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Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000008.fa

@@ -0,0 +1,83 @@
+>PROKKA_00711
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>PROKKA_01398
+MEGSLEGSHGDRVRLEDGRGHRGGLHHYPGLNSFTTWDPGASSIPAPTQQSLRTLEWLSR
+RENLVVCGPSGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARI
+LRADLIVIDDIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATAT
+VDRLLHHAHVCQTTGDSVRMTQAMAGKGVMPLN
+>PROKKA_01502
+MAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIGLLPVADDAAEGLYRIVDAA
+YEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQTTGDSVRMTQAMAGKGVMP
+LN
+>PROKKA_02225
+MLWKVRSKAPTVTASVSKMVVATGEGYTTIRDSTPKTLATATVDRLLHHAHVCQTTGDSV
+RMTQAMAGKGVMPLN
+>PROKKA_02227
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTVKSLEVV
+>PROKKA_00092
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>PROKKA_00343
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>PROKKA_01013
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>PROKKA_01394
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>PROKKA_02284
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>PROKKA_00606
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>PROKKA_01016
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPIADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>PROKKA_01158
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPIADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>PROKKA_01349
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>PROKKA_02164
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000012.fa

@@ -0,0 +1,42 @@
+>PROKKA_00156
+MKGAAQLDFIRRGQAVGLTLAQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQ
+LRTTIADLREDAAAGDPATCSPEDVCRYL
+>PROKKA_00159
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLGPAVG
+>PROKKA_01075
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAVGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATC
+SPEDVCRYL
+>PROKKA_02063
+MRIGEVAAASGVTTKALRFYEERGLLPQADRATNGYRDYPEDTIVRLEFIRRSQVAGLTL
+AEILDILQIRDAGTAPCGHVRDQLAEHLTNLDRHIAELTALRETVAGLHGTAAAGDPAQC
+NAEVICSYL
+>PROKKA_00297
+MRIGELAERAGTTAKTLRFYEEQGLLPPAERTPSGYRDYAPETAARIDFVHRGQAAGLTL
+AQIRQILDIRDDGAAPCEHVRDLLDARLAEIEQQIAQLAALRDTITELRRDAAQPDPDSC
+SADQVCRYL
+>PROKKA_00338
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC
+SPEDVCRYL
+>PROKKA_00345
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC
+SPEDVCRYL
+>PROKKA_00794
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC
+SPEDVCRYL
+>PROKKA_00720
+MLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATCSPEDV
+CRYL
+>PROKKA_00722
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGSSPMKWC
+SG
+>PROKKA_02223
+MRIGEVAAASGVTTKALRFYEERGLLPQADRATNGYRDYPEDTIVRLEFIRRSQVAGLTL
+AEILDILQIRDAGTAPCGHVRDQLAEHLTNLDRHIAELTALRETVAGLHGTAAAGDPAQC
+NAEVICSYL
+>PROKKA_01024
+MLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATCSPEDV
+CRYL

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000017.fa

@@ -0,0 +1,102 @@
+>PROKKA_00542
+MSIADAPQASVVPPVDPAAERRFSRVLIANRGEIAVRIIRACQDEGLTSVAVYAEPDRDA
+LHVTLADEAVALGGETAADSYLVIGKILDAAERAGADAVHPGYGFLSENADFARAVTDAG
+LVWIGPPAEAIDRLGDKVSARQLATKVGAPLAPGTTSPVTGTEEVVAFADEFGLPVAIKA
+AYGGGGRGIKVARTREEIPEFYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG
+DVVVISTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILQEAGYVGAGTCEFLVG
+QDGTISFLEVNTRLQVEHPVSEEITGIDLVREQFRLARGEALGYTDPQPRGHSIEFRLNG
+EDPGRNFLPAPGRLTTFRMPSGPGVRVDSGVVEGEAVSGAFDSMVAKLIVTGADRRQALQ
+RAARALREAEIVGMPSVLPFHRAVVRDPAFAPEIAGSEEPFSVHTRWIETEFANRIEPSA
+LTPAEPAPREARHTVTVEVNGKRVDVTLPTWGEALHTISGAAQRAGAGRRRPRGKRGAPV
+AAAVSTDALTAPMQGTVVKVAAENGQTVAEGDLIVVVEAMKMEQPLAAHRAGVVSGLEVE
+PGQTVTAGTVIATIADAE
+>PROKKA_01915
+MTTTPAARPVTRVLIANRGEIAVRVARAARDHGIASIAVYSDPDADALHVAVADEAFHLP
+GASSADTYLKIDAVLDVARRAGADAVHPGYGFLSENADFAQAVIDAGMTWIGPSPDAIRA
+LGDKITARSLAQQAGAPLVPGSDGPVPDAAAARAFAEEHGLPIAIKAAFGGGGRGIRVVR
+ELGDVEDAFEATVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHGHVAVLGTRDCSLQ
+RRNQKLVEEAPAPFLTDEQRERIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVNTR
+LQVEHPVTEEVFGVDLVREQFRIAAGELLSIPEDPTPRGHALEFRLNAEDPAYGFLPVPG
+PIDAFEAPTGPGVRMDSGVRTGSVVPGEYDSLLAKLIVWGEDRAQAIARARDALAELRID
+GVPTVVPFHRAVLEQDAFTSGDRLGVYTTWIESEFAEPLAESPYLGAEVPAGGRTSVTVE
+LDGRAVRLGLPADLYAALLGGGGAGAAAPADAAGAGKPDDDGAVASPVTGTLASWKVEDG
+AEVAEGDTVAIVEAMKMETPIRAPRAGRIQLLVAETPASVTRGQAISRLGA
+>PROKKA_00267
+MSIADAPQASVVPPVDPAAERRFSRVLIANRGEIAVRIIRACQDEGLTSVAVYAEPDRDA
+LHVTLADEAVALGGETAADSYLVIGKILGAAERAGADAVHPGYGFLSENADFARAVADAG
+LVWIGPPAEAIDRLGDKVSARQLATKVGAPLAPGTTSPVTGTEEVVAFADEFGLPVAIKA
+AYGGGGRGIKVARTREEIPEFYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG
+DVVVISTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILQEAGYVGAGTCEFLVG
+QDGTISFLEVNTRLQVEHPVSEEITGIDLVREQFRLARGEALGYTDPQPRGHSIEFRLNG
+EDPGRNFLPAPGRLTTFRMPSGPGVRVDSGVVEGETVSGAFDSMVAKLIVTGADRRQALQ
+RAARALREAEIVGMPSVLPFHRAVVRDPAFAPEIAGSEEPFSVHTRWIETEFANRIEPSA
+LTPAEPAPARRATP
+>PROKKA_01611
+MTTTPAARPVTRVLIANRGEIAVRVARAARDHGIASIAVYSDPDADALHVAVADEAFHLP
+GASSADTYLKIDAVLDVARRAGADAVHPGYGFLSENADFAQAVIDAGMTWIGPSPDAIRA
+LGDKITARSLAQQAGAPLVPGSDGPVPDAAAARAFAEEHGLPIAIKAAFGGGGRGIRVVR
+ELGDVEDAFEATVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHGHVAVLGTRDCSLQ
+RRNQKLVEEAPAPFLTDKQRERIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVNTR
+LQVEHPVTEEVFGVDLVREQFRVAAGEPLSIPEDPTPRGHALEFRLNAEDPAYGFLPVPG
+PIDAFEAPTGPGVRMDSGVRTGSVVPGEYDSLLAKLIVWGEDRAQAVARARDALAELRID
+GVPTVVPFHRAVLEQDAFTSGDRLGVYTTWIESEFAEPLAESPYLSAEVPAGGRTAVTVE
+LDGRAVRLGLPADLYAALLGGGGAGAAAPAGAAGAGKPDDDGAVASPVTGTLASWKVEDG
+AEVVEGDTVAIVEAMKMETPIRAPRAGRIQLLVAETPASVTRGQAIARLGA
+>PROKKA_02407
+MSIADAPQASVIPPRDPKAERRFSRVLIANRGEIAVRVVRACQDEGLTSVAVYAEPDRDA
+LHVKLADEAVALGGETAADSYLLVEKILDAAERSGADAVHPGYGFLSENADFARAVEAAG
+LVWIGPPAEAIDRLGDKVSARQLATKVGAPLAPGTTSPVTGTEEVVAFADEHGLPVAIKA
+AYGGGGRGIKVARSREEIPELYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG
+GVVVMSTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILKEAGYVGAGTCEFLVG
+QDGTISFLEVNTRLQVEHPVTEEVTGIDLVREQFRLARGEALGYEDPVVRGHSFEFRLNG
+EDPGRNFLPAPGRLTTFRMPSGPGVRVDTGVVEGETVSGAFDSMVAKLIVTGADRRQALQ
+RAARALGEAEIAGMPSVLPFHRAVVTDPAFAPEIAGAAEPFTVHTRWIETEFANHIEPSE
+HAPADPTSREPRRTVTVEVNGKRVDVTLPTWGEALHTISGAAQRAGAGRRRPRGRRGAPV
+AAAVSTDALTAPMQGTVVKVAAENGQTVAEGDLIVVVEAMKMEQPLTAHRAGVVSGLEVE
+PGQTVSAGTVIATIADAD
+>PROKKA_00880
+MSTPSTTASRPVTRVLIANRGEIAVRVARACRDHGIASIAVYSDPDAQAMHVAVADEAYA
+LPGSTSAETYLDIAAVLDVARRSGADAVHPGYGFLSENADFAQAVIDAGLTWIGPSPQAI
+RDLGDKITARAIAQRAGAPLVPGSDGPVPDAAAARAFAQEHGLPIAIKAAFGGGGRGIKV
+VRELSEVEDAFESAVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHGAVAVLGTRDCS
+LQRRNQKLVEEAPAPFLTDEQRQRIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVN
+TRLQVEHPVTEEVFGVDLVREQFRIAAGEPLSIPEDPAPRGHAIEFRLNAEDPAHGFLPV
+PGPVEAFEAPTGPGVRMDSGVRTGSVVPGEYDSLLAKLIVVGEDRSQAIARARDALAELR
+IEGVPTVVPFHRAVLEEEAFTSAEALGVYTTWIESEFAAPLAASPHLGASVPGGGRTTVT
+VEVDGRAVRLGLPADLHAALLGGGGARTGASAPAEQSVDEGAVTSPVTGTLASWKVEDGA
+QVAEGDTIAVVEAMKMETPVRAPRAGRVERAAGDAPAAVTRGQVLASVRA
+>PROKKA_02288
+MTNASAPQASADIAEAPGRPFSRVLIANRGEIAVRVIRACQDEGLTSVAVYAEPDRDALH
+VKLADEAVALGGETAADSYLVIQKVLDAAERSGADAVHPGYGFLSENAEFARAVEAAGLV
+WIGPPADAIDALGDKVSARRIATKVGAPLAPGTTSPVNGTDEVVAFADEFGLPVAVKAAY
+GGGGRGIKVARTREEIPELYESAVREAVAAFGRGECFVERFLDRPRHVETQCLADAHGNV
+VVVSTRDCSLQRRNQKLVEEAPAPFLTDEQNTRLVESSKALLKEAGYVGAGTCEFLVGQD
+GTLSFLEVNTRLQVEHPVSEEVTGIDLVREQFRIARGEALGYGDPEARGHSFEFRLNGED
+PGRNFLPAPGTLTRFRMPSGPGVRVDAGVTEGETVSGAFDSMVGKLIVTGADRRQALQRA
+ARALAEAEIAGMPSVLPFHRAVVADPAFAPELAGSEEPFAVHTRWIETEFAHQIEPTALT
+PAAAPDRPERHTVTVEVNGKRVDVTLPTWGEAMHQLQGAAARAGAGRRRPRGARRAGAAP
+AAPGTDSLTAPMQGTVVKVAAQNGDRVAEGDLIVVMEAMKMEQPLTAHRAGVVSGLEVAA
+GDALTAGAVIAVIADAE
+>PROKKA_00545
+MSIADAPQASVVPPVDPAAERRFSRVLIANRGEIAVRIIRACQDEGLTSVAVYAEPDRDA
+LHVKLADEAVALGGESAADSYLVVGKILDAAERAGADAVHPGYGFLSENADFARAVADAG
+LVWIGPPAAAIDRLGDKVSARQLATKVGAPLAPGTTSPVTGTEEVVAFADEFGLPVAIKA
+AYGGGGRGIKVARTREEIPEFYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG
+DVVVISTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILQEAGYVGAGTCEFLVG
+QDGTISFLEVNTRLQVEHPVSEEITGIDLVREQFRLARGEALGYTDPQPRGHSIEFRLNG
+EDPGRNFLPAPGRLTTFRMPSGPGVRVDSGVVEGETVSGAFDSMVAKLIVTGADRRQALQ
+RAARALREAEIVGMPSVLPFHRAVVRDPAFAPEIAGSEEPFSVHTRWIETEFANRIEPSA
+LTPAEPAPREARHTVTVEVNGKRVDVTLPTWGEALHTISGAAQRAGAGRRRPRGKRGAPV
+AAAVSTDALTAPMQGTVVKVAAENGQTVAEGDLIVVVEAMKMEQPLAAHRAGVVSGLEVE
+PGQTVTAGTVIATIADAE
+>PROKKA_01835
+MTTTPAARPVTRVLIANRGEIAVRVARAARDHGIASIAVYSDPDADALHVAVADEAFHLP
+GASSADTYLKIDAVLDVARRAGADAVHPGYGFLSENADFAQAVIDAGMTWIGPSPDAIRA
+LGDKITARSLAQQAGAPLVPGSDGPVPDAAAARAFAEEHGLPIAIKAAFGGGGRGIRVVR
+ELGDVEDAFEATVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHGHVAVLGTRDCSLQ
+RRNQKLVEEAPAPFLTDEQRERIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVNTR
+LQVEHPVTEEVFGVDLVREQFRVAAGEPLSIPEDPTPRGHALEFRLNAEDPAYGFLPVPG
+PIDAFEAPTGPGVRMDSGVRTGSVVPGEYDSLLAKLIVWGEDRAQAVARARDALAELRID
+GVPTVVPFHRAVLEQDAFTSGDRLGVYTTWIESEFAEPLAESPYLSAEVPAGGRTAVTVE
+LDGRAVRLGLPADLYAALLGGGGAGAAAPAGAAGAGKPDDDGAVASPVTGTLASWKVEDG
+AEVVEGDTVAIVEAMKMETPIRAPRAGRIQLLVAETPASVTRGQAIARLGA

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000020.fa

@@ -0,0 +1,73 @@
+>PROKKA_00524
+MTIVDFFRLLRANLLLLLAAALVGGLLGWGYSALQPRIYASESQGFLAARAADQSLITSN
+LPAESRAQAYVALINSEAVRERVAQDTGQDGDGSLSAVLVPESSMIKVTATSTDPETAAQ
+LANSALQATADVAADVDKNSPLEVVPLSDARVPSAPVSPDTRRNVLLGVVAGLGAGLAIA
+VLRRLLDVKVRSRADVKEITGAGVIGAVPENASLTRTGEEAVDLDPRAGEAIRALRTNLK
+FVSVDEPPRVVSFTSADPSEGKSTVASNLARALALAGERVLVVDADLRRPRQHDLFQVAG
+DVGLSEVLAGEVQPDDALAATGIPNLTLLPAGRTPPNPSELLGSKRMRALLKLASEDFFV
+IVDSPPLLPVTDGSLLATAVDGTVLVVRQGRTRKDHLEAAVENLAAVDAHLLGVVMNGVA
+RSQRGGGYSYGYGYESTYHKSHDKYLQGTGKGGKKSRRAARAKKG
+>PROKKA_00245
+MTIVDFFRLLRANLLLLLAAALVGGLLGWGYSALQPRIYASESQGFLAARAADQSLITSN
+LPAESRAQAYVALINSEAVRERVAQDTGQDGDGSLSAVLVPESSMIKVTATSTDPETAAQ
+LANSALQATADVAADVDKNSPLEVVPLSDARVPSAPVSPDTRRNVLLGVVAGLGAGLAIA
+VLRRLLDVKVRSRADVKEITGAGVIGAVPENASLTRTGEEAVDLDPRAGEAIRALRTNLK
+FVSVDEPPRVVSFTSADPSEGKSTVASNLARALALAGERVLVVDADLRRPRQHELFQVAG
+DVGLSEVLAGEVQPDDALAATGIPNLTLLPAGRTPPNPSELLGSKRMRALLKLASEDFFV
+IVDSPPLLPVTDGSLLATAVDGTVLVVRQGRTRKDHLEAAVENLAAVDAHLLGVVMNGVA
+RSQRGGGYSYGYGYESTYHKSHDKYLSGVGSSAKKGRRSRRKARTRG
+>PROKKA_00256
+MNIIDFLRVLRANRLVILGCAALGLALGLLYSLLQPTLYTATSTAFVTVEGEASISGTET
+AQTRAQSYIPLINSRTVRERIAAEGLDTAGATLSAALVPNSNLITVSAVAPDAQQAAALA
+NGALVATADVANELDPTSNVKVTAMEDALAPAAPSSPDRVRHLLYGLGAGLVLGLIVAFL
+RRLLDVNVRTTTDAQVAGGAGLLGAIPLDPSMKAERTAPMAPLSPRASEAVRQLRTNLRF
+AAVDDPPRTIAFTSSNPGEGKSTVIGNLALTVAAAGQPVILIDADLRRPRQALQFGVDGR
+VGLSEVLNGDVALQDVLIPVGEDGLLLLPAGRTPPNPSEQLGSERMRDLLTALAETHMVL
+VDAPPVLPVTDSTLLATAVDGTVLVIRHGKTRKEHLEVARDMLAGVNARVLGVVLNGTPA
+SGVGSDYYGGGYGADGGSYDAYYQAPRDAAEAAAGTAGDASRR
+>PROKKA_01211
+MDLQQYLQTFRKYWRSILTVLSVCVGAALVFTFLQTPKYSSTSSALIAVDTAATPGELSS
+GALYAERQVSSFVALADSALVLDPVINELGLNVTPQALRSRVSVSAPAGTSIVDVTVTDT
+NAGRAAEVANAITASLKNVTSDVVPTGPDGDEIVTVTVVEPAAASSRPVSPRPVVNIALG
+LIAGVVIGLGQALVRRLLDSRIRTRDDLVEITDAPVLASVVHHKGSDRPKDEAAPARGTA
+WASAESYRKLRTAVGFVALGGERRSSIVVTSSVQGEGKTETSTNLAKVLAETGARVLLVD
+ADLRRPQVGARLGLDDELGLSDVLTGRADLNDVLLSVDDLSVLTAGTVPPNPSELLGSEA
+MAELLALVEAHFEYVILDAPPLLPVTDAAILSHQAGGAIVVARSGVARQNQLAEALSILE
+AADASVYGVVLNDVPVSHIDGYSQYYR
+>PROKKA_02417
+MNIIDFLRVLRANRLVILGCAALGLVAGLVYSLLQPTLYTATSTGFVTVQGEATISGTET
+AQTRAQSYIPLINSRTVREKIAEGGLDTAGASLSAAVVPGSNLITVSAESEDPEQAAALA
+NSALVATAETANGLDPTSNVQVTAMEDALAPTSPTSPDYVRNMLYGLGAGLLLGLVIAVL
+RRILDVNVRTTTDAQVASGAGLLGAIPLDATLKAERDAPRGEPSPRAAEAVRQLRTNLRF
+AAVDDPPRTIAFTSANPGEGKSTVIGSLALAVAASGQPVILIDADLRRPRQALQFGVDGR
+VGLSEVLNGDVALQDVLVPVGDHGLLLLPAGRTPPNPSEQLGSARMRDLLTALAETHMVL
+VDAPPVLPVTDSTLLSTAVDGTVLVVRHGKARKEHVEVARDMLAGVNARVLGVVLNGTPA
+SGVGSDYYGGSYASKGDDYHAYYQASRDAESRPSDEAVPEGPAAQR
+>PROKKA_02299
+MNILDFLRVLRANRLVLLGGVVLGLLGGLVYSLLQPTLYTSTSTGFVTVAGEASISGTET
+ALTRAQSYVPLINSRTVREKVAESGVDVSGSTLSAQVVPNSNLITVTALAPDPQRAADLA
+NTALGATAEVANSLDPTSNVKVTAMEDALPPAGPSSPDHLRNALIGAGIGLLAALAVAFL
+RRVLDVNVRTTTDATEASGAGLLGAIPQDGTMKAERTAPLGVPSPRAAEALRQLRTNLRF
+AAVDDPPRVVMVTSSNPGEGKSTVIAGLAQAVAVSGQPVILVDADLRRPRQASQFGVDGR
+VGLSEVLSGDVLLEDAVQDLGDGLLLLPAGRTPPNPSEQLGSHRMQELLRVLAETHLVLV
+DAPPGAAGDGLHPAGGRRGRDRAGGAPRQDPEGPCGGGPGHAGQGQRPHAGRGAQRRARL
+RCGLGLLRRGLRRGRRQLRRLLPGAPGRRRRRGRDRGRHVATLIAPGGRARSSHRRRRPG
+DAEGPRL
+>PROKKA_00524
+MTIVDFFRLLRANLLLLLAAALVGGLLGWGYSALQPRIYASESQGFLAARAADQSLITSN
+LPAESRAQAYVALINSEAVRERVAQDTGQDGDGSLSAVLVPESSMIKVTATSTDPETAAQ
+LANSALQATADVAADVDKNSPLEVVPLSDARVPSAPVSPDTRRNVLLGAVAGLGAGLAIA
+VLRRLLDVKVRSRADVKEITGAGVIGAVPENASLTRTGEEAVDLDPRAGEAIRALRTNLK
+FVSVDEPPRVVSFTSADPSEGKSTVASNLARALALAGERVLVVDADLRRPRQHDLFQVAG
+DVGLSEVLAGEVQPDDALAATGIPNLTLLPAGRTPPNPSELLGSKRMRALLKLASEDFFV
+IVDSPPLLPVTDGSLLATAVDGTVLVVRQGRTRKDHLEAAVENLAAVDAHLLGVVMNGVA
+RSQRGGGYSYGYGYESTYHKSHDKYLQGTGTAGKGGKKSRRAARAKKG
+>PROKKA_00535
+MNIIDFLRVLRANRLVILGCAALGLAMGLVYSLLQPTLYTATSSAFVTVEGEASISGTET
+AQTRAQSYIPLINSRTVRERIASEGLDTAGATMSAALVPNSNLITVSAVAPDAQQAAALA
+NGALVATADVANELDPTSNVKVTAMEDALAPATPSSPDRVRHLLYGLGAGLVLGLIVALL
+RRLLDVNVRTTTDAQVAGGAGLLGAIPLDPSMKAERTAPMAPLSPRASEAVRQLRTNLRF
+AAVDDPPRTIAFTSSNPGEGKSTVIGNLALTVAAAGQPVILIDADLRRPRQAMQFGVDGR
+VGLSEVLNGDVALQDVLIPVGEDGLLLLPAGRTPPNPSEQLGSERMRDLLTALAETHMVL
+VDAPPVLPVTDSTLLATAVDGTVLVIRHGKTRKEHLEVARDMLAGVNARVLGVVLNGTPA
+SGVGSDYYGGGYGADGGSYDAYYQAPRDAPEAAAGTAGDTSRR

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000021.fa

@@ -0,0 +1,48 @@
+>PROKKA_00570
+MHAGWSLGAAAGAGLGAAVITVGGPAALHLGLNGAVCVAVLLGVRRLFLAEAPVDSASAR
+GAADQSPAPSETSAPPAPAAQALPRRAAVAVLVPAVVIAMAGFGVEEFGNAWATLFLITE
+RGLDPAAAVLGASTLLGAQFVGRLAGDRTLAVLGRRGALTAGLGAVVVGLGLALAPLPGP
+VAVPAAFAGLALAGLGCAVVVPVAYALGDEAPGLRPQTGLAVTSWCMRLAGVGLSPAVGA
+LAGAVGLAPALTVFLGLAAVGTVLAARLPAAP
+>PROKKA_00571
+MSEAPPHLPTADDGVARARRARWAVTAAFATNGALLGALIPHYPEAKAAFGLDPAAFGLL
+VIALAVGGTLAGPLPAPILRRFGARRVMLAGSVAIALLTTAAGLVLDIAGAGAGAGHGAG
+TAAAWLLWVFAGLVLASGVLDAVVDTAQNAQGLQV
+>PROKKA_00294
+MHAGWSLGAAAGAGLGAAVITVGGPAALHLGLNGAVCVAVLLGVRRLFLAEAPVDSASAR
+GAADQSPAPSETSTPPAPAAQALPRRAAVAVLVPAVVIAMAGFGVEEFGNAWATLFLITE
+RGLDPAAAVLGASTLLGAQFVGRLAGDRTLAALGRRGALTAGLGAVVVGLGLALAPLPEP
+VAVPAAFAGLALAGLGCAVVVPVAYALGDEAPGLRPQTGLAVTSWCMRLAGVGLSPAVGA
+LAGAVGLAPALTVFLGLAAVGAVLAARLPAAP
+>PROKKA_00295
+MSEAPPHLPTADDGVARARRARWAVTAAFATNGALLGALIPHYPEAKAAFGLDPAAFGLL
+VIALAVGGTLAGPLPAPILRRFGARRVMLAGSVAIALLTTAAGLVLDIAGAGAGAGHGAG
+TAAAWPLWVFAGLVVASGVLDAVVDTAQNAQGLQV
+>PROKKA_02374
+MPSASPSSPAARRARAHPVARRDVVRARWAATLAFLTNGGMLGALIPHYPQAKAAFGLDA
+DAFGLLVVALAAGAAAAGSLPAPVLRRWGSRRVMLAGTVVMAVVVVAAGLVVDLSAPAQG
+RPWAGAVWLFAALLGVAGILDAVVDTAQNAQGLTVQTRLARPVLTSMHAGWSLGAGLGAG
+LGALAVGAGMPAGLHLGLNGAACVAVLVAAGRRFLPDDARPAPDADAPEGTAAPAPGPSP
+RRPARPPPPRPAPPPGWPCSP
+>PROKKA_02375
+MAGFGVEEFGNAWTALFLQSERGLDVAAAGLGASTLLLAQFVGRLVGDRVLHRLGRRRTL
+AGSLAVVVAALVLVLTAPAAPAVFAGLALAGLGCAVVVPTAYALGDEVPGLPPRTGLAVV
+SWLMRVAGIGLSPLVGLLATGLPLPAALAVFPALAVLGLVGTGVVGRRRRRP
+>PROKKA_02254
+MTSAPADTPRIDRRAATRSRWAATAAFFTNGALAAAMIPHYPQAKAAFGLDPAGFGLLVT
+VMTLGAACAGPAGAPILRRAGSRATVLWGSLAIAVVLTGAGLALDLGARSDAAGPWLGAY
+AAAVFASGLCDAVVDTAQNAQGLRAQHALGRPVLTSMHAGWSLGAAVGAALGAAAVGAGV
+PAGLHLGLNGAACVLLLALTLPRFLPDTPDHAPAPALLTADDPGPESEATPASHRHPWLL
+LAPIVVISMAGFSVEEFGNSWTSLFLQAERGLDPATAGLGASTLLGAQFLGRLTGDRVLA
+ALGRTRALTGGLAVVLAGLTVTLLVPTPAAMFTGLALAGLGSAVVVPTAFALADEVPGLP
+AQTGLAVVSWLMRLAGLGLSPLVGLLAGVLPLTAALGAFVVLAALGTVLALTLRAPRLAP
+DFR
+>PROKKA_00572
+MSEAPPHLPTADDGFARARRARWAVTAAFATNGALLGALIPHYPEAKAAFGLDPAAFGLL
+VIALAVGGTLAGPLPAPILRRFGARRVMLAGSVAIALLTTAAGLVLDIAGAGAGAGHGAG
+TAAAWPLWVFAGLVLASGVLDAVVDTAQNAQGLQVQTRLARPVLTTMHAGWSLGAAAGAG
+LGAAVITVGGPAALHLGLNGAVCVAVLLGVRRLFLAEAPTDSASARDASDQSPAPSETST
+PPAPAAQALPRRAAVAALLPAVVIAMAGFGVEEFGNAWATLFLITERGLDPAAAVLGAST
+LLGAQFVGRLAGDRTLAALGRRGALTAGLGAVVVGLGLALAPLPGPVAVPAAFVGLALAG
+LGCAVVVPVAYALGDEAPGLRPQTGLAVTSWCMRLAGVGLSPAVGALAGAVGLAPALTVF
+LGLAAVGAVLAARLPAAP

