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Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000046.fa

@@ -0,0 +1,50 @@
+>GCF_002008305_PROKKA_01791
+MQPIDQTTSGPA-TSVGERPLAGIRVVSVAVNLPGPLAAARLAEFGAEVVKIEPPTGDPL
+AAAAPQWYAELIAGQRVLTLDLKTGPGQDHLATLLKGADLLLSSLRPSAADRLGLPASAH
+AA---GAVFLEVVGHDGDDADLPGHDLTYQAAAGTLDAPRM-----PLVPVADLLGGERA
+VSAALAALRSRDHGG---PVTRVRVTLEDAARAAAAPVRRGLLGPGGPLGGDLPTYSLYA
+SADGHVAVAAVEPHFAARLAEHIG-------STRDEIARTILTRPGAEWERIANELDLPL
+---AVVRPPR-
+>GCF_002008305_PROKKA_02047
+---------------MSAAPLAGVRVVTIALNLPGPAAAARLQELGADVVTVLPPSGDPV
+ATLVPALYEELHRGQSVRTVDMKSQAGVAEMEQILAEADVFLTSHRSGALRRLGLDADAV
+RARHRRICQVDITGYAGDRTDVPGHDINYQAAAGLLAPGAP-----PRILAADLHGAERA
+VSTALALLWARGADG---DGGHATVALAEAAHALALPNRHRMTDPRSPLGGALPHYGVYP
+AAEGHVAVGALEPHFAAALVEGLGLDADG--DVRAQLTEALSRHDAAHWQAWGEKRGIPL
+---TALVSPTA
+>GCF_003691675_PROKKA_01753
+---------------MSAAPLAGVRVVTIALNLPGPVAAARLQELGADIVTVLPPSGDPV
+ATLVPALYEELHRGQSVRTVDMKSQAGAAEMEQILAEADVFLTSHRSGALRRLGLDADAV
+RARHRRICQVDITGYDGDRTDVPGHDINYQAAAGLLAPGAP-----PRILAADLHGAERA
+VSAALALLWARGADG---DGGHATVALADAAHALALPNRHRMTGPRSPLGGALPHYGVYP
+AAEGHVAVGALEPHFAAALVEGLGLDADG--DVRAQLTEALSRHDAAHWQAWGEERGIPL
+---TALASPTA
+>GCF_005280335_PROKKA_01085
+MQPIDQTTSGPA-TSVGERPLAGIRVVSVAVNLPGPLAAARLAEFGAEVVKIEPPTGDPL
+AAAAPQWYAELIAGQRVLTLDLKTGPGQDHLATLLEGADLLLSSLRPSAADRLGLPASAH
+AA---GAVFLEVVGHDGDDADLPGHDLTYQAAAGTLDAPRM-----PLVPVADLLGGERA
+VSAALAALRSRDHGG---PATRVRVTLEDAARAAAAPVRRGLLGPGGPLGGDLPTYSLYA
+SADGHVAVAAVEPHFAARLAEHIG-------STRDEIARTILTRPGAEWERIANELDLPL
+---AVVRPPR-
+>GCF_020097155_PROKKA_00733
+MSAGDGASRVPAGDAVVPGPLADVAVVTIALNLPGPLAAFRLAELGAQVTTVLPPAGDPV
+ATLVPALYTELHAGMAELTLDLKQDGDRARMEELLAGADVLLTSHRSGALTRLGLDAAAT
+ARRHPRLVQVDITGFPGERADVPGHDLNYQAEAGLLEPGHP-----PRGLLADVHGAERA
+VSAALAGLHARDRDG---RGGGVVVALSDAAHAMALPTRHGMTDPGSPLGGANPFYGVYP
+ARSGHVALGALEPHFAHAMVEALQLDPDG--DVRAQLTAAFAERDADAWQSWGEEWGHPI
+---TALAGPTA
+>GCF_020097155_PROKKA_00743
+------------------------------------------------------------
+------------------------------------------------------------
+---------MDVVGFAGERAGVPGHDLTYQAETGLLLSGESQTPTLPRALVADMHGAEQA
+VSTAPALLLARDRAGRDAPGGHARVSLAEAAAAVGIPSRHGLLAPDALLGGGTPYYAVYR
+AAEGHVAVGALEPHFSDALRAELDLPAGAGDDLAAALSAALTARPARDWQEWGEERGIPT
+GRGAVNGQPR-
+>GCF_023573625_PROKKA_01981
+---------------MSAAPLAGVRVVTIALNLPGPAAAARLQELGADVVTVLPPSGDPV
+ATLVPALYEELHRGQSVRTVDMKSQAGVAEMEQILAEADVFLTSHRSGALRRLGLDADAV
+RARHRRICQVDITGYAGDRTDVPGHDINYQAAAGLLAPGAP-----PRILAADLHGAERA
+VSTALALLWARGADG---DGGHATVALAEAAHALALPNRHRMTDPRSPLGGALPHYGVYP
+AAEGHVAVGALEPHFAAALVEGLGLDADG--DVRAQLTEALSRHDAAHWQAWGEKRGIPL
+---TALASPTA
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000062.fa

@@ -0,0 +1,43 @@
+>GCF_002008305_PROKKA_00076
+MDESIDAAAREANRALLGRLPADRTLVMGILNVTPDSFSDGGEHATVRAAVEHARRMVAD
+GADIVDVGGESTRPGARAVPPAEEQERILPVIEALLAEDVVLSVDTRHTATARAALALGP
+VIVNDVSGLAHEPDMPALIAASGAPYILMHN--RGNPQTMDGLAVYEDTVPDVVCELRDV
+AGRFLAAGVEPAQLIVDPGLGF--AKAGEQNWELLRGLEWLR-AMGHPVLVAASRKRFLG
+TLLADDDGTPAPPAARDAATAAISA--LAAAQGAWGVRVH---DVRASADAVRTAAAWAG
+A----HAPGEPVSEDVLP
+>GCF_003691675_PROKKA_02089
+MDESIDAAAREANRALLGRLPAGRTLVMGILNVTPDSFSDGGEHATVRAAVEHARRMVAD
+GADIVDVGGESTRPGARAVPPAEEQERILPVIEALLAEDVVLSVDTRHTATARAALALGP
+VIVNDVSGLAHEPDMPALIAASGAPYILMHN--RGNPQTMDGLAVYEDTVPDVVCELRDV
+AGRFLAAGVEPAQLIVDPGLGF--AKAGEQNWELLRGLEWLR-AMGHPVLVAASRKRFLG
+TLLADDDGTPAPPAARDAATAAISA--LAAAQGAWGVRVH---DVRASADAVRAAAAWVG
+A----HAPGEPVSEDVLP
+>GCF_005280335_PROKKA_00317
+MDESIDAAAREANRALLGRLPADRTLVMGILNVTPDSFSDGGEHATVRAAVEHARRMVAD
+GADIVDVGGESTRSGARAVPPAEEQARILPVIEALLAEDVVVSVDTRHTATARAALALGP
+VIVNDVSGLVHEPEMPALIAASGAPYILMHN--RGNPQTMDGLAVYEDTVPDVVCELRDV
+AGRLLAAGVEPAQLIVDPGLGF--AKAGEQNWELLRGLEWLR-AMGHPVLVAASRKRFLG
+TLLADDDGAPAPPAARDAATAAISA--LAAAQGAWGVRVH---DVRASADAVRTAAAWVG
+A----HAPGEPVSEDVLP
+>GCF_005280335_PROKKA_02338
+M------------------LR-SRVTVFGILNLTEDSFFDESRRLDPAGAVTAAIEMLRV
+GSDVVDVGPAASHPDARPVSPADEIRRIAPLLDALSDQMHRVSIDSFQPETQRYALKRGV
+GYLNDIQGF-PDPALYPDIAEADCRLVVMHSAQRDGIATRTGHLRPEDALDEIVRFFEAR
+VSALRRSGVAADRLILDPGMGFFLSPAPETSLHVLSNLQKLKSALGLPLLVSVSRKSFLG
+ATV----GLP----VKDLGPASLAAELHAIGNGADYVRTHAPGDLRSAITFSETLAKFRS
+RDARDRGLDHA-------
+>GCF_020097155_PROKKA_00258
+M---LPKPFHE--------LP-DRTLVMGILNVTPDSFSDGGAHDRVDAAVAHGLDLLAQ
+GADLIDVGGESTRTGATPVDPAEEQRRILPVVEALLAEGAVLSIDTMHTATARACLALGP
+VIVNDVSGLVHEPDMPALVAESGAPCILMHN--RGHAQVMDSLAHYEDTLGEVVRELSEV
+TDRFLAAGASPEQIILDPGLGF--AKAGEQNWELLRGLERIE-SLGRPVLVAASRKRFLG
+TVLAGEDGTPRPALDRDHATAAVSA--ISAAHGAWGVRVH---DVRSSVDAVRVGDAWRG
+AAPRPAGPGEARA-----
+>GCF_023573625_PROKKA_00070
+MDESIDAAAREANRALLGRLPADRTLVMGILNVTPDSFSDGGEHATVRAAVEHARRMVAD
+GADIVDVGGESTRPGARAVPPAEEQERILPVIEALLAEDVVLSVDTRHTATARAALALGP
+VIVNDVSGLAHEPDMPALIAASGAPYILMHN--RGNPQTMDGLAVYEDTVPDVVCELRDV
+AGRFLAAGVEPAQLIVDPGLGF--AKAGEQNWELLRGLEWLR-AMGHPVLVAASRKRFLG
+TLLADDDGTPAPPAARDAATAAISA--LAAAQGAWGVRVH---DVRASADAVRTAAAWAG
+A----HAPGEPVSEDVLP
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000079.fa

@@ -0,0 +1,37 @@
+>GCF_002008305_PROKKA_00318
+MANTTYTLVLLRHGQSEWNEKNLFTGWVDVPLTEKGRAEAARGGELLEAEGIRPDVVHTS
+LLKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMVWRRS
+-FDTPPP-------ALDDDSEFSQVGDERYADLGKDAPRTEALKQVVDRLLPYWEEQVLP
+DLKAGKTVLIAAHGNSLRALVKHLDGISDEDITGLNIPTGIPLVYELDQNFKPITANGRY
+LDPEAAAAGAAAVAAQGSAH
+>GCF_003691675_PROKKA_00033
+MANTTYTLVLLRHGQSEWNEKNLFTGWVDVPLTEKGRAEAARGGELLEAEGIRPDVVHTS
+LLKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMVWRRS
+-FDTPPP-------ALDDDSEFSQIGDERYADLGKDAPRTEALKQVIDRLLPYWEEQILP
+DLKAGKTVLIAAHGNSLRALVKHLDGISDEDIAGLNIPTGIPLVYELDQNFKPITANGRY
+LDPEAAAAGAAAVAAQGSAH
+>GCF_005280335_PROKKA_00019
+MANTTYTLVLLRHGQSDWNEKNLFTGWVDVPLTEKGRAEASRGGELMKAEGIHPDVLHTS
+LLKRAITTANLALETADRQWIPVKRDWRLNERHYGALQGKDKAQVKEEFGEEQFTVWRRS
+-FDTPPP-------ALDDSSEFSQIGDERYAELGDDAPRTEALKNVIDRLIPYWEAEIVP
+DLKASKTVLVAAHGNSLRALVKHLDGISDEDIAGLNIPTGIPLVYELDEDLKPITANGRY
+LDPEAAAAGAAAVAAQGSAH
+>GCF_020097155_PROKKA_00015
+MAD-TFKLILLRHGQSDWNEKNLFTGWVDVPLTEKGRAEASRGGELLAAEGLLPDVLHTS
+LLKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMTWRRS
+-FDVPPP-------PLDDSSEFSQAGDERYRDIGPDAPRTEALKQVIDRLLPYWTEQIVP
+DLKAGKTVMVAAHGNSLRALVKHLDGISDEEISGLNIPTGIPLFYELDQNLKPVTPHGRY
+LDPEAAAAGAAAVAAQGDKK
+>GCF_020097155_PROKKA_00687
+M------LTLLRHGESTANEAGTFTGLLDVPLTHRGERQASAAGQLLRSNHITPDVVVTS
+TLRRAVRTAELVCDALGTQ-LPTEAVWQLNERNYGALTGMTKTDARRMLGDDEYVRLRRS
+RTGTPPPMSLHLWEELRSSSALRGLPDGALR-------RTEALSDVIKRVRPVLHDRLLP
+MVRSGRSVLVVAHGNSLRALCACIDDLTDPELEQLNLPTGQPVQYHLAPTGALVPRGGAF
+LDPVAAQHAAALVAAEGGT-
+>GCF_023573625_PROKKA_00325
+MANTTYTLVLLRHGQSEWNEKNLFTGWVDVPLTEKGRAEAARGGELLAAEGIRPDVVHTS
+LLKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMVWRRS
+-FDTPPP-------ALDDDSEFSQVGDERYADLGKDAPRTEALKQVIDRLLPYWEEQVLP
+DLKAGKTVLIAAHGNSLRALVKHLDGISDEDIAGLNIPTGIPLVYELDQNFKPITANGRY
+LDPEAAAAGAAAVAAQGSAH
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000085.fa

@@ -0,0 +1,60 @@
+>GCF_002008305_PROKKA_00423
+MPSPTTTTAPGPAS-------------PAGPLRPPHTAAESAERVKRRGALYFAEHQLRNMRRYGAVLIVGALGEPVLYL
+LAMGLGLAQLMGGGMPQDALGGVSYVAFIAPALLASGALMTASVEFSYPVMGGFQWHRTYYAAQATPLSPAQIALGHLAA
+VSLRFVFQAAVFLLVMLAFGVVSSPWAWVQVLTATLGGLAVGAPIMAFAASLKEDKGQFATLQRLVVMPLFLFSATFYPL
+DVLPVWLRWIGWLSPQWHAAQLGRMLSYGMAEPAWLTVAHVAFLLALALGGARLAVRIYTRRLGWVRGTPDRDAGTAARR
+DRAPRLGRRAPRLGRRAARTGAARADVAPAAAQADPAAPSSSVVREHAVAVPPLPEIPVRRGPLAGAYSGNVRAVMERAF
+LSLKSNNWVVFFSGFFEPVLYLASLGLGLGALVGDVAGPDGTPVPYGMYLAPALLAVSAMNGAIYDSTWNVFFKLRYAKT
+YQTMLSTRLGPLDVALGEIAMALLRGLIYAVGFLIVMTVAGLVTSWTALLMIPGALLVALGFASLGMAVTSWMKTFQHMD
+WVQIVLMPMFLFSATFFPLAVYPEPIQWVIRVFPLWHAVEMMRALAVGVLSWATAGHVLYFVVMAGVGVWLAARRLGALF
+LR
+>GCF_003691675_PROKKA_00144
+MPSPTTTTTPGPAS-------------PAEPLRPPVTAAASAERVKRRGVLLYAEHQLRSMRRYGAVLLVGALGEPVLYL
+LAMGLGLAQLMGGGMPQDALGGVSYVAFIAPALLASGALMTASVEFSYPVMGGFQWQRTYYAAQVTPLSPAQIALGHLVA
+VSLRFVFQAAVFLLVMLAFGVVSSPWAWVQVLTATLGGLAVGAPIMAFAASLREDKGQFATLQRLVVMPLFLFSATFYPL
+EALPVWLRWIGWLSPQWHAAQLGRVLSYGMAEPVWLTVVHVAFLLALALGGAWLAVRIYTRRLGWVRGTPDRDAVTVARR
+D-------RAPRLGCRAARTGAARADVAPAAAQADPAAPSSSVVREHAVAVPPLPEIPVRRGPLAGAYSGNVRAVMERAF
+LSLKSNNWVVFFSGFFEPVLYLASLGLGLGALVGDVAGPDGTPVPYGMYLAPALLAVSAMNGAIYDSTWNVFFKLRYAKT
+YQTMLSTRLGPLDVALGEIAMALLRGLIYAVGFLIVMTVAGLVTSWTALLMIPGALLVALGFASLGMAVTSWMKTFQHMD
+WVQIVLMPMFLFSATFFPLAVYPEPIQWVIRVFPLWHAVEMMRALAVGVLSWATAGHVLYFVVMAGIGVWLAARRLGALF
+LR
+>GCF_005280335_PROKKA_02534
+--------------------------------------------------------------------------------
+---------------------------------------MT---------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-----------------------------AAAGAEPAAPSSSVVLEHTAAVPPMPEITLRHGPLAGMYAGNVRAVMERAF
+LTLKSNNWVVFASGFFEPVLYLASMGIGLGALVGDVAGPDGTPIPYGMFIAPALLAVSAMNGAIYDSTWNVFFKLRHAKT
+YQTMLSTKLGPLDVALGEIVMALLRGLIYAVGFLIVMTVGGLVTSWTAVLMVPGALLVALGFASLGMAVTSYLKTFQHMD
+WIQIVLMPMFLFSATFFPLSVYPQAIQWVIQVLPLWHAVELMRALAVGVVTWGTAGHILYFVAMSAVGIWFTSRRLGALF
+LR
+>GCF_005280335_PROKKA_02535
+MDASTTTTAPGPAAP-------RASA-SPAPLSPPISAAESAERVTRRGALYYAEHQLRNMRRYGSVLIVGALGEPIVYL
+LAMGLGLAQLMGGGAAQEGLGGVSYVAFLAPALLASGALMTAAVEFSYPVMGGFQWQKTYYAAQATPLTPAQIAVGHLGA
+VSLRFLFQGLVFFLVMLAFGVVHSPWGWLQILTATLGGLAIGAPIMAFAASLTEDKGQFATVQRLVIMPLFLFSATFYPL
+EALPVWLRWIGWISPQWHAAQLGRVLSYGMAEPVWLTVLHVVVLVAMAAVGTWLAVRIYTRRLGWRRGTPDRDALARP--
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--
+>GCF_020097155_PROKKA_02405
+------MAAQIPAS---------------APLQPPITAAESAVRVKARGAWFYAEHVLRSMRRYGAVLIVGALGEPILYL
+LAMGLGMAQVMGGGAPQESLGGVSYVTFLAPALLASGALMTAATEFSYPVMGGFQWHRTYYAAQATPLSPAQIAVGHLGA
+VALRFLFQAAVFFGVMLAFGVVHGPWGWVQVLTAALGGLAIGAPIMAFSASLKEDHGQFATLQRLVIMPLFLFSATFYPL
+EALPVWLRWVGWISPQWHAAQLGRVLSYGMAEPRWLTVLHVAVLLALAFGGAWAAVRMYTRRLGWRPGTPDRDAVARPRA
+Q-------RASRLGRRATRVDRM------AGAHAE-AAAASSVVREHTAAVPPMPEITVRRGRLGGLYSGNVAAVMERAL
+LTLKSNNWVVFASGFFEPVLYLASMGLGLGALVGAVPGPGGAPIPYGMYIAPALLAVSAMNGAIYDSTWNVFFKLRYAKT
+YQTMLATRLGPLDVALGEIAMALLRGLLYAVGFLVVMAVAGMATSWTALLMVPGALLVALGFASLGMAVTSWMKTFQQMD
+WIQLVLMPMFLFSATFFPLTVYPEPIQWLIRVFPLWHAVEMMRALAVGAVTGATAGHALYFGVMSGLGVWLTSRRLRALF
+LR
+>GCF_023573625_PROKKA_00426
+MPSPTTTTTPGPASPGPRSGTSAPSATPAEPLRPPVTAAESAERVRRRGVLLYAEHQLRSMRRYGAVLLVGALGEPVLYL
+LAMGLGLAQLMGGGMPQDALGGVSYVAFIAPALLASGALMTASVEFSYPVMGGFQWQRTYYAAQATPLSPAQIALGHLVA
+VSLRFVFQATVFLLVMLAFGVVSSPWAWVQVLTATLGGLAVGAPIMAFAASLKEDKGQFATLQRLVVMPLFLFSATFYPL
+EALPVWLRWIGWLSPQWHAAQLGRVLSYGMAEPAWLTVVHVAFLLALALGGAWFAVRIYTRRLGWVRGTPDRDAVTAARR
+D-------RAPRLGRRAARTGAARADVAPAAAQAEPAAPSSSVVREHAVAVPPLPEIPVRRGPLAGAYSGNVRAVMERAF
+LSLKSNNWVVFFSGFFEPVLYLASLGLGLGALVGDVAGPDGTPVPYGMYLAPALLAVSAMNGAIYDSTWNVFFKLRYAKT
+YQTMLSTRLGPLDVALGEIAMALLRGLIYAVGFLIVMTVAGLVTSWTALLMIPGALLVALGFASLGMAVTSWMKTFQHMD
+WVQIVLMPMFLFSATFFPLAVYPEPIQWVIRVFPLWHAVEMMRALAVGVLSWATAGHVLYFVVMAGVGVWLAARRLGALF
+LR

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000088.fa

@@ -0,0 +1,48 @@
+>GCF_002008305_PROKKA_00495
+MIGSPGDESTALRMGSTARGRVLGRPWERGLPLLVLIVDVVAVLLATFVSAQLRFGGPRRTTLPGAEVIDYSVISLALSA
+AWVLALTIQGSRDIRILGVGSEEYKRVLQGTLYLFGTVAILAYAAGLEVARGYVGLALPLGVLLLLLGRFLVRGWVARQR
+HRGRFRRRLLLVGGPKAVRHIFQTLDSEAGAGYAPVAAALPGYKARREDYLPIPVSTDLDTVEDVVALVEVRDVEAVVIT
+SGHSFVPGDVRRLGWELQERGVSLIMAPALVDVAGPRLHTQPLAGLPLIHLS-TPRLSEGKAFAKRAFDVVASGLGLIAI
+SPLLIAVAIAVKATDGGPVLFRQERIGLGGRPFTMLKFRSMVVDAEEIRQRLVSDGGDADVLFKMKDDPRITRVGKLIRR
+TSIDELPQLVNVLRGEMSLVGPRPHLPHEVEAYGQYVHRRFLVQPGITGLWQVSGRSDLPWEEAVRLDLYYVENWSILGD
+LVILGRTVKAVV-------------------AADGAY--------------------------------
+>GCF_003691675_PROKKA_00216
+MIGSPGDESTALRMGSTARGRVLGRPWERGLPLLVLIVDVVAVLLATFVSAQLRFGGPRRTTLPGAEVIDYSVISLALSA
+AWVLALSIQGSRDIRILGVGTEEYKRVLQGTLYLFGTVAILAYAAGLEVARGYVGLALPLGVLLLLLGRFLVRGWVARQR
+HRGRFRRRLLLVGGPKAVRHIFQALDSEAGAGYAPVAAALPGYKARREDYLPIPVSTDLDTVEDVVAHVEERDVEAVVIT
+SGHPFVPSDVRRLGWELQERGVSLIMAPALVDVAGPRLHTQPLAGLPLIHLS-TPRLSEGKAFAKRAFDVVASGLGLIAI
+SPLLIAVAIAVKATDGGPVLFRQERIGLGGRPFTMLKFRSMVVDAEEIRQRLVSDGGDADVLFKMKDDPRITRVGKLIRR
+TSIDELPQLVNVLRGDMSLVGPRPHLPHEVEAYEQYVHRRFLVQPGITGLWQVSGRSDLPWEEAVRLDLYYVENWSILGD
+LVILGRTVKAVI-------------------AADGAY--------------------------------
+>GCF_005280335_PROKKA_01221
+MLTP-------------------DSPYEE------------------------RF--------------------AALNQ
+S-------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------LRWEVAD-----------------ELRRANLARVDELHPPVTPRDTFYTRHGKRALDVGVSGAALLFS
+SPVIGALCLVTLKDLGQPVLFTQQRPGKHGKPFQMVKLRTM--------REAYDDQGK-----PLLGELRVTKTGRLIRR
+ASLDELLNFWNIFKGDMSLIGPRPLVPEYVERFSRRHRQRLAVKPGLECPPPRPPQGPVTYDDQFENDCWYVENVSLKTD
+AWLTWRVLQTALDRRQNKARGSSTRGSFMGYDADGTVITTAALPDWALNTVLERHGLLTSNSADARQEG
+>GCF_005280335_PROKKA_02452
+MFSSPGDESPALRTGSTARGRLLGRPWERGLPLLVFIVDVVAVLLATFVSAQLRFGGPRRTTLPGTEVIDYSVISLALSA
+AWVLALSIQGSRDIRILGVGSEEYKRVLQGTLYLFGTVAILAYAAGLEVARGYVGLALPLGVLLLLLGRFLVRGWVARQR
+HLGRFRRRLLLVGGPKAVRHIFQALDSEAGAGYAPVAAALPGYKTRQEDYLPIPVSTDLDTVEDVVALVEVRDVEAVVIT
+SGHSFVPGDVRRLGWELQERGVSLIMVPALVDVAGPRLHTQPLAGLPLIHLS-TPRLSEGKAFAKRAFDVVASGLGLIAI
+SPLLIAVAIAVKATDGGPVLFRQERIGLGGRPFTMLKFRSMVVNAEEIKQRLVSDGGDADVLFKMKDDPRITKVGKFIRR
+TSIDELPQLVNVLRGDMSLVGPRPHLPHEVEAYEQYVHRRFLVQPGITGLWQVSGRSDLPWEEAVRLDLYYVENWSILGD
+LVILGRTVKAVV-------------------AADGAY--------------------------------
+>GCF_020097155_PROKKA_02336
+MTSSAVTTSQTGRGGSSVHARVLGAPWERGLPRLVLLADVVAVVLAAFLSSELRFGTARNAAVPGAESVNYLLVGAVLSA
+SWVVALGVDGSRDIRILGIGAEEYKRVLRGTLYLFGMIAILAYAFAFEVARGYVALALPIGLLLLMLGRFLIRGWVARGR
+HRGAMRRRLLLVGGPQAVKYVHDTLDSEAGAGYKPIAAVLPGYRARDEGWLPIPVTTEVDGVDELVAQVREMDIEAVVIT
+SGHPFVPDDVRRLGWDLQERGISLIMAPALVDVAGPRLHTQPLAGLPLLHLS-TPRLSRGKAFVKRSFDVVASGLGMLVI
+SPLLLTVAIAVKATDGGPVLFRQERVGLRGEHFTMLKFRSMVVDAEEIKQQLMSDRGEEDVLFKMKDDPRITRVGRFIRR
+TSIDELPQLVNVLRGDMSLVGPRPHLPHEVEQYGQYVHRRFLVQPGITGLWQVSGRSDLSWEDAVRLDLYYVENWSVLGD
+LVILGRTVKAVL-------------------AADGAY--------------------------------
+>GCF_023573625_PROKKA_00494
+MFASPGDESTTLRMGSTARGRVLGRPWERGLPRLVLVVDVVAVLLATFVSAQLRFGGPRRTTLPGAALVDYSVISLALSA
+AWVLALTIQGSRDIRILGVGTEEYKRVLQATLYLFGTVAILAYAAGLEVARGYVGLALPLGVLLLLLGRFLVRGWVARQR
+HRGRFRRRLLLVGGPKAVRHIFEALDSEAGAGYAPVAAALPGYKARQEDYLPIPVSTDLDTVEDVVALVEVRDVEAVVIT
+SGHSFVPGDVRRLGWELQERGVSLIMAPALVDVAGPRLHTQPLAGLPLIHLS-TPRLSEGKAFAKRAFDVVASGLGLIAI
+SPLLIAVAIAVKATDGGPVLFRQERIGLGGRPFTMLKFRSMVVDAEEIRQRLVSDGGDADVLFKMKDDPRITRVGKLIRR
+TSIDELPQLVNVLRGDMSLVGPRPHLPHEVEAYEQYVHRRFLVQPGITGLWQVSGRSDLPWEEAVRLDLYYVENWSILGD
+LVILGRTVKAVI-------------------AADGAY--------------------------------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000096.fa

