diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000008.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000008.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de04b300ec9c30caad59f53dd72ca02525c48eb4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000008.fa
@@ -0,0 +1,83 @@
+>PROKKA_00711
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>PROKKA_01398
+MEGSLEGSHGDRVRLEDGRGHRGGLHHYPGLNSFTTWDPGASSIPAPTQQSLRTLEWLSR
+RENLVVCGPSGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARI
+LRADLIVIDDIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATAT
+VDRLLHHAHVCQTTGDSVRMTQAMAGKGVMPLN
+>PROKKA_01502
+MAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIGLLPVADDAAEGLYRIVDAA
+YEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQTTGDSVRMTQAMAGKGVMP
+LN
+>PROKKA_02225
+MLWKVRSKAPTVTASVSKMVVATGEGYTTIRDSTPKTLATATVDRLLHHAHVCQTTGDSV
+RMTQAMAGKGVMPLN
+>PROKKA_02227
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTVKSLEVV
+>PROKKA_00092
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>PROKKA_00343
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>PROKKA_01013
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>PROKKA_01394
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>PROKKA_02284
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>PROKKA_00606
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>PROKKA_01016
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPIADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>PROKKA_01158
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPIADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>PROKKA_01349
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>PROKKA_02164
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000012.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000012.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e5945c2a5933ed6528ac363aabdaec38c0d85592
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000012.fa
@@ -0,0 +1,42 @@
+>PROKKA_00156
+MKGAAQLDFIRRGQAVGLTLAQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQ
+LRTTIADLREDAAAGDPATCSPEDVCRYL
+>PROKKA_00159
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLGPAVG
+>PROKKA_01075
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAVGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATC
+SPEDVCRYL
+>PROKKA_02063
+MRIGEVAAASGVTTKALRFYEERGLLPQADRATNGYRDYPEDTIVRLEFIRRSQVAGLTL
+AEILDILQIRDAGTAPCGHVRDQLAEHLTNLDRHIAELTALRETVAGLHGTAAAGDPAQC
+NAEVICSYL
+>PROKKA_00297
+MRIGELAERAGTTAKTLRFYEEQGLLPPAERTPSGYRDYAPETAARIDFVHRGQAAGLTL
+AQIRQILDIRDDGAAPCEHVRDLLDARLAEIEQQIAQLAALRDTITELRRDAAQPDPDSC
+SADQVCRYL
+>PROKKA_00338
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC
+SPEDVCRYL
+>PROKKA_00345
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC
+SPEDVCRYL
+>PROKKA_00794
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC
+SPEDVCRYL
+>PROKKA_00720
+MLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATCSPEDV
+CRYL
+>PROKKA_00722
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGSSPMKWC
+SG
+>PROKKA_02223
+MRIGEVAAASGVTTKALRFYEERGLLPQADRATNGYRDYPEDTIVRLEFIRRSQVAGLTL
+AEILDILQIRDAGTAPCGHVRDQLAEHLTNLDRHIAELTALRETVAGLHGTAAAGDPAQC
+NAEVICSYL
+>PROKKA_01024
+MLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATCSPEDV
+CRYL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000017.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000017.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45bd885c2476f52d248e173aa20f66954e8cf83a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000017.fa
@@ -0,0 +1,102 @@
+>PROKKA_00542
+MSIADAPQASVVPPVDPAAERRFSRVLIANRGEIAVRIIRACQDEGLTSVAVYAEPDRDA
+LHVTLADEAVALGGETAADSYLVIGKILDAAERAGADAVHPGYGFLSENADFARAVTDAG
+LVWIGPPAEAIDRLGDKVSARQLATKVGAPLAPGTTSPVTGTEEVVAFADEFGLPVAIKA
+AYGGGGRGIKVARTREEIPEFYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG
+DVVVISTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILQEAGYVGAGTCEFLVG
+QDGTISFLEVNTRLQVEHPVSEEITGIDLVREQFRLARGEALGYTDPQPRGHSIEFRLNG
+EDPGRNFLPAPGRLTTFRMPSGPGVRVDSGVVEGEAVSGAFDSMVAKLIVTGADRRQALQ
+RAARALREAEIVGMPSVLPFHRAVVRDPAFAPEIAGSEEPFSVHTRWIETEFANRIEPSA
+LTPAEPAPREARHTVTVEVNGKRVDVTLPTWGEALHTISGAAQRAGAGRRRPRGKRGAPV
+AAAVSTDALTAPMQGTVVKVAAENGQTVAEGDLIVVVEAMKMEQPLAAHRAGVVSGLEVE
+PGQTVTAGTVIATIADAE
+>PROKKA_01915
+MTTTPAARPVTRVLIANRGEIAVRVARAARDHGIASIAVYSDPDADALHVAVADEAFHLP
+GASSADTYLKIDAVLDVARRAGADAVHPGYGFLSENADFAQAVIDAGMTWIGPSPDAIRA
+LGDKITARSLAQQAGAPLVPGSDGPVPDAAAARAFAEEHGLPIAIKAAFGGGGRGIRVVR
+ELGDVEDAFEATVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHGHVAVLGTRDCSLQ
+RRNQKLVEEAPAPFLTDEQRERIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVNTR
+LQVEHPVTEEVFGVDLVREQFRIAAGELLSIPEDPTPRGHALEFRLNAEDPAYGFLPVPG
+PIDAFEAPTGPGVRMDSGVRTGSVVPGEYDSLLAKLIVWGEDRAQAIARARDALAELRID
+GVPTVVPFHRAVLEQDAFTSGDRLGVYTTWIESEFAEPLAESPYLGAEVPAGGRTSVTVE
+LDGRAVRLGLPADLYAALLGGGGAGAAAPADAAGAGKPDDDGAVASPVTGTLASWKVEDG
+AEVAEGDTVAIVEAMKMETPIRAPRAGRIQLLVAETPASVTRGQAISRLGA
+>PROKKA_00267
+MSIADAPQASVVPPVDPAAERRFSRVLIANRGEIAVRIIRACQDEGLTSVAVYAEPDRDA
+LHVTLADEAVALGGETAADSYLVIGKILGAAERAGADAVHPGYGFLSENADFARAVADAG
+LVWIGPPAEAIDRLGDKVSARQLATKVGAPLAPGTTSPVTGTEEVVAFADEFGLPVAIKA
+AYGGGGRGIKVARTREEIPEFYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG
+DVVVISTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILQEAGYVGAGTCEFLVG
+QDGTISFLEVNTRLQVEHPVSEEITGIDLVREQFRLARGEALGYTDPQPRGHSIEFRLNG
+EDPGRNFLPAPGRLTTFRMPSGPGVRVDSGVVEGETVSGAFDSMVAKLIVTGADRRQALQ
+RAARALREAEIVGMPSVLPFHRAVVRDPAFAPEIAGSEEPFSVHTRWIETEFANRIEPSA
+LTPAEPAPARRATP
+>PROKKA_01611
+MTTTPAARPVTRVLIANRGEIAVRVARAARDHGIASIAVYSDPDADALHVAVADEAFHLP
+GASSADTYLKIDAVLDVARRAGADAVHPGYGFLSENADFAQAVIDAGMTWIGPSPDAIRA
+LGDKITARSLAQQAGAPLVPGSDGPVPDAAAARAFAEEHGLPIAIKAAFGGGGRGIRVVR
+ELGDVEDAFEATVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHGHVAVLGTRDCSLQ
+RRNQKLVEEAPAPFLTDKQRERIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVNTR
+LQVEHPVTEEVFGVDLVREQFRVAAGEPLSIPEDPTPRGHALEFRLNAEDPAYGFLPVPG
+PIDAFEAPTGPGVRMDSGVRTGSVVPGEYDSLLAKLIVWGEDRAQAVARARDALAELRID
+GVPTVVPFHRAVLEQDAFTSGDRLGVYTTWIESEFAEPLAESPYLSAEVPAGGRTAVTVE
+LDGRAVRLGLPADLYAALLGGGGAGAAAPAGAAGAGKPDDDGAVASPVTGTLASWKVEDG
+AEVVEGDTVAIVEAMKMETPIRAPRAGRIQLLVAETPASVTRGQAIARLGA
+>PROKKA_02407
+MSIADAPQASVIPPRDPKAERRFSRVLIANRGEIAVRVVRACQDEGLTSVAVYAEPDRDA
+LHVKLADEAVALGGETAADSYLLVEKILDAAERSGADAVHPGYGFLSENADFARAVEAAG
+LVWIGPPAEAIDRLGDKVSARQLATKVGAPLAPGTTSPVTGTEEVVAFADEHGLPVAIKA
+AYGGGGRGIKVARSREEIPELYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG
+GVVVMSTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILKEAGYVGAGTCEFLVG
+QDGTISFLEVNTRLQVEHPVTEEVTGIDLVREQFRLARGEALGYEDPVVRGHSFEFRLNG
+EDPGRNFLPAPGRLTTFRMPSGPGVRVDTGVVEGETVSGAFDSMVAKLIVTGADRRQALQ
+RAARALGEAEIAGMPSVLPFHRAVVTDPAFAPEIAGAAEPFTVHTRWIETEFANHIEPSE
+HAPADPTSREPRRTVTVEVNGKRVDVTLPTWGEALHTISGAAQRAGAGRRRPRGRRGAPV
+AAAVSTDALTAPMQGTVVKVAAENGQTVAEGDLIVVVEAMKMEQPLTAHRAGVVSGLEVE
+PGQTVSAGTVIATIADAD
+>PROKKA_00880
+MSTPSTTASRPVTRVLIANRGEIAVRVARACRDHGIASIAVYSDPDAQAMHVAVADEAYA
+LPGSTSAETYLDIAAVLDVARRSGADAVHPGYGFLSENADFAQAVIDAGLTWIGPSPQAI
+RDLGDKITARAIAQRAGAPLVPGSDGPVPDAAAARAFAQEHGLPIAIKAAFGGGGRGIKV
+VRELSEVEDAFESAVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHGAVAVLGTRDCS
+LQRRNQKLVEEAPAPFLTDEQRQRIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVN
+TRLQVEHPVTEEVFGVDLVREQFRIAAGEPLSIPEDPAPRGHAIEFRLNAEDPAHGFLPV
+PGPVEAFEAPTGPGVRMDSGVRTGSVVPGEYDSLLAKLIVVGEDRSQAIARARDALAELR
+IEGVPTVVPFHRAVLEEEAFTSAEALGVYTTWIESEFAAPLAASPHLGASVPGGGRTTVT
+VEVDGRAVRLGLPADLHAALLGGGGARTGASAPAEQSVDEGAVTSPVTGTLASWKVEDGA
+QVAEGDTIAVVEAMKMETPVRAPRAGRVERAAGDAPAAVTRGQVLASVRA
+>PROKKA_02288
+MTNASAPQASADIAEAPGRPFSRVLIANRGEIAVRVIRACQDEGLTSVAVYAEPDRDALH
+VKLADEAVALGGETAADSYLVIQKVLDAAERSGADAVHPGYGFLSENAEFARAVEAAGLV
+WIGPPADAIDALGDKVSARRIATKVGAPLAPGTTSPVNGTDEVVAFADEFGLPVAVKAAY
+GGGGRGIKVARTREEIPELYESAVREAVAAFGRGECFVERFLDRPRHVETQCLADAHGNV
+VVVSTRDCSLQRRNQKLVEEAPAPFLTDEQNTRLVESSKALLKEAGYVGAGTCEFLVGQD
+GTLSFLEVNTRLQVEHPVSEEVTGIDLVREQFRIARGEALGYGDPEARGHSFEFRLNGED
+PGRNFLPAPGTLTRFRMPSGPGVRVDAGVTEGETVSGAFDSMVGKLIVTGADRRQALQRA
+ARALAEAEIAGMPSVLPFHRAVVADPAFAPELAGSEEPFAVHTRWIETEFAHQIEPTALT
+PAAAPDRPERHTVTVEVNGKRVDVTLPTWGEAMHQLQGAAARAGAGRRRPRGARRAGAAP
+AAPGTDSLTAPMQGTVVKVAAQNGDRVAEGDLIVVMEAMKMEQPLTAHRAGVVSGLEVAA
+GDALTAGAVIAVIADAE
+>PROKKA_00545
+MSIADAPQASVVPPVDPAAERRFSRVLIANRGEIAVRIIRACQDEGLTSVAVYAEPDRDA
+LHVKLADEAVALGGESAADSYLVVGKILDAAERAGADAVHPGYGFLSENADFARAVADAG
+LVWIGPPAAAIDRLGDKVSARQLATKVGAPLAPGTTSPVTGTEEVVAFADEFGLPVAIKA
+AYGGGGRGIKVARTREEIPEFYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG
+DVVVISTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILQEAGYVGAGTCEFLVG
+QDGTISFLEVNTRLQVEHPVSEEITGIDLVREQFRLARGEALGYTDPQPRGHSIEFRLNG
+EDPGRNFLPAPGRLTTFRMPSGPGVRVDSGVVEGETVSGAFDSMVAKLIVTGADRRQALQ
+RAARALREAEIVGMPSVLPFHRAVVRDPAFAPEIAGSEEPFSVHTRWIETEFANRIEPSA
+LTPAEPAPREARHTVTVEVNGKRVDVTLPTWGEALHTISGAAQRAGAGRRRPRGKRGAPV
+AAAVSTDALTAPMQGTVVKVAAENGQTVAEGDLIVVVEAMKMEQPLAAHRAGVVSGLEVE
+PGQTVTAGTVIATIADAE
+>PROKKA_01835
+MTTTPAARPVTRVLIANRGEIAVRVARAARDHGIASIAVYSDPDADALHVAVADEAFHLP
+GASSADTYLKIDAVLDVARRAGADAVHPGYGFLSENADFAQAVIDAGMTWIGPSPDAIRA
+LGDKITARSLAQQAGAPLVPGSDGPVPDAAAARAFAEEHGLPIAIKAAFGGGGRGIRVVR
+ELGDVEDAFEATVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHGHVAVLGTRDCSLQ
+RRNQKLVEEAPAPFLTDEQRERIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVNTR
+LQVEHPVTEEVFGVDLVREQFRVAAGEPLSIPEDPTPRGHALEFRLNAEDPAYGFLPVPG
+PIDAFEAPTGPGVRMDSGVRTGSVVPGEYDSLLAKLIVWGEDRAQAVARARDALAELRID
+GVPTVVPFHRAVLEQDAFTSGDRLGVYTTWIESEFAEPLAESPYLSAEVPAGGRTAVTVE
+LDGRAVRLGLPADLYAALLGGGGAGAAAPAGAAGAGKPDDDGAVASPVTGTLASWKVEDG
+AEVVEGDTVAIVEAMKMETPIRAPRAGRIQLLVAETPASVTRGQAIARLGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000020.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000020.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6e04b908c15cc32babe965ef49be493cada329c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000020.fa
@@ -0,0 +1,73 @@
+>PROKKA_00524
+MTIVDFFRLLRANLLLLLAAALVGGLLGWGYSALQPRIYASESQGFLAARAADQSLITSN
+LPAESRAQAYVALINSEAVRERVAQDTGQDGDGSLSAVLVPESSMIKVTATSTDPETAAQ
+LANSALQATADVAADVDKNSPLEVVPLSDARVPSAPVSPDTRRNVLLGVVAGLGAGLAIA
+VLRRLLDVKVRSRADVKEITGAGVIGAVPENASLTRTGEEAVDLDPRAGEAIRALRTNLK
+FVSVDEPPRVVSFTSADPSEGKSTVASNLARALALAGERVLVVDADLRRPRQHDLFQVAG
+DVGLSEVLAGEVQPDDALAATGIPNLTLLPAGRTPPNPSELLGSKRMRALLKLASEDFFV
+IVDSPPLLPVTDGSLLATAVDGTVLVVRQGRTRKDHLEAAVENLAAVDAHLLGVVMNGVA
+RSQRGGGYSYGYGYESTYHKSHDKYLQGTGKGGKKSRRAARAKKG
+>PROKKA_00245
+MTIVDFFRLLRANLLLLLAAALVGGLLGWGYSALQPRIYASESQGFLAARAADQSLITSN
+LPAESRAQAYVALINSEAVRERVAQDTGQDGDGSLSAVLVPESSMIKVTATSTDPETAAQ
+LANSALQATADVAADVDKNSPLEVVPLSDARVPSAPVSPDTRRNVLLGVVAGLGAGLAIA
+VLRRLLDVKVRSRADVKEITGAGVIGAVPENASLTRTGEEAVDLDPRAGEAIRALRTNLK
+FVSVDEPPRVVSFTSADPSEGKSTVASNLARALALAGERVLVVDADLRRPRQHELFQVAG
+DVGLSEVLAGEVQPDDALAATGIPNLTLLPAGRTPPNPSELLGSKRMRALLKLASEDFFV
+IVDSPPLLPVTDGSLLATAVDGTVLVVRQGRTRKDHLEAAVENLAAVDAHLLGVVMNGVA
+RSQRGGGYSYGYGYESTYHKSHDKYLSGVGSSAKKGRRSRRKARTRG
+>PROKKA_00256
+MNIIDFLRVLRANRLVILGCAALGLALGLLYSLLQPTLYTATSTAFVTVEGEASISGTET
+AQTRAQSYIPLINSRTVRERIAAEGLDTAGATLSAALVPNSNLITVSAVAPDAQQAAALA
+NGALVATADVANELDPTSNVKVTAMEDALAPAAPSSPDRVRHLLYGLGAGLVLGLIVAFL
+RRLLDVNVRTTTDAQVAGGAGLLGAIPLDPSMKAERTAPMAPLSPRASEAVRQLRTNLRF
+AAVDDPPRTIAFTSSNPGEGKSTVIGNLALTVAAAGQPVILIDADLRRPRQALQFGVDGR
+VGLSEVLNGDVALQDVLIPVGEDGLLLLPAGRTPPNPSEQLGSERMRDLLTALAETHMVL
+VDAPPVLPVTDSTLLATAVDGTVLVIRHGKTRKEHLEVARDMLAGVNARVLGVVLNGTPA
+SGVGSDYYGGGYGADGGSYDAYYQAPRDAAEAAAGTAGDASRR
+>PROKKA_01211
+MDLQQYLQTFRKYWRSILTVLSVCVGAALVFTFLQTPKYSSTSSALIAVDTAATPGELSS
+GALYAERQVSSFVALADSALVLDPVINELGLNVTPQALRSRVSVSAPAGTSIVDVTVTDT
+NAGRAAEVANAITASLKNVTSDVVPTGPDGDEIVTVTVVEPAAASSRPVSPRPVVNIALG
+LIAGVVIGLGQALVRRLLDSRIRTRDDLVEITDAPVLASVVHHKGSDRPKDEAAPARGTA
+WASAESYRKLRTAVGFVALGGERRSSIVVTSSVQGEGKTETSTNLAKVLAETGARVLLVD
+ADLRRPQVGARLGLDDELGLSDVLTGRADLNDVLLSVDDLSVLTAGTVPPNPSELLGSEA
+MAELLALVEAHFEYVILDAPPLLPVTDAAILSHQAGGAIVVARSGVARQNQLAEALSILE
+AADASVYGVVLNDVPVSHIDGYSQYYR
+>PROKKA_02417
+MNIIDFLRVLRANRLVILGCAALGLVAGLVYSLLQPTLYTATSTGFVTVQGEATISGTET
+AQTRAQSYIPLINSRTVREKIAEGGLDTAGASLSAAVVPGSNLITVSAESEDPEQAAALA
+NSALVATAETANGLDPTSNVQVTAMEDALAPTSPTSPDYVRNMLYGLGAGLLLGLVIAVL
+RRILDVNVRTTTDAQVASGAGLLGAIPLDATLKAERDAPRGEPSPRAAEAVRQLRTNLRF
+AAVDDPPRTIAFTSANPGEGKSTVIGSLALAVAASGQPVILIDADLRRPRQALQFGVDGR
+VGLSEVLNGDVALQDVLVPVGDHGLLLLPAGRTPPNPSEQLGSARMRDLLTALAETHMVL
+VDAPPVLPVTDSTLLSTAVDGTVLVVRHGKARKEHVEVARDMLAGVNARVLGVVLNGTPA
+SGVGSDYYGGSYASKGDDYHAYYQASRDAESRPSDEAVPEGPAAQR
+>PROKKA_02299
+MNILDFLRVLRANRLVLLGGVVLGLLGGLVYSLLQPTLYTSTSTGFVTVAGEASISGTET
+ALTRAQSYVPLINSRTVREKVAESGVDVSGSTLSAQVVPNSNLITVTALAPDPQRAADLA
+NTALGATAEVANSLDPTSNVKVTAMEDALPPAGPSSPDHLRNALIGAGIGLLAALAVAFL
+RRVLDVNVRTTTDATEASGAGLLGAIPQDGTMKAERTAPLGVPSPRAAEALRQLRTNLRF
+AAVDDPPRVVMVTSSNPGEGKSTVIAGLAQAVAVSGQPVILVDADLRRPRQASQFGVDGR
+VGLSEVLSGDVLLEDAVQDLGDGLLLLPAGRTPPNPSEQLGSHRMQELLRVLAETHLVLV
+DAPPGAAGDGLHPAGGRRGRDRAGGAPRQDPEGPCGGGPGHAGQGQRPHAGRGAQRRARL
+RCGLGLLRRGLRRGRRQLRRLLPGAPGRRRRRGRDRGRHVATLIAPGGRARSSHRRRRPG
+DAEGPRL
+>PROKKA_00524
+MTIVDFFRLLRANLLLLLAAALVGGLLGWGYSALQPRIYASESQGFLAARAADQSLITSN
+LPAESRAQAYVALINSEAVRERVAQDTGQDGDGSLSAVLVPESSMIKVTATSTDPETAAQ
+LANSALQATADVAADVDKNSPLEVVPLSDARVPSAPVSPDTRRNVLLGAVAGLGAGLAIA
+VLRRLLDVKVRSRADVKEITGAGVIGAVPENASLTRTGEEAVDLDPRAGEAIRALRTNLK
+FVSVDEPPRVVSFTSADPSEGKSTVASNLARALALAGERVLVVDADLRRPRQHDLFQVAG
+DVGLSEVLAGEVQPDDALAATGIPNLTLLPAGRTPPNPSELLGSKRMRALLKLASEDFFV
+IVDSPPLLPVTDGSLLATAVDGTVLVVRQGRTRKDHLEAAVENLAAVDAHLLGVVMNGVA
+RSQRGGGYSYGYGYESTYHKSHDKYLQGTGTAGKGGKKSRRAARAKKG
+>PROKKA_00535
+MNIIDFLRVLRANRLVILGCAALGLAMGLVYSLLQPTLYTATSSAFVTVEGEASISGTET
+AQTRAQSYIPLINSRTVRERIASEGLDTAGATMSAALVPNSNLITVSAVAPDAQQAAALA
+NGALVATADVANELDPTSNVKVTAMEDALAPATPSSPDRVRHLLYGLGAGLVLGLIVALL
+RRLLDVNVRTTTDAQVAGGAGLLGAIPLDPSMKAERTAPMAPLSPRASEAVRQLRTNLRF
+AAVDDPPRTIAFTSSNPGEGKSTVIGNLALTVAAAGQPVILIDADLRRPRQAMQFGVDGR
+VGLSEVLNGDVALQDVLIPVGEDGLLLLPAGRTPPNPSEQLGSERMRDLLTALAETHMVL