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000026.fa

@@ -0,0 +1,70 @@
+>PROKKA_00134
+MSTSPSGSRVAETGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFYGSAGGIQAAGPGV
+ILSFLVAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIV
+ADTAAITTYMAFWFPGVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMI
+FGGVILLFTGASTADGTQASLANLVDHGGFLPHGILGVLTALTIVTFSFGGIETLGVAAG
+EAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPFVQIFEGLGVPFAP
+HLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMV
+LGAVLITVDPNAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVG
+TYLGLAFVATVVITMATIPDSRQALIIGLVWVAVLTLAWFVTGTRTSAAAHDRTGTLPVV
+RTRQSHED
+>PROKKA_02148
+MSTSPSGSRVAETGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFYGSAGGIQAAGPGV
+ILSFLVAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIV
+ADTAAITTYMAFWFPGVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMI
+FGGVILLFTGASTADGTQASLANLVDHGGFLPHGILGVLTALTIVTFSFGGIETLGVAAG
+EAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPFVQIFEGLGVPFAP
+HLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMV
+LGAVLITVDPNAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVG
+TYLGLAFVATVVITMATIPDSRQALIIGLVWVAVLTLAWFVTGTRTSAAAHDRTGTLPVV
+RTRQSHED
+>PROKKA_00251
+MSTSPSGSRVAEPGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFYGSAGGIQAAGPGV
+ILSFLIAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIV
+ADTAAITAYMAFWFPEVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMI
+FGGVILLFTGASTADGTQAGLANLVDHGGFLPHGILGVLTALTIVTFSFGGIETLGVAAG
+EAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPFVQIFEGLGVPFAP
+HLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMV
+LGAVLITVDPNAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVG
+TYLGLAFVATVVITMATIPDSRQALIIGLVWVAVLTLAWFVTGVRKAAAVHDRTGTLPVA
+SGEEAAASHR
+>PROKKA_00186
+MNASPSGAHAVDHPRDDAAHAAQSQLHRGLSQRHIMFIALGTAIGTGLFYGSAGGIQTAG
+PGVILSFLIAGFAVYLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAV
+VIVADTAAVTKYMAFWFPGVPAWAWVAATILVIGLVNLTHVGNFGEAEFWLTLIKIGAIV
+AMIFGGLILMFTGASFTDGTPAGLHNLVDHGGFLPHGFGGVLIALTIVTFSFGGIETLGV
+AAGEAKDPETALPKAINTVPVRILLFYVLTMVVIMSLVPWSAVDGKTSPFVQIFEGLGVP
+FAPHILNFVVLTAAISAINACIYASGRLLYAMAHDGQAPRAFTRTTANGVPWLTVAVMLG
+VMVLGAILITVNPDAFGLIAGVASFAVVLTWTMIFLSHRAMRARVKEAGAPPSVYPMPFG
+IVGTVLGLAFVATVVITMATIPESRQALLIGLAWVVALTAAWFVTGVRKTAALHDRTGQL
+PVVHRHH
+>PROKKA_00187
+MQSTPAPEAPAQAQLQRGLNPRHITFIALGTAVGTGLFYGSAAGIQAAGPGVVLAFMLAG
+AAVYLVMRALGEMAVREPISGSFVAYASRYLGPFAGFLTGWTYVFELAVVIVADTTAVTV
+YMAFWYPDVPAWVWVAATMVVLGLINVTHVGSFGEAEFWFSLIKVLAIVGMIFGGVILMF
+SGASFQDGVTPGPHNLVEHGGFLPHGLMGVLTALTIVTFSFGGTETLGIAAGEAEDPASA
+LPRAVNTVPVRILFFYIGSMLVIMSLVPWTTVDGETSPFVQIFETLGVPFAPHLLNFVVL
+TAAVSAINACIFTNARLLHHMAHDGHAPRVFTAVTRGGVPWVTVVAMLGVMAAGAVFMSV
+KEDTFGIVAGVATFAVVFTWALILASHLGMRRALARHGQAPGAFPMPGGRVGAWLGLAFV
+AVVAGTMAFDQGGAVLGALGGPDALQTALAQPFVIGVLWLAVLAAAWAVPAVRRSAHRHD
+RHGTPPPLTWDV
+>PROKKA_02180
+MTPERRGPGTSPGGRYGVRVNEPPALPEPTGAAPPAPSPAGGATAAPSHGAADARLRRGL
+SMRHIQFIALGSAIGTGLFYGSATAIQLAGPAVILAYLVAGAAVFMVMRALGELAVRHPV
+PGSFGQYADRYLGPFAGFVTGWTFVFEMVVVAIADVTAFGVYMGFWFPDTPRWIWVTAVI
+LFIAAVNTRHVKVFGELEFWLSIVKVSAILAMVIGGVALLVMGVSLDAATPAGVQNLVDH
+GGFAPHGAAGVLAALSVVVFAFGGVETIGITAGEAQDPGRAIPRAVNAVPARILLFYVMT
+MVVIMSLVPWDRITGEASPFVEIFSTLGVPAAPAILNLVVITAAISAINADTFSAGRMLF
+GMAQQGRAPAVFASVSRGGVPWMAAVVMGLALAVGAVLNAVIPEDVFVVVASIATFATVW
+VWLMILLAHIAMRREVARRGLPASAFPVPLWPAASWAAVAFVLLVVGLLGWFSDTRVAMI
+VGLVWLVLLGAAYRLFLHGHGRSRPDLEEGAASSP
+>PROKKA_00142
+MSTSPFGSRVAETGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFYGSAGGIQAAGPGV
+ILSFLVAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIV
+ADTAAITTYMAFWFPGVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMI
+FGGVILLFTGASTADGTQASLANLVDHGGFLPHGILGVLTALTIVTFSFGGIETLGVAAG
+EAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPFVQIFEGLGVPFAP
+HLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMV
+LGAVLITVDPNAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVG
+TYLGLAFVATVVITMATIPDSRQALIIGLVWVAVLTLAWFVTGTRTSAAAHDRTGTLPVV
+RTRQSHED

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000027.fa

@@ -0,0 +1,14 @@
+>PROKKA_00161
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>PROKKA_01073
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>PROKKA_00336
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>PROKKA_00347
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>PROKKA_00792
+MAAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>PROKKA_00724
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>PROKKA_01022
+MAAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000028.fa

@@ -0,0 +1,49 @@
+>PROKKA_00162
+MSTPATRGRADGGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALL
+SDAGHMAADVVVLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVV
+EAISRLGDAPEVASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSV
+GVMVAGVLIILTGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGD
+LDAVEGVEEVHDLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQ
+VEGAGSDGCHDLSW
+>PROKKA_01072
+MGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALLSDAGHMAADVV
+VLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVVEAISRLGDAPE
+VASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSVGVMVAGVLIIL
+TGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGDLDAVEGVEEVH
+DLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQVEGAGSDGCHD
+LSW
+>PROKKA_00335
+MGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALLSDAGHMAADVV
+VLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVVEAISRLGDAPE
+VASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSVGVMVAGVLIIL
+TGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGDLDAVEGVEEVH
+DLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQVEGAGSDGCHD
+LSW
+>PROKKA_00348
+MGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALLSDAGHMAADVV
+VLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVVEAISRLGDAPE
+VASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSVGVMVAGVLIIL
+TGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGDLDAVEGVEEVH
+DLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQVEGAGSDGCHD
+LSW
+>PROKKA_00791
+MGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALLSDAGHMAADVV
+VLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVVEAISRLGDAPE
+VASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSVGVMVAGVLIIL
+TGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGDLDAVEGVEEVH
+DLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLHDRYGIAHATLQVEGAGSDGCHD
+LSW
+>PROKKA_00725
+MGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALLSDAGHMAADVV
+VLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVVEAISRLGDAPE
+VASGAMLAVGFAGLVINIISMLLLRSGTKDSLNVKGAYYEVIADAAGSVGVMVAGVLIIL
+TGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGDLDAVEGVEEVH
+DLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQVEGAGSDGCHD
+LSW
+>PROKKA_01021
+MGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALLSDAGHMAADVV
+VLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVVEAISRLGDAPE
+VASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSVGVMVAGVLIIL
+TGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGDLDAVEGVEEVH
+DLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQVEGAGSDGCHD
+LSW

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000029.fa

@@ -0,0 +1,28 @@
+>PROKKA_00163
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARALYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>PROKKA_01071
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARALYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>PROKKA_00334
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARALYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>PROKKA_00349
+MSVTLLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARALYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>PROKKA_00790
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARVLYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>PROKKA_00726
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLADPRRARVLYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>PROKKA_01020
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARVLYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000032.fa

@@ -0,0 +1,42 @@
+>PROKKA_00245
+MSEQTTPDGAESPIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIGAI
+LLSGSPKAFAAGADIKEMATKEFSEMYAADWFAGWDGLTRARTPIVACVTGYALGGGCEL
+AMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGRMIGAEEAER
+IGLVSRVVADEKALEEALEVAATIASKSKPASWMAKEAVNAAFETTLAQGIAFERRVFHA
+AFATADQKEGMDAFTAKREAGWQHR
+>PROKKA_00096
+MSTGLHIETVDRIGIIRLDRPAELNALTFATVEEIAAQVQRWEVDGETDGVVITGSGQKA
+FAAGADIRELQHKSVQEMTARGMQHAMTALRESSLISVAAVNGLALGGGFELALSCDIRL
+ATPQASFGLPELGLGIIPGAGGTQLLTRYTNASVASYHILTGQPISADRAHQLGLVSELH
+EAEDLMAAAMEVIGTIASKGPLARQLAKRAIHGAAHAGMDSGLEIELLAQAAIFGTQERE
+EGLNAFLERRTPSFIPRPRPRKD
+>PROKKA_00100
+MTDRIRTSVEQGVCTITLNRPGALNALENTMIATIVAELERAGADPDVRAILLRGEGKAF
+CAGDDLVDMGTEEHPESPDLVERYSRGYPAIVERMLTLEKPIVASVRRYALGAGLEMALA
+ADLIVAEPQAKLGLPFVLRGIAAGTSLLPKRAPVQLVQRMLYLGEMITAEDAHRMGVVGH
+LAEDEDVDELALATARRLAVGATRAIGLMKTALRTSETLSARDALAVQVGATAASVLTED
+FTEGKVAFTQKRDPEFGGR
+>PROKKA_02257
+MSEQTTPDGAESPIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIGAI
+LLSGSPKAFAAGADIKEMATKEFSEMYAADWFAGWDGLTRARTPIVACVTGYALGGGCEL
+AMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGRMIGAEEAER
+IGLVSRVVADEKALEEALEVAATIASKSKPASWMAKEAVNAAFETTLAQGIAFERRVFHS
+AFATADQKEGMDAFTAKREAGWQHR
+>PROKKA_00124
+MSEQTTPDGAESPIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIGAI
+LLSGSPKAFAAGADIKEMATKEFSEMYAADWFAGWDGLTRARTPIVACVTGYALGGGCEL
+AMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGRMIGAEEAER
+IGLVSRVVADEKALEEAQEVAAAIASKSKPAAWMAKETVNAAFETTLAQGIAFERRVFHS
+AFATTDQKEGMDAFANKREAGWQHR
+>PROKKA_00093
+MNEQNRTEAAEAEQPVIVGRDGRVGRIQLNRPKALNALNAATMEAVVAAAVEMDADPEVG
+AILLLGSAKAFAAGADIKEMKDKDAADMYAADWFRRWEDLARLRTPIVACVQGYALGGGC
+ELAMMADVLVAGRSAKFGQPEITLGVLPGMGGSQRLTKSVGKAKAMDMVLTGRMVEAEEA
+ERMGLVSRLVEDEDAVATAEEVAATIAGFSKPVAQMNKEVVLNAFETPLTQGLVFERRVF
+HGVFSSEDQAEGMAAFAEKRSPVWKHR
+>PROKKA_00245
+MSEQTTPDGAESPIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDLEIGAI
+LLSGSPKAFAAGADIKEMATKEFSEMYAADWFAGWDGLTRARTPIVACVTGYALGGGCEL
+AMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGRMIGAEEAER
+IGLVSRVVADEKALEEAKEVAAAIASKSKPAAWMAKETVNAAFETTLAQGIAFERRVFHS
+AFATADQKEGMDAFTAKREAGWRHR

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000035.fa

@@ -0,0 +1,21 @@
+>PROKKA_00627
+MPAAYPREFRQDVVAIARKGQIPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGITKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
+>PROKKA_00372
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGITKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
+>PROKKA_00389
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGVTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLVQSPK
+>PROKKA_00393
+MPAAYHREFRQDVIAIARKGQMPIAQVAKDFGIAESRLRRWLAQDDVEAGIRPGVTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLVQSPK
+>PROKKA_00410
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGVTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
+>PROKKA_02189
+MPAAYPREFRQDVVAIARNGQMPIAQVAKDLGITASCLRRWLAQDDVEAGIRPGLTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
+>PROKKA_00604
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGITKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK

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

@@ -0,0 +1,41 @@
+>PROKKA_01791
+MQPIDQTTSGPATSVGERPLAGIRVVSVAVNLPGPLAAARLAEFGAEVVKIEPPTGDPLA
+AAAPQWYAELIAGQRVLTLDLKTGPGQDHLATLLKGADLLLSSLRPSAADRLGLPASAHA
+AGAVFLEVVGHDGDDADLPGHDLTYQAAAGTLDAPRMPLVPVADLLGGERAVSAALAALR
+SRDHGGPVTRVRVTLEDAARAAAAPVRRGLLGPGGPLGGDLPTYSLYASADGHVAVAAVE
+PHFAARLAEHIGSTRDEIARTILTRPGAEWERIANELDLPLAVVRPPR
+>PROKKA_02047
+MSAAPLAGVRVVTIALNLPGPAAAARLQELGADVVTVLPPSGDPVATLVPALYEELHRGQ
+SVRTVDMKSQAGVAEMEQILAEADVFLTSHRSGALRRLGLDADAVRARHRRICQVDITGY
+AGDRTDVPGHDINYQAAAGLLAPGAPPRILAADLHGAERAVSTALALLWARGADGDGGHA
+TVALAEAAHALALPNRHRMTDPRSPLGGALPHYGVYPAAEGHVAVGALEPHFAAALVEGL
+GLDADGDVRAQLTEALSRHDAAHWQAWGEKRGIPLTALVSPTA
+>PROKKA_01753
+MSAAPLAGVRVVTIALNLPGPVAAARLQELGADIVTVLPPSGDPVATLVPALYEELHRGQ
+SVRTVDMKSQAGAAEMEQILAEADVFLTSHRSGALRRLGLDADAVRARHRRICQVDITGY
+DGDRTDVPGHDINYQAAAGLLAPGAPPRILAADLHGAERAVSAALALLWARGADGDGGHA
+TVALADAAHALALPNRHRMTGPRSPLGGALPHYGVYPAAEGHVAVGALEPHFAAALVEGL
+GLDADGDVRAQLTEALSRHDAAHWQAWGEERGIPLTALASPTA
+>PROKKA_01085
+MQPIDQTTSGPATSVGERPLAGIRVVSVAVNLPGPLAAARLAEFGAEVVKIEPPTGDPLA
+AAAPQWYAELIAGQRVLTLDLKTGPGQDHLATLLEGADLLLSSLRPSAADRLGLPASAHA
+AGAVFLEVVGHDGDDADLPGHDLTYQAAAGTLDAPRMPLVPVADLLGGERAVSAALAALR
+SRDHGGPATRVRVTLEDAARAAAAPVRRGLLGPGGPLGGDLPTYSLYASADGHVAVAAVE
+PHFAARLAEHIGSTRDEIARTILTRPGAEWERIANELDLPLAVVRPPR
+>PROKKA_00733
+MSAGDGASRVPAGDAVVPGPLADVAVVTIALNLPGPLAAFRLAELGAQVTTVLPPAGDPV
+ATLVPALYTELHAGMAELTLDLKQDGDRARMEELLAGADVLLTSHRSGALTRLGLDAAAT
+ARRHPRLVQVDITGFPGERADVPGHDLNYQAEAGLLEPGHPPRGLLADVHGAERAVSAAL
+AGLHARDRDGRGGGVVVALSDAAHAMALPTRHGMTDPGSPLGGANPFYGVYPARSGHVAL
+GALEPHFAHAMVEALQLDPDGDVRAQLTAAFAERDADAWQSWGEEWGHPITALAGPTA
+>PROKKA_00743
+MDVVGFAGERAGVPGHDLTYQAETGLLLSGESQTPTLPRALVADMHGAEQAVSTAPALLL
+ARDRAGRDAPGGHARVSLAEAAAAVGIPSRHGLLAPDALLGGGTPYYAVYRAAEGHVAVG
+ALEPHFSDALRAELDLPAGAGDDLAAALSAALTARPARDWQEWGEERGIPTGRGAVNGQP
+R
+>PROKKA_01981
+MSAAPLAGVRVVTIALNLPGPAAAARLQELGADVVTVLPPSGDPVATLVPALYEELHRGQ
+SVRTVDMKSQAGVAEMEQILAEADVFLTSHRSGALRRLGLDADAVRARHRRICQVDITGY
+AGDRTDVPGHDINYQAAAGLLAPGAPPRILAADLHGAERAVSTALALLWARGADGDGGHA
+TVALAEAAHALALPNRHRMTDPRSPLGGALPHYGVYPAAEGHVAVGALEPHFAAALVEGL
+GLDADGDVRAQLTEALSRHDAAHWQAWGEKRGIPLTALASPTA

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000047.fa

@@ -0,0 +1,78 @@
+>PROKKA_01806
+MSSKAARTRSEPVTLPRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVPQRRAG
+PEIVDQWIEDNPVWGPVLDALQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHAKALRQ
+PPARTPRNLTRLPASGVVVLEEGGPSPEEAVARAQAWLRKRRYRVERRLEAGGASVGAER
+GYLREIGNILFHVSLIGVLVFMAYGGMTKYGGQKIIVEGEGFANNLVAYDSFTPGTYFSA
+DDLQPFSLTLDSFDAVFDRESETHYGQPLDYTAVMDVREGSGGELQRQILKVNQPLDIDG
+VRVYLVGNGYAPVVTIRDGAGDVAFQGPVVTRVFDQNYGSQATIKVPDARPDQLGFVGFF
+LPSAVEDEEGAAFSADPELLNPELQLNSYYGDLGLDTGRPQNVYVLDTASLTELNSRTNE
+NGGIVLSPGQTYELPEGKGSISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLAISLFV
+RRRRVWVRARTDDDGRTRVEYALLARGEEFGLHEEHVALRAAMEKWWPIVAATETADDAA
+AGAAPQSTPTAPETPAGPADARSGD
+>PROKKA_01503
+MSSKAARTRSEPVTLPRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVPQRRAG
+PEIVDQWIEDNPVWGPVLDALQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHAKALRQ
+PPARTPRNLTRLPASGVVVLEDGGPGPEEAVARAQAWLRKRRYRVEHRPEAGGASVGAER
+GYLREIGNILFHVSLIGVLVFMAYGGMTKYGGQKIIVEGEGFANNLVAYDSFTPGTYFSA
+DDLQPFSLTLDSFDAVFERQSETTYGQPLDYTAVMDVREGTGGELQRQILKVNQPLDIDG
+VRVYLVGNGYAPVVTIRDGAGDVAFQGPVVTRVFDQNYGSQATIKVPDARPDQLGFVGFF
+LPSAVEDEEGAAFSADPELLNPELQLNSYYGDLGLDTGRPQNVYVLDTASLTELNSRTNE
+NGGIVLSPGQTYELPEGKGSISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLVISLFV
+RRRRVWVRARTDEAGRTRVEYALLARGEEFGLHEEHVALRSAMERWWPVAAPESEEEAVA
+SAAAVGHTGTTPETLAGPRTPRSGD
+>PROKKA_00397
+MSRTEDQDPGRRPEVALPALGFWGTLRFAWTQLTSMRTALMLLLLLAVAAVPGSLFPQRP
+AGPGIVQDYIDDNPVLGEWLDRFQMFDVYSSVWFSAIYLLLFISLIGCVAPRAVKHAQAL
+RSAPPRTPRRLSRLPEYGRVVLEPGGPAPVEAVEQAARYLKRRGYRIEVRQEDAGGASVG
+AARGYLREVGNIVFHLSLIGVLVFMATGSLLSYRGQKILVEGEGFANTLVAYDAFTPGSA
+FSEEMLTPFSMTLKRVEYVYDRQSPTHYGQPLD
+>PROKKA_01068
+MGDAPVSSKAARTRSEPVTLPRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVP
+QRRAGPEIVDQWIEDNPVWGPVLDALQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHA
+KALRQPPARTPRNLTRLPASGVVVLEEGGPSPEEAVARAQAWLRKRRYRVEHRPEASGAS
+VGAERGYLREIGNILFHVSLIGVLVFMAYGGMTKYYGQKIIVEGEGFANNLVSYDSFTPG
+TYFSADDLQPFSLTLDSFDVVFDRESEALYGQPLDYTAVMQVQEGGGGEPREEILKVNHP
+LSMDGVRVYLVGNGYAPVLTVRDGEGDIAFQGPVVTRVQDVNFNSLVTLKVPDARPDQLG
+FVGQFMPAAVEDESGVAVSVDPELYNPQLILDSYYGDLGLDGGVPQNVYVLDTETLTELN
+SRKNENGGIVLSQGQTYELPEGKGSISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLA
+ISLFVRRRRVWVRARTDEAGRTRVEYALLARGEEFGLHEEHVALRAAMEKWWPVAAATAP
+ETTPETPCRPRRRPIRRLTVFNPTAPVNEQLALYSDLFMLIAAFVYAAAFVLFTIDMATS
+SATIRRLEEDLAAQRGPARLAPARETVGAGFGGSSLGGSSSVGSTGAGSSAGGPGVLPGE
+ARAAGLGDEPGLVDEDMDYTGGGRRPIANVAVAVLAVGWALHAFAVIARGLAASRVPWGN
+LYEFMTTGALVITTVYLLFLFRKDLRFVGTFVTGLVVAMMCAATMGFPTPVGHLQPPLQS
+PWLVIHVSIAVLATALFTLTAAMSMLQLIQDRAEKRAAATGERPWAFLRLVPSAQALENW
+SYRINAVGFVMWTFTLIAGAIWAEASWGRYWNWDTKEVWTFVIWVVYAAYLHARATRGWT
+GARAAWLSIVGFLCVVFNYTIVNTYFPGLHSYAGLPG
+>PROKKA_02641
+MSRPSDYDDGTGAGGTLRAESPELGFAGWLRWFWRQLTSMRVALILLLLLAVAAIPGSLV
+PQRGADPNGVVQYQKDHPDLFPILDAFPIQAFDVYGSVWFSAIYLLLFISLIGCVLPRIA
+HHWKAWRGRPPKTPARLQRMAGFSEIRLSNPDATPAEREAFAARAVDEAAAILKKLRYRV
+EVQRASRRGVDEVSVSAERGYLRETGNLLFHVSLLGVLVSVGLGGVFTFNGQKVLIEGET
+MVNQLIDYDTATSGRSFDSSSLEPFSLRLDTLDVTYNTPDDGNVQAIGLVKDYTANMTLI
+SPEGDESEHVIRVNHPLRVHGSPIYLIANGYAPKITIRNAEGTVVYSEAMPFIPQDNLNM
+TSLGVVKVPDGIVDESGEPVQLGLRGFFYPTKADLDTGAYTSNYPDLENPVLTLDVFVGD
+LGINDGIPKSVYALDTSDMEQVTGRAVDLDSIELRPGEQTELPNGFGTIEFESVPRYASF
+DVMQNPAQEWILVFAVLALGGLMWSLFVPRRRMWVKALPSEDGVVLQYAALARGDDPALE
+RAVEELRDRHRELL
+>PROKKA_01003
+MGDAPVSSTSAPKDPAPRNRTRDDVTLPALGVGGTLRWAWTQLTSMRTALLLLLLLAVAA
+VPGSLVPQRRAGPEAVDQWIEDNPFWGPILDALQFFDVYTSVWFSAIYLLLFISLVGCVL
+PRALKHAKALRQPPARTPRNLGRLPESGVVVLEAGGPAPEEAVRQAQRWLKRKRYRVELR
+PEAGGASVGAERGYLREIGNILFHFSLIGVLAFMAYGGMTKYTGQKIIVEGEGFANNLVA
+YDSFTPGMYFDAASLQPFQLTLKSFDATFERQSQTHWGAPLDYTAVMEVRHGTGGDPEEQ
+VLKVNHPLEIDGAKVYLVGNGYAPVVTVRDGNGDIAFQGPVVTRVTDQNFNSLAVIKAPD
+ARPDQLGFVGQFMPAAADVGQGVEVSVDPEPLNPKLILNSYSGDLGLDAGVPQNVYVLDT
+STLTELNSRRSENGGITLSVGQTHVLPDGKGSISLDGVRRYVGLDIHYDAGKWGVGVFSV
+LALIGLAVSLFTRRRRVWVRARTGDDGRTRVEYALLARGEEFGLREEHVALREAFEKMWP
+VSAPEADTGETTPATPAPAAAPTPRSGD
+>PROKKA_01727
+MSSKAARTRSEPVTLPRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVPQRRAG
+PEIVDQWIEDNPVWGPVLDALQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHAKALRQ
+PPARTPRNLTRLPASGVVVLEEGGPSPEEAVARAQAWLRKRRYRVEHRPEAGGASVGAER
+GYLREIGNILFHVSLIGVLVFMAYGGMTKYGGQKIIVEGEGFANNLVAYDSFTPGTYFSA
+DDLQPFSLTLDSFDAVFDRESETHYGQPLDYTAVMDVREGSGGELQRQILKVNQPLDIDG
+VRVYLVGNGYAPVVTIRDGAGDVAFQGPVVTRVFDQNYGSQATIKVPDARPDQLGFVGFF
+LPSAVEDEEGAAFSADPELLNPELQLNSYYGDLGLDTGRPQNVYVLDTASLTELNSRTNE
+NGGIVLSPGQTYELPEGKGSISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLAISLFV
+RRRRVWVRARTDDDGRTRVEYALLARGEEFGLHEEHVALRAAMEKWWPIVAATETADDAA
+AGAAPQSTSTTPETPAGPADARSGD

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000048.fa

@@ -0,0 +1,35 @@
+>PROKKA_01808
+MQTPRPSRRTVLTGLSLLGLAPVLAACSGDDSLTRQAGNADGKNYIAGDGSVLEIAPAER
+GAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAPHLVSLHEQFAPQGVRFL
+GVNVRDTVTTAQAFERTFEIPYPSIEDARGEVLLNMTDYVPPQAVPSTLVLDVEGRVAAR
+VLGAVEESTLRALLTTVVDEAAA
+>PROKKA_01505
+MQTPRPSRRTVLTGLSLLGLAPVLAACSGDDSLTRQAGNADGKNYIAGDGSVLEIAPAER
+GAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAPHLVSLHEQFAPQGVRFL
+GVNVRDTVTTAQAFERTFEIPYPSIEDARGEVLLNMTDYVPPQAVPSTLVLDVEGRVAAR
+VLGAVEESTLRALLTTVVDEAAA
+>PROKKA_00398
+MPIPQPHREGHHRPPGLPPRPGRRQVLAGLAGVASLPLLAACSAEDPLAAQAGKADGKNY
+IAGDGSVLEIGPAERGEPVQFSSAMFSGEPIIAQDLAGDPAVLNFWYAACAPCRVEAPDL
+QALHEQFAPEGVRFLGINVRDTIATAQAFERKFGITYPSVEDRGGQVLLAMTDYVPPQAV
+PTTIVLDHQGRVSARILGIAERSTLRTLITTVLDEQA
+>PROKKA_01066
+MHTPPRPSRRTLLTGLALASLAPALAACSGGDDSLARQAGNADGKNYIAGDGSVLEIAPA
+ERGAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAPHLVSLHEQFAPQGVR
+FLGVNVRDTVTTAQAFERTFEIPYPSIEDTRGDVLLNMADYVPPQAVPSTLVLDVEGRVA
+ARVLGAVEESTLRALLTTVVDEAAA
+>PROKKA_02643
+MNRRRTGAALALPIAALFALAGCSGGDGNLAAEWNEASGKGYVSGDGSSLSIAPDQRTEP
+VEFSGETEDGDIYGSDDTVGSVTVVNFWYAGCAPCRAEAPDLVEAYDEFSPQGVKFVGVN
+TRDQVAQARQFSVRFDIEYPSIMDNAGGRAVQRAFAGQVPLNAVPTTLVLDAEGRVAHRV
+LGQLAGASQLRTLIGETLAEAGGGAAADPASDPAPADEATEQ
+>PROKKA_01001
+MPFPPRPSRRAALAGLSAAALAPLLAACSGTDDSLAQQAGNAGGKNYIAGDGSVVEYAAD
+QRGAPVEFSAAGFDGETVSGETLRGEPALLNFWYAACAPCRVEAPHLVKLHGEFEPKGVR
+FLGVNVRDTVTTAQAFERTFGIPYSSVDDTSGSVLLAMSDYVPPQAVPSTLVLDRQGRVA
+ARVLGAVEEGTLRALLDTVVAEA
+>PROKKA_01729
+MHTPPRPSRRTLLTGLALASLAPALAACSGGDDSLARQAGNADGKNYIAGDGSVLEIAPA
+ERGAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAPHLVSLHEQFAPQGVR
+FLGVNVRDTVTTAQAFERTFEIPYPSIEDARGDVLLNMTDYVPPQAVPSTLVLDVEGRVA
+ARVLGAVEESTLRALLTTVVDEAAA