@@ -0,0 +1,43 @@
+>GCF_002008305_PROKKA_00614
+MGS-------HHHAP--------TGHRGRLAIAFGITTAVLLAEVVGAVLTGSLALLVDA
+AHMLTDAGGLLMALLAATLMARPPTTRRTWGFLRAEVLAALAQAAVLLAVGTYAFIEGLQ
+RLFAPPEVASGPLLAFGILGLVGNLASLAVLGSGRGANLNMRAAFLEVLNDALGSVAVIA
+SALVIAATGWTRADAVAGMLIAVLIVPRTLKILGETTRILLESTPRGLDLAEVRTHLQAL
+PHVVSVHDLHASQIATGVPVLSAHIVVEDSCFHDGHAPQILDQLQHCVAEHFDVGVDHST
+FQLEPAAHAHHE-----HPTHH
+>GCF_003691675_PROKKA_00326
+-------------------------------MVFSITATIMVAEVIGALASGSLALLADA
+GHMFTDSAGLLIALTATTLALRPATDKRTWGYKRAEIIAAAAQAAVLLAVGGFVAVEGVR
+RLIEPPEVESTAMLWFGVIGLAGNLIGLAILASSRGENLNMKAAFLEVLNDALGSVAVIV
+SAIVIATTGWNRADAVVSLLIAALIVPRALILLRDTIDVLMETTPKGLDLEAVRIRLSEL
+PHVLEVHDLHASRIDSDTPVLSAHVTVHNGCLTAAHLGTVLTDLQRCVAQDFQVPIEHST
+FQIEPATHPHTETL---HP---
+>GCF_003691675_PROKKA_01774
+MGA-------HHHAS--------PAHRWRLAVAFAITTAVLLAEVAGALITGSLALLVDA
+AHMLTDAGGLLMALLASTLMARPPTARRTWGFLRAEVLAALAQAAILLAVGLYAFIEGLQ
+RLFAPPEVASGPLLLFGILGLAGNLASLAVLGSGRGANLNMRAAFLEVLNDALGSVAVIA
+SALVIATTGWAQADAVAGMLIAVLIVPRTLKILAEAAHILLESTPRDLDLAEVRDHLEAV
+PHVVSVHDLHASQIATGVPVLSAHVVVEDHCFHDGHAPQILDQLQHCVAEHFDVAIDHST
+FQLEPAAHAHHE-----HPTHH
+>GCF_020097155_PROKKA_00544
+MSTPHEHHHDHAHGPSPEEAAADPALRRRLWIALALAGTVVLAQAVGAALTGSLALLTDT
+AHAVTDASGLAVALVAAILMARPATPRRTWGLRRLEVVAALGQAALLLLVGAYSAVEAVR
+RLVEPPAVDGTGMLLFGVLGLAANLAAAAVLASSRGANLSMRAAFLEVVNDALGSLGVIA
+AAAVVAVTGWTRADAVAGLLIVVLIVPRAVSLLRQTLRVLLEFTPEGLDLDEVRTHLLEV
+EHVLEVHDLHASTVATGLPVLTAHVVVEDGCFTDGHAAQILEQLRECTREHFPLAVPHST
+FQLETAAIAADDAHHTAHP---
+>GCF_020097155_PROKKA_00702
+MGA------GHNHGPAASETGHPGDFRKKLWIAFSITATIVVAQAMGSVITGSLALLTDT
+AHAITDASGLLVALIAATLMLKPANSKRTWGFRRIEVIAALGQSALLLAVGTYAAIEGIR
+RLFEPPEVPASELLIFGIIGLVANIIAITILASSRGSNFNMRAAFLEVLNDALGSLGVII
+AAIVIATTGFMQADAIAGLLIAALIVPRAFKLMRETTGVLMEFTPKGLDLDKVRSHILEL
+DHVKDVHDLHASTVATGLPILTAHVVVEDECFTDGRAAQTLHEIKDCVAGHFEVSIHHST
+FQIETEHIAEHEPEISKHD---
+>GCF_023573625_PROKKA_02007
+MSG-----HDHSHAL------PAAGRRGRLAVVFSITATIMVAEVIGALASGSLALLADA
+GHMFTDSAGLLIALTAATLALRPATDKRTWGYKRAEIIAAAAQAAVLLAVGGFVAVEGVR
+RLIEPPEVESTAMLWFGVIGLAGNLIGLAILASSRGENLNMKAAFLEVLNDALGSVAVIV
+SAIVIATTGWNRADAVVSLLIAALIVPRALILLRDTIDVLMETTPKGLDLEAVRIRLSEL
+PHVLEVHDLHASRIDSDTPVLSAHVTVHNGCLTAAHLGTVLTDLQRCVAQDFQVPIEHST
+FQIEPATHPHTETL---HP---
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000108.fa

@@ -0,0 +1,60 @@
+>GCF_002008305_PROKKA_00838
+MSL-----------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------------------------------EF----------------RTSEESPDVTRVVA-THLPTRHGDFALLG
+YRDG-RGTDHVALTL---GDVAADDGELPL-VRLHSECLTGDALGSYRCDCGEQLDAALQAIGAAGRGVLIYIRGHEGRG
+IGLLDKLRAYALQDSGIDTVDANTHLGLPADARDYDQSAQILRELGVGKIRLLSSNPAKQEALEALGIHVEARVRLNVAD
+RPENSRYLSTKRARMRHDLPPERNAWDLLAGARVPTGPLTPQEEALVLRYGPLVEAGPRLVIGQLGQSLDGFIASRTGDA
+CFVTGEADREHLHRLRALVDAVLVGAQTVAADDCQLTVRAVNGADPARVVVDPHARIPLTAKVLTDPRSRTLWLVGSDAS
+VPASLAPHVSVHRLETSTGFEPAAILQYLADQGLGRVLIEGGGLTVSGFLHAGVLDRLYLTSAPLLVGDGVPGIRFDGAD
+ALSGALSAPVRRFVLGDDVCTEFDFSAAKPASPAALHRADQENQPTGQD
+>GCF_002008305_PROKKA_01065
+MSE----------HIRLDPVPVAIAAIAAGRPVVVVDDADRENEGDLIYAAALATDEVTAFTVRHTSGVICAPLPAGLAD
+RLALPPMTTVNEDPKGTAYTVSVDAAAGVTTGISAADRTRTLRLLADPGAAPGDLTRPGHVFPLRAVPGGVRARRGHTEA
+GVELCRLAGVAPVAAIAELVHDDGTMMRLPALREFSDEHGLVLISIEDLVAHLEETTPALTAVPAEATLPTRHGLFRVSV
+HVDAETGAEHLLLV------AGETDSERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALARAAAEG-GAVLYLRGHEGRG
+IGLANKIRAYRLQEEGMDTVEANLALGLPAEARDWAGAAAVLTAAGHRRIRLVTNNPAKVAGLRAAGIDVVERVPAPTPV
+TEHNVVYLRTKRDRMAHAL-----ADRVLEPPTATGGPATPAD-------------------------------------
+---------------------------------------------------DPT----------TDPTH-----------
+--------------------------------------------------------------------------------
+--------PTH-----------------------------QEDTP----
+>GCF_003691675_PROKKA_00784
+MSE----------HIRLDPVPAAIAAIAAGRPVVVVDDADRENEGDLIYAAALATDEVTAFTVRHTSGVICAPLPAGLAD
+RLALPPMTTVNEDPKGTAYTVSVDAAAGVTTGISAADRTRTLRVLADPGAAPGDLTRPGHVFPLRAVPGGVRARRGHTEA
+GVELCRLAGVAPVAAIAELVHDDGTMMRLPALREFSDEHGLVLISIEDLVAHLEETTPTLTAVPAEATLPTRHGLFRVSV
+HVDAETGAEHLLLV------AGETDPERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALARAAAEG-GAVLYLRGHEGRG
+IGLANKIRAYRLQEEGMDTVEANLALGLPAEARDWAGAAAVLTAAGHRRIRLVTNNPAKVAGLRAAGIDVVERVPAPTPV
+TEHNVVYLRTKRDRMAHAL-----ADRVLEPPTATGGPATPAD-------------------------------------
+---------------------------------------------------DPT----------TDPTH-----------
+--------------------------------------------------------------------------------
+--------PTH-----------------------------QEDTP----
+>GCF_005280335_PROKKA_01822
+MSD----------SIPLDAVPAAIAAFAAGRPVVVVDDADRENEGDLVYAAALATDAVTAFTVRHTSGVICAPMPADLAD
+RLALPPMTARNEDPKGTAYTVSVDAATEVSTGISAADRTRTLRILADPAAGPADLTRPGHVFPLRAVPGGVRARRGHTEA
+GVELCRLADVAPVAAIAELVHDDGTMMRLPALREFADEHGLVLISIEDLVRHLEEEGPTPVPVPAEATLPTRHGVFRVSV
+HADAVTGAEHVLLVAKKAGEAGEADPERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALSRAGSEG-GAVLYLRGHEGRG
+IGLANKVRAYRLQEQGLDTVEANIALGLPTEARDWAGAAAVLAAAGHTRVRLVTNNPAKVAGLQAAGIDVVERVPAPTPV
+TEHNLGYLRTKRDRMAHAL-----ADRVLEHPVAPG--------------------------------------------
+-----------------------------------------------------H----------EDPRHE----------
+--------------------------------------------------------------------------------
+-------TPTH-----------------------------QEDTP----
+>GCF_020097155_PROKKA_01711
+MSIDTAVEPAAPVDIRLDPVADAVAAIAQGRPVVVVDDADRENEGDLIYAAALATDAVTAFTVRHTSGVICAPLPAELAD
+RLNLPPMTARNEDPKGTAYTVSVDAVAGVTTGISAADRTVTLRVLAGEESTAADLTRPGHVFPLRAVPGGVRARRGHTEA
+GVELCELADLPPVAAIAELVHDDGTMMRLPALREFADEHSLVLISIEDLVAHLHEHRPEQRVVPAEAALPTAHGDFRISV
+HPDTATGAEHVLLVADRPGSATGGDADAPVTVRVHSECLTGDVFGSLRCDCGPQLQAALDAAARDG-GAVLYLRGHEGRG
+IGLTNKIRAYRLQEEGLDTVEANLALGLPAEGRAYAGAADLLREAGLTRIRLVTNNPAKVDALRAAGIDVVERVPAPTPV
+TEHNAAYLRTKRDRMHHEL-----ADRDL------G--------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------------------DA-----
+>GCF_023573625_PROKKA_01012
+MSE----------HIRLDPVPAAIAAIAAGRPVVVVDDADRENEGDLIYAAALATDEVTAFTVRHTSGVICAPLPAGLAD
+RLALPPMTTVNEDPKGTAYTVSVDAAAGVTTGISAADRTRTLRVLADPGAAPGDLTRPGHVFPLRAVPGGVRARRGHTEA
+GVELCRLAGVAPVAAIAELVHDDGTMMRLPALREFSDEHGLVLISIEDLVAHLEETTPTLTAVPAEATLPTRHGLFRVSV
+HVDAETGAEHLLLV------AGETDPERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALARAAAEG-GAVLYLRGHEGRG
+IGLANKIRAYRLQEEGMDTVEANLALGLPAEARDWAGAAAVLTAAGHRRIRLVTNNPAKVAGLRAAGIDVVERVPAPTPV
+TEHNVVYLRTKRDRMAHAL-----ADRVLEPPTATGGPATPAD-------------------------------------
+---------------------------------------------------DPT----------TDPTH-----------
+--------------------------------------------------------------------------------
+--------PTH-----------------------------QEDTP----

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000145.fa

@@ -0,0 +1,31 @@
+>GCF_002008305_PROKKA_01790
+MDAP----ASDLTGKARIRHAALRLFAHHGVEGTSMRAIAEEASVTVGLITHHYGSKAGL
+HREVDAAVADDFAAAIASVPAEGTARDVTLRRDAAVAEMLRARPDVLEYVRRHVLLGEPA
+ADSQLVEKLTALAREQVRQLRAAGLISGRRDEVPQVVSMIMRMLGELFFEPLVDRI----
+---VDAVDRDAARPAVVVRVQAAEDETARGGRA
+>GCF_002008305_PROKKA_02051
+MNTPLPFDQDDLSSPARLRLAALELYAERGVEMASVREIAQRAGVAPGLVRHHFGSKAGL
+TRAVDDDVLRLIAATLDEVPLVGTPQEVSAARDAAFADLLADHPVVGAYVRRSLLEAGGE
+TES-LLERLVDLTTEQTERLRRSGF-APRRSMPTSVFGTVIRQMGHLMVDPSADRIWRRI
+AETQEGAAEQAS-PRVRLVVDPP-----R----
+>GCF_003691675_PROKKA_01757
+MNTPLPFDQDDLSSPARLRLAALELYAERGVEMASVREIAQRAGVAPGLVRHHFGSKAGL
+TRAVDDDVLRLIAATLDEVPLVGTPQEVSAARDAAFADLLADHPVVGAYVRRSLLEAGGG
+TES-LLERLVDLTTEQTERLRRSGF-APRRSMPTSVFGTVIRQMGHLMVDPSADRIWRRI
+AETQEAAAEQRS-PRVRLVVDPP-----R----
+>GCF_005280335_PROKKA_01086
+MDAP----ASDLTGKARIRHAALRLFAHHGVEGTSMRAIAEEASVTVGLITHHYGSKAGL
+HREVDAAVADDFAAAIASVPAEGTARDVTLRRDAAVAEMLRARPDVLEYVRRHVLLGEPA
+ADSQLVEKLTALAREQVRQLRAAGLISGRRDEVPQVVSMIMRMLGELFFEPLVDRI----
+---VDAVDRDAARPAVVVRVQAAEDETARGGRA
+>GCF_020097155_PROKKA_00729
+MNTARPLTREDLSSAARLRLSALELYAERGEHAASIRDVGRHAGVAPGLVRHHFGSKDGL
+TRAVDDDIIDLVRATLEAVPLEGTPLEISAARDAAFQELLQERPLIGGYLAQALTASRAS
+GES-VLDRLVDLSAEQTRQLIDRGL-DPRRGLRTSVFTTVVRQVAVFLVAPVAERAWNRL
+GHTLEGASDVAPMPPVRVVVGPAPEEDRR----
+>GCF_023573625_PROKKA_01985
+MNTPLPFDQDDLSSPARLRLAALELYAERGVEMASVREIAQRAGVAPGLVRHHFGSKAGL
+TRAVDDDVLRLIAATLDEVPLVGTPQVVSAARDAAFADLLADHPVVGAYVRRSLLEAGGE
+TES-LLERLVDLTTEQTERLRRSGF-APRRSMPTSVFGTVIRQMGHLLVDPSADRIWRRI
+AETQEDAAEQAS-PRVRLVVDPP-----R----
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000164.fa

@@ -0,0 +1,78 @@
+>GCF_002008305_PROKKA_02122
+MTHP---------ASSTPAGPQSETTRRVDLDVTGMTCASCVGRVERKLGKLEGVTASVNLPLEQATVTAPAGVSDEELV
+AAVEKAGYGATVR-----RPA-----------PPAGHAGHAGHAHTS--------EHGEEHAADHDGVDHHDHMAHGPSE
+DVLTPRLIGAAVLTVPLVLISMVPALQFPHWGWVAFALAAPVALWAAWPFHSAAFRAARHGSSTMDTLVSLGVLVSFSFS
+AVELILA----PDMTAHVGGTMAEM-AHHSLYFETAAVITTFLLLGRWLEARAKREAGAALRALLDLGAAQATLY-----
+--------------------------------DPETH--------DERTVPAESLAPGDVVLIRPGEKVPTDAEVLEGTS
+AVDASLLTGESVPVEVGPGDALTGATLNTSGRLVARATRVGSDTTLAQMGRLVSEAQTGKARVARLADRISAVFVPIVLG
+IAVLTFAVWMIVT-GDLPSALRAGVAVLVIACPCALGLATPVGLLAGTGRAAQLGILIRGPEVLEDSRTVDTIVLDKTGT
+VTEGRMALADVLVLDPAFVAETGAS-----------RSAFVDETAPDQAADVLLTLAAAVERGSEHPIARAIVAGAEERG
+LTVPGVADFASTAGGGVSGLVALPHDDGAPGSGAHGAAGPDPVRVAVGRGSVLETALDGGIPAEHRAAFEAAEQAGATAV
+WVAVGGRVAGVLSVRDTVKETSADAIARLKELGLRPLLVTGDNAAVATQVAAAVGIPAEDVVAGVRPEDKVDVVRRLQSE
+GHVVAMVGDGVNDAPALAAADMGIAMGSGTDVAREAAQITVMGDDLHQVVQALDLSRRTLGIIRMNLFWAFAYNVLGIPV
+AALGLLNPMIAGGAMAASSVLVVLNSLRLTRYA----R
+>GCF_003691675_PROKKA_01830
+MTHP---------ASSTPAGPQSETTRRVDLDVTGMTCASCVGRVERKLGKLEGVTASVNLPLEQATVTAPAGVSDEELV
+AAVEKAGYGATVR-----RPA-----------PPAGHAGHAGHAHTSEHGEEHGEEHGEEHAADHDGVDHHDHMAHGPSE
+DVLTPRLIGAAVLTVPLVLISMVPALQFPHWGWVAFALAAPVALWAAWPFHSAAFRAARHGSSTMDTLVSLGVLVSFSFS
+AVELILA----PDMTAHVGGTMAEM-AHHSLYFETAAVITTFLLLGRWLEARAKREAGAALRALLDLGAAQATLY-----
+--------------------------------DPETH--------DERTVPAQSLAPGDVVLIRPGEKVPTDAEVLEGTS
+AVDASLLTGESVPVEVGPGDALTGATLNTSGRLVARATRVGSDTTLAQMGRLVSEAQTGKARVARLADRISAVFVPIVLG
+IAVLTFAVWMLVT-GDLPSALRAGVAVLVIACPCALGLATPVGLLAGTGRAAQLGILIRGPEVLEDSRTVDTIVLDKTGT
+VTEGRMALADVLVLDPAFVAETGAS-----------RSAFVAETAPDQAADVLLTLAAAVERGSEHPIARAIVAGAEERG
+LTVPDVADFASTAGGGVSGLVALPHDDGALGSGAHDAAGPAPVRVAVGRGSVLETALDGGIPAEHRAAFEAAEQAGATAV
+WVAVGGRVAGVLSVRDTVKETSADAIARLKELGLRPLLVTGDNAAVATQVAAAVGIPAEDVVAGVRPEDKVDVVTRLQSE
+GAVVAMVGDGVNDAPALAAADMGIAMGSGTDVAREAAQITVMGDDLHQVVQALDLSRRTLGIIRMNLFWAFLYNVLGIPV
+AALGLLNPMIAGGAMAASSVLVVLNSLRLTRYA----R
+>GCF_005280335_PROKKA_00658
+MAASPSPSDRAAEALGRTALQDAEGTRRVDLDVTGMTCASCVGRVERKLGKIEGVEASVNLPLERATVTVPASVSDQDLL
+DAVAKAGYTAAVRPDAQARPARRGRHDDGGTRPGADHAGHPDHR-------DH-ETPGEDHAG-HEG--HDDHMAHGPRA
+DVLRPRLIVAAILTVPIVLISMVPALQFPHWGWVALALSAPVALWCGWPFHSAAFRAARHGSSTMDSLVSVGVLVAWTYS
+AVELVLE----PGMTAHVGGTMAEM-MRHSLYFETAAVITTFLLLGRWLEARAKREAGRALRSLLDLGAAQATVLPNWDA
+QTPHPSTSAAATPVAAVSGDFSEVEAASTSDKSPQTHHDGGADALTERVIPAEELEPGDVVVIRPGEKVPTDAVVLEGTS
+AVDASLLTGESVPVEVGPGDEITGATVNTSGRLIARATRTGADTTLAQMGRLVSDAQTGKARVARLADRISAVFVPIVLV
+LAVLTFVVWMLVTGGDVAPALRAGVAVLVIACPCALGLATPVGLLAGTGRASQLGILIGGPEVLEDTRTVDTIVLDKTGT
+VTEGRMALSDV--------------------------HAFADDAALTE--DRILALAAAVEAGSEHPIARAIVAGARERG
+LTVPRVADFASTAGGGVTGTVALPE--------------AGSVRVAVGRGDLV-----GEPSPAQQAEFDAAEQAGATAV
+WVAVDGRVAGVLSVKDTVKPSSAAAIARLKELGLRPLLVTGDNAAVAAQVAAAVGIPAEDVVAGVRPEDKVDVVTRLQSE
+GRVVAMVGDGVNDAPALAAADMGIAMGSGTDVAREAAQITVMGDDLDQVVQALDLSRRTLGIIRMNLFWAFAYNVLGIPV
+AALGLLNPMIAGGAMAASSVLVVLNSLRLTRYA----R
+>GCF_020097155_PROKKA_00575
+MTHP---------ASSAPAGPQSETTRRVDLDVTGMTCASCVGRVERKLGKLEGVTASVNLPLEQATVTAPADVSDEELV
+AAVEKAGYGATVR-----RPA-----------PPA---GHAGHAHTS----EHGEGHGEEHAADHDGVDHHDHMAHGPGE
+DVLKPRLIGAAVLTVPLVLISMVPALQFPHWGWVAFALAAPVALWAAWPFHSAAFRAARHGSSTMDTLVSLGVLVSFSFS
+AVELILA----PDMTAHVGGTMAEM-AHHSLYFEAAAVITTFLLLGRWLEARAKREAGAALRALLDLGAAQATLY-----
+--------------------------------DPETH--------DERTVPAESLAPGDVVLIRPGEKVPTDAEVLEGTS
+AVDASLLTGESVPVEVGPGDAVTGATLNTSGRLVARATRVGADTTLAQMGRLVADAQTGKARVARLADRISAVFVPVVLG
+LAVLTFAVWMLVT-GDLPSALRAGVAVLVIACPCALGLATPVGLLAGTGRASQLGILIRGPEVLEDSRTVDTIVLDKTGT
+VTEGRMALADVLVLDPAFVTDTGASRSASVAETDAPRSAFVAETAPDRATDLLLTLAAAVERGSEHPIARAIVTGAEERG
+LTVPDVADFASTAGGGVSGLVALPHDDGALASGAHGAAGPAPVRVAVGRGSVLETALDGGIPAEHRAAFEAAEQAGATAV
+WVAVGGRVAGVLSVRDTVKDTSADAIARLKELGLRPLLVTGDNAAVATQVADAVGIPAEDVVAGVRPEDKVDVVRRLQSE
+GRVVAMVGDGVNDAPALAAADMGIAMGSGTDVAREAAQITVMGDDLHQVVQALDLSRRTLGIIRMNLFWAFLYNVLGIPV
+AALGLLNPMIAGGAMAASSVLVVLNSLRLTRYA----R
+>GCF_020097155_PROKKA_00718
+M--------------STSAPPT--GGPDIELEIGGMTCASCANRIEKKLNKLDGVAATVNYATEKAKVTVPAGYDPSLLV
+AEVEKTGYTAALP-----KPK-----------DTT--------ANTS----E--TEAGEE---------EDSELTS----
+--LRHRLIGAIVLTVPVIAMAMIPALQFTYWQWASLALAAPVIIWGAWPFHKAAWTNLKHGAATMDTLISMGTSVALLWS
+LYALFLGTAGTPGMTHPFEFTIAPSDGAANIYLEVGAGVTMFILAGRYFEKRSKRQAGAALRALLELGAKEVAVL-----
+-------------------------------------RDG-----VEVKIPTSELAVGDEFIVRPGEKIATDGLVTSGSS
+AVDASMLTGESVPVEVREGDSVTGATVNAGGRLVVRATRVGSDTQLAQMAKLVEDAQTGKAEVQRLADRISGIFVPIVIV
+VAFITLGAWLGGG-FPVAAAFTAAVAVLVIACPCALGLATPTALLVGTGRGAQMGVLIKGPEVLESTRKVDTVVLDKTGT
+VTSGKMTLTDV-----------------------------ITEPGVDR--AELLRFAGALEDSSEHPIAQAIAKGATQEV
+GQLPTPEDFANVEGKGVQGIVE-------------------GTPVVVGRESLL-ADWSQKLSPEVAQAKAQAEGEGKTVV
+AIGWDGAARGILVVADTVKPTSAEAIRGLKEIGLTPVLLTGDNEAVARQIASEVGI--DEVIAEVLPKDKVDVVTRLQEE
+GKIVAMVGDGVNDAPALAQADLGLAMGTGTDVAIEASDITLVRGDLRAAVDAIRLSRKTLSTIKTNLFWAFAYNTAAIPV
+AALGMLNPMLAGAAMAFSSVFVVGNSLRLRGFTSVASK
+>GCF_023573625_PROKKA_02060
+MTHP---------ASSTPAGPQSETTRRVDLDVTGMTCASCVGRVERKLGKLEGVTASVNLPLEQATVTAPAGVSDEELV
+AAVEKAGYGATVR-----RPA-----------PPAGHAGHAGHAHTS----EHGEEHGEEHAADHDGVDHHDHMAHGPSE
+DVLTPRLIGAAVLTVPLVLISMVPALQFPHWGWVAFALAAPVALWAAWPFHSAAFRAARHGSSTMDTLVSLGVLVSFSFS
+AVELILA----PDMTAHVGGTMAEM-AHHSLYFETAAVITTFLLLGRWLEARAKREAGAALRALLDLGAAQATLY-----
+--------------------------------DPETH--------DERTVPAESLAPGDVVLIRPGEKVPTDAEVLEGTS
+AVDASLLTGESVPVEVGPGDALTGATLNTSGRLVARATRVGSDTTLAQMGRLVSEAQTGKARVARLADRISAVFVPIVLG
+IAVLTFAVWMIVT-GDLPSALRAGVAVLVIACPCALGLATPVGLLAGTGRAAQLGILIRGPEVLEDSRTVDTIVLDKTGT
+VTEGRMALADVLVLDPAFVAETGAS-----------RSAFVDETAPDQAADVLLTLAAAVERGSEHPIARAIVAGAEERG
+LTVPGVADFASTAGGGVSGLVALPHDDGAPGSGAHGAAGPDPVRVAVGRGSVLETALDGGIPAEHRAAFEAAEQAGATAV
+WVAVGGRVAGVLSVRDTVKDTSADAIARLRQMGLRPLLVTGDNAAVAAQVAEAVGIPAEDVVAGVRPEDKVDVVTRLQSE
+GAVVAMVGDGVNDAPALAAADMGIAMGSGTDVAREAAQITVMGDDLHQVVQALDLSRRTLGIIRMNLFWAFLYNVLGIPV
+AALGLLNPMIAGGAMAASSVLVVLNSLRLTRYA----R

