diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000007.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000007.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20c01bc98e14f65c2181432142e5d71807ac5d7e
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000020.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000020.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b48230d6c070938c36cde07e87e12fcb3afd134f
--- /dev/null
+++ b/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---------------------------------------------------
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000027.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000027.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e298cea803794bad889a2165dd1a31b7f6eb5a50
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000028.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000028.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee189abaedf0d6af285c468cac693fe0a4a6c06c
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000029.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000029.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5572476c6b7d912f2aaf514531690b1d899dca34
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000046.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000046.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a6287003de07b782cb8f04dee53cb4e57dec42e
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000055.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000055.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d9ae23ccb84a86c377cc6cdadc6c23545d977027
--- /dev/null
+++ b/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--
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-------------------------------
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000056.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000056.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d48fa7d5c750d29c6c45a849f43ca6b9c699a938
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000058.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000058.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a29a909e4c5e8747847e7a4b44f5c45979539585
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000061.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000061.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a7eb6dd512335d592d4014deedef28d68ab70bc
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000062.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000062.fa
new file mode 100644
index 0000000000000000000000000000000000000000..570293666ed24838965e6d356bc4370ba99eb36b
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000066.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000066.fa
new file mode 100644
index 0000000000000000000000000000000000000000..be00d92e31a16e0b594141fdd09b626eaa445668
--- /dev/null
+++ b/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-------------------------
+----------------------------------------------
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000073.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000073.fa
new file mode 100644
index 0000000000000000000000000000000000000000..208e0f2aabd544089ab813505c0030f8ad6665cd
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000079.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000079.fa
new file mode 100644
index 0000000000000000000000000000000000000000..33a08144a432d4b325bf348d7c8be75864f005e4
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000085.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000085.fa
new file mode 100644
index 0000000000000000000000000000000000000000..96a5268054bf4d99a5edc8b0a87e9b39235bd056
--- /dev/null
+++ b/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
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000086.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000086.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef624d099a88326d8f3c7df34306a40f42e71af4
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000088.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000088.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7a0c264b79f91ccb21330068ce9b7e50cfa4bc4
--- /dev/null
+++ b/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--------------------------------
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000092.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000092.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e0d573a1916b46d55fc0619874176c304d5e236
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000096.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000096.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1dd77574bf47d063764562179542262331e1ce0b
--- /dev/null
+++ b/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---
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000098.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000098.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e3897fe86c2a0034f34b5f61a2d1fb9252b6692e
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000100.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000100.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cbafe3980ee6494c586374cd2913569fc57b7d63
--- /dev/null
+++ b/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--
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000108.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000108.fa
new file mode 100644
index 0000000000000000000000000000000000000000..55f683439ed756c3a06770994ecff8309e62ae51
--- /dev/null
+++ b/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----
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000109.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000109.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dded1de8915e4bea9c899dc15338ce5fa0c6a836
--- /dev/null
+++ b/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-
+-------
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000116.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000116.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b47c9b4a2a40ef3165bc36bc2a957d032a1e8aa
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000120.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000120.fa
new file mode 100644
index 0000000000000000000000000000000000000000..635d2b00010a8c263226eb459f9a73c670082b71
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000127.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000127.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5a69d841e505c60829f7eba2df6c5c5508c789a3
--- /dev/null
+++ b/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
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000129.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000129.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ff9e633fd264b4cc36d443d38ad3d96f1167e66
--- /dev/null
+++ b/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-------------
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000143.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000143.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3bf139403d4d434ea7a843cdb4e21f3e5fdbda21
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000144.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000144.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40e965cb5978229ddcb586b7aed0aa4ff31a999f
--- /dev/null
+++ b/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-
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000145.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000145.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3d0886bc2e5a65f0c906b80a8faa1114ec94b88d
--- /dev/null
+++ b/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----
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000151.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000151.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cebd3cdb797a0850ccbc9f6cdcca3bfedbd59b21
--- /dev/null
+++ b/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
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000159.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000159.fa
new file mode 100644
index 0000000000000000000000000000000000000000..49be263652d03ad35a7d006ead211b84e134e3dd
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000163.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000163.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d85fed49917fac32c4598fb443d45547370ec920
--- /dev/null
+++ b/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---------------------------------------------
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000164.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000164.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0cebf536d0344a032aa30d352041ea18bca1410f
--- /dev/null
+++ b/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
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000172.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000172.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6dd49b5b39eb4cec5d408e4e90390dc15e96434a
--- /dev/null
+++ b/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------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000173.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000173.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e89d3770caf5038441788f6c35e511cae9e8b321
--- /dev/null
+++ b/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--------------------------
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000177.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000177.fa
new file mode 100644
index 0000000000000000000000000000000000000000..39479b379763170329bc9d06edeeaf0c381000fe
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000182.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000182.fa
new file mode 100644
index 0000000000000000000000000000000000000000..75a55b286d1d5724a9a0b9fc4314b187862e7e64
--- /dev/null
+++ b/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----
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000188.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000188.fa
new file mode 100644
index 0000000000000000000000000000000000000000..91b37582cd342483a938df6a08a93691496c7047
--- /dev/null
+++ b/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-------------------
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000190.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000190.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8c088d7378723c41840d80d0f809fa2a8c07bfed
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000199.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000199.fa
new file mode 100644
index 0000000000000000000000000000000000000000..33dae68450ab224618d745219e236f948766f85c
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000200.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000200.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ca57413f34973ca2de67248f9974065d88a295f
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000206.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000206.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dd49b0f8efffa5f5daf7a7c1fa3bb1afbc932ee5
--- /dev/null
+++ b/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--
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000208.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000208.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee472ed3f92fd9ac9f1f9b0fa09da074f9b1a038
--- /dev/null
+++ b/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
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000218.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000218.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da77db0af15e01eeabe387f7a62d199f12ffa24f
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000223.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000223.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f44bc3c98198b93a542229fa324a9951b96752f
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000225.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000225.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d9e83820e40b541164a40455617add2a96784c77
--- /dev/null
+++ b/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-----
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000227.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000227.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b273b496724d0fd92c1972e34f8c8219ef4ab6e5
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000231.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000231.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cd65959bdc8853fbcf57ff26dc120847a4a44a25
--- /dev/null
+++ b/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
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000238.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000238.fa
new file mode 100644
index 0000000000000000000000000000000000000000..001699f9021b1bd73c69892c00072e03b49bafe5
--- /dev/null
+++ b/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
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000245.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000245.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b8a76c4c9f6b30e8c802cf5c7177f57ee81e3a0c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000245.fa
@@ -0,0 +1,16 @@
+>0_97
+-MGIGDLNNLANQHSDKIDEAVDNAQEQHGDKLGEHGDTVNKGVDGAQEKFLSGD----E
+GEQQA
+>1_2061
+-MGIGDLNNLANQHSDKIDEAVDNAQEQHGDKLGEHADTVNKGVDGAQEKFLSGD----E
+GEQQA
+>2_274
+-MGIGDLNNLANQHSDKINEAVDGAQEQHGDKLGEHADTVNKGVDGAQEKFLSGE--KNE
+GEQQA
+>3_221
+MVGFDDVKNLANENSDKINEQVDAAQAQHSDKLGQHADLADKGIDGAQDKFLNGQSAENE
+GEQQA
+>4_92
+-MGIGDLNNLANQHSDKIDEAVDNAQEQHGDKLGEHGDTVDKGVDGAQEKFLSGD----E
+GEQQA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000259.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000259.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5bd0f30cbb0e13b2e69907cbcf96cd40cba3fb1a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000259.fa
@@ -0,0 +1,46 @@
+>0_112
+MSLSPDPAQQ--LLSAGALERAAGLRRMKAVALGLLILLAVVFVVAFPLQDTHPVWGYVR
+AAAEGGMVGALADWFAVTALFRHPMGVPVPHTALIPRKKDQLGAALTEFVQENFLDSEVA
+HEKVDGLKVAEAAGGWLRREENAARTAREIATAARGAMAAADDDAVQELLRQLMERHMVA
+PDWSPTLAGVLEDVVAGRHHERVVDLVVAHTGDWVAAHPELFVETVRRRSPEWSPDLVDR
+LLAERLHAETLKYLAGIRRDREHEARRAVDDWLDRLADEMRNEPATRASVERFKRNLFAD
+ERLRAWAGRAWVSLRDSLLDALEDPSSDLHRALVAALRDLGARLQEDPELRDRVDGHARR
+AAAYALSSYGPALTGVIEETVARWDGEQTARTLELFVGKDLQFIRINGSVVGALAGLAIH
+GVATLFL
+>1_2076
+MSLSPDPAQQ--LLSAGALERAAGLRRMKAVALGLLILLAVVFVVAFPLQDTHPVWGYVR
+AAAEGGMVGALADWFAVTALFRHPMGVPVPHTALIPRKKDQLGAALTEFVQENFLDSEVA
+HEKVDGLKVAEAAGGWLRREENAARTAREIATAARGAMAAADDDAVQELLRQLMERHMVA
+PDWSPTLAGVLEDVVAGRHHERVVDLVVAHTGDWVAAHPELFVETVRRRSPEWSPDLVDR
+LLAERLHAETLKYLAGIRRDRQHEARRAVDDWLDRLADEMRNEPATRASVERFKRNLFAD
+ERLRAWAGRAWVSLRDSLLDALEDPSSDLHRALVAALRDLGARLQEDPELRDRVDGHARR
+AAAYALSSYGPALTGVIEETVARWDGEQTARTLELFVGKDLQFIRINGSIVGALAGLAIH
+GVATLFL
+>2_256
+MSLSPDPARQ--LLSAGTLERERGLRRMKAVALGLLVALAVVFAVAFPLQDVHPVWGYVR
+AAAEGGMVGALADWFAVTALFRHPMGIPVPHTALIPRKKDQLGAALTEFVQENFLDSDVA
+REKVEGLEVAAAAGGWLRRPENAERAAREVATAARGAMAAADDDAVQELLRQLMQRHMVE
+PEWSPTLAGVLQDVVTGRHHERVVDLVVEHTGDWVAAHPEMFVETVRRRSPEWSPDLVDR
+LLAERLHAEALKYLAGIRDDRDHEARRAVDDWLTRLSAEMRDDPHTRASVERFKHSLFAD
+ERLRAWAGRAWTSLRDSLLDALEDPASDLHRALVAALRDLGARLQEDPVLRDRVDGHARA
+AAAYALSTYGPAVTGVIEETVARWDGDQTARTLELFVGRDLQYIRINGSIVGALAGLTIH
+AVATLFL
+>3_188
+MAPSPVPADSPFPLTPAALERAAGLRRMKAVALGLLIVLAVVFAVAFPLQRVHPAWGFVR
+AAAEGGMVGALADWFAVTALFRRPLGLPIPHTALIPEKKDQLGAALTEFVQENFLDSDVA
+REKVAGLQVARAAGGWLRERPHAVHAAGEIAMAARGAVAATDDDAVQDLLQQLMQRHMVE
+PDWSPTLAGVLEDVLAGRHHEKVVDLVVEHTGDWVATHPEMFLETVRRRSPEWSPDLVDR
+LLAERLHAETLKYLAGVRADRDHEARRSVDDWLARLAGNMRDDPATRASAERFKADLFAD
+EQLRAWAGRAWITLRDSLLAALEDQDSDLHRALVDALVDLGVRLQEDPALQASVDGRARA
+AASYALSSYGPALTGVIEETVARWDGRQTADTLENLVGRDLQFIRINGSVVGALAGLAIH
+TLASLVF
+>4_117
+MSLSPDPAQQ--LLSAGALERAAGLRRMKAVALGLLILLAVVFVVAFPLQDTHPVWGYVR
+AAAEGGMVGALADWFAVTALFRHPMGVPVPHTALIPRKKDQLGAALTEFVQENFLDSEVA
+HEKVDGLKVAEAAGGWLRREENAARTAREIATAARGAMAAADDDAVQELLRQLMERHMVA
+PDWSPTLAGVLEDVVAGRHHERVVDLVVAHTGDWVAAHPELFVETVRRRSPEWSPDLVDR
+LLAERLHAETLKYLAGIRRDRQHEARRAVDDWLDRLADEMRNEPATRASVERFKRNLFAD
+ERLRAWAGRAWVSLRDSLLDALEDPSSDLHRALVAALRDLGARLQEDPELRDRVDGHARR
+AAAYALSSYGPALTGVIEETVARWDGEQTARTLELFVGKDLQFIRINGSIVGALAGLAIH
+GVATLFL
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000261.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000261.fa
new file mode 100644
index 0000000000000000000000000000000000000000..669bc8c6b2b556c4d8b40ed9dc7f4a9b0161c14c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000261.fa
@@ -0,0 +1,21 @@
+>0_118
+MIVAFSVAPSGQPADSAHLP-GDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGDW
+DEVMEVVRGAVDAVSSYGSRVSLVLKADIRPGHSGELDGKLERLEAALAEDGNGDAADAR
+------
+>1_2083
+MIVAFSVAPSGQPADSAHLP-GDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGDW
+DEVMEVVRGAVDAVSSYGSRVSLVLKADIRPGHTGELDGKLERLESALAEDEGRRAAPAP
+HDGDAG
+>2_249
+MIVAFSVAPSGTPADAAHQP-GDEDSASVHRAVAAAVAVVRESGLPHRTSSMFTEIEGDW
+DEVMDVVRGAVDAVAPYGSRVSLVLKADIRPGHTGELDGKLARLEAALASDDVS------
+------
+>3_183
+MIVAFSVSPSGAPADAAYAPSSDGDSASVHRAVAAAVAVVRASGLPHRTSSMFTEVEGEW
+DEVMGVVKRAVEAVEPYGSRVSLVLKADIRRGRTGELDGKLERLEAALT--DGTPATPDR
+FRA---
+>4_126
+MIVAFSVAPSGQPADAEHLP-GDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGEW
+DEVMEVVRAAVDAVSPYGTRVSLVLKADIRPGRTGELDGKLERLESALAEDEGRRAAPAP
+RDGDAG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000263.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000263.fa
new file mode 100644
index 0000000000000000000000000000000000000000..29076515b728bb5b105233c637bace845eb7eddd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000263.fa
@@ -0,0 +1,36 @@
+>0_120
+MSRRSGRSSGRSSAASSSSRGSAARRGR----AAEPEGIVPGVHEISHGTAEIREDPYEP
+GAFVLYVNGVESSPLDPDHPERMGFEYMRWAVAAVRAHW-PEPTPLRALHLGGAGCALAR
+WVDHAHPGSHQTAVEIDAGLAALARERFGLPRAPALRIRVADAAEVLATAHPASRDLIIR
+DVFAPDPTDLTG----ARHITPPGLTGLDAARAAARVLAPGGLYVLNVGGGPDLTSVRAD
+VAAVVAAFEHVEVIADPPMLKGRRRGNVIVAASDAPVARPAADAPPGSDPRDRLARALRM
+DAFPARLAEDPRGFPAGVAPGITGLVPGPEA---------------
+>1_2085
+M-----------------SRRSSARRGRAAGGSAGPAGIEPGVHAITHGTAEIREDAFEP
+DAFILYVNGVESSPLDPERPERMAFEYMRWAAAAVRAHW-PEPTPLRALHLGGAGCALAR
+WVDHAYPGSHQTAVEIDAGLAALARERFGLPRAPALRIRVADAAEVLATAHPASRDLIIR
+DVFAPDPTDLTG----ARHITPPGLTGLDAARAAARVLAPGGLYVLNVGGGPDLTSVRAD
+VAAVVAAFEHVEVIADPPMLKGRRRGNVIVAASDAPVARPAADAPPGSDPRDRLARALRM
+DAFPARLAEDPRGFPAGVAPGITGLVPGPEA---------------
+>2_247
+M-------------------------------------ITPGVFAISSGTAEILPDPWTD
+GVYLLKVNGVESSQLNPDRPETLGFEYMRWAAAVLAHRFAPDAERLRVLHLGGAGCTFAR
+WVTHTWPQAHQLAVELDAGLAELARTHFDLPRAPQLKIRVGEAGQVLAGLREATREVVFR
+DVFA--PADPLSLAPDSPHVTPAHLTGADAAAHAARVLVPGGVYVLNIGGGPDLASVRRE
+VAALRTAFAHVEVMADPAMLKGRRRGNVIAAASSVPLA---AEELGG---RAALARALRS
+DALPAQLVDDVARFAGGLAPDPTPLVQASDGTSEGASTQASPGPAQ
+>3_181
+M-------------------------------------ITPGTFPISSGTAEIVPDPWTD
+GVFLLKVNGVESSQLNPDRPETLGFEYMRWAAAVLTHRFAPDA-RLRVLHLGGAGCTFAR
+WVTHTYPASHQLAVELDAGLAAVAREHFDLPRAPQLKIRVGEAGEVLAGLRDATREVVFR
+DVFAPDPADPTG----ALHVTPAHLTGLDAAAHAARVLTPGGVYLLNIGGGPDLTSVRRE
+VAALTETFAHVEVMADPAMLKGRRRGNVIAAASSAPLS---ADGLGG---RSALARALRS
+DALPAQLLDDVVAFTAGLTPDATPLVTPAEG---------------
+>4_128
+M-----------------SRRSSARRGRAAGGAAGPAGIEPGVHAITHGTAEIRENAFEP
+GAFILYVNGVESSPLDPERPERMAFEYMRWAAAAVRAHW-PEPTPLRALHLGGAGCALAR
+WVDHAYPGSHQTAVEIDAGLAALARERFGLPRAPALRIRVADAAEVLATAHPASRDLIIR
+DVFAPDPTDLTG----ARHITPPGLTGLDAARAAARVLAPGGLYVLNVGGGPDLTSVRAD
+VAAVVAAFEHVEVIADPPMLKGRRRGNVIVAASDAPVARPAADAPPGSDPRDRLARALRM
+DAFPARLAEDPRGFPAGVAPGITGLVPGPEA---------------
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000267.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000267.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a807db0373de90696abd175e71cd05b1a888c9b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000267.fa
@@ -0,0 +1,50 @@
+>0_125
+MSDPTPPSTEPMIPEQPGNHPSS-------ATAPDAGV---APATSAAAGRDRV-LLPWVFWPSAVIVLSFVGATLLAPA
+QMTVGIGLVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGDITLGKPDEKPEFSTLSWFSLLFAAGMGIGLVFFGMTEP
+LMHFTSPRPDLAAANPTQAEAAQSALATTFLHWGLQPWAIYAVVGVAVALAIHRRGRPLALRWAFEPLIGERRVRGGWGH
+LIDNIALIGTVFGVATSLGLGVTQMSAGLRALGIVPEDSPWLEYVMIGAVTCVVLYTVVSGVERGMKWLSNTNLILAAGL
+LLFIAIVGPTAFLFKEMVQSLGSYMQYFFANSLNVSAFYGAEGDAWQAGWSAYYWGWWMSWTPFVGIFIARISRGRTVRE
+FIAGVLLVPTLVCVVWFGILGGTAIFLETTRPAGYTSVVGADGAIDSNTALFQVLEQLPAGMMLVVGAIILSGIFFITSA
+DSGSLVMGMLATGGDVNPKATVKIFFAIATSLMAAALLAAGGLSAIQVLAITIGLPFSVLMLLICLATFRSLGYSVARVE
+AVRRQAMLASIKDRLGLESDDDEVVDAGPVAASQWWASLSRDHQQRIADAAAGVPASE----------GPRRPRLRRHE-
+--H
+>1_2090
+MSDPTPPSTEPMIPEQPGNHPSS-------ATAPDAGV---APATSAAADRDRV-LLPWVFWPSAVIVLSFVVATLLAPE
+QMTVGISLVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGDITLGKPDEKPEFSTLSWFSLLFAAGMGIGLVFFGMTEP
+LMHFTSPRPDLAAANPTQAEAAQSALATTFLHWGLQPWAIYAVVGVAVALAIHRRGRPLALRWAFEPLIGERRVRGGWGH
+LIDNIALIGTVFGVATSLGLGVTQMSAGLRALGIVPEDSPWLEYAMIGAVTCVVLYTVVSGVERGMKWLSNTNLILAAGL
+LLFIAIVGPTAFLFKEMVQSLGSYMQYFFANSLNVSAFYGAEGDAWQAGWSAYYWGWWMSWTPFVGIFIARISRGRTVRE
+FIAGVLLVPTLVCVVWFGILGGTAIFLETTRPAGYTSVVGADGAIDSNTALFQVLEQLPAGMMLVVGAIILSGIFFITSA
+DSGSLVMGMLATGGDVNPKATVKIFFAIATSLMAAALLAAGGLSAIQVLAITIGLPFSVLMLLICLATFRSLGYSVARVE
+AVRRQAMLASIKDRLGLESDDDEVVDAGPVAASQWWASLSRDHQQRIADAAAGVPASE----------GPRRPRLRRHE-
+--H
+>2_242
+MSESIPPSHPSAPPGPASAHPAAPAAGAADAREASGAV---APASSDAATGARV-LLPWVFWPSTIVVLLFVGATLLFPE
+PMTAAIGTVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGAITLGKPDEKPEFSTLSWFALLFAAGMGIGLVFFGMTEP
+LMHFVSPRPDLAATDPNPAQAAQAALATTFLHWGLQPWAIYAVVGVAVGLAIHRRGRPLALRWAFEPLLGERRVRGGWGH
+LIDNIALIGTVFGVATSLGLGVTQMSAGLRSLGVVPEESAWVEYAMIGLVTLVVLYTVVSGVERGMKWLSNVNLVLAAGL
+LLFIAIVGPTAFLFKEMVQSFGAYLQTFFGASLNVSAFQGAEGDAWQAGWSAYYWGWWMSWTPFVGIFIARISRGRTVRQ
+FLAGVLLVPTLIGVVWFGVLGGTAIYLETVRPDGYTSVVGADGSIDSNTALFQVVEQLPAGALLVIGAIMLSAIFFVTSA
+DSGALVMGMLATGGDVNPKVPVKIFFAIATALMSAALLAAGGLSAIQTLAITIGLPFSVLMLVMCLATFRSLGYSVARVE
+AVRRQAMLASIKDRFGLDTDDDEVVDGGPVAASQWWASLSRDRQRTIAQAASAGPDDEIRLAGSSAEEPAGSPDARR---
+---
+>3_178
+MT-PAPAGRD----------ADAPAANRPHRTGPDPDVKHPAPATADQADRGHAGLLPWVFWPSTLIVLLFVVATLAFPA
+QMTDVIGDVQAAIIRNFSWWYAIVAFAFVVFCAYLVFSRKGSITLGKPDEKPEFSTMSWFALLFAAGMGIGLVFFGMTEP
+LMHFTSPRPDLAAANPTEAQAAQSALATTFLHWGLQPWAIYAVVGVAVGLAIHRRGRPLSLRWAFEPLLGERRVRGGWGH
+LIDNIALIGTVFGVATSLGLGVTQMAAGLRSLGIVPADSPWLEYAMIAAVTCVVMYTVVSGVERGMKWLSNINLVLAAGL
+LLFIALVGPTPFLLKETVQSFGAYLQNFFADSLNVSAFYGAEGDAWQAGWTAYYWGWWMSWTPFVGIFIARISRGRTVRE
+FLMGVLLVPTLVCVVWFGILGGTAIWLETVRPAGYTSVVGADGAIDSNSALFQVLEQLPAGLLLVIGAIILSGIFFVTSA
+DSGALVMGMLATGGDVNPKTAVKIFFAIATAFMAAALLAAGGLSAIQTLAITIGLPFSVLMLVMCVATFRSLGYSAARVE
+AVRRQAMLASIQDRLGKDTDDDEVVEGGPVAASQWWASLSRDHQRTIARLASPGPDDEIRLH-EDATATSARPDTTRGGS
+TAR
+>4_133
+MSDPTPPLKNPLDPERADTRPSS-------APTADGAV---APATSAAAARDRV-LLPWVFWPSAVIVLSFVGATLLAPE
+QMTVGISLVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGDITLGKPDEKPEFSTLSWFSLLFAAGMGIGLVFFGMTEP
+LMHFTSPRPDVAAANPTQAEAAQSALATTFLHWGLQPWAIYAVVGVAVALAIHRRGRPLALRWAFEPLIGERRVRGGWGH
+LIDNIALIGTVFGVATSLGLGVTQMSAGLRALGIVPEDSPWLEYAMIGAVTCVVLYTVVSGVERGMKWLSNTNLILAAGL
+LLFIAIVGPTAFLLKEMVQSLGSYMQYFFANSLNVSAFYGAEGDAWQAGWSAYYWGWWMSWTPFVGIFIARISRGRTVRE
+FIAGVLLVPTLVCVVWFGILGGTAIFLETTRPAGYTSVVGADGAIDSNTALFQVLEQLPAGMMLVVGAIILSGIFFITSA
+DSGSLVMGMLATGGDVNPKATVKIFFAIATSLMAAALLAAGGLSAIQVLAITIGLPFSVLMLLICLATFRSLGYSVARVE
+AVRRQAMLASIKDRLGLESDDDEVVDAGPVAASQWWASLSRDHQQRIADAAAGVPASE----------GPRRTRLRRHG-
+--H
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000268.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000268.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0bc4b34a0f1b6fc4d622906589d2af0024caca3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000268.fa
@@ -0,0 +1,45 @@
+>0_127
+MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLGVDAIWLSPFYLSPQHDAGYD
+VADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHTSSEHAWFQAALAAGPGSPERARYHFAEGRGEHGELPPNNW
+ESTFGGGAWTRVTEADGTPGQWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS
+RMGMVTDAGEDADPTFDPDTFEPLTPFMDQDRVHEVYRDWRRVLDSYDHEPMMVAEAWVAPLSRMFRYVRPGEMHQTFNF
+TYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTVRHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMV
+ELGLPGSAYIYQGDELGLPEHTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA
+PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWS-EHHDPTRGVLAFTVTSGGGRHLGSGEPIPAR
+TVLVMANLSTEPVDLPANHSRALFSLEEAEAVQDGRLAHDAAAWLLMD
+>1_2092
+MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLGVDAIWLSPFYLSPQHDAGYD
+VADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHTSSEHAWFQAALAAGPGSPERARYHFAEGRGEHGELPPNNW
+ESTFGGGAWTRVTEADGTPGQWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS
+RMGMVTDAGEDADPTFDPDTFEPLTPFMDQDRVHEVYRDWRRVLDSYDHEPMMVAEAWVAPLSRMFRYVRPGEMHQTFNF
+TYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTVRHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMV
+ELGLPGSAYIYQGDELGLPEHTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA
+PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWS-EHHDPTRGVLAFTVTSGGGRHLGSGEPIPAR
+TVLVMANLSTEPVDLPANHSRALFSLEEAEAVQDGRLAHDAAAWLLMD
+>2_240
+MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLGVDAIWLSPFYLSPQHDAGYD
+VADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHTSSEHAWFQAALAAGPDSPERARYHFAEGRGEHGELPPNNW
+ESTFGGGAWTRVTEADGTPGQWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS
+RMGMVTDAGEDADPTFDPDTFEPLTPFLDQDRVHEVYRDWRRVLDSYGHEPMMVAEAWVAPLSRMFRYVRPGEMHQTFNF
+TYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTVRHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMV
+ELGLPGSAYIYQGDELGLPEHTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA
+PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWS-EHHDPARGVLAFTVTSGGGRHLGSGEPIPAR
+TVLVMANLSTDPVDLPTGHSRALFSLEEAEAVQDGRLAHDAAAWLLMD
+>3_175
+MTTQRLTTPPSEARNRPETPWWVDAVVYQVYPRSFADGDGNGMGDLPGVTAKIPYLSRLGVDAIWLSPFYLSPQHDAGYD
+VADYRTVDPRFGTLADADALIDAAHAADIRVIVDLVPNHTSSEHPWFQAAMAAGPGSRERARYHFTEGRGEHGELPPSNW
+ESTFGGGAWSRVTEADGTPGQWYLHLFDTTQPDLNWENPEVREEFESILRFWLDRGVDGFRVDVAHGLVKKPGYPDADHT
+RMGMVTDAGEDQDPDFDVDAFEPAMPFLDQDGVHEVYRQWRRVLDSYPHEPMMVAEAWVSPLPRTFRYVRPGEMHQAFNF
+TYLMAGWDAESLTSAIDRSFTEAEKVGAPNTWVLSNHDTVRHTSRYGLSDPTAYPAGITAEDEQPDEALGRRRARAAAMI
+ELALPGSAYIYQGDELGLPEHTTLPAELREDPYFFRTGGAEPGRDGCRIPLPWAADEPALGFSGPDAD----------AA
+PWLPQPDSFRVLAADRQVGVEGSHFELYRHLLQIRAELDLGTGTFAWSAEHHRPEQGVLAFTVSSGGGRHLGSGVPIPAR
+TVLVMANIGDTPVALPGDHVRAQFSLPESEAVVDDRLAPDAAAWLLLR
+>4_135
+MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLGVDAIWLSPFYLSPQHDAGYD
+VADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHTSSEHAWFQAALAAGPGSPERARYHFAEGRGEHGELPPNNW
+ESTFGGGAWTRVTEADGTPGQWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS
+RMGMVTDAGEDADPTFDPDTFEPLTPFMDQDRVHEVYRDWRRVLDSYDHEPMMVAEAWVAPLSRMFRYVRPGEMHQTFNF
+TYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTVRHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMV
+ELGLPGSAYIYQGDELGLPEHTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA
+PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWS-EHHDPARGVLAFTVTSGGGRHLGSGEPIPAR
+TVLVMANLSTDPVDLPAGHSRALFSLEEAEAVQDGRLAHDAAAWLLMD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000275.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000275.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ed2729b77d87af5095cb1e2dfd38573d34c7ffb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000275.fa
@@ -0,0 +1,21 @@
+>0_134
+MKTPRHAPPVVRDGKTLLPAHAVSTAPVTAFGLIGGYLTARETGIRPLGGVVLAAAGLYA
+GRTWLAKRGPAVAGGLAALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDRSEA
+GR
+>1_2099
+MKTPRHAPPVVRDGKTLLPAHAVSTAPVTAFGLIGGYLTARETGIRPLGGVVLAAAGLYA
+GRTWLATRGPAVTGGLAALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDRSEA
+GR
+>2_232
+MNSPRHAAPVVRDGRTLLPAHAVTTAPIAAFGLIGGYLTARETGIRPLGGVVLAAAGAYA
+GRTWLAKRGPAVAGGLTALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDREGA
+-R
+>3_166
+M-SKDTSTPVARDGKTLLPADAVTTAPIAALGLVGGYLVARETGIRWLGGVVLGAAGLYA
+GRTWAAKGGPAVAGTLGALYLGGFGASHPLAKKIGAWPSVLSVAAASAGAAYAAVDRKDG
+RR
+>4_142
+MKTPRHAPPVVRDGKTLLPAHAVSTAPVTAFGLIGGYLTARETGIRPLGGVVLAAAGLYA
+GRTWLAKRGPAVAGGLAALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDRSEA
+GR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000276.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000276.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3589aa88869beafa83bab6e80f3e7332b1078729
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000276.fa
@@ -0,0 +1,26 @@
+>0_135
+------------------------------------------------------------
+-------------------MAIENWQHDLNIGTVVRTANAFNAAGVHIIGRRRWNRRGAM
+VTDRYLHVRHHETVAAFTEWAAGEGLPVLGVDLFPESVPVETFDFPRACVLVFGQEGPGL
+SAEVRAASSAVLSIAQYGSTRSINAGVAAGIAMHAWIRQHAA-VP----
+>1_2100
+------------------------------------------------------MLDHYR
+YWSLEAIVADLDARRHPFHVAIENWQHDLNIGTVVRTANAFNAAGVHIIGRRRWNRRGAM
+VTDRYLHVRHHETVAAFTEWAAGEGLPVLGVDLFPESVPVETFDFPRACVLVFGQEGPGL
+SAEVRAASSAVLSIAQYGSTRSINAGVAAGIAMHAWIRQHAA-VP----
+>2_231
+MGPGTSENSPETREKREEREGREEREVGVGPWEGPWPEDPRYDPELLRDGDRRNVVDGYR
+YWTLEAIVADLDARRHPFHVAIENWQHDLNIGTVVRTANAFNAAGVHVIGRRRWNRRGAM
+VTDRYLHVRHHATVEEFTAWAAAEGLPVLGVDLFPESVPLESFELPRECVLVFGQEGPGL
+SEEVRAASAAVLSIAQYGSTRSINAGVAAGIAMHAWVRQHGG-VPTSSS
+>3_165
+MGSGEGVDAREV-----------GREVGAPPWEGPWPEDPRYDPALLRDGDRRNVADRYR
+YWTVEAIVADLDRTRHPFHVAIENWQHDLNIGTVVRTANAFNAAGVHIIGRRRWNRRGAM
+VTDRYLHVHHHETVEAFTAWAAGEGLPVLGVDLFPESVPVETFDFPRACVLVFGQEGPGL
+SEEVRAASEAVLSIAQYGSTRSINAGVAAGIAMHAWIRQHGGPAPV---
+>4_143
+M----------------------PREVGVGPWLGPWPEDPRYDPELLAHGDRRNVLDRYR
+YWRLEAIVADLDARRHPFHVAIENWQHDLNIGTVVRTANAFNAAGVHIIGRRRWNRRGAM
+VTDRYLHVRHHETVAAFTEWAAGEGLPVLGVDLFPESVPVETFDFPRACVLVFGQEGPGL
+SAEVRAASSAVLSIAQYGSTRSINAGVAAGIAMHAWIRQHAA-VP----
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000278.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000278.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f51f90c86480967f9ebaf7a14682fb602a972152
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000278.fa
@@ -0,0 +1,36 @@
+>0_138
+MPIASPEKYAEMIDAAKNGAFAYPAINVTSSQTLNAAIRGFAEAGSDGIIQVSTGGAAYF
+SGSSVKDMVAGSLAFAAFAREVAKKHSVNIALHTDHCPQDKLEDFVLPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGRELLARTHANKQILEVEIGVVGGEEDGVAHEINEKL
+YTTVADGIATVEALGLGENGRYLTALTFGNVHGVYKPGNVKLRPEILQEIQQAVGEKFGR
+ERPFDLVFHGGSGSAAQEIADSVEYGVVKMNVDTDTQYAFTRPVAGHMFENYDGVLKVDG
+EVGDKKQYDPRVWGAKAEEAMAARVVQACTELNSAGKSIG
+>1_2103
+MPIASPEKYAEMIDAAKNGAFAYPAINVTSSQTLNAAIRGFAEAGSDGIIQVSTGGAAYF
+SGSSVKDMVAGSLAFAAFAREVAKKYSVNIALHTDHCPQDKLEGFVLPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGRELLARTHANKQILEVEIGVVGGEEDGVAHEINEKL
+YTTVADGIATVEALGLGEHGRYLTALTFGNVHGVYKPGNVKLRPEILQEIQQAVGEKFGK
+ERPFDLVFHGGSGSAAQEIADSVEYGVVKMNVDTDTQYAFTRPVAGHMFENYDGVLKVDG
+EVGDKKQYDPRVWGAKAEEAMAARVVQACTELNSAGKSIG
+>2_228
+MPIASPDKYAEMIDAAKNGAFAYPAINVTSSQTLNAAIRGFAEAGSDGIIQVSTGGAAYF
+SGASVKDMVTGSLAMAAFAREVAKNYSVNIALHTDHCPKDKLDAFVMPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGKELLARTHANKQILEVEIGVVGGEEDGVAHEINDKL
+YTTVEDGIATIEALGLGEQGRYLTALTFGNVHGVYKPGNVKLRPQILEDIQKAVGEKFGK
+ERPFDLVFHGGSGSAAQEIADSVSYGVVKMNVDTDTQYAFSRPVAGHMFENYAGVLKVDG
+EVGDKKMYDPRVWGAKAEEAMAARVVQACQELNSAGTSIG
+>3_163
+MPIASPDKYAEMIDAAKNGAFAYPAINVTSSQTLNAAVRGFAEAGSDGIIQVSTGGAAYF
+SGSSVKDMVAGSLAMAAFAREVAKKYSVNIALHTDHCPKDKLDGFVKPLLDASEAEVKAG
+RDPLFNSHMWDGSAETLEENLRIAQELLARTHANKQILEVEIGVVGGEEDGVANEINDKL
+YTTVEDGIATIEALGLGENGRYLTALTFGNVHGVYKPGGVKLRPQILQDIQQAVGEKFGR
+QRPFDLVFHGGSGSAAQEIADSVSYGVVKMNVDTDTQYAFSRPVAGHMFENYDGVLKVDG
+EVGNKKMYDPRVWGAKAEDGMAARVVQACQELNAAGKSIG
+>4_146
+MPIASPEKYAEMIDAAKNGAFAFPAINVTSSQTLNAAIRGFAEAGSDGIVQVSTGGAAYF
+SGSSVKDMVAGSLAFAAFAREVAKKYSVNIALHTDHCPQDKLEGFVLPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGRELLARTHANKQILEVEIGVVGGEEDGVAHEINEKL
+YTTVQDGIATVEALGLGEHGRYLTALTFGNVHGVYKPGNVKLRPEILQEIQQAVGEKFGK
+ERPFDLVFHGGSGSAAQEIADSVEYGVVKMNVDTDTQYAFTRPVAGHMFENYDGVLKVDG
+EVGDKKQYDPRVWGAKAEEAMAARVVQACTELNSAGKSIG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000283.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000283.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5dd4baa98a2a011f269048acbed0b549db3c469c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000283.fa
@@ -0,0 +1,21 @@
+>0_143
+MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDIVPVAPESSLVWALMAEDAWAEGR
+TVDSYAYARVGYHRGLDALRRAGWRGAGPVPYAHEPNRGFLRALYALGRAAAGIGESEEV
+ERIRTFLRDSDPTAAEQIEAGQGRARG
+>1_2108
+MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDIVPVAPESSLVWALMAEDAWAEGR
+TVDSYAYARVGYHRGLDALRRAGWRGAGPVPYAHEPNHGFLRALYALGRAAAGIGESEEV
+ERIRTFLRDSDPTAAEQIEAGQGRAQG
+>2_222
+MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDVVPVAPESSLVWALMAEDAWSEGR
+TVDSYAYARVGYHRGLDALRKAGWRGAGPVPYDHEPNRGFLRALYSLGRAAAGIGESEEV
+ERIRTFLKDSDPTAAEKIEATQGRSGS
+>3_161
+MSESLIGKNLMEPPATLLPEEPEVLARLDAGDLPEDLVPLAPESSLVWALMAEDAWSEGR
+AVDSYAYSRVGYHRGLDALRRAGWRGAGPVPWSHEPNRGFLRALYALGRAAAGIGESAEV
+DRIRTFLKDSDPTAAQQIEAAQA----
+>4_151
+MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDIVPVAPESSLVWALMAEDAWAEGR
+TVDSYAYARVGYHRGLDALRRAGWRGAGPVPYAHEPNRGFLRALYALGRAAAGIGESEEV
+ERIRTFLRDSDPTAAEQIEADQGRAQG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000284.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000284.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af88c8545a1b51d0f5326f5dccbf9419c132135e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000284.fa
@@ -0,0 +1,26 @@
+>0_144
+MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEGDVVSRLGVTRAVDF
+LVPAGADVRELFRRHATGDDPDALVGHVEAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG
+VPVIAYGLRTDFRTRSFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVDPATGAEHF
+VFEGDQVAIDGVQVTYESLCGTCYLAESGGALG
+>1_2109
+MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEGDVVSRLGVTRAVDF
+LVPAGADVRELFRRHATGDDPDALVGHVEAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG
+VPVIAYGLRTDFRTRSFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVDPATGAEHF
+VFEGDQVAIDGVQVTYESLCGTCYLAESGGALG
+>2_221
+MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEDEVVSRLGVTRTVDF
+LVPAGAGVRELFRRHASGDDPDALVDHVDAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG
+VPVIAYGLRTDFRTRCFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVNPATGAEHF
+VFEGDQVAIDGVEVTYESLCGSCYLAESGGRLG
+>3_160
+MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPAVDTKGDAAVVSRLGVTRAVDF
+LVPAGADVLALFRAHAAGDDPDALVDHVDAPPVACLLVDEAQFLEAGQVDDLLRIAVLED
+VPVMAYGLRTDFRTHSFPGSARLLELAHSLEELKTICRCGRKAVLNTRKVVDAATGRSRF
+VFEGDQVAIDGVEVTYESLCAACYLEESGGRLG
+>4_152
+MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEGDVVSRLGVTRAVDF
+LVPAGADVRELFRRHATGDDPDALVGHVEAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG
+VPVIAYGLRTDFRTRSFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVDPATGAEHF
+VFEGDQVAIDGVQVTYESLCGTCYLAESGGALG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000285.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000285.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b9ac97acf1d94ba43ad0e0d4813283c513207d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000285.fa
@@ -0,0 +1,26 @@
+>0_146
+MATPLLELAASRGVCFPLRARRLTLTPFRGLDAPAVWSFCRLEQVWSWTSGRPESENALR
+ESYLGAGDRLTVR--AGDVIVGVGKVAVQDAWSQDGPQEEARDAQAELGWTIDPRQAGQG
+YGTELARALLGFAFDDLGVRRVEAHAFADNAPSLRIMEKVGMRHEGTFKEESLHLTRGWV
+DGATYAMLASEFHSPL--TQE
+>1_2111
+MATPLLELAASRGVCFPLRTRRLTLTPFRGLDAPAVWSFCRLEQVWSWTSGRPESENALR
+ESYLGAGDRLTVR--AGDVIVGVGKVAVRDAWSQGGPREEGRDAQAEIGWTIDPRQAGQG
+YGTELARALLGFAFDDLGVRRVEAHAFADNAPSLRIMEKVGMRHEGTFKEESLHLTRGWV
+DGATYAMLASEFHSPL--TQE
+>2_452
+MATPLLDLAARRGVVFPLRTERLTLTSFAADDAPAVFDFCRLEEVWTWTSGRAGSAGELR
+ESYLAAGDRLTVR--AGEAIIGVGKLAVQDAWSQGGPREEARDAQAEIGWTIHPTHADQG
+YATELAGALLKLAFTGLGVHRVEAEAFADNAPTLRVMEKVGLRHEGTFREESLHLTRGWV
+DGVTYAMLASEFLARV-----
+>3_403
+MATPLLDLAARRGVAFPLRTERLTLTPFTAVDAPAVWDFCRLEEVRTWTSGRAGSAAELR
+EEYLATGDRLTVRDGAGDV-VGVGKLAVQDAWSQGGPHPDARDAQAELGWTVAPEHAGRG
+YATEIGRALLDLAFRGLGVRRVEAGAFADNAPSLRVMAKIGLRHEGTFLGESLHLTRGWI
+DGVTFALLASEYEGGAAASRA
+>4_159
+MAPPLLELAASRGVCFPLRARRLTLTPFRGLDAPAVWGFCRLEQVWSWTSGRPESEGALR
+ESYLAAGDRLTVR--VGDVIVGVGKAAVQDAWSQGGPREEARDAQAEIGWTIDPRQAGQG
+YGTELARALLGFAFNDLGVRRVEAHAFADNAPSLRIMEKVGMRHEGTFKEESLHLTRGWV
+DGATYAMLASEFHSPL--TQE
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000289.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000289.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a67d531914d2c6b4f4e527606b84311a0a477696
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000289.fa
@@ -0,0 +1,55 @@
+>0_172
+MTTQQPDIPGTPGPITPDLEEHTALTHPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAAQGCPYLTTAHGVRLQDSDHS
+LKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGAHGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGS
+MDLARDTRGFATKFYTDEGTWDLVGNNIPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTLW
+NMSDRGIPRSYRMMEGFGVHTYRLIAADGSTVLVKFHWKPMLGVHSVTWEEALLTNGMDPDFHRRDLADAIEAGAFPEWE
+LGVQVFEDNEEQMFEGIDLLDPTKLVPEELAPVQPLGRMTLNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFS
+YLDTQLTRLGGPNWNQLPINRPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHAFIEHPEPLPASVKER
+AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLAQQVADGLGIPVPAPTETPAD
+VQPSPVLSQIGGAWPLDGRQVGVVVGESVDEKELDALVQGIHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVV
+VASPAAPAADAAPGLDQKAGAADPEAVDPRVIKVLQEMWRHSKAILALEPAEAVLAAAQVSGK-GVESAADGASAVSRLT
+ELLPAHRVWDRFPTTGRLAD
+>1_2119
+MTTQQPDIPGTPGPITPDLEEHTALTHPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAAQGCPYLTTAHGVRLQDSDHS
+LKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGAHGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGS
+MDLARDTRGFATKFYTDEGTWDLVGNNIPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTLW
+NMSDRGIPRSYRMMEGFGVHTYRLIAADGSTVLVKFHWKPMLGVHSVTWEEALLTNGMDPDFHRRDLADAIEAGAFPEWE
+LGVQVFEDNEEQMFEGIDLLDPTKLVPEELAPVQPLGRMTLNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFS
+YLDTQLTRLGGPNWNQLPINRPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHAFIEHPEPLPASVKER
+AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLAQQVADGLGIPVPAPTETPAD
+VQPSPVLSQIGGAWPLDGRQVGVVVGESVDEKELDALVQGIHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVV
+VASPAAPAADAAPSLDQKAGAADSEAVDPRVVKVLQEMWRHSKAILALEPAEAVLAAAQVSGK-GVESAADGASAVSRLT
+DLLPAHRVWERFPTTGRLAD
+>2_211
+MTTQQPDIPGTPGPRTPDLEERTAPTSSDD-AAMPAPDQRGPASVSPTGQDTGADPATAAQGCPYLTTAHGVRLQDSDHS
+LKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGAHGMFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGS
+MDLARDTRGFATKFYTDEGTWDLVGNNMPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTIW
+NMSDRGIPRSFRMMEGFGVHTYRLIAADGSTVLVKFHWKPKLGVHSVTWEEALITNGADPDYHRRDLADAIEAGAFPEWE
+LGVQVFEDTEEQMFEGIDLLDPTKLVPEELVPVQPLGRMTLNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFS
+YLDTQLTRLGGPNWTQLPINRPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHALIEHPEPLPASVKER
+AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLAQQVADGLGIPVPAPTETPAD
+VQPSPVLSQIGGVWPLDGRQVGVVVGESVDEKELDALVQGIHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVV
+VASPAAPAADAAPGLDEKAGAAASEAVDPRVVKVLQEMWRHSKAILALEPAEGVLAAAQVSGK-GVESAADGASAVSRLT
+ELLPAHRVWERFGTTGRFAD
+>3_156
+-MAEQPKIPGTPGPITPDLEEHTALTDPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAAQGCPYLTTAHGVRLQDSDHS
+LKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGAHGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGS
+MDLARDTRGFATKFYTDEGTWDLVGNNMPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTIW
+NMSDRGIPRSFRMMEGFGVHTYRLIAADGSTVLVKFHWKPKLGVHSVTWEEALITNGADPDYHRRDLADAIEAGAFPEWE
+LGVQVFEDNEEQMFEGIDLLDPTKLVPEELVPVQTLGLMTLNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFS
+YLDTQLTRLGGPNWTQLPINRPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHALIEHPEPLPASVKER
+AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEETIRVRQLQNLGAIDPRLAQQVADGLGMPVPAPADAPAD
+VQPSAALSQVGGTWPLDGRQVGLVVGPQVDEKELGDAVQGIHGAGMVPLVIAPKGGPVAGEVVAQRAYLTAASIELDAVV
+VLGATPPAGDAQHGLDAKAAADAPDAVDPRVAKLVQEAWRHAKAIVAVGEGTSVLDELGLTGTPGVLTVDAGADAVAQLK
+ELMPAHRVWERFPTTGRLAD
+>4_169
+MTTQQPDIPGTPGPITPDLEEHTALTHPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAAQGCPYLTTAHGVRLQDSDHS
+LKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGAHGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGS
+MDLARDTRGFATKFYTDEGTWDLVGNNIPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTLW
+NMSDRGIPRSYRMMEGFGVHTYRLIAADGSTVLVKFHWKPMLGVHSVTWEEALLTNGMDPDFHRRDLADAIEAGAFPEWE
+LGVQVFEDNEEQMFEGIDLLDPTKLVPEELAPVQPLGRMTLNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFS
+YLDTQLTRLGGPNWNQLPINRPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHAFIEHPEPLPASVKER
+AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLAQQVADGLGIPVPAPTETPAD
+VQPSPVLSQIGGAWPLDGRQVGVVVGESVDEKELDALVQGIHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVV
+VASPAAPAADAAPGLDQKAGAADSEAVDPRVVKVLQEMWRHSKAILALEPAEAVLAAAQVSGK-GVESAADGASAVAALK
+QLLPAHRVWDRFPTTGRLAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000292.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000292.fa
new file mode 100644
index 0000000000000000000000000000000000000000..76c3e3f57a2cf15b9e606ff5466759511811125a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000292.fa
@@ -0,0 +1,26 @@
+>0_175
+MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD
+DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVATPPDSAVYLAIV
+EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV
+VGALSTLVPAYRCTDELADRCGAALVAATHELAHLLGAADTPRERPADSPGKPKARS
+>1_2122
+MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD
+DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVTTPPDSAVYLAIV
+EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV
+VGALSTLVPAYRCTDELADRCGAALVAATGELAHLLGAADTPRERPADSPGKPKASS
+>2_208
+MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD
+DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVTTPPASAVYLAIV
+EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV
+VGALSTLVPAYRCTDELADRCGAALVAATDELAHLLGAADTPRERPADSPGKPKASS
+>3_153
+MPTTPPASTRTVDRALALLAAVVAQPRLSLAEAARATDLPASTALRLLRSLETAGFVDRQ
+EEGEYRPGARLIQLGARAFSREPLVRLARAPMDGVAEATGESVYLSLRNGAQEAVYIAIV
+EGTHSVRHASWVGRTVPLEGTAVGEVYRGEVPPGGYAHGGHSVEQDVTALSSPVVVGGRV
+VAALSALVPDYRCTAEHADRCGRALAGATTRLASALGEEAPPED--AD---------
+>4_172
+MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD
+DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVTTPPDSAVYLAIV
+EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV
+VGALSTLVPAYRCTDELADRCGAALVAATHELAHLLGAADTPRERPADSPGKPKASS
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000293.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000293.fa
new file mode 100644
index 0000000000000000000000000000000000000000..327edc42e8a6e15214b198551d8b339deca6e334
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000293.fa
@@ -0,0 +1,45 @@
+>0_176
+MAVGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRAARSWEAYDAIVATLKDLEED
+ETLLVQSGKPVGVFRTNKWAPRVLIANSNLVGDWATWPEFRELEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGR
+KRYDGSLQGTLTLTGGCGGMGGAQPLAVTLNGGVCLIVDVSEDRLRRRMGKRYLDEVETDIDKAVERVMQAKNDGEAVSV
+GLVGNAAEVFPELLERQKAGTVEIDIVTDQTSAHDPLSYLPIEIDEKDWHAEAEADPDTFTKKAQESMARQVEAMVGFQD
+IGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFCEGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLD
+GAAEFVEFEGLPARICWLGYGERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGVADGTELAAAKLEALLTNDPGMGVIRHVDAGYSRAAEVAKERGVRVPME
+ATIRD
+>1_2123
+MAEGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRAARSWEAYDAIVATLKDLEED
+ETLLVQSGKPVGVFRTNKWAPRVLIANSNLVGDWATWPEFRKLEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGR
+KRYDGSLQGTLTLTGGCGGMGGAQPLAVTLNGGVCLIVDVSEDRLRRRMGKRYLDEVETDIDKAVERVMQAKRDGEAVSV
+GLVGNAAEVFPELLERQKAGTVEIDIVTDQTSAHDPLSYLPIEIDEKDWHAEAEADPDTFTKKAQESMARQVEAMVGFQD
+IGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFCEGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLD
+GAAEFVEFEGLPARICWLGYGERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGVADGTELAAAKLEALLTNDPGMGVIRHVDAGYSRAVEVAAERGVRVPME
+ATIRD
+>2_207
+MAVGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRAARSWEAYDAIVATLKDLEED
+ETLLVQSGKPVGVFRTNKWAPRVLIANSNLVGDWATWPEFRKLEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGR
+KRYDGSLKGTLTLTGGCGGMGGAQPLAVTLNGGACLIVDVSEGRLRRRMGKRYLDEVVTDIDKAVERVMQAKRDGEAVSV
+GLVGNAAEVFPELLERQKRGEIEIDIVTDQTSAHDPLSYLPIEIDEADWQAEAEGDPETFTKKAQESMARQVEAMVGFQD
+IGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFCEGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLD
+GAAEFVEFEGLPARICWLGYGERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGLADGTELAAAKLEALLTNDPGMGVIRHVDAGYSRAAEIAAERGVRVPME
+ATIRD
+>3_152
+MAAGFTQHDPSRTIRAPRGTELNAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRAARSWEAFDAIVETLKDLEED
+ETLLVQSGKPVGVFRTNVWAPRVLIANSNLVGDWADWKTFRELEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGR
+KKYDGTLKGTLTLTGGCGGMGGAQPLAVTLNGGVCLIVDVSEERLRRRMGKRYLHEVETDIDAAIARVMQAKRDGEAVSV
+GLVGNAAEVFPELLKRQKAGEVEIDIVTDQTSAHDPLSYLPIEIEEKDWHAEAEADPDTFTKKAQESMARQVEAMVGFQD
+IGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFCEGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLD
+GAAEFVEFEGLPARICWLGYGERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGLADGTELAAAKLTALLTNDPGMGVIRHVDAGYSRAVEVAAERGVRIPME
+PTVRD
+>4_173
+MAVGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRAARSWEAYDAIVATLKDLEED
+ETLLVQSGKPVGVVKTNVWAPRVLIANSNLVGDWADWKTFRELEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGR
+KRYDGSLKGTLTLTGGCGGMGGAQPLAVTLNGGVCLIVDVSEDRLRRRMGKRYLDEVETDIERAVERVMQAKRDGEAVSV
+GLVGNAAEVFPELLERQKAGTVEIDIVTDQTSAHDPLSYLPIEIDEKDWHAEAEADPDTFTKKAQESMARQVEAMVGFQD
+IGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFCEGLGPFRWAALSGDPEDIRVTDAALKELFPENEHLHRWLD
+GAAEFVEFEGLPARICWLGYGERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGVADGTELAAAKLEALLTNDPGMGVIRHVDAGYSRAAEVAKERGVRVPME
+ATIRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000296.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000296.fa
new file mode 100644
index 0000000000000000000000000000000000000000..deaa9511b884c33cef45f593733ca4db7e33ad64
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000296.fa
@@ -0,0 +1,40 @@
+>0_179
+MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGVSTGFGALADKHIPLESRAQL
+QKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVRPVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALA
+LMGEGDVVGTDGALRPAGEALAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR
+VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLRDTLAYVRTVAERELAATVDN
+PVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSERRTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVS
+DMKRLAVPASVDSIPSSAMQEDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV
+PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH
+>1_2126
+MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGVSTGFGALADKHIPLESRAQL
+QKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVRPVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALA
+LMGEGDVVGEDGALRPAGEALAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR
+VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLRDTLAYVRTVAERELAATVDN
+PVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSERRTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVS
+DMKRLAVPASVDSIPSSAMQEDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV
+PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH
+>2_204
+MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGVSTGFGALADKHIPLESRAQL
+QKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVRPVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALA
+LMGEGDVVGADGALRPAGEALAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR
+VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLRDTLAYVRTVAERELAATVDN
+PVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSERRTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVS
+DMKRLAVPASVDSIPSSAMQEDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV
+PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAWKSEGTEAEGH
+>3_149
+MTT---TVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGVSTGFGALADKHIPLESRAQL
+QKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVRPVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALA
+LMGEGDVVGADGALRPAGEALAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLDELVDTVDLTAAMSVEALLGTDR
+VFVPELHLPLRPHPGQAASADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLRDTLAYVRTVAERELAATVDN
+PVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSERRTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVS
+DMKRLAVPASVDSIPSSAMQEDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV
+PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGASADAEPQDLAEESAGAEAEGH
+>4_176
+MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGVSTGFGALADKHIPLESRAQL
+QKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVRPVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALA
+LMGEGDVVGTDGALRPAGEALAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR
+VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLRDTLAYVRTVAERELAATVDN
+PVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSERRTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVS
+DMKRLAVPASVDSIPSSAMQEDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV
+PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000297.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000297.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1524f0a5b9063b84aa6e53082bd5600d786df543
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000297.fa
@@ -0,0 +1,41 @@
+>0_184
+M------------------------TSELPSSSLSPAWTGRTDGDTPEHLRWHQVVRPAD
+GRGEPTTPQRDPGAGAPTSGARSTALIGFASDEGVRRNHGRVGAEDGPEALRGALASLAY
+LEGTGALVDAGDVSVDRGDDDAPGELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYAS
+ITGLTGSTRVAAGTRVGILNLDAHFDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGI
+SEANNTRALFDTARERGVTWVTDEQAQTADVTGVRRWVRSFINAVDVLYLTIDLDVLPAA
+VAPGVSAPAGFGVPYEVIHACALEATQSGKLALADVVELNPALDVDGRTAKAAARLIHTI
+VSRHRTDASLLA
+>1_2131
+M------------------------TSELPSPSLSPAWTGRTDGDTPEHLRWHQVVRPAD
+GRGEPTTTQRHPGAGAPTSGARSTALVGFASDEGVRRNHGRVGAEDGPEALRGALASLAY
+LEGTGALVDAGDVSVDRGDDDAPGELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYAS
+ITGLTGSTRVGAGTRVGILNLDAHFDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGI
+SEANNTRALFDTARERGVTWVTDEQAQTADVTGVRRWVRSFINAVDVLYLTIDLDVLPAA
+VAPGVSAPAGFGVPYEVIHACALEATQSGKLALADVVELNPALDVDGRTAKAAARLIHTV
+VSRHRTDASLLA
+>2_198
+M------------------------TSELPSPSLSSAWAGRTDGDAPEHLRWHQVVRPAD
+GRGEPTTTQRHPGAGAPTSGARSTALVGFASDEGVRRNHGRVGAEDGPEALRGALASLAY
+LEGTGALVDAGDVSVDRGDDDAPGELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYAS
+ITGLTGSTRVGEGTRVGILNLDAHFDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGI
+SEANNTRVLFDTAREHGVTWVTDEQAQIADVTGVRRWVRSFIDAVDVLYLTVDLDVLPAA
+VAPGVSAPAGFGVPYEVIHACAVEAATSGKLALADVVELNPSLDVDGRTAKAAARLIHTI
+VSRHRTDASLLA
+>3_145
+MSGVVRPSLRTRPSMAWNGAMTADRASELPSAALSPAWTGRTDGDAPEHLRWHQVVRSAD
+GGAPAQTVDAAP--------ARSTALVGFASDEGVRRNHGRVGAEDGPDALRGALASLAY
+LEGTGALVDAGDVSVDRGDDDAPGELEAGQAELATVVSGLLNAHDLAVVLGGGHETAYAS
+ITGLTGSTRVAAGTRVGILNLDAHFDLREAPRPSSGTPFLQALRDAEEAEHQLSYAVVGI
+SEANNTRALFDTARERGVTWVTDEQAQTADVTGVRRWVRSFIDAVDVLYLTIDLDVLPAA
+VAPGVSAPAGFGVPYEVIHACTLEATQSGKLALADVVELNPALDVDGRTAKAAARLIHTI
+VSRHRTDASLLA
+>4_184
+M------------------------TSELPSSSLSPAWTGRTDGDTPEHLRWHQVVRPAD
+GRGEPTTTQRHPGAGAPTSGARSTALIGFASDEGVRRNHGRVGAEDGPEALRGALASLAY
+LEGTGALVDAGDVSVDRGDDDAPGELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYAS
+ITGLTGSTRVGAGTRVGILNLDAHFDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGI
+SEANNTRALFDTARERGVTWVTDEQAQTADVTGVRRWVRSFINAVDVLYLTIDLDVLPAA
+VAPGVSAPAGFGVPYEVIHACALEATQSGKLALADVVELNPALDVDGRTAKAAARLIHTI
+VSRHRTDASLLA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000301.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000301.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ab9e38501a69f64cc298317c4e070948cbe3ff0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000301.fa
@@ -0,0 +1,21 @@
+>0_188
+MPDDVAVRLLLIADTHIPRRARALPAQVWAEVARADVVLHAGDWVTEDVLDDLDARAARL
+VGVWGNNDGPKLRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS
+HIPWDTVAGPDTANPGLRLLNPGSCTDRRRQPVCTLMRAVVRGGRLEDVELVSVDRTP
+>1_2135
+MPDDVAVRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDARAARL
+VGVWGNNDGPGPRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS
+HIPWDTVAGPETANPGLRLLNPGSCTDRRRQPVCTLIRAVARDGRLEDVELVPVDRTP
+>2_193
+MT--TETRLLLLADTHIPPRARAMPAQVWDEVARADVVLHAGDWVEESVLDELEARSRRL
+VGVWGNNDDGALRARLPEVARVEIGGVRIAMVHETGAARGRERRMAEAFPDADVLVFGHS
+HIPWDTVAGPETANPGLRLLNPGSPTDRRRQPVCTLMRAVVRDGGLADVELVPVDRTP
+>3_141
+----MTTRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDAQAARL
+VGVWGNNDGPRLRARLPEVARVEIGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS
+HIPWDTVAGPETANPGLRLLNPGSCTDRRRQPVCTLMRAVVRGGRLEDVELVPVDRTP
+>4_188
+MPDDVAVRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDARAARL
+VGVWGNNDGPGPRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS
+HIPWDTVAGPETANPGLRLLNPGSCTDRRRQPVCTLIRAVARDGRLEDVELVPVDRTP
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000307.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000307.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f82cef51863e6b8ea68c73d759e9cf3109c50e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000307.fa
@@ -0,0 +1,31 @@
+>0_201
+MRQRQTQT-----RRTRRGLSLAALG-AAALLLTGC-ASGDDAPGAWDRARTQLEEADSV
+RMVTELRSEAPSNGRAVPDAVDISGPVDGSSMRYVSVYKDDGLITRDESRIVDGTAYSRF
+TVERVGA-SGEDHPAYAERWTAT-PYEGDPSATGMGAMVSSLLGSLPESGGLDDVEADAD
+GIRRSGQDAIRYVLDEPVSGPQEGVELTAFTVSKEDGRLLTVETESAGTKAVVTLSEMGG
+VDPVQAPPADEVLKQD---------------------------------G
+>1_2145
+MRQRQTQT-----RRTRRGLSLAAVG-AAALLLTGC-ASGDDAPGAWDRARTQLEEADSV
+RMVTELRSEAPSNGRAVPDSVDISGPVDGSSMRYVSVYQDDGLITRDESRIVDGTAYSRF
+TVERAGA-SGEDRPAYVERWTAT-PYESDPRATGMGAMVSSLLGSLPESGGLDDVEADAD
+GIRRSGQDAIRYVLDEPVSGPQEGVELTAFTVSKEDGRLLTVETESAGTKAVVTLSEMGG
+VDPVQAPPADEVLKQD---------------------------------G
+>2_172
+M-PRQNPT-----GRARRGLPLAALGAAAALVLTGCGASGEDASAAWDRARTQLEETDSV
+RMVTELRSDAPQAGNRTPESVDLSGPVDGSSMRYVSTYEDGDLITRDESRVVDGTAYSRF
+TVERRGA-SGEDRPAYVERWTAA-PHTGDPRATGMGAMVSSLLGSLPESGGLEDVAVDAD
+GIRRSGQDAVRYVLDEPLSVADDGVAMTAFTVSEEDGRLLTVETESAGTKAVVTVSEMGD
+VEPLQAPPSDEVLPQQQGQGAPGAVPPGGAPQDGTAPGGTPAEPVPPTDG
+>3_118
+MRPTTPRTPAPHGGARRRALSLAALGAAAALSLSACGASGEDASAAWDAARTQLQDASSV
+RLTTEARNDSGAA-PGTPDGVEIAGDVHSSDLSYTGVFRTDGYITRDESRTVGGQRYERF
+TLEQPGGVSGEGRPAFAEKWKKAEPLPGD---ASMRSILDGVLTAVPQAGALQGADVRAT
+DIRRQGRDATRYVLDTPVKGGTTDSSLTAFTVADDDGTLLTVETTGPGTRGTVTFSDWNA
+VEPVTA-PATEDMAQD------------------TA-----------TAK
+>4_201
+MRQRQTQT-----RRTRRGLSLAAVG-AAALLLTGC-ASGDDAPGAWDRARTQLEEADSV
+RMVTELRSEAPSNGRAVPDSVDISGPVDGSSMRYVSVYQDDGLITRDESRIVDGTAYSRF
+TVERAGA-SGEDRPAYVERWTAT-PYESDPRATGMGAMVSSLLGSLPESGGLDDVEADAD
+GIRRSGQDAIRYVLDEPVSGPQEGVALTAFTVSKEDGRLLTVETESAGTKAVVTLSEMGE
+VDPVQAPPADEVLKQD---------------------------------G
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000311.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000311.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8f8ca01dca549f6caf9c29eecb72acd657fe014
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000311.fa
@@ -0,0 +1,16 @@
+>0_205
+MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTDEILAQAR
+TAAEEMLSNPVIEDVVNVAVLDEAEGAR
+>1_2149
+MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGKVTDEILAQAR
+TAAEEMLSNPVIEDVVNVAVLDEAEGAR
+>2_163
+MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTDAVLDQAR
+RAAEELLSNPVIEDVVNVAVLDEAEGAR
+>3_112
+MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTEEVLAAAR
+TAAEEMLSNPVIEDVVNVAVLDE--DAA
+>4_205
+MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTDEILAQAR
+TAAEEMLSNPVIEDVVNVAVLDEAEGAR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000325.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000325.fa
new file mode 100644
index 0000000000000000000000000000000000000000..78cf2cf22d21d8f3095aaf5d50589b89553faf3c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000325.fa
@@ -0,0 +1,45 @@
+>0_225
+M-------PLARLRAALPAAALSLLLLTGCT---ATDDGVTPASDADTSASVSTMP----ITSTPSVDAAATSRAAASSL
+AA--SSSAAQSSRAAASSSSGAAESRA---------AEGSR----------------------SAEPAAPAAPADVEGDV
+VTVESISDGDTLRVTLGEVSTRVRLLNIDTPETHHPSKPVECMGPEATAALKSMISPGDTVVLRYDRRLYDRYDRLLAGV
+YADGVLLNAEMARLGYGEPAVFDGNDRFLPEVEAAWEQARANGVGRFSG--ECG--------------------------
+------------------------------------TAAEPIPEAAPAPAPEAAPA------------------------
+--------------------------------------------------------------------------------
+-------------------------------------------------AGDAGPVSGADSVCPDSHPVKANDNSGIYHM
+PGQQHYGKTNARHCYASASAAQAGGYRAARR
+>1_2189
+M-------PLARLRAALPAAALSLLLLTGCT---ATDDGVTPESAADTSASVSTMP----TTPTPSVDAAATSRAAASSL
+AA--SSSAAQSSRAAASSSSGAAESRAARAAEESRTAEGSR----------------------SAEPAAPAAPADVEGDV
+VTVESISDGDTLRVTLGEVSTRVRLLNIDTPETRHPSKPVECMGPEATAALKSMISPGDTVVLRYDRRLYDRYDRLLAGV
+YADGVLVNAEMARLGYGEPAVFDGNDRFLPEVEAAWEQARANGVGRFSG--ECG--------------------------
+------------------------------------AAAEPIPEAAPAPAPEAAPA------------------------
+--------------------------------------------------------------------------------
+-------------------------------------------------SGDAGPVRGADSVCPDSHPVKANDNSGIYHM
+PGQQHYGKTNARNCYASAAAAQADGYRAARR
+>2_128
+M------TPRLFPRAGLVAAAALSLVLTGCTPAASGDDVAAPASAGAPSSGAAATTAAPAVSSTASAEAADRSRAAESSR
+AAAQASEAEQSRRAEESRAAEARRAEESRAAEASREAERSRRAEESRAAAAAAAEEEDLDAAGSAEDAAWGGTAGVEGDV
+AVVQSVADGDTLRVSLDGVSTPVRLLNIDTPETVHPSKPVQCQGPEATAALKSMIGPGDTVVLRYDRRVYDRYDRLLAGV
+FADGRLVNAEMARLGLGEPVVFDGNVRFLPEVEAAWEQARADGVGLFSG--ECAVE------------------------
+------------------------------------EAPEPVEDEAPTAVAEPAPA-P----------------------
+--------------------------------------------------------------------------------
+-------------------------------------------------AAGSGPVPGADFVCPDDFPVKGNDNSFIYHV
+PGQQHYGRTNARNCYASAAAAEVDGYRAAKR
+>3_93
+MPSSRPPAPRVRTRL-LVSAALVLLAATGCT--------ASPATSSSTSSTSSAAPAALAASASPPASGASSA-------
+-------------------------------------------------------------------------AAVEGDA
+ATVVRVVDGDTVDVRRGAEDVRVRLLNIDTPETKHPSRPVECLGPEATRKLEELLRPGDEVVLQYDEERFDRYGRTLAGV
+VEGETLVNAEIVRAGLGVPVVFEPNRRFLPPVEAAWAEAQREGAGLNQPGLECSLQTLQESVAQDPAPAAVSELAQALEA
+VEAEGQEWMKVHYAAVIPLAVSLVQQHGGRADVPSAGAASVAPRASTAPAVPAAPQAPAVGAGSDAAERDRQRAAEAQAA
+ADRAERKRQAEARAEAQRQAQAQEQVQARERAAQASREAEAAASAREKQKGASSGSSTAKGFADTSARDTSSGSPSSSGG
+TSQKAPNRCYAPGGETFVYCGEGSTGSSSGGSSSSASAGASSSGAGTSSGGAGGPVSGADGVCPAGYPVKVS-SSGKYHV
+PGGQYYDDTSAKRCYASTAAAAADGAVASKR
+>4_226
+M-------PLARLRAALPAAALSLLLLTGCT---ATDDGVTPESDADTSASVSTMP----TTPTPSVDAAATSRAAASSL
+AA---SSAAQSSRAAASSSIEAAQSRAARAAEESRTAEGSR----------------------SAEPAAPAAPADVEGDV
+VTVESISDGDTLRVTLGEVSTRVRLLNIDTPETHHPSKPVECMGPEATAALKSMISPGDTVVLRYDRRLYDRYDRLLAGV
+YAEGVLLNAEMARLGYGEPAVFDGNDRFLPEVEAAWEQARANGVGRFSG--ECG--------------------------
+------------------------------------TAAEPIPEAAPAPAPEAAPA------------------------
+--------------------------------------------------------------------------------
+-------------------------------------------------AGDAGPVSGADSVCPDSHPVKANDNSGIYHM
+PGQQHYGKTNARHCYASASAAQAGGYRAARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000340.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000340.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e44f604bfedb950a919864fdc999d29acc8fc3c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000340.fa
@@ -0,0 +1,26 @@
+>0_252
+MTTPAPVASAARARRRAAR--SGPRPQLRMGLNGFLVAWLLPNLVMAAVVAVLAVVPGLQ
+AFGSLTPLLTVVGVAGLVVGLPLCLLVNWAFRHVLNQWVHVLAYALIGMLYGLVVLTQGA
+AGILPMLIPVIGFPAAVLMALGRTAARPLVRTVTPE-----------PSPAEP-------
+--A
+>1_2216
+MTTPAPVASAARARRRAAR--SGPRPQLRMGLNGFLVAWLLPNLVMAAVVAILAVVPGLQ
+AFGSLTPLLTVVGVAGLVVGLPLCLLVNWAFRHVLNQWVHVLAYALIGMLYGLVVLTQGA
+AGILPMLIPVIGFPAAVLMALGRTAARPLVRTVTPE-----------PSPAEP-------
+--A
+>2_97
+-----------------------------MGLNGFLVAWLLPNLVMAALVAVLAVLPGLQ
+AFGSLTPLLTVVGIAGLVVGLPLCLLVNFAFRHVLNQWVHVLAYALIGMLYGLVVLTQGA
+AGILPMLIPVIGFPAAVLMALGRMAARPLVQVVTPGQEAEARSAAQTASPADPEPSERAA
+RGA
+>3_67
+MTTPAPVKSTARARRKAARAVSGPRPRLRMGLNGFLVAWLLPNLLMAAVVLALTLIPSLQ
+RFGTLTPLLTVVGIAGLVIGLPLCLLVNRAFRHVLNQWVHVLAYALVGMLYGLVVLAQGV
+GGVLPMLIPVIGFPAAVLMGLGRLAARPLV-DVVPG-----------AEPR---------
+--S
+>4_250
+MTTPAPVASAARARRRAAR--SGPRPQLRMGLNGFLVAWLLPNLVMAAVVAVLAVVPGLQ
+AFGSLTPLLTVVGVAGLVVGLPLCLLVNWAFRHVLNQWVHVLAYALIGMLYGLVVLTQGA
+AGILPMLIPVIGFPAAVLMALGRTAARPLVRTVTPE-----------PSPAEP-------
+--A
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000341.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000341.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6767c04dec8f50d8467c6b56ce119b2d4cca416d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000341.fa
@@ -0,0 +1,41 @@
+>0_253
+MKLPSPAPSAPGEVHHSASSVPVDGVEAVFPALRQRALAPGGRLYGLAAAAAVGGLTLLD
+PHARRGRERRALAELEAAVSGTVLAAETANALHTAAIADGEVAPSPAARALR--------
+------------------GLGGLAVGGAVAAVALRTAGLNDRIDGAVVRGLQRV-----G
+VPAPRVALAAAASLAMLLANEDARRTRRDAVEL-----------AVTGPAGLDEDPVDEV
+EPE------------ATAELPVEVRVLLETLLDPALAEGRDLPGAEALRSQLPHARTVAS
+VAEAIREAGEVPDWVPLVVQTDDDVRRAVPNDCVWPVRGRFASGSAGGHELELRLQVIDG
+EIGALTVTLPADAEADSDAWDAFQEIESFPGVEDLAFHVDGDRRA
+>1_2217
+MKLPSPAPSAPGEVHHSASSVPVDGVEAVFPALRQRALAPGGRLYGLAAAAAVGGLTLLD
+PHARRGRERRALAELEAAVSGTVLAAETANALHTAAIADGEVAPSPAARALR--------
+------------------GLGGLAVGGAVAAVTLRATGLNDRIDGALVRGLQRV-----G
+VPAPRVALAAAASLAMLLANEDARRTRRDAVEL-----------AVTGPAGLDEDPVDEV
+EPE------------ATAELPVEVRVLLETLLDPALAEGRDLPGAEALRSQLPHARTVAS
+VAEAIREAGEVPDWVPLVVQTDDDVRRAVPNDCVWPVRGRFASGSAGGHELELRLQVIDG
+EIGALTVTLPADAEADSDAWDAFQEIESFPGVEDLAFHVDGDRRA
+>2_96
+MRQNSPVPG-------SLPARYVDDPAAAFPALRQRALAPGGRPYGLLAAAVVGALTLVD
+PHRMGAAERRGLARTEAAASGAFVAAEAASSLRLAGLP-GRVGPAA--------------
+--------------------GGLAAGAATAALALSTVPLNDRIDGALVRFLERA-----G
+ASAPRAVLAGTAALSVLAGNESVRRERRNALEE-----------A-AWPAW--DDLSEEE
+QSE------------PTAPLPVEVRVLLETLLDPALAEGRELPGAAALRAQLPHVRTVAS
+MAEAIRDEDEVPDWTPLVVETDGPVDRAVPHDHVWPVRGRFAVGE-DGHEVELRLQVIDG
+ELGALVITLPADEDADPDAWDAFQELEAFPGVEDLTFQVDGERRD
+>3_66
+METP------------RTPE------------------------------------TRTD
+PPADRLAEPQHPAHADAPVVHDTAVPESERIERTVSTRTGETRP-PVVRTVVTESERIER
+PVVEVRDARVPGRLLWWIGGGTLAAGSLAALVRV----LRERLATPEPTPLERLADAGRG
+AGLP-LALSLAGTAAGVGVSLRARRRRRTEEVLAAPAVPFLLGEAVSAEAG--EDDVDGL
+PPVNEASDAYPAGALETEALPLEVVVLLDTLLDPSLDEGRELPGAAALRAQLPHVRTAAS
+VAEEIREDGKVPDWTPLVVEEETGVARAIPNDMVWPVRGRFT--TEDGHELELRLQVIDG
+ELGALVITLPEDVEDGVAAWDAFQELEAFPGVEELTFTVDGDRRP
+>4_251
+MKLPSPAPSVPGEVHHSASSVPVDDAEAVFPALRQRALAPGGRLYGLAAAAAVGGLTLLD
+PHARRGRERRALAELEAAVSGTFLAAETAGALHTAAIAEGEVAPSPAARALR--------
+------------------GLGGLAVGGAVAAVALRATGLNDRIDGAVVRGLQRV-----G
+VPAPRVALAAAASLAMLLANEDARRTRRDAVEL-----------AVTGPAGLDEDAVDEV
+EPE------------ATAELPVEVCVLLETLLDPALAEGRDLPGAEALRSQLPHARTVTS
+VAEAIREAGEVPDWVPLVVETDDDIRRAVPNDCVWPVRGRFASGSAGGHELELRLQVIDG
+EIGALTVTLPADAEADSDAWDAFQEIESFPGVEDLTFHVDGDRRV
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000353.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000353.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92e9ebb34127e8feec2e4d2022e7d30f753e1811
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000353.fa
@@ -0,0 +1,16 @@
+>0_271
+MPSYRARLQIGDLLPGHRPEEVMDLAEAAVQATHVLAAKDIEVVARVPRIVLRFTVPGSH
+RAGEDAEAAEVARRMAEAVSGVAVTGRLDVLRRDGGRWVPVPAGLGR
+>1_2237
+MPSYRARLQIGDLLPGHRPDEVMDLAEAAVQATHVLAAKDIEVVARVPRIVLRFTVPGSH
+RAGEDAEAAEVARRMAEAVSGVAVTGRLDVLRRDGGRWVPVPAGLGR
+>2_64
+MPSYRARLQIGDLLPGHRPEEVMDLAEAAVQATHVLAAKDIEVVARVPRIVLRFTVPGSH
+RAGEDAEAAEVARRMAEAVSGVAATGRLDVLRRDGGRWVPVPAGPGR
+>3_50
+MPSYRARLQIGDVLPGHRPEEVLDTAEAAIGATHEVAAKDVEVVARVPRIVLRFTVPAAH
+RAAEDAEAAAVAGRMAEAVADVATVGRLDVLRREGGRWLPVSA---R
+>4_270
+MPSYRARLQIGDLLPGHRPDEVMDLAEAAVQASHVLAAKDIEVVARVPRIVLRFTVHGSH
+RAGEDAEAAEVARRMAEAVSGVAVTGRLDVLRRDGGRWVPVPAGPGR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000356.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000356.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b73259af74c9889b19c97902c1441305a1db6d9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000356.fa
@@ -0,0 +1,55 @@
+>0_275
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------------------------------------MADPFPKDPEGAVVALVLAG
+GTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLRDVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQG
+RAEEGFARGNGHAIAQQLPLLEQFGAETVVVLSADHLYQLDLRPVLAEHARSGAELTVVTTETDEDPSRFGVVQVDDDGA
+VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSSLGDYGESIIPAFVARGRVRE
+HRLVGYWRDIGTLDAYVRAHREILDGTGLDLAAEGWPLITNPHQAPPAWVAPDARVSGSLLSPGCRIAGEVSDSVVGPGV
+VVAAGATVRGSLLLGDCEVPAGAVLDTVVVDVGGAVPAREVTGRAAPA-EEVVVLTPQDRGPA-EDETTGSGRPGRSD
+>1_2248
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------------------------------------MADPFPTDPEGAVVALVLAG
+GTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLRDVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQG
+RAEEGFARGNGHAIAQQLPLLEQFGAETVVVLSADHLYQLDLRPVLAEHARSGAELTVVTTETDEDPSRFGVVQVDDDGA
+VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSSLGDYGESIIPAFVARGRVRE
+HRLVGYWRDIGTLDAYVRAHREILDGTGLDVAAEGWPLLTNPHAAPPAWVAPEATVTGSLLSPGCRIAGEVTDSVVGPSV
+VVEAGAVVRGSILLGECTVPSGAVLDTVIADVGAAIPAEGATGRAEPA-DEVVVLEPGERGPASSDETTGSGAPVRD-
+>2_60
+MPEGDSLVRLAHRLRPVLAGRALTHADLRVPQHATADLTGWTVVEVEPRGKYLLMRLTPPAGRPAARPLTLVSHLKMEGR
+WLVSALDARWGAPAWQVRAVLETADHRVLGAQLGMLTLVPTDREDTVLGHLGPDLLDPAWDGSEEAAAALLAEGTRRLTA
+RPERPVGLALLDQRTTCGIGNIYRCESLLLAGIDPHRPVGAVPDVPGLLTIARDLLRANVPPAAPFLGWPRTTTGVRANP
+DRPYGIEVVVADRGFPPGLPAAVGSGTAADPAADPGADRTASGPALGRPPARPPADPGAAGRRRTGCTGTTAPPACAAAG
+ACARRTSAPPRTTRGSCGGARPASGEPRPNRGPGGGAPYAERRPSPQGRSARPPTPRRTRVADPFPDDPRSAVVALILAG
+GRGSRLAPLTDARSKPAVPFAGQYRLIDVALTTVAHSGLQDAWIVEQYRPFTLNQHVAGGRPWDLDGTRHGLRVLPPAQG
+RDEEGFAQGNGHAIHQQLAPLRRFGAKTVVIMSADHLYRMDLRPVLERHRERDAELTVVTTQVAEGASRFGVVSSDADGR
+VTAYDYKPDEPATDVVATEVFVADVDALTEVIESLLDSASE-------EQVDDDDPAGAQLGDYGETIIPALVERGRVHE
+FRHEGYWKDVGTIDAYYQAHMALLRGDGLDLDDPRWPLISNFHPRPPAFIHPEAEVNGSMLCPGSRVRGTVTESVIGPGV
+VVEAGATVHRSVLLGSATVPAGARLDAVIADVGARIP-EGATGQTKPGPGNITVLTPDDRSTAEGDETTGHA------
+>3_40
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------------------------------------MADPFPKDPAGSTVALVLAG
+GRGSRLDPLTAARSKPAVPFAGQYRLIDVVLSNLAHSGLKDVWIAEQYRPFTLNQHLAGGRPWDLDGTRHGLRILPPAEG
+REEEGFSAGNGHALAQQVPILRSFGAERVVVLSADHLYQLDLRPVLAAHADSGAELTMVTTVTDEDPSRFGVVQADEDGA
+VTAYDYKPEDPEGRLVATEVFVFDVAALHEVVAELVAREKAAGEHADGEEDEDGDPVASSLGDYGETIIPAFVERGRVRE
+HRLEGYWRDIGTLDAFYRAHMELLDGAGLDLAAPGWPLLTNPPAAPPARVGPRAEVSNALLSPGCVVKGTVEDSVLGPGV
+VVERGAHVRRSVLFGECIVPRGARLDAVIADVGAHIPAE-EVGRSRPGPGNLTVLTPATRDPDSEDETTGGA-AAKDG
+>4_281
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------------------------------------MADPFPKDPEGAVVALVLAG
+GTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLRDVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQG
+RAEEGFARGNGHAIAQQLPLLEQFGAETVVVLSADHLYQLDLRPVLAEHTRSGAELTVVTTETDEDPSRFGVVQVDDDGA
+VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSSLGDYGESIIPAFVARGRVRE
+HRLVGYWRDIGTLDAYVRAHREILDGTGLDVAAEGWPLLTNPHAAPPAWVAPEATVTGSLLSPGCRIAGEVTDSVVGPSV
+VVEAGAVVRGSILLGECTVPSGAVLDTVIADVGAAIPAEGATGRAEPA-DEVVVLEPGERGPASSDETTGSGAPVRD-
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000357.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000357.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c71dda491b2cb4286d6b3d537db4e3e5edec1074
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000357.fa
@@ -0,0 +1,21 @@
+>0_279
+----MSVRVLAIGKKHEAWVVDGIDRYERRLKKPYDLSWRLLPHSARQEEAARTEESDRI
+LGAVGADEHLILLDERGTAFDSPGLARHLQSRFDVGAPVTMVIGGAYGVDARVHARADRV
+WSLSPLVFPHQLVRLILAEQVYRAQEISAGRPYHHA
+>1_2252
+----MSVRVLAIGKKHEAWVVDGIDRYERRLKKPYDLSWRLLPHSARQEEAARTEESDRI
+LGAVGADEHLILLDERGAAFDSPGLARHLQSRFDVGAPVTMVIGGAYGVDARVHARADRV
+WSLSPLVFPHQLVRLILAEQVYRAQEISAGRPYHHA
+>2_57
+----MSVRVLAIGKKHEAWVSEGIDRYERRLKKPYDLSWRLLPHSARQEEAARTEESDRI
+LGAVGADEHLILLDERGTAFDSPGLARHLQSRFDVGAPVTVVIGGAYGVDARVHARADRV
+WSLSPLVFPHQLVRLILAEQVYRAQEISAGRPYHHA
+>3_36
+MMVLMAVRVVAIGKRHESWVSEGITRYEKRLKKPWDLTWQLLPHSSRQEDAARAEESERI
+LAKVGPDEQLILLDERGRGFDSPGLSAHLQGQFDLGRTVTLVIGGAYGVDASVHARADRV
+WSLSGLVFPHQLVRLILAEQVYRAQEIAGGRPYHHA
+>4_285
+----MSVRVLAIGKKHEAWVVDGIDRYERRLKKPYDLSWRLLPHSARQEEAARTEESDRI
+LGAVGADEHLILLDERGAAFDSPGLARHLQSRFDVGAPVTMVIGGAYGVDARVHARADRV
+WSLSPLVFPHQLVRLILAEQVYRAQEISAGRPYHHA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000359.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000359.fa
new file mode 100644
index 0000000000000000000000000000000000000000..805ec1b6162d1137664b94e1662c88e4b4415208
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000359.fa
@@ -0,0 +1,21 @@
+>0_281
+MGLALRAARAAGAAGDVPIGAALVAGDGTVLAVVGNEREQHHDPTAHAEVLALRRGAELR
+AAAGAGDGWRLTDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP
+RFNHQVQVRAGVRSEESAALLRGFFAAQR--D
+>1_2255
+MGLALRAARAAGAAGDVPIGAALVAGDGTVLAVVGNEREQHHDPTAHAEVLALRRGAELR
+AAAGAGDGWRLTDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP
+RFNHRVQVRAGVRSEESAALLRGFFAAQR--D
+>2_55
+MGLALDAARAAGEAGDVPIGAVLVAGDGTVLAAVGNEREQHHDPTAHAEVLALRRGARAL
+AEAGEADGWRLSDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP
+RFNHAVQVRAGVRAEESAALLRGFFAVQR--G
+>3_34
+MGLALDAARTAGEAGDVPIGAVLVDGDGRVLAAVGNEREQHHDPTAHAEVLALRRGAAAL
+AARGDADGWRLAECTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP
+RFNHTVQVRAGVRGDECAALLVDFFAARRPGG
+>4_288
+MGLALRAARVAGAAGDVPIGAALVAGDGTVLAVVGNEREQHHDPTAHAEVLALRRGAELR
+AAAGAGDGWRLTDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVIRDP
+RFNHQVQVRAGVRAEESAALLRGFFAAQR--S
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000365.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000365.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec674591dc86150cf841ba434f0732592f63b029
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000365.fa
@@ -0,0 +1,55 @@
+>0_288
+MDATSHPDAGPRLPETSVPGG---------------DAALHEEALAVLRRLVDRPDARFKDGQFEAIEALVAHRRRALVV
+QRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSSANATEWDEVRARLAADEVDVLLISP
+ERLTNPRFRDEQLPDLVARMGLLVVDEAHCISDWGHDFRPDYRRIRDLIGLLPAEGPRAVPVLATTATANARVVADVVEQ
+LGVASEQDVFVLRGPLARASLRLGVLRMPSPAARLAWLLDHLGDLPGSGIVYALTVSAAEDTARALREAGHEVVAYTGRT
+DPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHFGAPGSPVAYYQQVGRAGRGTDHADVLLLPGPEDRRIWEY
+FATASMPDEEQARAVLGALADHGGALSVAALEPAVRIKRTALELLLKVLAVDGAVERVGGGWRATGREWTYDAERYARVA
+EARRAEERLMLDYQTTDRCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDGAARERAEAALRRTGVPIEPRRMWPSGM
+DRLGVPVKGRIAPESQAEEGRALARLTDLGWGTVLRDLLDREDAPVPEEVLRGAVDVLAGWGWRTRPIAVVAMPSRTRPQ
+LVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGNSAYRLGSVYGRFAVPEAMAQMLRTAPDAGRHGPVLLVDDLVDSRW
+SLAEAARVLREAGAQGVLPLVLAQAG
+>1_5
+MDATSHPDAGPRLPETSAPGG---------------DAALHEEALAVLRRLVDRPDARFKDGQFEAIEALVAHRRRALVV
+QRTGWGKSAVYFVASLLLRARDAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSSANATEWDEVRARLAADEVDVLLISP
+ERLTNPRFRDEQLPGLVARMGLLVVDEAHCISDWGHDFRPDYRRIRDLIGLLPAEGPRAVPVLATTATANARVVADVVEQ
+LGVASEQDVFVLRGPLARASLRLGVLRMPSPAARLAWLLDHLADLPGSGIVYALTVSAAEDTARALREAGHEVVAYTGRT
+DPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHFGAPGSPVAYYQQVGRAGRGTDHADVLLLPGPEDRRIWEY
+FATASMPDEEQARAVLGALADHGGALSVAALEPAVRIKRTSLELLLKVLAVDGAVERVGGGWRATGREWTYDAERYARVA
+EARRAEERLMLDYQTTDRCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDGAARERAEAALRRTGVPIEPRRMWPSGM
+DRLGVPVKGRIAPESQAEEGRALARLTDLGWGTVLRDLLDREDAPVPEEVLRGAVDVLAGWGWRTRPIAVVAMPSRTRPQ
+LVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGNSAYRLGSVYGRFAVPEAMAQMLRTAPDAGRHGPVLLVDDLVDSRW
+SLAEAARVLREAGAQGVLPLVLAQAG
+>2_48
+MDTTQHPDAGPLPSESTAPIGPYGSGAAAPGAAAAREPELHAEALAVLRRLVDRPDAQFKDGQFEAIEALVAHRRRALVV
+QRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSSANATQWDEVRARLAADEVDVLLISP
+ERLTNPRFREEQLPDLVARMGLLVVDEAHCISDWGHDFRPDYRRIRDLIGLLPSTGPRAVPVLATTATANARVVGDVVEQ
+LGVDSAQDVFVLRGSLARASLRLGVLRMPSPAARLAWLLDHLEDLPGSGIVYALTVSAAEDTARALREAGHEAVAYTGRT
+DPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHFGAPSSPVAYYQQVGRAGRGTDHADVLLLPGPEDRRIWEY
+FATASMPDEEQARAVLQALAQHGGALSVAALEPAVRIKRTALELLLKVLAVDGAVERVGGGWRATGREWVYDAQRYARVA
+EARRAEERLMLDYQTTDTCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDTSARERAEAALRRTGVPIEPRRMWPSGM
+DRLGVPVKGRMAPEIQAEEGRALARLTDLGWGTVLRELLDKEDAPVPEDVLQGAVGVLAGWGWQTRPIAVVAMPSRTRPL
+LVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGNSAYRLGSVHGRFEVPEAMAHLLRTASDAGRHGPVLLVDDLVDSRW
+SLAEASRVLREAGAQGVLPLVLAQAG
+>3_26
+M------STSPQDPARPAAVA---------------DPALYAEALGVLRALVGRPDAEFKDGQYEAVEALVAHRRRALVV
+QRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAASLSSANATEWEDVRRSLEADEVDVLLISP
+ERLTNPRFRDEQLPDLVSRMGLLVVDEAHCISDWGHDFRPDYRRIRDLIRLLPSSGPRAVPVLATTATANARVVQDVVEQ
+LDVESRQDVFVLRGPLARASLRLGVLRLPSPAARLAWLLQHLGELPGSGIVYALTVSAAEDTARALREAGHEVVAYTGRT
+DPEQRARIEQDLKDNRVKAVIATSALGMGFDKPDLTFVVHLGAPSSPVAYYQQVGRAGRGTDHADVLLLPGQEDRAIWEY
+FATASMPDEVQARAVLEALEESGGAMSVAALEPVVSVKRTALELLLKVLSVDGAVERVGGGWRATGSPWTYDAERYARVA
+EARRAEERLMLDYQTTQTCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGWDGAAREQADRALRRTGVPLEPRRMWPSGM
+DRLHVPVKGRISPAEQAEEGRALARLTDLGWGSRLRELLAAPDAPVPEEVLQAAVRVLAEWGWQERPIAVVAMPSRGRPQ
+LVDSLARGLAGQGRLPFLGPLELVGGGPTAGPGGNSAYRLASVHGRFAVPEGMARMLATAPDAGRHGPVLLVDDLADSRW
+SLAEAARVLRGTGAQGVLPFVLAQNG
+>4_295
+MDATSHPDAGPRLPETSAPGG---------------DAALHEEALAVLRRLVDRPDARFKDGQFEAIEALVAHRRRALVV
+QRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSSANATEWDEVRARLAADEVDVLLISP
+ERLTNPRFRDEQLPDLVARMGLLVVDEAHCISDWGHDFRPDYRRIRDLIGLLPAEGPRAVPVLATTATANARVVADVVEQ
+LGVASEQDVFVLRGPLARASLRLGVLHLPSPAARLAWLLDHLGDLPGSGIVYALTVSAAEDTARALREAGHEVVAYTGRT
+DPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHLGAPGSPVAYYQQVGRAGRGTDHADVLLLPGPEDRRIWEY
+FATASMPDEEQARAVLGALADHGGALSVAALEPDVRIKRTSLELLLKVLAVDGAVERVGGGWRATGREWTYDAERYARVA
+EARRAEERLMLDYQTTDRCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDGAARERAEAALRRTGVPIEPRRMWPSGM
+DRLGVPVKGRIAPESQAEEGRALARLTDLGWGTVLRDLLDREDAPVPEEVLRGAVDVLAGWGWRTRPIAVVAMPSRTRPQ
+LVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGNSAYRLGSVYGRFAVPEAMAQMLRTAPDAGRHGPVLLVDDLVDSRW
+SLAEAARVLREAGAQGVLPLVLAQAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000371.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000371.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e17cbd5bae6c9c1f57069a894b3af2954021a8fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000371.fa
@@ -0,0 +1,65 @@
+>0_295
+MTPLPRFAARTAVTTAALALLAPAV-ALPSQASPAGDSLVINEAYTNGGSANAVYTHKFVELYNPTDQPINLDGWSLQYR
+SAAGTAATQGTVALSGTVPAKGHFLVSGGSNGTAGAALPQADLVAGGAFNPAGTKGTIVLARQAGTVTDLPVGSVVTGQV
+PGVADVLGYGATNTFETAAAGAPSANSDPKSLTRTNGVDTDDNSADFTVTGQVTPTNAAA--TGG-EPTPEPEPQPTPSE
+RITIAQLQGTGTATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGDTPDATPGASDGVFVYSPDTVGSVTLGDHVQV
+TGEAAEHYGLTQIKVAADGVLPVAEPGA-VAPTPVEFPLEEADREALEGMVLAPQGDWTVTDNYSLNQYGSLGVVPGTKP
+LDNPTSVARPGAEAQAVAAANAQQLIVLDDGASTNFMRSPGNQNPLPYLDADQPVRVGAGLEFSTGVILDWRFDAWSFQP
+LGHLTDATAAAVQPVTIEDTRPAEAAPEAVGGNVTVGSFNVLNYFTTLGQDVAGCGAYRDRAGTPVTTNGCLPRGAYTPE
+AFARQQEKIAAAINGLGTSVVALEEIENSEKFGLDRDHALAHLVEALNAQAGEQRWAYVASPSARPALADEDVIRSAFIY
+QPAEVTPLGESVILDDQTNFDNAREPMAQLFRAADGTAEGAAGTEFVAITNHFKSKGGSGATGDNVDAGDGQGAYNADRV
+GQAEALVAFAERMKAETGTDRVLLMGDFNAYEKEDPIRVLEAAGYVSQGALTGEYSYAFGGAVGSLDGIYASPSAAAAIT
+GQDIWMINANESVALEYSRHNYVAEDLYSADQWRSSDHNPILVGLQLDAPVTEPTPEPEPEPT-PGETCDGVTDPRGVPG
+KPANSVREWLRCIGATPGHGGDHPGKGHGGD----HPGKGRGP--VRP
+>1_19
+MTPLPRFAARTAVTTAALALLAPAV-ALPSQASPAGDSLVINEAYTNGGSANAVYTHKFVELYNPTDQPINLDGWSLQYR
+SAAGTAATQGTVALSGTVPAKGHFLVSGGSNGTAGAALPQADLVAGGAFNPAGTKGTIVLARQAGTVTDLPVGSVVTGQV
+PGVADVLGYGATNTFETAAAGAPSANSDPKSLTRTNGVDTDDNSADFTVTDQVTPTNAAA--TGG-EPTPEPEPQPTPAE
+RITIAQLQGTGTATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGDTPDATPGASDGVFVYSPDTVGSVTLGDHVQV
+TGEAAEHYGLTQIKVAAGGVLPVAEPGA-VAPTPVEFPLEEADREALEGMVLAPQGDWTVTDNYSLNQYGSLGIVPGTTP
+LDNPTSVARPGAEAQAVAAANAQQLIVLDDGATTNFMRSPGNQNPLPYLDADQPVRVGAGLEFTTGVILDWRFDAWSFQP
+LGHLTDATAAAVQPVTIEDTRPAEAAPEAVGGNVTVGSFNVLNYFTTLGQDVAGCSAYRDRAGTPVTTNGCLPRGAYTSE
+AFARQQEKIAAAINGLGTSVVALEEIENSEKFGLDRDHALAHLVEALNAQAGEQRWAYVASPATRPALADEDVIRSAFIY
+QPAEVTPVGESVILDDQTNFDNAREPMAQLFRAADGTSEGAAGTDFVAITNHFKSKGGSGATGDNVDAGDGQGAYNADRV
+GQAEALVAFAERMKAETGTDRVLLMGDFNAYEKEDPIRVLEAAGYLSQGALTGEYSYAFGGAVGSLDGIYASPSAATAIT
+GQDIWMINANESVALEYSRHNYVAEDLYSADQWRSSDHNPILVGLQLDAPVTEPT--PEPEPS-PGETCDGVTDPRGVPG
+KPANSVREWLRCVGATPGHGGDHPGKGHGPE----HPGKGRGP--VRP
+>2_24
+MTQRTFRLSRPAVALAALTLLAPAVVAGPAHAAPTGDGLVINEVYTNGGSANAVFTHKFVELYNPTDTPISLDGWSLQYR
+SATGTAAPNGVVALSGTVPAKGHFLIQGGSNGTTGAALPRPDLNAGGAFNPAGARGTVVLSDQAGALTALPVGSVTTGQA
+EGVADLLGYGTSNTFETAAAGAPSSNSDPKSLTRTDGVDTDDNAADFTVTAQVTPTSSTG--EAPVDPIPDPEPDPEPAP
+ALTIAQIQGDGAATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGSAEDATPGASDGLFVYSPDTVGSVALGDHVQV
+TGEAAEHYGLTQVRVGAAGVTPVAEPAA-VAPTAVDFPLSEADREALEGMLLAPTGEWTVTDNYDLNQYGSLGIVPGTEP
+LPNPTSVAAPGAEAQAVAADNASRLIVLDDGASTNFMRSPGNENPLPYLDADRPVRVGAGLDFTTGVILDYRFDAWSFQP
+LGHLTDATAAAVQPVAVEDTRPEEASPEAVGGNVSVGSFNVLNYFTALGQDFPGCRAYTDRFGEPVTTNGCLPRGAYTPE
+AFARQQEKIAAAIDGLDASVVALEEIENSAKFDLDRDRALAHLVDALNAQAGEQKWAYVASPADRPALSEEDVIRNAFVY
+QPAEVTPVGESVILRDEVNFDNAREPLAQHFRAADGTEAGVAGTDFVAVTNHFKSKGGSGAAGDNADSGDGQGAYNGDRT
+RQAQALVAFAEQVADDAGTDRVLLLGDFNAYEKEDPIRVLEEAGYVSQGALTGEYSYTFDGAVGSLDGVYASPAASAVVT
+GQDIWMINANESVALEYSRHDYVAEDLYAPDQWRSSDHNPLLVGLQLDAPVVEPEPQPGA----------------GHPG
+K------------GKGLDKGAGHPGKGKGLDKGAGHPGHGRVPEAARP
+>3_20
+MPTPRLRLVRTAATLAAATLLAPAVLALPAQASPAGDSLVINEAYTNGGSAGALFTHKFVELYNPTDQPISLDGWSLQYR
+SATGTTAPSTTVALSGTVPAKGHFLIQGGSNGATGAALPTPDLTT--SFNPAGTKGTIVLADQAGTVAGLPTGSVVTDQV
+AGVADVLGYGATNTFETAASGAPAANSDPKSIARTGGADTDDNAADFTVAADVTPQNAAGGGTAPVDPVDPVDPTPAPAP
+SVTVAEIQGTGATSPLEGRRVSTTGVVTAVYSTGGYDGFYIQTAGTGG-AEDATPGASDGVFVYAPAEVGSVTLGQTVTV
+TGDVAEYYGLTQVKAEAGGVRQAAEAGAPVTARELAFPLTEAEKEAHEGELLAPAGAWTVTDNYDVNQYGSLGLAPGTSP
+LPNPTSVALPGADAQAVAADNAQRLIVLDDGASTNFFRSPGNQNALPYIDADAPARVGSAVDFRTPVILDYRYGAWSFQP
+LGHLTDANKAEVQPVDIADTRPAEAVREDLGGNVTVGSFNVLNYFTTLGEDVPGCGYYADKDGAPVSTKGCLPRGAYTEE
+AFLEQQAKIATAINGMDTSVVALEEIENSEKFGLDRDHALAHLVDALNAQAGYAKWAYVASPTVRPALADEDVIRSAFIY
+QPAEVTPVGESVILDDQVNFANAREPMAQAFRVADGSAGGVVGTEFVAITNHFKSKGGSGATGDNVDTGDGQGAYNGDRT
+RMAQALVAFAEQMKVQAGTDRVLLMGDFNSYEKEDPIRVLEAAGYISQGAKTGEYSYTFDGAVGSLDGIYASPAADATVT
+GQDIWMINANESVAFEYSRDNYVGEEFYAPDQWRSSDHNPVLVGLQLDAPAAPVVPTPGTRPTPPADQCALITSPRGAKA
+SAGFSASEWMRCAGV--------------------HPGKGRG----RG
+>4_302
+MTPLPRFAARTAVTTAALALLAPAV-ALPSQASPAGDSLVINEAYTNGGSANAVYTHKFVELYNPTDQPINLDGWSLQYR
+SAAGTAATQGTVALSGTVPAKGHFLVSGGSNGTAGAALPQADLVAGGAFNPAGTKGTIVLARQAGTVTDLPVGSVVTGQV
+PGVADVLGYGATNTFETAAAGAPSANSDPKSLTRTNGVDTDDNSADFTVTDQVTPTNAAA--TGG-EPTPEPEPQPTPAE
+RITIAQLQGTGTATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGDTPDATPGASDGVFVYSPDTVGSVTLGDHVQV
+TGEAAEHYGLTQIKVAAGGVLPVAEPGA-VAPTPVEFPLEEADREALEGMVLAPQGDWTVTDNYSLNQYGSLGIVPGTTP
+LDNPTSVARPGAEAQAVAAANAQQLIVLDDGATTNFMRSPGNQNPLPYLDADQPVRVGAGLEFTTGVILDWRFDAWSFQP
+LGHLTDATAAAVQPVTIEDTRPAEAAPEAVGGNVTVGSFNVLNYFTTLGQDVAGCSAYRDRAGNPVTTNGCLPRGAYTSE
+AFARQQEKIAAAINGLGTSVVALEEIENSEKFGLDRDHALAHLVEALNAQAGEQRWAYVASPATRPALADEDVIRSAFIY
+QPAEVTPVGESVILDDQTNFDNAREPMAQLFRAADGTSEGAAGTDFVAITNHFKSKGGSGATGDNVDAGDGQGAYNADRV
+GQAEALVAFAERMKAETGTDRVLLMGDFNAYEKEDPIRVLEAAGYLSQGALTGEYSYAFGGAVGSLDGIYASPSAATAIT
+GQDIWMINANESVALEYSRHNYVAEDLYSADQWRSSDHNPILVGLQLDAPVTEPT--PEPEPS-PGETCDGVTDPRGVPG
+KPANSVREWLRCVGATPGHGGDHPGKGHGPE----HPGKGRGP--VRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000374.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000374.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab7c81884adb524cee84008fcb66b307c75ac633
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000374.fa
@@ -0,0 +1,31 @@
+>0_299
+MSLP--HAPRTPAPPAAASSAVPLRLAVVDMSGTSIVEHGLQDTAFARSLDQHGVPAGTP
+EHDDAARRFRALRPTSRTAVFPRVFADRAVAAAATRTFEATFDALLAEHGVRAVPGAEEA
+LIRLRALGLHVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMILTALLG
+LDLEDVRSVLVVGDTAEDMTAGRRAGAGLVVGVRTGRDADHVLLAAGSDRVVPGLADVPD
+LVVRTR-
+>1_23
+MSLP--HAPRTPAPPAAASSAAPLRLAVVDMSGTSIVEHGLQDTAFARTLDQHGVPAGTP
+EHDDAARRFRALRPTSRTAVFPRVFADRAVAAAATRTFEAAFDALLAEHGVQAVPGAEEA
+LVRLRALGLHVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMILTALLG
+LDLDDVRSVLVVGDTAEDMTAGRRAGAGLVVGVRTGRDADDVLLAAGADRVVPGLADVPD
+LVVRTR-
+>2_20
+MSLPPRPPPRGRAPRADGPPAPPLRLAVVDMSGTSIVERGLQDAAFAHALETHGLAADAP
+AHADAVRVFRARRATSRTAVFAQVFPDRPAAAAAARTFEEAFDSLLAEHGVQPVPGAEEA
+LLRLRALGLRVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPFPDMILTALLG
+LDLDDVRGVLVVGDTAEDMTAGRRAGAGLVAGVRTGRDADAALLAAGAHHVVDGLADVPA
+LVGAGG-
+>3_16
+MSLS------TAVPALSVGTPVPLRLAVVDMSGTSVVEGGLQDRAFAEVVAARGLAEGSP
+EHERAARLFRERRGTSRTAVFQALFEGRTAALEATRAFEAAFDRLLAEHGVTAVPGAEGA
+LVRLREAGLDLCLITGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMVLTALLA
+LDHDDVRSVLTVGDTAADILAGRRAGAGLVVGVRSGQDTGGVLAGAGADQVVDSLAQVPD
+LVATLRG
+>4_306
+MSLP--HAPRTPAPPAAASSAVPLRLAVVDMSGTSIVEHGLQDTAFARTLDQHGVPAGTP
+EHDDAARRFRALRPTSRTAVFPRVFADRAVAAAATRTFEATFDALLGQHGVQAVPGAEEA
+LVRLRALGLHVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMILTALLG
+LDLDDVRSVLVVGDTAEDMTAGRRAGAGLVVGVRTGRDADDVLLAAGADRVVPGLADVPD
+LVVRTR-
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000375.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000375.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec264535f5e6f697ef5138082c248ae13e78869e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000375.fa
@@ -0,0 +1,41 @@
+>0_300
+MTA-SAPVPPVFADLAGQEAAVAQLRRAAAEDRPTHAWMFTGPPGSGRSTAARAFAAALQ
+CEVADPAARGCGECHACRTVLGGTHPDVTVLATEAVSYRIEDVRALVEAGQSTPATGRWR
+IFLMEDADRMTERATNVLLKAIEEPPARTIWMLCTPSPADVLPTVRSRCRLITLSIPAVE
+QVAELLHRRDGLDRETALTTARISQSHVGMARRLARDPEALERRERILSLPLQATAVSDA
+MALAATLAEVSKAEAESAAEARDAEELEALRRSLGLEPGEPVPPKLRHHVKRLEEDQTRR
+RRRAVRDSLDRAMIDVMGLFRDVLRVQLGADGELINEHRRDEIEAYARGTAGDSAEVLAR
+IDAVTTTRERIAANVPEQLALEAMMLALLPRRVRTPRRR-
+>1_24
+M---TAPAPAVFADLAGQEAAVAQLRRAAAEDRPTHAWMFTGPPGSGRSTAARAFAAALQ
+CEVADPAARGCGECHACRTVLGGTHPDVTVLATEAVSYRIEDVRALVEAGQSTPATGRWR
+IFLMEDADRMTERATNVLLKAIEEPPARTIWMLCAPSPADVLPTVRSRCRLITLSIPAVE
+QVAELLHRRDGLDRETALTTARISQSHVGMARRLARDPEALERRERILSLPLQATAVSDA
+MALAATLAEVSKAEAESAAEARDAEELEALRRSLGLEPGEPVPPKLRHHVKRLEEDQTRR
+RRRAVRDSLDRAMIDVMGLFRDVLRVQLGADGELINEHRRDEIEAYARGAAGDSAEVLAR
+IDAVTTARERIAANVPEQLALEAMMLALLPRRVRTPRRR-
+>2_19
+MTALPDAVPAVFADLAGQGSAVEQLRRAAAEDRPTHAWMFTGPPGSGRSTAARAFAAALQ
+CEAPDPAARGCGRCHACRTVLAGTHPDVTVLATEAVTYRIEDVRSLVEAAQSTPATGRWR
+IFLMEDADRMTERATNVLLKAVEEPPARTVWMLCTPSPADVLPTVRSRCRLVTLSIPAVE
+DVADLLHRRDGLDRETALTTARISQSHVGMARRLARDPEALERRERILSLPLEATSVSDA
+MALAATLADVSKAEAESSAEARDAEELETLRRSLGLEPGEPVPPKLRQHVKRLEEDQTRR
+RRRSVRDSLDRAMIDVMGLFRDVLRVQLGAEGELINEHRRAEVEAYARGAAGDSAEVLAR
+IDAVATARERIAANVPEQLALEAMMLALLPRRVRTPRRR-
+>3_15
+MTG----APDVYSDLAGQDAAVAQLRRAATEDRPTHAWLFTGPPGSGRSTAARAFAAALQ
+CEQPDPANRGCGACHACRTVLGGTHPDVTVLATEAVSYRIEDVRALVEAAQSTPATGRWR
+IFLMEDADRMTERATNVLLKAIEEPPPRTIWMLCSPSPADVLPTIRSRCRLVTLRIPAPE
+DVAALLHRRDGLDEATALMTARISQSHVGMARRLARDPEALARREDVLSLPLQATAVSDA
+MAMAARLAEVSHAEAESSAAARDAEELAALRRQLGVAEGEAVPPKLRQQVKRLEEDQSRR
+RTRVTRDALDRAMIDVIGLFRDVLRVQLGAGGDLVNEHRRAEIERYAAGAAGSSAEVVAR
+IDAVHLARERLGQNVPEQLALEAMMLALLPARVRTPRGRR
+>4_307
+M---TAPAPAVFADLAGQEAAVAQLRRAAAEDRPTHAWMFTGPPGSGRSTAARAFAAALQ
+CEVADPAARGCGECHACRTVLGGTHPDVTVLATEAVSYRIEDVRALVEAGQSTPATGRWR
+IFLMEDADRMTERATNVLLKAIEEPPARTIWMLCAPSPADVLPTVRSRCRLITLSIPAVE
+QVAELLHRRDGLDRETALTTARISQSHVGMARRLARDPEALERRERILSLPLQATAVSDA
+MALAATLAEVSKAEAESAAEARDAEELEALRRSLGLEPGEPVPPKLRHHVKRLEEDQTRR
+RRRAVRDSLDRAMIDVMGLFRDVLRVQLGADGELINEHRRDEIEAYARGAAGDSAEVLAR
+IDAVTTARERIAANVPEQLALEAMMLALLPRRVRTPRRR-
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000384.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000384.fa
new file mode 100644
index 0000000000000000000000000000000000000000..65d936f69bc1843d5fbc36b5ee23296d13d12818
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000384.fa
@@ -0,0 +1,46 @@
+>0_310
+MPTALVIAAAGAGTRLGAGLPKALAPLADGRTLLRHCLESVAAARAAGLDLDAVVVLTPP
+AGADAGRVAAEVDAGPR--LDVPVHCVPGGAERADSVRAGLAAASHALADLA-PAG-APR
+RVLVHDAARALTPPSVFGAVTAALETGAVAAIPGLPLTDTVKQVTPGRGGVDVVAATPAR
+AGLRAIQTPQGFDLDTLLAAHEAVRTDPTLDAAALTDDAMVMEAAGHEVVVVTGDPAAFK
+VTAPADLDLARLELARRA----PQEEAPMDQ------------PARPAAAPAP---LPRV
+GIGTDVHAWAPEDAPRPLWLGGIHWPGERGVAATSDGDVAAHAACNALLSAAGLGDLGAV
+FGVDRPEMADASGADMLREVLRLLTEAGLAVGNVAVQVVAPRPKVGARRAEMEAALSAAL
+GGAPVSVSAATTDRLGFIGRKEGLVGIATALVIPAA
+>1_34
+MPTALVIAAAGAGTRLGAGLPKALAPLADGRTLLRHCLESVAAARAAGLGLDAVVVLTPP
+AEADAGRVAAEVDAGPR--LDVPVHCVPGGAERADSVRAGLAAASGALADLA-PAG-APR
+CVLVHDAARALTPPSVFGAVTAALGTGAVAAVPGLPLTDTVKQVTPGRGGVDVVAATPAR
+AGLRAIQTPQGFDLDTLLAAHEAVRTDPTLDAAALTDDAMVMEAAGHEVVVVTGDPAAFK
+VTAPADLDLARLELARRA----PQEEAPMDQ------------PARPAAAPAP---LPRV
+GIGTDVHAWAPEDAPRPLWLGGIHWPGERGVAATSDGDVAAHAACNALLSAAGLGDLGAV
+FGVDRPEMADASGADMLREVLRLLTEAGLAVGNVAVQVVAPRPKVGARRAEMEAALSAAL
+GGAPVSVSAATTDRLGFIGRKEGLVGIATALVIPAA
+>2_9
+MPTALVIAAAGAGTRLGAGMPKALVPLADGRTLLRHCLDSVAAARAAGAAVDAVVVLAPP
+AEEDAARVAAEVDAGPG--LGAPVACVPGGAERADSVRAGLAAAADALNALG-PAA-GPR
+RVLVHDAARALTPPAVFAAVEAALDAGAVAVVPGIAVTDTVKQVAPGPGGAEVVTTTPPR
+AALRAVQTPQGFDLDALLAAHEAVRADPALDAAALTDDAMVMEAAGHPVAVVAGDAAAFK
+VTAPADLELARLELARRADAPTPEEDPAMDQYGTAPGTGPEADAATDPAGPRPGAALPRV
+GVGTDVHRWAPEDAPRPLWLGGVHWPGERGVAATSDGDVAAHAACNALLSAAGLGDLGAV
+FGVDRPEMADASGTAMLAEVLRLLTEAGLAVGNVAVQVVAPRPKVGTRRAEMEAALSAAL
+GGAPVSVSAATTDRLGFIGRGEGLVGIATALVAPTA
+>3_5
+MPTALVIAAAGSGTRLGAGVPKALAPLTDGRPLLDHCLESVAAARATGLGLDALVVLVPP
+A-ADHARAVADVVARHETAVGAPVTCVPGGVERADSVRAGLAAADAALADRGHPAGQGVR
+HVLVHDAARAFTPPAVFEAVAGALVSGEVAAVPGLPLTDTVKEVT-GADGREVVVATPAR
+SALRAVQTPQGFDLDVLLAAHAAAQADPAADAAALTDDAMAMEAAGHAVVVVPGDERAFK
+VTSPADLEAAARILAVRD----AQSGPGTPS------------PAAVPAAP-P---LPRT
+GIGTDVHRWAPDDAPRPLWLGCVEWPGQNGVAATSDGDVAAHAACNALLSAAGLGDLGAV
+FGVDRWEMRGASGAAMLAEVLRLVTEAGCRIGSVAVQVVAPRPKVGTRRAEMEAAMSAAL
+GGAPVAVSAATTDGLGFIGAGEGLVGLATALVVPAA
+>4_317
+MPTALVIAAAGAGTRLGAGLPKALAPLADGRTLLHHCLASVATARAAGLALDAVVVLTPP
+AEADAGRVAAEVDAGPR--LDVPVHCVSGGAERADSVRAGLAAASYALADLA-PAG-APR
+RVLVHDAARALTPPSVFGAVTAALETGVVAAVPGLPLTDTVKQVTPGRGGVDVVAATPAR
+AGLRAIQTPQGFDLDTLLAAHEAVRTDPTLDAAALTDDAMVMEAAGHEVVVVTGDPAAFK
+VTAPADLDLARLELARRA----PREEAPMDQ------------PARPAAAPAP---LPRV
+GIGTDVHAWAPEDAPRPLWLGGIHWPGERGVAATSDGDVAAHAACNALLSAAGLGDLGAV
+FGVDRPEMADASGADMLREVLRLLTEAGVAVGNVAVQVVAPRPKVGTRRAEMEAALSAAL
+GGAPVSVSAATTDRLGFIGRREGLVGIATALVVPAA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000389.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000389.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b46236c146d136fa6dae893adc9d59d8410dc8b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000389.fa
@@ -0,0 +1,21 @@
+>0_318
+MSWWPFPR-PSASPSP-DDDGAPAAAELEEAVAALRQLLRAERHRLRPDSWALAWEMVEQ
+AAEYAPAWTRLQRTRPVETQELVLALTGRLEPLLCDFLALPDSEKPTHADAVHARLREQG
+TEHGRLRRRLTRALTARLRAGEEL----
+>1_43
+MSWWPFLR-SSASPSP-DDDGAPAAAELEEAVAALRRLLRAERHRLRPDSWALAWEMVEH
+AAEYGPAWTRLQRTRPVETQELVLALTGRLEPLLRDFLALPDSEKPAHADAVHARLREQS
+TEHGRLRRRLTRALTARLRAGEEL----
+>2_2620
+MAWWPFRG-PSGAPRD-DDASTAGRASLEAAVHSLRALMTAERHRLRPDSRDLAWTITER
+AAEYGPAWDRVSAQRPAEAQELLLLLSHRLEPALRDFLDLPDSQKPRHADELHGRLSELQ
+TEAQRLGRRLTRALSSRLRARGEL----
+>3_2431
+MAWWARRRLSSSGPAPLGKPPLVAAEELRRLTDELSEILQRESARIRPDAAAVLRSFLNR
+SRALLPAWDRTAPARSAEALAAYELLRDRVLPGLQDWLCLPDHLKPVHADDLLADAQAWE
+GDLSHHAARLTQVLTARGRAVRELDERQ
+>4_325
+MSWWPFLH-SSASPSP-DDDGAPAAAELEEAVAALRRLLRAERHRLRPDSWALAWEMVEH
+AAEYGPAWTRLQRTRPVETQELVLALTGRLEPLLRDFLAIPDSEKPAHADAVHARLREQS
+TEHGRLRRRLTRALTARLRAGEEL----
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000397.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000397.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7325815f5fa5fb25a1192ade4b47d8d407940237
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000397.fa
@@ -0,0 +1,60 @@
+>0_326
+MSTSTVRSAPASTYRLQVSPDLPLESVAGLVPYLRRLGVDWLYLSPLLEAEPGSDHGYDVVDPTRLDAARGGAEGLDAVA
+RAAHEAGMGVLVDIVPNHVGVATPQANPAWWDVLTHGPEAAHAAWFDVDWAAGGGSLLIPVLGDGPDGD---ADAELNRL
+VVD-E----GRLRYWDNVYPLAPGSLEAAEAETGLRAAEVFAEADPAKESTAERARLARAVHDRQHYRLVGWRRGDAELN
+YRRFFTVTTLAGVRVDEPEVFDAVHAEPARWVREGLVDGLRVDHPDGLADPAGYARRLRSHVLPEGYLVVEKILEPGEAL
+PADWPVDGTTGYDALGEVERVFMHPEAAGDAAEDARRRREWDEAVVRAKHDVATGSLAAETARLVREVRAVHALGAHPDE
+DVAAAFAAVLARLPVYRTYLPVGLAVLEGALADAAEAEPALAAVLGDLRPELTDPDSPVARRFQQTSGMVMAKGVEDRSF
+YRYTRWANLNEVGGDPSHVALSLADFHAAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEPDRWAAELAELRRLH
+PLGHPDAERLLWESIVGVWPTDGTAPEEERILGFLQKASREAALATSWTDQDPEFEARLAALAAAVTSPEGPARGVLQAV
+ADRIAEPGLVVQLGHKLVQLAAPGVPDVYQGTEVPFPTLVDPDNRRPVDFAARADLLDRLDAGHTPGLDDPAAAKLAVVA
+AVLRTRRDRPELFTGHRPLDVSGPAAEHAIAFDRGGALAVATRWPVRLAAAGGWGETVVTVPAGRWEDAVTGHPVHPDAR
+GAVRLDELLSTLPVALLVPAHAPSDRRERTAP
+>1_51
+MSTSTVRSAPASTYRLQVSPDLPLESVAGLVPYLRRLGVDWLYLSPLLEAEPGSDHGYDVVDPTRLDAARGGAEGLDMVA
+RAAHEAGMGVLVDIVPNHVGVATPRANPAWWDVLTHGPEAAHAAWFDVDWAAGGGSLLIPVLGDGPDGD---ADAELNRL
+VVD-E----GRLRYWDNVYPLAPGSLEAAEAETGLRAAEVFAEADPASEPTAEQARLARAVHERQHYRLVGWRRGDAELN
+YRRFFTVTTLAGVRVDEPEVFDAVHAEPARWVREGLVDGLRVDHPDGLADPAGYARRLRSHVLPEGYLVVEKILEPGEAL
+PADWPVDGTTGYDALGEVERVFMHPEAAGDAAEDARRRREWDEAVVRAKHDVATGSLAAETARLVREVRAVHALGAHPDE
+DVAAAFAAVLARLPVYRTYLPVGLAVLEGALADAAAAEPGLADVLGDLRPELTDPDSPVARRFQQTSGMVMAKGVEDRSF
+YRYTRWANLNEVGGDPSHVALSLADFHSAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEPDRWAAELAELRRLH
+PLGHPDAERLLWESIVGVWPTDGTAPEEERILGFLQKASREAALATSWTEQDPEFEARLAALAAAVTSPEGPARGVLQAV
+ADRLAEPGLVVQLGHKLVQLAAPGVPDVYQGTEVPFPTLVDPDNRRPVDFAARADLLDRLDAGHTPGLDDPAAAKLAVVA
+AVLRARRDRPELFTGHRPLDVSGPAAEHAIAFDRGGALAVATRWPVRLAAAGGWGETVVTVPAGRWEDAVTGHPVHPDAR
+GAVRLDELLSTLPVALLVPAHAPSDRRERTAP
+>2_2566
+MSTSTERPVPSSTYRLQVGPDLPLESVAGLVPYLRRLGVGWLYLSPILEAEPGSDHGYDVVDPTRLDAARGGAEGLEAVA
+RAAREAGLGVLVDIVPNHVGVATPEANPAWWDLLAHGSEAAHAPWFDVDWTAGEGRVLLPVLGDGPDGE---AEAELDRL
+VVE-TGDDGGRLRHWDTRYPLAPGSLAAAEEETGLRAADVFAGAEPAHEPTPERARLARAVHARQHYRLIGWRRGDAELN
+YRRFFTVTTLAGVRVEDPEVFDAVHAEPARWVREGLVQGLRVDHPDGLADPAGYVRRLRSHVLPEGYLVVEKILEPGEEL
+PADWDVDGTTGYDALGEVERVFMHPVAAGGPNEDERRRRDWDEVVAEAKRDVATGSLVAETARLVREVRGVHALGAHADE
+DVAAAFAAVLSRLPVYRTYLPVGLAVLERALADAGEAEPALAPVLADLGPELADPDSPVARRFQQTSGMVMAKGVEDRSF
+YRWTRWANLNEVGGDPAHVQLSLDAFHAAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEPDRWAGELAGLRALH
+PLGDEGAERLLWESIVGVWPTDGTAPSTERILGFLQKASREAALSTTWTDQDPEFEGRLEDLARAVTAPDSPARGAVQAV
+ADRIAEPGLVVQLGHKLVQLAAPGVPDVYQGTELPVPSLVDPDNRRPVDFHARADLLDRLDAGHVPGLDDADAAKLAVVA
+AVLRARRDRPELFTRHRRLDVSGPAAEHAVAFDRGGALAVATRWPVHLAAAGGWGETVVTLPPGRWEDAVTGRPVHPDAR
+GAVRLDELLSTLPVALLVPARA-----EEATP
+>3_2417
+MSHTDAVSAPASTYRLQVGPDLPLDSVAGLVPYLRRLGVDWLYLSPILAADPGSDHGYDVVDPARVDPARGGPEALAALA
+AAAHEAGMRLLVDVVPNHLGVATPLANPAWADLLAHGPEAAHAAWFDVDWEAGDGRVLLPVLGDGPEGDPRGAEAGLDQL
+IVDPSAGEHGVLRHWDTAYPLAPGSLAAAEEETGLRAAEVFAGADPAA-PTDDAARLGRAVHDRQHYRLVHWRRGDAELN
+YRRFFTVTTLAGLRVEDPEVFDATHVEIGRWVSEGLVHGLRIDHPDGLTDPGAYLRALRERVLPEGYLVVEKILEPGEDL
+PAAWPVDGTTGYDALGELERVFMPADPDGPAADDA-ARAAWEALIAEAKRDVATGSLAAETARLVREARAAVVLGAHSDE
+ALTEAFADVLASLDVYRTYLPVGAERLAAAVARARAAHPEPADVLDDVARVLADPDSPVARRFQQTSGMVMAKGVEDRSF
+YRWTRWANLNEVGGDPAHLDLPLAGFHALQRARQASWPTTMTALTTHDTKRSEDVRARITALAEEPASWEDALARLRTAH
+PLDAPGLEELVWESIVGVWPTDGTAPEADRLEEFLLKSAREGQEHTSWTAQDDAYEGRLRALAADVVAPDSAARAVVQEI
+ADRIAEPGLTVQLGRKLVQLAAPGVPDVYQGTEIPFPTLVDPDNRRAVDFEARADLLDRLDAGHAPTLDEPEAAKLLVVS
+RALRARRDRPELFHGYRPLDVDGPAAAHLIAFSRGGALALATRLPLTLAAAGGWRETVVSLPPGRWRCAVTGRAVTPDAR
+GAVRVDDVLSQLPVALLLPEEETA--------
+>4_333
+MSTSTVRSAPASTYRLQVSPDLPLESVAGLVPYLRRLGVDWLYLSPLLEAEPGSDHGYDVVDPTRLDAARGGAEGLDMVA
+RAAHEAGMGVLVDIVPNHVGVATPPANPAWWDVLTHGPEAAHAAWFDVDWAAGDGSLLIPVLGDGPDGN---ADAELDRL
+VVD-A--EGGRLRYWDNVYPLAPGSLEAAETETGLRAAEVFAAADSAKEPTAEQARLARAVHDRQHYRLVGWRRGDAELN
+YRRFFTVTTLAGVRVEEPEVFDAVHAEPARWVREGLVDGLRVDHPDGLADPAGYARRLRSHVLPEGYLVVEKILEPGETL
+PADWPVDGTTGYDALGEVERVFMHPEAAGDAAEDARRRREWDEAVVRAKHDVATGPLAAETARLVREVRAVHALGAHPDE
+DVAAAFAAVLARLPVYRTYLPVGLAVLEGALADAAEAEPGLADVLGDLRPELTDPDSPVARRFQQTSGMVMAKGVEDRSF
+YRYTRWANLNEVGGDPSHVALSLADFHAAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEPDRWAAELAELRRLH
+PLGHPDAERLLWESIVGVWPTDGTTPEEERILGFLQKASREAALATTWTDQDPEFEARLAALAAAVTSPEGPARGVLQAV
+ADRIAEPGLVVQLGHKLVQLAAPGVPDVYQGTEVPFPTLVDPDNRRPVDFAARADLLDRLDAGHTPGLDDPAAAKLAVVA
+GVLRARRDRPELFTGHRPLDVSGPAAEHAIAFDRGGALAVATRWPVRLAAAGGWGQTVVTVPAGRWEDAVTGHPVHPDAR
+GAVRLDELLSTLPVALLVPAHAPSDRRERTAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000402.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000402.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bdc535122e566e6a6835e0398d8d2939efd6a4cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000402.fa
@@ -0,0 +1,26 @@
+>0_332
+MEFIAPLDPGWEAALAPQAAAFEQVGERLRARRAGGEQVLPAPEHILRAFRQSFADVRVL
+VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLANIHRELHDDLGITPPAHGDLSAWTDQGV
+LLLNRALSVRAGAPGSHRGLGWEQITEAAVRALCARGTPLVGLLWGADARRMAPLLTAAG
+AGVVESPHPSPLSAHRGFFGSRPFSRVNRLLEAAGAAPVDWRLPD
+>1_57
+MEFIAPLDPGWEAALAPQAAAFEQVGEALRARRAAGEQVLPAPEHILRAFRQPFADVRVL
+VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLANIHRELHDDLGITPPAHGDLSAWTDQGV
+LLLNRALSVRAGAPGSHRGLGWEQITEAAVRALCARGTPLVGLLWGADARRMAPLLAAAG
+AGVVESPHPSPLSAHRGFFGSRPFSRVNRLLEAAGAAPVDWRLPD
+>2_2552
+MELIAPLDPGWEAALAPQAAALEQVGAALTQRRAAGEQVLPAPEHILRVFRRPFEDVRVL
+VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLVNIHRELQDDLGIAPPAHGDLSAWADQGV
+MLLNRALTVRAGAPGSHRGLGWEQITEAAVRALCERGTPLVGLLWGADARRMAPLLTQAG
+AGVVESPHPSPLSAHRGFLGSRPFSRVNRLLEEAGAEPVDWRLPD
+>3_2411
+MDLISPLDPGWAAALADQEEALVRVGAELTARRAAGEHVLPAPEHILRAFRQPFADVKVL
+IVGQDPYPTPGHPIGLCFACDRHVRPLPRSLANIHRELHDDLGVPPAAHGDLSAWTDQGV
+LLLNRVLTVRAGAAGSHRGIGWEQITEAAVRALVARGTPLVGLLWGNDARRLAPLLTAGG
+AGVVESAHPSPLSASRGFFGSRPFSRVNALLEAAGASPVDWRLPD
+>4_339
+MEFIAPLDPGWEAALAPQAAAFEQVGERLRARRAAGEQVLPAPEHILRAFRQPFADVRVV
+VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLANIHRELHDDLGIAPPAHGDLSAWTDQGV
+LLLNRALSVRAGAPGSHRGLGWEQITEAAVRALCARGTPLVGLLWGADARRMAPLLTAAG
+AGVVESPHPSPLSAHRGFFGSRPFSRVNRLLEAAGAAPVDWRLPD
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000419.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000419.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa85957df8cb4e0b326dc192ccaadb9bdc8a50c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000419.fa
@@ -0,0 +1,46 @@
+>0_353
+MTS------EHTSE------------------------------------TRRLRS----
+-----RTSFVLLAVF-GVAAIVALLTSA----VEPWPPLVLAPGL-----------IAGL
+WLLSQWHREVAAPTRWAVLALGTLTWALSALWDLTPLGALAFALAGALEVMWS-----RH
+ARAVVTLLVLTVGSAA----GALVFVTDP--QALWVYVGMGALLTGVACVTIPVSRISFD
+LMRLQDQR----AEQERAASLDAERLRFSQDLHDIQGHALHVVKLKIAVAQRMLSTD-TD
+AAQRELDEAQQTLRQTMAETKALAQDGHTLTLRGELANSVALLEATGITVTTDDDGGPRG
+--EEFEHVAGVVIREGTTNILRHSDARRVEISLAPG-------HVVISNDGAAGVSAEDH
+TGGLDNLRSRLAGVGGRLDVSCV-DGRFT-LGARWEADEEESV-------------
+>2_980
+MTPPSPLAPEPVPDRAPAQDPGSGHAPSPASAALPPGHRPTGALPVAPGFDRDLHRLWWY
+TAAGLLSAVVVVAGF-LVFVMARRLAVAEGPDASPLAVTVLVAGIAAAVAAAVGQTLATL
+RLRRAWEEEREPLRRTAVAAL-----LPALLVALTPLAVPSLSAWPVLSLWLSVCLIAPQ
+AAAHVRTAVLTSGAAATLGLTALALVRTPAGPAD-SAVGVLLWWAMVLLVVLPTVWVWRV
+AVRLEEAR-----AQAGELAVARERLRFAADLHDVQGHHLQVIALQAELAGRLLEKGRTD
+QAGAALRDVREQAAEALGETRALVRGLRQVSVASEIENAREVLAATGAVVEVDVDPAAAR
+LAREAARLVGLAVREATTNALRHAEPRRVRLALGPADGAAGGVRLTVTNDGARPPAA-PP
+GTGLAGLAARAAEVSGRLSAGPDDDGGFR-LELTVPSSSGATTR-TDPTTTTGEDA
+>2_2532
+MTS------EPTSE------------------------------------TRRLRS----
+-----RTSFVLLAVF-GVAAIVALLTSA----VEPWPPLVLAPGL-----------IAGL
+WLLSQWHREVAAPTRWAVLALGTLTWALSALWELTPLGALAFALAGALEVMWS-----RH
+ARAVVTLLVLTVGAAA----GALVFVTDP--PALWVYVGMGALLTGVACVTIPVSRTSFD
+LMRLQDQR----AEQERAASLDAERLRFSQDLHDIQGHALHVVKLKIAVAQRMLSTD-TD
+AARRELDEAQQTLRQTMAETKALAQDGHTLTLRGELANSVALLEAAGITVTTDDDGDPRR
+--EEFEHVAGVVIREGTTNILRHSDARRVEISLAPG-------HVVISNDGVAGAPAEDH
+TGGLDNLRSRLAGVGGRLDVSCG-DGRFT-LEARWEADEEETV-------------
+>3_1154
+MSP-------------------AGGPPAPARPTVGTAEHDPAVLP--------LHL--WP
+STMGFAGVWLISFGFVLVELLRRAFTPGDGRGEAILGVAAIAVFILVYLAA-----FVVP
+RPVRAWPAWANTVLTWFVLAG-----CVAVLTRIL----------GVHALLYSPFLVATW
+IFPHRLRVGLTGAGATMAAALATGLLFFPGDPA----LPVVLGNLAVLLVVL-------V
+GMRLAIARDDRVVEMTHELDLAGQRERLGRDLHDILGHSLTTINVKTQLVHRLIDTD-PA
+RAKEEAAEVIALSRTALAEARAAVAELAAPELGGQLSLSVGALRDAGMAVEAPPPGAVTE
+VPQRRRALAAWIVREAVTNVLRHAGARRVRISLDAH-------HVAVLDDGAGLPAAVVA
+GVGPRTLAERAAAEGARLEVGPGLGGAGTGVAVHWGGTTPEAARGVLPATEGRMDA
+>4_360
+MTS------EHTSE------------------------------------TRRLRS----
+-----RTSFVLLAVF-GVAAIVALLTSA----VEPWPPLVLAPGL-----------IAGL
+WLLSQWHREVAAPTRWAVLALGTLTWALSALWDLTPLGALAFALAGALEVMWS-----RH
+ARAVVTLLVLTVGSAA----GALVFVTDP--QALWVYVGMGALLTGVACVTIPVSRISFD
+LMRLQDQR----AEQERAASLDAERLRFSQDLHDIQGHALHVVKLKIAVAQRMLSTD-TD
+AAQRELDEAQQTLRQTMAETKALAQDGHTLTLRGELANSVALLEATGITVTTDDDGGPRG
+--EEFEHVAGVVIREGTTNILRHSDARRVEISLAPG-------HVVISNDGAAGVSAEDH
+TGGLDNLRSRLAGVGGRLDVSCV-DGRFT-LGARWEADEEESV-------------
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000421.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000421.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c9fb3a49dab73db81b232bac84d324a55128f480
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000421.fa
@@ -0,0 +1,41 @@
+>0_358
+MSPAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER
+RHEQHWRALLGEHAENPPRPSLHRILLRWLARIFGSVFVLALAQRAESDTPYAEDQDAPE
+GMVADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL
+FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELKLVYLARG
+MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA
+SGALIPILPYIFGMSGLWALGLAAAMVGVALLFTGGVVGLLSGSSPLARGLRQLAIGFGA
+AAVTYVLGLLFGANVG
+>1_91
+MSAAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER
+RHEQHWRILLGEHAENPPRPSFRRVLLRWLARIFGSVFVLALAQRAESDTPYEKDQDAPE
+GMAADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL
+FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELKLVYLARG
+MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA
+SGALIPILPYIFGMSGLWALGLAAAMVGAALLFTGGVVGLLSGSSPLARGLRQLAIGYGA
+AAVTYVLGLLFGANVG
+>2_2520
+MSPAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER
+RHEQHWRALLGEHAENPPRPSVHRILLRWLARIFGSVFVLALAQRAESDTPYAKDQDAPE
+GMVADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL
+FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELTLVYLARG
+MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA
+SGALIPILPYIFGMSGLWALGLAAAMVGVALLFTGGVVGLLSGSSPLARGLRQLAIGYGA
+AAVTYVLGLLFGANVG
+>3_2392
+MSPAHAATPAALPEPTREQVRRWRRYLADEIAEGQIYRDIAASKDGVERDILIGLAEAEK
+RHEEHWRALLGEHAAHPPRPSVHRILLRALARVFGSVFVLALAQRAESDTPYAKDQDATE
+HMAADEQIHEEVVRGLASRGREQLAGSFRAAVFGMNDGLVSNLALVMGIGATGVASSVVL
+FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAEHLDLDRNELELVYLARG
+MTPEDAKHRALERLGYLSCDCNPQFSARPDGSKGPVDHSESFAEIGSAWGASLSSFCFFA
+SGALIPILPYLFGMTGLGALVVAAVLVGIALLFTGGVVGLLSGSSPLWRGLRQLMIGYGA
+AAVTYLLGLLVGGSIG
+>4_364
+MSPAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER
+RHEQHWRALLGEHAENPPRPSLHRILLRWLARIFGSVFVLALAQRAESDTPYAEDQDAPE
+GMVADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL
+FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELKLVYLARG
+MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA
+SGALIPILPYIFGMSGLWALGLAAAMVGVALLFTGGVVGLLSGSSPLARGLRQLAIGFGA
+AAVTYVLGLLFGANVG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000423.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000423.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e2af7466ae8bd458be127635c7615c83ca54f07d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000423.fa
@@ -0,0 +1,16 @@
+>0_360
+MRLHHDPGLQPERTVMSWGRTALALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT
+QRRRYVAHADGIAREQARPALASVACMVALVVGLAALGITATLLHAA
+>1_93
+MRLHHDPGLQPERTVMSWGRTVLALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT
+QRRRYVAHADGIARERARPALASVACMVALVVGLAALGITATLLHAA
+>2_2518
+MRLHHDPGLQPERTVMSWGRTVLALGVLSLMFLRWWPAVGAWAFGPAVVAAVGGAAVLAT
+QRRRYVAQSRGIAGEWARPALASVAGMVALVVGLAALGITATLLHAA
+>3_2390
+MRLHHDPGLQPERTVMSWGRTVLALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT
+QRRRYVAQADGIAREQARPALASVACMVALVVGLAVLGITATLLHAA
+>4_366
+MRLHHDPGLQPERTVMSWGRTVLALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT
+QRRRYVAHADGIAREQARPALASVACMVALVVGLAALGITATLLHAA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000424.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000424.fa
new file mode 100644
index 0000000000000000000000000000000000000000..84ef71b9bfa2d4e8b6f272034f70beeebd3db0a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000424.fa
@@ -0,0 +1,41 @@
+>0_361
+-----------------------MTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHG
+VILKIVATNICGSDLHIYRGSFPAPEGMVLGHEMTGQVLEVGSDVQFLQEGDLVSVPFNV
+ACGRCRNCRAGRTEICETANPDQACAAYGFNLGGFQGGQAEYLFVPYADFQLLRFPDQEQ
+AMEKILDLTVLSDILPTAFHGLVEAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVG
+DQDASRLELVRKHGCETIDLSTTENLQDAVSDILGEPMVDCAVDCVGSEAHGLGSASDEM
+QPIAAVNQVLDITRPGGATGIIGIYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQA
+PVMRYNRQLMMSILWDRMPYLTEMVNPRVISLDEAPQAYAEFDQGSLEKFVIDPHGMIAR
+>1_94
+-----------------------MTTENRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHG
+VILKIVATNICGSDLHIYRGSFPAPEGMVLGHEMTGQVLEVGSDVQFLQEGDLVSVPFNV
+ACGRCRNCRAGRTEVCETTNPEQACAAYGFNLGGFQGGQAEYLFVPYADFQLLRFPDQEQ
+AMEKILDLAVLSDILPTAFHGLMEAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVG
+DQDASRLELVRKHGCETIDLSTTENLQDAVNDILGEPMVDCAVDCVGSEAHGLGSASDEM
+QPIAAVNQVLDVTRPGGATGIIGIYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQA
+PIMRYNRQLMMSILWDRMPYLTELVNPRVITLDEAPQAYAEFDQGSVEKFVIDPHGMIAR
+>2_2517
+MSPRGRSGSRLTQASLETEGNSFMTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHG
+VILKIVATNICGSDLHIYRGSFPVPEGMVLGHEMTGQVLEVGSDVQFLKEGDLVSVPFNV
+ACGRCRNCRAGRTEVCETANPEQACAAYGFNLGNFQGGQAEYLFVPYADFQLLRFPDQEQ
+AMEKILDLAVLSDILPTAFHGLMAAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVG
+DQDASRLELVRKHGCETIDLSVTENLQDAVNDILGEPMVDCAVDYVGSEAHGLGSESDEM
+QPIAAVNQVLDITRPGGATGIIGIYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQA
+PIMRYNRQLMMSILWDRMPYLTEMVNPRVISLDEAPQAYAEFDQGSVDKFIIDPHGMIAR
+>3_2389
+-----------------------MTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHG
+VILKIVATNICGSDLHIYRGSFPVPEGMVLGHEMTGQVLEVGSDVQFLKEGDLVSVPFNV
+ACGRCRNCRAGHTEICETANPEQACAAYGFNLGNFQGGQAEYLFVPYADFQLLRFPDQEQ
+AMEKILDLAVLSDILPTAFHGLMAAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVG
+DQDASRLELVRKHGCETIDLSVTENLQDAVNDILGEPMVDCAVDYVGSEAHGLGSESDEM
+QPIAAVNQVLDITRPGGATGIIGIYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQA
+PIMRYNRQLMMSILWDRMPYLTEMVNPRVISLDEAPQAYAEFDQGSVDKFIIDPHGMIAR
+>4_367
+-----------------------MTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHG
+VILKIVATNICGSDLHIYRGSFPAPEGMVLGHEMTGQVLEVGSDVQFLQEGDLVSVPFNV
+ACGRCRNCRAGRTEICETANPEQACAAYGFNLGGFQGGQAEYLFVPYADFQLLRFPGQEQ
+AMEKILDLAVLSDILPTAFHGLMEAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVG
+DQDASRLELVRKHGCETIDLSVTENLQDAVNDILGEPMVDCAVDCVGSEAHGLGSASDEM
+QPIAAVNQVLDITRPGGATGIIGIYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQA
+PIMRYNRQLMMSILWDRMPYLTEMVNPRVISLDEAPQAYAEFDQGSLEKFVIDPHGMIAR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000430.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000430.fa
new file mode 100644
index 0000000000000000000000000000000000000000..144cd806802d2da2fee2537b8ad57ad74ba2f7d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000430.fa
@@ -0,0 +1,46 @@
+>0_370
+MPAASDAPTPA----PRRGRLAPSGDPTPVENVATHLQEGWNRWHRARALRAGNVPTVMA
+FTGYGSTSWVRILSRVVIASDEEFMNGRRLSKVVADGVRGWRNFVAPPMAYAEVEVQVGD
+LRTTVRTDRMGVVDVVLDVELEPGWQTATLHVGGQEEHAVMDLYICEPGARIGLVSDIDD
+TVVVTSLPRPLLAAWNSFVIDEHARTPTPGIAVLLRRIAELEPKAPVLYLSTGAWNVAQT
+LTRFLGRNLYPLGALLLTSWGPTRDRWFRSGQEHKRVQLERLAEQFPDIQWILVGDDGQH
+DPEIYAEFAQRHPDRVKAIVIRQLTPSQALLAGGRAEDTRRSTPGIPWCYGPDGATLSNQ
+LEDLGILPVEFVDVQPEAWREDILGDDEAPATLD-------AAAQRDDRSTD--EEAAR-
+--------------------------
+>1_103
+MPAASDAPTPA----PRRGRLAPSGDPTPVENVATHLQEGWNRWHRARALRAGNVPTVMA
+FTGYGSTSWVRILSRVVIASDEEFMNGRRLSKVVADGVRGWRNFVAPPMAYAEVEVQVGD
+LRTTVRTDRMGVVDVVLDVELEPGWQTATLHVGGQEEHAVMDLYICEPGARIGLVSDIDD
+TVVVTSLPRPLLAAWNSFVIDEHARTPTPGIAVLLRRIAELEPKAPVLYLSTGAWNVAQT
+LTRFLGRNLYPLGALLLTSWGPTRDRWFRSGQEHKRVQLERLAEQFPDIQWILVGDDGQH
+DPEIYAEFAQRHPDRVKAIVIRQLTPSQALLAGGRAEDTRHSTPGIPWCYGPDGATLSNQ
+LEDLGILPVEFVDVQPEAWREDILGDDEAPATLD-------APGQRDGRPAD--EEAAR-
+--------------------------
+>2_2509
+MSAVSDAAPVS----PRRTRLAALGDPTPVENVATHLQEGWNRWHRSRALRAGHVPTIMA
+FTGYGSTSWVRILSRVVIAPDEEFLNGRRISKVVADGVRGWRNFVAPPMAYAEVEVEVGG
+TRTTVRTDRMGVVDAVLDVEMEPGWRTATLHV-GDDEHVTMDLYICHPDARIGLVSDIDD
+TVVVTSLPRPLLAAWNSFVIDEHARTPTPGMAVLLRRVAELEPKAPVLYLSTGAWNVAQT
+LTRFLGRNLYPLGALLLTSWGPTKDRWFRSGQEHKKTQLERLAEQFPDIKWILVGDDGQH
+DPEIYADFAQRHPDRVAAIVIRQLTPSEALLAGGRAEDTRRSTPGIPWCYGPDGASLSNQ
+LEDLGILPVGFVDVQPEGWKEDILGDDEVLSAAE-------HGAAALGDEADAPDTAAEP
+RVPAGEAAVGDGAADEAEAAEAGGSR
+>3_2380
+MPASESASIAAQNDPARRQRLAAAGGPTPAENVATHLQEQWNRWHRSRALRRGFVPTVMA
+FTGYGTTSWVRVLSRVVLAKDEDFLNGRRLSKVVADGVHGWRNFVAPPMAYAEVEVEVGD
+LVTTVRADRMGVVDVVLDVELEPGWRTAVLRV-GDEEEVTTDLYIASPDAKVGLVSDIDD
+TVVVTSLPRPLLAAWNSFVIDEHARTPTPGMAVLLRRIAAAEPMAPVLYLSTGAWNVAQT
+LTRFLGRNLYPLGALLLTSWGPTKDRWFRSGQEHKVTQLERLAQQFPDLQWILVGDDGQH
+DPEIYADFATKHPDKVKAIVIRQLTPSEALLAGGRAEATRHSTPGIPWCYGPDGAALSNQ
+LEDLGILPVDFVDVHPEGWLEDILGEDEASAAGRDGDEHGVHGGRADQDEARDVDVSAQ-
+----------D---------------
+>4_376
+MPAASDAPTPA----PRRGRLAPSGDPTPVENVATHLQEGWNRWHRARALRAGNVPTVMA
+FTGYGSTSWVRILSRVVIASDEEFMNGRRLSKVVADGVRGWRNFVAPPMAYAEVEVQVGD
+LRTTVRTDRMGVVDVVLDVELEPGWQTATLHVGGQEEHAVMDLYICEPGARIGLVSDIDD
+TVVVTSLPRPLLAAWNSFVIDEHARTPTPGIAVLLRRIAELEPKAPVLYLSTGAWNVAQT
+LTRFLGRNLYPLGALLLTSWGPTRDRWFRSGQEHKRVQLERLAEQFPDIQWILVGDDGQH
+DPEIYAEFAQRHPDRVKAIVIRQLTPSQALLAGGRAEDTRHSTPGIPWCYGPDGATLSNQ
+LEDLGILPVEFVDVQPEAWREDILGDDEAPATLD-------AAAQRDGRSAD--EEAAR-
+--------------------------
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000435.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000435.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea7eb0ef4bf9e6b072b5e447eed464392dc76aec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000435.fa
@@ -0,0 +1,40 @@
+>0_376
+MSSRPAAPRLLRPVPLPLWLQGVVEALVTAMISLLAVMVPTLAVWATGGFERPTIEGAVQVGGVLWLALHAVPVTVTTAM
+PTAPDHLITGTAWLVPWGLTLLPLALSWRAGRRLARASYRDQAWQAFVGAVGAYALVGLAVAFLPGTDELTAHPAPAALL
+PALLFGVAALAGARREAGTWAHLIGLDLTERISRRSQYERWAGSYAWSVVRAAAVAVLALTGLNALLVAGRLAVEWTAVV
+TVAEAIGGGPLGGLLLALLQIGWLPTFTAWSIAWTAGPGFSVGADSLYSVFGATPATAPALPALGALPGTWSPWQLLLLA
+VPIGAGAVAGVWLLREGENHLDDWLHTRHGSRAVSLTLSTLALAVLTGLLTGLLLLVPLALTSGTLGLGALTDLGSHVWA
+VSAAVAGWVALGCAAGYLTALAVA-----GHRDGTTTVPRSGDRA-SGLRDRPSPRR-----------------------
+-------------------------------------------ARD
+>1_109
+MSSRPAAPRLLRPVPLPLWLQGVVEALVTAMISLLAVMVPTLAVWATGGFERPTIEGAVQVGGVLWLALHAVPVTVATAM
+PTAPDHLITGTAWLVPWGLTLVPLALSWRAGRRLARASYRDQAWQAFVGAVGAYALVGLAVAFLPGTDELTAHPAPAALL
+PALLFGVAALAGARREAGTWAHLIGLDLTERISRRSQYERWAGSYAWSVVRAAAVAVLALTGLNALLVAGRLAVEWTAVV
+TVAQAIGGGPLGGLLVALLQIGWLPTFTAWSIAWTAGPGFSVGADSLYSVFGATPATAPALPALGALPGTWSPWQLLLLA
+VPISAGVVAGVWLLREGENHLDDWLHTRHGSRAVSLTLSTLALAVLTGLLAGLLLLVPLALTSGTLGLGTLTDIGPHVWA
+VCAAVAGWVALGCAAGYLTALAVA-----GHRDGTTTVPRSGDRA-SGLRDRPSPRR-----------------------
+-------------------------------------------ARD
+>2_2504
+---------------------------MTALLSLLAVMIPTLVVWATGGFQRPTIEGALQVGGTLWLALHAVPVTVATVL
+PTAEGHVLSGTAWLVPWGLTLIPLLLSWRAGRRLARASYRDQAWQAFAGAVVGYALAGLTVAFLPGTPELRVSPWAAALL
+PALLFGIAALAGARREAGTWAHLIGLDLTERIARRSQYERWAGSYAWSVVRAAVVALLVLAALSALLVAVRLAVEWPAVV
+TLAQAIDAGPFGGLLLAVLQIGWLPTLTGWAIAWTAGPGFSVGSDSLYSVFGATPAAAPALPALGALPAAWAPWHPLFLA
+VPIAAGVAAGVWLLREGENHLDDWLDARTGHRAVSLALSTLALAVLTGLLAGLLLLVPLALTSGTLGVGTLTDIGANVWA
+VCAAVAGWVALGCAAGYLVALALA-----GRR----FIPPA--EA-AVAAERPRPRR-----------------------
+-------------------------------------------SRD
+>3_2375
+MS--PRVPSLLRPVPLPLWLQGVVEALVTALTSLALVLVPTLAVWITGGFSSTRIEDVLQTGGALWLGLHAVPLAVTTVV
+AQADTPTVTGTVWLVPWALTALPVWLSWRAGRRLARASYREQAWQALAGAVAAYAVVALACALLPGEGRITVHPLPSVLL
+PCLLFTTSAVAGARREAGTWAHLIGLDLTERIARRSQYERWAGTYAWSVLRGAGVGLAALAGLHALLVTVAVLVRWPRII
+EVQQMVGAGPVGGLMLALLEIGWLPTFTAWAVAWTAGPGFAVGADGHYSVFGTTPAPVPALPLLEALPAPWAPWHPAFLL
+VPVLAGAVAGWWLLREGENHLDDWIDSRITARWASLTLSTLALALLLGLVSGVAVLVPLALTNGTLGVGSMREIGSNAPL
+VALAVAGWMALGCALGYLVALAVVDRPVRGRRRISLPLPGSAPRAVTGRARRLPPRRLPRGVADAEADEPEVAAPAAARE
+EIPGRETPAQETPSEEPPAAARPAPRRAGAPRVPRVPRPAPRRARD
+>4_382
+MSSRPAAPRLLRPVPLPLWLQGVVEALVTAMISLLAVMVPTLAVWATGGFERPTIEGAVQVGGVLWLALHAVPVTVATAM
+PTAPDHLITGTAWLVPWGLTLVPLALSWRAGRRLARASYRDQAWQAFVGAVGAYALVGLAVAFLPGTDELTVHPAPAALL
+PALLFGVAALAGARREAGTWAHLIGLDLTERISRRSQYERWAGSYAWSVVRAAVLAVLALTGLNALLVAGRLAVEWTAVV
+TVAEAIGAGPLGGLLLALLQIGWLPTFTAWSIAWTAGPGFSVGADSLYSVFGATPATAPALPALGALPGTWSPWQLLLLA
+VPIGAGAVAGVWLLREGENHLDDWLHTRHGSRAVSLTLSTLALAVLTGLLTGLLLLVPLALTSGTLGLGTLTDIGSHVWA
+VCAAVAGWVALGCAAGYLTALAVA-----GHRDGTTTVPRSGDRA-SGPRDRPSPRR-----------------------
+-------------------------------------------ARD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000444.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000444.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d7ece0d8ec21541cd851da3b7db0cac74cb44ce7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000444.fa
@@ -0,0 +1,65 @@
+>0_389
+MVPMPTP-------VDPVTVP---SALSAALGRLSAGLTFAAALPDLEAALDARGAAVVEAPPGTGKTTVVPPALAVRLA
+DHG-----GGRVLVTQPRRVAVRAAWRRLRTAVLAAAADSHPGADPDARARLADAAVGYAVRGDAVGGGASAVEFVTPGL
+LLRRLLADPGLDGVGAVVLDEVHERDLDTDVLFALLADLRQLRPELALVAMSATVDAAALAARWARGMGE-APLPVVSTP
+AVLHPLREEHAPFRGHRLTAEGRVDRAFLDHVAATAARAHAKALEADPTVDALVFLPGVAEVETVAGRVAALAPDTEVRV
+LHGRQEPADQDAALAGRTDPAVPRVVVATAVAESSLTVPGVRLVVDSGLAREPRRDRGRGMAGLVTVQASRAAAGQRAGR
+AARLGPGTVVRCHTAAALGTAPAAPTPALAVVDLAPVALAFAAWGAPGGRGLTLPEDPPADAMAAAERTLASLGAVDADG
+RITPHGAVLAELPLDPPLGHALLRAAPLTGPRPAAEATAALALDLRAPGADLEALVAALRDGRHPEAGRWHREADRLERL
+ARRHAHHAPETREPDEPGPEA-ATAPRHSAGLVAALAFPAWIARRAGEEGAYLLASGTRAALPRDAV-GGLAGQEWLAVA
+EVARVAGDAAGTGAAIRAAAPIDRSLVERAGAGLRRTEDTAEWRGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRDA
+LAADGLARFDPRGRAERLRRRVHLLHRVLGAPWPDLSDTALPDLDTLVDGLAADLAAGRPLARLDAEALLRGALPWPEAG
+RLDELAPERLPVPSGRAVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREPVVLHLLSPAGRPLAVTADLPSFWAG
+PYAQVRAENRGRYPKHPWPEDPAVAEPTARTNRRAL
+>1_118
+MDPMPTP-------VDPVAVP---SALSTALGRLSAGLTFAAALPELGSALDARGAAVVEAPPGTGKTTVVPPALAVRLA
+DHG-----GGRVLVTQPRRVAVRAAWRRLRTAVLAAAADAQPGADPDARARLADAAVGYAVRGDAAGGGASAVEFVTPGL
+LLRRLLADPGLDGVDAVVLDEVHERDLDTDVLFALLADLRQLRPELALVAMSATVDAAALAARWARGMGE-APLPVVSTP
+AVLHPLREEHAPFRGHRLTAEGRVDRAFLDHVAATAARAHAEALEADPTVDALVFLPGVAEVEAVAGRVAALAPDTEVRV
+LHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRRDRGRGMAGLVTVQASRAAAGQRAGR
+AARLGPGTVVRCHTAAALGTAPAAPTPALAVVDLAPVALAFTAWGAPGGRGLTLPEDPPADAMAAAERTLASLDAVDADG
+RITPHGAVLAELPLDPPLGHALLRAALWTGPRPAAEATAALALDLRAPGADLEALVASVRDGRHPEAGRWRREADRLERL
+ARRHAHHSLETRAPGEPGPEATAAARRHPAGLVAALAFPAWIARRAGEAGAYLLASGTRAALPRDAAGGGLAGQEWLAVA
+EVARVAGDAAGTGAAIRATAPIDRTLAELAGAGLRRTEDTADWRGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRAA
+LAADGLARFDPSGRTERLRRRVHLLHRVLGAPWPDLSDAALPGLDALVDGLAADLAAGRSLARLDAEALLRGALPWPEAG
+RLDELAPERLPVPSGRAVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREPVVLHLLSPAGRPLAVTADLPSFWAG
+PYAQVRAENRGRYPKHPWPEDPAAAEPTARTNRRAR
+>2_2493
+M-PAPSPHSSRPASVDTAVAP----ALSAALERLGSGLTFVAALPDLEAALDARGAAVVEAPPGTGKTTVVPPALAVRLA
+DHG-----GGRVLVTQPRRVAVRAAWRRLRSAVLDAADRT---SAPDA---LADAAVGYAVRGDAVGGGASAVEFVTPGL
+LLRRLLADPGLDGVDAVVLDEVHERDLDTDVLFALLADLRQLRPELALVAMSATVDAAALAARWARGMGEEAPLPVVSTP
+AVLHPLREEHAPFRGRRLTAEGRVDRAFLDHVAATAARAHAAALDADPTVDALVFVPGVAEVEAVAGRVAARAPDTEVRV
+LHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRRDRGRGMAGLVTVQASRAAAGQRAGR
+AARLGPGTVVRCHTAAALGAAPAAPTPALAVVDLAPVALAFAAWGAPGGRGLTLPKDPPADAMAAAERTLASLGAVDTDG
+RITPHGAVLAELPLDPPLGHALLRAAPLTGPRPAAEATAALALDLRASGADLEALVAALRDGRHPESRRWRREADRLERL
+ARRHAHRAPETREPDGPGPEA-ATARRHPAGLVAALASPAWIARRAGEAGAYLLASGTRAALPRNAVVGGLAGQEWLAVA
+EVARAAGDAAGTGAAIRAAAPIDRPLAELAGAGLRRTEDTADWRGDRLTGRRVDRMGALVLAETPAPVAPDAAAQAVRAA
+LAADGLARFDPSGRAERLRRRVHLLHRVLGAPWPDLSDTALPGLDALVDGLAADLAAGRSLAHVDAEALLRGALPWPEAG
+RLDELAPERLPVPSGRGVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGRELVVLHLLSPAGRPLAVTADLPSFWAG
+PYAQVRAENRGRYPKHPWPEDPAAAEPTARTNRRVR
+>3_2361
+---MSTS-------SASHSTPDLRAALAAASARLGADLAFSASLPALEAALDARAGAVVHAPPGTGKTTAVPPAVALWLA
+RRAESGGEGGRVLVTQPRRVAVRAAWRRLHGAVADALG---PESGPDT-GRLPDAVVGYAVRGDAVGRGASAVEFVTPGL
+LLRRLLGDPGLEGVGAVVLDEVHERDLDTDVLFALLADLRQLRPELALTAMSATLDADALAARWATGMGE-DPVPVVRTP
+SVQHPLTVEHAPFGGPRTTADGRVDRDFLDHVAATAARAHAEALDADPTVDALVFVPGVAEVEAVAGRVAALAPDTEVRV
+LHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRRDRGRGITGLATVQASRAAADQRAGR
+AARLGPGTAVRCHTAAALGAAPAAPTPALAVADLASVVLAFAVWGAPGGDGLVLPEDPPADAMAAAERTLASLDAVDTDG
+RITPHGTVLAELPLDPPLGHALLRAAPLTGPRSAAEATAALALDLRAPGADLEALVAALRDGRHPEAGRWRREADRLERL
+ARRHAHRAPETREPDEPGPAATATARRHPAGLVAALAFPAWIARRAGEEGAYLLASGTRAALPRDAVGGGLAGQEWLAVA
+EVARVAGDAAGTGAAIRAAAPIDRPLAELAGAGLRRTEDTAEWRGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRVA
+LAADGLARFDPSGRAERLRRRVHLLHRVLGAPWPDLSDATLPGLDALVDGLAADLAAGRSLTRLDAEALLRGALPWPEAG
+RLDELAPERLPVPSGRGVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREPVVLHLLSPAGRPLAVTADLPSFWAG
+PYAQVRAENRGRYPKHPWPEDPAAAEPTDRTNRRAR
+>4_392
+---MPTP-------VDPVSVP---SALSAALGRLSAGLTFAAALPDLEAALDARGAAVVEAPPGTGKTTVVPPALAVRLA
+DHG-----GGRVLVTQPRRVAVRAAWRRLRTAVLAAAADAQPGADPDAQARLGDAAVGYAVRGDAAGGGASAVEFVTPGL
+LLRRLLADPGLDGVGAVVLDEVHERDLDTDVLFALLADLRQLRPELALVAMSATVDAAALAARWARGMGEDAPLPVVSTP
+AVLHPLREEHTPFRGHRLTAEGRVDRAFLDHVAATAARAHAEALDADPTVDALVFLPGVAEVEAVAGRVAALAPDTEVRV
+LHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRRDRGRGMAGLVTVQASRAAAGQRAGR
+AARLGPGTVVRCHTAAALGTAPAAPTPALAVVDLAPVALAFAAWGAPGGRGLTLPEDPPADAMAAAERTLASLDAVDADG
+RITPHGAVLAELPLDPPLGHALLRAAPWTGPRPAAEATAALALDLRAPGADLEALVAAVRDGRHPEAGRWRREADRLERL
+ARRHAHHA-----PGEPGPEAAATVRRHPAGLVAALAFPAWIARRAGEAGAYLLASGTRAALPRDAAGGDLTGQEWLAVA
+EVARVAGDAAGTGAAIRAAAPIDRTLAELAGAGLRRTEDTADWRGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRAA
+LAADGLARFDPSGRTERLRRRVHLLHRVLGAPWPDLSDAGLPGLDALVDGLAADLAAGRPLTRLDAEALLRGALPWPEAG
+RLDELAPERLPVPSGRAVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREPVVLHLLSPAGRPLAVTADLPSFWAG
+PYAQVRAENRGRYPKHPWPEDPAAAEPTARTNRRAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000458.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000458.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d795fc6ae736891ae6dc73e0fb18ad2560355489
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000458.fa
@@ -0,0 +1,31 @@
+>0_407
+MSTAVPIPAVAEVPPGAEPVLETENLVKVYGRGASRFDALKGITLQIQRGESLAVVGKSG
+SGKSTLMHLLALLDQPSAGVVAMDGRPVSQLKAAEISQLRNERFGFVFQQFFLNPNQTVL
+ENTVLPLKIAGVGRAERARRGMAVLERLELADKAKNKATDLSGGQKQRVCIARALVNNPT
+VLFADEPTGNLDSATSAAVEDILFGLHRDEGITLVVVTHDDDLAAKCDRRVELQDGVVIA
+DERVG---TERDGARA
+>1_137
+MSTAVPIPAVAEVPPGAEPVLETENLVKVYGRGASRFDALKGITLQIQRGESLAVVGKSG
+SGKSTLMHLLALLDQPSAGVVAMDGRPVSQLKAAEISQLRNERFGFVFQQFFLNPNQTVL
+ENTVLPLKIAGVGRAQRTRRGMAVLERLELADKAKNKATDLSGGQKQRVCIARALVNNPT
+VLFADEPTGNLDSATSAAVEDILFGLHRDEGITLVVVTHDDDLAAKCDRRVELQDGVVIA
+DERVG---TERDGARA
+>2_2473
+MHT-VQQAAGAHAPAGREPVLETENLVKVYGRGESRFDALKGVTLQIQAGESVAIVGKSG
+SGKSTLMHLLALLDRPSAGVVAMDGRPVQDVSPAEVARLRNETFGFVFQQFFLNPAQTVL
+ENTVLPLKISGVPRAERRERGMAVLERLELADKAGNKATDLSGGQKQRVCIARALVNRPT
+VLFADEPTGNLDSATSAAVEDILFGLHRDEGITLVVVTHDDDLAARCDRRLVMQDGMIVD
+E-------TTTAGAQA
+>3_2343
+MSTVHTHPPETQASRGEEPVLETENLVKVYGRGASRFDALKGVTLQIHRGESVAVVGKSG
+SGKSTLMHLLALLDVPTSGVVAMDGRPVSQLKAAEVAHLRNERFGFVFQQFFLNADQTVL
+ENVVLPLKIAGVPRHEREARGREVLERLEIADKAKNRANDLSGGQKQRVCIARALINRPT
+VLFADEPTGNLDSATSRSVEEILFGLHRDEGITLVVVTHDDDLAAQCDRRLVMQDGVIVA
+AEGAGRAVAAGTGARA
+>4_410
+MSTAVPIPAVAEVPPGAEPVLETENLVKVYGRGASRFDALKGITLQIQRGESLAVVGKSG
+SGKSTLMHLLALLDQPSAGVVAMDGRPVSQLKAAEISQLRNERFGFVFQQFFLNPNQTVL
+ENTVLPLKIAGVGRAQRTRRGMAVLERLELADKAKNKATDLSGGQKQRVCIARALVNNPT
+VLFADEPTGNLDSATSAAVEDILFGLHRDDGITLVVVTHDDDLAAKCDRRVELQDGVVID
+DERVG---TEQDGARA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000460.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000460.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8cb61e98942a44b03e6df22c3b9a667a15c7e36e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000460.fa
@@ -0,0 +1,31 @@
+>0_409
+MTTDRP---NPDPNPEQP-------A----------------------------------
+---VGSRYGTQPYAAPGYGAQPGSPYGIVPEPAAFPALLTLTLTSLALYVLSSLPALFGG
+EESIE-RMRDSLRQSGLTPEQVEEI---APVVGASVTVGTIIVLLIGVALYALVYFNLRG
+AKNWARILGIVVGILGTLSAVGGIFSFVTYPGIGGVLASVLSLALVIVNILWLVKAFNPQ
+VAAYTRQGRRA--
+>1_139
+MTTDRP---N--PNPEQP-------A----------------------------------
+---AGSRYGTQPYAAPGHGAQPGSSYGIVPEPAAFPALLTLTLTSLALYVLSSLPALFGG
+EESIE-RMRDSLRQSGLTPEQVEEI---APVVGASVTVGTIIVLLIGVALYALVYFNLRG
+AKNWARILGIVVAILGTLSAVGGIFSFVTYPGIGGVLASVLSLALVIVNILWLVKAFNPQ
+VAAYTRQGRRA--
+>2_2471
+MSNQNPDFTNPAYNPANPPFEGESGQAGQ-APQQGQPGQAAQYGQPGPYGQAPQYGQPGQ
+YPATGTRYGTQPYGVDGR-------YGTVPEPRGFRTLLTLTLVSAALWVLSSLPAMFTM
+DDMMDVVMRDAASQPGVTAEDMEMV---SSFMRTAGITSIVISLIIGLGLYALVYFNLRG
+VKNWARILGIVFAILGALAIFSGI-GFLFSGSTMLILSGALTLAYAVVNIIWVITAFRSD
+VAEWFRQGRPAAA
+>3_2341
+MTDQNT------PYPQNP-------QGGQPAPQYGQPGQA-----------APQYGQPG-
+---EGSRFGTQAYGAPGL--QYGAP---LAEPAKFRTLLKLTLASAVVYVLSALPGLFVD
+QDAL---VRDQLRAQGMSAEQIDQAMQNAGMFSAMAGIGAVVGLLIALGLYALVYFGLRA
+GKNWARVLGIVLAILGTLSAVFGLFSLGSFPAGVMIASLVLSVLFIAVNVLWLVNAFNKD
+VAAYTKQGRLPAA
+>4_412
+MTTDRP---NPDPNPEQP-------AAGGPGPYPGQ---------------NPAYGQPT-
+---AGSRYGTQPYAAPGYGAQPGSPYGIVPEPAAFPALLTLTLTSLALYVLSSLPALFGG
+EESIE-RMRDSLRQSGLTPEQVEEI---APVVGASVTVGTIIVLLIGVALYALVYFNLRG
+AKNWARILGIVVAILGTLSAVGGIFSFVTYPGIGGVLASVLSLALVIVNILWLVKAFNPQ
+VAAYTRQGRRA--
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000477.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000477.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac195317bed6db2023b3833e59c326a6a76a643e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000477.fa
@@ -0,0 +1,31 @@
+>0_428
+MSPRRPRVPRVDPTTGAPRRTAVAAPAAPTTASPKADAPTPTPEATTPTPAATGAEVIDL
+HSVQERRQAGHHGHLDGHPDADRADTAP----AAPASPSAPPRRTAPARPAGRRTRPAPR
+RAASAAATAARRRAPLPEPVPARQITGRSLIVVAVLLVAAVLVAPTLRAFLNQQLEISAA
+REEIATMQAQREDYERRIQLWDDPAYVTQQARERLELVMPGETLYSVTGRPSETETETDT
+EAEDTPAARADEVVNTRLPWAEGLWDSAVRAGLE----------------
+>1_158
+MSPRRPRVPRVDPTTGAPRRTAVAAPAAPTTAFPEADTPTPTPAAPTPAPAATDAEVIDL
+QSIQERRQA-------GHPDVDRADTAPAGDTAAPASPSAPPRRTAPARPAGRRPRPAPR
+GAASAAATAARRRAPLPEPVPARQITGRSLIVVAVLLVAAVLVAPTLRAFLNQQLEISAA
+REEIATMQAQREDYERRIQLWDDPAYVTQQARERLELVMPGETLYSVTGRPSETDTATET
+--EDTPAAGADEVVNTRLPWAEGLWDSAVRAGLE----------------
+>2_2451
+------------------------------------------------------------
+------------------------------------------------------------
+-------MAARRRAPLPDPVPARQITGRSLLVVAVLLVAAVLVAPTLRAFLNQQLEIAAA
+EEEIAAMQAQREDYEERIRLWDDPGYVTQQARERLQLVMPGETLYSVTGVPEEAPR----
+--DPRPEAPAGEPVNTRLPWAEGLWDSAVRAGPRVSPGPRPDPGSGPARP
+>3_2323
+MSARRPRVPRVAVPDTAPER-ATPAVVEPVVVEPAPVAPA-APEAPAP-PAPPGPQVIDL
+QEAAQRRR----------------------HEATRPSPRPDAERAAAQRVA--RLREERR
+RATVREHAAARRRVPLPEPVPARQLTGRSLVVLAVLIIAAVLVAPTARLMLNQQLEISAA
+QQDIAEQQRRKAEYEEQIRRWDDPGYVAQQARQRLELVMPGETLYTVTGLPDESGA----
+--VPADSVP-QEKVNDRLPWVEGLWDSAVRAATE----------------
+>4_431
+MSPRRPRVPRVDPTTGAPRRTAVAAPAAPTTAFPEADTPTPTPAAPTPAPAATDAEVIDL
+QSVQERRQAGHPGHLDGHPDADRADTAPAGDTAAPASPSAPPRRTAPARPAGRRPRPAPR
+RAASAAATAARRRAPLPEPVPARQITGRSLIVVAVLLVAAVLVAPTLRAFLNQQLEISAA
+REEIATMQAQREDYERRIQLWDDPAYVTQQARERLELVMPGETLYSVTGRPSETDTATET
+--EDTPAAGADEVVNTRLPWAEGLWDSAVRAGLE----------------
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000482.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000482.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c80408bdc869544762030c32372a9b89da4d37f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000482.fa
@@ -0,0 +1,46 @@
+>0_436
+MSSTLAAQTKINKDVPYGLTVAAAWSWRLVAVVIGIGVVVYLLGFVSLVVIPILVAALLA
+TLLAPVFQAMRRIKVPGVAAALLCVLLLVVVVVGLMGLAGQQIVQGFAELGDQLGQAVDD
+AIAWLAGVGVEIPRSGAGLEGLWQTLRDNSATVMNSAVSLGSTAVNIGAGLFIALFSLIF
+FLYDGDRIWRFLLIFVPKAHRATVGRAGRSGWQSLGSYVRVQIFVAFIDAVGIGIGALIL
+GVPLAIPLAVLVFLASFIPMIGATLTGAMAVLLALMSNGLVNALLMLGVVLLVQQIESNV
+LQPLVMGKAVALHPLAVFLAVAAGSTVLGLAGAVFAVPVLAFVNSFVRALTADTP-----
+--EELTERTGHALEPGGAEDETAGSHRYRPSAHDDAALASEADAGTRHGDDA--------
+-----
+>1_163
+MSSTLAAQTKIDKDVPYGLTVAAAWSWRLVAVVIGIGVVVYLLGFVSLVVIPILVAALLA
+TLLAPVFQAMRRIKVPGVAAALLCVLLLVVVVVGLMGLAGQQIVQGFAQLGDQLGQAVDD
+TIAWLAGVGVEIPRSGAGLEGLWQTLRDNSATVMNSAVTFGSTAVNIGAGLFIALFSLIF
+FLYDGDRIWRFLLIFVPKAHRATVGRAGRSGWQSLGSYVRVQIFVAFIDAVGIGIGALIL
+GVPLAIPLAVLVFLASFIPMIGATLTGAMAVLLALMSNGLVNALLMLGVVLLVQQIESNV
+LQPLVMGKAVALHPLAVFLAVAAGSTVLGLAGAVFAVPVLAFVNSFVRALTADTP-----
+--EELTERTGHALEPGGAEDEAAGSHRYRPSAHDDAALASEADAGTRHGDDA--------
+-----
+>2_2434
+MSSTLAAQTKINKDVPYGLTVAAAWSWRLVAVLVGLGILWWLLSFVSLVLIPVLVAALLA
+TLLAPLFEGMRRIGIPGIAASLLCVVLLIVVVVGLVVVAGQQIAQGFSDLGDKLTQAVDG
+AIAWLASIGVELPTAGGGLEGLWQTLRDNSGTLLDSAMTFGSTAVNIGAGFFIALFSLIF
+FLYDGDRIWRFILVFVPKAHRATVGRAGQTGWRALGNYVRVQIFVAFVDAVGIGLGALIL
+GVPLAIPLAVLVFLASFIPMIGATVTGAIAVLFALMSNGLVNALLMLGVVLLVQQIESNV
+LQPLVMGKAVALHPLAVFLAVAAGSAVLGLAGAVFAVPVLAFVNSFIRALTADPP-----
+--EQLTDRSDQALAPGSAADEAVGSHVFEPTKHDDAALASEDDAGT-SGDLR--------
+-----
+>3_2318
+MSSTLSTDAKLEKDIPYGLTVAAGWSWRVIAVAAMLWVVWHFAGFASLVIIPVLVAALLA
+VLLAPIYRALRRARIPGVLAAVLSIVLLLAAVVLLAWVAGLELVQGFSDLSDQLGASVEH
+LVTWVQGMGVPVSFDAAALDNVWSTVKDNSGVLVDGALAFGSTAANVLTGLFIALFTLIF
+FLFDGERIWRFLLAFVPHTSRSRVDVAGRTGWNALGSFVRVQIVVAFIDAVGIGLGAWLL
+GVPLALPVAVIVFLFSFVPTIGAIASGALACVLALTANGLVNALLMLGVVILVQQIESNL
+LQPLIMGRAVSLHPLAVFLGVAAGGVALGLVGAVFAVPLLAFANAFVQALRAKGPGEEIL
+PGEKVFRPSDEVIA--AARRDAKLDPKLDPTSFDD-------DSGP-DGDVEDGRTGSTR
+TELKP
+>4_436
+MSSTLAAQTKIDKDVPYGLTVAAAWSWRLVAVVIGIGVVVYLLGFVSLVVIPILVAALLA
+TLLAPVFQAMRRIKVPGIAAALLCVLLLVVVVVGLMGLAGQQIVQGVAQLGDQLGQAVDD
+AIAWLAGVGVEIPRSGAGLEGLWQTLRDNSATLMNSAVSFGSTAVNIGAGLFIALFSLIF
+FLYDGDRIWRFLLIFVPKAHRATVGRAGRSGWQSLGSYVRVQIFVAFIDAVGIGIGALIL
+GVPLAIPLAVLVFLASFIPMIGATLTGAMAVLLALMSNGLVNALLMLGVVLLVQQIESNV
+LQPLVMGKAVALHPLAVFLAVAAGSTVLGLAGAVFAVPVLAFVNSFVRALTADTP-----
+--EELTERTDHALEPGGAEDEAAGSHRYRPSTHEDAALASEADAGTRHGDGA--------
+-----
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000485.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000485.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2665b93a5a03fa87036b28438b99ad03d49600e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000485.fa
@@ -0,0 +1,21 @@
+>0_439
+MTTSQSDAPWLTQEAYDRLSKELEYISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAADDESL
+EVYSERSPLGEAINGAKKGDKVSYTAPNGKDIKVEVKDVQPYSG
+>1_166
+MTTSQSDAPWLTQEAYDRLSKELEYISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAADDESL
+EVYSERSPLGEAINGAKKGDKVSYTAPNGKDIKVEVKDVQPYSG
+>2_2431
+MTTSQSDAPWLTQEAFDRLSKELEHISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAEDDEHL
+EVYSERSPLGEAINGAAKGDKVTYTAPNGKEIKVEIKDVKPYSG
+>3_2315
+MATTPSDAPWLTQEAFDRLSKELAHISGPGRQEIIERIEAAREEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGETQAADGVVTPGTVVTAVVAGDEMTFLFGNREIAADGEDL
+EVYSERSPMGEAINGAKQGDKVTYTAPNGKDIAVEITDVKPYQA
+>4_439
+MTTSQSDAPWLTQEAYDRLSKELEHISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAADDESL
+EVYSERSPLGEAINGAKKGDKVSYTAPNGKDIKVEVKDVQPYSG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000492.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000492.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9cae33fbfeb1c8933b918f8b198552b506fbd955
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000492.fa
@@ -0,0 +1,21 @@
+>0_447
+MSGVGWAWTHGAPATAVLWSLGLVWFAVCAGVLVRTDLREHRLPNRWTLRLALGGLTMMT
+GGALLAGRGDLTLCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV
+LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA----
+>1_174
+MSGVGWAWTHGAPATAVLWTLGLAWFAVCSGVLVRTDLREHRLSNRWTLRLALGGLAMMT
+GGALLAGRGDLALCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV
+LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA----
+>2_2424
+MDGVGWAWAQGLPATAVLWSAGLAWFAVCAAVLVRVDLREHRLPNRWTLRLALGGLAAMA
+GGAALAGRADLVLSSVLGGLGYAAAMLVLHVLSRGSLGMGDVKLAAGLGAYTGVLGGSAV
+VAAGLGAILLGGAVAAVLVAARRASRSTALPFGPPMILAAAAVLAFAPAGG
+>3_2307
+MTWWTGAWEAGERLTAMLWAAGLVWFLLCSVVLARTDLREHRLPNRWTGRLALGGVVAMG
+GGAVLGGLWSVVASCLLGGLGYALAMLALHVLTRGGLGLGDVKLAAGLGLYCGVAGLAAV
+LAAAVLAVLLGGVVAVVLVLARRADRHTALPFGPAMVAGALGVLLLA----
+>4_447
+MSGVGWAWTHGAPATAVLWTLGLAWFAVCSGVLVRTDLREHRLSNRWTLRLALGGLAMMT
+GGALLAGRGDLALCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV
+LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA----
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000495.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000495.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c8ae0f82d4f38a41362d6ccd7373cb97b04f2a13
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000495.fa
@@ -0,0 +1,26 @@
+>0_450
+MLTVSS------ADPHA-PAPRPVLTATQAQRARQPWMAMVLSLAALLAIVAVVLLLNPE
+PPQRPREDRVDVAAEAATIPHDDGDLPALAPEVPESWYANYARLQKLDGVSTWDVGWVVT
+DTVFAGLQQAEDVDPTWVSLRVDQVPTSETIEIDGIAWDLHADPKKPERRLVAEVDGSTV
+VLTTTGDQAVLEDLAHGVAKETR
+>1_177
+MLTVSS------ADPHA-PAPRPVLTATQAQRARQPWMAMVLSLAALLAIVAVVLLLNPE
+PPQRPREDRVDVAAEAATIPHDDGDLPALAPEVPESWYANYARLQKLDGVSTWDVGWVVT
+DTVFAGLQQAEDVDPTWVSLRVDQVPTSETIEIDGIAWDLHADPKKPERRLVAEVDGSTV
+VLTTTGDQAVLEDLAHGVAKETR
+>2_2421
+MLTVSSTHPTDPTDPNA-PAPRPVLTAKQAQRARQPWIGMVLSVVALLALVAVVLILNPE
+PPQRPREDRVDVAAAAATVPHDDGVLPALAPEVPESWYANFARLQTMDGVSTWDVGWVVT
+DTVFAGMQQAHDVDPTWVTLRVDSVPATETLEIDGLAWDLHADPRAPEKRLVTEVEDTTV
+VLTTTGDRAVLEDLARGVAKETR
+>3_2304
+MPGMSS------PDPAAPPAPRPVLTPKQAQRARAPWIAMVLSTLAVLGIVLVALMVNQP
+PPAPAQADRVDVAAAASTVPHDDGALPALAPDVPEPWDSTYARVERLQGVDTWDVGWAVN
+DAVFAGLKQTSRADPTWLALRVGSAPAVGTVDVDGITWDHYAPQDSKDQHLVAEVRGSTL
+VLTTSGDQAVLEDLARAVAKEIR
+>4_450
+MLTVSS------ADPHA-PAPRPVLTATQAQRARQPWMAMVLSLAALLAIVAVVLLLNPE
+PPQRPREDRVDVAAEAATVPHDDGDLPALAPEVPESWYANYARLQKLDGVSTWDVGWVVT
+DTVFAGLQQAEDVDPTWVSLRVDHVPTSETIEIDGIAWDLHADPKKPERRLVAEVDGSTV
+VLTTTGDRAVLEDLAHGVAKETR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000499.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000499.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e39db3f671219bd25ef0e871ef16fd22860776bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000499.fa
@@ -0,0 +1,45 @@
+>0_455
+---------MMAGAAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPTEHLRALQEAGV
+AVRPDPEALQHAQDKLVMRAAVERLGLPNPAWAPVDDLEAVLAFGDEHGWPMILKTARGGYDGKGVLKLDDADDARASAA
+DGTLAAWLGAGITPLLAEALVPFSRELSAQVARTPSGEVAVYPVVDSVQVAGVCDLVVAPAQDLDPAVAAAATAAAVRLA
+EELDVTGMLAVELFETPGVGPGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGETAPRGAGVVMKNVLGGAR
+EDLHAGSVAALAAHPQAKVHLYGKDVRPGRKVGHVNVVADHGLSLEEAVRTAESAAALLRD----DAPTTGTETEARP--
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------
+>1_182
+---------MMAGAAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPTEHLRALQEAGV
+AVRPDPEALQHAQDKLVMRAAVERLGLPNPAWAPVDDLEAVLAFGDEHGWPMILKTARGGYDGKGVLTLDDADDARASAA
+DGTLAAWLGAGIAPLLAEALVPFSRELSAQVARTPSGEVAVYPIVDSVQVAGVCDLVVAPAQDLDPAVAAAATAAAVRLA
+EELDVTGMLAVELFETPGVGPGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGETAPRGAGVVMKNVLGGAR
+EDLHAGSVVALAAHPQAKVHLYGKDVRPGRKVGHVNVVADHGLSLEEAVRTAESAAALLRD----DAPTTGTETEARP--
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------
+>2_2416
+---------MMAGPAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPTEHLRVLQEVGV
+AVRPGPEALQHAQDKLVMRAAVERLGLPNPAWAAVRDLDEVLAFGDEHGWPMILKTPRGGYDGKGVLKLDDADDARASAS
+DGTLGTWLGAGIAPLLAEALVPFTRELSAQVARTPSGRVAAYPVVDSVQVAGVCDLVVAPARDLDPAVAEAATAAAVRLA
+EELDVTGMLAVELFETPGVGPGFQINELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGDTAPRGAGVVMKNLLGGAR
+EDLHAGLADALAAHPQAKVHLYGKAVRPGRKVGHVNVVADHGLTLEQAVRAAESAAAVLRDGAAPDAVDASPSSPATPHP
+AGGPPMTATPQNPAQPLQDDAPVVSVVMGSDSDWPVMSAAAEALRELDVPVEVGVVSAHRMPHEMVEFGARAHERGIRVI
+VAGAGGAAHLPGMLASVTPLPVIGVPVKLKSLDGLDSLLSIVQMPAGVPVATVSVDGARNAGLLAARILASADTEEGERL
+RAALTEHAAELNAQAQAKGARLRERMAADR
+>3_2299
+MIGGGQLARMMAGPAAELGVPFRVLAEAPDASAAQVAPHMVGDHASLEDLRAFAATVDVVTFDHEHVPTEHLRTLEAAGV
+AVRPGPDALQYAQDKLLMRGLVERLGLPNPAWAPVSSLEEVIAFGDEHGWPMILKTARGGYDGKGVLKVDSADDARSGAA
+DGTLGTWLGAGIAPLLAEAMVPFARELSAQVARRPSGEVAAYPVVASLQTQGVCDVVTAPAPDLAPAVAEAASGAAVRIA
+EELDVTGMLAVELFETPGTDAGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDMPLGGTAPRGDGTVMKNVLGGAH
+EDLHSGFSEALAAHPEAKVHVYGKGVRPGRKVGHVNVVAEHGLSLADAERIAESTAAVLRDA---TAPSAPTPKA-----
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------
+>4_455
+---------MMAGAAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPTEHLRALQEAGV
+AVRPDPEALQHAQDKLVMRAAVERLGLPNPAWAPVDDLEAVLAFGDEHGWPMILKTARGGYDGKGVLKLDDADDARASAA
+DGTLAAWLGAGITPLLAEALVPFSRELSAQVARTPSGEVAVYPVVDSVQVAGVCDLVVAPAQDLDPAVAAAATAAAVRLA
+EELDVTGMLAVELFETPGVGPGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGETAPRGAGVVMKNVLGGAR
+EDLHAGSVAALAAHPQAKVHLYGKDVRPGRKVGHVNVVADHGLSLEEAVRTAESAAALLRD----DAPTTGTETEARP--
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000501.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000501.fa
new file mode 100644
index 0000000000000000000000000000000000000000..182f8a8c82efa84574c53a2ab0ec9d52b2b6a3ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000501.fa
@@ -0,0 +1,31 @@
+>0_457
+MVSLSAPRSTGPLVLRLASSPRPALVQEPGAPDE-----PGAVDQRIELSGRVTVNWAAK
+FAGLLGAEGIGAGDAVALDLPVHWLSHALALGVLCAEAEPALEG----------DSPAAV
+LTDRPEAWPDPSVAVFAVALPRGLEPEF-DGPAVDPAVVDVAAEIRAQPDALPGPVDHVR
+PASIPAG----------ADVAPDDDGP---------RPRLTWAGVRAALEAWDAGRAVTV
+RP
+>1_184
+MVSLSAPRSTGPLVLRLASSPRPALVQEPGAPDE-----PGAVDQRIELSGRVTVNWAAK
+FTGLLGAEGIGAGDAVALDLPVHWLSHALALGVLCAEAEPALEG----------DSPAAV
+LTDRPEAWPDPSVAVFAVALPRGLEPEF-DGPATDPAVVDVAAEIRAQPDALPGPVDHVR
+PASIPAG----------TDVAPDDDGP---------RPRLTWAGVRAALEAWDAGRAVTV
+RP
+>2_2414
+MVSLSAPRSTGPLVLRLASSPRPALVQEPGAPGE-----HGAVDQRIELSGRVTVNWAAK
+TAGLLADEGLGPGDPVALDLPAHWLSHALALGVLCAGAEPADDG----------AAPAAV
+LTDRPERWTDPATAVFAVALPRGLELPT-GGAVADPSVVDVAAEILGQPDALPGPVDHVR
+PEALPAADVAAADGDARTDEDQDDDGP---------RPRLTWAGMRAVLQAWDAGRAVQV
+RP
+>3_2297
+MVSLSAPRPDGPLVTRLASSPRPALVQEPAPAGEAAGAAHGAVDQRIELSGSVTVNWAAK
+AAGLLLDEGVAPGDAVLLDLPDHWLSRALALGVLCAGARPAFVAGPADRAQEAPDDAAAV
+LTDRPEHWDDPVLTVVAVRLPRGIEPDFGDDDAGDPSVVDLAAEIRAQPDALPGRVDHVT
+VDAVPADPADAA-------------GPLTEGGVGVGRARLDAPALRASLEAWDAGRAAHV
+PA
+>4_457
+MVSLSAPRSTGPLVLRLASSPRPALVQEPGAPDE-----PGAVDQRIELSGRVTVNWAAK
+FAGLLGAEGIGAGDAVALDLPVHWLSHALALGVLCAEAEPALEG----------DSPAAV
+LTDRPEAWPDPSVAVFAVALPRGLEPEF-DGPAVDPAVVDVAAEIRAQPDALPGPVDHVR
+PASIPAG----------ADVAPDDDGP---------RPRLTWAGVRAALEAWDAGRAVTV
+RP
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000504.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000504.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4744257dc1030d0e17917371c764ecf877644e0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000504.fa
@@ -0,0 +1,21 @@
+>0_460
+MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRRAEPHTYDLCGEHARRTTAPRGWEVLR
+LELPEHYEAVDADGGVRTVPTRPMAV----------------------------------
+-PPARPGLRVVRDGD-----
+>1_187
+MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRRAEPHTYDLCGEHARRTTAPRGWEVLR
+LELPEHYEAVDADGGVRTVPTRPMAV----------------------------------
+-PPARPGLRVVRDGD-----
+>2_2411
+MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRLAEPHTYDLCAEHARRTTAPRGWEVLR
+LELPGHYEAVAPDGTVHTVPTAPRAVPAAPPADVASRPSLAAPRPAPAVPPVDADEPEAP
+APPTRPGLRLVRDDDPLPPA
+>3_2294
+MRRCSKTGCQEPAEATLTYNYAGSQVVIGPLAQRAEPHAYDLCAAHAARTTAPRGWEVLR
+L--------------APAAPAAPGVA----------------------------------
+-APTHPALRLVTDPVEGTAG
+>4_460
+MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRRAEPHTYDLCGEHARRTTAPRGWEVLR
+LELPEHYEAVDADGGVRTVPTRPMAV----------------------------------
+-PPARPGLRVVRDGD-----
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000505.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000505.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b0a2bfebed3dfd2b693444cb903213e7685bda7b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000505.fa
@@ -0,0 +1,40 @@
+>0_461
+MTETSAEFRTPDVDPAFANRTTVPGASFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLREEYGEAQPLKGARIAGSLHMT
+VQTAVLIETLIALGAEVRWASCNIFSTQDEAAAAVVVGSGTPEDPQGVPVFAWKNESLEDYWWTASQILTWPGADEDPER
+GPNMILDDGGDATLLVHKGVEFEAAGAVPSATEDDPEEYRIILETLRRSLARDPQHWTRTAGTLRGVSEETTTGVLRLYQ
+LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGKGAAEALRGQGARVIVTEIDP
+ICALQAAMDGYQVARLEDVVGEGDIFVTTTGGKDIIMAEHMAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQV
+HEWTLGGGTEAERSIIVLSEGRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK
+VARLHLDALGVGLTELTKAQAEYLGVDVAGPYKADHYRY
+>1_188
+MTETSAEFRTPDVDPAFANRTTVPGASFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLREEYGEAQPLKGARIAGSLHMT
+VQTAVLIETLIALGAEVRWASCNIFSTQDEAAAAVVVGSGTPEDPQGVPVFAWKNESLEDYWWTASQILTWPGADEDPER
+GPNMILDDGGDATLLVHKGVEFEAAGAVPSATEDDPEEYRIILETLRRSLARDPQHWTRTAGTLRGVSEETTTGVLRLYQ
+LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGKGAAEALRGQGARVIVTEIDP
+ICALQAAMDGYQVARLEDVVGEGDIFVTTTGGKDIIMAEHMAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQV
+HEWTLDGGTEAERSIIVLSEGRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK
+VARLHLDALGVGLTELTKAQAEYLGVDVAGPFKADHYRY
+>2_2410
+MTETPAESRTPDVDPAYANRATVPGAAFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLREEYGESQPLAGARIAGSLHMT
+VQTAVLIETLTALGAEVRWASCNIFSTQDEAAAAVVVGSGTPEDPQGVPVFAWKNETLEDYWWTASQILTWPGAAEDPER
+GPNMILDDGGDATLLVHKGVEFEAAGAVPSATEDDPEEYRIILETLRRSLAEDPQRWTRTASTLRGVSEETTTGVLRLYQ
+LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGKGAAEALRGQGARVIVTEIDP
+ICALQAAMDGYQVARLEDVVGQGDLFVTTTGGKDIIMAEHMAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQV
+HEWTLDAGTDSERSIIVLSEGRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK
+VARLHLDALGVGLTELTKSQAEYLGVDVAGPYKADHYRY
+>3_2293
+MTETSSARPTPDVDPAFANRSTVPGATFDFAVRDLSLAEAGRHQIRLAEHEMPGLMALREEYGESQPLKGARIAGSLHMT
+VQTAVLIETLTALGAEVRWASCNIFSTQDEAAAAIVVGSGTPDAPAGVPVFAWKGESLEEYWWTASQILTWPGAAEDPDR
+GPNMILDDGGDATLLVHKGVEFEAAGAVPSATEDDPEEYRIILETLRRSLAEDPQRWTRTASTLRGVSEETTTGVLRLYQ
+LAQEGTLLFPAINVNDSVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGKGAAEALRGQGARVIVTEIDP
+ICALQAAMDGYQVARLEDVVEQGDLFVTTTGGKDIIMAEDMLRMKDKAIVGNVGHFDNEIDMAGLGRVDGVVKTEIKPQV
+HEWTFDTGTEDERSIIVLSEGRLLNLGNATGHPSFVMSASFTNQVMAQIELYDGSTGQGALTGEHYEKQVYTLPKVLDEK
+VARLHLDALGVGLTELTKAQAEYLGVDVAGPYKADHYRY
+>4_461
+MTETSAEFRTPDVDPAFANRTTVPGASFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLREEYGEAQPLKGARIAGSLHMT
+VQTAVLIETLIALGAEVRWASCNIFSTQDEAAAAVVVGSGTPEDPQGVPVFAWKNESLEDYWWTASQILTWPGADEDPER
+GPNMILDDGGDATLLVHKGVEFEAAGAVPSATEDDPEEYRIILETLRRSLARDPQHWTRTAGTLRGVSEETTTGVLRLYQ
+LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGKGAAEALRGQGARVIVTEIDP
+ICALQAAMDGYQVARLEDVVGEGDIFVTTTGGKDIIMAEHMAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQV
+HEWTLDGGTEAERSIIVLSEGRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK
+VARLHLDALGVGLTELTKAQAEYLGVDVAGPYKADHYRY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000509.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000509.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fbd30c6371865434194933b303668ed7182e86b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000509.fa
@@ -0,0 +1,31 @@
+>0_465
+M---------PEGRIVLAATPIGNLGDASARLRDLLAEADVIAAEDTRTARRLCAGLGVT
+PAGRVVAHHEHNEAASAQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVT
+CAPGPSAVTTALALSGLPTDRFAFDGFVPRKDGERRRWLTSLLTEARTVVAFESPQRLAD
+ALAVVAEVLGAERPVCVARELTKLHEEVVRGTAAGVHAWAAERHAGEGIRGEIVLVIGPA
+APGA--EGEASEADAVAEVAVLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAAR-G
+>1_194
+M----------TGRIVLAATPIGNLGDASARLRELMAEADVIAAEDTRTARRLCAGLGVT
+PAGRVVAHHEHNEAASTQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVT
+CAPGPSAVTTALALSGLPTDRFAFDGFVPRKDGDRRRWLTSLLTEARTVVAFESPQRLAD
+ALAVVVEVLGAERPVCVARELTKLHEEVVRGTAADVHAWAAERHAGEGIRGEIVLVIGPA
+APGA--EGEASEADAVAEVAVLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAAR-S
+>2_2405
+MTPRPTDLPSPSGRIVLAATPIGNLGDASARLRELLAEADVIAAEDTRTARRLCQGLGVT
+PAGRVVAHHEHNEAASTQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVT
+CAPGPSAVTTALALSGLPTDRFAFDGFVPRKDGERRRWLTSLLTEARTVVAFESPQRLAD
+ALAVVVEVLGAERPVCVARELTKLHEEVVRGTAAEVHAWAAERHAGEGIRGEIVLVIGPA
+SPDAASAGGATEADAVAEVGVLVDSGTRLKEAVATVAAAHGLRSRTLYQAVLAAR-G
+>3_2288
+M-----SLPAASGRIVLAATPLGNLGDATGRLRELLATADVIAAEDTRNTRRLCQGLGIT
+PAGRLMAHHEHNEAASAAGLLERVRAGETVVMVSDAGMPTVSDPGFRLVEAAVAAGLPVT
+CAPGASAVTTALALSGLPSDRFAFDGFLPRKDGERRRRLEEIRTDPRTVVYFESPQRTAS
+ALAVIAEVLGGARPVCVARELTKLHEEVVRGTADELVAWAVEREAGEGIRGEVAIVVGPA
+APDA--GAGADEADVLAEVAALTDSGTRLKEAVAAVAAAHGLRSRELYQAVLDARRG
+>4_465
+M---------PEGRIVLAATPIGNLGDASARLRDLLAEADVIAAEDTRTARRLCAGLGVT
+PAGRVVAHHEHNEAASAQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVT
+CAPGPSAVTTALALSGLPTDRFAFDGFVPRKDGERRRWLTSLLTEARTVVAFESPQRLAD
+ALAVVVEVLGAERPVCVARELTKLHEEVVRGTAAGVHAWAAERHAGEGIRGEIVLVIGPA
+APGA--EGEASEADAVAEVAVLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAAR-G
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000516.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000516.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a5d77d00ee858b38e65b3dba6db43a85844dca7a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000516.fa
@@ -0,0 +1,36 @@
+>0_477
+MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADHIRSSVEGEEVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVQILKDAGAKDVIIAATHPVFSDPAAQRLGECGAREVVVTNTLPIPEEKRFETLTVLS
+IAPLIARAIREVFEDGSVTSLFDGVA
+>1_207
+MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADHIRSSVEGEEVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVQILKDAGAKDVIIAATHAVFSDPAAQRLGECGAREVVVTNTLPIPEEKRFETLTVLS
+IAPLIARAIREVFEDGSVTSLFDGVA
+>2_2396
+MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADYIRTRVEGEEVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVQILKEAGAKDVIIAATHAVFSEPAAQRLGECGAREVVVTNTLPILEEKRFETLTVLS
+IAPLIARAIREVFEDGSVTSLFDGDA
+>3_2279
+MTELSRSEDKRLVLAAGRAHPGLAQEIAEALGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFVIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADYIRGQVEGEKVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVRILKEAGAKDVIIAATHAVFSDPAAQRLGESGAREVVVTNTLPIPEEKRFDNLTVLS
+IAPLIARAIREVFEDGSVTSLFDGDA
+>4_476
+MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADHIRSSVEGEEVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVQILKDAGAKDVIIAATHPVFSDPAAQRLGECGAREVVVTNTLPIPEEKRFETLTVLS
+IAPLIARAIREVFEDGSVTSLFDGVA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000517.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000517.fa
new file mode 100644
index 0000000000000000000000000000000000000000..78b0e32d84339058870b268edb01ac1be3753926
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000517.fa
@@ -0,0 +1,31 @@
+>0_478
+MAERVE--PAHGE--DG------------GAVAAP-QPHRPRLPFWASLLLNVVVALAVV
+AVVQALWVKVYSVPSGSMENTLEVGDRMLVNRTAYPDGAADAQDVVVFTANEDWA-HPMP
+PEGAVENAVRTFGDLTGIGRSHEQALVKRVIGTAGQTVECCTAEGAVTVDGEPLDEPYIH
+NDLPFIRDELDCESEVMSARCFGPVTVPEDSMLVLGDHRSNSADSVIACRGIPADQAGDC
+ARFVTREDIVGEVFVTVWPPTHWGGH
+>1_208
+MAERVE--PAHGE--DG------------GAVAAP-QPHRPRLPFWASLLLNVVVALAVV
+AVVQALWVKVYSVPSGSMENTLEVGDRMLVNRTAYPDGMADAQDVVVFTANEDWA-HPMP
+PEGAVENAVRTFGDLTGIGRSHEQALVKRVVGTAGQTVECCTAEGAVTVDGEPVDEPYIH
+NDLPFIRDELDCESEVMSARCFGPVTVPEDSMLVLGDHRSNSADSVIACRGIPADQAGDC
+ARFVTREDIVGEVFVTVWPPTHWGGH
+>2_2395
+MAERVE--PVRGEDGDD------------GSVAAP-ERRRSRLPGWASVLLNVVVAIAVV
+AVVQALWVKVYSVPSGSMEQTLEVGDRMLVNRTAYPDGMAASQDVVVFNANEDWA-QPLP
+PEGPVENAVRTFGDITGIGRSHDQALVKRVVGTEGQTVECCTSEGRVTVDGQPLDEPYLH
+NDLPFAPGRLDCESDVMSARCFGPITVPEDSMLVLGDHRSNSADSVIGCRGLPAEQAEGC
+ARFVTREDVVGEVFVTIWPPSNWGGH
+>3_2278
+MAHTPDAVPARDEAACDEAVRDDAAPAPASSAAAPGRRRRVQLPFWASVLLNVAVALLVV
+SVVQALWVKVYSVPSGSMEQTLQVGDRMLVNRTAYPDGVAERQDIVVFDANETWGVDTVG
+EEGPVEGAVRTFGDLTGIGRSHENALVKRVIGLPGETVECCTSQGAVTVGGTPLEEDYLY
+EDLPFVPGTLDCTTTPRSSRCFGPVTVPERSMLVMGDHRSNSADSVYQCRGLTAEQAGDC
+AHFVRDEDVVGRVFSTVWPPSNWSGH
+>4_477
+MAERVE--PAHGDDVDG------------GAVAAP-QPHRPRLPFWASLLLNVVVALAVV
+AVVQALWVKVYSVPSGSMENTLEVGDRMLVNRTAYPDGAADSQDVVVFTANEDWA-HPMP
+PEGAVENAVRTFGDLTGIGRSHEQALVKRVVGTAGQTVECCTAEGAVTVDGEPLDEPYIH
+NDLPFIRDELDCESEVMSARCFGPVTVPEDSMLVLGDHRSNSADSVIACRGIPADQVGDC
+ARFVTREDIVGEVFVTVWPPTHWGGH
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000519.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000519.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff48c56445a1e37bf015ba7d35ab6a5f126ab786
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000519.fa
