDEANLADTRRLATTDEQRDRIHLMGEFASDADSAGVREVPD
+PYGYPRPQFEEMYRQIEDAADGVVAAIRDGRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001782.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001782.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d29173ea16645f190a051b8e24be522bff20814d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001782.fa
@@ -0,0 +1,36 @@
+>0_137
+MAPVRRPSRPLALAAAVAVVAGFGAPHAALAQESAPAPDAPEVSSAVEDLSQPATTAEDA
+RWNAARDALAAASADDPFYLPPTTLPSTPGALIRTEPTAFYLDPVRLVQVPAHATRIMYA
+SQDAQGRPIAVTGTVLTPTAPWTGAGERPVIGYAVGTQGAADRCAPSRTLSTGVQYEGVG
+ITSLLSRGHAVVVTDYEGLGTPGTHTYMVREAQAHAVLDAVRAAAQVAGSGVTATAPVAL
+AGYSQGGGAAAAAAELAPDYAPELDLKGAYAGAPPADLVQVAGRIDGGLYAAFLLYAMAG
+QLAAYDVDPATHLNETGLTALDGAAETCLAGSLAYAHLDSATLTHTGQDFPELVRSDAEL
+AGILAEQRIGAQGRRPDVPVMIAHSVTDDVIPYRAGRDLGRRWCAEGARVRFDPLLTPTH
+VGGHVASLPRMGAFLDATLADRWTADSCGWF
+>1_2102
+MAPARRPSRPLALAAAVAVVAGFGAPHAALAQESAPAPDAPEVSSAVADLSQPATTAEDA
+RWNAARDALAAASVDDPFYLPPAVVPATPGALIRSEPAAFYLDPVRLVQVPAHATRIMYA
+SQDAQGRPVAVTGTVLTPTAPWTGGGERPVIGYAVGTQGAADRCAPSRTLSTGAQYEGVG
+ITSLLSRGHAVVVTDYEGLGTPGTHTYMVREAQAHAVLDAVRAAAQVSGSGVTSTAPVAL
+AGYSQGGGAAAAAAELASDYAPELDLKGAYVGAPPADLVQVADRIDGGLYAAFLLYAMAG
+QLAAYDVDPATHLNETGLTALAGAAETCVAGSLAYAHLDSATLTHTGQDFPELVRSDAEL
+AGILAEQRIGAPGRRPDVPVMIAHSVTDDVIPYRTGRDLGRRWCAEGARVRFDPLLTPTH
+VGGHVASLPRMGAFLDATLADRWTADSCGWF
+>2_229
+MSRRRRVRPLSTAAALAVVAGLCAPGALAQDPVPAPDAPEVRSAVEDLSRPASPAEERSW
+DAARAELAEDTAGDAFYRPPATIPARPGTLIRSEPSAFYLDPVKLIRVPARATRILYSSV
+DAQGRPMAVSGTVLTPTAPWTGGGERPVIGYAVGTQGAADRCAPSRTLSTGEQYEGVGIS
+SLLGRGHTVVVTDYEGLGTPGAHTYMVRESQAHAVLDSVRAAAQVDGAEVTASSPVALAG
+YSQGGGASAAAAELAPSYAPELDLKGAYAGAPPADLVQVADRIDGGSYSAFLLYAMSGQL
+AAYDVDPAVYLNEHGRQVLTDAVETCVTDSGEHGSLDSSALTHTGQSFPQLVRTDPQLAG
+ILAEQKLGAEGRRPEVPVMIAHSLTDDVIPYRTGRELGLRWCAEGARVRFDPILTPTHMG
+GYVAALPRMHSFLDAALADRWTPNSCGWF
+>4_145
+MAPSRPLALAAAVAVVAGFGAPHAALAQESAPAPDAPEVSSAVADLSQPATTAEDARWNA
+ARDALAAASADDPFYLPPATVPATPGALIRTEPTAFYLDPVRLVQVPAHATRIMYASQDA
+QGRPIAVTGTVLTPTAPWTGGGERPVIGYAVGTQGAADRCAPSRTLSTGVQYEGVGITSL
+LSRGHAVVVTDYEGLGTPGAHTYMVREAQAHAVLDAVRAAAQVSGSGVAATAPVALAGYS
+QGGGASAAAAELASEYAPELDLKGAYVGAPPADLVQVADRIDGGLYAAFLLYAMAGQLAA
+YDVDPATHLNETGLTALAGAAETCMVGGLAYAHLDSATLTHTGQDFPELVRSDAELAGIL
+AEQRIGAPGRRPDVPVMIAHSVTDDVIPYRTGRDLGRRWCAEGARVRFDPLLTPTHVGGH
+VASLPRMGAFLDATLADRWTADSCGWF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001802.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001802.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a081d2d0cd8d44aec7d94ff05038a7032d8fc051
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001802.fa
@@ -0,0 +1,28 @@
+>0_313
+MKHRSLPLTAALAVAALGLTACGDSGSGGSGSSSAAGGDGSYTVGINQLVSHPALDGAAE
+GFKEAFKDAGLDVTFEEQNAQGEQATVTSIASTFANDGDVDLVAAIATPAAQGTASAVKD
+KPVVFMAVTDPQGAELVASDEAPGGNVTGVSDRNPVKEQLQLLKDVKPDATTVGIVYNSG
+EANSKVQVDQAKEAGKELGLEVKEATITNSSEVQQGVQSLSGVDGIYVPTDNAVVSALET
+VVGYGEEQRVPVISADIDSVERGALGTYGIDYTAHGKQAGEMAVKILKDGAKPAELPVGY
+ADPANLQLVLNPKAAEAYGVEIPAELTDRADQLVEG
+>1_38
+MKHRSLPLTAALAVAALGLTACGDSGSGGSGSSSAAGGDGSYTVGINQLVSHPALDGAAE
+GFKEAFKDAGLDVTFEEQNAQGEQATVTSIASTFANDGDVDLVAAIATPAAQGTASAVKD
+KPVVFMAVTDPQGAELVASDEAPGGNVTGVSDRNPVKEQLQLLKDVKPDATTVGIVYNSG
+EANSKVQVDQAKEAGKELGLEVKEATITNSSEVQQGVQSLSGVDGIYVPTDNAVVSALET
+VVGYGEEQRVPVISADIDSVERGALGTYGIDYTAHGKQAGEMAVKILKDGAKPAELPVGY
+ADPANLQLVLNPKAAEAYGVEIPAELTDRADQLVEG
+>2_4
+MKHRSLTLTAALAVTALGLTACGDSGDAGAGGDEKYTVGINQLVSHPALDGAREGFKEAF
+SDAGLEVTFEEQNAQGEQATVTSIASTFANDGDVDLVAAIATPAAQGTAAAVKDKPVVFM
+AVTDPKGAELVASEEAPGGNVTGVSDRNPVQEQLQLLKDVNPDAKTVGIVYNSGEANSAV
+QVEQAKEAGQELGLEIKEATVTNSSEVQQGVQSLSDVDGIYVPTDNAVVSALETVVGFGE
+ENDIPVISADIDSVDRGALGTYGIDYKAHGKQAGEMAVKILKDGANPGEIAVGFADPANL
+QLVLNPAAAEAYGVEIPAELSDEADRLVEG
+>4_320
+MKHRSLPLTAALAVAALGLTACGDSGSGGSGSSSAAGGDGSYTVGINQLVSHPALDGAAE
+GFKEAFEDAGLDVTFEEQNAQGEQATVTSIASTFANDADVDLVAAIATPAAQGTASAVKD
+KPVVFMAVTDPKGAELVASDEAPGGNVTGVSDRNPVKEQLQLLKDVKPDATTVGIVYNSG
+EANSKVQVDQAKEAGKELGLEVKEATITNSSEVQQGVQSLSGVDGIYVPTDNAVVSALET
+VVGYGKEQRVPVISADIDSVERGALGTYGIDYTAHGKQAGEMAVKILKDGAKPAELPVGY
+ADPANLQLVLNPKAAEAYGVEIPAELTDRADQLVEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001818.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001818.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4f7b6f000dec2d1c457435af4dc50b120611726
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001818.fa
@@ -0,0 +1,40 @@
+>0_553
+MAAAVALVPIGYLFLRTAQGGFGPWLDAVVSPRVGALAATSLALTAVVTALCLVIGVGAA
+WLVTRTDTPGRGLLAVLLALPLAVPSYVAAFTWVSVSDLLPGVEAGRFEGFWAAVTVMTL
+YTYPYVYLPVAAALSRIDPGQEDVARSLGRGPAATLFTVTLAQVRPAIAGGALLVALYVL
+SDFGAVAILRLDTFTRAIFTALEVGFNRQLALTLATVLVLLTVLVLWGESRTRRADDGVR
+SGRTVRRVSVHRLGRSRWVGTGLLAVVTGAALGVPAVSLVRWMGEGTSLSAVRDRWLDAV
+SGSVVLAGAGAALTLALALPIGILAARHPGRVSRIAERAAFLAHGLPGVVVGLSLVFLGV
+SLVPALYQTTWMVAFAYATLFLPLAVTSVAGAVAQSSPALEEAARSLGSSGAEVLRRVTL
+PLALPGVGAGVALVALTAMKELPATLLLRPTGMDTLATRLWNATSVGRYAEAAPYALTLV
+LLAAVPTWVVVHRTGIVAAVRGRSSAPSTPNEVSE
+>1_294
+MAAAVALVPIGYLFLRTAQGGFGPWLDAVVSPRVGALAATSLALTAVVTALCLVIGVGAA
+WLVTRTDTPGRGLLAVLLALPLAVPSYVAAFTWVSVSDLLPGVEAGRFEGFWAAVTVMTL
+YTYPYVYLPVAAALSRIDPGQEDVARSLGRGPAATLFTVTLAQVRPAIAGGALLVALYVL
+SDFGAVAILRLDTFTRAIFTALEVGFNRQLALTLATVLVLLTVLVLWGESRTRRADDGVR
+SGRTVRRVSVHRLGRSRWVGTGLLAVVTGAALGVPAVSLVRWMGEGTSLSAVRDRWLDAV
+SGSVVLAGAGAALTLALALPIGILAARHPGRVSRIAERAAFLAHGLPGVVVGLSLVFLGV
+SLVPALYQTTWMVAFAYATLFLPLAVTSVAGAVAQSSPALEEAARSLGSSGAEVLRRVTL
+PLALPGVGAGVALVALTAMKELPATLLLRPTGMDTLATRLWNATSVGRYAEAAPYALTLV
+LLAAVPTWVVVHRTGIVAAVRGRSSAPSTPNEVSE
+>2_2304
+MAAAVAVVPIGYLFLRTAQGGFGPWLDAVVSPRVGALAATSLALTAVVTALCLVIGVGAA
+WLVTRTDTPGRGLLAVLLALPLAVPSYVAAFTWVSVSDLLPGVEAGRFEGFWAAVTVMTL
+YTYPYVYLPVAAALSRIDPGQEDVARSLGRGPAATLFTVTLAQVRPAIAGGALLVALYVL
+SDFGAVAILRLDTFTRAIFTALEVGFNRQLALTLATVLVLLTVLVLWGESRTRRADDGVR
+SGRTVRRVSVHRLGRSRWVGTGLLAVVTGAALGVPAVSLVRWMGEGTSLSAVRDRWLDAV
+SGSVVLAGAGAALTLALALPIGILAARHPGRVTRIAERAAFLAHGLPGVVVGLSLVFLGV
+SLVPALYQTTWMVAFAYATLFLPLAVTSVAGAVAQSSPALEEAARSLGSSGAEVLRRVTL
+PLALPGVGAGVALVALTAMKELPATLLLRPTGMDTLATRLWNATSVGRYAEAAPYALTLV
+LLAAVPTWVVVHRTGIVAAVRGRSSAPSTPNEVSE
+>4_554
+MAAAVALVPIGYLFLRTAQGGFGPWLDAVVSPRVGALAATSLALTAVVTALCLVIGVGAA
+WLVTRTDTPGRGLLAVLLALPLAVPSYVAAFTWVSVSDLLPGVEAGRFEGFWAAVTVMTL
+YTYPYVYLPVAAALSRIDPGQEDVARSLGRGPAATLFTVTLAQVRPAIAGGALLVALYVL
+SDFGAVAILRLDTFTRAIFTALEVGFNRQLALTLATVLVLLTVLVLWGESRTRRADDGVR
+SGRTVRRVSVHRLGRSRWVGTGLLAVVTGAALGVPAVSLVRWMGEGTSLSAVRDRWLDAV
+SGSVVLAGAGAALTLALALPIGILAARHPGRVSRIAERAAFLAHGLPGVVVGLSLVFLGV
+SLVPALYQTTWMVAFAYATLFLPLAVTSVPGAVAQSSPALEEAARSLGSSGAEVLRRVTL
+PLALPGVGAGVALVALTAMKELPATLLLRPTGMDTLATRLWNATSVGRYAEAAPYALTLV
+LLAAVPTWVVVHRTGIVAAVRGRSSAPSTPNEVSE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001841.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001841.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce4de2c3a7e793aba972044f28505944b244dddc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001841.fa
@@ -0,0 +1,44 @@
+>0_923
+MRPAAPATTGARGPRPSRVAAQPEPEAAVRRGTWASVLITVGSWGVGWLPMTPDSVFSGT
+TLLNPLRVYLPGVLLSTVLLAAGSLLLVRSWLELGRALRGRWEEHGRLVARAAWWWSAPL
+MLALPIFSRDVFSYLQQGRLLASGLDPYSQGVSALPGWFMQGADSIWAESPSPYGPLFLL
+FAETTWRATGGNIELSVTAFRLLALAGLALCLWAVPRLAAVAGRCGPWATWVAVANPLFL
+LYMIAGAHNDALMSGLMLAGILLMVRLPRRRVHALWGIVLIALSVAIKPLTALVLPFVAL
+LLPTGWARFRAADPRLRRRDRLGPWFTTAVISLAVLTILGAGSGLWFGWVPAMLTSGDAA
+FPYAPVGLLGLLLGAVVEAVTPLGARDVAAAFYTVMTVSALGFTAWLALRRRPLDPVFSA
+AAVLVVAVATAPIVQPWYLLWVLPLLACALRPLPWGADHPRWLGWVTALAVLLLTGVGVV
+DQLSVAQWLPVLAVRVFTLVLMLAGIGWIIHRDPVTAPLFPGRRRPPLEVVEPRAAAASP
+TPPEAGVPPDAPPDGPPSTAAHPASSSTRIPQERP
+>1_645
+MRPAAPATTGARGPRPSRVAAQPEPEAAVRRGTWASVLITVGSWGVGWLPMTPDSVFSGT
+TLLNPLRVYLPGVLLSTVLLAAGSLLLVRSWLELGRALRGRWEEHGRLVARAAWWWSAPL
+MLALPIFSRDVFSYLQQGRLLASGLDPYSQGVSALPGWFMQGADSIWAESPSPYGPLFLL
+FAETTWRATGGNIELSVTAFRLLALAGLALCLWAVPRLAAVAGRCGVWATWVAVANPLFL
+LYMIAGAHNDALMSGLMLAGILLMVRPPRRRVHALWGIVLIALSVAIKPLTALVLPFVAL
+LLPTGWARFRAADPRLRRRDRLGPWFTTAVISLAVLTILGAGSGLWFGWVPAMLTSGDAA
+FPYAPVGLLGLLLGAVVEAVTPLGARDVAAAFYTAMTVSALGFTAWLALRRRPLDPVFSA
+AAVLVVAVATAPIVQPWYLLWVLPLLACALRPLPWGADHPRWLGWVTALAVLLLTGVGVV
+DQLSVAQWLPVLAVRVFTLVLMLAGIGWIIHRDPVTAPLFPGRRRPPLEVVEPRAAAASP
+TPPEAGVPPDAPPDGPPSTAAHPASSSTRIPQERP
+>3_1839
+MTLAVDGARRDDGGPSGRGSRALNGPAAAPEPAAAVREGLWAALAVMVASWGVGWQPMTP
+LSVFSGSTLLVPLRTGLAGVLLCAVLLAVGVFALVRAWLRLGRSLQGRWTADGHLAARAA
+LFWSLPLLAALPIFSRDVFSYLQQGRLVALGLDPYEDGISRLPGWFMHGADSIWAESPSP
+YGPLFLLSAEGIWRLTGGQVELSVAAFRLLALAGLALCLWAVPRLAAAAGREPAWAVWVS
+VANPLFLLYMVAGAHNDALMTGLLLAGAALLVRVGRRRVVALAGLVLVALSVAIKPLTAL
+TLPFLAMLLPGGWSRFRVGARRLGRVERIGPWITAAVIAAAVLTVLGAGTGLWFGWVRAM
+TTSGDAAFPYAPVGLLGLGLGWAVDLVSDVPARQAAGWFYSAMTCAALAFTAWMALRRSP
+REPLVASAAVLVVAIVTAPIIQPWYLLWFLPLLACAPRPLPGVVDHPRWLGWVLTALVLA
+LCGVGVVDQISVAQWLPLGLVRVVAALACLVAAWALVRRDPSTAVLFPRRRRPPDETIEP
+RGRPAPRRALAAPTTPTAPVQE
+>4_869
+MRPAAPATTGARRPRPTRAAAQPEPGAAVRRGTWASVLITVGSWGVGWLPMTPDSVFSGT
+TLLNPLRVYLPGVLLSTVLLAAGSLLLVRSWLELGRALRGRWEEHGRLVAHAAWWWSAPL
+MLALPIFSRDVFSYLQQGRLLASGLDPYSQGVSALPGWFMQGADSIWAESPSPYGPLFLL
+FAETTWRATGGSIELSVTAFRLLALAGLALCLWAVPRLAAVAGRCGPWATWVAVANPLFL
+LYMIAGAHNDALMSGLMLAGILLMVRPPRRRVHALWGIVLIALSVAIKPLTALVLPFVAL
+LLPTGWARFRAADPRLRRRDRLGPWFTTAVISLAVLTILGAGSGLWFGWVPAMLTSGDAA
+FPYAPVGLLGLLLGAVVEAVTPLGARDVAAAFYTVMTVSALGFTAWLALRRRPLDPVFSA
+AAVLVVAVATAPIIQPWYLLWVLPLLACALRPLPWGADHPRWLGWVTALAVLLLTGVGVV
+DQLSVAQWLPVLAVRVFTLVLMLAGIGWIIHRDPVTAPLFPGRRRPPLEVVEPRAEAASS
+TPPEAGVPPDAPPDGPPSTAAHPASSSTRIPQERP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001842.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001842.fa
new file mode 100644
index 0000000000000000000000000000000000000000..50bf10e7b53173322dbb8b21d38324915ab77710
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001842.fa
@@ -0,0 +1,16 @@
+>0_957
+MTPDQPETGGATEQGRFGDEPWRPERETRAQRQWRPGTRRRRRSVRALFTSTILMLEAVL
+IFFLGLMLFGMHRDEPGAWWFVAGYSALAVVAVLTCALVRKPVGIAIGWAIQAVLLASGF
+WEYSMFVVGALFALTWAYAVIKGGAMDVENAQRDRLEAAWEAEHGR
+>1_680
+MTPDQPETGGATEQGRFGDESWRPARETRAQRQWRPGTRRRRRSVRALFTSTILMLEAVL
+IFFLGLMLFGMHRDEPGAWWFVAGYSALAVVAVLTCALVRKPVGIAIGWAIQAVLLASGF
+WEYSMFVVGALFALTWAYAVIKGGAMDVENAQRDRLEAAWEAEHGR
+>3_1801
+MSGPTEPRPGRPADERFGAEDWRPARETKTQRAWRPGQRKRARSVRAMFASTVLCLEAVL
+LFFLGMTLFGLNRGADHAPWVAVAFTALAAVAVLDCALVRKPLGVAIGWAIQAVLIASGF
+WEYSMFVIGPLFALTWWYAITKGDQIDRENAARARAQAAWEASHPEEAGPRT
+>4_900
+MTDDQPETGGATEQGRFGDEPWRPARETRAQRQWRPGTRRRRRSVRALFTSTILMLEAVL
+IFFLGLMLFGMHRDEPGAWWFVAGYSALAVVAVLTCALVRKPVGIAIGWAIQAVLLASGF
+WEYSMFVVGALFALTWAYAVIKGGAMDVENAHRDRLEAAWEAEHGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001856.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001856.fa
new file mode 100644
index 0000000000000000000000000000000000000000..360e0e05d64d66a68ccfd036bdb7383ead79d43a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001856.fa
@@ -0,0 +1,36 @@
+>0_1176
+MPALPLGEPVPDDGRLPADVGQRVRAAAGDGAARTFSLYVHVPFCTVRCGYCDFNTYTAV
+DLGPGAGRGDYWESAVAELDFAADVLASSDVPARPLHTVFFGGGTPTLLPAADLVRILQA
+AVDRFGIAPGAEVTTEANPDTITPEYARELAAGGFTRLSLGMQSAVPHVLATLERTHRPE
+SVPAAVAAAREAGLEVSLDLIYGTAGESLADWRATLEAAVALAPDHVSAYSLIVEEGTKL
+GAQVARGEVADVDPDDQADKYLLAEELLGAAGYRWYEVSNWARDPQGSGVHRARHNVAYW
+EDQDWWGIGPGAHSHLAGVRFWNAKHPAAYAQRLATGVTPAVGRERPDADARRLERIMLA
+VRTVDGLPTAELVSETPGEAARIRGAIAELIAAGLLDGRAAVDGRIIPTLEGRLRNDAIV
+RALAGF
+>1_904
+MPALPLGEPVPDDGRLPADVGQRVRAAARDGAARTFSLYVHVPFCTVRCGYCDFNTYTAV
+DFGPGAGRGDYWESAVAELDFAADVLASSDVPARPLHTVFFGGGTPTLLPAADLVRILQA
+AVDRFGIAPGAEVTTEANPDTITPEYARQLAAGGFTRLSLGMQSAMPHVLATLERTHRPE
+SVPAAVAAAREAGLEVSLDLIYGTAGESLADWRATLEAAVVLAPDHVSAYSLIVEEGTKL
+GAQVARGEVADVDPDDQADKYLLAEELLSAAGYRWYEVSNWARDPRGSGVHRARHNVAYW
+EDQDWWGIGPGAHSHLAGVRFWNAKHPAAYAQRLATGVTPAVGRERPDADARRLERIMLA
+VRTVGGLPTAELVSETPGEAARIRGAIAELIAAGLLDGRAAVDGRIIPTLEGRLRNDAIV
+RALAGF
+>2_1635
+MPALPLGAPVPDDGRLPAAVGERVRAAEDGAARTFSLYVHVPFCTVRCGYCDFNTYTAVD
+LGPGAGRGDYWESAVAELGFAQRALEASAVPARPLHTVFFGGGTPTLLPAADLVRILREA
+VERFGIVPGAEVTTEANPDTVTPEYARELAAGGFTRLSLGMQSAAPHVLATLERTHRPES
+VPAAVAAARDAGLEVSLDLIYGTAGESLQDWRDTLHAAVELAPDHVSAYSLIVEEGTKLG
+AQVARGEVADVDPDDQADKYLLAEEVLGAAGFRWYEVSNWAHDPEGAGVHRARHNVAYWE
+DQDWWGIGPGAHSHVAGVRFWNAKHPAAYAQRLATGVTPAVGREQPDAAARRLERIMLAA
+RTSEGLPAAEAVSDEPGDGERVRRVTAELIAAGLLDGRAALAGRLVPTLQGRLRNDAIVR
+ALAGF
+>4_1134
+MPALPLGEPVPDDGRLPADVGQRVRAAARDGAARTFSLYVHVPFCTVRCGYCDFNTYTAV
+DLGPGAGRGDYWESAVAELDFAADVLASSDVPARPLHTVFFGGGTPTLLPAADLVRILQA
+AVDRFGIAPGAEVTTEANPDTITPEYARQLAAGGFTRLSLGMQSAMPHVLATLERTHRPE
+SVPAAVAAAREAGLEVSLDLIYGTAGESLADWRATLEAAVALAPDHVSAYSLIVEEGTKL
+GAQVARGEVADVDPDDQADKYLLAEELLGAAGYRWYEVSNWARDPQGSGVHRARHNVAYW
+EDQDWWGIGPGAHSHLAGVRFWNAKHPAAYAQRLATGVTPAVGRERPDADARRLERIMLA
+VRTVGGLPTAELVSETPGEAARIRGAIAELIAAGLLDGRAAVDGRIVPTLEGRLLNDAIV
+RALAGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001869.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001869.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09c297df084c1450ab232005b79b34df98d2e457
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001869.fa
@@ -0,0 +1,16 @@
+>0_1401
+MARVKRAVNAHKKRRTMLERASGYRGQRSRLYRKAKEQMLHSFTYNYQHRHKRKGDFRRL
+WITRINAAARANGMTYNRFMQGLKLAGVEVDRRMLAEIAVSDAATFAVLVKTAREALPAD
+VNAPAVSR
+>1_1142
+MARVKRAVNAHKKRRTMLERASGYRGQRSRLYRKAKEQMLHSFTYNYQHRHKRKGDFRRL
+WITRINAAARANGMTYNRFMQGLKLAGVEVDRRMLAEIAVSDAATFAVLVQTAREALPAD
+VNAPAASR
+>3_1324
+MARVKRAVNAHKKRRTALNRASGYRGQRSRLYRKAKEQLLHSFTYNYQHRHKRKGDFRRL
+WITRINAAARANGMTYNRFMQGLKLAGIEVDRRMLAEIAVSDAATFTALVETARTALPAD
+VNAPAASR
+>4_1350
+MARVKRAVNAHKKRRTMLERASGYRGQRSRLYRKAKEQMLHSFTYNYQHRHKRKGDFRRL
+WITRINAAARANGMTYNRFMQGLKLAGVEVDRRMLAEIAVSDAATFAVLVKTAREALPAD
+VNAPAASR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001872.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001872.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cd4ea10afe12dad71c123d599fb59721feab2157
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001872.fa
@@ -0,0 +1,36 @@
+>0_1425
+MVGSFLVAIVTGTGALLLPASYQGRAPTPLEAAFTATSATTVTGLGVVDTQTFWTPLGQL
+VILTLIKLGGLGVMTFTSLLGLVILRRLGLTQRLDAAASTRAEGIGDLPRVLRALILYST
+AVEASVALLLSLRFWLGAGMSPGQALWQGVFHAVSAFNNAGFALFSDNLMGFVSDPFICL
+PIAAAIILGGLGLPVVLTLRRDLRRPERWNLTVRLVLVGTAVLLVGGTLMYLVLEWSNPR
+TLGGLDPASRVLAAFFQSVTTRTAGFNTLDYGQMHPVTLFATDVLMFIGGGPAGTASGVK
+ITTASVLLFIVLAEIRGEGAVHAFGRRLSRTTHREAITVIMLSATAIAVATMALMGLSSF
+TTDQILFECVSAFSTVGLSTGITAQLPPAAQGILMLLMFVGRIGPATVAGSLALTDRTRH
+FEYPKERPLIG
+>1_1166
+MVGSFLVAIVTGTGALLLPASYQGRAPTPLEAAFTATSATTVTGLGVVDTQTFWTPLGQL
+VILTLIKLGGLGVMTFTSLLGLVILRRLGLTQRLDAAASTRAEGIGDLPRVLRALILYST
+AVEASVALLLSLRFWLGAGMSPGQALWQGVFHAVSAFNNAGFALFSDNLMGFVSDPFICL
+PIAAAIILGGLGLPVVLTLRRDLRRPERWNLTVRLVLVGTAVLLVGGTLMYLVLEWSNPR
+TLGGLDPASRVLAAFFQSVTTRTAGFNTLDYGQMHPVTLFATDVLMFIGGGPAGTASGVK
+ITTASVLLFIVLAEIRGEGAVHAFGRRLSRTTHREAITVIMLSATAIAVATMALMGLSSF
+TTDQILFECVSAFSTVGLSTGITAQLPPAAQGILMLLMFVGRIGPATVAGSLALTDRTRH
+FEYPKERPLIG
+>3_1299
+MVGSFLVAIVTGTGALLLPASYQGRAPTPLEAAFTATSATTVTGLGVVDTQTFWTPLGQV
+VILALIKLGGLGVMTFTSLLGLVILRRLGLTQRLDAAASTRAEGIGDLPRVLQALILYST
+AVEASVALLLSLRFWLGAGMSPGQALWQGIFHAVSAFNNAGFALFSDNLMGFVSDPFICL
+PIAAAIILGGLGLPVVLTLRRHLRRPERWNLTVRLVLVGTAVLLVGGTLMYLVLEWSNPR
+TLGGLDPASRVLAAFFQSVTTRTAGFNTLDYGQMHPVTLFGTDVLMFIGGGPAGTASGVK
+ITTASVLLFIVLAEIRGEGAVHAFGRRLSRTTHREAITVIMLSATAIAVATMAIMGLSSF
+TTDQILFECVSAFGTVGLSTGITAQLPPTAQGILMLLMFVGRIGPATVAGSLALTDRTRH
+FEYPKERPLIG
+>4_1374
+MVGSFLVAIVTGTGALLLPASYQGRAPTPLEAAFTATSATTVTGLGVVDTQTFWTPLGQL
+VILTLIKLGGLGVMTFTSLLGLVILRRLGLTQRLDAAASTRAEGIGDLPRVLRALILYST
+AVEASVALLLSLRFWLGAGMSPGQALWQGVFHAVSAFNNAGFALFSDNLMGFVSDPFICL
+PIAAAIILGGLGLPVVLTLRRDLRRPERWNLTVRLVLVGTAVLLVGGTLMYLVLEWSNPR
+TLGGLDPASRVLAAFFQSVTTRTAGFNTLDYGQMHPVTLFATDVLMFIGGGPAGTASGVK
+ITTASVLLFIVLAEIRGEGAVHAFGRRLSRTTHREAITVIMLSATAIAVATMALMGLSSF
+TTDQILFECVSAFSTVGLSTGITAQLPPAAQGILMLLMFVGRIGPATVAGSLALTDRTRH
+FEYPKERPLIG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001882.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001882.fa
new file mode 100644
index 0000000000000000000000000000000000000000..982b61bd3491e9b8467ab9bdcd63c1494c158061
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001882.fa
@@ -0,0 +1,16 @@
+>0_1615
+MTGHDHPRPESISAAVDEQMLADFLNQHLLGSRSGVKAFRAAEQTWAGTPQEAALRRLGD
+AVQDDQDRLEALIGELGLRTPLVDRAAGAAAEVGGRLNPVNALRTRGSGWTQIELDLLQG
+MLQAKSAMWDVLEQLAPHLPAVDAAEMQALRQRTADQQREVQRITSATLEGRFLAG
+>1_1330
+MTGHEHPRPESTSAAVDEQMLEDFPNQHLLGSRSGVKAFRAAEQTWAGTPQEAALRRLGD
+AVQDDQDRLEALIGELGLRTPLVDRAAGAAAEVGGRLNPVNALRTRGSGWTQIELDLLQG
+MLQAKSAMWHVLEQLAPHLPAVDAAEMQALRQRAADQQREVQRITSATLEGRFLAG
+>2_1200
+MTGHEHPRPEPLSAAVDEQMLEDFLNQHLLGSRSGVKAFRAAEQTWAGTPQEDALRRLGD
+AVQDDQERLEALIGELGLRTPLVDRAAGAAAEVGGRLNPVNALRTRGSGWTQIELDLLQG
+MLQAKAAMWHVLEALAPHEPVLDAGEMAALYERAQDQQRAVQRIAEDTLLERFLR
+>4_1545
+MTGHEHPRPESTSAAVDEQMLADFLNQHLLGSRSGVKAFRAAEQTWAGTPQEAALRRLGD
+AVQDDQDRLEALIGELGLRTPLVDRAAGAAAEVGGRLNPVNALRTRGSGWTQIELDLLQG
+MLQAKSAMWHVLEQLAPHLPAVDAAEMHALRQRTGDQQREVQRITSATLEGRFLAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001887.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001887.fa
new file mode 100644
index 0000000000000000000000000000000000000000..baaf958801035cd34504bb33974a7817f22a7241
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001887.fa
@@ -0,0 +1,32 @@
+>0_1746
+MFNPTAPVNEQLALYSDLFMLIAALVYAAAFILFTIDMATASATIRRLEADLAAQRGQVR
+TAPARETVGAAVGGSTAVGASASDAARPTGAAERGVDADGALVDEDMDYTGGGRRPVANV
+AVAVLAVGWALHAFAVVARGLAASRVPWGNLYEFMTTGALVITTVYLLFLLRKDLRFVGT
+FVTGIVVAMMCAATMGFPTPVGHLQPPLQTPWLVIHVSIAVLASSLFALTAAMSVLQLVQ
+DRAEKRAAAGERSWAFLRLVPAAQGLENWSYRLNAVGFVMWTFTLIAGAIWAEAAWGRYW
+NWDTKEVWTFVIWVVYAAYLHARATRGWTGARAAWLSIVGFACIVFNYTIVNTYFPGLHS
+YAGLPG
+>1_1454
+MFNPTAPVNEQLALYSDLFMLIAALVYAAAFILFTIDMATASATIRRLEADLAAQRGQVR
+TAPARETVGVAVGGSTAVGASDSDTARPAAAEPGVDADDDLVDEDMDYTGGGRRPVANVA
+VAVLAVGWALHAFAVVARGLAAYRVPWGNLYEFMTTGALVITTVYLLFLLRKDLRFVGTF
+VTGIVVAMMCAATMGFPTPVGHLQPPLQTPWLVIHVSIAVLASSLFALTAAMSMLQLLQD
+RAEKRAAAGEPTWSFLCLVPSSDSLENWSFRINAVGFVMWTFTLIAGAIWAEAAWGRYWN
+WDTKEVWTFVIWVVYAAYLHARATRGWTGARAAWLSIVGFLCIVFNYTIVNTYFPGLHSY
+AGLPS
+>3_984
+MFNPTAPVNEQLAYYSDLFMFIAALVYAGAFILFAVDMATASATIRRLEAELDAQAGVDR
+DVASRVRERQLAGVGAGSGVGTPAGGAHALGTDASASSAGRSDAELVDDDMDYTGAGRRP
+VANVAVAVLAVGWALHAFAVVARGVAASRVPWGNLYEFMTTGALVIVTVYLAFLIRKDLR
+FVGTFVSGLVVAMMCAATMGFPTPVGHLQPPLQSGWLVIHVSIAVLSSSLFALSAAMSAL
+QLLQGSAEKRAAAGRRGWSFLRLVPSARALENWSYRINAVGFVMWTFTLIAGAIWAEAAW
+GRYWNWDTKEVWTFVIWVVYAAYLHARATRGWTGTRAAWLSITGFLCIVFNYTIVNTFFP
+GLHSYAGLPA
+>4_1668
+MFNPTAPVNEQLALYSDLFMLIAALVYAAAFILFTIDMATASATIRRLEADLAAQRGQVR
+TAPARETVGVAVGGSTAVGASDSDTARPAAAEPGVDADDDLVDEDMDYTGGGRRPVANVA
+VAVLAVGWALHAFAVVARGLAASRVPWGNLYEFMTTGALVITTVYLLFLLRKDLRFVGTF
+VTGIVVAMMCAATMGFPTPVGHLQPPLQTPWLVIHVSIAVLASSLFALTAAMSVLQLLQD
+RAEKRAAAGERSWAFLRLVPAAQGLENWSYRLNAVGFVMWTFTLIAGAIWAEAAWGRYWN
+WDTKEVWTFVIWVVYAAYLHARATRGWTGARAAWLSIVGFLCIVFNYTIVNTYFPGLHSY
+AGLPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001888.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001888.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00d12a564269fc94d83d49dfd39d276b716ec38c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001888.fa
@@ -0,0 +1,36 @@
+>0_1777
+MPLGLTWLDVLLIVALAMLLVQGHRRGLWVVLGNLVGLVGGAAIAFYALPEVAEFVTAPQ
+WRWAALIATLVLLVAAGQYVGAAIGEAIRLRVNLPALRLVDRLLGALAAGLAGALVLWLV
+AFSIAASGSTAVTREVNRSQVITALDTVMPDSLLAWAARSRSAVADLDVLPELELPAPVP
+ESDDGVRAAPAPAATPGLPSAASSPSDTATSAPSASATPEEPDDAAAASSSTAAAPSATT
+TAPASSTSTAAPSTPAASSASAAVVRLTGTAAQCNQVQSGSGVAVAPDRVLTNAHVVLGV
+DAPTVTDRARGVHAARIVHLDTAHDLAVLAVDDANLPVMPVGAELTGGASASVLGYPDGG
+PFASTPATVQAVGEVPLGDVLTGAASMVDVYTLAADIRHGYSGGPVVDTAGNLAGLVFAR
+APGSDAVGYALTADTIAPVVAAAPGMTATVPSGDCVPGG
+>1_1485
+MPLGLTWLDVLLIVALAMLLVQGHRRGLWVVLGNLVGLVGGAAIAFYALPEVAKFVTAPQ
+WRWAALIATLVVLVAAGQYVGAAIGEAIRLRVNLPALRLVDRLLGALATGLAGALVLWLV
+AFSIAASGSTAVTREVTRSRVIAALDTVMPDSLLAWAARSRSAVADLDVLPELELPAPVP
+ETDDGVRAAPAPAATPGLPSAASSPSAPPATSAAATPEEPDDAAAASSSTSAAPSATTTA
+PASSTSTAAPSTPAASSASAAVVRLTGTAAQCNQVQSGSGVAVAPDRVLTNAHVVLGVDA
+PTVTDRARGVHAARIVHLDTAHDLAVLAVDDADLPVMPVGAELTGGASASVLGYPDGGPF
+ASTPATVQAVGEVPLGDVLTGAASMVDVYTLAADIRHGYSGGPVVDAAGNLAGLVFARAP
+GSDAVGYALTADTIAPVVAAAPGMTATVPSGDCVPGG
+>2_1011
+MPLSLTWLDAVLLVLLVVLLVQGHRRGLWVVLGNLVGLVGGAAIAFYAMPEVAQLVTAPQ
+WRWAALLATLVLLVAAGQYVGAAIGEAIRLRVNLPALRLVDRILGALAAGVAGALVVWLV
+SFSMSTAGSGAVTREVARSQVIAAIDRVLPDSALAWAARSRSAVADLDMLPELRLPEPVP
+VPDDDGGVRAAPPTSSSPATTPARPAEPEDAAPASGGSATPEERPPAPPTTAPPPFPTPR
+PRRPPRPPPPRPPRPPIPSPRRPTPPNPPPPRPSRTAVPAEAAVVRLTGTAAQCGQVQSG
+SGVAVAPDRVLTNAHVVLGVDAPTVTDAQRGVHDARIVHLDTARDLAVLALDGADLPVMP
+LGAELVGGESALVMGHPDGGPFASTPATVQAVGEVPLGDVVTGAASMVDVYTLAADIRHG
+YSGGPVVDAAGSLAGLVFARAPGADPVGYALSADSIAPAVAAAPGMSATVPSGDCIPGA
+>4_1699
+MPLGLTWLDVLLIVALAMLLVQGHRRGLWVVLGNLVGLVGGAAIAFYALPEVAKFVTAPQ
+WRWAALIATLVVLVAAGQYVGAAIGEAIRLRVNLPALRLVDRLLGALATGLAGALVLWLV
+AFSIAASGSTAVTREVTRSRVIAALDTVMPDSLLAWAARSRSAVADLDVLPELELPAPVP
+ETDDGVRAAPAPAATPGLPSAASSPSAPPATSAAATPEEPDDAAAASSSTSAAPSATTTA
+PASSTSTAAPSTPAASSASAAVVRLTGTAAQCNQVQSGSGVAVAPDRVLTNAHVVLGVDA
+PTVTDRARGVHAARIVHLDTAHDLAVLAVDDADLPVMPVGAELTGGASASVLGYPDGGPF
+ASTPATVQAVGEVPLGDVLTGAASMVDVYTLAADIRHGYSGGPVVDAAGNLAGLVFARAP
+GSDAVGYALTADTIAPVVAAAPGMTATVPSGDCVPGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001898.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001898.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c6d4a5b0ddda6321982c77d38e7a83083688859
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001898.fa
@@ -0,0 +1,24 @@
+>0_1853
+MTTTTPLPPLDGATTPAQARERFRAGLVRPTSGIADGYAQANLVSIPQDHAYDVLLFAQR
+NPQALPLLGVFEAGEVNGPALDGDVRTDVPQYVVYRDGVETDRPTDLLDVWRDDLVTFVI
+GCSFTFESALVAEGIRMAHQDAGVNVPMYRTTRRCASAGRLSGPLVVSMRPLPADRVADA
+VRITSRYPAVHGAPVHVGDPAGLGITDLSAPDFGDAVEVPQGHLPVFWACGVTPQAAIME
+SRPPLAITHAPGHMLITDLPDRMFQVP
+>1_1560
+MTTTTPLPPLDAATTPAQARERFRAGLVRPTSGIADGYAQANLVSIPQDHAYDVLLFAQR
+NPKALPLLGVFEAGEVNGPALDGDVRTDVPQYVVYRNGVETDRPTDLLDVWRDDLVTFVI
+GCSFTFESALVAEGIRMAHQDAGVNVPMYRTTRRCASAGRLSGPLVVSMRPIPADRVADA
+VRITSRYPAVHGAPVHVGDPAGLGITDLSAPDFGDAVEVPQGHLPVFWACGVTPQAAIME
+SRPPLAITHAPGHMLITDLPDRMFQVP
+>3_863
+MTALHGGTGPAEARERFRAGLVRPTAGIADGFAQANLMVVPQDLAWDVLLFAQRNPKALP
+LLGVLEAGEVRGPAVDGDVRTDVPQYVVYEDGVPVGRPTDLLEVWRDDLVTFLIGCSFTF
+ESALVAEGIRIAHQDAGVNVPMYRTTRRCVPAGRLSGPLVVSMRPIPADRVADAVRITSR
+YPSVHGAPVHVGDPAALGIADLSAPDFGDAVEVPPGHLPVFWACGVTPQAAVMESRPPLA
+ISHAPGHMLITDIPDRTFQIP
+>4_1774
+MTTTTPLPPLDGATTPAQARERFRAGLVRPTSGIADGYAQANLVSIPQDHAYDVLLFAQR
+NPQALPLLGVFEAGEVNGPALDGDVRTDVPQYVVYRDGVETDRPTDLLDVWRDDLVTFVI
+GCSFTFESALVAEGIRMAHQDAGVNVPMYRTTRRCASAGRLSGPLVVSMRPLPADRVADA
+VRITSRYPAVHGAPVHVGDPAGLGITDLSAPDFGDAVEVPQGHLPVFWACGVTPQAAIME
+SRPPLAITHAPGHMLITDLPDRMFQVP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001921.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001921.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a9e512686ad58a9cf87a24f801d56706d776580
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001921.fa
@@ -0,0 +1,36 @@
+>0_2036
+MHRPSRSSTAAPAFAPSAPAPTAAPAFAPSVRSQVPPFTVMSILGRVAALRAAGHDVVSL
+CAGEPGGGAPPAVDAAAAAVHASGRALTYTPALGLPELRAAVAGHYRRWYGLDVRPEQVA
+ITTGSSGAFMLGFLAAFSPGDRVLLPRPGYPAYRNILTALGVEVVDVDVDAGTRYQPTVA
+HLEAALAEGPVAGLVLASPANPTGTMVSAAELAELARWCEERGVRLVSDEIYHGIVHTDG
+QGPGACAWRTSRTALVVSSFSKYWGMPGWRLGWMLMPDDLATAVDGLAGSVALCPPAAAQ
+EAAVHAFTEESYAFCAEQAGGFTATRGVVLAALPRLAWADAAPADGAFYLWARLASGMLA
+EFGSAVGYCAALLEEAGVALTPGDDFDAVHGPESVRLSFAAGPDAVHEALERIAAWHAAR
+GLA
+>1_1754
+MRRPSRSSTADPASTAAPAPTATPAFAPSARSQVPPFTVMSILGRVAELRAAGHDVVSLC
+AGEPGGGAPPAVDAAAAAVHASGRAFTYTPALGLPELRTAVAGHYRRWYGLDVRPEQVAI
+TTGSSGAFMLGFLAAFPPGDRVLLPRPGYPAYRNILTALGVEVVDVDVDAGTRYQPTVAH
+LEAALAEGPVAGLVLASPANPTGTMVSADELAELARWCEERGVRLVSDEIYHGIVHTDGE
+GLGACAWRTSRTALVVSSFSKYWGMPGWRLGWMLMPDDLAAAVDGLAGSVALCPPAAAQE
+AAVHAFSEESYAFCAEQAGGFTATRGVVLAALPRLGWADAAPADGAFYLWARLAPGMLAE
+FGSAVGYCAALLEEAGVALTPGDDFDAVHGPESVRLSFAAGPDAVHEALERIAAWHAARG
+LA
+>2_664
+MDPQPRLAPGTHHDVAALAPASPVADAAPEDQAAPGDPASPVAPAFAPSARSQVPPFTVM
+TILGRVAELRAAGRDVISLCAGEPGGGAPPTVSAAAAEVHASGSPLTYTPALGLPELRAA
+VAGHYRRWYGIDVRPEQVAITTGSSGAFMLGFLAAFSPGDRVVLPRPGYPAYRNILAALG
+CEVVEVGVDASTRYQPTVAHLEAALAEGPVAGLVLASPSNPTGTMVDADELAALASWCEA
+HGVRLVSDEIYHGIVHPRSGDDDGGPAGGGAAGGAPGASGAEGSRFPHESVGACAWATSR
+TAMVISSFSKYWGMPGWRLGWMLMPEDLAGAIDGLAGSVALCPPAAAQRAAVEAFGEDAY
+AFCEEQAGGFTATRGVVLAALPRLGWADAAPADGAFYLWARLGERQLAEFGDAVAYCTAL
+LEEAGVALTPGADFDGVHGGEFVRMSYAADAGAVAEALERIAAWHAARGLA
+>4_1977
+MRRPSRSSTADPASTAAPAPTATPAFAPSARSQVPPFTVMSILGRVAELRAAGHDVVSLC
+AGEPGGGAPPAVDAAAAAVHASGRAFTYTPALGLPELRTAVAGHYRRWYGLDVRPEQVAI
+TTGSSGAFMLGFLAAFPPGDRVLLPRPGYPAYRNILTALGVEVVDVDVDAGTRYQPTVAH
+LEAALAEGPVAGLVLASPANPTGTMVSADELAELARWCEERGVRLVSDEIYHGIVHTDGE
+GLGACAWRTSRTALVVSSFSKYWGMPGWRLGWMLMPDDLAAAVDGLAGSVALCPPAAAQE
+AAVHAFSEESYAFCAEQAGGFTATRGVVLAALPRLGWADAAPADGAFYLWARLAPGMLAE
+FGSAVGYCAALLEEAGVALTPGDDFDAVHGPESVRLSFAAGPDAVHEALERIAAWHAGRG
+LA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001924.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001924.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ecbcf0cfe492729ca28ac02eaa706a4b60fcd676
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001924.fa
@@ -0,0 +1,19 @@
+>0_2047
+MAFAALSRSARLAGLSAAALLALTACGGQDSSDADASASTTAPASASAQGAESSSASASS
+LSAAPADYEAGTCFTAPLGARDLSSFETTDCEGAHTAEYLWAVPAVAEGEEADPAAAQTC
+TAQAQRLSEEKEDQLNGAVLTSSELGNYGTDEKHCVVYGVSGEWEGQIVDPEITLETASA
+DA
+>1_1765
+MAFAALSRSARLAGLSAAALLALTACGGQDSSDADASASTTAPASASAQGVESSSASASS
+LSAAPADYEAGTCFTAPLGARDLSSFETTDCEGAHTAEYLWAVPAVAEGEEADPAAAQTC
+TAQAQRLSEEKEDQLNGAVLTSSELGNYGTDEKHCVVYGVSGEWEGQIVDPEITLETASA
+DA
+>2_652
+MAFAALSRSARLAGLSAAALLALTACGGQDSSDADASASTTAPASESAQSSESSSASASS
+LSAAPADYEAGTCFTAPLGARDLSTFETTDCEGAHIAEYLWAVPAVAEGEEADPAAAQTC
+TAQAQRLSEEKEDQLNGAVLTSSELGNYGTDEKHCVVYGVSGEWEGQIVDPELTLDEAIA
+ASAGA
+>4_1988
+MAFAALSRSARLAGLSAAALLALTACGGQDSSDADASASASAQGSESSSASASSLSAAPA
+DYAAGTCFTAPLGARDLSSFETTDCEGAHTAEYLWAVPAVAEGEEADPAAAQTCTAQAQR
+LSEEKEDQLNGAVLTSSELGNYGTDEKHCVVYGVSGEWEGQIVDPEITLETASADA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001933.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001933.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cfc7b765cfcf3fa47faee4b1c43ac24209a3bdb9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001933.fa
@@ -0,0 +1,13 @@
+>0_2127
+MSESTGFSAAEQAAIAERAQELRAQRGGKKKADALQDLLATIEEMPEPDRALAVAVHRIV
+TEVAPELDPRT
+>1_1852
+MSESTGFSAAEQAAIAERAQELRAQRGGRKKADALQDLLVKIEEMPEQDRAMAVGVHRIV
+TEAAPELEPRTWYGMPAYARGTDVLVFLQVSSKFGVRYTTLG
+>2_543
+MSESTGFSAAEKAAMAERAEELRAQRGGKKKADALQDLMEKIEAMPEQDRALAVAVHQIV
+TEVAPELEPRTWYGMPAYARGKDVLVFLQVSSKFDVRYTTLGFNESAALDDGPMWPTAYA
+LTALNDDVRARIADLVRRAVG
+>4_2073
+MTESTGFSAAEQAAIAERAQELRAQRGGKKKADALQDLLAKIEEMPEQDRAMAVAVHRIV
+TEAAPELEPRTWYGMPAYARGTDVLVFLQVSSKFGVRYTTLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001946.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001946.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5c28aaf5d14f62905fd02b4050784556c7d6819
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001946.fa
@@ -0,0 +1,32 @@
+>0_2202
+MSNDPRPTPWAVGWEERPWAAGPDDAGLRSRSARVRASGPYRAALPARIARLGLDLPSDL
+ATEVEEATAAVVRFDAEISHALPGLTGEIAPIDAVLLRTESASSSQIEHITAGARALALA
+TLGERTRPNATLVAANVRAMGAASRLAADLDEPALLAAHRALMDGQEHARPGAYRDAQGW
+IGGGAPTPHTAQFVPPHPERLRAGMDDLFAYLRRTDVPALVQAAIAHAQFETIHPFADGN
+GRTGRVLVHAVLHRAGAITRMGVPLSAGLLTDTAGYFDALTAYRDGDPAPIVRRFAQAAL
+AAVGNGRELVADLDEALTGWRERLTARRDAAVWRALAVIIAQPAVTVDHLAQALGVSRPA
+AQRAVDQLVEAGALQAASAQRRNRVWLATEVLACLDEFAARAGRRG
+>1_1908
+MSNDPRPTPWAVGWEERPWAAGPDDAGLRSRSARVRAAGPYRAALPARIARLGLDLPSDL
+ATEVEEATAAVVRFDAEISHALPGLTGEIAPIDAVLLRTESASSSQIEHITAGARALALA
+TLGERTRPNAALVAANVRAMGAASRLAADLEEPALLAAHRALMDGQEHARPGAYRDAQGW
+IGGGAPTPHTAQFVPPHPERLRAGMDDLFAYLRRTDVPALVQAAIAHAQFETIHPFADGN
+GRTGRVLVHAVLHRAGAITRMGVPLSAGLLTDTAGYFDALTAYRDGDPAPIVRRFAQAAL
+AAVGNGRELVADLDEALTGWRERLTARRDAAVWRALAVIIAQPAVTVDHLAQALGVSRPA
+AQRAVDQLVEAGALQAVSAQRRNRVWLATEVLTCLDEFAARAGRRG
+>3_411
+MGMDQTISTAVGWEERPWTADPDDAGALTRRARVRASGPYRAALPARIARLGLDLPSDLA
+TAVEEATAAVVRFDAEISHALPGLTGEIAPIDAVLLRTESASSSQIEHITAGARALALAT
+LGERTRPNAALVAANVKAMGAASRLAADLDEPALLAAHRALMDGQEHARPGAYRDAQGWI
+GGGAPTPHTAQFVPPHPERLHAEMDDLFAYLRRTDVPALVQAAIAHAQFETIHPFADGNG
+RTGRVLVHAVLYRAGAITRMGVPLSAGLLTDTAGYFDALTAYRDGDPEPIVRRFAMAALA
+AVGNGRELVADLDEALTGWRERLTARRDAAVWRALAVIIAQPAVTVDHLAQVLGVSRPAA
+QRAVDQLVEAGALQAVSAQRRNRVWLATEVLACLDEFAARAGRRG
+>4_2134
+MSNDPRPTPWAVGWEQRPWTADPHDAGLRSRRARVRAAGPYRAALPARIARLGLDLPSDL
+ATEVEEATAAVVRFDAEITHALPGFTGEIAPIDAVLLRTESASSSQIEHISAGARALALA
+TLGERTRPNAALVAANVRAMGAASRLAADLDEPALLAAHRALMDGQEHARPGAYRDAQGW
+IGGGAPTPHTAQFVPPHPERLRAGMDDLFAYLRRTDVPALVQAAIAHAQFETIHPFADGN
+GRTGRVLVHAVLHRAGAITRMGVPLSAGLLTDTAGYFDALTAYRDGDPAPIVRRFAQAAL
+AAVGNGRELVADLDEALTGWRERLTARRDAAVWRALAVIIAQPAVTVDHLAQALGVSRPA
+AQRAVDQLVEAGALQAASAQRRNRVWLATEVLACLDEFAARAGRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001955.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001955.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3eeeebc8db68ec03796dd5f33afcf523cab77ce7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001955.fa
@@ -0,0 +1,20 @@
+>1_241
+MQKNTSTLSRRKVTAGIAWSVPAVAAVAAAPFAAASPTGCAAVTTGTAEKFPGGGHPDGI
+KQAYGFTITITNTSPTPVYVDPGTVTVEFKGHPTRSGEALLYTASPCEGGTRLAAMDPEL
+LLQPGESETYYYVVNQTGNSAQESGCVKGKLQLALPKGAPEGADLCNDGVVDFSNCFDTT
+PPTAGC
+>2_2365
+MQQNTSSLSRRKVTTGIAWSVPAVVAVAAAPFAAASPSCITSSAGRVVKYPGNSSGYDLK
+QAYGFTVTVTNPTRGKLRVTAKSVSLILDKKVLRGSLLIYTADPCAGGVPVDPNSDLLVL
+EPGESQTLFLVANNTGNSANTSGCIYAKLGVKLVDGSVPVANLCDEHDVVEACFDETSPT
+ATC
+>3_2246
+MQTTPKTVNRRTVSAGIAWSVPAVAAVAAAPFAAASPTGCVNVTSGTAEKFPGGGHPDGI
+KQAYGFTITITNTSPTPVYVNPGTVTVVFGGHTTRNGEARLYTASPCRGGKRLAAMDPEL
+LLQPGQSKTYYYVVNNTGNSAQESGCVKGKLQLALPKGAPEGADLCNGGIVEFKNCFETT
+PPTAGC
+>4_511
+MQKNTSTLSRRKVTAGIAWSVPAVAAVAAAPFAAASPTGCAAVTTGTAEKFPGGGHPDGI
+KQAYGFTITITNTSPTPVYVDPGTVTVVFGGHTTRNGEARLYTANPCRGGKRLAAMDPAL
+LLQSGQSKTYYYVVNNTGNSANESGCVEGKLQLALPKGAPEGADLCNDGVVEFSNCFETT
+PPTARC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001963.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001963.fa
new file mode 100644
index 0000000000000000000000000000000000000000..22d2fd2288deb148b7d46b8032b88493dec27020
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001963.fa
@@ -0,0 +1,36 @@
+>1_1647
+MAWSEGLRDTLRFWPLVLVAFVHAVASCSLLGLSFQQASEAQEVDRHLQRWEQLGAASLR
+GFYLAAPGHLEGGGAAPGESQQEPPEPDLSADSKAASADDGRRAAALLALLEDPHRTAYT
+MDPYGDRFGDDLPGALLVTEDFFAGSGLAAAMSPTGQSPHRDADGTAAPYAVLGSDSSAK
+DPYALTVGGVLPPPTRVQFQDAMIPVTGRLAPGATALDPMMGSVPLDGAVLVVVPPSALA
+SLYPPDALEAILLRTIVLGQDAVPALDAAGRALETDALVVNAEPLTPQSSALLQSLSASS
+RTLLVLFGAAVLGAVVSLFGVLGVLARALAPTWRIAAMVGAARWQAAVRIIVPVLFAWVL
+PAAVGLTAGASALPGPPPTGLTSTALIAVMAIGAVATLSSWRALAATFGRRPRRHRPTKE
+TARASSKSTTWTRRSSPAGRRCPSSGGPLCWFRPVRCTPSPGLPGPGNPPCCGSSRAWTP
+RTRVASCSGANLSRSRGAGAGTGIGTSGAASSCRTSPSWSTPPHWRT
+>2_835
+MAWSDGLRDTLRFWPLVLVAFVHAVASCSLLGLSFQQASEAQEIGRHLQRWEQLGAASLR
+GFYLAGPGDLEGGGAAPGDSQQEPPEPDFSAGSRADSADDGRRTAALLALLADPHRTAYT
+MDPYGDRFGDDLPGALLVTEDFFAGSGLDETMSPTGQSSHRDAGGTAAPYAVLGSDSSAK
+DPYALTAGGVLPPTTRVQFQDAMIPVTGRLAPGATALDPMMGSVPLDEAVLVVVPPSMLA
+SLYPPDALEALLLRTIVLGQDAVPALDAAGRALETDALLVTAEPLTPQSSALLQSLSASS
+RTLLVLFGAAVLGAVVSLFGVLGVLARALAPTWRIAAMVGAARWQAAVRIIVPVLFAWVL
+PAAVGLTAGASALPGPPSTGLTSTALIAVMAIGAVATLSSWRALAATFGRRPRRRPTKET
+A
+>3_773
+MSTRALAVALADGLNDAARFWPLILGAFLHAVVSCLLLGLSFQQVSEAGEVSAHLHRWEQ
+QGAASLHGIYLAGVSARPAAEGMTPTLQDGLDETPVLDPEGEAGAASRTAGLLSLLEDPQ
+RLAYTMDPYGDRFGDDLPGAMVVTEDFLRATGVDDSMTPTGAAVPRDSDGAPAPYAVLGS
+ASRAKDPHALLVDGAPPPTTRVQFQGAMIPVVGRLAQGATTLDPMMGSVPLDEAALIVLP
+AASLPGLYPAEELEALLLRTVVLGPDAVPVLDASARPFESERLLVAAQPLTAESSGLLQS
+LTSSSRTLVLLFGSAVLGAVVSLFGALGVLARALAPTWRIAAMVGAARWQAAVRIAVPVL
+LAWVLPAGLGLLAGAAAVPGPSPTALAAVALALVLGVGCWAALSSWRALAATFGPRRRTP
+TRTTTKEAA
+>4_709
+MMAAMRAVADGLRDLFDTPGLLFLSLLHTTVASVVFGLALGVAGGVTTALEVLEDAESSG
+LVTARILDPAVTTDLHPRAVDTVSRAFAAHVDGVDPRAFLVTDAIGIEDPRLQGAVIATP
+GLAREFGAAAAVSPAEGVYFAPAAITSGGPGGTVYVGSTPHSYAGPLPGDAAAPRADGSL
+WPLGESPVIVTSTTTMAGLIEPAQLAAVYGSVVARQDAASEVRAALDVLEDETGVVAELA
+PIASARSPIAREARGAALMVTAYTAGLASAVVTVVSLLTTVTRRLTPTWLAHLTVGAPRR
+LIRLRIATSVAAVWGIPAVLGSLLGLGIASEAGGLRPAPAVVVVGLAVVLAIAAACTRHP
+LRQLHRAVRTAALVEGTV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001964.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001964.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c8752095117deda6cb17e5acd2e1226b7d4c0994
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001964.fa
@@ -0,0 +1,28 @@
+>1_1648
+MTGRGLRTLGLLVTRAVLLVALCGLALSLVGSLSVHHRQYFGAAECGPAVWDVGIGGGGE
+VWSVAEAATTGRNLTLMASGADPGVRHLAGPAAPCLAGIDVPTLESLRAARGFLLREGSI
+LADRAARSGELAGRPVALASAADWRGLPSDGVIQPTPAFDNAAAYVGFLVGDPADLDGFL
+QNLRTAGLEVDAAPAPSAMTASLGTPVLGVTSSLTGLTLMSVTAFWVLTLRAGDRPSLRV
+LRLLGVSPLRAAVSRARVSLVPFLGAAGISAALWQGMVLTGAVTEPSPLVASGVILVVLL
+GDAVLVSATHVVALWMRAPR
+>2_834
+MGSRTLGLLVTRAVLLAAVCGLALSLVGSMSVHQRQYFGAAECGDAVWDVGIGGSGEVWS
+ATEAALTGRNLTLMANGADPRVRHLTGPTAPCLAGVDEQMLNSLRMERGFLVREGSVLAD
+RAAGEGELAGRPVALASSARWRGLPSDGVIQPTPAFDNAAAYVGFLVGDPADLDGFLQNL
+RTAGLEVDAAPAPTAMTASLGTPVLGVTSSLTGLTLMSVTAFWVLTLRAGERPSLRVLRL
+LGVSPLRAAVSRARVSLVPFLGAAGISAALWQGMVLTGAVTEPSPLVASGVILVVLLGDA
+VLVAATHVVSLWMRAPR
+>3_772
+MGTGLLGRLLTRAVLLTALCGLALGIAGSMSVHRQQYFGAEGCGEAVWDVNVVGADRVWS
+ALEAALTGRDLTAMVTGADPGLFHVAGPAASCLTGVDEQTLGSTREAGGFLVRGGGMLAA
+RAGQDGELATRPAVVVPPDRWRGLPSVSLIQPTPVFDDSSSYVGFLVGDAGEIEDLVRRL
+RESGLEVEAAPAATAAEAALRAPTLSATTGLTALTCLSVTAFWALTLHAGQRPAVRVLRL
+LGVSPLRAAASRWAASAVPFAAAAALAAALWLGMILSGTLTTPAPGTAALIVAGAILADA
+ALVALTHVGALWMKRVPR
+>4_710
+MTRMLVSRFLLLLITLGTAALLASYVGVEKEDRWRMDGTVYEISAFPAGEAWPMIRTSLT
+GPDSGSAATSTSPHVTALAGRPALDVLPDGVAPTAVVPSTSPFAARAAAGELSWPDVDRV
+VVRDLSSAPDRATEADLLVPFLSTDSSSLAGVIGGSPAQVDELVQSLRRAGVVVDVVPLP
+PPWEAAMRRSVHVPLLAVIAGFALLGAQVVWRTTLRSRLLPAVTSHRLVGASPLRAARLG
+VRPAMLAWATAAASAGGVWLVAWPRWDAEIGLTGDTALLWSAVLVVDAILILGTTLSTLW
+VRRAHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001966.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001966.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e2786af4b7460d01a1280ea51f17be880f08bda9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001966.fa
@@ -0,0 +1,24 @@
+>1_1651
+MLEFVDTAAQAVSRITDGATVLIGGFGNAGQPMELIDALLESGATGLTVVNNNAGQADAG
+LALLIKERRVAKIICSFPRHSDSWHFDEAYRAGEIELELVPQGNLAERLRAGGAGIGGFF
+TPTGYGTQLAEGKEVREIDGTHYVLEAPIRGDVALIKAYAADRHGNLVYRKTARNFGPVM
+AAAAATTIVQVDEVREEPIDPEHVVTPGIYTDTVVRIDTESGEKERAERAALAEGRPKPC
+AATTTAAEPAAEGK
+>2_831
+MLEFVDTAAQAVSQVTDGATVLIGGFGNAGQPMELIDALLESGATGLTVVNNNAGQADAG
+LALLIKERRVAKIICSFPRQSDSWHFDEAYRAGEIELELVPQGNLAERLRAGGAGIGGFF
+TPTGYGTQLAEGKEVREIDGRHYVLESPIRGDVALIKAYAADRHGNLVYRKTARNFGPIM
+AAAAEHTVVQVDEVRDEPIDPEHVITPGIYTDVIVRIETESGAKEREEREALAAGKPKPC
+AATKTAAEKAAEGK
+>3_769
+MLEFVETAAEAVAQVRDGQTVLIGGFGNAGQPMELIDALLESGATGLTVVNNNAGQADAG
+LALLIKERRVAKIICSFPRQSDSWHFDEAYRAGEIELELVPQGNLAERLRAGGAGIGGFF
+TPTGYGTQLAEGKEVREIDGRHYVLESPIKGDVALIKAYAADRHGNLVYRKTARNFGPVM
+AAAAATTIVQVDEISEEPLNPEHVITPSIYVDTVVRIQTESGVKEREALAAGKPKPCLAT
+ETAAGQAAEGK
+>4_1869
+MLEFVDTAAQAVSRITDGATVLIGGFGNAGQPMELIDALLESGATGLTVVNNNAGQADAG
+LALLIKERRVAKIICSFPRQSDSWHFDEAYRAGEIELELVPQGNLAERLRAGGAGIGGFF
+TPTGYGTQLAEGKEVREIDGTHYVLEAPIRGDVALIKAYAADRHGNLVYRKTARNFGPVM
+AAAAATTIVQVDEVREEPIDPEHVVTPGIYTDTVVRIDTESGEKERAERAALAEGRPKPC
+AATTTAAEPAAEGK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001997.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001997.fa
new file mode 100644
index 0000000000000000000000000000000000000000..315d77c0101e77b3ec9a9d0845ab0640980ac999
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001997.fa
@@ -0,0 +1,18 @@
+>0_198
+MSVHAPSRATASTPVRDEDRHSLDVVFRGVGRTFPTADGPRVVLRDVDLTVAPGEVLAVI
+GASGCGKSTLLRAVAGLDPDFDGELLIDGSPVRPYDERTAVGFQEPRLLPWRTLRRNVEL
+GLPRELDRAAGRDRVQELLELVGLAPFAEHRPREVSGGMAQRASLARALARRPGVLLLDE
+PFGALDALTRLKMQDLLLDVHAATGTTVLLITHDVEEALQLADRVLLLARDVPAPDGGAR
+PGATVGRIVDVPGARPRDRADARLARLRAELLEGLGVESHAR
+>2_190
+MAHPAPPSDPPLAASPATAVDTAADDGAPATSRLSVRLEDVGRTFDTPHGAHTVLRDVSL
+TIAPGEVLAILGASGSGKSTLLRSVGGLDTAHSGRVLLGESPVTAYDPRVAVGFQEPRLL
+PWRTIRRNIALGLPRGTSRAEGEARVERLMELVGLTHAAERRPREVSGGMAQRASLARAL
+ARRPEVLLLDEPFGALDALTRMKMQDLLLDVHAKVSTTVLLVTHDVDEALQLADRILLLG
+PDEDGRPGATVQRLLTVPGERPRERGDDALAHLRTELFAGLGVDLHSAAGAAR
+>3_128
+MSVHAPSRATASTPVRGEDRNSLDVVFRGVGRTFPTADGPRVVLRDVDLTVAPGEVLAVI
+GASGCGKSTLLRAVAGLDPDFDGELLIDGSPVRPYDERTAVGFQEPRLLPWRTLRRNVEL
+GLPRGLDHAAGRDRVQELLELVGLAPFAEHRPREVSGGMAQRASLARALARRPGVLLLDE
+PFGALDALTRLKMQDLLLDVHAATGTTVLLITHDVEEALQLADRVLLLARDVPAPDGAAR
+PGATVGRIVDVPGARPRDRADARLAQLRSELLEGLGVESHAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002000.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002000.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2698b4c019253dda2eb8814d5858ebdead426f5d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002000.fa
@@ -0,0 +1,9 @@
+>0_354
+MKTIRTIAFILFLCATAFGVMLTLHYLPIPEILPSEITSWVPARDTADATWLIVGMVVAV
+VATAVGFSASHKAVERETQVTS
+>2_2531
+MKTIRTIAFILFLCATAFGVMLTLHYLPIPEILPSEVTSWVPARDTADATWLIVGMVVAV
+VATAVGFSASHKAVERETQVTS
+>4_361
+MKTIRTIAFILFLCATAFGVMLTLHYLPIPEILPSEITSWVPARDTADATWLIVGMVVAV
+VATAVGFSASHKAVERETQVTS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002002.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002002.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a964d52cf80d8344db0a810d8cb3e8701efce20c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002002.fa
@@ -0,0 +1,21 @@
+>0_394
+MGTMPTSSALPRTTPDDVPERLLVLPAAQDVAGTPYAHARRLAEQAVADVGGTVVAEGDA
+SATALLMVRPIPVEALAAALAAHPHVSWVQFPFAGIEPFIPLVRSRPDIVWTSAKGTYAP
+PVAEHALLLTLALLRDLPARVRATTWGPSSGRTLNGLNAVVVGGGGIAQEYVRLLKTWDV
+HVTAVRRRAGDVPGADRTVTTDSLDEVLPGAQVVMIAAAATDETRGLFDADRLALLNEDA
+VLVNIARGTLVDTDAVVRALAAGRLHGYGTDVTDPEPLPEGHPLWTEERALITPHTADTP
+QMCVPLLHARVERNLRARAAGTELEGLVDAEGGY
+>1_123
+MGTMPTSSALPRTRPDDVPERLLVLPAAQDVAGTPYAHARRLAEQAVADVGGAAVAEGDT
+SATALLMVRPIPVDALAAALTAHPHVSWVQLPFAGIEPFVPLVRSRPDIVWTSAKGTYAP
+PVAEHALLLTLALLRDLPARVRATTWGPSSGRTLNGLNAVVVGGGGIAQEYIRLLKTWDV
+HVTAVRRRAGDVPGADRTVTTDRLDEVLPGAQVVMIAAAATEETRGMFDADRLALLDEDA
+VLVNVARGALVDTDAVVQTLAAGRLHGYGTDVTDPEPLPDGHPLWTEERALITPHTADTP
+EMCVPLLHARVERNLRARAAGTELEGLVDAEGGY
+>4_397
+MGTMPTTSTLPRTRPDDVPERLLILPAAQDVADTPYAHARRLAEQAVADVGGTAVAEGDT
+SATALLMVRPIPVDALAAALAAHPHVSWVQLPFAGIEPFVPLVRSRPDIVWTSAKGTYAP
+PVAEHALLLTLALLRDLPARVRATTWGPSSGRTLNGLTAVVVGGGGIAQEYIRLLKTWDV
+HVTAVRRRAGDVPGADRTVTTDRLDEVLPGAQVVMIAAAATEETRGMFDADRLALLDEDA
+VLVNVARGALVDTDAVVQTLAAGRLHGYGTDVTDPEPLPDGHPLWTEERALITPHTADTP
+EMCVPLLHARVERNLRARAAGTELEGLVDAEGGY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002016.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002016.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5c7b954ec4b51e31043a30698a53711964e467a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002016.fa
@@ -0,0 +1,15 @@
+>0_741
+MRLFLAIRPPRAALDHLEPALDGVRDRAGRALCWTEPEQRHLTLAFHPEVPAGAVDDVVA
+VAGRIAAGHGPLDLHLAGAGEFSHRTLWVGVGGQVRELGALLAEPWLADDDGRDRRRAHL
+TVARASGAAPRPRGRRRGEPRPPAPATVLLAEAVHALAVYRGPEWTADEVEVVASRLGEG
+RSGGPLHEVLATVPLRG
+>1_480
+MRLFLAIRPPRAVLDHLEPAFDGVRDRAGRALCWTEPEQRHLTLAFHPEVPAGAVDDVVA
+VAGRIAAGHGPLDLHLAGAGEFSHRTLWVGVGGQVRELGALLAEPWLADDDGRDRRRAHL
+TVAPVSGAALRPRGRRRGEPRPPAPATVLLAEAVRALAVYRGPEWTADEVEVVASRLGEG
+RSGGPLHEVLATVPLRG
+>4_705
+MRLFLAIRPPRAALDHLEPALDGVRDRAGRALCWTEPEQRHLTLAFHPEVPAGAVDDVVA
+VAGRIAAGHGPLDLHLAGAGEFSHRTLWVGVGGQVRELGALLAEPWLADDDGRDRRRAHL
+TVAPVSGAALRPRGRRRGEPRPPAPATVLLAEAVRALAVYRGPEWTADEVEVVASRLGEG
+RSGGPLHEVLATVPLRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002018.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002018.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d933afd027531c24dcf52f6919e0a179782ac317
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002018.fa
@@ -0,0 +1,18 @@
+>0_799
+MEVVILPDAAALGRHGADAVAAHVAARPEAVLGLATGSSPLPVYDELARRVRDGELSLRS
+CRAFLLDEYVGLPAGHPESYRTVIEREFVARTDIAPEAVHGPDGGAADVPGACAAYEEAL
+REAGGVDVQLLGVGTDGHIAFNEPGSSLASRTRIKVLAEQTRRDNARFFDGDLDQVPTHC
+LTQGVGTILDARHLVLLARGEGKAEAVRQLVEGPVSARWPVTALQLHPHVTVLVDDAAAG
+RLELAGDYRHMWEAKPRWQGL
+>1_540
+MEVVILPDAAALGRHGADAVAAHVAARPEAVLGLATGSSPLPVYDELARRVRDGELSLRS
+CRAFLLDEYVGLPAGHPESYRTVIEREFVARTDIAPEAVHGPDGGAADVPGACAAYEEAL
+REAGGVDVQLLGVGTDGHIAFNEPGSSLASRTRIKVLAEQTRRDNARFFDGDLDQVPTHC
+LTQGVGTILDARHLVLLARGEGKAEAVRQLVEGPVSARWPVTALQLHPHVTVLVDDAAAG
+RLELAGDYRHMWEAKPRWQGL
+>4_768
+MEVVILPDAAALGRHGADAVAAHVAARPEAVLGLATGSSPLPVYDELARRVRDGELSLRS
+CRAFLLDEYVGLPAGHLESYRTVIEREFVARTDIAPEAVHGPDGGAADVPGACAAYEEAL
+REAGGVDVQLLGVGTDGHIAFNEPGSSLASRTRIKVLAEQTRRDNARFFDGDLDQVPTHC
+LTQGVGTILDARHLVLLARGEGKAEAVRQLVEGPVSARWPVTALQLHPHVTVLVDEAAAG
+RLELAGEYRHMWEAKPSWQGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002023.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002023.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7959665e490d01a58e7a804bca7017d1c86174cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002023.fa
@@ -0,0 +1,17 @@
+>0_914
+MGPRAVPLAIIGDLHLDLTDAQWVNSLYAVLLAALLLSTGNLADRWGRKRLFLTGSALIA
+PYPRRPAAQHPLCCYRFGVHFHATAGVRGRLLPLASHRRLVAMNDMHSLGRLIAPAQERN
+GWSLSDLAARADRAGYDMSHASFARLKSTPVTSIKGENITMLALVLRAPVAHVVTAALES
+IGVELDSALHPSVLDVVQESPDLSTYDQELLAAVLRVMLDRRRTDHHDERDHADQDQDRE
+RGTAERGGARGGDAGAEQKTAAADAPADFDLAAHPDFELTRDRQAREWGDVGEENQDPGD
+EAGA
+>2_1896
+MLNHSHTPAEADPVNEPDSLQALAKAVLDKQQASARQIAEYARKAGKRLSYTTLNHMAAG
+TYRSTPTAETLQTLAWLAGVSETVAFHAAGLPVPGPPLADELPPGSDNLSPKSRAAVIQM
+LRVLIDLESNHDEHDHPDQHQDRERGTAERGGARGGDASAEQKTAAAGAPADFDLAAHPD
+FELTRDRQAREWGDAGEESQDHGEGESA
+>2_2053
+MERIPTSLQELAQLVLDVQGTSARQVALRAEAKGLKLKDTTLNQMKSGSYKFVPREETLR
+ALADLAGVSVETAFHAAGLTAPGPPLADELPPGSDNLSPKSRAAVIQMLRVLIDLESNDD
+HHTTNPTPAHERAQHDDGADAAPDRRRGAGRGDARPGQKTAAAGGTPARSLNPADYDLAA
+HPSFELTRDRQDREWGDVGEENQDPDQEDRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002031.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002031.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd9237ce384a9b63740eda83b6a4e26f8445a247
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002031.fa
@@ -0,0 +1,21 @@
+>0_1342
+MSHPTVFFYPRPRVDVAEVPAASHAGAVLLTDTIHATGLASSLREALGSWTKPLAEHHAS
+KVLLDLAMTLAVGGEVARDTDLLRCEPGLFGDVASAPTISRTLTTLAEDAPAVMTAIARA
+RRTAREQAWALAGEHSPAEGTSAKTPLVIDLDATLINVHSEKEQAAPTFKRGFGYHPLYA
+FLDHGSEGTGEPLAIHLRPGNAGSNTASDHIAVTRLALAQLPPALLGRGGRGSKKVLIRT
+DGAGGPKDFAGWLERQRLAYSVGFTLPANTPDLLERIDEAKAWTPAYDTDTEGIRDGAWV
+AELTGLLDLPGWPPECG
+>1_1083
+MSHPTVFFYPRPRVDVAEVPAASHAGAVLLTDTIHATGLASSLREALGSWTKPLAEHHAS
+KVLLDLAMTLAVGGEVARDTDLLRCEPGLFGDVASAPTISRTLTTLAEDAPAVMTAIARA
+RRTAREQAWALAGEHSPAEGTSAKTPLVIDLDATLINVHSEKEQAAPTFKRGFGYHPLYA
+FLDHGSEGTGEPLAIHLRPGNAGSNTASDHIAVTRLALAQLPPALLGRGGRGSKKVLIRT
+DGAGGPKDFAGWLERQRLAYSVGFTLPANTPDLLERIDEAKAWTPAYDTDTEGIRDGAWV
+AELTGLLDLPGWPPECG
+>4_1292
+MSHPTVFFYPRPRVDVAEVPAASHAGAVLLTDTIHATGLASSLREALGSWTKPLAEHHAS
+KVLLDLAMTLAVGGEVARDTDLLRCEPGLFGDVASAPTISRTLTTLAEDAPAVMTAIARA
+RRTAREQAWALAGEHSPAEGTSAKTPLVIDLDATLINVHSEKEQAAPTFKRGFGYHPLYA
+FLDHGSEGTGEPLAIHLRPGNAGSNTASDHIAVTRLALAQLPPALLGRGGRGSKKVLIRT
+DGAGGPKDFAGWLERQRLAYSVGFTLPANTPDLLERIDEAKAWTPAYDTDTEGIRDGAWV
+AELTGLLDLPGWPPECG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002039.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002039.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d80c79c964a49e668bbedd21a22e03718e2a0c79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002039.fa
@@ -0,0 +1,28 @@
+>0_1563
+MTGIPFLLVFILAIALMIVMISRWKIHPFLSIMVVAFALGIIGGIPLVKSTGAEGEAPVK
+GIADVIGEGFSGIFTSIGIVIILGTLIGLILERTGGAFRIADALVRVVGKRYPVLAMQLM
+GWVVSIPVFCDSGFVILNPIRKALARRTGASPVAMTVALAAGLYTSHVFIPPTPGPIAAA
+QNLGIGDHLLLVIGLGVLVSIPALLVAYLYALYIGKRVTSPEETGTEDADELEAAYDALR
+RSYGRMPGTAASFAPIIAPILLMALGSLASVLKWTGPAGDFARFLGTPMIALAVGTLCAV
+GLLFSVRRGETFYDLTEETLRVVGPILFITAAGGVLGRVIAATDLVTFIESNAAQLSVIG
+LFFPFLVSAVLKTAQGSSTVALTTTSAMVFPMMPALGFETPVASALVVMAIAAGAMTVSH
+ANDSYFWVVTNFSGMTPSQGYRTQTMVTLLMGLTSIVFIWLLGLVLV
+>0_1978
+MSTDTRTATPHTRGSTRRGDRPMPVPRDPHPLVALLPLLALIALASASTLSWKIGMILPI
+VAGIVVAAVIGRLTGHSWKDMEAAMTDGVSRAMPAVFILLIIGMIIGTWISGGVIPTLIH
+YGLEFINPTFFLPMACLVTAFISLVLGSSFTSIATVGLAFMAIGGGMGVPLPIVAGAVIS
+GAFFGDKLSPLSDTTNVAPAMVGEGLFDHIRHMLWDTIPGLVLSAGLFWFIGLRVSPGGD
+VDTAARDTIQAGLSGQFTIHPALLLVVLATLVIIALRVPAIPALVLVAALGGLSGVLVQG
+RPVGAVLKDATTGYTSTTGQESVDSLLTNGGVASMFMTIGLVIVATALGGLLERTGVFRA
+LIDPLVRRIRRTGSLIAATVMASFLVGFSTGAQFLAVILPARGMVDAYRRMGLSPLNLSR
+VVEAAGTVGINLVPWGVPAVFAAGVFGLEPMEFIPWILFAFIVPALNVLYGYTGLSIKRI
+TPAEVDPEDQRD
+>2_1254
+MTGIPFLLVFILAVALMIVMISRWKIHPFLSIMVVAFALGIIGGIPLVKSTGAEGEEPVK
+GIADVIGEGFSGIFTSIGIVIILGTLIGLILERTGGAFRIADALVRVVGKRYPVLAMQLM
+GWVVSIPVFCDSGFVILNPIRKALARRTGASPVAMTVALAAGLYTSHVFIPPTPGPIAAA
+QNLGIGDHLLLVIGLGVLVSIPALLVAYLYALYIGKRVSSPEETGTEDADELEAAYDALR
+RSYGRMPGTAASFAPIIAPILLMALGSLASVLKWTGPAGDFARFLGTPMIALAVGTLCAV
+GLLFSVRRGETFYDLTEETLRVVGPILFITAAGGVLGRVIAATDLVTFIESNAAQLSVIG
+LFFPFLVSAVLKTAQGSSTVALTTTSAMVFPMMPALGFETPVASALVVMAIAAGAMTVSH
+ANDSYFWVVTNFSGMTPSQGYRTQTMVTLLMGLTSIVFIWVLGLVLV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002042.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002042.fa
new file mode 100644
index 0000000000000000000000000000000000000000..76eadf2e37d05e559691f6c31337a28985cc38bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002042.fa
@@ -0,0 +1,18 @@
+>0_1568
+MKTPVLSATDMRIVEQVLDMGDGYVLDFSNRTFADFFADLDVEIEPEDSGLSKAKRLRAF
+FRSASTSECARVLHALLEYRGEQDGDDESASIDKYRAIVSRLEGVAVPLSAAPVAPEVLT
+LAYVRELSDKAERRLAASDLEGAITVSRTLVEAVLEQLEIRLTGQSGNYAGDLQRQYKAV
+AKILRIDDKDDQVDEGFKQIARGLVQIVNGLAAIRNMASDGHARHVQPQARHARVAVNSA
+KTVASFLVEVYLAKRTGPTSPAAVRSGG
+>1_353
+MASTSPTLLPFRIDSLATSLFAKETGFSGPHLHDFFARYTDMLGPYRWNGSPSRWQIFQT
+GLHSLPLPQQRAVLLELCSYDGEFKNGRPPEGELTRLRGMLLSAGTPGAHAAQESLQKLE
+DWEAVNRSWQAALTKVQDDPDGAITATRTTIESVCKHICDERGVKYEDGWDLARLYKATS
+SAMQVAPDQHSEQIIKQILSGAATLVGGLAAMRNALSDAHGRGKRSVGPAPRHAKLAVNA
+GFAIAGFLIDTHVEKPPVSS
+>3_2152
+MASTSPTLLPFRIDSLATSLFAKETGFSGPQLHDFFARYTDVLGPYRWNGSPSRWQIFQT
+GLHSLPLPQQRAVLLELCSYDGEFKNGRPPEGELTRLRAMLLSAGTPGAQAAQESLQKLE
+DWEAVNRSWQAALTKVQDDPDGAITATRTTIESVCKHICDERGVKYEDGWDLARLYKATS
+SAMQVAPDQHSEQIIKQILSGAATLVGGLAAMRNALSDAHGRGKRSVGPAPRHAKLAVNA
+GFAIAGFLIDTHVEKPPVSS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002074.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002074.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f897501e7f6f41b4a01e8b92961f39bfdbeb90f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002074.fa
@@ -0,0 +1,24 @@
+>1_89
+MTTIPIHEAQVRHQPLHAYVEEHAQVSPDRTAIVCGGSQLTFGQLQSQVEQLSAYLSEQG
+VSHGDTVALFMQNSPQFVVSLLAVQRLGATAGPCNPMFKQWELEYQLNDLDTKVLITFDD
+LVPVFEKTDTGVQTVVLTRWSDVIEDVSQVPVEDGAEPVQQTKAPHTVRYAQIIGGERTV
+PPAAEIDLAQDPALIIYTSGTTGQPKGAMLSYRNVEFKTACTVQTYGFTSDDVFCAVMPI