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000049.fa

@@ -0,0 +1,70 @@
+>PROKKA_02005
+MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTR
+IIERRPHRLEIGQADGIQARSVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRT
+SLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARPDYGWAFETLEDTNDGEHPVL
+VTLRRTVDAEENALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGVM
+DALADTDFPDIRTKCAIHSSSGSILLIPREGGHLSRMYVDLGEVPADDDHKVRQTPLEEI
+IRRAQQILRPYTLDVKEVAWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAG
+QGMNVSMQDGWNLGWKLGQVLSGLAPVELVPTYAEERKEIAKNLIDFDKEWSTLMATPTS
+ELGDPNEVAEFYTKTAEFPAGFMTEYQPSLLTTDATGQALAQGYPIGKRFKSALVERSCD
+TNVKHLGHLHRADGRWRVYVFADAASPRAEDSKVAAWAKAIEEDPRSFRNRHTPSDGPED
+ARFDIKVVYQQKQTEFAHPDVPSIFRPTTGSLGLHDLNNIFATCRPQHGEDIFEARGISR
+DGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN
+>PROKKA_01715
+MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTR
+IIERRPHRLEIGQADGIQARSVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRT
+SLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARPDYGWAFETLEDTNDGEHPVL
+VTLRRTVDAQGNALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGVM
+DALADTDFPDIRTKCAIHSSSGSILLIPREGGHLFRMYVDLGEVPADDNHKVRQTPLEEI
+IRRAQQILRPYTLDVKEVAWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAG
+QGMNVSMQDGWNLGWKLGQVLSGMAPVELVPTYSEERKEIAKNLIDFDKEWSTLMAKPTS
+ELGDPNEVAEFYTKTAEFPAGFMTEYQPSLLTTDATGQALAQGYPIGKRFKSGLVERSCD
+TNVKHLGHLHRADGRWRVYVFADTASPRAEDSKVAAWAKAIVEDPRSFRNRHTPSDGPED
+ARFDIKVVYQQKQTEFAHPDVPSIFRPTTGPLGLHDLNNIFATCQPKHGEDIFEARGISR
+DGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN
+>PROKKA_00837
+MLFHHHGYVSTDPRVQPAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTR
+IIERRSHRLEIGQADGIQARSVETFQAFGFASQIIDEAYDLTSMAFWNPSSEDADTIVRT
+SLAEDDPEGVSEFPHLIVNQARILDWFAAYMKNSPTRAEPDYGWSFESLEDSAEGEYPVL
+VTLRRTVDAQGEPLADPESGETRQVRAKYVVGADGAGSRVRKAIGHSLAGGASNHAWGVM
+DALAVSDFPDIRTKCAIHSSTGSILHIPREGGHLFRMYVDLGEVPADDNHKVRQTPIEEI
+IRRAQQIIRPYTLEVKDVAWHSVYEVGHRLTSGFDNRERVDHPNVFLLGDACHTHSAKAG
+QGMNVSMQDGWNLGWKLGQVLSGVAPAELVPTYSEERKEIAKNLIDFDKEWSTLMAKPTS
+ELGDPNEVADFYTKTAEFPAGFMTEYKPSILTTDATGQSLAAGFPIGKRFKSALVERSCD
+TNVKHLGHLHRADGRWRVYVFADAASPRSADSKVAAWAKAVEEDPRSFRNRHTPADGPQD
+ARFDVKVVYQQKQTEFAHPDVPAVFRPTSGDLRLLDLNNIFATCQPKHGEDIFEARGISR
+DGAVVVVRPDHYVSGVFGLDEVERLNEFFAGVLLDAS
+>PROKKA_00774
+MLFHHHGYVSTDPRMKPAAGIGLDRPAELPDEMDVLIVGTGPAGMIAAAQLAMFPDVHTR
+IIERRGKRLEIGQADGIQARSVETFQAFGFASQIIDEAYDLTSMAFWNPSPEDEDAIVRT
+SLAEDDPHGVSEFPHLIVNQARILDWFAEFMKNSPTRATPDYGWEFVSLDDSDQDAERPV
+QVTLRRTVDAKGNPLAEGVAGEERVVRAKYVIGADGAGSRVRKAIGHSLSGDAANHAWGV
+MDVLADSNFPDIRTKCAIHSSSGSILHIPREGGHLFRMYVDLGEVPADDNHKVRQTPIEE
+VIRRAQQIIRPYTLDVKDVAWSSVYEVGHRLTSGFDNRERCTHPNVFLLGDACHTHSAKA
+GQGMNVSMQDGWNLAWKLGQVLSGIAPAELVPTYSEERKEIAKNLIDFDKEWSTLMAKPT
+SELGDPNEVAEFYTKTAEFPAGFMTEYRPSMLTTDAAGQELATGFPIGKRFKSAKVERSC
+DTNVKHLGHLHTADGRWRVYVFADAAAPHDADSKVAAWAEAVEEDPQSFRNRHTPAGAPQ
+DERFDLKVVYQQKQTEFAFPDVPAVFRPTTGPLGLHDLNNIFAVCRPEHAEDIFELRGVS
+RDGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN
+>PROKKA_00173
+MFIAGDACHTHSAKAGQGMNVSMQDGWNLAWKLGQVLEGRSDASLLATYSEERQQIAENL
+IEFDKAWEGMMSKRPDELEDPQAVGRFYKDNAEFPNGFATQYPASSVTGEDTHQALAAGV
+PIGKRFESAAVRRVADTSPRQLGHLFEADGRWRLYAFADEDRTAVGELADWLADSPDSPV
+RRFTPESADLNSVFDAKVVYQQPYQEVELADVPALFLPKMGPYQLTDKEVVFAADLADDI
+FEARGIDRGGALIIQRPDMYVAHVLPLSAREEITAFFEQNMVSASV
+>PROKKA_00174
+MRGAADPRRSLSTLPTTAVSEFPFLIVNQARVIDYFAEYAERGPQGQERTVRAKYVVGCD
+GSRSRVRDCTGIEVVRDPSAHAWSVMDVLLETDFPDNRQKCGIQSDKDGTILLIPREGGF
+LARFYVSLGSIDDAPRPRSGGGIRACSSPATPATPTPPRPARA
+>PROKKA_01943
+MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTR
+IIERRPHRLEIGQADGIQARSVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRT
+SLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARPDYGWAFETLEDTNDGEHPVL
+VTLRRTVDAQGNALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGVM
+DALADTDFPDIRTKCAIHSSSGSILLIPREGGHLFRMYVDLGEVPADDNHQVRQTPLEEI
+IRRAQQILRPYTLDVKEVAWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAG
+QGMNVSMQDGWNLGWKLGQVLSGMAPVELVPTYSEERKEIAKNLIDFDKEWSTLMAKPTS
+ELGDPNEVAEFYTKTAEFPAGFMTEYRPSLLTTDATGQALAQGYPIGKRFKSALVERSCD
+TNVKHLGHLHRADGRWRVYVFADAASPRAEDSKVAAWAKAIEEDPRSFRNRHTPSDGPED
+ARFDIKVVYQQKQTEFAHPDVPSVFRPTTGSLGLHDLNNIFATCRPTHGEDIFEARGISR
+DGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000053.fa

@@ -0,0 +1,35 @@
+>PROKKA_02246
+MDHKEILHQGLRRQRDALFAKLDGLPEREVRLPRTPTGTNLLGLLKHAATCELEYFGEVF
+GRPAGIPLPWDAPGVGEEDGADLFAAEDETLEDVLDYARRCFAHADATIEALVFDARGRV
+PWWPAHLAEVTLAQILSHVALDAARHAGHADILREGIDGQAGLRGPGDNLPGWDAERWAA
+HVRRLEGIARGAGPVR
+>PROKKA_02261
+MDHKQILHDGLRRQRAALLQKLEGLSERDARLPRTPTGTNLLGLVKHAAVVELEYFGETF
+DRPAEVQLPWAAAGQSEEDNVDMFAAEGESLEDVLEFARRCFAHADATITALGADAHGRV
+AWWPDDKAEVTLAQIIAHVALDEARHAGHADILREQIDGQAGLRAPGNNLPVWGADRWAA
+HVDRLTAIAEGSGGPGRN
+>PROKKA_01948
+MDHKEILHQGLRRQRDALFAKLDGLPEREVRLPRTPTGTNLLGLLKHAATCELECFGEVF
+GRPAGIPLPWDAPGVGEEDGADLFAAEDETLEDVLDYARRCFAHADATIEALVLDARGRV
+PWWPAHLAEVTLAQILSHVALDAARHAGHADILREGIDGQAGLRGPGDNLPGWDAERWAA
+HVRRLEGIARGAGPVR
+>PROKKA_00418
+MDHKQILHDGLRRQRAALLHKLEGLSERDARLPRTPTGTNLLGLVKHAAVIELEYFGGTF
+GRPAEVQLPWAAAGQPEEDNVDMFAAEGESLEDVLEFARRCFVHADATITALGADAPGRV
+AWWPDDKAEVTLAQIIAHVALDEARHAGHADILREQIDGQVGLRSPGNNLPPWDADRWAA
+HVDRLTAIAEGSGGVGWN
+>PROKKA_00422
+MGFLTPQAHGELAVLTTYALQQLAQMRTTVHGLTDEQAHSVPSASALNLTGLLLHTGEVA
+VYWTAAAASAPGEPVLPEDVNEDHSLDELVADGRPLAQVLERFDRCVEVARQNLAAVADL
+SAPVPVPDAPWFPADLKTWEARWALLHVTAEVARHVGHADLIRESIDGTGSYELNDLADA
+AAQG
+>PROKKA_02178
+MDHKEILHQGLRRQRDALFAKLDGLPEREVRLPRTPTGTNLLGLLKHAATCELEYFDEVF
+GRPAGIPLPWDAPGVGEEDGADLFAAEDETLEDVLDYARRCFAHADATIEALVFDARGRV
+PWWPAHLAEVTLAQILSHVALDAARHAGHADILREGIDGQAGLRGPGDNLPGWDAERWAA
+HVRRLEGIARGAGPVR
+>PROKKA_02192
+MDHKQILHDGLRRQRAALLQKLEGLSERNARLPRTPTGTNLLGLVKHAAVVELEYFGETF
+GRPAEVQLPWAAAGQPEEDNVDMFAAEGESLEDVLEFARRCFAHADATIAALDADAPGRV
+AWWPDDKAEVTLAQIIAHVALDEARHAGHADILREQIDGQAGLRAPGNNLPPWDADRWAA
+HVDRLTAIAEGSGGPGRN

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000055.fa

@@ -0,0 +1,42 @@
+>PROKKA_01696
+MEHATALENVMLPLRYGPDRVPRGEQRRRAGEALERVGLGMRTGHRARTLSGGEKQRVAV
+ARALINEPPLVLADEPTGALDQARTRDVVDLLRGAVGPERAVVVVTHDPRVAAACDRRWH
+LVDGELAPQD
+>PROKKA_00855
+MTLLEVHDVDKTFHSGGEAVPVLRGASLLVPAGEMHAVTGPSGSGKSTLLRILACLDSPD
+SGRVLLGGEPLPEPWSRGGDRYRNQRCGIVLQDFALMEHATALENVMLPLRYGPDRVPRG
+EQRRRAGEALERVGLGTRTGHRARTLSGGEKQRVAVARALINEPPLVLADEPTGALDQER
+TRDVVDLLRGAVGPERAVVVVTHDPRVAAACDRRWHLVDGGLAPQD
+>PROKKA_01010
+MSDGSAPPLLELAGVLKSFKGADRPALDGVDLTVRDGDFVAIVGPSGSGKSTLLNVLGLL
+DRPDGGSYRVSGTDTMSMGERERDRLRSRWFGFVFQSSHALGDEPVAVNAALGLRVQRTP
+PEQRDARAGEALALLGLSHRLDTRAKLLSGGERQRLAIARAIATRPRVILADEPTGNLDS
+VNSRIVIDHLRALHAQGATVLLITHDPEIARQADRQVRIEDGRITELAGHRTAASASADM
+AGTGHGWSAPGAARRHRSPRSSAMLDDLVEAVSSLSTRFLRTVLLMAAFAVGIGGLVASV
+GLTQTATDQVGALLTAAALDEVVVTVPQAEGLLDPGDGRLASWADGLAALPHVTAAGHVA
+QVAPADVVITRHDPSDPEPAVAISLVAASSSYAGLAGLTLPSETSRTLLDSPDARLAWAT
+PAAARALELPVTDTGMLSPGYRVWIQGHAVDVAGIVTLSERTPELDASLVVTPAVMTGVA
+QAHPQLVVRTEAGFPYPVSQAAPLVIAPENPGSVTVRTVADLRNLRAGVSDDLGAFVGVL
+SGVLLVLAVISASTAMYLSVQARTAEIALRRAIGSPRGLIARLFLLEGALIGLAGGAVGA
+AVGSGVILAVSQARGWAAVLPPGAVPLALGLGLVAGVVSALYPGWVASRQRPADALRG
+>PROKKA_00792
+MSLLEVHDVDKSFTTAASEVPVLRGVSLSVPAGQMHAVTGPSGSGKSTLLRILACLDSPD
+AGEVLLEGVPLPPPWSRGGDRHRNRRCGIVLQDFALMEHATALDNVLLPLRYGPGGGSRA
+EQRRRAALALDRVGLADRAHHRARTLSGGEKQRVAVARALINDPPLVLADEPTGALDQAR
+TRDVVKLLRSAVGPQRAVVVVTHDPEVAAACDQRWHLEDGRLHSQG
+>PROKKA_00870
+MTASAPVLTLDRVQVGYRHPDGGTRVLIESLDLTLAPGEVVGLWGRSGTGKSSLIRHLAG
+LSRPLAGRIAYRSPDGSLNGEVADLSAGDLARYRREHLGYVDQSCELIGELSALDNAAVW
+IHGGRIAGSACDAQETVQGLLERLGLGHRLGAPASRLSGGEAQRVALVRALSKRPHLIVA
+DEPTGHLDGVTAREAIALLREHAEAGAAVLVASHDPLVHAAVDRAVRVGED
+>PROKKA_00943
+MNTAPLTPPVLAARGLTKAYGSTHALTGVDLEIRPGESVAVMGPSGSGKTTLLHVLSGII
+APDGGRVTLAGADGTVHEVTALTEEQRARLRRERLGFVFQEGLLLPELTAVENVAMPLML
+NGVDRRAAEQTAARWLGSLGLAGMEDRRPGELSGGQRQRVAIARAQAVEPDVVFADEPTG
+ALDSDTSEAVLDSLIASTVARGRTLVVVTHDPSVAAACSRLIRVRDGRIESDQAQAAAGT
+TREQVR
+>PROKKA_00735
+MSLLTVHDVHRSYRGPAGDVPVLRGVSLQVPGGGVHAIMGPSGSGKSTLLRLLACLDTPD
+AGSIRVAGRSLPAPWSSDGDAYRNRTCGIVLQDHLLIDRATAVDNAALPLLYARPRTSKR
+ERRTMAAELLTRLGLGDRLHHPVGRLSGGERQRVAIARAVIMGPSLLLADEPTGALDEER
+TDEVMGLFRSMSQPERAIVVVTHDPAVAARCDHTWRLRAGRLE

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000056.fa

@@ -0,0 +1,35 @@
+>PROKKA_00025
+MERGPVVGLLDNLERGLERAVRSAFSAGGPRAVKPVEIASALRQAMDDESIALSEGHTVA
+PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRGGD
+LRVVTRLDDGSLTAPAPHDDGASPATAHGPGATAPAPDRLVEDPPAAAPREPSPAPRVGP
+RPAPRRAAAPAAPAAPSHADQPTVVMGRPVTEPAGPALELDGRMLPLDGDDLILGRSAER
+ADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRDGDVVTVGQTE
+LLFFGGTGGRA
+>PROKKA_02043
+MERGPVVGLLDNLERGLERVVRSAFSAGGPRAVKPVEIASALRQAMDDESLALSEGHTVA
+PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRAGD
+LRVVTRLDDGSLTAPAPHDDGASPATAHGPGASAAAPDRLVEDLPAAAPREPSPAPRVGP
+RPAPRRAAAPAAPAAPAAPAAPAHADQPTVVMGRPVTGPAGPALELDGRMLPLDGDDLIL
+GRSAERADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRDGDVV
+TVGQTELLFFGGTGGRA
+>PROKKA_00370
+MERGPVVGLLDNLERGLERAVRSAFSAGGPRAVKPVEIASALRQAMDDESFALSEGHTVA
+PNSYVVHFSPADFDRARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDTDVRAGD
+LRVVTGLDDGSLPAPAPHDDGASPATAHGPGATATAPDRLVEDLLGGRTP
+>PROKKA_00371
+MGRPVTEPSGPALELDGRMLPLDGDDLILGRSAERADLVIPDSSVSREHLRLLTVGSTVT
+LLDLGSRNGVLVNGRRVDGSVTLRDGDVVTVGQTELLFFSGTGGRA
+>PROKKA_00353
+MGLLDNLERGLEKAVRSAFSAGGARAVQPVEIASALRHAMDDESFALSEGHTVAPNDFTV
+HFAPADFDRARTWGSTLAGELCDEVIRHAQSQGYTLPGSVRVAFHEDAQVHAGQVEVDAR
+IDDGSSPVPSPPAATSAPAPAAARTADDRGPRPSRAPRHGATAAPAPRRDPSPAPRPAPT
+PARSESARRAPADEQATVVMPRRTSPAPAVPWLEADGVRHPLTHEDMVLGRSSERADVVV
+PDSSVSRQHARLVRVGRSVTLIDLGSRNGVTVNGRRVDGSTVLREGDRITVGQTDLVFHI
+DPADGRPRA
+>PROKKA_00025
+MERGPVVGLLDNLERGLERVVRSAFSAGGPRAVKPVEIASALRQAMDDESFALSEGHTVA
+PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRAGD
+LRVVTRLDDGSLTAPAPHDDGASPATAHGPGASAAAPDRLVEDLPAAAPRKPSPAPRVGP
+RPAPRRAAAPTAPAAPAHADQPTVVMGRPVAEPAGPALELDGRMLPLDGDDLILGRSAER
+ADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRDGDVVTVGQTE
+LLFFGGTGGRA

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000058.fa

@@ -0,0 +1,44 @@
+>PROKKA_00049
+MQRIHDPQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHFGEDA
+TVWPMFNGTGANVVGLQAMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDGKL
+TPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPDEVKAITDYAHEHGMRVYMDGAR
+IANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAADGLVYLRKNQMQL
+ASKMRFVSAQLLALFDGDLYLRSARHANAMAARLRAGIEAGVADGSLAGVEFTQATDANA
+VFAVLPEGVADRLRARFRFYDWDAARREVRWVCGFDTTEEDVDAFTAALRAELVPAA
+>PROKKA_02062
+MQRIHDPQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHFGEDA
+TVWPMFNGTGANVVGLQAMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDGKL
+TPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPEEVKAITDYAHEHGMRVYMDGAR
+IANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAADGLVYLRKNQMQL
+ASKMRFVSAQLLALFDGDLYLRSARHANAMAARLRAGIEAGVADGSLAGVEFTQATDANA
+VFAVLPEGVADRLRTRFRFYDWDAARREVRWVCGFDTTEEDVDAFTAALRAELVPAA
+>PROKKA_00354
+MQQIHDPASRGFASDNYSGVHPEVLAAIAEANGGHQTAYGEDAYTGRLAEVVRGHFGEDA
+QVWPMFNGTGANVVALQSMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLTVPTPDGKL
+TPELIDVQAWGWGDEHRAQPLVVAITQSTELGTLYTPEEIRAITEHAHARGMTVFLDGAR
+LANAAAALDLPLRAFTTDVGVDVLSLGGTKNGALGAEAVVALNPAATTGMTYLRKSQMQL
+ASKMRFVSAQLLALFDGDLYLRTARHANAMAQRLQDAVAAGIADGSLPGVALTQRAQVNA
+VFATLPAGVADRLRRSFRFYDWDEANGEVRWVCSFDTAEEDVDAFVAALRAELAPAD
+>PROKKA_01608
+MSAGAPAAGLRAFASDNYAGVHPDVWAALADVDAHHAPAYGADPHTERLQEAVREAFDAP
+DAVALPVFNGTGANVVALQSMLPPWGAVVAADTSHIHHDEGGAPERMGRTKLFTVPTPDG
+RLTPELVDREAHGWGFVHRAQPAVVEIAQVTELGTVYTPEQVRALADHAHGHGMGLYMDG
+ARLFNAAAALELPLSAFTTHAGVHVVSLGGTKAGALGAEAVVVLRPEAVTLASLVPERDL
+PADAGPRERARLAVEYVRKSSMQLASKMRYVSAQLTALLKGDLGIRLAGHANAMARELAG
+RVAGIDGVEVTRTPEANAVFAVLDPQAADRARVRHPFYDWDAARHEVRWMTSWDTTAADV
+DSFAAALGEALSPGRRR
+>PROKKA_01503
+MSAARPAGLRAFASDNYAGVHPDVWAAMADADADHAVSYGEDPTSAALQEKVREVFGERA
+FAVPVFTGTAANVLALQALTPPWGSVVTAASSHLIHDEGGAPERLGRTPLVPVPTPDGRL
+TGELAAAHVRRDGFVHASQPAVVEIAQATELGTVYSAAQVREVADAAHAAGAALYMDGAR
+LSNAAAALDLPLRAFTTDAGVDVVSYGGTKNGGLGAEAVIVLNPEAVVAARMVGPADVPG
+GDAADARDRARAALGYLRKQDMQLASKHRYLAAQLLALLTDDLGIALAAQANRMARVLAD
+AVAGLDDVELARAPEANAVFARLDPDVAAEVRLRHPFYDWDAAAHEVRWMTSWDTTDADV
+ESFVDALAAALRARRPR
+>PROKKA_00044
+MQRIHDPQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHFGKDA
+TAWPMFNGTGANVVGLQTMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDGKL
+TPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPDEVKAITDYAHEHGMRVYMDGAR
+IANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAADGLVYLRKNQMQL
+ASKMRFISAQLLALFDGDLYLRSARHANAMAARLRAGIEAGVADGSLAGVEFTQATDANA
+VFAVLPEGVADRLRARFRFYDWDAARREVRWVCGFDTTEEDVDAFTAALRAELVPAV

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000061.fa

@@ -0,0 +1,29 @@
+>PROKKA_00068
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+YLPGFDLVPGCVVEARPIGVFNMTDDGGGDAKLLCVPADKRYDHITELEHVEESLKQEIE
+HFFTRYKDLEPGKWVKAEGWEGRAAAEAELEASIQRFDAEGEESPTDEPQGRAVDTEEAQ
+PATEEGEATDEPQGR
+>PROKKA_02081
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+YLPGFDLVPGCVVEARPVGVFNMTDDGGGDAKLLCVPADKRYDHITELEHVEESLKQEIE
+HFFTRYKDLEPGKWVKAEGWEGRAAAEAELEASIQRFNAEGEESPTDEPQGRAVDTEEAQ
+PATEEGEATDEPQGR
+>PROKKA_00326
+MPHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDAMV
+LLPGFDLVPGCVVEARPVGVFNMTDDGGGDAKLLCVPADKRFDHITELEHIEESLKQEIE
+HFFTRYKDLEPGKWVKAEGWQGRADAEAELEASIARFDAAGEHSPTDEPQGRDVETEDPS
+PATEEGEEKDVPQGR
+>PROKKA_00266
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+FLPGFDLVPGCIVEARPVGVFNMTDDGGGDAKLLCVPADKRFDHIQELEDVEESLKQEIE
+HFFTRYKDLEPGKWVKADGWEGREAAEKELEASIERFAAEGEHSPSDEPQGRDVDTEEAA
+PAAEQEA
+>PROKKA_00684
+MLFDVTIEIPRGSGNKYEVDHTTGRIRLDRAVFTSMVFPQDYGSIDNTLGDDGDPLDALV
+LLPRPTFPGVVITVRPVGMLRMVDENGGDDKILTVPAGDDRFAQLRDITDVPEHTLAEIE
+HFFAHYKEIEHGKHVTTNGWADRAAAEAVIRTAQNAHTRHP
+>PROKKA_00062
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+YLPGFDLVPGCVVEARPIGVFNMTDDGGGDAKLLCVPADKRYDHITELEHVEESLKQEIE
+HFFTRYKDLEPGKWVKAEGWEGRAAAEAELEASIQRFDAQGEESPTDEPQGRDVDTEEAQ
+PATEEGEPQGR

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

@@ -0,0 +1,40 @@
+>PROKKA_00076
+MDESIDAAAREANRALLGRLPADRTLVMGILNVTPDSFSDGGEHATVRAAVEHARRMVAD
+GADIVDVGGESTRPGARAVPPAEEQERILPVIEALLAEDVVLSVDTRHTATARAALALGP
+VIVNDVSGLAHEPDMPALIAASGAPYILMHNRGNPQTMDGLAVYEDTVPDVVCELRDVAG
+RFLAAGVEPAQLIVDPGLGFAKAGEQNWELLRGLEWLRAMGHPVLVAASRKRFLGTLLAD
+DDGTPAPPAARDAATAAISALAAAQGAWGVRVHDVRASADAVRTAAAWAGAHAPGEPVSE
+DVLP
+>PROKKA_02089
+MDESIDAAAREANRALLGRLPAGRTLVMGILNVTPDSFSDGGEHATVRAAVEHARRMVAD
+GADIVDVGGESTRPGARAVPPAEEQERILPVIEALLAEDVVLSVDTRHTATARAALALGP
+VIVNDVSGLAHEPDMPALIAASGAPYILMHNRGNPQTMDGLAVYEDTVPDVVCELRDVAG
+RFLAAGVEPAQLIVDPGLGFAKAGEQNWELLRGLEWLRAMGHPVLVAASRKRFLGTLLAD
+DDGTPAPPAARDAATAAISALAAAQGAWGVRVHDVRASADAVRAAAAWVGAHAPGEPVSE
+DVLP
+>PROKKA_00317
+MDESIDAAAREANRALLGRLPADRTLVMGILNVTPDSFSDGGEHATVRAAVEHARRMVAD
+GADIVDVGGESTRSGARAVPPAEEQARILPVIEALLAEDVVVSVDTRHTATARAALALGP
+VIVNDVSGLVHEPEMPALIAASGAPYILMHNRGNPQTMDGLAVYEDTVPDVVCELRDVAG
+RLLAAGVEPAQLIVDPGLGFAKAGEQNWELLRGLEWLRAMGHPVLVAASRKRFLGTLLAD
+DDGAPAPPAARDAATAAISALAAAQGAWGVRVHDVRASADAVRTAAAWVGAHAPGEPVSE
+DVLP
+>PROKKA_02338
+MLRSRVTVFGILNLTEDSFFDESRRLDPAGAVTAAIEMLRVGSDVVDVGPAASHPDARPV
+SPADEIRRIAPLLDALSDQMHRVSIDSFQPETQRYALKRGVGYLNDIQGFPDPALYPDIA
+EADCRLVVMHSAQRDGIATRTGHLRPEDALDEIVRFFEARVSALRRSGVAADRLILDPGM
+GFFLSPAPETSLHVLSNLQKLKSALGLPLLVSVSRKSFLGATVGLPVKDLGPASLAAELH
+AIGNGADYVRTHAPGDLRSAITFSETLAKFRSRDARDRGLDHA
+>PROKKA_00258
+MLPKPFHELPDRTLVMGILNVTPDSFSDGGAHDRVDAAVAHGLDLLAQGADLIDVGGEST
+RTGATPVDPAEEQRRILPVVEALLAEGAVLSIDTMHTATARACLALGPVIVNDVSGLVHE
+PDMPALVAESGAPCILMHNRGHAQVMDSLAHYEDTLGEVVRELSEVTDRFLAAGASPEQI
+ILDPGLGFAKAGEQNWELLRGLERIESLGRPVLVAASRKRFLGTVLAGEDGTPRPALDRD
+HATAAVSAISAAHGAWGVRVHDVRSSVDAVRVGDAWRGAAPRPAGPGEARA
+>PROKKA_00070
+MDESIDAAAREANRALLGRLPADRTLVMGILNVTPDSFSDGGEHATVRAAVEHARRMVAD
+GADIVDVGGESTRPGARAVPPAEEQERILPVIEALLAEDVVLSVDTRHTATARAALALGP
+VIVNDVSGLAHEPDMPALIAASGAPYILMHNRGNPQTMDGLAVYEDTVPDVVCELRDVAG
+RFLAAGVEPAQLIVDPGLGFAKAGEQNWELLRGLEWLRAMGHPVLVAASRKRFLGTLLAD
+DDGTPAPPAARDAATAAISALAAAQGAWGVRVHDVRASADAVRTAAAWAGAHAPGEPVSE
+DVLP