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000177.fa

@@ -0,0 +1,26 @@
+>GCF_002008305_PROKKA_00004
+----------MAETPAPFEPDRPDLALVQLRRVREAARERGEAPLRARGTGAGLAGAMAG
+TPSAGR-----ERQDRRRPFGGADRDPATVSTVFGRLIRDRGWSTPVAVGSVLTRWAELV
+GPEIALHCRPESFEDSVVRVRTSSTAWATQLRLMSPVLLQRFDEALGPGVVTRIEVAGPQ
+APSWRKGPRTVRGGRGPRDTYG
+>GCF_003691675_PROKKA_02009
+----------MAETPAPFEPDRPDLALVQLRRVREAARERGEAPLRARGTGAGLAGAMAG
+TPSAGR-----ERQDRRRPFGGADRDPATVSTVFGRLIRDRGWSTPVAVGSVLTRWAELV
+GPEIALHCRPESFEDSVVRVRTSSTAWATQLRLMSPVLLQRFDEALGPGVVTRIEVAGPQ
+APSWRKGPRTVRGGRGPRDTYG
+>GCF_005280335_PROKKA_00420
+------------------------------------------------------------
+-----------------------------MSSVFGRLIRDRGWSTPVAVGSVLTRWDELV
+GPEIALHCRPESFEDSVVRVRTSSTAWATQLRLMTPVLLQRFDDALGPGVVTRLEVAGPQ
+APSWRKGPRTVRGGRGPRDTYG
+>GCF_020097155_PROKKA_00373
+MRERSPEPDALAELP----PDRPDLALVQLRRVRDAARQRGEAPLNRRGTAAGLAQSMAG
+SEAAAAAGGAVARSGHRRPGAPADRDPAVVSSVFGRLIRDRGWSTPVAVGSVLTRWADLV
+GPEIALHCRPESFEDSVVRVRTSSTAWATQLRLMSPMLLSRFDEALGPGVVTRIDVAGPA
+APSWRHGPRTVRGGRGPRDTYG
+>GCF_023573625_PROKKA_00004
+----------MAETPAPFEPDRPDLALVQLRRVREAARERGEAPLRARGTGAGLAGAMAG
+TTSAGR-----ERQDRRRPFGGADRDPATVSTVFGRLIRDRGWSTPVAVGSVLTRWAELV
+GPEIALHCRPESFEDSVVRVRTSSTAWATQLRLMSPVLLQRFDEALGPGVVTRIEVAGPQ
+APSWRKGPRTVRGGRGPRDTYG
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000188.fa

@@ -0,0 +1,60 @@
+>GCF_002008305_PROKKA_00019
+--MDEQRTLNGRYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRKEARSAASLNHPSIVSVYDTG
+EVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGPDRAVAWTRGVLEALEHAHEEDIVHRDVKPANVMVTDTGTVKV
+MDFGIAHALADTSATTSQTQAVVGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPP
+APSDVDPDLPPAFDPVVLRALRKDPQDRFPTGAAFLAALEEAAADPHAGPGRHTPPLDAVHPALV--GAGGAVLGATP--
+----AEHGADVADVPTA-------------AVPLT----RPAPSVP--AEPDTAQPQAVNHAVAGAGLPGAASAAQLAA-
+-AAAMDGPRPVTGG----QPVTPGAAATPRPEPPPRDTPAPATATPRRVRRRVRRR-TLLAAGVVLVALALVLAPWLAAA
+L------RTTAEVPAVVGLQQDEAVAALEDAGLVAVVSSAYMADAPDGTVTQSDPPTGTEVPRGAEVRIRVSRGEEGIAL
+SDSLHGLSEDAARRELERLGLRVSSVQYQDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARR
+QLALSAPELRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTTSSWIAPTAEPSEPAPPSSEAPEPT-PSASTSPS
+PPSSESPEPSESPEPSESAEPSPSPSASATPSPEPTTTATPSPTQSPSPPSAAPSTSSEP-TEQSPST-SPTATPVDPLP
+TLTPDP--EPSIDPPPST-------------------
+>GCF_003691675_PROKKA_02037
+MSVDEQRTLNGRYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRKEARSAASLNHPSIVSVYDTG
+EVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGTDRAVAWTRGVLEALEHAHEEGIVHRDVKPANVMVTETGAVKV
+MDFGIAHALADTSATTSQTQAVVGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPP
+APSDVDPDLPPAFDPVVLRALRKDPEDRFPTGTAFLAALEEAAADPHAGPGRHTPPLDAFPPALV-----GAVLGAAA--
+----AEHG---ADVPTA-------------AVPLT----RPTPSVP--AEPDAAQPQAANHAVAGAGLPGAASAAQLAA-
+-AAAMDGPRPVTVG----QPVMPGAAATPWPEPQG-DTPAPATATPRRVRRRLRRR-TLPAAGVVLVALALVLTPWLAAA
+L------RTTVEVPAVVGLQQDEAVVALEDAGLLAVVSSAYMADAPDGTVTQSDPPTGTEVPRGAEVRIRVSRGKEGIAL
+SDSLHGLSEDAARRELERLGLRVSSVQYQDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARR
+QLALSAPELRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTASSWIAPTAEPSEPAPPYSEAPEPT-PSASASPS
+PP------PSESSEPSESAEPSPSPSASATPSPEPTTTATPSPTQSPSPTSAAPS---EP-TEQPPST-SPTATPVDPLP
+TLTPDP--EPSIDPPPST-------------------
+>GCF_005280335_PROKKA_00377
+--MEEQWTLNGRYRIDALIGRGGMADVFRGTDLRLHRPVAVKLMRRDLARDPHFQARFRKEARSVASLNHPSIVSVYDTG
+EVSLEDGHHPVDCPYLVMELVTGRSLREVLHAEGAVGTERAVAWTREVLEALEHAHQEGIVHRDVKPANVMVTDAGSVKV
+MDFGIAHALADTSATTSQTQAVVGTALYLAPEQATGRTVDGRADLYATGCVLFELLTGRPPFTGDTPLAVAYQHVREAPP
+APSEVDPDLPRAFDPVLLRALEKDPEDRFPTGAAFREALEAAAADPHAAVDADTAALDLVRAGAA--GAGGAAVAAGREV
+RRDGARDS---ADVPTA-------------AVPLTPAPAPAAPAEP--AEPPGGEPRRGRGRAARRRLRRPAGGRRLRGR
+PAPGHRLPTPPSRGPRRPAPRPPPGSALPPPLPPP--DGAAAGGAACR--------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-------------------------------------------------------------------------------S
+PG---CCWPASSC-------------------------------------------------------------------
+-------------------------------------
+>GCF_020097155_PROKKA_00359
+--MQGQRILHERYRVDELIGRGGMADVFRGHDLRLNRTVAVKMMRPDLARDPAFQARFRTEARHAAALNHPNIVSVYDTG
+DALLDDGPQSVECPYLVMEHVDGRTLRELLDA-GEVAWRDAVEWTRGLLHALDHSHRQRIVHRDVKPANVMVTRDGGVKV
+MDFGIARALSDTSAHTGQTQAVVGTALYLPPEQAQGARVDARSDLYAAGCVLFELLTGRPPFTGETPLAIAYQHVREEPP
+APSAVDPSLSTEFDSVVLRALQKDPGLRHQHAREFLSALDFAAARAARAADDDAPTRVVPASGAAPLATGSGALAAAV--
+----AGST---AAGPTASGSTALGAGGAPEARPAT----GPPATTPLGAAAGPTEPLIAGHAVAGAAVPGAPSASQLAA-
+-AEAVE-----------------TAPAAASTTGGS--AGAGATSGAERAGRRHRLSWAVLAAVAAVAAVAAILA--LGAA
+LLIGSRDPGPVTVPALAGRTEAEAVSALTGLGLRSAISPDYHSTEPDGRVLKVHPGAGAAVEPGSTVNLSVARGGEGVVL
+PTSLRGASEARVRQELARLGLNVASVEDTPSGELDRGALVQTDPVLGSRVPPGSAVVLHLADGTARVPSLVGMTGADART
+TLAALDPEMTVRFQGAAGADPDTGVVVLQDPAAGTVVDNTAMITLITSAEATPTASAVTVAPPDPALPSATTTTAPAEPS
+PG-----VPAPTT-PAAPAVDTPAPAPATTPAPAPESSSTPGAGTDPAPTESAPTPDDGPGSTGTPSTEAPTEAPTDPVG
+TPAPSPSGEPVPQPSPSVEPLPEPTAPTEAPTADPAG
+>GCF_023573625_PROKKA_00019
+--MDEQRTLNERYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRKEARSAASLNHPSIVSVYDTG
+EVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGTDRAVAWTRGVLEALEHAHEEGIVHRDVKPANVMVTDTGTVKV
+MDFGIAHALADTSATTSQTQAVVGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPP
+APSDVDPDLPPAFDPVVLRALRKNPQDRFPTGAAFLAALEEAAADPHAGPGRHPPPLDAVHPALV-----GAVLGATP--
+----AGHG---ADVPTA-------------AVPLT----RPTPSVP--AEPDTTQPQAANHAVAGAGLPGAASAAQLAA-
+-AAAMDGPRPVTAG----QPVTAGQPVTPRPEPPPGDTPAPATATPRRVRRRVRRR-TLLAAGMVLVALALVLAPWLAAA
+L------RNTVEVPAVVGLQQDEAVAALEDAGLVAVVSSAYMADAPDGAVTQSDPQTGTEVPRGAEVRIRVSRGEEGIAL
+SDSLHGLSEDAARRELERLGLRVSSVQYQDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARR
+QLALSAPELRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTASSWIAPTAEPSEPAPPSSEAPEPT-PSASAPPS
+PP------PSESPEPSESAEPSPSPSASATPSPDP-TSATPSPTQSPSPPSAAPSTSPEP-TAQSPST-SPTGTPVDPLP
+TLTPDP--EPSIDPPPST-------------------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000206.fa

@@ -0,0 +1,26 @@
+>GCF_002008305_PROKKA_00050
+MAA-----LTDRAVLIAGATSASGRAAARTLLDAGAHVVATGRDAAKLAPL-----AGLG
+AETATL--DLTDETAVRGLVEDLHARGTRIDGLLHLVGGWRGGGGLAGQTEADYRALEAS
+FTALRHVSRALDDDLRASSAGRLAIVSSTAVTRPLAGGANYAAVKAASEAWTRAVAQGWA
+KATRDAETPLRSAAVVFRVKSLAGLEERLAEEYARLWKAEAGALNDAVLTLQEKGT---
+>GCF_003691675_PROKKA_02063
+MAA-----LTDRAVLIAGATSASGRAATRTLLDAGAHVVPTGRDAAKLAPL-----AALG
+AETAAL--DLTDEAAVRGLVEDLHARGTRIDGLLHLVGGWRGGGGLTGQTEDDYRALEAS
+FTALRHVSRALDDDLRASSAGRLAIVSSTAVTRPLAGGANYAAVKAASEAWTRAVAQGWA
+KAARDAEAPLRSAAVVFRVKSLAGLEERLAEEYARLWKAEAGALNDAVLTLQEKGTD--
+>GCF_005280335_PROKKA_00353
+MGT-----LTGRTVLISGATSASGLAAARALLAAGADVVATGRSPERLAPL-----AALG
+ADTAAL--DLSDEAAVRGLVEDLHARGVRVDGLLHLVGGWRGGGGLAGQSEEDYRALESS
+LTALRHVSRALDDDLRASSAGRLAIVSSTAVARPLAGGAAYAAVKAASEAWTRAVAQGWD
+KAARDAGTELRGAAVVLRVKSLAGLEDRLAEQFVRLWSADAAQLNDSILAVQEKETA--
+>GCF_020097155_PROKKA_01218
+MSAPAAPDLTGALVLVTGASSGIGSALARGLAAAGADLVLVARRAGRLAALADELRAAHR
+TEVTVLPRDLAAPDAGPALRAELSSRGPRVTGLVNNAG---FGSGLPFGREDPARLEAMP
+AEEERGRERVLCVSPSSTGTEFFDVAGT-----PGAGGG--FARRAAPDDVAAAVLRVLA
+RRGGPAEVVPHDRAVTVAARLLPRTVLR------------------GMGAMHRRGAARR
+>GCF_023573625_PROKKA_00045
+MAA-----LTDRAVLIAGATSASGRAAARTLLDAGAHVVATGRDAAKLAPL-----AELG
+AETAAL--DLTDETAVRGLVEDLHARGTRIDGLLHLVGGWRGGGGLAGQTEEDYRALEAS
+FTALRHVSRALDDDLRASSAGRLAIVSSTAVTRPLAGGANYAAVKAASEAWTRAVAQGWA
+KAARDAEAPLRSAAVVFRVRSLAGLEERLAEEYARLWKAEAGALNDAVLTLQEKGTD--
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000238.fa

@@ -0,0 +1,50 @@
+>GCF_002008305_PROKKA_00093
+MTATAEPEVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVREVGTGFDPAQARVQATAAAG
+AHRDVPLAPLDEEDAEGTEHPELKRRIAALYASFMDDETVEARGLEPIASDLAAVATVSTPAELLALSGRLQRQGVSGLI
+NTGALNDAGNPDRMLLHLLQGGLGLPDESYYRDEAYAEILEQYTEHTGRLLALAGIGADRDEAAALGVRVVELEKRIAAL
+HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGLLEGPEAADLEDWRHWLILQV
+LRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAFVNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRS
+IEELEWMGEETRQRALEKLAMFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHITPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGRLEDWWTEEDRAAFTERTSRL
+VAQYNALSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRALEIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVT
+RIASDPHSPNEFRCNQVVKNLDAFHEAFGTREGDPMWLAPEERVTIW
+>GCF_003691675_PROKKA_02106
+MTATAEPRVPSPREDLYRHVNTGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEGAVREVGAGFDPAQARVQATAAAG
+AHRDAPLAPLDAEDTEGMEHPELKRRIAALYASFMDDETVEARGLEPIASDLAAVATVTTPAELLTLSGRLQRQGVSGLI
+NTGALNDAGNPDRMLLHLLQGGLGLPDESYYRDEAYAEILEQYTEHTGRLLTLAGIGADRDEAAALGVRVVELEKRIAAL
+HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGLLEGPEAADLEDWRHWLILQV
+LRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAFVNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRS
+IEELEWMGEETRQRALEKLAMFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHMTPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGRLEDWWTEEDRAAFTERTSRL
+VAQYNALSPVEAPDHRVNGEFTLGENIGDLGGLGIAHRALEIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVT
+RIASDPHSPNEFRCNQVVKNIDAFHEAFGTREGDPMWLAPEERVTIW
+>GCF_005280335_PROKKA_00298
+MTATAEPRVPAPREDLYRHVNAAWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVREVGAGFDPAQARVDATAAAG
+AEHHTPLEPLDAEETEGMELPEVKRRIAALYASFMDDETVEARGLEPVATDMAAVASVQTPAELLELSGRLQRQGVSGLV
+NTGALNDAGNPDRMLLHLLQGGLGLPDESYYRDEAYAEILEQYTEHAGRLLGLAGIGADSAEAAEAGVRVVELEKRIAAL
+HWDVVRSRDAVARYNLMTHEQLVELFPLAEAWLEGVDAAGERSREVVVWQPDFLSGVQALLEGPEAADLEDWRHWLILQV
+LRSFAGFLPDAFVQENFSFYGRRLAGTEEVRHRWKRAVAFVNGAAGEDVARLYVDRHFPEGHVAAMDELVNLLQEAYRRS
+IDELEWMSEETRQRALEKLSMFRPMVGRPVRWVDYSSLEVHAGDLLGNARAASEFEWERDLRKIEDGPDPEEWHITPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEKSMAANLGAIGAVIGHEIGHGFDDQGSRYDGSGRLEDWWTQEDRAAFTELTSRL
+VAQYNVLSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRALEIWRDEGDGASLDAAAGDREFFSAWAAVWRQLTRPETMVT
+RIASDPHSPNEFRCNQVVKNIDAFHEAFGTQEGDPMWLAPEERVTIW
+>GCF_020097155_PROKKA_00243
+MTATAEPRVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRRIAEDAARDA------------AMAAPA
+PEVEAPAQDEASQDPAAAERAA-RERIAVLWSAFMDEEAVEAAGILPLAADLEAVDAVASPAELLALSGRLQREGVSGLI
+GTGALNDAGDPERMLLHLIQSGLGLPDESYYREEAYAEILAQYTEHVGRLFALAGVGGDEAGAAALGERVVALEKRIAAH
+HWDVVRSRDAVARYNLLTRDQLLELLPLAPGWLEGIGAADARADEVVVWQPDFLTGVQALLEGPDAADLADWKAWLTLQV
+LRSRAGFLPDAFVQENFSFYGRRLAGTQEVRPRWKRAVAFVNGGVGEDVGRLYVARHFPEGHVAAMDQLVGLLLEAYRRS
+IDALDWMGEQTRQSALEKLAMFRPMVGFPETWRDYSALELTPGDLVGCARAVDRFEWDRDLAKIETGPDPREWHMTPQTV
+NAYYTPLENAIVFPAALLQPPFFDPERSMAANLGGIGAVIGHEIGHGFDDQGSRYDGSGRLHDWWTEQDREAFAERTGRL
+VAQYSALSPAEAPDRQVNGEFTLGENIGDLGGLGIAHQALEIWREEQDGSTEDESSGDREFFQAWAAVWRQLTRPETMVT
+RIASDPHSPNQFRCNQVVKNLDAFHTAYGTREGDPMWLAPEERVTIW
+>GCF_023573625_PROKKA_00088
+MTATAEPEVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVREVGTGFDPAQARVQATAAAG
+AHRDVPLAPLDEEDAEGTEHPELKRRIAALYASFMDDETVEARGLEPIASDLAAVATVSTPAELLALSGRLQRQGVSGLI
+NTGALNDAGNPDRMLLHLLQGGLGLPDESYYRDEAYAEILEQYTEHTGRLLALAGIGADRDEAAALGVRVVELEKRIAAL
+HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGLLEGPEAADLEDWRHWLILQV
+LRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAFVNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRS
+IEELEWMGEETRQRALEKLAMFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHITPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGRLEDWWTEEDRAAFTERTSRL
+VAQYNALSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRALEIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVT
+RIASDPHSPNEFRCNQVVKNIDAFHEAFGTREGDPMWLAPEERVTIW

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000259.fa

@@ -0,0 +1,46 @@
+>GCF_002008305_PROKKA_00117
+MSLSPDPAQQ--LLSAGALERAAGLRRMKAVALGLLILLAVVFVVAFPLQDTHPVWGYVR
+AAAEGGMVGALADWFAVTALFRHPMGVPVPHTALIPRKKDQLGAALTEFVQENFLDSEVA
+HEKVDGLKVAEAAGGWLRREENAARTAREIATAARGAMAAADDDAVQELLRQLMERHMVA
+PDWSPTLAGVLEDVVAGRHHERVVDLVVAHTGDWVAAHPELFVETVRRRSPEWSPDLVDR
+LLAERLHAETLKYLAGIRRDREHEARRAVDDWLDRLADEMRNEPATRASVERFKRNLFAD
+ERLRAWAGRAWVSLRDSLLDALEDPSSDLHRALVAALRDLGARLQEDPELRDRVDGHARR
+AAAYALSSYGPALTGVIEETVARWDGEQTARTLELFVGKDLQFIRINGSVVGALAGLAIH
+GVATLFL
+>GCF_003691675_PROKKA_02130
+MSLSPDPAQQ--LLSAGALERAAGLRRMKAVALGLLILLAVVFVVAFPLQDTHPVWGYVR
+AAAEGGMVGALADWFAVTALFRHPMGVPVPHTALIPRKKDQLGAALTEFVQENFLDSEVA
+HEKVDGLKVAEAAGGWLRREENAARTAREIATAARGAMAAADDDAVQELLRQLMERHMVA
+PDWSPTLAGVLEDVVAGRHHERVVDLVVAHTGDWVAAHPELFVETVRRRSPEWSPDLVDR
+LLAERLHAETLKYLAGIRRDRQHEARRAVDDWLDRLADEMRNEPATRASVERFKRNLFAD
+ERLRAWAGRAWVSLRDSLLDALEDPSSDLHRALVAALRDLGARLQEDPELRDRVDGHARR
+AAAYALSSYGPALTGVIEETVARWDGEQTARTLELFVGKDLQFIRINGSIVGALAGLAIH
+GVATLFL
+>GCF_005280335_PROKKA_00270
+MSLSPDPARQ--LLSAGTLERERGLRRMKAVALGLLVALAVVFAVAFPLQDVHPVWGYVR
+AAAEGGMVGALADWFAVTALFRHPMGIPVPHTALIPRKKDQLGAALTEFVQENFLDSDVA
+REKVEGLEVAAAAGGWLRRPENAERAAREVATAARGAMAAADDDAVQELLRQLMQRHMVE
+PEWSPTLAGVLQDVVTGRHHERVVDLVVEHTGDWVAAHPEMFVETVRRRSPEWSPDLVDR
+LLAERLHAEALKYLAGIRDDRDHEARRAVDDWLTRLSAEMRDDPHTRASVERFKHSLFAD
+ERLRAWAGRAWTSLRDSLLDALEDPASDLHRALVAALRDLGARLQEDPVLRDRVDGHARA
+AAAYALSTYGPAVTGVIEETVARWDGDQTARTLELFVGRDLQYIRINGSIVGALAGLTIH
+AVATLFL
+>GCF_020097155_PROKKA_00201
+MAPSPVPADSPFPLTPAALERAAGLRRMKAVALGLLIVLAVVFAVAFPLQRVHPAWGFVR
+AAAEGGMVGALADWFAVTALFRRPLGLPIPHTALIPEKKDQLGAALTEFVQENFLDSDVA
+REKVAGLQVARAAGGWLRERPHAVHAAGEIAMAARGAVAATDDDAVQDLLQQLMQRHMVE
+PDWSPTLAGVLEDVLAGRHHEKVVDLVVEHTGDWVATHPEMFLETVRRRSPEWSPDLVDR
+LLAERLHAETLKYLAGVRADRDHEARRSVDDWLARLAGNMRDDPATRASAERFKADLFAD
+EQLRAWAGRAWITLRDSLLAALEDQDSDLHRALVDALVDLGVRLQEDPALQASVDGRARA
+AASYALSSYGPALTGVIEETVARWDGRQTADTLENLVGRDLQFIRINGSVVGALAGLAIH
+TLASLVF
+>GCF_023573625_PROKKA_00122
+MSLSPDPAQQ--LLSAGALERAAGLRRMKAVALGLLILLAVVFVVAFPLQDTHPVWGYVR
+AAAEGGMVGALADWFAVTALFRHPMGVPVPHTALIPRKKDQLGAALTEFVQENFLDSEVA
+HEKVDGLKVAEAAGGWLRREENAARTAREIATAARGAMAAADDDAVQELLRQLMERHMVA
+PDWSPTLAGVLEDVVAGRHHERVVDLVVAHTGDWVAAHPELFVETVRRRSPEWSPDLVDR
+LLAERLHAETLKYLAGIRRDRQHEARRAVDDWLDRLADEMRNEPATRASVERFKRNLFAD
+ERLRAWAGRAWVSLRDSLLDALEDPSSDLHRALVAALRDLGARLQEDPELRDRVDGHARR
+AAAYALSSYGPALTGVIEETVARWDGEQTARTLELFVGKDLQFIRINGSIVGALAGLAIH
+GVATLFL
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000278.fa