+FHIAGMTVCMNSPLMVGGTMVIEPRFEPGTMIRDLERHAVTVTYTTPPMNLALLDHPAMA
+EADLSAVRLSPGTSFGIKITREISDRWEEVTGAPLFEWAYGMSETHTGDTQMPPEAIRYG
+SHGKPTFDTDVRISDPEDPSREMPQGELGEILVSSPSVFLGYRGREEATQKTMHRHWYRS
+GDLGRIDSEGYLHFEGRNKDLIKSSGYSVFPEEVERMLVRHEAVAQAAVVGYPDPQRGES
+VRAFVILEEGQSVTPKELIEWSRERMAAYKYPRDVRIIQELPTTTTGKLQYAKLRDLD
+>1_2241
+MNTTVSGARIPIRPDDVVLAVLPFFHVYGLTSVLNICVRHACTMVLLPRFDAAAALDLVE
+RHGITRISAVPTMLIGMVEDPDTGRDLSSVSQVVSGGSALPQEVLRRFEAKFPRATILEG
+YGLSESTSSVAVNVSREERRVMSIGKPLWGTECRVVDAEGHLLGPGEDQVGELLFRGPTI
+MKGYYRNPEATAATLVDGWLRTGDMGYRDEDGFIYVVDRKKELILRGGYNVYPREVEEVI
+ATHPAVSEVAVVGRPHPSLGSEVVAVVSTRPGMSVTPAGVIEHAKVSLAAYKYPREVVVV
+DSLPKTATGKIRKRDLATTLAEPASPESHSATP
+>4_274
+MNTTVSGARIPIRPDDVVLAVLPFFHVYGLTSVLNICVRHACTMVLLPRFDAAAALDLVE
+RHGITRISAVPTMLIGMVEDPDTGRDLSSVSQVVSGGSALPQEVLRRFEAKFPRATILEG
+YGLSESTSSVAVNVSREERRVMSIGKPLWGTECRVVDAEGHLLGPGEDQVGELLFRGPTI
+MKGYYRNPEATAATLVDGWLRTGDMGYRDEDGFIYVVDRKKELILRGGYNVYPREVEEVI
+ATHPAVSEVAVVGRPHPSLGSEVVAVVSTRPGMSVTPAGVIEHAKVSLAAYKYPREVVVV
+DSLPKTATGKIRKRDLATTLAEPASPESHSATP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002086.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002086.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af03d91ea70cee61e9e7ae67fe3359d336616450
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002086.fa
@@ -0,0 +1,26 @@
+>1_1445
+MRPRSASAARTREALRDAVQIYAPSTVYAVGLGAMTPALAVAALALGLDAARAAAVVLLV
+GLGSLVANGPASALAARAGERVTMVVSAGLGTVGAGLAWATTAGVSSGPSAAGVAEPGRL
+ALFLAAVLAVGMAGAGFNLARQAYLAVAVPATHRARAMSTLGGTVRIGTFLGPFLGAAAQ
+APLGLDGAFAAAAAAMAVGALLCLRIRDLPVPASDPAAGEEPGPAGRPRLLDVARARRGA
+LLTAGFGVVAVSAARAARNAVIPLWATHLGLDAATASLVFGLAGAADLLLFYPSGRLMDR
+FGRRAVAVPCLTLLGAGFLAISLTREPTAFAAAAVLLGIGNGFGAGIVMTLGADHSPPNA
+RAPFLGLWRSMSDAGMLAGPLLLSGATAAAGLAVGVGSLAVVCGVGAVVFAAVLPRGPGA
+VADPPPVVVRPR
+>2_1069
+MPRRSASAARTRQALRGAVQIYAPSTVYAVGLGAMTPALAVAALALGLDAARAAAVVVLV
+GLGSLVANAPASALAARAGERVTIVVSAFLGTAGAALAWATTAGLSSSPGREGVVEPGRL
+ALYLTAVLAMGMAGSGFNLARQAYLAVAVPPSHRARAMSTLGGTIRIGVFLGPFLGAAVQ
+AAMGLDGAFAAATAAMAVGALLCLRIRDLPASGAAAPGADPGAQPVPAHRPRVADVARAR
+REVLLTAGFGVVAVSAARAARNAVIPLWATHLGMDAASASLVFGLAGAVDLLLFYPAGRL
+MDRHGRRAVAVPCLAVLGAGFLAVSLTRDPAAFAAATVLLGIGNGFGAGIVMTLGADYWL
+LGHPVGLGRAG
+>4_1657
+MRPRSASAARTREALRDAVQIYAPSTVYAVGLGAMTPALAVAALALGLDAARAAAVVLLV
+GLGSLVANGPASALAARAGERVTMVVSAGLGTVGAGLAWATTAGVSSGPSAAGVAEPGRL
+ALFLAAVLAVGMAGAGFNLARQAYLAVAVPATHRARAMSTLGGTVRIGTFLGPFLGAAAQ
+APLGLDGAFAAAAAAMAVGALLCLRIRDLPVPASDPAAGEEPGPAGRPRLRDVARARRGA
+LLTAGFGVVAVSAARAARNAVIPLWATHLGLDAATASLVFGLAGAADLLLFYPSGRLMDR
+FGRRAVAVPCLTLLGAGFLAISLTREPTAFAAAAVLLGIGNGFGAGIVMTLGADHSPPNA
+RAPFLGLWRSMSDAGMLAGPLLLSGATAAAGLAVGVGSLAVVCGVGAVVFAAVLPRGPGA
+VADPPPVVVRSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002088.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002088.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4e23750969290b3e63f81eb09500b89749f3d38
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002088.fa
@@ -0,0 +1,10 @@
+>1_1621
+MTLVVLALDTVFRLTPAETSAAIPGIAGLEHLLVTAGLALLFVALYGGVRERQAHLETGR
+AGGAVVEGA
+>3_798
+MTVGLTLHVLMWPVLVLAVLGLASGLFYREYTKAHEFTGATELGTVHTHLLGLGLTVTLV
+VLALDAVFGLTGRGPFTWFFWLFHLGVLVTSVMMAVRGGLTVDGLTPAEASAGIPGIAGL
+GHMLVTAGLALLFVALYSGVRERQDRLETGRTGGTVVEGA
+>4_1843
+MTLVVLALDTVVRLTPAETSAAIPGIAGLEHLLVTAGLALLFVALYSGVRERQDRLETGR
+AGGAVVEGV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002100.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002100.fa
new file mode 100644
index 0000000000000000000000000000000000000000..304f5ecbdc2a9a33353fca84f5448dd446ad563c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002100.fa
@@ -0,0 +1,9 @@
+>1_1878
+MSQNDLTVYGADWCRDCLRTKRQLDELGVAYDYVDLVADPAQADAAERISGRKNIPVVVF
+PDGDHQVEPTNEETAAKLTALGLI
+>2_508
+MTQNAPALTVYGADWCRDCLRTKRQLDELGVAYDYVDLVADPAQADVAERISGRKNIPVV
+VFPDGEHQVEPTNEETAQKLTALGLL
+>4_2094
+MSQNVLTVYGADWCRDCLRTKRQLDELGVAYDYVDLVADPAQADAAERISGRKNIPVVVF
+PDGDHQVEPTNEETAAKLTALGLI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002102.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002102.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d87c0fe8847077111edfca4ca68a830349b26a06
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002102.fa
@@ -0,0 +1,20 @@
+>1_2127
+MVPTADDAPRREPGAVWRGLLTIFLVSAGGSLMFYTWLIYLPTHAQVAHQMDKSTTLSAS
+LVAQVIFLAAILGAGLLGDRVGRRPLVIAFGLLFVVLPFPLFGMLDGTFASFLLVQTIAL
+LAVALLFGVNGAVWSEALPTAVRAKGVATMLSLATAIFGGTAPYLITWLTAQGWTSAFPI
+YLMVVGGLTGLVMKETKDVDLAA
+>3_148
+MSTAATGAARPAPVPRTRPRSLKDMLAVNFGNALEWYDWNVYTIFAPVFAAQIFHADNPT
+SELLATLAVFAVGFVARPIGGYVFGAYADRVGRKRSLFAAMMITALGSLIIAFTPTYGMV
+GVLASVILVIARLLQGLAHGGEMGTSVTYLVERAPQGRRGLFGATSWVSVVVGTILATLV
+GLTINTLLTHEQVASWGWRVAFGIGGVLGLYALYLRRSLTESEHFTAAQQVVPTADDAPR
+RESGAVWRGLLTIFLVSAGGSLMFYTWLIYLPTHAQVAHHMDKSTTLSASLLAQVIFLAA
+ILGAGLLGDRVGRRPLVIAFGLLFVLLPFPLFGMLDGTFASFLLVQTIALLAVALLFGVN
+GAVWSEALPTAVRAKGVATMLSLATAIFGGTAPYLITWLTAQGWTSAFPIYLMVVGGLTG
+LTGLVMKETKDVDLAA
+>4_177
+MGTSVTYLVERAPQGRRGLFGATSWVSVVVGTILATLVGLAVNTLLSPEQVASWGWRVAF
+GIGGVLGLYALYLRRSLTESEHFTAAQQVVPTADDAPRRELGAVWRGLLTIFLVSAGGSL
+MFYTWLIYLPTHAQVAHQMDKSTTLSASLLAQVIFLAAILGAGLLGDRVGRRPLVIAFGL
+LFVVLPFPLFGMLDGTFASFLLVQTIALLAVALLFGVNGAVWSEVLPTAVRAKGVATMLS
+LATAIFGGTAPYLITWLTAQGWASAFPIYLMVVGGLTGLTGLFMKETKDVDLAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002105.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002105.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7532d42a8316355dfe29475ff76d935fecad2c5c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002105.fa
@@ -0,0 +1,24 @@
+>2_121
+MPFALYMLALAVFVMGTSEFMLAGLLPAIATELDVSVGTAGLLTSAFAVGMVVGAPVMAA
+FARSWPPRLTLIVCLLVFAGSHVIGAMTPVFSLLLITRVLSALANAGFLAVALSTATTLV
+PANQKGRALSILLSGTTIATVVGVPAGALLGTALGWRTTFWAIAILCIPAAVGVIRGVTN
+NVGRSATSATSPRLRAELSQLAMPRLILAMALGALINGGTFAAFTFLAPVVTETAGLAEA
+WVSVALVMFGIGSFLGVTIAGRLSDQRPGLVLAVGGPLLLTGWIVLAVVASHPVALIVLV
+LVQGFLSFGVGSTLITRVLYAASGAPTMGGSYATAALNIGAAAGPVLGAFGLATGLGLLA
+PVWVASVLTAIALAIMLLTGRALTKTAAEAN
+>2_1477
+MPFALYLLALAVFAMGTSEFMLAGLVPDIAASVGVSVGTAGLLTSAFAVGMILGAPAMAA
+LTRRWPARTTLLGCVVIFAACHVVAATAETFSVLFATRVVAAVANAGFLAVALSTATRLV
+APSRKGRALAILLSGTTIAMVAGVPAGALLGTALGWRATFWAVAFLCVPAAIGILTGIRP
+QPRDTQDEANDGLSLAFELAQLRVPRLFTAMLLAALVNGGTFAAFTFLAPVVTGTAGLGQ
+VWVPVALVLFGIGSFMGVSIAGRLSDQHPRTLLVVAAPLLLVGWLLLAVLAGHSVPLLVL
+VFLLGMLAFAVGSTMIARVLYAASEAPTMGGSYATAALNIGAAAGPALGAVALESSRARA
+TLVPCGQRPR
+>2_2289
+MPFVLYLLAMVVFAMGTSEFMLSGLVPDISAYFGVSVGTAGLLTSAFAIGMVIGAPAMAA
+LTRRLPVKATLLGCVIVFALSHAVGALTPDFTVLFITRVIAAVVNAGFLAVALVAATKLV
+APDAKGRAVAILLAGTTVATVAGVPAGALLGAVLGWQSTFWAIALLCVPAAVGIAAGFTA
+QSDDSSREEPTSISLRAELSQLASPRLVLTMLLAALVNAGTFSTLTFLAPIVTHTAGLSQ
+WWVSVALVLFGVGSFIGVTVAGRLSDARPRIVIVGGGSVLVLGWLALATFATNPIALLGL
+VFAQGVLGFAVGSTLITRVLYAAAGAPSMAGSYATAALNVGAAAGPILAATALGVVPGAL
+GPVWVAVIVTAAALLLAIPVLRLVAPAESEVIK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002114.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002114.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b3276fc37ad79e9c7e4bd839c34053ac55de7c57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002114.fa
@@ -0,0 +1,10 @@
+>2_1284
+MLGALIAGGATFLTGKLADDRARQAERKEHVARVGAEFLREADRVEQYLLDYVHEHAAVP
+GDNEEWGETAELARIAWELRLFAPRPVNDAAAELVDVLEAWESGVDGRGRDVLEIHKRFV
+SVLRVYLHGEDD
+>3_2182
+MARVGAEFLREADRVEQYLLDYVHEHAAVPGDNEEWGETAELARIAWELRLFAPRPVNDA
+AAELVDVLEAWESGVDGRGRDVLEIHKRFVSVLRVYLHGEDD
+>4_114
+MDAWIGVVGTLLGAVVGGGVAYLNGTRDRKLEARRDQEKCVTEVAGELLQIVDARERYVH
+GYLEVVGEFPHDGAPDGEEDPARKTLALLELYAPAPVTTAAREYVDLMDKW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002129.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002129.fa
new file mode 100644
index 0000000000000000000000000000000000000000..46753e7f3c9506cc0ff9641ced6d4eaef908869b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002129.fa
@@ -0,0 +1,7 @@
+>0_491
+MGLGLNVALHDVVHRVAFSAAVPIQHRTAFLRRLGWTGITRSDIRDGCLFIGFDITMDRS
+YLNRQVLIDASAPVRIGAHVQFGPRSSIITSTHRIGDATMRGGDPEAQPVAVGDGCWIGA
+GAMILPGVIVAPGCIIAAGAVVTRDTEPNGIYAGTPARRVRDLD
+>2_261
+MRAAENSLRSRATGADVHPTVWVMRSAWIERGATVGGPGQRAGAVVTRSTEPNGLYAGVP
+GRRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002143.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002143.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9362ab0750bfd2d553c3f606271b0a167ce6f321
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002143.fa
@@ -0,0 +1,16 @@
+>0_915
+MSANTNFFTSQQPAAVFKLKVLEDYLTPWAMKVASKAPREVAYVDGYAGAGQYDDAHKGS
+PLYAVDIARKLAAQNRIMHIHLVERDRAHAETLRHAVAAQGQGAGPVYLHHGAVEEQIDA
+ILNDIGTRPALFFLDPFGTALPYDVVASKLLLRPARSTEVLLNFSLSTVWRIGGIVRKGA
+SASSGETVTLLRGDRFLGGPWWREVFAEARRQADVSGDSSSAATAASYVAREYMQRMTGE
+TAHNVISVPIRRTPSEGPIFTLMLFYQHFAAPMLFADAAARAHRKWRQVNSENYYQGLLN
+DTQGSLFDLQETFDQQVVAEQTDVRNRAIAAIQTRLSSHLGQGQAVRICDDVPHWLGEHL
+GTAGASEVRQAIKNLQKAGIAQGYTKDMVDGRAVILPARRGR
+>2_2055
+MVAHATFFTEQKPAAAFKLKVLEDYLTAWSMKVASRPPHEVAYIDGYAGAGQYDDAHKGS
+PLYALDIARKLAPQNRSMHIHLVERDRAHAETLRRAVAAQGRSASPIHLHHGAVEAQIDA
+ILHQIAARPALFFLDPFGTALPYDVVASKLLLRPARSTEVLLNFSLSTVWRIGGIVRKGA
+TASPAEQLTLLRGDHFLGGPWWQEVFAHARAKADASGEDSPAATAASYVAREYMQRMTGD
+TNHRVISVPIRRTPSEGPIFILMLFYQHHAAPMLFADAAARAHKRWRQVNAGNYYRGLLD
+DAQGSLFDLEETFNQQVVAEQTEVRNRAIAFIEATLSAQLVQGQAVRICDDVPRWLGAHL
+GTAGAPEVRQAVKNLKKAGIAQAYTKEMVDGRALILPSRPAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002144.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002144.fa
new file mode 100644
index 0000000000000000000000000000000000000000..130cf86d7a07d686d99d7031ec1c1901f121c882
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002144.fa
@@ -0,0 +1,12 @@
+>0_916
+MANTSAIEWTEVTWNPVTGCDRVAAGCDNCYALTLAKRLKAMGAEKYQNDGNPVTSGPGF
+GVTLHPKALGQPRSWKAPRVVFVNSMSDLFHAKVPLGFIRDIFDVMRETPQHTYQALTKR
+SLRMARLADRLDWPANLWMGVSVEDETVTGRIDHLREVPAAVRFLSCEPLIGPLRDLDLA
+GIDWVIAGGESGANHRPMDQAWVEDIRDQCVSADVAFFFKQWGGRTPKANGRLLEGRTWD
+EMPTSRAALAG
+>2_2056
+MAQTSAIEWTEVTWNPVTGCDRVAAGCDNCYALTLAKRLKAMGAAKYQQDGNPATSGPGF
+GVTLHRQALDQPRSWKTPRVVFVNSMSDLFHAKVPLEFIQDIFDVIRETPQHTYQALTKR
+SLRMARLADQLDWPPNLWMGVSVEDASVTNRIEHLRRVPAAVRFLSCEPLIGPVGALDLD
+GIDWVIAGGESGANHRPMDEEWVTDIRDQCVAAGVAFFFKQWGGRTPKANGRVLAGRTWD
+EMPNQPASMAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002146.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002146.fa
new file mode 100644
index 0000000000000000000000000000000000000000..53085bf04ede42fb38082522c54cbce6e35da93e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002146.fa
@@ -0,0 +1,6 @@
+>0_919
+MTTTTQAPACAGHLSVRDHMALQLWGRRWRHGAARDRAAEHLVGLQGTALAMRVATLAED
+PVAIAAYPVITRRAREARQTRERAVRVPAA
+>2_1892
+MTTTTQAPASAGHLSVRDHMVLQLWGRRWRHGAARDRAAEHLVGLRGTALAMRVAVLAED
+PVAIAAYPVITRRAREARQTRERAVRAPAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002155.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002155.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37dd70784c299866007ce5290aff224c3e93bb2e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002155.fa
@@ -0,0 +1,8 @@
+>0_1441
+MTASTTKSERARRQRTVYSKRLELRLTERQLQLASETAQRLSAIRGKRVTVSDYVRLLID
+DGGRGLVQRLERISQSPAGTLTQADADRVVAALQEVRDEVRRVGHNVNQMTVRAHQAKQV
+VDDLDEVKASLSQIDAHVLDAAKTFLGYEGTDEDEG
+>2_2152
+MTASTTKSGRARRQRTIFSKRLELRLTERQFRLASETAKRLSEIRDKKVTVSDYLRMLIE
+DGGKGLIQGLERVSHAPAGILSQADVDRIVAALQEVRDEVRRVGHNVNQMTKVAHQSGQV
+ADDLDGVKQALAGIDAHVLDAAKSFLGYEATDEEEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002156.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002156.fa
new file mode 100644
index 0000000000000000000000000000000000000000..413ef9c23ced180b389224e23ca1df974e7669b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002156.fa
@@ -0,0 +1,22 @@
+>0_1442
+MAAPIAAIVVASPTRNASRLLAYALNKKKGQTTDRFVVASGLNGAIPEVAAAQYRDNRKR
+HGKNGERQVRVPDDKGGMRTITEGAYVQGYHVIQSFARDGEGALDPNDPEAWEEAHRLGR
+KFALRLAGDGRMGVVVTQIDGRTGCIHNHLVLDSIDRQTGKSFASSNVKHKVLAQTHDEV
+LREAGYAQQNELQSTAAERREPSEERARLRHEQWGANGRQGPEPFSVAVMKQRVREGMSD
+PRSVSFETYAEVLAERGVRVERRGQDHPGLTYEMVLSDGKGGTVDPQPAYRRRASKLGRD
+FMLATVEQALERNRTKQAVQPTGHRPLLDPSKYVALVGRADQVPAPAVTATPNADETERP
+LLWRTYERMGLDWREARKVAPETEVEPAPTPDVAEPLPAPSAPAAEPIAAPTEPEDEAEA
+QDEAQRATAPAYRSPVRDRTVKRERSREFRERLAAADEHVVARLEAGEPVDDTVLKGLGP
+DKIRSYRTSLHPQTQRALRRRQSMQGAAARAYAAGQRELAQRIRAEVAAGEYRWIEPAPD
+AVAQHEQDEPELGG
+>2_2153
+MAQPIAAIVVASPTRNASRLIAYALNRKQGQTTDRFVAASGLNGAIPEIAAHQFRDNRKR
+HGKNGERQVQVPDGEGGTVTVTEGVYVQGYHVIQSFARDGDGALDPSDPDAWEEAHRLGR
+KLCRRLAGDGRMAVVVTQIDGATGCIHNHIVLDSIDRQTGKSFASSNVKHKMLAATHDEV
+LAEAGYVQQNELQSTAAERREPSEDRALLKHQQWVAGGRQGPEPYSVAIVKHRIREAQGD
+PRSVSFDTYAGVLLEHGVRVEKRGEKGAGLTYEMVLADGGGGVLKAQPAHRRRASKLGRD
+FMLPAVEAACARNRAREVGRLRGLGAPVLPPREESAVEALLRELTEARAKGRAGRRPGPT
+EAPAAPPRTPEPREPAEASQAAQRAAQAQQAAAVAAPVQSSAWRSRLWDLPPSNRTVRTQ
+QIIDAVAEWEPSARERLQSGERLDEPAIPKGVGARFLESYGQYLDPAVRTELEAREETRA
+QRREQFELEREHEEALQAVGRRPEAERTIYERGVRAQLDTARLRREAIEAAIAEGRYGRA
+DVDGIVSEAEQAEREASARRREQVAERAAAMRDEDRESDDPQPGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002157.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002157.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3cfe678dcbec3e5c41adaf128ef58ce45f67beb0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002157.fa
@@ -0,0 +1,10 @@
+>0_1443
+MSTTTTFRVLTVPEVRVCCLRCEDQGTRYGAWVPLDEVDDVCADQVHRGRVVRLERGVAL
+HADAPTTVLETRNLPMDGPLTAEQLEAWQDLYEVVGAEQWPALLAWVGSGTHVEDGDGLP
+DAAAFAESYAGIWGSFDEYAQELADETNLMDGWLETARTYFDWSRWARDLRYDYTVCDMP
+HGPGVYVFRDL
+>2_2157
+MTTETTTIRVLTTPEVYVGCTRCEAEGRRRGVWVPLDEAADVVTDQAHRGRVVTLTRDVD
+LHADPDVLQVLETRHMPVPGPLTSAQVAAWQDLYESVGEERWPALLAWVDSGAWVEDGDG
+LPSIGAFEERHCGQWEDFEAYARALAEETDLQAGWSETARTYFDWGRWTRDLRYEHTVVD
+GPQGGVYVFRDL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002161.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002161.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd8892f520f1c5054da126ecd82b6a2a9cbb5922
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002161.fa
@@ -0,0 +1,12 @@
+>0_1552
+MCHGHDREGSDAGQSVSGRPAAHRAAADEGAERLHRSLTVLTTTGFLGGVEITIGLLAYL
+LTLHETGSHLLAGLAFSIGLVSLFLAHSELFTEGFYYPITAIAAGRGTWMELLRLWAVTL
+VMNLLGGTVMIALVVAGFPDLHGTLAESAHHFLDIGFSWQGAALAVLAGVAITLVTRMQA
+GTDSPTAMIVASVAGAIVLAGGSLFHSVMDSILIIGAILSGAHGVGWLEWLSWVWWVIPL
+NILGGLALTTAPRLLRSKEVREETGR
+>1_1274
+MGPVCHGHDREGSDAGQSVSGRPAAHREAADEGAERLHRSLTALTTTGFLGGVEITIGLL
+AYLLTLHETGSHLLAGLAFSIGLVSLFLAHSELFTEGFYYPITAIAAGRGTWMELLRLWA
+VTLVMNLLGGTVMIALVVAGFPDLHGTLAESAHHFLDIGFSWQGAALAVLAGVAITLVTR
+MQAGTDSPTAMIVASVAGAVVLAGGSLFHSVMDSILIIGAIPSGAHGVGWLEWLSWVWWV
+IPLNILGGLALTTAPRLLRSKEMREEKGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002170.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002170.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a5a811bda345bc7902f426359a75bb2d604f2e26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002170.fa
@@ -0,0 +1,12 @@
+>0_1735
+MQIKDRTFLVTGGASGLGEATTRALLDRGGHVVVADRAGTAPEGAVFVEADVTDAVQVAH
+AVAEATRQPGPLSGVVNCAGIGSAAKVISRDGPQPLADFERIVGVNLIGTFNVIRLAAAA
+MAENEPDDDGGRGVIVNTASVAAYEGQVGQAGYSASKGGVVAMTLPIARELAAYGIRVNT
+IAPGLFLTPMMHQLPEKARASLGEQVPYPSRLGDPAEYAHLVTHIVENQMLNGETIRLDG
+AIRMAPR
+>2_1061
+MQIKDRTFLVTGGASGLGEATTRALLDRGGHVVVADRAGTAPEGAVFVEADVTDAVQVAH
+AVAEATRQPGPLSGVVNCAGIGSAAKVISRDGPQPLADFERIVGVNLIGTFNIIRLAAAA
+MAENEPDDDGGRGVIVNTASVAAYEGQVGQAGYSASKGGVVAMTLPIARELAAYGIRVNT
+IAPGLFLTPMMHQLPEKARASLGEQVPYPSRLGDPAEYAHLVTHIVENQMLNGETIRLDG
+AIRMAPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002176.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002176.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9696426fcdc46bd79cada07dcdd74e75fc288f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002176.fa
@@ -0,0 +1,8 @@
+>0_1998
+MNQPSMATLSSGKITLRDARRGTTRDVELEPFEMAVHPLHDRSTGRPLTPLTWFETINLC
+NELSNAEELQPAYTRAGDGRSVTWNTSADGYRLPTEAEWEYACRAGTTSPAYGPLEDIAW
+TGLDHLEGPQPVVRSENP
+>3_2167
+MTPPAAEGHFSRATLTDLLCEKFIACRVKSSLHLDSDARRGTTRDVELEPFEMAVHPLHD
+RSTGRPLTPLTWFETINLCNELSNAEELQPAYTRAGDGRSVTWNTSADGYRLPTEAEWEY
+ACRAGTTSPAYGPLEDIAWTGLDHLEGPQPVVRSENP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002181.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002181.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c535c4b869fdabe277b45d7cec509423527ea5e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002181.fa
@@ -0,0 +1,14 @@
+>0_2173
+MNMARTTEPVTLAGTWDVLLSHAALLGAAMIVEEELGAGAVRLRWTDEPDSRPQLCGAGL
+DAAAFGSLIHRHATRHVQNPGGWLYSTDAVAGSLFSARTKMPASEHGWADLLHDRTEVAR
+PLRGLDSALVVGLGERAWWHRTSKSFRPDHGAAAWEMRTRNKGMEFIAHSLLPTGRAVAG
+RAVEAVTSGLLGTTVEDEPGKNKPDSRTATGMAPLGPVDAARAWVGLWALAALPVWADSH
+GRSVSSAHIPARRESLARLLMPVPTSWVTVARMQAALRSRYLLVAGEDATGPSLGSAETT
+AAQAILEEWGFAQILSFPVNVTGSASAPERRTLAARALR
+>4_2106
+MNMARTTEPVTLAGTWDVLLSHTALLGAAMIVEEELGAGAVRLRWTDEPDSRPQLCGAGL
+DAAALGGLIHRHATRHVQDPRGWLCSTDAVAGSLFSARTKMPASEHGWVDLLHDRIEVAR
+PLRGLDSALVVGLGERAWWHRTSKLFRPDHGAAAWEMRTRNKGMEFIAHSLLPTGRAVAG
+RAVEAVTSGLLGTTVEDEPGKNKPDSRTATGMAPLGPVDAARAWVGLWALAALPVWADSH
+GRSVSSAHIPARRESLARLLMPVPTSWVTVARMQAALRSRYLLVAGEDATGPSLGSAETT
+AAQAILEEWGFAQILSFPVNVTGSASAPERRTLAARALR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002197.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002197.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c2a0688a59d3fdd070ec68009c57c4b8948a0af5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002197.fa
@@ -0,0 +1,5 @@
+>1_287
+MSANSAAFDHLTGFRWRQGDPSLADAEAQLYDLGVLRSVLERPSRSPSPTPEPMG
+>2_2318
+MSANSAAFDHVNGFRWRLGDPTLADAEAHLYDLGVLRSVLEEAVEIAVADARADGVTWAR
+IGDALGVTHQAVIKRYRRGGAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002200.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002200.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09c44b29d6c453963d2ab0de51706511b2ee2ea6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002200.fa
@@ -0,0 +1,12 @@
+>1_314
+MPPIDQWVTFEPLTGSPVGIAALLFAALYLRGAIWMWRNRRRWAIARTASFLIGCALIFA
+ITMFGVNRLATESITALVFQQITLLTVVPPLLIAGSPGLLLLRSTPHTGLGRLVLRAAHG
+GLRSRFWSAALHPVVAIVIAILLYPVLYLTDAISVIMRIPFGQDALLFVILVLGIVSATP
+LWSSDPLPRQPSFAARFVDIAVEIQIHAIFGLILLRTATPLFSAYATPTGSHDPVIDQAI
+AGTLVWTYAELPMFVVLIVCLSRWRARDVRTSRQRQKAEDAELDSYNEYLASLSRRRNES
+>2_375
+MPPIDQWVTFEPLTGSPVGIAALLFAALYLRGAIWMWRNRRRWAIARTASFLIGCALIFA
+ITMFGVNRLATESITALVFQQITLLTVVPPLLIAGSPGLLLLRSTPHTGLGRLVLRAAHG
+GLRSRFWSAALHPVVAIVIAILLYPVLYLTDAISVIMRIPFGQDALLFVILVLGIVSATP
+LWSSDPLPRQPSFAARFIDIAVEIQIHAIFGLILLRTATPLFSAYATPTGSHDPVIDQAT
+AGTLVWTYAELPMFVVLIVCLSRWRARDVRTSRQRQKAEDAELDSYNEYLASLSRRRNES
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002206.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002206.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a6ec54778f37fc5c008bbec09d9e4a92bfc727ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002206.fa
@@ -0,0 +1,24 @@
+>1_735
+MTPVPPSSPSRLDALTAPTARHAHRLLVAKAIREFTHERLLTPVRGERVDDAGRHAYTLT
+LGGVRWTFTARALPLEHLGVDPDSVCRAGDPDAVAVDRFVLDAAEVLGLAGEALDVYLEE
+LASTFAARCHTLAGERPSAADLVDADYTAVEAAMSEGHPGFVATNGRIGWGATEYAMFAP
+EGGRALHPVWLAFPSELGGRWTWPKTASAGAAVPAPPPPITEAVAGLWAERAAALDVDPE
+AYTLIPVHPWQWEHRIQVAFAPDLAVGRLVHVGEDPDAFTAMQAVRTLFNASDPHAPQLK
+TALSVQNMGFVRGLSPAYMSVTPAINAVVADLVDSDPLLARWGFGVLREYASAGYTGDAF
+HAVGSKGPHTKMLAALWRESPLPRLAEGERVMTMAALLHRDGGGRSVAGALVERSGLTAA
+QWLHGVVTAYVTPLVHLAAAYSTVFMPHGENIVLRLREGRVTGAFLKDIGEEVVVGADGV
+PLTEQTRRIRIDLTDEDLSLSFFTDMLDGVLRHLADVMDADALLPAEEFYAVVGRVLAEY
+TALGLADVERLGLDAEDFAHSCLNRLQLRNATQMVDLTDPSGSLLYAGRLANPVSAPLRR
+ALAELRQDAAA
+>4_954
+MTPVPPSRLDALTAPTARHAHRLLVAKAIREFTHERLLTPVRGERVDDAGRHAYTLTLGG
+VRWTFTARALPLEHLGVDPDSVCRAGDPDAVAVDRFVLDAAEVLGLAGEALDVYLEELAS
+TFAARCHTLAGERPSAADLVDADYTAVEAAMSEGHPGFVATNGRIGWGATEYAMFAPEGG
+RALHPVWLAFPSELGGRWTWPKTASAGAAVPAPPPPITEAVAGLWAERAAALDVDPEAYT
+LIPVHPWQWEHRIQVAFAPDLAAGRLVHVGEDPDAFTAMQAVRTLFNASDPHAPQLKTAL
+SVQNMGFVRGLSPAYMSVTPAINAVVADLVDSDPLLARWGFGVLREYASAGYTGDAFHAV
+GSKGPHTKMLAALWRESPLPRLAEGERVMTMAALLHRDGGGRSVAGALVERSGLTAAQWL
+HGVVTAYVTPLVHLAAAYSTVFMPHGENIVLRLREGRVTGAFLKDIGEEVVVGADGVPLT
+EQTRRIRIDLTDEDLSLSFFTDMLDGVLRHLADVMDADALLPAEEFYAVVGRVLAEYTAL
+GLADVERLGLDAEDFAHSCLNRLQLRNATQMVDLTDPSGSLLYAGRLANPVAAPLRRALA
+ELRQDAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002214.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002214.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4139960be23bb723a6dc576443f2317dd03ddd0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002214.fa
@@ -0,0 +1,6 @@
+>1_1695
+MNAKPEKDLRRTVDILFRPARVAVLIDGCYWHGCPQHYIAPKANGGYWSDKVATNRARDL
+ETTRILTERGWLVLRFWEHEDPAVVAERVVAVVNERRPRRTTGAS
+>4_1913
+MNAKPEKDLRRTVDILFRPARVAVLIDGCYWHGCPQHYIAPKANGGYWSDKVATNRARDL
+ETTRILTERGWLVLRFWEHEDPAVVAERVVAVVNERRPRRTTGAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002216.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002216.fa
new file mode 100644
index 0000000000000000000000000000000000000000..077b4b75a4b397c66718bbeed596bd6355edb351
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002216.fa
@@ -0,0 +1,10 @@
+>1_1699
+MIGALRYVLSGGAPLAVETLREAEAEAAFGVPVREAYGLSESCGPVCFNPMDGPSRPGTV
+GRPLEGVEFRIVTPEGVEVPERDTETPGELRIHRPVVMSGYLGLPEAGAAAFDDDGWLRT
+GDLARRDEEGYYRIVGRLKDINIRNGYNVYPREVEDALYVHPDVAEAEFSAFVRERLLSY
+KGPQPVTLMDSLPKNGTGKIVKDLLR
+>4_1917
+MIGALRYVLSGGAPLAVETLREAEAEAAFGVPVREAYGLSESCGPVCFNPMDGPSRPGTV
+GRPLEGVEFRIVTPEGVEVPERDTETPGELRIHRPVVMSGYLGLPEAGAAAFDDDGWLRT
+GDLARRDEEGYYRIVGRLKDINIRNGYNVYPREVEDALYVHPDVAEAEFSAFVRERLLSY
+KGPQPVTLMDSLPKNGTGKIVKDLLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002235.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002235.fa
new file mode 100644
index 0000000000000000000000000000000000000000..68bae614c3f48af0165426a6ee2d51c7e7f5ab78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002235.fa
@@ -0,0 +1,16 @@
+>1_2247
+MVQEAGVPEESGDAERRLREAWSALLEDADRIADEIAAATLGGDQGGAWSTPELRARLRR
+STREHVRRGLRGLAGVPSGEGAGGRLVDTWRATGVERARQGVPLETVISTYTSGNRLLWE
+ELGRRVREGRLDITTEELLEAGRRLWEDLSVTGEVLSAAYRRETARLTLRDLRRQEDCLA
+GLLEGKGADPVYAEQAEEILGVRATAPLACVVALAEDPGSDVLHHPEDRMGRLGATSRWA
+VREGALYGVVEPPSTDEEWLTEALGPLVEGQVGVAWARQGIPETAAAFRLATRAAHTLPP
+GERRLAWASHRLPEVLLESSPEVAALLVEEVLGPLRALPADQRATLMETLRALLRRSGSA
+TLAAEDLICHRNTVIYRTKRLVELTGCSLQDPRGRLMLELAVLAADRAGGPVRRARPISP
+>4_280
+MVQEAGVPEESGDAERRLREAWSALLEDADRIADEIAAATLGGDQGGAWSTPELRARLRR
+STREHVRRGLRGLAGVPSGEGAGGRLVDTWRATGVERARQGVPLETVISTYTSGNRLLWE
+ELGRRVREGRLDITTEELLEAGRRLWEDLSVTGEVLSAAYRRETARLTLRDLRRQEDCLA
+GLLEGKGADPVYAEQAEEILGVRATAPLACVVALAEDPGSDVLHHPEDRMGRLGATSRWA
+VREGALYGVVEPPSTDEEWLTEALGPLVEGQVGVAWARQGIPETAAAFRLATRAAHTLPP
+GERRLAWASHRLPEVLLESSPEVAALLVEEVLGPLRALPADQRATLMETLRALLRRSGSA
+TLAAEDLICHRNTVIYRTKRLVELTGCSLQDPRGRLMLELAVLAADRAGGPVRRARPISP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002236.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002236.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9fd69e8bcef9fe0a132e637ecae83b8d24f45a79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002236.fa
@@ -0,0 +1,20 @@
+>1_2254
+MMAVEAQRSRLVVLVAEAFAIQREFKTFLGKPRRGDKALRPVYEAETSKVHQRMAWACEA
+LHEGTVATASPLCDRPTGPRSLGEAANPVPVVAGIIGDMKYSESETAAYLKSTILRDFSA
+PLSTEPRKDKGTYYSRRVGCYEAPVPVLLRYPFDLLGIQHTGPGEKFAWAVEFNYKGFPA
+YLGYHKFGVKAGIICSLSRAESENHLNMMLDRIFSAAHVVEKLLSERAPEAIRQGNVTVA
+NQYRRLRAPYEYHRDRAINPVFVADEREHRRFNGGQSWTHISGKMVMKMHASHDLVASTV
+AFLSLLEHLFVLSLPFAGYNPESEDLTAFIGDRWGVKWERIIGDKNPEARDLRRRMSEVV
+EQWRNPYSHGGFEKGHGSSLYVHTPGLGALPMGLTRVRESTFFSFNPAPKGDIESIYSLF
+DEIESYLKSILPGAYTWIESGLDVRFDSEFAQELAEASQIDGGVEKLVDQYICRQEMIDN
+MDYY
+>4_287
+MMAVEAQRSRLVVLVAEAFAIQREFKTFLGKPRRGDKALRPVYEAETSKVHQRMAWACEA
+LHEGTVATASPLCDRPTGPRSLGEAANPVPVVAGIIGDMKYSESETAAYLKSTILRDFSA
+PLSTEPRKDKGTYYSRRVGCYEAPVPVLLRYPFDLLGIQHTGPGEKFAWAVEFNYKGFPA
+YLGYHKFGVKAGIICSLSRAESENHLNMMLDRIFSAAHVVEKLLSERAPEAIRQGNVTVA
+NQYRRLRAPYEYHRDRAINPVFVADEREHRRFNGGQSWTHISGKMVMKMHASHDLVASTV
+AFLSLLEHLFVLSLPFAGYNPESEDLTAFIGDRWGVKWERIIGDKNPEARDLRRRMSEVV
+EQWRNPYSHGGFEKGHGSSLYVHTPGLGALPMGLTRVRESTFFSFNPAPKGDIESIYSLF
+DEIESYLKSILPGAYTWIESGLDVRFDSEFAQELAEASQIDGGVEKLVDQYICRQEMIDN
+MDYY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002240.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002240.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c3f9fc7e021b81e93189db8959872ffc5311681
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002240.fa
@@ -0,0 +1,21 @@
+>2_82
+MGESRSGGIIRYAHLQEPHCVYGGWIQEDFTARQVLDSLTSQNEQGEVVPWIARAWEVSD
+DGLAWTFHLREGVHFTDGTPLDAQVVVDNFQYWADGGNSTAAVHLGGFFESAEVADAHTV
+RVHLLRPNGVLPSTLSQTYFGLQSPTALRTRSKEDNCRQPIGSGPFTVTEFQRGSHISYA
+RNPDYQWAPADARHQGPAYVDGIRWSFVPDNTSRYGALLSGEADAIGEVPAVNVAEAQER
+FAYQQYVTPGRPVVMSLNTREGIFTDVRVRKAFAHATDRESIVRSAFLGTVPFEPNGFIS
+RTTPGYDPTLADALPYDADAANRLLDEAGWTGRDPDGVRTKDGRRLQSRIVYGAGSILNP
+DGATAVASVAEQARAVGFDLGIRPATQSELFGGLFATPETRGIEVGYWTSPHAGILHINY
+RPSTPEEPNGANTSFLDSPETYSTVVDALSARSEEQRNALFAQAQHELNDLVPAIGLYDQ
+TNSVATSRGLTGVWLEGSQGAPVFHDAYFVAPAAPDGPPADARRTDQKD
+>3_124
+MSRPPHPARRRRRALRVSVAAAAALVLASGAAAVALPTGPDGPSDGQVLRVALGSDQGCL
+DPQQVSSNDSIYVARQVADSLTDQDPETGQIVPWLAERWEVSEDARAYTFTLRDGVTFSD
+GTPVDSEAVAANLDSLAEGLGPRASLATGYLAGYAETDVHDARTFTVRFHRPTVQFLQAT
+STVSLAVVSPASIAAGAEQRCAGVVGSGPFVVDAYSPGAGSTLSRRDDYAWGSSLWKETG
+RAGVDRVEFSIVQESGVRAGLLQSDQVDLIGSIAPQDEDPLAASGARLLQRANPGTPFGL
+LLNHEHEPFTDPRVRQAVSAALDRQEIVDVAFFRDSQPATSMVSRTTPGYADLSGRLQHD
+PQRAAAALQEAGYTRDPDGYWTKDGTPLTFTVTWSAVSPHNAPALEMLQQQLDDAGIRVR
+LREISTDQAGQILAESDFDAFWTNTTRADVDILRTSYHTGLANRSNAAASPTDGLLEQID
+ATTDSAARDRLAARAQDELLTSLPVIPVAELDTQLAARPEVSGVLFDSGSRLILHDARVD
+AEQKEQKEQEEH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002258.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002258.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a7d41ec564b8328601e88eca94f5b6eaf91239e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002258.fa
@@ -0,0 +1,6 @@
+>2_380
+MPKKYTPELRERAARMVLERQAAQGGPRSHSIRAIAPQVGVGEETLRMWCNRHGHEITQA
+PAGEDLQQENKRLKRELAEARRANEILKAASAFFARELDRPTTR
+>3_295
+MPKKYTPELRERAVRMVLERQVAEGGPRSHSIRAVAPQLRVGEETLRMWCNRHGHEITQA
+PAGEDLQQENKRLKRELAEARRANEILKAASAFFAADAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002259.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002259.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a64a80c71082eb142a6e56c11fc1026cb9978d34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002259.fa
@@ -0,0 +1,22 @@
+>2_420
+MIDAEIAAAHPIQPIARIAAEAGIAEDLLIPYGRHMAKVDVHALTAPEDGRVVLVTGISP
+TPAGEGKTTVTVGLADGLNMLAGQADAPAAVAGSRTVVALREPSLGPVFGIKGGATGGGH
+AQVVPMEAINLHFTGDFHAITSAHNLLCALVDNHVQQGNALGIDPRTIALKRALDMNDRS
+LRDVVTGLGGRTQGVPREGGFEITVATETMAVFCLAADLADLKERLGRITVGHTYDGEPV
+TASQIGPHGAQGAMAVLLKDAISPNLVQTLGGTPALVHGGPFANIAHGANSVIATRTARR
+LGDLVITEAGFGADLGGQKFMDITAVAGGFPPAAVVVVATVRALKLQAGLSLRDVKAGAA
+ETAAITGRDAEAVRAEHLDALRTGTANLARHVANMQEYGVPVVVGVNRFTQDEDAELEVL
+RAWGAEHGVPVAVADVWGGGGEGSLELARLLGEHLPAPGEPAAEVTRLWEEDMDVEEHIQ
+AVVRRVYRGARAELTPAARRQLAQLRDRGLDRLPVCMAKTQYSFSDDPALLNAPEGFTVT
+VRELSAKTGAGFVVALTGAVMTMPGLPASPAADRMDVAEDGTVTGLF
+>3_374
+MTEAPLTDAQIAAAHPIRPIARIAAEAGIDEELVIPYGRHMAKVDVHALTAPEDGRVVLV
+TGISPTPAGEGKTTVTVGLADGLNLLAGQEDAPAAVAGARAVVALREPSLGPVFGIKGGA
+TGGGHAQVVPMEDINLHFTGDFHAVTSAHNLLCALVDNHIQQGNVLGIDPRTVSIKRALD
+MNDRALRQVVTGLGGRAQGVPREGGFEITVATETMAVFCLAADLADLKARLGRITVGQTF
+DGEPVTASQIGPHGAQGAMAVLLKDAMRPNLVQTLGGTPALVHGGPFANIAHGANSVIAT
+RTARRLGEIVVTEAGFGADLGGQKFMDLTSVAGGFPPAAVVVVATVRALKLQAGISLTDV
+KAGVAAAAERAGRPAAEVEAEHVAALRAGTANLTRHVENMQSYGAPVVVAVNRFAQDADA
+ELDALRAWGAERGVAVAVADVHGGGGEGALELARTLGEALPAPGAPQAELTRLWTEEMDV
+AQRIEAVVRRIYRGTGVEYSAVARRQLRDLADRGLDRLPVCLAKTQYSFSDDPALLNAPE
+GFTVHVRELSAKTGAGFVVVLTGAVMTMPGLPASPAADRMDVSADGVVTGLF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002266.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002266.fa
new file mode 100644
index 0000000000000000000000000000000000000000..82a83234b35c6717bc2881af8f8908f9ed2acd2e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002266.fa
@@ -0,0 +1,7 @@
+>2_494
+MSTLSEMHVIDFPGFPTVVVRGPGQSVDGLHHFMDTSFRALGAAMGQGVFAPAGPAFALY
+RGMTGQGLGESMDLEVGHPVDVPPAVPLDVDGVRVEPSSLPAGRLAVAKHTGPYELLPEA
+WEAFLDALRADGHEPGDLCWEAYDTEPGPDVDPETLVTGLAVPVRTVA
+>3_432
+MRIEPSDLPAGSLGVAKHTGTYELLSEAWPAFLDALRENGHEPGGLCWEAYDTPPTPDTD
+PETLVTGLAVPVRPAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002279.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002279.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2dabc856b6660ca9b1cac99cc06d2939aff4c8e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002279.fa
@@ -0,0 +1,9 @@
+>2_653
+MGEARRGTEQARLLRQVVLLHQEVRIHLCRLMGMHDTDYAALALLMRGRLGPSALASALG
+LSSAAATAVVDRLEAAGHAERLPHPQDRRRTMVRLLPASQEPVQAEVDRMADATGALLED
+FDERERAAIARYLAGTRDALEQWRDDVAARVAARDDVAAVDAEAGR
+>3_570
+MARLLDFLEKGVDVPEAIQSLDAASTALRESPMLSPISEPAPAIRPVSGELKGVTSAART
+LRRIIRLNAQIRVQMRLLMGLNETDYAALSVLMRAPTGPTELARNLHLTTAATTAVVDRL
+VSGGHAVREPHPQDRRRTLVRALPESRSQAMAEVQPMVDMVGDAMSGMTDQDRAAVERFL
+DSVADHMDAWRDDLTARVTQQAEQP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002280.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002280.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5ed6ed95d18c65810e7005d9089233efe728833
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002280.fa
@@ -0,0 +1,30 @@
+>2_692
+MHQSLRAYASNRDLGHGAHAVTAAARTAGELTYDGLPREPLLYAGIATALLTLGLIPLAL
+WFRVRRRIDRLRRRLRSARTDLARVILDLEAVEVAVLTTPEGASGGSSGRSSAPDLRGGL
+ARLTDSAFALARGEEDLARRLRRPDRGAEADLQGHESAVARVRGQAAGLHDAATLQSRHA
+GAQTAADRLVAPLVMAAQAVVSRARRVSDGRSPEAPSDRPRSDAVADRLQSAADALLQVA
+ADAGSGDLTGLAPRVLEAEGELARASADLVQHLRAAAGPAGGPIDEAVTAVPSLRPDPED
+AARRANAGLPAVGPADAPQALSTAYAAVLVAGAADPQDVVAAVVDADRELRGSVAPTPDE
+WRAAVARVAEERRRAGERERSASSGPWWAAVGTAVGCLVLAGLIARPLAEAATAEPGWDL
+AGSDEVASLVVDGMPQGVLTEEHLSVEDVRGYLEETLPAGLDVTVAVRPAASHLVPDPSG
+PSSESIMALDRSATLDGLARLKAEFPDLLEPGTGDLRPGAVIVPVFTTAGGQVIVDASLT
+GVVAYGTESWLEGGGFERMNVSRGWEPDLTEVSVAHEIEDVARGVQSEGAFESDVETSTL
+WALLTVSGGIVLLMLALAARAVGGAMARRFGVGPARGTVARARGRLERLMLDLDLQRLDA
+VAVLGRGPAADAREAEQRLWESALVSAWREADEIERLPLPQQWDEDVKRRAAALAARVED
+LAAHRSDVAARAEL
+>2_750
+MRAPVLAWIAGACALLTAVLVGLAAWVTTVEPRHTVRIEVAEGTPVGISQGTVDAVLAQR
+PVRSWQPMTLRVTDEHLTFEETFRGEGLPEGVDVLLSTQTERLGAQRPDLDASERPERDA
+AGVGIRPGLGLDEDHADGHDLERMYLAGLGAGQGPTAVVNVARAMGEASYAGPARVPALH
+LGLALPALAGALVATALWARARRRQADVRRALDRGRASLARVLLEVEALEVSVAGVAPHA
+LPTGHSQRRAELRRSLQHEARRERDLTDAVERLTARDAIRGTASDDDAGGRPGGRGRGGR
+RRGGRSRGTRPASSWRDLGQRVAAFEDSTRGLEDAVEQLIDSADVLAATPRRTRVVDRVL
+APVAVEMLALTGLLREAPEGAVDPRIRRALDEAYDDLLAVAQHERLDRDAARRWRDAEKR
+LAGHAREVTAQLERFPLGADAGRVAAAPEDDSLAALRAGLGLSARPAGDLLTHLARARRT
+AVALLGPLTDEHRGAPSSSGEGAPGASRRADRSDALASAPHLRRAAWALVTVLAVLVSVP
+FAQRAADAALPPDPYRLVGSEALRSVSVDGPADGIDVERVAEHVDGTFPRALDVVVAVRA
+GEAYLTPRATRTDAEDGKGPWSELGVDLDPTATAEGLRRVVAESGALLDPATGELRRDAV
+VLPVFVFEDGRRVMGRVPLNTVDTAEPWTVAGVVLSSLPHAQGASLAGEVGSAVVRAGQA
+MQSADREGEAPAPDVEPAVLTTVLTLGFAAALLTLALALESLATTAAGLRGLGSLTSSGR
+RLQAITRRLEALMLGLDDSRLDAVAVLGRGPAGTAKEAGQRLYERELVAAWREAKALAGT
+SVVERLRGGMADRLDGLEATAAALEHREADVADRAAEVLERARRHPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002282.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002282.fa
new file mode 100644
index 0000000000000000000000000000000000000000..424e2238cf8fc6bf49191d9395d22103e3f9cbd8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002282.fa
@@ -0,0 +1,6 @@
+>2_717
+MLQRPLEPAQYVSLAYSDALIAAGVSASVGTVGDSYDNALAETVNGLYKAELIHSKRVWE
+SVEEVELATMGWVHWWNTARLHEALGYCTPAEVEATYTHDQDSAPVAS
+>2_727
+MLQRPLEPAQYVSLAYSDALIAAGVSASVGTVGDSYDNALAETVNGLYKAELIHSKRVWE
+SVEEVELATMGWVHWWNTARLHEALGYCTPAEVEATYTHDQDSAPVAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002292.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002292.fa
new file mode 100644
index 0000000000000000000000000000000000000000..39ec8531a45016c34a704b314489ed53c4f4919c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002292.fa
@@ -0,0 +1,8 @@
+>2_889
+MDGVRGTWAPGTVRGVLHASGVGAATGYPGVVLATPAATEHPAAQIADVPAQLLVSVDLP
+DHWDRLDAFEGAGYRRVPAVVALDDDAVRPAYLYELVPDAVPPSA
+>4_1809
+MALTGVPELGGWRVTPSPTPAGTTPPELTITYATDDFATALALANRIGEAAEAADHHPDL
+TVSYGRLTVGMHSHDVRALTSRDVRLARTVARLASEVLAPHALAAYGTLAPGRSNAHVMD
+GVRGTWIPGTLRGTLHASGIGAATGYPGVVLAGTAPAHATTDVPAQVLVSADLPDHWDRL
+DAFEGAGYRRVPGVVALEDDDAVRPAFVYELVPDAVPPSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002294.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002294.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a55e00e0e61e6bcb84e87f8d5d17cbc667dad1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002294.fa
@@ -0,0 +1,12 @@
+>2_913
+MAAGGFTLGLGQPLTMSLVTQAVPADWRSSALAVRLMGNRAGQVVLPATAGLLAAPLGPA
+AAVWFACAVLAASGLERTAAARRRR
+>3_845
+MTESRTGAAAGERTTAGPGAGWLWALIGAAVLTQAATNLARPVTSYHLLSLGAPDAAVGL
+ATAAYALLPLVGALWLGRVTDRLSSAAPLVVAGAAVVAAGAAGLALATDVAAVLAASAVL
+GVGHLAFTIAGQAAIARRAPAHLLDGAFGWFTAAFSLGQMLGPLLSGGILTAVGGTPRDA
+TTLALWVSAGLALAGALPVLLAPGAPPGTRDPAAREASAESGAAPGDDAGRPTVRAILAR
+PGVGSAMLASLALLAVLDILTAFLPVVGERHGVSAAWVGALLALRGAGSLVSRVFLPRLR
+RRFSRELLLAVALWASAATIAAVPVGMTSGLLWLAAAAAVAGGLTLGVGQPLTMSVISEA
+VPHAWRSTALAVRLMGNRLGQVVLPAAAGLAAAPLGPSAAVWTACAVLAVSGAERAARSR
+RRRPPRSVRSGGGRGGSASADQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002298.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002298.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf07a469f6af74787f28059a4a084daf91d75906
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002298.fa
@@ -0,0 +1,9 @@
+>2_957
+MGPGQHAKLTMEGIAARAGVSKQTVYRWWKTKVDVLVEAVGAGYLVIPLPVIPDTGDLRE
+DLAHWLREMQEEIDGGGATHLSQSLVAAIATADSQSRQIHGMLVAPVREQLHARFRSARL
+GDGVDREMLAETVGAQLVMRVLFAEPTDEEWVRRLLDLVAPEGS
+>3_922
+MTSLTPPRAGTIRPGGRTARVRAEVLRATRELLTQQGASAMRMELIAERSGVHRSTLYRR
+WKRPAGIIADLADDIAGTIAVPDTGDLGQDLRQLAGRLAHQLDGDGGALVRALLGWPDQE
+VQQHLEDFWRDRRADVGLVLQHHGIDADPALVTRLLASPLHYRSLIERHPVDDETITAAV
+ESTILAVLRTPRTSHR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002306.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002306.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a13de974e0a821077279eee2d8dea5bb79fade0b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002306.fa
@@ -0,0 +1,9 @@
+>2_1239
+MQDARRALEAVGSVPDLAGTAVAVMGVSGSGKTVLALRLAAALGVPFAEADEFHSPEAVA
+KMAGGTPLTDADRLPWLHRIRDWTAVAAAERGAVVTCSALKRSYRDLLRDGPARVVFLHV
+DAPQSEIRDRMARRRHYMPPTLLHSQAATLEPLGVDEPGAVLANDSTVEDLTERALRVLA
+AR
+>3_1149
+MTGQAGPARALLDLAGTAVVVMGVSGSGKTVLAQRLAQALGVPFAEGDEFHSAEAVARMA
+GGTPLTDEDRGPWLRRIRDWMGSGVAARGAVVTCSALKRSYRDVLREAPVRVVFLHVETP
+AEQVLHRMERRRHFMPPALLPGQLATLEPLEADEEGVVLANDSTMEELTERALRALADL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002314.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002314.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28772318d843c8e72fe47ee27facbd2611e04bce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002314.fa
@@ -0,0 +1,9 @@
+>2_1655
+MLSFGIREAAGSQPATGPRRTGRSPPLEASSGASGRQTHAPSSGSRRHPCTGACAGRTTS
+VSHSVVSGFHPARTVATSSSSGRQRVAEARQPRAVRWTASHSWATQSRSGTTHRPALPFT
+RCQSWPLEALTSRGTLRHSRTESSGLLILYVRRTPSTGVTAADPAPESSPLRSNPAGSCE
+TLATMPTGIDHQILYRFAVGSAGVLPLRGLPPAAPPVPRPRGRLGGPGAADSGRLVPTGR
+SSTGSPPAGRPSGEPALSPAHARSPVSGLHGRADPLPARPLRRDPASTSPPPPFRPEQHG
+RVLPPPGPRGRGQRGPARADRPRLPDGTRRRAARW
+>4_1109
+MRSNPAGTCETLATMATGIDHQIPYRFAVGSAGFLPLRGLPPAAPPAPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002315.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002315.fa
new file mode 100644
index 0000000000000000000000000000000000000000..981f7e4a3f60911ae25c8218f61e9ba99e13ea29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002315.fa
@@ -0,0 +1,8 @@
+>2_1879
+MRVHIATDHAGMELSAHLVEHLRGKGYEMVDHGPEEYDALDDYPGFCINAARAVVADREK
+GLDSLGIVLGGSGNGEQIAANKVAGVRAALAWNLDTAKLAREHNDANVVAVGGRQHSLEE
+ATAIIEAFLAEPFSEDERHVRRIGKIAQYEQTGEVVM
+>3_1826
+MRVHIATDHAGMELSAHLVEHLTAAGYEMVDHGPTEYDAQDDYPGFCINAARAVVADREQ
+GLDSLGIVLGGSGNGEQIAANKVAGVRAALAWNLDTAKLAREHNDANVVAVGGRQHSLEE
+ATAIIEAFLAEPFSEDERHVRRIGKIAHYEQTGEVVM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002318.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002318.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d1dda38b03a7619eb455be46ec69541c08b12740
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002318.fa
@@ -0,0 +1,12 @@
+>2_2074
+MRAAAGGGPGPDRAALDRLAWRLPVRRVTEHPRSPADRGTWPATVPAVRQLLDEGLDLSA
+ATVVVGANGAGKSTLVEAVAEAFGLNAEGGTRNVVHETRRTSSDLAEHLQLARGAQATRD
+GVFLRAETMYGLFTYYESVFRGADHHRRSHGEAFLQFCAERAGLTGLWVLDEPESALSFD
+GCLALIAHLRDILADGSQVILSTHSPVLAALPGARILLLDERGITPTEYDDLPFVYHHRS
+FLDSPQRYLRHLYDA
+>3_1964
+MPEVGIDATPTWPVRQVSEHPRAPMPRESWPATVPAIAQVLDAGLDLGPATVLVGANGAG
+KSTLVEGIAEAFGLNAEGGTRNVRHETRRTTSPLAGHLLLTRSAGAPRGGVFLRAETMYG
+LFTHLEQNLIGDVLHERSHGEAFLDYLQERAGVRGLWVLDEPESALSFDGCMALLVLLAD
+VLEGGSQVILSTHSPLLAALPGAQMLEVGPWGLRDTAWEDVEAVQHWRRFLDSPERYLRH
+LR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002347.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002347.fa
new file mode 100644
index 0000000000000000000000000000000000000000..229d7beb16a97954f90d328f43b9f61404413860
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002347.fa
@@ -0,0 +1,29 @@
+>3_625
+MTSTTHHQEQPVSNRDVIRVRGARTNNLRDVDVDIPKKQLTVVTGVSGSGKSSLAFDTIA
+AESQRLLAATYPAFVQNLMPHLPRPDVDTLEGLSASIVVDQAPLGANPRSTVGTATDAWS
+LLRQLYAGHGTPPVPGPHALSFNAATGMCPACEGTGRTATLDVDLVLDRSLSLNDGAITF
+PNFTVGSLFWKVYARSGAFDNDKPVQSYTPAELEHLLTGTGPNVDTGTYPMAYEGVLTKI
+TRLYLSKDPAALKPRLREALELAATTGPCPGCAGTRLNSAARACTIDNTPITTCHTMPAT
+DLHRWLADLDLPAAAPLIAQLQSLLANLTRVGLGYLALDRPTSTLSGGEGQRIRTVLHLD
+SALTDLTYVFDEPAAGLHAHDTAQVVTLLHALRDKGNTVLVVEHHPDVITAADHVIDLGP
+GAGTDGGTITFQGTPAQLTHTHTPTAAALAARPTLNLTPRTPTGTLRIRDATTHNLHHLD
+VDIPLGVLTCITGVAGAGKTSLLTNLPRRDDLAVIDQRPIRGSRRSTPATYTGVMDWLRD
+AFAKAGSTPGHKLKPAMFSANSAGACPDCTGLGVTYLDAPGSGPVPVTCTTCNGARYTAD
+VLTHTLDGLTIADVLGLPVADAATRYTNTPAGPPLAGLVDVGLGYLTLGQPLSTLSGGER
+QRLRLATRIAQSATVYALDEPTTGLHMSDVDTLTRLLHRLVDTGATVVVADHHLNLIATA
+DHVIDLGPDAGPGGGHITYQGPAADLATTDTHTGRALAARLAL
+>3_1204
+MPTPHASAAPAPHTAHPADGHDVIRVHGARTHNLQDVSLELPKRRLTVFTGVSGSGKSSL
+VFGTLAAESQRLVNETYPSFVQGFMAAMPRPDVDVLEGLTTAIVVGQERMGSNPRSTVGT
+ATDATALLRILFSRLGTPHIGSPQAFSFNVASVSGAGAVSTQKNGRTVKERREFSVTGGM
+CERCEGTGRVSDIDLAALYDEELSLEDGALKIPGYSMDGWCGRIFRGAGLFPVDTPIKKF
+TQRQLDALLHKEATTITVDGINLTYLGLIPQMERSMLSKDVESLQPHIRRFVESAVAFGT
+CPDCHGTRLNERARSVTLGGASIDQVCALQITDAAAWLRGLDAGPAAPLVAGLQELLDAF
+ERIGLGYLSLDRATGTLSGGESQRVKMIRHLGSALTDVTYVFDEPSVGLHPHDLARVNAL
+LTDLRDKGNTVLVVEHKPETIAIADHVVDMGPRAGADGGRVTFEGTVEELAASDTLTGRH
+LKDRAALKGEVRTPTGVVEIRGASEHNLQDVDVDIPLGVLVAVTGVAGSGKSSLVHGSLA
+GREGVVVIDQAPITGSRRSNPATYTGLLEPLRKAFAKANGVKPGLFSPNSDGACPACKGA
+GVIYTDLATLGGVESVCEECQGRRFLPEVLELTLAGRSIADVLEMSVDQAAAYVAEGEAR
+LPAAQKVLGRLQDVGLGYLTVGQPLTTLSGGERQRLKLAVQMGERAEVYVLDEPTTGLHL
+ADVDQLLALLDRLVDGGTSVVVIEHHQAVMAHADWIVDLGPGAGHDGGRIVFEGTPAALV
+ADASTLTGRHLKEYVGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002348.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002348.fa
new file mode 100644
index 0000000000000000000000000000000000000000..23d1aaccbcafe730342eeb82f0737374338c9da9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002348.fa
@@ -0,0 +1,10 @@
+>3_649
+MSAEPDGMRPHSPSAQEAYAARAVEYADLLGRMDAVADADKRLVEAWAQRTGGVLADVGC
+GPAHWTAYLHSLGHDVRGIEPVEEFVAHARRAHPEVRVERGSFETLPTAAVDGILAWYSI
+IHTPPAEMPHLFEHAHRSLRPGGSMLLGFFAGDEVEPFDHAVTTTWHWPVDALSRLLTTA
+EFTVVDRGTRQDPGARLHGWIEADRE
+>3_918
+MEAGTLDAEGGTTITADDVHGENISSCAAYGARAAEYAELLGTMAAVADDDRLLVEAWAH
+ETGGSLADVGCGPAHWTAHLAALGHDIVGVEPVDEFVAHARRVHPGVRVETGSFRTLPAS
+TFDGILAWYSMIHTPPPEATLLLEHAHEALRPGGSLLLGFFAGDRVEPFDHAVTTAWYWP
+LDDLTSVLTAAGFTVTDRGTRLDPGTRRHGWMRAHRN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002358.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002358.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2778c10ab9c4f47e3d6a9221911ac7a797dd5a6c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002358.fa
@@ -0,0 +1,18 @@
+>3_1171
+MGVLKDLKERFERERVELHLDDIQGLVLRERPEPYVGAHAMLTVEEAEGGRDFVRRLAEH
+VTSAQDWADDLQSWTGVAISFAGLRALGLPEDPLASFPLPYQQGMAARAQQLMDTGPNAP
+EHWDEAFTQDACHIALTIYAADADALDAALDQAQQVLDHSTGVTLVATHRFGVDELNKNP
+FGFRDSISQPTVAGSGVRPQPGQERSISAGEFILGENSETGSPLAVPQPDVLGRNGTYVV
+LRKFASRVGAFNEYLASQSPDPEEQHRIAAKMFGRWRSGAPLVLSPDHDDEALGNDPERR
+NDFTFEDDPKGLMCPHSSHMRRLNPRDSDLSIMTDVNIKRIIRRSSTYGPGWSPEVTSAD
+DAKEDRGIYFIFISARAFDTIEFMQQEWINGGNFVDLGSERDPIVGLHEDDPTQGRFTIP
+AEPARKRINGITTFNRMAGGEYLFMPSLRALRWIGEAGWTSDQSDAEA
+>4_1480
+MGVLKDLKERFDRERVELDLDDIQGLVLRSRPEPYVGAHAMLTVEEAEGGRDFVRRLAEH
+VTSAQDWADDLQSWTGVAISYAGLRALGLPEDSLASFPLPYQQGMAARAQQLMDTGPNAP
+EHWDEAFTQDACHIALTIYAADADALDAALDQAEEVLEHSTGVTLVATHRFGVDELNKNP
+FGFRDSISQPTVAGSGVRPQPGQERSISAGEFILGENSETGSPLAVPQPDVLGRNGTYVV
+LRKFASRVGAFNEYLASQSPDPEEQHRIAAKMFGRWRSGAPLVLSPDHDDEELGNDPERR
+NDFTFEDDPKGLMCPHSSHMRRLNPRDSDLSIMTDVNIKRIIRRSSTYGPGWSPEVSSAD
+DAKEDRGIYFIFISARAFDTIEFMQQEWINGGNFVDLGSERDPIVGLHEDDPTQGRFTIP
+AEPARKRIDGITTFNRMAGGEYLFMPSLSALRWIGEGGWTSDQSAAEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002367.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002367.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc4132f23bb67b7c92d2eee4ad0c1e40ac2c542c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002367.fa
@@ -0,0 +1,12 @@
+>3_2260
+MNTRCLVLTSGRAADGPYGIDQLGQFGYDLVEVEPARTRVHRKLRDVVEHRSGRPMDKTV
+RSVRQAWQADLVLAFLEKEALAASWAKRRGVAPFAGRPLVMIACWLADELQRMSPAQRTA
+VVTSYSGVDLIIVLSRNQVEILVEAGFDASRIEAVSFGYNPDQFPVAAFEERRGIVSVGA
+DRGRDFPTLLQAVEGSDLQLHLYTGEGHLNDVELPAEAVLHGRVPFERYQEVIATASMVA
+IPTHVMAYPSGQTVALEAAGTGACLILTDTPAMREYFTDETAVFVPPGDADGWRTALTEL
+TSDAEARRRLGRNAAAMVADHFTYADMWRQVDEAIRRRGWSAQ
+>4_497
+MEGVDRLLMFSSNQVRIFTDAGIDPKRLHPVLFGVDERFYHPSKEPRRFQVLAAGVDRGR
+DWQTLVEAARLLPHIRFELYTRPETVAPLAVPSNMTVHAPVGIDEHRHNLQSSDLVVVPT
+HDLAYPTGQSVMLEAMASGACVAVTATEAMADYQDDGVSTLALPLHDPEGVASVIEMPIE
+DAALRRQIAESGRAAIEERFTFTRMWDEIRQVVRDVARDGASTASAFR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002370.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002370.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4539a67f8746f5d875fa5247306dc0b01043c7cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002370.fa
@@ -0,0 +1,2 @@
+>0_26
+MFDILVALFVSSLAYLGFAVALGLTLPSGILGGGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002374.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002374.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf311cdb64ebed7b1f489949330c86f7bd71826c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002374.fa
@@ -0,0 +1,3 @@
+>0_233
+MSYYHGDDSHTLSPPAVSPPHHPVVDRPRGRPEPQEDEPMFPITDDQKALVDAVRDLAEQ
+RVAPHALDWDAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002385.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002385.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a5ed65baf626b6f95bc71a6e8182c1ec9ad2747
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002385.fa
@@ -0,0 +1,3 @@
+>0_567
+MSEQTEFEQSHDVPEGQEPRVVYVERDRGLVASVRRLRQRAGEAGRRWVAESVDAPLPTS
+WQERVPDAWDSARGRWVIAAVALAVLVVWVLVVQAMAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002386.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002386.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3cdac90dad347a108f8c1d8dbe14c78bd1cbbcc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002386.fa
@@ -0,0 +1,7 @@
+>0_570
+MWEKDFEEFLRGSILGLAKAAAGLIEQAFSVGALTPEWWVTVVGGQVTTTVAGGESTVID
+HPGMLNIIVVAMIPLLVIFVAVQVVLSAVRGSTAGMVRAFLAAVFSIPATYVVVGLVWMA
+MGATQQLTLWILRVGSGGTDGEDEAVAGVLGLFGLTYDAANDKILLDENFAQWEMASENS
+GNGMIVVAVIIALVIFFACFVLMAMMIFRLVLILILASFAPPAIFSLALEPAKALAGRWL
+SMMLGLIMAGPLAAAVVRLGMAMAALSTDWVQTVAGMVLVFVAAAMPIFMLAVTAWLAGG
+AGQAEQAGVMAASRAGRGAMNSMRGVSARAGRMRQRAGAMVMRGGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002405.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002405.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3df6c49a101c40f579076b453d1500c3bd0fd44b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002405.fa
@@ -0,0 +1,3 @@
+>0_1437
+MPAHGLPNTTEPVDLTSTVPPGALPPEEAAKYIGRPGALKTLTNYRSMGKGPKAISVLGK
+PVYRIEDLDAYLAAGGDAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002417.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002417.fa
new file mode 100644
index 0000000000000000000000000000000000000000..732a086c0b8824add54e2d6b149b7f68213ff226
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002417.fa
@@ -0,0 +1,21 @@
+>0_1894
+MIDAATLTKDLRALVLEVEEDLRGVLQSRPEEDAAWKSKHGILVKEEQTALSWTEFRDGR
+ITQVAVAWVLATVFVRFVEDNSLVAPVWLAGPTEGRRQEAQDAQLAYFRQHPEHTGREWI
+RQAIRHLETLPATRALVQDSAHLHLPISGRMADRIIAFWREDDPAGGLVRDFTDDRLDTR
+FLGDLYQDLSEYAQKTFALKQTPVFVEEFILDRTLEPALAERPLEGFRVIDPTCGSGHFL
+LGAFDRVADRWAAAGATADEAVDRALESVVGVDINPFATAIARFRLAVAALQRAGETSLE
+TATPRHVRVLTGDSLLHGRQRPGTGESFDAVDLQLGGFFASPEEIDELREALRSGSYDAV
+VGNPPYITVKDKALNQLYRRLYPATTKGSYALSAPFLERFFDLARPESATTPAGWTGQIT
+ANSFMKREFGTPVVEKFLPTKDLELVIDTSGAYIPGHGTPTVILVGRNAAPEGETVRAVL
+GIQGEPGRPTEASEGKVWRAIAGHVDEPGYEDPWVSVIDVPRASLATHPWSLQGGSAPQA
+MATLDEKAHATLGSLNPDIGLSVKSGMDGAYFAGIDVFRRRGFETEQVAVVIGEDVRDFS
+LINNLRTFFPYSADGTRRDPSEAARRYLWPNRAHLTNQRDFGKVKSERGLEWFEPSMFFA
+RRYTAPLSIAFAFVATHNHFVLDRGGKVFNRSAPVIKLPAGATEDDHFALLGVLNSSVAC
+FWLKQNSYPKGGDPVGDSGARVSQLPWADRYEFTSTTLKDFPLPAQMPADRARRLDALAG
+ERAALTPAALAERAVPTADALATAEAEYDRVTRQMIAEQEELDWKNYAAYGFTSEPLTFT
+GELPQVRLGERAFEIALARRVAAGEATSEWFTRHGSTPITEVPEHWPADYRALVQQRLEL
+IEADRSLNLLERPEYKRRWAAEPWDKQVDAALRTWLLDRLDVPELWRDRAGRPTPRSIAQ
+LADPLGRDADFMAVLRLWSGAEDISTVKELTRLLTDEAVPYLAALRFTESGLRKFRAWQH
+TWDLQRRQDAGEDVGHIPAPPTYSQADTRKATWWKHRGKLDVPKERFILYPDAGREGDPT
+LLLGWAGWDHAQQALALNRIVDERLAEDASAERLVPLVAGLAELQPWVEQWHAEEDPAFG
+LPLAEFTRGTLEEYRRELGVTAAQLEAWRPAPTGRGGRRKRT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002418.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002418.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1fa27f775bea41457746ccbe613d4c48737153a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002418.fa
@@ -0,0 +1,22 @@
+>0_1895
+MTDLLKDLLDIPATTGAEDYVLRLTDSVGERSRSALKDYVVTEDIAAAFDQALGLVSDAL
+AENTSRAAFLVGTFGSGKSHFMAVMHALLRQDPQARSIPELGPVLHRHDPALRERKILPL
+VFHMLGRTSFEEAIYGGYLTQVRALHPDAPLPALHATDQVLQDADTYRQDLGDAKFFARL
+NGRATDVDEDPDDPWGSVVEGEQWNAVRYAQARAAAPENPLRQELVTALTRTLFTSYTKQ
+ADHVPLDTGLRVISEHAKSLGYDAVTLFLDELVLWLAFAATDVGFFRRETQKLTQLVEAN
+DARRAVPIISFVARQMDLKQWFADAGASGNEQAALDQAFAHQSGRFAEIPLGDDNLPYVA
+HRRLLAPKDDDAAARLEDAFRAIKDESGAGWNVLLDGVNTDERHRGADEAAFRLTYPFSP
+ALISTLRSLASSMQRERTALKVMKQMLVDRRDRLTVDELIPVGDAYPYLVEGQKPLDATA
+QALFSSAQNLWAQKWEPLLRSKHGLTPEQASAPDENVPVGYRTDRRLARTLLLSAIAPKV
+PALRDLTPARLAALNHGSIVAPLPGKEAQIVLGKVKEWAQQIPEIHVDGDGRSPIIRLRL
+AEVDYEKVVERARAEDNPGRRRELIQQTLLELLGVDATARENLFNTKSVPVTWRGSAREV
+DLVFGNVREASWLPDDVFEERPGTWRLVIDHPFDEVGHTTAEDLARVEQLRSSSRERQTV