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000068.fa

@@ -0,0 +1,17 @@
+>PROKKA_00216
+MENTIPDERARLGWSQQRLADELGVSRQTVISLEKGRYDPSLPLAFRLAAVFGRRIEDLF
+TPDGNAG
+>PROKKA_02209
+MENTIPDERARLGWSQQRLADELGVSRQTVISLEKGRYDPSLPLAFRLAAVFGRRIEDLF
+TPDGNAG
+>PROKKA_00167
+MENSLPAERARLGWSQQRLADELGVSRQTVISLEKGRHDPSLALAFRLAETFGTRIEDLF
+SPDPPA
+>PROKKA_02206
+MSIDRLAEAAAIHRRTIIQIEAGRTAPRVTTLYAIAEATGTPLRDLLAPLDEALERGTR
+>PROKKA_00321
+MARLARAFKVHKANSGMTYDQLAEATGLARQTLLNLAAGRTYGDLRTWLILAKVWGVTLD
+DLTAAAWRGHAGG
+>PROKKA_00216
+MENTIPDERARLGWSQQRLADELGVSRQTVISLEKGRYDPSLPLAFRLAAVFGRRIEDLF
+TPDGNAG

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000072.fa

@@ -0,0 +1,66 @@
+>PROKKA_00250
+MTVQDPTAVAAPSPTEVFRVARDLLVECQTDDERARAEFEWPRFEHFNFGFDWFDRLAQD
+PARADVPALIIAEDDGRSTERTFAELSAASNRVANWLSAQGLRRGDRLILMLNNQVELWE
+FMLACIKLRVVMVPTTTQMTSGDLEDRVTRAGAAWAVAGAEDLAKFAGVGEGLHLVHVPG
+VFAEGPARRAPEVAGHTVLSYDDAADAATELAPAEPTPADETLLFYFTSGTTSKPKLVEH
+THTSYPVGHLTTLYWIGLEPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDP
+AALMANMARYGVTSFCAPPTVWRMLIKADLAQLTTPPTKTISAGEPLNAEVIDQVHKAWG
+TTIRDGFGMTETTLQVANTPGQKVVIGSMGRPLPGMDVTLIDPLTGQEAEEGEICLRLDP
+RPVGLLKSYYGNQEKTDEVFRDGVFHTGDIARRDENGVLTYVGRADDVFKSSDYKVSPFE
+LESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETARAILQFTLTQLPPYK
+RIRRIEFLELPKTISGKIRRVELRKAEVERAQTGAAPDGYGTEFREEDLDLHR
+>PROKKA_02262
+MTVQDPTAVAAPSPTEVFRAARDLLVECQTDYERARAEFEWPRFEHFNFGFDWFDRLAQD
+PARADVPALIIAEDDGRSTERTFAELSAASSRVANWLSAQGLRRGDRLILMLNNQVELWE
+FMLACIKLRVVMVPTTTQMTSGDLEDRVTRAGAAWAVAGAEDLAKFAGVGEDLHLVHVPG
+VFAEGPARRAPEVAGHTVLSYDDADDAATELTPAEPTPADETLLFYFTSGTTSKPKLVEH
+THTSYPVGHLTTLYWIGLEPGGVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDP
+AALMANMERYGVTSFCAPPTVWRMLIKADLAQLTTPPTKTISAGEPLNAEVIDQVHKAWG
+TTIRDGFGMTETTLQIANTPGQKVVIGSMGRPLPGMDVTLLDPLTGQEAEEGEICLRLDP
+RPVGLLKSYYGNQEKTDEVFRDGVFHTGDIARRDENGVLTYVGRADDVFKSSDYKVSPFE
+LESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETARAILQFTLTQLPPYK
+RIRRIEFLELPKTISGKIRRVELRKAEVERAQTGAAPDGYGTEFREEDLDLQR
+>PROKKA_00120
+MTVQDRTPADAASPTEVFRAARDLLVECQTDYERARAEFEWPRFEHFNFGFDWFDRLAQD
+PARQDVPALIIAEDDGRSTERTFAELSAASNRAANWLAEQGLRRGDRLILMLNNQVELWE
+FMLACIKLRVVMVPTTTQMTSADLEDRVSRADAAWAVAGAEDLAKFAGVGEGLRLVHVPG
+VFAEGEARRAPEVPGHTVLSYDDAAGASAELSPAEPTPADETLLFYFTSGTTSKPKLVEH
+THTSYPVGHLTTLYWIGLQPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDP
+AALMANMDRYGVTSFCAPPTVWRMLIKADLAQLKTPPTKTISAGEPLNAEVIDQVQKAWG
+ATIRDGFGMTETTLQVANTPGQKVVIGSMGRPLPGMDVVLIDPLTGQEAAEGEICLRLDP
+RPVGLLKSYFGNQEKTDEVFRDGVFHTGDIASRDENGVLTYVGRADDVFKSSDYKVSPFE
+LESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETAQSILQFTLTQLPPYK
+RIRRIEFLELPKTISGKIRRVELRKAEVERSETGTAPSGYGTEFREEDLDLTR
+>PROKKA_00088
+MTTTSVTERLRAARDLLVECQEDYDRARAEFEWPRFEHFNFGFDWFDQLAARPDRADVPA
+LIISDAGGGHLSRTYAELSAASNRAANWLRERGITPGDRVILMLDNQVELWELMLACIKL
+RVVMVPTTTQMTSADLADRVERAEARWVVASAENLAKFDGVDSGLHLVHIPGVAAQGDAR
+TAPVVAGHEVLSYDDAASASPELTPDSPTPADETLLLYFTSGTTSKPKLVEHTHTSYPVG
+HLTTVYWIGLQPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDAAALMADMD
+EFGVTSLCAPPTVWRMLIKADLSLLKTPPVKTISAGEPLNAEVIDQVHRAWGTTIRDGFG
+MTETTLQIANTPGQKLVIGSMGRPLPGMDVVLIDPLTGEEAAEGEICLRLDPRPVGLLKS
+YYGNEEKTAEVFRDGVFHSGDIASLDESGVLTYVGRADDVFKSSDYKISPFELESVLVEH
+PAVMEAAIVPSPDEVRLAVPKAFVTLAPSYEPTAETARQILQHTLTQLPPYKRIRRIEFR
+ELPKTISGKIRRVELRKAEAERAETGQAPEGYGIEHREEDLDLKR
+>PROKKA_02472
+MSVTARLRAARDLLVEHQQDYAGARAAFEWPRFETVNFGSDWFDAVAATPERADQDALVI
+VEEDGTVLRRSYARMSADTDRVAGWLQHLGVGRGDTVIVMLDNQVELWEAMLACMKIGAV
+VIPTTTQLVAADLQDRVDRAGARWAIANAGNLVKFADVVGDCTLIHVPGVYASEAEHALP
+EVPGHPVHSYGDAASFAGTWSLETPTSADDPLLLYFTSGTTSLPKLVEHTQASYTVGHLS
+TMYWVGLRPGDVHLNVASPGWGKHAWSSFFAPWLAEATIFVLNFRRFDAATLMRAMDEGG
+VTSFCAPPTVWRMLIKADLTQLQAPPRNAISAGEPLNAAVIDQVQRGWGVTVRDGFGQTE
+STLQIANTPGQRVVIGAMGRPLPGFDIELRDPQTGDRVDGEGEGEICVGLDPRPVGLFQR
+YHGDPEKTAEAFRDGVYHTGDIARRDEHGIYTYVGRADDLFKSSDYKLSPFELESVLMTH
+PAVLEAAVVPAPDELRLSVPKAFVTLAAGHEPGEEAARAILQHVTDRVPAYKRIRRIEFR
+PLPKTVSGKVRRVELRAEEEQRRAGVAGLGVEHREEDLGIRRQRRA
+>PROKKA_00250
+MTVQDPTAVAAPSPTEVFRAARDLLVECQTDDERARAEFEWPRFEHFNFGFDWFDRLAQD
+PARADVPALIIAEDDGRSTERTFAELSAASNRVANWLSAQGLRRGDRLILMLNNQVELWE
+FMLACIKLRVVMVPTTTQMTSGDLEDRVTRAGAAWAVAGAEDLAKFAGVGEDLHLVHVPG
+VFAEGPARRAPEVAGHTVLSYDDADDAATELTPAEPTPADETLLFYFTSGTTSKPKLVEH
+THTSYPVGHLTTLYWIGLEPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDP
+AALMANMERYGVTSFCAPPTVWRMLIKADLAQLTTPPTKTISAGEPLNAEVIDQVHKAWG
+TTIRDGFGMTETTLQIANTPGQKVVIGSMGRPLPGMDVTLLDPLTGQEAEEGEICLRLDP
+RPVGLLKSYYGNQEKTDEVFRDGVFHTGDIARRDENGVLTYVGRADDVFKSSDYKVSPFE
+LESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETARAILQFTLTQLPPYK
+RIRRIEFLELPKTISGKIRRVELRKAEVERAQTGAAPDGCGTEFREEDLDLQR

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000073.fa

@@ -0,0 +1,31 @@
+>PROKKA_00258
+MSEELRILIADDQPLMSGALRVLVDSAPGMTCVGVVANGVEAVEACAAIEPDVVLMDMQM
+PLMDGMEATRRIKDTHPAIRVLAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIQA
+VHRGESVLSPAVATKLLASIERDRPTVGPTSVQPGSPDGSDLTERELGVLRLLARGQSNP
+EIAANLFVSESTVKANLTRIMAKLEVRDRVQLIIRAAQLGLVTLALD
+>PROKKA_02272
+MSEELRILIADDQPLMSGALRVLVASAPGMTCVGVVANGVEAVEACAAVEPDVVLMDMQM
+PLMDGVEATRRIKEAHPEVRVLAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIQA
+VHRGESVLSPAVATKLLASIERDRPTVGPTSVQPGSPDGSDLTERELGVLRLLARGQSNP
+EIAANLFVSESTVKANLTRIMAKLEVRDRVQLIIRAAQLGLVTLALD
+>PROKKA_00111
+MHDAGHTDYSAAHIARTADGTAASGAVSAGPGGRRPGPTTPADAGRSRGSRYADRVSEDL
+RILIADDQPLMSGALRVLVSSAPGMTCVGVVANGAEAVEACAAVEPDVVLMDMQMPLMDG
+VEATSRIKEAHPGIRILAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIHAVHRGE
+SVLSPAVASKLLASIERDHPVVGPAQARPGDPDGSDLTDRERDVLRLLARGQSNPEIAAN
+LHVSESTIKSNLTRIMDKLEVRDRVQVIIRAAQLGLVTLSLD
+>PROKKA_00079
+MPDSPEDEIRVLIADDQPLMSGALRVLVDSAPGMRCVGLVADGVEAVEAVEATRVDVVLM
+DMQMPRMDGVEATRRITASRPGTRVLAVTTFSSEDYLVPALRAGAAGYLLKDAEPATVLG
+AVEAVRRGESVLSPAVAAKLIAAVERDHPVVGPAAAEPGDPDGSDLTEREHQVLTLLARG
+RSNPEIAAELQVSESTVKANVGRVIDKLEVRDRVQVVIRAAQLGLVTLSLD
+>PROKKA_00526
+MDAITVLIVEDEPLLTQAYTMILEADPGIRVVGTASDGAAGVAEHERLRPDVVLMDLRMP
+VLDGVEATGRIMREHPEAKVLVVTSMTTEDYLSPALANGAAGYLTKDTDAEGLVRAVRAV
+EAGTMALGPSIAREVVDLLLRSGVAPRTDAPASPRDLPEALTPREQDVLELLAEGLTNQE
+MAARLYVSDSTVKSNLARVMHKLGANNRVQALVLGVRAGLVSIPG
+>PROKKA_00257
+MSEELRILIADDQPLMSGALRVLVDSAPGMTCVGVVANGVEAVEACAAIEPDVVLMDMQM
+PLMDGVEATRRIKDTHPAIRVLAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIQA
+VHRGESVLSPAVATKLLASIERDRPTVGPTSVQPGSPDGSDLTERELGVLRLLARGQSNP
+EIAANLFVSESTVKANLTRIMAKLEVRDRVQLIIRAAQLGLVTLALD

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000075.fa

@@ -0,0 +1,30 @@
+>PROKKA_00282
+MTGGDPAALMDALGAWFHPLTALLVALDAPIPPVPSEVVVIGSGALAAEGRVSPVAAVLA
+AWLGCWAGDVGLYALFRHGLADRLDRWAWWRRIHRGIRSLLVRVGPAGSLAGLSVLRFVS
+GGRTASMAAAGIGGIRWPVFLWLSGAGSLAWSSSMVGLGWITGRATGLPWWASAMVGMVF
+GTLAGLMIAGIMAHRRRGRKG
+>PROKKA_02297
+MTGGDPAALMDALGAWFHPLTALLVALDAPIPPVPSEVVVIGSGALAAEGRVSPVAAVLA
+AWLGCWAGDVGLYALFRHGLADRLDRWAWWRRIHRGIRTLLVRVGPAGSLAGLSVLRFVS
+GGRTASMAAAGIGGIRWPVFLWLSGAGSLAWSGSMVGLGWLTGRATGLPWWASAVVGMVF
+GTLAGLMIAGIMAHRRRGRKG
+>PROKKA_00071
+MTVLTPAWFAASGGVPTMGAGAAAASGAGAWDPSALLDSLGAWFHPLTALLVALDAPIPP
+VPSEVFVIGSGALAAEGRVGLAAAVLTAWLGCWAGDVGLYALFRHGLADRLDRWAWWRRV
+HRGIRVLLVRVGPAGSLAGLSVLRFVSGGRTASMAAAGIGGIRWPVFLWLSGAGSLAWSG
+WMVGLGWLTGRTTGLPWWASAVVGMVFGTLAGLIIAGVVARRRARKG
+>PROKKA_00057
+MTDVTALLEGLGPWFHPLTFLLVALDAPVPPTPSEVLVIGSGSLAAAGRLGLATSVLTAW
+LGCWAGDVGLYALFRHRLTSVLDRWGWGRAVHAGIRRLMEKAGPASSLAGLFVLRFVSGG
+RTASMAAAGVAGVRWRPFLWLSGTGSLAWSVYMVGLGWITGSATGLPWWASAVVGVVLGT
+LLGAAVAAVIAWRRRGKEGA
+>PROKKA_00450
+MPVLTNILDAASILHSLGPWTLGGIGSMVFIESGVLFPFLPGDSLLVTAAALHVELGIAL
+WAIILVAGLAAILGDQVGFYLGHRYGRRLFKDDARVLKTERLAQAEAFFERRGPLALVLG
+RFVPIVRTYVPVAAGTAGMPYRSFVGWNIGGAVAWVCSMVAVGALLGQIPGITKSIDGIM
+ILIIVISVAPIAIQALRARRKARRDAVMTEGQPVA
+>PROKKA_00281
+MTGGDPAALMDALGVWFHPLTALLVALDAPIPPVPSEVVVIGSGALAAEGRVSPVAAVLA
+AWLGCWAGDVGLYALFRHGLADRLDRWAWWRRIHRGIRSLLVRVGPAGSLAGLSVLRFVS
+GGRTASMAAAGIGGIRWPVFLWLSGAGSLAWSGSMVGLGWITGRATGLPWWASAVVGMVF
+GTLAGLMIAGIMAHRRRGRKG

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000078.fa

@@ -0,0 +1,43 @@
+>PROKKA_00310
+MDVPAQMRAVRFTGAGDNGVVRVGHEPVPDPGPGEVLVHVAAAGLNRADIAQREGRYPPP
+RGASEIPGLEVSGTVAALGPEAGMPGEGRFAVGDRVCALLAGGGFAEYVAVPAGQLMAVP
+DGVGLVEAAALPEVACTVHSTLVGRAGVQAGDRVLVHGATGGIGSFAVQFLTAVGARVLG
+TAGGPEKVALGRGLGAEHMFDHRAAESGAFAPWVKEVTDGHGADVILDVVGAPYLAPNVS
+ALAPEGRIVTLAVQGGAVPEDFNIMKLVVKRGWLTGATLRSRSVTDKAGIVAAAERAVWP
+LVAAGRIDASVGACFPLAEAAEAFDWFDSATRTGKVVLVTDPADARRPSGDRA
+>PROKKA_00025
+MDVPAQMRAVRFTGAGDNGVVRVGHEPVPDPGPGEVLVHVAAAGLNRADIAQREGRYPPP
+RGASEIPGLEVSGTVAALGPEAGMPGEGRFAVGDRVCALLAGGGFAEYVAVPTGQLMAVP
+DGVGLVEAAALPEVACTVHSALVGRAGVQAGDRVLVHGATGGIGSFAVQFLAALGARVLG
+TAGGPEKVALGRRLGTEHMFDHRAAESGAFAPWVKEVTDGHGADVILDVVGAPYLAPNVS
+ALAPEGRIVTLAVQGGAVPEDFNIMKLVVKRGWLTGATLRSRSVVDKAGIVAAAERAVWP
+LVAAGRIDASVGACFPLAEAAEAFDWFDSATRTGKVVLVTDPADARRPSGDRA
+>PROKKA_00027
+MSETTRTPGTGRGTMRAVRFTGEGGAGSLAVGQEPIPTPGPGEVLVKVAAAGLNRADVMQ
+REGKYPPPPGASDVPGLEVSGVVVALGEEAGLPGEGRFAPGDEVCALLAGGGYAEHVVVP
+AGQLMAVPPGVDLVTAAALPEVACTVWSTMSERGGVRAGDVVLVHGGSGGIGTFAVQYLA
+AIGARVLATAGGPAKCERVRGLGAEDVFDHRSGEPGAFADWVLERTGGRGADVVLDVVGG
+PYLDANVRCLAEEGRIVVIAVQGGPKADGFNLMRLVSKRGWLTGATLRARSVVDKARIVA
+GTERAVAPLVAAGRIDLAVGARFPLDDAAAAHRRFEAEDRVGRVLLVTDPADALWPQEDR
+T
+>PROKKA_00023
+MDTAPDMLAVRFAGAGGTDVIRVGREPVPEPGPGEVLVRVAAAGLNRADVVQREGHYPVP
+PGASEVPGLEVSGTVVALGPQAGVAGEGRFAVGDRVCALLAGGGYAEHVAVPAGQLMSVP
+DGLDLVSAAGLPEVACTVHSNLEGRAGVRPGEWALVHGATGGIGAFAVQYLSAVGVRVLA
+TAGGPAKVARALELGADAAFDHRAAAPGAFADWVREITGGHGADVVLDVVGGPYLAPNVK
+ALAMDGRIVVIAAQDGPVPEDFHLMRLAARRGWVTGSLLRPRPPDEKAGIVAAAERAVWP
+LVAAGRIDPGVTARFPLREAAAAHAHFEGAARMGKVLLVTDDADALLPGGAA
+>PROKKA_00654
+MHPSLPRTMLAAIIPAPGGRPELRQCPVPEPGPGEVLVRVMASSVNPTDVMTWRRGMFVT
+GQTVPFVGGYDMSGIVVKLGRGVTALDVGDAVTGMPRFPAPAAAFAQYSAVPARHLARIP
+TGTEDLSAGAWGRWAGLPLAGLTAYQALVDTAHLQSGQTVLVHAASGGVGSLACQLAVNL
+GAQVTAVTSDRGRTLVEVLGTRHVVDRATVDWQRFAGCFDVVLDTVGGDTTPRSLAMASP
+DGVVVALHPYAHDDLAQRDPRLRRMLVEPDHHALELLIEQAARGRLTVQVGAGYPLSDLG
+DALLHVETNKTPGKTIIHIQGDNA
+>PROKKA_00317
+MDVPAQMRAVRFTGAGDNGVVRVGHEPVPDPGPGEVLVHVAAAGLNRADIAQREGRYPPP
+RGASEIPGLEVSGTVAALGPEAGMPGEGRFAVGDRVCALLAGGGFAEYVAVPAGQLMAVP
+DGVGLVEAAALPEVACTVHSALVGRAGVQAGDRVLVHGATGGIGSFAVQFLAALGARVLG
+TAGGPEKVALGRRLGAEHMFDHRAAESGAFAPWVKEVTDGHGADVILDVVGAPYLAPNVS
+ALAPEGRIVTLAVQGGAVPEDFNIMKLVVKRGWLTGATLRSRSVVDKAGIVAAAERAVWP
+LVAAGRIDASVGACFPLAEAAEAFDWFDSATRTGKVVLVTDPADARRPSGDRA

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

@@ -0,0 +1,36 @@
+>PROKKA_00318
+MANTTYTLVLLRHGQSEWNEKNLFTGWVDVPLTEKGRAEAARGGELLEAEGIRPDVVHTS
+LLKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMVWRRS
+FDTPPPALDDDSEFSQVGDERYADLGKDAPRTEALKQVVDRLLPYWEEQVLPDLKAGKTV
+LIAAHGNSLRALVKHLDGISDEDITGLNIPTGIPLVYELDQNFKPITANGRYLDPEAAAA
+GAAAVAAQGSAH
+>PROKKA_00033
+MANTTYTLVLLRHGQSEWNEKNLFTGWVDVPLTEKGRAEAARGGELLEAEGIRPDVVHTS
+LLKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMVWRRS
+FDTPPPALDDDSEFSQIGDERYADLGKDAPRTEALKQVIDRLLPYWEEQILPDLKAGKTV
+LIAAHGNSLRALVKHLDGISDEDIAGLNIPTGIPLVYELDQNFKPITANGRYLDPEAAAA
+GAAAVAAQGSAH
+>PROKKA_00019
+MANTTYTLVLLRHGQSDWNEKNLFTGWVDVPLTEKGRAEASRGGELMKAEGIHPDVLHTS
+LLKRAITTANLALETADRQWIPVKRDWRLNERHYGALQGKDKAQVKEEFGEEQFTVWRRS
+FDTPPPALDDSSEFSQIGDERYAELGDDAPRTEALKNVIDRLIPYWEAEIVPDLKASKTV
+LVAAHGNSLRALVKHLDGISDEDIAGLNIPTGIPLVYELDEDLKPITANGRYLDPEAAAA
+GAAAVAAQGSAH
+>PROKKA_00015
+MADTFKLILLRHGQSDWNEKNLFTGWVDVPLTEKGRAEASRGGELLAAEGLLPDVLHTSL
+LKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMTWRRSF
+DVPPPPLDDSSEFSQAGDERYRDIGPDAPRTEALKQVIDRLLPYWTEQIVPDLKAGKTVM
+VAAHGNSLRALVKHLDGISDEEISGLNIPTGIPLFYELDQNLKPVTPHGRYLDPEAAAAG
+AAAVAAQGDKK
+>PROKKA_00687
+MLTLLRHGESTANEAGTFTGLLDVPLTHRGERQASAAGQLLRSNHITPDVVVTSTLRRAV
+RTAELVCDALGTQLPTEAVWQLNERNYGALTGMTKTDARRMLGDDEYVRLRRSRTGTPPP
+MSLHLWEELRSSSALRGLPDGALRRTEALSDVIKRVRPVLHDRLLPMVRSGRSVLVVAHG
+NSLRALCACIDDLTDPELEQLNLPTGQPVQYHLAPTGALVPRGGAFLDPVAAQHAAALVA
+AEGGT
+>PROKKA_00325
+MANTTYTLVLLRHGQSEWNEKNLFTGWVDVPLTEKGRAEAARGGELLAAEGIRPDVVHTS
+LLKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMVWRRS
+FDTPPPALDDDSEFSQVGDERYADLGKDAPRTEALKQVIDRLLPYWEEQVLPDLKAGKTV
+LIAAHGNSLRALVKHLDGISDEDIAGLNIPTGIPLVYELDQNFKPITANGRYLDPEAAAA
+GAAAVAAQGSAH

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000084.fa

@@ -0,0 +1,54 @@
+>PROKKA_00418
+MPESTLYWIIAAIIVVLLILIILSVIASRRRREAEAEAAETRLERRGTTADTADTAGEQA
+AAPAAPTRLSRLDEVAAEQDARPAAAVKPAGGPAASETAAAGRETDESVAGVAGGAGVTV
+DQQDAPRTDATAETSRPTAAPTTRGTLRPAAAAPSTAREADTVGLGAAGVAGGSGITLDE
+QTPAADVAAAPASPSPVTETPAPAAPAAEAPQHRSHLTPAPEHVHGTVPAEEVAAEHTPT
+KEFATDAIPVAQGEHLETNTVATTAHGSVTVVAAESDQTQQNDADGAERSAAGSLRIDGT
+PGVPGRVAEAGREPARTEDHRADAAQPAAVEPAAERPSLEAAAERPSLEATPATRRAEAP
+ETHAGTTPATPLGGAPELDPTAASSGRAEDATPATRREARAAQSAAAAGTAATAGTAGTA
+APTSSTPTTVAPDTSTSSAPTNEEPAEDDTEGAALPDLRADRDETRGSDAEGESKLAQAG
+AVAASAFETVRDKVAIPLRDNVAVPAKDKAVKVVKDKLAQAQERRWGKR
+>PROKKA_00139
+MPQSTLYWIIAAIIVVLLILIIVSVIASRRRREAEAEAAETRLERRGVSADTAGEQAAAP
+AAPTRLSRLDEVAAEKDARPAPAVRPAGGLAAFDTAAADRETDESGAGVAGGAGVTVDQQ
+DAPSTEATAQTHRRDAAAPATRGTLRPAPAVPSTVREADTVGLGAAGVAGGSGVTLDEQT
+PAADVPATPASPSPVTETPAPAAPVAEAPQQRSHLTPAPEHVHGTVPADEVAAEHTPTKE
+FATDGIPVPQGEHLETHTVATTAHGSVTVVATESDQAQQTGVDGTERSAAGSLRIDGTPG
+VPGRVAEADREPARTDDHGADVAQPAAVEPAAERPPLEAAPATRRAEAPETHAGTTPATP
+LGGAPELDPTAASSGRAEDATPATRREARAAQSAAAAGTAGTAAPTSSTPTTVAPDTSTS
+SAPTDEEPAEDDTEGAALPDLRADRDETRASDAEGESKLAQAGAVAASAFETVRDKVAVP
+LRDNVAVPAKDKVVKVVKDKLSQAQERRWGKR
+>PROKKA_02541
+MPTDAEPAADDTEGAALPVQDATRADAVRPGTARTDASAGDSKLAQAGAAAGTVLETVRD
+KVAIPLRDNVAIPAKDKAVKVLKAKLAEAQERRRNKR
+>PROKKA_02542
+MGESTLYWIIGAIIVVLLILIILSVVASRRRRAAEAEAAEAQLERRRVTPTAAGVGASHE
+DALEETHDADARPHTVASTGGDVAPAAAAGAAAGTTRLSQLDDVAPVAAAAADADAESLP
+ADGVAAGSGVTVDQQDASDQSVRPAAPAAPAGADTRGPNASVKSAGAAAAAVGLGAAGVA
+GGRGVTVDQQDAAADVPSTPASPSPVAQTPAAPSSAGATTAQDDRADRTAQDAADAEPVK
+GTVPLSEDAHAVPPAADPPSGGDAVADDAHLEAHTVATTEHGSVVVVTAEQDEDDQATAA
+SRETETETDDSRGDDAGQDRDAERAVAEGVAGGTGVTVDQKAVAEAAATQGAPASAAGAA
+SAAGAAARRRDRGRRLDPACGGARLLQDRRHAGHARPRRLRGAGRGRGGDRPARPPRRRP
+GDARLHHPRDAPGRRAGAGPGRRRRGLPQGRGRDPAAPPRGRRPGAKPRRRPTSTRPRPR
+PPRRTAPAR
+>PROKKA_02410
+MPQSTLYWIIGIIIVVLVIILIVSSLRAKRGREEEAAAAGRHADSAPAPLAATAARGGTV
+GASTVPATGDAPADRTDGRAAGATALPSFDVDEVDRRAAEQREQDVVERRRATGAEAGAA
+GHAAVPGVTGGSGVSVDEAEGVAKDATGQDVTPVADAQRRNGSSAAPAATGAGLGLAAAG
+VAGGTGVTVDDAGTGADLPAPKGSPAGVVEVAETQAEAAQADAAPAEHTVVPGVAGGDAV
+TVDTADVQSSSAPQGAQAAAGRSDLTDAEARTYPVTGLPGVPSAVDPEQVAAARVQDAAE
+LKAAEGQGAEHERGASQPADPESVPGTVPLTGEEAVIEAPVHTHEMPEPVLGTPAYIQDS
+TTGQDPTEDLPEGQVYGTTPLSGEDAIVEPADQLPAEAAETEDRAASDAGTASAETAVVP
+VEETETAVVPVAETRSADAGPSEDSVALTGQGVETADRVEPAAPVAGTPARDEARTHDEH
+RSRLEIVKDAVAETAGTVATTAGTAAEKAAPVVRSAARTVGKAAGSAASTLKDKLAQAQE
+RRWGKR
+>PROKKA_00421
+MPESTLYWIIAAIIVVLLILIILSVIASRRRREAEAEAAETRLERRGTTADTADTAGEQA
+AAPAAPTRLSRLDEVAAEQDARPAAAVKPAGGPAASETAAAGRETDESVAGVAGGAGVTV
+DQQDAPRTDATAETSRPTAAPTTRGTLRPAAAAPSTAREADTVGLGAAGVAGGSGITLDE
+QTPAADVAAAPASPSPVTETPAPAAPAAEAPQHRSHLTPAPEHVHGTVPAEEVAAEHTPT
+KEFATDAIPVAQGEHLETNTVATTAHGSVTVVAAESDQTRQNDADGAERSAAGSLRIDGT
+PGVPGRVAEAGREPARTEDHRADAAQPAAVEPAAERPSLEAAAERPSLEATPATRRAEAP
+ETHAGTTPATPLGGAPELDPTAASSGRAEDATPATRREARAAQSAAAAGTAATAGTAGTA
+APTSSTPTTVAPDTSTSSAPTNEEPAEDDTEGAALPDLRADRDETRGSDAEGESKLAQAG
+AVAASAFETVRDKVAIPLRDNVAVPAKDKAVKVVKDKLAQAQERRWGKR