@@ -0,0 +1,36 @@
+>0_481
+MAAQSTTAAVTVVIPHYGDPAPTLALVDRLLTDPGDALAAVVVSDDASPTPYPEAHDPR-
+-LTVVRRERNGGFGANVNTGLAAVTTELALVLNSDAEITGAQIDALVVAAAPYQPAVVSP
+QVVNEDGTPQWSGRHFPTVLHQTVEWLTPLARFRHLDVLHEAVGHDVAATRSASPVAVDW
+VMGAVLLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSIVVPAVRVPHGLHGSSD
+PLRRRGWLVDSRYRYARKFGHPRVLKAALTAATGANFAVNALRQARGVDVDARAVLRDEH
+ALVWKGQRR
+>1_210
+MAAQSPTAAVTVVIPHYGDPAPTLALVDRLLTDPGDALAAVVVSDDASPTPYPEAHDPR-
+-LTVVRRERNGGFGANVNTGLAAVTTELALVLNSDAEITGAQIDALVAAAAPYQPAVVSP
+QVVNEDGTPQWSGRHFPTVLHQTVEWLTPLARFRHLDVLHEAVGHDVAATRSASPVAVDW
+VMGAVLLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSIVVPAVRVPHGLHGSSD
+PLRRRGWLVDSRYRYARKFGHPRVLKAALTAATGANFAVNVLRQARGVDVDARAVLRDEH
+ALVWKGKRR
+>2_2393
+MAAQSTAAAVTVVIPHYGDPAPTLALVDRLLADPGDALAAVVVSDDASPTPYPEAHDPR-
+-LTVVRRERNGGFGANVNTGLSEVDTDLALVLNSDALITGEQIDALVAAAAPFQPAVVSP
+QVVNEDGSPQWSGRHFPTVLHQGVEWLTPLARFRHLPLLHEAVGHDVAAARSAAPVAVDW
+VMGAVMLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRDRGVASIVVPSVRVEHGMHGSSD
+PLRRRGWLVDSRFRYARKFGRPRALKAVLTAATGVNYAVNRVRQARGTDVDAAAVLRDEH
+ALIWKGTRR
+>3_2276
+MPASRIAPSVTVVIPHYGDPEPTRALVDALLAAPGRSVAGVVVSDDASPEPYPQPAPGRE
+GLTVVRREANGGFGANVNTGLAEVRTELALVLNSDAEITGEQIDALVEAARPYQPAVVSP
+QVVNEDGSPQWSGRHFPTVTHQTVEWLTPLARFRHLPALHEAVGHDVRAAEADSPVAVDW
+VMGAVMLLPMAEVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSVVVPSVRVVHGLHGSSD
+PLRRRAWLVDSRFRYARKFGRPRLLRGALTAATGVNWAVNRVRQTRGTDVDANAVFRAER
+DLIWKGTRR
+>4_480
+MTAQSPTAAVTVVIPHYGDPAPTLALVDRLLSDPGDALAAVVVSDDASPTPYPEAHDPR-
+-LTVVRRERNGGFGANVNTGLAAVTTELALVLNSDADITGAQIDALVAAAAPYQPAVVSP
+QVVNEDGSPQWSGRHFPTVLHQTVEWLTPLARFRHLDVLHEAVGHDVAAARSASPVAVDW
+VMGAVLLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSIVVPAVRVPHGLHGSSD
+PLRRRGWLVDSRYRYARKFGHPRVLKAALTAATGANFAVNALRQARGVDVDARAVLRDEH
+ALVWKGRRR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000521.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000521.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ede63ee942dee69a36d4af452039b2fad6349e40
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000521.fa
@@ -0,0 +1,41 @@
+>0_483
+M-----TDAPLFWRSEDLPRWHAWQRAQWPLTRRAADTARSTVRGVAGALTRRR---STG
+DDAPRLLLPAGDVHTLVALESFGPTQLAALASPVAALATAR--------PEAAAGVGWVL
+PA----GDAPALPGAVGHREHAATADVVTDRLPGLRRVLVAGEYLPSGRAAVRWARQRGA
+RVGVVQHGLLAVSTPPVPRDATLYAFTSADADWWTQGRADVEAVAVGSALLEQARRAA--
+--PAPSDTAGDGPGVFLGQLHGAELPRRDFAAAAEQYVRATGAAYRPHPAERDRLSRGQH
+AAWRRAGVRIDDAGAPLVATRGPVAAVFSTGILEAAQAGRPAWAVHPDPPAWLEGFWRRY
+GMTRWRPGRTPEPTPPLASPTADPAAAIAEHVWKESA
+>1_212
+M-----TDAPLFWRSGDLPRWHAWQRAQWPLTRRAADTARSTVRGVAGALARRG---STG
+DDVPRLLLPPGDVHTLVALESFGPTQLAALASPVAALATAR--------PEAAAGVGWVL
+PA----GDAPALPGAAGHREHAATADVVTDRLSGLRRVLVAGEYLPSGRAAVRWARQRGA
+RVGVVQHGLLAVSTPPVPQDATLYAFTSADADWWTQGRADVEAVPVGSALLEQARRTA--
+--PALSGAGDDGPGVFLGQLHGAELPRRDFAAAAEQYVRATGAAYRPHPAERDRLSRGQH
+AAWRRAGVRIDDAGAPLVATRGPVAAVFSTGILEAAQAGRPAWAVHPDPPAWLEGFWRRY
+GMTRWRPGRVPEPTPPLASPTTDPAAAIAEHVWKESA
+>2_2391
+MSGVGSGDVPLFWRPEDLPAWQRWQRAQWPASRRLADTARRLARAGRGALAAGRGAAPAP
+ESGLRLVLPAGDVHTLVGVESAAPTQRAALVEPVRALAEGRAGHAAADAARTAAGVGWVV
+PADVVAAQLPDLPGSDALSVHAVDDVMVAERLGGLRCVLVAGEYLPAGRAAVRWARERGA
+RVGVVQHGLLAVSTPPVPRDVALYAFTDHDAHWWTQGRTDVQAVAVGSALLEAARRMASH
+A-VADAVPRAAGPGVFLGQLHGAELPRTDFARAAQEYVRATGAAYRPHPAERDRLSLAQH
+EAWRKAGMRIDATAGPLASTAGPVAAVFSTGILEAAQAGRPAWAVHPDPPAWLEGFWERY
+GMTRWRPGVETEPTPPLASPSADPAAAIAAHLWKETA
+>3_2274
+MTR-AVAQPPLFWRAEQLDAWRRWQRTQWPLARRAADLVRGGVARSRGAV-------QAP
+DAGLRLLLPAGDVHTLIAVESAGPTQRAALVEPTRALAEGRTGLDAAARTRLLGGVAWVV
+PADVAGALLPDLPAAAQLTGHAADPDTVGTRLAGLERVLVAGEYLPAGRAAVRWAHERGA
+SVHVVQHGLLAVSTPPVPRDATLYAFTARDADWWTQGRADVRAVPVGSALLEAARRGAAS
+ADPTATGSTGPGPGLFLGQLHGAELPRAQFAAAAEQYVRTTGAVYRPHPAERDRLSRAQH
+ARWEGAGIAVDRSGAPLTQTAGPVAAVFSTGILEAAQTGRPAWAVHPDPPRWLVEFWDRY
+GITRWMPGADPTPTPALVAPTADPAAAIARDLWKEHA
+>4_482
+M-----TDAPLFWRSEDLPRWHAWQRAQWPLTRRAADTARSTVRGVAGALTRRR---STG
+DDAPRLYLPAGDVHTLVALESFGPTQLAALASPVAALATAR--------PEAAAGVGWVL
+PA----GDAPALPGAVGHREHAATADVVTDRLSGLRRVLVAGEYLPSGRAAVRWARQRGA
+RIGVVQHGLLAVSTPPVPQDATLYAFTSADADWWTQGRADVEAVPVGSVLLEQARRTA--
+--PALSGAGDDGPGVFLGQLHGAELPRRDFAAAAEQYVRATGAAYRPHPAERDRLSRGQH
+AAWRRAGVRIDDAGAPLVATRGPVAAVFSTGILEAAQAGRPAWAVHPEPPAWLEGFWRRY
+GMTRWRPGRTPEPTPPLASPTADPAAAIAEHVWKESA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000526.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000526.fa
new file mode 100644
index 0000000000000000000000000000000000000000..79119a4f6330bced09388024fe5d5c4afd8d0b84
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000526.fa
@@ -0,0 +1,41 @@
+>0_490
+MT-----------DMTRGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTF
+PEFKDARIITSPLNRVGVLRKDPRRALPLLPLASSLLHVKEPVAVVSTSGWAHGFRYDGA
+TLVYCHTPARWVYLLDDYLGEGGRNSIKGRIARALRPGLRRWDRAAVRRRSRYVANSTVV
+KERIEDVYGLDGVDLVFPPHSVSTDGPQEPIPGAERLAEDGFLLSVARLMPYKHVDVAIE
+AAARAGRPLVVIGKGPEEARLRAMAGEDVVFGQDLTDAQLRWAYAHAIALIAASHEDFGI
+TPLEASAWGVPTVALRAGGYLDTIVDGVNGTFVLDASIDAVGEGIKKLQAARWDTAAMRR
+HVEKFSEREFALRIRALVEGLPGA-------
+>1_219
+MS-----------EQTPATIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTF
+PEFEDAHIVTSPLNRVGVLRKDPRRALPLLPLASSLMHVKEPIAVVSTSGWAHGFRYDGA
+TLVYCHTPARWVYLLDDYLGEDGRNSIKGRIARVLRPGLRRWDRAAVRRRSRYVANSTVV
+KKRIDDVYGLDGVDLVFPPHSVSTDGPQGPIPGAEQLAEDGFLLSVARLMPYKHVDVAIE
+AAARAGRPLVVIGKGPEEARLRAMAGEDVVFGQDLTDAQLRWAYAHATALIAASHEDFGI
+TPLEASAWGVPTVALRAGGYLDTIVDGVNGVFVEEPTVDAVAGGVERLLAHDWDRAAMQA
+HAERFSEAQFGRRIRALVAESPAGPAHRGRQ
+>2_2385
+MT-----------DTTRGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTF
+PEFKDARIITSPLNRVGVLRRDPRRALPLLPVASSLMHVKEPVAVVSTSGWAHGFRYHGD
+TLVYCHTPARWVYLLEDYLGEEGQKSMKGRVARVLRPGLRAWDRAAQRRRTRYVANSTVV
+KERIEEAYGLTDVPIVFPPHSVSTDGSQEPIPGAEHLAEGGYLLSVARLMPYKHVDVAIR
+AAERTGLRLLVIGKGPDEARLKAMAGDGVVFAQDLTDAQLRWAYAHATALIAASHEDFGI
+TPLEASAWGVPTVALRAGGYLDTITEGVNGVFVEAPTVEAVTDGVEQALARDWDPPAMRA
+HAERFSEDQIARQVRTQLGQLQNHARNKGAM
+>3_2267
+MKIHASRPLSARRASQPGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYNPEGTF
+PEFKKARIITSPLNRVGVLRSDPRRALPLLPLASSLMHVKEPLAVVSTSGWAHGFRYEGD
+TLVYCHTPARWVYLLEDYLGEGGQRSLKGRVARALRPALRAWDSAAQLRRTRYVANSTVV
+KRRIEEVYGVANVDLVFPPHSVSTDGPQAPIPGAEDLAEGGYLLSVARLMPYKHVDVAIR
+AAERTGRRLLVIGKGPEEARLRALAGQGVVFAQDLTDAQLRWAYAHAVALIAASHEDFGI
+TPLEASAWGVPTVALRAGGYLDTIVEGVNGVFVPEPTVEAVTDVVEQVLAQDWDRGAMQA
+HAEHFSEVAFRERLARLLDDPHGAV------
+>4_489
+MT-----------DTTRGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTF
+PEFKDARIITSPLNRVGLLRKDPRRALPLLPLASSLMHVKEPIAVVSTSGWAHGFRYDGA
+TLVYCHTPARWVYLLDDYLGEGGRDSIKGRIARVLRPGLRRWDRAAVRRRSRYVANSTVV
+KERIEEVYGLIDVPVVFPPHSVSTDGPQEPIPGAEHLAEGGYLLSVARLMPYKHVDVAIR
+AAERTGLRLLVIGKGPEEARLKAMAGDGVVFAQDLTEAQLRWAYAHATALIAASHEDFGI
+TPLEASAWGVPTVALRAGGYLDTIVEGVNGVFVNGTSVAAVAGGIEWVRAHNWDRAAMRS
+HARRFSEFEFGQQVQAQLGWIGISR------
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000537.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000537.fa
new file mode 100644
index 0000000000000000000000000000000000000000..90e11f36cc41aa0ae5ef37005e893080bcb27d6f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000537.fa
@@ -0,0 +1,36 @@
+>0_512
+MDALRLVSIAAVVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVWGRFRS
+LMVPYLVWAALMSVAAFAWFAD---DPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFT
+TVLRRFLERFPSAVAWAVGLAGLAWAHLVPDSAIARTPLGVGLALPCLLFVLSGEMFRRR
+VQPHVRRHRTLIGVGLVLLGMVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFG
+STVERLLRSFARRTGTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALA
+LALSWLAGLALLATPLSKPFTGARRRWHPVHRLRHVEPPHPVTSALPRVTTASERTHP
+>1_245
+-----------MVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVWGRFRS
+LMVPYLVWAALMSVAAFAWFAD---DPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFT
+TVLRRFLERFPSAVAWAVGLAGLAWAHLVPDSAIARTPLGVGLALPCLLFVLSGEMFRRR
+VQPHVRRHRTLIGVGLVLLGMVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFG
+STVERLLRSFARRTGTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALA
+LALSWLAGLALLATPLSKPFTGARRRWHPVHRLRHVEPPHPVTSALPRVTTASERTHP
+>2_2361
+MDALRLVSIAAVVLGHAYLADLTFSRYLEIWRMPLFFFLTGYFWTRGRPVARDARGRFKA
+LMVPYLVWAVVMSAAALAWFGD---DPERLQRLMAAGWYGGADQEPPWWAFWFISVLFFA
+TVLRRFLERFPTAVAWGVGLAGLAWAYLVPESAIARTPLGVGLALPCLLFILSGEAFRRR
+VQPRIRRHRTLLGLALVGLGLAAVALGLEPHNIKFGGFGTPLLTPLVGVLMSAGMVLVFG
+AAVERILREFARRTGSGQALRRVITALVRTGTVVVLLHGWVLMWVMRQGVEDNLLKFVLA
+LGISWLVGLALLATPLSKPLTGARRRWFPLHRLRGEEPPHPPTSALPRVTTASERTHP
+>3_2242
+MDALRLVSISAVVLGHAYLADLTFSPYLEIWRMPLFFFLTGYFWTRGRPWAADALSRFRS
+LMVPYLLWSVLMTLVVLSWSRRSQIDGVTLADLVSAGWYGGADQPPPWWAFWFISVLFFV
+ALLRRALERAPSWAGWAVALAGLAAAELVPESAIARTPLGIGLAAPCLFYVLAGEAFRRR
+VQPRIRRHRTLIGVALVAAGVGAVALGLPPHNIKWGGFGLFPWTPLTGIAMAAGMVLVFG
+AFVERRLRAFARDTGTGRAIRAGITALTRTGTVVVLLHGLVLMEAMRVGIEDNLMKFVVA
+LTVSWAVGLALLATPLARPLTGVPQQWFPFGREAGA----------------------
+>4_515
+MDALRLVSIAAVVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVRGRFRS
+LMVPYLVWAALMSVAAFAWFAD---DPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFT
+TVLRRFLERFPSAVAWAVGLAGLAWAHFVPDSAIARTPLGVGLALPCLLFVLSGETFRRR
+VQPHVRRHRTLIGVGLVLLGLVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFG
+STVEGLLRSFARRTGTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALA
+LALSWLAGLALLATPLSKPFTGARRRWHPVHRLRRVEPPHPVTSALPRVPTASERTHP
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000538.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000538.fa
new file mode 100644
index 0000000000000000000000000000000000000000..19e1ffb1d3c673879348f323a0f0eaa4dcdfd639
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000538.fa
@@ -0,0 +1,26 @@
+>0_514
+M--TVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELA
+GSDVLTCTVIGFPLGANASEVKAFEARQAIDAGADEVDMVLDVAAARAGDRDRLVADVRA
+VAEAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATV
+EHVALMRRTVGERIGVKASGGVRTRADALAMIEAGATRIGASSALAILGSD
+>1_247
+M--TVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELA
+DSDVLTCTVIGFPLGANTSEVKAFEARQAIDAGADEVDMVLDIAAARAGDRARLVADVRA
+VAEAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATV
+EHVALMRRTVGEDIGVKASGGVRTREDALAMIEAGATRIGASSALAILGSD
+>2_2359
+M--TRTLSTAELAQYIDATALKTETSEADVRRLVAEARQAGVKSVCVNPRWVPLVSAELA
+GSDVLTCTVIGFPLGANASEVKTFEARQAIEAGAHEVDMVIDVAAARAGDRARLVEDVRA
+VAEAAHAAGPAGQGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATV
+EHVALMRRTVGEHVGVKASGGVRTREDALAMIEAGATRIGASSALAILGTD
+>3_2241
+MSETPQLTTAELAKHIDHTLLKPEASREDILRVVAEAREAGVKSVCVNPRWVREVRAGLE
+GSDVLTCTVIGFPLGASSSAVKAFETTQAIADGADEVDMVIDIAAARAGDRARLEEDVRA
+VVAAAHASGPAGRAGTLVKVIIETALLDDAAKVLACEAAVAAGADFVKTSTGFSTGGATV
+EDVALMRRTVGPEIGVKASGGVRSREDALAMITAGATRIGASSALAILGDD
+>4_517
+M--TVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELA
+GSDVLTCTVIGFPLGANASEVKAFEARQAIDAGADEVDMVLDVAAARAGDRDRLVADVRA
+VAEAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATV
+EHVALMRRTVGERIGVKASGGVRTRADALAMIEAGATRIGASSALAILGSD
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000542.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000542.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3d3267feb2c694ea8d13447f70b1b2d42b951077
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000542.fa
@@ -0,0 +1,46 @@
+>0_518
+MSHSTPPVNPGAPTDLTSDAVATAEEVPRSRVIIASLVGTSIEFYDFYIYATAAVSVFPL
+IFFAGGDDNTALLASMATFGAAFIARPLGAVVFGHLGDRVGRKTTLIGSLLTMGIATFLI
+GLLPTYFQIGLWAPAMLTLLRFFQGLGLGGEWSGAALLATEYAKDGKRAQAAMWPQLGAP
+IGFLLANGLFLALVLGFDHDSTNPVLDGPFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP
+VFQRALDRDQRVKAPLSEVFRRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKPANGF
+LGVPYAEFLVLQLVGILFFAAFVPVSGLLADRFGRRPTLIVISVLMVLFGLSFGLWLSPE
+NMGVGAELNGPLMVAFLATGMTLMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA
+ALTPFIAAWLVQKFDVSYVGYYLAAASAITVIALVLSPETRHTDLDTVTSARERRAA-R
+>1_251
+MSHSTPPVNPGAPTDLTSDAVATAEEVPRSRVIIASLVGTSIEFYDFYIYATAAVSVFPL
+IFFAGGDDNTALLASMATFGAAFIARPLGAVVFGHLGDRVGRKTTLIGSLLTMGIATFLI
+GLLPTYFQIGLWAPAMLTLLRFFQGLGLGGEWSGAALLATEYAKDGKRAQAAMWPQLGAP
+IGFLLANGLFLALVLGFDHDSTNPVLDGPFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP
+VFQRALDRDQRVKAPLGEVFRRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKPANGF
+LGVPYAEFLVLQLVGILFFAAFVPVSGLLADRFGRRPTLIVISVLMVLFGLSFGLWLSPE
+NMGVGAELNVPLMLAFLATGMTLMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA
+ALTPFIAAWLVQKFDVAYVGYYLAAASAITVIALALSPETRHTDLDTVTSARERRAA-R
+>2_2355
+MSRTT------TPADGTAAGLEAAAEVPRGRVITASLVGTSIEFYDFYVYATAAVSVFPL
+IFFPGDDQTTALLASFAVFGTAFVARPIGSVLFGHFGDIMGRKVTLIGSLLTMGIATFLI
+GLLPTAFQIGLWAPAMLVVLRFCQGLGLGGEWSGAALLATEYAAEGKRARAAMWPQLGAP
+IGFFLANGLFLALVIGFGHDSTNPDHDGAFLNWVWRLPFLLSIVMVAVGLYVRVKLEETP
+VFQRAIANDTRVKAPLGEVFKRNWWELILGTFIMYATYVLFYLMTTWILSYAIGKTENGM
+LGVPYAEFLVLQLIGILFFAAFVPASGWLADRFGRKPTLLTVSALMVLFGLSFGLWLSAE
+RMGTGAGVNVPLMLAFLAVGMALMGLTFGPMSAVLPELFPTNTRYTGSGISYNVSSILGA
+ALTPFLAAWLVKEYGVAYVGYYLAAASVITMIALALAPETRHTDLDGVTSARERRAASV
+>3_2237
+MSHTT----------ARSAEAPSVEDVPKSRVILASLVGTSIEFYDFYVYATAAVSVFPL
+IFFPGDDPTTALLASFAVFGTAFVARPIGSILFGHFGDRMGRKVTLIGSLLTMGIATFLI
+GLLPTAFQIGLWAPAMLVVLRFCQGLGLGGEWSGAALLATEYADHGKRARAAMWPQLGAP
+IGFLLANGLFLILVRAFGHDSTNPQLEGSFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP
+VFQRALEDDTRVKAPLGEVFKRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKTQNGM
+LGVKYADFLVLQLVGILFFAAFVPVSGWLADRFGRKPTLLVVSGLMVVFGLSFGAWLSPA
+AMGQGDALNVPSMLAFLAVGMALMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA
+ALTPFLAGWLVKEFGVATVGWYLAIASVITMAALALSPETRHADLHEVTSARERRAAAR
+>4_521
+MSHSTPPVNPGAPTDLTSDAVATAEEVPRSRVIIASLVGTSIEFYDFYIYATAAVSVFPL
+IFFAGGDDNTALLASMATFGAAFIARPLGAVVFGHLGDRVGRKTTLIGSLLTMGIATFLI
+GLLPTYFQIGLWAPAMLTLLRFFQGLGLGGEWSGAALLATEYAKDGKRAQAAMWPQLGAP
+IGFLLANGLFLALVLGFDHDSTSPVLDGPFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP
+VFQRALDRDQRVKAPLGEVFRRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKPANGF
+LGVPYAEFLVLQLVGILFFAAFVPVSGLLADRFGRRPTLIVISVLMVLFGLSFGLWLSPE
+NMGVGAELNVPLMLAFLATGMTLMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA
+ALTPFIAAWLVQRFDVSYVGYYLAAASAITVIALALSPETRHADLDTVTSARERRAA-R
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000546.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000546.fa
new file mode 100644
index 0000000000000000000000000000000000000000..703491a3468d06b3acf33577cac38496ca09c581
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000546.fa
@@ -0,0 +1,40 @@
+>0_523
+MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELDALAVHRTTAFGMDAKHPAGD
+GLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQEFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVL
+ASGMIPQISLIMGPSAGGAAYSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE
+DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLEVIASIVDEGHLLQLQELYAPNVITGL
+ARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAFNIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATV
+PKLTVITRKAFGGAYIVMGSKKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN
+PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL
+>1_257
+MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELDALAVHRTTAFGMDAKHPAGD
+GLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQEFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVL
+ASGMIPQISLIMGPSAGGAAYSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE
+DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLAVIASIVDEGHLLQLQELYAPNVITGL
+ARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAFNIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATV
+PKLTVITRKAFGGAYIVMGSKKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN
+PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL
+>2_2348
+MSDPDLTTTAGRLADLHRRLEATAAPGGEGAVERQHARGKHTARERIDLLLDEGSFVELDALAVHRTTAFGMDAKHPAGD
+GLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQEFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVL
+ASGMIPQISLIMGPSAGGAAYSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNSTSGTAHYMASSEE
+DAIAYVQELLELLPSNNLAEAPTFEAADPETTDEDLALDEIVPDSANQPYDMLEVIGAIVDEGHLLQLQELYAPNVITGL
+ARLDGMSVGVVANQPQQLAGTLDIAASEKAARFVRFCDAFNIPILTLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATV
+PKLTVITRKAFGGAYIVMGSKKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATQDAGGDVDARRAEIVADYEAELLN
+PYQAAELGYVDAVVPPHATRGALIRALRATLHKREARPAKKHGNMPL
+>3_2231
+MSAPELSTTAGRLADLHRRLEATAAPGGEAAVERQHSRGKHTARERIDLLLDEGSFVELDALATHRTTAFGMDAKHPAGD
+GVVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQEFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVM
+ASGMIPQISLIMGPSAGGAAYSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNSTTGTAHYMATSEE
+DAIAYVQDLLEYLPSNNLAEAPVFEAESLEETEQDLALDTIVPDSANQPYDMLEVIAALVDDGHLLQLQEMYAPNVITGL
+ARLDGMSVGVVANQPQQLAGTLDIAASEKASRFVRFCDAFNIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATV
+PKLTVITRKAFGGAYIVMGSKKLGADLNLAWPSAQIGVMGPQGAVNILYRRELAAAEAAGEDVEARRAQIVADYEAELLN
+PYQAADLGYVDAVVPPRQTRAHLVRALRATFHKREARPAKKHGNMPL
+>4_526
+MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELDALAVHRTTAFGMDAKHPAGD
+GLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQEFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVL
+ASGMIPQISLIMGPSAGGAAYSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE
+DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLEVIASIVDEGHLLQLQELYAPNVITGL
+ARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAFNIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATV
+PKLTVITRKAFGGAYIVMGSKKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN
+PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000550.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000550.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2afcd2d740079cc55f34fa0abf7ccbde6702f47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000550.fa
@@ -0,0 +1,36 @@
+>0_528
+M----------SARTTVPGLLVVAKAAARAGADVLARRWTGHHPAVPLGIEEIGAQTKSS
+GSDWVTDYDRRAEQAVREVVAGYRPSDEITGEEYGATRPAEPSGYRWSIDPLDGTTNFVR
+GLPQFCTSVAVTGPVDAETADLLGVAEGTERWLAGVVAAPALGRTWYASAGRGAFSTADA
+TTAGVDLPDRDAAPVRLTGPLPGRSGRLLATGFGYDPARRALQVRALAALLPAFGDVRRI
+GSAALDLCMVADGTLDAYAEFGTQEYDWAAGALVAEEAGVAVTRPASADGTAHPDWMVAG
+DVDGSALAAMTGERA
+>1_262
+M----------SARTTVPGLLVVAKAAARAGADVLARRWTGHHPAVPLGIEEIGAQTKSS
+GSDWVTDYDRRAEQAVREVVAGYRPSDEITGEEYGATRPAEPSGYRWSIDPLDGTTNFVR
+GLPQFCTSVAVTGPVDAETADLLGVAEGTERWLAGVVAAPALGRTWYASAGRGAFSTADA
+TTAGVDLPDRDAAPVRLTGPLPGRSGRLLATGFGYDPARRALQVRALAALLPAFGDVRRI
+GSAALDLCMVADGTLDAYAEFGTQEYDWAAGALVAEEAGVAVTRPASADGTAHPDWMVAG
+DVDGSALAAMTGERA
+>2_2341
+MSSPTRVAHVPSQPPGISGLLVVAKAAARAGADVLARRWTGHHPAVPLGREEIGAETKTS
+GSDWVTDYDRRAEQAVREVLVAYRPQDEITGEEYGATVPAEPSGLRWSIDPLDGTTNFVR
+GLPQFCTSVAVTGPVDEETAALLGVPAGTRRWLAGVVAAPALGRTWFASAGRGAFSTADA
+TTAGVDVPDRDAAPVRITGPAPGRSGRLLATGFGYDPARRAMQVRALAALLPAFGDVRRI
+GSAALDLCMVADGTLDAYAEFGTQEYDWAAGALIAEEAGVRVRRPASGDGTAHPDWMVAG
+DVDEAALAAAQEETA
+>3_2225
+M------SAAPARPASPAGLLVIAKAAARAGADVLAERWAGHHPAVPLTSDELGADTKSS
+GSDWVTDYDRRAEDAVRAVLTGYRPHDEITGEEHGSTAPVEPSGYRWSIDPLDGTTNFIR
+GLPQFGTSVAVEGPVDEETAALLGVLPGSRRWLAGVVAAPALGRTWFASAGRGAFSTADA
+TTAGVAVPDRDAAPVRLTGPVPGRSGRLLATGFGYHPGRRAMQLRALAALLPAFGDVRRI
+GSAALDLCMVADGTLDAYAEFGTQEWDWAAGALIADEAGVPVDRPASGDGTGHPDWMTAG
+DVDAAALAAAKEATA
+>4_531
+M----------SARTTVPGLLVVAKAAARAGADVLARRWTGHHPAVPLGIEEIGAQTKSS
+GSDWVTDYDRRAEQAVREVVAGYRPSDEITGEEYGATRPAEPSGYRWSIDPLDGTTNFVR
+GLPQFCTSVAVTGPVDAETADLLGVAEGTERWLAGVVAAPALGRTWYASAGRGAFSTADA
+TTAGVDLPDRDAAPVRLTGPLPGRSGRLLATGFGYDPARRALQVRALAALLPAFGDVRRI
+GSAALDLCMVADGTLDAYAEFGTQEYDWAAGALVAEEAGVAVTRPASADGTAHPDWMVAG
+DVDGSALAAVTGERA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000555.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000555.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89928039da944952fec095bb4b6fade5aadff1d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000555.fa
@@ -0,0 +1,41 @@
+>0_534
+MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL
+RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLASALAERDVSWAVPVALSDPVSAG
+PGAAVLQRFLPGGPYPPHEGDPDVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPAR
+ARHVAALPGAVAARLGAWEGH------------DVDARLGAEAWPDAVAALTDAVTTWTA
+APPVPPSLVHGDLAGHNMRWR-----AVPEDEDPRAPLRWALAGVLDWDLACAWGPALNV
+AYLALWHGEQKVPDLARDAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLR
+KTLPRVARALTALDG
+>1_268
+MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL
+RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLAAALAERRVPWTVPIALSDPVPAG
+PGAAVLQRFLPGGPHPPHEGDPAVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPER
+ARHVAALPGAVAARLGAWEGH------------DVDARLGAEAWPDAVAALADAVTTWTA
+APPVPPSLVHGDLAGHNMRWR-----AVPEDEDPRAPLRWALAGVLDWDLACAWDPALNV
+AYLALWHGEEKVPDLARDAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLR
+KTLPRVARALTALDG
+>2_2333
+MASDPVDSELELVHRALGRLRPHVSPADARALHEADWSAGTVEEGGQFNRVLVCAGAGVL
+RMTRAHEVGAAPAARWSPERDPARQLGRRMALLDGLDAALAEQGVAWTVPVALSDPVPAG
+TGAAVLQRYLPGGPHPPHEGDPAVLRRLLDEIAAVDVADPRIAPHLGRPFSFRGPWTAQR
+AEHVAGIPGRLAPRLGAWPGD------------DVDARTGADAWADAVARVTRAVTAWTE
+EPPVPPSLVHGDLAGHNMRWR-----AMPAADDAPGEVRWELAGVLDWDLACAWDPALNV
+AYLSLWHGEDQVERLAVDAGEAARARVWLGAMALETLDDAAARDELVGGLPNGSWRRLLR
+KALPRVARALTAL-G
+>3_2216
+MASDPARSELDLVAAALQRLRPGLDDGVAARLRGADWSAGRVEEGGQFHRVLVLEDVGVL
+RMTRVHEAGAAPAARWTPERDPAVHLPRRLALLDGLAAVLAEAGVRWSLPTALSAVVEDG
+PGAAVLQRYVPGFPHPPHEGDPAVLRGVLADLAAVDVADPRVAPHLGRPFTFRGPWTPER
+AAHVAGLPARLAPRLGAWPGDALGHAGDETAAGEAAVRLRADAWGESVTALTGVVSAWTR
+EPPVPPALVHGDLAGHNMRWRVVPAAATPDAEVPDAPVRWELAGVLDWDLACAWDPALNV
+AYLGLWHGEDLVEAIAADPAEARRARVWLGAMALETLDDAGARDVLVGGLAESSWRRLLR
+KTLPRVGRALAAAAA
+>4_537
+MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL
+RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLAAALAERRVPWTVPIALSDPVPAG
+PGAAVLQRFLPGGPHPPHEGDPAVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPER
+ARHVAALPGAVAARLGAWEGH------------DVDARLGAEAWPDAVAAVTDAVTAWTA
+APPVPPSLVHGDLAGHNMRWR-----AVPEDEDPRAPLRWALAGVLDWDFACAWDPALNV
+AYLALWHGEEKVPDLARDAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLR
+KTLPRVARALTALDG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000563.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000563.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9b86bb5220f6b800a926888fcae37a23bea4c4a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000563.fa
@@ -0,0 +1,46 @@
+>0_542
+MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE
+DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHRRHRQDHLLEAFEAKKGRPAEGMA
+EIVCPDCGTQGAWTEPQLFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGAARK
+KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAGQHFDRWVEDCWDWFID
+LGIDPAHLRKFDVPADERAHYSDATIDLEYDFGFTGGDGWGELMGIANRTDYDLGRHTEH
+SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGVDVRTVLKLD
+PRLAPVKAAVLPLSKKPELQPTTQSLAAELRTLWNIETDDSGAIGRRYRRQDEIGTPFCI
+TVDFDTLEDQAVTIRERDTMAQERVALSQVKSYLLERLVK
+>1_276
+MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE
+DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHRRHRQDHLLEAFEAKKGRPAEGMA
+EIVCPDCGTQGAWTEPQLFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGAARK
+KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKQHFDRWVEDCWDWFID
+LGIDPAHLRKFDVPAEDRAHYSDGTIDLEYDFGFTGGDGWGELMGIANRTDYDLGQHTTH
+SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGVDVRTVLKLD
+PRLAPVKAAVLPLSKKPELQPATQSLAAELRGLWNIETDDSGAIGRRYRRQDEIGTPFCI
+TVDFDTLEDQAVTIRERDTMAQERVALSQVKSYLLERLVK
+>2_2325
+MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE
+DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHKRHRQDHLLEAFEAKKGRPSASMD
+EIVCPDCGTKGAWTEPQMFSGLVKTFLGPVDNEEGLHYMRPETAQGIFVNFLNVLGASRK
+KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKQHFDTWVEACWDWFID
+LGIDPENLRRLDVPEEERAHYSDGTIDLEYRFGFGGGDGWGELMGVANRTDYDLGRHTEH
+SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGTDVRTVLKLD
+PRLAPVKAAVLPLSKKPELQPATQALAAELRALWNIETDDSGAIGRRYRRQDEIGTPFCI
+TVDFDTLEDQAVTIRERDTMSQERVALSQVKSYLLERLVK
+>3_2208
+MAAKSPLDNVINLAKRRGFVFQAGDIYGGSRSAWDYGPLGVELKENIKAEWWRTFVRSRE
+DMVGLDSSIILPRQVWEASGHVATFTDPLVECQQCHRRHRQDHLLEAFEAKKGRAAAGME
+EITCPDCGTTGKWTEPQMFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGASRK
+KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKEHFDTWVEACWDWFID
+LGIDPANLRKFDVPEEERAHYSDGTIDLEYRFGFAGGDGWGELMGVANRTDYDLTSHANA
+SGAKLQYFDQANDVHYTPYVIEPSFGLTRSMMAFLVDAYTEDEAPNAKGGVDVRTVLKLD
+PRLAPVKAAVLPLSKKLELQEPSQRLAAELRAHWNIETDDSGAIGRRYRRQDEIGTPFCI
+TVDFDTLEDQSVTIRERDTMSQERVALAQVRAYLAERLTK
+>4_545
+MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE
+DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHRRHRQDHLLEAFEAKKGRPAEGMA
+EIVCPDCGTQGAWTEPQLFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGAARK
+KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKQHFDRWVEDCWDWFID
+LGIDPAHLRKFDVPADERAHYSDATIDLEYDFGFTGGDGWGELMGIANRTDYDLGRHTEH
+SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGVDVRTVLKLD
+PRLAPVKAAVLPLSKKPELQPATQSLAAELRTLWNIETDDSGAIGRRYRRQDEIGTPYCI
+TVDFDTLEDQAVTIRERDTMAQERVALSQVKSYLLERLVK
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000569.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000569.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09acbd0442b3ac24a2014b9f852e614869f45440
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000569.fa
@@ -0,0 +1,36 @@
+>0_555
+M-ADP-------------------------HPVLAASAPVLADPHPV---------LAAS
+APDLDPDALDAVRALVAAAERPVVLSGAGMSAESGIPTFRDARTGLWERFSAEELATEEA
+FLADPALVWSWYRWRARMVRARRPNPGHDAVAAWQRRTPGLEVVTQNVDDLHERAGARVL
+AHLHGSLFEHRCAECWAPADVDPGAP---ADEATAGSEADLEAMLREAPPACTVCGDGLI
+RPGIVWFGEMLPAEPWDRAFAALEDCDLCVVVGTSGIVQPAASLPFVALGAGAAVVEVNP
+VETELSGAVTHVLRGPAGAVLPALVAGVWPGPSGALSTARHVTW
+>1_296
+M-ADP-------------------------HPVLAASAPVLAASAPV---------LAAS
+APDLDPGALDAVRALVAAAERPVVLSGAGMSAESGIPTFRDAQTGLWERFSAEQLATEEA
+FLADPALVWSWYRWRARMVRARRPNPGHDAVAAWQRRTPDLEVVTQNVDDLHERAGARVL
+AHLHGSLFEHRCAECGAPADVDPGAP---SDVDAAGSEADLEAMLREAPPACPACGTGRI
+RPGVVWFGEMLPQEPWERAYEALERCDLALVVGTSGLIQPAASLPFVALGAGVAVVEVNP
+VKTELSGAVTHALRGSAGAVLPALVAGVWPGPSGALSTARHVTW
+>2_2302
+MPVEPGRDDVGPAGEAGRAVVGAGQRRRVVNPVAATPPSYLGRHYPVPMSHPSPGDLSET
+VPTAD---LDAVRALVAQARRPVVLTGAGMSAESGIPTFRDAQTGLWERYSPEQLATEDA
+FLADPDLVWSWYRWRARMVRARRPNPGHDAVAHWQRAVPGLEVVTQNVDDLHERAGARVL
+AHLHGSLFEHRCAECGAPADVDPGAP---ADAEAAGSEADLEAMLREAPPTCPACGTGRI
+RPGVVWFGEMLPQEPWERAYEALERCDLALVVGTSGLVQPAASLPFVALGAGAAVVEVNP
+VETELSGAVTHALRGSAGAVLPALVAGV----------------
+>3_2195
+--------------------------------------------------------MSPT
+QPS-DPAALGAVRRLILEAERPVVLTGAGVSAESGVPTFRDAQTGLWERYSPEQLATAEA
+FAADPSLVWSWYLWRARMVRAVEPNAGHRALAAWQARTPALRIVTQNVDDLHERAGADVL
+SHLHGSLFAFRCAECDTPADVDPSAVVALAESAAPGSEAGLEALMHLEPPLCAACRRGRV
+RPDIVWFGELLPERAWGDAQAALEECDLCVVVGTSGVVQPAASLPFLALGAGAPVVEVNP
+DRTALSDAMTHVLRGPAGTVLPALLG------------------
+>4_556
+M-ADP-------------------------HPVLAASAPVLADPHPV---------LAAS
+APDLDPGALDAVRALVAAAERPVVLSGAGMSAESGIPTFRDAQTGLWERFSAEQLATEEA
+FLADPALVWSWYRWRARMVRARRPNPGHDAVAAWQRRTPDLEVVTQNVDDLHERAGARVL
+AHLHGSLFEHRCAECGAPADVDPGAP---SDVDAAGSEADLEAMLREAPPACPACGTGRI
+RPGVVWFGEMLPQEPWERAYEALERCDLALVVGTSGLIQPAASLPFVALGAGVAVVEVNP
+VETELSGAVTHALRGSAGAVLPALVAGVWPGPSGALSTARHVTW
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000570.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000570.fa
new file mode 100644
index 0000000000000000000000000000000000000000..74f06ab49a8abc1638b8560888adec7e8bceea0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000570.fa
@@ -0,0 +1,40 @@
+>0_556
+MPTAPAPSEAAATPLHVAVRTLDAAALAAAGHTAATAVAAVYAHAVVRGAASFWLDSALPDPAEARWSVAGDGLDVLGEE
+QGRVPSPGPRLVRHDDPADPDRAWAGLAAAAAPRPVVGGEGLPLRGGLVGWLGYELGLADLGVTPPSRRAEDPAPLPAQF
+WVRPSRYVVADHAAGVLHCCVVSLDPTTAEAGADRWAADVRRALAAARRALETAAGDAVVPPPQDAVPGPRADEEAPGTW
+REDRAAYAEQIARCRAALHAGDSYELCLTTRFDADPGLRVDPLVLFHELAAHQPAPYAALLEHGTGSRRWAVVSASPERF
+LSGREGRYSTKPIKGTAARLADPAGDAEAARALAADPKTRAENLMIVDLLRNDLSRVCEPGSVQVPSLMAVESYASVHQL
+VSTVTGTARAGIEPVDVVRSLFPGGSMTGAPKRRSVELLAAWEASPRGVYSGALGMLSADGTTSLSVVIRTAVL------
+AGGRWSVGAGGAIVADSDPAAEHDEVLLKARGLRRALARAAGTGLPTTAPDIA-
+>1_298
+MPTAPAPSVAAATPLHVAVRTLDAAALAAAGHTAATAVAAVYAHAVVRGAASFWLDSALPDPAEARWSVAGDGLDVLGEE
+QGRTPSPGPRLVRHDDPADPDRAWADLAAAAAPRPVVGGEGLPLRGGLVGWLGYELGLADLGVTPPSPRPGDPASLPAQF
+WVRPSRYVVADHAAGVLHCCVVSLAPTAAETGADRWAADVRRALAAARRALETASGDVVVPPPRDAGPGPQADEEAPGTW
+REDRAAYAEQIARCRAALHAGDSYELCLTTRFDADPGLRVDPLVLFHELAAHQPAPYAALLEHGTGARRWAVVSASPERF
+LAGRAGRYSTKPIKGTAARLADPVADAEAARALAADPKTRAENLMIVDLLRNDLSRVCEPGSVEVPSLMAVESYASVHQL
+VSTVTGTARAGVEPVDVVRSLFPGGSMTGAPKRRSVELLAAWEASPRGVYSGALGMLSADGTTSLSVVIRTAVL------
+AGGRWSVGAGGAIVADSDPAAEHDEVLLKARGLRRALARAAGTGVPTTAPDVA-
+>2_2301
+-------------------------------------MAAVYAHAVQRGAGSFWLDSALPDPAEARWSVAGDGLDVLGEE
+QGRVPSPGPRLVRHADPADPERAWSDLAAAAAPRRVVGGEGLPLRGGLVGWLGYELGLADLGVRPPSRRAGDPAALPAQF
+WVRPSRYAVADHAAGTLSCCVVALDAAAAEAAADRWAADVRRALDAARRATQAAADDAAASEVRADVAPEAGTGEAAGAW
+REDRAAYDEHIARCHAALHAGDSYELCLTTRFDADPALRVDPLALFLELAAHQPAPYAALMEHGTGPRGWAVVSASPERF
+LAGRDGRYSTKPIKGTAARLPDPAADAEAARALAADPKTRAENLMIVDLLRNDLSRVCEPGSVQVPSLMAVESYATVHQL
+VSTVTGTARAGVAPVDVVRSLFPGGSMTGAPKRRSVELLAQWEDSPRGVYSGALGLLGADGAVSLSIVIRTAVL------
+AAGRWGIGAGGAIVADSTAEAEHEEVLLKARGLRRALARADGTARTTTAPPRSR
+>3_2194
+MPTAPGRPDASPAPLHVAVRTLDIATLAAVGHTAATAAGAVYAHAVQRGTASFWLDSALPDGGEARWSMVGDGVDVLGEE
+EGRIPSPGLRLIRHGDPADPDRAWADLAAAAAPREVHGGEGLPLRGGLVGWLGYELGLADLGVTPPPPRPGDPAALPAQF
+WVRPSRYAVADHVAGALSCCVVSLDADAAEAAADRWEADVRRALEAARTSTEEVEVDVDAP-------------EAPGVW
+REDGAAYAEQIARCRAALHAGDSYELCLTTRFDADPALRVDPLALFRDLAAHQPAPYAALMEHGTGAERWAVVSASPERF
+LSGRDGRYSTKPIKGTAARLPDPTEDAAAAAALAADPKTRAENLMIVDLLRNDLSRVCEPGTVQVPALMAVESYATVHQL
+VSTVTGVARAGVAPVDVVRSLFPGGSMTGAPKRRTVELLAAWEGSPRGVYSGALGMLGADGTVELSIVIRTAVLSPTTPD
+APARWSVGAGGAIVADSDAHAEHEEVLLKARGLRRALTRAAGTA----------
+>4_557
+MPTAPAPSEAAATPLHVAVRTLDAAALAAAGHTAATAVAAVYAHAVVRGAASFWLDSALPDPAEARWSVAGDGLDVLGEE
+QGRVPSPGPRLVRHDDPADPDRAWADLGAAAAPRSVVGGEGLPLRGGLVGWLGYELGMADLGVSPPSRRPEDPAPLPAQF
+WVRPSRYAVADHAAGVLHCCVVSLDPTAAEAGADRWAADVRRALAAARRDLETAAGDAVVPPPEDAGPEPRADEEAPGTW
+REDRAAYAEQIARCRAALHAGDSYELCLTTRFDADPGLRVNPLVLFHELAAHQPAPYAALLEHGTGARRWAVVSASPERF
+LAGREGRYSTKPIKGTAARLPDPAADAAAARALADDPKTRAENLMIVDLLRNDLSRVCEPGSVEVPSLMAVESYASVHQL
+VSTVTGTARAGVEPVEVVRSLFPGGSMTGAPKRRSVELLAAWEASPRGVYSGALGMLSADGTTSLSVVIRTAVL------
+AGGRWSVGAGGAIVADSDPAAEHDEVLLKARGLRRALARAAGTGVPTTAPDIA-
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000572.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000572.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e64043a7a7c1e98b7db71d86561b2528165ea2ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000572.fa
@@ -0,0 +1,26 @@
+>0_560
+MTITTLTRKTALTGTGMLAALALAACGTTSDNGDDGSASPEVDASSSLASTPATDDAS--
+GSA---TSSSASSASASSTAAAAGSDSATGQADDPAYAVIDAVLEKYGDGIIVAVDADDD
+DTTWEVDVVVGEEVKELDVTADGDITETDRESDLEDVQKAKDAEVTAQQALDTAREGRDG
+VTLDEMDLDDDNGTLQWEVGFDREDGSDGPEVEIDATSGEVLTVDEH
+>1_302
+MTITTLTRKTALTGTGVLAALALAACGTTADNGDDGSVSPEVDASSAVASTPATDDASTT
+SAS---ASSSASSTSASSTAAAASSGSGTGQADDPAYAVIDAVLEKHGDGIIVEVDANDD
+DTTWEVDVVVGEEVKELDVTADGDITETDRESDLEDVQKAKDAEVTAQQALDTAREGRDG
+VTLDEMDLEDDNGTLQWEVGFDREDGSDGPEVEIDATSGEVLTVDER
+>2_2298
+MNATSLARKTALTGTGLLAALALAACGTADDDTAANPQETAVQQSPTQAATTAPASAS--
+GSASASASGSASASASGSASPAAASGSVERQGDDPAYAAIDAILGLHDDGVIVEMDLDDD
+DAKWEVDVVVGDDVKEYDVTTGGQVSEGVRPQIDDDVRRAGEAQVTAETAISTALQGRTD
+QTVDEVDLDEEGGTLVWKVELDRENGEDGAEVKIDAKTGDVIEVEEG
+>3_2192
+MTITTLTRKTALTGTGVLAALALAACGTTADNGDDGSASLEVDASSAVASTPATEDASTT
+SAS----ASSASSAPASSTAAAAGRDSATGQADDPASAVIDAVLEKYGDGIIVGVDANDD
+DTTWEVDVVVDKEVKELDVTADGDITETDRESDPEDVQKAKDAEVTAQQALDTARKGRDG
+VTLDEMDLDDDNGTLQWEVEFDREDGSDGPEVEIDATSGEVLTVDEH
+>4_561
+MTITTLTRKTALTGTGMLAALALAACGTTSDNGDDGSASPGVDASSAVASTPTTDDAS--
+GSA----SSSASSASASSTAAAAGSGSATGQADEPAYAVIDAVLEKYADGIIVAVDANDD
+DTTWEVDVVVGEGAKELDVTADGDITETDRESDPEDVQKAKEAEVTAQQALDTAREGRDG
+VTLDEMDLEDDNGTLQWEVRFDREDGSDGPEVEIDATSGEVLTVDER
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000577.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000577.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f74b784e768680c78d5aa40284f0e561b72cd1e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000577.fa
@@ -0,0 +1,21 @@
+>0_612
+MTHHVSAMLDTYPKNVGNIDRQKLAECIQACFECAQTCTACADACLAEDMVADLRQCIRL
+NLDCADVCAATGRMLSRQTGNNVETTRALLEACRAACKTCGDECESHAQMHEHCKVCAEA
+CRRCEQACADLLVTLG
+>2_1952
+MTHHVNAMLDTHPKDLGGIDRQKLAECIEACFACAQTCTACADACLSEDMVAELRQCIRL
+NLDCADVCAATGAVLTRQTGEDASTVRALLEACRAACRSCGEECASHAGMHEHCAVCAEA
+CRRCEQACADLLAALG
+>3_2139
+MTHHVSAMLETYPKEVGNIDRQKLAECIQACFECAQTCTACADACLAEDMVADLRQCIRL
+NLDCAEVCAATGRVLSRQTGTNVETTRALLEACRAACKTCGDECESHAQMHEHCKVCAEA
+CRRCEQACADLLVTLG
+>4_569
+MTHHVSAMLDTYPKNVGNIDRQKLAECIQACFECAQTCTACADACLAEDMVADLRQCIRL
+NLDCADVCAATGRMLSRQTGNNVETTRALLEACRAACKTCGDECESHAQMHEHCKVCAEA
+CRRCEQACADLLVTLG
+>4_860
+MTHHVSAMLETHPKDLGGVDRRKLAECIEACLACAQTCTACADACLSDDMVAEMRRCIRL
+NLDCADVCGATAAVLTRQTGEDASTVRALLEACRTACRACGDECASHAEMHEHCKVCAES
+CRRCEQACADLLASLG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000590.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000590.fa
new file mode 100644
index 0000000000000000000000000000000000000000..90f8ff6a10258da3565f85e0362bae69a3248c10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000590.fa
@@ -0,0 +1,41 @@
+>0_632
+MTLVDHTRPTGGQSAGSPPPAGPAEAVMLQVLDTEGRRRPQPELDPWIEDVDADALAALY
+RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALRPDDFVFPSYRENGVALL
+RGVPALDLLRVWRGSTFSSWDPNETRVATQQIIIGAQALHAVGYAMGVQRDQADVATIVY
+FGDGATSQGDVNEAMVFSASYQSPVVFFCQNNHWAISEPVRLQTRRSIADRPWGFGIPSM
+RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA
+RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALEALEEDGADRLFDEIYAEPH
+QELERQRREHALYLQQFGDEEAGA
+>1_378
+MTLVDHTRPTGGQSAGSPLPAGPAEAVMLQVLDTEGRRRPQPELDPWIEDVDADALAALY
+RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALRPDDFVFPSYRENGVALL
+RGVPALDLLRVWRGSTFSSWDPNETRVATQQIIIGAQALHAVGYAMGVQRDQADVATIVY
+FGDGATSQGDVNEAMVFSASYQSPVVFFCQNNHWAISEPVRLQTRRSIADRPWGFGIPSM
+RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA
+RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALEALEEDGADRLFDEIYAEPH
+QELERQRREHALYLQQFDDEEAGA
+>2_2255
+MTLVDHTRPAGGEAATSPPPGEPAEAPMLQVLDAEGRRHAQPELDPWIEDVDADALAALY
+RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALREDDFVFPSYRENGVALL
+RGVPALDLLRVWRGSTFSGWDPQATGVATQQIIIGAQALHAVGYAMGVQRDQADAATIVY
+FGDGATSQGDVNEAMVFSASYRSPVVFFCQNNHWAISEPVKLQTRRSIADRPWGFGIPSL
+RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA
+RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALESLVEDGAELLFDEIYAEPH
+QELERQRREHALYLQQFDDEEAGA
+>3_2110
+MT--DVHLP---EQDA--PPRSDRPAEQLQVLTPDGRRSPSPELDPWLTDVDEEMLARLH
+RELTLVRRLDTEATHLQRQGRLALWPPLRGQEASQVGAAAALRPADHVFPSYRENGLCLL
+RGVEAGELLRVWSGSSFSGWDPAATGVATQQLVIGAQTLHAVGYAMGVQRDAADVSTLVC
+FGDGATSEGDVHEAMVFAASYQAPVVFFCQNNHWAISEPVGLQARRSIADRAWGYGIPAL
+RVDGNDVLAVLAAVRRGVDRAAAGAGPMFVEAVTYRMGAHTTADDPTRYQDPAELEAWAR
+RDPLERLTAHLRDVGADADAVVDASEAAADDLAARMRADLDALPEEGPEALFAHVYAEPH
+QELARQQRDLQLHLDGLDAGEEQA
+>4_602
+MTLVDHTRPTGGQSAGSPPPAGPAEAVMLQVLDAEGRRRPQPELDPWIEDVDADALAALY
+RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALRPDDFVFPSYRENGVALL
+RGVPALDLLRVWRGSTFSSWDPNETRVATQQIIIGAQALHAVGYAMGVQRDQADVATIVY
+FGDGATSQGDVNEAMVFSASYQSPVVFFCQNNHWAISEPVRLQTRRSIADRPWGFGIPSM
+RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA
+RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALEALEEDGADRLFDEIYAEPH
+QELERQRREHALYLQQFDDEEAGA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000598.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000598.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7bb399dde7223cb5ae2cf6dc2c7300ce61f6c380
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000598.fa
@@ -0,0 +1,46 @@
+>0_644
+MTHGSLTDYTLPAP-AP----AHDGGAPRAVALIGSTGSIGTQGLDVIAQDPARLRAVAL
+AGGANTTLLAEQAVRFEVEAVGSAAAGEEELRAALADAAARLG-RPAPRPVLFTGPRAAE
+QIAAWPGADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAARPGQLVP
+VDSEHSALAQALRGGTADEVRRLVLTASGGPFRGLDRAALHAVTPAQALAHPTWDMGRVV
+TTNSASLVNKALEVIEAHLLFDVPLDRIDVVVHPQSVVHSMVEFVDGSTLAQASPPDMRL
+PIALGLCWPRRLPGAAPACDWTRAATWTFEPLDEEAFPAVRAAKEAAAASPTHMAVFNAA
+NEESVDAFHAGALPFDGIVDTVRAVVADYAPEHVLAAAGHDPAPTGLTVDAVLAAEAWAR
+RAARARW
+>1_390
+MTHGSLTDYTLPAP-AP----ADDDGAPRAVALIGSTGSIGTQGLDVIAQDPTRLRAVAL
+AGGANTTLLAEQAVRFEVEAVGSAAAGEEELRAALADAAARLG-RPSPRPVLFTGPCAAE
+QIAAWPGADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAAAPGQLVP
+VDSEHSALAQALRGGTADEVRRLVLTASGGPFRGLDRAALHAVTPAQALAHPTWDMGRVV
+TTNSASLVNKALEVIEAHLLFDVPLDRIDVVVHPQSVVHSMVEFVDGSTLAQASPPDMRL
+PIALGLCWPRRLSGAAPACDWTRAATWTFEPLDEEAFPAVRAAKEAAAASPTHMAVFNAA
+NEESVDAFHAGALPFDGIVDTVRAVVADYAPEHVLAAAGHDPAPTGLTVDAVLAAEAWAR
+RAARARW
+>2_2242
+MTHGSLTDYTLPAAGAPSASNAHDDGAPRAVALIGSTGSIGTQGLDVIAQDPARFRAVAL
+SGGANTGLLAEQAVRFEVQAVGSATATEDELRAAIADAAARLGLKPAPRPALFTGPTAAE
+RIAAWKGADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAAAPGQLVP
+VDSEHSALAQALRGGTADEVRRLVLTASGGPFRGLDRAALAEVTPAQALAHPTWDMGRVV
+TTNSASLVNKALEVIEAHLLFDVPLERIDVVVHPQSVVHSMVEFTDGSTLAQASPPDMRL
+PIALGLAWPARVPGAAAGCDWTRAATWAFEPLDEDAFPAVRAAKEAAAASPTHMAVFNAV
+NEEAVDAFHDGRIRFDAIVDTVRAVVGEYEPARVLGAAGHGHVAQDLTVEAVLAAEDWAR
+TAARARW
+>3_2103
+MTHGSLTDYTFPADHGP----GASDGACRAVALVGSTGSIGTQGLDVIAQAPERFRAVAL
+SGGANTALLAEQAVAHGVEAVGSAAASEEELRAALADAAARLR-RPDPRPALFTGPEAAA
+RIAAWEGADTVLNGITGSIGLAPTLAALRAGHRLALANKESLIVGGALVKAAAAPGQLVP
+VDSEHSALAQALRGGTAGEVRRLVLTASGGPFRGFSAAQLAEVTPAQALAHPTWDMGRVV
+TTNSASLVNKALEVIEAHLLFDVPLERIDVVVHSQSVVHSMVEFTDGSTLAQASPPDMRL
+PIALGIGWPHRVLGAAAGCDWTQAAQWTFEPLDEAAFPAVSLAKEAAASSDTHMAVFNAA
+NEEAVDAFHGGRIRFDQIVETVRAVLGEYRPDGVLAAAGADP--DELTVEAVLAAEDWAR
+AAARGRW
+>4_614
+MTHGSLTDYTLPAP-AP----ADDDGAPRAVALIGSTGSIGTQGLDVIAQDPARLRAVAL
+AGGANTTLLAEQAVRFEVEAVGSAAAGEEELRAALADAAARLG-RPAPRPVLFTGPRAAE
+QIAAWPGADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAARPGQLVP
+VDSEHSALAQALRGGTADEVRRLVLTASGGPFRGLDRAALHAVTPAQALAHPTWDMGRVV
+TTNSASLVNKALEVIEAHLLFDVPLDRIDVVVHPQSVVHSMVEFVDGSTLAQASPPDMRL
+PIALGLCWPRRLPGAAPACDWTRAATWTFEPLDEEAFPAVRAAKEAAAASPTHMAVFNAA
+NEESVDAFHAGALPFDGIVDTVRAVVADYAPEHVLAAAGHDPAPTGLTVDAVLAAEAWAR
+RAARARW
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000601.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000601.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54d2e966d8837b5f98be84978f23a5bc2cf977ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000601.fa
@@ -0,0 +1,36 @@
+>0_647
+MTRLPPVPRWSPSTDREVRAATGDRVRLLTDADTAALAALSARAPVSNVFVDSLLEAGRL
+AGPRGGAA-GTLFLGI------DD-DAPGAGALRAAVWIGSNVVPVAASEAPDAGWAPGD
+AEALGAAAAALRRRYGSIYGPAGPVLAAGEALAAAGHRSRSVRPDQPLLVLG-TAGGIDP
+NPHVVQAQPHDFARVLPASAAMFEEELGFSPFAGGAAQYRDRVERLIHTGRVFIDPGP--
+-RDAGGPLRFKADIGLLSSRCAQIQGVWMAPAARGRGLAASAMAAVVDYVRLQAPVVSLY
+VNAYNTPALRTYERVGFERRGTFATVLY
+>1_393
+MTRLPPVPRWSPSTDREVRAATGDRVRLLTDADTAALAALSARAPVSNVFVDSLLEAGRL
+AGPRGGAA-GTLFLGI------DD-DAPGAGALRAAVWIGSNVVPVAASEAPDAGWAPGD
+AEALGAAAAALRRRYGSIYGPAGPVLAAGEALAAAGHRSRSVRPDQPLLVLG-TAGGIDP
+NPHVVQAQPHDFARVLPASAAMFEEELGFSPFAGGAAQYRDRVERLIHAGRVFIDPGP--
+-RDAGGPLRFKADIGLLSSRCAQIQGVWMAPAARGRGLAASAMAAVVDYVRLQAPVVSLY
+VNAYNTPALRTYERVGFERRGTFATVLY
+>2_2239
+MTRLPPVPRWSPSTDRQVRAATGGRVRLLTDADTPALAALSARAPVSNVFVDSLLEAGRL
+AGPRGGAA-GTLFLGIDAGEGRDD-DGAPVAGLRAALWVGSNVVPVAAAETPDAGWAPGD
+AEALGAAAVALRRRYGSLYGPAEPVLAVGSALAAAGHRARSVREDQPLLVLG-ADGAAET
+SPHVVQAHPRDFERVLPASAAMFEEELGFSPFLGGAAQYRDRVERLIRAGRVFIDPGP--
+-ADAGGPLRFKADIGLLSSRCAQIQGVWMAPAARGRGLAAAAMAAVVEYVRLQAPVVSLY
+VNAYNTPALRTYERVGFERRGTFATVLY
+>3_2100
+M---------------DLAAASDGRVRVLTDADTPALTALAAADPVANVHAASLLEAGRL
+AGPRGGRADGTLFLGV------EDPDRP--GALRSACWVGSTVVPLAGHD--------DD
+VPALAASVAALRRRFASVYGPAVTVLAVGRTLRDAGHRPRAVREEQPLMVHARTPGDLVP
+DPAVRAAAPGEWESVVPASAAMFEEELGFSPFLTGAAQYRDRVRRLVADGRVFTAPGEPV
+VDDPTSGVRFKADIGLLSASCVQVQGVWLHPSRRGRGEAAPAMAAAVALMARRAPAVSLY
+VNGFNTPALRTYERVGFERVGTFATVLY
+>4_617
+MTRLPPVPRWSPSTDREVRAATGDRVRLLTDADTAALAALSARAPVSNVFVDSLLEAGRL
+AGPRGGAA-GTLFLGI------DD-DAPGAGGLRAAVWIGSNVVPVAASEAPDAGWAPGD
+AEALGAAAAALRRRYGSIYGPAGPVLAAGEALAAAGHRSRSVRPDQPLLVLG-TAGGIDP
+NPSVVQAQPRDFARVLPASAAMFEEELGFSPFAGGAAQYRDRVERLIQAGRVFIDPGP--
+-RDAGGPLRFKADIGLLSSRCAQIQGVWMAPAARGRGLAVSAMAAVVDYVRLQAPVVSLY
+VNAYNTPALRTYERVGFERRGTFATVLY
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000604.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000604.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc26e81b66acbfaafb34d5139a8dd9e5e1856913
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000604.fa
@@ -0,0 +1,26 @@
+>0_650
+MDSTDRRDDLAELRTRVEEALAADDVVVEQVRATGTAEHRTVEVVLDRASGTQGLSLDDV
+ARLSGRVSAALDALGDHVPGVGAGEYLLEVTTAGVDRPLTEPRHFARNVGRLVEVSVDGA
+APVTARLKDVTDDDVELAVVRPPAKKGMKAKELPAERVALDRLGPAIVQVEWSPAQQAGD
+ADAAAGEDTAEHTEA
+>1_396
+MDSTDRRDDLAELRTRVEEALAADDVVVEQVRATGTAEHRTVEVVLDRASGTQGLSLDDV
+ARLSGRVSAALDALGDHVPGVGAGEYLLEVTTAGVDRPLTEPRHFARNVGRLVEVSVDGA
+APVTARLKDVTDDDVELAVVRPPAKKGMKAKELPAERVALDRLGPAIVQVEWSPAQQAGD
+ADAAAGEDTAEHTEA
+>2_2236
+MDSTDRHDDAASLRARVEEALASADVVVEEVRVAGAAAHPTVEVVVDRASGTEGLSLDEL
+AGLSGRVSAALDALGDHVPGVGAGEYLLELTTAGVDRPLTQPRHFARNVGRLVEVAVDGG
+EPFTARLLAADEDAVELAEVRPGAKKGMKAKELPAQRVELARLGPAVVQVEWTPAQQAAD
+A-AAAGEQTAEHTEA
+>3_2097
+METVP-----AALTELVEGAVSHRGVVVESVRVAGAADAPTVEVVLDRLEGTEGLSLDEV
+AELSGLVSDALDACGDEVPGVGAGEYLLEVSTAGVDRPLTGPRHWLRNVGRLVEVSIDAA
+LPVTARVLGVEASGVELEVVRPGAKKGMPAKVLPAEHVDFSRLGPGQVQVEWSTA-----
+AEQSGAEQTAEQTEA
+>4_620
+MDSTDRRDDLAELRTRVEEALAADDVVVEQVRATGAAEHRTVEVVLDRASGTQGLSLDDV
+ARLSGRVSAALDALGDHVPGVGAGEYLLEVTTAGVDRPLTEPRHFARNVGRLVEVSIDGA
+APVTARLKDVTDDDVELAVVRPPAKKGMKAKELPAERVALDRLGPAIVQVEWSPAQQAGD
+ADAAAGEDTAEHTEA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000622.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000622.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a0e4e54fec59f4a360894b38a4649b554a3488b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000622.fa
@@ -0,0 +1,26 @@
+>0_670
+MSAAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWGGDSLVARWVALALFAAAMY
+TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT
+LMRFVVIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPVVGGWWPWAGWVVIGAATVLTV
+LTGLEYVKDAWVLRRDALAAQRGA--
+>1_416
+MSTAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWGGDSLVARWVALALFAAAMY
+TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT
+LMRFVVIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPLVGGWWPWAGWVVIGAATVLTV
+LTGLEYVKDAWVLRRDALAAQRGA--
+>2_2208
+MSTGGEAERVSAWNLPNILTSVRILMVPLFAWALWAGGPWGGDSATARWIAVALFAAAMY
+TDKLDGDIARARGLITDFGKIADPIADKLLTGAALVLFSLLGELWWWVTVVILVREWGIT
+LMRFVVIRYGVMPAGRGGKLKTVLQAVGIGLLLMPLAPVVGGWWPWVGWTVIGAATVLTV
+LTGLEYVKDAWILRRDALAAPRGA--
+>3_2078
+M--NAQPERVSAWNLPNILTTVRILMVPFFVWAVWAGGPWGQDSLTARWIAVALFAAAMY
+TDKLDGDIARSRGLITDFGKIADPIADKLLTGSALVLFALLGELWWWVVIVILVREWGIT
+AMRFVVIRYGVMPAGRGGKLKTVLQAVGIGLLLMPLAPVLGGWWPWLGWTVIGAALALTV
+VTGVEYVRDAVRLRADWLASHPEARR
+>4_640
+MSTAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWSGDSLLARWVALALFAAAMY
+TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT
+LMRFVMIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPLVGGWWPWAGWVVIGAATVLTV
+LTGLEYVKDAWVLRRDALAAQRAA--
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000624.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000624.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a59618dc1d3e6c8cea2b121a7faf021f7c21d530
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000624.fa
@@ -0,0 +1,21 @@
+>0_673
+--------------------------------MPLLRHEIGDVLRDVRQLQGRTLREVSH
+DARVSLGYLSEVERGQKEASSELLASICQALDIPLSYLLREVSDRLVEQEGMVVPDTLPD
+DLT---DPSLGSLAGR
+>1_419
+--------------------------------MPLLRHEIGDVLRDVRQLQGRTLREVSH
+DARVSLGYLSEVERGQKEASSELLASICQALDIPLSYLLREVSDRLVEQEGMVVPDTLPD
+DLT---DPSLGSLAGR
+>2_2205
+MMRHPVQAHGITRWVDDQPRPRATTPDIKERSMPLLRHEIGDVLRDVRQLQGRTLREVSH
+DARVSLGYLSEVERGQKEASSELLASICQALEIPLSYLLREVSDRLVDQEGIQVPDTLPE
+DLTDAADPSLGTLAGR
+>3_2076
+MMRHPVQAHGITRWVDSQPRPSQPTPELKERSMPILRHEIGDVLRDVRQRQGRTLREVSH
+DARVSLGYLSEVERGQKEASSELLASICDALQIPLSFLLREVSDRLAEQEGVVVPDTVPA
+DMAEDGAADVAPLAVR
+>4_643
+--------------------------------MPLLRHEIGDVLRDVRQLQGRTLREVSH
+DARVSLGYLSEVERGQKEASSELLASICQALDIPLSYLLREVSDRLVEQEGMVVPDTLPD
+DLT---DPSLGSLAGR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000631.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000631.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c973148df7034e37b19146d4d67305660bcdb28b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000631.fa
@@ -0,0 +1,26 @@
+>0_683
+MVAVSSASHYFDADPSAPERRRTVRTRLAGRDVEVQTANGIFSPDGLDKGTAALFSAVPA
+PPARGRFLDVGAGWGPIALTLALRSPEAEVTAVEVNDRSLQLTRDNAAALGLDNLVALRP
+EDVPEGAEFDLIWSNPPIRIGKPALHALLERWLPRLAPGGEAWLVVQKNLGADSLLPWIG
+RMLEERAPGRFTAERADSVKGFRILRVARA----R
+>1_426
+MVAVSSASHYFDADPSAPERRRTLRTRLAGRDVEVQTANGIFSPDGLDKGTAALFSAVPA
+PPATGRFLDVGAGWGPIALTLALRSPEAEVTAVEVNDRSLQLTRDNAAALGLDNVVALRP
+EDVPEDAEFDLIWSNPPIRIGKPALHALLERWLPRLAPGGEAWLVVQKNLGADSLLPWIG
+RMLEERAPGRFTAERADSVKGFRILRVVRA----R
+>2_2196
+MVAVTSPAHYFSPDPGTPERRRSVDVELAGRRVTLQTANGVFSPDGIDKGTAALLSAVPA
+PPARGAFLDVGAGWGPLALTLALASPEAEVTGVEVNERSLALARDNAAAVGASNARFLTP
+EQIPDDARFDLIWSNPPIRIGKAALHDLLAQWLPRLAPGGEAWLVVQKNLGADSLLPWIA
+GMLQEQAPGEFTATRAATVKGFRILRISRAAESSS
+>3_2068
+MDAVTSPAHYFSPDPGTPERRRRVDVEIAGRRVTLQTANGVFSPDGIDKGTAALLSAVPA
+PPARGAFLDVGAGWGPLALTLALTSPEAEVTGVEVNERSLALARDNAAAVGAQNARFLTP
+EQVPDDARFDLIWSNPPIRIGKAALHDLLAQWLPRLAPGGEAWLVVQKNLGADSLLPWIS
+GMLQERAPGEFTATRAATVKGFRILRISRAAESSS
+>4_650
+MVAVSPASHYFDADPSAPERRRTLRTRLAGRDVEVQTANGIFSPDGLDKGTAALFSAVPA
+PPATGRFLDVGAGWGPIALTLALRSPEAEVTAVEVNDRSLQLTRDNAAALGLDNVVALRP
+EDVPEDAEFDLIWSNPPIRIGKPALHALLERWLPRLAPGGEAWLVVQKNLGADSLLPWIG
+RMLEERAPGRFTAERADSVKGFRILRVVRA----R
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000639.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000639.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d085d717e90b0b9eeb0ad3014838be2d200b39c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000639.fa
@@ -0,0 +1,26 @@
+>0_694
+MARPTTVPGVRPRVAVLDYGSGNVHSALRAVERAGAEVELTRDPQAVQEADGLLVPGVGA
+YASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERTAGMGEWPGVVAE
+LPAEVLPHMGWNTVRPPEGSALFAGIEDERFYFVHSYGVLEWEFDQTISAMRPPQVTWAH
+HGADFIAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL
+>1_434
+MARPTTVPGVRPRVAVLDYGSGNVHSALRAVERAGAEVELTRDPQAVQEADGLLVPGVGA
+YASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERTAGMGEWPGVVAE
+LPAEVLPHMGWNTVRPPEGSALFAGIEDERFYFVHSYGVLEWEFDQTISAMRPPQVTWAH
+HGADFIAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL
+>2_2188
+MARPTSVPGVRPSVAVLDYGSGNVHSAVRALERAGADVELTRDPEAVQSADGLLVPGVGA
+FASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERAEGMGEWPGVVEA
+LPAEVLPHMGWNTVRPPEGSALFAGIEDERFYFVHSYGVLRWEFDQTISAMRPPQVTWAH
+HGADFVAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL
+>3_2059
+MASPTSVPGVRPTVAVLDYGSGNVHSAVRAVEHAGARVELTKDPDAVLGADGLVVPGVGA
+FASVMEALRSSGGTRWIGRRVAGGRPVLGICVGHQVLFEAGVEHGVRTEGMGEWPGVVEP
+LPAATVPHMGWNTVRPAEGSALFAGIEDERFYFVHSYAVQSWEFDQGNEAMRPPQVTWSH
+HGADFIAAVENGPLSATQFHPEKSGDAGQALLRNWLETL
+>4_658
+MARPTTVPGVRPRVAVLDYGSGNVHSALRAVERAGAEVELTRDPQAVQEADGLLVPGVGA
+YASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERTAGMGEWPGVVAE
+LPAEVLPHMGWNTVRPAEGSALFAGIEDERFYFVHSYGVLEWEFDQTISAMRPPQVTWAH
+HGADFIAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000647.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000647.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa6317cf103745ac34ea3fe77f8b5297ee1e50ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000647.fa
@@ -0,0 +1,26 @@
+>0_702
+MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD
+VVDGDDGRVLFRLADPATFGRDRFAILDADGLPFANLVRQIAFLRTSVNVEVVDGTCFAV
+TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRSNG
+>1_442
+MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD
+VVDGDDGRVLFRLADPATFGRDRFAILDADGLPLAHLVRQFAFLRTSVNVEVVDGTCFAV
+TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRSNG
+>2_2179
+MNTAFDAGRLGRTDVLTLQQVTSFMSNDMQVTGPDGQTVATVVTTGGGLGRMVLGSRTFD
+VVDGEDGRVLFRLADPATFGRDRYAIVDADGLPLANLVREFALFRTSVSVEVVDGTRFAV
+TGNLWDHDYTMTVGQAPIARATATFGGFMNALAGRSRYELRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRRNN
+>3_2051
+M-TTFDAGRLALVNSLALQQVTSFLSNDMQVLGPDGEVVATVQTQGGGLSRMLMGSRRLL
+VCDGDDGRPLFELQDPATFGRDRFQVLDPAGLPLANLRREVAFFRTAVSVEVVDGTVFRV
+EGDLFDHDYRMIAGEVPIARAVSQWSGFGNALLGRSRYRLELDPAMPPVVRCAVLGTAIA
+LDLLRAKDARRND
+>4_666
+MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD
+VVDGDDGRVLFRLADPATFGRDRFAILDADGLPFANLVRQIAFLRTSVNVEVVDGTCFAV
+TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRSNG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000649.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000649.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f7b4a2e791ff09ccfdf44bc40b65b1de54648d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000649.fa
@@ -0,0 +1,26 @@
+>0_704
+MAQIVLFHHALGLTDGVRALAEQI-ASGGHTVHTPDLYDGRTFATVDEGVAHAQHL-GFE
+EIGRRGMRACAEHQEASVVAGISMGVMPAWRAAQVVPGFRACIAMAGVLALDAYAPLWQP
+HTALQIHLGTRDPWALEGDLATARSYAATAEHPDRPADLFEYDTDRHLFMNSSTADFDAD
+LTAVLVRRIHELLA
+>1_444
+MAQIVLFHHALGLTDGVRALAEQI-AGGGHTVHTPDLYDGRTFATVDEGVAHAQHI-GFE
+EIGRRGMRACAEHQEASVVAGISMGVMPAWRAAQVVPGFRACIAMAGALALDAYAPLWQP
+HTALQIHLGTRDPWALEGDLETARSYAATAEHPDRPADLFEYDTDRHLFMDSSTADFDAD
+LTAVLVRRIHELLA
+>2_2173
+MAQILLFHHALGLTDGVRALAAQI-EAGGHTVHTPDLYDGALFTDVEEGIAHVESLGGFD
+VIAERGMRAAAQHPQASVVAGISMGVVAAHKAAQAVPAFRACIDIAGIVPLDAFAPLWQP
+HTALQVHLATRDPWVMDEDLPLARSVAATEEDPDKPAVLFEYDTDAHLFMDSSTDGHDPA
+LTEVLVRRIHELLA
+>3_2048
+MAQIILFHHARGLTEGVLALAEQIEQASGHHVHTPDLFGGAVLPTVEDGLAHLQQI-GQD
+EVMTRAMHACAEHKEASVVAGISMGVMPAWKAAQTAPGFRACIAMSSALPLDAYARLWQP
+HTSLQIHLAAQDPWVKDEDLPLARTYAATAEHPDRPADLFEYETASHLFMDSSTDQYDAR
+HTEVMVERIRELLA
+>4_668
+MAQIVLFHHALGLTDGVRALAEQI-ASGGHTVHTPDLYDGRTFATVDEGVAHAQHL-GFE
+EIGRRGMRACAEHQEASVVAGISMGVMPAWRAAQVVPGFRACIAMAGVLALDAYAPLWQP
+HTALQIHLGTRDPWALEGDLETARSYAATAEHPDRPADLFEYDTDRHLFMDSSTADFDAD
+LTAVLVRRIHELLA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000672.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000672.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6c8c5455aa685c310167d742be54286805612ee2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000672.fa
@@ -0,0 +1,41 @@
+>0_732
+MNGDVVGLLWLVVLLAANAFFVAGEFAVMGARRAQIEPRAEAGSRQAQVALYAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLVVPMAALGVPSAAADVTAFVLALLVVTFLHVTL
+GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPVVAALNWTANLVLHALRIEPKDEVASS
+YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHRAGDVMVPLERVVTVPEGITPHDFE
+WTVGRVGFSRFVVEDPDGGYTGYLHLKDVLTVGPSGHDEPIPLTRVRSLANVRLEDEVED
+ALALMQRTGSHLARVITPEGETAGILFLEDVLEELVGEINDVTQSPRRFRPA--------
+----------
+>1_471
+MNGDVVGLLWLVVLLAANAFFVAGEFAVMGARRAQIEPRAEAGSRQAQVALYAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLVVPMAALGVPSAAADVTAFVLALLVVTFLHVTL
+GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPVVAALNWTANLVLHALRIEPKDEVASS
+YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHRAGDVMVPLERVVTVPEGITPHDFE
+WTVGRVGFSRFVVEDPDGGYTGYLHLKDVLTVGPSGHDEPIPLTRVRSLANVRLEDEVED
+ALALMQRTGSHLARVITPEGETAGILFLEDVLEELVGEINDVTQSPRRFRPA--------
+----------
+>2_2122
+MNEDVIGLLWLVVLLVANAFFVAGEFAVMGARRSQIEPKAEAGSRPAQVALYAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLVGPMTALGVPDAAADVTAFVLALLVVTFLHVTF
+GEMVPKNAAVSFADRAVMILARPLVGLSKLLHPIVTVLNWAANVVLRAFRIEPKDEVASS
+YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHTAGDVMVPLEKVVTVPEGITPHDFE
+WTVGRVGYSRFVVEDPDGGYTGYLHLKDVLTVGPSGHEEPIPLTRVRSLANVRLEDEVED
+ALALMQRTGSHLARVITPEGETAGVLFLEDVLEELVGEINDVTQSPRRFRPA--------
+----------
+>3_2016
+MSQDVVGLLWLAVLLAANAFFVAGEFAVMGARRSQIEPRAEAGSRQAQVALFAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLAAPMEALGLPLAAADVVAFVLALLIVTFLHVTM
+GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPLIVVLNWAANTVLRAFGIEPKDEVASS
+FTLEEVQTIVAESTRSGTLEDESGVLHSALEFSSYTAGDVMVPIEKVVSVPEDVTPQQFE
+WAVGRVGYSRFVVEDSQGGYAGYLHLKDVLAGGPSRYADPVPVTRVRSLANVRVADEVED
+ALGLMQRTGSHLARVISEDGATVGVLFLEDVLEELVGEIHDVTQSPRRFRPTTGSHAAPE
+PTRMRDLPAR
+>4_696
+MNGDVVGLLWLVVLLAANAFFVAGEFAVMGARRAQIEPRAEAGSRQAQVALYAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLVVPMGALGVPAAAADVTAFVLALLVVTFLHVTL
+GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPVVAALNWTANLVLHALRIEPKDEVASS
+YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHRAGDVMVPLERVVTVPEGITPHDFE
+WAVGRVGFSRFVVEDPDGGYTGYLHLKDVLTVGPSGHDEPIPLTRVRSLANVRLEDEVED
+ALALMQRTGSHLARVITPEGETAGILFLEDVLEELVGEINDVTQSPRRFRPA--------
+----------
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000676.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000676.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c39499879f44ca132b1ba265fa7e172a995b3eb4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000676.fa
@@ -0,0 +1,41 @@
+>0_737
+MHSETPDPSPVPDRDGAAPDRPDPLIVVDEGQARVVPAPTAAPSSSHDAGGDPDA----D
+TDGVDPEAAEPPTLVTVDVLAGWLGLAPVEDLPPVPEGPAYAQPGRCRPNRVILLDVRFR
+ATA-GGPDHAAYLQGHLPGAVYVSLPSQLAGHAGPAAGRHPLPDARQFAETVRMWGIDEG
+DTIVVYDDDHGLSAARAWWLLRHAGLRDSMLLDGGLEAWRAAGLPLQPGEVIPVPGTARP
+SWGRMPVVDTAGAEAMASGGLLLDARAAERYRGEVEPFDPVAGHIPGARNVPTAESIAED
+GRLRPAAELAERFDAVGVDDATPVAVYCGSGITAAHAVLTLAVAGRPGVALYPGSWSAWV
+QDPSNAVAVGPEPDGASGRD
+>1_476
+MHSETPDPSPVPDRDGAAPDRPDPLIVVDEGQGRVVPAPTAAPSSSHDAGGDPDA----D
+IDGVDPEAAEPPTLVTVDVLAGWLGLAPVEDLPPVPGGPAYAQPGRCRPNRVILLDVRFR
+ATG-GGPDHAAYLQGHLPGAVYVSLPSQLAGHAGPAAGRHPLPDARQFAETVRMWGIDEG
+DTIVVYDDDHGLSAARAWWLLRHAGLRDSVLLDGGLEAWRAAGLPLQPGEVIPVPGTARP
+SWGRMPVVDTAGAEAMASGGLLLDARAAERYRGEVEPFDPVAGHIPGARNVPTAESIAED
+GRLRPAAELAERFDAVGVDDATPVAVYCGSGITAAHAVLTLAVAGRPGVALYPGSWSAWV
+QDPSNAVAVGPEPDGASGRD
+>2_2116
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------------------------------------------MWGIDDG
+DTVVVYDDDRGLSAARAWWLLRHAGLRDSMLLDGGLAAWRAGGLPLQPGEVIPMPGSART
+SWGRMPVVDTAGAEAMASGGLLLDARAAERYRGETEPIDPVTGHIPGARSLPTAGSLAED
+GRLRPAEELAARFDAVGVDDETPVAVYCGSGVTAAHAVLTLAVAGRPGVALYPGSWSAWI
+QDPSNAVAVGPDPHGEPGRD
+>3_2011
+MK--------------------------DSTEGR-PPSPASSPAADAPTDQTPLAELAED
+ATAPDPAAAEPPSLVDVGVLAGWLGLTPAEPVPAPPPGPVFDR--RVDPGRVILLDVRYA
+VAGAGGSGHDAYLRGHLPGAVFVSLPNQLAGHAGPRQGRHPLPDPVQFAHSLRMWGIDDG
+DTVVVYDDDRSLAAARAWWLLRHAGLRDSVLLDGGLGAWRAAGLPLQPGEVIPQPGSVHP
+SWGRMPVVDTDGAEAIAAGGLLLDARSAERYRGEEEPLDPVAGHIPGARSLPTSGNVAAD
+GRLLDPAALAARFEDAGLSDEVPAAVYCGSGVTAAHQVLALAVAGRHGVALYPGSWSAWI
+QDPDRPVATGPRPEG----D
+>4_701
+MHSETPDPSPVPDRDGAAPDRPDPLIVVDEGQGRVVPAPTAAPSSSHDAGGDPDA----D
+IDGVDPEAAEPPTLVTVDVLAGWLGLAPVEDLPPVPGGPAYAQPGRCRPNRVILLDVRFR
+ATG-GGPDHAAYLQGHLPGAVYVSLPSQLAGHAGPAAGRHPLPDARQFAETVRMWGIDEG
+DTIVVYDDDHGLSAARAWWLLRHAGLRDSVLLDGGLEAWRAAGLPLQPGEVIPVPGTARP
+SWGRMPVVDTAGAEAMASGGLLLDARAAERYRGEVEPFDPVAGHIPGARNAPTAESIAED
+GRLRPAAELAERFDAVGVDDATPVAVYCGSGITAAHAVLTLAVAGRPGVALYPGSWSAWV
+QDPSNAVAVGPEPYGASGRE
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000678.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000678.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4d67f51e2fd5aeeb57faa71c0d1bb856b7b06000
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000678.fa
@@ -0,0 +1,95 @@
+>0_739
+MTQTPPPSTPAAQPSATPHDAVAITFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKTTQLPKMCLALGLGEAGSIGH
+TQPRRIAARSVAERIAQELGEEIGQTVGYQVRFTAQTSKATRVKVMTDGILLAEIPHDPQLRRYSVIIVDEAHERSLNID
+FLLGYLRNLLPQRPDLKVIITSATIDPERFARHFGRPLAEGEDHADAVEADDGGRVVPAPIIEVSGRTYPVEIRYRPLTD
+EPSPDDPEDDADDAAETRDPLDAIGDAVLELASEPPGDILVFLPGEREIREAADHLTGVVAGTTRLAGTEILPLFGRLSM
+AEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDTGTARISRYSHRTKVQRLPIERVSQASANQRSGRSGRTSDG
+IAIRLYSEEDYLSRPEFTDPEILRTSLASVILQMLSLGVARTPGDVKEFPFVQPPDGRQVTDGATTLTELGAL-------
+--------EAGG---ARA---GTITRVGRRLARLPVDPRLGRMILEAGERGCVREVMVIAAALTIQDPRERPTEQREAAD
+ELHRRFADENSDFSAILNLWAYLRERQQELSGSQFRKLCRREHINWLRVQEWQDLVRQLRQLAKDVGLTVEAGPVDPVGR
+HEAVHKSLLTGLLAQIGAYDERRREYAGARGTRFAVFPGSALFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEVAGH
+LVKRAYNEPHWSRRAGSVVAREKVTLFGVTLIPDRSVRYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDA
+LETRLRRRDLRIGDEDLFAFYDARIPANVVSERHFDAWWKKARQEQPDLLDLDVAALLTADAEDLDTDAFPTTFSYPMPG
+GDVELDLEYTFDPTGAAGTDGVTVAVPILLLNQVSPGPFAWLVPGLRVELVTALIKALPKAVRKNLVPAPDVAQQLVADL
+EAHADPLRDELPEALSAAVRRVRGVVVEPGLWAPDAVPLHLRMDYRVVDARGAVMGAGQDLPALQARLAQANRSAIAARL
+AGTDDPASARPGP------------------RGTGRGGRAQADARAGAEGRRRPE------GPGRSG-ATPAFEERHRLT
+SWSIGTVPKTVSTAAGARGPAITGYPSLVPETTPDGGPAAGLTVARSAEDQAAWHRAGVIRLLLATLPSPQRYVLDHLDN
+REKLTFTQNPHGSVDSLVADCTQAAVDRLVGDELPFDEAAFRALFDRVRADLIDTVFAVTSLVEQVLSRAAQVRRRLKGS
+VSLALAPALSDVKAHLEQLVFPGFVAATGWERLQHLPRYLQGMLTRLDRLDAGGHLQRDGQHMAVVQGLEDEFDAAVAAH
+RARFAGTPVPAELERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALARATRA
+>1_478
+MTQTPPPSTPAAQPSATPHDAVAITFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKTTQLPKMCLALGLGEAGSIGH
+TQPRRIAARSVAERIAQELGEEIGQTVGYQVRFTAQTSKATRVKVMTDGILLAEIPHDPQLRRYSVIIVDEAHERSLNID
+FLLGYLRNLLPQRPDLKVIITSATIDPERFARHFGRPLAAGEDHADAVEADDGGRVVPVPIIEVSGRTYPVEIRYRPLTD
+EPSPDDPEDDADDAAETRDPLDAIGDAVLELAAEPPGDILVFLPGEREIREAADHLTGVVAGTTRLAGTEILPLFGRLSM
+AEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDTGTARISRYSHRTKVQRLPIERVSQASANQRAGRSGRTSDG
+IAIRLYSEEDYLSRPEFTDPEILRTSLASVILQMLSLGVARTPGDVKEFPFVQPPDGRQVTDGATTLTELGAL-------
+--------EAGG---ARA---GTITRVGRRLARLPVDPRLGRMILEAGERGCVREVMVIAAALTIQDPRERPTEQREAAD
+ELHRRFADENSDFSAILNLWAYLHERQKELSGSQFRKLCRREHINWLRVQEWQDLVRQLRQLAKDVGLTVEAGPVDPVGR
+HEAVHKSLLTGLLSQIGAYDERRREYAGARGTRFAVFPGSALFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEVAGH
+LVKRAYNEPHWSRRAGSVVAREKVTLFGVTLIPDRSVRYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDA
+LETRLRRRDLRIGDEDLFAFYDARIPGNVVSERHFDAWWKKARQDQPDLLDLDVAALLTADAEDLDTDAFPTTFAYPMPG
+GDVELDLEYTFDPTGAAGTDGVTVAVPILLLNQVSPGPFAWLVPGLRVELVTALIKALPKAVRKNLVPAPDVAQQLVADL
+EAHADPLRDELPDALSAAVRRVRGVVVEPGLWAPDAVPLHLRMDYRVVDARGAVMGAGQDLPALQARLAQANRSAIAARL
+AGTDDPASARPGP------------------RGTGRGGRAPADARAGAEGHRRPE------GPGRSG-ATPVFEERHGLT
+SWSIGTVPKTVSTAAGARGPAITGYPSLVPETTPDGGPAAGLTVARSAEDQAAWHRAGVIRLLLATLPSPQRYVLDHLDN
+REKLTFTQNPHGSVDSLVADCTQAAVDRLVGDELPFDEAAFRALFDRVRADLIDTVFAVTSLVEQVLSRAAQVRRRLKDS
+VSLALAPALSDVKAHLEQLVFPGFVAATGWERLQHLPRYLQGMLTRLDRLDAGGHLQRDGQHMAVVQGLEDEFDAAVAAH
+RARFAGTPVPAELERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALARATRA
+>2_2114
+MTETPTP--PAAASSAP-----AIVFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKTTQLPKMCLALGLGEAGVIGH
+TQPRRIAARSVAERIAEELGEDIGRTVGYQVRFTAQTSKATRVKVMTDGILLAEIPHDPQLRRYSVVIVDEAHERSLNID
+FLLGYLRTLLPQRPDLKVIITSATIDPERFARHFGRALAEGEEHEDAVPADDGGLVVPAPVIEVSGRTYPVEVRYRPLTG
+EPSPDDPEDDSDDAAETRDPLDAIGEAVLELAAEPPGDILVFLPGEREIRDAADHLSGVVASSKRLAGTEVLPLFGRLSM
+AEQHRVFGRAAAGVRRRIVLATNVAETSLTVPGIKYVIDTGTARISRYSHRTKVQRLPIERVSQASANQRAGRSGRTSPG
+IAIRLYSEEDYLSRPEFTDPEILRTSLASVILQMLSLGVAATPADVQGFPFVQPPDGRQVSDGATTLTELGALHPPRPSG
+AKDGHDGGRGRG---GRAPEPGTITPIGRRLARLPVDPRLGRMILESGERGCVREVMVLAAALTIQDPRERPVEQREAAD
+ELHRRFADENSDFSAILNLWAYLQEQQKELSGSQFRKLCRREHINWLRVHEWQDLVRQLRQLAKDVGVAVHAGPVDPVGQ
+HEAVHRSLLTGLLSQIGSYDERRREYAGARGTRFAVFPGSALFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEAAGG
+LVKRTYNEPHWSRRAGAVVAREKVTLFGVTLIPDRSVKYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDA
+LETRLRRRDLRIGDEDLFAFYDARVPANVVSERHFDAWWKKARQERPDLLDLDVAALLTADAEDLDTDAFPTVFPYPLSG
+GDVDLDLEYTFDPTGASGTDGVTVSVPVLLLNQVSPGPFAWLVPGLRVELVTALIKALPKAVRKQLVPAPDVARQLVADL
+DAHADPLADELTEALSAAVRRVRGIVVEPGLWAPDAVPAHLRMDYRVVDARGAVMGAGQDLAALQARLAKANRSAIAARL
+AGTDDPANARPGPGRQGGRRDGGGNDGGAGRRGSGRGVRGR-----GRDGTGRPEAG----AQGAGG-AAAAFAERHGLT
+SWSIGTVPRRITTDPGARGPAITGYPALVPETTAEGGPAAGLTVARSAEDQAAWHRAGVIRLLLATLPSPQRYVLDHLDN
+REKLTFTQNPHGSVDSLVADCSQAAVDRLVGDELPFDEAAFRALFDRVRADLIDTVFAVTRLVEQVLSRAAEVRRRLKGS
+VSLAMAPALSDVKAHLEQLVFPGFVAATGWERLQHLPRYLQGILVRLDRLDAGGHLQRDGQHMAVVQRLEDEFDAAVQAH
+RARFSGVPVPADLERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALAQAARA
+>3_2009
+MTDFPQP--PAAAP--------VITFPAHLPVAERREEIMDAVRENQVVIVAGETGSGKTTQLPKMLLALGLGGAGVVGH
+TQPRRIAARSVAERIAEELGEDVGRTVGYQVRFTAQTSTRTRVKVMTDGILLAEIPHDPDLRKYSAIIVDEAHERSLNID
+FLLGYLKRLLPRRPDLKVIITSATIDPERFARHFGT-----EDE-------------PAPIIEVSGRTYPVEIRYRPLTE
+EPSPDDPDDDADDHAETRDPIDAVGDAVLELAGEAPGDILVFFPGEREIREAADHLAGVVASTPRLAGTEVLPLYGRLSM
+AEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDTGTARISRYSHRTKVQRLPIERISQASANQRSGRSGRTSDG
+IAIRLYSEEDFLSRPEFTDPEILRTSLASVILQMLSLGVADTPREVMDFPFVQPPDSRQVTDGAATLTELGALHADAPT-
+----RGGGRGRGKGAGNRSAAGTITDIGRRLARLPVDPRLGRMILESGRRDCTREVMVLAAALTIQDPRERPVEQRQAAD
+ELHARFADDRSDFSAYLNLWEYLREQQRELSGSQFRKLCRREHINWLRVHEWQDLVRQLRQLSKDVGVSVHPGPVDPVGK
+HDDVHKSLLTGLLSQIGAYDERRREYQGARNTRFAVFPGSALFKKRHPFVMAAELVETSRLWARAVARIEPEWIEEVAGD
+LVLRSYAEPHWSRKAGAAVAMEKVTLFGVTIVPERSVRYGRIDPVLSRELFLRHALVEGDWRTRHRFFARNRRLLEEVDE
+LETRLRRRDLRVGDEELFAFYDARVPANVVSERHFDAWWKKARQETPDLLDLDLDALLTQDADELDTDAFPTAFRYPLPG
+GDADLALDYTYDPTGASGTDGVTVAVPILLLNEVAPGPFAWLVPGLRGELVTALIKALPKAVRKNLVPAPDVARLLVEDL
+DAHADPLRDELPAALSSAVRRVRGAVVEPELWRLDAVPDHLRMDYRVVDARGAVMGAGQDLPALQARLAKANRSAIAARL
+AGTDDPRNARPG-------------------QGAGR-GRGKTEPKGGDGGARGPAADTGRPGPSRTADGAPAFRERHGLT
+SWTVGEVPRQITTAPGDRGPAITGYPSLIPETTADGSPAAGLVVARSAQDQAAWHRAGVIALLLATLPSTHRYVLDHLDN
+KEKLTFTQNPHGSVESLVRDATHVAVDRLVGTDLPFTEVGFRALFDRVRADLIDTVFAVTALVEQVLSRAAEVRRRLKGG
+VSLAMAPAKSDVQAHLEQLVFPGFLAATGWQQLQHLPRYVQGMLARLDKLDAGGHLQRDGQHMAVVQGLEDEFDAAVTAH
+RSRFPGTPVPAELERVRWLLEELRVSYFAQELGTAVSVSEKRVRQALAQARQG
+>4_703
+MTQTPPPSTPAAQPSATPHDAVAITFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKTTQLPKMCLALGLGEAGSIGH
+TQPRRIAARSVAERIAQELGEEIGQTVGYQVRFTTQTSKATRVKVMTDGILLAEIPHDPQLRRYSVIIVDEAHERSLNID
+FLLGYLRNLLPQRPDLKVIITSATIDPERFARHFGRPLAAGEDHADAVEADDGGRVVPAPIIEVSGRTYPVEIRYRPLTD
+EPSPDDPEDDADDAAETRDPLDAIGDAVLELAAEPPGDILVFLPGEREIREAADHLTGVVAGTTRLAGTEILPLFGRLSM
+AEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDTGTARISRYSHRTKVQRLPIERVSQASANQRAGRSGRTSDG
+IAIRLYSEEDYLSRPEFTDPEILRTSLASVILQMLSLGVARTPGDVKEFPFVQPPDGRQVTDGATTLTELGAL-------
+--------EAGG---ARA---GTITRVGRRLARLPVDPRLGRMILEAGERGCVREVMVIAAALTIQDPRERPTEQREAAD
+ELHRRFADENSDFSAILNLWAYLHERQKELSGSQFRKLCRREHINWLRVQEWQDLVRQLRQLAKDVGLTVEAGPVDPVGR
+HEAVHKSLLTGLLSQIGAYDERRREYVGARGTRFAVFPGSALFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEVAGH
+LVKRTYNEPHWSRRAGSVVAREKVTLFGVTLIPDRSVRYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDA
+LETRLRRRDLRIGDEDLFAFYDARIPGNVVSERHFDAWWKKARQDQPDLLDLDVAALLTADAEDLDTDAFPTTFTYPMPG
+GDVELDLEYTFDPTGAAGTDGVTVAVPILLLNQVSPGPFAWLVPGLRVELVTALIKALPKAVRKNLVPAPDVAQQLVADL
+EAHADPLRDELPDALSAAVRRVRGVVVEPGLWAPDAVPLHLRMDYRVVDARGAVMGAGQDLPALQARLAQANRSAIAARL
+AGTDDPASARPGP------------------RRTGRGGRAQADGRAGAEGRRRPE------GPGRSG-ATPAFEERHGLT
+SWSIGTVPRTVSTAAGARGPAITGYPSLVPETTPDGGPAAGLTVARSADDQAAWHRAGVIRLLLATLPSPQRYVLDHLDN
+REKLTFTQNPHGSVDSLVADCTQAAVDRLVGDELPFDEAAFRALFDRVRADLIDTVFAVTSLVEQVLSRAAQVRRRLKGS
+VSLALAPALSDVKAHLEQLVFPGFVAATGWERLQHLPRYLQGILTRLDRLDAGGHLQRDGQHMAVVQGLEDEFDAAVAAH
+RARFAGTPVPAELERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALARATRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000682.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000682.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a16f997bfd31ed0e6badb8a4ed0d19b70a3ec3a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000682.fa
@@ -0,0 +1,41 @@
+>0_745
+MSHVTESSPAHPGRAEESAPLRPTSPLGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG
+TGALVIAGALFFLLAVIVLRLAQKLRTTDIHRIVNPTTSRVPTWFADLSITTSLLGTLVI
+MLAGAGAAVHTAFGLPSLVGSLVMATVCVVSVLAGITGLVRVQAVVVPLIIVVAVGVAVW
+GLANPGAAVDDVAALVTSSPLINQWWLSGVLYVAFNIQLAYAVLAPIGEESSSSGRSLVA
+GAGLGALGLVVMAGAVMAAMTAHAQLIGRAELPMVELAAMIGGWAALLYTVVLLLAQFTT
+AVSCLYGGVERIALLSSMRRVPGWVIAVVTALAATLLSSVGFSDLVGTVYPVLGYAGLVI
+IVMLVVTWIVERSTVRRRAARAARA
+>1_485
+MSHVTESSPAHPGRAEESTPLRPTSPLGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG
+TGALVIAGALFFLLAVIVLRLAQKLRTTDIHRIVNPTTSRVPTWFADLCITTSLLGTLVI
+MLAGAGAAVHTAFGLPSLVGSLVMAAVCVVSVLAGITGLVRVQAVVVPLIIVVAVGVAVW
+GLANPGAAVDDVAALVTSSPLINQWWLSGVLYVAFNIQLAYAVLAPIGEESSSSGRSLVA
+GAGLGALGLVVMAGAVMAALTVHAQLIGRAELPMVELAAMIGGWAALLYTVVLLLAQFTT
+AVSCLYGGVERIALLSSMRRVPGWAIAVVTALAATLLSSVGFSDLVGTVYPVLGYAGIVI
+IVMLIVTWIVERTTVRRRAARAARA
+>2_2109
+MSPVTESSPAHRGRAEESAPLRPTSRLGIAATFIGTTIGAGYASGNEILQYFVSFGFWGG
+TLALVIAGALFFLLSAIVLKMAQKLRTTDIHRLVNPTTSRVPTWFADLCITASLLGTLVI
+MLAGAGAAVNTSFGLPTMVGSLLMAAVCVLSVLAGISGLVRVQAVVVPLIIVVAVGVAWW
+GLANPGAPVEDVASLVTSSPLINQWWMSGILYVAFNFQLAYAVLAPIGRDSSSSGRTLVA
+GAGLGAVGLVVMAGAIMFAMAAHAHLIGRADLPMVELAAMIGGWAALVYTVILLLAQFTT
+AVSCLFGGVERIALLSPLRRVPGWAIAVATALAATLLSSVGFSDLVGTVYPVLGYAGIAI
+IVMLIITWIAERTLVRRRAARAARA
+>3_2003
+MSHVAQSTHENRPAQDGGNGLRPMSALGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG
+TGALVIAGVLFFLLSAIVLKMAQQLRTTDIHRLVNPTSSRIPTWFADLCITASLLGTLVI
+MFAGAGAALDTWLGLPAWAGAALMAAVCVLTVLGGISGLVKVQGLVVPLIILVAVGVAWW
+GLTHPGAGADDVASLVTSSPLINTWWMSGILYVAFNFQLAYAVLAPIGKGSSSPGTSLVA
+GAGLGAIGLVVMAGAIMAAMGAHATLIGRAELPMVELAGMVAPWVAAVYTVILLLAQFTT
+AVSCLFGGVERIALLSPLRDVPGWLIAVVTAVVAVLLSSVGFSDLVGIVYPVLGYAGIAI
+VAMLIATWILDRTLVRRRAARADRA
+>4_712
+MSHVTESSPAHPGRAEESAPLRPTSPLGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG
+TGALVIAGALFFLLAVIVLRLAQKLRTTDIHRIVNPTTSRVPTWFADLCITTSLLGTLVI
+MLAGAGAAVHTAFGLPSLVGSLVMAAVCVVSVLAGITGLVRVQAVVVPLIIVVAVGVAVW
+GLANPGAAVDDVAALVTSSPLINQWWLSGVLYVAFNIQLAYAVLAPIGEESSSSGRSLVA
+GAGLGALGLVVMAGAVMAAMTAHAQLIGRAELPMVELAAMIGGWAALLYTVVLLLAQFTT
+AVSCLYGGVERIALLSSMRRVPGWVIAVVTALAATLLSSVGFSDLVGTVYPVLGYAGIVI
+IVMLVVTWIVERSTVRRRAARAARA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000683.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000683.fa
new file mode 100644
index 0000000000000000000000000000000000000000..48ed4719b0a1d81e2a84b387cbf1ed2779046895
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000683.fa
@@ -0,0 +1,36 @@
+>0_746
+MT---------------SAVPRVLSIAGSDSGGGAGVQADLKTIAAWGGYGMTAITAITA
+QNTQGVQAVHPLPVDVVRAQLDSVAADIAVDAVKIGMLGTVELMRAVAGWLEETRPAVVV
+LDPVMVASSGDALTAVGDDDGRAAWARLLRVAHLVTPNLPELARLTGRDATDWDAALDAA
+RGLAAEHGVTVLLKGGHLDETEAPEAAAAE----------VPDAVVRVGGAVHEVRGPRV
+TTRASHGTGCTLSSALATLAGAGLSWDDALERAKPWLADAMRAGEALAVGDASRPTWHGP
+VDHGHAQRG
+>1_486
+MT---------------PAVPRVLSIAGSDSGGGAGVQADLKTIAAWGGYGMTAITAITA
+QNTQGVQAVHPLPVDVVRAQLDSVAADIAVDAVKIGMLGTVELMRAVAGWLEETRPAVVV
+LDPVMVASSGDALTAVGDDDGRAAWARLLRVAHLVTPNLPELARLTGRDATDWDAALDAA
+RGLAAEHGVTVLLKGGHLDETEAPEAAAAE----------VPDAVVRVGGAVHEVRGPRV
+TTRASHGTGCTLSSALATLAGAGLSWEDALERAKPWLADAMRAGEALAVGDASRPTWHGP
+VDHGHAQRG
+>2_2108
+----------------------MLSIAGSDSGGGAGVQADLKTIAVWGGYGMTAITAITA
+QNTQGVQAVHPLPVDVVRAQLDSIAADIAVDAVKIGMLGTAELMGAVAGWLEETRPAVVV
+LDPVMVASSGDALTAVGDDDGRAAWSRLLRAAHLVTPNLPELARLTGRDSTDWEAALDAA
+GGLAAEHEVTVLLKGGHLD-----EAAAAE----------VPDAVVRVAGAVHEVRGPRV
+ATRASHGTGCTLSSALATLAGAGLSWEDALERAKPWLADAMRAGEALAVGDASRPTWHGP
+VDHGHARRG
+>3_2002
+MAPSPSTPPSSSPAAEGPAVPRVLSIAGSDSGGGAGIQADLKTIAEWGGYGMTAITAITA
+QNTQGVQAVHPLPAEVVRAQLDSVASDIAVDAVKVGMLGTAELMRVVADWLEEARPAVVV
+VDPVMAATSGHALTPVGDAEAHAAWGRLLRAAHLVTPNLPELARLAGRPLDSWAAALDAA
+RELAAAHAVTVLAKGGHLADLTRADPEGAEAGDDPDAEGGVPDALVRPDGSVHEVRGPRV
+ESGATHGTGCTLSAALATLAAGGLGWEDAIERAKPWLAQAMVAGEALAVGDRTRPTWHGP
+VDHGHARRG
+>4_713
+MT---------------SAVPRVLSIAGSDSGGGAGVQADLKTIAAWGGYGMTAITAITA
+QNTQGVQAVHPLPVDVVRAQLDSVAADIAVDAVKIGMLGTVELMRAVAGWLEETRPAVVV
+LDPVMVASSGDALTAVGDDDGRAAWARLLRVAHLVTPNLPELARLTGRDATDWDAALDAA
+RGLAAEHGVTVLLKGGHLDETEAPEAAAAE----------VPDAVVRVGGAVHEVRGPRV
+TTRASHGTGCTLSSALATLAGAGLSWEDALERAKPWLADAMRAGEALAVGDASRPTWHGP
+VDHGHAQRG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000691.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000691.fa
new file mode 100644
index 0000000000000000000000000000000000000000..889c309a9761b58d4b0ef95bf3fd10d66764899c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000691.fa
@@ -0,0 +1,46 @@
+>0_754
+M-------PQHTDAPT--ALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAV
+RDTGATRDWQADPALYTTDAEALVDGADVVIELMGGIEPARTLILRALAAGTSVVTGNKA
+LLAQHGEELYAAAAATGAQLSFEAAVAGAIPILRPLRDSLGGDRVTRVMGIANGTTNFIL
+DRMDSEGADFDDALAEAQRLGYAEADPTADVEGHDAAAKAAILATIAFGAPYTLDQVAVA
+GITAITAEDNAAAAEAGYVIKLLAIAERGRAADGAQGAVLRVHPTLLPREHPLASVRGAF
+NAVFVEAENAGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVTALPALDP
+AEAHTSFMVVLRAADQPGVLRRVAGVFEEHGVSIETLRQVPSEREDAPGASLRLITHRAR
+QRDLDATVEALAALDVVHEVASVLRVEGN
+>1_494
+M-------PQHTDAPT--ALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAV
+RDTGATRDWQADPALYTTDAEALVDGADVVIELMGGIEPARTLILRALAAGTSVVTGNKA
+LLAQHGEELYAAAAATGAQLSFEAAVAGAIPILRPLRDSLGGDRVTRVMGIANGTTNFIL
+DRMDSEGADFDDALAEAQRLGYAEADPTADVEGHDAAAKAAILATIAFGAPYTLDQVAVA
+GITAITAEDNAAAAEAGYVIKLLAIAERGRAADGAQGAVLRVHPTLLPREHPLASVRGAF
+NAVFVEAENAGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVTALPALDP
+AEAHTSFMVVLRAADQPGVLRRVAGVFEEHGVSIETLRQVPSEREDAPGASLRLITHRAR
+QRDLDATVEALAALDVVHEVASVLRVEGN
+>2_2100
+M-------PQHTDAPT--ALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAV
+RNTGATRDWQADPALYTTDAEALVDGADVVIELMGGIEPARTLILRALAAGTSVVTGNKA
+LLAQHGEELYAAAAATGAQLSFEAAVAGAIPILRPLRDSLAGDRVTRVMGIANGTTNYIL
+DKMDSEGAGFDEALAEAQRLGYAEADPTADVEGHDAAAKAAILATLAFGAPYTLDQVAVS
+GITAITAEDNEAAADAGYVIKLLAIAERARAADSAEGAVLRVHPTLLPREHPLASVRGAF
+NAVFVEAENAGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVAELPALDP
+AEAVTSCLVVLRVADEPGVLRRVAGVFEEQGVSIETLRQVQSDRDDAPGASLRLITHRAR
+QRDLDATVEALAALDAVHEVASVLRVEGN
+>3_1993
+MAEPTASAAQTAPAPARDALRVALLGGGTVGSQAARILTEDAAVLADRVGVRLELTGIAV
+RDTAAVRDWQADPSLYTTDAEALVDGADLVIELMGGIEPARSLIRRALQVGTSVVTGNKA
+LLAEHGEELYRLASETGAQLSFEAAVAGAIPILRPLRDSLSGDTVNRVMGIANGTTNFIL
+DRMDTEGASFADALAEAQRLGYAEADPTADVGGFDAAAKAAILATLAFGSSYTLDQVSVE
+GITEVTAEDNAAAADAGYVIKLLAIAERDTARDGTAGAILRVHPTLIPREHPLGSVRGAY
+NAVFVEAENAGQLMFYGPGAGGAPTASAVMGDAVAIGQRIVRGGPARLRTPVAALPALDV
+SEARTSCMVVLRVADQPGVLRRVAGVFEEHGVSIETLRQVQGA-DDAAGASLRLITHRAR
+QRDLDDVVAELTTLDAVHEVASVLRVEGN
+>4_721
+M-------PQHTDAPT--ALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAV
+RDTGATRDWQADPALYTTDAEALVDGADVVIELMGGVEPARTLILRALAAGTSVVTGNKA
+LLAQHGEELYAAAAATGAQLSFEAAVAGAIPILRPLRDSLGGDRVTRVMGIANGTTNFIL
+DRMDSEGADFDDALAEAQRLGYAEADPTADVEGHDAAAKAAILATIAFGAPYTLDQVAVA
+GITAITAEDNAAAAEAGYVIKLLAIAERGRAADGAQGAVLRVHPTLLPREHPLASVRGAF
+NAVFVEAENAGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVTALPALDP
+AEAHTSFMVVLRAADQPGVLRRVAGVFEEHGVSIETLRQVPSEREDAPGASLRLITHRAR
+QRDLDATVEALAALDVVHEVASVLRVEGN
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000692.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000692.fa
new file mode 100644
index 0000000000000000000000000000000000000000..17dcfd8060b14f92357b62395d1a9e4523925c95
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000692.fa
@@ -0,0 +1,41 @@
+>0_755
+MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS
+FKDRGMTMAITAAVADGAKAVVCASTGNTSASAAAYAAQAGITCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDTLGDAP
+DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDAELPAVATKTPVMWGFQAAGAAPI
+VQGHPVTDPDTIATAIRIGNPASWEQAEAARDESGGMIDSVTDEEILEAHRWLSAKEGVF
+VEPASAAGVAGLLKHHAAGNVPAGKSWVITVTGHGLKDPQWALRGADGADVTPRSVPFDV
+VTVAQALGLS
+>1_495
+MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS
+FKDRGMTMAITAAVADGAKAVVCASTGNTSASAAAYAAQAGITCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDTLGDAP
+DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDAELPAVATKTPVMWGFQAAGAAPI
+VQGHPVTDPDTIATAIRIGNPASWEQAEAARDESGGMIDSVTDEEILEAHRWLSAKEGVF
+VEPASAAGVAGLLKHHAAGNVPAGKSWVITVTGHGLKDPQWALRGADGADVTPRSVPFDV
+VTVAQALGLS
+>2_2099
+MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS
+FKDRGMTMAITAAVDQGAKAVVCASTGNTSASAAAYAAQAGLTCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDALGDAP
+DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDEELPAVSTKTPVMWGFQAAGAAPI
+VLGHPVTEPDTIATAIRIGNPASWEQAEAARDGSGGMIDSVTDEEILAAHRWLSAKEGVF
+VEPASAAGVAGLIKHHAAGNVPAGKSWVITVTGHGLKDPQWALRDADGEDVTPRTVPFDV
+VTVAQALGLA
+>3_1992
+MAHVWRGVIREYAGRLPVTEDTRVVSLGEGGTPLIRAPHLSELVEGEVYVKFEGMNPTGS
+FKDRGMTMAITAAVENGAKAVVCASTGNTSASAAAFAAQAGLTCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDNCLDIARKLSENYPVFLVNSVNPARIEGQKTAAFEVVDLLGDAP
+DYHLLPVGNAGNITAYWKGYQEYSRPYVNPHPGTSDEELPAVATKTPVMWGFQAAGAAPL
+VLGHPVTEPETIATAIRIGNPASWDQATAARDASGGMIDSVTDEEILAAHRWLSSKEGVF
+VEPASAAGVAGLIKHHAAGNVPAGKTWVITVTGHGLKDPQWALKGADGDDVTPRSVPFDV
+VTVAEALGLT
+>4_722
+MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS
+FKDRGMTMAITAAVADGAKAVVCASTGNTSASAAAYAAQAGITCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDTLGDAP
+DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDAELPAVATKTPVMWGFQAAGAAPI
+VQGHPVTDPDTIATAIRIGNPASWEQAEAARDESGGMIDSVTDEEILEAHRWLSAKEGVF
+VEPASAAGVAGLLKHHAAGNVPAGKSWVITVTGHGLKDPQWALRGADGADVTPRSVPFDV
+VTVAQALGLS
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000694.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000694.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b9eda40d0482c5fc74042333afe51b56c52c81a6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000694.fa
@@ -0,0 +1,55 @@
+>0_757
+MTESTEQTTPTNGGGLASLKLAQLQALASQLGIAGGSRMRKADLVTAISDHQRGGSVADRDAAERAAQAPAAPAAEAAPA
+A-ASSQDAAPAAERPARRRSRRADADTSAPA-AAQDGQPQAEAREDQTEQAPRETASDQDRSEGSETRDEGEGRPQSERR
+S-RG-RRAGDDDAQ-----QGQDRRSDGA-----QGEDG--ADRRGDREDRDDNGRENGRGRNGRNGRDRDNGR----DR
+ENGRENNRDRENG----RDGSREQ---RGDKSEDGGRGDGGRGDR------SRRDDRDDEGGRNRRNRRNRNERGRNRRG
+RGGPEVDETELTEDDVLQPVAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKYGLRKGDAVVGAIRAPRDGEKQQHHG
+GGSNRQKFNALVKISSVNGQPAVEHPQRVEFGKLVPLYPQERLRLETDPKLIGPRVIDLVSPIGKGQRGLIVSPPKAGKT
+MILQSIANAIKTNNPEVHLMMVLVDERPEEVTDMQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLD
+SMTRLGRAYNLAAPASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKGTGNMELRL
+SRHLAERRIFPAVDVNASGTRREEALLSQEEVKIMWKLRRVLSGLEQQQALDLLTNKIKDTASNAEFLMLVSKTTLGSKG
+DD
+>1_497
+MTESTEQTTPTNGGGLASLKLAQLQALASQLGIAGGSRMRKADLVTAISDHQRGGSVADRDAAERAAQAPAAPAAEAAPA
+A-ASSQDAAPAAERPARRRSRRADADTSAPAAAAQDGQPQAEAREDQTEQAPRETASDQDRSGGSEARDEGEDRPQSERR
+S-RNRRRAGDDDAQ-----QGQDRRSDGA-----QGEDG--ADRRGDREDRDDNGRENGRGRNGRNGRDRENGR----DR
+ENGRENNRDRENG----RDGSREQ---RGDKSEDGGRGDGGRGDR------SRRDDRDDEGGRNRRNRRNRNERGRNRRG
+RGGPEVDETELTEDDVLQPVAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKYGLRKGDAVVGAIRAPRDGEKQQHHG
+GGSNRQKFNALVKISSVNGQPAVEHPQRVEFGKLVPLYPQERLRLETDPKLIGPRVIDLVSPIGKGQRGLIVSPPKAGKT
+MILQSIANAIKTNNPEVHLMMVLVDERPEEVTDMQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLD
+SMTRLGRAYNLAAPASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKGTGNMELRL
+SRHLAERRIFPAVDVNASGTRREEALLSQEEVKIMWKLRRVLSGLDQQQALDLLTNKIKDTASNAEFLMLVSKTTLGSKG
+DD
+>2_2097
+MTESTEQTTPTTGGGLAALKLAQLQALASQLGIPGGSRMRKADLVTAISDHQRGGSVADRAAAERAAKAAAAPAAEAAPA
+ADKAAEQPAEAAERPARRRSRRADADTSAAAQSAESGKDQAERRAEQPAEG-RDAEGSQD--SGDRAQDSGD-RTQGERR
+S-RGRRRAGDDDAR-----GQDRRRQDGEDAGQDQAHDS--AEDRGG--DREDGGRENGRGNRGRNG--RDNGR----DR
+ENG--NGRDRDNGNGRDRDGSREQ---KQDKSEDGGR-DGGRNDR------NRRDDRDDEGGRGRRNRRNRNERGRNRRG
+RGGPDVDETELTEDDVLQPVAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKHGLRKGDAVVGAIRAPREGEKPQHQG
+GGSNRQKFNALVKISSVNGQPAVEHPERVEFAKLVPLYPQERLRLETDPKQVGPRVIDLVSPIGKGQRGLIVSPPKAGKT
+MILQSIANAIKTNNPEVHLMMVLVDERPEEVTDMQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLD
+SMTRLGRAYNLAAPASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKGTGNMELRL
+SRHLAERRIFPAVDVNASGTRREEALLSPEEVKIMWKLRRVLSGLEQQQALELLTNKIKDTGSNAEFLMLVSKTTLGAKG
+ED
+>3_1990
+MTESPDQTTA--GGGLASLKLAQLQALASQLGITGGSRMRKSDLVAAISDHQRGGSVADRDA---AAQAAAAPAAQAEAA
+E-APAAEQAPR----SRRRSRRADSDGAVAA-------DQPAEATQAPADE-QPAAETED--APARAEASAE-SGAQEAG
+SGRSRRRRGDRAARDEQQDGAQDEKQESG-----RG-----AGEETRREQDGDEERAEGRSRSRRGRGDRDRGERQNADR
+QNGERANGERANG----QGEDRSQGGRREDREEESGRGQGGDGQKRSDRGNGRREDR-DEDGRRGRNRRNRNDRGRNRRS
+R-GPEVDDVEVTEDDVLQPVAGILDVLDNYAFVRTSGYLPGEKDVYVSLAMVKKFGLRKGDAVVGAIRAPREGEKP--HS
+GGGRNQKFNALVKVTTVNGQPAEENPQRVEFGKLVPLYPTERLRLESDHKLVGPRVIDLISPIGKGQRGLIVSPPKAGKT
+MILQSIANAITRNNPEVHLMMVLVDERPEEVTDMQRSVAGEVIASTFDRPAEDHTTVAELAIERAKRLVEMGRDVVVLLD
+SMTRLGRAYNLAAPASGRILSGGVDSAALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKGTGNMELRL
+SRQLAERRIFPAVDVNASGTRREEVLLSPEEVKIMWKLRRVLSGLDTQQALELLTNKIKDTASNAEFLMLVSKTTLGSKG
+DD
+>4_724
+MTESTEQTTPTNGGGLASLKLAQLQALASQLGIAGGSRMRKADLVTAISDHQRGGSVADRDAAERAAQAPAAPAAEAVPA
+A-ASSQDAAPAAERPARRRSRRADADTSAPAAVAQDGQPQAEAREAQTEQGPRETASDQDRSGGSETRDEGEDRPQSERR
+S-RGRRRAGDDDAQ-----QGQDRRSDGA-----QGEDGADADRRGDREDRDDNGRENGRGRNGRNGRDRDNGR----DR
+DNG----RDRENG----RDGSREQ---RGDKSEDGGRGDGGRGDR------SRRDDRDDEGGRNRRNRRNRNERGRNRRG
+RGGPEVDETELTEDDVLQPAAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKYGLRKGDAVVGAIRAPRDGEKQQHHG
+GGSNRQKFNALVKISSVNGQPAVEHPQRVEFGKLVPLYPQERLRLETDPKLIGPRVIDLVSPIGKGQRGLIVSPPKAGKT
+MILQSIANAIKTNNPEVHLMMVLVDERPEEVTDMQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLD
+SMTRLGRAYNLAAPASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKGTGNMELRL
+SRHLAERRIFPAVDVNASGTRREEALLSQEEVKIMWKLRRVLSGLEQQQALDLLTNKIKDTASNAEFLMLVSKTTLGSKG
+DD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000697.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000697.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ffa73a2a47c9ed33404eff5450e2c0a98852a7d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000697.fa
@@ -0,0 +1,41 @@
+>0_761
+MRAYLVLVMVTAVACGALTPLMRRLGLRARVFTPLRQRDVHRHPVPKLGGVAMAAAVLVG
+FAVGGVVPFLQGIYADDAAMRGLLVAVAVVLVVGIADDMWDLRWWVKMAGQVLAGLAVAL
+GGIRIEAMPVGWIPVGNETTQVILTVFAVVLTMNAINFVDGLDGLAAGVALIGGSAFFVY
+SYLLTRTINQFDYANLATLLMALLVGACVGFLPWNLAPARIFMGEVGAMLIGLLMAAAAV
+AVTADVNALDGMRFRNVPAYMPILLPVAVLALPLADLALAVLRRTAKGTSPFSADRGHLH
+HKLVDGGYTQAQAVGLLWLWAFLVAWGAVSLNFVDHMVVLPVLAVALAGAGYLTLHPIVE
+RRRADRNDA--AAHPDERGDA
+>1_501
+MRAYLVLVMVTAVACGALTPLMRRLGLRARVFTPLRQRDVHRHPVPKLGGVAMAAAVLVG
+FAVGGVVPFLQGIYADDAAMRGLLVAVAVVLVVGIADDMWDLRWWVKMAGQVLAGLAVAL
+GGIRIEAMPVGWIPVGNETTQVILTVFAVVLTMNAINFVDGLDGLAAGVALIGGSAFFVY
+SYLLTRTINQFDYANLATLLMALLVGACVGFLPWNLAPARIFMGEVGAMLIGLLMAAAAV
+AVTADVNALDGMRFRNVPAYMPILLPVAVLALPLADLALAVLRRTAKGTSPFSADRGHLH
+HKLVDGGYTQAQAVGLLWLWAFLVAWGAVSLNFVDHMVVLPVLAVALAGAGYLTLHPIVE
+RRRADRNDA--AAHPDERGDA
+>2_2094
+MRAYLVLVVVTALACGALTPLMRRIGLRARVFTPVRQRDMHRRPIPKLGGVAMAAAVLVG
+LAVGGTVPFLQGIYADDAAMVGLLVAVAVVFVVGIADDLWDLRWWVKMAGQVCAGLAVAL
+GGIRIEAMPVGWIPVGSEAMQIALTVFAVVLTMNALNFVDGLDGLAAGVALIGGSAFFVY
+SYLLTRTINQFDYANLATLLMALLVGACLGFLPFNRFPARIFMGEVGAMLLGLLMAAAAV
+AVTADVKALDGMRFRNVPAYMPILLPIAVLALPLLDLALAVVRRTARGASPFSADRGHLH
+HKLVDGGYTHAQAVWLLWLWAFLVAWGAVSLNFVDDMIVLPVLGLALLGAGYLTLRTPVR
+RRRAGAPAAGPALDPEE--GA
+>3_1986
+MRAYLLVAAVTALTCLALTPWVRRVGVRARAYTPHRDRDVHRAPVPKLGGVAMVAAVLAG
+LAVAGTVPFLGGIFTDASAMRGLLAALGIILVLGVVDDLVDLRWWAKLGGQSLAALAVAL
+GGIRIAALPVGWIHVGSEAVQVALTVFVVVLTMNAINFIDGLDGLAAGVALIGGSAFFVY
+SYLLTRTIDQFDYSNLATLLMALLIGACAGFLPYNRHPARIFMGESGALLLGLLLSTAAV
+AVTADLDALEGFRFRNVPAYMPVLLPIAVLALPLADLTISVIRRAAHGESPFGADRGHLH
+HRLVDGGFTHAQAVRVLWLWSFIVAWGVLSLNFADDAVVLLLAAAGLAVATWLTVHPL--
+RARAARPASRPDAQPKD--QP
+>4_728
+MRAYLVLVVVTAVACGALTPLMRRLGLRARVFTPLRQRDVHRHPVPKLGGVAMAAAVLVG
+FAVGGVVPFLQGIYADDAAMRGLLVAVAVVLVVGIADDMWDLRWWVKMAGQVLAGLAVAL
+GGIRIEAMPVGWIPVGNETTQVILTVFAVVLTMNAINFVDGLDGLAAGVALIGGSAFFVY
+SYLLTRTINQFDYANLATLLMALLVGACVGFLPWNLAPARIFMGEVGAMLIGLLMAAAAV
+AVTADVNALDGMRFRNVPAYMPILLPVAVLALPLADLALAVLRRTAKGTSPFSADRGHLH
+HKLVDGGYTQAQAVALLWLWAFLVAWGAVSLNFVDPMIVLPVLAVALAGAGYLTLHPIVE
+RRRAVRNDA--AAHPDERGDA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000698.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000698.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d9d93e47424a269ea52158c5f24f49cd0455f98f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000698.fa
@@ -0,0 +1,21 @@
+>0_762
+MTG------------AGGRRRRRRWENRRGWWGILGWSLAAAGVALAITCAAWLLSVGGE
+AAGSALLGGGAVLALSALTGVTTALVWDRAREAALPVSVGLFVLKIAVFAVLLGVLPRPG
+WVRADAAAIAALVTILVWQAAEVLVFARTRRGIYAD
+>1_502
+MTG------------AGGRRRRRRWENRRGWWGILGWSLAAAGVALAITCAAWLLSVGGE
+AAGSALLGGGAVLALSALTGVTTALVWDRAREAALPVSVGLFVLKIAVFAVLLGVLPRPG
+WVRADAAAIAALVTILVWQAAEVLVFARTRRGIYAD
+>2_2093
+MSPRTAPDAAPRSARARRRPRRRRWENRRGWWGILAWSLAATAAAVAVVCAVALAAGGPD
+AAASALLGGGAVLVLSALTGATTALVWDRAREAALPVSVGLFVLKIAVFAVLLGTVPRPD
+WILPDAAAIAALVAILVWQGVEVLVFARTRRGIYAD
+>3_1985
+MT-------------ASARPARRRWENRAGWWGILRWCCAATAVGVLACGAVAAVLHGGP
+AGLSALTGGGAVLVLSALTGATTAVAWDRARAAALPLSVGAFVVKLVLYALLLATLRMPE
+WMSGTAVAVGALVGVVVWQAVEVLVFARTRRGIYAD
+>4_729
+MTG------------AGGRRRRRRWENRRGWWGILGWSLAAAGAALAITCAAWLLSAGGE
+AAGSALLGGGAVLALSALTGATTALVWDRAREAALPVSVGLFVLKIAVFAVLLGVLPRPG
+WVRADAAAIAALVTILVWQAAEVLVFARTRRGIYAD
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000712.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000712.fa
new file mode 100644
index 0000000000000000000000000000000000000000..36b806a2d2a9e3fd7a04c62fb7ec5924ae66059d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000712.fa
@@ -0,0 +1,31 @@
+>0_776
+M----------------TPH---ASEPAPTHL-AAATRRRAVDAPDPDLALVTRGLTQRF
+GDKLALDALDLDVPAGSFFGVVGPNGAGKTTALSMATGLLRPDHGRAWIHGVDVWEQPLE
+AKRRVGVLADGVRTFDRLTGAQLVTYAGLLHGLDADTVAERTADLLRVMDLEDAGRTLVA
+DYSAGMTKKVSLAAAMVHAPDLLVLDEPFEAVDPVSAANIRDILHSYVERGGTVIVSSHV
+MDLVQRMCTHVAVIAAGTLRAAGTLEEVRDGRDLEDRFVELVGGRHGSEGLAWL
+>1_516
+M----------------TPH---APEPAPAHL-AAAARRRAADAPDPDLALVTRGLTQRF
+GDKLALDALDLDVPAGSFFGVVGPNGAGKTTALSMATGLLRPDHGRAWIHGVDVWEQPLE
+AKRRVGVLADGVRTFDRLTGTQLVTYAGLLHGLDADTVAERTADLLRVMDLEDAGRKLVA
+DYSAGMTKKVSLAAAMVHAPDLLVLDEPFEAVDPVSAANIRDILHSYVERGGTVIVSSHV
+MDLVQRMCTHVAVIAAGTLRAAGTLEEVRDGRDLEDRFVDLVGGRHGSEGLAWL
+>2_2078
+MSEHPAEPHRTAPSSAEAPHAGPAPAEAPAVVPSAAARRRAVDAPDPDLALVTRGLTKRF
+GDKTALDGLDLDVPAGSFYGVVGPNGAGKTTALSMATGLLRPDLGQAWIHGVDVWAQPLE
+AKRRVGVLADGVRTFDRLTGAQLVTYAGLLHGVDADTVAARTEDLLRVMDLADAGRKLVV
+DYSAGMTKKISLAAAMVHAPDVLVLDEPFEAVDPVSAANIRDILHDYVGRGGTVIVSSHV
+MDLVQRMCSHVAVIAGGTLRAAGTLEEVRAGRDLEDRFVDLVGGRHEQEGLAWL
+>3_1970
+M--------------------------------------RAQDAPDPNLALVTRGLAKRF
+GEKVALAGLDLEVPAGSFFGVVGPNGAGKTTALSMATGMLRPDAGRVWIHGVDVWEQPLE
+AKRRVGVLADGVRTFDRLTGAQLITYAGLLHGLDRDTVDVRTADLLRVMDLEEAGRKLVV
+DYSAGMTKKVNLAAAMVHAPDVLVLDEPFEAVDPVSAANIRDILHDYVGRGGTVIVSSHV
+MDLVQRMCSHVAVIAGGVLRAAGTLEEVRAGRDLEERFVDLVGGRHTGEGLAWL
+>4_743
+M----------------TPH---APEPAPAHL-AAAARRRAVDAPDPDLAFVTRGLTQRF
+GDKLALDALDLDVPAGSFFGVVGPNGAGKTTALSMATGLLRPDHGRAWIHGVDVWEQPLE
+AKRRVGVLADGVRTFDRLTGAQLVTYAGLLHGLDADTVAERTTDLLRVMDLEDAGRKLVA
+DYSAGMTKKVSLAAAMVHAPDLLVLDEPFEAVDPVSAANIRDILHSYVERGGTVIVSSHV
+MDLVQRMCTHVAVIAAGTLRAADTLEEVRDGRDLEDRFVDLVGGRHGSEGLAWL
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000719.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000719.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b6ab34ab1ccd86334916e67312c1c65324ef9b87
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000719.fa
@@ -0,0 +1,31 @@
+>0_784
+MAERFRWTRRGYTAQLELPEVRLLRGLVRDVVALLEGRRADVRPAEAD--PAEAPAA---
+-EDGVDTPEDPPAAPPSVSAAQDAGPVAGLDAS---DAAFWGLVSGLHLSQDPEPQRSAP
+TDPAVARLLPDAMPQAGAAEQGAHRALTEDALSEGKLADARLALELLRSTRVEVPHDQAP
+AFGRALNDVRLVLAARLGVETEEDAARVHAVDDWRSAEDVESTMALLYNFTSWLLETLMT
+EMLSELPEGADESAPGAGDAEDEQ
+>1_525
+MAERFRWTRRGYTAQLELPEVRLLRGLVRDVVALLEGRRADVRPAEAD--PAEAPAA---
+-EDGVDTPEDPPAAPPSVSAAQDAGPVAGLDAS---DAAFWGLVSGLHLSQDPEPQRSAP
+TDPAVARLLPDAMPQAGAAEQGAHRALTEDALSEGKLADARLALELLRSTRVEVPHNQAP
+AFGRALNDVRLVLAARLGVETEEDAARVHAVDDWRSAEDVESTMALLYNFTSWLLETLMT
+EMLSELPEGSDESAPGAGDAEGEQ
+>2_2070
+MAERFRWTRRGYTAQLEKPEVRLLRGLVKDVITLLEGRRRNVL-SEADDLPADAPGAPEP
+SADVAPVPQGPEAG---------AGPAAGLDEA---DAAFWELVSGLHLSQDRVPHRAAP
+ADPAVARLLPEAMPQADAQERGAHRALTEDALSEGKLADARLALELLRSTRVEVPHHQAP
+AFGRALNDVRLVLAARLGVETEEDAERVHAVDDWRSAEDVESTMALLYNFTTWLLETLMT
+EMLSELPEGADEDAPGADEAGDDA
+>3_1960
+MAQRFRWTRRGYVAELEDAELRLLRGLVKDVVTLLENRQDEVAPPGSD--AG--------
+------TAEDAPEAGAEPVADARPGDAVGPGEETPHDAAFWALVGGLDLVADPVAERSAP
+EDPAVARLLPDAMPHAEPAERARQRALTEDALTAAKLADARRALEALRSVRVTVPHEHAV
+SFGRALNDVRLVLAARLGIETEQDAARVHAVDDWRDAQDVEATMALLYNFTTWLQETLMA
+EMLSELPL---EGAAGPDEEE-RA
+>4_753
+MAERFRWTRRGYTAQLELPEVRLLRGLVRDVVALLEGRRADVRPAEAD--PAEAPAA---
+-EDGVDTPEDPPAAPPSVSAAQDAGPVAGLDAS---DAAFWGLVSGLHLSQDPEPQRSAP
+TDPAVARLLPDAMPQAGAAEQGAHRALTEDALSEGKLADARLALELLRSTRVEVPHDQAP
+AFGRALNDVRLVLAARLGVETEEDAARVHAVDDWRSAEDVESTMALLYNFTSWLLETLMT
+EMLSELPEGSDESAPGAGDAEGEQ
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000721.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000721.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca1eb19c5d9022571f2cb0434ebdf085124fceb7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000721.fa
@@ -0,0 +1,31 @@
+>0_786
+MKLTIIGASGSFPGPGSPASCYLLTAEGVAEDGVTPRTWRILLDLGNGALGVLQRYVELE
+DLDGILLSHLHPDHFMDLCGMHVAIRWNPAGWDRGRLPVYGPAGTADRIAEAYGMDPEPG
+MHQDFEFRCWAAGRTERLGPFRFTPVPVRHPIDEAYAIRVEVDRVDDDGDVTTRVLTYSG
+DTDACEGLVEAARDADVFLCEAAFHEGRDDGIDGVHLTGRRAGETAAQAGARKLLLTHLP
+VWNDPQRAVQEARAVYDGPLAVAVSGLSYGV
+>1_527
+MKLTIIGASGSFPGPGSPASCYLLTAEGVAEDGVTPRTWRILLDLGNGALGVLQRYVELE
+DLDGILLSHLHPDHFMDLCGMHVAIRWNPAGWGRGRLPVYGPAGTADRIAEAYGMDPEPG
+MHQDFEFRCWAAGRPERLGPFRFTPVPVRHPIDEAYAIRVEVDRVDDDGDVTTRVLTYSG
+DTDACEGLVEAARDADVFLCEAAFHEGRDDGIDGVHLTGRRAGETAAQAGARKLLLTHLP
+VWNDPQRAVQEARAVYDGPLAVAVSGLSYGV
+>2_2068
+MKLTVIGASGSFPGPGSPASCYLVTAQGVAEDGVTPRTWRILLDLGNGSLGVLQRYIELE
+ELDGILLSHLHPDHCMDLCGMHVAIRWNPEGWHRDRMPVYGPTATADRIAEAYGMDPEPG
+MHEDFDFRVWRPGRTERFGPFRLTPVPVRHPIDEAYAIRVEADEPDGEGGTVTRVLTYSG
+DTDACEGLVEAARDADLFLCEAAFHEGRDDGIDGVHLTGLRAGQTAAQAGAKKLLLTHLP
+VWNDPQRAVLEAREAYEGPMAVAVSGLSYGV
+>3_1958
+MKLTVIGASGSFPGPGSPASCYLVTADGPDGNGGT-RPWRILLDLGNGSLGVLQRHIELE
+QIDGVLLSHLHPDHCIDLCGLHVAVRWNPEGWDAGRIPVYGPAATATRIAEAYGMDPEPG
+MQEDFDFRAWEAGRTEGLGPFRLTPFAVRHPIDEAYAIRVETTEPGPDGEPVTRVLAYSG
+DSDTCDGLVEAARDADLFLCEAAYHEGRDDHIDGVHLTGRRAGQMAAEAGARKLLLTHLP
+VWNDPQRCAQEAREAYVGPLAVAVSGLSYGL
+>4_755
+MKLTIIGASGSFPGPGSPASCYLLTAEGVAEDGVTPRTWRILLDLGNGALGVLQRYVELE
+DLDGILLSHLHPDHFMDLCGMHVAIRWNPAGWGRGRLPVYGPAGTADRIAEAYGMDPEPG
+MHQDFEFRCWAAGRPERLGPFRFTPVPVRHPIDEAYAIRVEVDRVDDDGDVTTRVLTYSG
+DTDACEGLVEAARDADVFLCEAAFHEGRDDGIDGVHLTGRRAGETAAQAGARKLLLTHLP
+VWNDPQRAVQEAREVYDGPLAVAVSGLSYGV
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000724.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000724.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7d7a693ee506aafe190e84736ec68b5a05f2560
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000724.fa
@@ -0,0 +1,41 @@
+>0_789
+MSGGRVPV--PGLDFTAIDFETANGFRGSPCAVGAVRVRDGVMVDRAEWLIRPPVGFDRF
+DPRNVRIHGITEDRVLDAPRFAQVYDELADFVGTDVLAAHNAGFDVGVIESGLEVSGRDV
+PGLEFVCTLVLARRVYDLPSYALPSAAREAGFTPGRHHDALADAEACAAILVDIGRRVLG
+APPADADVLPGLTDAPAG-RG------VDRLMRAQGLGVSVLAPRAAGAGAESKATRQAR
+RTEGVFDARVPLRDERAMPDFMRWPDEGVNPLPNPAADPGHPLFGQTVVFTGGIGMSRQR
+AKTRAAAHGAQTANRVGAATTMLVVGDGFEAADL----------HRPRAEDGAPQAVTT-
+-ALAHRKTRDALRRRDRG------------------------
+>1_530
+MSGGRAPV--PGLDFTAIDFETANGFRGSPCAVGAVRVRDGVMVDRAEWLIRPPVGFDRF
+DPRNVRIHGITEDRVLDAPRFAQVYDELADFVGTDVLAAHNAGFDVGVIESGLEVSGRDV
+PGLEFVCTLVLARRVYDLPSYALPSAAREAGFTPGRHHDALADAEACAAILVDIGRRVLG
+APPADAEILPGLTDAPAG-RG------VDRLMRAQGLGVSVLAPRAAGSGAESKATRQAR
+RTEGVFDARVPLRDERAMPDFMRWPDEGVNPPPNPTADPGHPLFGQTVVFTGGIGMSRQS
+AKTRAAAHGAQTANRVGAATTMLVVGDGFEAADL----------HRPRAEDGAPQAVTT-
+-ALAHRKTRDALRRRDRGQAIALVSEGEFLQMLDGNWPDAAR
+>2_2065
+MSGVLAPV--PGLDFTAIDFETANGFRGSPCALGAVRVRDGVMVERAEWLIRPPVGFDRF
+DPRNVRIHGITEDRVLDAARFADVYDELAGFVGADVLAAHNAGFDVGVIESGLEVSGRDV
+PRLDFVCTLVLARRVYDLASYALPSAAREAGFAPGPHHDALADAEACAAILVDVARRVLG
+TEAGD-----GAAVAPAGARGLPEPFDVPRLMRAQGLTVNTLAQRAAGEGPESKATRQAR
+RAQGVFDARVPLKDERAMPDFLRWPDEGTNPVPNPDADPGHPLHGQTVVFTGGIGMSRQT
+AKVRAARLGAQTANRVGAATTMLVVGDGFEAADL----------DRPAPAPGTREAVTT-
+-ALAHRKTRDALRRRERGQHISLVSEGEFLQMLDGNWPDAAR
+>3_1955
+MTAGIAPVRQPGLDFTAIDFETANGFRGSACQLGAVRVRDGLPASRAVWLMRPPAGFDRF
+DPRNVRIHGIHADRVVDAPRFAEVYDAFAAFAGDDVLVAHNAGFDLGVIESGLEVSGRDV
+PAHDYACTLTLARRIYDLPSYSLPSAAREAGFVPGRHHDALADAEACAAILVDLARRV--
+CPPGEAT--------------------VDALLASQGLRRSRLTARAAGTGRESRATRQAR
+TMPGLFDATIPLADDRTLPDLMRWPDEGVNPEPAADADPGHPLYGQVVVFTGGIGMSRQE
+AKNRAAQRGAATANRVNGRTTMLVVGDGVDPAELVGAPEVHGVVVDPGATDPAGRGVDPG
+GAVTHRKTREALQRRAKGQAIALVSEAEFLQMVDGAWPAGAR
+>4_758
+MSGGRVPV--PGLDFTAIDFETANGFRGSPCAVGAVRVRDGVMVDRAEWLIRPPVGFDRF
+DPRNVRIHGITEDRVLDAPRFAQVYDELADFVGTDVLAAHNAGFDVGVIESGLEVSGRDV
+PGLEFVCTLVLARRVYDLPSYALPSAAREAGFTPGRHHDALADAEACAAILVDIGRRVLG
+APPADAEILPGLTDAPAG-RG------VDRLMRAQGLSVSVLAPRAAGSGAESKATRQAR
+RTEGVFDARVPLRDERAMPDFMRWPDEGVNPLPNPAADPGHPLFGQTVVFTGGIGMSRQS
+AKTRAAAHGAQTANRVGAATTMLVVGDGFEAADL----------HRPRAEDGAPQAVTT-
+-ALAHRKTRDALRRRDRGQAIALVSEGEFLQMLDGNWPDAAR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000732.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000732.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dea4bbc3848d0b2af32a3f485d38b54d00f6977a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000732.fa
@@ -0,0 +1,26 @@
+>0_797
+MTRADGSAYVGPMDTPTLHRRLRRVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLE
+MLLCPFDPTSTPDDHDRRAPG--VAEDDPHGPVTEASADRADVVEVGLANVATVADTGSG
+YQVETVTGFRTWFDVPEHTRVPVGDLTEDGTAELDQAEDATDFHAFMTAFMDELDRLYAT
+PETDATDVTPPDLH----GV
+>1_538
+------------MDTPTLHRRLRRVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLE
+MLLCPFDPTSTPDDHDRRAPG--VAEDDPHGPVTEASADRADVVEVGLANVATVADTGSG
+YQVETVTGFRTWFDVPEHTRVPVGDLTEDGTAELDQAEDATDFHAFMTAFMDELDRLYAT
+PETDATDVTPPDLH----GV
+>2_2049
+------------MDSPTLQRRLRGVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLE
+MLLCPFDPTSTPDDAPADAPAADAPEEDPHGPVAEPSSHGTDVVGVALGNVATVADTGSG
+YQVETVTGFRTWFDVPEHARVPVGDLTEDGTAGLDQAEDAVDFHAFMTAFMDELDRLYAA
+PEAGGTDVTGPDLH----AR
+>3_1947
+------------MDSPTLARRIRGAFDARVFNHGDYNLVYGQRSGGSLPLVIGYRHSPLE
+MLLCPLDP-------------------------VEAVAAVPE--EVALANVATVADTGSG
+YQVETVTGFRTWFEVVDRPRVPVGEASEDGLAELDQADDAADFHAFMTAFMDELDRLYAE
+P-------ADPDLHPPQKSV
+>4_766
+------------MDTPTLHRRLRRVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLE
+MLLCPFDPTSTPDDHDRRAPG--VAEDDPHGPVTEASADRADVVEVGLANVATVADTGSG
+YQVETVTGFRTWFDVPEHTRVPVGDLTEDGTAELDQAEDATDFHAFMTAFMDELDRLYAT
+PETDATDVTPPDLR----GV
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000733.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000733.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ede2c7a556664c1b7a658f093e4bcf42b0a3b14
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000733.fa
@@ -0,0 +1,45 @@
+>0_798
+MLTRLRGMDSAAS--TPSTPSAAPDIKPRSRDVTDGMERTAARGMLRAVGMGDEDFGKPQIGIASSWNEITPCNLSLDRL
+AQASKDGVHAAGGYPLEFGTVSVSDGISMGHEGMHFSLVSREVIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARL
+DLASVFVYAGSIMPGVARLTDGTERQVTIIDAFEAVGACARGLMSEEDLLRIEKSIAPGEGACGGMYTANTMASIGEALG
+MSLPGSAAAPSADRRRDAFARRSGKAVVNMLRQGITARDIMTKPAFENAIAVTMAFGGSTNAVLHLLAIAREAGVDLQLS
+DFNRIADRTPHIADLKPFGQYVMTDVDRIGGVPVVMKALLDEGLLHGDTLTVTGKTLAENLAALDPDPVDGKVIRTMDDA
+MHPNGGIAILHGSLAPEGAVVKSAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPKGGPGMREMLAITG
+AIKGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAAEGGPIGLVQDGDRIRVDIAGRTMDLLVDEAELAARRESWEPVEP
+KFTTGVLGKYAKLVHSAAEGAYLG
+>1_539
+MLTRLRGMDSAAS--TPSTPSAAPDIKPRSRDVTDGMERTAARGMLRAVGMGDEDFGKPQIGIASSWNEITPCNLSLDRL
+AQASKDGVHAAGGYPLEFGTVSVSDGISMGHEGMHFSLVSREVIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARL
+DLASVFVYAGSIMPGVARLTDGTERQVTIIDAFEAVGACARGLMSEEDLLRIEKSIAPGEGACGGMYTANTMASIGEALG
+MSLPGSAAAPSADRRRDAFARRSGKAVVNMLRQGITARDIMTKPAFENAIAVTMAFGGSTNAVLHLLAIAREAGVDLQLS
+DFNRIADRTPHIADLKPFGQYVMTDVDRIGGVPVVMKALLDEGLLHGDTLTVTGKTLAENLAALDPDPVDGKVIRTMDDA
+MHPNGGIAILHGSLAPEGAVVKSAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPKGGPGMREMLAITG
+AIKGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAAEGGPIGLVQDGDRIRVDIAGRTMDLLVDEAELAARRESWEPVEP
+KFTTGVLGKYAKLVHSAAEGAYLG
+>2_2048
+-------MDTAAS--TPRTPSAAPDMKPRSRDVTDGMERAASRGMLRAVGLGDADFAKPQIGIASSWNEITPCNLSLDRL
+AQAAKEGVHADGGFPLEFGTVSVSDGISMGHEGMHFSLVSREVIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARL
+DLASVFVYAGSTMPGHARLSDGTEKQVTIIDAFEAVGACARGLMSEEDLLRIEKAIVPTEGACGGMYTANTMASVGEALG
+MSLPGSATPPSPDRRRDDFARRSGAAVVNLLRQGITARDIMTKEAFENAIAVTMAFGGSTNAVLHLLAIAREAGVDLSLE
+DFNRVGDRTPHIADLKPFGRYVMTDVDRVGGVPVVMKALLDEGLLHGDALTVTGRTVAENLAELAPDPVDGDVIRTMDRP
+MHPNGGIAILHGSLAPEGAVVKSAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPRGGPGMREMLAITG
+AIKGAGLGKDVLLLTDGRFSGGTTGLCIGHIAPEAADGGPIGLVRDGDRIRVDIAGRTLDVQVAEEELEARRREWTPVPP
+KFTTGVLGKYAKLVHSAAEGAYLG
+>3_1946
+-------MDTSAADRTPQDVVTAPDMKPRSRDVTDGMERTAARGMLRAVGLGDEDFAKPQIGIASSWNEITPCNLSLDRL
+AQASKDGVHAAGGFPLEFGTVSVSDGISMGHEGMHFSLVSREVIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARL
+DLASVFVYAGSIMPGVARLTDGTEKQVTIIDAFEAVGACARGLMSEEDLLRIEKAIAPGEGACGGMYTANTMASIGEALG
+MSLPGSAAAPSADRRRDAFARRSGEAVVNMLRLGITARDVMTKPAFENAIAVTMAFGGSTNAVLHLLAIAREAGVDLQLS
+DFNRIADRTPHIADLKPFGQYVMTDVDRVGGVPVVMKALLDEGLLHGDTLTVTGKTLAENLAALDPDPVDGTVIRTMENA
+LHPNGGIAILHGSLAPEGAVVKSAGFDADVFEGTARVFDRERAAMDALEEGVIQAGDVVVIRYEGPKGGPGMREMLAITG
+AIKGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAADGGPIGLVRDGDRIRVDIASRTLDLLVEEAELEARRTSWQPVPP
+KFTTGVLGKYAKLVHSAAEGAYLG
+>4_767
+MLTRLRGMDSAAS--TPSTPSAAPDIKPRSRDVTDGMERTAARGMLRAVGMGDEDFGKPQIGIASSWNEITPCNLSLDRL
+AQASKDGVHAAGGYPLEFGTVSVSDGISMGHEGMHFSLVSREVIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARL
+DLASVFVYAGSIMPGVARLTDGTERQVTIIDAFEAVGACARGLMSEEDLLRIEKSIAPGEGACGGMYTANTMASIGEALG
+MSLPGSAAAPSADRRRDAFARRSGEAVVKMIRQGITARDIMTKPAFENAIAVTMAFGGSTNAVLHLLAIAREAGVDLQLS
+DFNRIADRTPHIADLKPFGQYVMTDVDRIGGVPVVMKALLDEGLLHGDTLTVTGKTLAENLAALDPDPVDGKVIRTMDDA
+MHPNGGIAILHGSLAPEGAVVKSAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPKGGPGMREMLAITG
+AIKGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAAEGGPIGLVQDGDRIRVDIAGRTMDLLVDEAELAARRESWKPVEP
+KFTTGVLGKYAKLVHSAAEGAYLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000747.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000747.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1096777caa25462ec3e09ccf5c2b1eba8e57ce41
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000747.fa
@@ -0,0 +1,41 @@
+>0_827
+M------TVRDPAAAAGATVGDLTEAELLEVVLTGLAPAVRDGHWPAGTVAPGDDAALVP
+APRGGTLISTDAMGEGTDFLHRWPAGPRTRGHDAGWKAVAQNLSDVNAMGGSASALVTAL
+TLPPTTPVAWVRSFAAGIVGAVRHLGAPDCRVAGGDLGTGGRVHAAVTVLGDPHPGGVLC
+RTPAAADRDRVLAEGADLVHAQAVPDGPRAA----------APPGPGWAAAGLAVLLTDR
+AELERRADALPAADRPSPRELARAVRAQLRPRPPLALGPAAVTAGLLTLMDVSDGLGKDA
+HRMAAATGGA----GPAPAPWLDEAWLAQAAAPLRRVAALAGTSPEALVTGGGEDYGLLG
+LAWPETELPRGFTRIGRLVPAGARAPAGHRPLPGSGWDPFA---G
+>1_558
+M------TVRDPAAAAGATVGDLTESELLEVVLTGLAPAVRDGHWPAGTVAPGDDAALVP
+APRGGTLISTDAMGEGTDFLPRWPAGPRTRGHDAGWKAVAQNLSDVNAMGGTASALVTAL
+TLPPTTPVAWVRSFAAGIVGAVRHLGAPDCRVAGGDLGTGGRVHAAVTVLGDPHPGGVLC
+RTPAAADRDRVLVEGADLVHAQAVPDGPRAA----------APPGPGWAAAGLTLLLTDR
+AELERRADALPAADRPSPRELARAVRAQLRPRPPLALGPAAVTAGLLTLMDVSDGLGKDA
+HRMAAATGGA----GPAPAPWLDEAWLAEAAAPLRRVAALAGTSPEALVTGGGEDYGLLG
+LAWPETELPRGFTRIGRLVPAGARPPAGHRPLSESGWDPFA---G
+>2_2032
+M------TPAGGRPADGRTVGEVTEAQLLRVVLDGLAPAVRPGHWPPGTVAPGDDAALVP
+APRGGTLVSTDAMGEGTDFLHRWPAGVRTRGHDAGWKAVAQNLSDVNAMGGTASALVTAL
+TLPPTTPLAWVRSFAAGVVGAVDRLGAPGCRVAGGDLGTGERVHAAVTVLGDPHPAGVLR
+RAPAPAARERVLAEGADLVHAQDAPGSSGAARSGALRPSA-ARPGPGWAAAGLALLLTDR
+DELARRAAALPPEDRPGARDLARAVRAQLRPRPPLALGPAAVEAGILTLMDVSDGLGRDA
+HRMAAATGAAASAEAPPPVPWIDAAWLAEAAAPLRGVAALAGVSAESLVTGGGEDYGLLG
+LAWPETALPAGFVRIGRLEPAGAPAPAGHRELPEAGWDPFG---G
+>3_1925
+MSTPASTASAGGRPAPARTVGEASEAELLDLIQDALAPVARDVPWPAGTVPPGDDCAVVP
+APRGLVAVSTDAMGEGTDFLRRWPAGVRTRGHDVGWKAAAQNLSDVNAMGATPSALVTAL
+ALPAPTPLDWVASLAGGFTAAVRALGADRCRVAGGDLGAGESVQVAVTALGDPDPAGALR
+RAAGGERGARIARRGADLVLAA---GSPRAAAAGEGQDSAWGPAGPGWAAAGLALLLTDR
+AVLTRRWADLAAHERPSARELARAVRGQLRPRPPLAAGPAAARAGLAALMDVSDGLGRDG
+HRLARASSAP----GAPLVPWVDRRWLAEAAEPLRRVASLAGTTPEALVLGGAEDYGLLG
+LAEPGLALPSGFRRVGRLAPAG-ETPDGHVRLPEAGWDHFDAGRG
+>4_786
+M------TMRDPAAAAGATVGDLTEAELLEVVLTGLAPAVRDGHWPAGTVAPGDDAALVP
+APRGGTLISTDAMGEGTDFLHRWPAGPRTRGHDAGWKAVAQNLSDVNAMGGTASALVTAL
+TLPPTTPVAWVRSFAAGIVGAVRHLGAPDCRVAGGDLGTGGRVHAAVTVLGDPHPGGVLR
+RTPAAADRDRVLAEGADLVHAQAVPDGPRAA----------APSGPGWAAAGLTLLLTDR
+AELERRADALPAADRPSPRELARAVRAQLRPRPPLALGPAAVTAGLLTLMDVSDGLGKDA
+HRMAAATGGA----GPAPAPWLDEAWLAEAAAPLRRVAALAGTSPEALVTGGGEDYGLLG
+LAWPETELPRGFTRIGRLVPAGARPPAGHRPLSESGWDPFA---G
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000748.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000748.fa
new file mode 100644
index 0000000000000000000000000000000000000000..33f3f14864ee80a5e221f98719fb19d8bec7a3b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000748.fa
@@ -0,0 +1,51 @@
+>0_828
+MTETTAPAAPAEQEAA---PRLSVIGTGYLGATHAACMAELGFEVLGVDVDPAKIERLAR
+GEVPFHEPGLPELLRTHVASGRLRFTTDVAEAARWADVHFIGVGTPQKVGETAADLSYVD
+AAVASLAAAIDRDALIVGKSTVPVGTARRLAELVRTVRAEAGLPGEVELAWNPEFLREGF
+AVRDTLTPDRLVIGMHGPRAEGILRRVYARQLAADTPWISTDLETAELVKVAANAFLATK
+ISFINAFSEITENVGGDIGTLADAIGHDARIGRRFLNAGVGFGGGCLPKDIRALQARVSE
+LGLDRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARDGRIRRAEASG-PAPTPASVQVLN
+GTRIAVLGVTFKPDSDDVRDSPALDVANRLYTAGADVRVYDPEGNANAAARFPRLDYVDS
+LEAAVDGAELTLLLTEWRQFREMDPDTVGARVASRLLIDGRNVLDVAAWREHGWDVIGLG
+HRFDPERLLRA-------A
+>1_559
+MTETTAPAAPAEQEAA---PRLSVIGTGYLGATHAACMAELGFEVLGVDVDPAKIERLAR
+GEVPFHEPGLPELLRTHVASGRLRFTTDVAEAARWADVHFIGVGTPQKVGETAADLSYVD
+AAVASLAAAIDRDALIVGKSTVPVGTARRLAELVRTVRAEAGLPGEVELAWNPEFLREGF
+AVRDTLTPDRLVIGTHGPRAEGILRRVYARQLAADTPWISTDLETAELVKVAANAFLATK
+ISFINAFSEITENVGGDIGTLADAIGHDARIGRRFLNAGVGFGGGCLPKDIRALQARVSE
+LGLDRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARDGRIRRAEASG-PAPTPASVQVLN
+GTRIAVLGVTFKPDSDDVRDSPALDVANRLYTAGADVRVYDPEGNANAAARFPRLDYVDS
+LEAAVDGAELTLLLTEWRQFREMDPDTVGARVASRLLIDGRNVLDVAAWREHGWDVIGLG
+HRFDPERLLRA-------A
+>2_2031
+M---THPSAPAEQDRA---PRLSVIGTGYLGATHAACMAELGFEVLGVDVDPEKIARLSR
+GEVPFHEPGLPELLRTHVESGRLRFTTDVAEAARWADVHFVGVGTPQKVGESGADLRYVD
+AAVASLAAAIDRDALIVGKSTVPVGTARRLAAMVRRVRAEAGLPGEVELAWNPEFLREGF
+AVKDTLTPDRLVIGTDGPRAEQVLRRVYARQLAADTPWISTDLETAELVKVAANAFLATK
+ISFINAFSEITEAVGGDIGTLADAIGHDARIGRRFLNAGVGFGGGCLPKDIRALQARVSE
+LGLDRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARDAGRGEAAAYG-GKTTASGVEVLR
+GARIAVLGVTFKPDSDDVRDSPALDVANRLYTAGADVRVHDPEGNANAAARFPRLDYVDS
+LEEAVEGAELTLLLTEWQAFREMDPAAVGALVDARLLIDGRNVLDLAAWAEHGWTVVGLG
+HRFDPAALG---------A
+>3_1924
+MTETAVVPAAAESEEAPARPRLSVIGTGYLGATHAACMAELGFEVLGVDVDPAKIERLAR
+GEVPFHEPGLPELLRAHVASGRLRFTTDVAEAASWADVHFIGVGTPQKVGEAAADLTYVD
+AAVESLARAIDRDALIVGKSTVPVGTARRLAARVAEIRAAEGLPGEVELAWNPEFLREGY
+AVKDTLTPDRLVIGTHGPRAELLLRTVYATPLAAGTPWISTDLETAELVKVAANAFLATK
+ISFINAFSEITETVGGDIGTLADAIGHDGRIGRRFLNAGVGFGGGCLPKDIRALQARVSE
+LGLDRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARQGVVRSAPGGARTAPTPAGVQVLN
+GTRIAVLGVTFKPYSDDVRDSPALDVANRLFTAGAEVAVYDPEGNANAAARFPRLGYVDS
+LDAALQGAELVLLLTEWDEFRQMDPAAAGELVAQRILIDGRNVLDVDAWGEHGWTVLGLG
+HRFDPAALNGGRPGDDAQA
+>4_787
+MTETTAPAAPAEQEAA---PRLSVIGTGYLGATHAACMAELGFEVLGVDVDPAKIERLAR
+GEVPFHEPGLPELLRTHVASGRLRFTTDVAEAARWADVHFIGVGTPQKVGETAADLSYVD
+AAVASLAAAIDRDALIVGKSTVPVGTARRLAELVRTVRAEAGLPGEVELAWNPEFLREGF
+AVRDTLTPDRLVIGTHGPRAEGILRRVYARQLAADTPWISTDLETAELVKVAANAFLATK
+ISFINAFSEITENVGGDIGTLADAIGHDARIGRRFLNAGVGFGGGCLPKDIRALQARVSE
+LGLDRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARDGRVRRADASG-TAPTPASVQVLN
+GTRIAVLGVTFKPDSDDVRDSPALDVANRLYTAGADVRVYDPEGNANAAARFPRLDYVDS
+LEAAVDGAELTLLLTEWRQFREMDPDAVGARVASRLLIDGRNVLDAAAWREHGWDVIGLG
+HRFDPERLLRA-------A
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000749.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000749.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb0f7d07b83be1af76ad61e194dc25e34f8313eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000749.fa
@@ -0,0 +1,31 @@
+>0_829
+MTTEPVRPPTEDDLIGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVIATGIARPTL
+HRLAAALTHHRMVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV
+FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT
+PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRLHAD
+AVVSAATRLTELIRAGEA
+>1_560
+MTTEPVRPPTEDDLIGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVIATGIARPTL
+HRLAAALTHHRMVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV
+FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT
+PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRLHAD
+AVVSAATRLTELIRAGEA
+>2_2030
+MTAEPARAQADDDVLGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVTATGIARPTL
+HRLAAALTHHRLVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV
+FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT
+PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRNHAD
+AVVAAATRLTELIRAGEA
+>3_1923
+MTTTPLPDAGAD--IGPALHVHPSGVGVVDKSVAILDALESGPATLAQLVTATGIARPTL
+HRLAAALTHHRLVAKDLQGRYVLGSRLAELASAAGEDRLTSAAGPVLQWLRDACGESAQV
+FRRQADSRVCVASAERPWGLRDTIPVGTRMSMKAGSAAQVLLAWEDNERLVDGLVGAVFT
+PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPNGKVIAALSISGPLERLSRQPGRLHAG
+SVVAAADRLTELIRAGEA
+>4_788
+MTTEPVRPPTEDDLIGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVTATGIARPTL
+HRLAAALTHHRMVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV
+FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT
+PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRLHAD
+AVVSAATRLTELIRAGEA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000750.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000750.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1ae3fe88c4d92570000def4bb7cf0c46ae8f92df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000750.fa
@@ -0,0 +1,51 @@
+>0_830
+--MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLA
+GRPVRRPDLTIATEDHNTPTLDIDQPIADATSRTQIETLRANCAEFGVRLHPLGDAEQGI
+VHVVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMA
+VTVDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAG
+ARAGMVAPDETTFAYLKGRPHAPEGDDWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPF
+VTWGTNPGQGVSLNDTVPAPEDFADPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSC
+TNSRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGC
+SMCLGMNPDQLSPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPA
+LTPQEA
+>1_561
+--MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLA
+GRPVRRPDLTIATEDHNTPTLDIDQPIADPTSRTQIETLRANCAEFGVRLHPLGDAEQGI
+VHVVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMA
+VTVDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAG
+ARAGMVAPDETTFAYLKGRPHAPEGADWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPF
+VTWGTNPGQGVSLNDTVPAPEDFTDPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSC
+TNSRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGC
+SMCLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPA
+LTLQEA
+>2_2029
+--MTSETTRPRTLAEKVWDEHVVVRGEGEGSSRTPDLLYIDLHLVHEVTSPQAFEGLRLA
+GRPVRRPDLTIATEDHNTPTLEIDKPIADPTSRTQIETLRANAAEFGVRLHPLGDAEQGI
+VHVVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMA
+ITVDGTLRPGVTAKDVILAVIAKIGTGGGQGFVLEYRGEAIRSLSMEGRMTICNMSIEAG
+ARAGMVAPDETTFAYLKGRPHAPEGADWDAAVEHWRTLATDEGAEFDAEVVIDADELEPF
+VTWGTNPGQGVSLNGAVPAPEDFDDPVAQESARKALGYMDLTPGTPMKEVAVDTVFMGSC
+TNSRIEDLRAFAEVVKGRKKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGC
+SMCLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPA
+LTPQEA
+>3_1922
+MSTQTQTPRPRTLAEKVWDEHVVVRGEGEGARRTPDLLYIDLHLVHEVTSPQAFDGLRLA
+DRPVARPELTIATEDHNTPTLEIDRPIADETSRVQIETLRANAEEFGVRLHSLGDREQGI
+VHVVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLRLKPFRTMA
+ITVDGTLRPGVTAKDVILAVIAKIGTGGGQGYVLEYRGEAIRSLSMEGRMTLCNMSIEAG
+ARAGMVAPDDTTFEYLKGRPHAPQGADWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPF
+VTWGTNPGQGVSLNDAVPAPEDFSDPAAQEAARKALSYMDLTPGTPMKDVAVDTVFMGSC
+TNSRIEDLRAFAEVVKGRTKADGLRVMVVPGSARVRLQAMDEGLDKVFEDFGAEWRFAGC
+SMCLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPLVAAATAVLGRLASPSDLPA
+LENQEA
+>4_789
+--MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLA
+GRPVRRPDLTIATEDHNTPTLDIDQPIADATSRTQIETLRANCAEFGVRLHPLGDAEQGI
+VHVVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMA
+VTVDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAG
+ARAGMVAPDETTFAYLKGRPHAPEGDDWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPF
+VTWGTNPGQGVSLNDTVPAPEDFADPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSC
+TNSRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGC
+SMCLGMNPDQLSPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPA
+LTPQEA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000758.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000758.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0c339e94b5444036a1091b9bf3cda7d5e658da90
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000758.fa
@@ -0,0 +1,36 @@
+>0_838
+---------------------MGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADAC
+PAQDDAGAVLAHAGAAALDSARGNSGMLLAVSLAGMAEPLRGRERVDAFALAAAFGAADR
+AARQALSDPREGTILTVLSAAARSLARSSTQAPDTPAVAGDADPAVRLGPAVTLMLADCV
+QAVEETESLLAPLTRAHVVDAGAVGLLWVFEALRAVVTGTPVDEELATALPGYGEGAHAA
+EAEPAA-AAEAPAEGAVEVMGTLALTPLAAAELRRRLTEVGDAVILAPLGTARDGQGRVP
+WRVHVHVPRAEDAIGPLRAAGDVEGLTVTDLAGPSH--------GDDA--APDGCHGR
+>1_569
+-MSTPSRPSLVRHWLALAEELVGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADAC
+PAQDDAGAVLAHAGAAALDSARGNSGMLLAVSLAGMAEPLRGRERVDAFALAAAFGAADR
+AARQALSDPREGTILTVLSAAARSLARSSTQAPDTPAVAGDADPAVRLGPAVTVMLADCV
+QAVEETESLLAPLTGAQVVDAGAVGLLWVFEALRAVVTGTPVDEELATALPGYGEGVHAA
+EGEPAA-AAEAPAEGAVEVMGTLTLTPLAAAELRRRLADVGDAVILAPLGTARDGQGRVP
+WRVHVHVPRAEDAIGPLRAAGDVEGLTVTDLAGPSH--------GDDA--APDGCHGR
+>2_2021
+-MSTPPRPSLVRHWLALAEELVGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADAC
+PAQDDAGAVLARAGAAALDLARGNSGTLLAVALAGMAEPLRGRARADAFALAAAFGAADR
+AARQALSDPREGTILTVLSAASRSLARSATQAPDSPAVAADVDPAVRLGPAVTAMMADCL
+RAVEQTESQLAPLAQARVVDAGAVGLLWVLEALRAAVTDTAPDEELATALHGYVEGVRPG
+P-EPA-------GEDAVEVMGTLALTPLAAADLRRRLAETGDSVILAPVGTERDEHGRVP
+WRVHVHVPRAADAVELMRAAGEVQGLAVTELSGDAA--------GPDA----DGCHGR
+>3_1914
+MIRARLRGALA--WLRGAEAALAQAAPRLDALNLFPVPDADTGSNMLATVRAARQAAER-
+SAGTDMSAVLRDAGAAALDSARGNSGTLLAVALVGLAAPLTPDAPLTTAELAAGARAADR
+AARAALSDPREGTILTVLREAATVL---------EAAAAGGREPAEALGSVVEA----AR
+RAVEDTEGQLAPLTRARVVDAGAVGLLLVLEALRAEVTRTPFDEGVVAALHGWADGPGAA
+GEDPQADGREAP---GVEVMCSIDLTPVDAAGLRRGLEEAGDSVILAPLSRAVDGAGRLR
+WRVHVHVARAEDAVALLEAAGAPEEVAVTDLWDPAHRHPDDPAEGDAASPAPDG-HGR
+>4_797
+-MSTPSRPSLVRHWLALAEELVGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADAC
+PAQDDVGAVLAHAGAAALDSARGNSGMLLAVSLAGMAEPLRGRERVDAFALAAAFGAADR
+AARQALSDPREGTILTVLSAAARSLARSSTQAPDTPAVAGDADPAVRLGPAVTVMLADCV
+QAVEETESLLAPLTRAHVVDAGAVGLLWVFEALRAVVTGTPVDEELATALPGYGEGVHAA
+EGEPAA-AAETPAEGAVEVMGTLALTPLAAAELRRRLADVGDAVILAPVGTARDGQGRVP
+WRVHVHVPRAEDAIGPLRAAGDVEGLAVTDLAGPSH--------G-DA--APDGCHGR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000763.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000763.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d800bda56538d716d88c71c5e02fcbbeaad7913
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000763.fa
@@ -0,0 +1,36 @@
+>0_843
+M----TVPPPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVTEARRAG
+LADVLMITGRNKRALEDHFDRHPALEAALEHKGDTKRLAQIHESDLVGDIHYVRQGEALG
+LGHAVNCARRHVGEEPFAVLLGDDIIGDGEALLERMIDVQQRLGGSVIALMEVPEEAVSA
+YGVAAVQAVPGEGDDVVRVTDLVEKPAREDAPSTLAIIGRYVLAPQVFDVLDETPPGRGG
+EIQLTDALQRLATEDGEGRGVHAVVFDGRRYDTGDKLGYLQAVIEFGTRHEDLGADLRAW
+LREFTAGL
+>1_574
+M----TVPPPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVTEARRAG
+LADVLMITGRNKRALEDHFDRHPALEAALEHKGDAKRLAQIHESDLVGDIHYVRQGEALG
+LGHAVNCARRHVGEEPFAVLLGDDIIGDGEALLERMIDVQQRLGGSVIALMEVPEEAVSA
+YGVAAVEAVPGEGDDVVRVTDLVEKPAREDAPSTLAIIGRYVLAPQVFDVLDETPPGRGG
+EIQLTDALQRLATEDGEGRGVHAVVFDGRRYDTGDKLGYLQAVIEFGARHEDLGADLRAW
+LREFTAGL
+>2_2016
+M----TV--PSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVAEARRAG
+LQDVLMITGRNKRALEDHFDRHPALEATLERKGDATRLAQIRESDLVGDIHYVRQGEALG
+LGHAVNCARRHVGDEPFAVLLGDDIIGDGEALLARMIDVQQRLGGSVVALMEVPEEAVSA
+YGVAAVEAVPGEGEDVVRVTGLVEKPAREDAPSTLAVIGRYVLASQVFDVLDRTPPGRGG
+EIQLTDALQTLADDDGEGGGVHAVVFDGRRYDTGDKLGYLQAVVEFGTRHEELGGDLRAW
+LKAFAAGL
+>3_1909
+MTEQSTAASPTRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVAEAVSAG
+LGDVLMITGRNKRALEDHFDRHPALEQVLEAKGDTKRIDLIRASDLVGDIHYVRQGEALG
+LGHAVGCARRHVGDEPFAVLLGDDLIGEDEGLLARMIDVQHRLGGSVIALMEVPEDAVSA
+YGVAAVAPVDGEDDDVVAVTSLVEKPARGDAPSNLAIIGRYVLAPQVFEVLERTAPGRGG
+EIQLTDALQTLAAGEGEGFGVHAVVFRGRRYDTGDKLGYLQAVVELGVRHPELGGDLREW
+LKGFAAGL
+>4_802
+M----TVPPPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVTEARRAG
+LADVLMITGRNKRALEDHFDRHPALEAALEHKGDATRLAQIHESDLVGDIHYVRQGEALG
+LGHAVNCARRHVGEEPFAVLLGDDIIGDGEALLERMIDVQQRLGGSVIALMEVPEEAVSA
+YGVAAVQAVPGEGDDVVRVTDLVEKPAREDAPSTLAIIGRYVLAPQVFDVLDETPPGRGG
+EIQLTDALQRLATEDGEGRGVHAVVFDGRRYDTGDKLGYLQAVIEFGTRHEDLGADLRAW
+LREFTAGL
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000772.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000772.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d11d1870d75abf234c0613114b053a7eb95c0447
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000772.fa
@@ -0,0 +1,31 @@
+>0_863
+MSDTG-DPRVPSGTAVLTVDGATLRRVGARPGLARYLASLWEYRSFILFDSRSRIAGANS
+VNALGRVWMVLNPILDGAAYFLVFGLLLGTGRGVPNFLGYLIIGVFLFRYTSSAITAGSR
+SISTNLSIVRAFRFPRATLPIATNIRELMLFGPTLVVMLVLVLAIPPMEQITWRWLLLIP
+LLALQTLFNVGASLLLARYVARWSDLSNLIAFGTRIWLYVSAVFFSADRFA-DFPPMMTA
+MHLNPLFCVLDIARQSLLYASDADPMRWVVLAAWTAALLVVGTVVFWRAEETYGEE--R
+>1_594
+MADTG-DPRVPSGTAVLTVDGATLRRVGARPGLARYLASLWEYRSFILFDSRSRIAGANS
+VNALGRVWMVLNPILDGAAYFLVFGLLLGTGRGVPNFLGYLIIGVFLFRYTSSAITAGSR
+SISTNLSIVRAFRFPRATLPIATNIRELMLFGPTLVVMLVLVLAIPPMEQITWRWLLLIP
+LLALQTLFNVGASLLLARYVARWSDLSNLIAFGTRIWLYVSAVFFSADRFA-DIPPLMTA
+MHLNPLFCVLDIARQSLLYASDADPMRWIVLAAWTAALLVVGTVVFWRAEETYGEE--R
+>2_2000
+MSGTGMAASGPVNTVV--VDAAPLGVVGARPSLRDYVLSLFRYRSFILFDSRSRISGANA
+VNTLGRLWMVLNPILDGGAYFLVFGVLLGTGRGIPNFIAYLIIGVFFFRYSSQAITAGSK
+AVSSNLTLVRAFRFPRATLVLATNLRALLEFVPTLAVMVVLILAIPPLEVFTWRWLLLVP
+LLILQTLFNVGLSLVLARFVAHWPDLANMIAFGMRIWLYLSAVFFSVERFD-GQPIVQTA
+MHLNPLYCVLDIARQSLLYGQDAEPHRWLVLAGWAALVAVVGLVVFWRAEETYGEE--R
+>3_1897
+MTDRV-EATSPP--VELRVDESRLERVGRRPSLGDYVTRLWRLRHYVRYDAVAAVQAQNR
+RHRLGNVWLLLNPILNGATYFLVFGVLLRTSLGVENFIGYLTVGVFMFTFTTRAVTALSR
+SLTARNNVADAFQLPRAVLPLTALAREVLAYGFTLAAMLLAVLILPPHAQVTWWWLLFPV
+VVALQLMLVAGVGLLLARAVSRVRDLSQIVGFGIRLWMYGSAVFYSFDRFV-SQPNVLAV
+LQLNPMYQVLDISRDLLLYGRSPSPVAWGILAAWSVGLLVVGVVVFWLGEERYAKDLNR
+>4_814
+------------------------------------------------------------
+-------------MLDAIFYWLIFGLLLRFDHGMDNFVAFVIVGVFMFQMTSAALTSGTR
+TIASNLSLTRAFRFPRMALPLADLVYDVLQRLPAIAVMFILVIAIPPHETPEWSWLVFPG
+VLGLHVILNFGIMLLLARLSTLLPDVSRMVPFVSRLLMYGSGVIFPITRFTDNHPALHAI
+IQLNPLYVLITMYRQVIIEGVTPPASSWAMLAAYAVCLTIVGGIVFWLGEESYGRDQYR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000773.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000773.fa
new file mode 100644
index 0000000000000000000000000000000000000000..821eb4f605d55e97811d941e1cfc1a8fb30a6762
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000773.fa
@@ -0,0 +1,41 @@
+>0_864
+MP-KVMPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDL
+NIIQPRQTLNGVFARTLDGLDAVLEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEA
+GLRSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAAEDIYVTGNTVIDALL
+EAVGHQVPFEDERLAELEAS-----GRRVVLVTTHRRENQGDAMRGVGRALARLAADHPE
+VTFVLPAHRNPVVREAILPEIEGRENVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAP
+SLGKPVLVMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLLTDEAAYTAMSQAVNPYGD
+GRAAERTVSAIAELLGVGERLPAFDGGDPA
+>1_595
+MP-KVMPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDL
+NIIQPRQTLNGVFARTLDGLDAVLEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEA
+GLRSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAPEDVYVTGNTVIDALL
+EAVSHQVPFEDERLAGLEAS-----GRRVVLVTTHRRENQGDAMRGVGRALARLAADHPE
+VTFVLPAHRNPVVREAILPEIEGRENVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAP
+SLGKPVLVMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLLTDEAAYSAMSQAVNPYGD
+GRAAERTVSAIAELLGVGERMPEFAPDDRG
+>2_2001
+M--KVMPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDL
+NIIQPRQTLNGVFARTLDGLDAILEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEA
+GLRSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAPEDVYVTGNTVIDALL
+EAVGHQVPFEDERLAELEAS-----GRRVVLVTTHRRENQGDAMRGVGRALARLAADHPE
+VTFVLPAHRNPVVREAILPEIEGRANVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAP
+SLGKPVLVMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLLTDEAAYTAMSQAVNPYGD
+GRAAERTVSAIAELLGVGERLPAFDGA---
+>3_1898
+MPLKIMPIYGTRPEAIKMAPIVNALRADDRFECFTTVTGQHREMLDQVNAIFGITPDADL
+DIMRPNQTLNGIMSVMLEGLDELLVRERPDAVVVQGDTTTSTAGAIAAFYRGIPVVHAEA
+GLRSGDLFSPFPEEANRKITSQIASLHLAPTSVSRANLEREAIDSAAITVTGNTVIDALL
+ETVAQQLPFTDPRLAELAERRAADPQSRVLLVTTHRRENQGEAMRGVGRALARLAQSHPN
+LTIVLPAHRNPVVREAVLPTLEGIDSVIVTEPLPYGEFTRMMDLADVVLTDSGGVQEEAP
+SLGKPVLVMRDNTERPEAVHAGTVRLIGTDEERLVEETSLLLTDPDAYAAMAHAVNPYGD
+GRAGLRTVAAIAQLLGVGDRLDEFGA----
+>4_815
+-----MPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDL
+NIIQPRQTLNGVFARTLDGLDAVLEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEA
+GLRSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAAEDIYVTGNTVIDALL
+EAVSHQVPFEDERLAELEAS-----GRRVVLVTTHRRENQGDAMRGVGRALARLAADHPE
+VTFVLPAHRNPVVREAILPEIEGRENVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAP
+SLGKPVLVMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLVTDEAAYTAMSQAVNPYGD
+GRAAERTVSAIAELLGVGERLPAFDGA---
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000776.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000776.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9bd9812c7dd58c4aff27f4a483d5dd112fecb93b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000776.fa
@@ -0,0 +1,46 @@
+>0_870
+MNEMT-LDAGTVWMVVSAGLVLLMTPGLALFYGGMTRSKSALNMMMMSFVSMGLVGVVWI
+LWVSGMTGGEGWLGLVGSPLADPGLTTAMEEGGLIAAGFGATFAIITVALISGAVADRAR
+FLTWCVFVPVWVTLVYAPLAYMVWGGGLLAEEGAIGSRLGEALDFAGGLVVHISAGVAAL
+VLALMMGKRKGFGVDPGHKPHNVPFTMLGAALLWFGWFGFNGGAAGDTGQLGLIWINTLA
+AAAAGMLGWVVVEWVRRGRPTSIGTASGIVAGLVGITPACAFVSPLGALVIGVASGAASA
+LAVNLKYRLGFDDSLDVVGVHLTAGILGTVLIGFFALPSEGPAGLFYGGDGRLLLAQTVA
+VVVAVVFTAVLTFLIALVLKATLGLRVSEEDEERGVDLTLHDESAYHYDVGFGGVPVPAD
+AQAHRGGAAG
+>1_598
+MEESNVLDAGTVWMVTSAAMVLLMTPGLAIFYGGMTRAKSSLNMIMMSFVSMGLVGVVWV
+LWVHGMTGGDGWAGVVGNPAGDLGLTGTMAEGGLVAAAYGATFAIIAVALISGAVADRFK
+FVTWCVFVPVWTTVVYAPLAYMVWGGGLLSEDGAIGARLGEALDFAGGLVVHISAGVAAL
+VLALLLGKRHGFGVDPGHRPHNVPFTMLGAALLWFGWFGFNGGAAGGVDELGLIWVDTLA
+AGAAGMLGWVFVEWLRRGRPTSIGTASGIVSGLVAITPACAYVSPLGAVVIGLVSGAASA
+LAVNLKYRLGFDDSLDVVGVHLTSGILGTVLIGFFALPGEGRAGLFYGGDAGLLVAQTVA
+VLVAVVFTAVVTTAIALVLRGTMGLRVSKEDEERGVDLTLHDESA--YDVGFGGVPVPAE
+AR--------
+>2_1996
+MNEMT-LDAGTVWMVVSAGLVLLMTPGLALFYGGMTRSKSALNMMMMSFVSMGLVGVVWI
+LWVSGMTGGEGWLGLVGSPLADPGLTTAMEEGGLIAAGFGATFAIITVALISGAVADRAR
+FLTWCVFVPVWVTLVYAPLAYMVWGGGLLAEEGAIGSRLGEALDFAGGLVVHISAGVAAL
+VLALMMGKRKGFGVDPGHKPHNVPFTMLGAALLWFGWFGFNGGAAGDTGQLGLIWINTLA
+AAAAGMLGWVVVEWVRRGRPTSIGTASGIVAGLVGITPACAFVSPLGALVIGVASGAASA
+LAVNLKYRLGFDDSLDVVGVHLTAGILGTVLIGFFALPSEGPAGLFYGGDGRLLLAQTVA
+VVVAVVFTAVLTFLIALVLKATLGLRVSEEDEERGVDLTLHDESAYHYDVGFGGVPVPAD
+AQAHRGGAAG
+>3_1893
+MTETTPLDAGAVWTVTAAALVLLMTPGLALFYGGMTRAKSALNMMMMSFVSMGLIGVAWI
+LWAYGMTSGDGLAGIVGSPLNDLGAVQSMADGDLISVGFSATFAIIAVALISGAVADRAK
+FSTWCVFVPVWVTLVYAPLAYMVWGGGLLSADGAIGARLGEALDFAGGLVVHISAGVAAL
+VLAMMMGKRQGFGVDAAHRPHNVPFTMLGAALLWFGWFGFNSGAASDVEQLGLTWVTTLV
+AAAAGMLGWVLVEWLRRGRPTSIGTASGIVSGLVAITPACAFVSPLGAVVIGLVAGAACA
+LAVNLKYRWGFDDSLDVVGVHLTAGILGTLLIGLFALPETGHAGLFHGGDGSLLLAQTVA
+VVVAVVFTAVVTAVIAFVLRATLGLRVSVEEEERGVDLTLHDETA--YDVGFGGVPVPTD
+AQARSTAAAE
+>4_818
+MEESNVLDAGTVWMVTSAAMVLLMTPGLAIFYGGMTRAKSSLNMIMMSFVSMGLVGVVWV
+LWVHGMTGGDGWAGVVGNPAGDLGLTGTMAEGGLVAAAYGATFAIIAVALISGAVADRFK
+FVTWCVFVPVWTTVVYAPLAYMVWGGGLLSADGAIGARLGEALDFAGGLVVHISAGVAAL
+VLALLLGKRHGFGVDPGHRPHNVPFTMLGAALLWFGWFGFNGGAAGSVDELGLIWVATLA
+AGAAGMLGWVFVEWLRRGRPTSIGTASGIVSGLVAITPACAYVSPLGAVVIGLVSGAASA
+LAVNLKYRLGFDDSLDVVGVHLTAGILGTVLIGFFALPDEGRAGLFYGGDAGLLVAQTVA
+VLVAVVFTAVVTTAIALVLRGTMGLRVSKEDEERGVDLTLHDESA--YDVGFGGVPVPAE
+AR--------
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000778.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000778.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b38ca43f43c615674c5dfd4967a474a216c3651c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000778.fa
@@ -0,0 +1,21 @@
+>0_872
+MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL
+SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE
+APAESEQAAEAP---A--AEAPAEDAEKSE
+>1_600
+MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL
+SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE
+APAESEQAAEAPAEEA--AEAPAEDAEKSE
+>2_1994
+MAVKIRLKRFGKIRAPYYRIVVADSRTRRDGRAIEEIGKYHPTEEPSYIEVDSERAQYWL
+SVGAQPTEQVAALLKITGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKAEE
+PKAKESAEAETPAEEA--PEAPAEDAEKSE
+>3_1891
+MAVKIRLKRFGKIRAPYYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL
+SVGAQPTEQVAALLKITGDWQKFKGEAGAEGTLKTKGEKEAFVAPAKESVILPEEPKQEE
+APAESAE-AEAPVEEAADAEAPAEDAEKAE
+>4_820
+MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL
+SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE
+APAESEQAAEAPAEEA--AEAPAEDAEKSE
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000780.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000780.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0f1cc550bc5982c75981baa315bd629e24fae55
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000780.fa
@@ -0,0 +1,26 @@
+>0_874
+MSPAAQ----DDLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGERLVVRDGAPGLPAE
+LTVTRARWNKQILVVGFEESPDRNVAETLRGAQLFAVPAAPEESDEWYEEDLVDLEVRVD
+GERVGVVTALTTGAVQDLLHVALDGVEEEALVPFVEEIVPEIDPEAGVLVLTPPPGLLEL
+ATGE-----DEGAADGPTDADA--ED
+>1_602
+MSPAAQ----DDLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGERLVVRDGAPGLPAE
+LTVTRARWNKQILVVGFAESPDRNVAETLRGAQLFAVPAVPEESDEWYEEDLVDLEVRVE
+GERVGVVTALTTGAVQDLLHVALDGVEEEALVPFVEEIVPEIDSEAGVLVLTPPPGLLEL
+ATGE-----DEGAVDGPADADA--ED
+>2_1992
+MSPAPQ----DGLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGATLTVRDGGPSLPAE
+LTVTRARWNKQILVVGFEQSPDRNTAETLRGAQLFAAPAAPEESDEWYEDDLVDLEVRVD
+GRRVGVVTALTTGAVQDLLHVALDGVDEEALVPFVEEIVPEIDPEAGVLVLTPPPGLLEL
+ASGEAEQDDDAAASDAEADADAGREG
+>3_1889
+MSPAPQPAETEGQVRVARIGKPHGIRGEVTVQLFTDDPEARFAADSRLEVRQGPPGAPAA
+LTVTRARWNKAILVVGFAEVPDRNAAEALRGAQLYAAPLEKVEDDAWYEDDLLDLEVHVD
+GARVGVVTGLLTGTVQDLLQVRLDATGDDALVPFVEEIVPEVDQEAGVVVVAPPPGLLEL
+ASET-----TAG------------EG
+>4_822
+MSPAAQ----DDLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGERLVVRDGAPGLPAE
+LTVTRARWNKQILVVGFAESPDRNVAETLRGAQLFAVPAAPEESDEWYEEDLVDLEVRVE
+GERVGVVTALTTGAVQDLLHVALDGVEEEALVPFVEEIVPEIDSEAGVLVLTPPPGLLEL
+ATGE-----DEDAADGPADADA--ED
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000783.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000783.fa
new file mode 100644
index 0000000000000000000000000000000000000000..81aa5036059b64b2301cf34bd793fa7998d4754d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000783.fa
@@ -0,0 +1,31 @@
+>0_877
+MRTSEPRDPRRSRGSVAS---GAGSSPGTTAAPASGASRWWAWLGLTVVAAVVVAAVLRA
+LTGPVYLIPSGSMEPTLQPGDRVRVDAAAAGGQGLHHGDVVVFDGAGSLAPYRSAGSLER
+GLEDVARWWGVGAAEDVFVKRVLALPGDRLECCAPDGRLLREGEPLDEPYLGRPVTADEP
+AAAGTWSFEVPDGRMVVLGDHRAASRDSRALLGAPGGGLIPLERVEGRAAEIVWPLSRRG
+TVDAPSGDT-----P
+>1_605
+MRTSEPRDPRRSRGSVAS---GAGSSSGPTAAPASGTSRWWAWLGLTVVAAVVVAAVLRA
+LTGPVYLIPSGSMEPTLQPGDRVRVDAAAAGGQGLHHGDVVVFDGAGSLAPYRSAGSLER
+GLEDVARWWGVGAAEDVFVKRVLALPGDRLECCAPDGRLLRNGEPLDEPYLGRPVTADEP
+AAAGTWSFEVPDGRMVVLGDHRAASRDSRALLGAPGGGLIPLERVEGRAAEIVWPLSRRG
+TMDAPSGDT-----P
+>2_1989
+MSHPEPRDPRRSRGSAVSRSVAPGSGRGTTPARGSGGTAWWAWIGLTVAAAVGAAAVLRA
+LTGPVYLIPSGSMEPTLHPGDRVRVDASAAGGEGVRRGDVVVFDGAGSLAPYRSVGSLER
+GLEDVARSWGLGASGDAFVKRVLALPGDRLECCAPDGRLLRDGAPVDEPYLGRPVTAQDP
+AADGSWTFEVPEGRMVVLGDNRSASRDSRALLGGAGGGLIPLKRVEGRAAEVVWPLDRRG
+PVDASAPEAAPGAAP
+>3_1886
+MRAQEPRDRNRSRGSRAS---GEAGRP------------WWALVLLTLAGAVVAAALLRA
+FTGPVYLVPSGSMEPTLLPGDRVHVDTAAADGAGLEHGDVVVFDGAGSLAPYRSRTALDR
+GLEDVAAFWGVGAAQDVYVKRVLALPGDTLSCCTADGRLERNGAPLDESYLGRTVDAAAP
+ASRSTWAFEVPEGRMVVLGDNRDVSRDSRALLGAPGGGLIPVEKVIGRVDSVAWPLDRRG
+DVPAGAQDGSRG---
+>4_825
+MRTSEPRDPRRSRGSVAS---GAGSSSGPTAAPASGTSRWWAWLGLTVVAAVVVAAVLRA
+LTGPVYLIPSGSMEPTLQPGDRVRVDAAAAGGQGLQRGDVVVFDGAGSLAPYRSAGSLER
+GLEDVARWWGVGAAEDVFVKRVLALPGDRLECCAPDGRLLREGEPLDEPYLGRPVTADEP
+AAAGTWSFEVPDGRMVVLGDHRAASRDSRALLGAPGGGLIPLERVEGRAAEIVWPLSRRG
+TVDAPSGDT-----P
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000795.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000795.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2b281e7a74e945faf2f9261efa4bdb67005e5f37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000795.fa
@@ -0,0 +1,36 @@
+>0_889
+MLAIVCPGQGSQTPGFLAPWLELDGTRDLLASLSDAAGVDLIRHGTESDEETIKDTAVAQ
+PLIVAAGLVAAAALEADAAAPKSTVVAGHSVGEVTAAAVTGVLSPAEALSLVRVRATGMA
+RAAAATPTGMAAVVGGDQDEVLAAIDAAGLAPANVNGAGQIVAAGTAEALGALAESAPAR
+ARVIPLKVAGAFHTEHMRPAVDDLATHVAGLSPSDPRLPLLSNRDGETVESGTDVLARIV
+DQVTRPVRWDLCMATMAARQVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA
+FLAEHSA
+>1_617
+MLAIVCPGQGSQTPGFLAPWLELDGTRDLLASLSDAAGVDLIRHGTESDEETIKDTAVAQ
+PLIVAAGLVAAAALEADAAAPKSTVVAGHSVGEVTAAAVTGVLSPAEALSLVRVRATGMA
+RAAAATPTGMAAVVGGDQDEVLAAIDAAGLTPANVNGAGQIVAAGTAEALGALAESAPAR
+ARVIPLKVAGAFHTEHMRPAVDDLAAHVAGLSPSDPRLPLLSNRDGEAVESGTDVLARIV
+DQVTRPVRWDLCMATMATRQVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA
+FLAEHSA
+>2_1976
+MLAIVCPGQGSQTPGFLSPWLELDGTRALLESLSDAAGVDLVRHGTESDEETIKDTAVAQ
+PLIVAAGLVAAAALEADAAAPASTLVAGHSVGEITAAAVTGVLSPADALALVRVRATGMA
+RAAAATPTGMAAVVGGDQDEVLAAIEAADLAPANVNGAGQIVAAGTAEALAALGESAPAR
+ARVIPLKVAGAFHTEHMRPAVEELAAHVAGLSPADPRLTLLSNRDGQAVDAGAEVLSRIV
+DQVTRPVRWDLCMEAMAEREVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA
+FLAEHTA
+>3_1874
+MLAIVCPGQGSQTPGFLAPWRELEGVPSLLDRLSAAAGVDLTAHGTVSDEETIKDTAVAQ
+PLIVAAGLVAADVLGLDALAPDRVLAAGHSVGEITAAAVAGVLSPEDALALVRVRATGMA
+EAAAATPTGMAAVVGGDQDEVLAAVEAAGLTPANVNGGGQIVAAGTQDALDALAAQPPAR
+ARVIPLKVAGAFHTEHMRPAVDALAAHVTGLSPADPRLTLLSNREGAAVASGTEVLERIV
+NQVTRPVRWDLCMEAMAERGVTGIMEVLPGGTLAGLAKRGLKGVPSLAVKAPDDLDAARA
+FIAEHTA
+>4_837
+MLAIVCPGQGSQTPGFLAPWLELDGTRDLLASLSDAAGVDLIRHGTESDEETIKDTAVAQ
+PLIVAAGLVAAAALEADAAAPKSTVVAGHSVGEVTAAAVTGVLSPAEALSLVRVRATGMA
+RAAAATPTGMAAVVGGDQDEVLAAIDAAGLAPANVNGAGQIVAAGTAEALGALAESAPAR
+ARVIPLKVAGAFHTEHMRPAVDDLAAHVAGLSPSDPRLPLLSNRDGEAVESGTDVLARIV
+DQVTRPVRWDLCMATMATRQVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA
+FLAEHSA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000802.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000802.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5a9b63e5277c5b78f20c355a7090e32029e9c8c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000802.fa
@@ -0,0 +1,31 @@
+>0_896
+MGLLRDLLTRRS--ARDRSSDPPATLGRHLDNAAAIVAAARRADVPLAVAAALAELESGG
+RNVFGHDAGGVHSAPRGTDVLVTRERYEELVARVAQGETSNGVGPAQITWPPYFAQAAER
+GLHLWEPEDNLAFGLEILRGHLRGDLSAEGIARAGTLYNAGTLSDGVTAYGRRLAAASRA
+WAERLGEPAPPPVRPG--------------------------------------------
+--------------------
+>1_624
+MGLLRDLLTRRS--ARDRSSDPTATLGRHLDNAAAIVAAARRADVPLAVAAALAELESGG
+RNVFGHDAGGVHSAPRGTDVLVTRERYEELVARVAQGEKSNGVGPAQITWPPYFAQAAER
+GLHLWEPEDNLAFGLEILRGHLRGDLSAEGIARAGTLYNAGTLSDGVTAYGRRLAAATRA
+WAERLGESAPPPVRPG--------------------------------------------
+--------------------
+>2_1968
+MATTPS-VGRMSWFPRRRAASAPRALAARLENADAIAAAARRADVPLPVAAALAQLESGG
+RNVFGHDAGGVHAAPRGTDVPVTRELFEELEARVAAGETSNGVGPAQITWPPYFAQARRR
+GLRLWEPEDNMAFGLEILRGHLGGDLTEEGIARAGTLYNAGTLQGGVTDYGRRLARASRD
+WARRLGEPAPPSSSPGRGAGRDGDRGRARSGAPGRTHVIEPGDTLWAIARANGTDVATLR
+RLNPDLVPEALAVGAPVRLP
+>3_1865
+M-------------------DPVTVLSASLAHPEAIVAAAGRARVPVSVAAALAELESGG
+RNVFGNDVGGVFSSPGAPDVEVTPERVAELRRRVADGERSNGVGPAQITWPPLFDRADAE
+GLDLADPEDNMTLGLSLLRDSARGDFSVAGLERAGTLYNAGTLAGGVTDYGRRLAAAAAA
+WERRL-------TARG--------------------------------------------
+--------------------
+>4_844
+MGLLRDLLTRRS--ARDRPSDPTATLGRHLDNAATIVAAARRADVPLPVAAALAELESGG
+RNVFGHDAGGVHSAPRGTDVPVTRERYEELVARVAQGETSNGVGPAQITWPPYFAQAAER
+GFRLWEPEDNLAFGLEILRGHLRGDLSAEGIARAGTLYNAGTLTHGVTAYGRRLAAATRV
+WAERLGELAPPPVRPG--------------------------------------------
+--------------------
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000803.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000803.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b0d7aeffafa708b7d7e378c4b677df85c97da115
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000803.fa
@@ -0,0 +1,21 @@
+>0_897
+MSATPLGFWKLPARPDGAARHLAVITGGEAQQTMLFLQDGQ-WSILALFQDELAGKAAAR
+TLDALLQSVTCLRMGGRDVLDGADTPRPGIEWAGYDREFEEADVAEQRDVEPRGRIWILP
+ATDGASVGLKLPGHRRYDDAVAQFADVDAARAAVAAIDELLGVGPRG-------
+>1_625
+MSATPLGFWKLPARPDGAARHLAVITGGEAQQTMLFLQDGQ-WSILALFQDELAGKAAAR
+TLDALLQSVTCLRMGGRDVLDGADTPRPGIEWAGYDREFEEADVAEQRDVEPRGRIWILP
+ATDGASVGLKLPGHRRYDDAVAQFADVDAARAAVAAIDELLGVGPRG-------
+>2_1967
+---------------------------------MLFLQDGQ-WSILGLFQDELAGKATAR
+TLDALLQSVTCLRMGGRDVLDGADTPRPGVEWAGYDREFEEADVAESRDVEPHGRIWILP
+ATDGATVGLKLPGHRRYHDAVAQFADVDAARAAVAAIDELLGVGPRG-------
+>3_1864
+MPATPHGFWKLPAPSDAGPRHLAVITGGEAEQTMLFLQDAAGWHVLALFQDELAGRTTAR
+TLDRLLQSVTYLRMGGADLMDGADTERPGVEWAGYDREFEEQDAADETAADPAARLWILP
+ATDGASVGLKLPGHPRYADAVAQFVDAGTARAAVDAVDALIGARRPGAARPAAD
+>4_846
+MSATPLGFWKLPARPDGAARHLAVITGGEAQQTMLFLQDGQ-WSILALFQDELAGKAAAR
+TLDALLQSVTCLRMGGRDVLDGADTPRPGIEWAGYDREFEEADVAEQRDVEPRGRIWILP
+ATDGASVGLKLPGHRRYDDAVAQFADVDAARAAVAAIDELLGVGPRG-------
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000836.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000836.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45104b11f61f4b06e6110343317234ef871e827e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000836.fa
@@ -0,0 +1,31 @@
+>0_945
+MSAPVLHVIACAHGTHDAAGRDVIDGLRADLAALLAAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPGTIAAAPLAGAGDDVEPRLVTVLAER
+VARAVPAGEAATSDVILAAAGTRAADGQAQVHALAGALARATGLPVTAAFGAAATPRVPD
+AVARVHAAGRRAVVAAHLLAPGYFHDRLGEAGADAVTDPLLPHPLVARIALDRLRSALVE
+APRGAAGGR
+>1_668
+MSAPVLHVIACAHGTHDAAGRDVIDGLRADLAALLAAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPGTIAAAPLAGAGDDVEPRLVTVLAER
+VAQAVPAGEAATSDIILAAAGTRAADGQAQVHALAGALARATGLPVTAAFGAAATPRVPD
+AVSRVRAAGRRAVVAAHLLAPGHFHDRLGESGADAVTDPLLPHPLVARIALDRLRSALAE
+APRGAAGGR
+>2_1867
+MSAPVLHVIACAHGTHDAAGRVVIDGLRADLAALLDAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPDTIAAAPLAGAGDDVEPRLVAVLAER
+VAQAVPAGEAATSEVILAAAGTRAADGQAQVHALAAALARATGLPVTAAFGAAATPPVPD
+AVSRVRATGRRAVAAAHLLAPGYFHDRLGESGADAVTDPLLPHPLVARIALDRLRSALAE
+APRGAAGGR
+>3_1813
+MSAPVLHVIACAHGTHDAAGRVVIDGLRADLAALLDAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPDTIAAAPLAGAEDDVEPRLVTVLAER
+VAQAVPAGEAATSDIILAAAGTRAADGQAQVHALAAALARATGLPVTAAFGAAATPRVPD
+AVARVRATGRRAVVAAHLLAPGYFHDRLGESGADAVTDPLLPHPLVARIALDRLRSALAE
+APRGAAGGR
+>4_888
+MSAPVLHVIACAHGTHDAAGRDVIDGLRADLAALLAAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPGTIAAAPLAGAGDDVEPRLVTVLAER
+VARAVPAGEAATSDVILAAAGTRAADGQAQVHALAGALARATGLPVTAAFGAAATPRVPD
+AVARVHAAGRRAVVAAHLLAPGYFHDRLGEAGADAVTDPLLPHPLVARIALDRLRSALVE
+APRGAAGGR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000840.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000840.fa
new file mode 100644
index 0000000000000000000000000000000000000000..29dc0aeed74d3d74635bad8c34d334c6fba0d2cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000840.fa
@@ -0,0 +1,46 @@
+>0_949
+MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARKGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYAEEVFTAIAEDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPHDGATLAAGMVRGGDEA
+>1_672
+MSTALLDRRAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARKGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYAEEVFTAIAEDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPVRTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPHDGATLAAGMVRGGDEA
+>2_1863
+MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARSGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYSEEVFTAIADDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVLRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPQDGATLAAGMVRGGDEA
+>3_1809
+MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARKGVVEQTRRHLSVVALLRVPQVIVAVNKIDLVDYSEEVFTAIAEDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPQDGATLAAGMVRGGDEA
+>4_892
+MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARKGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYAEEVFTAIAEDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPHDGATLAAGMVRGGDEA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000847.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000847.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e932ad234a7cde6a8896427897ef64026df2c96
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000847.fa
@@ -0,0 +1,26 @@
+>0_959
+--------MPATPLTDDIRLSPADDIPAEEARLTWYARPAGTAALLLITSLVALTATIII
+IVERTLLTADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLL
+AGARFARWYWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRN
+LQTGTLPAPAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID
+>1_682
+--------MPATPLTDDIRLSPADDIPAEEARLTWYARPAGTAALLLITSLVALTATIII
+IVERTLLTADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLL
+AGARFARWYWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRN
+LQTGTLPAPAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID
+>2_1854
+--------MPSTPTADRVRPAQPAETPASDGTLSWYARPAGMAWTLLVTSLVALTATIVI
+IVERSILAADPGHRTSCDLNPWVSCGRVMQSWQAMTFGFPNTYIGIVAFSVLITVAVSLF
+AGARFARWYWLLMNVGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRN
+IQTGTLPASPGAARLARELAWPVILILYVLVFATILLELGFGVIGLD
+>3_1799
+MDVTETAENPPAP-----RAHHAAHALPEDRSLSWYARPLGTAWMLLITSIVAVTATIII
+IVERSILAENPNYRTSCDINPWLSCGTVMQSWQAHTFGFPNTFVGIVAFPVLITVAVSLF
+AGARFARWYWVLMNVGILAGFAFAAWLWYSAVYSIGTLCLYCMIVWAMVILQLVLVTSRN
+LQTGALPSSPGLARLAQDFAWPVIVLLYALVFASILLQLGLGVIGIR
+>4_902
+MS------MPTTPPTDDVRLSPADDVPAEEARLTWYARPAGTAALLLITSLVALTATIVI
+IVERALLTADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLL
+AGARFARWYWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRN
+LQTGTLPAPAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000848.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000848.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d57648bc03d6bfc3cc423e181d222951e98a0c73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000848.fa
@@ -0,0 +1,85 @@
+>0_960
+MAANNEDTTRADERVEETAEQ----------------------AVTQTAADTADGA-EPERTAASDDAAD----------
+-PAEEPSAPTLQVDPTDPFAVPANLIEVLRTETTSRQRSED---------------------------------------
+-------EDAGESEDRAEGAVVSRRRRRRRRGEVDMELDGGEAGDPEHTVTRVRAPRQAVGTASDTVQSVKGSTRLEAKR
+QRRRDSRSGGRRRTVITEAEFLARREAVDRKMLVRQRDQRIQIAVLEDGVLAEHFVSHTTQDSMIGNVYLGKVQNVLPSM
+EAAFVDIGRGRNAVLYAGEVNWDAAQLDGKPRKIENALKSGDTVLVQVTKDPVGHKGARLTSQVSLPGRYLVYVPGGSMT
+GISRKLPDVERSRLKKILKDHLPQDAGVIVRTAAEGTSEQELQNDINRLRAQWEGIQEKASGTKVLAPELLYAEPDLTIK
+TVRDVFNEDFSAMLVQGEATWDNIEAYVTYVAPHLLGRLHHWVPEDHDGEDLYATHRVDEQLHKALERKVYLPSGGSLVI
+DRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEIVRQLRLRDIGGIIVIDFIDMVLEANRDLVLRRLVECLGRDRT
+KHQVAEVTSLGLVQMTRKRMGTGLVEVFSETCEHCAGRGILIQDTPVERGRSGGEQRGEAEGRRR-RRRRG--DGEGEHA
+HAAAATTT-GAEHADSEDERQRRERAEAARVALHSIAKASGKVAEDEAPAQESAPAEQAADAAEDSAAEAVEAASAGPAE
+AGQPAGT-------DEEETPRRRRRRGRRRSRGRAEESGDTGAEDAGSEDAARSHDDGPAESAGQTRQTEEEAAEPAAAA
+APEHQDPVVQAEEAVAAVAEAEADAEAESPEDAAE-----QDDRPRRSRRRRGGRGRSRRGGEAASTEADADAE------
+-----DHGA--ERATPSRHEAADADSSVAVSSEVASEPVPAEDAPAPV---PAEDAPAPRRRRSRRASS------DGVVR
+PAAGAD-ASAERTADRTDAAPVEAT------------------------EPSPEESTDATEVHEQPAAPAAVEEAVMVEP
+AATEPTAEPTADADQASAADAPTEAQAAPTAPVPGSPRRRSRRAVSSDGVHVQVQAAPGGAQGGRFTAAVAEASTPAEPQ
+GAAPVMLGVGVKAADLARRGR
+>1_683
+MAANNEDTTRADERVEETAEQ----------------------AVTQTAADTADGA-EPERTAASDDAAD----------
+-PAEEPSAPTLQVDPTDPFAVPANLIEVLRTETTSRQRSED---------------------------------------
+-------EDAGESEDRAEGAVVSRRRRRRRRGEVDMELDGGEAGDPEHTVTRVRAPRQAVGTASDTVQSVKGSTRLEAKR
+QRRRDSRSGGRRRTVITEAEFLARREAVDRKMLVRQRDQRIQIAVLEDGVLAEHFVSHTTQDSMIGNVYLGKVQNVLPSM
+EAAFVDIGRGRNAVLYAGEVNWDAAQLDGKPRKIENALKSGDTVLVQVTKDPVGHKGARLTSQVSLPGRYLVYVPGGSMT
+GISRKLPDVERSRLKKILKDHLPQDAGVIVRTAAEGTSEQELQNDINRLRAQWEGIQEKASGTKVLAPELLYAEPDLTIK
+TVRDVFNEDFSAMLVQGEATWDNIEAYVTYVAPHLLGRLHHWVPEDHDGEDLYATHRVDEQLHKALERKVYLPSGGSLVI
+DRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEIVRQLRLRDIGGIIVIDFIDMVLEANRDLVLRRLVECLGRDRT
+KHQVAEVTSLGLVQMTRKRMGTGLVEVFSETCEHCAGRGILIQDTPVERGRSGGEQRGEAEGRRR-RRRRG--DGEGEHA
+HAAAATTT-GAEHADSEDERQRRERAEAARVALHSIAKASGKVAEDEAPAQESAPAEQAADAAEDSAAEAVEAASAGPAE
+AGQPAGT-------DEEETPRRRRRRGRRRSRGRAEESGDTGAEDAGSEDAARSHDDGPAESAGQTRQTEEEAAEPAAAA
+APEHQDPVVQAEEAVAAVAEAEADAEAESPEDAAE-----QDDRPRRSRRRRGGRGRSRRGGEAASTEADADAE------
+-----DHGA--ERATPSRHEAADADSSVAVSSEVASEPVPAEDAPAPV---PAEDAPAPRRRRSRRASS------DGVVR
+PAAGAD-ASAERTADRTDAAPVEAT------------------------EPSPEESTDATEVHEQPAAPAAVEEAVMVEP
+AATEPTAEPTADADQASAADAPTEAQAAPTAPVPGSPRRRSRRAVSSDGVHVQVQAAPGGAQGGRFTAAVAEASTPAEPQ
+GAAPVMLGVGVKAADLARRGR
+>2_1853
+M-AANEDTTGAEERAEQTEQTTAETSAAVAGQAAAESPVEDGGTVTQAQADAAEGADAPERTAEAADIEDEAETDTAAEP
+EPDEAPGAPALQFDPTDPFAVPANVMEILRTEKSERRPARDERPARGAEDEEEAPGRSRRRRRPSRDRDQAETEAGAEDE
+AVETAEGEQDAETAERGEGAVVSRRRRRRRRGDVDMELDGGEDGDPENTVTRVRAPRQALSTGSDAVQGVKGSTRLEAKR
+QRRRDSRSGGRRRTVITEAEFLARREAVDRKMLVRQREHRIQIAVLEDGVLAEHFVSNTTQDSLIGNVYVGKVQNVLPSM
+EAAFVDIGRGRNAVLYAGEVNWDAAQLDGKPKKIENALKSGDTVLVQVTKDPVGHKGARLTSQVSLPGRYLVYVPGGSMT
+GISRKLPDVERSRLKKILKDHLPQDAGVIVRTAAEGTSEQELQNDINRLRAQWEGIQEKASSTKVLAPELLYAEPDLTIK
+TVRDVFNEDFSAVLVQGEATWDNIEAYVTYVAPHLLDRLHHWVPQDHDGEDLYATHRVDEQLHKALERKVYLPSGGSLVI
+DRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEVVRQLRLRDIGGIIVIDFIDMVLEANQDLVLRRLVECLGRDRT
+KHQVAEVTSLGLVQMTRKRMGTGLVEVFSETCEHCAGRGILIHDTPVERGRSGGEPRGEGEGRRR-RRRKG--AGEGEQA
+QPAESTTTAGGEEVDAEDERQRRERAEAARAALHSIAKASGKVSEDEDPAEQAAPAEQAADAAEDQAAEAVEAARQDAAE
+ETGEAGAQDGEGAEDEDEAPRRRRRRGRRRGRGRSEEAAE--AAEAASEDGSRDADAAP---AGQAPAADEEEA-PAA--
+-----DPVAQAEAAVTAVAEAEADAESGGEEREAEPAGDEEGARPRRARRRRGGRGRSRRGADREASTADADDEAAQPAQ
+EPAQADAGAAGDRARASRAGRVGAARAARVRPGRGRGGRRAASRPAPP---PF----APRFERRCRAPGRGPGRRPGVVR
+PGDPVPRGGGRRRGDRAHRGAVHGRHRGARAPGRPRPGGGGRDGRAGGGRPRPGRAGRA-----RPAARPELRARRPPSP
+GAVGPVARCPRTACACRSRTPPGRHGADASRRPPPSPRPPPSRA-------------------------------PRRP-
+---------------------
+>3_1780
+M----------------AADE----------------------STTQDTHETAEGSTTP---VEATEEETAAEVAESPAG
+EAAEATAAPDVRFDPTNPFAVPEGLLPLIEAETVE-----------------------RRRRRPAAD----PVPEGAADD
+AHADDEDDEDR--------PAVSRRRRRRRRGTVDMELAGGEDGDPEDTVTRVRAPRRALSTGPEAVQGVKGSTRLEAKR
+QRRRESRSGGRRRTVITEAEFLARRESVDRKMLVRQREHRIQIAVLEDGVLAEHFVSNTTQDSMIGNVYLGKVQNVLPSM
+EAAFVDIGRGRNAVLYAGEVDWDAAQLDGKAKKIENALKSGDTVLVQVTKDPVGHKGARLTSQISLPGRYLVYVPGGTMT
+GISRKLPDVERARLKKILKDHLPQDAGVIVRTAAEGTSEQELQNDINRLRVQWEGIQEKASSTKTLAPELLYAEPDLTIK
+TVRDVFNEDFSAMLVQGEATWDSIEAYVTYVAPHLLDRLHHWVPEDHDGEDLYATHRVDEQLHKALERKVYLPSGGSLVI
+DRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEVVRQLRLRDIGGIIVIDFIDMVLESNQDLVLRRLVECLGRDRT
+KHQVAEVTSLGLVQMTRKRMGTGLVEVFSEVCEHCGGRGILIQDTPVERNRWGHEHRAEPEARRRNKRRRGTESGEGGPA
+EPTAAELT--------EEERLRAERAAAARTALMSIAKASGKAADEE-------PSEEAAPRAEDAPEEAADEVRPSPAG
+DAEEQG--------ESESGGRRRKRRGRRRGRGRG---GDDAARSAEEQDAPAEH---PAEAAGE-PAPAEAGA-P----
+-----DP------AETATEDADADSASDAPAAQAEADEDGRSGGRRRSRRRGGRRAESPQGSGAPASAPEASVEAEQDPE
+EPAGA---AEAEEA-------------------LAAEEAPASPEPAAVVTFDGEPVAVPRRRRSRRATS------DGVSA
+PRPSGM-DALEAAVDRRAEDAAAAA------------------------QRS-------------PATPAAT--------
+----PTAAP-----------EPAPAPVAGEGPAAAAPRRRSRRAVSADGATVQVQEG-AAAGGGRFTAQAAQAAPAGET-
+-AAPVMLGVGVKAADIVR-GE
+>4_903
+MAANNEDTTRADERVEETAEQ----------------------AVTQTAADTAAGAVQPERTPASDDAAD----------
+-APEEPSAPTLQVDPTDPFAVPANLIEVLRTETTSRQRSED-------EDDPDTSGRSRRRRRPSREDD--RAEEGAADA
+SADAEDREDASESEDRAEGAVVSRRRRRRRRGEVDMELDGGEAGDPEHTVTRVRAPRQAVSTASDTVQSVKGSTRLEAKR
+QRRRDSRSGGRRRTVITEAEFLARREAVDRKMLVRQRDQRIQIAVLEDGVLAEHFVSHTTQDSMIGNVYLGKVQNVLPSM
+EAAFVDIGRGRNAVLYAGEVNWDAAQLDGKPRKIENALKSGDTVLVQVTKDPVGHKGARLTSQVSLPGRYLVYVPGGSMT
+GISRKLPDVERSRLKKILKDHLPQDAGVIVRTAAEGTSEQELQNDINRLRAQWEGIQEKASGTKVLAPELLYAEPDLTIK
+TVRDVFNEDFSAMLVQGEATWDNIEAYVTYVAPHLLDRLHHWVPEDHDGEDLYATHRVDEQLHKALERKVYLPSGGSLVI
+DRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEIVRQLRLRDIGGIIVIDFIDMVLEANRDLVLRRLVECLGRDRT
+KHQVAEVTSLGLVQMTRKRMGTGLVEVFSETCEHCAGRGIIIKDTPVERGRSGGEQRGEAEGRRR-RRRRG--NGEGEHA
+HAAAATTT-GAEHADSEDERQRRERAEAARVALHSIAKASGKVAEDETPAQEPAPAEQAADAAEDSVAEAVEAASTGPAE
+AGQPAAA-------DEEETPRRRRRRGRRRSRGRAEESGDTGAEDAGSEDAARSHDDGPAESAGQTRQTEEEAAEPAAAA
+APEHQDPVVQAEEAVAAVAEAEADAEAESPEDAAE-----QGDRPRRSRRRRGGRGRSRRGGEAASTEADADAE------
+-----DHGA--ERATPSRHEAADADSSVAVSSEVASEPVPAEDAPAPV---PAEDAPAPRRRRSRRASS------DGVVR
+PAAGAD-ASAERTADRTDAAPVEAT------------------------EPSPEESTDATEVHEQPAAPAAVEEAVMVEP
+AATEPTAEPTADADQASAADAPTEAQAAPTAPVPGSPRRRSRRAVSSDGVHVQVQAAPGGAQGGRFTAAVAEASTPAEPQ
+GAAPVMLGVGVKAADLARRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000859.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000859.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d73f380bf6b00be763dd8c792d229de24feaa688
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000859.fa
@@ -0,0 +1,21 @@
+>0_976
+MYPTPMTF-DVARAGRALAQVSARTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALL
+KYGVGLVPEDEFGGAGVRRIFSAEKSRRIKAMENEGGPA---------------------
+----YEDDI-------------------------------
+>1_699
+MYPTPITF-DVARAGRALAQVSVRTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALL
+KYGVGLVPEDEFGGTGVRRIFTAEKSRRIEAMENEGGPA---------------------
+----YEDDI-------------------------------
+>2_1834
+MYPTPMTF-DVARAGRALAQVSVRTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALR
+KYGVGLVPEDEFGGTGVRRIFTAEKSRRLEAMENEGGPA---------------------
+----YEDDI-------------------------------
+>3_688
+MESQHISNGDMTRAARILVKVSAQYIAREANVTKEELRDFEKGRHDLSEKKQERVRAALE
+ELGAEFLPDGPNGGYGIRLKFGRSRIYSLERCEGEGGPRLTTESDRRTQAHVPFSEPDSN
+LPFHLEDRTTASLRILVPLRLGRLWPSHLASVPGMEARAR
+>4_920
+MYPTPMTF-DVARAGRALAQVSVRTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALR
+KYGVGLVPEDEFGGAGVRRIFTAEKSRRLEVLENEGGPA---------------------
+----YEDDI-------------------------------
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000860.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000860.fa
new file mode 100644
index 0000000000000000000000000000000000000000..25cdae9dc0f615d365c43828ea2ca1d23c4384ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000860.fa
@@ -0,0 +1,46 @@
+>0_977
+M-TATPDLEQTRHLATELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGN
+RLIDLASGIAVTSVGASHPRVVAAVQDQVAQFTHTSFMITPYEGYVAVAEQLDRTSPIPG
+ETRTALFNSGAEAVENAVKVARAYTGKQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGP
+FAPEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEG
+FLPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVT
+GRAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIREHFEQNAD
+DRIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRATGVILLTCGTYGNVVRFLPPL
+TIGEDLLKEGLSEVTKALQSA
+>1_700
+M-TATPDLEQTRHLATELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGN
+RLIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTSPIPG
+ETRTALFNSGAEAVENAVKVARAYTGKQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGP
+FAPEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEG
+FLPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVT
+GRAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIREHFAQNAD
+DRIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRAAGVILLTCGTYGNVVRFLPPL
+TIGEDLLKEGLSEVTNALQSA
+>2_1833
+M-SSTPDLEQSRHLATALPGPRSQALAERQKAAVPAGVATTMPVYAARAAGGILEDVDGN
+RLIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTAPISG
+QTRTALFNSGAEAVENAVKVARSYTGKQAVAAFDHAYHGRTTLTMALTAKNMPYKHHFGP
+FAPEVYRVPGSYPLRDGLSGAEAARRAIGALETQIGAENLAAVIMEPIQGEGGFIVPAEG
+FLPAVVEWCRANDVLFIADEVQSGVARTGSWFACEAEGVEPDLMTTAKGIAGGMPLSGVT
+GRAEVMDSVHPGGLGGTYGGNPVAAAAALAVFEAIEDEDLLAKATRIEEVIREHFAAHAD
+DRIAEVRGRGAMMAIELVEPGTGEPDAALTAAVAAAVRATGVILLTCGTYGNVIRFLPPL
+TIGEDLLKEGLSEVTKALQSA
+>3_1724
+MTSPVTAPEQSRHIATELPGPKSRELAARQAGAVPAGVATTMPVFASRAGGGIIEDVDGN
+RLIDLGSGIAVTSVGASHPKVVEAVQEQVADFTHTCFMITPYEGYVAVAEKLGEKAPISG
+ETRTALFNSGSEAVENAVKVARAYTRKQAVVAFDHAYHGRTTLTMSLTAKSMPYKHSFGP
+FAPEVYRVAGSYPLRDGLNGAAAAKKAISAMEKQIGADNLAAVIMEPLQGEGGFIVPAEG
+FLQAIVEWCTANDVLFIADEVQSGFARTGAWSASELEGIEPDLMCTAKGIAGGMPLSAVT
+GRAEVMDAVHPGGLGGTYGGNPVATAASLAVFEAIEEDGLLQEAQMIERVIREHFEQNAD
+ERIAEVRGRGGMMAIEFVDPASGEPDAALTGKLAAAVRAAGVVLLTCGTYGNVVRFLPPL
+TIGEELLREGLAEVTTALQSA
+>4_921
+M-TATPDLEQTRHLVTELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGN
+RLIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTCPIPG
+ETRTALFNSGAEAVENAVKVARAYTGRQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGP
+FAPEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEG
+FLPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVT
+GRAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIRDHFEQNAD
+DRIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRATGVILLTCGTYGNVVRFLPPL
+TIGEDLLKEGLSEVTKALQSA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000864.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000864.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e2b0e981d8247a2d74ffd8974a34b4b6c223cab8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000864.fa
@@ -0,0 +1,41 @@
+>0_981
+M---RTARPTRLAVALGAGVLLTGVGAT---PALASPAHPA-GWTAEHGLPGGSFLVAGA
+EGETGASFGTEFEVDESDVRLTVAPA-------------MEGEARGAETEVPFTYDDELE
+RGDFDVAAARRSLGESGTGPVVYTLYVLGGEVAALTYGPDADLTDADPGEPLRADQRHEL
+GFHMLPTAWDTTLLAAPGERHVFIS-SYTGD---EAAPLTLVAGPAEGRVVEV-------
+---TEEETGGPRGYVYQAPEGFTGSDTV--TLRATRDGVTTTRTVTVRFGDPRVDLYDWE