+VWVPAFLSEERLRDLSRLVILDWLFEGVGDRWDQHSDHLNENDRRIARAMLEGQRDALRD
+SLRLTLEQAYGIAQPSTGALEAGTAEHKMLTSLHRGFADTELTEPSFSTAFSALVDRMFS
+FSHPDHPRFEPGDQPVTVRQLTHVYQHMERAMADPDRRVTLGDGAADVRRIAEPLRVGKT
+AETVFLFGSNQFAFWNGVISRASGDRAQDAEERLTVATLRSWIGTADPDWGLSRELENLI
+ILGWALQHQRSWYMGGAAMAAPDVHKVHDAMELRQQPMPTPEEWARTVETAGILFGTRVN
+PYLTGPAMTEMTGLVNDAAADALPATQALATALTAARAQAPAELGLREDADRERLAHLAV
+DLLGRWSRLGGKALVESLAAVRDSVDPVHLSTSIGTQAADVARAVKAVRWKPMSDAVGKG
+TDEARQLAQDVRRVWHASQHEVHLPQVLPGLEERAYDLAVSGDGPAPGPTPPAVVPEPLT
+NPEQISLPSVRQGAATGRGRLGLTDALQRARTAAEAVLDEHPDANVEITWRVVE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002420.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002420.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9be3ade77facde78361f355e78a50812493002b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002420.fa
@@ -0,0 +1,9 @@
+>0_1897
+MTRVSSRRRAEILSALRKGTVPQDGLDRLAVGLDRFSAALDEEIDLATGGAAAFKAVRGE
+YGAGKTFFTRHLAARARARGMATAEVQISEKETPLHRLQTVYRRVTESLRTANVPPSAFR
+SVLDSWLFTLQSEAAAQNPSDLESTVDRLLEQRLRTVSERNPTFAVALRAYHRATVAEDH
+ELADGLAAWLGGQPHVAASVKRTAGVRGDLDHDGALSFLQGLLVVLRDAGHPGLLLVLDE
+VETLQRMRRDTQEKSLNGLRQLIDEIDAGRLPGLYVVITGTPAFFTGRSGVNLLPPLAQR
+LEVDFTTDSRFDNPRAVQIRLPGFTHDSLAEVGARVRDLFADGSPQGDRVRAIVDDAYLG
+DLAAAVAGKLGGQTGVSPRLYLKKLVQDVLDRVELHPAFDPRRDYALTVSAADLTEQERA
+AAGRRQIMAGQDDPDAVDLDLS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002426.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002426.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e12595bd8cd3b80ea74c8025ba87b40edabf4360
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002426.fa
@@ -0,0 +1,5 @@
+>0_2081
+MTRTSTYGFREGTLDTVRRSMRTVAVHRDDGELVGRVVRGELAGCERTGTFRWESIGGAA
+TTVGIRRATWRSAVGRLLRPTYAVTHRPEVTAPAEGEPPAPVHDELKEIWGENVLYFAVD
+GTVQGRRVVARADWDGSVEVRAQGEDGGRPRRVARFHSGGMFSLTRVEVDHEAAGTTRDG
+ALFGVLMLLPFVARLHREESSLIEELLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002429.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002429.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9a827dbb99a163d43572f04681444ef033edc596
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002429.fa
@@ -0,0 +1,3 @@
+>0_2220
+MSRFQMLSRAQWELITPRLPTRTGRAGRPFTDARTMVEAIIYRYRYRCFDSLEGPARGLR
+ALADRVDLAPPDGGRGHLGHGADKANRRH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002452.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002452.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a2462b14f8879604dbb7ed78d855aca919d7ba8e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002452.fa
@@ -0,0 +1,3 @@
+>1_1102
+MLAGDGALDGQEQVDAVFRVSRERRAEALPKGLTESTLREVVELLGADPETALSAAEVGE
+RLGISRVTARRYLEHLERIRRVRRSARHGGRGRPEQEYRWAGRT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002456.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002456.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cbedd7f906167739ef28a7e019930561f8d4b8bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002456.fa
@@ -0,0 +1,6 @@
+>1_1601
+MQLTATETCEQLAGNRGGLALDVLDFSVDFYMEDLVMSDRDRRVAGLVEQGDQLRAVAHP
+KYLDTLDRLMAEPEEIQRIVKSGGGRYTMPMQDIVQSVTGAATDCYQPGEELNRFVENMT
+PIINRIPEYAALEVDGASEGASSTPAASSTSTPTAGSAPASEPTPTPEPTPTLSEETEAA
+AEHEAGDVPMEYQSALRKAYSYEENMDMSKMGIYGQLVSEYGEQFSPEAAQYAIDNMTDV
+DWNANALAKAKSYQEMMDMSPSAIYDQLVSEYGEEFTPDQAQYAIDNLSQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002472.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002472.fa
new file mode 100644
index 0000000000000000000000000000000000000000..119d145be53f0bd9ca408d771630ccbaa40020a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002472.fa
@@ -0,0 +1,4 @@
+>1_2159
+MYGDGFAEERSWGINDGPRVGNVGSSWAPDRGFFLEVGPCGIDNLIVGDLTPRQARTLGS
+RLLEVADRIEELQAEDVRDAVRAIASKKGGGTITDLARAADRLGVQVVTMGAAWEAAWAE
+LGGEQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002501.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002501.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5a092d4bb08490142258293cc0180e10f552b1de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002501.fa
@@ -0,0 +1,6 @@
+>2_130
+MVPNEFAGDESAAAAGNAATDNFRRAGKTGTAQVDQARVDELAGALIKAANDIVLEKKVT
+YEEYNALKAWLIKVGDDGEWPLFLDVWLEHSVEDVATEHREGNKGSIEGPYYVPDAPVPA
+DGRTIPMREDEGGTAMVFHGQVRSTDGTPLKDAKVELWHADNDGFYSQFAPNLPEWNLRG
+SFPVDAEGNYSINTVQPAPYQIPTDGACGQLIAAAGWHAWRPAHLHLKVSAPGHELLTAQ
+LYFPGDEHNDDDIASAVKPELILDPKPAGEGVDVEYDFVLDPVSEKTPETVRGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002502.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002502.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a83366bc4f3ad344ad600cc456996b6ed743bdbf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002502.fa
@@ -0,0 +1,3 @@
+>2_131
+MLFLARMDVTFPETMTDETKAGFQAREKEYSGDLQRRGVMKGIWRIVGEYANHSVFDVDS
+HDELHAILSGFPMFPYMNVRVTPLATHPNAIAEDFFTTAEDRAAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002504.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002504.fa
new file mode 100644
index 0000000000000000000000000000000000000000..190c35906fb7c7ba9450cc0319778a00dfa14bf4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002504.fa
@@ -0,0 +1,6 @@
+>2_135
+MPMSDAPDAVVLALPYRRPFAFDHLLRFHAARAVPGVEHVDQAAYTRVLALPRGPAVAVV
+SDDDGAVRLELRHAHPDDVAAAAGLVRRMFDLDADPQAVDAALRQDPAAARSVTRFPGLR
+VPGSPDPHESLFRAIVGQQITVARATARLADMAARMPSLGFDGPVDRLFPTAERMAEGLH
+ALYRGPAARREALRGAAEALVEDPDLLERTRDPEALSETLVGLRGVGPWTAAYVSMRVLN
+APDVPLPGDAAVATGARLLGFDDVAAAYERVRPFRSSFTIHAWNAAAGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002515.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002515.fa
new file mode 100644
index 0000000000000000000000000000000000000000..80ef08e33c88987286de321a27ad4e8cae424c69
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002515.fa
@@ -0,0 +1,9 @@
+>2_259
+MPRPARLVAPPYERYADAIAALPAADRSRSLGVLDLDAFRANAAAMAARAAGVPVRVASK
+SLRIRRAVVEALEQPGFRGVMAYALAEALWWAESGQPDVLVAYPTADEAALDALLRSPRA
+RAAVVLTVDSAEHLRWIEDRVRAAGVHPGQGAADLPPLRLCLDVDTAWRPLARLRVGALR
+SPVRTPDQARELADRILRMPGVRLSGVLAYEAQVAGLPDASGPRAAAVRVVKSGSRRDLA
+RRRPAIVAAVRQAVRAAGAELDFVNGGGTGSLAETAAEGVVTELGAGSGLLAPASFDGFH
+GLGLRPAASYVRPVVRRPAPDVVTVAGGGWIASGAPGADRWPTVAWPEGLRLTRQEGAGE
+VQTPLHGPGAARLALGDPVFFRHAKGGEPAEHLDAVAVYSAQADAIVDLWPTYRGEGRMF
+T
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002539.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002539.fa
new file mode 100644
index 0000000000000000000000000000000000000000..438acf05c2b691d97a795b177c566ec3af6f873d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002539.fa
@@ -0,0 +1,20 @@
+>2_461
+MTAPHPAQEQDTFDLGIEFPGRDTADIRQWRLEEVQIANWGTMDGRIHRFPVSRRGHLIT
+GPSGSGKSSILDAIAAVLTPDKWLRFNQAAQGGAERTATRGLVSYVRGAWTRRQDEDEDR
+VVSAYLRPGATWAGVVLTYRDGAGGVVSLCRQFFLRGTAMSRADMKDLCLLERSAVDLAE
+LQTLIDDGIRTRRVQARWPQAVVTTNGGHGPFYARLRSVFGIRDDAALHLLHRTQSAKGL
+DSLDQLFRNHMLERPPTFAMADRAVEEFGALRTAYERVVDLRRQRDHLLEVRTAAQEYET
+AVAEESRLRRLEAAIHPYHQARFLAEIRRALEEVQASLAGLHAARTEADAEQERAEQRRQ
+HALIALASVGGDRVAELGRQIDAAQEQHRERLARRAVLANRLRAADVDAEPSTAVEFGEL
+QAAIAADLEAPPEHPGPSHAQLTELSRLREAVRELEADITALRRRGSTVPRHLASVREDL
+AEHLGVRTDAVPFVAELLDVDARHQEWTGAIERVLAPLSLTLLIPTRLLSAARTWIDRRH
+LGVRLRFEEVRPTRAAIRPASSQDSLVHKVTVKQGVFHDWLQARLSERFDLACVSTAAEL
+ARHERAVTAAGQVKLSATRYEKDDRFRLDDRSRWVLGDPAAKLEVLVEERAARQAAFAVV
+EGEVQRAQERADAERRRRATLRSVLETPWTDVDHAALERRIADLRAQADELSAASGDLQA
+ARRRDEAAQQDLRTARQAADEARLAAAQAERRRAELTQEARELEAESTGREPLPAELTAE
+LDARFRAVRRSATRSALTESADLVRRDVSALAERARSAGAQAGERCTVLTTQFSRQWAVA
+AADASPGVEDRGTYLAILERIVGQGLPEHEDRFHQILHERSSVLFGELHRAISTAPGEIE
+DRVDPINSALRRSPFDEGRFLHLRVRVRRPEAAQQFLRDLSAVAENAWADDSLDDAERRY
+TALAGIMDRLASSDHVDRVWRQQCLDTREHVTFLAQEVDDAGAVHATYDSGAAMSGGQQQ
+KLVVFCLAAALRYQLAAPEDPRPRYGTVILDEAFDKADARYTRMAMDVFVEFGFQMVLAT
+PQKLLQTIAPYVGGITTVENPTRRLTQIAEVMWEDEEK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002541.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002541.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a5a86d9dfa2de86d3909a4736c953e6d781f7287
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002541.fa
@@ -0,0 +1,10 @@
+>2_463
+MSSLAQALRVHRLVQDDVALRMLRMDSLPLVAGVLATHLGAPNASLPTHELHDALDAELD
+TLRDHLDLSGRTAKAYCEDWRQAGLLERRIADEAREEVYELTPAARQGLRVVEQLLAPRA
+SVTESRLVSLLTALHQLALETDPDTSRRLAALRAEQQALAERIERIASGEDTVLDERRAV
+ERLDDVLTQAADLPVDFARVRARFGELNQELRRRILTDEGLPGDVLENVFRGVDLIESSD
+EGQTFAAFSRMVRDPAMSAAFQADIRAVLERDFAADLPPATRRAVRGLARTLQDGSSAVQ
+DTLTEFARGLRRYVLSQEYHRDRRLHVALREALSAAADAAPATRPYRQTGRDLDLTGMSL
+RSVGEISLHDPREFDVGPALEDAAVATVDMAALRALARETEIDFTELRENVNRTLEGKDG
+APASATVADVLELHPATQGVASVVGLLSLAAQHGQVDPEAVDLLRWPSAAGMHSAHVIRH
+RFTERLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002549.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002549.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a170c1b83f01cd8b2ed421facfec57d2bf19757f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002549.fa
@@ -0,0 +1,4 @@
+>2_476
+MELAPAAPWVRDLGLGPVDAAMTMHDVGDEGSEAPRRVRARLLRVREARFDRRSAAGGQG
+RKLIPGSVRRPDVDGLPGRNEPEAEEAEPPAADTGTPLIGTVSYEASFNPPPGWVSGPDG
+WLLDLEVLEELGPAW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002556.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002556.fa
new file mode 100644
index 0000000000000000000000000000000000000000..072cd193fec20b60dbf3b5dc0e348dd3dc636fb5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002556.fa
@@ -0,0 +1,7 @@
+>2_501
+MSASLAAGAGLVVVGLAARATVQDAGLFLVMTVVALSGMALGNVLIPAWVKLHAGSRTTA
+LMTVYSVFLTLGGSAGALVTAPIAAAARDDGEGWRWALGAWGAVALLPLVVWIVLARRTG
+HDFPAVGAASGDGGSLLRSPTALALTLLFGVQSMNAYVQFAWVPQILRDAGLSAGVAGAA
+VAVTAGLGIAGALLMPTVISRSRTLASWMVLFGAMTALGYVGMLVAPVAGVWLWAVILGV
+GGFAFPTVIALIPARSRDPHVTARLSGFAQPLGYVLAAIGPFAVGLLHEATGGWTAVLVL
+LACSGAVMTAAGLRVAGRVFVDDELLAPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002557.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002557.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c8279f9c95d7673374df8c07bb00c30e4bb8fa96
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002557.fa
@@ -0,0 +1,4 @@
+>2_502
+MTASAPDPATTASPLTVLPVLRDAPAADPDGERGVVRRHHTGDGASLITFTFAPGQGWPE
+HQAAHPITVQCLAGRLDFTVGDRTERLVPGVVAHLPARVRHDVAAPADSPDAANVLLLTM
+LT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002565.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002565.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7da04a8563a73cb004730148607fc39aa029be88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002565.fa
@@ -0,0 +1,2 @@
+>2_585
+MKKLVTALALTASLAAAGAAPAAAQATPVEGFPVTAPVSAKGQEDADNIWCLILNRCR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002569.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002569.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d83830a827b3e0a3f4aed3b6c841eb2147dbc985
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002569.fa
@@ -0,0 +1,3 @@
+>2_590
+MTTPAASTESRAVRRTERTITFLLIALATAVVVVLGLTTELTTLPRLGITLGALVVAYPV
+LRMLLYPRSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002581.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002581.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2fedd9d62e8f75eb1d70f2f3e5ea3ad17ca914a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002581.fa
@@ -0,0 +1,4 @@
+>2_696
+MTRTLEEIWPPSGLVVESDDLRMTALREADVPEVLDVVAGGIHDPSWTPFAFPWTDAPAE
+EIPANYLRFFASTLARTQGGGASIELVVRRGGRVVGVQAMNGADVAGSRRMETGRGQAER
+RGMPTTDVFFELRPDEFVRGDDPVRITGADELRRFLGLT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002589.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002589.fa
new file mode 100644
index 0000000000000000000000000000000000000000..623555b8c46926380d4d9dc6236ba124936d8f69
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002589.fa
@@ -0,0 +1,3 @@
+>2_737
+MGDKISVLSEIDLDGAYVRLIATGHLTETNQQGLHPLIQQARTLAPDGAISVDLSHAEEV
+ESATVDLLRWAIAHNDDTGSGAGPVHILVPDED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002593.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002593.fa
new file mode 100644
index 0000000000000000000000000000000000000000..58bac5fe9d06aae11a1af90d60517ba1b8741f7f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002593.fa
@@ -0,0 +1,8 @@
+>2_767
+MSTAPALVTVVERPHSIRHMSPLRRLFRPFWVIPALVSLAAVVVGLTLPLVDAGLRHQIG
+VAFPGGPDGARSVLGTIASAMISVTGLVFSITMVVMQLASSQFSPRILQDFLSTRITQWT
+LGAFVASFVYSLTVLREVRGASGGGEVFVPQLSVSLAYVLVLTAFALFLAFIRTIMSLIQ
+VSDVVSRIGEATCRAVEEHLPEAGQTPERGLWAPQGDVRVLRLGERHGHVVEVDERRIAA
+LAHEHDLHVELLVGPGDFAAPGTALARVWGAAPEDVGERLEKALALGSHRSLPQDPAFGV
+RQLVDVAERALSPGINDPTTATQVLAELRVILGQAVSRPDAPRHVADEDGTPRVALRRAT
+VEDLLRLAVEEVAHYGADTLQVSRALEQLLGELDAVALPEHRPALGRTRALVARRTEDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002597.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002597.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9e338e6cbb783d2fa29494e7ffddfea6af28c9db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002597.fa
@@ -0,0 +1,7 @@
+>2_794
+MTSTPQHITLEQLYSEWTELMTEYPTMNMRLFRAVFDEWHQPTVEPEGVTYREDVVGGVP
+GIWTLPEGADEKQVLVYTHGGGFAVGSASSHRKLAGHLAKALGVVSFVLDYRRAPEHPHP
+AAVEDGVAVIDALIEAGIRPEDITTVGDSAGGNLAVAVPLSRREQGKPLPGQVIAFSPWL
+DMENKGETLATNNDTDKLITPELLEGMIAGVLGGTTEPTAPLANPLYAEYQDFPRTYITA
+GSVESLVDNATRLEERMKAAGVDVTLVVSEGQQHVYPFEAGASDVADREIQSITAWYGQG
+R
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002609.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002609.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6d6c5879119395105e92ee39c5b7d94d326b18a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002609.fa
@@ -0,0 +1,4 @@
+>2_895
+MRADHRFEATLDEDLEAASASALHHRLVTEIPPLTDTQLRAFRRARIEIRADHVPSFDTG
+LTGLRLVVAAVALGLSAAALYNVAPNGIVLVWAVVALAVVLLLAMLGMTLLHGRNRRRSQ
+TLEMAVALAEIVEPLGARPRVRH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002610.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002610.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2eb97df9a8162b87b4a94a73bf6c1d7bd8e3138f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002610.fa
@@ -0,0 +1,2 @@
+>2_897
+MTATMHAHVEDPTDGLATRRINVQVAAEPVVPGIGVVELA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002629.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002629.fa
new file mode 100644
index 0000000000000000000000000000000000000000..756980827f902cb616a9e12f31478023ab6468ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002629.fa
@@ -0,0 +1,4 @@
+>2_1258
+MTTPQLFHCLRYTDADRGIDFLQAIGFTTAMIVRDPDDATLVAHAQLAWRDNGGIMLGSV
+RDDDPHYGPGICNLVVASDEDVDSLFAAALAHGATTVTEPNDAPHGGRNACVADFDSHWW
+NLDSYPGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002636.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002636.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a73a89dd1a8b1f6736c15991780e0dc07605f7a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002636.fa
@@ -0,0 +1,3 @@
+>2_1295
+MTRCRTSVRHTDAMHRDVAPYRPPLWWTVLSVLAGLLVVAVGAMVTWAGQVDDSPGLGGL
+GLINALVGVVIVVRTLLARRLLSPAAPPSPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002638.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002638.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1ac3f354a49789af1424362d2e2b1dce13739c07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002638.fa
@@ -0,0 +1,2 @@
+>2_1300
+MLNWPLRARRLRGDVNAVRSGPRAMGRRAGSRLARRLVSRLFR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002640.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002640.fa
new file mode 100644
index 0000000000000000000000000000000000000000..11295919ec3b309861cc735316e3db6ba1f01cd2
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002640.fa
@@ -0,0 +1,4 @@
+>2_1303
+MTVTDALPPCPACAEEYAYEDGALLVCPMCGHEWSPESEAADRAEPAAAVVKDAVGNPLA
+DGDDVTIAKDLKVKGGAGIKAGTKVRGIRLLETPVDGHDIAAKVPGAGQMYLKSSVVKKA
+T
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002649.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002649.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a10df09799fd98bd4dd33f83e98584773be21eb5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002649.fa
@@ -0,0 +1,3 @@
+>2_1464
+MSENTPTGFSAAYKVLSVRTSEDTRAQLEVLAQLNERSVTEETRIALEHWVEKSKSDPAV
+LKRAEQVRAEIERDAETKRNAINAVLGGKNSKAASARTTKQTQTPQGT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002650.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002650.fa
new file mode 100644
index 0000000000000000000000000000000000000000..02f1d25538dbb1ab973dc6361dfba3a02ac57fd4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002650.fa
@@ -0,0 +1,5 @@
+>2_1465
+MVKGIYVPADDSKALEVRELTKLEDYQTAVDGWIEAVDVPVLGVTIYVNEEGLIRRLPLN
+PRASFLWWYHVPGAHHAMLVGNVILVGAPDENGDGTDVPEEVVDLLTVAREYAVAVRIGG
+SSTPSESDGKLSSVLLPLVHGDPSWCLSLTRHEDYLSAAAWAVVFRERWVAAVDVTVVSS
+VEVPRRMQILMDALPPVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002658.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002658.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b69c3bfa469be16dd59053f3557501629e317b0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002658.fa
@@ -0,0 +1,5 @@
+>2_1493
+MTLLLTGVALLLGWTLGSGGLGVGATAVVPELDGLAREAAEERLVAAGLATAVTARHDEL
+RTEGTVVATSPQAGQQVDRGTPVEVTVSAGPAPVPVPDLAGVSVRHAHGVARDARFAVEV
+DARRTDPHVPAGAVLEQRPAAGERATPGTVVRVVLSEGRAVRAVPDVTGLSLAAARTSLQ
+DDGWDVREHRVPVPLPAGDEARVLHQSPAAGTPLLEGTRVELWSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002665.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002665.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c43d6976cc7af93e697bda9e5ff64a7d7b569570
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002665.fa
@@ -0,0 +1,7 @@
+>2_1708
+MYFFLNDEEAGALVMAAGYYAADQWGEDEWLSFGRETGTTDIIKKHDRLLRSWSFGDPDY
+TDACIAVMGQILKEGPDPQAGQAGKMDLLRDSMPDLPDWVRKNGPGRTRRLFHEYISARA
+NSEIPKEWLPASAPTTSTSAGKPEILPKELDGLNSRSVPTQLENSSQSGPDVNDKWDSVN
+ELTDKEPAPREQVVPTYDPTSSPREVFIVHGHDTAAVDSLKVFIQERFGVMPRNLQSAPG
+IGRTIIEKFEDSGSRVDIAVILLTPDDIGAAKAAVDNGEEPQPRARQNVVLEMGYFIARV
+GRSRVVVLNGGVELPSDIHGVSYISYPGDSWKDELFHELKSMGLVASSD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002671.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002671.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88cf34d1ab8f691684d76283f7135da87f83de3f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002671.fa
@@ -0,0 +1,2 @@
+>2_1819
+MRARLLPALLDLTLTSLVSVPSVTAPARVRAGVIVGEGWIDLSTLWKGDVT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002680.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002680.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bbd055f325a659e33273198121cc805466304846
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002680.fa
@@ -0,0 +1,3 @@
+>2_1897
+MRVKDPDALRRRRLNCNYTQRQLAFLVNKSQNAISKLETGRMKTLSEGFAIALAARLDRD
+WEELFALEEQEVVPEVTHGACTAERSAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002716.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002716.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5ed905ba2d15a32612322aa5951fdf6630941b42
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002716.fa
@@ -0,0 +1,2 @@
+>2_1934
+MSEKTTFTKGDLSITTTDPAEKVRLRSQGFAAADTTAPAKATPKRADAPATDQKN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002730.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002730.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1abcb4f66051cfefa6281c9c4a643744c32ae885
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002730.fa
@@ -0,0 +1,2 @@
+>2_1956
+MITTMNVFGVVFPFVLAVIVVAMIVGIRSSGREHTQASEVELRLRERTFTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002743.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002743.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e3bd2abacc1b393c8dcd1bdb5d4b1ac7fbce3193
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002743.fa
@@ -0,0 +1,3 @@
+>2_2149
+MTTYSPASARDHYLTLREAVELGYGAYSTLRSWIAQGRLPAVKTGGRVKILRADLDALAR
+PIGPDPAPNDDLDAAIERLVAQAPALSPRQIRELQSILGGVAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002744.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002744.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ae8b5b6ca69b796bb08d503a2940436f3e95b8bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002744.fa
@@ -0,0 +1,5 @@
+>2_2154
+MADQNPTITDEQRGRLDQALTVVLTEGVPIQEVTAAQLTSRLDGGARKTVVLAYLREMKA
+KAPDTEDAIPAPPEDLATASVQALVRAVWEAAYTAARAEVAETVAEAVSARQAAEDAAAQ
+AQDELDTAREEFQRESSQLEARLNKAKEQVTRDAGAARDAATAATEARAREGEVRAQLAR
+EQERTAALEARMDALIVKLTEPVQETPEPKEAPTRSRRTGAKKTPASPTEPTKS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002745.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002745.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2dd2a12c61510c3518161043166d6473edf75535
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002745.fa
@@ -0,0 +1,6 @@
+>2_2155
+MPRVPIRVPLTIAACAALLTGCASGADSTDPGSTTGTTAGQGQSQSAQEGASQPADPQDK
+PKTGEQPEFASGNDLLASVNTDLINAGATACVWDIKSEGPKYNNPEAYFWAECDHKSAGE
+LEFEGSTDKPHGVEVIYWHPDPAVLKENVIGDSENPVWATGKNWVILTDSYISPNYPFYG
+ENAEASDEEKQSWRDRADRVRTETGQMLGVRFTDGRDAGNQLTTGIDGNGSGTSGSSTDA
+P
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002749.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002749.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c861f6e5056a6d92d854b930fa0064ac6c39dcfa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002749.fa
@@ -0,0 +1,5 @@
+>2_2165
+MTRRSGVDRNAIRRIARQIERDFNKEFERRPLRIPVEHEIAPGSPQPHPHVVNHYAGPVV
+TINGDHAQVAWNGGTNIGHREESQTVTPGFEQVAKVVSDVLAQADALELEEDERLELQQT
+GEEILTEVVKEEPDTGAIRRTLRTLKGFLAPALTAGASAAVSTEAQEAAQAAFDAIQALS
+F
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002756.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002756.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7952b23e57661c43a1038a7fa149c71b9b3ce3bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002756.fa
@@ -0,0 +1,5 @@
+>2_2180
+MGGMGEGILSDRLRAAPTLHVRVIRTPGADFAAEVTDDDGARLALAATVHPVADWRGAGH
+AVELVCADTGRPMITVLDRADLGLGAGEVLDDGALPLGVVRPWDTGFHAAARVEAADGAE
+FELQDGWNSAVVRIMHHGRVVGLLAPAAAVPWRSRLPGGPTPEPVTLRWERLDRDGRAGQ
+GDGADPGAGPWGLAGDAAARELVALPGRLMP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002762.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002762.fa
new file mode 100644
index 0000000000000000000000000000000000000000..407500fbdb3b414f1f9155a72a2e6104e4d51d1e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002762.fa
@@ -0,0 +1,3 @@
+>2_2276
+MPKKYTPELRERAVRMVLERQAAEGGPRSHSIRAIAPQVGVGEETLRMWCNRHGHEVAPV
+PAGESPAEEIRRLKRELAEARRANEILKAASAFFARELDRPTTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002763.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002763.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1cf2769227e1cd81f24d90ab8919df6bb85f29a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002763.fa
@@ -0,0 +1,4 @@
+>2_2290
+MDSEEPPNVRVACSGDIDEVVRLMHDAAAWMSAKGTPAWDVARIDRTFAETFVLRSELLV
+ASCSDGIVGCCTLSAEDPEFWPDALKGEAAYLHKLAVRRTHAGRGVSSALIEACRHAART
+QGCAKLRLDCHPNLRGLYERLGFTHVDTFNPGWDPTFIAERLELEI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002771.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002771.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24fdd16079f00953c2307459a661124e7ed1ba54
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002771.fa
@@ -0,0 +1,2 @@
+>2_2438
+MSLCQTKWICVRDTTTKMPAVLAIWSGGELNDLAAVEQANYLFPRACAEMVGLVDIQALT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002772.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002772.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4f82c377aefd7d2aeaa1abb0b0a05d125daacee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002772.fa
@@ -0,0 +1,5 @@
+>2_2439
+MARVRSVKRAEEIIKLYEEIGSEFSPIRIDTGMAESTRRKRREKLFNRESRIVICVNMLG
+EGFDLPSLKIAAIHDPQKSLAVTLQFVGRFTRVGDESLGEASAFVPLQVAGVDEQLRKLY
+GEDADWNEVIRDLTERGVGQEKDRTDFELAFGSVPREVAMRSIHPKMSTVTYQSETSLTW
+NPENIYDVFEDRLLTTRLGINNKGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002775.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002775.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d8defd31e788d15512f885600aa4dc9032703de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002775.fa
@@ -0,0 +1,3 @@
+>2_2446
+MILAFIDEMRAEGYAVESILRVLRQQGLRIAARTYRAWKKPTRIAGRTITDALVEGKIRD
+LVWTIDEVAGRRRMRPEGLYGRRKMLSLIRRQGGARQVW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002777.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002777.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54a6b6110ad4e84025373f2b24664c0d519309fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002777.fa
@@ -0,0 +1,7 @@
+>2_2522
+MADAPLGPVPRLGSPPEGSGRRPTRTAGMLCLGGRPRRLWDHPTYPPEVLVDWSSVTKTV
+TAAAASHLAAAGALDLDAPFRTWVPEIGNVPATVRDLAVHRSGMPTMHPTAARGLLRDPA
+RGALDEEELLGHCPGLFRSLREDHGRPRYSNLGYAFLGLVVERASGEDWWTAVRRLVLPA
+DRLPTVTVDPAPDLQRRPGLGPLRVSPWRLSSSAYRPAGGLWSTLSDLLAHAELASLPTA
+SRLGWHRDPSGLLVHTGSGRYSSCCAVLVPATGDSGVAHSTAVPAPRLQRRLVKALLSHL
+R
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002788.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002788.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b696d6a29a5a7a64786cd8ef59ba05140e8b341b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002788.fa
@@ -0,0 +1,7 @@
+>2_2588
+MTAAQYPPAEHFILHLSDTHFVGGPGLLHGKVDSDANLKKLFRDFAETKARPEAIVLTGD
+LADTGDADAYRRLRALVEPAAEAIGAQVIWVMGNHDTRTPFRKHLLDSDAGEQSVDLVHD
+VNGLRIIALDSTVPGQHHGEITDEQYAWLAEVLSTPAPHGTVIALHHPPVPSLLDTLSFV
+ELREQARFAEAIRGTDVRAVLGGHLHFNTFSEIGGVPVSVASATCYTQDLNVERGGMRGQ
+DGAQGFNLVHFYDDRVMHTVVPIGEFSTVYKVSAEQLRSWTSLTLEEISVEMEKTANEPE
+REPSLV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002810.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002810.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20d7ecc3d4b5198eba134e6f8e6f5f41962a1b8d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002810.fa
@@ -0,0 +1,3 @@
+>3_64
+MMFSLRPAWKVPTVTTARPVGAASRETMHCRRVTAEEAMRIGSMERSGMEPWAPLPWNVT
+LKESARDMASPLT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002825.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002825.fa
new file mode 100644
index 0000000000000000000000000000000000000000..872f48c10b9ae5d1c546a0921461f9965f615e98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002825.fa
@@ -0,0 +1,2 @@
+>3_200
+MSAPESHAAAAVAVRRIQAQAWADGYAAGRVDEFHGVTRPNPYALDAGPEDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002827.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002827.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a601f13b19577dfa9dfa3a36cf69faa8749a8793
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002827.fa
@@ -0,0 +1,5 @@
+>3_202
+MSHFPTDQEIGRRVRDAREDAGIKQQGDLVPLLRAAGLPWSQGTLSRVELGQRSVKVTEA
+AVLAEVLGVTVPALIGAPESTTREVLWEAYLGAENVAKVLRTVEDVYWETVRGVRDKARQ
+DDELRSRVQERRDKYLAIRSEDLRRQAIRDGDDVSTPEAWAAYTKLWGLDAIPAIRAATD
+VLEGLESADDTVGGEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002846.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002846.fa
new file mode 100644
index 0000000000000000000000000000000000000000..15155319fe45bf11dbda569ea033d811a5c2918a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002846.fa
@@ -0,0 +1,3 @@
+>3_325
+MDHDAQLIEAVTVRRHRLLTALTHGTNPTEQRWHGRGRLYVAGAVLAAVICALCVLVSLV
+ISILTAWLDNREQVEQQRQQQQIEQQQRQEERERAQQELDDERQVTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002848.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002848.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2b333e20b91ae423ba0adda027b5a7cbe1e4e0b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002848.fa
@@ -0,0 +1,8 @@
+>3_327
+MTRTESFAHDADRRLRGRAARNPAQSAPHAVWHAFHRSTDLRRLEEAAVRLQAPVGTGRR
+IAVTSSRGGTGRTTLTAVLAQTLGRFRLEPIGAVDLDPGHGALRLRLGPLVDGPDAEDGG
+EGGEAAEREGAGPGERGAATADRVAQHIRDHGTGGAADFLAPLEASPHRVYHTAARTTRQ
+VLPQDHVAGLLTGFSRFFPVTLSDCAAGHLPVETAAAVASSHAVLHVVPADALAVDEALH
+FLTATGQHTRRTPEPHVVVAVVQHRSRTNADARDAAAALRRRGFPVHVVPFDRHLDTGVS
+VTPRLMLPRSRAVAAELAADLLERATARSAQSGHTAEDEAVDAAAEAHPAGPPVRSGSTA
+RPRGRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002850.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002850.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ecda801ee1c14ca81293de0ce1850de5faf2f7a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002850.fa
@@ -0,0 +1,3 @@
+>3_335
+MGRRARLKPNQVSERWPNTPVDDPIHETLRRYVHNLTEAIGDTSIKAAAERTQVNYSTLY
+AILKGETWPDAITVARTEEGLQARLWEGPASLPED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002859.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002859.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c854d2dc988e2c21b23fdc63b51b85a35db5301
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002859.fa
@@ -0,0 +1,2 @@
+>3_409
+MRVRIQEVTRTVVTVAPTVNGAVGEVAKSIDPAASITLSLPTERLCPAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002876.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002876.fa
new file mode 100644
index 0000000000000000000000000000000000000000..be184e3325a9e1aeab05305bb1a9fcd0e4cb9028
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002876.fa
@@ -0,0 +1,7 @@
+>3_545
+MITSAGGTWLALLLCGLQAVLTTGTVTLVTSGVQTFTASLVSAVPADQAQLAVLNIDDAG
+VSTRLAQEVRREIDAPEDFGYRQVEAPTSAQDGPVVVVETPRQAADVLGLRKLDPQAEEG
+LRQGGALRALQAPEGELSVVDPHAADPTRVSARLATFPVIVVEGAQGSLAQGGAVILAST
+AARLPAPVSREVAHVFPRLTPEQQALAARLPQELHVNPDWMDLPKPPDTMPIPPAVTCGA
+AVLSAVDSALGVLTVTALQGVPLDLHVPWTLVGIMAGGTVLAFVGALWLALRNLSVRERM
+E
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002878.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002878.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7da4b5127acceb1ae5db73e1e890e690c99170e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002878.fa
@@ -0,0 +1,4 @@
+>3_588
+MSCRCILLGSVGCAVAVGLHLLAYADLAHAGPWLLAGAALWGFMVLLGNITQAAVTARAC
+PEGTLGRVTAMRRTLTRGSVPLATLAGGALGAMLGVGWALAGWQVLAVVSLAAVVPASRW
+VDAGLDDVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002887.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002887.fa
new file mode 100644
index 0000000000000000000000000000000000000000..60777046efabac1c0acfd1879941d46590d0cf31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002887.fa
@@ -0,0 +1,4 @@
+>3_630
+MVTRTESLTDEQWALVESLMPRPDEAGRPFRDHRMVVEGIIYRYRTGIAWRDLPSCFGPW
+QTVWKRHRRFSGDGTWDAILTALLGRADHQGLIDWEVSIDSTINRAHQHATNLPRTTGGL
+GELHETAPGAC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002889.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002889.fa
new file mode 100644
index 0000000000000000000000000000000000000000..97d4bd2d55a7f47009056a9c34df5764535f5283
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002889.fa
@@ -0,0 +1,3 @@
+>3_640
+MPLTPDMWWPPAVLALALFSDAAMSLRPPRFIRDCLNGVGFPREWWWTLIVIKTLAVIGL
+IAGIWIPGIALAANTGVIVYFLSAAAAHIRTRFTGQAFWLNCLGMLALSIAVLILSFAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002894.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002894.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9f63983362ed1a08abcfc68b653a79471d72616d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002894.fa
@@ -0,0 +1,7 @@
+>3_665
+MHPSCACAPWFGNGGLVGRAQWLLVALRRLTDRILDLDTLEVLVRVAETGSLTRAAEVLG
+VTQQAVSARLRAAEQATGQPLAHRTASGTALTDAGRVVLGLAVPVLEASRRLEAGVAALR
+EPAGSLVIAASQTIAELLLPGWLLTHRAATPDASVRLIAGNSADVTDLVRSGAADVGFTE
+TPAAPIGLSSLVVDEDELVVVVAPHHPWASASAITSDDLAETPLLLREEGSGTRSTVEAW
+LDDAGLTLVPPAAVLETTGIIRANARAGIAPAVMSLRTVDTDLEDGALVRALLLGPPLIR
+PLRAIWSGRPGPAVTAFLDTARSSSTGGQISP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002899.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002899.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f784b7897cd2a80173442ffd732977e300506c96
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002899.fa
@@ -0,0 +1,2 @@
+>3_684
+MKNFRPFPKYGGTKTAAITVVVGAFLLTGCTAANDSSSASRH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002916.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002916.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fbbced413de3d902c7d6ed3c5b2f990802795c60
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002916.fa
@@ -0,0 +1,8 @@
+>3_816
+MSTPDLSGLKRVTTADVYKAGHLAGTLERNAQGGVAFAYQPGYDGPPVASTLPVTDAAVT
+APGGGLPTFFSGLLPEGHRLSVLRAAAKTSLDDELTLLLAVGADVPGDTQIVPGGTTPHE
+PAPLAAENPTDLDFTALAGGVDRTGLPGVQAKASASMVNVPLTLAGRSALLKLDPPEHPH
+LVENEALHLTAAARLGVPVSGHAVVTDRKGTPGLLVGRFDRRHQEDGTVHRLALEDGAQV
+LDVYPAQKYNVTTEDLISALAARAAARPVAARNLYLQFLFAWLTGNGDLHAKNVSVLQGP
+DGRWQVAPVYDVPCTALYRDMTMALSVDGRVEDLRRRHWEALADAIGLPQRAADAAMRKA
+LAAADRIDLSTLPFEGSPLRGAERELRHRRGELRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002919.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002919.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f8c6f9d97f6a9ace72c95c91ecf4c14a59cb9737
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002919.fa
@@ -0,0 +1,5 @@
+>3_866
+MAGQRLRDVRNGMTIPPKISLKTVLDASYRPEWWFDFLTTEPLTFASLSDSAGDLPSIIN
+GMFDPTLDLHDLEWIRSVWLGRLMVKGVLTREDTRRALDTGADGLVVSNHGGRQLDRAPV
+SLQALPEVRDEAGPDVPIILDSGITTGEDIVAALALGADFTLIGRAYLSGLMAGGQEGVR
+RVIELLAQEVRVAMSLMGAATTADLTPASVRAPWLRDGQVVRSGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002929.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002929.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e3f9386bbcaf570ce0dd6e48bc4c08351cefb5e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002929.fa
@@ -0,0 +1,3 @@
+>3_928
+MNGVPSPSAREMNGVPSPSAREMNGVPSPSARETNGVPSPSAREMNGVPSPSARETDAAW
+HA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002950.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002950.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1563e926ac2ae25dadcdf0a510a8d8c1cc135eab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002950.fa
@@ -0,0 +1,5 @@
+>3_1274
+MATVFEGGDRPWLCVLAGRAGTGKTTLAQALAQATGACCLRVDAVETALGRVQDHVGAAG
+YAVVHELAVSNLPLGHDVVVDAVHPVPASRAAWTQTAARAGARLVVLETVLPDGREHRRR
+VETREADIPGHRVPTWEDVQADGWVAWDVERDGPPDRDRHHHPRGRAARRAGGPATPVTR
+TRASEGPGAVPSGTAHP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002953.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002953.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a0d6205d5a26124f6221ddd16e91faff08395d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002953.fa
@@ -0,0 +1,3 @@
+>3_1333
+MAVLAEGERTQAQVATAIAVDPRNVGATIRKLIEARWVQARPNPADARSRLLSLTPEGRQ
+WWNDLQPGLRQGRNAFFHALTPDELTALEALLGKLDASHAADSINVPGQYI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002954.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002954.fa
new file mode 100644
index 0000000000000000000000000000000000000000..887728f87b80a5d719f52c0cf81f70d517f719e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002954.fa
@@ -0,0 +1,4 @@
+>3_1334
+MPSLTPPTGHNTINPFAIVPDAMGFIRFVESVFDGHEAAHVRTPDRDGSIIHGEVTIGDA
+TIMLCDRKPDWPFTPAFLQVYVPDAQDCLDKAVAAGGRIVTPVSDFYGGYRIARALDPWR
+NLWWIYEPTTQPLHQDERDSDTDWHDRKPSLVYTSLMDAMRSLDRPEPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002955.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002955.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d644d1a10b790fad280f2e55b29cdf47d120174f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002955.fa
@@ -0,0 +1,3 @@
+>3_1489
+MTQAPLILLADDGANPLVPAGAELLAGAVGAVCTVLVVTAVLLLAVTRMDAYRRLLWLAV
+AVLVPFLGAIASIVIALRQRRRPEAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002964.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002964.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e6fd7471fdb2d542401df7bcd61d16b649f27292
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002964.fa
@@ -0,0 +1,4 @@
+>3_1729
+MNLTSLYTDLVFDHDRHPRHAGLREPFDAEVHHVNPTCGDEVTLRVRLTGEGPDVVVEDV
+SYEAAGCAMSRASASIMAELLHGRPEAEAQAVWDHFDHVMHQRGKEAGDEELIGDGVALV
+GAAKFPGRVKCVLLPWKAWQAAFAQARAARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002968.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002968.fa
new file mode 100644
index 0000000000000000000000000000000000000000..81775be0264778f86c5f58add48a2f819753be3a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002968.fa
@@ -0,0 +1,7 @@
+>3_1740
+MPMSSASQAPAATTEPPGTPSGWIALTAIAPVVWGTTYIVTTHLLPSGHPLFAAFMRTLP
+AGLIAVMIARKLPHGEWWWKSFVLGTLNMGVFFPLLFVAAQRLPGGVAATLGAAQPIVVA
+LLASAILHERLTSWRLSWAVVGLLGVGMVVLGPGASLDPIGLMAGLGGAVSMGSGVVLSK
+KWRQPQGVGAVAFAGWQLTGGGLFLALPTLVVDGIPNGIDSRAVAGYAWLGLIGALMAYT
+IWFAGIRRLSVTPTALLGLLSPLTAAALGSLVAGEALNIIQLCGFATALTALIAGQLSPR
+ARRRVLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002969.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002969.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d70b53f218884ca21fb235e1cba901381169b364
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002969.fa
@@ -0,0 +1,8 @@
+>3_1741
+MATSGKDARAAREAKLDALHERLTGAVEQLVSGEDWARALAFAARFRARSFANTILIFTQ
+HQEAYGLGLVPDPVPSHVAGYRQWQQLGRQVSKGQPGYQILAPVTGRFASATPQDAESWR
+RLGKGEKPRAGETVRTKMVGVRPAYVWDASQTTGEPIPEPPAPRLLEGHAPAGLWEGLAA
+QVLSAGFELRQVADASEIFGANGLTDYASRVVSVRTDMDPAAQVKTLAHELGHVLLHGPD
+ASEARQHRGIGEVEAESVALMVGAAHGMDTSGYTVPYVSTWAARVEGQDPVEVVKTTGER
+VRKTALGILEQLDTVQVGNGTPPGLERDTPTRDPATRQAPVAPAVSEPAGRVVSGPEAVA
+L
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002982.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002982.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d7cfb71d0f9c688524b17569ba165c077376bcd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002982.fa
@@ -0,0 +1,3 @@
+>3_1766
+MVRRYRRATARVEADRPLRVRYEPREEIDAAKVAEVLIRIALRTAGDQPGGQSGAHLRRL
+LVAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002984.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002984.fa
new file mode 100644
index 0000000000000000000000000000000000000000..180e3e9f0e6345d4e60b798313e6e41fac1602e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002984.fa
@@ -0,0 +1,8 @@
+>3_1769
+MINDPVLVLGVVVGLAGLLIALESYTGWKVFKYLPAFVLMYLGCAALNTFGVLGDAEGSR
+DALKATKDLLLPSMIFVLLLGCDLRRIAKLGPKLLLTFFVTVLSIMAAFFLVFGLFRSLL
+DGQALDPQSWIPMASLLASWTGGSSNMVAVNDILQGPENLFGFALITDTVVYSFWLMLMF
+SSVAVAGAFNRWTKADTSRIDEHAARVEHDDTPITRTSLAVLVFGSILVGALSIEAGKLL
+PKVGDVINGTAWTIIIVSILGLIAAQTPLGKVAGSSEVGSLMLFVVVGQIASGSDFSGIT
+QAPVYLLMGVLIVLVHGAIMVVYAKLAKADLFSLTVASTANVGGMASAPVVAAAYDKRLV
+PVGVLFALMGQLIGTFAGLGGGAVMRLFG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002992.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002992.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e5bcc3966210c096885087095b7d95076fe70f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002992.fa
@@ -0,0 +1,9 @@
+>3_1833
+MTGNAGRTATEDTHGTMPAEHAAHDDDGGVTPGVRGTSRVVASRMLSRWSGEHPGGGLSL
+ADRAVDHELGMLASTFRFLLDVTPTNVESARRAFLERDELEPFAYRRLEDDPEVLRQVLY
+DIPVQDVEDPVLGTLLRNKEREIDLQLEMLQARDTSDFMPLSIELYGAITPALRETAEHI
+LDQVPVPEPDADEAVDAPTFLALAREEIERYRDQDADIEAHAEIRRDVSGVMVSGDTLLV
+GPESTVQRRRADALVQHEVGTHLVTHVNGSAQPIACLATGLAGYDETQEGLAVLAEIAAG
+QLTAFRLRQLAARVVTVHRMVAGADFRECHRALVDDGIPASSAFTTVMRAFRSGGMTKDA
+VYLRGLLDLVDHVQRGNELDLFLLGKFSLADLPLLEDLRTRGILRPARIRSRWLTDPVHL
+ARLRALADVTDPAALVNA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003002.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003002.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7fd20f346420108ae705a87c899a5747237c5ab1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003002.fa
@@ -0,0 +1,6 @@
+>3_1966
+MQHVDKPDEMIGLGLDGADDLESVVLDPVSGIAAYASPEEEFTYVPVLRDDGTVQAHTVI
+DTPGAPTRFEYTVDIPEGGHLEMVGTSVLILDAQGDMVGGIAPAWAKDAVGNDVPTHYEI
+DGATLTRVVEHDSSFAYPVTADPWLRINLFGHVYKDTYRDHPRVNASLSAWGWSVYSGAS
+VGGPAKGQQILNTSGLSEVLSRGQDIRDAFYGKASMYAQYACHALGAVAAGQWNLERIRP
+NLTVPWTTNLANHRCNWNYSNGGV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003018.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003018.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28359ca985600fdfa29d631436c73ae412b2f2bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003018.fa
@@ -0,0 +1,7 @@
+>3_2187
+MDESGEVWTYSPSGSTAGSKDGDVQPARIEWLDVRGLPGYLVHPPSNDEGVSPWRRVYPF
+ADALALDVVAIETWTVPVSGDPPGAVNGWRWEEPATGLGEQALEVFDPLMYGRPAATLSQ
+LAGQADGVGRKLMNLREALMGCTTPVDLTVIWDQLDEALRLVVDAERSLTYAHRVIAEDL
+PLRKQLSRGEPPWVSSTGVNRWLTPKQMKRARRRHDVVPEDQLITYREAVVMADDLIPPL
+LAKTLAAMDKQILLDELLDDLLSRQCPGCGAGAGAYCTTASGRIAEVVHAGRRDASPMMR
+GHMELYMEVRQPNEFVPDPECGRVGPAPWDETLPGV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003019.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003019.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45d13bbde698c06ede35b4d63c7a700c97848924
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003019.fa
@@ -0,0 +1,4 @@
+>3_2188
+MWSRGLGRGWDLRWVRDVARMQFDLYEEDRTGAWWADQDSGHQLALVSDGGWRMSLNGAS
+YPSRYRVFDFDGVEIVEQTEEVLGRLGHGGHFDPQQEGAGRYQRVREECVSAVEDVLHLG
+GKR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003044.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003044.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a720167790c98363c0f605996fa2bcf640e9c44
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003044.fa
@@ -0,0 +1,2 @@
+>4_178
+MHQRGRMRQEVTREHPGPGSVPLGLSTLGRIGQVLGLSVDGIRAIARLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003060.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003060.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a53b9babd4d42556655eebd9e989a0b061c31db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003060.fa
@@ -0,0 +1,6 @@
+>4_1973
+MTPSPPSLRSARHALPATTAALTLALTLAGCSGGGGPATASGTTPSPAASSDTTPSPSST
+SETTTPSAGGPASGTTAPSTPAPASGSATQGSGGGSTAGAGFVPEGADPARNGALPLSEG
+FLAALPEAAVTHRAGSPTEDPLARALEGVELPGTPTTDVNVIASELQGLQTPGEGGAAMG
+GERPEGTLRLMLLCDDPDAGPSSVGILGADGFAAYQPLGWSDRCGGYVVMVPESDAEDLV
+VSAEAPEGTRYRLSVITDHDPVAN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003061.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003061.fa
new file mode 100644
index 0000000000000000000000000000000000000000..750a7a15f964ddbcecf9cb1cfc241ca3882dba85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003061.fa
@@ -0,0 +1,4 @@
+>4_1975
+MSHFAPQRRSTRTAAFSATFAAAAIALTACGGDATPSGPTSAPASASGGAESPAGEATAA
+SSVSAEDRVDPTQTTEVSAVTPRILLSHEDGLTLLDAESGEVVKEQDITGFKRLSNAGNG
+KDVLVTTGKGWEVCSPPASRPRPTAITSTTTSPRPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003064.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003064.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f18f4cace469d374516bac2a24bfeb9417213e5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003064.fa
@@ -0,0 +1,5 @@
+>4_2147
+MWALENGGGPLTTTGSRMRTITLTTQKPVAFELQRVWVTYTRQDLPEGTAFYDVSDGLGA
+GEREPARFVAALGHEGRATNRFAAKHVSDFDLPQKEAPVPYRLSDATHLDIDLLLSFLTE
+GVYTYSVEVEVAVNGVSRTLKVEKAPIGDQELPLKMVFAREPAMVHEEFTEYPHTRWLPG
+PRPEM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000000_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000000_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..47c27c2b24767e87da8d9c2b81182be191cc1fa8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000000_tree_id.txt
@@ -0,0 +1 @@
+((4_1516:0.002912777,(4_770:0.000000006,4_1128:0.002880187)0.899:0.005763499)0.817:0.002500317,(4_845:0.000000005,(1_1192:0.009428983,((1_10:0.006388848,(((1_36:0.019453289,((((2_1469:0.0,2_2418:0.0):0.000000005,2_2555:0.002876771)0.000:0.000000005,2_761:0.075818515)0.717:0.003562628,(((2_1737:0.0,2_2285:0.0):0.000000005,2_2578:0.002897630)0.485:0.000000005,2_137:0.000000005)0.904:0.041998311)0.784:0.031140912)0.977:0.044256205,(1_1079:0.009994891,(2_2573:0.061305716,(2_37:0.000000005,(2_538:0.002887090,2_674:0.000000005)0.899:0.000000006)0.966:0.041196453)0.820:0.016226034)0.953:0.037473432)0.957:0.025179729,((1_125:0.000000005,1_1921:0.035370896)0.313:0.007021435,((2_217:0.002847703,(2_1706:0.0,2_2499:0.0):0.003007921)0.999:0.043212988,((4_2042:0.000000005,4_2046:0.002882492)0.938:0.020652467,(1_336:0.042443047,(2_1475:0.258790137,2_2288:0.304882289)0.997:0.287255181)0.822:0.028725864)0.792:0.020666842)0.931:0.022268013)0.919:0.017161715)0.904:0.012240551)0.978:0.023211452,((1_297:0.011894952,(0_1892:0.000000005,0_1289:0.043248220)0.003:0.013026071)0.333:0.004300812,((0_2217:0.000000005,(0_2050:0.000000005,1_1768:0.000000005)0.829:0.002928616)0.982:0.027024683,((1_2024:0.016813058,(0_60:0.005550227,(0_2007:0.008898229,1_1771:0.011917887)0.990:0.027727601)0.944:0.015465063)0.245:0.003480740,(4_265:0.0,4_1492:0.0):0.016486305)0.703:0.009293130)0.962:0.019040427)0.675:0.000000005)0.456:0.002873587)0.972:0.016993171)0.716:0.000801834,(1_1117:0.003856630,(1_1918:0.005151224,(4_1937:0.006935756,4_495:0.013894110)0.798:0.003003457)0.785:0.002981653)0.800:0.004347377);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000003_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000003_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..10f09ea553a250a74563de6e80afe3388d32fce0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000003_tree_id.txt
@@ -0,0 +1 @@
+((1_1283:0.0,2_740:0.0,2_2280:0.0,4_1485:0.0):0.000000005,(3_1759:0.0,3_1797:0.0,3_2155:0.0):0.007389841,(0_1338:0.000000005,(2_2556:0.007953412,((4_109:0.000000006,(1_1077:0.000000005,4_1825:0.006428966)0.854:0.006425584)0.839:0.006454198,((((2_1256:0.0,2_1287:0.0):0.007525926,((2_2296:0.000000006,2_2572:0.015054550)0.900:0.015091691,((0_2219:0.135022201,3_303:0.049728394)0.883:0.047262267,2_1279:0.000000005)0.793:0.007571284)1.000:0.000000005)0.870:0.007588932,3_608:0.007455794)0.000:0.000000005,(0_1023:0.014983195,(1_1609:0.006465133,(((1_303:0.0,1_2209:0.0):0.007402723,1_752:0.000000005)0.858:0.007385580,2_1292:0.007463203)0.000:0.000000006)0.903:0.012963549)0.777:0.006551171)0.859:0.006482147)1.000:0.000000005)1.000:0.000000005)0.000:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000004_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000004_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a0dd48ba5b199bc0412a2c3b898c3c1570c38028
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000004_tree_id.txt
@@ -0,0 +1 @@
+(((2_879:0.362442419,3_1790:0.405774430)1.000:0.491080568,((2_218:0.0,2_875:0.0):0.000000005,(1_973:0.008797146,2_2052:0.008895920)0.000:0.000017795)0.453:0.000039136)0.602:0.000000005,((4_1493:0.0,4_1495:0.0,4_1821:0.0):0.000000005,(0_2008:0.023503058,((0_355:0.0,0_1345:0.0,0_2051:0.0,0_2216:0.0,1_339:0.0,1_1086:0.0,1_1696:0.0,1_1769:0.0,1_1964:0.0,4_111:0.0,4_1914:0.0):0.000000851,1_976:0.026067414)0.000:0.000000017)0.011:0.002215115)0.941:0.002216766,((2_625:0.0,2_1476:0.0):0.000000005,2_219:0.000000005)0.847:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000005_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000005_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..83a63a18ae1e59f42219f34a8c2c2f7edbb96f03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000005_tree_id.txt