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

@@ -0,0 +1,61 @@
+>PROKKA_00423
+MPSPTTTTAPGPASPAGPLRPPHTAAESAERVKRRGALYFAEHQLRNMRRYGAVLIVGAL
+GEPVLYLLAMGLGLAQLMGGGMPQDALGGVSYVAFIAPALLASGALMTASVEFSYPVMGG
+FQWHRTYYAAQATPLSPAQIALGHLAAVSLRFVFQAAVFLLVMLAFGVVSSPWAWVQVLT
+ATLGGLAVGAPIMAFAASLKEDKGQFATLQRLVVMPLFLFSATFYPLDVLPVWLRWIGWL
+SPQWHAAQLGRMLSYGMAEPAWLTVAHVAFLLALALGGARLAVRIYTRRLGWVRGTPDRD
+AGTAARRDRAPRLGRRAPRLGRRAARTGAARADVAPAAAQADPAAPSSSVVREHAVAVPP
+LPEIPVRRGPLAGAYSGNVRAVMERAFLSLKSNNWVVFFSGFFEPVLYLASLGLGLGALV
+GDVAGPDGTPVPYGMYLAPALLAVSAMNGAIYDSTWNVFFKLRYAKTYQTMLSTRLGPLD
+VALGEIAMALLRGLIYAVGFLIVMTVAGLVTSWTALLMIPGALLVALGFASLGMAVTSWM
+KTFQHMDWVQIVLMPMFLFSATFFPLAVYPEPIQWVIRVFPLWHAVEMMRALAVGVLSWA
+TAGHVLYFVVMAGVGVWLAARRLGALFLR
+>PROKKA_00144
+MPSPTTTTTPGPASPAEPLRPPVTAAASAERVKRRGVLLYAEHQLRSMRRYGAVLLVGAL
+GEPVLYLLAMGLGLAQLMGGGMPQDALGGVSYVAFIAPALLASGALMTASVEFSYPVMGG
+FQWQRTYYAAQVTPLSPAQIALGHLVAVSLRFVFQAAVFLLVMLAFGVVSSPWAWVQVLT
+ATLGGLAVGAPIMAFAASLREDKGQFATLQRLVVMPLFLFSATFYPLEALPVWLRWIGWL
+SPQWHAAQLGRVLSYGMAEPVWLTVVHVAFLLALALGGAWLAVRIYTRRLGWVRGTPDRD
+AVTVARRDRAPRLGCRAARTGAARADVAPAAAQADPAAPSSSVVREHAVAVPPLPEIPVR
+RGPLAGAYSGNVRAVMERAFLSLKSNNWVVFFSGFFEPVLYLASLGLGLGALVGDVAGPD
+GTPVPYGMYLAPALLAVSAMNGAIYDSTWNVFFKLRYAKTYQTMLSTRLGPLDVALGEIA
+MALLRGLIYAVGFLIVMTVAGLVTSWTALLMIPGALLVALGFASLGMAVTSWMKTFQHMD
+WVQIVLMPMFLFSATFFPLAVYPEPIQWVIRVFPLWHAVEMMRALAVGVLSWATAGHVLY
+FVVMAGIGVWLAARRLGALFLR
+>PROKKA_02534
+MTAAAGAEPAAPSSSVVLEHTAAVPPMPEITLRHGPLAGMYAGNVRAVMERAFLTLKSNN
+WVVFASGFFEPVLYLASMGIGLGALVGDVAGPDGTPIPYGMFIAPALLAVSAMNGAIYDS
+TWNVFFKLRHAKTYQTMLSTKLGPLDVALGEIVMALLRGLIYAVGFLIVMTVGGLVTSWT
+AVLMVPGALLVALGFASLGMAVTSYLKTFQHMDWIQIVLMPMFLFSATFFPLSVYPQAIQ
+WVIQVLPLWHAVELMRALAVGVVTWGTAGHILYFVAMSAVGIWFTSRRLGALFLR
+>PROKKA_02535
+MDASTTTTAPGPAAPRASASPAPLSPPISAAESAERVTRRGALYYAEHQLRNMRRYGSVL
+IVGALGEPIVYLLAMGLGLAQLMGGGAAQEGLGGVSYVAFLAPALLASGALMTAAVEFSY
+PVMGGFQWQKTYYAAQATPLTPAQIAVGHLGAVSLRFLFQGLVFFLVMLAFGVVHSPWGW
+LQILTATLGGLAIGAPIMAFAASLTEDKGQFATVQRLVIMPLFLFSATFYPLEALPVWLR
+WIGWISPQWHAAQLGRVLSYGMAEPVWLTVLHVVVLVAMAAVGTWLAVRIYTRRLGWRRG
+TPDRDALARP
+>PROKKA_02405
+MAAQIPASAPLQPPITAAESAVRVKARGAWFYAEHVLRSMRRYGAVLIVGALGEPILYLL
+AMGLGMAQVMGGGAPQESLGGVSYVTFLAPALLASGALMTAATEFSYPVMGGFQWHRTYY
+AAQATPLSPAQIAVGHLGAVALRFLFQAAVFFGVMLAFGVVHGPWGWVQVLTAALGGLAI
+GAPIMAFSASLKEDHGQFATLQRLVIMPLFLFSATFYPLEALPVWLRWVGWISPQWHAAQ
+LGRVLSYGMAEPRWLTVLHVAVLLALAFGGAWAAVRMYTRRLGWRPGTPDRDAVARPRAQ
+RASRLGRRATRVDRMAGAHAEAAAASSVVREHTAAVPPMPEITVRRGRLGGLYSGNVAAV
+MERALLTLKSNNWVVFASGFFEPVLYLASMGLGLGALVGAVPGPGGAPIPYGMYIAPALL
+AVSAMNGAIYDSTWNVFFKLRYAKTYQTMLATRLGPLDVALGEIAMALLRGLLYAVGFLV
+VMAVAGMATSWTALLMVPGALLVALGFASLGMAVTSWMKTFQQMDWIQLVLMPMFLFSAT
+FFPLTVYPEPIQWLIRVFPLWHAVEMMRALAVGAVTGATAGHALYFGVMSGLGVWLTSRR
+LRALFLR
+>PROKKA_00426
+MPSPTTTTTPGPASPGPRSGTSAPSATPAEPLRPPVTAAESAERVRRRGVLLYAEHQLRS
+MRRYGAVLLVGALGEPVLYLLAMGLGLAQLMGGGMPQDALGGVSYVAFIAPALLASGALM
+TASVEFSYPVMGGFQWQRTYYAAQATPLSPAQIALGHLVAVSLRFVFQATVFLLVMLAFG
+VVSSPWAWVQVLTATLGGLAVGAPIMAFAASLKEDKGQFATLQRLVVMPLFLFSATFYPL
+EALPVWLRWIGWLSPQWHAAQLGRVLSYGMAEPAWLTVVHVAFLLALALGGAWFAVRIYT
+RRLGWVRGTPDRDAVTAARRDRAPRLGRRAARTGAARADVAPAAAQAEPAAPSSSVVREH
+AVAVPPLPEIPVRRGPLAGAYSGNVRAVMERAFLSLKSNNWVVFFSGFFEPVLYLASLGL
+GLGALVGDVAGPDGTPVPYGMYLAPALLAVSAMNGAIYDSTWNVFFKLRYAKTYQTMLST
+RLGPLDVALGEIAMALLRGLIYAVGFLIVMTVAGLVTSWTALLMIPGALLVALGFASLGM
+AVTSWMKTFQHMDWVQIVLMPMFLFSATFFPLAVYPEPIQWVIRVFPLWHAVEMMRALAV
+GVLSWATAGHVLYFVVMAGVGVWLAARRLGALFLR

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000086.fa

@@ -0,0 +1,54 @@
+>PROKKA_00448
+MALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAAVPSGASTGEFEAVERRDGDKKRYG
+GKGVLDAVAAVEGIAEELEGEFAADQRAVDRAMRDLDGTPNKGKLGANAILGVSMAVAVA
+AAQASDLMLYKYLGGPNAHVLPVPMMNILNGGAHADSNVDIQEFMIAPIGAPSFREALRW
+GTEVYHALKTVLQEKGLSTGLGDEGGFAPSLESNRAALDLIAEAVTKAGYRLGEDIALAL
+DVASSEFFDNGSYTFEGQQRSAEEMAAYYTELVDNYPIVSIEDPLDEDDWDGWQHLTAQL
+GDRVQLVGDDLFVTNVERLQRGIDEKAGNALLVKVNQIGSLTETFDAIALAQRHMFHCMI
+SHRSGETEDTFIADLAVATNAGQIKTGAPARSDRVAKYNQLLRIEEDLADAAVYAGRSAF
+PRFRG
+>PROKKA_00169
+MALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAAVPSGASTGEFEAVERRDGDKKRYG
+GKGVLDAVAAVEGIAEELEGEFAADQRAVDRAMRDLDGTPNKGKLGANAILGVSMAVAVA
+AAQASDLMLYKYLGGPNAHVLPVPMMNILNGGAHADSNVDIQEFMIAPIGAPSFREALRW
+GTEVYHALKTVLQEKGLSTGLGDEGGFAPSLESNRAALDLIAEAVTKAGYRLGEDIALAL
+DVASSEFFDNGSYTFEGQQRSAEEMAAYYTELVDNYPIVSIEDPLDEDDWDGWQHLTAQL
+GDRVQLVGDDLFVTNVERLQRGIDEKAGNALLVKVNQIGSLTETFDAISLAQRHMFHCMI
+SHRSGETEDTFIADLAVATNAGQIKTGAPARSDRVAKYNQLLRIEEDLADAAVYAGRSAF
+PRFRG
+>PROKKA_02509
+MALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAAVPSGASTGEFEAVERRDGDTKRYL
+GKGVLDAVAAVEEIADELEDEFAVDQRAVDRLMLDLDGTPNKGKLGANAILGVSMAVAAA
+AAQSSDLMLYKYLGGPNAHVLPVPMMNILNGGAHADSNVDIQEFMIAPIGAPSFREALRW
+GTEVYHSLKKVLQEKGLSTGLGDEGGFAPSLESNRAALDLIAEAVEKAGYTLGEDIALAL
+DVASSEFCEKGAYTFEGQKRSAEDMVAYYTELADNYPIVSIEDPLDENDWDGWRLLTEKL
+GDRVQLVGDDLFVTNVERLQRGIDDKAGNALLVKVNQIGSLTETFDAIALAQRHMFHCMI
+SHRSGETEDTFIADLAVATNAGQIKTGAPARSDRVAKYNQLLRIEEDLADAAVYAGRSAF
+PRYRG
+>PROKKA_00683
+MNDYISGIHHHGAHQGEYVTHHDHPVTIDAVHGARILDSRGYPTVRVSLELDDGRTVTGD
+APAGASTGAHEAVELRDGGSAFGGRDVTQALHLIDTDISGLLTGRSWSAIGQIDAALAEL
+DGTTGYRRLGANSVVATSIAASRALAHAADLPLWQWIAEITGSTPRMPVPHFNVLNGGAH
+AANELDFQEFMIAPVNAGSMADAVRIGADVYHALAALVRDRFGSLGLGDEGGFAPSIAAP
+EEALDLLVDAIRTAGYEPGVDQVAIALDPAANEFSQGDGSYRVLNDSLDRDGLVDYYRHL
+IDTYPIRSIEDAFAEDDHEGFRRMQAALGDRIQIVGDDLYVTDPQRIRDGGEQQLTNAAL
+IKPNQIGTVSQTLGAIATAKSIGMASMVSHRSGETTDTFIADLVVGTGTGQIKSGAPGRG
+ERVAKYNRLTEIAEQHPELPYGLI
+>PROKKA_02380
+MAQIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAAVPSGASTGEFEAVERRDGDTERYL
+GKGVQDAVNAVFEIAEELEDELATDQRAVDQMMLDMDGTENKGKLGANAILGVSMAVAVA
+AADSADLPLYKYLGGPNAHVLPVPMMNILNGGAHADSNVDIQEFMIAPIGAPSFREALRM
+GAEVYHSLKKVLQEKGLSTGLGDEGGFAPNLESNRAALDLIAEAVQKAGYTLGEDVALAL
+DVASSEFCENGSYTFEGRQRSAEEMSAYYAELVDAYPIVSIEDPLDENDWEGWEHLTEQL
+GDRVQLVGDDLFVTNVARLQRGIDEKAGNALLVKVNQIGSLTETFDAIALAQRHMFHCMI
+SHRSGETEDTFIADLAVATNAGQIKTGAPARSDRVAKYNQLLRIEEDLADAAVYAGRSAF
+PRFQG
+>PROKKA_00451
+MALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAAVPSGASTGEFEAVERRDGDKKRYG
+GKGVLDAVAAVEGIAEELEGEFAADQRAVDRAMRDLDGTPNKGKLGANAILGVSMAVAVA
+AAQASDLMLYKYLGGPNAHVLPVPMMNILNGGAHADSNVDIQEFMIAPIGAPSFREALRW
+GTEVYHALKTVLQEKGLSTGLGDEGGFAPSLESNRAALDLIAEAVTKAGYRLGEDIALAL
+DVASSEFFDNGSYTFEGQQRSAEEMAAYYTELVDNYPIVSIEDPLDEDDWDGWQHLTAQL
+GDRVQLVGDDLFVTNVERLQRGIDEKAGNALLVKVNQIGSLTETFDAIALAQRHMFHCMI
+SHRSGETEDTFIADLAVATNAGQIKTGAPARSDRVAKYNQLLRIEEDLDDAAVYAGRSAF
+PRFRG

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

@@ -0,0 +1,56 @@
+>PROKKA_00495
+MIGSPGDESTALRMGSTARGRVLGRPWERGLPLLVLIVDVVAVLLATFVSAQLRFGGPRR
+TTLPGAEVIDYSVISLALSAAWVLALTIQGSRDIRILGVGSEEYKRVLQGTLYLFGTVAI
+LAYAAGLEVARGYVGLALPLGVLLLLLGRFLVRGWVARQRHRGRFRRRLLLVGGPKAVRH
+IFQTLDSEAGAGYAPVAAALPGYKARREDYLPIPVSTDLDTVEDVVALVEVRDVEAVVIT
+SGHSFVPGDVRRLGWELQERGVSLIMAPALVDVAGPRLHTQPLAGLPLIHLSTPRLSEGK
+AFAKRAFDVVASGLGLIAISPLLIAVAIAVKATDGGPVLFRQERIGLGGRPFTMLKFRSM
+VVDAEEIRQRLVSDGGDADVLFKMKDDPRITRVGKLIRRTSIDELPQLVNVLRGEMSLVG
+PRPHLPHEVEAYGQYVHRRFLVQPGITGLWQVSGRSDLPWEEAVRLDLYYVENWSILGDL
+VILGRTVKAVVAADGAY
+>PROKKA_00216
+MIGSPGDESTALRMGSTARGRVLGRPWERGLPLLVLIVDVVAVLLATFVSAQLRFGGPRR
+TTLPGAEVIDYSVISLALSAAWVLALSIQGSRDIRILGVGTEEYKRVLQGTLYLFGTVAI
+LAYAAGLEVARGYVGLALPLGVLLLLLGRFLVRGWVARQRHRGRFRRRLLLVGGPKAVRH
+IFQALDSEAGAGYAPVAAALPGYKARREDYLPIPVSTDLDTVEDVVAHVEERDVEAVVIT
+SGHPFVPSDVRRLGWELQERGVSLIMAPALVDVAGPRLHTQPLAGLPLIHLSTPRLSEGK
+AFAKRAFDVVASGLGLIAISPLLIAVAIAVKATDGGPVLFRQERIGLGGRPFTMLKFRSM
+VVDAEEIRQRLVSDGGDADVLFKMKDDPRITRVGKLIRRTSIDELPQLVNVLRGDMSLVG
+PRPHLPHEVEAYEQYVHRRFLVQPGITGLWQVSGRSDLPWEEAVRLDLYYVENWSILGDL
+VILGRTVKAVIAADGAY
+>PROKKA_01221
+MLTPDSPYEERFAALNQSLRWEVADELRRANLARVDELHPPVTPRDTFYTRHGKRALDVG
+VSGAALLFSSPVIGALCLVTLKDLGQPVLFTQQRPGKHGKPFQMVKLRTMREAYDDQGKP
+LLGELRVTKTGRLIRRASLDELLNFWNIFKGDMSLIGPRPLVPEYVERFSRRHRQRLAVK
+PGLECPPPRPPQGPVTYDDQFENDCWYVENVSLKTDAWLTWRVLQTALDRRQNKARGSST
+RGSFMGYDADGTVITTAALPDWALNTVLERHGLLTSNSADARQEG
+>PROKKA_02452
+MFSSPGDESPALRTGSTARGRLLGRPWERGLPLLVFIVDVVAVLLATFVSAQLRFGGPRR
+TTLPGTEVIDYSVISLALSAAWVLALSIQGSRDIRILGVGSEEYKRVLQGTLYLFGTVAI
+LAYAAGLEVARGYVGLALPLGVLLLLLGRFLVRGWVARQRHLGRFRRRLLLVGGPKAVRH
+IFQALDSEAGAGYAPVAAALPGYKTRQEDYLPIPVSTDLDTVEDVVALVEVRDVEAVVIT
+SGHSFVPGDVRRLGWELQERGVSLIMVPALVDVAGPRLHTQPLAGLPLIHLSTPRLSEGK
+AFAKRAFDVVASGLGLIAISPLLIAVAIAVKATDGGPVLFRQERIGLGGRPFTMLKFRSM
+VVNAEEIKQRLVSDGGDADVLFKMKDDPRITKVGKFIRRTSIDELPQLVNVLRGDMSLVG
+PRPHLPHEVEAYEQYVHRRFLVQPGITGLWQVSGRSDLPWEEAVRLDLYYVENWSILGDL
+VILGRTVKAVVAADGAY
+>PROKKA_02336
+MTSSAVTTSQTGRGGSSVHARVLGAPWERGLPRLVLLADVVAVVLAAFLSSELRFGTARN
+AAVPGAESVNYLLVGAVLSASWVVALGVDGSRDIRILGIGAEEYKRVLRGTLYLFGMIAI
+LAYAFAFEVARGYVALALPIGLLLLMLGRFLIRGWVARGRHRGAMRRRLLLVGGPQAVKY
+VHDTLDSEAGAGYKPIAAVLPGYRARDEGWLPIPVTTEVDGVDELVAQVREMDIEAVVIT
+SGHPFVPDDVRRLGWDLQERGISLIMAPALVDVAGPRLHTQPLAGLPLLHLSTPRLSRGK
+AFVKRSFDVVASGLGMLVISPLLLTVAIAVKATDGGPVLFRQERVGLRGEHFTMLKFRSM
+VVDAEEIKQQLMSDRGEEDVLFKMKDDPRITRVGRFIRRTSIDELPQLVNVLRGDMSLVG
+PRPHLPHEVEQYGQYVHRRFLVQPGITGLWQVSGRSDLSWEDAVRLDLYYVENWSVLGDL
+VILGRTVKAVLAADGAY
+>PROKKA_00494
+MFASPGDESTTLRMGSTARGRVLGRPWERGLPRLVLVVDVVAVLLATFVSAQLRFGGPRR
+TTLPGAALVDYSVISLALSAAWVLALTIQGSRDIRILGVGTEEYKRVLQATLYLFGTVAI
+LAYAAGLEVARGYVGLALPLGVLLLLLGRFLVRGWVARQRHRGRFRRRLLLVGGPKAVRH
+IFEALDSEAGAGYAPVAAALPGYKARQEDYLPIPVSTDLDTVEDVVALVEVRDVEAVVIT
+SGHSFVPGDVRRLGWELQERGVSLIMAPALVDVAGPRLHTQPLAGLPLIHLSTPRLSEGK
+AFAKRAFDVVASGLGLIAISPLLIAVAIAVKATDGGPVLFRQERIGLGGRPFTMLKFRSM
+VVDAEEIRQRLVSDGGDADVLFKMKDDPRITRVGKLIRRTSIDELPQLVNVLRGDMSLVG
+PRPHLPHEVEAYEQYVHRRFLVQPGITGLWQVSGRSDLPWEEAVRLDLYYVENWSILGDL
+VILGRTVKAVIAADGAY

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000090.fa

@@ -0,0 +1,42 @@
+>PROKKA_00521
+MTPRGSCWSSLPVGARFRLWNTLDPMHLLVTGGAGFIGSNFVHHVVRETGHDVVVLDKLT
+YAGNRENLAGLPEDRVTLEVGDICDAALVDRLVAESDAVVHYAAESHNDNSLNDPSPFIQ
+TNIVGTFVLLEAARKHGKRFHHVSTDEVYGDLELDDPAKFTETTPYNPSSPYSASKAGSD
+HLVRAWVRSFGVQATLSNCSNNYGPYQHIEKFIPRQITNLIDGVRPRLYGQGVNVRDWIH
+TEDHSSAVLRILERGEIGRTYLIGADGEKNNREVVEILLELFDRPADDYDLVADRPGHDL
+RYAIDNTALRTELGWEPRFTDIRAGLADTVRWYRENEAWWRPAKAAVEATYRAQGQ
+>PROKKA_00243
+MHLLVTGGAGFIGSNFVHHVVRETGHDVVALDKLTYAGNRENLAGLPEDRVTLEVGDICD
+AALVDRLVAESDAVVHYAAESHNDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVST
+DEVYGDLELDDPAKFTETTPYNPSSPYSASKAGSDHLVRAWVRSFGVRATLSNCSNNYGP
+YQHIEKFIPRQITNLIDGVRPRLYGQGVNVRDWIHTEDHSSAVLRILERGEIGRTYLIGS
+DGERNNREIVEILLELFDRPADDYDLVADRPGHDLRYAIDNTALRTELGWEPRFTDIRAG
+LADTVRWYRENEAWWRPAKAAVEATYRAQGQ
+>PROKKA_01219
+MRFVVTGAGGFLGSNVVRELLAETDHDVVAVSSQTDRELAAQLERAPYPALRRFPQVHPR
+TRLLEAGFLRDGDIVINCAFPWNRGGRAMADGLEYLTRLFQSAHAVALHTFVNVSSQSVY
+SQARTEAADESSPVECDTPYSTGKYAMELAAELVLPPKVLVNARMSSLIGPGYDVRIVNR
+FIARFLADEPVSIQGGDQVFDFMDVRDAARALIAVALAGPPEGSAALNIGSGAPRTLRDI
+AQTVADVVRTHTGHDPRIAWEPSAGDDRTLGLDSGLLRREYGFAPRHTLEDSALSILQAM
+TSAQSASVGETPTGSVEGGRR
+>PROKKA_02428
+MHLLVTGGAGFIGSNFVHHVVRETGHDVVVLDKLTYAGNRENLAGLPEDRVTLEVGDICD
+AALVDRLVAQSDAVVHYAAESHNDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVST
+DEVYGDLELDDPAKFTETTPYNPSSPYSASKAGSDHLVRAWVRSFGVQATLSNCSNNYGP
+YQHIEKFIPRQITNLIDGVRPRLYGQGVNVRDWIHTEDHSSAVLRILERGEIGRTYLIGS
+DGERNNREIVEILLELFDRPADDYDLVADRPGHDLRYAIDNTALRTELGWEPQFTDIRAG
+LADTVRWYRENEAWWRPAKAAVEAKYRAAGQ
+>PROKKA_02311
+MHLLVTGGAGFIGSNFVHHVVRETGHDVVVLDKLTYAGNRENLAGLPEDRVTLEVGDICD
+AALVDRLVAESDAVVHYAAESHNDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVST
+DEVYGDLELDDPAKFTETTPYNPSSPYSASKAGSDHLVRAWVRSFGVQATLSNCSNNYGP
+YQHIEKFIPRQITNLIDGVRPRLYGQGINVRDWIHTEDHSSAVLRILERGEIGRTYLIGS
+DGERNNKEIVEILLELFDRPADDYDLVADRPGHDLRYAIDNTALRTELGWEPQFTDIRAG
+LADTVRWYRENEAWWRPAKDAVEATYRAQGQ
+>PROKKA_00521
+MRILVTGGAGFIGSNFVHHLVRETDHDVVVLDKLTYAGNRDNLVGLPESRVRLEIGDICD
+AALVDRLVAESDAVVHYAAESHNDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVST
+DEVYGDLELDDPAKFTETTPYNPSSPYSASKAGSDHLVRAWVRSFGVQATLSNCSNNYGP
+YQHIEKFIPRQITNLIDGVRPRLYGHGVNVRDWIHTEDHSSAVLRILERGEIGRTYLIGS
+DGERNNREIVEILLELFDRPADDYDLVADRPGHDLRYAIDNTALRTELGWEPRFTDIRAG
+LADTVRWYRENEAWWRPAKAAVEATYRAQGQ

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

@@ -0,0 +1,41 @@
+>PROKKA_00614
+MGSHHHAPTGHRGRLAIAFGITTAVLLAEVVGAVLTGSLALLVDAAHMLTDAGGLLMALL
+AATLMARPPTTRRTWGFLRAEVLAALAQAAVLLAVGTYAFIEGLQRLFAPPEVASGPLLA
+FGILGLVGNLASLAVLGSGRGANLNMRAAFLEVLNDALGSVAVIASALVIAATGWTRADA
+VAGMLIAVLIVPRTLKILGETTRILLESTPRGLDLAEVRTHLQALPHVVSVHDLHASQIA
+TGVPVLSAHIVVEDSCFHDGHAPQILDQLQHCVAEHFDVGVDHSTFQLEPAAHAHHEHPT
+HH
+>PROKKA_00326
+MVFSITATIMVAEVIGALASGSLALLADAGHMFTDSAGLLIALTATTLALRPATDKRTWG
+YKRAEIIAAAAQAAVLLAVGGFVAVEGVRRLIEPPEVESTAMLWFGVIGLAGNLIGLAIL
+ASSRGENLNMKAAFLEVLNDALGSVAVIVSAIVIATTGWNRADAVVSLLIAALIVPRALI
+LLRDTIDVLMETTPKGLDLEAVRIRLSELPHVLEVHDLHASRIDSDTPVLSAHVTVHNGC
+LTAAHLGTVLTDLQRCVAQDFQVPIEHSTFQIEPATHPHTETLHP
+>PROKKA_01774
+MGAHHHASPAHRWRLAVAFAITTAVLLAEVAGALITGSLALLVDAAHMLTDAGGLLMALL
+ASTLMARPPTARRTWGFLRAEVLAALAQAAILLAVGLYAFIEGLQRLFAPPEVASGPLLL
+FGILGLAGNLASLAVLGSGRGANLNMRAAFLEVLNDALGSVAVIASALVIATTGWAQADA
+VAGMLIAVLIVPRTLKILAEAAHILLESTPRDLDLAEVRDHLEAVPHVVSVHDLHASQIA
+TGVPVLSAHVVVEDHCFHDGHAPQILDQLQHCVAEHFDVAIDHSTFQLEPAAHAHHEHPT
+HH
+>PROKKA_00544
+MSTPHEHHHDHAHGPSPEEAAADPALRRRLWIALALAGTVVLAQAVGAALTGSLALLTDT
+AHAVTDASGLAVALVAAILMARPATPRRTWGLRRLEVVAALGQAALLLLVGAYSAVEAVR
+RLVEPPAVDGTGMLLFGVLGLAANLAAAAVLASSRGANLSMRAAFLEVVNDALGSLGVIA
+AAAVVAVTGWTRADAVAGLLIVVLIVPRAVSLLRQTLRVLLEFTPEGLDLDEVRTHLLEV
+EHVLEVHDLHASTVATGLPVLTAHVVVEDGCFTDGHAAQILEQLRECTREHFPLAVPHST
+FQLETAAIAADDAHHTAHP
+>PROKKA_00702
+MGAGHNHGPAASETGHPGDFRKKLWIAFSITATIVVAQAMGSVITGSLALLTDTAHAITD
+ASGLLVALIAATLMLKPANSKRTWGFRRIEVIAALGQSALLLAVGTYAAIEGIRRLFEPP
+EVPASELLIFGIIGLVANIIAITILASSRGSNFNMRAAFLEVLNDALGSLGVIIAAIVIA
+TTGFMQADAIAGLLIAALIVPRAFKLMRETTGVLMEFTPKGLDLDKVRSHILELDHVKDV
+HDLHASTVATGLPILTAHVVVEDECFTDGRAAQTLHEIKDCVAGHFEVSIHHSTFQIETE
+HIAEHEPEISKHD
+>PROKKA_02007
+MSGHDHSHALPAAGRRGRLAVVFSITATIMVAEVIGALASGSLALLADAGHMFTDSAGLL
+IALTAATLALRPATDKRTWGYKRAEIIAAAAQAAVLLAVGGFVAVEGVRRLIEPPEVEST
+AMLWFGVIGLAGNLIGLAILASSRGENLNMKAAFLEVLNDALGSVAVIVSAIVIATTGWN
+RADAVVSLLIAALIVPRALILLRDTIDVLMETTPKGLDLEAVRIRLSELPHVLEVHDLHA
+SRIDSDTPVLSAHVTVHNGCLTAAHLGTVLTDLQRCVAQDFQVPIEHSTFQIEPATHPHT
+ETLHP

