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Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000007.fa

@@ -0,0 +1,52 @@
+>0_150
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>0_992
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKAEDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>0_1245
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>0_1335
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWR------------------KQNATLKRLLAEAELEKAALKELAEGNF
+>0_2015
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>1_977
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>1_1064
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>1_1072
+MRVVLLPAVADRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>1_1076
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>1_1970
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>2_1188
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>4_564
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>4_566
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>4_1202
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>4_1289
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>4_1827
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>4_2144
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+ 

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

@@ -0,0 +1,64 @@
+>0_501
+MTIVDFFRLLRANLLLLLAAALVGGLLGWGYSALQPRIYASESQGFLAARAADQSL----ITSNLPAESRAQAYVALINS
+EAVRERVAQD-TGQDGDGSL----SAVLVPESSMIKVTATSTDPETAAQLANSALQATADVAADVDKNSP-----LEVVP
+LSDARVPSAPVSPDTRRNVLLGVVAGLGAGLAIAVLRRLLDVKVRSRADVKEITGAGVIGAV--PENASLT--RTGEEAV
+DLDPRAGEAIRALRTNLKFVSVDEPPR-VVSFTSADPSEGKSTVASNLARALALAGERVLVVDADLRRPRQHDLFQVAGD
+VGLSEVLAGEVQPDDALAATGIPNLTLLPAGRTPPNPSELLGSKRMRALLKLASEDFF--VIVDSPPLLPVTDGSLLATA
+VDGTVLVVRQGRTRKDHLEAAVENLAAVDAHLLGVVMNGVARSQRGGGYSYGYGY-------ESTYHKSHDKYLQ-GTG-
+--KGGKKSRRAAR----------AKKG----------------------------------
+>1_231
+MTIVDFFRLLRANLLLLLAAALVGGLLGWGYSALQPRIYASESQGFLAARAADQSL----ITSNLPAESRAQAYVALINS
+EAVRERVAQD-TGQDGDGSL----SAVLVPESSMIKVTATSTDPETAAQLANSALQATADVAADVDKNSP-----LEVVP
+LSDARVPSAPVSPDTRRNVLLGVVAGLGAGLAIAVLRRLLDVKVRSRADVKEITGAGVIGAV--PENASLT--RTGEEAV
+DLDPRAGEAIRALRTNLKFVSVDEPPR-VVSFTSADPSEGKSTVASNLARALALAGERVLVVDADLRRPRQHELFQVAGD
+VGLSEVLAGEVQPDDALAATGIPNLTLLPAGRTPPNPSELLGSKRMRALLKLASEDFF--VIVDSPPLLPVTDGSLLATA
+VDGTVLVVRQGRTRKDHLEAAVENLAAVDAHLLGVVMNGVARSQRGGGYSYGYGY-------ESTYHKSHDKYLS-GVGS
+SAKKGRRSRRKAR----------TR-G----------------------------------
+>1_242
+MNIIDFLRVLRANRLVILGCAALGLALGLLYSLLQPTLYTATSTAFVTVEG--EAS----ISGTETAQTRAQSYIPLINS
+RTVRERIAAE-GLDTAGATL----SAALVPNSNLITVSAVAPDAQQAAALANGALVATADVANELDPTSN-----VKVTA
+MEDALAPAAPSSPDRVRHLLYGLGAGLVLGLIVAFLRRLLDVNVRTTTDAQVAGGAGLLGAI--PLDPSMKAERTAPMAP
+-LSPRASEAVRQLRTNLRFAAVDDPPR-TIAFTSSNPGEGKSTVIGNLALTVAAAGQPVILIDADLRRPRQALQFGVDGR
+VGLSEVLNGDVALQDVLIPVGEDGLLLLPAGRTPPNPSEQLGSERMRDLLTALAETHM--VLVDAPPVLPVTDSTLLATA
+VDGTVLVIRHGKTRKEHLEVARDMLAGVNARVLGVVLNGTPASGVGSDY-YGGGYGADGGSYDAYYQAPRDAAEA-AAGT
+A---GDASRR---------------------------------------------------
+>2_1186
+MDLQQYLQTFRKYWRSILTVLSVCVGAALVFTFLQTPKYSSTSSALIAVDT--AATPGELSSGALYAERQVSSFVALADS
+ALVLDPVINELGLNVTPQALRSRVSVSAPAGTSIVDVTVTDTNAGRAAEVANAITASLKNVTSDVVPTGPDGDEIVTVTV
+VEPAAASSRPVSPRPVVNIALGLIAGVVIGLGQALVRRLLDSRIRTRDDLVEITDAPVLASVVHHKGSDRPKDEAAPARG
+-TAWASAESYRKLRTAVGFVALGGERRSSIVVTSSVQGEGKTETSTNLAKVLAETGARVLLVDADLRRPQVGARLGLDDE
+LGLSDVLTGRADLNDVLLSV--DDLSVLTAGTVPPNPSELLGSEAMAELL-ALVEAHFEYVILDAPPLLPVTDAAILSHQ
+AGGAIVVARSGVARQNQLAEALSILEAADASVYGVVLNDVPVSHIDG--------------YSQYYR-------------
+-------------------------------------------------------------
+>2_2364
+MNIIDFLRVLRANRLVILGCAALGLVAGLVYSLLQPTLYTATSTGFVTVQG--EAT----ISGTETAQTRAQSYIPLINS
+RTVREKIAEG-GLDTAGASL----SAAVVPGSNLITVSAESEDPEQAAALANSALVATAETANGLDPTSN-----VQVTA
+MEDALAPTSPTSPDYVRNMLYGLGAGLLLGLVIAVLRRILDVNVRTTTDAQVASGAGLLGAI--PLDATLKAERDAPRGE
+-PSPRAAEAVRQLRTNLRFAAVDDPPR-TIAFTSANPGEGKSTVIGSLALAVAASGQPVILIDADLRRPRQALQFGVDGR
+VGLSEVLNGDVALQDVLVPVGDHGLLLLPAGRTPPNPSEQLGSARMRDLLTALAETHM--VLVDAPPVLPVTDSTLLSTA
+VDGTVLVVRHGKARKEHVEVARDMLAGVNARVLGVVLNGTPASGVGSDY-YGGSYASKGDDYHAYYQASRDAESR-PSDE
+AVPEGPAAQR---------------------------------------------------
+>3_2245
+MNILDFLRVLRANRLVLLGGVVLGLLGGLVYSLLQPTLYTSTSTGFVTVAG--EAS----ISGTETALTRAQSYVPLINS
+RTVREKVAES-GVDVSGSTL----SAQVVPNSNLITVTALAPDPQRAADLANTALGATAEVANSLDPTSN-----VKVTA
+MEDALPPAGPSSPDHLRNALIGAGIGLLAALAVAFLRRVLDVNVRTTTDATEASGAGLLGAI--PQDGTMKAERTAPLGV
+-PSPRAAEALRQLRTNLRFAAVDDPPR-VVMVTSSNPGEGKSTVIAGLAQAVAVSGQPVILVDADLRRPRQASQFGVDGR
+VGLSEVLSGDVLLEDAVQDLG-DGLLLLPAGRTPPNPSEQLGSHRMQELLRVLAETHL--VLVDAPP----------GAA
+GDG--LHPAGGRRGRDR-------------------AGGAPRQDPEGPCGGGPGHAGQGQRPHAGRGAQRRARLRCGLGL
+LRRGLRRGRRQLRRLLPGAPGRRRRRGRDRGRHVATLIAPGGRARSSHRRRRPGDAEGPRL
+>4_501
+MTIVDFFRLLRANLLLLLAAALVGGLLGWGYSALQPRIYASESQGFLAARAADQSL----ITSNLPAESRAQAYVALINS
+EAVRERVAQD-TGQDGDGSL----SAVLVPESSMIKVTATSTDPETAAQLANSALQATADVAADVDKNSP-----LEVVP
+LSDARVPSAPVSPDTRRNVLLGAVAGLGAGLAIAVLRRLLDVKVRSRADVKEITGAGVIGAV--PENASLT--RTGEEAV
+DLDPRAGEAIRALRTNLKFVSVDEPPR-VVSFTSADPSEGKSTVASNLARALALAGERVLVVDADLRRPRQHDLFQVAGD
+VGLSEVLAGEVQPDDALAATGIPNLTLLPAGRTPPNPSELLGSKRMRALLKLASEDFF--VIVDSPPLLPVTDGSLLATA
+VDGTVLVVRQGRTRKDHLEAAVENLAAVDAHLLGVVMNGVARSQRGGGYSYGYGY-------ESTYHKSHDKYLQ-GTGT
+AGKGGKKSRRAAR----------AKKG----------------------------------
+>4_512
+MNIIDFLRVLRANRLVILGCAALGLAMGLVYSLLQPTLYTATSSAFVTVEG--EAS----ISGTETAQTRAQSYIPLINS
+RTVRERIASE-GLDTAGATM----SAALVPNSNLITVSAVAPDAQQAAALANGALVATADVANELDPTSN-----VKVTA
+MEDALAPATPSSPDRVRHLLYGLGAGLVLGLIVALLRRLLDVNVRTTTDAQVAGGAGLLGAI--PLDPSMKAERTAPMAP
+-LSPRASEAVRQLRTNLRFAAVDDPPR-TIAFTSSNPGEGKSTVIGNLALTVAAAGQPVILIDADLRRPRQAMQFGVDGR
+VGLSEVLNGDVALQDVLIPVGEDGLLLLPAGRTPPNPSEQLGSERMRDLLTALAETHM--VLVDAPPVLPVTDSTLLATA
+VDGTVLVIRHGKTRKEHLEVARDMLAGVNARVLGVVLNGTPASGVGSDY-YGGGYGADGGSYDAYYQAPRDAPEA-AAGT
+A---GDTSRR---------------------------------------------------

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

@@ -0,0 +1,15 @@
+>0_153
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>0_1028
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>1_320
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>1_331
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>1_756
+MAAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>2_706
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>4_977
+MAAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+ 

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

@@ -0,0 +1,50 @@
+>0_154
+MSTPATRGRADGGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALL
+SDAGHMAADVVVLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVV
+EAISRLGDAPEVASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSV
+GVMVAGVLIILTGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGD
+LDAVEGVEEVHDLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQ
+VEGAGSDGCHDLSW
+>0_1027
+M-----------GAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALL
+SDAGHMAADVVVLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVV
+EAISRLGDAPEVASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSV
+GVMVAGVLIILTGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGD
+LDAVEGVEEVHDLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQ
+VEGAGSDGCHDLSW
+>1_319
+M-----------GAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALL
+SDAGHMAADVVVLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVV
+EAISRLGDAPEVASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSV
+GVMVAGVLIILTGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGD
+LDAVEGVEEVHDLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQ
+VEGAGSDGCHDLSW
+>1_332
+M-----------GAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALL
+SDAGHMAADVVVLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVV
+EAISRLGDAPEVASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSV
+GVMVAGVLIILTGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGD
+LDAVEGVEEVHDLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQ
+VEGAGSDGCHDLSW
+>1_755
+M-----------GAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALL
+SDAGHMAADVVVLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVV
+EAISRLGDAPEVASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSV
+GVMVAGVLIILTGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGD
+LDAVEGVEEVHDLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLHDRYGIAHATLQ
+VEGAGSDGCHDLSW
+>2_707
+M-----------GAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALL
+SDAGHMAADVVVLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVV
+EAISRLGDAPEVASGAMLAVGFAGLVINIISMLLLRSGTKDSLNVKGAYYEVIADAAGSV
+GVMVAGVLIILTGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGD
+LDAVEGVEEVHDLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQ
+VEGAGSDGCHDLSW
+>4_976
+M-----------GAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALL
+SDAGHMAADVVVLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVV
+EAISRLGDAPEVASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSV
+GVMVAGVLIILTGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGD
+LDAVEGVEEVHDLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQ
+VEGAGSDGCHDLSW
+ 

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

@@ -0,0 +1,29 @@
+>0_155
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARALYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>0_1026
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARALYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>1_318
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARALYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>1_333
+MSVTLLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARALYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>1_754
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARVLYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>2_708
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLADPRRARVLYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>4_975
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARVLYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+ 

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

@@ -0,0 +1,50 @@
+>0_1732
+MQPIDQTTSGPA-TSVGERPLAGIRVVSVAVNLPGPLAAARLAEFGAEVVKIEPPTGDPL
+AAAAPQWYAELIAGQRVLTLDLKTGPGQDHLATLLKGADLLLSSLRPSAADRLGLPASAH
+AA---GAVFLEVVGHDGDDADLPGHDLTYQAAAGTLDAPRM-----PLVPVADLLGGERA
+VSAALAALRSRDHGG---PVTRVRVTLEDAARAAAAPVRRGLLGPGGPLGGDLPTYSLYA
+SADGHVAVAAVEPHFAARLAEHIG-------STRDEIARTILTRPGAEWERIANELDLPL
+---AVVRPPR-
+>0_1986
+---------------MSAAPLAGVRVVTIALNLPGPAAAARLQELGADVVTVLPPSGDPV
+ATLVPALYEELHRGQSVRTVDMKSQAGVAEMEQILAEADVFLTSHRSGALRRLGLDADAV
+RARHRRICQVDITGYAGDRTDVPGHDINYQAAAGLLAPGAP-----PRILAADLHGAERA
+VSTALALLWARGADG---DGGHATVALAEAAHALALPNRHRMTDPRSPLGGALPHYGVYP
+AAEGHVAVGALEPHFAAALVEGLGLDADG--DVRAQLTEALSRHDAAHWQAWGEKRGIPL
+---TALVSPTA
+>1_1703
+---------------MSAAPLAGVRVVTIALNLPGPVAAARLQELGADIVTVLPPSGDPV
+ATLVPALYEELHRGQSVRTVDMKSQAGAAEMEQILAEADVFLTSHRSGALRRLGLDADAV
+RARHRRICQVDITGYDGDRTDVPGHDINYQAAAGLLAPGAP-----PRILAADLHGAERA
+VSAALALLWARGADG---DGGHATVALADAAHALALPNRHRMTGPRSPLGGALPHYGVYP
+AAEGHVAVGALEPHFAAALVEGLGLDADG--DVRAQLTEALSRHDAAHWQAWGEERGIPL
+---TALASPTA
+>2_1064
+MQPIDQTTSGPA-TSVGERPLAGIRVVSVAVNLPGPLAAARLAEFGAEVVKIEPPTGDPL
+AAAAPQWYAELIAGQRVLTLDLKTGPGQDHLATLLEGADLLLSSLRPSAADRLGLPASAH
+AA---GAVFLEVVGHDGDDADLPGHDLTYQAAAGTLDAPRM-----PLVPVADLLGGERA
+VSAALAALRSRDHGG---PATRVRVTLEDAARAAAAPVRRGLLGPGGPLGGDLPTYSLYA
+SADGHVAVAAVEPHFAARLAEHIG-------STRDEIARTILTRPGAEWERIANELDLPL
+---AVVRPPR-
+>3_715
+MSAGDGASRVPAGDAVVPGPLADVAVVTIALNLPGPLAAFRLAELGAQVTTVLPPAGDPV
+ATLVPALYTELHAGMAELTLDLKQDGDRARMEELLAGADVLLTSHRSGALTRLGLDAAAT
+ARRHPRLVQVDITGFPGERADVPGHDLNYQAEAGLLEPGHP-----PRGLLADVHGAERA
+VSAALAGLHARDRDG---RGGGVVVALSDAAHAMALPTRHGMTDPGSPLGGANPFYGVYP
+ARSGHVALGALEPHFAHAMVEALQLDPDG--DVRAQLTAAFAERDADAWQSWGEEWGHPI
+---TALAGPTA
+>3_725
+------------------------------------------------------------
+------------------------------------------------------------
+---------MDVVGFAGERAGVPGHDLTYQAETGLLLSGESQTPTLPRALVADMHGAEQA
+VSTAPALLLARDRAGRDAPGGHARVSLAEAAAAVGIPSRHGLLAPDALLGGGTPYYAVYR
+AAEGHVAVGALEPHFSDALRAELDLPAGAGDDLAAALSAALTARPARDWQEWGEERGIPT
+GRGAVNGQPR-
+>4_1921
+---------------MSAAPLAGVRVVTIALNLPGPAAAARLQELGADVVTVLPPSGDPV
+ATLVPALYEELHRGQSVRTVDMKSQAGVAEMEQILAEADVFLTSHRSGALRRLGLDADAV
+RARHRRICQVDITGYAGDRTDVPGHDINYQAAAGLLAPGAP-----PRILAADLHGAERA
+VSTALALLWARGADG---DGGHATVALAEAAHALALPNRHRMTDPRSPLGGALPHYGVYP
+AAEGHVAVGALEPHFAAALVEGLGLDADG--DVRAQLTEALSRHDAAHWQAWGEKRGIPL
+---TALASPTA
+ 

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

@@ -0,0 +1,70 @@
+>1_1646
+--------------------------------------------------------------------------------
+------------------------------MEHATALENVMLPLRYGPDRVPRGEQRRRAGEALERVGLGMRTGHRARTL
+SGGEKQRVAVARALINEPPLVLADEPTGALDQARTRDVVD-LLRGAVGPERAVVVVTHDPRVAAACDRRWHLVDGELAPQ
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------D
+>2_836
+MT-------LLEVHDVDKTFHSG-GEAVPVLRGASLLVPAGEMHAVTGPSGSGKSTLLRILACLDSPDSGRVLLGGEP--
+----LPEPWSRGGDRYRNQRCGIVLQDFALMEHATALENVMLPLRYGPDRVPRGEQRRRAGEALERVGLGTRTGHRARTL
+SGGEKQRVAVARALINEPPLVLADEPTGALDQERTRDVVD-LLRGAVGPERAVVVVTHDPRVAAACDRRWHLVDGGLAPQ
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------D
+>2_989
+MSDGS-APPLLELAGVLKSFK---GADRPALDGVDLTVRDGDFVAIVGPSGSGKSTLLNVLGLLDRPDGGSYRVSGTD--
+----TMSMGERERDRLRSRWFGFVFQSSHALGDEPVAVNAALGLRVQRTPPEQRDAR--AGEALALLGLSHRLDTRAKLL
+SGGERQRLAIARAIATRPRVILADEPTGNLDSVNSRIVID-HLRALHAQGATVLLITHDPEIARQADRQVRIEDGRITEL
+AGHRTAASASADMAGTGHGWSAPGAARRHRSPRSSAMLDDLVEAVSSLSTRFLRTVLLMAAFAVGIGGLVASVGLTQTAT
+DQVGALLTAAALDEVVVTVPQAEGLLDPGDGRLASWADGLAALPHVTAAGHVAQVAPADVVITRHDPSDPEPAVAISLVA
+ASSSYAGLAGLTLPSETSRTLLDSPDARLAWATPAAARALELPVTDTGMLSPGYRVWIQGHAVDVAGIVTLSERTPELDA
+SLVVTPAVMTGVAQAHPQLVVRTEAGFPYPVSQAAPLVIAPENPGSVTVRTVADLRNLRAGVSDDLGAFVGVLSGVLLVL
+AVISASTAMYLSVQARTAEIALRRAIGSPRGLIARLFLLEGALIGLAGGAVGAAVGSGVILAVSQARGWAAVLPPGAVPL
+ALGLGLVAGVVSALYPGWVASRQRPADALRG
+>3_774
+MS-------LLEVHDVDKSFTTA-ASEVPVLRGVSLSVPAGQMHAVTGPSGSGKSTLLRILACLDSPDAGEVLLEGVP--
+----LPPPWSRGGDRHRNRRCGIVLQDFALMEHATALDNVLLPLRYGPGGGSRAEQRRRAALALDRVGLADRAHHRARTL
+SGGEKQRVAVARALINDPPLVLADEPTGALDQARTRDVVK-LLRSAVGPQRAVVVVTHDPEVAAACDQRWHLEDGRLHSQ
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------G
+>3_851
+MTA---SAPVLTLDRVQVGYRHPDGGTRVLIESLDLTLAPGEVVGLWGRSGTGKSSLIRHLAGLSRPLAGRIAYRSPDGS
+LNGEVADLSAGDLARYRREHLGYVDQSCELIGELSALDNAAVWIHGGRIAGSACDAQETVQGLLERLGLGHRLGAPASRL
+SGGEAQRVALVRALSKRPHLIVADEPTGHLDGVTAREAIA-LLREHAEAGAAVLVASHDPLVHAAVDRAVRVGED-----
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-------------------------------
+>3_923
+MNTAPLTPPVLAARGLTKAY-----GSTHALTGVDLEIRPGESVAVMGPSGSGKTTLLHVLSGIIAPDGGRVTLAGADGT
+VH-EVTALTEEQRARLRRERLGFVFQEGLLLPELTAVENVAMPLMLN--GVDRRAAEQTAARWLGSLGLAGMEDRRPGEL
+SGGQRQRVAIARAQAVEPDVVFADEPTGALDSDTSEAVLDSLIASTVARGRTLVVVTHDPSVAAACSRLIRVRDGRIESD
+QAQAAAGTTREQV-------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------R
+>4_708
+MS-------LLTVHDVHRSYRGP-AGDVPVLRGVSLQVPGGGVHAIMGPSGSGKSTLLRLLACLDTPDAGSIRVAGRS--
+----LPAPWSSDGDAYRNRTCGIVLQDHLLIDRATAVDNAALPLLYARPRTSKRERRTMAAELLTRLGLGDRLHHPVGRL
+SGGERQRVAIARAVIMGPSLLLADEPTGALDEERTDEVMG-LFRSMSQPERAIVVVTHDPAVAARCDHTWRLRAGRLE--
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-------------------------------

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

@@ -0,0 +1,43 @@
+>0_22
+MERGPVVGLLDNLERGLERAVRSAFSAGGPRAVKPVEIASALRQAMDDESIALSEGHTVA
+PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRGGD
+LRVVTRLDDGSLTAPAPHDDGASPATAHGPGATAPAPDRLVEDPPAAAPRE---PSPAPR
+VGPRPAPRRA------AAPAAPAAPSHADQPTVVMGRPVT-EPAGPALELDGRMLPLDGD
+DLILGRSAERADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRD
+GDVVTVGQTELLFFGG-TGGR--A
+>1_1991
+MERGPVVGLLDNLERGLERVVRSAFSAGGPRAVKPVEIASALRQAMDDESLALSEGHTVA
+PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRAGD
+LRVVTRLDDGSLTAPAPHDDGASPATAHGPGASAAAPDRLVEDLPAAAPRE---PSPAPR
+VGPRPAPRRAAAPAAPAAPAAPAAPAHADQPTVVMGRPVT-GPAGPALELDGRMLPLDGD
+DLILGRSAERADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRD
+GDVVTVGQTELLFFGG-TGGR--A
+>2_354
+MERGPVVGLLDNLERGLERAVRSAFSAGGPRAVKPVEIASALRQAMDDESFALSEGHTVA
+PNSYVVHFSPADFDRARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDTDVRAGD
+LRVVTGLDDGSLPAPAPHDDGASPATAHGPGATATAPDRLVEDL----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------LGGRT-P
+>2_355
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------MGRPVT-EPSGPALELDGRMLPLDGD
+DLILGRSAERADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRD
+GDVVTVGQTELLFFSG-TGGR--A
+>3_338
+------MGLLDNLERGLEKAVRSAFSAGGARAVQPVEIASALRHAMDDESFALSEGHTVA
+PNDFTVHFAPADFDRARTWGSTLAGELCDEVIRHAQSQGYTLPGSVRVAFHEDAQVHAGQ
+VEVDARIDDGSSPVPSPPAATSAPA----PAAARTADDR--GPRPSRAPRHGATAAPAPR
+RDPSPAPRPAPTPA--RSESARRAPAD-EQATVVMPRRTSPAPAVPWLEADGVRHPLTHE
+DMVLGRSSERADVVVPDSSVSRQHARLVRVGRSVTLIDLGSRNGVTVNGRRVDGSTVLRE
+GDRITVGQTDLVFHIDPADGRPRA
+>4_22
+MERGPVVGLLDNLERGLERVVRSAFSAGGPRAVKPVEIASALRQAMDDESFALSEGHTVA
+PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRAGD
+LRVVTRLDDGSLTAPAPHDDGASPATAHGPGASAAAPDRLVEDLPAAAPRK---PSPAPR
+VGPRPAPRRA------AAPTAPAAPAHADQPTVVMGRPVA-EPAGPALELDGRMLPLDGD
+DLILGRSAERADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRD
+GDVVTVGQTELLFFGG-TGGR--A
+ 

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

@@ -0,0 +1,49 @@
+>0_45
+MQRIHD-PQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHF-GE
+DATVWPMFNGTGANVVGLQAMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDG
+KLTPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPDEVKAITDYAHEHGMRVYMDG
+ARIANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAAD----------
+--------------GLVYLRKNQMQLASKMRFVSAQLLALFDGDLYLRSARHANAMAARL
+RAGIEAGVADGSLAGVEFTQATDANAVFAVLPEGVADRLRARFRFYDWDAARREVRWVCG
+FDTTEEDVDAFTAALRAELVPA--A
+>1_2009
+MQRIHD-PQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHF-GE
+DATVWPMFNGTGANVVGLQAMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDG
+KLTPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPEEVKAITDYAHEHGMRVYMDG
+ARIANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAAD----------
+--------------GLVYLRKNQMQLASKMRFVSAQLLALFDGDLYLRSARHANAMAARL
+RAGIEAGVADGSLAGVEFTQATDANAVFAVLPEGVADRLRTRFRFYDWDAARREVRWVCG
+FDTTEEDVDAFTAALRAELVPA--A
+>2_339
+MQQIHD-PASRGFASDNYSGVHPEVLAAIAEANGGHQTAYGEDAYTGRLAEVVRGHF-GE
+DAQVWPMFNGTGANVVALQSMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLTVPTPDG
+KLTPELIDVQAWGWGDEHRAQPLVVAITQSTELGTLYTPEEIRAITEHAHARGMTVFLDG
+ARLANAAAALDLPLRAFTTDVGVDVLSLGGTKNGALGAEAVVALNPAATT----------
+--------------GMTYLRKSQMQLASKMRFVSAQLLALFDGDLYLRTARHANAMAQRL
+QDAVAAGIADGSLPGVALTQRAQVNAVFATLPAGVADRLRRSFRFYDWDEANGEVRWVCS
+FDTAEEDVDAFVAALRAELAPA--D
+>2_1578
+MSAGAPAAGLRAFASDNYAGVHPDVWAALADVDAHHAPAYGADPHTERLQEAVREAFDAP
+DAVALPVFNGTGANVVALQSMLPPWGAVVAADTSHIHHDEGGAPERMGRTKLFTVPTPDG
+RLTPELVDREAHGWGFVHRAQPAVVEIAQVTELGTVYTPEQVRALADHAHGHGMGLYMDG
+ARLFNAAAALELPLSAFTTHAGVHVVSLGGTKAGALGAEAVVVLRPEAVTLASLVPERDL
+PAD--AGPRERARLAVEYVRKSSMQLASKMRYVSAQLTALLKGDLGIRLAGHANAMAREL
+AGRV-AGI-----DGVEVTRTPEANAVFAVLDPQAADRARVRHPFYDWDAARHEVRWMTS
+WDTTAADVDSFAAALGEALSPGRRR
+>3_1473
+MSAARP-AGLRAFASDNYAGVHPDVWAAMADADADHAVSYGEDPTSAALQEKVREVF-GE
+RAFAVPVFTGTAANVLALQALTPPWGSVVTAASSHLIHDEGGAPERLGRTPLVPVPTPDG
+RLTGELAAAHVRRDGFVHASQPAVVEIAQATELGTVYSAAQVREVADAAHAAGAALYMDG
+ARLSNAAAALDLPLRAFTTDAGVDVVSYGGTKNGGLGAEAVIVLNPEAVVAARMVGPADV
+PGGDAADARDRARAALGYLRKQDMQLASKHRYLAAQLLALLTDDLGIALAAQANRMARVL
+ADAV-AGL-----DDVELARAPEANAVFARLDPDVAAEVRLRHPFYDWDAAAHEVRWMTS
+WDTTDADVESFVDALAAALRARRPR
+>4_40
+MQRIHD-PQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHF-GK
+DATAWPMFNGTGANVVGLQTMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDG
+KLTPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPDEVKAITDYAHEHGMRVYMDG
+ARIANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAAD----------
+--------------GLVYLRKNQMQLASKMRFISAQLLALFDGDLYLRSARHANAMAARL
+RAGIEAGVADGSLAGVEFTQATDANAVFAVLPEGVADRLRARFRFYDWDAARREVRWVCG
+FDTTEEDVDAFTAALRAELVPA--V
+ 