@@ -0,0 +1 @@
+(3_610:0.000000005,((((3_614:0.0,3_2111:0.0):0.002904931,((3_301:0.0,3_628:0.0):0.020801028,(((1_1728:1.083394266,3_661:0.747436635)1.000:1.026001527,(3_213:0.736291367,((2_1257:0.047193185,(3_635:0.040806351,3_1781:0.048772794)0.374:0.035024320)0.989:0.100840286,(3_1335:0.066493578,(3_624:0.071321333,3_1793:0.034742642)0.231:0.014301880)0.946:0.058738344)0.968:0.178415735)0.947:0.154764175)0.909:0.161534004,2_2224:0.010295174)0.799:0.009485229)0.950:0.012905581)0.000:0.000000005,(3_733:0.0,3_1757:0.0):0.000000005)0.930:0.002904321,3_1847:0.011672960)0.000:0.000000005,(((3_212:0.000000005,3_1796:0.002877802)0.464:0.000000005,(3_431:0.000000005,3_2154:0.000000005)0.809:0.003424367)0.872:0.005762608,3_298:0.000000006)0.946:0.005801750);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000006_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000006_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5f4d4871da7ea0fd5f79688cd507a719af44e1fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000006_tree_id.txt
@@ -0,0 +1 @@
+(4_1290:0.000000005,((4_563:0.0,4_2145:0.0):0.003717745,(1_1073:0.000000005,(4_565:0.033520419,(0_1336:0.000000005,(1_1971:0.002784487,4_1826:0.016620739)0.496:0.000941071)0.000:0.000000005)0.047:0.003723445)0.845:0.003726926)0.000:0.000000005,((0_149:0.0,0_993:0.0,0_1244:0.0,0_2016:0.0,1_1065:0.0,4_1201:0.0):0.000000005,(1_1075:0.007473851,(1_972:0.004641539,2_1189:0.002567099)0.644:0.001148377)0.909:0.000000005)0.705:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000012_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000012_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dfb415f736f8a981b7c918ef827c9c44d8d5642f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000012_tree_id.txt
@@ -0,0 +1 @@
+(0_148:0.026678410,(2_702:0.0,4_979:0.0):0.014818142,(0_151:0.021898112,(((2_704:0.139128212,(1_322:0.0,1_329:0.0,1_758:0.0):0.000000005)0.743:0.006247567,((0_2002:0.0,3_2171:0.0):0.445773272,1_282:0.255798096)0.990:0.240536395)0.281:0.009327576,0_1030:0.000000005)0.811:0.000000005)0.657:0.005990244);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000014_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000014_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cafdf198cd60eb792ae1c0577390ddc29636790d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000014_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000019_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000019_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e23b43d81327518e1dd59102466befb7cfd79024
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000019_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000020_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000020_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..58c3c660589f4083a5f94e6ed1b95d37c7a22347
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000020_tree_id.txt
@@ -0,0 +1 @@
+(1_242:0.003533249,4_512:0.017307905,(2_2364:0.097178562,(3_2245:0.266165747,(2_1186:0.992211400,(1_231:0.014194181,(0_501:0.000000005,4_501:0.002534472)0.706:0.010437412)1.000:0.463804842)0.980:0.195629523)0.960:0.109911854)0.998:0.079471700);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000021_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000021_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7bd673ce7c057887fe67a0a8358e62b913821cb9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000021_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000027_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000027_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed5cc0ee23e61f5b636398ca9b5a54a5e2eca4e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000027_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000029_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000029_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e0fd4e061724a5b365d3e8c665a12acb93816f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000029_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000037_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000037_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..39f09c98fd09681c70cb518fb1505b6381cf448a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000037_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000042_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000042_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d12696d645fcbecdc58f8d9d4e1a4f2342402d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000042_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000043_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000043_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2573a8148b0849fe0f3510b0d71bd842bf0695aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000043_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000048_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000048_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fe23231c03e9ddf31e3aeb825332ef6fcdff5086
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000048_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000056_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000056_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a518fec8fe31cf4b87174be3cd1351cb3b4027fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000056_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000057_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000057_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a04f90550933d686a6311d84ded478cd7731bb2f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000057_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000059_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000059_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..993561f6df3e746778432dfe167c961ff24c5c74
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000059_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000062_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000062_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d538d57cae91f4b6955fae004778bf95fc253af8
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000062_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000063_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000063_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..24ebb7b26e70bb6c42dfc176a8530d8fa7d78b99
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000064_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000064_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..224b08949a38ac7d320f4bf0f3a2b71815c60d9b
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000064_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000070_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000070_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ea2a22259a8df4f934b74ca42716464a83476381
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000071_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000071_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..198a763a5a0b2e7acb5c209064395cd7b26337c5
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000074_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000074_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..53f8258c07bfd1b8d78ce81769dae41dfda01bca
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000080_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000080_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b5392e834a56cb8e08427df9c49327743a4628fd
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000080_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000083_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000083_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..355aecf932eb580db43e9de47ba3e15f4e6dc6ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000083_tree_id.txt
@@ -0,0 +1 @@
+((0_391:0.0,4_394:0.0):0.000000005,1_120:0.003111543,(2_2491:0.008110340,(2_2587:1.819885880,3_2359:0.032336234)0.817:0.043616418)0.960:0.020294488);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000087_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000087_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5222df6119d1e4604412276d7899b62e07191ba5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000087_tree_id.txt
@@ -0,0 +1 @@
+((0_467:0.0,1_197:0.0):0.001997572,4_466:0.000000005,(2_2404:0.003884340,(3_2287:0.050649499,4_1499:1.314494467)0.951:0.075344932)0.749:0.002121728);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000090_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000090_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ba054c4816148cd35a157a0e851d34a1d67f5afd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000090_tree_id.txt
@@ -0,0 +1 @@
+(2_2375:0.008927892,3_2257:0.008897350,((2_1194:1.794042030,4_498:0.000000005)1.000:0.030117316,(1_229:0.005920328,0_498:0.011853919)0.000:0.000000005)0.774:0.002961095);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000093_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000093_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f2614e67374096b1d0da022abe666e7e3b749d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000093_tree_id.txt
@@ -0,0 +1 @@
+((0_2113:0.0,1_1838:0.0,4_2059:0.0):0.107953292,2_560:0.115181965,(0_579:1.544779234,3_488:0.058490513)0.821:0.097732605);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000094_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000094_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b33e3c6a0e6889c223632819ff6ed49d892243ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000094_tree_id.txt
@@ -0,0 +1 @@
+(2_2583:0.836623849,(0_585:0.025246713,1_1720:0.009121174)0.880:0.073960153,((2_383:0.000000005,3_2150:0.008495586)0.994:0.113143289,4_1944:0.185888716)0.805:0.056407918);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000096_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000096_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bec0e4827c9a6257486c60bab2dbbfdeb259e2ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000096_tree_id.txt
@@ -0,0 +1 @@
+(3_527:0.256101246,3_685:0.272870539,((1_310:0.006844695,4_1947:0.000000005)1.000:0.358885799,(0_589:0.027487390,1_1724:0.084295529)0.996:0.183974371)0.996:0.147834794);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000100_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000100_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b53e303e6ebfa163cac4bc4754adb954afdfddff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000100_tree_id.txt
@@ -0,0 +1 @@
+((3_567:1.102572247,4_589:0.003425987)0.821:0.010778807,1_365:0.007203700,((2_2268:0.057492373,3_2126:0.101592237)0.999:0.099133996,0_619:0.010323516)0.564:0.007752945);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000101_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000101_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f45ad014a88f3f6b710f811e3554d7948b3395d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000101_tree_id.txt
@@ -0,0 +1 @@
+(1_370:0.007385002,4_594:0.004858197,(0_624:0.016522113,(2_2263:0.067391824,(0_811:1.919877534,3_2119:0.123532683)0.891:0.150211536)0.967:0.039318700)0.982:0.027080495);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000103_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000103_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4d653b350f3e0e134a5336813c810cde77c17408
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000103_tree_id.txt
@@ -0,0 +1 @@
+(0_666:0.000000005,1_412:0.004795866,(4_636:0.007958667,(2_2213:0.281755071,(2_2212:0.292903789,3_2387:1.364317717)0.645:0.048050920)0.853:0.089221387)0.863:0.021260271);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000108_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000108_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8f883a976da95106f83a4cb7a999b736728975d0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000108_tree_id.txt
@@ -0,0 +1 @@
+(0_1020:0.008498174,(1_748:0.0,4_967:0.0):0.000000005,(2_1790:0.075062539,(0_808:0.715086106,3_1678:0.081202453)0.971:0.102232650)0.992:0.051912585);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000111_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000111_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..68d6bb99df33fa1c6f99e5c1a328d163bc5fe18c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000111_tree_id.txt
@@ -0,0 +1 @@
+((2_1785:1.202039617,3_1804:0.151940965)0.848:0.093757717,4_897:0.004649971,(0_954:0.013934453,(2_1858:0.047811870,1_677:0.000000005)0.036:0.013900722)0.883:0.014146755);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000112_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000112_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e7a489ff9751b05b1e602308979b52ac27829964
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000112_tree_id.txt
@@ -0,0 +1 @@
+(2_1841:0.038364403,(2_1840:0.042798092,4_914:0.019078652)0.726:0.015145333,((0_971:0.0,1_694:0.0):0.011002953,3_1727:0.918150651)0.646:0.013126112);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000113_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000113_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..39a4553b20b5c165181fa679004aa0f2b12cd052
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000113_tree_id.txt
@@ -0,0 +1 @@
+((0_987:0.0,1_711:0.0,4_931:0.0):0.059136399,3_1707:0.000036670,(2_175:1.036232106,2_1816:0.802572135)1.000:0.942112306);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000115_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000115_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b5f377819a1c2038d92adc30f8059da9c880908f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000115_tree_id.txt
@@ -0,0 +1 @@
+((0_989:0.0,1_713:0.0,4_933:0.0):0.000000005,3_1705:0.017734492,(2_176:0.500751812,2_1817:0.482676942)1.000:0.815193297);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000119_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000119_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6ac0fb3f5ac1afc59b2bde74b33b373e220119d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000119_tree_id.txt
@@ -0,0 +1 @@
+(0_1071:0.001062653,4_1021:0.000939070,(1_799:0.001053944,(2_1745:0.035456678,(1_357:0.895192288,3_1637:0.070875498)0.957:0.050612721)0.990:0.024246003)0.789:0.003015128);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000121_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000121_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..959ae53d7f834cc486cb00a853ab860cd71f00f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000121_tree_id.txt
@@ -0,0 +1 @@
+(3_1607:0.087854560,(0_1101:0.003744384,(1_829:0.0,4_1051:0.0):0.003864927)0.983:0.042568511,(2_1714:0.011062484,2_753:1.434347777)0.507:0.007755692);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000123_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000123_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..981ccdbbc733d463ab143bab4e1a36dc6c1657a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000123_tree_id.txt
@@ -0,0 +1 @@
+((0_1224:0.0,1_952:0.0,4_1181:0.0):0.044873234,2_1585:0.032730534,(3_1480:0.039941075,4_1823:1.525377161)0.855:0.046490721);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000125_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000125_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..299c0e7ba8cbb4b82d7511c8312e4d9329a40c8a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000125_tree_id.txt
@@ -0,0 +1 @@
+((0_1286:0.0,4_1241:0.0):0.000000005,1_1016:0.002876097,(2_1527:0.047566710,(3_121:1.364137549,3_1423:0.141500319)0.934:0.125849894)0.968:0.040351459);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000131_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000131_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..61b210f2aee9c3350761a08ce0e68a270f20f8a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000131_tree_id.txt
@@ -0,0 +1 @@
+((2_1351:0.034349107,(3_1243:0.008634276,3_1272:1.472626698)0.871:0.114300325)0.982:0.048165478,4_1422:0.000000005,(1_1215:0.004375167,0_1495:0.000000005)0.777:0.004354452);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000141_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000141_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c495239a86ebf1df6c4cc0aab5264b1ebf4a33a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000141_tree_id.txt
@@ -0,0 +1 @@
+((3_1144:0.004624839,(0_1582:0.020893770,4_1511:0.020639916)0.987:0.041762550)0.951:0.028967020,2_1234:0.037541433,(3_1186:0.777982753,1_1297:0.000000005)0.733:0.012083218);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000151_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000151_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5230a903e1b431fea4531f57be86101dd5b81d1e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000151_tree_id.txt
@@ -0,0 +1 @@
+((4_1782:0.013439375,(2_919:0.055332318,3_855:0.457429256)0.977:0.052728176)0.858:0.009425114,1_1568:0.011185572,(2_768:1.783136313,0_1861:0.000000005)0.773:0.001979605);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000153_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000153_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0d1aef7c86a9d7fe6f4f0e4d17b1823e190d9292
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000153_tree_id.txt
@@ -0,0 +1 @@
+((3_799:0.061740785,(0_1914:0.000000006,2_863:0.113069838)0.842:0.008575152)0.583:0.000000005,1_1619:0.000000005,(0_1915:0.008524205,4_1841:0.004072481)0.965:0.008216894);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000158_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000158_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..175f740d61595c7d409c28dff1e0f19552d4ed00
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000158_tree_id.txt
@@ -0,0 +1 @@
+(3_732:0.308544045,(0_1968:0.018906404,(2_771:0.027381724,4_1906:0.002094288)0.794:0.042382776)0.888:0.119490321,(0_1970:0.022106830,1_1688:0.000000005)1.000:0.064532667);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000162_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000162_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d509663bb50c7cba54909e1f3b8f4ffdb7c4d880
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000162_tree_id.txt
@@ -0,0 +1 @@
+(2_667:0.031804399,3_584:0.032121404,(1_1750:0.065079296,(3_538:1.171605609,(0_2032:0.026387147,1_1751:0.042273014)0.427:0.069941553)0.786:0.121927829)1.000:0.294598414);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000163_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000163_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..882078b24f33a9156ae0a1e1369daae19ad8732f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000163_tree_id.txt
@@ -0,0 +1 @@
+((0_2037:0.0,1_1755:0.0):0.003450448,4_1978:0.000000005,(2_663:0.041273751,(2_1470:1.411621724,3_578:0.143863397)0.507:0.061947987)1.000:0.025744405);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000164_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000164_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f7daab5d6b4de96dd5f8f9ef2d8ad9d941997f50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000164_tree_id.txt
@@ -0,0 +1 @@
+(0_2061:0.003612376,4_2000:0.006984856,(1_1780:0.002418505,(3_558:0.016626809,(2_640:0.103516336,3_700:0.629619476)0.994:0.077398655)0.867:0.012314512)0.945:0.005882962);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000171_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000171_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9baba28ed7a410a9f0624c8d26cfb51a272ec356
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000171_tree_id.txt
@@ -0,0 +1 @@
+((0_2244:0.0,1_1948:0.0):0.003057686,4_2186:0.000000005,(2_414:0.163476363,(2_1906:1.891734817,3_367:0.110694305)0.981:0.174568540)0.682:0.008405580);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000178_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000178_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d7439b0bcae57bdb515bcc2c5a6e7c48b9b89111
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000178_tree_id.txt
@@ -0,0 +1 @@
+(0_4:0.002750315,(1_1960:0.0,4_4:0.0):0.000000005,(2_401:0.024561785,3_354:0.091669950)0.997:0.032601098);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000190_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000190_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5ba60f812d641274db27241dff4008182752e97
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000190_tree_id.txt
@@ -0,0 +1 @@
+((0_18:0.001973842,1_1987:0.000000005)0.755:0.002487045,3_342:0.410496678,(4_18:0.011318617,2_359:0.025710572)0.276:0.004554508);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000191_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000191_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..105b125cdad2240145772d5e0bc24e868fdd58cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000191_tree_id.txt
@@ -0,0 +1 @@
+(0_19:0.002179857,1_1988:0.002170334,(4_19:0.001997268,(2_358:0.013749527,3_341:0.172256479)0.163:0.006361803)0.884:0.004532877);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000192_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000192_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..39433024141e925e99659c5f59d2c0e3941df727
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000192_tree_id.txt
@@ -0,0 +1 @@
+(0_20:0.017964076,1_1989:0.009340606,(2_357:0.024748977,(4_20:0.011867292,3_340:0.377714710)0.836:0.007914018)0.961:0.010137786);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000193_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000193_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7f50763960dabf4c7455d3a16f86e52c152df53b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000193_tree_id.txt
@@ -0,0 +1 @@
+(2_356:0.005238457,(0_21:0.005224530,1_1990:0.000000005)0.792:0.005235653,(3_339:0.239516139,4_21:0.000000005)0.254:0.005235689);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000194_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000194_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d0db3ecd65e70877c53f6f8349fd7c31036a02c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000194_tree_id.txt
@@ -0,0 +1 @@
+(1_1996:0.003090895,4_27:0.006156842,(0_28:0.000000005,(2_351:0.020538962,3_290:0.132880148)0.879:0.011239383)0.396:0.003069560);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000195_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000195_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c2aa4eb7a69fe1be01603fbc61f589d78542bf55
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000195_tree_id.txt
@@ -0,0 +1 @@
+(4_28:0.004567542,1_1997:0.000000005,(0_29:0.000000005,(2_350:0.094744268,3_446:0.193130502)1.000:0.116082002)0.234:0.004556167);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000200_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000200_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..991ff00020f7ab9a8c645518e1a859bb5ce78a7e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000200_tree_id.txt
@@ -0,0 +1 @@
+(1_2002:0.000000006,4_33:0.002227990,(0_38:0.006021610,(2_343:0.041181238,3_286:0.087073216)1.000:0.055132211)0.850:0.007421209);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000204_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000204_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..16ed864fa6c2925d067887974e6876bd222c0f41
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000204_tree_id.txt
@@ -0,0 +1 @@
+((0_42:0.0,1_2006:0.0):0.000000005,4_37:0.011653077,(2_334:0.145256553,3_280:0.415690427)0.942:0.077309443);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000206_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000206_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ce54f78770f26fc6df2311a65207721e8fd1ee0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000206_tree_id.txt
@@ -0,0 +1 @@
+(0_46:0.020848264,4_41:0.007874400,(1_2010:0.018203540,(2_338:0.085352385,3_1194:1.477372615)0.881:0.124639381)0.311:0.005269975);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000214_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000214_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..44ef8e24df30238da9c0d08d062ff7449d90c3f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000214_tree_id.txt
@@ -0,0 +1 @@
+(1_2022:0.009476278,4_53:0.003147654,(0_58:0.003120985,(2_318:0.203360233,3_260:0.075722759)1.000:0.255438384)0.745:0.003181419);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000216_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000216_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..afdff9f4be17ce09c3eb228e930a1384bee22bf3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000216_tree_id.txt
@@ -0,0 +1 @@
+(0_62:0.000000005,4_56:0.010923537,(1_2026:0.007247653,(2_314:0.092528225,3_254:0.083551214)0.987:0.056524715)0.750:0.003682952);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000219_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000219_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fcdf101bd1b977b1dfd4012227e6f035c99dc44
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000219_tree_id.txt
@@ -0,0 +1 @@
+(1_2030:0.016782946,4_60:0.007163345,(0_66:0.000000005,(2_307:0.149360559,3_250:0.138951754)0.996:0.088070802)0.929:0.007134431);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000220_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000220_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..88279cdfd1897d1aa8266060af11ed370a28267b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000220_tree_id.txt
@@ -0,0 +1 @@
+((2_306:0.291632417,3_249:0.196699525)0.999:0.152308782,4_61:0.019837243,(1_2031:0.029304553,0_67:0.014298690)0.435:0.008572013);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000224_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000224_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7d47e592a814b9791b55a748cdee94c3c33b59db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000224_tree_id.txt
@@ -0,0 +1 @@
+(1_2037:0.007572030,4_67:0.007532281,(0_73:0.000000005,(2_301:0.034333059,3_243:0.175909414)0.681:0.021815345)0.795:0.007516176);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000226_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000226_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2ca5d161711870d086ab24facf1a57fb2fb8c654
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000226_tree_id.txt
@@ -0,0 +1 @@
+(2_299:0.101091936,3_241:0.389037128,(0_75:0.028755445,(1_2039:0.0,4_69:0.0):0.007280752)0.961:0.099978582);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000227_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000227_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5aca906897450a65596e51fe6882b2c9ca1ae85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000227_tree_id.txt
@@ -0,0 +1 @@
+(0_76:0.000000005,(1_2040:0.0,4_70:0.0):0.005972477,(2_298:0.064754788,3_240:0.341514490)0.952:0.102624315);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000229_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000229_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eb772c97c9d26f90d0b190535aec5bb692ad28e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000229_tree_id.txt
@@ -0,0 +1 @@
+(0_78:0.006176397,(1_2042:0.0,4_72:0.0):0.003073305,(2_296:0.102885990,3_238:0.108010205)1.000:0.099315352);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000236_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000236_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9a3f7f7eca2eeed39aa9a4c7a4a51b7a60d400cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000236_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000237_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000237_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d1f02d681d775afebe8910ab9ab70f8287d7ddae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000237_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000238_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000238_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c5be4eb7b25e05ff9ffa7f6b6645fcef4151974a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000238_tree_id.txt
@@ -0,0 +1 @@
+(0_89:0.001467856,4_84:0.000000005,(1_2053:0.008923963,(2_283:0.057328366,3_229:0.241134245)0.992:0.037502644)0.950:0.010353082);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000239_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000239_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a3587770a1864aa096cbad53f7a2aef171a884c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000239_tree_id.txt
@@ -0,0 +1 @@
+(0_90:0.000000005,4_85:0.005877548,(1_2054:0.029783860,(2_282:0.154894872,3_228:0.611321363)0.999:0.320201739)0.880:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000240_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000240_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1266416eaa7817af7cb76fdf3847161b64fd80e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000240_tree_id.txt
@@ -0,0 +1 @@
+(4_86:0.000856846,(2_281:0.151283600,3_227:0.128962426)1.000:0.107215423,(1_2055:0.000000005,0_91:0.012403963)0.285:0.005322909);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000242_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000242_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5672f449d9e7924d5f920daf3222a905c9d192e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000242_tree_id.txt
@@ -0,0 +1 @@
+(0_93:0.000000005,4_88:0.005836924,(1_2057:0.001958778,(2_279:0.028887628,3_225:0.099851318)0.962:0.018391215)0.835:0.003874175);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000243_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000243_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a92430670ddb8ba85ce69c0f4d136b7ad4201cef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000243_tree_id.txt
@@ -0,0 +1 @@
+((0_94:0.0,4_89:0.0):0.000000005,1_2058:0.013118309,(2_278:0.207121999,3_224:0.170767496)0.977:0.193887989);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000253_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000253_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5202e16608552ef2354d0cccb1a6293c20dadd00
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000253_tree_id.txt
@@ -0,0 +1 @@
+(2_265:0.015406316,3_207:0.023520004,((0_106:0.0,1_2070:0.0):0.000000005,4_101:0.007583860)1.000:0.059364827);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000259_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000259_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1860fa70832111e4425ad48c4c90758856de57c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000259_tree_id.txt
@@ -0,0 +1 @@
+(2_256:0.065344825,3_188:0.190865151,(0_112:0.001386455,(1_2076:0.0,4_117:0.0):0.003292670)0.996:0.060479046);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000265_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000265_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2b22bfd6c7eee8f6400774071c5b3c852a8066ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000265_tree_id.txt
@@ -0,0 +1 @@
+((2_245:0.030254308,3_179:0.142055564)0.868:0.023736036,4_130:0.000000005,(1_2087:0.015477867,0_122:0.000000005)0.879:0.007711030);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000266_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000266_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..97a4d5bfb6ba676e07971d0a4342f6b4d72dc3cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000266_tree_id.txt
@@ -0,0 +1 @@
+(0_123:0.000000005,1_2088:0.004784926,(4_131:0.024040612,(2_244:0.234324930,3_634:1.747794044)0.852:0.000000005)0.928:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000267_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000267_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c87af2121b9e373f1e245f8eb74eb9e649fee341
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000267_tree_id.txt
@@ -0,0 +1 @@
+(0_125:0.006264501,1_2090:0.001886058,(4_133:0.021994275,(2_242:0.108645345,3_178:0.124687631)1.000:0.104837401)0.811:0.012216308);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000269_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000269_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..427d0762dcaf5645575aa151f62983269ea482ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000269_tree_id.txt
@@ -0,0 +1 @@
+(1_2093:0.006724514,4_136:0.000000005,(0_128:0.013193427,(2_238:0.092440265,3_172:0.339138830)0.952:0.052881905)0.866:0.011167719);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000270_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000270_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e434fa3e55429849ef2a495006b104122568f485
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000270_tree_id.txt
@@ -0,0 +1 @@
+(1_2094:0.000000005,4_137:0.003704572,(3_171:0.018593111,(0_129:0.003726421,2_237:0.071589101)0.656:0.003707415)0.613:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000277_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000277_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5651b7a873c3ce65a20a656bd9bf7dbffdae4c0e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000277_tree_id.txt
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+(1_2101:0.003387411,4_144:0.003404907,(0_136:0.000000005,(2_230:0.024471080,3_164:0.165901133)0.990:0.065619304)0.721:0.006850211);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000280_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000280_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3f32aa2defc928eaf40f347ae7be89d48a74e687
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000280_tree_id.txt
@@ -0,0 +1 @@
+((0_140:0.0,1_2105:0.0,4_148:0.0):0.006294254,2_225:0.014051845,3_802:0.121879073);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000281_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000281_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bfc1ea92b83695a708828c5f8fa7507239f7020f
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000281_tree_id.txt
@@ -0,0 +1 @@
+(0_141:0.003368752,4_149:0.000000005,(1_2106:0.000000005,(2_224:0.090526454,3_801:0.318608812)1.000:0.061410502)0.406:0.001682225);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000284_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000284_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b3da514287a3987b2121987f15b7cdceccf87a43
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000284_tree_id.txt
@@ -0,0 +1 @@
+((0_144:0.0,1_2109:0.0,4_152:0.0):0.028699598,2_221:0.031460475,3_160:0.118973954);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000285_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000285_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..228742ea958c0a00884fb3cfcaab05e0557aa9be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000285_tree_id.txt
@@ -0,0 +1 @@
+(0_146:0.016274061,1_2111:0.015110879,(4_159:0.018359118,(2_452:0.084898595,3_403:0.192082100)1.000:0.201624691)0.861:0.019395083);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000286_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000286_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..008ca45007c9f8e928af5b7a71c763b3cf60959d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000286_tree_id.txt
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+(2_2282:0.000000005,4_1951:0.005002567,((1_343:0.000000005,3_659:1.544410678)0.835:0.004995332,0_160:0.009991453)0.935:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000295_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000295_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2269ecdf9c96a93df98a586c9fa2a712443cff07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000295_tree_id.txt
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+(3_150:0.062595872,(0_178:0.002422638,1_2125:0.002462357)0.911:0.010961036,(2_205:0.007369852,4_175:0.009916271)0.663:0.004079178);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000297_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000297_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4301b6fb6322bc5c408b470fd6b6c1dbf3385408
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000297_tree_id.txt
@@ -0,0 +1 @@
+(1_2131:0.002728605,2_198:0.037238597,(4_184:0.000000005,(0_184:0.001861331,3_145:0.059836946)0.552:0.006629655)0.888:0.005661101);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000301_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000301_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4c5a95ed4a99b37069036c67cf8f9d19bfefc52
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000301_tree_id.txt
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+(0_188:0.026137370,(1_2135:0.0,4_188:0.0):0.029737884,(2_193:0.154051978,3_141:0.014365621)0.437:0.019360674);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000306_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000306_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..88f17f60f73162469efec549fcde2f05cd97b983
--- /dev/null
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@@ -0,0 +1 @@
+(0_200:0.007863058,4_200:0.003914530,(1_2144:0.030948707,(2_173:0.220780777,3_119:0.655048908)0.643:0.066858456)0.679:0.006996097);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000307_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000307_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2275c234f8dce54572a45509a610a66ec9620197
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000307_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000310_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000310_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ac0007d636d9cf0069079a7e1c8a989a6c5936f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000310_tree_id.txt
@@ -0,0 +1 @@
+(0_204:0.003774943,1_2148:0.000000005,(4_204:0.003842097,(2_164:0.049144798,3_113:0.085331949)0.936:0.027418143)0.758:0.003756928);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000315_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000315_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f0e8f18dbb67e3cac62eddd2b142d2f4d61bc490
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000315_tree_id.txt
@@ -0,0 +1 @@
+(0_212:0.028665585,(2_150:0.236542097,3_108:0.103358457)1.000:0.181465619,(1_2176:0.008318878,4_213:0.000000005)0.915:0.018106379);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000317_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000317_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..31406e86247148716682b03df07fd770b228dd96
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000317_tree_id.txt
@@ -0,0 +1 @@
+((2_146:0.186023649,3_104:0.470055028)0.996:0.185075651,1_2180:0.001246990,(4_217:0.019974211,0_216:0.009917357)0.488:0.006249479);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000318_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000318_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2b8fad99ce25213b2ce38968c17fdc578be70743
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000318_tree_id.txt
@@ -0,0 +1 @@
+((0_217:0.0,1_2181:0.0,4_218:0.0):0.010170920,2_145:0.000000005,3_103:0.042595875);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000322_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000322_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..299726106e323b4ea0b6ea27d1d1d090b0738452
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000322_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000323_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000323_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3371afee32e65bfb98c448a66def1e580ca962fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000323_tree_id.txt
@@ -0,0 +1 @@
+(0_223:0.003252590,1_2187:0.003361203,(4_224:0.006303145,(2_138:0.111508653,3_96:0.112654413)1.000:0.160374874)0.915:0.020536484);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000325_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000325_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..26cb228e92fce256902decb432d43f76093c5c75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000325_tree_id.txt
@@ -0,0 +1 @@
+(0_225:0.008047423,4_226:0.010625296,(1_2189:0.002870661,(2_128:0.242520496,3_93:0.592314079)0.977:0.152619133)0.841:0.021058366);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000332_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000332_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e8746491b4af2050d2be55a637516cd597c006b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000332_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000333_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000333_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b9c05f2b7ea3275060a62cbc582fedd761c7f4f
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000333_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000338_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000338_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fe43c33c5367cf30d1df4fdfcb4d3b6870c43b33
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@@ -0,0 +1 @@
+(1_2212:0.002530667,4_246:0.005073435,(0_247:0.000000005,(2_104:0.044996030,3_72:0.175246157)0.991:0.043891765)0.498:0.002537438);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000341_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000341_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c6aac6b21006e85a23b23da92a2e8ef14e95a4e0
--- /dev/null
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+(0_253:0.005361978,1_2217:0.005569937,(4_251:0.015146115,(2_96:0.296022100,3_66:0.684943094)0.983:0.174657636)0.886:0.021330688);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000343_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000343_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1389614a0ebe4e7ad7b8816854822c29f0cdc930
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000343_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000356_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000356_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8f991ebae20f8b84b7f56290c91c3a62e5db7b0c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000356_tree_id.txt
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+(1_2248:0.002275988,4_281:0.002192768,(0_275:0.051759861,(2_60:0.316955333,3_40:0.147382516)0.999:0.147954445)0.924:0.021702755);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000361_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000361_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee92351735de823ffdec74483400f28367b1a803
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000361_tree_id.txt
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+((0_283:0.0,1_0:0.0,4_290:0.0):0.016138150,2_53:0.030396727,3_32:0.081384363);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000365_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000365_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9322258d7559d17f7e34da713cb39336c4439dc3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000365_tree_id.txt
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+(1_5:0.004130418,4_295:0.005517838,(0_288:0.001376616,(2_48:0.042306272,3_26:0.146314579)0.996:0.027094661)0.763:0.001364135);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000377_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000377_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..25e61f60e83239175acde077628d8f636204e3df
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000377_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000381_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000381_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..070465088a9e35fdc836cf0efb4421ec204d6b11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000381_tree_id.txt
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+((0_307:0.0,1_31:0.0,4_314:0.0):0.033720051,2_12:0.007095402,3_8:0.084016033);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000394_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000394_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cf10bfd58c26c77ba0cd52493ebd29b0a6f8b68f
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000394_tree_id.txt
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+(0_323:0.000000005,4_330:0.006717033,(1_48:0.009570041,(2_2569:0.072071089,3_2420:0.110181993)0.999:0.071869555)0.732:0.003852172);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000400_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000400_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..56e9dab34f79da545cac68b0b141b76c16606bce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000400_tree_id.txt