+VDAPPVLPVTDSTLLATAVDGTVLVIRHGKTRKEHLEVARDMLAGVNARVLGVVLNGTPA
+SGVGSDYYGGGYGADGGSYDAYYQAPRDAPEAAAGTAGDTSRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000021.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000021.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1264f648bbb318dc071287399612ceca81a7b17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000021.fa
@@ -0,0 +1,48 @@
+>PROKKA_00570
+MHAGWSLGAAAGAGLGAAVITVGGPAALHLGLNGAVCVAVLLGVRRLFLAEAPVDSASAR
+GAADQSPAPSETSAPPAPAAQALPRRAAVAVLVPAVVIAMAGFGVEEFGNAWATLFLITE
+RGLDPAAAVLGASTLLGAQFVGRLAGDRTLAVLGRRGALTAGLGAVVVGLGLALAPLPGP
+VAVPAAFAGLALAGLGCAVVVPVAYALGDEAPGLRPQTGLAVTSWCMRLAGVGLSPAVGA
+LAGAVGLAPALTVFLGLAAVGTVLAARLPAAP
+>PROKKA_00571
+MSEAPPHLPTADDGVARARRARWAVTAAFATNGALLGALIPHYPEAKAAFGLDPAAFGLL
+VIALAVGGTLAGPLPAPILRRFGARRVMLAGSVAIALLTTAAGLVLDIAGAGAGAGHGAG
+TAAAWLLWVFAGLVLASGVLDAVVDTAQNAQGLQV
+>PROKKA_00294
+MHAGWSLGAAAGAGLGAAVITVGGPAALHLGLNGAVCVAVLLGVRRLFLAEAPVDSASAR
+GAADQSPAPSETSTPPAPAAQALPRRAAVAVLVPAVVIAMAGFGVEEFGNAWATLFLITE
+RGLDPAAAVLGASTLLGAQFVGRLAGDRTLAALGRRGALTAGLGAVVVGLGLALAPLPEP
+VAVPAAFAGLALAGLGCAVVVPVAYALGDEAPGLRPQTGLAVTSWCMRLAGVGLSPAVGA
+LAGAVGLAPALTVFLGLAAVGAVLAARLPAAP
+>PROKKA_00295
+MSEAPPHLPTADDGVARARRARWAVTAAFATNGALLGALIPHYPEAKAAFGLDPAAFGLL
+VIALAVGGTLAGPLPAPILRRFGARRVMLAGSVAIALLTTAAGLVLDIAGAGAGAGHGAG
+TAAAWPLWVFAGLVVASGVLDAVVDTAQNAQGLQV
+>PROKKA_02374
+MPSASPSSPAARRARAHPVARRDVVRARWAATLAFLTNGGMLGALIPHYPQAKAAFGLDA
+DAFGLLVVALAAGAAAAGSLPAPVLRRWGSRRVMLAGTVVMAVVVVAAGLVVDLSAPAQG
+RPWAGAVWLFAALLGVAGILDAVVDTAQNAQGLTVQTRLARPVLTSMHAGWSLGAGLGAG
+LGALAVGAGMPAGLHLGLNGAACVAVLVAAGRRFLPDDARPAPDADAPEGTAAPAPGPSP
+RRPARPPPPRPAPPPGWPCSP
+>PROKKA_02375
+MAGFGVEEFGNAWTALFLQSERGLDVAAAGLGASTLLLAQFVGRLVGDRVLHRLGRRRTL
+AGSLAVVVAALVLVLTAPAAPAVFAGLALAGLGCAVVVPTAYALGDEVPGLPPRTGLAVV
+SWLMRVAGIGLSPLVGLLATGLPLPAALAVFPALAVLGLVGTGVVGRRRRRP
+>PROKKA_02254
+MTSAPADTPRIDRRAATRSRWAATAAFFTNGALAAAMIPHYPQAKAAFGLDPAGFGLLVT
+VMTLGAACAGPAGAPILRRAGSRATVLWGSLAIAVVLTGAGLALDLGARSDAAGPWLGAY
+AAAVFASGLCDAVVDTAQNAQGLRAQHALGRPVLTSMHAGWSLGAAVGAALGAAAVGAGV
+PAGLHLGLNGAACVLLLALTLPRFLPDTPDHAPAPALLTADDPGPESEATPASHRHPWLL
+LAPIVVISMAGFSVEEFGNSWTSLFLQAERGLDPATAGLGASTLLGAQFLGRLTGDRVLA
+ALGRTRALTGGLAVVLAGLTVTLLVPTPAAMFTGLALAGLGSAVVVPTAFALADEVPGLP
+AQTGLAVVSWLMRLAGLGLSPLVGLLAGVLPLTAALGAFVVLAALGTVLALTLRAPRLAP
+DFR
+>PROKKA_00572
+MSEAPPHLPTADDGFARARRARWAVTAAFATNGALLGALIPHYPEAKAAFGLDPAAFGLL
+VIALAVGGTLAGPLPAPILRRFGARRVMLAGSVAIALLTTAAGLVLDIAGAGAGAGHGAG
+TAAAWPLWVFAGLVLASGVLDAVVDTAQNAQGLQVQTRLARPVLTTMHAGWSLGAAAGAG
+LGAAVITVGGPAALHLGLNGAVCVAVLLGVRRLFLAEAPTDSASARDASDQSPAPSETST
+PPAPAAQALPRRAAVAALLPAVVIAMAGFGVEEFGNAWATLFLITERGLDPAAAVLGAST
+LLGAQFVGRLAGDRTLAALGRRGALTAGLGAVVVGLGLALAPLPGPVAVPAAFVGLALAG
+LGCAVVVPVAYALGDEAPGLRPQTGLAVTSWCMRLAGVGLSPAVGALAGAVGLAPALTVF
+LGLAAVGAVLAARLPAAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000026.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000026.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0178dab530d769538855b03121dac49d16863c85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000026.fa
@@ -0,0 +1,70 @@
+>PROKKA_00134
+MSTSPSGSRVAETGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFYGSAGGIQAAGPGV
+ILSFLVAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIV
+ADTAAITTYMAFWFPGVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMI
+FGGVILLFTGASTADGTQASLANLVDHGGFLPHGILGVLTALTIVTFSFGGIETLGVAAG
+EAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPFVQIFEGLGVPFAP
+HLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMV
+LGAVLITVDPNAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVG
+TYLGLAFVATVVITMATIPDSRQALIIGLVWVAVLTLAWFVTGTRTSAAAHDRTGTLPVV
+RTRQSHED
+>PROKKA_02148
+MSTSPSGSRVAETGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFYGSAGGIQAAGPGV
+ILSFLVAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIV
+ADTAAITTYMAFWFPGVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMI
+FGGVILLFTGASTADGTQASLANLVDHGGFLPHGILGVLTALTIVTFSFGGIETLGVAAG
+EAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPFVQIFEGLGVPFAP
+HLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMV
+LGAVLITVDPNAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVG
+TYLGLAFVATVVITMATIPDSRQALIIGLVWVAVLTLAWFVTGTRTSAAAHDRTGTLPVV
+RTRQSHED
+>PROKKA_00251
+MSTSPSGSRVAEPGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFYGSAGGIQAAGPGV
+ILSFLIAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIV
+ADTAAITAYMAFWFPEVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMI
+FGGVILLFTGASTADGTQAGLANLVDHGGFLPHGILGVLTALTIVTFSFGGIETLGVAAG
+EAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPFVQIFEGLGVPFAP
+HLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMV
+LGAVLITVDPNAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVG
+TYLGLAFVATVVITMATIPDSRQALIIGLVWVAVLTLAWFVTGVRKAAAVHDRTGTLPVA
+SGEEAAASHR
+>PROKKA_00186
+MNASPSGAHAVDHPRDDAAHAAQSQLHRGLSQRHIMFIALGTAIGTGLFYGSAGGIQTAG
+PGVILSFLIAGFAVYLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAV
+VIVADTAAVTKYMAFWFPGVPAWAWVAATILVIGLVNLTHVGNFGEAEFWLTLIKIGAIV
+AMIFGGLILMFTGASFTDGTPAGLHNLVDHGGFLPHGFGGVLIALTIVTFSFGGIETLGV
+AAGEAKDPETALPKAINTVPVRILLFYVLTMVVIMSLVPWSAVDGKTSPFVQIFEGLGVP
+FAPHILNFVVLTAAISAINACIYASGRLLYAMAHDGQAPRAFTRTTANGVPWLTVAVMLG
+VMVLGAILITVNPDAFGLIAGVASFAVVLTWTMIFLSHRAMRARVKEAGAPPSVYPMPFG
+IVGTVLGLAFVATVVITMATIPESRQALLIGLAWVVALTAAWFVTGVRKTAALHDRTGQL
+PVVHRHH
+>PROKKA_00187
+MQSTPAPEAPAQAQLQRGLNPRHITFIALGTAVGTGLFYGSAAGIQAAGPGVVLAFMLAG
+AAVYLVMRALGEMAVREPISGSFVAYASRYLGPFAGFLTGWTYVFELAVVIVADTTAVTV
+YMAFWYPDVPAWVWVAATMVVLGLINVTHVGSFGEAEFWFSLIKVLAIVGMIFGGVILMF
+SGASFQDGVTPGPHNLVEHGGFLPHGLMGVLTALTIVTFSFGGTETLGIAAGEAEDPASA
+LPRAVNTVPVRILFFYIGSMLVIMSLVPWTTVDGETSPFVQIFETLGVPFAPHLLNFVVL
+TAAVSAINACIFTNARLLHHMAHDGHAPRVFTAVTRGGVPWVTVVAMLGVMAAGAVFMSV
+KEDTFGIVAGVATFAVVFTWALILASHLGMRRALARHGQAPGAFPMPGGRVGAWLGLAFV
+AVVAGTMAFDQGGAVLGALGGPDALQTALAQPFVIGVLWLAVLAAAWAVPAVRRSAHRHD
+RHGTPPPLTWDV
+>PROKKA_02180
+MTPERRGPGTSPGGRYGVRVNEPPALPEPTGAAPPAPSPAGGATAAPSHGAADARLRRGL
+SMRHIQFIALGSAIGTGLFYGSATAIQLAGPAVILAYLVAGAAVFMVMRALGELAVRHPV
+PGSFGQYADRYLGPFAGFVTGWTFVFEMVVVAIADVTAFGVYMGFWFPDTPRWIWVTAVI
+LFIAAVNTRHVKVFGELEFWLSIVKVSAILAMVIGGVALLVMGVSLDAATPAGVQNLVDH
+GGFAPHGAAGVLAALSVVVFAFGGVETIGITAGEAQDPGRAIPRAVNAVPARILLFYVMT
+MVVIMSLVPWDRITGEASPFVEIFSTLGVPAAPAILNLVVITAAISAINADTFSAGRMLF
+GMAQQGRAPAVFASVSRGGVPWMAAVVMGLALAVGAVLNAVIPEDVFVVVASIATFATVW
+VWLMILLAHIAMRREVARRGLPASAFPVPLWPAASWAAVAFVLLVVGLLGWFSDTRVAMI
+VGLVWLVLLGAAYRLFLHGHGRSRPDLEEGAASSP
+>PROKKA_00142
+MSTSPFGSRVAETGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFYGSAGGIQAAGPGV
+ILSFLVAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIV
+ADTAAITTYMAFWFPGVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMI
+FGGVILLFTGASTADGTQASLANLVDHGGFLPHGILGVLTALTIVTFSFGGIETLGVAAG
+EAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPFVQIFEGLGVPFAP
+HLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMV
+LGAVLITVDPNAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVG
+TYLGLAFVATVVITMATIPDSRQALIIGLVWVAVLTLAWFVTGTRTSAAAHDRTGTLPVV
+RTRQSHED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000027.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000027.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dbe3e6eeb01c499e867c650b5a79413d976e6848
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000027.fa
@@ -0,0 +1,14 @@
+>PROKKA_00161
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>PROKKA_01073
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>PROKKA_00336
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>PROKKA_00347
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>PROKKA_00792
+MAAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>PROKKA_00724
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>PROKKA_01022
+MAAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000028.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000028.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fafb3377d33c9897f84ae47f8dd06015ae95ce22
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000028.fa
@@ -0,0 +1,49 @@
+>PROKKA_00162
+MSTPATRGRADGGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALL
+SDAGHMAADVVVLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVV
+EAISRLGDAPEVASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSV
+GVMVAGVLIILTGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGD
+LDAVEGVEEVHDLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQ
+VEGAGSDGCHDLSW
+>PROKKA_01072
+MGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALLSDAGHMAADVV
+VLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVVEAISRLGDAPE
+VASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSVGVMVAGVLIIL
+TGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGDLDAVEGVEEVH
+DLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQVEGAGSDGCHD
+LSW
+>PROKKA_00335
+MGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALLSDAGHMAADVV
+VLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVVEAISRLGDAPE
+VASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSVGVMVAGVLIIL
+TGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGDLDAVEGVEEVH
+DLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQVEGAGSDGCHD
+LSW
+>PROKKA_00348
+MGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALLSDAGHMAADVV
+VLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVVEAISRLGDAPE
+VASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSVGVMVAGVLIIL
+TGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGDLDAVEGVEEVH
+DLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQVEGAGSDGCHD
+LSW
+>PROKKA_00791
+MGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALLSDAGHMAADVV
+VLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVVEAISRLGDAPE
+VASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSVGVMVAGVLIIL
+TGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGDLDAVEGVEEVH
+DLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLHDRYGIAHATLQVEGAGSDGCHD
+LSW
+>PROKKA_00725
+MGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALLSDAGHMAADVV
+VLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVVEAISRLGDAPE
+VASGAMLAVGFAGLVINIISMLLLRSGTKDSLNVKGAYYEVIADAAGSVGVMVAGVLIIL
+TGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGDLDAVEGVEEVH
+DLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQVEGAGSDGCHD
+LSW
+>PROKKA_01021
+MGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALLSDAGHMAADVV
+VLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVVEAISRLGDAPE
+VASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSVGVMVAGVLIIL
+TGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGDLDAVEGVEEVH
+DLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQVEGAGSDGCHD
+LSW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000029.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000029.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51da731a3257a73f9c94d9a79bc9c4521b8d3ac2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000029.fa
@@ -0,0 +1,28 @@
+>PROKKA_00163
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARALYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>PROKKA_01071
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARALYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>PROKKA_00334
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARALYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>PROKKA_00349
+MSVTLLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARALYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>PROKKA_00790
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARVLYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>PROKKA_00726
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLADPRRARVLYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>PROKKA_01020
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARVLYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000032.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000032.fa
new file mode 100644
index 0000000000000000000000000000000000000000..748068e718095aa9d28e25c758c32f7541ac1d0e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000032.fa
@@ -0,0 +1,42 @@
+>PROKKA_00245
+MSEQTTPDGAESPIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIGAI
+LLSGSPKAFAAGADIKEMATKEFSEMYAADWFAGWDGLTRARTPIVACVTGYALGGGCEL
+AMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGRMIGAEEAER
+IGLVSRVVADEKALEEALEVAATIASKSKPASWMAKEAVNAAFETTLAQGIAFERRVFHA
+AFATADQKEGMDAFTAKREAGWQHR
+>PROKKA_00096
+MSTGLHIETVDRIGIIRLDRPAELNALTFATVEEIAAQVQRWEVDGETDGVVITGSGQKA
+FAAGADIRELQHKSVQEMTARGMQHAMTALRESSLISVAAVNGLALGGGFELALSCDIRL
+ATPQASFGLPELGLGIIPGAGGTQLLTRYTNASVASYHILTGQPISADRAHQLGLVSELH
+EAEDLMAAAMEVIGTIASKGPLARQLAKRAIHGAAHAGMDSGLEIELLAQAAIFGTQERE
+EGLNAFLERRTPSFIPRPRPRKD
+>PROKKA_00100
+MTDRIRTSVEQGVCTITLNRPGALNALENTMIATIVAELERAGADPDVRAILLRGEGKAF
+CAGDDLVDMGTEEHPESPDLVERYSRGYPAIVERMLTLEKPIVASVRRYALGAGLEMALA
+ADLIVAEPQAKLGLPFVLRGIAAGTSLLPKRAPVQLVQRMLYLGEMITAEDAHRMGVVGH
+LAEDEDVDELALATARRLAVGATRAIGLMKTALRTSETLSARDALAVQVGATAASVLTED
+FTEGKVAFTQKRDPEFGGR
+>PROKKA_02257
+MSEQTTPDGAESPIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIGAI
+LLSGSPKAFAAGADIKEMATKEFSEMYAADWFAGWDGLTRARTPIVACVTGYALGGGCEL
+AMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGRMIGAEEAER
+IGLVSRVVADEKALEEALEVAATIASKSKPASWMAKEAVNAAFETTLAQGIAFERRVFHS
+AFATADQKEGMDAFTAKREAGWQHR
+>PROKKA_00124
+MSEQTTPDGAESPIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIGAI
+LLSGSPKAFAAGADIKEMATKEFSEMYAADWFAGWDGLTRARTPIVACVTGYALGGGCEL
+AMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGRMIGAEEAER
+IGLVSRVVADEKALEEAQEVAAAIASKSKPAAWMAKETVNAAFETTLAQGIAFERRVFHS
+AFATTDQKEGMDAFANKREAGWQHR
+>PROKKA_00093
+MNEQNRTEAAEAEQPVIVGRDGRVGRIQLNRPKALNALNAATMEAVVAAAVEMDADPEVG
+AILLLGSAKAFAAGADIKEMKDKDAADMYAADWFRRWEDLARLRTPIVACVQGYALGGGC