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

@@ -0,0 +1,31 @@
+>0_64
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+YLPGFDLVPGCVVEARPIGVFNMTDDGGGDAKLLCVPA-DKRYDHITELEHVEESLKQEI
+EHFFTRYKDLEPGKWVKAEGWEGRAAAEAELEASIQRFDAEGEESPTDEPQGRAVDTEEA
+QPATEEGEATDEPQGR
+>1_2028
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+YLPGFDLVPGCVVEARPVGVFNMTDDGGGDAKLLCVPA-DKRYDHITELEHVEESLKQEI
+EHFFTRYKDLEPGKWVKAEGWEGRAAAEAELEASIQRFNAEGEESPTDEPQGRAVDTEEA
+QPATEEGEATDEPQGR
+>2_311
+MPHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDAMV
+LLPGFDLVPGCVVEARPVGVFNMTDDGGGDAKLLCVPA-DKRFDHITELEHIEESLKQEI
+EHFFTRYKDLEPGKWVKAEGWQGRADAEAELEASIARFDAAGEHSPTDEPQGRDVETEDP
+SPATEEGEEKDVPQGR
+>3_252
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+FLPGFDLVPGCIVEARPVGVFNMTDDGGGDAKLLCVPA-DKRFDHIQELEDVEESLKQEI
+EHFFTRYKDLEPGKWVKADGWEGREAAEKELEASIERFAAEGEHSPSDEPQGRDVDTEEA
+APAAEQEA--------
+>3_667
+MLFDVTIEIPRGSGNKYEVDHTTGRIRLDRAVFTSMVFPQDYGSIDNTLGDDGDPLDALV
+LLPR-PTFPGVVITVRPVGMLRMVDENGGDDKILTVPAGDDRFAQLRDITDVPEHTLAEI
+EHFFAHYKEIEHGKHVTTNGWADRAAAEAVIRTA--------QNAHTRHP----------
+----------------
+>4_58
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+YLPGFDLVPGCVVEARPIGVFNMTDDGGGDAKLLCVPA-DKRYDHITELEHVEESLKQEI
+EHFFTRYKDLEPGKWVKAEGWEGRAAAEAELEASIQRFDAQGEESPTDEPQGRDVDTEEA
+QPATEEGE----PQGR
+ 

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

@@ -0,0 +1,43 @@
+>0_72
+MDESIDAAAREANRALLGRLPADRTLVMGILNVTPDSFSDGGEHATVRAAVEHARRMVAD
+GADIVDVGGESTRPGARAVPPAEEQERILPVIEALLAEDVVLSVDTRHTATARAALALGP
+VIVNDVSGLAHEPDMPALIAASGAPYILMHN--RGNPQTMDGLAVYEDTVPDVVCELRDV
+AGRFLAAGVEPAQLIVDPGLGF--AKAGEQNWELLRGLEWLR-AMGHPVLVAASRKRFLG
+TLLADDDGTPAPPAARDAATAAISA--LAAAQGAWGVRVH---DVRASADAVRTAAAWAG
+A----HAPGEPVSEDVLP
+>1_2036
+MDESIDAAAREANRALLGRLPAGRTLVMGILNVTPDSFSDGGEHATVRAAVEHARRMVAD
+GADIVDVGGESTRPGARAVPPAEEQERILPVIEALLAEDVVLSVDTRHTATARAALALGP
+VIVNDVSGLAHEPDMPALIAASGAPYILMHN--RGNPQTMDGLAVYEDTVPDVVCELRDV
+AGRFLAAGVEPAQLIVDPGLGF--AKAGEQNWELLRGLEWLR-AMGHPVLVAASRKRFLG
+TLLADDDGTPAPPAARDAATAAISA--LAAAQGAWGVRVH---DVRASADAVRAAAAWVG
+A----HAPGEPVSEDVLP
+>2_302
+MDESIDAAAREANRALLGRLPADRTLVMGILNVTPDSFSDGGEHATVRAAVEHARRMVAD
+GADIVDVGGESTRSGARAVPPAEEQARILPVIEALLAEDVVVSVDTRHTATARAALALGP
+VIVNDVSGLVHEPEMPALIAASGAPYILMHN--RGNPQTMDGLAVYEDTVPDVVCELRDV
+AGRLLAAGVEPAQLIVDPGLGF--AKAGEQNWELLRGLEWLR-AMGHPVLVAASRKRFLG
+TLLADDDGAPAPPAARDAATAAISA--LAAAQGAWGVRVH---DVRASADAVRTAAAWVG
+A----HAPGEPVSEDVLP
+>2_2287
+M------------------LR-SRVTVFGILNLTEDSFFDESRRLDPAGAVTAAIEMLRV
+GSDVVDVGPAASHPDARPVSPADEIRRIAPLLDALSDQMHRVSIDSFQPETQRYALKRGV
+GYLNDIQGF-PDPALYPDIAEADCRLVVMHSAQRDGIATRTGHLRPEDALDEIVRFFEAR
+VSALRRSGVAADRLILDPGMGFFLSPAPETSLHVLSNLQKLKSALGLPLLVSVSRKSFLG
+ATV----GLP----VKDLGPASLAAELHAIGNGADYVRTHAPGDLRSAITFSETLAKFRS
+RDARDRGLDHA-------
+>3_244
+M---LPKPFHE--------LP-DRTLVMGILNVTPDSFSDGGAHDRVDAAVAHGLDLLAQ
+GADLIDVGGESTRTGATPVDPAEEQRRILPVVEALLAEGAVLSIDTMHTATARACLALGP
+VIVNDVSGLVHEPDMPALVAESGAPCILMHN--RGHAQVMDSLAHYEDTLGEVVRELSEV
+TDRFLAAGASPEQIILDPGLGF--AKAGEQNWELLRGLERIE-SLGRPVLVAASRKRFLG
+TVLAGEDGTPRPALDRDHATAAVSA--ISAAHGAWGVRVH---DVRSSVDAVRVGDAWRG
+AAPRPAGPGEARA-----
+>4_66
+MDESIDAAAREANRALLGRLPADRTLVMGILNVTPDSFSDGGEHATVRAAVEHARRMVAD
+GADIVDVGGESTRPGARAVPPAEEQERILPVIEALLAEDVVLSVDTRHTATARAALALGP
+VIVNDVSGLAHEPDMPALIAASGAPYILMHN--RGNPQTMDGLAVYEDTVPDVVCELRDV
+AGRFLAAGVEPAQLIVDPGLGF--AKAGEQNWELLRGLEWLR-AMGHPVLVAASRKRFLG
+TLLADDDGTPAPPAARDAATAAISA--LAAAQGAWGVRVH---DVRASADAVRTAAAWAG
+A----HAPGEPVSEDVLP
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000066.fa

@@ -0,0 +1,49 @@
+>0_190
+MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG
+PRGWAAVVGLGAAMTGMNLAIYEA--FARIPQGVAVTFEVLGPLALSVAAR---PSWRSA
+AW---AALALAGIGVLGREGFSADGGIGGAGLDPVGVALALAAAACWAGYILLSR---RA
+GTHLPGVQGLALATAAGSLVALPVGVATAGAALLSPVVLGVGLAVALLSTAVPYGIDLQV
+LRRMPTALFSLLTCLSPIAAALTAWAVRGQELTPLDLAGMLLV-----IAACAAAVWTS-
+---------------------RSPGVA---GGGRG-------------------------
+----------------------------------------------
+>1_1974
+M-----------------------------------------------------------
+------------AVAVYPLAFYTSIHWAGVAIGSVVSLAS-APLASGLLERIVEYRRLSR
+WWMLAAALGGTGAALLCLSQLDQ--EAASSTATLAGVLLGLVAGATYATYSWAAHRLIHD
+GISRAASMGAVFG--AGGALLLPVLVLTGAPLIATPQAFAVAAYMALVPMFLGYVLFGYG
+LTRVPASTATTITLTEPAIAAILAVAVVGERLTPVGWTGLGIIAAVLFILALTPTNTTAD
+RHGRTPTSEAIQPALAPSPRRHNERTSPRDDAGRGSDVMWVSQTMRCQGATRPSRWEGVR
+GRFRKPYRLRPVSPDHGRATCGERTEIMRPARGLDARSVLAATMET
+>1_2137
+MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG
+PRGWAAVVGLGAAMTGMNLAIYEA--FARIPQGVAVTFEVLGPLALSVAAR---PSWRSA
+AW---AALALAGIGVLGREGFSADGRIGGAGLDPVGVALALAAAACWAAYILLSQ---RA
+GTHLPGVQGLALATAAGSLVALPVGVATAGAALLSPVVLGVGLAVALLSTAVPYGIDLQV
+LRRMPTALFSLLTCLSPIAAALTAWAVRGQQLTPLDLAGMLLV-----IAACAAAVWTS-
+---------------------RSPGVS---GGARG-------------------------
+----------------------------------------------
+>2_187
+MRLIPLVLLSLLCQQLGASVAGLMFGTTGPAGMVALRLAFSALVLLVLTRPRMRTLAGLS
+RRGWVAVVMLGVTMAGMNLLIYAA--FDRIPQGVAVTFEVLGPLALSVLAN---RRWLSV
+VW---AALAFAGIALLGRDGFSA--GMDGAGLDPLGVAFALAAAACWAGFILANR---HA
+GTHLPGVQGLALAMVVGSAVAVPVGAADAGPVLLEPWVLAVGLGVALLSSSIPYGIEMQV
+LRTMPTGLFSLITCLSPVVAALTAWAVRGQRLAVLDLGGMGLV-----VLACGAAVWAAE
+RAAR--------------PSRRAPRTS---------------------------------
+----------------------------------------------
+>3_139
+MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG
+PRGWAAVVGLGAAMTGMNLAIYEA--FARIPQGVAVTFEVLGPLALSVAAR---PSWRSA
+AW---AALALAGIGVLGREGFSADGGIGGAGLDPVGVALALAAAACWAAYILLSR---RA
+GTHLPGVQGLALATAAGSLVALPVGVATAGAALLSPVVLGVGLAVALLSTAVPYGIDLQV
+LRRMPTALFSLLTCLSPIAAALTAWAVRGQELTPLDLAGMLLV-----IAACAAAVWTS-
+---------------------RSPGVA---GGGRG-------------------------
+----------------------------------------------
+>4_190
+MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG
+PRGWAAVVGLGAAMTGMNLAIYEA--FARIPQGVAVTFEVLGPLALSVAAR---PSWRSA
+AW---AALALVGIGVLGREGFSADGGIGGAGLDPVGVALALAAAACWAAYILLSR---RA
+GTHLPGVQGLALATAAGSLVALPVGVATAGTALLSPVVLGVGLAVALLSTAVPYGIDLQV
+LRHMPTALFSLLTCLSPIAAALTAWAVRGQELTPLDLAGMLLV-----IAACAAAVWTG-
+---------------------RSPGVA---GGGRS-------------------------
+----------------------------------------------
+ 

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

@@ -0,0 +1,37 @@
+>0_249
+M-------------------------------------------------------SEEL
+RILIADDQPLMSGALRVLVDSAPGMTCVGVVANGVEAVEACAAIEPDVVLMDMQMPLMDG
+MEATRRIKDTHPAIRVLAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIQAVHRGE
+SVLSPAVATKLLASIERDRPTVGPTSVQPGSPDG--SDLTERELGVLRLLARGQSNPEIA
+ANLFVSESTVKANLTRIMAKLEVRDRVQLIIRAAQLGLVTLALD
+>1_2214
+M-------------------------------------------------------SEEL
+RILIADDQPLMSGALRVLVASAPGMTCVGVVANGVEAVEACAAVEPDVVLMDMQMPLMDG
+VEATRRIKEAHPEVRVLAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIQAVHRGE
+SVLSPAVATKLLASIERDRPTVGPTSVQPGSPDG--SDLTERELGVLRLLARGQSNPEIA
+ANLFVSESTVKANLTRIMAKLEVRDRVQLIIRAAQLGLVTLALD
+>2_102
+MHDAGHTDYSAAHIARTADGTAASGAVSAGPGGRRPGPTTPADAGRSRGSRYADRVSEDL
+RILIADDQPLMSGALRVLVSSAPGMTCVGVVANGAEAVEACAAVEPDVVLMDMQMPLMDG
+VEATSRIKEAHPGIRILAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIHAVHRGE
+SVLSPAVASKLLASIERDHPVVGPAQARPGDPDG--SDLTDRERDVLRLLARGQSNPEIA
+ANLHVSESTIKSNLTRIMDKLEVRDRVQVIIRAAQLGLVTLSLD
+>3_70
+M---------------------------------------------------PDSPEDEI
+RVLIADDQPLMSGALRVLVDSAPGMRCVGLVADGVEAVEAVEATRVDVVLMDMQMPRMDG
+VEATRRITASRPGTRVLAVTTFSSEDYLVPALRAGAAGYLLKDAEPATVLGAVEAVRRGE
+SVLSPAVAAKLIAAVERDHPVVGPAAAEPGDPDG--SDLTEREHQVLTLLARGRSNPEIA
+AELQVSESTVKANVGRVIDKLEVRDRVQVVIRAAQLGLVTLSLD
+>3_509
+M--------------------------------------------------------DAI
+TVLIVEDEPLLTQAYTMILEADPGIRVVGTASDGAAGVAEHERLRPDVVLMDLRMPVLDG
+VEATGRIMREHPEAKVLVVTSMTTEDYLSPALANGAAGYLTKDTDAEGLVRAVRAVEAGT
+MALGPSIAREVVDLLLRSG--VAPRTDAPASPRDLPEALTPREQDVLELLAEGLTNQEMA
+ARLYVSDSTVKSNLARVMHKLGANNRVQALVLGVRAGLVSIP-G
+>4_248
+M-------------------------------------------------------SEEL
+RILIADDQPLMSGALRVLVDSAPGMTCVGVVANGVEAVEACAAIEPDVVLMDMQMPLMDG
+VEATRRIKDTHPAIRVLAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIQAVHRGE
+SVLSPAVATKLLASIERDRPTVGPTSVQPGSPDG--SDLTERELGVLRLLARGQSNPEIA
+ANLFVSESTVKANLTRIMAKLEVRDRVQLIIRAAQLGLVTLALD
+ 

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

@@ -0,0 +1,37 @@
+>0_304
+MANTTYTLVLLRHGQSEWNEKNLFTGWVDVPLTEKGRAEAARGGELLEAEGIRPDVVHTS
+LLKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMVWRRS
+-FDTPPP-------ALDDDSEFSQVGDERYADLGKDAPRTEALKQVVDRLLPYWEEQVLP
+DLKAGKTVLIAAHGNSLRALVKHLDGISDEDITGLNIPTGIPLVYELDQNFKPITANGRY
+LDPEAAAAGAAAVAAQGSAH
+>1_28
+MANTTYTLVLLRHGQSEWNEKNLFTGWVDVPLTEKGRAEAARGGELLEAEGIRPDVVHTS
+LLKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMVWRRS
+-FDTPPP-------ALDDDSEFSQIGDERYADLGKDAPRTEALKQVIDRLLPYWEEQILP
+DLKAGKTVLIAAHGNSLRALVKHLDGISDEDIAGLNIPTGIPLVYELDQNFKPITANGRY
+LDPEAAAAGAAAVAAQGSAH
+>2_15
+MANTTYTLVLLRHGQSDWNEKNLFTGWVDVPLTEKGRAEASRGGELMKAEGIHPDVLHTS
+LLKRAITTANLALETADRQWIPVKRDWRLNERHYGALQGKDKAQVKEEFGEEQFTVWRRS
+-FDTPPP-------ALDDSSEFSQIGDERYAELGDDAPRTEALKNVIDRLIPYWEAEIVP
+DLKASKTVLVAAHGNSLRALVKHLDGISDEDIAGLNIPTGIPLVYELDEDLKPITANGRY
+LDPEAAAAGAAAVAAQGSAH
+>3_11
+MAD-TFKLILLRHGQSDWNEKNLFTGWVDVPLTEKGRAEASRGGELLAAEGLLPDVLHTS
+LLKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMTWRRS
+-FDVPPP-------PLDDSSEFSQAGDERYRDIGPDAPRTEALKQVIDRLLPYWTEQIVP
+DLKAGKTVMVAAHGNSLRALVKHLDGISDEEISGLNIPTGIPLFYELDQNLKPVTPHGRY
+LDPEAAAAGAAAVAAQGDKK
+>3_670
+M------LTLLRHGESTANEAGTFTGLLDVPLTHRGERQASAAGQLLRSNHITPDVVVTS
+TLRRAVRTAELVCDALGTQ-LPTEAVWQLNERNYGALTGMTKTDARRMLGDDEYVRLRRS
+RTGTPPPMSLHLWEELRSSSALRGLPDGALR-------RTEALSDVIKRVRPVLHDRLLP
+MVRSGRSVLVVAHGNSLRALCACIDDLTDPELEQLNLPTGQPVQYHLAPTGALVPRGGAF
+LDPVAAQHAAALVAAEGGT-
+>4_311
+MANTTYTLVLLRHGQSEWNEKNLFTGWVDVPLTEKGRAEAARGGELLAAEGIRPDVVHTS
+LLKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMVWRRS
+-FDTPPP-------ALDDDSEFSQVGDERYADLGKDAPRTEALKQVIDRLLPYWEEQVLP
+DLKAGKTVLIAAHGNSLRALVKHLDGISDEDIAGLNIPTGIPLVYELDQNFKPITANGRY
+LDPEAAAAGAAAVAAQGSAH
+ 

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

@@ -0,0 +1,60 @@
+>0_402
+MPSPTTTTAPGPAS-------------PAGPLRPPHTAAESAERVKRRGALYFAEHQLRNMRRYGAVLIVGALGEPVLYL
+LAMGLGLAQLMGGGMPQDALGGVSYVAFIAPALLASGALMTASVEFSYPVMGGFQWHRTYYAAQATPLSPAQIALGHLAA
+VSLRFVFQAAVFLLVMLAFGVVSSPWAWVQVLTATLGGLAVGAPIMAFAASLKEDKGQFATLQRLVVMPLFLFSATFYPL
+DVLPVWLRWIGWLSPQWHAAQLGRMLSYGMAEPAWLTVAHVAFLLALALGGARLAVRIYTRRLGWVRGTPDRDAGTAARR
+DRAPRLGRRAPRLGRRAARTGAARADVAPAAAQADPAAPSSSVVREHAVAVPPLPEIPVRRGPLAGAYSGNVRAVMERAF
+LSLKSNNWVVFFSGFFEPVLYLASLGLGLGALVGDVAGPDGTPVPYGMYLAPALLAVSAMNGAIYDSTWNVFFKLRYAKT
+YQTMLSTRLGPLDVALGEIAMALLRGLIYAVGFLIVMTVAGLVTSWTALLMIPGALLVALGFASLGMAVTSWMKTFQHMD
+WVQIVLMPMFLFSATFFPLAVYPEPIQWVIRVFPLWHAVEMMRALAVGVLSWATAGHVLYFVVMAGVGVWLAARRLGALF
+LR
+>1_132
+MPSPTTTTTPGPAS-------------PAEPLRPPVTAAASAERVKRRGVLLYAEHQLRSMRRYGAVLLVGALGEPVLYL
+LAMGLGLAQLMGGGMPQDALGGVSYVAFIAPALLASGALMTASVEFSYPVMGGFQWQRTYYAAQVTPLSPAQIALGHLVA
+VSLRFVFQAAVFLLVMLAFGVVSSPWAWVQVLTATLGGLAVGAPIMAFAASLREDKGQFATLQRLVVMPLFLFSATFYPL
+EALPVWLRWIGWLSPQWHAAQLGRVLSYGMAEPVWLTVVHVAFLLALALGGAWLAVRIYTRRLGWVRGTPDRDAVTVARR
+D-------RAPRLGCRAARTGAARADVAPAAAQADPAAPSSSVVREHAVAVPPLPEIPVRRGPLAGAYSGNVRAVMERAF
+LSLKSNNWVVFFSGFFEPVLYLASLGLGLGALVGDVAGPDGTPVPYGMYLAPALLAVSAMNGAIYDSTWNVFFKLRYAKT
+YQTMLSTRLGPLDVALGEIAMALLRGLIYAVGFLIVMTVAGLVTSWTALLMIPGALLVALGFASLGMAVTSWMKTFQHMD
+WVQIVLMPMFLFSATFFPLAVYPEPIQWVIRVFPLWHAVEMMRALAVGVLSWATAGHVLYFVVMAGIGVWLAARRLGALF
+LR
+>2_2478
+--------------------------------------------------------------------------------
+---------------------------------------MT---------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-----------------------------AAAGAEPAAPSSSVVLEHTAAVPPMPEITLRHGPLAGMYAGNVRAVMERAF
+LTLKSNNWVVFASGFFEPVLYLASMGIGLGALVGDVAGPDGTPIPYGMFIAPALLAVSAMNGAIYDSTWNVFFKLRHAKT
+YQTMLSTKLGPLDVALGEIVMALLRGLIYAVGFLIVMTVGGLVTSWTAVLMVPGALLVALGFASLGMAVTSYLKTFQHMD
+WIQIVLMPMFLFSATFFPLSVYPQAIQWVIQVLPLWHAVELMRALAVGVVTWGTAGHILYFVAMSAVGIWFTSRRLGALF
+LR
+>2_2479
+MDASTTTTAPGPAAP-------RASA-SPAPLSPPISAAESAERVTRRGALYYAEHQLRNMRRYGSVLIVGALGEPIVYL
+LAMGLGLAQLMGGGAAQEGLGGVSYVAFLAPALLASGALMTAAVEFSYPVMGGFQWQKTYYAAQATPLTPAQIAVGHLGA
+VSLRFLFQGLVFFLVMLAFGVVHSPWGWLQILTATLGGLAIGAPIMAFAASLTEDKGQFATVQRLVIMPLFLFSATFYPL
+EALPVWLRWIGWISPQWHAAQLGRVLSYGMAEPVWLTVLHVVVLVAMAAVGTWLAVRIYTRRLGWRRGTPDRDALARP--
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--
+>3_2349
+------MAAQIPAS---------------APLQPPITAAESAVRVKARGAWFYAEHVLRSMRRYGAVLIVGALGEPILYL
+LAMGLGMAQVMGGGAPQESLGGVSYVTFLAPALLASGALMTAATEFSYPVMGGFQWHRTYYAAQATPLSPAQIAVGHLGA
+VALRFLFQAAVFFGVMLAFGVVHGPWGWVQVLTAALGGLAIGAPIMAFSASLKEDHGQFATLQRLVIMPLFLFSATFYPL
+EALPVWLRWVGWISPQWHAAQLGRVLSYGMAEPRWLTVLHVAVLLALAFGGAWAAVRMYTRRLGWRPGTPDRDAVARPRA
+Q-------RASRLGRRATRVDRM------AGAHAE-AAAASSVVREHTAAVPPMPEITVRRGRLGGLYSGNVAAVMERAL
+LTLKSNNWVVFASGFFEPVLYLASMGLGLGALVGAVPGPGGAPIPYGMYIAPALLAVSAMNGAIYDSTWNVFFKLRYAKT
+YQTMLATRLGPLDVALGEIAMALLRGLLYAVGFLVVMAVAGMATSWTALLMVPGALLVALGFASLGMAVTSWMKTFQQMD
+WIQLVLMPMFLFSATFFPLTVYPEPIQWLIRVFPLWHAVEMMRALAVGAVTGATAGHALYFGVMSGLGVWLTSRRLRALF
+LR
+>4_405
+MPSPTTTTTPGPASPGPRSGTSAPSATPAEPLRPPVTAAESAERVRRRGVLLYAEHQLRSMRRYGAVLLVGALGEPVLYL
+LAMGLGLAQLMGGGMPQDALGGVSYVAFIAPALLASGALMTASVEFSYPVMGGFQWQRTYYAAQATPLSPAQIALGHLVA
+VSLRFVFQATVFLLVMLAFGVVSSPWAWVQVLTATLGGLAVGAPIMAFAASLKEDKGQFATLQRLVVMPLFLFSATFYPL
+EALPVWLRWIGWLSPQWHAAQLGRVLSYGMAEPAWLTVVHVAFLLALALGGAWFAVRIYTRRLGWVRGTPDRDAVTAARR
+D-------RAPRLGRRAARTGAARADVAPAAAQAEPAAPSSSVVREHAVAVPPLPEIPVRRGPLAGAYSGNVRAVMERAF
+LSLKSNNWVVFFSGFFEPVLYLASLGLGLGALVGDVAGPDGTPVPYGMYLAPALLAVSAMNGAIYDSTWNVFFKLRYAKT
+YQTMLSTRLGPLDVALGEIAMALLRGLIYAVGFLIVMTVAGLVTSWTALLMIPGALLVALGFASLGMAVTSWMKTFQHMD
+WVQIVLMPMFLFSATFFPLAVYPEPIQWVIRVFPLWHAVEMMRALAVGVLSWATAGHVLYFVVMAGVGVWLAARRLGALF
+LR

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

@@ -0,0 +1,55 @@
+>0_427
+M------------------------ALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAA
+VPSGASTGEFEAVERRDGDKKRYGGKGVLDAVAAVE-GIAEELEGEFAADQRAVDRAMRD
+LDGTPNKGKLGANAILGVSMAVAVAAAQASDLMLYKYLGGPNAHV--LPVPMMNILNGGA
+HADSNVDIQEFMIAPIGAPSFREALRWGTEVYHALKTVLQEKGLSTGLGDEGGFAPSLES
+NRAALDLIAEAVTKAGYRLGED-IALALDVASSEFFD-NGSYTFEGQQRSAEEMAAYYTE
+LVDNYPIVSIEDPLDEDDWDGWQHLTAQLGDRVQLVGDDLFVTNVERLQRGIDEKAGNAL
+LVKVNQIGSLTETFDAIALAQRHMFHCMISHRSGETEDTFIADLAVATNAGQIKTGAPAR
+SDRVAKYNQLLRIEEDLADAAVYAGRSAFPRFRG
+>1_157
+M------------------------ALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAA
+VPSGASTGEFEAVERRDGDKKRYGGKGVLDAVAAVE-GIAEELEGEFAADQRAVDRAMRD
+LDGTPNKGKLGANAILGVSMAVAVAAAQASDLMLYKYLGGPNAHV--LPVPMMNILNGGA
+HADSNVDIQEFMIAPIGAPSFREALRWGTEVYHALKTVLQEKGLSTGLGDEGGFAPSLES
+NRAALDLIAEAVTKAGYRLGED-IALALDVASSEFFD-NGSYTFEGQQRSAEEMAAYYTE
+LVDNYPIVSIEDPLDEDDWDGWQHLTAQLGDRVQLVGDDLFVTNVERLQRGIDEKAGNAL
+LVKVNQIGSLTETFDAISLAQRHMFHCMISHRSGETEDTFIADLAVATNAGQIKTGAPAR
+SDRVAKYNQLLRIEEDLADAAVYAGRSAFPRFRG
+>2_2453
+M------------------------ALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAA
+VPSGASTGEFEAVERRDGDTKRYLGKGVLDAVAAVE-EIADELEDEFAVDQRAVDRLMLD
+LDGTPNKGKLGANAILGVSMAVAAAAAQSSDLMLYKYLGGPNAHV--LPVPMMNILNGGA
+HADSNVDIQEFMIAPIGAPSFREALRWGTEVYHSLKKVLQEKGLSTGLGDEGGFAPSLES
+NRAALDLIAEAVEKAGYTLGED-IALALDVASSEFCE-KGAYTFEGQKRSAEDMVAYYTE
+LADNYPIVSIEDPLDENDWDGWRLLTEKLGDRVQLVGDDLFVTNVERLQRGIDDKAGNAL
+LVKVNQIGSLTETFDAIALAQRHMFHCMISHRSGETEDTFIADLAVATNAGQIKTGAPAR
+SDRVAKYNQLLRIEEDLADAAVYAGRSAFPRYRG
+>3_666
+MNDYISGIHHHGAHQGEYVTHHDHPVTIDAVHGARILDSRGYPTVRVSLELDDGRTVTGD
+APAGASTGAHEAVELRDGGSA-FGGRDVTQALHLIDTDISGLLTGRSWSAIGQIDAALAE
+LDGTTGYRRLGANSVVATSIAASRALAHAADLPLWQWIAEITGSTPRMPVPHFNVLNGGA
+HAANELDFQEFMIAPVNAGSMADAVRIGADVYHALAALVRDRFGSLGLGDEGGFAPSIAA
+PEEALDLLVDAIRTAGYEPGVDQVAIALDPAANEFSQGDGSYRVLNDSLDRDGLVDYYRH
+LIDTYPIRSIEDAFAEDDHEGFRRMQAALGDRIQIVGDDLYVTDPQRIRDGGEQQLTNAA
+LIKPNQIGTVSQTLGAIATAKSIGMASMVSHRSGETTDTFIADLVVGTGTGQIKSGAPGR
+GERVAKYNRLTEIAEQ---------HPELPYGLI
+>3_2324
+M------------------------AQIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAA
+VPSGASTGEFEAVERRDGDTERYLGKGVQDAVNAVF-EIAEELEDELATDQRAVDQMMLD
+MDGTENKGKLGANAILGVSMAVAVAAADSADLPLYKYLGGPNAHV--LPVPMMNILNGGA
+HADSNVDIQEFMIAPIGAPSFREALRMGAEVYHSLKKVLQEKGLSTGLGDEGGFAPNLES
+NRAALDLIAEAVQKAGYTLGED-VALALDVASSEFCE-NGSYTFEGRQRSAEEMSAYYAE
+LVDAYPIVSIEDPLDENDWEGWEHLTEQLGDRVQLVGDDLFVTNVARLQRGIDEKAGNAL
+LVKVNQIGSLTETFDAIALAQRHMFHCMISHRSGETEDTFIADLAVATNAGQIKTGAPAR
+SDRVAKYNQLLRIEEDLADAAVYAGRSAFPRFQG
+>4_430
+M------------------------ALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAA
+VPSGASTGEFEAVERRDGDKKRYGGKGVLDAVAAVE-GIAEELEGEFAADQRAVDRAMRD
+LDGTPNKGKLGANAILGVSMAVAVAAAQASDLMLYKYLGGPNAHV--LPVPMMNILNGGA
+HADSNVDIQEFMIAPIGAPSFREALRWGTEVYHALKTVLQEKGLSTGLGDEGGFAPSLES
+NRAALDLIAEAVTKAGYRLGED-IALALDVASSEFFD-NGSYTFEGQQRSAEEMAAYYTE
+LVDNYPIVSIEDPLDEDDWDGWQHLTAQLGDRVQLVGDDLFVTNVERLQRGIDEKAGNAL
+LVKVNQIGSLTETFDAIALAQRHMFHCMISHRSGETEDTFIADLAVATNAGQIKTGAPAR
+SDRVAKYNQLLRIEEDLDDAAVYAGRSAFPRFRG
+ 