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000105.fa

@@ -0,0 +1,22 @@
+>PROKKA_00747
+MLSGFCLALGTWSTVAAEAADAALARRWGAAARLWTAHLGLGLVAVVVGWGAGLGLHAVL
+AG
+>PROKKA_00748
+MSGAGYEVFALFQVALLACLAAGGVLGALARRRLTDRLGPRGLLTANTTAALLLGVTVGL
+AVPELVYASGG
+>PROKKA_00478
+MSGAGYEVFALFQVALLACLAAGGALGALARGRLTDRLGPRGLLTANTTAALVLGATVGL
+AVPELVYASESWGDGQGLMLVAAVSAVVSGFCLALGTWSTVAAEAADAALARRWGAAARL
+WTAHLGLGLVAVVVGWGAGLGLHAVLAG
+>PROKKA_02182
+MSPALMGASPWEWVLGLAVLAAGGALGALLRLTLQEHLPRRGVLAANTLAAGVLGFSLAL
+ALPSLVYASGLAGDPLGVAGLLVASLTAGFCLALGTWSTVAGQAADAVLAGRWGAAGRIW
+AAHLGLGLLAAAAGWGLGLGARLLVA
+>PROKKA_02077
+MSAGTVLLTVLLAGLAAAVGAGLRHLADHRWGGRGVLLANVTASALAGALFAIGFGPGSA
+DPEGPAGAALALGAAGAFVLALGTWSTVAFQAAQEVLAGRTRRAVRVWLVHLASGTAAAV
+VGVLAVGFLVR
+>PROKKA_00712
+MSGAGYEVFALLQVALLACLAAGGALGALVRRRLTDRLGPRGLLTANTTAALLLGVTVGL
+AVPELVYASGGGGDGQGLVLVAAVSAVVSGFCLALGTWSTVAAEAADAVLARRWGTAARL
+WAAHLGLGLVAVVVGWGAGLGLHAVLAG

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000106.fa

@@ -0,0 +1,35 @@
+>PROKKA_00762
+MNASFPAGAAAATPPLAVARALELRHGSHVAVRPSDFTLPARRLIAVIGPNGSGKSTLLT
+ALAGLSDPASGALEVLGEDPRRRSQRTSFVMQSIGVPQGVPVTVRDVVGMGRYPTLGWFR
+RFRREDRDIVRAAMERMQVADLARRHLDQLSGGQRQRAYVAQGLAQDHDVLLLDEPMTGL
+DIVSARTIDDLLHEEPTRGVSVVYTTHDLDEAAEADHVVLMGGRVVASGSPRDVLTVENL
+DIAYGRGALHGPSTAVEDAADFLDDPAGGRRH
+>PROKKA_00492
+MNASFPAGAAATPPPLAVARALELRHGSHVAVRPSDFTLPARRLIAVIGPNGSGKSTLLT
+ALAGLSDPASGALEVLGEDPRRRSQRTSFVMQSIGVPQGVPVTVRDVVGMGRYPTLGWFR
+RFRREDRDIVRAAMERMQVADLARRHLDQLSGGQRQRAYVAQGLAQDHDVLLLDEPMTGL
+DIVSARTIDDLLHEEPTRGVSVVYTTHDLDEAAEADHVVLMGGRVVASGPPRDVLTVENL
+DIAYGRGALHGPSTAVEDAADFLDDPAGGRRH
+>PROKKA_02168
+MSRSAAVVPEAAPAPLAVAEHLELRHGDHLAVEASSFTLPAGCVVAVIGPNGSGKSTLLQ
+ALAGVLDPAAGRLEVRGESPSRHGRLTSFVMQSLQFPQGVPLTVRDVVTMGRYTTAGWFR
+RLGATDRAAVAAAMERVRVTDLADRHLDQLSGGQRQRVYVAQGLAQEHDVLMLDEPVTGL
+DIVSARTIDEIIHEQPERGVSVVYTTHDLDEAAAADHVVLMDGRVVASGPPAQVLTAANL
+DAVYGRGALHAPLLVHLDDPADCSPDRG
+>PROKKA_00528
+MNPAAPAPAIRLADVSAAYDRRRPVFTGADLVIDGPGLVRVHGRNGGGKSTLIELVSGYL
+RPSDGQVRIGGLPAHDPRAHERRRVCRTEPALYPLMDVHDHVVFASRWAGADPAEGLARA
+ERYGLGPWMHAPAQTLSTGNRRRLWIVQCTVGAFDTVVLDEPFNGLDDESSAVLAAELAA
+WARTRCVVLICHLPPPGLAFDRVVRWPPGQAAADPAPPADPGVRP
+>PROKKA_02063
+MTRTVPTAPTPGAGVLAEARGLELRRAAHVAVAPSDLTLPAGVLVAVIGPNGSGKSTLLH
+ALAGTLEPAAGSLTVRGESPSRHARRTAFVMQTIPVPQGVPLTVRDVVRMGRYPRVGWFG
+RFGAADREAVDAAMERMSVTDLARRHLDELSGGQRQRVYVAQALAQEHDVLMLDEPLTGL
+DLVSARTIDRLLHEEPARGVSVVHTTHDLDEAAAADFVVLMSGRVVAAGTPRQVLTEANL
+EAAYGHGVLHGPRLPFLDDPVDGVR
+>PROKKA_00726
+MNASFPAGAAAAPPPLAVARALELRHGSHVAVRPSDFTLPARRLIAVIGPNGSGKSTLLT
+ALAGLSDPASGALEVLGEDPRRRSQRTSFVMQSIGVPQGVPVTVRDVVGMGRYPTLGWFR
+RFRREDRDIVGAAMERMQVADLARRHLDQLSGGQRQRAYVAQGLAQDHDVLLLDEPMTGL
+DIVSARTIDDLLHEEPTRGVSVVYTTHDLDEAAEADHVVLMSGRVVASGPPRDVLTVENL
+DIAYGRGALHGPSTAVEDAAEFLDDPAGGIRH

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

@@ -0,0 +1,54 @@
+>PROKKA_00838
+MSLEFRTSEESPDVTRVVATHLPTRHGDFALLGYRDGRGTDHVALTLGDVAADDGELPLV
+RLHSECLTGDALGSYRCDCGEQLDAALQAIGAAGRGVLIYIRGHEGRGIGLLDKLRAYAL
+QDSGIDTVDANTHLGLPADARDYDQSAQILRELGVGKIRLLSSNPAKQEALEALGIHVEA
+RVRLNVADRPENSRYLSTKRARMRHDLPPERNAWDLLAGARVPTGPLTPQEEALVLRYGP
+LVEAGPRLVIGQLGQSLDGFIASRTGDACFVTGEADREHLHRLRALVDAVLVGAQTVAAD
+DCQLTVRAVNGADPARVVVDPHARIPLTAKVLTDPRSRTLWLVGSDASVPASLAPHVSVH
+RLETSTGFEPAAILQYLADQGLGRVLIEGGGLTVSGFLHAGVLDRLYLTSAPLLVGDGVP
+GIRFDGADALSGALSAPVRRFVLGDDVCTEFDFSAAKPASPAALHRADQENQPTGQD
+>PROKKA_01065
+MSEHIRLDPVPVAIAAIAAGRPVVVVDDADRENEGDLIYAAALATDEVTAFTVRHTSGVI
+CAPLPAGLADRLALPPMTTVNEDPKGTAYTVSVDAAAGVTTGISAADRTRTLRLLADPGA
+APGDLTRPGHVFPLRAVPGGVRARRGHTEAGVELCRLAGVAPVAAIAELVHDDGTMMRLP
+ALREFSDEHGLVLISIEDLVAHLEETTPALTAVPAEATLPTRHGLFRVSVHVDAETGAEH
+LLLVAGETDSERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALARAAAEGGAVLYLRGHE
+GRGIGLANKIRAYRLQEEGMDTVEANLALGLPAEARDWAGAAAVLTAAGHRRIRLVTNNP
+AKVAGLRAAGIDVVERVPAPTPVTEHNVVYLRTKRDRMAHALADRVLEPPTATGGPATPA
+DDPTTDPTHPTHQEDTP
+>PROKKA_00784
+MSEHIRLDPVPAAIAAIAAGRPVVVVDDADRENEGDLIYAAALATDEVTAFTVRHTSGVI
+CAPLPAGLADRLALPPMTTVNEDPKGTAYTVSVDAAAGVTTGISAADRTRTLRVLADPGA
+APGDLTRPGHVFPLRAVPGGVRARRGHTEAGVELCRLAGVAPVAAIAELVHDDGTMMRLP
+ALREFSDEHGLVLISIEDLVAHLEETTPTLTAVPAEATLPTRHGLFRVSVHVDAETGAEH
+LLLVAGETDPERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALARAAAEGGAVLYLRGHE
+GRGIGLANKIRAYRLQEEGMDTVEANLALGLPAEARDWAGAAAVLTAAGHRRIRLVTNNP
+AKVAGLRAAGIDVVERVPAPTPVTEHNVVYLRTKRDRMAHALADRVLEPPTATGGPATPA
+DDPTTDPTHPTHQEDTP
+>PROKKA_01822
+MSDSIPLDAVPAAIAAFAAGRPVVVVDDADRENEGDLVYAAALATDAVTAFTVRHTSGVI
+CAPMPADLADRLALPPMTARNEDPKGTAYTVSVDAATEVSTGISAADRTRTLRILADPAA
+GPADLTRPGHVFPLRAVPGGVRARRGHTEAGVELCRLADVAPVAAIAELVHDDGTMMRLP
+ALREFADEHGLVLISIEDLVRHLEEEGPTPVPVPAEATLPTRHGVFRVSVHADAVTGAEH
+VLLVAKKAGEAGEADPERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALSRAGSEGGAVL
+YLRGHEGRGIGLANKVRAYRLQEQGLDTVEANIALGLPTEARDWAGAAAVLAAAGHTRVR
+LVTNNPAKVAGLQAAGIDVVERVPAPTPVTEHNLGYLRTKRDRMAHALADRVLEHPVAPG
+HEDPRHETPTHQEDTP
+>PROKKA_01711
+MSIDTAVEPAAPVDIRLDPVADAVAAIAQGRPVVVVDDADRENEGDLIYAAALATDAVTA
+FTVRHTSGVICAPLPAELADRLNLPPMTARNEDPKGTAYTVSVDAVAGVTTGISAADRTV
+TLRVLAGEESTAADLTRPGHVFPLRAVPGGVRARRGHTEAGVELCELADLPPVAAIAELV
+HDDGTMMRLPALREFADEHSLVLISIEDLVAHLHEHRPEQRVVPAEAALPTAHGDFRISV
+HPDTATGAEHVLLVADRPGSATGGDADAPVTVRVHSECLTGDVFGSLRCDCGPQLQAALD
+AAARDGGAVLYLRGHEGRGIGLTNKIRAYRLQEEGLDTVEANLALGLPAEGRAYAGAADL
+LREAGLTRIRLVTNNPAKVDALRAAGIDVVERVPAPTPVTEHNAAYLRTKRDRMHHELAD
+RDLGDA
+>PROKKA_01012
+MSEHIRLDPVPAAIAAIAAGRPVVVVDDADRENEGDLIYAAALATDEVTAFTVRHTSGVI
+CAPLPAGLADRLALPPMTTVNEDPKGTAYTVSVDAAAGVTTGISAADRTRTLRVLADPGA
+APGDLTRPGHVFPLRAVPGGVRARRGHTEAGVELCRLAGVAPVAAIAELVHDDGTMMRLP
+ALREFSDEHGLVLISIEDLVAHLEETTPTLTAVPAEATLPTRHGLFRVSVHVDAETGAEH
+LLLVAGETDPERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALARAAAEGGAVLYLRGHE
+GRGIGLANKIRAYRLQEEGMDTVEANLALGLPAEARDWAGAAAVLTAAGHRRIRLVTNNP
+AKVAGLRAAGIDVVERVPAPTPVTEHNVVYLRTKRDRMAHALADRVLEPPTATGGPATPA
+DDPTTDPTHPTHQEDTP

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000109.fa

@@ -0,0 +1,68 @@
+>PROKKA_00886
+MTARERPAPSRRPLLRSLALTAQTVREHVTDDPVLLALQVSRRLPPAAVGGAAGILTRLG
+RNGVVPALGHEMRGERAAALAALGVDEAGRPVRASRPGAGNVRGLVHRADAALGMGRPDI
+AETLLGSVPEKRRGAAWTAAAARLAAHRGDLGGAAALAARHPRNRHLARRMAGERDAFRG
+VAPTVPTEPGYRPVPGRVLHVLTNSLPHTGSGYAQRSHAILTSLRDEGFDAAAVTRPGYP
+VQIGVPWAAQRDVVDGIRYARLLPARLAQGQAARIQQHAELLAAHVRRHRPALLHTTTHF
+VNALAVEAVARAFGIPWVYEVRGQLADTWAAVRGPEALASERYRLFQEREAEAARRADGV
+VTLGAGMRDRLVAAGVAEDAVVLCPNAVGPAFVAERVDRDEARARLGWDLPTDAFVVGTV
+SSLVDYEGLDILLRAAARLAPHRPGLRVHIAGDGVARPGLQALAAELGIAELCAFPGRVD
+REDARLHHAALDVFTVPRRDLPVTRAVTPMKTVEASATGRPVVASDLPALAELVEDERTG
+LLVPAEDPAALAAALDRLAGDPAERARLGAAGREWALQTRTWEANARRYRTLYDRLGVHP
+R
+>PROKKA_00608
+MTARERPAPSRRPLLRSLALTAQTVREHVTDDPVLLALQVSRRLPPAAVGGAAGILTRLG
+RNGVVPALGHEMRGERAAALAALGVDEAGRPVRASRPGAGNVRGLVHRADAALGMGRPDI
+AETLLGSVPEKRRGAAWTAAAARLAAHRGDLGGAAALAARHPRNRHLARRMAGERDAFRG
+VAPTVPTEPGYRPVPGRVLHVLTNSLPHTGSGYAQRSHAILTSLRDEGFDAAAVTRPGYP
+VQIGVPWAAQRDVVDGIRYARLLPARLAQGQAARIQQHAELLAAHVRRHRPALLHTTTHF
+VNALAVEAVARAFGIPWVYEVRGQLADTWAAVRGPEALASERYRLFQEREAEAARRADGV
+VTLGAGMRDRLVAAGVAEDAVVLCPNAVGPAFVAERVDRDEARARLGWDLPTDAFVVGTV
+SSLVDYEGLDILLRAAARLAPHRPGLRVHIAGDGVARPGLQALAAELGIAELCAFPGRVD
+REDARLHHAALDVFTVPRRDLPVTRAVTPMKTVEASATGRPVVASDLPALAELVEDERTG
+LLVPAEDPAALAAALDRLAGDPAERARLGAAGREWALQTRTWEANARRYRTLYDRLGVHP
+R
+>PROKKA_02050
+MDRPGGLEGAFDRHWRKIRRELGSVYRDYRAGRASTGSALKRATRIGLKHGVLAPRDALA
+EFLRLRDEAVGPTLAGAGPMTMLPGELDSERARIWLSVLERHYPSGPARTAYFEQLRRLA
+LRDGQISTALDATAELASSNTSMARAAVDVNGRMTELSGWLPRLPGPVEPVSGCGTNVVL
+HLLKESRPYLSNGFTSRTQWNLLAEKDAGWTPVVLTEPGFPEGMTEGRPSTVEEVDGIEH
+RRILTGVSYRGVPFDRWLEDFAFLALDHVRNVRPDVLHVSSGRRGYETALVGLALREKTG
+LPLVYEVRSFFEGNWTPDLDIEEHSEVFRRRREVETRCMIAADRVLTLGEAMRDEIVARG
+VPAEKVDIVPNGVQLDRFTPAPRDPAIAARHGITLPTFGYVSNMDHPREGHELLIRAALL
+LQERGVEAQCVLVGGGRRFDELRALARELGIANRVVFTGPVDHEEVAALYGLIDVFVVPR
+INERAARYVTPLKPFEAMALRRPVIVSDLPALREIVAAPRRGLTFPVGDVMVLAETIARL
+LEEPAERQRLGAAGREWVEAERQWVHNGPRYDRAYHAAINARRRAGKG
+>PROKKA_02052
+MTSILLDFVRALGHAPLVLRTVVDHLRDDPAVLGLQISRRLPLAARVGLGRLAESLPARP
+GVVLGAVGLAAAGRHVDLLEHVEAVLPSAGAPDRVRLADVLTAAQEPDRAQAVLDAVPVN
+TPGLAAARARVAWHRGDVEAAISLLGGTGRDGVVRARFASEVRALRGGALPLPRADRDRA
+VGYRPRPGSALFVLTNSLPHTGSGYAQRSHSLACALRDEGWDVEAVTRLGWPVQTGVLTA
+ARRDMVDGIVYHRLLPSSLARGFDGRLAQHARMLLDLVLERRPAVLHTTTHWVNAVVTRA
+VAEAVGVPWVYEVRGQLADTWASTRGPEALRSDRYALFTAREDDAVRSADGVVTLGEQMA
+RRIAVAGMDRDAVVLSPNGVGGAFLEEPAPREDARRRLGLSMDDEIVGTVSSVVPYEGLD
+DLVRAVAALVDERPRLRLAVVGDGVALPALRRLAADLGIEDRLLAPGRVDRSLAPVWHQA
+LDVFCVPRKDTGVTRAVTPMKPLEAMATSRPVLVSDLPALSEIVEDGVTGRVLPAEEPEA
+WAAALAALLDDPAEARGLGARAREWVLGHRTWAANARRYDALYRRLGVMAPSA
+>PROKKA_01946
+MSPRAPRVRRLAANAALTGRTVADHLLDDPVVLALQVSRRLPTGLRARVGGVLADVPARV
+AVPRGIGLAMLGREEQLQAALVDADDAPGPRERARRAEVLLAAGRDEDAERLLADVPADA
+PGAAEARARLRWHRGDMTGAVLVLSPHGRQGRLRARLAAERDSLLGRPVCLSAEDRALAA
+DYEPRPGHVLFVLTNSLPHTGSGYVQRSHSLLTAVRDAGWSVAAVTRLGWPVQTGVLAAE
+DVDRVDGVAYHRLLPAALAPGFGARLDQHAAALLRLVLRERPAVLHTTTHWVNAAVTAAV
+AEAVGIPWVYEVRGQLADTWASTRGPQALMSERYRAFRTREAEAAARADGVVTLAETMRA
+RLAEDGVDPEDVVLSPNAVGGAFLDAPGERAAARRALGLAPDAEYIGTVSSVVPYEGLDD
+LVRVVALLADRRPRLRLLVAGDGTALPGLAALAEQLGVRDRVDLLGRVERARAPLCHQAL
+DVFCVPRRDTSVTRDVTPMKPLEAMASARPVLLSRLPALQELVAEGETGATVPASDPEAW
+AEAVEALLADPNAAAAMGDRARAWVLAERTWAANARRYTELYARLGAVVDVADRGAVRGG
+>PROKKA_00842
+MTSILLDSVRALGHAPLVLRTVVDHLRDDPAVLGLQISRRLPLAARVGLGRLAESLPARP
+GVVLGAMGLAAAGRHVDLLEHVEAVLPSAGAPDRVRLADVLTAAQEPDRAQAVLDAVPVD
+TPGLAAARARVAWHRGDVEAAISLLGGTGRDGVVRARFASEVRALRGGALPLPRADRDRA
+VGYRPRPGSALFVLTNSLPHTGSGYAQRSHSLACALRDEGWHVEAVTRLGWPVQTGVLTA
+ARRDMVDGIVYHRLLPSSLARGFDGRLAQHARMLLDLVLERRPAVLHTTTHWVNAVVTRA
+VAEAVGVPWVYEVRGQLADTWASTRGPEALRSDRYALFTAREDDAVRSADGVVTLGEQMA
+RRIAAAGMDRDAVVLSPNGVGGAFLEEPAPREDARRRLGLSMDDEIVGTVSSVVPYEGLD
+DLVRAVAALVDERPRLRLAVVGDGVALPALRRLAADLGIEDRLLAPGRVDRSLAPVWHQA
+LDVFCVPRKDTGVTRAVTPMKPLEAMATSRPVLVSDLPALSEIVEDGVTGRVLPAEEPEA
+WAAALAALLDDPAAARGLGARAREWVLGHRTWAANARRYDALYRRLGVTAPSA

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000112.fa

@@ -0,0 +1,35 @@
+>PROKKA_01012
+MSVIRTRRPSLRHLPAAVAAAGLITTVALAGPAAAWDDAHGPQAGYFQAVDHENVTAAFF
+QTYDGYDPEDLTLTLTPVAEDGTRLEGGQEVEFTALDVIDGGAVDVLETRRALGAAGEGL
+VRYDVEVDGQMLNMGITLQADADLADDQGAAVHAVDGPQTADLGDRPLVWDSAMQLAPGV
+AGAEIVHLVAAPTMEDAYAAVVAEPAHGEVFAFRDSEHSELRAWYIPDEGFVGTDTFTVD
+FHSDHVAHVQTVTVHVGEEISAAYDGFLDAEDGVLNGKPLDLTDPDTAAALAAFRADEAA
+PAPEDEEEQPAPVEDDADEQHTTPDTVETGQSTGWWLAGLGAAAAGVLVAARRRLGLTD
+>PROKKA_00726
+MSVIRTRRPSLRHLPAAVAAAGLITTVALAGPAAAWDDAHGPQAGYFQAVDHENVTAAFF
+QTYDGYDPEDLTLTLTPVAEDGTRLEGGQEVEFTALDVIDGGAVDVLETRRALGAAGEGL
+VRYDVEVDGQMLNMGITLQADADLADDQGAAVHAVDGPQTADLGDRPLVWDSAMQLAPGV
+AGAEIVHLVAAPTMEDAYAAVVAEPAHGEVFAFRDSEHSELRAWYIPDEGFVGTDTFTVD
+FHSDHVAHVQTVTVHVGEEISAAYDGFLDAEDGVLNGKPLDLTDPDTAAALAAFRADEAA
+PAPEDEEEQPAPVEDDADEQHTTPDTVETGQSTGWWLAGLGAAAAGVLVAARRRLGLTD
+>PROKKA_01876
+MTHLGDRPLVWDSAMQLAPGVEGAEIVHLVAAPTMENTYAEVVTEPAHGEVFAFRDSEHS
+ELRAWYIPEEGFVGTDTAAALAAFRGDEAAPAPEDEEE
+>PROKKA_01877
+MSVIRTRRPSLRHLPAAVAAAGLITTVALAGPAAAWDDAHGPQAGSFQAVDHENVTTAFF
+QTYDGYDPEDLTLTITPVAEDGTRLEGGQEVGFTALDVIDGGAVDVLETRRALGAAGEGL
+VRYDVVADGQMLNMGITLQADADLADDQGTAVHSVEARR
+>PROKKA_01764
+MFVTRPSCAPRLAAAVLASGLAAAALAAPASAEQAYDWTDDHGYPHGLFFGMDPESVDEA
+TFQTFYGFDPADLTVTVSPSDAEGTPTGPAAAVPFTAVDVLDGGTIDVLETRRVLGEAGT
+GTVAYHVFSGDQKELDMALVVGPDADLADATGGALVAAPGPVRAVLGDMPLSWSADVVMA
+PGVRAMEVRYPVDPALFDDVHPMVMTEAAHGTVVTFRDREDLSVRTWYVPDAGFTGTDTF
+SLDLTSDHVAHLPTVTVHVGQELPAAAAGAPDAQDGVLGGMPLDVEDPAIAAMLQQMGAL
+PPAPEATVPETTVSAEQHTRPGKVQTGGEPIWWLASAAVLGAGALVAARRRPGMAG
+>PROKKA_00955
+MSVIRTRRPSLRHLPVAVAAAGLVTTVALAGPAAAWDDAHGPQAGYFQAVDHENVTTALF
+QTYDGYDPEDLTLTLTPVAEDGTRLEGGQEVEFTALDVIDGGAVDVLETRRALGAAGAGL
+VRYDVVADGQMLNMGITLQADTDLADDQGAAVHSVDGPQMAHLGDRPLIWDSAMQLAPGV
+AGAEIVHLVAAPTMESTYAEVVAEPAHGEVFAFRDSGHSELRAWYIPEEGFVGTDTFTVD
+FHSEHVAHVQTVTVHVGEEIPAAYDGFLDAEEGVLNGKPLDLTDPDTAAALAAFRADEAA
+PAPEDEEEQPAPVEDDADEQHTTPDTVETGQSTGWWLAGLGAAAAGVLVAARRRLGLTD

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000115.fa

@@ -0,0 +1,30 @@
+>PROKKA_01030
+MIDRFQNLDWGYYGPELMTAVGDTLYMVGWSFILGGILGLLVGLVLYTTRPGGIFANRAV
+YLVTNFIVNLIRPIPFVILIAALQPLTIAVLGTGIGNTAVVFCMIWASTFGIARIVEQNL
+VSLDPGVIEAARAMGASRMRIVRAVVLPEALGPLILGFTFVIISLVDMSAMAGIIGGGGV
+GNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR
+>PROKKA_00745
+MIDRFQNLDWGYYGPELMTAVGDTLYMVGWSFILGGILGLLVGLVLYTTRPGGIFANRAV
+YLVTNFIVNLIRPIPFVILIAALQPLTIAVLGTGIGNTAVVFCMIWASTFGIARIVEQNL
+VSLDPGVIEAARAMGASRMRIVRAVVLPEALGPLILGFTFVIISLVDMSAMAGIIGGGGV
+GNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR
+>PROKKA_00186
+MSEALSRILQVWPEIVVALGQTLTMLAVTIPLAVLLGTPLGIWLFTHAPGGLSPSPRLHR
+VVDAAVSMLRSFPFLILLIAIIPVTRLIVGTTIGTAAVIVPLTVNAIPYFARFVEQNLAQ
+LGPGPVEAARAMGATRGQIVRDVLLVDARPALVGSLTIMSVSFISYSAMAGLVGGGGIGD
+FAIRYGYYRYETPLMVVAILLMIGLVALLQFAGTRLSQRLDHRRPRTARRPRRRALAPAG
+>PROKKA_01853
+MTWLETLTTNPAITDALPEALVETLLMVAISGVATVLIGGLLGIVLHVTRPGGLNPMPAL
+YTVLSTVIVNITRSVPYAILMVALIPLTKWLVGTAIGPIAATVSLTIGTAPFFARLVESA
+LREIPSGTVDAAQVMGSTRGQVIRKVLLPEAMPGLIAATTTTLVTLVGYSAMAGLIGGGG
+LGRLAYNYGYQRFQTEVMVVTIVVIVILVQLIQWIGDLLIRRVDHR
+>PROKKA_01742
+MIDRFQNLDWGYYGPELMTAVGDTLYMVGWAFILGGILGLLVGLVLYTTRPGGIFANRAV
+YLVTNFVVNLIRPIPFVILIAALQPLTIAVLGSGIGNTAVVFCMIWASTFGIARIVEQNL
+VSLDPGVIEAARAMGASRMRIVRTVVLPEALGPLILGFTFVIISLVDMSAMAGIIGGGGV
+GNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR
+>PROKKA_00974
+MIDRFQNLDWGYYGPELMTAVGDTLYMVGWSFILGGILGLLVGLVLYTTRPGGIFANRAV
+YLVTNFIVNLIRPIPFVILIAALQPLTIAVLGTGIGNTAVVFCMIWASTFGIARIVEQNL
+VSLDPGVIEAARAMGASRMRIVRAVVLPEALGPLILGFTFVIISLVDMSAMAGIIGGGGV
+GNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000116.fa