+NGRIPGFVTFPVAGLF--------DD--APGQPADPDTPTSPA-------EPETPADPAD
+GEHTVPDTVETGRGPAAWPVAVAVLAAGVLAVVRRH-RVAA
+>1_704
+M---RTARPTRLAAALGAGVLLTGLGAT---PVLASPAHPA-GWTAEHDLPGGSFLVASA
+EGETGASFGTEFEVDESDVRLTVAPV-------------LEGEARGAETEVPFTYDDELE
+RGDFDVAAARRSLGESGTGPVVYTLY----------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------R
+>1_705
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---MLPTAWDTTLLAAPGERHVFIS-SYTGD---EAAPLTLVAGPAEGRVVEV-------
+---AEEETGGPRGYVYQAPEGFTGSDTV--TLRATRDGVTTTRTVTVRFGDPRVDLYDWE
+NGRIPGFVTFPVAGLF--------DDAPAPGQPADPDTPTSPA-------EPETPADPAD
+GEHTVPDTVETGRGPAAWPVAVAVLAAGVLAVVRRH-RVAA
+>2_764
+MSARRTTRP--LSTALAAAVLAGGLAASTAAPALAAPAETTDGWQNGH-FVGGTFGSTEL
+SPRTG-SFYTQHAV--KDVRVTVAPFYPAFTDLEEISYKVPGEM-GPETDVEFTYDAELE
+AGYVDVLEQRRVLDEEGTAGAVFTLYVDGKATATLVFGEDRNLGDDVPGMFLDATGPQAY
+DFSARPTVDHQTRLAAPGSRLVHLQGNSTGDAPVEDSTRTVVEQPEHGTLVELPRIGDPT
+NWTSDGANGSFASTVYVADEGFTGTDQAVFTLTDGSTGEQKTLVVTFSIGDPRAA--DPH
+LGVQGTGLPFDEARVWEALEAQGEDD--ASEAPA-PESPATPAPDSTDAPEASEPSEPAD
+-EHTVPETVETGSGQAWWLAAVAAAGTGALVAGRRRFGLAR
+>4_925
+M---RTARPTRLAAALGAGVLLTGLGAT---PALASPAHPA-GWTAEHGLPGGSFLVAGA
+EGETGASFGTEFEVDESDVRLTVAPV-------------LEGEARGAETEVPFTYDDELE
+RGDFDVAAARRSLGESGTGPVVYTLYVLGGEVAALTYGPDADLTDADPGEPLRADQRHEL
+GFHMLPTAWDTTLLAAPGERHVFIS-SYTGD---EAAPLTLVAGPAEGRVVEV-------
+---TEEETGGPGGYVYQAPEGFTGSDTV--TLRATRDGVTTTRTVTVRFGDPRVDLYDWE
+NGRIPGFVTFPVAGPF--------DD--APGQPADPDTPTSPA-------EPETPADPAD
+GEHTVPDTVETGRGPAAWPVAVAVLAAGVLAVVRRH-RVAA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000865.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000865.fa
new file mode 100644
index 0000000000000000000000000000000000000000..621a8e44efa65118076fa7a3de9d6f65318157d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000865.fa
@@ -0,0 +1,16 @@
+>0_982
+--------MSTSPTV-TRNDAESRYELHDG-GTLLAVLDFRDNGAAVSLNRAFTIPVHRG
+RGHAAALTAGAVEDIATNGGPAGGRRIVPMCWYVAQWFDEHPEKSALLAPR
+>1_706
+--------MSTSPTV-TRNDAESRYELHDG-GTLLAVLDFRDNGAAVSLNRAFTIPVHRG
+RGHAAALTAGAVEDIETNGGPAGGRRIVPMCWYVAQWFDEHPEKSALLAPR
+>2_1829
+MTARD---AAGGPAV-TRNDAESRYELHDG-GTLLAVLDYRDNGTAVALTRAFTIPVHRG
+HGHAATLTAGAVEDIEARGGAAGGRQIVPLCWYVAQWLEEHPEKAHLVAPR
+>3_1721
+M---D---ASDSPTTFTRNDAASRYELHDASGELLAALDYRDNGTAVSLTRAFTVPVHRR
+QGHAATLTAGAVADIEARGGAAGGTTVVPMCWYVARWFEEHPEKAGLLDAR
+>4_926
+MTTGGCPGMSTSPTV-TRNDAESRYELHDG-GTLLAVLDFRDNGAAVSLNRAFTIPVHRG
+RGHAAALTAGAVEDIATNGGPAGGRRIVPMCWYVAQWFDEHPEKSALLAPH
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000867.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000867.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df19fb62bb997fdfdc0f02e0b200c74bbd407fee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000867.fa
@@ -0,0 +1,21 @@
+>0_984
+-MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREP
+TLGATAPYVLMTPTYGGGSGPGA-VPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLA
+GYIISRKCQVPLMYKFELMGTPDDVERVRGGLEGM----WT
+>1_708
+-MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREP
+TLGATAPYVLMTPTYGGGSGPGA-VPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLA
+GYIISRKCQVPLMYKFELMGTPDDVERVRGGLEGL----WT
+>2_1824
+-MTVAADPGHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVQKLELPEDRVARLPLITREP
+TLGATAPYVLLTPTYGGGDGPGA-VPKQVIKFLNVPGNRTWIRGVIASGNTNFHEAYCLA
+GYIIARKCQVPLMYKFELMGTPEDVDSVRGGLEGL----WT
+>3_1713
+MTTATAGPNHMRDAEAQGLVPTDARLIYFSSASGYTHRFVEKLGLPLGQAARLPLLTREP
+TLGATAPYVLLTPTYGGGGDTGGEVPKQVIKFLNVPGNRALIRGVIASGNTNFSGAYAAA
+GYIISRKCQVPLMYKFELMGTPEDVVAVREGLERLEEGQHA
+>4_928
+-MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREP
+TLGATAPYVLMTPTYGGGSGPGA-VPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLA
+GYIISRKCQVPLMYKFELMGTPDDVERVRGGLEGL----WT
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000884.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000884.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6e4a14d8d9712998bb2579aa0223e6859dd2579
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000884.fa
@@ -0,0 +1,31 @@
+>0_1010
+MTDTAAKFSEYAHPEKLVSTQWVADHVGDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE
+LNDPVTRDFVGPEAFAEFAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD
+GGRDKWIAEGRETTREVPTVARA-EYPVIERDDHTERAAREDVLQAIGTTPLIDVRSRPE
+YTGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRAGAGLQEGD
+DVIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR
+>1_732
+MTDTAAKFSEYAHPEKLVSTQWVADHVDDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE
+LNDPVTRDFVGPEAFAEVAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD
+GGRDKWIAEGRETTREVPTVARA-EYPVIERDDHTERAAREDVLQAIGTTPLIDVRSRPE
+YTGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRTDAGLREGD
+DVIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR
+>2_1799
+MTETATEFSQYAHPEKLVSTQWVADHVGEEGVVVLESNEDALLYATGHIPGAQRIDWHTE
+LNDPVTRDFIGPEAFAEMAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDVRLMN
+GGRDKWIAEGRETTREVPTVARG-EYPVVPRDDTTERAAREDVLQAVGTTPLIDVRSRPE
+YTGETTHMDGYPQEGTLRGGHIPTAASVPWAQAANEDGTFKSREELEAVYRDGAGLKDGD
+DVIAYCRIGERSSHTWFVLKHLLGHENVRNYDGSWTEWGNSVRLPIVVGEEPGAAPAR
+>3_1688
+MTETPAEFAEYAHPEKLVSTQWVADHIDDEGVVVLESNEDTLLYSTGHIPGAVKIDWHTE
+LNDPVSRDFVGPEAFAELVASKGIGPDTTVVFYGDKSNWWAAYALWVFTLYGHRDVRLMN
+GGRDKWIAEGRPTTREVPEVTPAPSYPVSQRDDATDRAAREDVLAAIGSTPLVDVRSPKE
+YTGETTHMDGYPQEGTLRGGHIPTAASVPWAKAANEDGTFKSRAELEEIYKEGAGLGESD
+SVIAYCRIGERSSHTWFVLKQLLGYENVRNYDGSWTEWGNGVRLPIALGDEPGEAPAR
+>4_951
+MTDTAAKFSEYAHPEKLVSTQWVADHVGDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE
+LNDPVTRDFVGPEAFAEFAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD
+GGRDKWIAEGRETTREVPTVARA-EYPVIERDDHTDRAAREDVLQAIGTTPLIDVRSRPE
+YTGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRAGAGLQEGD
+DVIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000887.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000887.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3bd68bf1c0c24129d5a9e8bb82179da0fcb0f82c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000887.fa
@@ -0,0 +1,26 @@
+>0_1013
+MTVLPVRTIPDPVLRTAASPVPAGADVRALVADMIETMHAVGGVGLAAPQVGVGLRVFVF
+DVAGVAGHVVNPVLETAGQALREPGEGCLSVPGLRYHPARAAEAVVRGTDVDGNPVEHRG
+TGLLARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRAARRIGAARAAAVSSVF
+GAPGAPAAGTGAAR--------
+>1_741
+MTVLPVRTIPDPVLRTAASPVPAGADVRALVADMIETMHAVGGVGLAAPQVGVGLRVFVF
+DVAGVAGHVVNPVLETAGQALREPGEGCLSVPGLRYHPARAAEAVVRGTDVDGNPVEHRG
+TGLLARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRAARRIGAARAAAVSSVF
+GAPAVPAAGTGAAR--------
+>2_1796
+MSVLPVRTVPDPVLRTPARPVPAGMDVRALVADMVETMHAVGGVGLAAPQVGVGLRVFVF
+DVQGVAGHVVNPVLETGEETVREPGEGCLSVPGLRYHPARAAEAVVRGVNVDGHPVEHRG
+TGLVARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRTARRVGAERAAAVGSVF
+AAPAAPPTPARAPR----GGTR
+>3_1685
+MTVLTLRTVPDPVLRTPAAPVAAGQDVRALVEDMVETMHAVGGVGLAAPQVGVGLRVFVF
+DCAGASGHVLNPVLETFGSPVREPGEGCLSVPGLRYHPARAERAVVRGVDVDGNPVEHRG
+EGLLARCLQHETDHLDGILYVDRLDGDDRREARRRLRADAPDPEAERIRARRDALAGSVF
+GAR--PSVSPSAARTTPRRGAQ
+>4_960
+MTVLPVRTVPDPVLRTAASPVPAGADVRALVADMIATMHAVGGVGLAAPQVGVGLRVFVF
+DVAGVAGHVVNPVLETAGQALREPGEGCLSVPGLRYHPTRAAEAVVRGTDVDGNPVEHRG
+TGLLARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRAARRIGAARAAAVSSVF
+GAPAVPAAGTGAAR--------
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000892.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000892.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0358f40e24dafff2f296dfbeec2fc0953c398e36
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000892.fa
@@ -0,0 +1,45 @@
+>0_1018
+MNAA-----ETPS-ADPMDLAVGAALRGVRGANPLVGAVLTDAAGRILAVGHHRGRGTAHAEVDALTRWRAARAADPALA
+TLDPAGLTLHVTLEPCDHTGSTGPCSQAVLDAGIGALRYAVADPTGHDGGGAARLAAHGVHVTGPTGEAAALTLTARWRE
+VRDAGRPWVTGHLAQSLDGHAAAADGTSQWITGPDSRVHAHEVRSRVDAIVVGTGTVLADDPRLTARDAAGAELAHQPVP
+VVQGHRPVPDGAALRTHPVLLHVPDHDPHAVLAALAAHPGPWPH-GRRAEHVLIEGGPRVLGAWLRAGLVDELMVYTAPL
+LLGPGRAAVAGLDVATLSEGPRWHPDPAEGGPARALGVDVWTHLSPVPAPRLPTAPAPTRFQED----------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------------------------
+>1_746
+MSAA-----ETPS-ADPMDLAVRAALRGVRGANPLVGAVLTDEAGRVLAVGHHRGRGTAHAEVDALTRWRAARATDPALA
+ALDPAGLTLHVTLEPCNHTGSTGPCSQAVLDAGVGALRYAVADPTGHDGGGAARLAAHGVRVTGPTGEVAALALTARWRE
+ARDAGRPWVTGHLAQSLDGHAAAADGTSQWITGPDSRVHAHEVRSRVDAIVVGTGTVLADDPRLTARDAAGAELAHQPVP
+VVQGHRPVPDGAALRAHPVLLHVPDHDPHAVLAALAAHPGPWPH-GRRAEHVLIEGGPRVLGAWLRAGLVDELMVYTAPL
+LLGPGRAAVAGLDVATLSEGPRWHPDPAEGGPARALGDDVWTHLSPVPAPRLPTAPAPTRFQED----------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------------------------
+>2_1791
+M---------SGA-PDPMALAVGAALRGVRGANPLVGAVLTDDAGRVLAAGHHRGRGTAHAEVDALARWEAARAADPALA
+ALDPAGLTLHVTLEPCDHTGSTGPCSGAILASGVGAVRYAVADPTGVDGGGAARLAAHGVRVSGPTGEPAALALTERWRR
+ARDAGRPWITGHLAQSLDGHAAAADGTSRWITGAASRAHAHRVRARVDAIVVGTGTVLADDPRLTVRDAAGAETGPQPVP
+VVQGRTPIPAGAALRARPETLHVPAHEPEAVLAALAARPGPWPHGGARPGHVLIEGGPRVLGAWIRAGLVDELMVYTAPL
+LLGAGRPAVAGLDVGTLADGLRWHPDPAEDGPVRALGEDVWTHLAPVPAPA-PEGPDP---QEDCMFTGIVTHLGTVLAL
+EPDPAADTARLVLDAGGALEGLPAGGSLAVDGVCLTALDGPGAEPGVFRADLMGQTLRMTSLGGRTPGDRVNLERCLRPT
+DHLDGHVVQGHVDGVGEVLSVTPQGAWTTVRIGLPAALARYVPAQGAIALQGVSLTVSAVSEPGADAHWFEVGLIPATLE
+ATTLGALRPGDRVNLETDVLARYAERLALLPAAPAASPSAAPAEEVRP
+>3_1680
+MSAPAARHDDAGRPAEPLDLAAAAALAGVRGANPLVGAVITGPDGAVLAVGHHRGRGTAHAEVDALNRWAAARAADPSL-
+HVDPAACTIHVTLEPCDHTGSTGPCAGAILDAGLGAVRYAVADATGTAGGGAARLTRAGLRVEGPTGHAASAALTARWRR
+VRDAGRPWITVHLAQSLDGRAAAADGTSRWITGPASRAHAHAVRARVDAVVCGTGTVAADDPRLTARDAAGEQLPVQPVP
+VVMGERDLPAGAALAARADLIHVRSHDPRAVLAALASRPGPWPHGGSRPGHVLIEGGPHVLGAWLAAGLVDEVFAYTAPV
+LLGDGLPGVAGLDVPTLAAGHRWAPDPAEDGPVRALGDDVLTHLAPVTDPA------------D----------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------------------------
+>4_965
+MNAA-----ETPS-ADPMDLAVRAALRGVRGANPLVGAVLTDEAGRVLAVGHHRGRGTAHAEVDALTRWRAARATDPALA
+ALDPAGLTLHVTLEPCDHTGSTGPCSQAVLDAGIGALRYAVADPTGHDGGGAARLAAHGVHVTGPTGEAAALTLTARWRE
+VRDAGRPWVTGHLAQSLDGHAAAADGTSQWITGPDSRVHAHEVRSRVDAIVVGTGTVLADDPRLTARDAVGAELAHQPVP
+VVQGHRPVPDGAVLRTHPVVLEVLDHDPHAVLAALAAHPGPWPH-GRRAEHVLIEGGPRVLGAWLRAGLVDELMVYTAPL
+LLGPGRAAVAGLDVATLSEGLRWHPDPAEGGPVRALGVDVWTHLSPVPAPRLPTAPAPTRFQED----------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------------------------
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000893.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000893.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b4d1dc94d388ae08ea3c6310cbb1b2d921e8db5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000893.fa
@@ -0,0 +1,21 @@
+>0_1021
+MSGAGAPTFT------PDPAAASGLNVAIVAAQWHTEIMDGLIAGAQAAAADLGLEPVLV
+RVPGTVELTVAAARLAERFDVVVVLGVVVRGDTPHFDYVCQSVTQGVTEVSVRTGVPVGF
+GVLTVDTEQQARDRAGLPGSREDKGREALEAAVLTELALRSVTPRD
+>1_749
+MSGAGAPTFT------PDPAAASGLNVAIVAAQWHTEIMDGLIAGAQAAAADLGLEPVLV
+RVPGTVELTVAAARLAERFDVVVVLGVVVRGDTPHFDYVCQSVTQGVTEVSVRTGVPVGF
+GVLTVDTDQQARDRAGLPGSREDKGREALEAAVLTELALRSVTPRD
+>2_1789
+--------------------------MAVVAAQWHTEIMDGLIAGARAAAADLGLEPVLV
+RVPGTVELSVAAARLAEDFDAVVVLGVVVRGDTPHFDYVCQAVTQGVTEVSVRTGTPVGF
+GVLTVDTEQQARDRAGLPGSREDKGRESLEAAVLTELALRDV--QA
+>3_1677
+MSGAGAPTLALTTLTDADRAAAGSLRVAVVAAQWHTEIMDGLIAGSRAAAADLGIDVDLV
+RVPGTVELSVAAARLAATHDVVVVLGVVVRGGTPHFDYVCQSVTQGVTEVSVRTGVPVGF
+GVLTVDTVEQARDRAGLPGSQEDKGREALEAAVLTELALRAA--LG
+>4_968
+MSGAGAPTFT------PDPAAASGLNVAIVAAQWHTEIMDGLIAGAQAAAADLGLEPVLV
+RVPGTVELTVAAARLAERFDVVVVLGVVVRGDTPHFDYVCQSVTQGVTEVSVRTGVPVGF
+GVLTVDTDQQARDRAGLPGSREDKGREALEAAVLTELALRSVTPRD
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000894.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000894.fa
new file mode 100644
index 0000000000000000000000000000000000000000..930672a2f064cf8247eef48d39e806329ce5508e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000894.fa
@@ -0,0 +1,16 @@
+>0_1033
+MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE
+EISQLLYHVQTMMIARGISLEDVYRHL
+>1_761
+MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE
+EISQLLYHVQTMMIARGISLEDVYRHL
+>2_1788
+MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE
+EISQLLYHVQTMMIARGIALEDVYRHL
+>3_1674
+MKTFEELFAELTRKVAERPEGSGTVAQIDAGVHAIGKKIVEEAAEVWMAAEYESHDAAAE
+EISQLLYHVQTMMIAKGIGLKDVYRHL
+>4_982
+MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE
+EISQLLYHVQTMMIARGISLEDVYRHL
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000895.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000895.fa
new file mode 100644
index 0000000000000000000000000000000000000000..032528457169bec9bb88161f8c16c351a5f1fb78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000895.fa
@@ -0,0 +1,31 @@
+>0_1034
+MLRIAVPNKGALSESAREILTEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG
+TLDVGLTGRDLFCDAQVGDTAEEIMALGFGRSVFRLAAPVGSFTSAEQLAGKRIATSYDG
+LLSDYLARTGLDATVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMEVFGEPILDSE
+AVLIGRAGERPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEAATAVTPGLESPTVSPL
+RDETMVAVRSMVRKPDANRVMDELYALGARGILISAIHAIRL
+>1_762
+MLRIAVPNKGALSESAREILTEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG
+TLDVGLTGRDLFCDAQVGDTAEEIMALGFGRSVFRLAAPVGSFTSAEQLAGKRIATSYDG
+LLSDYLARTGLDATVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMEVFGEPILDSE
+AVLIGRAGERPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEAATAVTPGLESPTVSPL
+RDETMVAVRSMVRKPDANRVMDELYALGARGILISAIHAIRL
+>2_1787
+MLRIAVPNKGALAEAAREILQEAGYRQRRDSRELVLVDPENQVEFFYLRPRDIAVYVGQG
+TLDVGLTGRDLFRDAQVDGGAEEIMALGFGRSVFRLAAPVGAFSSEAELSGKRIATSYDG
+LLSAYLERTGLDAEVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMETFGESILDSE
+AVMIARVGARPEGLDVLLRRLKGVLVARRWVMIDYDVRRELLEQATAVTPGLESPTISPL
+RDESMVAVRSMVRKADANRAMDDLYALGARGILISAIHAIRL
+>3_1673
+MLRIAVPNKGALSESAREILIEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG
+TLDVGLTGRDLFRDARVGETAEEIMALGFGKSVFRLAAPVGSFTSAEELAGRRIATSYDG
+LLTEYLAESGLDARVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMETFGEPILDSE
+AIMIARVGARPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEQATAVTPGLESPTVSPL
+RDESMVAVRSMVRKADANRAMDDLYDLGARGILISAIHAIRL
+>4_983
+MLRIAVPNKGALSESAREILTEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG
+TLDVGLTGRDLFCDAQVGDTAEEIMALGFGRSVFRLAAPVGSFTSAEQLAGKRIATSYDG
+LLSDYLARTGLDATVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMEVFGEPILDSE
+AVLIGRAGERPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEAATAVTPGLESPTVSPL
+RDETMVAVRSMVRKPDANRVMDELYALGARGILISAIHAIRL
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000906.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000906.fa
new file mode 100644
index 0000000000000000000000000000000000000000..359a96756704875b927d92ecae6d9ea2a00fbb47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000906.fa
@@ -0,0 +1,51 @@
+>0_1045
+MADPRGFLKNRERVDRPTRPVPVRIMDFKDVYVRQDEAIVRTQAGRCMDCGIPFCHSGCP
+LGNLIPEWNDLVRRRRWDEAAARLHSTNNFPEVTGRICPAPCEDSCTLGINQPAVTIKQT
+EVAIAEQIFDNDWLEPVVPARLNGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDERLG
+GLLRLGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGVDLPWDQLKARFDAVIVATGAP
+VARELPVPGRGLDGIHLAMDYLVQSNRAVAGDEVPDQISAEGRHVVILGGGDTGADCIGT
+AHRQGAASVTTLAIGQQLPVERPVHQPWPTIPKVHQQTTADAEGGARAHLASTVEFLGDE
+HGRVRALRVAETEYREDGTRGPKAGTEREVQADLVLLALGFTGIEEGLLTQQLGVHVTRG
+LVARKDGYETDEPGVFACGDAGRGASLVVWAIAEGRACAQEVDESLERWSRLPHPVDPDD
+RGLVLG
+>1_773
+MADPRGFLKNRERVERPTRPVPVRIMDFKDVYVRQDEAIVRTQAGRCMDCGIPFCHSGCP
+LGNLIPEWNDLVRRRRWDEAAARLHSTNNFPEVTGRICPAPCEDSCTLGINQPAVTIKQT
+EVAIAEQIFDNDWLEPVVPARLNGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDERLG
+GLLRLGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGVDLPWDQLKARFDAVIVATGAP
+VARELPVPGRGLDGIHLAMDYLVQSNRAVAGDEVPDQISAEGRHVVILGGGDTGADCIGT
+AHRQGAASVTTLAIGQQLPVERPVHQPWPTIPKVHQQTTADAEGGARAHLASTVEFLGDE
+HGRVRALRVAETEYREDGTRGPKAGTEREVQADLVLLALGFTGIEEGLLTQQLGVHVTRG
+LVARKDGYETDEPGVFACGDAGRGASLVVWAIAEGRACAQEVDESLERWSRLPHPVDPDD
+RGLVLG
+>2_1774
+MADPRGFLKHRERVARPSRPVPVRIMDFKDVHVRQDEAIVRTEASRCMDCGVPFCHAGCP
+LGNLIPEFNDLVYRDDWDEAGARLEATNNFPEFTGRICPAPCEASCVLGINQPAVSIKQV
+EQSIADHLFDAPSLTPHPPQRQNGLTVAVVGSGPAGLAAAQQLTRSGYTVVVYEKDEALG
+GLLRFGIPDFKLEKHLIDRRIAQMTEEGTRFRTGVRIGTDMSWEALQRRYDAVVLATGAP
+VGRELPLPGRGLDGIHLAMDYLVPVNRRVAGGE-PEPISAQGRHVVILGGGDTGADCIGT
+AHRQGAASVTTLAIGRRPPEQRPEHQPWPTVPTLFEVASAHAEGGERTYLASTVEFLGDA
+EGRVRALKVAETEIRADGTRGPRAGTEHEIPADLVLLALGFTGADLDELVDRSAVSLERG
+LVVRDETYATQAPGVFACGDVSRGASLVVWAIAEGRAVAAEVDRFLTGDTMLPAPVRPSD
+HGFVLR
+>3_1662
+MADPRGFLKNRERVERPTRPVPVRIMDFKDVYVRQDEAVVRTQASRCMDCGIPFCHSGCP
+LGNLIPEWNDLVRRGRWEDAAARLHSTNNFPEVTGRICPAPCEDACTLGINQPAVTIKQT
+EVAIAEQIFDHDWLEPVVPTRINGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDDRPG
+GLLRYGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGRDLAWDALKARFDAVIVATGAP
+VGRELPVPGRGLDGIHLAMDYLVQSNHATAGDDVPGQITAEGRHVVVLGGGDTGADCIGT
+AHRQGAASVTTLAIGQQLPVDRPVHQPWPTVPKVHQMTTADAEGGQREHLASTVEFLGDE
+NGRVRALRVAETEYRADGTRGPKAGTEREVKADLVLLALGFTGVEEEALTAQLAVRTERG
+LVARAGTYETDEPGVFVCGDAGRGASLVVWAIAEGRACAQAVDESLESWSRLPHPVDPTD
+RGLVLG
+>4_994
+MADPRGFLKNRERVERPTRPVPVRIMDFKDVYVRQDEAIVRTQAGRCMDCGIPFCHSGCP
+LGNLIPEWNDLVRRGRWDEAAARLHSTNNFPEVTGRICPAPCEDSCTLGINQPAVTIKQT
+EVAIAEQIFDNDWLEPVVPARLNGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDERLG
+GLLRLGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGVDLPWDQLKARFDAVIVATGAP
+VARELPVPGRGLDGIHLAMDYLVQSNRAVAGDEVPDQISAEGRHVVILGGGDTGADCIGT
+AHRQGAASVTTLAIGQQLPVERPVHQPWPTIPKVHQQTTADAEGGARAHLASTVEFLGDE
+HGRVRALRVAETEYREDGTRGPKAGTEREVQADLVLLALGFTGIEEGLLTQQLGVHVTRG
+LVARKDGYETDEPGVFACGDAGRGASLVVWAIAEGRACAQEVDESLERWSRLPHPVDPDD
+RGLVLG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000908.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000908.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fab875cf84c3c226ede99081bcbb9be647b7b67e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000908.fa
@@ -0,0 +1,26 @@
+>0_1047
+MSTLTPPEE----TGLRAVVAEDETLIRLDLVEVLTGAGYRVVAEAGDGRAAVEAVREHR
+PDIVVMDVKMPVMDGIAAAGEIAGERLAPVVMLTAFSQRELVERARTAGAMAYVVKPFTE
+ADLVPAIELAVARFDELRSLEAEVRDLGDRLETRKIVDRAKALLQERMRLTEAESFRWIQ
+KTSMDRRLTMREVAQAVIDQVG-
+>1_775
+MSTLTPPEE----TGLRAVVAEDETLIRLDLVEVLTGAGYRVVAEAGDGRAAVEAVREHR
+PDIVVMDVKMPVMDGIAAAGEIAGERLAPVVMLTAFSQRELVERARTAGAMAYVVKPFTE
+ADLVPAIELAVARFDELRSLEAEVRDLGDRLETRKIVDRAKALLQERMRLTEAESFRWIQ
+KTSMDRRLTMREVAQAVIDQVG-
+>2_1772
+MPMTTPAEG----TGLRAVVAEDETLIRLDLVEVLTGAGYEVVAEAGDGAAAVAAVREQR
+PDIVVMDVQMPVMDGIAAASEIAQDRLAPVVMLTAFSQRDLVERARTAGAMAYVVKPFTE
+HDLVPAVELAVARFEELRSLESEVRDLGDRLETRKLVDRAKSVLQDRLRLSEAESFRWIQ
+KTSMDRRLTMREVAQAVIDQVR-
+>3_1660
+--MTIPAESADPTAGLRVVVAEDEALIRLDVVETLTHAGHTVVAEVGDGQAAVAAVREHR
+PDIVVMDVMMPVMDGIAAAGEIAAERLAPVVMLTAFSQRDLVERASQVGAMAYVVKPFTE
+KDLLPAMELAVARFDQLRGLEEEVRGLEDRLATRKLVDRAKSLLQAHMGLSEAESFRWIQ
+KTSMDRRLTMREVAQTVVDQIGA
+>4_996
+MSTLTPPEE----TGLRAVVAEDETLIRLDLVEVLTGAGYRVVAEAGDGRAAVEAVREHR
+PDIVVMDVKMPVMDGIAAAGEIAGERLAPVVMLTAFSQRELVERARTAGAMAYVVKPFTE
+ADLVPAIELAVARFDELRSLEAEVRDLGDRLETRKIVDRAKALLQERMRLTEAESFRWIQ
+KTSMDRRLTMREVAQAVIDQVG-
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000911.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000911.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a7ef156bd059b0e5536627d69282091db82f382b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000911.fa
@@ -0,0 +1,45 @@
+>0_1050
+MSAVPLGQLLPLFAAVPLLSAGLLVLAGERPRLHRAVLFAVLGLVTTGGLALGVHALDGSVLATSLGGWPGGIGIGFAAD
+MLSALMLVLTSALTIVGAAFAYGSRVANSQFFAPLLLILIGGVNGALLTADLFNLFVFIEVMLVPSYGLYVLSANRREPL
+RRVDGARLYVTLNLLTSTILLVGVGFVYGLTGSVNLAMLAGSAAADPRIAIAAGMVLFALSIKASVAPLHGWLAWAYSST
+SPAVTALFAALHTKVAVYGLYRIYSVMYDGDARLLPLILVLSLATLVVGALASVGEHGVRAVLSWQMVSGIGGILVGLGL
+STRLGLAAGLFYLVHHMVAMGCLLMAAGAIEVRYGTGRLADLQGLARREPLIAVAFFVGLLSLVGIPPFSGFVGKLMLVS
+AGLDAGRGVTAALVLGASLVSLWVLLRVWDAWFWGAPTAPHGHRERLATAAMPIVGRAGSVPS------PSGRGSSTDHE
+RTESWASQETLDPPTGVLPVTVDPDEDVTRSRIPGRLAAPAVVLAMATLALGLGGQALWTVTDLAAQGLMDPSRYIEAVL
+NP
+>1_778
+MSAVPLGQLLPLFAAVPLLSAGLLVLAGERPRLHRAVLFAVLGLVTTGGLALGVHALDGSVLATSLGGWPGGIGIGFAAD
+MLSALMLVLTSALTIVGAAFAYGSRVANSQFFAPLLLILIGGVNGALLTADLFNLFVFIEVMLVPSYGLYVLSANRREPL
+RRVDGARLYVTLNLLTSTILLVGVGFVYGLTGSVNLAMLAGSAAADPRIAIAAGMVLFALSIKASVAPLHGWLAWAYSST
+SPAVTALFAALHTKVAVYGLYRIYSVMYDGDARLLPLILVLSLATLVVGALASVGEHGVRAVLSWQMVSGIGGILVGLGL
+STRLGLAAGLFYLVHHMVAMGCLLMAAGAIEVRYGTGRLADLQGLARREPLIAVAFFVGLLSLVGIPPFSGFVGKLMLVS
+AGLDAGRGVTAALVLGASLVSLWALLRVWDAWFWGAPTAPHGHRERLATAAMPIVGRAGSVPS------PSGRGSSTDHE
+RTESWASQETLDPPTGVLPVTVDPDEDVTRSRIPGRLAAPAVVLAMATLALGLGGQALWTVTDLAAQGLMDPSRYIEAVL
+NP
+>2_1768
+MSPEALGQLLPLFVAVPLITAGLLTLAGDRPRVHRLVVALVLCLTAGAGALIVARSLDGDVLATSVGGWPGGIGIGFAAD
+MLTGLMLLLTSLLTLVGVNLAHGTRVVNSLYFGPLMLVLMAGVNGALLTADLFNLFVFIEVMLLPSYGLYVLSANRREPL
+RRVDGARLYVTLNLLTSTILVVAVGFLYALTGTVNLAVMAGAAARDERVAIAGGLVLFALSIKASVVPLHGWLARAYPST
+SPAVTAIFAALHTKVAVYALYRVFSVLFDNDARFLPLLLALAGLTLAVGALASVGVHGVRLVLSWQMVSGIGGILVGLGL
+STQLGLSAGLFYLVHHMVAMGCLLAATAAVEVRYGTGRLADLRGLARREPLIAVVFFVGLLSIVGIPPFSGFVGKLMLVT
+AGVEAGRLVTVAVVLVGSLVSLWALLRVWDAWFWGEPGTPHGLRERLATAALPVVGRGAERTG------PSGRGSSTDHE
+RTESWTSTQTIDPPTGVLPVTFAADEDVTRSRIPVRLAMPGVVLAAATLVLGLAGQALWTLTDVAAQGLLDPARYIEAVL
+AP
+>3_1657
+MSDHAVGLLLPLFVAVPLLSAGLLVVAGSRPRLHRAVLAAVLAGGTVGGGLLMARAADGSVAAAGVGGWPDGIAIAFAAD
+MLTGLMVALTAGLTLVGAWFAYGSRVANSAHFAPFMLVLMAGVHGALLTADLFNLFVFIEVMLLPSYGLYVLSANRREPL
+RRVDGARMYVTLNLLTSTILVTGVGFVYALTGSVNMAVLAGAARGDVRVALAAGLVLFALSIKASMLPMHGWLARAYPST
+SPAVTAIFAALHTKVAVYAMYRIYMVVYDGDPRLLGLILTLCLATLMVGAVASVGEHGARAVLSWQMVSGIGGIMVGLGL
+ATQAGLSAGLFYLVHHMVVMACLLTATGAIEVRYGSGRLADLQGLAVREPLIAAAFFVGMLSLVGIPPFSGFAGKLALVL
+AGVAAGRTVTVVLVLVASLISLWALLRIWDAWFWGRPRAPHGHRERLDTAALPLVHGDGVMPAAGAPVHPAGRGSSTDSE
+RAEAWASTETLDTPTGVLPVVVDPDEDHTASRIPLRLAGPAALMAAATLALGLGAEGLWSVTDQAARGLADPTAYIEAVL
+GR
+>4_999
+MSAVPLGQLLPLFAAVPLLSAGLLVLAGERPRLHRAVLFAVLGLVTTGGLALGVHALDGSVLATSLGGWPGGIGIGFAAD
+MLSALMLVLTSALTIVGAAFAYGSRVANSQFFAPLLLILIGGVNGALLTADLFNLFVFIEVMLVPSYGLYVLSANRREPL
+RRVDGARLYVTLNLLTSTILLVGVGFVYGLTGSVNLAMLAGSAAADPRIAIAAGMVLFALSIKASVAPLHGWLAWAYSST
+SPAVTALFAALHTKVAVYGLYRIYSVMYDGDARLLPLILVLSLATLVVGALASVGEHGVRAVLSWQMVSGIGGILVGLGL
+STRLGLAAGLFYLVHHMVAMGCLLMAAGAIEVRYGTGRLADLQGLARREPLIAVAFFVGLLSLVGIPPFSGFVGKLMLVS
+AGLDAGRGVTAALVLGASLVSLWALLRVWDAWFWGAPTAPHGHRERLATAAMPIVGRAGSVPS------PSGRGSSTDHE
+RTESWASQETLDPPTGVLPVTVDPDEDVTRSRIPGRLAAPAVVLAMATLALGLGGQALWTVTDLAAQGLMDPSRYIEAVL
+NP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000914.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000914.fa
new file mode 100644
index 0000000000000000000000000000000000000000..52ddab8e081843b20923fbe90ac39dc8bc2c99c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000914.fa
@@ -0,0 +1,21 @@
+>0_1053
+MDVVLTAAGSVLVVIGALAFVTAGLGLIRFPDPYTRVSAVGTAGGVGMILIVVGALLLAP
+GVAAFVKVALIVVLQLGSASVATMALGRSAYLTGVPMNPGHYDELAEDTPGREHGEPAPR
+APDEV
+>1_781
+MDVVLTAAGSVLVVIGALAFVTAGLGLIRFPDPYTRVSAVGTAGGVGMILIVVGALLLAP
+GVAAFVKVALIVVLQLGSASVATMALGRSAYLTGVPMNPGHYDELAEDTPGREHGEPAPR
+APDEV
+>2_1765
+MDLVLTVIGSVLVVAGALVFVTAGLGLIRFPDPYTRISATGTAGGVGMILIVVGGLVLAP
+SVANVVKVALIVVLQLGSAAVATMALGRSAYLTGVPMNPGHYDELAEDTPGREHGEPAPR
+TPDAS
+>3_1654
+MDLVMTVAGSVLAVAGAVVFLGAAVGLIRFPDPYTRISATGTAGGVGMILIVTGGLLLMP
+SVANLVKVVLIVVLQLGTAAIATMALGRSAYLTGVPMNLAHYDELAEDTPGREHGEPAPR
+HPED-
+>4_1002
+MDVVLTAAGSVLVVIGALAFVTAGLGLIRFPDPYTRVSAVGTAGGVGMILIVVGALLLAP
+GVAAFVKVALIVVLQLGSASVATMALGRSAYLTGVPMNPGHYDELAEDTPGREGGRAAPR
+LPDMD
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000916.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000916.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8430b5c7950c10e5a08cf4e5849a467c0b8cdd8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000916.fa
@@ -0,0 +1,65 @@
+>0_1055
+MAADPTPEAPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQRPTHVAVAFDLSGPTFRSEEY
+GEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTLEGYEADDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYP
+KKGVSDIPPMDADAVKAKYGVAPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLKQYGDLDGVLAHAHEITGKKGEALR
+EHLEDVRRNRRLNALVRDLDLPIGLETMRLEMPEREPVEELFDALQFHRIRERVFEVFGERVGEDAPPPEVEAAPEFTEA
+TTAEDVRAFLAAEAGNLLGVHVDVEGPALLPRRKVPVPGTFGTPVGVALVGEHAGLHVTLDGDAPDPALVAAVREALGEG
+GLAKAVHDLKRTLKALAAPTEGDGLGPDAALDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLTAPRESAQQRAQGS
+FDLDGGQAAAERADRAADAVRAAWVVRRLSTQFTPQVLDRGAQRLLQELEIPLSRLLARMELTGIAVDVDALTGLREDFT
+DAADAAKESAWASVAEETGGMQVNLGSPKQLQEVLFERLNMPRTRKTKTGYSTDVDSLQDLLEQTRHPFLENLMAHRDAT
+KLRQTVEGLLETVAPDGRIHTTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIREVFVADEVAGEQAVLLSADYSQIEMR
+IMAHLSEDEGLIQAFREGEDLHSFVGSQVFGVDPDDVTAEQRAKVKAMSYGLAYGLSSFGLSKQLKISVDEARGLMKGYF
+DRFGGVRDYLRDVVAQARQDGYTSTIEGRRRYLPDLSSDNRQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLEEHGL
+ASRLLLQVHDELILEVPAAELEKATALLKERMGRAAELSVPLDVHVGQGRSWHDAAH
+>1_783
+MAADPTPEAPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQRPTHVAVAFDLSGPTFRSEEY
+GEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTLEGYEADDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYP
+KKGVSDIPPMDADAVMAKYGVAPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLKQYGDLDGVLAHAHEITGKKGEALR
+EHLEDVRRNRRLNALVRDLDLPIGLEAMRLEMPEREPVEELFDALQFNRIRERVFEVFGERVGEDAPPPEAEAAPEFTEA
+TTAEDVRSFLAAEAGNLLGVHVDVEGPALLPRRKVPVPGTFGTPVGVALVGEHAGLHVTLDGDAPDPALVAAVREALGEG
+GLAKAVHDLKRTLKALAAPTEGDGLGRDAALDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLTAPREPAQQRAQGT
+FDLDGGQAAAERADRAADAVRAAWVVRRLSTQFTPQVLDRGAQRLLQELEIPLSRLLARMELTGIAVDVDALTGLREDFT
+DAADAAKESAWASVAEETGGMQVNLGSPKQLQEVLFERLNMPRTRKTKTGYSTDVDSLQDLLEQTRHPFLENLMAHRDAT
+KLRQTVEGLLETVAPDGRIHTTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIREVFVADEVAGEQAVLLSADYSQIEMR
+IMAHLSEDEGLIQAFREGEDLHSFVGSQVFGVDPDDVTAEQRAKVKAMSYGLAYGLSSFGLSKQLKISVDEARGLMKGYF
+DRFGGVRDYLRDVVAQARQDGYTSTIEGRRRYLPDLSSDNRQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLEEHGL
+ASRLLLQVHDELILEVPAAELEQATALLKERMGRAAELSVPLDVHVGRGRSWHDAAH
+>2_1763
+MAADPTPEDPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQRPTHVAVAFDLSGPTFRSEEY
+GEYKAGRSETPAEFAGQIELTVKVMEALGIPTITLEGYEADDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYP
+KKGVSDIPPMDADAVMAKYGVSPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLTQYGDLDGVLAHADEIKGKKGEALR
+AHLDDVRRNRRLNALVRDLDLPIGLEAMALEMPEREPVEELFDALQFNRIRERVFEVFSERIGETAPAAQVEEAPEFTEA
+ATAQDVADFLAAEAGNLLGVHVDVEGPALLPKRKVPVPGTFGTAVGVALVGEHAGLHVSLDADAPDPALLAALREALGEG
+GLSKAVHDLKRVLKAIAEPAEATALEAGTPLDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLAAPREPAEADAQGA
+FDLDGGAAAAERAARAADAVRAAWVVRRLSVLFTPQVLERGAQRLLQELEIPLARLLARIELTGIAVDAQALETLRADFS
+EAAAAAQESAWASVAEETGGMKVNLGSPKQLQEVLFEHLDMPRTRKTKTGWSTDVDSLQDLLEQTRHPFLENLMRHRDAT
+KLRQTVEGLLETVAPDGRIHTTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIREVFVADRVAGEDAVLLSADYSQIEMR
+IMAHLSEDAGLIQAFREGEDLHSFVGSQVFGVAPDEVSSEQRAKVKAMSYGLAYGLSSFGLSKQLKISVDEARGLMKGYF
+DRFGGVRDYLRDVVAQARRDGYTSTIEGRRRYLPDLSSDNRQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLAEHGM
+ASRLLLQVHDELILEVPAAELEQATALLQERMGRAAELAVPLDVHVGQGRSWHDAAH
+>3_1652
+M-GENSTEARPRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTSMLLTMIRQQAPTHVAVAFDLSGPTFRSAEY
+GEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTKEDFEADDIVATLSAQAEAQGWDVCVVSGDRDAFQLISERTQVLYP
+KKGVSDIPPMTAADVEAKYGVRPEQYPELAALVGESADNLPGVPGVGPGFAAKWLQKYGDLDGVLAHADEITGKKGEALR
+AHLDDVRRNRRLNALVRDLDLDVSLDAMELTMPEREVVEELFDALQFQRIRERVFEVFAERLGSAAPAAPVAEAPAAVLA
+ATADDVHAFVSAHAGTLLGLHVEIDGPDLLPKRKVPVPGTFGTPVGLALAAEDAALYVDLTDADADPGLVAALGDLLAED
+GAAKAVHDLKRTLKAIAVPTGPTALPADTSLHGVVDDVALSAYLIQPDRRDTDLATLSQAHLQEPLEAP-ESAAAGAQGA
+FDLDGAQEEAERTARAARAARSAWVVRRLSQAFTPQVLERGAQRLLQEMEIPLARLLARMELAGIAVDGDALSALLADFT
+DRAEAAKESAWASVAEETGGMKVNLGSPKQLQEVLFEHLDMPKTRKTKTGWSTDVDSLQDLLEQTQHPFLENLMAHRDAT
+KLRQTVEGLRETVAPDGRIHTTYSQTVAATGRLSSLHPNLQNIPVRTEAGRRIREAFVAAPVDGEPAELLSADYSQIEMR
+IMAHLSEDAGLIEAFNSGEDLHSFVGSQVFGVDPDDVTSEQRSKVKAMSYGLAYGLSSFGLSKQLKISVDEARGLMKGYF
+DRFGGVRDYLRDVVAQARRDGFTSTIEGRRRYLPDLTSDNRQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLVEQGL
+RSRLLLQVHDELILEVPASELDAATALLQERMGRAADLSVPLDVHVGHGGTWHAAAH
+>4_1004
+MAADPTPEAPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQRPTHVAVAFDLSGPTFRSEEY
+GEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTLEGYEADDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYP
+KKGVSDIPPMDADAVKAKYGVAPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLKQYGDLDGVLAHAHEITGKKGEALR
+EHLEDVRRNRRLNALVRDLDLPIGLEAMRLEMPEREPVEELFDALQFNRIRERVFEVFGERVGEDAPPPEVEAAPEFTEA
+TTAEDVRAFLAAEAGTLLGVHVDVEGPALLPRRKVPVPGTFGTPVGVALVGEHAGLHVSLDGDAPDPALVGAVREALGEG
+GLAKAVHDLKRTLKALAAPTEGDGLGRDAALDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLTAPREPAQQRAQGT
+FDLDGGQAAAERADRAADAVRAAWVVRRLSTQFTPQVLDRGAQRLLQELEIPLSRLLARMELTGIAVDVDALTGLREDFT
+VAADAAKESAWASVAEETGGMQVNLGSPKQLQDVLFERLNMPRTRKTKTGYSTDVDSLQDLLEQTRHPFLENLMAHRDAT
+KLRQTVEGLLETVAPDGRIHTTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIRGVFVADEVAGEQAVLLSADYSQIEMR
+IMAHLSEDEGLIQAFREGEDLHSFVGSQVFGVDPDDVTAEQRAKVKAMSYGLAYGLSSFGLSKQLKISVDEARGLMKGYF
+DRFGGVRDYLRDVVAQARQDGYTSTIEGRRRYLPDLSSDNRQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLEEHGL
+ASRLLLQVHDELILEVPAAELEQATALLKERMGRAAELSVPLDVHVGRGRSWHDAAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000918.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000918.fa
new file mode 100644
index 0000000000000000000000000000000000000000..756e69c347af43df671ed9c108d3e5efdd065470
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000918.fa
@@ -0,0 +1,46 @@
+>0_1058
+M---SEPLPRG-----------VTPDVAHGGLPDDLTAGVDFAALDRWPLPPEPDRQAHD
+AADLLLLDTLAGWIASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDAN
+LAAWR-AAGRLGGEAGELERTATPEDAARGARTVLLPLPRSLDELDRLSRIVAAAADPGV
+VLLAGGRDKHMSPRMNAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTPRPPEEADRDVP
+GVGSLHLVAHAGAFGGAAADPGSRLLLASLADD----PRP-PGR----------------
+-----LVDLGCGNGLLSVGAARLWPHVTVLATDQSAVAVASTLATARANRVADRVRAVRD
+DALATWPDGTEECVLLNPPFHDGNAVDPSVAHRLVAAAARVLEPGGRLWCVWNSHLRYRP
+VLEDLVGPTRQTARDRTFTVTVSERR
+>1_786
+M---SEPLPRG-----------VTPDVARGGLPDDLTAGVDFAALDRWPLPTEPDRQAHD
+TADLLLLDTLAGWIASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDAN
+LAAWR-AAGRLGGETGELERTATPEEAARGARTVLLPLPRSLDELDRLSRIVSAAADPGV
+VLLAGGRDKHMSPRMNAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTARPPEEADRDVP
+GVGRLHLVAHAGTFGGAAADPGSRLLLASLADD----PRP-PGR----------------
+-----VVDLGCGNGLLSVGAARLWPHVTVVATDQSAVAVASTLATARANRVADRVRAVRD
+DALATWPDGEEECVLLNPPFHDGNAVDPSVAHRLVAAAARVLEPGGRLWCVWNSHLRYRS
+VLEDLVGPTRQTARDRTFTVTVSERR
+>2_1759
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------MDLGCGNGLLGVGAARLWPHVRVLATDQSAVAVASTLATARANGVADRLEAVRD
+DALAGRPDASEECILLNPPFHDGNAVDPAVAHRLVAEAARVLAPGGRLWCVWNSHLRHRP
+VLEAEVGPTRQVARDRTFTVTVSTRR
+>3_1649
+MDAIAQTPPRDPGPARLTATELVTPDAAGRGLPRDWTAEFPFERLGRWPLPESRERQAHD
+AADLLLVDTLAGWTADGRVPGPVAVLHDQHGAVSLPLLARGLNVRLGLDEASAARSVERN
+LDLFRDADGALPAGWGRLTVGGVDAATLADARTVLLLLPRALDALHLTAARIAVHAAPDV
+LVLGAGRDKHMTPSMNDVLARSFAAVVPGRGRSKSRVITAARPVDDATEPAPRRAQHRLG
+RLGAVTLVGGWATFGGAAADPGSLLLAGTLADRAPALPVPAPHRMRTDSGLGVDIPWATR
+AGAPDVVDAGSGNGMLSVVAARVWPEAAVLASDQSADAVASSAATAEANGLAERITAVQD
+DALGALPDASVRAVLLNPPFHDGTAVDPTVAHRMIEAAGRILAPGGELWCVWNSHLRHRP
+VLETAVGPTRQVARNRTFTVTVSTRR
+>4_1007
+M---SEPLPRG-----------VTPDVARGGLPDDLTAGVDFAALDRWPLPTEPDRQAHD
+AADLLLLDTLAGWIASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDAN
+LAAWR-AAGRLGGETGELERTATPEEAARGARTVLLPLPRSLDELDRLSRIVSAAADPGV
+VLLAGGRDKHMSPRMNAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTARPPEEADRDVP
+GVGRLHLVAHAGTFGGAAADPGSRLLLASLADD----PRP-PGR----------------
+-----VVDLGCGNGLLSVGAARLWPHVTVVATDQSAVAVASTLATARANRVADRVRAVRD
+DALATWPDGEEECVLLNPPFHDGNAVDPSVAHRLVAAAARVLEPGGRLWCVWNSHLRYRS
+VLEDLVGPTRQTARDRTFTVTVSERR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000921.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000921.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c22f237896b5102de215903c5ab9953f7db03fd2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000921.fa
@@ -0,0 +1,50 @@
+>0_1062
+MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAWLVERLQRPTLVMVQNKTLAA
+QLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEKDSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTP
+EEYIEQMVTLRRGAEMDRDVLLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG
+QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDRLLEAQRLRMRTTYDLEMMQQMGYCNGIENYSRH
+IDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYEGDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYL
+SATPGAYELGQADGYVEQIIRPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTTSLIQTIGRAARNVSGEVHMY
+ADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRIADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSL
+DRAPATGE-GAEAPAVDPASLPAKDLADLIEQMSQQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ
+>1_790
+MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAWLVERLQRPTLVMVQNKTLAA
+QLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEKDSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTP
+EEYIEQMVTLRRGAEMDRDVLLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG
+QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDKLLEAQRLRMRTTYDLEMMQQMGYCNGIENYSRH
+IDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYEGDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYL
+SATPGAYELGQADGYVEQIIRPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTTSLIQTIGRAARNVSGEVHMY
+ADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRIADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSL
+DRDATTGE-GTEAPAVDPASLPAKDLADLIEQMSKQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ
+>2_1754
+MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAWLVERLQRPTLVMVQNKTLAA
+QLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEKDSSVNEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTP
+EEYIEQMVTLRRGEEMDRDVLLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG
+QVVREETEMYIFPASHYVAGDERMGRAVTAIEDELRERLQELESQDRLLEAQRLRMRTTYDLEMMQQMGYCNGIENYSRH
+IDGRPDGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYEGDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYL
+SATPGAYELGQADGYVEQIIRPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLDAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTTSLIQTIGRAARNVSGEVHMY
+ADNVTDSMRRAIEETERRRAVQIAYNEEHGIDPQPLRKRIADITDQLAREDADTADFLKGMGGVKSGFDYGMGHRGLSSL
+DREEGQER-AGGGPAVDAASLPAKDLADLIEQMSLQMHQAAADLQFELAARLRDEVGELKKELRQMRREQ
+>3_1645
+MSLAKQINRVVAPFEVVSPYQPSGDQPTAIAEIAERVQAGEKDVVLMGATGTGKSATTAWVIEQLQRPTLVMVQNKTLAA
+QLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEKDSSINEEVERLRHSATNALLTRRDVVVVATVSCIYGLGTP
+EEYIAQMVTLRRGQEMDRDALLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEVESIQTLHPLTG
+QVVREEEEMYIFPASHYVAGDERMGRAIATIEDELRERLQELESQDKLLEAQRLRMRTTYDLEMMQQMGYCNGIENYSRH
+IDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYEGDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYL
+SATPGQYELSQADGVVEQIIRPTGLVDPTVVVKPTQGQIDDLLEQIRTRTEKDERVLVTTLTKRMAEDLTEYLLEAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVSILDADKEGFLRSTTSLIQTIGRAARNVSGEVHMY
+ADRVTDSMRRAIEETERRREVQIRYNAEHGIDPQPLRKKIADITDALAREDADSADFLKGMGGVKAGFDYGMGHRGLGSL
+DHEPPAGEVPSGSPAVDPAALPAKDLAQLIEQMSAQMHQAAADLQFELAARLRDEIGDLKKELRQMKREQ
+>4_1011
+MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAWLVERLQRPTLVMVQNKTLAA
+QLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEKDSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTP
+EEYIEQMVTLRRGAEMDRDVLLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG
+QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDKLLEAQRLRMRTTYDLEMMQQMGYCNGIENYSRH
+IDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYEGDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYL
+SATPGAYELGQADGYVEQIIRPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTTSLIQTIGRAARNVSGEVHMY
+ADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRIADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSL
+DRDATTGE-GTEAPAVDPASLPAKDLADLIEQMSKQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000922.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000922.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f540fe58d61361cd54a031640ad29d2af05f0f58
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000922.fa
@@ -0,0 +1,26 @@
+>0_1063
+MS---AAP-PVAAVIADIVGSRALPDRDRAQEQILAAFAAAEQDVPPLRPAWASVGDEFQ
+ALHRTWPDALRLTVRVTLALPPGLDLRFGIGLGQRR----ALDAG-GDGIEDGPAWYRAR
+EAVERAHERAVGAATAFRAADPSLTAAVDGLVLLRDHVLGRLKARERRIAAALLGGATQA
+EAARAERITQSAVSQAVARSGIDRLLELDAELAA-AAT----------------EVAP
+>1_791
+MS---AAP-PVAAVIADIVGSRALPDRERAQEQILAAFAAAEQDVPPLRPAWASVGDEFQ
+ALHRTWPDALRLTVRVTLALPPGLDLRFGIGLGQRR----ALDAG-GDGIEDGTAWYRAR
+EAVEHAHERAAGAATAFRAADPSLTAAVDGLALLRDHVLGRLKARERRIAAALLGGATQA
+EAARAERITQSAVSQTVARSGIGRLLELDAELAA-AAT----------------EVAP
+>2_1752
+MT---RAP-QAAAVIADIVGSRRLPDREAAQEQILAAFAVAEKDVPPLRAAWATVGDEFQ
+ALHGVWPQAVRAVVRVSLALPPGLELRFGIGVGERR----SLDDGAGDRIEDGTAWYRAR
+AAVERAHARADGAATAFVAADPSLTAAVDGVLLLRDHVLGRLKARERRLAAALLGGATQT
+QAARAERITQSAVSQAVTRSGIDRLLELDAALAE-AAAGRPGHAGAAGEGAGDEGDAG
+>3_1644
+MSLTDEGPVRGTAVIADIVGSRGLRDRAAAQEAILAAFAAAEEAVPARIPAWATVGDEFQ
+ALHADWAAAVRATLRVAVALPEGVELRFGLGDGVHREVTGAADDD-GRPILDGSAWHRAR
+EALEAAEHRTRGLAGAYRGPDADLTAAVDGQLLVRDHVLRRLKARERRIAAALLAGRTQA
+ETATAERITQGAVSQAVARSGVRELLALDAALGALPGAGRGAKATA-------EEDRP
+>4_1012
+MS---AAP-PVAAVIADIVGSRALPDRERAQEQILAAFAAAEQDVPPLRPAWASVGDEFQ
+ALHRTWPDALRLTVRVTLALPPGLDLRFGIGLGQRR----ALDAG-GDGIEDGTAWYRAR
+EAVEHAHERAAGAATAFRAADPSLTAAVDGLALLRDHVLGRLKARERRIAAALLGGATQA
+EAARAERITQSAVSQTVARSGIGRLLELDAELAA-AAT----------------EVAP
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000924.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000924.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5032df2c22ee6b3b871d4a5c9a3a0158a2078c1f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000924.fa
@@ -0,0 +1,40 @@
+>0_1067
+-----------MAGDPRGFAPLEPARHRVGERTELYDGTVTVDHWFSVPIDHALGLAEAEAQDAAGTGVGPHGRGTLTVF
+AREIRAKDDPEGERPWALYLQGGPGSAGPRPARLSGWLGALAESHRVLLLDQRGTGRSTPATVATLTAPGAFATDEARAE
+HLVHLRAPSIVRDAEMLRLALGAGPWTTLGQSFGGFCTLSYLSFHPEGLQRSLVTGGLAPLTGHADRVYRATYARMRART
+EEFFDRHPADRDAWSEAVGLIRAAEAAGAPIPLPGGGPLTVGRAQGLGMLLGGNTRVDRLHWVLAEAVDRTGPAPRLSET
+FLAAVADQDDRLVNPLYTVLHEAIYAQPADLAGGRADTGWSASRMLAEHPDFDPEATTVPLPTGEHVMPWSVEVDPRLRP
+LAGTARLLAERTQWGPLYDVAALAQNTVPVAAAVYADDVYVDRDLSLETARRVRGLQVWETDAFHHDGIADDGPAILERL
+LAMT-----------------APDGAGTTTAPDPVD
+>1_795
+-----------MAGDPRGFAPLEPARHRVGERTELYDGTVTVDHWFSVPIDHALGLAEAEAQDAAGTGVGPHGRGTLTVF
+AREIRAKDDPEGERPWALYLQGGPGSAGPRPARLSGWLGALAESHRVLLLDQRATGRSTPATVATLTAPGAFATDEARAE
+HLVHLRAPSIVRDAEMLRLALGAGPWTTLGQSFGGFCTLSYLSFHPEGLQRSLVTGGLAPLTGHADRVYRATYARMRART
+EEFFDRHPADRDAWSEAVGLIRAAEAAGAPIPLPGGGPLTVGRAQGLGMLLGGNTRVDRLHWVLAEAVDRTGPAPRLSET
+FLAAVADQDDRLVNPLYTVLHEAIYAQPADLAGGRADTGWSASRMLAEHPDFDPEATTVPLPTGEHVMPWSVEVDPRLRP
+LAGTARLLAERTQWGPLYDVAALAQNTVPVAAAVYADDVYVDRDLSLETARRVRGLQVWETDAFHHDGIADDGPAILERL
+LAMT-----------------APDGAGTTTASDPVN
+>2_1749
+M----SAPAPRVPGDPRGFAPLEPARHRVGERTELYDGTVAVDHWFTVPVDHALTLAEAEAQDAAGTGVGPHGRGTLTVF
+AREIRAAGDADGARPWALYLQGGPGGAGPRPARGGGWIGALASEHRVLLLDQRGTGRSTAASVAALTAPGAFASDEALAE
+HLVHLRAPSIVRDAEMVRLALGAAPWTTLGQSFGGFCTLTYLSFHPEGLRRCLVTGGLAPLTGHADRVYQATYARMRDRA
+HEFFARHTGDRAAWAEAVALIRAAEQAGEPVRLPDGGLLTVARAQALGMLLGGNTRVDRLHWILAEAVDRSGPAPRLSET
+FLAAVAEQNDRHVNPLYTVLHESIYAQPAELAGGRAATDWSAARVLAEHPDFDPDAADAPLPTGEHVMPASLELDPHLRP
+LRGAARLLAERTDWGPLYDVEALARNIVPVAAAVYTDDVYVDRDLSLETAGRVRGLRVWETDAFHHDGLADDGPAIVRRL
+LEMTGEGAAPAAAEGAERSDSAPAASETTTAPGPVD
+>3_1641
+MTRTGTGDAAFVPGDPRGFAPVGPAAHREGERTVLFDGTVAVDHWFTVPVDHALTLAEALAQDAAGTGLGPGGRGTLEVF
+AREVRHPEDPEGERPWLLYLQGGPGSGGPRPARLGGWQCELAQHHRLLLLDQRGTARSTPVTAATL---AGLPDDAARAA
+YLTHLRAPQIVQDAEMIRVALGAPPWTTLGQSFGGFCTLSYLSWRAEGLERCLVTGGLAPLTGHADRVYRATTARMHARW
+QEFLERHPQDAGHWAEAVALIRAAQDDGDPYVLPDGTALTVGRAQQLGMLLGGNTRVDGLHWVLAEAVDRSGGEPRLSPG
+FLAAVAAQTTRAVNPLYAVLHEAIYAQPAALTDGRGATAWSAQRVLAEHPDSSPAADPAPVPTGEHVLPWSFETEPELRA
+LAGVAALLAAKDDWGALYDLDALAANEVPVAAAVYTDDVYVDRDLSLETAARVRGLQVWETDAFHHDGLADDGPGIVRRL
+RGMLG----------------A--------------
+>4_1017
+-----------MAGDPRGFAPLEPARHRVGERTELYDGTVTVDHWFSVPIDHALGLAEAEAQDAAGTGVGPHGRGTLTVF
+AREIRAKDDPEGERPWALYLQGGPGSAGPRPARLSGWLGALAESHRVLLLDQRGTGRSTPATVATLTAPGAFATDEARAE
+HLVHLRAPSIVRDAEMLRLALGAGPWTTLGQSFGGFCTLSYLSFHPEGLQRSLVTGGLAPLTGHADRVYRATYARMRART
+EEFFDRHPADRDAWSEAVGLIRAAEAAGAPIPLPGGGPLTVGRAQGLGMLLGGNTRVDRLHWVLAEAVDRTGPAPRLSET
+FLAAVADQDDRLVNPLYTVLHEAIYAQPADLAGGRADTGWSASRMLAEHPDFDPEATTVPLPTGEHVMPWSVEVDPRLRP
+LAGTARLLAERTQWGPLYDVAALAQNTVPVAAAVYADDVYVDRDLSLETARRVRGLQVWETDAFHHDGIADDGPAILERL
+LAMT-----------------APDGAGTTTAPDPVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000925.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000925.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1e3935acfee539b77d774f0720f784cd40f9bdb2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000925.fa
@@ -0,0 +1,60 @@
+>0_1068
+MTSAATNPPSLTDRIDALPPAPDADDVFGAFAAWTEDRGISLYPAQEEAALELVQGRHVILATPTGSGKSLVALAAHADA
+LAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDSTVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYY
+ADPSRGWAWQVPLLELPQARFLLMSATLGDTTRLEADLTERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEEFVSTHQA
+PVYIVHFSQLDAVETAQGLSSISVTSREEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGVHHAGMLPKYRRLVEKLAQDG
+LLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQAREFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAA
+AKFANVKDEAERAKRMKQSVKSGKRKTPPAGFVSWGPATFERLVSAEPEPLVSRMRITHSMLLNILDRPGDPVIAVRRLL
+RGTHETPARQAVLMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLSPFALAALDLLDPADPDHALD
+VVSVIEATLDPPRQVLSAQVKHAKGEAVAAMKAEGMDYNDRMRALDEITHPRPLAELLEQQFELYRQDAPWLAEFELTPK
+SVVRDMFERAMGFGDYVRFYGIARSEGVLLRYLTDAVKALRHTVPEAARTEELQVLLDWLDEMVKQTDSSLLEEWEDLVA
+GDIDELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEALARLSGELSADDWADALDAYFDDHEDIDDG
+PAARGPELFRVAAAPDVAAPLELAGPRWWAVRQVLKDPDGDLDHGINAVVDLDASDEAGHPVIRVVSVGAPESGWGL
+>1_796
+MTSAATNPPSLTDRIDALPPTPDADDVFGAFAAWTEDRGISLYPAQEEAVLELVQGKHVILATPTGSGKSLVALAAHADA
+LAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDSTVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYY
+ADPSRGWAWQVPLLELPQARFLLMSATLGDTTRLEADLTERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEELVSTHQA
+PVYIVHFSQLDAVETAQGLSSISVTSREEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGVHHAGMLPKYRRLVEKLAQDG
+LLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQAREFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAA
+AKFANVKDEAERAKRMKQSVKSGKRKTPPAGFVSWGPATFERLVSAEPEPLVSRMRITHSMLLNILDRPGDPVIAVRRLL
+RGTHETPARQAVLMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLSPFALAALDLLDPADPDHALD
+VVSVIEATLDPPRQVLSAQVKHAKGEAVAAMKAEGMDYNDRMRALDEITHPRPLAELLEQQFELYRQDAPWLAEFELTPK
+SVVRDMFERAMGFGDYVRFYGIARSEGVLLRYLTDAVKALRHTVPEAARTEDLQVLLDWLDEMVKQTDSSLLEEWEDLVA
+GDIDELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEALARLSGELSADDWADALDAYFDDHEDIDDG
+PAARGPELFRVAAAPDVAAPLELAGPRWWAVRQVLKDPDGDLDHGINAVVDLDASDEAGHPVIRVVSVGAPESGWGL
+>2_1748
+MTSPATNPPSLTDRIDALPPTPDADDVFGAFAAWTEVRGISLYPAQEEAALELVQGRHVILATPTGSGKSLVALAAHADA
+LAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDSTVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYY
+ADPSRGWAWQVPLLELPQARFLLMSATLGDTTRLEADLIERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEELVSTHQA
+PVYIVHFSQLDAVETAQGLSSISVTSKEEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGVHHAGMLPKYRRLVEKLAQDG
+LLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQAREFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAA
+AKFANVKDEAERAKRMKQSVKSGKRKSPPAGFVSWGPATFERLVAAEPEPLVSRMQITHSMLLNILDRPGDPVVAVRRLL
+RGTHETPARQAILMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLSPFALAALELLDPAEPDHALD
+VVSVIEATLDPPRQVLSAQVKKAKGEAVAAMKAEGMDYNDRMRALDEVTHPQPLADLLEQQFEVYRASAPWLAEFELTPK
+SVVRDMFERAMGFGDYVRFYGIARSEGVLLRYLTDAVKALRQTVPEASRTEELQVLLDWLDEMVKQTDSSLLEEWEDLVA
+GDIEELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEELARLSGDLSADDWADALDAYFGDHEDIDDG
+PAARGTELFRVAESPDVAPPVELAGSRWWAVRQVLKDPDGVHDHGVNAVVDLDASDEAGHPVIRVVSVGAPESGWGL
+>3_1640
+MTPSATNPPSLTDRLDALPASPDADDVFGAFAAWTEDRGISLYPAQEEAVLELVQGRHVILATPTGSGKSLVALGAHADA
+LAHGKVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDSSVNADAPIICCTAEILANRALREGSGMEIGTVVMDEFHYY
+ADPSRGWAWQLPLLELPQARFLLMSATLGDTSMLERDLAERTGREVAVVAHAERPIPLSFEWSEVPLQEKVEELVSTHQA
+PVYIVHFSQLDAVETAVGLASISVTTKEEKEAIAERIAGFRFSAGFGKTLNRLVRAGIGVHHAGMLPKYRRLVEKLAQEG
+RLKVISGTDTLGVGINVPIRTVLLTALSKFDGEKTRILQSREFHQIAGRAGRAGFDTQGYVVVQAPEHVIENKAAERKAA
+AKFAGIKDEAERAKRMKQSVKGSKRKTPPQGFVSWGPATFDKLVASEPEPLVSRMRITHSMLLNILDRPGDPVLAVRRLL
+RATHETPARQAQLMRRALGIFRELLATGVVEVLPEPDAEGRTVDLTVDLQPDFALNQPLSPFALAALDLLDPAAPDHHLD
+VVSVIEATLDAPRQVLSAQVKKAKGEAVAAMKAEGMDYSDRMRALDEVTHPQPLAELLEQAFERYRQDAPWLAEFELSPK
+SVVRDMFERAMGFGDYVRFYGLARSEGVLLRYLTDAVKALRQTVPQEDRTEDLQVLLDWLDEMVKQTDSSLLEEWEDLMS
+GDIAELRRDLESLEPTPPPRLTDNAAVFRVMVRNAMFHRVRLFGDEQDARLAELSGDLSANDWADALDAYFDEHEDIDDG
+PDARGQEFFRVATAPGARCPVELEGSRWWAVRQVLKDHDGDHDHGINAVVDLEASDEAGHPAIRVVSVGAPVPGWDL
+>4_1018
+MTSAATNPPSLTDRIDALPPTPDADDVFGAFAAWTEDRGISLYPAQEEAVLELVQGKHVILATPTGSGKSLVALAAHADA
+LAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDSTVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYY
+ADPSRGWAWQVPLLELPQARFLLMSATLGDTTRLEADLTERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEELVSTHQA
+PVYIVHFSQLDAVETAQGLSSISVTSKEEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGVHHAGMLPKYRRLVEKLAQDG
+LLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQAREFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAA
+AKFANVKDEAERAKRMKQSVKSGKRKTPPAGFVSWGPATFERLVSAEPEPLVSRMRITHSMLLNILDRPGDPVIAVRRLL
+RGTHETPARQAVLMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLSPFALAALDLLDPADPDHALD
+VVSVIEATLDPPRQVLSAQVKHAKGEAVAAMKAEGMDYNDRMRALDEITHPRPLAELLEQQFELYRQDAPWLAEFELTPK
+SVVRDMFERAMGFGDYVRFYGIARSEGVLLRYLTDAVKALRHTVPEAARTEDLQVLLDWLDEMVKQTDSSLLEEWEDLVA
+GDIDELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEALARLSGELSADDWADALDAYFDDHEDIDDG
+PAARGPELFRVTAAPDVAAPLELAGPRWWAVRQVLKDPDGDLDHGINAVVDLDASDEAGHPVIRVVSVGAPESGWGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000928.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000928.fa
new file mode 100644
index 0000000000000000000000000000000000000000..94ba71e54d1819803015de1d0a350bfda987de23
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000928.fa
@@ -0,0 +1,50 @@
+>0_1073
+MPVADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLSSYFQDPARLATKTRTMVFTAAAVEWTVVGSELEA
+LQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQVMRGDRKPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSA
+GVFKRARAQDRPCLLGYIGKCSAPCVGRISPADHRALAQDFCDFMAGDANRFIRELEKAMARAVEELRYEDAARLRDDIA
+ALRRVFERNAVVLPENTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVAEPEMVAHLLQQVYGDLEGPERI
+PHEILVPVEPDDAAQLTEWLSGLRGSRVAVRVPRRGSKADLMETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEI
+TEPLLRIECYDISHSQGTNVVGSMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARLAKERAEGAPLSGQVE
+ADDQEAG-RRFAYPPSLVVVDGGPPQVAAAAAVLEELGLDDLPVVGLAKRLEEVWLPGDEFPVVLPRTSEGLYLLQRIRD
+ESHRFAIAGHRSRRSKAMTVSALDGIPGLGPAKRTALLNHFGSVAEIRAAGVDRLTEVAGIGPRLAEAVHTALTADTPAD
+TVES
+>1_801
+--MADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLSSYFQDPARLATKTRAMVFTAAAVEWTVVGSELEA
+LQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQVMRGDRKPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSA
+GVFKRARAQDRPCLLGYIGKCSAPCVGRISPADHRALAQDFCDFMAGDANRFIRELEKAMARAVEELRYEDAARLRDDIA
+ALRRVFERNAVVLPENTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVAEPEMVAHLLQQVYGDLEGPERI
+PHEILVPVEPDDAAQLTEWLSGLRGSRVAVRVPRRGSKADLMETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEV
+TEPLLRIECYDISHSQGTNVVGSMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARLAKERAEGAPLSGQVE
+GDDQEAG-RRFAYPPSLVVVDGGPPQVAAAAAVLAELGLDDLPVVGLAKRLEEVWLPGDEFPVVLPRTSEGLYLLQRIRD
+ESHRFAIAGHRSRRSKAMTVSALDGIPGLGPAKRTALLNHFGSVAEIRAAGVDRLTEVAGIGPRLAEAVHTALTADTPAD
+TVES
+>2_1743
+--MADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLGSYFQDPARLTTKTRTMVFTAAAVEWTVVGSELEA
+LQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQVMRGDRRPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSA
+GVFKRARAQDRPCLLGYIGKCSAPCVGRISPAEHRELAQDFCDFMAGDAQRFIRELERAMQGAVEELRYEDAARLRDDIA
+ALRRVFERNAVVLPESTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVSEPEMVTHLLQQVYGDLAGEDRI
+PHEILVPAEPDDAAQLVEWLSGLRGARVNVRVPRRGTKADLMETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEI
+AEPLLRIECYDISHSQGTNVVGSMVVMEDGLPKKKDYRRFNVTGEAARDDTASMKDVLSRRFARLAEERAEGAPLSGQLE
+GEEEGRD-RRFAYPPSLVVVDGGPPQVAAAAAVLEELGLDDLPVVGLAKRLEEVWLPGDEFPVVLPRTSEALYLLQRIRD
+ESHRFAIAGHRGRRAKAMTASALDGISGLGPAKRTALLNHFGSVAQIRAAGVERLTEVAGIGPTLAQTVHAALAPAEPTD
+TVEP
+>3_1635
+--MADPRTYRPAPGEISTSPGVYRFRDPDGRVIYVGKAKNLRARLSSYFQDPARLATKTRTMVFTASAVEWTVVASELEA
+LQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNERFPRVQVMRGDKRPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSA
+GVFKRAQAQDRPCLLGYIGKCSAPCVGRISPDEHRALAQDFCDFMAGDADRFVRELEKAMAGAVEELRFEDAARLRDDIA
+ALRRVFERNAVVLAESTEADVFALHSDELETAVQVFHVRQGRIRGQRGWIMERVEDVGEDEAVAELLTQVYGDVPDTERI
+PHEVLVPVLPAGAEQVTEWLSGLRGARVQVRVPQRGPKADLMGTVRENAEMALKLHKTRRSGDLTTRSAALRELQDALEI
+DEPLLRIECYDISHSQGTNVVGSMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARMAEDRREGGVLTGQID
+AEEAEGERRRFAYPPSLVVVDGGPPQVAAAAEVLAELGLDDLPVVGLAKRLEEVWLPGDEFPVVLPRTSEGLFLLQRIRD
+ESHRFAIAGHRSRRTKAMTASALDDVPGLGPTRRRALLTHFGSVERMRQAGPAGLTEVAGIGPALAEAVHAALTASDGGD
+TVAP
+>4_1023
+MPVADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLSSYFQDPARLATKTRTMVFTAAAVEWTVVGSELEA
+LQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQVMRGDRKPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSA
+GVFKRARAQDRPCLLGYIGKCSAPCVGRISPADHRALAQDFCDFMAGDANRFIRELEKAMARAVEELRYEDAARLRDDIA
+ALRRVFERNAVVLPENTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVAEPEMVAHLLQQVYGDLEGPERI
+PHEILVPVEPDDAAQLTEWLSGLRGSRVAVRVPRRGSKADLMETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEI
+TEPLLRIECYDISHSQGTNVVGSMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARLAKERAEGAPLSGQVE
+GDDQEAG-RRFAYPPSLVVVDGGPPQVAAAAAVLEELGLDDLPVVGLAKRLEEVWLPGDEFPVVLPRTSEGLYLLQRIRD
+ESHRFAIAGHRSRRSKAMTVSALDGIPGLGPAKRTALLNHFGSVAEIRAAGVDRLTEVAGIGPRLAEAVHTALTADTPAD
+TVES
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000935.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000935.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a6b690e3019e373387f347a2186da7919205953a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000935.fa
@@ -0,0 +1,31 @@
+>0_1080
+MA-EQTTRVPLIAGNWKMNLDHLEAVTLVQRLTWLLSDADHDQEAVEVAVFPPFTGLRSV
+QTLVTGDRLDLVYGAQDLSPEDAGAYTGDVSGAFLAALGCRYAIVGHSERRTLHGEDDAL
+VARKAAAALRHGLTPVICVGEGLEVRQAGRHVEHTLAQLEGSIAGLSAQDVAGVVVAYEP
+VWAIGTGEVAGPEDAQQMCAALRARVAALHGDDVAAGLRILYGGSVKSSSAPALLAQPDV
+DGALVGGASLDADEFAKIVRFDQA-
+>1_808
+MA-EQTTRVPLIAGNWKMNLDHLEAVTLVQRLTWLLTDADHDQEAVEVAVFPPFTGLRSV
+QTLVTGDRLDLVYGAQDLSPEDAGAYTGDVSGAFLAALGCRYAIVGHSERRTLHGEDDAL
+VARKAAAALRHGLTPVICVGEGLEVRQAGRHVEHTLAQLEGSIAGLSAQDVAGVVVAYEP
+VWAIGTGEVAGPEDAQQMCAALRARVAALHGDDVAAGLRILYGGSVKSSSAPALLAQPDV
+DGALVGGASLDADEFAKIVRFDQA-
+>2_1735
+MA-ETAARVPLIAGNWKMNLDHREAVTLVQRLAWLLTDADHDHEDVEVAVFPPFTDLRAV
+QVLVTGDRLDVAYGAQDLSPEDSGAYTGDVSGAFLAALGCRYAIVGHSERRTIHGEDDAL
+VARKAAAALRHGLSPVVCVGEGLDVRQAGRHVAHTVAQLEGSLVGLSAEDVARTVVAYEP
+VWAIGTGEVAGAGDAQEMCAALRARVGELHGDDVAAGLRILYGGSVKSTSAPELLAQPDV
+DGALVGGASLDAEEFARIVRFDQA-
+>3_1628
+MSVVQPVRVPLIAGNWKMNLDHQEAVTLVQRLGWLLGDADHEQGNVEAAVFPPFTDLRSV
+QTLVAADRIGVAYGAQDVSAEDSGAFTGEVSGAFLAKLGCAYAIVGHSERRTLHHEDDAL
+VARKAAAALRHGLVPVVCVGEGLDVRQAGRHVEHTVAQLRGSLDGLSSEDVARVVVAYEP
+VWAIGTGEVASAADAQEMCAALRADLAERHGAEVAERVRVLYGGSVKSSSAPELLAQPDV
+DGALVGGASLDADEFARIVRSDAAH
+>4_1030
+MA-EQTTRVPLIAGNWKMNLDHLEAVTLVQRLTWLLTDADHDQEAVEVAVFPPFTGLRAV
+QTLVTGDRLDLAYGAQDLSPEDAGAYTGDVSGAFLAALGCRYAIVGHSERRTLHGEDDAL
+VARKAAAALRHGLTPVICVGEGLEVRQAGRHVEHTLAQLEGSIAGLSAQDVAGVVVAYEP
+VWAIGTGEVAGPEDAQQMCAALRARVAALHGDDVAAGLRILYGGSVKSSSAPALLAQPDV
+DGALVGGASLDADEFAKIVRFDQA-
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000945.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000945.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85552b16a97ff4227f4b17782f3b0bd85550825b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000945.fa
@@ -0,0 +1,36 @@
+>0_1090
+-----------MPRDEPVLRLSDVHRSLGRGRSRTPVLRGVDLTARAGAVTVLLGPNGAG
+KSTTLGLCHGMDRPDAGTVRVFGADPWRASADLRARIGVMWQEGGLPPAIPARRFVGHVA
+SLYRDPLPVEPLLERLLIAEVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLD
+PETRPVVHDVVREQTDRGAAVLLTTHLLDDAERLADDVAILRAGRVVRSGSLAELTRVAE
+GDVVDVDFGDASPDAVRAWADTLPAPLRAAGLDESARLRVAGVRGPDDLAVLAASWREHA
+LMPTRFERAGLRLEQILRETAA---------
+>1_818
+-----------MPRDEPVLRLSDVHRSLGRGRSRTPVLRGVDLTARAGAVTVLLGPNGAG
+KSTTLGLCHGMDRPDAGTVRVFGADPWRASADLRARIGVMWQEGGLPPAIPARRFVGHVA
+SLYRDPLPVEPLLERLLIAEVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLD
+PETRPVVHDVVREQTDRGAAVLLTTHLLDDAERLADDVAILRAGRVVRSGSLAELTRVAE
+GDVVDVDFGDASPDAVRAWADTLPAPLRAAGLDESARLRVAGVRGPDDLAVLAASWREHA
+LMPTRFERAGLRLEQILRETAA---------
+>2_1725
+MVPRPVLTPDPAPRDEPVLRLRDVHRSLGRGRARTPVLRGVDLTARAGAVTVLLGPNGAG
+KSTTLGLCHGMDRPDAGAVRVFGADPWRAPADLRARIGVMWQEGGLPPSVPARRFVGHVA
+SLYRDPMPVEPLLERLLIADVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLD
+PETRPVVHEVVREQTARGAAVLLTTHLLDDAERLADDVAILRAGRVVRAGSLADLTRVAE
+GDVVDVDFGDAAPEAVRAWADALPEPLRAAGLAEPARLRVAGVHGPAELAALAASWHRHA
+LMPTRFERAGLRLEQILRETAA---------
+>3_1618
+M---PETSPHP---DAPALRLHEVRRTLGRGAARTEVLRGVDLEARRGAVTVLLGPNGAG
+KSTTLALCHGSDRPDSGTVRVFGRDPWRADADLRARLGVMWQEGGLPPSVTARRFVRHVA
+SLHGDPLDPDALLGRLRIDRVADRPIRRLSGGQRQRVALAAAVVGRPDLLFLDEPTAGLD
+PETRPVVHDVVREHTARGAAVLLTTHLLDDAERLADDVAILRAGRVVRAGTLAELTRVQD
+GDVVDVRFDEARAADVRAWVAAAPASFRAVASAGAPAARVAGVRSPADLEALAASWTRAG
+LFPTRLERAVLRLEELLQSPDADTPSPERSR
+>4_1040
+-----------MPRDEPVLRLSDVHRSLGRGRSRTPVLRGVDLTARAGAVTVLLGPNGAG
+KSTTLGLCHGMDRPDAGTVRVFGADPWRASADLRARIGVMWQEGGLPPAIPARRFVGHVA
+SLYRDPLPVEPLLERLLIAEVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLD
+PETRPVVHDVVREQTDRGAAVLLTTHLLDDAERLADDVAILRAGRVVRSGPLSELTRVAE
+GDVVDVDFGDASPDAVRAWADTLPAPLRAAGLGESARLRVAGVRGPDDLAVLAASWREHA
+LMPTRFERAGLRLEQILRETAA---------
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000977.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000977.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ade7893d17ff2e6a6957a7e33999594711488cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000977.fa
@@ -0,0 +1,41 @@
+>0_1127
+MT---------------------EPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGE
+FHSYQGVLRHDDLIGGFEGVVVENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIV
+QQADIFPGAVVVEAGVGSGALSMSLLRAVGDHGRLHSYERRPEFADVARANVEAFFGAEH
+PAWSVHLGDAQEEMPKVHEPGSVDRVVLDMLAPWECLDAVAEVLAPGGVWLNYVATATQL
+SRVAEAIRDSGRFTQVEANETLVRGWHLDGLAVRPDHRMVAHTGFLLTARRLASGEEALR
+LKKRSKVSEFRAEDVEAWQPADEARWTPEALGERPITDKKARKAAKEARLMAARSRAAEQ
+GVDAYGGRTPTGEQD
+>1_855
+MT---------------------EPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGE
+FHSYQGVLRHDDLIGGFEGVVVENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIV
+QQADIFPGAVVVEAGVGSGALSMSLLRAVGDHGRLHSYERRPEFADVARANVEAFFGAEH
+PAWSVHLGDAQEEMPKVHEPGSVDRVVLDMLAPWECLDTVAEVLAPGGVWLNYVATATQL
+SRVAEAIRDSGRFTQVEANETLVRGWHLDGLAVRPDHRMVAHTGFLLTARRLASGEEALR
+LKKRSKVSEFKAEDVEAWQPADEARWTPEALGERPVTDKKARKAAKEARLMAARSRAAEQ
+GVDAYGGRTPTGEQD
+>2_1685
+MT---------------------EPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGE
+FHSYQGVLRHDDLIGGFEGVVVENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIV
+QQADIFPGAVVVEAGVGSGALSMSLLRAVGDHGRLHSYERREEFADVARANVEAFFGAEH
+PAWSIHLGDAQEQMTRVHEPGSVDRVVLDMLAPWECLDAVAEVLAPGGVWLNYVATATQL
+SRVAEAIRDSGRFTQVEANETLVRGWHLDGLAVRPDHRMVAHTGFLLTARRLATGEEALR
+LKKRSKVSEFKAEDVEAWQPADEARWTPEALGERPVTDKKARKAAKEARLMAARSRAAER
+GVDAYGGSIQEQDQD
+>3_1582
+MSDATAPETPAAPTTPDTAAPAGRPAGVTARRGPLRAGQRVQIKDAKGRLNTITLLPGGE
+FHSYQGVLRHDDLIGGPEGIVVQNSSGHAYQVLRPLLNDFVLSMPRGATVVYPKDAGQIV
+QQADIFPGAVVVEAGVGSGALSMSLLRAVGDAGRLHSYERRAEFAEIARGNVESFFGGVH
+PAWSIHLGDAQEEMPKVHEPHSVDRVVLDMLAPWECLDAVATVLAPGGVWLNYVATATQL
+SRVAEAIRASGKFTQIEATETLVRGWHLDGLAVRPDHRMVAHTGFLLTARRLAAGEDALV
+MKKRLKVSEFTTEDVEAWTPSDGARWTPQALGERTVTDKKARKAAKEARLTARRARAALE
+GRDP---RTVGQDKD
+>4_1077
+MT---------------------EPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGE
+FHSYQGVLRHDDLIGGFEGVVVENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIV
+QQADIFPGAVVVEAGVGSGALSMSLLRAVGDHGRLHSYERRPEFADVARANVEAFFGAEH
+PAWSVHLGDAQEEMPKVHEPGSVDRVVLDMLAPWECLDAVAEVLAPGGVWLNYVATATQL
+SRVAEAIRDSGRFTQVEANETLVRGWHLDGLAVRPDHRMVAHTGFLLTARRLASGEEALR
+LKKRSKVSEFKAEDVEAWQPADEARWTPEALGERPVTDKKARKAAKEARLMAARSRAAEQ
+GVDAYGGRTPTGEQD
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000982.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000982.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aebaf50e975eb226af4f437417d89d6922fe5b6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000982.fa
@@ -0,0 +1,16 @@
+>0_1132
+MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQRLDSLLDEIDSVLESNAEEFVKGFVQK
+GGQ
+>1_860
+MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQRLDSLLDEIDSVLESNAEEFVKGFVQK
+GGQ
+>2_1680
+MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQGLDSLLDEIDSVLESNAEEFVKGFVQK
+GGQ
+>3_1577
+MAQEQIRPRPAGGPEDEGAAA-QAQAKAAPQDTGLDGLLDEIDSVLESNAEEFVKGFVQK
+GGQ
+>4_1082
+MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQGLDSLLDEIDSVLVSNAEEFVKGFVQK
+GGQ
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000993.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000993.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08bfcf78ccdd9fff4ce5cf2ba078c25e701019a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0000993.fa
@@ -0,0 +1,21 @@
+>0_1144
+MEWIEANAGWLWLVLAAGLAGVELLTLDLVFLMIAAGAGAAGVVALVGGPLALQLAAFAA
+VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITGDAGTLAVDGDTWSARV
+EPGAPEVAPGDEVTVLRIDGATLVVRPLPRIDWEADG-A
+>1_872
+MEWIEANAGWLWLVLAAGLAGVELLTLDLVFLMIAAGAGAAGVVALVGGPLALQLAAFAA
+VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITGDAGTLAVDGDTWSARV
+EPGAPDVAPGDEVTVLRIDGATLVVRPLPRIDWQADG-A
+>2_1667
+MDWIEANAGWLWLVAAAGLIGVELLTLDLVFLMIAAGAGAAGVVALAGGPLPLQLAAFAV
+VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITAEAGTLTVDGDTWSARV
+EDGAPDAAPGAEVTVLRVEGATLVVRPLPQIDWE-DGRS
+>3_1565
+MEWIEANADWLWLVLALGLVGAELLSLDLVLAMLAAGALSAGVAALAGAPLGLQLGVFVV
+VSLLTLVAVRPAAMRRLHPDPAVGASWLDGLSGRRLTATGPVTDEGGRIDVDGETWSARV
+EPGAAPAAHGQGVTVLRVEGAHLILRPDPVIDWDAPAHD
+>4_1094
+MEWIEANAGWLWLVLAAGLAGVELLTLDLVFLMIAAGAGAAGVVALVGGPLALQLAAFAA
+VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITGDAGTLAVDGDTWSARV
+EPGAPEVAPGDEVTVLRIDGATLVVRPLPRIDWEADG-A
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001007.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001007.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98f2e1f58289e1d8cb33309dffd06b6bbf8ec31f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001007.fa
@@ -0,0 +1,21 @@
+>0_1159
+MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAG
+GSCACGDSFH
+>1_887
+MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAG
+GSCACGDSFH
+>2_1651
+MALSADETGVEIGATQDSEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVQVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAV
+GSCACGDSFH
+>3_1548
+MALSAEETGVEIGATEDATGLPPHEVELTDVAAAKVRALLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAV
+GSCACGDSFH
+>4_1116
+MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYIMGATIDFEDTISKQGFTIDNPNAG
+GSCACGDSFH
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001022.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001022.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1b2107bd32bb03c72ce00665196963680e645dde
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001022.fa
@@ -0,0 +1,21 @@
+>0_1175
+M--NTRAQP----------DAGRTGHGPPAWLVSAGGRGAPLTAKQDRDRAALAHLSLAF
+GVLGPLVVWLLYRDRGPFTSQESREALNFSGPPTLITLLFFFLSLLPVVGPIFAILGALT
+WAAMAVYGVMGASHVSKGRPFRYPFNLRILR
+>1_903
+M--NTRAQP----------DAGRTGHGPPAWLVSAGGRGAPLTAKQDRDRAALAHLSLAF
+GVLGPLVVWLLYRDRGPFTSQESREALNFSGPPTLITLLFFFLSLLPVVGPIFAILGALT
+WAAMAVYGVMGASHVSKGRPFRYPFNLRILR
+>2_1636
+M--NPSAQP----------DAGRPGHEPPAWLASAGGRATPLTAKQDRDRAALAHLSLAF
+GVLGPLVVWLLYRDRGPFTSQESKEALNFSGPPTLITTLFFFLALLPVIGAIFAILGALS
+WAVMAVYGVMGASNVSKGRPFRYPFNLRILR
+>3_1532
+MATTPSTTPAGETATPRRAAGGSAAHEAPAWLRDAAGGRAPLTAKQDRDRAALSHLSLAC
+GLPGPLVMWLLYRDRGPFTAQESREALNFSLAPTLLIVLLFLLGGVPLLGGLLAILGALL
+WIALALYGVMGASQVAKGRPFRYPFSPRLLR
+>4_1133
+M--NTRAQP----------DAGRTGHGPPAWLVSAGGRGAPLTAKQDRDRAALAHLSLAF
+GVLGPLVVWLLYRDRGPFTSQESREALNFSGPPTLITLLFFFLSLLPVVGPIFAILGALT
+WAAMAAYGVMGASHVSKGRPFRYPFNLRILR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001025.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001025.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b8e8340215d9ec36b690fcdcb2d1a1d27dded8f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001025.fa
@@ -0,0 +1,16 @@
+>0_1179
+MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEPEAAAAALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG
+>1_907
+MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG
+>2_1632
+MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG
+>3_1529
+MANIKSQKKRILTNEKARQRNIAVKSELKTAIRAVDKAVAAGEQDAAVEALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG
+>4_1137
+MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001040.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001040.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca936c95c28211af9215d3699a7185da62188de7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001040.fa
@@ -0,0 +1,75 @@
+>0_1194
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPELADATYVEPITPAVVAKIIEK
+ERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANIEAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVE
+DLKYPVVVRPSFTMGGLGSGMAYDEADLYRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPVDGRVVVIEMNPRVSRSSALASKATGFAIA
+KIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPRFAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRS
+LEQKGSELAFPQDADPQALLAAASTATTDRLSQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADEIRDAEVLDEA
+LLRRAKRHGFSDAQIGSLRHMDAAVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSYDLETEVAPHEGESVIILGSG
+PNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVSTDYDISDRLYFEPLTLEDVLEVIAAEEASGGVRGVFVQLGG
+QTPLKLAQQLADAGVPILGTSPAAIDLAEHRGEFALVLERAGLVAPKNGTAVSFDDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVEHATEITPDQPMLVDRFLEDAIEIDVDALYDGTELYLGGVMEHIEEAGIHSGDSACVLPPVTLGPD
+VLERVHRATERIAAGVGVRGLINIQFALASDVLYVIEANPRASRTVPFVSKATGVQLAKAAARIGVGESIADLRAAGMLP
+TAYDGGTLPIGAPVAVKEAVLPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDKHFDTAFAKSQSAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQVVSTGGTAEVLRRNGIPAEVVAKIADAGHEDGAGTVLEQLHAGTVDLVLNTPSGGDART
+DGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRSYEWSVTSLQEHDARLQQAVAGPEAAA
+>1_922
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPELADATYVEPITPAVVAKIIEK
+ERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANIEAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVE
+DLKYPVVVRPSFTMGGLGSGMAYDEADLYRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPVDGRVVVIEMNPRVSRSSALASKATGFAIA
+KIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPRFAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRS
+LEQKGSELAFPQDADPQALLAAASTATTDRLSQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADEIRDAEVLDEA
+LLRRAKRHGFSDAQIGSLRHMDAAVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSYDLETEVAPHEGESVIILGSG
+PNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVSTDYDISDRLYFEPLTLEDVLEVIAAEEASGGVRGVFVQLGG
+QTPLKLAQQLADAGVPILGTSPAAIDLAEHRGEFALVLERAGLVAPKNGTAVSFDDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVAHATEITPDQPMLVDRFLEDAIEIDVDALYDGTELYLGGVMEHIEEAGIHSGDSACVLPPVTLGPD
+VLERVHRATERIAAGVGVRGLINIQFALASDVLYVIEANPRASRTVPFVSKATGVQLAKAAARIGVGESIADLRAAGMLP
+TAYDGGTLPIGAPVAVKEAVLPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDKHFDTAFAKSQSAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQVVSTGGTAEVLRRNGIPAEVVAKIADAGHEDGAGTVLEQLHAGTVDLVLNTPSGGDART
+DGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRSYEWSVTSLQEHDARLQQAVAGPEAAA
+>2_1617
+MPKRPDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPELADATYVEPITPAVVAKIIEK
+ERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANIEAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVE
+DLKYPVVVRPSFTMGGLGSGMAYDEADLHRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPADGRVVVIEMNPRVSRSSALASKATGFAIA
+KIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPRFAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRS
+LEQKGSELAFPQDADPRELLRRARTATTDRLAQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADQIRDAEVLDES
+LLRHAKRHGFSDAQIGSLRHMGADVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSYDLETEVAPHEGRSVIILGSG
+PNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVSTDYDISDRLYFEPLTLEDVLEVIAAEEASGGVLGVYVQLGG
+QTPLKLAQQLADAGVPILGTSPEAIDLAEHRGEFARVLDRAGLVAPKNGTAVSFEDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVEHATEITPDQPMLVDRFLEDAIEIDVDALYDGERMYLGGVMEHIEEAGIHSGDSACVLPPVTLGPD
+VLERVHRATEQIAAGVGVRGLINIQFALASDVLYVIEANPRASRTVPFVSKATGVQLAKAAAMIGVGKSIADLQAEGVLP
+TAYDGATLPLGAPVAVKEAVLPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDRHYDTAFAKSQAAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQIVSTGGTAEVLRRNGIPAETVAKIAEAGGEDGAGTVLEQLHAGTVDLVLNTPSGGDART
+DGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRAYEWSVTSLQEHDARLQQAV---EASA
+>3_1514
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVILVNSNPATIMTDPELADATYVEPITPEVVAKIIEK
+ERPDAVLPTLGGQTALNTAIALDKDGVLEKFGVELIGANIAAIELGENRELFKGVVERAGGESARSHIVHTMEEAFAAVE
+DLKYPVVVRPSFTMGGLGSGMAYDEADLRRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPEDGRVVVIEMNPRVSRSSALASKATGFAIA
+KIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPRFAFEKFPAADATLTTTMKSVGEAMAIGRSFSEALQKALRS
+LEQKGSELSFDRDADPASLLASARTATTQRLAQTQRALYAGATLEEAFEATAIDPWFLDQLMLINEVADEVREAPQLDEA
+VLRRAKRHGFSDAQIGSLRHMDPAVVRGLRHALGVRPVYKTVDTCAAEFEAFTPYRYSSYDLESEVDEHAAPSVVILGSG
+PNRIGQGIEFDYSCVHATLALREAGYETVMVNCNPETVSTDYDISDRLYFEPLTLEDVLEVIAAEEATGGVAGVFVQLGG
+QTPLKLAQQLADAGVPILGTSPEAIDLAEHRGEFARVLDEAGLIAPKNGTAVSFEDARRVADEIGYPVLVRPSYVLGGRG
+MEIVYTEEALAHYVTNATEITPTQPMLVDRFLEDAIEIDVDALYDGHELYLGGVMEHIEEAGIHSGDSACVLPPVTLGPD
+VLERVRTATEKIAAGVGVRGLINIQFALASDVLYVIEANPRASRTVPFVSKATGVQLAKAAAMIGMGRTIAELRAAGTLP
+TAFDGASLPMGASVAVKEAVLPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDRHFDTAFAKSQAGAGGPLPTEGRVFVSV
+ANRDKRAVVGQAKRLVDLGFEIVSTGGTAEVLRRNGVPAEVVAKIADASDADGAGTVLEQLHEGRVDLVLNTPSGGEART
+DGYEIRAAATSLGVPVITTTAEFAACLQAIEAMRTYEWSVTSLQEHEERLAQAVAAEASA-
+>4_1152
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPELADATYVEPITPAVVAKIIEK
+ERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANIEAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVE
+DLKYPVVVRPSFTMGGLGSGMAYDEADLYRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPVDGRVVVIEMNPRVSRSSALASKATGFAIA
+KIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPRFAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRS
+LEQKGSELAFPQDADPQALLAAASTATTDRLSQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADEIRDAEVLDEA
+LLRRAKRHGFSDAQIGSLRHMDAAVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSYDLETEVAPHEGESVIILGSG
+PNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVSTDYDISDRLYFEPLTLEDVLEVIAAEEASGGVRGVFVQLGG
+QTPLKLAQQLADAGVPILGTSPAAIDLAEHRGEFALVLERAGLVAPKNGTAVSFDDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVEHATEITPDQPMLVDRFLEDAIEIDVDALYDGTELYLGGVMEHIEEAGIHSGDSACVLPPVTLGPD
+VLERVHRATERIAAGVGVRGLINIQFALASDVLYVIEANPRASRTVPFVSKATGVQLAKAAARIGVGESIADLRAAGMLP
+TAYDGGTLPIGAPVAVKEAVLPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDKHFDTAFAKSQSAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQVVSTGGTAEVLRRNGIPAEVVAKIADAGHEDGAGTVLEQLHAGTVDLVLNTPSGGDART
+DGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRSYEWSVTSLQEHDARLQQAVAGPEAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001047.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001047.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5a81298e7771ef85ecf20f370b46831ee5ee000
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001047.fa
@@ -0,0 +1,41 @@
+>0_1201
+MTDREPDITEQETPGAAPAAAPAAP--EDVTVIPVAGGHEAAVHGGYDVVVGRGLLARLP
+DLLGPTVRRVLVIHPRALRATGDVVKNDLEAVGLTALTAEIPDAEEGKHLQVAGFCWQVL
+GQNDFTRSDAIVSVGGGAVSDLAGFVAATWLRGIRVVHMPTTLLGMVDAAVGGKTGINTA
+EGKNLVGAFHNPAGVLADLDTLLTLPANELISGLAEVVKCGFIADPAILDLIEEDPAQAQ
+NPHSPRLRELIERSIRVKADVVSRDPRESGAREALNYGHTMGHAIELAERYQWRHGAAVS
+VGLVFAAELARSLGRLDDATADRHWSVLTALGLPVSYRGDRWQTLLEGIRRDKKNRGDQL
+RFVLLDGLAQPTTVDIPDASLLFAAYQEIAE
+>1_929
+MTDREPDITEQETPGAAPAAAPAAP--EDVTVIPVAGGHEAAVHGGYDVVVGRGLLARLP
+DMLGPTVRRVLVIHPRALRATGDVVKNDLEAVGLTALTAEIPDAEEGKHLQVAGFCWQVL
+GQNDFTRSDAIVSVGGGAVSDLAGFVAATWLRGVRVVHMPTTLLGMVDAAVGGKTGINTA
+EGKNLVGAFHNPAGVLADLDTLLTLPANELISGLAEVVKCGFIADPAILDLIEEDPAQAQ
+NPHSARLRELIERSIRVKADVVSRDPRESGAREALNYGHTMGHAIELAERYQWRHGAAVS
+VGLVFAAELARSLGRLDDATADRHWSVLTALGLPVSYRGDRWQTLLEGIRRDKKNRGDQL
+RFVLLDGLAQPTTVDIPDASLLFAAYQEIAE
+>2_1609
+MTDRHPDPAEPEIPGEPPAAEPAAAGQEDVTVIPVSGGQEAAAHGGYDVVVGRGLLARLP
+EMLGPGVQRVLVIHPRALRATGDVVKNDLEAVGLTALTAEIPDAEEGKHLQVAGFCWQVL
+GQNDFTRSDAVVSVGGGAVSDLAGFVAATWLRGVRVVHMPTTLLGMVDAAVGGKTGINTS
+EGKNLVGAFHPPAGVLADLDTLLTLPANELISGLAEVVKCGFIADPAILDLIEQDPAQSQ
+NPHSARLRELIERSIRVKADIVSRDLRESGEREALNYGHTMGHAIELAERYQWRHGAAVS
+VGLVFAAELARSLGRLDDATADRHWSVLTALGLPVSYRGDRWQTLLEGIRRDKKNRGDQL
+RFVLLDGLAQPSTVDIPDPSLLFAAYQEIAE
+>3_1506
+MTEHQPD---QSDPIAEHSAA-APE--QDVTVIPVAGGPENRAGGGYDVVVGRGLLGRLP
+AVLGPQVRRVLVIHPRALRATGDVVKNDLEAAGLVSLTAEIPDAEEGKHLQVAGFCWQVL
+GQNDFTRSDAIVSVGGGAVSDLAGFVAATWLRGIRVVHMPTTLLGMVDAAVGGKTGINTA
+EGKNLVGAFHPPAGVLADLDTLLTLPSNELVSGLAEVVKCGFIADPRILELIEEAPEQAQ
+NPHSAVLRELIERAVRVKAEVVSGDLREAGPREALNYGHTLGHAIEHAERYQWRHGAAVS
+VGLVFAAELARSLGRLDDATADRHWSVLQSLGLPVSYRGDRWQTLLEGIKRDKKNRGDQL
+RFVLLDGLARPTTVDIPDASLLFAAYQEIAE
+>4_1159
+MTDREPDITEQETPGAAPAAAPAAP--EDVTVIPVAGGHEAAVHGGYDVVVGRGLLARLP
+DMLGPTVRRVLVIHPRALRATGDVVKNDLEAVGLTALTAEIPDAEEGKHLQVAGFCWQVL
+GQNDFTRSDAIVSVGGGAVSDLAGFVAATWLRGVRVVHMPTTLLGMVDAAVGGKTGINTA
+EGKNLVGAFHNPAGVLADLDTLLTLPANELISGLAEVVKCGFIADPAILDLIEEDPAQAQ
+NPHSARLRELIERSIRVKADVVSRDPRESGAREALNYGHTMGHAIELAERYQWRHGAAVS
+VGLVFAAELARSLGRLDDATADRHWSVLTALGLPVSYRGDRWQTLLEGIRRDKKNRGDQL
+RFVLLDGLAQPTTVDIPDASLLFAAYQEIAE
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001058.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001058.fa
new file mode 100644
index 0000000000000000000000000000000000000000..76aa999be69aa2f56f96200610f96a4c2b16daae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001058.fa
@@ -0,0 +1,45 @@
+>0_1213
+---MPRLARLATAVTAAALSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHETGVFGESAAEIPAFDAVS
+GRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVTDKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTT
+TLRYLGGVRVGALPDSLAFSPNGAYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTAL
+PAGVRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLEDLWALTPTDWSTEGVLDA
+SDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGREWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLK
+VLTDLGYDSERECHSSLTTLGGRSFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPE
+PESVVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGAEGLTFVPADESPSGTAL
+LIVANEVSGSTTVYEVNPTR---RQ
+>1_941
+---MPRLARLATAVTAATLSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHETGVFGESAAEIPAFDAVS
+GRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVTDKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTT
+TLRYLGGVRVGALPDSLAFSPNGAYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTAL
+PAGVRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLEDLWALTPTDWSTEGVLDA
+SDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGREWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLK
+VLTDLGYDSERECHSSLTTLGGRSFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPE
+PESVVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGAEGLTFVPADESPSGTAL
+LIVANEVSGSTTVYEVNPTR---RQ
+>2_1597
+---MRTLSRLAAATSMVALSAAVVAPLTVAAP------------AANPSGRSIELTAAGTHATGVFDASAAEIPAFDKTT
+GRLFVVNAQKGAIDVLTVGEDAEPAAESVLSVAGLPAADGSVTGAGAVVNSVAVAGAVMAATVEAEDKTGHGWLVFFDTR
+TLGFLGGVRVGALPDSVALAPNGAYAVVANEGEPADDFSSDPEGTISVVSVPKNARQFARLGQDAVRTVDFRAYDEGAAL
+PEGVRVFGPDVAVPSGHEEAGRIARNLEPEYASIDPTGRTAYVSVQEANAVVAVDLASASLADFWALHLTDWSTEGVLDV
+SDKDGAISPAYQPVLGVPMPDGLATYKHRGQTLVVTANQGDSREWGDFVDAERVKDLELCGDVFPHAKALQKNEALGRLN
+VLTDLGYDAERGCHTELHALGGRGFSIYTADGQRLFDSSGMLEEQIARLIAAGELPAHAFNANNDETPSFDSRSDDKGVE
+PESVVVGEVQGRQYAFVGLERIGGVMVFDITDPTDARYVDYINERAWDAVGEDGDAGLGDMGAEGLAFVPASDSPSGTAL
+LIVATEVSGSTTVYEVDPVKGGKRT
+>3_1494
+MSRIVRLTRLGAAAGALALSAAVVAPSAVSAPVTATAA------AANPSGKTVELSLAGTHETGVFGESAAEIPAFDAAT
+GRLFVVNAEKGAVDVLRVGADGAPAAETVLSAEGLRTADGSVTDGGATVNSVAVSGGVLAVAVEAADKTGLGWVAFFDTT
+TLSYLGGVRVGALPDSIAFSPDGAYAVVANEGEPADDFSADPEGTISVISVPKNVRQFARLTQAAVRTVDFRAYDAGTAL
+PEGVRVFGPDVQVPEGQEPAGRIARNLEPEYVTIDDTGRTAYVSVQEANAVVAVDLKSATLKDFWALQLTDWSKEGVLDA
+SNEDKAITLRNQPVLGVPMPDGVDTYRYRGQDLVVTANEGDSREWGDFVDAARVKDLELCTAEYPDAKALQKKPALGRLN
+VVTDLGYDADRDCFSQLHAFGGRSFSIYTADGTRLFDSAGMIEEQIAQLIADGELPESAFNANNDETPSFDSRSDDKGPE
+PEAVVVGRVQGRTYAFVGLERIGGVMVFDITDPTKATYVDYVNERNWDAEGDDAAAGLGDMGAEGLTFVPANESPSGTAL
+LVVANEVSGSTTVYEVNPVR---R-
+>4_1170
+---MPRLARLATAVTAATLSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHETGVFGESAAEIPAFDAVS
+GRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVTDKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTT
+TLRYLGGVRVGALPDSLAFSPNGAYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTAL
+PAGVRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLEDLWALTPTDWSTEGVLDA
+SDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGREWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLK
+VLTDLGYDSERECHSSLTTLGGRSFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPE
+PESVVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGAEGLTFVPADESPSGTAL
+LIVANEVSGSTTVYEVNPTR---RQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001060.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001060.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c5129ee29fb0de299ab7721a99f449c429756435
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001060.fa
@@ -0,0 +1,50 @@
+>0_1215
+-----------------MLRTHSLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVRDEADFDPLRNEW
+VLQVTGTVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARLRHRYLDLRRPQPSRIMRLRSEVN
+RTARELLHGEGFVEVETPTLTRSTPEGARDFLVPARLAPGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADR
+QPEFTQLDIEASFVEQDDVIALGEKIVKALWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKDTPFR
+VFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGELTGPVSKNISEEEKAGLAAAVGANPGDCVFFA
+AGKPKESRALLGAARVEIGRRCGLFTDAGDGVAAKDADWAFVWVVDAPMFEPAADAVASGDVAVGAGAWTAVHHAFTSPK
+PEFADTFDTDPGAALAYAYDIVCNGNEIGGGSIRIHRQDVQERVFEVMGLSPEEANEKFGFLLEGFKYGAPPHGGIAFGW
+DRVVALLAGTDSIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAQPEPKQAEAE-------PEA------------
+---
+>1_943
+-----------------MLRTHSLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVREEADFDPLRNEW
+VLQVTGTVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARLRHRYLDLRRPQPSRIMRLRSEVN
+RTARELLHGEGFVEVETPTLTRSTPEGARDFLVPARLAPGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADR
+QPEFTQLDIEASFVEQDDVIALGEKIVKALWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKHTPFR
+VFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGELTGPVSKNISEEEKAGLAAAVGANPGDCVFFA
+AGKPKESRALLGAARVEIGRRCGLFTDAGDGVAAKDADWAFVWVVDAPMFEPAADAVASGDVAVGAGAWTAVHHAFTSPK
+PEFADTFDTDPGAALAYAYDIVCNGNEIGGGSIRIHRQDVQERVFEVMGLSPEEANEKFGFLLEGFKYGAPPHGGIAFGW
+DRVVALLAGTDSIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAQPEPKQAEAE-------PEA------------
+---
+>2_1594
+MNPTISSGRSPDGEDAFVLRTHQLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVRDEADFDPLRNEW
+VLQVSGVVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARLRHRYLDLRRPEPSRIMRLRSEVN
+RTAREMLHGEGFTEVETPTLTRSTPEGARDFLVPARLAPGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADR
+QPEFTQLDIEASFVEQDDVIALGEKIVKAVWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTAYFKDTPFR
+VFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGSLTGPVSKNISDEEKAGLAAAVGANPGDCVFFA
+AGKPKESRALLGAARVEIGRRCELFTDAGNGVEAKDADWAFVWVVDAPMFEPAADAVASGDVAVGSGAWTAVHHAFTSPK
+PEFADTFDTDPGSALAYAYDIVCNGNEIGGGSIRIHRQDMQERVFSVMGLSQEDAQEKFGFLLEGFKYGAPPHGGIAFGW
+DRVVALLAGTESIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAKPEPKKAEGEKAEAAGQPQA------------
+---
+>3_1491
+-----------------MLRTHHLGELNASLIGQTVTVTGWVAKRRDHGGVAFVDLRDASGRAQVVVRDEADFDPLRNEW
+VLQVTGTVERRPEGNENPNLPTGEVELIADDVVVLNTAAALPFQIDEHVEVGEEARLRHRYLDLRRPQPARIMRLRSEAN
+RVARELLNEQGFVEVETPTLTRSTPEGARDFLVPARLAPGSWYALPQSPQLFKQLLQVGGLEKYYQIARCYRDEDFRADR
+QPEFTQLDIEASFVEQDDVIALGEQIVKALWGLVGVEVQTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKDTPFR
+VFQNEYVGAVVMPGGASQPRRTLDAWQEWAKQRGAKGLAHVLIQEDGTLTGPVSKNITDEEKAGLAAAVGANPGDCVFFA
+AGKAKESRALLGAARVEIGRRCELFTDAGDGVEAKDADWAFVWVVDAPLFEPAADAVASGDVAVGAGQWTAVHHAFTSPK
+PEFMDTFDTDPGSALAYAYDIVCNGNEIGGGSIRIHRQDVQKRVFSVMGLSEEDANEKFGFLLEGFKYGAPPHGGIAFGW
+DRVVALLAGTESIREVIAFPKTGGGYDPLTAAPAPITPQQRKEAGVDAKPEAKKAEGAASEGA-EAQAKANDEKTAADEA
+QLR
+>4_1172
+-----------------MLRTHSLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVRDEADFDPLRNEW
+VLQVTGTVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARLRHRYLDLRRPQPSRIMRLRSEVN
+RTARELLHGEGFVEVETPTLTRSTPEGARDFLVPARLAPGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADR
+QPEFTQLDIEASFVEQDDVIALGEKIVKALWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKDTPFR
+VFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGELTGPVSKNISEEEKAGLAAAVGANPGDCVFFA
+AGKPKESRALLGAARVEIGRRCGLFTDAGDGVAAKDADWAFVWVVDAPMFEPAADAVASGDVAVGAGAWTAVHHAFTSPK
+PEFADTFDTDPGSALAYAYDIVCNGNEIGGGSIRIHRQDVQERVFEVMGLSPEEANEKFGFLLEGFKYGAPPHGGIAFGW
+DRVVALLAGTDSIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAQPEPKQAEAE-------PGA------------
+---
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001061.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001061.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0cf37270f6d64cb7c458e72096e532d785b0d08a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001061.fa
@@ -0,0 +1,46 @@
+>0_1216
+--MTAALQRRLTLLHAVAIGLGSMIGAGVFTAIGLAAALTGGHPGLLYGALAVAAVAALC
+NALSTAQLATVHPESGGAYVYGRRQLHPWAGFVAGWGFVTGKTASVAAVAATLGLYLVPD
+DAAAARWTGVAAVVVLTGVAMAGVTRTAQATLAILVPVLAVLVLAIGAGLAREAPGGSAA
+ALGV-DSPVQ-----GVLMGAGVLFFAFAGYARVATMGEEVIDPARTIPRAILIALAVTV
+ALYLLLATALISGLGTSGLARSPAPVRELLETALGSGWGWVAVAGAALAAAGAMLTLLTG
+ISRTALAMAREADLPRPLARVHAGTGTPWTAQLTVAAAVVLLLLTTDILTVVGFSSFGVL
+VYYAVANLSALTLRGDDHGHRPARP---RPLRVPRAVNVLGLALCLLLAFSLPPMSVAAM
+AGVFLIGVGGRAFVRAGR-----RGG---
+>1_944
+--MTAALQRRLTLLHAVAIGLGSMIGAGVFTAIGLAAALTGGHPGLLYGALAVAAVAALC
+NALSTAQLATVHPESGGAYVYGRRQLHPWAGFVAGWGFVTGKTASVAAMAATLGLYLFPD
+DDAAARWTGVAAVVVLTGVAMAGVTRTAQATLAILVPVLAVLVLAIGAGLAREAPGGSAA
+ALGV-DSPVQ-----GVLMGAGVLFFAFAGYARVATMGEEVIDPARTIPRAILIALAVTV
+ALYLLLATALISGLGTSGLARSPAPVRDLLETALGSGWGWVAVAGAALAAAGAMLNLLTG
+ISRTALAMARESDLPRPLARVHAGTGTPWTAQLTLAAAVILLLLTTDILTVVGFSSFGVL
+VYYAVANLSALTLRGDDDGRRPARPRPLRPLRVPRAVNVLGLALCLLLALSLPPMSVAAM
+AGVFLIGVGGRAFVRAGR-----RGR---
+>2_1593
+-----MLQRRLTLTHAVVIGLGSMIGAGVFTAIGLAAALTGGHPGLLYAALALALLTALC
+NALSTAQLATVHPESGGAYVYGRRQLHPLAGFVAGWGFVTGKTASVAAMAATIGLYLFPD
+DAAAARLTGVAAVVVLTAVAMAGVTRTAQATMAILVPVAAVLALAIGAGLALGAPSEADA
+FAGVADSPVT-----GVLMGAGILFFAFAGYARVATMGEEVIDPRRSIPRAILIALGLTA
+GLYVLLTAALFAGLGPTGLALSPAPVRELLETTLGATWGWAALAGAALAAAGAALNLLTG
+ISRTALAMARESDLPRPLARVNARTGTPWVGQLTIAVAVILLLLTTDILTVVGFSSFGVL
+VYYAVANLAAATLRGGEDGRDPALP---RPLRVPRAVNVLGLVLCAVLAATLPPMAVVAM
+LAVFLVGVGGRAFVLAGRGRPGRRGAVAP
+>3_1490
+MTATSPAPRGLPLRGALAIGVGSMVGAGAFTSLGLAALLTGGHVGALAAALGLAVAVATC
+NALSTAQLAAVHPASGGTYVYGRRQIGPTAGFVAGWGFVTGKTASVAAMATTAGLYLFPD
+SPLAARLAGAAAVVILTAVALRGITRTAQATVAILVPVLAVLGLTIVAGLA----GGRAA
+A----DTPVSAADPAGVLAAAGVLFFAFAGYARVATMGEEVEDPRRTIPRAVLGALAFTV
+VLYALLAAALVAALGGTGLAASEAPVRATLEASLGAGWGWAAVVGAVLACAGAMLNLLAG
+ISRTGMAMAREGDLPRPLARVDERTAVPWAGQVTVAVAVILLVLTTDVLTVVGFSSFGVL
+VYYAVANLSALTLRPEQ-----------RTLRVPRAVNVLGLGLCLVIAFTLPPASVAAM
+VGVFLIGLGGRWFVRSRR--PDRIG----
+>4_1173
+--MTAALQRRLTLLHAVAIGLGSMIGAGVFTAIGLAAALTGGHPGLLYGALAVAAVAALC
+NALSTAQLATVHPESGGAYVYGRRQLHPWAGFVAGWGFVTGKTASVAAMAATLGLYLFPD
+DAAAARWTGVAAVVVLTGVAMAGVTRTAQATLAILVPVLAVLVLAIGAGLAREAPGGSAA
+ALGV-DSPVQ-----GVLMGAGVLFFAFAGYARVATMGEEVIDPARTIPRAILIALAVTV
+ALYLLLATALISGLGTSGLARSPAPVRDLLETALGSGWGWVAVAGAALAAAGAMLNLLTG
+ISRTALAMARESDLPRPLARVHAGTGTPWTAQLTVAAAVILLLLTTDILTVVGFSSFGVL
+VYYAVANLSALTLRGDDDGRRPARP---RPLRVPRAVNVLGLALCLLLALSLPPMSVAAM
+AGVFLIGVGGRAFVRAGR-----RGR---
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001064.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001064.fa
new file mode 100644
index 0000000000000000000000000000000000000000..03196679fe2a694b813f36dc5ce8aaf2308f4289
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001064.fa
@@ -0,0 +1,26 @@
+>0_1219
+MTTVTIEETAPAGALMLAGDPFTEPELQALGARGAVRPLLPGVWARPDAADDPAVRAAAL
+WTLGGPLLAAGWTAIGPSAAWILAGGAAPGRLHAAVPHFHRRPAGGGQLPWTLTQSDVAA
+DATGVAPAEQDVLRFGPVRVTTPARTVEDLLLSADPDAARRAAAVIGAHGAAGLRERLAR
+RTRRAGVVAARRRLGALLTALDVPD
+>1_947
+MTTVTIEETAPTGALVLAGDPFTEPELQALGARGAVRPLLPGVWARPDAADDPAVRAAAL
+WTLGGPLLAAGWTAIGPSAAWILAGGAAPGRLHAAVPHFHRRPAGGGLLPWTLTQSDVAA
+DATGVAPAEHDVLRFGPVRVTTPARTVEDLLLSADPDAARRAAAVIGAHGAAGLRERLAR
+RTRRAGVVAARRRLGALLAALDVPD
+>2_1590
+ME-----------GLILAGEPFTPAELQALGSRGVVVPLVPGVWARPEAARRPGVRAEAL
+WMLGGPVLAGGWTAIGSSAAWVLTGGAVPERLHAAVPHFHRLPAGGSPLPWTLTQSDVAA
+GPDGRAPAEEDVLRIGPLRVTTPERTVEDLLLSPDPDAARTAAAVIAAHGAAGLRERLAR
+HSRRSGVVAARRRLDVLLGALEAAG
+>3_1485
+MHQG--HGSRGGAAWELAGMTFTEPELRLLAARGTLEAVLPGVYRPVDVPSEPAGRAAAL
+GLLGGPVLASGWTAVGPSAAWVHVGGPAPHRLHAAVPHFHRLPAGGAAPAWRLVQSDVAA
+GPTGAAPAEEDVQVLEGVRVTVPARTVEDLLLTGDPDDARRAARVIAAHGAEGLRDRLDR
+PSRRPGSVGARRRLRMLLDALGADG
+>4_1176
+MTTVTIEETAPTGALVLAGDPFTEPELQALGARGAVRPLLPGVWARPDAADDPAVRAAAL
+WTLGGPLLAAGWTAIGPSAAWILAGGAAPGRLHAAVPHFHRRPAGGGLLPWTLTQSDVAA
+DATGVAPAEHDVLRFGPVRVTTPARTVEDLLLSADPDAARRAAAVIGAHGAAGLRERLAR
+RTRRAGVVAARRRLGALLAALDVPD
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001075.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001075.fa
new file mode 100644
index 0000000000000000000000000000000000000000..845f5eff42ce7ddf5d6806a28fffa71a1a34e39a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001075.fa
@@ -0,0 +1,26 @@
+>0_1231
+MSVIGPRRLS--AAPGAVEAPVP---PGVFRRALADLRDARPRTEVRLREIPAPEGQAPF
+AVALAADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLA
+GAVAWTWLVEALERHHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLG
+SHLEAWSDMICAFAGLPPEHAADVHTAGP---
+>1_959
+MSVIGPRRLS--AAPGAVEAPVP---PGVFRRALADLRDARPRTEVRLREIPAPEGQAPF
+AVALAADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLA
+GAVAWTWLVEALERRHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLG
+SHLEAWSDMICAFAGLPPEHAADVHTAGP---
+>2_1577
+MTVIGPRRLAPVTGPRGAVAPAPAPLPAAFRRALADLRTARPRPEVRLREIAAPAGQAPH
+AVALAAEVCGSPGAD-DVLATGRFVLLHDPSPAARWPGGFRAVTWIRASLEPDVALDQLA
+GAVAWTWLVEALERRHAEHTQAGGTATRSIAEGFGTLGTAPDATDIELRASWTPAPRDLG
+AHLEAWSDMIGAFAGLPPR-------------
+>3_1472
+MTESGPRAPA--PAAGGA--------SGAFADALADLRAAHPRPEVRLRPIPDPPGLAPF
+AVTLAADVLDPHGAEADPLATGRFVLLHDPAGSPVWRGDFRVVTYIRASLEPDVATDHLA
+GAVAWDWLAEALERRHAAHTEAGGTATRQLAEHFGTLALEPGWTDIELRASWTPGPRDLG
+AHLEAWSDMICAFAGLPPLADDDVPAAVPLRP
+>4_1188
+MSVIGPRRLS--AAPGAVEAPVP---PGVFRRALADLRDARPRTEVRLREIPAPEGQAPF
+AVALAADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLA
+GAVAWTWLVEALERRHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLG
+SHLEAWSDMICAFAGLPPEHAADVHTAGP---
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001077.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001077.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b41accd51b8ad05859ede093f7b46add4212c4d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001077.fa
@@ -0,0 +1,55 @@
+>0_1233
+M--TSVSLASFDHLPALAPDEVVTTVTVTDHALPEGAGTLALLTLDNGQGPRRPATLGPATLLGLGRVLDEQAARAAAGE
+IQALAVTGVEGTFAAGADLSLIASIT-D-DVGRDLALLGHAVYDRLAALEIPTVALVNGLALGGGLELALAAGHRVVAAD
+AKGFGLPEVRLGLIPGWSGVWRVPHLIGPEAAVDVVLKNPLDDNRMLDARAAHGLGLMDRIVEGDLLDAGLELAAALVTG
+DESVAAELAAHRDRDVSDAAWDRALAALERLQAARPGRHLPARRHLEALFTGARTRTRAESAQAEADALGTLLHSPEFRR
+TVYAFLGLVQGRAKRPAGDPGRELAREVRKVGIVGAGLMAGQLALVFARHLRVPVVMTDIDAERVERGLAGVRAQVEKMV
+SRGRLSAEDGQALAGLITADTDKAVYADADIVIEAVFEELEVKRTVFRELEGIVREDAILMTNTSSLSVAAMAEVLERPE
+RLVGFHFFNPVAVMPLVEIVRTEATTDEVVATAFELTRRLRKTGVLVHDATAFVVNRVLLRMMGEVQNSFDEGTDAHEAD
+HALDPLALPMTPFTLLAMVGIPVAQHVSESLSASFGAERFPVSANLQRLIDAGKTAIWAKDVRPDRRDEEAAGATGEQIP
+EATAALLEQGSTPQTSEELLRRVEDALAEEIGLLLDERVVAAPEDVDLCMILGANWPLHLGGITPYLDDCGAAERVNGRR
+FHPAAQA
+>1_961
+M--TSVSLASFDHLPALAPDEVVTTVTVTDHALPDGAGTLALLTLDNGQGPRRPATLGPATLLGLGRVLDEQAARAAAGA
+IQALAVTGVEGTFAAGADLSLIAGLT-D-DVGRDLALLGHAVYDRLAALEIPTVALVNGLALGGGLELALAAGHRVVAAD
+AKGFGLPEVRLGLIPGWSGVWRVPHLIGPEAAVDVVLKNPLDDNRMLDARAAHGLGLMDRIVEGDLLDAGLELAAALVAG
+DESVAAELAAHRDRDVSDAAWDRALAALERLQAARPGRHLPARRHLEDLFTGARTRTRAESAQAEADALGTLLHSPEFRR
+TVYAFLGLVQGRAKRPAGDPGRELAREVRKVGIVGAGLMAGQLALVFARHLRVPVVMTDIDAERVERGLAGVRAQVEKMV
+SRGRLSAEDGEALAGLITADTDKAVYADADIVIEAVFEELEVKRTVFRELEGIVREDAILMTNTSSLSVAAMAEVLEHPE
+RLVGFHFFNPVAVMPLVEIVRTEATTDEVVATAFELTRRLRKTGVLVHDATAFVVNRVLLRMMGEVQNSFDEGTDAHEAD
+HALDPLALPMTPFTLLAMVGIPVAQHVSESLSASFGAERFPVSANLQRLIDAGKTAIWAKDVRPDRRDEEAAGATGEQIP
+EATAALLEQGSTPQTSEELLRRVEDALAEEIGLLLDERVVAAPEDVDLCMILGANWPLHLGGITPYLDDCGAAERVNGRR
+FHPAAQA
+>2_1575
+MTFTPAPLAPFESLLPLVPDEVLTHVAATDHVLPGGAGTLVLLTLDNGQGPRRPATLGPASLLELGRAVDAQAERARAGE
+VQALALTGVEGTFAAGADLSLIAGIE-DRTVGRDLARLGHAVHDRIDAFPAPTLALVNGTALGGGLELALAADHRVVAAD
+ARGFGLPEVRLGLIPGWSGVWRVPHLIGPEAAVEVVLKNPLDNNRMLDARTAHGLGLMDEVAEGDLLEAGLAFAARIVAG
+DDAALAAVRDHRDRDVSDAAWDRALEAMEALQAGRPGRDLPARRALQELFAGARTRTREESAEAEAEALHGLIGSDEFRR
+TVYAFLDLLQRRAKRPVGDPGKELAREVTKVGVVGAGLMAGQLALVFAQHLRVPVVMTDMDQERVDRGLAGVRGQVEKMV
+SRGRITAEQGEALAGLITASTDKSVYADADVVIEAVFEELEVKRTVFRELEPIVREDAVLMTNTSSLSVAAMAEVLEHPE
+RLVGFHFFNPVAQMPLIEVVRVAETSDEAVATAFELSRRLRKTGVLVHDAAAFVVNRVLLRMMGEVQASFDEGTDAHTAD
+HALDPLALPMTPFTLLAMVGIPVAQHVSESLQAAFGAERFPVSANLQRLIDAGKTAIWAKDVRRDKVEEEAAGATGETIP
+AGTAALIERGSSPQTAEELRRRVEDALAEEIGLLLAEGVVAAPEDVDLCMILGAGWPLHLGGITPYLDDCGAAERVNGTR
+FHG----
+>3_1470
+MSHTPAPLDQFEHLSTIAPDEILTRATATDHALPDGAGTLALITLDNGQGPRRPATLGSASLLELARAVDEQAARASAGE
+IQALGITGVEGVFAAGADLALVASLPADAETGRALGRLGHAVYDRIDAFPVPTVALVNGTALGGGLELALACDRRVIAPE
+VKALGLPEVRLGLIPGWSGVWRAPHLVGPEAAVALLLTNPLDNGRMIGAADAVRLGLMDSLAEGDLLAAGLTAAADAVAG
+R-------TVQRTADVSDAAWDRALQAFGAAQSARPGRDLPARRHLEELFAGARTRTRAESAEAEADALADLIGSAEFRR
+TVYAFLGLVQGRAKRPAGDPGVEQAHTVHRVGVVGAGLMAGQLALLFATALRVPVVMTDLDQERVDRGLAYVRSQLERSV
+TKGRMKAEDAEAVAGLITGATDVSAHAEAEFVIEAVFEELEVKRTVFRQLEQVVSPTAILATNTSSLSVAGMAEVLEHPE
+RLVGFHFFNPVAQMPLVEIVRVAETTDAAVATAFELARRLRKTAVLVNDAAAFVVNRVLLRMMGEIQNSFDQGTDAHTAD
+HALDPLAFPMTPFTLAAMVGLPVAQHVSESLQAAFGAERFPVSENLQRLIEAKKTAIWAKDV---KSPEEAGGATGETIP
+ADTAALIEQGDTPQTADELRVRVEDALAEEIGLLLDEGVVAAPDDVDLCMILGAGWPLHLGGITPYLDDCGASERVRGAR
+FHQA---
+>4_1190
+M--TSVSLASFDHLPALAPDEVVTTVTVTDHALPEGAGTLALLTLDNGQGPRRPATLGPATLLGLGRVLDEQAARAAAGE
+IQALAVTGVEGTFAAGADLSLIAGLT-D-DVGRDLALLGHAVYDRLAALEIPTVALVNGLALGGGLELALAAGHRVVAAD
+AKGFGLPEVRLGLIPGWSGVWRVPHLIGPEAAVDVVLKNPLDDNRMLDARAAHGLGLMDRIVEGDLLDAGLELAAALVAG
+DESVAAELAAHRDRDVSDAAWDRALAALERLQAARPGRHLPARRHLEDLFTGARTRTRAESAQAEADALGTLLHSPEFRR
+TVYAFLGLVQGRAKRPAGDPGRELAREVRKVGIVGAGLMAGQLALVFARHLRVPVVMTDIDAERVERGLAGVRAQVEKMV
+SRGRLSAEDGEALAGLITADTDKAVYADADIVIEAVFEELEVKRTVFRELEGIVREDAILMTNTSSLSVAAMAEVLEHPE
+RLVGFHFFNPVAVMPLVEIVRTEATTDEVVATAFELTRRLRKTGVLVHDATAFVVNRVLLRMMGEVQNSFDEGTDAHEAD
+HALDPLALPMTPFTLLAMVGIPVAQHVSESLSASFGAERFPVSANLQRLIDAGKTAIWAKDVRPDRRDEEAAGATGEQIP
+EATAALLEQGSTPQTSEELLRRVEDALAEEIGLLLDERVVAAPEDVDLCMILGANWPLHLGGITPYLDDCGAAERVNGRR
+FHPAAQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001078.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001078.fa
new file mode 100644
index 0000000000000000000000000000000000000000..269b374540fb177bf616771a7df97faf733e7343
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001078.fa
@@ -0,0 +1,31 @@
+>0_1234
+MTDPAP-RPTGAARFDLTPFERWEAVTLDDVHVGFLHRVLEDGVLTTRTGFAPTTAQRAA
+RDGLPERYLAQTQVGFTPDGDGWAWTTHEDSAGAQRVRIDRERAGIDAAVLPSYAEYLLL
+ARVAA---EGPLAV-DRLEEASPLQGGLRVPRAELR-----------PADAGGSD-----
+VRVAVVADGVELGAHLVREGA------VVASDWGGGTASTPVADQAAATAGLDAHVVTFA
+GLPIA
+>1_962
+MTHPAP-RPTGAARFDLTPFERWEAVTLDDVHVGFLHRVLEDGVLTTRMGFAPTPAQRAA
+RGGLPERYLAQTQVGFTPDGDGWAWTTHEDSAGAQRVRIDRERAGIDAAVLPSYAEYLLL
+ARVAA---EGPLAV-DRLEEASPLQGGLRVPRAELR-----------PADAGGSD-----
+VRVAVVADGVELGAHLVREGA------VVASDWGGGTASTPVADQAAATAGLDAHVVTFA
+GLPIA
+>2_1573
+MTDPAPVRPS----LDLTPFERWEAVTLDGEHVGFLHRVLDGTLLTTRMGFAPTPAQRRA
+RPELPERYLAQSQVSFTADGTSWDWTSHEDSAGAQRVRIDRERAGLDADVLPSYAEYLLL
+AVAAA---DGPVVVAARLEESSPLQGGLRMPRAELR-----------PADAGDGD-----
+VSVTVVADGAALGAHLVRDGA------VVASDWGGGTASTPVAGRAEATEGLDEHVVTFS
+GMPLV
+>3_1469
+M----------SARYDLTPFETWEAVALDGVHAGFLHRRLADGILTTRMAFQPTGAQRRE
+RADLPQRYLAQARVRFSADGSTWEVCDFEDSLTTQNVRIARERAGLGAEVVPSWAEHLLI
+TAQRTPEHDGAPYL--RLEESSPLQGPVRMPPAVLRIGAREAVPAAGPAGSEAGQARPEG
+LRVEVVSEGHVLAVHWLGEPATEGRRPLVASDWGGGTVSVPVATAAEALEGLPADLHTFA
+QLPTD
+>4_1191
+MTHPAP-RPTGAARFDLTPFERWEAVTLDDVHVGFLHRVLEDGVLTTRMGFAPTPAQRAA
+RGGLPERYLAQTQVGFTPDGDGWAWTTHEDSAGAQRVRIDRERAGIDAAVLPSYAEYLLL
+ARVAA---EGPLAV-DRLEEASPLQGGLRVPRAELR-----------PADAGGSD-----
+VRVAVVADGVELGAHLVREGA------VVASDWGGGTASTPVADQAAATAGLDAHVVTFA
+GLPIA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001084.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001084.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc653ce0cd7583e0a7797a7f3e4c1ead92aee05c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001084.fa
@@ -0,0 +1,51 @@
+>0_1248
+MAVVDTSTDVTGIGRTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEDG
+ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF
+RDTVHRIADLAVEPEVCFAGSEDEPTGQRWRTRNAFAVTPQGHIAMHAYRSATLLPVRNM
+PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEVKLGRLRTRIRQ
+AANACGVDVSTGLALPGPKQFQPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH
+QHAPATLVDAVLEDARVEPGQVVADLYGGAGLFSAYLADAVGPEGRVYSVEASRQASKDA
+RRNLHDQPQASVLNGPTDKVLGSWLKYPERPVADGGLGGAALDTVVLDPPRAGAGRRAIE
+RILALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPAAQ
+SAPAAAVVEI
+>1_980
+MAVVDTSTDVTGIGRTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEDG
+ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF
+RDTVHRIADLAVEPEVCFAGSEDEPTGQRWRTRNAFAVTPQGHIAMHAYRSATLLPVRNM
+PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEVKLGRLRTRIRQ
+AANACGVDVSTGLALPGPKQFQPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH
+QHAPATLVDAVLEDARVEPGQVVADLYGGAGLFSAYLADAVGPEGRVYSVEASRQASKDA
+RRNLHDQPQASVLNGPTDKVLGSWLKYPERPVADGGLGGAALDTVVLDPPRAGAGRRAIE
+RILALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPAAQ
+SAPAAAVVEI
+>2_1566
+MAVIDTSTGVTGIGGTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEEG
+ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF
+RDTVHRIAGLTVEPEVCFAGPEDEPTGQRWRTRNAFTVTPQGHIAMHAYRSATLLPVRNM
+PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEAKLGRLRTRIRQ
+AANACGVDVSTGLALPGPKRHSPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH
+RHAPATLVDAVLEDARIEPGQTVADLYGGAGLFSAYLADAVGPEGRVFSVEAAGQASKDA
+RRNLHGQPQATVLNGPTDKALGSWIKYPERTVADGGLEGASLDTVVLDPPRAGAGRRAIE
+RLLALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPATQ
+LAAVPAIVEI
+>3_1462
+---MDTSTEVVAPGGVIEVEAGAMAHGGHCVARHEGRVVFVRHAIPGEIVRVALTEAEPG
+ARFWRGDVVEVVRPSEFRRIHQWKLADSLRAHASGRLPVGGAEYGHIVVHHQRRLKAQVF
+RDTVARIAGVTIEPEALHAGHEDEPTGQHWRTRTAFAVTPQGRIAMHAHRSAVLLPVRNM
+PLGVHALDALALWDWDFTGAARVDVATPADGTQPLVLATPTPQTLADEARLGKLRTRIRQ
+AANACPVDVSTGFAVPGPKKFSPTGIQRITGRTWVHETVSSERGGERTFRVTGDGFWQVH
+QHAPATLVDAVLEDVDPQPGEVIADLYAGAGLFSAFLSDAVGEEGRVYSVEASRQASKDA
+RRNLLSLPQAGVLNGPTDKVLGSWIKEPERTTRDGGLDGDRLDAVVLDPPRAGAGRRAIE
+RILALAPGRICYVSCDPASFARDLAWLREGGYEVERARVFDLYPDTHHLESVTLLRPAGE
+VEQTT----L
+>4_1205
+MAVVDTSTDVTGIGRTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEDG
+ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF
+RDTVHRIADLAVEPEVCFAGSEDEPTGQRWRTRNAFAVTPQGHIAMHAYRSATLLPVRNM
+PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEVKLGRLRTRIRQ
+AANACGVDVSTGLALPGPKQFQPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH
+QHAPATLVDAVLEDARVEPGQVVADLYGGAGLFSAYLADAVGPEGRVYSVEASRQASKDA
+RRNLHDQPQASVLNGPTDKVLGSWLKYPERPVADGGLGGAALDTVVLDPPRAGAGRRAIE
+RILALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPAAQ
+SAPAAAVVEI
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001085.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001085.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fbe316032257bd8d5c5fd094f82741d39616b2f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001085.fa
@@ -0,0 +1,50 @@
+>0_1249
+MATLSSLLRRGLLGRPVTSHAADEPRMNRWRALPVTSSNALSSLAYAPDEVILTLVAAGTSALALGPAVGWAVVAVMLLI
+VVSFRAAVAAVPHGGIYHMAGMKLGPRAGVVASAALLLDFVFTAAVSVAAFAHFVAALAPGLTVGSRVLVASAALVGVLL
+AALRGVRLSRWVLPVLVSVFVALTALLVLAGLWQEGRGLLGAAPTAGWTQEGAGVGGTVGTVATALLALRAFSAGSVLLT
+GVEVPVSSTRLMARPAVPTVRWVLTVMALTLGALTVGVMHLAQRTGVVVGLELENLRDAAGAEVTPDRAPAPVLAQLADT
+VYGPGSILSVATIAATALLLLFAAKSAFRSFPALAARVAEDGYLPRQLRVRSDRLVHTWSVLGMGAVALSLVLFFEARTA
+LLVQLYVIGVLLAFTLAQAGMLRLWRRRLVHTPGARARAAVRLRLIITAVAWVVTALAGVVVLVTRFTQGAWVALLAIVL
+GSLVMGRIRRHYADVDRELAPDPQDDARALPSRVHVVVVVTTLDRPALRALAYARASRPSSLEAVVVDAERAATLEVIDA
+WERAGLPMSLTVIASPYRDTVAPLVRHVREHRRRSPRDLTMVFIPEYVVRPGWRTLLHNRTATRQTRRLQREPGVMVGSV
+PWQVHEGQ---------------GS--------
+>1_981
+MATLSSLLRRGLLGRPVTSHAADEPRMNRWRALPVTSSNALSSLAYAPDEVILTLVAAGTSALALGPAVGWAVVAVMLLI
+VVSFRAAVAAVPHGGIYHMAGMKLGPRAGVVASAALLLDFVFTAAVSVAAFAHFVAALAPGLTVGSRVLVASAALVGVLL
+AALRGVRLSRWVLPVLVSVFVALTALLVLAGLWQEGRGLLGAAPTAGWTQEGAGVGGTVGTVATALLALRAFSAGSVLLT
+GVEVPVSSTRLMARPAVPTVRWVLTVMALTLGALTVGVMHLAQRTGVVVGLELENLRDAAGAEVTPDRAPAPVLAQLADT
+VYGPGSILSVATIAATALLLLFAAKSAFRSFPALAARVAEDGYLPRQLRVRSDRLVHTWSVLGMGAVALSLVLFFEARTA
+LLVQLYVIGVLLAFTLAQAGMLRLWRRRLVHTPGARARAAVRLRLIITAVAWVVTALAGVVVLVTRFTQGAWVALLAIVL
+GSLVMGRIRRHYADVDRELAPDPQDDARALPSRVHVVVVVTTLDRPALRALAYARASRPSSLEAVVVDAERAATLEVIDA
+WERAGLPMSLTVIASPYRDTVAPLVRHVREHRRRSPRDLTMVFIPEYVVRPGWRTLLHNRTATRQTRRLQREPGVMVGSV
+PWQVHEGQ---------------GS--------
+>2_1565
+MATLSSLLRRGLLGRPVASHDVAEPRMSRWQALPVTSSNALSSLAYAPDEIVLTLVAAGTAALALGPLVGWGVVVVMLLI
+VASFRAAVAAVPQGGIYQMARTKLGPRAGVVASAALLLDFVFTAAVSVAAFAHFAAALLPGLGLESRVLVACAALVGVLL
+TSLRSARLSRWALPVLVSAFVALTALLVAAGLWQEGQGLLGRAATSGWTQEGAGIGGTVGAVATALLALRAFSAGSVLLT
+GVEVPVSSSSAMARPAVATVRWVLAVMALTLGALTLGVMHLAQRTGVVVALDPARLRDAAGRPVAEADTPAPVIAQLADT
+VFGPGSVLSLATIAATALLLLFAARSAFRSFPALASRLAEDGYLPRQLRVRGDRLVHTWGVLALGAAALALVLLFRAQTA
+LLVQLYVIGVLLAFTLAQAGMLRLWRRRLAQTPGARARAAVRLRLTITAVAWVVTALAGVVVLVTRFAQGAWVALLAIVL
+GSLVMGRIRRHYEDVGRELAPDPEDDARALPSRVHVVVVVSTLNRPALRALAYARATRPSSLEAVVVDAERAVTEDVIDA
+WSRAGLPVPLTVVAAPYRDTVVPLVRHLRERRRRSPRDLTMVFIPEYVVRPGWRTLMHNRTATRQKRRLQREAGVMIGSV
+PWQIHEGQ---------------GD-GQRSTTV
+>3_1461
+MSTPPSTLRRLLLGRPVASGARPAPRRGRWLALPATASNALSSLAYAPDEVILTLVASGTGALALGPLVGWAVVAVMVLI
+VLAFRAAVVAVPRGGIYRMARTKLGPRSGVVAAAALLLDFVFTAAVSVAAFAHHASALVPALR-GHVGIVSAVALVLVLV
+SALRGERGSGALVTVLVAAFVGLLGTLVAVGLWQSGQGTLAAAPSAGLHVDGAGL-GPVGDAATALLALRAFSAGSVLLS
+GVEVPLSATDRMARPAVRTARWVLTVLAVVVGTLTVGVMHLAQRTGVVVALHPDRLRTADGAPLAPDTAPAPVVAQLAET
+VFGAGSPGAVATVAVTSLLLLVAARGAFRSFPTLTARLAEDGWLPRQLRVRGDRMVHTGGTLALATATLLLLVLFRGRTA
+LLVQLYVIGVLLAFALALVGMLRLWRLKLAHTPGARARASVRVKLVVTAVGLGATALAGVVVLVTRFAQGAWVALLAIGV
+SAVVMGRIRRHYRAVEAELAPDPQDDARALPSRVHAVVVVSTLNRPALRALAYARATRPATLEAVVVDADRRQTERVVED
+FARAGLPVPLTVIAAPYRDTVVPLVRHVRGRRLRSPRDLTMVFIPEHVVRGGWRRLLHNRTASRQKARLQREAGVMVGSV
+PWQIREGDPHRPVEGGIVACAAPGDVPEGVESS
+>4_1206
+MATLSSLLRRGLLGRPVTSHAADEPRMNRWRALPVTSSNALSSLAYAPDEVILTLVAAGTSALALGPAVGWAVVAVMLLI
+VVSFRAAVAAVPHGGIYHMAGMKLGPRAGVVASAALLLDFVFTAAVSVAAFAHFVAALAPGLTVGSRVLVASAALVGVLL
+AALRGVRLSRWVLPVLVSVFVALTALLVLAGLWQEGRGLLGAAPTAGWTQEGAGVGGTVGTVATALLALRAFSAGSVLLT
+GVEVPVSSTRLMARPAVPTVRWVLTVMALTLGALTVGVMHLAQRTGVVVGLELENLRDAAGAEVTPDRAPAPVLAQLADT
+VYGPGSILSVATIAATALLLLFAAKSAFRSFPALAARVAEDGYLPRQLRVRSDRLVHTWSVLGMGAVALSLVLFFEARTA
+LLVQLYVIGVLLAFTLAQAGMLRLWRRRLVHTPGARARAAVRLRLIITAVAWVVTALAGVVVLVTRFTQGAWVALLAIVL
+GSLVMGRIRRHYADVDRELAPDPQDDARALPSRVHVVVVVTTLDRPALRALAYARASRPSSLEAVVVDAERAATLEVIDA
+WERAGLPMSLTVIASPYRDTVAPLVRHVREHRRRSPRDLTMVFIPEYVVRPGWRTLLHNRTATRQTRRLQREPGVMVGSV
+PWQVHEGQ---------------GS--------
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001086.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001086.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a2ecce858439b9add2805a41f90d47582d0f73da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001086.fa
@@ -0,0 +1,26 @@
+>0_1250
+MAHYVIVGGGRVGTRLAAALDAAGHGVALVDRDPRTVEGLAPGFSGELVAGVGFDRSALL
+AAGIDRAQGLAAVTADDNTNIIAARVARETFHVDHVVARIYDADRARLYQRLGIPTVASI
+QWTADQVLHRLLPAGTADAEHRDASGRLLVTELVPHSSWWGRRLTDVESTVGMRIAYLTR
+LGDGQLPRPGDRLQEGDVLHAVYPVDRRDRVEAALQGEARVP--DGTDEDEEGRA
+>1_982
+MAHYVIVGGGRVGTRLAAALDAAGHGVALVDRDPRTVEGLAPGFSGELVAGVGFDRSALL
+AAGIDRAQGLAAVTADDNTNIIAARVARETFHVDHVVARIYDADRARLYQRLGIPTVASI
+QWTADQVLHRLLPAGTADAEHRDASGRLLVTELVPHSSWWGRRLTDVESTVGMRIAYLTR
+LGDGQLPRPGDRLQEGDVLHAVYPVDRRDQVEAALQGEARVP--DGTDEDEEGRA
+>2_1564
+MAHYVIVGGGRVGTRLACALDAAGHSVALVDRDPRTVDGLVPGFSGELVAGVGFDRAALL
+AAGVDRAQGLAAVTAEDNTNIIAARVARETFHVEHVVARIYDADQAKVYQRLGIPTVASI
+QWTADQVLHRLLPAGTADVERRDASGRLLVTGLVPHPSWWGRRLTDVESGAGLRIAYLTR
+RGEGLLPRPGDRLQEGDLLHAVYPVDRRDQVEAALQGEAVRSDRDAEDEDEEGRA
+>3_1460
+MAHYVIVGAGRVGTRLAGALDTAGHSVAVIERSPELTAGLGPDFGGTVVAGIGFDRDALR
+RAGIEQAQGLAAVTTEDTTNVIAARVARETFGVQHVVARIYDAQRARVFQRLGIPTVASV
+EWTADQVLHRLLPAGTAEPSRRDASGRLAMGDYMPHRSWWGSPLHAVEAAVGARIAYLTR
+YGEGVLPSPDGVLQEGDVLHVAYPAARRDRVEAALQGEA-GDVRAGEDEDQEEDA
+>4_1207
+MAHYVIVGGGRVGTRLAAALDAAGHGVALVDRDPRTVEGLAPGFSGELVAGVGFDRSALL
+AAGIDRAQGLAAVTADDNTNIIAARVARETFHVDHVVARIYDADRARLYQRLGIPTVASI
+QWTADQVLHRLLPAGTADAEHRDASGRLLVTELVPHSSWWGRRLTDVESTVGMRIAYLTR
+LGDGQLPRPGDRLQEGDVLHAVYPVDRRDQVEAALQGEARVP--DGTDEDEEGRA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001094.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001094.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6de2347ebaa37e51ff00944c6d2cd2665c18ff9c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001094.fa
@@ -0,0 +1,41 @@
+>0_1259
+M--------TGPALPAGVVPADRALRSVLTSAAAALGVPGCENALAVPAGRRVVVALVDG
+LGRSLLKRFGGHAPTLRSAMADGGRVLEVAVPTTTAASLTSLGTGLDVGEHGVAGYDVLD
+PDRDVVINQLGGWDEATDPVGWQPKPTVFERAAAAGVDAVTVSLPAFERSALTRAGLRGG
+RFVAGRTLIARAQAAERALKDARVPTLVYFYVNELDRAGHRDGVGSDRWLHALEEIDAAV
+RRLVDRVPAGTVVLATGDHGMVDVPPSRRVDYAALDEAGELADAALLEGVAHTAGEPRLV
+QLHFRSDAGPDVRARVRRAWAERYGAHAWVLTRDEAVDAGWFGAVVEDRVRARIGDLLVA
+VHGDLALYDGRRVPPHAFEMVGQHGAPTRAEREVPLLTWHR
+>1_991
+M--------TGPALPAGVVPADRALRSVLTSAAAALGVPGCENALAVPAGRRVVVALVDG
+LGRSLLKRFGGHAPTLRSAMADGGRVLEVAVPTTTAASLTSLGTGLDVGEHGVAGYDVLD
+PDRDVVINQLGGWDEATDPVGWQPKPTVFERAAAAGVDAVTVSLPAFERSALTRAGLRGG
+RFVAGRTLIARAQAAERVMKDARVPTLVYFYVNELDKAGHRDGVGSERWLHALEEIDAAV
+RRLVDRVPAGTVVLATGDHGMVDVPPSRRVDYAALDEAGELADPALLEGIAHTAGEPRLV
+QLHFRSDAGPDVRARVRRTWAERYGAHAWVLTRDEAVDAGWFGAVVEDRVRARIGDLLVA
+VHGDLALYDGRRVPPHAFEMVGQHGAPTRAEREVPLLTWHR
+>2_1555
+M--------SGPAVPVGVVPPERALRSVLTSAAAALGVPGCENALGVPASRRVVVALVDG
+LGRSVLKRFGGHAPTLRAAMADGGRVLQAAVPTTTAASLTSLGTGLDVGEHGVAGYDVLD
+PERDAVVNQLGGWDEATDPVAWQPRPTVFERAGAAGVDAVTVSLPAFEHSGLTRAGLRGG
+RFVAGRGLLARAQAAERVLKDAREPTLVYFYVNELDKAGHRDGVGSDRWLHALEEIDGAL
+RRLVDRVPAGTVVLATGDHGMVDVPPTRRVDYAAADESGALADPALLEGIAHTAGEPRLV
+QLHFRPDADADVRARVRRAWEDRFGAHAWVLTRDEAVAAGWFGTVVEERVRGRIGELLVA
+VHGDLALYDGRRVAPHAFEMVGQHGSPTRAEREVPLLTWRR
+>3_1451
+MTGPDAAAPAGPGLPPGPVPPERALRSVLTSAAAALGVPGCANALGVPVTRRVVVALVDG
+LGRGVLKRFSGHAPTLRAAMADGGRVLTAATPTTTAASLTSLGTGLDVGEHGVAGYDVLD
+PDRGVVVNMLGGWDEATDPLAWQPHPTVFERAVEAGVDAVTVSLPEFEHSALTRAGLRGG
+RFVGGRGLLARAGHAERVLADACVPTLVYFYVNELDKAGHRDGVGSRSWLHALEEVDAAL
+RRLVSRVPAGTVVLATGDHGMVDVAESRRVDYAALGDDGAPVRPGLLAGVAHTAGEPRLV
+QLHFAPTATPAEREGTRRAWEDAYGDQAWILTRDEAVAAGWFGERVADRVLPRIGDLLVA
+CHGELALYDGRRVSPRAFAMVGQHGSPTRAEREVPLLTWRR
+>4_1216
+M--------TGPALPAGVVPADRALRSVLTSAAAALGVPGCENALAVPAGRRVVVALVDG
+LGRSLLKRFGGHAPTLRSAMADGGRVLEVAVPTTTAASLTSLGTGLDVGEHGVAGYDVLD
+PDRDVVINQLGGWDEATDPVGWQPKPTVFERAAAAGVDAVTVSLPAFERSALTRAGLRGG
+RFVAGRTLIARAQAAERVMKDARVPTLVYFYVNELDKAGHRDGVGSERWLHALEEIDAAV
+RRLVDRVPAGTVVLATGDHGMVDVPPSRRVDYAALDEAGELADPALLEGIAHTAGEPRLV
+QLHFRSDAGPDVRARVRRTWAERYGAHAWVLTRDEAVDAGWFGAVVEDRVRARIGDLLVA
+VHGDLALYDGRRVPPHAFEMVGQHGAPTRAEREVPLLTWHR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001096.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001096.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6bd55409bf41b3df0e0af5f656f1d3612408b3d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001096.fa
@@ -0,0 +1,65 @@
+>0_1261
+MGETEADRGYPSHWEADVVLRDGATAHLRPISPEDAAELQRMHAGQSENSIYLRYFTYKSELSAKDLDRFTHVDHRDRVA
+FVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLGSILMEHLAAAARENGIRRFTAEVLPENRKMLSVFQESGFE
+VTRRFEDGVVAVEFPIDPTARWRAVVESREHRAESRSVAELVEPASVAVVGASRDPQAVGSLVLRHVLEAGFTGTVHAVN
+RAAEDVQGLTAHRSLADIGEPVDLVVVAVPADEVEALIPEAAAAGAQGLVVLTSGYADAGAEGLEAQRRLVSLARAHGMR
+VIGPASTGLVRTDPAIRLNASPSPGLAQRGPVSLFSQSGAVGAMVSAGVKRRGVGISTSISAGNRADVSGNDAMQFFEAD
+PHTAAVGVYLESFGNPRKFSRIARRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGTVDSMLDQTGVLEAHTHEAMLD
+ILMAVASQPLPTGHRVVLVADSLALDRLGRDAAAEAGLEVTATVGLVGSEQGIAPPADTLVSAVRDAVCHEQADAVVVLA
+RLGLHQADDEPERLAHALADATREARIPVLGCLTDVVSPRYRGATLGAAGPVDDDAEPGSLQPGLPFYPSPQQAMAVLGA
+LADYVHWRHQEVGEPLEPTGLHPHEAEELVEAAAARAEGTELVRLSDEETETLLGHYGITVLPSVRFETAEEAVAAAERL
+GFPVALKAVDPHLRHRLDLGGVRLNVVDADSLRRNVEHMRRLLAPFGVRELEVQAMAPAGQACMLTALEDPLLGPVVSFG
+IAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAVKLRGTGGVPPVDLAALEDLVGRVSVLKDDLPQVARLRFAPVLAAP
+ERVTVLQAEVHVANAARRTDSARRALRGR
+>1_993
+MGETEAVRGYPSHWEADVVLRDGATAHLRPISPEDAAELQRMHAGQSENSIYLRYFTYKSELSAKDLDRFTHVDHRDRVA
+FVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLGSILMEHLAVAARENGIRRFTAEVLPENRKMLSVFQESGFE
+VTRRFEDGVVAVEFPIDPTARWRAVVESREHRAESRSVAELVEPASVAVVGASRDPQAVGSLVLRHVLEAGFTGAVHAVN
+RAAEDVQGLTAHRSLADIGEPVDLVVVAVPADEVEALIPEAAAAGAQGLVVLTSGYADAGAEGLEAQRRLVSLARAHGMR
+VIGPASAGLVRTDPAIRLNASPSPGLAQRGPVGLFSQSGAVGAMVSAGVKRRGVGISTSISAGNRADVSGNDAMQFFEAD
+PHTAAVGVYLESFGNPRKFSRIARRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGTVDSMLDQTGVLEAHTHEAMLD
+ILMAVASQPLPTGHRVVLVADSLALDRLGRDAAAEAGLEVTATVGLVGSEQGIAPPAETLVSAVRDAVRHEQADAVVVLA
+RLGLHQADDEPERLAHALADATRDARIPVLGCLTDVVSPRYRGATLGAAGPVDDDAEPGSLQPGLPFYPSPQQAMTVLGA
+LADYVHWRRQEVGEPLEPTGLHPHEAEELVEAAAARAEGTELVRLSDEETETLLGHYGITVLPSARFETADEAVAAAERL
+GFPVALKAVDPHLRHRLDLGGVRLNVVDADSLRRNVEHMRRLLAPFGVRELEVQAMAPAGQACMLTALEDPLLGPVVSFG
+IAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAVKLRGTGGVPSVNLAALEDLVGRVSVLKDDLPQVARLRFAPVLAAP
+EGVTVLQAEVHVANAARRTDSARRALRGR
+>2_1553
+MGDTEPVRDYPSHWEADVVLRDGATARLRPITPEDADELQRMHAGQSENSIYLRYFTYKSELSAKDLDRFTHVDHKDRVA
+FVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLGSILMEHLAVAAREHGIRRFTAEVLPENRKMLSVFQESGFE
+VTRRFEDGVVAVEFPIDPTARWRAVVESREHRAEARSVAELVAPESVAVVGASRDPQAVGSMVLRHILEGGFAGPVHAVN
+RAAGEVQGLTAHASLAEIGEEVELVVVAVPVDQVEALVPEAAAAGAAGLLVLTSGYADAGAEGLEAQRRLVSLARAHGMR
+VIGPASAGLVRTDPAVRLNASPSPGLAQRGPVGLFSQSGAVGAMVSAGAKRRGVGVSTSISAGNRADVSGNDAMQFFEAD
+PHTAAVGVYLESFGNPRKFTRITRRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGAVDSMLDQTGVLEVHTHEAMLD
+LLMAVASQPLPTGRRVVLVADSLAVDRLARDAAAEAGLDVVATVGLAGSEQGVAPPAETLVASVREAVAHEQADAVVVVG
+RLGLHQEDDDPETVARALAEATAGARMPVLVCLTDVVSPRYAGATLGASGPVADDAEPGSLQPGVPFYPSPQQAMSVLGA
+LADYVRWRGEEAGEPLEPADVRLHAAEDLVEAAAARAEGTELVRLSAAETEELLGHYGIAVLPSARFETADEAVAAAERL
+GFPVAVKAVDPHLRHRLDLGGVRLNVVDAASLRRNVEQMRRVLAPFGVTELEVQAMAPAGQACMVTALEDPLLGPVVSFG
+IAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAAKLEGRGGVPAVDLAALEDLVGRVSVLKDDLPQVARLRFSPVLASP
+EGVTVLQAEVDVANAAGRTDSARRALRGS
+>3_1449
+MAEPDTETAYPSQWEADVVLRDGATARLRPIREDDVDGLRALHAGQSESSIYLRYFTFKSELSAKELERFTHVDHRDRVA
+LVIERGGRILGVGRYDRYGDSDAAEVAFNISDAAQGQGLGSILMEHLAVAAREQGIRRFTAEVLPENRKMLSVFQDSGFE
+VARHFEDGVVAVEFPIDPTARWRAVVESREHRAEARSVAELVEPESVAVVGASRDPHAVGSIVLRHILEAGFTGRVHAVN
+RAAEDVQGLTAHASLKDIGEPVDLVVVAVPVAEVDAVVAEAAEAGAQGLLVLTSGYADAGEDGLRAQRRLVARARARGMR
+VIGPASAGLVRTAPDVRLNASPSPGLASRGPVGVFSQSGAVGAMITAGMKRRGVGMSTSLSAGNRADVSGNDAMQFFEDD
+PHTAAVGVYLESFGNPRKFSRIARRLSRTKPVVVVRSDVTGRALPPGHETRTTQAPEGAVDSMLEQTGVLEAATHEDMLD
+LLMAVATQPLPTGRRVTLVADSLALDRLGRDAAAVAGLEVVATHGLGGSEQGIAPTADDVVASVEAALAAGDTDAVVVVT
+RLGLHQDEDAAHEVAQALARVAEGATVPVLGCLTDVVSARYGGARVGGAAAPAADAEPGALQPGLPLYPSPRKAMTVLGR
+LCDYVAWRREDAGEPIELTDVDVRAAEALVDRALERALGTELIRLTGAETEELLRIYGIGVLRSRRFTTPDEAVAAAEEL
+GFPVAVKAVDPYLRHRLDLGGVRLNLEDAESLRQNVRQMRAVLAPFGVTELEVQSMAPSGQPCMVTALEDPLLGPVVSFG
+MAGDATDLLGDWVHRVPPLTDQDVRRMVRSPRAAVKLDGVGGVPAVDLDALEDLLARVSCLKDDLPAVARLRFAPVLAAP
+TGTTVLSAEVDVANAAGRTDSARRALRAS
+>4_1218
+MGETEAVRGYPSHWEADVVLRDGATAHLRPISPEDAAELQRMHAGQSENSIYLRYFTYKSELSAKDLDRFTHVDHRDRVA
+FVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLGSILMEHLAVAARENGIRRFTAEVLPENRKMLSVFQESGFE
+VTRRFEDGVVAVEFPIDPTARWRAVVESREHRAESRSVAELVEPASVAVVGASRDPQAVGSLVLRHVLEAGFTGAVHAVN
+RAAEDVQGLTAHRSLADIGEPVDLVVVAVPADEVEALIPEAAAAGAQGLVVLTSGYADAGAEGLEAQRRLVSLARAHGMR
+VIGPASAGLVRTDPAIRLNASPSPGLAQRGPVGLFSQSGAVGAMVSAGVKRRGVGISTSISAGNRADVSGNDAMQFFEAD
+PHTAAVGVYLESFGNPRKFSRIARRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGTVDSMLDQTGVLEAHTHEAMLD
+ILMAVASQPLPTGHRVVLVADSLALDRLGRDAAAEAGLEVTATVGLVGSEQGIAPPAETLVSAVRDAVRHEQADAVVVLA
+RLGLHQADDEPERLAHALADATRDARIPVLGCLTDVVSPRYRGATLGAAGPVDDDAEPGSLQPGLPFYPSPQQAMTVLGA
+LADYVHWRRQEVGEPLEPTGLHPHEAEELVEAAAARAEGTELVRLSDEETETLLGHYGITVLPSARFETADEAVAAAERL
+GFPVALKAVDPHLRHRLDLGGVRLNVVDADSLRRNVEHMRRLLAPFGVRELEVQAMAPAGQACMLTALEDPLLGPVVSFG
+IAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAVKLRGTGGVPSVNLAALEDLVGRVSVLKDDLPQVARLRFAPVLAAP
+EGVTVLQAEVHVANAARRTDSARRALRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001100.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001100.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a87f911fd121b7f83a8bc7b6908fed836c3e4776
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001100.fa
@@ -0,0 +1,40 @@
+>0_1265
+MDPLDLARWQFGITTVYHFLMVPLTIGLGLVVAVMQTLWVRTGREQYLRMTKFWGKLFLINFIMGVATGIVQEFQFGMAW
+SEYSRFVGDVFGAPLALEALIAFFLESVFLGVWIFGWGRVPRRLHLAAIWCAVIGAHLSAYFIMTANAFMQHPVGYEVVD
+GRPVLNDIGAVLANPIVLTHFPHTIAGSWAVAGGFLLGISWYHLWKRRRDGIDTVDEHGRVVVGTTGSKARDRLDHRVWI
+TSLRAGAAVAIVGFLGTAFTGHAQAQQMIEFQPTKMASAEAACHDGTAFSVLTLGDLGAGDRTTCTDVTTVIELPGLLSY
+LAYEDFTTPVPGLNSLLPDFEERYGTHLPDDPLYGERAGAPIDYQPLMEVTYWGFRLMITFGGLGALAGALTLWMTRRGT
+VPDSRGWTATAVASIGAPFAANVAGWVFTEMGRQPFVVYPNPAMGVDEVYMFTAAAVSPGVSAQEVLASLIVLVGIYAVL
+LVVEVVLMVRYVRGGVPAGMPELTADEHRDPDEDRHDRDDVLAFAY
+>1_997
+MDPLELARWQFGITTVYHFLMVPLTIGLGLVVAVLQTLWVATGKDHYLRMTKFWGKLFLINFIMGVATGLVQEFQFGMAW
+SEYSRFVGDVFGAPLALEALIAFFLESVFLGIWIFGWDRIPRRLHLAALWCAVLGINLSAYFIMVANGFMQHPVGYEVVD
+GRPVLNDLGAVLTNPIVLTHYPHTIFGSWAVAGGFLVGIAWYHLWKRRRDGIDVVDEAGRVVVGDAGTAARDRTDHRVWL
+TSLRAGAAVALIGFVGTAFSGHAQAQQMIHFQPTKMAAAEAACHDGTAFSVLTLGDVRSGGATTCEDVQGVIEVPGLLSY
+LAYEDFTTPVRGINTLLPEFEQKYGTHLPDSELYGDRAGSEISYLPLMEVTYWGFRLMILFGGLGALAALGALWFSRRGT
+VPASRGWMRLAVASIGAPFAANMTGWVFTEMGRQPFVVYPNPAMGVDQVYMFTAAAVSPGVTGEEVLVSLIVLVGIYAVL
+LGVEVFLLTRFVRGGVPAAMPELTAAEHS--DEQKRDRDDVLAFAY
+>2_1549
+MDPLDLARWQFGITTVYHFLMVPLTIGLGLVVAVMQTLWVRTGREQYLRMTKFWGKLFLINFIMGVATGIVQEFQFGMAW
+SEYSRFVGDVFGAPLALEALIAFFLESVFLGVWIFGWGRVPRRLHLAAIWCAVIGAHLSAYFILTANAFMQHPVGYEVVD
+GRPVLNDIGAVLANPIVLTHFPHTIAGSWAVAGGFLLGISWYHLWKRRRDGIDTVDEHGRVVVGTTDSKARDRLDHRVWI
+TSLRAGAAVAIVGFLGTAFTGHAQAQQMIEFQPTKMASAEAACHDGTAFSVLTLGDLGAGDRTTCTDVTTVIELPGLLSY
+LAYEDFTTPVPGLNSLLPDFEERYGTHLPDDPLYGERAGAPIDYQPLMEVTYWGFRLMITFGGLGALAGALTLWMTRRGT
+VPDSRGWTATAVASIGAPFAANVAGWVFTEMGRQPFVVYPNPAMGVDEVYMFTAAAVSPGVSAQEVLASLIVLVGIYAVL
+LVVEVVLMVRYVRGGVPAGMPELTADEHRDPDEDRHDRDDVLAFAY
+>3_1445
+MDPLELARWQFGITTVYHFLMVPLTIGLGLVVAVLQTLWVRTGREHYLRMTKFWGKLFLINFIMGVATGLVQEFQFGMAW
+SEYSRFVGDVFGAPLALEALIAFFLESVFLGMWIFGWDRLPRRLHLAAIWCAVIGAHLSAYFIMAANAFMQHPVGYEVVD
+GRPVLNDIVAVLTNPIVLTHFPHTIAGSWAVAGGFLLGISWYHLWKRRRDGIDTVDAEGRVVVGTTGSKARDALDHRVWI
+TSLRAGAAVVIVGFLGTAFTGHAQAQQMIHYQPTKMASAEAACHDGTAFSVLTLGDVNTPGATTCDDVTGVIEIPGLLSF
+LAYSDFTTPVPGITTLLPQFEARYGTQLPDDPMYGERAGQEISYLPLMEVTYWGFRLMITFGGLAALAGALTLWMTRKGT
+VPDSKPWMITAVASIGASFAANVAGWVFTEMGRQPFVVYPNPAMGVDEVYMFTAAAVSPGVSGEEVLTSLIVFVVLYAVL
+LVVEVALLARYVRGGVPAGMPELTADEHRDPDDDRHDRDDVLAFAY
+>4_1222
+MDPLELARWQFGITTVYHFLMVPLTIGLGLVVAVLQTLWVATGKDHYLRMTKFWGKLFLINFIMGVATGLVQEFQFGMAW
+SEYSRFVGDVFGAPLALEALIAFFLESVFLGIWIFGWDRIPRRLHLAALWCAVLGINLSAYFIMVANGFMQHPVGYEVVD
+GRPVLNDLGAVLTNPIVLTHYPHTIFGSWAVAGGFLVGIAWYHLWKRRRDGIDVVDEAGRVVVGDAGTAARDRTDHRVWL
+TSLRAGAAVALIGFVGTAFSGHAQAQQMIHFQPTKMAAAEAACHDGTAFSVLTLGDVRSGGATTCEDVQGVIEVPGLLSY
+LAYEDFTTPVRGINTLLPEFEQKYGTHLPDSELYGDRAGSEISYLPLMEVTYWGFRLMILFGGLGALAALGALWFSRRGT
+VPASRGWMRLAVASIGAPFAANMTGWVFTEMGRQPFVVYPNPAMGVDQVYMFTAAAVSPGVTGEEVLVSLIVLVGIYAVL
+LGVEVFLLTRFVRGGVPAAMPELTAAEHS--DEQKRDRDDVLAFAY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001105.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001105.fa
new file mode 100644
index 0000000000000000000000000000000000000000..36d9feefcde45e60060ae6aae6fbadff71bd44d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001105.fa
@@ -0,0 +1,16 @@
+>0_1272
+MSITAVAEPAALTRSDRCDRCGAQAYVRAVLHSGGALQFCAHHARAVEDALRPQAALWQD
+ETDRLTAGA--
+>1_1002
+MSITAVAEPAALTRSDRCDRCGAQAYVRAVLHSGGALQFCAHHARAVEDALRPQAALWQD
+ETDRLTAGA--
+>2_1541
+MSITAVAEPAALTRSDRCDRCGAQAYVRAVLPSGGALQFCGHHARAVEDALRPQAAHWQD
+ETDRLTAGA--
+>3_1437
+MSITAVAEPAALTRADRCDRCGAQAYVRAVLPSGGELLFCGHHARGVEASLRPQAALWQD
+QTEELDGSTAA
+>4_1227
+MSITAVAEPAALTRSDRCDRCGAQAYVRAVLHSGGALQFCAHHARAVEDALRPQTALWQD
+ETDRLTAGA--
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001107.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001107.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c5a7f32d4bad295389135709e653d4182ee9b5c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001107.fa
@@ -0,0 +1,41 @@
+>0_1274
+--------MEAP-----------TSLDVPVLPARGPEDLLAYVGHALGRLPEGSLVLLTL
+RDGRLRAVVRVDLPPEEVDVGA--WACAVAEVCRRDAAADATLCLALPDGARATLARPGW
+AAALDDALASAGRPLTAAWTCARGRARPWWGSGVAEEGPL---DPRAAPLSLHLMTRGSV
+WDRAAVPDPVPRRGPAAARADDARWRPPEQDAPAARRAWLAQWESVLTGAARDRGAPAP-
+-------------------AVLGSPLTRPAWRDGLLLHAAAPSGAATGDPGDEERILTAA
+SGRAPAWDRLDALRAGLRALVPVATPAVAAQALALAGWVGWARGHGSDADAHLTAAAALS
+PDDPFVSVLRRIVAAGCVAGWATDPATAWRP-------DGGRP
+>1_1004
+--------MEAP-----------TSLDAPVLPARGPEDLLAYVGHALGRLPEDSLVLLTL
+HDGRLRAVVRVDLPPEEVDVDA--WACAVAEVCRRDAAADATLCLALPDGARATLTRPGW
+AAALDDALASAGRPLAAAWTCAHGRARPWWGSSIAEEGTL---DPRAAPLSLHLMTRGSV
+WDRAAVSDPVPRRGPAAARPDDARWRPPEQDAPPARRAWLAQWEPVLTGTARGRGAPAP-
+-------------------AVLGSPLTRPAWRDGLLLHAAAPSGAATGDPGDEERILTAA
+SRRAPAWDRLDALRAGLRALVPVATPAVAAQALALAGWVGWARGHGSDADAHLTAAAALS
+PGDPFVSVLRRIVAAGCVAGWATDPATAWRP-------DGGRP
+>2_1539
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------------MWLSQWESVLAG---ERGAAGPV
+TAEGTAPVSGTEEHPSADAAVLGAPLTLPSWRDALVLHAAVRPGDPPPEPAERERFLIAG
+SEQAPPWERLDRLRAGLRRLVPAAPPPAAAQALALAGWVGWARGQGSDAAAHLAAAAELA
+PDDPFVTLMRRVVDTGCVAGWAAHPDTAWRP----------GA
+>3_1435
+MRPRTLEGMDHPPAVPSAVPAGVTPPHLPVLRARGVDDLLGYAFHVLGTEPRESILLVTL
+ARARLRAVVRVDRPGRETPPAARHWAEAVAAVARRDAAADAVVCVSL-TGRAGGLEPPGW
+WPPLVRALRDRGIPAREGWGVVAGHAARWPVEPGAGPGPLEEVDPRHSDLSLHLIGAGSV
+WGLRAGHRSVPTPAALDPAAPDRPHWTAARARPEAPGPWLAAWERVLDGGGLPERPAGR-
+-------------------ARLGAGLEHPARRDALLIAAAGAAADELP-AAERAALLTGT
+RDPGPDWRRLDRLWDALRALAADAPAPCAAPALALAAWICWARGEGTAAGAHLDVARRLA
+PRDPLVGVLRRILDAGAVCAWAADPRRAWTPWDPQDPASGMRG
+>4_1229
+--------MEAP-----------TSLDVPVLPARGPEDLLAYVGHALGRLPEGSLVLLTL
+RDGRLRAVVRVDLPPEEVDVGA--WACAVAEVCRRDAAADATLCLALPDGARATLARPGW
+AAALDDALASAGRPLTAAWTCARGRARPWWGSGVAEEGPL---DPRAAPLSLHLMTRGSV
+WDRAAVPDPVPRRGPAAARADDARWRPPEQDAPAARRAWLAQWESVLTGAARDRGAPAP-
+-------------------AVLGSPLTRPAWRDGLLLHAAAPSGAATGEPGDEERILTAA
+TGRAPAWDRLDALRAGLCALVPAATPAVAAQALALAGWVGWARGHGSDADAHLTAAAALN
+PGDPFVSVLRRIVAAGCVAGWATDPATAWRP-------DGGGP
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001111.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001111.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5277d2a97bb33103caeae0f57ddc12c7ef0f39a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001111.fa
@@ -0,0 +1,45 @@
+>0_1278
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEILVEEDDTVEVGAPLATIGDGS
+GGGSADASEDDAA--AEEPAVEEAQQDDAQQEPAGEPAPEERASTDQGSDGAPS---AGGEASEVTLPALGESVTEGTVT
+RWLKSVGDEVEVDEPLLEVSTDKVDTEIPSPVAGTLLEIRAEEDDTVEVGAVLALVGSGSAGGGSAPSEGS----SGQDE
+ASAEEIEDKATEAEAPEETEEAAEAAGAEKSEKTPEASPSEEASRRESAERDSAQAESAEAPSATEPGQGYVTPLVRRLA
+HQNNVDLSTVRGTGVGGRIRKQDVLAAALASQAAAGGSEAPAEQASEAAAPSSAPAAASAPAASSSVDPSVRGEVEKAPR
+IRQVIAQRMRESLDLSAQLTQVHEVDVTRIVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEI
+TYHASEDIAIAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVGALFDTPIINQP
+QVAILGIGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAGRFLRTLRQRLEGGEFANELGL
+>1_1008
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEILVEEDDTVEVGAPLATIGDGS
+GGGSADASEDDAA--AEEPAVEEAQQDDAQQEPAGEPAPEERASTDQGSDGAPS---AGGEASEVTLPALGESVTEGTVT
+RWLKSVGDEVEVDEPLLEVSTDKVDTEIPSPVAGTLLEIRAEEDDTVEVGAVLALVGSGSAGGGSAPSEGS----SGQDE
+ASAEEIEDKATEAEAPEETEEAAEAAGAEKSEKTPEASPSEEASRRESAERDSAQAESAEAPSATEPGQGYVTPLVRRLA
+HQNNVDLSTVRGTGVGGRIRKQDVLAAALASQAAAGGSEAPAEQASEAAAPSSAPAAASAPAASSSVDPSVRGEVEKAPR
+IRQVIAQRMRESLDLSAQLTQVHEVDVTRIVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEI
+TYHASEDIAIAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVGALFDTPIINQP
+QVAILGIGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAGRFLTTLRQRLEGGEFANELGL
+>2_1535
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLQEILADEDETVEVGAPLATIGDGD
+GGGSSESDDDAQAEESEEPAAEEAQEDEEQQEPEGEPAPEERSST-QDSEEKSSGGASGGDASEVTLPALGESVTEGTVT
+RWLKAVGDEVEVDEPLLEVSTDKVDTEIPSPVAGTLLEIRAEEDETVEVGAVLALVGSGSAGGSSDSSDDSAKDDSAPDE
+ASAEEIEDKATEAETGEETEEAAQDAGEEKEEKAPEASASENASREESAEQEKAAA--ADAPEATSPGQGYVTPLVRRLA
+HQNDVDLSTVRGTGVGGRIRKQDVLAAALAQQAGSAESAPAQEQGSK----EQAAAASSAPAVASSVDPSVRGEVEKAPR
+IRQVIAQRMRESLDLSTQLTQVHEVDVTRIVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEI
+TYHASEDIAIAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVGALFDTPIINQP
+QVAILGTGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAGRFLTTLRQRLEGGEFANELGL
+>3_1431
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEILVEEDDTVEVGAPLATIGDGS
+GGGSADASEDDAA--AEEPAVEEAQQDDAQQEPAGEPAPEERASTDQGSDEAPS---AGGEDSEVTLPALGESVTEGTVT
+RWLKSVGDEVEVDEPLLEVSTDKVDTEIPSPVAGTLVEILANEDDTVEVGAVLARVGSGAA--PAASQDPA----PAADT
+ASPEEIEDKATEAPTGEQTEEAAEQAGDVKQEQAPAASPAETASAAPAASAPAAET------SASEPGPGYVTPLVRRLA
+KQNGVDLSTVRGTGVGGRIRKQDVLAASLANQASSGSASPAA------AEEQQTPAAASAPAPA-----AVRGETEKAPR
+IRQVIAQRMRESLDLSTQLTQVHEVDMTRIVQLRGKAKASFQEKNGVKLTYLPFITQAVTEALKQHPKLNASFSEDNKEI
+TYHASEDIAIAVDTDRGLLVPVVKDAGTLNLAGLAQKIADVAERTRTNKINPDELSGGTFSITNIGSVGALFDTPIINQP
+QVAILGTGAIVKRPMVVADADGNDTIAIRHMMYLSLTYDHRLVDGADAGRFLQTLKARLEGGEFAAELGL
+>4_1233
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEILVEEDDTVEVGAPLATIGDGS
+GGGSADASEDDAA--AEEPAVEEAQQDDAQQEPAGEPAPEERASTDQGSDEAPS---AGGEASEVTLPALGESVTEGTVT
+RWLKSVGDEVEVDEPLLEVSTDKVDTEIPSPVAGTLLEIRAEEDDTVEVGAILALVGSGSAGGGSAPSEGS----SGQDE
+ASADEIEDKATEAEAPEETEEAAEAAGAEKSEETPEASPSEEASRRESAERDSAQGESAEAPAATEPGQGYVTPLVRRLA
+HQNNVDLSTVRGTGVGGRIRKQDVLAAALASQAAAGGSEAPAEQASEAAAPSSAPAAASAPAASSSVDPSVRGEVEKAPR
+IRQVIAQRMRESLDLSTQLTQVHEVDVTRIVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEI
+TYHASEDIAIAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVGALFDTPIINQP
+QVAILGTGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAGRFLTTLRQRLEGGQFADELGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001114.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001114.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a528bca9ce65286bcf39268c528e5a1f083dee48
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001114.fa
@@ -0,0 +1,26 @@
+>0_1281
+MPETLLPPLRLLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE
+DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF
+GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG
+IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA
+>1_1011
+MPETPLPPLRVLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE
+DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF
+GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG
+IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA
+>2_1532
+MPETLLPPLRVLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE
+DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF
+GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG
+IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA
+>3_1428
+MPHALLPPVRVLGLAPDLIDYEEGWALQRTLHADVVAGRSDGEILLLEHEAVYTAGRRTE
+DADRPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEEVLIRTAAEF
+GVTAVRVDGRAGIWITA---REGDPRPDRKLGAIGLSIHDGVSMHGFSFNCSNSLTPYET
+IIACGIADASTTTLSVETGREVTPVDVLPVLVRHLEDLGPEHIALTPTEGTPA
+>4_1236
+MPETLLPPLRVLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE
+DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF
+GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG
+IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001115.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001115.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b78e55189f449628dbd707b89519b5ad0311ab0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001115.fa
@@ -0,0 +1,36 @@
+>0_1282
+MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC
+PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMEEPQKVAENIREMDLRYATV
+TGVARDDQKDGAAWLYAETIRRIHALNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN
+LETVPRIFKRIRPAFTYEKSLRVLTMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG
+CDIITITQYVRPSKLHHPIDRWVKPQEFVQWSQRAEEIGFQGVMAGPLVRSSYRAGKLYA
+QAMQRLGRTLPENLAHLAGEKTARQEASAVVAQMS
+>1_1012
+MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC
+PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMEEPQKVAENIREMDLRYATV
+TGVARDDQKDGAAWLYAETIRRIHALNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN
+LETVPRIFKRIRPAFTYEKSLRVLTMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG
+CDIITITQYVRPSKLHHPIDRWVKPQEFVHWSQRAEEIGFQGVMAGPLVRSSYRAGKLYA
+QAMQRLGRTLPENLAHLAGEKTARQEASAVVAQMS
+>2_1531
+MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC
+PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMDEPQKVAENIREMDLRYATV
+TGVARDDQKDGAAWLYAETIRRIHAFNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN
+LETVPRIFKRIRPAFTYEKSLKVLSMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG
+CDIITVTQYVRPSKLHHPIDRWVKPQEFVEWSRRAEEIGFQGVMAGPLVRSSYRAGKLYA
+QAMQRLGRTLPENLEHLAGEKTARQEASAVVAQMS
+>3_1427
+MTTAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNTVKGSGLHTVCEEAGC
+PNIFECWEDREATFLIGGDICTRRCDFCDIASGRPLPLDMDEPQKVAENIREMDLRYATV
+TGVARDDQKDGAAWLYAETIRRIHELNPSTGVEILPPDFGAVPELVQQVFDARPEVFAHN
+LETVPRIFKRIRPAFTYEKSLRVLTMAKEQELVTKSNLILGMGETDEEIDQALVDLHEAG
+CDIITITQYVRPSKLHHPIDRWVKPQEFVAWSQRAEEIGFAGVMAGPLVRSSYRAGKLYA
+QAMERLGREVPEHLAHLRGERTARQEAAAVVARMS
+>4_1237
+MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC
+PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMEEPQKVAENIREMDLRYATV
+TGVARDDQKDGAAWLYAETIRRIHALNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN
+LETVPRIFKRIRPAFTYEKSLRVLTMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG
+CDIITITQYVRPSKLHHPIDRWVKPQEFVQWSQRAEEIGFQGVMAGPLVRSSYRAGKLYA
+QAMQRLGRTLPENLAHLAGEKTARQEASAVVAQMS
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001116.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001116.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38f22dc01f10b6cb3a275621bdc228e32404d45c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001116.fa
@@ -0,0 +1,31 @@
+>0_1283
+MTKNSQPPASSSGSTSATLKEVKAMQRERRLREKEQAKAQRRDKRATKGPGVISQLKQAY
+AMTKAHDPKVGLWMLLAFLGALVVGLVIGLLLDNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVSEQPAAVNPKTQDLVYRAVGRPGVVLVTEGPSPR
+VAALVVKEEKAMRRFLPGVPVTVVESGNGQGQVPLHELPGTLKGMKKALTAQEVQAVDKR
+LTALNTNRLPIPKGVDPNKVRPSRRAMRGR
+>1_1013
+MTKNSQPPASSSGSTSATLKEVKAMQRERRLREKEQAKAQRRDKRATKGPGVISQLKQAY
+AMTKAHDPKVGLWMLLAFLGALVVGLVIGLLLDNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVSEQPAAVNPKTQDLVYRAVGRPGVVLVTEGPSPR
+VAALVVKEEKAMRRFLPGVPVTVVESGNGQGQVPLHELPGTLKGMKKALTAQEVQAVDKR
+LTALNTNRLPIPKGVDPNKVRPGRRAMRGR
+>2_1530
+MTKNSQPPASSSGSTSADLKQVKAMQRDRRRRVKEETRAQRRDKRANRGPGIISQLKQAY
+AMTKANDPKVGLWMLLAFVGVLVLGLVIGLLLNNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVPEQPVAVNPKTQDVVYRAVGRPGVVLVTEGPSNR
+IAALVGKEEKAMRRFLPGVPVTVVEAGNGQGQVPLHELPRTLKSMKKALTAQEVQAVDKR
+VNALNVNRLPIPKGVDPMKARPSRRAMRGR
+>3_1426
+MAKNPSTSPSSSGSSS--LKEVKAMQRDRRAQLKADAKAERAQKRANAGPGIISQLKQVF
+AITRQQNPRLVLWMVLAFASVLVLGLVVGLLLHNWITWLLLAIPFGVLAAVIVMNRLGER
+AMFDRLEGQTGAAGATLSSLGRGWIVGEQPSAVNPKTHDLVYRAIGKPGVVLVTEGPASR
+VGKLVSKEQKAMERFLPGVPVHVVETGRGEGQIPLREVPKTLKALPKKLTAQEVSAVDKR
+LSALGTQKPPIPKGVDPMRARPDRRGMRGR
+>4_1238
+MTKNSQPPASSSGSTSATLKEVKAMQRERRLREKEQAKAQRRDKRATKGPGVISQLKQAY
+AMTKAHDPKVGLWMLLAFLGALIVGLVIGLLLDNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVSEQPAAVNPKTQDLVYRAVGRPGVVLVTEGPSPR
+VAALVVKEEKAMRRFLPGVPVTVVESGNGQGQVPLHELPGTLKGMKKALTAQEVQAVDKR
+LTALNTNRLPIPKGVDPNKVRPSRRAMRGR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001117.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001117.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a3ab6c43a02b0d569642e380fcca5a80da4f95ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001117.fa
@@ -0,0 +1,26 @@
+>0_1284
+-------------------MARRAPDPA----QEPEPTRRDEPLITRRDLAGWVDGPGGG
+LAGGRWPGDLLGLPEHGPTSMATAARRAVALVIDWFLALGVSWLLFDSDAIATLMVFATM
+HILGITLLATTVGKAVCRTQVVRLG-GRTAPVHRVVVRTALLCLVLPAVVVGPDGRGMHD
+KVAGTVEIRM
+>1_1014
+-------------------MARRAPDPA----QEPEPTRRDEPLITRRDLAGWVDGPGGG
+LAGGRWPGDLLGLPEHGPTSMATAARRAVALVIDWFLALGVSWLLFDSDAIATLMVFATM
+HILGITLLATTVGKAVCRTQVVRLG-GRTAPVHRVVVRTALLCLVLPAVVVGPDGRGMHD
+KVAGTVEIRM
+>2_1529
+-------------------MARRAPDPA----QEPEPTRRDEPLITRRDLAGWVDGPGGG
+LAGGRWPGDLLGLPEHGPTSMATAARRAVALVIDWFLALGVSWLLFDSDAIATLMVFATM
+HILGITLLATTVGKAVCRTQVVRLG-GRTAPVHRVVVRTALLCLVLPAVVVGPDGRGMHD
+KVAGTVEIRM
+>3_1425
+MSCVFPACNASSGPDYPGGVAHRASDPAPRDRSERDAAGRAEPLISRADLAGWIDGPGGG
+RAGGRWPGDLLGLPEHGPASMATAARRAGALMIDWALALVVSNLAFGGDAIATLLVFAAM
+HVVGLTLLATTVGKALCRIQVVREGTGGTAPVHRVLIRTALLCLVLPAVVVGPDGRGMHD
+RVAGTVELHM
+>4_1239
+MVA-----------HYAGGVARRAPDPQ----DRTETTGRAEPLITRRDLAGWVDGPGGG
+RAGGRWPGDLLGLPERGPASMATAARRMGALVLDWFIALGISWLAFDADAIATLLVFAAM
+HVIGLTLLATTVGKAVCRIQVVRVG-GRPAGLLRILLRTALLCLVLPAVVVGPDGRGMHD
+KLADTVEIRM
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001118.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001118.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f34bb86f020f7769918cc62306aa0b717b6f1944
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001118.fa
@@ -0,0 +1,46 @@
+>0_1285
+MFTSPADVLAYIKDEGIEFVDVRFTDLPGMQHHFNVPASSVDEDFFVTGQLFDGSSIRGF
+AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS
+SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG
+GYFPVSPTDKQADLRDEICSVLAEVGLEVERSHHEVGAAGQAEINYRFNTLTHSADDLQK
+FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW
+YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR
+IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD
+EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV
+>1_1015
+MFTSPADVLAYIKDEGIEFVDVRFTDLPGMQHHFNVPASSVDEDFFVTGQLFDGSSIRGF
+AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS
+SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG
+GYFPVSPTDKQADLRDEICSVLAEVGLEVERSHHEVGAAGQAEINYRFNTLTHSADDLQK
+FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW
+YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR
+IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD
+EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV
+>2_1528
+MFTSPADVLAYIKEEGIEFVDIRFTDLPGMQHHFNVPASTVDEDFFTTGQLFDGSSIRGF
+AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS
+SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG
+GYFPVSPTDKQADLRDEICSVLAEVGLEVERSHHEVAAAGQAEINYRFNTLTHSADDLQK
+FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW
+YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR
+IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD
+EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV
+>3_1424
+MFTSVEDVLAYIKDEGVEFVDIRFTDLPGMQHHFNVPASTVDEDFFVTGQLFDGSSIRGF
+AGLAESDMQLIPDVTTAFVDPFRVRKTLAMNFSIVNPRTGEDYRRDPRGVAQRAEAYLAS
+TGIADTAFFAPEAEFYVFDDVRYESSARSSFYRVDSTEAHWNTSRDEEGGNLGHKTPRQG
+GYFPVTPVDKQADLRDEICAVLAEVGLEVERSHHEVGSAGQAEINYRFNTLTHSADDLQK
+FKYVVKNVAEMFGKSVTFMPKPVFGEAGSGMHCHQSLWLGGEPLFYDEKGYANLSDTARW
+YIGGLLQHASAVLAFTNPTVNSYRRLVPGFEAPVSMVYSQGNRSAGVRIPVTGSNPKAKR
+LEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPPEEAADIQKAPTSLE
+EALNALEEDHEFLLAGDVFTEELIRTWIDYKREMELTPLAARPNPYEFELYYSC
+>4_1240
+MFTSPQEVLTYIREEGVEFVDVRFTDLPGLQHHFNVPASSVDEDFFVTGQLFDGSSIRGF
+AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS
+SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG
+GYFPVSPTDKQADLRDEICAVLAEVGLTVERSHHEVGAPGQAEINYRFNTLTHSADDLQK
+FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW
+YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR
+IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD
+EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001119.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001119.fa
new file mode 100644
index 0000000000000000000000000000000000000000..59609b3e6293e8194a20506c13faed3f4d842081
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001119.fa
@@ -0,0 +1,75 @@
+>0_1287
+MSSLSTTGALPAVPDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRALLLWVRLAEREPRVHHALRD
+PETTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAATAPALAQPDPADGEPWGDASATLRRLLLDSVGADPDTDRPV
+AAVTGKDAAVALRRAYRRQLAAIALRDLDSAEPTAAMPSVGRWLADLAGATVDAALAVSRAVLTEREGPVVDRVDLAVIG
+MGKCGAGELNYVSDVDVVFAH---------AVREAADGADPDAE-VPDGPRAAALAAELAAGIGRVIQGAAPEPGLWEVD
+ANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGERYIAEIWPRVWESSSRDGFVESVRAMRARVL
+DTLAPAEREREIKLGPGGLRDVEFTAQLLQLVHGRADESLRVRGTLDAVRALHAASYITTRDARAFDEHYRWLRTLEHRI
+QLVHLRRTHLMPVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALSAEDVRLSAEA
+VRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGADPDGGLLAFRRLSESLGGTAWYLRMLRDSSD
+AARRLCLVLSGSRFVGDLLEHSPEAVAWVGDDRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVAL
+ADISGLLDLEAVTGALSDIDQVTVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVHRPRPGVDEGR
+AREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGRQGPLVRTLDSYREYYGRWAEVWERQALLRARPLAGDDDL
+ATDFRRWADGVRYAGDLTTADAREIRRIKARVEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGT
+LPALRAIARHGLLPEAEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTAGG-ELEERYLRVTRL
+ARQVFETRFYGL
+>1_1017
+MSALPDAATADA-PDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRALLLWVRLAEREPRVHHALRD
+PGTTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAATAPALAQPDPTAGEPWGDASAALRRLLLDSVGADPDADRPL
+AAVTGKDAAVALRRAYRRQLAAIALRDLDSAEPTAAMPSVGRWLADLAGATVDAALAVSRAVLTEREGPVVDRVDLAVIG
+MGKCGAGELNYVSDVDVVFAH---------AVREAADGADPDAQ-VPDGPRAAALAAELAAGIGRVIQGAAPEPGLWEVD
+ANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGERYIAEIWPRVWESSARDGFVESVRAMRARVL
+DTLAPAEREREIKLGPGGLRDVEFTAQLLQLVHGRADESLRVRGTLDAVRALHAASYVTTRDARAFDEHYRWLRTLEHRI
+QLVHLRRTHLMPVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALSAEDVRLSAEA
+VRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGADPDGGLLAFRRLSESLGGTAWYLRMLRDSSD
+AARRLCLVLSGSRFVGDLLEHSPEAVAWVGDDRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVAL
+ADISGLLDLEAVTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVHRPRPGVDEGR
+AREQAEEVVRTLMALLQKPVAPPLPGERRLEVDADLRPEGRQGPLVRTLDSYREYYGRWAEVWERQALLRARPLAGDDDL
+ATDFRRWADGVRYAQDLSAADAREIRRIKARVEAERLPRGADPARHVKLGRGGLSDVEWLVQSMQLKHAGQIEDLRVTGT
+LPALRAIARHDLLPESEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTTGG-ELEERYLRVTRL
+ARQVFETRFYGL
+>2_1526
+MSALPDAATADA-PDRRALAQAGVADARRVQSLLASPEFEGADVAPLVKRLGHAADPDRALLLWVRLAEREPRVHRALRD
+PETTARLLRLLGASEALGEFLIRRPEHLDLVLEPESAAATAPALAQPDPADGEEWADEPAALRRLLLEAVEADPDADRPR
+AGLTGADAAVALRRAYRRQLAAIALRDLDSADPAAVMPSVGRWLADLAGAAVDAALAVSRATLAEREGPAVDRVDLAVIG
+MGKCGARELNYISDVDVVFVHELLDPGPDAAGEAGADGADGEASDAVDGTRAAVLAAELAAGIGRVIQAAAPEPGLWEVD
+ANLRPEGKDGALSRTLDSHAEYYRRWAHGWEFQALLKARPIAGSADLGARYLERIWPRVWESSAREGFVDSVRAMRSRVL
+ETIAPAEREREIKLGSGGLRDVEFTAQLLQLVHGRADESIRVRGTLDAVRALHEASYISTRDAAAFDEHYRWLRTLEHRI
+QLVHLRRTHLMPVKDEALRIVARSLRGAQETGPATGEDLQAAFTRVRRAVRGLHETVFYRPLLSTTAALSDDEVRLSAEA
+VRERLAALGYRDPKGALRHIEALTQGVSRRAAIQRQLLPAMLGWFAEGADPDGGLLAFRRLSESLGGTAWYLRMLRDSSD
+AARRLCLVLAASRFVGDLLEHSPEAVAWVGDDRELEPRGTVQLWRQADARLDRRIEAQETPAAVRHVRQVRRSETLRVAL
+ADISGLLDLEAVTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVHRPRPGVDEGR
+AREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGRQGPLVRTLDSYREYYGRWAEVWERQALLRARPLAGDDDL
+ATDFRRWADGVRYAGDLTTADAREIRRIKARVEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGT
+LPALRAIARHGLLPEAEVAVLEEAWLLASRIRAAVLLWTGKVGDVLPTNMRDLEAIARLSGVGTAGG-ELEERYLRVTRL
+ARQVFEARFYGL
+>3_1422
+MAPTPDSHVPGP---RRALVHAGVADLTRAERLLSSPELAEQDADAALAALAHAADPDSALLLYIRLAERDPQVHRVLAE
+ADRARDLLRLLGASEALGEFLIRRPEHLDLVLDPARAAATAPALAQQDPTDGGDWHDEPAALRALLLEAVGADPAADQPV
+AGLTGADASVALRRAYRRQLTAIALADLASREPTLVMPAVGRWLADLAGAALEAALAVSRAELRAREGAAVDCVELAVIG
+MGKCGARELNYVSDVDVVFVHDVLEPG------------APDA---PSAQEAARLAAELAAGISRVLSGPAPEPGLWEVD
+ANLRPEGRDGALSRTLDSHVEYYRRWAHGWEFQALLKARPVAGSPALGERYVAAVWPRVWESSAREGFVENVRAMRTRVL
+DTIARDERDREIKLGAGGLRDVEFTAQLVQLVHGRADESVRVRGTLDALRVLHAASYISSRDMRAFDAAYRWLRLLEHRI
+QLVHLRRTHLMPVKEGPRRVVARSMRGAGDVHPVAGDDLQDRFSRVRREVRALHETVFYRPLLSTTAALSDEDVRLSADA
+VQARLSALGYRDPRRALAHIEALTRGVSRRAAVQRQLLPAMLGWFADGADPDAGLLAFRRLSESLGSSPWFLRMLRDSTD
+AARRLCLVLAGSRRVGDLLEHAPESVAWIGETRELAPRGLSALTSEVTARLDRRSPEESAAQVIRHVRQIRQREILRTAL
+ADITGVVGLEEVGHALADVDQAAVQGALRVAGQAVLDGADPLTEVVVVAMGRQGGREIAYGSDLDAMFVHRPLAGADETA
+AAAQAEAVARQLMALLQQPAAPPLPSEQPLDVDADLRPEGRQGPLVRTLDSYREYYARWAEVWERQALLRARVVAGPAGL
+AEEFTAWADGVRYGDELSAGDAREIRRIKARVEAERLPRGADPARHVKLGRGGLSDVEWLVQSLQLRHAHDEPELRVTGT
+LPALRALARLDLLPPSEAALLEEAWLLATRVRSALVLWTGKGSDVLPTNARDLGALARLAGDACGGGVAFEERYLRVTRQ
+ARQVFEQRFYGL
+>4_1242
+MSALPDAATADA-PDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRALLLWVRLAEREPRVHHALRD
+PGTTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAATAPALAQPDPTAGEPWGDASAALRRLLLDSVGADPDADRPL
+AAVTGKDAAVALRRAYRRQLAAIALRDLDSAEPTAAMPSVGRWLADLAGAAVDAALAVSRAVLTEREGPVVDRVDLAVIG
+MGKCGAGELNYVSDVDVVFAH---------AVREAADGADPDAQ-VPDGPRAAALAAELAAGIGRVIQGAAPEPGLWEVD
+ANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGERYIAEIWPRVWESSARDGFVESVRAMRARVL
+DTLAPAEREREIKLGPGGLRDVEFTAQLLQLVHGRADESLRVRGTLDAVRALHAASYVTTRDARAFDEHYRWLRTLEHRI
+QLVHLRRTHLMPVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALSAEDVRLSAEA
+VRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGADPDGGLLAFRRLSESLGGTAWYLRMLRDSSD
+AARRLCLVLSGSRFVGDLLEHSPEAVAWVGDDRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVAL
+ADISGLLDLEAVTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVHRPRPGVDEGR
+AREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGRQGPLVRTLDSYREYYGRWAEVWERQALLRARPLAGDDDL
+ATDFRRWADGVRYAGDLTTADAREIRRIKARVEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGT
+LPALRAIARHGLLPEAEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTAGG-ELEERYLRVTRL
+ARQVFETRFYGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001120.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001120.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4f257009c7484b0180597b0cf839c630ea65c475
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001120.fa
@@ -0,0 +1,46 @@
+>0_1288
+MDRQQDYVLRTIEDRDVRFVRLWFTDVIGTLKSVALSPAEVENAFTEGLGFDGSSIDGYT
+RISESDMLLQPDPSTFQILPWRGDQGQSSRMFCDVLTPDGRPAPADPRHVLRRVLDRAAD
+RGFTCFTHPEIEFYLLQSDQPGPDGEPVPVDRAGYFDNVPGSDAADFRRDAVSLLEGMGI
+SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSHHPG
+SGMHTHFSLFEGDANAFYDPADEFRLSVTGRRFIAGLLRHSVEITAVTHQFVNSYKRLWG
+GGEAPSYTSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLIAAGLKGI
+EEGYEVPEAAAEDISALTTHERRVLGHVPLPGTLHDALRTAEESEFVASVLGEHVFDALL
+RNKRQEWDDYRVEVTPYELRRYLSGL
+>1_1018
+MDRQQDYVLRTIEDRDVRFVRLWFTDVIGTLKSVALSPAEVENAFTEGLGFDGSSIDGYT
+RISESDMLLQPDPSTFQILPWRGDQGQSSRMFCDVLTPDGRPAPADPRHVLRRVLDRAAD
+QGFTCFTHPEIEFYLLQSDQPGPDGEPVPVDRAGYFDNVPGSDAADFRRDAVSLLEGMGI
+SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSEHPG
+SGMHTHISLFEGDSNAFYDPADEFRLSVTGRRFIAGLLRHSVEISAVTHQFVNSYKRLWG
+GGEAPSYVSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLIAAGLKGI
+EEGYELPESAAEDVSALTTHERRVLGHVPLPGTLHDALRAAEESEFVASVLGEHVFDALL
+RNKRQEWDDYRVEVTPYELRRYLSGL
+>2_1525
+MDRQQDYVLRTIEDRDVRFVRLWFTDVVGTLKSVALSPAEVENAFAEGLGFDGSSIDGYT
+RISESDMLLQPDPATFQILPWRGDGGQSSRMFCDVLTPDGRPAPADPRHVLRRVLEKASD
+MGFSCFMHPEIEFYLLTSDQPGPDGRPVPVDRAGYFDNVPGSDAADFRRDAVTLLESMGI
+SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSEHPG
+SGMHTHISLFEGDSNAFYDPADEFRLSVTGRRFIAGLLRHSVEISAVTHQFVNSYKRLWG
+GGEAPSYVSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLLAAGLKGI
+EEGYELPESAAEDVSALTTHERRVLGHDPLPGTLHDALRAAEESEFVASVLGEHVFDALL
+RNKRQEWDDYRVEVTPYELRRYLSGL
+>3_1421
+MDRQQDFVLRTIEDRDVRFVRLWFTDVIGTLKSVALAPAEVEAAFTEGLGFDGSSIDGYT
+RISESDMLLQPDPATFQILPWRGEAGQTSRMFCDVLTPDGRPAPADPRNVLRRVLDKASD
+MGFSCYTHPEIEFYLLASDRPGPDGRPVPVDSAGYFDHVPGGAAQDFRRDAVTLLEDMGI
+SVEFSHHENGPGQNEIDLRAADALTTADNVQTFRTIMKEVAARQGHYATFMPKPFGDQPG
+SGMHTHFSLFEGDSNAFYDPADEFRLSVTGRRFIAGLLKHSVEISLVTHQFVNSYKRLWG
+ADEAPAYVSWGHNNRSALVRVPLYKPDKAGSARIEYRGLDASANPYLAYALLLAAGLKGV
+EENYDLPEPASEDVGALTPQERRVLGHVSLPGTLHDAVRAAEESEFVADVLGEHVYEALL
+RNKRQEWDDYRVEITPYELRRYMTGL
+>4_1243
+MDRQQDYVLRTIEDRDVRFVRLWFTDVIGTLKSVALSPAEVENAFTEGLGFDGSSIDGYT
+RISESDMLLQPDPSTFQILPWRGDQEQSSRMFCDVLTPDGRPAPADPRHVLRRVLDRAAD
+RGFTCFTHPEIEFYLLQSDQPGPDGEPVPVDRAGYFDNVPGSDAADFRRDAVSLLEGMGI
+SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSHHPG
+SGMHTHFSLFEGDANAFYDPADEFRLSVTGRRFIAGLLRHSVEITAVTHQFVNSYKRLWG
+GGEAPSYTSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLLAAGLKGI
+EEGYELPESAAEDVSALTTHERRVLGHVPLPGTLHDALRAAEESEFVASVLGEHVFDALL
+RNKRQEWDDYRVEVTPYELRRYLSGL
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001123.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001123.fa
new file mode 100644
index 0000000000000000000000000000000000000000..236986a22f5ebc65bdb7b74f76caa95a73df629f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001123.fa
@@ -0,0 +1,36 @@
+>0_1292
+MSQRQNPVAPSSHNGPRPAGPTAPEPGSFAPVGTLTPGAPSPAPPVPAAIPRPEYVGKAT
+PDEGKASDVYDAAGVERIRAAGRLAAQAMEHTAAHIRPGVTTDELDRIAHAFLVERGAYP
+SCLGYRGFPRSICTSINEVICHGIPDGTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHDRLLVPGMVFTIEPMLTLGTIEWDQWDDGWTVVTRDRRRTAQFEHT
+IVVTDDGAEILTLP
+>1_1021
+MSQRQNPAVPSSHNGPRPAGPTAPEPGSLAPVGTLTPGAPSPAPPVPAAIPRPEYVGKAT
+PDEGNASDVYDAAGIERIRAAGRLAAQAMEHTAAHIRPGVTTDELDRIAHAFLVERGAYP
+SCLGYRGFPRSICTSINEVICHGIPDGTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHDRLLVPGMVFTIEPMLTLGTIEWDQWDDGWTVVTRDRRRTAQFEHT
+IVVTDDGAEILTLP
+>2_1522
+MSHRQSTASPSSHNGPRPEGPAAPQPGSLAPVGTLTPGAPSPAPPVPASIPRPEYVGRAT
+ADEGNASDVYDAAGIERIRAAGRLAARAMEHTAAYIRPGVTTDELDRIAHAYLVEHGAYP
+SCLGYRGFPRSICTSMNEVICHGIPDSTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHDRLLEPGMVFTIEPMLTLGTIDWDQWDDGWTVVTRDRRRTAQFEHT
+LVVTDDGAEILTLP
+>3_1418
+MSTTARPTSQPSHNGPRPEGPPAPEPGSRAPLGTLTPGAPSPAPAVPASIVRPEYVGRAT
+ADEGNASDVYDTEGIGRIREAGRIAAQAMEHTAEHIRPGITTDELDRIAHEFIVAAGAYP
+SCLGYRGFPRSICTSVNEVICHGIPDGTVLEDGDIVNLDITAYKDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIKAVKPGREINVIGRAIESYARRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHNRLMVPGMVFTIEPMITLGGIDWEQWDDGWTVVTKDRRRTAQFEHT
+LVVTEDGAEILTLP
+>4_1246
+MSQRQNPAVPSSHNGPRPAGPTAPEPGSLAPVGTLTPGAPSPAPPVPAAIPRPEYVGKAT
+PDEGKASDVYDAAGIERIRAAGRLAAQAMEHTAAHIRPGVTTDELDRIAHAFLVERGAYP
+SCLGYRGFPRSICTSINEVICHGIPDGTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHDRLLVPGMVFTIEPMLTLGTIEWDQWDDGWTVVTRDRRRTAQFEHT
+IVVTDDGAEILTLP
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001124.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001124.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0bf93e2a7cd42e54a2d86163b43c0807c367d133
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001124.fa
@@ -0,0 +1,21 @@
+>0_1294
+MHCPFCRHEDSRVVDSRSLDDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRATGNAEVDAHDVGLAILDPLRRLDQVA
+FLRFASVYRDFESLDDFEEAIAELRAGDGDDRGRPAVQPRLFTR
+>1_1023
+MHCPFCRHEDSRVVDSRSLDDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRATGNAEVDAHDVGLAILDPLRRLDQVA
+FLRFASVYRDFESLDDFEEAIAELRAGDGDDRGRPAVQPRLFTR
+>2_1520
+MHCPFCRHEDSRVVDSRSLEDGSAIRRRRQCQSCGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRASGNAEVDAHDVGLAILDPLRRLDQVA
+FLRFASVYRDFESLDDFADAIAELRAGT-DERGRPAVQPRLFSR
+>3_1416
+MHCPYCRHEDSRVVDSRSLEDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVSSDDLAVLAQEVEEAVRASGNAEVDAHEVGLAILGPLRRLDQVA
+YLRFASVYRDFESLSDFEDAIAELRAQEGEAPGRPAVQPRLFSR
+>4_1248
+MHCPFCRHEDSRVVDSRSLDDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRATGNAEVDAHDVGLAILDPLRRLDQVA
+FLRFASVYRDFESLDDFEEAIAELRAGDGDDRGRPAVQPRLFTR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001126.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001126.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f9de8c799982095bc208a21955294f817b61ba6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001126.fa
@@ -0,0 +1,36 @@
+>0_1296
+MGMRPGLTERLEVTEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA
+KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG
+PTVVGALAALGYDITTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK
+VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLEDGRPSVTHYETLEVFGRATLLEVHL
+ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLAFPHPVTGEPVTI
+TSPYPDDLAHALAALRGDE------D
+>1_1025
+MGMRPGLTERLQVAEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA
+KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG
+PTVVGALAALGYDITTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK
+VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDDGRPSVTHYATLEVFGRATLLEVHL
+ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLAFPHPVTGEPVTI
+TSPYPDDLAHALAALRGDE------D
+>2_1518
+MEPIPGATARIEVTPDRAGRRADAVLAEVLGLSRSALADWFSRGLVRAESRTGRRDRVLA
+KSAKAVAGEVLAVDVPDDPDPLEVRAERVDALRILHEDEHLIAVDKPTGVAAHPSPGWAG
+PTVVGALAALGHDISTSGAPERQGIVHRLDVGTTGVMVVAKTEQAYAALKDQFRRRVPEK
+VYHALVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDGGRPSVTHYETLEVFGRATLLEVHL
+ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLSFPHPVTGEPVSV
+TSEHPDDLAHALARLRRDG------S
+>3_1414
+MGLRPGLTERLAVTEDDAGRRADAVLADAFGVSRASLADLFSRGLVRAESRTGRRDRVLA
+KSAKAVAGETLAVDVPVDPDPLEVRAERVDAMTVLYEDDDLLAVDKPTGVAAHPSPGWFG
+PTVVGGLAGLGRRISTSGAPERQGIVHRLDVGTTGVMVVAKSERAYTALKDQFRERVPEK
+VYHAVVQGMPDPLEGTIDAPIGRDPNHHWRFAVLEGGRPSVTHYETVEAFGRATLLEIHL
+ETGRTHQIRVHTSALRHPCAGDLTYGADPRLAAELGLTRQWLHAHRLALPHPATGERLEI
+VSPYPDDLAHALRVLRGEDRGAAPDA
+>4_1250
+MGMRPGLTERLEVTEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA
+KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG
+PTVVGALAALGRDISTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK
+VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDDGRPSVTHYETLEVFGRATLLEVHL
+ETGRTHQIRVHTSALRHPCVGDLTYGADPRMAAELGLTRQWLHAHRLAFPHPVTGEPVTI
+TSPYPDDLAHALAALRGDA------D
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001128.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001128.fa
new file mode 100644
index 0000000000000000000000000000000000000000..95e3c25ca50580f7d02bb9f3bfa3b0a5efd1ae61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001128.fa
@@ -0,0 +1,26 @@
+>0_1298
+MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA
+APAAGPAADTP----EAAATPASAEESAPAA-------------APESADAAATSAAGVL
+AMAQRLHDEHVAAGEQRSTELVAEAEATAARLVSDAEEQKARTLEALAEEKAGLEGEVEQ
+LRSFETDYRSRLTSYIEGQLREIRAQKRVEPPTPTA
+>1_1027
+MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA
+A----PVADTP----EAAETPSPVEEPAPAA-------------APEAADAAATSAAGVL
+AMAQRLHDEHVAAGEQRSTELVAEAEATAARLVSDAEEQKARTLEALAEERAGLEGEVEQ
+LRSFETDYRSRLTSYIEGQLREIRAQKRVEPPTPTA
+>2_1516
+MALSWEDVVNKQFQPTKFREGYDQGEVDDFLDEIVGELKRLQGLNEQLTAENEALRAGGA
+VPDADAAVDAPVADADAAAVVDAGQSPAPAALAD-AEPGLEVEPTPSSADPASASAAGVL
+AMAQRVHDEHVAAGEQRRDELISEAEARAEALVAEAEETRTRTLEELAADKAGLEAEVEQ
+LRGFETDYRSRLTAYIEGQLREIRSQERVEPAQRPA
+>3_1412
+MVLSWEDVVNKEFQLTKFREGYDREEVEDFLDEVVEELKRLTEENDRLRSDLDACREGAP
+---AQAEASAPAAGEAAPAL----QAPAPVAPVEPSAPG-----EPVAPTDSATSAAGVL
+AMAQRLHDEYVAEGEQRRDRIIADAEAEATTVVRQAEETRTRTLSDLESRRKGLEADVER
+LRAFETDYRSRLTAYIEGQLREITAQERLEPAKGTV
+>4_1252
+MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA
+APAAAPAADTP----EAAATPASVEEAAPAA-------------APESADAAATSAAGVL