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+(4_337:0.020415977,(2_2554:0.137910589,3_2413:0.321153697)0.999:0.106984939,(0_330:0.024821227,1_55:0.023550921)0.291:0.002621839);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000401_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000401_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..28b773a58d0f7e9a5b55d0b2ea5e530ada7ee8eb
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000403_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000403_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c2cc0a3f5249e577d28f0f4c7ca02fd8105c0684
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000405_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000405_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e0c39cfea1dca2c14295c46d179c9eeed9723b9
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+(1_61:0.003117369,4_343:0.000000005,(0_336:0.006425881,(2_2548:0.090275086,3_2407:0.357732563)0.999:0.103188953)0.756:0.002968112);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000408_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000408_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..797019520130774000245da10120b1411b91f314
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000409_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000409_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9115d89f1f5d8c26a9b5bbed053d5518b1ba14dc
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@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000413_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000413_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d43e6b02dc41dc89f9ae60390f96fc7ffdd480b8
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000414_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000414_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..84ddfa6f5468746d34eff7881ab4a51254952f60
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000415_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000415_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..30c099163e347eb23b592bbbd57f248fe0141fd5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000415_tree_id.txt
@@ -0,0 +1 @@
+(1_74:0.003446196,4_356:0.003450683,(0_349:0.006917140,(2_2536:0.025681821,3_2395:0.116450439)0.993:0.024202913)0.548:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000418_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000418_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bba42728593ff65f900944a5750d79408d7156be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000418_tree_id.txt
@@ -0,0 +1 @@
+((0_352:0.0,4_359:0.0):0.028600894,2_2533:0.000000006,(2_981:0.367141642,3_1153:0.519351522)1.000:0.511712556);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000420_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000420_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3bfae6715cbe7319be6728895f236cdaa8b6dfb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000420_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000423_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000423_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5380f2ad798922d0f495c7665348f071b098920d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000423_tree_id.txt
@@ -0,0 +1 @@
+(0_360:0.009319738,4_366:0.000000005,(1_93:0.009351754,(2_2518:0.061203426,3_2390:0.009353069)0.339:0.009321591)0.807:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000425_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000425_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..637866a086097e3ee5b0234ffcb4426bf9e658eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000425_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000427_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000427_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b5f74f749e0089fc981246c0fe23344edaf31e09
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000427_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000436_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000436_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9805327650e6de79cbb2a50b22803d84dc1398fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000436_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000441_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000441_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f8f170ca8ac18f36df73ca791352b398583b76cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000441_tree_id.txt
@@ -0,0 +1 @@
+(0_383:0.004999591,4_389:0.005031327,(1_115:0.010265818,(2_2496:0.027369892,3_2364:0.283650558)0.879:0.024216245)0.782:0.004795420);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000444_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000444_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f2dffe115aa9d7d5b4fb483919bce0b10b2638e1
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000444_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000449_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000449_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0a9649bfddf042d7b93ae2fd16e3af1be4dd3e22
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000451_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000451_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1955b7e8c367274a29ab98b969491821952f5a9b
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000451_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000452_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000452_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f66ed0f8a29c5be00f16c3a2e7ed5147deddf50d
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000456_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000456_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..26db50551cf369f5b6afb3081896121f01687de7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000456_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000459_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000459_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..42ab5892029c7450d2261ad4cde9548e33809503
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000463_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000463_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cd7cec378eb5b534b38805c6749605dab418215b
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000467_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000467_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cfcae6b4505c0cd0162884002c887da7914dc7c9
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000468_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000468_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0d255679b301f47fb39ca0f491b8181fd636c9d7
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000470_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000470_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2cd236d092a417d3c0208749a2485994795cade3
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000477_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000477_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7687c6d5633e7981ae01f71193e6ddf1fef98937
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000477_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000480_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000480_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fe78f70af47a81466cf38eb178876676e57be98c
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000483_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000483_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6c7515e7238c91c1930a427b6c43060b6a6d74cb
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000485_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000485_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..919a6b938c8c880ee014efa8069f001578b2ea73
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000486_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000486_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a859cb63b7c2f38f4523b0a9e8468dc37d170e0
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000489_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000489_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..744c7e3ec129a8b3973993d0f2ad9bb4161d868a
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000490_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000490_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d2375bcf2d3faea7893c8c775e060944cd1589cc
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000490_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000491_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000491_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9d74f1168c0e079e345ef5d2fe705f2223da15d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000491_tree_id.txt
@@ -0,0 +1 @@
+(0_446:0.004110893,4_446:0.002051687,(1_173:0.000000005,(2_2425:0.090581539,3_2308:0.176957426)0.997:0.075363332)0.801:0.002053147);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000493_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000493_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eeef88663b44b612b422fc4dd8066d45a89fb5fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000493_tree_id.txt
@@ -0,0 +1 @@
+((0_448:0.0,1_175:0.0,4_448:0.0):0.028175751,2_2423:0.025257219,3_2306:0.059993034);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000494_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000494_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e90188da40520033b317c6d67a6b0405e467aa79
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000494_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000495_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000495_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..68245dd1677fb0cdaf538c4dc56dc269f5f4e0d8
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000495_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000496_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000496_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6ef4f9d890423f251721536db090dc7086d4db00
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000496_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000498_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000498_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e62a1909ab90bacb7a15e25c79e4d54d61c5c27
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000498_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000499_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000499_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f1b8c7ab5f576beef0f75ceb8fff20969107d0ee
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000502_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000502_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2eb9dbb8b7d570da4797e694372aade7be2db57d
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000513_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000513_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bab93830d43f386ce6d8d69ebc57bb0f5229e4ce
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000516_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000516_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..963661cc128a4211bbd66bcae6d2ddb983c8271b
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000517_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000517_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..38ce1ab7df97a853ea57e35d3ae32416cf12e7b9
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000518_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000518_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5d7f113fbd8c9dd077888d34fad56ddf5643bd18
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000519_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000519_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2610380277370b5d54e3d06a70a45f8af7626544
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000522_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000522_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..71ea3a5169742f40d1ecd33b7fd27622f7814eaf
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000524_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000524_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b1ca9f6d486385b7892b75eea85057c96e0725d
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000528_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000528_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..03aaffb4be4d5fcbf540bc43c89098e14493d5a9
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000530_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000530_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..32c6c669932ae0528bd532cbec0989f44aeeff50
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000531_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000531_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c35b02ce905038b1952f638607b8411677d6553b
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000533_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000533_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4b4087cad9f34c07a71ea4c2dc25f820528abaf
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000535_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000535_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b1ddbd1475ec093ab990c57c3e52a9f33b21d02b
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000537_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000537_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1747331034fd14157d3b1caf3a56337f14bfb9d9
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000540_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000540_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..93d336fbc986e4e8bbb169fa712d9b6cdac6da49
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000543_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000543_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e62907bc8a9c2e213296d0edc05324893a692b20
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000544_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000544_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..882a7d8b8bdf326cdfd9673706568706c6cde20c
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000558_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000558_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ab3192e75737bbe7728b2cd2da7a3e7de50d5611
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000558_tree_id.txt
@@ -0,0 +1 @@
+(0_537:0.004335519,1_271:0.002173579,(4_540:0.002165732,(2_2330:0.028347603,3_2213:0.174069113)0.966:0.025153829)0.747:0.002191263);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000561_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000561_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..470c3a22c1be04a4d71543965b40c412117fee1d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000561_tree_id.txt
@@ -0,0 +1 @@
+(0_540:0.003548157,4_543:0.005404115,(1_274:0.004576560,(2_2327:0.086857352,3_2210:0.270905865)1.000:0.179634542)0.756:0.008626079);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000565_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000565_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..10ba784878c2ccf4259804577de44c102e539afb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000565_tree_id.txt
@@ -0,0 +1 @@
+(0_548:0.000000005,4_549:0.014777358,(1_281:0.022590267,(2_2321:0.080693069,3_2200:0.063368221)0.998:0.087169148)0.566:0.018910079);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000566_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000566_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..502c5a92cf74866b7e3dc75c52e5a2c82b2de463
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000566_tree_id.txt
@@ -0,0 +1 @@
+((2_2308:0.000000005,3_2198:0.182736102)1.000:0.519179624,1_290:0.000000005,(4_550:0.027358680,0_549:0.012521008)0.611:0.011204557);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000572_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000572_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..79bbcb7f73e64684808aa418be8234872f067960
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000572_tree_id.txt
@@ -0,0 +1 @@
+((1_302:0.034627696,3_2192:0.055925475)0.842:0.024719218,4_561:0.044075421,(0_560:0.011356566,2_2298:0.702042693)0.715:0.011404857);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000577_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000577_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..40df710e33de95ecf5d6689c257c27d10b243486
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000577_tree_id.txt
@@ -0,0 +1 @@
+((0_612:0.0,4_569:0.0):0.015566110,3_2139:0.024365341,(2_1952:0.034022774,4_860:0.098746952)1.000:0.172368800);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000579_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000579_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..42be71b6eb85500462c3dd62a4508bbf7878d3dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000579_tree_id.txt
@@ -0,0 +1 @@
+(2_2269:0.162510229,(3_2131:0.009537567,4_587:0.009455360)0.761:0.006279302,(0_617:0.009493317,1_363:0.000000005)0.657:0.003274288);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000581_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000581_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a36ee5246b357711e82fd42c1bb5268a89113b06
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000581_tree_id.txt
@@ -0,0 +1 @@
+(4_590:0.016091869,(0_620:0.000000005,1_366:0.003217444)0.972:0.019795540,(2_2267:0.069657570,3_2125:0.193046266)0.744:0.006632319);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000588_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000588_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..05029afa1fc9de731f3d458aa3b667591b23e48c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000588_tree_id.txt
@@ -0,0 +1 @@
+((0_629:0.0,1_375:0.0,4_599:0.0):0.034761275,2_2258:0.018748425,3_2114:0.079997467);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000593_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000593_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2848debb7394d25a9d282e32750f38ffaea094c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000593_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000594_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000594_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6b65b0ddf7274288f74005a28158eaf8854b3dbc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000594_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000597_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000597_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..24df151d26c0e4e7bcc53071df9b6bfa168bb569
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000597_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000598_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000598_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d53e86e568da8058cef0210945bad8b545c48275
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000598_tree_id.txt
@@ -0,0 +1 @@
+(1_390:0.011699531,4_614:0.000000005,(0_644:0.002333525,(2_2242:0.043393882,3_2103:0.131801163)1.000:0.085993602)0.291:0.002320837);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000601_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000601_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5678547d14543412c4642ce804b8d164a66894ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000601_tree_id.txt
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+(0_647:0.003131523,1_393:0.000000005,(4_617:0.008203990,(2_2239:0.064950923,3_2100:0.459194206)0.939:0.050828134)0.821:0.007668908);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000602_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000602_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3a0eafc8d62d34d2eaccc2132e15d75459853103
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000602_tree_id.txt
@@ -0,0 +1 @@
+(0_648:0.003300980,1_394:0.003310371,(4_618:0.000000005,(2_2238:0.158968566,3_2099:0.066301733)0.999:0.061062921)0.751:0.001651562);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000603_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000603_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..faecb84a067fd56fe5416dcbdc43414f18d2998d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000603_tree_id.txt
@@ -0,0 +1 @@
+(2_2237:0.020880395,3_2098:0.322130352,((0_649:0.0,4_619:0.0):0.004044875,1_395:0.000000005)0.985:0.065666814);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000606_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000606_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5cac29fb31ba1075178c6dd82d2c225b3cd5e10b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000606_tree_id.txt
@@ -0,0 +1 @@
+(1_399:0.003183604,4_623:0.000000006,(0_653:0.002122439,(2_2234:0.027096984,3_2094:0.059982125)0.992:0.027877089)0.800:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000608_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000608_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fcebb44c4e38d56f08fb0e2725b0f124ff01f7bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000608_tree_id.txt
@@ -0,0 +1 @@
+(0_655:0.000000005,1_401:0.003216495,(4_625:0.003217462,(2_2232:0.050293568,3_2092:0.177851938)0.869:0.021250168)0.149:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000610_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000610_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0800b6215e6a59239f024cd78600d3559a2a07c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000610_tree_id.txt
@@ -0,0 +1 @@
+((0_657:0.0,1_403:0.0,4_627:0.0):0.086483276,2_2230:0.118886188,3_2090:0.230748153);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000611_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000611_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f2ffd3e392d1e59d7c4cb8e83cda1383033a176
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000611_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000613_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000613_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc14a11cea613092f864d5dab799634afbc03480
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000613_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000620_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000620_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..38682bb5b7df79992834a0ca1bb8a2aeb5a9ac01
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000620_tree_id.txt
@@ -0,0 +1 @@
+((2_2210:0.008200023,3_447:0.644439481)0.824:0.012909194,1_414:0.000000005,(4_638:0.005239549,0_668:0.000000005)0.902:0.001743438);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000621_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000621_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c916fa1530f828f03d6eefb13bb7b5a809c88601
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000621_tree_id.txt
@@ -0,0 +1 @@
+(0_669:0.004706264,4_639:0.006743145,(1_415:0.011513041,(2_2209:0.026782017,3_2079:0.198863742)0.999:0.062686753)0.868:0.008337937);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000630_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000630_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..314cc52ed796326a58f62e8db6bea9c36b464a29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000630_tree_id.txt
@@ -0,0 +1 @@
+(0_682:0.004663417,4_649:0.011096499,(3_2070:0.020681943,(2_2199:0.170167161,1_425:0.000000005)0.853:0.007957073)0.330:0.003132073);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000638_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000638_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..017a98131f2235ffb2870f18ae28e74b9907c5cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000638_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000640_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000640_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6c81d47a7aa2678d675e2fb9d1761a5630fa7bcc
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000640_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000641_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000641_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4a509731bd10401f5961a7461b50abac9a6f8cb7
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000644_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000644_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..17c23a0f5d985398a852d7123400bf8434c93bc4
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000646_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000646_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5785c5331f9a59152bdc7c36fb4e83747b8ade8
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000647_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000647_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..49ce25d442cc51c8503d45f03e1ab2547eb298ae
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000649_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000649_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..118eb4afd683363174bef280c8adbcf6f3f58c43
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000657_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000657_tree_id.txt
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index 0000000000000000000000000000000000000000..9a150a83abb4147baba21e9e37f44b2003629add
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000661_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000661_tree_id.txt
new file mode 100644
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000662_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000662_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000663_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000663_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..987010a527f41428a1226376384d9c81782976d8
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000666_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000666_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000670_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000670_tree_id.txt
new file mode 100644
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000673_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000673_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..31adb022e078d0cfa31914cebed8e72e2d0d6948
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000676_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000676_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..658fabf4795a5e760248998554ffe5d9641048cc
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000678_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000678_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..235076db752a7d7f08e8dbf246a06b05c22d891b
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000684_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000684_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bef58e12eec17742c193ceec069ab7afd1d2bbab
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000685_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000685_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3fee494b12a741d37f7277c1807da4ec983d325c
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000690_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000690_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d64d97b6e801cc5e114ed685315ca50823d20a52
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index 0000000000000000000000000000000000000000..a8ba221afaf01d61bfa043061b32b6bfae5db19b
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000704_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000704_tree_id.txt
new file mode 100644
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000706_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000706_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000707_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000707_tree_id.txt
new file mode 100644
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000714_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000714_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b71cf4b0f683f2e172cc45a6a2d94cf77a5fc40
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000714_tree_id.txt
@@ -0,0 +1 @@
+((0_778:0.0,1_518:0.0):0.000000005,4_745:0.000000005,(2_2076:0.030034197,3_1968:0.170554107)0.992:0.089563798);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000716_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000716_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed12e391aeaca7a469bf70c5a1a149af59194cd7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000716_tree_id.txt
@@ -0,0 +1 @@
+(0_781:0.004218822,(1_522:0.0,4_750:0.0):0.004297311,(2_2073:0.027391805,3_1963:0.377222857)0.000:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000717_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000717_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1161000b9df7258799eb5771182e8b5ee23da6f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000717_tree_id.txt
@@ -0,0 +1 @@
+((0_782:0.0,1_523:0.0,4_751:0.0):0.000885626,2_2072:0.020962481,3_1962:0.202200719);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000724_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000724_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..88fce2ffd20a604cee9c6f3b538ff5cc20539e38
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000724_tree_id.txt
@@ -0,0 +1 @@
+(0_789:0.011127341,4_758:0.002510406,(1_530:0.003607024,(2_2065:0.110437630,3_1955:0.331171836)0.958:0.051654170)0.442:0.004263718);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000726_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000726_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a774e52f6b6736ac99e4bea5df546b165a06159d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000726_tree_id.txt
@@ -0,0 +1 @@
+(0_791:0.002453330,4_760:0.000000005,(1_532:0.005288644,(2_2063:0.101473562,3_1953:0.107551236)1.000:0.236312865)0.723:0.002080447);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000731_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000731_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f6df46e76d5288f8f1d27ab84fc0c819b2e29fdb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000731_tree_id.txt
@@ -0,0 +1 @@
+((0_796:0.0,1_537:0.0):0.000000005,4_765:0.006118833,(2_2050:0.027432284,3_1948:0.095632559)0.961:0.055951632);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000732_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000732_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..384c63f78cd38ec582ab1ec8d84a5847904c4669
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000732_tree_id.txt
@@ -0,0 +1 @@
+((2_2049:0.110588337,3_1947:0.234894146)0.913:0.081106424,4_766:0.005301889,(1_538:0.000000005,0_797:0.000000005)0.000:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000734_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000734_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..90aedfedbdb4edbe1ad16e8e20e1d60ef3c4f67d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000734_tree_id.txt
@@ -0,0 +1 @@
+(4_769:0.039706655,1_541:0.044283215,(0_800:0.010562021,(2_2083:0.431352478,3_1975:0.167774859)1.000:0.951464313)0.617:0.001119485);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000742_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000742_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc6f14c175c29d6b7cf90e8441992d1c866075a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000742_tree_id.txt
@@ -0,0 +1 @@
+(2_2039:0.028363179,3_1938:0.151916572,(0_820:0.004515903,(1_551:0.0,4_779:0.0):0.045170381)0.933:0.040094103);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000760_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000760_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3fa13d124110051b448559cfc3433d6397e61c4c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000760_tree_id.txt
@@ -0,0 +1 @@
+(0_840:0.005337709,4_799:0.010686896,(1_571:0.010567923,(2_2019:0.033899700,3_1912:0.235627129)0.988:0.074285500)0.764:0.005582138);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000762_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000762_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..18c498b9652f297f874bef2d8667a9400114f96e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000762_tree_id.txt
@@ -0,0 +1 @@
+(0_842:0.000000005,1_573:0.006240254,(4_801:0.006243811,(2_2017:0.040841482,3_1910:0.202269350)0.977:0.065483646)0.868:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000764_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000764_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..abc16e4ff3bfc2a75f90df826253de0ed6c1bf3b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000764_tree_id.txt
@@ -0,0 +1 @@
+(2_2015:0.025252437,3_1908:0.244094107,((0_844:0.0,1_575:0.0):0.000000005,4_803:0.005365338)0.938:0.040916102);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000767_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000767_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1fcdfb6fef9a63cbdee74fc9ffc6cad1b5e9bd82
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000767_tree_id.txt
@@ -0,0 +1 @@
+((2_2012:0.041866157,3_1905:0.214565615)0.984:0.058434838,1_578:0.010430398,(4_806:0.009969475,0_847:0.003318725)0.716:0.002787399);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000770_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000770_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ea87cbaa9419b164337cff0053d694131f82fc9c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000770_tree_id.txt
@@ -0,0 +1 @@
+(2_2008:0.003681825,4_810:0.008083313,(3_1901:0.098951221,(0_852:0.000000005,1_583:0.002325606)1.000:0.116678032)1.000:0.110735784);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000771_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000771_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2bc2ad386608d156293e4cd139000d768e0863e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000771_tree_id.txt
@@ -0,0 +1 @@
+(0_862:0.013261872,1_593:0.000000005,(2_1999:0.267655980,(3_1896:0.589961178,4_813:0.811427126)0.973:0.310235966)0.967:0.157647980);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000774_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000774_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..08a78d1223269da3c3b5bc25a332bdccbd629dbc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000774_tree_id.txt
@@ -0,0 +1 @@
+(4_816:0.069500612,2_1998:0.038900583,(1_596:0.083849509,(0_867:0.109689281,3_1895:0.078418666)1.000:0.131480122)0.397:0.024294923);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000775_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000775_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0f25721fe76a803798d93c1dc5779c22993c52ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000775_tree_id.txt
@@ -0,0 +1 @@
+(0_869:0.012356783,2_1997:0.032881042,(3_1894:0.170588687,(1_597:0.004527269,4_817:0.002969020)0.995:0.055469687)0.979:0.036335987);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000781_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000781_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e278f66fc055076eb6d28d9baadf06bae8421abc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000781_tree_id.txt
@@ -0,0 +1 @@
+((0_875:0.0,4_823:0.0):0.000000005,1_603:0.004147859,(2_1991:0.046290592,3_1888:0.183102169)0.844:0.029515733);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000784_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000784_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a3b0ee280ca2fddb1c9bdb7357b654410f80a924
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000784_tree_id.txt
@@ -0,0 +1 @@
+((0_878:0.0,1_606:0.0,4_826:0.0):0.067096462,2_1988:0.132174837,3_1885:0.598523616);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000789_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000789_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..849570667caea5d6325c5239198443581d31ba9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000789_tree_id.txt
@@ -0,0 +1 @@
+(1_611:0.013813695,4_831:0.005607364,(0_883:0.003533059,(2_1983:0.162714667,3_1880:0.298535339)0.998:0.101176006)0.703:0.010157428);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000792_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000792_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3fefa1cad1e94dfda4a4299d67ba4be666bda813
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000792_tree_id.txt
@@ -0,0 +1 @@
+(0_886:0.000000005,4_834:0.002346055,(1_614:0.004741885,(2_1979:0.024631344,3_1877:0.130280659)0.992:0.037512893)0.741:0.002309373);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000795_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000795_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1eea39c91de70e121a9ee987d03547c1ae7ecb19
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000795_tree_id.txt
@@ -0,0 +1 @@
+(1_617:0.003111776,4_837:0.000000005,(0_889:0.009301273,(2_1976:0.029139078,3_1874:0.184641619)0.998:0.064368213)0.570:0.000059844);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000799_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000799_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..002ab95a71376645ffd1b60b5d2a00f25c719cf3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000799_tree_id.txt
@@ -0,0 +1 @@
+((0_893:0.0,4_841:0.0):0.005777494,1_621:0.018616442,(2_1972:0.098225316,3_1870:0.570008684)0.993:0.166308027);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000801_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000801_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a3cc872876e51c721bcd15bc13ae5d234d4aa331
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000801_tree_id.txt
@@ -0,0 +1 @@
+(0_895:0.017403635,1_623:0.000000005,(4_843:0.000000005,(2_1969:0.054894074,3_1867:0.255114762)0.945:0.074232975)0.868:0.008598104);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000802_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000802_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5f46d24c52ec34f8eee843a4a4ebd232d4855f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000802_tree_id.txt
@@ -0,0 +1 @@
+(4_844:0.051565836,1_624:0.007711366,(0_896:0.000000005,(2_1968:0.191531360,3_1865:0.471520794)0.922:0.122020129)0.414:0.012540118);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000803_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000803_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..041efbf78ea2d716786e74457917dac23ee3c5a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000803_tree_id.txt
@@ -0,0 +1 @@
+((0_897:0.0,1_625:0.0,4_846:0.0):0.012559077,2_1967:0.042457298,3_1864:0.345216722);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000808_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000808_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2783692761d4a65362965cbf840ef58821e5de13
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000808_tree_id.txt
@@ -0,0 +1 @@
+(1_630:0.015271181,2_1961:0.010143132,(4_851:0.000000005,(0_902:0.004862722,3_1857:0.293962710)0.762:0.005361153)0.773:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000816_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000816_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..19aa3b1b7d032800a534fba590d038bfd24c4083
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000816_tree_id.txt
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+(1_641:0.000000005,4_861:0.010094282,(0_913:0.010104638,(2_1948:0.111966912,3_1848:0.031467668)0.742:0.009512512)0.232:0.000000006);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000819_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000819_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a6c82bc0330335acbb7446349a996e90aeb625aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000819_tree_id.txt
@@ -0,0 +1 @@
+(0_924:0.002105889,4_870:0.014717378,(1_646:0.002737147,(2_1888:0.058242783,3_1838:0.218045103)0.999:0.071353808)0.767:0.003595849);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000820_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000820_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f68fb62b5a527f2758dee6237c6baa382ad056f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000820_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000821_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000821_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dc5762bbd2fb70bdf7957307719adf5db2253926
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000821_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000831_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000831_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..39831c138802dc3a0360858ec158c6ba2ab08bc9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000831_tree_id.txt
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+((0_940:0.0,1_663:0.0,4_883:0.0):0.033843728,2_1873:0.018703137,3_1819:0.047920131);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000832_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000832_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..53f6b716392e8b192fc574f92231b0ecbba7fbdc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000832_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000837_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000837_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..51069fde8f303ab18ebba9e0f998f6eed8f1019b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000837_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000841_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000841_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c2a4d5b9b4af2f81368cd6ea0bfa0de0b1891e26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000841_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000843_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000843_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..89c9fafaf01e9ce983f1955adfadcab7bbc7e3b2
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000843_tree_id.txt
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+(2_1860:0.003746025,4_895:0.012580075,(1_675:0.003227225,(0_952:0.006951925,3_1806:0.004660664)0.891:0.006063999)0.347:0.002322452);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000844_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000844_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4cdcacdeef2ac33da14c62ec2806f0ab01714e8f
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000849_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000849_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..619fec3045fc1deb4e807dfe2e558d6dba7e193d
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000849_tree_id.txt
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+((0_961:0.0,1_684:0.0,4_904:0.0):0.009546877,2_1852:0.009599677,3_1779:0.039596551);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000852_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000852_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d6f1b69d1906854a5f96643ebe457b53a3a35086
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000853_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000853_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ef66ab3b4bcf85dbe63a4928c087a6bbf3827abb
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000856_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000856_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..27910f3258b086230d43f9236f1e92c9aa25f65b
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000857_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000857_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..54bc6f624352b2696547ae96aa0ef20bbacbab9e
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000858_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000858_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e5d1c9ecc4e68867e3f4540b3d94773b4cb7f5b2
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000866_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000866_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2726af6e6ce9f7c311a882ce597b8af09a42cb8c
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000869_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000869_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3dd1eaaa9c032b423595eb3c05fb7166d23c9f15
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000871_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000871_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c294e0ebecb372b27ae47033614fd0f63d7141f0