@@ -0,0 +1,29 @@
+>PROKKA_01042
+MLEPEIRSDNGGRGIRNAETNFYADAETRTLVTTLNGVEVELRATPVSFHWDYGDGSPTK
+TTSVAGQSQPEFNVPTPTSHVYEDTGQYTVRLTTVYIGEYREAGGEWVLIPGTISLDSAP
+VTANIWRTITRNVADDCSVDSSAWGCTGPIESAPAG
+>PROKKA_00755
+MLKPEIRSDNGGRGIRNAETNFYADAETRTLVTTLNGVEVELRATPVSFRWDYGDGSPTK
+TTSVAGQSQPEFNVPTPTSHVYEDTGQYTVRLTTVYIGEYREAGGEWVLIPGTISLDSAP
+VTADIWRTITRNVADDCSVDSSAWGCTGPIESTPAG
+>PROKKA_00331
+MPHQLDNADYGSCLNQDESFCPDGEWVQARTVDITRPDADPLYGRPTCTSDVAAGAGGAR
+SFTLEEVRTLLLLDPTIESDNAGRGVRNAETNFYTDAGVETLSTTINGVPVELRATPVSF
+HWNYGDGTAPRVTHVGGHAQAEFNTPTPTSHVYEETGEYTVTLTTVYIGEYREADGDWVL
+IPGTITLDAAPVTADIWRTVTRNVAEDCAADPSAWGCTGPIEAPDAP
+>PROKKA_00544
+MPHQLDNADYGSCLNQDESFCPDGEWVQARTVDITRPDADPLYGRPTCTSDAAAGADGAR
+SFTLEEVRTLLLLDPTIESDNAGRGVRNAETNFYTDAGVETLSTTINGVPVELRATPVSF
+HWNYGDGTAPRVTHVGGHAQAEFNTPTPTSHVYKETGEYTVTLTTVYIGEYREADGDWVL
+IPGTITLDAAPVTADIWRTVTRNVAEDCAADPSAWGCTGPIEAPDAP
+>PROKKA_01735
+MTSRRGDFPACMAVLFALIFLVSAVTLVTPSQAHASSCDTAGRKAQLTDDSLIVGQRCHK
+SSIAEIVGDGLADDQEKSAKATSPTTKVTTLQNACYENLPEPGFENCATQQELICGDQNV
+AWLQPSTKDTARPEDAPVKGDAFCADGSAAPSAPPQPSRPAVSIDDMGEVIAPEPRILAD
+TDGRGVRNAETNFYSPEAVRHETAVIDGVSVEMRLTPVSFIWDYGDGTAPVTTDVGGNPQ
+DGFDVRTPTSHVYDETGTYEVTLTTVYTGEIRYPGQGWEAVPGTIRRTATPVTADIWTTS
+TRNVADDCSADASAWGCAGPVEAPNGG
+>PROKKA_00983
+MSIDEVRTLLVLEPEIRSDNGGRGIRNAETNFYADAETRTLVTTLNGVEVELRATPVSFH
+WDYGDGSPTKTTSVAGQSQPEFNVPTPTSHVYEDTGQYTVRLTTVYIGEYREAGGEWVLI
+PGTISLDSAPVTANIWRTITRNVADDCSVDSSAWGCTGPIESAPAG

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000117.fa

@@ -0,0 +1,54 @@
+>PROKKA_01102
+MTPHTDAPEGPSLRRLADAAEDRLGEHGLALRDLGVLGPEDPAASHFAAAVERGFYETVP
+TGAALRQQLEAHAADGRRRLGVYAPGDDPAARRPAATFEDFVQPLTTSPGRTVDAWLITD
+VTVSPDARRRGVLRAMMLRSLADARDAGLCAAALTATEAAIYGRFGFGAATRWHAVRIDV
+SGAPAFTGAPAGGRVTVEEPREIPGLVDELYGRVLPATPGSVQRTSFSVPRWEDREASRN
+EGRGSGLYAAVHRDDDGRVQGVALYRFEGWEKEPPTITVTAFLAATADARRGLVHHLARL
+DLVERIEWGRAPEPGWLEALFVDERRVSRHRGSDDLYLRVLNLPAAMAARGWAGDGEVVV
+AVEDALGAIDGTWRLTVRQGRGAAERLGPAADAVGLDAGLRLDAARFSALWLGGHSRGAG
+AAVLAEAGVVAELRAGAAEAFDGLVRPSRPLHTLVGF
+>PROKKA_00821
+MTPHTDTPEGPSLRRLADAAEARLGEHGLALRDLGVLGPEDPAASHFAAAVERGFYETVP
+TGAALRQQLEAHAADGRRRLGVYAPGEDPAARRPAATFEDFVQPLTTWPGRAVDAWLITD
+VTVSPDARRRGVLRAMMLRSLADARDAGLCAAALTATEAAIYGRFGFGAATRWHAVRIDV
+SGAPALTGAPAGGRVTVEEPREMPGLVDELYGRVLPATPGSVQRTSFSVPRWEDREASRN
+EGRGSGLYAAVHRDDDGRVQGVALYRFEGWEKEPPTITVTAFLAATADARRGLVHHLARL
+DLVERIEWGRAPEPGWLEALFVDERRVSRHRGSDDLYLRVLNLPAAMAARGWAGDGEVVV
+AVEDALGAIDGTWRLTVRQGRGAAERLGPAADAVRMGAGLRLDAARFSALWLGGHSRGAG
+AAVLAEAGVVAELRAGAAEAFDGLVRPSRPLHTLVGF
+>PROKKA_01792
+MSINPAAAAHAADATAAQDALARHGLVLRTLAPLSRGFDGADPARAEHPAHVRHTAAVEK
+GFYEEVPQGAAADQDLGVSADDAKVLRGVYLSADDPARREPVGTFVDWTSRLTTSPGAEL
+PVWMISNVTVSPGHRRRGILRAMMTASLEEAVAAGVPVAALTASESTIYGRFGFGAASTA
+RTVRVDVRGDVVLAADAAGRTDEDAGTVLREDPRELAGVVEALHDRVRRGTPGSVHRPTG
+HVIRWEDRSAAKNDGRGSGLFAAVHRDADGAVQGVALYRFDGWGKEPTTVSVEVFLAATD
+AAARQLWRYLTRLDLIERLRMTRCPDDGGLEQVLADRRRVRTKSVWDDLYLRVLDVPVCL
+GGRGYAPEVVGEVVLAVADAAGHAAGTWRLRVADGVGRAERLADDARADLALDVAHLSAV
+WLGGVRAGALVRAGVVDEREPGAAARLDALLAPAAAVHLLTGF
+>PROKKA_01793
+MTPRTDAPDAWLDPAPATAEALAAHGLELLRVPSPWETGDADPDAPFDHARRWADAPAVR
+RHTAVLQRNFHEVGDPDFALADRFIGVEQGDRRRLSGVYPQGADPAATDPVGTLVDFTKD
+LNVGDGRMLPAWCLTEVTVSPTHRRRGILRAMMTESLRRAHAARVPIALLTATEATLYRR
+FGFGVSTYHRSVWLDVTRGVQLRGRRPDGSFRFVEPTASGALIDGLWRRAFEAQAGSVER
+IRFHAARETDRDPRVGEGRPQGLRAVVYSAPDGEDLGVAVYRVTGSTAELVADDPVTATV
+VALWAATPEAHRALLEFLGNLDLVVRLRLPAVAADRLLEFLVLDESRIYTRGVHHHLWHR
+VLDVAACFEARPYLHEGAVTVTVEDDLGYAAGTWEIAAADGVGRVRPAPQDAAELTLDVA
+ELGSVLLGGVKAEMMREAGILLAHRPGAAADLDTLLRQARPPYSLTGF
+>PROKKA_01683
+MRPHTDLQPTATPRADAEVLAEQGLALVVAPGRAADPAFERHTTAVERGFYEQVPSGEAM
+AQLLEAGEADGRRMVDVLPLGADPATTRPVATFEDFRSELTVSPGVAVSAWLISGVTVDP
+GFRRRGLLRTMMTRSLADAVAAGVPVAALTASEAAIYGRFGFGAATRWRRARLDTRGDVR
+LRGAPSAGRVTREEPREVGALADELYQHVRRLTPGATQRPTMTAIGWEDRSRFKNDGKGS
+GLYAAVHRDAAGTAQGIALYRPQGWDVEPPTVTMELFLALTPDARRGLLTHLTSLDLIER
+IVWERAPEAGWPEALLEDERRLRTERDGDDLYLRILDVPAALGARADLGDGEVVVDVTDP
+LGHAAGAWRIRARDGVAEVTEAAEGEAELGLDVADLSAVWLGGHGSAGGVAARVATGLVR
+EVVPGAGARLDALLRPSVPVRSLVGF
+>PROKKA_01051
+MTPHTDAPEGPSLRRLADAAEDRLGEHGLALRDLGVLGPEDPAASHFAAAVERGFYETVP
+TGAALRQQLEAHAADGRRRLGVYAPGDDPAARRPAATFEDFVQPLTTWPGRTVDAWLITD
+VTVSPDARRRGVLRAMMLRSLADARDAGLCAAALTATEAAIYGRFGFGAATRWHAVRIDV
+SGAPAFTGAPAGGRVTVEEPREIPGLVDELYGRVLPATPGSVQRTSFSVPRWEDREASRN
+EGRGSGLYAAVHRDDDGRVQGVALYRFEGWEKEPPTITVTAFLAATADARRGLVHHLARL
+DLVERIEWGRAPEPGWLEALFVDERRVSRHRGSDDLYLRVLNLPAAMAARGWAGDGEVVV
+AVEDALGAIDGTWRLTVRQGRGAAERLGPAADAVRMGAGLRLDAARFSALWLGGHSRGAG
+AAVLAEAGVVAELRAGAAEAFDGLVRPSRPLHTLVGF

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000119.fa

@@ -0,0 +1,106 @@
+>PROKKA_01117
+MPKNSSTTVSSAVEAHPGGLASGSGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVF
+TGLSGSGKSSLAFDTIFAEGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKS
+TNRNPRSTVGTITEIYDYMRLLWARVGVPHCPQCGEPVSRQTPQQIVDQLEELPERTRFQ
+VLAPVVRGRKGEFVDLFKDLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRLAM
+KEGIRQRLTDSVETALKLADGLVVAEFVDVEPVAEKGRKNTAEFGGRDAEGNPRYRSFSE
+KLSCPNGHEQTVDEIEPRSFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVV
+PWSLGKSTSDYWLRVLGGLGKEMGFSLDTPWKDLTEAERDAVLHGKDFKVEVTFRNRFGR
+ERRYTTGFEGVIPYVMRKHGETESDGARERYESFMREIPCPACHGARLNPTVLNVLVGGL
+SIADATRLPMREAMEFFSGLRLTDRERQIADQVLKEILARLAFLLDVGLEYLNLERPAGT
+LSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEH
+DEDTIAEADWIVDIGPRAGEHGGEVVHSGSLADLKANTRSVTGDYLSGRRSIAVPERRRV
+PEKGRVLTVRGAQENNLKDVSVEVPLGVLTAVTGVSGSGKSTLINEILYKVLANRLNGAK
+LVPGRHRSVEGLEHLDKVVHVDQSPIGRTPRSNPATYTGVFDAIRKLFAETPEAKVRGYQ
+QGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTYKGKNIAE
+VLDMPIEEAADFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKR
+SNGRTIYVLDEPTTGLHFDDIRKLLHVLQSLVDKGNTVLTIEHNLDVIKSADHVIDLGPE
+GGSGGGTIVAAGTPEEVAHVAESHTGRFLAELLA
+>PROKKA_00373
+MVESSSFVPPKLSVQPDVRVLGARENNLQDVDLTVPRDATVVFTGVSGSGKSSLAFGTLY
+AESQRRYLESVAPYARRLIDQAGVPDVDSITGMPPAVALQQQRGSGNARSTVGSITTLSS
+LVRMLYSRAGDYPEGQPMLYAEDFSANTVQGACSECHGIGRVYEVNEQQMVPDPSLTIRE
+RAIASWPTAWHGHQLRDVLVALGYDVDVPWRDLPKKDRDWILYTDETPFVPVHSRLTLSE
+SKAAIEAGVEPSYSGTFVGARRYILDTFANTKSASMKRRVAQFLTAAICPTCNGKRLKPE
+ALSVTFEGFDIAEFSQLPLRELATILSGVVAREEDHEAASSDVRPTASRTPEKRAAAVQL
+ASGVLQRLRPLVDLGLGYLSLSRTTPTLSGGELQRLRLATQLSSDLFGVVYVLDEPSAGL
+HPQDVAALLEILDGLKGRGNSLFIVEHSVAVMRHADWLVDIGPGAGEHGGRVLYSGPPDG
+LAGVTESVTRGYLFGGRGLPLRTPREARSWLRLENVTRNNLHDLTVDIPLGVFTAVTGVS
+GSGKSSLVSQALPSLLGDRLGLAARADDEPVSDESLLADAPEHLEGRVAGPVTGVQRLVV
+IDQRPIGRTPRSNVATYTGLFDHVRRRFADTPEARSRGYKPGRFSFNVAGGRCPTCEGEG
+SVMVELLFLPSVYTECPDCHGTRYKASTLEVTWRGRTIADVLSMSVEEANLFFVGDEEIT
+RSLAALSDVGLEYLRLGQPATELSGGEAQRVKLATELQRAQRGDTLYVLDEPTSGLHCAD
+TDRLVAHLQTLVDAGNTVVAAELDMRVVAVADHVIDLGPGAGDAGGTVVAAGTPAHVADQ
+GVGASAGYLAAALQAATNVTPS
+>PROKKA_00836
+MPKNSSTTVSSAVEAHPGGLASGSGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVF
+TGLSGSGKSSLAFDTIFAEGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKS
+TNRNPRSTVGTITEIYDYMRLLWARVGVPHCPQCGEPVSRQTPQQIVDQLEELPERTRFQ
+VLAPVVRGRKGEFVDLFQDLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRLAM
+KEGIRQRLTDSVETALKLADGLVVAEFVDVEPVAEKGKKNTAEFGGRDAEGNPRYRSFSE
+KLSCPNGHEQTVDEIEPRSFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVV
+PWSLGKSTSDYWLRVLGGLGKEMGFSLDTPWKDLTEAERDAVLHGKDFKVEVTFRNRFGR
+ERRYTTGFEGVIPYVMRKHGETESDGARERYESFMREIPCPACHGARLNPTVLNVLVGGL
+SIADATRLPMREAMEFFSGLRLTDRERQIADQVLKEILARLAFLLDVGLEYLNLERPAGT
+LSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEH
+DEDTIAEADWIVDIGPRAGEHGGEVVHSGSLADLKANTRSVTGDYLSGRRSIAVPERRRV
+PEKGRVLTVRGAQENNLKDVSVEVPLGVLTAVTGVSGSGKSTLINEILYKVLANRLNGAK
+LVPGRHRSVEGLEHLDKVVHVDQSPIGRTPRSNPATYTGVFDAIRKLFAETPEAKVRGYQ
+QGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTYKGKNIAE
+VLDMPIEEAADFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKR
+SNGRTIYVLDEPTTGLHFDDIRKLLHVLQSLVDKGNTVLTIEHNLDVIKSADHVIDLGPE
+GGSGGGTIVATGTPEEVARAAESHTGRFLAELLA
+>PROKKA_01776
+MPKNSSTTVSSAVETHAGGLASGPGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVF
+TGLSGSGKSSLAFDTIFAEGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKS
+TNRNPRSTVGTITEVYDYLRLLWARVGVPHCPQCGEPVSRQTPQQIVDQLEELPERTRFQ
+VLAPVVRGRKGEFVDLFADLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRLAM
+KEGIRQRLTDSVETALKLADGLVVAEFVDVEVVAEKGKKNTAEFGGRDAEGNPRYRSFSE
+KLSCPNGHEQTVDEIEPRSFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVV
+PWSLGKSTSDYWLRVLGGLAKEMGFSLDTPWRELEPAQREAVLHGKDFKVEVTFRNRFGR
+ERRYTTGFEGVVPYVLRKHGETESDGARERYESFMREIPCPVCHGARLNPTVLNVLVGGL
+SIAEATRLPLREARDFLAGLELSARERQIADQVLKEILARLAFLLDVGLEYLNLERPAGT
+LSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEH
+DEDTIAEADWIVDIGPRAGEHGGEVVHSGSLEDLKANTASITGDYLAGRRAITAPQTRRA
+PQEGRTLTVRGARENNLKDVSVDIPLGVLTAVTGVSGSGKSTLINEILYKVLANRLNGAK
+LVPGRHRAVDGLEHLDKVVHVDQSPIGRTPRSNPATYTGVFDAIRKLFAETPEAKVRGYQ
+QGRFSFNIKGGRCEACSGDGTLKIEMNFLPDVYVPCEVCDGARYNRETLEVTYKGKNIAE
+VLDMPIEEAAQFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKR
+SNGRSVYVLDEPTTGLHFDDIRKLLQVLQSLVDKGNTVITIEHNLDVVKCADHVIDLGPE
+GGSGGGTIVATGTPEEVARVEASHTGRFLAELLA
+>PROKKA_01669
+MPKNSSSAAAPARPDAAARGGLASGPARGSAQHERIVVKGAREHNLKNVDVSIPRDSMVV
+FTGLSGSGKSSLAFDTIFAEGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQK
+STNRNPRSTVGTITEIYDYMRLLWARVGVAHCPVCGEVVSKQTPQQIVDQLEQLPERTRF
+QVLAPVVRGRKGEFVDLFSSLSTQGYARALVDGELIQLSDPPALKKQNKHTIAVVVDRLA
+VKEGIRQRLTDSVETALKLADGLVAVEFVDVDVVAQAGKKNQGDLAGEDAEGNPRFRTFS
+EKLSCPHGHPQTVDEIEPRSFSFNNPFGACPECTGIGSRLQVDPDLVVPNDELSLNEGAI
+LPWSLGKSTSDYWLRVLGGLAKEMKFSLDTPFKDLTAQQRDAVLNGKDFKVEVSFRNRFG
+RERRYTTGFEGVLPYVMRKHGETESDNARERYESFMRQIPCPACHGARLNPTVLNVRVGG
+LSIADATRLPLRESLAFLDGLQLTERELAIADQVVREIRARLEFLLDVGLDYLNLERNAG
+TLSGGEAQRIRLATQIGAGLVGVLYVLDEPSIGLHQRDNRRLIDTLIRLRDLGNTLIVVE
+HDEDTIAEADWIVDIGPRAGEHGGEVVHSGSLDELKANTRSVTGDYLAGRRRIEVPAARR
+PVDPKRRLTVKGATENNLKDVTVDIPLGVFTAVTGVSGSGKSTLINEILYKVLADKLNGA
+KMVPGRHRSVAGLEHLDKVVHVDQSPIGRTPRSNPATYTGVFDQIRKLFAETPEAKVRGY
+QQGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTYKGKNIA
+EVLDMPIEEAAEFFGAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQK
+RSTGRTVYVLDEPTTGLHFEDIRKLLQVLQTLVDKGNTVLTIEHNLDVVKCADHVIDLGP
+EGGSGGGTVVATGTPEEVAAVPESHTGRFLAELLG
+>PROKKA_01067
+MPKNSSTTVSSAVEAHPGGLASGPGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVF
+TGLSGSGKSSLAFDTIFAEGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKS
+TNRNPRSTVGTITEIYDYMRLLWARVGVPHCPQCGEPVSRQTPQQIVDQLEELPERTRFQ
+VLAPVVRGRKGEFVDLFQDLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRLAM
+KEGIRQRLTDSVETALKLADGLVVAEFVDVEPVAEKGRKNTAEFGGRDAEGNPRYRSFSE
+KLSCPNGHEQTVDEIEPRSFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVV
+PWSLGKSTSDYWLRVLGGLGKEMGFSLDTPWKDLTEAERDAVLHGKDFKVEVTFRNRFGR
+ERRYTTGFEGVIPYVMRKHGETESDGARERYESFMREIPCPACHGARLNPTVLNVLVGGL
+SIADATRLPMREAMEFFSGLRLTDRERQIADQVLKEILARLAFLLDVGLEYLNLERPAGT
+LSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEH
+DEDTIAEADWIVDIGPRAGEHGGEVVHSGSLADLKANTRSVTGDYLSGRRSIAVPERRRV
+PEKGRVLTVRGAQENNLKDVSVEVPLGVLTAVTGVSGSGKSTLINEILYKVLANRLNGAK
+LVPGRHRSVEGLEHLDKVVHVDQSPIGRTPRSNPATYTGVFDAIRKLFAETPEAKVRGYQ
+QGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTYKGKNIAE
+VLDMPIEEAADFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKR
+SNGRTIYVLDEPTTGLHFDDIRKLLHVLQSLVDKGNTVLTIEHNLDVIKSADHVIDLGPE
+GGSGGGTIVAAGTPEEVAHVAESHTGRFLAELLA

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000120.fa

@@ -0,0 +1,31 @@
+>PROKKA_01118
+MATSEPVRRSAAALLRLTCRPEVVGMEHVPARGPFVMASNHLSFVDSVILQALAPRPVHF
+FAKEEYFTGTGLRGRVRRRFFESVGSVPVRRGEQAASVAALESLVGLLESGQGVGIYPEG
+TRSRDGRLYRGRTGAAWLALATGARVVPVGLVGTQHLQPPDTNGFRPHRFSVRVGAPLDF
+GHPGRRHTLPQRRDATAAIMDAIGALSGQERVDAYNAAPGARG
+>PROKKA_00837
+MATSEPVRRSAAALLRLTCRPEVVGMEHVPARGPFVMASNHLSFVDSVILQALAPRPVHF
+FAKEEYFTGTGLRGRVRRRFFESVGSVPVRRGEQAASVAALESLVGLLESGQGVGIYPEG
+TRSRDGRLYRGRTGAAWLALATGAPVVPVGLVGTQHLQPPDTNGFRPHRFSVRVGAPLDF
+GHPGRRHTLPQRRDATAAIMDAIGALSGQERVDAYNAAPGARG
+>PROKKA_00163
+MSALAARARAGLAHAVLAVAGARIHASGPDGAEEAEITRERLAALLPRQAVFYANHTSHL
+DFVTLWAVLPPALQRRVRPVAAADYWGSGLRRRVAEGLFHAYLVERGKTRRRGPGAASGS
+GVSPDGGSQLEGMLEILAGGDSLIIFPEGTRGSGEDVARFQRGLHALAAAFPQVPVVPVS
+LVNLGRILPKGEPIPVPHLSTVRFHPPLDPPEPARPPGPGAPASGTAATDAPEPGRGEDE
+AARTAWLERARAVLVQDLSASLRG
+>PROKKA_01775
+MATSEPVRRSAAALLRLTCRPEVTGMDQVPAEGPFIMASNHLSFFDSVILQALAPRPVHF
+FAKEEYFTGAGVRGRAQRWFFESVGSVPVRRGEQAASVAALESLVGLLDSGQGVGIYPEG
+TRSRDGRLYRGRTGAAWLALTTGAPVVPVGLVDTQHLQPPDTNGFRPHRFAVRVGAPLDF
+GHPGRRHTLPQRRDATAAIMDAIGALSGQERLDAYNAAPGARG
+>PROKKA_01668
+MATSEQLRRAVAGAIRLSCRPHVRGLEHVPPEGPFIVASNHLSFVDSVILQALCPRPVGF
+FAKAEYFEAPGLRGRAQRRFFEAVGSIPVRRGEQAASVAALEDLVALLDGGHGVGIYPEG
+TRSRDGRLYRGRTGAAWLALTTGAPVVPVGLRGTERLQPPGTNGFRPHRFTVEMGEPLDF
+GHPGRRHSLPQRREATATIMAAIAALSGQERVDEYNAAPAARG
+>PROKKA_01068
+MATSEPVRRSAAALLRLTCRPEVVGMEHVPARGPFVMASNHLSFVDSVILQALAPRPVHF
+FAKEEYFTGTGLRGRVRRRFFESVGSVPVRRGEQAASVAALESLVGLLESGQGVGIYPEG
+TRSRDGRLYRGRTGAAWLALATGAPVVPVGLVGTQHLQPPDTNGFRPHRFSVRVGAPLDF
+GHPGRRHTLPQRRDATAAIMDAIGALSGQERVDAYNAAPGARG

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000121.fa

@@ -0,0 +1,36 @@
+>PROKKA_01147
+MADQTTTPTADAQAAGRSVLVTGGNRGIGLAIARAFAANGDRVAITSRSGEGPEGVLAVR
+ADVTDAASVDAAFREVEEVHGPVEVLVANAGITHDQLLLRMSEDDFTSVIDTNLTGAFRV
+VQRATKGMMRLKRGRIVLVSSVVGLLGSPGQVNYAASKSGLVGMARSITRELGARGVTAN
+VVAPGYIDTEMTQSLDDELKAQYKTSIPAGRFAAPEEVAGVVRWLASDEAAYISGAVIPV
+DGGLGMGH
+>PROKKA_00866
+MADQTTTPAADAQAAGRSVLVTGGNRGIGLAIARAFAAHGDRVAITSRSGEGPEGVLAVR
+ADVTDAASVDAAFREVEEVHGPVEVLVANAGITHDQLLLRMSEDDFTSVIDTNLTGAFRV
+VQRATKGMMRLKRGRIVLVSSVVGLLGSPGQVNYAASKSGLVGMARSITRELGARGVTAN
+VVAPGYIDTEMTQSLDDELKAQYKTSIPAGRFAAPEEVAGVVRWLASDEAAYISGAVIPV
+DGGLGMGH
+>PROKKA_00771
+MAEFDGKVALVTGGGSGIGEACAKDLARGGAKVLVTDINLEAAERVAEEIKADGGEAAAY
+RLDSASPDDNEKAVAFAEETFGALHLAVNNAGIGAGTEPAGELKIEDWDRVIDIDLNGVL
+YGMRHQLPAMERAGGGAVVNMASIHGTVATGLGASAYTAAKHGVVGLTKQAGVDYGPRGV
+RVNAVGPGYIETPLLAELPDEVHEALVAKHPIGRLGRAEEVAHLVSFLLSDKASFLTGAY
+YLVDGGYTAP
+>PROKKA_01745
+MADQTTPTAADAKASGRSVLVTGGNRGIGLAIARAFAANGDRVAVTSRSGEGPEGVLAVR
+ADVTDAASVDAAFREVEEAHGPVEVLVANAGITNDQLLLRMSEEDFTSVVDTNLTGAFRV
+VQRATKGMMRLKRGRIVLVSSVVGLLGSPGQVNYAASKSGLVGMARSITRELGARGVTAN
+VVAPGYIDTEMTQSLGEDLKAQYKKSIPAGRFAQPEEVADVVRWLASDEAAYISGAVIPV
+DGGLGMGH
+>PROKKA_01639
+MAEQTEPGGRSVLVTGGNRGIGRAIAEAFLANGDRVAVTSRSGEGGPEGALTVAADVTDA
+ASVDAAFRAVEEAHGPVEVLVANAGVTNDQLLLRMSEDDFTSVVDTNLTGAFRVVQRATK
+GMMRLKRGRIVLVSSVVGLLGSPGQVNYAASKSGLIGMARSITRELGARGITANVVAPGY
+IDTEMTRSLDEELKAQYRKSIPAGRFAEPEEVADVVRWLASPGAGYVSGAVIPVDGGLGM
+GH
+>PROKKA_01097
+MADQTTTPAADAQAAGRSVLVTGGNRGIGLAIARAFAAHGDRVAITSRSGEGPEGVLAVR
+ADVTDAASVDAAFREVEEVHGPVEVLVANAGITHDQLLLRMSEDDFTSVIDTNLTGAFRV
+VQRATKGMMRLKRGRIVLVSSVVGLLGSPGQVNYAASKSGLVGMARSITRELGARGVTAN
+VVAPGYIDTEMTQSLDDELKAQYKTSIPAGRFAAPEEVAGVVRWLASDEAAYISGAVIPV
+DGGLGMGH