+AMAQRLHDEHVAAGEQRSTELVAEAEATAARLVSDAEEQKARTLEALAEEKAGLEGEVEQ
+LRSFETDYRSRLTSYIEGQLREIRAQKRVEPPTPTA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001131.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001131.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d7e854d7b364e3ff42afea92a69030bb6b07fea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001131.fa
@@ -0,0 +1,31 @@
+>0_1301
+MTAPATAGPTPTDP----RAREIADALAAVHARIADAARDAGREAEPALVVVTKTHPAED
+VVRLAALGVTDVGENRDQEARPKAEAVAAALGAD---APRWHFVGQLQTNKAKYVVRYAS
+VVESVDRPELAEALSRALVLRREREPEAAIPDLECLVQVDVDDRADEDRPEGIGPRGGAR
+PEDVPALADVIAGLPGLRLGGLMCVAPRGLDPEHAFRRLAALGARLRQTHPEATALSMGM
+SADLEAAVRAGATQVRIGSDVLGARDAVG
+>1_1030
+MTAPATAGPTPTDP----RTREIADALAAVRARLADAARDAGREAEPALVVVTKTHPAED
+VVRLAALGVTDVGENRDQEARPKAEAVAAALGAD---APRWHFVGQLQTNKAKYVVRYAS
+VVESVDRPELAEALSRALLLRREREPEAAIPDLECLVQVDVDDRADEDRPEGIGPRGGAR
+PEDVPALTDAIAGLPGLRLGGLMCVAPRGLDPEDAFRRLAALGAHLRQTHPEATALSMGM
+SADLEAAVRAGATQVRIGSDVLGARDAVG
+>2_1513
+MSTPEQH-PTPHDAAAETRTREIAAGLAAVRERIARAAREAGRADEPALVVVTKTHPAED
+VVRLAGLGVAAVGENRDQEARPKAAAVAEALGDA---APRWHFIGQLQTNKAKHAARYAS
+VVESVDRTELAEALSRALVLRREREPGVEVPDLECLVQVDVDDRADEDRPEGIGPRGGAA
+PEDVPALAAAIAALPGLRLGGLMCVAPRGLDPEASFRRLAALGEELRSAHPDASTLSMGM
+SADLESAVRAGATQVRIGSDVLGARPAVG
+>3_1409
+MAE-----PLQDDP----RVAEIAAGLDGVRRRIADAAAAAGRADLPELIVVSKTHPAED
+VVALAGLGVRQVGENRDQEARPKAAAVAEALGGAGVPAPAWHFIGQLQTNKAKHVARYAS
+AVHSVDRLDLVDALSRAVVLRREREGADAVSALDCLVQVDVDDRADEDRPEGIGPRGGAA
+PEDVPELARAIAAADGLRLRGLMCVAPRAADPAAAFARLAALSARVRAEHPDADALSMGM
+SGDLEAAVAAGATHVRVGSDILGARGAVG
+>4_1255
+MTAPATAGPTPTDP----RAREIADALAAVRARIADAARDTGRAAEPALVVVTKTHPAED
+VVRLAALGVTDVGENRDQEARPKAEAVAAALGAD---APRWHFVGQLQTNKAKYVVRYAS
+VVESVDRPELAEALSRALLLRREREPEAAIPDLECLVQVDVDDRADEDRPEGIGPRGGAR
+PEDVPALADVIAGLPGLRLGGLMCVAPRGLDPEDAFRRLAALGAGLRQTHPEATALSMGM
+SADLEAAVRAGATQVRIGSDVLGARDAVG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001133.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001133.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2e20ef204ae708e777dbc37af7c88e1dc887fdc2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001133.fa
@@ -0,0 +1,46 @@
+>0_1303
+---MAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLD
+VGRELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARI
+ARSLGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVM
+DAFRQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKA
+AELAIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDD
+ALGDEVRVTVIAAGFDKVDVTSAPAAPQAVQQQAAPQRAAAPAQPQPA-AQPQPA-----
+-APAQ---PQQAERPAVRGTVPL--------APQEQQ--------------PRRQQDLPT
+VVEPDLGAGSSDLDVPDFLK
+>1_1032
+---MAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLD
+VGRELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARI
+ARSLGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVM
+DAFRQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKA
+AELAIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDD
+ALGDEVRVTVIAAGFDKVDVTSAPAAPQAAQQQAAPQRAAAPAQPQP-------------
+-VPAQ---PQQAERPAVRGTVPL--------APQEQQ--------------PRRQQDLPT
+VVEPDLGAGSSDLDVPDFLK
+>2_1511
+MDTVAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLD
+VGRELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARI
+ARSLGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVM
+DAFRQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKA
+AELAIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDD
+ALGDEVRVTVIAAGFDKVDATSAPASPQAGQFQQAPQRPAQQAQPQQQ-A---PAPQQHQ
+AQPAQQEQPQQVQPQSVRGTVPL--------APQQPQQTE-----------QRRQQDLPT
+VVEPDLGAGSSDLDVPDFLK
+>3_1407
+MDTVAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLD
+VGRELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARI
+ARSLGALTIGVVTRPFTFEGRRRAGSAENGIDALRDEVDTLIVIPNDRLLSISDRNVSVM
+DAFRQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKA
+AELAIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDD
+ALGDEVRVTVIAAGFDKVDATSAPAAP--FQQQAAPQRAAAPQQPAQQ-A--------QQ
+APVSQQAAPQ---RPSVPGTMPLNSSSAFGGAPAQPAATQQPAAPQQPAAPQRAQQDLPT
+VVEPEF--GSSDLDVPDFLK
+>4_1257
+---MAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLD
+VGRELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARI
+ARSLGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVM
+DAFRQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKA
+AELAIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDD
+ALGDEVRVTVIAAGFDKVDVTSAPAAPQAVQQQAAPQRAAAPTQPHPVPAQPQPAPAQPQ
+PAPAQ---PQQAERPAVRGTVPL--------APQEQQ--------------PRRQQDLPT
+VVEPDLGAGSSDLDVPDFLK
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001136.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001136.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac8fdbd614f2a4ab6ce442a00f42191d92a4eb47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001136.fa
@@ -0,0 +1,41 @@
+>0_1306
+MTQTSHPSGPLRVVLAGGGTAGHISPMLAIARALEGDGGGPVECTMVGTASGMETRLVPE
+AGYELDLIDRVPMPRRPSMDVVRFPARMRAAVATAARILRDRRADVVVGVGGYVATPVYL
+AAFRAGVPVVVHEANARPGLANRIGALRATHVGTALPDTRLRGARWVGMPMRPEISGLDR
+AAARRAAREALGLDPDRTTVVVTGGSSGALAVNRTVRAALGDLLDAGLQVFHLTGRDKAL
+TEDDGSLLVRDGYVQREYLAGMEQAYAAADLIVARSGAGTVCEVSAVGLPAVYVPLPIGN
+GEQALNARPVVEAEGALLVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV
+TMAGLVRSAAQEGARR
+>1_1035
+MTQTSHPSGPLRVVLAGGGTAGHISPMLAIARALEGDGGGPVECTMVGTASGMETRLVPE
+AGYELDLIDRVPMPRRPSMDVVRFPARMRAAVATAARILRDRRADVVVGVGGYVATPVYL
+AAFRAGVPVVVHEANARPGLANRIGALRAAHVGTALPDTRLRGARWVGMPMRPEISGLDR
+AAARRAAREALGLDPDRTTVVVTGGSSGALAVNRTVRAALGDLLDAGLQVFHLTGRDKAL
+TEDDGSLLVRDGYVQREYLAGMEQAYAAADLIVARSGAGTVCEVSAVGLPAVYVPLPIGN
+GEQALNARPVVEAEGALLVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV
+TMAGLVRSAAQEGARR
+>2_1508
+MPQTPDPARELRVVLAGGGTAGHISPMLAIARALESDDAGPVRCTMVGTASGMETRLVPE
+AGYELDLIERVPMPRRPSMDVVHFPARMRAAVAAAGRILAERRADVVVGVGGYVATPVYL
+AAFRAGVPVVVHEANARPGLANRIGALRAAHVGTALPDTRLRGARWVGMPMRPEISGLDR
+AAQRRAARAALGLDPERTTVVVTGGSSGALAVNRTVRDSLDDLLGAGLQVFHLTGRDKAL
+TEADGTPLRREGYVQREYLDGMEQAYAAADLLVARSGAGTVCEVSAVGLPAVYVPLPIGN
+GEQALNARPVVEAEGALTVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV
+TMAGLVRSAAEEGARR
+>3_1404
+MTTPNDASRPLRVVLAGGGTAGHISPMLAIARALGRQDPSTV-CTMVGTDSGMETRLVPQ
+AGYELDFVERVPMPRRPSMDVVRFPGRFQASVRQAGEILRRRGADVLVGVGGYVSTPMYL
+AASRAGVPVVVHEANARPGLANRVGALRAARVGTALPDTRLPKAQWVGMPMRPEISGLDR
+AAARDAARAELGLDPERTTVVVTGGSSGALNVNRTVRESLDDLLGAGLQVFHLTGRGKEL
+TDEAGQRVTRPGYVQREYLDGMEKAYAAADLIVARSGAGTVCEIAAVGLPAVFVPLPVGN
+GEQALNARPVVDAGGALLVRDETFRADWVRRELIPLATDPQRLAAMGEAAARLGVRDADV
+RTADLVREAAREGARR
+>4_1260
+MTQTSHPSGPLRVVLAGGGTAGHISPMLAIARALEDDGGGPVECTMVGTASGMETRLVPE
+AGYELDLIDRVPMPRRPSMDVVRFPARMRAAVATAARILRDRRADVVVGVGGYVATPVYL
+AAFRAGVPVVVHEANARPGLANRIGALRATHVGTALPDTRLRGARWVGMPMRPEISGLDR
+AAAGRAAREALGLDPDRTTVVVTGGSSGALAVNRTVRAALGDLLDAGLQVFHLTGRDKAL
+TEDDGSLLVRDGYVQREYLAGMEQAYAAADLIVARSGAGTVCEVSAVGLPAVYVPLPIGN
+GEQALNARPVVEAEGALLVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV
+TMAGLVRSAAQEGARR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001142.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001142.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df2097b150f994a1cc94fc7d07c7125269e43aa2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001142.fa
@@ -0,0 +1,26 @@
+>0_1313
+MTLHEEMSMAAHARIAESL----RPGSTPVAPARPTPQERTPLSVVPAPLPRSRSGVTVL
+CVLVVLAALAAVLVMNITMSNRQYALLDLRQEQQAVTETNERLAEQVGHLEAPQNLAARA
+DALGMVAPAGTASVDAGTGQFSGEAQAAQDGDISATYVAPPADADAVRQGTAGDG---QD
+EIEGPRTLG------GEDASAAPDQDAAD----R
+>1_1042
+MTLHEEMSMAAHARIAESL----RPGSTPVAPARPAPQERTPLSVVPAPLPRSRSGVTVL
+CVLVVLAALAAVLVMNITMSNRQYALLDLRQEQQAVIETNERLAEQVGNLEAPQNLAARA
+DALGMVAPAGTASVDAGTGEFGGEAQAAQDGDVSATYVAPPADADVVRQGASAEG---QD
+EIEGPRTLG------GEDASAAADQDAAD----R
+>2_1502
+MTLHEEMSMAAHARIAEPL----RHTG---APARPAPQERTPLSVVPAPLPRSRSGMTVL
+CVVVLLAALAAVLVMNITMSNRQYALLDLRQEQQAVTEVNERLAEQVGYLEAPQNVAARA
+DALGMVAPAGTASVDAATGEFRGEAQPAREGEISATFVAPPVNADAVRQGSAGSADADRG
+DIEGPRTLG--APAAAPGAAASDDRDASD----R
+>3_1397
+MTAYEETGMSAQAWRDEARTAWPRTGATPEREHR----QRTPLSVVPTPLPRSGSGVAVL
+CGLVLLVALGLVLVMNITMSNRQFTLLDLRAQQTTLTETNERLAEQAGYLDAPQNLAARA
+GAMGMVSPGATSTVDVASGAVAGPSTGAGSTTLPEGRIAPPADADLARQGEA------QG
+QIPGPRTVDPAAPTAAPSGETAPTPAPTDAPAGR
+>4_1267
+MTLHEEMSMAAHARIAESL----RPGSTPVAPARPTPQERTPLSVVPAPLPRSRSGVTVL
+CVLVVLAALAAVLVMNITMSNRQYALLDLRQEQQAVTETNERLAERVGHLEAPQNLAARA
+DALGMVAPAGTASVDAGTGQFSGEAQAAQDGDISATYVAPPADADAVRQGTAGDG---QD
+EIEGPRTLG------GEDASAAPDQDAAD----R
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001143.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001143.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c5171ab16dd99d6343cc6fd88c71e3a8db20046d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001143.fa
@@ -0,0 +1,36 @@
+>0_1314
+MDAGQPRPEDRHLPVMRDRVVDLLAPAVQAALEAGRTPVAVDGTLGMGGHTEALLTRFPH
+LRVIGIDRDVHAQAMAVERLGPLAERLIPFHGTYDRVPEAMAAAGVTKVDAALYDLGVSS
+YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEQELRRIIRRDGEERFAGPIAR
+AIVRARDEAPIETTGRLVEVIRSAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP
+AILDALHVGGRLVVMSYHSLEDRITKRHLSAWATSTAPPGFPVVLEEHEPVVRVLTRGTE
+KPTEEEISENRRASSARVRAVEKIRTSRTTA
+>1_1043
+MDAGQPRPEDRHLPVMRDRVVDLLAPAVQAALEAGRTPVAVDGTLGMGGHTEALLTRFPH
+LRVIGIDRDVHAQAMAAERLGPLADRLIPFHGTYDRVPEAMAAAGVTKVDAALYDLGVSS
+YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEQELRRIIRRDGEERFAGPIAR
+AIVRARAEAPIETTGRLVEVIRSAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP
+AILDALHVGGRLVVMSYHSLEDRITKRHLSAWATSTAPPGFPVVLEEHEPVVRVLTRGTE
+KPTEEEISENRRASSAKVRAVEKIRTSRTTA
+>2_1501
+MDADQLRPEDRHVPVMRDRVVDLLAPAVQAALDAGRAPVAVDGTLGMGGHTEAMLTRFPE
+LTVIGIDRDAHAQALAAERLGPLAERLVPFHGTYDLVPEAMAAAGVEKVDAALYDLGVSS
+YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEHELRRIIRRDGEERFAGPIAR
+AIVRARAEAPIETTGRLVEVIRTAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP
+AILDALHVGGRLVVMSYHSLEDRIAKRHLSAWAASTAPPGFPVVLEEHEPVVRTLTRGTE
+KPTEEEILENRRASSAKVRAVEKIRTSRTPA
+>3_1396
+MDPTQPLPRDRHVPVMRDRVVDLLAPAVEAAAAAGRTPVAVDGTLGMGGHTEVLLRRFPT
+LRVVGIDRDPNALAMAQERLGPLAERLVPFHGTYDQVPEALAAAGAERMDAALYDLGVSS
+YQLDARERGFAYSYDAPLDMRMDTTAPVTAADLVAELDEQSLRRIIRRDGEDRFAGPIAR
+AIVRAREEEPILTTGRLVDVIRAVVPVSAGNKGGHPAKRTFQALRIAVNEELDILDAAVP
+AVLDALEVGGRLVVMSYHSLEDRIAKRHLQEWAASTAPPGFPVELPEHRPLVKVLTRGTE
+KPTEEEIEENRRASSAKVRAVEKIRTSRTTA
+>4_1268
+MDAGQPRPEDRHLPVMRDRVVDLLAPAVQAALEAGRTPVAVDGTLGMGGHTEALLTRFPH
+LRVIGIDRDVHAQAMAVERLGPLAERLIPFHGTYDRVPEAMAAAGVTKVDAALYDLGVSS
+YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEQELRRIIRRDGEERFAGPIAR
+AIVRARDEAPIETTGRLVEVIRSAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP
+AILDALHVGGRLVVMSYHSLEDRITKRHLSAWATSTAPPGFPVVLEEHEPVVRVLTRGTE
+KPTEEEISENRRASSARVRAVEKIRTSRTTA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001146.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001146.fa
new file mode 100644
index 0000000000000000000000000000000000000000..73d9e715159d90b1331ede50909f14566ec2a91a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001146.fa
@@ -0,0 +1,46 @@
+>0_1317
+M-------SETAPAAPRDEATILHVDMDAFFLSVELRERPDLEGRPAAVAAPSGRSVVLS
+ASYAARAYGVRSAMPLAHARALCPPLVVIPPRQQLYRAVSAEVMAVLADVTPVMEQLSVD
+EAFLDVAGARRRLGPPEHIGHLIRERVRSALGLPCTVGGSAVKFVAKTASTAAKPDGLLI
+VPPERTLDFLHPLPVGRLWGVGPKAAERLARRGVATIGDLARVDPARLEASFGAAGREWA
+SLARGIDPRPVAPRPAARSIGADHTFDVDPVDVAGVDPEVLRLCHRVAARLRAEQATAGA
+VTVRLKAPDGSVRSRTARLARPTATGHDLLGPARRLVRELHAERPHPVRLVGVRAERLGD
+EADQPPAQEALFGGPAWGTEGEAS-EAGDWAGAEAALDAVARRFPTAAVRPASLLGRREA
+RADARRDAPRPGPGGPDRE
+>1_1046
+M-------SESAPAAPRDEATILHVDMDAFFLSVELREQPDLEGRPAAVAAPSGRSVVLS
+ASYAARAYGVRSAMPLAHARALCPPLVVIPPRQQLYRAVSAEVMAVLADVTPVMEQLSVD
+EAFLDVAGARRRLGPPEHIGHLIRERVRSALGLPCTVGGSAVKFVAKTASTAAKPDGLLI
+VPPQRTLDFLHPLPVGRLWGVGPKAAERLARRGVATIGDLARVDPARLEASFGAAGREWA
+SLARGIDPRPVAPRPAARSIGADHTFDVDPVDVAGVDPEVLRLCHRVAARLRAEQVTAGA
+VTVRLKAPDGSVRSRTARLARPTATGHDLLGPARRLVRELHAERPHPVRLVGVRAERLGD
+EADQPPAQEALFGGPAWGTEGEAS-EAGDWAGAEAALDAVARRFPTAAVRPASLLGRREA
+RADARRDAPRPGPGGPDRE
+>2_1498
+M-------SDTAAAQARPEASILHVDMDAFFLSVELRERPDLTGRPAAVAAPSGRSVVLS
+ASYEARAYGVRSAMPLAHARALCPPLVVVPPRQDVYRSVSADVMALLGQVTPVLEQLSVD
+EAFLDVAGARRRLGPPARIGGLIRRRVREELGLPCTVGAAGVKFVAKMASTAAKPDGLLV
+VPPERTLEFLHPLPVGRLWGVGPKAAEALRRRGMATIRDLAAADPEQLERAFGAAGRSWA
+QLSRGIDPRPVAPRPAARSIGADHTFDVDPLDVAGVDLEVLRLCHRVAARLRAEEVAAGA
+VTVRLKDPDGRVRSRTARLARPTTTAHGLLGPARRLVAELHAQRPHPVRLVGVRAERLTD
+ADEPAPEQEALFGGSGFGDDDAAEGGAGDWAGAEAAADAVARRFPTAAVRPASLLRRAAG
+RPDTRRDVPGP--------
+>3_1393
+MSAPDPGPAPSSPPPPRREPSILHVDMDAFFLSVERRERPELRGVPAAVAHPEGRSVVLS
+ASYEARAYGVRSAMPLAQARALCPPLRVTPPRQELYRSTSARVMDLFGRVTPVVEQLSVD
+EAFLDVAGARRLLGPPERIAALIRERVRAELGLPCTVGGAGVKFVAKMASTAAKPDGMLL
+VPPQCTLAFLHPRPVGALWGVGPQAARRLRERGVETIGDLAARDPRWLREAFGAAGAAWA
+ELAAGRDPRPVAPREPARSVGADHTFDVDARDPAALDREVLSLCHRVAARLRSGGHTAAA
+VTVRVKDPALATRARTVRLPAPTASGRVLHAHAGPAVAGLLTERPHPVRLVGVRAERLSD
+AEAHGAVQEALFAPE--GHEGPTD-DAG-WRRAEEAADAVARRFPGAGVRPASLLGPPEG
+S------------------
+>4_1271
+M-------SETAPAAPRDEATILHVDMDAFFLSVELREQPDLEGRPAAVAAPSGRSVVLS
+ASYAARAYGVRSAMPLAHARALCPPLVVIPPRQQLYRAVSAEVMAVLADVTPVMEQLSVD
+EAFLDVAGARRRLGPPEHIGHLIRERVRSELGLPCTVGGSAVKFVAKTASTAAKPDGLLI
+VPPERTLDFLHPLPVGRLWGVGPKAAERLARRGVATIGDLARVDPARLEASFGAAGREWA
+SLARGIDPRPVAPRPAARSIGADHTFDVDPVDVAGVDPEVLRLCHRVAARLRAEGVTAGA
+VTVRLKAPDGSVRSRTARLARPTATGHDLLGPARRLVRELHAERPHPIRLVGVRAERLGG
+EADQPPAQEALFGGPAWGTEGEAS-EAGDWAGAEAALDAVARRFPTAAVRPASLLGRREA
+RADARRDAPRPGPGGPDRE
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001149.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001149.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d32225f0cb5fd1e6c872d986da8e2edb32a74b4c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001149.fa
@@ -0,0 +1,41 @@
+>0_1320
+----------MPRSAVPH-TPVRSRCLRSVLTGGAVPLLLLTGLPAQAHAQEAA-----V
+HTVRPGDSLTRISAARGVSVADLLRFNGLGLETVLYPGDELRLTGAAAPAPAAGTYTVQP
+NDGWWVIARRTGVSAAQLQRLNGMSASSMLHPGMVLTTQRTAAAPKAPASPAPTTTPATA
+PASTTPTAAGGTVRYTVVSGDSLWGISQRFEVSIPRLRELNGLTRASTLHPGDVLVISDG
+TLEVEPVSAVQAVGDTFLGRTYAPHVTASANENLRLLRAVPQPTPEQMQQIVRETAERMG
+VDPRLALGHAYTESRFRMASVSPGNAVGAMQVIPITGEFASELVGRELNLLDPHDNAVAG
+VAFIKYVQDRTPTLDEGIGAYYQGLGGVLDSGLNPEARDYVAKVRAAMAMF
+>1_1049
+----------MPRSAVSH-TPVRSRRLRSVLTGGAVPLLLLTGLPAQAHAQEAA-----V
+HTVRPGDTLTRISAARGVSVADLLRFNGLGLETVLYPGDELRLTGAAAPAPAVGTYTVQP
+NDGWWIIARRTGVSAAQLQRLNGMSASSMLHPGMVLTTQRTAAAPKTPASTAPATTPASA
+PASTAPAAAGGTVRYTVVSGDSLWGISQRFEVSIPRLRELNGLTRASTLHPGDVLVISDG
+TLEVEPVSAVQAVGDTFLGRTYAPHVTASANENLRLLRSVPQPTPEQMQQIIRETAERMG
+VDPRLALGHAYTESRFRMASVSPGNAVGAMQVIPITGEFASELVGRELNLLDPHDNAVAG
+IAFIKYVQDRTPTLDQGIGAYYQGLGGVLDSGLNPEARDYVAKVRAAMAMF
+>2_1495
+----------MPRSSVSH-TP--SRRLRHALAGGAVPLLLLTGLPAQAQAQEAP-----V
+HTVRPGDTLTAISAAHGVPLVDLFRLNGLDHESIIYPGDAIRLTGEAAPAAAAGTYTVQP
+DDGWWIIARRTGVSAAELQRLNGMSASTMLHPGMVLTTAGKAAA------PAPTPAP---
+PRCSLAPATRDVVRYAVVSGDSMWGISQRFEMSIPRLRELNGLTRSSMLHPGQVLVISDG
+TLEVEPVSDVQPIGDTFLGRTYPAHVTASANENLRLLQSVPQPSPEQMREIVRETAVRMD
+VDPRLALGHAYTESRFRMASVSPANAIGAMQVIPITGEFASELVGRELNLLDPYDNAVAG
+VAYIKYVQDRTPTLDTGIGAYYQGLGGVLQGGLSAEGRTYVATVRAAMAMF
+>3_1390
+MPPARKVTPLMPQPAAPRASATTARRSLGLVAGGVVPLLMTGALPVAAQAAEAAHAAPRT
+HTVRAGENPYRIAEAEGVRLSDLLRLNGLRADSVIYTGQVLALTGAPAPAAAPGTVEVER
+GEGWWQVSRRAGVDAAVLQRINGLGARSMLHPGQILLTE----APARP--TTPATPVAAA
+P---APVRQAAPTTYTVRNGDSMWSISQRVEVSIPRLRELNGLTWRSVLHTGDVLVIADG
+TEQAPVIDG--PVGSTFLSTTYAPHVTASANDNLRALQAVPQPSPAEVQALVRQTALELG
+VDPALALGHAYTESRFQHASVSPGNAIGAMQVIPITGEFASQLVGRELNVLDVRDNVTAG
+VVLIKYLQEHTDTVDQGISAYFTGLGGSDDPVKQQEARNYVARVKAAAAMF
+>4_1274
+----------MPRSAVPH-TPVRSHRLRSVLTGGAVPLLLLTGLPAQAHAQEAA-----V
+HTVRPGDSLTRISAARGVSVADLLRFNGLGLETVLYPGDELRLTGAAAPAPAAGTYTVQP
+NDGWWVIARRTGVSAAQLQRLNGMSASSMLHPGMVLTTQRTAAAPKAPASPAPTTTPATA
+PASTAPTAAGGTVRYTVVSGDSLWGISQRFEVSIPRLRELNGLTRASTLHPGDVLVISDG
+TLEVEPVSAVQAVGDTFLGRTYAPHVTASANENLRLLRSVPQPTPEQMQQIVRETAERMG
+VDPRLALGHAYTESRFRMASVSPGNAVGAMQVIPITGEFASELVGRELNLLDPHDNAVAG
+VAFIKYVQDRTPTLDEGIGAYYQGLGGVLDSGLNPEARDYVAKVRAAMAMF
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001152.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001152.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f922c894730c9952211bfa892b36119d7780d369
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001152.fa
@@ -0,0 +1,31 @@
+>0_1324
+M--------------PRPVAVAPEDLPLRLMPAAPARRDHCVVLLHGFTSTPASVRAWAE
+GLAAGGSPVSVPLLPGHGTRWEDLAATGADEIRAAVRAVVDLELARHGRVVMAGISMGGA
+LALDAAAHRPVAGVLVVNPALRFASPLAPFAPLLAPFVPTVAPIADDIADPTARERAYPR
+TPVAGVAALGRIQRAARRALPRITAPVTVYRSARDAVVPASSHRTLVRGLRQAPVEVVGL
+PRSRHVATLDYDLPLLIDHGRSAVAAMTTH
+>1_1053
+M--------------PRPVAVAPEDLPLRLMPAAPARRDHCVVLLHGFTSTPASVRAWAE
+GLAAGGSPVSVPLLPGHGTRWEDLAATGADEIRAAVRAVVDLELARHGRVVMAGISMGGA
+LALDAAAHRPVAGVLVVNPALRFASPLAPFAPLLAPFVPTVAPIADDIADPTARERAYPR
+TPVAGVAAVGRIQRAARRALPRITAPVTVYRSARDAVVPASSHRTLVRGLRQAPVEVVGL
+PRSRHVATLDHDLPLLIDHGRSAVAAMTTH
+>2_1490
+MDRPVPPVEPAPPAVPAP-AVDPVHLPLRLAPGSGAGADRCVVVLHGFTSGPDSVRAWAE
+GIAAGGSHVSVPLLPGHGTRWQDLAATGADEIRGAVRETVDRELSRHRHVVVAGISMGGA
+LALDAAAHRPVSAAIVVNPALRFASPLAPLAPALAPFVPSVAPIANDIADPDARELAYPR
+TPVAGVAAVGRIQRAARRALPRITAPVTVFRSARDAVVPAASHRTLLRGLRRAPVDVVPL
+PRSRHVATLDYDLPLLIERSRAAVEAATRA
+>3_1386
+MTRLRP---AAPDRRPAP-GVDPAQRPFRLPATSLPGV--AVVMLHGFTSGPDSVRAWAE
+GVAAGGAAVHVPLLPGHGTRWEDLGTTDADELRAAVRDAVDAALATHRRVVVAGISMGGA
+LALDAAAHRDVAGVLVVNPALRFGSPLAVAAPLLRHVVPSVPSIAGDIADPDARELAYER
+APVAGVAQVGRIQTAARRGLGRITAPVTVFRSAEDAVVPERSHHTLLRGLTAAPVEVVRL
+LHSRHVATLDRDLPLLVARSRDAVAAAAR-
+>4_1278
+M--------------PRPVAVAPEDLPLRLMPAAPARRDHCVVLLHGFTSTPASVRAWAE
+GLAAGGSPVSVPLLPGHGTRWEDLAATGADEIRAAVRAVVDLELARHGRVVMAGISMGGA
+LALDAAAHRPVAGVLVVNPALRFASPLAPFAPLLAPFVPTVAPIADDIADPTARERAYPR
+TPVAGVAALGRIQRAARRALPRITAPVTVYRSARDAVVPASSHRTLVRGLRQAPVEVVGL
+PRSRHVATLDYDLPLLIDHGRSAVAAMTTH
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001159.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001159.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08117c95e9ebb9716f86af991304fe089d003e0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001159.fa
@@ -0,0 +1,21 @@
+>0_1331
+MNQPGREPDLSTSAINLTELAPLVSADLTREESDAIRALPAGSALLLAHEGPDQSARFLL
+DKDVVSVGRHPDADIFLDDVTVSRRHAEFRAEDGGHRLVDLNSLNGTFVNHDRVDEILLR
+SGMHVQIGKYRLTYYAAPARG
+>1_1060
+MNQPGREPDLSTSAINLTELAPLVSADLTREESDAIRALPAGSALLLAHEGPDQSARFLL
+DEDVVSVGRHPDADIFLDDVTVSRRHAEFRAEDGGHRLVDLNSLNGTFVNHDRVDEILLR
+SGMHVQIGKYRLTYYAGPARG
+>2_1483
+MNQPGREPDLSTSSINLTELAPLVAADLSAEESDAIRALPAGSALLLADGGPEKAARFLL
+DQDVVTVGRHPDADIFLDDVTVSRRHAEFRAEAGGHRLVDMNSLNGTFVNHDRVDDVLLR
+SGTHVQIGKYRLTYFTSTQRG
+>3_1378
+MTQ--QEPSLHTSSISLTDLAPVAETGLSPEETAAVRALPAGAALLVAHEGPDAGARFLL
+DTPVVTVGRHPESDILLDDVTVSRRHAEFRAVDGGHELVDLSSLNGTYVNNDRVDQVRLR
+TGMQLQIGRYRLSYHAA-EPA
+>4_1285
+MNQPGREPDLSTSAINLTELAPLVSADLTREESDAIRALPAGSALLLAHEGPDQSARFLL
+DEDVVSVGRHPDADIFLDDVTVSRRHAEFRAEDGGHRLVDLNSLNGTFVNHDRVDEILLR
+SGMHVQIGKYRLTYYAGPARG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001170.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001170.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a888fb5050b3f25442869bec32caa612f91cb80
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001170.fa
@@ -0,0 +1,41 @@
+>0_1367
+MTETEIKKGLAGVVVDTTAISKVNPETNSLLYRGYPVQDLAAQLSFEAVALLLWTGELPT
+DEELAAFEHFERAHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAQALFAAFPAVVAYDQRRRRGQDVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESRQDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLQSAMDEAKQIKPNLDYPAGPTYHLMGFDTEMFTPLFIASRITGWTAHIMEQRAA
+NALIRPLSAYDGPEQRELPAG
+>1_1107
+MTETEIKKGLAGVVVDTTAISKVNPETNSLLYRGYPVQDLAAQLPFEAVALLLWTGELPT
+DEELTAFERFERTHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAQALFAAFPAVVAYDQRRRRGQEVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLEQAMDEAKQIKPNLDYPAGPTYHLMGFDTELFTPIFIASRITGWTAHIMEQRAA
+NALIRPLSAYDGPEQRELPAG
+>2_1454
+MTETEIKKGLAGVVVDTTAISKVNPDTNSLLYRGYPVQDLAAKLPFESVALLLWNGELPT
+DEELAEFQRFERAHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAKALFAAFPAAVAYDQRRRRGQDVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLQSAMDEAKQIKPNLDYPAGPTYHLMGFDTEMFTPLFIASRITGWTAHIMEQRAA
+NALIRPLSSYDGPEQRELPAG
+>3_1361
+MTETEIKKGLAGVVVDTTAVSKVNPETNSLLYRGYPVQDLAAQLPFEAVALLLWNGELPT
+DAELEEFQRFERAHRALDPEVKAAVDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAKALFAAFPAVVAYDQRRRRGQEVVEPRADLDYAQNFLWMSFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLEQAMDEAKQIKPNLDYPAGPTYHLMGFDTEMFTPIFIAARITGWTAHIMEQRAA
+NALIRPLSAYNGPEQRELPGK
+>4_1316
+MTETEIKKGLAGVVVDTTAISKVNPETNSLLYRGYPVQDLAAQLSFEAVALLLWTGELPT
+DEELAAFERFERAHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAQALFAAFPAVVAYDQRRRRGQDVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLEQAMDEAKQIKPNLDYPAGPTYHLMGFDTELFTPIFIASRITGWTAHIMEQRAA
+NALIRPLSAYDGPEQRELPAG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001171.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001171.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40830eb878e9de382861a7daf038d6c208e0043a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001171.fa
@@ -0,0 +1,36 @@
+>0_1369
+MSADPA--------PRGSRGGRGAESALAAPFRRHLEHLAVERGLAANTLAAYRRDLERY
+RRWLEAQGVRAPADVDPGHVSGFLRALGTGEDGGRPLAVRSAARVLAAVRGLHRFWALEG
+LTPADPALDVHPPKPGARLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARIS
+EVVGLDVDDVVGLAQT-----GDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGR
+PTIMAGAARSTPALFVNACGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLA
+GGADVRVVQELLGHASVTTTQVYTLVTVDSLREVYSAAHPRAR---
+>1_1109
+MSTDPAARGSGEAEA---RGGRGAESALAAPFRRHLEHLAVERGLAANTLAAYRRDLERY
+RRWLEAHGVRAPADVDPGHVSGFLRALGTGEDGGRPLAVRSAARVLAAVRGLHRFWALEG
+LTPADPARDVHPPKPGDRLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARIS
+EVVGLDVDDVVGLAQT-----GDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGR
+PTIMTGVTRSTPALFVNARGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLA
+GGADVRVVQELLGHASVTTTQVYTLVTVDSLREVYSAAHPRAR---
+>2_1452
+MSTDPAARGSGEAEARGSRGGRGAESALAAPFRRHLEHLAVERGLAANTLAAYRRDLERY
+RRWLEAHGVRAPADVDPGHVSGFLRALGTGEDGGRPFAVRSAARVLAAVRGLHRFWALEG
+LTPADPARDVHPPKPGDRLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARIS
+EVVGLDVDDVVGLAQT-----GDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGR
+PTIMTGAARSTPALFVNARGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLA
+GGADVRVVQELLGHASVTTTQVYTLVTVDSLREVYAAAHPRAR---
+>3_1360
+MS---------------------ASPELHRALDRHLDHLAVERGLASATLAAYRRDLGRY
+LAWLEASRVDRPADVDPGHVAGFLSALGTGDDGGRPLGARSAARVLSAVRGMHRFWALEG
+LTPTDPAADVAPPRPPERLPKALPVETVTRILEAVPTAEPADLRDRALLEFLYGTGARVS
+EAVGLDVDDVVGVAGDRGAGRGDDDRLPVVRLFGKGSKERLVPVGSHAADALAAWLVRGR
+PALAAAATRPVPALFLNLRGGRLSRQSAWSILKAAAERAGVAQDVSPHTLRHSFATHLMQ
+GGADVRVVQELLGHASVTTTQVYTRVTAEALREVYASAHPRARWTT
+>4_1318
+MS--PHAP---------------QTSALAAPFRRHLDHLAVERGLAENTLAAYRCDLARY
+RRWLEAAGVRAPGDVDPGHVAGFLQALATGDDGGRPLAVRSAARVLAAVRGLHRFWALEG
+LTPADPARDVHPPKPGDRLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARIS
+EVVGLDVDDVVGLAQT-----GDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGR
+PTIMTGVTRSTPALFVNARGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLA
+GGADVRVVQELLGHASVTTTQVYTLVTVDSLREVYSAAHPRAR---
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001173.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001173.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa528225bf6f19ec81268f213df618089fbf368a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001173.fa
@@ -0,0 +1,45 @@
+>0_1371
+MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSSRAVVDAGVRVTADHAALRLA
+QEAGAVVDEGDNGTHDLVLSRSVTASGDGTRSRATAGGRSVPVGLLSEIGATLVAVHGQNDQVRLQGADAQRHALDAFGG
+AELAAALRAYRADHAAWTAARREREELTAHRQERAREAEALQRSLEEIDLAEPREGEDEELRALIRRLEDVEELRAASGE
+AHARLAGPDVDAMDETPGAVSLVEAARQAVLAAPGDDPDLAAAAARLAEAAVVLTDIAGDLARYTADLDADAASDLDAAQ
+SRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGRLEELEAEVDRLDAALRERAATLTALRTAAAERLETAVTEE
+LHALFMPDASFHVGLTPVAGDGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV
+DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVVTLTADERVEELARMLAGHGD
+SAAAREHARELLESSARERG
+>1_1111
+MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSSRAVVDAGVRLPEAHAALALA
+EDAGAVLDEADEGVRELVLSRSVTASGEGTRSRAAAGGRTVPVGLLAEIGATLVAVHGQNDQVRLQGADAQRHALDAFGG
+AELAAALRAYRADHAAWTAARREREELTAHRQERAREAEALQRSLEEIDLAEPQEGEDEELRALIRRLEDVEELRAASGE
+AHARLAGPDVDTMDETPGAVSLVEAAQQAVLAAPGDDPELAAAAARLAEAAVVLTDIAGDLARYTADLDADAASDLDAAQ
+SRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGRLEELEAEVDRLDAALRERAATLTALRTAAAERLETAVTEE
+LHALFMPDASFHVGLTPVAGDGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV
+DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVVTLTADERVEELARMLAGHGD
+SAAAREHARELLESSARERG
+>2_1450
+MIEHLRISGLGVIGEATVDLDPGLTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGAARAVVDAGVRLPEAHAALALA
+EDAGAVLDEADDGVRELVLSRSVTASGEGTRSRAAAGGRTVPVGLLAEIGATLVAVHGQNDQVRLQGAEAQRRALDAFGG
+AELAASLRAYRADHAAVSAARRERDELTAHRQERAREAEALQRSLEEIDLAEPLAGEDAELRELIRRLEDVEELRAASGE
+AHARLAGAEMDALEETPGAVSLVEGARQAVLAAPGDDPALAAAAERLAEAAVVLTDIAADLARYTADLDTDAASDLDAAQ
+SRLAELTRLQRLYGPELEDVIGWAETQRPRLDELQGDSGRLEELEGELERLESALRERAAALTALRTAAAGRLEEAVTQE
+LHALFMPDASFHVDLAPVGGDGLGPHGAEDVALALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV
+DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVVTLSAEERVEELARMLAGHGD
+SAAAREHARELLEASARERG
+>3_1358
+MIDWMQITGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGRRADAGAVRRGSRRAAVDAGVRLPADHPALSLA
+VEAGAVLDDAGDGSADLVLSRSVTASGDGTRSRAGLGGRAVPVGVLAEVGSALVAVHGQNDQVRLQSAAAQRHALDAFGG
+PQLVAAAAAYRADHTAYVAARRERDLLVERQQERAREAEALQRGLEEIDRAEPEAGEDETLRALIRRLEDVEELRAAADG
+GHAHLAGPDIESGDDLPGAITLVESARAAVQAAPGDDPELAAAAGRLAEASVILGDIAADLARFSADLDGDAVSDLDAAQ
+TRLAELSRLQRLYGPELTDVLAWAEAQRPRLEELQGDSGRIDELEADLARLDASRRERAAELTTLRTAAAGRLEQAVTAE
+LHALFMPDASFHVSLVPLDDGDPGPHGAEDVALALRPHAGAEPRPLGRGASGGELSRVMLALEVVLAETDPVPTFVFDEV
+DAGVGGEAAVSIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPEAGVTTSDVVTLGQQERVDELARMLAGHGD
+SAAARAHARELLEASAAERA
+>4_1320
+MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSSRAVVDAGVRLPEAHAALALA
+EDAGAVLDEADEGVRELVLSRSVTASGEGTRSRAAAGGRTVPVGLLAEIGATLVAVHGQNDQVRLQGADAQRHALDAFGG
+AELAAALRAYRADHAAWTAARREREELTAHRQERAREAEALQRSLEEIDLAEPQEGEDEELRALIRRLEDVEELRAASGE
+AHARLAGPDVDAMDETPGAVSLVEAARQAVLAAPGDDPELAAAAARLAEAAVVLSDIAGDLARYTADLDADAASDLDAAQ
+SRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGRLEELEAEVDRLDAALRERAATLTALRTEAAERLETAVTEE
+LHALFMPDASFHVGLTPVAGDGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV
+DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVVTLTADERVEELARMLAGHGD
+SAAAREHARELLESSARERG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001176.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001176.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf40e5a31cd3abfa174a5c88ccab95634041954c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001176.fa
@@ -0,0 +1,31 @@
+>0_1374
+----MSTTFFDGHDGLLCDLDGVVYAGDGAIAGAVETLSTLQERGVPVGFVTNNASRAPE
+SVAEHLRTLGVPAEAGQVFGSAPAGVDLLEETLGRR----TGRVLVVGSAYLRAVVEERG
+YEVVASAAQCPDAVIQGFDPGLGWADLAEAAYAVRAGATWVATNLDTSIPRAEGIAPGNG
+ALVEAVGRATGTAPVAAGKPEPRLFRTAADALGLARPLVVGDRLDTDIRGGNAAGFDTVL
+VLTGIDTRETAAAAPGPDRPTWVRAHLPALLA--GGAEASADPRRG
+>1_1114
+----MSATFFAGHDGLLCDLDGVVYAGGGAIAGAVETLSTLQERGVPVGFVTNNASRAPE
+SVAEHLRTLGVPAQAGQVFGSAPAGVDLLEETLGRR----TGRVLVVGSAYLRAVVEERG
+YEVVASAAQRPDAVIQGFDPGLGWADLAEAAYAVRAGATWVATNLDTSIPRAEGIAPGNG
+ALVEAVGRATGTAPVAAGKPEPRLFRTAAEALGLARPLVVGDRLDTDIRGGNAAGFDTVL
+VLTGIDTRETAAAAPGPDRPTWVRAHLPALLA--GGAEAFADPRRG
+>2_1447
+----MSPTLPRGHDGLLCDLDGVVYAGGGAVPGAVETLTALAERGVPVGFVTNNASRAPE
+SVAEHLRSLGVPARPEQVFGSAPAGVDLLEETLGAR----TGRVLVVGSDYLRQVVRDRG
+FEVVAASQDRPDAVIQGFDPGVGWAELAQAAYAVNAGAAWVATNLDASIPRAEGIAPGNG
+ALVGAVGQATGTAPAAAGKPEPLLFRTAARALGLTRPLVVGDRLDTDIRGGNAAGFDTVL
+VLTGIDTRENAGSAPEADRPTWIVEDLPALLSEPDGQAGTADGRRG
+>3_1355
+MTDPAASTFFGGHDGLLCDLDGVVYAGGEAIPGAVETVSALAERGVPVGFVTNNASRPPE
+AVAEQLRRFGLEVSPSHVFGSAPVGVDLLEERLTAAGHEGPARVLVVGSVHLADLVAARG
+HHVVETAAERPDAVLQGFDPRVDWSRLAEAAYAVNAGAAWVATNLDLSIPRAEGVAPGNG
+ALALAVTQATGVIPVAAGKPEPRLFHTAAAALGLQAPLMVGDRLDTDIRGGNAAGMETVL
+VLTGVGSRHAAGEAPEEDRPTWIVDDMTALLGEP------AEAARG
+>4_1323
+----MSATFFAGHDGLLCDLDGVVYAGGGAIAGAVETLSTLQERGVPVGFVTNNASRAPE
+SVAEHLRTLGVPAQAGQVFGSAPAGVDLLEETLGRR----TGRVLVVGSAYLRAVVEERG
+YEVVASAAQRPDAVIQGFDPGLGWADLAEAAYAVRAGATWVATNLDTSIPRAEGIAPGNG
+ALVEAVGRATGTAPVAAGKPEPRLFRTAAEALGLARPLVVGDRLDTDIRGGNAAGFDTVL
+VLTGIDTRETAAAAPGPDRPTWVRAHLPALLA--GGAEAFADPRRG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001177.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001177.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d110283d231c3341d11a90c4be5eb627046c2e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001177.fa
@@ -0,0 +1,40 @@
+>0_1375
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-------------------------------------MTGKELDRGTLKEINGLDERAASWVAKHLVMAGRYLDVDPTLA
+FQHALAASRKGGRLSRVREAVALTAYAAGEYADALREFRTYRRMTGDDTHIAAQVDSERALGRTEKALQLAAEVDASRLD
+RAARAELAMVVSGIREDAGDLQGAHEALQIPELDRRRGYPFSPRLFQRQADVLLALGRRDEARLWARAVRVAEKALGVGG
+FADPEIIDVDTEPVEDP------RNRRPSPRERRHERYAAEAGAEPTADGSPAEEPEAAAEPTLVPRQEAVA--QPPAAV
+DTPDEVDPNQLSLFDALEAPEADER
+>1_1115
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-------------------------------------MTGQELDRGTLKEINGLDERPASWVAKHLVMAGRYLDVDPALA
+FQHALAASRKGGRLSRVREAVALTAYAAGEYADALREFRTYRRMTGDDTHIAAQVDSERALGRTEKALQLAAEVDASRLD
+RAARAELAMVVSGIREDAGDLQGAHEALQIPELDRRRGYPFSPRLFQRQADVLLALGRRDEARLWARAVRVAEKALGVGG
+FADPEIIDVDTEPVEDP------RDRRPSPRERRHERYAAEAGAEPTADGSPAEEPEAATEPTEAPRPEAAA--EPPAAV
+DAPDEVDPNQLSLFDALEAPEADER
+>2_1446
+MAEDTPRGRRDDRRSPGDGAGRSRGGSGDARRFGGPRDGRRSGGSGEGRSGQDRRDRSSEGFRGGRSGDGPRRERSSDGP
+RRERSSDGFRRDRSSDGPRGERSGDGPRGPRAGGDRRQSGAGSARGGFEGRRGGERREGAGGERRDRRSASSSPRWEGRG
+QDRTERTERRERPAHNPRDLRAANRVDQERSPDIDADVTGQELDRGTLKEVNGLDERPASWVAKHLVMAGRYIDVDPALA
+FQHALAASRKGGRLSRVREAVALTAYAAGEYADALREFRTYRRMTGDDTHVAAQVDSERALGRPAKALQLAAEIDTARLD
+RAARVELAMVVSGIREDAGDLQGAHDALQIPELDRRRGYPFSPRLFQRQADVLLLLGRADEARLWARAVRVAEKALGIGG
+FAEPEIVDVDTEPVDDR------RERGPSPRERRYAENAAPA-AEEVPDTPEADDEVAADADTEAPASTESELDAPPAAV
+AQADEVDPNQMSLFDELDGGEGEGR
+>3_1354
+MA------------------------------------------------------------------------------
+--ERSAREPRDDRRGDGHDGTRSGT-PRGRRDGDGGRRQGEGRP---FRPHRDG---EGVGRSRNVGGRDGAAPR-----
+PGRPERAQ-RERPAHSPSDLRAANRVDQQRSPDIDGDVTGKELDRGTLKEIGGLDERPATWVAKHLVMAGRYIDEDPELA
+FQHALAASRKGGRLARVREAVALTAYAAGEYHEALREFRTYRRMTGDDTHIAAQVDSERALGRHEKALQLAGEVDTSRLD
+RAARVELAMVVSGVREDLGDLEGALAALKIPELDRRRGYPFSPRLFQRQADVLTALGRTQEAAVWQRSVHVAERALGIGG
+FAEPEIVDVEVEPAEDDRPVRGHRERHTGPRVSDASQSSAESA--PVGEGSAEEHGQAA------PAERES---------
+-------------------------
+>4_1324
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-------------------------------------MTGQELDRGTLKEINGLDERPASWVAKHLVMAGRYLDVDPALA
+FQHALAASRKGGRLSRVREAVALTAYAAGEYADALREFRTYRRMTGDDTHIAAQVDSERALGRTEKALQLAAEVDASRLD
+RAARAELAMVVSGIREDAGDLQGAHEALQIPELDRRRGYPFSPRLFQRQADVLLALGRRDEARLWARAVRVAEKALGVGG
+FADPEIIDVDTEPVEDP------RDRRPSPRERRHERYAAEAGAEPTADGSPAEEPEAATEPTEAPRPEAAA--EPPAAV
+DAPDEVDPNQLSLFDALEAPEADER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001178.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001178.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e790db6fc0f1d1ebc245dc036e6087a9bcdc04db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001178.fa
@@ -0,0 +1,46 @@
+>0_1376
+MAPQNEERAARLRAQANDPSFENVWQELRWRGLVHVSTDEAALEQALAGEPVSYYCGFDP
+TAPSLHLGHLVQLLTLRRLQLAGHRPYALVGGATGLIGDPRQTSERVLNSQETVAAWVES
+LRAQIEPYLSFEGENAATMVNNLDWTAGMSALDFLRDVGKNFRVGTMVKKEIVAKRLNSD
+EGISYTEFSYQVLQGNDFLELHRRHGVTLQTGGSDQWGNLTAGTELIRKVEGTHAHALGT
+PLITNADGTKFGKSEGNAVWLDAEMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE
+YAQKVADEPFRREAQRRLAWEVTALAHGEETTTKVIEASQAVFGGGDLTTVDPDTLTAVL
+AELPQADRTQWEGEPGTVTAVELLVSTGLVASRSEARRTVRDGGASVNNVRVTDADQVFT
+RDDALAGRHLLVRRGKKNMAGADLGEA-----
+>1_1116
+MAPQNEERAARLRAQANDPSFENVWQELRWRGLVHVSTDEAALEQALAGEPVSYYCGFDP
+TAPSLHLGHLVQLLTLRRLQLAGHRPYALVGGATGLIGDPRQTSERVLNSQETVAAWVES
+LRAQIEPYLSFEGENAATMVNNLDWTAGMSALDFLRDVGKNFRVGTMVKKEIVAKRLNSD
+EGISYTEFSYQVLQGNDFLELHRRHGVTLQTGGSDQWGNLTAGTELIRKVEGTHAHALGT
+PLITNADGTKFGKSEGNAVWLDAKMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE
+YAQKVADEPFRREAQKRLAWEVTALAHGEETTTKVIEASHAVFGGGDLTTVDPDTLTAVL
+AELPQADRTQWEGEPGTVTAVELLVSTGLVASRSEARRTVRDGGASVNNVRVTDADQVFT
+RDDALAGRHLLVRRGKKSMAGADLGEG-----
+>2_1445
+MAPDNEERAARLRAQANDPSFENVWQELLWRGLVHVSTDEAALEEALAGEPISYYCGFDP
+TAASLHLGHLVQLLTLRRLQLAGHRPMALVGGATGLIGDPRQTSERVLNSQETVAGWVES
+LREQIQPYLSFEGENAATMVNNLDWTAGMSALDFLREVGKNFRVGTMMKKEIVAKRLNSE
+EGISYTEFSYQVLQGNDFLELYRRHGVSLQTGGSDQWGNLTAGTELIRKVEGVPAHALGT
+PLITNADGTKFGKSEGNAIWLDAAMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE
+YAQKVADEPFRREAQKRLAWEVTSLAHGEEATTKVIEASQAVFGGGDLGEVDAETLGAIL
+SELPQADRTQWEGEPGTVTAVELLVSTGLVGSKSEARRTVKEGGASVNNERVSDADRVYT
+REDALAGRHLLVRRGKKNMAGADFGSQDADRG
+>3_1352
+MAETTVTRAERLRQQANDPSFENVWQELTWRGLVHVSTDEAALEEALAGEPISYYCGFDP
+TAPSLHLGHLVQLLLMRRLQLAGHRPVALVGGATGLIGDPRQTSERVLNTREVVQEWVES
+LRAQIEPYLAFEGDNGARMVNNLDWTASMSALDFLREVGKNFRVGTMVKKEIVAKRLHSE
+EGISYTEFSYQVLQGNDFLELYRQHGVTLQSGGSDQWGNLTSGTELIRKVEGAHVHALGT
+PLITNSDGTKFGKSEGNAIWLDADMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE
+YAAKVDAEPFRREAQKRLAWEVTALAHGEEAARTVIDASAAVFGGGDLSEVDVDVLSAVL
+AELPQADAAQW-GAAGKPTAVELLVSTGLVSSNSEARRTIKEGGASVNNVKVADAEQVFG
+ADEALAGRYLLVRRGKKNMAAADLRSGE----
+>4_1325
+MAPQNEERAARLRAQANDPSFENVWQELRWRGLVHVSTDEAALEQALAGEPVSYYCGFDP
+TAPSLHLGHLVQLLTLRRLQLAGHRPYALVGGATGLIGDPRQTSERVLNSQETVAAWVES
+LRAQIEPYLSFEGENAATMVNNLDWTAGMSALDFLRDVGKNFRVGTMVKKEIVAKRLNSD
+EGISYTEFSYQVLQGNDFLELHRRHGVTLQTGGSDQWGNLTAGTELIRKVEGTHAHALGT
+PLITNADGTKFGKSEGNAVWLDAEMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE
+YAQKVADEPFRREAQRRLAWEVTALAHGEETTTKVIEASQAVFGGGDLTTVDPDTLTAVL
+AELPQADRTQWEGEPGTVTAVELLVSTGLVASRSEARRTVRDGGASVNNVRVTDADQVFT
+RDDAFAGRHLLVRRGKKNMAGADLGEA-----
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001184.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001184.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c87540835f290f4100e59b149986aa62855edc6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001184.fa
@@ -0,0 +1,36 @@
+>0_1382
+MTPA------AAVRHFLVDTDLTPAEQAEVLDLAAQMKADRFRHRPLAGPRTGIVFFDKT
+STRTRVSFAAGIAELGGTPLIVNPGESQLGHKESVADTARVLERMVGVIVWRTFAQAGLE
+EMAAHSSVPVVNALSDDYHPCQILADLLTVREHLGGTAGRTLTYLGDAANNMAHSYLLGC
+ATAGMHVRVAGPEGHLPAEDVVAAARQRAAETGGSVLVTTDAAEALAGADVVVTDTWVSM
+GQEEEKEARLALFRDYQVDAAAMARAADDAIFLHCLPAYRGYEVTAEVIDGPRSVVFDEA
+ENRLHAQKALIAWLLYRSGLAEEPR
+>1_1123
+MTPA------AAVRHFLVDTDLTPAEQAEVLDLAAQMKADRFRHRPLAGPRTGIVFFDKT
+STRTRVSFAAGIAELGGTPLIVNPGESQLGHKESVADTARVLERMVGVIVWRTFAQAGLE
+EMAAHSSVPVVNALSDDYHPCQILADLLTVREHLGGTAGRNLTYLGDAANNMAHSYLLGC
+ATAGMHVRVAGPEGHLPAEDVVAAARQRAAETGGSVLVTTDAVEALAGADVVVTDTWVSM
+GQEEEKEARLALFRDYQVDAAAMARAADDAIFLHCLPAYRGYEVTAEVIDGPRSVVFDEA
+ENRLHAQKALIAWLLYRSGLAEEPR
+>2_1438
+MTPAP-TPAPAAVRHFLVDTDLTPGEQAEVLDLAAQMKTDRFAHRPLAGPRTGVVFFDKT
+STRTRVSFAAGIAELGGSPLIVNPGESQLGHKESVADTARVLERMVGIIVWRTFAQSGLE
+EMAAHSRVPVVNALSDDYHPCQILADLLTVREHLGGTQGRVLAYLGDAANNMAHSYLLGC
+ATAGMHVRIAGPAGHLPAEHVVAAARERAAETGGSVLVTTDAAEALDGADVVVTDTWVSM
+GQEDEKEARLALFRDYQVDAAAMARAGSDAIFLHCLPAYRGYEVSAEVIDGPQSVVFDEA
+ENRLHAQKALMAWLLYRSGLAEDPR
+>3_1346
+MTAAPGTDVP--VRHFLVDTDLSPAEQAEVLDLALEMKADRFRHRPLAGPQTGIVFFDKT
+STRTRVSFAAGIADLGGTPLIVNPGESQLGHKESIADTARVLERMVGVIVWRTYAQSGLE
+EMAAHSRVPVVNALSDDYHPCQLLADLLTVREHKGRTRGLTMAYLGDAANNMANSYLLGG
+VTAGMHVRVAGPEGFLPDPAVVRAAEERAGETGGSVLVTTDAAAALDGADVVVTDTWVSM
+GQEDEKEERLRLFADYRVDAAAMARAASDAVFLHCLPAYRGYEVTEDVIDGPQSVVFDEA
+ENRLHAQKALMAWLLYRSGLAQDPR
+>4_1331
+MTPA------AAVRHFLVDTDLTPAEQAEVLDLAAQMKADRFRHRPLAGPRTGIVFFDKT
+STRTRVSFAAGIAELGGTPLIVNPGESQLGHKESVADTARVLERMVGVIVWRTFAQAGLE
+EMAAHSSVPVVNALSDDYHPCQILADLLTVREHLGGTAGRNLTYLGDAANNMAHSYLLGC
+ATAGMHVRVAGPEGHLPAEDVVAAARQRAAETGGSVLVTTDAVEALAGADVVVTDTWVSM
+GQEEEKEARLALFRDYQVDAAAMARAADDAIFLHCLPAYRGYEVTAEVIDGPRSVVFDEA
+ENRLHAQKALIAWLLYRSGLAEEPR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001189.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001189.fa
new file mode 100644
index 0000000000000000000000000000000000000000..15577cb329851d0008085d389f6d122e275edf2d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001189.fa
@@ -0,0 +1,36 @@
+>0_1387
+MTTANTPAVPRTHHAVVVSATGGPEVLQWTETEVPSPAPGHVLVRTAAAGLNFIETYQRS
+GVYTMDLPFTPGTEGSGEVVALGEGVDAGLLGARVATATATGAYAEHFTAPADRLLTVPE
+GIDLAEAAALPLQGMTAHYLCRSTFPVEEGHTVVVTAGAGGVGLLLTQLATARGARVVTT
+ASTEEKRELSRGAGAVAAVDYPDLAATVAELTDGEGAHVVYDGVGKDTFDTSLEVLRVRG
+TLVLFGGASGQVPPFDLQRLNAAGSLYVTRPSLVHYTRTGEETRWRGGEVFGAWASGELD
+VRIGERFPLADAAAAHAALESRSTTGKVLLTLS
+>1_1128
+MTTANTPAVPRTHHAVVVSATGGPEVLQWTETEVPSPAPGHVLVRTAAAGLNFIETYQRS
+GTYAMDLPFTPGTEGSGEVVALGEGVDAALLGARVATATATGAYAEHFTAPADRLLAVPE
+GIDLAEAAALPLQGMTAHYLCRSTFPVEEGHTVVVTAGAGGVGLLLTQLATARGARVVTT
+ASTEEKRELSRGAGAVAAVDYPDLAATVAELTDGEGAHVVYDGVGKDTFDTSLEVLRVRG
+TLVLFGGASGQVPPFDLQRLNAAGSLYVTRPSLVHYTRTGEETRWRGGEVFGAWASGELD
+VRIGERFPLADAAAAHAALESRSTTGKVLLTLS
+>2_1433
+MPHASSPAVPRTHHAVVVAETGGPEVLRWTQADVPAPGPGRVLVRTAAVGLNYIETYQRA
+GVYPMDLPFVPGTEASGTVVGLGEGVDPTLLGARVATATAQGAYAEHFTAPADRLLTVPE
+GVDLADAAALPLQGMTAHYLCRSTFPVEEGQTVVVTAGAGGVGLLLTQLAAARGARVITT
+ASTEAKRELSRAAGAAAAVDYPELAATVDRLTDGHGAHAVFDGVGKDTFETSLRVLRVRG
+TLVLFGGASGQVPPFDLQRLNAAGGLYVTRPSLVHYTRTEEETRGRSDELFAAWAAGELD
+VRIGERIPLAEAAAAHAALESRATTGKVLLTLG
+>3_1341
+M--STHAEIPARHHAIIAEEVGGPEVLRWTETAVPTPGAGEVLVRTAAAGLNFIETYQRS
+GVYAVPHPFTPGSEGSGVVVALGPGVDEALRGARVATAAGRGTYAEHFTAPADQLLHVPA
+GVDLADAAALPLQGMTAHYLCRSTFPVEPGHVVALTAGAGGVGLLLTQLAAARGATVITA
+ASTEDKRALSAAAGASAAVPYAELRQTVLDATGGEGAHAVFDGVGADTFEDSLASLRVRG
+TLVLFGGASGQVPPFDLQRLNSGGGLYVTRPSLAHYTRTAEETAWRGRELFDAWSAGALD
+VRIGARVPLAEAGRAHTLLASRATTGKVLLPLS
+>4_1336
+MTTANTPAVPRTHHAVVVSATGGPEVLQWTETEVPSPAPGHVLVRTAAAGLNFIETYQRS
+GVYTMDLPFTPGTEGSGEVVALGEGVDAGLLGARVATATATGAYAEHFTAPADRLLTVPE
+GIDLAEAAALPLQGMTAHYLCRSTFPVEEGHTVVVTAGAGGVGLLLTQLATARGARVVTT
+ASTEEKRELSRGAGAVAAVDYPDLAATVAELTDGEGAHAVYDGVGKDTFDTSLEVLRVRG
+TLVLFGGASGQVPPFDLQRLNAAGSLYVTRPSLVHYTRTGEETRWRGGEVFGAWASGELD
+VRIGERFPLADAAAAHAALESRSTTGKVLLTLS
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001192.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001192.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa769f355aa256cd0a3fdb6d0e48977d7a54219d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001192.fa
@@ -0,0 +1,60 @@
+>0_1391
+MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPAAELQGPIVVGQVLSKEPEPQKNGKTINWCSVRVVPEGAA
+QPLTGEGIEPSGVQGIVCGAHNFEVGDKVVVALPGAVLPGDFRISPRKTYGHVSAGMIASSTELGMGDDGTDGIIVLGDL
+GLDPEPGTDARDVLDLHGEAAEINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAAVHPPAADDAGPAVRIDDDAPIHGE
+PGATRFVARTVSGVDATRPTPPWLAARLRLAGIRTISLPVDISNYVMWELGQPLHFYDADTLSGEIVVRRARAGETLTTL
+DGKERELDPEDLLITDDSGPIGLAGVMGGAATEVTDATTTIVVESANFDPVSIARTRRRHRLPSEASKRNERGVDWEIAD
+EAAERAVQLLVELAGGTAEPGVTDVGTRPQPAVVEMAADFPSALVGVAYTTDEVVETLRALGAEVAVAEAAADVAPRLTV
+TAPSWRTDLRIPEDLAEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGLTEVLAYPFVSEEQNRRFGAD
+SDAQGQALAMVALANPIASQYRYLRLSLLPGLVETARRNLGRGFRDLALYEMGLVFLPG-AQLGSATIPPRAVHPSAEVL
+ADLEAGIPAQPWHVAGLYAGHDSAPGPDHDPRPVDWQDAIAGALDVADVLGVELTVRQGRHHAFHPGRVAELVVVTEHGD
+RVVGVAGELHPQWLEAEDLPARTSVWELDLDALCAAAPEIVVAAPLSTFPVSTQDVALVVDEAVVAGDVRATLAEGAGEL
+LEAVELFDVYRGAGVPEGRKSLAFSLRFRAPDRTLTAEEVSEARAAATALAAQRHGAVQR
+>1_1132
+MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPAAELQGPIVVGQVLSKEPEPQKNGKTINWCSVRVVPEGAA
+QPLTGEGIEPSGVQGIVCGAHNFEVGDKVVVTLPGAVLPGDFRISPRKTYGHVSAGMIASSTELGVGDDGTDGIIVLGDL
+GLDPEPGTDARDVLDLHGEAAEINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAAVHPPAADDAGPAVRIDDDAPIHGE
+PGATRFVARTVSGVDATRPTPPWLAARLRLAGIRTISLPVDISNYVMWELGQPLHFYDADTLSGEIVVRRARAGETLTTL
+DGKERELDPEDLLITDDSGPIGLAGVMGGAATEVTDATTTIVVESANFDPVSIARTRRRHRLPSEASKRNERGVDWEIAD
+EAAERAVQLLVELAGGTAEPGVTDVGTRPQPAVVEMAADFPSALVGVAYTTDEVVETLRALGAEVAVAEAAADVAPRLTV
+TAPSWRTDLRIPEDLAEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGLTEVLAYPFVSEEQNRRFGAD
+SDAQGQALAMVALANPIASQYRYLRLSLLPGLVETARRNLGRGFRDLALYEMGLVFLPG-AQLGSATIPPRAVHPSAEVL
+ADLEAGIPAQPWHVAGLYAGHDSAPGPDHDPRPVDWQDAIAGALDVADVLGVELTVRQGRHHAFHPGRVAELVVVTEHGD
+RVVGVAGELHPQWLEAEDLPARTSVWELDLDALCAAAPEIVVAAPLSTFPVSTQDVALVVDEAVVAGDVRATLAEGAGEL
+LEAVELFDVYRGAGVPEGRKSLAFSLRFRAPDRTLTAEEVSEARAAATALAAQRHGAVQR
+>2_1429
+MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPSDELRGPIVVGQVLSKEPEPQKNGKTINWCTVRVVPEGAE
+QTLTGEGIDPSGVQGVVCGAHNFEVGDKVVVTLPGAVLPGDFRISPRKTYGHVSAGMIASVRELGIGDD-HDGILVLSTL
+GLDPEPGTDALEVLDLQGEAAEINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAALTPPAADDAGHPVRIADDAPIYGA
+PGATRFVARTVSGVDASRPTPPWMAARLRLAGIRSISLPVDISNYVMWELGQPLHFYDAQKLAGEIVVRRARAGETLRTL
+DDKERTLDPEDLLITDDSGPIGLAGVMGGLATEVTDATTTIVIESANFDPISIARTRRRHRLPSEASKRNERGVDWEIAD
+EAAERAVQLLVELAGGTAEPGVTDVGTRPELAVVEMAADFPTALVGVEYTADEVAETLRALGAQVEAAEAADGAAPRLRV
+TAPSWRTDLRIPEDLVEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGHTEVLAYPFVSAEQNRRFGVD
+SEEQGEALEMVALANPISSQYRYMRLSLLPGLVEIARRNLGRGFRDLALYEAGLVFLPG-TQLGSASIPPRAAHPAPEVL
+ADLEAGIPAQPWRVAGLYAGHDSAPGPDHAPRPVDWQDAVSGALAVADVLGVELAVRQGRHHAFHPGRVAELVVLGERGD
+QVVGVAGELHPQWLEAEDLPARTSVWELDLDALCAAAPPAVVAVPLSTYPMSTQDVALVVEEAVVAGDVRASLAEGAGEL
+LESVELFDVYRGPGVPEGSKSLAFSLRFRAPDRTLTAEEASEARAAATALAAQRHGAVQR
+>3_1337
+MRIPLDWLREFAQVPADATAEDVLADLVTVGLEEEDVHRPSDELTGPLVVGQVLTREPEPQKNGKTINWCSVRVVPEGAE
+QTLTGEGIDPSGVQGIVCGAHNFEVGDKVVVCLPGAVLPGDFRISPRSTYGHVSAGMMASARELGLGDD-HDGIIVLGDM
+GLDPEVGTDVVDLFHLREEAAEVNVTPDRSYAFSIRGIAREYAHATGTAFTDPAAAVTAPEANDAGPAVTLADGAGIYGV
+PGCDRFVARVVEGIDPAAATPPWMAARLRLAGIRPHSLAVDVSNYVMWELGQPLHFYDADRLTGGITVRRAAAGETLRTL
+DDKERTLDPEDLVIADESGAIGLAGVMGGAATEVSEGTTRVLIESAHFDAVSIARTRRRHRLPSEASKRNERGVDWEIAD
+EAAERAVQLLVELAGGTPAQGVTDVGTRPEPVVVELDPEYPARRIGVDYPRERVVELLTGLGASVE------DAGDLLQV
+TAPTWRHDLRIPEDLVEEVARLDGYANIPSTLPVAPPGRGLTRAQVHRRRVADTLAAAGLTEVLDYPFVSEGQNRLFGSA
+TPEEGAAQRMVRLANPISSEFGWMRTTLLPNLLETVRRNVSRGFKDVALFEVGAVFLPGDGALGSPSNEPIGVKPSAETL
+AELDAGIPAQPRHVAGAFAGHEAAPGAGFAPRAFDWQDPIAAALAVGRAVGVELTVVQGTHQAFHPGRTATLSLPD---G
+TAVGVAGELLPAWLEDADMPARTGAFELDLDAVLAAAADRVVARPLSTYPASQQDVALVVADDVVAGDVRATLAEGAGEL
+LEEVALFDVYAGKGVPEGHKSLAFSLRFRAPDRTLTADEASEAREAATALAAERHGAVQR
+>4_1340
+MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPAAELQGPIVVGQVLSKEPEPQKNGKTINWCSVRVVPEGAA
+QPLTGEGIEPSGVQGIVCGAHNFEVGDKVVVTLPGAVLPGDFRISPRKTYGHVSAGMIASSTELGMGDDGTDGIIVLGDL
+GLDPEPGTDARDVLDLHGEAAEINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAAVHPPAADDAGPAVRIDDDAPIHGE
+PGATRFVARTVSGVDATRPTPPWLAARLRLAGIRTISLPVDISNYVMWELGQPLHFYDADTLSGEIVVRRARAGETLTTL
+DGKERELDPEDLLITDDSGPIGLAGVMGGAATEVTDATTTIVVESANFDPVSIARTRRRHRLPSEASKRNERGVDWEVAD
+EAAERAVQMLVELAGGTAEPGVTDVGTRPQPAVVEMAADFPSALVGVAYTTDEVVETLRALGAEVAVTEAADGAAPRLTV
+TAPSWRTDLRIPEDLAEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGLTEVLAYPFVSEEQNRRFGAD
+SDAQGQVPAMVALANPIASQYRHLRLSLLPGLVETARRNLGRGFRDLALYEMGLVFLPG-AQLGSATIPPRAVHPSPEVL
+ADLEAGIPAQPWHVAGLYAGHDSAPGPDHAPRPVDWQDAVAGALDVADVLGVELTVRQGRHHAFHPGRVAELVVVTEHGD
+RVVGVAGELHPQWLEAEDLPARMSVWELDLDALCAAAPETVVAAPLSTFPVSTQDVALVVDEAVVAGDVRATLAEGAGEL
+LEAVELFDVYRGAGVPEGRKSLAFSLRFRAPDRTLTAEEASEARAAATALAAQRHGAVQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001196.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001196.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f8b992a557ffb4d7e364cf6d9df6b5dfdb5b0b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001196.fa
@@ -0,0 +1,41 @@
+>0_1396
+MRWEAQTLRSEGGAQRATAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNSV
+PSASAMPFRWTVNPYRGCTHACRYCYARSTHTFLELDAGADFDRQIVVKVNVAEVLRAEL
+ARPTWGREAVALGTNTDPYQRAEGRYALMPGIIRALADSGTPFSVLTKGTLLARDVPLLQ
+AASRQVPVQVSLSLAMLDPAIAAAVEPGTPSPTARLRLIERLAAAGADVTVMAMPLLPWL
+TDGDREIDALMRALADAGAARVMPGALHLRPGAKEWYLDWIRREHPDLLAGYEQMYARSA
+YAPESYRRMLTRMAGEAAARHGLARGGAHGIRREDGPPARRRPASRP---SAPA------
+-------------AQPALF
+>1_1137
+MRWEAQTLRSEGGAQRATAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNSV
+PSASAMPFRWTVNPYRGCTHACRYCYARSTHTFLELDAGADFDRQIVVKVNVAEVLRAEL
+ARPTWGREAVALGTNTDPYQRAEGRYALMPGIIRALADSGTPFSVLTKGTLLARDVPLLQ
+AASRQVPVQVSLSLAMLDPAIAAAVEPGTPSPTARLRLIERLAAAGADVTVMAMPLLPWL
+TDGDREIDALMRALADAGAARVMPGALHLRPGAKEWYLDWIRREHPDLLAGYEQMYARSA
+YAPESYRRMLTRMAGEAAARHGLARGGAHGIRREDGPPARRRPASRP---SAPA------
+-------------AQPALF
+>2_1425
+MRWEAQTLRSESGAQRAAAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNAV
+PAASAMPFRWTVNPYRGCTHACRYCYARSTHAFLDLDAGEDFDRQIVVKVNVAQVLRAEL
+ARPTWGREAVALGTNTDPYQRAEGRYSLMPGIIEALADSGTPFSVLTKGTLLARDVPLLQ
+AASRSVPVQVSLSLAMLDPAVAAAVEPGTPSPAARLRLIERLAAAGADVTVMAMPLLPWL
+TDGDRDLDALMRALAAAGAARVMPGALHLRPGAKEWYLRWIRQEHPDLLAGYEQMYARSA
+YAPESYRRTLARAAGEAAARHGLTRGGAHGIRREDGPVARPVPRSTPVAVPAPA--AP--
+-------------AQPALF
+>3_1329
+MRWEAQTLRTGGGAQRPGAGTPAGSPATLPLPGLQRIVSPPEFAGVTFHEVLARSALNKV
+PASSAMPFRWTVNPYRGCTHACVYCYARGTHRYLDLGPGEDFDRQIVVKTNAPEVLRAEL
+SRPGWTREPVALGTNTDPYQRAEGRYRLMPGIITALADTGTPFSILTKGTLLGRDAPALQ
+AAAAQTSVQVGLSLALLDPSLAAAVEPGTPSPAARLRLISRLAEAGVEVSVMAMPLLPWL
+TDSDRQLDRLMAALADAGAHSVLAGTLHLRPGAREWFLGWIDREHPHLAADYRRMYARSA
+YAPQAYRRVVSQAAREAAARHGLRHGGAHTITREDGPGPRGGASAPL---SAPAGTTGAE
+QADTAADAVRPVIAQPTLF
+>4_1345
+MRWEAQTLRSEGGAQRATAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNSV
+PSASAMPFRWTVNPYRGCTHACRYCYARSTHTFLELDAGADFDRQIVVKVNVAEVLRAEL
+ARPTWGREAVALGTNTDPYQRAEGRYALMPGIIRALADSGTPFSVLTKGTLLARDVPLLQ
+AASRQVPVQVSLSLAMLDPAIAAAVEPGTPSPTARLRLIERLAAAGADVTVMAMPLLPWL
+TDGDREIDALMRALADAGAARVMPGALHLRPGAKEWYLDWIRREHPDLLAGYEQMYARSA
+YAPESYRRMLTRMAGEAAARHGLARGGAHGIRREDGPPARRRPASRP---SAPA------
+-------------AQPALF
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001203.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001203.fa
new file mode 100644
index 0000000000000000000000000000000000000000..546d96056779c59cf070392419406994d60bacc4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001203.fa
@@ -0,0 +1,21 @@
+>0_1405
+MAQSRRPDPVAPSESSGADATTVPPRPGRGLPVAVLVVAAALVLEAGALLWLAVDAVVHA
+ADGVLPAGARVMLVVIYALLTLWILATAVALLRGRAWSRGAAVAIQLFGVLLSSWLFSVD
+AAALGGPLLAVSGVALLTLFTTPVTRHLTPAPEASTDA------
+>1_1146
+MAQSRRPDPVAPSESSGADATTVPPRPGRGLPVAVLVVAAALVLEAGALLWLAVDAVVHA
+ADGVLPAGARVMLVVIYALLTLWILATAVALLRGRAWSRGAVVAIQLFGVLLSSWLFSVD
+AAALGGPLLAVSGVALLTLFTTPVTRHLTPAPEASTDA------
+>2_1417
+MAQSRRPDPVDPREAPAAPAPEGPRTGGR-APVAALVVAAALALQAAALLWLAGDAIAHL
+GDGVLPAGARVMLIVIYVLLGLWILVTSVALLRGRAWSRGAATAVQLFGVLLSSRLLSVG
+EPVVGGVLLAVSGIALVTLFSRPVTAHLSQAAREPSAE------
+>3_1320
+M---------------SSSIPASPSGRRR-MPAQAVVVAGVLGLEALTLVWLAVDGVAHL
+GAGALPTAAGVFLVVVYVLLAAWVGAVCGGMVRGRRFSRGAAVAIQLFAVILSTWLMSIG
+APIAGGLLLVGSGAALLCLFSGAVQAHLAGPDAGRPDAGRPDVG
+>4_1354
+MAQSRRPDPVAPSESSGADATTVPPRPGRGLPVAVLVVAAALVLEAGALLWLAVDAVVHA
+ADGVLPAGARVMLVVIYALLTLWILATAVALLRGRAWSRGAVVAIQLFGVLLSSWLFSVD
+AAALGGPLLAVSGVALLTLFTTPVTRHLTPAPEASTDA------
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001205.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001205.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c1ab02c3dec2d0d974cb95994da9afa05ddaac8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001205.fa
@@ -0,0 +1,40 @@
+>0_1407
+MVSSLAQDPLTSHPDIGDEDRAWLQRLVGDWQLVADLALADLVLWCPVPRRDEAGGFVALAQVRPFTAPTLFHRDIVGSR
+ARADLRAVVGQTWHGGERAEGAGPVEAPGGTLQVRLWPVVRAGRVIAVVSAHADPNGRPARSVIEENYSRTASTLLDMMQ
+HGRWPAPEEPSGLWAGGTPRVGDGLVVLGPDSVAEFTSPNAVSALRRLGIASTLEGHRLTDVLASTEAARVPTDEGTWAV
+LTGLRAGRREVQSGGASLTVRSVPLLGPDGWQGALLLLRDVTELRRQEQRLLTKDATIREIHHRVKNNLQTVGSLLRMQA
+RRTSSPEAERALRQAMQRVDTIALVHQTLSEEIEDQVPVDGLLQRQFRLAVEVAGDGRPLQVAVTGEFGELPSHVTTPLA
+LVLNELAANAVEHGTAPGGGCVGLHADRESTPAGTVLVVSVTDGGPAAPDGWVPGE-SPRAGEGSGLGLRIVHSLVEGDL
+RGTLRWERSDDGGTRVVLRLPLT
+>1_1148
+MVSSLAQDPLTSHPDIGDEDRAWLQRLVGDWQLVADLALADLVLWCPVPRRDEAGGFVALAQVRPFTAPTLFHRDIVGSR
+ARADLRAVVGQTWHGGERAEGAGPVEAPGGTLQVRLWPVVRAGRVIAVVSAHADPNGRPARSVIEENYSRTASTLLDMMQ
+HGRWPAPEEPSGLWAGGTPRVGDGLVVLGPDSVAEFTSPNAVSALRRLGIASTLEGHRLTDVLASTEAARVPTDEGTWAV
+LTGLRAGRREVQSGGASLTVRSVPLLGPDGWQGALLLLRDVTELRRQEQRLLTKDATIREIHHRVKNNLQTVGSLLRMQA
+RRTSSPEAERALRQAMQRVDTIALVHQTLSEEIEDQVPVDGLLQRQFRLAVEVAGDGRPLQVAVTGEFGELPSHVTTPLA
+LVLNELAANAVEHGTAPGGGCVGLHADRESTPAGTVLVVSVTDGGPAAPDGWVPGE-SPRAGEGSGLGLRIVHSLVEGDL
+RGTLRWERSDDGGTRVVLRLPLT
+>2_1415
+MVSSLAQDPLTSHPDLADEDRSWLQLLVGDWQLVADLALADLVLWCPAPRPDPAEGFVAVAQVRPFTAPTLFHRDIVGSR
+ARADLRAVVASTWSGGERPEGAGPVETPDGTLQVRLWPVVRRGRVVAVLSAHGDPNGRPSRSVIEENYIRTADSLLDMMQ
+HGRWPAPEESAGLWAGGTPRVGDGLVVLGPDSVARFTSPNAVSALRRLGIGATLEGHRLTDVLAGTDAARQPSEEGTWAV
+LTGLRAGRREVQSRGASLTVRSVPLLGPDGWHGALLLLRDVTELRRQEQRLVSKDATIREIHHRVKNNLQTVGSLLRMQA
+RRTSSPEADRALRQAMRRVDTIALVHQTLSEEIDGQVPVDDLLKRQFRLAVEVSGDGRPLEAAASGEFGELPSHVTTPLA
+LVLNELAANAVEHGTAPAGGRVELHAERELTPAGSVLVVSVTDGGSGVQDGWSPGE-FQPAADGAGLGLRIVQTMVEGDL
+RGTLRWERLPDGGTRVVLRIPTA
+>3_1318
+MVSTIASDPLNTHPDLGAEDRAWLQQLVGDWQLIADLALADLVLWCPLPVEVDGTGHLAMAQVRPFTAPTLFHRDIVGSR
+ARADLRALVDRVWAAGAPADGTGPLVEPGATLKVRLWPVVRAGRVVGVVSAHEDPRTRPARSAVEDNYRTSADTLLDMVQ
+HGRWPNPEDPPAYWIGGTPRVGDGLVVLGDDSRATFTSPNAVSALRRLGLPTTLAGHSLTELLGGTEAARRPVEEGSWAM
+LNGQRAGRTEVQANGATLTVRSVPLRNRDGWCGALIMLRDVTELRRQEQRLISKDATIREIHHRVKNNLQTVGSLLRMQA
+RRSDSPETGRALRQAMQRVDTIALVHQTLSEQIDAQLSVDALMARQFRLAVEVAGDGRPLGTRVEGTFGELASHVVTSVA
+LVLNELATNAVEHGTGEEGGVVSLQAHREDTPAGDVLVFSVTDGAS-VEDG--PGEGFVPQPAPNGLGLRIVHSLVEGDL
+RGSIQWRRMPDGGTRVTVRLPVE
+>4_1356
+MVSSLAQDPLTSHPDIGDEDRAWLQRLVGDWQLVADLALADLVLWCPVPRRDEAGGFVALAQVRPFTAPTLFHRDIVGSR
+ARADLRAVVGQTWHGGERAEGAGPVEAPGGTLQVRLWPVVRAGRVIAVVSAHADPNGRPARSVIEENYSRTASTLLDMMQ
+HGRWPAPEEPSGLWAGGTPRVGDGLVVLGPDSVAEFTSPNAVSALRRLGIASTLEGHRLTDVLASTEAARVPTDEGTWAV
+LTGLRAGRREVQSGGASLTVRSVPLLGPDGWQGALLLLRDVTELRRQEQRLLTKDATIREIHHRVKNNLQTVGSLLRMQA
+RRTSSPEAERALRQAMQRVDTIALVHQTLSEEIEDQVPVDGLLQRQFRLAVEVAGDGRPLQVAVTGEFGELPSHVTTPLA
+LVLNELAANAVEHGTAPGGGCVGLHADRESTPAGTVLVVSVTDGGPAAPDGWVPGE-SPRAGEGSGLGLRIVHSLVEGDL
+RGTLRWERSDDGGTRVVLRLPLT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001210.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001210.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07a7054317a272c5737de28a26f6cf6d05b84a9c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001210.fa
@@ -0,0 +1,41 @@
+>0_1412
+ME--RSTSPA------------GPAPTRPVDAADAVGLTVLLLAGPGLLACAAALLQTGT
+SAPGAELTRVLGLGAGLAGLGLLAWWAVGLIGLALVALGRRAGRPAWARLGRSLTPALLG
+RVAGAVVGAQLLAAPAAWAD----AAHPVPDASWTVAAVPAHATGVEAPA--PDAAWTP-
+RPPAPAPPGAGTGRADPDHPTVTVRRGDCLWHLAAAELGPDATPREIDARWRRWYEANRR
+VIGDDPHLLLPGTVLTSPVFTPHAGVDG-----PRP------------------------
+------------------------------------------------------------
+--
+>1_1153
+ME--RSTSPA------------GPAPTRPVDAADAVGLTVLLLAGPGLLACAAALLQTGT
+SAPAAELTRVLGLGAGLAGLGLLAWWAVGLTGLALVALGRRAGRPAWARLGRSLTPALLG
+RVAGAVVGAQLLAAPAAWAD----AAHPVPDASWTVAASPTHATGVEAPA--PDAAWTP-
+RPPAPAPPGAGTGRADPDHPTVTVRRGDCLWHLAAAELGPDATPREIDARWRRWYEANRR
+VIGDDPHLLLPGTVLTSPVFAPHAGVDG-----PRP------------------------
+------------------------------------------------------------
+--
+>2_1410
+MQ--RITEPARRGRAALSEADGHRADGHRVDTVDAVGLVVLALAAPALLIGAAALLEPGE
+GAASSELVRLLGLGAGIAGLGLVAWWAVGLLGLVLATVGRRTGRLGFARLGARLTPALLG
+RVAGAVLGAHMLAAPAAWAEQP--AVGPVPDAGQTVSHAAPASTTASAPAAVPEAAWTP-
+RTPVPAPPGATAARNLSDRPTVTVRRGDCLWDIAAAELGPDATPREIDARWRRWHEANRR
+VIGDDPHLLLPGTVLTAPVFSPHAAPQEGLAMTPRPRTTPTTTRPQEPAMTALAARPPSP
+PSTAAPAVSPGTPTVAPTVPPPRCCTVPPTARPCCPAARRSPAGPPSSRAGRSCVGSAPW
+PR
+>3_1313
+MSFVASQPPA------------AGVHAPRASALDVAALAVLAAAVPALGWAAATLLGPAA
+PTPDAALGRALGLGAAGLGLALAAWWALGLLGLAALALGRRTGHRGWSRLGERMTPALLR
+RAGAAVLGAQLLAAPAAWADAPPAPSAAVVDASWT---------SAAASPTLPDAAWTPG
+APPTPQPGSPAAPRDTGDRPTVTVRAGDCLWDIAADELGPDATPREVDRRWREWHRHNRD
+LIGEDPNLILPGTVLTAPDFTPHVQRGG----TP--------------------------
+------------------------------------------------------------
+--
+>4_1361
+ME--RSTSPA------------GPAPTRPVDAADAVGLTVLLLAGPGLLACAAALLQTGT
+SAPGAELTRVLGLGAGLAGLGLLAWWAVGLIGLALVALGRRAGRPAWARLGRSLTPALLG
+RVAGAVVGAQLLAAPAAWAD----AAHPVPDASWTVAAVPAHATGVEAPA--PDAAWTP-
+RPPAPAPPGAGTGRADPDHPTVTVRRGDCLWHLAAAELGPDATPREIDARWRRWYEANRR
+VIGDDPHLLLPGTVLTSPVFTPHAGVDG-----PRP------------------------
+------------------------------------------------------------
+--
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001215.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001215.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38d4bedf79474b4160f62b874119a97e6bb5d76e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001215.fa
@@ -0,0 +1,45 @@
+>0_1417
+MTTVDPQPP-RPPRVAVVAVIVALVLALSGCTQIPQSSEVRSADPVDGASAAADAPQFHPPGPAESDTAEEAIRGFLLAG
+TSPQDDYAVAREFLDGPAATQWTPGQRTLVYSAEPRITRGDGDGDYQIQVEVDSEIDEYGLRTVAPPGTTRAWAVTVQER
+PQGMRITSTENGTLLSQAQFGQLFAPHELAFYDTAKRYIVPDVRWFVNRGTTVTAVTRALLRGPAPYLAGAVETAFPLRT
+GTDLAAPTVPVDDDGVAHVDLTQAAAEGADAERRHRMREQLELTLRGLQSVKEVEVTVAGAQLSTSGDDGPAP---VQTD
+PAVRSVQVGIDAATGGLVYVQGSSVTPVGGAPDVTALDPVRPTMSGDRSRFAFVTGDRTAVHVAGTDGSLREVLRGTGLT
+VPSLDLLGWVWAADRGTTSRIRAVSAQPGGQERIVTATWLRPGERIVDLRLARSGARAAMLVDDGQRTTLRVSGVVRGSD
+GVPNALTEPILLPSSGSEDSVEWAGDTNLLVSAYAEKPDERVVPRIVSIDGTVRELNPLGGLRGISAGDDGAYYAETEEL
+VFLLVGSSWRAQELDRGVRDLSFPD
+>1_1158
+MTTVDPQSP-RPPRLAVVGVIVALMLALSGCTQIPQSSEVRSADPVDGATADADAPQFHPPGPAESDTAEEAIRGFLLAG
+TSPQDDYAVAREFLDGPAATQWTPGQRTLVYSAEPRITRGDGAGDYQIQVEVDSEIDEYGLRTIAPPGTTRAWAVTVQER
+PQGMRITSTENGTLLSQAQFGQLFAPHELAFYDTAKRYVVPDVRWFVNRGTTVTAVTRALLRGPAPYLAGAVDTAFPLRT
+GTDLAAPTVPVDDDGVAHVDLTQAAAEGADAERRHRMREQLELTLRGLQSVKEVEVTVAGAQLSTSGDDGPAP---VQTD
+PAVRSVQVGIDAATGGLVYVQGSSVTPVGGAPDVTALDPVRPTMSGDRSRFAFVTGDRTAVHVAGTDGSLREVLRGTGLT
+VPSLDLLGWVWAADRGTTSRIRAVSAQPGGQERIVTATWLRPGERIVDLRLARSGARAAMLVDDGQRTTLRVSGVVRGSD
+GVPNALTEPILLPSSGSEDSVEWAGDTNLLVSAYAAKPDERVVPRIVSVDGTVRELNPLGGLRGISAGDDGAYYAETEEF
+VFLLVGSSWRAQELDRGVRDLSFPD
+>2_1405
+MSPTRPTGPRRARRLAGVGLAAALALALGGCTQIPQSSDVRSAEPLDGATAAPEAPQFRPPGPSADDTAEDVIRGFLLAG
+TSPQDDYAVAREFLDGPAAARWAPGQRTLVYSAQPRITRGEGTGNYQVQVEVDSEIDEFGLRTIAPEGTTRAWQVSVQER
+PEGMRITATENGTLLSQSQFGQLFAPHELAFYDTAQRYAVPDVRWFVNRGTTVTAVTRALLRGPAPYLTGAVETAFPLRT
+GADLAGPTVPVDEDGVAHVDLTEAAAEGADADRRHRMREQLEITLLGLQSVSDVRVTVDGAELSASGENPPPP---VQDE
+PTTGSVQVGIDSATGDLAYFQGMSVGPVGGAPDVSALDPVDPTMSRDRSRFAFVTRDRTAVHVAGTDGSLREAMRGTGLT
+SPSIDGLGWVWAADGAETSRVRAVPAEPGQEARIVTATWLRPAERIVDLRVSRSGARAALLVDDGDRRTVRVAGIVRGSD
+GVPSALTEPILLPSTGRAASVEWAGDTNLLVSPRAATPDERVVPRIVSIDGTVRELNPLGGLTGVSAGDGGALYAETDEL
+VFLLVGSSWRAQELERGVRDLSFPG
+>3_1307
+---MRPSGPARP-RRRLCAAALAGALALAGCAQIPQSSPVRSGAPLDVGSRAADAPQFRPPGPAEDATAEQLVRGFAQAG
+IAPEDGYAIARQYLSAEASDGWEPDRGVVVYSGEPTVTRGLGEGTYEVQLEVESEVDEFGQRTMAPPNTTQAREVTVEEV
+DGVLRITGVQDGVLLSRSQFAQLYAPHPLYFFDQSQAFAVPDVRWFVNRGTAVTALTRALLRGPAPYLTGAVATAFPLRT
+GADLTGPSVPVAEDGTAAVDLTGATVDGADPARLSRMREQLERTLTGVSGVERVEVTVEGRSLTSSAPSGSVPSARIGED
+P--GTVQVGVSDA-GELVFFQGLDAVPVGGLPSVADLGPEDPAMDRERRRFVFLDRTRTVLHGVGTDGGEHRLLDGGRLT
+APSLDSSGWAWTVDRARSSRISVVRADGSEPARVVTTPWLAEGESIVALHIGPAGARAALIVDDGQQRTLRVAGVVRGGD
+GVPTALTPPVYIPTLDPPDDVEWMGDGSLVSTPLAPDAETRVRPEVVSLDGTSRQLNPLAGLTGISAREEGTLYAETAED
+VFLLVGSSWRAQDVATPVHDLAFPD
+>4_1366
+MTTVDPQPP-RPLRVAVFAVIVALVLALSGCTQIPQSSEVRSADPVDGATAAADAPQFHPPGPAESDTAEEAIRGFLLAG
+TSPQDDYAVAREFLDGPAATQWTPGQRTLVYSAEPRITRGDGAGDYQIQVEVDSEIDEYGLRTVAPPGTTQAWAVTVQER
+PQGMRITSTENGTLLSQAQFGQLFAPHELAFYDTAKRYVVPDVRWFVNRGTTVTAVTRALLRGPAPYLAGAVDTAFPLRT
+GTDLAAPTVPVDDDGVAHVDLTQAAAEGADADRRHRMREQLELTLTGLQSVKEVEVTVAGAQLSTSGDDGPAP---VQTD
+PAVGSVQVGIDTATGGLVYVQGTSVTPVGGAPDVTALDPVRPTMSGDRSRFVFVTRDRTAVHVAGTDGTLREVLRGTGLT
+VPSLDLLGWVWAADRETTSRIRAVPAQPGGQERIVTATWLRPGERIVDLRLSRSGAQAAMLVDDGQRTTLRVSGVVRGSD
+GVPNALTEPILLPSSGSEDSVEWAGDTNLLVSAYAEKPDERVVPRIVSIDGTVRELNPLGGLRGISVGDDGAYYAETEEL
+VFLLVGSSWRAQELDRGVRDLSFPD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001221.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001221.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aea4df6768945d9b83856f7e05c18d2d25343356
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001221.fa
@@ -0,0 +1,41 @@
+>0_1426
+MSREGNIVLPGRTVTVRRRWLNGRVPTPSVPLVHPVHRFAHHEIDFRRRIVTMAVVNRTP
+DSFYDDGAGAVLEDALAQAHAAADAGAEWVDVGGVPFAPGAELDPTEEAARVVPLIAALR
+SGDGAGSSEASRRLILSADTFQPAVAEAALAAGADVVNDTTGLFHADLGRVVAAAGAHLV
+VTHSLAHVRGPRAVVPRPTYGDVVREVRDHLRRTVDRAVALGVPEERIIVDPGHDLNKNT
+RHTLEITRRLDEIATLGLPVLAAVSNKDFIGESLDRHRHERLPGSLAAAAACVYGGARIL
+RMHDADASVSAARMLECVFGWRQPARLVHNMGAENPPPDRSTLAGH-RAHR---------
+----GGRA
+>1_1167
+MSREGNIVLPGRTVTVRRRWLNGRVPTPSVPLVHPVHRFAHHEIDFRRRIVTMAVVNRTP
+DSFYDDGAGAVLEDALAQAHAAADAGAEWVDVGGVPFAPGAELDPTEEAARVVPLIAALR
+SGDGAGSSEASRRLILSADTFQPAVAEAALAAGADVVNDTTGLFHADLGRVVAAAGAHLV
+VTHSLAHVRGPRAVVPRPTYGDVVREVRDHLRRTVDRAVALGVPEERIIVDPGHDLNKNT
+RHTLEITRRLDEIATLGLPVLAAVSNKDFIGESLDRHRHERLPGSLAAAAACVYGGARIL
+RMHDADASVSAARMLECVFGWRQPARLVHNMGAENPPPDRSTLAGH-RAHR---------
+----GGRA
+>2_1398
+MRQ------------------NVAMALTELALRHPVRRFARREVDFRRRILTMAVVNRTP
+DSFYDDGAAFALEAAVDQARAAAEAGAEWVDVGGVPFAPGPALDPGEEARRVVPLIAALR
+-GEAAEHSEAVAGLILSADTFEPAVAEAAIAAGADVVNDTSGLVHADLGRVVAASQAHLV
+LTHSLAHVHGPRAVVPRPRYGDVVAEVREHLLRTVERAVALGVPEERIIVDPGHDLNKNT
+LHTLEITRRLDEIAGLGLPVLAAVSNKDFIGESLDQHRHERLAGSLAAAVACVHGGARIL
+RMHDAAASVSAARLLECVFGWREPARLVHNMGEANPAPDRTSLAEH-RAGRVRA------
+----GGTR
+>3_1298
+------------------------MPTPSVPLAHPVHRFAHHEIDFRRRIVTMAVVNRTP
+DSFFDDGAGFAFDAALAQVHTAADAGAEWVDVGGVPFAPGRELDPAEEAARVAPFVAAVR
+AGRGEGASEAARRLILSADTFQPAVAEAAIDAGADVVNDTTGLYYPDLGRVVAASNAHLV
+VTHSLAHVSGPRTVVPRPRYDDVVAEVREHLLRTVDRAVALGVPEERIIVDPGHDLNKTT
+VHTLEVTRRLDEIADLGFPVLAAVSNKDFIGESLDRHRHDRLAGTLASAAFCALAGARIL
+RMHDADASVSTAHMLECILGWREPLLAVHNTGDVNPAADRTTPADRVPADRPPAAVPAPT
+HDPEEARP
+>4_1375
+MSREGNIVLPGRTVTVRRRWLNGRVPTPSVPLVHPVHRFAHHEIDFRRRIVTMAVVNRTP
+DSFYDDGAGAVLEDALAQAHAAADAGAEWVDVGGVPFAPGAELDPTEEAARVVPLIAALR
+SGDGAGSSEASRRLILSADTFQPAVAEAALAAGADVVNDTTGLFHADLGRVVAAAGAHLV
+VTHSLAHVRGPRAVVPRPTYGDVVREVRDHLRRTVDRAVALGVPEERIIVDPGHDLNKNT
+RHTLEITRRLDEIATLGLPVLAAVSNKDFIGESLDRHRHERLPGSLAAAAACVYGGARIL
+RMHDADASVSAARMLECVFGWRQPARLVHNMGAENPPPDRSTLAGH-RAHR---------
+----GGRA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001222.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001222.fa
new file mode 100644
index 0000000000000000000000000000000000000000..882b2bc5cdce718e0a6dea26034738d3e4eefef2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001222.fa
@@ -0,0 +1,31 @@
+>0_1427
+MRRLTETGPGLDDDALRTALAAPAAEDTGPGPWVRVVFIASADGAATLDGRAGGLGSPAD
+QRLLSLSRHDADVVLVGAGTIRAEGYEGALLSEEDRRRRAEAGGPADPPVAVVSGSLDLD
+PASAFFTAAPVRPWILTSRAALAAEPERAAALAARADVLAVGEEHVDPQTVVATLHARGA
+RVVHCEGGPRLFGSLAAAGLVDEVHLTVAPLLAGPAAGRVLTGEDGPGLPARLQLVQVLH
+DDGMLFLRLHHERHA-----SPGPDPTP----------
+>1_1168
+MRRLTETGPGLDDDALRTALAAPAAEDTGPGPWVRVVFIASADGAATLDGRAGGLGSPAD
+QRLLSLSRHDADVVLVGAGTIRAEGYEGALLSEEDRRRRAEAGGPADPPVAVVSGSLDLD
+PASAFFTAAPVRPWILTSRAALAAEPERAAALAARADVLAVGEEHVDPQTVVATLHARGA
+RVVHCEGGPRLFGSLAAAGLVDEVHLTVAPLLAGPAAGRVLTGEDGPGLPARLQLVQVLH
+DDGMLFLRLHHERHA-----SPGPDPTP----------
+>2_1397
+MRRLAAVGPELSDEDLLALRRAPSTQD-APGPWVRAVFVSSLDGATALDGRSGTLGSPAD
+RRQFALARTDADVILVGAGTVRAEGYAGPLVDAAARARRAARGLPEHPAVAVVTGSLDLD
+PDGEFFRAAPVRPWVIASERAVAAQPERAAALAEVADVLTAGVRDVEPRELLALLAGRGA
+RVVHCEGGPTLLGALAAAGAVDELLLTLSSLLAGGAGPRLIPAVEGIGLPARMLPHHVLT
+QDGDLYLRLLHERHAALLADAPGLDGRAGTGR------
+>3_1297
+MRLLTATGPEIDDDALLALRRAPAPDL-VPGPWVRAVFVSSLDGAATLDGRAGGLGSPAD
+QRQFTLARTDADVVLVGAGTVRAEGYEGPLVGPAARARREEAGLPAHPGIAVVSGALGLD
+PDGDFLRQAPVRPLILTTQTALERCPDRAEALAARADVVASGAEVVEAPALVDALTARGH
+RVLHCEGGPRLFGTLAAADLVDELLLTISPLLAGGDGPRVLSGGDGPGLPTRLRPHHVLT
+EDGELYLRLVHERHAAVLAEAPGLEADPADADPAPGAP
+>4_1376
+MRRLTETGPGLDDDALRTALAAPAAEDTGPGPWVRVVFIASADGAATLDGRAGGLGSPAD
+QRLLSLSRHDADVVLVGAGTIRAEGYEGALLSEEDRRRRAEAGGPADPPVAVVSGSLDLD
+PASAFFTAAPVRPWILTSRAALAAEPERAAALAARADVLAVGEEHVDPQTVVATLHARGA
+RVVHCEGGPRLFGSLAAAGLVDEVHLTVAPLLAGPAAGRVLTGEDGPGLPARLQLVQVLH
+DDGMLFLRLHHERHA-----SPGPDPTP----------
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001234.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001234.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cdeb046db3abe8f24645750a6f6fac4b0e59760b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001234.fa
@@ -0,0 +1,31 @@
+>0_1462
+M-----RTVAETVTTVPHDAAASALEPG----AWAPPTDVHVAGLDAVGAAIAHALAGAG
+ALRLALWDPRPVDAADLGTGLLPGDLGRPRAGALARRLGDVAPGLRLYAHHGPVPVLVGQ
+ATVAVGSVLDADLAAHALAADHPLLPVTVGPRAVTVGPWCAPVVRGCPLCRWPADPAGVP
+GAPTAPGPSAHRGQ-----VDGLAALRAAVLTVDAL--RTGPAPGVLRADRVTGRTRRVK
+VRPRPGCACDPDALG-------WAF------------------
+>1_1181
+M-----RTVAETVTTVPHDAAASALEPG----AWAPPTDVHVAGLDAVGAAIAHALAGAG
+ALRLALWDPRPVDAADLGTGLLPGDLGRPRAGALARRLGDVAPGLRLYAHHGPVPVLVGQ
+ATVAVGSVLDADLAAHALAADHPLLPVTVGPRAVTVGPWCAPGVRGCPLCRWPADPAGVP
+GAPTAPGPSAHRGQ-----VDGLAALRAAVLTVDAL--RTGPAPGVLRADRVTGRTRRVK
+VRPRPGCACDPDALG-------WAF------------------
+>2_1384
+MPAAPSSALSDALSSAEPGAVRPEVEPGPPGAGWEPPVDVHVAGLDAVGVAVAHALAGAG
+AHRMALWDPRPVDAADLGTGLLPGDLGRPRARALERRLLDVAPGLRVYAHHGPLPVLVGQ
+ASVAVGDVLDADLAAQALAADHPLLPVHVGPRAVTVGPWCAPDVVGCPLCSLPADPVGPP
+GRRSARGRATSSGESGAAAVDALTAQRAAVLVADAL--RAGPSAGVVRADRASGRTRRAR
+VRPRAGCACDPDALA-------WGT------------------
+>3_1284
+M------ATTD---------AHGPRESG----LLADPAGIQVAGLGPAGGALAAALAAGG
+VAALALWDPTPVGASDLGLGLLPADLGRPRDRAWEARLSRTWPALPVYAGAGTRPGALGA
+ATVAVDLPGLPDLAARAIAAQHPLLPVRTDLHGVSAGPWTGGGAPGCVLCTEDVPGTALT
+APPAAPPRRDPGAA-----REPGHALRAVVLALDVLTGRRDATSAVLRVDAATGRLTRIP
+VRTRPGCGC-ADLLAGDGTGDDWAAALAAVEESLDGALADARP
+>4_1389
+M-----RTVAETVTTVPHDAAASALEPG----AWAPPTDVHVAGLDAVGAAIAHALAGAG
+ALRLALWDPRPVDAADLGTGLLPGDLGRPRAGALERRLGDVAPGLRVFAHHGPVPVLVGQ
+ATVAVGSVLDADLAAQALAADHPLLPVTVGPRAVTVGPWCAPGVRGCPLCRWPADPAGVP
+GVPTAPGPSAHRGQ-----VDGLAALRAAVLTVDAL--RTGPAPGVLRADRVTGRTRRVK
+VRPRPGCACDPDALG-------WAF------------------
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001240.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001240.fa
new file mode 100644
index 0000000000000000000000000000000000000000..70bb9acc06949193ade24d1a9f23eb1eb59adfc1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001240.fa
@@ -0,0 +1,21 @@
+>0_1468
+MT---DHPVLPGARHRDDGPLTLGEGLEALARLVPPGRAVSYGGLAGLLGVGGPRQAGRA
+MAESSPGTPWWRVVRADGSLPPELAARAAVEHEREAMPRTPAG-----RVDLPRARWEPD
+DGAARAIRAIADRIVSGPGARMRP
+>1_1187
+MT---DHPVLPGARHRDDGPLTLGEGLEALARLVPPGHAVSYGGLAGLLGVGGPRQAGRA
+MAESSPGTPWWRVVRADGSLPPELAARAAVEHEREATPRTPAG-----RVDLPRARWEPD
+DGAARAIRAIADRIVSGPGARMRP
+>2_1378
+MT---TPPADP--RPVPDGPLTLGEGLEAVARLVPAGRAVSYGDLAGLLGVGGPRQAGRA
+MAKSAPGTPWWRVVSADGSLPGELARRAAVEHAREGTPVRPGG-----RVDLPRARWEPD
+EAALGAVAAIAARIVSGPGARMQA
+>3_1278
+MSPVPSTPPDPDPHLPTDGPVTLGEALAAAARLIPSGRAASYGALAGLLGRGGPRQAGRA
+MAESEPGTPWWRVVRADGSLPEPLRRQARERWAAEGTPVRGSGTVRDQRVDLAQAGWEPD
+AAARAALADLAARV---------G
+>4_1395
+MT---DHPVLPGARHRDDGPLTLGEGLEALARLVPPGRAVSYGGLAGLLGVGGPRQAGRA
+MAESSPGTPWWRVVRADGSLPPELAARAAVEHEREGTPRTPAG-----RVDLRRARWEPD
+DGAARAIRAIADRIVSGPGARMGP
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001241.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001241.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5333adaa33337bdcda20b47c712bd6db6012a25d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001241.fa
@@ -0,0 +1,26 @@
+>0_1469
+---MTWHESIRAGFDLETTGRDPRTALIVTATLVMVDEQGRAASSAEWLVDPGVPIPAEA
+AEVHGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARHHGL
+TPLEARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALA
+ARYEQLRVAPVDLHERQVRWKAEQAESFEQYLRRKDPQATVSRHWPVEAER
+>1_1188
+---MTWHESIRAGFDLETTGRDPRTALIVTATLVMVDEQGRAASSAEWLVDPGVPIPAEA
+AEVHGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGL
+TPLEARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALA
+AQYEQLRVAPADLHERQVRWKAEQAESFEQYLRRKDPQATVSRHWPVDAER
+>2_1377
+MSPVNWHQSIRAGFDLETTGRDPRSALIVTATLVMVDAQGRATASAEWLLDPGVPIPAEA
+AEVHGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGL
+APVEARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALA
+ERHEQLRVDPAELHERQVRWKAEQAESFEEYLRRKDPQATVSRDWPVESGR
+>3_1277
+---MSWNEQIRAGFDLETTGRDPRQARIVTATIVMVDAAGKAVSSAEWLLDPGVPIPEEA
+AAVHGVTTERARAEGLEARRGVSEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGV
+APLEPRPVVDPYVVDKQVDRFRKGKRTLGAVSEHYDVVLEDAHTSAADALAAVQVMDELV
+RRHPKADLPLDELHAAQARWKAEQAESFEEYLRRKDPQATVSRAWPVEPDV
+>4_1396
+---MTWHESIRAGFDLETTGRDPRTALIVTATLVMVDEHGRAASSAEWLVDPGVPIPAEA
+AEVHGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGL
+TPLEARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALA
+ARYEQLRVAPTDLHERQVRWKAEQAESFEQYLRRKDPQATVSRHWPVEAER
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001249.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001249.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0b5092c105454c74d9fcc7275db3fc5902eecc12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001249.fa
@@ -0,0 +1,46 @@
+>0_1477
+----------MTTAPEPRADAPVHTGPDAGVAPALRTPEKAAAGVDYDVCGVMAPKDYDA
+LLLASFGGPEGQDDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALKAAI
+EAELAARGLDLPVYWGNRNWEPYFPDTLARMHADGHRRILTVTTSAYSCYSSCRQYREDM
+GMAMEQTGLTGKVDLDKTRQYFNHPGFIEPFRDGLRADLASLRAELGDDARIHVLFATHS
+IPTSDAAAAGPRGLAADLRAQAGAEPGD-EGADVYSAQHLDVAREILAGVPEAADVPWSL
+VYQSRSGPPSVPWLEPDINDAMEHLAGEGAETDAQGRAVAGFVVVPLGFVSDHMEVVWDL
+DTEAKETAEGLGVGFRRSPTPGTDPRFVAGLVDIVEERLGRREGRAAVGCFPAWYDVCRP
+DCCVKVMRDGSTRPTTSAVDAAVRGLAEHEAGAAAPAEEA-----
+>1_1197
+----------MTTAPEPRADAPVHTGPDAGVAPALRTPEKAAAGVDYDVCGVMAPKDYDA
+LLLASFGGPEGQDDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALKAAI
+EAELAARGLDLPVYWGNRNWEPYFPDTLARMHADGHRRILTVTTSAYSCYSSCRQYREDM
+GMALEQTGLTGKVDLDKTRQYFNHPGFIEPFRDGLRADLASLRAELGDDARIHVLFATHS
+IPTSDAAAAGPRGLAADLRAQAGAEPGD-EGADVYSAQHLDVAREILAGVPEAADVPWSL
+VYQSRSGPPSVPWLEPDINDAMEHLAGEGAETDAQGRAVAGFIVVPLGFVSDHMEVVWDL
+DTEAKETAEGLGVGFRRSPTPGTDPRFVAGLVDIVEERLGRREGRAAVGCFPAWYDVCRP
+DCCVKVMRDGSTRPTTSAVDAAVRGLAEHEAGAAAPAEEA-----
+>2_1369
+MSTAPENAAAASPAPEPRADAPVHAGPRAGVAPTLRAPEEAAAGVDFDVCGVMAPKEYDA
+LLLASFGGPEGQDDVIPFLRNVTRGRGIPDERLEEVATHYRANDGVSPINAQNRALKAAI
+EAELAARGLALPVYWGNRNWEPYVPDTLERMHADGHRRILTVTTSAYSCYSSCRQYREDM
+GMALRRTGLEGVVDLDKTRQYFNHPGFIEPFRDGLRADLASLREELGEDARIHVLFATHS
+IPTSDAAAAGPRGLAADLRAQAGAEPGE-EGADVYSAQHLDVAREILAGVPEAADVPWSL
+VYQSRSGPPSVPWLEPDINDAMEHLAGEDAEADAAGRAVAGFVVVPLGFVSDHMEVLWDL
+DTEARQTAADLGVAFRRSPTPGTDPRFVSGLVDIVEERMGRREGRASLGCFGAWYDVCRP
+DCCSKVMRDGTVRPTTSAVDADVRGLAEHEAGTAPAGRTEE---S
+>3_1261
+MTA-----------------VPTHRVPEDARRP-VHEPERAAAGVDYDACGAMAPKAYDA
+LILASFGGPEGQEDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALISAI
+EAELVRRGLELPVYFGNRNWEPYFPDALQRAYDDGHRRILTVTTSAYSCYSSCRQYREDM
+GLAMERTGLEGKVDLDKTRQYFNHPGFVEPFAEGLRADLASLREEVGEDARVHLLFATHS
+IPTADAAAAGPRGLAAALREQAGGEPGDVEGADAYSAQHLDVIREVLARVPEAEGVDWSL
+VYQSRSGAPHVPWLEPDINDALEALAGPDAPADADGRALAGVVVVPVGFVSDHMEVVWDL
+DTEAKDTAAELGVAFRRTPTPGTDPRFVSGLVDIVEERLGRREGREAVGCFPAWYDVCRP
+DCCVKVMRDGSVRPTTSAVDAPVRGLAEHR-GEQDGADDAGAQDS
+>4_1404
+----------MTTAPEPRADAPVHTGPDAGVAPALRTPEKAAAGVDYDVCGVMAPKDYDA
+LLLASFGGPEGQDDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALKAAI
+EAELAARGLDLPVYWGNRNWEPYFPDTLARMHADGHRRILTVTTSAYSCYSSCRQYREDM
+GMAMEQTGLTGKVDLDKTRQYFNHPGFIEPFRDGLRADLASLRAELGDDARIHVLFATHS
+IPTSDAAAAGPRGLAADLRAQAGAEPGD-EGADVYSAQHLDVAREILAGVPEAADVPWSL
+VYQSRSGPPSVPWLEPDINDAMEHLAGEGAETDAQGRAVAGFVVVPLGFVSDHMEVVWDL
+DTEAKETAEGLGVGFRRSPTPGTDPRFVAGLVDIVEERLGRREGRAAVGCFPAWYDVCRP
+DCCVKVMRDGSTRPTTSAVDAAVRGLAEHEAGAAAPAEEA-----
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001252.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001252.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eaa4ae604c680f04f7c5ae749249ae745461c2e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001252.fa
@@ -0,0 +1,41 @@
+>0_1480
+MSALSQTPETPAAVPALPAEHPLRTEDPSRSTVASPLLRALRGQRPDRHPVWFMRQAGRS
+LPEYRRVREGIGMLDSCLMPDLVREITMQPVRRHDVDAAIFFSDIVVPLRLAGVDVEIQP
+GVGPVLGQAVRTADDVAALPVLEDAALDVIREAVAATVAELGPRPLIGFAGAPFTLAAYM
+VEGRPSRDHFGPRRMMHADPETWAALAGWAATVSGQFLRAQLESGASAAQLFDSWAGSLS
+ADDYLEHVQPHSTAALAHVADLAGPGVPDGAPLLHFGTGTGEFLHHMRDAGATAVGVDHR
+LTLAEAHRRLSANPGPDGRGAVPLQGNIDPALLAAPWEVLEAHVRDVVASGAVAPGHVVN
+LAHGVPPETDAAVLTRVVELIHSLPVPEREGQDPAPGAETAEREERA
+>1_1200
+MSALSQTPETPAAVPALPAEHPLRTEDPSRSTVASPLLRALRGQRPDRHPVWFMRQAGRS
+LPEYRRVREGIGMLDSCLMPDLVREITMQPVRRHDVDAAIFFSDIVVPLRLAGVDVEIQP
+GVGPVLGQAVRTADDVAALPVLEDAALDVIREAVAATVAELGPRPLIGFAGAPFTLAAYM
+VEGRPSRDHFGPRRMMHADPETWAALAGWAATVSGQFLRAQLESGASAAQLFDSWAGSLS
+ADDYLEHVQPHSTAALAHVADLAGPGVPDGAPLLHFGTGTGEFLHHMRDAGATAVGVDHR
+LTLAEAHRRLSANPGPDGRGAVPLQGNIDPALLAAPWEVLEAHVRDVVASGAVAPGHVVN
+LAHGVPPETDAAVLTRVVELIHSLPVPEREGQDPAPGVETAEREERA
+>2_1366
+MSDLSQTSEIRAGAPALPADHPLRTQDPARSTAASPLVRALRGQRPDRHPVWFMRQAGRS
+LPEYREARAGIGMLESCLMPDLVREITLQPVRRHDVDAAIFFSDIVVPLRLAGVDVEIQP
+GVGPVLGRAVRTAEDVAALPVLEDSALDVIREAVSSTVAELGPRPLIGFAGAPFTLAAYM
+VEGRPSRDHFGPRRMMHGDPEAWAALAGWAATVSGQFLRAQLEAGASAAQLFDSWAGSLA
+AEDYLEHVQPHSRAALAHVDDLAGPGVDGGAPLLHFGTGTGEFLHHLRDAGASAVGVDHR
+LTLSEAHRRLSERPGPDGRTVVPLQGNIDPALLAAPWPVVEAHVRDVVASGAAAPGHVVN
+LAHGVPPETDPTVLTRVVELIHSLPVPEREGQDPAPPAGAAAGEGRA
+>3_1258
+MSAMT-TP------PGLPAEHPLSTADPARSTADAPLVCALRGRRPHRHPVWFMRQAGRS
+LPEYRKAREGVGMLESCLRPELAAEITLQPVRRHDVDAAIFFSDIVVPLKLAGVGVEIVP
+GVGPVLDHPVRTAEDAAALPELEDSALDVIREAVSRTVAELGPTPLIGFAGAPFTLAAYM
+VEGRPSRDHLGPRRMMHGDPQTWAALAAWAATVSGQFLRAQLEAGASAAQLFDSWAGSLS
+AADYRKHVQPHSAAALSAVSDLAGPGVEGGAPLLHFGTGTGEFLDLMRDAGASAVGVDHR
+ITLAEAHRRLSSRPGPDGRAAVPLQGNIDPALLGAPWEVLEAHVREVVASGAAAPGHVVN
+LAHGVPPETDPEVLTRVVELIHSIPVAD--------GAEK-------
+>4_1407
+MSALSQTPETPAAVPALPAEHPLRTEDPSRSTVASPLLRALRGQRPDRHPVWFMRQAGRS
+LPEYRRVREGIGMLDSCLMPDLVREITMQPVRRHDVDAAIFFSDIVVPLRLAGVDVEIQP
+GVGPVLGQAVRTADDVAALPVLEDAALDVIREAVAATVAELGPRPLIGFAGAPFTLAAYM
+VEGRPSRDHFGPRRMMHADPETWAALAGWAATVSGQFLRAQLESGASAAQLFDSWAGSLS
+ADDYLEHVQPHSTAALAHVADLAGPGVPDGAPLLHFGTGTGEFLHHMRDAGATAVGVDHR
+LTLAEAHRRLSANPGPDGRGAVPLQGNIDPALLAAPWEVLEAHVRDVVASGAVAPGHVVN
+LAHGVPPETDAAVLTRVVELIHSLPVPEREGQDPAPGAETAEREERA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001253.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001253.fa
new file mode 100644
index 0000000000000000000000000000000000000000..abdc76530ae15c4289ca694b39d25862801dea08
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001253.fa
@@ -0,0 +1,46 @@
+>0_1481
+----MTVFSLVASHHDLDLDTVARLSAGATGVGPALPGSGAAGAVVLATCNRVEIYAEAD
+AAGVEAARAGLLSAVAASTSLPDEDVHAAFRTLDADATARHLFEVGAGLDSAVVGEREIA
+GQVRRALTAAQEAGTASGPLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLAEELRG
+LTDAAAQRDFWAGATILLIGTGAYAGTTLAQLADRGATTVGVHSASGRAEQFVADRGGWA
+LALGGEAVAGAVAEADVIIGSSGGERQISPERLQELRKGGRRPLTVVDLALSRDFDPAVA
+DLPDVDLITLESVRLAAPEQAQVAVAEARALVDDAVEEYRAAQRGRSADAAIKALRRHTL
+GVLDRELERVRARHGCTAAAEEVEFALRRMVNQLLHEPSVRAKRLAAEGRLDRYEDALEA
+VFGIEAPG-RPAPAVGTVEAVCPAHEDEGGAARIA
+>1_1201
+----MTVFSLVASHHDLDLDTVARLSAGATGVGPALPGSGAAGAVVLATCNRVEIYAEAD
+AAGVEAARAGLLSAVAASTSLPDEDVHTAFRTLDADATARHLFEVGAGLDSAVVGEREIA
+GQVRRALTAAQEAGTASGPLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLAEELRG
+LTDAAAQRDFWAGATILLIGTGAYAGTTLAQLADRGATTVGVHSASGRAEQFVADRGGWA
+LALGGEAVAGAVAEADVIIGSSGGERQISPERLQELRKGGRRPLTVVDLALSRDFDPAVA
+DLPDVDLITLESVRLAAPEQAQVAVAEARALVDDAVEEYRAAQRGRSADAAIKALRRHTL
+GVLDRELERVRARHGCTAAAEEVEFALRRMVNQLLHEPSVRAKRLAAEGRLDRYEDALEA
+VFGIEAPG-RPAPAVGTVEAACPAHEDDGGAARIA
+>2_1365
+MADVVTVFSLVASHQHLDLDTVARLSAGATGVGPALPGSGAAGAVVLATCNRVEIYAEAD
+ESGVEAAREGLVAAVAAHSSLPDEAVRSAFRVLDSEATARHLFEVGAGLDSAVVGEREIA
+GQVRRALSMARESGTASGSLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLTEELRG
+LADDDAKAAFWADASVLLIGTGAYAGTTLAQLAERGATAVAVHSASGRAEQFVEDRGGWA
+LALGGGAVAGAVAEADVIIGSSGGERQISPERLQELREDVDRPLTVVDLALSRDFDPAVG
+DLPDVDLITLESVRLAAPEQARAAVAEARVLVDGAVAEYRAAQRGRSADASIKALRRHTL
+AALDREMERVRARHGCTAAAEEVEFALRRMVNQLLHEPIVRAKRLAAEGRLDRYEDGLEA
+VFGIEPPG-STSSPAERPDAGCPAHEDEAGTARIA
+>3_1257
+MDVAVTVFSLVASHKDLSLDTVARLSAGSAGVGSALASSTDDGAVVLATCNRVEVYADAR
+DA--DAARERIVAAIAEQSGLPEDAVRSAFRVLDDDASARHLFEVGAGLDSAVVGEREIA
+GQVRRALVDARDAGTATGSLTRLFESATRTAKDVGSHTALGATGRSVVSVALDLAEELRG
+LTDAMARRTFWQEANVLLIGTGAYAGTTLAQLADRGAQAVGVHSASGRAAQFVADRGGWA
+LALGGADVAGAVAEADVIIGSSGGDRQISPERMAGLRRGAERPVTVVDLALSRDFDPAVG
+ELEGVDLITLESVRLAAPEQAQAAVAEARGLVETALEEYTSARRGRTADAAIKALRGHTM
+AALDREMERVRARHGCTAAADEVQFALRRMVNQLLHTPSVRARELAAQGRLDEFEHALEV
+LFDIPVPGTRPADAPGD---ACPATEAD-DARRTA
+>4_1408
+----MTVFSLVASHHDLDLDTVARLSAGATGVGPALPGSGAAGAIVLATCNRVEIYAEAD
+GAGVEAARTGLLSAVAASTSLPDEDVHTAFRTLDADATARHLFEVGAGLDSAVVGEREIA
+GQVRRALTAAQEAGTASGPLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLAEELRG
+LTDAAAQRDFWAGATILLIGTGAYAGTTLAQLADRGATTVGVHSASGRAEQFVADRGGWA
+LALGGEAVAGAVAEADVIIGSSGGERQISPERLQELREGGRRPLTVVDLALSRDFDPAVA
+DLPDVDLITLESVRLAAPEQAQVAVAEARALVDDAVEEYRAAQRGRSADAAIKALRRHTL
+GVLDRELERVRARHGCTAAAEEVEFALRRMVNQLLHEPSVRAKRLAAEGRLDRYEDALEA
+VFGIEAPG-RPAPAVGTVEAACPAHEDDGGAARIA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001255.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001255.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d5550e3f8a522368ee62268f1cda578c78bee8a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001255.fa
@@ -0,0 +1,16 @@
+>0_1483
+MEIRIGVQHVGREVVIDSEQSADEVRSLVDAAVSDGTPLVLADAKGRQVVVPGDRIGFVE
+IGAKKSGPLGFAAS
+>1_1203
+MEIRIGVQHVGREVVIDSEQSADEVRSLVDAAVADGTPLVLADAKGRQVVVPGDRIGFVE
+IGAKKSGPLGFAAS
+>2_1363
+MEIRIGVQHVGREVVIESEQPAEEVRSLVDAAVADGSTLVLADAKGRQVVVPGDRIGFVE
+INAKKSGPLGFAAS
+>3_1255
+MEIRIGVQHVGREVVLESDHTAQEVRALVDAALADGTTLALTDTKGRQVIVPADRIGFVE
+IGAKKSAPLGFAAV
+>4_1410
+MEIRIGVQHVGREVVIDSEQSADEVRSLVDAAVADGTPLVLTDAKGRQVVVPGDRIGFVE
+IGAKKSGPLGFAAS
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001256.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001256.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e439d2bb4319902e6dbfa88db496a5360d51dbc3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001256.fa
@@ -0,0 +1,40 @@
+>0_1484
+MTPHALGLRGPADPTLLERLAALRTELELPPAFPAPVLAEAEAAAREVHAGLTGSPDHADRTALPFVTVDPAGSTDLDQA
+LLLTPADD-DGILVRYAIADVPAFVTPGGAVDGEARRRGQTVYLPDGRVPLHPEVLSEDAASLLPDREHPAFVWTFLLDA
+AGAVVETGLERARIRSRAQLTYGQVQAFLDAQPGAQAPTTPRPGVTDADRAAAEGWPAEVRDSLALLPEVGRRRAAQEAA
+RGGASLNLPDQEVRVTEDGAHELVHRAPLPAEEHNAQLSLLTGMAAAELMLAAGVGILRTMPAPDTDAVAAFRERTRALG
+APWDEGQDYGAYLRSLDPADARHLAVLHAATGLFRGAGYTAFDAQAEDPALRTPPDEPAQAALAAPYAHATAPLRRLVDR
+FVLALCHAHAIGAPAPAWVRSALPALPALMADSSRRASAASRTAADLVEAAALESRVGAELEGIAVREAKDGTEVWLLDP
+AVSLRVPGSVPAGTRVRVRIEGVDRASGAITAAGVDWPHSSR
+>1_1204
+MSSHALGLRGPADPALLERLAALRTELELPSAFPTPVLAEAEAAAHGVHVGLAGSPDHADRTALPFVTVDPAGATDLDQA
+LLLTPSDD-DGILVRYAIADVPAFVAPGGAVDAEARRRGQTVYLPDGRVPLHPEVLSEDAASLLPDRERPAFVWTFLLDA
+AGAVVETGLERARVRSRAQLTYGQVQAFLDARPGAQAPATPRPGVTDADRAAAEGWPAEVRDSLALLPEVGRRRAAQEAA
+RGGASLNLPDQEVLVTEDGAHELVHRAPLPAEEHNAQLSLLTGMAAAELMLAAGVGILRTMPAPDADAVAAFRERTRALG
+VPWDEGQDYGAYLRSLDPADARHLAVLHAATGLFRGAGYTAFDAQAEDPALRTPPAEPAQAALAAPYAHATAPLRRLVDR
+FVLALCHAHASGAPAPAWVRSALPELPALMADSSRRASAASRTAADLVEAAALESRVGAELEGIAVREAKDGTEVWLLDP
+AVSLRVPGSVPAGTRVRVRIEGVDRASGAITAAGVDWSHSSR
+>2_1362
+MPHRAVALRGRPDPALIERLAALRTELELPAGFPPEVLEEADAAARDVLAALASDPAYADRTDVPFVTVDPAGSTDLDQA
+LYLEAADG-DAITVRYAIADVPAFVAPGGAVDVEARRRGQTVYLPDGRVPLHPEALSEDAASLLPDRERPAFVWTFVLDA
+AGAVVDTSLERARIRSRAQLTYAQVQAFLDALPDAKAPAAPRPGLDEADHAAHRGWDAPLRDSLALLPEVGRRRAAQEAA
+RGGASLNLPDQEVHVAEDGRHCLVQRAPLPAEDHNAQLSLMTGMAAARLMLEAGVGILRTMPAPDAEAVAAFRSRTRALG
+APWEEGQDYGAYLRTLDPADPGHLAVLHEATSLFRGAGYTAFDAHAEDPELRTPPSEPEQAALAAPYAHATAPLRRLVDR
+FVLALCHAHATGAPAPEWARAALPEVPALMTESSRRTSAADRAATDLVEAAALQDHVCAELEGIAVRRVKGGAEVWLLDP
+AVTLRVPGEAEPGTRVRVRIEGVDRASGEVTASGVDWPHSSR
+>3_1254
+MPHHALEVRGGPDAALAARLRALRAELDVPGEFPADVLTEAERAAAEVPGRVAADPDRADLTAVPFVTVDPAGSTDLDQA
+LHLQAGPGRDELTVRYAIADVPGFVAPEGAVDAEARRRGQTVYLPDGRVPLHPEVLSEDAASLLPEVERPTFVWTFVLDA
+EGAVASTDLVRARIRSRAQLAYPQVQALLD---------------DDAAPEAAD-WPAEVRASLALLPEVGARRTAQEAA
+RGGASLSMPDQEISVV-DGAYTLVQRVPLAAEDHNAQLSLMTGMAAARIMLEAGVGILRTMPAPDPDAVDAFRARTRALG
+LPWGEELDYGAYLRTVDPTDPRGLAVMHAATTLFRGAGYTAFDRGSVDPALRALPEDPEQAALAAPYAHTTAPLRRLVDR
+FVLVLCHAHVAGEPVPDWVRRALPDLPALMAESGRRASAADRAATDLVEAALLAARVGSVLEGTAVRTSEKGTDVQLTDP
+AVSLRVPGRAEPGTVVRVRVDAVDVAAGKVTASGVDWPHSAR
+>4_1411
+MSSHALGLRGPADPALLERLAALRTELELPSAFPTPVLAEAEAAAHGVHVGLAGSPDHADRTALPFVTVDPAGATDLDQA
+LLLTPSDD-DGILVRYAIADVPAFVAPGGAVDAEARRRGQTVYLPDGRVPLHPEVLSEDAASLLPDRERPAFVWTFLLDA
+AGAVVETGLERARIRSRAQLTYGQVQAFLDAQPGAQAPTTPRPGVTDADRAAAEGWPAEVRDSLALLPEVGRRRAAQEAA
+RGGASLNLPDQEVRVTEDGAHELVHRAPLPAEEHNAQLSLLTGMAAAELMLAAGVGILRTMPAPDTDAVAAFRERTRALG
+APWDEGQDYGAYLRSLDPADARHLAVLHAATGLFRGAGYTAFDAQAEDPALRTPPDEPAQAALAAPYAHATAPLRRLVDR
+FVLALCHAHAIGAPAPAWVRSALPALPALMADSSRRASAASRTAADLVEAAALESRVGAELEGIAVREAKDGTEVWLLDP
+AVSLRVPGSVPAGTRVRVRIEGVDRASGAITAAGVDWPHSSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001259.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001259.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e766eb4ad3903b9d72c75b85963ca9c095b5364d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001259.fa
@@ -0,0 +1,45 @@
+>0_1488
+MG------------------------IDLTTELTALRDRLLSAEAEHADLISRVRDRHRASARNLVHYVALRGTDLRPLQ
+EALSDAGLSSLGRMEAGVLGHVDAVLAAARALDGDLATAP-EDDALTSAEGRAILARNAASLLGPARGDRDARIMVTMPS
+EAATDPELVARIAEAGMDLARVNCAHDDEQAWAAMIAAVRRCA-GAGRPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPAR
+DPSGIVTEPSRVWLAAGPHDAVAVADRPDGAVVVPLAAPD---GKTLAGLQRGDEIELTDARGAHRRLEVERVSGEGVLV
+RADKTVYWATGTALTTPHGPLEVGPLPPLEQSMRVHEGEQIVLTRSLEPVPAVDTPPYRIGLTLAQAFADATVGDRVSLD
+DGRIGTRITGVSDDEITLEVTQAGPRGAKLKAEKGVNFPDTHLDIPALTDEDLAHIPFAARHADMVNMSFVRSAEDVAQL
+IDALEAEDAPDVDITLKIETVEAFRQLPRMLLEAMRWRDVGVMIARGDLAVEAGFARMAELQEEILWLCEAAHVPAIWAT
+QVLESLAKTGLPSRAEITDAAMAQRAEAAMLNKGPYIDRAVTVLGDILGRMHGHASKKRDMLRRLESWSL
+>1_1208
+MG------------------------IDLTTELTALRDRLLSAEAEHADLISRVRERHRASARNLVHYVALRGTDLRPLQ
+EALSDAGLSSLGRMEAGVLGHVDAVLAAARALDGDPAPAP-EDDALTSAEGRAILARNAASLLGPARGDRDARIMVTMPS
+EAATDPELVARIAEAGMDLARVNCAHDDEQAWAAMIAAVRRCA-GAGLPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPAR
+DPSGIVTEPSRVWLAAGPHDAVATADRPDGAVVVPLADPE---GTTLAVLQRGDEIELTDARGAHRRLEVEQVDGEGVLV
+RAEKTVYWATGTALTTPHGPLEVGPLPPLEQSMRVHEGEEIVLARSLEPVPAVDTPPYRIGLTLAQAFADAAVGDRVSLD
+DGRIGARITAVSADEITLEVTQAGPRGAKLKAEKGVNFPDTHLAIPALTDEDLAHIPFAARHADMVNMSFVRSAEDVAQL
+IDALEAEDAPDVDITLKIETVEAFRQLPRMLLEAMRWRDVGVMIARGDLAVEAGFARMAELQEEILWLCEAAHVPAIWAT
+QVLESLAKTGLPSRAEITDAAMAQRAEAAMLNKGPYIDRAVTVLGDILGRMHGHASKKRDMLRRLESWSL
+>2_1358
+MD------------------------IDLTTELTALRDRLLSAEAEHADLISRVRDRHRASARNLVHYVALRGTDLRPLQ
+DALSDVGLSSLGRMEAGVLGHVDAVLAAARALDGEDAPSP-DDDALTPARGREILARDADRLLGPARPDRAARIMVTLPS
+EAAQDPDLVARMAEAGMDLARVNCAHDDEAAWAAMIEAVRACA-TPERPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPAR
+TPAGLVTEPSRVWLAAA-----GAADAPAGAVVVPVTEAG---AEVLAGLAAGDEVELTDARGSHHVLTVEQAGAAGALV
+RADKTVYWGTGLAVDTPRGTLTVGELAPLEQSMRVRRRDQVVLTRSLDPVPAASAPPYRIGLTLAQAFEDVAVGDRVSID
+DGKIDAVVRAANADEITLEVTEAGPNGTKLKAEKGVNFPDTALSIPALTDEDLAHIPFVARHADMVNLSFVRSAEDVAQL
+IDALAAEDATDVDITLKIETVGAFEQLPRMLLEAMRWRDVGVMIARGDLAVEAGFERMAELQEEILWLCEAAHVPAIWAT
+QILESLAKTGLPSRAEITDAAMAQRAEAAMLNKGPYIEEAITALGDILGRMGGHARKKRDMLRRLESWSL
+>3_1250
+MSTLPENAPDSRPTAESPVVAPGAAVTELIEAIDALRARIVAAEQAHAERLDRVADRHRASARNLVHYVTLRGEDLRPLQ
+DALSAVGLSSLGRMEAGVLGHLDAVRTALHPLGGRPAPDPADDDPLSPAEGRALLAANAESLLGPSRPGRETRIMVTMPS
+EAATNAALVQGMADAGMDLARVNAAHDGEAAWAAMVANIRGVARDGGRPAPRICMDLAGPKLRTGPLEPGPGVVKVKPRR
+DVDGTVLERSRVWLGEA--DAPEAAD----AVVLPLDPAGSGHSPVLSALRPGDHAMLTDARDSDRTLHVLAATEAGVLL
+ACRKTVYWHTGLEVDTPRGTLVVGALPSVPQAMRVHAGDEIVLTRSMDPRPAVSEGPFTIGCSLPQAFQDVRPGERVLID
+DGKITGEVVSNDGEAITLTVTEAGPTGAKLRAEKGVNFPDTDLRLPALTDEDRSHLPFAAAHADVVNMSFVRSPADVAAL
+IDALDAEDARGVGVSLKIETVGAFERLPAMLLEAMRWNDVGVMIARGDLAVEAGFERMAELQEEILWLCEAAHVPAVWAT
+QILETLAKQGLPSRAEITDAAMAQRAEAAMLNKGPYIDEAIGALSDILTRMGGHADKKRDMLRRLRSWSL
+>4_1415
+MG------------------------IDLTTELTALRDRLLSAEAEHADLISRVRERHRASARNLVHYVALRGTDLRPLQ
+EALSDAGLSSLGRMEAGVLGHVDAVLAAARALDGDPAPAP-EDDALTSAEGRAILARNAASLLGPARGDRDARIMVTMPS
+EAATDPELVARIAEAGMDLARVNCAHDDEQAWAAMIAAVRRCA-GAGRPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPTR
+DPSGTVTEPSRVWLAAGPHDAVAAADRPDGAVVVPLADPE---GTTLAVLQRGDEIELTDARGAHRRLEVEQVDGEGVLV
+RAEKTVYWATGTALTTPHGPLEVGPLPPLEQSMRVHEGEQIVLTRSLEPVPAVDTPPYRIGLTLAQAFADATVGDRVSLD
+DGRIGTRITGVSDDEITLEVTQAGPRGAKLKAEKGVNFPDTHLDIPALTDEDLAHIPFAARHADMVNMSFVRSAEDVAQL
+IDALEAEDAPDVDITLKIETVEAFRQLPRMLLEAMRWRDVGVMIARGDLAVEAGFARMAELQEEILWLCEAAHVPAIWAT
+QVLESLAKTGLPSRAEITDAAMAQRAEAAMLNKGPYIDRAVTVLGDILGRMHGHASKKRDMLRRLESWSL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001269.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001269.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1b3b39394c83c62db8f67ff9693b533b356158f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001269.fa
@@ -0,0 +1,31 @@
+>0_1499
+MTQITPEQPHGAHLPDEAGVRRRRGAAGDDLIVLEGVNKHFGDFHALRQIDLRIPRGQVA
+IVLGPSGSGKSTLCRTINRLETIDDDGGRILIDGRPLPTEGRQLAQLRAEIGMVFQSFNL
+FAHKSILENVTLGPIKVKGKRRADAERHAMELLERVGVAQQARKMPAQLSGGQQQRVAIA
+RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF
+MADGAILEDTDPDTFFTNPRHERAQDFLGKILAH
+>1_1219
+MTQITPEQPHGAHLPDEAGVRRRRGAAGDDLIVLEGVNKHFGDFHALRQIDLRIPRGQVA
+IVLGPSGSGKSTLCRTINRLETIDDDGGRILIDGRPLPTEGRQLAQLRAEIGMVFQSFNL
+FAHKSILENVTLGPIKVKGKRRADAERHAMELLERVGVAAQARKMPAQLSGGQQQRVAIA
+RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF
+MADGAILEDTDPDTFFTNPRHERAQDFLGKILAH
+>2_1347
+MTQITPEEPHGAHARDEAAPRRPRAAPGDDLIVLENVNKHFGDFHALKDIDLRIPRGQVA
+IVVGPSGSGKSTLCRTINRLETIDDDGGRILLDGQPLPAEGKQLAQLRAEVGMVFQSFNL
+FAHKSILENVTLGPIKVKGKRKADAERHAMELLERVGVAQQAKKMPAQLSGGQQQRVAIA
+RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF
+MADGAILEDTDPESFFTAPQHERARDFLGKILAH
+>3_1239
+MSEITSGTVHGS----TAASGPAPAAASDALIRLEHVNKHFGEFHALKDIDLAIPRGQVA
+IVLGPSGSGKSTLCRTINRLETIDDDGGRILIDGRPLPSEGRELARLRAEVGMVFQSFNL
+FAHKSILENVTLGPIRVKGRKKAEAERHALELLERVGVAHQAKKMPAQLSGGQQQRVAIA
+RALAMEPQALLFDEPTSALDPEMVQEVLDVMVGLAREGMTMVVVTHEMGFARKAGDRVVF
+MADGEILEDTDPESFFTRPQHPRAQEFLGKILVH
+>4_1426
+MTQITPEQPHGAHLPDEAGVRRRRGAAGDDLIVLEGVNKHFGDFHALRQIDLRIPRGQVA
+IVLGPSGSGKSTLCRTINRLETIDDDGGRILVDGRPLPTEGRQLAQLRAEIGMVFQSFNL
+FAHKSILENVTLGPIKVKGKRRADAERHAMELLERVGVAQQARKMPAQLSGGQQQRVAIA
+RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF
+MADGAILEDTDPDTFFTNPRHERAQDFLGKILAH
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001270.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001270.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b8fafc5380f9bf894286e34255f94e262680e050
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001270.fa
@@ -0,0 +1,31 @@
+>0_1500
+MLRTKLLTLSAVTAAAALSLTACAPSSSQGGGGDAAGSSSAGESTSSGSGESLRIGIKFD
+QPGLGYREGSAQPTGFDTDVARYVADKLGVAEQDIEWVQTPSANRENALENGEVDMIFAT
+YSITDARKERVAFAGPYFVAGQDLLVRADDTAITGPESLDGKNLCSVTGSTSAQKIKDQF
+ASGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAAADANKGKFKVVGNTFTTERYG
+VGLPKDSERCEDINEAIKEMKDSGEWEKALESNTEGTGYTYDETLNSGEDAEFEPCA
+>1_1220
+MLRTKLLTLSAVTAAAALSLTACAPSSSQGGGGDAAGSSSAGESTSSGSGERLRIGIKFD
+QPGLGYREGSAQPTGFDTDVARYVADKLGVAEKDIEWVQTPSANRENALENGEVDMIFAT
+YSITDARKERVDFAGPYFVAGQDLLVRADDTAITGPESLEGKNLCSVTGSTSAQKIKDQF
+ASGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAAADANKGKFKVVGNTFTTERYG
+VGLPKDSERCEDINEAIKEMKDSGEWEKALESNTEGTGYTYDETLNSGEDAEFEPCA
+>2_1346
+MFRKKLLTLSAVTAAAALSLTACSPSAQQ-GGGEGSGSASAGGSQSAGSGEGLRIGIKFD
+QPGLGFREGSGAPTGFDTDVARYVADKLGVAEGDIEWVQTPSANRENALENGEVDMIFAT
+YSITDARKERVDFAGPYFVAGQDLLVRADDTEITGPDALDGKNLCSVTGSTSAQKIKDQF
+ASGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAATDANKGKFKVVGNTFTTERYG
+VGIAKGDDRCEDINDAIKEMKDSGAWKESLDANTEGTGYEYDEALNSGADAEFESCS
+>3_1238
+MARSRILSVAAVAAAAALSLSACSPSSS--GGSGSASSASGSTAAQSGSSDTLRIGIKYD
+QPGLGFREGQNAPTGFDTDVARYVAGKLGVAEDKIEWVQTPSANRENALENGEVDMIFAT
+YSITDARKQRVDFAGPYFVAGQDLLVRQDDTSITGPDSLNGKNLCSVTGSTSAQKIKDNY
+ASGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAATDANKGKFKVVGQPFTTERYG
+VGLQKGSDKCKDINEAIKAMKDSGEWEKSLKANTEGTGYEYSEDKNSGADAEFEPCA
+>4_1427
+MLRTKLLTLSAVTAAAALSLTACAPSSSQGGGGDAAGSSSAGESTSSGSGESLRIGIKFD
+QPGLGYREGSAQPTGFDTDVARYVADKLGVAEQDIEWVQTPSANRENALENGEVDMIFAT
+YSITDARKERVAFAGPYFVAGQDLLVRADDTAITGPESLDGKNLCSVTGSTSAQKIKDQF
+ASGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAAADANKGKFKVVGNTFTTERYG
+VGLPKDSERCEDINEAIKEMKDSGEWKKALESNTEGTGYTYDETLNSGEDAEFEPCA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001271.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001271.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e342321a5a724cf9eef121a58db533726a590290
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001271.fa
@@ -0,0 +1,26 @@
+>0_1501
+MESISSLLADYGADIPLAFWMNIRLAFLATLGSFVLGVVLALFRISPVPSLRALGAGYVN
+VVRNTPLTIIMLLGVLAVWGQLKISFSSDFTLNFFIYAVIALSLYHAAFMCEAIRSGVNT
+VPLGQAEAARSIGLGFLPAARHVILPQALRGAITPLGNTVIALTKNTTVAAAASVAEASG
+LMKRMIEFSPDVMVAIFLTFAIGFCLIVIPIGLLTTWASEKWAVAR
+>1_1221
+MESISSLLADYGADIPLAFWTNIRLAFLATLGSFVLGVVLALFRISPVPSLRALGAGYVN
+VVRNTPLTIIMLLGVLAVWGQLKISFSSDFTLNFFIYAVIALSLYHAAFMCEAIRSGVNT
+VPLGQAEAARSIGLGFLPAARHVILPQALRGAITPLGNTVIALTKNTTVAAAASVAEASG
+LMKRMIEFSPDLMVAIFLTFAIGFCLIVIPIGLLTTWASEKWAVAR
+>2_1345
+MESISSLLADYGADIPLAFWTNIRLAFLATLGSFVLGVVLALFRISPVPSLRAIGTAYVN
+VVRNTPLTIVMLLGVLAVWGQLKITFSSDFTLNFFIYAVIALSLYHAAFMCEAIRSGVNT
+VPLGQAEAARAIGLGFLPAARHVILPQALRGAITPLGNTVIALTKNTTVAAAASVAEASG
+LMKRMIEFSPDVMVAIFLTFAIGFCLIVIPIGLLTTWASDKWAVAR
+>3_1237
+MESLSTLVEQYGAAVPQAFWMNIRLAALATLGAFVLGVLLALCRISPVPSLRAVGAGYVH
+IVRNTPLTIIMLIGVLAVWGQLKVTFAPDFKVNFFVYAVLALSLYHAAFMCEAIRSGVNT
+VPLGQAEAARAIGLGFLPAARLVILPQALRGAITPIGNTVIALTKNTTVAAAASVAEASG
+LMKTMIEFRPDAMVAIFLTIAIGFCLIVIPIGLLTTWASDKWAVSR
+>4_1428
+MESISSLLADYGADIPLAFWTNIRLAFLATLGSFVLGVVLALFRISPVPSLRALGAGYVN
+VVRNTPLTIIMLLGVLAVWGQLKISFSSDFTLNFFIYAVIALSLYHAAFMCEAIRSGVNT
+VPLGQAEAARSIGLGFLPAARHVILPQALRGAITPLGNTVIALTKNTTVAAAASVAEASG
+LMKRMIEFSPDLMVAIFLTFAIGFCLIVIPIGLLTTWASEKWAVAR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001272.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001272.fa
new file mode 100644
index 0000000000000000000000000000000000000000..163842893761bb23aa4ade3a3c02055fef5997d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001272.fa
@@ -0,0 +1,31 @@
+>0_1502
+MSAQASVLFDAPGPIARRRILLANLVSLAAVLVVAVLVLIQMNATGQLSGRRWLAAVDGN
+AWRNYYLPGLQFTLQSAGIAVVSSVVFGLVFGFLRLAPVGPVRWLAAVVVEFFRAVPVLV
+MMVFFYQLFAQVARSGAIQPQDGPYYAVIAALTLYNGSVIAELVRSGVRSLPRGQREAAA
+AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGNG
+NILQSLVVAAMIFIVINFLLTWAATRLSRRLSSRTAGDASAPTTPRVGAPTDTAG--
+>1_1222
+MSAQASVLFDAPGPIARRRILLANLVSLAAVLVVAVLVLIQMNATGQLSGRRWLAAVDGN
+AWRNYYLPGLQFTLQSAGIAVVSSVVFGLVFGFLRLAPVGPVRWLAAVVVEFFRAVPVLV
+MMVFFYQLFAQVARSGAIQPQDGPYYAVIAALTLYNGSVIAELVRSGVRSLPRGQREAAA
+AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLHYARQLGSGNG
+NILQSLVVAAMIFIVINFLLTWAATRLSRRLSSRTAGDASAPTTPRVGAPTDTAG--
+>2_1344
+MSSQASVLFDAPGPLARRRILIANLVALAAVLALAVAVLMRMADADQLEARRWTAALDAN
+AWTNYYLPGLQFTVQAAAIAVLTSVVFGLVLGFLRLAPFAPVRGAAGLVVEFFRAVPVLI
+MMVFFYQVFAQVARTGVIAPADGPYYAVIVALTLYNGSVIAELVRSGVRSLPKGQREAAA
+AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGQG
+NILQSLVVAALIFIVINFLLTWVATRLSRRLSSRTAGDAGAPTTPVVGAPTDKPA--
+>3_1236
+MSAQASVLFDAPGPATRRRILIVNLVALALVLAVAVVVGMALQDRGQLEPRRWLAALDAN
+AWTNYYLPGLQFTLQSAGIAVVTSVVFGLVFGFLRLAPVAPVRWLAAVVVEFLRAVPVLV
+MMVFFYQAFALAARGGAINAADSPYYAVIVGLTLYNGSVIAELVRSGVTGLPKGQREAAA
+AIGMTPNQSLRLVEVPQALVAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGQG
+NILQTLVVAAVIFILINMLLTWLATLLSRRLSSRTSGR----TKPHAGSTAVTIGKD
+>4_1429
+MSAQASVLFDAPGPIARRRILLANLVSLAAVLVVAVLVLIQMNATGQLSGRRWLAAVDGN
+AWRNYYLPGLQFTLQSAGIAVVSSVVFGLVFGFLRLAPVGPVRWLAAVVVEFFRAVPVLV
+MMVFFYQLFAQVARSGAIQPQDGPYYAVIAALTLYNGSVIAELVRSGVRSLPRGQREAAA
+AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGNG
+NILQSLVVAAMIFIVINFLLTWAATRLSRRLSSRTAGDASAPTTPRVGAPTDTAG--
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001273.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001273.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b35a09ad29640c134b9bdbfb37ed249c7691aea1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001273.fa
@@ -0,0 +1,41 @@
+>0_1503
+M--SLTPNTLPDLADPDLDVAALTATLLDVRSVSGEEGPLADAVEQALRALGGLEVRRFG
+DAVVARTALGRSTRVILAGHLDTVPLPTVPGSRGTVPSAWDGDVLYGRGAVDMKSGVAVQ
+LALAGRFGRADGPTPVHDVTWVFYDHEEVSSDLSGLARVARQAPELLEGDFAVLLEPTDG
+VVEGGCNGTCRYRVTFSGVAAHSGRAWRGDNAIHKLAPVLTALAAYEPATVTVEGLEYRE
+GLHAIRVAGGVAGNVIPDEASVDLNYRFAPDKTLEQAHAHVRAVLEGAGVDWDAQVRIDD
+ASPAARPGLDRPAAAAFVAAVGGEPQPKYGWTDVARFSQLGVPAVNFGPGDALLAHTDDE
+HVSREAVHACLAALTAWLAG
+>1_1223
+M--SLTPVSLPDLADPDLDVAALTATLLDVRSVSGEEGPLADAVEHALRALGGLEVRRFG
+DAVVARTALGRPTRVILAGHLDTVPLPTVPGSRGTVPSAWDGDVLYGRGAVDMKSGVAVQ
+LALAGRFGRADGPTPVHDVTWVFYDHEEVSSDLSGLARVARQAPELLEGDFAVLLEPTDG
+VVEGGCNGTCRYRVTFSGVAAHSGRAWRGDNAIHKLAPVLTALAAYEPATVTVEGLEYRE
+GLHAIRVAGGVAGNVIPDEASVDLNYRFAPDKTLEQAHAHVRAVLEGAGVDWDAQVRIDD
+ASPAARPGLDRPAAAAFVAAVGGEPQPKYGWTDVARFSQLGVPAVNFGPGDALLAHTDDE
+HVSREAVHACLAALTAWLAG
+>2_1343
+MTETSAP-ALPDLADPGLDVAELTAVLLDVPSVSGDEGPLADAVETALRALGGLEVRRFG
+DAVVARTDLGRDTRVILAGHLDTVPLPTVPGSRGTVPSAWEGDVLYGRGAVDMKSGVAVQ
+LALAGRYGRADGPAPAHDVTWVFYDHEEVASDLSGLARVARQAPELLEGDFAVLLEPTDG
+VVEGGCNGTCRYRVSFSGVAAHSGRAWRGENAIHKLGAVLTALAAHEPATVTVEGLDYRE
+GLNAIRVAGGVAGNVIPDAAHVDVNYRFAPDKTLEQAHARVREVLEGAGVDWDAQVRIDD
+ASPAARPGLDRPAAAAFVAAVGGEPQPKYGWTDVARFSELGVPAVNFGPGDALLAHTDDE
+HVHRAAVHACLDALDAWLAG
+>3_1235
+MTDAVAP-VLPDLAAADLDVAALTATLLDAPSVSDDEGPLADAVEAALARLPRLGVRRFG
+DAIVARTELGLPGRVILAGHLDTVPLPTAPGARGTVPSAWEGDVLYGRGAVDMKSGVAVQ
+LALAGLFGRADGPDPVHDVTWVFYDHEEVDSARSGLARIARQAPELLEGDFAVLLEPTDG
+VVEGGCNGTCRYRVRFEGVAAHSGRAWRGDNAIHKLGALLSALAAYEPATVTVEGLDYRE
+GLNAIRVSGGVAGNVIPDAAATEVNYRFAPDKTLEQAHAHVREVFAAAGVDWDAQVEVTD
+ASPAARPGLDRPAAAAFVAAVGGEPMPKYGWTDVARFSELGVPAVNFGPGDALLAHTDDE
+HVERAAVERCRDALEAWLRG
+>4_1430
+M--SLTPVSLPDLADPDLDVAALTATLLDVRSVSGEEGPLADAVEQALRALGGLEVRRFG
+DAVVARTALGRSTRVILAGHLDTVPLPTVPGSRGTVPSAWDGDVLYGRGAVDMKSGVAVQ
+LALAGRFGRADGPTPVHDVTWVFYDHEEVSSDLSGLARVARQAPELLEGDFAVLLEPTDG
+VVEGGCNGTCRYRVTFSGVAAHSGRAWRGDNAIHKLAPVLTALAAYEPATVTVEGLEYRE
+GLHAIRVAGGVAGNVIPDEASVDLNYRFAPDKTLEQAHAHVRTVLEGAGVDWDAQVRIDD
+ASPAARPGLDRPAAAAFVAAVGGEPQPKYGWTDVARFSQLGVPAVNFGPGDALLAHTDDE
+HVHREAVHACLAALAAWLAG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001284.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001284.fa
new file mode 100644
index 0000000000000000000000000000000000000000..059f41bf55ea96f6e9654a55aad5e0c0d6a5a3d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001284.fa
@@ -0,0 +1,41 @@
+>0_1517
+M-TPPGWPPRARRSPLAFVIALFGVLGALVLAGGLTALLAGRMV-DVAADSAPTVPAAEA
+P---AREAGELAAGLTHIHDGVAVDWSASAHDGSSLDPGQPVADAPGILLVETALGARTG
+TGTGMVLSPDGLAVTNYHVVEDSSEVHVVVADTGARHTATVLGRDAEHDIAVLDVEGVSD
+LPVASVSLDPVRRGDQVAAVGNGGGQGHLTAVRGTVLGTDRSIMAAAEGTDQYARLSGLI
+QTDADVVPGYSGGPVVDDAGQVVGVTVAASDGTTADEVDGFAIPLEVAFDVVDQVLTGEE
+TDTVSIGADGALGIMVGADPDVGVVVMQVDAGSAAEQIGLVEGDVILEIEGRAVGDDASR
+MSRLVNDHNVGDRITVQWRTADGEVREAEAVLQPALVN
+>1_1237
+M-TPPGWPPRARRAPLAFVIALFGVLGALVLAGGLTALLAGRMV-DVAADSAPTVPAAEA
+P---AREAGELAAGLTHVHDGVAVDWSASAHDGSSLDPGQPVADAPGILLVETALGARTG
+TGTGMVLSPDGLAVTNYHVVEDSSEVHVVVADTGARHTATVLGRDAEHDIAVLDVEGVSD
+LPVASVSLDPVRRGETVAAVGNGGGQGHLTAVRGTVLGTDRSIMAAAEGTDQYARLSGLI
+QTDADVVPGYSGGPVVDDAGQVVGVTVAASDGTTAEEVDGFAIPLDVAFDVVDQVLSGEE
+TDTVSIGADGALGIMVGADPDVGVVVMQVDAGSAAEQIGLVEGDVILEIEGRPVGDDAFR
+MSRLVNDHNVGDRITVQWRTASGEVREAEAVLQPALVN
+>2_1328
+MSVPPGWPPRRRRSPLALAISFFGVLGALVLAVGVTLLVAGRMV-DVVGAPDPVVSARES
+A---PPDAGALAQELAGAHEGVAVDWDAPAHAGSELDPGLAVDHAPGILLVETVLGQRMG
+TGTGMVLTPEGLALTNYHVVEDSSEVFVVEADTGERHTATVLGRDAEHDVAVLDVHGVTD
+LPVASVSLDPVRRGDEVAAVGNGRGQGHLTAVRGTVLGTDRSIMAASQGSDEYARLTGLI
+QTDADVVPGYSGGPVVDDDGQVVGVTVAASDGTGAQEVDGFAIPLGVALGVVDQVLSGEE
+TDTVSIGADGALGIMVAADPEAGVVVMQVDADSAAEAIGLVPGDVVLAVDGQAVEGNASR
+MSRLVNDHNVGDRITVTWRTASGEVREAEAVLQEAVVN
+>3_1222
+-----------------MAIAVFGVLGAVVLAVGLTLLAGGRLIAAVGAGSSSSAAAPSG
+PQVTTRSLDALAASLDHAHAGIAVPAADAPPADGSLDPGERVRRAPGVLLVETRLEAMQG
+TGTGMVLTSDGLALTNYHVVEDSTAVSVVVADTGARHAATVLGRDAKNDVAVLQIDGVSG
+LTTTSVSRDPVRPGEAVAAVGNGGGQGYLTSVGGEVLRVDQSILAATEGTDDFERLTGLI
+QTDADVVPGYSGGPLVDGEGQVVGVTVAASEGRTAAQVDGYAIPLSTAFDVVAQVLSGEE
+TDSVSIGADGSLGISVAGSRD-GVEVLSVDRGSAGEELGLRPGDVITAIDGRTLDGNATA
+MSRLVNDHEVGDRLSVQWRTADGEARQGEAVLQKARHN
+>4_1444
+M-TPPGWPPRARRSPLAFVIALFGVLGALVLAGGLTALLAGRMV-DVAADSAPTVPAAEA
+P---AREAGELAAGLTHIHDGVAVDWSASAHDGSSLDPGQPVADAPGILLVETALGARTG
+TGTGMVLSPDGLAVTNYHVVEDSSEVHVVVADTGARHTATVLGRDAEHDIAVLDVEGVSD
+LPVASVSLDPVRRGDQVAAVGNGGGQGYLTAVRGTVLGTDRSIMAAAEGTDQYARLSGLI
+QTDADVVPGYSGGPVVDDAGQVVGVTVAASDGTTADEVDGFAIPLEVAFDVVDQVLSGEE
+TDTVSIGADGALGIMVGADPDVGVVVMQVDAGSAAEQIGLVEGDVILEIEGRAVGDDASR
+MSRLVNDHNVGDRITVQWRTADGEVREAEAVLQPALVN
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001288.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001288.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3cde970723717531a058e182382222233b8b8a83
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001288.fa
@@ -0,0 +1,21 @@
+>0_1521
+MKLTDDLLQKFNDQITLEFEASMVYRQLAIAADDLDLSGMAAWLRHQADEEIVHANKFID
+HVADRDSFPTIGAIPAPPVQAGLSALEIFRAALAHEQKVSEAIRELYRATESAGDLNSRP
+LLNWFLDEQIEEEATVSEIVGQLELVGDDGSGLLRIDGRLGSRPVETTENDA
+>1_1241
+MKLTDDLLQKFNDQITLEFEASMVYRQLAIAADDLDLSGMAAWLRHQADEEIVHANKFID
+HVADRDSFPTIGAIPAPPVQAGLSALEIFRAALAHEQKVSEAIRELYRATESAGDLNSRP
+LLNWFLDEQIEEEATVSEIVGQLELVGDDGSGLLRIDGRLGSRPVETTENDA
+>2_1324
+MT-----------GVT--------------AADGLDLSGMAAWLRHQADEEIVHANKFID
+HVTDRGS-------------------------------------------DAAGDLSSRP
+LLNWFLEEQIEGEAT---------------------------PPL-------
+>3_1218
+MSIDKDLTRKFNEQITLEFEASMVYRQLAIAADMQDLSGMAAWLRHQADEEIVHANKFID
+HVVDREASAVIGAIPAPDVPEHITPVQIFEAALAHERKVSEAIRELYRAAEAAGDLSSRP
+LLNWFLEEQIEEEATVGEIVGQLKLVGEDGSGLLRIDSALGARPVETTENAG
+>4_1448
+MKLTDDLLQKFNDQITLEFEASMVYRQLAIAADDLDLSGMASWLRHQADEEIVHANKFID
+HVADRDSFPTIGAIPAPPVQAGLSALEIFRAALAHEQKVSEAIRELYRATESAGDLNSRP
+LLNWFLDEQIEEEATVSEIVGQLELVGDDGSGLLRIDGRLGSRPVETTENDA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001290.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001290.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1eda222a802996af5998147c2f1f02a0513ce3d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001290.fa
@@ -0,0 +1,31 @@
+>0_1523
+MN-----------------TT---AAASDPSDAPLASTRIGEGPRGVAFLHGLMGRGRNF
+TGPAKELGDDFTVELIDLPDHGASPWTDRVDYREIADRVAAHLRAGLAADGPVHLLGHSM
+GGKVAMVLALRHPELVDRLIVEDISPRLSPQATDEFVHLLGTMLRMDLDAYDSRAEADAA
+MAEHVHDARVRGFLLQNLRRTAGHFAWQPNVAMLFEHLREIGSFPDPVVPEDPERVFDHP
+VLWLAGAESDYVQDEDVPRMKELFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD
+>1_1243
+MN-----------------TT---AAASDPSDAPLASTRIGEGPRRVAFLHGLLGRGRNF
+TGPAKELGDDFTVELIDLPDHGASPWTDRVDYREIADRVAAHLRAGLAADGPVHLLGHSM
+GGKVAMVLALRHPDLVDRLIVEDISPRVSPQATDEFVHLLGTMLRMDLDAYDSRAEADAA
+MAEHVHDARVRGFLLQNLRRTAGHFAWQPNVAMLFEHLREIGSFPDPVVPEDPERVFDHP
+VLWLAGAESDYVQDEDVPRMKELFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD
+>2_1321
+MTISDQGSPRRLPDSLERVSTPDPSASAAPSDAALASDVIGDGPHRVAFLHGLMGRGRNF
+TGPAKALADDFTVELLDLPDHGRSPWTDRVDYQEIADRVAEHLRAGLAADGPVHVLGHSM
+GGKVAMVLALRHPDLVDRLIVEDISPRLLPQATDEFVHLLGTMLRMDLDSYESRAEADAV
+MAKHVHDARVRGFLLQNLRREGGRFAWQPNVAMLFEHLEAVGSFPDPAAPEDPDRVFDRP
+VLWLAGANSDYVRDEDVPRMKDLFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD
+>3_1215
+M-------PTWSRASLSRVNT---TAASAPSDAPLASTRIGEGSRRVAFLHGLMGRGRNF
+TGVATALADDFTVELIDLPDHGQSPWTDAVDYQDMADRVADHLRAGLAADGPVHLLGHSM
+GGKVAMVLALRHPELVERLVVVDISPRMSPSATGEFVHLLGTMLRMDLASYTSRAEADAA
+MAEHVHDARVRGFLLQNLRREDGHFAWQPNVRMLFEHLDEIGAFPDPVVPEDPDRVFDRP
+VLWLGGADSDYIRDGDAPEMKALFPRVVRVTVRGASHWVHADQPEAFVSAVRTFLTAD
+>4_1450
+MN-----------------TT---AASA-PSDAPLASTRIGEGPRRVAFLHGLMGRGRNF
+TGPAKELGDDFTVELIDLPDHGASPWTDRVDYREIADRVAAHLRAGLAADGPVHLLGHSM
+GGKVAMVLALRHPELVDRLIVEDISPRLSPQATDEFVHLLGTMLRMDLDAYDSRAEADAA
+MAEHVHDARVRGFLLQNLRRTAGHFAWQPNVAMLFEHLREIGSFPDPVVPEDPERVVDHP
+VLWLAGAESDYVQDEDVPRMKELFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001291.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001291.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3584a68f5d07da41c22a60b4aea3f43ab7adb297
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001291.fa
@@ -0,0 +1,31 @@
+>0_1524
+MPVAEARVSVAVSTAVFGVRPDPHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD
+VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPVLDDDGAAPASRPDPD
+VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR
+AVHEAVLGRGLDAANFRRATLAAGTLEETGEVRGGTPHRPPKLYRYRPAGPGTDPDPAGP
+DAR---R
+>1_1244
+MPVAEARVSVAVSTAVFGVRPDPHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD
+VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPALDDDGAAPASSPDPD
+VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR
+AVHEAVLGRGLDAANFRRATLAAGALEETGEVRGGTPHRPPKLYRYRPAGPGTDPDPAGP
+DAR---R
+>2_1320
+MPAPEARVTVAVSTAVFGVRPDPSGAPRLHVALVPRMREPFLDRWALPGTWLAADEELAD
+AAARVAAETVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPALDDDGAAPSHGGGLD
+VAGLPAGVHVRWQRADAPPAMAFDHAEILTAAVARLRADLPRAGVAHALLGPSFTLAELR
+AVHEAVLGRTLDAANFRRATLATGVLEETGEVRAGTRHRPPKLYRYRPADGA--PPPAAP
+DDPGDLS
+>3_1214
+MPVAEARVSVAVSTAVFGVRPDAHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD
+VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPTLDDDGAAPASRPDPD
+VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR
+AVHEAVLGRGLDAANFRRATLAAGTLEETGEVRDGTPHRPPKLYRYRPAGPGTDPNPAGP
+DAS---R
+>4_1451
+MPVAEARVSVAVSTAVFGVRPDPHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD
+VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPALDDDGAAPASSPDPD
+VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR
+AVHEAVLGRGLDAANFRRATLAAGTLEETGEVRGGTPHRPPKLYRYRPAGPGTDPDPAGP
+DAR---R
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001292.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001292.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5cb861598bc5fd1158445c4ca10e0d1ba62a5b66
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001292.fa
@@ -0,0 +1,46 @@
+>0_1525
+MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA
+PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR
+ASQGRPEAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL
+EAVYGTEPDDDGRVPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL
+FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALRDAKVLLWHGFCSVHRRFTVA
+QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ
+RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPASVAEPART
+ALERMLAVAPK----QSAAQSAGAGT
+>1_1245
+MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA
+PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR
+ASQGRPEAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL
+EAVYGTEPDDDGRVPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL
+FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALRDAKVLLWHGFCSVHRRFTVA
+QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ
+RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPASVADPART
+ALERMLAVAPK----QSAAQSAGAGT
+>2_1319
+MTATPETTASVARTLTLVARDPARGSACSSDLTTGPWAFDAGLPAYGPGASQDDAIPADA
+PVQGRIPEEYQQASDEELHARIAAAKAALGDRAVVLGHFYQRDEVVRHADFVGDSFQLAR
+ASQGRPEAEAIVFCGVHFMAETADLLSTPEQAVILPNLAAGCSMADMADLDSVQDAWEQL
+EEVYGTEPDADGRVPLLPVTYMNCSAALKGFVGERGGIVCTSSNASAVLEWAFERAQRVL
+FFPDQHLGRNTGRAMGIELERMPMWNPRLPLGGNTEETLRDARVLLWHGFCSVHRRFTVA
+QIEQARAEHPDVRVIVHPECPLPVVEAADESGSTDHIVKAIQAAPAGSTFAIGTEINLVQ
+RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPDAVADPARA
+ALERMLAVAPR----QSVAQGAGA--
+>3_1213
+MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA
+PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR
+ASQGRPAAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL
+EAVYGTEPDDDGRMPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL
+FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALREAKVLLWHGFCSVHRRFTVA
+QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ
+RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPVSVADPART
+ALERMLAVAPKQSAAQSAAQSAGAGT
+>4_1452
+MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA
+PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR
+ASQGRPEAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL
+EAVYGTEPDDDGRVPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL
+FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALRDAKVLLWHGFCSVHRRFTVA
+QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ
+RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPASVADPART
+ALERMLAVAPK----QSAAQSAGAGT
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001310.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001310.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f8ab5b522994ae2aed49324c64a1d4996181f763
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001310.fa
@@ -0,0 +1,26 @@
+>0_1574
+MQLTIAPGDITATHADAVVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPEGL
+PAGQAVATTAGRLPARWVIHTVGPVWAKTIDKSDTLASCYRESLKVAAGLGARTVAFPAI
+SAGIYGWPMEDAARIAVETCHAMADEVGDTVDEVLFVPYGETAEAAFRAALGHLEAPQTT
+DDEG-DTGR
+>1_1289
+MQLTIAPGDITATHADAVVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPEGL
+PAGQAVATTAGRLPARWVIHTVGPVWAKTIDKSDTLASCYRESLKVAAGLGARTVAFPAI
+SAGIYGWPMEDAARIAVETCHAMADEVGGTVEEVLFVPYGDTAEAAFRTALDRVERG---
+---------
+>2_1243
+MELLIAPGDITATTADVVVNAANSTLLGGGGVDGAIHRRGGPEILAACRRLRETELPDGL
+PVGQAVATTAGRLPARWVVHTVGPVWAKTIDKSATLASCYRESLRVAAELGARSVAFPAI
+SAGVYGWPMDDAARIAVTTCREVAAQGAGSVERVLFVPFGERAEAAFRAALD------AP
+DETGAPAAS
+>3_1152
+MKLSIAPGDITATHADAIVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPDGL
+PAGQAVATTAGRLPARWVIHTVGPVWAKTIDKSDTLASCYRESLRVARELGARTVAFPAI
+SAGVYGWPMDDAARIAVETSHAMADEVGDVVEEVLFVPFGDRAEAAFRAALEHLT-----
+---------
+>4_1503
+MQLTIAPGDITATRADAVVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPEGL
+PAGQAVATTAGRLPARWVIHTVGPVWAETIDKSDTLASCYRESLKVAAGLGARTVAFPAI
+SAGIYGWPMEDAARIAVETCHAMADEVGGTVDEVLFVPYGETAEAAFRAALGHLEDPQAT
+DDEG-DTGR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001316.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001316.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b9c913c3f9f2ed1e7e3aeaf08ceda76ea36c4482
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001316.fa
@@ -0,0 +1,46 @@
+>0_1580
+MDQPVTEGASAASDVPVSAPARAGETSAERPWPLRRLSENLKAHIERAPATWIEGQLIEF
+KNNRGNVYMTMRDLEEEVSLPLTAWRNVAMTLDGTVQQGSRVVARVKPNFWLKAGRLSMN
+VQEMRPVGLGDLLARVELLRRALAEEGLTSPARKRPLPLLPRRIGLITGRDSDAKKDVLR
+NTLLRWPAAEFEIREVAVQGAEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS
+DEALVRAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQEAAGLADA
+RLRLAAAVERRVRAEAEGLAALRSRPVLARPHVMVDTRQEETDRWRERGRSALGHRLVRE
+EDALTQLRARVRALSPQRTLDRGYAVVQHAGQVVRDADQVAPDDRLDILVAAGRIAADVV
+ATH------------RTTPTPSHERTRQA
+>1_1295
+MDQPVTEGASAASDVPVSAPARAGETSAERPWPLRRLSENLKAHIERAPATWIEGQLIEF
+KNNRGNVYMTMRDLEEEVSLPLTAWRNVATTLDGTVQQGSRVVARVKPNFWLKAGRLSMN
+VQEMRPVGLGDLLARVELLRRALAEEGLTSPARKRPLPLLPHRIGLITGRDSDAKKDVLR
+NTLLRWPAAEFETREVAVQGAEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS
+DEALVRAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQEAAGLADA
+RLRLAAAVERRVRAEAEGLAALRSRPVLARPHVMVDIRQEETDRWRERGRSALGHRLVRE
+EDALTQLRARVRALSPQRTLDRGYAVVQHAGQVVRDADQVAPDDRLDILVAVGRIAADVV
+ATH------------RPTPTPSHERTRQA
+>2_1236
+MDPSSTAHVEADALLDAGVPATASQTSAERPWPLRRLSENLKLHIERAPATWIEGQLIEY
+KTNRGNVYMTMRDLEEEYSLPVTAWRNVAVTFEGTVQQGSRVVARVKPNFWTKAGRLSMV
+VQEMRPVGLGDLLARVELLRRRLGEEGLLDPARKRPLPLLPGLVGLITGRDSDAKKDVLR
+NAQLRWPAVRFEVREVAVQGPEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS
+DEALVRAVAAARTPVVSAIGHEADRPVLDDVADVRASTPTDAAKRIVPDAAQEAAGIAEA
+RRRLAAAVERRVQREGEGLAQLRSRPVLADPVVMVDGREQDLHAWRERARRATAHRLTRE
+RDAVEHLVARVRALSPQQTLDRGYAVVQQEGRLIRDAAQVAPGEDVDILVASGRISAEVT
+AVRPGRVGGVGTVQDEDEQAGTKE---QA
+>3_1146
+M-----EESAAREEGTVVVPATASETSPERPWPLHRLSENLKLHIERAPATWIEGQLIEH
+KNNRGNLYMTMRDLEEEVSLPLTAWRAVAAGIDPSVQQGSRVVARVKPNFWVKGGRLSMV
+VQEMRPVGLGDLLARVELLRRRLAEEGLTSPARKRQLPVLPGVIGLITGRDSDALKDVVR
+NTHLRWPAAVFEVREVAVQGPDAPRQVAAALAELDARPEVEVIVIARGGGALEEVVLPFS
+DEALVRAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQESVGIREA
+RLRLAGAVERRVRGEADALAALRSRPVLAHPHVMVDTRTEDLGRWQERGRVALGHRLARE
+ADAVSALRAQVRALSPQQTLDRGYAVVQHAGHVVRRAEDVTPGDDLDVLVAAGRIEAYVT
+DVTP-----------VETPSPTQE---DA
+>4_1509
+MDQPVTEGASAAPDVPVSAPARAGETSAERPWPLRRLSENLKAHIERAPATWIEGQLIEF
+KNNRGNVYMTMRDLEEEVSLPLTAWRNVAMTLDGTVQQGSRVVARVKPNFWLKAGRLSMN
+VQEMRPVGLGDLLARVELLRRALAEEGLTSPARKRPLPLLPHRIGLITGRDSDAKKDVLR
+NTLLRWPAAEFEIREVAVQGAEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS
+DEALVRAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQEAAGLADA
+RLRLAAAVERRVRAEAEGLAALRSRPVLARPHVMVDTRQEETDRWRERGRSALGHRLVRE
+EDALTQLRARVRALSPQRTLDRGYAVVQHAGQVVREADQVATDDRLDILVAAGRIAADVV
+ATH------------RTTPTPSHERTRQA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001320.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001320.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a585f147e4eddae0a3b9fdfe4ad12c9a676518f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001320.fa
@@ -0,0 +1,41 @@
+>0_1585
+MSRPAHRRPT-----ALAASALALSLALGAC-ARQADAPPTPSASGTPITVVHGGEGLEG
+AVAAVLARHLRLHGHAVADEDGVAVEQPAWSAAGGDTVAVVDTLALAVAADPAVALPSPP
+--PPTSTPSSTPTGTEAG--PSADAVPTPSATASTAVPSPTALPVGDPAADAQAAGRVLE
+TLLAEETA-------------AAGTPQ-DEAPAVLSSSAGVLRLTAVVTQTTAARLELES
+ITDLNGWCESLTAVAPPPLTAAADPDAATALRARLDRLAGCRPETWLADTEDPSAALVAD
+EAQVALLTDTDPEIDANTLVPLEDDGRVLPEGRLTAVGSAATLDDDAERRIAEVMSALDG
+DGLRELERLTTGADPLPAAEAAQYWLVDHGLEDAPEDWFVPRGSWF
+>1_1300
+MSRPAHRRPT-----ALAASALALSLALGAC-ARQADAPPTPSASGAPITVVHGGEGLEA
+AVAAVLARHLRLHGHAVADEDGVAVEQPAWSAAGGDTVAVVDTLALAAAADPAAALPSPP
+--TPTPTP--TPTGTEAG--TSTGTVPTPSATASTAAPSPTALPVGDPAADAPAAGRVLE
+TLLAGQTA-------------AAGTPQ-DEAPAALSSSAGVLRLTAVVTQTTAARLELES
+ITDLNGRCESLTAVAPPALTSA--ADAATALRARLDRLAGCRPETWLADTEDPTAAVVAD
+EAQVALLTGTDPEIDANTLIPLEDDGRVLPEGRLTAVGSAATLDDDAERRIAEVMSALDG
+DGLRELERLTTGADPLPVAEAAQYWLVDQGLEDAPEDWFVPRGSWF
+>2_1231
+------------------------------------------------------------
+------------------------------------------------------------
+----------MPTASESS-----------DAADASATPEPTPLPDGEPAADAAEAGRVVE
+RLLQGDAE-------------AGASPEPGDAVAVLGSSAGVLRLSAVVTATTAARLELDA
+LEDLNGRCEGLTAALPAGLAG--DPQANAALHARLDRLAGCRPGTWREEDASAAAVVVAD
+QAQLGLLSATDPEIPASMLVPLEDPERVLPEGRLAAVGAPDALDDDAQRRIEEVLSALDE
+DGLRELERITTGADALPPAEAARYWLVDQGLEDVPEGWFMPRDSWF
+>3_1141
+MTRPAERPRTSRVRAAAGASALSLALALSGCGAPRAGAPADP--TGAPVTVVHTSDPLDS
+AVAAVVARHLRHRGHPVTLED--AGDATPWSAAAGDTVAVVDTLRLALQADPAAVLPPEP
+EDAAASRAAAAPTPSESSLEPIDPSAPARVPATGSATPSPTPLASGLPAADADAAQAVVD
+AALSRVAAGADAAAPTPAASRSAATPT-GPSPRVLADSAGTLRLAAVVTATTASREGLDS
+IDDLDGRCGDLTLAVPAALAA---AVSDGLLAHRLDDFAGCRPADWRTDAADVGPAVVAD
+AAQVGLTYRTDPDIPPNGLVLLEDPDRVLPEGRIAVVGERETLDDDAQSALGEVMDRLDD
+DGIAELARLTEGGDALPADEAAQYWLVSQRLEDAPEDWVVPADPWF
+>4_1514
+MSRPAHRRPT-----ALAASALALSLALGAC-ARQADAPPTPSASGTPITVVHGGEGLEG
+AVAAVLARHLRLHGHAVADEDGVAVEQPAWSAAGGDTVAVVDTLALAAAADPAAALPSPP
+--SPTSTPSSTPTGTEAG--TSADAVP----TASTAAPSPTALPVGDPAADAPAAGRVLE
+TLLAEETA-------------AAGTPQ-AEAPAVLSSSAGVLRLTAVVTQTTAARLELES
+ITDLNGRCESLTAVAPPTLTAAADADAATALRTRLDRLAGCRPETWLADTEDPTAAVVAD
+EAQVALLTGTDPEIDANTLVLLEDDGRVLPEGRLTAVGSAATLDDDAERRIAEVMSALDG
+DGLRELERLTTGDDPLPVAEAAQYWLVDHGLEDAPEDWFVPRGSWF
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001321.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001321.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c3e88eb337cd0d3c9182d862b43dbee0619b3b05
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001321.fa
@@ -0,0 +1,21 @@
+>0_1586
+MSTTPAAPDAAGAH---PAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIEL
+GESPEEACLREVWEETGHTAELTGLLGVTTGTIPVEKRLRGEPLPLLTVQVLYTARITGG
+VLRPEVGGSSTDARWFDLAELSELRTASWVTEALARAGVDT--------
+>1_1301
+MSTTPAAPDAAGAH---PAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIEL
+GESPEEACLREVWEETGHTAELTGLLGVTTGTIPVERRLRGEPLPLLTVQVLYTARITGG
+VLRPEVGGSSTDARWFDLAELSGLRTASWVTEALARAGVAT--------
+>2_1230
+MSPTP-VPDAEPARADAPAGPFQTRAGAYALIVDGGRVLLSSWQGPEHLVWTLPGGGIEL
+GESPEEACRREVWEETGHTAELTGLLGVTTGVIPAERRLRGEALPLLTVQVLYTARITGG
+VLRPEVGGSSTDARWFDLAGLDAVRTAPWVREALARAGAAA--------
+>3_1140
+M--SAASPTAASTA---P-GPFETRAGAYALIVEDGRVLMSAWAGPTGIVWTLPGGGIEL
+GESPEEACVREVEEETGHTAELTGLLGVTTGTIPVERRLRGEPLPLLTVQVLYTARLTGG
+VLRPEADGSSVDAAWFALDGLADVRTSAWVDRALALAGLAADDAAGTAR
+>4_1515
+MSTTPAAPDAAGAH---PAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIEL
+GESPEEACLREVWEETGHTAELTGLLGVTTGTIPVEKRLRGEPLPLLTVQVVYTARITGG
+VLRPEVGGSSTDARWFDLAELSELRTASWVTEALARAGVDT--------
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001324.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001324.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5488e6c1a3ed639526545f59ce4f70ee0d291f90
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001324.fa
@@ -0,0 +1,36 @@
+>0_1589
+MDETTAPTRAVQAALDALADARVSASLVIVALVAFLAWRLVLRRHRLASAPARPSMPRSF
+MHRLQSSPAVRALTARFSGRLSAAADAARAA-RGRTGLHIRWGRTALFLAALVALLVFLV
+AGLAAAFGAGTLALAGWSLLFAVAGLAGLRALAVRDRTRRARPAAVVVPERPAAPAAEER
+QAPPA--DPERDRRVLETVLAFETEAPR-PAAAPAAPRVEPVVVTASAA-APAADRVVTI
+PAVPRPTYLDAPEMARPLPAPLETPAPTGA-DTRLTDAARTADDQ--ISAAAEQDIAA--
+LDLDNVLARRRAC
+>1_1304
+MDETTPPTTAVQAALDALADARVSASLVIVALVAFLAWRLVLRRHRLASAPARPSMPRSF
+MHRLQSSPAVRALTARFSGRLGAAADAARAA-RGQTGLHIRWGRTALFLAALAALFVFLV
+AGLAAAFGAGTLSLAGWSLLFAVAGLAGLRALAVRDRTRRARPAADVVPARPAAPAAEER
+QAPPA--DPERDRRVLETVLAFETEAPR-PAAAPAASRVEPVVVTASAA-APAADRAVTI
+PAVPRPTYLDAPEMARPLPAPLETPAPTGA-DTRLQDAASTADDR--ISAAAEQDIAA--
+LDLDNVLARRRAC
+>2_1225
+MEDTTAPASAGRAALDALADARVSASFVILALVAYFAWRLVVRRRRVESAPARPTMLRST
+MHRLQSSPAVRALTERLSGRVSGLADSARAAGRRTAGLQVRWGRTALFLAALAALAVALV
+AGVAAAFGAGTAGLAGACLLFAVAAVAGLRALAVRDRARRAPAAVVEAPA-EAAPHAAP-
+EAPRV--DPERDRRVFETVLGLEDEAARVSAAAPAAPAAAPTVVAASAVRAPEATDTVTL
+PVVPRPTYLDAPEMLRPAPAPLTAPEAAGS-DVRLKDAARAAEHEEALSATAEQDVAA--
+LDLDHVLARRRAS
+>3_1137
+------------------------------------------------------------
+------------MTETPSPREDARLDA--EPGHADSGFHVHWDRASLFLVGVGALAVALV
+TALCALAGLPTAGLAGWSLLVTVGAVVGLRVLAARDQREHHDDLADDADEPNLAEEDLDT
+HELPVVPDPERDRRVLAAALSLTDEAEDEEPAAEPVPVVVDALQRRRAPRIPLG--GIVI
+PEVPRPTYLDAPE-APAAEAQAEYPAEDDAVATRPEAEEQAASAE--VVEIPEPAARAVV
+LDLDGVLARRRAS
+>4_1519
+MDETTAPTRAVQAALDALADARVSASLVIVALVAFLAWRLVLRRHRLASAPARPSMPRSF
+MHRLQSSPAVRALTARFSGRLSAAADAARTA-RGRTGLHIRWGRTALFLAALVALLVFLV
+AGLAAAFGAGTLSLAGWSLLFAVAGLAGLRALAVRDRTRRARPAAVVVPERPTAPAAEER
+QAPPA--DPERDRRVLETVLAFETEAPR-PAAAPAAPRVEPVVVTASAA-APAADRAVTI
+PTVPRPTYLDAPEMARPLPAPLETPAPTGA-DTRLTDAARTADDQ--ISAAAEQDIAA--
+LDLDNVLARRRAC
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001325.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001325.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5b8d752c22a6ae205a16f802ca3b2f483e2a2071
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001325.fa
@@ -0,0 +1,26 @@
+>0_1590
+MSWQRSPWPVTLRHGTLALRPLRRRDREAWEEQRAHNREWLTPWDATSPVPGAGPASFGQ
+MVRWHGRQGRDGSAYTWGMAL-DDDRPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREA
+GRGLTPTAVAMATDWAFRSAGLHRVEVNIRPENAASLRVVAKLGLRDEGLRRAYLHVDGA
+WRDHRTFAVTAEEVPDGLLAGWLATRPRP-------------------------
+>1_1305
+MSWQRSPWPVTLRHGTLALRPLRRRDREAWEEQRAHNREWLTPWDATSPVPGAGPASFGQ
+MVRWHGRQGRDGSAYTWGMVLDDDDRPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREA
+GRGLTPTAVAMATDWAFRSAGLHRVEVNIRPENAASLRVVAKLGLRDEGLRRAYLHVDGA
+WRDHRTFAVTAEEVPDGLLARWLASRPRA-------------------------
+>2_1224
+MSWQRSPWPVTLRHGTLSLRPLRRRDRDAWEAQRAHNHAWLTPWDATSPVPGAGPSSFGQ
+MVRWHGRQGREGSSFTWGVAL-DDDAPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREA
+GRGLTPTAVAMAADWAFRSAGLHRVEVNIRPENAASLRVVEKLGLRDEGVRRSYLHVDGD
+WRDHRTFAITAEEVPEGLLARWLASRPRA-------------------------
+>3_1136
+MDVSGSLWPVALRHGTLTLRPLRRGDRRAWEEQRAANRDWLTPWDATSPVPGAAPASFAQ
+MVRWQHRQARAGTSYTWGMAL-DDDAPGRDRLIGLLSLGGVQHGSVMSGAVGYWIDRRQA
+GRGLTPTAVAMATDWAFHGLGLHRVEVNIRPENTASLRVAEKLGLREEGLRRAYLHVDGA
+WRDHLSFAVTAEEVPEGLLPRWLARREAAAGTAEPRDTAHTPGVAGDVPGPSGR
+>4_1520
+MSWQRSPWPVTLRHGTLALRPLRRRDREAWEEQRAHNREWLTPWDATSPVPGVGPASFGQ
+MVRWHGRQGRDGSAYTWGMVL-DDDRPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREA
+GRGLTPTAVAMATDWAFRSAGLHRVEVNIRPENAASLRVVAKLGLRDEGLRRAYLHVDGA
+WRDHRTFAVTAEEVPDGLLARWLATRPRP-------------------------
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001341.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001341.fa
new file mode 100644
index 0000000000000000000000000000000000000000..041178afa51b10316a5ddc0ee3228804f5546c53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001341.fa
@@ -0,0 +1,46 @@
+>0_1609
+MA-----------RPRPAARPSRPSAAASEEDDTALAPVLESEGRALLDSLAGYREADAL
+AVSSRLRAAGHPPERVAAALTQAALRSRAEARLGPEARRMLFTRDGLEQATRPLVAGLHA
+DRLAAAGARRVADLGCGLGLDARAFADRGLDVVAVERDAVVAAAAEVNLAG---HRGARV
+VHGDAVAWARAHVPAEADAVWLDPARRQVGGGGSARVFDPEAFSPPLSVVTDIAATGVPV
+GVKLGPGLPHEAVPAGAEAEWVSVDGDVVEAALWFNAAARPGVRRAARVMTVHGGKTTTA
+QLVSGADFGDSPEVEAVGEEGMAGLVGAVLHEPDGAVIRAGLVTDLAVSWPVPTRQLDPH
+LAYLVAPEPVHDGLARAHRIEAVHGFHLASLRRWAKETGVGRLDVKKRGIRETPEEVRRA
+VLGGAKPGRRGGAGRHATLVLARVGRSRFALEVTPL--D
+>1_1324
+MA-----------RPRPASRSPRPTAAASEADDTALAPVLEPEGRALLDSLAGYREADAL
+AVSSRLRAAGHPPERVAAALTQAALRSRAEARLGPEARRMLFTRDGLEQATRPLVAGLHA
+DRLAAAGARRVADLGCGLGLDARAFADRGLDVVAVERDAVVAAAAEVNLAG---HRGARV
+VHGDAVAWARAHVPAEADAVWLDPARRQVGGGGSARVFDPEAFSPPLSVVTDIAATGVPV
+GVKLGPGLPHEAVPEGAEAEWVSVDGDVVEAALWFNAAARPGVRRAARVMTVRGGETTTA
+QLVSGADFGDSPEVEAVGEEGMAGLVGAVLHEPDGAVIRAGLVTDLAASWPVPTRQLDPH
+LAYLVAPEPVRDGLARAHRIEAVHGFHLASLRRWAKETGVGRLDVKKRGIRETPEEVRRA
+VLGGAKPGRRGGAGRHATLVLARVGRSRFALEVTPL--D
+>2_1206
+------------------------------------------------------------
+------------------MLTQADLRARAVPRLGPDARGMLFTRDGLEQATRPVVAALHA
+QRMAAAGARTVADLGCGLGLDARAFADAGLGVVAVERDAVVAAAAEVNLTD---RPGARV
+VHGDAVPWAREHVPAQADAVWLDPARRQVGGGGSARVFDPEAFSPPLSVVEELAATGVPV
+GVKLGPGLPHEAVPAGAEAEWVSVDGDVVEAALWFNAAARPGVRRAARVIDTRGGQATTA
+ELVSGADFGDSPGVEAVGEEGMPGLVG-----------RCSTSRTAPSSGPGSSRTWR--
+-------SPGRRRPASWTRTWPIWWPPSTRPTRWPGRTGSTRSTISTSSL----------
+CAGGRR--RRGSAAW-----------------------T
+>3_1118
+MARSQRPARPSRPRPRPADRPGRPRAAESAADATRLEPVLDPAGRVLLDGLGDVSGQDPL
+ALSSRLRAAGHDADTVAAALTQAGLRHAGRAKLGALADGMLLTRDGLEQATRAVVAEHRA
+RRLQEAGVRSLADLGCGIGADALVYARAGLDVTAVERDPTVAAAAAANLATLAPAGAASV
+VTGDAEAWAAAHAD-EVDALWLDPARRRLGSSGTARVFDPEAFSPPLSFVLGLADGGRPV
+GVKLGPGLPHEHVPAAAEAEWVSVDGDVVEVTLWFGPLAQAPGRRTATLLDTRG--SAVH
+RLVPAA--ASSPAVEAVGEEGVDGLVGQVLLEPDGAVIRAGLVTDLAVELGPAVRLLDPH
+LAYLVAPDAAPHPLARGYRVLAVHEFRTKALARWARETGVGRLDVKKRGVRETPEQVRAA
+VLGRGTPG-----GRHATLVLARVGERRVAFEVEPLPAG
+>4_1539
+MA-----------RPRPASRSPRPTAAASEADATALTPVLEPEGRALLDSLAWYREADAL
+AVSSRLRAAGHPPERVAAALTQAALRSRAEARLGRQARRMLFTRDGLEQATRPLVAGLHA
+DRLAAAGARCVADLGCGLGLDARAFADRGLDVVAVERDAVVAAAAEVNLAG---HRGARV
+VHGDAVAWARAHVPAEADAVWLDPARRQVGGGGSARVFDPEAFSPPLSVVTDIAATGVPV
+GVKLGPGLPHEAVPAGAEAEWVSVDGDVVEAALWFNAAARPGVRRAARVMTVRGGETTTA
+QLVSGADFGDSPEVEAVGEEGMAGLVGAVLHEPDGAVIRAGLVTDLAASWPVPTRQLDPH
+LAYLVAPEPVHDGLARAHRIEAVHGFHLASLRRWAKETGVGRLDVKKRGIRETPEEVRRA
+VLGGAKPGRRGGAGRHATLVLARVGRSRFALEVTPL--D
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001345.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001345.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dbd236c09627340c7e8ea9fefd7e85a1409ae7f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001345.fa
@@ -0,0 +1,21 @@
+>0_1613
+MRTRTLTRRAALTGLLGSAALGFTACTSSGYPADPDGTLDRVTGGVLRVGVVHHPPHVDV
+SGAEPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHA
+SITRDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR
+>1_1328
+M---TITRRAALAGLLGGAALGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDA
+SGAEPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHA
+SITRDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR
+>2_1202
+M---TITRRAALTGLLGGAVLGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDA
+SGAEPVGPEPDLIRGFAAAHDAEIAWTVSGEEALLTALEKGDVDLVAGGLTSDSPWTTHA
+SLTRDYAEAAGPDGEPVKLVMAVPPGENQMLAALEAHLDAQAREAGR
+>3_1114
+M---QTPRRTLLTGALAAAGVVLTGCTSSGYPADPDGTLDRITGGTLRVGASHHPPHVDA
+AGAEPQGPEPDLVRAFAAERDARVEWTVSGEEALMTALKQGDLDLVVGGLTKKSPWTTDA
+GLTRPYAETTGPDGEKAELVMAVPLGENQFQSALERFLDAHGEEAGA
+>4_1543
+M---TITRRAALAGLLGGAALGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDA
+SGAEPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHA
+SITRDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001346.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001346.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3eb0efb642d120e0d54dd7a5a66a0f2a20147a02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001346.fa
@@ -0,0 +1,36 @@
+>0_1614
+MTRR-DTRETGPSGRRFGATELPPEIERVVQQAKRLEWATLGVIVVTIVLVAFVMGSSQA
+MRAAWIEDLLSLIPPIAFLVALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLV
+GDSLLGLVTAEHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLKLAEQLHDRV
+LYADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAILVGVSIVLDGWKNLKEAVTNLA
+DRRAATIDGARPHPLIDRAERVAWAEPWVRHAGARVRDEGHVFHVEMFVVPHEGADVTVA
+RCCALRDAIAALDWKLQDVVVAPVDELPAEVHGGRSGEHQT-GEE
+>1_1329
+MTRQ-DTRETGPSGRRFGATELPPEIERVVQQAKRLEWVTLGVIVVTIVLVAIVMGSSQA
+MRAAWIEDLLSLIPPIAFLIALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLV
+GDSLLGLVTAEHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLTLAEQLHDRV
+LYADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAIFVGVSIVLDGWKNLKEAVTNLA
+DRRATTIDGARPHPLIDRAERVAWAEPWVRHAGARVRDEGHVFHVEMFVVPHEGADVTVA
+RCCALRDAIAALDWKLQDVVVAPVDELPAEVHGGRSGEHQT-GEE
+>2_1201
+MTHHASTTHRSPGGRRFGATELPPEIERALRRAVRLEWATLAVLAVTIALVAVVMGSSQA
+MRAAWIEDLLSLVPPIAFLVAVRVTRRHPTRARPYGSHRSVGVGHLVAAVALSVMGVILV
+ADSALGLVTGEHPPIGTLDLFGHTVWQGWFMMAVMALSIPGPVLLGRAKLKLAEQLHDRV
+LYADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAIFVGVSIVLDGWRNLREAVGNLA
+DRRATTIDGDRPHPLIDRAERVAWAQPWVRHAGTRVRDEGHVLHVEMFVVPHEGAGATVG
+RCAQLREEIVALDWKLEDVVVVPVAELPAEVHGGASGDEQS-GEE
+>3_1113
+MSEK----------RTIGRAELPDDVARAAHQAVVLEWVSLGWLVLTVSLVAVVMGSSQA
+MRAAWIEDLLSLIPPIAFLVALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLV
+GDSLLGLLTAEHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLKLAEQLHDRV
+LYADADMNKADWQTGVATIVGVAGIGLGWWWADAAAAIFVGVSIVLDGWKNLKEAVTNLA
+DRRATTIDGARPHPIIDRAERVAWAQPWVRHAGARVRDEGHVFHLEMFVVPRHGADVTVG
+RCADLRERIEELDWKLEDVVVVPVAELPEEVHGGRSGDEQSKGSE
+>4_1544
+MTRR-DTRETGPSGRRFGATELPPEIERVVQQAKRLEWATLGVIVVTIVLVAIVMGSSQA
+MRAAWIEDLLSLIPPIAFLVALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLV
+GDSLLGLVTAEHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLKLAEQLHDRV
+LYADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAIFVGVSIVLDGWKNLKEAVTNLA
+DRRAATIDGARPHPLIDRVERVAWAEPWVRQAGARVRDEGHVFHVEMFVVPHEGADVTVG
+RCCALRDAIAALDWKLQDVVVAPVDELPAEVHGGRSGEHQT-GEE
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001355.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001355.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b8a765f187f2f122b273c650361d24e83d8600e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001355.fa
@@ -0,0 +1,50 @@
+>0_1624
+MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHAHVAGIGHGQRYGYRVHGPWD
+PARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPDRIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYE
+THVKGMTKLHPAVPEELRGTYAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS
+SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEGDERHYMDYTGTGNSVDLSSP
+KALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPDMFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGL
+WSEWNGMYRDAVRDFWRGEPGTLGEFATRLTGSADLYEGDGRGPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG
+EAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNVYCQDNEISWIDWSAMDDSLV
+AFTRDLIALRRDHAVFRRRHHFDGRPAARDVEAPLPDIVWLEPDATAKTEDDWGAEARSIGFYLNGHMLTRGDEEGEEPY
+RDFYVLMNAWWEPVPYTLPGPTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQV--PEGA
+>1_1339
+MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHAHVAGIGHGQRYGYRVHGPWD
+PARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPDRIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYE
+THVKGMTKLHPAVPEELRGTYAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS
+SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEGDERHYMDYTGTGNSVDLSSP
+KALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPDMFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGL
+WSEWNGMYRDAVRDFWRGEPGTLGEFATRLTGSADLYEGDGRGPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG
+EAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNVYCQDNEISWIDWSAMDDSLV
+AFTRDLIALRRDHAVFRRRHHFDGRPAARDVEAPLPDIVWLEPDATAKTEDDWGAEARSIGFYLNGHMLTRGDEEGEEPY
+RDFYVLMNAWWEPVPYTLPGPTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQV--PEGA
+>2_1175
+MHTVDIGQPYPLGATVDETGTNFAVALAREAESVELCLVDEDGVETRLPVVERHGTTWHVHVAGVGHGQRYGYRVTGPWD
+PSRGLWHNPAKILVDPYARAFAGEHEWGQQHHSYDFDEPDRMDTSDNLGTTMLGVVTDDDFDWGEDAPPNIEMTDTVVYE
+THVKGMTMRHPAVPEELRGTYAGMAHPEVVRHLTDLGVTAVELMPVHQFVDDATLQEKGLSNYWGYNTLGFFAPHAAYAA
+SQEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSMRGLDNAGYYHLVEADERHYMDYTGTGNSVDLSSP
+KALQLVMDSLRHWVTEMHVDGFRFDLATTLTRVEGEQGPDMFSAFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGI
+WSEWNGMYRDTVRDFWRGEPGTLGEFATRLTGSADLYEGDGRSPGASVNFVTAHDGFTLRDLVSYNEKHNAANGEDNNDG
+ESHNRSWNCGVEGETDDPEVLTLRARQQRNFLATLLISQGVPMISHGDELGRTQGGNNNVYCQDNEISWIDWSAVDDSLV
+AFTRDLIALRHDHAVFRRRHHFDGRPAARDVEAPLPDIVWLEPDATAKTEDDWGAEARSIGFYLNGHTLTRGDEDEEGPY
+RDFYVLMNAWWEPVPYTLPGPLFPETWEVVVDTSSHVAPSGSRPRVRAGEVLEVPARSTVILRQV--PEGA
+>3_1104
+MHTVDIGQPYPLGATVDEAGTNFAVAVGREVEAVELCLIAEDGSEERIPVTERHDTTWHVHVAGIGGGQRYGWRVHGPWD
+PARGLWHNPHKLLADPYARAFTGDYAWGQQHFSYAFDEPDRMDTADSRGTSMVGVVVDDDFDWGDDAPPQRLLTDTVVYE
+THVKGLTALHPDVPEELRGTYAGVAHPSVLEHLTSLGVTAVELMPVHQFVNDSILQEKGLSNYWGYNSLGYLAPHAAYSS
+ADTVGGQVHEFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPLLSFRGFDNAGYYHLVEGDERHYMDYTGTGNSVDLSSP
+KALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPDMFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGI
+WSEWNGMYRDTVRDFWRGEPGTLGEFATRLTGSADLYEGDGRNPGASVNFVTAHDGFTLRDLVSYNEKHNHANGEDNNDG
+DSHNRSWNCGVEGETDDPEVLTLRARQQRNFLTTLMVSEGVPMLSHGDELGRTQKGNNNVYCQDNELSWIDWSTRDDALI
+AFTRDVIALRRDHAVFRRRQHFDGRPAERDVEAPLPDIVWLEPDATAKTEADWGAEARSIAFYLNGHDLQRREGEPDEAF
+RDFYVLMNAWWEPVPYTLPGPLFPGEWEIVVDTSSHVAPAGTRPHVVAGEVIEVPGRSTMILREVVRQEQG
+>4_1554
+MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHAHVAGIGHGQRYGYRVHGPWD
+PARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPDRIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYE
+THVKGMTKLHPAVPEELRGTYAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS
+SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEGDERHYMDYTGTGNSVDLSSP
+KALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPDMFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGL
+WSEWNGMYRDTVRDFWRGEPGTLGEFATRLTGSADLYEGDGRSPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG
+DAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNVYCQDNEISWIDWSAMDDSLV
+AFTRDLIALRRDHAVFRRRHHFDGRPAARDIEAPLPDIVWLEPDATAKTEDDWGAEARSLGFYLNGHTLPRGDEEGEEPY
+RDFYVLMNAWWEPVPYTLPGPTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQV--PEGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001360.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001360.fa
new file mode 100644
index 0000000000000000000000000000000000000000..23aa11817579ab15e01df48defefb2f761059648
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001360.fa
@@ -0,0 +1,46 @@
+>0_1632
+MSRLFGTDGVRGLANETLTVELSVQLAQAASPVLGAEAFDAGRRPVAVVARDPRISGEFI
+TAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLDADFGVMISASHNPAPDNGIKFLARGG
+EKLTDAQEDEIIRHLEGVTPRRPQGADVGRVRVFADAEDRYVLHLLQTLPHRLDGLKVVL
+DCAHGAAAGCSPEAFRAAGAEVVVIGASPDGLNINDGYGSTHLEKLQAAVREHGADLGIA
+HDGDADRCLAVDERGEVVDGDQIMGVMAVALKDRGVLRDDTLVVTVMSNLGLKLAMGREG
+VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLASRVAETGTP
+LSELAAVMDRLPQVLVNVRGVDKSRAAEDEAVQAAVAEAEARLGETGRVLLRPSGTEPVV
+RVMVEAPDEETAGREAQVLADVVQRELRLHD
+>1_1346
+MSRLFGTDGVRGLANETLTVELSVQLAQAASPVLGAEAFDAGRRPVAVVARDPRISGEFI
+TAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLDADFGVMISASHNPAPDNGIKFLARGG
+EKLTDAQEDEIIRHLEGVTPRRPQGADVGRVRVFADAEDRYVLHLLQTLPHRLDGLKVVL
+DCAHGAAAGCSPEAFRAAGAEVVVIGASPDGLNINDGYGSTHLEKLQAAVREHGADLGIA
+HDGDADRCLAVDEHGEVVDGDQIMGVMAVALKDRGVLRDDTLVVTVMSNLGLKLAMGREG
+VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLASRVAETGTP
+LSELAAVMDRLPQVLVNVRGVDKSRAAEDEAVQAAVAEAEARLGETGRVLLRPSGTEPVV
+RVMVEAPDEETAGREAQVLADVVQRELRLHD
+>2_1167
+MSRLFGTDGVRGLANETLTVELSVQLAQAAAPVLGAEALEAGRRPVAVVARDPRISGEFI
+AAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLGADFGVMISASHNPAPDNGIKFLARGG
+EKLTDAQEDEIIRHLEGVEPRRPQGADVGRVKVFSDAEDRYVVHLLQALPHRLEGLKVVL
+DCAHGAAAGCSPEAFRDAGAEVVVIGASPDGLNINEGYGSTHLEKLQAAVLEHGADLGIA
+HDGDADRCLAVDERGEVVDGDQIMGVMAVAMKDRGVLRDDTLVVTVMSNLGLKLAMGREG
+VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLAARVAETGRP
+LSALAAVMDRLPQVLVNVRGVDKSRAAEDVAVQAAVAEAEARLGETGRVLLRPSGTEPVV
+RVMVEAPDEETAGREAEALADVVQRELRLHV
+>3_1098
+MSRLFGTDGVRGLANDVLTVELSVQLAQAAAPVLGADALAAGRRPVAVVARDPRISGQFI
+AAAVIAGLASSGVDVHDAGVVPTPAAAFLVGDLDADFGVMISASHNPAPDNGIKFLARGG
+EKLTDEQEDEIIQHLESEHPLRPTGAEVGRVRTFSDAEDRYVVHLLQTLPHRLDGLTVVL
+DCAHGAASGCSPDAFRDAGAQVIVIGAEPDGLNINEGVGSTHLEKLQAAVKEHGADLGIA
+HDGDADRCLAVDELGEVVDGDQIMGIMALALKDRGQLKEDTLVVTVMSNLGLKLAMRGAG
+IELVETQVGDRYVLAGMRLGEYSLGGEQSGHVIFADHATTGDGVLTGLQIAARVAETGTP
+LSQLAAVMTRLPQVLVNVRGVDKSRAAEDAAVQSAVREAEARLGETGRVLLRPSGTEPVV
+RVMVEAPDEETARREAEALAEVVQRELRLHD
+>4_1561
+MSRLFGTDGVRGLANETLTVELSVQLAQAASPVLGAEAFDAGRRPVAVVARDPRISGEFI
+AAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLDADFGVMISASHNPAPDNGIKFLARGG
+EKLTDAQEDEIIRHLEGVTPRRPQGADVGRVRVFADAEDRYVLHLLQTLPHRLDGLKVVL
+DCAHGAAAGCSPEAFRAAGAEVVVIGASPDGLNINDGYGSTHLEKLQAAVREHGADLGIA
+HDGDADRCLAVDERGEVVDGDQIMGVMAVALKDRGVLRDDTLVVTVMSNLGLKLAMGREG
+VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLASRVAETGTP
+LSELAAVMDRLPQVLVNVRGVDKSRAAEDEAVQAAVAEAEARLGETGRVLLRPSGTEPVV
+RVMVEAPDEETAGREAQVLADVVQRELRLHD
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001367.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001367.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bd8f33a10c0ba777dc8dbdc6d9c8c7fd974006b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001367.fa
@@ -0,0 +1,21 @@
+>0_1640
+MPPKTRASAARKPRRKANKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS
+RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP
+MAHNGARPAKRRRV
+>1_1357
+MPPKTRASAARKPRRKANKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS
+RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP
+MAHNGARPAKRRRV
+>2_1159
+MPPKTRASAARKPRRKDKKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS
+RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP
+MAHNGARPAKRRRV
+>3_1090
+MPPKTR-SAVRKPRRKDKKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS
+RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP
+QAHNGARPAKRRRV
+>4_1569
+MPPKTRASAARKPRRKANKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS
+RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP
+MAHNGARPAKRRRV
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001372.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001372.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1ca06dadee527202681ac33d1c0f0fe4be3d605
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001372.fa
@@ -0,0 +1,26 @@
+>0_1645
+MTRMLLMGPPGSGKGTQATRIADKLGIVPISTGDIFRHNVKSMTPLGVEAKKYIDNGDFV
+PDEVTNRMVADRIAQADAEHGFLLDGYPRTKGQVEALDAMLAEAGLSLSAVVELEVPDEE
+LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETESVIQEYVERGIVARVDGTGQIDDVTE
+RLLQAVYSVRAATGSLPVIQPGAES
+>1_1362
+MTRMLLMGPPGSGKGTQAARIADKLGIVPISTGDIFRHNVKSMTPLGVEAKKYIDNGDFV
+PDEVTNRMVADRIAQADAEHGFLLDGYPRTKGQVEALDAMLAESGQSLSAVVELEVPDEE
+LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETESVIQEYVERGIVARVDGTGQIDDVTE
+RLLQAVYSVRAATGSLPVIQPGAES
+>2_1154
+MTRMLLMGPPGSGKGTQATRIADKLGIVAISTGDIFRHNVKSMTPLGVEAKKYIDNGDFV
+PDDVTNRMVADRIAQPDAEHGFLLDGYPRTKGQVEALDAMLTEAGLALSAVVELEVPDAE
+LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETEAVIQEYVERGIVARVDGTGQIDDVTE
+RLLQSVYAVRAATGSLPVIAPDTES
+>3_1085
+MTRMLLMGPPGSGKGTQATRIADKLGIVAVSTGDIFRHNVKNMTELGKEAKRYMDAGDFV
+PDEVTNRMVADRLSQSDAETGFLLDGYPRTAGQVDALDAMLKDTGQALSAVVELEVPDAE
+LVARLLKRAEIEGRADDTEEVIQHRLDLYHRETESVIESYAERGIVARVDGTGQIDDVTE
+RVLQSVYSVRAATGTLPIITPDTQA
+>4_1574
+MTRMLLMGPPGSGKGTQAARIADKLGIVPISTGDIFRHNVKSMTPLGVEAKRYIDNGDFV
+PDEVTNRMVADRIAQADAEHGFLLDGYPRTKGQVEALDAMLAEAGQSLSAVVELEVPDEE
+LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETESVIQEYVERGIVARVDGTGQIDDVTE
+RLLQAVYSVRAATGSLPVIQPGAES
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001380.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001380.fa
new file mode 100644
index 0000000000000000000000000000000000000000..924ccd015c2d4e2e6a17c077cc93a9850754169b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001380.fa
@@ -0,0 +1,26 @@
+>0_1653
+MTEVQQTEKVTPRLKTKYRDEIRGALQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII
+DGAVADLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR
+IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL
+KALGFPFKTDQ
+>1_1370
+MTEVQQTEKVTPRLKTKYRDEIRGALQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII
+DGAVADLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR
+IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL
+KALGFPFKTDQ
+>2_1146
+MTEVQQTEKVAPRLKTKYREEIRATLQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII
+DGAVTDLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR
+IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL
+KALGFPFKTDQ
+>3_1077
+MTEVQQTEKVTPRLKTKYREEIRASLQEQFEYANVMQVPGLVKVVVNMGVGEAAKDSKII
+DGAIADLTAITGQKPMVTKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR
+IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL
+KALGFPFKTDK
+>4_1582
+MTEVQQTEKVTPRLKTKYRDEIRGALQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII
+DGAVADLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR
+IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL
+KALGFPFKTDQ
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001381.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001381.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f4c8fc064497503cfe5cfdbbd0e4e01bbe1833c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001381.fa
@@ -0,0 +1,16 @@
+>0_1654
+MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGL
+QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKDGVSKTVKVRFAKASGKEL
+>1_1371
+MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGL
+QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKDGVSKTVKVRFAKASGKEL
+>2_1145
+MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGR
+QVAEAPIHISNVAVVDPETKKPTRVGYRFETVEKNGESKTVKVRFAKASGKEL
+>3_1076
+MAKIKKDDLVQVLSGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQNNNGSTEGGL
+QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKNGEQVTVKVRFAKASGKEL
+>4_1583
+MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGL
+QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKDGVSKTVKVRFAKASGKEL
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001383.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001383.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee42cb07c79987c24f820207315841e6ccf0e93b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001383.fa
@@ -0,0 +1,16 @@
+>0_1656
+MTEQTPAVSEERGYRKALRGIVVSDKMDKTIVVEVEDRKKHSLYGKVLKTSKRVKAHDED
+NTAGVGDRVRLAETRPLSASKRWRLVEIVERAK
+>1_1373
+MTEQTPAVSEERGYRKALRGIVVSDKMDKTIVVEVEDRKKHSLYGKVLKTSKRVKAHDED
+NTAGVGDRVRLAETRPLSASKRWRLVEIVERAK
+>2_1143
+MTEQTPAVSEERGYRKALRGVVVSDKMDKTIVVEVEDRKKHSLYGKVMKTSKRVKAHDED
+NTAGIGDRVRIAETRPLSASKRWRLVEIVERAK
+>3_1074
+MTEQTAAPVEERNYRKSLRGVVVSDKMDKTIVVEVEDRKKHALYGKVMKTSKRVKAHDED
+NTAGVGDRVLIVETRPLSADKHFRLVEIVERAK
+>4_1585
+MTEQTPAVSEERGYRKALRGIVVSDKMDKTIVVEVEDRKKHSLYGKVLKTSKRVKAHDED
+NTAGVGDRVRLAETRPLSASKRWRLVEIVERAK
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001391.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001391.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e7670359df9a25700a6eb1fba63b0e79f23760eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001391.fa
@@ -0,0 +1,26 @@
+>0_1664
+MAENSVKTVQVDLPAELFDVQSNVPLMHQVVVAQLAAARQGTHKTKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGVVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ
+>1_1381
+MAENSVKTVQVDLPAELFDVQSNVPLMHQVVVAQLAAARQGTHKTKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGVVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ
+>2_1135
+MAENSVKTVQVDLPAEIFDVQSNVPLMHQVVVAQLAAARQGTHKVKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGIVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ
+>3_1066
+MAENTVKTVQVELPAEIFDVQANVPLMHQVVVAQLAAARQGTHKVKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGIVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLESLNTGRKNVLLVIDRADDLTALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTKVAYEAYVAQASGAKKEDAQ
+>4_1593
+MAENSVKTVQVDLPAELFDVQSNVPLMHQVVVAQLAAARQGTHKTKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGVVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001395.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001395.fa
new file mode 100644
index 0000000000000000000000000000000000000000..78bfb7629078252e3800ea6d174db3903c738cdb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001395.fa
@@ -0,0 +1,11 @@
+>0_1668
+MSDDGAAAAARLGSMPELILLIAVLAVVVVAVRWALRTFRPEIDRARRIRRANRGGELER
+>1_1385
+MSDDGAAAAARLGSMPELLILIVVLAVAVVAVRWALRTFRPEIDRARRIRRANRGGELER
+>2_1131
+--------------MPELLITLLVLAAAVVAVVWALRTFRPEIDRARRIRRANRNGELRR
+>3_1062
+M---------------EWLIALVVIAAVVAGGLWARRAFAPEIERARRIRRAERGGRLER
+>4_1597
+MSDDGAAAAARLGSMPELILLIAVLAVVVVAVRWALRTFRPEIDRARRIRRANRGGELER
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001396.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001396.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab4937a371740971e2294782a12517e7c741a04f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001396.fa
@@ -0,0 +1,41 @@
+>0_1669
+MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEARDFATIDSAPEERQ
+RGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE
+HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQDFDGDEAPVIRTSGLKA
+LEGDAQWVKSVEDLMEAVDEFIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLK
+INSEVEIVGIRDVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVEPGS
+ITPHTNFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE
+MSVELIQPIAMEEGLGFAIREGGRTVGSGRVTKITK
+>1_1386
+MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEARDFATIDSAPEERQ
+RGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE
+HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQDFDGDEAPVIRTSGLKA
+LEGDPQWVKSVEDLMEAVDEFIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLK
+INSEVEIVGIRDVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVEPGS
+ITPHTNFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE
+MSVELIQPIAMEEGLGFAIREGGRTVGSGRVTKITK
+>2_1130
+MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEARDFATIDSAPEERQ
+RGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE
+HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQEFDGDDAPVIRTSGLKA
+LEGDAQWVKSVEDLMDAVDEYIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLA
+INSEVEIVGIRDVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVAPGS
+ITPHTNFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE
+MTVELIQPIAMEEGLGFAIREGGRTVGSGRVTKITK
+>3_1061
+MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEKRDFASIDSAPEERQ
+RGITINISHVEYQTDKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE
+HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQEFDGDEAPVIRTSGLKA
+LEGDAQWVKSVEDLMDAVDEYIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLA
+INSEVEIVGIRPVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVQPGS
+ITPHTDFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE
+MSVELIQPIAMEEGLGFAIREGGRTVGSGRVTKINK
+>4_1598
+MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEARDFATIDSAPEERQ
+RGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE
+HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQDFDGDEAPVIRTSGLKA
+LEGDAQWVKSVEDLMEAVDEFIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLK
+INSEVEIVGIRDVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVEPGS
+ITPHTNFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE
+MSVELIQPIAMEEGLGFAIREGGRTVGSGRVTKITK
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001410.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001410.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f8f2294a943b1ab16877d5010af10f6745ea91a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001410.fa
@@ -0,0 +1,46 @@
+>0_1683
+MP---------------------------------TPSAPAPA---PRPPLMRHGADRPV
+SGVAAGLARHLGMPAGRVRAALALLSLLGGAGLALYVWLWLLVPEEGPDGAPAADAPTLR
+GRAPEVLERVREGGWPVLLAAVVLGVGVLTVADGLGLAVDWALVGPVAVLVIGLGLAWMQ
+LDLAGGPRAGRSGRLVRLVLGTALVLLAVLAIVLGAVSSGELWRALLAAVAMLAGAALVA
+MPYVLAWLRRRDAERTAFAVQAQRAEIAAHLHDSVLQSLALIQRRAQDADAVARVARAQE
+RELRQFLALDSRGGPHSLAEALEQHAAAVEDAHGARVEVVAVGRAAGAWLEPLAAAAREA
+MQNAARHAGDAQVFAEAGEDDRGRTVAEVFVRDRGPGFDLPTVPADRLGVRESILGRMGR
+AGGTARIRSGPGGTEVHLTLAEP--EGARARTGQEHP
+>1_1400
+MP---------------------------------TPSAPAQA---PRPPLMRHGADRPV
+SGVAAGLARHLGVPVGRVRAALALLSLMGGAGLALYVWLWLLMPEEGPDGAPAADAPTLR
+GRAPEVLERVREGGWPVLLAAVVLGVGVLTVADGLGLAVDWALVGPVAVLVIGLGLAWMQ
+LDLAGGPRAGRSGRLVRLVLGTALVLLAVLAIVLGAVSSGELWRALLAAVAMLAGAALVA
+MPYVLAWLRRRDAERTAFAVQVQRAEIAAHLHDSVLQSLALIQRRAHDADAVARVARAQE
+RELRQFLALDSRGGPRSLAEALEEHAAAVEDAHGSRVEVVAVGRAAGAWLEPLAAAAREA
+MQNAARHAGDAQVFAEAGEDDHGRTVAEVFVRDRGPGFDLHTVPADRLGVRESILGRMER
+AGGAARIRSGPGGTEVHLTLTEP--EGARARAGQEHP
+>2_1116
+MPASAVPPSAPSGRAGPRRAAADDARTRPIGADPRTSEARASG---TRAPLMRHRADRPV
+SGVAAGAARHLGLSPRTARAGFAVLALAGGAGLALYVWLWLLMPEEGADGAPTGEAPSLR
+GRAPEVLERVREGGWPVLLAAVVLGVGVITIADGLGLAVDWALVGPVAVLVIGLGLAWMQ
+LDLAGGPPAGRVGRVVRLALGTALVLLAVLAIVLGGVTSGDLWLGLLVAVALIAGVAMVA
+MPYALSWLRRRDAERTAFAVQAQRAEIAAHLHDSVLQSLALIQRRAHDPEAVARAARAQE
+RELRRFLALDDRGGHDSLAATLREHAAAVEDAHGRRVEVVAVGEASGAWLEPLTAAAREA
+MLNAARHAGDAQVFAEVAEDDDGRTVAEVFVRDRGPGFDPGAVPADRLGVRESVVGRMER
+AGGAARIRSGPGGTEVHLTLTRP--DRVPPHAAQERP
+>3_1046
+MP---------------------------------APAIPPPADLSARPALLRHAADRPV
+SGVAGGVARHLGLDPRLARAGFAVLALAGGAGIALYAWLWLLMPEEGPDGAPAGPAPTLR
+GRAPEVLERLREGGWPILLAVVVLGVGVLTVADGLGVPVDWALVGPVAVLVIGLGLAWMQ
+LGAADGPEGGRWARRARLGLGTALVLLGVLAIVVGAVTAGDLWLGLLVAVALLAGGALVA
+MPFVLARRRRRDEERTGAAVRAQRDEIAAHLHDSVLQSLALIQRRADDPETVARVARAQE
+RELRQFLALDSARAHGTLAEAVEDHAAAVEDAFGRRVEVVSVGEASGPWLEPLASAAREA
+MVNAARHAGDVQVFVEVSEDDGGRTLAEVFIRDRGTGFDLADVPADRLGVRESILGRMRR
+AGGTARIRSGPSGTEVQLSLADPGAPGVGLREGRGRA
+>4_1612
+MP---------------------------------TPSAPAPA---PRPPLMRHGADRPV
+SGVAAGLARHLGMPAGRVRAALALLSLLGGAGLALYVWLWLLMPEERPDGAPAADAPTLR
+GRAPEVLERVREGGWPVLLAAVVLGVGVLTVADGLGLAVDWALVGPVAVLVIGLGLAWMQ
+LDLAGGSRAGRSGRLVRLVLGTALVLLAVLAIVLGAVSSGELWRALLAAVAMLAGAALVA
+MPYVLAWLRRRDAERTAFAVQAQRAEIAAHLHDSVLQSLALIQRRAQDADAVARVARAQE
+RELRQFLALDSRGGPHSLAEALEQHAAAVEDAHGARVEVVAVGRAAGAWLEPLAAAAREA
+MQNAVRHAGDAQVFAEAGEDERGRTVAEVFVRDRGPGFDLHTVPADRLGVRESIVGRMER
+AGGTARIRSGPGGTEVHLTLTEP--EGARARTGQEHP
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001415.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001415.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f8b93086a862c7479e017a47fe1e8c6130153ffe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001415.fa
@@ -0,0 +1,26 @@
+>0_1688
+MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSAGTEIFYQRVDFTEHGLPFVEYRAESW
+LCEADGTLLRPLTVESGFWQVDRARRDGDVGPGMRPADIVPAFRSAEDVERLRAGDEGFG
+LTATITHPGSLSELYYGRIKGPQLQLATDAVLRGSAAGPYHRATRMAGLVNGQLFWRWDV
+ADAAGAELEAHASAILDRMPSAAEGRLAPGAERPRGARGEQ----S
+>1_1405
+MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSAGTEIFYQRVDFTEHGLPFVEYRAESW
+LCEADGTLLRPLTVESGFWQVDRARRDGDVGPGMRPADIVPAFRSAEDVERLRAGDEGFG
+LTATITHPGSLSELYYGRIKGPQLQLATDAVLRGSAAGPYHRATRMAGLVNGQLFWRWDV
+ADAAGAELEAHASAILDRMPSAAEGRLAPGAERPRGARGEQ----S
+>2_1110
+MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSDGTEIFYQRVDFTEHGLPFVEYRAESW
+LCEADGTLLRPLTVESGFWQVDRERRDGDVGPGMRPADIVPAFRSAEDVESLRAGDEGFG
+ITATITHPGSLAELYYGRIKGPQLQLVTDAVLRGSAAGDYHRATRMAGLVNGQLFWRWDS
+SGSEGAELEAHASAILDRMPSESEGRLAPGAPRPRGAGGAEPGERP
+>3_1040
+MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSEGTDIFYQRVDFVEHGLPFVEYRAESW
+LCEADGTLLRPLTVESGFWQVDRARQDGDVGPGMVPADIVPAYRSAEDVEALRSEDGAFR
+ITATITHPGSLAELYYGRIKGPQVQIVMDSLLRGAAAGEYARATRMAGLVNGQLFWRWDS
+SPAVEGPMEVHASAILDRMPDPSEGRLAPGAPRPRGERGRAPEQGA
+>4_1617
+MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSAGTEIFYQRVDFTEHGLPFVEYRAESW
+LCEADGTLLRPLTVESGFWQVDRARRDGDVGPGMRPADIVPAFRSAEDVERLRAGDEGFG
+LTATITHPGSLSELYYGRIKGPQLQLATDAVLRGSAAGPYHRATRMAGLVNGQLFWRWDV
+ADAAGAELEAHASAILDRMPSAAEGRLAPGAERPRGARGEQ----S
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001417.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001417.fa
new file mode 100644
index 0000000000000000000000000000000000000000..64b7badc15fe221a42c0edaa73353fe9593516d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001417.fa
@@ -0,0 +1,31 @@
+>0_1690
+MAREVRPAVARPGPSRCAPGRMGQVMRLSMALSAAVAALVLGGAALLGPVPAALAAAVVI
+LVIAWGWPRQMGAPARLSLSVTLAVAGGAAVLLMLLWPPLEDGHSGAWTLFEPLAVVVAW
+STMASFVVQLVRGTGRPLRLESTVATMGGAFMAVVTACWVAVSRWTDTPAVAGLVITLAV
+TVAAVSLVGLTPWMQGRPGVLALVVIPLGTVLAWPVSALAGVGARDRPAVTAAALAVAVL
+VSLTAATAPSSRPRPEDRPVGTTLRPRRAGYALALAPVGAAGVVAHVMVGFLA
+>1_1407
+MAREVRPAVARPGPSRCAPGRMGQVMRLSMALSAAVAALVLGGAALLGPVPAALAAAVVI
+LVIAWGWPRQMGAPARLSLSVTLAVAGGAAVLLMLLWPPLEDGHSGAWTLFEPLAVVVAW
+STMASFVVQLVRGTGRPLRLESTVATMGGAFMAVVTACWVAVSRWTDTPAVAGLVITLAV
+TVAAVSLVGLTPWMQGRPGVLALVVIPLGTVLAWPVSALAGVGARDRPAVTAAALAVAVL
+VSLTAATAPSSRPRPEDRPVGTTLRPRRAGYALALAPVGAAGVVAHVMVGFLA
+>2_1108
+------------------------MMRLSMALSAAVAALVLGGATLLGPVPAAVAAMAVI