+ELAMMADVLVAGRSAKFGQPEITLGVLPGMGGSQRLTKSVGKAKAMDMVLTGRMVEAEEA
+ERMGLVSRLVEDEDAVATAEEVAATIAGFSKPVAQMNKEVVLNAFETPLTQGLVFERRVF
+HGVFSSEDQAEGMAAFAEKRSPVWKHR
+>PROKKA_00245
+MSEQTTPDGAESPIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDLEIGAI
+LLSGSPKAFAAGADIKEMATKEFSEMYAADWFAGWDGLTRARTPIVACVTGYALGGGCEL
+AMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGRMIGAEEAER
+IGLVSRVVADEKALEEAKEVAAAIASKSKPAAWMAKETVNAAFETTLAQGIAFERRVFHS
+AFATADQKEGMDAFTAKREAGWRHR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000035.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000035.fa
new file mode 100644
index 0000000000000000000000000000000000000000..db70a0c07640c8eacfd1aa2e1cd1f06a665904cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000035.fa
@@ -0,0 +1,21 @@
+>PROKKA_00627
+MPAAYPREFRQDVVAIARKGQIPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGITKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
+>PROKKA_00372
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGITKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
+>PROKKA_00389
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGVTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLVQSPK
+>PROKKA_00393
+MPAAYHREFRQDVIAIARKGQMPIAQVAKDFGIAESRLRRWLAQDDVEAGIRPGVTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLVQSPK
+>PROKKA_00410
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGVTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
+>PROKKA_02189
+MPAAYPREFRQDVVAIARNGQMPIAQVAKDLGITASCLRRWLAQDDVEAGIRPGLTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
+>PROKKA_00604
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGITKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000046.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000046.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e6ec3b704c65d2288a4ffe567a4424a47dfdcce6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000046.fa
@@ -0,0 +1,41 @@
+>PROKKA_01791
+MQPIDQTTSGPATSVGERPLAGIRVVSVAVNLPGPLAAARLAEFGAEVVKIEPPTGDPLA
+AAAPQWYAELIAGQRVLTLDLKTGPGQDHLATLLKGADLLLSSLRPSAADRLGLPASAHA
+AGAVFLEVVGHDGDDADLPGHDLTYQAAAGTLDAPRMPLVPVADLLGGERAVSAALAALR
+SRDHGGPVTRVRVTLEDAARAAAAPVRRGLLGPGGPLGGDLPTYSLYASADGHVAVAAVE
+PHFAARLAEHIGSTRDEIARTILTRPGAEWERIANELDLPLAVVRPPR
+>PROKKA_02047
+MSAAPLAGVRVVTIALNLPGPAAAARLQELGADVVTVLPPSGDPVATLVPALYEELHRGQ
+SVRTVDMKSQAGVAEMEQILAEADVFLTSHRSGALRRLGLDADAVRARHRRICQVDITGY
+AGDRTDVPGHDINYQAAAGLLAPGAPPRILAADLHGAERAVSTALALLWARGADGDGGHA
+TVALAEAAHALALPNRHRMTDPRSPLGGALPHYGVYPAAEGHVAVGALEPHFAAALVEGL
+GLDADGDVRAQLTEALSRHDAAHWQAWGEKRGIPLTALVSPTA
+>PROKKA_01753
+MSAAPLAGVRVVTIALNLPGPVAAARLQELGADIVTVLPPSGDPVATLVPALYEELHRGQ
+SVRTVDMKSQAGAAEMEQILAEADVFLTSHRSGALRRLGLDADAVRARHRRICQVDITGY
+DGDRTDVPGHDINYQAAAGLLAPGAPPRILAADLHGAERAVSAALALLWARGADGDGGHA
+TVALADAAHALALPNRHRMTGPRSPLGGALPHYGVYPAAEGHVAVGALEPHFAAALVEGL
+GLDADGDVRAQLTEALSRHDAAHWQAWGEERGIPLTALASPTA
+>PROKKA_01085
+MQPIDQTTSGPATSVGERPLAGIRVVSVAVNLPGPLAAARLAEFGAEVVKIEPPTGDPLA
+AAAPQWYAELIAGQRVLTLDLKTGPGQDHLATLLEGADLLLSSLRPSAADRLGLPASAHA
+AGAVFLEVVGHDGDDADLPGHDLTYQAAAGTLDAPRMPLVPVADLLGGERAVSAALAALR
+SRDHGGPATRVRVTLEDAARAAAAPVRRGLLGPGGPLGGDLPTYSLYASADGHVAVAAVE
+PHFAARLAEHIGSTRDEIARTILTRPGAEWERIANELDLPLAVVRPPR
+>PROKKA_00733
+MSAGDGASRVPAGDAVVPGPLADVAVVTIALNLPGPLAAFRLAELGAQVTTVLPPAGDPV
+ATLVPALYTELHAGMAELTLDLKQDGDRARMEELLAGADVLLTSHRSGALTRLGLDAAAT
+ARRHPRLVQVDITGFPGERADVPGHDLNYQAEAGLLEPGHPPRGLLADVHGAERAVSAAL
+AGLHARDRDGRGGGVVVALSDAAHAMALPTRHGMTDPGSPLGGANPFYGVYPARSGHVAL
+GALEPHFAHAMVEALQLDPDGDVRAQLTAAFAERDADAWQSWGEEWGHPITALAGPTA
+>PROKKA_00743
+MDVVGFAGERAGVPGHDLTYQAETGLLLSGESQTPTLPRALVADMHGAEQAVSTAPALLL
+ARDRAGRDAPGGHARVSLAEAAAAVGIPSRHGLLAPDALLGGGTPYYAVYRAAEGHVAVG
+ALEPHFSDALRAELDLPAGAGDDLAAALSAALTARPARDWQEWGEERGIPTGRGAVNGQP
+R
+>PROKKA_01981
+MSAAPLAGVRVVTIALNLPGPAAAARLQELGADVVTVLPPSGDPVATLVPALYEELHRGQ
+SVRTVDMKSQAGVAEMEQILAEADVFLTSHRSGALRRLGLDADAVRARHRRICQVDITGY
+AGDRTDVPGHDINYQAAAGLLAPGAPPRILAADLHGAERAVSTALALLWARGADGDGGHA
+TVALAEAAHALALPNRHRMTDPRSPLGGALPHYGVYPAAEGHVAVGALEPHFAAALVEGL
+GLDADGDVRAQLTEALSRHDAAHWQAWGEKRGIPLTALASPTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000047.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000047.fa
new file mode 100644
index 0000000000000000000000000000000000000000..373482d9efd984b5b928979d7d963d9b44a6eb55
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000047.fa
@@ -0,0 +1,78 @@
+>PROKKA_01806
+MSSKAARTRSEPVTLPRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVPQRRAG
+PEIVDQWIEDNPVWGPVLDALQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHAKALRQ
+PPARTPRNLTRLPASGVVVLEEGGPSPEEAVARAQAWLRKRRYRVERRLEAGGASVGAER
+GYLREIGNILFHVSLIGVLVFMAYGGMTKYGGQKIIVEGEGFANNLVAYDSFTPGTYFSA
+DDLQPFSLTLDSFDAVFDRESETHYGQPLDYTAVMDVREGSGGELQRQILKVNQPLDIDG
+VRVYLVGNGYAPVVTIRDGAGDVAFQGPVVTRVFDQNYGSQATIKVPDARPDQLGFVGFF
+LPSAVEDEEGAAFSADPELLNPELQLNSYYGDLGLDTGRPQNVYVLDTASLTELNSRTNE
+NGGIVLSPGQTYELPEGKGSISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLAISLFV
+RRRRVWVRARTDDDGRTRVEYALLARGEEFGLHEEHVALRAAMEKWWPIVAATETADDAA
+AGAAPQSTPTAPETPAGPADARSGD
+>PROKKA_01503
+MSSKAARTRSEPVTLPRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVPQRRAG
+PEIVDQWIEDNPVWGPVLDALQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHAKALRQ
+PPARTPRNLTRLPASGVVVLEDGGPGPEEAVARAQAWLRKRRYRVEHRPEAGGASVGAER
+GYLREIGNILFHVSLIGVLVFMAYGGMTKYGGQKIIVEGEGFANNLVAYDSFTPGTYFSA
+DDLQPFSLTLDSFDAVFERQSETTYGQPLDYTAVMDVREGTGGELQRQILKVNQPLDIDG
+VRVYLVGNGYAPVVTIRDGAGDVAFQGPVVTRVFDQNYGSQATIKVPDARPDQLGFVGFF
+LPSAVEDEEGAAFSADPELLNPELQLNSYYGDLGLDTGRPQNVYVLDTASLTELNSRTNE
+NGGIVLSPGQTYELPEGKGSISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLVISLFV
+RRRRVWVRARTDEAGRTRVEYALLARGEEFGLHEEHVALRSAMERWWPVAAPESEEEAVA
+SAAAVGHTGTTPETLAGPRTPRSGD
+>PROKKA_00397
+MSRTEDQDPGRRPEVALPALGFWGTLRFAWTQLTSMRTALMLLLLLAVAAVPGSLFPQRP
+AGPGIVQDYIDDNPVLGEWLDRFQMFDVYSSVWFSAIYLLLFISLIGCVAPRAVKHAQAL
+RSAPPRTPRRLSRLPEYGRVVLEPGGPAPVEAVEQAARYLKRRGYRIEVRQEDAGGASVG
+AARGYLREVGNIVFHLSLIGVLVFMATGSLLSYRGQKILVEGEGFANTLVAYDAFTPGSA
+FSEEMLTPFSMTLKRVEYVYDRQSPTHYGQPLD
+>PROKKA_01068
+MGDAPVSSKAARTRSEPVTLPRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVP
+QRRAGPEIVDQWIEDNPVWGPVLDALQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHA
+KALRQPPARTPRNLTRLPASGVVVLEEGGPSPEEAVARAQAWLRKRRYRVEHRPEASGAS
+VGAERGYLREIGNILFHVSLIGVLVFMAYGGMTKYYGQKIIVEGEGFANNLVSYDSFTPG
+TYFSADDLQPFSLTLDSFDVVFDRESEALYGQPLDYTAVMQVQEGGGGEPREEILKVNHP
+LSMDGVRVYLVGNGYAPVLTVRDGEGDIAFQGPVVTRVQDVNFNSLVTLKVPDARPDQLG
+FVGQFMPAAVEDESGVAVSVDPELYNPQLILDSYYGDLGLDGGVPQNVYVLDTETLTELN
+SRKNENGGIVLSQGQTYELPEGKGSISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLA
+ISLFVRRRRVWVRARTDEAGRTRVEYALLARGEEFGLHEEHVALRAAMEKWWPVAAATAP
+ETTPETPCRPRRRPIRRLTVFNPTAPVNEQLALYSDLFMLIAAFVYAAAFVLFTIDMATS
+SATIRRLEEDLAAQRGPARLAPARETVGAGFGGSSLGGSSSVGSTGAGSSAGGPGVLPGE
+ARAAGLGDEPGLVDEDMDYTGGGRRPIANVAVAVLAVGWALHAFAVIARGLAASRVPWGN
+LYEFMTTGALVITTVYLLFLFRKDLRFVGTFVTGLVVAMMCAATMGFPTPVGHLQPPLQS
+PWLVIHVSIAVLATALFTLTAAMSMLQLIQDRAEKRAAATGERPWAFLRLVPSAQALENW
+SYRINAVGFVMWTFTLIAGAIWAEASWGRYWNWDTKEVWTFVIWVVYAAYLHARATRGWT
+GARAAWLSIVGFLCVVFNYTIVNTYFPGLHSYAGLPG
+>PROKKA_02641
+MSRPSDYDDGTGAGGTLRAESPELGFAGWLRWFWRQLTSMRVALILLLLLAVAAIPGSLV
+PQRGADPNGVVQYQKDHPDLFPILDAFPIQAFDVYGSVWFSAIYLLLFISLIGCVLPRIA
+HHWKAWRGRPPKTPARLQRMAGFSEIRLSNPDATPAEREAFAARAVDEAAAILKKLRYRV
+EVQRASRRGVDEVSVSAERGYLRETGNLLFHVSLLGVLVSVGLGGVFTFNGQKVLIEGET
+MVNQLIDYDTATSGRSFDSSSLEPFSLRLDTLDVTYNTPDDGNVQAIGLVKDYTANMTLI
+SPEGDESEHVIRVNHPLRVHGSPIYLIANGYAPKITIRNAEGTVVYSEAMPFIPQDNLNM
+TSLGVVKVPDGIVDESGEPVQLGLRGFFYPTKADLDTGAYTSNYPDLENPVLTLDVFVGD
+LGINDGIPKSVYALDTSDMEQVTGRAVDLDSIELRPGEQTELPNGFGTIEFESVPRYASF
+DVMQNPAQEWILVFAVLALGGLMWSLFVPRRRMWVKALPSEDGVVLQYAALARGDDPALE
+RAVEELRDRHRELL
+>PROKKA_01003
+MGDAPVSSTSAPKDPAPRNRTRDDVTLPALGVGGTLRWAWTQLTSMRTALLLLLLLAVAA
+VPGSLVPQRRAGPEAVDQWIEDNPFWGPILDALQFFDVYTSVWFSAIYLLLFISLVGCVL
+PRALKHAKALRQPPARTPRNLGRLPESGVVVLEAGGPAPEEAVRQAQRWLKRKRYRVELR
+PEAGGASVGAERGYLREIGNILFHFSLIGVLAFMAYGGMTKYTGQKIIVEGEGFANNLVA
+YDSFTPGMYFDAASLQPFQLTLKSFDATFERQSQTHWGAPLDYTAVMEVRHGTGGDPEEQ
+VLKVNHPLEIDGAKVYLVGNGYAPVVTVRDGNGDIAFQGPVVTRVTDQNFNSLAVIKAPD
+ARPDQLGFVGQFMPAAADVGQGVEVSVDPEPLNPKLILNSYSGDLGLDAGVPQNVYVLDT
+STLTELNSRRSENGGITLSVGQTHVLPDGKGSISLDGVRRYVGLDIHYDAGKWGVGVFSV
+LALIGLAVSLFTRRRRVWVRARTGDDGRTRVEYALLARGEEFGLREEHVALREAFEKMWP
+VSAPEADTGETTPATPAPAAAPTPRSGD
+>PROKKA_01727
+MSSKAARTRSEPVTLPRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVPQRRAG
+PEIVDQWIEDNPVWGPVLDALQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHAKALRQ
+PPARTPRNLTRLPASGVVVLEEGGPSPEEAVARAQAWLRKRRYRVEHRPEAGGASVGAER
+GYLREIGNILFHVSLIGVLVFMAYGGMTKYGGQKIIVEGEGFANNLVAYDSFTPGTYFSA
+DDLQPFSLTLDSFDAVFDRESETHYGQPLDYTAVMDVREGSGGELQRQILKVNQPLDIDG
+VRVYLVGNGYAPVVTIRDGAGDVAFQGPVVTRVFDQNYGSQATIKVPDARPDQLGFVGFF
+LPSAVEDEEGAAFSADPELLNPELQLNSYYGDLGLDTGRPQNVYVLDTASLTELNSRTNE
+NGGIVLSPGQTYELPEGKGSISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLAISLFV
+RRRRVWVRARTDDDGRTRVEYALLARGEEFGLHEEHVALRAAMEKWWPIVAATETADDAA
+AGAAPQSTSTTPETPAGPADARSGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000048.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000048.fa
new file mode 100644
index 0000000000000000000000000000000000000000..68bc6a1af6472b40f9856e00c7f4930f611b4788
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000048.fa
@@ -0,0 +1,35 @@
+>PROKKA_01808
+MQTPRPSRRTVLTGLSLLGLAPVLAACSGDDSLTRQAGNADGKNYIAGDGSVLEIAPAER
+GAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAPHLVSLHEQFAPQGVRFL
+GVNVRDTVTTAQAFERTFEIPYPSIEDARGEVLLNMTDYVPPQAVPSTLVLDVEGRVAAR
+VLGAVEESTLRALLTTVVDEAAA
+>PROKKA_01505
+MQTPRPSRRTVLTGLSLLGLAPVLAACSGDDSLTRQAGNADGKNYIAGDGSVLEIAPAER
+GAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAPHLVSLHEQFAPQGVRFL
+GVNVRDTVTTAQAFERTFEIPYPSIEDARGEVLLNMTDYVPPQAVPSTLVLDVEGRVAAR
+VLGAVEESTLRALLTTVVDEAAA
+>PROKKA_00398
+MPIPQPHREGHHRPPGLPPRPGRRQVLAGLAGVASLPLLAACSAEDPLAAQAGKADGKNY
+IAGDGSVLEIGPAERGEPVQFSSAMFSGEPIIAQDLAGDPAVLNFWYAACAPCRVEAPDL
+QALHEQFAPEGVRFLGINVRDTIATAQAFERKFGITYPSVEDRGGQVLLAMTDYVPPQAV
+PTTIVLDHQGRVSARILGIAERSTLRTLITTVLDEQA
+>PROKKA_01066
+MHTPPRPSRRTLLTGLALASLAPALAACSGGDDSLARQAGNADGKNYIAGDGSVLEIAPA
+ERGAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAPHLVSLHEQFAPQGVR
+FLGVNVRDTVTTAQAFERTFEIPYPSIEDTRGDVLLNMADYVPPQAVPSTLVLDVEGRVA
+ARVLGAVEESTLRALLTTVVDEAAA
+>PROKKA_02643
+MNRRRTGAALALPIAALFALAGCSGGDGNLAAEWNEASGKGYVSGDGSSLSIAPDQRTEP
+VEFSGETEDGDIYGSDDTVGSVTVVNFWYAGCAPCRAEAPDLVEAYDEFSPQGVKFVGVN
+TRDQVAQARQFSVRFDIEYPSIMDNAGGRAVQRAFAGQVPLNAVPTTLVLDAEGRVAHRV
+LGQLAGASQLRTLIGETLAEAGGGAAADPASDPAPADEATEQ
+>PROKKA_01001
+MPFPPRPSRRAALAGLSAAALAPLLAACSGTDDSLAQQAGNAGGKNYIAGDGSVVEYAAD
+QRGAPVEFSAAGFDGETVSGETLRGEPALLNFWYAACAPCRVEAPHLVKLHGEFEPKGVR
+FLGVNVRDTVTTAQAFERTFGIPYSSVDDTSGSVLLAMSDYVPPQAVPSTLVLDRQGRVA
+ARVLGAVEEGTLRALLDTVVAEA
+>PROKKA_01729
+MHTPPRPSRRTLLTGLALASLAPALAACSGGDDSLARQAGNADGKNYIAGDGSVLEIAPA
+ERGAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAPHLVSLHEQFAPQGVR
+FLGVNVRDTVTTAQAFERTFEIPYPSIEDARGDVLLNMTDYVPPQAVPSTLVLDVEGRVA
+ARVLGAVEESTLRALLTTVVDEAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000049.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000049.fa
new file mode 100644
index 0000000000000000000000000000000000000000..534ce5b8b3b34b3d2a7a1e9eaa8095ca685e657e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000049.fa
@@ -0,0 +1,70 @@
+>PROKKA_02005
+MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTR
+IIERRPHRLEIGQADGIQARSVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRT
+SLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARPDYGWAFETLEDTNDGEHPVL
+VTLRRTVDAEENALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGVM
+DALADTDFPDIRTKCAIHSSSGSILLIPREGGHLSRMYVDLGEVPADDDHKVRQTPLEEI
+IRRAQQILRPYTLDVKEVAWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAG
+QGMNVSMQDGWNLGWKLGQVLSGLAPVELVPTYAEERKEIAKNLIDFDKEWSTLMATPTS
+ELGDPNEVAEFYTKTAEFPAGFMTEYQPSLLTTDATGQALAQGYPIGKRFKSALVERSCD
+TNVKHLGHLHRADGRWRVYVFADAASPRAEDSKVAAWAKAIEEDPRSFRNRHTPSDGPED
+ARFDIKVVYQQKQTEFAHPDVPSIFRPTTGSLGLHDLNNIFATCRPQHGEDIFEARGISR
+DGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN
+>PROKKA_01715
+MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTR
+IIERRPHRLEIGQADGIQARSVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRT
+SLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARPDYGWAFETLEDTNDGEHPVL
+VTLRRTVDAQGNALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGVM
+DALADTDFPDIRTKCAIHSSSGSILLIPREGGHLFRMYVDLGEVPADDNHKVRQTPLEEI
+IRRAQQILRPYTLDVKEVAWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAG
+QGMNVSMQDGWNLGWKLGQVLSGMAPVELVPTYSEERKEIAKNLIDFDKEWSTLMAKPTS
+ELGDPNEVAEFYTKTAEFPAGFMTEYQPSLLTTDATGQALAQGYPIGKRFKSGLVERSCD
+TNVKHLGHLHRADGRWRVYVFADTASPRAEDSKVAAWAKAIVEDPRSFRNRHTPSDGPED
+ARFDIKVVYQQKQTEFAHPDVPSIFRPTTGPLGLHDLNNIFATCQPKHGEDIFEARGISR
+DGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN
+>PROKKA_00837
+MLFHHHGYVSTDPRVQPAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTR
+IIERRSHRLEIGQADGIQARSVETFQAFGFASQIIDEAYDLTSMAFWNPSSEDADTIVRT
+SLAEDDPEGVSEFPHLIVNQARILDWFAAYMKNSPTRAEPDYGWSFESLEDSAEGEYPVL
+VTLRRTVDAQGEPLADPESGETRQVRAKYVVGADGAGSRVRKAIGHSLAGGASNHAWGVM
+DALAVSDFPDIRTKCAIHSSTGSILHIPREGGHLFRMYVDLGEVPADDNHKVRQTPIEEI
+IRRAQQIIRPYTLEVKDVAWHSVYEVGHRLTSGFDNRERVDHPNVFLLGDACHTHSAKAG
+QGMNVSMQDGWNLGWKLGQVLSGVAPAELVPTYSEERKEIAKNLIDFDKEWSTLMAKPTS
+ELGDPNEVADFYTKTAEFPAGFMTEYKPSILTTDATGQSLAAGFPIGKRFKSALVERSCD
+TNVKHLGHLHRADGRWRVYVFADAASPRSADSKVAAWAKAVEEDPRSFRNRHTPADGPQD
+ARFDVKVVYQQKQTEFAHPDVPAVFRPTSGDLRLLDLNNIFATCQPKHGEDIFEARGISR
+DGAVVVVRPDHYVSGVFGLDEVERLNEFFAGVLLDAS
+>PROKKA_00774
+MLFHHHGYVSTDPRMKPAAGIGLDRPAELPDEMDVLIVGTGPAGMIAAAQLAMFPDVHTR
+IIERRGKRLEIGQADGIQARSVETFQAFGFASQIIDEAYDLTSMAFWNPSPEDEDAIVRT
+SLAEDDPHGVSEFPHLIVNQARILDWFAEFMKNSPTRATPDYGWEFVSLDDSDQDAERPV
+QVTLRRTVDAKGNPLAEGVAGEERVVRAKYVIGADGAGSRVRKAIGHSLSGDAANHAWGV
+MDVLADSNFPDIRTKCAIHSSSGSILHIPREGGHLFRMYVDLGEVPADDNHKVRQTPIEE
+VIRRAQQIIRPYTLDVKDVAWSSVYEVGHRLTSGFDNRERCTHPNVFLLGDACHTHSAKA