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

@@ -0,0 +1,48 @@
+>0_473
+MIGSPGDESTALRMGSTARGRVLGRPWERGLPLLVLIVDVVAVLLATFVSAQLRFGGPRRTTLPGAEVIDYSVISLALSA
+AWVLALTIQGSRDIRILGVGSEEYKRVLQGTLYLFGTVAILAYAAGLEVARGYVGLALPLGVLLLLLGRFLVRGWVARQR
+HRGRFRRRLLLVGGPKAVRHIFQTLDSEAGAGYAPVAAALPGYKARREDYLPIPVSTDLDTVEDVVALVEVRDVEAVVIT
+SGHSFVPGDVRRLGWELQERGVSLIMAPALVDVAGPRLHTQPLAGLPLIHLS-TPRLSEGKAFAKRAFDVVASGLGLIAI
+SPLLIAVAIAVKATDGGPVLFRQERIGLGGRPFTMLKFRSMVVDAEEIRQRLVSDGGDADVLFKMKDDPRITRVGKLIRR
+TSIDELPQLVNVLRGEMSLVGPRPHLPHEVEAYGQYVHRRFLVQPGITGLWQVSGRSDLPWEEAVRLDLYYVENWSILGD
+LVILGRTVKAVV-------------------AADGAY--------------------------------
+>1_203
+MIGSPGDESTALRMGSTARGRVLGRPWERGLPLLVLIVDVVAVLLATFVSAQLRFGGPRRTTLPGAEVIDYSVISLALSA
+AWVLALSIQGSRDIRILGVGTEEYKRVLQGTLYLFGTVAILAYAAGLEVARGYVGLALPLGVLLLLLGRFLVRGWVARQR
+HRGRFRRRLLLVGGPKAVRHIFQALDSEAGAGYAPVAAALPGYKARREDYLPIPVSTDLDTVEDVVAHVEERDVEAVVIT
+SGHPFVPSDVRRLGWELQERGVSLIMAPALVDVAGPRLHTQPLAGLPLIHLS-TPRLSEGKAFAKRAFDVVASGLGLIAI
+SPLLIAVAIAVKATDGGPVLFRQERIGLGGRPFTMLKFRSMVVDAEEIRQRLVSDGGDADVLFKMKDDPRITRVGKLIRR
+TSIDELPQLVNVLRGDMSLVGPRPHLPHEVEAYEQYVHRRFLVQPGITGLWQVSGRSDLPWEEAVRLDLYYVENWSILGD
+LVILGRTVKAVI-------------------AADGAY--------------------------------
+>2_1196
+MLTP-------------------DSPYEE------------------------RF--------------------AALNQ
+S-------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------LRWEVAD-----------------ELRRANLARVDELHPPVTPRDTFYTRHGKRALDVGVSGAALLFS
+SPVIGALCLVTLKDLGQPVLFTQQRPGKHGKPFQMVKLRTM--------REAYDDQGK-----PLLGELRVTKTGRLIRR
+ASLDELLNFWNIFKGDMSLIGPRPLVPEYVERFSRRHRQRLAVKPGLECPPPRPPQGPVTYDDQFENDCWYVENVSLKTD
+AWLTWRVLQTALDRRQNKARGSSTRGSFMGYDADGTVITTAALPDWALNTVLERHGLLTSNSADARQEG
+>2_2398
+MFSSPGDESPALRTGSTARGRLLGRPWERGLPLLVFIVDVVAVLLATFVSAQLRFGGPRRTTLPGTEVIDYSVISLALSA
+AWVLALSIQGSRDIRILGVGSEEYKRVLQGTLYLFGTVAILAYAAGLEVARGYVGLALPLGVLLLLLGRFLVRGWVARQR
+HLGRFRRRLLLVGGPKAVRHIFQALDSEAGAGYAPVAAALPGYKTRQEDYLPIPVSTDLDTVEDVVALVEVRDVEAVVIT
+SGHSFVPGDVRRLGWELQERGVSLIMVPALVDVAGPRLHTQPLAGLPLIHLS-TPRLSEGKAFAKRAFDVVASGLGLIAI
+SPLLIAVAIAVKATDGGPVLFRQERIGLGGRPFTMLKFRSMVVNAEEIKQRLVSDGGDADVLFKMKDDPRITKVGKFIRR
+TSIDELPQLVNVLRGDMSLVGPRPHLPHEVEAYEQYVHRRFLVQPGITGLWQVSGRSDLPWEEAVRLDLYYVENWSILGD
+LVILGRTVKAVV-------------------AADGAY--------------------------------
+>3_2281
+MTSSAVTTSQTGRGGSSVHARVLGAPWERGLPRLVLLADVVAVVLAAFLSSELRFGTARNAAVPGAESVNYLLVGAVLSA
+SWVVALGVDGSRDIRILGIGAEEYKRVLRGTLYLFGMIAILAYAFAFEVARGYVALALPIGLLLLMLGRFLIRGWVARGR
+HRGAMRRRLLLVGGPQAVKYVHDTLDSEAGAGYKPIAAVLPGYRARDEGWLPIPVTTEVDGVDELVAQVREMDIEAVVIT
+SGHPFVPDDVRRLGWDLQERGISLIMAPALVDVAGPRLHTQPLAGLPLLHLS-TPRLSRGKAFVKRSFDVVASGLGMLVI
+SPLLLTVAIAVKATDGGPVLFRQERVGLRGEHFTMLKFRSMVVDAEEIKQQLMSDRGEEDVLFKMKDDPRITRVGRFIRR
+TSIDELPQLVNVLRGDMSLVGPRPHLPHEVEQYGQYVHRRFLVQPGITGLWQVSGRSDLSWEDAVRLDLYYVENWSVLGD
+LVILGRTVKAVL-------------------AADGAY--------------------------------
+>4_472
+MFASPGDESTTLRMGSTARGRVLGRPWERGLPRLVLVVDVVAVLLATFVSAQLRFGGPRRTTLPGAALVDYSVISLALSA
+AWVLALTIQGSRDIRILGVGTEEYKRVLQATLYLFGTVAILAYAAGLEVARGYVGLALPLGVLLLLLGRFLVRGWVARQR
+HRGRFRRRLLLVGGPKAVRHIFEALDSEAGAGYAPVAAALPGYKARQEDYLPIPVSTDLDTVEDVVALVEVRDVEAVVIT
+SGHSFVPGDVRRLGWELQERGVSLIMAPALVDVAGPRLHTQPLAGLPLIHLS-TPRLSEGKAFAKRAFDVVASGLGLIAI
+SPLLIAVAIAVKATDGGPVLFRQERIGLGGRPFTMLKFRSMVVDAEEIRQRLVSDGGDADVLFKMKDDPRITRVGKLIRR
+TSIDELPQLVNVLRGDMSLVGPRPHLPHEVEAYEQYVHRRFLVQPGITGLWQVSGRSDLPWEEAVRLDLYYVENWSILGD
+LVILGRTVKAVI-------------------AADGAY--------------------------------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000092.fa

@@ -0,0 +1,31 @@
+>0_530
+MSAL------------VRPLRPEDHEAVAEL---TLASYVDGGHIAPDDAYVKTLMDVAD
+RAGRAEVLVAEVDGEVAGSVVLTPPGSPLAETSGDGEYEFRMLAVHPRFHRRGVGGALLA
+EIVARARAEEGVDAVVLTTMPSMTGAHRMYERAGFVRVPERDWFLADVVPDLDPADETGP
+FLVYRLALD
+>1_264
+MSAL------------VRPLRPEDHEAVAEL---TLASYVDGGHIAPDDAYVKTLMDVAD
+RAGRAEVLVAEVDGEVAGSVVLTPPGSPLAETSGDGEYEFRMLAVHPRFHRRGVGGALLA
+EIVARARAEEGVDAVVLTTMPSMTGAHRMYERAGFVRVPERDWFLADVVPDLDPADETGP
+FLVYRLALD
+>2_622
+MERPAPTA-------EICPVRPEDTDAVVALWERTLPEY--GDPTRPQRAPRPSIRRKLD
+-WGDGLFWLAVSDEEVVGTV--------MAGYDGHRGWIYS-LAVHPDHRRGGLGTALVA
+H-AEQELARLGCPKVNLQVLATNADGAEFWAATGYQPDPVLG------------------
+-LGKRLG-G
+>2_2339
+MTETAPTVPTPPARPQVRPLRPEDHEAVAAL---TVASYVDGGHIAPGSRYVKTLRDVAG
+RAARAEVLVAEVDGQVAGSVVLTPLGSPMAETAAPGEYEFRMLAVHPDHHRRGVARTLMA
+VIEERARALPGIEAIALTTMPTMTDAHRLYEALGYVRVPERDWYLRDVIPDLDPADETGP
+FLVYRLPLA
+>3_2222
+MSDVT-----------VRALRPEDHEAVAAL---TLASYTTGGHFEAESDYLETLADVAG
+RAAVAEVLVAELDGQVAGSLVLTPHGSPMAETSVPGEYEFRMLAVDPAVHRRGVATALLA
+EVVRRARATPGVEAIALSTMTSMTDAHRMYERLGFVRVPDRDWRLSDLEPGLDPAEDAGP
+FLVYRLPLT
+>4_533
+MSAL------------VRPLRPEDHEAVAEL---TLASYVDGGHIAPDDAYVKTLMDVAD
+RAGRAEVLVAEVDGEVAGSVVLTPPGSPLAETSGDGEYEFRMLAVHPRFHRRGVGGALLA
+EIVARARAEEGVDAVVLTTMPSMTGAHRMYERAGFVRVPERDWFLADVVPDLDPADETGP
+FLVYRLALD
+ 

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

@@ -0,0 +1,43 @@
+>0_589
+MGS-------HHHAP--------TGHRGRLAIAFGITTAVLLAEVVGAVLTGSLALLVDA
+AHMLTDAGGLLMALLAATLMARPPTTRRTWGFLRAEVLAALAQAAVLLAVGTYAFIEGLQ
+RLFAPPEVASGPLLAFGILGLVGNLASLAVLGSGRGANLNMRAAFLEVLNDALGSVAVIA
+SALVIAATGWTRADAVAGMLIAVLIVPRTLKILGETTRILLESTPRGLDLAEVRTHLQAL
+PHVVSVHDLHASQIATGVPVLSAHIVVEDSCFHDGHAPQILDQLQHCVAEHFDVGVDHST
+FQLEPAAHAHHE-----HPTHH
+>1_310
+-------------------------------MVFSITATIMVAEVIGALASGSLALLADA
+GHMFTDSAGLLIALTATTLALRPATDKRTWGYKRAEIIAAAAQAAVLLAVGGFVAVEGVR
+RLIEPPEVESTAMLWFGVIGLAGNLIGLAILASSRGENLNMKAAFLEVLNDALGSVAVIV
+SAIVIATTGWNRADAVVSLLIAALIVPRALILLRDTIDVLMETTPKGLDLEAVRIRLSEL
+PHVLEVHDLHASRIDSDTPVLSAHVTVHNGCLTAAHLGTVLTDLQRCVAQDFQVPIEHST
+FQIEPATHPHTETL---HP---
+>1_1724
+MGA-------HHHAS--------PAHRWRLAVAFAITTAVLLAEVAGALITGSLALLVDA
+AHMLTDAGGLLMALLASTLMARPPTARRTWGFLRAEVLAALAQAAILLAVGLYAFIEGLQ
+RLFAPPEVASGPLLLFGILGLAGNLASLAVLGSGRGANLNMRAAFLEVLNDALGSVAVIA
+SALVIATTGWAQADAVAGMLIAVLIVPRTLKILAEAAHILLESTPRDLDLAEVRDHLEAV
+PHVVSVHDLHASQIATGVPVLSAHVVVEDHCFHDGHAPQILDQLQHCVAEHFDVAIDHST
+FQLEPAAHAHHE-----HPTHH
+>3_527
+MSTPHEHHHDHAHGPSPEEAAADPALRRRLWIALALAGTVVLAQAVGAALTGSLALLTDT
+AHAVTDASGLAVALVAAILMARPATPRRTWGLRRLEVVAALGQAALLLLVGAYSAVEAVR
+RLVEPPAVDGTGMLLFGVLGLAANLAAAAVLASSRGANLSMRAAFLEVVNDALGSLGVIA
+AAAVVAVTGWTRADAVAGLLIVVLIVPRAVSLLRQTLRVLLEFTPEGLDLDEVRTHLLEV
+EHVLEVHDLHASTVATGLPVLTAHVVVEDGCFTDGHAAQILEQLRECTREHFPLAVPHST
+FQLETAAIAADDAHHTAHP---
+>3_685
+MGA------GHNHGPAASETGHPGDFRKKLWIAFSITATIVVAQAMGSVITGSLALLTDT
+AHAITDASGLLVALIAATLMLKPANSKRTWGFRRIEVIAALGQSALLLAVGTYAAIEGIR
+RLFEPPEVPASELLIFGIIGLVANIIAITILASSRGSNFNMRAAFLEVLNDALGSLGVII
+AAIVIATTGFMQADAIAGLLIAALIVPRAFKLMRETTGVLMEFTPKGLDLDKVRSHILEL
+DHVKDVHDLHASTVATGLPILTAHVVVEDECFTDGRAAQTLHEIKDCVAGHFEVSIHHST
+FQIETEHIAEHEPEISKHD---
+>4_1947
+MSG-----HDHSHAL------PAAGRRGRLAVVFSITATIMVAEVIGALASGSLALLADA
+GHMFTDSAGLLIALTAATLALRPATDKRTWGYKRAEIIAAAAQAAVLLAVGGFVAVEGVR
+RLIEPPEVESTAMLWFGVIGLAGNLIGLAILASSRGENLNMKAAFLEVLNDALGSVAVIV
+SAIVIATTGWNRADAVVSLLIAALIVPRALILLRDTIDVLMETTPKGLDLEAVRIRLSEL
+PHVLEVHDLHASRIDSDTPVLSAHVTVHNGCLTAAHLGTVLTDLQRCVAQDFQVPIEHST
+FQIEPATHPHTETL---HP---
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000098.fa

@@ -0,0 +1,37 @@
+>0_601
+MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYQWLAEPVSAREWSDAHAANAVLDAHAGDP
+EFGYRFLADELRGRGLAVSDHQVLKACRLVRVRCCHWFRRGSGKRPGPAVHDDLVRREFR
+AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLALDALQMALARR
+GGKAEVQGCRVHSDRGSQGGFNR--SSQHPLGITGGMGD-GKQG----------------
+--------------------------------LGE---------------EDQ
+>1_355
+MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP
+EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFR
+AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLAVDALQMALARR
+GGKAEVQGCRVHSDRGSQFRARRFVETLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNV
+LNRRRWQSFDQLRLAIVSWIERTYHRRRRQARLRKLTPVEFEMVQSVQAAAAA
+>2_376
+MTYPVVKDLARDGIPVRLCCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP
+EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFR
+AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLAVDALQMALARR
+GGKAEVQGCRVHSDRGSQFRARRFVETLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNV
+LNRRRWQSFDQLRLAIVSWIERTYHRRRRQAPLGRLTPVEFEMVQSVQAAAAA
+>2_395
+MTYPVVKDLARDGIPVRLCCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP
+EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFR
+AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFLKR--------------------------
+--------------PGSD------------------------------------------
+--------------------------------------------------EDS
+>3_2136
+MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYPWLAEPVSAREWSDAHAANAVFDAHADDP
+EFGYRFLADELRGRGLDVSDHQVLKACRLVRVRCCHSIRRGSGKRPGPAVHDDLVRRQFR
+ADKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSIDRRMSSQLAVDALQMALARR
+GGKAGVQGCRVHSDRGSQFRARRFVETLRVNSLIGSMGRVGAAGDNAAMESFFALLQKNV
+LNRRRWDSFAQLRLAIVSWIERTYHRRRRQARLGKLTPVEFEMVQSVQAAAAA
+>4_580
+MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP
+EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFA
+AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLAVDALQMALGRR
+GGKAEVQGCRVHSDRGSQFRARRFVETLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNV
+LNRRRWQSFDQLRLAIVSWIERTYHRRRRQARLGKLTPVEFEMVQSVQAAAAA
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000100.fa

@@ -0,0 +1,43 @@
+>0_619
+M-------------TSVPTV-----PFHDGQQIPQLGFGVWKVEDDVAADVVEQAIRAGY
+RHIDTAAIYGNEEGVGRGIAAS----GVAREELFLTTKVWNSDQGYEEAL-AALDVSLDK
+LGTDYVDLYLIHWAKPAQGKYLETWKALIEAQKQGKVRSIGVSNFPAAQLEEIIEATGVV
+PVIHQVETHPYWQQRELREVEGRHGIVHESWSPLGQGGDLLA--DPVVTEIAEARGATPA
+QVVIAWHLAHGFVVIPKSVTPERIVSNLEAAGVELTDDDVARIDALDREDG-RLGPDPAV
+IDF--
+>1_365
+M-------------TDVPTV-----PFHDGQQIPQLGLGVWQVEDDVAADVVEQAIRAGY
+RHIDTAAIYGNEEGVGRGIAAS----GVAREELFLTTKVWNSDQGYEEAL-AALDVSLDK
+LGTDYVDLYLIHWAKPAQGKYLDTWKALIEAQKRGKVRSIGVSNFPAAQLEEIIEATGVV
+PVIHQVETHPYWQQRELREVEGRHGIVHESWSPLGQGGDLLA--DPVVTEIAEVRGATPA
+QVVIAWHLAQGFVVIPKSVTPERIVSNLEAAGVELTDDDVARIDALDREDG-RLGPDPAV
+IDF--
+>2_2268
+M-------------TSVPTV-----PFHDGQSIPQLGYGVWRVEDEVAADVVAQAIRAGY
+RHIDTAAIYGNEEGVGRAVAAS----GVPREELFITTKVWNSAHGYDEAL-AALEESLGK
+LGTDYVDLWLIHWAKPTQGRYVDTWKALIEAQRQGKVRSIGVSNFPAEQLEEIIEATGVV
+PVIHQVETHPYWQQRELRELEERHGILHESWSPLGQGGELLE--DPEITAIAEAHGATPA
+QVVIAWHLAKGFVVIPKSVTSERIVSNLAAADVELTEDEVARIDALDREDG-RIGPDPAT
+IEF--
+>3_567
+MSTDSRHTAIPVDETPVPETLTLTGTGVDGVEMPRIGLGTWPLRGAEARDAVEQALRIGY
+RHVDTAQNYGNEDAVGEGIAAAIHAGVLDRDQLFVTTKVNREHHGDARTVRAAVECRLRV
+LGLEHVDLVLVHWPNPDQDRYLETAWSLSELAEDGRIRAWGVSNFTPAHLDRLAGAGLRA
+PV-DQIEVGPLRQSPAWQEGVRAHGAAITAYSPLGRADQDLGALEP-VAAAAARTGRTPA
+QVVLRWHLQSGRAAVPKSVDPARQAQNLDVFSFALTAEEMAAIDALDTGEGPRRHPD---
+-EFGH
+>3_2126
+M-------------TTVPQT-----PFRDGQSIPQLGYGVWQVEDAVAADVVEQAVRAGY
+RHIDTAAVYGNEEGVGRAVAAA----GVPREELFITTKVWNSDQGYDEAL-AALEASLAK
+LGTDYVDLWLIHWAKPAQGKYVDTWKALIEAQRQGRARSIGVSNFPAEQLEEIISATGVV
+PVIHQVETHPYWQQRELREVESRHGIVHESWSPLGQGGELLS--DPVITAIAEAHGATPA
+QVVIAWHLAEGFVVIPKSVTPERIVSNLTAAELELTAEEVDQIRGLDRADG-RIGPDPAS
+ITF--
+>4_589
+M-------------TDVPTV-----PFHDGQQIPQLGLGVWQVEDDVAADVVEQAIRAGY
+RHIDTAAIYGNEEGVGRGIAAS----GVAREELFLTTKVWNSDQGYEEAL-AALDASLDK
+LGTDYVDLYLIHWAKPAQGKYLDTWKALIEAQKQGKVRSIGVSNFPAAQLEKIIEATGVV
+PAIHQVETHPYWQQRELREVEGRHGIVHESWSPLGQGGDLLA--DPVVTEIAEARGATPA
+QVVIAWHLAQGFVVIPKSVTPERIVSNLEAAGVELTADDVARIDALDREDG-RLGPDPAV
+IDF--
+ 

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

@@ -0,0 +1,60 @@
+>0_808
+MSL-----------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------------------------------EF----------------RTSEESPDVTRVVA-THLPTRHGDFALLG
+YRDG-RGTDHVALTL---GDVAADDGELPL-VRLHSECLTGDALGSYRCDCGEQLDAALQAIGAAGRGVLIYIRGHEGRG
+IGLLDKLRAYALQDSGIDTVDANTHLGLPADARDYDQSAQILRELGVGKIRLLSSNPAKQEALEALGIHVEARVRLNVAD
+RPENSRYLSTKRARMRHDLPPERNAWDLLAGARVPTGPLTPQEEALVLRYGPLVEAGPRLVIGQLGQSLDGFIASRTGDA
+CFVTGEADREHLHRLRALVDAVLVGAQTVAADDCQLTVRAVNGADPARVVVDPHARIPLTAKVLTDPRSRTLWLVGSDAS
+VPASLAPHVSVHRLETSTGFEPAAILQYLADQGLGRVLIEGGGLTVSGFLHAGVLDRLYLTSAPLLVGDGVPGIRFDGAD
+ALSGALSAPVRRFVLGDDVCTEFDFSAAKPASPAALHRADQENQPTGQD
+>0_1020
+MSE----------HIRLDPVPVAIAAIAAGRPVVVVDDADRENEGDLIYAAALATDEVTAFTVRHTSGVICAPLPAGLAD
+RLALPPMTTVNEDPKGTAYTVSVDAAAGVTTGISAADRTRTLRLLADPGAAPGDLTRPGHVFPLRAVPGGVRARRGHTEA
+GVELCRLAGVAPVAAIAELVHDDGTMMRLPALREFSDEHGLVLISIEDLVAHLEETTPALTAVPAEATLPTRHGLFRVSV
+HVDAETGAEHLLLV------AGETDSERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALARAAAEG-GAVLYLRGHEGRG
+IGLANKIRAYRLQEEGMDTVEANLALGLPAEARDWAGAAAVLTAAGHRRIRLVTNNPAKVAGLRAAGIDVVERVPAPTPV
+TEHNVVYLRTKRDRMAHAL-----ADRVLEPPTATGGPATPAD-------------------------------------
+---------------------------------------------------DPT----------TDPTH-----------
+--------------------------------------------------------------------------------
+--------PTH-----------------------------QEDTP----
+>1_748
+MSE----------HIRLDPVPAAIAAIAAGRPVVVVDDADRENEGDLIYAAALATDEVTAFTVRHTSGVICAPLPAGLAD
+RLALPPMTTVNEDPKGTAYTVSVDAAAGVTTGISAADRTRTLRVLADPGAAPGDLTRPGHVFPLRAVPGGVRARRGHTEA
+GVELCRLAGVAPVAAIAELVHDDGTMMRLPALREFSDEHGLVLISIEDLVAHLEETTPTLTAVPAEATLPTRHGLFRVSV
+HVDAETGAEHLLLV------AGETDPERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALARAAAEG-GAVLYLRGHEGRG
+IGLANKIRAYRLQEEGMDTVEANLALGLPAEARDWAGAAAVLTAAGHRRIRLVTNNPAKVAGLRAAGIDVVERVPAPTPV
+TEHNVVYLRTKRDRMAHAL-----ADRVLEPPTATGGPATPAD-------------------------------------
+---------------------------------------------------DPT----------TDPTH-----------
+--------------------------------------------------------------------------------
+--------PTH-----------------------------QEDTP----
+>2_1790
+MSD----------SIPLDAVPAAIAAFAAGRPVVVVDDADRENEGDLVYAAALATDAVTAFTVRHTSGVICAPMPADLAD
+RLALPPMTARNEDPKGTAYTVSVDAATEVSTGISAADRTRTLRILADPAAGPADLTRPGHVFPLRAVPGGVRARRGHTEA
+GVELCRLADVAPVAAIAELVHDDGTMMRLPALREFADEHGLVLISIEDLVRHLEEEGPTPVPVPAEATLPTRHGVFRVSV
+HADAVTGAEHVLLVAKKAGEAGEADPERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALSRAGSEG-GAVLYLRGHEGRG
+IGLANKVRAYRLQEQGLDTVEANIALGLPTEARDWAGAAAVLAAAGHTRVRLVTNNPAKVAGLQAAGIDVVERVPAPTPV
+TEHNLGYLRTKRDRMAHAL-----ADRVLEHPVAPG--------------------------------------------
+-----------------------------------------------------H----------EDPRHE----------
+--------------------------------------------------------------------------------
+-------TPTH-----------------------------QEDTP----
+>3_1678
+MSIDTAVEPAAPVDIRLDPVADAVAAIAQGRPVVVVDDADRENEGDLIYAAALATDAVTAFTVRHTSGVICAPLPAELAD
+RLNLPPMTARNEDPKGTAYTVSVDAVAGVTTGISAADRTVTLRVLAGEESTAADLTRPGHVFPLRAVPGGVRARRGHTEA
+GVELCELADLPPVAAIAELVHDDGTMMRLPALREFADEHSLVLISIEDLVAHLHEHRPEQRVVPAEAALPTAHGDFRISV
+HPDTATGAEHVLLVADRPGSATGGDADAPVTVRVHSECLTGDVFGSLRCDCGPQLQAALDAAARDG-GAVLYLRGHEGRG
+IGLTNKIRAYRLQEEGLDTVEANLALGLPAEGRAYAGAADLLREAGLTRIRLVTNNPAKVDALRAAGIDVVERVPAPTPV
+TEHNAAYLRTKRDRMHHEL-----ADRDL------G--------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------------------DA-----
+>4_967
+MSE----------HIRLDPVPAAIAAIAAGRPVVVVDDADRENEGDLIYAAALATDEVTAFTVRHTSGVICAPLPAGLAD
+RLALPPMTTVNEDPKGTAYTVSVDAAAGVTTGISAADRTRTLRVLADPGAAPGDLTRPGHVFPLRAVPGGVRARRGHTEA
+GVELCRLAGVAPVAAIAELVHDDGTMMRLPALREFSDEHGLVLISIEDLVAHLEETTPTLTAVPAEATLPTRHGLFRVSV
+HVDAETGAEHLLLV------AGETDPERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALARAAAEG-GAVLYLRGHEGRG
+IGLANKIRAYRLQEEGMDTVEANLALGLPAEARDWAGAAAVLTAAGHRRIRLVTNNPAKVAGLRAAGIDVVERVPAPTPV
+TEHNVVYLRTKRDRMAHAL-----ADRVLEPPTATGGPATPAD-------------------------------------
+---------------------------------------------------DPT----------TDPTH-----------
+--------------------------------------------------------------------------------
+--------PTH-----------------------------QEDTP----