+LVIAWGWPRQMGAPARLSLSVTLAAVGLVAVLLMLLWPPIEDGRSGAWTLFEPLAVALAW
+STMASFVVQLVRGTGRPLRLESTVATMGGGLIAVMTACWVAVSRWTDAPAVAGLVLTLAI
+SVAAFSLIGLIPGVQGRPGVLALVVVPLGALLAWPVSALLGVGPQDRAAVVAAVVAVATL
+VSLTAATAPSARPRPEDRPVGTTLRPRRAGYALALAPVGAAGVVAHVMVGFLA
+>3_1038
+------------------------MMRLSMALSAALAALVLGGAALLGPVPAAVAACLVI
+AVIAFGWPRQMGAPARLSLTLTMLVAGVLGVLVMVLWPRGDAGPRGAWALFEPLAVVLAF
+GTMASFIVQLVRGTGRPLRLESTVTTMGGVLVCLLAASWVPLAHHREAPGATGLVVTLAA
+TLIVTSLIGLTPFMQGRPRVLALVMVPASGVVAALVSLLLGAPAHTAWVYAAAALGTAGL
+VSLTAAAAPSSRPLPEDRVVGTTLSPRRAGYALAMAPVGAAGVVGHVMLGFLA
+>4_1619
+------------------------MMRLSMALSAAVAALVLGGAALLGPVPAALAAAVVI
+LVIAWGWPRQMGAPARLSLSVTLAVAGGIAVLLMLLWPPLEDGHSGAWTLFEPLAVVVAW
+STMASFVVQLVRGTGRPLRLESTVATMGGAFMAVVTACWVAVSRWSDTPAVAGLVITLAV
+TVAAVSLVGLTPWMQGRPGVLALVVIPLGTVLAWPVSALAGVGARDRPAVTAAALAVAVL
+VSLTAATAPSSRPRPEDRPVGTTLRPRRAGYALALAPVGAAGVVAHVMVGFLA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001429.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001429.fa
new file mode 100644
index 0000000000000000000000000000000000000000..27b384c76ac07a4bd675a6750f3415e2837546bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001429.fa
@@ -0,0 +1,55 @@
+>0_1702
+M-------SDILDPQTTAEV---APELAEAEQEAT-GTVPQV------------DAAPEAPAEPAAPEAPAEPAGPTFLD
+LGLDARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETTDVTGRADTPQVLVLAPTR
+ELALQVADAFDSYAKHLDDVSVLAVYGGSPYGPQLAGLRRGAQVVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRM
+GFAEEVDRILASTPDTKQTALFSATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKFEALSRILETEE
+HDGVIAFVRTRAGTEELAQKLTRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAARGLDVERISHVVNYDIPQ
+DAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQVEEMAVPSVADVNAARKRRFADGITRTLERASEEELA
+VFGEIVAAYVDEHEAEPARVAAALGMMAQGGRPLLAREQEIPFGGARGRKDRDGGREGGRDGGRERGTSDGRGSRGPARE
+PAAGNVTYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTSAQLEAAANAEINGRRLGLRKDT
+GRPTRAERDGE--------DRGER------RGGFRKDRGERG------ERGGFRGDRDG-GQRGGYRKDRDDRG------
+-----------SREDRGGFRKDRDDRSFRGDRRGRPGGRKPRWGAQERSDRGARR
+>1_1419
+M-------SDILDPQTTAEV---APELAEAEQEAT-GTVPQV------------DAAPEAPAEPAAPEAPAEPAGPTFLD
+LGLDARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETTDVTGRADTPQVLVLAPTR
+ELALQVADAFDSYAKHLDDVSVLAVYGGSPYGPQLAGLRRGAQVVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRM
+GFAEEVDRILASTPDTKQTALFSATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKFEALSRILETEE
+HDGVIAFVRTRAGTEELAQKLTRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAARGLDVERISHVVNYDIPQ
+DAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQVEEMAVPSVADVNAARKRRFADGITRTLERASEEELA
+VFGEIVAAYVDEHEAEPARVAAALGMMAQGGRPLLAREQEIPFGGARGRKDRDGGREGGRDGGRERGTSDGRGSRGPARE
+PAAGNVTYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTSAQLEAAANAEINGRRLGLRKDT
+GRPTRAERDGE--------DRGER------RGGFRKDRGERG------ERGGFRGDRDG-GQRGGYRKDRDDRG------
+-----------SREDRGGFRKDRDDRSFRGDRRGRPGGRKPRWGAQERSDRGARR
+>2_1096
+M-------SDALDPQTTPEAQVDAAELAEARQEAAEAAAPKAETPETAAAATETDSAPEAET-AEEPEAPAEPAGPTFLD
+LGLDARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALARLAETADVNGRADTPQVLVLAPTR
+ELALQVADAFDSYAKHLEDVSVLAVYGGSPYGPQLAGLRRGAQVVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRM
+GFAEEVDRILASTPDTKQTALFSATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKLEAFTRILETED
+HDGVIAFVRTRAGTEELAQKLNRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAARGLDVERISLVVNYDIPQ
+DAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQVEEMAVPAVKDVNAARKRRFADGITRTLERASEEELA
+VFGEIVAAYVEEHDAEPSRVAAALGMMAQGGRPLLAKEQEIP-TGPRGRKERD----GGRDGGREHGTADGRGSRGPARE
+PAAGNATYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTPAQLEAAANIEISGRRLGLRKDT
+GRPTRAERDGDERRGGFRKDRGERGGHGGHRGGFRKDRDERGFRGDREERGGFRGDRDDRGDRGGFRKDREDRGGFRKDR
+EDRGDRGGFRKDREDRGGFRKDRDERG--GFRGGKAGGRKPRWGAQERSDRGPRR
+>3_1022
+MTPHETIPADDQAPVDLTEF---DPELAETTAE-----------------------APAAEQDADDAEADAEPAGPTFLS
+LGLDARVLAAVEDLGYQRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETQDVNGRSQAPQILALAPTR
+ELALQVAEAFESYAKHLDDVSVLAVYGGAPYGPQLAGLRRGAQVVVGTPGRVIDHLERGNLDLSQLQTLVLDEADEMLRM
+GFAEEVDRILAETPDSKQTALFSATMPPAIRRISAQYLNDPEEVAVARQSTTGTNIRQRYLQIAHQWKFEAMTRILETED
+HEGVIAFVRTRAGTDELAQRLNQAGFSAVAISGDVAQKQREKTVDDLKAGRVDILVATDVAARGLDVERISLVVNYDIPQ
+DAESYVHRIGRTGRAGRSGDAVLFMTPRERFLLKQIERTTRQEVEEMQVPTVAQVNEARTRGVVAGIGRTLETASEADLD
+TYARMVAEYVEANDVDPARAAAALALMAQGGRPLLTEADEVP-AGGRVRRDRDRDDRRERGDRSERGDRDGRGSRGPRRE
+PAAGNATYWIGVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHALVELPADLTAAQLDAAANTEINGRRLNLRKDT
+GRPTRAERDGD---G----ERGHRGPRED-RGGFRRD---RG------DRGGFRRDRGERPERGGFRKDRDDRG------
+-----------PREDRGGFRHDRDDRG------GRPGARKPRWGSDDRRDRGPRR
+>4_1631
+M-------SDILDPQTTAEA---APELAEAEQEAT-GTVPQV------------DA-----AEPAAPEAPAGPAGPTFLD
+LGLDARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETTDVTGRADTPQVLALAPTR
+ELALQVADAFDSYAKHLDDVSVLAVYGGSPYGPQLAGLRRGAQVVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRM
+GFAEEVDRILASTPDTKQTALFSATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKFEALSRILETEE
+HDGVIAFVRTRAGTEELAQKLTRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAARGLDVERISHVVNYDIPQ
+DAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQVEEMAVPSVADVNAARKRRFADGITRTLERASEEELA
+VFGEIVAAYVDEHEAEPARVAAALGMMAQGGRPLLAREQEIPFGGARGRKDRDGGREGGRDGGRERGTSDGRGSRGPARE
+PAAGNATYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTSAQLEAAANAEINGRRLGLRKDT
+GRPTRAERDGE--------D----------RGGFRKDRGERG------ERGGFRGDRDG-GQRGGYRKDRDDRG------
+-----------SREDRGGFRKDRDDRSFRGDRRGRPGGRKPRWGAQERSDRGARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001433.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001433.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00b9e722e60f6d2d03aee3ce0fb97dbb7df8cdb2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001433.fa
@@ -0,0 +1,40 @@
+>0_1706
+M---------------QYAENVLELIGHTPLVKLHSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEEAEREGLLGPGG
+TVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLSAYGAELVVTPTAVDPTSEESYYGVADRLVREIPGAYQP
+NQFFNPAAPASHYETTGPEIWEDTAGRVTHVVMGAGTGGTITGTGRYLKEVSADRPSGAVRVIGADPSGSVYSGGAGRPY
+FVEGVGEDMWVDNYDPAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARELGPEDVMVIVLPDSGRGY
+LAKIFNDPWMDERGFDYDVRETVLPAWARGRTRSAVPQTDDDGATGAAGGAGTPVEALEHADAEPATRAG----APAEAD
+RWSATAGELLTEKADLFPGSVPTLVTAAPTTSVADAVATMNRYGVDALPVILEPRHDLRIGEVRGTVSSAALADALAEGR
+ATAQTPVADVMGPVLPCLGARTPLRAVARRLAQDPVLLVLEAGRVQGVVTLHDVLAHVTA
+>1_1423
+M---------------QYAENVLELIGHTPLVKLHSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEEAEREGLLGPGG
+TVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLSAYGAELVVTPTAVDPTSEESYYGVADRLVREIPGAYQP
+NQFFNPAAPASHYETTGPEIWEDTAGRVTHVVMGAGTGGTITGTGRYLKEVSADRPSGPVRVIGADPSGSVYSGGAGRPY
+FVEGVGEDMWVDNYDPAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARELGPEDVMVIVLPDSGRGY
+LAKIFNDPWMDERGFDYDVRETVLPAWARGRTRSAVPQMDDDGATGAAGGAGTPVEVLEHADAEPATRAG----APAEAD
+RWSATAGELLTEKADLFPGSVPTLVTAAPTTSVADAVATMNRYGVDALPVILEPRHDLRIGEVRGTVSSAALADALAEGR
+ATAQTPVADVMGPVLPCLGARTPLRAVARRLAQDPVLLVLEAGRVQGVVTLHDVLAHVTA
+>2_1092
+M---------------QYAENVLELIGHTPLVKLNSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEDAEKAGKLAPGG
+TVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLTAYGAEIVVTPTSVAPESEESYYGVANRLERDIPGAYQP
+NQFFNPAAPASHYETTGPEIWEDTAHRVTHVVIGAGTGGTITGTGRYLKEVSADRESGPVRVIGADPSGSVYSGGTGRPY
+FVEGVGEDMWVDNYDPAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARDLGPKDVMVIVLPDSGRGY
+LAKIFNDPWMDERGFDYDVQDTVLPEWARGRTRSAAPEADDDGAQGAAGGAGTPVEALEQADAAAGADAGQVADAPAEAD
+RWAATAGELLAEKADLFPGSVPTLVTASPTTSVADAVATMNRYGVDALPVVAEPRHDLRIGEVRGTVSAAALGEALAAGR
+VHPGTPVAEAMGPVLPCIGARTPLRAVARRLAQDPTLLVLSAGRVAGVVTLHDVLAHVTA
+>3_1018
+MGAVNEINPAPAHGQPRWAENVLDLIGRTPLVKLNRVTEGVEATVLVKVEYLNPGGSVKDRIALRMLEEAERDGKLAPGG
+TVVEPTSGNTGVGLALVAQQKGYRAVFVTPDKVGQEKRDVLTAYGAEIVVTPTSVEPSSDESYYGVANRLEKEIPGAFQP
+NQFFNPAAPASHYETTGPEIWEDTAGTVTHVVIGAGTGGTITGTGRYLKEVSADRASSPVRVIGADPEGSVYSGGTGRPY
+FVEGVGEDMWPGNYDPSVPDEVIAVSDDAAFEMTRRLAAEEGLLVGGSSGMAVVAGLQAARELGPDDVMVIVLPDSGRGY
+LAKIFNDDWMDERGFHYAQEETVLPAWAQGRTRSAVATAPSDSREGARGGVGTPVEAPGEGSPQDGAATA----TPAPGS
+RWDASLADVLADKEDLFPGSVPTLVTASPDTTVADAVATLARYGVDALPVIAEPRHDLRINEVRGTVSAPALAAALAAGR
+VQPGSAVSDVMEPALPSVGAAMTLRAAARRLQEDPILLVMDAGIVQGVVTLHDVLVYATA
+>4_1635
+M---------------QYAENVLELIGRTPLVKLHSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEEAEREGLLGPGG
+TVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLSAYGAELVVTPTAVDPTSEESYYGVADRLVREIPGAYQP
+NQFFNPAAPASHYETTGPEIWEDTAGRVTHVVMGAGTGGTITGTGRYLKEVSADRPSGPVRVIGADPSGSVYSGGAGRPY
+FVEGVGEDMWVDNYDPAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARELGPEDVMVIVLPDSGRGY
+LAKIFNDPWMDERGFDYDVRETVLPAWARGRTRSAVPQTDDDGATGAAGGAGTPVEVLEHADAELATRAG----APAETD
+RWSATAGELLTEKADLFPGSVPTLVTAAPTTSVADAVATMNRYGVDALPVILEPRHDLRIGEVRGTVSTAALADALAEGR
+ATAQTPVADVMGPVLPCLGARTPLRAVARRLAQDPVLLVLEAGRVQGVVTLHDVLAHVTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001435.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001435.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a69fb8f3d40c0c3507a0388fdca9eba68aa94374
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001435.fa
@@ -0,0 +1,21 @@
+>0_1708
+MTTAFEPRPHTAAAPREPD---PHGPGTPGSLRPGERGSVLIVTRHPDPDEAMRHAMAWI
+TAFEEDCGLVLDTDETALYAVGRAGDLGEALRRGPLVHEDGSPADTSAFVDAVLADGTWR
+LRDADPRA--------WSTTYRATILGAAPEAVCTIWDVFPLPAA-
+>1_1425
+MTTAFEPRPHAAAAPREPD---PHGPGTAGSLRPGARGSVLIVTRHPDPDEAMRHAMAWI
+TAFEEDCGLVLDTDETALYAVGRAGDLGEALRRGPLVHEDGSPADTSAFVDAVLTDGTWR
+LRDADPRA--------WSTTYRATILGAAPEAVCTIWDVFPLPAA-
+>2_1090
+MTTAFEPRPHTGLAPREPE---PHGPGTPGPLRPGVRGSVLIVSEHADPDTAMRHAMAWI
+TAFEDDCGLVLDADGTELYAVGLAGELGASLRRSPGVAEDGTPTDTSEFVDAILTGGVWR
+LREPDARA--------WSTAYRAAILGAAPHAVCTVWDVLPLPAA-
+>3_1016
+MTAQH-------AEPTRTDRAEPHGPGTPATLRPGERGSVLVLSPAGPPEAAMGHAVAWI
+TAFEDDCGLVLDRDATSLYAVSPA----DGLRREGDVPSDGGIAE---HLDFVLAGDVWH
+HRGTCPPAPAGSDVDGWALLVHRLQREAPRGALGTVWDVFPLPAAG
+>4_1637
+MTTAFEPRPHTAAAPREPD---PHGPGTPGSLRPGERGSVLIVTRHPDPDEAMRHAMAWI
+TAFEEDCGLVLDTDETALYAVGRAGDLGEALRRGPLVHEDGSPADTSAFVDAVLTDGTWR
+LRDADPRE--------WSTTYRAAILGAAPEAVCTIWDVFPLPAA-
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001438.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001438.fa
new file mode 100644
index 0000000000000000000000000000000000000000..75d943bba4caea282174a56b2381fc1e1ed41dc4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001438.fa
@@ -0,0 +1,46 @@
+>0_1712
+MARLLVDITPLRVSPAYRRLWLGNTLAYVGTQLTLVAVSLEVFALTGSSFAVGLLGLAAL
+VPLVVAGLYGGAIADRHDRRRVALTSSAVMWLTTVGIAAQAWAGFESVPVLYALVALHSG
+ASGINQPTRGAIIPALVGLPLVPAANALNMMTFSVALMVGPVLGGVLVAAVGYAWTYSID
+VVTFLAALYAVWRLPSLPPQQAEAAAASGTRGGLASVVEGLRFLGSRPNLRMTFLADIVA
+MTTAFPRALLPAIGAVVLGGGEAAVGVLLAAMAAGAFLAGLFSAPFTRLHAQGWGVYVSI
+LVWGGAVAAFGGVVWWAQSLPDGDPRLTLAFALAALCMAVGGAADSLSGVFRGSILQSAT
+PDHLRGRLQGVFVVVVAGGPRLGELITGGASVVLGEGPTLLAGGVLCMLGVSALMRWQPG
+FLRYDARNPTP
+>1_1429
+MARLLVDITPLRVSPAYRRLWLGNTLAYVGTQLTLVAVSLEVFALTGSSFAVGLLGLAAL
+VPLVVAGLYGGAIADRHDRRRVALTSSAVMWLTTVGIAAQAWAGLESVPVLYALVALHSG
+ASGINQPTRGAIIPALVGLPLVPAANALNMMTFSVALMVGPVLGGVLVAAVGYAWTYSID
+VVTFLAALYAVWRLPSLPPQRAETATASGTRWGLASVVEGLRFLGSRPNLRMTFLADIVA
+MTTAFPRALLPAIGAVVLGGGEAAVGVLLAAMAAGAFLAGLFSAPFTRLHAQGWGVYVSI
+LVWGAAVAAFGGVVWWAQSLPDGDPRLTLAFALAALCMAVGGAADSLSGVFRGSILQSAT
+PDHLRGRLQGVFVVVVAGGPRLGELLTGGASVGLGEGPTLLAGGVLCMLGVTALMRWQPG
+FLRYDARNPTP
+>2_1086
+MARLLVDLTPLKVSPAYRRLWVGNTLSFVGTQLTLVAVSLEVFALTGSSFAVGLLGLAAL
+VPLVVAGLYGGAVADRHDRRTVALASSAVMWLTTVGIAAHAWAGIESVPLLYALVALHSG
+ASGINQPTRGAIIPALVGMKLVPAANALNMMTFSVAMMAGPVLGGVLVASVGYAWTYSID
+VVTFLAALYAVWRLPSLPPQRAEGEAAPTGRVGVRSVVEGLRFLGSRPNLRMTFLADIVA
+MATAFPRALLPAVGGVVLGGGEAAVGVLLAAMAAGAFLAGLFSGPFTRLHAQGWGVYVSI
+LVWGASVAAFGGVVWWAQGLPDGDPRLTGAFVAAALCLAVGGAADSISGVFRTTILQSAT
+PDHLRGRLQGVFVVVVAGGPRVGELLTGGASVAVGEGLTLLLGGLACVLGVSLLMRRQPE
+FLKYDARSPTP
+>3_1013
+MPRLLVDLAPLEASPAYRRLWLGNALAFVGTQLTLVAVSLEVFALTGSSFAVGMLGLAAL
+IPLVVAGLYGGAVADRHDRRTVALASGAVMWAATALIAAHAWAGVESVGVLYGLVALHSA
+ASGINQPTRGAIIPALVGPALLPAANALNMLTFSTAMMAGPLLGGVLVASVGYAWTYTVD
+VVTFLAALWAVWRLPSLPPDRSAAPDDAG-RGGLSSVLDGFRFLGTRRNVRMTFVADIVA
+MATAFPRALLPAVGGTILGGGEAAVGVLLASMAAGTFLAGLFSGTFTRVHRQGRGVAVAI
+AAWGLSVAAFGAVVLWAAPLPDGDPRLGPALAACAACLVVAGAADSVSAVFRTTILQSAT
+PDHLRGRLQGVFVVVVAGGPRVGEMIQGTASAALGEGATLVLGGVLCVAGIALLMRVQPG
+FLHYDARRPTP
+>4_1641
+MARLLVDITPLRVSPAYRRLWLGNTLAYVGTQLTLVAVSLEVFALTGSSFAVGLLGLAAL
+VPLVVAGLYGGAIADRHDRRRVALTSSAVMWLTTVGIAAQAWAGLESVPVLYALVALHSG
+ASGINQPTRGAIIPALVGLPLVPAANALNMMTFSVALMVGPVLGGVLVAAVGYAWTYSID
+VVTFLAALYAVWRLPSLPPQRGEAAAASGTRGGLASVVEGLRFLGSRPNLRMTFLADIVA
+MTTAFPRALLPAIGAVVLGGGEAAVGVLLAAMAAGAFLAGLFSAPFTRLHAQGWGVYVSI
+LVWGAAVAAFGGVVWWAQSLPDGDPRLTLAFALAALCMAVGGAADSLSGVFRGSILQSAT
+PDHLRGRLQGVFVVVVAGGPRLGELLTGGASVGLGEGPTLLAGGVLCMLGVSALMRWQPG
+FLRYDARNPTP
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001439.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001439.fa
new file mode 100644
index 0000000000000000000000000000000000000000..15e592d29df33ee892f678f606092f89f64ae841
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001439.fa
@@ -0,0 +1,36 @@
+>0_1714
+MVRV----SPSSP-AVRPGVTPDGAAPDTGALPTVSPAPADDPRGLALGFTAYFVWGLLP
+LYMAVLAPAGALEIVVVRIGFALIFCLLLLTVMRRLRELGTALATPGRWGTTGLAAGIIA
+VNWLLYAVSVTTGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWVAVGIAVAAVVVMS
+AAMGQVPWIALGLATSFGLYGFVKKRFPSPVHAVTAMTAETVVLIPVFVVGSVLLAQAGL
+LTTVTEGPGHFWLMAGLGVLTAVPLILFSAAARSLTLTTLGMLQYTAPILQFLVAVTVLG
+EQMPAARWAGFGLIWLSLAVFTLDQLNASRLQRRAVRAGQGAHA
+>1_1431
+MVRV----SPSSP-AVRPGVTPDGAAPDTGALPTVSPAPADDPRGLALGFTAYFVWGLLP
+LYMAVLAPAGALEIVVVRIGFALIFCLLLLTVMRRLRELGTALATPGRWGTTGLAAGIIA
+VNWLLYAVSVTTGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWVAVGIAVAAVVVMS
+AAMGQVPWIALGLATSFGLYGFVKKRFPSPVHAVTAMTAETVVLIPVFVVGSVLLAQAGL
+LTTVTEGPGHFWLMAGLGVLTAVPLILFSAAARSLTLTTLGMLQYTAPILQFLVAVTVLG
+EQMPAARWAGFGLIWLSLAVFTLDQLNASRLQRRAVRAGQGAHA
+>2_1084
+MARV----SPSPA-SRRPGVPPDAAAPDTGALPAVSPAPANDPRGLALGFTAYFLWGLLP
+LYMARLAPAGAVEIVVVRVGFALVFCLVLLALMRRLRELRTSLATPARWGATALAAGFIG
+TNWLLYAVSVTTGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWAAVGIAVAAVVVMS
+VAMGQVPWIALGLAFSFGLYGFVKKRFPTPVHAVTTMTAETVVLLPAFAVGMVWLGQAGL
+LTTFTEGPAHFWLMAGLGVLTAVPLILFSAAAKALTLTTLGMLQYTAPILQFIVAVTVLG
+EQMPVARWAGFGLIWVSLLVFTLDQVRVSRLHRRAARAGHGARA
+>3_1011
+MAQVSHSPSPSGPDAPRDGVPVEAAAPDTGALPTITPAPANDPRGLALGFAAYVIWGLLP
+LYMAATAPAGAVEIVVVRVVFALIFCLLLLAVMRRLPELRTALATRARWGSITLAAAFIA
+VNWLLYAHSVTSGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWIAVGIAVVAVVVMS
+VAMGQVPWIALGLAFTFGMYGFVKKRFPVPVHAVTTMTAETVVLLPAFAVGMVFLVQAGL
+LTTVSEGPGHFWMMAGLGVLTAVPLILFSAATQSLTLTTLGMLQYIAPIMQFLVAVAVLG
+EHMPAARWAGFALIWLSLVVFTLDQANASRVQRRAARAAGRART
+>4_1643
+MVRV----SPSSP-AVRPGVTPDGAAPDTGALPTVSPAPADDPRGLALGFTAYFVWGLLP
+LYMAMLAPAGALEIVVVRIGFALIFCLLLLTVMRRLRELGTALATPGRWGTTGLAAGIIA
+VNWLLYAVSVTTGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWVAVGIAVAAVVVMS
+AAMGQVPWIALGLATSFGLYGFVKKRFPSPVHAVTAMTAETVVLIPVFVVGSVLLAQAGL
+LTTVTEGPGHFWLMAGLGVFTAVPLILFSAAARSLTLTTLGMLQYTAPILQFLVAVTVLG
+EQMPAARWAGFGLIWLSLAVFTVDQLNASRLQRRPVRVRRGAHA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001446.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001446.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1ec06059d0363952dfac1294b8f30c5505e82ebc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001446.fa
@@ -0,0 +1,40 @@
+>0_1724
+MSNTFLLPDLGEGLTEADIVRWLVAEGDTVAVDQPMVEVETAKALVEVPSPYAGTVLTLHGAEGETMDVGSPLITIGAAG
+ES-GEGSAPAAGTEALAVPPATGAAAAEAARPGALSYREEEMAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHR
+ATSRSRPSKRGRGAARPT-----PAPTAGA------GAPRVTSPIVRKLAREKGVDVAALTGTGPDGLITRADVLAAAEG
+-SAPQAAPAQAPLVAAVPAAEA--AAQPGAVDGRTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVTALLEL
+RASLKAKDSENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDGVHLGLAVQTDRGLMVPSVEHAEKLSADE
+LTAAVNDTVSRARAGRAAPAELTRGTFTLNNYGPLGTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTF
+DHRVTDGATASAFLTFVADCLHDPTAALARI
+>1_1441
+MSNTFLLPDLGEGLTEADIVRWLVAEGDTVAVDQPMVEVETAKALVEVPSPYAGTVLTLHGAEGETMDVGSPLITIGAAG
+ES-GEGSAPAAGTEALAVPPATGAAAAEAARPGALSYREEEMAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHR
+ATSRSRPSKRGRGAARPT-----PAPTAGA------GAPRVTSPIVRKLAREKGVDVAALTGTGPDGLITRADVLAAAEG
+-SAPQAAPAQAPLVAAVPAAEA--AAQPGAVDGRTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVTALLEL
+RAALKAKDPENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGQDEIVEVDGVHLGLAVQTDRGLMVPSVEHAEKLSADE
+LTAAINDTVSRARAGRAAPAELTRGTFTLNNYGPLGTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTF
+DHRVTDGATASAFLTFVADCLHDPTAALARI
+>2_1075
+MSNTFLLPDLGEGLTEADIVRWLVAEGDEVVVDQPIVEVETAKALVEVPSPYAGTVLTLHGAEGQTMEVGRPLITVGAAG
+ES-GEGSAPVAGTEAQAVPPATGEDAAEADRPGALSYREEEMAGVQPKPDKARGGDGDVAGSDEEASGAVLIGYGTSGHS
+ATSRTRPSKRGRRGAGTTTAGGSGAASGQGEQAGQARAPRVTSPIVRKLAREQGVDVAALTGTGPDGLITRADVLSAAQG
+GDAPQAAAAPAAQPAATAGAAS--TVGAGSADARTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVTALLEL
+RAALKAKDAENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDGVHLGLAVQTDRGLMVPSVEHAERLSADE
+LTAAINETVTRAREGKAAPAELTRGTFTLNNYGPLGTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTF
+DHRVTDGATASAFLTFVADCLNDPQSALARI
+>3_999
+MSNTFLLPDLGEGLTEADIVRWLVAEGDEVAVDQPMVEVETAKALVEVPSPFAGTVLTLHGAEGETMEVGAPLITVGAVG
+ESAGDAPPPSSAADAGTAP------AADGAVPGALSYREEERAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHT
+ATSRSRPSKRARGGAGTTQAAAGAAPAASG------RAPRVTSPIVRKLARERGVDVATLTGTGPDGLITRADVLGAAGG
+ASAPQDAQAPAPVQTAPSAAAQAPAVAAGATDARTGLAVVARTPISGVRKVIADQLSRSRREVPDVTAWLDVDVTALLEL
+RAQLKAKDPENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDGVHLGLAVQTDRGLMVPSVEHAEKMSADE
+LTRAINDTVSRAREGRAAPAELTRGTFTLNNYGPLGTDGATPILNIPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTF
+DHRVTDGATASAFLTFVADCLNDPQAALARI
+>4_1653
+MSNTFLLPDLGEGLTEADIVRWLVAEGDTVAVDQPMVEVETAKALVEVPSPYAGTVLTLHGAEGETMDVGSPLITIGAAG
+ES-GEGSAPVAGTEALAVPPSTGADAAEAARPGALSYREEEMAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHR
+ATSRSRPSKRGRGATRPT-----PAPTAWA------GAPRVTSPIVRKLAREKGVDVAALTGTGPDGLITRADVLAAAEG
+-SAPQAAPAQAPSVAAVPAAEA--AAQPGAVDGRTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVTALLEL
+RAALKAKDPENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDGVHLGLAVQTDRGLMVPSVEHAEKLSADE
+LTAAVNDTVSRARAGRAAPAELTRGTFTLNNYGPLGTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIMVRKVTEMTVTF
+DHRVTDGATASAFLTFVADCLHDPTAALARI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001447.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001447.fa
new file mode 100644
index 0000000000000000000000000000000000000000..835d7485db5c23b8d280990991f24a031bb6f4cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001447.fa
@@ -0,0 +1,36 @@
+>0_1725
+MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTARFGEERCFDTPLAE
+SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPITIRIPYG
+GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRSAIRLDDPVVFMEPKKMYWTK
+AELDLDQLRAEFEEGWARVEDKKEHGEAWARAAVVREGTDVTLVSYGPSVPTCLAAAHAA
+AEEGLSVEVVDLRTVNPLDEDTMAASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS
+LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLDAEEARA
+>1_1442
+MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTARFGEERCFDTPLAE
+SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPITLRIPYG
+GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRSAIRLDDPVVFMEPKKMYWTK
+AELDLDQLRAEFEEGWARVEDKKEHGEAWARAAVVREGTDVTLVSYGPSVPTCLAAAHAA
+AEEGLSVEVVDLRTVNPLDEDTMAASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS
+LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLDAEEARA
+>2_1074
+MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTKRFGEERCFDTPLAE
+SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPMTIRIPYG
+GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRAAIRLDDPVVFMEPKKMYWTK
+AELDLEDLRAEFEERWGRVEEKKEHGEAWARAAVVRAGSDVTLVSYGPSVPTCLAAARAA
+EEEGLSVEVVDLRTVNPLDEDTMVASVSKTGRAVVVAEPQGFASVASELVARIQQRCFHS
+LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLDAEEARA
+>3_998
+MANLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTQRFGDERCFDTPLAE
+SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQVASHVAKMRNRTKGGAPMPIVIRIPYG
+GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYLMLRSAIRLDDPVVFMEPKKMYWTK
+ADLDLDELRAEFDEQWARAQEKTAQGEAWARAAVVRQGADVTLVSYGPSVPTCLAAAQAA
+AEEGLSVEVVDLRTVNPLDEDTMAASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS
+LAAPVGRVTGFDIPFPAPKLEEHHLPNVDRILDAIDDLNWDLDAEEARA
+>4_1654
+MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTARFGEERCFDTPLAE
+SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPITIRIPYG
+GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRSAIRLDDPVVFMEPKKMYWTK
+AELDLDQLREEFEEGWARVEDKKEHGEAWARAAVVREGTDVTLVSYGPSVPTCLAAAHAA
+AEEGLSVEVVDLRTVNPLDEDTMTASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS
+LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLGAEEARA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001448.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001448.fa
new file mode 100644
index 0000000000000000000000000000000000000000..428b952bd36bf60b3e829c38c1523c46db3beccf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001448.fa
@@ -0,0 +1,41 @@
+>0_1726
+M--SDPTPAVPGAARTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQG
+TEPGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVC
+LGEDDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHA
+VGMAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFA
+KQSAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAH
+TNTDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQIARDAEDVAQQLRDAM
+NAETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA
+>1_1443
+M--SDPTPAVPGAVRTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQG
+TEPGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVC
+LGEHDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHA
+VGMAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFA
+KQSAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAH
+TNTDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQITRDAEDVAQQLRDAM
+NAETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA
+>2_1073
+M--SDPTPAVSGSARTDQAEARPNAGAAFGISLEEYLLPATRRIQLIGEDGTLLSPEEQG
+AEPGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVC
+LGKQDWLFPTYRDTVAVIARGVPPLEVMVSYQGTWHQGYDPNEHHVSVQSTPLTTQLLHA
+VGMAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFA
+KQSAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVDLCRQGQGPFLVEADTYRMQAH
+TNTDDPTRYREDAEVQEWEARDPLRRMTAYLESTGALTEEVSAEIAQAAEDVAKDLRDAM
+NAEAELDPLELFDHVYSVQTPQLAAQRAQLTEELSRSENQEA
+>3_997
+MTSTRPGPATP--------DTRTEAAAAFGITLEEYLLPAARRIQLISPEGELLPAEEQG
+TAPGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVC
+LGQDDWLFPTYRDTVAVIARGVAPLDVMVSFQGTWHQGYDPKEHRVSVQSTPLTTQLLHA
+VGMAKAARLRGEDVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFLVQNNKFAISVPFA
+KQSAAPSLAHKAVGYGLAGERVDGNDLAALLAVLGRAVDLCREGKGPFLVEADTYRMQAH
+TNTDDPTRYREDSEVKEWEVRDPLRRMTAYLESTGALTAEVSTSIAKDAEDVAQQLRDAM
+NADVELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENKEA
+>4_1655
+M--SDPTPAVPGAVRTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQG
+TEPGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVS
+LGEDDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHA
+VGMAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFA
+KQSAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAH
+TNTDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQIARDAEDVAQQLRDAM
+NAETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001451.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001451.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2fd7c98b58aa5c8f4eea5ade51d5d8f9cc86269
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001451.fa
@@ -0,0 +1,55 @@
+>0_1739
+MPQTTSHAPVPPSASAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTADQAPLREAIVGEIKARTVETD
+RSVPARRDGWWYFVRTREGAEYPIHCRVPARDTGDLEADWTPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPD
+ATRVAYAVDHTGDERFTLRVREIATGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVRAHVLGTDPAEDVLLHE
+EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLADVEPVTDADGVRRLLVVHDRA
+L-----DDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVKVDGVMVTLTHAALAVRRETTPRVVVAELDAVLAGQ
+AAHWREPAFDEELYACHLSATAAESPFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPS
+SVTGEDVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGGGELGRRWYEDGKKLA
+KRHSFTDFVDATRHLVGLGWADPARVACMGGSAGGLLMGAVLNLAPELYRACLAVVPFVDALTTILDPELPLSALEWEEW
+GNPIEDAAVYAAMRAYTPYENVRAVDYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQATPLAEGGAPILLRTEMDG
+GHGGASGRYQGWEDTAWEYAFLLTALGATARIV
+>1_1447
+MPQTTSHAPVPPSASAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTADQAPLREAIVGEIKARTVETD
+RSVPARRDGWWYFVRTREGAEYPIHCRVPARDTGDLEADWTPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPD
+ATRVAYAVDHTGDERFTLRVREISTGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVKAHVLGTDPAEDVLLHE
+EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLADVEPVTDADGVRRLLVVHDRA
+L-----DDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVKVDGVMVTLTHAALAVRRETTPRVVVAELDAVLAGQ
+AAHWREPAFEEELYACHLSATAAQSPFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPS
+SVTGEDVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGGGELGRRWYEDGKKLA
+KRHSFTDFVDATRHLVDLGWADPARVACMGGSAGGLLMGAVLNLAPELYRACLAVVPFVDALTTILDPELPLSALEWEEW
+GNPIEDAAVYEAMRAYTPYENVRAVDYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQATPLAEGGAPILLRTEMDG
+GHGGASGRYQGWEDTAWEYAFLLTALGATARID
+>2_1057
+MPQTTSHAPVPPSVSAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTADQAPLRAAIFGEIKARTVETD
+RSVPSRRDGWWYFARTKEGAEYPVHCRVPAADTGDLEADWTPPVVTPDAPLEGEQVILDGNAEAEGHPFFALGGLHISPD
+STRVAYAVDHTGDERFTLRVREIATGEDLPDVVENIAHGVRFDRSGARVLYTVWDDSWRPYQVKAHVLGTDPAQDQLLYE
+ESDPGMWTGFTGTADRTQLLIGVGNSEVSETHVVDLPESPDAPLPAPRLLIPRAWGMLADVEPVTGADGVRRLLVVHDRT
+VARQDAADAGADAPAPNGMLSLVAEADVADRGAWRTVVPHREDVKVDGVMVTLTHAALAVRRETTPRVVVAPLDSVLAGE
+AADWREPAFEEELYACHLASTAAESPFLRLAYTSWISPARVLDVSAATGEVHLRRETEVPGYDPSLYVAERVWAPASEPS
+SVTGEPVRIPVTVIRRKDVAADGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVYAVAHVRGGGELGRRWYEDGKKLA
+KRHSFTDFVDATRHLVDLGWADPARVACTGGSAGGLLMGAVLNLAPELYRACLAVVPFVDALTSILDPELPLSALEWEEW
+GNPIEDPEVYAAMRDYTPYENVRAVDYPTIAAVTSLHDTRVLYVEPAKWVARLRRTVTSDQATPLAEGGAPVLLRTEMDG
+GHGGASGRYQGWEDTAWEYAFLLTALGATQRVD
+>3_993
+MYE--TSLPTPPRAAARPTARTVHGETFTDDFEWMRAKTEQEVLDHLQAENAYTEAATADQADLRAAIYGEIKAHTVETD
+QSVPARRDGWWYFVRTVEGKDYAVHCRVPAQDTGDALADWTPPVVPADAALPGEQVILDGNAEAAGHPFFSLGGMHISPD
+GALAAYAVDLAGDERYTLRVREIATGTDLPDVVRNIAPGVRFDRSGTRLIYTVWDETWRPYQVRVHTLGTDAAEDAVLYE
+ESDPGMWTGFDASADRTQLLIGVGNSEVSETWAVDLPVD-ASPLPAPRVLVPRTARMLADVEPF-DMDGRRRLLIVHDRL
+A-----DG----TTAPNGMLSIVDEADVADRDAWRPVVPHADDVRVDGVLVTRTHVGLAVRRDTTPRVLIAPLEGLREGS
+APAWTEPSFDEELYMCRLAGVNLDSPFLRLSYASWTTPARVLDVVAATGEVRLRREVEVPGFDREDYVAERWWAPASEPS
+SLTGEQVRIPLTVIRRRDVAQDGTAPAVVYGYGSYEMSMDPVFGVARLSLLDRGVVYVVAHVRGGGELGRAWYEDGKKAA
+KRHSFTDFVDATRFVADSGWVDPARIACTGGSAGGLLMGAVLNLAPELYRACLAVVPFVDALTSILDPDLPLSALEWEEW
+GNPIEDPEVYATMKAYTPYENVRAVDYPAIAAVTSLNDTRVLYVEPAKWVAQLRRTVTSDQTTPIAAGGSPILLRTEMDG
+GHGGASGRYQGWEDTAWEYAFLLTALGATARVD
+>4_1659
+MPQTTTHAPVPPSVAAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTADQAPLREAIVGEIKARTVETD
+RSVPARRDGWWYFVRTREGAEYPIHCRVPARETGDLEADWTPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPD
+ATRVAYAVDHTGDERFTLRVREIATGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVKAHVLGTDPAEDVLLHE
+EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLADVEPVTDADGVRRLLVVHDRA
+L-----DDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVKVDGVMVTLTHAALAVRRETTPRVVVTELDAVLAGQ
+AAHWREPAFDEELYACHLSATAAESPFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPS
+SVTGEDVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGGGELGRRWYEDGKKLA
+KRHSFTDFVDATRHLVDLGWADPARVACMGGSAGGLLMGAVLNLAPELYRACLAVVPFVDALTTILDPELPLSALEWEEW
+GNPIEDAAVYAAMRAYTPYENVRAVDYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQARPLADGGAPVLLRTEMDG
+GHGGASGRYQGWEDTAWEYAFLLTALGATRRVV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001461.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001461.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9e3b57d39d21e88a5189f2e1e993cc1f340c6a92
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001461.fa
@@ -0,0 +1,11 @@
+>0_1753
+MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK
+>1_1461
+MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK
+>2_1041
+MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK
+>3_977
+MGSVIKKRRKRMAKKKHRKLLRKTRHQRRNKK
+>4_1675
+MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001462.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001462.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7eb49b5113065c8f30d2d4736c74b7729759b493
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001462.fa
@@ -0,0 +1,41 @@
+>0_1754
+-MSTTSTPPAPTPAAVVWDSSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVRIVE
+PPVATDEQLALVHDPEYVAAVRRAAATSSAEDGRFGLGTEDCPVFPDLHESAARIAGGSL
+VAAEAIWSGEVDRAVNFAGGMHHAARSSASGFCIYNDCAVAIQRLLDLGAERVAYVDVDA
+HHGDGTQSIFYDDPRVLTISLHETGISLFPGTGFANEIGGSAAQGTAVNVALPPRTGDAG
+FLRAAHAVVPPLLEAFAPDVLVSQHGCDGHLTDPLADLRLSVDGQRQLAFDVGDWADRFA
+YGRWLATGGGGYNPLRVVPRAWAHLTAAVLQTPIPVRSEIPAAWIEHVRALTADELTGDM
+SVHEGDDAERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRREVFPLHGLDPWFD
+>1_1462
+-MSTTSTPPAPTPAAVVWDSSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVRIVE
+PPVATDEQLALVHDPEYVAAVRRAAATSSAEDGRFGLGTEDCPVFPDLHESAARIAGGSL
+VAAEAIWSGEVDRAVNFAGGMHHAARSSASGFCIYNDCAVAIQRLLDLGAERVAYVDVDA
+HHGDGTQSIFYDDPRVLTISLHETGISLFPGTGFANEIGGSAAQGTAVNVALPPRTGDAG
+FLRAAHAVVPPLLQAFAPDVLVSQHGCDGHRTDPLADLRLSVDGQRQLAFDVGDWADRFA
+HGRWLATGGGGYNPLRVVPRAWAHLTAAVLQTPIPVKSEIPAAWIEHVRTLTADELTGDM
+SVHEGDDAERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRREVFPLHGLDPWFD
+>2_1040
+-MSTTSQRPAPTPAAVVWDPSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVSIIE
+PPVATDAQLALVHDPDYIAAVRRASEAASDEDAPFGLGTEDCPVFPDLHEASARIAGGTL
+AAAEAVWSGQVRRAVNFAGGMHHAARAKASGFCIYNDCALAIQRLLDLGAERVVYLDVDA
+HHGDGTQAIFYDDPRVMTISVHETGISLFPGTGFANEIGGPDAQGTAVNVAVPPRTGDAG
+FLRAVHAVVPQLLQGFDPDVIVSQHGCDGHHADPLADLRLSVDGQRQLAFDIGDWAEKFA
+DGRWVATGGGGYNPLRVVPRVWTHLTAAVLQTPIPVKAEIPQSWIEHARTLTAEELTGDM
+SLHEGDESERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRRELFPLHGLDPWFD
+>3_976
+MTSATSDCSQPAPSAVVWDPSLLKYRFSAQHPMAPLRLDLTHRLASSLGLLDAEHVRILQ
+PPVATDEQLATVHDPAFIAAVRAASREDAEADEPHGLGSEDCPTFPDLHESAARIAGGSL
+VAAEAVWSGEVSRAVNVAGGMHHAARAKASGFCIYNDCAVAIQRLLDLGAERVAYVDVDA
+HHGDGTQSIFYDDPRVLTISLHETGISLFPGTGFANETGGPGAEGTAVNVALPPGTGDAG
+FLRAVHAVVPQLLGAFQPDVLVTQHGADAHRGDPLADLRLSVDGQRQLAFDLGDWADRYA
+HGRWLATGGGGYNHVRVVPRAWTHLIGAVTGQPVPSSTPVPESWLEHVRSLTPDDLEGDM
+SLFEGAEEDRYPLTMTEDADVWWRSWEVGYDPADPVDQTIMATRREVFPIHGLDPWFD
+>4_1676
+-MSTTSTPPAPTPAAVVWDSSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVRIVE
+PPVATDEQLALVHDPEYVAAVRRAAATSSAEDGRFGLGTEDCPVFPDLHESAARIAGGSL
+AAAEAIWSGEVDRAVNFAGGMHHAARSSASGFCIYNDCAVAIQRLLDLGAERVAYVDVDA
+HHGDGTQSVFYDDPRVLTISLHETGISLFPGTGFANEIGGAAAQGTAVNVALPPRTGDAG
+FLRAAHAVVPPLLEAFAPDVLVSQHGCDGHRTDPLADLRLTVDGQRQLAFDVGDWADRFA
+HGRWLATGGGGYNPLRVVPRAWAHLTAAVLQTPIPVKSEIPAAWIEHVRALTADELTGDM
+SVHVGDDAERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRREVFPLHGLDPWFD
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001465.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001465.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37f7eaa0ad219acc818d1b6541f137bf829da0eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001465.fa
@@ -0,0 +1,31 @@
+>0_1757
+M----KLTILGLGTMTGAILAGALDAGAVRAEDVTATTRSAASAEKAAAQH-GVTVTSQE
+RDERANHAAVAEADIVLVGVKPKDMVATLTDLASSLRPETVVVSVAAGVTAATMAAVLPA
+GQPIVRTMPNTPLTVGSGVVGVAPGPGVTEEQATAVRALFEGSGLVVPVAEEQLSAVVAT
+AGSAPAYVFLLAELIAAHGAEMGLDAASAEAMAAATVKGAGIMLQ----QEGARAGALRK
+AVMSPNGTTEKAVEAFLDGGMGDLVNRAMDAAAQRDREMAEEFGA
+>1_1465
+M----KLTILGLGTMTGAILAGALEAGAVRAEDVTATTRSAASAEKAAAQH-GVTVTSQE
+RDERANHAAVAEADIVLVGVKPKGMVATLTDLAPSLRPETVVVSVAAGVTAATMAAVLPA
+GQPIVRTMPNTPLTVGSGVVGVAPGPGVTEEQTTAVRALFEGSGLVVPVAEEQLSAVVAT
+AGSAPAYVFLLAELIAAHGAEMGLDAASAEAMAAATVKGAGIMLQ----QEGARAEALRK
+AVMSPNGTTEKAVEAFLDGGMGDLVNRAMDAAAQRDKEMAEEFGA
+>2_1033
+M----KLTILGLGTMTGAILTGAIEAGAVRAEDVRATTRSAASAERARGRHPGVEVLAAE
+EDAHANKRAVEGADVVLLGVKPKDIAATAAEVAQALGTDTTVVSVAAGVRAETIAAALRE
+GQPLVRTMPNTPLTVGSGVVGVAPARGVTDAQTQAVEALFAGSGLVVRVAEEQLAAVVAA
+AGSAPAYVFLLAESIAKHAEQLGLDRANAEAMAAATVKGAGLMLQNGIREGDQTAEDLRR
+GVMSPGGTTEQAIRTFQEGGFERLVADAMDAAARRDEEMGRELAG
+>3_972
+MTAQPRIAILGLGSMTGAILTGLLAASVTTPERVVATTRTAASAQAKGNRFPGVRVLSGE
+QDVDANLTAVAEADVVLLGVKPKDIVVTARQIAPALRPEAVVVSVAAGVRAETLAGALPE
+GQPLVRTMPNTPLTVGSGVVGVAPAAGVTADQRALVESLFSGSGVVVPVSEEQLPAVVAA
+SGSAPAYVFLLAEAIAAHAVELGLSAEAAEAMAAATVKGAGAMLVDAVTSGEQTAEGLRR
+AVMSPNGTTERAIAAFEDGGFAGLVADAMDAAARRDEEMGREFGA
+>4_1679
+M----KLTILGLGTMTGAILAGALDAGAVRAEDVTATTRSAASAEKAAAQH-GVTVTSQE
+RDERANHAAVAEADIVLVGVKPKDMVATLTDLAPSLRPETVVVSVAAGVTAATMAAVLPA
+GQPIVRTMPNTPLTVGSGVVGVAPGPGVTEEQATAVRALFEGSGLVVPVAEEQLSAVVAT
+AGSAPAYVFLLAELIAAHGAEMGLDAASAEAMAAATVKGAGIMLQ----QEGARAEALRK
+AVMSPNGTTEKAVEAFLDGGMGDLVNRAMDAAAQRDKEMAEEFGA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001469.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001469.fa
new file mode 100644
index 0000000000000000000000000000000000000000..998eec79277c4390a7f30f8837d5663b499b3bf0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001469.fa
@@ -0,0 +1,45 @@
+>0_1761
+M---SPVPTPPSPPAPRLTPATAVALAADLAALPFTTAAVEGLLGPVATLALDREHAEAARRVVAGHL-AGPGRHDDA--
+-------------AGPGDRPGTRGLAAAVGAWLLGDPVPAADLDAALPSLGLAGAVAAGLVV-EGPDG---RVRGAVDLS
+PYEADEPGRMWIASDLTALQRRGPLPPEHVLGVGRASLTLAGATQRRPVARALDVGVGCGIQTLHLLAHADHVTATDLSE
+RALAFTRFNLLLNADVLGLDRERLEDRVRLAAGDLLAPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGREGDRIVA
+ELIAALPDVLAEGGTAQLLANWEIPAG---------DTADADTA------PWDARPRSWVASGMQAWFIQRDRQDPAGYA
+ETWLQDSSLELDPPAYEAAYRGYLDDFAARGVAGVGFGHVWLRRPAADGSQGRGWVVAEELTQAVDEALGTAWAAAVARR
+DRLTAG--AGAGDAV--GDPALAALRGLHLRVAADVTEERHQRFGAEHPEVILARQGSGFRRVARLDTATAGVLSASDGE
+LSVGQLVGAVAALLELDDVGRAGLLAALRELYEDGFLVE---G
+>1_1469
+M---SPVPTPPSPPAPRLTPATAVALAADLAALPFTTAAVEGLLGPVATRALDREHAEAARRVVAGHL-AGPGRHDDA--
+-------------AGPGDRHGTRGLAAAVGAWLLGDSVPAADLDAALPRLGLAGAVAAGLVV-EGPDG---RVRGAVDLS
+PYEADEPGRMWIASDLTALQRRGPLPPEHVLGVGRASLTLAGATQRRPVARALDVGVGCGIQTLHLLAHADHVTATDLSE
+RALAFTRFNLLLNADVLGLDRDRLEDRVRLAAGDLLAPVTGERFDLVVSNPPFVITPRTDPGAPVLIYRDGGREGDRIVA
+ELIAALPDVLAEGGTAQLLANWEIPAG---------DTANADTA------PWDARPRSWVAPGMQAWFLQRDRQDPAGYA
+ETWLQDSSLELDPPAYEAAYRGYLDDFAARGVAGVGFGHVWLRRPAADGSQGRGWVVAEELTQPVDEALGAAWAAAVARR
+DRLAAG--AGAGDAV--GDPALAALRGLHLRVAADVTEERHQRFGAEHPEVILARQGSGFRRVARLDTATAGVLSASDGE
+LSVGQLVGAVAALLELDDVGRAGLLAALRELYEDGFLVE---G
+>2_1028
+MKPPAPSPSSPSLPAPRLTPATAAALDADLAALPYTTAAVEELLGPVATAALDREHAEPARRVVARVLTAAPGDHTQALY
+DDGALGSGARPLEAGIGSPAARRALAALVSVWMLGDAADAADVAAALPALGLDGAREAGLVA-EEGGG---TVRGTVDLS
+PYEADEPGRMWVASDQTALQRRGPLPEDHVLGIGRASLTLAGATQRRPVACALDVGVGCGIQTLHLLAHAEHVTATDLSE
+RALEFTRFNLLLNADVLGLDRERLEDRVRLAAGDMLAPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGREGDRIVA
+ELVAALPAHLTEGGTAQLLANWEIPAGAAAIPAAAAASADGDLADTAGPAPWDARPRSWIAPGMQGWIIQRDAQDPAGYA
+ETWLQDSSLELDPHRYEAAYRGYLEDFAARGVAGVGFGHVWLRRPVDDGAQGRAWTVAEELTQPVDEALGAAWAAAVARR
+DRLA----AGAPDGA--GDPALAALRGLHLRVAEDVSEERHGRFGAEHPEVILARQGAGFRRTARLDTATAGVLSASDGE
+LSVGQLVGAVAALLELDDAGRAGLLAAIRELYEDGFLVERAED
+>3_968
+M----------SLPAPHLSPAAAAALAADLTALPYTTDVVETLLGPVATAALDREHAVAARRVVAGVL-AAPAARDAA--
+-------------------AASRPLAAVVGAFMLGEPVPAADLAAALPALGLDGAVEAGLVVLDGADTGAERARATVDLS
+PYAADEPGPMWVASDQTALQRRGPLPEDHVLGIGRASLTLAGATQRRPVARALDLGVGCGVQTLHLLAHAEHVTATDLSE
+RALDFTRFNLLLNADVLRLDRERLEDRVRLAAGDLLGPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGREGDRLVA
+ELIAALPEHLVEGGTAQLLANWEIPAGAAEIPAGAAEVPAGDDA----PPAWDARPRSWVGPGMQAWFVQRDRQDPAGYA
+ETWLQDSSLELDPAAYEAAYRGYLDDFAARGVTGVGFGHVWLRRPAADRSQGRAWTVAEELTQPLDEALGTAWAAAVARR
+DRLAAGPEAGATDAVVTGDPALAALRGLHLRVAEDVTEERHSRFGAEHPEVILARQGAGFRRTARLDTATAGVLSASDGE
+LSVGQLVGAVAALLELDDAGRAGLLAAVRELHEDGFLLE---A
+>4_1683
+M---SPVPTPPSPPAPRLTPATAVALAADLAALPFTTAAVEGLLGPVATLALDREHAEAARRVVAGHL-AGPGRHDDA--
+-------------AGPGDRPGTRGLAAAVGAWLLGDPVPAADLDAALPSLGLAGAVAAGLVV-EGPDG---RVRGAVDLS
+PYEADEPGRMWIASDLTALQRRGPLPPEHVLGVGRASLTLAGATQRRPVARALDVGVGCGIQTLHLLAHADHVTATDLSE
+RALAFTRFNLLLNADVLGLDRERLEDRVRLAAGDLLAPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGGEGDRIVA
+ELIAALPDVLAEGGTAQLLANWEIPAG---------DTADADTA------PWDARPRSWVAPGMQAWLLQRDRQDPAGYA
+ETWLQDSSLELDPPAYEAAYRGYLDDFAARGVAGVGFGHVWLRRPAADGSQGRAWVVAEELTQPVDEALGTAWAAAVARR
+DRLAAG--AGAGDAV--GDPALAALRGLHLRVAADVTEERHQRFGAEHPEVILARQGSGFRRVARLDTATAGVLSASDGE
+LSVGQLVGAVAALLELDDVGRAGLLAALRELYEDGFLVE---G
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001472.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001472.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da4682c8a8d73515738e7fa1ed4bb0ad49913fe4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001472.fa
@@ -0,0 +1,65 @@
+>0_1764
+MTG---HLPEH-------DPWADPAGGWGPPGTA-----DAAPPVD--DAAPDSSGP---EPQPVGEVVADVVAGLSVTA
+PGDLCPDTPAGAGLRAALGRTGLPEQIRHVTELPARQARHTDWPADAPEGLVRAFAARGVERPWLHQVRAAALAGAGTHT
+VLATGTASGKSLGYQLAVGTRLAADPRATALYLAPTKALAADQLTSWRALERDGAPGLRSAPYDGDTAPQDRIWAREHAS
+VLMTNPDMLHVGILPHHERWATFFRNLAFVVVDESHTYRGVFGSQVGILLRRLRRIAAHYRGDRPETVFIGASATSADPA
+GHFARLIGAP---AAAVTEDASPHGAVTVAFWEPELTDRRGENGAPVRRSAMAAAADLVTDLALQQVRTLAFIRSRRGAE
+AIASAAKRQLEEVEPGLGTRIAAYRSGYLPEERRELEADLRSGRLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQ
+QIGRAGRGGQDALAFFVASDDPLDTFVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPITPEAFGWFGEPERVR
+ALLDVLVDQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAESGALLGTMDSPQTHYQAHPGAVYVHQDRTYLVE
+ELDEDAHAVVVTRAWPDFTTQARDVTEVEIVAVHRRLDAREGTLRWCLGDVQVRTQVVSFQRKALASGEVLGEEPLDLPA
+RDLFTSAVWFQAASDELIAAGLTTDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSPAVFVYDGRPGGAG
+FAERGFEQARRWVEATAGAIAACECAEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLMDHADHLVPADASTDGSGGGASG
+GSSGGATDAAPGA------
+>1_1472
+MTG---HLPEH-------DPWADPAGGWGPPGTA-----DSAPPVD--DAAPDFSGP---EPQPVGAVLADVVAGLSVTA
+PGDLRPDTPAGAGLRAALGRTGLPEQIRHVTELPARQARHTDWPADAPEGLVRAFAARGVERPWLHQVRAAALAGAGTHT
+VLATGTASGKSLGYQLAVGTRLAADPRATALYLAPTKALAADQLTSWRALERDGAPGLRAAPYDGDTAPQDRIWAREHAT
+VLMTNPDMLHVGILPHHERWAAFFRNLTFVVVDESHTYRGVFGSQVGILLRRLRRIAAHYRGDRPETVFIGASATSADPA
+GHFARLIGAP---ATAVTEDASPHGAVTVAFWEPELTDRRGENGAPVRRSAMAAAADLVTDLALQQVRTLAFIRSRRGAE
+AIASAAKRQLEEVEPGLGTRIAAYRSGYLPEERRELEADLRSGRLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQ
+QIGRAGRGGQDALAFFVASDDPLDTFVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPITPEAFGWFGEPERVR
+ALLDVLVEQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAESGALLGTMDSPQTHYQAHPGAVYVHQDRTYLVE
+ELDEDAHAVVVTRAWPDFTTQARDVTEIEIVAVHRRLDAREGTLRWCLGDVQVRTQVVSFQRKALVSGEVLGEEPLDLPA
+RDLFTSAVWFQAASDELIAAGLTTDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSPAVFVYDGRPGGAG
+FAERGFEQARRWVEATAGAIAACECTEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLMDHADHLVPADASTDGSG----G
+GASGGSADPAPGA------
+>2_1025
+MST---PPPEPAAAGVAFDPWADPAAGWGAPDDGPSDRRDAPADVDETDHPGDEAHP-WDEPAPLADAVADVVAGLSVSR
+PGDPVAGGEAADVLRGALGRHGLPEQIRHVVTLPAREARHADWPSEAPEALVGAFAGRGIERPWAHQVRAATVAGAGTHT
+VVATGTASGKSLAYQLAAGIRLSGDPHATVLHLSPTKALAADQLLAWRALERDGATWLRAAPYDGDTAPPDRIWAREHAN
+VLMTNPDMLHVGILPHHERWARFFRHLAFVVVDESHSYRGVFGSQVGILLRRLRRVAAHWRGDRPEPVFIGASATSADPA
+GHFSRLIGAP---ATAVAEDASPHGAVTVAFWEPELTDRRGENGAPVRRSAMAASADLLTDLALQQVRTLAFIRSRRGAE
+AIASAARRQLEELEAGLGSRIAAYRSGYLPEERRALEADLRSGRLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQ
+QIGRAGRGGQDALAFFVASDDPLDTYVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPLTPEAFERFGDPERVR
+ALLDVLVEQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAESGTLLGTMDSPQTHYQAHPGAVYVHQDRTYLVE
+ELDEDAHAVIVTRAWPDFTTQARDVTEIEIVDVHRRLDAREGTLRWCLGDVQVRTQVVSFQRKALVSGEVLGEEPLELPA
+RDLFTSAVWFQASSEELIAAGLTMDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSPAVFVYDGRPGGAG
+FAERGFAQARRWVEATAGAIAACECEAGCPSCVQSPKCGNRNSPLDKAGALTVLRFLLGQADHLVPVVAEGSGETDGGTD
+DGVGVDGEDASGSGSSGTA
+>3_965
+MTGGPVPWPDD-------DPWA----ARGPAEDRSA--RDVP--------TPAPGGPGWEPPQELAT-------------
+-GDP----EARAAFAAALGRRSLPAQIRHVTTIPARTPRSAPWPAGTPAGLVRAFAARGVQAPWEHQARGTAAALAGRHT
+VLATGTASGKSLAYQLAVGATLAADPRATVLYLAPTKALAADQLASWRALERDGAAWLRAAPYDGDTAPQDRIWAREHAN
+VLLTNPDMLHVGILPHHERWAVFFRNLAYVVLDESHTYRGVFGSQVGILLRRLRRVVAHYRGERPETVFIGASATSAAPA
+EHLATLIGAAPGEVEAVTEDASPHGAVHVAFWEPELTDRRGENGAPVRRSATATAADLLTDLALQQVRTLAFIKSRRGAE
+TIAGAAKRQLEEVEAGLGSRIAAYRSGYLPEERRALEEALRSGRLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQ
+QIGRAGRGGQDALAFFVASDDPLDTFVVEHPGAVFDLGVEDTVLDPANPHLLGPQLCAAAAELPLRPEDLPWFGGPERVR
+ELLDVLVEQGLLRRRPAGWFWTHTEHAASLVSLRDDGGGPMDIIDVESGALLGTMDSPQTHYQAHPGAVYVHQDRTFLVE
+DLDEDAHAVLVQRAWPDFTTQARDVTEIEIVAVHRRLDAAGSSLRWCLGDVQVTTQVISFQRKALLSGEVLGEEPLDLPA
+RDLFTSAVWFQAASEELVAAGLTMDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGVPTVFVYDGRPGGAG
+FAERGFAQARRWVEATAGAIAACECAEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLAERFDGLIEVPAHLPDV------
+-----------------TA
+>4_1686
+MTG---HLPEH-------DPWADPAGGWGPPGTA-----DAAPPVD--DAAPDSSGP---EPQPVGEVVADVVAGLSVTA
+PGDLRPDTPAGAGLRAALGRTGLPEQIRHVTELPARQARHTDWPADAPEGLVRAFAARGVERPWLHQVRAAALAGAGTHT
+VLATGTASGKSLGYQLAVGTRLAADPRATALYLAPTKALAADQLTSWRALERDGAPGLRSAPYDGDTAPQDRVWAREHAS
+VLMTNPDMLHVGILPHHERWAAFFRNLAFVVVDESHTYRGVFGSQVGILLRRLRRIAAHYRGDRPETVFIGASATSADPA
+GHFARLIGAP---ARAVTEDASPHGAVTVAFWEPELTDRRGENGAPVRRSAMAAAADLVTDLALQQVRTLAFIRSRRGAE
+AIASAAKRQLEEVEPGLGTRIAAYRSGYLPEERRELEADLRSGRLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQ
+QIGRAGRGGQDALAFFVASDDPLDTFVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPITPEAFGWFGEPERVR
+ALLDVLVEQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAESGALLGTMDSPQTHYQAHPGAVYVHQDRTYLVE
+ELDEDAHAVVVTRAWPDFTTQARDVTEIEIVAVHRRLDARAGTLRWCLGDVQVRTQVVSFQRKALVSGEVLGEEPLDLPA
+RDLFTSAVWFQAASDELIAAGLTTDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSPAVFVYDGRPGGAG
+FAERGFEQARRWVEATAGAIAACECAEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLMDHADHLVPADASSDGS-----G
+GASGGATDAAPGA------
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001473.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001473.fa
new file mode 100644
index 0000000000000000000000000000000000000000..600666fe0e784bc2c399376fc908d5b3b3eaa7e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001473.fa
@@ -0,0 +1,21 @@
+>0_1765
+MTRGRAP------ARGERGSGTVSVLGTAALGAGLLLAVAALGQASATGSRAAGAADLAA
+LAASDARRGLSD------HEPCVLAGRTAERNGAAVVACEVREDGTVRVAVELARAPLPA
+ATADAVAGPPRSQAPGAASVAP------PEDPPEAPPP-------EPSVEASAGTR
+>1_1473
+MTRGRAP------VRGERGSGTVSVLGTAALGAGLLLAVAALGQASVTGARAAGAADLAA
+LAASDARRGLSD------HEPCVLAGRTAERNGAAVVACEAREDGTVRVAVELARAPLPA
+ATADAVAGPPRSQAPGAGSADP------PE----APPP-------EPSVEASAGTR
+>2_1024
+MT-GRAPGGVPRGAASETGSGTVSVLGTAALGAGLLLAVAALGQASVAGAQAAGAADLAA
+LAASDARRGLSA------GEPCLVAGQTAARNRAVVVECEVRENGTVRVSVERGRAPLPP
+ALAAAVAGPPRLQAPQAVPEDPLPDASSPS----TPTPSSVPPSVSPDPSATTGTR
+>3_964
+M------------------SGTATALGTALLGAGLLTGVLAVGHASATAARASGAADLAA
+LAASDARRGLGAVPDAGVLEPCPLAEESARRNGAEVTECVLLPDGSVRVAVVIAADPLPA
+STAVAVAGPP--VGPRGPVAGPGRDDA-PE----DAPD-------TPGAPPEAATP
+>4_1687
+MTRGRAP------ARGERGSGTVSVLGTAALGAGLLLAVAALGQASVTGSRAAGAADLAA
+LAASDARRGLSD------HEPCVLAGRTAERNGAAVVACEVREDGTVRVAVELARAPLPA
+ATADAVAGPPRSQAPGAASVAP------PE-----APP-------EPSLEASAGTR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001476.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001476.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3feaee8153f1132e32839036b5234c4cad15c733
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001476.fa
@@ -0,0 +1,41 @@
+>0_1768
+------------------------------------MLVGALRRWAALVAAGLTEEQAWR
+ETACTLPACGSGPGEAGAACCAHHRARRRAEALAWDVPA---------------------
+--SHAPTGEAARGGGTLPWRTPARDPGWALVDAALAAGARAGAAPAAVARRLAHSLEADV
+DAARARRSAAAGPGATSRLLQWLPLGGLGLAWLLGTSPWDLARSPFGAVVAAVGLLFWLA
+GRSWTRLLLRAAAREPAAVGAAVVLDVLAALLSAGRSLPAALDDLGRTLPGARGLRATAA
+LLLWGRDWDEAWAGLDTDPVWIETAARLRPLHRSGMAGARTLAETAAAVRQQTRRADERA
+AEELAVRLVMPLGLCLLPAFVCWGVVPVVMALLGAGPG
+>1_1476
+MSPTTATGPARRSHAGRAVALLPWRAGRVPPEEETEVLIGVLRRWAALVAAGLTEEQAWR
+ETACTLPACGSEPSEAGTACCAHHHARRRAEALAWDVPA---------------------
+--AHAPTGEAARRGGTLPWRTPARDPGWALVDAALAAGARAGAAPAAVARRLAHSLEADV
+DAARARRSAAAGPGATSRLLQWLPLGGLGLAWLLGTSPGDLVRSPFGAVVAAVGLLFWLA
+GRSWTRLLLRAAAREPAAVGAAVVLDVLAALLSAGRSLPAALDDLGRTLPGARGLRATAA
+LLLWGRDWDEAWVGLDTDPVWAETAARLRPLHRSGMAGARTLAETAAAVRQQTRRADERA
+AEELAVRLVMPLGLCLLPAFVCWGVVPVVMALLGAGPG
+>2_1021
+MS-TAA------------------------PEDATEELVVVLRRWAALVSAGLTEEAAWR
+ETVRMLPDDDGH---------ARHAARLRAERLAWDAAGDLSTGRDAPDVRGLRRDEHPP
+GDTHDASPDRSRRRWCPPWRTPPPDPGWALVDAALAAGARAGAAPAVVVRRLAESLEADV
+DAARARRSAAAGPAATARLLQWLPLGGVGLAWLLGSSPWETVSTPFGAVVAAVGLLFWLA
+GRSWTRLLLRSAAREPAALTAPVVLDVLAALLGAGRSLPAALDDLARTLPGARGLRVTSA
+LLLWGRGWDEAWAGIGEETVWAEAAARLRPLHRSGMAGARTLAESAAAARQQGRRADERA
+AEELAVRLVMPLGLCLLPAFVCWGVIPVVMALLGAG-A
+>3_961
+MI------------------ALPGRAEER-AEERAQEVVEALRRWAGLTAAGMTPAEAWT
+AVAQASSPCG----RPTPGCCPRHEALRRAALARWGGPG-----------RGAEGGQPRP
+GE-----------------RSP-----WDLADAALAAAARAGASFSRTAARLADALEADV
+DASRARRTAAAGPRATARLLSWLPVGGLGLAWLLGMGPADLLATGFGWVLLVLGGVLTAA
+GRAWTRLALRRGARPLGEASPGVVVDVAAVLLGAGRSLPAALDDVSAHLPGAADLRVVAV
+LLRWGADWDEAWAPVTEEPRWAALGERLRPLHRTGMAGEAVLHQTAAALRQETRRADERG
+AEELAVRLVVPLGLCQLPAFVCWGVAPMALALLGA--R
+>4_1690
+------------------------------------MLVGVLRRWAALVSAGLTEEQAWR
+ETACTLPACGPGPSEAGTACCAHHRARRRAEALAWDVPA---------------------
+--SHAPTGEAARGGGTLPWRTPARDPGWALVDAALAAGARAGAAPAAVARRLAHSLEADV
+DAARARRSAAAGPGATSRLLQWLPLGGLGLAWLLGTSPWDLARSPFGAVVAAVGLLFWLA
+GRSWTRLLLRAAAREPAAVGAAVVLDVLAALLSAGRSLPAALDDLGRTLPGARGLRTTAT
+LLLWGRDWDEAWAGLDTDPVWIETAARLRPLHRSGMAGARTLAETAAAVRQQTRRADERA
+AEELAVRLVMPLGLCLLPAFVCWGVVPVVMALLGAGPG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001494.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001494.fa
new file mode 100644
index 0000000000000000000000000000000000000000..508d6baa07fbe998883196dfc9c484280e9736fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001494.fa
@@ -0,0 +1,51 @@
+>0_1791
+M-SVAPRAAVPPAPTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPEASSGPFPA
+TTLVLLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVAHHGDFAWV
+AFPLFFVVLHVVDRVARQAWVRHVVGPALVVAMAVVVVAGMAAGAG-GVRVPAVIGPLVG
+AAVAVVLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLT
+QGLASIVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGT-------
+---GAPSLIEALERAVAGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLA
+NVGAHAGARRARVTLGYLGDELTVDVADDGAGFDPAVVAA-------------RPRAG-A
+AGADPGA------GTGVGLASVRERLAAVGGEATVESAPGEGTVVALRVPLVAAGAGRSA
+DPEQTESEETA
+>1_1498
+M-SVAPRAAVPPAPTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPDA-SGPFPA
+TTLVLLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVGHHGDFAWV
+AFPLFFVVLHVVDRVARQAWVRHVVGPALVVAMAAVVVAGMAAGAG-GVRVPAVIGPLVG
+AAVAVVLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLT
+QGLASIVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGT-------
+---GAPSLVEALERAVTGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLA
+NVGAHAGARRARVTLGYLGDELTVDVADDGAGFDPAVVVA-------------RARAG-A
+AGADPGA------GTGVGLASVRERLAAVGGEATVESAPGEGTVVALRVPLAAAGAGRSA
+DPEQTESEETA
+>2_997
+MPTTRPSADTAGAPAETGAAAVLAGLRVALHVAFAVLLAVGLGRALADLSRTGAPAP-AV
+LALTGCTALLAGVYLAGTLVERRRWGRGEDVGRGPALLWLALVLALWGLLVAQHRDFAWV
+AFPLFFVALHVVARTARTAMARRIAGPVLVAAMAAVVVAGMAAGVDEGVRPAAVIGPLVG
+AAVAVVLSGAYRALHQESERQRDVAEQLRAAQAELARTQHRAGVGEERERLAREIHDTLT
+QGLASIVLVSRAAQDALDAQDPALARTRMETVRTTAAENLDESRRFVRDLRAT-------
+---GGASLVAAVERAVAGFAERQAAAGTPVAADVEVVGTPVPLAEAVEAALLRAVQASLA
+NVAAHARATRARVTLAWMPGELAVDVADDGVGFRPEAVVTGDAGTQGTGAGTQGARAG-R
+A-SRPGA------GTGVGLASVRERLAGVGGHASVESAPGEGTVVALRVPLPAA-AGRAE
+EDEGRER---G
+>3_940
+MRTSDPADGPRGA---NGTAALLSGLRVAVHVGFAVLLALALVRALAGPDAGARLTGRPA
+LALVGLTVVLAGVYLTGTVAERRLHAAGRAPGRTAAGTWLAVLLGVWALAVLRHPDMMWV
+AFPLFFVALHAVHVI----LGRPRLALACVAAMTVVVV---VASLERGTAPGAVLGPAVG
+AAVAVVVFHACRLLVVESERQRSVAEQLRATRAELAASERHAGVLAERERLAREIHDTLT
+QGLASIVLVSRAAQDAVRAGDAALADERLETVRTTAAENLAESRAFVRGLRAPVDGVQGG
+ADRAGSALEAALGAAVRGFRARRQALGRPVEAELAVVGEPVAVGEAVETVLVRAAQSSLA
+NVDQHARTDRCRVTLTWMDGEVALDVADDGVGFDPEAA---------------RARASRA
+AVSDPAAPRPAEEGTGVGLAGLAERVAGVGGRVDVESAPGQGCVVAVRIPVPRQHERRGA
+-----------
+>4_1712
+M-SVAPRAA---APTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPEASSGPFPV
+TTLVLLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVAHHGDFAWV
+AFPLFFVVLHVVDRVARQAWVRHVVGPALVVAMAVVVVAGMAAGAG-GVRVPAVIGPLVG
+AAVAVVLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLT
+QGLASIVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGT-------
+---GAPSLIEALERAVTGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLA
+NVGAHAGAHRARVTLGYLGDELTVDVADDGAGFDPAVVAA-------------RPRAG-A
+AGADPGA------GTGVGLASVRERLAAVGGEATVESAPGEGTVVALRVPLVAAGAGRSA
+DPEQTESEETA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001499.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001499.fa
new file mode 100644
index 0000000000000000000000000000000000000000..39c9ff8b66c6324b18dd366f97cab20f01f15e7e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001499.fa
@@ -0,0 +1,40 @@
+>0_1797
+MIAPRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAGIAVSDGGRIAVYKDIGLVSQ
+VFDEATLTALSGHIAVGHCRYSTTGVNKWANAQPTLGATADDGTVALAHNGNLVNSAELLRMVHAADGRHTHGEMKQGNT
+TDTALVTALLHGAPGDRLEETALELLPKIRGAYCFVFMDEHTLYAARDPQGVRPLVLGRLERGWVVASEQSALATVGASF
+IREVEPGEMIAIDEEGIRSTRFAESKPAGCVFEYVYLARPDATIAGRSVYESRVEMGRRLALEQPVEADVVIPVPESGTP
+AAVGYADASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIRLKLNVESTVVAGKRVVVVDDSIVRGNTQRAVVRMLKEAGA
+AEVHVKISSPPVKWPCFYGIDFATRAELIANGAAVDQIAASIGADSLAYISEEGMIEATGQPRERLCTACFTGDYPIPLA
+DEGERGKGLLEPVAVSPASTVVLDEDGETTTVTATGCEPGPDADDEKLLTETDRTPL
+>1_1504
+MIAPRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAGIAVSDGGRIAVYKDIGLVSQ
+VFDEATLTALSGHIAVGHCRYSTTGVNKWANAQPTLGATADDGTVALAHNGNLVNSAELLRMVHAADGRHTHGEMKQGNT
+TDTALVTALLHGAPGDRLEETALELLPKIRGAYCFVFMDERTLYAARDPQGVRPLVLGRLERGWVVASEQSALATVGASF
+IREVEPGEMIAIDEEGIRSTRFAESKPAGCVFEYVYLARPDAAIAGRSVYESRVEMGRRLALEQPVDADVVIPVPESGTP
+AAVGYADASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIRLKLNVQSTVVAGKRVVVVDDSIVRGNTQRAVVRMLKEAGA
+AEVHVKISSPPVKWPCFYGIDFATRAELIANGAAVDQIAASIGADSLAYISEKGMIEATGQPRERLCTACFTGDYPIPLA
+DEGERGKGLLEPVAVSPASTVVLDEDGETTTVTATGCEPGPDADDEKLLTETDRIPL
+>2_987
+MIASRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAGIAASDGKRIGVYKDIGLVSQ
+VFDESTLATFTGHIAVGHCRYSTTGANKWANAQPTLGATAGGDTVALAHNGNLVNSGELLRMVQARDGLQLRGEMKQGNT
+TDTALVTALLHGEEGRKLEETALELLPKVRGAYCFVFMDEHTLYAARDPHGVRPLVLGRLERGWVVASEQSALATVGASF
+IREVEPGEMIAIDEEGIRSTRFAEATPAGCVFEYVYLARPDASIAGRSVYESRVDMGRRLALEGPVDADVVIPVPESGTP
+AAVGYAEASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIRLKLNVQPSVVAGKRVVVVDDSIVRGNTQRAIVRMLKEAGA
+AEVHVKISSPPVKWPCFYGIDFASRAELIANGAGVAEIASSIGADSLGYISEEAMIAATGQPRERLCTACFTGTYPIELA
+DESERGKSVLETDAGSAAVT-VMAPDGDATTVASTGCEPGPDADDEKLLTETDRTPL
+>3_932
+MISARTRRGDGRLTAALDPQEAGPQDECGVFGVWAPGEEVAKLTYYGLYALQHRGQESAGIAASDGKRIAVYKDMGLVSQ
+VFDEPTLAALTGHVAVGHCRYSTTGVNKWANAQPTLGATADDGTVALAHNGNLVNSAELLRMVESKEGAHTLGEIKQGNT
+TDTALVTALLHGEKGVSVEETALELLPKVRGAYCFVFMTERTLYAARDPHGVRPLVLGRLERGWVVASEQSALATVGASF
+IREVEPGEMIAIDEEGIRSTRFAEATPAGCVFEYVYLARPDAAINGRSVYESRVEMGRRLAQEHPVDADVVIPVPESGTP
+AAVGYADASGIPFRQGFVKNAYVGRTFIQPSQTLRQLGIRLKLNVQPSVVAGKRVVVVDDSIVRGNTQRAIVRMLKEAGA
+AEVHVKISSPPVKWPCFYGIDFATRAELIANGAGVQEIASSIGADSLAYISEEGMIAATEQPRERLCTACFTGTYPIELA
+DEKERGKAVLENGTPTAEATDVVSEDGTVTTVASTGCEPGPDSEDEKLLTQTDRTPL
+>4_1718
+MIAPRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAGIAVSDGGRIAVYKDIGLVSQ
+VFDEATLTALSGHIAVGHCRYSTTGVNKWANAQPTLGATADDGTVALAHNGNLVNSAELLRMVHAADGRHTHGEMKQGNT
+TDTALVTALLHGAPGDRLEETALELLPKIRGAYCFVFMDEHTLYAARDPQGVRPLVLGRLERGWVVASEQSALATVGASF
+IREVEPGEMIAIDEEGIRSTRFAESKPAGCVFEYVYLARPDATIAGRSVYESRVEMGRRLALEQPVDADVVIPVPESGTP
+AAVGYADASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIRLKLNVQSTVVAGKRVVVVDDSIVRGNTQRAVVRMLKEAGA
+AEVHVKISSPPVKWPCFYGIDFATRAELIANGAAVDQIAASIGADSLAYISEEGMIEATGQPRERLCTACFTGDYPIPLA
+DEGERGKGLLEPVAVSPASTVVLDVDGETTTVTATGCEPGPDADDEKLLTETDRTPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001530.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001530.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7524df3204ed8c8b7aaccd30caf6ad77b5351dca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001530.fa
@@ -0,0 +1,46 @@
+>0_1831
+-----------------MTDVALPPVASAAPRRQVAAWALWDWGSAAFNAVMVTFVFGTY
+LASDAFGPDERGTAWLSTAMAVAGVVIAVTAPVLGRRADGAGRRRLWLALTTGAVIACTA
+ACFWVTPEESSLLLGVTLIALGTVFFEFAEVQVNAILVHISTPATIGRISGIGWGAGYLG
+GILLLLIVFVGFVSGDAHWFGVTEDAALNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPA
+ADGGPRRESVLGSYRELGATLARMWREDRNTLWFLVASAVFRDGVGAVFVYGAILGTTVY
+GLAASDVILFAIAANVVAALGAFVGGRLDDAVGPRRVILGSLAAMVLVAGALFFASGTLA
+FWVGGLALCLFVGPVQSASRAFLGRLTTPRTAGEVFGLYATTGRAVGFITPALVTLALAL
+HPDNRVVIPVIAVVLVAGGLLFARVTEPITRSAESVR---------
+>1_1538
+-----------------MTDVALPPVASAAPRRQVAAWALWDWGSAAFNAVMVTFVFGTY
+LASDAFGPDERGTAWLSTAMAVAGVVIAVTAPVLGRRADGAGRRRRGLGLTTGAVIACTA
+ACFWVTPEESSLLLGVTLIALGAVFFEFAEVQVNAILVHISTPATIGRISGIGWGAGYLG
+GILLLLIVFVGFVSGDAHWFGVTEDEGLNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPS
+PGGGPRRESLAASYRALGSTLARMWREDRNTLWFLLSSAVFRDGVGAVFVYGAILGTTVY
+GLAASDVILFAIAANVVAALGAFVGGRLDDAVGPRRVILGSLAAMVLVAGALFFASGTLA
+FWVGGLALCLFVGPVQSASRAFLGRLTTPRTAGEVFGLYATTGRAVGFITPALVTLALAL
+HPDNRVVIPVIAVVLVAGGLLFARVTEPITRSAESVR---------
+>2_947
+-------MPGMDPAASAVPDAALPRLATAAPRRQVVAWALWDWGSAAFNAVMVTFVFGTY
+LASDAFGPDERGTAWLSTALAVAGVVIALTAPVMGRRADGAGRRRLWLGVMTAAVIACTT
+ACFLVTPQESSLLLGVTMIALGTVFFEFAEVQVNAILVQISTPATIGRISGIGWGAGYLG
+GILLLLIVFVGFVSGDAHWFGITGDEALNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPT
+PGGGPRRESLAASYRALGSTLARMWRQDRNTLWFLVSSAVFRDGVGAVFVYGAILGTTVY
+GLAASDVILFAIVANVVAAAGAFAGGRLDDAIGPRRVILGSLAAMVLVAAGLALASGTLA
+FWIGGLALCLFVGPVQSASRAFLGRLTTERTAGEVFGLYATTGRAVGFITPMLVTLALAA
+VPDNRVVIPVIVLVLIVGGVLFARVTDPVTRSAEPAP---------
+>3_886
+MPRMSSPAPHAAPQPCPAPHGGAGPAPARVPRGRVVAWAAWDWGSAAFNAVMVTFVFGTY
+LASDAFGPDDRGTQWLSAANALAGVVIALTAPALGRLADGTGRRRLWIALTTGAVIACTA
+ACFLVTPEESMLGLGVTLIALGTVFFEIASVHINAILLQISTPATIGRVSGFGWGAGYLG
+GIVLLLIVFVGFVSGDDHWFGVGEERALNIRVVALVAAAWFLVFALPVLAASPEPPAARG
+ADGSPRRESLVESYRGLGRTLARMWRQDRLTLRFLAASAVFRDGVGAVFVYGAILGTTLY
+GLAAQDVVLFAIVANVVAALGAFAGGRLDDALGPRRVILGSLAAMVVVAAALVLAEGTAA
+FWAGGLALCLFVGPVQSASRAFLGRLTVPETAGEAYGLYATTGRAIGFITPALVSAALAV
+WGDSRVIIPVIALVLLAGGALLLGVREPEGPTVAGARPGTGPRAAR
+>4_1752
+-----------------MTDVALPPVASAAPRRQVAAWALWDWGSAAFNAVMVTFVFGTY
+LASDAFGPDERGTAWLSTAMAVAGVVIAVTAPVLGRRADGAGRRRRGLALTTGAVIACTA
+ACFWVTPEESSLLLGVTLIALGTVFFEFAEVQVNAILVHISTPATIGRISGIGWGAGYLG
+GILLLLIVFVGFVSGDAHWFGVTEDAALNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPA
+ADGGPRRESVLGSYRELGATLARMWREDRNTLWFLVASAVFRDGVGAVFVYGAILGTTVY
+GLATSDVILFAIAANVVAALGAFVGGRLDDAVGPRRVILGSLAAMVLVAGALFFASGTLA
+FWVGGLALCLFVGPVQSASRAFLGRLTTPRTAGEVFGLYATTGRAVGFITPALVTLALAL
+HPDNRVVIPVIAVVLVAGGLLFARVTEPITRSAESVR---------
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001532.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001532.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ef26756cdbb074d3359ec0c0d99c2c793a06998
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001532.fa
@@ -0,0 +1,36 @@
+>0_1836
+MTQVLSGFAVVWVIILVGVLVGRTGVLGEHGRTVLSRAAFFIGNPALLFVTLSRADVGAV
+LGPQLWVATLSAFTAAALYLAVTVPLLKGRSASERIMSALSASLVNSANLGIPIAAYVLG
+DAALAAPALIFQLAIYTPLYVAAMDAATAREARRRTT---------AGRRRAVRRSPGRA
+VADQVRHTVTNPLILGSVAGLVFSLTGWSLQGPLMESVELIGGLSIPAMLLAFGMSLVGS
+RPLERAGGRRADVLLASAVKLVVHPLLAWLLAQFVFGLDARHVFVAVVLASLPTAQNVFV
+TAVRYDTGLRVSKDTILVTTIVAIPAMIAVALLLA
+>1_1543
+MTQVLSGFAVVWVIILVGVLVGRTGVLGEHGRTVLSRAAFFIGNPALLFVTLSRADVGAV
+LGPQLWVATLSAFTAAALYLAVTVPLLKGRSASERIMSALSASLVNSANLGIPIAAYVLG
+DAALAAPALIFQLAIYTPLYVAAMDAATAREVRRRTT---------AGRRRAVRRSPGRA
+VADQVRHTVTNPLILGSVAGLVFSLTGWSLPGPLMESVELIGGLSIPAMLLAFGMSLVGS
+RPLERAGGRRADVLLASAVKLVVHPLLAWLLAQFVFGLDARHVFVAVVLASLPTAQNVFV
+TAVRYDTGLRVSKDTILVTTIVAIPAMIAVALLLA
+>2_942
+MTQVLSGFVVVWVIIAVGFLVGRSGVLGEDARTVLSRTAFYIGSPALLFVTLSGADVAAV
+LGPQLWVATLSALAAAALFLAISIPVFKQRPASERIMAALSASMVNSANLGIPIAAYVLG
+DAALAAPVLIFQLAIYTPLYVAAMDVATTSEARARA----------AGGRPAVRRSRGQA
+LAAQLRQTGTNPMILGSAAGLLFSLNDWTLPGPLMQSVELIGGLSIPAMLLAFGMSLVGS
+RPLERAGGRRADVLLASGVKLLVHPLIAWVLAQFVLGLDAREVFVAVVLASLPTAQNVFV
+SAVRYDAGLRVAKDTILITTIVAIPAMIAVALLLA
+>3_882
+MIEVLSGFSVVWVIILVGLLLGRTGVLGDEAREVLSRTAFFVGNPALLFVTLSRADVGAV
+LGPQLWVACLSAFAAAVVFLGLSIPLLKGRPASERVMSGLSASLVNSANLGIPIATYVLG
+DAALAAPALIFQLAIYTPVYVAVMDWATTHEAAARASSAGAAHDAGAPAPRTVR--PRNP
+VLAQLRQTATNPMILGAFGGLLLSFTGWTLPGPLMTSVELIGGLSIPAMLIAFGMSLAGS
+RPLARDSGRRADVLLASAVKLVVHPLVAWMIAQFVFGLDARRVFVAVVLASLPTAQNVYV
+SAVRYRAGETVSKDTILVTTIVAIPAMIAVALLLA
+>4_1757
+MTQVLSGFAVVWVIILVGVLVGRTGVLGEHGRTVLSRAAFFIGNPALLFVTLSRADVGAV
+LGPQLWVATLSAFTAAALYLAVTVPLLKGRSASERIMSALSASLVNSANLGIPIAAYVLG
+DAALAAPALIFQLAIYTPLYVAAMDAATAREARRRTT---------AGRRRAVRRSPGRA
+VADQVRHTVTNPLILGSVAGLVFSLTGWSLQGPLMESVELIGGLSIPAMLLAFGMSLVGS
+RPLERAGGRRADVLLASAVKLVVHPLLAWLLAQFVFGLDARHVFVAVVLASLPTAQNVFV
+TAVRYDTGLRVSKDTILVTTIVAIPAMIAVALLLA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001543.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001543.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f2305c1598fa9971d59cb3042d2339aaafd8370
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001543.fa
@@ -0,0 +1,11 @@
+>0_1849
+MAKDKDVRPIIKLKSTAGTGFTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER
+>1_1556
+MAKDKDVRPIIKLKSTAGTGFTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER
+>2_929
+MAKDKDVRPIIKLKSTAGTGYTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER
+>3_870
+MAKDKDVRPIIKLKSTAGTGYTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER
+>4_1770
+MAKDKDVRPIIKLKSTAGTGFTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001546.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001546.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e37a063d53deaa8db093a0699c44c459266e8d5e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001546.fa
@@ -0,0 +1,41 @@
+>0_1858
+MENQQTGQAADRGTIDTREGFTGNYVQSGAEFTRDTNYIADRIVADPEAVRALPVAEPST
+VGRVGGGLTEGAEAWPVEEGRYRLVAARACPWANRTIIVRRLLGLEDAISLGTPGPTHDE
+RSWTFDLDEGGKDPVLGTERIQENYFTRFPDYPRGITVPAIVDVPTGGVVTNDYPQITLD
+LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIERVFTEVNNGVYRCGFAGSQEAYDAAYER
+LWTAMDWLEERLTTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNRLTEMSALWG
+YARDLFQTPGFGDTIDFAQIKEHYYVVHEDINPTGIVPAGPELASWLSEHGREAFGGDPW
+GGGTAPGPVREGERVDPEHTPLR
+>1_1565
+MENQQTGQAADRGTIDTREGFTGNYVQSGAEFTRDTNYIADRIVADPEAVRALPVAEPST
+VGRVGGGLTEGAEAWPVEAGRYRLVAARACPWANRTIIVRRLLGLEDAISLGTPGPTHDE
+RSWTFDLDEGGKDPVLGTERIQENYFTRFPDYPRGITVPAIVDVPTGGVVTNDYPQITLD
+LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIERVFTEVNNGVYRCGFAGSQEAYDAAYER
+LWTAMDWLEERLSTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNRLTEMPALWG
+YARDLFQTPGFGDTIDFAQIKEHYYVVHEDINPTGIVPAGPELASWLSEHGREAFGGDPW
+GGGTAPGPVREGERVDPEHTPLR
+>2_922
+MENQQTGQAADRGTIDTREGLKGNYVQSGAEFTRDTNYITDRIVADPEAVRALPVAEPST
+VGRVGGGLTEGAEAWPVEAGRYRLVAARACPWANRAIIVRRLLGLEDAISLGTPGPTHDE
+RSWTFDLDEGGKDPVLGTERLQENYFARFPDYPRGITVPAVVDVPTGDVVTNDYPQMTLD
+LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIKRVFTEVNNGVYRCGFAGSQEAYDAAYDR
+LWTAMDWLEERLTTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNRLTEMPALWG
+YARDLFQTPGFGDTIDFAQIKEHYYVVHEDINPTGIVPAGPELASWLSEHGREAFGGDPW
+GGGTAPGPVREGEEVEPAHTPLR
+>3_858
+MEDQQTGQAADRGTIDTREALTGNYVQSGAEFTRDTDYIADRIVADPEAVRALPVAEPST
+VGRVGGGLTEGAEAWPVEAGRYRLVAARACPWANRTIIVRRLLGLEDAISLGTPGPTHDE
+RSWTFDLDAGGKDPVLGTERLQENYFTRFPDYPRGITVPAIVDVPTGGVVTNDYPQITLD
+LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIERVFTEVNNGVYRCGFAGSQEAYDAAYER
+LWAAMDWLEERLTTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNKLTEMPALWG
+YARDLFQTPGFGDTIDFAQIKEHYYVVHEDINPTGIVPAGPDLSGWTTEHGRADLGGDPW
+GGGTAPGPVRDDERVDPEHTPLR
+>4_1779
+MENQQTGQAADRGTIDSREGLKGNYVQSGAEFTRDTNYIADRIVADPEAVRALPVAEPST
+VGRVGGGLTEGAEAWPVEAGRYRLVAARACPWANRTIIVRRLLGLEDAISLGTPGPTHDE
+RSWTFDLDEGGKDPVLGTERIQENYFTRFPDYPRGITVPAIVDVPTGGVVTNDYPQITLD
+LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIERVFTEVNNGVYRCGFAGSQEAYDAAYER
+LWTAMDWLEERLTTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNKLTEMPALWG
+YARDLFQTPGFGDTIDFVQIKEHYYVVHEDINPTGIVPAGPELASWLSEHGREAFGGDPW
+GGGTAPGPVREGERVDPEHTPLR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001556.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001556.fa
new file mode 100644
index 0000000000000000000000000000000000000000..93f3833355ca37c082e5ad3e67db9b50ae8009a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001556.fa
@@ -0,0 +1,26 @@
+>0_1870
+-MHLIPRTIWVVARARRRPRAGLWEPTTLPMRALPTDVDMALHVNNGQYFGLFDLGRFDA
+MVRTGLWDEIRRRGWTPVVQAEQIAFRRSVTLGQRFDVETRMIGLDERAVWFEQRVVVDG
+DVAVRAYICTRLRKKDGRPVENDEVRAIAAAAGHDLAGEPTLPEWLHEWRRSVALPSART
+PLPHTWDLDTVRRG
+>1_1577
+-MHLIPRTIWVVARARRRPRAGLWEPTTLPMRALPTDVDMALHVNNGQYFGLFDLGRFDA
+MVRTGLWDEIRRRGWTPVVQAEQIAFRRSVTLGQRFDVETRMIGLDERAVWFEQRVVVDG
+DVAVRAYICTRLRKKDGRPVENDEVRAIAAAAGHDLAGEPTLPEWLHEWRRSVALPSART
+PLPHTWDLDTVRRG
+>2_908
+-MHLIPRTLWVLARARRRPPLSIWDSASLPMRALPTDVDIAGHVNNGQYFGLFDLGRFDL
+MARSGLMRAVRRRGWLPVVQAEQIAFRRSVTLGTAFTLETRIIGLDERAVWFEQRVVVAG
+DVAVRGYVCTRLRGRDGTPVGNDEVRALAVELGHDPAAEPELPGWLHDWREQVALPSART
+PLPHAWGR------
+>3_843
+MLHLLPRTALVVVRARRRPRLGIWEASTLPLRALPTDVDFAGHINNGQYFGLFDLGRFDL
+MVRAGVWDGAKRRGWLPVVQAEQIAFRRSVTLGTRFTVESRIIGLDERAVWFEQRAVVDG
+DVAVRAFICTRLRAKDGTPVSNEDVRDLARELGHDLAAEPVLPEWLHGWRSDIALPSART
+PLPHAWGTPAPAGV
+>4_1790
+-MHLIPRTIWVVARARRRPRAGLWEPTTLPMRALPTDVDMALHVNNGQYFGLFDLGRFDA
+MVRTGLWDEIRRRHWTPVVQAEQIAFRRSVTLGQRFDVETRMIGLDERAVWFEQRVVVDG
+DVAVRAYICTRLRKKDGRPVENDEVRAIAAAAGHDLAGEPTLPEWLHEWRRSVALPSART
+PLPHTWDLDTVRRG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001557.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001557.fa
new file mode 100644
index 0000000000000000000000000000000000000000..188a8be00c8ca7487a8f9bdcc118aaa11122acca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001557.fa
@@ -0,0 +1,41 @@
+>0_1872
+MAA-VDPAPTDARERRDLVVPVPGPEDPPERAWLVLPHRHPVPTLLEETRDAVVGLAETL
+AAVLPVTVLAHPRDAGAARLVPPEVDLLRAPVGSPLLGRTGPSFVRRP---EGLAAVAWR
+SAAGLTGTGPLDGAAATAVAEAAGLPLLTPLLCAPRGAWVSDGEGTAVVAADPVLDGRIN
+GAWTPGQVAAEFAALLGITRVLWVPPAPRPDTGPWGGPG----HLASWVRLQGDGEAAVH
+WRGDRFNPEHPYAAAALRFLQGADDAAGRPLRVRTVTGAAQPAEYDPAERGPRSLLDTLP
+LG-AAVLRPAFEDAAGEEAAAAACAALHPGRPQLSFPAPPLLRLAGALNDLVLLQP----
+----------------RP
+>1_1579
+MAA-VDPAPTDARERRDVVVPVPGPEDPPERAWLVLPHRHPVPTLLDETRDAVVGLAETL
+AAVLPVTVLAHPRDAGAARLVPPEVDLLRAPVGSPLLGRTGPSFIRRP---EGLAAVAWR
+SAAGLTGTGPLDGAAATAVAEAAGLPLLTPLLCAPRGAWVSDGEGTAVVAADPVLDGRIN
+GAWTPGQVAAEFAALLGITRVLWVPPAPRPGTGPWGGPG----HLASWVRLRGDGEAAVH
+WRGDRFHPEHPYAAAALRFLQGADDAAGRPLRVRTVTGAAQPAAYDPAERGPRSLLDTLP
+LG-AAVLRPAFEDAAGEEAAAAACAALHPGLPQLSFPAPPLLRLAGALNDLVLLQP----
+----------------RP
+>2_907
+MPA-AETVPADAAGRPDARPRVPGPREQPERAWLALPRRHPVPALLDEARDAVAGLAETL
+AEVLPVTVLTDPADHAVRSLIPPEVDLLAAPVDSPLLGRTGPGFVRRP---EGLAAIAWR
+PAAGAGGPGPRDAGVAAAVAAAAGLPLLTPMLRAPRDAWVADGEGTAVVAADPVLDGRTN
+PAWTPEQVEAEFAALLGITRVAWLPPVPRIPTGPWGGAG----HLGAWVRLLGGGEAAVH
+WRADRFHPEHLHGAAALRILQDAPDAAGRPLRVRTVPGGALPPEHDPAEIGPRSLVDTVP
+LG-SAVLRPAFEDAATEEAAAAACAALHPGLRPVPFPGPPLLRLAGSLSDLVLVQP----
+----------------HP
+>3_842
+MSTPAVPEP----------PRAPAPWEVPERLWLALPAVHPVPGLLAEARDAVAGLAETL
+GAHAPVAVLTDPDDADAARLLPGVVERVPVRGASPLPGREGPTFVHAAGTRGSVEAVHWR
+LPSDAAGTAGRAAATADAVARSAGLPLRTPLFSAPAGTWAADGDGTAVVSA-ALLDPAVN
+EGWTRAQAEDALAGLLGAERVLWLPPVAGHAAGPWDGGGAAQPHPHPWLRFVAPGEVAVH
+WQPGRLHPDHAASAAALHALTGARDARGRALSVRTVRALPPGPDADLEARGPLSALDLLP
+LAPGVVLRPAHADPEADAATAEAAAALFPGAEQVPFPGPPLLRLLGTLSDLVLPQPPGAR
+TRRPSPAPAHPEGPRAAP
+>4_1792
+MAA-ADPVPTDARERRDVVVPVPGPEDPPERAWLVLPHRHPVPTLLDETRDAVVGLAETL
+AAVLPVTVLAHPRDAGAARLVPPEVDLLRAPVGSPLLGRTGPSFIRRP---EGLAAVAWR
+SAAGLTGTGPLDGAAATAVAEAAGLPLLTPLLCAPRGAWVTDGEGTAVVAADPVLDGRIN
+GAWTPGQVAAEFAALLGITRVLWVPPAPRPGTGPWGGPG----HLASWVRLRGDGEAAVH
+WRGDRFHPEHPYAAAALRFLQGADDAAGRPLRVRTVTGAVQPAEYDPAERGPRSLLDTLP
+LG-AAVLRPAFEDAAGEEAAAAACAALHPGLAQLSFPAPPLLRLAGALNDLVLLQP----
+----------------RP
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001558.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001558.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e9907dff7cefaaef5c6596c96cbfe89fe7ca4e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001558.fa
@@ -0,0 +1,51 @@
+>0_1873
+MSAAQPAGVTPPPASSSPASDWDIRRPHRMWPRMLVIVLTLAGLVLVVQFFQGIASIAAP
+VFLGLNLVIVAYPLQAWLIRRGLHPVLGAATTVLLVVAVMAVFGGMMVWSGLELVAELPK
+YADRFQQIVLDVSHWLNERGVTPDMVSQQLASIDMSAVTGTAVSAITKIATNVYAVFGLL
+VTVIMGMFFLAMDSMDVERRVRLLSTARHEFGHALVEFAQGVRRYWVVTTVFGLIVAVLD
+VIALMLIGVPLALVWGVLSFLTNYIPNIGFIIGLLPPAVLGLAAGGWSDFLWVVVSYSVL
+NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN
+ARWINALIASDLKGMERRQSSLLERLR-------------PAAWRSDAHGKDEDRAPTDG
+GDDDGPATDEVTG--GAGA-----------------------------------------
+-APGR
+>1_1580
+MSAAQPAGVTPPSASSSPASDWDIRRPHRMWPRMLVIVLTLAGLVLVVQFFQGIASIAAP
+VFLGLNLVIVAYPLQAWLIRRGLHPVLGAATTVLLVVAVMAVFGGMMVWSGLELVAELPK
+YADRFQQIVLDVSHWLNERGVTPDMVSQQLASIDMSAVTGTAVSAITKIATNVYAVFGLL
+VTVIMGMFFLAMDSMDVERRVRLLSTARHEFGHALVEFAQGVRRYWVVTTVFGLIVAVLD
+VIALMLIGVPLALVWGVLSFLTNYIPNIGFIIGLLPPAILGLAAGGWSDFLWVVVSYSVL
+NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN
+ARWINALIASDLKGMERRQSSLLERLR-------------PAAWRSDAHGGDEDRASADG
+GDDDGPATDEVTG--EAGA-----------------------------------------
+-APGR
+>2_906
+MSAAQPVGAAPTPSAAGPVSDWDIRRPHRMWPRMLVIVLTLAGLVLLVQFFQGIASIAAP
+VFLGLNLVIVAYPLQAWLIRRGVHPVLGAAASVVVVVAVLGAFVGMIVWSGLELVAELPK
+YSGQFQQIVLDVSNWLNARGVTPDMVSQQLASIDVSAVTSAAVSALTKIATNLYAVLGLL
+VTVVMGMFFLAMDSMDVERRVRLLSTARLELGEALIDFAHGVRRYWVVTTVFGLIVAALD
+VIALVLIGVPLALVWGVLSFLTNYIPNVGFIIGLIPPAILGLAAGGWTSFLWVVVSYSVL
+NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN
+SRWVNSLIASDLKGMERRQHSLLERLR--------------VGRRGEGRAGKADAEAVAG
+ADVAAAGVEAALDVDDAAAGARRPEAAPTGSTLTEPARTEPGPAAPADAADGPGLTGGAA
+PAPGR
+>3_841
+MSASAPPAVT---GTSTPATEWDNRRPHRMWPRMLVIVLTLAGLVVLVQFFQGIASIAAP
+VFLGLNLVIVAYPLQAWLIRRGLHPVLGAATTVVVVCAVIAAFLGMIAWSGMELLTELPK
+YAGQFQQIMHDASQWLSDHGVTPDMVNQQLASVDMSAVTGAAVSALTTIASNLYAVLGLL
+ITVIMGMFFLAMDSMAVERRVRLLSTARHELGQALIDFADGVRRYWIVTTVFGLIVAVLD
+MVALVIIGVPLALVWGVLSFLTNYIPNVGFIIGLVPPAILGLAAGGWPAFLWVVVSYSVL
+NFVLQSIIQPKVAGDAVGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLVKAVLIDADPN
+SRWVNSLIASDLKGMERRQSSMLERLRLPRELIRHGGSTASHATAADVQ-GDDDVAPERT
+AEDAAPAQDRRRV--RAAAQEARLEGPPP-STLRAPRVDLPGEPEPATADGSAPPEAGA-
+-APGR
+>4_1793
+MSAAQPAGVTPPPASSSPASDWDIRRPHRMWPRMLVIVLTLAGLVLVVQFFQGIASIAAP
+VFLGLNLVIVAYPLQAWLIRRGLHPVLGAATTVLLVVAVMAVFGGMMVWSGLELVAELPK
+YADRFQQIVLDVSHWLNERGVTPDMVSQQLASIDMSTVTGTAVSAITKIATNVYAVFGLL
+VTVIMGMFFLAMDSMDVERRVRLLSTARHEFGHALVEFAQGVRRYWVVTTVFGLIVAVLD
+VIALMLIGVPLALVWGVLSFLTNYIPNIGFIIGLLPPAVLGLAAGGWSDFLWVVVSYSVL
+NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN
+ARWINALIASDLKGMERRQSSLLERLR-------------PAAWRSDAHGGDEDRASADG
+GDDEGPAADEVTG--EAGA-----------------------------------------
+-APGR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001559.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001559.fa
new file mode 100644
index 0000000000000000000000000000000000000000..01d4cd3901f3795c4e1e94334060797e33406e63
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001559.fa
@@ -0,0 +1,41 @@
+>0_1874
+MSRTPHR---------ALAALSVAALALTGCSVS----GSSGDGASSSAA----------
+-----GA-GGEPTTVTIMTHDSFNLPQELVQKFEQESGYTLKTTAPGDAGSVVNQLLLAK
+DEPTVDGVYGVEDHSAHRLVREGVVAEYTPQDLPASAQDRMVEDRMTPVDQGQVCFNTDP
+AWFEAHDVEAPTSIDQLDDPEYAKLTVATSPVASSPGLALLAATTEKYGDDGWQDWWRGL
+KENGGKVADSWSDAYNSDFSGGEGKGRFPVVLSYSSSPAFAPETEVIEDSCTPQVEYAGV
+LEGAKNPEGAQAFVDFMLTEEVQSALPESMYMYPIDESVQLPEEWAQNAPLVEDAITPDP
+ARIDERREDLLKEWTALAEASRR-
+>1_1581
+MSRTPHR---------ALAALSVAALALTGCSVS----GSSGDGASSSAS----------
+-----GAGGGEPTTVTIMTHDSFNLPQELVQKFEQESGYTLKTTAPGDAGSVVNQLLLAK
+DEPTVDGVYGVEDHSAHRLVREGVVAEYTPQDLPASAQDRMVEDRMTPVDQGQVCFNTDP
+AWFEAHDVEAPTSIDQLDDPEYAKLTVATSPVASSPGLALLAATTEKYGDDGWQDWWRGL
+MENGGKVADSWSDAYNSDFSGGEGKGRFPVVLSYSSSPAFAPETEVIEDSCTPQVEYAGV
+LEGAKNPEGAQAFVDFMLTEEVQSALPESMYMYPIDESVQLPEEWAQNAPLVEDAITPDP
+ARIDERREDLLKEWTALAEASRR-
+>2_905
+MTTAPHRVRTRPRRHGALAALSVAALALTGCSVA--DRGGSGDQGSSSA-----------
+----------EARTVTIMTHDSFSLPDELIARFEQESGHTLVTTAPGDAGSVVNQLLLAK
+DAPTVDGVYGIEDHSAHRLVSEGVIAEHVPADLPDSARDLVVDGRMTPVDQGQVCLNVDT
+PWFQEQGLAAPTTLEQVAAPEYAELTVVTSPVSSSPGLALLAATVAEFGEDGWQDWWRTA
+LQGGMQVDASWSDAYNTSFSGGEGTGTRPIVLSYSSSPAFAPDTDVVAASCTPQVEYAGV
+VEGAENPEGARAFVDFLLTEDVQAAIPDAMYMYPVDSSVPLPEAWAEHAPLVEDPIVPDA
+GLLDSRREDLLKEWTALHEEAAS-
+>3_840
+MSV--HR--TATTRRGVLAAACLSALALTGCSVSAPSTGSSSSAASSSAAPSSASGSSST
+SASGTAA-AGSKGTVTIMTHDSFALPKELIAQFEAESGYRLVTTAPGDAGAVVSQVLLSK
+DAPVADGVYGVENHSAHRLVDQGAVQDVAPADLPASAEDLVVDGKMIPVDQGQVCFNTDP
+AWFTEHGVAEPTSIDQLRDPEYAKLTAVTSPVTSSPGLALLAATTEKYGDDGWQGWWEDL
+LKGGAKVDSTWSDAYSTDFSGGEGKGEFPVVLSYSSSPAFAPQTAVIEDSCTPQVEYAGV
+LTGAENPEGAKAFVEFLLSKDVQAAIPENMYMYPVDDTVELPAEWAANGPLVEDPITPDP
+AEIDTEREGLLKEWTALSESAGSR
+>4_1794
+MSRTPHR---------ALAALSVAALALTGCSVS----GSSGDGASSSAA----------
+-----GA-GGEPTTVTIMTHDSFNLPQELVQKFEQESGYTLKTTAPGDAGSVVNQLLLAK
+DEPTVDGVYGVEDHSAHRLVREGVVAEYTPQDLPASAQDRMVEDRMTPVDQGQVCFNTDP
+AWFEAHDVEAPTSIDQLDDPEYAKLTVATSPVASSPGLALLAATTEKYGDDGWQDWWQGL
+MENGGKIADSWSDAYNSDFSGGEGKGQFPVVLSYSSSPAFAPETEVIEDSCTPQVEYAGV
+LEGAKNPEGAQAFVDFLLTEEVQSALPESMYMYPIDESVQLPEEWAQNAPLVEDAITPDP
+ARIDERREDLLKEWTALAEASRR-
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001562.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001562.fa
new file mode 100644
index 0000000000000000000000000000000000000000..69ffe5f1662fd7518030124fb00697094415aebf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001562.fa
@@ -0,0 +1,21 @@
+>0_1877
+M-TPP---APRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAGVLGVQASALYWHVPDKQS
+LLARVADRIVAEAEETVRARRVTDLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLH
+RLLTEAADTPEDGERALALLLGTVSLRQQRAQAQALGVATGPDVQRHRTDPL
+>1_1584
+M-TPP---APRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAAVLGVQASALYWHVPDKQS
+LLARVADRIVAEAEETVRARRITDLAGRAEAAEAALLRHRDGADLVLSALALGLGGLGLH
+RLLTEAADTPEDGERALALLLGTVSLRQQRAQAQALGVPTGPDVQRHRTDPL
+>2_902
+MSSPPRAGSSRGRLSATDVVDAAVGILQDFGMGDLSMRRVASVLGVQASALYWHVPDKQT
+LLARVADRIVAEAEEAVRHRGIADLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLH
+ALLTEAAPTPEEGERALALLLGGVSLRQQRAQAEALGVRVGPDVQRHRTDPL
+>3_837
+M-STS---SARGRLSAEDVVDAAVGILQDFGMGDLSMRRVASMLGVQASALYWHVPDKQT
+LLARVADRIVADVERACAARRVEDLAGRAEEAEAVLLRHRDGADVVLSALALGLGGLGLH
+RLLVDAAHTPEEGERALAALLGTAALRQQRNQAAALGLRLGPDVQARRTGAL
+>4_1797
+M-TPP---APRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAGVLGVQASALYWHVPDKQS
+LLARVADRIVAEAEETVRARRVTDLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLH
+RLLTEAADTPEDGERALALLLGTVSLRQQRAQAQALGVATGPDVQRHRTDPL
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001563.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001563.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0b134fd30747bb32959f2dfb6420cdf6ef50c896
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001563.fa
@@ -0,0 +1,40 @@
+>0_1878
+MGARINHPRTVVDRTLHHDVEPAHPAALVDVGWDFRGPGA----------------KAEEQHRPLRVVRARR-------P
+RGTP-RDRNGV----------------DLTRTGPVVPRPSPPRTRIRRDGVRVVASPLAMLPGVDHGPALRLDLHPTTGG
+IVYVARELELRELGDDVRGHVYTGMVGTAHLSVFWSTVTVDLPPERPVIVRLRSDRDAELLSLLEVLAPVDTRVVSYRLD
+ESPVGTQRSSYLLPDVDPETVAQTGAARIPLEAIEAAQEEEDALRRSSGVFLSRRRTDRFLRRNLPGVTHSLTFADEADV
+TDVYVDGSVLRGSRIGGAAAVAGPSMWAVQAVAGATMPLEVELEALVLGHVICAWAGTPGGRVTIHSDSRAALALLNAAR
+RERLTLGGARGERIRRTLRRLLAAVDLAQAADVQVDTTWVKGHVGVHGNELADDLARAAARHASVGTPEGDLPERMGQLI
+QLRVEDDAAG--------------------------
+>1_1585
+MGARINHPRTVVDRTLHHDVEPAHPAALVDVGWEFRGPGA----------------KAEEQHRPLRVVRARR-------P
+RGTP-RDRNGV----------------DLTRTGPVVPRPSPPRTRIRRDGVRVVASPLAMLPGVDHGPALRLDLHPTTGG
+IVYVARELELRELGDDVRGHVYTGMVGTAHLSAFWSTVTVDLPPERPVIVRLGSDRDAELLSLLEVLAPVDTRVVSYRLD
+ESPVGTQRSSYLLPDVDPETVAQTGAARIPLEAIEAAQEEEDALRRSSGVFLSRRRTDRFLRRNLPGVTHSLTFADEADV
+TDVYVDGSVLRGSRIGGAAAVAGPSMWAVQAVAGATMPLEVELEALVLGHVICAWAGTPGGRVTIHSDSRAALALLNAAR
+RERLTLGGARGERIRRTLRRLLAAVDLAQAADVQVDTTWVKGHVGVHGNELADDLARAAARHASVGTPEGDLPERMGQLI
+RLRVEDDAAAG-------------------------
+>2_901
+--------------------------------------------------------------------------------
+--------------------------------------------------MRVVAAPLAMLPGVDHGPALRMDLHPVPGG
+IVYVARDLVLRELGDDVRGHVHAGMVGTAQLHAFWSTVTVDLPPDRPVIVRLRSDRDAELLSLLEVLAPVEMRVVSYRLD
+ESPVGTQRSSYLLPDVDPEIVARAESPRVPLEAIEATQEEEDALRRSSGVFLSRRRTDRFLRRTLPTVTHSLSFSDEADV
+ADVYVDGSVLRSSRIGGAAAVGGPSMWAVQAVNGATTPLEVELEALVLGHVVSAWAGVPGERVTIHSDSRAALALLNAAR
+RERLTLGGARGERVRRTLRRLLAAVDLAQAADVRVETTWVKGHVGVQGNELADDLARAAARHAGVGTSEEDLRRRLDRLI
+DLHEEAEAEAGQTPARAVAAEGHRPMPPGRRPGPRL
+>3_836
+MDNSSTHPREGQVRSLHFDTDASSPDALLDPMWAFTGPRASRAGAPAPDGADVLARRARPAHPGAALVRAATSLFTLPGP
+PGMPHRSRSAALEAARAPAGYLSPVPHRLALPRPARPRPAPPRMRVRQDGVRVVARPLAMLPGVDHGRALRLDLHPVRDG
+IVFVSRHLELRELGDDVKGLVLTGVVPAARLGYFWDTVAGDLPEGRPVIVRLRSNDDAELLTLLRAIAPPWLRVVSYRLD
+ESPVGSQRSSYLLPDVDGEAVAASGAERVPLETLREAHQASAEVERASRVFLARRRVDRFVRRSVPDLMHSLSYTDPAEV
+RHVYVDGSVLRGTRTGGAAAVTRSGPWAAHALPGATIPLEAELEALTLGHLMAAWSGTPDERVLIHSDSRAALALLREAH
+RERLTLGDARGERIRRALRRLLAAVDLAGSAGVEVSTLWVKGHAGTHGNELADDLARSAARNTAAGVSADEMRRRMRHVV
+QLW---DATTH----------------------PQA
+>4_1798
+MGARINHPRTVVDRTLHHDVEPAHPAALVDVGWDFRGPGA----------------KAEEQHRPLRVVRARR-------P
+RGTP-RDRNGV----------------DLTRTGPVVPRPSPPRTRIRRDGVRVVASPLAMLPGVDHGPALRLDLHPTTGG
+IVYVARELELRELGDDVRGHVYTGMVGTAHLSVFWSTVTVDLPPERPVIVRLRSDRDAELLSLLEVLAPVDTRVVSYRLD
+ESPVGTQRSSYLLPDVDPETVAQTGAARIPLEAIEAAQEEEDALRRSSGVFLSRRRTDRFLRRNLPGVTHSLTFADEADV
+TDVYVDGSVLRGSRIGGAAAVAGPSMWAVQAVAGATMPLEVELEALVLGHVICAWAGTPGGRVTIHSDSRAALALLNAAR
+RERLTLGGARGERIRRTLRRLLAAVDLAQAADVQVDTTWVKGHVGVHGNELADDLARAAARHASVGTPEGDLPERMGQLI
+QLRVEDDAAG--------------------------
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001574.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001574.fa
new file mode 100644
index 0000000000000000000000000000000000000000..208fafccf5f2c79ae206eb5fbdc345a09b24164a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001574.fa
@@ -0,0 +1,41 @@
+>0_1909
+MKGIVDVDSQPQGRVLYVTVGAPEHGVVRHGRQTAAALQRVGAEVELLTAEDVAAFRGLV
+PLLEEARALGAAVHLDVTDALFGPTATAAADLLVDVLPAGTTLTLHDIPQPAEGDGRYRR
+RGEAYARLAQAVAGVVVSSQHERALLADLVDVAADVVPLPVQDRRAAAARAEPVVPESMA
+GLDQDLVLFGFVYPGKGHALALEALTELHRQWGPDSGAPRRLTALGPVSAGHDDLVAELT
+RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRAIASAGR
+YTEEMERLRPGTLRLVHPNGS-PAFAMAEAIAEAVEDPERTWLDPAVDLSPGAEGCARML
+FDVLRRVHRWT---
+>1_1614
+MKGIVDVDSQPQGRVLYVTVGAPEHGVVRHGRQTAAALRRVGAEVELLTAEDVAAFRGLV
+PVLEEARALGAAVHLDVTDALFGPTATAAADLLVDVLPEGTTLTLHDIPQPAEGDGRYRR
+RGEAYARLAQAVDGVVVSSQHERALLADLVDVAADVVPLPVEDRRAAAARAEPVVPESMA
+GLDRDLVLFGFVYPGKGHALALEALTELHRQWGPDSGAPRRLTALGPVSAGHDDLVAELT
+RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRAIASAGR
+YTEEMERLRPGTLRLVHPNGS-PAFAMAEAIAEAVEDPERTWLGPGVDLSPGAEDCARML
+FDVLRRVHRWT---
+>2_870
+------MESQPQGRVLYVIVGPPEHGVVRHARQTAAALRRVGAEVELLTAEDVAAFHGLV
+PLMAEARSLGAAVHLDVTDALFGPTAAAAADLLVDVLPEGTTLTLHDIPQPAEGDGRYRR
+RGEAYARLARHAAGVVVSSQHERALLAELVDADADVVPLPVEDRRAEAARAESVVPENMA
+GLDQDVVLFGFVYPGKGHALALEALTELHRQWGPNSGAPRRLTALGPVSAGHDDLVAELT
+RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRAIASAGR
+YTEEMERLRPGTLRLVHPNGS-PAFAMAEAIAEAVEDPEHTWLDPAVDLSPGAEDCARML
+FDVLRRVHRWT---
+>3_812
+------MTSHAQGRVLYLSVGSRGHGVVHHGLLTAEELAQVGLDVESLHTEDATGFVGLA
+PVLARAREARRAVHVDVTDSLFGPSPAAAADTLSRILPDGATVTLHDVPQPAEGEARFLE
+RAEAYVRIAQAAAGVVVSSEHERALLHAIVDVDAHVVPLPVEDRR--AAREAVRLPEALE
+GLDRDVVIFGHLYPGKGHAEAIDALAELDRQWGPSPHRPRRVTALGAVAARHEFLVDELT
+ARAEVSGLQFRVTGFVPDEVLDPALRAAAVPLAAHHNVSASGSLASWMSVGRRPIVPAGR
+YTQEMARLRPGTLRIVQVGTSGPEYALAEAVAEAVEEPSRTWQARGTSLAPGPRACARML
+AAALADVHGWAWPR
+>4_1836
+MKGIVDVDSQPQGRVLYVTVGAPEHGVVRHGRQTAAALRRVGAEVELLTAEDVAAFRGLV
+PVLEEARALGAAVHLDVTDALFGPTATAAADLLVDVLPEGTTLTLHDIPQPAEGDGRYRR
+RGEAYARLAQAVDGVVVSSQHERALLADLVDVAADVVPLPVEDRRAAAARAEPVVPESMA
+GLDRDLVLFGFVYPGKGHALALEALTELHRQWGPDSGAPRRLTALGPVSIGHDDLVAELT
+RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRTIASAGR
+YTEEMERLRPGTLRLVHPNGS-PAFAMAEAIAEAVEDPERTWLDPAVDLSPGAEDCARML
+FDVLRRVHRWT---
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001575.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001575.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b3ef0e955a2e532b6d239a44997087c5568ba341
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001575.fa
@@ -0,0 +1,50 @@
+>0_1910
+MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPGAPAHQWWPPRALHAEWLAEHRPDVLHVHFGFEHFSPAQLAA
+ALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGRADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVAQ
+GDDDAPGAEPGLLPPDASDDGD--GAAAPARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQDTVQDED
+ALAALRAGCAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAVADIGHIADQSGAWLTPDS
+LAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVAAAHVAVYREALARARGALPGVSVLVITGHRDEHLARVI
+AGLERSHRRPDQVVVVFMGQPDGRVPATDLPVTVGHVAAEAGLPLAQARNRAAELATGEILVFLDVDCIPAAETVGVLAT
+EVAAHPGSVVMGRPRYLRPGWTRDVGE--ADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHLVWTLILALRRADLARI
+GGFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMTPPLHHLEDILVNARRFRQVHGRWAMEGWLRAFADAG
+LIAWDPEGERLELLRHPTEAELTAARRDDAAY
+>1_1615
+MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPDAPAHQWWPPRALHAEWLAEHRPDVLHVHFGFEHFSPAQLAA
+ALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGRADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVAQ
+GDDDAPGL----LPPDASDDGD--GAPVPARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQDTVQDED
+ALAALRAGCAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAVADIGHIADQSGAWLSPDS
+LAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVAAAHVAVYREALARARGALPSVSVLVITGHRDEHLARVI
+AGLERSHRRPDQVVVVFMGQPDGRVPATDLPVTVGHVAADAGLPLAQARNRAAELAIGEILVFLDVDCIPAAETVGVLAT
+EVAAHPGSVVMGRPRYLRPGWTRDVGE--ADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHLVWTLILALRRADLARI
+GCFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMTPPLHHLEDILVNARRFRQVHGRWAMEGWLRAFADAG
+LIAWDPEGERLELLRHPTEAELTAARRDDAAY
+>2_869
+MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPGAPAHQWWPPRALHAEWLAEHRPDVLHVHFGFEHFNPAQLAA
+ALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGRADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVSQ
+GDDDAPGL----LPPDASD--D--GAAAPARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQATVQDED
+ALAALRAGCAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAVADIGHIADQSGAWLAPDS
+LAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVAAAHVAVYREALARARGALPSVSVLVITGHRDEHLARVI
+AGLERSHRRPDQVVVVFMGQPDGRVPATGLPVTVGHVAAEAGLPLAQARNRAAELATGEILVFLDVDCIPAAETVGVLAT
+EVAAHPGSVVMGRPRYLRPGWTRAVEE--ADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHLVWTLILALRRADLARI
+GGFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMTPPLHHLEDILVNARRFRQVHGRWAMEGWLRAFADAG
+LIAWDPEGERLELLRTPTADELAVARRDDAAY
+>3_811
+MSLTVQHVPAGHPYARSVRPLDGAAAPDVEFWPDPPVPGAAEGVWWPPRALDPAWIAEHRPDVLHVHFGFEHFTPEQLRA
+ALDAQHAHGGAVVVTVHDLQNPHLQDQDPHRARLRVLLDAADAVITLTPGAAAAVEAASGRAPLVLPHPHVVPLDA----
+------------LPDDGAADGERPGVDRPARLLMHAKDLRAQVDPVGLLPVLAAARDALAARGLAVEVTVDVQDGVRDEA
+ALAELEAGAEAHGFALWRHARLDDAELHAALRDADVSVLPYRVGTHSGWVEMCRDLGVPVAVAEVGHIADQARAWTTPEL
+LAAFDPDDPASLADALAALLTAAPDARAAAPAARAAQRRRVAAAHVAVYRQALAVRRGTAATVSVLVITGHRDAHLARVL
+AGLERSHRRPDQVVVVFMGQPDGAVPATDLPVTVGHVAADHGLPLATARNRAAELATGEVLVFLDVDCIPAADTVGVLAA
+EVAAHPGSLVMGAPRYLAPDWTAALAAEGVDADAAPTDGDLRRHAVPHRARTHLRPGPSEEWALVWTLVMAIGAADLARI
+DGFDEGFAGYGAEDTDLAFRARDAGLTLRISPAEAFHQHHGVHRPPLHHVADIVVNARRFRTLHGTWPMGGWLAAFAERG
+LIRWDPDGDLLELVREPTPDDVAAARVDDAAY
+>4_1837
+MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPGAPAHQWWPPRALHAEWLAEHRPDVLHVHFGFEHFSPAQLAA
+ALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGRADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVAQ
+GDDDAPGA----LPPDASDDGD--GAAAPARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQDTVQDED
+ALAALRAGCAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAVADIGHIADQSGAWLSPDS
+LAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVAAAHVAVYREALARARGALPGVSVLVITGHRDEHLARVI
+AGLERSHRRPDQVVVVFMGQPDGRVPATDLPITVGHVSAEAGLPLAQARNRAAELATGEILVFLDVDCIPAAETVGVLAT
+EVAAHPGSVVMGRPRYLRPGWTRDVGE--ADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHLVWTLILALRRADLARI
+GGFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMVPPLHHLEDILVNARRFRQVHGRWAMEGWLRAFADAG
+LIAWDPEGERLELLRHPTEAELTAARRGDAAY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001581.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001581.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7045fa61be94991cd4d6e47e84ee6f10b0d8b547
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001581.fa
@@ -0,0 +1,31 @@
+>0_1919
+MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYMEDALPVVR
+NHVRTFMKADYDLAVAPSASCVASLGHQQPDVARSGGDEGLARDAEVVASRTLELSQLLT
+DVLGVTDAGAQLGSWFPHTVTYHPSCHGMRLLRLGSRQEDLLRTVADIDLRPLPDAEECC
+GFGGTFSLKNPDVSAAIAEEKIEKVTASGASLCTGGDASCLLHLDGAMHRREARGQDGRP
+LRTVHLAEILAATRENPLEVDGPVELSIPASAGARRGPSARVEEARR
+>1_1624
+MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYMEDALPVVR
+NHVRTFMKADYDLAVAPSASCVASLGHQQPDVARSGGDEGLARDAEVVASRTLELSQLLT
+DVLGVTDAAAQLGSWFPHTVTYHPSCHGMRLLRLGSRQEDLLRTVADIDLRPLPDAEECC
+GFGGTFSLKNPDVSAAIAEEKIEKVTASGASLCTGGDASCLLHLDGAMHRREARGQDGRP
+LRTVHLAEILAATRENPLEVDGPVELSIPTSAGVRRGPSARVEEARR
+>2_859
+MRVALFATCIVDAMYPKVALATVRILERLGHEVVFPRGQGCCAQMHVNSGYLDDALPVVK
+NHVRTFQGADYDVAVAPSGSCVASLGHQQPMVARAAGDEALARDAEEVAANTYELAALLT
+DVLGVTDAAAQLGSWFPHTVTYHPSCHGMRLLRLGDRQERLLRSVADIDYRALPDAEECC
+GFGGTFSLKNPDVSGAMAEEKIGNIERTQARLCTGGDASCLLHLGGVMSRRGTTAPDGSP
+VTTLHFAEILAATRENPLDVSGPVDLSIPAQGPARR---RRQKEATR
+>3_795
+MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYVEDALPVVR
+NHVRTFMKADYDLAVAPSGSCVASLGHQQPDVARSCGDEGLARDAEVVASRTLELSQLLT
+DVLGVTDAAAQLGSWFPHTVTYHPSCHGMRLLRLGTRQEDLLRTVADIDLRPLPDAEECC
+GFGGTFSLKNPDVSAAIAEEKIEKVTASGASICTGGDASCLLHLGGAMHRREARGQDGRP
+LRTVHLAEILAATRENPLEVDGPVELSIPASAGARRGPSARVEEAHR
+>4_1846
+MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYMEDALPVVR
+NHVRTFMKADYDLAVAPSASCVASLGHQQPDVARSGGDEGLARDAEVVASRTLELSQLLT
+DVLGVTDAGAQLGSWFPHTVTYHPSCHGMRLLRLGSRQEDLLRTVADIDLRPLPDAEECC
+GFGGTFSLKNPDVSAAIAEEKIEKVTASGASLCTGGDASCLLHLDGAMHRREARGQDGRP
+LRTVHLAEILAATRENPLEVDGPVELSIPASAGARRGPSARVEEARR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001583.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001583.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b1a41eb1d5c3fa596540744ab7db2db6a71d97c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001583.fa
@@ -0,0 +1,31 @@
+>0_1921
+MTA---------------APAYTIVLDWLEAELRSGAVVVGDKLPGERTLAERFGISRAS
+VREATRMLEAMGLIRASAGSGPNSGAVVVSEPSAALGWALRLHIATRSLPMADVVAARVL
+LETDAAQAAAATSGDPESVAVLAEVETLLDRMDDPALPEEDFHLLDTEFHVRLATLGGNV
+VTAMMLDSLRQATIGYVTETVAGLSDWPAVRAGLQADHRRILAASAAGDGRAAAQELREH
+VLGFAALAQAGRVPAGG
+>1_1626
+MTA---------------APAYTIVLDWLEAELRSGAVVVGDKLPGERTLAERFGISRAS
+VREATRMLEAMGLIRASAGSGPNSGAVVVSEPSAALGWALRLHIATRSLPMADVVAARVL
+LETDAAQAAAATSGDPESVAVLAEVETLLDRMDDPALPEEDFHLLDTEFHVRLATLGGNV
+VTAMMLDSLRQATIGYVTETVAGLSDWPAVRAGLQADHRRILAASAAGDGRAAAQELREH
+VLGFAALAQAGRVPAGG
+>2_857
+MTARPPTPPAEPEPGRRRAPGHAVILDWLEGELRSGRIQVGDKLPSERTLAERFGMSRSS
+VREAGRVMDAMGLVRSATGSGPRAGAIVVSEPSAALAWALRMHVATRALPVADLVTTRVL
+LETEAA-LEAAEHDVPGRGAILATAHAHLDRMDVPDFPAREFHRLDAEFHVLLSTLSGNV
+VLETILRSLREATIGYVEEAMAGVEDWGAVRDELQRQHRDILAAAVERDGPRAAQAVREH
+IHWFSRFTTAGPDAAGG
+>3_793
+MTA---------------APAYTIVLDWLEAELRSGAVAVGDKLPGERTLAERFGISRAS
+VREATRMLEAMGLIRASAGSGPNSGAVVVSEPSAALGWALRLHIATRSLPMADVVAARVL
+LETDAAQAAAATSGDPESVAVLAEVETLLDRMDDPALPEEDFHLLDTEFHVRLATLGGNV
+VTAMMLDSLRQATIGYVTETVAGLSDWPAVRAGLQADHRRILAASAAGDGRAAAQELREH
+VLGFAALAQTGRVPAAG
+>4_1848
+MTA---------------APAYTIVLDWLEAELRSGAVVVGDKLPGERTLAERFGISRAS
+VREATRMLEAMGLIRASAGSGPNSGAVVVSEPSAALGWALRLHIATRSLPMADVVAARVL
+LETDAAQAAAATSGDPESVAVLAEVETLLDRMDDPALPEEDFHLLDTEFHVRLATLGGNV
+VTAMMLDSLRQATIGYVTETVAGLSDWPAVRAGLQADHRRILAASAAGDGRAAAQELREH
+VLGFAALAQAGRVPAGG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001588.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001588.fa
new file mode 100644
index 0000000000000000000000000000000000000000..03f1cd35c7fa4edd1bff4ea5893a5df70849317a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001588.fa
@@ -0,0 +1,41 @@
+>0_1929
+MRNL-----RDHLSQRAVGVKQSAVRDVFDIAMDPNLVSLAGGNPWLADLPLDELGRIAS
+DLMTRFGTESLQYGPGQGTEEMRAAAATVMAADGIPDADPDLVVITPGSQAAIDTACRAF
+ANPGDVVVVEDPTFVGALTTFATWQLEAVATGTDDQGLVPAALDETLTRLAAEGRRVAFL
+YTIPSFANPSGALLPPGRRAEVGAICEKHGVLIVEDNPYGQIAFDGEPVAPIAADHRDNV
+VHLGTMSKIFSPGVRIGWALVPAALKREFYLCAESAYIHASTYSQMLSTAFVTQLDWQGH
+VRHVTGLYRERAGALVDAVREHWDPGVEFITPQGGFFLWATLPAGVDTLEVMHRGIEAGA
+VFVPGAAFTPVEGTHSTLRLAYSFVDAEKLVEGVRRLAPAVNESIARAR
+>1_1634
+MRNL-----RDHLSQRAVGVKQSAVRDVFDIAMDPNLISLAGGNPWLADLPLDELGRIAS
+DLMTRFGTESLQYGPGQGTEAMRAAATAVMAADGIPDADPDLVVITPGSQAAIDTACRAF
+ANPGDVVVVEDPTFVGALTTFTTWQLEAVATGTDDHGLVPAALDETLTRLAAEGRRVAFL
+YTIPSFANPSGALLPPGRRAEVGAICEKHGVLIVEDNPYGQIAFDGEPVAPIAADHRDNV
+VHLGTMSKIFSPGVRIGWALVPAALKREFYLCAESAYIHASTYSQMLSTAFVTQLDWQGH
+VRHVTGLYRERAAALVDAVREHWDPAVEFITPQGGFFLWATLPVGVDTLEVMHRGIEAGA
+VFVPGAAFTPVEGTHSTLRLAYSFVAAEKLVEGVRRLAPAVNESIARAR
+>2_848
+MRHL-----RDHLSHRAVGVKQSAVRDVFDIAMDPNLVSLAGGNPWLADLPLDELGRIAS
+DLMTRFGTESLQYGPGQGTEEMRAAAAAVMAADGIPDADPELVVITPGSQAAIDTACRAF
+GNPGDVVVVEDPTFVGALTTFNTWELDAVATGTDEHGLVPAALDETLTRLAAEGRRVAFL
+YTIPSFANPSGALLPADRRAEVAAICERHGVLIVEDNPYGQIAFDGDPVAPIAAEHRDGV
+VYLGTMSKIFSPGVRIGWALVPAELKREFYLSAESAFIHASTYSQMLSTAFVTQLDWQGH
+VRHVTGLYRERAGVLVDAVREHWDPGVEFITPRGGFFLWATLPGGVDTIELMHRGIEAGA
+VFVPGGAFTPVEGVHSTLRLAYPFVEAERLVEGVRRLAPVVNDAVARAR
+>3_1720
+MSTLDPAGARAHLARRATTVQQSAVRDVFDIAMDPDLVSLAGGNPWLAGLPLEELGATAA
+RLVAEQGTASLQYGPGQGLECMRVAACAVMAADGIPDADPELVVITPGSQAAIDTACRAF
+ADPGDVVVVEDPTFVGALTSFQTWELEAVATPTDEHGLVPADLDATLARLEAEGRRVAFL
+YTIPSFANPSGLLLPADRRDDVAAVCERHGVLIVEDNPYGQIAFDGAPVAPIAAAHRERT
+VYLGTMSKIFSPGVRVGWALVPEALHREFYLCAESAFIHASTTSQMLSTAFVTEYDWQDH
+VRGVTGLYRSRAQALQAAIAEHWDPGFTFTPPAGGFFLWGSLPAGVDAVELMHRGIAAGA
+VFVPGAAFTPVPGTHSTLRLAYSFVDEETLAEGVRRLAPVVNTAVEGAR
+>4_1856
+MRNL-----RDHLSQRAVGVKQSAVRDVFDIAMDPNLVSLAGGNPWLADLPLDELGRIAS
+DLMTRFGTESLQYGPGQGTEEMRAAATAVMAADGIPDADPDLVVITPGSQAAIDTACRAF
+ANPGDVVVVEDPTFVGALTTFTTWQLEAVATGTDDHGLVPAALDETLTRLAAEGRRVAFL
+YTIPSFANPSGALLPPGRRAEVGAICEKHGVLIVEDNPYGQIAFDGEPVAPIAADHRDNV
+VHLGTMSKIFSPGVRIGWALVPAALKREFYLCAESAYIHASTYSQMLSTAFVTQLDWQGH
+VRHVTGLYRERAGALVDAVREHWDPGVEFITPQGGFFLWATLPAGVDTLEVMHRGIEAGA
+VFVPGAAFTPVEGTHSTLRLAYSFVDAEKLVEGVRRLAPAVNESIARAR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001589.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001589.fa
new file mode 100644
index 0000000000000000000000000000000000000000..861475af3ae1a27acd2d39d7e0f3580188a95221
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001589.fa
@@ -0,0 +1,40 @@
+>0_1930
+MTQSTPEPTPTVTEHDFTVRENRPGKVLAVHLNYPSRIAQRGRPPQAPGYFLKAGTSLARSGDTIERPAGTELLAYEGEI
+ALIIGRTARRVSPEEGWSHVSGITAANDWGLYDLRHADKGSNVKNKSGDGYTPLGPAVISAAGLDPAALRVRTWVNGEIV
+QDDTTEGLVFPFGRLVADLSQLMTLEEGDVILTGTPAGSSVAQPGDVVEVEVDAPSAPGAPTTGRLVTTVVDSEHALAPF
+GAQPQVDDVQREEAWGSREAAGLAP-------QAEAASSSAVDENGHWVASAPQPDRSLLTPELRAKIDAIAVATLTAQL
+QKRGVQNATIDGPRPVHRGRRVLGYAKTLRYVPKREDLAKEFGGGFNAQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLA
+LRAQVNGANAVITDGGIRDSAAVAEVGLQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDIIVGDDDGVVVIPPSL
+LQEVVDDAYEQELQDAWAYEQVKAGYPVDGMFPPNAEWKAKFAEYRKTLPDAPAPEGDA
+>1_1635
+MTQSTPDPTPTVTEHDFTVRENRPGKVLAVHLNYPSRIAQRGRSPQAPGYFLKAGTSLAGSGDTIERPAGTELLAYEGEI
+ALIIGRTARRVSPEEGWSHVSGITAANDWGLYDLRHADKGSNVKNKSGDGYTPLGPAVISAAGLDPAALRVRTWVNGEIV
+QDDTTEGLVFPFGQLVADLSQLMTLEEGDVILTGTPAGSSVAQPGDVVEVEVDAPSAPGAPTTGRLVTTVVDSEHSLAPF
+GAQPQVDDVQREEAWGSREAAGLAP-------QAAAPSSSAVDENGHWVASAPQPDRSLLTPELRAKIDAIAVATLTAQL
+QKRGVQNATIDGPRPIHRGRRVLGYAKTLRYIPKREDLAKEFGGGFNAQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLA
+LRAQVNGANAVITDGGIRDSAAVAEVGLQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDIIVGDDDGVVVIPPSL
+LQEVVDDAYEQELQDAWAYEQVKAGYPVDGMFPPNAEWKAKFAEYRKTLPDAPAPEGDA
+>2_847
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-----------------------------------------MDENGHWVASAPQPDRSLLTPELRAKIDAVAVATLTAQL
+QKRGIQNATIDGPRPIHQGRRVLGYAKTLRYVPKREDLFKEFGGGFNAQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLA
+LRAQVNGANAVITDGGIRDSAAVAEVGLQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDVIVGDDDGVVVIPPSL
+LQEVVDDAYEQELQDAWAYEQVKAGHPVDGMFPPNAEWKATFDEYRKTLPDAPAPEGDA
+>3_786
+MTQNTSPATPSVTEHDFTVRQNRPGKVLALHLNYPSRIAQRGRSPQFPGYFIKAGTSIARSGDAVERPAGTELLAYEGEI
+ALIIGRTARRVRPEEGWSYVSGITAANDWGLYDLRHADKGSNVKNKSGDGYTPLGPAVIAAANLDPAALRVRTWVNGALV
+QDDTTEGLVFPFGQLVADLSQLMTLEEGDVILTGTPAGSSVAQPGDVVEVEVDAPTAPGAPSTGRLITHVTDSDIPMADY
+GHGPRVDDLQREEAWGSREAAGLAPVEDAPAQDDAAPASTAVDENGHWVASAPQPDRSLLTPELRAKIDAIAVATLTAQL
+QKRGIQNATIDGPRPIHQGRRVLGYAKTLRYIPKREDLFKEFGGGFNAQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLA
+LRAQVNGANAVITDGGIRDSAAVAEVGLQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDIIVGDDDGVVVVPPSL
+LQEVVDDAYEQELQDAWAYEQVKAGHPVDGMFPPNAEWKAKFDEYRKTLPDAPAPEGDA
+>4_1857
+MTQSTPDPTPTVTEHDFTARENRPGKVLAVHLNYPSRIAQRGRSPQAPGYFLKAGTSLARTGDTIERPAGTELLAYEGEI
+ALIIGRTARRVSPKEGWSHVSGITAANDWGLYDLRHADKGSNVKNKSGDGYTPLGPAVISAAGLDPAALRVRTWVNGEIV
+QDDTTEGLVFPFGQLVADLSQLMTLEEGDVILTGTPAGSSVAQPGDVVEVEVDAPSAPGAPTTGRLVTTVVESEHALAPF
+GAQPQVDDVQREEAWGSREAAGLAP-------QAAAPSSSAVDENGHWVASAPQPDRSLLTPELRAKIDAIAVATLTAQL
+QKRGVQNATIDGPRPIHQGRRVLGYAKTLRYIPKREDLAKEFGGGFNAQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLA
+LRAQVNGANAVITDGGIRDSAAVAEVGLQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDIIVGDDDGVVVIPPSL
+LREVVDDAYEQELQDAWAYEQVKAGYPVDGMFPPNAEWKAKFAEYRKTLPDAPAPEGDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001591.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001591.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed426253cb08461ef7fe199bad3a2476080215fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001591.fa
@@ -0,0 +1,40 @@
+>0_1932
+MTEKTSIEARKPAGLPDVLRHYIDGEFVDSIDGDTFEVLDPVTNEPYLTAASGKAADIDRAVAAAKRAFESGEWSQALPR
+QRSRVLHAIADIMETRGNQLAEMECFDTGLPIKQARGQAARAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAG
+LITPWNTPFMLESWKLAPAIATGNSVVLKPAEFTPLSASLWGGIFEEAGLPKGVFNMVHGFGEEGYAGDPLVKHPDVPLI
+SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERCTAGSRILVQRSVYDEFVERY
+AAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKTEARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIF
+GPVVAITPFDTEEEALQLANNTKYGLAAYIWTNDLKRAHNVAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS
+IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG
+>1_1637
+MTEKTSIEARKPEGLPDVLRHYIDGEFVDSIDGDTFEVLDPVTNEPYLTAASGKAADIDRAVAAAKRAFESGEWSQALPR
+QRSRVLHRIADIMETRGDQLAEMECFDTGLPIKQARGQAARAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAG
+LITPWNTPFMLESWKLAPAIATGNSVVLKPAEFTPLSASLWGGIFEEAGLPQGVFNMVHGFGEEGYAGDPLVKHPDVPLI
+SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERCTAGSRILVQRSVYDEFVERY
+AAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKTEARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIF
+GPVVAITPFDTEEEALQLANNTKYGLAAYIWTNDLKRAHNVAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS
+IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG
+>2_845
+M---TEINDRKPEGLPDLIRHYIDGQSVDSVDGDTFDVLDPVTNQPYIKAASGKTADVDKAVAAAKAAFESGVWSQALPR
+ERSRVLHKIADIMETRGDQLAAMECFDTGLPIKQAKGQAARAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAG
+LITPWNTPFMLESWKLAPAIATGNSVVLKPAEFTPLSASLWPGIFEEAGLPKGVFNMVHGFGEEGFAGDPLVKHPDVPLI
+SFTGESRTGQIIFGNAAPHLKGLSMELGGKSPAVVFADADLDAAIDATIFGVFSLNGERCTAGSRILVAREVYDEFVERY
+AAQASRVKVGMPNDETTEVGAIVHPEHFEKVMSYVEIGKSEAHLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIF
+GPVVAITPFDSDEEALELANNTKYGLAAYIWTNDLKRAHNFAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS
+IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG
+>3_784
+MTEKTSIAARTPEGMPDVIRHYIDGEFVDSIDGDTFDVLDPVTNEPYIKAASGKSADVDAAVAAAKRAFESGEWSQALPR
+QRSRVLHRIADIMETRGDQLAEMECFDTGLPIKQAKGQAARAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAG
+LITPWNTPFMLESWKLAPAIATGNSVVLKPAEFTPLSASLWGGIFEEAGLPTGVFNMVHGFGEEGYAGDPLVKHPDVPLI
+SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERCTAGSRILVQRSVYDEFVERY
+AAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKAEARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIF
+GPVVAITPFDTEEEALQLANNTKYGLAAYIWTNDLKRAHNFAQDVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS
+IDFYTDQQAVHINLGEVHNPVFGKQESKETG-DA
+>4_1859
+MTEKTSIEARKPQGLPDVLRHYIDGEFVDSIDGDTFEVLDPVTNEPYLTAASGKAADIDRAVAAAKRAFESGEWSQALPR
+QRSRVLHRIADIMETRGDQLAEMECFDTGLPIKQARGQAARAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAG
+LITPWNTPFMLESWKLAPAIATGNSVVLKPAEFTPLSASLWGGIFEEAGLPKGVFNMVHGFGEEGYAGDPLVKHPDVPLI
+SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERCTAGSRILVQRSVYDEFVERY
+AAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKTEARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIF
+GPVVAITPFDTEEEALELANNTKYGLAAYIWTNDLKRAHNVAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS
+IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001600.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001600.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34846aeb3e4e1b1dda972164434c23e7176c47f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001600.fa
@@ -0,0 +1,21 @@
+>0_1946
+MPPLIGPQQIATALRAVGLDDDAARLVAWADPARREREAAEQALADLAVAQTQLRAALGG
+LVSAATDVRSAIQTGWRGEAAGAYGEAVRRAAALAAELEREAGEWLALRATAERDAEDAR
+RNAEARQRAAEETALAVLRSLAVAA
+>1_1667
+MSPLIGPQQIATALRAVGLDDDAARLAAWADPARREREAAEQALADLAAAQTQLRTALGG
+LVSAATDVRSAMHTAWRGEAAGAYGEAVRRAATLAAELEREAGEWLALRATAERDAEDAR
+RNAEARQRAAEETALAVLRSLAVAA
+>2_816
+MLQLIGPQHLAAALQAAGLDDDAARLLAWADPARRDRDAAQAALDELAVAQESLRGALAG
+LVAAARDVRAGAAVAWRGPAAGEYADAVAEAVGAAEGLEREAGEWLALRATAEREAEDAR
+QDAEARLRAAEETARAALRALAVAA
+>3_754
+MLLPPTAQALLRTLVAAGLDDDAARLAVGLTDAHADLQAARAAQDALADAAEDLRDLLAL
+LEELTRGVAAALDVDWRSEAGAEYGERTDGLHRTATDRQDEAREWAGLLGRARSEAEQAE
+RDAELRVRRAEEGASALLRAMAAA-
+>4_1885
+MSPLIGPQQIATALRAVGLDDDAARLVAWADPARREREAAEQALADLAVAQTQLRTALGG
+LVSAATDVRSAMHTAWRGEAAGAYGEAVRRAATLAAELEREAGEWLALRATAERDAEDAR
+RDAEARQRAAEETALAVLRSLAVAA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001613.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001613.fa
new file mode 100644
index 0000000000000000000000000000000000000000..778015fa5cec82ae23b34bc5e686cb9b28f1e53c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001613.fa
@@ -0,0 +1,50 @@
+>0_1962
+MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGARLTGVSTDGLDTAAAIEHARTVGQQALGALTIHERALKLKE
+LALYLNSRVQELYDVSFATGATQRDHAFDVDGGIGTLFTFSGKGRRELPNSNVIIDGDVEPLSRDGSFIGEHIYQRIPGV
+AVQINAFNFPVWGMLEKFAPAFVAGVPTVVKPATPTGYVAQKCVELMLESGVLPEGSIQLISGSARDLLDHLDYRDHVAF
+TGSAATAATLKKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVKAGQKCTAIRRVIVPQDRVEA
+VTAALTERLAAKVVLGDPRVEGTTMGALASKEQQGEVRGAVQRLVDAGGQVRLGGPEGSTGDADAESGAFFAPTVLTFED
+ARTPEVHSVEAFGPVTSVIGYTDVADAVALAALGSGSLVATVATNDGETARAFAAGIGAHHGRVHVLNRQTATTTTGHGA
+PVPVLIHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTREDVEAGTAVHPFYKSLAELTV
+GDQFASGLRTVTLEDITAFAEETGDRFYAHTDEEAAMANPFFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFI
+TPVTYDDAIRVTLTAKRITPRVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG
+>1_1682
+MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGARLTGVSTDGLDTAAAIEHARTVGQQALGELTIHERALKLKE
+LALFLNSRVQELYDVSFATGATQRDHAFDVDGGIGTLFTFSGKGRRELPNSTVIIDGDVEPLSRDGSFIGEHIYQRIPGV
+AVQINAFNFPVWGMLEKFAPAFVAGVPTVVKPATPTGYVTQKCVELMLESGVLPEGSIQLISGSARDLLDHLDYRDHVAF
+TGSAATAATLKKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVKAGQKCTAIRRVIVPQDRVEA
+VTAALTERLAAKVVLGDPRVEGTTMGALASKDQQGEVRGAVQRLVDAGGQVRLGGPEGSTGDADAESGAFFAPTVLTFED
+ARTPEVHSVEAFGPVTSVIGYTDVADAVALAALGSGSLVATVATNDGETARAFAAGIGAHHGRVHVLNRQTAATTTGHGA
+PVPVLIHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTREDVEAGTAVHPFYKSLAELTV
+GDQFASGLRTITLEDITAFAEETGDRFYAHTDEEAAMANPFFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFI
+TPVTYDDAIRVTLTAKRITPRVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG
+>2_778
+MTVTLPSLPEILPSYVNGAWWTPQSPSKVTDVTDANTGERLTGVSTDGLDTAAAIEHARTVGRKSLGELTIHERALKLKE
+LALYLNSRIQELYDVSFATGATQRDHAFDVDGGIGTLFTFSGKGRRELPNSNVITDGPVEPLSRDGSFIGEHIYQRIPGV
+AVQINAFNFPVWGMLEKFAPSFVAGVPTVVKPATPTGYVTQKCVELMLESGVLPEGSLQLISGSARDLLDHLDYRDHVSF
+TGSAATAQTLRKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVKAGQKCTAIRRVIVPQDRVDA
+VVEALSARL-GKVVLGDPRVEGTTMGALASKEQQGEVRGAVQRLVDAGGQVRLGGPDASTGDADAESGAFFAPTVLSFED
+ARTPEVHAVEAFGPVTSVVGYTDVEDAVALAALGSGSLVATVATDDGETARAFAAGIGAHHGRVHFLNRQTATTTTGHGA
+PVPVLVHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTREDVEAGTAVHPFYKSLAELTV
+GDQFASGLRTVTLQDITDFAEETGDKFYAHTDEEAAMANPFFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFI
+TPVTYDDAIRVTLTAKRITPRVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG
+>3_739
+MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGELMARVSTDGIDTAGAIEHARTVGQRNLGELTIHERALKLKE
+LALYLNSRIQELYDLSFATGSTQRDHAFDVDGGIGTLFTFSGKGRRELPNSNVIIDGDVEPLSRDGSFIGEHIYQRIPGV
+AVQINAFNFPVWGMLEKFAPAFVAGVPTVVKPATPTGYVTEACVRMMVESGVLPEGSIQLISGSARDLLDHLDYRDHVAF
+TGSAGTAQTLRQHENVLNGGVRFTAETDSLNAAILGPDAGVDTPEFEAFVKVVFQEMTVKAGQKCTAIRRVIVPEAMVED
+VTAALTERLSSTVVLGDPRAEGTTMGALASKEQQSEVRKAVQTLVDAGGQVRLGGPEGSTGDADAEAGAFFAPTVLTFAD
+ADTPQVHSVEAFGPVTSVIGYTDVADAVRLAALGSGSLVATLATNDGATASEFIAGIGAHHGRVHVLNRQTAKTTTGHGA
+PVPVLIHGGPGRAGGGEELGGVRAVKHYMQRTAVQGSPDMLTAITGVWHQGAAAQTATREDVEAGKAKHPFYKALDELQI
+GDQFASGLRTVTIEDITAFAESTGDKFYAHTDEEAAMANPFFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLDDLRFI
+TPVTYDDAIRVTLTAKRITPRVTDEYGEVAWDCRLHNQKDELVAQYDVLTLVAKTWPMPEAE-PKA
+>4_1900
+MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGARLTGVSTDGLDTAAAIEHARTVGQQALGALTIHERALKLKE
+LALYLNSRVQELYDVSFATGATQRDHAFDVDGGIGTLFTFSGKGRRELPNSTVIIDGDVEPLSRDGSFIGEHIYQRIPGV
+AVQINAFNFPVWGMLEKFAPAFVAGVPTVVKPATPTGYVTQKCVELMLESGVLPEGSIQLISGSARDLLDHLDYRDHVAF
+TGSAATAATLKKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVKAGQKCTAIRRVIVPQDRVEA
+VTAALTERLAAKVVLGDPRVEGTTMGALASKEQQSEVRGAVQRLVDAGGQVRLGGPEGSTGDADAESGAFFAPTVLTFED
+ARTPEVHSVEAFGPVTSVIGYTDVADAVALAALGSGSLVATVATNDGETARAFTAGIGAHHGRVHVLNRQTATTTTGHGA
+PVPVLVHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTREDVEAGTAVHPFYKSLAELTV
+GDQFASGLRTVTLEDITAFAEETGDRFYAHTDEEAAMANPFFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFI
+TPVTYDDAIRVTLTAKRITPRVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001618.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001618.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ab65929ddc30e5f1644c37c39ac3cae46942ca7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001618.fa
@@ -0,0 +1,21 @@
+>0_1967
+MTETAHHPMLAEDRVARWLGVTLEAAEKDHARIRMTLTEDQHNGFGLAHGGAVFAFADTC
+FALTCNDPASDGSTLTVASGVDVNFLAATRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG
+TPVAAFRGRSRTIPAPGR
+>1_1687
+MTETAHHPMLAEDRVARWLGVTLEAAEKDHARIRMTLTEDQHNGFGLAHGGAVFAFADTC
+FALTCNDPASDGSTLTVASGVDVNFLAATRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG
+TPVAAFRGRSRTIPAPGR
+>2_773
+----------------------------------MTLTEDHHNGFGMAHGGAVFAFADSC
+FALTCNDPGGDGSTITVASGVDVNFLAGTRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG
+TPVAAFRGRSRTIPAPGR
+>3_734
+MTETPHHPALVGDRVARWLGVTLEAAEKDHARIRMTLGEEHHNAFGMAHGGVVFAFADCC
+FALTCNDPASDGSTLTVASGVDVNFLSGTRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG
+TLVAAFRGRSRTVAVKGA
+>4_1905
+MTETAHHPMLAEDRVARWLGVTLEAAEKDHARIRMTLTEDQHNGFGLAHGGAVFAFADTC
+FALTCNDPASDGSTLTVASGVDVNFLAATRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG
+TPVAAFRGRSRTIPAPGR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001622.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001622.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e1041f26a680ed0faba6092f3fa08315afe68ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001622.fa
@@ -0,0 +1,41 @@
+>0_1975
+MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT
+RDILLDRGLPASLENPVYLAPPLLVSLLVYVKVIHPNRLNLTITLFDAAGLALFTVSGVL
+LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM
+NGALNAFTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLARLRRLATQAQEAAARRV
+ERTLERRLRSPGAP--------------------------------------AFPDDDAD
+G--SYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRLDRGTGVMDVTDLRTGRTRSF
+DDPEHDWIADDPEDE-KG
+>1_1693
+MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT
+RDILLDRGLPASLENPVYLAPPLLVSLLVYVKVIHPNRLNLTITLFDAAGLALFTVSGVL
+LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM
+NGALNGYTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLERLRRLATQAQEAAARRV
+ERTLERRLRSPGAP--------------------------------------AFPDDDTH
+G--SYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRLDRGTGVMDVTDLRTGRTRSF
+DDPEHDWIADDPADP-RD
+>2_762
+MDVQQFFADLSDVPWLLTTLDLIGIFFFATSGALLASRKEFDLVGSMALALLAGLGGGFT
+RDILLDRGLPASLENPIYLAPPVLVSLLVYVKALHPNRLNLTITLFDAGGLALFTVSGVL
+IAHSMDVHPVSTVVVAMVAALGGGVLRDIVANEVPSIFDPRGVYVMPTFVGATVATIAAM
+NGVLNAFTGFLIAFLIFAVRMLAYRYQWRLFGADISQDKESLDRLRRLATQAQDAAARRV
+ERARERRLRSASGPGGMDVGEAEAIADRAVHHPPAPAGYHYDAVEDAYTRDHAFDDDGEP
+GSASYGPRQEYEDQVRVDEYDPETQTITVIDPASRQQVRLDPATGVMDVTDLRTGRTRSY
+DDPEHDWIADDAEDDARG
+>3_729
+MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT
+RDILLDRGLPASLENPVYLAPPVLVSLLVYVKLIHPNRLNLTITLFDAAGLALFTVSGVL
+LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM
+NGALNAFTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLERLRRLATQAQEAAARRV
+ERTLERRLRAPGAP--------------------------------------AFPDDDTH
+G--SYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRLDRGTGVMDVTDLRTGRTRSF
+DDPEHDWIADDPEDS-RD
+>4_1911
+MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT
+RDILLDRGLPASLENPVYLAPPLLVSLLVYVKVIHPNRLNLTITLFDAAGLALFTVSGVL
+LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM
+NGALNGYTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLERLRRLATQAQEAAARRV
+ERTLERRLRSPGAP--------------------------------------AFPDDDTH
+G--SYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRLDRGTGVMDVTDLRTGRTRSF
+DDPEHDWIADDPADP-RD
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001630.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001630.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b18928337df1ff0e1f943e49a3076ffc80171ad9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001630.fa
@@ -0,0 +1,26 @@
+>0_1997
+MSTSVPSSHDGHVRPAATTTA--DRP---TDAGRPRRGSAGGSLARIAVMTALMAVLGLV
+PPIAVAGVPAPIVLQNIAVILAGVILGPWRGAASMALFAGLVALGLPLLSGGRGGLGVFA
+GPTAGFILGWIPSALIVGLIFWALTSRARPGLDAGRVALGAAVAGLIGGVVMVYFFGVLG
+FVGIAGMEFGAAVLSMAPFVPGDLIKLVVSVILIVGLWKAYPRAFR
+>1_1714
+MSTSVPSSHDGHVRPAATTTA--DRP---TDAGRPRRGSAGGSLARIAVMTALMAVLGLV
+PPIAVAGVPAPIVLQNIAVILAGVILGPWRGAASMALFAGLVALGLPLLSGGRGGLGVFA
+GPTAGFILGWIPSALIVGLIFWALTSRARPGLGAGRVALGAAVAGLIGGVVMVYFFGVLG
+FVGIAGMEFGAAVLSMAPFVPGDLLKLVVSVILVVGLWKAYPRAFR
+>2_742
+MPT------------SDTLAS--GRPAHSTDDRRPRRSSAGSGLARVAVFAALMAVLGLV
+PPVPVAGIPAPIVLQNLAVTLAGVILGPWRGAAAILLFNVLVALGLPLLTGGRGGLGVFV
+GPSSGFILGYVVAAAAVGLVFWALTGRARPGLRPGRVLAAALVAGLVGMVVL-YAAGAVG
+FIVAAHMEPGAAVLAMGAFVPGDTVKVVLAALLVTGLWKAYPRAFR
+>3_705
+MTS-----------PSAPQTAVVDAP----ATHRPRR-SPGADLARIAVMAALIAVLGAM
+PGIPVPGIPTPITLQTLGVMLAGLVLGAWRGAASVALFHLLVALGLPLLAGGRGGAAVFV
+GPSAGFLWGWIPGAFVVGLLFHLYLRGRRDGRNTGGLVAAALTACVVGGIAVIYLFGIPG
+MNLFGGVPLDKAAIGSLAFIPGDLLKAVVAALLAAGLWKAYPRAFA
+>4_1934
+MSTSVPSSHDGHVRPAATTTA--DRP---ADAGRPRHGSAGGSLARIAVMTALMAVLGLV
+PPIAVAGVPAPIVLQNIAVILAGVILGPWRGAASMALFNALVALGLPLLTGGRGGLGVFV
+GPSVGFILGWIPSAMIVGLIFWALTSRSRPGLSAGRIALAAAVAGLIGGVIMVYVFGAFG
+FVGVQGMEFGAAMLSMAVFVPGDLTKLVIAVLLCAGLWKAYPRAFR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001631.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001631.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9be3076904ad92ac7d6f9860dccd955ebd799892
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001631.fa
@@ -0,0 +1,40 @@
+>0_2010
+M-----------STTTKDVEQPRVMKEMSFLDRWLPVWILAAMAVGLLMGRFIPGLNTALEAVKIGSVSLPIAIGLLVMM
+YPVLAKVRYDETRRIGADRRLLVTSLVLNWIVGPALMFALAWIFLADLPEYRTGLIIVGLARCIAMVLIWNDLACGDREA
+AAVLVAINSVFQVIAFGALGWFYLQALPSWLGLPTTSAEFSIGAIVLSVLIFLGIPLVAGFLTRILGERAKGRTWYEERF
+LPKIGPWALYGLLFTIVLLFALQGDAIISAPGDVARIALPLLVYFVVMFLGSFLLGRAIGLDYAKSTTVAFTASGNNFEL
+AIAVAIGTFGVTSGQALAGVVGPLIEVPVLVALVYVALAMGRRLFP-GDTTAPTR-------------------------
+--------------------------------------------------------------------------------
+-------------------------------------------------
+>2_541
+MPSRAVAPSPATGPAARPAERP-VLQEMSFLDRWLPVWILAAMAAGLLLGRLVPGLAEALDAFTVAGVSVPIALGLLVMM
+YPVLAKVRYDETHRIAADRRLMGTSLVLNWIVGPALMFALAWLFLADLPEYRTGLIIVGLARCIAMVLIWNDLACGDREA
+AVVLVAVNSVFQVVAFGALGWFYMQVLTGWLGLPTTTAGFSVGAIVLSVLVFLGVPLLAGFLTRVLGERARGRAWYEGRF
+LPRIGPWALYGLLFTIVLLFALQGEAITTSPGDVARIALPLLVYFTVMFLLGLVASRAVGLDYARSTTVAFTASGNNFEL
+AIAVAIATFGVHSGQALAGVVGPLIEVPVLVGLVYVARWLAPRLFP-GDPTVPP---PRPRPHRQEHPVTEHAPTDRRPS
+VLFVCVHNAGRSQMAAGWLEHLSGGRVEVRSAGSAPKDRINPSAVAVMAEAGIDLSANTPKVLTTEAVRESDVVITMGCG
+DTCPVFPGKRYEDWAVEDPAGQGVNAVRPIRDEIRGRVEALLADLLPEG
+>2_724
+MS---------VSTTAPAPHQP-VLKEMSFLDRWLPAWILLAMAAGLLLGRFVPGLNTALEAVKIGEVSLPIAIGLLVMM
+YPVLAKVRYDEAHRVAGDKWLMITSLVLNWIVGPALMFALAWMLLPDLPEYRTGLIIVGLARCIAMVFIWNDLACGDREA
+AAVLVAINSVFQVVAFGALGWFYLQVLPSWLGLPTTSADFSVWAIVLSVLVFLGVPLLAGFLTRLLGERAKGRTWYEERF
+LPRIGPWALYGLLFTIVLLFALQGEAITSNPWDVARIALPLLAYFVLMFGIALLASKAVGLNYAKSTTVAFTAAGNNFEL
+AIAVAIGTFGVTSGQALAGVVGPLIEVPVLVGLVYVSLWAGRKLFP-GDPTVPARP-QAAAAHRA---------------
+--------------------------------------------------------------------------------
+-------------------------------------------------
+>3_470
+MS---------STPRTTAEAAP-VAARLSSLDRLLPVWIGAAMLVGLLLGRLVPGLGGVLAAVEVDGVSLPIALGLLVMM
+YPVLAKVRYDRLDSVTGDRRLLVASLVLNWVFGPLLMFALAWIFLADLPEYRTGLIIVGLARCIAMVIIWNDLACGDREA
+AAVLVALNSIFQVIAFAALGWFYLSVLPGWLGLPQTGLDVSPWDIARSVLIFLGIPLLAGFLSRVIGERRWGRAAYEGSF
+LPTIGPWALYGLLFTIVVLFALQGEQIAARPWDVARIALPLLVYFAVMWGLGYTVGRRLGLGYERTTTLAFTAAGNNFEL
+AIAVAIATFGATSGQALAGVVGPLIEVPVLVGLVYVSLWLRRRFPPAADAGTPASAMTVPATTAQENR------------
+--------------------------------------------------------------------------------
+-------------------------------------------------
+>4_1939
+M-----------STTTKDVEQPRVMKEMSFLDRWLPVWILAAMAVGLLLGRLIPGLNTALEAVKIGSVSLPIAIGLLVMM
+YPVLAKVRYDETRRIGADRRLLVTSLVLNWIVGPALMFALAWIFLADLPEYRTGLIIVGLARCIAMVLIWNDLACGDREA
+AAVLVAINSVFQVIAFGALGWFYLQALPSWLGLPTTSAEFSIGAIVLSVLIFLGIPLVAGFLTRILGERAKGRTWYEERF
+LPKIGPWALYGLLFTIVLLFALQGDAIISAPVDVARIALPLLVYFVVMFLGSFLLGRAIGLDYAKSTTVAFTASGNNFEL
+AIAVAIGTFGVTSGQALAGVVGPLIEVPVLVALVYVALAMGRRLFP-GDTTAPTR-------------------------
+--------------------------------------------------------------------------------
+-------------------------------------------------
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001633.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001633.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea2b8d6239e0a80cfcc567ba85693d5fc6a1da2f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001633.fa
@@ -0,0 +1,26 @@
+>0_2020
+MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA
+LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVVATTLALTWLN
+PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPKAWRV
+VDVVIAVVMAVLAVRLIAGSGVWG
+>1_1735
+MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA
+LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVIATTLALTWLN
+PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPKAWRV
+VDVVIAVVMAVLAVRLIAGSGVWG
+>2_685
+MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA
+LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALHPQGLVAEQAPRTAGSVIATTLALTWLN
+PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPTAWRV
+VDVVIAVVMAVLAVRLIAGSGVWG
+>3_596
+MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA
+LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVIATTLALTWLN
+PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASILWFTALGYGARLLARVLADPKAWRV
+VDLVIAVVMAVLAVRLIAGSGVWG
+>4_1959
+MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA
+LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVVATTLALTWLN
+PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPKAWRV
+VDVVIAVVMAVLAVRLIAGSGVWG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001638.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001638.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a34c791c5d88e16041ae94cb9c8eef2d10452d03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001638.fa
@@ -0,0 +1,46 @@
+>0_2025
+MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE
+YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH
+RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH
+DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA
+EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG
+LPDHPGHALAARQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE
+MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGAPPSSAVPRPA
+PAHHRTTRARTPERTR
+>1_1741
+MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE
+YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH
+RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH
+DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA
+EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG
+LPDHPGHALAARQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE
+MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGAPPSSAVPRPA
+PAHHRTTRARTPERTR
+>2_679
+MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE
+YSRGSNPTRNGFETQLAALEHGERAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH
+RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH
+DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA
+EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG
+LPDHPGHDLAARQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE
+MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAVGRGTPSSSAVPRPA
+PAHHRTTRVRTPERTR
+>3_590
+MTAVHHPTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE
+YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH
+RLITTVLEPWGVSNTPVDITDTTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH
+DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA
+EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG
+LPDHPGHDLATRQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE
+MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGTPSSSAVPRPA
+PAHHRTTRVRTPERTR
+>4_1965
+MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE
+YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH
+RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH
+DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA
+EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG
+LPDHPGHALAARQMDGFGGIVSIRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE
+MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGAPSSSAVPRPA
+PAHHRTTHARTPERTR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001643.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001643.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0497d1e107e4677a3f1336b3c9bd78cb9d57651d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001643.fa
@@ -0,0 +1,45 @@
+>0_2038
+M--------------ASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRAGARNPS
+DLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRIADIVGTAADTAGVAQLVYLSGLHPDT
+VPVAELSDHMRSRALVAERLERAATPALTFEAGVIIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQ
+ACALPEPVQLRAQIGNGHPQSFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLAEEAVVE
+DRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPSDPEWAGTTVYTDERERESDLPAQEVW
+PVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGLTRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQL
+STEPREGGGSVYRQRAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRLPLRRNP
+LDRRARGAGGAQSRD
+>1_1756
+M--------------ASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRAGARNPS
+DLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRIADIVGTAADTAGVAQLVYLSGLHPDT
+VPVAELSDHMRSRALVAERLERAATPALTFEAGVIIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQ
+ACALPEPVQLRAQIGNGHPQSFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLAEEAVVE
+DRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPSDPEWAGTTVYTDERERESDLPAQEVW
+PVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGLTRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQL
+STEPREGGGSVYRQRAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRLPLRRNP
+LDRRARGAGGAQSRD
+>2_662
+--------------------------------------------------------MGGRLIPELLAAGFDVRAGARNPS
+DLADRPWSEGVEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVTQEQRIADIVGTAADTAGVAQLVYLSGLHPDT
+IPVAELSDHMRSRALVAERLEQAATPALTFEAGVIIGSGSTSFEMIRHLAERLPVMPGPSWLKNRVEPLAIRDVLYYLLQ
+ACALPEPVQLRAQIGNGHPQSFASVLVDYAKAAGLSRRIVIPTPFPLQTLAGFWIGTVTPIPVAVALPLAASLAEEAVVE
+DRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADVHAAADPADPLPSDPAWSGTTVYTDERERESDLPPQDVW
+PVIESVGGANGWYSTPMLWKVRGLADKLVGGPGLIRGRRDQDRLRRGDAVDWWRVEDVEHGRRLTLRAEMKAGGRAWLQM
+STEPRDGGGSVYRQRAIFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEAQRRTTGGERRRPRSLARALVDRLPLRRNP
+LDRGASA--------
+>3_577
+MSTPSTSRGSGLTSAAASGDTPAGTGATTAS-LSPLGLALPDGHDRRVLVTGATGYVGGRLIPELLAAGFRVRAGARTPR
+DLEDRPWSDRVEVVELDLEKPDLVKAAMQDVHTALYLVHSMGAGGDFVEQEQKIADIVATAADEAGITQLVYLSGLHPAG
+KPVEELSDHMRSRALVAERLEAAATPALTFEAGVVIGSGSASFEMIRHLSERLPIMPGPSLLKNRVEPIAVRDVLHYLVQ
+ACALEEPVQLHAQIGNGRPQSFASVLVDYAEVAGLSKRIVIPTPLPLSRLAGLWVGVVTPIPVKVALPLAASLAEDAVVE
+DHAIRDVIPAPEGGLTSYKEAVRRALAAEKNGPLDVTFEADVYDSSDPAAPLPSDPEWAGHTVYTDDRERESDLAPEDVW
+PVIESIGGRNGWYSTPLLWKVRGYMDKVVGGPGLMRGRRDQDHLRRGDAVDWWRVEEVDPGHRLTLRAEMKAGGRAWLQL
+TTEPREQGGSVYRQRAIFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEAERRRTGGARRRTRGLVRALADRLPLRRSP
+LDRRAG---------
+>4_1979
+M--------------ASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRAGARNPS
+DLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRIADIVGTAADTAGVAQLVYLSGLHPDT
+VPVAELSDHMRSRALVAERLERAATPALTFEAGVIIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQ
+ACALPEPVQLRAQIGNGHPQPFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLAEEAVVE
+DRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPSDPEWAGTTVYTDERERESDLPAQEVW
+PVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGLTRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQL
+STEPREGGGSVYRQRAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRLPLRRNP
+LDRRARGAGGAQSRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001649.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001649.fa
new file mode 100644
index 0000000000000000000000000000000000000000..535e2acbb34ab910a9e283510812a7ca0d5981fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001649.fa
@@ -0,0 +1,41 @@
+>0_2046
+MG--EARTGGEA----------------ALSGVTAELDAALRHAAAQAPGSAAFAELLDS
+LHVHVGAGKLIRPRLVELGWRLATADP----VPPSGRA--------AVDRLGAAFELLHT
+ALLVHDDVIDRDVLRRGQPAVHASARHRLEARGVPAADAAHAGVAVALIAGDVLLTQAFR
+LAATCAADTARAAEAAAVVFDAAAVTAAGELEDVLLGLSRHTGEEPDPDRILAMQRLKTA
+HYTVGAPLRAGALLAGADPDLARAMGEAGADLGA-AYQVIDDVLGVFGDPGETGKSADGD
+LREGKATVLTAHGRRIPAVRALLDAGPAT----------PADIEAARRALEAAGAREHAL
+DVAAELTVRARERIAALPLDETVRAEFADACHAVLTRRS
+>1_1764
+MG--EARTGGEA----------------ALSGVTAELDAALRHAAAQAPGSAAFAELLDS
+LHVHVGAGKLIRPRLVELGWRLATADP----VPPSGRA--------AVDRLGAAFELLHT
+ALLVHDDVIDRDVLRRGQPAVHASARHRLEARGVPAADAAHAGVAVALIAGDVLLTQAFR
+LAATCAADTARAAEAAAVVFDAAAVTAAGELEDVLLGLSRHTGEEPDPDRILAMQRLKTA
+HYTVGAPLRAGALLAGADPDLARAMGEAGADLGA-AYQVIDDVLGVFGDPGETGKSADGD
+LREGKATVLTAHGRRIPAVRALLDAGPAT----------PADIEAARRALEAAGAREHAL
+DVAAELTVRARERIAALPLDETVRAEFADACHAVLTRRS
+>2_654
+M---------SA----------------GREGVVAELEAALSRAAGLAPESAAFAELLAG
+LRTHAGAGKLIRPRLVELGWRAAADGP----VPAAERP--------AVDRLGAAFELLHT
+GLLVHDDVIDRDVVRRGERTVHEATRRRLAARGVPEAEAAHAGTAVALIGGDVLLVEALR
+LAMTCTPDPGRAAPVAAVVLDAATASAAGELEDVLLGLARHTGEEPEPERILAMQRLKTA
+HYTVSAPLRVGGAAGGGGSRRRRGAGEAAAPTWAWPTRWWTTCSGCSAPRSRPASPPTAT
+CARARPPCSPRTAAATPPSAPCSTPAPAT----------PEELEAARRALEAAGAREHAL
+QVAEELTRRAAEHLAVLPLGEAACAEFADACHAVLTRSS
+>3_571
+MNPLAAGIGGAAPWSASAATPGLDDAGRARAAVRAELDRVFAETPLCADAPDSFHLLWAR
+LREAVSGGKLVRPRLVDLGWRTVRRAPASSGVPRGGTGEEEAADLRAVARVGAAFELLHA
+ALIVHDDVIDRDDLRRGRPTVAEQYRRDAVRDGVPAGEAEHVGRSAGIIAGDLLLTAAFR
+LAAASGA-RVRAAEAAESVFRAASAAAAGELEDVLLALHRHTGHHPEAGRILTMERLKTA
+GYSFEEPLRAGALLAGADPAHAEALAEAGALLGV-AYQVVDDVLGTAGDPAVTGKPHDAD
+LREGKATLLTAHGRRDPRARAALDRVARAERHGEDLGELAAAVAEARAALVDAGSVEHAL
+GVAEELVDQARALLDALPMAPAERAEFAATCGQILQREA
+>4_1987
+MG--EARTGGEA----------------ALSGVTAELDAALRHAAAQAPGSAAFAELLDS
+LHVHVGAGKLIRPRLVELGWRLATADP----VPPSGRA--------AVDRLGAAFELLHT
+ALLVHDDVIDRDVLRRGQPAVHASARHRLEARGVPAADAAHAGVAVALIAGDVLLTQAFR
+LAATCAADTVRAAEAAAVVFDAAAVTAAGELEDVLLGLSRHTGEEPDPDRILAMQRLKTA
+HYTVGAPLRAGALLAGADPDLARAMGEAGADLGA-AYQVIDDVLGVFGDPGETGKSADGD
+LREGKATVLTAHGRRIPAVRALLDAGPAT----------PADIEAARRALEAAGAREHAL
+DVAAELTVRARERIAALPLDETVRAEFADACHAVLTRRS
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001653.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001653.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ecb37360c1453e89d384a7f74077376a6fdf3645
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001653.fa
@@ -0,0 +1,21 @@
+>0_2053
+MGTQDPRARLLEKLAKVNVCMLTTAEPDGTLVTRPMGLQQAE-DGGTLWFLTRATSDVAA
+DAPQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNPATEAFFGEGSSPEDPQIVLVR
+VDVQTAQFWESPGAVATAVELVKAKVTGGEAHPGDSETVRF
+>1_1772
+MGTQDPRTHLLEKLAKVHVCMLTTAEADGTLVTRPMGLQQAE-DGGTLWFMTRSTSDVAA
+DAPQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNSATEAFFGEGSSPEDPQIVLVR
+VDVNTAQFWESPGAVATAVEMVKAKVTGGTAEPGDSETVRF
+>2_648
+MGHKDPRTHLLEKLEKSNVCMLTTSETDGTLTTRPMGLQKAE-ETGTLWFMTRAASDVAS
+DASQRPVNVSVQDKDFWASVAGHGQVVRDDARKKEFWNPATEAFFGEGAKPEDPQIVLVR
+VDVESAQYWESPGAVGTVVELIKAKVTGGEAHPGESTTVQF
+>3_565
+MTEQDPRTALLEKIEKAGVVMLTTAEEDGTLASRPMAVQEVEQEPGVLWFITRATGDAAQ
+DSAGRPVNVAVQEKGFWASVAGHGEIVRDEARKTEYWNSATEAFFGEGARPEDPQIVLVR
+VQADSAEYWDGGGA-ASVVEIVKAKVTGGEARPGDHDTVEF
+>4_1992
+MGTQDPRARLLEKLAKVNVCMLTTAEQDGTLVTRPMGLQQAE-DGGTLWFLTRATSDVAA
+DAPQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNPATEAFFGEGSSPEDPQIVLVR
+VDVDTAQFWESPGAVATAVELVKAKVTGGTAEPGDSETVRF
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001655.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001655.fa
new file mode 100644
index 0000000000000000000000000000000000000000..830dac9478dd8c096804692230cb2c3c40633bb1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001655.fa
@@ -0,0 +1,16 @@
+>0_2056
+----------MSINTTSHHLPTAPSPLMQRHVLQRVEETLLRRFEGTVTAETVRSVVREV
+VADLKRGARITTFLPALAEREATRRLQ--AATPAHEAMAVA---A
+>1_1775
+----------MSINTTSHHLPTAPSPLMQRHVLQRVEETLLRRFEGTVTAETVRSVVREV
+VADLKRGARITTFLPALAEREATRRLQ--ATTPAHEAMAVA---A
+>2_645
+----------MSINTV-HHLPAAPSPLMQRHVLKRVEETLARRFEGVATAEAVRATVREV
+ASELKRSARMTMFLPALTEREAARRLQ--AGAPAHEPLAAA---A
+>3_563
+--------MTATLTTQ-HHMPVHPDTTMQQRVLERIAGTLIRRFDGSVPAADVRTTVAEV
+TAELEAEARLTTYLPALTEREALNRLEAMAAAPAHMTITHARHAA
+>4_1995
+MVRQPKEVLTVSINTTSHHLPTAPSPLMQRHVLQRVEETLLRRFEGTVTAETVRSVVREV
+VADLKRGARITTFLPALAEREATRRLQ--AATPAHEAMAVA---A
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001666.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001666.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c38f1d10be7c81684fe6bbc063ea1473ecd1423e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001666.fa
@@ -0,0 +1,51 @@
+>0_2069
+MSSTLATGAYRRAVDRAHESLDSVRLSLAPSSSTAPTGADQGLRAALQGLRREVRESWLR
+SLGALTPAGSALDAGASAAAPAVPGQTDPATLADDDLAAARREQRLAVALPVVRRMLIQP
+AAEAGMLAAIGNARGHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAP
+TQVSRGEHLSPRVHPWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLLSTVDAVH
+AAWRDLPAPSRGRPRGTVPTPGPSAPPSASPGPSPAGAPHRHDEAAGLLRVTGHLPPTLD
+GVELTGRHAEILTLLAWHGPGLTGAELEVALYPEETAGPRSAPGDAPARAISLRAEVHRL
+RRALRDVGAPVELLSRPYRLVGEVHADLLCAREALRAGDLDRALHAAVGPVLPRSASPGV
+ASIRAELGEALREAVAQDADVDQLWAYLGRPEARDDVELWGAALRLLPTDSPRRALAVAT
+LERIERDLA
+>1_1788
+MSSTLATGAYRRAVDRAHESLAAVRLSLAPSSPTAPAGADQGLRAALQGLRREVRESWLR
+SLGALT--------------PAVPGQTDPATLSDDDLAAARRDQRLAVALPVVRRMLIHP
+AAEAGMLAAIGNARGHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAP
+TQVSRGEHLSPRVHPWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQATVDAVH
+AAWRDLPAPSRGRPRGTAPTPGPSAPPSASPGPSPAAAPHRHDAAAGLLRVTGHLPPTLD
+GVELTGRHAEILTLLAWHGPGLTGAELEVALYPEETAGPRPAPGDSPARAISLRAEVHRL
+RRALRDVGAPVALLSRPYRLVGEVHADLLCAREALRAGDLDRALHAAAGPVLPRSTSPGV
+ASIRAELGEALREAVAQDADVDQLWAYLGRPEARDDVELWGAALRLLPTDSPRRALAVAT
+LERIERDLA
+>2_632
+MSSTLATGAYRRAVDRAHESLDSVRLSLAPSSPTAPTGADQGLRTALQGLRREVRESWLR
+SLGALTPAGSALDAEAAATAPAVPGQTDPATLADDDLAAARREQRLAVALPVVRRMLIHP
+AAEAGMLAAIGNARGHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAP
+TQVSRGEHLSPRVHPWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQATVDAVH
+AAWRDLPAPSRGRPRGTVPTPGPSAPPSASPGPSPAAAPHRHDAAAGLLRVTGHLPPTLD
+GVELTGRHAEILTLLAWHGPGLTGAELEVALYPEETAGPRSAPSDAPARAISLRAEVHRL
+RRALQDAGAPVELLSRPYRLVGEVHADLLCAREALRAGDLDRALHAAAGPVLPRSVSPGV
+ASIRAELGEALREAVAQDADVEQLWAYLGRPEARDDVELWGVALRLLPADSPRRALAVAT
+LERIERDLA
+>3_549
+MSSTLATGAYRRAVDRAHESLAAVRLSLAPSSPTAPTGADQGLRAALQGLRREVRESWLR
+SLGVLTPAGSALDAGASATAPAVPGQTDPATLSDDDLAAARREQRLAVALPVVRRMLIQP
+AAEAGMLAAIGNARGHLLWVEGDRTAVRHAEALGFVAGADWSEASMGTSAPGIVLATGAP
+TQVSRGEHLSPRVHPWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQTTVDAVH
+AAWRDLPAPSRGRSRGTVPTPGPSAPPSVSPGPSPAAAPHRHDAAAGLLRVTGHLPPTLD
+GVELTGRHAEILTLLAWHGPGLTGAELEVALYPEETVGPRSAPGDAPARAISLRAEVHRL
+RRALRDVGARVELLSRPYRLVGAVHADLLCAREALRAGDLDRALHAAAGPVLPRSASPGV
+ASIRAELGEALREAVAQDADVEQLWAYLGRPEARDDVELWGAALRLLPADSPRRALAVAT
+LERIERDLT
+>4_2008
+MSSTLATSAYRRAVDRAHESLAAVRLSLAPSSPTAPAGADQGLRAALQGLRREVRESWLR
+SLGALT--------------PAVPGQTDPATLSDDDLAAARRDQRLAVALPVVRRMLIHP
+AAEAGMLAAIGNARGHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAP
+TQVSRGEHLSPRVHPWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQATVDAVH
+AAWRDLPAPSRGRPRGTAPTPGPSAPPSASPGPSPAAAPHRHDAAAGLLRVTGHLPPTLD
+GVELTGRHAEILTLLAWHGPGLTGAELEVALYPEETAGPRPAPGDSPARAISLRAEVHRL
+RRALRDVGAPVALLSRPYRLVGEVHADLLCAREALRAGDLDRALHAAAGPVLPRSASPGV
+ASIRAELGEALREAVAQDADVEQLWAYLGRPEARDDVELWGAALRLLPADSPRRALAVAT
+LERIERDLA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001674.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001674.fa
new file mode 100644
index 0000000000000000000000000000000000000000..95cc50011a42817d40d8a30188bf42845dee76b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001674.fa
@@ -0,0 +1,36 @@
+>0_2078
+MSVPPSG-------PPAGP----------PAGWPPSGRPSARRAAVAPSLHGHPGAPGGV
+PAGWPGRRPAARPAPDWTPGRFHWGDAVVVLVYVALMVLGLGLWLAVSLGLVPGDLEAFD
+LVRDGFTVNIVSYAILVVLVLAVAWRPLVTSLRVFRTGTWWKLLLLPATWLACIVVNVIV
+LSLIGEAQTSANQAALEEMTTQAPPVLMILMTVVAAPLVEEYLFRHLLIGKLSRWINVWV
+CAVVSVLAFTLLHFLGTGGDFRLVETVPYLTLAVAITVSYILMGRSFGYAVLLHMVNNGI
+AIAMLYLVAPLLPDTLPGPTAPTTALAPLLALLG
+>1_1797
+MSVPPSG-------PPAGP----------PAGWPPSGRPSARRAAVAPSLHGHPGAPGGV
+PAGWPGRRPAARPAPDWTPGRFHWGDAVVVLVYVALMVLGLGLWLAVSLGLVPGDLEAFD
+LVRDGFTVNIVSYAILVVLVLAVAWRPLVTSLRVFRTGTWWKLLLLPATWLACIVVNVIV
+LSLIGEAQTSANQAALEEMTTQAPPVLMILMTVVAAPLVEEYLFRHLLIGKLSRWINVWV
+CAVVSVLAFTLLHFLGTGGDFRLVETVPYLTLAVAITVSYILMGRSFGYAVLLHMVNNGI
+AIAMLYLVAPLLPDTLPGPTAPTTALAPLLALLG
+>2_615
+-----------------------------------------------------------M
+PAGWPGRTPGPRTAPDWEPGRFHWGDAVVVLAYAGLMLFGLGLPLAMLLGLVPGDLAAFD
+LVRDGFTVNMVSYAILTALVLIVAWRPLVTSLRVFRTGTWWKILLLPAVWFTCILVNVLV
+LSLIGEAQTSANQAALEEMSAQAPPVLMILMTVVGAPLVEEYLFRHLLVGKLSRWVNVWV
+CAVVSMLAFTLLHFLGTGGQFDLVETVPYLTLAIAITVTYILMGRSFGYAVLLHMVNNGI
+AIAMLYLVAPLLPDVLPEPTAPAAALSPLLALLG
+>3_540
+MSVPPPGPHDAGALPPPGSTAPTSAAGEAPEGWPPAGWPGRASAGGAPQ--------GWP
+PSGWPGRTASARTAPSWEPGRLHWGDAAVVVLYVLMMVVGLGYLLAVLLGLAPRDPAAMD
+-VMDGFRVNLVSYAVLVVAVLAVSWRPLVASLRVFATHTWLKILLLPALWLVTVLVNALL
+LSLIGQAQTSANQAALEEMTTQAPALGMVLMTVVGAPIVEEYLFRHLLVGKLSRWINVWV
+CAAISVAAFTLLHFLGTGGDFQWVETVPYLTLAVTITVTYVLIGRSFGYAVLLHMVNNGI
+AIAMLYLVAPLLP-SAPAPVGPGALLSPLLALLG
+>4_2017
+MSVPPSG-------PPAGP----------PAGWPPSGRPSARRAAVAPSLHGHPGAPGGV
+PAGWPGRRPAARPAPDWTPGRFHWGDAVVVLVYVALMVLGLGLWLAVSLGLVPGDLEAFD
+LVRDGFTVNIVSYAILVVLVLAVAWRPLVTSLRVFRTGTWWKLLLLPATWLACIVVNVIV
+LSLIGEAQTSANQAALEEMTTQAPPVLMILMTVVAAPLVEEYLFRHLLIGKLSRWINVWV
+CAVVSVLAFTLLHFLGTGGDFRLVETVPYLTLAVAITVSYILMGRSFGYAVLLHMVNNGI
+AIAMLYLVAPLLPDTLPGPTAPTTALAPLLALLG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001680.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001680.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc7fd486a3aee02e8acadcb4187877d0c979adc6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001680.fa
@@ -0,0 +1,31 @@
+>0_2085
+MVGL----------VGALLLAGCASGADAGASAHAETGSTPS----KVWDAATWKPTEVI
+EPVLATEPEKEAAYREQMDRLAESGGTPEILQVQRKDWSTTPLESDQKVASCMRADGFPV
+EVSPTG-GLRYSTPPAAQARAWALAMNTCIAQHPVDPSYTQDWSEPQLRLVYDYWDQYLI
+PCLEAQGFTVDTSTRPSKESFVTAFFTPGRHDWWPLQATMRGVPEERQTQVVQTCPELPP
+QDVFWGTSG
+>1_1803
+MTSLRIPATAALVAAVALTLTGCVGRESAGLGGSSTVAAPPTATAEKTWDASQWVPTERI
+EPLLTTEAEKERAYREQVARHAQGAGMPAPPQVERSGWYATSLESDRMVSTCLAEAGWPN
+SVGPTG-GIQIDTPPESQRSAFEAAYVTCYAQHPVDPSYTQDWTDPQLRLVYDYWDQYLI
+PCLEAYGYTVDTSARPSKEAFVSAFYTPGRHQWWPFADSMRGVSAERQAEVAQTCPELPP
+QDVFWGSSG
+>2_608
+MKTKFAAVTAAAVTAV-LTLSGC------ATTAPSTSAAATGSPTEKVWDPETWTPTEKI
+ERRMTEADERERWYESQLARNAAFLGIRNPPAVTRRGWATSRQEQARWSAQCMTERGVPA
+TYNEVMVGVTYDTPPPSQEAAVKLVSWTCDALFPIDPSLDQEFSDAQLRLLYDYWDQYAI
+PCLEDHGITVDTSQRPSKETWLAAFNTPERISWWPVQDSIMGLTDARSAEVSEACPVQPP
+DSMLFGYSE
+>3_533
+MTSLRIPATAALVAAVALTLTGCVGRESAGLGGSSTVAAPPTATAEKTWDASQWVPTERI
+EPLLTTEAEKEAAQREQVERMAREAGTPELLQVRRMDWSSTTLESSQKIGECMAAAGFPV
+EVTPTG-GLRYPTPPESQKRAWNLAENTCAVKHPVDPAYAHDWTEPQLRLVYDYWDQYLI
+PCLEAQGLHVDTSSRPSKESFVTSFFTQDRHDWWPFSTTMVGVSEERKAHIAQTCPELPP
+PDVFWGTAP
+>4_2023
+MTSLRIPATAALVAAVALTLTGCVGRESAGLGGSSTVAAPPTATAEKTWDASQWVPTERI
+EPLLTTEAEKERAYREQVARHAQGAGMPAPPQVERSGWYATSLESDRMVSTCLAEAGWPN
+SVGPTG-GIQIDTPPESQRSAFEAAYVTCYAQHPVDPSYTQDWTDPQLRLVYDYWDQYLI
+PCLEAYGYTVDTSARPSKEAFVSAFYTPGRHQWWPFADSMRGVSAERQAEVAQTCPELPP
+QDVFWGSSG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001681.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001681.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a83c0f07a903971cb2b90c75a7bf3fb4cba93324
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001681.fa
@@ -0,0 +1,50 @@
+>0_2086
+MS---------------EHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLVVVALMVLVAVVLN
+VWAPHVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTPGEGIDFTELGRLILIVLGMYLVAQT
+FMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSYFDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMM
+FWLSWQLALIALIALPVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNEELYEA
+AFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFNQPLGQIAGMSNMLISGVASAERIFE
+LLDEPEETPDGTPARTPARTFVRETAPSEGTFVRETAPSAASGPDVVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNLV
+AEPGQTVAIVGPTGAGKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRSELRAATGMVLQDAVLFGGTIRENIRYGRLDAT
+DEEVVAAAKATYVDRFVHTLPEGYDTVIEHDASNVSAGERQLITIARAFLAQPSLLILDEATSSVDTRTEVLVQGAMAAL
+RSDRTSFVIAHRLSTIRDADVILVMEHGDIVEQGSHAELLAAKGAYHRLYMSQFKGGE-----DDDGA-ASRDDAR
+>1_1805
+MS---------------EHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLVVVALMVLVAVVLN
+VWAPHVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTPGEGIDFTELGRLILIVLGMYLVAQT
+FMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSYFDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMM
+FWLSWQLALIALVALPVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNEELYEA
+AFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFNQPLGQIAGMSNMLISGVASAERIFE
+LLDEPEETPDGTPARTPDGTFVWETAPSESAFVRETAPSAIPGPDGVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNFV
+AEPGQTVAIVGPTGAGKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRGELRAATGMVLQDAVLFGGTIRENIRYGRLDAT
+DEEVVAAAKATYVDRFVHTLPDGYDTVIEQDAANVSAGERQLITIARAFLAQPSLLILDEATSSVDTRTEVLVQGAMAAL
+RSDRTSFVIAHRLSTIRDADVILVMEDGDIVEQGSHDQLLAARGAYFRLYRSQFQGGEQAEEQDDDGAPAAREDAR
+>2_604
+MSGTEKHGSTAAPQGEVGELTDAEIAAFQEAGVTDEWGEGPPRKAKAFWPSAMRLLGLFAPERTGLILVSLMVLVAVVLN
+VWAPHVLGQAMDVIFGGLISRDMPAGLTREQVIEGLRGQGQGQAADMLSGMAFVPGQGIDFAELARLILIVLGMYVVAQL
+FMWLQGRVLNDLVMRIVFRLREDIEAKLNRLPLSYFDTRQRGDLLSRTTNDVDNVQQAMQQAFATLVYSVLTIIGIVGMM
+FWLSWQLALIALIALPVAGVMVGVIGSKSQKLFTAQWRETGRLNGHIEESFTGHELVTVFGRQADMAERFDERNEAMYEA
+SFKAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFNQPLGQVAGMSNMLISGVASAERIFE
+LLDEDEQDSDAEVARRASDDDVAEPADAS---VRET---GASADDDVAHLPQPVAGRVEFEHVRFSYTEAKPLITDLNLV
+AEPGQTIAIVGPTGAGKTTLVNLIMRFYEVDGGRILVDGVDTRTVSREELRSHTGMVLQDAVLFGGTIRENIRYGRQDAT
+DEEVVAAAKATFVDRFVHTLPEGYDTVIEQDASNVSAGERQLITIARAFLAQPSLLILDEATSSVDTRTEVLVQGAMAAL
+RSDRTSFVIAHRLSTIRDADVILVMEHGDIVEQGNHAELLAARGAYHRLYMSQFKGGE-----DDGGGAASGEDAR
+>3_530
+MS---------------EQLTDQEIVELQESGATDEWGGGPGRKAKAFWPSAKRLLGLFRTEKAGLALVAAMVLVAVVFN
+VWAPHVLGRAMDVLFGGVISKGMPAGVSREQVIEGLRGQGQGQAADMLSGMDFTPGQGIDFDALARLILTVLGMYVVAQG
+FMWLQGRVLNDVVMRIVFRLREQIEAKLNRLPLSHFDTRQRGDLLSRATNDVDNVQQAMQQAFATLVYSVLTIFGIVGMM
+FWLSWELALIALIALPVAGVVVGVVGKKSQALFTAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAERFDERNDAMYEA
+SFKAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFNQPLGQVAGMSNMLISGVASAERIFE
+LLDEPEEEPDDVVAAR--------------------------ADDDVAHLPQPVAGRVEFEHVRFSYTEAKPLITDLNLV
+AEPGQTIAIVGPTGAGKTTLVNLIMRFYEVDGGRILLDGVDTRRVPRQELRAATGMVLQDAVLFGGTIRENIRYGRLEAT
+DEEVLAAAKATYVDRFVHTLPDGYDTVIEQDASNISAGERQLITIARAFLAQPSLLILDEATSSVDTRTEVLVQQAMAAL
+RNDRTSFVIAHRLSTIRDADVILVMEHGDIVEQGSHEELLAARGAYHRLYTSQFRGGE--DEHHDDGAPASR----
+>4_2025
+MS---------------EHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLAVVAVMVLVAVVFN
+VWAPRVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTPGEGIDFTELGRLILIVLGMYLVAQT
+FMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSYFDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMM
+FWLSWQLALIALVALPVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNEELYEA
+AFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFNQPLGQIAGMSNMLISGVASAERIFE
+LLDEPEETPDGTPARTPDGTFVWETAPSESAFVRETAPSAIPGPDGVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNFV
+AEPGQTVAIVGPTGAGKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRGELRAATGMVLQDAVLFGGTIRENIRYGRLDAT
+DEEVVAAAKATYVDRFVHTLPDGYDTVIEQDAANVSAGERQLITIARAFLAQPSLLILDEATSSVDTRTEVLVQGAMAAL
+RSDRTSFVIAHRLSTIRDADVILVMEDGDIVEQGSHDQLLAARGAYFRLYRSQFQGGEQAEEQDDDGAPAAREDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001683.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001683.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d00563d5ed440c4b7a1a37c6584dd31014d688b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001683.fa
@@ -0,0 +1,46 @@
+>0_2088
+MRRPSLPS--LSRLPVRRLLRGAAVAAGVGLVGLPLTVAAGLTGVDMVKRGGRVRRPAPN
+PGVFDAHVEGSELRIFTSGEDLYKEMIAAIDGAQRIIKFETFIWKGDPTGQRFMDAFNRA
+AARGVEVYVSYDGFGNLVVPPRFYRQLDPRIHVFRLPAFARPIWRGVVRHSGFNHSKIMV
+VDDEVGFAGGFNIGDDYARLWRDTHVRERGPAVWALGQSISIKWNAHHRAGEQMSWRPPD
+TWDPRVTVAANQPPLLVYPIRLSYLDAIQRAQHRILINTPYFIPDQQVLEALLHAARRGV
+DVQVMVPEDSNHIVADWASRGFFGKMLEAGITILLYRASMIHAKTATVDGIWSTVGSANV
+DRLSLGFNYESNVVVVDRDFAARMEEIFALDAQRAVRIDTPRWEDRHGLARVVEALLVPL
+RPLL
+>1_1812
+------------------------MAAGVGLVGLPLTVAAGLTGVDMVKRGGRVRRPAPN
+PGVFDAHVEGSELRIFTSGEDLYKEMIAAIDGAQRIIKFETFIWKGDPTGQRFMDAFNRA
+AARGVEVYVSYDGFGNLVVPPRFYRQLDPRIHVFRLPAFARPIWRGVVRHSGFNHSKIMV
+VDDEVGFAGGFNIGDDYARLWRDTHVRERGPAVWALGQSISIKWNAHHRAGEQMSWRPPD
+TWDPRVTVAANQPPLLVYPIRLSYLDAIQRAQHRILINTPYFIPDQQVLEALLHAARRGV
+DVQVMVPEDSNHIVADWASRGFFGKMLEAGITILLYRASMIHAKTATVDGIWSTVGSANV
+DRLSLGFNYESNVVVVDRDFAARMEEIFALDAQRAVRIDTPRWEDRHGLARVVEALLVPL
+RPLL
+>2_595
+M--SPLPASPLHRIPVRRIVRGAALAAGTGLVGVPMAVAAGLTGVDMVKRRGRRRRPAHN
+PGVFDAPVKDCHLRIFTSGEDLYEEMLAAIDSAERIVKFETYIWKADPTGQRFIEAFNRA
+AARGVEVYVSYDGFGNLVVPRAFYRQLDPRIRVFRLPAFARPFWRGPVRNTGFNHSKIMV
+VDDEIGFVGGFNIGDDYATFWRDTHVCERGPAVWALDQSISIKWNAHHREGEQMSWRPPE
+SWDPRVTVSANQPPLLVYPIRLTYLEAIQRAQHRILINTPYFIPDQQVLQALLHAARRGV
+DVQVMVPRDSNHIVADWASRGFYAGMLEAGITILLYEASMIHAKTATVDGIWSTVGTANI
+DRLSLGFNYESNVVVVDRDFAARMEEIFAIDAEQSERVESPRWQDRHGVARMVERLLVPL
+RPLL
+>3_520
+M---------------GYALRRAAVAGTTAFVGVPLATAVAVSAYDAFKHRGRKLRPAER
+PGTFQAQVGPDALTIYTAGDDVYDAMIQAIDDARETVKFETFIWKDDATGQRFVDALNRA
+AARGVQVWASYDGFGNLLIPPSFYRQFDPRVRVFRLPAFARPLWRGVVRYSGFNHSKILT
+VDGRVGFVGGYNVGDLYAAHWRDTHLRVEGPAVWGLEHSLSVLWNEGYTDMAEMPWTRPE
+EWEERTVVAANLPTQLVYPIRNTYLNAIARAQDHIYISTPYFVPDRQVLDALKEAARRGV
+DVQVLVPKDSNHVVADWVSRGFYSEMLDAGITILLYAAGMIHAKTATIDGRWATVGTANI
+DRLSLSFNYETNVSVVDRDFAARMEDVFRADAARSERIQSPRWKDRHGLARVVEKLLVPL
+RPLM
+>4_2032
+MHRPPLPS--LSRLPVRRLLRGAAVAAGVGLVGLPLTVAAGLTGVDMVKRRGRVRRPAPN
+PGVFDAHVKGSELRIFTSGEDLYEEMIAAIDGAQRIIKFETFIWKGDPTGQRFMDAFNRA
+AARGVEVYVSYDGFGNLVVPPRFYRQLDPRIHVFRLPAFARPIWRGVVRHSGFNHSKIMV
+VDDEVGFAGGFNIGDDYARLWRDTHVRERGPAVWALGQSISIKWNAHHRAGEQMSWRPPD
+TWDPRVTVAANQPPLLVYPIRLSYLDAIQRAQHRILINTPYFIPDQQVLEALLHAARRGV
+DVQVMVPEDSNHIVADWASRGFFGKMLEAGITILLYRASMIHAKTATVDGIWSTVGSANV
+DRLSLGFNYESNVVVVDRDFAARMEEIFALDAQRAVRIDTPRWEDRHGLARVVEALLVPL
+RPLL
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001684.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001684.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c2f9265cf803688edb9f6a1983be2b63125a0d0b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001684.fa
@@ -0,0 +1,36 @@
+>0_2089
+MRPPGALALEFRADSFDHPTGLVDAGTVISWIEKAGYAVAASWAGTFVRARYMGHTQFRH
+PVPVDRRAVVQARVVHTDGAEVHVQTRLLLPEIRDDDGDPVVATSSLVVYAAEEGGVPVT
+VPVWEPSTPGQIERDEQARRSTVARRAVERGMARLPFPAPGEAPEEMSTLAFLAPNAEAT
+VGGTINAGAILRWVDEAAAVCAARWTGHESVVAVFGGGVRFVRNIHVGDLVRVEALLVNT
+TERSMHVALRVYASRRTGAESRLVAHSIAVMVDVSAEDQAQRVRQYIPESESARRLQETA
+IELVRMRSEVSAAWTEMRRSTDPR
+>1_1813
+MRPPGALALEFRADSFDHPTGLVDAGTVISWIEKAGYAVAASWAGTFVRARYMGHTQFRH
+PVPVDRRAVVQARVVHTDGAEVHVQTRLLLPEIRDDDGDPVVATSSLVVYAAEEGGVPVT
+VPVWEPSTPGQIERDEQARRSTVARRAVERGMARLPFPAPGEAPEEMSTLAFLAPNAEAT
+VGGTINAGAILRWVDEAAAVCAARWTGHESVVAVFGGGVRFVRNIHVGDLVRVEALLVNT
+TERSMHVALRVYASRRTGAESRLVAHSIAVMVDVSAEDQAQRVRQYIPESESARRLQETA
+IELVRMRSEVSAAWTEMRRSTDPR
+>2_594
+MKPAGALALEFRADSFDHPGGLVDAGTVISWIEKAGYAVAASWAGTFVRARYMGHTQFRH
+SVPVDHRAVVQARVVHTDGADVHVQTRLLLPEVKDESGDPVVATSSLVVYSAEEDGARVT
+VPAWVPSTPGQIERDEQASRSTVARRAVERGMARLPFPSPGQAPEEMSTLAFLAPASEAT
+VGGTMNAGAILRWLDEAAAVCAARWTGHESVVAVFGGGVRFVRNILVGDLVRVDALLVNT
+TERSMQVALRVYAGRPTGVQPRLVAHSIAVMVDVSAEDKAQPVRQYVPESEGARSLQEAA
+VQLVRLRSEVGAAWTETRRSPESR
+>3_519
+MMRSGALSLDFRADSFDHPSGLVDAGTAIGWIDKVGYAVAASWSGTYVRARYMGTMQFRH
+PVPVDMRVTVQGRVVRTHGAAVHVQLRLLLPEVLDDDGRPVVSTSTLSVYYAEEDGQMLQ
+VPEWTPSTPDQIERDERARVSSVERRGIEQVMARLPFPEPGQEHEEMTTLAFIAPMAEAS
+VGGTVAAGAVMRWLDEAAGVCAARWTGHENVVAVFAGGVRFVRPVKVGDLVRVDALLVHT
+SERSMHVALRVHAGPRHQRDHRLVAHSIAVMVDVTREGRAESVRPYAPGSPAAHRLEESA
+VELVRLRSEAGAVWSD------PS
+>4_2033
+MRPPGALALEFRADSFDHPTGLVDAGTVVSWIEKAGYAVAASWAGTFVRARYMGHTQFRH
+PVPVDRRAVVQARVVHTDGAEVHVQTRLLLPEIRDDDGDPVVATSSLVVYAAEEDGVPVT
+VPAWEPSTPGQIERDEQARRSTVARRAVERGMARLPFPAPGEAPEEMSTLAFLAPNAEAT
+VGGTINAGAILRWVDEAAAVCAARWTGHESVVAVFGGGVRFVRNIHVGDLVRVEALLVNT
+TERSMHVALRVYASRRTGAESRLVAHSIAVMVDVSAEGQAQPVRQYVPESESARRLQETA
+IELVRMRSEVSAAWTETRRSTDPR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001685.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001685.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08a0039b082049e751de386f9c9020b5bdccd61c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001685.fa
@@ -0,0 +1,26 @@
+>0_2090
+MTAFDRFPLPAEPQTPHDRLRRRTEAAVAERGEAAVAGLAVRLMTGAATPDDVTSGAARA
+LTGDDGDLSPAATGALALMHAWHRSALPALTGALTAPEADVRSAAHLVLASRAGSLRRDA
+AVDRTLVDAVRAGCADPDPEVRASAASALGALARPEDLESALPVLTGMVMDVDADLAAAA
+ELALEQLAIRLDRPGLRVSLEG
+>1_1814
+MTAFDRLPLPAEPQTPHDRLRRRTEAAVAERGEAAVAGLAVRLMTGAATPDDVTSGAARA
+LTGDDGDLSPAATGALALMHAWHRSALPALTGALTAPEADVRSAAHLVLASRAGSLRRDA
+AVDRTLVDAVRAGCADPDPEVRASAASALGALARPEDLESALPVLTGMVMDVDADLAAAA
+ELALEQLAIRLDRPGLRVSLEG
+>2_593
+MTAFDRLPLPAEPQTPHDRLRRRVAAAVAERGEAAVAGLAVRLLTGSVTPADVTSGAARA
+LTGDDGDLTAGATGALALGHAWHRSALPALTSALSAPEPDVRSAAHLVLAARAGSLRADV
+AVDRALVDAVRAGCADPDPQVRASAASALGALAGPQDLEAALPVLTGMVMDVDADLATAA
+ELALDHLAERLDRPDLRVGAEG
+>3_518
+MTSRD-LPLPVEPQTPHTRLARRVEAAVSARGEAAVAGLAVRLLTGAPTPEDVTSGAARD
+LIGDDGELTPGATGALALGVVWHRGAAGALAAALDAPEPEVRAAALLVLAARADRLRADA
+QAGRALVEAVTARASDADPQVREAAASALGALARAEDLSAVEPVLSALVMDVDPELATAA
+ELALAHLAARLDRPELDPTPQA
+>4_2034
+MTAFDRLPLPAEPQTPHDRLRRRTEAAVAERGEAAVAGLAVRLMTGAATPEDVTSGAARA
+LTGDDGDLSPAATGALALMHAWHRSALPALTGALTAPEADVRSAAHLVIASRAGSLRRDA
+AVDRALVDAVRAGCADPDPEVRASAASALGALARPEDLESALPVLTGMVMDVDADLAAAA
+ELALEQLAIRLDRPGLRVSLEG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001686.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001686.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f968a7e32361cac66559f5d5751743d8d165c74a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001686.fa
@@ -0,0 +1,46 @@
+>0_2091
+MQCPHFDVGECRSCPLMGVPYARQLADKQAAVLAALADALDADTVVAEPFASAEAGFRNK
+AKLVVTGSAAAPRLGILDPRQHPRHHDGAGVDLRDCGLYEAGMEGVFEACAAAVTAAGLE
+PYDVAARTGELKNVIVTLSPDREAMVRFVLRSADRLDALRAAVPGLLDDLAARGTPAAVV
+SANLLPEHVALPEGDEEIVLAGGPTLRMELNGIGLRLRPQGFFQTNTAVTEGLYATAAAW
+VAEG----GVPA-SAWDLYCGVGGFAFHLAR------AGVRDVWGMESSAEAVAAARETA
+AELGLADRARFSAGDATSALSFEKRRAPEALSFEKRR--------SR-------------
+-----PDAVVVNPPRRGIGAELADALEDSGAPTVLYSSCNPTTLAQDLARMPSYRVARVQ
+LFDMFPQTLHAEVLTLLTRR
+>1_1815
+MQCPHFDVGECRSCPLMGVPYARQLADKQAAVLAALADAVDADTVVAEPFASAEAGFRNK
+AKLVVTGSAAAPRLGILDPRQHPRHHDGAGVDLRDCGLYEAGMEGVFDACAAAVTAAGLE
+PYDVAARTGELKNVIVTLSPDREAMVRFVLRSADRLDALRAAVPGLLDDLAARGTPAAVV
+SANLLPEHVALPEGDEEIVLAGGPTLRMELNGIGLRLRPQGFFQTNTAVTEGLYATAAAW
+VAEG----GVPA-SAWDLYCGVGGFAFHLAR------AGVRDVWGMESSAEAVAAARETA
+AELGLADRARFSDGDATSALSFEKRRAPEALSSKKRR--------PR-------------
+-----PDAVVVNPPRRGIGAELADALEDSGVPTVLYSSCNPATLAQDLARMPSYRVARVQ
+VFDMFPQTRHAEVLTLLTRR
+>2_592
+MQCHHYDAGRCRSCALMGVPYGVQLTDKDAAVCARLDAAVPAEA-WLPPQASAESGFRNK
+AKLVATGTAAAPRLGILDPEQHPRHHDGTGHDLRDCGLYEDGMEAAFHAIAETIPAAGLE
+PYDVAARTGELKSVIVTLSPDRELMVRFVLRSAARLDALRAAVPGLRSALAGLGTPAAVV
+TANLHPEHVALPEGPDEVHLAGDPTLRMELNGIGLRLRPQGFFQTNTDVTRRLYATAAAW
+LAEAAAADGTPVHSAWDLYCGVGGFAFHLARPVAEGGAGVAEVWGLETSEDAVAAARDTA
+AELGLAGAVRFTAGDATRALSPGRREPSEALSSGKREAWDALSSGSREPSDAGAHPDDDA
+APAAMPDAVVVNPPRRGIGPELAARLQDSGVPHVLYSSCNAASLAKDLAAMPAYRARRAQ
+VFDMFPQTGHAETLVLLSRA
+>3_517
+MQCPHFDAGECRSCALMGVPYGAQLADKDAAVRARLAEATDARTRWEAPAASAESGFRNK
+AKLVVTGTAAAPRLGILDPRQHPRHHDGTGVDLRDCGLYEDGMEAAFHAIAGAVTAAGLE
+PYDVAARTGELKNVIVTRSPDRELMVRFVLRSADRLEALRPEVPALREALAALGTPAAVV
+TANLHPEHVALPEGPEEVHLAGDATLRMELNGIGLRLRPQGFFQTNTDITQRLYATAAAW
+LAEAAAEGGTPVERAWDLYCGVGGFAFHLARPVAEGGAGVAEAWGLEVSAEAIEAAREAA
+AELGVAERVRFTAGDATTALA--------------------APGGTR-------------
+-----PDAVVVNPPRRGIGAELAGRFEESGVPFVLYSSCNAATLATDLTAMPSYRVARAQ
+VFDMFPQTGHAETLVLLARR
+>4_2035
+MQCPHFDVGECRSCPLMGVPYARQLADKQAAVLAALADAVDADTVVAEPFASAEAGFRNK
+AKLVVTGSAAAPRLGILDPRQHPRHHDGAGVDLRDCGLYEAGMEGVFDACAAAVTAAGLE
+PYDVAARTGELKNVIVTLSPDREAMVRFVLRSADRLDALRAAVPGLLDDLAARGTPAAVV
+SANLLPEHVALPEGDEEIVLAGGPTLTMRLNGVGLRLRPQGFFQTNTAVTEGLYATAAAW
+VAEA----GLPA-AAWDLYCGVGGFAFHLAR------AGVRDVWGMESSAEAVAAARETA
+AELGLADRARFSAGDATSALSFEKRRAPEALSSKKRR--------PR-------------
+-----PDAVVVNPPRRGIGAELADALEDSGVPTVLYSSCNPATLAQDLARMPSYRVARVQ
+VFDMFPQTRHAEVLTLLTRR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001688.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001688.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad6359d8c570386adf2fd18a42fd3e1a1f9cf5b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001688.fa
@@ -0,0 +1,51 @@
+>0_2096
+MEVLLALSPILLTLVLLLTRLPAWVAPAAGTAVAVLLALTAFGVAPGDLGGAIGAGVPTL
+LEILAIIAGGITLSRVMEYSGGHARLAAWLSAGNGPTIATALLMVHGVIPFLETVTGFGV
+SLIVGVPLLLGLGYTAFRSALISVLALTIGPWGSMAPGTLMGARLFGLDFREIGVTAAVF
+NLPACLVAGVATVLLLRGARGMRVDVGPARTLPWLGVAVLSGVAQWALILGANLVVGTAP
+AGAVATFVLTVAWLLVIRGGRLLPGPGRDVVPYLTLMAGTVLGTTVKGAFGLEGAAALVG
+TPALWAFVAVGVGVQLLHLDAAARRRVPREAGKLWVGTAIPNALYVAFGLILSAGGVSQA
+LAGALSGMGESYLVAMPFLGAFAGFITASNTGAMALIGPLQMDTGAALGVPPPWSNGLHN
+AAAGWGIVAGPARIQVAHGMAAGAQSPHMPGWAVTRRNLFVVLLPAMLAGILGMAVMGWF
+LLPR-
+>1_1820
+MEVLLALSPILLTLVLLLTRLPAWVAPAAGTAVAVLLALTVFGVAPGDLGGAVGAGVPTL
+LEILAIIAGGITLSRVMEYSGGHARLAAWLSAGNGPTIATALLMVHGVIPFLETVTGFGV
+SLIVGVPLLLGLGYTAFRSALISVLALTIGPWGSMAPGTLMGARLFGLDFREIGVTAAVF
+NLPACLVAGVATVLLLRGARGMRVDVGPARTLPWLGVAVLSGVAQWALILGANLVVGTAP
+AGAVATFVLTVAWLLVIRGGRLLPGPGRDVVPYLTLMAGTVLGTTVKGAFGLEGAAALVG
+TPALWAFVAVGVGVQLLHLDAAARRRVPREAGKLWVGTAIPNALYVAFGLILSAGGVSQA
+LAGALSGMGESYLVAMPFLGAFAGFITASNTGAMALIGPLQMDTGAALGVPPPWSNGLHN
+AAAGWGIVAGPARIQVAHGMAAGAQSPQMPGWAVTRRNLFVVLLPAMLAGILGMAVMGWF