@@ -0,0 +1,36 @@
+>GCF_002008305_PROKKA_00146
+MPIASPEKYAEMIDAAKNGAFAYPAINVTSSQTLNAAIRGFAEAGSDGIIQVSTGGAAYF
+SGSSVKDMVAGSLAFAAFAREVAKKHSVNIALHTDHCPQDKLEDFVLPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGRELLARTHANKQILEVEIGVVGGEEDGVAHEINEKL
+YTTVADGIATVEALGLGENGRYLTALTFGNVHGVYKPGNVKLRPEILQEIQQAVGEKFGR
+ERPFDLVFHGGSGSAAQEIADSVEYGVVKMNVDTDTQYAFTRPVAGHMFENYDGVLKVDG
+EVGDKKQYDPRVWGAKAEEAMAARVVQACTELNSAGKSIG
+>GCF_003691675_PROKKA_02160
+MPIASPEKYAEMIDAAKNGAFAYPAINVTSSQTLNAAIRGFAEAGSDGIIQVSTGGAAYF
+SGSSVKDMVAGSLAFAAFAREVAKKYSVNIALHTDHCPQDKLEGFVLPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGRELLARTHANKQILEVEIGVVGGEEDGVAHEINEKL
+YTTVADGIATVEALGLGEHGRYLTALTFGNVHGVYKPGNVKLRPEILQEIQQAVGEKFGK
+ERPFDLVFHGGSGSAAQEIADSVEYGVVKMNVDTDTQYAFTRPVAGHMFENYDGVLKVDG
+EVGDKKQYDPRVWGAKAEEAMAARVVQACTELNSAGKSIG
+>GCF_005280335_PROKKA_00238
+MPIASPDKYAEMIDAAKNGAFAYPAINVTSSQTLNAAIRGFAEAGSDGIIQVSTGGAAYF
+SGASVKDMVTGSLAMAAFAREVAKNYSVNIALHTDHCPKDKLDAFVMPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGKELLARTHANKQILEVEIGVVGGEEDGVAHEINDKL
+YTTVEDGIATIEALGLGEQGRYLTALTFGNVHGVYKPGNVKLRPQILEDIQKAVGEKFGK
+ERPFDLVFHGGSGSAAQEIADSVSYGVVKMNVDTDTQYAFSRPVAGHMFENYAGVLKVDG
+EVGDKKMYDPRVWGAKAEEAMAARVVQACQELNSAGTSIG
+>GCF_020097155_PROKKA_00173
+MPIASPDKYAEMIDAAKNGAFAYPAINVTSSQTLNAAVRGFAEAGSDGIIQVSTGGAAYF
+SGSSVKDMVAGSLAMAAFAREVAKKYSVNIALHTDHCPKDKLDGFVKPLLDASEAEVKAG
+RDPLFNSHMWDGSAETLEENLRIAQELLARTHANKQILEVEIGVVGGEEDGVANEINDKL
+YTTVEDGIATIEALGLGENGRYLTALTFGNVHGVYKPGGVKLRPQILQDIQQAVGEKFGR
+QRPFDLVFHGGSGSAAQEIADSVSYGVVKMNVDTDTQYAFSRPVAGHMFENYDGVLKVDG
+EVGNKKMYDPRVWGAKAEDGMAARVVQACQELNAAGKSIG
+>GCF_023573625_PROKKA_00154
+MPIASPEKYAEMIDAAKNGAFAFPAINVTSSQTLNAAIRGFAEAGSDGIVQVSTGGAAYF
+SGSSVKDMVAGSLAFAAFAREVAKKYSVNIALHTDHCPQDKLEGFVLPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGRELLARTHANKQILEVEIGVVGGEEDGVAHEINEKL
+YTTVQDGIATVEALGLGEHGRYLTALTFGNVHGVYKPGNVKLRPEILQEIQQAVGEKFGK
+ERPFDLVFHGGSGSAAQEIADSVEYGVVKMNVDTDTQYAFTRPVAGHMFENYDGVLKVDG
+EVGDKKQYDPRVWGAKAEEAMAARVVQACTELNSAGKSIG
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000285.fa

@@ -0,0 +1,26 @@
+>GCF_002008305_PROKKA_00154
+MATPLLELAASRGVCFPLRARRLTLTPFRGLDAPAVWSFCRLEQVWSWTSGRPESENALR
+ESYLGAGDRLTVR--AGDVIVGVGKVAVQDAWSQDGPQEEARDAQAELGWTIDPRQAGQG
+YGTELARALLGFAFDDLGVRRVEAHAFADNAPSLRIMEKVGMRHEGTFKEESLHLTRGWV
+DGATYAMLASEFHSPL--TQE
+>GCF_003691675_PROKKA_02168
+MATPLLELAASRGVCFPLRTRRLTLTPFRGLDAPAVWSFCRLEQVWSWTSGRPESENALR
+ESYLGAGDRLTVR--AGDVIVGVGKVAVRDAWSQGGPREEGRDAQAEIGWTIDPRQAGQG
+YGTELARALLGFAFDDLGVRRVEAHAFADNAPSLRIMEKVGMRHEGTFKEESLHLTRGWV
+DGATYAMLASEFHSPL--TQE
+>GCF_005280335_PROKKA_00470
+MATPLLDLAARRGVVFPLRTERLTLTSFAADDAPAVFDFCRLEEVWTWTSGRAGSAGELR
+ESYLAAGDRLTVR--AGEAIIGVGKLAVQDAWSQGGPREEARDAQAEIGWTIHPTHADQG
+YATELAGALLKLAFTGLGVHRVEAEAFADNAPTLRVMEKVGLRHEGTFREESLHLTRGWV
+DGVTYAMLASEFLARV-----
+>GCF_020097155_PROKKA_00420
+MATPLLDLAARRGVAFPLRTERLTLTPFTAVDAPAVWDFCRLEEVRTWTSGRAGSAAELR
+EEYLATGDRLTVRDGAGDV-VGVGKLAVQDAWSQGGPHPDARDAQAELGWTVAPEHAGRG
+YATEIGRALLDLAFRGLGVRRVEAGAFADNAPSLRVMAKIGLRHEGTFLGESLHLTRGWI
+DGVTFALLASEYEGGAAASRA
+>GCF_023573625_PROKKA_00167
+MAPPLLELAASRGVCFPLRARRLTLTPFRGLDAPAVWGFCRLEQVWSWTSGRPESEGALR
+ESYLAAGDRLTVR--VGDVIVGVGKAAVQDAWSQGGPREEARDAQAEIGWTIDPRQAGQG
+YGTELARALLGFAFNDLGVRRVEAHAFADNAPSLRIMEKVGMRHEGTFKEESLHLTRGWV
+DGATYAMLASEFHSPL--TQE
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000301.fa

@@ -0,0 +1,21 @@
+>GCF_002008305_PROKKA_00196
+MPDDVAVRLLLIADTHIPRRARALPAQVWAEVARADVVLHAGDWVTEDVLDDLDARAARL
+VGVWGNNDGPKLRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS
+HIPWDTVAGPDTANPGLRLLNPGSCTDRRRQPVCTLMRAVVRGGRLEDVELVSVDRTP
+>GCF_003691675_PROKKA_02192
+MPDDVAVRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDARAARL
+VGVWGNNDGPGPRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS
+HIPWDTVAGPETANPGLRLLNPGSCTDRRRQPVCTLIRAVARDGRLEDVELVPVDRTP
+>GCF_005280335_PROKKA_00203
+MT--TETRLLLLADTHIPPRARAMPAQVWDEVARADVVLHAGDWVEESVLDELEARSRRL
+VGVWGNNDDGALRARLPEVARVEIGGVRIAMVHETGAARGRERRMAEAFPDADVLVFGHS
+HIPWDTVAGPETANPGLRLLNPGSPTDRRRQPVCTLMRAVVRDGGLADVELVPVDRTP
+>GCF_020097155_PROKKA_00151
+----MTTRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDAQAARL
+VGVWGNNDGPRLRARLPEVARVEIGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS
+HIPWDTVAGPETANPGLRLLNPGSCTDRRRQPVCTLMRAVVRGGRLEDVELVPVDRTP
+>GCF_023573625_PROKKA_00196
+MPDDVAVRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDARAARL
+VGVWGNNDGPGPRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS
+HIPWDTVAGPETANPGLRLLNPGSCTDRRRQPVCTLIRAVARDGRLEDVELVPVDRTP
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000356.fa

@@ -0,0 +1,55 @@
+>GCF_002008305_PROKKA_00284
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------------------------------------MADPFPKDPEGAVVALVLAG
+GTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLRDVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQG
+RAEEGFARGNGHAIAQQLPLLEQFGAETVVVLSADHLYQLDLRPVLAEHARSGAELTVVTTETDEDPSRFGVVQVDDDGA
+VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSSLGDYGESIIPAFVARGRVRE
+HRLVGYWRDIGTLDAYVRAHREILDGTGLDLAAEGWPLITNPHQAPPAWVAPDARVSGSLLSPGCRIAGEVSDSVVGPGV
+VVAAGATVRGSLLLGDCEVPAGAVLDTVVVDVGGAVPAREVTGRAAPA-EEVVVLTPQDRGPA-EDETTGSGRPGRSD
+>GCF_003691675_PROKKA_02306
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------------------------------------MADPFPTDPEGAVVALVLAG
+GTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLRDVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQG
+RAEEGFARGNGHAIAQQLPLLEQFGAETVVVLSADHLYQLDLRPVLAEHARSGAELTVVTTETDEDPSRFGVVQVDDDGA
+VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSSLGDYGESIIPAFVARGRVRE
+HRLVGYWRDIGTLDAYVRAHREILDGTGLDVAAEGWPLLTNPHAAPPAWVAPEATVTGSLLSPGCRIAGEVTDSVVGPSV
+VVEAGAVVRGSILLGECTVPSGAVLDTVIADVGAAIPAEGATGRAEPA-DEVVVLEPGERGPASSDETTGSGAPVRD-
+>GCF_005280335_PROKKA_00069
+MPEGDSLVRLAHRLRPVLAGRALTHADLRVPQHATADLTGWTVVEVEPRGKYLLMRLTPPAGRPAARPLTLVSHLKMEGR
+WLVSALDARWGAPAWQVRAVLETADHRVLGAQLGMLTLVPTDREDTVLGHLGPDLLDPAWDGSEEAAAALLAEGTRRLTA
+RPERPVGLALLDQRTTCGIGNIYRCESLLLAGIDPHRPVGAVPDVPGLLTIARDLLRANVPPAAPFLGWPRTTTGVRANP
+DRPYGIEVVVADRGFPPGLPAAVGSGTAADPAADPGADRTASGPALGRPPARPPADPGAAGRRRTGCTGTTAPPACAAAG
+ACARRTSAPPRTTRGSCGGARPASGEPRPNRGPGGGAPYAERRPSPQGRSARPPTPRRTRVADPFPDDPRSAVVALILAG
+GRGSRLAPLTDARSKPAVPFAGQYRLIDVALTTVAHSGLQDAWIVEQYRPFTLNQHVAGGRPWDLDGTRHGLRVLPPAQG
+RDEEGFAQGNGHAIHQQLAPLRRFGAKTVVIMSADHLYRMDLRPVLERHRERDAELTVVTTQVAEGASRFGVVSSDADGR
+VTAYDYKPDEPATDVVATEVFVADVDALTEVIESLLDSASE-------EQVDDDDPAGAQLGDYGETIIPALVERGRVHE
+FRHEGYWKDVGTIDAYYQAHMALLRGDGLDLDDPRWPLISNFHPRPPAFIHPEAEVNGSMLCPGSRVRGTVTESVIGPGV
+VVEAGATVHRSVLLGSATVPAGARLDAVIADVGARIP-EGATGQTKPGPGNITVLTPDDRSTAEGDETTGHA------
+>GCF_020097155_PROKKA_00049
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------------------------------------MADPFPKDPAGSTVALVLAG
+GRGSRLDPLTAARSKPAVPFAGQYRLIDVVLSNLAHSGLKDVWIAEQYRPFTLNQHLAGGRPWDLDGTRHGLRILPPAEG
+REEEGFSAGNGHALAQQVPILRSFGAERVVVLSADHLYQLDLRPVLAAHADSGAELTMVTTVTDEDPSRFGVVQADEDGA
+VTAYDYKPEDPEGRLVATEVFVFDVAALHEVVAELVAREKAAGEHADGEEDEDGDPVASSLGDYGETIIPAFVERGRVRE
+HRLEGYWRDIGTLDAFYRAHMELLDGAGLDLAAPGWPLLTNPPAAPPARVGPRAEVSNALLSPGCVVKGTVEDSVLGPGV
+VVERGAHVRRSVLFGECIVPRGARLDAVIADVGAHIPAE-EVGRSRPGPGNLTVLTPATRDPDSEDETTGGA-AAKDG
+>GCF_023573625_PROKKA_00290
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------------------------------------MADPFPKDPEGAVVALVLAG
+GTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLRDVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQG
+RAEEGFARGNGHAIAQQLPLLEQFGAETVVVLSADHLYQLDLRPVLAEHTRSGAELTVVTTETDEDPSRFGVVQVDDDGA
+VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSSLGDYGESIIPAFVARGRVRE
+HRLVGYWRDIGTLDAYVRAHREILDGTGLDVAAEGWPLLTNPHAAPPAWVAPEATVTGSLLSPGCRIAGEVTDSVVGPSV
+VVEAGAVVRGSILLGECTVPSGAVLDTVIADVGAAIPAEGATGRAEPA-DEVVVLEPGERGPASSDETTGSGAPVRD-

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000371.fa

@@ -0,0 +1,65 @@
+>GCF_002008305_PROKKA_00307
+MTPLPRFAARTAVTTAALALLAPAV-ALPSQASPAGDSLVINEAYTNGGSANAVYTHKFVELYNPTDQPINLDGWSLQYR
+SAAGTAATQGTVALSGTVPAKGHFLVSGGSNGTAGAALPQADLVAGGAFNPAGTKGTIVLARQAGTVTDLPVGSVVTGQV
+PGVADVLGYGATNTFETAAAGAPSANSDPKSLTRTNGVDTDDNSADFTVTGQVTPTNAAA--TGG-EPTPEPEPQPTPSE
+RITIAQLQGTGTATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGDTPDATPGASDGVFVYSPDTVGSVTLGDHVQV
+TGEAAEHYGLTQIKVAADGVLPVAEPGA-VAPTPVEFPLEEADREALEGMVLAPQGDWTVTDNYSLNQYGSLGVVPGTKP
+LDNPTSVARPGAEAQAVAAANAQQLIVLDDGASTNFMRSPGNQNPLPYLDADQPVRVGAGLEFSTGVILDWRFDAWSFQP
+LGHLTDATAAAVQPVTIEDTRPAEAAPEAVGGNVTVGSFNVLNYFTTLGQDVAGCGAYRDRAGTPVTTNGCLPRGAYTPE
+AFARQQEKIAAAINGLGTSVVALEEIENSEKFGLDRDHALAHLVEALNAQAGEQRWAYVASPSARPALADEDVIRSAFIY
+QPAEVTPLGESVILDDQTNFDNAREPMAQLFRAADGTAEGAAGTEFVAITNHFKSKGGSGATGDNVDAGDGQGAYNADRV
+GQAEALVAFAERMKAETGTDRVLLMGDFNAYEKEDPIRVLEAAGYVSQGALTGEYSYAFGGAVGSLDGIYASPSAAAAIT
+GQDIWMINANESVALEYSRHNYVAEDLYSADQWRSSDHNPILVGLQLDAPVTEPTPEPEPEPT-PGETCDGVTDPRGVPG
+KPANSVREWLRCIGATPGHGGDHPGKGHGGD----HPGKGRGP--VRP
+>GCF_003691675_PROKKA_00022
+MTPLPRFAARTAVTTAALALLAPAV-ALPSQASPAGDSLVINEAYTNGGSANAVYTHKFVELYNPTDQPINLDGWSLQYR
+SAAGTAATQGTVALSGTVPAKGHFLVSGGSNGTAGAALPQADLVAGGAFNPAGTKGTIVLARQAGTVTDLPVGSVVTGQV
+PGVADVLGYGATNTFETAAAGAPSANSDPKSLTRTNGVDTDDNSADFTVTDQVTPTNAAA--TGG-EPTPEPEPQPTPAE
+RITIAQLQGTGTATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGDTPDATPGASDGVFVYSPDTVGSVTLGDHVQV
+TGEAAEHYGLTQIKVAAGGVLPVAEPGA-VAPTPVEFPLEEADREALEGMVLAPQGDWTVTDNYSLNQYGSLGIVPGTTP
+LDNPTSVARPGAEAQAVAAANAQQLIVLDDGATTNFMRSPGNQNPLPYLDADQPVRVGAGLEFTTGVILDWRFDAWSFQP
+LGHLTDATAAAVQPVTIEDTRPAEAAPEAVGGNVTVGSFNVLNYFTTLGQDVAGCSAYRDRAGTPVTTNGCLPRGAYTSE
+AFARQQEKIAAAINGLGTSVVALEEIENSEKFGLDRDHALAHLVEALNAQAGEQRWAYVASPATRPALADEDVIRSAFIY
+QPAEVTPVGESVILDDQTNFDNAREPMAQLFRAADGTSEGAAGTDFVAITNHFKSKGGSGATGDNVDAGDGQGAYNADRV
+GQAEALVAFAERMKAETGTDRVLLMGDFNAYEKEDPIRVLEAAGYLSQGALTGEYSYAFGGAVGSLDGIYASPSAATAIT
+GQDIWMINANESVALEYSRHNYVAEDLYSADQWRSSDHNPILVGLQLDAPVTEPT--PEPEPS-PGETCDGVTDPRGVPG
+KPANSVREWLRCVGATPGHGGDHPGKGHGPE----HPGKGRGP--VRP
+>GCF_005280335_PROKKA_00030
+MTQRTFRLSRPAVALAALTLLAPAVVAGPAHAAPTGDGLVINEVYTNGGSANAVFTHKFVELYNPTDTPISLDGWSLQYR
+SATGTAAPNGVVALSGTVPAKGHFLIQGGSNGTTGAALPRPDLNAGGAFNPAGARGTVVLSDQAGALTALPVGSVTTGQA
+EGVADLLGYGTSNTFETAAAGAPSSNSDPKSLTRTDGVDTDDNAADFTVTAQVTPTSSTG--EAPVDPIPDPEPDPEPAP
+ALTIAQIQGDGAATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGSAEDATPGASDGLFVYSPDTVGSVALGDHVQV
+TGEAAEHYGLTQVRVGAAGVTPVAEPAA-VAPTAVDFPLSEADREALEGMLLAPTGEWTVTDNYDLNQYGSLGIVPGTEP
+LPNPTSVAAPGAEAQAVAADNASRLIVLDDGASTNFMRSPGNENPLPYLDADRPVRVGAGLDFTTGVILDYRFDAWSFQP
+LGHLTDATAAAVQPVAVEDTRPEEASPEAVGGNVSVGSFNVLNYFTALGQDFPGCRAYTDRFGEPVTTNGCLPRGAYTPE
+AFARQQEKIAAAIDGLDASVVALEEIENSAKFDLDRDRALAHLVDALNAQAGEQKWAYVASPADRPALSEEDVIRNAFVY
+QPAEVTPVGESVILRDEVNFDNAREPLAQHFRAADGTEAGVAGTDFVAVTNHFKSKGGSGAAGDNADSGDGQGAYNGDRT
+RQAQALVAFAEQVADDAGTDRVLLLGDFNAYEKEDPIRVLEEAGYVSQGALTGEYSYTFDGAVGSLDGVYASPAASAVVT
+GQDIWMINANESVALEYSRHDYVAEDLYAPDQWRSSDHNPLLVGLQLDAPVVEPEPQPGA----------------GHPG
+K------------GKGLDKGAGHPGKGKGLDKGAGHPGHGRVPEAARP
+>GCF_020097155_PROKKA_00026
+MPTPRLRLVRTAATLAAATLLAPAVLALPAQASPAGDSLVINEAYTNGGSAGALFTHKFVELYNPTDQPISLDGWSLQYR
+SATGTTAPSTTVALSGTVPAKGHFLIQGGSNGATGAALPTPDLTT--SFNPAGTKGTIVLADQAGTVAGLPTGSVVTDQV
+AGVADVLGYGATNTFETAASGAPAANSDPKSIARTGGADTDDNAADFTVAADVTPQNAAGGGTAPVDPVDPVDPTPAPAP
+SVTVAEIQGTGATSPLEGRRVSTTGVVTAVYSTGGYDGFYIQTAGTGG-AEDATPGASDGVFVYAPAEVGSVTLGQTVTV
+TGDVAEYYGLTQVKAEAGGVRQAAEAGAPVTARELAFPLTEAEKEAHEGELLAPAGAWTVTDNYDVNQYGSLGLAPGTSP
+LPNPTSVALPGADAQAVAADNAQRLIVLDDGASTNFFRSPGNQNALPYIDADAPARVGSAVDFRTPVILDYRYGAWSFQP
+LGHLTDANKAEVQPVDIADTRPAEAVREDLGGNVTVGSFNVLNYFTTLGEDVPGCGYYADKDGAPVSTKGCLPRGAYTEE
+AFLEQQAKIATAINGMDTSVVALEEIENSEKFGLDRDHALAHLVDALNAQAGYAKWAYVASPTVRPALADEDVIRSAFIY
+QPAEVTPVGESVILDDQVNFANAREPMAQAFRVADGSAGGVVGTEFVAITNHFKSKGGSGATGDNVDTGDGQGAYNGDRT
+RMAQALVAFAEQMKVQAGTDRVLLMGDFNSYEKEDPIRVLEAAGYISQGAKTGEYSYTFDGAVGSLDGIYASPAADATVT
+GQDIWMINANESVAFEYSRDNYVGEEFYAPDQWRSSDHNPVLVGLQLDAPAAPVVPTPGTRPTPPADQCALITSPRGAKA
+SAGFSASEWMRCAGV--------------------HPGKGRG----RG
+>GCF_023573625_PROKKA_00314
+MTPLPRFAARTAVTTAALALLAPAV-ALPSQASPAGDSLVINEAYTNGGSANAVYTHKFVELYNPTDQPINLDGWSLQYR
+SAAGTAATQGTVALSGTVPAKGHFLVSGGSNGTAGAALPQADLVAGGAFNPAGTKGTIVLARQAGTVTDLPVGSVVTGQV
+PGVADVLGYGATNTFETAAAGAPSANSDPKSLTRTNGVDTDDNSADFTVTDQVTPTNAAA--TGG-EPTPEPEPQPTPAE
+RITIAQLQGTGTATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGDTPDATPGASDGVFVYSPDTVGSVTLGDHVQV
+TGEAAEHYGLTQIKVAAGGVLPVAEPGA-VAPTPVEFPLEEADREALEGMVLAPQGDWTVTDNYSLNQYGSLGIVPGTTP
+LDNPTSVARPGAEAQAVAAANAQQLIVLDDGATTNFMRSPGNQNPLPYLDADQPVRVGAGLEFTTGVILDWRFDAWSFQP
+LGHLTDATAAAVQPVTIEDTRPAEAAPEAVGGNVTVGSFNVLNYFTTLGQDVAGCSAYRDRAGNPVTTNGCLPRGAYTSE
+AFARQQEKIAAAINGLGTSVVALEEIENSEKFGLDRDHALAHLVEALNAQAGEQRWAYVASPATRPALADEDVIRSAFIY
+QPAEVTPVGESVILDDQTNFDNAREPMAQLFRAADGTSEGAAGTDFVAITNHFKSKGGSGATGDNVDAGDGQGAYNADRV
+GQAEALVAFAERMKAETGTDRVLLMGDFNAYEKEDPIRVLEAAGYLSQGALTGEYSYAFGGAVGSLDGIYASPSAATAIT
+GQDIWMINANESVALEYSRHNYVAEDLYSADQWRSSDHNPILVGLQLDAPVTEPT--PEPEPS-PGETCDGVTDPRGVPG
+KPANSVREWLRCVGATPGHGGDHPGKGHGPE----HPGKGRGP--VRP

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000374.fa

@@ -0,0 +1,31 @@
+>GCF_002008305_PROKKA_00313
+MSLP--HAPRTPAPPAAASSAVPLRLAVVDMSGTSIVEHGLQDTAFARSLDQHGVPAGTP
+EHDDAARRFRALRPTSRTAVFPRVFADRAVAAAATRTFEATFDALLAEHGVRAVPGAEEA
+LIRLRALGLHVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMILTALLG
+LDLEDVRSVLVVGDTAEDMTAGRRAGAGLVVGVRTGRDADHVLLAAGSDRVVPGLADVPD
+LVVRTR-
+>GCF_003691675_PROKKA_00028
+MSLP--HAPRTPAPPAAASSAAPLRLAVVDMSGTSIVEHGLQDTAFARTLDQHGVPAGTP
+EHDDAARRFRALRPTSRTAVFPRVFADRAVAAAATRTFEAAFDALLAEHGVQAVPGAEEA
+LVRLRALGLHVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMILTALLG
+LDLDDVRSVLVVGDTAEDMTAGRRAGAGLVVGVRTGRDADDVLLAAGADRVVPGLADVPD
+LVVRTR-
+>GCF_005280335_PROKKA_00024
+MSLPPRPPPRGRAPRADGPPAPPLRLAVVDMSGTSIVERGLQDAAFAHALETHGLAADAP
+AHADAVRVFRARRATSRTAVFAQVFPDRPAAAAAARTFEEAFDSLLAEHGVQPVPGAEEA
+LLRLRALGLRVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPFPDMILTALLG
+LDLDDVRGVLVVGDTAEDMTAGRRAGAGLVAGVRTGRDADAALLAAGAHHVVDGLADVPA
+LVGAGG-
+>GCF_020097155_PROKKA_00020
+MSLS------TAVPALSVGTPVPLRLAVVDMSGTSVVEGGLQDRAFAEVVAARGLAEGSP
+EHERAARLFRERRGTSRTAVFQALFEGRTAALEATRAFEAAFDRLLAEHGVTAVPGAEGA
+LVRLREAGLDLCLITGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMVLTALLA
+LDHDDVRSVLTVGDTAADILAGRRAGAGLVVGVRSGQDTGGVLAGAGADQVVDSLAQVPD
+LVATLRG
+>GCF_023573625_PROKKA_00320
+MSLP--HAPRTPAPPAAASSAVPLRLAVVDMSGTSIVEHGLQDTAFARTLDQHGVPAGTP
+EHDDAARRFRALRPTSRTAVFPRVFADRAVAAAATRTFEATFDALLGQHGVQAVPGAEEA
+LVRLRALGLHVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMILTALLG
+LDLDDVRSVLVVGDTAEDMTAGRRAGAGLVVGVRTGRDADDVLLAAGADRVVPGLADVPD
+LVVRTR-
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000397.fa