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

@@ -0,0 +1,60 @@
+>0_853
+MTARERPAPSRRPLLRSLALTAQTVREHVTDDPVLLALQVSRRLPPAAVGGAAGILTRLGRNGVVPALGHEMRGERAAAL
+AALGVDEAGR------PVRASRPGAGNVRGLVHRADAALGMGRPDIAETLLGSVPEKRRGAAWTAAAARLAAHRGDLGGA
+AALAARHPRNRHLARRMAGERD----AFRGVAPTVPTEP-----GYRPVPG----RVLHVLTNSLPHTGSGYAQRSHAIL
+TSLRDEGFDAAAVTRPGYPVQIGVPWAAQRDVVDGIRYARLLPARLAQG--QAARIQQHAELLAAHVRRHRPALLHTTT-
+--HFVNALAVEAVARAFGIPWVYEVRGQLADTWAAVRGPEALASERYRLFQER---EAEAARRADGVVTLGAGMRDRLVA
+AGVAEDAVVLCPNAVGPAFVAERVDRDEA-RARLGWDLPTDAFVVGTVSSL-VDYEGLDILLRAAARLAPHRPGLRVHIA
+GDGVARPGLQALAAELGIAELCAFPGRVDREDARLHHAALDVFTVPRRDLPVTRAVTPMKTVEASATGRPVVASDLPALA
+ELVEDERTGLLVPAEDPAALAAALDRLAGDPAERARLGAAGREWALQTRTWEANARRYRTLY-------DRLGVHPR---
+-------
+>1_584
+MTARERPAPSRRPLLRSLALTAQTVREHVTDDPVLLALQVSRRLPPAAVGGAAGILTRLGRNGVVPALGHEMRGERAAAL
+AALGVDEAGR------PVRASRPGAGNVRGLVHRADAALGMGRPDIAETLLGSVPEKRRGAAWTAAAARLAAHRGDLGGA
+AALAARHPRNRHLARRMAGERD----AFRGVAPTVPTEP-----GYRPVPG----RVLHVLTNSLPHTGSGYAQRSHAIL
+TSLRDEGFDAAAVTRPGYPVQIGVPWAAQRDVVDGIRYARLLPARLAQG--QAARIQQHAELLAAHVRRHRPALLHTTT-
+--HFVNALAVEAVARAFGIPWVYEVRGQLADTWAAVRGPEALASERYRLFQER---EAEAARRADGVVTLGAGMRDRLVA
+AGVAEDAVVLCPNAVGPAFVAERVDRDEA-RARLGWDLPTDAFVVGTVSSL-VDYEGLDILLRAAARLAPHRPGLRVHIA
+GDGVARPGLQALAAELGIAELCAFPGRVDREDARLHHAALDVFTVPRRDLPVTRAVTPMKTVEASATGRPVVASDLPALA
+ELVEDERTGLLVPAEDPAALAAALDRLAGDPAERARLGAAGREWALQTRTWEANARRYRTLY-------DRLGVHPR---
+-------
+>2_2007
+MDRPGGLEGAFDRHWRKIRRELGSVYRDYRAGRASTGSALKR----ATRIG----------------LKHGVLAPRDA--
+----LAEFLRLRD--EAVGPTLAGAGPMTMLPGELDSERARIWLSVLERHYPSGPART---AYFEQLRRLALRDGQISTA
+LDATAELASSNTSMARAAVDVNGRMTELSGWLPRLPG-------PVEPVSGCGTNVVLHLLKESRPYLSNGFTSRTQWNL
+LAEKDAGWTPVVLTEPGFPEGMTEGRPSTVEEVDGIEHRRILTGVSYRGVPFDRWLEDFAFLALDHVRNVRPDVLHVSSG
+RRGYETALVGLALREKTGLPLVYEVRSFFEGNWT----PDLDIEEHSEVFRRRREVETRCMIAADRVLTLGEAMRDEIVA
+RGVPAEKVDIVPNGVQLDRF-TPAPRDPAIAARHGITLPT----FGYVSNMDHPREGHELLIRAALLLQERGVEAQCVLV
+GGGRRFDELRALARELGIANRVVFTGPVDHEEVAALYGLIDVFVVPRINERAARYVTPLKPFEAMALRRPVIVSDLPALR
+EIVAAPRRGLTFPVGDVMVLAETIARLLEEPAERQRLGAAGREWVEAERQWVHNGPRYDRAYHAAINARRRAG-------
+-----KG
+>2_2009
+MTSI---LLDFVRALGHAPLVLRTVVDHLRDDPAVLGLQISRRLPLAARVG-------LGR------LAESLPARPGVVL
+GAVGLAAAGRHVDLLEHVEAVLPSAG-APDRVRLADVLTAAQEPDRAQAVLDAVPVNTPGLA--AARARVAWHRGDVEAA
+ISLLGGTGRDGVVRARFASEVR----ALRGGALPLPRADRDRAVGYRPRPG----SALFVLTNSLPHTGSGYAQRSHSLA
+CALRDEGWDVEAVTRLGWPVQTGVLTAARRDMVDGIVYHRLLPSSLARG--FDGRLAQHARMLLDLVLERRPAVLHTTT-
+--HWVNAVVTRAVAEAVGVPWVYEVRGQLADTWASTRGPEALRSDRYALFTAR---EDDAVRSADGVVTLGEQMARRIAV
+AGMDRDAVVLSPNGVGGAFLEEPAPREDA-RRRLG--LSMDDEIVGTVSSV-VPYEGLDDLVRAVAALVDERPRLRLAVV
+GDGVALPALRRLAADLGIEDRLLAPGRVDRSLAPVWHQALDVFCVPRKDTGVTRAVTPMKPLEAMATSRPVLVSDLPALS
+EIVEDGVTGRVLPAEEPEAWAAALAALLDDPAEARGLGARAREWVLGHRTWAANARRYDALY-------RRLGVMAPSA-
+-------
+>3_1902
+MSPR---APRVRRLAANAALTGRTVADHLLDDPVVLALQVSRRLPTGLRAR-------VGG------VLADVPARVAVPR
+G-IGLAMLGREEQLQAALVDADDAPG-PRERARRAEVLLAAGRDEDAERLLADVPADAPGAA--EARARLRWHRGDMTGA
+VLVLSPHGRQGRLRARLAAERD----SLLGRPVCLSAEDRALAADYEPRPG----HVLFVLTNSLPHTGSGYVQRSHSLL
+TAVRDAGWSVAAVTRLGWPVQTGVLAAEDVDRVDGVAYHRLLPAALAPG--FGARLDQHAAALLRLVLRERPAVLHTTT-
+--HWVNAAVTAAVAEAVGIPWVYEVRGQLADTWASTRGPQALMSERYRAFRTR---EAEAAARADGVVTLAETMRARLAE
+DGVDPEDVVLSPNAVGGAFLDAPGERAAA-RRALG--LAPDAEYIGTVSSV-VPYEGLDDLVRVVALLADRRPRLRLLVA
+GDGTALPGLAALAEQLGVRDRVDLLGRVERARAPLCHQALDVFCVPRRDTSVTRDVTPMKPLEAMASARPVLLSRLPALQ
+ELVAEGETGATVPASDPEAWAEAVEALLADPNAAAAMGDRARAWVLAERTWAANARRYTELY-------ARLGAVVDVAD
+RGAVRGG
+>4_809
+MTSI---LLDSVRALGHAPLVLRTVVDHLRDDPAVLGLQISRRLPLAARVG-------LGR------LAESLPARPGVVL
+GAMGLAAAGRHVDLLEHVEAVLPSAG-APDRVRLADVLTAAQEPDRAQAVLDAVPVDTPGLA--AARARVAWHRGDVEAA
+ISLLGGTGRDGVVRARFASEVR----ALRGGALPLPRADRDRAVGYRPRPG----SALFVLTNSLPHTGSGYAQRSHSLA
+CALRDEGWHVEAVTRLGWPVQTGVLTAARRDMVDGIVYHRLLPSSLARG--FDGRLAQHARMLLDLVLERRPAVLHTTT-
+--HWVNAVVTRAVAEAVGVPWVYEVRGQLADTWASTRGPEALRSDRYALFTAR---EDDAVRSADGVVTLGEQMARRIAA
+AGMDRDAVVLSPNGVGGAFLEEPAPREDA-RRRLG--LSMDDEIVGTVSSV-VPYEGLDDLVRAVAALVDERPRLRLAVV
+GDGVALPALRRLAADLGIEDRLLAPGRVDRSLAPVWHQALDVFCVPRKDTGVTRAVTPMKPLEAMATSRPVLVSDLPALS
+EIVEDGVTGRVLPAEEPEAWAAALAALLDDPAAARGLGARAREWVLGHRTWAANARRYDALY-------RRLGVTAPSA-
+-------

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

@@ -0,0 +1,43 @@
+>0_1001
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------------MLEPEIRSD
+NGGRGIRNAETNFYADAETRTLVTTLNGVEVELRATPVSFHWDYGDGSPTKTTSVAGQSQ
+PEFNVPTPTSHVYEDTGQYTVRLTTVYIGEYREAGGEWVLIPGTISLDSAPVTANIWRTI
+TRNVADDCSVDSSAWGCTGPIESAPAG
+>1_723
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------------MLKPEIRSD
+NGGRGIRNAETNFYADAETRTLVTTLNGVEVELRATPVSFRWDYGDGSPTKTTSVAGQSQ
+PEFNVPTPTSHVYEDTGQYTVRLTTVYIGEYREAGGEWVLIPGTISLDSAPVTADIWRTI
+TRNVADDCSVDSSAWGCTGPIESTPAG
+>2_316
+MP----------------------------------------------------------
+------------------------------------HQLDNADYGSCLNQDESFCPDGE-
+-WVQARTVDITRPDADPLYGRPTCTSDVAAGAGGAR----SFTLEEVRTLLLLDPTIESD
+NAGRGVRNAETNFYTDAGVETLSTTINGVPVELRATPVSFHWNYGDGTAPRVTHVGGHAQ
+AEFNTPTPTSHVYEETGEYTVTLTTVYIGEYREADGDWVLIPGTITLDAAPVTADIWRTV
+TRNVAEDCAADPSAWGCTGPIEAPDAP
+>2_526
+MP----------------------------------------------------------
+------------------------------------HQLDNADYGSCLNQDESFCPDGE-
+-WVQARTVDITRPDADPLYGRPTCTSDAAAGADGAR----SFTLEEVRTLLLLDPTIESD
+NAGRGVRNAETNFYTDAGVETLSTTINGVPVELRATPVSFHWNYGDGTAPRVTHVGGHAQ
+AEFNTPTPTSHVYKETGEYTVTLTTVYIGEYREADGDWVLIPGTITLDAAPVTADIWRTV
+TRNVAEDCAADPSAWGCTGPIEAPDAP
+>3_1698
+MTSRRGDFPACMAVLFALIFLVSAVTLVTPSQAHASSCDTAGRKAQLTDDSLIVGQRCHK
+SSIAEIVGDGLADDQEKSAKATSPTTKVTTLQNACYENLPEPGFENCATQQELICGDQNV
+AWLQPSTKDTARPEDAPVKGDAFCADGSAAPSAPPQPSRPAVSIDDMGEVIAPEPRILAD
+TDGRGVRNAETNFYSPEAVRHETAVIDGVSVEMRLTPVSFIWDYGDGTAPVTTDVGGNPQ
+DGFDVRTPTSHVYDETGTYEVTLTTVYTGEIRYPGQGWEAVPGTIRRTATPVTADIWTTS
+TRNVADDCSADASAWGCAGPVEAPNGG
+>4_942
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------------------------------MSIDEVRTLLVLEPEIRSD
+NGGRGIRNAETNFYADAETRTLVTTLNGVEVELRATPVSFHWDYGDGSPTKTTSVAGQSQ
+PEFNVPTPTSHVYEDTGQYTVRLTTVYIGEYREAGGEWVLIPGTISLDSAPVTANIWRTI
+TRNVADDCSVDSSAWGCTGPIESAPAG
+ 

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

@@ -0,0 +1,37 @@
+>0_1072
+MAT-------------------------------SEPVRRSAAALLRLTCRPEVVGMEHV
+PARGPFVMASNHLSFVDSVILQALAP----RPVHFFAKEEYFTGTGLRGRVRRRFFESV-
+--GSVPVRRGEQAASVAA--------LESLVGLLESGQGVGIYPEGTRSRDGRLYRGRTG
+AAWLALA-TGARVVPVGLVGTQHLQPPDTNGFRPHRFSVRVGAPLDFGHPGRRHTLPQRR
+DATAAIMDAIGALSGQERVDAYNAAPGAR------------G
+>1_800
+MAT-------------------------------SEPVRRSAAALLRLTCRPEVVGMEHV
+PARGPFVMASNHLSFVDSVILQALAP----RPVHFFAKEEYFTGTGLRGRVRRRFFESV-
+--GSVPVRRGEQAASVAA--------LESLVGLLESGQGVGIYPEGTRSRDGRLYRGRTG
+AAWLALA-TGAPVVPVGLVGTQHLQPPDTNGFRPHRFSVRVGAPLDFGHPGRRHTLPQRR
+DATAAIMDAIGALSGQERVDAYNAAPGAR------------G
+>2_153
+MSALAARARAGLAHAVLAVAGARIHASGPDGAEEAEITRERLAALL--------------
+PRQAVFY--ANHTSHLDFVTLWAVLPPALQRRVRPVAAADYW-GSGLRRRVAEGLFHAYL
+VERGKTRRRGPGAASGSGVSPDGGSQLEGMLEILAGGDSLIIFPEGTRGSGEDVARFQRG
+LHALAAAFPQVPVVPVSLVNLGRILPKGEPIPVPHLSTVRFHPPLDPPEPARPPGPGAPA
+SGTAA-TDAPEPGRGEDEAARTAWLERARAVLVQDLSASLRG
+>2_1744
+MAT-------------------------------SEPVRRSAAALLRLTCRPEVTGMDQV
+PAEGPFIMASNHLSFFDSVILQALAP----RPVHFFAKEEYFTGAGVRGRAQRWFFESV-
+--GSVPVRRGEQAASVAA--------LESLVGLLDSGQGVGIYPEGTRSRDGRLYRGRTG
+AAWLALT-TGAPVVPVGLVDTQHLQPPDTNGFRPHRFAVRVGAPLDFGHPGRRHTLPQRR
+DATAAIMDAIGALSGQERLDAYNAAPGAR------------G
+>3_1636
+MAT-------------------------------SEQLRRAVAGAIRLSCRPHVRGLEHV
+PPEGPFIVASNHLSFVDSVILQALCP----RPVGFFAKAEYFEAPGLRGRAQRRFFEAV-
+--GSIPVRRGEQAASVAA--------LEDLVALLDGGHGVGIYPEGTRSRDGRLYRGRTG
+AAWLALT-TGAPVVPVGLRGTERLQPPGTNGFRPHRFTVEMGEPLDFGHPGRRHSLPQRR
+EATATIMAAIAALSGQERVDEYNAAPAAR------------G
+>4_1022
+MAT-------------------------------SEPVRRSAAALLRLTCRPEVVGMEHV
+PARGPFVMASNHLSFVDSVILQALAP----RPVHFFAKEEYFTGTGLRGRVRRRFFESV-
+--GSVPVRRGEQAASVAA--------LESLVGLLESGQGVGIYPEGTRSRDGRLYRGRTG
+AAWLALA-TGAPVVPVGLVGTQHLQPPDTNGFRPHRFSVRVGAPLDFGHPGRRHTLPQRR
+DATAAIMDAIGALSGQERVDAYNAAPGAR------------G
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000127.fa

@@ -0,0 +1,120 @@
+>0_1321
+M-------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------------------------SSARRDPL---VGGIVDGRYRVVERLARGGMSTVYLAVDERLDRQVALKVMHP
+HLAEDPVLVGRFEQEAKTTARLS-HPHVVAVLDQGHTEAEDGDVLAYLVMEHVPGRTLRTVIRDRAPLSPREALRFLRPL
+VDGLAAAHGAGLVHRDVKPENV-LVRDDG---RVTVADFGLSRAATAHTMAGQAVVGTPAYLAP--EHIAGAPADARSDV
+YAVGIILFELLTGRQPYTAATALQVAYRHVHERVPVPSTL-HPGLPEDLDDLVLWCTEPDPADR------PAGAGELLHR
+IEAVAAGL--------DP-DAPDRRPA--AQP-----AEGPGADPAPAGPAADGLEDAAP----DGNLETRALDAGDHHA
+TRVLPALA-ESDLDEDMTDVIDTRVATHGGDPRPAA-------RPAEPIGPLGLDPAPAD------RHPGRGSRRRLRRA
+ARRPALDLGQGTGRAAAIGAAVTLLLTGVALLLGWTLGSGGLGVGGVAVVPDLDGLAREA----AEERLTAAGFTAAVTA
+RHDELRTEGTVVASSPAAGEPAGRGAPVELTVS-------AGPAPVP-------VPDLTGVVIRQAHGVARDARFTVEVA
+ERRTDPAVPAGA-------VIEQHPAPGEQATPGTA------VRVVLSEGRAVRPVPDMTGQDPETAHTTLADEGWDARV
+HRLP-LPLSARGESRVLHQSPAAGTAL----------------------------------------------------P
+EGT-----------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-------------AVHVWV---------------------------------------------------G
+>0_1893
+MSLPDARWHVVSPSPFEHEQQGLDILREVLPDESPFQVWTNFEFPDEDGQWHEVDALVLARTKFILVELKYYSGVLRGTG
+LRWERPGHSPQRSPLALAKKKAERFRSLLERTIESKMPGAGRQRIVPYVDYAVFLHHDRFRNEMAPQDSGRLFGLPHNET
+ASNLPSIEHLVLAPATDRFPLIGEPREQVLVALMEHLNLADARQPEVGSWLLEERLGEPTPDGQDWLASHRFQERHFARI
+RFQQPREGAPSSDLARVREAARREFDLTRALHHEGLLTASDRVDNELGVGLVFPYDESLAPLPLWLESRAATLSQQNRLD
+LLRQLAETLEYVHSNGIVHRALSPEALWVKTPKQGEPRILVADWQLAGVADRDKVDHAASLTQLSTQFGTTVRSTEELAP
+TSGALFRAPEDARRVSSLGRYKLDVFSVGALAAYLLTGAPAANTVAELHEHLATHQGLDVSVALPSVPEPVRQAILHATD
+PRPTARTATLNDFLAGLTEAQATAPQPASPALDPLEAAPGQALDSRFTLVRRLGKGSTAVGLLVDDAQTGSRQVLKV---
+--ALDDEAATRLDDEAQVLRLLPLHKRLVRLLDGPF--DVGGR--RALLLTSAGTRTLSEVLRERQRLSLDHLERFGSEL
+LEAAQALDAAGLRHRDVKPANIGVVRTPKHGEHLVLFDFSLARARSTDVRA-----GTPPYLDPFLEQGGRTGYDSAAEL
+YAVAVVLYEMASGQKPFYGDPEANPA--AVRDDLTVPDGIFDPSLQAPLSALFERALARDAQARFHTVAELAAAWEALFR
+NDA-------------DPVTAQDAETLAARAT-----LETPLSEAGLSARGLSALEAIKV----TAGPGGVAVEPHDVRT
+VRDLVLVD-PIKLNSLAGSTTETRAEVRARAKQWRAAFKKELMRQATQV-PQGTLPTPLDAAELLLRHAGAAHAEGVRAQ
+LR---LVLGLDGEVPALSTHAVLADARGVT----------------PGLVPQLFGRAQQAWTDVAETRSLLDSLDGALRA
+----------------AVAERGGVSTPDELTSALEQTLSPATPAEVRDAEPRRIVQGLLWLLLDRERAAARGEADVPALV
+QRRREGRVVAVAEMPVLLDVAETLGAAAEAAVDGAGDPESALVPADLVQTR-VAAVLDAVDGLPEALRSWRRAAALAAHV
+SATTCLSAAGEWHHRLLAPATAAHHALQGASGTVQLSRERAAERVGARFPALSPLPRDAALDRVLAEAELGLVFDEDLGP
+QGAYRSRQTLAPTTGFATRAETRLVEHQRPLSELGVEGQRLLDSQRNRSYLALGVPAQRLARLESALVRRFHAEPLDLTD
+LFIRLLKDQAAAHPKMTWDHVTAADAEPDGSRPAQGLNVLVRNLLPELEQHLSRTIGDPGRAASPVLLTGAAVLARYGHL
+GVLARWADLAEYRARPVWLVVPQVAGNVGPRLDGVSVPKNTPGQYVPLTPEWIDGLAALMAAQPLTEESRT
+>1_1050
+M-------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------------------------SSARRDPL---VGGIVDGRYRVVERLARGGMSTVYLAVDERLDRQVALKVMHP
+HLAEDPVLVGRFEQEAKTTARLS-HPHVVAVLDQGHTEAEDGDVLAYLVMEHVPGRTLRTVIRDRAPLSPREALRFLRPL
+VDGLAAAHRAGLVHRDVKPENV-LVRDDG---RVTVADFGLSRAATAHTMAGQAVVGTPAYLAP--EHIAGAPADARSDV
+YAVGIILFELLTGRQPYTAATALQVAYRHVHERVPVPSTL-HPGLPEDLDDLVLWCTEPDPADR------PAGAGELLHR
+IDAVAAGL--------DP-DEPDRH------P-----AEGPGAEPAVAAPAADGPEDAAP----DGNLQTRALDAGDHHA
+TRVLPALA-ESDLDADMTDVIDTRAATRGADRRPAA-------HPAEPIGPLGLDPAPAD------RHPGRESPRRLRRA
+ARRPALDLGQGTGRAAAIGAAVTLLLTGVALLLGWTLGSGGLGVGGVAVVPDLDGLAREA----AEERLTAAGFTAAVTA
+RHNELRTEGTVVASSPAAGEPAGRGTPVELTVS-------AGPAPVP-------VPDLTGVVIRRAHGVARDARFTVEVA
+ERRTDPAVPAGA-------VIEQHPAPGEQATPGTA------VRVVLSEGRAVRPVPDVTGQDPETARTTLADDGWDARV
+HRLP-LPLAGRGESRVLHQSPAAGTAL----------------------------------------------------P
+EGT-----------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-------------AVHVWV---------------------------------------------------G
+>2_1494
+M-------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------------------------SSTRRDPL---VGGIVDGRYEVLARLARGGMSTVYLALDTRLDREVALKVMHP
+HLAEDPVLVGRFEQEAKTAARLS-HPHVVAVLDQGHTEDASGEVLAYLVMEHVPGHTLRTVIREQAPLTPREALRHLRPL
+VDGLAAAHRAGLVHRDAKPENV-LVRTDG---RITVADFGLSRAATAHTSAGQAVVGTPAYLAP--EHIAGAPADARSDV
+YAAGIILFELLTGRQPFTAGTALQVAYRHVHERVPVPSSL-QPGLPEALDDLVLWCTEPDPADR------PADAGEVLDR
+LDAVAAEL--------GP-AELDRPPV--LVPDAVEGRPGPEHDETTTLDALDRLDPKDPLDDADGD-ETTSLDAGDHHA
+TRVLPSLP-ADALPTE---------------------------------------ALAAD------DVVRRSPARRRRR-
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-------------------------------------------------------------------------------P
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-----------------------------------------------------------------------
+>3_1389
+M-------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------------------------SSTRRDPL---IGDLVDGRYEVLDRVARGGMSTVYRALDHRLDREVALKVMHP
+HLAEDPALVGRFEREAKTAARIS-HPHVVAVLDQGHTADEAGDVLAYLVMEHVPGRTLRAVIREEAPVAPRRAVALLEPV
+VEGLAAAHRAGLVHRDVKPENV-LVRTDG---RITVADFGLSRAATGHTSAGQTVFGTPAYLAP--ELISGTGGDARADV
+YGVGIMLFELLTGTQPFTAATPLQVAYRHVHERVPVPSSV-RPGLPEALDDIVLWCTEPRPADR------PEDAAALLPE
+LRRVAALLPQTAPADEAP-AADDAPTVALAVSPTVPTVPVPD-----AADATARLEPRRP--DPRRA-EPVPTPAT---A
+TAASPSSDLSSAVPEA---------------------------------------PRPAP------VAPRPASARQRRRT
+ARTPEVVLGAGMGRTVAVGAAVTLLLAGMALLLGWILGSGGISGPAGVVVPPLWGLEQQE----AAARLAEAGLTSAVVS
+RHDERFSDGVVLDVSPAAGSTVDAGGPVRLTVS-------DGPAPVP-------APDLAGLTVTDAHAVAEDGRVGVVVA
+DRVADRAVPAGA-------VVSQSPEAGAEMTPGDE------VAVVLSTGPATHPLPDLGGLTVGEARTRLADLGFVPDV
+RTLP-LPGPSGDAARVLRQGTPAGTVL----------------------------------------------------P
+EGA-----------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-------------SVQLWT---------------------------------------------------L
+>4_1275
+M-------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------------------------SSARRDPL---VGGIVDGRYRVVERLARGGMSTVYLAVDERLDRQVALKVMHP
+HLAEDPVLVGRFEQEAKTTARLS-HPHVVAVLDQGHTEAEDGDVLAYLVMEHVPGRTLRTVIRDRAPLSPREALRFLRPL
+VDGLAAAHRAGLVHRDVKPENV-LVRDDG---RVTVADFGLSRAATAHTMAGQAVVGTPAYLAP--EHIAGAPADARSDV
+YAVGIILFELLTGRQPYTAATALQVAYRHVHERVPVPSTL-HPGLPEDLDDLVLWCTEPDPADR------PAGAGELLHR
+IDAVAAGL--------DP-DEPDRR------P-----AEGPGTDPAAAAPAADGLEGAAP----DGDLPTRALDAGDHHA
+TRVLPALA-ESALDDDVTDVIDTRAATHGGDPRPAA-------RPAEPVGPLAVDPAPAD------RHPGRGSRRRLRRA
+ARRPALDLGQGTGRAAAIGAAVTLLLTGVALLLGWTLGSGGLGVGGVAVVPDLDGLAREA----AEERLTAAGFTAAVTA
+RHDELRTEGTVVDSSPAAGEPAGRGAPVELTVS-------AGPAPVP-------VPDLTGVVIRQAHGVARDARFTVEVA
+ERRTDPAVPAGA-------VIEQHPAPGEQATPGTA------VRVVLSEGRAVRPVPDMTGQDPETAHTTLADEGWDARV
+HRLP-LPLSARGESRVLHQSPAAGTAL----------------------------------------------------P
+EGT-----------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-------------AVHVWV---------------------------------------------------G

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

@@ -0,0 +1,55 @@
+>0_1398
+-----------------------------------MPPGPGALLGGRRVRLLPAILALAL
+GSFAIGTTEFAMMGLLPQAVADLGVGLEAGGVLISMYALGVVIGAPLLAASFARVDRRVT
+SIVLMLLFVVGHVAAFLAPDMGSMMAARFVSGLPHGAYFSAAALAAADLAGPARRGQAVA
+WVMAGLSVANVLGVPGATALGQAVGWRWMFVIVAVCAALCVGATAWLVPSVPAPAGASVG
+-----RELRGLASGRLWATVAVGVIGFAGMFALYTYIAPLLTEVAGLEERWVPAVLALYG
+VGMVIGTLVSGALTDRDPVGTLRLSFGLSAVSLAAVAL-TAPWA-PVMIVFLFCVA----
+-VSGSGIAPSLQVLLVDSAPTAPQLAGSLNHSALNMANAMGAWVGAAAIGAGASLRTPPL
+VGAGIALAGLVLAFLLVRRDVAASPGVRADDGGSPR-------------
+>1_1139
+MPTPTPAADGAHDRSPRAPRPTRPDPS----IPPTAPTGPGALLGGRRVRLLPAILALAL
+GSFAIGTTEFAMMGLLPQAVADLGIGLEAGGVLISMYALGVVIGAPLLAASFARVDRRVT
+SIVLMLLFVVGHVAAFLAPDAATMMAARFICGLPHGAYFSAAALAAADLAGPARRGQAVA
+WVMAGLSVANVLGVPAATALGQSAGWRWMFVIVATCAALCVAATAWLVPPVPAPEGASVR
+-----RELRGLASGRLWATVAVGVLGFAGMFALYTYIAPLLTTVSGLDERWVPAVLALYG
+VGMVVGTLVGGALTDRDPVRTLRLSFALSAVFLLGVGL-TAQWA-PVMVVFLFLVA----
+-VSGSGIAPSLQVLLVDSAPTAPQLAGSLNHSALNMANAMGAWVGAAAIGAGASLRTPPL
+IGAAIALGGLVLALLLVRRT-PAVGAVPHDGPSAATV------------
+>2_1423
+MTTP---ASGDPAASPSV--SARPDPADAAGSPAAGAVGPQSLLGGRRVRLLPAILALAL
+GSFAIGTTEFAIMGLLPQAVADLGIGLEAGGVLISMYALGVVVGAPLLAAAFARVDRRTT
+GIVLMLLFTVGHTGAFLAPDTATMMAARFVSGLPHGAYFSAAALAAADLAGPARRGQAIA
+WVMAGLSVANVVGVPAATAIGQAAGWRWMFVIVAACALACVAATAWLVPPVPAPEGASVR
+-----RELRGLASGRLWATVAVGVIGFAGMFALYTYIAPLLTEVAGLDERWVPAVLALYG
+IGMVVGTLVSGALTDRDPVGTLRLSFGLSAVSLLAVGL-TAQWA-PVMVLLLFCVA----
+-VSGSGIAPSLQVLLVDSAPGAPQLAGSLNHSALNMANAMGAWVGAAAIGAGASLRTPPL
+VGAAIALAGLVLAFVLVRRASPTSAATAADAR-----------------
+>3_1327
+------------------------------------------------MRLLPAILALAL
+GSFAIGTTEFTMMGLLPEAVTDLGVGLETGGVLISMYALGVVVGAPVLAAALARMDRKLS
+SILLMGLFVVGHLASLLAPSLGALMAARFVSGLPHGAFFSAAALAAADLAGPARRGQAIG
+WVMAGLSVANVVGVPAATALGQAAGWRWMFAVVAACALGCIAATALLVPRVPAPAGASVA
+-----AEIRGLASGRLWATVAIGVVGFAGMFCLYTYIAPLLTEVSGLHPRWVPAVLALYG
+VGMVIGTLVSGALTDRDPIRTLRWSFGVSALGLLAVSL-TAPWW-PALLVSLLVVA----
+-LSGSGIAPALQVLLVDAAPTAPQLSGSLNHSALNMANAMGAWVGAAAVGAGASLRMPSL
+IGAGIALVGLLMSVALLRRPASAPPGA----------------------
+>3_1738
+MSAVS-----------NAPRPRLP---------------------------WGALLALSA
+SGFLAIFTETIPAGLLPELSRGLGVTESAAGQLVTLYAMGSVVAAIPLVAATQTVNRKKV
+LLAAVATLGAFNLVTAAAPWLPVILAARFVAGAAAALVWGVLAGFARSLVAPQLQGRALA
+VTGLGQPIALAGGVPLGSFAASVMDWRWVFVAISVAAG---GLAVWIAAAVQNVEGSPRR
+QREPLRRVVMLPGVRLIFAVTGCWILAHNM--LYTYAAPLLNRT----DLRLDVGLGLFG
+VASMIGISLVGMVIDR----ALRL---VSAICVTAMCLATTVWLLPQVGIALAVASVVAW
+GLSFGGAPVLLQTALADRAGEHTDAAQSVFVTVFNLAVAGGGFMGGMLLASSGT------
+--AGIATTSAVLCLVAVGMIVLARAAFPAGHRHKDETDESVVAPSECSA
+>4_1347
+MPTPTPAADGAHDRSPRAPRPTRPDPS----IPPTAPTGPGALLGGRRVRLLPAILALAL
+GSFAIGTTEFAMMGLLPQAVADLGIGLEAGGVLISMYALGVVIGAPLLAASFARVDRRVT
+SIVLMLLFVVGHVAAFLAPDMGSMMAARFVSGLPHGAYFSAAALAAADLAGPARRGQAVA
+WVMAGLSVANVLGVPGATALGQAVGWRWMFVIVAVCAALCVGATAWLVPSVPAPAGASVG
+-----RELRGLASGRLWATVAVGVIGFAGMFALYTYIAPLLTEVAGLEERWVPAVLALYG
+VGMVIGTLVSGALTDRDPVGTLRLSFGLSAVSLAAVAL-TASWA-PVMIVFLFCVA----
+-VSGSGIAPSLQVLLVDSAPTAPQLAGSLNHSALNMANAMGAWVGAAAIGAGASLRTPPL
+VGAGIALAGLVLAFLLVRRDVAARPGVRADDDGSPR-------------
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000143.fa