+LLPR-
+>2_583
+MQVLLALTPILLTLALLLTRLPAWVAPAAGGVLAAALAPTVFGVDPGVLAAEVGRGVPTV
+VEILAIIAGGITLSRVMEHSGAHARLALWLSAGNGPTLATALLMVHGIIPFLETVTGFGV
+SLIVGVPLLLGLGFTAFRSALLAVLALTIGPWGSMAPGTLMGARLYDLDFQAVGVTAALF
+NLPASLVAGAATVLLLRGAQGMRGDGEPARTVPWLAVGLLSGAAQWALILGANLSVGTAP
+AGAVGTFVLTVAWLLVIRRGRLTPGPGRDVVPYVTLMAGTVFGTTVEDALGLTGVLSVVG
+TPALWSFVAVGAGVALLGLGPHARRTVPGEAARLWVGTAIPNALYVAFGLTLSAGGVSQA
+LAGALSGMGPAYLAAIPVIGAFSGFVTASNTGAMALMGPLQMDTGAALGVPPTWTNGLHN
+AAAGWGIIAGPARIQVAHAMAVGAQTPEMPGWAVSRRALLAVLLPAMVVGIALMSLLGLA
+VLPRV
+>3_506
+MQVLLALAPILLTLGLLMTRLPAWAAPAAGSVAAVVLGLTVFGVDPAVLGAAVGHGVPTV
+LEILAIIAGGITLSRVMEHSGAHARLGGWLSAGNGPTLATALLMVHGVIPFLETVTGFGV
+SLVVGVPLLLGLGFTAYRAALLSVLSLTIGVWGSMAPGTLMGARLAGLDVQEVGVTAAVF
+NLPASLVAGVATVLAVRGARGLRDDSAPARLAPWLGVALASGTAQWALILGANLLVGTAP
+AGAVATFALTLAWLLVIRRGRLTPGPGRDVVPYVTLMAGTVLGTTAEDALGLTGPLSVVG
+TPALWSFVAVGVGLRLLDLDAAARRTVPRESLRLWRGTAVPNALYVAFGLVLSAGGASPA
+LAGALSGLGESYLAAMPFIGAFAGFVTASNTGAMALVGPLQMDTGAALGVPPAWSNGLHN
+AAAGWGIIAGPARIQVAHGMAAPAQTPDMPGRAVSPRGLVAALLPASLAGVAGMSLMGWL
+LLPR-
+>4_2040
+MEVLLALSPILLTLVLLLTRLPAWVAPAAGTAVAVLLALTAFGVAPGDLGGAIGAGVPTL
+LEILAIIAGGITLSRVMEYSGGHARLAAWLSAGNGPTIATALLMVHGVIPFLETVTGFGV
+SLIVGVPLLLGLGYTAFRSALISVLALTIGPWGSMAPGTLMGARLFGLDFREIGVTAAVF
+NLPACLVAGVATVLLLRGARGMRVDVGPARTLPWLGVAVLSGVAQWALILGANLVVGTAP
+AGAVATFVLTVAWLLVIRGGRLLPGPGRDVVPYLTLMAGTVLGTTVKGAFGLEGAAALVG
+TPALWAFVAVGVGVQLLHLDAAARRRVPREAGKLWVGTAIPNALYVAFGLILSAGGVSQA
+LAGALSGMGESYLVAMPFLGAFAGFITASNTGAMALIGPLQMDTGAALGVPPPWSNGLHN
+AAAGWGIVAGPARIQVAHGMAAGAQSPQMPGWAVTRRNLFVVLLPAMLAGILGMAVMGWF
+LLPR-
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001689.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001689.fa
new file mode 100644
index 0000000000000000000000000000000000000000..11ca22094e18bd1270952402c8fadb6a6a59a61e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001689.fa
@@ -0,0 +1,41 @@
+>0_2097
+M---TQPSHPDDVTRARLIPPVPVAVAPMAGGPSTPELVAAVVGAGGGGFLAGGMRTAAQ
+MRAQVDALRALL--------GAERPDRWGVNLFVPDAVNTAIPAAARTEAARSARAAAVA
+AYRAG---LTAD--------------GAADLPAVADVVPDPDAERADFEAMLVAAEEQAW
+PLVSFTFGLPAADVFARLAAAGVPAGATVTDAAEARAALEHGAAFLVVQGHRAGGHRGTS
+DPAAEPTRAELPTVLAAVRDVVGTGAASAAPVVAAGGVGTAEDVRALLTAGADAVSAGTA
+FLLTPEAGTSAAHRAAVAACAAGTRFS-ADDGRARTALTRAYTGRWARSLATAFMAEHPD
+APAAYPEVNVLTKGLRAAAAAVGDLERVHLWAGTEAHRVREAPAADVLASLTP----
+>1_1821
+M---TQPSHPDDVTRARLIPPVPVAVAPMAGGPSTPELVAAVVGAGGGGFLAGGMRTAAQ
+MRAQVDALRALL--------GAEGPDRWGVNLFVPDAVNTAIPDAARTEAARSARAAAVA
+AYRAD---LTAD--------------GAADLPTAADVVPDPDAERADFDALLTAAEEQAW
+PLVSFTFGLPAADVFARLAAAGIPAGATVTDATEARAALEHGAAFLVVQGHRAGGHRGTS
+DPAAEPPRAELPAVLPAVRDVVGTGATSAVPVVAAGGVGTAEDVRALLTAGADAVSAGTA
+FLLTPEAGTSAAHRAAVAACAAGTRFS-ADDGRARTGLTRAYTGRWARSLATAFMAEHPD
+APAAYPEVNVLTKGLRAAAAAAGDLERVHLWAGTEAHRVREAPAVDVLASLTP----
+>2_582
+M---SAAQLPDDVVRARLIPPARVLAAPMAGGPSTPELVAAVVRAGGSGFLAGGMRTAAQ
+VREQVDALRGLLGGGDGSVDGSDAARRWGVNLFVPDAVNTAIPAADRTERARAERRAAVA
+AYRER---LAAEGERAAGGAAAEGAGGAPTLPSPDDVTPDPARERAEFAAMLTAAEEQAW
+PLVSFTFGLPEPAVFARLAAAGIPAGVTVTDADEARSARAHGAAFLVVQGHRAGGHRGTL
+DPAADPVERELPSVLAQVRAVVGT----RVPVVAAGGVGAAAHVRSLLAAGADAVAAGTA
+FLLAAEAGTSVAHRAGIRRCAAGEGFV-GPDGAARTVLTRAYTGRWARTLATDFAAAHPD
+APAAYPELNALTTGLRAAAATAGDLERVHLWAGTQAHTAREAGAADVVAGLTP----
+>3_505
+MSSTTVPSVPAPVP-APLDPPVPVLAAPMAGGPSTPELAAAVIRAGGGAFLAGGMRSAAQ
+VREQVDGLRALL-------TAPEEAGRFGVNLFVPDAVNTAVAASARGGAARIARAQAVA
+SYRERLAPLAAD--------------LGAELPSVLTVTPDPDAERAAFEDMLAAAEEQSW
+PAVSFTFGLPAPDVFARLDAAGIPAGVTVTSPAEAMAAVASGARFLVVQGPKAGGHRATL
+DPQGRPGITDLRTLVFAVRHALG---PAAVPLVAAGGITDGAQVRPLLEAGAVAVAAGTA
+FLLTPEAGTSAAHRTALRQASAGVAFAHPDDGAASTALTRAYTGRWARGLVTPFMDEHHD
+APAAYPEVNGLTGPLRRAAAEEGDLEHVHLWAGTGAHRVEEVGAAEVLASLAPRAEP
+>4_2041
+M---TQPSHPDDVTRARLIPPVPVAVAPMAGGPSTPELVAAVVGAGGGGFLAGGMRTAAQ
+MRAQVDALRALL--------GAEGPDRWGVNLFVPDAVNTAIPDAARTEAARSARTAAVA
+AYRAG---LTAD--------------GAAGLPTAADVVPDPDAERADFDALLTAAEEQAW
+PLVSFTFGLPAADVFARLAAAGIPAGATVTDATEARAALDHGAAFLVVQGHRAGGHRGTS
+DPAAEPTRAEMPTVLAAVRDVVGTGAASAAPVVAAGGVGTAEDVRALLTAGADAVSAGTA
+FLLTPEAGTSAAHRAAVAACAAGTRFS-ADDGRARTGLTRAYTGRWARSLATAFMAEHPD
+APAAYPEVNVLTKGLRAAAAAAGDLERVHLWAGTEAHRVREAPAADVLASLAP----
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001692.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001692.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bbe0c25a759272712e1f049b7752903ac9132897
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001692.fa
@@ -0,0 +1,31 @@
+>0_2102
+MDTSSPAHPFSPTTPGPVAPGPGTPSSSATTTTAPAVCARGLTRAYGRGDAQVHALRGVD
+VDFASGAFTAIMGPSGSGKSTLLHCLAGLDARTSGSVRIGGTEITGLDDTALTRLRRDRV
+GFVFQAFNLVPTLTAEQNIVLPLELAGRTPDRAWLDEITRALGLADRLGHRPHELSGGQQ
+QRVAVARALLTRPDVVFGDEPTGNLDTATSAEVLGLLRRSAREMGQTVIMVTHDPVAASA
+ADRVVLLADGRLAGELVDPTVESVTAALTALSA------------PAEGGVR
+>1_1827
+MDTSSPAHPFSPTTPGPVAPGPGTPSSSATTTTAPAVCARGLTRAYGRGDAQVHALRGVD
+VDFASGAFTAIMGPSGSGKSTLMHCLAGLDAPTSGSVRIGGTEITGLDDTALTRLRRDRV
+GFVFQAFNLVPTLTAEQNIVLPLELAGRTPDRAWLDEITRTLGLADRLGHRPHELSGGQQ
+QRVAVARALLTRPDVVFGDEPTGNLDTATSAEVLGLLRRSAREMGQTVIMVTHDPVAASA
+ADRVVLLADGRLAGELVDPTVESVTAALTALSA------------PAEGGVR
+>2_576
+MSTTADSHSAHSTPPGAGASGPGMPSSSTTTTTAPAASARALTKTYGRGDAEVHALRGVD
+VDFAAGAFTAIMGPSGSGKSTLMHCLAGLDTPTSGSVVLGGTEITGLGDTALTRLRRDRV
+GFVFQAFNLVPTLTAEQNIVLPLELAGRKPDRAWLDEITATLGLTDRLKHRPHELSGGQQ
+QRVAVARALLTRPDVVFGDEPTGNLDSATSAEVLGLLRRSAREMGQTVIMVTHDPVAASA
+ADRVVLLADGRLAGELLDPTVESVTNALAALSAPGAADAAGTFDAPADGG-R
+>3_500
+MDITSPRSAAHDAGAHALA----TPLAHAAAPPAPAVSARGLTKTYGRGDAAVHALRGVD
+VDVETGRFTAIMGPSGSGKSTLMHCLAGLDTPDAGVVTLGDTVITGLSDAALTRVRRDRV
+GFVFQAFNLVPTLTAEQNIVLPMELAGRTPDRAWLAEIVDRLGLSDRLAHRPHELSGGQQ
+QRVAVARALLTRPDVVFGDEPTGNLDSATGAQVLDLLRRATRETGQTVIMVTHDPVAAAA
+ADRVVLLADGALAGELHAPTAERVAEALTALQQGRPLPQGRPL--PQDGG-R
+>4_2048
+MDTSSPAHPFSPTTPGPVAPGPGTPSSSATTTTAPAVCARGLTRAYGRGDAQVHALRGVD
+VDFASGAFTAIMGPSGSGKSTLMHCLAGLDAPTSGSVRIGGTEITGLDDTALTRLRRDRV
+GFVFQAFNLVPTLTAEQNIVLPLELAGRTPDRAWLDEITRTLGLADRLGHRPHELSGGQQ
+QRVAVARALLTRPDVVFGDEPTGNLDTATSAEVLGLLRRSAREMGQTVIMVTHDPVAASA
+ADRVVLLADGRLAGELVDPTVESVTAALTALSA------------PAEGGVR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001695.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001695.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98841880fb61c1302b7d59d4c9d0751bf323123a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001695.fa
@@ -0,0 +1,36 @@
+>0_2108
+MARTWDGSYPRSVTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLTVCFVADVA
+LLVLGAGGVGVVAERWPWLVPALTVAGVVYLLGFAAGALRSAWRGDRTLSTAAADVEGTG
+HGPDRIDLAVLTGELPLIDPVTGRLA----------EREPAGAGVGH---HDD-------
+------GAPGF--------GAPSG-GGSVTVRQR----VQPRRVALDRPQTPLPRIILLA
+LSVSLVNPHAILDTVVMMGTFAQTFGAAKWAYVGGAVAASLVWFTALGWGGTKLAPSMDS
+ARTWRIVDAVVGVLMLGIAVKVGLTLL
+>1_1833
+MARTWGDSYPRSVTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLTVCFVADVA
+LLVLGAGGVGVVAERWPWLVPALTVAGVVYLLAFAVGALRSAWRGDRTLTTAAADAAGTG
+HGPDRIDLAVLTGELPLIDPATGRLA----------EREPAGAGVGQ---HDD-------
+------GAPGV--------GAPSG-GGSVAARQR----VQPRRVALDRPQTPLPRIILLA
+LSVSLVNPHAILDTVVMMGTFAQTFGAAKWTYVGGAVAASLVWFTALGWGGTKLAPSMDS
+ARTWRIVDAVVGVLMLGIAVKVGLTLL
+>2_565
+------------MTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLIVCFLGDVA
+LLALGAAGIGVVAERWPWLVTALTVAGVVYLVWFAAGALRSAVRGQRTLA-AAAEAEGPA
+VGLTDGEIAALTGELPLIDPATGRLSADFTGRTAEGRAVPVGAGVGMGRGHDPLGDESRT
+VGGIPVGNPRLCGTRPGERGADGR-SGGVAVKQR----VQPRRVVLSAPQTPLPRIVLLA
+LSVSFLNPHAVLDTVVMMGTFAQTYGPGKWVYVGGAVAASLVWFTALGWGGTRLAPYMNT
+PRTWRIVDAAVGVLMLVIAAKVGLTLL
+>3_492
+------------MTVFSAGFLTYLALIVAIGAQTLFLLRQVVRGDRAWTAIGVCFLSDIV
+LLLAGAAGVGAAAERAPWLVPALTVAGVAYLVWFGVSALRSAHRGDRTLAGAAAEVEDDA
+WAPTAEEVAAMTGSLPVVAAG-----------------------------PDA-------
+------GADAA--------TAPAGTGGGVALRTRPVSTTAPASAAPRPALTPLPRLVLLC
+LSVSLLNPHAILDAVVMMGTFAQGYGADKWLYVAGAVASSALWFLVLGWGGAKLAPLMNT
+PRTWRIVDGAVGVVVLGIAGKVALTLF
+>4_2054
+MARTWDGSYPRSVTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLTVCFVADVA
+LLVLGVGGVGVVAERWPWLVPALTVAGVVYLLAFAVGALRSAWRGDRTLTTAAADGAGTG
+HGPDRIDLAVLTGELPLIDPATGRLA----------DREPAGAGVGR---HDD-------
+------GAPGV--------GAPSG-GGSVAVRQR----VQPRRVALDRPQTPLPRIILLA
+LSVSLVNPHAILDTVVMMGTFAQTFGAAKWVYVGGAVAASLVWFTALGWGGTKLAPSMDS
+ARTWRIVDAVVGVLMLGIAVKVGLTLL
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001699.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001699.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eed06171cbc4fe0139b6c25d4a6a8ccfc8db7387
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001699.fa
@@ -0,0 +1,36 @@
+>0_2115
+MPSTALASPARVRAGVLMGALPAALLLAALVAGVALGARTVPATTALDTL-GAILTGHPV
+PEGIEAAAVASRVPRVVTGALVGAALAVAGAALQGATRNPLGDPGLLGLSAGAGLAVAAG
+MALGVAGSTFGVLALAAVGTLVAAALGYAVAAAATRSGR-TPGAPSPMALVLAGAALTAG
+ATAGTTALLVLSPTVQDRLRFWAVGTVARADLGEALALAPVIAVGLLAAVAVAPGLDALA
+LGDDLAHGLGGRPERVRAVLLGAVVLLTAAAVALAGPVGFVGLLVPHALRRLRPPSTRAL
+MVGCALWGAVLVILADLAGRLVVAPGEIHLGVTTVLLGVPVLLALLRRPGVAA
+>1_1840
+MPSTALASPARVRAGVLMGALPAALLLAALVAGVALGARTVPATTALDTL-GAVLTGHPV
+PEGIEAAAVASRVPRVVTGALVGAALAVAGAALQGATRNPLGDPGLLGLSAGAGLAVAAG
+MALGVAGSTFGVLALAAVGTLVAAALGYAVAAAATRRGRTTPGAPSPMALVLAGAAITAG
+ATAGTTALLVLSPTVQDRLRFWAVGTVARADLGEALALAPVIAVGLLAAVAVAPGLDALA
+LGDDLAHGLGGRPERVRAVLLGAVVLLTAAAVALAGPVGFVGLLVPHALRRLRPPSTRAL
+MAGCALWGAVLVILADLAGRLVVAPGEIHLGVTTVLLGVPVLLALLRRPGVAA
+>2_558
+MPR------------ALLLIAPAVLAVLAALASLALGARPVPVDAAVGALTEAALHGPAA
+VTGMDGAAVLSRVPRTLAAILVGAGLAVAGAALQGATRNPLGDPGLLGLTAGAVLAFALG
+IALGVAGSLPAVMALAILGTLAAAALVTAVAAGAARVSG-VPGPPSPLSLVLAGAATTAG
+ATAVTSALVVLHPAVRDRLRLWTVGSVARADLGDALWLAPVVLAAVAAVVVLGPGMDALA
+LGTDLAHGLGARPERVRALLLAAAVVLTAAAVALAGTVGFLGLVIPHAVRRLRPPDARTL
+VLACALWGAVLVLVADTLGRLVIAPAEVHLGVTTAVLGVPVLLALLRRRGVAA
+>3_486
+MPSSP------TRGALLFGLLPLALLLTAGLAALALGARPVPLTTTATTL-QAMLAGEGV
+PAGVDAAAVASRVPRTLTAALVGAALAVAGAALQGATRNPLGDPGLLGLSAGASLATAIG
+LALGVSGSTFWVLALAAAGTLAAALLVYAVAAAASRGAG-AGGAPTPIGLVLAGAAVTAG
+AGAVTTALLVLSPVVRDRFRFWAVGTVARADLGEAALLTPVIGLGIVLALAAARGLDALA
+LGDDLAHGLGARPGRTRALLLAAVVLLTAAAVALAGPVGFVGLVVPHALRRLRPGGTRTL
+LIGSALWGAVLLVAADLLGRLVIAPAEIHLGVTTVLLGVPVLLVLLRRTGLGS
+>4_2061
+MPSTALASPARVRAGVLMGALPAALLLAALVAGVALGARTVPATTALDTL-GAVLTGHPV
+PEGIEAAAVASRVPRVVTGALVGAALAVAGAALQGATRNPLGDPGLLGLSAGAGLAVAAG
+MALGVAGSTFGVLALAAVGTLVAAALGYAVAAAATRRGR-TPGAPSPMALVLAGAAITAG
+ATAGTTALLVLSPTVQDRLRFWAVGTVARADLGEALALAPVIAVGLLAAVAVAPGLDALA
+LGDDLAHGLGGRPERVRAVLLGAVVLLTAAAVALAGPVGFVGLLVPHALRRLRPPSTRAL
+MVGCALWGAVLVILADLAGRLVVAPGEIHLGVTTVLLGVPVLLALLRRPGVAA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001707.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001707.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b00ac16e533c1cd393dcd2c2c80ab8f59dbc2de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001707.fa
@@ -0,0 +1,21 @@
+>0_2124
+MTQP------TTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLAEEARVRALA
+AWATTTASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRC
+VLCDAVFVQVDPAAGRPVAVSDEERAAFERVLIPAED---
+>1_1849
+MTQP------TTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLAEEARVRALA
+AWATTTASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRC
+VLCDAVFVQVDPAAGRPVAVSDEERAAFERVLIPAED---
+>2_547
+MNGQDGGQGRTTTDGATGREAPVPFETEIQVRWSDEDRYGHVNNARLLTLTEEARVRATR
+AWSGVTPGRDVHRVVRAMEVQYEAPVVY-GPELTAKVWIARIGTSSYTLRHELWQDGRRC
+VLCDAVFVHVDPETGRSVALAEDERVTLERVLIPAEADAT
+>3_473
+MSDS----------------QPRPYEGVLDLRWSDMDLYGHVNNVRILTLTEEARVRALK
+AWDEGDVGRDVMRVVRAMTTEYERPVEY-GPELTAKVWVRALGRTSYTLHHELWQEGVRC
+VTCDAVMVHLDPETGAPLPHDDARRARLQAVLVPAEG---
+>4_2070
+MTQP------TTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLTEEARVRALA
+AWATTTASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRC
+VLCDAVFVQVDPAAGRPVAVSDEERAAFERVLIPAED---
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001713.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001713.fa
new file mode 100644
index 0000000000000000000000000000000000000000..640dabd2824a4decb19b8dda0cf01af4a8ebdc83
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001713.fa
@@ -0,0 +1,31 @@
+>0_2135
+M----SSTPTDAD----HHGPGPAPVPAHLDDLPPATLVARGLTLRGGRGPVFGPLDLVL
+PPQTHLAVLGTQGSGRSALLLALTGRLQGVRGELVLTGGPVDVALDGPERPAARAYRPPI
+DAARHPHALRARTAVAHTTDVVELEPALTAAEVVDERCLADGVRRRAGRARFALLADAVR
+LSVAPEAVVGELPAPERALLAAVVACLRPARLVTFDDVDATLTIDELVALHAALDVLKDH
+GHPFAVSAVASAPVPRDAVVLTLP--------------PVREN
+>1_1859
+M----SSTPTDAD----HHGPGPAPDPAHLDDLPPATLVARGLTLRGSRGPVFGSLDLVL
+PPQTHLAVLGTQGSGRSALLLALTGRLQGVRGELVLTGGPVDVALDGPERPAARAYRPPI
+DAARHPHALRARTAVAHTTDVVELEPALTAAEVVDERCLTDGVRRRAGRARFALLADAVR
+LTVAPEAVVRELSAPDRALLAAVVACLRPARLVTFDDVDATLTIDELVALHAALDVLKDH
+GHPFAVSAVASAPVPRDAVVLTLP--------------PVREN
+>2_530
+M----SSTPTDAD----HHGPGPVSVPAHLDDLPPATLVARGLTLRGGRGPVFGPLDLVL
+PPQTHLAVLGTQGSGRSALLLALTGRLRGVRGELVLTGGPVDVALDGPERPAARAYRPLI
+DATRHPYALRARTAIAHTTDVVELEPALTAAEVVDERCLADGVRRRAGRARFALLADAVR
+LTVAPEAVVGELSAPDRALLAAVVACLRPARLVTFDDVDATLTLDELVALHAALDVLKDH
+GHPFAVSAVASAPVPRDAVVLTLP--------------PVREN
+>3_462
+MTEDQTPAPIETDDVVAERAPEPAPGGSHQVG---RALTARGLTLRSIRGTVFGPVDVDL
+PPGVPGAVLGTQGSGRSALLLALVGRLQGVGGELTLGD---------------------M
+DGIRHPHRLRRATTVARITDYVELEPLLTIRECIDEHCLAEGISRRTGRKRFARLEAAVG
+FHPDHGDQVSSLPVEDRTILTCMLACLRPADVIVYDDIDSSLTRPQLEHVYRVLETLGRL
+GHRFVVSALTSAPVPRGAVVVELPTPGHDDLPAALPTRPSLED
+>4_2080
+M----SSTPTDAD----HHGPGPAPVPAHLDDLPPATLVARGLTLRGGRGPVFGPLDLVL
+PPQTHLAVLGTQGSGRSALLLALTGRLQGVRGELVLTGGPVDVALDGPERPAARAYRPPI
+DAARHPHALRARTAVAHTTDVVELEPALTAAEVVDERCLADGVRRRAGRARFALLADAVR
+LSVAPEAVVGELPAPERALLAAVVACLRPARLVTFDDVDATLTIDELVALHAALDVLKDH
+GHPFAVSAVASAPVPRDAVVLTLP--------------PVREN
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001720.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001720.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0566b59a451db2c64b162292707b733d37695d29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001720.fa
@@ -0,0 +1,46 @@
+>0_2147
+MTQTPTAPDRTGATAPDDLALAIPGTTVRGRAARVLPQDRPDTTSWAPRTAES-------
+---------R-------AAATTPGLPGVVGSPAVRPPGAAHLTDAQVAELGRELDAIRDD
+VLARRGTSDAAYIRRVIRWQRRLELGGRALLLNARHPAAFVAGTAMLTVAKIVENMEIGH
+NVLHGQWDWMRDPDIHSTTWEWDFVTPSRAWQNTHNDLHHRWTNVVGKDRDVGYNVLRMD
+ESEPWRPRHLLNPVINAGLAPIFEWGIALYDLELDRVQSGEKSREELMTDLRSVGVKAAR
+QFAKDYVATPAVAEVLTGSGKAALVGTLLANGLRNIWAHAVIFCGHFPEGAETFSEEMVD
+GETRGDWYVRQMIGSANISGSKLMHFMTGNLSHQVEHHLFPDLPSSRYAEVAPRVREICA
+RYGLPYTTGPLLRQVGSAWKKVFRLALP
+>1_1871
+MTQTPTTPSRTGATAPDDLALAIPGTTVRGRAARVLPQDRPDTTSWAPHTAES-------
+---------RAATSRSTAAATTPGLPGVVGSPAVRPPGAAHLTDAQVAELGRELDAIRDD
+VLARRGTSDAAYIRRVIRWQRRLELGGRALLLNARHPAAFVAGTAMLTVAKIVENMEIGH
+NVLHGQWDWMRDPDIHSTTWEWDFVTPSRAWQNTHNDLHHRWTNVVGKDRDVGYNVLRMD
+ESEPWQPRHLLNPVINAGLAPIFEWGIALYDLELDRVQSGEKSREELMTDLRSVGVKAAR
+QFAKDYVATPAVAEVLTGSGKATLAGTLLANGLRNIWAHSVIFCGHFPEGAETFSEEMVD
+GETRGDWYVRQMIGSANISGSKLMHFMTGNLSHQVEHHLFPDLPSSRYAEVAPQVREICA
+RYGLPYTTGPLLRQVGSAWKKVFRLALP
+>2_519
+MTQTLPATERTGATAPDDLSLAIPGTTVRGRTARVLPEDRPDTTSWAPQTADAGTDAAAP
+AASETPEAPTADAATRPAANAKPGLLGVVGSPAVRPPGAAHLTDEQVAELGRELDAIRDD
+VLSRRGASDAAYIRRVIRLQRWLEIGGRAALLNARHPAAFVAGTTMLTVAKIVENMEIGH
+NVLHGQWDWMRDPDIHSTTWEWDFVTPSRAWQNTHNDLHHRWTNVIGKDRDVGYNVLRMD
+ESEPWRPRHLLNPVINAGLAPIFEWGIALYDLELDRVHAGEKSRKELMTDLRSVGVKASR
+QFAKDYVATPAVAEFLTGSGKAALVAGLLANGLRNIWAHSVIFCGHFPEGAETFSEEMVD
+GETRGDWYVRQMIGSANISGSKLMHFMTGNLSHQVEHHLFPDLPSNRYAEVAPKVREICA
+RYGLPYTTGPLLKQVGSAWKKVFRLALP
+>3_451
+MI----------------------------RSA---------------------------
+------------------------------------------------------------
+-----------------------------------------------TAGKIIENMEIGH
+NVLHGQWDWMRDPDIHSTTWEWDFVTPSSAWQHTHNDAHHRWTNVTGLDEDLGYNVLRMD
+EAEPWEPRHLLNPVINAILAPFFEWGIAIYDLELAKVRAGEKPVADLRRDLASVAVKAVR
+QLAKDSLATPIAAELVSRSGSA--------------------------------------
+------------------------------------------------------------
+------------------WRKVFRLALP
+>4_2092
+MTQTPTTPSRTGATAPDDLALAIPGTTVRGRAARVLPQDRPDTTSWAPHTAES-------
+---------RAATSRSTAAATTPGLPGVVGSPAVRPPGAAHLTDAQVAELGRELDAIRDD
+VLARRGTSDAAYIRRVIRWQRRLELGGRALLLNARHPAAFVAGTAMLTVAKIVENMEIGH
+NVLHGQWDWMRDPDIHSTTWEWDFVTPSRAWQNTHNDLHHRWTNVVGKDRDVGYNVLRMD
+ESEPWQPRHLLNPVINAGLAPIFEWGIALYDLELDRVQSGEKSREELMTDLRSVGVKAAR
+QFAKDYVATPAVAEVLTGSGKATLAGTLLANGLRNIWAHSVIFCGHFPEGAETFSEEMVD
+GETRGDWYVRQMIGSANISGSKLMHFMTGNLSHQVEHHLFPDLPSSRYAEVAPQVREICA
+RYGLPYTTGPLLRQVGSAWKKVFRLALP
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001726.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001726.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a9fb450ba7199d17a8df83bd13d496d9a7e4f2c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001726.fa
@@ -0,0 +1,45 @@
+>0_2180
+MTSGPP-SPAL--------PAGPAAHLRGEHLTVSLGGHRVLTDATVRINAGSRLGIVGENGRGKTTLLHVLTGRITPDV
+GRVTRAGTLAFVPQALRARADGRSRTVGDLVRDALTGPHAALEALDAAAAALAEAPDDAGAGHRYSTALERAHLYDAWDA
+GRRVDMDLEGLHACTDREHPLTSLSVGQRHRVRLAVTLGSRPDLLLLDEPTNHLDDVALDFLTRRLVEHPGGVAVVSHDR
+ALLRAVCTDIVDLDPSQDGRPRRYSGGYAGWAKGRRRARAAWEQEYAEQNAERERLELAVEDAREQM-QGSWRPPKGTGK
+HQRSSRSAGIVQMFNRRFDELEAHRITVPEPPLRLDWPFADMPDGDPRDGADAAAGTAGGPGTAGDDVLLTADAVRVAGR
+LEQPMGAALVPGGRVLVTGPNGAGKSTLLRVLAGDLEPTSGLVTVGADVRVRLVAQETPAWDEERTAAAVFEEHVRRVG-
+-ADEAGVDDLGRPLPAPTLPSLGLLTAEAADTPVGRLSQGQQARLHLAMVLIERPHVLLLDEPTNHLSPALVDEMTEALQ
+VTEQAVVVVTHDRQMLADLADWPRVELRTDAAAV
+>1_1893
+MTSGPP-SPAL--------PAGPAAHLRGEHLTVSLGGHRVLTDATVRINAGSRLGIVGENGRGKTTLLHVLTGRITPDV
+GRVTRAGTLAFVPQALRARADGRSRTVGDLVRDALTGPHAALEALDAAAAALAEAPDDAGAGHRYSTALERAHLYDAWDA
+GRRVDMDLEGLHACTDRERPLTSLSVGQRHRVRLAVTLGSRPDLLLLDEPTNHLDDVALDFLTRRLVEHPGGVAVVSHDR
+ALLRAVCTDIVDLDPSQDGRPRRYSGGYAGWAKGRRRAQAAWEQEYAEQNAERERLELAVEDAREQM-QGSWRPPKGTGK
+HQRSSRSAGIVQMFNRRFDELEAHRITVPEPPLRLDWPFADMPDGDPRDGADAAAGTAGGPGTAGDDVLLTADAVRVAGR
+LEQPMGAALVPGGRVLVTGPNGAGKSTLLRVLAGDLEPTSGLVTVGADVRVRLVAQETPAWDEERTAAAVFEEHVRRVG-
+-ADEAGVDDLGRPLPAPTLPSLGLLTAEAADTPVGRLSQGQQARLHLAMVLIERPHVLLLDEPTNHLSPALVDEMTEALQ
+VTEQAVVVVTHDRQMLADLADWPRVELRTDAAAV
+>2_697
+MTLTPPHAPAL--------PAGASAHIRAECITLTLGDRTVLDQADVTVSAGSRLAIVGENGRGKTTLLHVLAGTLAPDA
+GTVTRAGTLALVEQDLDADDD---RTVGDLIHDAVGESLAVLDRLEAATRALAEG--RPGADDDYARALETATALEAWDA
+ERRIDVALEGLSACTDRTRPLNSLSVGQRYRVRLAVVLGSAVDLLLLDEPTNHLDAGALEHLTRALREHPGGVAVVTHDR
+ALLKDVAETFLDLDPTSDGRPRQYAGGYAGWEKGRSAERAAWEQAHEQQVAEHAALAEAAEAARGRL-QDRWRPDKGTGK
+HQRATRAAGVVQAFNRRVRDLEAHEVTVPEPPRALAWPASSTRAARP---------------------LLNAEGVDVAGR
+LRGPVSADLTGGDRLLLTGPNGAGKSTLLHVLAGRLDPTAGRVLRHTGARIALLTQEAPAWNPRHTARQAFEVHLHRRGL
+LADDDG--------GAPPLASLGLLEPRSMDAPVGRLSQGQQRRLHLALCLAERPDLLMLDEPSNHLSATLVDELTEALR
+ATRSAVVVATHDRQMLRDLSDWPRLELTAEAVAR
+>4_2113
+MTSGPP-SPAL--------PAGPAAHLRGEHLTVSLGGHRVLTDATVRINAGSRLGIVGENGRGKTTLLHVLTGRITPDV
+GRVTRAGTLAFVPQALRARADGRSRTVGDLVRDALTGPHAALEALDAAAAALAEAPDDAGAGHRYSTALERAHLYDAWDA
+GRRVDMDLEGLHACTDRERPLTSLSVGQRHRVRLAVTLGSRPD-LLLDEPTNHLDDVALDFLTRRLVEHPGGVAVVSHDR
+ALLRAVCTDIVDLDPSQDGRPRRYSGGYAGWAKGRRRARAAWEQEYAEQNAERERLELAVEDAREQM-QGSWRPPKGTGK
+HQRSSRSAGIVQMFNRRFDELEAHRITVPEPPLRLDWPFADRPDGDPRDGADAAAGTAGGPGTAGDDVLLTADAVRVAGR
+LEQPMGAALVPGGRVLVTGPNGAGKSTLLRVLAGDLEPTSGLVTVGADVRVRLVAQETPAWDEERTAAAVFEEHVRRVG-
+-ADEAGVDDLGRPLPAPTLPSLGLLTAEAADTPVGRLSQGQQARLHLAMVLIERPHVLLLDEPTNHLSPALVDEMTEALQ
+VTEQAVVVVTHDRQMLADLADWPRVELRTDAAAV
+>4_2153
+M----PTSRSLRSCVWNGTPQGHAAHIRAESIHITLGDRHVLNGVDVTVSVGSRLAIVGDNGRGKTTLLHLLAGILQPDS
+GVVTQAGSLVLVKQDMATEGD---RTVGDLIAEATGPSKSALEALDATSAALAEGDDAADA---YSAALERATLLDAWDA
+ERRVDIALEGLNACSDRDRVLSTLSVGQRYRVRLAVALGSTPDLLLLDEPTNHLDAAGLSFLTERLRDHAGGLALVSHDR
+ALLRDVATTFLDLDPTRDGRPRTYAGGYQGWVEGRQRERVSWEQDHAAQVARHAQLTRAAAEARSRLSQGGWRPDKGTGK
+HQRATRAAGVVQAFNRRVEDLERHEIDVPEPPLRLAWPKSSARRGMS---------------------IVNASMLTVERR
+LDTPVSIGVNGGDRLVVTGPNGAGKSTLLAVLGQRLVPTTGYVQVNPSARIALLSQEVPDWDRTSPAHVAYETYLGKLGC
+RSQ------------APSLGSLGLLEASATSTPVGRLSQGQQRRLHLALCLAQDPDLLLLDEPTNHLSSSLVDDITTELL
+QTPCAVIVATHDRQMLDDLADWPHLDLDPKDMP-
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001732.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001732.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1511ed70dff42bb78248378ded68224245cf601
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001732.fa
@@ -0,0 +1,21 @@
+>0_2195
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTASHHLLQ
+HLPLLFVPAGVGVVAVLGLIEEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTD-KEDA
+Q
+>1_1906
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTASHHLLQ
+HLPLLFVPAGVGVVAVLGLIEEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTD-KEDA
+Q
+>2_457
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTTSHHLLQ
+HLPLLFVPAGVGVVAVLGLIGEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTNKKENA
+Q
+>3_413
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVITASHQLLQ
+HLPLLFVPAGVGVVAVLGLIQEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTNKKEDA
+Q
+>4_2127
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTASHHLLQ
+HLPLLFVPAGVGVVAVLGLIEEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTD-KEDA
+Q
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001734.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001734.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e64d27b78de8e9ebe8752a577e73a359c6a592c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001734.fa
@@ -0,0 +1,45 @@
+>0_2207
+MPTLRTVPLSAATREDHLARLRATSPEAPLDILVVGGGSTGVGAAFDAATRGLDVGIVEARDWASGTSSRSSRLMHGGLR
+YLEMLDVKLVYEALRERDLLLTQTAPHLVRPLRFVFPFFHKVIDRGFIGAGVTMYDAMQSLGRRRAMGAHRHLSRRSMAA
+TFPSLDDEKIVGAVEYADAQFDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGDDGRVQGVRVREETSGEEFDVHARAVI
+LAGGVWTQEQQELAGADGGLEVLASKGAHITVPRDRIRADAATGVITKTEKSVLFLIPWDEYWVIGTTDTPWAEDVAHPA
+TTADDIDYILEHANAVLKEDLTRDDVVATYAGLRPLLQPVTGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTYRAMAED
+VVDFVVRETHPTRPSLTERIPVLGGLGYSEIEAEADRIAADYGLDEARVDRLLFRYGTVLRHVLDLIDADPSLSVPLAEA
+PRYLRAEIVYAARAEGVVHLDDVIERRTRLSTEVRDRGVAAAEEIASLVAPELGWDEERIAGEIRAYKNLVAARLRGETA
+HDDVTAAAALAAADADA--APT-----------P-------
+>1_1911
+MPTLRTVSLSAATREDHLARLRATSPEAPLDILIVGGGSTGVGAAFDAATRGLDVGIVEARDWASGTSSRSSRLMHGGLR
+YLEMLDVKLVYEALRERDLLLTQTAPHLVRPLRFVFPFFHKVIDRGFIGAGVTMYDAMQSLGRRRAMGAHRHLSRRSMAA
+TFPSLDDEKIVGAVEYADAQFDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGDDGRVQGVRVREETSGEEFDVHARAVI
+LAGGVWTQEQQELAGADGGLEVLASKGAHITVPRDRIRADAATGVITKTEKSVLFLIPWDEYWVIGTTDTPWAEDVAHPA
+TTADDIDYILEHANAVLKEDLTRDDVIATYAGLRPLLQPVTGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTYRAMAED
+VVDFVVRETHPTRPSLTEHIPVLGGLGYSEIEAEADRIAADYGLDEARVDRLLFRYGTVLRHVLDLIDGDPSLSVPLAEA
+PRYLRAEIVYAARAEGVVHLDDVIERRTRLSTEVRDRGVAAAEEIASLVAPELGWDEERIAGEIRAYKNLVAARLRGETA
+HDDVTAAAALAAADA----APVHGKEPVHGHDLPA------
+>2_444
+----------------------------------MGGGSTGVGAAFDAATRGLDVGIVEARDWASGTSSRSSRLMHGGLR
+YLEMLDVKLVYEALRERDLLLTQTAPHLVRPLRFVFPFFHKVIDRGFIGAGVTMYDAMQSLGRRRAMSAHRHLSRRSMAA
+TFPSLDDEKIVGAVEYADAQFDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGDDGRVQGVRVREETSGEEFDVHARAVI
+LAGGVWTQEQQELAEADGGLEVLASKGAHITVPRDRIRADAATGVITKTEKSVLFLIPWDEYWVIGTTDTPWAEDVAHPA
+ATADDIDYILEHANAVLKEDLTRDDVIATYAGLRPLLQPVTGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTYRAMAED
+VVDFVVRETHPTRPSLTERIPVLGGLGYSEIEAEADRIAADYGLDEARVDRLLFRYGTVLRHVLDLIDADPSLSVPLAEA
+PRYLRAEIVHAARAEGVVHLDDVIERRTRLSTEVRDRGVAAAEEIASLVAPELGWDEERIAGEIRAYKSLVAARLRGETA
+HDDVTAAAALAAADA----ASTH------------------
+>3_476
+MPTLRTVELSPATRADHLARLRAADADHPLDVLVVGGGSAGVGAAFDAATRGLDVGIVDAGDWAGGTSSRSSRLMHGGLR
+YLEMLDVKLVYEALRERDLLLTRTAPHVVRPLRFVFPLEH-ARDRGWIGAGVGVYDAMQSVGRRRAVGGHRHLGRKALAE
+TFPGLDPEAAVGAVEYADAQFDDARLALLLVRSAVDLGAAALNHAPVVGYLKDGAGAVVGARVRESLTGEELQVHARAVI
+LAGGVWTQEQQELAGVDGGLEVLASKGVHVTVPRERIAAEPGVGVITRTEKSVLFVIPSDEHWIIGTTDTPWRQDVDHPA
+ATAADVDYVLEHANAVLSEDLTRADVVAVYAGLRPLLQPAAGADDASTKVSREHTVTELAPGLTAVAGGKWTTYRAMAED
+TVDFAVRDLFPTRPSLTAHTPVLGGLGYAEIAARAAEIAAERGFDAARVDRLLRRYGTLLPHVLALVDADPALGEPLPGG
+EAYLRAEVVYAARAEGAVHLDDVLERRLRLSTEVPDRGADAASEAAALVADVLGWDAARRDAEVAAYRALVAARRRAEGL
+DDDAAAAAELAAAGERAGVVPVTSRETVT----PEEKGGAR
+>4_2140
+MPTLRTVSLSAATREDHLARLRATSPEAPLDILIVGGGSTGVGAAFDAATRGLDVGIVEARDWASGTSSRSSRLMHGGLR
+YLEMLDVKLVYEALRERDLLLTQTAPHLVRPLRFVFPFFHKVIDRGFIGAGVTMYDAMQSLGRRRAMGAHRHLSRRSMAA
+TFPSLDDEKIVGAVEYADAQFDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGDDGRVQGVRVREETSGEEFDVHARAVI
+LAGGVWTQEQQELAEADGGLEVLASKGAHITVPRDRIRADAATGVITKTEKSVLFLIPWDEYWVIGTTDTPWAEDVAHPA
+TTADDIDYILEHANAVLKEDLTRDDVVATYAGLRPLLQPVTGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTYRAMAED
+VVDFVVRETHPTRPSLTEHIPVLGGLGYSEIEAEADRIAADYGLDEARVDRLLFRYGTVLRHVLDLIDADPSLSVPLAEA
+PRYLRAEIVYAARAEGVVHLDDVIERRTRLSTEVRDRGVAAAEEIASLVAPELGWDEERIADEIRAYKNLVAARLRGETA
+HDDVTAAAALAAADA----APT-----------P-------
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001737.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001737.fa
new file mode 100644
index 0000000000000000000000000000000000000000..55488c51f8e6dbc86617684e3fde5002db30d231
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001737.fa
@@ -0,0 +1,41 @@
+>0_2224
+MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA
+VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV
+RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV
+EESKGTDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM
+GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR
+LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTCVFPNPADTKVLEEGD
+RLLCFGKTENMRALIPARARRPKRVRRLPATPIL-ASVAEEAPAPEAPADDA
+>1_1926
+MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA
+VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV
+RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV
+EESKGTDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM
+GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR
+LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTSVFPNPADTKVLEEGD
+RLLCFGKTENMRALIPARARRPKRVRKLPATPIL-ASVAEEAPAPEAPADDA
+>2_434
+MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA
+ILPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV
+RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV
+EESKGKDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM
+GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR
+LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTSVFPNPADTKVLEEGD
+RLLCFGKTENMRALIPARARRPKRVRKLPATPIL-ASVAEEAPAPEAPADDA
+>3_388
+MKLAILSRSLRAYSTQRLKSAALDRGHDVKVLDTLRFGIDLAGDEPDMMFRGKPLSSYDA
+VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRASQILSRHGIAQPATVFV
+RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV
+EESKGKDVRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVEQVELSEEYAETAVRAAHIM
+GLRVAGVDMLEGEDGPLVMEVNSSPGLEGIERATTLDVAGAIVDYIADQAGFPEVDVRQR
+LAVSTGYGVAEIAVLAGSDMAGQSIEDSGLLEKDLQVLTLHRGASVFPNPADSKVLEEGD
+RLLCFGKTENMRALIPARSQRPKRVKKLPKNPIIEAPPAEPAVRPDAESGES
+>4_2164
+MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA
+VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV
+RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV
+EESKGTDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM
+GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR
+LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTSVFPNPADTKVLEEGD
+RLLCFGKTENMRALIPARARRPKRVRKLPATPIL-ASVAEEAPAPEAPADDA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001749.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001749.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc9a031deaecd2628df2e9f344b641e603c10ba4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001749.fa
@@ -0,0 +1,60 @@
+>0_2240
+M-------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-----------------------DPADETPEGERRAGRSTAIMASGTLLSRVLGLVRATLVTVAIGLS-ADMADIFEIAN
+SLPNVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGTLVMLAGTVVVMLAAAPLMTALTRGWSPEKLEMATV
+FALWCLPQVFFYGMYALVGQVLNANGRFGAYMWAPVLNNVVAIGAIVLYLGMFGAYRAGDDLAGWTSAQTVVLAGGHTLG
+VVLQAVILFLPLRGLGLGLRPRFGWKGIGLRDTGRIAGYTLITMVATNVVLLLCQRYVTSATEARDRGELRIPGTETWSA
+EMAQAAIPGVAAYNMAMLMAVLPHSVFVLSLATVLFNRLARAMGRQDMSAVRRTTAQGLRAFTVPLMFCLAGVVVLAGPL
+GRVFGSTAETAMVAGVAVGSVLLALALSIPFRSGSFYLLRVFYAAEDAKVPMVVQVSGSLLMLLLSWAGAMLLPLWSMAL
+WVAVASSVSYVYQFVLTHVLTVRRFGDYGLASVLRAHVQTGLAALAAAAAGAVVVWLLGGYTGGFAWNSIGTALLTCAVA
+AVAMGPVYLMVLRAMRFPELDDALRPLVARVPALGRLLRVG
+>1_1944
+M-------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-----------------------DPADETPEGERRAGRSTAIMASGTLLSRVLGLVRATLVTVAIGLS-ADMADIFEIAN
+SLPNVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGTLVMLAGTVVVMLAAAPLMTALTRGWSPEKLEMATV
+FALWCLPQVFFYGMYALVGQVLNANGRFGAYMWAPVLNNVVAIGAIVLYLGMFGAYRAGDDLAGWTSAQTVVLAGGHTLG
+VVLQAVILFLPLRGLGLGLRPRFGWKGIGLRDTGRIAGYTLITMVATNVVLLLCQRYVTSATEARDRGELRIPGTETWSA
+EMAQAAIPGVAAYNMAMLMAVLPHSVFVLSLATVLFNRLARAMGRQDMSAVRRTTAQGLRAFTVPLMFCLAGVVVLAGPL
+GRVFGSTAETAMVAGVAVGSVLLALALSIPFRSGSFYLLRVFYAAEDAKVPMVVQVSGSLLMLLLSWAGAMLLPLWSMAL
+WVAVASSVSYVYQFVLTHVLTVRRFGDYGLASVLRAHVQTGLAALAAAAAGVVVVWLLGGYTGGFAWNSIGTALLTCAVA
+AVAMGPVYLMVLRAMRFPELDDALRPLVARVPALGRLLRVG
+>2_418
+MASPDPSAHRGAPLPSALGAWHRRPQPPARPEPAPAPGPRPAASGLPTVEEVSAGGVVVREHDGGLEVAIIARYNRGGRL
+EWCLPKGHPEGVEDHRQAAVREVEEETGIAGDILEPLGAIDYWFTVSRHRVHKTVHHFLLRATGGELTTENDPDHEAVDV
+AWVRLEDVARRLSFANERRIVDLARQVVDRHFPRAPPGAPAPDPPPRTRGSSDHDWVTLEQQPLPAPRAGTPPAPAVADE
+EPTTADPA----PATDPEAPAREDRPDETPEGERRAGRSTAIMASGTLISRVLGLVRAMLVTVAIGLS-TDMADIFEIAN
+SLPNVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGTLVMLGGTLVVMAVAAPLMTALTRGWSPEKLEMATV
+FALWCLPQVFFYGMYALVGQVLNANGRFGAYMWAPVLNNVVAIAAIGLYLAMFGAYRAGEDVAGWTSTQTLVLAGGHTLG
+VILQAVILFLPLRGLGLGMRPRFGWKGIGLRETGRIAGYTLVTMMVTNVVLLLCQRYVTSATEARDRGELRIPGTEAWST
+EMAQAAIPGVAAYNMAMLIAVLPHSVFVLSLATVLFNRLARAMTRQDMPAVRRTTAQGLRAFTVPLMFSLAGIVVLAGPL
+GRVFGSTAETSMVAGIAVGAVLLALALSIPFRSGSFYLLRVFYAAEDAKVPMVVQVSSSLLMLLLSWAGAMLLPLWSMAL
+WVAIASSVSYVYQFALTHVLTVRRFGDYGFASVLRAHGQTGLAALAAAAAGAVVVWLLGGYTGGFAWETIVTALITCAVA
+AAVMAPVYVVTLKLLRFPELDDALRPVVSRVPALGRLLRVG
+>3_371
+MSS-----------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+----------------------------------------------RT-----------------APRRALP-----ADD
+APRPKEVEDVVLPASDPEAPAQAQ--EEVPEGERRAGRSTAIMAAGTMISRVLGFVRAALLTIAIGTTVGTVADIFEVAN
+SLPNVIYLLLVGGVFNVVLVPQLIKHAKDADRGADYTSRLMTLAVLVMLAATVLVTAAAAPLMAALTRGWSPEMLQLGTV
+FALWCLPQMFFYGMYALVGQILNANGRFGAYMWAPVLNNVVAIAAIGLYLVMFGRYSGGDLLGRWTPEQTLVLAGGHTLG
+VILQALILFLPLRGLGLGLRPRFGWRGMGLRHTGRIAGYTLFTMAASNIVLLLSHRYINGASAAREDPSVRVPGTEGWDP
+AMADALIPGLTAYNQAMLISVLPHSVFVLSLATVLFNKLARSMAAGDHAAVRETTARGLRTFAAPIMFSLAGVVVLAGPL
+GRLFGSTAESAQVTGMAVGAVILLMSLSMPFRSGSFYLLRVFYAAESARIPMVVQVTTSLLTLAVTAAGAYLLPLWAITY
+WAALASVVSHAFQFFFAHVLAVRRFGDYGFTHVLAAYATTGAAGVVAGAAGAVVAWLLGAYSGGWAWGSILSALVTCAVV
+GLVMAPVYVVALRVLRFPELASAAAPLARRVPALGRLLGAR
+>4_2182
+M-------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-----------------------DPADETPEGERRAGRSTAIMASGTLLSRVLGLVRATLVTVAIGLS-ADMADIFEIAN
+SLPNVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGTLVMLAGTVVVMLAAAPLMTALTRGWSPEKLEMATV
+FALWCLPQVFFYGMYALVGQVLNANGRFGAYMWAPVLNNVVAIGAIVLYLGMFGAYRAGDDLAGWTTAQTVVLAGGHTLG
+VVLQAVILFLPLRGLGLGLRPRFGWKGIGLRDTGRIAGYTLVTMVATNVVLLLCQRYVTSATEARDRGELRIPGTETWSA
+EMAQAAIPGVAAYNMAMLMAVLPHSVFVLSLATVLFNRLARAMGRQDMSAVRRTTAQGLRAFTVPLMFCLAGVVVLAGPL
+GRVFGSTAETAMVAGIAVGSVLLALALSIPFRSGSFYLLRVFYAAEDAKVPMVVQVSGSLLMLLLSWAGAMLLPLWSMAL
+WVAFASSVSYVYQFVLTHVLTVRRFGDYGLASVLRAHVQTGLAALAAAAAGAVVVWLLGGYTGGFAWNSIGTALLTCAAA
+AVAMGPVYLVVLRAMRFPELDDALRPLVARVPALGRLLRVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001759.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001759.fa
new file mode 100644
index 0000000000000000000000000000000000000000..21baed197c66086acaded2c6a36e07c80146f765
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001759.fa
@@ -0,0 +1,50 @@
+>1_193
+MTV-----------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------ESVDVSVIIPMHNGGELIHEQLDALAAQRTDLNWEVIVGDNRSTDGSPDAVRARADSFPV
+PLAVVDAFRVQGASHARNAAAAAARGEVLAMCDADDRVAPDWVEQAFRGVREIAPMVAGANRLLSHPQRPDAPLL-----
+-----------NPRI------LHGRGAQTC--NAAVRRDVFLASGGFDESLPPYGVEDSDLSARVLAAGHTIAPHPGLVL
+YFRETTGLKAKLRKIHSSGQAEAVLWSRGHEAQGTPLAESQFVVALAA--LPAD-AVRTARARELRSLPKWTLREAAVRT
+GRWRGYRRWVKTGKAGEPRLPFLDGRGGA-------A
+>1_223
+M-------------------------------------------------------------------------------
+--------------------FADADDVVSRWWVRNGARAFESSDLWSGGAPFMTDEQMREGVEGARRAFDDSDEWHAPVP
+GDLRNAFPVLMGGDFGVTREVFERVGGFDHSLGAVYEDNDFAVRAHLKGIRVDEAAAVRIAFRGKWDMRFRTRLVRRSAK
+AHSLVTTRYELGRQSHFPNPWVEFVRTGASAALMTLGCKTPDWEGVRLRAQTAAGAAAGRVEYRWMRRGPQPQIGLGYRR
+ADSS-PFSQADAAGAGENSEEVLAASVVIPARNAEGWIGEQLDSLAAQCDAPLFEVVVADNGSYDRTAQIA--LSHPTPF
+QVRVVDASGVPSASHARNVGARLARGHVLLFCDADDFVGDRWAGELYRAVTSGPQLVARGV--LEHSRFNDVDVLAAYRI
+DPAQDLHDTEDSPRIERVSDGFAGYLATVPGNNFAIRRDDYLKLGGMDPAYPG-GSEETDFVWRAQEAGFTVVQAAGAVV
+YYRLRTTPAAIFRQQRNQQRGRMYLWTRY-RGRGMSGPSVKASVFAISRHMPMWPFLRRDRGRALA-----WAYTVGAHV
+GALEGMARYRRPALLRSRR-PGSDGGTA--------A
+>2_2379
+MSTRARSSSTPTAPSVSVVIPVYNGAPTLPLQLEALHTQVGAPAFEVVVVDNRSTDDLDGAVRPFMESGPPLRVVRADGH
+QGSSYARNRGIAAARAPYVMFCDADDVVSRHWVATGAAAFATAPIWTGSVTHLPAAVFEQGLEAVRDLLGDGPRPQDGPG
+REVPGPFPVLMGGDFGASRELLVAVGGFDQSFPHAGDDNDLAFRVLRAGHRLVEMPQVRVASRGKTSLQTAHRIAFRSAR
+AHALLADRYGLWERSRATTWASEPVRCLGAAVKMAAHPTRADWRGLACRTAMASGTLAGAVEYHLLRRRPAPQVGLGLDP
+DDTALPGEEPQGAGGPGHP---ELVSVIIPAYNAEAYIAEQIESLAVQVDAPEFEVIVADNGSTDRTASTAREAAERWGL
+TLTVVDARGPASASHARNVGAMAAAGGVLLFCDADDFVGPEWVRELAAAVRSREDALAVGT--LLHRRFNDAAVLAAYGI
+PPEAGEPRT-DAAGYPVVHGGFAGHLPTVAGNDFGVRRSLYLAVGGMDSSFPG-GSEETDFSWRAQRRGAVVVHAPRAIV
+HYRLRSTPQTVFRQQRIQQVGRMLLWMRH-RGDGMSGPSWRVSVTEVARHLPAY-LLVRERAARLR-----HARIAGGHL
+GALQGMVRYRLLKRIPPRRL--VDGSSVPR------A
+>3_2262
+MN------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+----------------------QAVSVVIPCHNAAGSMQRQVDALLPQLEETD-ELLLVENRSADGTRRIA-EEAALRDA
+RVRVLNAPDKAGANHARNIGAARAHNPIILFCDADDVVHSGWVR-SLRQVLGTDGIAGGSATPVDEEGR---------RL
+GPDLGLHET-------------FGGPAYPLGATMGVRREVLETIGGFDESYAG-GHDETDLAWRAARAGWPTHFVPEARI
+DYVQRPDARSALQQRRLYARTSIQVWVQNPDLVDQSAVSLRGALNGVRLGLPL--GIKMIRGTATAR----DAARWGWAL
+GVLEGHLRYRVLGRPPARVAPPIPPAPHPAEPNRPCA
+>4_493
+MS------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+----------------------RPVSVIIPCHNAAAWVDRQISAVLAQLRADD-ELVLVDNRSTDTTYERL-EAAAAGDR
+RVRTVSAPERPGANHARNVGIAAARNPLLLFCDADDLVTGGWVE-AFRAALQNAGITGGAATPVDADGC---------RI
+GSDLGLHEI-------------FGGPAYPLGACMAIRKDVVNAVGGFDESFAG-GHDETDLAWRAERAGWPTAFVPDARI
+DYLQRPDAAATVRQRRAYARTSIQLWARHPETVNPHGVSVKGAVRGVLRGLPN--AVRVLRGRASAD----QAAQWGWSL
+GLLEGHLRYRILGKPPAAHTPRPDAS----------A
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001762.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001762.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92dccd5b6fc38768804ac2d86f5976fab68be0fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001762.fa
@@ -0,0 +1,31 @@
+>1_1808
+----MWIVLALALVVGLLLGLMGGGGSILMVPLLTYVAGLEPKQAIAGSLFVVGVTSLVS
+VLLHSRHGTVRWRTGLIFGAASMVGALLGGVVGGFLPGTLLLIAFAVMMLFTAWAMI--R
+PKKTQPAAAPSVEASADVEPRRHPLGKILLEGVVVGFVTGIIGAGGGFLVVPALVLLGGL
+PMSAAVGTSLLVIAMKSFAGLGGYLTSVTLPWDLLLWVTGVAVVGGLIGVPLVKRVPEKA
+LKKGFGWFVLAMGLVILVREL----------IGLLV------------------------
+>2_598
+M---AWLAVVLAVAVGLLLGLMGGGGSILMVPLLTYVAGLDPKEAIAGSLFVVGVTSLVS
+VGLHARAGNVRWRTGLVFGLAGMVGAALGGVVGGFLPGTVLLIAFAVMMLVTAWAMI--R
+PKR--PTAAPAEGGHA---PGR-ALGRIVLDGVVVGFVTGIVGAGGGFLVVPALVLLAGL
+PMSAAVGTSLLVIALKSFAGLGGYLTSVTLDWPFLLAVTGVAVLGALIGAALVNRVPDKA
+LEKGFGWFVLAMGVVMLVTEL----------VGLLA------------------------
+>2_2599
+MSGTLILTLVLAVGVGLALGTLGGGGSILTVPLLTYIAGMPPKEAIAASLLIVGVTSLSS
+LVVHARHRRVRWRTGLIFGAAGMVGAFAGGLIGGQLPGAVLMVAFAIMMIATAIAMVTRK
+PRR--DTDQPTADAGTE-RAHSLPMLRTMLEGIVVGLITGIVGAGGGFLVVPALVLLGGL
+SMPVAVGTSLLVIAMKSFAGLAGYLTTVTLDWPLVAAVTAMAVLGALLGARLSGRIPADA
+LQKVFGVFVLLTGTLVLVIELPPAWAIAAGGLGLITVVLVLVCRLTALNCPFGLARPTPG
+>3_523
+MV-PLALLVVLAAVVGLLLGLMGGGGSILTVPLLTLTAGMDPQEAIAGSLVMVGASSLVA
+ALVHATRGAVAWRTGLTFGAASMVGALAGGFVGRDLPGPVLMVGFAVIMLISAVKMI--R
+PRRK--------GAGHD-DAAPVPLGRVLLQGVGVGLITGVVGAGGGFLIVPALVLLARL
+PMPVAVGTSLLVIAMNSAMGLVSQLGATALDWAVLGPMAAAAAAAGVVGVVLAHRVPAAA
+LKRGFGWFVLAMGVLILAQQA----------LELLP------------------------
+>4_2028
+----MWIVLALALVVGLLLGLMGGGGSILMVPLLTYVAGLEPKQAIAGSLFVVGVTSLVS
+VLLHSRHGTVRWRTGLIFGAASMVGALLGGVVGGFLPGTLLLIAFAVMMLFTAWAMI--R
+PKKTQPAAAPSVEASADVEPRRHPLGKILLEGVVVGFVTGIVGAGGGFLVVPALVLLGGL
+PMSAAVGTSLLVIAMKSFAGLGGYLTSVTLPWDLLLWVTGVAVVGALIGVPLMKRVPEKA
+LKKGFGWFVLAMGLVILVREL----------IGLLV------------------------
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001764.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001764.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e2c3269d3c6c3a2a82900c790f08db1f4de92134
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001764.fa
@@ -0,0 +1,41 @@
+>1_2079
+M-------------------------------------LRLIGKRLLLLIPTLFGLSVLL
+FVWVRSLPGGPATALLGDRA------TPEAVARVNAAYGFDKPLLEQYVTYMGRLLRGDF
+GTSIMTNRPVVEEFADRFPATLELSIFAIVFAVVIGIPLGYWAARHVGRWQDDVAVVLSL
+IGVVVPVFFLAFILKWVFAVKLGWLPTDGRQDPRIDATHYTNFYVWDGIITAEWDAALNA
+LTHLVLPGIALGTIPLAIIARITRASVLDVQDADFVRTARAKGLAPRLIRDRFIMRNALL
+PVSTTLGLQLGLLISGAVLTETVFAFNGIGRFLAQAIFQLDFPVLQGFIIFIALLYSLIN
+LVVDVSYGLIDPRVRVS---
+>2_81
+MTALASRPGAASRASRSAPVSPASRSTRRTHRRRTLVGAGTVLRRLAGAVGVVWATATLT
+FLMQFLLPGDRATLVFNLRAGQAQPRTAEELAPLNALFGFQDPVLVQYLHFLGGLLRGDL
+GTSYVTFEPVTTVIGDQLAPTLLLTGASIAIAWAVALVL-LVATVRRARWVSGLASAVEA
+LLAALPHYWLGVILLVVFALGLGLFPVVGG----------------------------TG
+PAALVLPALTMGLPLAGYLAQTMRSEYASVLDQPFILTARTRGQSDAGIRVRHALRHALL
+PGLSLTGWAVGAQFSAAVIAEGVFSRPGIGGVLVDAANGRDLPVVCGVVVLIAIVYVLAN
+LAVDVLYTVVDPRLRSAR--
+>2_254
+M-------------------------------------LRLIGKRLLLLIPTLFGLSVLL
+FLWVRSLPGGPATALLGDRA------TPEAVARVNAAYGFDKPLLEQYTTYMGRLLRGDF
+GTSTMTNRPVLEEFADRFPATLELSLFAIVFAVAIGIPLGYWAARHVGRWQDNIAVVLSL
+IGVVVPVFFLAFILKWVFAVKLGWLPTDGRQDPRLDATHYTNFYVWDGISTGEWDAALNA
+LTHLVLPGIALGTIPLAIIARITRASVLDVQNADFVRTARAKGLAPRLIRDRFIMRNALL
+PVSTTLGLQLGLLISGAVLTETVFAFNGIGRFLAQAIFQLDFPVLQGFIIFIALIYSLIN
+LVVDVSYGLIDPRVRVS---
+>3_125
+M-------------------------------------ARRILLRLALALAVLLGAYTAA
+FLILYVMPGDPVTAMAAGGL-EAGAISDADLQALRAEHGLDRPLPVQYLSQLAAAVTGDL
+GTSVQTGQPVTEAILDRLPTTLRLAWAALLVAVVAGPAIALVAAGTRRRWVRATASAIPA
+LGAALPTFWTGLLLVQVFSFGLGWLPALGD----------------------------DG
+LAGLVMPALTLGLPLSALIAQVMLRALDESGTQEYVETALASGQSRRRVLITHMLPNAAL
+PTLAMLGVITGNVVAGAVVVETVFSRPGVGQLTVQAVTAQDLPVVLGVVLLSSLVFVLVT
+LTVDLLSPLLDPRVGPAGAV
+>4_120
+M-------------------------------------LRLIGKRLLLLIPTLFGLSVLL
+FVWVRSLPGGPATALLGDRA------TPEAVARVNAAYGFDKPLLEQYVTYMGRLLRGDF
+GTSIMTNRPVVEEFADRFPATLELSIFAIVFAVVIGIPLGYWAARHVGRWQDDVAVVLSL
+IGVVVPVFFLAFILKWVFAVKLGWLPTDGRQDPRIDATHYTNFYVWDGIITAEWDAALNA
+LTHLVLPGIALGTIPLAIIARITRASVLDVQDADFVRTARAKGLAPRLIRDRFIMRNALL
+PVSTTLGLQLGLLISGAVLTETVFAFNGIGRFLAQAIFQLDFPVLQGFIIFIALLYSLIN
+LVVDVSYGLIDPRVRVS---
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001765.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001765.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa0a2e5509f00c7bb3c69013cde4252c83d9d9f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001765.fa
@@ -0,0 +1,36 @@
+>1_2080
+M----SVNLPPSPGGGPTEHAVEHALAPVEAGATQATTEAAADTRGTSVWGAAFQRLRRN
+PAAIAGAVIVLLFVLVAVLAP-VLA---PYAGTATPGMREIRPTHVPGPGEVAGYPLGLD
+RFGGDVLSKLIWGAQASLLIGVVSTAFGLAGGMLLGLLAGTFGGWVDSVVMRVVDILLSV
+PNLLLAVSIAAILGQTPFAVMIAIGVAQVPVFARLLRSSMLTQKGSDYVLAAQTLGLSRG
+RITMSHVLPNSLGPVIVQATLTLATAVIDAAALSFLGLGGGRPETAEWGRMLTYAQAELG
+INPWLAFLPGLCIAITALGFTLLGESLREALDPTSRRR
+>2_80
+MTAVLTSSQTPPP--------------PSDSSAAASPVSLV----------PATRRPRRA
+DLGLAFALTGAAVLLVAALWPQLLATHDPRALDLAA------PLQAPSL----DHWFGTD
+QNGRDLYSRIVHGTGPSLLIGLGAAAVGVGLGMLLGIVAAFGGRWADAAVSRTVEVLFAF
+PSLLLALMLITVYGPSVSTLILAVGVGTAPGYARLVRGQVLAVRGSAYVQAAEVIGHPPM
+TILLQHIVPNAVRPLVAVFMLGVGQAIVWASGLAFLGFGVAPP-SPEWGALLEAGRPYIT
+AAWWLEIFPGLAVLATALTATALGRHLEARLQGET--R
+>2_253
+M----SVNLPPSPGSGPAEHAVDHALAPVEAGATQETTEAAADARGTSVWGAAFQRLRRN
+PAAIAGAVIVALFVLVAVLAP-VLA---PYAGTDTPGMREIRPTHVPGPGEVDGYPLGLD
+RFGGDVLSKLIWGAQASLIIGVVSTAFGLVGGMLLGLLAGTFGGWVDSVVMRTVDILLSV
+PNLLLAVSIAAILGQTPFAVMIAIGVAQVPIFARLLRSSMLTQKGSDYVLAAQTLGLSRG
+RITMSHVLPNSLGPVIVQATLTLATAVIDAAALSFLGLGGGRPETAEWGRMLTYAQAELG
+INPWLAFLPGLCIAIAALGFTLLGESLREALDPTSRRR
+>3_126
+MTSAPAVAAEPTP------------------AASATPSDPA----------GARRRA-RP
+RLGLLLSAGFLVVVLLAALFPSLLAPGDPFAGASGA------TLEPPGP----GHWLGTD
+HLGRDLYTRVVHGTGLTVATAAAAVAGALVVGGTLGLASGYVGGVADTLLMRVVDVLLSI
+PSLLLSLAVVAGLGFGPVQVAVAVGIGSVASFARIGRAQALRISQAPFVEAAPSFGTRRI
+LVLLHHVVPNAVGPLVSLAVLEFGSALLAVSALSFLGYGEPRP-AAEWGGLISDGRSYLA
+VAPWLTALPGLVIAATVLALQQVATSPAPADAP----R
+>4_121
+M----SVNLPPSPGGGPTEHAVEHALAPVEAGATQATTEAAADTRGTSVWGAAFQRLRRN
+PAAIAGAVIVLLFVLVAVLAP-VLA---PYAGTATPGMREIRPTHVPGPGEVAGYPLGLD
+RFGGDVLSKLIWGAQASLLIGVVSTAFGLAGGMLLGLLAGTFGGWVDSVVMRVVDILLSV
+PNLLLAVSIAAILGQTPFAVMIAIGVAQVPVFARLLRSSMLTQKGSDYVLAAQTLGLSRG
+RITMSHVLPNSLGPVIVQATLTLATAVIDAAALSFLGLGGGRPETAEWGRMLTYAQAELG
+INPWLAFLPGLCIAITALGFTLLGESLREALDPTSRRR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001772.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001772.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71d0c5fe510d6e0910ae1dcdd1a26ea585c7bf72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001772.fa
@@ -0,0 +1,32 @@
+>0_44
+MD-TSAPRTSPSTPPASAAHITPEGGSLRRTLKSRHLTMIAMGGAIGTGLFVASGNTIATAGPGGALAAYVAIGFMVFLL
+MQSLGEMSTYLPVSGAFEEYSTRFVSPSFGFAIGWNYWYNWAITVAAELVAAALIMRYWLPDVPSWIWSATFLALLFGLN
+ALSTRAYGESEFWFSLIKVATVVIFLVLGVLMIVGILGGSSPGFHNWTDGEAPFVGGGAGILAIFMVAGFSFQGTELVGV
+AAGEAEDPEKNVPKAIRTVFVRILLFYVGAITVVGFLIPYTSPHLLGSDVEDISISPFTLVFENAGVLAAASVMNAVILT
+AILSAGNSGLYASTRMLWALADSGKAPRFLAKVNRRGVPMNALYATTAVGAACFLTTFIGDGAAYVWLVSASGLAGFIVW
+MGIAWSHYRFRRAYVAQGHDPKDLPYRAFLFPLGPIVALVMCAVVILGQNYQAFMGDVDLVAVASAYIGLPLFLALWLGH
+KLVTGSKPVRYEDADLTRVLD
+>1_2008
+MD-TSAPRTSPSTPAASAAHATHEGGSLQRTLKSRHLTMIAMGGAIGTGLFVASGNTIATAGPGGALVAYVAIGFMVFLL
+MQSLGEMSTYLPVSGAFEEYSTRFVSPSFGFAIGWNYWYNWAITVAAELVAAALIMRYWLPDVPSWIWSAIFLALLFGLN
+ALSTRAYGESEFWFSLIKVATVVIFLVLGVLMIVGILGGSSPGFHNWTDGEAPFVGGGAGILAIFMVAGFSFQGTELVGV
+AAGEAEDPEKNVPKAIRTVFVRILLFYVGAITVVGFLIPYTSPHLLGSDVEDISISPFTLVFENAGVLAAASVMNAVILT
+AILSAGNSGLYASTRMLWALADSGKAPRFLAKVNRRGVPMNALYATTAVGAACFLTTFIGDGAAYVWLVSASGLAGFIVW
+MGIAWSHYRFRRAYVAQGHDPKDLPYRAFLFPLGPIVALVMCAVVILGQNYQAFMGDVDLVAVASAYIGLPLFLALWLGH
+KLVTGSKPVRYEDADLTRVLD
+>3_282
+MNPTDSPRTAGPAGSTAAAASPEPHTGLKRTLAARHLMMIAMGGAIGTGLFVASGNSIATAGPGGALLAYVVIGFMVFLL
+MQSLGEMATYLPVSGAFEEYATRFVSPSFGFAIGWNYWYNWAITVAAELVAAALVMRYWFPDVPSWAWSALFLALLFGLN
+ALSTRAYGESEFWFSLIKVVTVVVFLVLGVLMIVGVLGDAAVGTDNWTTGEAPFVGGAPGILAIFLVAGFSFQGTELVGV
+AAGEAEDPERTVPKAIRTVFWRILLFYVGAITVIGFLIPYTSPNLLGSDIEDIAISPFTLVFENAGVLAAAAVMNAVILT
+AILSAGNSGLYASTRMLWALADSGKAPRFLAKVNRRGVPMNALVVTTAVGALCFLTTFIGDGAAYVWLVSASGLAGFIVW
+MGIAWSHYRFRKAYVAQGNDITDLPYRAALFPLGPIVALLLCTVVILGQNYEAFLNGVDLVAVASAYIGLPLFLALWIGH
+KLVTGSKGVRPEEADLTRGRA
+>4_39
+MD-TSAPRTSPSTPAASAAHATHEGGSLQRTLKSRHLTMIAMGGAIGTGLFVASGNTIATAGPGGALVAYVAIGFMVFLL
+MQSLGEMSTYLPVSGAFEEYSTRFVSPSFGFAIGWNYWYNWAITVAAELVAAALIMRYWLPDVPSWIWSAIFLALLFGLN
+ALSTRAYGESEFWFSLIKVATVVIFLVLGVLMIVGILGGSSPGFHNWTDGEAPFVGGGAGILAIFMVAGFSFQGTELVGV
+AAGEAEDPEKNVPKAIRTVFVRILLFYVGAITVVGFLIPYTSPHLLGSDVEDISISPFTLVFENAGVLAAASVMNAVILT
+AILSAGNSGLYASTRMLWALADSGKAPRFLAKVNRRGVPMNALYATTAVGAACFLTTFIGDGAAYVWLVSASGLAGFIVW
+MGIAWSHYRFRQAYVAQGHDPKDLPYRAFLFPLGPIVALVMCAVVILGQNYQAFMGDVDLVAVASAYIGLPLFLALWLGH
+KLVTGSKPVRYEDADLTRVLD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001780.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001780.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce07af8b93a8a3785aebb7efc46adb474880dc5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001780.fa
@@ -0,0 +1,33 @@
+>0_115
+----------------------MLVLVINSGSSSLKYQLRELADDGTDAPVPVLAQGLVE
+RIGVPGSGVPDHAAALEQVEAELAEATGGRTIDAAGHRVVHGGERFTAPARVTNEVIRAI
+ERLAPLAPLHNPAAAQGLRAMAERWPDMPQVVVFDTSFHQTMPREAWQYALPDEVYTEHG
+IRRYGFHGTSDDLVTGLAAEHLGIPRGEFRAVVLHLGNGASATAIRDGVSVDTSMGYTPL
+AGLVMGTRSGDLDPSVVTHLMRNHGYDAEELDTLMNRRSGLLGLAGEADMRQVLENAASG
+DGRARNALDVASYRLAKYVGGYHVAVGGAQAIVFTAGIGENSAPFRARVLDRLEALGVAY
+DAEANRARVA-----GPHTISAPESAIPVLVVPTDEEQAIARLTWELAR--------
+>2_251
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------------MLHLGNGASATAIRDGASVDTSMGFTPL
+AGLVMGTRTGDLDPSVVTHLMRTQGHSAEEMDTLMNKESGLLGLAGHADMRQVVEAADAG
+DRRARTAPDVASYRLAKYVGGYHVAVGGAQAIVFTAGIGENSAPFRARVVERLGALGVEL
+DAAANEAGLSAAGDDGVAVISAPGSAIPVLVIPTDEEQAIARLTWELTR-------G
+>3_186
+MTASPATMTLPTVSARQLPEDALLVLVVNSGSSSLKYQVRELTPDGRDTDQPVVLKGLVE
+RIGVAGSDVPDHAAALERVEAEITAVVGSRRLAAAGHRVVHGGERFQRPELVTNEVIRAI
+ERLAPLAPLHNPAAAQGLRAVAQRWPDLPQVVVFDTSFHQSMPREAWQYAIPDELYTEHG
+IRRYGFHGTSHDLVTGLAAEHLGLERSEFDGVVLHLGNGASATAIRGGRSIDTSMGYTPL
+AGLVMGTRSGDLDPSIVTHLITAHGMSAEDVDAMLNKESGLLGLSGNADMRQVLEAAEAG
+HRASRDALRIASYRLAKYVGGYHVAVGGAKAIVFTAGIGENSAPFRARVLDRLEPLGVRY
+DHARNMVR-----GDEPRTISTDDSAIPVLVVPTDEEMAIAQLTHHVVEQAEAWTLG
+>4_123
+----------------------MLVLVINSGSSSLKYQLRELADDGTDAPVPVLAQGLVE
+RIGVPGSGVPDHAAALEQVEAELAEATGGRTIDAAGHRVVHGGERFTAPARVTNEVIRAI
+ERLAPLAPLHNHAAAQGLRAMAERWPDMPQVVVFDTSFHQTMPREAWQYALPDEVYTEHG
+IRRYGFHGTSHDLVTGLAAEHLGIPRGEFRAVVLHLGNGASATAIRDGVSVDTSMGYTPL
+AGLVMGTRSGDLDPSVVTHLMRNHGYDAEELDTLMNRRSGLLGLAGEADMRQVLENAASG
+DGRARNALDVASYRLAKYVGGYHVAVGGAQAIVFTAGIGENSAPFRARVLDRLEALGVAY
+EAEANRARVA-----GPHTISAPESAIPVLVVPTDEEQAIARLTWELAR--------
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001781.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001781.fa
new file mode 100644
index 0000000000000000000000000000000000000000..73b1b1cf39ead32e08f4fecfcb1dd119b0d29b3c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001781.fa
@@ -0,0 +1,13 @@
+>0_124
+MTDVPFEDREDERELETDLLADPNAAGDPEPEDGRDGQPVRGGSDDPQHWAGEGRAPDSL
+RNAESAAMHIEEDAQDRTRADEGDVEIL
+>1_2089
+MTDVPFEDREDERELETDLLADPNAAGDPEPEDGRDGQPVRGGSDDPQHRAGEGRAPDSL
+RNAESAAMHIEEDAQDRTRADEGDVEIL
+>2_243
+MTSTPYEDGIDQRELQEDLLAEPDSATDPGPQDGRDGQPVRGSSDDPQHWAGDGRAEDSL
+RNAESEAMHIQQDAEDRTRADEGDVEIL
+>4_132
+MTDVPFEDREDERELETDLLADPNAAGDPEPEDGRDGQPVRGGSDDPQHRAGEGRAPDSL
+RNAESAAMHIEEDAQDRTRADEGDVEIL
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001784.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001784.fa
new file mode 100644
index 0000000000000000000000000000000000000000..980ac3738a44becc5e23781785b4e8bd2b6c7399
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001784.fa
@@ -0,0 +1,29 @@
+>0_147
+--------MSGVGNEREWR------------------------WRIGVASPLVGSAGVFA
+GLRQDLGLGWGLTLVAVTALGAMLALRGVHHRVEAEQARRNVFDAGAGSTAWVML-LMGA
+AVIPGLVLNAIDDAGVRAVVAGLLGAVVEMQRRVHTTRGELFAYQAGSGRRENWVSRWAP
+PRAPGIARNVGAVAALAGWLWRVMWRADRAGGSAHDAWRDPSPQTTDKGSGPSPSLAGAR
+LSVWLAPLYGGVLSELSGGLQARGQEGAASEAHVPQADPSPGQRPTAGRRNRRRDRVHPA
+QQNRCERSNTPTQQSGPPCAATGP
+>1_2112
+--------MSRVGNEREWR------------------------WRIGVAPALVGSAGVFA
+GLRQDLGLGWGLTLVAVTALGAMLALRGVHHRVEAEQARRNVFDAGAGSTAWVML-LMGA
+AVIPGLVLNAIDDAGVRAVVAGLLGAVLAAAAHGILAA-------TTTLEEQ--------
+------------------------------------------------------------
+----------------------------------PRPEPVPLDR-------RRR------
+------------------------
+>3_1439
+MDAVAQNTGRRVGEPLTERSDAGTGHTAASQGRDGTLRGDAPAWRAAGVGAAFGLASVVC
+SLQDHLAEWSAIGGAAAFMALGLLSMTGLRFVVDQEKARRTVFYAGERQGAWFLLNFLGI
+FQIPRFLISGIADPTGLVLAAAGLGIVVAVANQALVSR-------YMTGRRQ--------
+------------------------------------------------------------
+----------------------------------PDPEPVPLG-----------------
+------------------------
+>4_160
+M--CQHGAVSRVGNEREWR------------------------WRIGVASALVGSAGVFA
+GLRQDLGLGWGLTLVASTALGAMLALRGVHHRVEAERARRNVFYAGAGSTAWVML-LMGA
+AVIPGLVLNVIDDAGVRAVGAGVLGATLAAAAHGILAA-------TTTLEEQ--------
+------------------------------------------------------------
+----------------------------------PRPEPVPLDR-------RRR------
+------------------------
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001789.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001789.fa
new file mode 100644
index 0000000000000000000000000000000000000000..895ddf68f7471fef67bad3830859b92f93e659d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001789.fa
@@ -0,0 +1,21 @@
+>0_209
+M--TANHSRHTAAADGQGAAAEHAGTGTATTDPRRDTRSRWGCSSRLGGGTGRLMGVSLA
+VGVVGALGLGSAAWATTVAAGHADS-LAWIAAGAMALNGLLFGLLLTWLALVDRHSIRGA
+DTNPEESIEGRWYEKATSGAFHDTLVVVGLGAAILSFGGYVISPAAVGAALFVLMGCAAA
+IRYQIQKRRG
+>1_2153
+M----------------------ATTPHTTTDLARDRRPRWGRSARLGGGSGRLILVSLV
+AGVVIALLIGAASYGLASSQGDAGPRFPAVTGAVMAASALPVGAALAWLFLVDRTTLRGA
+VRDTEETIEGRWLEKAQSGAFGDLLVVLGLGTFVVALAGWQPSLPLVGAGLLLFAGASVA
+VRYALQKRRG
+>2_158
+MNTTADPRSRSASGPERA-----ASTSAAATPAGSAAPSAWGRSARLGGGTGRLVVVSLV
+FGVLLAAMLGVIAYGLAGTADPADPRRPWVLGLVVASGALPVLAGTVWMLLVDRATIKGA
+VRDPEESIESRWYDAAAGGAFHDLLVVLGLGTFVVSMTGWTAELSLVGAGLVLFMMADVA
+IRYRVQKRRG
+>4_209
+M----------------------ATTPHTTTDLARDRRPRWGRSARLGGGSGRLILVSLV
+AGVVIALLIGAASYGLASSQGDAGPRFPAVTGAVMAASALPVGAALAWLFLVDRTTLRGA
+VRDTEETIEGRWLEKAQSGAFGDLLVVLGLGTFVVALAGWQPSLPLVGAGLLLFAGASVA
+VRYALQKRRG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001790.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001790.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b15efdd75915c5ca7fec4b4f02209673c8dfa6ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001790.fa
@@ -0,0 +1,36 @@
+>0_211
+MTRTVPARRRTTLAAAV-AAVSLAVTAAAPALSAPGNGNGNGNGNG----SASQGQARSNDLSATRGNKVNDAAALAPHL
+VGQTLDWEACDFGSERLNARFNAIPGTACADVTVPRDWKNPEDGHTITLRVAKTETSKGNPERQGIALVNPGGPGGSGLP
+WGPAMAERAPELAEQYDFIGFDPRGVGQSTALECTYTPNPEHDVWQDTKAQVDACLENELTPYITTEQTVYDMDFIRAVL
+GEEKTSYIGYSYGTWLGSWYQRVFPQHTHRFLLDSAVDISRDGLQTTWDLQPRSRDRQFQDAMLPYVARHDEIFGLGDNP
+MQIRQRWEDVGGTRTQLGMIVAGSFLLPAMYDTSQYLDAGSVIAAYIRIMESEAAATDPAGQRTQIERILAEARASLPAE
+ERDSFDRFAARGLETVGEREQLVAATQAGDAVTFEGAFSAIRCQDGQWNTSQGYWTSWVDDLGRKAPWIGVLMGPSECMY
+WPAQTSMPAQPGGKGAPNTVIVQSELDAATPYEGGHRAAGVLRNTSLISVDNEGTHGLFPYRTECVDAPIRDYFLTGAQP
+AEKSLCDAVPLPLETQPVQVAGTPTHKGDIKISMRTDAVREANRITHDAIERQLIDSRAVTPDVEAFLED
+>1_2156
+MTRTVPARRRTTLAAAV-AAVSLAVAAAAPALSAP----GNGNGNG----SASQGQARSNDLSATRGNKVNDAAALAPHL
+VGQTLDWDACDFGSERLNARFNAIPGTACADVTVPRDWKNPEDGHTITLRVAKTETSKGNPERQGIALVNPGGPGGSGLP
+WGPAMAERAPELAEQYDFIGFDPRGVGQSTALECTYTPNPEHDVWQDTKAQVDACLENELTPYITTEQTVYDMDFIRAVL
+GEEKTSYIGYSYGTWLGSWYQRVFPQHAHRFLLDSAVDISRDGLQTTWDLQPRSRDRQFQDAMLPYVARHDEIFGLGDDP
+MQIRQRWEDVGGTRTQLGMIVAGSFLLPAMYDTSQYLDAGSVIAAYIRIMESEAAATDPAGQRTQIERILAEARASLPAE
+ERDSFDRFAARGLETVGEREQLVAATQAGDAVTFEGAFSAIRCQDGQWNTSQGYWTSWVDDLGRKAPWIGVLMGPSECMY
+WPAQTSMPSQPGGKGAPNTVIVQSELDAATPYEGGHRAAGVLRNTSLISVDNEGTHGLFPYRTECVDAPIRDYFLTGAQP
+AEKSLCDAVPLPLETQPVQVAGTPTHKGDIKISMRTDAVREANRITHDAIERQLIDSRAVTPDVEAFLED
+>2_151
+MTRTAPTRRRTTLAAAVAAAAALTISAAAPALSAP----GNGNGNGNGQSSASQGQARSNDLSTTRGNQVNDAAALAPHL
+LDQELAWEACDFGSPALNTRFGAIPGTACADVTVPRDWKDPQDGHTITVRVAKTETSKGNPDRQGIALVNPGGPGGSGLP
+WGPAMAERAPELAEQYDFIGFDPRGVGQSTALECTYTPNPEHDVWQDTKAQVDACLENELTPYITTEQTVYDMDFIRAVM
+GEEKTSYIGYSYGTWLGSWYQRVFPQHAHRFLLDSAVDVSRDGLQTTWNLQPRSRDRQFQDMMLPYVARQDAVYGLGTDP
+MEIRQRWEDAGGTRTILGQIVAGSYLLPAMYSTSQYPMAASMIAAFISIMETETAATDEAGMQAQLERITAEARATVPAA
+DRAAFDRFIEQGSEVVAERDELAAAVRTGQPVTFSGTFSAIRCQDGQWNTSEGYWTSWVNDLGRKAPWIAAFMGPSECMY
+WPAQTSMPSQPGGKDTPSAVIVQSELDAATPYEGGHRAAGVLRNTSLISVDNEGTHGLFPYRTECVDAPIRDYFLTGEMP
+AEKSLCEAHPLPGETQTHQVAGTPTHKGDIKISMRTDAVREANRITLDAIERQLLDSRAVTPDVEAFLER
+>4_212
+MTRTVPARRRTTLAAAV-AAVSLAITAAAPALSAP----GNGKGNG----SASQGQARSNDLSATRGNKVNDAAALAPHL
+VGQTLDWEACDFGSESLNARFNAIPGTACADVTVPRDWKNPEDGHTITLRVAKTETSKGNPERQGIALVNPGGPGGSGLP
+WGPAMAERAPELAEQYDFIGFDPRGVGQSTALECTYTPNPEHDVWQDTKAQVDACLENELTPYITTEQTVYDMDFIRAVL
+GEEKTSYIGYSYGTWLGSWYQRVFPQHAHRFLLDSAVDISRDGLQTTWDLQPRSRDRQFQDAMLPYVARHDEIFGLGDDP
+MQIRQRWEDGGGTRTQLGMIVAGSFLLPAMYDTSQYMSAGAVIAAYIRIMESEAAATDPAGQRAQIERILAEARASLPTE
+ERDSFDRFADRGLETVGEREQLIAATQAGDAVTFEGAFSAIRCQDGQWNTSQGYWTSWVDDLGRKAPWIGVLMGPSECMY
+WPAQTSMPSQPGGKGAPSTVIVQSELDAATPYEGGHRAAGVLRNTSLISVDNEGTHGLFPYGTECVDAPIRDYFLTGAQP
+AEKSLCDAVPLPLETQPVQVAGTPTHKGDIKISMRTDAVREANRITHDAIERQLIDSRAVTPDVEAFLED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001794.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001794.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f77fbd3903a53da8d969d847a65bef2cfc7bfb9c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001794.fa
@@ -0,0 +1,25 @@
+>0_243
+MLNLCAPERTVRRNTHLALVLTAIAGILNSVGFVAVATYTSHMTGIVASMADAAVLHAPG
+LVGTGLLALAMFILGAVVCALVFNWGRVNGLRSRYANILLLEGVGMLVFGLLAEHVRDAH
+RPLVVVAVLCFTMGLQNALITRIGAWPIRTTHVTGMVTDIGVELGKILYRNGPGAAAPVV
+GEPRRVGLLALLVALFFLGGVAGAAGYLWLGFEVVIPVAGVLLLIAHRPLVQDLQDA---
+------
+>1_2206
+MLNLCAPERTVRRNTHLALVLTAIAGILNSVGFVAVATYTSHMTGIVASMADAAVLHAPG
+LVGTGLLALAMFILGAVVCALVFNWGRVNGLRSRYANILLLEGVGMLVFGLLAEHVRDAH
+RPLVVVAVLCFTMGLQNALITRIGAWPIRTTHVTGMVTDIGVELGKILYRNGPGAAAPVV
+GEPRRVGLLALLVALFFLGGVAGAAGYLWLGFEVVIPVAGVLLLIAHRPLIQDLQDAWLT
+RRPRRP
+>2_109
+MLNLCAPERTVRRNTHLALVLTAIAGILNSVGFVAVATYTSHMTGIVASMADATVLHAPG
+LVSTGLLALAMFILGAVVCALVFNWGRVNGLRSRYANILLLEGVGMLAFGLLAEHVRDAH
+RPLVVVAVLCFTMGLQNALITRIGAWPIRTTHVTGMVTDLGVELGKILYRNAPGTAAPVV
+GEPRRVGLLALLVALFFLGGVAGAAGYLWLGFEVVIPVAGVLLLIAHRPLIQDLRDAWLT
+RRPRRR
+>4_243
+MLNLCAPERTVRRNTHLALVLTAIAGILNSVGFVAVATYTSHMTGIVASMADAAVLHAPG
+LVGTGLLALAMFILGAVVCALVFNWGRVNGLRSRYANILLLEGVGMLVFGLLAEHVRDAH
+RPLVVVAVLCFTMGLQNALITRIGAWPIRTTHVTGMVTDIGVELGKILYRNGPGAAAPVV
+GEPRRVGLLALLVALFFLGGVAGAAGYLWLGFEVVIPVAGVLLLIAHRPLIQDLQDAWLT
+RKPRRR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001797.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001797.fa
new file mode 100644
index 0000000000000000000000000000000000000000..535d7801279e642a554d8334881041956af34a80
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001797.fa
@@ -0,0 +1,60 @@
+>0_264
+MIDAPLAQLAETYARDVRLASTSGVSAEPEAQLTVPVSEFLRAFSSVTGIGDLSLLREAQLDGVRPDFAALIDGRPCGWV
+ELKAPGHTVIGEKWRGREKGQWDLLSQLDALLVSNGDEIALYVSGSPVDTAFLPVDGVAGWDADRLRTVLEQFTLAQPRP
+ITRVSQLADRLAPLARFLRERLQEGLSNNYRSVREAKAAWDHTVHHTTTDAQFAGDVAQVVAYSMAIAGLSGQADRNADG
+VVTLEEAKHALETAHRNVLAASLGPIIGIPALMEYIAPEVGAIMRLVSSMDVAAIERSTDSRGEPWLWFYEDFLQRYDPA
+ARNRAGVYYTPISVVQCQVRVVDALLRERFGQTLGFGAPSVVTLDPATGSGTYPLAVIDRAEAAAREERGPAGVAQVAKN
+LTKNLLAFELLPGPYSVAHLRIGQRLAEAQGHAFQAEEIGVYLTDTLEDPSAGMAEGLFGDARVLAEAAEAARRIKRDRR
+ITVAIGNPPYDRVTSGTGGWVEHGDGE-DALFDDVIGPAQEQGVIFSAQASLYNLYVYFWRWAIWKAFQQDPGDQAIISF
+ITASSWLTGPAFVGLRDLARRTASEIWVMDLGGEGRGARQEENVFDIQTPVAIVTLVRTGKAAREASVYYRRFRGTRAEK
+FAALDEVARLDPDDGTWECLPGGAGDPLAPASGGEDWAAMPALADLFPWQQPGIKYNRAWPVAPDQDTLQRRWRELLADP
+SADARAEKYVTGHSGRTIHTAVSGLTPLAALPADAEHRPITRVAWRSFDRQWTFDDPRLINLERPALWQALSDRQLFFVS
+PKTARISGGPAVTVATAVPDLHYFVGSYGGKDVIPLYRDAEAAQPNVTGGLLPLLGERYGREVTPEDLAAYVMGIAGHDA
+YVQRFDEALEGSPVRVPLTVDPALFARAVELGKRLLWLQTYGERFTGVDRPAGRVPRIPGLGWEAPVTALPASPRAVSYD
+PATQRLKVGDGVVTGVSPEVRAFAVSGMNILDKWLGARTATGIGRAAGKAATPLDRIRPTEWADEWNDELLDLLRVLTET
+VSLGGDQADLLDEILARDLIPANELPEPTPAERKVPKTIKRDFSTAQEEMF
+>1_2230
+MIDAPLAQLAETYARDVRLASTSGVSAEPEAQLTVPVSEFLRAFSSVTGIGDLSLLREAQLDGVRPDFAALIDGRPCGWV
+ELKAPGHTVIGEKWRGREKGQWDLLSQLDALLVSNGDEIALYVSGSLVDTAFLPVDGVAGWDADRLRTVLEQFTLAQPRP
+ITRVSQLADRLAPLARFLRERLQEGLSNNYRSVREAKAAWDHTVHHTTTDAQFAGDVAQVVAYSMAIAGLSGQADRNADG
+VVTLEEAKHALETAHRNVLAASLGPIIGIPALMEYIAPEVGAIMRLVSSMDVAAIERSTDSRGEPWLWFYEDFLQRYDPA
+ARNRAGVYYTPISVVQCQVRVVDALLRERFGQTLGFGAPSVVTLDPATGSGTYPLAVIDRAEAAAREERGPAGVAQVAKN
+LTKNLLAFELLPGPYSVAHLRIGQRLAEAQGHAFQAEEIGVYLTDTLEDPSAGMAEGLFGDARVLAEAAEAARQIKRDRR
+ITVAIGNPPYDRVTSGTGGWVEHGDGE-DALFDDVIGPAQEQGVIFSAQASLYNLYVYFWRWAIWKAFQQDPGDQAIISF
+ITASSWLTGPAFVGLRDLARRTASEIWVMDLGGEGRGARQEENVFDIQTPVAIVTLVRTGKAAREASVYYRRFRGTRAEK
+FAALDEVARLDPDDGTWECLPGGAGDPLAPASGGEDWAAMPALADLFPWQQPGIKYNRAWPVAPDQDTLQRRWRELLADP
+SADARAEKYVTGHSGRTIHTAVSGLTPLAALPADAEHRPITRVAWRSFDRQWTFDDPRLINLERPALWQALSDRQLFFVS
+PKTARISGGPAVTVATAVPDLHYFVGSYGGKDVIPLYRDAEAAQPNVTGGLLPLLGERYGREVTPEDLAAYVMGIAGHDA
+YVQRFDEALEGSPVRVPLTVDPALFARAVELGKRLLWLQTYGERFTGVDRPAGRVPRIPGLGWEAPVTALPASPRAVSYD
+PATQRLKVGDGVVTGVSPEVRAFAVSGMNILDKWLGARTATGIGRAAGKAATPLDRIRPTEWADEWNDELLDLLRVLTET
+VSLGGDQADLLDEILAGDLIPANELPEPTPAERKVPKTIKRDFSTAQEEMF
+>2_74
+MDRDAVNALAEEYSRGIGQALSMGVAAEPEAQLTVPFAAFLSRFAQEVELGRLDLLREAQLDGVRPDFAAALDGRPCGWI
+ELKAPGHTVVGERWRGREKSQWALLSQLDALLVSNGELLALYVAGAPVETCALPVDGAAGWDPDRLRRVLEQFTLAQPRP
+ITRVSQLADRLAPLARFLRERLAEGLEHSYDSVVEAKAAWDHTMQHTTSPEEFSGDVAQVVAYSMAIAGLSGQADRNADG
+VVSLEEAKHALETAHRNVLAASLGPILGIPALMQHIAPEVGAITRLVAGMDVAAIERSTDSRGEPWLWFYEDFLQRYDPE
+ARSRAGVYYTPISVVECQVRVVDALLRERFGQNLGFGAPSVVTLDPATGSGTYPLAIIDRAESVAREERGDAGAKQVAMN
+LTKNLLAFELLPGPYSVAHLRIGQRLAEAQGHAFQAEEIGVYLTDTLEDPSAGMPTGLFGDARVLAEAAESARRVKRDQQ
+ITVAIGNPPYDRVTSGTGGWVEQGSGSGDALFDDVIKPAQDSGVIFSAQASLYNLYVYFWRWAIWKAFQQDPKDHAVISF
+ITASSWLTGPAFVGLRRLAQATASEIWVMDLGGEGRGARKEENVFDIQSPVAIVTLVRTGKASREAKVFYRRFRGSRAEK
+FTALDRIQRLDAADG-WEQIAAPGGAPFMPASGGEDWTAMPQLADLFPWQQPGIMYNRAWPVASDQNTLRRRWQELLSDD
+DADARAGKYVTGNSGRTIHTAVAGLPTLASLPADAEPRPIVRVAWRSFDRQWTFDDPRLINLERPALWQALSDRQLFLVS
+PKTARINGGPAVTVSTAVPDKHHYVGSFGGKDVIPLYRDAAAAEPNVTVGLLELLADRLGHDVTPEDLAAYVMAVAAHDG
+YAQTFDEALETSPVRIPFTADASLWDAAVALGERLLWLQTYGERFTSADRPRGRVPRVPGLGWSEAVTHIPADTASLSYD
+AASRELRVGDGVVTGVSPEVRAFSVSGMNIVDKWLGARTAKGIGRAAGKAATPLDRIRPTEWADEWNDELLDLLRVLTET
+VALGDQQAELLAAILAGELITAADLPVPTAAERKVPKTIKRGVSPHQEGLL
+>4_262
+MIDAPLAQLAETYARDVRLASTSGVSAEPEAQLTVPVSEFLRAFSSVTGIGDLSLLREAQLDGVRPDFAALIDGRPCGWV
+ELKAPGHTVIGEKWRGREKGQWDLLSQLDALLVSNGDEIALYVSGSLVDTAFLPVDGVAGWDADRLRTVLEQFTLAQPRP
+ITRVSQLADRLAPLARFLRERLQEGLSNNYRSVREAKAAWDHTVHHTTTDAQFAGDVAQVVAYSMAIAGLSGQADRNADG
+VVTLEEAKHALETAHRNVLAASLGPIIGIPALMEYIAPEVGAIMRLVSSMDVAAIERSTDSRGEPWLWFYEDFLQRYDPA
+ARNRAGVYYTPISVVQCQVRVVDALLRERFGQTLGFGAPSVVTLDPATGSGTYPLAVIDRAEAAAREERGPAGVAQVAKN
+LTKNLLAFELLPGPYSVAHLRIGQRLAEAQGHAFQAEEIGVYLTDTLEDPSAGMAEGLFGDARVLAEAAEAARQIKRDRR
+ITVAIGNPPYDRVTSGTGGWVEHGDGE-DALFDDVIGPAQEQGVIFSAQASLYNLYVYFWRWAIWKAFQQDPGDQAIISF
+ITASSWLTGPAFVGLRDLARRTASEIWVMDLGGEGRGARQEENVFDIQTPVAIVTLVRTGKAAREASVYYRRFRGTRAEK
+FAALDEVARLDPDDGTWECLPGGAGDPLAPASGGEDWAAMPALADLFPWQQPGIKYNRAWPVAPDQDTLQRRWRELLADP
+SADARAEKYVTGHSGRTIHTAVSGLTPLAALPADAEHRPITRVAWRSFDRQWTFDDPRLINLERPALWQALSDRQLFFVS
+PKTARISGGPAVTVATAVPDLHYFVGSYGGKDVIPLYRDAEAAQPNVTGGLLPLLGERYGREVTPEDLAAYVMGIAGHDA
+YVQRFDEALEGSPVRVPLTVDPALFARAVELGKRLLWLQTYGERFTGVDRPAGRVPRIPGLGWEAPVTALPASPRAVSYD
+PATQRLKVGDGVVTGVSPEVRAFAVSGMNILDKWLGARTATGIGRAAGKAATPLDRIRPTEWADEWNDELLDLLRVLTET
+VSLGGDQADLLDEILAGDLIPANELPEPTPAERKVPKTIKRDFSTAQEEMF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001800.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001800.fa
new file mode 100644
index 0000000000000000000000000000000000000000..48e41f07f4f79b3e9ff1298bffd5aba08832ca9c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001800.fa
@@ -0,0 +1,17 @@
+>0_277
+---MSIDAAPPEDG----GTAPTGTSPAPEALEDALPHPSDPSVTPFLLFEGDAGAAMDA
+YLTAFVEYLPVTEVRRDLFDDSSPRGAEWAGKVLHGELEIAGQRLRFFDSFTPHGFTFTP
+AISLFVELPDATAVDAIHDTLLAGGGRDYMPPDDYGFSRRFAWVGDRFGVTWQLNAA
+>1_2250
+---MSIDAAPPEDV----GTAPTGTSPAPEALEDSLPHPSDPSVTPFLMFEGDAGAAMDA
+YLTAFVEHLPVTEVRRDLFDDSSPRGAAWAGKVLHGELEIAGQRLRFFDSFTPHGFTFTP
+AISLFVELPDATAVDAVHDALLAGGGRDYMPPDDDGFSRRFAWVGDRFGVTWQLNAA
+>2_59
+MSETTTDPGLPDDVGVDAGADPTGTAPAPAALEESMPHPSDPSVTPFLMFEGDAGAAMDA
+YLSVFVEHLPVTEVRRDLFDGSSPRGAEWAGKVLHGELEVAGQRLRFFDSFTSHGFTFTP
+AISLFVELPDPTAVDAVHDALIAGGGQDYMPPGDYGFSRRFAWVGDRFGVTWQLNAA
+>4_283
+---MSIDAAPPEDV----GTAPTGTSPAPEALEDSLPHPSDPSVTPFLLFEGDAGAAMDA
+YLTAFVEHLPVTEVRRDLFDESSPRGAAWAGKVLHGELEIAGQRLRFFDSFTPHGFTFTP
+AISLFVELPDATAVDAIHDALLAGGGRDCMPPDDDGFSRRFAWVGDRFGVTWQLNAA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001806.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001806.fa
new file mode 100644
index 0000000000000000000000000000000000000000..891178f16de99991f635b39b493cf799bfe2ed51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001806.fa
@@ -0,0 +1,33 @@
+>0_348
+MSTTPTPPVSHGSAPSRMTWMDAMRGFAVLLVMFTHTYTMPQGLDATFSSVAFANVVQVF
+QSWRMPMLVFLSGVLLPRSVSKPLGTYYRGKAERILWPFLVWMVVLALATGKPGSLLSVE
+FWRGGAWHLWFLWVLMLCYLIGPVIRRVPALVVAAVLFVLLLEFVSGPRDWV-RPLYWGV
+YFFLGAASARLL--------PRIRTAPAALGVIAVILMVLTVTATRTGALV-----VAER
+QPWSVFAALPGILVVLWLGPRLPRLPFLEFCGRRSMVLYVAHMPVLILAVAAFR----DL
+AAVRPVDFYVAIASFTFLVPLALALGYRRV---RWLFELPTAGRVRARPRTRATVPGAAD
+AVPAQTAEPASTTAPLPVVEPASPPQPAAGPTPAAEPAAGAPARVRAPRPRPRHAD
+>1_73
+MSTTPTPPMSHGSTPSRMTWMDAMRGFAVLLVMFTHTYTMPQGLDATFSSVAFANVVQVF
+QSWRMPMLVFLSGVLLPRSVSKPLGTYYRGKAERILWPFLVWMVVLALATGRPGSLLSGE
+FWRGGAWHLWFLWVLMLCYLIGPVIRRVPALVVAAVLFVLLLEFVSGPRDWV-RPLYWGV
+YFFLGAASARLL--------PRIRTAPAALGVIAVILMVLTVTATRTGALV-----VAER
+QPWSVFAALPGILVVLWLGPRLPRLPFLEFCGRRSMVLYVAHMPVLILAVAAFR----DL
+AAVRPVDFYVAIASFTFLVPLALALGYRRV---RWLFEFPTAGRGRERPRTRAAVPEAAD
+AVPAQTAEPAPTTAPLPVVEPASEPQSTAGPAPATEPASDAPAQV--PRPRPRHAD
+>2_2342
+--------------------MDAIRGTAILLMLLLHATMIPAVVGGMEPVPWLVAITDAT
+APFRMPVLMFLSGMLLDRALAKPAKRYLSGKFRVLLWSYVVWAVVYFMVMGRPGELFRPW
+TWV-QTLYLWFLAFLLAYYVLALVLRRIPAIVVAVAALVPHVVLVGAERGFLARFFLYMT
+VFFAGAAFTRFLAARPGILEPRRRDGHLLVG---LPLLVVGVVAIRSGGALPHPAGAVVG
+AVAAVAVAMGLVLVVQALVPR-PRGPLVR-VGQQSLVYYCVHYPVMVLVVRLGERLSWDV
+VVVSLVSLVAAV-----VVCAVIAEGRDRVPVLDALFRAPAPPR-RRRPVTH--------
+--------------------------------------------------------
+>4_355
+MSTTPTPPMSHGSTPSRMTWMDAMRGFAVLLVMFTHTYTMPQGLDATFSSVAFANVVQVF
+QSWRMPMLVFLSGVLLPRSVSKPLGTYYRGKAERILWPFLVWMVVLALATGRPGSLLSGE
+FWRGGAWHLWFLWVLMLCYLIGPVIRRVPALVVAAVLFVLLLEFVSGPRDWV-RPLYWGV
+YFFLGAASARLL--------PRIRTAPAALGVIAVILMVLTVTATRTGALV-----VAER
+QPWSVFAALPGILVVLWLGPRLPRLPFLEFCGRRSMVLYVAHMPVLILAVAAFR----DL
+AAVRPVDFYVAIASFTFLVPLALALGYRRV---RWLFEFPTAGRGRERPRTRAAVPEAAD
+AVPAQTAEPAPTTAPLPVVEPASEPQSTAGPAPATEPASDAPAQV--PRPRPRHAD
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001808.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001808.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a19ede549820d1fdff04bb936cc20537469c2e0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001808.fa
@@ -0,0 +1,17 @@
+>0_369
+MTEHPLPTPDDDATLTGPQTPTPQRVAAVRALRELLAAGYGTEARPIASYGAPAPGTLGG
+VYPDYDDRVFPGLVAAQELAGIDVDYLRNVDRVSEAGIAEASLADLGTLFTYLVRGERFA
+DGHVAAAIENGKVGRMLDRLTALVPEIR
+>1_102
+MTEHPLPTPDDDATLTGPQTPTPQRVAAVRALRELLAAGYGTEARPIASYGAPAPGTLGG
+VYPDYDDRVFPGLVAAQELAGIDVDYLRNVDRVSEAGIAEASLADLGTLFTYLVRGERFA
+DGHVAAAIENGKVGRMLDRLTALVPEIR
+>2_2510
+-------------------------MAAVRALRTLLAEGYATPEAPVAVTGAG-------
+-WPDYDARVLPGLAAAQELAGVDVDYLRHVDRVSDAGIDAASLADLGTLFTYVLRGERFS
+EGHIGAALANGKVGRMLDRLAELVPQVR
+>4_375
+MTEHPLPTPDDDATLTGPQTPTPQRVAAVRALRELLAAGYGTEARQIASYGAPAPGTLGG
+VYPDYDDRVFPGLVAAQELAGIDVDYLRNVDRVSEAGIAEASLADLGTLFTYLVRGERFA
+DGHVAAAIENGKVGRMLDRLTALVPEIR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001815.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001815.fa
new file mode 100644
index 0000000000000000000000000000000000000000..653aa4f5d00c526d276fd4800b27d55558c093b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001815.fa
@@ -0,0 +1,13 @@
+>0_513
+MIRNGKAIDHSNVGGVWGSLIAFIVAFGAFLGCLYAMGFWSLESVWIPGLIALALATVAF
+MIPKAFLGRSDTVDTTAIHTRPV-VEHAAS-------GAAHR-
+>1_246
+MIRNGKAIDHSNVGGVWGSLIAFIVAFGAFLGCLYAMGFWSLESVWIPGLIALALATVAF
+MIPKAFLGRSDTVDTTAIHTRPV-VEHAASGAHAVETGAAHR-
+>2_2360
+MIRNGKAIDHSNVGGVWGSLIAFLVAYVAFLGSLYAMGFWTLENAWVPGLIALALAMVTF
+MIPQVFLGRSDTVDTAAIHTRPVAVEHPVSGAHAVETGAARRH
+>4_516
+MIRNGKAIDHSNVGGVWGSLIAFIVAFGAFLGCLYAMGFWSLESVWIPGLIALALATVAF
+MIPKAFLGRSDTVDTTAIHTRPV-VEHAASGAHAVETGAAHR-
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001816.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001816.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bcbdde56f1eeb34435f2fa2f09eeca09f2ca7ce3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001816.fa
@@ -0,0 +1,21 @@
+>0_545
+MDSRVNSGGVVGKVDNLTCLAGLVTTEDPARVRALRGTVLAVALLNGAYLVVEIILALGI
+GSVALVADSVDFFEDFAVNLLIFVALGWTAARQAVIGKVMAGIIVLPAVAALVMAATKIG
+DPDPPAAGVLLGAAVGSLLVNLVCVALLARVRTDGGSLTRAAWLAARNDLVAGAVLIALS
+GITVLTASGWADIIVGVLLVLLNGSAAKEIWEAATEEHLAAQALAGEVDDD
+>1_278
+MNR--------------------AAVADRRRTRTLRGTVLAVALLNGAYLVVEIILAVGI
+GSVALVADSVDFFEDFAVNLLIFVALGWTAARQAVIGKVMAGIIVLPAVAALVMAATKIG
+DPEPPAAGVLLGAAVGSLLVNIVCVVLLARVRVDGGSLTRAAWLAARNDLVAGVVLIALS
+GITVLTASGWADIIVGVLLVLLNGSAAKEIWEAATEEHLAAQALAGEVDDD
+>3_2206
+MDAMTETS---------------HPRPDPARVRALRGTVLAVSLLNLAYMLVEIGVALGI
+GSVSLVADSVDFFEDFAVNMLIVIALGWPLARRARVGKVMAGIIVLPAIAALAMAAVKVG
+DPEPPATGPLFWTGVGSLLVNLVCVGLLARFRADGGSLTRAAWLAARNDLIAGIVLIALA
+GATALTASGWADIIVGVLLVVLNGGAAKEVWQAATEERLAAQALAGEFDDD
+>4_547
+MNE--------------------VPEADRRRTRALRGTVLAVALLNGAYLVVEIILALGI
+GSVALVADSVDFFEDFAVNLLIFVALGWTAARQAVIGKVMAGIIVLPAVAALVMAATKVG
+DPDPPAAGVLLGVAVGSILVNLVCVALLARVRTDGGSLTRAAWLAARNDLVAGVLLIALS
+GITVLTASGWADIIVGVLLVLLNGSAAKEIWEAATEEHLAAQALAGEVDDD
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001826.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001826.fa
new file mode 100644
index 0000000000000000000000000000000000000000..563e33ec38ee74cad2f1ffb2bbf4822568aff513
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001826.fa
@@ -0,0 +1,29 @@
+>0_610
+MQDKIKVAVNGYGVIGKRVADAVRAQEDMALVGVSDVIADYRIATAAGKGIPVYASTEQA
+LPVMADAGLPVVGGLHDLLENVDVVVDCTPAQVGAGNLELYRAHGVKSVFQGGEKHDLTG
+HSFVAHANYATALGRDSTRVVSCNTTATVRALTALKDVGLLSKARGVLIRRATDPWESDH
+SGIMNTIVPEGRIPSHQGPDAQSVVPDLDVVTMAAKGAHTQNHLHYWTIELTRPAEKQEV
+LETFRAMPRIAFVRRSDGVVAVNSTVELMEDLGRPRGDMYEVALWEDILTVDGNELYYTY
+TVDNQAIVIPENIDAIRALTGTVDDGGESIRCTDRALGVRQDFVRSSVAAR
+>2_391
+MQDKIKVAVNGYGVIGKRVADAVRAQEDMALVGVSDVIADYRIATAAGKGIPVYASTEQA
+LPVMADAGLPVVGGLHDLLENVDVVVDCTPAQVGAGNLELYRAHGVKSVFQGGEKHDLTG
+HSFVAHANYATALGRDSTRVVSCNTTATVRALTALKDVGLLSKARGVLIRRATDPWESDH
+SGIMNTIVPEGRIPSHQGPDAQSVVPDLDVVTMAAKGAHTQNHLHYWTIELTRPAEKQEV
+LEAFRAMPRIAFVRRSDGVVAVNSTVELMEDLGRPRGDMYEVALWEDILTVDGNELYYTY
+TVDNQAIVVPENIDAIRALTGTVDDGGESIRRTDRALGVRQDFVRSSVAAR
+>3_2142
+MQDKIKVAVNGYGVIGKRVADAVRAQEDMALVGVSDVIADYRIATAAGKGIPVYASTEQA
+LPVMADAGLPVVGGLHDLLENVDVVVDCTPAQVGAGNLELYRAHGVKSVFQGGEKHDLTG
+HSFVAHANYATALGRDSTRVVSCNTTATVRALTALKDVGLLSKARGVLIRRATDPWESDH
+SGIMNTIVPEGRIPSHQGPDAQSVVPDLDVVTMAAKGAHTQNHLHNWTIELTRPAEKQEV
+LEAFRAMPRIAFVRRSDGVVAVNSTVELMEDLGRPRGDMYEVVLWEDILTVDGNELYYTY
+TVDNQAIVVPENIDAIRALTGTVDDGGESIRRTDRALGVRQDFVRSSVAAR
+>4_571
+MQDKIKVAVNGYGVIGKRVADAVRAQEDMALVGVSDVIADYRIATAAGKGIPVYASTEQA
+LPVMADAGLPVVGGLHDLLENVDVVVDCTPAQVGAGNLELYRAHGVKSVFQGGEKHDLTG
+HSFVAHANYATALGRDSTRVVSCNTTATVRALTALKDVGLLSKARGVLIRRATDPWESDH
+SGIMNTIVPEGRIPSHQGPDAQSVVPDLDVVTMAAKGAHTQNHLHYWTIELIRPAEKQEV
+LEAFRAMPRIAFVRRSDGVVAVNSTVELMEDLGRPRGDMYEVALWEDILTVDGNELYYTY
+TVDNQAIVVPENIDAIRALTGTVDDGGESIRRTDRALGVRQDFVRSSVAAR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001830.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001830.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de70562d27b3290db60053e53d7f3c189099caab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001830.fa
@@ -0,0 +1,32 @@
+>0_637
+MTASTPAPAAQSAPTVAERNAAGHARLEQELADLVARTSLGGPERSRERHTGRGKLLVRDRIDALLDEGSPFLEVGALAA
+HGLYDGDSPAAGVVAGIGLVHGRLVMVVGNDATVKGGTYYPMTVKKHLRAQEIALENRLPCIYLVDSGGAFLPRQDEVFP
+DREHFGRIFRNQALLSSQRIPQLAAVCGSSTAGGAYVPAMSDETVIVREQGTIFLGGPPLVKAAIGEDVSPEDLGGGRLH
+AERSGVADHLADDDLHAMQILRDIVATLPPAEAPAWEVAPAAEPAKDPAELTRVVPVDVNTPYDVREVIDRLVDGGSVHE
+FKPLYGTTLVTAFARIDGHPVGVLANNGILFGDSARKGAHFIELCDQRGIPLLFLQNISGFMVGRDAEAGGIARDGAKMV
+TAVATARVPKLTVVIGGSFGAGNYAMCGRAYSPRFLWMWPNARISVMGGPQASSVLTQIKQDQRAAAGEEPMSSEEVEAF
+QAPVRRQYEDQGSPLYSTARLWDDGVITPGQTRRVLSLALDVISRSPLPDSRFGLFRM
+>1_383
+MTASTPAPAAQSAPTVAERNAAGHARLEQELADLVARTSLGGPERSRERHTGRGKLLVRDRIDALLDEGSPFLEVGALAA
+HGLYGGDSPAAGVVAGIGLVHGRLVMVVGNDATVKGGTYYPMTVKKHLRAQEIALENRLPCIYLVDSGGAFLPRQDEVFP
+DREHFGRIFRNQALLSSQRIPQLAAVCGSSTAGGAYVPAMSDETVIVREQGTIFLGGPPLVKAAIGEDVSPEDLGGGRLH
+AERSGVADHLADDDLHAMQILRDIVATLPPAEAPAWEVAPAAEPAKDPAELTSVVPVDVNTPYDVREVIDRLVDGGSVHE
+FKPLYGTTLVTAFARIDGHPVGVLANNGILFGDSARKGAHFIELCDQRGIPLLFLQNISGFMVGRDAEAGGIARDGAKMV
+TAVATARVPKLTVVIGGSFGAGNYAMCGRAYSPRFLWMWPNARISVMGGPQASSVLTQIKQDQRAAAGEEPMSSEEVEAF
+QAPVRRQYEDQGSPLYSTARLWDDGVITPGQTRRVLSLALDVISRSPLPDSRFGLFRM
+>2_2250
+MTASTTAPDSESAPTAAERNAAGHARLEQEVAELVARTALGGPERSRERHTARGKLLVRDRIDALLDEGSPFLEVGALAA
+HGLYDGDSPAAGVVAGIGLVHGRLVMVVGNDATVKGGTYYPLTVKKHLRAQEIALENHLPCLYLVDSGGAFLPRQDEVFP
+DREHFGRIFRNQALLSSRRIPQLAAVCGSSTAGGAYVPAMSDETVIVREQGTIFLGGPPLVKAAIGEDVSPEDLGGGRLH
+AERSGVADHLADDDLHAMQILRDIVATLPPPPAPAWEVAPAQEPAKDPAELTSVVPVDVNTPYDVREVIDRIVDGGSVHE
+FKPLYGTTLVTAFARIDGHPVGILANNGILFGDSARKGAHFIELCDQRGIPLLFLQNISGFMVGRDAEAGGIARDGAKMV
+TAVATARVPKLTVVIGGSFGAGNYAMCGRAYSPRFLWMWPNARISVMGGPQASSVLTQIKQDQRAAAGEEPMDAAEVEAF
+QAPVRQQYEDQGSPLYSTARLWDDGIITPGQTRRVLSLALDVISRPPLPDTRFGLFRM
+>4_607
+MTASTPAPAAQSAPTVAERNAAGHARLEQELADLVARTSLGGPERSRERHTGRGKLLVRDRIDALLDEGSPFLEVGALAA
+HGLYGGDSPAAGVVAGIGLVHGRLVMVVGNDATVKGGTYYPMTVKKHLRAQEIALENRLPCIYLVDSGGAFLPRQDEVFP
+DREHFGRIFRNQALLSSQRIPQLAAVCGSSTAGGAYVPAMSDETVIVREQGTIFLGGPPLVKAAIGEDVSPEDLGGGRLH
+AERSGVADHLADDDLHAMQILRDIVATLPPAEAPAWEVAPAAEPAKDPAELTSVVPVDVNTPYDVREVIDRLVDGGSVHE
+FKPLYGTTLVTAFARIDGHPVGVLANNGILFGDSARKGAHFIELCDQRGIPLLFLQNISGFMVGRDAEAGGIARDGAKMV
+TAVATARVPKLTVVIGGSFGAGNYAMCGRAYSPRFLWMWPNARISVMGGPQASSVLTQIKQDQRAAAGEEPMSSEEVEAF
+QAPVRRQYEDQGSPLYSTARLWDDGVITPGQTRRVLSLALDVISRSPLPDSRFGLFRM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001837.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001837.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af0ae43f1ec0a2b41302c1f40e1b1f0ef3258b87
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001837.fa
@@ -0,0 +1,29 @@
+>0_759
+M--SAPA-----WSALLRDAAARLTTVGIDSPRVDAELLLAHVLGLDRGALLARVFAGAV
+AEPAQAAAFEALIGRRAAREPVQHLTGVAHFHGLDLAVGPGVFVPRPETELLVETVVADL
+AARPTAGVVVDLCTGSGAIAAAVAAWGEARGRPLAVTAVELDPTAADWARRNLAPRGVDL
+RQGDALVACPDLEGRVDVVVSNPPYVPEAEVPAQPEARLDPARALYGGDAPGLRIPQAIV
+HRAAELLVPGGLFAMEHHETQGPALLAALGADPRFMGVRVHRDLTGRDRFLTARRSGEAA
+A---GAEVEE
+>1_499
+M--SAPA-----WSALLRDAAARLTTVGIDSPRVDAELLLAHVLGLDRGALLARVFAGAV
+AEPAQAAAFEALIGRRAAREPVQHLTGVAHFHGLDLAVGPGVFVPRPETELLVETVVADL
+AARPTAGVVVDLCTGSGAIAAAVAAWGEARGRPLAVTAVELDPTAADWARRNLAPRGVDL
+RQGDALVACPDLEGRVDVVVSNPPYVPEAEVPAQPEARLDPARALYGGDAPGLRIPQAIV
+HRAAELLVPGGLFAMEHHETQGPALLAALGADPRFMGVRVHRDLTGRDRFLTARRSGEAA
+A---GAEVEE
+>3_1988
+MTSSGPATPPADWSALLRQAAATLRAAGVDSPRADAELLLSHLLGGDRGTLLARVLAGAA
+PGPGQAEAFGALVERRAVREPLQHITGAAAFHGLTLEVGPGVFVPRPETELLVEEGIRAL
+AVLDGPARVVDLCTGSGAIAAAVAAWAEERHRDVAVTAVEREDAALAWARRNLEPRGVDL
+RQGDALVACADLDGTVDVVLSNPPYVPDAELPVQAEALADPPTALYGGDAAGLRIPRGII
+ARAAGLLRPGGRLVMEHHEAQGEALAAEARLGGRFEDVRVLPDHTGRERFLAAVRTGALV
+APPSDGRMEP
+>4_726
+M--SAPA-----WSALLRDAAARLTAVGIDSPRVDAELLLAHVLGLDRGALLARVFAGAV
+AEPAQAAAFEALVGRRAAREPVQHLTGVAHFHGLDLAVGPGVFVPRPETELLVETVVADL
+AARPAAGAVVDLCTGSGAIAAAVAAWGEARGRPLAVTAVELDPTAADWARRNLAPRGVDL
+RQGDALVACPDLEGRVDVVVSNPPYVPEAEVPAQPEARLDPARALYGGDTPGLRIPRAIA
+HRAADLLAPGGLFAMEHHETQGPALLSALGADRRFTGERVHQDLTGRDRFLTARRSGEAA
+A---GAEVEE
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001844.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001844.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7c0c2eb7869b9cbac6078f46f44c062b2ef3f9a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001844.fa
@@ -0,0 +1,21 @@
+>0_972
+MDETTEPPRARRRRGRPLSPALSREAIADAALAVARTEGYEGLTMAAVGRRLGVAPSALY
+NHISGKHELLVLLQDAVMGEVSLVELEAAIRGEVPVVAALRAWARSYRDVFAAHPPLIPL
+IATLPIEGAPSTQRVYETVCAVLARTGLAPEQVLARVIALESFIYGSAYDVDAPADIFEV
+AGAQERLPALGAAAEAFRAGGGTRATGARNPYADAPFEEGLDLLLAGLGD
+>1_695
+--------------------------------------------MAAVGRRLGVAPSALY
+NHISGKHELLVLLQDAVMGEVSLVELEAAIRGEVPVVAALRAWARSYRDVFAAHPPLIPL
+IATLPIEGAPSTQRVYETVCAVLARTGLAPEQVLARVIALESFIYGSAYDVDAPADIFEV
+AGAQERLPALGAAAEAFRAGGGTRATGARNPYADAPFEEGLDLLLAGLGD
+>2_1839
+MDETPEPPRTRRRRGRPLSPALSREAIADAALAVARTEGYEGLTMAAVGRRLGVAPSALY
+NHISGKHELLVLLQDAVMGEVSLVELEAAIRGEAPVVAALRAWARSYRDVFAAHPPLIPL
+IATLPIEGAPSTQRVYETVCAVLARTGLAPGQVLARVIALESFIYGSAYDVDAPADIFEV
+AGAQERLPAFGAAAEAFREGGGTRATGARNPYADAPFEEGLDLLLAGLDD
+>4_915
+MDETTEPPRARRRRGRPLSPALSREAIADAALAVARTEGYEGLTMAAVGRRLGVAPSALY
+NHISGKHELLVLLQDAVMGEVSLVELEAAIRGEVPVVAALRAWARSYRDVFAAHPPLIPL
+IATLPIEGAPSTQRVYETVCAVLARTGLAPEQVLARVIALESFIYGSAYDVDAPADIFEV
+AGAQERLPALGAAAEAFRAGGGTRATGARNPYADAPFEEGLDLLLAGLGD
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001845.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001845.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e895f8ec3f06a773438ed0e4f3d9b2f0597c6ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001845.fa
@@ -0,0 +1,37 @@
+>0_975
+MSTPTGYRVQDPSTDQVVETFPALADGEVDQVLAAAETAQRAWAARPIEERATIVQKVAD
+LFEERKDELAQIIATEMGKRVTEGVEEAEFSSAIFGYFADKGPTLAADRPIETYGGGRAM
+IRHLPLGVLLGVMPWNFPYYQIARFAAPNLMLGNAIVLKHAEICPRSALAVQQIMDDAGV
+PAGVYTNVFATHDQIAEFIADPRVAGVSLTGSERAGSVIGALAGQHLKKAVLELGGSDPY
+IVLDAEDPAEAARTAWATRMYNMGQACNSNKRMIVSADIHDAFVAELVSLAEAMKPGEAA
+DEDPTVFTPLSSRGAAEGLAEQVERARQQGATVHVGGTVTDEAGARFAPAVITGVTSEMD
+AYREELFGPVAVVYKVESADEALALANDSQYGLGGAVFSQDEAKAERIARQLEVGMANVN
+TPAGEGAEIPFGGVKRSGFGRELGPLGMDEFVNKQTYFVQD
+>1_698
+MSTPTGYRVQDPSTDQVVETFPALADGEVDQVLAAAETAQRAWAARPIEERATIVQKVAD
+LFEERKDELAQIIATEMGKRVTEGVEEAEFSSAIFGYFADKGPTLAADRPIETYGGGRAM
+IRHLPLGVLLGVMPWNFPYYQIARFAAPNLMLGNAIVLKHAEICPRSALAVQQIMDDAGV
+PAGVYTNVFATHDQIAEFIADPRVAGVSLTGSERAGSVIGALAGQHLKKAVLELGGSDPY
+IVLDAEDPAEAARTAWATRMYNMGQACNSNKRMIVTADIHDAFVAELVSLAEAMKPGEAA
+DEDPTVFTPLSSRGAAEGLAEQVERARQQGATVHVGGTVTDEAGARFAPAVITGVTSEMD
+AYREELFGPVAVVYKVESADEALALANDSQYGLGGAVFSQDEAQAERIARQLEVGMANVN
+TPAGEGAEIPFGGIKRSGFGRELGPLGMDEFVNKQMYFVQD
+>2_1836
+MSTPTGYRVQDPSTDQVVETFPTLADGEVDQLLAAAETAQRAWAARPIEERATIVQKVAD
+LFEERKDELAQIIATEMGKRVTEGVEEAEFSSAIFGYFADKGPTLAADRPIETFEGGRAM
+IRHLPLGVLLGVMPWNFPYYQIARFAAPNLMLGNAIVLKHAEICPRSALAVQQIMDDAGV
+PAGVYTNVFATHDQIAEFIADPRVAGVSLTGSERAGSVIGALAGQHLKKAVLELGGSDPY
+IVLDAEDPAEAARTAWATRMYNMGQACNSNKRMIVSADIHDAFVAELVSLAEAMKPGEAA
+DEDPTVFTPLSSRGAAEGLAEQVERARQQGATVHVGGTVTDEAGARFAPAVITGVTSEMD
+AYREELFGPVAVVYKVESADEALALANDSQYGLGGAVFSQDEAQAERVARQLEVGMANVN
+TPAGEGAEIPFGGVKRSGFGRELGPLGMDEFVNKQMYFVQD
+>4_919
+MSTPTGYRVQDPSTDQVVETFPALADGEVDQVLAAAETAQRAWAARPIEERATIVQKVAD
+LFEERKDELAQIIATEMGKRVTEGVEEAEFSSAIFGYFADKGPTLAADRPIETYGGGRAM
+IRHLPLGVLLGVMPWNFPYYQIARFAAPNLMLGNAIVLKHAEICPRSALAVQQIMDDAGV
+PAGVYTNVFATHDQIAEFIADPRVAGVSLTGSERAGSVIGALAGQHLKKAVLELGGSDPY
+IVLDAEDPAEAARTAWATRMYNMGQACNSNKRMIVSADIHDAFVAELVSLAEAMKPGEAT
+DEDPTVFTPLSSRGAAEGLAEQVERARQQGATVHVGGTVTDEAGARFAPAVITGVTSEMD
+AYREELFGPVAVVYKVESADEALALANDSQYGLGGAVFSQDEAQAERIARQLEVGMANVN
+TPAGEGAEIPFGGVKRSGFGRELGPLGMDEFVNKQMYFVQD
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001854.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001854.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eec62adbc01b5506e71a76a2d3b0e19a74b2176a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001854.fa
@@ -0,0 +1,21 @@
+>0_1114
+MNPVTSTARDGRSVRWDRHRAERRLELVRAARSAVHALGAHASMEEIASHAGTSKTVYYR
+YFGDREGLRLAVSERVTAHMERRLLEVADEPVSEPEALRRMVEVYLTVAATSPEVYAFAV
+APSPAA-AEAPVLGPFLERVYAMLESGLARGMAARGHAPAPADPLALWPRAAVGLVRAAA
+ETWLRTPAAGRIPVEAMARAIADWLLTGLIGAAPGAALEPAAADAVRARPHSRT--GASS
+>1_842
+MNPVTSTARDGRSVRWDRHRAERRLELVRAARSAVHALGAHASMEEIASHAGTSKTVYYR
+YFGDREGLRLAVSERVTAHMERRLLEVADEPVSEPEALRRMVEVYLTVAATSPEVYAFAV
+APSPAA-AEAPVLGPFLERVYAMLESGLARGMAARGHAPAPADPLALWPRAAVGLVRAAA
+ETWLRTPAAGRIPVEAMARAIADWLLTGLIGAAPGAALEPAAADADRARPHSRT--GASS
+>3_1595
+M-------------------------LVRAARAAVHELGPTASMDEIAAHAGTSKSVFYR
+YFGDRAGLRQAVAERVTASMERRLREAAVDAPDGVSALHRMVAECLSVAASSPAVYAFAV
+TQGGAADGTGPDLGPFFERIAALLAEGLARTLPAADAGPGTT--LVLWPRVAVGTVRAAV
+EAWLATEESVRPDPVRTAHDVAGWLLAGLRSADPSAS--PAA------DTHTPTQQGEPS
+>4_1064
+MNPVTSTARDGRSVRWDRHRAERRLELVRAARSAVHALGAHASMEEIASHAGTSKTVYYR
+YFGDREGLRLAVSERVTAHMERRLLEVADEPVSEPEALRRMVEVYLTVAATSPEVYAFAV
+APSPAA-AEAPVLGPFLERVYAMLESGLARGMAARGHAPAPADPLALWPRAAVGLVRAAA
+ETWLRTPAAGRIPVEAMARAIADWLLTGLIGAAPGAALEPAAADADRARPHSRT--GASS
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001855.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001855.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1da651879c93d83c768f91cdeff809d7aaf8af2e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001855.fa
@@ -0,0 +1,25 @@
+>0_1165
+MSGSGSSRRGARHGGYAANSFRTEAIVLRTHRLGEADRIIEALTPEHGLVRAVAKGVRKT
+SSRLGSVVEPFMHSTLQLARGRGELHIVSQAQLLHPYATMLAADYDAYTVAGALAEAVER
+VPAVDDDGRRAQYRLFHGALAALARGAHDPRLILHSFLLRALAQAGWAPTFDRCARCGAP
+GPHTALHVGLGGAVCPACRPPGAAHPAPETFDLLSALAAGGWATADASGAPARREAAGIV
+AAYLQFHAERRLVSLSVLDQDLGLPAPRVERRP
+>1_893
+MSGSGSSRRGARHGGYAANSFRTEAIVLRTHRLGEADRIIEALTPEHGLVRAMAKGVRKT
+SSRLGSVVEPFMHSTLQLARGRGELHTVSQAQLLHPYATMLAADYDAYTVAGALAEAVER
+VPAVDDDGRRAQYRLFHGALAALARGAHNPRLILHSFLLRALAQAGWAPTFDRCARCGAP
+GPHTALHVGLGGAVCPECRPPGAAHPAPETFDLLSALAAGDWATADTSGAPARREAAGIV
+AAYLQFHAERRLVSLSVLDQDLGLPAPRVERRP
+>3_1542
+MS-------GARHGGYSANSFRTEAIVLRTHRLGEADRIVEAITPEHGVLRCVAKGVRKS
+SSRFGSVVEPFMHSTLQVARGRGELHTITQAQLLHPYATAVAADYEAFAVAAALAEGVER
+IPALDADGRRAQYLLFHGALAALARRAHDPRMILHSFLLRTLTQAGWAPTFDRCARCGAP
+GPHTAVNVALGGAVCAEHRPPGSASPAPETFALLTALTAGDWAVVDTAGPLARREAAGIV
+SAYLQFHAERRLVALSVLDQEIAPPAPRAERSA
+>4_1122
+MSASGSSRRGARHGGYAANSFRTEAIVLRTHRLGEADRIIEALTPEHGLVRAVAKGVRKT
+SSRLGSVVEPFMHSTLQLARGRGELHTVSQAQLLHPYATMLAADYDAYTVAGALAEAVER
+VPAVDDDGRRAQYRLFHGALAALARGAHDPRLILHSFLLRALAQAGWAPTFDRCARCGAP
+GPHTALHVGLGGAVCPECRPPGAAHPAPETFDLLSALAAGDWATADASGAPARREAAGIV
+AAYLQFHAERRLVSLSVLDQDLGLPAPRVERRP
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001861.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001861.fa
new file mode 100644
index 0000000000000000000000000000000000000000..267489e64ce85dc18e6e1d45f13e767bf2d0691a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001861.fa
@@ -0,0 +1,33 @@
+>0_1309
+MIGLLIGGVLGLVLSAVGTPLFIRFLVKRGYGQFVRDDGPTTHKTKRGTPTMGGAVIIGS
+MVLAYLITHGLLAVFGVDFGGPTASGLILLLLTVGMAFVGFVDDFTKITKQRSLGLTPRG
+KIILQALIGTAFAVLALNFPDERGLTPASTAISFARDIPWLDLAFAGPAIGVILFVIWSN
+LITTATTNAVNLTDGLDGLATGATAMITGAYVLISLFQSSQSCAL-EGTRGCYEVRDPMD
+LALLAAILTGSLLGFLWWNTSPAKIFMGDTGSLGLGGALAGFAIFTRTEILVAVLAGLMV
+AITLSVIIQVGWFKVSGGKRVFLMAPLQHHFELKGWAEVTVVVRFWLLSLMCVTVGLAIF
+YGDWLIRQGGLAGVTP
+>1_1038
+MIGLLIGGVLGLVLSAAGTPLFIRFLVKRGYGQFVRDDGPTTHKTKRGTPTMGGAVIIGS
+LVLAYLITHGLLAVLGVDFGGPTASGLILLLLTVGMAFVGFVDDFTKITKQRSLGLTPRG
+KIILQALIGTAFAVLALNFPDERGLTPASTAISFARDIPWLDLAFAGPASGVILFVIWSN
+LITTATTNAVNLTDGLDGLATGATAMITGAYVLISLFQSSQSCAL-EGTRGCYEVRDPMD
+LALLAAILTGSLLGFLWWNTSPAKIFMGDTGSLGLGGALAGFAIFTRTEILVAVLAGLMV
+AITLSVIIQVGWFKVSGGKRVFLMAPLQHHFELKGWAEVTVVVRFWLLSLMCVTVGLAIF
+YGDWLIRQGGLAGVTP
+>3_1401
+MIGLLIGGVLGLILSGLGTPLFIRYLVKRGYGQQVRDDGPQTHKSKRGTPTMGGFVIISA
+LVLGYLLTHGILALLGSELAGPTASGWIVLLLTVGMAFVGWIDDYTKIAKQRSLGLTPKG
+KIILQGLIGTAFAVLALLFPNADGVTPASTAVSFVRDIPWLELAFAGPVVGVVLFVIWSN
+IITTATTNAVNLTDGLDGLAAGATAMVTGAYVLVSLFQASQSCGLTEGAEACYVVRDPMD
+LGLLAAVLTGALLGFLWWNTSPAKIFMGDTGSLGLGGALAGLAILSRTEILVVILAGLMV
+AITLSVIIQVGWFKISGGKRVFLMAPLQHHFELKGWAEVTVVVRFWLISLVCVIIGLALF
+YGEWLLQHGALQAVAR
+>4_1263
+MIGLLIGGVLGLVLSAVGTPLFIRFLVKRGYGQFVRDDGPTTHKTKRGTPTMGGAVIIGS
+MVLAYLITHGLLAVFGVDFGGPTASGLILLLLTVGMAFVGFVDDFTKITKQRSLGLTPRG
+KIILQALIGTAFAVLALNFPDERGLTPASTAISFARDIPWLDLAFAGPAIGVILFVIWSN
+LITTATTNAVNLTDGLDGLATGATAMITGAYVLISLFQSSQSCAL-EGTRGCYEVRDPMD
+LALLAAILTGSLLGFLWWNTSPAKIFMGDTGSLGLGGALAGFAIFTRTEILVAVLAGLMV
+AITLSVIIQVGWFKVSGGKRVFLMAPLQHHFELKGWAEVTVVVRFWLLSLMCVTVGLAIF
+YGDWLIRQGGLAGVTP
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001866.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001866.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d19d7cd9231677a6b17b8dea5049ccb8c34eda3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001866.fa
@@ -0,0 +1,25 @@
+>0_1362
+MTA-RPYRVLVVEDEQLTAETYVAHLDRLPGFEVAAVAGSLLAARQVAAAGLHANGRFPF
+DVVLLDMNLPDGHGLDFLRQLRAAGFHGGVLALTAATDLPVVRRAVAYGVTQYLVKPFGF
+DEFADRLGGFRAASAMLAGDGALDGQEQVDAVFRVSRERRAEALPKGLTESTLREVVELL
+GADPETALSAAEVGERLGISRVTARRYLEHLERIRRVRRSARHGGRGRPEQEYRWA---G
+RT
+>1_1101
+MTA-RPYRVLVVEDEQLTAETYVAHLDRLPGFEVAAVAGSLLAARQVAAAGLHADGRFPF
+DVVLLDMNLPDGHGLDFLHQLRAAGFHGGVLALTAATDLPVVRRAVAYGVTQYLVKPFGF
+D-----------------------------------------------------------
+------------------------------------------------------------
+--
+>3_1366
+MSAERPYRVLIVEDEELTAQTCADHVTRLPGFTVVGAVGTVDAARRLVAAALDRDGRFPF
+DVLLLDMNLPDGHGLDLLQQLRAAGFQGGVLALTAATELSVVRRAIALGVVQYLVKPFGF
+EAFAQRMTGFRSAAALLAGPGRLSGQEHVDDVFRAGQRRGVEELPKGLSAGTLQAVLDLV
+-HDADGGRSASEAAAGLGLSRVTARRYLEHLERIGRVRRRARHGGRGRPEQEYVWAPGAP
+SA
+>4_1311
+MTA-RPYRVLVVEDEQLTAETYVAHLDRLPGFEVAAVAGSLLAARQVAAAGLHANGRFPF
+DVVLLDMNLPDGHGLDFLRQLRAAGFHGGVLALTAATDLPVVRRAVAYGVTQYLVKPFGF
+DEFADRLGGFRAASAMLAGDGALDGQEQVDAVFRVSRERRAEALPKGLTEGTLREVVELL
+GADPETALSAAEVGERLGISRVTARRYLEHLERIRRVRRSARHGGRGRPEQEYRWA---G
+RT
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001867.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001867.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb098b438d80b342cd730cfc93c9d8b2df2443a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001867.fa
@@ -0,0 +1,32 @@
+>0_1368
+MFVTGGVASSLGKGLTASSLGHLLKARGLRVVMQKLDPYLNVDPGTMNPFQHGEVFVTEDGAETDLDIGHYERFLDEDLD
+GLDNVTTGQVYSTVIARERRGEYLGDTVQVIPHITDEICRRMRLPAEPRGDRPAPDVIITEIGGTVGDIESQPFLEAARQ
+VRQDVGRDDVFFLHVSLVPYIGPSQELKTKPTQHSVAALRSIGIQPDAIVLRSDRAVPDDVRGKIARMCDVPQDAVVNCA
+DAPSIYDIPRVIHDQGLDAHVVQSLDLKFKDVDWTAWDALMDAVHHPEHELTVALVGKYVDLPDAYLSVTEALRAGGFAH
+RAKVGIRWVAADECATPEGAAVALADVDAVCVPGGFGVRGLEGKLGALRHAREQRIPTLGLCLGLQSMVIEYARNVLGLE
+DADSTEFDPETASPVIATMAEQEQIVAGEGDLGGTMRLGAFPATLRPGSVVAEAYGTTEVTERHRHRYEVNNAYRDRLEE
+AGLAICGTSPDGALVEFVELPRDVHPYYVSTQAHPEFSSRPTRPHPLFAGLVAAGLARRADAAARR
+>1_1108
+MFVTGGVASSLGKGLTASSLGHLLKARGLRVVMQKLDPYLNVDPGTMNPFQHGEVFVTEDGAETDLDIGHYERFLDEDLD
+GLDNVTTGQVYSTVIARERRGEYLGDTVQVIPHITDEICRRMRLPAEPRGDRPAPDVIITEIGGTVGDIESQPFLEAARQ
+VRQDVGRDDVFFLHVSLVPYIGPSQELKTKPTQHSVAALRSIGIQPDAIVLRSDRAVPDDVRGKIARMCDVPQDAVVNCA
+DAPSIYDIPRVIHDQGLDAHVVQSLDLKFKDVDWTAWDALMDAVHHPEHELTVALVGKYVDLPDAYLSVTEALRAGGFAH
+RAKVGIRWVAADECATPEGAAVALADVDAVCVPGGFGVRGLEGKLGALRHAREQRIPTLGLCLGLQSMVIEYARNVLGLE
+DADSTEFDPETASPVIATMAEQEQIVAGEGDLGGTMRLGAFPATLRPGSVVAEAYGTTEVTERHRHRYEVNNAYRDRLEE
+AGLAICGTSPDGALVEFVELPRDVHPYYVSTQAHPEFSSRPTRPHPLFAGLVAAGLARRADAAARR
+>2_1453
+MFVTGGVASSLGKGLTASSLGHLLKARGLRVVMQKLDPYLNVDPGTMNPFQHGEVFVTEDGAETDLDIGHYERFLDEDLD
+GLDNVTTGQVYSTVIARERRGEYLGDTVQVIPHITDEICRRMRLPAEPRGDRPAPDVIITEIGGTVGDIESQPFLEAARQ
+VRQDVGRDDVFFLHVSLVPYIGPSQELKTKPTQHSVAALRSIGIQPDAIVLRSDRAVPDDVRGKIARMCDVPQDAVVNCA
+DAPSIYDIPRVIHDQGLDAHVVQSLDLKFKDVDWTAWDALMDAVHHPEHELTVALVGKYVDLPDAYLSVTEALRAGGFAH
+RAKVGIRWVAADECATPEGAAAALADVDAVCVPGGFGVRGLEGKLDALRHAREQRIPTLGLCLGLQSMVIEYARNVLGLE
+DADSTEFDPETASPVIATMAEQEQIVAGEGDLGGTMRLGAFPATLRPGSVVAEAYGTTEVTERHRHRYEVNNAYRDRLEE
+AGLAICGTSPDGALVEFVELPRDVHPYYVSTQAHPEFSSRPTRPHPLFAGLVAAGLARRADAAARR
+>4_1317
+MFVTGGVASSLGKGLTASSLGHLLKARGLRVVMQKLDPYLNVDPGTMNPFQHGEVFVTEDGAETDLDIGHYERFLDEDLD
+GLDNVTTGQVYSTVIARERRGEYLGDTVQVIPHITDEICRRMRLPAEPRGDRPAPDVIITEIGGTVGDIESQPFLEAARQ
+VRQDVGRDDVFFLHVSLVPYIGPSQELKTKPTQHSVAALRSIGIQPDAIVLRSDRAVPDDVRGKIARMCDVPQDAVVNCA
+DAPSIYDIPRVIHDQGLDAHVVQSLDLKFKDVDWTAWDALMDAVHHPEHELTVALVGKYVDLPDAYLSVTEALRAGGFAH
+RAKVGIRWVAADECATPEGAAVALADVDAVCVPGGFGVRGLEGKLGALRHAREQRIPTLGLCLGLQSMVIEYARNVLGLE
+DADSTEFDPETASPVIATMAEQEQIVAGEGDLGGTMRLGAFPATLRPGSVVAEAYGTTEVTERHRHRYEVNNAYRDRLEE
+AGLAICGTSPDGALVEFVELPRDVHPYYVSTQAHPEFSSRPTRPHPLFAGLVAAGLARRADAAARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001873.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001873.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0460076dee787e95b510f433b9ec20008c136ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001873.fa
@@ -0,0 +1,17 @@
+>0_1453
+--------------------------------------------------MLATTLEQIS
+VAGARGRPRIRPDRLIADKGYPSKANRAWLRRHGIAATIPERADQITHRRRRPGRPIDFG
+EDQRQRYRGRNVVERCFNRLKQWRGIAMRSDKYARNYHAGLSLAATLHWLTTLL
+>3_623
+---------------------MTTKIHLVCDGKGRTLAFVLTGGQVADTSMFPDTIDEIR
+VVGVKGRPRTRPERVIADKGYPSKKNRAWLRQRGIATTIPERDDQIAHRRKKPGRPIDFG
+RDQKRRYKGRNAVERCFNKLKQWRGIAARSDKTPRNFHAGLSLAATLQWV----
+>3_1709
+MNYKKSGDEPADHAIGRSRGGLTTKSHLVCDGKGRVLAFVVTGGQVADTSMLATTLELIS
+VAGARGRPRARPDRLIADKGYPSKANRSWLRRHGIAATIPERADQIAHRRRRPGRPIDFG
+EDQRQRYRGRNVVERCFNRLKQWRGIAMRSDKYARSYHAGLCLAATLHWLTTTL
+>3_2184
+MNYKKSGDEPADHAIGRSRGGLTTKSHLVCDGKGRVLAFVVTGGQVADTSMLATTLELIS
+VAGARGRPRARPDRLIADKGYPSKANRSWLRRHGIAATIPERADQIAHRRRRPGRPIDFG
+EDQRQRYRGRNVVERCFNRLKQWRGIAMRSDKYARSYHAGLCLAATLHWLTTTL
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001884.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001884.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc84497a04633eb71c916a67853fa1c46bb476d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001884.fa
@@ -0,0 +1,25 @@
+>0_1629
+-MRRTLPLAALAALALLVAGCGTPAAGPSSTPTTPTSGSASAAASSGAASSTAPSS----
+GTHADPATLDVVVNKTRPVAPPDWAPSDLVAVPGSELPLRAEAATAAGDLLDAAAAAGHR
+LTTLSAYRSYDYQVRTYGHWVDELGRAEADRVSARPGYSEHQTGLAWDVGDAATPACDLE
+ACFGDTAAGRWVAAHAAEYGFVIRYPVGAEDVTGFAHEPWHLRYVGSAEAARVEAAGGVL
+ETAWGLPPAPDYAD
+>1_1343
+-MRRTLPLAALAALALLAAGCGTPAAGPSSTPTTPTSGSASAAASSRAASSTAPSS----
+GTHADPATLDVVVNKTRPVAPPDWAPSDLVAVPGSELPLRAEAATAAADLLDAAAAAGHR
+LTTLSAYRSYDYQVRTYGHWVDELGRAEADRVSARPGYSEHQTGLAWDVGDAATPACDLE
+ACFGDTAAGRWVAAHAAEYGFVIRYPAGAEDVTGFDHEPWHLRYVGSAEAARVEAAGGVL
+ETAWGLPPAPDYAD
+>2_1170
+MARRALPAAGLAVLAALAAGCSLSDGQPAPSETT-SAPAASSASPSGTATGPAPSSAAPA
+GAHSDPAALDVVVNKARPLSPVDWAPQDLVPVPGSDLPLRAEAARAAGGLIEAAARSGHA
+LSTLSAYRSHAYQAQTYGHWVDELGRQEADRVSARPGHSEHQTGLAWDVGDPESPQCHLE
+ACFGDTAAGRWVAEHAAEHGFVVRYPAGAEHVTGYAPEPWHLRFVGREAAAAVEAAGGVL
+ETAWGLPAAPDYPG
+>4_1558
+-MRRTLPLAALAALALLVAGCGTPAAGPSSTPTTPTSGSASAAASSGAASSTAPSS----
+GTHADPAALDVVVNKTRPVAPPDWAPSDLVAVPGSELPLRAEAATAAGDLLDAAAAAGHR
+LTTLSAYRSYDYQVRTYGHWVDELGRAEADRVSARPGYSEHQTGLAWDVGDAATPACDLE
+ACFGDTAAGRWVAAHAAEYGFVIRYPAGAEDVTGFDHEPWHLRYVGSAEAARVEAAGGVL
+ETAWGLPPARDYAD
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001886.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001886.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb6a2cee3174ca3659ae94049ab203b0bfb4839e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001886.fa
@@ -0,0 +1,21 @@
+>0_1722
+MTR-VPPAHGHRPALRDSTGSAHGPG-VEPGARPRLSAEDLLAARDALAPFGRLSRQEPI
+EWAAEEPLAPDLADFYRYVGPEWLEIDTLGLPVMFFPLDRLWDEQAGYRWNPRTGALLVD
+WNDDWTVVAKQGADPFIHAASTGQVLMAPGDEGWEDRLDEPRPVFRDLTEMTRALAAVGT
+AWARFDDPFTADWHLTEEVTAAVVAGLEGVLGAHDRAVDLARALGYLGAV
+>1_1439
+MTR-VPPAHGHRPALRDSTGSAHGPG-VEPGARPRLSAEDLLAARDALAPFGRLSRQEPI
+EWAAEEPLAPDLADFYRYVGPEWLEIDTLGLPVMFFPLDRLWDEQAGYRWNPRTGALLVD
+WNDDWTVVAKQGADPFIHAASTGQVLMAPGDEGWEDRLDEPRPVFRDLTEMTRALAAVGT
+AWARFDDPFTADWHLTEEVTAAVVAGLEGVLGAHDRAVDLARALGYLRAV
+>3_1001
+MDRHLLPA---------------GPGEVTPRPRIALDPARLHAARAALSVFGPVHRQEPI
+EWAAEEPLAPDLAEFYREVGPDWVEIDTLGLPLLMFPLERLWDEQAGYRWNHRTGAMLAD
+WNEDWTVVAKQGAEPFIHEAATGHVLMAHGEEGWEDRLGEPVPVFRDVAEMTLALCAAGA
+AWAGSDDPFTADWHVRPEVTSAVVDGLEQVLGDRARAVDVARRLGHLRAA
+>4_1651
+MTR-VPPAHGHRPALRDSTGSAPGPG-VEPGARPQLSAEDLLAARDALAPFGRLSRQEPI
+EWAAEEPLAPDLADFYRYVGPEWLEIDTLGLPVMFFPLDRLWDEQAGYRWNHRTGALLVD
+WNEDWTVVAKQGADPFIHAASTGQVLMAPGDEGWEDRLDEPEPVFRDLAEMTRALAAVGT
+AWARFDDPFTVDWHLTEEVTTAVVAGLEAVLGAHDRAVDLARALGYLRAV
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001889.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001889.fa
new file mode 100644
index 0000000000000000000000000000000000000000..77b905b0f918f0fbbde9361977bff837dab15b7f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001889.fa
@@ -0,0 +1,29 @@
+>0_1787
+MSGERV-------------GFTGAEALWLPGWRHVYSGKVRDLYEPADAEPGRSATLLVV
+ASDRISAYDHVLEPPIPDKGTILTRLTLWWFEKLAEGYNGAHAEPVEHHVVGTDVPAAVA
+GRAMVVKRLDMFPVECIARGYLTGSGLAEYRASGTVAGLPLPAGLVDGSRVDPPIFTPSA
+KAEVGEHDENITFEQMVERVGTEAAERLRFLTLDLYARAEAIAREAGIILADTKVEFGVD
+PATGQVVLGDEVLTPDSSRFWDAEDYEPGRPQASFDKQFVRDWLTGPDSGWDKTSGEAPP
+ELPADVVAKTRDRYVEAYERLTGRPFDA
+>1_1494
+MSGERV-------------GFTGAEALWLPGWRHVYSGKVRDLYEPADAEPGRSATLLVV
+ASDRISAYDHVLEPPIPDKGTILTRLTLWWFEKLAEGYNGAHAEPVEHHVVGTDVPAAVA
+GRAMVVKRLDMFPVECIARGYLTGSGLAEYRASGTVAGLPLPAGLVDGSRVDPPIFTPSA
+KAEVGEHDENITFEQMVERVGTEAAERLRFLTLDLYARAEAIAREAGIILADTKVEFGVD
+PATGQVVLGDEVLTPDSSRFWDAEDYEPGRPQASFDKQFVRDWLTGPDSGWDKTSGEAPP
+ALPADVVAKTRDRYVEAYERLTGRPFDA
+>2_1001
+MSHETPASDTTPHSGAAPRGFAGAEALELPGWRHVYSGKVRDLYEPADAAPGESETLLVV
+ASDRISAYDHVLSPPIPDKGAVLTQLTLWWFERLSEGYNGAAGAPVEHHVVSTDVPEAVA
+GRAMVVKRLRMFPVECIARGYLTGSGLAEYRESGTVTGLPLPTGLVDGSRLDPAIFTPSA
+KAEVGEHDENITFEQMSERVGAEAAERLRYLTLDLYSRAEAIARDAGIILADTKVEFGVD
+PATGQVVLGDEVLTPDSSRFWDAEDYEPGRAQASFDKQFVRDWLTSDASGWDRASGAEPP
+ELPADVVEKTRARYVEAYERLTGRPFEA
+>4_1708
+MSGERV-------------GFTGAEALELPGWRHVYSGKVRDLYEPADAEPGRSATLLVV
+ASDRISAYDHVLEPPIPDKGTILTRLTLWWFEKLAEGYNGAHAEPVEHHVVGTDVPAAVA
+GRAMVVKRLDMFPVECIARGYLTGSGLAEYRASGTVAGLPLPAGLVDGSRVDPPIFTPSA
+KAEVGEHDENITFEQMVERVGTEAAERLRFLTLDLYARAEAIAREAGIILADTKVEFGVD
+PATGQVVLGDEVLTPDSSRFWDAEDYEPGRAQASFDKQFVRDWLTGPDSGWDKAGGEAPP
+ALPADVVAKTRDRYVEAYERLTGRPFDG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001891.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001891.fa
new file mode 100644
index 0000000000000000000000000000000000000000..90ef90a8b53469d5528e8fe1b0f3745a763a362c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001891.fa
@@ -0,0 +1,48 @@
+>0_1819
+MPTPPDLSAFRTPAA-------------------------------------------TGRPPRGLRLGLAAALAVVWFA
+VLGLGGPVFGRIGDVSSNDQATFLPASAESTRAGQEAAAFQDGEAVPAVVVGPASTADPAAAFPALADLAGRLGEVPGVT
+DVAGPIPSDDGAAVQFLAFVDSSAGAERPVADVVADLREVVADPAAADPALAGTVAADTEWHVGGPAGLVAELGGAFAGI
+DGLLLLVALAVVFVILVAVYRSVLLPVLVLLTAVAALCGAIVAVYGMALAGWIQLNGQAQGILSILVIGAATDYCLLLVA
+RHREELLVRADVGEALRAAVRGSFGAITASASTVALALLILMASDLNSTRSLGPVAATGVAFAWLAALTLLPALLRLTGR
+AAFWPTIPSPERARRRAQRRAARGRAFTPPLDGAGRPVAGLEEDHGVWTRVGAVVARRPRLVWVATTVVLLALCGGLLQL
+RADGVAQEDVLLGDSDARQAQALLSEHFDAGAGAPAQILAPAGDAEAVLAAVAEDPGVAEAEVTTDAPEAAAGPPPGVTD
+------AEGGAG---AASAPEPQPRVVDGRVLVSATLADPGESLAAQQTVARLRDRLADLPATGEILVGGPAAQALDTNV
+TTQRDLRVVIPLILAMLLVILAVLLRSLLAPVLLVAATVVSFGAALGVSALVFRHVFGFEDADPTVPLYGFVFLVALGID
+YTIFLMTRAREETPRHGTRAGVLRALTVTGGVITSAGVVLAATFAALAVIPLMFMVQLAFIVAFGVLLDTLIVRSLLIPA
+LVRDIGPKVWWPAKVD
+>1_1526
+MPTPPDLSAFRTPAA-------------------------------------------TGRPPRGLRLGLAAALTVVWFA
+VLGLGGPVFGRIGDVSSNDQATFLPASAESTRAGQEAAAFQDGEAVPAVVVGPASTADPAAAFPALADLAGRLGEVPGVT
+DVAGPIPSDDGAAVQFLAFVDSSAGAERPVADVVADLREVVADPAAADPALAGTVAADTEWHVGGPAGLVAELGGAFAGI
+DGLLLLVALAVVFVILVAVYRSVLLPVLVLLTAVAALCGAIVAVYGMALAGWIQLNGQAQGILSILVIGAATDYCLLLVA
+RHREELLVRADVGEALRAAVRGSFGAITASASTVALALLILMASDLNSTRSLGPVAATGVAFAWLAALTLLPALLRLTGR
+AAFWPTIPSPERARRRAERRAARGRAFTPPRDGAGRPVAGLEEDHGVWTRVGAVVARRPRLVWVATTVVLLALCGGLLQL
+RADGVAQEDVLLGDSDARQAQALLSEHFDAGAGAPAQILAPAEDAEAVLAAVAEDPGVAEAEVTTDAPEAAAGPPPGALD
+------AEGGAG---AASAPEPQPRVVDGRVLVSATLADPGESLAAQQTVARLRDRLADLPTSGEILVGGPAAQALDTNV
+TTQRDLRVVIPLILAMLLVVLAVLLRSLLAPVLLVAATVVSFGAALGVSALVFRHVFGFEDADPTVPLYGFVFLVALGID
+YTIFLMTRAREETPRHGTRAGVLRALTVTGGVITSAGVVLAATFAALAVIPLMFMVQLAFIVAFGVLLDTLVVRTLLIPA
+LVRDIGPKVWWPAKVD
+>2_960
+MRTPPDLSALRSPDARRAAGSADPDSAAGRPEGLGASAAGRDGERTDGRTGDRTGERTAGRPSAWLRFGLAAALFVVWFA
+VMGLGGPTFGKIGDVSSNDQSTFLPASAESTRAGEEAAAFRDGEAVPAVIVAEADLSDPAQAFPALGGLAETLRGVDGVT
+DVAGPIPAEDGEAVQFLAFVDSSDGAEREVADVVEDLKGILADPAAADADLADTVAADADWHLGGPAGLATELGGAFAGI
+DGLLLLVALVVVFVILVIVYRSVLLPILVLLTAVGALCAAILAVYGMAVAGWIQLNGQAQGILSILVIGAATDYCLLLVA
+RHREELLVREEVTASLLAAVRGSFGAITASASTVALALLILLVSDLNSNSSLGPIAATGILFAWLAALTLLPALLQLAGR
+AAFWPTVPSPENARRRATRRAERGRAFVQPEDAAGRPLAGLEEDHGVWTKVGAAVARRPRPVWLATLAVLLVMSAGLLQL
+QASGVAQEDVLLGESDSRQAQALLTEHFDAGSGAPAQIVAPAEDADAVLAAVEADPGVAEASVTTDEAPAPAGPPPGVTG
+GGEGTPAEGGAGRPEAAPQPDPEPKVVDGTVLISATLADPGESLAAQATVERLRAELADVGSGGEVLVGGPAAQALDTNT
+TSQRDLVVVIPLILAMLLVILSMLLRSILAPVLLVAATVISFGAAMGVSALVFRHVFGFENADPTVPLYGFVFLVALGID
+YTIFLMTRAREETPRHGTRAGVLRALTVTGGVITSAGVVLAATFAALAVIPLMFMLQLAFIVAFGVLLDTLVVRTLLIPA
+LVRDIGPKVWWPARAE
+>4_1740
+MPTAPDLSAFRTPAA-------------------------------------------PGRPSRGLRLGLAAALAVVWFA
+VLGLGGPVFGAIGDVSSNDQATFLPASAESTRAGEEAAAFQDGEAVPAVVVGPASTADPAAAFPALADLAGLLGEVPGVV
+DVAGPIPSEDGAAVQFLAFVDSSAGAERPVADVVADLREVVADPAAAAPALAGTVAADTEWHVGGPAGLVAELGGAFAGI
+DGLLLLVALVVVFVILVAVYRSVLLPVLVLLTAVAALCGAIVAVYGMALAGWIQLNGQAQGILSILVIGAATDYCLLLVA
+RHREELLVRAEVGEALRAAVRGSFGAITASASTVALALLILMASDLNSTRSLGPVAATGVAFAWLAALTLLPALLRLTGR
+AAFWPTIPSPERARRRTERRAARGRAFTPPRDGAGRPIAGLEEDHGVWTRVGTVVARRPRPVWVATTVGLLALCGGLLQL
+RADGVAQEDVLLGDSDARQAQALLSEHFDAGAGAPAQILAPAGDAEAVLAAVAEDPGVAEAEVTADAPEAAAGPPPGVTD
+------AEGGAG---AASAPEPQPRVVDGRVLVSATLADPGESLAAQQTVARLRDRLADLPTSGEILVGGPAAQALDTNV
+TTQRDLRVVIPLILAMLLVILAVLLRSLLAPVLLVAATVVSFGAALGVSALVFRHVFGFEDADPTVPLYGFVFLVALGID
+YTIFLMTRAREETPRHGTRAGVLRALTVTGGVITSAGVVLAATFAALAVIPLMFMVQLAFIVAFGVLLDTLVVRTLLIPA
+LVWDIGPKVWWPAKAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001893.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001893.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c27fd40ae68528372df8cba0f4381a56ef54ed8f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001893.fa
@@ -0,0 +1,32 @@
+>0_1833
+MRDTTADAAQVPARPDDAAVYRYLAFGEADRPFLVGGPRPAPPAPAATPSPVADLESVRAAIRAHGGPLASTAHVCGRPA
+PTPSAADASRGLRGAARTLTATRRDVAARLADSRERADVPVEALLNSAFVDAHADERPADRGVPRGRLAGLVDAVLPPAR
+PAGDDAAAGLLLALREPVREVFASDSFAARPYADAPTVRALFEDFLAHPRRHDPERFWRLLNLELWLRDAVDADAAPAGP
+ATAVDEAPTAPAPVKPDHEPNPGKELDLVSAEDGRRYRRFPVQTGLVDRDTDLQAYLRGEIEDFFRDLPADAMPQDAPWH
+FSVSEKIVAITQGRSYYTWEVRPSVAARVLSRLVTRTPAGIGLGDPTTMQLAIQEAGLPRIVLSAAAGAAGKVAGKRGVF
+YNVVGGNVRAIDGPTTYSTFPANVSAKLPPAEPDRVAAEVSAMIRAADIPAWAKASFAGTVVMDANDIGRNALGKDTAAS
+AAVLEAAFADNPLGQGRERTPLAVVVRMD
+>1_1540
+MRDTTADAAQVPARPDDAAVYRYLAFGEADRPFLVGGPRPAPLAPAATPSPVADLESVRAAIRAHGGPLASTAHVCGRPA
+PTPSAADASRGLRGAARTLTATRRDVAARLADSRERADVPVEALLNSAFVDAHADERPADRGVPRWRLAGLVDAVLPPAR
+PADDDAAAGLLLALREPVREVFASDSFAARPYADAPTVRALFEDFLAHPRRHDPERFWRLLNLELWLRDAVDPDAAPASP
+AAAVDEAAGAPAPAKPDHEPNPGKELDLVSAEDGRRYRRFPVQTGLVDRDTDLQAYLRGEIEDFFRDLPAEAMPQDAPWH
+FSVSEKIVAITQGRSYYTWEVRPSVAARALSRLVTRTPAGIGLGDPTTMQLAIQEAGLPRIVLAAAAGAAGKVAGKRGVF
+YNVVGGNVRAIDGPTTYSTFPANVSAKLPPAEPDRVAAEVSAMIRAADIPAWAKASFAGTVVMDANDIGRNALGKDTAAS
+AAVLEAAFADNPLGQGRERTPLAVVVRMD
+>2_945
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------------------------------------------------------MF
+YNVVGGNVRAIDGPTTYSAFPANVSAKLPPADPDGVAREVSAMIRAADIPEWARRSFAGTVVMDANDIGRNALGRDTAAS
+AAVLEAAFADNPLGQGRERTPLAVVVRMD
+>4_1754
+MRDTTADAAQVPARPDDAAVYRYLAFGEADRPFLVGGPRPAPLAPAATPSPVADLESVRAAIRAHGGPLASTAHVCGRPA
+PTPSAADAPRGLRGAARTLTATRRDVAARLADSRERADVPVEALLNSAFVDAHADERPADRGVPRGRLAGLVDAVLPPAR
+HADDDAAAGLLLALREPVREVFASDSFAARPYADAPTVRALFEDFLAHPRRHDPERFWRLLNLELWLRDAVDADAAPAGP
+ATAVDEAPTAPAPAKPDHEPNPGKELDLVSAEDGRRYRRFPVQTGLVDRDTDLQAYLRGEIEDFFRDLPADAMPQDAPWH
+FSVSEKIVAITQGRSYYTWEVRPSVAARALSRLVTRTPAGIGLGDPTTMQLAIQEAGLPRIVLSAAAGAAGKVAGKRGVF
+YNVVGGNVRAIDGPTTYSTFPANVSAKLPPAEPDRVAAEVSAMIRAADIPAWAKASFAGTVVMDANDIGRNALGKDTAAS
+AAVLEAAFADNPLGQGRERTPLAVVVRMD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001910.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001910.fa
new file mode 100644
index 0000000000000000000000000000000000000000..52ba07edf5e2ba9190e9b6ef1682bd5186ab3b78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001910.fa
@@ -0,0 +1,40 @@
+>0_1940
+MKILPPRSAASPRPLAPAVAVAALSILVGGLLPQSPSATTEGAPDARPRDDAARATT---VGAAATPASAAPVEGAGVAT
+VPQEGENLVPAEEAPAGVVLGEPVVDRPFTVAAAVWDAAADDAVKRVEIRVRQDGAWGPWQVLDRPVLPEDAAPARTGTD
+PFVAFGADGAQLRVTTVDGAAPAGLELSLIDPGTAATDETVASAHPAVAAEQAAETAGLPRGVKSSAVVGGEEPAEARTV
+ATVSDARAKILPDVITRAQWGADESWAEDSPQFDQVRALTIHHTAGTNDYTRAQAVEQMRGIYAYYTKTLGWGDFPYHLI
+TDRFGNIYEGRRGALDSNPLGTHAGGFNRGTMGVSTMGNYDVVAPSEEVVDAMARATAYYLYRDGIDARGRVTLTSGGST
+KYAAGTPVTVDTIFPHRATSATACPGQHLMARFDDLRDRAEAIATAAGQP---------PAAVT-----PAPTPAPTTER
+STAGTYTVQPNDGWWTIARRTGVPAATLQELNGMTESTVLHPGMVLRTVADPTAPEPTPITTGTYTVQPNDGWWVIARRT
+GVSAAELQRLNGMTASTVLHPGMVLITAATAPASPPAPAPAPG----TYTVREGDGWWIIAHRTGVTMETLQRLNGMTAT
+TVLHPGMVLRTGQ--TASAPAPSPATYVVQANDGWWLIAQRTGVSMERLQRLNGMTVSTMLHPGMVLRTA
+>1_1645
+MKILLPGSAASPRPLAPAVAVAALSVLVGGLLPQQPSATTEGAPDARPLDDAARATT---AGTATTPASAAPVEGAGVAT
+VPQEGENLVPAEEAPAGVVLGEPVVDRPFTVAAAVWDAAADDAVERVEIRVRQDGAWGPWQVLERPVLPEDAAPARTGTD
+PFVAFGADGAQLRVTTVDGAAPAGLELSLIDPGTAATDETVASAHPAVAAEQAAETAGLPRGVKSSAVVGGAAPAEAHTV
+ATASDARAKILPDVITRAQWGADESWAEDSPQFDQVRALTIHHTAGTNDYTRAQAVEQMRGIYAYYTKTLGWGDFPYHLI
+TDRFGNIYEGRRGALNSNPLGTHAGGFNRGTMGISTMGDYDVVAPSEEVVDAMARATAYYLYRDGIDARGRVTLTSGGST
+KYAAGTPVTVDTIFPHRATSATACPGQHLMARFDDLRDRAEAIATAAGQP---------PTPAT-----PAPTPAPTTEP
+STAGTYTVQPNDGWWIIARRTGVPAATLQELNGMTESTVLHPGMVLRTVADPTAPEPTPITTGTYTVQPNDGWWVIARRT
+GVSAAELQRLNGMTASTVLHPGMVLITAATAPTSPPAPAPAPAPAPDTYTVREGDGWWIIAHRTGVTMETLQRLNGMTAT
+TVLHPGMVLRTGQ--TASAPAPSPATYVVQANDGWWLIAQRTGVSMERLQRLNGMTVSTLLHPGMVLRTA
+>2_837
+MKLSAPRSAAPARS-PPAVVVAALSVLVGGLLPQQPVPTTAVPPPPPRLADAAALRTLAPAGSGRAPAAASEVRGAAVAA
+VPQEGEALA---DAPAGVVLGEPVVDRPFTVAAAVWDAAADHAVERVEIRVRQDGAWGPWQVLERAVLPEGAAVTRTGTD
+PFVAFGADGAQLRLTTADGAAPAGLELSLIDPGTAATDEAVASAHPAVSADQAAQDAALPRGVKSSAVVGGAEPAPARTV
+STASEARARILPDVITRAQWGADESWAQASPQFEQVRALTIHHSAGTNDYTRAQAVEQMRAIYAYYTKTLDWGDFPYHLI
+TDRFGNIYEGRRGALDANPLGTHAGGFNTGTMGISTMGNYDVVAPSEEVVDAMARATAYYLYRDGLDPYGRVTLTSGGST
+KYAAGTPVTVDTIFPHRTTSNTACPGRHLMARFDDVRDRAATIAAAAGQEAPAPEPEPIPTPEPEPTPRPEPEPIPMPEP
+TTPTTYTVQDGDGWWVIARRTGVPAATIQELNGMTESTVLHPGMVLRLVADVSAPAPTPVTTGTYTVQPNDGWWVIARRT
+GVPAEELQRLNGMTADSLLHPGMVLITAATAPAPAPAPAPAPAPAPGTYTVRDGDGWWVIAHRTGVTMETLQRLNGMTAD
+TLLHPGMVLVTGQNATAAAPAPAPATYTVRPNDGWWIIADRTGISMAELQRLNRMTASTLLHPGMVLRIA
+>4_1867
+MKILLPGSAASPRPLAPAVAVAALSVLVGGLLPQQPSATTEGAPDARPLDDAARATT---AGTATTPASAAPVEGAGVAT
+VPQEGENLVPAEEAPAGVVLGEPVVDRPFTVAAAVWDAAADDAVERVEIRVRQDGAWGPWQVLERPVLPEDAAPARTGTD
+PFVAFGADGAQLRVTTVDGAAPAGLELSLIDPGTAATDETVASAHPAVAAEQAAETAGLPRGVKSSAVVGGAAPAEAHTV
+ATASDARAKILPDVITRAQWGADESWAEDSPQFDQVRALTIHHTAGTNDYTRAQAVEQMRGIYAYYTKTLGWGDFPYHLI
+TDRFGNIYEGRRGALDSNPLGTHAGGFNRGTMGISTMGDYDVVAPSEEVVDAMARATAYYLYRDGIDARGRVTLTSGGST
+KYAAGTPVTVDTIFPHRATSATACPGQHLMARFDDLRDRAEAIATAAGQP---------PTPAT-----PAPTPAPTTEP
+STAGTYTVQPNDGWWIIARRTGVPAATLQELNGMTESTVLHPGMVLRTVADPTAPEPTPITTGTYTVQPDDGWWVIARRT
+GVCAAELQRLNGMTASTVLHPGMVLITAATAPASTPAPAPAPAPG--TYTVREGDGWWIIAHRTGVTMETLQRLNGMTAT
+TVLHPGMVLRTGQ--TASAPAPSPATYVVQANDGWWLIAQRTGVSMERLQRLNGMTVSTLLHPGMVLRTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001916.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001916.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40fa80169ada7d2767c3424e3e9f95eb73a39fee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001916.fa
@@ -0,0 +1,33 @@
+>0_1988
+MTQDAFLYDALRTPRGAGKPSGSLHEVKPIDLVVGLTHALRDRHEGLDPADIEDMILGCV
+SPVGDQGAVLPRVAALKAGLPQTVAGVQLNRFCASGLEAMNQAAARIRSGWESLLVAGGV
+ESMSRVPMGSDGGAWAMDPATSLATDFVPQGVSADLIATREGFSRAELDRFAAQSHRRAA
+AAWQEGRFARSVVPVTDMNGMTVLDRDETIRPDSSVETLATLKPSFEALGREAGFDAVAL
+EKYSSLAGIEHLHHPGNSSGIVDGAALTLIGSEEAGRRAGMSPRARIVSAAVVGSEPTIM
+LTGPTPACRKALEVAGMTAADIDLVEINEAFAAVPLLLMKEMGWTEEQTNVNGGAIAMGH
+PLGATGAMILGTLVDELERRDLRTGIATLCIGAGMGVATIVERV
+>1_1705
+MTQDAFLYDALRTPRGAGKPSGSLHEVKPIDLVVGLTHALRDRHEGLDPADIEDMILGCV
+SPVGDQGAVLPRVAALKAGLPQTVAGVQLNRFCASGLEAVNQAAARIRSGWESLLVAGGV
+ESMSRVPMGSDGGAWAMDPATSLATDFIPQGVSADLIATREGFSRAELDSFAAQSHRRAA
+AAWQEGRFARSVVPVTDMNGMTVLDRDETIRPDSTVETLAKLKPSFEALGREAGFDAVAL
+EKYSSLAEIEHLHHPGNSSGIVDGAALTLIGSEEAGRRAGMSPRARIVSAAVVGSEPTIM
+LTGPTPACRKALEVAGMTAADIDLVEINEAFAAVPLLLMKEMGWTEEQTNVNGGAIAMGH
+PLGATGAMILGTLVDELERRDLRTGIATLCIGAGMGVATIVERV
+>3_713
+MTRDAYLFDAVRTPRGLGKPTGSLHEVKPVGLLGGLFDALRERHPEWDPAGVDDVVLGVV
+TPVGDQGGDIARVAALKAGMPESVAGVQLNRFCGSGLEAVNQVAARIRSGWEDMLIAGGV
+EAMSRVPMGSDGSAWAMDPATALDLHFVPQGISADLIATRQGFSREDLDRFAVQSHHRAA
+QAWSEGRFEGSVIPVTDMNGLTVLDRDETIRPDASLETLAGLRPSFAAMGEQAGFDAVAL
+NRYTDVDEIHHVHHAGNSSGIVDGAALTLIGGEEAGRRAGLTPRARIVSAAVVGSEPTIM
+LTGPTPACRKALDVAGMTASDIDLVEINEAFAAVPLQLMRDLGWNEEQTNVNGGAIAMGH
+PLGATGAMILGTLVDELERRDLQTGIATLCIGAGMGVATIVERV
+>4_1923
+MTQDAFLYDALRTPRGAGKPSGSLHEVKPIDLVVGLTHALRDRHEGLDPADIEDMILGCV
+SPVGDQGAVLPRVAALKAGLPQTVAGVQLNRFCASGLEAVNQAAARIRSGWESLLVAGGV
+ESMSRVPMGSDGGAWAMDPATSLATDFIPQGVSADLIATREGFSRAELDRFAAQSHRRAA
+AAWQEGRFARSVVPVTDMNGMTVLDRDETIRPDSTVETLATLKPSFEALGREAGFDAVAL
+EKYSSLAGIEHLHHPGNSSGIVDGAALTLIGSEEAGRRAGMSPRARIVSAAVVGSEPTIM
+LTGPTPACRKALEVAGMTAADIDLVEINEAFAAVPLLLMKEMGWTEEQTNVNGGAIAMGH
+PLGATGAMILGTLVDELERRDLRTGIATLCIGAGMGVATIVERV
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001918.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001918.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d657ecb7be39db8b3c4b84d99a87ea2870f1e29d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001918.fa
@@ -0,0 +1,40 @@
+>0_2001
+MS---------------------EHFDVAVLGLGPGGEVAADRLLKAGK-NVVVFEREL---IGGECAYWACIPSKTVLR
+PPEARTEVQRAAGVSGAELDWAATAKYR---DYMIRNLDDQAQVDGYIKEGA----------------VVIKDEARITGP
+GRIQ------AGDREITAEH-IIIATGSDAVIPPLDGIDQITAWTNRETYTTSTLPERAVIIGGSAVGV-----------
+------ETATFLARFGVAITLIHCGERLLDREG------PRVGELAHQYLQEAGIDIRLATSAVQARREGADSIIELQTR
+DGDP-------AGE-VAADVVIFGTG-----------------RTPRTEGLGFEHAGVTLGD----HGEIQIDDHCRAGE
+NTW------------AIGDVTGIMPFTHVAKYQGRIAADAI----LGRPHPAT----------------------YDGIP
+RVVFTDPEIAGAGLTQEQATKQG----IRTIATELDLADAIARPWTYEQDSRGHLGLLADADRKILIGAW--------AV
+GPMAGEWIHHASLAIRTQLPIDTLLDQVAQFPTYHEAYQVALEQ--------------LDLT------------------
+--P
+>3_2170
+MS---------------------EHFDVAVLGLGPGGEVAADRLLKAGK-NVVVFEREL---IGGECAYWACIPSKTVLR
+PPEARTEVQRAAGVSGAELDWAATAKYR---DYMIRNLDDQAQVDGYIKEGA----------------VVIKDEARITGP
+GRIQ------AGDREITAEN-IIIATGSDAVIPPLDGIDQITAWTNRETYTTSTLPERAVIIGGSAVGV-----------
+------ETATFLARFGVAITLIHCGERLLDREG------PRVGELAHQYLQEAGIDIRLATSAVQARREGADSIIKLQTR
+DGDP-------AGE-VAADVVIFGTG-----------------RTPRTEGLGFEHAGVTLGD----HGEIQIDDHCRAGE
+NTW------------AIGDVTGIMPFTHVAKYQGRIAADAI----LGRPHPAT----------------------YDGIP
+RVVFTDPEIAGAGLTQEQATKQG----IRTIATELDLADAIARPWTYEQDPRGHLGLLADADRKILIGAW--------AV
+GPMAGEWIHHASLAIRTQLPIDTLLDQVAQFPTYHEAYQVALEQ--------------LDLT------------------
+--P
+>3_2370
+MTEDLAPTTGPDDATP--GAPDEEAVDVVVIGAGPVGENAAQYAHTAGGLEVALVEADL---LGGECSYWACMPSKALLR
+PLEVAGAAAHLGGLTDPDIDLPGLLARR---DEWRSHLDDAGQVEWAEDAGL----------------RVVRGHGRLAGP
+RRVEVLGDDGAPARVLRARHAVVVATGSTAVVP--GELRGVSPWTSRDATGVREVPGRLAIVGGGVVAV-----------
+------EAATWMAALGSDVQLLVRGDRLLSGQE------PVASRLVLEGLVDAGVRVRFGTSVERAERADVHAESDVGVP
+HGGPVRLTLAGSGETLEVDELLVAAG-----------------RRPALDGLGLEALGLSAEDLQDESGTAVVPASDGAAP
+WLY------------AVGDVTGGPALTHWGKHRARLLGERIAALATGRPAPSG---------------EEAGEGVPEAVP
+QVVFTSPQVARVGVTEAQAREEGGEGELRVVDVPLTSAAGAA---LLRDDAAGRAVLVLRGDR--VVGAT--------FV
+GFEVAELLHAATVAIVGEVPLDRLRHAVAAYPTASEVWLRLVEEALGRG-------------------------------
+---
+>3_2384
+MSSVI-----PDTARPSSGHAGVHRADVVVLGHGLAGLVAACELLEAGR-SVVLVDQERAADLGGQ-AWWSFGGLFLVDS
+PEQRRLRVRDSVDLAWS--DWRETAGFTGGDDALPR-----AWAEAYVHFAAGEKRAWLRERGHRLFPVVGWAERKVPAP
+G---------VGGNSVPRFH-ITWGTGP-GIVEPFAAVVEQAAFDGRLTYLPRHRVTELVTQNGAVCGVRGDRLADDDGA
+RGTSSSRTVTGAFEVRAQAVLIASGGIGADHDAVRAAWPDRLGTPPERML--SGVPAYVDGSGVAAARAVGAHMLHPDRM
+WHYT-------EGV-ANWDPVWPGHGIRILPGPSSLWLDAAGRRLPHPRWPGFDTLG-ALGEICRPGGARRAEG----AD
+HTWFVLNERIIGREFALSGSEQNPDLT--GRSLGHVLGRAT----QGVPAPVRAFLDHGEDFVQAATVEELVDQMNELQD
+RTGGGGPRVELHAVRQAVAEHEDG------------AARAGVDP---QLDAVRRARQYL-GDR--LIRTAAPHRLTDPAA
+GPLIAVRLRTLTRKTLGGLHTD-LRGRVLDELGGPVPGLYAAGEAAGFGGGGMHGFRALEGTFLGGCLFSGRTAGRALAE
+DVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001920.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001920.fa
new file mode 100644
index 0000000000000000000000000000000000000000..836714b285ece97bbb943066a6851eb583fdc2b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001920.fa
@@ -0,0 +1,17 @@
+>0_2030
+MTDADLDDMFRLLGDAEVMRYYPRAKSRNEVRRWINWSKDNYATHGFGLWVIEHRTTGDF
+IGDCGLTWQNVDGQEVLEVGYHVLPEHQGQGLATEGASACLRHGFETLDATMVTAIINPD
+NMASRRVAERIGMTVWKSTRDPRGAPIVVYSSHGHEA
+>1_1749
+MTDADLDDMCRLRGDAEVMRYYPRAKSRNEVQRWINWSKDNYAKHGFGLWVIEHRTTGDF
+IGDCGLTWQNVDGQEVLEVGYHVLPERQGQGLATEGASACLRHGFETLDATMVTAIINPD
+NMASRRVAERIGMTVWKRTRDPSRAPIVVYSSHGQEA
+>2_669
+MTDADLDDMCRLLGDAEAMRYYPRAKSRNEVQRWINWSKDNYAKHGFGLWVIEHRTTGDF
+IGDCGLTWQNVDGQEVLEVGYHVLPERQGQGLATEGASACLRHGFETLDATMVTAIINPD
+NMASRRVAERIGMTVWKSTRDPSGAPIVVYSSHGQEA
+>3_586
+MTDADLDDMCRLLGDAEVMRYYPRAKSRNEVQRWINWSKDNYAEHGFGLWVIEHRATGDF
+IGDCGLTWQNVDGQEVLEVGYHVLPERQGQGLATEGASACLRYGFETLCATMVTAIINPD
+NMASRRVAERIGMTVWKSTRDPSGAPIVVYSSHGQEA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001927.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001927.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4d22d05cbb59d528452790618823e37c1cb70331
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001927.fa
@@ -0,0 +1,29 @@
+>0_2074
+MSEHTPAH---TPASLGPAHRKVGVVGAGGVGTAICYAALIRGVAREVALYDIDEPKVRA
+EVLDLAHGTPFTSASAMTGGADPDVLAGCEVVVITAGAKQKPGQTRLDLGAHNVEILRGL
+LPQVQAHAPDALIVLVTNPVDVLTLVAQRLTGLPAGRVIGSGTLLDTSRLRWLLASRAQV
+HASSVHAAILGEHGDTEFPAWSSARIGPTPLLEWPTPADPLFTRADLDEVADTVVNAAYE
+VIQGKGATTYAVGVATTRLLEAILRDQHAILPVSTVLDGVHGLSDVALSMPSVVGRDGVT
+RVIQPELDAAEMRALHASADALRREARSLGF
+>1_1793
+MSEHTPAHSPAAPASLGPAHRKVGVVGAGGVGTAICYAALIRGVAREVALYDIDEPKVRA
+EVLDLAHGTPFTSASAMTGGADPDVLAGCEVVVITAGAKQKPGQTRLDLGAHNVEILRGL
+LPQVQAHAPEALIVLVTNPVDVLTLVAQRLTGLPAGRVIGSGTLLDTSRLRWLLASRAQV
+HPSSVHAAILGEHGDTEFPAWSSARIGPTPILEWPTPVDPLFTRADLDEVADTVVHAAYE
+VIQGKGATTYAVGVATTRLLEAILRDQHAILPVSTVLDGVHGLSDVALSMPSVVGRDGVT
+RVIQPELDDAEMRALHASADALRREARSLGF
+>2_619
+MSEHTPA----APASLGPAHRKVGVVGAGGVGTAICYAALIRGVAREVALYDIDEPKVRA
+EVLDLAHGTPFTSASAMTGGADPDVLADCEVVVITAGAKQRPGQTRLDLGAHNVEILRGL
+LPQVQAHAPDALIVLVTNPVDVLTLVAQRLTGLPAGRVIGSGTLLDTSRLRWLLASRAQV
+HASSVHAAILGEHGDTEFPAWSSARIGPTPILEWPTPAAPLFTRADLDEVADTVVHAAYE
+VIRGKGATTYAVGVATTRLLEAILRDQHAILPVSTVLDGVHGLSDVALSMPSVVGRDGVT
+RVIQPELDAAEMRALHSSADALRREARSLGF
+>4_2013
+MSEHTPAHSPAAPASLGPAHRKVGVVGAGGVGTAICYAALIRGVAREVALYDIDEPKVRA
+EVLDLAHGTPFTSASAMTGGADPDVLAGCEVVVITAGAKQKPGQTRLDLGAHNVEILRGL
+LPQVQAHAPEALIVLVTNPVDVLTLVAQRLTGLPAGRVIGSGTLLDTSRLRWLLASRAQV
+HPSSVHAAILGEHGDTEFPAWSSARIGPTPILEWPTPVDPLFTRADLDEVADTVVHAAYE
+VIQGKGATTYAVGVATTRLLEAILRDQHAILPVSTVLDGVHGLSDVALSMPSVVGRDGVT
+RVIQPELDDAEMRALHASADALRREARSLGF
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001929.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001929.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2fa78e135dde575095456942c68cb0b279b30848
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001929.fa
@@ -0,0 +1,21 @@
+>0_2095
+MIRVVVADDQALMRTALEHFVAQAEDLEVVGSAEDGVQALEAARTLAPDVVLMDMQMPRM
+DGVEATARISAEAPGVRVLAITTFSSEQYLVPALRAGAAGYLVKDAPPAEVVDAIRRVHA
+GDAVFSARVAADLVEAVTAAPEHTAPCPAEPLAPHERLTERELDVVRELAKGASNAEIAG
+APFLAEATVKSHIGKVLDKWQVRDRVQILIRAARAGLVDIG-
+>1_1819
+MIRVVVADDQALMRTALEHFVAQAEDLEVVGSAEDGVQALEAARTLAPDVVLMDMQMPRM
+DGVEATARISAEAPGVRVLAITTFSSEQYLVPALRAGAAGYLVKDAPPAEVVDAIRRVHA
+GDAVFSARVAADLVEAVTAAPEHTAPCPAEPLAPHERLTERELDVVRELAKGASNAEIAG
+ALFLAEATVKSHIGKVLDKWQVRDRVQILIRAARAGLVDIG-
+>2_586
+---MLVADDQQLMRTALAHFVSTAEDLEVVGTAADGVEAVEMAKDLRPDVVLMDMQMPRM
+DGIEATTAIMAEAPEVRVLAITTFSSEAYLVPALRAGASGYLVKDAPPEEVVEAVRQVHR
+GDAVFSPRVARELIETVTQQSERRESAAAHALTELEELTPRELEVVTELAKGSSNAEIAQ
+ALFLAEATVKSHLGKIMDKWQARDRVQVLIRASRAGLVSFDD
+>4_2039
+MIRVVVADDQALMRTALEHFVAQAEDLEVVGSAEDGVQALEAARTLAPDVVLMDMQMPRM
+DGVEATARISAEAPGVRVLAITTFSSEQYLVPALRAGAAGYLVKDAPPAEVVDAIRRVHA
+GDAVFSARVAADLVEAVTAAPEHAAPCPAEPLAPHERLTERELDVVRELAKGASNAEIAG
+ALFLAEATVKSHIGKVLDKWQVRDRVQILIRAARAGLVDIG-
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001935.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001935.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab37c0847e6468868a43902693dd8b6f8b41e106
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001935.fa
@@ -0,0 +1,21 @@
+>0_2132
+MSPADPTADVAAG-PAGPAAVAEAFAAAWNAADADALADLFAEDADFVNVVGVWWTRRRQ
+IRVNHALGFRWMFPASRLVLGQVRVRELGDVAVVHAPWTMTG-----------------Q
+TAPDGDEA--GERTGVLLLVVRRTEAGAWEAVAGQNTDSVPEAQTHLAD-DDGLAAVHYH
+PSAWIDPDDDPDGPEA-------------------------------------C----
+>1_1856
+MSPADPTADVAAR-PTGPAAVAEAFAAAWNAADADALAELFAEDADFVNVVGVWWRRRRQ
+IRVNHALGFRWMFPHSRLELGRVRVRELGDVAVVHAPWTMTG-----------------Q
+TAPDGDEA--GERTGVLLLVVRRTETGAWEAVAGQNTDSVPGAQTHLAD-DEGLAAVHYH
+PSAWFDPDEDPDGPEA-------------------------------------C----
+>2_535
+MSPADPSPRLLARPPASPAAVAEAFEAAWNAADADALADLFAEDADFVTVLGVWWTRRRQ
+IRLDHARAFRWMFPESRLEMDEVRVRDLGDVAVVHAPWTMTGPGVGGEVGEATGTVGVRE
+AGGDGSGGGDGERTGVLLLVVRRDEAGAWEVVAAQNTDRSPEPRPRPADEDDLLAEVHPH
+PSAWLHPDD--DGPASRLSARPRLGWAVHEPVPPLPLPNSPSPPLPLPQGELSCRWPV
+>4_2077
+MPPADPTADVAAR-PAGPAAVAEAFAAAWNAADADALAELFAEDADFVNVVGVWWTRRRQ
+IRVNHALGFRWMFPASRLVLGQVRVRELGDVAVVHAPWTMTG-----------------Q
+TAPDGDEA--GERTGVLLLVVRRTEAGAWEAVAGQNTDSVPEAQTHLAD-DDGLAAVHYH
+PSAWIDPDDDPDGPEA-------------------------------------C----
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001945.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001945.fa
new file mode 100644
index 0000000000000000000000000000000000000000..caadc09d3285c8c2c756575e1e4e96abf8c47ee7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001945.fa
@@ -0,0 +1,17 @@
+>0_2198
+M--------------------------------NVSAEQL--------------------
+------------------------------------------------------------
+--------IGDESGVHRGLYRRVVDHVPWLRGFVCDDLHNFGPEDRWILAR-----
+>2_445
+MTRLLPGDSLTLDLAPEDPADLLARLRAAGVAMNESAERLITDARVCAVVPER--VTVVE
+RTLAELGLPDGGTLPELRRAVEAAGLRECPPTVAPLLRLVTLDQANAPDSLLRHGRAPDD
+SAHVFSPSLSDEPGVHRGLYLRVVDHVPWLRGFVCDDLHVFGPEDRWILAL-----
+>3_683
+MADLIDRAGIELTLA-GDPHELLTQLQAAGVRFNDSARTLLFRPALARDLQTSRPVRVVE
+RSLTDLGLPNGGTLPQLRRAALAAGLAPCPPAVAPLLRLRTLDQVNAPDSVLRHGRAPEG
+SVHVLSPSLGEDPRVHRGFYLRVVDEAPWLRGFMCDDLHVMGADDRWVLSAPTSAP
+>4_2130
+M--------------------------------NVSAEQL--------------------
+------------------------------------------------------------
+--------IGDESGVHRGLYRRVVDHVPWLRGFVCDDLHNFGPEDRWILAR-----
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001947.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001947.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c8444da955a5e1991ca33e41f2305e5b5889035
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001947.fa
@@ -0,0 +1,60 @@
+>0_2211
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------MGVNGLPGTGKTTTLRDILASNVVERARRLSACENPFDALTERTHEWTGEGRMRRRARELRPEVAGFE
+MVVASANNAAGESISEEIPQVESRIVV-----------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-----------------------------------------------------------------------
+>1_1914
+M------------------------------------------------------------PAPS---------------
+-----------------------------------LGEEDKRAI------------------------------------
+--------------------------------------------------------------------------------
+--------------PALQPSLSSSNVTAHEHTGHPQAARIDVVARADVVEAG----------------------------
+--------GPGLMGVNGLPGTGKTTTLGDILASNVVERARRLSACENPFDALTERTHEWTGEGRMRRRVRELRPEVVGFE
+MVVASANNAAVENLSEEIPQ---RSAIKDSRNVDADYFAELA-AALG---GSRGEEDALGEDSLTSEQPGTSGLATAPMA
+TAPTPPRS------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------------------------------ARRR----------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------PTR--------------------------------------------------------------------
+----------------------------------------------------------------------G
+>2_442
+M------------------------------------------------------------PAPS---------------
+-----------------------------------LGEEDKRAI------------------------------------
+--------------------------------------------------------------------------------
+--------------PALQPSLSSSNVTAHEHTGHLQAACIDVVARSEVVEVG----------------------------
+--------GPGLMGVNGLPGTGKTTMLRDILASNVVERARRLSACENPFDALTERTHEWTGEGRMRRRARELRPEVVGFE
+MVVASANNAAVENLSEEIPQ---RSAIKDGRHVDADYFACLATAAVG---GSGGGRGRPG--------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-----------------------------------------------------------------------
+>3_393
+MGDTRGRTQQDIVRFWQLQELFDPQPLPKLTPRTSPPFGKRVITWRAEDGDVALPWNRLAPPPPTTKGAAREWRHTLYLR
+IYALEDAYQTLHSAFPADADAYDERPGGRSAAAGALVDADGRLIGGTGVLSSALWGIGRLCRGEGFDDSLVDGFEAAGEA
+FVDAADRAAGVPDDDAFGEQPVLTAGMLVALIRLAQHSAGVEGMPALAGHEVRIASQVVSASSGDETPDIDFLNSFYLSD
+LHRVGEAIARGDVGPALDAYLTPDGDVDTQR-------RVDVVARPDIVDAGVEPARVPAGRWPAKTSYALARSQQFAVN
+RALNELGAEPGLMGVNGPPGTGKTTMLRDILAANVVERARKLAGFADPSGAFTGRTLAWTGEGRRHRTVHELRPELTGFE
+MVVASANNAAVENISEEIPH---RDAIKDSGRADADYFADLATAALGLGVENADEDGAPG-------------ACDGPAA
+EQPAAASSGAWGLVAARLGNKVNRARFRDAVLFGGASGGRGARGRGLDTLLKDWAASPSAPAQWTAAREAFHRALHEVDR
+GLTERRDAAQRTVRTAAAREAVRAAERRLAELSRQRTAKWAGAEAIRRELSAAQAEAGRIRDALDLHRDAKPGFWETITS
+FGVAGQQWRETYQPLLEAWSTADAGRAALAADTEAAERRLSELEAQIVHLDGECARRRGDLADLEAAVRADEERFGGRHP
+SAVVDAQTRETTTPWLDEEMEKARTELFLAALELHRAFIAAAARDLRPSFQAAMEVMAGAAPRDLEAEKRRAAWQVFFLL
+VPLVSTTFASFDRMFTGMGRESLGWLFVDEAGQASPQYAAGAIWRANRAVVVGDPLQLEPVVTIPVTVSRSLAKAHGVSS
+TWIAPEASVQRLADRVSRYGTTLPQGEDDVWVSSPLRVHRRCDDPMFALSNDLAYGGLMVSGVQRKGPEEDPFERTGDGE
+IFASSWMDTPARTPGTHLQPNQIERVRRGIEACRRWGIPCTEIIAISPFREVADALRVLSDEFPGLTAGTIHTAQGREAD
+VVFFVLGGAPDKPGARNWASSRVNLANVAVSRAKRRLYVIGDREAWSRHNYFRQIAEALPRAAEPDAGRER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001949.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001949.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f916f241c5e465b79d4ad7415d9b85c47fd9a4f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001949.fa
@@ -0,0 +1,33 @@
+>0_2222
+MPPATTAPSPASLPLDGVLVADFSRVLAGPLATMTLADLGARVIKVEHPVRGDDTRGWAP
+PRSATGATYFESVNRNKESVGWDLKDPEDQRRAAALAARADVVVHNLKPGTMERLGLGYD
+DVARENPSVVYAAVSGFGDREGRDLPGYDFIVQAAGGLMSITGEPD-APMKAGVALVDVL
+TAKDLTAGVLAALLRRERTGEGAHLRLNLLSSLQGALANQGQAWLGAGVVPRRMGNDHPS
+IAPYQLLACRDAPLAVAIGNDAQFRTFAAALGVPELAEDPRFTTNTDRVEHREELRTALE
+DALSAQTAAHWRDVLQAERLPAGLVSTVAEGVELAESLGLEPTVEVQDRSGAPAGRQFRH
+PVQWDPPVAHPRHAPPALGADTAAVNTWLD---------AR
+>1_1924
+MPPATTAPSPASLPLDGVLVADFSRVLAGPLATMTLADLGARVIKVEHPERGDDTRGWAP
+PRSATGATYFESVNRNKESVGWDLKDPEDQRRAAALAARADVVVHNLKPGTMERLGLGYD
+EVARENPSVVYAAVSGFGDREGRDLPGYDFIVQAAGGLMSITGEPD-APMKAGVALVDVL
+TAKDLTAGVLAALLRRERTGEGAHLRLNLLSSLQGALANQGQAWLGAGVVPRRMGNDHPS
+IAPYQLLACRDAPLAVAIGNDAQFRTFAAALGVPELAEDPRFTTNTDRVEHREELRTALE
+DALSAETAAHWRDVLQAERLPVGLVSTVAEGVELAESLGLEPTVEVQDRSGAPAGRQFRH
+PVQWDPPVAHPHHAPPALGADTAAVNTWLD---------TR
+>2_790
+M-EHTDEPRGGG-PLEGIVIADFTRVLAGPYATMLLADMGATVIKVESP-GGDDTRTWRP
+PEHEGVSTYYLSVNRNKRAVALDLSDREDLDTAYALLDRADVFLENFKPGGLAKFGLDPD
+SVAERWPHLVHASITGFGTASGTALPGYDLLAQAVSGMMTVTGEPDGAPQRSGVAIFDVI
+TGLHAAIGVLGALQERTRSGRGQHLELNLLSSALSGLVNQTSAAIAGGVTPHRMGNEHPS
+LYPYGPFRAADRELIIAVGNDRQFARLVEQLGRPELAEDPRFLTMKDRNAHRGELGPLLE
+EALAAQSAGEWFEQLRDAGIPCSPILTLPEGVEFAAGLGLDPVVEV----GEQRIPTVRH
+PIRFSRTPARHELAPPALDADRDWVRAWIDQTPPSTAADAD
+>4_2162
+MPPATTAPSPASLPLDGVLVADFSRVLAGPLATMTLADLGARVIKVEHPVRGDDTRGWAP
+PRSATGATYFESVNRNKESVGWDLKDPEDQRRAAALAARADVVVHNLKPGTMERLGLGYD
+DVARENPSVVYAAVSGFGDREGRDLPGYDFIVQAAGGLMSITGEPD-APMKAGVALVDVL
+TAKDLTAGVLAALLRRERTGEGAHLRLNLLSSLQGALANQGQAWLGADVVPRRMGNDHPS
+IAPYQLLACRDAPLAVAIGNDAQFRTFAAALGVPELAEDPRFTTNTDRVEHREELRTALE
+DALSAQTAAHWRDVLQAERLPVGLVSTVAEGVELAESLGLEPTVEVQDRSGAPAGRQFRH
+PVQWDPPVAHPHHAPPALGADTAAVNTWLD---------AH
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001951.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001951.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a6f6685531aa076cf849e84020eb4e8b3a1c9b8c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001951.fa
@@ -0,0 +1,13 @@
+>0_2237
+MAEKKTEKNGAPMGPGTSNIKDPEVYEALRREGASEEKAARIANASARDGRDEVAERGGE
+AGSYEDWTKDELAKRARELDIEGRSTMTKDELIEALRNH
+>1_1941
+MAEKKAEKNGAPMGPGTSSIKDPEVYEALRREGASEEKAARIANASARDGRDEVAERGGE
+AGSYEDWTKDELEKRARELDIEGRSTMTKDELIEALRDH
+>2_925
+MATQKKSESDTP------QIKDPEMYEALRRDGASKEKAARISNAAARDGREEVAERGGE
+SESYEEWTVDELEDRAKELDLTGYSDKRKDELIAMLREH
+>4_2179
+MAEKKTEKNGAPMGPGTSNIKDPEVYEALRREGASEEKAARIANASARDGRDEVA-----
+-------------KRARELDIEGRSTMTKDELIEALRDH
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001952.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001952.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8bcc95b37129bf561ff5baaff393536f181705d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001952.fa
@@ -0,0 +1,21 @@
+>0_2239
+MTRPDPSAHRGAPLPSALGAWRRRPQPPLRPVTPAPAGPRSAAAASLPTVEEVSAGGVIV
+REHDGGLEVAVIARYNRGGRLEWCLPKGHPEGEEDHRQAAVREVEEETGIAGHILEPLGA
+IDYWFTVARHRVHKTVHHFLLRATGGELTTENDPDHEAVDVAWVRLEDVARRLSFANERR
+IVDLARQVVDQHFPPGGARGPRP
+>1_1943
+MTRPDPSAHRGAPLPSALGAWRRRPQPPLRPVTPAPAGPRSAAAASLPTVEEVSAGGVIV
+REHDGGLEVAVIARYNRGGRLEWCLPKGHPEGEEDHRQAAVREVEEETGIAGHILEPLGA
+IDYWFTVARHRVHKTVHHFLLRATGGELTTENDPDHEAVDVAWVRLEDVARRLSFANERR
+IVDLARQVVDQHFPPGGARGPRP
+>3_372
+MSSPDPTAHRGAPLPSALGAWRRRPPQPPRPLAPGAPAARPQSGAGLPTVEEVSAGGIVI
+REHAGDLEVAVIARYNRGGRLEWCLPKGHPEGAEDHRQAAVREVEEETGIAGCILEPLGS
+IDYWFTVSRHRVHKTVHHFLLRATGGELTTENDPDHEAVDVAWVSIDDVARRLSFANERR
+IVDLARQVIPQHFPTGRPPG-RP
+>4_2181
+MTRPDPSAHRGAPLPSALGAWRRRPQPPLRPVTPAPAGPRSAAAASLPTVEEVSAGGVIV
+REHDGGLEVAVIARYNRGGRLEWCLPKGHPEGEEDHRQAAVREVEEETGIAGHILEPLGA
+IDYWFTVARHRVHKTVHHFLLRATGGELTTENDPDHEAVDVAWVRLEDVARRLSFANERR
+IVDLARQVVDQHFPPGGARGPRP
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001953.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001953.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0c7263e9c5ab9d5eafbab50b41649bbfdfecb085
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001953.fa
@@ -0,0 +1,33 @@
+>1_82
+MTRSTSTRIQGAVLQTLSATAPYAQSRPLEVQDLQLAPPQGREVLVRIEAASVCHSDLSV
+VQGLRPRPVPMLLGHESAGIVESTGPEVASVAVGDRVIMTFLPRCGECPACRTEGRLPCS
+EGTAANERGDLLSGGRRLSTEDG--PVAHHLGVSGFATHAVVDARSVVRVEHDVPADIAA
+VLGCAVLTGGGAVMNAVSVPKGSTVVVVGLGGVGMAAAIVARALG-HEVIGVDGISTKRD
+LAVELGAQQVY------APQEALDAEVRG-DLVVDATGNPRGFETAVELTGPGGATVTVG
+LPP--ADAMSSVSPMALVAQARTIVGSYLGSAVPQRDIPRFVELWRAGRLPIERLISSHI
+SLEDINQAMDRLDSGAEMRQVIL-FDQEQPSQGQE
+>1_1746
+----------------MRAALAMKVGGKFEIHDVVIDDPVGREVLVDVKASGLCHSDLHL
+IDHDFGLPLPAAGGHEISGVVAAVGPSVTSLKPGDRVVACLIAYCGACARCLAGQTTLCL
+NQEAVVRGP---EEKPRLTLQDG-TPVAQSVNVGGFAEQVLVHENQLAVVNEDIPFPQAA
+LIGCSVVTGAGAAINTAHVRPGDTVAVVGVGGIGLNAVSGARLCGAKRVIAIDLDDSKLE
+AARRFGATDVVNSGSGDAVEAVLGITGTGVDHAFEAIGLPVTQQLAQDVLGPGGTAYLIG
+IAPPGTTAQFGASLDSLFAQ-RRLQAVAMGSSNIQRDIPLYADLYVQGRMDLDHMVSQEI
+SLDEINTGYERLLNGEVIRSVITSF----------
+>2_672
+----------------MRAALAMKVGGKFEIHDVVIDDPVGREVLVDVKASGLCHSDLHL
+IDHDFGLPLPAAGGHEISGIVAAVGPSVTSLKPGDRVVACLISYCGACARCLSGQTTLCL
+NQEALVRGP---EEKPRLTLEDG-TPVAQSVNVGGFAEQVLVHENQLAVVNEDIPFPHAA
+LIGCSVVTGAGAAINTAHVRPGDTVAVVGVGGIGLNAVSGARLCGAKRVIAIDLDDSKLE
+AARRFGATDVVNSGSGDAVGAVLGITGTGVDHAFEAIGLPVTQQLTQDVLGPGGTAYLIG
+IAPPGTTAQFGASLDSLFAQ-RRLQAVLMGSSNIQRDIPLYADLYVQGRMELDHMVSQEI
+SLDEINAGYERLLNGEVIRSVITSF----------
+>2_757
+M--------------KTTAAVATAAETPLTITEVEIDDLRADELRIRMVASGVCHTDAIV
+RDQWYPTPLPAVLGHEGAGVVEEVGDGVHGFSAGDRVLLSF-SSCGHCRACHEGQPAYCA
+DMFALNFGGRRLEDGSTSYTLDGEQVSSHFFGQSSFAALANVPARCAVKVDDDAPLELLA
+PLGCGIQTGAGAVLNVLRPEPGASLVVFGAGAVGLSAVMAAKVARCGTIIAVDMHPDRLR
+LAEELGATHTLQAGEP-VAERIRELTDGGTEYAVDTTGVAAIFGDNVDALAPRGVLGVVG
+AAALGTEASFDIGTN--LPKGITIRTIVEGESIPQVFVPRLMALHAAGEFPFDRLVKSY-
+PFAQINQAFEDSKSGETLKPVVV-FDQ-------A
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001958.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001958.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c53250d47a601958f54f8cad9ada50dc7618520
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001958.fa
@@ -0,0 +1,40 @@
+>1_1594
+MQTEKHVPEALTIEEVFTAARHYRVPVYQRAYAWTQVEISTLLADVRRARLRSEKPDTQGASSDYYLGSLVVNRATTPEG
+VPIDEVVDGQQRLTTLTVLAAVAERVIRAGVLDPRALAVLDYEGRPEAGEDLATLRRRGAPAGTSFQVDAIGVAVETIAA
+ACRRALERQTPADDQEVMFDGDDLAYLWKHVRLLRTELPKGTDLNHYFEVMNTRGEQLAKHEILKATLMRPLQDATDRKV
+FAHVWDACAVLDRHIQLQFSTERPKDGGEAARDAVFGGSWSALLTRDFASLRAALAPSQTAMASGARTIIGVLLAAGQTA
+VESGPSSDQCQDDADTGAYGTIVDFPNLLLHVLRVMQEKGEGAEPGLPRWGQDSTGAVRLEDGSLLEQFAQHGQGDAAWS
+QRFLVTLLRMRLLLDTYVIRTLATTGTQADEENWVLSRAQKLETESGE-RSPRRRLGVKNTFQDPQVQDAVRNLQAMFQV
+TDTRRTSKYFLYRILRWLDAQPEDGVDGVAFQHMLEDLARERLRAYEADKTWDAGVNVPNFVFNALDYILWDAGRTSPME
+REHLREPLSDVEQEVLRRRADAFRFRYRTSVEHFYPVVPGEEQEALTAEDVNRFGNLCIMGRRENSQRNNLMPVSKVKQY
+SSDEQSLKFQLMAGILHAEGDWDVPQIKEHGNSMRRVIQEWQGKRP
+>2_885
+MQTEKHVPEALTIEEVFTAARHYRVPVYQRAYAWTQVEISTLLTDVRRARLRSEKPDTQGALSDYYLGSLVVNRATTPED
+VPIDEVVDGQQRLTTLTVLAAVAERVIRAGVLDPRALAVLDYEGRPEAGEDLATLRHRGAPAGTSFQVDAIGVAVETIAA
+ACRRAMDRQTPADDQEVMFDGDDLAYLWKHVRLLRTELPKGTDLNHYFEVMNTRGEQLAKHEILKATLMRPLQDATDRKV
+FAHVWDACAVLDRHIQLQFSTERPKDGVEAARDAVFGASWSALLTRDFASLRAALAPSLTATVSGARTIIGALRAAGQTA
+VESGSSSDQRQDDADTGAYGTIVDFPNLLLHVLRVMQEKGEGAEPGLPRWSQDSTGAVRLEDGSLLEQFAQHGQDDAAWS
+QRFLVALLRMRLLLDTYVIRTLATTGTQADEENWVLSRAQKLETESGE-RSPRRRLGVKNTFQDPQVQDAVRNLQAMFQV
+TDTRRTSKYFLYRILRWLDAQPVDSVDGVAFQHMLENLARERLRAYEADKTWDAGVNVPNFVFNALDYILWDAGRTSPME
+REHLREPLSDVEQEVLRRRADAFRFRYRTSVEHFYPVVPGEEQEVLTAEDVNRFGNLCIMGRRENSQRNNLMPVSKVKQY
+SSDEQSLKFQLMAGILHAEGDWDVPQIKEHGNRMRRVIQEWQGKRP
+>3_825
+MQTEKHVPEALTIEEVFTAARHYRVPVYQRAYAWTQVEISTLLTDVRRARLGSEKPDTQGALSDYYLGSLVVNRATTPED
+VPIDEVVDGQQRLTTLTVLAAVAEHVIRAGVLDPRALAVLDYEGRPEAGEDLATLRHRGAPAGTSFQVDAIGVAVETIAA
+ACRRAMDRQTPADDQEVMFDGDDLAYLWKHVRLLRTELPKGTDLNHYFEVMNTRGEQLAKHEILKATLMRPLQDATDRKV
+FAHVWDACAVLDRHIQLQFSTERPKDGGEAARDAVFGASWSALLTRDFASLRAALAPSLTATVSGARTIIGALRAAGQTA
+VESGSSSDQRQDDADTGAYGTIVDFPNLLLHVLRVMQEKGEGAEPGLPRWGQDSTGAVRLEDGSLLEQFAQHGQDDAAWS
+QRFLVALLRMRLLLDTYVIRTLATTGTQADEENWVLSRAQKLETESGE-RSPRRRLGVKNTFQDPQVQDAVRNLQAMFQV
+TDTRRTSKYFLYRILRWLHAQPVDSVDGVAFQHMLENLARERLRAYEADKTWDAGVNVPNFVFNALDYILWDAGRTSPME
+REHLREPLSDVEQEVLRRRADAFRFRYRTSVEHFYPVVPGEEQEVLTAEDVNRFGNLCIMGRRENSQRNNLMPVSKVKQY
+SSDEQSLKFQLMAGILHAEGDWDVPQIKEHGNRMRRVIQEWQGKRP
+>4_1814
+-MSERNAPETLTIGEVFAAGRHYRVPVYQRSYAWTEVEVSTLLADVRRARLRSKALESRGNVSDYYLGAMVVNRTQTPAG
+DQIDEVVDGQQRLTTLTVLAAVAEQITQAGVLDPVALAVLDYEGRAEAGEDLATLRRRGGHRHGAFQVEAIGIAAQTVRG
+ACERATDRQATADGQTVVFDADDLAYLWNHVRLLRTELPEGTDLNHYFEVMNTRGEQLAKHEVLKAMLMRPLRDESERQV
+FAQVWDACAVLDRPVQLQFASEQLDPDISPARDAVFGDTWSTLVTTDFESLRAALEPSLAETELGGRTSLDSLLSSRGAG
+EGTSASAEKRSD--ETGSYGTIIDFPNLLLHVLRVMEESGMASGSGRPAWGQEPKNAVRLEDNSLLEQCAERRQDDARWS
+KRFLVMLLRIRFLLDTYVIRTLSTTGTRADEENWVLVGALKVESGAEEGSSRRRRLGVKNTFEDPAVQEAVRNLQAMFQV
+TDTRRASKYFLYRILRWLAERPVDRVDGEAFQRMLEDLARERLRAYDADEGLDLGVKVPNFVFNVLDYILWDLGRNPSAE
+AGALGAALGDVERSVLSQRAGSFRFRYRTSVEHFYPVVPGEGQKVLTSTEVNRFGNLCIMGRRENSQRNNLMPVSKVKQY
+SSDEQSLKFQLMAGILHAEGDWDVPQIKEHGNSMRRVIQEWQGKRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001959.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001959.fa
new file mode 100644
index 0000000000000000000000000000000000000000..84351d61aac386c624cb7dd4364344f4dd80e9c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001959.fa
@@ -0,0 +1,32 @@
+>1_1595
+MRTRPTALDAAVDHPRGAQSDARGPGTGRSGSLTANVMTVADALRDPRLRIPEYQRPYTWSTTNTGQLVEDIRRFRAAAS
+YRIGTMIVHAEDGWLDIVDGQQRYMTFALIALALQEVLGDTAERAEHQRAALDRAAAIELPPGRRDVSERHIVENHRLIL
+QTFRSWDSTEVEDFADYFLDHCTLVRLVVSDLDAAFQMFDSQNTRGRALLPTDLLKAYHLRAYGEATSDRAAILAAVREW
+EATPPFEIHHLFSRLLYPILRWSAGESLPRDGFTASRIGAFKGISAGPTGLGRLPWAHGLLMAKAHVDDYNGRNAALIAH
+GALPPLEFPFQLTQPVIDGEMFFRLVRHYTRLARDLGVSATDAEQTAGDDARRGRENRQFQTITRLVRATGTGAGYRYTQ
+ELYGALLLAYADRFGDHDIERAALVFARHAFALRTRLTRVYPRSVELHALGQHGAPDLEDRVNLFRLMRSSVDPAVVTGR
+VAALPGPYVDEASPVERLYSDTPWDTEEAHDAD
+>2_884
+MEMHSTAADAAVDHPWGAQNDAQGPGTGRSGSLTANVMTVADALRDPRLRVPEYQRPYTWSTKNAVQLVEDIRRFRAAAS
+YRIGTMIVHAEDGWLDIVDGQQRYMTFALIALALQEVLGDTAERAEHQRAALDRAAAIELPPGRRDVSERHVVENHRLIL
+QTFRSWKSSEVEDFADYFLDHCTLVRLVVNDLDAAFQMFDSQNTRGRALLPTDLLKAYHLRAYGEATSDRAAILAAVREW
+EATPPFEIHHLFSRLLYPILRWSAGESLPRDGFTASRIGAFKGISAGPTGLGRLPWAHGLLMAKAHVDDYNGRNATLIAH
+GALPPLEFPFQLTQPVIDGEMFFRLVRHYTRLARDLGVSATDAEQTAGDDARRGRENGRFQTITRLVRATGTGAGYRYTQ
+ELYGALLLAYADRFGDHDIERAALVLARHAFALRTRLTRVYPRSVELHALGQHGAPDLEDRVNLFRLIRSSLDPAAVTGR
+VAALPGPYVDEASPVERLYSDTPWDTEEAHDAD
+>3_824
+MEMHSTAADAAVDHPWGAQNDAQGPGTGRSGSLTANVMTVADALRDPRLRVPEYQRPYTWSTKNAVQLVEDIRRFRAAAS
+YRIGTMIVHAEDGWLDIVDGQQRYMTFALIALALQEVLGDTAERAEHQRAALDRAAAIELPPGRRDVSERHVVENHRLIL
+QTFRSWKSSEVEDFADYFLDHCTLVRLVVNDLDAAFQMFDSQNTRGRALLPTDLLKAYHLRAYGEATSDRAAILAAVREW
+EATPPFEIHHLFSRLLYPILRWSAGESLPRDGFTASRIGAFKGISAGPTGLGRLPWAHGLLMAKAHVDDYNGRNATLIAH
+GALPPLEFPFQLTQPVIDGEMFFRLVRHYTRLARDLGVSATDAEQTAGDDARRGRENGRFQTITRLVRATGTGAGYRYTQ
+ELYGALLLAYADRFGDHDIERAALVLARHAFALRTRLTRVYPRSVELHALGQHGAPDLEDRVNLFRLMRSSLDPAAVTGR
+VAALPGPYVDEASPVERLYSDTPWDTEEAHDAD
+>4_1815
+MRTRPTALDAAVDHPRGAQSDAQEPGTGRSGSLTANVMTVADALRDPRLRIPEYQRPYTWSTTNTGQLVEDIRRFRAAAS
+YRIGTMIVHAEDGWLDIVDGQQRYMTFALIALALQEVLGNTAERAEHQRAALDSAAAIELPPGRRDVSERHVIENHRLIL
+QTFRSWDSTEVEDFADYFLDRCTLVRLTVTDLDAAFQMFDSQNTRGRPLLPTDLLKAYHLRAYGETTTDRGAIMAAVKDW
+EFTPPDEINHLFSRLLYPVVRWSAGESSPRDGFTSAQIGAFKGISAGAASFGRLPWAHGLLMAKAHVDDYNTRNAALIAH
+GALAPLEFPFQLSQPIIDGEMFFRFVRHYTSLARTLGVSATEADQTVQDDARRHREIRRVHAITGLVRSSGNGAGYRYTQ
+ELYGALLLAYADRFGAEDLERAALVLARHAFALRTRLRRVYPRSTELHALGLNKAVDSAEQVNLFRLMMGTMDPAAITGR
+VPARPGDVDNAPEPVRRLYSDRPWDPEEESHHV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001961.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001961.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f92a0e19a6ef22b175562c929f9567e69f6918de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001961.fa
@@ -0,0 +1,60 @@
+>1_1597
+MAIHNESELETYICEYLEQHDWLYSPNDAGYDRKNAIFPEDVHAWLAENQPEDYGRIVKADAPASAQQAQRDQITTRLID
+VLNKPQDTGVGGTLNVLRKGFKVGTSATLRMAEPRPATNLNPAAVASYERMRLRVMRQVHFNPA-TNQSVDLVLFVNGLP
+VATIELKTDSTQSIGHAKKQYRDRNPKATPLFGFGTRAVVHFAVSNREVWMTTKLAGKDTFFLPFNQGDDGHAGNPLNPN
+-GSSTAYLWERILQRDTWLEILQKFVFLKKETVEDEHGRSRRKSTLIFPRFHQWEAVTTMLAAVREEGAGASYLIEHSAG
+SGKTNTIAWTAHRLLSTYGVDEQRVFDSVIVVTDRTVLDDQLQEAVRQIERTSGTVVAVDRKNLGGEATSKSALVKQTLL
+QGNRIIVVTLQTFPAVLELLKGDSTLAGRTYAVIADEAHSSQTGSAAAKLKRVLTPDEQADLDDGGEADTESILAAEVAA
+TGRPQNISFFAFTATPKDKTLQMFGRPSGEYDEKGQEIPASFHRYTMQQAIEEEFILDVLKNFTNYDTAFKLALAGQQGE
+FRPEGDRAAVGKPTTEVDQTEASKKLMRWVKLHPTNIAQKVKIIVEHFRANVAGLLDGQAKAMVVTDSRAAAVRYKRQMD
+QYIQDMGYTDVGTLVAFSGEITDDEFGLEKVTERSMNPSVTGDLAKAFDGDGYQVMIVANKYQTGFDQPKLCALYVDKKL
+SGVLAVQTLSRLNRAAPGKDTTYVLDFVNSEDDIQAAFEPYYAGAKLEAVTDPNLIHDLGTKLDAAGVYDWDEVDAFAEV
+WVAWKPGSGQEGLQAALEPVAYRFRKELAHARMNQDETRVNELVLVRKDMRSFVSLYDFLSQIYEFGDTEHYKRALFLRH
+LVQLVGDQPGGEELIDLSDVQLVSIRQKKTSSGDIGLTGGAALKGTTAVGGGQVREEQRGPLEEVIEKINEIFAGEGVDA
+SPSQQEAWVSALVAPLMEDEKLLGQAGANSLEQFLASPNLERSAMGAVYANEDAFAKMTDIVGRGGDPSKMIVAAIGEYL
+YWKVRSEGTGPVDVAHGRSAVFADETAPSQGTSVDERARATPSRVRKGS
+>2_882
+MAIHNESELETYICEYLQSHGWLYSANDEGYDRKNAIFPEDVHAWLVENQPEDYGRIVKADAPASAQQAQRDQITTRLVD
+VLNKPQDTGVGGTLNVLRKGFKVGTSATLRMAEPRPATNLNPAAVASYERMRLRVMRQVHFTGAHESESVDLVLFVNGLP
+VATIELKTDSTQSIGHAKKQYRDRNPKATPLFGFGTRAVVHFAVSNREVWMTTKLAGKDTFFLPFNQGDDGHAGNPLNPN
+GGSSTAYLWERILQRDTWLEILQKFVFLKKETVEDEYGRSRRKSTLIFPRFHQWEAVTKMLAAVREEGVGKSYLIEHSAG
+SGKTNTIAWTAHRLLSTYGVDEQRVFDSVIVVTDRTVLDDQLQEAVRQIERTSGTVVAVDRKNLGGEPTSKSALVKQTLL
+QGNRIIVVTLQTFPAVLELLKGDSTLAGRTYAVIADEAHSSQTGSAAAKLKRVLTPDEQADLEDGGEADTESILAAEVAA
+TGRPQNISFFAFTATPKDKTLQMFGRPSGEYDEKGQEIPASFHRYTMQQAIEEEFILDVLKNFTNYDTAFKLALAGQQGE
+FRPEGDRAAVGKPTTEVDQTEASKKLMRWVKLHPTNIAQKVRIIVEHFRANVAGLLDGQAKAMVVTDSRAAAVRYKRQMD
+QYIQDMGYTDVGTLVAFSGEITDDDFGLEKVTERSMNPPVTGDLAKAFDGDGYQVMIVANKYQTGFDQPKLCALYVDKKL
+SGVLAVQTLSRLNRAAPGKDTTYVLDFVNSEDDIQAAFEPYYAGAKLETVTDPNLIHDLGTKLDAAGVYDWAEVDAFAEV
+WVVWKPGSGQEGLQAALEPVAYRFRKELAHARMNQDETRVNELVLVRKDMRSFVSLYDFLSQIYEFGDTEHYKRALFLRH
+LVQLVGDQPGGEELIDLSDVQLVSIRQNKTSSGDIGLTGGTALKGTTAVGGGQVHEKQRGPLEDVIEKINEIFAGEGVDA
+SPSQQEAWVSALVAPLMEDEKLLGQAGANSLEQFLASPNLERSAMGAVYANEDAFAKMTDIVGRGGDPSKMIVAAIGEYL
+YLTVRGEGAGPVDVAHGRSAVFADETAPSQGTSVDERASATPSRVRKGN
+>3_822
+MAIHNESELETYICEYLERHGWLYSANDDGYDRKNAIFPEDVHAWLAENQPEDYGRLVKADAPASAQQAQRDQITTRLID
+VLNKPQDTGVGGTLNVLRKGFKVGTSATLRMAEPRPATNLNPAAVASYEHMRLRVMRQVHFNPA-TNQSVDLVLFVNGLP
+VATIELKTDSTQSIGHAKKQYRERNSKATPLFGFGTRAVVHFAVSNREVWMTTKLAGKDTFFLPFNQGDDGHAGNPLNPN
+GGSSTAYLWERILQRDTWLEILQKFVFLKKETVEDEYGRSRRKSTLIFPRFHQWEAVTTMLAAVREEGAGKSYLIEHSAG
+SGKTNTIAWTAHRLLSTYGADEQRVFDSVIVVTDRTVLDDQLQEAVRQIERTSGTVVAVDRKNLGGEATSKSALVKQTLL
+QGNRIIVVTLQTFPAVLELLKGDSTLAGRTYAVIADEAHSSQTGSAAAKLKRVLTPDEQADLEDGGEADTESILAAEVAA
+TGRPENISFFAFTATPKDKTLQMFGRPSGEYDEKGQEIPASFHRYTMQQAIEEEFILDVLKNFTNYDTAFKLALAGQQGE
+FRPEGDRAAVGKPTTEVDQTEASKKLMRWVKLHPTNIAQKVKIIVEHFRANVAHLLDGQAKAMVVTDSRAAAVRYKRQMD
+QYIHDMGYTDVGTLVAFSGEITDDDFGLEKVTERSMNPSVTGDLAKAFDGDGYQVMIVANKYQTGFDQPKLCALYVDKKL
+SGVLAVQTLSRLNRAAPGKDTTYVLDFVNSENDIQAAFEPYYAGAKLETVTDPNLIHDLGTKLDAAGVYDWDEVDAFADV
+WVAWKPGSGQEGLQAALEPVAYRFRKELAHARMNHDETRVNELVLVRKDMRSFVSLYDFLSQIYEFGDTEHYKRALFLRH
+LVQLVGDQPGGEELIDLSDVQLVSIRQKKTSSGDIGLTGGAALKGTTAVGGGQAREKQRGPLEEVIEKINEIFAGEGVDA
+SPSQQEAWVSALVAPLMEDEKLLGQAGANSLEQFLASPNLERSAMGAVYANEDAFAKMTDIVGRGGDPSKMIVAAIGEYL
+YWKVRGEGAGPVDVAHGRSAVFADETAPSQGTSVDERASATPSRVRKGN
+>4_1817
+MAIHNESELETYICEYLEQHGWLYSPNDDGYDRKNAIFPEDVHAWLAENQPEDYGRLVKADAPASAQQAQREQITTRLVD
+VLNKPQDTGVGGTLNVLRKGFKVGTSATLRMAEPRPATNLNPAAVASYERMRLRVMRQVHFNPA-TNQSVDLVLFVNGLP
+VATIELKTDSTQSIGHAKKQYRDRNPKATPLFGFGTRAVVHFAVSNREVWMTTKLAGKDTFFLPFNQGDDGHAGNPLNPY
+GGSSTAYLWERILQRDTWLEILQKFVFLKKETVEDEHGRSRRKSTLIFPRFHQWEAVTTMLAAVREEGAGKSYLIEHSAG
+SGKTNTIAWTAHRLLSTYGADEQRVFDSVIVVTDRTVLDDQLQEAVRQIERTSGTVVAVDRKNLGGEATSKSALVKQTLL
+QGNRIIVVTLQTFPAVLELLKGDSTLAGRTYAVIADEAHSSQTGSAAAKLKRVLTPDEQADLEDGGEADTESILAAEVAA
+TGRPQNISFFAFTATPKDKTLQMFGRPSGEYDEKGQEIPASFHRYTMQQAIEEEFILDVLKNFTNYDTAFKLALAGQKGE
+FRPEGDRAAVGKQTTEVDQTEASKKLMRWVKLHPTNIAQKVKIIVEHFRANVAGLLDGQAKAMVVTDSRAAAVRYKRQMD
+QYIQDMGYTDVDTLVAFSGEITDDEFGLEKVTERSMNPSVTGDLAKAFDGDGYQVMIVANKYQTGFDQPKLCALYVDKKL
+SGVLAVQTLSRLNRAAPGKDTTYVLDFVNSEDDIQAAFEPYYAGAKLETVTDPNLIHDLGTKLDAAGVYNGDEVDVFADV
+WVAWKPGSGQEGLQAALEPVAYRFRKELAHARMNQDETRVNELVLVRKDMRSFVSLYDFLSQIYEFGDTEHYKRALFLRH
+LVQLVGDQPGGEELIDLSDVQLVSIRQKKTSSGEIGLTGGAALKGTTAVGGGQVREKQRGPLEEVIEKINEIFAGEGVDA
+SPSQQEAWVSALVAPLMEDEKLLGQAGANSLEQFLASPNLERSAMGAVYANEDAFVKMTDIVGRGGDPSKMIVAAIGEYL
+YWKVRSEGAGPVDVAHGRSAVFVDETAPSQGTSVDERASATPSRVRKGN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001965.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001965.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89bcd8af76c988992ee197bc587b0efa135dc544
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001965.fa
@@ -0,0 +1,21 @@
+>1_1650
+MSITQTDTPLTQDELARTIAADIAPGSFVNLGIGQPTTVSNYLEAEKNVTLHTENGMLGF
+GPQAEGEQIDEDLINAGKIPVTELPGAAYFHHADSFAMMRGGHLDVCVLGAYQVSATGDL
+ANWSTGKPGAIPAVGGAMDLAIGAKDTYVMMDLFTKKGDPKLLAECTFPLTGVGCVSRIY
+ADRGVFLLDASGVVRVRELHGITWEELEAAHPGVRFEKLED--
+>2_832
+MSFTQTDTPLTQDELAKVIAADIAPGSFVNLGIGQPTTVSNYLEAEKNVTLHTENGMLGF
+GPQAEGEQVDEDLINAGKIPVTELPGAAYFHHADSFAMMRGGHIDVSVLGAYQVSATGDL
+ANWSTGKPGAIPAVGGAMDLAIGAKDTYVMMDLFTKKGDPKLLAACTFPLTGVGCVSRIY
+ADRGVFLLDASGVVRVRELHGITWEELEEAHPGVRFEKLEA--
+>3_770
+MGFTHTENPLSHEELAQVIAADIAPGSYVNLGIGQPTTVSDYLDADQHVTLHTENGMLGF
+GPQAHGEQVDEDLINAGKIPVTELPGASYFHHADSFAMMRGGHLDVCVLGAYQVSATGDL
+ANWSTGKPGAIPAVGGAMDLAIGAKDTYVMMDLFTKKGDRKLMPECTFPLTGVGCVSRIY
+ADKGVFLLDSSGVVKVRELHGITFEELQATHEGVTFEEVDASA
+>4_1868
+MSITQTDTPLTQDELARTIAADIAPGSFVNLGIGQPTTVSNYLEAEKNVTLHTENGMLGF
+GPQAEGEQIDEDLINAGKIPVTELPGAAYFHHADSFAMMRGGHLDVCVLGAYQVSATGDL
+ANWSTGKPGAIPAVGGAMDLAIGAKDTYVMMDLFTKKGDPKLLAECTFPLTGVGCVSRIY
+ADRGVFLLDASGVVRVRELHGITWEELEAAHPGVRFEKLED--
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001968.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001968.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c57b5693ef18d34a2d13be6b5e61e41d41d408c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001968.fa
@@ -0,0 +1,25 @@
+>1_1653
+MTDDVDAPGAR---PASGGDVVRALASGLAVLRAFTPDTPTLSVSEAATAAGVTRATARR
+MLLTLTELGYAVQDGRRFALTPRVLELGHGYWSGRSVSEILRPILTQASQRLHQSCSAGV
+LHGAHLMYIARVHTERILRVNLDVGTRLPAFTTSMGRVLLADLPEDEACALLAGAPRTPA
+TEHTLTDVDALMAELARVREQGHAVVTAELDAHLSSVAVPVRDAEGRVAVAINTALSLGP
+DHRDPGARRAALRTGARVPAPRTPEVAAAVVQALPVLRAAADDAEAALAALQR
+>2_829
+------------------------------MLRSFTPGRPSLTVSDAAAAAGTTRATARR
+VLHTLVHEGYAVQEGRDFRLTPRVLELGHGYWTGTSLAEILSPVLTRASQELEQSCSAAV
+LDGPFLLYIARVHTERIIRVNLDVGTRMPAFLTSMGRVLLADLPPATVRRVLEAAPRTPR
+TPRTVTDVEALLEEIAQVRRQDHAVVTAELDDHLSSVAVPVRGPDGAVVAAINTALP---
+-HRTPGA--------AEPSADEQTRAAVA--QALPVLRAAARDAEDALVALRR
+>3_767
+MS----LPSTEITSPAPGDGYVRALATGLAVLRAFTPDVPRLTLTEAADAAGVSRATARR
+SLLTLVELGYAVQDGRAFELTPKVLELGHGYWSGRSTSEVLRPVLTRASQRLHQSCSAGV
+LHGAHLMYIARVHTERILRVNLDVGTLLPAFSTSMGRVLLAGLDDAEVRRVLEGAPRTPA
+TAQTLTDVDALLEEVRRVRERGHALVHGELDPNLSSVAVPVRDRDGRVVLAVNTALS---
+------TRRGRL---GEALSPAAAEAAAA--EALPVLREAADDAEAALELLGR
+>4_1871
+MTDDVDAPGAR---PASGGDVVRALASGLAVLRAFTPDTPTLSVSEAATAAGVTRATARR
+MLLTLTELGYAVQDGRRFALTPRVLELGHGYWSGRSVSEILRPILTQASQRLHQSCSAGV
+LHGAHLMYIARVHTERILRVSLDVGTRLPAFTTSMGRVLLADLPEDEACALLAGAPRTPA
+TEHTLTDVDALMAELARVREQGHAVVTAELDAHLSSVAVPVRDAEGRVAVAINTALSLGP
+DHRDPGARRAALRTGARVPAPRTPEVAAAVVQALPVLRAAADDAEAALAALQR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001971.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001971.fa
new file mode 100644
index 0000000000000000000000000000000000000000..52d3823313e2bb675d51939fd817231111e2f8de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001971.fa
@@ -0,0 +1,41 @@
+>1_1658
+MTSA-AADLAAVADVGLLDPAWAGSRAEAATADRTFLGHLLDVEAAWVRVLARHGLATEA
+EAAAAAAAGDPDAYDLAALARAAQGGGTPLIPALKALRAQLPAGSRAVHLGATSQDVVDS
+ALMVMVGRVGAILAEDLAAAQDALAELARAHRSTPMVARSLAQHSLPSTFGLRAANWLDG
+LGQAADRLAAAVADLPVQWGGAAGTLASLSGHVDRAHRAGTLGPEVTAFTLVEDLAAELG
+L--AAPAGPWDTNRMAVTGVAAALADVVAACGKIANDVLTSARIENGELGEPLAAGRGGS
+SPMPHKQNPVLSVLIRSAALSAPGLAARVYTAAGAADDERPDGAWHAEWPALRRLLRVAG
+GTAALTRELVSGLRVHEDRMRRNLELTGPLLVSEPIMAELAPELDEASGEPGSGKRLIQD
+VVDRSLACEGNFRALLRAAVPESVPDARLDDLLDPAAYTGEAEALVDRLLAARRGTTTPP
+RT
+>2_825
+MTDLDALDLS--ADAGLLNPAWAGRPVARATADRAFLQRMLEVEAAWVAVLAAHGLATDE
+QARQAEEACDPAGYDLVALARAAQGGGNPLIPALKALRERLPAGSTAVHMGATSQDVIDT
+ALMAMAAEVGRGLGEDLRGLAAALAGLAREHRGTPMVARSLAQHSLPSTFGLRAANWLDA
+VGQAAQRLERATAALPVQWGGAAGTMASLAGHVDRAHRAGRLDESVTVFTLVEDLAARLG
+L--SAPAGPWDTNRMAVTGVAAALADVTAACGKIANDVLLSSRIENGELGEPLAAGRGGS
+SAMPHKQNPVLSVLVHSAALSAPGMLAQVYTAAGAANDERPDGAWHAEWPALRQLLRVAG
+GAASLTRELAEGLRVNADRMAENLAQTGPVLVSERLMAELAPAIDEACGEPGAGKAAIQG
+AVDDSLAGRGEFRALLREAVPDTVSDDRLDELLDPAGYTGEAGALVDRILAAHAELIDT-
+--
+>3_759
+MT----------------------RP----------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------------------RVG
+IVGAAPAGPWDTNRMAVTGVAAALADVVAACGKVANDVLTSARIENGELGEPLAAGRGGS
+SAMPHKQNPVLSVLIHSAALSTPGLLAQVYTAAGAANDERPDGSWHAEWPALRQLLCVAG
+GAAALTRELVSGLRVHTGRMAANLALTGPLLVSERIMAELAPELDALFGGPGSGKAVIQG
+AVDASLAGEGDFAELLRAAVPAEVSDARLADLLDPVAYTGEAETLVDRILAAHAPRLRAS
+A-
+>4_1876
+------------------------------------------------------------
+-----------------------------------------------MHLGATSQDVVDS
+ALMVMVGRVGAILAEDLAAAQDALAELARAHRSTPMVARSLAQHSLPSTFGLRAANWLDG
+LGQAADRLAAAVADLPVQWGGAAGTLASLSGHVDRAHRAGTLGPEVTAFTLVEDLAAELG
+L--AAPAGPWDTNRMAVTGVAAALADVVAACGKIANDVLTSARIENGELGEPLAAGRGGS
+SAMPHKQNPVLSVLIRSAALSAPGLAARVYTAAGAADDERPDGAWHAEWPALRRLLRVAG
+GTAALTRELVSGLRVHEDRMRRNLELTGPLLVSERIMAELAPELDEASGEPGSGKRLIQD
+VVDRSLACEGNSRALLRAAVPESVPDARLDDLLDPAAYTGEAEALVDRLLAARRGTTTPP
+RT
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001972.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001972.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d08f264806cb8aff514c418245301f96e649b2a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001972.fa
@@ -0,0 +1,21 @@
+>1_1736
+MARFSAVLDACVLVPIAQADTLLHLAEAGLYRPVWSGRILDETVRALEAMHPDMRASGAA
+RHRAGVMDAAFDDARVEGWEQLVPGIDLPDPDDRHVVAAAIQGRADLIVTANLKDFPREV
+VESFDIEVQSPDEFFMNQLDLDPARVMTALAAQAGATRNPPLTVRDVLERLVPCGAPLFA
+EAARAQLWRVDVERP
+>2_684
+MARFSAVLDACVLVPIAQADTLLHLAEAGLYRPVWSGRILDETVRTLEAMHPDMRASGAA
+RHRAGVMDAAFDDARVEGWEQLVPGIDLPDPDDRHVVAAAIQGRADLIVTANLKDFPREV
+VGSFDIEVQSPDEFFMNQLDLDPARVMTALAAQASATRNPPLTVRDVLERLVPCGAPLFA
+EAARAQLWRVDVERP
+>3_595
+MARFSAVLDACVLVPIAQADTLLHLAEAGLYRPVWSGRILDETVRTLETMHPDMRASGAA
+RHRAEVMDAAFDDARVEGWEQLVLGIDLPDPDDRHVVAAAIQGRADLIVTANLKDFPREV
+VESFDIEVQSPDEFFMNQLDLDPARVMTALAAQAGATRNPPLTVSDVLERLVPCGAPLFA
+EAARAQLWRVDAERP
+>4_1960
+MARFSAVLDACVLVPIAQADTLLHLAEAGLYRPVWSGRILDETVRALEAMHPDMRASGAA
+RHRAGVMDAAFDDARVEGWEQLVPGIDLPDPDDRHVVAAAIQGRADLIVTANLKDFPREV
+VESFDIEVQSPDEFFMNQLDLDPARVMTALAAQAGATRNPPLTVRDVLERLVPCGAPLFA
+EAARAQLWRVDVERP
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001976.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001976.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b45b3322ec9683ff31cecf726875bb6c7f5338d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001976.fa
@@ -0,0 +1,41 @@
+>2_186
+M---------------TASR-LIPPAVDPASLPRDLPGLRAHFRPVVEEIARGALERDRA
+RLLPFEAVRALGCAGFSVLRVPREAGGPDVDVRTVTALLVDLAAADSNVAHLYRSHLGFL
+DAL-RFQPQPVRDRWHALVLAGATVGNASTERGGNALGTLNTRLTAPAGGDDDGAPGAAW
+TLTGTKYYATGSIFSSHTRVSAAVVRADGSLAPGRGFAVVPVDAPGVCLEDDWDGFGQRL
+TGTGTAVFEDVAVDPRDVLERIPGSPEAVHEAAWFQLILLAVLAGIARAARDDAAARVAA
+RVRTFNTGLGVPFREDPLIQEAVGRIAAKASAAEAVVLAAADALDASLAAGA--------
+-ATGADRWGFTGPVPPAFAEAELAVEHAQITVPELALGAAQELFLTGGASDTSVAKGLDR
+HWRNAQTVATHNPIAFRARAVGDYWINGT-LPEGLNAIGDAPAAPSSSAVDAAQPAPEPA
+EAGA-R
+>3_138
+MPLTDPTDA-------PTPLGTVPPLVRPADLPRDLAGLRRHFAPVFARVAEGSRERDRR
+RILPFAEVRALNEAGFATLRVPAEAGGPGVDVRTAVALLIDLAEADANVAHLYRSHLGFL
+DSL-RFQPAAVRERWHARILAGATVGNASTEKGGNALGTLNTVLTPPAAGD------GPW
+TLTGTKFYATGSIFSSHTRVSAAQTDADGHPAPGRRFAVVPVEAPGVRLDDDWDGFGQRL
+TGTGTAVFDGVAVPPQDVLDRVPGSAEAVYEAAWFQLILLAVLAGIARAARRDAADAVAA
+RVRTFNTGLGLPFREDPLIQEAVGRIAAKAFTAEAAVLSAADALDAALADHD--------
+-A-GRTGSGAPEEVPASFTWAELAVEHAQVTVPELALGAAQELFLTGGASATSTAKGLDR
+HWRNAQTVATHNPIAFRARAIGDYWINGT-VPEGLNAIGDAPAASAPLG-D----APAPG
+EAA--R
+>3_580
+M---------------TTPV-LDRPAPTSAADAPDTAELRARFAPVFARIAANEARRRDA
+AVPPHAAVRLLAETGFTALRLPRERGGSDATLTQLLDLLVDLAAADANLPQALHGHFMFT
+EQVARDVHPRLTDWWLDEVAAGKVFANALVDPPA------ATGLPGVTARRDPRDP-EAF
+LLTGTKQYSTGTLLADWTLVAAH--DDAGALQP----LVVEVAGPGVEARDDWDGIGQRG
+TASGTTVYTDAPAPAWRRVDLERPAAAPGYPFLW--LILAATQAGIAQRALDDFAEILRR
+RSRSYQHAASASPAHDPVLQHQLGAAAAQVRALRSVVLGAVPALEAAYTAAAGAAPAIGA
+AATESPDDGAAEAFEAAHTEAWVAAASASSVAADLTLRLTSDLFETAGASAVVAGPGLDR
+HWRNARVLASHTPLPHRRRQIGECLLHGTPAPHSADAVETASSTDADPSRDSVSPSPSTP
+AATKEQ
+>4_191
+MPLTDPTDASAPPAATPVPLGAVPPLERPADLPRDLAGLRRHFAPVFARIAEGSRERDRR
+RILPFEEVRALNEAGFATLRVPAEAGGPGVDVRTAVALLIDLAEADANVAHLYRSHLGFL
+DSL-RFQPEAVRERWHARILAGATVGNASTEKGGNALGTLNTVLTPAPAGD------GPW
+TLTGTKFYATGSIFSSHTRVSAAQTDADGRPAPGRRFAVVPVEAPGVRLDDDWDGFGQRL
+TGTGTAVFDGVAVPPQDVLDRAPGSAEAVYEAAWFQLILLAVLAGIARAARRDAADAVAV
+RVRTFNTGLGLPFREDPLIQEAVGRIAAKAFTAEAAVLSAADALDAALADHE--------
+-A-GRTGSGAPEEVPASFTWAELAVEHAQVTVPELALGAAQELFLTGGASATSTAKGLDR
+HWRNAQTVATHNPIAFRARAIGDFWINGT-VPEGLNAIGDAPAASAPLGAD----APASG
+EAA--R
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001995.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001995.fa
new file mode 100644
index 0000000000000000000000000000000000000000..acb4dc95a21b79575409a8f5b74fc8b8b31261bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001995.fa
@@ -0,0 +1,16 @@
+>0_168
+MTRTLEEIWPPYGLVVEAGDLRMTALREADVPEVLDVVAGGIHDPSWTPFLFPWTDAPAE
+EMPANYLRFYASTLTRTVDGDVSLELVVRRNGQVIGMQGMNGPDVAGTRRLETGSWLGLP
+FQGQGLGTRMRRMMCALAFDGLGLDAVTSSAWEDNAASRRVSEKVGYLETGRGQAERRGV
+PTGEVFFELRPEGFVRGDEPVRITGAEELRRFLGLG
+>2_624
+MTRTLEEIWPPYGLVVEAGDLRMTALREADVPEVLDVVAGGIHDPSWTPFLFPWTDAPAE
+EMPANYLRFYASTLTRTVDGDVSLELVVRRNGQVIGMQGMNGPDVAGTRRLETGSWLGLP
+FQGQGLGTRMRRMMCALAFDGLGLDAVTSSAWEDNAASRRVSEKVGYLETGRGQAERRGV
+PTGEVFFELRPEGFVRGDEPVRIMGAEELRRFLGLG
+>3_41
+MTRTLEEIWPPSGLVVEAGDLRMTALREADVPEVLDVVAGGIHDPSWTPFLFPWTDAPAE
+EMPANYLRFYASTLTRTVDGDVSLELVVRRNGQVIGMRGMNGPDVAGTRRLETGSWLGLP
+FQGQGLGTRMRRMMCALAFDGLGLDAVTSSAWEDNAASRRVSEKVGYLETGRGQAERRGV
+PTPEVYFELLPEGFVHGDEPVRITGADELRRFLGLA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001996.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001996.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5cca6982b7a9fb931cab28afb3111a82e991e1ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001996.fa
@@ -0,0 +1,25 @@
+>0_197
+-----MSGAGSARLTRRTALGLLAASLPLG---LSGCVLQGEAT-TGPVNGPD---TLSI
+DYATYNPLSLVIRHQGWLEETLAPRGVRVNWVFSAGSNKANELLRSNSVDIGSTAGSAAL
+LNRANGAPTRIVGVASRPEWSALMVPPGSDITDVAQLAGRTVAATRGTDPYFFAVQALEA
+AGVDPADVEIQNLQHADGRAALAGGSVAAWSGLDPIMAKAEAEGARFLYRDLALNTFSVL
+NATESFLEADPETAQTVLDTYERARAWAL---EHPDETVGILAEAAKISPDVARTVILER
+TNADVSPVPGQELLDALTGVGRILVGTGSVDYQHQVDAALASILDTRFAEEAIR------
+---
+>2_189
+MRRPVVARPGARTLGRR---ALLAGGLGLGAAAAAGCVVPGEQTRPGPVDGGDWAWTLNI
+DYATYNPLSLVIRAKGWLDEALNPDDVGVHWVFSAGSNKANENLRAEAIEVGSTAGSAAL
+LSRANGTPIRTIAVANRPEWAALVRAPGSDVDDVAALAGSVAAATRGTDPYFFLVQALRE
+FDVPRERVEILNLQHADGRTALFGGSVQAWSGLDPIMADAQRDGAELFYRNLAFNTFDVL
+NATQRFLDERPEVAQTVVDVYQQARAWVLASDANLAETARILAEEAGLDAAVARTVLAER
+TNLDVSPVPGADFTTALNGVGPIMAESGDARSLDAVQQAIEQIVEPAFAQRAAARPTPAG
+GNA
+>3_129
+-----MSGAGSARLTRRTALGLLAASLPLG---LSGCVLQGEAG-AGPVNDRD---TLSI
+DYATYNPLSLVIRHQGWLEETLAPRGVRVNWVFSAGSNKANELLRSNSVDIGSTAGSAAL
+LNRANGAPTRIVGIASRPEWSALMVPPGSDITDVAQLAGRTVAATRGTDPYFFAVQALEA
+AGVDPADVEIQNLQHADGRAALAGGSVAAWSGLDPIMAKAEAEGARFLYRDLALNTFSVL
+NATESFLEEDPETAQTVLDTYERARAWAL---EHPDETVGILAEAAKISPDVARTVILER
+TNADVSPVPGQELLDALTGVGRILVDTGSVDYQHQVDAALASILDTRFAEEAIR------
+---
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001998.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001998.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6aeae864f010e9f3ecda03a070644eec039077de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0001998.fa
@@ -0,0 +1,13 @@
+>0_262
+MFNGKDDWTAAPVGVRAWASQRAVELIAAHTPWFGFQGVDVDRLRQRPGWEDAKPHIVVS
+AQLLNRVHRRTSLRADGLLVIADDHHLRDDSRLTYRRMRAASVQGLSDGALDHLLDTMYF
+GPSNQSRLLQAVDVLTYFEQRRRHVTERHRDAVRRMNAIGRSLNKIRQHSYVWTP
+>1_2228
+MFNGKDDWTAAPVGVRAWASQRAVELIAAHTPWFGFQGVDVDRLRQRPGWEDAKPHIVVS
+AQLLNRVHRRTSLRADGLLVIADDHHLRDDSRLTYRRMRAASVQGLSDGALDHLLDTMYF
+GPSNQSRLLQAVDVLTYFEQRRRHVTERHRDAVRRMNAIGRSLNKIRQHSYVWTP
+>4_260
+MFNGKDDWTAAPVGVRAWASQRAVELIAAHTPWFGFQGVDVDRLRQRPGWEDAKPHIVVS
+AQLLNRVHRRTSLRADGLLVIADDHHLRDDSRLTYRRMRAASVQGLSDGALDHLLDTMYF
+GPSNQSRLLQAVDVLTYFEQRRRHVTERHRDAVRRMNAIGRSLNKIRQHSYVWTP
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002004.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002004.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6043df5a1fa413843fb2d1d168021b9f3e7b373c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002004.fa