@@ -0,0 +1,60 @@
+>GCF_002008305_PROKKA_00344
+MSTSTVRSAPASTYRLQVSPDLPLESVAGLVPYLRRLGVDWLYLSPLLEAEPGSDHGYDVVDPTRLDAARGGAEGLDAVA
+RAAHEAGMGVLVDIVPNHVGVATPQANPAWWDVLTHGPEAAHAAWFDVDWAAGGGSLLIPVLGDGPDGD---ADAELNRL
+VVD-E----GRLRYWDNVYPLAPGSLEAAEAETGLRAAEVFAEADPAKESTAERARLARAVHDRQHYRLVGWRRGDAELN
+YRRFFTVTTLAGVRVDEPEVFDAVHAEPARWVREGLVDGLRVDHPDGLADPAGYARRLRSHVLPEGYLVVEKILEPGEAL
+PADWPVDGTTGYDALGEVERVFMHPEAAGDAAEDARRRREWDEAVVRAKHDVATGSLAAETARLVREVRAVHALGAHPDE
+DVAAAFAAVLARLPVYRTYLPVGLAVLEGALADAAEAEPALAAVLGDLRPELTDPDSPVARRFQQTSGMVMAKGVEDRSF
+YRYTRWANLNEVGGDPSHVALSLADFHAAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEPDRWAAELAELRRLH
+PLGHPDAERLLWESIVGVWPTDGTAPEEERILGFLQKASREAALATSWTDQDPEFEARLAALAAAVTSPEGPARGVLQAV
+ADRIAEPGLVVQLGHKLVQLAAPGVPDVYQGTEVPFPTLVDPDNRRPVDFAARADLLDRLDAGHTPGLDDPAAAKLAVVA
+AVLRTRRDRPELFTGHRPLDVSGPAAEHAIAFDRGGALAVATRWPVRLAAAGGWGETVVTVPAGRWEDAVTGHPVHPDAR
+GAVRLDELLSTLPVALLVPAHAPSDRRERTAP
+>GCF_003691675_PROKKA_00060
+MSTSTVRSAPASTYRLQVSPDLPLESVAGLVPYLRRLGVDWLYLSPLLEAEPGSDHGYDVVDPTRLDAARGGAEGLDMVA
+RAAHEAGMGVLVDIVPNHVGVATPRANPAWWDVLTHGPEAAHAAWFDVDWAAGGGSLLIPVLGDGPDGD---ADAELNRL
+VVD-E----GRLRYWDNVYPLAPGSLEAAEAETGLRAAEVFAEADPASEPTAEQARLARAVHERQHYRLVGWRRGDAELN
+YRRFFTVTTLAGVRVDEPEVFDAVHAEPARWVREGLVDGLRVDHPDGLADPAGYARRLRSHVLPEGYLVVEKILEPGEAL
+PADWPVDGTTGYDALGEVERVFMHPEAAGDAAEDARRRREWDEAVVRAKHDVATGSLAAETARLVREVRAVHALGAHPDE
+DVAAAFAAVLARLPVYRTYLPVGLAVLEGALADAAAAEPGLADVLGDLRPELTDPDSPVARRFQQTSGMVMAKGVEDRSF
+YRYTRWANLNEVGGDPSHVALSLADFHSAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEPDRWAAELAELRRLH
+PLGHPDAERLLWESIVGVWPTDGTAPEEERILGFLQKASREAALATSWTEQDPEFEARLAALAAAVTSPEGPARGVLQAV
+ADRLAEPGLVVQLGHKLVQLAAPGVPDVYQGTEVPFPTLVDPDNRRPVDFAARADLLDRLDAGHTPGLDDPAAAKLAVVA
+AVLRARRDRPELFTGHRPLDVSGPAAEHAIAFDRGGALAVATRWPVRLAAAGGWGETVVTVPAGRWEDAVTGHPVHPDAR
+GAVRLDELLSTLPVALLVPAHAPSDRRERTAP
+>GCF_005280335_PROKKA_02625
+MSTSTERPVPSSTYRLQVGPDLPLESVAGLVPYLRRLGVGWLYLSPILEAEPGSDHGYDVVDPTRLDAARGGAEGLEAVA
+RAAREAGLGVLVDIVPNHVGVATPEANPAWWDLLAHGSEAAHAPWFDVDWTAGEGRVLLPVLGDGPDGE---AEAELDRL
+VVE-TGDDGGRLRHWDTRYPLAPGSLAAAEEETGLRAADVFAGAEPAHEPTPERARLARAVHARQHYRLIGWRRGDAELN
+YRRFFTVTTLAGVRVEDPEVFDAVHAEPARWVREGLVQGLRVDHPDGLADPAGYVRRLRSHVLPEGYLVVEKILEPGEEL
+PADWDVDGTTGYDALGEVERVFMHPVAAGGPNEDERRRRDWDEVVAEAKRDVATGSLVAETARLVREVRGVHALGAHADE
+DVAAAFAAVLSRLPVYRTYLPVGLAVLERALADAGEAEPALAPVLADLGPELADPDSPVARRFQQTSGMVMAKGVEDRSF
+YRWTRWANLNEVGGDPAHVQLSLDAFHAAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEPDRWAGELAGLRALH
+PLGDEGAERLLWESIVGVWPTDGTAPSTERILGFLQKASREAALSTTWTDQDPEFEGRLEDLARAVTAPDSPARGAVQAV
+ADRIAEPGLVVQLGHKLVQLAAPGVPDVYQGTELPVPSLVDPDNRRPVDFHARADLLDRLDAGHVPGLDDADAAKLAVVA
+AVLRARRDRPELFTRHRRLDVSGPAAEHAVAFDRGGALAVATRWPVHLAAAGGWGETVVTLPPGRWEDAVTGRPVHPDAR
+GAVRLDELLSTLPVALLVPARA-----EEATP
+>GCF_020097155_PROKKA_02477
+MSHTDAVSAPASTYRLQVGPDLPLDSVAGLVPYLRRLGVDWLYLSPILAADPGSDHGYDVVDPARVDPARGGPEALAALA
+AAAHEAGMRLLVDVVPNHLGVATPLANPAWADLLAHGPEAAHAAWFDVDWEAGDGRVLLPVLGDGPEGDPRGAEAGLDQL
+IVDPSAGEHGVLRHWDTAYPLAPGSLAAAEEETGLRAAEVFAGADPAA-PTDDAARLGRAVHDRQHYRLVHWRRGDAELN
+YRRFFTVTTLAGLRVEDPEVFDATHVEIGRWVSEGLVHGLRIDHPDGLTDPGAYLRALRERVLPEGYLVVEKILEPGEDL
+PAAWPVDGTTGYDALGELERVFMPADPDGPAADDA-ARAAWEALIAEAKRDVATGSLAAETARLVREARAAVVLGAHSDE
+ALTEAFADVLASLDVYRTYLPVGAERLAAAVARARAAHPEPADVLDDVARVLADPDSPVARRFQQTSGMVMAKGVEDRSF
+YRWTRWANLNEVGGDPAHLDLPLAGFHALQRARQASWPTTMTALTTHDTKRSEDVRARITALAEEPASWEDALARLRTAH
+PLDAPGLEELVWESIVGVWPTDGTAPEADRLEEFLLKSAREGQEHTSWTAQDDAYEGRLRALAADVVAPDSAARAVVQEI
+ADRIAEPGLTVQLGRKLVQLAAPGVPDVYQGTEIPFPTLVDPDNRRAVDFEARADLLDRLDAGHAPTLDEPEAAKLLVVS
+RALRARRDRPELFHGYRPLDVDGPAAAHLIAFSRGGALALATRLPLTLAAAGGWRETVVSLPPGRWRCAVTGRAVTPDAR
+GAVRVDDVLSQLPVALLLPEEETA--------
+>GCF_023573625_PROKKA_00351
+MSTSTVRSAPASTYRLQVSPDLPLESVAGLVPYLRRLGVDWLYLSPLLEAEPGSDHGYDVVDPTRLDAARGGAEGLDMVA
+RAAHEAGMGVLVDIVPNHVGVATPPANPAWWDVLTHGPEAAHAAWFDVDWAAGDGSLLIPVLGDGPDGN---ADAELDRL
+VVD-A--EGGRLRYWDNVYPLAPGSLEAAETETGLRAAEVFAAADSAKEPTAEQARLARAVHDRQHYRLVGWRRGDAELN
+YRRFFTVTTLAGVRVEEPEVFDAVHAEPARWVREGLVDGLRVDHPDGLADPAGYARRLRSHVLPEGYLVVEKILEPGETL
+PADWPVDGTTGYDALGEVERVFMHPEAAGDAAEDARRRREWDEAVVRAKHDVATGPLAAETARLVREVRAVHALGAHPDE
+DVAAAFAAVLARLPVYRTYLPVGLAVLEGALADAAEAEPGLADVLGDLRPELTDPDSPVARRFQQTSGMVMAKGVEDRSF
+YRYTRWANLNEVGGDPSHVALSLADFHAAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEPDRWAAELAELRRLH
+PLGHPDAERLLWESIVGVWPTDGTTPEEERILGFLQKASREAALATTWTDQDPEFEARLAALAAAVTSPEGPARGVLQAV
+ADRIAEPGLVVQLGHKLVQLAAPGVPDVYQGTEVPFPTLVDPDNRRPVDFAARADLLDRLDAGHTPGLDDPAAAKLAVVA
+GVLRARRDRPELFTGHRPLDVSGPAAEHAIAFDRGGALAVATRWPVRLAAAGGWGQTVVTVPAGRWEDAVTGHPVHPDAR
+GAVRLDELLSTLPVALLVPAHAPSDRRERTAP

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000402.fa

@@ -0,0 +1,26 @@
+>GCF_002008305_PROKKA_00352
+MEFIAPLDPGWEAALAPQAAAFEQVGERLRARRAGGEQVLPAPEHILRAFRQSFADVRVL
+VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLANIHRELHDDLGITPPAHGDLSAWTDQGV
+LLLNRALSVRAGAPGSHRGLGWEQITEAAVRALCARGTPLVGLLWGADARRMAPLLTAAG
+AGVVESPHPSPLSAHRGFFGSRPFSRVNRLLEAAGAAPVDWRLPD
+>GCF_003691675_PROKKA_00068
+MEFIAPLDPGWEAALAPQAAAFEQVGEALRARRAAGEQVLPAPEHILRAFRQPFADVRVL
+VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLANIHRELHDDLGITPPAHGDLSAWTDQGV
+LLLNRALSVRAGAPGSHRGLGWEQITEAAVRALCARGTPLVGLLWGADARRMAPLLAAAG
+AGVVESPHPSPLSAHRGFFGSRPFSRVNRLLEAAGAAPVDWRLPD
+>GCF_005280335_PROKKA_02609
+MELIAPLDPGWEAALAPQAAALEQVGAALTQRRAAGEQVLPAPEHILRVFRRPFEDVRVL
+VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLVNIHRELQDDLGIAPPAHGDLSAWADQGV
+MLLNRALTVRAGAPGSHRGLGWEQITEAAVRALCERGTPLVGLLWGADARRMAPLLTQAG
+AGVVESPHPSPLSAHRGFLGSRPFSRVNRLLEEAGAEPVDWRLPD
+>GCF_020097155_PROKKA_02468
+MDLISPLDPGWAAALADQEEALVRVGAELTARRAAGEHVLPAPEHILRAFRQPFADVKVL
+IVGQDPYPTPGHPIGLCFACDRHVRPLPRSLANIHRELHDDLGVPPAAHGDLSAWTDQGV
+LLLNRVLTVRAGAAGSHRGIGWEQITEAAVRALVARGTPLVGLLWGNDARRLAPLLTAGG
+AGVVESAHPSPLSASRGFFGSRPFSRVNALLEAAGASPVDWRLPD
+>GCF_023573625_PROKKA_00359
+MEFIAPLDPGWEAALAPQAAAFEQVGERLRARRAAGEQVLPAPEHILRAFRQPFADVRVV
+VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLANIHRELHDDLGIAPPAHGDLSAWTDQGV
+LLLNRALSVRAGAPGSHRGLGWEQITEAAVRALCARGTPLVGLLWGADARRMAPLLTAAG
+AGVVESPHPSPLSAHRGFFGSRPFSRVNRLLEAAGAAPVDWRLPD
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000495.fa

@@ -0,0 +1,26 @@
+>GCF_002008305_PROKKA_00472
+MLTVSS------ADPHA-PAPRPVLTATQAQRARQPWMAMVLSLAALLAIVAVVLLLNPE
+PPQRPREDRVDVAAEAATIPHDDGDLPALAPEVPESWYANYARLQKLDGVSTWDVGWVVT
+DTVFAGLQQAEDVDPTWVSLRVDQVPTSETIEIDGIAWDLHADPKKPERRLVAEVDGSTV
+VLTTTGDQAVLEDLAHGVAKETR
+>GCF_003691675_PROKKA_00190
+MLTVSS------ADPHA-PAPRPVLTATQAQRARQPWMAMVLSLAALLAIVAVVLLLNPE
+PPQRPREDRVDVAAEAATIPHDDGDLPALAPEVPESWYANYARLQKLDGVSTWDVGWVVT
+DTVFAGLQQAEDVDPTWVSLRVDQVPTSETIEIDGIAWDLHADPKKPERRLVAEVDGSTV
+VLTTTGDQAVLEDLAHGVAKETR
+>GCF_005280335_PROKKA_02475
+MLTVSSTHPTDPTDPNA-PAPRPVLTAKQAQRARQPWIGMVLSVVALLALVAVVLILNPE
+PPQRPREDRVDVAAAAATVPHDDGVLPALAPEVPESWYANFARLQTMDGVSTWDVGWVVT
+DTVFAGMQQAHDVDPTWVTLRVDSVPATETLEIDGLAWDLHADPRAPEKRLVTEVEDTTV
+VLTTTGDRAVLEDLARGVAKETR
+>GCF_020097155_PROKKA_02359
+MPGMSS------PDPAAPPAPRPVLTPKQAQRARAPWIAMVLSTLAVLGIVLVALMVNQP
+PPAPAQADRVDVAAAASTVPHDDGALPALAPDVPEPWDSTYARVERLQGVDTWDVGWAVN
+DAVFAGLKQTSRADPTWLALRVGSAPAVGTVDVDGITWDHYAPQDSKDQHLVAEVRGSTL
+VLTTSGDQAVLEDLARAVAKEIR
+>GCF_023573625_PROKKA_00472
+MLTVSS------ADPHA-PAPRPVLTATQAQRARQPWMAMVLSLAALLAIVAVVLLLNPE
+PPQRPREDRVDVAAEAATVPHDDGDLPALAPEVPESWYANYARLQKLDGVSTWDVGWVVT
+DTVFAGLQQAEDVDPTWVSLRVDHVPTSETIEIDGIAWDLHADPKKPERRLVAEVDGSTV
+VLTTTGDRAVLEDLAHGVAKETR
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000504.fa

@@ -0,0 +1,21 @@
+>GCF_002008305_PROKKA_00482
+MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRRAEPHTYDLCGEHARRTTAPRGWEVLR
+LELPEHYEAVDADGGVRTVPTRPMAV----------------------------------
+-PPARPGLRVVRDGD-----
+>GCF_003691675_PROKKA_00200
+MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRRAEPHTYDLCGEHARRTTAPRGWEVLR
+LELPEHYEAVDADGGVRTVPTRPMAV----------------------------------
+-PPARPGLRVVRDGD-----
+>GCF_005280335_PROKKA_02465
+MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRLAEPHTYDLCAEHARRTTAPRGWEVLR
+LELPGHYEAVAPDGTVHTVPTAPRAVPAAPPADVASRPSLAAPRPAPAVPPVDADEPEAP
+APPTRPGLRLVRDDDPLPPA
+>GCF_020097155_PROKKA_02349
+MRRCSKTGCQEPAEATLTYNYAGSQVVIGPLAQRAEPHAYDLCAAHAARTTAPRGWEVLR
+L--------------APAAPAAPGVA----------------------------------
+-APTHPALRLVTDPVEGTAG
+>GCF_023573625_PROKKA_00482
+MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRRAEPHTYDLCGEHARRTTAPRGWEVLR
+LELPEHYEAVDADGGVRTVPTRPMAV----------------------------------
+-PPARPGLRVVRDGD-----
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000509.fa

@@ -0,0 +1,31 @@
+>GCF_002008305_PROKKA_00487
+M---------PEGRIVLAATPIGNLGDASARLRDLLAEADVIAAEDTRTARRLCAGLGVT
+PAGRVVAHHEHNEAASAQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVT
+CAPGPSAVTTALALSGLPTDRFAFDGFVPRKDGERRRWLTSLLTEARTVVAFESPQRLAD
+ALAVVAEVLGAERPVCVARELTKLHEEVVRGTAAGVHAWAAERHAGEGIRGEIVLVIGPA
+APGA--EGEASEADAVAEVAVLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAAR-G
+>GCF_003691675_PROKKA_00207
+M----------TGRIVLAATPIGNLGDASARLRELMAEADVIAAEDTRTARRLCAGLGVT
+PAGRVVAHHEHNEAASTQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVT
+CAPGPSAVTTALALSGLPTDRFAFDGFVPRKDGDRRRWLTSLLTEARTVVAFESPQRLAD
+ALAVVVEVLGAERPVCVARELTKLHEEVVRGTAADVHAWAAERHAGEGIRGEIVLVIGPA
+APGA--EGEASEADAVAEVAVLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAAR-S
+>GCF_005280335_PROKKA_02459
+MTPRPTDLPSPSGRIVLAATPIGNLGDASARLRELLAEADVIAAEDTRTARRLCQGLGVT
+PAGRVVAHHEHNEAASTQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVT
+CAPGPSAVTTALALSGLPTDRFAFDGFVPRKDGERRRWLTSLLTEARTVVAFESPQRLAD
+ALAVVVEVLGAERPVCVARELTKLHEEVVRGTAAEVHAWAAERHAGEGIRGEIVLVIGPA
+SPDAASAGGATEADAVAEVGVLVDSGTRLKEAVATVAAAHGLRSRTLYQAVLAAR-G
+>GCF_020097155_PROKKA_02343
+M-----SLPAASGRIVLAATPLGNLGDATGRLRELLATADVIAAEDTRNTRRLCQGLGIT
+PAGRLMAHHEHNEAASAAGLLERVRAGETVVMVSDAGMPTVSDPGFRLVEAAVAAGLPVT
+CAPGASAVTTALALSGLPSDRFAFDGFLPRKDGERRRRLEEIRTDPRTVVYFESPQRTAS
+ALAVIAEVLGGARPVCVARELTKLHEEVVRGTADELVAWAVEREAGEGIRGEVAIVVGPA
+APDA--GAGADEADVLAEVAALTDSGTRLKEAVAAVAAAHGLRSRELYQAVLDARRG
+>GCF_023573625_PROKKA_00487
+M---------PEGRIVLAATPIGNLGDASARLRDLLAEADVIAAEDTRTARRLCAGLGVT
+PAGRVVAHHEHNEAASAQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVT
+CAPGPSAVTTALALSGLPTDRFAFDGFVPRKDGERRRWLTSLLTEARTVVAFESPQRLAD
+ALAVVVEVLGAERPVCVARELTKLHEEVVRGTAAGVHAWAAERHAGEGIRGEIVLVIGPA
+APGA--EGEASEADAVAEVAVLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAAR-G
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000526.fa

@@ -0,0 +1,41 @@
+>GCF_002008305_PROKKA_00513
+MT-----------DMTRGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTF
+PEFKDARIITSPLNRVGVLRKDPRRALPLLPLASSLLHVKEPVAVVSTSGWAHGFRYDGA
+TLVYCHTPARWVYLLDDYLGEGGRNSIKGRIARALRPGLRRWDRAAVRRRSRYVANSTVV
+KERIEDVYGLDGVDLVFPPHSVSTDGPQEPIPGAERLAEDGFLLSVARLMPYKHVDVAIE
+AAARAGRPLVVIGKGPEEARLRAMAGEDVVFGQDLTDAQLRWAYAHAIALIAASHEDFGI
+TPLEASAWGVPTVALRAGGYLDTIVDGVNGTFVLDASIDAVGEGIKKLQAARWDTAAMRR
+HVEKFSEREFALRIRALVEGLPGA-------
+>GCF_003691675_PROKKA_00233
+MS-----------EQTPATIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTF
+PEFEDAHIVTSPLNRVGVLRKDPRRALPLLPLASSLMHVKEPIAVVSTSGWAHGFRYDGA
+TLVYCHTPARWVYLLDDYLGEDGRNSIKGRIARVLRPGLRRWDRAAVRRRSRYVANSTVV
+KKRIDDVYGLDGVDLVFPPHSVSTDGPQGPIPGAEQLAEDGFLLSVARLMPYKHVDVAIE
+AAARAGRPLVVIGKGPEEARLRAMAGEDVVFGQDLTDAQLRWAYAHATALIAASHEDFGI
+TPLEASAWGVPTVALRAGGYLDTIVDGVNGVFVEEPTVDAVAGGVERLLAHDWDRAAMQA
+HAERFSEAQFGRRIRALVAESPAGPAHRGRQ
+>GCF_005280335_PROKKA_02438
+MT-----------DTTRGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTF
+PEFKDARIITSPLNRVGVLRRDPRRALPLLPVASSLMHVKEPVAVVSTSGWAHGFRYHGD
+TLVYCHTPARWVYLLEDYLGEEGQKSMKGRVARVLRPGLRAWDRAAQRRRTRYVANSTVV
+KERIEEAYGLTDVPIVFPPHSVSTDGSQEPIPGAEHLAEGGYLLSVARLMPYKHVDVAIR
+AAERTGLRLLVIGKGPDEARLKAMAGDGVVFAQDLTDAQLRWAYAHATALIAASHEDFGI
+TPLEASAWGVPTVALRAGGYLDTITEGVNGVFVEAPTVEAVTDGVEQALARDWDPPAMRA
+HAERFSEDQIARQVRTQLGQLQNHARNKGAM
+>GCF_020097155_PROKKA_02321
+MKIHASRPLSARRASQPGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYNPEGTF
+PEFKKARIITSPLNRVGVLRSDPRRALPLLPLASSLMHVKEPLAVVSTSGWAHGFRYEGD
+TLVYCHTPARWVYLLEDYLGEGGQRSLKGRVARALRPALRAWDSAAQLRRTRYVANSTVV
+KRRIEEVYGVANVDLVFPPHSVSTDGPQAPIPGAEDLAEGGYLLSVARLMPYKHVDVAIR
+AAERTGRRLLVIGKGPEEARLRALAGQGVVFAQDLTDAQLRWAYAHAVALIAASHEDFGI
+TPLEASAWGVPTVALRAGGYLDTIVEGVNGVFVPEPTVEAVTDVVEQVLAQDWDRGAMQA
+HAEHFSEVAFRERLARLLDDPHGAV------
+>GCF_023573625_PROKKA_00512
+MT-----------DTTRGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTF
+PEFKDARIITSPLNRVGLLRKDPRRALPLLPLASSLMHVKEPIAVVSTSGWAHGFRYDGA
+TLVYCHTPARWVYLLDDYLGEGGRDSIKGRIARVLRPGLRRWDRAAVRRRSRYVANSTVV
+KERIEEVYGLIDVPVVFPPHSVSTDGPQEPIPGAEHLAEGGYLLSVARLMPYKHVDVAIR
+AAERTGLRLLVIGKGPEEARLKAMAGDGVVFAQDLTEAQLRWAYAHATALIAASHEDFGI
+TPLEASAWGVPTVALRAGGYLDTIVEGVNGVFVNGTSVAAVAGGIEWVRAHNWDRAAMRS
+HARRFSEFEFGQQVQAQLGWIGISR------
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000537.fa

@@ -0,0 +1,36 @@
+>GCF_002008305_PROKKA_00535
+MDALRLVSIAAVVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVWGRFRS
+LMVPYLVWAALMSVAAFAWFAD---DPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFT
+TVLRRFLERFPSAVAWAVGLAGLAWAHLVPDSAIARTPLGVGLALPCLLFVLSGEMFRRR
+VQPHVRRHRTLIGVGLVLLGMVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFG
+STVERLLRSFARRTGTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALA
+LALSWLAGLALLATPLSKPFTGARRRWHPVHRLRHVEPPHPVTSALPRVTTASERTHP
+>GCF_003691675_PROKKA_00259
+-----------MVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVWGRFRS
+LMVPYLVWAALMSVAAFAWFAD---DPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFT
+TVLRRFLERFPSAVAWAVGLAGLAWAHLVPDSAIARTPLGVGLALPCLLFVLSGEMFRRR
+VQPHVRRHRTLIGVGLVLLGMVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFG
+STVERLLRSFARRTGTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALA
+LALSWLAGLALLATPLSKPFTGARRRWHPVHRLRHVEPPHPVTSALPRVTTASERTHP
+>GCF_005280335_PROKKA_02414
+MDALRLVSIAAVVLGHAYLADLTFSRYLEIWRMPLFFFLTGYFWTRGRPVARDARGRFKA
+LMVPYLVWAVVMSAAALAWFGD---DPERLQRLMAAGWYGGADQEPPWWAFWFISVLFFA
+TVLRRFLERFPTAVAWGVGLAGLAWAYLVPESAIARTPLGVGLALPCLLFILSGEAFRRR
+VQPRIRRHRTLLGLALVGLGLAAVALGLEPHNIKFGGFGTPLLTPLVGVLMSAGMVLVFG
+AAVERILREFARRTGSGQALRRVITALVRTGTVVVLLHGWVLMWVMRQGVEDNLLKFVLA
+LGISWLVGLALLATPLSKPLTGARRRWFPLHRLRGEEPPHPPTSALPRVTTASERTHP
+>GCF_020097155_PROKKA_02296
+MDALRLVSISAVVLGHAYLADLTFSPYLEIWRMPLFFFLTGYFWTRGRPWAADALSRFRS
+LMVPYLLWSVLMTLVVLSWSRRSQIDGVTLADLVSAGWYGGADQPPPWWAFWFISVLFFV
+ALLRRALERAPSWAGWAVALAGLAAAELVPESAIARTPLGIGLAAPCLFYVLAGEAFRRR
+VQPRIRRHRTLIGVALVAAGVGAVALGLPPHNIKWGGFGLFPWTPLTGIAMAAGMVLVFG
+AFVERRLRAFARDTGTGRAIRAGITALTRTGTVVVLLHGLVLMEAMRVGIEDNLMKFVVA
+LTVSWAVGLALLATPLARPLTGVPQQWFPFGREAGA----------------------
+>GCF_023573625_PROKKA_00538
+MDALRLVSIAAVVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVRGRFRS
+LMVPYLVWAALMSVAAFAWFAD---DPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFT
+TVLRRFLERFPSAVAWAVGLAGLAWAHFVPDSAIARTPLGVGLALPCLLFVLSGETFRRR
+VQPHVRRHRTLIGVGLVLLGLVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFG
+STVEGLLRSFARRTGTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALA
+LALSWLAGLALLATPLSKPFTGARRRWHPVHRLRRVEPPHPVTSALPRVPTASERTHP
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000538.fa

@@ -0,0 +1,26 @@
+>GCF_002008305_PROKKA_00537
+M--TVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELA
+GSDVLTCTVIGFPLGANASEVKAFEARQAIDAGADEVDMVLDVAAARAGDRDRLVADVRA
+VAEAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATV
+EHVALMRRTVGERIGVKASGGVRTRADALAMIEAGATRIGASSALAILGSD
+>GCF_003691675_PROKKA_00261
+M--TVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELA
+DSDVLTCTVIGFPLGANTSEVKAFEARQAIDAGADEVDMVLDIAAARAGDRARLVADVRA
+VAEAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATV
+EHVALMRRTVGEDIGVKASGGVRTREDALAMIEAGATRIGASSALAILGSD
+>GCF_005280335_PROKKA_02412
+M--TRTLSTAELAQYIDATALKTETSEADVRRLVAEARQAGVKSVCVNPRWVPLVSAELA
+GSDVLTCTVIGFPLGANASEVKTFEARQAIEAGAHEVDMVIDVAAARAGDRARLVEDVRA
+VAEAAHAAGPAGQGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATV
+EHVALMRRTVGEHVGVKASGGVRTREDALAMIEAGATRIGASSALAILGTD
+>GCF_020097155_PROKKA_02294
+MSETPQLTTAELAKHIDHTLLKPEASREDILRVVAEAREAGVKSVCVNPRWVREVRAGLE
+GSDVLTCTVIGFPLGASSSAVKAFETTQAIADGADEVDMVIDIAAARAGDRARLEEDVRA
+VVAAAHASGPAGRAGTLVKVIIETALLDDAAKVLACEAAVAAGADFVKTSTGFSTGGATV
+EDVALMRRTVGPEIGVKASGGVRSREDALAMITAGATRIGASSALAILGDD
+>GCF_023573625_PROKKA_00540
+M--TVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELA
+GSDVLTCTVIGFPLGANASEVKAFEARQAIDAGADEVDMVLDVAAARAGDRDRLVADVRA
+VAEAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATV
+EHVALMRRTVGERIGVKASGGVRTRADALAMIEAGATRIGASSALAILGSD
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000555.fa