@@ -0,0 +1,43 @@
+>0_1633
+M----PDVT---P-PPPSRSWTRRSVLGGTGLAIAAGVAGCGRDEQAEQSSEGDEQAT--
+--RLPAPDIITTAQWGAMQPNYYLQTLNERPSYLVIHHTTTPNVTDGSREAAESIAQVVQ
+NAHMGSANDWGDTGQHFTVSRGGFAMEGRHGSRHALEGGQTFMLGVHALGFNAYALGIEC
+EGLYMLNPPPQSLYAGLVPLVAYICQQYELPPSRIIGHRDVTATSCCGDAFYAKLPILRE
+DVRLSLASGEYHVSEGFG------AD----------------------------------
+------------------------------NLFDDAHVTP---EYVEE--ERG
+>1_1347
+M----PDVT---P-PPLPHSWTRRSVLGGTGLAIAAGVAGCGRDEQAEQSSEGDEQAT--
+--RLPAPDIITTAQWGAMQPNYYLQTLNERPSYLVIHHTTTPNVTDGSREAAESIAQVVQ
+NAHMSPANDWGDTGQHFTVSRGGFAMEGRHGSRHALEGGQTFMLGVHALGFNAYALGIEC
+EGLYMLNPPPQSLYAGLVPLVAYICQQYELPPSRIIGHRDVTATSCCGDAFYAKLPILRE
+DVRLSLASGEYHVSEGFG------AD----------------------------------
+------------------------------NLFDDAHVTP---EYVEE--ERG
+>2_1166
+M----PEQS---P-TPSSRPWARRTVLGGTGLAIAAGVAGCSRPEAGEEAEETEAAPK--
+--RLPAPDILTTAQWGALQPNYHLQTLDERPSYLVIHHTTTPNVTDGSREAAESIAKSIQ
+NAHMSTLNDWGDTGQHFTVSRGGFALEGRHGSRYTLEQGQTFMLGVHALGFNAYALGIEC
+EGLYTLNPPPQSLYAGLVPLAAYICQQYELPPSRIIGHRDVTATSCCGDAFYGKLPVLRE
+DVRLSLATGEYHVSEGFG------AD----------------------------------
+------------------------------NLFDDAHVTP---DYLQE--QGY
+>3_30
+MKHALPRHVQHAPVPPAAASPGRRAVLVG-GLA-AAGAAGA--------AAAGAVPAA--
+--AFAGPVVHSTAQWGARSPRSAAEVVRARPTRLVIHHMASPNTAETSLAHAYGLARACQ
+QDHMG--RGFDDSGQHFTVSRGGHCLEGRAGSLAALRAGDRHVKGAHVSGQNTGKIGIEC
+EGSYVTGLPTPAQYRALVQLAAHICRQYGIRPADIVGHGDLMATQCPGGAFHARLGVLRA
+DVARTLATGRLSVSDPSGRAASIPADPRRAATTTPSAAAPASRRVLGPGSRGADVKRVQA
+LLTTAGHRVPRTGLYAARTTAAVRAFQRRSGLAQDGFTGPLTWAALEAAGRR-
+>3_1097
+M----PDHQ------ILSSSWPRRAVLGGAGLAIAGTVAGCGTGGDAAQSTSADGSAAST
+GPRLPEPEILSTIDWGARIPENWQQTLYEKPSYLVIHHTTTPNVTDGSRDAAIALAQRVQ
+NQHIN--QQWGDSGQQFTMSRGGFAMEGRHGSLYALQGGETFILGVHALGFNAYAVGIEC
+EGFYMVSPPPQSLYAGLVKLSAFICQQYELPPSRIIGHRDVVKTSCCGDAFYAKLPILRE
+DVKRSLETGEYQITEGFG------AD----------------------------------
+------------------------------NLLDDAKINV---ENYEDFQKRS
+>4_1562
+M----PDVT---P-PPLPHSWTRRSVLGGTGLAIAAGVAGCGRDEQAEQSSEGDEQAT--
+--RLPAPDIITTAQWGAMQPNYYLQTLNERPSYLVIHHTTTPNVTDGSREAAESIAQVVQ
+NAHMSPANDWGDTGQHFTVSRGGFAMEGRHGSRHALEGGQTFMLGVHALGFNAYALGIEC
+EGLYMLNPPPQSLYAGLVPLVAYICQQYELPPSRIIGHRDVTATSCCGDAFYAKLPILRE
+DVRLSLASGEYHVSEGFG------AD----------------------------------
+------------------------------NLFDDAHVTP---EYVEE--ERG
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000144.fa

@@ -0,0 +1,55 @@
+>0_1721
+MS-----------TAPALPPLPGA-------------PGGPALPSVEELLADAVAVAVPM
+RVRFRGTDLRHALLLRGPAGWGEFSPFPEYGPHESAAWLAAAIEAGWQGWPAPVR-----
+---------ETIPVNATVP--------------------AVDADDVEAVLARYGDGITA-
+---VKVKVAEHGPEGGLVPGGREADLARVRRVRALLPHAQVRVDANAGWTPAEAVDVLTE
+LADVGL--EYAEQPVPG--ITDLAEVRAELRARGVPTPIAADEAVRKAEDPLAVAAAGAA
+DLIVVKVQPLGGVRRAAAI---VAAAGLPAVVSSALDTSVGIAGGAALAACLPSLPHACG
+LGTAALFEHDVVAPAWRPRAGALPAPGERAPAPDPELLDRIRADGTRQAWWADRVRAAHA
+VLAAQG-
+>1_1438
+MS-----------TAPALPPLPGA-------------PGGPALPSVEELLADAVAVALPM
+RVRFRGTDLRHALLLRGPAGWAEFSPFPEYGPHECAAWLAAAIEAGWQGWPGPVR-----
+---------QTVPVNATVP--------------------AVAADDVEAVLARYGDGITA-
+---VKVKVAEHGPEGGLVPGGREADLARVRRVRALLPHAQVRVDANAGWTPAEAVDVLTA
+LADVGL--EYAEQPVPG--ITALAEVRAELRARGVPTPIAADEAVRKAEDPLAVAAAGAA
+DLIVVKVQPLGGVRRAAAI---VAAAGLPAVVSSALDTSVGIAGGAALAACLPSLPHACG
+LGTAALFEHDVVAPAWRPRAGALPAPGERAPAPDPELLDRIRADGTRQAWWADRLRAAHA
+VLAAQG-
+>2_1077
+-----------------------------------------------------------M
+RVRFRGTDARQALLLRGPAGWAEFSPFPEYGPAESSAWLAAAIEAGWQGWPAPVR-----
+---------DVVPVNATVP--------------------AVEAEAVESVLARYGEGITA-
+---VKVKVAEHRPGGGLVPGSHSADLARVRRVRELLPDAHVRIDANAGWTPAEAIAMLTD
+LADVGL--EYAEQPVPG--IKKLARVRRELRARGVSTPIAADEAVRKAEDPLAVAAAGAA
+DLIVVKVQPLGGVRRAAAV---VAAAGLPAVVSSALDTSVGIAGGAALATHLPALPHACG
+LGTAALFDDDVVTPAWTPRQGVLEAPGERAPEPDPALLARVRADERTHAWWRDRVAAAHA
+VLAAGGR
+>3_1002
+MTVPAAHDDADPRPGSALPPLPGA-------------PGGPALPDVDELLEHAVAVTLPM
+TVRFRGTTERRALLLRGPAGWAEFSPFPEYGPAEASRWLAAAVEAGWQGWPAPVR-----
+---------SEVPVNATVP--------------------AVDAADVESVLARYGDGITA-
+---VKVKVAEHRPGGGLVDPTHAADVARVRRVRELLPEAAVRIDANAGWDEDRAFAVLGA
+LQDVGL--EYAEQPVPG--IAGLAALRSRLRAAGIATPIAADEAVRKETDPLAVAQAGAA
+DLIVVKVQPLGGVRRAAAI---VAAAGLDAVVSSALDTSVGIAGGAALAAHLPSLPFACG
+LGTASLFAHDVVSPAWRPADGSLPAPGERAPEPDPALLAAARADAAEHAWWAERLRAAHA
+VLAARGR
+>3_1768
+MS-----------PAPGQAPVSVAAVRRHRHRAPLLHPFVTAARRTEAVEYVVVEVELSD
+GTVGQGSAAETVAVTGEDAASIETAVDGVFGPALTGA--TGGLDGLLARLPAPARGATSA
+RSAVDVAVHDAVARAAGVPLTALLAPAGTAVKQTLENDMTVSLEDPATMAARAAEAVAAG
+TRILKIKLGRDV----------AEDRRRLHAVLEAAPQARLRLDANQGWSVEDAIAIISG
+MEDEGLPVDLVEQPVAAADVAGLARVRA-----AVTTPIMADEALWSSEDARRLIEAGAA
+DLFNVKLAKTGGLADAVAIADLAAEHGIGCMVGSMMEPRISIAAAVQLSLAHPAVTMV--
+---------DLDAPLWFASDA--PAGGYTQEGADLRLLPG-------EGLALERLDPGTD
+PV-----
+>4_1650
+MS-----------TAPALPPLPGA-------------PGGPALPSIEELLADAVAVALPM
+RVRFRGTDLRHALLLRGPAGWAEFSPFPEYGPHESAAWLAAAIEAGWQGWPAPVR-----
+---------QAVPVNATVP--------------------AVDAADVEAVLARYGDGITA-
+---VKVKVAEHGPEGELVPGSREADLARVRRVRALLPHAQVRVDANAGWTPTEAVDVLTA
+LADVGL--EYAEQPVPG--ITDLAEVRAELRARGVPTPIAADEAVRKAEDPLAVAAAGAA
+DLIVVKVQPLGGVRRAAAI---VAAAGLPAVVSSALDTSVGIAGGAALAACLPSLPHACG
+LGTAALFEHDVVAPAWRPRAGALPAPGERASAPDPELLDRVRADGARQAWWADRVRAAHA
+VLAAQG-
+ 

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

@@ -0,0 +1,31 @@
+>0_1731
+MDAP----ASDLTGKARIRHAALRLFAHHGVEGTSMRAIAEEASVTVGLITHHYGSKAGL
+HREVDAAVADDFAAAIASVPAEGTARDVTLRRDAAVAEMLRARPDVLEYVRRHVLLGEPA
+ADSQLVEKLTALAREQVRQLRAAGLISGRRDEVPQVVSMIMRMLGELFFEPLVDRI----
+---VDAVDRDAARPAVVVRVQAAEDETARGGRA
+>0_1990
+MNTPLPFDQDDLSSPARLRLAALELYAERGVEMASVREIAQRAGVAPGLVRHHFGSKAGL
+TRAVDDDVLRLIAATLDEVPLVGTPQEVSAARDAAFADLLADHPVVGAYVRRSLLEAGGE
+TES-LLERLVDLTTEQTERLRRSGF-APRRSMPTSVFGTVIRQMGHLMVDPSADRIWRRI
+AETQEGAAEQAS-PRVRLVVDPP-----R----
+>1_1707
+MNTPLPFDQDDLSSPARLRLAALELYAERGVEMASVREIAQRAGVAPGLVRHHFGSKAGL
+TRAVDDDVLRLIAATLDEVPLVGTPQEVSAARDAAFADLLADHPVVGAYVRRSLLEAGGG
+TES-LLERLVDLTTEQTERLRRSGF-APRRSMPTSVFGTVIRQMGHLMVDPSADRIWRRI
+AETQEAAAEQRS-PRVRLVVDPP-----R----
+>2_1065
+MDAP----ASDLTGKARIRHAALRLFAHHGVEGTSMRAIAEEASVTVGLITHHYGSKAGL
+HREVDAAVADDFAAAIASVPAEGTARDVTLRRDAAVAEMLRARPDVLEYVRRHVLLGEPA
+ADSQLVEKLTALAREQVRQLRAAGLISGRRDEVPQVVSMIMRMLGELFFEPLVDRI----
+---VDAVDRDAARPAVVVRVQAAEDETARGGRA
+>3_711
+MNTARPLTREDLSSAARLRLSALELYAERGEHAASIRDVGRHAGVAPGLVRHHFGSKDGL
+TRAVDDDIIDLVRATLEAVPLEGTPLEISAARDAAFQELLQERPLIGGYLAQALTASRAS
+GES-VLDRLVDLSAEQTRQLIDRGL-DPRRGLRTSVFTTVVRQVAVFLVAPVAERAWNRL
+GHTLEGASDVAPMPPVRVVVGPAPEEDRR----
+>4_1925
+MNTPLPFDQDDLSSPARLRLAALELYAERGVEMASVREIAQRAGVAPGLVRHHFGSKAGL
+TRAVDDDVLRLIAATLDEVPLVGTPQVVSAARDAAFADLLADHPVVGAYVRRSLLEAGGE
+TES-LLERLVDLTTEQTERLRRSGF-APRRSMPTSVFGTVIRQMGHLLVDPSADRIWRRI
+AETQEDAAEQAS-PRVRLVVDPP-----R----
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000151.fa

@@ -0,0 +1,48 @@
+>0_1861
+M----VLPVLPALATPPLLTALDRLL-AGETVPSGVEGDIQDGAAATTRAFGVEWGTLLTVLMAFAIGAAVVYLALQVAR
+VVLVRRPAFQHGAARLSLPAAVAAGLLASRIWLGVMAEEQAWYRPASFLLLIAVAAAGAWAAWRLVGVIEAGILGRYQET
+GVEHRRERRIRTQTILIRRILNAVIVVVVVAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDA
+IRVGDVVDMEGVFGTVEEITLSNVVVKLWDGRRVVYPSSHFTTQPFENWTRVGTEVSGVVELDVDWRVPMDALRARLAQL
+LESTDLWDG-REHALQVTDATGGVVRI----RAVVSARNSGDLWDLRCLVREDLVAFLRHEHPEGIVVQRMVVRHP----
+--AHDDAAPASEGSDAGARGGDRTGEPGPDGSGVAAR-EPRPRTAPLPRVDGADPRPHTLTTPLTRVGDHSGLYTGSMTA
+VQRNRELAGPGEEAFAERRAQQAKQAAEAAAADEAGRRSGAGSHADGPLDDAVTRRRQDDED
+>1_1568
+M----VLPVLPALATPPLLTALDRLL-AGETVPSGVEGDIQDGAAATTRAFGVEWGTLLTVLMAFAIGAAVVYLALQVAR
+VVLVRRPAFQQGAARLSLPAAVAAGLLASRIWLGVMAEEQTWYRPASFLMLIAVAAAGAWAAWRLVGVIEKGILGRYQET
+SVEHRRERRIRTQTILIRRILNAVIVVVAVAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDA
+IRVGDVVDMEGVFGTVEEITLSNVVVKLWDGRRMVYPSSHFTTQPFENWTRVGTEVSGVVELDVDWRVPMDALRARLAQL
+LESTDLWDG-REHALQVTDATGGVVRI----RAVVSARNSGDLWDLRCLVREDLVAFLRHEHPEGIVVQRMVVRHP----
+--AHDDAAPASEGSDAGARGGDRTGEPGPDGSGVAAR-EPRPRTAPLPRVDGADPRPHTLTTPLTRVGDHSGLYTGSMTA
+VQRNRELAGPGEEAFAERRAQQAKQAAEAAAADEAGRRSGAGSHADGPLDDAVTRRRQDDED
+>2_768
+MDLPQITP------------------------------------------------------------------------
+-------------------------------------------------LAVAVGLAVAVVGWLLGRLLGAGVAWLFA--
+----RRGRSPSSARVFGKLVAAGITVLSLGAAVTVVFPSVKPV--DLLGGIGVISIAAGIAFQTVLGNMFAGMVILARDR
+FRVGDQIQVGEHAGNVVEMGLSSTAVKTFDGRLVLIPNQMLHSQAVTVQTGFSAVRS---SLRVDVETGNDLARTREIAV
+RAMSELPQVLRDPAPQALLASVGVTTVGMDLRFWSGARQMETKEAMDAVIHAVLTAFEKNGVATGDDV-RVVDAGP-ELR
+RILEGPGAPRGQG--------------GPDYPG------------------G----------------------------
+------LAGPGE---------------PDRAARP-------------------------GSD
+>2_919
+M----LLAALSGPASPPVLGSLARLF-AGENVPAGVEGNVQDGAAATTAALGVEWGTLLTVLVAFAVGATLVYAALQVTR
+VVLVRRPAFQHGAARLSLPAAVAAGLLASRIWLGVMAEEQTWYRPASFLLLIAVAAAGAWAAWRLVGVIEAGILGRYQET
+GVEHRRERRIRTQTILIRRILNAVIVVVAIAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDA
+IRVGDVVDMEGVFGTVEEITLSNVVLKLWDGRRMVYPSSHFTTQPFENWTRVGTEVSGVVELDVDWRVPMPALRERLTQL
+LDSTDLWDG-RESSMQVTDAIGGTVRI----RAVVSARNSGDLWDLRCLVREDLVTFLRSEHPEAIVVQRVVERHP----
+--AHDDAVPASEGSDAGARGGDPTGEPGPDGSGVAAR-EPRPRTAALPRVEGGEPRPDTVTTPLTRVDDHAGLYTGSITA
+VQRNRELHGPGEDAFAERRAQQAKQAAEAATADEAGRRSGAGSHADGLLDDAVTRRRQDDED
+>3_855
+MPVPALLPVLAQTASSDAALSDAVLSAADQVVPGSVEQDVQQGASAASAALGVEWATVAAVLGAFLAGGLVVLGVFLVAR
+LALFRRDRLKADAARLTVPVSLFAGFLTARVGLEVMAHGQPWFEAAAFVLLLAVAASAAWAAWRVVDVVESGILARYHQP
+GVNDRRERKIRTQTMLLRRVLNAVIVVVALAVVLLAIPQVRSLGAGLLASAGLISVIAGLAVQSTLTNVIAGFQLAFTDS
+IRVGDVVDMQGVFGTVEEITLSNVVVKLWDGRRMVYPSKHFTSEPFENWTRTGAAVAGVVEMDVDWRVPMDPLRARLTEL
+LESTDLWDG-RENAMQVIDAVGGMVRI----RAVVSAKNSGELWDLRCLVREDLVGFLRAEYPEGIYTQRLVERRPSDPA
+PEAHDDPAPDAHDDAAPAAA---PAAPAPSDRGSSTRAEPTPQTRPMPTVTG--------SVPLARAGENASLYTGSIRA
+VERNQEMDGPGEEAYAERRARAAER--EDRAARDAGR---GGAHA--------------ARS
+>4_1782
+M----VLPVLPALATPPLLTALDRLL-AGETVPSGVEGDIQDGAAATTRAFGVEWGTLLTVLMAFAIGAAVVYLALQVAR
+VVLVRRPAFQHGAARLSLPAAVAAGLLASRIWLGVMAEEQAWYRPASFLLLIAVAAAGAWAAWRLVGVIEAGILGRYQET
+GVEHRRERRIRTQTILIRRILNAVIVVVVVAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDA
+IRVGDVVDMEGVFGTVEEITLSNVVLKLWDGRRMVYPSSHFTTRPFENWTRVGAEVSGVVELDVDWRVPMDALRARLTQL
+LESTDLWDG-REHALQVTDATGGIVRI----RAVVSARNSGDLWDLRCLVREDLVSFLRHEHPEGIVVQRMVVRHP----
+--AHGDASPASEGSDAEARGGDRTGEPGPDGSGVAAR-EPRPRTAPLPRVDGADPRPDTLTTPLTRVGDHSGLYTGSMTA
+VQRNRELAGPGEEAFAERRAQQAKQAAEAAAADEAGRRSGAGSHTDGLLDDAVTRRRQDDED

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000159.fa

@@ -0,0 +1,25 @@
+>0_2009
+M-----------------STTTSITAAGLETMNGPEG--------CCTLSAGP--VDSVE
+AERIASLLKALSDPTRLRLLSHVAAQGCNSVCA-CDLTEPLGISQPTVSHHMKKLVDAGL
+LTREQKGRWAHYSVVPSAFAELRSFLD-------IA
+>1_1068
+MDVKVYVPEFAVEFDTCQYVPMSMSGL--SARDAALG-------YCTPLAREP--ITPAQ
+AEGVSRMLKALADPVRLRLMSMILSHEGAEACAMCDLTEGFDLSQSTLSHHLKVLHDAGL
+VDRDKRGVWVYYKARTEAMDALRTLFSGDLAAPQLA
+>2_542
+M-------------TACSVPVSTAAAP--VLADD-----------CCSLADGP--LGAED
+AAELAVLLKALADPMRLRLLSHVAARGCADVCA-CDLTEELGIAQPTVSHHMKRLVDAGL
+LTREQRGRWAHYTVVPEAFARLRRVLV-------LG
+>2_725
+M-----------------VATTTIPAP--EDTDRPEGDDALGSVACCSLSAGP--IDAAQ
+AQRAAGMFKALADPMRLRLLSHVAAQGCAAVCS-CDLTEELGISQPTVSHHMKKLVEAGL
+LTREQRGRWAHYTVVPAAFAELGRMLE-------LG
+>3_469
+---------------------MTTTAP--SPSD------------TCCAPAGPALLPAEH
+AARLAAVFKALADPTRVRVLAHVAASPEGTVCA-CHLPEPLGISQPTLSHHLKTLTAAGL
+VTREQRGRWAHYTAVPAALDAARAFLADPAGA----
+>4_1938
+M-----------------STTTAITAAGLETMNGPEE--------CCTLSAGP--VDSVE
+AERIASLLKALSDPTRLRLLSHVAAQGCNSVCA-CDLTEPLGISQPTVSHHMKKLVDAGL
+LTREQKGRWAHYSVVPSAFAELRSFLD-------IA
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000163.fa