@@ -0,0 +1,13 @@
+>0_433
+MVTMRQAGAKRGNPYEQGCPTRHILDRIGDKWTVLIVGALGEESLRFSELRRRIEGISQK
+MLTQTLRALEEDGLVTRTVYAEVPARVEYRLTEAGHSLRAPLQALEEWSITHLADVLHAR
+NHYQT--
+>2_2447
+--------MKRGNPYEQGCPTRHILDRIGDKWTVLIVGALGEESLRFSELRRRIEGISQK
+MLTQTLRALEEDGLVMRTVYAEVPARVEYRLTEAGHSLRAPLEALEKWSITHLADVLHAR
+THYQT--
+>3_131
+M-------NRSWNPLLASCPSRTSLARIANKWTALIVIALAEGPLRFGGLHDGVDGISRK
+VLTDTLRDLERDGIVARTDHGGVPRRVEYELTALGRTLETPLAALVDWAAEHHDAVEAAR
+VDYDERR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002006.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002006.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e38b13504590686f81b2ca0adcb38d0ea13f2196
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002006.fa
@@ -0,0 +1,22 @@
+>0_476
+MGVPVDRARRLLGAVIVAQMLPEGVVVKGGNGVRLRHGATGTRATRDLDLLARDPQQALK
+DLTGFVDRGWGAAPGSKRELKADPAATRVAFFGTVHEDDPAEPLGVPDPYVLSRAKVTLH
+FLSARTSWVSVPIEIGRDEFEGSTLAQPVEVVAPQVAEAVTALGCGTPRSVAVMAVEQQL
+AQKIHAVTDPHQTRGHDLVDIQLLWHGAEAEGGVDIPLLADLVSRTFMFRSPGRTAAGHT
+PHEWPPPVAHVRTLEQGYLDALEETRVGAEGQARLLQPRVSDAADWLESLITRIARAAGA
+EGSGAQG
+>1_206
+MGVPVDRARRLLGAVIVAQMLPEGVVVKGGNGVRLRHGATGTRATRDLDLLARDPQQALK
+DLTGFVDRGWGAAPGSKRELKADPAATRVAFFGTVHEDDPAEPLGVPDPYVLSRAKVTLH
+FLSARTSWVSVPIEIGRDEFEGSTLAQPVEVVAPQVAEAVTALGCGTPRSVAVMAVEQQL
+AQKIHAVTDPHQTRGHDLVDIQLLWHGAEAEGGVDIPLLADLVSRTFMFRSPGRTAAGHT
+PHEWPPPVAHVRTLEQGYLDALEETRVGAEGQARLLQPRVSDAADWLESLITRIARAAGA
+EGSGAQG
+>4_475
+MGVPVDRARRLLGAVIVAQMLPEGVVVKGGNGVRLRHGATGTRATRDLDLLARDPQQALK
+DLTGFVDRGWGAAPGSKRELKADPAATRVAFFGTVHEDDPAEPLGVPDPYVLSRAKVTLH
+FLSARTSWVSVPIEIGRDEFEGSTLAQPVEVVAPQVAEAVTALGCGTPRSVAVMAVEQQL
+AQKIHAVTDPHQTRGHDLVDIQLLWHGAEAEGGVDIPLLADLVSRTFMFRSPGRTAAGHT
+PHEWPPPVAHVRTLEQGYLDALEETRVGAEGQARLLQPRVSDAADWLESLITRIARAAGA
+EGSGAQG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002007.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002007.fa
new file mode 100644
index 0000000000000000000000000000000000000000..410ebfc636bb1f81823f233a3e690c9ca35088a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002007.fa
@@ -0,0 +1,22 @@
+>0_492
+MASFDILYIRPAGSGWGPVHELVQLTRRLFDARLIEVDDTGDVNRLQRASALLPRGPRVR
+DRHLLVMGPQPAAIAHVAHPRLWLPGYRSVAVWIIDSFWTDRTPRLLRDRPHVDRLFITD
+PQLVSEWSGQTGLPVGVLPWGSDTTRFTSAQEGTDRPVDVLRVGRQPRAWSDDARTSRDA
+AAHGLHFAGRPPFSDDPARNQMLVREAMGRARVVLAFSNLVSPAPYTHPTRDYLTGRWTD
+ALAAGCLVAGTAPASAASLLWPGATVEISPTSRDDAWPVLAQLASEWTPQAAADRQSEAR
+RRLDWRYRLRDLCMAMDWAVPDRLTAELATL-------
+>1_226
+-MSVDVLYVRPGGSGWGPVDVLARLAARLLEGRLVEVEDRGAASWAQRASVLLPRGRRAR
+GRRLLVLAGNPAALALAARRDLWWPGHESTAAWIVDSFWTDRIAGIARHRPHFDRLFVTD
+PDLVDEWSALTGRPVDALPWGSDT--LAVAADDGPRPVDLLRLGRQPEAWDDDARTAREA
+QDHGLVFRGRPPSSPDPLQNQEAVRAALAQARLVLAFSNLVSPAPYTHPTRDYLTGRWTD
+ALAAGCRVAGVAPRSAATLLWPEATLEVSPNSRAEAWPVLAEAAAAWTPERAAEQRRRAR
+RELDWRLRLQRLCTAMGWPLPPTLDAELAAL------G
+>2_2383
+-MTLDILYVRPRGSGWGPVAELVALAARLFDARVAVVDDHGEVSLFRKTAASLPRGRRRP
+GHHLLVVAPHAGMAAYAARPRLWFPGYDSTAVWVIDSFWTDRTPRLLRGTAHVDRVFITD
+PQLVEEWEQITGTPVSVLPWGADTALYPSAAH--HRDIDLLRLGRQPKAWADDDATAADA
+RRRGLRFAGRPPMNDDPGQNQHNVREALMGAKLVLAFSNLVSPAPYTHPTRDYLTGRWMD
+ALAAGCLVAGTAPAAATSTLWDGATLEISPTSREDAWPVLTAAAEGWSPERAAEQQERAR
+RTLDWRWRLRQMSSVMGWPEPPRLTQELERLISSPQQG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002008.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002008.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e61ee61783e060172cc9c31da26660978c8ea3a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002008.fa
@@ -0,0 +1,28 @@
+>0_502
+--------------MGAVAPPEARPARRHASLGLVPDGQAAWTRSPWNPLVTPASPRLFE
+AVLAIGLVMEAFTAPGLPIPFAEFSAILLLLLASFRQPRRDLSQYGVLALVALALVAYLV
+AVTVHNDLDPTRRATRITLLILLIYAIASERIDIKGVLYGMTAGALINVPLFYAGLAPDT
+YGGYLTGFLGDKNVSGLFYALLPVLLVATMQRMGPKLLVLGAGFALTFLTGSRTSMAGLL
+CAVVWILVSPYLGRVLRIALGVVLGWFVSWAEVNLADLGIFGDRTGTDWFREQIQEASAE
+KVADTSFFGQGLSTAFVELDNVTMFFHNSYLGLLVEGGWPFLIVVVGAYLWLCLRPFART
+HRSPSRVAVEAAALIILVTSLQLGEVFITIFGAVVLGCGLLLSAQENEESQGAPAKDRAH
+RRKLDRIIERSRRAGV
+>1_232
+MRPSTPRDRTAARAMGAVAPPEARPARRHASLGLVPDGQAAWTRSPWNPLVTPASPRLFE
+AVLAIGLVMDAFTAPGLPIPFAEFSAILLLLLASFRQPRRDLSHYGVLALVALALVAYLV
+AVTVHNDLDPTRRATRITLLILLIYAIASERIDIKGVLYGMTAGALINVPLFYAGLAPDT
+YGGYLTGFLGDKNVSGLFYALLPVLLVATMQRMGPKLLVLGAGSVLTFLTGSRTSMAGLL
+CAVVWILVSPYLGRVLRIALGVVMGWFVSWAEENLADLGIFGDRTGTDWFRAQIQEASAE
+KVADTSFFGQGLSTAFVELDGVTMFFHNSYLGLLVEGGWPFLVVVVGAYLWLCLRPFART
+HRSPSRVAVEGAALIILVTSLQLGEVFITIFGAVVLGCGLLLSAQESDESHGAPAKDRAH
+RRKLDRIVERSRRAGR
+>4_502
+MRPSTPRDRTAARAMGAVAPPEARPARRHPSLGLFPDGQAAWTRSPWNPLVTPASPRLFE
+AVLAIGLVMDAFTAPGLPIPFAEFSAILLLLLASFRQPRRDLSHYGVLALVALALVAYLV
+AVTVHNDLDPTRRATRITLLILLIYAIASERIDIKGILYGMTVGALINVPLFYAGLAPDT
+YGGYLTGFLGDKNVSGLFYALLPVLLVATMQRMGPKLLVLGAGAALTFLTGSRTSMAALL
+CAVVWILVSPYLGRVLRIALGVVMGWFVSWAEENLADLGIFGDRTGTDWFRAQIQEASAE
+KVADTSFFGQGLSTAFVELDGVTMFFHNSYLGLLVEGGWPFLVVVVGAYLWLCLRPFART
+HRSPSRVAVEGAALIILVTSLQLGEVFITIFGAVVLGCGLLLSAQESDESHGAPAKDRAH
+RRKLDRIVERSRRANR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002010.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002010.fa
new file mode 100644
index 0000000000000000000000000000000000000000..290357a56d375b0515dfe468896347d09de87a63
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002010.fa
@@ -0,0 +1,10 @@
+>0_558
+MVGDMSLSFVSSARRRHGGLASAALFHPLVEAATGALPVIDPATGRPASEGAGAARTEAP
+RTAGTGPAQAAAEAEPSTEAGSARG
+>1_300
+----MSLSFVSSARRRHGGLASAALFHPLVEAATGALPVIDPATGRPASEGVDAARTEAS
+RAAGTGPAQAAAETEPSTQAGSARG
+>4_559
+----MSLSFVSSARRRHGGLASAALFHPLVEAATGALPVIDPATGRPASEGVDAARTEAS
+RAAGTGPAQAAAETEPSTQGGSARG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002011.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002011.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d420265b405becf8baab2d9115b431b4e1d577c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002011.fa
@@ -0,0 +1,25 @@
+>0_563
+MSAQQMWEARTSGPKRAEAPASGQAVGASENAQSETVHIPKNTLVEHSKDSTGARPTDSG
+IRTLPRRVNPNDGRFIRAVVAGTAVAGLVAFSISFAALYEVAAWLGLPPFMHWAVPVFID
+LAILVYAGSVLVHESRGESARASWWALGAFTGLSMIANGAHAWSAENASVWQSVVGALIA
+VMVPVAVFVATDQLARVAVENPDSRRAERASQVSEEAEQLKAQAELDRQRAELEAELAAS
+RWQIEAQRREA---EREAEVAEARHRQELERMERQAKLETEREAREVPQAVVEESQVAQG
+IEVVETVASSEPVAAETKTVEKASGADITAWIVSRAQEGQVPSAAEVAEKFGCSERTGRR
+RLVKS-------------LEVV
+>1_306
+MSAQQMWEARTSGPKRAEAPSSGQAVGASENAQSETVHIPKNTLVEHSQDSTGTRPTGSG
+IRSLPRRVNPNDGRFIRAVVAGTAVAGLVAFSISFAALYEVAAWLGLPPFMHWAVPVFID
+LAILVYAGSVLVHESRGE------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------
+>3_1743
+MRARR-WA----------------------------------------------------
+---------------VRTAVAGTVFIAIGAFWLSFTALADLAARSGIGAGQAWAWPLIVD
+GIIVVATVAVVALAGQKA-AWYPWALLIGGAVVSVTANALHAIVAADADVPALLAAAIAA
+--VPPVVLLAITHLTVILT---------RATSPETQTVIWQTIAQQNDQPT------PAP
+RPGIEAEPPPAALLQHDVSDTVGLGDERPTTPESGPSPMKHAEAKPAPEA---STPTAPN
+GETVRGVSEMAGVGRR----ERAAGLRSEGW-----------SNKQIASELGVHPSTVGR
+WLTSTPTRSSEPDTNPSIKEES
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002015.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002015.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7cd8e18b17e4b04ea050522baf13605a1e10dc76
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002015.fa
@@ -0,0 +1,42 @@
+>0_676
+MHRLGPELQGILAWCRSRGVPTAFWNKEDPVHFNTFLTAAGEFDAVFTT---DLDCVPRYKRELGHENVHFLPFAAQTAQ
+SNPVEVFDRVEGCAFAGAYYAKYPERLADLRELSAELSADGRRFDIYDRNHGRATSGYTFPEDYQRYIVGGALTPGLLDV
+PYKGYTVNLNLNSVKQSQSMFARRVFELLASNTLTVSNFSRGLRLMFGDLVVSTDSGRQMRRRLEAIEAQPNGNERLRAV
+ALRKVLREHTYTERLEFVASRSGVTLPDAAVERPLMVVPSTLGRDAAAVVELVRRWAGQTWNDWVLAVQGKVEEFAPMPL
+ELQDPRVVLFDELADLDGLARTRGCTLAGMLDPNDWYGPHYLEDMVLTLRWADVKTCGHVEHYAVDSVDGSLERRELGTA
+WRLQDKILPCRSLSRLDWAQVADCNGVARQLDAAQLSGLAVSPLEYCAGGATSEEPALAPASSLDVYEGLTLTEIRQHAD
+DLVFAESSDDMPVMDLGTIFEGMKSFDEMTLTWEDGVPRVTSSLGAGRHQYWINSLARPVEFHQNGNDQPVYFDVSVGLD
+IMLVAYWLDADGQRFGHAMIPARQYTTVKIPEQARAMRWGLRVSGSGSAVVHRVVNGPYVAPSVPMLAGSS--DVLITNI
+YPAYDNLYRNGFVHSRLRRYREMGHRLETILVGEGDGPRFREFEDVDVAVLRVQDLIATLATGEVKTLVVHCLLPETWNV
+LKATSDLPPTTVWVHGFEIQPWWRRRFNYATEEELDAAKMLTEQRLAMWREVFDSSPDNMHFIFVSRWFAETVFEDVGIR
+LPDHRYSVIHNPIDDTVFPYQEKTAQHRLRVLSIRPYHSHVYANDLAVAAVLELSNEPWFNELDFTFIGDGPLFEETLAP
+LWDFENVLIRKGFLTHAEIASEHARHGVLLVPTRSDTQGVSRDEAMSSGLVPITSAVAAIPEFVDEEVAFLAPPEDHRAL
+ADAVRTLRAEPARYLRMSAAAARRVRRQSGADHVLDAELRLAFRTDGDHSAPSVRPHPEREAHRP
+>0_858
+MLR-----------------------------------------AVFDTLPQDSDAVRRLRAAAAP------PRRRRTSP
+PRPA---------APAGA--------------------------------HGD--------------------TPG----
+-YRGY---LHLADV---------------------------------GD-------------------------------
+---------TYTAQ----EASTLLQLENAALKRRLFAEPA----------------------------------------
+--------------------------------------------------------------------------------
+-------------------------------------------------------PPLPPTG---------------HED
+E-------------DL----------------------------------------------------------------
+-----------------------------------------------AAAPRRVADHLARADAADQLGDDAPRHLVVVGV
+YPTLENPYGNGFVHRRVKYFQAAGVRVDVAVIDRSAEPRSYEYDGVHVLVGRGAEAAEMLRTRHYESVAAHFLVRSLWEP
+IQDALAGHRFFVFMHGFESRRWIRTVRNHRTQGQVDDAIVDTLERQRFWREVLEHPHGPERFVFVSRWWRRAAQEDMELV
+FPGQRTAIVHNVIDTDLFRFVPKDPEQRFRVLWVRSAANLNYGADLAVRALERLRDTPLWDRMQVTVIGDGKHFGLFEAA
+FADDANVTVERRYAVQEEIAALHREHGVFLVPTRLDSQGVSRDEAMASGLVPVTNDAGAVREFVDEDCAMIAGVEDVAGL
+ADGLRRLMEDPDLFLRMSQAAAARVRAQTSPEHTVDHEMALM----GLAAGPGGR--GEENA---
+>1_589
+MLR-----------------------------------------AVFDTLPQDSDAVRRLRAAAAP------PRRRRTSP
+PRPA---------APAGA--------------------------------HGD--------------------TPG----
+-YRGY---LHLADV---------------------------------GD-------------------------------
+---------TYTAQ----EASTLLQLENAALKRRLFAEPA----------------------------------------
+--------------------------------------------------------------------------------
+-------------------------------------------------------PPLPPTG---------------HED
+E-------------DL----------------------------------------------------------------
+-----------------------------------------------AAAPRRVADHLARADAADQLGDDAPRHLVVVGV
+YPTLENPYGNGFVHRRVKYFQAAGVRVDVAVIDRSAEPRSYEYDGVHVLVGRGAEAAEMLRTRHYESVAAHFLVRSLWEP
+IQDALAGHRFFVFMHGFESRRWIRTVRNHRTQGQVDDAIVDTLERQRFWREVLEHPHGPERFVFVSRWWRRAAQEDMELV
+FPGQRTAIVHNVIDTDLFRFVPKDPEQRFRVLWVRSAANLNYGADLAVRALERLRDTPLWDRMQVTVIGDGKHFGLFEAA
+FADDANVTVERRYAVQEEIAALHREHGVFLVPTRLDSQGVSRDEAMASGLVPVTNDAGAVREFVDEDCAMIAGVEDVAGL
+ADGLRRLMEDPDLFLRMSQAAAARVRAQTSPEHTVDHEMALM----GLAAGPGGR--GEENA---
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002019.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002019.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d7882f579acb85871dce748521c4c6989cabf52
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002019.fa
@@ -0,0 +1,16 @@
+>0_855
+MSGNVFTAASADVAEDAVLGDGTKVWHLAQVREQARLGERCIVGRAAYIGTGVE------
+-------LGDDCKVQNLALVYEP--ARLGRGVFIGPGVVLTNDTYPRAVNPDLSQKSGDD
+WEAVG--VDIGDGAAIGARSVCVAPVRIGEWALVAAGSVVTRDVPDFGLVAGVPAKRIG-
+-------WVGRTGR-----RLEEKDGVWVCPDTGETFIERDGALRPAEPAQEEENHG
+>1_586
+MSGNVFTAASADVAEDAVLGDGTKVWHLAQVREQARLGERCIVGRAAYIGTGVE------
+-------LGDDCKVQNLALVYEP--ARLGRGVFIGPGVVLTNDTYPRAVNPDLSQKSGDD
+WEAVG--VDIGDGAAIGARSVCVAPVRIGEWALVAAGSVVTRDVPDFGLVAGVPAKRIG-
+-------WVGRTGR-----RLEEKDGVWVCPDTGETFIERDGALRPAEPAQEEENHG
+>2_1190
+M---------------------------SKLRMLSRMPKK---GRFMFIISGGDRARYMS
+RKGLVRGMGENVWFQPRALPNDPNLIRFHNNIVVASGVTFVAHD---VINLMIGRKNGVR
+LPVNEDCIEVMDDVFIGSGSVILPGVGIGPRAIIAAGTVVTKDVPPDSIVRGVPAKRLGD
+FSVLEAQRLADAGRFDGMTRAQIDDVLW----------------------------E
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002026.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002026.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5387b5880c1bc8530983022898af38c76fb6246
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002026.fa
@@ -0,0 +1,19 @@
+>0_999
+-MAALDDETAGIPEGNRGPSAGLVYAWGEHSRADPVFGDYPERVLALKYAEPGVELPLWS
+KRQGDDASVAELSWGPRWGTLWRDTALEFSPGF-----TTSPT-----------------
+------------------------------------------------------------
+-------------RHTRPTTA----------------------SFATG------------
+-----------------------RW-----------------TG
+>1_721
+-MAALDDETAGIPEGNRGPSAGLVYAWGEHSRADPVFGDYPERVLALKYAEPGVELPLWS
+KRQGDDASVAELSWGPRWGTLWRDTALEFSPGF-----TTSPT-----------------
+------------------------------------------------------------
+-------------RHTRPTTA----------------------SFATG------------
+-----------------------RW-----------------TG
+>4_941
+MAAALYDEAAGTPEGNRGPSAGLVYAWGEHSLADPVFGDNPEWFFTLEHAESGVLLPFRS
+EGLGDDAAVAELSWGPRWGTLWRDTTVDSFTGFHYLADATYPTDDRLVLDWSLDGMTKSE
+DVIITQDAARSDVFALVELLADGQKPWALNVPAGEDAPSPGEADPVPPAEQEPVDTPAPV
+AGEEPGEGTGGEETHTTPDTVETGREVRRARSERSRPSARDSCSWPGGGCAGSDTPGRRG
+GRGAVDGRPSAAPRSVLSRPERIRWGRCSPRLRSRRCSHRRHCG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002030.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002030.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e7ec79aba17c83ab47e4ba5e2a653fa1151f6936
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002030.fa
@@ -0,0 +1,22 @@
+>0_1337
+MGNAVGSNIINVLLILGLSALVVPLAVKRRLIRFDLPLMVVLSVLLLLVSLDGRISAVDG
+LILFFGVVVHTIMSVVISRRDAKTAVNAREGTGDSATVDPADEEGAALGASVSRSLFFVL
+LGVALLVAGATLLVEGAVNIATTLGVSSLVVGLTVVAVGTSLPELATSIIAVRRGERDLA
+VGNVVGSNIFNIGVVLGLTALISLEGIPVSGAAVAFDIPVMLAAAVALLPIAFTGFAVAR
+WEGGLFVVLYAAYTGYLVLAATAHDALEGFTVAMAWFVLPLIALTLISFTAYEIGLRKGR
+RDLDQTTTST
+>1_1074
+MGNAVGSNIINVLLILGLSALVVPLAVKRRLIRFDLPLMVVLSVLLLLVSLDGRISAVDG
+LILFFGVVVHTIMSVVISRRDAKTAVNAREGTGDSATVDPADEEGAALGASVSRSLFFVL
+LGVALLVAGATLLVEGAVNIATTLGVSSLVVGLTVVAVGTSLPELATSIIAVRRGERDLA
+VGNVVGSNIFNIGVVLGLTALISLEGIPVSGAAVAFDIPVMLAAAVALLPIAFTGFAVAR
+WEGGLFVVLYAAYTGYLVLAATAHDALEGFTVAMAWFVLPLIALTLISFTAYEIGLRKGR
+RDLDQTTTST
+>4_1291
+MGNAVGSNIINVLLILGLSALVVPLAVKRRLIRFDLPLMVVLSVLLLLVSLDGRISAVDG
+LILFFGVVVHTIMSVVISRRDAKTAVNAREGTGDSATVDPADEEGAALGASVSRSLFFVL
+LGVALLVAGATLLVEGAVNIATTLGVSSLVVGLTVVAVGTSLPELATSIIAVRRGERDLA
+VGNVVGSNIFNIGVVLGLTALISLEGIPVSGAAVAFDIPVMLAAAVALLPIAFTGFAVAR
+WEGGLFVVLYAAYTGYLVLAATAHDALEGFTVAMAWFVLPLIALTLISFTAYEIGLRKGR
+RDLDQTTTST
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002033.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002033.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ddd20b98749e1964d57a5fb541e3cd152640ebcf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002033.fa
@@ -0,0 +1,10 @@
+>0_1347
+MAMPETDLLRIGRWCRERVPEHLWDQVRVEAEIADRHVTIIETRPPWDGQGDWTRFPVAR
+LRYTVKTGQWSIYWRDRHMKFHEYTKRRPTKNVQSLLDYIGSHQDPIFWG
+>1_1089
+MAMPETDLLRIGRWCRERVPEHLWDQVRVEAEIADRHVTIIETRPPWDGQGDWTRFPVAR
+LRYTVKTGQWSIYWRDRHMKFHEYTKRRPTKNVQSLLDYIGSHQDPIFWG
+>4_1296
+MAMPETDLLRIGRWCRERVPEHLWDQVRVEAEIADRHVTIIETRPPWDGQGDWTRFPVAR
+LRYTVKTGQWSIYWRDRHMKFHEYTKRRPTKNVQSLLDYIGSHQDPIFWG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002041.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002041.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ecb78367141c5e4279761b1abf1a00969d4d963b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002041.fa
@@ -0,0 +1,28 @@
+>0_1567
+MTLPANSIRIIEANNWVSAETAARMKLKLTP--PGAVAFAKIGE-----GLKA-------
+--ERLRRITVPTAMD--------------NNMMAAI-PKPAVV-----------------
+--------DSGFLIYLIESVHIAEWAQG--SALPYLSQKLLADIPVHVPSLPEQRAIAAT
+LGAFDDKIESNRQAMATGESLIRAVVESTLDASE---------GED--------------
+------GTLGDY-CALVKAPVEIDKIDPDDNYIG--LEHMPRGSI--FLTEWKKAKGLGS
+NKTAFKR-GDLLFGKLRPYFKKVGIAPIDGVCSTDILVVR--PKSPRDIALVTAVAASDA
+LIDSLSASSTGTRMPRASWKDLAAWRVPVLTATERIELSARVDPLVERLTQLTFESHRLV
+ALRD---ALLPELLSGGLRVPVTS
+>2_200
+MK-PG----------WTTVALGDVAEVRRTSVHP---AHMRPDD--PYLGLEN-------
+-IERGGRLLSVSTVAGEGVKSTKFRFSPGDVLYGKLRPNLAKILKVDFEGLCSTDILPIA
+VNSGTLSADFLAYYLSQPQVVAQAASRASGANLPRLAPAEFLALRIPLPPLDEQRRIAAA
+LDRATVVIG---------------------GIGDL-RRRTRSIGESVVQQSSTGAGRWST
+IGKSLTLRSGSTLPATRRRP-------------GGVPVYGANGAIGE--------HDEAT
+HEQPHVTIGRV------GAVGAVNVTAGRAWISDNALIVVKAPEHLS-NGYLAIALAMAD
+----LGRFASQSAQPLITQRKVADVPLWI-PS---QAEALRIDAILDRLAEV--ERANVE
+RVARAD-ALFASLQSRAFRGEL--
+>4_181
+MK-PG----------WTTVALGELCELKYGKSLP---AKARSGEGFPVFGSSGLVGAHEK
+AIQRGPGIIVGRKGSIGEVHWSEDDFWPIDTTYFAL-PRRANV-----------------
+--------DLRWLYLALRWLPLKTLNKA--AAVPGLNREDAYRLTLALPPLDEQRRIAAI
+LGTSLHSIGCRVRACIWIDDFLDNVYNSTLRSGDIPRRPIRSLGE---------------
+------VSTGKT-PATSKAD-----------YFGGVIPFVAPGDLGGLVSAKRTLTDLGA
+QESRLVRAGATMVCCIGATIGKVGIVAEQSAFNQQINAIEWGPDMDDLYGYFTMRAQSDV
+----VAARGSSTTMPILAKSKFEELLIPV-APFEVQEEFARVASIVSRV------RSNLV
+AAWEAERQLFASLQSRAFRGEL--
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002051.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002051.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e1afbe8c3d58e6f000c04d64ea89279e7007c88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002051.fa
@@ -0,0 +1,31 @@
+>0_1981
+MTPTTSTPATFHDTRVDQQFIAGQWRDGASGDRASDINPYTDDVVAEFALATAEDLDEAY
+RAAAAAQEEWAAMPPKDRAAVLRRAAEILEERRDEVIDWLVKEAGSTRIKADSEVSLAIA
+ITQEAASFPTRVHGKIFDSNTPNRETRVYRKPIGVVGVISPWNFPLHLSQRSVAPALALG
+NAVVLKPASDTAVTGGTLIARVFEEAGLPAGVLSVVVGSGSEIGDAFVTHPVPRLISFTG
+STVVGKQVAANAVTGDTIKKVALELGGNAPLVVLDDADLDAAVDQAVLGGYLHSGQICMS
+VQRVIVDESVYDEFLPKYEGAVKALKVGDPAEEGVLVGPIINDSQVESLRKKIASAEADG
+ARALVGGEIQGRVVPPFVWVDATADMDIAREEIFGPMTVVLKAHDEAHALELANDHEYGL
+SSAVFTQDLDRGLRFANGLAAGMSFINEMTVQDEAHVAFGGARNSGLGRFNGEWALEEFT
+TDHTIGVTRVG
+>2_758
+MSPTTHAAATFHSNDVSKQFIAGQWRDGAAGSTKQDLNPYDDAVVAEFALASEADLDEAY
+RAAADAQKEWAAVAPAKRAAVLRRAAELLEERRAEIVDWLVKESGSTVIKANIEVSLAVG
+ITQEAASFPTRVHGTIHPSNTPDREMRVYRKPIGVVGVISPWNFPLHLSQRSVAPALALG
+NAVVIKPASDTPVTGGTLIARLFEEAGLPAGVLSVVVGAGSEIGDAFVKHPVPRLISFTG
+STPVGKQVGANAVSGDHIKKVTLELGGNAPVVVLDDADLDAAVEQSVTGGYLHSGQICMS
+VQRVIVDEKVYDEFLPKYEGAVKSLKFGDPREEGVLVGPVVNDQQLETLKKKIASAEADG
+ARALVSGEIEGRVVPPFLWVGAEPDMEIARDEIFGPMTVVLKARDEAHALELANDHEFGL
+SSAVFTQDLDRGLRFADGLAAGMSFINEMTVQDEAHVAFGGARNSGLGRFNGEWAIEEFT
+TAHTIGVKRLG
+>3_726
+MTPTTHASGTFLGNDVGKQFIAGQWRDGAAGSTKQDVNPYDDSVVAEFALASEADLDEAY
+RSAAEAQKGWAETGPKERAAVMRRAAELLEEHRDEVVDWLVQEAGSTVIKANIEVSLAIA
+ITEEAATFPTRVHGKIFDSNTSNRESRVYRSPIGVVGVISPWNFPLHLSQRSVAPALALG
+NAVVIKPASDTPVTGGTLIARLFEQAGLPAGVLSVVVGAGSEIGDAFVKHPVPRLISFTG
+STPVGKQVAANAVLGENIKKVALELGGNAPLVVLDDADLDTAVEQAVTGGYLHSGQICMS
+TQRVIVDAKVYDEFLPKYEQAVKALKVGDPRGEGVLVGPIINDSQVEGLQKKIASAEADG
+ARALVGGEVEGRVVPPFVWVDVDPDMEIAKEEIFGPMTVVLKARDEEHALELANHHEFGL
+SSSVFTQDTGRGVRFAQRVAAGMTFVNEMTVQDEAHVAFGGARNSGLGRFNGEWAVEEFT
+TDHTIGVTTVG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002054.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002054.fa
new file mode 100644
index 0000000000000000000000000000000000000000..270d6c34a2180b568957af5ee8cdb90e4af01870
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002054.fa
@@ -0,0 +1,28 @@
+>0_2035
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------MGGASATLRTRGLGRHGRNARVLASHNPLIYRARLLGDRAVN
+GTPLERHYRLGG
+>3_579
+MTTTTDRTDTISRPADVGTADSGVPTTAHPADRPQFLAARARLAPVFAWLAETAAERDRE
+RVTDREATDRLAAAGFPGLRVPEDAGGAGLTFPEAARLYVELAEADSNVLQALRVHVVNV
+ETVLGSPDGPRRERWLHRFATGETVANATTEIGNRTGHYETRLTTRPDGSAVVNGRKAYS
+TGTLYADWTIVVVEDEDGAERAATVRSDAPGVTLHDDWDGFGQRLSASGTTEFTDVVVDP
+EELTPVGQSLDDGSSIFASQAIFQFVHLVGLTGIARAVVRDAAAYVAGRTRGFSHGAAPR
+PGDDPQVLQVVGELEAAAFGAQAALDAVVGPLDRALRAEAAGAPLAEAEVDAVYTAVYAA
+QQVIARAALD-AATRLFEVGGASATLRTRGLDRHWRNARVLASHNPLIYRARLLGDRAVN
+GTPLERHYRLGG
+>4_1976
+MRLIHNK-----------------------------------------------------
+-----------------------DCCG---------------------------------
+--------------WF----------------------------------AIRRGASARH
+TG---------------GA-------------------DG--------------------
+---------------------------------------------------------AP-
+PSREP-------------------------------------------------------
+----ARDALERAATRLFEVGGASATLRTRGLDRHGRNARVLASHNPLIYRARLLGDRAVN
+DTPLERHYRLGG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002058.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002058.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fe16d5a1efa450478967b8137b3aa84cbb834963
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002058.fa
@@ -0,0 +1,19 @@
+>0_2130
+M-----------------------------------------------------------
+------------------------------------------------------------
+------------G-----------------------------------------------
+------------------------------------------------------------
+-----------GRPAAGLDPPQTAQSGHADDPSSARTVFDRFVFGNHIRSFSVD
+>2_533
+MTTTIQDPWAQPTPAGAYDDLLVRALPVTRAQRRWEPADGPMPSLFVSHGAPPTLDDPQW
+LADLFDWAQSMPKPRAIVIVSAHWEDAPVAISSAAAGTPLVYDFGGFHPRYYELQYATPD
+ATDLAARVAGVLG-QGRPGSVHQ-TGRGLDHGAYIPLMAMYPDADVPVVQVSMPSMDPSA
+LLDLGVKLRSLREEGVLVIGSGFMTHSFAAMRDPRLFGHVDAFDKWAAEMTHAGDVDSLI
+GYLDKAPGARIAHPTADHYVPLLLTMGAANDPSSARTVFDRFVFSNHIRSFSVD
+>3_457
+M--TLADPWAQPTPAGAYDDLLARALPLTRRQKLWEPSDGRMPALFISHGAPPTLDEPQW
+LNDLFEWAQTMPKPRAIVIVSAHWENAPAAISASAAGTPLVYDFGGFHPRYYTLRYDTPD
+ATDLARRLAGVLGAQGQ--EVHQHTDRGLDHGAYIPLMAMYPDADVPVLQVSMPSQDPAD
+LLRLGERLRELRDEGVLVIGSGFMTHSFAAMRDPRLFGHVDAFDTWAAEMAHAGDVDALM
+GYLDRAPGARIAHPTADHYVPLLLTMGAAHDPSTTRTVFNRFVFSNHIRSFTVD
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002059.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002059.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7cbcd8129009981f6cff3cb2077180584e84b62
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002059.fa
@@ -0,0 +1,25 @@
+>0_2138
+MAQHSSTPYPLVIVGSGPAGVSAARAYVDAGGPGPVLMLTSDVDHPYERPPLSKELLRGT
+AEPDPTVLDELPDAVELRRGVTVTHADLGARTLWAAEEPVRFERLILALGAHPKPLPVAD
+DDAEVHLLRSLDHARRLVASAGHARSAVVVGSGFIGCEAAASLALRGVATTLVTPDEVPQ
+QKRLGREAGDRIAQWLIGAGVELRTGVRVGQVRAPRTVHLDDGATLAPDLILAAVGVEPG
+GGWLEDSELTMHEGRIVADEHLAAAPGVWVAGDVARAHHAVAGRPIPVEHWGDALGMGEV
+AGHNAARTEVGVPGGAGQASVLAHAATADPESLRRWEAVPGFWSTIGEHTLKHAAWGDGH
+EQARMVERTGGFTLWYTDAQDRVVGVLTYNADEDYERGRELVAGRDAVGEGRGRPDPA
+>1_1862
+MAQHSSTPFPLVIVGSGPAGVSAARAYVDAGGPGPVLMLTSDVDHPYERPPLSKELLRGT
+AEPEPTVLEDLPDAVELRRGVTVTHADLGARTLRVGEEPVRFERLILALGAHPKPLPVAD
+DDAEVHLLRSLDHARRLVASAGHARSAVVIGSGFIGCEAAASLALRGVATTLVTPDEVPQ
+QKRLGREAGDRIAQWLIGAGVELRTGVRVGQVRAPRTVHLDDGATLAPDLILAAVGVEPG
+GGWLEDSELTMHEGRIVADEHLAAAPGVWVAGDVARAHHAVAGRPIPVEHWGDALGMGEV
+AGHNAARTEVGVPGGAGQASVLAHAATADPESLRRWEAVPGFWSTIGEHTLKHAAWGDGH
+EQARMVERTGGFTLWYMDAQDRVVGVLTYNADEDYERGRELVAGRDAVGEGRGRPDPA
+>4_2083
+MAQHSSTPYPLVIVGSGPAGVSAARAYVDAGGPGPVLMLTSDVDHPYERPPLSKELLRGT
+AEPDPTVLDELPDAVELRRGVTVTHADLGARTLWAAEEPIRFERLILALGARPVPLPDVE
+ADAEVHLLRSFADARRLVTSAGHARSAVVVGSGFIGCEAAASLALRGVETTLVTPDEVPQ
+QKRLGREAGDRIAQWLIGAGVELRTGVRVGQVRAPRTVHLDDGATLAPDLILAAVGVEPG
+GGWLEDSELTMHEGRIVADEHLAAAPGVWVAGDVARAHHAVAGRPIPVEHWGDALGMGEV
+AGHNAARTEVGVPGGAGQASVLAHAATADPESLRRWEAVPGFWSTIGEHTLKHAAWGDGH
+EQARMVERTGGFTLWYTDAQDRVVGVLTYNADEDYERGRELVAGRDAVGEGRGRPDPA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002066.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002066.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c558b135d6ac77469baac630284032edc8e44ecf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002066.fa
@@ -0,0 +1,13 @@
+>0_2181
+MIRTPWTRTPAGARRARRPRQFRRVTTTGPAAVDVAWARYADLRLWPRWAPQIRAVEAPR
+RRLRAGLRGVVHAPLGLRVPFVVEEVDDDARTWRWTVRVAGTAVSMTHDLTATPRGTRAG
+LTVHGPAVVALAYRLPARVALRRLCRAHL
+>1_1894
+MIRTPWTRTPAGARRARRPRQFRRVTTTGPAAVDVAWARYADLRLWPRWAPQIRAVEAPR
+RRLRAGLRGVVHAPLGLRVPFVVEEVDDDARTWRWTVRVAGTAVSMTHDLTATPRGTRAG
+LTVHGPAVVALAYRLPARVALRRLCRAHL
+>4_2114
+MIRTPWTRTPAGARRARRPRQFRRVTTTGPAAVDVAWARYADLRLWPRWAPQIRAVEAPR
+RRLRAGLRGVVHAPLGLRVPFVVEEVDDDARTWRWTVRVAGTAVSMTHDLTATPRGTRAG
+LTVHGPAVVALAYRLPARVALRRLCRAHL
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002069.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002069.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6524cfb3bc34f443ba6771044d55c2f0e2c170ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002069.fa
@@ -0,0 +1,19 @@
+>0_2201
+M-----------------------------------------------------------
+------------------------------------------------------------
+------RNGQSGAGPPATA---------PSPRSTRD---------------------VDV
+GWVPRFDVDVLEAALRPVHERPRWEEWGQIAAPTLLITGENGYVPAGELDEMRRRRPDVR
+HVQVPGAGRDVHLDAPERVAELVRGFAA
+>3_400
+MSGLGRRSAGPVTREDGTRLHVLDSGGSGPALLLLHGLAGYAREWAQVAERLAAACRVVA
+FDQRGHGSSTRRPADLSRTAHVGDVVAVADALGLQRFTLVGQSMGAHTALLAAAAHPARV
+GRLVLIEGGVGGEGPEATAGVIDWFRAWPIPFATVDDAVAHLGGGPAARVWAEGLEETDA
+GGVPRFDVDVLEAALRPVHERPRWEEWGQIAAPTLLITGENGYVPAGELDEMRRRRPDVR
+HVQMPGAGHDVHLDAPERVAELVRGFAA
+>4_2133
+M-----------------------------------------------------------
+------------------------------------------------------------
+------RNGQSGARPPAIA---------PSPRSTRD---------------------VDA
+GWVPRFDVDVLEAALRPVHERPRWEEWGQIAAPTLLITGENGYVPAGELDEMRRRRPEVR
+HVQVPGAGHDVHLDAPDRVAELVRGFAA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002070.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002070.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92efbc51af67a9287e3331662ad311ef8291d684
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002070.fa
@@ -0,0 +1,10 @@
+>0_2203
+MEAHAFADNAPILRVMEKVGLRHEGTFKEESLHRTRGWVDGVTYAMLASEHRARGRRLST
+SRRPEVRNSLDITLRKVAA
+>1_1909
+MEAHAFADNAPILRVMEKVGLRHEGTFKEESLHRTRGWVDGVTYAMLASEHRARGRRLST
+SRRPEVRNSLDITLRKVAA
+>4_2135
+MEAHAFADNAPILRVMEKVGLRHEGTFKEESLHRTRGWVDGVTYAMLASEHRARGRRLST
+SRRPEVRNALDITLRKVVA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002071.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002071.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca723f7e341c16e685f61aff9bcc2a83c61419ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002071.fa
@@ -0,0 +1,13 @@
+>0_2206
+MDITVGAVGRASLSDWEQECCGDPIAVGEVHELILLPSRGVSQAGPLASAGWVVTHHDDG
+SPAGSIPLRRVRAVVRAAHEVWPSGRLAEIDRVPGHADLTILEPEEATGLGLGEVVYVGA
+YEPVLPETPRPDEWLLDLEILEDLGPHTW
+>2_450
+MDITVGAVGRASLSDWEQECCGDPIAVGEVHELIVLPSRGMSQAGPLASAGWVVTYHDDG
+SPAGSIPLRRVRAVVRAAHEVWPSGRLAEIDRVPGHADLTILEPEEATGLGLGEVVYVGA
+CEPVLPETPRPDEWLLDLEILEDLGPHTW
+>4_2139
+MDITVGAVGRASLSDWEQECCGDPIAVGEVHELILLPSRGVSQAGPLASAGWVVTHHDDG
+SPAGSIPLRRVRAVVRAAHEVWPSGRLAEIDRVPGHADLTILEPEEATGLGLGEVVYVGA
+YEPVLPETPRPDEWLLDLEILEDLGPRTW
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002077.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002077.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4666f0f86737fb1017dea0a7e42bdc3c29b81414
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002077.fa
@@ -0,0 +1,10 @@
+>1_308
+------------MPKKFDPEVKDRAVRMVLDRVEEAGSVTKAVALVSPKVDVGRETLRRW
+VCQHRVDAGLKDGPTSDDLAELKRLRGEVKRLREDNEILRKASIFFAGELDPRNR
+>2_2222
+------------MPKKFDPEVKDRAVRMVLDRVEEAGSVTKAVALVSPKVDVGRETLRRW
+VCQHRVDAGLKDGPTSDDLAELKRLRGEVKRLREDNEILRKASIFFAGELDPRNR
+>3_1787
+MPLPFEFERMLFMPKKFDPEVKDRAVRMVLDRVEEAGSVTKAVALVSPKVDVGRETLRRW
+VCQHRVDAGLKDGPTSDDLAELKRLRGEVKRLREDNEILRKASIFFAGELDPRNR
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002079.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002079.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6c70a5578ff9f847a075ac28e3363d967deeff7f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002079.fa
@@ -0,0 +1,16 @@
+>1_342
+MQAMSLDEITPVAQDYLKAIWSATEWGDAPLSTKSLAARMGTTAPNVTETVKRLAAQGLV
+EYQPYKPVTLTGKGCEHAIAMVRRHRLLESFLAASLGYSWDEVHAEAERLEHAASDELIE
+RIDQMLGHPTHDPHGDPIPTPVGQRERPAHAVRLDAAEPGFYRVLRISDADPQRLIRFQQ
+AGIVPDSVVEVAEAGHFRLRVVAVGPVELIETDAAAIWLVPSSTRG
+>3_655
+MQAMSLDEITPVAQDYLKAIWSATEWGDAPLSTNSLAARMGTTAPNVTETVKRLAAQGLV
+EYQPYKPVTLTGKGREHAIAMVRRHRLLESFLAATLGYSWDEVHAEAERLEHAASDELIE
+RIDQMLGRPTRDPHGDPIPTPEGQRAQPAHAVRLDVAEPGFYRVLRISDADPQRLVRFQQ
+AGLVPGTVVEVTEAGHSRLRVVAVGPVELIETDAAAIWLVPSATRG
+>4_1952
+MQAMSLDEITPVAQDYLKAIWSATEWGDAPLSTNSLAARMGTTAPNVTETVKRLAAQGLV
+EYQPYKPVTLTGKGREHAIAMVRRHRLLESFLAATLGYSWDEVHAEAERLEHAASDELIE
+RIDQMLGRPTRDPHGDPIPTPEGQRAQPAHAVRLDVAEPGFYRVLRISDADPQRLVRFQQ
+AGLVPGTVVEVTEAGHSRLRVVAVGPVELIETDAAAIWLVPSATRG
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002080.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002080.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26d71eee44335c67c4d272c31f568c59b2444905
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002080.fa
@@ -0,0 +1,25 @@
+>1_350
+MTRISPLSAAGTDFDGTRLTVARRLRRKTKATLAREVGVTPTAIAQFEKNLSKPTQSVLA
+RLCLQLGLPREFFG--AGRPLALLPASGAHFRSLRSTSATSREQALAYGELCLELVDLIG
+AYVDLPPVSLPELELPEELTDEAIVEAARLTRSTWGIAPGPLPSVVQTLEAHGIIALRLP
+VETDAAVDAFSTYSGARPLVFLSPTKDDKARSRFDAAHELGHLVLHPDTEPGSKLV----
+EQQAHQFAAEFLMPRDEIIEDLPRRINWPAFHELKRHWGVSLRALVYRAHSLGRLSEASY
+RRANQQLSAWG--HPEPGPLGPAESPQVLG----IARQLITDGGYDFEGIMAAGRIAPE-
+-----VAEAVMDAAST----------VRPKLRFVI----
+>3_306
+MT----------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------------------------MMHELGHVIYDRDVSTPWRSTKSPE
+EERAFRFAGAMLIPANVMKKRVTESLTLHGYLAIKADYGVSVGALVKRAESLGIISKSRA
+RSLYIQISSQGWRYNEPVPVA-AERSLL------IQQATARAFGENLEGVAQSTGVPHR-
+-----LVEHWTGFKRD----------LRAPMADVIPLRR
+>4_163
+MS-----------LEPSRIVRARRRAGISKKRLADLIGATPRTISNYETR--GAPDALAA
+TLADVLNVDPTFFSMPATSPLE---EDRVFFRARRRTSAAVRHAASEAGRTGVEFYSLIA
+EHFKLPEVDLP------DLVGMGPAIAARQLRAHWKVGAGPLPNLIQLAESRGLRVMSLP
+GTTD-EVDAFSVWEKGVPYIFLSQRKTAE-RSRFDLAHEIGHLVLHSGLGNGDSVE-RDA
+EREADAFASEFLLPGEVLRGAMPRQPSTEAVLKAKVSFGVSAMAMAYALFRNGLLSEWAH
+RQMCIDLTRRGYRSSEPGGIH-RETSRVFGLTLSLARQRL---GLGTEEIAQALGVCPQE
+IHELTFGHAVTPVASVGGSSAAPEPGPRPSLRVV-----
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002085.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002085.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b9484dd944c86d1acc2518c7525749ba4ef7804
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002085.fa
@@ -0,0 +1,13 @@
+>1_1080
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGIS--
+-------------------------------AYG--T
+>1_1916
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGLSRL
+RDLTP-------------GQVPGSGVTV-FEAVG--A
+>2_136
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGRIP
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002089.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002089.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a54802cda4c28e5325349a65c36fdd57a1b97a07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002089.fa
@@ -0,0 +1,28 @@
+>1_1654
+MRERVALIGAGPSGMALLRSLALAEDAGAAVPEVVAFERQDDWGGQWNLDWRTGADRHGE
+PVHSAMYRDLWINGPKECMEYPDYPFDAHFGRAVSSYLPREAMRDYIVGRVAEVAGRIRP
+QIRFATAVRWVQPLDDGGFGVTSEDLVTREAVTERFDRVVVATGHFHTPHLPSWPGVETF
+PGQVQHAHDYRSPEPYTGRRVLVVGSSYSGQDLALQLHRAGAAHVTTAYRARPQDIAWPA
+GMDEAPEVQGFDGAEVTFADGSTAEYDAVLLCTGYRHHYPFLPGELALAGPNLLAPFGLW
+KGVVWHADPRVLYLGATQQLFTLTLLDAQAFFARDVLLGRVPVPGDEERRADMDAWFERM
+TRIDGPPAALAYQGAYIQDLSSHTDCPEVDVEAVARTFLEMRDARIEDVRTFRDRRHRST
+VTGTLAAAHPVPWMDRPDDSLEEYLRRFPA
+>3_765
+MTERVALIGAGPSGMALLRALALAEDEGAVVPEVVAFERQADWGGQWNLDWRTAADRFGE
+PVHSAMYRDLWINGPKECMEYPDYSFDAHFGRPVSSYLPQEAMKDYILGRVAHVAERIRP
+LIRFGTVVRWVQPLDDGTFEVTSVDLTTGAARTEAFDRIVVATGHFHAAHTPSWPGVEDF
+PGLVQHAHDYRTPEPFAGRRVLVIGSSYSGQDLALQLHRGGAAHVTTAYRKAPQELDWPA
+GMDERPEVQGFAGSRVAFADGSSAEYDAVLLCTGYRHHYPFLPAELALSGPNLPFVPSLW
+KSVVWQADPRVLYLGATQQWFTLTLLDAQAFFARDVLLGRAPVPSAQERQADIDAWTARM
+AAIDSTPVALAFQADQIRDLTAGTGYPEMDLDGVIATFLQMGEDKRESLTRYRDRTHRSL
+VTGTRAAAHPVPWMHHPDGSLEGYLAHFPG
+>4_1872
+MRERVALIGAGPSGMALLRSLALAEDAGAAVPEVVAFERQDDWGGQWNLDWRTGADRHGE
+PVHSAMYRDLWINGPKECMEYPDYPFDAHFGRAVSSYLPREAMRDYIVGRVAEVAGRIRP
+QIRFATAVRWVQPLDDGGFGVTSEDLVTREAVTERFDRVVVATGHFHTPHLPSWPGVETF
+PGQVQHAHDYRSPEPYTGRRVLVVGSSYSGQDLALQLHRAGAAHVTTAYRARPQDIAWPA
+GMDEAPEVQGFDGAEVTFADGSTAEYDAVLLCTGYRHHYPFLPGELALAGPNLLAPFGLW
+KGVVWHADPRVLYLGATQQLFTLTLLDAQAFFARDVLLGRVPVPGDEERRADMDAWFERM
+TRIDGPPAALAYQGAYIQDLSSHTDCPEVDVEAVARTFLEMRDARIEDVRTFRDRRHRST
+VTGTLAAAHPVPWMDRPDDSLEEYLRRFPA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002095.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002095.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ba49bf458a515219cb8e87cd7fc719d2d55a33c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002095.fa
@@ -0,0 +1,16 @@
+>1_1725
+M-------RVSKADGSQATDLQRDALLEAGVEPEALYEDKASGKSDDRPHLAACLKALRA
+GDTLLVWKLDRLGRDLRHLVNIVHELTERGVGLKVLTGQGAAIDTTTASGKLVFGIFAAL
+AEFERELISERTKAGLASARARGRKGGRPYKMTPAKIRLAMASMGNKDTNVGALCKELGI
+TRQTLYR----HVSPTGELREAGQKVLAQRR
+>2_713
+------------------------------MEPEALYEDKASGKSDDRPHLAACLKALRA
+GDTLLVWKLDRLGRDLRHLVNIVHELTERGVGLKVLTGQGAAIDTTTASGKLVFGIFAAL
+AEFERELISERTKAGLASARARGRKGGRPYKMTPAKIRLAMASMGNKDTNVGALCKELGI
+TRQTLYR----HVSPTGELREAGQKVLAQRR
+>3_662
+MGHLLGYARVSTTD--QDASLQIDALGAAGC--YRVFVDTMSGSLQHRPELDKLLDQLRP
+GDTLVVWRLDRLGRSIRHLIDQLHALAERGIGFRSLQ---ETIDTTSPGGRLVFHVFAAL
+AEFERDLIKERTNAGLAAARARGRTGGRPSRLSADQVRTARRLYEQQDMTVAQIGDVLGV
+SRTTIYRTLAKHAEPVARRRAKPSPTM----
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002098.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002098.fa
new file mode 100644
index 0000000000000000000000000000000000000000..13c00d114aac3bdf5119e5f10651fd0a49b1540c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002098.fa
@@ -0,0 +1,24 @@
+>1_1747
+MTETSNSPMTARVRAFLDRPHRLLIGGEWVDAASGKTFETRDPATGEVLATVAHAEQADIDAAVAAARAAFDEGSWVRMR
+PNVREDLLWRISNLITERLEDFALLESLDQGKGV--GIASAFDVRAAADCFRYYAGWPSKLQGAVNAPSMLLAPPEAEFH
+SYTRREPVGVCGQIIPWNFPLLMAAWKIAPALATGNTVVLKPAEQTPLTALMLGELLTEAGVPAGVVNIVTGHGDAGAAL
+TAHPDVDKVAFTGSTEVGKKIVGAAAENLKKVSLELGGKSPNIVFADANIDAAVDGALMGFTLNSGQACESGTRVFVHAD
+VYDRFNEALAAKMRQMSIGPGTEDAAIT-PLVSQEQLDRVMGFVEEGKRDGAVALTGGQRHGD-AGFYVEPTLFTETTPE
+MSIVREEIFGPVAVSVKFTDEDEVIRAANDSVYGLAAALWTRDVSRAHRVAARLKAGTVWVNTFHALDSQLPFGGFRQSG
+WGRELGAESLELYTQVKSVTIAL
+>2_671
+MTETSNSPMTARVRAFLDRPHRLLIGGEWVDAASGKTFETRDPATGEVLATVAHAEQADIDAAVAAARAAFDEGSWVRMR
+PNVREDLLWRISNLITERLEDFALLESLDQGKGV--GIASAFDVRAAADCFRYYAGWPSKLQGAVNAPSMLLAPPEAEFH
+SYTRREPVGVCGQIIPWNFPLLMAAWKIAPALATGNTVVLKPAEQTPLTALMLGELLTEAGVPAGVVNIVTGHGDAGAAL
+TAHPDVDKVAFTGSTEVGKKIVGAAAENLKKVSLELGGKSPNIVFADADIDAAVDGSLMGFTLNSGQACESGTRVFVHAD
+VYDRFNEALAAKMRQMSIGPGTEDAAIT-PLVSQEQLDRVMGFVEEGKRDGAVALTGGQRYGD-AGFYVEPTLFTETTPE
+MSIVREEIFGPVAVSVKFTDEDEVIRAANDSVYGLAAALWTRDVSRAHRVAARLKAGTVWVNTFHALDSQLPFGGFRQSG
+WGRELGAESLELYTQVKSVTIAL
+>2_805
+MTET---------LTYAD----LLAA---VVAPEGAGTEIKDPATGDLIGYAPQSTTADLDAAVELARTA--QRDWAKLS
+HAERSAALNRAADAIEANSAALAELLSREQGKPVKNGPNAAFEVGGCVAWTRATAGFEVQPETIVDDET-----GRAELH
+WM----PIGVVGGIGPWNWPMMISVWQIAPALRMGNTVVLKPSEYTPLSVLGLVHVMNQA-LPEGVLQVLAGDGELGRAF
+TSHDGIDKITFTGSTATGKAIMKGAADDLKRLTLELGGNDAGIVLDDADPKAIAEGLFWGAFINTGQTCAALKRLYVPDS
+LYDAVCEELVAVARRMPMGPGLEEENVLGPLQNRAQYEIVERLVQAAKDGGGRVLLGGDPDPERPGLFYPTTIVADIDND
+NPLVAEEQFGPALPIVRYTDLEQAIEWANGLDVGLGASVWSADPERAKEVAMRLEAGSVWINKHGTIDPRVPFGGVKHSG
+MGREFGVLGLKEMAEAKSISV--
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002099.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002099.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f40ec82ea2fc1ba1a54df5d9fd7f799c68a0ad64
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002099.fa
@@ -0,0 +1,10 @@
+>1_1804
+MGMKQRISKVGAGVAVAGPLAVSGAVPAQALTDSGRQDCSAG------------------
+----------------------------------LLLSGTYGYCYYPY
+>3_532
+MGMKQRISKVGADVAVAGLLAVSGAVPGQALTDSGRQDCSAGGGYVGARGEQQRYGDRMS
+FDVGGRTTKVVNRYTYGFDSGLRMSQNWRVSSESLLLSGTYGYCYYPY
+>4_2024
+MGMKQRISKVGAGVAVAGPLAVSGAVPAQALTDSGRQDCSAG------------------
+----------------------------------LLLSGTYGYCYYPY
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002103.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002103.fa
new file mode 100644
index 0000000000000000000000000000000000000000..50cf5d9b88416b9717959dd5ecc8c6770bc761ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002103.fa
@@ -0,0 +1,16 @@
+>1_2129
+MKYRPQHEANPLPFSP-----------FKSSTVPRPIGWLSSVSTDGRENIAPYSQWQNL
+TFDPPMVMFSANQYPDGRRKDTVLNAEQTGWFVWNMATYDLREAVNVSAMALEPGESEWD
+RIAEHGVTKVYADNHPIPMVAESPVRFECRYHSTHRIKGDSNVGTIDVVFAHVDTIHIDD
+DVITADGR----LDIPRIQPIARLGYFDYTVVRETFEMRVPGADGDAQAGLEGRS
+>2_806
+MSARTE-------FDPAALGDRETTLLVKSLLIPRPIAWVGTLSADGVPNLAPHSFFTVA
+SSEPPIVLIGS-----AGRKDTLRNAEATGEFTVSLVTRALAEAANRTSAPFAP---EVD
+EFAAASLTPEPSVVVGPPRVAASPAALECRLHEVHPV-GDSFLLMGRVVHVSVDT-----
+DVLTTDARGRTLPDPAALGPVSRLGRMEWGGLGEVFELERPSA-----------G
+>3_147
+MKYRPQHEANPLPFSP-----------FKSSTVPRPIGWLSSVSTDGRENIAPYSQWQNL
+TFDPPMVMFSANQYPDGRRKDTVLNAEQTGWFVWNMATYDLREAVNVSAMALEPSESEWD
+RIAEHGVTKVYADNHPIPMVAESPVRFECRYHSTHRIKGDSNVGTIDVVFAHVDTIHIDD
+DVITADGR----IDIPRIQPIARLGYFDYTVVRETFEMRVPGADGDAQAGLEGRA
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002104.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002104.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd82eeb3754f056b15ef888045b19d18845ff9e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002104.fa
@@ -0,0 +1,25 @@
+>1_2246
+MSETRSGVLPDHDIYLLDDELTEEQREVRDRVRAFVDAELMPVINDYWERAEFPFELVPK
+LAELNVAGTVIEGYGCPGMSRMAGALVSMELARGDGSFNTFFGVHSGLAMGSINAFGSDE
+QKERWLPRMARMEMIGAFALTEPDHGSDSVALETTARREGDTWVLDGAKRWIGNASYAHV
+IVIYARDVADGQVKAFVLEREPDTEFPAGFEPTVITGKIGKRAILQPDIVISGLRIPEAD
+RLPGCSSFKDVNRVLSTTRGGVAVETLGHAVAAYEAAVAYAGQRVQFGKPIAGHQLVQGQ
+LATMLADVTNIKLTCFRLLELQDQGRLTGPMASLAKMSAARQARRVTSMARDILGGNGLL
+LENHVARHLTDMEVVYTYEGTDSMQSLIVGRAITGVSAFA------
+>2_791
+MAD-RPAVIDHPDYFLLDSDLTDAQRALRDRVRDFGREQVLPIINEWWEKAEFPEPLLPG
+LADLGIIGTYIEGYGCPGMSRIEAGLVAREMGRIDGSVNTFLGVHSNLCMGSIYILGSDE
+QRQRWLPAMAKLEKTGAFALTEPKHGSDSVSLETSARRDGDEWVITGHKRWIGNGHAADV
+VVLYARDEADGEVKAFVVEKQEDGSFPAGYNPTVITGKVGKRAILQADIVIENLRVKEEN
+RLVNCESFAGVNRVLKATRGGASWEAVGHGMAAFEIAAAYALEREQFGAQIGGYQLVQER
+LATMLTDLTTMQLMCVRMAELQERDELTLAMASMVKMHTSRKALDMTRTARDIVAGNGLL
+LERHIGRHLTDMEVVSTYEGTDSMQALIVGRDITGISAFTRSRRKS
+>4_279
+MSETRSGVLPDHDIYLLDDELTEEQREVRDRVRAFVDAELMPVINDYWERAEFPFELVPK
+LAELNVAGTVIEGYGCPGMSRMAGALVSMELARGDGSFNTFFGVHSGLAMGSINAFGSDE
+QKERWLPRMARMEMIGAFALTEPDHGSDSVALETTARREGDTWVLDGAKRWIGNASYAHV
+IVIYARDVADGQVKAFVLEREPDTEFPAGFEPTVITGKIGKRAILQPDIVISGLRIPEAD
+RLPGCSSFKDVNRVLSTTRGGVAVETLGHAVAAYEAAVAYAGQRVQFGKPIAGHQLVQGQ
+LATMLADVTNIKLTCFRLLELQDQGRLTGPMASLAKMSAARQARRVTSMARDILGGNGLL
+LENHVARHLTDMEVVYTYEGTDSMQSLIVGRAITGVSAFA------
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002116.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002116.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa868b88b9dae6e6317c8285201df2eaaed6ebb7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002116.fa
@@ -0,0 +1,19 @@
+>2_2378
+---------------------MSQPTAAGFRFYDAFNGSAADPSPHFNVARYRAHYPGPP
+TPGQAGCAISHFRVLESFASSLGHEDGVALVSEDDVLMPPETEAVLEGILKDDS-FEIAV
+LADR--GPT-NPSLAFQRL----LMTEAELSLLSRPI--VCGGRIRRLGRFEGNPYMAAL
+YLVTRSGARKLASGLVDDAGGPWTIADDWPLFRDRYGLDIRVLRPGLVTYMGGS----TT
+R---DAESLARDALSAAGDGRPLTRLKTAVGLRSRSRAARLVVRATLRDIATR
+>3_2223
+MPDIVDYRVIALADSTRLEGFLAQPLGRRFRPFEAVDARKGYGPEDFDAEGFEVRFGRPP
+LNGEVGCTLSHMSVLREFAVEDGAVTDVLVVAEDDARFSRFTSEVLNRLLETSAVRGLVV
+LA----DPY-GPVDMRGRLGAPTLEDKLQQSLLRRRLRPLAGAPRFAVGRWSRGLVGTGF
+YLVSRDAAKY---------DIAW-------------------------------------
+---------------------RLRH------RRGGAR----------------
+>3_2258
+MGQITDRYVISLEGSPRREAFFSQPGVADFVVWDAFDGRTGAGRDRFDVVAFERRAGRPP
+EGGEIGCTLSHAGLLADFAAGLGRPDDLMLVAEDDVVFTPDFEAVLGRVARTRG-WGWTL
+LAQGLEDPFRDPFWAKSRDRAP-------QSLLAKPVGPPSSPWRYRLGNWDGELWGTGL
+YLVTREAARALTDHATRE-GLSWA-ADDYVTWHAAAGVKVWILLPTIAGWVGESEINATT
+RPHLQIQSYAAHPMGRQAWSRRVSR------FRAGARIAWKEMRGDTRPWAS-
+ 
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002127.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002127.fa
new file mode 100644
index 0000000000000000000000000000000000000000..696846944cef33bed393f027435b74e9302e9199
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002127.fa
@@ -0,0 +1,12 @@
+>0_466
+----------------------MVNETRAISRRQVTKGVTWSVPAIAATAAAPAFAVSSV
+GVVAGATLYANPLMTKYVQAQNGTTALYLNATPGVGIPDATACQSVQNKKISIVYTAPAG
+IVDFRKVLNARKAGTPYNTYTNGSVGDSKTFYTLKVGDRFVTGTNPAYWEVTKLASDGSS
+ITLTYSAPITGCYYYAQPSFNPYFWAKDVASMVNQVHLTAYIGTQRVAFDTGAASNVTWS
+ADRLEIIGPKTTN
+>1_195
+MSECLMPVEVPQVLRSATKGIGMVNETRVISRRQVTKGVSWSVPAIAATAAAPAFAVSNP
+GVVAGATLYANPLMTKYVQPQNGTTALYLNATPGVGIPDATACQSVQNKKISIVYTAPAG
+IVDFRKVLNAQKAGTPYNTYTNGSVGDS-NFFTLKVGDRFVTGTNPAYWEVTKLASDGSS
+ITLTYSAPITGCYYYAQPSFNPYFWAKDVASMVNQVHLTAYIGTQRVAFEKGAGTNVTWS
+DDRLEIIGPKTTN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002132.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002132.fa
new file mode 100644
index 0000000000000000000000000000000000000000..97e628e6cf9d93699503ee8d94483d9edee039ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002132.fa
@@ -0,0 +1,20 @@
+>0_571
+MATMIQ------ESMDSEYDDVRFPQERTQGLILGLTLEQVIVV-LAGVLIGMAFILRGG
+PAMFVGIGLMAVIGAFGATRFRGRSLPGWVWVAAQYLRRGATDQLEYRQGMAPAHVLELV
+DGEPQAPVSEAGPQAQRDAKGRIKPGEPARFRLPGVAGELMVYAMP-NGAGFVWDPRARE
+AVVCAKVMTTRGFDLESFDAQEERSLSWGSSLAALSRLPGVVRIQASDQTTLISGAAVED
+FYESKQEGAGRTGASIDPFLDQAFRELMKEA-QSMPVHEQWLTLVVSPSKITSQVKALGG
+GTPALMEHMLKLMTTVESTLPRSGTQVTAWHSPRTLAGLSRSAFDPDASVMVSTMKADGK
+TAGTAPSSAGPMAVEVHAGHMVTDGNYHRTYKVSELPQNLARLGFLDELVFAGDFRHTVS
+VFLAPVERGAAVRSVQRRKTDWHTNSRLMNKLGRIGSLEHDQSLEDVEREEAELRRRHTG
+VEVVVLVTVTGASRSELESAAAEVVASGITAECELRPVWMEQDAAFVAGALPFGRMKL
+>3_1755
+MSSRKKNNSHEPEATGSELVPVKFSRLTRRGILLGLSAAQLVTVGIAIATIITALYAGGG
+MWLAYTAPVWATAVLLTWVPVAGRPVIEWVPVAGWWVYRTTIGQLLYRRRI---------
+----------------------VTPRPAGTLALPGDQARLREYEDPTTGAGMIHDPHQNT
+LTVVCEI-THPAFVLLDPAEQERRVTAWGRVLATVCRSGRIATLQILERTLPDSGTGLAE
+WWTTHGQPDDTSWAA------TTYAELINRAGPAGERHATTLSLSLDMRNAARQIRTAGG
+GIRGAAAVLRQEMNTLTAALRSADLTPSGWLTPGQIAVILRSAYDP---AIAATLERHGE
+I-GHDLATAGPVAVNETWSRIRTDSAHHAVLWISEWPRSMVYPGFLSPILLSSGIQRSFS
+LICTPMRSDQAARDIRKKKVEHISDQAQRAKIGQIEDASQTAEYHDVLQQEADLTAGHGI
+LRYTGLITVTATTIEDLDAHVAALEQAAIQANCETRLLAGQQAKAFTAAALPLCR-QV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002141.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002141.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f23cff07458781925634064c6ddb70ed3e3e41a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002141.fa
@@ -0,0 +1,26 @@
+>0_859
+MSTVLLLTTGTGPAEGLLLQDLRDSGHVVDVLDVASHAWLRRRPGLAPAPLYPWTGTHAL
+RAAGAQIAREMRRVTAAGAYDAILASGLGAAGFAARHVEEEFIPLLRRGDLDFSAARRHA
+EEDFAALTRAVDRLFLADEWEFDKALSKGSRSAHLRHPRVGLAPQTLAPLAAEAETPRVV
+VLHPEHVDADRLAAQMEALQTAVDTVPGASLRSLSASALYRTRDLAAGRAFDAVAATRLG
+GATHVVLVGSSRDHAAVGELLVGTGFAERLVVEDTIGSGAWAAGHPGVRTGRGLRLVTEL
+AAALHGGPETHSAVDTVDGGTTDLLSAYRAAMTGRVDRTFEDLAVLRHDGPLDVFFSTSP
+LEDRTDGARPQRVRNMNDALSEPAAALRLSSVPGVFDRRLRVLDEALAAGRPLGLLYGEN
+STSPIPVDRVTAALADVMARFSAGGGTSVWFVRDLHWLDEIDGYLEDADARRDVQERGLA
+EFDAMAEAAYRLAAPSAESGAGFDALLARHGRGPVDWLPLPPAVSPANTVPADAPAIGEE
+GVTLLYAGGVGGIYGLGQYLTAVGTLDPQVRLDFVVRAGERSVLEDMLAEHGLADRPGLR
+ITTVPLEWYVPATRTVVGVVLLGGKYARFSFPYKTMSLIERGYPVLCFADMGIADFLERN
+RVGLGVARSSEAIRAGIVTLVRDGAPGMAEAQRSQSWAVRVATARAALED
+>1_590
+MSTVLLLTTGTGPAEGLLLQDLRDSGHVVDVLDVASHAWLRRRPGLAPAPLYPWTGTHAL
+RAAGAQIAREMRRVTAAGAYDAILASGLGAAGFAARHVEEEFIPLLRRGDLDFSAARRHA
+EEDFAALTRAVDRLFLADEWEFDKALSKGSRSAHLRHPRVGLAPQTLAPLAAEAETPRVV
+VLHPEHVDADRLAAQMEALQTAVDTVPGASLRSLSASALYRTRDLAAGRAFDAVAATRLG
+GATHVVLVGSSRDHAAVGELLVGTGFAERLVVEDTIGSGAWAAGHPGVRTGRGLRLVTEL
+AAALHGGPETHSAVDTVDGGTTDLLSAYRAAMTGRVDRTFEDLAVLRHDGPLDVFFSTSP
+LEDRTDGARPQRVRNMNDALSEPAAALRLSSVPGVFDRRLRVLDEALAAGRPLGLLYGEN
+STSPIPVGRVTSALADVMARFSAGGGTSVWFVRDLHWLDEIDGYLEDADARRDVQERGLA
+EFDAMAAAADRLAAPSAESGAGFDALLARHGRGPVDWLPLPPAVSPANTVPADAPAIGEE
+GVTLLYAGGVGGIYGLGQYLTAVGTLDPQVRLDFVVRAGERSVLEDLLAEHGLADRPGLR
+ITTVPLEWYVPATRTVVGVVLLGGEYARFSFPYKTMSLIERGYPVLCFADMGIADFLERN
+RVGLGVARSSEAIRAGIAALVRDGAPGMAEAQRSQSWAARVATARASAED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002142.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002142.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3565ce22462810d4325f38fda95b7e10c7b2f66
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002142.fa
@@ -0,0 +1,32 @@
+>0_860
+MAVATPAPRRPRMAMLVGNQVVGDSRVEKAAVSAVRAGYEVVVVGVSHRTTFNLGRYGSV
+PILRVPVTFRRHLAWQTLHGTARPDVTDWSAVLDPEEAAAMTAWDLAHEVGAGLLQAVVR
+GLSPHALPDRARGRLGRAARRLGRLGPARGRRDPAAMRGRRALKNFAAGRTGAWREVWPL
+IADYEDGFLRALIDLAPDLVHVHDRHPLPAAAAYDHYRAARGLPPVPWVYDAHEWLPGQM
+MPGPVDQRIAWKAAEAELIHEADAVVAVTDELAERMREYHALQERPVTVINGPWGTQLPM
+GPAERLPLRTELGLSDDVPLLVYLGKLAAVRGVGTLVDALPLLPGVHIAFVGSPDPDARQ
+GLRDRAAQLDVADRMHIVDYVPSASVTWYVSSATAGVSPLLPTPAHESAVPTKLRECLLA
+GLPLTVSDLREQARFVREQGVGTVFAPGDAADLARAVRDLLARRTELTAAARSPEIAARH
+GWEAAERALHGLWRRLVPTPAAPPPVEIAPDPAREPQPRGLLVVGDPPTVRPLADAWPAG
+AGPVTLRPPRDFPEGRGLVVGGPEAVWGVLQDWVTDDRAHGTVLIGGEGPLWGRAEQSPV
+HELLSLRARGRQVALVAGERILAGVERRLAAVPGHPWGGLDPDARAALDRRIRRQGRPFQ
+AALAAGVPVLSHRRVEALLTPGVLWLPAPIPTPTDRGPGRDGASAPRSVLILPGDRTSAE
+SAAVDELVAELAARGIPVEAPSGPRFRRRPDAFHGDVVVAPLHTEDLEVAALQALAAGSA
+VVAGPPVTPAPDECAPPVTETDDATLLATVLGLLEETSAAAGERRERAREHHARLHAPEA
+VLVRLQALLSPAETTDGPAAV
+>1_591
+MPVDTPAPRRPRMAMLVGNQVVGDSRVEKAAVSAVRAGYEVVVVGVFHRTTFNLGRYGSV
+PILRVPVTFRRHLAWQTLHGTARPDATDWSAVLDPEEAAAMTAWDLAHETGAGLPQAVVR
+GLSPHALPDGARGRLGRAARRLDRLGPARGRRGPAATRGRRALKNFAAGRTGAWREVWPL
+IADYEDGFLRALIDLAPDIVHVHDLHPLPAAAAYDRYRAARGLPPVPWVYDAHEWLPGQM
+MPGPVDQRIAWKAAEAELIHEADAVVAVTDGLADRMREYHALQERPVTVINGPWGAQVPM
+DPAERLPLRTELGLSDDVPLLVYVGKLAEVRGVRTLVDALPLLPGVHVAYVGSPDPGARQ
+GLRDRAAQLDVADRMHIVDYVPSASVTWYVSSATAGVSPLLPTPAHESAVATKLRECLLA
+GLPLIVSDLREQARFVRDQGVGTVFAPGDAADLARAVRALLARQAELTAAARAPEITARH
+GWEAAERALHGLWRRLVPTPAAPQPVEIAPDPARDPRPRGLLVVGDPPTVRPLLDAWPAD
+AGSATQRPPRDVPEGRGLAVGGPEAVWGVLQDWVTDDRAHGTVLSGGEGPLWGRAEQSPV
+HELLSLRARGRHVALVAGERILAGIDRRLAAVPGHPWGGLDPDARAALDRRIRRQGRPFQ
+AALAAGVPVLSHRRVEALLTPGVLWLPAPIPTPTDRGPGHDGASAPRSVLILPGDRTSAE
+SAAVDELVAELAARGIPVEAPSGPRFRRRPDAFRSDVVVAPLHTGELEIAALQALAAGSA
+VVAGPPVTAAPDGCAPPVIETDDATLLATVLSLLEETSAAARERRERAHEHHARLHAPEA
+VLVRLQALLSPAETTDGPAAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002148.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002148.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bea11b6f613f624baec4f06eec31b29fcf4d5a13
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002148.fa
@@ -0,0 +1,12 @@
+>0_932
+MTPPTGVLPRAALVMRLLHEAGPAGLRLSQLVQRTGLPQPTAHRLLADLAEQGAVTRRGA
+AYALGDRWGPVGFEPVTPRCLIEREASRAVVQAAADELGDTVYLAARAAGGVAYLLRCDG
+DSPVRVFTVEVGEVKRLAAGYAGIALLASLPPERRRAEVDAVVARPPRRWNLTDDGALHD
+LLDTLLRQMDEQGWCGGVPVVPGVAGVACGVPARTGGIPQVSLTASAAEQRMPPARVPEV
+AEVLRAAATRLAEIGG
+>1_654
+MTPPTGVLPRAALVMRLLHEAGPAGLRLSQLVQRTGLPQPTAHRLLADLAEEGAVTRRGA
+AYALGDRWGPVGFEPVTPRCLIEREASRAVVQAAADELGDTVYLAARAAGGVAYLLRCDG
+DSPVRVFTVEVGEVKRLAAGYAGIALLAALPPERQRAEVDAVVARPPRRWNLTDDGALHD
+LLDTLLRQMDEQGWCGGVPVVPGVAGVACGVPARTGGIPQVSLTASAAEQRMPPARVPEV
+AEVLRAAATRLAEIGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002158.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002158.fa
new file mode 100644
index 0000000000000000000000000000000000000000..35329bad9e63890b575da985f11ff76121d6d6ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002158.fa
@@ -0,0 +1,6 @@
+>0_1444
+MSAPATAVTFPGVTLFLPDGVMTGDLTYDARTSQLAITYADGETEVLSIDLTLEGYVAAP
+GEALIKDWSEHSGFTAALVDAGIVMRVETLQIGPFDSRAYRVLVLTEAVTGR
+>2_2159
+MSASTATATFPGVTLFLPDGVMVGDLIYDARTSQLAIVYSDGETEVLSIDLTLEGYLPTP
+GEALIKDWSEHSGVTSALVDAGLVMRTETLVVGPFSSRAYRVLVLTPEVTGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002163.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002163.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a2bef4b2d5f61bbd99e580393b46d6fca8624eef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002163.fa
@@ -0,0 +1,10 @@
+>0_1554
+------------------------------------------------------------
+---MSFLIPSVPVSCGCRREVREETGLEVTAGRLVAVDTRPSKADGRIGLRFLFRAVHPL
+TAADVAAIRLQEDEASEHSFVTCQEARKLLRPAIARRVDAAWDAAHCVYLEDGRPAAGVD
+QPAG
+>1_1276
+MVNLLLSVTFACGVAIAGLHVVNRRFIAPMYDVVLNLAAFLAAVASSVLLGHVLPAVFAA
+LAVLAWLILAVRTV----RARRAGHKLEVTAGRLVAVDTRPSKADGRIGLRFLFRAVHPL
+TAADVAAIRLQEDEASEHRFVTCQEARKLLRPAIARRVDAAWDAAHCVYLEDGRPAAGVD
+QPAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002164.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002164.fa
new file mode 100644
index 0000000000000000000000000000000000000000..49c14840cbf7928b20fb1865c1e48f7bae7362c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002164.fa
@@ -0,0 +1,8 @@
+>0_1559
+-------------------------------------------MSGNAFQDLPFPVSGPI
+LGSVGERFRLETASDEGTATFSAGGTEGGTYSCGAGQTLLIGDSALLCRAVGENSLDFTI
+SRPR
+>2_1251
+MRTRVTTSLLGLGLTAAALVGCQTQTWISMCFTDATLRSCEVSVSGNAFQDLPFPVSGPI
+LGGVGDRFRLETASVEGTATFSA----GGTYSCGAGQTLLIGDSALLCRAVGENSLDFTI
+SRTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002171.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002171.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a6050efd476b75bf14116e903dc5360a378dd547
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002171.fa
@@ -0,0 +1,12 @@
+>0_1737
+MTRDIIRTERIGPVTVIHLQDDRALNALGSALVAGLADALEHAQQDPEVRAVVITGSDRA
+FCAGAHIPEVLALREALTADPDAEVYLDRLFDLLAASPQPVIAAVRGLALGGGCELALAC
+DLVVAGESASFGLPEVRLGVIPGAGGTQRLVHAIGKAKATRMLMTGESVDAAWAESAGLV
+AEVAADEDVVARAVDIARRAADNAPGAVRLAVGCARRAQDLSLTDGLAHERRAFLEALAS
+DDAAEGMSAFAQKRRPVFGSR
+>2_1059
+MTRDIIRTERIGPVTVIHLQDDRALNALGSALVAGLADALEHAQQDPEVRAVVITGSDRA
+FCAGAHIPEVLALREALTADPDAEVYLDRLFDLLAASPQPVIAAVRGLALGGGCELALAC
+DLVVAGESASFGLPEVRLGVIPGAGGTQRLVHAIGKAKATRMLMTGESVDAAWAESAGLV
+AEVAADEDVVARAVDIARRAADNAPGAVRLAVGCARRAQDLSLTDGLAHERRAFLEALAS
+DDAAEGMSAFAQKRRPVFGSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002172.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002172.fa
new file mode 100644
index 0000000000000000000000000000000000000000..053eab253fe3fa8d1c0455f860aa2481e88a645c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002172.fa
@@ -0,0 +1,16 @@
+>0_1738
+MILDSYRSPWLTEDAEALLEHCRDFLAREVVPHEERWAEQHGVDRDLWTKAGEAGLLCPS
+LPEEYGGAGGTFALEAAILTEQGRCFDDAWGFSIHSPIVAHYILAYGTEEQKQRWLPGLA
+SGELVGAIAMTEPNTGSDLQAVRTRATRDGDHYVINGSKTFISNATHCGLLLIVARTGDE
+PGGRGLSLIVAETDGLEGFERGRVLKKIGQHGQDTRELSFSDMRVPVSHLLGPDEGQGFV
+QLMAQLPQERLTLAVLAAGVCEAAVRETIRYTKERHAFGEPLMSFQNTQFVLAECVADTL
+ATRTLVDQCIVAHVDGTLTAADASMVKFFASDMQNKVVDRCLQLFGGYGYMEEYPIARAF
+TGARVQKIYGGTNEIMKMLVARAL
+>2_1058
+MILDSYRSPWLTEDAEALLEHCRDFLAREVVPHEERWAEQHGVDRDLWTKAGEAGLLCPS
+LPEEYGGAGGTFALEAAILTEQGRCFDDAWGFSIHSPIVAHYILAYGTEEQKQRWLPGLA
+SGELVGAIAMTEPNTGSDLQAVRTRATRDGDHYVINGSKTFISNATHCGLLLIVARTGDE
+PGGRGLSLIVAETDGLEGFERGRVLKKIGQHGQDTRELSFSDMRVPVSHLLGPDEGQGFV
+QLMAQLPQERLTLAVLAAGVCEAAVRETIRYTKERHAFGEPLMSFQNTQFVLAECVADTL
+ATRTLVDQCIVAHVDGTLTAADASMVKFFASDMQNKVVDRCLQLFGGYGYMEEYPIARAF
+TGARVQKIYGGTNEIMKMLVARAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002179.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002179.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a5d94452364e8809674ea8af7fc008c446587a1d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002179.fa
@@ -0,0 +1,14 @@
+>0_2154
+MLRPRLARPTALLTAGLAALALLTGCSVDGDAAAGSSA------------GSPSAASSSS
+GASSSGRVSDGAAPSSSRAAGSSSAVASASRAVESSQAAEASRAAAASREAEKSAAAAAA
+EASRSAEAEAEAVAEAEREAEASAEVEVGAAEEESAASAGGDGLSAEGQQAVRQAQSYLS
+FTAFSRSGLIDQL-EFEGFSNADATAAVDSLDVDYAAQAVKQAQSYLTHTAFSRTGLIDQ
+L-EFEGYSNADATAAVDGLGIDYNEQAAKQAQSYLSHSAFSRAGLIDQLM-FEGYSASQA
+EYGVDAAGL
+>2_511
+MLRPRHTRPALLLTAGLTSLALLTGCA-DGDPAPGAAATTAAATTAAATSSAPTTQAASS
+SPASSPRTSSAAASSSAKASDAAAAASSSAAAASASEAAESSRAAEAEAEASRE-AEAEA
+EAARAREAEESAAAEAEREAEAAATV------EEDSSTTAGEGTVSSG-QAVRAAKNYLE
+VLPFSRDGLVHQLVAGDGYSDADAAAAVDSLTVDYEAQARRAAQNYLDVLPFSRDGLVHQ
+LIAGDEYSDADAAAAVDSLTVDYQEQAARAAQNYLDVMPFSRDGLIRQLMDGDDYSASQA
+EYGVDAVGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002180.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002180.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee714b73c6288111bd8c66f50ef65155b1d95b12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002180.fa
@@ -0,0 +1,20 @@
+>0_2169
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------MSAGRITVVKGDERLASIPLERVSAVVVHGNVDLSGALLRELMWRGLP
+CVWCTGAGRVVGWTNGVKPPNGGARFRQFAASAEGRVDIAREFVVAKVANQATILRRFGG
+MPAVVKRLRSATRLASTATSTGQLFGIEGRAAAEYFAGFPGLLAPGVDAGVAESFPGRVG
+RGATDPLNIALNYGYGMLLSEVIRAVLACGLDPHAGVLHSSGRNKPALALDLMEEFRPPV
+VDSAILAAFNNGELGRLSFTHVLGGARLTQS-----------------------------
+---------------------------
+>4_2105
+MDEKAPKVAQIQQGVADHARVDVPTTREAQTMRGIDVRDPSLGLHGRVDRVERLPSGRLR
+VVEHKATPVKRAVRINDANRLQLVLQTMALESQGNTVEDAEVYFTTHHRRVPVEISAADR
+KAARDAVASARSVVNGETAPAPLLGDPRCMRCSHASVCLPEERQEEEVLSRIVPPDPAGE
+TLHLTVPGSRASMSAGRITVVKGDERLASIPLERVLAVVVHGNVDLSGALLRELMWRGLP
+CVWCTGAGRVVGWTNGVKPPNGGARFRQFAASAEGRVDIAREFVVAKVANQATILRRFGG
+MPAVVKRLRSATRQASTATSTGQLFGIEGRAAAEYFAGFPGLLAPGVDAGVAESFPGRVG
+RGATDPLNIALNYGYGMLLSEVIRAVLACGLDPHAGVLHSSGRNKPALALDLMEEFRPPV
+VDSAILAAFNNGELGRLSFTHVLGGARLTQTGRRKVIAAVERRLGTEFKHPVFGYRVTWR
+RAIEVQARMFLGVLDGSQEVYKGVRVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002189.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002189.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8abebdc190df1073a444ef443ca241d5ad8c1f26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002189.fa
@@ -0,0 +1,6 @@
+>1_14
+M----SAPLPS-----HLTIVQSADLLQVSRDTIRRLIASGDLKAYRIGPSTNRRRPIRV
+DRDSLLALREPVTSLAALKAGEAA
+>2_28
+MAAAASKPRPSFDPRPRLTIAEVADYTGTSPSSVRRWIARGELRAYKYGP-----RAIRI
+DPADVDAMRQPVTSLADLRGGDAQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002194.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002194.fa
new file mode 100644
index 0000000000000000000000000000000000000000..008e2e98e2d31ed8f0dfc5b9860d0f3ca7ba84e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002194.fa
@@ -0,0 +1,12 @@
+>1_284
+MSAALDRLKQQNAQSGSQQQLDSPETMEALTSILAAVEAQNARLDRLAEQQKKLAGFVKV
+MDEETTRRLERITASASTSSPSSDASARIASIESRLNEIASTLGEFAQSLNGESLNAASQ
+SLVAEAQRNHAATASAIEGLKAQAAANQKLVSQVGGAVQRIEKRTEERVVKAVEQVAGEA
+SATIAANLDASNERAERIIAATAKLEARQLWSAAAAMCLALLPVVVVVAGLWMGIAGLIT
+GAQWALDVDGSVWLGIGRWLVIAAGLAAAGYGVFASVRWVAGLVETWKGRGMPTWPNWRR
+>2_2315
+MSAALDRLKQQNAHEQPPQQLGSPATMEVLTSILTAVEAQNARLDRLAEQQKKLAGFVKV
+MDEETTRRLERIAAPASTSSPSSDVSARIASIESRQNEIASTLGEFARSLNGESLNAASR
+SLVAEAQKNHAATASAIEGLKAQAAANQKLVSQVGGAVQRIEKRTEERVEKAVEQVTGEA
+SATMTANLDASNERAERIIAATAKLETRQLWSAAAAMCLALLPVVVVIAGLWMGIAGLIT
+GAQWALDVNGSVWLGIGRWLVVGVGLAGASYGLFASVRWVAGLVETWKDRGLPKWPRWRK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002195.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002195.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f76b0b984a5b04f9c0ebc4fb791f4f620829b637
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002195.fa
@@ -0,0 +1,10 @@
+>1_285
+MSTERDALFQGVEGAGGPSQAAGEDMSASETSDTATACHSGVQVEQQTDSQVNTGRADAE
+AVRQSHGGAKRRRGGGGRLDTRFDDATLAALRTRAKRLGLAPSTWVRTVVRDALHASRSE
+ELDAAVAAQLLGVEERVQASADARELAAQVRPLAINVNDLDRRARAGEPVALSAEVPELI
+ELLHEVRALLGDRAAS
+>2_2316
+MSADQHPLFQGIEGGGAPSQAGLEDTSVSDVSDRPTACHSGVQVEQQADSQVKTGRADAE
+AVRQSHGGAKRRRGGGGRLDTRFDEATLGALRTRAERLGLAPSTWVRSVVRDALHASRSE
+ELDAAVAAHLLGVEARVQASADARELAAQVRPLAINVNDLDRRARAGEAVALSAEVPELI
+ELLREVRTLLGDRTAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002196.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002196.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce6bec0b756f5b63cdd5d1c911b54114f49dafa4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002196.fa
@@ -0,0 +1,18 @@
+>1_286
+-------MAKQENNPTSIGLTQYLDPSYWAWAAEDPNGAALLQQGAEAILAYVVQRLEAT
+GCQVVEAYGIVHDKDEREVWSDTEKALVVEPKPEHLHAVIKFASRAKSAPLDRLAFGIGV
+EPQYVEKPGRGRYAFDNMLSYLTHVKYADKHQYAPSEVATVRGPDYLGIDAQRRETWLKG
+RAHVKKKIVAENFEDMRERVLQGEITRDQIMLTDELFDIYSRHQREIDDALSAYGQRRAY
+RAAAKLRAGEFSTHVVFVHGDAGIGKTRFATDFITEAINAANAHGERWQVYRAATGNPLD
+DWRGEEVLLLDDLRASAMDANDWLLLLDPYNASPAKARYKNKGEVAPRLIVITATIEPVE
+FFYYARQKGNVDEALDQFIRRLASVVKVYRADDINRYLVQHIGKIEPYEWHQCSVPTAAH
+TPGMYGNAYHQNVG-SRELTYGPETSAEHDAEGAVAELLGGLAVRSPDVPLALIGGAA
+>2_2317
+MSRAVVAVAKQENNPTSIGLTQYLDPSYWTWAAEDANGAALLQQGAGPILTYIVQRLEAV
+GCEVVEAYGIVHDKDEREVWSDTEKALVVEPKPDHLHAVIKFASRSKSAPLDRLAFGIGV
+EPQYVEKPGRGRYAFDNMLSYLTHVKYADKHQYAPSEVATVRGPDYLGIDALRRETWLKG
+RAHVKKRVVAENFEDMRERVLQGEITRDQIMLTDGLFDIYSRHQREIDDALSAYGQRRAY
+RAAAKLRAGDFSTHVVFVHGDAGIGKTRFATDFIMAAIDAANANGERWQVYRAATGNPLD
+DWRGEEVLLLDDLRASAMDANDWLLLLDPYNASPAKARYKNKGEVAPRLIVITATIEPVE
+FFFYARQKGNVDEALDQFIRRLASVVKVFRADDINRYLVQHIGKIEPYEWHQCSLPAAAH
+TPGVNGNSYHQQVAPSRELTYGPETSAEHDAESAVVELLSGLAVRSPDVPLALIGGAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002207.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002207.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4fb0b4e7e126504d321e1d9d38af134abe93d02f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002207.fa
@@ -0,0 +1,10 @@
+>1_736
+MSAVTPPQTTVDGAAASAARRVELRPVGAQDHPLLHRWVTSPHAVYWEMTEAGLADVVAE
+YEAIAAHPHHHAHVGLVDGTATFLVEVYDPAHSELAGRYAGAPGDVGLHVLVAPTDTPVP
+GTTDLVMAAVVRWCLAQPGARRVVVEPDERNAAIRAKNLAAGFTELGPVALGSKTAMLSI
+ATPESFTASRIGVLAAGLDLTLPEPPLLLTPDRQVSA
+>4_955
+MSAVTPPQTTVDGAAASAARRVELRPVGAQDHPLLHRWVTSPHAVYWEMTEAGLADVVAE
+YEAIAAHPHHHAHVGLVDGTATFLVEVYDPAHSELAGRYAGAPGDIGLHVLVAPTDTPVP
+GTTDLVMAAVVRWCLAQPGARRVVVEPDERNAAIRAKNLAAGFTELGPVALGSKTAMLSI
+ATPESFTASRIGVLAAGLDLTLPEPPLLLTPDRQVSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002210.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002210.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0506384aa9ffda109bd641a1df0d8f9f336e0ec7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002210.fa
@@ -0,0 +1,12 @@
+>1_739
+MKAYRGLAALGQAMPVDRDEYPQWTMTVRATWLLAPRLRRLTFAAEEFRTFTPQGCDEYF
+GLLTPPPGRALVMPDPAALNARRAVGRIPEDVRPDLRWYTVAEHRPSVGEIDVDVVVHDH
+AGPAGTWARTARPGDVAGFRTGTGAYRLPAAGESHLVVGDETAVPSIAAALAAQRRTPRG
+GRMDVVLEVPGRDHVPALEVPEGATLTVLHRGDAVPGALLTPHLEDLPAAPRDHVWACGE
+QSLATAARRVIVRRGIAPKRAIMFSGYWRVDGPRL
+>4_958
+MKAYRGLAALGQAMPVDRDEYPQWTMTVRATWLLAPRLRRLTFAAEEFRTFTPQGCDEYF
+GLLTPPPGRALVMPDPAALNARRAVGRIPEDVRPDLRWYTVAEHRPSVGEIDVDVVVHDH
+AGPAGTWARTARPGDVAGFRTGTGAYRLPAAGESHLVVGDETAVPSIAAALAAQRRTPRG
+GRMDVVLEVPGRDHVPALEVPEGATLTVLHRGDAVPGALLTPHLEDLPAAPRDHVWACGE
+QSLATAARRVIVRRGIAPKRAIMFSGYWRVDGPRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002220.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002220.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2da027fcbefa1cb6cd5d76bd0258435ca7a6275
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002220.fa
@@ -0,0 +1,10 @@
+>1_1919
+MTAPQLHLPRTVVSDQTDRAVDLLGHYFTPGKFIGGRWDGFDPSGTRAASANVFTSDDVA
+SAALLNTPVPGHAVVHLLITQRVHFAGLLEAVGPDRDFIDVDPDPSGKDMAPVYELYEAL
+KTLPKIGPTIASKLVARKRPRLFPIIDAELRQTVFHETRKDGYVGRALLHAEFSAQERTI
+WQRLASYHSAASLPTEVSVLRVFDVLAWMEAKAYWGPVP
+>2_440
+MTAPQLHLPRTVASDQTERAVDLLQLYFKSRKFIGSQWDGFDPSGRRAASANVFTADDVA
+SAALLNTPVPGHAVVHLLITQRERFSELLRIVGPDRDFIDADPDPSGKDMAPVYELYEAL
+KDLPKIGPTIASKLVARKRPRLFPIIDSDLRRTVFHETRKDGHVGRALLHADFSAQERTM
+WQRLESYRCAAALPAEVTTLRVFDVLAWMEAKAY-----
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002221.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002221.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e41aed49580788285175c80a4dcb2633cf5ff024
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002221.fa
@@ -0,0 +1,12 @@
+>1_1929
+MTARPVAPGIHLVQHANVNCYLIEDTDGLTLVDAGLPAVWRPLGHAVRALGRRPEDIKAL
+VLTHAHFDHVGAARRLVERLGVPVYAHRAEHYLAAHPYSYAHENPRALYPLRHPAALPIL
+GSMVAAGVFTVKGVRATAELTPGETVPVPGRPVVVPSPGHTHGHCALHLPDRDVLISGDA
+LVTLDPYTGRRGPRIIAGAATADSGLALRSLDALAATGAGTVLPGHGEPWHSGVASAVEE
+ARRHGPA
+>4_2167
+MTARPVAPGIHLVQHANVNCYLIEDTDGLTLVDAGLPAVWRPLGHAVRALGHRPEDIKAL
+VLTHAHFDHVGAARRLVERLGVPVYAHRAEHYLAAHPYSYAHENPRALYPLRHPAALPIL
+GSMVAAGVLAVKGVRATAELTPGETVPVPGRPVVVPSPGHTHGHCALHLPDRDVLISGDA
+LVTLDPYTGRRGPRIIAGAATADSGLALRSLDALAATGAGTVLPGHGEPWHSGVASAVEE
+ARRHGPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002223.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002223.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85b945b86a2caae9b7dbcff33d5173b215f3d350
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002223.fa
@@ -0,0 +1,4 @@
+>1_1972
+MRVTSPQTLISAVFEAAERATNDLTHLIPDLDRDRAEYAVASVLLEEAWLSNR
+>4_1100
+MRATNQQALITAVFEAAERATDSITHLVPDLDRDRAEYALVSVLLEEAWVAQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002234.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002234.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e2fed3a1fbddfd0a957cbb7958b4bcdb2af49f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002234.fa
@@ -0,0 +1,16 @@
+>1_2245
+MPEAVIVSAVRSPIGRARKGSLRDLRADDMAAQMVTAALDRVPELDRAEVEDLILGCGAP
+GGEQGGNLGRVVAVLAGLPSVPGTTITRFCSSSLQSTRMAFHAIRAGEGDVFVSAGVESA
+SRLDRGASDEDTRNPAFRSAWERSARRAEGDAPVWTDPAEEGELPDVYIAMGQTAENVAQ
+LRGVSRQAQDEYAVRSQQLTEKSQASGFWDREISPLVLPDGIRVTRDDSPRAGTTLEAVS
+QLNPVFRPDGTVTAGNACPLNDGAAALVVMSDTRAAELGLTPLARIVSTGLSALSPEIMG
+LGPVEASRQALARAGMSIDDVDLVEINEAFAAQVLPSAEDLGIPLDKLNVNGGAIALGHP
+WGMTGARITATLLNSLREHDKHIGLETMCVGGGQGMAMVIERLS
+>4_278
+MPEAVIVSAVRSPIGRARKGSLRDLRADDMAAQMVTAALDRVPELDRAEVEDLILGCGAP
+GGEQGGNLGRVVAVLAGLPSVPGTTITRFCSSSLQSTRMAFHAIRAGEGDVFVSAGVESA
+SRLDRGASDEDTRNPAFRSAWERSARRAEGDAPVWTDPAEEGELPDVYIAMGQTAENVAQ
+LRGVSRQAQDEYAVRSQQLTEKSQASGFWDREISPLVLPDGIRVTRDDSPRAGTTLEAVS
+QLNPVFRPDGTVTAGNACPLNDGAAALVVMSDTRAAELGLTPLARIVSTGLSALSPEIMG
+LGPVEASRQALARAGMSIDDVDLVEINEAFAAQVLPSAEDLGIPLDKLNVNGGAIALGHP
+WGMTGARITATLLNSLREHDKHIGLETMCVGGGQGMAMVIERLS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002244.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002244.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e0c97b89a3058e917a0e7b187c1d2a09106972f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002244.fa
@@ -0,0 +1,24 @@
+>2_108
+MNPTFSRRTGLRTLAAAVVAGTVTIQAPAVLARTAASTPA--AGADGFRVLPYLMEPTAT
+SMDLVWFSEREVPGTVVVSGPGLGDNHRGGRTRPAGTRVSTPEFQPLLAYTEKERAQSIK
+GLAQGSWLLGPASYKHRVSLTGLKAGKEYRYTVTQGGQRHTAAFRTADDGANWSDLRLIA
+FSDTETEPYGRIENREWELSMVTPYTEGSLPRPGEGSVWHQTFGSTTRYGQFTLKYPLTQ
+DVALRENIRHIDAAAPDLLLVAGDLGQGGGYQPGWDEFFRHFAGEHSDIASRVPLITSLG
+NWETFAALNDGYGTAADRSPVVRSRNKYHAYFERTSAGTDRENPRFRGSYYRTDHGPLTI
+LTLDSTNGVPDESVGAGLLSGAPFSGDDRNLTAATMPSDTQGSFTQAEYEAAFPTVFPGS
+TPADADLPVLNPGHEQWAWTERQLADARAAGRIVIVEFHHAAYSVGVHGTPPNHEFPDDQ
+SGVAMRVYTPLFEKYGVAVVISGHDEMFQRSWVDEDGDGVGFHSYDVGVAADGLRGEQYA
+KDASGQWKPVRFNTHMEWTANTHEPETWADVDGVRQLVDGGMHYGHLQIDLKRRGREAEM
+TLTPMYVFPILDDEYRLVRTERRAYDDVQTVRFDRRGVPKPRR
+>3_76
+MNPAFSRRTGLRALAAAVVTGTVATTAPAALAKTAQHAPAVPAGADGFRVLPYLMEPTAT
+SMDLVWFSERPVAGTVVVSGPGLGNNHGNGRTRPAGTRVSAPELQPLLAYTQKELTQTLT
+GLPQGSWLLGAENWKHRVSLAGLKPGKEYTYTVTQGGRRHTASFRTADDGRDWSDLRLIA
+FSDTETEPYGRIENREWELSQVTPYTEGSLPRPGEGSLWQQTFGSTVRYGAFTLKYPLTQ
+DVGLRENIAHIDAADPDLLLVAGDLGQGSAYQPGWDEFFRHVAGEHSDIASRVPLITALG
+NWETFAALNGGYGTPADRSPVVRSRNKYHAYFERTGAGTDRQNPRFRGSYYRTDHGPLTI
+ITLDSTNGVPDESVN-GPLSGAPISGDDRGLTAATMPTDTQGSFTQAEYEAAFPKVFPGS
+TPADADLPVFNPGHAQWAWAEEQLADARAKGQIILVEFHHVPLSIGEHGTPPNHAVPDDQ
+SGVAMRVYAPLLEKHGVAVVISGHDEMFQRSWVDADGDGVGFHSYDVGVASDGLRGEKYA
+KNAAGEYEPVRFNTHMEWTANTHEPETWADVDGVRQLVDGGMHYGHLQIDLKRRGQSAEM
+TLTPMYVFPILDSQYRLVRTERRAYGDVQLIRFDRNGVPLPRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002250.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002250.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab8252464ae5fac9ab98e9dc5cad6e9eaff87bd6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002250.fa
@@ -0,0 +1,28 @@
+>2_325
+MSAEEKNLPHGEESTTVGEMNDTVATGLPEEPRTEEGADAPQGARAENPQSDAAAGQCPV
+AHG-GAALPHPTSGDANQQWWPNRLNLKILAKDQPVQSPHEADFDYPAAFEALDLAEVKE
+TIAEVLTTSKDWWPADFGNYGPFMIRMAWHSAGTYRVTDGRGGAGEGQQRFAPLNSWPDN
+ASLDKARRLLWPVKKKYGQSLSWADLIVLAGNVAHEIMGMPTFGFSGGRIDAYEPADDVY
+WGPETEWTNGGAERYKGERDLDNPLAAVEMGLIYVNPEGPEGEPDPLKSAKDIHETFSRM
+GMDAEETVALIGGGHTFGKTHGAGPVEPHIGPEPEAADLEQMGLGWKNTYGQGKGRDTIT
+SGLEVTWTYHPTRWDNEFFHILYAYEWELMESPAGAKQWRPVNGGGSDMVPESDFQGRRE
+PRMLTSDLALRFDPVFGEISRRFKDDFAAFQDAYSRAWFKLTHRDMGPRPRHRGVEVPQE
+ELLWMDPVPAPESVPGDAEVKAVKDAVAQAGLSVTDVVKTAWAAASSFRSSDFRGGANGG
+RIRLEPQRSWEVNEPAVTGPVIDALEKIAQEAGVSFADTVVIAGNWAVEKAAADGGVQVT
+VPFTPGRGDATAEQTDVTSFGHLEPKVDGFRNWDPRGSKTFPAEFALVDRANLLGVSAPE
+MTVLVAGLRVLGAVHGDSQDGVWTDRVGVLSQDFLTAVTDIDTQWEKVAEGRYRGVTADG
+RELTGTRNDLVFGSNPELRTLAEVYAADDAREKFVQDFVRAWAKVMDADRFDAK
+>3_266
+------------------------------------------------------------
+MHGKGASLPHPTSGDANQQWWPNRLNLKILAKEQQVINAHDADFDYPTAFAALDLDEVKK
+TIAEVLTTSKDWWPADVGNYGPFMIRMAWHSAGTYRSGDGRGGAGTGQ----PLTARP--
+------------------------------------------------------AADD--
+-----------------------------------------GRP----------------
+---------------------------PH-------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------------------------------------------RVGARSA
+------------------------------------------------------------
+--FPPGAG----------------------------------------------------
+------------------------------------------------------------
+---------------PCL-----------------------------------Q
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002260.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002260.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7cc199036f926d2362ec3a3e03c00b31992c5ecc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002260.fa
@@ -0,0 +1,4 @@
+>2_455
+MTVAITRLDPVGADRAEPIALLTGSAWPFPVRPHVTRPVAKEAIEDGGRHHTLSGHQLPM
+>4_2136
+MDVTFTPLDPAGADRDALVALLTENAWPFHTRPRVTRPEAEKAVDDGS------------
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002262.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002262.fa
new file mode 100644
index 0000000000000000000000000000000000000000..27c34f295aabafb9afc0bff203e86729ade33e40
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002262.fa
@@ -0,0 +1,8 @@
+>2_473
+MDEDQGKILATHRQELRRGTLVVACL-------LACRTPRYGYALLEHLAD---ARLDAE
+ANTLYPLLRRLEGQGLLQAEWNTDEPRP-RKYYRTTPEGEAIVAELRGDWLRLTDSMTRL
+GKDPS---------
+>2_747
+MNEPTDRPPSGTAPEAWPSAWVRAALEPAILGSLA-GGPLHGYGIAHALADHGFGRL--R
+GGSLYPVLGRLEEAGHITARWAPGDAGPGRKDYELTDAGRAAYRDAVANWRRLGDALADL
+GATPRLTAQEGTAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002265.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002265.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08f0f2948a79ce224414fdf66213ef951445d413
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002265.fa
@@ -0,0 +1,12 @@
+>2_492
+M---------TATPRPAARRFLEVDVFATGPLTGNPLAVVVDAEGLPAERMQALAAWTGF
+SETAFLLPPTDPEADYRVRIFTPREEFDFAGHPTLGSALAWLHAGGTPRTPGR------L
+VQECGVGLVPVTVADDGVLAFATPPLRRSGPLNEADVVRIAAGLGVEREAIVDHAWGENG
+PAWQLVRLTDADAVRALRPRGHAELKVGVVGLEAAGAETACEVRAFAYGSEDPVTGSLNG
+ALAQWLRGAGLVSPRYVAAQGSQVGRRGRIHVHDDGARIWVGGRAAVLVDGTIAL
+>3_427
+MTESHAPFPDSSPARP--RRFLEVDVFATGPLTGNPLAVVVDAEGLTDGQMQAVAAWTGF
+SETTFLLPPTDPAADYRVRIFTPREEFDFAGHPTLGTALAWLHTGGTPRTPGRGGGSTAL
+VQECGAGLVPVTLAGDGLLAFATPPLRRSGPLGEEDVRAIAAGLRIDRDAILDHGWGDNG
+PGWQLVRVADAEAVRALEPRGHEELKVGVVGLEPEGAETAYEVRAFAYGGEDPVTGSLNG
+ALAQWLRGAGLVPPRYAAAQGSQVGRRGRIHVHDDGARIWVGGRAAVLVDGTLTL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002271.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002271.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba53f814a046c36a344088069695c155bcf1ee7a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002271.fa
@@ -0,0 +1,10 @@
+>2_540
+MSETIERAYPHAPTADDAPLDTAALAVCTTVLQQGAADLRRRFGPVLGEAVVDRQIEDSL
+EELRRSGVPRTHRESTAIHFAESRLLALAETTGVVEPSVPRVLFVCLQNAGRSQLAAALL
+AERAGDAVRVSSAGSRPTPEVHDDVAPVLSEIGADPAAAYPKPVTPELLAAADYVISLGC
+SDECRERTGVEVRDWPVGDPAEADWERLQEIVADIERRVDALWAEIQGRFAA
+>3_468
+MAEAHPAVAGTGPSPSTGPLPRIGEHV--GILAHGAAELRRVFGPALGEETVDRIVEESA
+AGLSPAAADPAHRESIAVRFAHDRLASLADARGVTRSGVPHVLFVCVQNAGRSQLAAALL
+AERAGDAVRVSSAGSQPAGRIHGNVQPVLTAHGADPARIFPKPITEEVLASADYVITMGC
+GDDCPVRLGQDARDWPVGDPAEVDWDRLQEIVADIEVRVDALWREISG---A
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002277.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002277.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4420aee4fabb13f1eb5bd26daed6159e1bf8f1ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002277.fa
@@ -0,0 +1,8 @@
+>2_626
+MSGGAQSVSVRVHGDSILGQECLKSMMWPWSVERLGLPCVGLSWGVPGETFKVQGAYARE
+PVRYEDLNFQEIGLVGEDFGRGRPAWPDRCFSLELFPEYSPEVAWLRLRVVEEAGAQVFR
+AQVTLRPRSEGRGCEADLDWWESRLGALPAQMREWARS
+>3_2172
+MSGGAQSVSVRVHGDSILGQECLKSMMWPWSVERLGLPCVGLSWGVPGETFKVQGAYAQE
+PVRYEDLNFQEIGLVGEDFGRGRPAWPDRCFSLELFPEYSPEVAWLRLRVVEEAGAQEFR
+AQVTLRPRSQGRGCQADLDWWESRLGALPAQMREWARS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002281.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002281.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cd622785f907a91ed481f80d6dbf638de749969b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002281.fa
@@ -0,0 +1,10 @@
+>2_695
+MTQRRTRWRSAASQDAEYRAHWKA-AASADVGTPDALTWAVLGDSAAVGVGAARVEESYV
+AQVAAGVAERTGRPVRVLNLAVSGATAAHVLADQLPLLPADGVDAVTCVVGGNDVAWPVR
+FRVDRFAAPLEKIAQRLPAGATLGTVPVFRIPPYESRVECANAAVRVIAARHGLGVADVH
+AATRRTSLRHQVSMLSHDLFHPNGAGYRDWARAVLPEVLRQVRGEAPTR
+>4_1972
+MPS-PSGWQ--AQHDADYRAHWHALAARAD---PDALTWVVLGDSAAVGIGAESVERTYV
+AQVAERVAAETGRPVRVVNLAVSGAMAKDVLADQLPLMPASGVDAVTCVVGGNDVTWAWR
+FREAAFEEPLEAIARALPAGATLGLVPTFRIPPFEARVRRANTVVRRVAARHGLGVADVH
+AATWRRNLRHQVSRLARDLFHPNGAGYEDWAAAVAPEVLRQVRGQAPAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002285.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002285.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f39270b96ef47a861b923c5bb0d63b337f7d5906
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002285.fa
@@ -0,0 +1,14 @@
+>2_755
+M--------AGGEAAVAWILGALRRELGAANLGEEDLEIVVERDRVWGSLWTVTAQGRRF
+WFKRPHACLRREVPLRRVLSARAPGELLSTVAACAETGWQLTADQGPVLAQRARED-GPS
+HYVELARSLARVQKSLTAADVA----ELRNIGLPVFETGDAVARLDEQLGWFSGLPAGHP
+AQCTAAERERAIEGMSVLVERWAVDARMLEGVVPELSVDHNDLHGGNAFVTAEG-VRLSD
+WGDTVLAHPFASLRALLVPVRNVFETEAMEQIRGAYLAEWGLGEDVG-DVLDLAMMLAVP
+QRLSCWSALADADAWAEYAEYIAPLWREIGTPVAEVEVP
+>3_2348
+MTGTGVLDVAGRTAARDWIAGVL-------DLPAAALTVRVVRERSWGDVWRLSSPAGVH
+WFKAPHPRLRGEVPLRALLESRAAERVLPLVAADHERGWQLTADAGRTLAALARDDAGAP
+RPGEVARLYAGLAGALAAMQEAVGEDDLRGRGLTEFDPAKAELSLLRELAPFRALPAAHP
+AHCTAEEEARAVAVRAALAMRW----EDCGGPADPLGLDHNDLHGGNAFLGADGRVLVSD
+VGDAVLGHPGASLRALLVPVRAEHGADAAETVRTAWLAARGQDHAAGRERLELAMLLAVP
+QRLRAWGALRSPETWAAYAEWITALWRDIGTPVDQLTTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002287.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002287.fa
new file mode 100644
index 0000000000000000000000000000000000000000..14b7fc3950459817b8af2ea99772768dc17bc92e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002287.fa
@@ -0,0 +1,8 @@
+>2_833
+MALFRKTAAWGATAAGAVALAAAAMAATWTGPGYTVVNDHSNIFDYKGSIKTTSCVRQSD
+GTHLIGGYIRYVQGGRDTGRLWTPTATSCGQTVSRSTTFKDSLALNAPKTQFYYGLNKAP
+YGALSEPLGGN
+>3_771
+MG----------------------------------------------------------
+-------------------------DSRCGQTVSCSTTFGDSLGLNAPRTYFNFDLNDVP
+YGALSEPVDGN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002291.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002291.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a1eae05c69d8761d555fd5fb3f9d96e5b5024d53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002291.fa
@@ -0,0 +1,10 @@
+>2_888
+MSTRSSI----PDAVDTDRTAGTIELLEPPREAVEWMASPAPATDLWWTATVCGEADPDW
+HRLET-------------------------------------------------------
+-------------------------TVAETIEVLVSWAQGHGLPLPYGAALRTYGNPPDL
+GL--VA
+>4_1811
+MSAPGSITADGARGLATHRAPGAVELVEPPREAVEWMASSAPATDLWWTATVCGEEDPGW
+HRLESAAQIADLVHALTDPRDKLILEDEPPTRYAQIMLLGDGLFMVEIAKRFEGLGAYNW
+RIGRGRAADEAANDPQDLVQPLQELTAAETVEVLVSWAQGHGLPLPYGAALRTYGTPPDP
+GLGFDS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002297.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002297.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e08d7fa6ef852f1b7cb8d181a3f85e248cbba4bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002297.fa
@@ -0,0 +1,22 @@
+>2_940
+MAQNTAGEGLLESIRQGYSFEDATVTLGAAVVDGQVHADAPVRLPLRMMNRHGLVAGATG
+TGKTKTLQMMAEQLSSAGVPVFLADVKGDLSGLAVAGEASEKLAERTTATGMPWQSQAYP
+VEFLALGGDGVGVPVRATVDAFGPVLLSRIMELNETQESSLQLMFHWADQRGLAMDDLAD
+LKAVVTHLTSDEGKADLKGLGGVATSTANVILREVTGLEAAGMAAFFGVPEFETAELLRV
+APDGRGVISCLELPTLAAKPQLFSTFMVWLLADLFAELPEAGDLDQPKLVFFLDEAHLLF
+DGASKAFLDAITTTVRLIRSKGVGLFFVTQTPQDLPAEVLGQLANRVQHALRAFTPQDAK
+ALKQTVQTFPTTEYDLAETLTSAKVGEAVVTVMDPEGAPTPVALTRMWSPQSAMEPAPEE
+AMRQIVGASALLPVYGTAQDRESASEVLSAQAAA-----AAPSTGGSARGSAAGAGDTRV
+ADGHGGGTVVSGVDLGDIEALRREEEKATARARKEADKPSDFERAMGNFMKSAGTQLGRE
+VVRSVLGTRGRRGGGLLGGLFRR
+>3_881
+MAENTA---LLDTLRAGYTFDDPTITLGAAVVDGEVHADVPVRLPLRMMNRHGLVAGATG
+TGKTKTLQMMAEQLSAAGVPVFLADVKGDLSGLATAGTASDTLTERTRATGMPWQAQAYP
+VEFYALGGDGVGVPVRATVDSFGPVLLSRIMELNETQESCLQLMFHWADQRDLPLDDLKD
+LKAVVVHLTSDEGKADLKGLGGVSTATANVILRKVTGLEASGMDQFFGVPEFETAELLRV
+APDGRGVVSCLELPTLQSKPELFSTFMIWLLADLFAELPEAGDLDKPKLVFFLDEAHLLF
+DGASRAFLEAITTTVRLIRSKGVGLFFITQTPKDVPGDVLAQLANRVQHALRAFTPEDAK
+ALKATVQTFPKTDYDLEEVLTGAKVGEAVVTVMDPDGAPTPVALTRMWSPQSTMGPTPED
+AMKAAVAASPLMGQYGTAQERESAAEKLAAQAAAPQGETAVPATGESAR-----------
+---DGGNVTVSGVDLGNIEEIRREEDARARRAQEKADKPSDFEKAMGNFMKSAGTQIGRE
+VVRSVFGTRRRSGGGLLGGLF-G
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002300.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002300.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e4cd32ba4b06c742090849507fbb7a9f33b13e3c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002300.fa
@@ -0,0 +1,16 @@
+>2_990
+MTDAGPQGPAVPVRTRRVAHPGRVTAVVLVVAALVAAAFLAGRFFQPPSTAADNEAAATP
+IDVWAHAEERVIDDGSSYVATVAAGRTRTVTVAADGPAVVLRQAAEVGEMVRPGDAAGEV
+SGVAYVFLPEPLALYRDLTEGDRGEDVASLQRALRQTGRWTATDGVFGDSTARALRETFR
+GAGSPLPEDEPVTVGWRQFIPVSDDGAVVTAAATYGATL------TEDRPLLELQVSAPT
+IRFTADVTQATALEKGQEVEVSGAFGSLHGTIAKIGEFAAAEGSERAGHPVTVAFDATAE
+DAPPVGQSVTVSTTAAEDVPAMLTVPQTAVRVEGASSYVVVQVPASAREGSASSAPAERR
+VPVTVERTGGGYAAVSGDLAPGDRVKVS
+>3_934
+----------------------------MLVLALLAASFVAGRFFQPPTT-ADPAAVARP
+IDVWAAVEQRAVDTTASFAGTVAAGKTRSVAVQAEGPAVVLRQTAKPGESVRPGDVAGEV
+SGVTYVFLAEPLALYRDLTEGDEGEDVASLQRALQKAGHATDTDGVLDSGTARALRELFA
+EAGDPLPEDAPVTVSWHQFIPLGKDGAQVTAAAGVVSALYPAWVASRQRPADALR-----
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------G
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002320.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002320.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92c9904e6cee60e6d7f08387c86ccfd2f7f8a4eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002320.fa
@@ -0,0 +1,6 @@
+>2_2273
+MTAFGIIWLIAVTLVSAVAVRGILRQSTGVHAADRNGSTSFLWFLVALAFLLTNLPSGID
+PFRAVGLHLGAAALLGFLLHVLTRGAPAARD
+>3_2135
+MTVIGIIWLSELTLVSGVAVRGL---------------------------LLTHLPSGID
+PFRAVGLHLGAAALSGFILHVLTRGSASRAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002326.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002326.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5e93a2b5633ef8ede8335c1bcb226c67b6e88ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002326.fa
@@ -0,0 +1,14 @@
+>2_2593
+MATLAEQVQGERMARVALSMIAEPNDPITGYVLARHGGVETLRLIESDDEVPGLARADTL
+MWRERLTARVTPGLLDQMAQA-ERHGFGTLIPADKEWPAGLNDLSDRAPYLLWTRGAVSF
+LMTALSDRATITGARAATAYGEQVAGELAAGLADEERVVVSGGAYGIEGAAHKSVLAASG
+QTIAVLAGGLDRPYPAGHSELLNRIGDVGLLVSELPPGAAPTRHRFLARNRLLAALSGAT
+VIPEAGPRSGSMTTVIAARELSRGVGAVPGPVTSVASAGPNELIKQGFASLVTQPSDVID
+LLDADRTPDRTVTRPEVGREFG-HRHPSPGTPGRSL
+>3_1734
+MSGVAGLGVDERRARVVLALLAEPDDPVTGGLLRRLGAVETLGLLDTDTTVPGLGRVDGQ
+VWRDRLTSQGRLDGLDQRLRVLEESGIVILIPGDAQWPRALDDLGERAPYVLFVRGAASF
+LARPMQDLVTVTGSRAASAYGEYVAAELAGDLANRERVLVAGGAYGVESAVHRAALAAGG
+DTIAVLAGGVDRPYPSGNRDLLDRVGDVGALVSELPPGSVPTRHRFLARSRLLGAMSAAT
+VVVEAGARSGAIGVAAEAHQLGRQVGAVPGPVTSVTSHGPHELLRAGHARLVTSAADVEE
+L-----TANRATHRPGLSADFTRHTAPAAGPPERSL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002330.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002330.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e26edd37e4b316363052df066a05a0d2c349ab0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002330.fa
@@ -0,0 +1,12 @@
+>3_42
+MAAVPDSLKLEGARFVGRSLRGARFIDSDLSHVRARGVMLDGADFDSPWLLDGEGSLVVN
+GVDVAPLVEVELNRRFPGRAQRRAEDAEGLRGAWGAVEASWRQATDRASALPDGAVDVSV
+EGEWSFSQTLRHLVFATDAWLSRGIQGAEEPFHPLGQPRAGAEDDGVDLAFFASTPPPYE
+QVLAVRSERLAQVREFLASVDDAGLDEERRHPWSPEYPETVRSCLHVILEEEWEHLRYAL
+RDLDALDDAAAQGR
+>3_1184
+MPAL-------SAGACG-------------------------------------------
+-------------------TQRRAEDAEGLRGAWGAVEASWRQATDRASALPDGAVDVSV
+EGEWSFSQTLRHLVFATDAWLSRGIQGAEEPFHPLGQPRAGAEDDGVDLAFFASTPPPYE
+QVLAVRSERLAQVREFLESVDDAA------------------------------------
+----------AQGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002331.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002331.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e8cd24afbf999126274f1a5e97667f3821175c87
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002331.fa
@@ -0,0 +1,12 @@
+>3_44
+MRLIALPSGESIPVLGQGTWGWGEDPGRRGDEVAALHAGLELGMTLVDTAEMYADGGAEE
+VAGEALAGRRDEAFVVSKVMPSHASRSGTIAACERSLKRLGTDRIDLYLLHSQGRYPLED
+TVSAFHQLVEDGKIRYWGVSNFDHRDLADLQDVPGSSGLATDQVLYNLSRRGPEYDLLPW
+CADHQLPVMAYSPIEQGRILHDTTLNDVAARHSVSPAAAALAWVLRRDSLCTIPKASSPQ
+HVRDNATALDVELTRDDLDALDRAFPPPSGPRPLEML
+>4_1935
+---MTLPSGESIPVLGQGTWGWGEDPGRRGDEVAALHAGLELGMTLVDTAEMYADGGAEE
+VVGEALAGRRDEAFVVSKVMPSHASRSGTIAACERSLKRLGTDRIDLYLLHWQGRYPLQD
+TVAAFHQLVEDGKIRYWGVSNFDHRALAELQDVPGSSGLATDQVLYNLSRRGPEYDLLPW
+CTDHQLPVMAYSPIEQGRILDDTTLNDVAARHSVSPAAAALAWVLRRDSLCTIPKASSPQ
+HVRDNATALDVQLTREDLDALDRAFPPPSGP--VKSF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002334.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002334.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1e374ff4fd95230e02f470b8431bb06168c4d40b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002334.fa
@@ -0,0 +1,18 @@
+>3_293
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------MRQDAGAQTVGNVVSTIAVSAGTGALA
+GSVLPGLGNVVGFAAGVVSGVAMAVPVADTDGDGQKDSVAEMAGDVAEGAWNWIRGK
+>3_321
+MTTSYVTKVGMSEWESADSMDQLAHGVTVAASSLAEVVSDQDATWQSLGNHYEGDGEGDL
+VNGFFVPVENAARVVLAAEALDKAFLDFSNALRGLWADRRVFETEVDTYNSMYGAQAIET
+LPPGVDSWRAALASMPADLERRYQQAASTCASAVRTIDIEALDLDSVSEGRPGQLGREIV
+AEAAKNALPLDPENPSTSALGLLDVARVREPWLRFDDVIPETWQARFMGLNVGPLGASVY
+AGGAAMVRAAQTRSWAPLRNVPLAMSMTMRNYSNDMAALALRYEDPRKFRRPTWPAFKSQ
+FLDGLPVTGFIRSTVPLWGKRTPATVGAPAPAMAGAYRVESRGAFRLNAGVKGLGAAGTL
+VGAGLTYRDEYDQQLRENQAETPGASREEVESEARQDAGAQTAGNVLSTIAVSAGTGALA
+GSVLPGPGNVVGFAAGVVSGVAMAVPVKDTDGDGQKDSVAEVAGDLAEGAWNWIRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002337.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002337.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a800c52d9106aefea5cb506ee22c9e3174a41a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002337.fa
@@ -0,0 +1,14 @@
+>3_313
+MGAPREL---------------FAEHALRGEIVV-----LDYAAGRTRSGLPVRRHHVVV
+RAGDRLVHSFRWYVGAAREVFEVTLT----FDEEWLPHRLWEPVAEAVRSARAPLAGEVD
+VPAVVPGAWDERPETVVVESGPGLDVAESLVEGLEVISASRKRWRSWSEADEVEQ-AVVR
+SMAPTLSARGGLRGRRTEVDVYAVLD----EAVVVRRRWWGDQGTEIIEREVLRVPGRVA
+PWAMFVGMDVRAGWMREVSARRPVDAEARSSDAEWEVIAGGERALGLLHGPRDVWAVSTG
+GGGLVAEWWQLPGEGLLGVFRDADSAQMMVG-PVDGWTIYLLVLEAWLA--------
+>3_319
+MHPTVALRHFTEPADGNVASASFREAFLGGQEVVEGFLLLSYEAFFTGRGLPGRRHHVIG
+WEEDLVWHSVRWYVGSGAEIVELTLTAEAGADLEIWGGQCDRMIRNVVCQGAPEPASNLC
+WPEVPADVRAQDSWEVVTEQGLNPPWLESLRAGYDAVQ-EQAPWSAWAREPSLEQRRVLE
+QELPILSGVGERSGQGFRIE--ACLDGRGGAVVVVVPEGEGD-GTN-VRRGVRTVPVSLV
+VPVLLTWAGLRADWLRDEVMEAPGDVAPTEMAELWRGRRGADGVGS--EASADWWRWWNQ
+EGEVVAEWVQPLHRAPLAVFRDESRC---VGVPVMPGVLY-SVLQATVQEIAGSPHM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002340.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002340.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0b36d7ebb1f53121fa7cb1f7fcc2f01caf46f0e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002340.fa
@@ -0,0 +1,22 @@
+>3_408
+M--------------------------------------------------------GK-
+----------------VRGDQAVQS----------------LQPHKVL---------DSD
+SSHGRLIRQQGERVPTDGDFTLSDRAQKEIVKLFIASESSLEGRTIGEWFSEDFFESNFW
+TYWATMFAFETWHSLAEMRRYLLRFVHAIDGLADFSALKFNRYDQYDSMVKPLLAYLEPH
+GVDFRYSTTVRDVRVETADGKVRAERLLLTVDGVQQEQEVGEDDLVSVTNGSITESTTYG
+DHHTPAPSTTEPGGSWTLWENLAEQSPLFGRPGVFYRGLPERSWFVSATATVESREVEEH
+IERLTQRPLHDGKVNTGGIVTATDSPWMLSFTVHRQPHFPTQRPDQTIVWIHALYSDTEG
+AYVKKPVTECTGEEITQEWLYHLGVPEDRIPEPAAQESVNTVLVYMPFITSYFMPRRAGD
+RPAVMPEGSMNLAFIGNFAESPTRDTVFTTEYSVRTAMEAVYTLFDVERGVPEVFASATD
+LRELI-------------------------------------------
+>3_1162
+MQYTAGNYEAFARPRPAQHAQETKAYIVGSGLAGLAAAVFLIRDAGVPGANVTILEKGEI
+AGGALDGLDVPEKGFVIRGGRELENHMECLWDMMRSIPSLELEDASVLDEFYWLNKDDPN
+YSLRRATVRRGEDAGHEGRFDLPKRAQKDLLKIFLAERAEMEGKRIDEVMGREFLDSPFW
+MYWRTMFAFEEWHSALEFKLYLHRFIHHIGGLPDFTALKFTKYNQYESFVLPLMHYLTEH
+GVVFRSGTEVLDVDFAHRNGEIRATAIRCRRDGAEETIELGEHDLALMTIGSLVDNSDEG
+DHHTPAALNEGPAPAWDLWKRIAKKDPAFGRPEVFCSSIEETKW-ESATVTTLDERIPAY
+IERIAQRDPFSGRVVTGGIVTAEDSSWLLSWTVNRQPHFKKQPKDQIVVWVYGLFVDVDG
+DYVKKPLAQCTGEEITQEWLYHLGVPVEEIPELAAT-GARCVPVMMPYVTSFFMPRRAGD
+RPQVVPEGAANFAFLGQFAET-GRDTIFTTEYSVRTGMEAVYELLDVERGVPETWGSTYD
+VRDLLEASARMRDGKKVEMPGPAALRGYLRGKLEHGEIGQLLEEHGLI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002350.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002350.fa
new file mode 100644
index 0000000000000000000000000000000000000000..112147ffa12cb6655e4d69f41009941f002bcf11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002350.fa
@@ -0,0 +1,6 @@
+>3_651
+MHAPFYSRAIPVHQIATITCGPDDGMNHGLLNWFVTGLATSPDGLRINNGGQAHIDMSTT
+EGLRSVVVVDDLSQTEQLICAVRTTCSR
+>4_1956
+MHAPFYSRAIPVHQIATITCGPDDGMNHGLLNWFVTGLATSPDGLRINNGGQAHIDMSTT
+EGLRSVVVVDDLSQTEQLICAVRTTCSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002353.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002353.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1f6a978a483f2dbcd464aedc54448b0ec3505e1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002353.fa
@@ -0,0 +1,16 @@
+>3_678
+M-----------------------------------------------------------
+-------------SRRSLASLATAAAFVVTAVLGGAG------PAAAGTTYSAPLRTAVA
+SLPVAAEN-NAGYDRAAQFGD-WKDANRDCQNTRAEVLIAESKTTPKFTTARKCTVATGK
+WVSSWD------LRTHTSASTVQIDHMVPVHEAWGSGARYWTKAKRVAFYNDLGDARSLN
+AQTSALNSAKQARGPEQWLPP--KNQCQYIADWTAVKIRWGLKADATEKAFLVKKAASCA
+NTTL--------------------------------------------------KVTRY-
+------------------------
+>3_2127
+MLGCSGCLGLVALGLLLLSLLVGGFTGSPSPSAASQAPDGRSAAPSAPDAPGDPAGSAPA
+PAPTPDRAEAPVSDRAEAPAPAPAPASAPAPAPGDAGEAAPSSPAAEAPAADGTALAALQ
+SLPVKGRAPKTGYSR-EQFGPAWADVDRNGCDTRNDVLRRDLADVVLKAGTNGCVVLSGT
+LHGPYTGEVIAFQRGPGTSTAVQIDHVVSLSDAWQKGAQGLSAGRRAAFGN---DPLNLL
+AVQGSVNQSKSDGDAATWLPPLRSARCPMVARQIAVKARYGLWVTPAERDAMARVLRECP
+GQGLPAEGGPVDPSPETAAEPTPQAPAPTVQAPAPAPAAPAGGADPSFSSCRKAKAAGYG
+PYVQGVDPEYAWYRDGDGDGMNCE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002355.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002355.fa
new file mode 100644
index 0000000000000000000000000000000000000000..886c56a7902a3b3caaa5267b3019985b80af80f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002355.fa
@@ -0,0 +1,10 @@
+>3_919
+MHGEERSTRAALERAGHVGLASRIGLDGTLVPPDGRAGPGAPDAAGVGYASRVPEQRIIA
+RRSLGNAPTRPDGLRLASLAALGEEQFSTHMLAASGGDPFDTSTEESALEDLLEIIEGAG
+DHFDPHAWYVVGDGEGEIGVVLPQPLPDKPGTGTVFYVAVLPSRRGRGKGRQLHQFGLSE
+LARRGCTEYVGSTSVDNAPMVAVFQANGCELEH
+>3_1270
+M-----------------------------------------------------------
+------------------------------------------------------------
+--------------------------------------AVLPSRRGQGMGRRLHALGLAE
+LARRGARKYIGSTGRKKAAMVAVSRANDCIVEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002356.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002356.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a10c590edb15a5bacacb787a0d2f985979bea64
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002356.fa
@@ -0,0 +1,12 @@
+>3_1163
+M---------------------DTR----------------------------DDTELAP
+SATLGRRERAKAEKRARILAAARALFEERGFERTSMSEVARAADVAEGTVFQYAATKVEL
+LMMVVDALWGAHERATTTPSLSAFAAPGAATAGGETADRIAELISPLVTAMWRWSELATW
+VAREILFGADMPHRRRVLDHVDRLEEEIAARLQDGRADASGAIGAARDGATGTAGEEPGA
+AAAAGARLIVAGVLAELNRSRQRRIDGEDVDVVLRRLIDLVVAGAGAAR
+>3_2236
+MPVTLVSPRARGGEFATNVHMVDARPPLPSRSIDCAVVSHSRLAPESEPEPEPEPEPATP
+TRVPGLRERNKAAQRERILAAVRERLGRQGYRAMTTAQIAQDAGVAAGTVFTYAATKPEM
+LMMATHDRW-----KDSVPSALAGSLPEDRT------EAVRALVDPIVATAVAEPENSAA
+IARELLFGQPGAHHDAVLVLVRRLEEAIARIIADG---------------------DPGP
+RERTAADLVVMGVVLELHRDRTEGGRVEGLEERIERVIGLFI------D
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002363.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002363.fa
new file mode 100644
index 0000000000000000000000000000000000000000..39efe03d1d414d03ee6c16286db7d61ea0440158
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002363.fa
@@ -0,0 +1,20 @@
+>3_1784
+MEGLERVGSVLGMMLQVCVNGARDIAEHPALSADPVRVAAECAEAVAAGADAVHVHPKDA
+HGQDSLQNPDVGRWVREVRARCAGVPVGVTTGAWALPSVEDRRQAIVGWQTLPDFASVNW
+HEPGADQIAATLLDRGIGVEAGIWHQEGLTAWLASPLRSRCLRVLIEVQDIPAEEVESEA
+LVLVQGVRRAEPAMPLLLHGEERSAWPALKLAGRLGLDTRAGLEDMVTFADGRPAPGNAE
+LITVASHLRGRSLEEEPTVMKPYSVPLAEARTAFLAALDAFEEGASSLDDLTLLGVSHVH
+GWSRLDCLVHVRLGLQEMLAGLAARTDDTPDVDAASYWTTYEP-EKDPVPGILMTRRTAS
+AYARPRNALEHLNQVSAGLRHAADTLIEESIAFQGHVLTAGDMLATWAVELAVHHHDLAL
+PAGAPAPAPAAVHIGRLTAEAL-GSTSGARAGAEDDLAVMLAG--------------FGR
+R
+>3_1829
+M-----------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------SVAGEAERFAQQAHQFAEAASGLDDLALLDPSLCR
+GWSRLDLVVHVRLGLEEMAAGLGVRADDAPDHDDVTYWSSFAADEQDPVPGHMWLRRTAS
+AYARPTDATAHLRDAAERACAASALQDPRPVRFQGKVLSVMDFLRTWSVELALHLVQLDV
+-----GVVPSAAGLARRTLEALTGAPLPVRLTDHSALRVALGADPWPADEPGGGAYPLG-
+L
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002368.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002368.fa
new file mode 100644
index 0000000000000000000000000000000000000000..006c24255e8b41b9d7eeab929b4d458a187ca9b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Alignments_ids/OG0002368.fa
@@ -0,0 +1,28 @@
+>3_2261
+MALHVGLYSPWNTTDPRAWSGVISPMAEALRDVFDVTVIPPVGQRDARGERIRTRLRGMT
+GRRSLPTHTMATARLRSAVLAHQLRRHTGAPLDALVTIAASTDVLSLPDDLPIVQVTDAT
+FPAIRGFYPLATGLGRRNEREGMRVEEAGAQATDRYLVASEWAALSLTDVVGVAPHRVTV
+APFGPGTPPPADARRREPGSSLRVLAVIADWERKRGDDIVAAVARAREFRDLTLTIVGRA
+PEGLPSWVNAPGVVDRARLAELYRGHDVLVDLALANAAGVVMTDALASGLPVIATHVGGV
+DTIVRDGKTGWLVQPSGAVDATARVLTTL----DAAAVTRASAAALADARARLSWRAWAA
+TADEVVRAAVAERRGQASPEAQRRRALMVTPILPSTGGQESAGEHLVNDIAQVI-AERSE
+LTMLSSDGPANRRALERGVAFAHRLLTSAPLRCDRLPRLLGVAPALNARTVEQVRGLVAS
+ADLVDLQWEESALLLGPLRRMNADARIVVTLHDVLSQRFARQRELQSSRLRKGVWAARQA
+AATMLEAHIVREADAVVVLSQKDADLLPKRGRRARIHVVPPAITGPLRPLR---DGTGAP
+FLLFVAYMARWENEDAMHWFVTEILPRVRAEAPDVRVAVAGGGLRDHVVAELEANDVEVL
+GFVHDLEPLYEEASAVVVPLRYGAGVKFKVVDALVRGVPVVTTTVGNEGIHPADAAIVAD
+EPAAFAEAVTAVLANLPCAERYARSRATDVAREFGPNRFRARLQEVYR
+>4_494
+MTPRIGLYSPWDLTDPRAWSGAAHQMAEALAAVADVEIVPPVQVDDAPLERARTRARGAR
+GRRSLPRHTMATARRRSQALSQALEARVGPSLDALVAIAGSTDVLRIPANLPLVQVTDAT
+FPAICGFYPMATGLGRRGEREGQRVEHASAVRTDRWAVASQWAADSLVADVGVPASAVRV
+APFGPGVTPTSAPRVRRPQRPMRVLAVIADWQRKRGDAVVDAVQQARRHADIELTIVGHA
+PDDLPIWVHLEGVVQSDRLSDIYADHDVLLDLASANAAGVVMTDALASGLPVIATRVGGV
+ASIVQDGRTGWLVDADRAAEQAANQLRLLGESGGADQVAAASKAAAEDAARRLTWRSWAA
+AVMESVEEAV------AAHAATERRIVMISPLLPSAAHQETAGEKLVRQTVDTLTADGAR
+VTLVSTPGPANRRAILRGGVPDHRLLSPARRITGRAARLLDLAPVLSPADLAPVRGLLRT
+ADVVDLQWEESGILLPALRLTAPGARTVVTLHDVLSQRFARQRDLQLRPARRAVWEARRR
+AALAVERLVLAMADDVVVLSDKDAALLSSRG-RARVHVVPPPIPGSLRPERRDLQPTAEP
+QLLFVGFMARWANEEGMHWFVTEVLPRIRAELPGARVAVAGGGHRDHVVEELENSEIEVL
+GFVEDLEALYNAADIVVVPLLSGAGVKFKVVEALVRGVPVVTTSVGNEGIHPADAALVAD
+DPQDFADAVLDVARYPQIAESHARAHASAVAEEFGVAGFRQRIKEIYR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000007_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000007_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..627b604cfa79acb05e8931b09e800746e7ef14c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000007_tree_id.txt
@@ -0,0 +1 @@
+((0_150:0.0,0_1245:0.0,0_2015:0.0,1_977:0.0,1_1064:0.0,1_1076:0.0,1_1970:0.0,2_1188:0.0,4_564:0.0,4_566:0.0,4_1202:0.0,4_1289:0.0,4_1827:0.0,4_2144:0.0):0.000000005,1_1072:0.009163421,(0_992:0.009149845,0_1335:0.000000005)0.784:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000025_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000025_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..833d26e52e45932923aad807665e258eb5ebe469
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000025_tree_id.txt
@@ -0,0 +1 @@
+(3_600:0.327506200,(3_653:0.0,4_1954:0.0):0.322720823,((0_95:0.0,1_2059:0.0,4_90:0.0):0.000000005,2_277:0.024703622)1.000:0.571752836);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000030_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000030_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fd4114db1241266551b10258a4e5d86e1b4c2615
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000030_tree_id.txt
@@ -0,0 +1 @@
+(1_344:0.000000005,4_1950:0.001990689,(0_161:0.006030839,(2_2283:0.000000005,(2_161:0.589657773,(2_181:1.122251921,2_2167:0.747882878)0.989:0.326334220)1.000:0.628862628)0.801:0.003973462)0.858:0.004001438);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000036_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000036_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..97c8b16969be6936dcc2bedf9e1e611f17bdda02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000036_tree_id.txt
@@ -0,0 +1 @@
+((3_434:1.085881316,(2_1228:0.820278434,2_1305:1.082570731)0.899:0.273356692)0.999:0.665845858,2_387:0.000000005,(3_2146:0.012756068,(0_606:0.0,4_575:0.0):0.007769457)0.614:0.009599865);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000040_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000040_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb3949d5e6aaac5c60fbec36146eac4155aa058c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000040_tree_id.txt
@@ -0,0 +1 @@
+((((2_804:1.339378938,3_2203:1.285070097)0.934:0.386898143,1_697:0.000000005)0.563:0.003616369,2_1837:0.005431302)0.734:0.000000005,4_918:0.002239510,(4_917:0.000000005,0_974:0.000000005)0.947:0.003612358);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000045_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000045_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0723d8c60fbe104ffc6b926f03e0e529ab915709
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000045_tree_id.txt
@@ -0,0 +1 @@
+(0_1536:0.010479020,1_1258:0.000000005,(4_1463:0.001796520,(3_1216:0.199431498,(3_1789:1.165489093,(3_696:1.597567971,3_626:0.664171331)0.752:0.128767607)0.996:0.427506781)0.991:0.156698023)0.869:0.006605470);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000052_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000052_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..85e70bc0cb5b7f9bd150593ed9d9b8761bea352c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000052_tree_id.txt
@@ -0,0 +1 @@
+((0_2099:0.0,1_1823:0.0):0.008104447,4_2044:0.000000005,(2_580:0.044011955,(3_503:0.055143929,(2_571:0.530802322,2_2524:1.523732894)0.855:0.287950074)0.911:0.058663291)0.907:0.021444016);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000053_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000053_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1c82d6e279d29a178a03e6cd4265593591bafed3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000053_tree_id.txt
@@ -0,0 +1 @@
+(0_2185:0.000000005,4_2118:0.005373016,(1_1898:0.010758424,(3_405:1.584514796,(3_401:0.032566304,(0_2200:0.026166446,4_2132:0.015097899)0.663:0.009215260)0.958:0.231562567)0.776:0.119768049)0.598:0.000002422);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000058_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000058_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..689598d1378cb0502a2f9ece1eeb8895dc29c3b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000058_tree_id.txt
@@ -0,0 +1 @@
+((2_339:0.109287997,(2_1578:0.131403844,3_1473:0.326445083)1.000:0.365245103)0.997:0.128130387,1_2009:0.000000006,(4_40:0.014095729,0_45:0.000000005)0.832:0.005617349);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000065_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000065_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a450a87f34feca4a074139154c174a3575003fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000065_tree_id.txt
@@ -0,0 +1 @@
+(0_824:0.000000005,(1_555:0.0,4_783:0.0):0.019109217,(2_2034:0.112439049,(0_167:1.706142014,3_1928:0.469315808)0.713:0.162918542)0.951:0.096861662);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000067_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000067_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..57febd7ede2771551248674ac6463401935e768a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000067_tree_id.txt
@@ -0,0 +1 @@
+((0_199:0.0,4_199:0.0):0.006252564,1_2143:0.002207454,(3_120:0.013037414,(2_174:0.019867697,3_122:1.697296944)0.839:0.052780945)0.865:0.004205905);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000069_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000069_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9cfae4b7e36b7390271d673da57f1c2084637dd3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000069_tree_id.txt
@@ -0,0 +1 @@
+(0_213:0.006583145,1_2177:0.005648734,(4_214:0.000901637,(2_149:0.099004683,(2_77:1.016801820,3_107:0.207948263)0.958:0.093140675)1.000:0.087987654)0.879:0.005719319);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000073_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000073_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2343349ad8c00775ce9a6526098828cc3ddeb9fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000073_tree_id.txt
@@ -0,0 +1 @@
+(0_249:0.004113967,4_248:0.000000005,(1_2214:0.010742430,(2_102:0.051593739,(3_70:0.126938700,3_509:0.889958557)0.912:0.104449608)0.980:0.060983368)0.862:0.014807957);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000075_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000075_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e92d2c717ba88253186a2c19a0832f31efdcde0e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000075_tree_id.txt
@@ -0,0 +1 @@
+(0_273:0.010059350,4_272:0.004999555,(1_2239:0.000000005,(2_62:0.017218346,(3_48:0.263979983,3_433:1.728936640)0.733:0.070948932)0.951:0.072353061)0.909:0.010112685);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000076_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000076_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e86b4fab21d77d78aef9e95435560b1f6e503c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000076_tree_id.txt
@@ -0,0 +1 @@
+(1_2251:0.003522818,4_284:0.002428942,(0_278:0.008703145,(2_58:0.035046518,(0_1898:1.500178278,3_37:0.101022109)0.741:0.065184420)1.000:0.038973807)0.939:0.003241634);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000079_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000079_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..28700d1d856bf32c763cb49f1430d44e2349cf4a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000079_tree_id.txt
@@ -0,0 +1 @@
+(0_304:0.008025716,4_311:0.004047512,(1_28:0.000000005,(2_15:0.061712610,(3_11:0.096562928,3_670:1.090057021)0.703:0.021780519)0.940:0.032591121)0.789:0.007978513);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000089_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000089_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4c63f0aea35fe8db6e00ea1f9a4315be1b1a86bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000089_tree_id.txt
@@ -0,0 +1 @@
+(2_2388:0.050491655,(0_486:0.009923027,4_485:0.018885414)0.947:0.015689664,(1_215:0.030587262,(2_1193:1.780791281,3_2271:0.022626982)0.830:0.036128906)0.509:0.006538547);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000092_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000092_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f062d8dea30933794afbc135da7f18506cf26e78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000092_tree_id.txt
@@ -0,0 +1 @@
+((0_530:0.0,1_264:0.0,4_533:0.0):0.181141102,3_2222:0.243764191,(2_622:1.605050268,2_2339:0.018882596)0.862:0.124957202);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000099_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000099_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..daea3a1f477740002d978276f86e94a861ab3abc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000099_tree_id.txt
@@ -0,0 +1 @@
+(2_386:0.004079981,3_2147:0.004099724,(0_605:0.000000005,(4_576:0.000000005,(3_435:0.916914262,3_1037:1.106285486)0.961:0.495220609)0.878:0.004082340)0.801:0.004097015);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000105_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000105_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3c6f87945f27860a53da547f1e26c89d60c9bd20
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000105_tree_id.txt
@@ -0,0 +1 @@
+(((2_2133:0.355195371,3_2027:0.820199726)0.970:0.341552303,4_685:0.000000006)0.867:0.024840602,0_721:0.014376199,(1_460:0.000000005,0_720:0.037961107)0.950:0.063380881);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000118_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000118_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3079ea127d10658e36f1921a3396bbbdb3de8c2b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000118_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000120_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000120_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0598084681b3c5edf7add05cfa3ad7a75b32e029
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000120_tree_id.txt
@@ -0,0 +1 @@
+(0_1072:0.004348563,(1_800:0.0,4_1022:0.0):0.000000005,(2_153:1.534365832,(2_1744:0.038812245,3_1636:0.212383996)0.452:0.034481264)0.991:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000122_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000122_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..16ed2acd38a44054109c3b0f8411d8fca84f864a
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000122_tree_id.txt
@@ -0,0 +1 @@
+(0_1106:0.006208055,(1_834:0.0,4_1056:0.0):0.004846934,(3_1602:0.154248206,(3_528:1.478711684,2_1709:0.000000006)0.946:0.049136441)0.991:0.047065764);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000124_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000124_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..300094224d584a19780598b607489ebbc6290c60
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000124_tree_id.txt
@@ -0,0 +1 @@
+(3_2030:1.306357283,(0_1237:0.006232137,(1_965:0.0,4_1194:0.0):0.000000005)0.720:0.015783939,(3_1466:0.110753924,2_1570:0.050928741)0.841:0.023923353);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000126_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000126_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7f50ed95fc7bdb2c5410876c15c9b040aaa5ea31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000126_tree_id.txt
@@ -0,0 +1 @@
+(0_1293:0.007081995,(1_1022:0.0,4_1247:0.0):0.003398036,(2_1521:0.062269623,(3_1385:1.228892366,3_1417:0.050899912)0.988:0.203581043)0.938:0.040177865);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000127_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000127_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3421e35837837d347371dcd35b8ee2a6da2b51c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000127_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000129_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000129_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5eb945c675fedc640eb0b31cca7bb78dcec1a856
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000129_tree_id.txt
@@ -0,0 +1 @@
+((3_1327:0.232177922,(0_1398:0.007841360,4_1347:0.006429934)0.905:0.029532230)0.342:0.023451608,3_1738:1.685527917,(2_1423:0.114844878,1_1139:0.056213462)0.709:0.010670601);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000132_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000132_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4348c3bdd0b50670bf36cb0ba36573c3434afacf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000132_tree_id.txt
@@ -0,0 +1 @@
+(1_1229:0.022652788,4_1436:0.000000005,(0_1509:0.018187725,(2_1338:0.037888634,(2_2218:1.552502776,3_1230:0.160993136)0.976:0.544262979)0.866:0.052856828)0.875:0.028217203);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000133_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000133_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ed5d44e95d68e4f9a525ec8e5bfeffa81092d36
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000133_tree_id.txt
@@ -0,0 +1 @@
+(0_1515:0.000000005,1_1235:0.004145493,(4_1442:0.007658135,(2_1330:0.070140226,(2_2521:0.292769096,3_1224:0.120453985)0.991:0.079721645)1.000:0.112050612)0.101:0.007085316);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000135_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000135_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2e17bd75a9d9f38cd84d483178f91324d539de14
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000135_tree_id.txt
@@ -0,0 +1 @@
+(3_1210:0.007225825,4_1455:0.008974687,(0_1528:0.000000005,((1_1249:0.006150287,2_1315:0.009239836)0.217:0.006147509,1_1248:0.003341181)0.013:0.000000005)0.848:0.003587629);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000137_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000137_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5c63de21e31c8df299f3941aaee67fef332a3363
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000137_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000139_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000139_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3ed166fb14e3cc3458c46da694faaa9d638d0f68
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000139_tree_id.txt
@@ -0,0 +1 @@
+(0_1550:0.001794200,1_1272:0.000000005,(4_1477:0.005402580,(3_1174:0.026242025,(2_1250:0.849016789,2_1265:0.041818255)0.808:0.026537444)0.929:0.011050844)0.792:0.001797618);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000142_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000142_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2851a8a0654e75a43892004681bba85f27dff794
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000142_tree_id.txt
@@ -0,0 +1 @@
+(0_1627:0.008486256,4_1556:0.002812842,(1_1341:0.002720916,(2_1172:0.115888130,(2_1184:0.218085960,3_1102:0.175687174)0.988:0.110620836)1.000:0.103973331)0.753:0.002905412);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000143_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000143_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5cd8027388464326de4524d417dcea6efe1297a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000143_tree_id.txt
@@ -0,0 +1 @@
+(0_1633:0.004963877,(1_1347:0.0,4_1562:0.0):0.013381252,(2_1166:0.154711270,(3_30:0.928311972,3_1097:0.245857542)0.937:0.142983847)0.891:0.042001348);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000144_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000144_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..507a0199e8d776c21ef817a0673d6248f9afcab1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000144_tree_id.txt
@@ -0,0 +1 @@
+(0_1721:0.013839788,1_1438:0.014147980,(4_1650:0.013503569,(2_1077:0.091671404,(3_1002:0.163285841,3_1768:1.463280825)0.568:0.016411343)1.000:0.090198520)0.843:0.011617126);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000149_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000149_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3a8edaba201e294f02c15c9e19e1805c067883d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000149_tree_id.txt
@@ -0,0 +1 @@
+(2_1306:1.829703287,3_945:0.070651494,(2_1003:0.064487504,((0_1785:0.0,1_1493:0.0):0.001549693,4_1707:0.003132203)1.000:0.148158989)0.114:0.004721188);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000150_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000150_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc8219e11681bc60099fe67d9084b5583bc99167
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000150_tree_id.txt
@@ -0,0 +1 @@
+(1_1500:0.025541362,4_1714:0.003632596,(0_1793:0.003506942,(2_995:0.113085401,(2_1037:1.560452016,3_938:0.116035758)0.897:0.123397397)0.971:0.059545576)0.857:0.007331164);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000156_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000156_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d4f1567dfd139a66e137fdd863a590949781be17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000156_tree_id.txt
@@ -0,0 +1 @@
+((3_747:0.027797061,(2_120:1.408235950,2_807:0.101622503)0.966:0.121620384)0.999:0.059043032,4_1892:0.007294278,(1_1674:0.016925499,0_1953:0.008265949)0.427:0.004190153);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000161_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000161_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..38d9e1f05233a1b420381e5e7430900790c51d90
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000161_tree_id.txt
@@ -0,0 +1 @@
+(2_687:0.017365247,3_602:0.358046905,(4_1957:0.013911648,(1_1733:0.024540753,(0_2018:0.007716552,3_598:0.011601778)0.348:0.002754199)0.765:0.003367512)0.723:0.005065140);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000172_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000172_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4b01ec5be873c63c1a3425ea24ec38a25f436fe6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000172_tree_id.txt
@@ -0,0 +1 @@
+(2_1471:0.727312161,3_274:0.441995556,(1_1967:1.117171926,(3_677:0.197337794,(3_333:0.080255263,4_106:0.098424134)0.999:0.287637882)1.000:1.019963765)0.968:0.334289581);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000174_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000174_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5d036eac04f946c94badd77c5d42972c719ab7f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000174_tree_id.txt
@@ -0,0 +1 @@
+(0_0:0.005632711,1_1956:0.000000005,(4_0:0.002802949,(2_405:0.040602182,3_359:0.125896569)0.967:0.026154959)0.803:0.004719240);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000182_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000182_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2cbedac322cae817d75b24e272b44acbc0aac456
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000182_tree_id.txt
@@ -0,0 +1 @@
+((2_370:0.068541662,3_2129:0.298981651)0.946:0.052537660,4_8:0.000000005,(1_1977:0.011511816,0_8:0.003843828)0.829:0.003778875);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000187_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000187_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6c4c96b09ec8358b685537d806fef2ba6a37f7cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000187_tree_id.txt
@@ -0,0 +1 @@
+(0_15:0.004536665,4_15:0.004546084,(1_1984:0.004534928,(2_363:0.051646576,3_345:0.102269261)0.963:0.041800673)0.675:0.000000006);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000197_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000197_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0f46235aaea81c7abd9c082020d44137fb626589
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000197_tree_id.txt
@@ -0,0 +1 @@
+(2_199:0.020381542,4_182:0.005930396,(0_182:0.000000006,(0_31:0.892665976,1_1968:1.452609901)0.999:0.608316445)0.969:0.017773843);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000201_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000201_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d07efbcca7d11bc3353263be5d19c0c320ab64ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000201_tree_id.txt
@@ -0,0 +1 @@
+(0_39:0.003046852,(1_2003:0.0,4_34:0.0):0.000000005,(2_342:0.048045006,3_285:0.172893905)0.996:0.070347326);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000202_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000202_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5b1c18dfb1cc82f0c26eb55ae495f37eb2048829
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000202_tree_id.txt
@@ -0,0 +1 @@
+(1_2004:0.005131582,4_35:0.002573215,(0_40:0.020819000,(2_341:0.050334880,3_284:0.141115452)0.980:0.039724272)0.774:0.003997790);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000203_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000203_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3dfe6b67aa14aa847ff1917a848959b12e693ffc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000203_tree_id.txt
@@ -0,0 +1 @@
+(0_41:0.012396364,(1_2005:0.0,4_36:0.0):0.012285227,(2_340:0.140268950,3_283:0.249771782)0.999:0.181311621);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000217_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000217_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..02f9b40ad3bb6a5083ffd802076250654fbe11e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000217_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000223_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000223_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..753795e8ede818fd76490af3e60fbaf1f2d2491c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000223_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000232_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000232_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b8070453831bd742c39c47e1f56c6696515202b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000232_tree_id.txt
@@ -0,0 +1 @@
+(1_2047:0.000000005,4_78:0.003542460,(0_83:0.012634919,(2_289:0.047154730,3_235:0.577111827)0.822:0.019296305)0.765:0.012820610);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000233_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000233_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..373da17bda2682756144cf99677b8a47102e7f10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000233_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000235_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000235_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..59f2e66ac786f1e81d337228440e0d1cc37732f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000235_tree_id.txt
@@ -0,0 +1 @@
+((0_86:0.0,1_2050:0.0,4_81:0.0):0.083867562,2_286:0.204798165,3_232:0.078233735);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000246_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000246_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ce20f91eff506cf097a5a015e025e09296c57a45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000246_tree_id.txt
@@ -0,0 +1 @@
+(0_98:0.005537363,1_2062:0.000000005,(4_93:0.011138268,(2_273:0.047552690,3_220:0.164985455)0.961:0.057268173)0.290:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000254_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000254_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b52ade4b7fbdc50513f1648999dadb7d2e2ee3c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000254_tree_id.txt
@@ -0,0 +1 @@
+(0_107:0.000000005,1_2071:0.003006403,(4_102:0.002999433,(2_264:0.103003517,3_206:0.556429522)0.998:0.124263856)0.752:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000255_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000255_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b778f99b6794c9991a8e9407e5472f422055a86b
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000255_tree_id.txt
@@ -0,0 +1 @@
+((0_108:0.0,1_2072:0.0,4_103:0.0):0.077321732,2_263:0.065381343,3_205:0.413903609);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000256_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000256_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc7ca17033bf172e8d34e0efb1a99aa9bd5c405b
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000256_tree_id.txt
@@ -0,0 +1 @@
+((0_109:0.0,1_2073:0.0,4_104:0.0):0.097445893,2_262:0.035356552,3_204:0.142824559);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000261_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000261_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c3aabcccfdcef86612f75ace9f008e0a6051feb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000261_tree_id.txt
@@ -0,0 +1 @@
+(1_2083:0.000000005,4_126:0.062964969,(0_118:0.046135454,(2_249:0.046199363,3_183:0.185140072)0.968:0.101598473)0.453:0.028134789);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000262_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000262_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..142d4a7b64e00f4f0b36305297084c13aa529982
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000262_tree_id.txt
@@ -0,0 +1 @@
+(2_248:0.203627404,3_182:0.908329004,(0_119:0.130888925,(1_2084:0.018681128,4_127:0.018908267)0.971:0.099232592)0.810:0.068502196);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000264_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000264_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f43936fc262edd56a255fc9ae84d936194789047
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000264_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000268_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000268_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..510fb50f1a23a69043acf2fcc62ba2d06d409155
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000268_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000274_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000274_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dd4d3027396c466d8aa0ebf79ea9718fa338bee0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000274_tree_id.txt
@@ -0,0 +1 @@
+(0_133:0.003114035,(1_2098:0.0,4_141:0.0):0.005157270,(2_233:0.107544503,3_167:0.337730465)0.964:0.076429509);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000275_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000275_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..76fd9b90ebaadd4500b3ad105ed3359bbe941a38
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000275_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000276_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000276_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b09f64b38f0e7bd6e80309658450ab9f8b5db81e
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000276_tree_id.txt
@@ -0,0 +1 @@
+(4_143:0.005935093,(2_231:0.086582820,3_165:0.074242345)0.987:0.059295643,(1_2100:0.013098353,0_135:0.006817026)0.019:0.000281041);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000288_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000288_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4edaea3bae827b41ff79d5d0298a81fd6bd2f929
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000288_tree_id.txt
@@ -0,0 +1 @@
+(0_171:0.000000005,1_2118:0.002343559,(4_168:0.002345650,(2_212:0.019094939,3_158:0.023867152)0.939:0.009379410)0.762:0.002339528);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000290_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000290_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7782d9c1af0f45044c8ce3987aff3296a180381e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000290_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000292_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000292_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a2928d8d60485880d08593b2ea77ba39ad9b3a0a
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000292_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000303_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000303_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e1a69061607c58eaaf7922f4699760299b9ba6d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000303_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000304_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000304_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..28efa64b2df6a5a9875718ab647149af5169a8a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000304_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000305_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000305_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..16780397055592fce125415dc7c05781f37d396a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000305_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000309_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000309_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f00e0ff62806ebc11489753e2d45271584fc618
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000309_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000321_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000321_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dc989c27c77ac1d628c04abd0f1130e19e548f8b
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000321_tree_id.txt
@@ -0,0 +1 @@
+(0_221:0.001957984,1_2185:0.001880029,(4_222:0.002299157,(2_142:0.135635612,3_99:0.067005559)0.998:0.058500029)0.862:0.009303669);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000324_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000324_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4745de8871005800af9c4ddac54dd079335a1e51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000324_tree_id.txt
@@ -0,0 +1 @@
+(0_224:0.003279977,1_2188:0.000000005,(4_225:0.008892536,(2_129:0.055625436,3_94:0.324513081)0.993:0.089191735)0.743:0.004306708);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000326_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000326_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b84dab4904402d116a69448cb9ab8042c2a2d0cb
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000327_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000327_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4088f6ec135eb5d29462229bf5dc73bfac1408ad
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000328_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000328_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..89810edee9635a19084cc7bfcd03290cda4f8328
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000328_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000335_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000335_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1803b7be5e496dcf6dc43e46e062b02668df6bb5
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000336_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000336_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..559e50a29f3780eae300b7476d61564ffc6f6f74
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000348_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000348_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7f959d43861caead67853b0d10a8bcdc0cfd09e0
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000349_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000349_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc786950507ab971d84ee4f26c2ef6941d8e4e8e
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000355_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000355_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ba72784086d6dfa89834cc0c98ab50851363b5b7
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000358_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000358_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8a366664031f1f856d8fa369c7b6226ccf73031e
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000360_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000360_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..643958ecfec432ba4d6094c08937e08ed4f8f2e0
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000367_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000367_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..664440076bf7e5d40a310b2444816666442d2382
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000367_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000369_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000369_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..187ea6fcc1eb9eb68b9c0562c058ef96f146e502
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000369_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000371_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000371_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b61e27c47d1d56db2cc5fe31db13f4863a3a2d2d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000371_tree_id.txt
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+(1_19:0.000000005,4_302:0.001061363,(0_295:0.009908818,(2_24:0.129961174,3_20:0.212276112)1.000:0.109483757)0.966:0.011711316);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000372_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000372_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..68b8c0a271b36ccdc093d10c2ff0d098490e07ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000372_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000374_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000374_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..344d4c8bf13c71c038dc8a70265dfec5d918a92e
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000374_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000375_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000375_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7d37504be8a1c36f8cce4e1b57a5d7b4be998f5e
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000375_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000376_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000376_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..997ffa6795a71e53f2c5e7f2cc413f1c2c2b42e5
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000376_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000380_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000380_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b70e9ff3d6b8af3ef823d62f62a0ff5a6a5b8a6
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000380_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000384_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000384_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b95129cb7a3bcfd46a13b4ce12e2824eba4d9e3e
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000385_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000385_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..33e191e1c90b77d86424db560d0e71f5798b516c
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000386_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000386_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..45600d0dfc515cbfb77bbab689610f633544dff2
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000388_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000388_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..68a53df3de0052cf6e2bb1bcd2e438284ce60b1e
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000395_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000395_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7e822173e4936c700b13389a44346a075e56516d
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000398_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000398_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b7d16e3129c17b45fbe8f1f9fe92b7dd119fea90
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000404_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000404_tree_id.txt
new file mode 100644
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000407_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000407_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b91cb3866fcc84d30aef6b0c02e66e23f3ee936
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000411_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000411_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..09333b501a17f43dbebd91f9a1f2bf592442bbb8
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000416_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000416_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4bc5ced04c58029ae18b2d2c1ac3f98f08f40c83
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000421_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000421_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52bd8a788896f2e548163d367dd327977c18de82
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000426_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000426_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..81d03fce95280543a8d04afff6ca17d388a7ddab
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000433_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000433_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..56825d398765d4946b81c1e2479a65be37fbaaac
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new file mode 100644
index 0000000000000000000000000000000000000000..3d295b7cdb91d327badb4ec28ae5bca224422798
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000438_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000438_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..880896a1555c0043a3c646c8a7b2a46de1c66305
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000442_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000442_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..26421e683c8b0dc4a2858e952d0a1ccf61e2aa11
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000450_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000450_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cad157022377a1d9e6aa05c9d39af7b7b723fdf2
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000454_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000454_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d42dc98dfce2b06cadef9b40a914f2e4b856055f
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000458_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000458_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..566deb89f4018e936565b555e5d30942f8f9e417
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000458_tree_id.txt
@@ -0,0 +1 @@
+(4_410:0.011601448,1_137:0.000000005,(0_407:0.000000005,(2_2473:0.127203816,3_2343:0.146043436)0.992:0.100595213)0.866:0.007691048);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000469_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000469_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9005a17f8e747db103f009270a4aa7d2a387711c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000469_tree_id.txt
@@ -0,0 +1 @@
+(1_149:0.001928227,4_422:0.001713520,(0_419:0.007401854,(2_2461:0.126107674,3_2332:0.045575603)0.999:0.059577109)0.382:0.003709292);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000478_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000478_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2115ee3e61dd55a1020d1330016cb6e3715df752
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000478_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000500_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000500_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e2354bc557458a9c11ee7328c77b3ff3e7482f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000500_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000501_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000501_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fafd374ba5ec13e759d349ebab6f27029f2e4207
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000501_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000505_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000505_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0bf3bc965f91ce295aa53a757397ac1ccc8db766
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000505_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000506_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000506_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4b850d6b2f80e87519d42f97ebc0e41bfe4a8e8d
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000506_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000508_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000508_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c29def9beb8ee7d2ea75372719bfc945743b2c3a
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000508_tree_id.txt
@@ -0,0 +1 @@
+(0_464:0.008242937,1_192:0.005455419,(4_464:0.017313764,(2_2407:0.053121035,3_2289:0.241399582)1.000:0.059133504)0.604:0.004686393);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000509_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000509_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8d5eae089160678be5584b0f53ab0137792dd2e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000509_tree_id.txt
@@ -0,0 +1 @@
+(1_194:0.012462165,(2_2405:0.016424235,3_2288:0.231834250)0.967:0.031319147,(0_465:0.003395317,4_465:0.000000005)0.932:0.013156826);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000512_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000512_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..292c75a06f254cbfdccdd4c37ea78997dfad002a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000512_tree_id.txt
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+(1_200:0.006317399,4_469:0.000000005,(0_470:0.000000006,(2_2401:0.106072892,3_2284:0.107129920)0.978:0.049735538)0.916:0.006375511);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000514_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000514_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..980f80bf8d206e7753af81bd4bdc10f673af4449
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000514_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000515_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000515_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b3729a02994e98f966a98c2244ec762763847294
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000523_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000523_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..28fc266b6cd8b5efa0fdbb76c668d0f6693e2c60
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000523_tree_id.txt
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+(1_214:0.010716499,4_484:0.004116259,(0_485:0.009913434,(2_2389:0.039178348,3_2272:0.081239250)1.000:0.043714647)0.739:0.002105740);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000529_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000529_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3e06a7f36ad6e67fafbdda1dff257bd8bee21afd
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000534_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000534_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a9611554dfad40fd1e34caf26486eb171ea3340
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000546_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000546_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64d04dfca72005cec1463bcbeb67c55b1a434083
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000546_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000562_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000562_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..911e259c3b0cbd12243944f8d2d053725fd714ee
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000563_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000563_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e83a655c83551027e65ffc2ee546d38945d5f342
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000563_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000568_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000568_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..07a17ac08601d23c4e39050aa997e36fb5b54b30
--- /dev/null
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+(0_551:0.003800134,1_292:0.007869776,(4_552:0.008036835,(2_2306:0.034335969,3_2196:0.185319662)0.982:0.037226222)0.751:0.003800113);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000569_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000569_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..00bc92ccc24d0662ce24ce4d1a2a3c83f9081f60
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+(1_296:0.013046948,4_556:0.000000005,(2_2302:0.123322578,(0_555:0.036107370,3_2195:0.362476653)0.925:0.042283150)0.864:0.014048484);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000570_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000570_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b3ef00354962032264b917cfadaa514d8e4ebce
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000575_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000575_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dd5ae6c10987518768ce72c2164c803b41eaf686
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000578_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000578_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b9e69348cbf9703c0a1853097939516cfbdfdb5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000578_tree_id.txt
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+(2_2270:0.094906436,4_586:0.003185551,(1_362:0.000000005,(0_616:0.000000005,3_2132:0.003141254)0.963:0.009456659)0.882:0.009395229);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000580_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000580_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..40ede371fb385b4a168455b2f995076122ed2950
--- /dev/null
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+(0_618:0.005532997,1_364:0.008310881,(4_588:0.019321283,(2_369:0.203280047,3_2130:0.075477435)0.981:0.052277544)0.919:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000582_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000582_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..63393ee66dc55c0e9e197f56bb19b9db3e69682e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000582_tree_id.txt
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+(0_622:0.000000005,1_368:0.004796091,(4_592:0.009562735,(2_2265:0.035815234,3_2123:0.242513909)0.992:0.045642422)0.739:0.002465528);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000583_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000583_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2fdac8bf46121de7f9a23cf69dcb284cc1368d47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000583_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000584_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000584_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a41d3e26ccc4bd53aa5206cd2b0cdbf218c0fa5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000584_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000586_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000586_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b08cfe1e25f2ced960df9f74750c7fc5a82e3d7e
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000586_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000589_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000589_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..79d8a21877e2f4209f65ae495382b815a85831fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000589_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000590_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000590_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..062149a73b617f779328951c5ebaa4f0856d4471
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000590_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000592_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000592_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..80d56d8f461e12e2e2b5d20d270e5ec36b313caf
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000592_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000596_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000596_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ebf586fa70741c68bf4d90792e48a4e46a46ddf8
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000609_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000609_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ccb767f3d792bce98d3be76b0e7a48977bb2656
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000609_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000614_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000614_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..99de3906dffa92906a84a083fc55a27373ac2b75
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000614_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000615_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000615_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4e77b68f9ccfc5ffd56206c4eeb91c8f39746f66
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000617_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000617_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..616a4c91d0ed50b1a84020bc86c6f66ece65a30d
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000619_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000619_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b2cbcceb2e39e298f5d124fb46c603ab12fc4da5
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000622_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000622_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad4a7a39567f1a3ff54906cfd74ebd1975167638
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000632_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000632_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ded184476283e1856edf14bcfa730a82fd43ca5f
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000634_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000634_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dff825f0b76747992f401098f32427f6f84c5b33
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000642_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000642_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0865b67151a2ed488d870a56042388eecd9fa433
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000643_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000643_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..015157fa4ea1a7cff93de72e8a121c9528aceacf
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000651_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000651_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d912e3120451d1c4eec7903c0e2b5f506eb0e631
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000671_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000671_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..41bc712de1764d6623f0bb929746a83811262fd4
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000675_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000675_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2662ae2e25a8fade5394c1cc456b231041a556b2
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+(0_736:0.013289538,1_475:0.006387322,(4_700:0.000000006,(2_2118:0.131736401,3_2012:0.248228144)0.930:0.069747286)0.899:0.012911830);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000688_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000688_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..96cc22e699830af9e447284f0137f873c32100ac
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000689_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000689_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..41a6115804e138fc0d0b95241bc328f4bece3e2f
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000692_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000692_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c4f547d8b882f659e34cdbb505f572c064f015d4
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+((0_755:0.0,1_495:0.0,4_722:0.0):0.029036324,2_2099:0.013371405,3_1992:0.094581568);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000693_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000693_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..13b991534b26ae6986010e6e78239ea9997932de
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000693_tree_id.txt
@@ -0,0 +1 @@
+(0_756:0.012453163,1_496:0.002918210,(4_723:0.003298599,(2_2098:0.081942946,3_1991:0.342822189)0.995:0.089431541)0.763:0.009242688);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000695_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000695_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..695654fa13ad8efd1b3b89aef1785a786a17a8f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000695_tree_id.txt
@@ -0,0 +1 @@