+GQGMNVSMQDGWNLAWKLGQVLSGIAPAELVPTYSEERKEIAKNLIDFDKEWSTLMAKPT
+SELGDPNEVAEFYTKTAEFPAGFMTEYRPSMLTTDAAGQELATGFPIGKRFKSAKVERSC
+DTNVKHLGHLHTADGRWRVYVFADAAAPHDADSKVAAWAEAVEEDPQSFRNRHTPAGAPQ
+DERFDLKVVYQQKQTEFAFPDVPAVFRPTTGPLGLHDLNNIFAVCRPEHAEDIFELRGVS
+RDGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN
+>PROKKA_00173
+MFIAGDACHTHSAKAGQGMNVSMQDGWNLAWKLGQVLEGRSDASLLATYSEERQQIAENL
+IEFDKAWEGMMSKRPDELEDPQAVGRFYKDNAEFPNGFATQYPASSVTGEDTHQALAAGV
+PIGKRFESAAVRRVADTSPRQLGHLFEADGRWRLYAFADEDRTAVGELADWLADSPDSPV
+RRFTPESADLNSVFDAKVVYQQPYQEVELADVPALFLPKMGPYQLTDKEVVFAADLADDI
+FEARGIDRGGALIIQRPDMYVAHVLPLSAREEITAFFEQNMVSASV
+>PROKKA_00174
+MRGAADPRRSLSTLPTTAVSEFPFLIVNQARVIDYFAEYAERGPQGQERTVRAKYVVGCD
+GSRSRVRDCTGIEVVRDPSAHAWSVMDVLLETDFPDNRQKCGIQSDKDGTILLIPREGGF
+LARFYVSLGSIDDAPRPRSGGGIRACSSPATPATPTPPRPARA
+>PROKKA_01943
+MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTR
+IIERRPHRLEIGQADGIQARSVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRT
+SLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARPDYGWAFETLEDTNDGEHPVL
+VTLRRTVDAQGNALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGVM
+DALADTDFPDIRTKCAIHSSSGSILLIPREGGHLFRMYVDLGEVPADDNHQVRQTPLEEI
+IRRAQQILRPYTLDVKEVAWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAG
+QGMNVSMQDGWNLGWKLGQVLSGMAPVELVPTYSEERKEIAKNLIDFDKEWSTLMAKPTS
+ELGDPNEVAEFYTKTAEFPAGFMTEYRPSLLTTDATGQALAQGYPIGKRFKSALVERSCD
+TNVKHLGHLHRADGRWRVYVFADAASPRAEDSKVAAWAKAIEEDPRSFRNRHTPSDGPED
+ARFDIKVVYQQKQTEFAHPDVPSVFRPTTGSLGLHDLNNIFATCRPTHGEDIFEARGISR
+DGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000053.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000053.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a0eb9eb6864014977f2b98047e656afed6eb3c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000053.fa
@@ -0,0 +1,35 @@
+>PROKKA_02246
+MDHKEILHQGLRRQRDALFAKLDGLPEREVRLPRTPTGTNLLGLLKHAATCELEYFGEVF
+GRPAGIPLPWDAPGVGEEDGADLFAAEDETLEDVLDYARRCFAHADATIEALVFDARGRV
+PWWPAHLAEVTLAQILSHVALDAARHAGHADILREGIDGQAGLRGPGDNLPGWDAERWAA
+HVRRLEGIARGAGPVR
+>PROKKA_02261
+MDHKQILHDGLRRQRAALLQKLEGLSERDARLPRTPTGTNLLGLVKHAAVVELEYFGETF
+DRPAEVQLPWAAAGQSEEDNVDMFAAEGESLEDVLEFARRCFAHADATITALGADAHGRV
+AWWPDDKAEVTLAQIIAHVALDEARHAGHADILREQIDGQAGLRAPGNNLPVWGADRWAA
+HVDRLTAIAEGSGGPGRN
+>PROKKA_01948
+MDHKEILHQGLRRQRDALFAKLDGLPEREVRLPRTPTGTNLLGLLKHAATCELECFGEVF
+GRPAGIPLPWDAPGVGEEDGADLFAAEDETLEDVLDYARRCFAHADATIEALVLDARGRV
+PWWPAHLAEVTLAQILSHVALDAARHAGHADILREGIDGQAGLRGPGDNLPGWDAERWAA
+HVRRLEGIARGAGPVR
+>PROKKA_00418
+MDHKQILHDGLRRQRAALLHKLEGLSERDARLPRTPTGTNLLGLVKHAAVIELEYFGGTF
+GRPAEVQLPWAAAGQPEEDNVDMFAAEGESLEDVLEFARRCFVHADATITALGADAPGRV
+AWWPDDKAEVTLAQIIAHVALDEARHAGHADILREQIDGQVGLRSPGNNLPPWDADRWAA
+HVDRLTAIAEGSGGVGWN
+>PROKKA_00422
+MGFLTPQAHGELAVLTTYALQQLAQMRTTVHGLTDEQAHSVPSASALNLTGLLLHTGEVA
+VYWTAAAASAPGEPVLPEDVNEDHSLDELVADGRPLAQVLERFDRCVEVARQNLAAVADL
+SAPVPVPDAPWFPADLKTWEARWALLHVTAEVARHVGHADLIRESIDGTGSYELNDLADA
+AAQG
+>PROKKA_02178
+MDHKEILHQGLRRQRDALFAKLDGLPEREVRLPRTPTGTNLLGLLKHAATCELEYFDEVF
+GRPAGIPLPWDAPGVGEEDGADLFAAEDETLEDVLDYARRCFAHADATIEALVFDARGRV
+PWWPAHLAEVTLAQILSHVALDAARHAGHADILREGIDGQAGLRGPGDNLPGWDAERWAA
+HVRRLEGIARGAGPVR
+>PROKKA_02192
+MDHKQILHDGLRRQRAALLQKLEGLSERNARLPRTPTGTNLLGLVKHAAVVELEYFGETF
+GRPAEVQLPWAAAGQPEEDNVDMFAAEGESLEDVLEFARRCFAHADATIAALDADAPGRV
+AWWPDDKAEVTLAQIIAHVALDEARHAGHADILREQIDGQAGLRAPGNNLPPWDADRWAA
+HVDRLTAIAEGSGGPGRN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000055.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000055.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00e8045ec126944afea25c92a72b2c9760780d96
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000055.fa
@@ -0,0 +1,42 @@
+>PROKKA_01696
+MEHATALENVMLPLRYGPDRVPRGEQRRRAGEALERVGLGMRTGHRARTLSGGEKQRVAV
+ARALINEPPLVLADEPTGALDQARTRDVVDLLRGAVGPERAVVVVTHDPRVAAACDRRWH
+LVDGELAPQD
+>PROKKA_00855
+MTLLEVHDVDKTFHSGGEAVPVLRGASLLVPAGEMHAVTGPSGSGKSTLLRILACLDSPD
+SGRVLLGGEPLPEPWSRGGDRYRNQRCGIVLQDFALMEHATALENVMLPLRYGPDRVPRG
+EQRRRAGEALERVGLGTRTGHRARTLSGGEKQRVAVARALINEPPLVLADEPTGALDQER
+TRDVVDLLRGAVGPERAVVVVTHDPRVAAACDRRWHLVDGGLAPQD
+>PROKKA_01010
+MSDGSAPPLLELAGVLKSFKGADRPALDGVDLTVRDGDFVAIVGPSGSGKSTLLNVLGLL
+DRPDGGSYRVSGTDTMSMGERERDRLRSRWFGFVFQSSHALGDEPVAVNAALGLRVQRTP
+PEQRDARAGEALALLGLSHRLDTRAKLLSGGERQRLAIARAIATRPRVILADEPTGNLDS
+VNSRIVIDHLRALHAQGATVLLITHDPEIARQADRQVRIEDGRITELAGHRTAASASADM
+AGTGHGWSAPGAARRHRSPRSSAMLDDLVEAVSSLSTRFLRTVLLMAAFAVGIGGLVASV
+GLTQTATDQVGALLTAAALDEVVVTVPQAEGLLDPGDGRLASWADGLAALPHVTAAGHVA
+QVAPADVVITRHDPSDPEPAVAISLVAASSSYAGLAGLTLPSETSRTLLDSPDARLAWAT
+PAAARALELPVTDTGMLSPGYRVWIQGHAVDVAGIVTLSERTPELDASLVVTPAVMTGVA
+QAHPQLVVRTEAGFPYPVSQAAPLVIAPENPGSVTVRTVADLRNLRAGVSDDLGAFVGVL
+SGVLLVLAVISASTAMYLSVQARTAEIALRRAIGSPRGLIARLFLLEGALIGLAGGAVGA
+AVGSGVILAVSQARGWAAVLPPGAVPLALGLGLVAGVVSALYPGWVASRQRPADALRG
+>PROKKA_00792
+MSLLEVHDVDKSFTTAASEVPVLRGVSLSVPAGQMHAVTGPSGSGKSTLLRILACLDSPD
+AGEVLLEGVPLPPPWSRGGDRHRNRRCGIVLQDFALMEHATALDNVLLPLRYGPGGGSRA
+EQRRRAALALDRVGLADRAHHRARTLSGGEKQRVAVARALINDPPLVLADEPTGALDQAR
+TRDVVKLLRSAVGPQRAVVVVTHDPEVAAACDQRWHLEDGRLHSQG
+>PROKKA_00870
+MTASAPVLTLDRVQVGYRHPDGGTRVLIESLDLTLAPGEVVGLWGRSGTGKSSLIRHLAG
+LSRPLAGRIAYRSPDGSLNGEVADLSAGDLARYRREHLGYVDQSCELIGELSALDNAAVW
+IHGGRIAGSACDAQETVQGLLERLGLGHRLGAPASRLSGGEAQRVALVRALSKRPHLIVA
+DEPTGHLDGVTAREAIALLREHAEAGAAVLVASHDPLVHAAVDRAVRVGED
+>PROKKA_00943
+MNTAPLTPPVLAARGLTKAYGSTHALTGVDLEIRPGESVAVMGPSGSGKTTLLHVLSGII
+APDGGRVTLAGADGTVHEVTALTEEQRARLRRERLGFVFQEGLLLPELTAVENVAMPLML
+NGVDRRAAEQTAARWLGSLGLAGMEDRRPGELSGGQRQRVAIARAQAVEPDVVFADEPTG
+ALDSDTSEAVLDSLIASTVARGRTLVVVTHDPSVAAACSRLIRVRDGRIESDQAQAAAGT
+TREQVR
+>PROKKA_00735
+MSLLTVHDVHRSYRGPAGDVPVLRGVSLQVPGGGVHAIMGPSGSGKSTLLRLLACLDTPD
+AGSIRVAGRSLPAPWSSDGDAYRNRTCGIVLQDHLLIDRATAVDNAALPLLYARPRTSKR
+ERRTMAAELLTRLGLGDRLHHPVGRLSGGERQRVAIARAVIMGPSLLLADEPTGALDEER
+TDEVMGLFRSMSQPERAIVVVTHDPAVAARCDHTWRLRAGRLE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000056.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000056.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1cb3d59adf3ee64729015040de8c50119295928d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000056.fa
@@ -0,0 +1,35 @@
+>PROKKA_00025
+MERGPVVGLLDNLERGLERAVRSAFSAGGPRAVKPVEIASALRQAMDDESIALSEGHTVA
+PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRGGD
+LRVVTRLDDGSLTAPAPHDDGASPATAHGPGATAPAPDRLVEDPPAAAPREPSPAPRVGP
+RPAPRRAAAPAAPAAPSHADQPTVVMGRPVTEPAGPALELDGRMLPLDGDDLILGRSAER
+ADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRDGDVVTVGQTE
+LLFFGGTGGRA
+>PROKKA_02043
+MERGPVVGLLDNLERGLERVVRSAFSAGGPRAVKPVEIASALRQAMDDESLALSEGHTVA
+PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRAGD
+LRVVTRLDDGSLTAPAPHDDGASPATAHGPGASAAAPDRLVEDLPAAAPREPSPAPRVGP
+RPAPRRAAAPAAPAAPAAPAAPAHADQPTVVMGRPVTGPAGPALELDGRMLPLDGDDLIL
+GRSAERADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRDGDVV
+TVGQTELLFFGGTGGRA
+>PROKKA_00370
+MERGPVVGLLDNLERGLERAVRSAFSAGGPRAVKPVEIASALRQAMDDESFALSEGHTVA
+PNSYVVHFSPADFDRARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDTDVRAGD
+LRVVTGLDDGSLPAPAPHDDGASPATAHGPGATATAPDRLVEDLLGGRTP
+>PROKKA_00371
+MGRPVTEPSGPALELDGRMLPLDGDDLILGRSAERADLVIPDSSVSREHLRLLTVGSTVT
+LLDLGSRNGVLVNGRRVDGSVTLRDGDVVTVGQTELLFFSGTGGRA
+>PROKKA_00353
+MGLLDNLERGLEKAVRSAFSAGGARAVQPVEIASALRHAMDDESFALSEGHTVAPNDFTV
+HFAPADFDRARTWGSTLAGELCDEVIRHAQSQGYTLPGSVRVAFHEDAQVHAGQVEVDAR
+IDDGSSPVPSPPAATSAPAPAAARTADDRGPRPSRAPRHGATAAPAPRRDPSPAPRPAPT
+PARSESARRAPADEQATVVMPRRTSPAPAVPWLEADGVRHPLTHEDMVLGRSSERADVVV
+PDSSVSRQHARLVRVGRSVTLIDLGSRNGVTVNGRRVDGSTVLREGDRITVGQTDLVFHI
+DPADGRPRA
+>PROKKA_00025
+MERGPVVGLLDNLERGLERVVRSAFSAGGPRAVKPVEIASALRQAMDDESFALSEGHTVA
+PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRAGD
+LRVVTRLDDGSLTAPAPHDDGASPATAHGPGASAAAPDRLVEDLPAAAPRKPSPAPRVGP
+RPAPRRAAAPTAPAAPAHADQPTVVMGRPVAEPAGPALELDGRMLPLDGDDLILGRSAER
+ADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRDGDVVTVGQTE
+LLFFGGTGGRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000058.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000058.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ae7a03950a6f290230e4c253196bf5105112a10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000058.fa
@@ -0,0 +1,44 @@
+>PROKKA_00049
+MQRIHDPQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHFGEDA
+TVWPMFNGTGANVVGLQAMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDGKL
+TPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPDEVKAITDYAHEHGMRVYMDGAR
+IANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAADGLVYLRKNQMQL
+ASKMRFVSAQLLALFDGDLYLRSARHANAMAARLRAGIEAGVADGSLAGVEFTQATDANA
+VFAVLPEGVADRLRARFRFYDWDAARREVRWVCGFDTTEEDVDAFTAALRAELVPAA
+>PROKKA_02062
+MQRIHDPQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHFGEDA
+TVWPMFNGTGANVVGLQAMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDGKL
+TPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPEEVKAITDYAHEHGMRVYMDGAR
+IANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAADGLVYLRKNQMQL
+ASKMRFVSAQLLALFDGDLYLRSARHANAMAARLRAGIEAGVADGSLAGVEFTQATDANA
+VFAVLPEGVADRLRTRFRFYDWDAARREVRWVCGFDTTEEDVDAFTAALRAELVPAA
+>PROKKA_00354
+MQQIHDPASRGFASDNYSGVHPEVLAAIAEANGGHQTAYGEDAYTGRLAEVVRGHFGEDA
+QVWPMFNGTGANVVALQSMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLTVPTPDGKL
+TPELIDVQAWGWGDEHRAQPLVVAITQSTELGTLYTPEEIRAITEHAHARGMTVFLDGAR
+LANAAAALDLPLRAFTTDVGVDVLSLGGTKNGALGAEAVVALNPAATTGMTYLRKSQMQL
+ASKMRFVSAQLLALFDGDLYLRTARHANAMAQRLQDAVAAGIADGSLPGVALTQRAQVNA
+VFATLPAGVADRLRRSFRFYDWDEANGEVRWVCSFDTAEEDVDAFVAALRAELAPAD
+>PROKKA_01608
+MSAGAPAAGLRAFASDNYAGVHPDVWAALADVDAHHAPAYGADPHTERLQEAVREAFDAP
+DAVALPVFNGTGANVVALQSMLPPWGAVVAADTSHIHHDEGGAPERMGRTKLFTVPTPDG
+RLTPELVDREAHGWGFVHRAQPAVVEIAQVTELGTVYTPEQVRALADHAHGHGMGLYMDG
+ARLFNAAAALELPLSAFTTHAGVHVVSLGGTKAGALGAEAVVVLRPEAVTLASLVPERDL
+PADAGPRERARLAVEYVRKSSMQLASKMRYVSAQLTALLKGDLGIRLAGHANAMARELAG
+RVAGIDGVEVTRTPEANAVFAVLDPQAADRARVRHPFYDWDAARHEVRWMTSWDTTAADV
+DSFAAALGEALSPGRRR
+>PROKKA_01503
+MSAARPAGLRAFASDNYAGVHPDVWAAMADADADHAVSYGEDPTSAALQEKVREVFGERA
+FAVPVFTGTAANVLALQALTPPWGSVVTAASSHLIHDEGGAPERLGRTPLVPVPTPDGRL
+TGELAAAHVRRDGFVHASQPAVVEIAQATELGTVYSAAQVREVADAAHAAGAALYMDGAR
+LSNAAAALDLPLRAFTTDAGVDVVSYGGTKNGGLGAEAVIVLNPEAVVAARMVGPADVPG
+GDAADARDRARAALGYLRKQDMQLASKHRYLAAQLLALLTDDLGIALAAQANRMARVLAD
+AVAGLDDVELARAPEANAVFARLDPDVAAEVRLRHPFYDWDAAAHEVRWMTSWDTTDADV
+ESFVDALAAALRARRPR
+>PROKKA_00044
+MQRIHDPQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHFGKDA
+TAWPMFNGTGANVVGLQTMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDGKL
+TPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPDEVKAITDYAHEHGMRVYMDGAR
+IANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAADGLVYLRKNQMQL
+ASKMRFISAQLLALFDGDLYLRSARHANAMAARLRAGIEAGVADGSLAGVEFTQATDANA
+VFAVLPEGVADRLRARFRFYDWDAARREVRWVCGFDTTEEDVDAFTAALRAELVPAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000061.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000061.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c2117c1bd8ff1bac5f53899c993c599d01455f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000061.fa
@@ -0,0 +1,29 @@
+>PROKKA_00068
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+YLPGFDLVPGCVVEARPIGVFNMTDDGGGDAKLLCVPADKRYDHITELEHVEESLKQEIE
+HFFTRYKDLEPGKWVKAEGWEGRAAAEAELEASIQRFDAEGEESPTDEPQGRAVDTEEAQ
+PATEEGEATDEPQGR
+>PROKKA_02081
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+YLPGFDLVPGCVVEARPVGVFNMTDDGGGDAKLLCVPADKRYDHITELEHVEESLKQEIE
+HFFTRYKDLEPGKWVKAEGWEGRAAAEAELEASIQRFNAEGEESPTDEPQGRAVDTEEAQ
+PATEEGEATDEPQGR
+>PROKKA_00326
+MPHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDAMV
+LLPGFDLVPGCVVEARPVGVFNMTDDGGGDAKLLCVPADKRFDHITELEHIEESLKQEIE
+HFFTRYKDLEPGKWVKAEGWQGRADAEAELEASIARFDAAGEHSPTDEPQGRDVETEDPS
+PATEEGEEKDVPQGR
+>PROKKA_00266
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+FLPGFDLVPGCIVEARPVGVFNMTDDGGGDAKLLCVPADKRFDHIQELEDVEESLKQEIE
+HFFTRYKDLEPGKWVKADGWEGREAAEKELEASIERFAAEGEHSPSDEPQGRDVDTEEAA
+PAAEQEA
+>PROKKA_00684
+MLFDVTIEIPRGSGNKYEVDHTTGRIRLDRAVFTSMVFPQDYGSIDNTLGDDGDPLDALV
+LLPRPTFPGVVITVRPVGMLRMVDENGGDDKILTVPAGDDRFAQLRDITDVPEHTLAEIE
+HFFAHYKEIEHGKHVTTNGWADRAAAEAVIRTAQNAHTRHP
+>PROKKA_00062
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+YLPGFDLVPGCVVEARPIGVFNMTDDGGGDAKLLCVPADKRYDHITELEHVEESLKQEIE
+HFFTRYKDLEPGKWVKAEGWEGRAAAEAELEASIQRFDAQGEESPTDEPQGRDVDTEEAQ
+PATEEGEPQGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000062.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000062.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb77e7700ccc76edf532cce9116000622be7a4a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000062.fa
@@ -0,0 +1,40 @@
+>PROKKA_00076
+MDESIDAAAREANRALLGRLPADRTLVMGILNVTPDSFSDGGEHATVRAAVEHARRMVAD
+GADIVDVGGESTRPGARAVPPAEEQERILPVIEALLAEDVVLSVDTRHTATARAALALGP
+VIVNDVSGLAHEPDMPALIAASGAPYILMHNRGNPQTMDGLAVYEDTVPDVVCELRDVAG
+RFLAAGVEPAQLIVDPGLGFAKAGEQNWELLRGLEWLRAMGHPVLVAASRKRFLGTLLAD
+DDGTPAPPAARDAATAAISALAAAQGAWGVRVHDVRASADAVRTAAAWAGAHAPGEPVSE
+DVLP
+>PROKKA_02089
+MDESIDAAAREANRALLGRLPAGRTLVMGILNVTPDSFSDGGEHATVRAAVEHARRMVAD
+GADIVDVGGESTRPGARAVPPAEEQERILPVIEALLAEDVVLSVDTRHTATARAALALGP
+VIVNDVSGLAHEPDMPALIAASGAPYILMHNRGNPQTMDGLAVYEDTVPDVVCELRDVAG
+RFLAAGVEPAQLIVDPGLGFAKAGEQNWELLRGLEWLRAMGHPVLVAASRKRFLGTLLAD
+DDGTPAPPAARDAATAAISALAAAQGAWGVRVHDVRASADAVRAAAAWVGAHAPGEPVSE
+DVLP
+>PROKKA_00317
+MDESIDAAAREANRALLGRLPADRTLVMGILNVTPDSFSDGGEHATVRAAVEHARRMVAD
+GADIVDVGGESTRSGARAVPPAEEQARILPVIEALLAEDVVVSVDTRHTATARAALALGP
+VIVNDVSGLVHEPEMPALIAASGAPYILMHNRGNPQTMDGLAVYEDTVPDVVCELRDVAG
+RLLAAGVEPAQLIVDPGLGFAKAGEQNWELLRGLEWLRAMGHPVLVAASRKRFLGTLLAD
+DDGAPAPPAARDAATAAISALAAAQGAWGVRVHDVRASADAVRTAAAWVGAHAPGEPVSE
+DVLP
+>PROKKA_02338
+MLRSRVTVFGILNLTEDSFFDESRRLDPAGAVTAAIEMLRVGSDVVDVGPAASHPDARPV
+SPADEIRRIAPLLDALSDQMHRVSIDSFQPETQRYALKRGVGYLNDIQGFPDPALYPDIA
+EADCRLVVMHSAQRDGIATRTGHLRPEDALDEIVRFFEARVSALRRSGVAADRLILDPGM
+GFFLSPAPETSLHVLSNLQKLKSALGLPLLVSVSRKSFLGATVGLPVKDLGPASLAAELH
+AIGNGADYVRTHAPGDLRSAITFSETLAKFRSRDARDRGLDHA