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000124.fa

@@ -0,0 +1,42 @@
+>PROKKA_01285
+MRHTRLGRSGLTVSVVGLGCNNLGRPGTATLEQAGTDDVVHAALDAGITFFDVADVYGAE
+PGLSEERLGRALGARRDEVVIGTKFGMDMGGVAGDDGGARGSRRYIVRAVEDSLRRLGTD
+WIDLYQFHTPDPATPIEETLRALDDLVRAGKVRYVGHSNRAGWQIAQAEYVARELGVERF
+VSAQNHYNLLDRRAELEVVPAAAEFGLGVLPYFPLANGLLTGKYSQGDAPEGSRLSHVRQ
+HMVADADLEQLAGFGRFARERGITEVQAAIGWLAAQGPVSSVIAGATRAAQVVENAAAAD
+WLATAEDLAELDALFPGPEKVALF
+>PROKKA_01004
+MRHTRLGRSGLTVSVVGLGCNNLGRPGTATLEQAGTDAVVHAALDAGITFFDVADVYGAE
+PGLSEERLGRALGARRDEVVIGTKFGMDMGGVAGDDGGARGSRRYIVRAVEDSLRRLGTD
+WIDLYQFHTPDPATPIEETLRALDDLVRAGKVRYVGHSNRAGWQIAQAEYVARELGVERF
+VSAQNHYNLLDRRAELEVVPAAAEFGLGVLPYFPLANGLLTGKYSQGDAPEGSRLSHVRQ
+HMVADADLEQLAAFGRFARERGITEVQAAIGWLAAQGPVSSVIAGATRAAQVVENAAAAD
+WLATAEDLAELDALFPGPEKVALF
+>PROKKA_01600
+MRHTRLGRSGLTVSVVGLGCNNLGRPGTVTLEQDGTDAVVHAALDAGITFFDVADIYGAQ
+PGLSEERLGRALGARRDDVVIGTKFGMDMAGANGVDHDARGSRRYIVRAVEASLRRLGTD
+WIDLYQFHTPDPATPIDETLRALDDLVRDGKVRYVGHSNRTGWQIAQAEYVARELGTERF
+VSAQNHYNLLDRRAELEVVPAAAEFGLGVLPYFPLANGLLTGKYSQGAAPEGSRLSHVRQ
+HMVADADLEQLAAFGEFARARGITEVQAAIGWLAAQGPVSSVIAGATRTGQVAENARAAD
+WEATEADLAELDALFPGPEKVALF
+>PROKKA_01496
+MRTVRLGRSGLTVSVVGLGCNNLGRPGTATMEQEGTDAVVHAALDAGITLFDVADVYGAR
+PGLSEERLGRALGSRRDEVVLATKFGMDMGGAAGADGGARGSRRYIVRAVEDSLRRLGTD
+WIDLYQFHTPDPATPIEETLRALDDLVRSGKVRYIGHSNRTGWQIAQAEHAAREIGVERF
+VSAQNHYNLLDRRAELEVLPASAEYGLGVLPYFPLANGLLTGKYSDGTAPAGSRLSHVRQ
+HMVEEADRGQLAAFGAFARERGITEVQAAIGWLAAQRPVASVIAGATRPGQIAENARAAD
+WEATPADLAELDALFPAPPPVALF
+>PROKKA_02080
+MSDMIYNRLGSSGLQVSQFSFGSWVTFGNQVDMGLAKDQLAAAKEGGVNFFDNAEVYAGG
+ESESIMGRAIAELGWKRHEYVVSTKLFWGIHGDVVNMKNTLNRKYLMQGIDGSLERLGLD
+FVDLVFCHRPDPHTPIEETVWAMSDMINRGKALYWGTSEWSADEIRAAWNIAERHHLHKP
+VMEQPQYNLLHRTKVEEEYARLYEDIGLGLTTWSPLASGILSGKYVDGVPEGSRGALKGY
+DFVKDSIADQETTAKVRQLVDIAAELDVTPAQLALAWTASNPRVSTVILGASSVAQVQEN
+LKALDVIELVTPEVRERLEAVFA
+>PROKKA_01243
+MRHTRLGRSGLTVSVVGLGCNNLGRPGTATLEQAGTDAVVHAALDAGITFFDVADVYGAE
+PGLSEERLGRALGARRDEVVIGTKFGMDMGGVAGDDGGARGSRRYIVRAVEDSLRRLGTD
+WIDLYQFHTPDPATPIEETLRALDDLVRAGKVRYVGHSNRAGWQIAQAEYVARELGVERF
+VSAQNHYNLLDRRAELEVVPAAAEFGLGVLPYFPLANGLLTGKYSQGDAPEGSRLSHVRQ
+HMVADADLEQLAAFGRFARERGITEVQAAIGWLAAQGPVSSVIAGATRAAQVVENAAAAD
+WLATAEDLAELDALFPGPEKVALF

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000129.fa

@@ -0,0 +1,51 @@
+>PROKKA_01450
+MPPGPGALLGGRRVRLLPAILALALGSFAIGTTEFAMMGLLPQAVADLGVGLEAGGVLIS
+MYALGVVIGAPLLAASFARVDRRVTSIVLMLLFVVGHVAAFLAPDMGSMMAARFVSGLPH
+GAYFSAAALAAADLAGPARRGQAVAWVMAGLSVANVLGVPGATALGQAVGWRWMFVIVAV
+CAALCVGATAWLVPSVPAPAGASVGRELRGLASGRLWATVAVGVIGFAGMFALYTYIAPL
+LTEVAGLEERWVPAVLALYGVGMVIGTLVSGALTDRDPVGTLRLSFGLSAVSLAAVALTA
+PWAPVMIVFLFCVAVSGSGIAPSLQVLLVDSAPTAPQLAGSLNHSALNMANAMGAWVGAA
+AIGAGASLRTPPLVGAGIALAGLVLAFLLVRRDVAASPGVRADDGGSPR
+>PROKKA_01182
+MPTPTPAADGAHDRSPRAPRPTRPDPSIPPTAPTGPGALLGGRRVRLLPAILALALGSFA
+IGTTEFAMMGLLPQAVADLGIGLEAGGVLISMYALGVVIGAPLLAASFARVDRRVTSIVL
+MLLFVVGHVAAFLAPDAATMMAARFICGLPHGAYFSAAALAAADLAGPARRGQAVAWVMA
+GLSVANVLGVPAATALGQSAGWRWMFVIVATCAALCVAATAWLVPPVPAPEGASVRRELR
+GLASGRLWATVAVGVLGFAGMFALYTYIAPLLTTVSGLDERWVPAVLALYGVGMVVGTLV
+GGALTDRDPVRTLRLSFALSAVFLLGVGLTAQWAPVMVVFLFLVAVSGSGIAPSLQVLLV
+DSAPTAPQLAGSLNHSALNMANAMGAWVGAAAIGAGASLRTPPLIGAAIALGGLVLALLL
+VRRTPAVGAVPHDGPSAATV
+>PROKKA_01449
+MTTPASGDPAASPSVSARPDPADAAGSPAAGAVGPQSLLGGRRVRLLPAILALALGSFAI
+GTTEFAIMGLLPQAVADLGIGLEAGGVLISMYALGVVVGAPLLAAAFARVDRRTTGIVLM
+LLFTVGHTGAFLAPDTATMMAARFVSGLPHGAYFSAAALAAADLAGPARRGQAIAWVMAG
+LSVANVVGVPAATAIGQAAGWRWMFVIVAACALACVAATAWLVPPVPAPEGASVRRELRG
+LASGRLWATVAVGVIGFAGMFALYTYIAPLLTEVAGLDERWVPAVLALYGIGMVVGTLVS
+GALTDRDPVGTLRLSFGLSAVSLLAVGLTAQWAPVMVLLLFCVAVSGSGIAPSLQVLLVD
+SAPGAPQLAGSLNHSALNMANAMGAWVGAAAIGAGASLRTPPLVGAAIALAGLVLAFVLV
+RRASPTSAATAADAR
+>PROKKA_01353
+MRLLPAILALALGSFAIGTTEFTMMGLLPEAVTDLGVGLETGGVLISMYALGVVVGAPVL
+AAALARMDRKLSSILLMGLFVVGHLASLLAPSLGALMAARFVSGLPHGAFFSAAALAAAD
+LAGPARRGQAIGWVMAGLSVANVVGVPAATALGQAAGWRWMFAVVAACALGCIAATALLV
+PRVPAPAGASVAAEIRGLASGRLWATVAIGVVGFAGMFCLYTYIAPLLTEVSGLHPRWVP
+AVLALYGVGMVIGTLVSGALTDRDPIRTLRWSFGVSALGLLAVSLTAPWWPALLVSLLVV
+ALSGSGIAPALQVLLVDAAPTAPQLSGSLNHSALNMANAMGAWVGAAAVGAGASLRMPSL
+IGAGIALVGLLMSVALLRRPASAPPGA
+>PROKKA_01775
+MSAVSNAPRPRLPWGALLALSASGFLAIFTETIPAGLLPELSRGLGVTESAAGQLVTLYA
+MGSVVAAIPLVAATQTVNRKKVLLAAVATLGAFNLVTAAAPWLPVILAARFVAGAAAALV
+WGVLAGFARSLVAPQLQGRALAVTGLGQPIALAGGVPLGSFAASVMDWRWVFVAISVAAG
+GLAVWIAAAVQNVEGSPRRQREPLRRVVMLPGVRLIFAVTGCWILAHNMLYTYAAPLLNR
+TDLRLDVGLGLFGVASMIGISLVGMVIDRALRLVSAICVTAMCLATTVWLLPQVGIALAV
+ASVVAWGLSFGGAPVLLQTALADRAGEHTDAAQSVFVTVFNLAVAGGGFMGGMLLASSGT
+AGIATTSAVLCLVAVGMIVLARAAFPAGHRHKDETDESVVAPSECSA
+>PROKKA_01400
+MPTPTPAADGAHDRSPRAPRPTRPDPSIPPTAPTGPGALLGGRRVRLLPAILALALGSFA
+IGTTEFAMMGLLPQAVADLGIGLEAGGVLISMYALGVVIGAPLLAASFARVDRRVTSIVL
+MLLFVVGHVAAFLAPDMGSMMAARFVSGLPHGAYFSAAALAAADLAGPARRGQAVAWVMA
+GLSVANVLGVPGATALGQAVGWRWMFVIVAVCAALCVGATAWLVPSVPAPAGASVGRELR
+GLASGRLWATVAVGVIGFAGMFALYTYIAPLLTEVAGLEERWVPAVLALYGVGMVIGTLV
+SGALTDRDPVGTLRLSFGLSAVSLAAVALTASWAPVMIVFLFCVAVSGSGIAPSLQVLLV
+DSAPTAPQLAGSLNHSALNMANAMGAWVGAAAIGAGASLRTPPLVGAGIALAGLVLAFLL
+VRRDVAARPGVRADDDGSPR

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000130.fa

@@ -0,0 +1,79 @@
+>PROKKA_01539
+MTQNSEHTPASADLDPTVAAIAEDIVTEDAAPVAPEQTFADFGVHPAIVEALEAKGIVHP
+FPIQAMTLPVALGGHDIIGQAKTGTGKTLGFGIPALQRAIGPGEPGWDGLEAKGTAGAPQ
+ALIVAPTRELAVQVAGDLTAAAARRPLRIATIYGGRAYEPQIEELQRGVEIVVGTPGRLI
+DLMRQRHLRLDLVNTVVLDEADEMLDLGFLPDVETLLAAVPAVRQTMLFSATMPGPVVAM
+ARRYMTQPTHIRAADPEDEGLTKKDIRQLVYRAHHMDKDELVARALQAEGRGRTIIFTRT
+KRTAARVADELTARGFAAGALHGDLGQGAREQALRAFRNGKVDILVATDVAARGIDVDDV
+THVFNFQAPEDEKTYVHRVGRTGRAGNKGVAVTLVDWEDMPRWSLIDKALGLGQPEPVET
+YSSSPHLFSDLGIPKGTKGRLPQAKRVLEGLEGETLEDLGGPEAKQRDGGRGRGREGGRS
+RDGERGGREGGRGGRGGRGRGGRSGEGRDAARGGSRGERSERSGRGRGEAPAEQRAEGRG
+RGRGEGRKRTASRSETPAARTSEPVAGVELTEARRAERAEARAEARRRRGGRSRTRRRNG
+EVVDG
+>PROKKA_01249
+MTQNSEHTPAPADVDPTVAEIAEDIVTEDAAPVAPEQTFADFGVHPKIVEALEAKGIVHP
+FPIQAMTLPVALGGHDIIGQAKTGTGKTLGFGIPALQRAIGPGEPGWDGLEAKGTAGAPQ
+ALIVAPTRELAVQVAGDLTAAAARRPLRIATIYGGRAYEPQIEELQRGVEIVVGTPGRLI
+DLMRQRHLRLDLVNTVVLDEADEMLDLGFLPDVETLLAAVPAVRQTMLFSATMPGTVVAM
+ARRYMTQPTHIRAADPEDEGLTKKDIRQLVYRAHHMDKDELVARALQAEGRGRTIIFTRT
+KRTAARVADELTARGFAAGALHGDLGQGAREQALRAFRNGKVDILVATDVAARGIDVDDV
+THVFNFQAPEDEKTYVHRVGRTGRAGNKGVAVTLVDWEDMPRWSLIDKALGLGQPEPVET
+YSSSPHLFSDLDIPKGTKGRLPQAKRVLEGLEGETLEDLGGPEAKQRDGGRGRGREGGRS
+RDGERGGRGRGGRSGEGRDRARGGGRGERTERSPRGRDEARAEGRGRGEAPAEQRAEGRG
+RGRGEGRERTASRPETPAARTPEPVAGVELTEARRAERAEARAEARRRRGGRTRTRRSNG
+EVVDG
+>PROKKA_01386
+MNRAHGASGPSRPPCRRPNRNASRHDPELRAHPRPGRRRPPQVADIAEEIVTEEAVETAP
+EQTFADFGVHPAIVQALEAKGIVHPFPIQAMTLPVALGGHDIIGQAKTGTGKTLGFGIPA
+LQRAIGPGEPGWDKLEAQGSAGAPQALIVAPTRELAVQVAGDLTAAAAQRPLRIATIYGG
+RAYEPQIEELQRGVEVVVGTPGRLIDLMRQRHLRLDLVNTVVLDEADEMLDLGFLPDVET
+LLGAVPAVRQTMLFSATMPGPVVAMARRYMTQPTHIRAADPEDEGLTKKDIRQLVYRAHH
+MDKDELVARALQAEGRGRTIIFTRTKRTAARVADELTARGFAAGALHGDLGQGAREQALR
+AFRNGKVDILVATDVAARGIDVDDVTHVFNFQAPEDEKTYVHRVGRTGRAGNKGVAVTLV
+DWEDMPRWSLIDKALGLGQPEPQETYSSSPHLFADLGIPKGTKGRLPKEKRVLEGLEGEV
+LEDLGGPESAPRGRGGRSRDGERDGGRGGRGGRGERGGRGGRSRDDERGGREGGRGGRGE
+RAGREGGRGRDAEQSSARGEEAGESKGRGRGGERAGREGGRGESTGRGRGGRSGESRTRG
+ESRTEASEARAAQPVAGVERTEARMAERAEARAEARRRRGGRTRTRRRNGEVVDG
+>PROKKA_00286
+MKSIDNVNVKLGDDLKAEITAGSKVRIAASAFSIYAFEALREELEGLEELQFIFTDPAFS
+ASSIDGTPRREHRRYFIPPLDIESSLTGTEFEVRLRNRLTQRAIARECADWVRRKVRFRS
+NTSGKGMQPIIGVGDDAAYLPVQDFSTSALGYEAGGALSNVVGKFEGPLEAAGLLTVFDQ
+VWNDPSALEDVTSTVLERIEQVYAENSPRHIYFLILNSIFSDFLADLSEDALPNDRTGYR
+ETKVWRALYDFQRDAAESIIQKLETYNGCILADSVGLGKTFTALAVIQYYEKRNKSVLVL
+CPKKLAENWTTYNNNYVTNPFVEDRFNYDVLAHTDLSRTRGESLGVRLDRINWGNYDLVV
+IDESHNFRNATYGEDRDTRYQRLMEKVIREGVRTKVLMLSATPVNNRFNDLKNQLQLAYE
+GEEENLSQHLNLSTTIDGVFRGAQAAFNEWSKLPAEERTPGRILGMLDFDFFELLDAVTI
+ARSRKQIQRFYDTAAIGAFPTRLPPLSLQEPLSEDKSVPSYNDIFEQLQALNLAVYTPLA
+FVHASRRYKYETGPGEENTDNFRSGRGQAGRETGLKRLMTVNLLKRLESSVHAFRKTLVS
+IESQVDALHRRLESEALGPLRVDAPAVEEDILREDDDVAEALFALPGDLELDLNDVDVLS
+WTSALWHDRETLRELIGEMDKITPERDLKLQRLRRLIRDKATSPLNEGNRKVLVFSAFAD
+TADYLYEQLSPALSAAGLETGIITGGSHSARSTLDGAVDFQTLMTLFSPVSKNRSALMPE
+ETREVDVLIGTDVISEGQNLQDCDFLVNYDIHWNPVRIVQRFGRIDRIGSTNERIQLVNF
+WPDMDLDAYIQLKDRVENRMVMVDVTGTADDNVLTPQQEQDAAYRTAQLKRMREEVVELE
+DTQAGVSITDLGLNEFRSALMAYVREHGDLTRAPRGLHAVVPADPDAGLPAGVIFALHNL
+QADPAMHRGNRLHPYYLVYVGEDGATVLEHTKAKPLLDLLRSAAEKQSVPLADAVRAFNT
+ATAEGTDMAAYSALLTRAIESMVEADEEQDVASLFTAGPTTALTSAIRGLEDFELIAFLA
+VVDTAGTDA
+>PROKKA_01277
+MTENTAAAEAVAPTAPEQTFADFGVQEPIVRALSEKGIVHPFPIQAMTLPVALGGHDIIG
+QAKTGTGKTLGFGIPALQRAVGPDEAGWDTRVAAGAAGAPQALVVAPTRELAVQVAGDLV
+AAAKHRPLRIATIYGGRAYEPQIEELQRGVEVVVGTPGRLIDLLRQKHLRLDAVNTVVLD
+EADEMLDLGFLPDVETLLAAVPEVRQTMLFSATMPGPVIAMARRYMTRPTHIRASDPEDE
+GLTKKDIRQLVYRAHHMDKDELVARALQAEGRGRTIIFTRTKRTAARVAEELTNRGFAAG
+PLHGDLGQGAREQALRAFRNGKVDILVATDVAARGIDVDDVTHVINFQAPEDAKTYVHRV
+GRTGRAGHKGTAVTLVDWEDMPRWSLIDKALGLNQPEPVETYSSSPHLFSDLGIPKGTKG
+RLPKEKRVLAGLDAERLEDLGGPEAKEKAARGGRDERSGSRSGGRGERSGGRGGRAGGGS
+RASREDRPPREDRTPRGERAPRPEKTVKAERAPRAERAPRAEKADRPAAAERSEGASGER
+RRRTRTRRRGGDVIDG
+>PROKKA_01466
+MTQNSEHTPASADLDPTVAAIAEDIVTEDAAPVAPEQTFADFGVHPAIVEALEAKGIVHP
+FPIQAMTLPVALGGHDIIGQAKTGTGKTLGFGIPALQRAIGPGEPGWDGLEAKGTAGAPQ
+ALIVAPTRELAVQVAGDLTAAAARRPLRIATIYGGRAYEPQIEELQRGVEIVVGTPGRLI
+DLMRQRHLRLDLVNTVVLDEADEMLDLGFLPDVETLLAAVPAVRQTMLFSATMPGPVVAM
+ARRYMTQPTHIRAADPEDEGLTKKDIRQLVYRAHHMDKDELVARALQAEGRGRTIIFTRT
+KRTAARVADELTARGFAAGALHGDLGQGAREQALRAFRNGKVDILVATDVAARGIDVDDV
+THVFNFQAPEDEKTYVHRVGRTGRAGNKGVAVTLVDWEDMPRWSLIDKALGLGQPEPVET
+YSSSPHLFSDLGIPKGTKGRLPQAKRVLEGLEGETLEDLGGPEAKQRDGGRGRGRDGGRS
+RDGERGGRGRGGRSGEGRDRARGGGRGERNRGGRSGEGRDDARGGGRGERSGRGRGEAPA
+EQRAEGRGRGRGEGRERTASRSETPAARTSEPVAGVELTEARRAERAEARAEARRRRGGR
+SRTRRRNGEVVDG

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000134.fa

@@ -0,0 +1,49 @@
+>PROKKA_01581
+MSTTLDLDHAATAPVRRSALEAMWPALTGVYGNPSSAHEAGRAAAALLEDARARVACAIG
+ARAGQVVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGADLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFEEAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARR
+LPRHASFALPGVNGESVLEEAARRGVLASAGSACSAHDAEPSPALLALGLSEDEARTALR
+CTFGPDADAPLLDAAADAIVDAVRTVSALR
+>PROKKA_01291
+MSTTLDLDHAATAPVRRSALEAMWPALTGVYGNPSSAHEAGRAAVALLEDARARVARAIG
+ARAGQVVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGADLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFEEAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARR
+LPRHASFVLPGVNGESVLEEAARRGVLASAGSACSAHDAEPSPALLALGLSEDEARTALR
+CTFGPDADAPLLDAAADAIVDAVRTVAALR
+>PROKKA_01342
+MSAALYLDHAATAPVRRVALEAMWPALTGVYGNPSSAHEAGRAAAALLEDARARVARAIG
+ARAGQVVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGSDLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFAEAEAERAAAADAWSGLRDRFAARALDGVQELVPDARLTGHPARR
+LPRHASFVLPGVNGESVLEEAARRGVLASAGSACSAHSTEPSPALLALGLSEDEARTALR
+CTFGPDADEAMLAAAADAIVDAVRTVSALR
+>PROKKA_01235
+MSTILDLDHAATAPVRRSALEAMWPALTGVYGNPSSAHEAGRAAAALLEDARARVARAIG
+ARAGQIVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGADLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFEEAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARR
+LPRHASFVLPGVNGESVLEEAARRGVLASAGSACSAHDAEPSPALLALGLSEDEARTALR
+CTFGPDADAPLLDAAADAIVDAVRTVTALR
+>PROKKA_01767
+MALDVAAVRQDFPILRSTLADGRPLVYLDSGATSQRPRQVIEAEVEFLTISNAAVKRGAH
+QLAEAATDRYESARETVAAFVGATDPRELVFTRNATEALNLVAYALGNGDDATPEHLRVR
+AGDEILVTEMEHHANLVPWQELARRTGATLRHIPLGEDFALDLVDLGSLVTERTKVVAFT
+HQSNVTGTVNPVATLGEAARAVGALTVLDACQSVPHMPVDVAALGVDFLAFSGHKMLGPT
+GIGALWGRYELLAELPPFLLGGSMIEVVHLDRSTYAEPPARFEAGTPPISQAVGLAAACD
+YLSALGMDAVAEHEHALTARALEHLAGMDRVRVIGAPAGPERSGAVSFAVEGIHPHDVGQ
+VLDSLGVQVRVGHHCAWPLHRRYGVPGTTRASFSVYSTLDEVDAFADGLAQTLAFFQGFG
+R
+>PROKKA_01508
+MSTTLDLDHAATAPVRRSALEAMWPALTGVYGNPSSAHEAGRAAAALLEDARARVARAIG
+ARAGQVVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGADLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFEEAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARR
+LPRHASFVLPGVNGESVLEEAARRGVLASAGSACSAHDAEPSPALLALGLSEDEARTALR
+CTFGPDADAPLLDAAADAIVDAVRTVAALR

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000135.fa

@@ -0,0 +1,48 @@
+>PROKKA_01582
+MSLACVPHPGPVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVA
+SRLTLPSGVATGDVTSNSAVLWARSSGRSRLHATLRAVDEDGKVLRGRFARGLTLRSGWV
+DGATDHTAKILADTLPSDTRFEVTYAFEDEAGRLGESAVARFTTAPGARFGRKTSAAQSF
+VWTADTAGQGYGINPEIGGMRGYAAMHATKPDFFLHSGDTIYADNPIPETLEVAGEPTWR
+NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYADVPVIAQWDDHETTNNWWPGEVLED
+PRYTQVRDVDTLAARARRAWQEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDM
+RTHKGENTPGLETHETPILGEEQLQWLIRGLRASTATWKVIANDLPLGLVVPDGTGQESL
+SNGDDGAPLGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWE
+FVAGPINAGSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRL
+INAAGRTVYSRTLTAA
+>PROKKA_01292
+MRLACVPHPGPVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVA
+SRLTLPSGVATGDVTSNSAVLWARSSGRSRLHATLRAVDEDGKVLRGRFARGLTLRSGWV
+DGATDHTAKILADTLPSDTRFEVTYAFEDEAGRLGESAVARFTTAPGARFGRKTSAAQSF
+VWTADTAGQGYGINPEIGGMRGYAAMHATKPDFFLHSGDTIYADNPIPETLEVAGEPTWR
+NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYADVPVIAQWDDHETTNNW
+>PROKKA_01293
+MDTLAARARRAWQEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDMRTHKGENT
+PGLETHETPILGEEQLQWLIRGLRASTATWKVIANDLPLGLVVPDGTGQESLSNGDDGAP
+LGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFESFWEFVAGPINA
+GSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRLINAVGRTV
+YSRTLTAA
+>PROKKA_01340
+MKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWEFVAGPINAGSFGPNTLDGTFGPRLDF
+EAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRLINAVGRTVYSRTLTAA
+>PROKKA_01234
+MSLACVPHPGSVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVA
+SRLTLPSGVATGDVTSNSAVLWARSSGRSRLHATLRAVDEDGKVLRGRFARGLTLRSGWV
+DGATDHTAKILADTLPSGTRFEVTYAFEDEAGRLGESAVARFTTAPGARFGRKTSAAQSF
+VWTADTAGQGYGINPEIGGMRGYAAMHATQPDFFLHSGDTIYADNPIPETLEVAGEPTWR
+NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYADVPVIAQWDDHETTNNWWPGEVLED
+PRYTQVRDVDTLAARARRAWQEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDM
+RTHKGENTPGLETHETPILGEEQLQWLIHGLRASTATWKVIANDLPLGLVVPDGTGQESL
+SNGDDGAPLGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWE
+FVAGPINAGSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRL
+INANGRTVYARTLTAA
+>PROKKA_01509
+MSLACVPHPGPVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVA
+SRLTLPSGVATGDVTSNSAVLWARSSGRSRLHATLRAVDEDGKALRGRFSRGLTLRSGWV
+DGATDHTAKILADTLPSGTRFEVTYAFEDEAGRLGESAVARFTTAPGARFGRKTSAAQSF
+VWTADTAGQGYGINPEIGGMRGYAAMHATQPDFFLHSGDTIYADNPIPETLEVAGEPTWR
+NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYTDVPVIAQWDDHETTNNWWPGEVLED
+PRYTQVRDVDTLAARARRAWQEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDM
+RTHKGENTPGLETHETPILGEEQLQWLIRGLRASTATWKVIANDLPLGLIVPDGTGQESL
+SNGDDGAPLGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWE
+FVAGPINAGSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEGGREFRVRL
+INAAGRTVYSRTLTAA

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

@@ -0,0 +1,30 @@
+>PROKKA_01790
+MDAPASDLTGKARIRHAALRLFAHHGVEGTSMRAIAEEASVTVGLITHHYGSKAGLHREV
+DAAVADDFAAAIASVPAEGTARDVTLRRDAAVAEMLRARPDVLEYVRRHVLLGEPAADSQ
+LVEKLTALAREQVRQLRAAGLISGRRDEVPQVVSMIMRMLGELFFEPLVDRIVDAVDRDA
+ARPAVVVRVQAAEDETARGGRA
+>PROKKA_02051
+MNTPLPFDQDDLSSPARLRLAALELYAERGVEMASVREIAQRAGVAPGLVRHHFGSKAGL
+TRAVDDDVLRLIAATLDEVPLVGTPQEVSAARDAAFADLLADHPVVGAYVRRSLLEAGGE
+TESLLERLVDLTTEQTERLRRSGFAPRRSMPTSVFGTVIRQMGHLMVDPSADRIWRRIAE
+TQEGAAEQASPRVRLVVDPPR
+>PROKKA_01757
+MNTPLPFDQDDLSSPARLRLAALELYAERGVEMASVREIAQRAGVAPGLVRHHFGSKAGL
+TRAVDDDVLRLIAATLDEVPLVGTPQEVSAARDAAFADLLADHPVVGAYVRRSLLEAGGG
+TESLLERLVDLTTEQTERLRRSGFAPRRSMPTSVFGTVIRQMGHLMVDPSADRIWRRIAE
+TQEAAAEQRSPRVRLVVDPPR
+>PROKKA_01086
+MDAPASDLTGKARIRHAALRLFAHHGVEGTSMRAIAEEASVTVGLITHHYGSKAGLHREV
+DAAVADDFAAAIASVPAEGTARDVTLRRDAAVAEMLRARPDVLEYVRRHVLLGEPAADSQ
+LVEKLTALAREQVRQLRAAGLISGRRDEVPQVVSMIMRMLGELFFEPLVDRIVDAVDRDA
+ARPAVVVRVQAAEDETARGGRA
+>PROKKA_00729
+MNTARPLTREDLSSAARLRLSALELYAERGEHAASIRDVGRHAGVAPGLVRHHFGSKDGL
+TRAVDDDIIDLVRATLEAVPLEGTPLEISAARDAAFQELLQERPLIGGYLAQALTASRAS
+GESVLDRLVDLSAEQTRQLIDRGLDPRRGLRTSVFTTVVRQVAVFLVAPVAERAWNRLGH
+TLEGASDVAPMPPVRVVVGPAPEEDRR
+>PROKKA_01985
+MNTPLPFDQDDLSSPARLRLAALELYAERGVEMASVREIAQRAGVAPGLVRHHFGSKAGL
+TRAVDDDVLRLIAATLDEVPLVGTPQVVSAARDAAFADLLADHPVVGAYVRRSLLEAGGE
+TESLLERLVDLTTEQTERLRRSGFAPRRSMPTSVFGTVIRQMGHLLVDPSADRIWRRIAE
+TQEDAAEQASPRVRLVVDPPR