@@ -0,0 +1,41 @@
+>GCF_002008305_PROKKA_00558
+MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL
+RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLASALAERDVSWAVPVALSDPVSAG
+PGAAVLQRFLPGGPYPPHEGDPDVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPAR
+ARHVAALPGAVAARLGAWEGH------------DVDARLGAEAWPDAVAALTDAVTTWTA
+APPVPPSLVHGDLAGHNMRWR-----AVPEDEDPRAPLRWALAGVLDWDLACAWGPALNV
+AYLALWHGEQKVPDLARDAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLR
+KTLPRVARALTALDG
+>GCF_003691675_PROKKA_00283
+MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL
+RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLAAALAERRVPWTVPIALSDPVPAG
+PGAAVLQRFLPGGPHPPHEGDPAVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPER
+ARHVAALPGAVAARLGAWEGH------------DVDARLGAEAWPDAVAALADAVTTWTA
+APPVPPSLVHGDLAGHNMRWR-----AVPEDEDPRAPLRWALAGVLDWDLACAWDPALNV
+AYLALWHGEEKVPDLARDAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLR
+KTLPRVARALTALDG
+>GCF_005280335_PROKKA_02385
+MASDPVDSELELVHRALGRLRPHVSPADARALHEADWSAGTVEEGGQFNRVLVCAGAGVL
+RMTRAHEVGAAPAARWSPERDPARQLGRRMALLDGLDAALAEQGVAWTVPVALSDPVPAG
+TGAAVLQRYLPGGPHPPHEGDPAVLRRLLDEIAAVDVADPRIAPHLGRPFSFRGPWTAQR
+AEHVAGIPGRLAPRLGAWPGD------------DVDARTGADAWADAVARVTRAVTAWTE
+EPPVPPSLVHGDLAGHNMRWR-----AMPAADDAPGEVRWELAGVLDWDLACAWDPALNV
+AYLSLWHGEDQVERLAVDAGEAARARVWLGAMALETLDDAAARDELVGGLPNGSWRRLLR
+KALPRVARALTAL-G
+>GCF_020097155_PROKKA_02269
+MASDPARSELDLVAAALQRLRPGLDDGVAARLRGADWSAGRVEEGGQFHRVLVLEDVGVL
+RMTRVHEAGAAPAARWTPERDPAVHLPRRLALLDGLAAVLAEAGVRWSLPTALSAVVEDG
+PGAAVLQRYVPGFPHPPHEGDPAVLRGVLADLAAVDVADPRVAPHLGRPFTFRGPWTPER
+AAHVAGLPARLAPRLGAWPGDALGHAGDETAAGEAAVRLRADAWGESVTALTGVVSAWTR
+EPPVPPALVHGDLAGHNMRWRVVPAAATPDAEVPDAPVRWELAGVLDWDLACAWDPALNV
+AYLGLWHGEDLVEAIAADPAEARRARVWLGAMALETLDDAGARDVLVGGLAESSWRRLLR
+KTLPRVGRALAAAAA
+>GCF_023573625_PROKKA_00561
+MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL
+RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLAAALAERRVPWTVPIALSDPVPAG
+PGAAVLQRFLPGGPHPPHEGDPAVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPER
+ARHVAALPGAVAARLGAWEGH------------DVDARLGAEAWPDAVAAVTDAVTAWTA
+APPVPPSLVHGDLAGHNMRWR-----AVPEDEDPRAPLRWALAGVLDWDFACAWDPALNV
+AYLALWHGEEKVPDLARDAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLR
+KTLPRVARALTALDG
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000569.fa

@@ -0,0 +1,36 @@
+>GCF_002008305_PROKKA_00579
+M-ADP-------------------------HPVLAASAPVLADPHPV---------LAAS
+APDLDPDALDAVRALVAAAERPVVLSGAGMSAESGIPTFRDARTGLWERFSAEELATEEA
+FLADPALVWSWYRWRARMVRARRPNPGHDAVAAWQRRTPGLEVVTQNVDDLHERAGARVL
+AHLHGSLFEHRCAECWAPADVDPGAP---ADEATAGSEADLEAMLREAPPACTVCGDGLI
+RPGIVWFGEMLPAEPWDRAFAALEDCDLCVVVGTSGIVQPAASLPFVALGAGAAVVEVNP
+VETELSGAVTHVLRGPAGAVLPALVAGVWPGPSGALSTARHVTW
+>GCF_003691675_PROKKA_00311
+M-ADP-------------------------HPVLAASAPVLAASAPV---------LAAS
+APDLDPGALDAVRALVAAAERPVVLSGAGMSAESGIPTFRDAQTGLWERFSAEQLATEEA
+FLADPALVWSWYRWRARMVRARRPNPGHDAVAAWQRRTPDLEVVTQNVDDLHERAGARVL
+AHLHGSLFEHRCAECGAPADVDPGAP---SDVDAAGSEADLEAMLREAPPACPACGTGRI
+RPGVVWFGEMLPQEPWERAYEALERCDLALVVGTSGLIQPAASLPFVALGAGVAVVEVNP
+VKTELSGAVTHALRGSAGAVLPALVAGVWPGPSGALSTARHVTW
+>GCF_005280335_PROKKA_02354
+MPVEPGRDDVGPAGEAGRAVVGAGQRRRVVNPVAATPPSYLGRHYPVPMSHPSPGDLSET
+VPTAD---LDAVRALVAQARRPVVLTGAGMSAESGIPTFRDAQTGLWERYSPEQLATEDA
+FLADPDLVWSWYRWRARMVRARRPNPGHDAVAHWQRAVPGLEVVTQNVDDLHERAGARVL
+AHLHGSLFEHRCAECGAPADVDPGAP---ADAEAAGSEADLEAMLREAPPTCPACGTGRI
+RPGVVWFGEMLPQEPWERAYEALERCDLALVVGTSGLVQPAASLPFVALGAGAAVVEVNP
+VETELSGAVTHALRGSAGAVLPALVAGV----------------
+>GCF_020097155_PROKKA_02248
+--------------------------------------------------------MSPT
+QPS-DPAALGAVRRLILEAERPVVLTGAGVSAESGVPTFRDAQTGLWERYSPEQLATAEA
+FAADPSLVWSWYLWRARMVRAVEPNAGHRALAAWQARTPALRIVTQNVDDLHERAGADVL
+SHLHGSLFAFRCAECDTPADVDPSAVVALAESAAPGSEAGLEALMHLEPPLCAACRRGRV
+RPDIVWFGELLPERAWGDAQAALEECDLCVVVGTSGVVQPAASLPFLALGAGAPVVEVNP
+DRTALSDAMTHVLRGPAGTVLPALLG------------------
+>GCF_023573625_PROKKA_00580
+M-ADP-------------------------HPVLAASAPVLADPHPV---------LAAS
+APDLDPGALDAVRALVAAAERPVVLSGAGMSAESGIPTFRDAQTGLWERFSAEQLATEEA
+FLADPALVWSWYRWRARMVRARRPNPGHDAVAAWQRRTPDLEVVTQNVDDLHERAGARVL
+AHLHGSLFEHRCAECGAPADVDPGAP---SDVDAAGSEADLEAMLREAPPACPACGTGRI
+RPGVVWFGEMLPQEPWERAYEALERCDLALVVGTSGLIQPAASLPFVALGAGVAVVEVNP
+VETELSGAVTHALRGSAGAVLPALVAGVWPGPSGALSTARHVTW
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000572.fa

@@ -0,0 +1,26 @@
+>GCF_002008305_PROKKA_00584
+MTITTLTRKTALTGTGMLAALALAACGTTSDNGDDGSASPEVDASSSLASTPATDDAS--
+GSA---TSSSASSASASSTAAAAGSDSATGQADDPAYAVIDAVLEKYGDGIIVAVDADDD
+DTTWEVDVVVGEEVKELDVTADGDITETDRESDLEDVQKAKDAEVTAQQALDTAREGRDG
+VTLDEMDLDDDNGTLQWEVGFDREDGSDGPEVEIDATSGEVLTVDEH
+>GCF_003691675_PROKKA_00317
+MTITTLTRKTALTGTGVLAALALAACGTTADNGDDGSVSPEVDASSAVASTPATDDASTT
+SAS---ASSSASSTSASSTAAAASSGSGTGQADDPAYAVIDAVLEKHGDGIIVEVDANDD
+DTTWEVDVVVGEEVKELDVTADGDITETDRESDLEDVQKAKDAEVTAQQALDTAREGRDG
+VTLDEMDLEDDNGTLQWEVGFDREDGSDGPEVEIDATSGEVLTVDER
+>GCF_005280335_PROKKA_02350
+MNATSLARKTALTGTGLLAALALAACGTADDDTAANPQETAVQQSPTQAATTAPASAS--
+GSASASASGSASASASGSASPAAASGSVERQGDDPAYAAIDAILGLHDDGVIVEMDLDDD
+DAKWEVDVVVGDDVKEYDVTTGGQVSEGVRPQIDDDVRRAGEAQVTAETAISTALQGRTD
+QTVDEVDLDEEGGTLVWKVELDRENGEDGAEVKIDAKTGDVIEVEEG
+>GCF_020097155_PROKKA_02245
+MTITTLTRKTALTGTGVLAALALAACGTTADNGDDGSASLEVDASSAVASTPATEDASTT
+SAS----ASSASSAPASSTAAAAGRDSATGQADDPASAVIDAVLEKYGDGIIVGVDANDD
+DTTWEVDVVVDKEVKELDVTADGDITETDRESDPEDVQKAKDAEVTAQQALDTARKGRDG
+VTLDEMDLDDDNGTLQWEVEFDREDGSDGPEVEIDATSGEVLTVDEH
+>GCF_023573625_PROKKA_00585
+MTITTLTRKTALTGTGMLAALALAACGTTSDNGDDGSASPGVDASSAVASTPTTDDAS--
+GSA----SSSASSASASSTAAAAGSGSATGQADEPAYAVIDAVLEKYADGIIVAVDANDD
+DTTWEVDVVVGEGAKELDVTADGDITETDRESDPEDVQKAKEAEVTAQQALDTAREGRDG
+VTLDEMDLEDDNGTLQWEVRFDREDGSDGPEVEIDATSGEVLTVDER
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000631.fa

@@ -0,0 +1,26 @@
+>GCF_002008305_PROKKA_00709
+MVAVSSASHYFDADPSAPERRRTVRTRLAGRDVEVQTANGIFSPDGLDKGTAALFSAVPA
+PPARGRFLDVGAGWGPIALTLALRSPEAEVTAVEVNDRSLQLTRDNAAALGLDNLVALRP
+EDVPEGAEFDLIWSNPPIRIGKPALHALLERWLPRLAPGGEAWLVVQKNLGADSLLPWIG
+RMLEERAPGRFTAERADSVKGFRILRVARA----R
+>GCF_003691675_PROKKA_00443
+MVAVSSASHYFDADPSAPERRRTLRTRLAGRDVEVQTANGIFSPDGLDKGTAALFSAVPA
+PPATGRFLDVGAGWGPIALTLALRSPEAEVTAVEVNDRSLQLTRDNAAALGLDNVVALRP
+EDVPEDAEFDLIWSNPPIRIGKPALHALLERWLPRLAPGGEAWLVVQKNLGADSLLPWIG
+RMLEERAPGRFTAERADSVKGFRILRVVRA----R
+>GCF_005280335_PROKKA_02246
+MVAVTSPAHYFSPDPGTPERRRSVDVELAGRRVTLQTANGVFSPDGIDKGTAALLSAVPA
+PPARGAFLDVGAGWGPLALTLALASPEAEVTGVEVNERSLALARDNAAAVGASNARFLTP
+EQIPDDARFDLIWSNPPIRIGKAALHDLLAQWLPRLAPGGEAWLVVQKNLGADSLLPWIA
+GMLQEQAPGEFTATRAATVKGFRILRISRAAESSS
+>GCF_020097155_PROKKA_02119
+MDAVTSPAHYFSPDPGTPERRRRVDVEIAGRRVTLQTANGVFSPDGIDKGTAALLSAVPA
+PPARGAFLDVGAGWGPLALTLALTSPEAEVTGVEVNERSLALARDNAAAVGAQNARFLTP
+EQVPDDARFDLIWSNPPIRIGKAALHDLLAQWLPRLAPGGEAWLVVQKNLGADSLLPWIS
+GMLQERAPGEFTATRAATVKGFRILRISRAAESSS
+>GCF_023573625_PROKKA_00676
+MVAVSPASHYFDADPSAPERRRTLRTRLAGRDVEVQTANGIFSPDGLDKGTAALFSAVPA
+PPATGRFLDVGAGWGPIALTLALRSPEAEVTAVEVNDRSLQLTRDNAAALGLDNVVALRP
+EDVPEDAEFDLIWSNPPIRIGKPALHALLERWLPRLAPGGEAWLVVQKNLGADSLLPWIG
+RMLEERAPGRFTAERADSVKGFRILRVVRA----R
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000647.fa

@@ -0,0 +1,26 @@
+>GCF_002008305_PROKKA_00728
+MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD
+VVDGDDGRVLFRLADPATFGRDRFAILDADGLPFANLVRQIAFLRTSVNVEVVDGTCFAV
+TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRSNG
+>GCF_003691675_PROKKA_00459
+MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD
+VVDGDDGRVLFRLADPATFGRDRFAILDADGLPLAHLVRQFAFLRTSVNVEVVDGTCFAV
+TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRSNG
+>GCF_005280335_PROKKA_02229
+MNTAFDAGRLGRTDVLTLQQVTSFMSNDMQVTGPDGQTVATVVTTGGGLGRMVLGSRTFD
+VVDGEDGRVLFRLADPATFGRDRYAIVDADGLPLANLVREFALFRTSVSVEVVDGTRFAV
+TGNLWDHDYTMTVGQAPIARATATFGGFMNALAGRSRYELRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRRNN
+>GCF_020097155_PROKKA_02102
+M-TTFDAGRLALVNSLALQQVTSFLSNDMQVLGPDGEVVATVQTQGGGLSRMLMGSRRLL
+VCDGDDGRPLFELQDPATFGRDRFQVLDPAGLPLANLRREVAFFRTAVSVEVVDGTVFRV
+EGDLFDHDYRMIAGEVPIARAVSQWSGFGNALLGRSRYRLELDPAMPPVVRCAVLGTAIA
+LDLLRAKDARRND
+>GCF_023573625_PROKKA_00692
+MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD
+VVDGDDGRVLFRLADPATFGRDRFAILDADGLPFANLVRQIAFLRTSVNVEVVDGTCFAV
+TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRSNG
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000672.fa

@@ -0,0 +1,41 @@
+>GCF_002008305_PROKKA_00759
+MNGDVVGLLWLVVLLAANAFFVAGEFAVMGARRAQIEPRAEAGSRQAQVALYAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLVVPMAALGVPSAAADVTAFVLALLVVTFLHVTL
+GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPVVAALNWTANLVLHALRIEPKDEVASS
+YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHRAGDVMVPLERVVTVPEGITPHDFE
+WTVGRVGFSRFVVEDPDGGYTGYLHLKDVLTVGPSGHDEPIPLTRVRSLANVRLEDEVED
+ALALMQRTGSHLARVITPEGETAGILFLEDVLEELVGEINDVTQSPRRFRPA--------
+----------
+>GCF_003691675_PROKKA_00489
+MNGDVVGLLWLVVLLAANAFFVAGEFAVMGARRAQIEPRAEAGSRQAQVALYAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLVVPMAALGVPSAAADVTAFVLALLVVTFLHVTL
+GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPVVAALNWTANLVLHALRIEPKDEVASS
+YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHRAGDVMVPLERVVTVPEGITPHDFE
+WTVGRVGFSRFVVEDPDGGYTGYLHLKDVLTVGPSGHDEPIPLTRVRSLANVRLEDEVED
+ALALMQRTGSHLARVITPEGETAGILFLEDVLEELVGEINDVTQSPRRFRPA--------
+----------
+>GCF_005280335_PROKKA_02171
+MNEDVIGLLWLVVLLVANAFFVAGEFAVMGARRSQIEPKAEAGSRPAQVALYAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLVGPMTALGVPDAAADVTAFVLALLVVTFLHVTF
+GEMVPKNAAVSFADRAVMILARPLVGLSKLLHPIVTVLNWAANVVLRAFRIEPKDEVASS
+YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHTAGDVMVPLEKVVTVPEGITPHDFE
+WTVGRVGYSRFVVEDPDGGYTGYLHLKDVLTVGPSGHEEPIPLTRVRSLANVRLEDEVED
+ALALMQRTGSHLARVITPEGETAGVLFLEDVLEELVGEINDVTQSPRRFRPA--------
+----------
+>GCF_020097155_PROKKA_02066
+MSQDVVGLLWLAVLLAANAFFVAGEFAVMGARRSQIEPRAEAGSRQAQVALFAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLAAPMEALGLPLAAADVVAFVLALLIVTFLHVTM
+GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPLIVVLNWAANTVLRAFGIEPKDEVASS
+FTLEEVQTIVAESTRSGTLEDESGVLHSALEFSSYTAGDVMVPIEKVVSVPEDVTPQQFE
+WAVGRVGYSRFVVEDSQGGYAGYLHLKDVLAGGPSRYADPVPVTRVRSLANVRVADEVED
+ALGLMQRTGSHLARVISEDGATVGVLFLEDVLEELVGEIHDVTQSPRRFRPTTGSHAAPE
+PTRMRDLPAR
+>GCF_023573625_PROKKA_00723
+MNGDVVGLLWLVVLLAANAFFVAGEFAVMGARRAQIEPRAEAGSRQAQVALYAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLVVPMGALGVPAAAADVTAFVLALLVVTFLHVTL
+GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPVVAALNWTANLVLHALRIEPKDEVASS
+YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHRAGDVMVPLERVVTVPEGITPHDFE
+WAVGRVGFSRFVVEDPDGGYTGYLHLKDVLTVGPSGHDEPIPLTRVRSLANVRLEDEVED
+ALALMQRTGSHLARVITPEGETAGILFLEDVLEELVGEINDVTQSPRRFRPA--------
+----------
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000683.fa

@@ -0,0 +1,36 @@
+>GCF_002008305_PROKKA_00773
+MT---------------SAVPRVLSIAGSDSGGGAGVQADLKTIAAWGGYGMTAITAITA
+QNTQGVQAVHPLPVDVVRAQLDSVAADIAVDAVKIGMLGTVELMRAVAGWLEETRPAVVV
+LDPVMVASSGDALTAVGDDDGRAAWARLLRVAHLVTPNLPELARLTGRDATDWDAALDAA
+RGLAAEHGVTVLLKGGHLDETEAPEAAAAE----------VPDAVVRVGGAVHEVRGPRV
+TTRASHGTGCTLSSALATLAGAGLSWDDALERAKPWLADAMRAGEALAVGDASRPTWHGP
+VDHGHAQRG
+>GCF_003691675_PROKKA_00504
+MT---------------PAVPRVLSIAGSDSGGGAGVQADLKTIAAWGGYGMTAITAITA
+QNTQGVQAVHPLPVDVVRAQLDSVAADIAVDAVKIGMLGTVELMRAVAGWLEETRPAVVV
+LDPVMVASSGDALTAVGDDDGRAAWARLLRVAHLVTPNLPELARLTGRDATDWDAALDAA
+RGLAAEHGVTVLLKGGHLDETEAPEAAAAE----------VPDAVVRVGGAVHEVRGPRV
+TTRASHGTGCTLSSALATLAGAGLSWEDALERAKPWLADAMRAGEALAVGDASRPTWHGP
+VDHGHAQRG
+>GCF_005280335_PROKKA_02157
+----------------------MLSIAGSDSGGGAGVQADLKTIAVWGGYGMTAITAITA
+QNTQGVQAVHPLPVDVVRAQLDSIAADIAVDAVKIGMLGTAELMGAVAGWLEETRPAVVV
+LDPVMVASSGDALTAVGDDDGRAAWSRLLRAAHLVTPNLPELARLTGRDSTDWEAALDAA
+GGLAAEHEVTVLLKGGHLD-----EAAAAE----------VPDAVVRVAGAVHEVRGPRV
+ATRASHGTGCTLSSALATLAGAGLSWEDALERAKPWLADAMRAGEALAVGDASRPTWHGP
+VDHGHARRG
+>GCF_020097155_PROKKA_02052
+MAPSPSTPPSSSPAAEGPAVPRVLSIAGSDSGGGAGIQADLKTIAEWGGYGMTAITAITA
+QNTQGVQAVHPLPAEVVRAQLDSVASDIAVDAVKVGMLGTAELMRVVADWLEEARPAVVV
+VDPVMAATSGHALTPVGDAEAHAAWGRLLRAAHLVTPNLPELARLAGRPLDSWAAALDAA
+RELAAAHAVTVLAKGGHLADLTRADPEGAEAGDDPDAEGGVPDALVRPDGSVHEVRGPRV
+ESGATHGTGCTLSAALATLAAGGLGWEDAIERAKPWLAQAMVAGEALAVGDRTRPTWHGP
+VDHGHARRG
+>GCF_023573625_PROKKA_00740
+MT---------------SAVPRVLSIAGSDSGGGAGVQADLKTIAAWGGYGMTAITAITA
+QNTQGVQAVHPLPVDVVRAQLDSVAADIAVDAVKIGMLGTVELMRAVAGWLEETRPAVVV
+LDPVMVASSGDALTAVGDDDGRAAWARLLRVAHLVTPNLPELARLTGRDATDWDAALDAA
+RGLAAEHGVTVLLKGGHLDETEAPEAAAAE----------VPDAVVRVGGAVHEVRGPRV
+TTRASHGTGCTLSSALATLAGAGLSWEDALERAKPWLADAMRAGEALAVGDASRPTWHGP
+VDHGHAQRG
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000721.fa

@@ -0,0 +1,31 @@
+>GCF_002008305_PROKKA_00814
+MKLTIIGASGSFPGPGSPASCYLLTAEGVAEDGVTPRTWRILLDLGNGALGVLQRYVELE
+DLDGILLSHLHPDHFMDLCGMHVAIRWNPAGWDRGRLPVYGPAGTADRIAEAYGMDPEPG
+MHQDFEFRCWAAGRTERLGPFRFTPVPVRHPIDEAYAIRVEVDRVDDDGDVTTRVLTYSG
+DTDACEGLVEAARDADVFLCEAAFHEGRDDGIDGVHLTGRRAGETAAQAGARKLLLTHLP
+VWNDPQRAVQEARAVYDGPLAVAVSGLSYGV
+>GCF_003691675_PROKKA_00546
+MKLTIIGASGSFPGPGSPASCYLLTAEGVAEDGVTPRTWRILLDLGNGALGVLQRYVELE
+DLDGILLSHLHPDHFMDLCGMHVAIRWNPAGWGRGRLPVYGPAGTADRIAEAYGMDPEPG
+MHQDFEFRCWAAGRPERLGPFRFTPVPVRHPIDEAYAIRVEVDRVDDDGDVTTRVLTYSG
+DTDACEGLVEAARDADVFLCEAAFHEGRDDGIDGVHLTGRRAGETAAQAGARKLLLTHLP
+VWNDPQRAVQEARAVYDGPLAVAVSGLSYGV
+>GCF_005280335_PROKKA_02116
+MKLTVIGASGSFPGPGSPASCYLVTAQGVAEDGVTPRTWRILLDLGNGSLGVLQRYIELE
+ELDGILLSHLHPDHCMDLCGMHVAIRWNPEGWHRDRMPVYGPTATADRIAEAYGMDPEPG
+MHEDFDFRVWRPGRTERFGPFRLTPVPVRHPIDEAYAIRVEADEPDGEGGTVTRVLTYSG
+DTDACEGLVEAARDADLFLCEAAFHEGRDDGIDGVHLTGLRAGQTAAQAGAKKLLLTHLP
+VWNDPQRAVLEAREAYEGPMAVAVSGLSYGV
+>GCF_020097155_PROKKA_02007
+MKLTVIGASGSFPGPGSPASCYLVTADGPDGNGGT-RPWRILLDLGNGSLGVLQRHIELE
+QIDGVLLSHLHPDHCIDLCGLHVAVRWNPEGWDAGRIPVYGPAATATRIAEAYGMDPEPG
+MQEDFDFRAWEAGRTEGLGPFRLTPFAVRHPIDEAYAIRVETTEPGPDGEPVTRVLAYSG
+DSDTCDGLVEAARDADLFLCEAAYHEGRDDHIDGVHLTGRRAGQMAAEAGARKLLLTHLP
+VWNDPQRCAQEAREAYVGPLAVAVSGLSYGL
+>GCF_023573625_PROKKA_00783
+MKLTIIGASGSFPGPGSPASCYLLTAEGVAEDGVTPRTWRILLDLGNGALGVLQRYVELE
+DLDGILLSHLHPDHFMDLCGMHVAIRWNPAGWGRGRLPVYGPAGTADRIAEAYGMDPEPG
+MHQDFEFRCWAAGRPERLGPFRFTPVPVRHPIDEAYAIRVEVDRVDDDGDVTTRVLTYSG
+DTDACEGLVEAARDADVFLCEAAFHEGRDDGIDGVHLTGRRAGETAAQAGARKLLLTHLP
+VWNDPQRAVQEAREVYDGPLAVAVSGLSYGV
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000776.fa