+>PROKKA_00258
+MLPKPFHELPDRTLVMGILNVTPDSFSDGGAHDRVDAAVAHGLDLLAQGADLIDVGGEST
+RTGATPVDPAEEQRRILPVVEALLAEGAVLSIDTMHTATARACLALGPVIVNDVSGLVHE
+PDMPALVAESGAPCILMHNRGHAQVMDSLAHYEDTLGEVVRELSEVTDRFLAAGASPEQI
+ILDPGLGFAKAGEQNWELLRGLERIESLGRPVLVAASRKRFLGTVLAGEDGTPRPALDRD
+HATAAVSAISAAHGAWGVRVHDVRSSVDAVRVGDAWRGAAPRPAGPGEARA
+>PROKKA_00070
+MDESIDAAAREANRALLGRLPADRTLVMGILNVTPDSFSDGGEHATVRAAVEHARRMVAD
+GADIVDVGGESTRPGARAVPPAEEQERILPVIEALLAEDVVLSVDTRHTATARAALALGP
+VIVNDVSGLAHEPDMPALIAASGAPYILMHNRGNPQTMDGLAVYEDTVPDVVCELRDVAG
+RFLAAGVEPAQLIVDPGLGFAKAGEQNWELLRGLEWLRAMGHPVLVAASRKRFLGTLLAD
+DDGTPAPPAARDAATAAISALAAAQGAWGVRVHDVRASADAVRTAAAWAGAHAPGEPVSE
+DVLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000068.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000068.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f19b24d96ad06418ad1055044ef3609a72fe0674
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000068.fa
@@ -0,0 +1,17 @@
+>PROKKA_00216
+MENTIPDERARLGWSQQRLADELGVSRQTVISLEKGRYDPSLPLAFRLAAVFGRRIEDLF
+TPDGNAG
+>PROKKA_02209
+MENTIPDERARLGWSQQRLADELGVSRQTVISLEKGRYDPSLPLAFRLAAVFGRRIEDLF
+TPDGNAG
+>PROKKA_00167
+MENSLPAERARLGWSQQRLADELGVSRQTVISLEKGRHDPSLALAFRLAETFGTRIEDLF
+SPDPPA
+>PROKKA_02206
+MSIDRLAEAAAIHRRTIIQIEAGRTAPRVTTLYAIAEATGTPLRDLLAPLDEALERGTR
+>PROKKA_00321
+MARLARAFKVHKANSGMTYDQLAEATGLARQTLLNLAAGRTYGDLRTWLILAKVWGVTLD
+DLTAAAWRGHAGG
+>PROKKA_00216
+MENTIPDERARLGWSQQRLADELGVSRQTVISLEKGRYDPSLPLAFRLAAVFGRRIEDLF
+TPDGNAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000072.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000072.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5ee8ddedc2c9cd9cd216ba5beb05d6a5b24a9a59
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000072.fa
@@ -0,0 +1,66 @@
+>PROKKA_00250
+MTVQDPTAVAAPSPTEVFRVARDLLVECQTDDERARAEFEWPRFEHFNFGFDWFDRLAQD
+PARADVPALIIAEDDGRSTERTFAELSAASNRVANWLSAQGLRRGDRLILMLNNQVELWE
+FMLACIKLRVVMVPTTTQMTSGDLEDRVTRAGAAWAVAGAEDLAKFAGVGEGLHLVHVPG
+VFAEGPARRAPEVAGHTVLSYDDAADAATELAPAEPTPADETLLFYFTSGTTSKPKLVEH
+THTSYPVGHLTTLYWIGLEPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDP
+AALMANMARYGVTSFCAPPTVWRMLIKADLAQLTTPPTKTISAGEPLNAEVIDQVHKAWG
+TTIRDGFGMTETTLQVANTPGQKVVIGSMGRPLPGMDVTLIDPLTGQEAEEGEICLRLDP
+RPVGLLKSYYGNQEKTDEVFRDGVFHTGDIARRDENGVLTYVGRADDVFKSSDYKVSPFE
+LESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETARAILQFTLTQLPPYK
+RIRRIEFLELPKTISGKIRRVELRKAEVERAQTGAAPDGYGTEFREEDLDLHR
+>PROKKA_02262
+MTVQDPTAVAAPSPTEVFRAARDLLVECQTDYERARAEFEWPRFEHFNFGFDWFDRLAQD
+PARADVPALIIAEDDGRSTERTFAELSAASSRVANWLSAQGLRRGDRLILMLNNQVELWE
+FMLACIKLRVVMVPTTTQMTSGDLEDRVTRAGAAWAVAGAEDLAKFAGVGEDLHLVHVPG
+VFAEGPARRAPEVAGHTVLSYDDADDAATELTPAEPTPADETLLFYFTSGTTSKPKLVEH
+THTSYPVGHLTTLYWIGLEPGGVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDP
+AALMANMERYGVTSFCAPPTVWRMLIKADLAQLTTPPTKTISAGEPLNAEVIDQVHKAWG
+TTIRDGFGMTETTLQIANTPGQKVVIGSMGRPLPGMDVTLLDPLTGQEAEEGEICLRLDP
+RPVGLLKSYYGNQEKTDEVFRDGVFHTGDIARRDENGVLTYVGRADDVFKSSDYKVSPFE
+LESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETARAILQFTLTQLPPYK
+RIRRIEFLELPKTISGKIRRVELRKAEVERAQTGAAPDGYGTEFREEDLDLQR
+>PROKKA_00120
+MTVQDRTPADAASPTEVFRAARDLLVECQTDYERARAEFEWPRFEHFNFGFDWFDRLAQD
+PARQDVPALIIAEDDGRSTERTFAELSAASNRAANWLAEQGLRRGDRLILMLNNQVELWE
+FMLACIKLRVVMVPTTTQMTSADLEDRVSRADAAWAVAGAEDLAKFAGVGEGLRLVHVPG
+VFAEGEARRAPEVPGHTVLSYDDAAGASAELSPAEPTPADETLLFYFTSGTTSKPKLVEH
+THTSYPVGHLTTLYWIGLQPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDP
+AALMANMDRYGVTSFCAPPTVWRMLIKADLAQLKTPPTKTISAGEPLNAEVIDQVQKAWG
+ATIRDGFGMTETTLQVANTPGQKVVIGSMGRPLPGMDVVLIDPLTGQEAAEGEICLRLDP
+RPVGLLKSYFGNQEKTDEVFRDGVFHTGDIASRDENGVLTYVGRADDVFKSSDYKVSPFE
+LESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETAQSILQFTLTQLPPYK
+RIRRIEFLELPKTISGKIRRVELRKAEVERSETGTAPSGYGTEFREEDLDLTR
+>PROKKA_00088
+MTTTSVTERLRAARDLLVECQEDYDRARAEFEWPRFEHFNFGFDWFDQLAARPDRADVPA
+LIISDAGGGHLSRTYAELSAASNRAANWLRERGITPGDRVILMLDNQVELWELMLACIKL
+RVVMVPTTTQMTSADLADRVERAEARWVVASAENLAKFDGVDSGLHLVHIPGVAAQGDAR
+TAPVVAGHEVLSYDDAASASPELTPDSPTPADETLLLYFTSGTTSKPKLVEHTHTSYPVG
+HLTTVYWIGLQPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDAAALMADMD
+EFGVTSLCAPPTVWRMLIKADLSLLKTPPVKTISAGEPLNAEVIDQVHRAWGTTIRDGFG
+MTETTLQIANTPGQKLVIGSMGRPLPGMDVVLIDPLTGEEAAEGEICLRLDPRPVGLLKS
+YYGNEEKTAEVFRDGVFHSGDIASLDESGVLTYVGRADDVFKSSDYKISPFELESVLVEH
+PAVMEAAIVPSPDEVRLAVPKAFVTLAPSYEPTAETARQILQHTLTQLPPYKRIRRIEFR
+ELPKTISGKIRRVELRKAEAERAETGQAPEGYGIEHREEDLDLKR
+>PROKKA_02472
+MSVTARLRAARDLLVEHQQDYAGARAAFEWPRFETVNFGSDWFDAVAATPERADQDALVI
+VEEDGTVLRRSYARMSADTDRVAGWLQHLGVGRGDTVIVMLDNQVELWEAMLACMKIGAV
+VIPTTTQLVAADLQDRVDRAGARWAIANAGNLVKFADVVGDCTLIHVPGVYASEAEHALP
+EVPGHPVHSYGDAASFAGTWSLETPTSADDPLLLYFTSGTTSLPKLVEHTQASYTVGHLS
+TMYWVGLRPGDVHLNVASPGWGKHAWSSFFAPWLAEATIFVLNFRRFDAATLMRAMDEGG
+VTSFCAPPTVWRMLIKADLTQLQAPPRNAISAGEPLNAAVIDQVQRGWGVTVRDGFGQTE
+STLQIANTPGQRVVIGAMGRPLPGFDIELRDPQTGDRVDGEGEGEICVGLDPRPVGLFQR
+YHGDPEKTAEAFRDGVYHTGDIARRDEHGIYTYVGRADDLFKSSDYKLSPFELESVLMTH
+PAVLEAAVVPAPDELRLSVPKAFVTLAAGHEPGEEAARAILQHVTDRVPAYKRIRRIEFR
+PLPKTVSGKVRRVELRAEEEQRRAGVAGLGVEHREEDLGIRRQRRA
+>PROKKA_00250
+MTVQDPTAVAAPSPTEVFRAARDLLVECQTDDERARAEFEWPRFEHFNFGFDWFDRLAQD
+PARADVPALIIAEDDGRSTERTFAELSAASNRVANWLSAQGLRRGDRLILMLNNQVELWE
+FMLACIKLRVVMVPTTTQMTSGDLEDRVTRAGAAWAVAGAEDLAKFAGVGEDLHLVHVPG
+VFAEGPARRAPEVAGHTVLSYDDADDAATELTPAEPTPADETLLFYFTSGTTSKPKLVEH
+THTSYPVGHLTTLYWIGLEPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDP
+AALMANMERYGVTSFCAPPTVWRMLIKADLAQLTTPPTKTISAGEPLNAEVIDQVHKAWG
+TTIRDGFGMTETTLQIANTPGQKVVIGSMGRPLPGMDVTLLDPLTGQEAEEGEICLRLDP
+RPVGLLKSYYGNQEKTDEVFRDGVFHTGDIARRDENGVLTYVGRADDVFKSSDYKVSPFE
+LESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETARAILQFTLTQLPPYK
+RIRRIEFLELPKTISGKIRRVELRKAEVERAQTGAAPDGCGTEFREEDLDLQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000073.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000073.fa
new file mode 100644
index 0000000000000000000000000000000000000000..715ba80cc89674dcbb359cadde57e967f7b73f9e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000073.fa
@@ -0,0 +1,31 @@
+>PROKKA_00258
+MSEELRILIADDQPLMSGALRVLVDSAPGMTCVGVVANGVEAVEACAAIEPDVVLMDMQM
+PLMDGMEATRRIKDTHPAIRVLAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIQA
+VHRGESVLSPAVATKLLASIERDRPTVGPTSVQPGSPDGSDLTERELGVLRLLARGQSNP
+EIAANLFVSESTVKANLTRIMAKLEVRDRVQLIIRAAQLGLVTLALD
+>PROKKA_02272
+MSEELRILIADDQPLMSGALRVLVASAPGMTCVGVVANGVEAVEACAAVEPDVVLMDMQM
+PLMDGVEATRRIKEAHPEVRVLAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIQA
+VHRGESVLSPAVATKLLASIERDRPTVGPTSVQPGSPDGSDLTERELGVLRLLARGQSNP
+EIAANLFVSESTVKANLTRIMAKLEVRDRVQLIIRAAQLGLVTLALD
+>PROKKA_00111
+MHDAGHTDYSAAHIARTADGTAASGAVSAGPGGRRPGPTTPADAGRSRGSRYADRVSEDL
+RILIADDQPLMSGALRVLVSSAPGMTCVGVVANGAEAVEACAAVEPDVVLMDMQMPLMDG
+VEATSRIKEAHPGIRILAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIHAVHRGE
+SVLSPAVASKLLASIERDHPVVGPAQARPGDPDGSDLTDRERDVLRLLARGQSNPEIAAN
+LHVSESTIKSNLTRIMDKLEVRDRVQVIIRAAQLGLVTLSLD
+>PROKKA_00079
+MPDSPEDEIRVLIADDQPLMSGALRVLVDSAPGMRCVGLVADGVEAVEAVEATRVDVVLM
+DMQMPRMDGVEATRRITASRPGTRVLAVTTFSSEDYLVPALRAGAAGYLLKDAEPATVLG
+AVEAVRRGESVLSPAVAAKLIAAVERDHPVVGPAAAEPGDPDGSDLTEREHQVLTLLARG
+RSNPEIAAELQVSESTVKANVGRVIDKLEVRDRVQVVIRAAQLGLVTLSLD
+>PROKKA_00526
+MDAITVLIVEDEPLLTQAYTMILEADPGIRVVGTASDGAAGVAEHERLRPDVVLMDLRMP
+VLDGVEATGRIMREHPEAKVLVVTSMTTEDYLSPALANGAAGYLTKDTDAEGLVRAVRAV
+EAGTMALGPSIAREVVDLLLRSGVAPRTDAPASPRDLPEALTPREQDVLELLAEGLTNQE
+MAARLYVSDSTVKSNLARVMHKLGANNRVQALVLGVRAGLVSIPG
+>PROKKA_00257
+MSEELRILIADDQPLMSGALRVLVDSAPGMTCVGVVANGVEAVEACAAIEPDVVLMDMQM
+PLMDGVEATRRIKDTHPAIRVLAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIQA
+VHRGESVLSPAVATKLLASIERDRPTVGPTSVQPGSPDGSDLTERELGVLRLLARGQSNP
+EIAANLFVSESTVKANLTRIMAKLEVRDRVQLIIRAAQLGLVTLALD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000075.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000075.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9099a598da91e4eecc1b6f4b99fcdf2e6f10d03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000075.fa
@@ -0,0 +1,30 @@
+>PROKKA_00282
+MTGGDPAALMDALGAWFHPLTALLVALDAPIPPVPSEVVVIGSGALAAEGRVSPVAAVLA
+AWLGCWAGDVGLYALFRHGLADRLDRWAWWRRIHRGIRSLLVRVGPAGSLAGLSVLRFVS
+GGRTASMAAAGIGGIRWPVFLWLSGAGSLAWSSSMVGLGWITGRATGLPWWASAMVGMVF
+GTLAGLMIAGIMAHRRRGRKG
+>PROKKA_02297
+MTGGDPAALMDALGAWFHPLTALLVALDAPIPPVPSEVVVIGSGALAAEGRVSPVAAVLA
+AWLGCWAGDVGLYALFRHGLADRLDRWAWWRRIHRGIRTLLVRVGPAGSLAGLSVLRFVS
+GGRTASMAAAGIGGIRWPVFLWLSGAGSLAWSGSMVGLGWLTGRATGLPWWASAVVGMVF
+GTLAGLMIAGIMAHRRRGRKG
+>PROKKA_00071
+MTVLTPAWFAASGGVPTMGAGAAAASGAGAWDPSALLDSLGAWFHPLTALLVALDAPIPP
+VPSEVFVIGSGALAAEGRVGLAAAVLTAWLGCWAGDVGLYALFRHGLADRLDRWAWWRRV
+HRGIRVLLVRVGPAGSLAGLSVLRFVSGGRTASMAAAGIGGIRWPVFLWLSGAGSLAWSG
+WMVGLGWLTGRTTGLPWWASAVVGMVFGTLAGLIIAGVVARRRARKG
+>PROKKA_00057
+MTDVTALLEGLGPWFHPLTFLLVALDAPVPPTPSEVLVIGSGSLAAAGRLGLATSVLTAW
+LGCWAGDVGLYALFRHRLTSVLDRWGWGRAVHAGIRRLMEKAGPASSLAGLFVLRFVSGG
+RTASMAAAGVAGVRWRPFLWLSGTGSLAWSVYMVGLGWITGSATGLPWWASAVVGVVLGT
+LLGAAVAAVIAWRRRGKEGA
+>PROKKA_00450
+MPVLTNILDAASILHSLGPWTLGGIGSMVFIESGVLFPFLPGDSLLVTAAALHVELGIAL
+WAIILVAGLAAILGDQVGFYLGHRYGRRLFKDDARVLKTERLAQAEAFFERRGPLALVLG
+RFVPIVRTYVPVAAGTAGMPYRSFVGWNIGGAVAWVCSMVAVGALLGQIPGITKSIDGIM
+ILIIVISVAPIAIQALRARRKARRDAVMTEGQPVA
+>PROKKA_00281
+MTGGDPAALMDALGVWFHPLTALLVALDAPIPPVPSEVVVIGSGALAAEGRVSPVAAVLA
+AWLGCWAGDVGLYALFRHGLADRLDRWAWWRRIHRGIRSLLVRVGPAGSLAGLSVLRFVS
+GGRTASMAAAGIGGIRWPVFLWLSGAGSLAWSGSMVGLGWITGRATGLPWWASAVVGMVF
+GTLAGLMIAGIMAHRRRGRKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000078.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000078.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ed1809c671abce50bf6d3ed89fc204f6a014f96
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000078.fa
@@ -0,0 +1,43 @@
+>PROKKA_00310
+MDVPAQMRAVRFTGAGDNGVVRVGHEPVPDPGPGEVLVHVAAAGLNRADIAQREGRYPPP
+RGASEIPGLEVSGTVAALGPEAGMPGEGRFAVGDRVCALLAGGGFAEYVAVPAGQLMAVP
+DGVGLVEAAALPEVACTVHSTLVGRAGVQAGDRVLVHGATGGIGSFAVQFLTAVGARVLG
+TAGGPEKVALGRGLGAEHMFDHRAAESGAFAPWVKEVTDGHGADVILDVVGAPYLAPNVS
+ALAPEGRIVTLAVQGGAVPEDFNIMKLVVKRGWLTGATLRSRSVTDKAGIVAAAERAVWP
+LVAAGRIDASVGACFPLAEAAEAFDWFDSATRTGKVVLVTDPADARRPSGDRA
+>PROKKA_00025
+MDVPAQMRAVRFTGAGDNGVVRVGHEPVPDPGPGEVLVHVAAAGLNRADIAQREGRYPPP
+RGASEIPGLEVSGTVAALGPEAGMPGEGRFAVGDRVCALLAGGGFAEYVAVPTGQLMAVP
+DGVGLVEAAALPEVACTVHSALVGRAGVQAGDRVLVHGATGGIGSFAVQFLAALGARVLG
+TAGGPEKVALGRRLGTEHMFDHRAAESGAFAPWVKEVTDGHGADVILDVVGAPYLAPNVS
+ALAPEGRIVTLAVQGGAVPEDFNIMKLVVKRGWLTGATLRSRSVVDKAGIVAAAERAVWP
+LVAAGRIDASVGACFPLAEAAEAFDWFDSATRTGKVVLVTDPADARRPSGDRA
+>PROKKA_00027
+MSETTRTPGTGRGTMRAVRFTGEGGAGSLAVGQEPIPTPGPGEVLVKVAAAGLNRADVMQ
+REGKYPPPPGASDVPGLEVSGVVVALGEEAGLPGEGRFAPGDEVCALLAGGGYAEHVVVP
+AGQLMAVPPGVDLVTAAALPEVACTVWSTMSERGGVRAGDVVLVHGGSGGIGTFAVQYLA
+AIGARVLATAGGPAKCERVRGLGAEDVFDHRSGEPGAFADWVLERTGGRGADVVLDVVGG
+PYLDANVRCLAEEGRIVVIAVQGGPKADGFNLMRLVSKRGWLTGATLRARSVVDKARIVA
+GTERAVAPLVAAGRIDLAVGARFPLDDAAAAHRRFEAEDRVGRVLLVTDPADALWPQEDR
+T
+>PROKKA_00023
+MDTAPDMLAVRFAGAGGTDVIRVGREPVPEPGPGEVLVRVAAAGLNRADVVQREGHYPVP
+PGASEVPGLEVSGTVVALGPQAGVAGEGRFAVGDRVCALLAGGGYAEHVAVPAGQLMSVP
+DGLDLVSAAGLPEVACTVHSNLEGRAGVRPGEWALVHGATGGIGAFAVQYLSAVGVRVLA
+TAGGPAKVARALELGADAAFDHRAAAPGAFADWVREITGGHGADVVLDVVGGPYLAPNVK
+ALAMDGRIVVIAAQDGPVPEDFHLMRLAARRGWVTGSLLRPRPPDEKAGIVAAAERAVWP
+LVAAGRIDPGVTARFPLREAAAAHAHFEGAARMGKVLLVTDDADALLPGGAA
+>PROKKA_00654
+MHPSLPRTMLAAIIPAPGGRPELRQCPVPEPGPGEVLVRVMASSVNPTDVMTWRRGMFVT
+GQTVPFVGGYDMSGIVVKLGRGVTALDVGDAVTGMPRFPAPAAAFAQYSAVPARHLARIP
+TGTEDLSAGAWGRWAGLPLAGLTAYQALVDTAHLQSGQTVLVHAASGGVGSLACQLAVNL
+GAQVTAVTSDRGRTLVEVLGTRHVVDRATVDWQRFAGCFDVVLDTVGGDTTPRSLAMASP
+DGVVVALHPYAHDDLAQRDPRLRRMLVEPDHHALELLIEQAARGRLTVQVGAGYPLSDLG
+DALLHVETNKTPGKTIIHIQGDNA
+>PROKKA_00317
+MDVPAQMRAVRFTGAGDNGVVRVGHEPVPDPGPGEVLVHVAAAGLNRADIAQREGRYPPP
+RGASEIPGLEVSGTVAALGPEAGMPGEGRFAVGDRVCALLAGGGFAEYVAVPAGQLMAVP
+DGVGLVEAAALPEVACTVHSALVGRAGVQAGDRVLVHGATGGIGSFAVQFLAALGARVLG
+TAGGPEKVALGRRLGAEHMFDHRAAESGAFAPWVKEVTDGHGADVILDVVGAPYLAPNVS
+ALAPEGRIVTLAVQGGAVPEDFNIMKLVVKRGWLTGATLRSRSVVDKAGIVAAAERAVWP
+LVAAGRIDASVGACFPLAEAAEAFDWFDSATRTGKVVLVTDPADARRPSGDRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000079.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000079.fa
new file mode 100644
index 0000000000000000000000000000000000000000..783ca763dce2a86d54e245225eacd71e85ac27f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000079.fa
@@ -0,0 +1,36 @@
+>PROKKA_00318
+MANTTYTLVLLRHGQSEWNEKNLFTGWVDVPLTEKGRAEAARGGELLEAEGIRPDVVHTS
+LLKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMVWRRS
+FDTPPPALDDDSEFSQVGDERYADLGKDAPRTEALKQVVDRLLPYWEEQVLPDLKAGKTV
+LIAAHGNSLRALVKHLDGISDEDITGLNIPTGIPLVYELDQNFKPITANGRYLDPEAAAA
+GAAAVAAQGSAH
+>PROKKA_00033
+MANTTYTLVLLRHGQSEWNEKNLFTGWVDVPLTEKGRAEAARGGELLEAEGIRPDVVHTS
+LLKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMVWRRS
+FDTPPPALDDDSEFSQIGDERYADLGKDAPRTEALKQVIDRLLPYWEEQILPDLKAGKTV
+LIAAHGNSLRALVKHLDGISDEDIAGLNIPTGIPLVYELDQNFKPITANGRYLDPEAAAA
+GAAAVAAQGSAH
+>PROKKA_00019
+MANTTYTLVLLRHGQSDWNEKNLFTGWVDVPLTEKGRAEASRGGELMKAEGIHPDVLHTS
+LLKRAITTANLALETADRQWIPVKRDWRLNERHYGALQGKDKAQVKEEFGEEQFTVWRRS
+FDTPPPALDDSSEFSQIGDERYAELGDDAPRTEALKNVIDRLIPYWEAEIVPDLKASKTV
+LVAAHGNSLRALVKHLDGISDEDIAGLNIPTGIPLVYELDEDLKPITANGRYLDPEAAAA
+GAAAVAAQGSAH
+>PROKKA_00015
+MADTFKLILLRHGQSDWNEKNLFTGWVDVPLTEKGRAEASRGGELLAAEGLLPDVLHTSL
+LKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMTWRRSF
+DVPPPPLDDSSEFSQAGDERYRDIGPDAPRTEALKQVIDRLLPYWTEQIVPDLKAGKTVM
+VAAHGNSLRALVKHLDGISDEEISGLNIPTGIPLFYELDQNLKPVTPHGRYLDPEAAAAG
+AAAVAAQGDKK
+>PROKKA_00687
+MLTLLRHGESTANEAGTFTGLLDVPLTHRGERQASAAGQLLRSNHITPDVVVTSTLRRAV
+RTAELVCDALGTQLPTEAVWQLNERNYGALTGMTKTDARRMLGDDEYVRLRRSRTGTPPP
+MSLHLWEELRSSSALRGLPDGALRRTEALSDVIKRVRPVLHDRLLPMVRSGRSVLVVAHG
+NSLRALCACIDDLTDPELEQLNLPTGQPVQYHLAPTGALVPRGGAFLDPVAAQHAAALVA
+AEGGT
+>PROKKA_00325
+MANTTYTLVLLRHGQSEWNEKNLFTGWVDVPLTEKGRAEAARGGELLAAEGIRPDVVHTS
+LLKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMVWRRS
+FDTPPPALDDDSEFSQVGDERYADLGKDAPRTEALKQVIDRLLPYWEEQVLPDLKAGKTV
+LIAAHGNSLRALVKHLDGISDEDIAGLNIPTGIPLVYELDQNFKPITANGRYLDPEAAAA
+GAAAVAAQGSAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000084.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000084.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a18fdc9bf7cca965de4b7e6e032a3bc5086b89ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000084.fa
@@ -0,0 +1,54 @@
+>PROKKA_00418
+MPESTLYWIIAAIIVVLLILIILSVIASRRRREAEAEAAETRLERRGTTADTADTAGEQA
+AAPAAPTRLSRLDEVAAEQDARPAAAVKPAGGPAASETAAAGRETDESVAGVAGGAGVTV
+DQQDAPRTDATAETSRPTAAPTTRGTLRPAAAAPSTAREADTVGLGAAGVAGGSGITLDE
+QTPAADVAAAPASPSPVTETPAPAAPAAEAPQHRSHLTPAPEHVHGTVPAEEVAAEHTPT
+KEFATDAIPVAQGEHLETNTVATTAHGSVTVVAAESDQTQQNDADGAERSAAGSLRIDGT
+PGVPGRVAEAGREPARTEDHRADAAQPAAVEPAAERPSLEAAAERPSLEATPATRRAEAP
+ETHAGTTPATPLGGAPELDPTAASSGRAEDATPATRREARAAQSAAAAGTAATAGTAGTA
+APTSSTPTTVAPDTSTSSAPTNEEPAEDDTEGAALPDLRADRDETRGSDAEGESKLAQAG
+AVAASAFETVRDKVAIPLRDNVAVPAKDKAVKVVKDKLAQAQERRWGKR
+>PROKKA_00139
+MPQSTLYWIIAAIIVVLLILIIVSVIASRRRREAEAEAAETRLERRGVSADTAGEQAAAP
+AAPTRLSRLDEVAAEKDARPAPAVRPAGGLAAFDTAAADRETDESGAGVAGGAGVTVDQQ
+DAPSTEATAQTHRRDAAAPATRGTLRPAPAVPSTVREADTVGLGAAGVAGGSGVTLDEQT
+PAADVPATPASPSPVTETPAPAAPVAEAPQQRSHLTPAPEHVHGTVPADEVAAEHTPTKE
+FATDGIPVPQGEHLETHTVATTAHGSVTVVATESDQAQQTGVDGTERSAAGSLRIDGTPG
+VPGRVAEADREPARTDDHGADVAQPAAVEPAAERPPLEAAPATRRAEAPETHAGTTPATP
+LGGAPELDPTAASSGRAEDATPATRREARAAQSAAAAGTAGTAAPTSSTPTTVAPDTSTS
+SAPTDEEPAEDDTEGAALPDLRADRDETRASDAEGESKLAQAGAVAASAFETVRDKVAVP
+LRDNVAVPAKDKVVKVVKDKLSQAQERRWGKR
+>PROKKA_02541
+MPTDAEPAADDTEGAALPVQDATRADAVRPGTARTDASAGDSKLAQAGAAAGTVLETVRD
+KVAIPLRDNVAIPAKDKAVKVLKAKLAEAQERRRNKR
+>PROKKA_02542
+MGESTLYWIIGAIIVVLLILIILSVVASRRRRAAEAEAAEAQLERRRVTPTAAGVGASHE
+DALEETHDADARPHTVASTGGDVAPAAAAGAAAGTTRLSQLDDVAPVAAAAADADAESLP
+ADGVAAGSGVTVDQQDASDQSVRPAAPAAPAGADTRGPNASVKSAGAAAAAVGLGAAGVA
+GGRGVTVDQQDAAADVPSTPASPSPVAQTPAAPSSAGATTAQDDRADRTAQDAADAEPVK
+GTVPLSEDAHAVPPAADPPSGGDAVADDAHLEAHTVATTEHGSVVVVTAEQDEDDQATAA
+SRETETETDDSRGDDAGQDRDAERAVAEGVAGGTGVTVDQKAVAEAAATQGAPASAAGAA
+SAAGAAARRRDRGRRLDPACGGARLLQDRRHAGHARPRRLRGAGRGRGGDRPARPPRRRP
+GDARLHHPRDAPGRRAGAGPGRRRRGLPQGRGRDPAAPPRGRRPGAKPRRRPTSTRPRPR
+PPRRTAPAR
+>PROKKA_02410
+MPQSTLYWIIGIIIVVLVIILIVSSLRAKRGREEEAAAAGRHADSAPAPLAATAARGGTV
+GASTVPATGDAPADRTDGRAAGATALPSFDVDEVDRRAAEQREQDVVERRRATGAEAGAA
+GHAAVPGVTGGSGVSVDEAEGVAKDATGQDVTPVADAQRRNGSSAAPAATGAGLGLAAAG
+VAGGTGVTVDDAGTGADLPAPKGSPAGVVEVAETQAEAAQADAAPAEHTVVPGVAGGDAV
+TVDTADVQSSSAPQGAQAAAGRSDLTDAEARTYPVTGLPGVPSAVDPEQVAAARVQDAAE
+LKAAEGQGAEHERGASQPADPESVPGTVPLTGEEAVIEAPVHTHEMPEPVLGTPAYIQDS
+TTGQDPTEDLPEGQVYGTTPLSGEDAIVEPADQLPAEAAETEDRAASDAGTASAETAVVP
+VEETETAVVPVAETRSADAGPSEDSVALTGQGVETADRVEPAAPVAGTPARDEARTHDEH
+RSRLEIVKDAVAETAGTVATTAGTAAEKAAPVVRSAARTVGKAAGSAASTLKDKLAQAQE
+RRWGKR
+>PROKKA_00421
+MPESTLYWIIAAIIVVLLILIILSVIASRRRREAEAEAAETRLERRGTTADTADTAGEQA
+AAPAAPTRLSRLDEVAAEQDARPAAAVKPAGGPAASETAAAGRETDESVAGVAGGAGVTV
+DQQDAPRTDATAETSRPTAAPTTRGTLRPAAAAPSTAREADTVGLGAAGVAGGSGITLDE
+QTPAADVAAAPASPSPVTETPAPAAPAAEAPQHRSHLTPAPEHVHGTVPAEEVAAEHTPT
+KEFATDAIPVAQGEHLETNTVATTAHGSVTVVAAESDQTRQNDADGAERSAAGSLRIDGT
+PGVPGRVAEAGREPARTEDHRADAAQPAAVEPAAERPSLEAAAERPSLEATPATRRAEAP
+ETHAGTTPATPLGGAPELDPTAASSGRAEDATPATRREARAAQSAAAAGTAATAGTAGTA
+APTSSTPTTVAPDTSTSSAPTNEEPAEDDTEGAALPDLRADRDETRGSDAEGESKLAQAG
+AVAASAFETVRDKVAIPLRDNVAVPAKDKAVKVVKDKLAQAQERRWGKR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000085.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000085.fa
new file mode 100644
index 0000000000000000000000000000000000000000..345dd71602adb8d1c857349d2c7c3d58dfb6518e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000085.fa
@@ -0,0 +1,61 @@
+>PROKKA_00423
+MPSPTTTTAPGPASPAGPLRPPHTAAESAERVKRRGALYFAEHQLRNMRRYGAVLIVGAL
+GEPVLYLLAMGLGLAQLMGGGMPQDALGGVSYVAFIAPALLASGALMTASVEFSYPVMGG
+FQWHRTYYAAQATPLSPAQIALGHLAAVSLRFVFQAAVFLLVMLAFGVVSSPWAWVQVLT
+ATLGGLAVGAPIMAFAASLKEDKGQFATLQRLVVMPLFLFSATFYPLDVLPVWLRWIGWL
+SPQWHAAQLGRMLSYGMAEPAWLTVAHVAFLLALALGGARLAVRIYTRRLGWVRGTPDRD
+AGTAARRDRAPRLGRRAPRLGRRAARTGAARADVAPAAAQADPAAPSSSVVREHAVAVPP
+LPEIPVRRGPLAGAYSGNVRAVMERAFLSLKSNNWVVFFSGFFEPVLYLASLGLGLGALV
+GDVAGPDGTPVPYGMYLAPALLAVSAMNGAIYDSTWNVFFKLRYAKTYQTMLSTRLGPLD
+VALGEIAMALLRGLIYAVGFLIVMTVAGLVTSWTALLMIPGALLVALGFASLGMAVTSWM
+KTFQHMDWVQIVLMPMFLFSATFFPLAVYPEPIQWVIRVFPLWHAVEMMRALAVGVLSWA
+TAGHVLYFVVMAGVGVWLAARRLGALFLR
+>PROKKA_00144
+MPSPTTTTTPGPASPAEPLRPPVTAAASAERVKRRGVLLYAEHQLRSMRRYGAVLLVGAL
+GEPVLYLLAMGLGLAQLMGGGMPQDALGGVSYVAFIAPALLASGALMTASVEFSYPVMGG
+FQWQRTYYAAQVTPLSPAQIALGHLVAVSLRFVFQAAVFLLVMLAFGVVSSPWAWVQVLT
+ATLGGLAVGAPIMAFAASLREDKGQFATLQRLVVMPLFLFSATFYPLEALPVWLRWIGWL
+SPQWHAAQLGRVLSYGMAEPVWLTVVHVAFLLALALGGAWLAVRIYTRRLGWVRGTPDRD
+AVTVARRDRAPRLGCRAARTGAARADVAPAAAQADPAAPSSSVVREHAVAVPPLPEIPVR
+RGPLAGAYSGNVRAVMERAFLSLKSNNWVVFFSGFFEPVLYLASLGLGLGALVGDVAGPD
+GTPVPYGMYLAPALLAVSAMNGAIYDSTWNVFFKLRYAKTYQTMLSTRLGPLDVALGEIA
+MALLRGLIYAVGFLIVMTVAGLVTSWTALLMIPGALLVALGFASLGMAVTSWMKTFQHMD
+WVQIVLMPMFLFSATFFPLAVYPEPIQWVIRVFPLWHAVEMMRALAVGVLSWATAGHVLY
+FVVMAGIGVWLAARRLGALFLR
+>PROKKA_02534
+MTAAAGAEPAAPSSSVVLEHTAAVPPMPEITLRHGPLAGMYAGNVRAVMERAFLTLKSNN
+WVVFASGFFEPVLYLASMGIGLGALVGDVAGPDGTPIPYGMFIAPALLAVSAMNGAIYDS
+TWNVFFKLRHAKTYQTMLSTKLGPLDVALGEIVMALLRGLIYAVGFLIVMTVGGLVTSWT
+AVLMVPGALLVALGFASLGMAVTSYLKTFQHMDWIQIVLMPMFLFSATFFPLSVYPQAIQ
+WVIQVLPLWHAVELMRALAVGVVTWGTAGHILYFVAMSAVGIWFTSRRLGALFLR
+>PROKKA_02535
+MDASTTTTAPGPAAPRASASPAPLSPPISAAESAERVTRRGALYYAEHQLRNMRRYGSVL
+IVGALGEPIVYLLAMGLGLAQLMGGGAAQEGLGGVSYVAFLAPALLASGALMTAAVEFSY
+PVMGGFQWQKTYYAAQATPLTPAQIAVGHLGAVSLRFLFQGLVFFLVMLAFGVVHSPWGW
+LQILTATLGGLAIGAPIMAFAASLTEDKGQFATVQRLVIMPLFLFSATFYPLEALPVWLR
+WIGWISPQWHAAQLGRVLSYGMAEPVWLTVLHVVVLVAMAAVGTWLAVRIYTRRLGWRRG
+TPDRDALARP
+>PROKKA_02405
+MAAQIPASAPLQPPITAAESAVRVKARGAWFYAEHVLRSMRRYGAVLIVGALGEPILYLL
+AMGLGMAQVMGGGAPQESLGGVSYVTFLAPALLASGALMTAATEFSYPVMGGFQWHRTYY
+AAQATPLSPAQIAVGHLGAVALRFLFQAAVFFGVMLAFGVVHGPWGWVQVLTAALGGLAI
+GAPIMAFSASLKEDHGQFATLQRLVIMPLFLFSATFYPLEALPVWLRWVGWISPQWHAAQ
+LGRVLSYGMAEPRWLTVLHVAVLLALAFGGAWAAVRMYTRRLGWRPGTPDRDAVARPRAQ
+RASRLGRRATRVDRMAGAHAEAAAASSVVREHTAAVPPMPEITVRRGRLGGLYSGNVAAV
+MERALLTLKSNNWVVFASGFFEPVLYLASMGLGLGALVGAVPGPGGAPIPYGMYIAPALL
+AVSAMNGAIYDSTWNVFFKLRYAKTYQTMLATRLGPLDVALGEIAMALLRGLLYAVGFLV
+VMAVAGMATSWTALLMVPGALLVALGFASLGMAVTSWMKTFQQMDWIQLVLMPMFLFSAT
+FFPLTVYPEPIQWLIRVFPLWHAVEMMRALAVGAVTGATAGHALYFGVMSGLGVWLTSRR
+LRALFLR
+>PROKKA_00426
+MPSPTTTTTPGPASPGPRSGTSAPSATPAEPLRPPVTAAESAERVRRRGVLLYAEHQLRS
+MRRYGAVLLVGALGEPVLYLLAMGLGLAQLMGGGMPQDALGGVSYVAFIAPALLASGALM
+TASVEFSYPVMGGFQWQRTYYAAQATPLSPAQIALGHLVAVSLRFVFQATVFLLVMLAFG
+VVSSPWAWVQVLTATLGGLAVGAPIMAFAASLKEDKGQFATLQRLVVMPLFLFSATFYPL
+EALPVWLRWIGWLSPQWHAAQLGRVLSYGMAEPAWLTVVHVAFLLALALGGAWFAVRIYT
+RRLGWVRGTPDRDAVTAARRDRAPRLGRRAARTGAARADVAPAAAQAEPAAPSSSVVREH
+AVAVPPLPEIPVRRGPLAGAYSGNVRAVMERAFLSLKSNNWVVFFSGFFEPVLYLASLGL
+GLGALVGDVAGPDGTPVPYGMYLAPALLAVSAMNGAIYDSTWNVFFKLRYAKTYQTMLST
+RLGPLDVALGEIAMALLRGLIYAVGFLIVMTVAGLVTSWTALLMIPGALLVALGFASLGM
+AVTSWMKTFQHMDWVQIVLMPMFLFSATFFPLAVYPEPIQWVIRVFPLWHAVEMMRALAV
+GVLSWATAGHVLYFVVMAGVGVWLAARRLGALFLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000086.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000086.fa
new file mode 100644
index 0000000000000000000000000000000000000000..44919c05b8aa4e508021e54393d2f7154ba69b1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000086.fa
@@ -0,0 +1,54 @@
+>PROKKA_00448
+MALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAAVPSGASTGEFEAVERRDGDKKRYG
+GKGVLDAVAAVEGIAEELEGEFAADQRAVDRAMRDLDGTPNKGKLGANAILGVSMAVAVA
+AAQASDLMLYKYLGGPNAHVLPVPMMNILNGGAHADSNVDIQEFMIAPIGAPSFREALRW
+GTEVYHALKTVLQEKGLSTGLGDEGGFAPSLESNRAALDLIAEAVTKAGYRLGEDIALAL
+DVASSEFFDNGSYTFEGQQRSAEEMAAYYTELVDNYPIVSIEDPLDEDDWDGWQHLTAQL
+GDRVQLVGDDLFVTNVERLQRGIDEKAGNALLVKVNQIGSLTETFDAIALAQRHMFHCMI
+SHRSGETEDTFIADLAVATNAGQIKTGAPARSDRVAKYNQLLRIEEDLADAAVYAGRSAF
+PRFRG
+>PROKKA_00169
+MALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAAVPSGASTGEFEAVERRDGDKKRYG
+GKGVLDAVAAVEGIAEELEGEFAADQRAVDRAMRDLDGTPNKGKLGANAILGVSMAVAVA
+AAQASDLMLYKYLGGPNAHVLPVPMMNILNGGAHADSNVDIQEFMIAPIGAPSFREALRW
+GTEVYHALKTVLQEKGLSTGLGDEGGFAPSLESNRAALDLIAEAVTKAGYRLGEDIALAL
+DVASSEFFDNGSYTFEGQQRSAEEMAAYYTELVDNYPIVSIEDPLDEDDWDGWQHLTAQL
+GDRVQLVGDDLFVTNVERLQRGIDEKAGNALLVKVNQIGSLTETFDAISLAQRHMFHCMI
+SHRSGETEDTFIADLAVATNAGQIKTGAPARSDRVAKYNQLLRIEEDLADAAVYAGRSAF
+PRFRG
+>PROKKA_02509
+MALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAAVPSGASTGEFEAVERRDGDTKRYL
+GKGVLDAVAAVEEIADELEDEFAVDQRAVDRLMLDLDGTPNKGKLGANAILGVSMAVAAA
+AAQSSDLMLYKYLGGPNAHVLPVPMMNILNGGAHADSNVDIQEFMIAPIGAPSFREALRW
+GTEVYHSLKKVLQEKGLSTGLGDEGGFAPSLESNRAALDLIAEAVEKAGYTLGEDIALAL
+DVASSEFCEKGAYTFEGQKRSAEDMVAYYTELADNYPIVSIEDPLDENDWDGWRLLTEKL
+GDRVQLVGDDLFVTNVERLQRGIDDKAGNALLVKVNQIGSLTETFDAIALAQRHMFHCMI
+SHRSGETEDTFIADLAVATNAGQIKTGAPARSDRVAKYNQLLRIEEDLADAAVYAGRSAF
+PRYRG
+>PROKKA_00683
+MNDYISGIHHHGAHQGEYVTHHDHPVTIDAVHGARILDSRGYPTVRVSLELDDGRTVTGD
+APAGASTGAHEAVELRDGGSAFGGRDVTQALHLIDTDISGLLTGRSWSAIGQIDAALAEL
+DGTTGYRRLGANSVVATSIAASRALAHAADLPLWQWIAEITGSTPRMPVPHFNVLNGGAH
+AANELDFQEFMIAPVNAGSMADAVRIGADVYHALAALVRDRFGSLGLGDEGGFAPSIAAP
+EEALDLLVDAIRTAGYEPGVDQVAIALDPAANEFSQGDGSYRVLNDSLDRDGLVDYYRHL
+IDTYPIRSIEDAFAEDDHEGFRRMQAALGDRIQIVGDDLYVTDPQRIRDGGEQQLTNAAL
+IKPNQIGTVSQTLGAIATAKSIGMASMVSHRSGETTDTFIADLVVGTGTGQIKSGAPGRG
+ERVAKYNRLTEIAEQHPELPYGLI
+>PROKKA_02380
+MAQIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAAVPSGASTGEFEAVERRDGDTERYL
+GKGVQDAVNAVFEIAEELEDELATDQRAVDQMMLDMDGTENKGKLGANAILGVSMAVAVA
+AADSADLPLYKYLGGPNAHVLPVPMMNILNGGAHADSNVDIQEFMIAPIGAPSFREALRM
+GAEVYHSLKKVLQEKGLSTGLGDEGGFAPNLESNRAALDLIAEAVQKAGYTLGEDVALAL
+DVASSEFCENGSYTFEGRQRSAEEMSAYYAELVDAYPIVSIEDPLDENDWEGWEHLTEQL
+GDRVQLVGDDLFVTNVARLQRGIDEKAGNALLVKVNQIGSLTETFDAIALAQRHMFHCMI
+SHRSGETEDTFIADLAVATNAGQIKTGAPARSDRVAKYNQLLRIEEDLADAAVYAGRSAF
+PRFQG
+>PROKKA_00451
+MALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAAVPSGASTGEFEAVERRDGDKKRYG
+GKGVLDAVAAVEGIAEELEGEFAADQRAVDRAMRDLDGTPNKGKLGANAILGVSMAVAVA
+AAQASDLMLYKYLGGPNAHVLPVPMMNILNGGAHADSNVDIQEFMIAPIGAPSFREALRW
+GTEVYHALKTVLQEKGLSTGLGDEGGFAPSLESNRAALDLIAEAVTKAGYRLGEDIALAL
+DVASSEFFDNGSYTFEGQQRSAEEMAAYYTELVDNYPIVSIEDPLDEDDWDGWQHLTAQL
+GDRVQLVGDDLFVTNVERLQRGIDEKAGNALLVKVNQIGSLTETFDAIALAQRHMFHCMI
+SHRSGETEDTFIADLAVATNAGQIKTGAPARSDRVAKYNQLLRIEEDLDDAAVYAGRSAF
+PRFRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000088.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000088.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fe4e4fcb78b5405774bd919579477713da0d700c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000088.fa
@@ -0,0 +1,56 @@
+>PROKKA_00495
+MIGSPGDESTALRMGSTARGRVLGRPWERGLPLLVLIVDVVAVLLATFVSAQLRFGGPRR
+TTLPGAEVIDYSVISLALSAAWVLALTIQGSRDIRILGVGSEEYKRVLQGTLYLFGTVAI
+LAYAAGLEVARGYVGLALPLGVLLLLLGRFLVRGWVARQRHRGRFRRRLLLVGGPKAVRH
+IFQTLDSEAGAGYAPVAAALPGYKARREDYLPIPVSTDLDTVEDVVALVEVRDVEAVVIT
+SGHSFVPGDVRRLGWELQERGVSLIMAPALVDVAGPRLHTQPLAGLPLIHLSTPRLSEGK
+AFAKRAFDVVASGLGLIAISPLLIAVAIAVKATDGGPVLFRQERIGLGGRPFTMLKFRSM
+VVDAEEIRQRLVSDGGDADVLFKMKDDPRITRVGKLIRRTSIDELPQLVNVLRGEMSLVG
+PRPHLPHEVEAYGQYVHRRFLVQPGITGLWQVSGRSDLPWEEAVRLDLYYVENWSILGDL
+VILGRTVKAVVAADGAY
+>PROKKA_00216
+MIGSPGDESTALRMGSTARGRVLGRPWERGLPLLVLIVDVVAVLLATFVSAQLRFGGPRR
+TTLPGAEVIDYSVISLALSAAWVLALSIQGSRDIRILGVGTEEYKRVLQGTLYLFGTVAI
+LAYAAGLEVARGYVGLALPLGVLLLLLGRFLVRGWVARQRHRGRFRRRLLLVGGPKAVRH
+IFQALDSEAGAGYAPVAAALPGYKARREDYLPIPVSTDLDTVEDVVAHVEERDVEAVVIT
+SGHPFVPSDVRRLGWELQERGVSLIMAPALVDVAGPRLHTQPLAGLPLIHLSTPRLSEGK
+AFAKRAFDVVASGLGLIAISPLLIAVAIAVKATDGGPVLFRQERIGLGGRPFTMLKFRSM
+VVDAEEIRQRLVSDGGDADVLFKMKDDPRITRVGKLIRRTSIDELPQLVNVLRGDMSLVG
+PRPHLPHEVEAYEQYVHRRFLVQPGITGLWQVSGRSDLPWEEAVRLDLYYVENWSILGDL
+VILGRTVKAVIAADGAY
+>PROKKA_01221
+MLTPDSPYEERFAALNQSLRWEVADELRRANLARVDELHPPVTPRDTFYTRHGKRALDVG
+VSGAALLFSSPVIGALCLVTLKDLGQPVLFTQQRPGKHGKPFQMVKLRTMREAYDDQGKP
+LLGELRVTKTGRLIRRASLDELLNFWNIFKGDMSLIGPRPLVPEYVERFSRRHRQRLAVK
+PGLECPPPRPPQGPVTYDDQFENDCWYVENVSLKTDAWLTWRVLQTALDRRQNKARGSST
+RGSFMGYDADGTVITTAALPDWALNTVLERHGLLTSNSADARQEG
+>PROKKA_02452
+MFSSPGDESPALRTGSTARGRLLGRPWERGLPLLVFIVDVVAVLLATFVSAQLRFGGPRR
+TTLPGTEVIDYSVISLALSAAWVLALSIQGSRDIRILGVGSEEYKRVLQGTLYLFGTVAI
+LAYAAGLEVARGYVGLALPLGVLLLLLGRFLVRGWVARQRHLGRFRRRLLLVGGPKAVRH
+IFQALDSEAGAGYAPVAAALPGYKTRQEDYLPIPVSTDLDTVEDVVALVEVRDVEAVVIT
+SGHSFVPGDVRRLGWELQERGVSLIMVPALVDVAGPRLHTQPLAGLPLIHLSTPRLSEGK
+AFAKRAFDVVASGLGLIAISPLLIAVAIAVKATDGGPVLFRQERIGLGGRPFTMLKFRSM
+VVNAEEIKQRLVSDGGDADVLFKMKDDPRITKVGKFIRRTSIDELPQLVNVLRGDMSLVG
+PRPHLPHEVEAYEQYVHRRFLVQPGITGLWQVSGRSDLPWEEAVRLDLYYVENWSILGDL
+VILGRTVKAVVAADGAY
+>PROKKA_02336
+MTSSAVTTSQTGRGGSSVHARVLGAPWERGLPRLVLLADVVAVVLAAFLSSELRFGTARN
+AAVPGAESVNYLLVGAVLSASWVVALGVDGSRDIRILGIGAEEYKRVLRGTLYLFGMIAI
+LAYAFAFEVARGYVALALPIGLLLLMLGRFLIRGWVARGRHRGAMRRRLLLVGGPQAVKY
+VHDTLDSEAGAGYKPIAAVLPGYRARDEGWLPIPVTTEVDGVDELVAQVREMDIEAVVIT
+SGHPFVPDDVRRLGWDLQERGISLIMAPALVDVAGPRLHTQPLAGLPLLHLSTPRLSRGK
+AFVKRSFDVVASGLGMLVISPLLLTVAIAVKATDGGPVLFRQERVGLRGEHFTMLKFRSM
+VVDAEEIKQQLMSDRGEEDVLFKMKDDPRITRVGRFIRRTSIDELPQLVNVLRGDMSLVG
+PRPHLPHEVEQYGQYVHRRFLVQPGITGLWQVSGRSDLSWEDAVRLDLYYVENWSVLGDL
+VILGRTVKAVLAADGAY
+>PROKKA_00494
+MFASPGDESTTLRMGSTARGRVLGRPWERGLPRLVLVVDVVAVLLATFVSAQLRFGGPRR
+TTLPGAALVDYSVISLALSAAWVLALTIQGSRDIRILGVGTEEYKRVLQATLYLFGTVAI
+LAYAAGLEVARGYVGLALPLGVLLLLLGRFLVRGWVARQRHRGRFRRRLLLVGGPKAVRH
+IFEALDSEAGAGYAPVAAALPGYKARQEDYLPIPVSTDLDTVEDVVALVEVRDVEAVVIT
+SGHSFVPGDVRRLGWELQERGVSLIMAPALVDVAGPRLHTQPLAGLPLIHLSTPRLSEGK
+AFAKRAFDVVASGLGLIAISPLLIAVAIAVKATDGGPVLFRQERIGLGGRPFTMLKFRSM
+VVDAEEIRQRLVSDGGDADVLFKMKDDPRITRVGKLIRRTSIDELPQLVNVLRGDMSLVG
+PRPHLPHEVEAYEQYVHRRFLVQPGITGLWQVSGRSDLPWEEAVRLDLYYVENWSILGDL
+VILGRTVKAVIAADGAY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000090.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000090.fa
new file mode 100644
index 0000000000000000000000000000000000000000..208ffd0d40592b93fad154f1567ca06db1e957fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000090.fa
@@ -0,0 +1,42 @@