@@ -0,0 +1,132 @@
+>0_2037
+MATADSGDVLPHLRTEAIRAVVGPTSADRGFAVAASGAVGRLRYDAATGRLSASVQGTAPSPYRVQVQLQEAYDDAAEDG
+AGALMEPVGGRCTCPVGTDCKHVAAALYQVVRLDADQALDDARRKLAEMVTTADALPAPAGRGHD-----GGGPAGLDA-
+PAADGAAPPPP-AGLDWRRVMEPLAGLH-GPRRVGTPPALAIGVELVAESSRNAFQQWGPATAGEEQVREGRPLYVTVRP
+LKRGAKGTWIKGGLTWKAFQFPRAEFAPAQERAMRLIWRQVQAEDSYPGDAWFGLHVFDSPRIWQLLAEAREVGVELVPL
+GLLTDVVLEAPVAVGLDVTAAPDGGLDVAPSLDPA---------------PPGPGLSGVHAVGGIGFYRV-ELTDEEAVL
+HLIPAARPVPEAVQQLVLAGGPVRVPAADREEFLGRIYPRLRGALPVTSGDASVELPEFEPPVLRLRADFRPGHELVLRW
+SWLYFDPPRELGLDAGGDPLRDTRHEDAVLRAVAELWPRAGRAEEQVLEGVGAARFSEQVLPLLQRADHVRVDVTGDRPD
+YRELKAAPRIEVGTKATQNDWFDLGVQVSVDGHVLPFVELFTALVQGRTTLILADGSYLGLDHPAFDRLRALLSEAATLQ
+EWTPEHTPVSRHQVGFWEDLKELADEVDEDPEWTAAVGRLAAVERLPEAPRPAGLKADLRPYQEEGLRWLAFLWEQDL-G
+GILADDMGLGKTVQTLALFAHARQARPEPPPFLVVAPSSVVSVWAAEA-EKFTPDLDVRVLDTTTRKRGTAVADEVAG--
+ADVVVTSYTL-LRIDAGQYGGLDWGGVVFDEAQFLKN----RAAKVHTVARDLRAPFR-LAITGTPMENSLSDLWALLDV
+VVPGLFPSHRRFRETYVTPIETGGDP---ERMAALRRRVRPFMLRRSKEL---VAKDLPSKQEQILQVELEPA--HRKLY
+DRV---LQRER----------------RKVLGL----------------------------LGDMDGNRFTIFTSLT---
+-----------------------------------LLRMLALAPQIVDDQYASVPSSKLERFLDDLTEVIGEGHRVIVFS
+QFTSFLRVIAEEL-------------------DHLEIEHAYLDGSTRG-----------RADVIRGFR-EGEAPVFLISL
+KAGGFGLTLTEADYVFLMDPWWNPAAEAQAVDRAHRIGQERTVMVYRLVSEGTI-EEKVLELQRRKAELFGALMDESDDS
+GAGAFTDSL--------------TAEDI----REMLG-------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---AEE---------------------------------------------
+>1_1755
+MATADSGDVLPHLRTEAIRAVVGPTSADRGFAVAASGAVGRLRYDAATGRLSASVQGTAPSPYRVQVQLQEAYDDAAEDG
+AGALMEPVGGRCTCPVGTDCKHVAAALYQVVRLDADQALDDARRKLAEMVTTADALPAPAGRGHD-----GGGPAGLDA-
+PAADGAAPPPP-AGLDWRRVMEPLAGLH-GPRRVGTPPALAIGVELVAESSRNAFQQWGPATAGEEQVREGRPLYVTVRP
+LKRGAKGTWIKGGLTWKAFQFPRAEFAPAQERAMRLIWRQVQAEDSYPGDAWFGLHVFDSPRIWQLLAEAREVGVELVPL
+GLLTDVVLEAPVAVGLDVTAAPDGGLDVAPSLDPA---------------PPGPGLSGVHAVGGIGFYRV-ELTDEEAVL
+HLIPAARPVPEAVQQLVLAGGPVRVPAADREEFLGRIYPRLRGALPVTSGDASVELPEFEPPVLRLRADFRPGHELVLRW
+SWLYFDPPRELGLDAGGDPLRDTRHEDAVLRAVAELWPRAGRAEEQVLEGVGAARFSEQVLPLLQRADHVRVDVTGDRPD
+YRELKAAPRIEVGTKATQNDWFDLGVQVSVDGHVLPFVELFTALVQGRTTLILADGSYLGLDHPAFDRLRALLSEAATLQ
+EWTPEHTPVSRHQVGFWEDLKELADEVDEDPEWTAAVGRLAAVERLPEAPRPAGLKADLRPYQEEGLRWLAFLWEQDL-G
+GILADDMGLGKTVQTLALFAHARQARPEPPPFLVVAPSSVVSVWAAEA-EKFTPDLDVRVLDTTTRKRGTAVADEVAG--
+ADVVVTSYTL-LRIDAGQYGGLDWGGVVFDEAQFLKN----RAAKVHTVARDLRAPFR-LAITGTPMENSLSDLWALLDV
+VVPGLFPSHRRFRETYVTPIETGGDP---ERMAALRRRVRPFMLRRSKEL---VAKDLPSKQEQILQVELEPA--HRKLY
+DRV---LQRER----------------RKVLGL----------------------------LGDMDGNRFTIFTSLT---
+-----------------------------------LLRMLALAPQIVDDQYASVPSSKLERFLDDLTEVIGEGHRVIVFS
+QFTSFLRVIAEEL-------------------DHLEIEHAYLDGSTRG-----------RADVIRGFR-EGEAPVFLISL
+KAGGFGLTLTEADYVFLMDPWWNPAAEAQAVDRAHRIGQERTVMVYRLVSEGTI-EEKVLELQRRKAELFGALMDESDDS
+GAGAFTDSL--------------TAEDI----REMLG-------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---AEE---------------------------------------------
+>2_663
+MATADSGDVLPHLRTEAIRAVVGPTSADRGFAVAASGAVGRLRYDAATGRLSASVQGTAPSPYRVQVQLQEAYDDAAEAG
+AGALMEPVGGRCTCPVGTDCKHVAAALYQVVRLDAHQALDDARRKLAEMVTTADALPAPAGRGHDDAARPDAGPRGAAAG
+PDGESAAPEAPHSGLDWRRVMEPLAGLD-APRRLGAPPALAIGVELVAESSRNAFQQWGPAPAGEDQVREGRPLYVTLRP
+LKRGAKGTWIKGGLTWKNFQFGRAEFAPAQERAMRLIWRQLQAEDSYPTDAWFGLHSFDSPRIWQLLAEAREVGVELVPL
+GLLTDVVLEAPAAVGLDVARAPDGGLDVAPSLDPA---------------PPGRGLAGVHAVGGIGFYRV-ELTDEEAVL
+HLIPAERPVPEAVQQLVLAGGPVRVPAVDREEFLGRIYPRLRGALPVTSGDASVELPEFEPPVLRLRADFRPDHELVLRW
+SWLYFDPPRELGLDAGGDPLRDTRHEDAVLRAVAELWPRAGRAEEQVLEGVAAARFSEQVLPLLQQAEHVRVDVTGHRPD
+YRELKSAPRIEVGTKATKNDWFDLGVQVSVDGHVLPFVELFTALVQGKTTLILADGSYLGLDHPAFDRLRALLSEAATLQ
+EWTPENTAVSRHQVGFWEDLKELADEVEEDPEWTAAVGRLAAVERLPEAPEVPGLQADLRPYQEDGLRWLAFLWEQDL-G
+GILADDMGLGKTVQTLALSAHARQARPERPPFLVVAPSSVVSVWAAEA-QTFTPDLDVRVLDTTVRKRGTDVAAEAAG--
+ADVVVTSYTL-LRIDAGQFGGIDWGGVVFDEAQFLKN----RAAKVHTVARDLRAPFR-LAITGTPMENSLTDLWALLGV
+VVPGLFPSHRRFREAYVTPIETGEDP---ERMVALRRRVRPFMLRRSKEL---VAKDLPPKQEQVLNVELEPA--HRKLY
+DRV---LQRER----------------RKVLGL----------------------------LGDMDGNRFTIFKSLT---
+-----------------------------------LLRMLALAPQIVDEQYASVPSSKLERFLDDLTEVIAEGHRVIVFS
+QFTSFLRVIAEEL-------------------DHMEVAHAYLDGSTRG-----------RADVIRGFR-EGQAPVFLISL
+KAGGFGLTLTEADYVFLMDPWWNPAAEAQAVDRAHRIGQERTVMVYRLVSEGTI-EEKVLELQRRKAELFGALMDESDDS
+GAGAFTDSL--------------TAEDI----RELLG-------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---AED---------------------------------------------
+>2_1470
+M-------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-----NLPLTDYQAKYYA--HELQRSYAND-----HVGKLAGL--------LFDAQVEPKPHQIDAA--LFALQTPFLPG
+VILADEVGLGKTIEAGIVISQYWAER--RRSILIVAPSSLRQQWQQELYEKFL--IPSAILDPKSKD---SLLAAAGGRS
+AQVLICSYEFALRHETSLLKA--WDLVVADEAHRLRNYWTGKTKAAEAVAHVVSGAHKTVLLTATPLQNKLEELYGLVSI
+FDPNYFYSLDAFRERYVKNRDLGGDDDLVERVATVSKRT----LRRDADKYIHFTKRLP------LTVEFTPSPDEARLY
+DLVNDYLQRDELFAFAGSQRHLSALIIRKRLGSSTYAVASTLENIANRLAEEVAAGQRRDGRGGLVTADFTVDDEITSEE
+LEEAEEIEGAGPASRPSSSPLDESLLEAMRAEVAELRDYAALARSITENQKAVKLGEALDLGFERLRE-LGAPQKAIIFT
+DSTKTQEYIARSLREAGRGDGLVLFNGSNNGPEQTAIYQAWLKANQDGDLITGIAAVDRRKALVDYFRTEG---TIMIAT
+EAAAEGINLQFCSMLVNYDLPWNPQRVEQRIGRVHRFGQKHNVVVVNFSNKGNIAEQRILELLTNKFQLFSSVFGASDEV
+-LGAIEDGLDFEKTISDILTRCRTADELDAAFRELEGQYASEISREMASAKAKVFDNLDPHVQDRLKAYDTQSGEVLNKF
+ERLLLAVTRHELDRFATFEGDGRAFVLNESPVQDVPTGRYFFKSQPLENAHQYRYASSLAQYVVDTSKGHETPARELTFS
+LGQSERVSSAIRALEGTSGELTVNLATFRMKARDEDVSESYMLAGALTDDGQWLDEEYVADILDLACISVGEQPVAIDES
+RFTPHLDARRAELEKEVQGRNSRYYDQQEELLYRNQQDRKAEHEGKIREYRAKEKEARKLARQADDPMEQLRLKKEARKW
+EQRAEEADEDFRDTRKKLRAEADKYLELIEQSLQGTQETEHLFTIRWRITT
+>3_578
+MAPGVSGDPLPHLRTEAIRALVGPTSADRGFDIAAEGGVLRVTYDASRLRLTSAVRGTAPQPYRQAVRLQPS-GETGPDG
+E-PLLEPTAGRCQCPVGEDCKHVAAALYEITRRHADAARHAAREELASRVTTADRLPSPE-RA-------GAAPARPDA-
+--------PAPEAGLPWRGVLESLAGLDGGPRRLAPPPDLAIGVELVAESSRNAFAQWGPAPAGEEHLREARLLYVIVRP
+LKRGAKGTWIKGGLTWKAFQFPRAEYDPAQERALRLIWRQLQAEDSYPTEGWFGLHAFDSPRIWQLLAEAQEAGVELVPQ
+GILADVVLDAPVEVGLDVASAPDGGLEVAPSLAPAGGAGEGAPADDAAARPDAERLRDTHAIGSIGFYRADEEEDGTWTL
+HLLPAVRRVPEPVQEMVLAGRPVHVPTADREEFLGRIYPRLRAALDVGSADASVELPEFEPPVLRLQADFRPGHRLVLRW
+SWLYFDPPRELGL--GHDGLRDPRHEEAVLRAAAQVWPRVGRAEEQELEGVGAARFSESVLPQLQRLDHVRVDVTGERPD
+YRELKAAPRIEVSTKAAQNDWFDLGVQVSVDGHVLPFVELFTALVHGKTTLMLQDGTWLGLDHPAFDRLRALLSEAAALQ
+EWTPEHTTLSRHQVGFWEDLKELADEAEEDPEWTAAVGRLAAVERLPEAPAVPGLKAELRPYQEDGLRWLRFLHDQDL-G
+GILADDMGLGKTVQTLALMAYARAEHPDRPPFLVVAPSSVLSVWASEA-AKFTPGLDVRVLDTTTRKRGTSVTEAAEG--
+ADVVVTSYTL-LRIDAAQHADASWAGIVLDEAQFLKN----RASKVHQVARDLRAPFR-LAITGTPMENSLSDLWALLEV
+VVPGLFPSHRRFRETYVTPIETGEHP---ERMASLRRRVRPFMLRRSKEL---VAKDLPPKQEQVLRVELDAA--HRKVY
+DRV---LARER----------------RKVLGL----------------------------LGDMDGNRFTIFKSLT---
+-----------------------------------LLRMLALAPQIVDREYAAVPSSKLERFLDDLEEVLAEGHRVIVFS
+QFTSFLRVVAEEL-------------------DAMEVEHAYLDGSTRN-----------RAEVIQDFR-EGDAPVFLISL
+KAGGFGLTLTEADYVFLMDPWWNPAAENQAVDRAHRIGQERTVMVYRMVSEGTI-EEKVLELQQRKAELFGALMDESDDS
+GAGAFTDSL--------------TADDI----RELLG-------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---AEE---------------------------------------------
+>4_1978
+MATADSGDVLPHLRTEAIRAVVGPTSADRGFAVAASGAVGRLRYDAATGRLSASVQGTAPSPYRVQVQLQEAYDDAAEDG
+AGALMEPVGGRCTCPVGTDCKHVAAALYQVVRLDADQALDDARRKLAEMVTTADALPAPAGRGHD-----GGGPAGLDA-
+PAADGAAPPPP-AGLDWRRVMEPLAGLH-GPRRVGTPPALAIGVELVAESSRNAFQQWGPATAGEEQVREGRPLYVTVRP
+LKRGAKGTWIKGGLTWKAFQFPRAEFAPAQERAMRLIWRQVQAEDSYPGDAWFGLHVFDSPRIWQLLAEAREVGVELVPL
+GLLTDVVLEAPVAVGLDVTRAPDGGLDVAPSLDPA---------------PPGLGLSGVHAVGGIGFYRV-ELTDEEAVL
+HLIPAARPVPEAVQQLVLAGGPVRVPAADREEFLGRIYPRLRGALPVTSGDASVELPEFEPPVLRLRADFRPGHELVLRW
+SWLYFDPPRELGLDAGGDPLRDTRHEDAVLRAVAELWPRAGRAEEQVLEGVGAARFSEQVLPLLQRADHVRVDVTGDRPD
+YRELKAAPRIEVGTKATQNDWFDLGVQVSVDGHVLPFVELFTALVQGRTTLILADGSYLGLDHPAFDRLRALLSEAATLQ
+EWTPEHTPVSRHQVGFWEDLKELADEVDEDPEWTAAVGRLAAVERLPEAPRPAGLKADLRPYQEEGLRWLAFLWEQDL-G
+GILADDMGLGKTVQTLALFAHARQARPERPPFLVVAPSSVVSVWAAEA-EKFTPDLDVRVLDTTTRKRGTAVADEVAG--
+ADVVVTSYTL-LRIDAGQYGGLDWGGVVFDEAQFLKN----RAAKVHTVARDLRAPFR-LAITGTPMENSLSDLWALLGV
+VVPGLFPSHRRFRETYVTPIETGGDP---ERMAALRRRVRPFMLRRSKEL---VAKDLPSKQEQILQVELEPA--HRKLY
+DRV---LQRER----------------RKVLGL----------------------------LGDMDGNRFTIFTSLT---
+-----------------------------------LLRMLALAPQIVDDQYASVPSSKLERFLDDLTEVIGEGHRVIVFS
+QFTSFLRVIAEEL-------------------DHLEIEHAYLDGSTRG-----------RADVIRGFR-EGEAPVFLISL
+KAGGFGLTLTEADYVFLMDPWWNPAAEAQAVDRAHRIGQERTVMVYRLVSEGTI-EEKVLELQRRKAELFGALMDESDDS
+GAGAFTDSL--------------TAEDI----REMLG-------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---AEE---------------------------------------------

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

@@ -0,0 +1,78 @@
+>0_2061
+MTHP---------ASSTPAGPQSETTRRVDLDVTGMTCASCVGRVERKLGKLEGVTASVNLPLEQATVTAPAGVSDEELV
+AAVEKAGYGATVR-----RPA-----------PPAGHAGHAGHAHTS--------EHGEEHAADHDGVDHHDHMAHGPSE
+DVLTPRLIGAAVLTVPLVLISMVPALQFPHWGWVAFALAAPVALWAAWPFHSAAFRAARHGSSTMDTLVSLGVLVSFSFS
+AVELILA----PDMTAHVGGTMAEM-AHHSLYFETAAVITTFLLLGRWLEARAKREAGAALRALLDLGAAQATLY-----
+--------------------------------DPETH--------DERTVPAESLAPGDVVLIRPGEKVPTDAEVLEGTS
+AVDASLLTGESVPVEVGPGDALTGATLNTSGRLVARATRVGSDTTLAQMGRLVSEAQTGKARVARLADRISAVFVPIVLG
+IAVLTFAVWMIVT-GDLPSALRAGVAVLVIACPCALGLATPVGLLAGTGRAAQLGILIRGPEVLEDSRTVDTIVLDKTGT
+VTEGRMALADVLVLDPAFVAETGAS-----------RSAFVDETAPDQAADVLLTLAAAVERGSEHPIARAIVAGAEERG
+LTVPGVADFASTAGGGVSGLVALPHDDGAPGSGAHGAAGPDPVRVAVGRGSVLETALDGGIPAEHRAAFEAAEQAGATAV
+WVAVGGRVAGVLSVRDTVKETSADAIARLKELGLRPLLVTGDNAAVATQVAAAVGIPAEDVVAGVRPEDKVDVVRRLQSE
+GHVVAMVGDGVNDAPALAAADMGIAMGSGTDVAREAAQITVMGDDLHQVVQALDLSRRTLGIIRMNLFWAFAYNVLGIPV
+AALGLLNPMIAGGAMAASSVLVVLNSLRLTRYA----R
+>1_1780
+MTHP---------ASSTPAGPQSETTRRVDLDVTGMTCASCVGRVERKLGKLEGVTASVNLPLEQATVTAPAGVSDEELV
+AAVEKAGYGATVR-----RPA-----------PPAGHAGHAGHAHTSEHGEEHGEEHGEEHAADHDGVDHHDHMAHGPSE
+DVLTPRLIGAAVLTVPLVLISMVPALQFPHWGWVAFALAAPVALWAAWPFHSAAFRAARHGSSTMDTLVSLGVLVSFSFS
+AVELILA----PDMTAHVGGTMAEM-AHHSLYFETAAVITTFLLLGRWLEARAKREAGAALRALLDLGAAQATLY-----
+--------------------------------DPETH--------DERTVPAQSLAPGDVVLIRPGEKVPTDAEVLEGTS
+AVDASLLTGESVPVEVGPGDALTGATLNTSGRLVARATRVGSDTTLAQMGRLVSEAQTGKARVARLADRISAVFVPIVLG
+IAVLTFAVWMLVT-GDLPSALRAGVAVLVIACPCALGLATPVGLLAGTGRAAQLGILIRGPEVLEDSRTVDTIVLDKTGT
+VTEGRMALADVLVLDPAFVAETGAS-----------RSAFVAETAPDQAADVLLTLAAAVERGSEHPIARAIVAGAEERG
+LTVPDVADFASTAGGGVSGLVALPHDDGALGSGAHDAAGPAPVRVAVGRGSVLETALDGGIPAEHRAAFEAAEQAGATAV
+WVAVGGRVAGVLSVRDTVKETSADAIARLKELGLRPLLVTGDNAAVATQVAAAVGIPAEDVVAGVRPEDKVDVVTRLQSE
+GAVVAMVGDGVNDAPALAAADMGIAMGSGTDVAREAAQITVMGDDLHQVVQALDLSRRTLGIIRMNLFWAFLYNVLGIPV
+AALGLLNPMIAGGAMAASSVLVVLNSLRLTRYA----R
+>2_640
+MAASPSPSDRAAEALGRTALQDAEGTRRVDLDVTGMTCASCVGRVERKLGKIEGVEASVNLPLERATVTVPASVSDQDLL
+DAVAKAGYTAAVRPDAQARPARRGRHDDGGTRPGADHAGHPDHR-------DH-ETPGEDHAG-HEG--HDDHMAHGPRA
+DVLRPRLIVAAILTVPIVLISMVPALQFPHWGWVALALSAPVALWCGWPFHSAAFRAARHGSSTMDSLVSVGVLVAWTYS
+AVELVLE----PGMTAHVGGTMAEM-MRHSLYFETAAVITTFLLLGRWLEARAKREAGRALRSLLDLGAAQATVLPNWDA
+QTPHPSTSAAATPVAAVSGDFSEVEAASTSDKSPQTHHDGGADALTERVIPAEELEPGDVVVIRPGEKVPTDAVVLEGTS
+AVDASLLTGESVPVEVGPGDEITGATVNTSGRLIARATRTGADTTLAQMGRLVSDAQTGKARVARLADRISAVFVPIVLV
+LAVLTFVVWMLVTGGDVAPALRAGVAVLVIACPCALGLATPVGLLAGTGRASQLGILIGGPEVLEDTRTVDTIVLDKTGT
+VTEGRMALSDV--------------------------HAFADDAALTE--DRILALAAAVEAGSEHPIARAIVAGARERG
+LTVPRVADFASTAGGGVTGTVALPE--------------AGSVRVAVGRGDLV-----GEPSPAQQAEFDAAEQAGATAV
+WVAVDGRVAGVLSVKDTVKPSSAAAIARLKELGLRPLLVTGDNAAVAAQVAAAVGIPAEDVVAGVRPEDKVDVVTRLQSE
+GRVVAMVGDGVNDAPALAAADMGIAMGSGTDVAREAAQITVMGDDLDQVVQALDLSRRTLGIIRMNLFWAFAYNVLGIPV
+AALGLLNPMIAGGAMAASSVLVVLNSLRLTRYA----R
+>3_558
+MTHP---------ASSAPAGPQSETTRRVDLDVTGMTCASCVGRVERKLGKLEGVTASVNLPLEQATVTAPADVSDEELV
+AAVEKAGYGATVR-----RPA-----------PPA---GHAGHAHTS----EHGEGHGEEHAADHDGVDHHDHMAHGPGE
+DVLKPRLIGAAVLTVPLVLISMVPALQFPHWGWVAFALAAPVALWAAWPFHSAAFRAARHGSSTMDTLVSLGVLVSFSFS
+AVELILA----PDMTAHVGGTMAEM-AHHSLYFEAAAVITTFLLLGRWLEARAKREAGAALRALLDLGAAQATLY-----
+--------------------------------DPETH--------DERTVPAESLAPGDVVLIRPGEKVPTDAEVLEGTS
+AVDASLLTGESVPVEVGPGDAVTGATLNTSGRLVARATRVGADTTLAQMGRLVADAQTGKARVARLADRISAVFVPVVLG
+LAVLTFAVWMLVT-GDLPSALRAGVAVLVIACPCALGLATPVGLLAGTGRASQLGILIRGPEVLEDSRTVDTIVLDKTGT
+VTEGRMALADVLVLDPAFVTDTGASRSASVAETDAPRSAFVAETAPDRATDLLLTLAAAVERGSEHPIARAIVTGAEERG
+LTVPDVADFASTAGGGVSGLVALPHDDGALASGAHGAAGPAPVRVAVGRGSVLETALDGGIPAEHRAAFEAAEQAGATAV
+WVAVGGRVAGVLSVRDTVKDTSADAIARLKELGLRPLLVTGDNAAVATQVADAVGIPAEDVVAGVRPEDKVDVVRRLQSE
+GRVVAMVGDGVNDAPALAAADMGIAMGSGTDVAREAAQITVMGDDLHQVVQALDLSRRTLGIIRMNLFWAFLYNVLGIPV
+AALGLLNPMIAGGAMAASSVLVVLNSLRLTRYA----R
+>3_700
+M--------------STSAPPT--GGPDIELEIGGMTCASCANRIEKKLNKLDGVAATVNYATEKAKVTVPAGYDPSLLV
+AEVEKTGYTAALP-----KPK-----------DTT--------ANTS----E--TEAGEE---------EDSELTS----
+--LRHRLIGAIVLTVPVIAMAMIPALQFTYWQWASLALAAPVIIWGAWPFHKAAWTNLKHGAATMDTLISMGTSVALLWS
+LYALFLGTAGTPGMTHPFEFTIAPSDGAANIYLEVGAGVTMFILAGRYFEKRSKRQAGAALRALLELGAKEVAVL-----
+-------------------------------------RDG-----VEVKIPTSELAVGDEFIVRPGEKIATDGLVTSGSS
+AVDASMLTGESVPVEVREGDSVTGATVNAGGRLVVRATRVGSDTQLAQMAKLVEDAQTGKAEVQRLADRISGIFVPIVIV
+VAFITLGAWLGGG-FPVAAAFTAAVAVLVIACPCALGLATPTALLVGTGRGAQMGVLIKGPEVLESTRKVDTVVLDKTGT
+VTSGKMTLTDV-----------------------------ITEPGVDR--AELLRFAGALEDSSEHPIAQAIAKGATQEV
+GQLPTPEDFANVEGKGVQGIVE-------------------GTPVVVGRESLL-ADWSQKLSPEVAQAKAQAEGEGKTVV
+AIGWDGAARGILVVADTVKPTSAEAIRGLKEIGLTPVLLTGDNEAVARQIASEVGI--DEVIAEVLPKDKVDVVTRLQEE
+GKIVAMVGDGVNDAPALAQADLGLAMGTGTDVAIEASDITLVRGDLRAAVDAIRLSRKTLSTIKTNLFWAFAYNTAAIPV
+AALGMLNPMLAGAAMAFSSVFVVGNSLRLRGFTSVASK
+>4_2000
+MTHP---------ASSTPAGPQSETTRRVDLDVTGMTCASCVGRVERKLGKLEGVTASVNLPLEQATVTAPAGVSDEELV
+AAVEKAGYGATVR-----RPA-----------PPAGHAGHAGHAHTS----EHGEEHGEEHAADHDGVDHHDHMAHGPSE
+DVLTPRLIGAAVLTVPLVLISMVPALQFPHWGWVAFALAAPVALWAAWPFHSAAFRAARHGSSTMDTLVSLGVLVSFSFS
+AVELILA----PDMTAHVGGTMAEM-AHHSLYFETAAVITTFLLLGRWLEARAKREAGAALRALLDLGAAQATLY-----
+--------------------------------DPETH--------DERTVPAESLAPGDVVLIRPGEKVPTDAEVLEGTS
+AVDASLLTGESVPVEVGPGDALTGATLNTSGRLVARATRVGSDTTLAQMGRLVSEAQTGKARVARLADRISAVFVPIVLG
+IAVLTFAVWMIVT-GDLPSALRAGVAVLVIACPCALGLATPVGLLAGTGRAAQLGILIRGPEVLEDSRTVDTIVLDKTGT
+VTEGRMALADVLVLDPAFVAETGAS-----------RSAFVDETAPDQAADVLLTLAAAVERGSEHPIARAIVAGAEERG
+LTVPGVADFASTAGGGVSGLVALPHDDGAPGSGAHGAAGPDPVRVAVGRGSVLETALDGGIPAEHRAAFEAAEQAGATAV
+WVAVGGRVAGVLSVRDTVKDTSADAIARLRQMGLRPLLVTGDNAAVAAQVAEAVGIPAEDVVAGVRPEDKVDVVTRLQSE
+GAVVAMVGDGVNDAPALAAADMGIAMGSGTDVAREAAQITVMGDDLHQVVQALDLSRRTLGIIRMNLFWAFLYNVLGIPV
+AALGLLNPMIAGGAMAASSVLVVLNSLRLTRYA----R

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000172.fa

@@ -0,0 +1,78 @@
+>1_1967
+MK--------------------------------------------------------------------------RSPK
+GRLEL----TWM---------GKDSALIPVEDGKYDYSFVDPNDPRALEVKSIEV--------------------LEQVG
+EVEGPTGANENLLIIGDSGDALRSLGTIPEYAEKYGGKVKLVYIDPPFNTE-QAFDHYADQLE-----------------
+------------HSIWLTMMRDRIRDFKPLLHPDASIW-VHLDDSEVHRMRALMDEEFGAE--NFIATVVWQKKYSRDNR
+PA-IGTVHDYILVYAPAGAQRW--------KTLRNR--------------------------IPRISAAQYRNPNNDPNG
+----------PWRPVPMDVQGGHATASQFYDVITPSGKIV----RPANGRA-WSVTAPVMQAMRDRGEVYFGL----DGS
+GKPNTIRY-----LKD---------------------DEGLVPWTWWPHEEVGNNDDAKKEIIALFGEDQVFDTPKPERL
+LERVIRIAT--NADDLVLDCFAGSGTSAAVAHKLG------RRWLTVELSQ------------------------EVADT
+FTVPRLRKVQRGTDSIGISV----------REAEGFA----DADMDGRVKPDDAKALLRAIKEVQKVGLKSLSP----EA
+GAA----LVQELRERLKPVSARQSVCQDGGF-------TVAKMG-----PSMYEVDDEHGMVFLSPEATNGAWSKAIAGQ
+LKF--TLTPDDPVFCGVRKRQRLAVIDGVADETVVRTVVEHLGEKERAVIVAKGVLP------EAGDLLQRLSPGSRIKK
+APEDMFPKGTVN
+>2_1471
+MT---DEIYETPSTTPNFQTELAAQLAD------LIPEAIADGK---------VDV--------EKLK-ELLDGDAADSN
+ERFGL----FWP---------GKKRALRAA------------------QEPTTAT--------------------LKPDF
+EDSKDWDTTQNVFIEGDNLEVLKIL------QKHYHAKIKLIYIDPPYNTG-KDFVYPDNYKEGLDTYLEWTRQVNEEGK
+KVTTNAETEGRYHSNWLNMMYPRLKLARNLLTDDGVIF-ISIDDNEIDNLLRLAKEVFGEP--NVSTTFIRQKKKKPSFL
+HANVGSMTEYLVCITRNKAFTF--PFSVDTTTAGKK--------------------------YPINNAGNSLGKLTFPAG
+-AVRFSQKFAEYEP--QDMSEGNIVTRLLDHVVVSEGVNR----NAFTLEGEWRYSQVTLDEFITAGDLITIS----KAP
+FRPNHVKA--------------GGEIKKM--------HNLLTPSTY----GVGTNEDGTAELEDLM-EGSYFDNPKPTSL
+VRVLAQAVTYDDPSAIVLDFFAGSGTTADAVFRLNAQDGGNRRVISVQLPE-PLDERSEAWAAGYRT----------ISQ
+LAKERIRRA-------GVRV------LD--REALLLEGRGVPLDTGFRAYKLSDTNFSK-----WRLSSD-VEE----DA
+LQQHLLSLRDSATDDANADELLTEILLKQGYSLTEAVSPAEVAG-----LDVRFVRDRDGDV-----AVLAYLNEHVKPT
+LEQLRALVDEEPT---------------------------------RIIVLEDAFQGDDELKTNLAQLAK--SKGIELW-
+----------TA
+>3_274
+ME---MSMDKLRGTSPDLTQDNVARLAE------LFPTVVTEARDEDGQVTRAVDF--------DLLRQELSDHVVEGPQ
+ERYHL----DWP---------GKRAAAFAA------------------NAPTTAT--------------------LRPDR
+EESVDFDTTKNVFIEGDNLEVLKVL------QESYLGKVKMIYIDPPYNTG-NDFVYADDFAESTADYLQRSGEIDDDGA
+RLRANPETNGRFHSDWLSMMYPRLKLARNLLTEDGAIL-ASIGEREVSNLRAILNELFGET--NFVGELVWEKKKKGAFL
+SSHVTNVKEYILVFCRDRSSFG--GLIGEVTHAAET--------------------------YPVIKSTNSRGIRTIPAG
+IASNYSERDHEVGA-GTRLTSGNMEMILLSDLIIRDGRLA----HDVEVESNWIYSQTLIDQFSLSGDLYIT-----RDL
+YIRRHVREPRTKMLKD-LLMMRGESTSGS--------TFTLEPSLH--SDGWGTNEDAFGELHSILGEQNLMDFPKPSKL
+IAKLIRSVTWADSDAIILDFFAGSGTTGQAVTQLNAADGGRRQYLLVQLNE-AAEESSALRRAGFSS----------ISA
+LSRERLRRS-------AAAV----------RETSGTE----RLDLGFRAFRLDASPFVE-----RNHSADSITP----DM
+LAE----LENPVLADRSPEDLLTHVLLAWGLDLSATIETVSLAG-----EEVYDVEDG---------ALLAALGSTVSDE
+LAH--AMAERHPD---------------------------------RALFLDSGFVS-DAARINVEQIFREVSPGTDVK-
+----------VL
+>3_333
+MSSLSDLLGQVRATNPDLAANLEREIKNRTRRQRQFGLVFEEHRPE------AVELPSREVRKGDKVR-------ILPPR
+GETKKGDQTLWRVQRINRADD--IAHLVEVD-----------GEQG-------AEAALADLVVVAEFRDHMYPGLVETGR
+VERGG-DKPFHTVINAENFHALEML------TYTHRHQVHCIYIDPPYNTGAKDWKYNNDYVASDDDYR-----------
+------------HSKWLSFMERRLQVARELLNPEDSVLIVTIDEKEYLRLGMLLEQTFPQARMQMVSTVINPK---GSHR
+AGGFARSDEYVFFLFVGASQPAPMPLSSEWKVVQDSRALGLRWADLLRTADGSTRAARPNMFYPVFIRLAGDGPVFVSVG
+EPF-YDADLTAVEA--------------------PEDAVAIWPIKADGSQGRWQIGADTLRDLITKGYVRIGRWR--GSK
+TTLTYLKAGEQAKVEDGRFPVRGRRADGSVLVDASEYSASFVPTSQWRISSHNAEQGGTNLLKSIM-GDKRFPFPKSLYA
+VEDALRFLIKKNPDAVVLDFFSGSGTTAHAVMRLNKQDGGRRQCISVTNNEVSAEEQKGLRKQGLRPGDPEWEQWGICDY
+VTKPRVTAAITGRTPTGDPIKGDYKFTDEFPMSDGFE-----ENAAFFTLTYESPLMVR-----QDLAFKRIAPLLWMRA
+GSRG--RVITEVHAR--------------GWDVAEAYGVLTKVDRATPFAEAV-AEAGVGTVYVVTDDERRYQAVC----
+-----ALLPEDVT----------------------------------PVRLYESYLT------NF-EINTGGRAG-----
+-----------A
+>3_677
+MSRLTDLLAQARKTDPQLAADLEAEFRQLTQRS-QFGLVFERHQPE------AVELPGRPVRRGDTVR-------VLPPR
+GTLTIGDTRHWVVTDLERTPDGKQAHLTEAD-----------VDPE-VREPATSTAALEDLVVVARFEDPIYPGLVETGR
+VENGGPDKPFHTVINAENFHALEML------TYTHRHKVDCIYIDPPYNTGAKDWKYNNDYVEADDDYR-----------
+------------HSKWLSFMERRLQVARELLNPDDSVLIATIDEKEYLRLGMLLEQTFPEARIQMISAIINPK---GSSR
+RDQFSRFDEYIFFVMNGSARPA--AVAGDMTMRQARSKEKVRWAGLMRQGANGRRSARPNLFYPIFV--ANETGRVHSVG
+DSLPLDVPRSEVSP--------------------PPGTTAIWPLSKAGGESTWGRDPESLRKALSAGYVKIGRFTPGSER
+CGFTHLQSGQIKAIEEGALVVTGRDSDGSLQVEFAEGGQTAMPGTAWHRPAHSASEHGSTLLNAIL-PDRKFPFPKSLYA
+VEDAVRFFVHGKPDAVVLDFFSGSGTTAHAVMRLNRQDGGRRQCISVTNNEVSAEEQKGLRKKGLRPGDPEWERWGICDY
+ITKPRITAAITGKTPAGDPIKGNYKFTDEFPMADGFE-----ENAAFFTLTYEAPRQVR-----RNRAFARVAPMLWFKA
+GSRG--RIISSLPER--------------GWDVAQAYGVLEDMDHAPEFLAALEADPQVGMAFIVTDSEVAFQSVA----
+-----RQLPEHAT----------------------------------AVRLYESYLH------NF-QINRRA--------
+------------
+>4_106
+MSSLSDLLGQVRATNPDLAANLEREIKNRTRRQRQFGLVFEGHRPE------AVELPSRPVRKGDKVR-------ILPPR
+GETKKGDQTLWHVDHIDRTTG--TARLTAVD-----------GEQE-------AQAAISDLVVVAEFRDHMYPGLVETGR
+VENGG-GKPFHTVINAENFHALEML------TYTHHRKV-----------------------------------------
+--------------------------------------------------------------------------------
+----------------------------------DS--------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-----------------------------------------------------------------------------C--
+------------------------------------------------------------------------------RA
+SDLG--HV------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000173.fa