+((0_758:0.0,1_498:0.0):0.002716897,4_725:0.002562072,(2_2096:0.050817437,3_1989:0.137687764)0.908:0.015624113);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000696_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000696_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..48c188efd5cfec68e8851a35a3aa77f95203ebd0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000696_tree_id.txt
@@ -0,0 +1 @@
+((0_760:0.0,1_500:0.0):0.000000005,4_727:0.011321126,(2_2095:0.067982975,3_1987:0.157380929)0.962:0.049130146);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000699_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000699_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d1a75e747a3d685369e8c4f2f47271f2f21396b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000699_tree_id.txt
@@ -0,0 +1 @@
+(2_2092:0.026745440,3_1984:0.177304853,((0_763:0.0,1_503:0.0):0.000000005,4_730:0.003869043)0.858:0.012850439);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000700_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000700_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d083cea6b399815385298c3fb468ce2aab519f98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000700_tree_id.txt
@@ -0,0 +1 @@
+((0_764:0.0,1_504:0.0,2_2091:0.0,4_731:0.0):0.022812828,3_1983:0.022812828);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000703_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000703_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2b92aabd7cc2786cb9693841fa51463f04828f7b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000703_tree_id.txt
@@ -0,0 +1 @@
+(1_507:0.001759639,4_734:0.000000005,(0_767:0.005290318,(2_2088:0.006512399,3_1980:0.063985629)0.987:0.017151716)0.824:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000708_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000708_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d57381ee43842a15edb76c26048de8dcdf5780d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000708_tree_id.txt
@@ -0,0 +1 @@
+(2_2082:0.065725361,3_1974:0.067568748,((0_772:0.0,1_512:0.0):0.000000005,4_739:0.004309185)0.935:0.032229426);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000709_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000709_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aa9f96447741fe14c0c2e419a74d41bdbfc0db7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000709_tree_id.txt
@@ -0,0 +1 @@
+(0_773:0.025930030,1_513:0.017304326,(4_740:0.008699019,(2_2081:0.048599580,3_1973:0.078388605)0.953:0.071681885)0.752:0.008405557);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000711_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000711_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..162d37efd48c99cb439ccd2501f6ca5d9ababd49
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000711_tree_id.txt
@@ -0,0 +1 @@
+(1_515:0.006161630,4_742:0.002947327,(0_775:0.012305092,(2_2079:0.075681031,3_1971:0.262651564)0.964:0.047666072)0.745:0.003001091);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000715_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000715_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d27a2ea2ed70152a38e9fc943759d4020ebfd32c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000715_tree_id.txt
@@ -0,0 +1 @@
+(0_779:0.006529934,1_519:0.001604583,(4_746:0.000854569,(2_2075:0.058748534,3_1967:0.082172064)0.963:0.021763828)0.801:0.005657428);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000719_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000719_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..10cbad187e41baa18e3907030df8c35990b73a20
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000719_tree_id.txt
@@ -0,0 +1 @@
+(1_525:0.003864067,4_753:0.000000006,(0_784:0.000000005,(2_2070:0.110907912,3_1960:0.398455060)0.966:0.089351398)0.887:0.007757216);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000721_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000721_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..091e15f839990a13df404afc3dcbd194899088fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000721_tree_id.txt
@@ -0,0 +1 @@
+(1_527:0.000000006,4_755:0.003811378,(0_786:0.000000005,(2_2068:0.055456613,3_1958:0.179426852)0.999:0.101155404)0.527:0.007625787);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000735_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000735_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5f64506e7416ab05c220af7813adbcc3e64a247f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000735_tree_id.txt
@@ -0,0 +1 @@
+((2_2047:0.022832565,3_1945:0.132643205)0.907:0.011003517,4_771:0.000000005,(0_801:0.007765545,1_542:0.004655255)0.613:0.001532965);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000740_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000740_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..71898f326cea28b8e3298c9abfde610314463b83
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000740_tree_id.txt
@@ -0,0 +1 @@
+(0_818:0.003309220,(1_549:0.0,4_777:0.0):0.002127804,(2_2041:0.021029084,3_1940:0.148262344)1.000:0.062540943);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000744_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000744_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..23f17d9445749c757e5e4ea3d76c44e30578f6a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000744_tree_id.txt
@@ -0,0 +1 @@
+(2_2036:0.028578157,3_1930:0.058638488,(0_822:0.005674423,(1_553:0.0,4_781:0.0):0.013266415)0.944:0.022626793);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000747_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000747_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..22b1688088e70b69a431eb8047623a6d82008718
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000747_tree_id.txt
@@ -0,0 +1 @@
+(1_558:0.008107429,4_786:0.007913076,(0_827:0.011030178,(2_2032:0.085180185,3_1925:0.385457366)1.000:0.122280424)0.488:0.007783997);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000752_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000752_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..544ef78637073b7c116fa3c2a4b6cf934522f64f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000752_tree_id.txt
@@ -0,0 +1 @@
+((2_2027:0.015056349,3_1920:0.049793662)0.975:0.021345475,4_791:0.002241516,(0_832:0.000000005,1_563:0.002245194)0.449:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000759_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000759_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f0fa6d7ec1b6167cae6b500e5f0bc1e4a46027b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000759_tree_id.txt
@@ -0,0 +1 @@
+(0_839:0.007017579,4_798:0.006520959,(1_570:0.005487119,(2_2020:0.050994456,3_1913:0.164267384)0.970:0.025348831)0.802:0.004258932);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000769_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000769_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee3b8c465adfff930f940ba9039a1135d73eb4c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000769_tree_id.txt
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+(0_849:0.008726885,1_580:0.009433925,(3_1903:0.358928174,(2_2010:0.077467486,4_808:0.001841294)0.999:0.105848804)0.911:0.030406638);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000777_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000777_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..632d7da50767b5e465d0b3272b95cc2ef6fef19f
--- /dev/null
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@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000785_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000785_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..037b9b3f9be2ab8bc8a1c7a0cd1353affbdf9e6d
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000785_tree_id.txt
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+((0_879:0.0,1_607:0.0,4_827:0.0):0.078713227,2_1987:0.093892811,3_1884:0.341580611);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000793_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000793_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..77a7702f6292416ab9252860fafdb2ef8f57f660
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000794_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000794_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cefe24539fd39a576cb2b53a5b1f00805df29986
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000797_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000797_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..efc6436dc3ff6c933cbf7396bdddeb0474b3609c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000797_tree_id.txt
@@ -0,0 +1 @@
+(1_619:0.001095590,4_839:0.000000005,(0_891:0.003198760,(2_1974:0.079276556,3_1872:0.019144660)0.802:0.006221996)0.774:0.001191663);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000805_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000805_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b9b2ff6b205efb7ea6aef9db9964c26c249ac456
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000805_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000812_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000812_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb577a4d4a4a49247489c14365d81d1aaa6a8c83
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000812_tree_id.txt
@@ -0,0 +1 @@
+(0_906:0.011284352,4_855:0.018895161,(1_634:0.020731932,(2_1957:0.117891024,3_1853:0.211206369)0.997:0.103734074)0.774:0.007347395);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000815_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000815_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7b33e40013a770a18d4a70c4c45b4c93d41fb33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000815_tree_id.txt
@@ -0,0 +1 @@
+(1_637:0.000000005,(2_1953:0.142223958,3_1849:0.223615399)0.950:0.050539603,(0_909:0.009658588,4_859:0.015928487)0.773:0.004784808);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000822_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000822_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1235de39ed06581c84b1a47e5fe37a3d31a8f2b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000822_tree_id.txt
@@ -0,0 +1 @@
+(0_927:0.001811618,1_649:0.000000005,(4_873:0.001809365,(2_1885:0.018247794,3_1835:0.075772157)0.856:0.005658681)0.905:0.000000006);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000823_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000823_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..98da8a2e1b332c96e8fdc46de3ce3168401d6c10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000823_tree_id.txt
@@ -0,0 +1 @@
+(4_874:0.018820766,(2_1883:0.095954156,3_1831:0.129655226)0.435:0.013828893,(0_928:0.000000005,1_650:0.006256637)0.835:0.009708524);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000829_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000829_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..84c77c7f901525f00a4f598d157c8c512bda3675
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000829_tree_id.txt
@@ -0,0 +1 @@
+(2_1875:0.005422163,3_1821:0.099106703,(0_938:0.000000005,(1_661:0.0,4_881:0.0):0.004772611)0.792:0.004158918);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000836_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000836_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7eacd5c1b45ba0da2a1da750888909506fc5207a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000836_tree_id.txt
@@ -0,0 +1 @@
+(2_1867:0.021042130,3_1813:0.006205954,((0_945:0.0,4_888:0.0):0.021554752,1_668:0.005839595)0.974:0.019860218);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000838_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000838_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3e8b8a98d1e2179382017bad5c8468203a56ad64
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000838_tree_id.txt
@@ -0,0 +1 @@
+(2_1865:0.012690082,(0_947:0.000000005,4_890:0.004199877)0.930:0.008457426,(1_670:0.004212349,3_1811:0.000000005)0.884:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000842_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000842_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a21cfe4d59ebdf2e60f5afe02b8d860f6b9b7fd9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000842_tree_id.txt
@@ -0,0 +1 @@
+(1_674:0.003883712,4_894:0.002785856,(0_951:0.003856594,(2_1861:0.027098551,3_1807:0.006665375)0.977:0.019924209)0.905:0.013474729);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000846_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000846_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bdadc93a7f9dd98741629574a3a44801a473550d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000846_tree_id.txt
@@ -0,0 +1 @@
+((0_958:0.0,1_681:0.0,4_901:0.0):0.027772766,2_1855:0.070120321,3_1800:0.226706662);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000850_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000850_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..416f734d5b36c92814672b76b48ea1168d534b1d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000850_tree_id.txt
@@ -0,0 +1 @@
+((0_962:0.0,1_685:0.0,2_1851:0.0,4_905:0.0):0.048607128,3_1778:0.048607128);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000859_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000859_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..655c402cedcfee9d667c9add8dd9bc69b97fa80f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000859_tree_id.txt
@@ -0,0 +1 @@
+(4_920:0.028550914,(2_1834:0.000000005,3_688:1.442655365)0.000:0.000000005,(0_976:0.038154166,1_699:0.009367851)0.874:0.019111046);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000860_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000860_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9a5d4d41d328191a0b4c0d9f33b10bcb37bc18cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000860_tree_id.txt
@@ -0,0 +1 @@
+(0_977:0.002203436,4_921:0.008842278,(1_700:0.006619944,(2_1833:0.081980691,3_1724:0.153778033)0.295:0.016344616)0.888:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000862_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000862_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3f5a1c7c79a1db844984b9ac39252ac14286c786
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000862_tree_id.txt
@@ -0,0 +1 @@
+((2_1831:0.113458289,3_1726:0.636608944)0.932:0.117271285,1_702:0.000000005,(4_923:0.022875530,0_979:0.011059214)0.510:0.005513015);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000863_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000863_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..80d9475be274ef0bf03ce4911fcca72343cfce5f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000863_tree_id.txt
@@ -0,0 +1 @@
+(4_924:0.021570360,1_703:0.010740790,(0_980:0.000000005,(2_1830:0.126426304,3_1725:0.854210847)0.988:0.188764924)0.757:0.002644042);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000872_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000872_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..925e00fc3d4999bbbcc67dd59caccc576587ffca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000872_tree_id.txt
@@ -0,0 +1 @@
+(0_994:0.019655878,1_716:0.005110034,(4_936:0.000000005,(2_1813:0.005147010,3_1702:0.000000005)0.769:0.004838271)0.775:0.004857728);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000876_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000876_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..601714ade08961bd864944da3f88dd412f245e27
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000876_tree_id.txt
@@ -0,0 +1 @@
+(0_1002:0.240948174,(1_724:0.014206204,4_943:0.005572196)1.000:0.292654029,(2_525:0.457529025,3_1697:0.830767373)0.933:0.168611214);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000880_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000880_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..67cc3ad9099d96a95732cd43c66827a6026779db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000880_tree_id.txt
@@ -0,0 +1 @@
+(0_1006:0.004321322,1_728:0.000000005,(4_947:0.007930488,(2_1805:0.103587931,3_1692:0.345839888)0.966:0.079977962)0.784:0.009465039);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000881_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000881_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..090807203711d9b7e4ff008dc9b6aa94ea3a83c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000881_tree_id.txt
@@ -0,0 +1 @@
+(1_729:0.004943517,4_948:0.009923877,(0_1007:0.018165190,(2_1804:0.051148391,3_1691:0.262554669)0.991:0.088682498)0.725:0.007587370);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000886_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000886_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fe050d36206b254bf3c12739b8b0db8ca3f37b5e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000886_tree_id.txt
@@ -0,0 +1 @@
+(0_1012:0.003146647,1_740:0.000000005,(4_959:0.006292777,(2_1797:0.033009549,3_1686:0.144317487)0.894:0.020868333)0.835:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000888_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000888_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..59f3150c33d0007cc9b8e9a4f3872a565aeec284
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000888_tree_id.txt
@@ -0,0 +1 @@
+(0_1014:0.013590910,1_742:0.021399629,(4_961:0.006209120,(2_1795:0.133007923,3_1684:0.332162119)0.989:0.082338673)0.539:0.010249971);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000889_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000889_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..767e271ba52b92186d05d75007d7a448df92bac3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000889_tree_id.txt
@@ -0,0 +1 @@
+(0_1015:0.009155388,4_962:0.001791911,(1_743:0.001607595,(2_1794:0.091854435,3_1683:0.182455117)0.998:0.057067926)0.663:0.005792838);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000895_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000895_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..22f241452333940bcb7b6b92c5856e0287e8a7c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000895_tree_id.txt
@@ -0,0 +1 @@
+((0_1034:0.0,1_762:0.0,4_983:0.0):0.051999894,2_1787:0.070370764,3_1673:0.036029387);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000899_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000899_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..18859edde6d193ee578d3fb91312ee36429e2b27
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000899_tree_id.txt
@@ -0,0 +1 @@
+(0_1038:0.000000006,(1_766:0.0,4_987:0.0):0.004723560,(2_1782:0.243569502,3_1669:0.349525789)0.938:0.088107126);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000903_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000903_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c4e7de03d1de7b7b4d15a942a264cc461b44dc47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000903_tree_id.txt
@@ -0,0 +1 @@
+(2_1778:0.021732878,3_1665:0.276696678,(0_1042:0.010419669,(1_770:0.0,4_991:0.0):0.014787870)0.950:0.039562409);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000908_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000908_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c2a57341b8e3a4d79d6f3338561cf7bcf783457
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000908_tree_id.txt
@@ -0,0 +1 @@
+((0_1047:0.0,1_775:0.0,4_996:0.0):0.070323829,2_1772:0.069312551,3_1660:0.174917417);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000918_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000918_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..43ea5911b2a6972a04b445197827ef3106a24f9c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000918_tree_id.txt
@@ -0,0 +1 @@
+(1_786:0.002455053,4_1007:0.000000005,(0_1058:0.009706623,(2_1759:0.045468788,3_1649:0.497303309)0.976:0.176924737)0.896:0.020699596);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000928_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000928_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c5e8003c047478282e2e219379842759b42a08e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000928_tree_id.txt
@@ -0,0 +1 @@
+(0_1073:0.001541070,4_1023:0.000000006,(1_801:0.004486052,(2_1743:0.049941313,3_1635:0.127032998)0.992:0.033920949)0.753:0.001708316);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000930_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000930_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f960b9b4e588331a7355319dd78cff82c4fc83d0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000930_tree_id.txt
@@ -0,0 +1 @@
+(0_1075:0.011267504,4_1025:0.000000005,(1_803:0.007303483,(2_1741:0.038192562,3_1633:0.229834318)0.976:0.041800549)0.796:0.006799607);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000931_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000931_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..075cf2885cf264f07990770e9a0c80ebca5dcca4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000931_tree_id.txt
@@ -0,0 +1 @@
+((0_1076:0.0,4_1026:0.0):0.003029642,1_804:0.003030069,(2_1740:0.028269339,3_1632:0.090136550)0.984:0.036789803);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000939_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000939_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3535b518cd8a09a9f72f6355be6e454f93f0565
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000939_tree_id.txt
@@ -0,0 +1 @@
+(2_1731:0.080739842,3_1624:0.301222262,((0_1084:0.0,1_812:0.0):0.001885958,4_1034:0.000000005)0.977:0.054263543);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000941_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000941_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..510ba15a6098714451986f11f711c7df0674c358
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000941_tree_id.txt
@@ -0,0 +1 @@
+((0_1086:0.0,1_814:0.0):0.002739948,4_1036:0.000000005,(2_1729:0.045284212,3_1622:0.097086234)1.000:0.050986139);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000943_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000943_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..776f9653f1fb5c146f4971004703339eb04c7793
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000943_tree_id.txt
@@ -0,0 +1 @@
+((0_1088:0.0,1_816:0.0):0.007988687,4_1038:0.007619490,(2_1727:0.065836056,3_1620:0.637169084)0.981:0.122541737);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000948_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000948_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b49a5279b26a69d2c45c5f01b75bd3eddd3795e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000948_tree_id.txt
@@ -0,0 +1 @@
+(0_1093:0.000000005,1_821:0.002322832,(4_1043:0.004739600,(2_1722:0.030981072,3_1615:0.203154535)0.987:0.041363339)0.792:0.004588787);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000949_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000949_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f651858744a585a7954d56cfdaa8f738a19aa952
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000949_tree_id.txt
@@ -0,0 +1 @@
+(1_822:0.002500539,(2_1721:0.009111786,3_1614:0.034941400)0.921:0.015855589,(0_1094:0.003890206,4_1044:0.000000005)0.177:0.005283604);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000953_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000953_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..89fe547759f59c267db85e9b3553d411affe8b86
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000953_tree_id.txt
@@ -0,0 +1 @@
+(0_1098:0.026730545,(1_826:0.0,4_1048:0.0):0.000000005,(2_1716:0.122223998,3_1610:0.229938066)0.995:0.098540753);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000957_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000957_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..12f251d454785740e339edaf386a1796a2927236
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000957_tree_id.txt
@@ -0,0 +1 @@
+(2_1711:0.074999633,3_1604:0.198457350,(0_1104:0.000000005,(1_832:0.0,4_1054:0.0):0.010923872)0.995:0.082362583);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000961_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000961_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..569f99d8f7b3e5bcca67fc517158d1795b777944
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000961_tree_id.txt
@@ -0,0 +1 @@
+(0_1110:0.000000005,(1_838:0.0,4_1060:0.0):0.001113690,(2_1702:0.101856085,3_1599:0.327800274)1.000:0.106454744);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000963_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000963_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0fd968c98aa4ac8560cbc1a007ba1d32b02c0bdc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000963_tree_id.txt
@@ -0,0 +1 @@
+(2_1700:0.030504419,3_1597:0.150462712,((0_1112:0.0,4_1062:0.0):0.002480610,1_840:0.000000005)0.998:0.045572279);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000966_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000966_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6fb592a0aa2fb37bbd55c6374d531f19b0f2b533
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000966_tree_id.txt
@@ -0,0 +1 @@
+(0_1116:0.002150907,4_1066:0.002145751,(1_844:0.005432771,(2_1697:0.071731314,3_1593:0.295034804)0.984:0.049914569)0.774:0.005423315);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000972_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000972_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..271aebdbcb6f3debb72fe1977f43b61ce8cce2f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000972_tree_id.txt
@@ -0,0 +1 @@
+((0_1122:0.0,1_850:0.0,4_1072:0.0):0.091066971,2_1690:0.044598632,3_1587:0.100644563);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000974_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000974_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9825beb48d9395aaabdb12dc24228a3f61b4706d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000974_tree_id.txt
@@ -0,0 +1 @@
+(2_1688:0.036928247,3_1585:0.269785830,(0_1124:0.006352021,(1_852:0.0,4_1074:0.0):0.003208373)0.990:0.068529378);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000976_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000976_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eaebf2003753a026d896611b1574a372c58f3c7a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000976_tree_id.txt
@@ -0,0 +1 @@
+(1_854:0.007961633,4_1076:0.005267562,(0_1126:0.012933237,(2_1686:0.124207956,3_1583:0.447960546)1.000:0.174246033)0.934:0.016562389);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000984_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000984_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5d37188908fcfd2ba161f6f59ec193210f8ea664
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000984_tree_id.txt
@@ -0,0 +1 @@
+((0_1135:0.0,1_863:0.0,4_1085:0.0):0.000000005,2_1676:0.032162958,3_1574:0.023909374);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000987_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000987_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..14e960ee21f8ac4d4c60b2b0660bd403d59aa6b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000987_tree_id.txt
@@ -0,0 +1 @@
+(2_1673:0.076263655,3_1571:0.510970265,((0_1138:0.0,4_1088:0.0):0.014407478,1_866:0.003658520)0.986:0.085903315);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000998_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000998_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4e8466028c6b21f31bc91bcff2fa3aec0a309547
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0000998_tree_id.txt
@@ -0,0 +1 @@
+(0_1149:0.010344598,1_878:0.000000005,(2_1661:0.053662077,(3_1558:0.155636511,4_1103:0.000000005)0.446:0.010344619)0.000:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001001_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001001_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..388c32bce6339f79063879295cd4c21e01ac9e08
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001001_tree_id.txt
@@ -0,0 +1 @@
+(2_1658:0.013231767,3_1554:0.126076048,((0_1152:0.0,4_1106:0.0):0.026163262,1_881:0.003924830)0.333:0.013236903);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001002_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001002_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9cb336a8decddf0600637dfe525b2ab97ef2fe74
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001002_tree_id.txt
@@ -0,0 +1 @@
+(0_1153:0.014173049,1_882:0.000000006,(4_1107:0.005478481,(2_1657:0.015215948,3_1553:0.128434169)0.446:0.007567695)0.757:0.003397115);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001008_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001008_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..14d68161f550a5e6a992cd37686fba944ec5a2ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001008_tree_id.txt
@@ -0,0 +1 @@
+(0_1160:0.013080447,4_1117:0.007959344,(1_888:0.010392893,(2_1650:0.060906137,3_1547:0.216702415)0.997:0.055474993)0.607:0.002333757);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001015_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001015_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3798d895206dd57df7b668bc1579174237d4711f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001015_tree_id.txt
@@ -0,0 +1 @@
+((0_1168:0.0,4_1125:0.0):0.000820604,1_896:0.008044335,(2_1643:0.059875724,3_1539:0.271647455)0.993:0.057543163);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001017_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001017_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9d7347180368fded4b680ac715cb58bf185cef51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001017_tree_id.txt
@@ -0,0 +1 @@
+((0_1170:0.0,1_898:0.0,4_1127:0.0):0.040679167,2_1641:0.034469202,3_1537:0.183057955);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001019_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001019_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed542ccbaf88085a8aaf2c8ed00b0d7d27bcdb4e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001019_tree_id.txt
@@ -0,0 +1 @@
+(2_1639:0.049894066,3_1535:0.209948918,((0_1172:0.0,1_900:0.0):0.000000005,4_1130:0.002679480)0.943:0.030946749);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001027_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001027_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ebba0d65d8e390a7fac4de70b942ea29a7563e87
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001027_tree_id.txt
@@ -0,0 +1 @@
+(1_909:0.000000006,4_1139:0.001133865,(0_1181:0.023919016,(2_1630:0.189018722,3_1527:0.416662577)1.000:0.162425762)0.946:0.021005317);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001030_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001030_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7237141920dca0e0c2c4e8a5c581d3e7a377e219
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001030_tree_id.txt
@@ -0,0 +1 @@
+(0_1184:0.005384937,(1_912:0.0,4_1142:0.0):0.004234997,(2_1627:0.033294507,3_1524:0.090631203)0.995:0.028505078);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001033_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001033_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..feb43a6bea0adcc2e672a71e1486d2c7dae333c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001033_tree_id.txt
@@ -0,0 +1 @@
+(0_1187:0.005799357,1_915:0.005813502,(4_1145:0.005327565,(2_1624:0.066067132,3_1521:0.285597023)0.995:0.053530582)0.886:0.005008058);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001044_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001044_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b65749da7d5caca858e3b6baabf9cf373b79c445
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001044_tree_id.txt
@@ -0,0 +1 @@
+((0_1198:0.0,1_926:0.0,4_1156:0.0):0.034109058,2_1612:0.066855318,3_1509:0.147060063);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001046_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001046_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2cb9cba8209f0baa9d0d8d86172924846f605a6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001046_tree_id.txt
@@ -0,0 +1 @@
+((0_1200:0.0,1_928:0.0,4_1158:0.0):0.020133639,2_1610:0.017889442,3_1507:0.070134973);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001049_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001049_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..98dcbc50df6c0bfd36b7a4f8a330e1384ce829e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001049_tree_id.txt
@@ -0,0 +1 @@
+(1_931:0.000000005,4_1161:0.002409389,(0_1203:0.002789031,(2_1607:0.027381418,3_1504:0.059073923)0.994:0.033782325)0.893:0.006955131);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001052_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001052_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e147373fe23b00622113847e86820a95fe903e42
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001052_tree_id.txt
@@ -0,0 +1 @@
+(1_935:0.000000005,4_1164:0.001095962,(0_1207:0.009962641,(2_1603:0.040636471,3_1500:0.052153087)1.000:0.022530667)0.950:0.006767832);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001057_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001057_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c22931c76a91f094a7fb79b641eb3d155b941238
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001057_tree_id.txt
@@ -0,0 +1 @@
+(0_1212:0.027548829,(1_940:0.0,4_1169:0.0):0.007350529,(2_427:0.885196305,3_1495:0.339755668)0.934:0.177284417);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001063_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001063_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3c22397003850663e47c033f45b9f19a64cdf600
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001063_tree_id.txt
@@ -0,0 +1 @@
+(0_1218:0.011479198,(1_946:0.0,4_1175:0.0):0.011401281,(2_1591:0.037204005,3_1486:0.154887637)0.984:0.052546831);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001067_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001067_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3322183e0988ee69077ec868b2d3d04c12d3dd29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001067_tree_id.txt
@@ -0,0 +1 @@
+(0_1222:0.000000005,(1_950:0.0,4_1179:0.0):0.003256265,(2_1587:0.101481469,3_1482:0.213297372)0.993:0.060140053);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001072_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001072_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a59e386a309d4c66331e46cc1e9842f69a1132c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001072_tree_id.txt
@@ -0,0 +1 @@
+(1_956:0.000000005,4_1185:0.001422741,(0_1228:0.003515366,(2_1581:0.079887284,3_1476:0.188072028)0.998:0.055908465)0.932:0.006563777);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001073_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001073_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b283417f2e6739e4f8305000175de1c357685f59
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001073_tree_id.txt
@@ -0,0 +1 @@
+(0_1229:0.014830070,(1_957:0.0,4_1186:0.0):0.000000005,(2_1580:0.119941593,3_1475:0.217328754)0.975:0.052009410);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001078_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001078_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5fac29e9b56c96150740346c2ea9b18b10083ecd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001078_tree_id.txt
@@ -0,0 +1 @@
+(0_1234:0.013105057,(1_962:0.0,4_1191:0.0):0.005330229,(2_1573:0.100986237,3_1469:0.596235968)0.986:0.144523157);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001080_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001080_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e9285b4ffc5490166dcc87698d25a97bba014fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001080_tree_id.txt
@@ -0,0 +1 @@
+((0_1236:0.0,1_964:0.0,4_1193:0.0):0.167370334,2_1571:0.138074678,3_1467:0.507532963);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001087_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001087_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..14692fb671ae82da99d78655bbcae94079b13342
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001087_tree_id.txt
@@ -0,0 +1 @@
+((0_1251:0.0,1_983:0.0,4_1208:0.0):0.070571933,2_1563:0.086738408,3_1459:0.182429862);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001088_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001088_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..acbd5b8979804f04dd3cd277eaf68944880ea566
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001088_tree_id.txt
@@ -0,0 +1 @@
+((0_1252:0.0,1_984:0.0,4_1209:0.0):0.126816273,2_1562:0.035578827,3_1458:0.445569404);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001094_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001094_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3498aa95b8f06ed57e044f72c8d6a6fbad2c9855
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001094_tree_id.txt
@@ -0,0 +1 @@
+(2_1555:0.046428548,3_1451:0.183605157,(0_1259:0.010123666,(1_991:0.0,4_1216:0.0):0.007621834)0.999:0.068164566);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001095_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001095_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..efb13471e04ed724c9771c2b0e1b5d14cc1c9f73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001095_tree_id.txt
@@ -0,0 +1 @@
+(0_1260:0.008787004,(1_992:0.0,4_1217:0.0):0.004481120,(2_1554:0.074048394,3_1450:0.324418440)0.955:0.057397619);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001098_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001098_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..174d90eece2ca6ff2e6d7b04bfc6fec24c0565f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001098_tree_id.txt
@@ -0,0 +1 @@
+(0_1263:0.003829696,2_1551:0.005172311,(3_1447:0.222862202,(1_995:0.012020330,4_1220:0.003369719)1.000:0.321027499)1.000:0.174600176);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001111_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001111_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..41f9c0e7e33ab1096687a509bdae663f31fcf61f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001111_tree_id.txt
@@ -0,0 +1 @@
+(0_1278:0.001521080,1_1008:0.000000005,(4_1233:0.010517507,(2_1535:0.086523942,3_1431:0.123123523)0.991:0.034554603)0.898:0.004734627);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001114_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001114_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f711dba846faf38aa2ac686b5114da204c7278bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001114_tree_id.txt
@@ -0,0 +1 @@
+((2_1532:0.0,4_1236:0.0):0.000000005,1_1011:0.004278798,(0_1281:0.004293205,3_1428:0.192513895)0.429:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001117_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001117_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6257a1f65349573618aa8d931f795c60a82c6029
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001117_tree_id.txt
@@ -0,0 +1 @@
+((0_1284:0.0,1_1014:0.0,2_1529:0.0):0.120400841,3_1425:0.167199753,4_1239:0.140900675);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001121_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001121_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d16c792eac06219b15eefb756b6295a94d2efc02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001121_tree_id.txt
@@ -0,0 +1 @@
+(1_1019:0.000000005,4_1244:0.003391533,(0_1290:0.004140759,(2_1524:0.038144420,3_1420:0.214085144)0.918:0.034941972)0.798:0.006051304);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001131_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001131_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2163a4a52c70a41b1ce6d659eb31c8ed4ee92dc5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001131_tree_id.txt
@@ -0,0 +1 @@
+(0_1301:0.011318755,4_1255:0.011245855,(1_1030:0.011895636,(2_1513:0.071890732,3_1409:0.254151203)0.998:0.128493764)0.051:0.007188466);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001137_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001137_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..98b9ef8b4e63bfb173ef4a143470343c060bea75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001137_tree_id.txt
@@ -0,0 +1 @@
+(0_1307:0.009443452,4_1261:0.006538360,(1_1036:0.000000005,(2_1507:0.078241358,3_1403:0.489228666)0.997:0.106271267)0.870:0.005697423);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001139_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001139_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..50ef0dcf2d71dbcab9c124ef4769fccf03e42876
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001139_tree_id.txt
@@ -0,0 +1 @@
+(0_1310:0.003960964,4_1264:0.001522890,(1_1039:0.003949352,(2_1505:0.083242877,3_1400:0.110648991)0.999:0.054967554)0.363:0.001845059);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001140_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001140_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8326b985068c5cd96bf7e8aac20e9d89842ed209
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001140_tree_id.txt
@@ -0,0 +1 @@
+(0_1311:0.006702711,4_1265:0.003267986,(1_1040:0.017984330,(2_1504:0.101114257,3_1399:0.248261673)1.000:0.091469406)0.911:0.011179684);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001141_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001141_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..414be7639c0beef16f29f1b01205bd61895c2251
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001141_tree_id.txt
@@ -0,0 +1 @@
+(0_1312:0.000000005,4_1266:0.001665457,(1_1041:0.004134812,(2_1503:0.078327542,3_1398:0.362230734)0.994:0.058926048)0.924:0.007589621);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001142_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001142_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..58268bb93aefc080f45735f7b2061dfea99ae076
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001142_tree_id.txt
@@ -0,0 +1 @@
+(0_1313:0.000000005,4_1267:0.004780425,(1_1042:0.047508068,(2_1502:0.129982917,3_1397:0.585656992)0.869:0.054721129)0.770:0.011794379);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001143_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001143_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..44aa2e868ff659f8ca1ebc7a9dfb2839e77fcd80
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001143_tree_id.txt
@@ -0,0 +1 @@
+(2_1501:0.039838870,3_1396:0.167163487,((0_1314:0.0,4_1268:0.0):0.008836933,1_1043:0.002836472)0.926:0.022597153);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001147_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001147_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..af1bb59c7fda87304a30b13c260f099674de6f6a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001147_tree_id.txt
@@ -0,0 +1 @@
+(0_1318:0.008027472,1_1047:0.008024961,(4_1272:0.005211710,(2_1497:0.095610637,3_1392:0.297854963)1.000:0.147051626)0.822:0.005524510);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001148_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001148_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..30158fd8af8df7229c31a624b6537c43622dae1e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001148_tree_id.txt
@@ -0,0 +1 @@
+(2_1496:0.062391810,3_1391:0.221194621,((0_1319:0.0,1_1048:0.0):0.007327502,4_1273:0.000000005)0.959:0.068324133);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001153_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001153_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e84a110dc6f084586236d9af2d801f507e72f53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001153_tree_id.txt
@@ -0,0 +1 @@
+(0_1325:0.000516384,(2_1489:0.055640084,3_1384:0.264229318)1.000:0.094598622,(1_1054:0.000000006,4_1279:0.001586187)0.864:0.007456677);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001155_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001155_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0fcfe2c19da108cbad584b6cb3d714b948300fd6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001155_tree_id.txt
@@ -0,0 +1 @@
+(2_1487:0.002660698,3_1382:0.113608641,(0_1327:0.003993937,(1_1056:0.001067420,4_1281:0.003974263)0.949:0.004194635)0.945:0.004356584);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001156_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001156_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..03f66b46014899acb94a71da5220ef1a241e0c12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001156_tree_id.txt
@@ -0,0 +1 @@
+(2_1486:0.025916262,3_1381:0.180416059,(4_1282:0.009532906,(0_1328:0.000000005,1_1057:0.005346547)0.876:0.013189756)0.865:0.017508311);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001163_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001163_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c35d6cff81b790ccdec35e8bf4da7a62a55841d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001163_tree_id.txt
@@ -0,0 +1 @@
+(1_1094:0.001908425,4_1304:0.000000005,(0_1355:0.001912891,(2_1462:0.012086707,3_1374:0.101728950)0.962:0.013179125)0.777:0.001904631);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001165_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001165_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..20277e5bc91a1bc6e6a6069f5e018fa6974a46a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001165_tree_id.txt
@@ -0,0 +1 @@
+((0_1358:0.0,1_1097:0.0,4_1307:0.0):0.028180519,2_1460:0.013236540,3_1371:0.111444318);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001166_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001166_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fec87193e207a835e2a5c584f27d31e7e65d71b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001166_tree_id.txt
@@ -0,0 +1 @@
+(0_1363:0.007397657,4_1312:0.008076732,(1_1103:0.003682711,(2_1458:0.031241788,3_1365:0.156823255)0.985:0.027180245)0.158:0.003097795);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001167_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001167_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cd33a044034fa2f449447520d29e9783a42424fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001167_tree_id.txt
@@ -0,0 +1 @@
+(2_1457:0.019790500,3_1364:0.282746882,((0_1364:0.0,1_1104:0.0):0.000000005,4_1313:0.004265783)0.957:0.048332416);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001179_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001179_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..74f413fb1b8e55fea3e2cfa61151a65bbdecd4cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001179_tree_id.txt
@@ -0,0 +1 @@
+(1_1118:0.003879280,4_1326:0.002590926,(0_1377:0.003020072,(2_1444:0.051758797,3_1351:0.202374703)1.000:0.062528916)0.850:0.003476663);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001185_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001185_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc6282b133661fa9987174228cdb0af345e6a526
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001185_tree_id.txt
@@ -0,0 +1 @@
+(0_1383:0.002336583,1_1124:0.002334526,(4_1332:0.004323135,(2_1437:0.093477896,3_1345:0.217203243)0.998:0.087999906)0.742:0.005017746);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001188_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001188_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f04457a96c2de790c6a8d554c3506305c9596a60
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001188_tree_id.txt
@@ -0,0 +1 @@
+((2_1434:0.052494868,3_1342:0.114154884)0.987:0.038752046,1_1127:0.002952245,(4_1335:0.005817440,0_1386:0.005731101)0.582:0.002798931);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001191_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001191_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aaef947bc61dbb98868102bfc44fe4754bcb43c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001191_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001199_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001199_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..87c1a4a535a9f2d2294d3c07461a878d345e1561
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001199_tree_id.txt
@@ -0,0 +1 @@
+(1_1141:0.071345436,2_1421:0.046142163,(3_1325:0.273872785,(0_1400:0.011985806,4_1349:0.020354597)0.989:0.073251213)0.993:0.090107822);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001201_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001201_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8de4bd965298c278190a48d9eb4521bcf6d4697
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001201_tree_id.txt
@@ -0,0 +1 @@
+(4_1352:0.003165909,(2_1419:0.060746743,3_1322:0.202746135)0.994:0.107096480,(0_1403:0.000000005,1_1144:0.006564762)0.764:0.003749082);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001204_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001204_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1d3ec41e94a0ce3d311891761ab6f327068246bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001204_tree_id.txt
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+((0_1406:0.0,1_1147:0.0,2_1416:0.0,4_1355:0.0):0.012404401,3_1319:0.012404401);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001205_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001205_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ae4576ff3173906f23f06b2b4494f7fc419a8f86
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001205_tree_id.txt
@@ -0,0 +1 @@
+((0_1407:0.0,1_1148:0.0,4_1356:0.0):0.069671915,2_1415:0.098865112,3_1318:0.328434604);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001208_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001208_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..23a563bcbbe82c1203b2f6a29c85d4043bf72574
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001208_tree_id.txt
@@ -0,0 +1 @@
+(1_1151:0.013126892,4_1359:0.000000005,(0_1410:0.000000005,(2_1412:0.113692135,3_1315:0.404989856)0.698:0.027280459)0.831:0.013134293);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001225_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001225_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cd211b5582d5c7c7bc22dc3542b7d79f86ec5036
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001225_tree_id.txt
@@ -0,0 +1 @@
+(1_1171:0.008152068,4_1379:0.004622012,(0_1430:0.016267948,(2_1394:0.107654664,3_1294:0.422860705)0.999:0.119535946)0.350:0.007345079);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001227_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001227_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ad10927852ba8ecff37e5f054522a31ffdccd37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001227_tree_id.txt
@@ -0,0 +1 @@
+((2_1392:0.148540398,3_1292:0.363117574)0.999:0.119444373,4_1381:0.003855765,(0_1432:0.017662399,1_1173:0.000000005)0.754:0.002679214);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001229_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001229_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0d6848ed04588087a86ec0294e2c8606d50f8afa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001229_tree_id.txt
@@ -0,0 +1 @@
+(0_1434:0.003460847,(1_1175:0.0,4_1383:0.0):0.000000005,(2_1390:0.032020409,3_1290:0.126912179)0.994:0.055888220);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001238_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001238_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..39c099ea5e741e1b778f82f52c16d08decf4dff9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001238_tree_id.txt
@@ -0,0 +1 @@
+(1_1185:0.002577953,4_1393:0.004279966,(0_1466:0.005852146,(2_1380:0.082757411,3_1280:0.316912957)1.000:0.051053478)0.932:0.004563059);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001243_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001243_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d9b7881a4280ba0cc17120e29a16d924cc6d235c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001243_tree_id.txt
@@ -0,0 +1 @@
+(1_1190:0.000000005,4_1398:0.002963822,(0_1471:0.005928644,(2_1375:0.084971884,3_1275:0.012029549)0.324:0.006454340)0.914:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001246_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001246_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3758dd95e0618fe3e7dc6c4004fdc6e6cee4de95
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001246_tree_id.txt
@@ -0,0 +1 @@
+(2_1372:0.040671435,3_1264:0.418092241,((0_1474:0.0,1_1194:0.0):0.010477544,4_1401:0.020515840)0.867:0.057385458);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001248_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001248_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c2c763b5d628740931f0fee0298939ee0f542b74
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001248_tree_id.txt
@@ -0,0 +1 @@
+(0_1476:0.002818590,1_1196:0.004974888,(4_1403:0.005181296,(2_1370:0.049344154,3_1262:0.147218866)0.956:0.032234628)0.407:0.005497455);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001251_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001251_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e7b41e90926e804455bbf23f23db016459662eee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001251_tree_id.txt
@@ -0,0 +1 @@
+(0_1479:0.001983426,(1_1199:0.0,4_1406:0.0):0.000000005,(2_1367:0.102267416,3_1259:0.219433933)1.000:0.070100343);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001252_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001252_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e40b27e8cc313f58427e3f83fdbedc76a4ad486
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001252_tree_id.txt
@@ -0,0 +1 @@
+((0_1480:0.0,4_1407:0.0):0.000000005,1_1200:0.002423180,(2_1366:0.065740737,3_1258:0.133684667)0.999:0.066391634);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001254_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001254_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..90b0c1d7dc003df95a0b4490101d163cc107dba7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001254_tree_id.txt
@@ -0,0 +1 @@
+(0_1482:0.008936978,4_1409:0.026978111,(1_1202:0.000000006,(2_1364:0.108024369,3_1256:0.705364311)0.859:0.064865238)0.837:0.004366206);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001259_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001259_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..991e17f17f1f5f0fe9c904df5f5a7aaf58878282
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001259_tree_id.txt
@@ -0,0 +1 @@
+(0_1488:0.018032456,4_1415:0.003223927,(1_1208:0.006612405,(2_1358:0.081281436,3_1250:0.349344402)1.000:0.119127405)0.620:0.008058323);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001260_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001260_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..56766182a3483bbd18f9e6a17662f3b0fe6c99a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001260_tree_id.txt
@@ -0,0 +1 @@
+(0_1489:0.000000005,4_1416:0.003931758,(1_1209:0.007540438,(2_1357:0.123216527,3_1249:0.364470513)0.986:0.119332823)0.954:0.037649146);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001263_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001263_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..856c85e9282f0a7ae053560addc1cbbc78d4c147
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001263_tree_id.txt
@@ -0,0 +1 @@
+(2_1354:0.064834914,3_1246:0.180550671,((0_1492:0.0,1_1212:0.0):0.020369370,4_1419:0.011444502)0.968:0.041206596);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001264_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001264_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..39e9e61a5c98c6aea6d462ae1278aae4306a2dbd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001264_tree_id.txt
@@ -0,0 +1 @@
+(0_1493:0.000000005,1_1213:0.000000005,(3_1245:0.385521150,(2_1353:0.134008578,4_1420:0.008669476)0.585:0.010750550)0.721:0.009569636);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001270_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001270_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1395703c1a6417fcf4c94d5ca8ac1a1807b71af4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001270_tree_id.txt
@@ -0,0 +1 @@
+(0_1500:0.000000005,4_1427:0.003271517,(1_1220:0.008487913,(2_1346:0.082904717,3_1238:0.165857324)0.982:0.058390751)0.753:0.004831928);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001271_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001271_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..30c15501572e675c1332e0b896904d16450a85c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001271_tree_id.txt
@@ -0,0 +1 @@
+(2_1345:0.015205247,3_1237:0.149281354,(0_1501:0.002958699,(1_1221:0.0,4_1428:0.0):0.005746521)0.418:0.016988712);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001273_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001273_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db6bcdb2b5352d24f4c21953a00e65240de17507
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001273_tree_id.txt
@@ -0,0 +1 @@
+(0_1503:0.005302853,1_1223:0.005250661,(4_1430:0.000809455,(2_1343:0.035475398,3_1235:0.143776237)0.998:0.060561061)0.779:0.007135078);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001276_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001276_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..428e72e4537252648619d7e4c67e95c49684483f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001276_tree_id.txt
@@ -0,0 +1 @@
+(0_1507:0.006713624,(2_1340:0.048916445,3_1232:0.174824348)0.999:0.053123777,(1_1227:0.002580939,4_1434:0.000000005)0.858:0.006352319);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001277_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001277_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2ed8f62a197644643b0acca7523b7f4db0972d86
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001277_tree_id.txt
@@ -0,0 +1 @@
+(2_1339:0.009096450,3_1231:0.062939483,((0_1508:0.0,1_1228:0.0):0.000000005,4_1435:0.009626329)0.940:0.030496342);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001286_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001286_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..91902a0ed51b20ee53107f228c581c1106f78d7f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001286_tree_id.txt
@@ -0,0 +1 @@
+(0_1519:0.000000005,4_1446:0.010014180,(1_1239:0.003346662,(2_1326:0.040693439,3_1220:0.126998638)0.998:0.061478358)0.860:0.006613291);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001289_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001289_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4019ad958b734681f3fe1444edec612cdc5fbe7e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001289_tree_id.txt
@@ -0,0 +1 @@
+(1_1242:0.003184704,4_1449:0.000000005,(0_1522:0.003332755,(2_1323:0.085536878,3_1217:0.170128308)1.000:0.134236991)0.762:0.003041487);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001291_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001291_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5be04baf9606326342bf9d7b748143ac9222bc3f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001291_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001296_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001296_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fcc6c4eb8a96aa1ceeb253b368f661998f772d54
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001296_tree_id.txt
@@ -0,0 +1 @@
+((0_1537:0.0,1_1259:0.0):0.006105696,4_1464:0.019856261,(2_1275:0.122236047,3_1195:0.141673174)0.972:0.084359506);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001315_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001315_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a9aec193c8b27070db920cd45ebfddb9da357400
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001315_tree_id.txt
@@ -0,0 +1 @@
+(0_1579:0.011066533,1_1294:0.000000005,(4_1508:0.021012194,(2_1237:0.370656584,3_1147:0.345129470)1.000:0.337219067)0.669:0.004245132);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001316_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001316_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..97cffe52e2ea741cfdf1482fa6056e3a637931b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001316_tree_id.txt
@@ -0,0 +1 @@
+(1_1295:0.011084954,4_1509:0.006607211,(0_1580:0.000000005,(2_1236:0.176778730,3_1146:0.146196479)0.999:0.099734937)0.806:0.002195449);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001318_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001318_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ff2be3cd8ef8407bf6719de69ae80c0e6d81fd5d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001318_tree_id.txt
@@ -0,0 +1 @@
+(0_1583:0.000000005,1_1298:0.009916385,(4_1512:0.024944901,(2_1233:0.102795284,3_1143:0.422040268)0.953:0.060719019)0.928:0.019988907);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001331_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001331_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b32724f0ca5305955c9c6b0613dc99d544b4beff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001331_tree_id.txt
@@ -0,0 +1 @@
+(1_1311:0.011347240,4_1526:0.000000005,(0_1596:0.000000005,(2_1218:0.085298803,3_1130:0.206999833)0.983:0.104124176)0.827:0.005646973);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001336_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001336_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6e3975dcc0ad9edab437f1e5f5f8029a754bdd0c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001336_tree_id.txt
@@ -0,0 +1 @@
+(0_1603:0.009962695,(1_1318:0.0,2_1212:0.0,4_1533:0.0):0.000000005,3_1124:0.009993142);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001337_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001337_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ed1b34bb6aa337cddfb4c73d545141b8db8ef70
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001337_tree_id.txt
@@ -0,0 +1 @@
+(4_1535:0.003947313,3_1122:0.003942237,((0_1605:0.000000005,2_1210:0.052567688)0.830:0.003936351,1_1320:0.003947320)0.599:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001338_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001338_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1069241b49ac8f49ec94479d390b0f1426f38a85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001338_tree_id.txt
@@ -0,0 +1 @@
+(0_1606:0.010902429,1_1321:0.002687006,(4_1536:0.008146203,(2_1209:0.104046590,3_1121:0.000000005)0.260:0.008152257)0.869:0.005447180);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001352_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001352_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52ae275932204bfc4848398592c648e40ecbbe64
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001352_tree_id.txt
@@ -0,0 +1 @@
+(1_1336:0.013349922,4_1551:0.009339194,(0_1621:0.012572990,(2_1178:0.100987896,3_1107:0.407280985)1.000:0.110853682)0.260:0.006685845);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001357_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001357_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..437c30427cdb5e72ffb4776f7f18ac1101569888
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001357_tree_id.txt
@@ -0,0 +1 @@
+((0_1628:0.0,4_1557:0.0):0.000000005,1_1342:0.002852867,(2_1171:0.034709402,3_1101:0.198790898)0.994:0.070139220);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001358_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001358_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5b18c2eb0944eade5451d1780d037c86e71843f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001358_tree_id.txt
@@ -0,0 +1 @@
+(0_1630:0.000000005,4_1559:0.006897066,(1_1344:0.006898363,(2_1169:0.130754321,3_1100:0.130013253)0.998:0.196843613)0.760:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001359_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001359_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..19beb17eb5352f76829aebc09470f52bd00006fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001359_tree_id.txt
@@ -0,0 +1 @@
+((0_1631:0.0,1_1345:0.0,4_1560:0.0):0.146514753,2_1168:0.223961577,3_1099:0.608393138);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001361_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001361_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fe1b3cf230ca48e7ed623f2e12598c439a56a88f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001361_tree_id.txt
@@ -0,0 +1 @@
+(1_1348:0.000000006,4_1563:0.035314639,(0_1634:0.011024560,(3_1096:0.137461339,2_1165:0.522321465)0.619:0.013907139)0.801:0.038784105);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001363_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001363_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4ee1458fae36d7224140b0cb25ba5f9e07f5693
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001363_tree_id.txt
@@ -0,0 +1 @@
+(2_1163:0.000000005,3_1094:0.055595058,((0_1636:0.0,1_1353:0.0):0.000000005,4_1565:0.006721507)0.969:0.020267841);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001365_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001365_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a12d55eabc22179d1878aaf237133e0fadb23d75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001365_tree_id.txt
@@ -0,0 +1 @@
+(2_1161:0.021321957,3_1092:0.040390133,((0_1638:0.0,4_1567:0.0):0.003918398,1_1355:0.000000005)0.980:0.030735915);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001367_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001367_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3cc996c69fd41132a3123ef61c297c701760470a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001367_tree_id.txt
@@ -0,0 +1 @@
+((0_1640:0.0,1_1357:0.0,4_1569:0.0):0.014021728,2_1159:0.000000005,3_1090:0.014209689);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001370_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001370_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9eccc9de8006690374bd9c9762af992aefb516d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001370_tree_id.txt
@@ -0,0 +1 @@
+((0_1643:0.0,1_1360:0.0,2_1156:0.0,4_1572:0.0):0.006717005,3_1087:0.006717005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001376_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001376_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4aa5a21bc255bebbf0c003135dcbaa843d12c6fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001376_tree_id.txt
@@ -0,0 +1 @@
+((0_1649:0.0,1_1366:0.0,4_1578:0.0):0.018454605,2_1150:0.005189958,3_1081:0.064357016);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001379_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001379_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..95c10d65d1f71bcef57b10bdd2584e240910cfc2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001379_tree_id.txt
@@ -0,0 +1 @@
+((0_1652:0.0,1_1369:0.0,4_1581:0.0):0.000000005,2_1147:0.007480552,3_1078:0.038387307);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001383_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001383_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e1437c34fb75646aa69663d229dd4b2afbfdde51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001383_tree_id.txt
@@ -0,0 +1 @@
+((0_1656:0.0,1_1373:0.0,4_1585:0.0):0.035748381,2_1143:0.005303664,3_1074:0.135188484);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001384_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001384_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d377c94ca6d7312b04b3532c22850a2ed3943323
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001384_tree_id.txt
@@ -0,0 +1 @@
+((0_1657:0.0,1_1374:0.0,4_1586:0.0):0.010779375,2_1142:0.021962216,3_1073:0.058154787);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001386_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001386_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3d4ba4d5089908f79c6dc22fc3d7c5b75c9d6ab8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001386_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001388_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001388_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b7f198b31367f2eaa30ad64369539255b447639e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001388_tree_id.txt
@@ -0,0 +1 @@
+((0_1661:0.0,1_1378:0.0,2_1138:0.0,4_1590:0.0):0.005374529,3_1069:0.005374529);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001390_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001390_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..993bc49ffc1cc2f3d2603058d1e96b37eacbe620
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001390_tree_id.txt
@@ -0,0 +1 @@
+((0_1663:0.0,1_1380:0.0,2_1136:0.0,4_1592:0.0):0.029826498,3_1067:0.029826498);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001394_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001394_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0ce21f929fa77282a1a9f178b052389bec9f6aa5
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001394_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001396_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001396_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aad089650e73419c2398c4097c2cd73d4504a786
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001396_tree_id.txt
@@ -0,0 +1 @@
+(2_1130:0.006973756,3_1061:0.017114871,((0_1669:0.0,4_1598:0.0):0.000000005,1_1386:0.002470487)0.953:0.010940704);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001399_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001399_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6a2e11e08ea4dd7d9cbf820888e9a2518bf2985
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001399_tree_id.txt
@@ -0,0 +1 @@
+(2_1127:0.000000005,3_1058:0.016111057,(0_1672:0.000000005,(1_1389:0.0,4_1601:0.0):0.008004046)0.410:0.008020230);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001400_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001400_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5dc72dfd1b75e9d80f56e1be2ec9a7e8021cd207
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001400_tree_id.txt
@@ -0,0 +1 @@
+(2_1126:0.018509936,3_1056:0.046356940,((0_1673:0.0,4_1602:0.0):0.000761500,1_1390:0.000767390)0.978:0.010074852);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001403_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001403_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4bf68857689c5532194bfe4d7db585bc45139c7e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001403_tree_id.txt
@@ -0,0 +1 @@
+(2_1123:0.011073477,3_1053:0.070540918,(0_1676:0.005623831,(1_1393:0.0,4_1605:0.0):0.000000005)0.913:0.017343619);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001406_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001406_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d4a19977cc9ac82f07cae3895a2c9d3cf4c8d234
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001406_tree_id.txt
@@ -0,0 +1 @@
+(1_1396:0.007026500,(2_1120:0.078116563,3_1050:0.147182406)0.898:0.032430038,(0_1679:0.002830832,4_1608:0.003047244)0.778:0.004746515);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001407_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001407_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a345e48a045e27f6a1a5606e9cb453cb41ed9b88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001407_tree_id.txt
@@ -0,0 +1 @@
+(2_1119:0.029071875,3_1049:0.306649309,((0_1680:0.0,4_1609:0.0):0.012408479,1_1397:0.000000005)0.567:0.036136465);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001408_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001408_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ac6b254df8f96492bed0a7552c8a6761319d883f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001408_tree_id.txt
@@ -0,0 +1 @@
+(0_1681:0.004831154,1_1398:0.000000005,(4_1610:0.002997138,(2_1118:0.057497530,3_1048:0.062551709)0.996:0.044841174)0.903:0.009121542);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001409_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001409_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3964461988157d56193a82ac0e44fa530c0a5bc0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001409_tree_id.txt
@@ -0,0 +1 @@
+(4_1611:0.012540383,1_1399:0.008347740,(0_1682:0.004317302,(2_1117:0.023090773,3_1047:0.144809214)0.968:0.040511590)0.772:0.003984545);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001410_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001410_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cd72257ed58fb7c99d4d569251d2cdb5ffa0da33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001410_tree_id.txt
@@ -0,0 +1 @@
+(0_1683:0.009603261,4_1612:0.011907130,(1_1400:0.013308211,(2_1116:0.109620094,3_1046:0.220582403)0.999:0.102444671)0.889:0.015752794);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001411_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001411_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cd6250b8dac90883240c8d0882ef1bec04596f43
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001411_tree_id.txt
@@ -0,0 +1 @@
+(0_1684:0.005786934,4_1613:0.002846633,(1_1401:0.012829103,(2_1115:0.183205828,3_1045:0.420789750)1.000:0.242818221)0.734:0.004563198);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001418_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001418_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d3afc2d39a32ca59d4fd3617adfd60175939d2a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001418_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001428_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001428_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..26bcda7058cce89ccc3ac0d1ce136b21c2bc6d7b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001428_tree_id.txt
@@ -0,0 +1 @@
+((0_1701:0.0,1_1418:0.0,4_1630:0.0):0.071557682,2_1097:0.213955429,3_1023:0.340845966);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001430_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001430_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5832e7e5eaace788e5037febdd5e24aa07eb6b95
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001430_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001433_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001433_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d1f3566f49b8146294ccaa02f447e59273a1a8dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001433_tree_id.txt
@@ -0,0 +1 @@
+(4_1635:0.007570085,1_1423:0.001887305,(0_1706:0.001906923,(2_1092:0.043854451,3_1018:0.215334837)1.000:0.065850941)0.762:0.001863780);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001438_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001438_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fae37e1a13f523cc5e14248834b3034a3bea37a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001438_tree_id.txt
@@ -0,0 +1 @@
+(1_1429:0.009496205,4_1641:0.002369887,(0_1712:0.011897420,(2_1086:0.053427842,3_1013:0.221351197)1.000:0.079007494)0.897:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001439_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001439_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d610c0d7d5b09130059d67abe6fbc42404b62109
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001439_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001446_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001446_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f2239c145943b7182dd4cebd8ed4779e65da2c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001446_tree_id.txt
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+(0_1724:0.004306498,1_1441:0.003516995,(4_1653:0.010693628,(2_1075:0.070776923,3_999:0.090073779)0.999:0.057835999)0.507:0.003542206);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001470_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001470_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a965e47c4775b8a7d694b9ce6d2c8df5758291a
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001474_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001474_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b6e8500d01ebb6996c3fe02c0c1f9d85ac3182c
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001478_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001478_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b19e6588a7c63644590ffe8d431771934efa55ae
--- /dev/null
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001479_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001479_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6015970deee19a535dc116a4af109480ce447067
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001483_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001483_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c86262d25cf1e4c8fd25d2ce99efdad2170c80f
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001485_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001485_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..01354605c502c88feae78441a1ca0e35389d82f4
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001490_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001490_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ba5ade36f1feee78ccb0a857ed9c3a4104d2b79
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001494_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001494_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e2adf59676ceb6b63b33c215ebdf4475485d0c8a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001494_tree_id.txt
@@ -0,0 +1 @@
+(0_1791:0.002072839,4_1712:0.004306574,(1_1498:0.002122147,(2_997:0.132506965,3_940:0.511305896)0.999:0.158771020)0.908:0.012895444);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001498_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001498_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df02d4def22c00098609cb3f9c1de7a9aa10a921
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001498_tree_id.txt
@@ -0,0 +1 @@
+(2_988:0.091210982,3_933:0.495875083,((0_1796:0.0,4_1717:0.0):0.017896631,1_1503:0.018664382)0.924:0.089205539);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001501_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001501_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3c9ed24716ec5312b7913cfa91d550d9ac8e23c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001501_tree_id.txt
@@ -0,0 +1 @@
+((2_985:0.249675393,3_930:0.153476435)1.000:0.164108506,4_1720:0.002632487,(1_1506:0.012339872,0_1799:0.002794212)0.259:0.009758177);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001506_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001506_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..296838150ed306340fa2b69c6b4767d33689ddfc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001506_tree_id.txt
@@ -0,0 +1 @@
+((2_976:0.077888419,3_916:0.451364084)0.996:0.108455529,4_1725:0.000000005,(1_1511:0.023262247,0_1804:0.002522537)0.764:0.002506856);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001508_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001508_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..23086cc1208fc120e3a9aefac4781f1b5e0f673e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001508_tree_id.txt
@@ -0,0 +1 @@
+(0_1806:0.000000005,4_1727:0.007220925,(1_1513:0.004917762,(2_974:0.081023013,3_913:0.266430720)0.975:0.069936869)0.614:0.002283702);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001514_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001514_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..326574f52c9d6a15e18e8040fc932466667a7d24
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001514_tree_id.txt
@@ -0,0 +1 @@
+(0_1812:0.003034954,1_1519:0.003073835,(4_1733:0.011074072,(2_968:0.024218573,3_906:0.200648866)1.000:0.113488282)0.758:0.004337371);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001523_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001523_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d216efed07c3a8acb6dd5f0e18cd661a984e5acb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001523_tree_id.txt
@@ -0,0 +1 @@
+(2_954:0.029559130,3_893:0.398963202,((0_1824:0.0,4_1745:0.0):0.022406600,1_1531:0.008574643)0.864:0.072386115);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001524_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001524_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c4b7891cea2f7bf2ade50d14e8059c0e0d3d4e18
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001524_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001526_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001526_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..162c14feb8412a5550236c485747797d8049d1e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001526_tree_id.txt
@@ -0,0 +1 @@
+(2_951:0.089998529,3_890:0.506648463,((0_1827:0.0,4_1748:0.0):0.112935057,1_1534:0.001774660)0.982:0.133061358);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001536_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001536_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..da25c9193d301dbc73d8a8e4743ddc4f84378143
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001536_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001546_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001546_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9a80c3c2d18e6b48893e46d2c66ba70b124899ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001546_tree_id.txt
@@ -0,0 +1 @@
+(3_858:0.046067904,(0_1858:0.005345456,1_1565:0.002662860)0.769:0.003263355,(2_922:0.033406758,4_1779:0.007450586)0.548:0.002714989);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001547_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001547_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64711777eadae79ae42c8505a26386376603806f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001547_tree_id.txt
@@ -0,0 +1 @@
+(0_1859:0.007149528,1_1566:0.007121090,(4_1780:0.000000005,(2_921:0.027677179,3_857:0.296444695)0.876:0.022562176)0.729:0.003570873);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001550_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001550_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d247d392651c059e4cfceec0d8ac5ce73ef9aeb6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001550_tree_id.txt
@@ -0,0 +1 @@
+((0_1863:0.0,1_1570:0.0,4_1784:0.0):0.028266176,2_917:0.243359834,3_853:0.005305192);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001551_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001551_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b4356e1a0abd8111c54f448777a634128560efd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001551_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001552_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001552_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c0a2c6294380845faca75f181ae97cfb443a6986
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001552_tree_id.txt
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+(0_1866:0.000000005,4_1786:0.005643549,(1_1573:0.011358534,(2_915:0.209810132,3_847:0.019841748)0.662:0.003500334)0.754:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001554_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001554_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e5ffc8f29d25770700b8bcd6815e078abd80e40d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001554_tree_id.txt
@@ -0,0 +1 @@
+(0_1868:0.012316872,1_1575:0.004576073,(4_1788:0.007364103,(2_911:0.062754707,3_844:0.222639529)1.000:0.103544402)0.535:0.002647746);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001559_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001559_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c3f664912121a079ecf44b8e95b294bf07183b21
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001559_tree_id.txt
@@ -0,0 +1 @@
+(0_1874:0.002779688,1_1581:0.002762484,(4_1794:0.004886193,(2_905:0.241094032,3_840:0.226400223)0.999:0.135218780)0.777:0.006245968);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001570_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001570_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4555e62d56b27110033615c1b9094a3baeb3d126
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001570_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001571_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001571_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..936de8c67de1575009b8d4c289f91c700e294b46
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001571_tree_id.txt
@@ -0,0 +1 @@
+(0_1903:0.004305013,2_874:0.023458650,(4_1830:0.007597696,(3_422:0.936182947,3_815:0.424046487)0.944:0.221904800)0.569:0.010744488);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001572_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001572_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..28057921121c2db6d4d24436db5757a543b9e1b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001572_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001578_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001578_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a843265c38534d46ab36d3bb585e249d1ef610f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001578_tree_id.txt
@@ -0,0 +1 @@
+(1_1618:0.021627098,4_1840:0.021648834,(0_1913:0.015622417,(2_865:0.298026968,3_808:0.621246884)0.875:0.106897543)0.712:0.005746477);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001580_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001580_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..828bcc458d136134085174e2ca637a7ccfee2419
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001580_tree_id.txt
@@ -0,0 +1 @@
+(3_796:0.018333892,1_1623:0.007235671,(0_1918:0.003598631,(2_860:0.249919566,4_1845:0.000000005)0.973:0.009022473)0.753:0.001777523);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001584_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001584_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6fbfc34a8d76f3cbc9d91c037ee44fa13dc17fe8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001584_tree_id.txt
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+(2_854:0.094266900,3_791:0.005545984,((0_1923:0.0,4_1850:0.0):0.005367867,1_1628:0.002356166)0.237:0.005086509);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001586_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001586_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c08b7309aa5d506604054a70b933b233541c8b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001586_tree_id.txt
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001588_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001588_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f7c3576d7f382f019ba40636c00a16d42a3b5ccc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001588_tree_id.txt
@@ -0,0 +1 @@
+(1_1634:0.014717622,4_1856:0.000000005,(0_1929:0.007411842,(2_848:0.036171943,3_1720:0.224298047)0.994:0.048370610)0.741:0.002385507);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001591_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001591_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..67c6db832906499cb9eea43af9017ddad1b5817e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001591_tree_id.txt
@@ -0,0 +1 @@
+(0_1932:0.005834650,4_1859:0.003870934,(1_1637:0.001940826,(2_845:0.056544362,3_784:0.026292211)0.972:0.016551519)0.721:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001594_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001594_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..88fca75ebadb249a43f832cc6a2e749a86dd0d0e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001594_tree_id.txt
@@ -0,0 +1 @@
+(1_1642:0.009603413,4_1864:0.015196826,(0_1937:0.013189738,(2_840:0.321123031,3_777:0.457494408)0.919:0.053572811)0.561:0.000100259);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001597_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001597_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b1cb917f5962d7f363c11fa0b2548ee91714eacf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001597_tree_id.txt
@@ -0,0 +1 @@
+(1_1663:0.012614856,4_1881:0.012555272,(0_1942:0.000341227,(2_820:0.031942124,3_758:0.201482448)0.989:0.048582206)0.621:0.007003934);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001601_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001601_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..914c1e8250b220493e518e5c63e5e69edc9667d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001601_tree_id.txt
@@ -0,0 +1 @@
+(0_1947:0.002983685,1_1668:0.000000005,(4_1886:0.008972132,(2_815:0.035293842,3_753:0.023107051)0.926:0.017901621)0.912:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001604_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001604_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b220ca578f8ee1065b578b53375415e1b684daa0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001604_tree_id.txt
@@ -0,0 +1 @@
+(1_1671:0.005701635,2_812:0.049559671,(4_1889:0.011558575,(0_1950:0.006683449,3_750:0.145817814)0.821:0.011079432)0.886:0.011853881);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001619_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001619_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1eb38c28ad33e3de9dad3a5904e0b633fafac8e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001619_tree_id.txt
@@ -0,0 +1 @@
+((0_1972:0.0,1_1690:0.0,4_1908:0.0):0.053455370,2_769:0.000000005,3_1202:0.561052429);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001628_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001628_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6e7dbebf9a2592e7e54adf1094fffcd82f34c7f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001628_tree_id.txt
@@ -0,0 +1 @@
+(2_746:0.142387848,3_710:0.152236588,(0_1995:0.015044777,(1_1712:0.0,4_1930:0.0):0.004374153)1.000:0.167929833);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001630_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001630_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e1cb7525d91eca15ed616413aa6fe2e0647f4c4e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001630_tree_id.txt
@@ -0,0 +1 @@
+(0_1997:0.009209579,1_1714:0.004692885,(4_1934:0.064385984,(2_742:0.279180613,3_705:0.620367232)0.912:0.097789402)0.985:0.071663233);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001631_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001631_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee515c47d949a74ff0847f026e214891c4421333
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001631_tree_id.txt
@@ -0,0 +1 @@
+(2_724:0.101279471,(0_2010:0.004796832,4_1939:0.003479833)0.999:0.100727780,(2_541:0.105859747,3_470:0.335980220)0.585:0.055171478);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001632_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001632_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fbc051362821d40245affecb33103e326cf377bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001632_tree_id.txt
@@ -0,0 +1 @@
+((1_1734:0.003386602,4_1958:0.006783089)0.845:0.000000005,3_597:0.017312290,(0_2019:0.020758887,2_686:0.036443148)0.246:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001634_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001634_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ff945be1a2ea5901353509b3198ede8be8b7ce1d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001634_tree_id.txt
@@ -0,0 +1 @@
+((0_2021:0.0,1_1737:0.0):0.000000005,3_594:0.017796064,(2_683:0.017851831,4_1961:0.000000005)0.603:0.005900130);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001644_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001644_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..44ada93a8fb62935a6ebf5fbbf3b3d123d154e96
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001644_tree_id.txt
@@ -0,0 +1 @@
+((0_2041:0.0,1_1759:0.0):0.000000005,4_1982:0.008904993,(2_659:0.025042309,3_575:0.999920267)0.995:0.476135580);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001645_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001645_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..baf56c70330846479b78c78572db5b1ddffb000c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001645_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001648_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001648_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2215e2ca234a62c18b59a91ad804439d02022f03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001648_tree_id.txt
@@ -0,0 +1 @@
+(0_2045:0.003227718,1_1763:0.000000005,(4_1986:0.003074744,(2_655:0.048440763,3_572:0.273099590)0.999:0.104728247)0.758:0.003568677);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001649_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001649_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..79cb4e8f5ca75f02dea8dddff3b369cbf77196be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001649_tree_id.txt
@@ -0,0 +1 @@
+((0_2046:0.0,1_1764:0.0):0.002674762,4_1987:0.000000005,(2_654:0.517615456,3_571:0.642618280)0.680:0.054503917);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001654_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001654_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5de8e633d4954dc6e53bf05b7094d10d599de866
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001654_tree_id.txt
@@ -0,0 +1 @@
+(1_1773:0.002151990,4_1993:0.004326402,(0_2054:0.002152954,(2_647:0.019006778,3_564:0.068453099)0.984:0.020034658)0.627:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001656_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001656_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f02fc738a55566f864979b649dde6954cab381b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001656_tree_id.txt
@@ -0,0 +1 @@
+(1_1776:0.009557002,4_1996:0.014428331,(0_2057:0.000000005,(2_644:0.086167824,3_562:0.345205717)0.985:0.067175560)0.828:0.009794619);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001658_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001658_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..94ce5357c4910526c4830ff1bfe19ab9f8b29b57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001658_tree_id.txt
@@ -0,0 +1 @@
+((0_2059:0.0,1_1778:0.0,4_1998:0.0):0.066822381,2_642:0.150062506,3_560:0.240324391);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001665_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001665_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..82249d42a5c570c2ab50ec6e2656554b8501fdf0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001665_tree_id.txt
@@ -0,0 +1 @@
+(0_2068:0.005911241,(1_1787:0.000000006,4_2007:0.003944176)0.793:0.001980843,(2_633:0.001972052,3_550:0.005928160)0.770:0.001968444);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001677_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001677_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..10cc788f95367263a57d6a6b71a0e6e65b99c3b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001677_tree_id.txt
@@ -0,0 +1 @@
+(3_536:0.002461627,(0_2082:0.023428581,2_611:0.053500173)1.000:0.144500503,(1_1800:0.002652953,4_2020:0.000000005)0.812:0.002866741);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001682_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001682_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7259dbbf94548f6abea1bd10826e0df813b76b5f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001682_tree_id.txt
@@ -0,0 +1 @@
+(0_2087:0.008311922,4_2026:0.008251406,(1_1806:0.004645941,(2_603:0.080264674,3_529:0.067514824)1.000:0.077037515)0.760:0.001951001);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001684_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001684_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6993cf25bb364718a7301280820395a0b4a33e3b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001684_tree_id.txt
@@ -0,0 +1 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001685_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001685_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f2a00f078d72eb47172c6eccd110dfaffd7ad1aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001685_tree_id.txt
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+(0_2090:0.004784526,1_1814:0.000000005,(4_2034:0.005479912,(2_593:0.054317991,3_518:0.337605098)0.993:0.091272653)0.846:0.008926587);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001688_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001688_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4cd4e20b6577eaf27cb951764f2f5d9946587000
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001688_tree_id.txt
@@ -0,0 +1 @@
+(0_2096:0.002112566,4_2040:0.000000005,(1_1820:0.000000005,(2_583:0.121364850,3_506:0.113640654)1.000:0.132662860)0.896:0.004228470);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001696_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001696_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..717ba434e9328b57549bec1c715977a9927d2dbf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001696_tree_id.txt
@@ -0,0 +1 @@
+((2_564:0.098506494,3_491:0.273012118)0.969:0.068222689,1_1834:0.003214599,(4_2055:0.009636927,0_2109:0.003255925)0.311:0.003233874);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001697_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001697_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..84210bc5292701d3ae48d87dc4b5a63db6934a42
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001697_tree_id.txt
@@ -0,0 +1 @@
+((0_2112:0.0,1_1837:0.0):0.008218082,4_2058:0.000000005,(2_561:0.036768828,3_489:0.351748518)0.939:0.037040599);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001717_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001717_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a28e2517efa71dac694f2307160ca9053cec120
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001717_tree_id.txt
@@ -0,0 +1 @@
+((0_2140:0.0,1_1864:0.0,4_2085:0.0):0.362127652,2_478:0.278267915,3_1273:0.345665914);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001725_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001725_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..87afeacfef297535336ab72645a41ec0ca958e4d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001725_tree_id.txt
@@ -0,0 +1 @@
+((0_2179:0.0,4_2112:0.0):0.002515553,1_1892:0.000000005,(2_487:0.089390291,3_424:0.061207435)1.000:0.084772542);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001727_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001727_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fedb2b45c86a8b556295792fa1e34231510bce37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001727_tree_id.txt
@@ -0,0 +1 @@
+(0_2183:0.003657918,4_2116:0.000000006,(1_1896:0.000000005,(2_484:1.063115706,3_2037:0.619471417)0.685:0.073890988)0.853:0.003642577);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001736_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001736_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..96496c7793377829b964a88cb9029ffc57b04a26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001736_tree_id.txt
@@ -0,0 +1 @@
+((2_436:0.008576561,3_389:0.014996936)0.873:0.004217252,1_1923:0.000000005,(4_2161:0.006382253,0_2221:0.002120273)0.690:0.000000006);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001737_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001737_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b010143961c87bfcb44b9667ee4a9350d6f2a561
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001737_tree_id.txt
@@ -0,0 +1 @@
+(2_434:0.002106521,3_388:0.129790476,(0_2224:0.004726364,(1_1926:0.0,4_2164:0.0):0.000000005)0.766:0.002619794);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001744_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001744_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..949504922d242e9a66dfaf39613cb55733c186c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001744_tree_id.txt
@@ -0,0 +1 @@
+(1_1936:0.006023337,4_2174:0.000000005,(0_2232:0.011518423,(2_425:0.044430659,3_379:0.280680173)0.979:0.047611092)0.588:0.000556321);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001746_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001746_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a956f568d1834c0166e0deb22e23a57c0afacdf3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001746_tree_id.txt
@@ -0,0 +1 @@
+(1_1938:0.001989209,4_2176:0.006143829,(0_2234:0.004793752,(2_423:0.076748258,3_377:0.249532896)1.000:0.097512966)0.681:0.003375897);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001747_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001747_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..defe82df94c77231e5cd6b2dc4b7620ff1fde612
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001747_tree_id.txt
@@ -0,0 +1 @@
+(1_1939:0.005388940,4_2177:0.000000005,(0_2235:0.005463537,(2_422:0.023187381,3_376:0.073559120)0.903:0.013026620)0.756:0.002598711);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001757_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001757_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cee438fd8371d93d5eee2305c98b5a33c68cccb8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001757_tree_id.txt
@@ -0,0 +1 @@
+(0_2250:0.026253841,(1_1954:0.0,4_2192:0.0):0.020838269,(2_407:0.061050618,3_361:0.531002119)0.268:0.034278910);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001760_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001760_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c4ef15b972f21488791c6d7a2e2516f79305eaf6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001760_tree_id.txt
@@ -0,0 +1 @@
+(1_2175:0.625711683,(1_288:0.027582238,2_2320:0.044308931)1.000:0.850655711,(2_2146:0.636494586,2_2148:0.812302543)0.952:0.212797568);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001762_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001762_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..30ece50a2ccd0af202b405f1425097ac01a3d215
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001762_tree_id.txt
@@ -0,0 +1 @@
+(2_598:0.108591829,(1_1808:0.008363100,4_2028:0.003610569)0.992:0.129258861,(2_2599:0.305771727,3_523:0.421853266)0.990:0.167230546);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001763_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001763_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ae4a8fa60acd09457c37e517f58095072c7a5f5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001763_tree_id.txt
@@ -0,0 +1 @@
+(2_596:0.048203513,3_521:0.073552448,((1_1810:0.0,4_2030:0.0):0.162127961,2_2601:0.406326732)1.000:0.130634234);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001768_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001768_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7da6ee80008ffd7f2544dd142196d2c0054ca167
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001768_tree_id.txt
@@ -0,0 +1 @@
+(2_372:0.004466420,3_639:0.003425050,(3_1792:0.101037469,(3_316:0.236543194,3_1185:0.136665950)1.000:1.233932193)0.623:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001777_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001777_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5852345f666fcee99ce9a6ace4ead56b5c3db2ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001777_tree_id.txt
@@ -0,0 +1 @@
+(1_2043:0.006445557,4_73:0.032225494,(2_294:0.243597428,0_79:0.006996613)0.773:0.005260004);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001784_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001784_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ce4dd3ebefbda694a06f13d05f67132dfa47d717
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001784_tree_id.txt
@@ -0,0 +1 @@
+(4_160:0.006541072,3_1439:1.457070512,(1_2112:0.001379282,0_147:0.219475497)0.845:0.052078211);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001789_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001789_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b45fed66b366c28f6163b13a065d5e0c764f7ef2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001789_tree_id.txt
@@ -0,0 +1 @@
+(0_209:0.636560757,(1_2153:0.0,4_209:0.0):0.278941309,2_158:0.423604049);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001792_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001792_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3af5f0668b4adad617d184a71207c174818a2902
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001792_tree_id.txt
@@ -0,0 +1 @@
+(1_2197:0.010497033,4_234:0.005558250,(0_234:0.012867048,2_118:0.044261022)0.888:0.012189278);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001796_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001796_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a84e69e8c4fba4ff43e99554d5ae8eb73de6412c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001796_tree_id.txt
@@ -0,0 +1 @@
+((0_263:0.0,1_2229:0.0,4_261:0.0):0.221093776,2_75:0.221093776);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001797_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001797_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d65d86fbb3e9438c40ad9e49a8256e807dad96ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001797_tree_id.txt
@@ -0,0 +1 @@
+(0_264:0.000896394,(1_2230:0.0,4_262:0.0):0.001866152,2_74:0.238243818);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001798_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001798_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..37b5918e8cdcff17253ae1a0b748b9e85865b3e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001798_tree_id.txt
@@ -0,0 +1 @@
+(0_267:0.000000006,2_70:0.449261623,(1_2233:0.000000005,4_266:0.010351260)1.000:0.042003602);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001802_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001802_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db06f19e0c33da28ba7d82f4e1264d703f0d8176
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001802_tree_id.txt
@@ -0,0 +1 @@
+((0_313:0.0,1_38:0.0):0.003404290,2_4:0.113664700,4_320:0.008154007);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001803_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001803_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4a33b09f6bf36c5c9dd8ce009b99f0cbeadd2b01
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001803_tree_id.txt
@@ -0,0 +1 @@
+((0_314:0.0,1_39:0.0):0.005311505,2_3:0.103131138,4_321:0.010203598);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001805_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001805_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2b3d8b8cba3a09f6f1719a50401ebce8c5a57399
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001805_tree_id.txt
@@ -0,0 +1 @@
+(0_327:0.000000005,1_52:0.001539999,(2_2565:0.116504412,4_334:0.009792758)0.988:0.019162276);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001806_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001806_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..011ea5c0a5ba7c92741627e774fb5f4ce71ec75b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001806_tree_id.txt
@@ -0,0 +1 @@
+(0_348:0.030530580,(1_73:0.0,4_355:0.0):0.017919327,2_2342:1.462601044);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001808_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001808_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c9098cc5bebbba517e7fcfd0241fd3cdcbbdcdbb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001808_tree_id.txt
@@ -0,0 +1 @@
+((0_369:0.0,1_102:0.0):0.000000005,2_2510:0.350091846,4_375:0.006786396);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001810_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001810_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..891c32b45ccc04a5ec358abe6433d6189438f2dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001810_tree_id.txt
@@ -0,0 +1 @@
+(4_413:0.004765596,2_2470:0.319360813,(1_140:0.000000005,0_410:0.024737596)0.670:0.005066393);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001812_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001812_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc46f412d033272e95845801e41ff8b76e2b27c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001812_tree_id.txt
@@ -0,0 +1 @@
+((0_454:0.0,1_181:0.0,4_454:0.0):0.113002449,3_2300:0.113002449);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001814_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001814_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7128f8ae14c92831b6b1348c524b05df597a13a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001814_tree_id.txt
@@ -0,0 +1 @@
+(0_500:0.007277037,4_500:0.005907290,(2_2373:0.198887272,3_2255:0.191704932)0.998:0.172823669);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001817_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001817_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..75f325c08bc5902f07d65817767d1e3d0bbe7a6f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001817_tree_id.txt
@@ -0,0 +1 @@
+((0_552:0.0,1_293:0.0):0.000000005,2_2305:0.002595508,4_553:0.002596949);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001819_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001819_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7b967fcb0f6a1cec4cfe835bce7c4b61933ce5fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001819_tree_id.txt
@@ -0,0 +1 @@
+((0_554:0.0,1_295:0.0):0.000000005,2_2303:0.008390053,4_555:0.002782071);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001831_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001831_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..70638883a8dbca2e20c33a88b3334802ee52b282
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001831_tree_id.txt
@@ -0,0 +1 @@
+(0_639:0.010174802,(1_385:0.0,4_609:0.0):0.002486879,2_2247:0.033598173);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001842_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001842_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fc218304e5bb388b9ac857b3c641d9bf644fda7f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001842_tree_id.txt
@@ -0,0 +1 @@
+(0_957:0.006203426,4_900:0.012489377,(1_680:0.000000006,3_1801:0.525480756)0.840:0.006146218);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001843_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001843_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..58e74debc432ccef38730afec5779d1998874bad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001843_tree_id.txt
@@ -0,0 +1 @@
+((0_970:0.0,1_693:0.0):0.032555408,2_1842:0.029690262,4_913:0.015914016);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001844_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001844_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ec7e202e15af105d9cc6574d42d714dace3e0e7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001844_tree_id.txt
@@ -0,0 +1 @@
+((0_972:0.0,4_915:0.0):0.000000005,1_695:0.000000005,2_1839:0.031028382);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001845_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001845_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cf22ddbea09feac65d1c73f5c96df7d1b9ae6f91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001845_tree_id.txt
@@ -0,0 +1 @@
+(1_698:0.004254224,2_1836:0.010671349,(4_919:0.002124880,0_975:0.004256214)0.362:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001848_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001848_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c5f24a29b0a305f98099164310f62537f35a6898
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001848_tree_id.txt
@@ -0,0 +1 @@
+((0_1031:0.0,1_759:0.0,4_980:0.0):0.205979810,2_2271:0.205979810);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001856_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001856_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..06becc17a87cda2df579c0a77c597a69d7784176
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001856_tree_id.txt
@@ -0,0 +1 @@
+(1_904:0.009454858,4_1134:0.004686663,(0_1176:0.000000005,2_1635:0.128137723)0.941:0.009493707);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001858_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001858_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c1d231964bb2a463dd05ee811429590929a315ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001858_tree_id.txt
@@ -0,0 +1 @@
+((0_1242:0.0,1_970:0.0):0.017233678,3_692:0.168952441,4_1199:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001860_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001860_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5c4d84cad1934e4bdac3e06c1bb2b50808e20d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001860_tree_id.txt
@@ -0,0 +1 @@
+(0_1267:0.000000005,2_1547:0.006167459,(2_2607:1.370403763,3_1443:0.246385257)0.957:0.185530606);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001874_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001874_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a040fe88a379eddb948ad36a11f85ca605ad0863
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001874_tree_id.txt
@@ -0,0 +1 @@
+((0_1460:0.0,1_1179:0.0):0.002927854,2_1386:0.078796936,4_1387:0.005819298);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001878_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001878_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f284d2cf97ba4174931fc9a2a560528507517f54
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001878_tree_id.txt
@@ -0,0 +1 @@
+(3_1197:0.288755458,4_1465:0.000000005,(0_1538:0.005892814,1_1260:0.000000005)0.965:0.005884971);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001883_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001883_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e0e9a1cadce3fce09251eae5018fc0e61272d663
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001883_tree_id.txt
@@ -0,0 +1 @@
+(0_1625:0.201935351,2_1174:0.292849317,(3_1193:1.250174177,3_2066:1.775960756)0.621:0.268355591);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001884_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001884_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..178207e3f17b4ed45f9c12378e783ebf9c9ca158
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001884_tree_id.txt
@@ -0,0 +1 @@
+(1_1343:0.011816242,4_1558:0.007848801,(0_1629:0.003681684,2_1170:0.359926005)0.716:0.004251143);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001892_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001892_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..728ae0371526fe2c4ac977cc0cffdeea6fdb74bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001892_tree_id.txt
@@ -0,0 +1 @@
+((0_1820:0.0,1_1527:0.0):0.011655988,2_959:0.305734823,4_1741:0.012357134);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001894_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001894_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ae526398c2e1f89a3840ced68f659b1fe41db05
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001894_tree_id.txt
@@ -0,0 +1 @@
+((0_1834:0.0,1_1541:0.0):0.000000006,3_883:0.369270357,4_1755:0.044819366);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001901_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001901_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0192b105e07d4fc7147c5b94f7ace75168b1897c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001901_tree_id.txt
@@ -0,0 +1 @@
+(4_1778:0.000000005,3_859:0.108420144,(0_1857:0.000000005,1_1564:0.007647390)0.875:0.003816610);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001905_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001905_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..86b577c44a7cfb2884284c852dd6b4fbe82a8bc7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001905_tree_id.txt
@@ -0,0 +1 @@
+((0_1907:0.0,1_1612:0.0,4_1834:0.0):0.067805514,2_872:0.067805514);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001908_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001908_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7524fd390def060968751c5b3ba60253c8e4856a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001908_tree_id.txt
@@ -0,0 +1 @@
+((0_1935:0.0,1_1640:0.0):0.010610212,3_779:0.328912682,4_1862:0.013692857);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001910_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001910_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee8b31037016c6b8b4bc11c6d3323215621f30be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001910_tree_id.txt
@@ -0,0 +1 @@
+(1_1645:0.002825152,4_1867:0.005593407,(0_1940:0.025783207,2_837:0.193683273)0.876:0.006979840);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001912_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001912_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2b9d8138ef2337067a45cc813b7ecaffdd2edb9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001912_tree_id.txt
@@ -0,0 +1 @@
+(0_1976:1.261266847,2_789:0.669052189,(2_133:0.195112755,3_95:0.198876516)0.971:0.391367370);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001913_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001913_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1d02b3c041e059916759c106acd1cd568423b47f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001913_tree_id.txt
@@ -0,0 +1 @@
+(0_1983:0.023628332,2_754:0.201353622,(1_1700:0.020529318,4_1918:0.007634897)0.423:0.005626013);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001915_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001915_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ea45eb26caf172a3bd37af77ac86dd58bff94a7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001915_tree_id.txt
@@ -0,0 +1 @@
+(4_1922:0.005466662,1_1704:0.006836266,(3_714:0.334948499,0_1987:0.000000005)0.364:0.002725956);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001919_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001919_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..79e29bbf0f9d1c2c9fbb58e53394b39d2e43ddf8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001919_tree_id.txt
@@ -0,0 +1 @@
+(0_2029:0.015093927,3_587:0.022901980,(1_1748:0.007378960,2_670:0.022891510)0.893:0.015626559);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001920_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001920_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..66842bfade712df6fafc599d9efa603069547a85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001920_tree_id.txt
@@ -0,0 +1 @@
+(1_1749:0.019253823,2_669:0.006350159,(0_2030:0.038929645,3_586:0.026075529)0.804:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001922_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001922_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ce131e3a11f4b45616f4dff3a21ef8d6174809e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001922_tree_id.txt
@@ -0,0 +1 @@
+((0_2039:0.0,1_1757:0.0):0.005798725,2_661:0.464935185,4_1980:0.001742717);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001925_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001925_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cb5c6252b354bc64e96969433c14214627204bec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001925_tree_id.txt
@@ -0,0 +1 @@
+(0_2055:0.021143302,4_1994:0.010290786,(1_1774:0.015684368,2_646:0.238114985)0.284:0.028154194);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001929_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001929_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e1affac734766dde6f084e5a18aa80adbcd221bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001929_tree_id.txt
@@ -0,0 +1 @@
+(0_2095:0.004307311,1_1819:0.000000005,(2_586:0.342892686,4_2039:0.004311727)0.757:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001931_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001931_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7d99dced8b874f738275c113f9acba3d10e79c5a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001931_tree_id.txt
@@ -0,0 +1 @@
+(4_2057:0.028358771,1_1836:0.000000006,(2_562:0.473903532,0_2111:0.000000005)0.840:0.003493606);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001941_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001941_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1d1851f70dae365cb0ad4116e637ad40c493fd50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001941_tree_id.txt
@@ -0,0 +1 @@
+(0_2157:0.002421361,1_1881:0.002406083,(3_456:0.558238210,4_2097:0.000000005)1.000:0.016966287);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001944_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001944_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..718ccd1b761a6c57da69f9cebe535f5212ab76d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001944_tree_id.txt
@@ -0,0 +1 @@
+(1_1889:0.008557016,4_2102:0.004344555,(0_2163:0.009829649,3_1205:0.387388490)0.672:0.003095577);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001946_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001946_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dfca2f2eafddaeec9025052bd2b81528d9ab843e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001946_tree_id.txt
@@ -0,0 +1 @@
+(0_2202:0.004361849,1_1908:0.007730758,(3_411:0.049070405,4_2134:0.013355047)0.844:0.007292606);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001949_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001949_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64012796d29a50937d526be48b625200eb60993a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001949_tree_id.txt
@@ -0,0 +1 @@
+(1_1924:0.010263358,4_2162:0.005110591,(0_2222:0.003089634,2_790:0.923782923)0.718:0.002297193);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001967_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001967_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6eb28e9862805022a139fa0473a28ef24f8c8702
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001967_tree_id.txt
@@ -0,0 +1 @@
+((1_1652:0.0,4_1870:0.0):0.057572677,2_830:0.083245044,3_768:0.041250454);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001973_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001973_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..79d1640063e540ebda620c167dabaeb22082f103
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001973_tree_id.txt
@@ -0,0 +1 @@
+(1_1807:0.010119654,4_2027:0.021953068,(2_599:0.042441452,3_524:0.000000005)1.000:0.144793739);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001974_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001974_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..443af783ad6bf069392c11276242493f5ffe3f22
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001974_tree_id.txt
@@ -0,0 +1 @@
+((1_1809:0.0,4_2029:0.0):0.134854898,2_597:0.473986575,3_522:0.204414905);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001975_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001975_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c6addea860b18389acd116da4dab93f4ae0d6aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001975_tree_id.txt
@@ -0,0 +1 @@
+(1_1900:0.004199440,4_2120:0.000000005,(2_1299:0.977022707,3_419:0.020123171)0.516:0.027219444);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001982_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001982_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e2391fabb1a52193abf4bc4883e73b98f42cbb03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001982_tree_id.txt
@@ -0,0 +1 @@
+(3_296:0.214149085,3_1736:0.216173515,(3_392:1.248935012,3_638:0.634764414)1.000:1.375207566);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001984_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001984_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..545c63dedfea6a42f22dcb0997641018a133a27d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001984_tree_id.txt
@@ -0,0 +1 @@
+(3_681:0.005395611,3_704:0.023332029,(3_644:0.155872371,3_1369:1.376057841)0.880:0.117664919);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001987_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001987_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..effc3aa21b7bd0fd2821cb81b9040319038dea77
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001987_tree_id.txt
@@ -0,0 +1 @@
+(0_23:0.008279868,(1_1992:0.0,4_23:0.0):0.008279868);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001988_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001988_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d2dbd0f377e0809a990d29672eb92781aca56b36
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001988_tree_id.txt
@@ -0,0 +1 @@
+(0_24:0.002896488,1_1993:0.014550715,4_24:0.011619856);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001999_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001999_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ace2aed9302e2986256970d6e3e14fdd8be4ba78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0001999_tree_id.txt
@@ -0,0 +1 @@
+(0_265:0.006101328,1_2231:0.015179413,4_263:0.049881900);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002001_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002001_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0dc9e0e14339c2c81a06af8adaf43fc41ff76fb2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002001_tree_id.txt
@@ -0,0 +1 @@
+((0_357:0.0,4_363:0.0):0.010354612,2_2529:0.010354612);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002003_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002003_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..31d7f4983ab9d0a4abe790ce9e34b53912d3e210
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002003_tree_id.txt
@@ -0,0 +1 @@
+(0_431:0.049324105,2_2448:0.000000005,3_2430:1.430079636);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002011_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002011_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..475fa7559a1a419245fbedaaa993e65b1ee61993
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002011_tree_id.txt
@@ -0,0 +1 @@
+(0_563:0.038326405,1_306:0.000000005,3_1743:1.682269286);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002016_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002016_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f1dfc7e75a1c87ae118a65db3af2f598929d56f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002016_tree_id.txt
@@ -0,0 +1 @@
+(0_741:0.021233021,1_480:0.010552516,4_705:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002020_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002020_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1eeff02daaeacdf93e3cab551fdfa0fde05bb17e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002020_tree_id.txt
@@ -0,0 +1 @@
+((0_856:0.0,1_587:0.0):0.774349543,2_1198:0.774349543);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002024_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002024_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..083595ae8ddb0c76122f5ed3e746a8cb06ea3be1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002024_tree_id.txt
@@ -0,0 +1 @@
+(0_934:0.024115560,1_656:0.009774654,2_795:1.719848028);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002028_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002028_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fcf6aa898c01cbfd05a0cab4c64f25c78ed31a70
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002028_tree_id.txt
@@ -0,0 +1 @@
+((0_1246:0.0,1_978:0.0):0.000000003,4_1203:0.000000003);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002032_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002032_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1b2230dfd0aaaa94fd2d5edf86ca04c00e3ff4f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002032_tree_id.txt
@@ -0,0 +1 @@
+(0_1343:0.0,1_1084:0.0,4_1293:0.0);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002033_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002033_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c783cc8b603cd04decd2c94c09f1aff26757ba22
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002033_tree_id.txt
@@ -0,0 +1 @@
+(0_1347:0.0,1_1089:0.0,4_1296:0.0);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002037_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002037_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a5ec73136cc6052c6a9fe23757db9ea9472c96c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002037_tree_id.txt
@@ -0,0 +1 @@
+((0_1542:0.0,1_1264:0.0):0.004453939,4_1469:0.004453939);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002042_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002042_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8f35e29e9550e31fd5aba490147fa808a8d06aed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002042_tree_id.txt
@@ -0,0 +1 @@
+(0_1568:1.739876878,1_353:0.015622955,3_2152:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002044_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002044_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..88712af96143d5b6c734930342db182146a50b32
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002044_tree_id.txt
@@ -0,0 +1 @@
+((0_1837:0.0,4_1758:0.0):0.001541975,1_1544:0.001541975);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002050_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002050_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0983d87abfb93e4373ae0f002d1cd46a0342a0f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002050_tree_id.txt
@@ -0,0 +1 @@
+(0_1980:0.026147231,2_759:0.029156452,3_727:0.613015864);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002051_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002051_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c86e1fb29eb28e9705fd91d60842578906a1c26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002051_tree_id.txt
@@ -0,0 +1 @@
+(0_1981:0.106556354,2_758:0.082989932,3_726:0.095410966);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002052_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002052_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0a4dec864398bbc1651d2ba849b49c2752ed9dcd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002052_tree_id.txt
@@ -0,0 +1 @@
+(0_1982:0.323837588,2_756:0.213166506,3_724:0.303087724);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002054_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002054_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..66e0d228978c7ba3f10ea91c4c0d125619968d1e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002054_tree_id.txt
@@ -0,0 +1 @@
+(0_2035:0.035175022,3_579:0.138180701,4_1976:0.138535752);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002057_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002057_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b186ad80b4ef204b7eae2a3f5f587f48cabf5404
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002057_tree_id.txt
@@ -0,0 +1 @@
+(0_2105:0.0,1_1830:0.0,4_2051:0.0);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002059_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002059_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1dba2c6cfe74e62d9d83dc88d43c886ab98b5039
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002059_tree_id.txt
@@ -0,0 +1 @@
+(0_2138:0.000000005,1_1862:0.021761426,4_2083:0.029528408);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002062_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002062_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d7935be9c1ddeb26f5710d88d19f57c25e85e9dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002062_tree_id.txt
@@ -0,0 +1 @@
+(0_2149:0.001865254,1_1873:0.000000005,2_516:0.154325245);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002063_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002063_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0dca222390a57b405ad9f1f9cae7617774f37ea9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002063_tree_id.txt
@@ -0,0 +1 @@
+(0_2150:0.021822888,1_1874:0.000293294,2_515:0.135062105);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002064_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002064_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c7aca4141ed1119feb865bf5d5a8467d92771ef9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002064_tree_id.txt
@@ -0,0 +1 @@
+(0_2151:0.006012862,1_1875:0.011229025,2_514:0.198917414);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002068_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002068_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0c7c99ce64da89972a0a42485275f9e9d95f54cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002068_tree_id.txt
@@ -0,0 +1 @@
+(0_2197:0.009076618,2_454:0.049929575,4_2129:0.009179696);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002073_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002073_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..27eb20645e46e2ed938639e62d70b38c0f261d20
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002073_tree_id.txt
@@ -0,0 +1 @@
+(0_2227:0.005002373,1_1930:0.000000005,4_2168:0.015036003);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002080_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002080_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f26e642b9f65db6019ff2f670bd34f83feb443c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002080_tree_id.txt
@@ -0,0 +1 @@
+(1_350:0.522423638,3_306:1.259485109,4_163:0.908144146);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002086_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002086_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4fe181b2eb820ae7ced6fc09a1ed20249b2cba5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002086_tree_id.txt
@@ -0,0 +1 @@
+(1_1445:0.004622683,2_1069:0.171890567,4_1657:0.000000005);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002088_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002088_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4ea01449ffcfe05f7e364fc9cd1dfdbc94a61dbe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002088_tree_id.txt
@@ -0,0 +1 @@
+(1_1621:0.043721850,3_798:0.135792303,4_1843:0.028174441);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002091_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002091_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..907a602752a283780ece98a946b3d0b9ba029a20
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002091_tree_id.txt
@@ -0,0 +1 @@
+((1_1660:0.0,4_1878:0.0):0.072400559,2_823:0.072400559);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002093_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002093_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..04ecb13d82c6864f53fae8cedb1c262d58283649
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002093_tree_id.txt
@@ -0,0 +1 @@
+(1_1662:0.018042884,2_821:0.218511644,4_1880:0.000729912);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002103_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002103_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e5253c00addb28172ba241d611de97a6d95d26aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002103_tree_id.txt
@@ -0,0 +1 @@
+(1_2129:0.000695248,2_806:1.274254745,3_147:0.012781117);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002104_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002104_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9900045c5a89adfdce3a805cdd03fbaacbec989a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002104_tree_id.txt
@@ -0,0 +1 @@
+((1_2246:0.0,4_279:0.0):0.281327888,2_791:0.281327888);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002107_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002107_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9dc07a15038a49a2c7bd3d46968282b8521efea1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002107_tree_id.txt
@@ -0,0 +1 @@
+(2_573:0.310884929,2_1297:0.642122218,3_497:0.337288737);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002111_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002111_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0968ed8ff81a4d671e09568bc6fe6640fbabbb0e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002111_tree_id.txt
@@ -0,0 +1 @@
+(2_1055:0.127610295,3_991:0.191449347,4_1661:0.327985035);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002113_tree_id.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002113_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7c9291381c1dfb2a854a1c1f376d488d4670287
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Trees_ids/OG0002113_tree_id.txt
@@ -0,0 +1 @@
+(2_1272:0.166263109,3_1182:0.000000006,4_585:0.653522851);