+>PROKKA_00521
+MTPRGSCWSSLPVGARFRLWNTLDPMHLLVTGGAGFIGSNFVHHVVRETGHDVVVLDKLT
+YAGNRENLAGLPEDRVTLEVGDICDAALVDRLVAESDAVVHYAAESHNDNSLNDPSPFIQ
+TNIVGTFVLLEAARKHGKRFHHVSTDEVYGDLELDDPAKFTETTPYNPSSPYSASKAGSD
+HLVRAWVRSFGVQATLSNCSNNYGPYQHIEKFIPRQITNLIDGVRPRLYGQGVNVRDWIH
+TEDHSSAVLRILERGEIGRTYLIGADGEKNNREVVEILLELFDRPADDYDLVADRPGHDL
+RYAIDNTALRTELGWEPRFTDIRAGLADTVRWYRENEAWWRPAKAAVEATYRAQGQ
+>PROKKA_00243
+MHLLVTGGAGFIGSNFVHHVVRETGHDVVALDKLTYAGNRENLAGLPEDRVTLEVGDICD
+AALVDRLVAESDAVVHYAAESHNDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVST
+DEVYGDLELDDPAKFTETTPYNPSSPYSASKAGSDHLVRAWVRSFGVRATLSNCSNNYGP
+YQHIEKFIPRQITNLIDGVRPRLYGQGVNVRDWIHTEDHSSAVLRILERGEIGRTYLIGS
+DGERNNREIVEILLELFDRPADDYDLVADRPGHDLRYAIDNTALRTELGWEPRFTDIRAG
+LADTVRWYRENEAWWRPAKAAVEATYRAQGQ
+>PROKKA_01219
+MRFVVTGAGGFLGSNVVRELLAETDHDVVAVSSQTDRELAAQLERAPYPALRRFPQVHPR
+TRLLEAGFLRDGDIVINCAFPWNRGGRAMADGLEYLTRLFQSAHAVALHTFVNVSSQSVY
+SQARTEAADESSPVECDTPYSTGKYAMELAAELVLPPKVLVNARMSSLIGPGYDVRIVNR
+FIARFLADEPVSIQGGDQVFDFMDVRDAARALIAVALAGPPEGSAALNIGSGAPRTLRDI
+AQTVADVVRTHTGHDPRIAWEPSAGDDRTLGLDSGLLRREYGFAPRHTLEDSALSILQAM
+TSAQSASVGETPTGSVEGGRR
+>PROKKA_02428
+MHLLVTGGAGFIGSNFVHHVVRETGHDVVVLDKLTYAGNRENLAGLPEDRVTLEVGDICD
+AALVDRLVAQSDAVVHYAAESHNDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVST
+DEVYGDLELDDPAKFTETTPYNPSSPYSASKAGSDHLVRAWVRSFGVQATLSNCSNNYGP
+YQHIEKFIPRQITNLIDGVRPRLYGQGVNVRDWIHTEDHSSAVLRILERGEIGRTYLIGS
+DGERNNREIVEILLELFDRPADDYDLVADRPGHDLRYAIDNTALRTELGWEPQFTDIRAG
+LADTVRWYRENEAWWRPAKAAVEAKYRAAGQ
+>PROKKA_02311
+MHLLVTGGAGFIGSNFVHHVVRETGHDVVVLDKLTYAGNRENLAGLPEDRVTLEVGDICD
+AALVDRLVAESDAVVHYAAESHNDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVST
+DEVYGDLELDDPAKFTETTPYNPSSPYSASKAGSDHLVRAWVRSFGVQATLSNCSNNYGP
+YQHIEKFIPRQITNLIDGVRPRLYGQGINVRDWIHTEDHSSAVLRILERGEIGRTYLIGS
+DGERNNKEIVEILLELFDRPADDYDLVADRPGHDLRYAIDNTALRTELGWEPQFTDIRAG
+LADTVRWYRENEAWWRPAKDAVEATYRAQGQ
+>PROKKA_00521
+MRILVTGGAGFIGSNFVHHLVRETDHDVVVLDKLTYAGNRDNLVGLPESRVRLEIGDICD
+AALVDRLVAESDAVVHYAAESHNDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVST
+DEVYGDLELDDPAKFTETTPYNPSSPYSASKAGSDHLVRAWVRSFGVQATLSNCSNNYGP
+YQHIEKFIPRQITNLIDGVRPRLYGHGVNVRDWIHTEDHSSAVLRILERGEIGRTYLIGS
+DGERNNREIVEILLELFDRPADDYDLVADRPGHDLRYAIDNTALRTELGWEPRFTDIRAG
+LADTVRWYRENEAWWRPAKAAVEATYRAQGQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000096.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000096.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1ef07e0d87e905dd263dfda8859684e9155917c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000096.fa
@@ -0,0 +1,41 @@
+>PROKKA_00614
+MGSHHHAPTGHRGRLAIAFGITTAVLLAEVVGAVLTGSLALLVDAAHMLTDAGGLLMALL
+AATLMARPPTTRRTWGFLRAEVLAALAQAAVLLAVGTYAFIEGLQRLFAPPEVASGPLLA
+FGILGLVGNLASLAVLGSGRGANLNMRAAFLEVLNDALGSVAVIASALVIAATGWTRADA
+VAGMLIAVLIVPRTLKILGETTRILLESTPRGLDLAEVRTHLQALPHVVSVHDLHASQIA
+TGVPVLSAHIVVEDSCFHDGHAPQILDQLQHCVAEHFDVGVDHSTFQLEPAAHAHHEHPT
+HH
+>PROKKA_00326
+MVFSITATIMVAEVIGALASGSLALLADAGHMFTDSAGLLIALTATTLALRPATDKRTWG
+YKRAEIIAAAAQAAVLLAVGGFVAVEGVRRLIEPPEVESTAMLWFGVIGLAGNLIGLAIL
+ASSRGENLNMKAAFLEVLNDALGSVAVIVSAIVIATTGWNRADAVVSLLIAALIVPRALI
+LLRDTIDVLMETTPKGLDLEAVRIRLSELPHVLEVHDLHASRIDSDTPVLSAHVTVHNGC
+LTAAHLGTVLTDLQRCVAQDFQVPIEHSTFQIEPATHPHTETLHP
+>PROKKA_01774
+MGAHHHASPAHRWRLAVAFAITTAVLLAEVAGALITGSLALLVDAAHMLTDAGGLLMALL
+ASTLMARPPTARRTWGFLRAEVLAALAQAAILLAVGLYAFIEGLQRLFAPPEVASGPLLL
+FGILGLAGNLASLAVLGSGRGANLNMRAAFLEVLNDALGSVAVIASALVIATTGWAQADA
+VAGMLIAVLIVPRTLKILAEAAHILLESTPRDLDLAEVRDHLEAVPHVVSVHDLHASQIA
+TGVPVLSAHVVVEDHCFHDGHAPQILDQLQHCVAEHFDVAIDHSTFQLEPAAHAHHEHPT
+HH
+>PROKKA_00544
+MSTPHEHHHDHAHGPSPEEAAADPALRRRLWIALALAGTVVLAQAVGAALTGSLALLTDT
+AHAVTDASGLAVALVAAILMARPATPRRTWGLRRLEVVAALGQAALLLLVGAYSAVEAVR
+RLVEPPAVDGTGMLLFGVLGLAANLAAAAVLASSRGANLSMRAAFLEVVNDALGSLGVIA
+AAAVVAVTGWTRADAVAGLLIVVLIVPRAVSLLRQTLRVLLEFTPEGLDLDEVRTHLLEV
+EHVLEVHDLHASTVATGLPVLTAHVVVEDGCFTDGHAAQILEQLRECTREHFPLAVPHST
+FQLETAAIAADDAHHTAHP
+>PROKKA_00702
+MGAGHNHGPAASETGHPGDFRKKLWIAFSITATIVVAQAMGSVITGSLALLTDTAHAITD
+ASGLLVALIAATLMLKPANSKRTWGFRRIEVIAALGQSALLLAVGTYAAIEGIRRLFEPP
+EVPASELLIFGIIGLVANIIAITILASSRGSNFNMRAAFLEVLNDALGSLGVIIAAIVIA
+TTGFMQADAIAGLLIAALIVPRAFKLMRETTGVLMEFTPKGLDLDKVRSHILELDHVKDV
+HDLHASTVATGLPILTAHVVVEDECFTDGRAAQTLHEIKDCVAGHFEVSIHHSTFQIETE
+HIAEHEPEISKHD
+>PROKKA_02007
+MSGHDHSHALPAAGRRGRLAVVFSITATIMVAEVIGALASGSLALLADAGHMFTDSAGLL
+IALTAATLALRPATDKRTWGYKRAEIIAAAAQAAVLLAVGGFVAVEGVRRLIEPPEVEST
+AMLWFGVIGLAGNLIGLAILASSRGENLNMKAAFLEVLNDALGSVAVIVSAIVIATTGWN
+RADAVVSLLIAALIVPRALILLRDTIDVLMETTPKGLDLEAVRIRLSELPHVLEVHDLHA
+SRIDSDTPVLSAHVTVHNGCLTAAHLGTVLTDLQRCVAQDFQVPIEHSTFQIEPATHPHT
+ETLHP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000105.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000105.fa
new file mode 100644
index 0000000000000000000000000000000000000000..48c3be91a50191d7aec6881afd8e47a7b28aa981
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000105.fa
@@ -0,0 +1,22 @@
+>PROKKA_00747
+MLSGFCLALGTWSTVAAEAADAALARRWGAAARLWTAHLGLGLVAVVVGWGAGLGLHAVL
+AG
+>PROKKA_00748
+MSGAGYEVFALFQVALLACLAAGGVLGALARRRLTDRLGPRGLLTANTTAALLLGVTVGL
+AVPELVYASGG
+>PROKKA_00478
+MSGAGYEVFALFQVALLACLAAGGALGALARGRLTDRLGPRGLLTANTTAALVLGATVGL
+AVPELVYASESWGDGQGLMLVAAVSAVVSGFCLALGTWSTVAAEAADAALARRWGAAARL
+WTAHLGLGLVAVVVGWGAGLGLHAVLAG
+>PROKKA_02182
+MSPALMGASPWEWVLGLAVLAAGGALGALLRLTLQEHLPRRGVLAANTLAAGVLGFSLAL
+ALPSLVYASGLAGDPLGVAGLLVASLTAGFCLALGTWSTVAGQAADAVLAGRWGAAGRIW
+AAHLGLGLLAAAAGWGLGLGARLLVA
+>PROKKA_02077
+MSAGTVLLTVLLAGLAAAVGAGLRHLADHRWGGRGVLLANVTASALAGALFAIGFGPGSA
+DPEGPAGAALALGAAGAFVLALGTWSTVAFQAAQEVLAGRTRRAVRVWLVHLASGTAAAV
+VGVLAVGFLVR
+>PROKKA_00712
+MSGAGYEVFALLQVALLACLAAGGALGALVRRRLTDRLGPRGLLTANTTAALLLGVTVGL
+AVPELVYASGGGGDGQGLVLVAAVSAVVSGFCLALGTWSTVAAEAADAVLARRWGTAARL
+WAAHLGLGLVAVVVGWGAGLGLHAVLAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000106.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000106.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b4e550aaed8ad697208e2fe49f8d7b50e3d574f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000106.fa
@@ -0,0 +1,35 @@
+>PROKKA_00762
+MNASFPAGAAAATPPLAVARALELRHGSHVAVRPSDFTLPARRLIAVIGPNGSGKSTLLT
+ALAGLSDPASGALEVLGEDPRRRSQRTSFVMQSIGVPQGVPVTVRDVVGMGRYPTLGWFR
+RFRREDRDIVRAAMERMQVADLARRHLDQLSGGQRQRAYVAQGLAQDHDVLLLDEPMTGL
+DIVSARTIDDLLHEEPTRGVSVVYTTHDLDEAAEADHVVLMGGRVVASGSPRDVLTVENL
+DIAYGRGALHGPSTAVEDAADFLDDPAGGRRH
+>PROKKA_00492
+MNASFPAGAAATPPPLAVARALELRHGSHVAVRPSDFTLPARRLIAVIGPNGSGKSTLLT
+ALAGLSDPASGALEVLGEDPRRRSQRTSFVMQSIGVPQGVPVTVRDVVGMGRYPTLGWFR
+RFRREDRDIVRAAMERMQVADLARRHLDQLSGGQRQRAYVAQGLAQDHDVLLLDEPMTGL
+DIVSARTIDDLLHEEPTRGVSVVYTTHDLDEAAEADHVVLMGGRVVASGPPRDVLTVENL
+DIAYGRGALHGPSTAVEDAADFLDDPAGGRRH
+>PROKKA_02168
+MSRSAAVVPEAAPAPLAVAEHLELRHGDHLAVEASSFTLPAGCVVAVIGPNGSGKSTLLQ
+ALAGVLDPAAGRLEVRGESPSRHGRLTSFVMQSLQFPQGVPLTVRDVVTMGRYTTAGWFR
+RLGATDRAAVAAAMERVRVTDLADRHLDQLSGGQRQRVYVAQGLAQEHDVLMLDEPVTGL
+DIVSARTIDEIIHEQPERGVSVVYTTHDLDEAAAADHVVLMDGRVVASGPPAQVLTAANL
+DAVYGRGALHAPLLVHLDDPADCSPDRG
+>PROKKA_00528
+MNPAAPAPAIRLADVSAAYDRRRPVFTGADLVIDGPGLVRVHGRNGGGKSTLIELVSGYL
+RPSDGQVRIGGLPAHDPRAHERRRVCRTEPALYPLMDVHDHVVFASRWAGADPAEGLARA
+ERYGLGPWMHAPAQTLSTGNRRRLWIVQCTVGAFDTVVLDEPFNGLDDESSAVLAAELAA
+WARTRCVVLICHLPPPGLAFDRVVRWPPGQAAADPAPPADPGVRP
+>PROKKA_02063
+MTRTVPTAPTPGAGVLAEARGLELRRAAHVAVAPSDLTLPAGVLVAVIGPNGSGKSTLLH
+ALAGTLEPAAGSLTVRGESPSRHARRTAFVMQTIPVPQGVPLTVRDVVRMGRYPRVGWFG
+RFGAADREAVDAAMERMSVTDLARRHLDELSGGQRQRVYVAQALAQEHDVLMLDEPLTGL
+DLVSARTIDRLLHEEPARGVSVVHTTHDLDEAAAADFVVLMSGRVVAAGTPRQVLTEANL
+EAAYGHGVLHGPRLPFLDDPVDGVR
+>PROKKA_00726
+MNASFPAGAAAAPPPLAVARALELRHGSHVAVRPSDFTLPARRLIAVIGPNGSGKSTLLT
+ALAGLSDPASGALEVLGEDPRRRSQRTSFVMQSIGVPQGVPVTVRDVVGMGRYPTLGWFR
+RFRREDRDIVGAAMERMQVADLARRHLDQLSGGQRQRAYVAQGLAQDHDVLLLDEPMTGL
+DIVSARTIDDLLHEEPTRGVSVVYTTHDLDEAAEADHVVLMSGRVVASGPPRDVLTVENL
+DIAYGRGALHGPSTAVEDAAEFLDDPAGGIRH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000108.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000108.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7455b441001b1611c855367c6f0458dfbb0e73a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000108.fa
@@ -0,0 +1,54 @@
+>PROKKA_00838
+MSLEFRTSEESPDVTRVVATHLPTRHGDFALLGYRDGRGTDHVALTLGDVAADDGELPLV
+RLHSECLTGDALGSYRCDCGEQLDAALQAIGAAGRGVLIYIRGHEGRGIGLLDKLRAYAL
+QDSGIDTVDANTHLGLPADARDYDQSAQILRELGVGKIRLLSSNPAKQEALEALGIHVEA
+RVRLNVADRPENSRYLSTKRARMRHDLPPERNAWDLLAGARVPTGPLTPQEEALVLRYGP
+LVEAGPRLVIGQLGQSLDGFIASRTGDACFVTGEADREHLHRLRALVDAVLVGAQTVAAD
+DCQLTVRAVNGADPARVVVDPHARIPLTAKVLTDPRSRTLWLVGSDASVPASLAPHVSVH
+RLETSTGFEPAAILQYLADQGLGRVLIEGGGLTVSGFLHAGVLDRLYLTSAPLLVGDGVP
+GIRFDGADALSGALSAPVRRFVLGDDVCTEFDFSAAKPASPAALHRADQENQPTGQD
+>PROKKA_01065
+MSEHIRLDPVPVAIAAIAAGRPVVVVDDADRENEGDLIYAAALATDEVTAFTVRHTSGVI
+CAPLPAGLADRLALPPMTTVNEDPKGTAYTVSVDAAAGVTTGISAADRTRTLRLLADPGA
+APGDLTRPGHVFPLRAVPGGVRARRGHTEAGVELCRLAGVAPVAAIAELVHDDGTMMRLP
+ALREFSDEHGLVLISIEDLVAHLEETTPALTAVPAEATLPTRHGLFRVSVHVDAETGAEH
+LLLVAGETDSERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALARAAAEGGAVLYLRGHE
+GRGIGLANKIRAYRLQEEGMDTVEANLALGLPAEARDWAGAAAVLTAAGHRRIRLVTNNP
+AKVAGLRAAGIDVVERVPAPTPVTEHNVVYLRTKRDRMAHALADRVLEPPTATGGPATPA
+DDPTTDPTHPTHQEDTP
+>PROKKA_00784
+MSEHIRLDPVPAAIAAIAAGRPVVVVDDADRENEGDLIYAAALATDEVTAFTVRHTSGVI
+CAPLPAGLADRLALPPMTTVNEDPKGTAYTVSVDAAAGVTTGISAADRTRTLRVLADPGA
+APGDLTRPGHVFPLRAVPGGVRARRGHTEAGVELCRLAGVAPVAAIAELVHDDGTMMRLP
+ALREFSDEHGLVLISIEDLVAHLEETTPTLTAVPAEATLPTRHGLFRVSVHVDAETGAEH
+LLLVAGETDPERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALARAAAEGGAVLYLRGHE
+GRGIGLANKIRAYRLQEEGMDTVEANLALGLPAEARDWAGAAAVLTAAGHRRIRLVTNNP
+AKVAGLRAAGIDVVERVPAPTPVTEHNVVYLRTKRDRMAHALADRVLEPPTATGGPATPA
+DDPTTDPTHPTHQEDTP
+>PROKKA_01822
+MSDSIPLDAVPAAIAAFAAGRPVVVVDDADRENEGDLVYAAALATDAVTAFTVRHTSGVI
+CAPMPADLADRLALPPMTARNEDPKGTAYTVSVDAATEVSTGISAADRTRTLRILADPAA
+GPADLTRPGHVFPLRAVPGGVRARRGHTEAGVELCRLADVAPVAAIAELVHDDGTMMRLP
+ALREFADEHGLVLISIEDLVRHLEEEGPTPVPVPAEATLPTRHGVFRVSVHADAVTGAEH
+VLLVAKKAGEAGEADPERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALSRAGSEGGAVL
+YLRGHEGRGIGLANKVRAYRLQEQGLDTVEANIALGLPTEARDWAGAAAVLAAAGHTRVR
+LVTNNPAKVAGLQAAGIDVVERVPAPTPVTEHNLGYLRTKRDRMAHALADRVLEHPVAPG
+HEDPRHETPTHQEDTP
+>PROKKA_01711
+MSIDTAVEPAAPVDIRLDPVADAVAAIAQGRPVVVVDDADRENEGDLIYAAALATDAVTA
+FTVRHTSGVICAPLPAELADRLNLPPMTARNEDPKGTAYTVSVDAVAGVTTGISAADRTV
+TLRVLAGEESTAADLTRPGHVFPLRAVPGGVRARRGHTEAGVELCELADLPPVAAIAELV
+HDDGTMMRLPALREFADEHSLVLISIEDLVAHLHEHRPEQRVVPAEAALPTAHGDFRISV
+HPDTATGAEHVLLVADRPGSATGGDADAPVTVRVHSECLTGDVFGSLRCDCGPQLQAALD
+AAARDGGAVLYLRGHEGRGIGLTNKIRAYRLQEEGLDTVEANLALGLPAEGRAYAGAADL
+LREAGLTRIRLVTNNPAKVDALRAAGIDVVERVPAPTPVTEHNAAYLRTKRDRMHHELAD
+RDLGDA
+>PROKKA_01012
+MSEHIRLDPVPAAIAAIAAGRPVVVVDDADRENEGDLIYAAALATDEVTAFTVRHTSGVI
+CAPLPAGLADRLALPPMTTVNEDPKGTAYTVSVDAAAGVTTGISAADRTRTLRVLADPGA
+APGDLTRPGHVFPLRAVPGGVRARRGHTEAGVELCRLAGVAPVAAIAELVHDDGTMMRLP
+ALREFSDEHGLVLISIEDLVAHLEETTPTLTAVPAEATLPTRHGLFRVSVHVDAETGAEH
+LLLVAGETDPERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALARAAAEGGAVLYLRGHE
+GRGIGLANKIRAYRLQEEGMDTVEANLALGLPAEARDWAGAAAVLTAAGHRRIRLVTNNP
+AKVAGLRAAGIDVVERVPAPTPVTEHNVVYLRTKRDRMAHALADRVLEPPTATGGPATPA
+DDPTTDPTHPTHQEDTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000109.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000109.fa
new file mode 100644
index 0000000000000000000000000000000000000000..512f65931ddb06eead39fddbdf10572b6ad6468b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000109.fa
@@ -0,0 +1,68 @@
+>PROKKA_00886
+MTARERPAPSRRPLLRSLALTAQTVREHVTDDPVLLALQVSRRLPPAAVGGAAGILTRLG
+RNGVVPALGHEMRGERAAALAALGVDEAGRPVRASRPGAGNVRGLVHRADAALGMGRPDI
+AETLLGSVPEKRRGAAWTAAAARLAAHRGDLGGAAALAARHPRNRHLARRMAGERDAFRG
+VAPTVPTEPGYRPVPGRVLHVLTNSLPHTGSGYAQRSHAILTSLRDEGFDAAAVTRPGYP
+VQIGVPWAAQRDVVDGIRYARLLPARLAQGQAARIQQHAELLAAHVRRHRPALLHTTTHF
+VNALAVEAVARAFGIPWVYEVRGQLADTWAAVRGPEALASERYRLFQEREAEAARRADGV
+VTLGAGMRDRLVAAGVAEDAVVLCPNAVGPAFVAERVDRDEARARLGWDLPTDAFVVGTV
+SSLVDYEGLDILLRAAARLAPHRPGLRVHIAGDGVARPGLQALAAELGIAELCAFPGRVD
+REDARLHHAALDVFTVPRRDLPVTRAVTPMKTVEASATGRPVVASDLPALAELVEDERTG
+LLVPAEDPAALAAALDRLAGDPAERARLGAAGREWALQTRTWEANARRYRTLYDRLGVHP
+R
+>PROKKA_00608
+MTARERPAPSRRPLLRSLALTAQTVREHVTDDPVLLALQVSRRLPPAAVGGAAGILTRLG
+RNGVVPALGHEMRGERAAALAALGVDEAGRPVRASRPGAGNVRGLVHRADAALGMGRPDI
+AETLLGSVPEKRRGAAWTAAAARLAAHRGDLGGAAALAARHPRNRHLARRMAGERDAFRG
+VAPTVPTEPGYRPVPGRVLHVLTNSLPHTGSGYAQRSHAILTSLRDEGFDAAAVTRPGYP
+VQIGVPWAAQRDVVDGIRYARLLPARLAQGQAARIQQHAELLAAHVRRHRPALLHTTTHF
+VNALAVEAVARAFGIPWVYEVRGQLADTWAAVRGPEALASERYRLFQEREAEAARRADGV
+VTLGAGMRDRLVAAGVAEDAVVLCPNAVGPAFVAERVDRDEARARLGWDLPTDAFVVGTV
+SSLVDYEGLDILLRAAARLAPHRPGLRVHIAGDGVARPGLQALAAELGIAELCAFPGRVD
+REDARLHHAALDVFTVPRRDLPVTRAVTPMKTVEASATGRPVVASDLPALAELVEDERTG
+LLVPAEDPAALAAALDRLAGDPAERARLGAAGREWALQTRTWEANARRYRTLYDRLGVHP
+R
+>PROKKA_02050
+MDRPGGLEGAFDRHWRKIRRELGSVYRDYRAGRASTGSALKRATRIGLKHGVLAPRDALA
+EFLRLRDEAVGPTLAGAGPMTMLPGELDSERARIWLSVLERHYPSGPARTAYFEQLRRLA
+LRDGQISTALDATAELASSNTSMARAAVDVNGRMTELSGWLPRLPGPVEPVSGCGTNVVL
+HLLKESRPYLSNGFTSRTQWNLLAEKDAGWTPVVLTEPGFPEGMTEGRPSTVEEVDGIEH
+RRILTGVSYRGVPFDRWLEDFAFLALDHVRNVRPDVLHVSSGRRGYETALVGLALREKTG
+LPLVYEVRSFFEGNWTPDLDIEEHSEVFRRRREVETRCMIAADRVLTLGEAMRDEIVARG
+VPAEKVDIVPNGVQLDRFTPAPRDPAIAARHGITLPTFGYVSNMDHPREGHELLIRAALL
+LQERGVEAQCVLVGGGRRFDELRALARELGIANRVVFTGPVDHEEVAALYGLIDVFVVPR
+INERAARYVTPLKPFEAMALRRPVIVSDLPALREIVAAPRRGLTFPVGDVMVLAETIARL
+LEEPAERQRLGAAGREWVEAERQWVHNGPRYDRAYHAAINARRRAGKG
+>PROKKA_02052
+MTSILLDFVRALGHAPLVLRTVVDHLRDDPAVLGLQISRRLPLAARVGLGRLAESLPARP
+GVVLGAVGLAAAGRHVDLLEHVEAVLPSAGAPDRVRLADVLTAAQEPDRAQAVLDAVPVN
+TPGLAAARARVAWHRGDVEAAISLLGGTGRDGVVRARFASEVRALRGGALPLPRADRDRA
+VGYRPRPGSALFVLTNSLPHTGSGYAQRSHSLACALRDEGWDVEAVTRLGWPVQTGVLTA
+ARRDMVDGIVYHRLLPSSLARGFDGRLAQHARMLLDLVLERRPAVLHTTTHWVNAVVTRA
+VAEAVGVPWVYEVRGQLADTWASTRGPEALRSDRYALFTAREDDAVRSADGVVTLGEQMA
+RRIAVAGMDRDAVVLSPNGVGGAFLEEPAPREDARRRLGLSMDDEIVGTVSSVVPYEGLD
+DLVRAVAALVDERPRLRLAVVGDGVALPALRRLAADLGIEDRLLAPGRVDRSLAPVWHQA
+LDVFCVPRKDTGVTRAVTPMKPLEAMATSRPVLVSDLPALSEIVEDGVTGRVLPAEEPEA