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000873_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000873_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..09ad76f7710fd473f8e8c4373e0f82665533c4b2
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000874_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000874_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a2c151642a24bf2c24af1b812892bd999c1e8e2d
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+(2_1811:0.022296252,3_1700:0.030649669,(4_938:0.000000005,(0_996:0.000000005,1_718:0.002757572)0.974:0.011095874)0.406:0.003203135);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000875_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000875_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b935e879a78440a68d08c30592f8501981c5cabb
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000875_tree_id.txt
@@ -0,0 +1 @@
+(0_998:0.004867819,4_940:0.007269884,(1_720:0.004971481,(2_1810:0.057266302,3_1699:0.228868709)1.000:0.154596915)0.758:0.004493858);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000879_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000879_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1d1a95e03cf78ed2eca9c5d4ad376619421d6567
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000879_tree_id.txt
@@ -0,0 +1 @@
+(0_1005:0.001502753,4_946:0.001504478,(1_727:0.000000005,(2_1806:0.059010544,3_1693:0.048520541)1.000:0.060982992)0.803:0.001507954);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000884_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000884_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9bf76b95bb3d0a63d00d6ceae42e5ea82bb46b10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000884_tree_id.txt
@@ -0,0 +1 @@
+(0_1010:0.000000005,4_951:0.003348226,(1_732:0.011516841,(2_1799:0.056352901,3_1688:0.146280361)0.989:0.053860428)0.708:0.005873053);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000885_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000885_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d6e17e523bf585a258139b4c0e8030ee9fa0375a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000885_tree_id.txt
@@ -0,0 +1 @@
+(0_1011:0.002868976,4_952:0.002867855,(1_733:0.002867807,(2_1798:0.043165207,3_1687:0.081799099)0.997:0.043076793)0.544:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000890_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000890_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6020c23d7301bf788b145f0c781182d1b69360c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000890_tree_id.txt
@@ -0,0 +1 @@
+(0_1016:0.000000005,1_744:0.008898457,(4_963:0.004503142,(2_1793:0.056710979,3_1682:0.163308485)0.924:0.028329362)0.861:0.008821569);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000892_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000892_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0eff2785c8364b0242269155f282f5e9d12e7501
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000892_tree_id.txt
@@ -0,0 +1 @@
+(0_1018:0.012379845,4_965:0.017913106,(1_746:0.005172020,(2_1791:0.075496642,3_1680:0.237766376)1.000:0.110498094)0.941:0.017866511);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000902_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000902_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ca1feaaa463caca125bb3e942810b9d53bef6a82
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000902_tree_id.txt
@@ -0,0 +1 @@
+(1_769:0.002048843,4_990:0.002481237,(0_1041:0.003885206,(2_1779:0.030500298,3_1666:0.093172162)0.982:0.026614808)0.418:0.005477472);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000904_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000904_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2900ed95a42a592a3515b278cc8dd399fba3eb3c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000904_tree_id.txt
@@ -0,0 +1 @@
+(0_1043:0.003302189,(1_771:0.0,4_992:0.0):0.000000005,(2_1776:0.258886511,3_1664:0.107089428)0.984:0.060866718);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000907_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000907_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4847d914db551e0f9ca7bb7b913b6e14b850cdc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000907_tree_id.txt
@@ -0,0 +1 @@
+(1_774:0.003881426,4_995:0.001942853,(0_1046:0.005848756,(2_1773:0.048674145,3_1661:0.100816450)0.998:0.053095655)0.767:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000911_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000911_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..607de70e4da658f1559f146ad73d36291da33064
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000911_tree_id.txt
@@ -0,0 +1 @@
+(2_1768:0.172800235,3_1657:0.210516636,(0_1050:0.001808187,(1_778:0.0,4_999:0.0):0.000000005)1.000:0.110354396);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000912_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000912_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5cec989d5f40f5eaa475db9504d50ed8024dbdf6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000912_tree_id.txt
@@ -0,0 +1 @@
+((0_1051:0.0,1_779:0.0,4_1000:0.0):0.041775316,2_1767:0.111828492,3_1656:0.128755781);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000920_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000920_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..08e2b29a9658879e259a30c0c26b2ca34bc09c21
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000920_tree_id.txt
@@ -0,0 +1 @@
+((0_1061:0.0,1_789:0.0,4_1010:0.0):0.041077842,2_1755:0.060144301,3_1646:0.254948620);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000921_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000921_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0703b451bc5348ab4e5ce70733dc89bd1e2f55c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000921_tree_id.txt
@@ -0,0 +1 @@
+(2_1754:0.023595788,3_1645:0.065687857,(0_1062:0.001313203,(1_790:0.0,4_1011:0.0):0.007643677)0.877:0.008230864);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000922_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000922_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..02e8535b4309fe0fb7403bf3594caecd81872eab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000922_tree_id.txt
@@ -0,0 +1 @@
+(0_1063:0.012187731,(1_791:0.0,4_1012:0.0):0.020929741,(2_1752:0.125907043,3_1644:0.437662367)0.976:0.093000155);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000924_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000924_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..540f812ed1cf1ea9a69029ad64d55b5e726f9ac7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000924_tree_id.txt
@@ -0,0 +1 @@
+((0_1067:0.0,4_1017:0.0):0.000000005,1_795:0.006190966,(2_1749:0.103713762,3_1641:0.296358884)0.999:0.099735956);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000926_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000926_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e0b60ea847596b3a777b30d8c7a73c0715833890
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000926_tree_id.txt
@@ -0,0 +1 @@
+((1_797:0.0,4_1019:0.0):0.003215852,2_1747:0.013286229,(0_1069:0.006204527,3_1639:0.215921224)0.735:0.003774614);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000933_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000933_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df48ed81d579e1b65d22bd74684096ab3c8fc829
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000933_tree_id.txt
@@ -0,0 +1 @@
+(0_1078:0.002904151,4_1028:0.000000005,(1_806:0.005852086,(2_1738:0.031599584,3_1630:0.127208266)0.987:0.036887298)0.805:0.000000006);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000938_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000938_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f2ccd66e46f05f92ac97444530ade5d2783dd105
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000938_tree_id.txt
@@ -0,0 +1 @@
+((0_1083:0.0,1_811:0.0,4_1033:0.0):0.033215262,2_1732:0.026376611,3_1625:0.077184669);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000940_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000940_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b88e02cdb43d8dd24fa4314e9b23b594dba88e55
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000940_tree_id.txt
@@ -0,0 +1 @@
+(2_1730:0.058083099,3_1623:0.203104330,((0_1085:0.0,1_813:0.0):0.002570348,4_1035:0.000000005)0.992:0.047302927);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000952_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000952_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6c5d210a7c8233e92515c0659ba2ff2774b0c048
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000952_tree_id.txt
@@ -0,0 +1 @@
+(0_1097:0.003708128,1_825:0.000000005,(4_1047:0.001864925,(2_1717:0.017169503,3_1611:0.068277198)0.877:0.007265219)0.787:0.001837293);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000955_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000955_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e793d22459ebf453ecc44e9b54b7e0c75f630e27
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000955_tree_id.txt
@@ -0,0 +1 @@
+(2_1713:0.050420697,3_1606:0.054466795,(0_1102:0.006738232,(1_830:0.0,4_1052:0.0):0.008911815)0.970:0.035759348);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000956_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000956_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..42892734f9e429ab85dd9940191f51d12033724d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000956_tree_id.txt
@@ -0,0 +1 @@
+(0_1103:0.002885138,(1_831:0.0,4_1053:0.0):0.004268350,(2_1712:0.066817551,3_1605:0.224654746)0.920:0.031708055);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000964_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000964_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52fd8f98960a8516b27d3bb1f412089eb34d59ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000964_tree_id.txt
@@ -0,0 +1 @@
+(0_1113:0.001400550,(1_841:0.0,4_1063:0.0):0.000000005,(2_1699:0.073340187,3_1596:0.198236517)1.000:0.077368792);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000967_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000967_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b0e7a8505b008a2210a52bc3cc700eecc3ffa8b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000967_tree_id.txt
@@ -0,0 +1 @@
+(0_1117:0.003428185,4_1067:0.013955299,(1_845:0.008527114,(2_1696:0.145151395,3_1592:0.418328442)0.991:0.114969782)0.690:0.012395242);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000968_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000968_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cebe38d753797a900f0378a6b6212f0b915a2f81
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000968_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000970_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000970_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1eeabbeee41436d1dd8ce9afaa56e63554ea8798
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000970_tree_id.txt
@@ -0,0 +1 @@
+((0_1120:0.0,1_848:0.0):0.012322269,4_1070:0.000000005,(2_1692:0.113247517,3_1589:0.070144363)0.964:0.096243646);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000975_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000975_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e9b695eede3dbfe6172964b440d06cf6e69bd9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000975_tree_id.txt
@@ -0,0 +1 @@
+(0_1125:0.024120505,1_853:0.010325550,(4_1075:0.011238559,(2_1687:0.117687302,3_1584:0.192371072)0.999:0.139990218)0.855:0.016990149);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000978_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000978_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f93cfe8ed770572fd01d4b4a289f2d1a7ca0991d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000978_tree_id.txt
@@ -0,0 +1 @@
+(0_1128:0.000000005,4_1078:0.004999345,(1_856:0.006674883,(2_1684:0.028107229,3_1581:0.245629624)0.771:0.008265124)0.912:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000979_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000979_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9f67dc1bec5c2d592fc3f8920cca7c256aea32e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000979_tree_id.txt
@@ -0,0 +1 @@
+(0_1129:0.000000005,4_1079:0.008717443,(1_857:0.001737420,(2_1683:0.007175375,3_1580:0.258484797)0.754:0.006800068)0.783:0.001728530);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000981_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000981_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b22780f5f469749d593277140038a5db0ea0257
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000981_tree_id.txt
@@ -0,0 +1 @@
+(2_1681:0.008870864,3_1578:0.386045676,((0_1131:0.0,1_859:0.0):0.006514830,4_1081:0.007067457)0.287:0.011907203);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000989_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000989_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3686e38562cdb3c83f2a3f2095932c8fd9976ca6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000989_tree_id.txt
@@ -0,0 +1 @@
+((0_1140:0.0,4_1090:0.0):0.006225128,1_868:0.004331159,(2_1671:0.170886700,3_1569:0.336305141)0.998:0.117166801);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000991_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000991_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..601b8cd4255e0b2d3ec717390d357ee9624d4309
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000991_tree_id.txt
@@ -0,0 +1 @@
+(2_1669:0.035435529,1_870:0.000000005,((0_1142:0.0,4_1092:0.0):0.000000005,3_1567:0.181830117)0.862:0.008567981);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000997_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000997_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..762317aebc672c13394c3eae947d088f994924f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000997_tree_id.txt
@@ -0,0 +1 @@
+((2_1662:0.214459848,3_1559:0.478185021)0.994:0.221971182,1_877:0.000000005,(4_1102:0.038014096,0_1148:0.030353088)0.393:0.022470088);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000999_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000999_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bf7817fd8714da3cf4386e9bb028067ea15775a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000999_tree_id.txt
@@ -0,0 +1 @@
+(0_1150:0.005540952,(1_879:0.0,4_1104:0.0):0.000000005,(2_1660:0.051453587,3_1556:0.106116278)0.998:0.073665145);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001006_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001006_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fc06a2ca60b03191096548141f705e241bb09d99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001006_tree_id.txt
@@ -0,0 +1 @@
+((2_1652:0.022423743,3_1549:0.200608001)0.872:0.020585531,1_886:0.007839147,(4_1115:0.007100603,0_1158:0.021365487)0.714:0.002702272);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001009_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001009_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ea03db3b24868d97a8069ba43dc1bd1bcd2ec752
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001009_tree_id.txt
@@ -0,0 +1 @@
+(2_1649:0.138367008,3_1546:0.316639125,((0_1161:0.0,4_1118:0.0):0.006277387,1_889:0.023728594)0.584:0.034096668);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001010_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001010_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..53d78c55e06f694402b58b668bd4966cf24b0b85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001010_tree_id.txt
@@ -0,0 +1 @@
+(0_1162:0.005312729,4_1119:0.008044348,(1_890:0.011367695,(2_1648:0.030520770,3_1545:0.225795271)0.984:0.048229894)0.803:0.005248528);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001022_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001022_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..29b1d67bd8b98b31b355e99b1f45fe6121a38c10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001022_tree_id.txt
@@ -0,0 +1 @@
+(2_1636:0.055731729,3_1532:0.446652245,((0_1175:0.0,1_903:0.0):0.000000005,4_1133:0.007381194)0.901:0.065950920);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001023_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001023_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..96f58bdc558d9c9056596894cfcd1393e4d6fee9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001023_tree_id.txt
@@ -0,0 +1 @@
+(1_905:0.003183601,4_1135:0.000000005,(0_1177:0.009020977,(2_1634:0.016459497,3_1531:0.059749767)0.987:0.023704197)0.501:0.004150480);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001029_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001029_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8d0dba7a16169bb9fb2a97d9efcd94eaf7d81e07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001029_tree_id.txt
@@ -0,0 +1 @@
+(2_1628:0.059320520,3_1525:0.378886920,(0_1183:0.009083362,(1_911:0.0,4_1141:0.0):0.006097640)0.865:0.025739819);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001034_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001034_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5265a588998d61ab647f59fe6acced0702c6f5d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001034_tree_id.txt
@@ -0,0 +1 @@
+(1_916:0.000000005,4_1146:0.002298302,(0_1188:0.004599901,(2_1623:0.025059988,3_1520:0.115447352)0.945:0.016205795)0.892:0.000000006);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001036_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001036_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..541ea2d6153ec3b79e67412365fa2060de6d1037
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001036_tree_id.txt
@@ -0,0 +1 @@
+(2_1621:0.047739212,(1_918:0.0,4_1148:0.0):0.008202531,(0_1190:0.013834284,3_1518:0.391667873)0.342:0.011342918);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001037_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001037_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e515b5073d5dedfeff576526ddc174125c92447f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001037_tree_id.txt
@@ -0,0 +1 @@
+(2_1620:0.028800967,3_1517:0.202555236,(0_1191:0.004629077,(1_919:0.0,4_1149:0.0):0.000000005)0.960:0.045856945);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001038_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001038_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..668b1beafc4951fec18e95cbd8a00ae00e34f7a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001038_tree_id.txt
@@ -0,0 +1 @@
+(2_1619:0.031409839,3_1516:0.242884134,((0_1192:0.0,4_1150:0.0):0.016056494,1_920:0.032946459)0.989:0.124275104);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001042_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001042_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3d3be01f6ab892e910131911a2c3e9ff9310de59
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001042_tree_id.txt
@@ -0,0 +1 @@
+((0_1196:0.0,1_924:0.0,4_1154:0.0):0.110314475,2_1615:0.130070610,3_1512:0.405195238);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001043_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001043_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..74e437dd831ce51d6a88643a56376be4684d9d1f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001043_tree_id.txt
@@ -0,0 +1 @@
+(2_1613:0.039427792,3_1510:0.160051481,((0_1197:0.0,1_925:0.0):0.000000005,4_1155:0.005904103)0.842:0.009225388);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001047_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001047_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..335cd64e5a08fe8d220d2c98812f3a81f7148a2f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001047_tree_id.txt
@@ -0,0 +1 @@
+(0_1201:0.007624949,(1_929:0.0,4_1159:0.0):0.000000005,(2_1609:0.054103424,3_1506:0.123637968)0.894:0.015393421);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001061_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001061_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a5e445a8c1cd29dafe7518b618f0b62a257fea92
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001061_tree_id.txt
@@ -0,0 +1 @@
+(1_944:0.004602405,4_1173:0.000000005,(0_1216:0.019443028,(2_1593:0.117295734,3_1490:0.277219470)0.999:0.074892430)0.720:0.003760138);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001062_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001062_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..470e65a32baff0847c7ba15a9d331db468fe9074
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001062_tree_id.txt
@@ -0,0 +1 @@
+(0_1217:0.006122647,(1_945:0.0,4_1174:0.0):0.009210688,(2_1592:0.031440792,3_1487:0.103816526)0.990:0.029708551);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001066_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001066_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cde35fe37bfe05c3c9ae742342da3467fe984d80
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001066_tree_id.txt
@@ -0,0 +1 @@
+((0_1221:0.0,1_949:0.0,4_1178:0.0):0.052364466,2_1588:0.032214322,3_1483:0.226449816);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001074_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001074_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..24613218c01955ebe436e910d2b457aa25e4fe0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001074_tree_id.txt
@@ -0,0 +1 @@
+((0_1230:0.0,1_958:0.0,4_1187:0.0):0.098480680,2_1579:0.151797118,3_1474:0.172700490);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001079_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001079_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3fc6fb39c0cf4d3b6085623db65a1edd70766502
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001079_tree_id.txt
@@ -0,0 +1 @@
+(0_1235:0.000873251,(1_963:0.0,4_1192:0.0):0.039704663,(2_1572:0.150286141,3_1468:0.431105099)0.896:0.066864568);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001083_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001083_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..47d22b0f627560ca07b58b06572db334a6ac909e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001083_tree_id.txt
@@ -0,0 +1 @@
+(2_1567:0.010495957,3_1463:0.068430953,((0_1247:0.0,1_979:0.0):0.001090170,4_1204:0.000000006)0.996:0.018702974);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001084_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001084_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..080b6f97bc47f0f3b8691151d5960a7120a27bfe
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001084_tree_id.txt
@@ -0,0 +1 @@
+((0_1248:0.0,1_980:0.0,4_1205:0.0):0.029044210,2_1566:0.039587336,3_1462:0.207319542);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001085_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001085_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ae2d262fb94eceadcf4cfa19184cadb15714bb5c
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001085_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001089_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001089_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c2153a017031346241f05bf90b8b758751c070aa
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001089_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001090_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001090_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cff457be9ff9c450f1a93502008a626878295b26
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001090_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001092_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001092_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..44f222b9161c6e6db2414149c50cca43b7dc9ab0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001092_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001093_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001093_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df761ec0bc62a663f2a629c305ca146a64993ecf
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001093_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001097_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001097_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..77c3c251ce7bf5a8ca4efacb4d26c974f0967f93
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@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001100_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001100_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a18563e102e3ae6a38374debfb1bcf8016f853ad
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001100_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001101_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001101_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..715dee2d1d1d2a7876ecd56169c3c378463b701c
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001101_tree_id.txt
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+(3_1442:0.135424546,(1_998:0.002798590,4_1223:0.000000005)1.000:0.083472527,(0_1268:0.000000005,2_1546:0.002789174)0.999:0.081521589);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001104_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001104_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a18883c91a0181c20ca8d0990a395f16841d72bb
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001104_tree_id.txt
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+(0_1271:0.002780352,1_1001:0.001390041,(4_1226:0.002377123,(2_1542:0.029921739,3_1438:0.082990437)0.420:0.006603889)0.611:0.000397999);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001129_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001129_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..406a3a2d4e1192c1f06395594d277385034027aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001129_tree_id.txt
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+(0_1299:0.020558892,(1_1028:0.0,4_1253:0.0):0.000000005,(2_1515:0.035810351,3_1411:0.296312919)0.958:0.107423881);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001133_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001133_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d8f5b93441d7ed54233f30dfd0c2ef1b3f7cc090
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+(0_1303:0.000000005,4_1257:0.008445156,(1_1032:0.004905983,(2_1511:0.033592288,3_1407:0.040731756)0.989:0.028465908)0.825:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001136_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001136_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d391d37a9b60a0479edb5b37df81a7ab87df2273
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001136_tree_id.txt
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+(0_1306:0.000000005,4_1260:0.005244525,(1_1035:0.000000005,(2_1508:0.041747727,3_1404:0.213657775)0.991:0.049600106)0.841:0.002616924);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001138_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001138_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..779540082960db1a989e394cbb1e712dc69051a6
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001146_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001146_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..92c6f4a57f0f580e1a7079bb7cc17107aa16b35e
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001152_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001152_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a2b7b4abd8803b54d8b0240f63b31948b13b5283
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001154_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001154_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..929f2e7b4546c15260e7c9c669f5e8c6505a7a8c
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001159_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001159_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1d339ddebdde73ece576d1e9a8139fd1afe84c0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001159_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001160_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001160_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..494354b05590873493b44bc38dbc468091bee202
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001160_tree_id.txt
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+(2_1482:0.038469542,3_1377:0.260559149,((0_1332:0.0,4_1286:0.0):0.000000005,1_1061:0.007588384)0.812:0.025306333);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001162_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001162_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..180a0ea2a85c17c76d98e0a01490842acee8e246
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001162_tree_id.txt
@@ -0,0 +1 @@
+(0_1354:0.012177981,(1_1093:0.0,4_1303:0.0):0.005505545,(2_1463:0.135581965,3_1375:0.831253818)0.958:0.152048402);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001169_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001169_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e2ca55129b3300564a585a37528d3d89c24df129
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001169_tree_id.txt
@@ -0,0 +1 @@
+(0_1366:0.008189342,1_1106:0.001739038,(4_1315:0.000000005,(2_1455:0.029364495,3_1362:0.016575718)0.964:0.019488980)0.941:0.012667249);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001173_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001173_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a6a370825ac0b8a013c5befe37a00f0144aaac22
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001173_tree_id.txt
@@ -0,0 +1 @@
+(1_1111:0.003345278,4_1320:0.003346674,(0_1371:0.032584552,(2_1450:0.048577304,3_1358:0.206409416)0.932:0.031766958)0.899:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001174_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001174_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5f6672246f0dd826ac8605f3b6b87ef49e12694b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001174_tree_id.txt
@@ -0,0 +1 @@
+(2_1449:0.053626827,3_1357:0.223215261,(0_1372:0.013779195,(1_1112:0.0,4_1321:0.0):0.014023068)0.956:0.037670120);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001176_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001176_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..266768fb4732113edc9e9e50d87d93768235fbbe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001176_tree_id.txt
@@ -0,0 +1 @@
+(0_1374:0.021054226,(1_1114:0.0,4_1323:0.0):0.004432651,(2_1447:0.095935317,3_1355:0.315462431)0.999:0.127137405);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001178_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001178_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..32d9f3ea9b17a84098199ccb8b2ebee76f53d9fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001178_tree_id.txt
@@ -0,0 +1 @@
+(0_1376:0.000000005,4_1325:0.002205154,(1_1116:0.006841741,(2_1445:0.057469075,3_1352:0.146587922)0.986:0.040638000)0.825:0.004253944);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001181_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001181_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c1511e034218e2cf23d4d584e55bb4a798a1038
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001181_tree_id.txt
@@ -0,0 +1 @@
+(0_1379:0.004791124,4_1328:0.000000005,(1_1120:0.002436124,(2_1442:0.020968198,3_1349:0.036726179)0.864:0.006104416)0.765:0.002364652);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001182_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001182_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0f687dac3746f22fae3c2447959d3b41e6561b29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001182_tree_id.txt
@@ -0,0 +1 @@
+((2_1441:0.120485126,3_1348:0.371042202)0.924:0.053773477,4_1329:0.003074258,(0_1380:0.011907708,1_1121:0.005604963)0.772:0.002942957);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001189_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001189_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cab7470a83a5cf3f3969e843548b3e9e5b659a46
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001189_tree_id.txt
@@ -0,0 +1 @@
+((2_1433:0.086930571,3_1341:0.272066101)0.995:0.087933105,4_1336:0.000000005,(1_1128:0.011823649,0_1387:0.000000006)0.642:0.002932380);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001193_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001193_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..66e7c001259ce6b56cbd7e8768a5eb441e624fe7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001193_tree_id.txt
@@ -0,0 +1 @@
+(1_1133:0.000000005,4_1341:0.002787425,(0_1392:0.000000005,(2_1428:0.022703975,3_1336:0.157166739)0.964:0.025781480)0.882:0.002794395);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001195_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001195_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cb2cecfca3131b07b802859b75dba8003d63c820
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001195_tree_id.txt
@@ -0,0 +1 @@
+(0_1395:0.008692428,4_1344:0.000000005,(1_1136:0.017393418,(2_1426:0.085404310,3_1330:0.181012839)0.986:0.095959879)0.828:0.013645360);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001196_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001196_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..58df4ef02c9abc10269a70317ad8a84bae93126f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001196_tree_id.txt
@@ -0,0 +1 @@
+((0_1396:0.0,1_1137:0.0,4_1345:0.0):0.035367500,2_1425:0.051859116,3_1329:0.314466956);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001198_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001198_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52819bb075eef9999fcbdcb7a2a074b2cb8f2989
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001198_tree_id.txt
@@ -0,0 +1 @@
+(1_1140:0.327971633,3_1326:0.105023096,(2_1422:0.010490559,(0_1399:0.059444523,4_1348:0.001863215)0.999:0.300060133)0.891:0.076521510);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001207_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001207_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..895d93f8f26a61b9987521ce488dc8b4f974f7ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001207_tree_id.txt
@@ -0,0 +1 @@
+(0_1409:0.009440602,4_1358:0.000000005,(1_1150:0.005841624,(2_1413:0.143931255,3_1316:0.519428535)0.857:0.053058127)0.871:0.013152276);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001211_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001211_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d2008973e4191f98b7d1c591b459d3e248972fef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001211_tree_id.txt
@@ -0,0 +1 @@
+(0_1413:0.005665052,4_1362:0.000000005,(1_1154:0.016972300,(2_1409:0.133021934,3_1312:0.405245758)0.868:0.087613276)0.952:0.000000006);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001212_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001212_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb93ffb72ff8bddf8e0a3daa5735d9f69a0b4826
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001212_tree_id.txt
@@ -0,0 +1 @@
+(0_1414:0.003214676,4_1363:0.003220476,(1_1155:0.009668878,(2_1408:0.040741281,3_1311:0.130806889)0.982:0.023447504)0.842:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001214_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001214_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b571c7807cee196686702eee6301a2d641d40f7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001214_tree_id.txt
@@ -0,0 +1 @@
+((2_1406:0.146099837,3_1308:0.403981755)0.988:0.172401374,1_1157:0.000000005,(4_1365:0.015660953,0_1416:0.000000005)0.480:0.008061957);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001215_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001215_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f581fe359ac1f9c9da743c4a2335229fb5af4c5d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001215_tree_id.txt
@@ -0,0 +1 @@
+(0_1417:0.006671078,1_1158:0.015480996,(4_1366:0.014002938,(2_1405:0.101722604,3_1307:0.608873995)0.999:0.129443681)0.623:0.013989895);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001217_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001217_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..38dbf86c3dc31ea150e8d7d68105d87ebc908d6c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001217_tree_id.txt
@@ -0,0 +1 @@
+(0_1420:0.019382892,1_1161:0.006894204,(4_1369:0.017724098,(2_1402:0.119630271,3_1304:0.169937347)1.000:0.153232310)0.863:0.011755590);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001218_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001218_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..48cfcd84a91334812dd3c2e23886621adf80eab8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001218_tree_id.txt
@@ -0,0 +1 @@
+(2_1401:0.132086290,3_1303:0.262016642,((0_1421:0.0,1_1162:0.0):0.014924314,4_1370:0.008523980)0.880:0.071811194);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001221_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001221_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d344fa316000335b254a7f94b6190b75b8d9bd9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001221_tree_id.txt
@@ -0,0 +1 @@
+((0_1426:0.0,1_1167:0.0,4_1375:0.0):0.081295246,2_1398:0.161920071,3_1298:0.170999923);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001222_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001222_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a1745a32b64e94cb2b1e71684313156f6fe2904
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001222_tree_id.txt
@@ -0,0 +1 @@
+((0_1427:0.0,1_1168:0.0,4_1376:0.0):0.340322031,2_1397:0.312596331,3_1297:0.188759839);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001226_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001226_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..341482cdc69123786a59d7d557bcf05c90d54d54
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001226_tree_id.txt
@@ -0,0 +1 @@
+(0_1431:0.017345981,(2_1393:0.026727854,3_1293:0.241413161)0.987:0.061025582,(1_1172:0.000000005,4_1380:0.011389526)0.746:0.003899005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001228_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001228_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..333dc30facb07e430e54484021448e16dbac6e28
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001228_tree_id.txt
@@ -0,0 +1 @@
+(0_1433:0.025628690,4_1382:0.000000005,(1_1174:0.008440264,(2_1391:0.077912128,3_1291:0.441401580)0.999:0.101960917)0.577:0.011289462);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001231_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001231_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..78b5957f5ac0699552772a258777c2434c3aa5b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001231_tree_id.txt
@@ -0,0 +1 @@
+(1_1177:0.000000005,4_1385:0.003815925,(0_1458:0.004768914,(2_1388:0.058100344,3_1287:0.194889435)1.000:0.052261668)0.732:0.001051010);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001235_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001235_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..93c0a758801334d0bbafa590f0643c378b62d7cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001235_tree_id.txt
@@ -0,0 +1 @@
+((0_1463:0.0,1_1182:0.0):0.001357048,4_1390:0.001439836,(2_1383:0.043676613,3_1283:0.148782748)0.986:0.021173246);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001237_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001237_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d5071be19011143846fe2e7e8abb90f85e8718a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001237_tree_id.txt
@@ -0,0 +1 @@
+(0_1465:0.011059257,4_1392:0.005043740,(1_1184:0.003299020,(2_1381:0.110116608,3_1281:0.504530307)0.870:0.028402119)0.660:0.007759395);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001239_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001239_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5603dd9c383954118cfffcfd285dff7d32337c6f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001239_tree_id.txt
@@ -0,0 +1 @@
+((2_1379:0.074882827,3_1279:0.309210119)1.000:0.065310752,4_1394:0.002614835,(1_1186:0.006924902,0_1467:0.003456492)0.634:0.002607061);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001242_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001242_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a3124a79ebd46244447d6029410641f5040adac7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001242_tree_id.txt
@@ -0,0 +1 @@
+(2_1376:0.030460599,3_1276:0.033054003,(0_1470:0.006712914,(1_1189:0.0,4_1397:0.0):0.000000005)0.990:0.024275478);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001247_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001247_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9bb28d4bbf65b3a9490bf38e6649ff51bf227cd3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001247_tree_id.txt
@@ -0,0 +1 @@
+(0_1475:0.000000005,1_1195:0.003650769,(2_1371:0.018778031,(4_1402:0.011757774,3_1263:0.840517431)0.673:0.006945181)0.864:0.007244424);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001249_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001249_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6a6a174552a2f13c787d93601d9b2c7c8846449d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001249_tree_id.txt
@@ -0,0 +1 @@
+((0_1477:0.0,4_1404:0.0):0.000000005,1_1197:0.004439237,(2_1369:0.080496053,3_1261:0.187649339)0.974:0.037938909);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001255_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001255_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..70a62a90b6de46156b6d7a8cdf84d9b594915517
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001255_tree_id.txt
@@ -0,0 +1 @@
+(0_1483:0.012895179,1_1203:0.000000005,(4_1410:0.012897835,(2_1363:0.040168414,3_1255:0.205058219)0.430:0.040835351)0.801:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001256_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001256_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a433315d6e6fdd87638e7c97e7351b290e096fd8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001256_tree_id.txt
@@ -0,0 +1 @@
+(1_1204:0.019183546,4_1411:0.000000005,(0_1484:0.013615044,(2_1362:0.108180161,3_1254:0.256253159)1.000:0.120908321)0.714:0.013195690);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001257_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001257_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8cb303cb5c697b37a150b933fcff4c167f14c9a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001257_tree_id.txt
@@ -0,0 +1 @@
+(0_1486:0.004842665,(1_1206:0.0,4_1413:0.0):0.008944142,(2_1360:0.139423470,3_1252:0.141049164)1.000:0.120021966);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001258_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001258_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2204656909bd3f400fe6a576f8b4de3ccd03b349
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001258_tree_id.txt
@@ -0,0 +1 @@
+(0_1487:0.001839971,1_1207:0.003695933,(4_1414:0.009305047,(2_1359:0.044618327,3_1251:0.134490434)1.000:0.052519453)0.808:0.003720474);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001262_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001262_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ef7735b0ae50cb0446bf940cb4580f887bcf97bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001262_tree_id.txt
@@ -0,0 +1 @@
+((0_1491:0.0,1_1211:0.0):0.006119069,4_1418:0.017822356,(2_1355:0.079099476,3_1247:0.367825851)0.997:0.138083778);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001266_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001266_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6b42c264dfa6a1c0c1aa8211e15aaaf39a56a9c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001266_tree_id.txt
@@ -0,0 +1 @@
+((0_1496:0.0,1_1216:0.0,4_1423:0.0):0.000000005,2_1350:0.018230138,3_1242:0.073848271);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001268_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001268_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..13ee86a7ac9cc0ca89b1bad75354a9cefdad8944
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001268_tree_id.txt
@@ -0,0 +1 @@
+(1_1218:0.031286520,4_1425:0.000000006,(0_1498:0.023614541,(2_1348:0.132514826,3_1240:0.287206575)0.972:0.083453180)0.662:0.011107351);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001269_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001269_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..788d9023faec3a3c33457acff95d41e13899a8b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001269_tree_id.txt