@@ -0,0 +1,48 @@
+>2_83
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------MDLTYKLWEGSWDEGAVLQDKGGSRHADPEKVHKIHHVSERYRVEGPHLPAPSP-QRTPVLF
+QAGSSGPGRAFAARNAEAVFLIAPSVEAARQQIEDPRRQAVEFGRRPEDIKFFQGLSFVIGDTEEEAQAKLEEYERYVSV
+DGYLA-HAALV---DPDGRVYPPDTPLRELETNTQ-KGFAESLQKAITDREPVVADVA--------------WRSHRDSR
+VVGTPEQIADELQRWQ-DAGVDGVNVINWVIPGSFEEFIEKVLPVLRERSLAQSDYG--EGTLRHRLFGEGDRLPDRHPA
+AKYRGAFTGTPRSQRAPRTEPQGADPAPAA
+>2_84
+MT---------KTARRRPLHLNAFAMNTTSHIHHGQWRRPDARQHEFADLRTWTELARTLEDAAFDAMFFADVVGHYGDA
+DADYAVYVEEGLQIPSNDPTVLLGALAAVTERIGLATTSNVFQAHPFQFARQLSTLDHLSRGRIAWNIVTGT--------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------
+>2_185
+-------------------------MMTPVHQSPGLWRHPESRIAEFDRLAYWTGLARTVEDGGFSALFLADVLGLYDVY
+GGGIEATVRGGVQWPVLDPAVAVPAMAAATERIGFGVTASVTYERPYLLARTLATLDHFTGGRVAWNIVTSYQDSAARNL
+GLDRQIPHDARYDLADEALDALYRLWEGSVEPGAVAFDRAAGVVADPDRVHPAAVAGAHVRVPDAALTHPGP-QGTPYLF
+QAGASARGRRFALDHAEAVFAIGPTPAHVRRFVDQTRAGLTEAGRSADAIRVLAMVTVVVAETDEAAAQRLAGYAEHVDV
+AGALALWGGWT---GVDVAGLDPDAPLEHVVTDAN-RSALAAFTEDPSGRTWTLRDVAEF-----------VAIGGRGPV
+IVGSPETVADELQRWQAETGVDGFNVSAAVRPADLERFAALVSPELRRRGVLREPEP--GRTLRENLSGAGPALPADHRG
+HAFRTA-----------------------G
+>3_123
+MTGTHPSTPRPRTADRQLILGAHF----PGVNNTTVWSDPESGSQIAPE--SFIRFAEIAERGRLDFIFLAEGLRLREQR
+GLLHDLDVVGR---PATLP--ILAALAAATEHIGLIGTLSTTYNEPYELARQLAGLDALSGGRAGWNVVTSPDAFTGENF
+RRGGYLPRERRYQHAGEFLATAQQIWDAA---------SGRPPHVDVD--------VEDFSVHGT-VDAPAPVHGRPVIL
+QAGDSDEGRDLAAREADAVFTRHGDWEAGQEFTADMRRRAAAAGRPDGAVRVLPGVTVVVGDTDEEAAAEAEQIRR-AQV
+SGATA-VLTLERIWNRDLSGWDPDGPLPDVEPVLEDTGLSQGRVRHVADPHAEVARLREISQRQGLTLRETVIATGQRQD
+FVGSPETVAQELIRHVEHDVCDGFILIPHLTPGGLEPFVDRVVPLLQERGALRTDYPEDGGGLRGLLGAA--VHPTAGRA
+S-----------------------------
+>3_136
+MT---------ATPAPAPFILSAFDMVTPVHQSPGLWRHPESRAHEFDRLSFWTDLARTVEEGGFTAVFLADILGLYDVH
+GGGVDATVRGGVQWPLLDPFTVVSAMAAVTERVGFGVTASVTYEQPYLLARTLTSLDHFTGGRIAWNVVTGYQDSAARNL
+GLDRQPGHDERYDRADAYLDAMYRQFEGSVERDAVVADRESGVFADPAKVHPIDVEGPHVRLPGVALAHPGP-QGTPFLF
+QAGASSRGRRFALEHAEAVFYIGPTTAHVRRFVEQTREGLREAGRPEDAIRVLAMVTVVVADTDEEAQARLASYHEHVDV
+ESALALFGGWT---GVDLSGLDPDAELEHVESEAS-RTALAAFTTQSPDRRWTVREVAEF-----------VSVGGRGPV
+IVGSPATVADELERWHRETGVDGFNISAAVRPTDLERFARLVSPELRRRGVLREPEA--GRTLRENVAGAGPLLPEDHRG
+AGFRR-------------------------
+>4_193
+MT---------AT--PAPFILSAFDMVTPVHQSPGLWRHPESRAHEFDRLSFWTDLARTVEEGGFTAVFLADILGLYDVH
+GSGVDATVRGGVQWPLLDPFTVVSAMAAVTERVGFGVTASVTYEQPYLLARTLTSLDHFTEGRIAWNVVTGYQDSAARNL
+GLDRQPGHDERYDRADAYLDAMYRQFEGSVERDAVVADRESGVFADPAKVHPIGVEGPHVRLPGVALAHPGP-QGTPFLF
+QAGASSRGRRFALEHAEAVFYIGPTTAHVRRFVEQTREGLREAGRPEDAIRVLAMVTVVVADTDEEAQARLAEYHEHVDV
+ESALALFGGWT---GVDLSGLDPDAELEHVESEAS-RTALAAFTTQSPDRRWTVREVAEF-----------VSVGGRGPV
+IVGSPATVADELERWHRETGVDGFNISAAVRPTDLERFARLVSPELRRRGLLREPEA--GRTLRENVAGGGPLLPEDHRG
+ARFR--------------------------

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

@@ -0,0 +1,26 @@
+>0_3
+----------MAETPAPFEPDRPDLALVQLRRVREAARERGEAPLRARGTGAGLAGAMAG
+TPSAGR-----ERQDRRRPFGGADRDPATVSTVFGRLIRDRGWSTPVAVGSVLTRWAELV
+GPEIALHCRPESFEDSVVRVRTSSTAWATQLRLMSPVLLQRFDEALGPGVVTRIEVAGPQ
+APSWRKGPRTVRGGRGPRDTYG
+>1_1959
+----------MAETPAPFEPDRPDLALVQLRRVREAARERGEAPLRARGTGAGLAGAMAG
+TPSAGR-----ERQDRRRPFGGADRDPATVSTVFGRLIRDRGWSTPVAVGSVLTRWAELV
+GPEIALHCRPESFEDSVVRVRTSSTAWATQLRLMSPVLLQRFDEALGPGVVTRIEVAGPQ
+APSWRKGPRTVRGGRGPRDTYG
+>2_402
+------------------------------------------------------------
+-----------------------------MSSVFGRLIRDRGWSTPVAVGSVLTRWDELV
+GPEIALHCRPESFEDSVVRVRTSSTAWATQLRLMTPVLLQRFDDALGPGVVTRLEVAGPQ
+APSWRKGPRTVRGGRGPRDTYG
+>3_356
+MRERSPEPDALAELP----PDRPDLALVQLRRVRDAARQRGEAPLNRRGTAAGLAQSMAG
+SEAAAAAGGAVARSGHRRPGAPADRDPAVVSSVFGRLIRDRGWSTPVAVGSVLTRWADLV
+GPEIALHCRPESFEDSVVRVRTSSTAWATQLRLMSPMLLSRFDEALGPGVVTRIDVAGPA
+APSWRHGPRTVRGGRGPRDTYG
+>4_3
+----------MAETPAPFEPDRPDLALVQLRRVREAARERGEAPLRARGTGAGLAGAMAG
+TTSAGR-----ERQDRRRPFGGADRDPATVSTVFGRLIRDRGWSTPVAVGSVLTRWAELV
+GPEIALHCRPESFEDSVVRVRTSSTAWATQLRLMSPVLLQRFDEALGPGVVTRIEVAGPQ
+APSWRKGPRTVRGGRGPRDTYG
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000182.fa

@@ -0,0 +1,31 @@
+>0_8
+------MNTTIDTPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYG
+PTVPVISDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAAL
+TYTVVSWTTPVEGFEVWDQALAPMLRITVAGVVAFLVGSLLNASIVVRLKERMKERHVAF
+RLILSTVVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRAL
+KRREPTYRAPGFEIHRDDDPALAPAASR----
+>1_1977
+------MNTTTHAPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYG
+PTVPVISDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAAL
+TYTVVSWTTPVEGFEVWDQALAPMLRITVAGFVAFLVGSLLNASIVVRLKERMKERHVAF
+RLILSTVVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRAL
+KRREPTYRAPGFEIHRDDDPALAPAASR----
+>2_370
+MVLDGPVNTTIDTPSPDQPVSGQGTPAYARVPASYYDIFVGVFVALLILSGVTAAKLFYG
+PTVPVFSDVFYGGGPLIFDGGAFLFPFAYIIGDILAEVYGWRRARRAILLGFAMLVLAAL
+TYTVVSWTTPVEGFEVWDQALAPMLRITVAGFVAFLAGSLINATIVVRLKERMRERHVAF
+RLILSTIVGQFFDTLIFCTIAFAGTITLLELANYTFTGFLYKTLVEILIVPITLLVIRRV
+KASEPTYR-----------PASSPARAAADAA
+>3_2129
+------MNTT--PASRSEPTSGQGAAASAAAPHSHYDIFVGVFVALLILSGVTAAKLFYG
+PTVPGVSDVFYGGGPLIFDGGAFLFPLSYVVGDILAEVYGLRRARRAIYIGFAMLVVAAL
+TYRLVALTTPVEGFEAWDQALAPTLRITLAGLAGYIVGSLLNATVVARMKARMAERAVAW
+RLIASTLVGEFFDTLIFCLVAFAGTITLADLANYTVTGYVYKCLVEICIVPVTLLVIRWL
+KRHEPTYRA-----QPTPAPVSAPTA------
+>4_8
+------MNTTIDTPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYG
+PTVPVISDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAAL
+TYTVVSWTTPVEGFEVWDQALAPMLRITVAGFVAFLVGSLLNASIVVRLKERMRERHVAF
+RLILSTVVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRAL
+KRREPTYRAPGFEIHRDDDPALAPAASR----
+ 

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

@@ -0,0 +1,60 @@
+>0_16
+--MDEQRTLNGRYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRKEARSAASLNHPSIVSVYDTG
+EVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGPDRAVAWTRGVLEALEHAHEEDIVHRDVKPANVMVTDTGTVKV
+MDFGIAHALADTSATTSQTQAVVGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPP
+APSDVDPDLPPAFDPVVLRALRKDPQDRFPTGAAFLAALEEAAADPHAGPGRHTPPLDAVHPALV--GAGGAVLGATP--
+----AEHGADVADVPTA-------------AVPLT----RPAPSVP--AEPDTAQPQAVNHAVAGAGLPGAASAAQLAA-
+-AAAMDGPRPVTGG----QPVTPGAAATPRPEPPPRDTPAPATATPRRVRRRVRRR-TLLAAGVVLVALALVLAPWLAAA
+L------RTTAEVPAVVGLQQDEAVAALEDAGLVAVVSSAYMADAPDGTVTQSDPPTGTEVPRGAEVRIRVSRGEEGIAL
+SDSLHGLSEDAARRELERLGLRVSSVQYQDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARR
+QLALSAPELRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTTSSWIAPTAEPSEPAPPSSEAPEPT-PSASTSPS
+PPSSESPEPSESPEPSESAEPSPSPSASATPSPEPTTTATPSPTQSPSPPSAAPSTSSEP-TEQSPST-SPTATPVDPLP
+TLTPDP--EPSIDPPPST-------------------
+>1_1985
+MSVDEQRTLNGRYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRKEARSAASLNHPSIVSVYDTG
+EVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGTDRAVAWTRGVLEALEHAHEEGIVHRDVKPANVMVTETGAVKV
+MDFGIAHALADTSATTSQTQAVVGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPP
+APSDVDPDLPPAFDPVVLRALRKDPEDRFPTGTAFLAALEEAAADPHAGPGRHTPPLDAFPPALV-----GAVLGAAA--
+----AEHG---ADVPTA-------------AVPLT----RPTPSVP--AEPDAAQPQAANHAVAGAGLPGAASAAQLAA-
+-AAAMDGPRPVTVG----QPVMPGAAATPWPEPQG-DTPAPATATPRRVRRRLRRR-TLPAAGVVLVALALVLTPWLAAA
+L------RTTVEVPAVVGLQQDEAVVALEDAGLLAVVSSAYMADAPDGTVTQSDPPTGTEVPRGAEVRIRVSRGKEGIAL
+SDSLHGLSEDAARRELERLGLRVSSVQYQDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARR
+QLALSAPELRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTASSWIAPTAEPSEPAPPYSEAPEPT-PSASASPS
+PP------PSESSEPSESAEPSPSPSASATPSPEPTTTATPSPTQSPSPTSAAPS---EP-TEQPPST-SPTATPVDPLP
+TLTPDP--EPSIDPPPST-------------------
+>2_361
+--MEEQWTLNGRYRIDALIGRGGMADVFRGTDLRLHRPVAVKLMRRDLARDPHFQARFRKEARSVASLNHPSIVSVYDTG
+EVSLEDGHHPVDCPYLVMELVTGRSLREVLHAEGAVGTERAVAWTREVLEALEHAHQEGIVHRDVKPANVMVTDAGSVKV
+MDFGIAHALADTSATTSQTQAVVGTALYLAPEQATGRTVDGRADLYATGCVLFELLTGRPPFTGDTPLAVAYQHVREAPP
+APSEVDPDLPRAFDPVLLRALEKDPEDRFPTGAAFREALEAAAADPHAAVDADTAALDLVRAGAA--GAGGAAVAAGREV
+RRDGARDS---ADVPTA-------------AVPLTPAPAPAAPAEP--AEPPGGEPRRGRGRAARRRLRRPAGGRRLRGR
+PAPGHRLPTPPSRGPRRPAPRPPPGSALPPPLPPP--DGAAAGGAACR--------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-------------------------------------------------------------------------------S
+PG---CCWPASSC-------------------------------------------------------------------
+-------------------------------------
+>3_344
+--MQGQRILHERYRVDELIGRGGMADVFRGHDLRLNRTVAVKMMRPDLARDPAFQARFRTEARHAAALNHPNIVSVYDTG
+DALLDDGPQSVECPYLVMEHVDGRTLRELLDA-GEVAWRDAVEWTRGLLHALDHSHRQRIVHRDVKPANVMVTRDGGVKV
+MDFGIARALSDTSAHTGQTQAVVGTALYLPPEQAQGARVDARSDLYAAGCVLFELLTGRPPFTGETPLAIAYQHVREEPP
+APSAVDPSLSTEFDSVVLRALQKDPGLRHQHAREFLSALDFAAARAARAADDDAPTRVVPASGAAPLATGSGALAAAV--
+----AGST---AAGPTASGSTALGAGGAPEARPAT----GPPATTPLGAAAGPTEPLIAGHAVAGAAVPGAPSASQLAA-
+-AEAVE-----------------TAPAAASTTGGS--AGAGATSGAERAGRRHRLSWAVLAAVAAVAAVAAILA--LGAA
+LLIGSRDPGPVTVPALAGRTEAEAVSALTGLGLRSAISPDYHSTEPDGRVLKVHPGAGAAVEPGSTVNLSVARGGEGVVL
+PTSLRGASEARVRQELARLGLNVASVEDTPSGELDRGALVQTDPVLGSRVPPGSAVVLHLADGTARVPSLVGMTGADART
+TLAALDPEMTVRFQGAAGADPDTGVVVLQDPAAGTVVDNTAMITLITSAEATPTASAVTVAPPDPALPSATTTTAPAEPS
+PG-----VPAPTT-PAAPAVDTPAPAPATTPAPAPESSSTPGAGTDPAPTESAPTPDDGPGSTGTPSTEAPTEAPTDPVG
+TPAPSPSGEPVPQPSPSVEPLPEPTAPTEAPTADPAG
+>4_16
+--MDEQRTLNERYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRKEARSAASLNHPSIVSVYDTG
+EVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGTDRAVAWTRGVLEALEHAHEEGIVHRDVKPANVMVTDTGTVKV
+MDFGIAHALADTSATTSQTQAVVGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPP
+APSDVDPDLPPAFDPVVLRALRKNPQDRFPTGAAFLAALEEAAADPHAGPGRHPPPLDAVHPALV-----GAVLGATP--
+----AGHG---ADVPTA-------------AVPLT----RPTPSVP--AEPDTTQPQAANHAVAGAGLPGAASAAQLAA-
+-AAAMDGPRPVTAG----QPVTAGQPVTPRPEPPPGDTPAPATATPRRVRRRVRRR-TLLAAGMVLVALALVLAPWLAAA
+L------RNTVEVPAVVGLQQDEAVAALEDAGLVAVVSSAYMADAPDGAVTQSDPQTGTEVPRGAEVRIRVSRGEEGIAL
+SDSLHGLSEDAARRELERLGLRVSSVQYQDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARR
+QLALSAPELRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTASSWIAPTAEPSEPAPPSSEAPEPT-PSASAPPS
+PP------PSESPEPSESAEPSPSPSASATPSPDP-TSATPSPTQSPSPPSAAPSTSPEP-TAQSPST-SPTGTPVDPLP
+TLTPDP--EPSIDPPPST-------------------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000190.fa

@@ -0,0 +1,51 @@
+>0_18
+MNEAIRRTWTVMAAMILVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE
+PIAESVPSDDAYHYQRVYHEPELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA
+MEIITGATPEGDQVELTIDPELQRLAYDALPDGVRASAVVTDPTTGEILAMVSKPSFDSN
+ALSSHSPAEAQAAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT
+VDIPAAWTLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVELGQDRIREVA
+ERFGFNDSFDYPLPVTGSVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM
+EPQLIKAVRRSDLTTVQEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA
+AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGVGHQTIVSGMKAIMEAVVT
+E
+>1_1987
+MNEAIRRTWTVMAAMILVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE
+PIAESVPSDDAYHYQRVYHEPELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA
+MEIITGATPEGDQVELTIDPELQRLAYDALPDGVRASAVVTDPTTGEILAMVSKPSFDSN
+ALSSHSPAEAQAAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT
+VDIPAAWTLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVELGQDRIREVA
+ERFGFNDSFDYPLPVTGSVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM
+EPQLIKAVRRSDLTTVQEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA
+AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGVGHQTVVSGMKAIMEAVVT
+E
+>2_359
+MNEAIRRTWTVMAAMMLVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE
+PIAESVPSDDAYHYQRVYHDPELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA
+MEIITGATPEGDQVELTIDPELQRVAYDALPDGVRASAVVTDPTTGEILAMVSKPGFDSN
+ALSSHSATEAQSAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT
+VDIPAAWPLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVKLGQDRIREVA
+ERFGFNDSFDYPLPVTASVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM
+EPQLIKAVRRPDLTTVEEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA
+AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGIGHQTIVSGIKAITEAVVT
+E
+>3_342
+MNEAIRRTWTVMVAMFLVLAVAASVIQVVAADSLKENKLNNRQLFLEFGAPRGPILVDGT
+PVAQSVPSGDAYNYQRVYRDSLLYAPLTGHYSLAYGTAGMEKAMNGELAGTSSSQFLDRA
+LEIVTGSTPEGDQVELTLDSELQKLAYESIPDGVKGSVVATDPKTGRVLAMASKPSYDAN
+TISSHTRSEATAAMSAYEGVPGLTVGQNRPTQQRVAPGSTFKLIDLVAMLESGDYAPDQV
+LDVPAAWTLPGTRTQMSNFDGGRCNGVGRATLTWIVANSCNTPFAQAAVALGQDEIRSVA
+ERFGFNQDGSMPLPVTASVFPEDLDDAALAQSAIGQRDVQATALQMNMVAAGIANDGMVM
+EPNLVQAVRRPDLTTVSEFSPREHGRAMDPDVAHQVRDMMVATVEDGTASAAKSSTLQIA
+AKTGTAEKDGTANVNTWVTGFAPAQDPKVAVTIVYEDQNSSSAHTQAVESMQRIMEAVVA
+E
+>4_18
+MNEAIRRTWTVMAAMLLVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE
+PIAESVPSGDAYHYQRVYHETELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA
+MEIITGATPEGDQVELTIDPELQRLAYDALPDGVRASAVVTDPTTGEILAMVSKPGFDSN
+ALSSHSPAEAQSAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT
+VDIPAAWTLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVELGQDRIREAA
+ERFGFNDSFEYPLPVTASVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM
+EPQLIEAVRRSDLTTVQEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA
+AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGVGHQTVVSGMKAIMEAVVT
+E
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000199.fa

@@ -0,0 +1,36 @@
+>0_36
+M-------------------------------------------AKGVKP-----AGRAG
+GEGRRRPAPAPPADLPVPPETLFLATIPGATPSTWVERFTTRQRTVQLVNHDDAAQLAHL
+AHDDAGQPRHFLPQLGYVRRRRDVSAEEFLRAGDVDPRHVHLVGVYSELPVVCVGRDHLL
+AAWDVDADGPVPPAELDPDEELDPARFAPAP--SPEPMDAAELPGAGERMALEIAASGAG
+HVVLPMSVARMFGRKDVIVLPLASTLDDTVGLSRADREAAATRSALADEQARAEAEAGAA
+VVDGADPAGHGDDDARHPVWDVALAWLKAADSELVQAFVGVARGRRGASSR
+>1_2000
+M-------------------------------------------AKGVKP-----AGRAG
+GEGRRRPAPAPPADLPVPPETLFLATIPGATPSTWVERFTTRQRTVQLVNHDDAAQLAHL
+AHDDAGQPRHFLPQLGYVRRRRDVSAEEFLRAGGVDPRHVHLVGVYSELPVVCVGRDHLL
+AAWDVDADGPVPPAELDPDEELDPARFAPAP--SAEPMDAAELPGAGERMALEIAASGAG
+HVVLPMSVARMFGRKDVIVLPLASTLDDTVGLSRADREAAATRSALADEQARAQAEAGAA
+VVDGADPAGQGDDDARHPGWDVALAWLKAADSELVQAFVGVARGRRGASSR
+>2_345
+MGPRRGLPEGEGPLSGARGGRGAGRQRASRGGPARSTRTGGRAGAKGGGPQRAGSGSRAG
+GEGRRR-APSAPADLAAPPETLFLATIPGATPSTWVDRFTTRQRVVQLVNHDEASQLAHL
+AHDDAGMPRHPLPQLGYVRRRRDVEAEEMLRAAGVDPRRVHLVGVYAELPVVCVGRDHLL
+AAWDAEADGPVPLAELDSHEELDPARFAAAP--VEDPLDSAELPGAGERMALEIAASGAG
+HVVLPMSVARMFGRKDVVVLPLASALDDTVGMSRADREAAATR-------AEVEADAGDA
+GTAAAGPGEADDDAARHPGWDVALAWLKEADSELVQSFVGVARGRRGNSSR
+>3_287
+------------------------------------------------------------
+-------MPAAPADLPTPPETLFLATIPGATPSTWVQRFSSRARTVQLVNHEEAQQAAHL
+AHDAAGAPLHPLPQLGYVRWLRDAGVESVLRESGVDPRFVHVVGVYSELPVVCVGKEHLL
+AAWDLEADGPVPLAELDPAEHMDPARFAPEPGAASNPLDSAELPGAGERMALEIVASGVG
+HVVLPQSVARVFGRKDVVVLPVACELDDVVGLSRADREAAATRAEVAE-------EGDGV
+VPDGAD--APATTAPRHPGWDVGLAWLKEQDSELVQSFVGVARGRRGGTSR
+>4_31
+-----------------------------------------------MKP-----AGRAG
+GEGRRRPAPAPPADLPVPPETLFLATIPGATPSTWVERFTTRQRTVQLVNHDDAAQLAHL
+AHDDAGQPRHFLPQLGYVRRRRDVSAEEFLRAGDIDPRHVHLVGVYSELPVVCVGRDHLL
+AAWDVDADGPVPPAELDPDEELDPARFAPAP--SPEPMDAAELPGAGERMALEIAASGAG
+HVVLPMSVARMFGRKDVIVLPLASTLDDTVGLSRADREAAATRSALADEQARAEAEAGAA
+VVDGADPAGQGDDEARHPGWDVALAWLKAADSELVQAFVGVARGRRGASSR
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000200.fa

@@ -0,0 +1,46 @@
+>0_38
+M--SPTPTRPSRG--PG-------WRLHGDGRTITPGTVVAPDERLSWPRTVGIGVQHVM
+AMFGATVLVPALTGMPATTALLFSGLGTLLFLVITGNRLPSYLGSSFAFIAPLTAATTIG
+GTGAALGGILVTGLLLTVIGVIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQ
+EVPVTTFGTALAVVLTAVAFRGLLGRLSILVGIVVGYVLALAQGQVDFAAVREAAWIGLP
+PFHGPELRWDLLPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTMLSG
+AGGGVGTTTYAENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAG
+IILYGMIGMMGVRIWVQNRVDFSNTVNLMAAGAGLIIAIADPQLVVGGLVFGGITLGTVA
+ALVVYHLMTAIARARGTEPVPEDEE---QFEASEAGRLG
+>1_2002
+M--SPTPTRPSRG--PG-------WRLHGDGRTITPGTVVAPDERLSWPRTVGIGVQHVM
+AMFGATVLVPALTGMPATTALLFSGLGTLLFLVITGNRLPSYLGSSFAFIAPLTAAAAIG
+GTGAALGGILVTGLLLTVIGAIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQ
+EVPVTTFGTALAVVLTAVTFRGLLGRLSILVGIVVGYVLALAQGQVDFAAVGEAAWIGLP
+PFHGPELRWDLLPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTMLSG
+AGGGVGTTTYAENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAG
+IILYGMIGMMGVRIWVQNRVDFSNTVNLMTAGAGLIIAIADPQLVVGGLVFGGITLGTVA
+ALVVYHLMTAIARARGTEPVPEDEE---QFEASEAGRLG
+>2_343
+M--SSSPSRPAPG--FG-------WRLHGDGRTITSGTVVAPDERLSWPRTVGIGVQHVM
+AMFGATVLVPALTGMPATTALLFSGVGTLLFLLLTGNRLPSYLGSSFAFIAPITAATTAG
+GVGAALGGVLVTGVLLAVIGLIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQ
+EVPLTTFGTALAIVLTAVLFRGLLGRLSILVGIVVGYLLALAQGQVDFTAVGEAGWLGLP
+PFHAPELHWNLLPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTTLSG
+LGGGVGTTTYAENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAG
+IILYGMIGVMGVRIWVQNRVDFSSTINLMTAGAGLIIAIADPQLVLGGLVFGGITLGTIA
+ALVVYHLMTAIARVRGTEPVSEDDE---AYEASEAGRLG
+>3_286
+MSSSPTPSAPRAGHVPGPGPAVRSWRLHGDGRTITPGTVVAPDERLSWGRTVGIGVQHVM
+AMFGATVLVPAITGMPATTALLFSGLGTLLFLLITGNRLPSYLGSSFAFIAPLTAASASH
+GVGAALGGIAATGVLLMVIGVVVGWAGTGWIHALMPPAVMGTIVALIGLNLAGATTQAMQ
+EVPLTTFGTALAVVLTAVLFKGLLGRLSILVGIVVGYLLALAQGQVDFTAVGQAAWVGLP
+PFHTPELHWSLLPLFLPVVLVLIAENIGHVRTVGLMTKRDLDPLTGRALLADGLATTLSG
+LGGGVGTTTYAENIGVMASSKVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAG
+IILYGMIGVMGVRIWVQNRVDFSNTINLMTAGAGLIVAIANPELVVGGLVFGGITLGTLT
+ALVVYHLMTLVARVRGTEPVDEDTEDPASYRAAEAGRLG
+>4_33
+M--SPTPTRPSRG--PG-------WRLHGDGRTITPGTVVAPDERLSWPRTVGIGVQHVM
+AMFGATVLVPALTGMPATTALLFSGLGTLLFLVITGNRLPSYLGSSFAFIAPLTAAAAIG
+GTGAALGGILVTGLLLTVIGAIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQ
+EVPVTTFGTALAVVLTAVTFRGLLGRLSILVGIVVGYVLALAQGQVDFAAVGEAAWIGLP
+PFHGPELRWDLLPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTMLSG
+AGGGVGTTTYAENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAG
+IILYGMIGMMGVRIWVQNRVDFSNTVNLMTAGAGLIIAIADPQLVVGGLVFGGITLGTVA
+ALVVYHLMTAIARARGTEPVPEDEE---EFEASEAGRLG
+ 