@@ -0,0 +1,46 @@
+>GCF_002008305_PROKKA_00903
+MNEMT-LDAGTVWMVVSAGLVLLMTPGLALFYGGMTRSKSALNMMMMSFVSMGLVGVVWI
+LWVSGMTGGEGWLGLVGSPLADPGLTTAMEEGGLIAAGFGATFAIITVALISGAVADRAR
+FLTWCVFVPVWVTLVYAPLAYMVWGGGLLAEEGAIGSRLGEALDFAGGLVVHISAGVAAL
+VLALMMGKRKGFGVDPGHKPHNVPFTMLGAALLWFGWFGFNGGAAGDTGQLGLIWINTLA
+AAAAGMLGWVVVEWVRRGRPTSIGTASGIVAGLVGITPACAFVSPLGALVIGVASGAASA
+LAVNLKYRLGFDDSLDVVGVHLTAGILGTVLIGFFALPSEGPAGLFYGGDGRLLLAQTVA
+VVVAVVFTAVLTFLIALVLKATLGLRVSEEDEERGVDLTLHDESAYHYDVGFGGVPVPAD
+AQAHRGGAAG
+>GCF_003691675_PROKKA_00622
+MEESNVLDAGTVWMVTSAAMVLLMTPGLAIFYGGMTRAKSSLNMIMMSFVSMGLVGVVWV
+LWVHGMTGGDGWAGVVGNPAGDLGLTGTMAEGGLVAAAYGATFAIIAVALISGAVADRFK
+FVTWCVFVPVWTTVVYAPLAYMVWGGGLLSEDGAIGARLGEALDFAGGLVVHISAGVAAL
+VLALLLGKRHGFGVDPGHRPHNVPFTMLGAALLWFGWFGFNGGAAGGVDELGLIWVDTLA
+AGAAGMLGWVFVEWLRRGRPTSIGTASGIVSGLVAITPACAYVSPLGAVVIGLVSGAASA
+LAVNLKYRLGFDDSLDVVGVHLTSGILGTVLIGFFALPGEGRAGLFYGGDAGLLVAQTVA
+VLVAVVFTAVVTTAIALVLRGTMGLRVSKEDEERGVDLTLHDESA--YDVGFGGVPVPAE
+AR--------
+>GCF_005280335_PROKKA_02039
+MNEMT-LDAGTVWMVVSAGLVLLMTPGLALFYGGMTRSKSALNMMMMSFVSMGLVGVVWI
+LWVSGMTGGEGWLGLVGSPLADPGLTTAMEEGGLIAAGFGATFAIITVALISGAVADRAR
+FLTWCVFVPVWVTLVYAPLAYMVWGGGLLAEEGAIGSRLGEALDFAGGLVVHISAGVAAL
+VLALMMGKRKGFGVDPGHKPHNVPFTMLGAALLWFGWFGFNGGAAGDTGQLGLIWINTLA
+AAAAGMLGWVVVEWVRRGRPTSIGTASGIVAGLVGITPACAFVSPLGALVIGVASGAASA
+LAVNLKYRLGFDDSLDVVGVHLTAGILGTVLIGFFALPSEGPAGLFYGGDGRLLLAQTVA
+VVVAVVFTAVLTFLIALVLKATLGLRVSEEDEERGVDLTLHDESAYHYDVGFGGVPVPAD
+AQAHRGGAAG
+>GCF_020097155_PROKKA_01937
+MTETTPLDAGAVWTVTAAALVLLMTPGLALFYGGMTRAKSALNMMMMSFVSMGLIGVAWI
+LWAYGMTSGDGLAGIVGSPLNDLGAVQSMADGDLISVGFSATFAIIAVALISGAVADRAK
+FSTWCVFVPVWVTLVYAPLAYMVWGGGLLSADGAIGARLGEALDFAGGLVVHISAGVAAL
+VLAMMMGKRQGFGVDAAHRPHNVPFTMLGAALLWFGWFGFNSGAASDVEQLGLTWVTTLV
+AAAAGMLGWVLVEWLRRGRPTSIGTASGIVSGLVAITPACAFVSPLGAVVIGLVAGAACA
+LAVNLKYRWGFDDSLDVVGVHLTAGILGTLLIGLFALPETGHAGLFHGGDGSLLLAQTVA
+VVVAVVFTAVVTAVIAFVLRATLGLRVSVEEEERGVDLTLHDETA--YDVGFGGVPVPTD
+AQARSTAAAE
+>GCF_023573625_PROKKA_00851
+MEESNVLDAGTVWMVTSAAMVLLMTPGLAIFYGGMTRAKSSLNMIMMSFVSMGLVGVVWV
+LWVHGMTGGDGWAGVVGNPAGDLGLTGTMAEGGLVAAAYGATFAIIAVALISGAVADRFK
+FVTWCVFVPVWTTVVYAPLAYMVWGGGLLSADGAIGARLGEALDFAGGLVVHISAGVAAL
+VLALLLGKRHGFGVDPGHRPHNVPFTMLGAALLWFGWFGFNGGAAGSVDELGLIWVATLA
+AGAAGMLGWVFVEWLRRGRPTSIGTASGIVSGLVAITPACAYVSPLGAVVIGLVSGAASA
+LAVNLKYRLGFDDSLDVVGVHLTAGILGTVLIGFFALPDEGRAGLFYGGDAGLLVAQTVA
+VLVAVVFTAVVTTAIALVLRGTMGLRVSKEDEERGVDLTLHDESA--YDVGFGGVPVPAE
+AR--------
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000884.fa

@@ -0,0 +1,31 @@
+>GCF_002008305_PROKKA_01051
+MTDTAAKFSEYAHPEKLVSTQWVADHVGDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE
+LNDPVTRDFVGPEAFAEFAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD
+GGRDKWIAEGRETTREVPTVARA-EYPVIERDDHTERAAREDVLQAIGTTPLIDVRSRPE
+YTGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRAGAGLQEGD
+DVIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR
+>GCF_003691675_PROKKA_00764
+MTDTAAKFSEYAHPEKLVSTQWVADHVDDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE
+LNDPVTRDFVGPEAFAEVAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD
+GGRDKWIAEGRETTREVPTVARA-EYPVIERDDHTERAAREDVLQAIGTTPLIDVRSRPE
+YTGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRTDAGLREGD
+DVIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR
+>GCF_005280335_PROKKA_01835
+MTETATEFSQYAHPEKLVSTQWVADHVGEEGVVVLESNEDALLYATGHIPGAQRIDWHTE
+LNDPVTRDFIGPEAFAEMAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDVRLMN
+GGRDKWIAEGRETTREVPTVARG-EYPVVPRDDTTERAAREDVLQAVGTTPLIDVRSRPE
+YTGETTHMDGYPQEGTLRGGHIPTAASVPWAQAANEDGTFKSREELEAVYRDGAGLKDGD
+DVIAYCRIGERSSHTWFVLKHLLGHENVRNYDGSWTEWGNSVRLPIVVGEEPGAAPAR
+>GCF_020097155_PROKKA_01725
+MTETPAEFAEYAHPEKLVSTQWVADHIDDEGVVVLESNEDTLLYSTGHIPGAVKIDWHTE
+LNDPVSRDFVGPEAFAELVASKGIGPDTTVVFYGDKSNWWAAYALWVFTLYGHRDVRLMN
+GGRDKWIAEGRPTTREVPEVTPAPSYPVSQRDDATDRAAREDVLAAIGSTPLVDVRSPKE
+YTGETTHMDGYPQEGTLRGGHIPTAASVPWAKAANEDGTFKSRAELEEIYKEGAGLGESD
+SVIAYCRIGERSSHTWFVLKQLLGYENVRNYDGSWTEWGNGVRLPIALGDEPGEAPAR
+>GCF_023573625_PROKKA_00992
+MTDTAAKFSEYAHPEKLVSTQWVADHVGDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE
+LNDPVTRDFVGPEAFAEFAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD
+GGRDKWIAEGRETTREVPTVARA-EYPVIERDDHTDRAAREDVLQAIGTTPLIDVRSRPE
+YTGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRAGAGLQEGD
+DVIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000906.fa

@@ -0,0 +1,51 @@
+>GCF_002008305_PROKKA_01090
+MADPRGFLKNRERVDRPTRPVPVRIMDFKDVYVRQDEAIVRTQAGRCMDCGIPFCHSGCP
+LGNLIPEWNDLVRRRRWDEAAARLHSTNNFPEVTGRICPAPCEDSCTLGINQPAVTIKQT
+EVAIAEQIFDNDWLEPVVPARLNGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDERLG
+GLLRLGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGVDLPWDQLKARFDAVIVATGAP
+VARELPVPGRGLDGIHLAMDYLVQSNRAVAGDEVPDQISAEGRHVVILGGGDTGADCIGT
+AHRQGAASVTTLAIGQQLPVERPVHQPWPTIPKVHQQTTADAEGGARAHLASTVEFLGDE
+HGRVRALRVAETEYREDGTRGPKAGTEREVQADLVLLALGFTGIEEGLLTQQLGVHVTRG
+LVARKDGYETDEPGVFACGDAGRGASLVVWAIAEGRACAQEVDESLERWSRLPHPVDPDD
+RGLVLG
+>GCF_003691675_PROKKA_00809
+MADPRGFLKNRERVERPTRPVPVRIMDFKDVYVRQDEAIVRTQAGRCMDCGIPFCHSGCP
+LGNLIPEWNDLVRRRRWDEAAARLHSTNNFPEVTGRICPAPCEDSCTLGINQPAVTIKQT
+EVAIAEQIFDNDWLEPVVPARLNGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDERLG
+GLLRLGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGVDLPWDQLKARFDAVIVATGAP
+VARELPVPGRGLDGIHLAMDYLVQSNRAVAGDEVPDQISAEGRHVVILGGGDTGADCIGT
+AHRQGAASVTTLAIGQQLPVERPVHQPWPTIPKVHQQTTADAEGGARAHLASTVEFLGDE
+HGRVRALRVAETEYREDGTRGPKAGTEREVQADLVLLALGFTGIEEGLLTQQLGVHVTRG
+LVARKDGYETDEPGVFACGDAGRGASLVVWAIAEGRACAQEVDESLERWSRLPHPVDPDD
+RGLVLG
+>GCF_005280335_PROKKA_01806
+MADPRGFLKHRERVARPSRPVPVRIMDFKDVHVRQDEAIVRTEASRCMDCGVPFCHAGCP
+LGNLIPEFNDLVYRDDWDEAGARLEATNNFPEFTGRICPAPCEASCVLGINQPAVSIKQV
+EQSIADHLFDAPSLTPHPPQRQNGLTVAVVGSGPAGLAAAQQLTRSGYTVVVYEKDEALG
+GLLRFGIPDFKLEKHLIDRRIAQMTEEGTRFRTGVRIGTDMSWEALQRRYDAVVLATGAP
+VGRELPLPGRGLDGIHLAMDYLVPVNRRVAGGE-PEPISAQGRHVVILGGGDTGADCIGT
+AHRQGAASVTTLAIGRRPPEQRPEHQPWPTVPTLFEVASAHAEGGERTYLASTVEFLGDA
+EGRVRALKVAETEIRADGTRGPRAGTEHEIPADLVLLALGFTGADLDELVDRSAVSLERG
+LVVRDETYATQAPGVFACGDVSRGASLVVWAIAEGRAVAAEVDRFLTGDTMLPAPVRPSD
+HGFVLR
+>GCF_020097155_PROKKA_01695
+MADPRGFLKNRERVERPTRPVPVRIMDFKDVYVRQDEAVVRTQASRCMDCGIPFCHSGCP
+LGNLIPEWNDLVRRGRWEDAAARLHSTNNFPEVTGRICPAPCEDACTLGINQPAVTIKQT
+EVAIAEQIFDHDWLEPVVPTRINGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDDRPG
+GLLRYGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGRDLAWDALKARFDAVIVATGAP
+VGRELPVPGRGLDGIHLAMDYLVQSNHATAGDDVPGQITAEGRHVVVLGGGDTGADCIGT
+AHRQGAASVTTLAIGQQLPVDRPVHQPWPTVPKVHQMTTADAEGGQREHLASTVEFLGDE
+NGRVRALRVAETEYRADGTRGPKAGTEREVKADLVLLALGFTGVEEEALTAQLAVRTERG
+LVARAGTYETDEPGVFVCGDAGRGASLVVWAIAEGRACAQAVDESLESWSRLPHPVDPTD
+RGLVLG
+>GCF_023573625_PROKKA_01039
+MADPRGFLKNRERVERPTRPVPVRIMDFKDVYVRQDEAIVRTQAGRCMDCGIPFCHSGCP
+LGNLIPEWNDLVRRGRWDEAAARLHSTNNFPEVTGRICPAPCEDSCTLGINQPAVTIKQT
+EVAIAEQIFDNDWLEPVVPARLNGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDERLG
+GLLRLGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGVDLPWDQLKARFDAVIVATGAP
+VARELPVPGRGLDGIHLAMDYLVQSNRAVAGDEVPDQISAEGRHVVILGGGDTGADCIGT
+AHRQGAASVTTLAIGQQLPVERPVHQPWPTIPKVHQQTTADAEGGARAHLASTVEFLGDE
+HGRVRALRVAETEYREDGTRGPKAGTEREVQADLVLLALGFTGIEEGLLTQQLGVHVTRG
+LVARKDGYETDEPGVFACGDAGRGASLVVWAIAEGRACAQEVDESLERWSRLPHPVDPDD
+RGLVLG
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000945.fa

@@ -0,0 +1,36 @@
+>GCF_002008305_PROKKA_01136
+-----------MPRDEPVLRLSDVHRSLGRGRSRTPVLRGVDLTARAGAVTVLLGPNGAG
+KSTTLGLCHGMDRPDAGTVRVFGADPWRASADLRARIGVMWQEGGLPPAIPARRFVGHVA
+SLYRDPLPVEPLLERLLIAEVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLD
+PETRPVVHDVVREQTDRGAAVLLTTHLLDDAERLADDVAILRAGRVVRSGSLAELTRVAE
+GDVVDVDFGDASPDAVRAWADTLPAPLRAAGLDESARLRVAGVRGPDDLAVLAASWREHA
+LMPTRFERAGLRLEQILRETAA---------
+>GCF_003691675_PROKKA_00855
+-----------MPRDEPVLRLSDVHRSLGRGRSRTPVLRGVDLTARAGAVTVLLGPNGAG
+KSTTLGLCHGMDRPDAGTVRVFGADPWRASADLRARIGVMWQEGGLPPAIPARRFVGHVA
+SLYRDPLPVEPLLERLLIAEVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLD
+PETRPVVHDVVREQTDRGAAVLLTTHLLDDAERLADDVAILRAGRVVRSGSLAELTRVAE
+GDVVDVDFGDASPDAVRAWADTLPAPLRAAGLDESARLRVAGVRGPDDLAVLAASWREHA
+LMPTRFERAGLRLEQILRETAA---------
+>GCF_005280335_PROKKA_01756
+MVPRPVLTPDPAPRDEPVLRLRDVHRSLGRGRARTPVLRGVDLTARAGAVTVLLGPNGAG
+KSTTLGLCHGMDRPDAGAVRVFGADPWRAPADLRARIGVMWQEGGLPPSVPARRFVGHVA
+SLYRDPMPVEPLLERLLIADVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLD
+PETRPVVHEVVREQTARGAAVLLTTHLLDDAERLADDVAILRAGRVVRAGSLADLTRVAE
+GDVVDVDFGDAAPEAVRAWADALPEPLRAAGLAEPARLRVAGVHGPAELAALAASWHRHA
+LMPTRFERAGLRLEQILRETAA---------
+>GCF_020097155_PROKKA_01650
+M---PETSPHP---DAPALRLHEVRRTLGRGAARTEVLRGVDLEARRGAVTVLLGPNGAG
+KSTTLALCHGSDRPDSGTVRVFGRDPWRADADLRARLGVMWQEGGLPPSVTARRFVRHVA
+SLHGDPLDPDALLGRLRIDRVADRPIRRLSGGQRQRVALAAAVVGRPDLLFLDEPTAGLD
+PETRPVVHDVVREHTARGAAVLLTTHLLDDAERLADDVAILRAGRVVRAGTLAELTRVQD
+GDVVDVRFDEARAADVRAWVAAAPASFRAVASAGAPAARVAGVRSPADLEALAASWTRAG
+LFPTRLERAVLRLEELLQSPDADTPSPERSR
+>GCF_023573625_PROKKA_01086
+-----------MPRDEPVLRLSDVHRSLGRGRSRTPVLRGVDLTARAGAVTVLLGPNGAG
+KSTTLGLCHGMDRPDAGTVRVFGADPWRASADLRARIGVMWQEGGLPPAIPARRFVGHVA
+SLYRDPLPVEPLLERLLIAEVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLD
+PETRPVVHDVVREQTDRGAAVLLTTHLLDDAERLADDVAILRAGRVVRSGPLSELTRVAE
+GDVVDVDFGDASPDAVRAWADTLPAPLRAAGLGESARLRVAGVRGPDDLAVLAASWREHA
+LMPTRFERAGLRLEQILRETAA---------
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001022.fa

@@ -0,0 +1,21 @@
+>GCF_002008305_PROKKA_01222
+M--NTRAQP----------DAGRTGHGPPAWLVSAGGRGAPLTAKQDRDRAALAHLSLAF
+GVLGPLVVWLLYRDRGPFTSQESREALNFSGPPTLITLLFFFLSLLPVVGPIFAILGALT
+WAAMAVYGVMGASHVSKGRPFRYPFNLRILR
+>GCF_003691675_PROKKA_00941
+M--NTRAQP----------DAGRTGHGPPAWLVSAGGRGAPLTAKQDRDRAALAHLSLAF
+GVLGPLVVWLLYRDRGPFTSQESREALNFSGPPTLITLLFFFLSLLPVVGPIFAILGALT
+WAAMAVYGVMGASHVSKGRPFRYPFNLRILR
+>GCF_005280335_PROKKA_01666
+M--NPSAQP----------DAGRPGHEPPAWLASAGGRATPLTAKQDRDRAALAHLSLAF
+GVLGPLVVWLLYRDRGPFTSQESKEALNFSGPPTLITTLFFFLALLPVIGAIFAILGALS
+WAVMAVYGVMGASNVSKGRPFRYPFNLRILR
+>GCF_020097155_PROKKA_01563
+MATTPSTTPAGETATPRRAAGGSAAHEAPAWLRDAAGGRAPLTAKQDRDRAALSHLSLAC
+GLPGPLVMWLLYRDRGPFTAQESREALNFSLAPTLLIVLLFLLGGVPLLGGLLAILGALL
+WIALALYGVMGASQVAKGRPFRYPFSPRLLR
+>GCF_023573625_PROKKA_01180
+M--NTRAQP----------DAGRTGHGPPAWLVSAGGRGAPLTAKQDRDRAALAHLSLAF
+GVLGPLVVWLLYRDRGPFTSQESREALNFSGPPTLITLLFFFLSLLPVVGPIFAILGALT
+WAAMAAYGVMGASHVSKGRPFRYPFNLRILR
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001040.fa

@@ -0,0 +1,75 @@
+>GCF_002008305_PROKKA_01241
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPELADATYVEPITPAVVAKIIEK
+ERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANIEAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVE
+DLKYPVVVRPSFTMGGLGSGMAYDEADLYRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPVDGRVVVIEMNPRVSRSSALASKATGFAIA
+KIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPRFAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRS
+LEQKGSELAFPQDADPQALLAAASTATTDRLSQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADEIRDAEVLDEA
+LLRRAKRHGFSDAQIGSLRHMDAAVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSYDLETEVAPHEGESVIILGSG
+PNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVSTDYDISDRLYFEPLTLEDVLEVIAAEEASGGVRGVFVQLGG
+QTPLKLAQQLADAGVPILGTSPAAIDLAEHRGEFALVLERAGLVAPKNGTAVSFDDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVEHATEITPDQPMLVDRFLEDAIEIDVDALYDGTELYLGGVMEHIEEAGIHSGDSACVLPPVTLGPD
+VLERVHRATERIAAGVGVRGLINIQFALASDVLYVIEANPRASRTVPFVSKATGVQLAKAAARIGVGESIADLRAAGMLP
+TAYDGGTLPIGAPVAVKEAVLPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDKHFDTAFAKSQSAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQVVSTGGTAEVLRRNGIPAEVVAKIADAGHEDGAGTVLEQLHAGTVDLVLNTPSGGDART
+DGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRSYEWSVTSLQEHDARLQQAVAGPEAAA
+>GCF_003691675_PROKKA_00960
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPELADATYVEPITPAVVAKIIEK
+ERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANIEAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVE
+DLKYPVVVRPSFTMGGLGSGMAYDEADLYRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPVDGRVVVIEMNPRVSRSSALASKATGFAIA
+KIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPRFAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRS
+LEQKGSELAFPQDADPQALLAAASTATTDRLSQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADEIRDAEVLDEA
+LLRRAKRHGFSDAQIGSLRHMDAAVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSYDLETEVAPHEGESVIILGSG
+PNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVSTDYDISDRLYFEPLTLEDVLEVIAAEEASGGVRGVFVQLGG
+QTPLKLAQQLADAGVPILGTSPAAIDLAEHRGEFALVLERAGLVAPKNGTAVSFDDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVAHATEITPDQPMLVDRFLEDAIEIDVDALYDGTELYLGGVMEHIEEAGIHSGDSACVLPPVTLGPD
+VLERVHRATERIAAGVGVRGLINIQFALASDVLYVIEANPRASRTVPFVSKATGVQLAKAAARIGVGESIADLRAAGMLP
+TAYDGGTLPIGAPVAVKEAVLPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDKHFDTAFAKSQSAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQVVSTGGTAEVLRRNGIPAEVVAKIADAGHEDGAGTVLEQLHAGTVDLVLNTPSGGDART
+DGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRSYEWSVTSLQEHDARLQQAVAGPEAAA
+>GCF_005280335_PROKKA_01647
+MPKRPDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPELADATYVEPITPAVVAKIIEK
+ERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANIEAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVE
+DLKYPVVVRPSFTMGGLGSGMAYDEADLHRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPADGRVVVIEMNPRVSRSSALASKATGFAIA
+KIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPRFAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRS
+LEQKGSELAFPQDADPRELLRRARTATTDRLAQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADQIRDAEVLDES
+LLRHAKRHGFSDAQIGSLRHMGADVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSYDLETEVAPHEGRSVIILGSG
+PNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVSTDYDISDRLYFEPLTLEDVLEVIAAEEASGGVLGVYVQLGG
+QTPLKLAQQLADAGVPILGTSPEAIDLAEHRGEFARVLDRAGLVAPKNGTAVSFEDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVEHATEITPDQPMLVDRFLEDAIEIDVDALYDGERMYLGGVMEHIEEAGIHSGDSACVLPPVTLGPD
+VLERVHRATEQIAAGVGVRGLINIQFALASDVLYVIEANPRASRTVPFVSKATGVQLAKAAAMIGVGKSIADLQAEGVLP
+TAYDGATLPLGAPVAVKEAVLPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDRHYDTAFAKSQAAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQIVSTGGTAEVLRRNGIPAETVAKIAEAGGEDGAGTVLEQLHAGTVDLVLNTPSGGDART
+DGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRAYEWSVTSLQEHDARLQQAV---EASA
+>GCF_020097155_PROKKA_01544
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVILVNSNPATIMTDPELADATYVEPITPEVVAKIIEK
+ERPDAVLPTLGGQTALNTAIALDKDGVLEKFGVELIGANIAAIELGENRELFKGVVERAGGESARSHIVHTMEEAFAAVE
+DLKYPVVVRPSFTMGGLGSGMAYDEADLRRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPEDGRVVVIEMNPRVSRSSALASKATGFAIA
+KIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPRFAFEKFPAADATLTTTMKSVGEAMAIGRSFSEALQKALRS
+LEQKGSELSFDRDADPASLLASARTATTQRLAQTQRALYAGATLEEAFEATAIDPWFLDQLMLINEVADEVREAPQLDEA
+VLRRAKRHGFSDAQIGSLRHMDPAVVRGLRHALGVRPVYKTVDTCAAEFEAFTPYRYSSYDLESEVDEHAAPSVVILGSG
+PNRIGQGIEFDYSCVHATLALREAGYETVMVNCNPETVSTDYDISDRLYFEPLTLEDVLEVIAAEEATGGVAGVFVQLGG
+QTPLKLAQQLADAGVPILGTSPEAIDLAEHRGEFARVLDEAGLIAPKNGTAVSFEDARRVADEIGYPVLVRPSYVLGGRG
+MEIVYTEEALAHYVTNATEITPTQPMLVDRFLEDAIEIDVDALYDGHELYLGGVMEHIEEAGIHSGDSACVLPPVTLGPD
+VLERVRTATEKIAAGVGVRGLINIQFALASDVLYVIEANPRASRTVPFVSKATGVQLAKAAAMIGMGRTIAELRAAGTLP
+TAFDGASLPMGASVAVKEAVLPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDRHFDTAFAKSQAGAGGPLPTEGRVFVSV
+ANRDKRAVVGQAKRLVDLGFEIVSTGGTAEVLRRNGVPAEVVAKIADASDADGAGTVLEQLHEGRVDLVLNTPSGGEART
+DGYEIRAAATSLGVPVITTTAEFAACLQAIEAMRTYEWSVTSLQEHEERLAQAVAAEASA-
+>GCF_023573625_PROKKA_01199
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPELADATYVEPITPAVVAKIIEK
+ERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANIEAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVE
+DLKYPVVVRPSFTMGGLGSGMAYDEADLYRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPVDGRVVVIEMNPRVSRSSALASKATGFAIA
+KIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPRFAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRS
+LEQKGSELAFPQDADPQALLAAASTATTDRLSQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADEIRDAEVLDEA
+LLRRAKRHGFSDAQIGSLRHMDAAVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSYDLETEVAPHEGESVIILGSG
+PNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVSTDYDISDRLYFEPLTLEDVLEVIAAEEASGGVRGVFVQLGG
+QTPLKLAQQLADAGVPILGTSPAAIDLAEHRGEFALVLERAGLVAPKNGTAVSFDDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVEHATEITPDQPMLVDRFLEDAIEIDVDALYDGTELYLGGVMEHIEEAGIHSGDSACVLPPVTLGPD
+VLERVHRATERIAAGVGVRGLINIQFALASDVLYVIEANPRASRTVPFVSKATGVQLAKAAARIGVGESIADLRAAGMLP
+TAYDGGTLPIGAPVAVKEAVLPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDKHFDTAFAKSQSAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQVVSTGGTAEVLRRNGIPAEVVAKIADAGHEDGAGTVLEQLHAGTVDLVLNTPSGGDART
+DGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRSYEWSVTSLQEHDARLQQAVAGPEAAA