@@ -0,0 +1 @@
+((2_1347:0.032924383,3_1239:0.154013366)0.991:0.062832236,4_1426:0.003626816,(1_1219:0.003643776,0_1499:0.000000006)0.796:0.000000006);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001272_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001272_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..227f494864cbe66e2b8f73e90e64ba85b59e088a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001272_tree_id.txt
@@ -0,0 +1 @@
+((0_1502:0.0,4_1429:0.0):0.000000005,1_1222:0.003315500,(2_1344:0.099325826,3_1236:0.161628377)0.999:0.082202602);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001275_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001275_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc609d99ba77e49fd01eb98abbfe93b425e504f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001275_tree_id.txt
@@ -0,0 +1 @@
+(0_1506:0.004729106,1_1226:0.002358686,(4_1433:0.000000005,(2_1341:0.016412639,3_1233:0.078655314)0.825:0.015280711)0.762:0.002367050);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001278_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001278_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ae8778cb569dc85e4f31e78406ed3f6fea69e3f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001278_tree_id.txt
@@ -0,0 +1 @@
+(0_1510:0.001533666,1_1230:0.001534236,(4_1437:0.000000005,(2_1337:0.065307442,3_1229:0.038868236)0.973:0.019028438)0.417:0.001531662);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001280_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001280_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d20e8ff07441cb13e6a7db687bec517739119893
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001280_tree_id.txt
@@ -0,0 +1 @@
+(0_1512:0.007538208,1_1232:0.002500262,(4_1439:0.000000005,(2_1335:0.045092609,3_1227:0.269101965)0.984:0.050253019)0.897:0.004998335);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001283_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001283_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..105dd5ef41f8cc6735a45d4002debafcbdd5d7a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001283_tree_id.txt
@@ -0,0 +1 @@
+(0_1516:0.003594603,4_1443:0.004385738,(1_1236:0.016298005,(2_1329:0.105035371,3_1223:0.650588487)0.952:0.090675619)0.793:0.011256711);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001284_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001284_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a69259a7c4285bb46a9a1309bdda5a6a277e4eb3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001284_tree_id.txt
@@ -0,0 +1 @@
+(0_1517:0.002451080,4_1444:0.002451329,(1_1237:0.017397489,(2_1328:0.153486506,3_1222:0.391731367)0.991:0.088103586)0.662:0.005072855);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001285_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001285_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f60c0604be66b6b44cf271ee32a05276b2ff1bab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001285_tree_id.txt
@@ -0,0 +1 @@
+(0_1518:0.017593205,4_1445:0.005814323,(1_1238:0.005438459,(2_1327:0.043353949,3_1221:0.279385443)0.982:0.068014085)0.768:0.006226222);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001292_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001292_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..541186e15d45ade027a34875d0b9972a01b2bb6c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001292_tree_id.txt
@@ -0,0 +1 @@
+(0_1525:0.002212513,(1_1245:0.0,4_1452:0.0):0.000000005,(2_1319:0.103173481,3_1213:0.008888409)0.833:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001295_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001295_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a406a269a1abbb475c36c3e15054ba6e663a25ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001295_tree_id.txt
@@ -0,0 +1 @@
+(0_1535:0.001722577,4_1462:0.001716036,(1_1256:0.014380833,(2_1308:0.020463359,3_1207:0.383544664)0.973:0.031837690)0.940:0.011593093);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001299_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001299_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f1ae27de18eea7881f14da0e71d47b3b16012bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001299_tree_id.txt
@@ -0,0 +1 @@
+(2_1273:0.054277645,3_1183:0.078167701,((0_1543:0.0,1_1265:0.0):0.004947663,4_1470:0.006556360)1.000:0.063314148);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001300_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001300_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b3dc3a0344df067226a2c1565a538c9bea242040
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001300_tree_id.txt
@@ -0,0 +1 @@
+((0_1544:0.0,1_1266:0.0):0.014878043,4_1471:0.014814453,(2_1270:0.000000006,3_1180:0.000000005)0.856:0.014861750);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001303_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001303_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ec0b94186cbb39cf0da68926b17e2e45201cc0b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001303_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001305_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001305_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b6a36e00173dc74beeebb12af9c5aa765ec9816e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001305_tree_id.txt
@@ -0,0 +1 @@
+(0_1556:0.008359032,2_1263:0.098030492,(1_1277:0.000000005,(3_1169:0.036968280,4_1482:0.012095709)0.296:0.008033210)0.860:0.007792373);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001307_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001307_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a14f6797d5a8c85298ba5bc0c39eeb6b2cf7c285
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001307_tree_id.txt
@@ -0,0 +1 @@
+((0_1558:0.043626495,2_1261:0.028455993)0.896:0.013594545,4_1484:0.035007630,(3_1167:0.045578044,1_1279:0.034551466)0.831:0.008338022);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001309_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001309_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..40c89412edd37fd6ac9c6cea7f22d05ebf13d808
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001309_tree_id.txt
@@ -0,0 +1 @@
+(1_1288:0.115661442,3_1157:0.125560781,(2_1246:0.095043195,(0_1572:0.000000005,4_1501:0.006224690)0.960:0.053355114)0.960:0.070796985);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001317_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001317_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d6d70210f69bfbe7418b380a4e94b0fe4ce0364f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001317_tree_id.txt
@@ -0,0 +1 @@
+((0_1581:0.0,4_1510:0.0):0.000000005,1_1296:0.032256769,(2_1235:0.161375641,3_1145:0.066428617)0.909:0.051055644);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001321_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001321_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..94b8e5b18fc3f54f7d87a23d31d01e507e70959f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001321_tree_id.txt
@@ -0,0 +1 @@
+(0_1586:0.000000005,4_1515:0.006439015,(1_1301:0.000000005,(2_1230:0.089112664,3_1140:0.267900742)0.922:0.056127478)0.879:0.019574560);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001323_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001323_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..57ce97b36cdda2951f16e8fa0a6c0d9e1fc8fe57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001323_tree_id.txt
@@ -0,0 +1 @@
+(4_1518:0.029048413,1_1303:0.015043611,(0_1588:0.014985344,(2_1226:0.285132102,3_1138:0.809264182)0.900:0.071927605)0.636:0.007037072);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001328_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001328_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4fcf7601494bdfe13b6e095bd754935860be076d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001328_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001334_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001334_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8f0e23c2343a74f8268021bb56084290fd0c00ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001334_tree_id.txt
@@ -0,0 +1 @@
+(1_1314:0.001797712,4_1529:0.000000005,(0_1599:0.007000530,(2_1215:0.015064139,3_1127:0.042231225)0.997:0.024326246)0.731:0.003859665);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001341_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001341_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..be320cf0744e53f0f4cc199ffbd3488ec6102c82
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001341_tree_id.txt
@@ -0,0 +1 @@
+(1_1324:0.004430348,4_1539:0.013604176,(0_1609:0.013562868,(2_1206:0.360410482,3_1118:0.485591631)0.469:0.031228096)0.361:0.006814637);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001349_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001349_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5233725313431604ae88af6931f2756858568059
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001349_tree_id.txt
@@ -0,0 +1 @@
+(0_1618:0.004493760,1_1333:0.009039952,(4_1548:0.014065833,(2_1181:0.016928360,3_1110:0.236365982)0.986:0.056434038)0.716:0.003984349);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001351_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001351_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0f64271781ecacea80c57d72021d46ad81a3b88a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001351_tree_id.txt
@@ -0,0 +1 @@
+(0_1620:0.007487478,1_1335:0.007367674,(4_1550:0.000000006,(2_1179:0.105729191,3_1108:0.328501186)0.998:0.110484357)0.942:0.014806426);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001353_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001353_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..74c04e97ab279e493bcdb3c94e81d41f2f761f11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001353_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001362_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001362_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f63466abe820d2cacee40223b7de1314c3b6ac12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001362_tree_id.txt
@@ -0,0 +1 @@
+(2_1164:0.020692642,3_1095:0.048131755,((0_1635:0.0,4_1564:0.0):0.005980190,1_1352:0.006018849)0.863:0.016894723);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001375_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001375_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..54acceeaf666da5c8085f63506c8f2e78a594673
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001375_tree_id.txt
@@ -0,0 +1 @@
+((0_1648:0.0,1_1365:0.0,4_1577:0.0):0.017998196,2_1151:0.011997937,3_1082:0.074764639);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001377_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001377_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3820d7ed4e1f3b82e0474b81d59cd63ea2592158
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001377_tree_id.txt
@@ -0,0 +1 @@
+(0_1650:0.007744409,3_1080:0.023384192,((1_1367:0.0,4_1579:0.0):0.000000005,2_1149:0.015625617)0.679:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001387_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001387_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..650e4308a63cd1e3518e3199d1a7f30149c16e65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001387_tree_id.txt
@@ -0,0 +1 @@
+((0_1660:0.0,1_1377:0.0,2_1139:0.0,4_1589:0.0):0.012077720,3_1070:0.012077720);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001405_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001405_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3eb76bfe146b5288293d39b550c54a004fbf7bb6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001405_tree_id.txt
@@ -0,0 +1 @@
+((0_1678:0.0,1_1395:0.0,4_1607:0.0):0.017422707,2_1121:0.010058732,3_1051:0.047040907);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001412_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001412_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3a70b4885f5769474fcd5d8bf34c6ceff63a3610
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001412_tree_id.txt
@@ -0,0 +1 @@
+(0_1685:0.002845587,4_1614:0.002863585,(1_1402:0.000000006,(2_1113:0.041733196,3_1043:0.070245821)0.995:0.036785430)0.455:0.002860834);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001417_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001417_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..861387b463bfc67dd391a41d267d79c024f13fab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001417_tree_id.txt
@@ -0,0 +1 @@
+(2_1108:0.104769519,3_1038:0.378381800,((0_1690:0.0,1_1407:0.0):0.007724354,4_1619:0.003783591)0.936:0.046771113);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001420_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001420_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c3f8159e9e72fc84c5b1626ac63dd8eb539df1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001420_tree_id.txt
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+((0_1693:0.0,1_1410:0.0,4_1622:0.0):0.080816388,2_1105:0.063636583,3_1034:0.203780865);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001425_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001425_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..20c59cfd80df5e274d0a21f53884fa27b41a5b91
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001427_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001427_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5af128bcfd643421c03144ec366e065b474b0cec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001427_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001434_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001434_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..86e6ce9e34fad418d0f580835b719a21bce2f356
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001434_tree_id.txt
@@ -0,0 +1 @@
+(1_1424:0.015956061,4_1636:0.010384143,(0_1707:0.024993539,(2_1091:0.067999218,3_1017:0.300194321)0.968:0.057116581)0.430:0.005726824);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001435_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001435_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3ad15e7332715a946a554f8578b42173ec1061f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001435_tree_id.txt
@@ -0,0 +1 @@
+(0_1708:0.006498570,1_1425:0.019650515,(4_1637:0.007854826,(2_1090:0.183523771,3_1016:0.756975828)0.805:0.088171187)0.736:0.005143841);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001437_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001437_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5d81293115c7c1ad866f8645aed97584b240dcb6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001437_tree_id.txt
@@ -0,0 +1 @@
+(0_1711:0.013568322,(1_1428:0.0,4_1640:0.0):0.016085059,(2_1087:0.109519659,3_1014:0.453793088)0.949:0.074432978);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001441_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001441_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0c7a5868519559cf6184a008b38420b2bfaba3ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001441_tree_id.txt
@@ -0,0 +1 @@
+(0_1716:0.012500474,1_1433:0.006225641,(4_1645:0.012805641,(2_1082:0.073139581,3_1008:0.072333378)0.947:0.049542870)0.758:0.006304799);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001442_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001442_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b7090a384dd290d21bd70499e582dcce7fc4746
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001442_tree_id.txt
@@ -0,0 +1 @@
+(0_1717:0.000000005,1_1434:0.005575995,(4_1646:0.004972139,(2_1081:0.081932724,3_1006:0.197908545)0.968:0.035651585)0.732:0.006243731);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001448_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001448_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..972e2586caaeabce252c0490d95405813ec28fac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001448_tree_id.txt
@@ -0,0 +1 @@
+(1_1443:0.004967905,4_1655:0.002476383,(0_1726:0.000000005,(2_1073:0.039888805,3_997:0.098031317)0.961:0.026390829)0.789:0.002474949);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001451_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001451_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..06834785b90011f8a3dffdeeb77caba7f5e7caa0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001451_tree_id.txt
@@ -0,0 +1 @@
+((2_1057:0.052151860,3_993:0.231878340)0.996:0.037768327,1_1447:0.004479020,(4_1659:0.013330616,0_1739:0.002667622)0.769:0.002184140);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001453_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001453_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2b8368f6e260f5a357d3fdb50dcf30b134baaf04
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001453_tree_id.txt
@@ -0,0 +1 @@
+(0_1741:0.013315128,4_1663:0.005972688,(3_989:0.003579523,(1_1449:0.011104155,2_1052:0.004299157)0.897:0.007503678)0.251:0.002356004);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001454_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001454_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9427d2e86072bfba84b101473f27efb5b722cbde
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001454_tree_id.txt
@@ -0,0 +1 @@
+(0_1742:0.020386135,4_1664:0.015419349,(3_988:0.003786111,(1_1450:0.014340321,2_1051:0.016097182)0.998:0.039330930)0.732:0.003637348);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001457_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001457_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..12b0a3901761092dd756080a7d7c4cdbe6824d39
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001457_tree_id.txt
@@ -0,0 +1 @@
+(1_1453:0.000000005,2_1048:0.007750094,(3_985:0.392197199,(0_1745:0.000000005,4_1667:0.023739173)0.985:0.161956326)0.923:0.098725965);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001459_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001459_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bce460d119bed654fd1ba243ab71aad4baa1d6f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001459_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001460_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001460_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5d760c534641d503c1254e260b433221f8b502ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001460_tree_id.txt
@@ -0,0 +1 @@
+(1_1460:0.000000005,4_1674:0.022729982,(0_1752:0.013453337,(2_1042:0.093742179,3_978:0.209600599)0.661:0.036159277)0.791:0.020873404);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001461_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001461_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5767414084d8db75a68118b399a8bd645ba12ee0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001461_tree_id.txt
@@ -0,0 +1 @@
+((0_1753:0.0,1_1461:0.0,2_1041:0.0,4_1675:0.0):0.015450835,3_977:0.015450835);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001463_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001463_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..20316b2162796afc67842dfa61fb204d68c388eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001463_tree_id.txt
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+(0_1755:0.002306618,1_1463:0.012010861,(4_1677:0.006015253,(2_1039:0.066619903,3_975:0.129828688)0.999:0.080237118)0.668:0.003898419);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001467_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001467_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..481d19d94310b65bf459aa463bcacf07b6b13d5d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001467_tree_id.txt
@@ -0,0 +1 @@
+(1_1467:0.000000005,4_1681:0.002912391,(0_1759:0.005244339,(2_1031:0.031967125,3_970:0.152858390)0.995:0.060415826)0.885:0.009439007);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001469_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001469_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..30757468cad8a8b810c67a79ae530eeb916a00a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001469_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001477_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001477_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b68cca54c2ef845a10230dba611b19b3b406649
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001477_tree_id.txt
@@ -0,0 +1 @@
+(4_1691:0.027464522,1_1477:0.010612168,(0_1769:0.008323845,(2_1020:0.097097556,3_960:0.368547429)0.995:0.112484327)0.824:0.008945160);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001481_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001481_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..940317822c717f2542013cc3879ba92f5c601b6c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001481_tree_id.txt
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+(4_1696:0.036824030,3_1032:0.953182937,((2_1014:0.122953082,1_1482:0.000000005)0.423:0.005881514,0_1774:0.030171616)0.616:0.007622757);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001486_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001486_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d2e34bdcfc21f519cf06368b9c2e610c55ed2260
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001486_tree_id.txt
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+(0_1780:0.004149327,(1_1488:0.0,4_1702:0.0):0.025730113,(2_1008:0.066494808,3_950:0.157234592)0.861:0.039949152);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001493_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001493_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0d69816fe60e8711be1839e60ba99424de602104
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001493_tree_id.txt
@@ -0,0 +1 @@
+(0_1790:0.000000005,4_1711:0.004520798,(1_1497:0.004525818,(2_998:0.053231178,3_941:0.256196627)0.968:0.059512185)0.788:0.004522117);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001495_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001495_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a9b55123781d3e96f386da435686e3da06b871ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001495_tree_id.txt
@@ -0,0 +1 @@
+(0_1792:0.007670827,4_1713:0.007688348,(1_1499:0.009293090,(2_996:0.103401360,3_939:0.441384422)0.958:0.047823305)0.793:0.006274456);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001502_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001502_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8a03be20a0d2bfb46503cbad7f1e66bb6bab7085
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001502_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001504_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001504_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2ea07ce990b11a24caf6d4ab3a6611bf881ec74f
--- /dev/null
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@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001509_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001509_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2fa61328800e0cba098c0560ca2263dd7838c0c0
--- /dev/null
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+(0_1807:0.000000005,4_1728:0.007263766,(1_1514:0.000000005,(2_973:0.061667128,3_912:0.131494431)0.926:0.036480527)0.839:0.003626109);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001510_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001510_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..219c531ac48d47be982e7dc1ff755f25c596e911
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001510_tree_id.txt
@@ -0,0 +1 @@
+(1_1515:0.000000005,4_1729:0.003667217,(0_1808:0.003658522,(2_972:0.051434888,3_911:0.147976658)0.983:0.047932348)0.750:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001511_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001511_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b187786f229b810c0c683e2304bc35f86cfcf99b
--- /dev/null
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@@ -0,0 +1 @@
+(0_1809:0.000000005,4_1730:0.009977163,(1_1516:0.000000005,(2_971:0.054084743,3_910:0.160392010)0.993:0.087847845)0.840:0.015076937);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001515_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001515_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..372b301ab37b4658a5e0105f34c183818c506ccd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001515_tree_id.txt
@@ -0,0 +1 @@
+(0_1813:0.015022347,1_1520:0.024282533,(4_1734:0.016004594,(2_967:0.100207067,3_905:0.629694254)0.919:0.072718340)0.924:0.021033928);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001517_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001517_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..89684a1c7689885bdbe60450b067da2fe3c69d00
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001517_tree_id.txt
@@ -0,0 +1 @@
+(3_903:0.247840704,(0_1815:0.012416208,1_1522:0.009047095)0.966:0.031680817,(2_965:0.031653012,4_1736:0.013664277)0.713:0.005933086);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001518_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001518_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eaa08e242177d95d2c1f5691326c12dac0617ec4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001518_tree_id.txt
@@ -0,0 +1 @@
+(0_1816:0.000000005,4_1737:0.017686296,(1_1523:0.026934398,(2_963:0.019008202,3_902:0.261696044)0.748:0.008540376)0.725:0.008552122);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001520_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001520_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..65d6219ffe019f4faabe1ecbfd3bf49246ea73d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001520_tree_id.txt
@@ -0,0 +1 @@
+((0_1821:0.0,1_1528:0.0):0.016206168,4_1742:0.007095322,(2_958:0.091647204,3_899:0.346888692)0.997:0.146357937);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001521_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001521_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bbe8b59771f4c3e32e2d168beff652295ab3c9c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001521_tree_id.txt
@@ -0,0 +1 @@
+((2_956:0.058397642,3_895:0.295123984)1.000:0.071419301,1_1529:0.002669699,(4_1743:0.019149540,0_1822:0.000000005)0.720:0.008167065);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001522_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001522_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ebd2424012a033bfb25eb373129b4fc05d8686bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001522_tree_id.txt
@@ -0,0 +1 @@
+(1_1530:0.005686426,2_955:0.057630724,((0_1823:0.0,4_1744:0.0):0.066757257,3_894:0.287099139)0.827:0.052404329);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001527_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001527_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c9065a37a466ad4c247752f3a11ca709467878c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001527_tree_id.txt
@@ -0,0 +1 @@
+((0_1828:0.0,4_1749:0.0):0.005474950,1_1535:0.003650038,(2_950:0.048353804,3_889:0.160938825)1.000:0.050692011);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001530_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001530_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7e353c9ec452108944e61127cb015ac975138510
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001530_tree_id.txt
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+(0_1831:0.002993666,4_1752:0.003779266,(1_1538:0.009733700,(2_947:0.069101097,3_886:0.275774561)0.959:0.049539511)0.835:0.024175929);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001534_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001534_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..568a1612ad5f4625efdb327b243591c1b1764e81
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001534_tree_id.txt
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+(1_1547:0.002330584,4_1761:0.002259715,(0_1840:0.006948295,(2_938:0.025586980,3_879:0.177780921)1.000:0.085109844)0.948:0.009928827);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001535_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001535_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df884ff7d8d44f4193fee23d3860e83fcbe998e8
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001538_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001538_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e86126186c876956b130c5e0cb575028c903675
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+(0_1844:0.014696229,4_1765:0.008774939,(1_1551:0.000000005,(2_934:0.197315799,3_875:0.418446961)0.986:0.158655575)0.891:0.010880261);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001544_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001544_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a173d643d45d6edffa5c8fcb3a01b761155318a8
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@@ -0,0 +1 @@
+((0_1850:0.0,2_928:0.0,4_1771:0.0):0.000000005,1_1557:0.012384983,3_869:0.024969467);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001545_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001545_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8c8cee1389d47478acb534d4ba3260d697a3f983
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001545_tree_id.txt
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+(1_1558:0.004026750,4_1772:0.003854640,(0_1851:0.024455687,(2_923:0.168952788,3_865:0.105204807)1.000:0.134835263)0.731:0.007403764);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001549_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001549_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fcbd7036163c34e3982d3ba99070efaddeaf4335
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001549_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001557_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001557_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..995b3cbb11820314a34d92dadfec0f835fdbe910
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001557_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001562_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001562_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..48dee3625d37e0afb864ddbf32e2a9b282c1bf54
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001562_tree_id.txt
@@ -0,0 +1 @@
+(2_902:0.042806610,3_837:0.184579876,((0_1877:0.0,4_1797:0.0):0.012051378,1_1584:0.012189959)0.990:0.084084059);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001568_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001568_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6f02ac85fa52577c5a06a77657a25dbc4f5d9bee
--- /dev/null
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@@ -0,0 +1 @@
+(0_1887:0.011338083,1_1592:0.022233001,(2_891:0.466071693,(3_828:0.018238879,4_1807:0.007600721)0.728:0.003690302)0.729:0.003627949);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001576_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001576_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..acd4edaecb5c9103ffa6d264486fb79be53a50d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001576_tree_id.txt
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+(1_1616:0.002514706,4_1838:0.005530124,(0_1911:0.008565673,(2_868:0.060337767,3_810:0.384732296)1.000:0.145811814)0.363:0.010634122);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001581_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001581_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..21418717fb5c22470c267f2e457f7e0fc9e4b8e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001581_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001583_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001583_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..535c9c3bf580100db39983a2c789cc208a5f36f2
--- /dev/null
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@@ -0,0 +1 @@
+((0_1921:0.0,1_1626:0.0,4_1848:0.0):0.000000005,2_857:0.543698482,3_793:0.011799423);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001585_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001585_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b3de5574c2b979ab3fbc31c8783abb25dbd08d45
--- /dev/null
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@@ -0,0 +1 @@
+(1_1630:0.003051581,4_1852:0.003056873,((0_1925:0.0,2_852:0.0):0.000000005,3_789:0.024820765)0.788:0.003053190);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001596_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001596_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a71b4c2f6e43359e3039cea317eee30dfd2114ce
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+((0_1939:0.0,1_1644:0.0,4_1866:0.0):0.121820133,2_838:0.099086983,3_775:0.459445431);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001600_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001600_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..04657654a5eb1756409874220aec2f6bfd16df10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001600_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001602_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001602_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c920d42675d92ec4ef165f6d63ed9e1c81abe6d3
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+((0_1948:0.0,1_1669:0.0,4_1887:0.0):0.032061649,2_814:0.018403553,3_752:0.070513377);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001603_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001603_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c2fd8a5fbb16871556013514f729a6205cdbcc45
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001605_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001605_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d79f2495d268ec5e54ddf75a5d1d645da7ba428a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001605_tree_id.txt
@@ -0,0 +1 @@
+(0_1951:0.007537873,1_1672:0.004993518,(4_1890:0.004449328,(2_811:0.033427447,3_749:0.107399720)0.996:0.039138954)0.748:0.003056764);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001609_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001609_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15a55eb793385aadebe71b18b060d75ff0a017d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001609_tree_id.txt
@@ -0,0 +1 @@
+((0_1958:0.0,1_1678:0.0):0.413119506,4_1896:0.024542851,(3_743:0.000000005,2_2481:0.656441150)0.695:0.015234675);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001610_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001610_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..be5ac1b56442f216f46ef80218badc8717e9e9dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001610_tree_id.txt
@@ -0,0 +1 @@
+(3_742:0.037179717,(0_1959:0.006376195,1_1679:0.021358193)0.843:0.014476354,(2_784:0.453847630,4_1897:0.016749419)0.567:0.020120416);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001611_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001611_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..46c05d7b8b4192ab1a9e78834116f407635de0ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001611_tree_id.txt
@@ -0,0 +1 @@
+(2_780:0.085277255,3_741:0.006802493,(0_1960:0.000000005,(1_1680:0.006671900,4_1898:0.013665941)0.764:0.006853943)0.759:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001616_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001616_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c5da6b06682a23cd0585eaa7fd88e7c576caa498
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001616_tree_id.txt
@@ -0,0 +1 @@
+(2_775:0.236973567,3_736:0.019795377,(0_1965:0.013566242,(1_1685:0.0,4_1903:0.0):0.006590257)0.965:0.051339250);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001618_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001618_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9f7dacafcce271be05d60b8361784f15a96ffe05
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001618_tree_id.txt
@@ -0,0 +1 @@
+((0_1967:0.0,1_1687:0.0,4_1905:0.0):0.034905528,2_773:0.029689531,3_734:0.118332269);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001622_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001622_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7e72225b48b8ccf18857863ca669eb8bacdfd8e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001622_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001623_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001623_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d30881ccb7ce5f73893c1415ca9813b15491b209
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001623_tree_id.txt
@@ -0,0 +1 @@
+(2_760:0.119066686,3_728:0.061905945,(0_1979:0.003744379,(1_1694:0.0,4_1912:0.0):0.001964031)0.688:0.007414467);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001624_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001624_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d2cb013105163f6dda681b7f588d84c69211208f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001624_tree_id.txt
@@ -0,0 +1 @@
+(0_1984:0.006314538,4_1919:0.021007608,(1_1701:0.011080326,(3_717:0.025180238,3_723:0.789079514)0.695:0.004648001)0.823:0.007818427);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001633_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001633_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5d305b861d9161c818d8463d85b7f25b4b467b20
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001633_tree_id.txt
@@ -0,0 +1 @@
+(2_685:0.009939262,1_1735:0.000000005,((0_2020:0.0,4_1959:0.0):0.004954482,3_596:0.009965132)0.387:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001636_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001636_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..56ba0d732c2801b1daf5603e9d711cc446f7fa96
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001636_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001638_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001638_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50c28084a75688a0fe0d086f2734245f1819fb26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001638_tree_id.txt
@@ -0,0 +1 @@
+(2_679:0.004504743,3_590:0.006816059,((0_2025:0.0,1_1741:0.0):0.002258200,4_1965:0.004508945)0.937:0.006813765);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001641_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001641_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f8da31095a661c63276840eca7ef00c57ac1b4d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001641_tree_id.txt
@@ -0,0 +1 @@
+(2_668:0.011631128,3_585:0.027655573,(0_2031:0.009564026,(3_396:0.142611953,3_917:1.530119302)0.961:0.229955303)0.863:0.013955751);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001643_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001643_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..14dbfc4a552632206e5ae9f8745637844a438c98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001643_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001646_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001646_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..368593a2a310bc01a836928e459ca0fb7b8f2beb
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001646_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001647_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001647_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0ef10d51e9b584776dd6e4222bd296e67dca8512
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001647_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001651_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001651_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e5e0e82f4f703a2bd745aee8402c9ae90d9f2e86
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001651_tree_id.txt
@@ -0,0 +1 @@
+((2_650:0.058410328,3_568:0.133444006)0.983:0.089736823,1_1767:0.013667723,(4_1990:0.027572856,0_2049:0.000000006)0.762:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001652_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001652_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d967ebf81878514d8de7e0c37d07d646ed3845c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001652_tree_id.txt
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+(0_2052:0.011437172,1_1770:0.019776037,(4_1991:0.022340773,(2_649:0.083316857,3_566:0.224601021)0.926:0.059928428)0.608:0.013380185);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001662_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001662_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5008baf9697b39f4bdf7133d6355a9c52fbe3ddd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001662_tree_id.txt
@@ -0,0 +1 @@
+(2_636:0.006599106,3_553:0.026585420,(1_1784:0.000000005,(0_2065:0.006575333,4_2004:0.013202807)0.904:0.000000005)0.931:0.000000006);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001668_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001668_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d23d4e492065f140677306b6a1b231cf09384dc2
--- /dev/null
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+(2_630:0.025838898,3_547:0.018345267,((0_2071:0.0,4_2010:0.0):0.012726546,1_1790:0.009270338)0.792:0.016455646);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001670_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001670_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ffc0bad447885008b1e00cfbc36ffba1bac7519
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001670_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001674_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001674_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..30944941cd03a9881776f3cc469d20ee5584c56e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001674_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001680_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001680_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dfbe88b9a5acccb8d665362c9d6e3ff881d17be8
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001681_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001681_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..532403b8eb2aceb05e734601abb68e94a29c0fc3
--- /dev/null
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+(1_1805:0.000000005,4_2025:0.005648759,(0_2086:0.006849967,(2_604:0.078662972,3_530:0.055199735)1.000:0.093006224)0.998:0.027062762);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001690_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001690_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a12e4be52e9ac4c75212c7279cb4821dd0bbea5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001690_tree_id.txt
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+(0_2098:0.000000005,1_1822:0.004419270,(4_2043:0.017932118,(2_581:0.211138112,3_504:0.281019151)0.999:0.149046542)0.882:0.009430680);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001692_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001692_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..984d3e2c2355a71c092a0f06781b54bd2e382be5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001692_tree_id.txt
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+(0_2102:0.010489361,(1_1827:0.0,4_2048:0.0):0.000000005,(2_576:0.070185117,3_500:0.272010979)0.990:0.075478695);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001693_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001693_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b7a34fe6fb52aeb867d64a4687d506ffaae39a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001693_tree_id.txt
@@ -0,0 +1 @@
+(0_2103:0.029059107,(1_1828:0.0,4_2049:0.0):0.018940523,(2_575:0.158089203,3_499:0.405398276)1.000:0.174880962);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001695_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001695_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..22493706efd17816538e53db9f6a5943200bad6f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001695_tree_id.txt
@@ -0,0 +1 @@
+(1_1833:0.015858352,4_2054:0.013552675,(0_2108:0.021678453,(2_565:0.125254883,3_492:0.407597402)0.997:0.151479292)0.817:0.012510192);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001703_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001703_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..23a5dfb4061c5c50c56278ab473e41600f92945a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001703_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001704_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001704_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e7dabe610dbe7871477b48addfd21107a06126b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001704_tree_id.txt
@@ -0,0 +1 @@