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

@@ -0,0 +1,26 @@
+>0_46
+MAA-----LTDRAVLIAGATSASGRAAARTLLDAGAHVVATGRDAAKLAPL-----AGLG
+AETATL--DLTDETAVRGLVEDLHARGTRIDGLLHLVGGWRGGGGLAGQTEADYRALEAS
+FTALRHVSRALDDDLRASSAGRLAIVSSTAVTRPLAGGANYAAVKAASEAWTRAVAQGWA
+KATRDAETPLRSAAVVFRVKSLAGLEERLAEEYARLWKAEAGALNDAVLTLQEKGT---
+>1_2010
+MAA-----LTDRAVLIAGATSASGRAATRTLLDAGAHVVPTGRDAAKLAPL-----AALG
+AETAAL--DLTDEAAVRGLVEDLHARGTRIDGLLHLVGGWRGGGGLTGQTEDDYRALEAS
+FTALRHVSRALDDDLRASSAGRLAIVSSTAVTRPLAGGANYAAVKAASEAWTRAVAQGWA
+KAARDAEAPLRSAAVVFRVKSLAGLEERLAEEYARLWKAEAGALNDAVLTLQEKGTD--
+>2_338
+MGT-----LTGRTVLISGATSASGLAAARALLAAGADVVATGRSPERLAPL-----AALG
+ADTAAL--DLSDEAAVRGLVEDLHARGVRVDGLLHLVGGWRGGGGLAGQSEEDYRALESS
+LTALRHVSRALDDDLRASSAGRLAIVSSTAVARPLAGGAAYAAVKAASEAWTRAVAQGWD
+KAARDAGTELRGAAVVLRVKSLAGLEDRLAEQFVRLWSADAAQLNDSILAVQEKETA--
+>3_1194
+MSAPAAPDLTGALVLVTGASSGIGSALARGLAAAGADLVLVARRAGRLAALADELRAAHR
+TEVTVLPRDLAAPDAGPALRAELSSRGPRVTGLVNNAG---FGSGLPFGREDPARLEAMP
+AEEERGRERVLCVSPSSTGTEFFDVAGT-----PGAGGG--FARRAAPDDVAAAVLRVLA
+RRGGPAEVVPHDRAVTVAARLLPRTVLR------------------GMGAMHRRGAARR
+>4_41
+MAA-----LTDRAVLIAGATSASGRAAARTLLDAGAHVVATGRDAAKLAPL-----AELG
+AETAAL--DLTDETAVRGLVEDLHARGTRIDGLLHLVGGWRGGGGLAGQTEEDYRALEAS
+FTALRHVSRALDDDLRASSAGRLAIVSSTAVTRPLAGGANYAAVKAASEAWTRAVAQGWA
+KAARDAEAPLRSAAVVFRVRSLAGLEERLAEEYARLWKAEAGALNDAVLTLQEKGTD--
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000208.fa

@@ -0,0 +1,45 @@
+>0_51
+MTENTAALPAAERPGTPALPQDLIDVDALLEAYHTGHPDVTDPAQKVVFGTSGHRGSAFTTSFNDDHIAAITQAVVEYRA
+HHGITGPVLVGRDTHALSGPAQDTAVEVLLGNDVEVLVDSRGGYTPTPAVSHAILHLNAGRELSPSGFAVDGDNAGLVDG
+LVITPSHNPPADGGFKYNPPHGGPADTEATTWIADRANELLAAGLAGVHRVASADVAGHAKLGGFDFLDRYVSDLPQVID
+VEAIREAGVRIGADPMGGASVAYWGEIADRHGLDLTVVNPEVDPRFGFMTLDWDGKIRMDCSSPNAMASLIERMTPDADG
+HAPFDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYLYRHRQQWPQSAGVGKTLVSSSMIDRVAGDLGRELVEVPVG
+FKWFVPGLLTGTGVFGGEESAGASFVQFDGSPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGDPAYARIDAPA
+TAEQKAKLKTLSPDDVPVTELAGETILATLTNAPGNDAPIGGLKVVTQHAWFAARPSGTEDVYKIYAESFRGPEHLKQVQ
+AEAQKLVDAVIG
+>1_2015
+MTENTAALPAAERPGTPALPQDLIDVDALLEAYRTGHPDVTDPAQKVVFGTSGHRGSAFTTSFNDDHIAAITQAVVEYRA
+HHGITGPVLVGKDTHALSGPAQDTAVEVLLGNDVEVLVDSRGGYTPTPAVSHAILHLNAGRELSPSGFAVDGDNAGLVDG
+LVITPSHNPPADGGFKYNPPHGGPADTEATTWIADRANELLAAGLAGVHRVASADVAGHAKLGGFDFLDRYVSDLPQVID
+VEAIREAGVRIGADPMGGASVAYWGEIADRHGLDLTVVNPEVDPRFGFMTLDWDGKIRMDCSSPNAMASLIERMTPDADG
+QAPFDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYLYRHREQWPQSAGVGKTLVSSSMIDRVAGDLGRELVEVPVG
+FKWFVPGLLTGTGVFGGEESAGASFVQFDGSPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGDPAYARIDAPA
+TAEQKAKLKTLSPDDVPVTELAGETILATLTNAPGNDAPIGGLKVVTQHAWFAARPSGTEDVYKIYAESFRGPEHLTQVQ
+AEAQRLVDAVIG
+>2_327
+MTEHTAAPPASERPGTPALPQDLIDVDALLTAYRTGRPDVSDPAQKVVFGTSGHRGSALKTSFNDDHIAAITQAVVEYRA
+EHGITGAVLVGKDTHALSGPAQDTAVEVLLGNDVEVLVDSRGGYTPTPAVSHAILHLNAGRDLTPAGFSADGDNAGLVDG
+LVITPSHNPPADGGFKYNPPHGGPADTEATTWIADRANALLAAGLEGVRRVAAADVDGHAKLGGFDFLDRYVTDLPDVID
+VEAIREAGVRIGADPMGGASVAYWGEIARRHGLDLTVVNPDADPRFGFMTLDWDGKIRMDCSSPHAMASLIERMTPDADG
+QAPYDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYLYRHRERWPADAGVGKTLVSSSMIDRVAGDLGRELVEVPVG
+FKWFVPGLLTGTGVFGGEESAGASFVKLDGGPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGSPAYARIDAPA
+TAEQKARLKTLSPDDVTVTELAGETILATLTNAPGNDAPIGGLKVVTQNAWFAARPSGTEDVYKIYAESFRGPEHLKQVQ
+EEAQRLVDAVIG
+>3_267
+-----MSTPAAGRAGTPALPEDLIDVEALLAAYRDLHPDPADPAQKVVFGTSGHRGSALKSSFNDDHIAAITQAVVEYRA
+EHGITGAILVGKDTHALSGPAQDTAVQVLLANDVEVLVDSRGGFTPTPAVSHAILHLNAGRDLTAAGFSADGDNAGLVDG
+LVITPSHNPPADGGFKYNPPHGGPADTDATSWIAARANDLLAARLDGVTRLAPEDVEGHAKLGSFDFLDRYVTDLPQVID
+LDAIREAGVRIGADPMGGASVAYWGEIGRRHGLDLTVVNPDVDPQFGFMTLDWDGKIRMDCSSPNAMASLIERMTPDADG
+HAPFDVATGNDADSDRHGIVTPDGGLMNPNHFLAVSIDYLYRNRSQWPQNAGVGKTLVSSSMIDRVATDLGRELVEVPVG
+FKWFVPGLLSGTGVFGGEESAGASFVKFDGGAWSTDKDGLLLCLLAAEIQAVTGQSPSERYRDLVALHGDPAYARIDAPA
+TAEQKAALKALSPDDVTATELAGETILAALTNAPGNDAPIGGLKVVTKNAWFAARPSGTEDVYKIYAESFLGEEHLKQVQ
+QEAQAIVDAVIS
+>4_46
+MTENTAALPAAERPGTPALPQDLIDVDALLEAYHTGHPDVTDPAQKVVFGTSGHRGSAFTTSFNDDHIAAITQAVVEYRA
+HHGITGPVLVGKDTHALSGPAQDTAVEVLLGNDVEVLVDSRGGYTPTPAVSHAILHLNAGRELSPSGFAVDGDNAGLVDG
+LVITPSHNPPADGGFKYNPPHGGPADTEATTWIADRANELLAAGLAGVHRVASADVAGHAKLGGFDFLDRYVSDLPQVID
+VEAIREAGVRIGADPMGGASVAYWGEIADRHGLDLTVVNPEVDPRFGFMTLDWDGKIRMDCSSPNAMASLIERMTPDADG
+QAPFDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYLYRHREQWPQSAGVGKTLVSSSMIDRVAGDLGRELVEVPVG
+FKWFVPGLLTGTGVFGGEESAGASFVQFDGSPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGDPAYARIDAPA
+TAEQKAKLKTLSPDDVPVTELAGETILATLTNAPGNDAPIGGLKVVTQHAWFAARPSGTEDVYKIYAESFRGPEHLTQVQ
+AEAQKLVDAVIG

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000218.fa

@@ -0,0 +1,51 @@
+>0_65
+MGQVDTGRTGRRDRRTERPRSRSLHAVLLAALAAVLVACG--PVTAPPA-PSSAPASSTT
+AAPTSSSPSAGPTA--------------AEVAAAVEPGLETSPGTASAEFRDLATGEVLY
+ARDADEPVAPASSLKVLAAAAIVSALGPETTLQTTVVAQPTADDAATELVLVGGGDVLLG
+TGASDSTHVSGRAGLRTLAQRTVAGLVEDGVTGQVVVSTDLRLFTDRTALNPRWTSDIPE
+SGNIAPVQPLATYGGREAPGTGEDRIEDPAQFAALTFQAALDDAVAASGADLEVGLRDTL
+PATEVPRATVLAAAPVAAVESASVGEQVAYLLAHSENQVVEALAHTAAPATDLPATHEGA
+TRLLTATVEDLGVDTAGMALVDSSGLSPDNRVSAGQLAGVVAGVARTPALATVLEGLPRP
+GEDSTLGDRFPDAPARQAVAAKTGTLDQTVSLTGTVTTTSGRVLAFSIICSDLQWKLEPA
+RAAVDEAVSAVAGL
+>1_2029
+MGQVDTGRAGRRDRRTEHRRSRSLPAVLLAALAAVLVACG--PVTAPTA-PSSASASTST
+AAPTSSSPSAGPTA--------------AEVAAAVEPGLETSPGTVSAEFRDLATGEVLY
+ARDADEPVAPASSLKVLAAAAIVSALGPETTLQTTVVAQPTADGAATELVLVGGGDVLLG
+TGASDSKAVSGRAGLRTLAERTVAGLVEDGVTGRVVVSTDLRLFADRTALNPRWTSDIPE
+SGNIAPVQPLATYGGREAPGTGEDRIEDPAQFAALTFQAALDDAVAASGADLEVGLRDTF
+PATEVPRATVLAAAPVAAVESAPVGQQVAYLLAHSENQVVEALAHTAAPATDLPATHEGA
+TQLLTATAEDLGVDTAGMALVDSSGLSPDNRVSAGQLAGVVAGVARTPALGTVLEGLPRP
+GEDSTLGDRFPDAPARQAVAAKTGTLDQTVSLTGTVTTTSGRVLAFSIICSDLQWKLEPA
+RAAVDEAVSAVAGL
+>2_308
+MTPG------------------SPFASLLAALAAALLSAA--PVLTPLAGPAALAPGNPV
+TAEAVAAPS--PDA--------------RALASAVDAALDASPGRVAAQVRDAATGEVLH
+ARDADFLAAPASSLKVLTAAAALRTLGPERTLRTRVVAVPAADDGATELVLVGGGDVLLG
+DGASDPDAVAGRAGLRTLAERTVAGLAEAGVSGDVVVSVDLRLF-DGAAVNPAWTPDLLE
+DGHVSAVQPLATWGGREVPGVDEERIEDPAGHAALVFQRLLDEEIERTGADLDLGLRDSI
+PATTAVRDDVVAAEPTAQVESAPVAEVAAYMLAHSENQVAEALGHLSAYAVGRPATHEGA
+ADLLEDVAADLGADTAGMAVLDASGLAEGSLVSPAQLAAVVSAASRVPWLAPVLDGLPRP
+GEDSTLDERFRGTAAEGAVAAKTGTLDHTVSLTGTVTTQDGRVLAFSIVASDLDWRLDEA
+REAVDAAVTAMAGL
+>3_251
+MTPSN--RAAR-----VAAVTRVLLALAICALLGLLAHDVLLPRLPTPAAPAASAPSAPV
+PA---ASPSGGATAPSSTALASVAPVDPADVAAAVAPALAQAPGTASAEVRDAATGEVLY
+ARSADQAVAPASALKILTAVTAVDVLGADRALTTSVVALPG--GGATELVLVGGGDALLG
+AGASDPGRVDGRAGLRTLARRTVAGLRERGVTGPVAVSTDLRLFTDASPLNPAWSAGLVE
+SGNITAVQPLATYGGRTAPGTGEDRIADPAAFAALAFQRELTAAVADSGADLSVRARDVV
+PATSAPRGDVLATEPVARVESAPVGQQVAYLLAHSENQVAEVLARVAAAADGRPATHAAV
+PGLLRDRAAAHGVDTAGMRLVDASGLSPQNRVTAHQLAGLVEAVQADPALAPVRDGLPRP
+GEDSTLAERFPGSPAREAVAAKTGTLDQTVSLTGTVTTGSGRVLAFSIVCSGVDWRIAPA
+RAAIDEAVSALAAL
+>4_59
+MGQVDTGRAGRRDRRTEHRRSRSLPAVLLAALAAVLVACG--PVTAPPA-PSSAPAASTT
+AAPTSTSPSAGPTA--------------AEVAAAVEPGLATSPGTVSAEFRDLATGEVLY
+ARDADEPVAPASSLKVLAAAAIVSALGPETTLQTTVVAQPTADGAATELVLVGGGDVLLG
+TGASDSTHVSGRAGLRTLAERTVAGLVEDGVTGQVVVSTDLRLFTDRTALNPRWTSDIPE
+SGNIAPVQPLATYGGREAPGTGEDRIEAPAQFAALTFQAALDDAVAASGADLEVGLRDTL
+PATEVPRATVLAAAPVAAVESASVGEQVAYLLAHSENQVVEALAHTAAPATDLPATHEGA
+TRLLTATAEDLGVDTAGMALVDSSGLSPDNRVSAGQLAGVVAGVARTPALATVLEGLPRP
+GEDSTLGDRFPDAPARQAVAAKTGTLDQTVSLTGTVTATSGRVLAFSIICSDLQWKLEPA
+RAAVDEAVSAVAGL
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000223.fa

@@ -0,0 +1,26 @@
+>0_71
+M----------------------------TAHTPDD------AVPGTFDPDSTAVDRPRI
+EAAVREILLAIGEDPDREGLADTPARVAKAYAEFFAGLHQSPDQVLGTTFDIAHEELVLV
+KDIPFYSTCEHHLVPFHGTAHIGYIPSAEGRVTGLSKLARLVELYARRPQVQERLTTQVV
+EALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAKTVTSAVRGQLRDPSTRSEAMSLIMHG
+>1_2035
+M----------------------------TAHTPDD------AVPGTFDPDSTAVDRPRI
+EAAVREILLAIGEDPDREGLADTPARVAKAYAEFFAGLHQSPDQVLGTTFDIAHEELVLV
+KDIPFYSTCEHHLVPFHGTAHIGYIPSAEGRVTGLSKLARLVELYARRPQVQERLTTQVV
+EALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAKTVTSAVRGQLRDPSTRSEAMSLIMHG
+>2_303
+MTEQTHHDDAARGPV----PAADGSAAAPTASTPAA-----AGVPGTFDPDSTAIDRPRI
+EAAVREILLAIGEDPDREGLQDTPKRVAKAYAEFFAGLHQGPEQVLGTTFDIAHEELVLV
+KDIPFYSTCEHHLVPVHGTAHIGYIPSAAGRVTGLSKLARLVELYARRPQVQERLTTQVV
+EALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAKTVTSAVRGQLRDPSTRSEAMSLIMHG
+>3_245
+MTEQ--HRDAALADAHLHRPHEAAADVAPTTGAGAALAGAVPGVPGTFDPDQDTVDRPRI
+EAAVREILLAIGEDPDREGLQDTPKRVAKAYAEFFAGLHQRPEQVLGTTFDLSHEELVLV
+KDIPFYSTCEHHLVPFHGAAHIGYIPSAEGRVTGLSKLARLVELYARRPQVQERLTTQVV
+EALMEHLQPKGAIVVVEAEHMCMSMRGVRKPGAKTVTSAVRGQLRDPSTRAEAMSLIMHG
+>4_65
+M----------------------------TAHTPDD------AVPGTFDPDSTAVDRPRI
+EAAVREILLAIGEDPDREGLADTPARVAKAYAEFFAGLHQSPDQVLGTTFDIAHEELVLV
+KDIPFYSTCEHHLVPFHGAAHIGYIPSAEGRVTGLSKLARLVELYARRPQVQERLTTQVV
+EALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAKTVTSAVRGQLRDPSTRSEAMSLIMHG
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000225.fa

@@ -0,0 +1,26 @@
+>0_74
+MSTVDWSHLAEGPAPVPALGARPDAPVAAVLALGANLREPAQTLDAAVAALSALPHITDV
+RASPRAVTAPVGGPPGQPDYLNQVVTLRTDLAPWELLAVAHRLEQDHHRRREVRWGARTL
+DVDVIAYGDVRSDHPDLTLPHPRAAERAFVLLPWLWLDADATLAGTPVADLAAVAADAPG
+VRRQEPERHRLLAG------TDDVVPLRPACPDALG-------REDT-----
+>1_2038
+MSTVDWSHPAEGPAPIPELGARPDAPVAAVLALGANLREPAQTLDAAVAALSALPHITDV
+RASPRAVTTPVGGPPGQPDYLNQVVTLRTDLAPWELLAVAHRLEQDHHRRREVRWGARTL
+DVDVIAYGDVRSDHPDLTLPHPRAAERAFVLLPWLWLDADATLAGTPVADLAAVAADAPG
+VRRQEPERHRLLAG------TDDVAPLRPARPDALG-------REAT-----
+>2_300
+MSGVDWRHPAEDPAPTPALGARPAEPVAAVLALGANLREPAQTLDAAVAALSALPHVTDV
+QASPRAVTAPVGGPPGQPDYLNQVLTLRTTLSAWELLAVAHRLEQEHHRRREVRWGARTL
+DVDVIAYGDLVSDHPDLTLPHPRAAERGFVLLPWLWLDPDAVLAGRPVAELAALAADAPG
+VRRAEPERHRLLAG------RDDVVPVRPRAVRAPG-------RDAIDGSGP
+>3_242
+MSRPEAAHPAEGPAPTPELAARPSSPVTAVLALGANLGDPSETLDASVAVLTVTPGIEAV
+AASPRALTAPVGGPPGQPDYLNQVVRIRTALSPWELLGVAHRLEQDHHRRRTVRWGARTL
+DVDLIVYGDLTSDHPDLVLPHPRAAERGFVLLPWAWLDPEAELAGESVAELGARAADAPH
+VRR-EPARTAHLDGPRPDVLRPDSTPGLPSAPLPDGAAIARPWSDPT-----
+>4_68
+MSTVDWSHPAEGPAPIPELGARPDAPVAAVLALGANLREPAQTLDAAVAALSALPHITDV
+RASPRAVTTPVGGPPGQPDYLNQVVTLRTDLAPWELLAVAHRLEQDHHRRREVRWGARTL
+DVDVIAYGDVRSDHPDLTLPHPRAAERAFVLLPWLWLDADATLAGTPVADLAAVAADAPG
+VRRQEPERHRLLAG------TDDVAPLRPARPDALG-------REAT-----
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000227.fa

@@ -0,0 +1,21 @@
+>0_76
+MPGIDLSGVAFTPASPRLTTVKLIATTIGHLIWLAAFSVPLILKLTGPWAGMAAWVAWGL
+PAVVVVSWIVDLILIPRRVRAMGWAEREDDVLWREGILFRSVHAVPYGRLQYVDVSDGPL
+LRRVGLQTLTLKTAAAGGDVTLEGVPRERAEELREVLMARGQARLAGL
+>1_2040
+MPGIDLSGVAFTPASPRLATVKLIATTIGHLIWLAAFSVPLILKLTGPWAGMAAWVAWGL
+PAVVVVSWIVDLILIPRRVRAMGWAEREDDVLWREGILFRSVHAVPYGRLQYVDVSDGPL
+LRRVGLQTLTLKTAAAGGDVTLEGVPRERAEELREVLMARGQARLAGL
+>2_298
+MPGIDLTGVTFAPASPKLTPVKLISSSIGHLIWLVVFSVPLVLKLLGPWEGLWAWTAWGL
+PAIVVVSWLVDLVLIPRRVRAMGWAEREDDVLWREGLLFRSVHAVPYGRLQYVDVSDGPL
+LRRVGLQTLTLKTAASGSDVTLEGLPRETADELREVLMARGQARLAGL
+>3_240
+MPGIDLQGVEFTPVSPALVRVEAVRELIALVIWLAVVSVPLVLKLTGVWPDMWSWTAWGL
+PALVLAWSLVELVLIPRRVVAKGWAEREDDVLWREGILFRRVVAVPYGRLQYVDVTDGPL
+LRWAGLQKLTLKT-AGGADVELVGLPRETCDRLREVLMARGQARLAGL
+>4_70
+MPGIDLSGVAFTPASPRLATVKLIATTIGHLIWLAAFSVPLILKLTGPWAGMAAWVAWGL
+PAVVVVSWIVDLILIPRRVRAMGWAEREDDVLWREGILFRSVHAVPYGRLQYVDVSDGPL
+LRRVGLQTLTLKTAAAGGDVTLEGVPRERAEELREVLMARGQARLAGL
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000231.fa

@@ -0,0 +1,46 @@
+>0_82
+MTSVRRHAARGLVALAAAVAVSAPLAAPAAAAPAAPTTPAAAQSVTGKPVVRPDVVGHRG
+ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRK
+TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER
+LSARYGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEYGLNKRNAPATVQSFELANLRD
+LNENLGLKAETVFLSSVTGAPYDSVAAGDGLRDYDFYETAAGMREVRAAGVDTLGPAFAQ
+IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDPNARGDMVGMIQ
+PFLDAGIDGFFTDHPDLGVQAVDTWMQGK-----KEHPGRG---------VGKTA-----
+--------------QRGLKVR
+>1_2046
+MTSVRRHAARGLVALAAAVAVSAPLAAPAVAAPAATETPAAAQSVTGKPVVRPDVVGHRG
+ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRR
+TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER
+LSARHGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD
+LNENLGLKAETVFLSSVTGAPYDSVAAGDELRDYDFYETAAGMREIRAAGVDTLGPAFAQ
+IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDRNAQGDMVGMIQ
+PFLDAGIDGFFTDHPDLGVQAVDVWMQGK-----KEHPGRG---------VGKTA-----
+--------------QRGLQGR
+>2_290
+MISVRRHAARGLVALAAAVAVSAPLAAPAVAAPAAPTAPAAAQSATGKPVVRPEVVGHRG
+ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRK
+TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYNGRYQVPTFEEVLELRER
+LSDRYGRQIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD
+LNENLGLKAETVFLSSVTGTPYDSVAAGDTVRDYDFYETAAGMREVRAAGVDTLGPAFAQ
+VITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSADSNAQGDMVGMIQ
+PFLDAGIDGFFTDHPDLGVQAVDTWMQGK-----KEHPGRG---------VGKSA-----
+--------------QRGLQVR
+>3_236
+MTALRT-TARGLAALTAAVAVAAPLAVPASAAIPAKEPITQAE--------RPDVVAHRG
+ASAYRPEHTLAAYELAVAQGADVIEPDLVSTKDGVLVDRHENDITGTTDVSERPEFADRK
+TTKTVDGVEITGWFTEDFTLAELKTLRAKERLPEARPGSAAYDGMYQVPTFEEDLKLREE
+LSAKYGREIGIIPEIKHPSYFDGIGLSQEEEVIELLEEHGLNHADGRAVVQSFEFSNLAE
+MNTRLGLQADTAYLLWYEGSGYDAVLSGDTARDYAYFSTPAGAAEAAFNGIDIYGPELRQ
+VIALNQDGSLGAPTGLVEVAHDAGLTVVPYTFRAENQSLPLQFRSSENPVEHGDLAAYIT
+EVLDAGVDGFFTDFPDVGVAARDAWLAEKPAEQPSEQPSDGSHAVPGKVQTGDAAAWLPA
+GLAAAAAGVLVALRRRLTAAR
+>4_77
+MTSVRRHAARGLVALAAAVAVSAPLAAPAVAAPAATETPAAAQSVTGKPVVRPDVVGHRG
+ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRR
+TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER
+LSARHGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD
+LNENLGLKAETVFLSSVTGAPYDSVAAGDELRDYDFYETAAGMREIRAAGVDTLGPAFAQ
+IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDRNAQGDMVGMIQ
+PFLDAGIDGFFTDHPDLGVQAVDVWMQGK-----KEHPGRG---------VGKTA-----
+--------------QRGLKGR
+ 

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

@@ -0,0 +1,50 @@
+>0_89
+MTATAEPEVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVREVGTGFDPAQARVQATAAAG
+AHRDVPLAPLDEEDAEGTEHPELKRRIAALYASFMDDETVEARGLEPIASDLAAVATVSTPAELLALSGRLQRQGVSGLI
+NTGALNDAGNPDRMLLHLLQGGLGLPDESYYRDEAYAEILEQYTEHTGRLLALAGIGADRDEAAALGVRVVELEKRIAAL
+HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGLLEGPEAADLEDWRHWLILQV
+LRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAFVNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRS
+IEELEWMGEETRQRALEKLAMFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHITPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGRLEDWWTEEDRAAFTERTSRL
+VAQYNALSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRALEIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVT
+RIASDPHSPNEFRCNQVVKNLDAFHEAFGTREGDPMWLAPEERVTIW
+>1_2053
+MTATAEPRVPSPREDLYRHVNTGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEGAVREVGAGFDPAQARVQATAAAG
+AHRDAPLAPLDAEDTEGMEHPELKRRIAALYASFMDDETVEARGLEPIASDLAAVATVTTPAELLTLSGRLQRQGVSGLI
+NTGALNDAGNPDRMLLHLLQGGLGLPDESYYRDEAYAEILEQYTEHTGRLLTLAGIGADRDEAAALGVRVVELEKRIAAL
+HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGLLEGPEAADLEDWRHWLILQV
+LRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAFVNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRS
+IEELEWMGEETRQRALEKLAMFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHMTPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGRLEDWWTEEDRAAFTERTSRL
+VAQYNALSPVEAPDHRVNGEFTLGENIGDLGGLGIAHRALEIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVT
+RIASDPHSPNEFRCNQVVKNIDAFHEAFGTREGDPMWLAPEERVTIW
+>2_283
+MTATAEPRVPAPREDLYRHVNAAWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVREVGAGFDPAQARVDATAAAG
+AEHHTPLEPLDAEETEGMELPEVKRRIAALYASFMDDETVEARGLEPVATDMAAVASVQTPAELLELSGRLQRQGVSGLV
+NTGALNDAGNPDRMLLHLLQGGLGLPDESYYRDEAYAEILEQYTEHAGRLLGLAGIGADSAEAAEAGVRVVELEKRIAAL
+HWDVVRSRDAVARYNLMTHEQLVELFPLAEAWLEGVDAAGERSREVVVWQPDFLSGVQALLEGPEAADLEDWRHWLILQV
+LRSFAGFLPDAFVQENFSFYGRRLAGTEEVRHRWKRAVAFVNGAAGEDVARLYVDRHFPEGHVAAMDELVNLLQEAYRRS
+IDELEWMSEETRQRALEKLSMFRPMVGRPVRWVDYSSLEVHAGDLLGNARAASEFEWERDLRKIEDGPDPEEWHITPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEKSMAANLGAIGAVIGHEIGHGFDDQGSRYDGSGRLEDWWTQEDRAAFTELTSRL
+VAQYNVLSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRALEIWRDEGDGASLDAAAGDREFFSAWAAVWRQLTRPETMVT
+RIASDPHSPNEFRCNQVVKNIDAFHEAFGTQEGDPMWLAPEERVTIW
+>3_229
+MTATAEPRVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRRIAEDAARDA------------AMAAPA
+PEVEAPAQDEASQDPAAAERAA-RERIAVLWSAFMDEEAVEAAGILPLAADLEAVDAVASPAELLALSGRLQREGVSGLI
+GTGALNDAGDPERMLLHLIQSGLGLPDESYYREEAYAEILAQYTEHVGRLFALAGVGGDEAGAAALGERVVALEKRIAAH
+HWDVVRSRDAVARYNLLTRDQLLELLPLAPGWLEGIGAADARADEVVVWQPDFLTGVQALLEGPDAADLADWKAWLTLQV
+LRSRAGFLPDAFVQENFSFYGRRLAGTQEVRPRWKRAVAFVNGGVGEDVGRLYVARHFPEGHVAAMDQLVGLLLEAYRRS
+IDALDWMGEQTRQSALEKLAMFRPMVGFPETWRDYSALELTPGDLVGCARAVDRFEWDRDLAKIETGPDPREWHMTPQTV
+NAYYTPLENAIVFPAALLQPPFFDPERSMAANLGGIGAVIGHEIGHGFDDQGSRYDGSGRLHDWWTEQDREAFAERTGRL
+VAQYSALSPAEAPDRQVNGEFTLGENIGDLGGLGIAHQALEIWREEQDGSTEDESSGDREFFQAWAAVWRQLTRPETMVT
+RIASDPHSPNQFRCNQVVKNLDAFHTAYGTREGDPMWLAPEERVTIW
+>4_84
+MTATAEPEVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVREVGTGFDPAQARVQATAAAG
+AHRDVPLAPLDEEDAEGTEHPELKRRIAALYASFMDDETVEARGLEPIASDLAAVATVSTPAELLALSGRLQRQGVSGLI
+NTGALNDAGNPDRMLLHLLQGGLGLPDESYYRDEAYAEILEQYTEHTGRLLALAGIGADRDEAAALGVRVVELEKRIAAL
+HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGLLEGPEAADLEDWRHWLILQV
+LRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAFVNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRS
+IEELEWMGEETRQRALEKLAMFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHITPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGRLEDWWTEEDRAAFTERTSRL
+VAQYNALSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRALEIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVT
+RIASDPHSPNEFRCNQVVKNIDAFHEAFGTREGDPMWLAPEERVTIW