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001058.fa

@@ -0,0 +1,45 @@
+>GCF_002008305_PROKKA_01261
+---MPRLARLATAVTAAALSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHETGVFGESAAEIPAFDAVS
+GRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVTDKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTT
+TLRYLGGVRVGALPDSLAFSPNGAYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTAL
+PAGVRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLEDLWALTPTDWSTEGVLDA
+SDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGREWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLK
+VLTDLGYDSERECHSSLTTLGGRSFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPE
+PESVVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGAEGLTFVPADESPSGTAL
+LIVANEVSGSTTVYEVNPTR---RQ
+>GCF_003691675_PROKKA_00980
+---MPRLARLATAVTAATLSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHETGVFGESAAEIPAFDAVS
+GRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVTDKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTT
+TLRYLGGVRVGALPDSLAFSPNGAYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTAL
+PAGVRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLEDLWALTPTDWSTEGVLDA
+SDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGREWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLK
+VLTDLGYDSERECHSSLTTLGGRSFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPE
+PESVVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGAEGLTFVPADESPSGTAL
+LIVANEVSGSTTVYEVNPTR---RQ
+>GCF_005280335_PROKKA_01627
+---MRTLSRLAAATSMVALSAAVVAPLTVAAP------------AANPSGRSIELTAAGTHATGVFDASAAEIPAFDKTT
+GRLFVVNAQKGAIDVLTVGEDAEPAAESVLSVAGLPAADGSVTGAGAVVNSVAVAGAVMAATVEAEDKTGHGWLVFFDTR
+TLGFLGGVRVGALPDSVALAPNGAYAVVANEGEPADDFSSDPEGTISVVSVPKNARQFARLGQDAVRTVDFRAYDEGAAL
+PEGVRVFGPDVAVPSGHEEAGRIARNLEPEYASIDPTGRTAYVSVQEANAVVAVDLASASLADFWALHLTDWSTEGVLDV
+SDKDGAISPAYQPVLGVPMPDGLATYKHRGQTLVVTANQGDSREWGDFVDAERVKDLELCGDVFPHAKALQKNEALGRLN
+VLTDLGYDAERGCHTELHALGGRGFSIYTADGQRLFDSSGMLEEQIARLIAAGELPAHAFNANNDETPSFDSRSDDKGVE
+PESVVVGEVQGRQYAFVGLERIGGVMVFDITDPTDARYVDYINERAWDAVGEDGDAGLGDMGAEGLAFVPASDSPSGTAL
+LIVATEVSGSTTVYEVDPVKGGKRT
+>GCF_020097155_PROKKA_01524
+MSRIVRLTRLGAAAGALALSAAVVAPSAVSAPVTATAA------AANPSGKTVELSLAGTHETGVFGESAAEIPAFDAAT
+GRLFVVNAEKGAVDVLRVGADGAPAAETVLSAEGLRTADGSVTDGGATVNSVAVSGGVLAVAVEAADKTGLGWVAFFDTT
+TLSYLGGVRVGALPDSIAFSPDGAYAVVANEGEPADDFSADPEGTISVISVPKNVRQFARLTQAAVRTVDFRAYDAGTAL
+PEGVRVFGPDVQVPEGQEPAGRIARNLEPEYVTIDDTGRTAYVSVQEANAVVAVDLKSATLKDFWALQLTDWSKEGVLDA
+SNEDKAITLRNQPVLGVPMPDGVDTYRYRGQDLVVTANEGDSREWGDFVDAARVKDLELCTAEYPDAKALQKKPALGRLN
+VVTDLGYDADRDCFSQLHAFGGRSFSIYTADGTRLFDSAGMIEEQIAQLIADGELPESAFNANNDETPSFDSRSDDKGPE
+PEAVVVGRVQGRTYAFVGLERIGGVMVFDITDPTKATYVDYVNERNWDAEGDDAAAGLGDMGAEGLTFVPANESPSGTAL
+LVVANEVSGSTTVYEVNPVR---R-
+>GCF_023573625_PROKKA_01219
+---MPRLARLATAVTAATLSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHETGVFGESAAEIPAFDAVS
+GRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVTDKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTT
+TLRYLGGVRVGALPDSLAFSPNGAYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTAL
+PAGVRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLEDLWALTPTDWSTEGVLDA
+SDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGREWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLK
+VLTDLGYDSERECHSSLTTLGGRSFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPE
+PESVVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGAEGLTFVPADESPSGTAL
+LIVANEVSGSTTVYEVNPTR---RQ

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001060.fa

@@ -0,0 +1,50 @@
+>GCF_002008305_PROKKA_01263
+-----------------MLRTHSLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVRDEADFDPLRNEW
+VLQVTGTVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARLRHRYLDLRRPQPSRIMRLRSEVN
+RTARELLHGEGFVEVETPTLTRSTPEGARDFLVPARLAPGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADR
+QPEFTQLDIEASFVEQDDVIALGEKIVKALWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKDTPFR
+VFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGELTGPVSKNISEEEKAGLAAAVGANPGDCVFFA
+AGKPKESRALLGAARVEIGRRCGLFTDAGDGVAAKDADWAFVWVVDAPMFEPAADAVASGDVAVGAGAWTAVHHAFTSPK
+PEFADTFDTDPGAALAYAYDIVCNGNEIGGGSIRIHRQDVQERVFEVMGLSPEEANEKFGFLLEGFKYGAPPHGGIAFGW
+DRVVALLAGTDSIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAQPEPKQAEAE-------PEA------------
+---
+>GCF_003691675_PROKKA_00982
+-----------------MLRTHSLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVREEADFDPLRNEW
+VLQVTGTVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARLRHRYLDLRRPQPSRIMRLRSEVN
+RTARELLHGEGFVEVETPTLTRSTPEGARDFLVPARLAPGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADR
+QPEFTQLDIEASFVEQDDVIALGEKIVKALWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKHTPFR
+VFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGELTGPVSKNISEEEKAGLAAAVGANPGDCVFFA
+AGKPKESRALLGAARVEIGRRCGLFTDAGDGVAAKDADWAFVWVVDAPMFEPAADAVASGDVAVGAGAWTAVHHAFTSPK
+PEFADTFDTDPGAALAYAYDIVCNGNEIGGGSIRIHRQDVQERVFEVMGLSPEEANEKFGFLLEGFKYGAPPHGGIAFGW
+DRVVALLAGTDSIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAQPEPKQAEAE-------PEA------------
+---
+>GCF_005280335_PROKKA_01624
+MNPTISSGRSPDGEDAFVLRTHQLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVRDEADFDPLRNEW
+VLQVSGVVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARLRHRYLDLRRPEPSRIMRLRSEVN
+RTAREMLHGEGFTEVETPTLTRSTPEGARDFLVPARLAPGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADR
+QPEFTQLDIEASFVEQDDVIALGEKIVKAVWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTAYFKDTPFR
+VFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGSLTGPVSKNISDEEKAGLAAAVGANPGDCVFFA
+AGKPKESRALLGAARVEIGRRCELFTDAGNGVEAKDADWAFVWVVDAPMFEPAADAVASGDVAVGSGAWTAVHHAFTSPK
+PEFADTFDTDPGSALAYAYDIVCNGNEIGGGSIRIHRQDMQERVFSVMGLSQEDAQEKFGFLLEGFKYGAPPHGGIAFGW
+DRVVALLAGTESIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAKPEPKKAEGEKAEAAGQPQA------------
+---
+>GCF_020097155_PROKKA_01521
+-----------------MLRTHHLGELNASLIGQTVTVTGWVAKRRDHGGVAFVDLRDASGRAQVVVRDEADFDPLRNEW
+VLQVTGTVERRPEGNENPNLPTGEVELIADDVVVLNTAAALPFQIDEHVEVGEEARLRHRYLDLRRPQPARIMRLRSEAN
+RVARELLNEQGFVEVETPTLTRSTPEGARDFLVPARLAPGSWYALPQSPQLFKQLLQVGGLEKYYQIARCYRDEDFRADR
+QPEFTQLDIEASFVEQDDVIALGEQIVKALWGLVGVEVQTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKDTPFR
+VFQNEYVGAVVMPGGASQPRRTLDAWQEWAKQRGAKGLAHVLIQEDGTLTGPVSKNITDEEKAGLAAAVGANPGDCVFFA
+AGKAKESRALLGAARVEIGRRCELFTDAGDGVEAKDADWAFVWVVDAPLFEPAADAVASGDVAVGAGQWTAVHHAFTSPK
+PEFMDTFDTDPGSALAYAYDIVCNGNEIGGGSIRIHRQDVQKRVFSVMGLSEEDANEKFGFLLEGFKYGAPPHGGIAFGW
+DRVVALLAGTESIREVIAFPKTGGGYDPLTAAPAPITPQQRKEAGVDAKPEAKKAEGAASEGA-EAQAKANDEKTAADEA
+QLR
+>GCF_023573625_PROKKA_01221
+-----------------MLRTHSLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVRDEADFDPLRNEW
+VLQVTGTVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARLRHRYLDLRRPQPSRIMRLRSEVN
+RTARELLHGEGFVEVETPTLTRSTPEGARDFLVPARLAPGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADR
+QPEFTQLDIEASFVEQDDVIALGEKIVKALWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKDTPFR
+VFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGELTGPVSKNISEEEKAGLAAAVGANPGDCVFFA
+AGKPKESRALLGAARVEIGRRCGLFTDAGDGVAAKDADWAFVWVVDAPMFEPAADAVASGDVAVGAGAWTAVHHAFTSPK
+PEFADTFDTDPGSALAYAYDIVCNGNEIGGGSIRIHRQDVQERVFEVMGLSPEEANEKFGFLLEGFKYGAPPHGGIAFGW
+DRVVALLAGTDSIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAQPEPKQAEAE-------PGA------------
+---

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001064.fa

@@ -0,0 +1,26 @@
+>GCF_002008305_PROKKA_01267
+MTTVTIEETAPAGALMLAGDPFTEPELQALGARGAVRPLLPGVWARPDAADDPAVRAAAL
+WTLGGPLLAAGWTAIGPSAAWILAGGAAPGRLHAAVPHFHRRPAGGGQLPWTLTQSDVAA
+DATGVAPAEQDVLRFGPVRVTTPARTVEDLLLSADPDAARRAAAVIGAHGAAGLRERLAR
+RTRRAGVVAARRRLGALLTALDVPD
+>GCF_003691675_PROKKA_00986
+MTTVTIEETAPTGALVLAGDPFTEPELQALGARGAVRPLLPGVWARPDAADDPAVRAAAL
+WTLGGPLLAAGWTAIGPSAAWILAGGAAPGRLHAAVPHFHRRPAGGGLLPWTLTQSDVAA
+DATGVAPAEHDVLRFGPVRVTTPARTVEDLLLSADPDAARRAAAVIGAHGAAGLRERLAR
+RTRRAGVVAARRRLGALLAALDVPD
+>GCF_005280335_PROKKA_01620
+ME-----------GLILAGEPFTPAELQALGSRGVVVPLVPGVWARPEAARRPGVRAEAL
+WMLGGPVLAGGWTAIGSSAAWVLTGGAVPERLHAAVPHFHRLPAGGSPLPWTLTQSDVAA
+GPDGRAPAEEDVLRIGPLRVTTPERTVEDLLLSPDPDAARTAAAVIAAHGAAGLRERLAR
+HSRRSGVVAARRRLDVLLGALEAAG
+>GCF_020097155_PROKKA_01515
+MHQG--HGSRGGAAWELAGMTFTEPELRLLAARGTLEAVLPGVYRPVDVPSEPAGRAAAL
+GLLGGPVLASGWTAVGPSAAWVHVGGPAPHRLHAAVPHFHRLPAGGAAPAWRLVQSDVAA
+GPTGAAPAEEDVQVLEGVRVTVPARTVEDLLLTGDPDDARRAARVIAAHGAEGLRDRLDR
+PSRRPGSVGARRRLRMLLDALGADG
+>GCF_023573625_PROKKA_01225
+MTTVTIEETAPTGALVLAGDPFTEPELQALGARGAVRPLLPGVWARPDAADDPAVRAAAL
+WTLGGPLLAAGWTAIGPSAAWILAGGAAPGRLHAAVPHFHRRPAGGGLLPWTLTQSDVAA
+DATGVAPAEHDVLRFGPVRVTTPARTVEDLLLSADPDAARRAAAVIGAHGAAGLRERLAR
+RTRRAGVVAARRRLGALLAALDVPD
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001116.fa

@@ -0,0 +1,31 @@
+>GCF_002008305_PROKKA_01331
+MTKNSQPPASSSGSTSATLKEVKAMQRERRLREKEQAKAQRRDKRATKGPGVISQLKQAY
+AMTKAHDPKVGLWMLLAFLGALVVGLVIGLLLDNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVSEQPAAVNPKTQDLVYRAVGRPGVVLVTEGPSPR
+VAALVVKEEKAMRRFLPGVPVTVVESGNGQGQVPLHELPGTLKGMKKALTAQEVQAVDKR
+LTALNTNRLPIPKGVDPNKVRPSRRAMRGR
+>GCF_003691675_PROKKA_01052
+MTKNSQPPASSSGSTSATLKEVKAMQRERRLREKEQAKAQRRDKRATKGPGVISQLKQAY
+AMTKAHDPKVGLWMLLAFLGALVVGLVIGLLLDNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVSEQPAAVNPKTQDLVYRAVGRPGVVLVTEGPSPR
+VAALVVKEEKAMRRFLPGVPVTVVESGNGQGQVPLHELPGTLKGMKKALTAQEVQAVDKR
+LTALNTNRLPIPKGVDPNKVRPGRRAMRGR
+>GCF_005280335_PROKKA_01560
+MTKNSQPPASSSGSTSADLKQVKAMQRDRRRRVKEETRAQRRDKRANRGPGIISQLKQAY
+AMTKANDPKVGLWMLLAFVGVLVLGLVIGLLLNNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVPEQPVAVNPKTQDVVYRAVGRPGVVLVTEGPSNR
+IAALVGKEEKAMRRFLPGVPVTVVEAGNGQGQVPLHELPRTLKSMKKALTAQEVQAVDKR
+VNALNVNRLPIPKGVDPMKARPSRRAMRGR
+>GCF_020097155_PROKKA_01456
+MAKNPSTSPSSSGSSS--LKEVKAMQRDRRAQLKADAKAERAQKRANAGPGIISQLKQVF
+AITRQQNPRLVLWMVLAFASVLVLGLVVGLLLHNWITWLLLAIPFGVLAAVIVMNRLGER
+AMFDRLEGQTGAAGATLSSLGRGWIVGEQPSAVNPKTHDLVYRAIGKPGVVLVTEGPASR
+VGKLVSKEQKAMERFLPGVPVHVVETGRGEGQIPLREVPKTLKALPKKLTAQEVSAVDKR
+LSALGTQKPPIPKGVDPMRARPDRRGMRGR
+>GCF_023573625_PROKKA_01287
+MTKNSQPPASSSGSTSATLKEVKAMQRERRLREKEQAKAQRRDKRATKGPGVISQLKQAY
+AMTKAHDPKVGLWMLLAFLGALIVGLVIGLLLDNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVSEQPAAVNPKTQDLVYRAVGRPGVVLVTEGPSPR
+VAALVVKEEKAMRRFLPGVPVTVVESGNGQGQVPLHELPGTLKGMKKALTAQEVQAVDKR
+LTALNTNRLPIPKGVDPNKVRPSRRAMRGR
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001128.fa

@@ -0,0 +1,26 @@
+>GCF_002008305_PROKKA_01346
+MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA
+APAAGPAADTP----EAAATPASAEESAPAA-------------APESADAAATSAAGVL
+AMAQRLHDEHVAAGEQRSTELVAEAEATAARLVSDAEEQKARTLEALAEEKAGLEGEVEQ
+LRSFETDYRSRLTSYIEGQLREIRAQKRVEPPTPTA
+>GCF_003691675_PROKKA_01066
+MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA
+A----PVADTP----EAAETPSPVEEPAPAA-------------APEAADAAATSAAGVL
+AMAQRLHDEHVAAGEQRSTELVAEAEATAARLVSDAEEQKARTLEALAEERAGLEGEVEQ
+LRSFETDYRSRLTSYIEGQLREIRAQKRVEPPTPTA
+>GCF_005280335_PROKKA_01546
+MALSWEDVVNKQFQPTKFREGYDQGEVDDFLDEIVGELKRLQGLNEQLTAENEALRAGGA
+VPDADAAVDAPVADADAAAVVDAGQSPAPAALAD-AEPGLEVEPTPSSADPASASAAGVL
+AMAQRVHDEHVAAGEQRRDELISEAEARAEALVAEAEETRTRTLEELAADKAGLEAEVEQ
+LRGFETDYRSRLTAYIEGQLREIRSQERVEPAQRPA
+>GCF_020097155_PROKKA_01442
+MVLSWEDVVNKEFQLTKFREGYDREEVEDFLDEVVEELKRLTEENDRLRSDLDACREGAP
+---AQAEASAPAAGEAAPAL----QAPAPVAPVEPSAPG-----EPVAPTDSATSAAGVL
+AMAQRLHDEYVAEGEQRRDRIIADAEAEATTVVRQAEETRTRTLSDLESRRKGLEADVER
+LRAFETDYRSRLTAYIEGQLREITAQERLEPAKGTV
+>GCF_023573625_PROKKA_01301
+MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA
+APAAAPAADTP----EAAATPASVEEAAPAA-------------APESADAAATSAAGVL
+AMAQRLHDEHVAAGEQRSTELVAEAEATAARLVSDAEEQKARTLEALAEEKAGLEGEVEQ
+LRSFETDYRSRLTSYIEGQLREIRAQKRVEPPTPTA
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001133.fa

@@ -0,0 +1,46 @@
+>GCF_002008305_PROKKA_01351
+---MAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLD
+VGRELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARI
+ARSLGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVM
+DAFRQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKA
+AELAIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDD
+ALGDEVRVTVIAAGFDKVDVTSAPAAPQAVQQQAAPQRAAAPAQPQPA-AQPQPA-----
+-APAQ---PQQAERPAVRGTVPL--------APQEQQ--------------PRRQQDLPT
+VVEPDLGAGSSDLDVPDFLK
+>GCF_003691675_PROKKA_01071
+---MAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLD
+VGRELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARI
+ARSLGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVM
+DAFRQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKA
+AELAIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDD
+ALGDEVRVTVIAAGFDKVDVTSAPAAPQAAQQQAAPQRAAAPAQPQP-------------
+-VPAQ---PQQAERPAVRGTVPL--------APQEQQ--------------PRRQQDLPT
+VVEPDLGAGSSDLDVPDFLK
+>GCF_005280335_PROKKA_01541
+MDTVAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLD
+VGRELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARI
+ARSLGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVM
+DAFRQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKA
+AELAIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDD
+ALGDEVRVTVIAAGFDKVDATSAPASPQAGQFQQAPQRPAQQAQPQQQ-A---PAPQQHQ
+AQPAQQEQPQQVQPQSVRGTVPL--------APQQPQQTE-----------QRRQQDLPT
+VVEPDLGAGSSDLDVPDFLK
+>GCF_020097155_PROKKA_01437
+MDTVAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLD
+VGRELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARI
+ARSLGALTIGVVTRPFTFEGRRRAGSAENGIDALRDEVDTLIVIPNDRLLSISDRNVSVM
+DAFRQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKA
+AELAIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDD
+ALGDEVRVTVIAAGFDKVDATSAPAAP--FQQQAAPQRAAAPQQPAQQ-A--------QQ
+APVSQQAAPQ---RPSVPGTMPLNSSSAFGGAPAQPAATQQPAAPQQPAAPQRAQQDLPT
+VVEPEF--GSSDLDVPDFLK
+>GCF_023573625_PROKKA_01306
+---MAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLD
+VGRELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARI
+ARSLGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVM
+DAFRQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKA
+AELAIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDD
+ALGDEVRVTVIAAGFDKVDVTSAPAAPQAVQQQAAPQRAAAPTQPHPVPAQPQPAPAQPQ
+PAPAQ---PQQAERPAVRGTVPL--------APQEQQ--------------PRRQQDLPT
+VVEPDLGAGSSDLDVPDFLK
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001142.fa

@@ -0,0 +1,26 @@
+>GCF_002008305_PROKKA_01361
+MTLHEEMSMAAHARIAESL----RPGSTPVAPARPTPQERTPLSVVPAPLPRSRSGVTVL
+CVLVVLAALAAVLVMNITMSNRQYALLDLRQEQQAVTETNERLAEQVGHLEAPQNLAARA
+DALGMVAPAGTASVDAGTGQFSGEAQAAQDGDISATYVAPPADADAVRQGTAGDG---QD
+EIEGPRTLG------GEDASAAPDQDAAD----R
+>GCF_003691675_PROKKA_01081
+MTLHEEMSMAAHARIAESL----RPGSTPVAPARPAPQERTPLSVVPAPLPRSRSGVTVL
+CVLVVLAALAAVLVMNITMSNRQYALLDLRQEQQAVIETNERLAEQVGNLEAPQNLAARA
+DALGMVAPAGTASVDAGTGEFGGEAQAAQDGDVSATYVAPPADADVVRQGASAEG---QD
+EIEGPRTLG------GEDASAAADQDAAD----R
+>GCF_005280335_PROKKA_01532
+MTLHEEMSMAAHARIAEPL----RHTG---APARPAPQERTPLSVVPAPLPRSRSGMTVL
+CVVVLLAALAAVLVMNITMSNRQYALLDLRQEQQAVTEVNERLAEQVGYLEAPQNVAARA
+DALGMVAPAGTASVDAATGEFRGEAQPAREGEISATFVAPPVNADAVRQGSAGSADADRG
+DIEGPRTLG--APAAAPGAAASDDRDASD----R
+>GCF_020097155_PROKKA_01427
+MTAYEETGMSAQAWRDEARTAWPRTGATPEREHR----QRTPLSVVPTPLPRSGSGVAVL
+CGLVLLVALGLVLVMNITMSNRQFTLLDLRAQQTTLTETNERLAEQAGYLDAPQNLAARA
+GAMGMVSPGATSTVDVASGAVAGPSTGAGSTTLPEGRIAPPADADLARQGEA------QG
+QIPGPRTVDPAAPTAAPSGETAPTPAPTDAPAGR
+>GCF_023573625_PROKKA_01316
+MTLHEEMSMAAHARIAESL----RPGSTPVAPARPTPQERTPLSVVPAPLPRSRSGVTVL
+CVLVVLAALAAVLVMNITMSNRQYALLDLRQEQQAVTETNERLAERVGHLEAPQNLAARA
+DALGMVAPAGTASVDAGTGQFSGEAQAAQDGDISATYVAPPADADAVRQGTAGDG---QD
+EIEGPRTLG------GEDASAAPDQDAAD----R
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0001184.fa

@@ -0,0 +1,36 @@
+>GCF_002008305_PROKKA_01434
+MTPA------AAVRHFLVDTDLTPAEQAEVLDLAAQMKADRFRHRPLAGPRTGIVFFDKT
+STRTRVSFAAGIAELGGTPLIVNPGESQLGHKESVADTARVLERMVGVIVWRTFAQAGLE
+EMAAHSSVPVVNALSDDYHPCQILADLLTVREHLGGTAGRTLTYLGDAANNMAHSYLLGC
+ATAGMHVRVAGPEGHLPAEDVVAAARQRAAETGGSVLVTTDAAEALAGADVVVTDTWVSM
+GQEEEKEARLALFRDYQVDAAAMARAADDAIFLHCLPAYRGYEVTAEVIDGPRSVVFDEA
+ENRLHAQKALIAWLLYRSGLAEEPR
+>GCF_003691675_PROKKA_01166
+MTPA------AAVRHFLVDTDLTPAEQAEVLDLAAQMKADRFRHRPLAGPRTGIVFFDKT
+STRTRVSFAAGIAELGGTPLIVNPGESQLGHKESVADTARVLERMVGVIVWRTFAQAGLE
+EMAAHSSVPVVNALSDDYHPCQILADLLTVREHLGGTAGRNLTYLGDAANNMAHSYLLGC
+ATAGMHVRVAGPEGHLPAEDVVAAARQRAAETGGSVLVTTDAVEALAGADVVVTDTWVSM
+GQEEEKEARLALFRDYQVDAAAMARAADDAIFLHCLPAYRGYEVTAEVIDGPRSVVFDEA
+ENRLHAQKALIAWLLYRSGLAEEPR
+>GCF_005280335_PROKKA_01464
+MTPAP-TPAPAAVRHFLVDTDLTPGEQAEVLDLAAQMKTDRFAHRPLAGPRTGVVFFDKT
+STRTRVSFAAGIAELGGSPLIVNPGESQLGHKESVADTARVLERMVGIIVWRTFAQSGLE
+EMAAHSRVPVVNALSDDYHPCQILADLLTVREHLGGTQGRVLAYLGDAANNMAHSYLLGC
+ATAGMHVRIAGPAGHLPAEHVVAAARERAAETGGSVLVTTDAAEALDGADVVVTDTWVSM
+GQEDEKEARLALFRDYQVDAAAMARAGSDAIFLHCLPAYRGYEVSAEVIDGPQSVVFDEA
+ENRLHAQKALMAWLLYRSGLAEDPR
+>GCF_020097155_PROKKA_01372
+MTAAPGTDVP--VRHFLVDTDLSPAEQAEVLDLALEMKADRFRHRPLAGPQTGIVFFDKT
+STRTRVSFAAGIADLGGTPLIVNPGESQLGHKESIADTARVLERMVGVIVWRTYAQSGLE
+EMAAHSRVPVVNALSDDYHPCQLLADLLTVREHKGRTRGLTMAYLGDAANNMANSYLLGG
+VTAGMHVRVAGPEGFLPDPAVVRAAEERAGETGGSVLVTTDAAAALDGADVVVTDTWVSM
+GQEDEKEERLRLFADYRVDAAAMARAASDAVFLHCLPAYRGYEVTEDVIDGPQSVVFDEA
+ENRLHAQKALMAWLLYRSGLAQDPR
+>GCF_023573625_PROKKA_01384
+MTPA------AAVRHFLVDTDLTPAEQAEVLDLAAQMKADRFRHRPLAGPRTGIVFFDKT
+STRTRVSFAAGIAELGGTPLIVNPGESQLGHKESVADTARVLERMVGVIVWRTFAQAGLE
+EMAAHSSVPVVNALSDDYHPCQILADLLTVREHLGGTAGRNLTYLGDAANNMAHSYLLGC
+ATAGMHVRVAGPEGHLPAEDVVAAARQRAAETGGSVLVTTDAVEALAGADVVVTDTWVSM
+GQEEEKEARLALFRDYQVDAAAMARAADDAIFLHCLPAYRGYEVTAEVIDGPRSVVFDEA
+ENRLHAQKALIAWLLYRSGLAEEPR
+