+(0_2120:0.007835634,4_2066:0.007761703,(1_1845:0.000000005,(2_551:0.110787341,3_479:0.281229541)0.922:0.051465426)0.422:0.007794726);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001705_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001705_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..22ad8aad2a804eb1c1d453d6952a49cac75f8a1a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001705_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001707_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001707_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e1e45092df729eceafc74448aa38a694e32f8712
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001707_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001710_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001710_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0342a8fc3e759880c5cb10edea32f9f9b8b9e45
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001710_tree_id.txt
@@ -0,0 +1 @@
+(1_1854:0.002463134,4_2075:0.009818384,(0_2129:0.005711221,(2_536:0.150306822,3_466:0.457281273)0.997:0.129917843)0.433:0.004118550);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001711_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001711_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..13e97fd716978c54578425f52f5f60e183095c21
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001711_tree_id.txt
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+(0_2133:0.026678309,4_2078:0.000000006,(1_1857:0.000000005,(2_528:0.214185945,3_465:0.799371440)0.809:0.080425882)0.372:0.005288319);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001712_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001712_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..468d5e93c84dd9e6f6477b4f3e2bc3e61c5dd6b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001712_tree_id.txt
@@ -0,0 +1 @@
+(0_2134:0.004809337,1_1858:0.003667466,(4_2079:0.000623869,(2_531:0.008646492,3_461:0.509690783)0.920:0.015916500)0.953:0.006695647);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001713_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001713_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fc32b7b72995c787f01e177a1e04fa7122116c1d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001713_tree_id.txt
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+(1_1859:0.019216042,2_530:0.030831511,((0_2135:0.0,4_2080:0.0):0.002017378,3_462:0.775759212)0.796:0.009266208);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001714_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001714_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8244768eb8a09b7f68988013ba0d89c255c380cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001714_tree_id.txt
@@ -0,0 +1 @@
+((0_2136:0.0,1_1860:0.0,4_2081:0.0):0.000000005,2_529:0.039717803,3_463:0.874245402);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001715_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001715_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e7dbd0ac8b1f35357e2c0fd21fffdf4411355ba2
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001715_tree_id.txt
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+(0_2137:0.000000005,1_1861:0.007869583,(4_2082:0.007879809,(2_527:0.210804665,3_464:0.377821620)0.958:0.099170871)0.890:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001716_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001716_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f4f8ac800b2fe6a8f1b7341372f81e76917efcaa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001716_tree_id.txt
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+((0_2139:0.0,1_1863:0.0,4_2084:0.0):0.212895816,2_524:0.063568153,3_1750:1.223015331);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001724_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001724_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2950b6bb57796e541d897d3169b81cfa01ae25eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001724_tree_id.txt
@@ -0,0 +1 @@
+(1_1891:0.003692140,2_488:0.068157088,(3_425:0.005538779,(0_2178:0.011126646,4_2111:0.005532892)0.761:0.001846431)0.885:0.000000006);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001731_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001731_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..24e035a0f69359d01900e99761a0f05ecf87ab3c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001731_tree_id.txt
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+(0_2194:0.004056978,(1_1905:0.0,4_2126:0.0):0.000000005,(2_458:0.020481751,3_414:0.004484623)0.875:0.007784576);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001734_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001734_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..22c80f6cb1c55db69cd5d3d573ba0068bac38a22
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001734_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001739_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001739_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0d90c730be9e788cf672ff542da264537496b2c
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001739_tree_id.txt
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+(0_2226:0.002684016,4_2166:0.007918980,(1_1928:0.013254463,(2_432:0.031655331,3_386:0.164216089)0.950:0.023826549)0.853:0.005521561);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001750_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001750_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2ec85ac8b953731ba13b1fd97a857cdfc538b4c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001750_tree_id.txt
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+(1_1945:0.004587258,4_2183:0.015902684,(0_2241:0.009718916,(2_417:0.314776113,3_370:0.409877046)0.978:0.087409320)0.954:0.014343830);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001752_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001752_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f8c9a362406f9f477babab1e3be73f0307151370
--- /dev/null
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+(0_2245:0.009285889,4_2187:0.000000006,(1_1949:0.009290688,(2_412:0.028776838,3_366:0.121636821)0.966:0.036197954)0.747:0.003080327);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001754_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001754_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1b61d2f2cc750ba96ea55eb09d887ed61564588e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001754_tree_id.txt
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+(0_2247:0.004930016,1_1951:0.009870897,(4_2189:0.004843978,(2_410:0.083099074,3_364:0.222386158)0.992:0.099946843)0.770:0.005039325);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001755_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001755_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..29b10aa94f4f059dbad8d83b57f92d6c9a4aaa40
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+(0_2248:0.000000005,2_409:0.018642121,(3_363:0.142019372,(1_1952:0.002085934,4_2190:0.004932277)0.938:0.026918653)0.975:0.035853210);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001756_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001756_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64cf5deabe48271b2f85e598048f61eb11491a0f
--- /dev/null
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+(3_362:0.177434348,4_2191:0.000000005,(2_408:0.035921989,(0_2249:0.0,1_1953:0.0):0.000000005)0.286:0.008750273);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001767_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001767_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a5d5a55038c90c84ef99d2d3bd34364d4e8567b3
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001767_tree_id.txt
@@ -0,0 +1 @@
+((2_1827:0.525036478,3_1715:0.197757275)0.993:0.733943575,3_1728:0.412876978,(2_140:0.869659081,3_1722:0.222491003)0.933:0.317597149);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001769_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001769_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..31b7c618c7db3a14ea51bd11de9ecccc2bc7cab1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001769_tree_id.txt
@@ -0,0 +1 @@
+(2_793:0.643041313,2_2335:1.256910627,(2_500:1.155247690,(2_926:0.096859555,3_867:0.121634838)1.000:0.761260029)0.934:0.327199544);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001771_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001771_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64ea332860125779077d82aff487851aeb542272
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001771_tree_id.txt
@@ -0,0 +1 @@
+(0_37:0.014933470,1_2001:0.006356707,(1_2114:1.558886595,4_32:0.000000005)0.549:0.008482974);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001776_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001776_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8ea40bdb2a73978d1ec28d2749d0b175474ec65b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001776_tree_id.txt
@@ -0,0 +1 @@
+(0_69:0.022432365,4_63:0.021780430,(1_2033:0.052826330,3_247:1.029921621)0.614:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001778_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001778_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c1b7d216926517fdba0b4eeb042ca1632f6fc9db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001778_tree_id.txt
@@ -0,0 +1 @@
+(1_2045:0.006630989,4_76:0.016727086,(0_81:0.004307560,2_291:0.085483230)0.752:0.001822623);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001780_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001780_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a3b4c3be0b69f50f618668627ed26c5ffa33aa4c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001780_tree_id.txt
@@ -0,0 +1 @@
+(0_115:0.002569351,4_123:0.005064839,(2_251:0.133957694,3_186:0.223412393)0.972:0.067705582);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001782_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001782_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..61a4845ade148f766418015446e1f915b093cbed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001782_tree_id.txt
@@ -0,0 +1 @@
+(1_2102:0.016510504,4_145:0.014685393,(0_137:0.020941018,2_229:0.258725611)0.877:0.009948824);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001786_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001786_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6bea2d1d493ffb40cc76d8d0943ece4a589b3859
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001786_tree_id.txt
@@ -0,0 +1 @@
+((0_191:0.0,4_194:0.0):0.032183785,1_2138:0.006041217,2_184:0.283885892);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001788_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001788_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..274ac68c75172b7c17144287eec2531c9cccdb9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001788_tree_id.txt
@@ -0,0 +1 @@
+(1_2139:0.015478535,4_195:0.019620086,(0_193:0.004848304,2_195:0.258550112)0.785:0.004323281);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001790_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001790_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1aff947dbcac7a3e690aebcf73d7cfdaaa4c726e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001790_tree_id.txt
@@ -0,0 +1 @@
+(2_151:0.161607258,4_212:0.011758982,(0_211:0.004794421,1_2156:0.003152087)0.905:0.009585765);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001791_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001791_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..757b7595a7300a526fed7ad67be6d7d355192342
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001791_tree_id.txt
@@ -0,0 +1 @@
+((0_219:0.0,1_2183:0.0):0.000000005,3_101:0.018127492,4_220:0.004514391);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001795_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001795_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b262c2c082a2325313c62c3b91f41a5f4ec37604
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001795_tree_id.txt
@@ -0,0 +1 @@
+(0_244:0.007956506,(1_2207:0.0,4_244:0.0):0.000000005,2_107:0.016032321);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001809_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001809_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52cb60280641cee47bbf804f90d129f75b763c16
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001809_tree_id.txt
@@ -0,0 +1 @@
+(0_374:0.002838534,1_107:0.000000005,(3_2377:0.361123573,4_380:0.000000005)0.815:0.005688009);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001811_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001811_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f6c4c2a001249789eda71cd715081e664af4f73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001811_tree_id.txt
@@ -0,0 +1 @@
+(1_168:0.006072396,4_441:0.003010614,(0_441:0.000000005,3_2313:0.446937602)0.478:0.003035304);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001813_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001813_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b5f0d855af3289d2650c3f8d47222f84ab09b6df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001813_tree_id.txt
@@ -0,0 +1 @@
+(0_487:0.019288950,1_216:0.024815896,(3_2270:0.645871093,4_486:0.026856497)0.729:0.017343536);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001816_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001816_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ccbc445b1837a8fd805be2a4d5b9d9fdc37caaa2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001816_tree_id.txt
@@ -0,0 +1 @@
+(1_278:0.043948159,4_547:0.027696009,(0_545:0.014518073,3_2206:0.277624132)0.922:0.026269638);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001820_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001820_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f1f8faacb01ed63f8c9154e4034a59d2deab63e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001820_tree_id.txt
@@ -0,0 +1 @@
+(2_2300:0.268446235,4_558:0.026460836,(0_557:0.044734725,1_299:0.023511029)0.781:0.024630923);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001824_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001824_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d8e444d04fe8b23656c6c72284445d0f5236aa44
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001824_tree_id.txt
@@ -0,0 +1 @@
+(3_2148:0.003433994,4_577:0.000000005,(0_604:0.003422441,2_385:0.010425691)0.776:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001827_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001827_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d6620ae7cbcf925e531c21adf786db16f3af7b07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001827_tree_id.txt
@@ -0,0 +1 @@
+(0_614:0.018049600,3_2134:0.021577808,(1_360:0.007139595,4_583:0.003560126)0.740:0.003490964);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001834_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001834_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..704c937fb8f25d2fa0777c6c09f542f60759c499
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001834_tree_id.txt
@@ -0,0 +1 @@
+(1_398:0.010063290,3_2095:0.363385475,(0_652:0.000000005,4_622:0.009983767)0.773:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001835_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001835_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1eae3b10d786bb930221591dad18f18c5d472c50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001835_tree_id.txt
@@ -0,0 +1 @@
+(0_672:0.011579485,4_642:0.009243317,(1_418:0.000000005,2_2206:0.298326665)0.777:0.006941832);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001837_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001837_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6a0ab71c0015606c33f7662a613c14f6db1923e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001837_tree_id.txt
@@ -0,0 +1 @@
+((0_759:0.0,1_499:0.0):0.029185741,3_1988:0.467163338,4_726:0.018324116);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001838_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001838_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..532215e55cf060a17e6e4e742c128a0df8df0506
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001838_tree_id.txt
@@ -0,0 +1 @@
+(0_816:0.014661921,2_2043:0.446002596,(1_547:0.000000005,4_775:0.000000005)0.844:0.020870368);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001841_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001841_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a1c1a849a9d504efde9665cfc87927ef2215a51b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001841_tree_id.txt
@@ -0,0 +1 @@
+(3_1839:0.474540063,1_645:0.000000005,(0_923:0.001793898,4_869:0.016246678)0.709:0.003607152);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001846_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001846_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..169593fe3c81a3bf81c78818c4b6b0aeb6372b4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001846_tree_id.txt
@@ -0,0 +1 @@
+(4_966:0.004609094,1_747:0.004601321,(3_1679:0.210017703,0_1019:0.000000005)0.845:0.004581232);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001853_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001853_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..47b3a557f2c2a06697d1e385732a3ff4094c75e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001853_tree_id.txt
@@ -0,0 +1 @@
+((0_1109:0.0,1_837:0.0,4_1059:0.0):0.261638229,2_1703:0.261638229);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001854_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001854_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0794b7afae7798030743e56a2ba652a569e7bf13
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001854_tree_id.txt
@@ -0,0 +1 @@
+(0_1114:0.000066751,(1_842:0.0,4_1064:0.0):0.004033188,3_1595:0.625393454);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001855_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001855_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64bffb2ee047bf2343542154d634fa947604847b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001855_tree_id.txt
@@ -0,0 +1 @@
+(0_1165:0.011090540,4_1122:0.003658392,(1_893:0.007724374,3_1542:0.210924988)0.746:0.003299446);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001857_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001857_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15adc07b30c3f1677b44c8d0c3a25f7363ca58aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001857_tree_id.txt
@@ -0,0 +1 @@
+(0_1205:0.025185829,1_933:0.020995710,(2_1605:0.138452828,3_1502:0.524384651)0.996:0.133354493);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001867_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001867_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..309e6023334147af3b15702ea7942cabab36e09f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001867_tree_id.txt
@@ -0,0 +1 @@
+((0_1368:0.0,1_1108:0.0,4_1317:0.0):0.001826225,2_1453:0.001826225);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001869_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001869_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0ac023f16beb61d61e37722dd7b2bf9c76871294
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001869_tree_id.txt
@@ -0,0 +1 @@
+(1_1142:0.000000006,3_1324:0.064347658,(0_1401:0.007505752,4_1350:0.000000005)0.667:0.007513879);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001870_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001870_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6e102d2f55f79dace9128d5278636ef1cc412fc5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001870_tree_id.txt
@@ -0,0 +1 @@
+(3_1306:0.349565357,4_1367:0.003592419,(1_1159:0.032829560,0_1418:0.013292479)0.832:0.008000704);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001871_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001871_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4ea22fbf11e127d8820a17b29ff4824c09e9e99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001871_tree_id.txt
@@ -0,0 +1 @@
+((0_1424:0.0,1_1165:0.0,4_1373:0.0):0.004344082,3_1300:0.004344082);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001872_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001872_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ab453f80e4248494dd789df6d4f0047765dcc596
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001872_tree_id.txt
@@ -0,0 +1 @@
+((0_1425:0.0,1_1166:0.0,4_1374:0.0):0.010561616,3_1299:0.010561616);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001877_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001877_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..859604cc405a454988c00321f48481a2b8bbe17e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001877_tree_id.txt
@@ -0,0 +1 @@
+((0_1534:0.0,4_1461:0.0):0.002043498,1_1255:0.001981498,2_1309:0.024516406);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001882_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001882_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e4cebc4060b821df1716ca38d204135faf56668
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001882_tree_id.txt
@@ -0,0 +1 @@
+(0_1615:0.017046865,4_1545:0.011334321,(1_1330:0.005732569,2_1200:0.141814359)0.843:0.011338499);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001886_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001886_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..635904f2269f10065226735ac9f473451cdbe60c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001886_tree_id.txt
@@ -0,0 +1 @@
+(0_1722:0.004553128,1_1439:0.000000005,(3_1001:0.370704388,4_1651:0.005929559)0.887:0.036435143);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001890_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001890_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..44621c670f9c97bb4908b5e9c55a289719f3e9c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001890_tree_id.txt
@@ -0,0 +1 @@
+(0_1818:0.000000005,1_1525:0.009415123,(2_961:0.074763609,3_900:0.367995363)0.990:0.164275993);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001895_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001895_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8c1b202c439fbf0e7b9f20a9997f9b7b641c702d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001895_tree_id.txt
@@ -0,0 +1 @@
+((0_1835:0.0,4_1756:0.0):0.012599974,1_1542:0.008214941,2_943:0.108490301);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001898_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001898_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f7fa70eb2691140924f83cb5fd6e23c39e62ddc7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001898_tree_id.txt
@@ -0,0 +1 @@
+((0_1853:0.0,4_1774:0.0):0.007517354,1_1560:0.007364063,3_863:0.152639808);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001899_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001899_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0d4ff2bc0b8ebf1b75a0ec3c4bab6d7748204c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001899_tree_id.txt
@@ -0,0 +1 @@
+(3_862:0.416132311,4_1775:0.000000005,(0_1854:0.025786002,1_1561:0.000000005)0.858:0.004272961);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001903_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001903_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..80924a4149cb32616ede47ee8a9268140a3e2d36
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001903_tree_id.txt
@@ -0,0 +1 @@
+((0_1880:0.0,4_1800:0.0):0.028231531,1_1587:0.011838699,2_899:0.402765094);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001904_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001904_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c238ea3faa849c72a80d96c9f106ac31f4343ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001904_tree_id.txt
@@ -0,0 +1 @@
+((0_1886:0.0,4_1806:0.0):0.000000005,2_896:0.424540152,3_829:0.005366688);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001924_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001924_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..04f4093fd90cba1ade7c28797dcc354c021aa652
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001924_tree_id.txt
@@ -0,0 +1 @@
+(2_652:0.054669669,4_1988:0.005521790,(0_2047:0.000000005,1_1765:0.005191049)0.785:0.005078442);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001926_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001926_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a1075f0e40379e8dccaf0acdbd940bba0d7460d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001926_tree_id.txt
@@ -0,0 +1 @@
+(1_1782:0.005298638,4_2002:0.000000005,(0_2063:0.000000005,3_556:0.021567242)0.850:0.005326959);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001928_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001928_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ec4f9632d80a66858afee6ad562740f7166cc09b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001928_tree_id.txt
@@ -0,0 +1 @@
+(2_584:1.176586541,4_2038:0.000000005,(0_2094:0.040461394,1_1818:0.015522479)0.616:0.011080458);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001930_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001930_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ffdbf4eb0ed452be16b7f96d0cba8d0434687317
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001930_tree_id.txt
@@ -0,0 +1 @@
+(0_2110:0.000000005,4_2056:0.006833720,(1_1835:0.015576007,3_490:0.341557173)0.723:0.014525441);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001935_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001935_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..20006033f3ba3fafec3f19353caf7b2750555c71
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001935_tree_id.txt
@@ -0,0 +1 @@
+(0_2132:0.010307249,4_2077:0.005965621,(1_1856:0.050504226,2_535:0.303468738)0.685:0.007547659);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001936_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001936_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ed98ffa83b26b5532714839f33aa517c8e2d3c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001936_tree_id.txt
@@ -0,0 +1 @@
+((0_2142:0.0,1_1866:0.0,4_2087:0.0):0.105077231,2_522:0.105077231);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001937_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001937_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0b6723e05d9e436d05760228e3b7a1d195e5696
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001937_tree_id.txt
@@ -0,0 +1 @@
+(1_1870:0.008516580,2_520:0.067207491,(0_2146:0.041230140,4_2091:0.000000005)0.983:0.033512937);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001939_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001939_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2e89b3ef23d0ac521bb5ced1b9570db2f3c3f488
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001939_tree_id.txt
@@ -0,0 +1 @@
+(0_2152:0.004086443,1_1876:0.003998448,(2_513:0.050755749,2_2591:0.869068314)0.852:0.037070085);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001940_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001940_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6f86706c7bcfae71a0c0b1985d909fa66c71596a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001940_tree_id.txt
@@ -0,0 +1 @@
+(1_1877:0.012682559,2_512:0.158160222,(0_2153:0.012704869,4_2093:0.012736109)0.775:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001945_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001945_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e528e6dcb59019f76a6c2a62aecb0146dd4fdae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001945_tree_id.txt
@@ -0,0 +1 @@
+((0_2198:0.0,4_2130:0.0):0.177181658,2_445:0.036801606,3_683:0.586609129);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001953_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001953_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..324b0dea4f10a4d5a71085e3feb458a69cb357a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001953_tree_id.txt
@@ -0,0 +1 @@
+(1_1746:0.015688067,2_672:0.014317886,(1_82:0.618319041,2_757:0.869187122)1.000:0.857100041);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001954_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001954_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2bd17359e466d0e757b46d2653ae0b3565996d4e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001954_tree_id.txt
@@ -0,0 +1 @@
+(1_224:0.176584801,2_2384:0.189976749,(2_1199:1.559630064,4_811:0.533979598)0.833:0.162337514);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001957_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001957_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c62460e9ae212a53426c792fc9494f18f55c1ae0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001957_tree_id.txt
@@ -0,0 +1 @@
+((1_307:0.0,2_2223:0.0):0.000000005,3_1786:0.006379386,4_567:0.004515534);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001962_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001962_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..41ab700cab4a7fb363b3f89701e9abff1569fc0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001962_tree_id.txt
@@ -0,0 +1 @@
+(2_881:0.011897538,4_1819:0.050643845,(1_1598:0.100840148,3_821:0.230758003)0.984:0.000000006);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001963_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001963_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d1e4295ae042a818e09f86ade6171ac193ee25ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001963_tree_id.txt
@@ -0,0 +1 @@
+(1_1647:0.044768924,2_835:0.016252636,(3_773:0.299389694,4_709:1.696135064)0.730:0.109978540);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001965_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001965_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e63b9aa4e32d02e245426f0cccf9fa4189cc8295
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001965_tree_id.txt
@@ -0,0 +1 @@
+((1_1650:0.0,4_1868:0.0):0.020632611,2_832:0.021343210,3_770:0.149992692);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001966_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001966_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e5c094357619c7b46748259cc56344d191b8dd13
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001966_tree_id.txt
@@ -0,0 +1 @@
+(1_1651:0.003849424,4_1869:0.000000005,(2_831:0.034734195,3_769:0.071730362)0.992:0.049800254);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001968_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001968_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..554ba1555530aab76ba0d291f626a9454a7e917e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001968_tree_id.txt
@@ -0,0 +1 @@
+(1_1653:0.000000005,4_1871:0.003293367,(2_829:0.303103720,3_767:0.193763937)0.995:0.129208969);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001971_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001971_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7d7a294f3244433548ed6184e4ccd84b5ccc339
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001971_tree_id.txt
@@ -0,0 +1 @@
+(1_1658:0.005923548,4_1876:0.005044528,(2_825:0.160030946,3_759:0.104040255)1.000:0.156862980);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001976_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001976_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c6fc5328c7de49acf1532ef842b70ee7af76ac2c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001976_tree_id.txt
@@ -0,0 +1 @@
+(3_138:0.005953410,4_191:0.025145243,(2_186:0.151935924,3_580:1.256473105)0.952:0.123931988);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001979_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001979_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..884a2cc2a8ca403c255b88c3d7ce4264e69b7a71
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001979_tree_id.txt
@@ -0,0 +1 @@
+(2_2140:0.197534376,3_2038:0.182824477,(2_2525:1.444572394,2_2610:0.628905998)0.763:0.179975912);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001980_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001980_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..da325c645674390a828f09a623226c7a50b2c0f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001980_tree_id.txt
@@ -0,0 +1 @@
+(3_385:0.829222697,3_697:1.072011871,(2_2197:0.085241047,3_2069:0.000000005)1.000:0.859698712);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001981_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001981_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bfdf3f0daaf50c0c4b36a6d03faf0fa55adacc23
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001981_tree_id.txt
@@ -0,0 +1 @@
+(2_2286:0.0,2_2291:0.0,2_2581:0.0,2_2592:0.0);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001983_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001983_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f72514d8617ee2202eea3cceb50658e61444d1a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001983_tree_id.txt
@@ -0,0 +1 @@
+(3_406:0.500192650,3_627:0.847738489,(3_1747:0.363418304,3_1783:0.250330565)1.000:0.777737641);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001985_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001985_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..648d2d25c97529e33e92a8afc6037e8c78004765
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001985_tree_id.txt
@@ -0,0 +1 @@
+(3_658:0.335732954,3_2174:0.307760715,(3_657:0.550357737,3_2173:0.292005631)0.916:0.199923184);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001989_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001989_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ef5e69db363b7950946711f8c962d91d4e875220
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001989_tree_id.txt
@@ -0,0 +1 @@
+(0_25:0.046061767,1_1994:0.011389409,4_25:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001990_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001990_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b8fc5fe9eea6feb0b99865b306c4e81eb46e9d89
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001990_tree_id.txt
@@ -0,0 +1 @@
+(0_27:0.008137090,1_1995:0.006109787,4_26:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001995_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001995_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..03cf393f5fcddb37c016fd0522ee68437794e57e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001995_tree_id.txt
@@ -0,0 +1 @@
+(0_168:0.000000005,2_624:0.004827236,3_41:0.039628864);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001997_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001997_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0e36e76c224add53625b6fc8ceb10be7c06eb44
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001997_tree_id.txt
@@ -0,0 +1 @@
+(0_198:0.007200058,2_190:0.440179887,3_128:0.018126371);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002002_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002002_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..87667371d6a317d145758bb7870b43a674e3d500
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002002_tree_id.txt
@@ -0,0 +1 @@
+(0_394:0.051602262,1_123:0.005727996,4_397:0.015080815);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002004_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002004_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d8d7ce4d04ce9f5f5d847d0d96d4e3b9aa3e8e3f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002004_tree_id.txt
@@ -0,0 +1 @@
+(0_433:0.000468254,2_2447:0.044023154,3_131:0.961238544);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002006_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002006_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..197bdfa24d05ac88010659f25a433f00429c6374
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002006_tree_id.txt
@@ -0,0 +1 @@
+(0_476:0.0,1_206:0.0,4_475:0.0);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002013_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002013_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aa9d56380b8cc3909aab773d1a360d729350b6fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002013_tree_id.txt
@@ -0,0 +1 @@
+(0_582:0.069427907,1_1717:0.062404941,2_2312:0.911033802);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002014_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002014_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..749b132c07e28728ffd8e55aef1f2110ec298d2e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002014_tree_id.txt
@@ -0,0 +1 @@
+(0_588:0.000000005,1_1723:0.067649841,3_686:0.935591633);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002019_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002019_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..29b0a3d2feeb2c7f6939c11bb6a2ab861f8a938d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002019_tree_id.txt
@@ -0,0 +1 @@
+((0_855:0.0,1_586:0.0):0.678783659,2_1190:0.678783659);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002026_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002026_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5c59cd16d24b6d14efeab892fc918c10b14ff6e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002026_tree_id.txt
@@ -0,0 +1 @@
+((0_999:0.0,1_721:0.0):0.205513986,4_941:0.205513986);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002038_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002038_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..438d48cc1da58b3138f51a1e06a7ec1f8623ecd5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002038_tree_id.txt
@@ -0,0 +1 @@
+(0_1561:0.015438841,1_1281:0.009390823,3_1164:0.406405648);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002041_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002041_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f2326484bc09d4b7a1f314b963bd230715989b35
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002041_tree_id.txt
@@ -0,0 +1 @@
+(0_1567:1.534678726,2_200:0.970039002,4_181:0.494199293);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002045_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002045_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..21813c611236f157da2190e4bd1b6155a1de90ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002045_tree_id.txt
@@ -0,0 +1 @@
+(0_1885:0.015307085,3_830:0.007578362,4_1805:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002048_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002048_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c6aa80390489a968874b2e8402314d9b1eba33e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002048_tree_id.txt
@@ -0,0 +1 @@
+(0_1904:0.007951246,1_1607:0.007945396,4_1831:0.012008709);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002053_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002053_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b3f5dce5156e849eaa707db4d99c9f246fc7d24
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002053_tree_id.txt
@@ -0,0 +1 @@
+(0_2012:0.040964884,2_719:0.326208726,4_1941:0.006261785);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002060_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002060_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c9ca53392260a2bf3a1b0359e6d0594f9b1de8a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002060_tree_id.txt
@@ -0,0 +1 @@
+(0_2143:0.0,1_1867:0.0,4_2088:0.0);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002066_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002066_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..56fbf2ae5d9c93f4294919e4513c4a21c77d019a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002066_tree_id.txt
@@ -0,0 +1 @@
+(0_2181:0.0,1_1894:0.0,4_2114:0.0);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002069_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002069_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4339cff24bde3b40be6722d7e98a09f4382603e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002069_tree_id.txt
@@ -0,0 +1 @@
+(0_2201:0.017217013,3_400:0.141307038,4_2133:0.034712011);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002072_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002072_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6aed7bc5fef143eb0b7ad4c0bb3454e6741ab8b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002072_tree_id.txt
@@ -0,0 +1 @@
+(0_2208:0.017459120,1_1912:0.008649623,4_2141:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002078_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002078_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..acce76626cfabbd51069e459e30901c1732829ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002078_tree_id.txt
@@ -0,0 +1 @@
+(1_341:0.022146534,(3_654:0.0,4_1953:0.0):0.022146534);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002083_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002083_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1b646c45939aff5919ff03f48fa8303e274c57aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002083_tree_id.txt
@@ -0,0 +1 @@
+((1_875:0.0,4_1097:0.0):0.148820836,2_1664:0.148820836);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002087_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002087_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6c65a56dd9be1bd45a63842f95144e7d349f33c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002087_tree_id.txt
@@ -0,0 +1 @@
+(1_1603:0.190740935,3_194:1.060667085,3_817:0.157695826);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002092_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002092_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..477c6ea4c9162a9cca45f4469b9f9fa80d93fb38
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002092_tree_id.txt
@@ -0,0 +1 @@
+((1_1661:0.0,4_1879:0.0):0.059637409,2_822:0.059637409);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002096_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002096_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6a1675d353cb1280ca451fc65754a5991b95f9ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002096_tree_id.txt
@@ -0,0 +1 @@
+(1_1727:1.670648243,3_618:0.523534429,4_2157:0.214524466);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002098_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002098_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..95a46f66e6a547906632c395d2dd1a2d5fd2e0cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002098_tree_id.txt
@@ -0,0 +1 @@
+(1_1747:0.004488212,2_671:0.001367607,2_805:1.219296998);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002099_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002099_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5a3fcac15f2c3e019b9e21c5fca725e4ede50a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002099_tree_id.txt
@@ -0,0 +1 @@
+((1_1804:0.0,4_2024:0.0):0.028344918,3_532:0.028344918);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002100_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002100_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e60a094184997ea380944e1f9287c4708d15eb8e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002100_tree_id.txt
@@ -0,0 +1 @@
+(1_1878:0.012014814,2_508:0.074042236,4_2094:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002101_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002101_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f37dc77f8407b111156365c6812e6a837cadf946
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002101_tree_id.txt
@@ -0,0 +1 @@
+((1_2078:0.0,4_119:0.0):0.064688755,2_255:0.064688755);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002105_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002105_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..440e0c1979f5a65a1cf30c3f2b4e7108a0b6f83b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002105_tree_id.txt
@@ -0,0 +1 @@
+(2_121:0.273643380,2_1477:0.245014956,2_2289:0.306426752);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002109_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002109_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df02b3702573bd12d79bcdefabf24d36b480122e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002109_tree_id.txt
@@ -0,0 +1 @@
+(2_744:0.204031726,3_707:0.168728270,4_1932:0.301978970);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002114_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002114_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..17a2efa83a824a99ddc4107a61007c4fc015dd14
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002114_tree_id.txt
@@ -0,0 +1 @@
+(2_1284:0.000000005,3_2182:0.009879092,4_114:1.492586618);