+WAAALAALLDDPAEARGLGARAREWVLGHRTWAANARRYDALYRRLGVMAPSA
+>PROKKA_01946
+MSPRAPRVRRLAANAALTGRTVADHLLDDPVVLALQVSRRLPTGLRARVGGVLADVPARV
+AVPRGIGLAMLGREEQLQAALVDADDAPGPRERARRAEVLLAAGRDEDAERLLADVPADA
+PGAAEARARLRWHRGDMTGAVLVLSPHGRQGRLRARLAAERDSLLGRPVCLSAEDRALAA
+DYEPRPGHVLFVLTNSLPHTGSGYVQRSHSLLTAVRDAGWSVAAVTRLGWPVQTGVLAAE
+DVDRVDGVAYHRLLPAALAPGFGARLDQHAAALLRLVLRERPAVLHTTTHWVNAAVTAAV
+AEAVGIPWVYEVRGQLADTWASTRGPQALMSERYRAFRTREAEAAARADGVVTLAETMRA
+RLAEDGVDPEDVVLSPNAVGGAFLDAPGERAAARRALGLAPDAEYIGTVSSVVPYEGLDD
+LVRVVALLADRRPRLRLLVAGDGTALPGLAALAEQLGVRDRVDLLGRVERARAPLCHQAL
+DVFCVPRRDTSVTRDVTPMKPLEAMASARPVLLSRLPALQELVAEGETGATVPASDPEAW
+AEAVEALLADPNAAAAMGDRARAWVLAERTWAANARRYTELYARLGAVVDVADRGAVRGG
+>PROKKA_00842
+MTSILLDSVRALGHAPLVLRTVVDHLRDDPAVLGLQISRRLPLAARVGLGRLAESLPARP
+GVVLGAMGLAAAGRHVDLLEHVEAVLPSAGAPDRVRLADVLTAAQEPDRAQAVLDAVPVD
+TPGLAAARARVAWHRGDVEAAISLLGGTGRDGVVRARFASEVRALRGGALPLPRADRDRA
+VGYRPRPGSALFVLTNSLPHTGSGYAQRSHSLACALRDEGWHVEAVTRLGWPVQTGVLTA
+ARRDMVDGIVYHRLLPSSLARGFDGRLAQHARMLLDLVLERRPAVLHTTTHWVNAVVTRA
+VAEAVGVPWVYEVRGQLADTWASTRGPEALRSDRYALFTAREDDAVRSADGVVTLGEQMA
+RRIAAAGMDRDAVVLSPNGVGGAFLEEPAPREDARRRLGLSMDDEIVGTVSSVVPYEGLD
+DLVRAVAALVDERPRLRLAVVGDGVALPALRRLAADLGIEDRLLAPGRVDRSLAPVWHQA
+LDVFCVPRKDTGVTRAVTPMKPLEAMATSRPVLVSDLPALSEIVEDGVTGRVLPAEEPEA
+WAAALAALLDDPAAARGLGARAREWVLGHRTWAANARRYDALYRRLGVTAPSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000112.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000112.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6161752b4961c49ac5a5c49625dd46dbdcc1d1d0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000112.fa
@@ -0,0 +1,35 @@
+>PROKKA_01012
+MSVIRTRRPSLRHLPAAVAAAGLITTVALAGPAAAWDDAHGPQAGYFQAVDHENVTAAFF
+QTYDGYDPEDLTLTLTPVAEDGTRLEGGQEVEFTALDVIDGGAVDVLETRRALGAAGEGL
+VRYDVEVDGQMLNMGITLQADADLADDQGAAVHAVDGPQTADLGDRPLVWDSAMQLAPGV
+AGAEIVHLVAAPTMEDAYAAVVAEPAHGEVFAFRDSEHSELRAWYIPDEGFVGTDTFTVD
+FHSDHVAHVQTVTVHVGEEISAAYDGFLDAEDGVLNGKPLDLTDPDTAAALAAFRADEAA
+PAPEDEEEQPAPVEDDADEQHTTPDTVETGQSTGWWLAGLGAAAAGVLVAARRRLGLTD
+>PROKKA_00726
+MSVIRTRRPSLRHLPAAVAAAGLITTVALAGPAAAWDDAHGPQAGYFQAVDHENVTAAFF
+QTYDGYDPEDLTLTLTPVAEDGTRLEGGQEVEFTALDVIDGGAVDVLETRRALGAAGEGL
+VRYDVEVDGQMLNMGITLQADADLADDQGAAVHAVDGPQTADLGDRPLVWDSAMQLAPGV
+AGAEIVHLVAAPTMEDAYAAVVAEPAHGEVFAFRDSEHSELRAWYIPDEGFVGTDTFTVD
+FHSDHVAHVQTVTVHVGEEISAAYDGFLDAEDGVLNGKPLDLTDPDTAAALAAFRADEAA
+PAPEDEEEQPAPVEDDADEQHTTPDTVETGQSTGWWLAGLGAAAAGVLVAARRRLGLTD
+>PROKKA_01876
+MTHLGDRPLVWDSAMQLAPGVEGAEIVHLVAAPTMENTYAEVVTEPAHGEVFAFRDSEHS
+ELRAWYIPEEGFVGTDTAAALAAFRGDEAAPAPEDEEE
+>PROKKA_01877
+MSVIRTRRPSLRHLPAAVAAAGLITTVALAGPAAAWDDAHGPQAGSFQAVDHENVTTAFF
+QTYDGYDPEDLTLTITPVAEDGTRLEGGQEVGFTALDVIDGGAVDVLETRRALGAAGEGL
+VRYDVVADGQMLNMGITLQADADLADDQGTAVHSVEARR
+>PROKKA_01764
+MFVTRPSCAPRLAAAVLASGLAAAALAAPASAEQAYDWTDDHGYPHGLFFGMDPESVDEA
+TFQTFYGFDPADLTVTVSPSDAEGTPTGPAAAVPFTAVDVLDGGTIDVLETRRVLGEAGT
+GTVAYHVFSGDQKELDMALVVGPDADLADATGGALVAAPGPVRAVLGDMPLSWSADVVMA
+PGVRAMEVRYPVDPALFDDVHPMVMTEAAHGTVVTFRDREDLSVRTWYVPDAGFTGTDTF
+SLDLTSDHVAHLPTVTVHVGQELPAAAAGAPDAQDGVLGGMPLDVEDPAIAAMLQQMGAL
+PPAPEATVPETTVSAEQHTRPGKVQTGGEPIWWLASAAVLGAGALVAARRRPGMAG
+>PROKKA_00955
+MSVIRTRRPSLRHLPVAVAAAGLVTTVALAGPAAAWDDAHGPQAGYFQAVDHENVTTALF
+QTYDGYDPEDLTLTLTPVAEDGTRLEGGQEVEFTALDVIDGGAVDVLETRRALGAAGAGL
+VRYDVVADGQMLNMGITLQADTDLADDQGAAVHSVDGPQMAHLGDRPLIWDSAMQLAPGV
+AGAEIVHLVAAPTMESTYAEVVAEPAHGEVFAFRDSGHSELRAWYIPEEGFVGTDTFTVD
+FHSEHVAHVQTVTVHVGEEIPAAYDGFLDAEEGVLNGKPLDLTDPDTAAALAAFRADEAA
+PAPEDEEEQPAPVEDDADEQHTTPDTVETGQSTGWWLAGLGAAAAGVLVAARRRLGLTD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000115.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000115.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9badee24091984c27f79c89bcc24fbe4652ee106
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000115.fa
@@ -0,0 +1,30 @@
+>PROKKA_01030
+MIDRFQNLDWGYYGPELMTAVGDTLYMVGWSFILGGILGLLVGLVLYTTRPGGIFANRAV
+YLVTNFIVNLIRPIPFVILIAALQPLTIAVLGTGIGNTAVVFCMIWASTFGIARIVEQNL
+VSLDPGVIEAARAMGASRMRIVRAVVLPEALGPLILGFTFVIISLVDMSAMAGIIGGGGV
+GNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR
+>PROKKA_00745
+MIDRFQNLDWGYYGPELMTAVGDTLYMVGWSFILGGILGLLVGLVLYTTRPGGIFANRAV
+YLVTNFIVNLIRPIPFVILIAALQPLTIAVLGTGIGNTAVVFCMIWASTFGIARIVEQNL
+VSLDPGVIEAARAMGASRMRIVRAVVLPEALGPLILGFTFVIISLVDMSAMAGIIGGGGV
+GNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR
+>PROKKA_00186
+MSEALSRILQVWPEIVVALGQTLTMLAVTIPLAVLLGTPLGIWLFTHAPGGLSPSPRLHR
+VVDAAVSMLRSFPFLILLIAIIPVTRLIVGTTIGTAAVIVPLTVNAIPYFARFVEQNLAQ
+LGPGPVEAARAMGATRGQIVRDVLLVDARPALVGSLTIMSVSFISYSAMAGLVGGGGIGD
+FAIRYGYYRYETPLMVVAILLMIGLVALLQFAGTRLSQRLDHRRPRTARRPRRRALAPAG
+>PROKKA_01853
+MTWLETLTTNPAITDALPEALVETLLMVAISGVATVLIGGLLGIVLHVTRPGGLNPMPAL
+YTVLSTVIVNITRSVPYAILMVALIPLTKWLVGTAIGPIAATVSLTIGTAPFFARLVESA
+LREIPSGTVDAAQVMGSTRGQVIRKVLLPEAMPGLIAATTTTLVTLVGYSAMAGLIGGGG
+LGRLAYNYGYQRFQTEVMVVTIVVIVILVQLIQWIGDLLIRRVDHR
+>PROKKA_01742
+MIDRFQNLDWGYYGPELMTAVGDTLYMVGWAFILGGILGLLVGLVLYTTRPGGIFANRAV
+YLVTNFVVNLIRPIPFVILIAALQPLTIAVLGSGIGNTAVVFCMIWASTFGIARIVEQNL
+VSLDPGVIEAARAMGASRMRIVRTVVLPEALGPLILGFTFVIISLVDMSAMAGIIGGGGV
+GNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR
+>PROKKA_00974
+MIDRFQNLDWGYYGPELMTAVGDTLYMVGWSFILGGILGLLVGLVLYTTRPGGIFANRAV
+YLVTNFIVNLIRPIPFVILIAALQPLTIAVLGTGIGNTAVVFCMIWASTFGIARIVEQNL
+VSLDPGVIEAARAMGASRMRIVRAVVLPEALGPLILGFTFVIISLVDMSAMAGIIGGGGV
+GNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000116.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000116.fa
new file mode 100644
index 0000000000000000000000000000000000000000..32ffac2349e34ebd2401418c944ee7c93f7cbd55
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000116.fa
@@ -0,0 +1,29 @@
+>PROKKA_01042
+MLEPEIRSDNGGRGIRNAETNFYADAETRTLVTTLNGVEVELRATPVSFHWDYGDGSPTK
+TTSVAGQSQPEFNVPTPTSHVYEDTGQYTVRLTTVYIGEYREAGGEWVLIPGTISLDSAP
+VTANIWRTITRNVADDCSVDSSAWGCTGPIESAPAG
+>PROKKA_00755
+MLKPEIRSDNGGRGIRNAETNFYADAETRTLVTTLNGVEVELRATPVSFRWDYGDGSPTK
+TTSVAGQSQPEFNVPTPTSHVYEDTGQYTVRLTTVYIGEYREAGGEWVLIPGTISLDSAP
+VTADIWRTITRNVADDCSVDSSAWGCTGPIESTPAG
+>PROKKA_00331
+MPHQLDNADYGSCLNQDESFCPDGEWVQARTVDITRPDADPLYGRPTCTSDVAAGAGGAR
+SFTLEEVRTLLLLDPTIESDNAGRGVRNAETNFYTDAGVETLSTTINGVPVELRATPVSF
+HWNYGDGTAPRVTHVGGHAQAEFNTPTPTSHVYEETGEYTVTLTTVYIGEYREADGDWVL
+IPGTITLDAAPVTADIWRTVTRNVAEDCAADPSAWGCTGPIEAPDAP
+>PROKKA_00544
+MPHQLDNADYGSCLNQDESFCPDGEWVQARTVDITRPDADPLYGRPTCTSDAAAGADGAR
+SFTLEEVRTLLLLDPTIESDNAGRGVRNAETNFYTDAGVETLSTTINGVPVELRATPVSF
+HWNYGDGTAPRVTHVGGHAQAEFNTPTPTSHVYKETGEYTVTLTTVYIGEYREADGDWVL
+IPGTITLDAAPVTADIWRTVTRNVAEDCAADPSAWGCTGPIEAPDAP
+>PROKKA_01735
+MTSRRGDFPACMAVLFALIFLVSAVTLVTPSQAHASSCDTAGRKAQLTDDSLIVGQRCHK
+SSIAEIVGDGLADDQEKSAKATSPTTKVTTLQNACYENLPEPGFENCATQQELICGDQNV
+AWLQPSTKDTARPEDAPVKGDAFCADGSAAPSAPPQPSRPAVSIDDMGEVIAPEPRILAD
+TDGRGVRNAETNFYSPEAVRHETAVIDGVSVEMRLTPVSFIWDYGDGTAPVTTDVGGNPQ
+DGFDVRTPTSHVYDETGTYEVTLTTVYTGEIRYPGQGWEAVPGTIRRTATPVTADIWTTS
+TRNVADDCSADASAWGCAGPVEAPNGG
+>PROKKA_00983
+MSIDEVRTLLVLEPEIRSDNGGRGIRNAETNFYADAETRTLVTTLNGVEVELRATPVSFH
+WDYGDGSPTKTTSVAGQSQPEFNVPTPTSHVYEDTGQYTVRLTTVYIGEYREAGGEWVLI
+PGTISLDSAPVTANIWRTITRNVADDCSVDSSAWGCTGPIESAPAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000117.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000117.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8686b0b5538a6f4e8037df783b702eef6f32e04e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000117.fa
@@ -0,0 +1,54 @@
+>PROKKA_01102
+MTPHTDAPEGPSLRRLADAAEDRLGEHGLALRDLGVLGPEDPAASHFAAAVERGFYETVP
+TGAALRQQLEAHAADGRRRLGVYAPGDDPAARRPAATFEDFVQPLTTSPGRTVDAWLITD
+VTVSPDARRRGVLRAMMLRSLADARDAGLCAAALTATEAAIYGRFGFGAATRWHAVRIDV
+SGAPAFTGAPAGGRVTVEEPREIPGLVDELYGRVLPATPGSVQRTSFSVPRWEDREASRN
+EGRGSGLYAAVHRDDDGRVQGVALYRFEGWEKEPPTITVTAFLAATADARRGLVHHLARL
+DLVERIEWGRAPEPGWLEALFVDERRVSRHRGSDDLYLRVLNLPAAMAARGWAGDGEVVV
+AVEDALGAIDGTWRLTVRQGRGAAERLGPAADAVGLDAGLRLDAARFSALWLGGHSRGAG
+AAVLAEAGVVAELRAGAAEAFDGLVRPSRPLHTLVGF
+>PROKKA_00821
+MTPHTDTPEGPSLRRLADAAEARLGEHGLALRDLGVLGPEDPAASHFAAAVERGFYETVP
+TGAALRQQLEAHAADGRRRLGVYAPGEDPAARRPAATFEDFVQPLTTWPGRAVDAWLITD
+VTVSPDARRRGVLRAMMLRSLADARDAGLCAAALTATEAAIYGRFGFGAATRWHAVRIDV
+SGAPALTGAPAGGRVTVEEPREMPGLVDELYGRVLPATPGSVQRTSFSVPRWEDREASRN
+EGRGSGLYAAVHRDDDGRVQGVALYRFEGWEKEPPTITVTAFLAATADARRGLVHHLARL
+DLVERIEWGRAPEPGWLEALFVDERRVSRHRGSDDLYLRVLNLPAAMAARGWAGDGEVVV
+AVEDALGAIDGTWRLTVRQGRGAAERLGPAADAVRMGAGLRLDAARFSALWLGGHSRGAG
+AAVLAEAGVVAELRAGAAEAFDGLVRPSRPLHTLVGF
+>PROKKA_01792
+MSINPAAAAHAADATAAQDALARHGLVLRTLAPLSRGFDGADPARAEHPAHVRHTAAVEK
+GFYEEVPQGAAADQDLGVSADDAKVLRGVYLSADDPARREPVGTFVDWTSRLTTSPGAEL
+PVWMISNVTVSPGHRRRGILRAMMTASLEEAVAAGVPVAALTASESTIYGRFGFGAASTA
+RTVRVDVRGDVVLAADAAGRTDEDAGTVLREDPRELAGVVEALHDRVRRGTPGSVHRPTG
+HVIRWEDRSAAKNDGRGSGLFAAVHRDADGAVQGVALYRFDGWGKEPTTVSVEVFLAATD
+AAARQLWRYLTRLDLIERLRMTRCPDDGGLEQVLADRRRVRTKSVWDDLYLRVLDVPVCL
+GGRGYAPEVVGEVVLAVADAAGHAAGTWRLRVADGVGRAERLADDARADLALDVAHLSAV
+WLGGVRAGALVRAGVVDEREPGAAARLDALLAPAAAVHLLTGF
+>PROKKA_01793
+MTPRTDAPDAWLDPAPATAEALAAHGLELLRVPSPWETGDADPDAPFDHARRWADAPAVR
+RHTAVLQRNFHEVGDPDFALADRFIGVEQGDRRRLSGVYPQGADPAATDPVGTLVDFTKD
+LNVGDGRMLPAWCLTEVTVSPTHRRRGILRAMMTESLRRAHAARVPIALLTATEATLYRR
+FGFGVSTYHRSVWLDVTRGVQLRGRRPDGSFRFVEPTASGALIDGLWRRAFEAQAGSVER
+IRFHAARETDRDPRVGEGRPQGLRAVVYSAPDGEDLGVAVYRVTGSTAELVADDPVTATV
+VALWAATPEAHRALLEFLGNLDLVVRLRLPAVAADRLLEFLVLDESRIYTRGVHHHLWHR
+VLDVAACFEARPYLHEGAVTVTVEDDLGYAAGTWEIAAADGVGRVRPAPQDAAELTLDVA
+ELGSVLLGGVKAEMMREAGILLAHRPGAAADLDTLLRQARPPYSLTGF
+>PROKKA_01683
+MRPHTDLQPTATPRADAEVLAEQGLALVVAPGRAADPAFERHTTAVERGFYEQVPSGEAM
+AQLLEAGEADGRRMVDVLPLGADPATTRPVATFEDFRSELTVSPGVAVSAWLISGVTVDP
+GFRRRGLLRTMMTRSLADAVAAGVPVAALTASEAAIYGRFGFGAATRWRRARLDTRGDVR
+LRGAPSAGRVTREEPREVGALADELYQHVRRLTPGATQRPTMTAIGWEDRSRFKNDGKGS
+GLYAAVHRDAAGTAQGIALYRPQGWDVEPPTVTMELFLALTPDARRGLLTHLTSLDLIER
+IVWERAPEAGWPEALLEDERRLRTERDGDDLYLRILDVPAALGARADLGDGEVVVDVTDP
+LGHAAGAWRIRARDGVAEVTEAAEGEAELGLDVADLSAVWLGGHGSAGGVAARVATGLVR
+EVVPGAGARLDALLRPSVPVRSLVGF
+>PROKKA_01051
+MTPHTDAPEGPSLRRLADAAEDRLGEHGLALRDLGVLGPEDPAASHFAAAVERGFYETVP
+TGAALRQQLEAHAADGRRRLGVYAPGDDPAARRPAATFEDFVQPLTTWPGRTVDAWLITD
+VTVSPDARRRGVLRAMMLRSLADARDAGLCAAALTATEAAIYGRFGFGAATRWHAVRIDV
+SGAPAFTGAPAGGRVTVEEPREIPGLVDELYGRVLPATPGSVQRTSFSVPRWEDREASRN
+EGRGSGLYAAVHRDDDGRVQGVALYRFEGWEKEPPTITVTAFLAATADARRGLVHHLARL
+DLVERIEWGRAPEPGWLEALFVDERRVSRHRGSDDLYLRVLNLPAAMAARGWAGDGEVVV
+AVEDALGAIDGTWRLTVRQGRGAAERLGPAADAVRMGAGLRLDAARFSALWLGGHSRGAG
+AAVLAEAGVVAELRAGAAEAFDGLVRPSRPLHTLVGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000119.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000119.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5537df46aec924320a725458b881b68e6d15cc14
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000119.fa
@@ -0,0 +1,106 @@
+>PROKKA_01117
+MPKNSSTTVSSAVEAHPGGLASGSGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVF
+TGLSGSGKSSLAFDTIFAEGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKS
+TNRNPRSTVGTITEIYDYMRLLWARVGVPHCPQCGEPVSRQTPQQIVDQLEELPERTRFQ
+VLAPVVRGRKGEFVDLFKDLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRLAM
+KEGIRQRLTDSVETALKLADGLVVAEFVDVEPVAEKGRKNTAEFGGRDAEGNPRYRSFSE
+KLSCPNGHEQTVDEIEPRSFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVV
+PWSLGKSTSDYWLRVLGGLGKEMGFSLDTPWKDLTEAERDAVLHGKDFKVEVTFRNRFGR
+ERRYTTGFEGVIPYVMRKHGETESDGARERYESFMREIPCPACHGARLNPTVLNVLVGGL
+SIADATRLPMREAMEFFSGLRLTDRERQIADQVLKEILARLAFLLDVGLEYLNLERPAGT
+LSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEH
+DEDTIAEADWIVDIGPRAGEHGGEVVHSGSLADLKANTRSVTGDYLSGRRSIAVPERRRV
+PEKGRVLTVRGAQENNLKDVSVEVPLGVLTAVTGVSGSGKSTLINEILYKVLANRLNGAK
+LVPGRHRSVEGLEHLDKVVHVDQSPIGRTPRSNPATYTGVFDAIRKLFAETPEAKVRGYQ
+QGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTYKGKNIAE
+VLDMPIEEAADFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKR
+SNGRTIYVLDEPTTGLHFDDIRKLLHVLQSLVDKGNTVLTIEHNLDVIKSADHVIDLGPE
+GGSGGGTIVAAGTPEEVAHVAESHTGRFLAELLA
+>PROKKA_00373
+MVESSSFVPPKLSVQPDVRVLGARENNLQDVDLTVPRDATVVFTGVSGSGKSSLAFGTLY
+AESQRRYLESVAPYARRLIDQAGVPDVDSITGMPPAVALQQQRGSGNARSTVGSITTLSS
+LVRMLYSRAGDYPEGQPMLYAEDFSANTVQGACSECHGIGRVYEVNEQQMVPDPSLTIRE
+RAIASWPTAWHGHQLRDVLVALGYDVDVPWRDLPKKDRDWILYTDETPFVPVHSRLTLSE
+SKAAIEAGVEPSYSGTFVGARRYILDTFANTKSASMKRRVAQFLTAAICPTCNGKRLKPE
+ALSVTFEGFDIAEFSQLPLRELATILSGVVAREEDHEAASSDVRPTASRTPEKRAAAVQL
+ASGVLQRLRPLVDLGLGYLSLSRTTPTLSGGELQRLRLATQLSSDLFGVVYVLDEPSAGL
+HPQDVAALLEILDGLKGRGNSLFIVEHSVAVMRHADWLVDIGPGAGEHGGRVLYSGPPDG
+LAGVTESVTRGYLFGGRGLPLRTPREARSWLRLENVTRNNLHDLTVDIPLGVFTAVTGVS
+GSGKSSLVSQALPSLLGDRLGLAARADDEPVSDESLLADAPEHLEGRVAGPVTGVQRLVV
+IDQRPIGRTPRSNVATYTGLFDHVRRRFADTPEARSRGYKPGRFSFNVAGGRCPTCEGEG
+SVMVELLFLPSVYTECPDCHGTRYKASTLEVTWRGRTIADVLSMSVEEANLFFVGDEEIT
+RSLAALSDVGLEYLRLGQPATELSGGEAQRVKLATELQRAQRGDTLYVLDEPTSGLHCAD
+TDRLVAHLQTLVDAGNTVVAAELDMRVVAVADHVIDLGPGAGDAGGTVVAAGTPAHVADQ
+GVGASAGYLAAALQAATNVTPS
+>PROKKA_00836
+MPKNSSTTVSSAVEAHPGGLASGSGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVF
+TGLSGSGKSSLAFDTIFAEGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKS
+TNRNPRSTVGTITEIYDYMRLLWARVGVPHCPQCGEPVSRQTPQQIVDQLEELPERTRFQ
+VLAPVVRGRKGEFVDLFQDLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRLAM
+KEGIRQRLTDSVETALKLADGLVVAEFVDVEPVAEKGKKNTAEFGGRDAEGNPRYRSFSE
+KLSCPNGHEQTVDEIEPRSFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVV
+PWSLGKSTSDYWLRVLGGLGKEMGFSLDTPWKDLTEAERDAVLHGKDFKVEVTFRNRFGR
+ERRYTTGFEGVIPYVMRKHGETESDGARERYESFMREIPCPACHGARLNPTVLNVLVGGL
+SIADATRLPMREAMEFFSGLRLTDRERQIADQVLKEILARLAFLLDVGLEYLNLERPAGT
+LSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEH
+DEDTIAEADWIVDIGPRAGEHGGEVVHSGSLADLKANTRSVTGDYLSGRRSIAVPERRRV
+PEKGRVLTVRGAQENNLKDVSVEVPLGVLTAVTGVSGSGKSTLINEILYKVLANRLNGAK
+LVPGRHRSVEGLEHLDKVVHVDQSPIGRTPRSNPATYTGVFDAIRKLFAETPEAKVRGYQ
+QGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTYKGKNIAE
+VLDMPIEEAADFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKR
+SNGRTIYVLDEPTTGLHFDDIRKLLHVLQSLVDKGNTVLTIEHNLDVIKSADHVIDLGPE
+GGSGGGTIVATGTPEEVARAAESHTGRFLAELLA
+>PROKKA_01776
+MPKNSSTTVSSAVETHAGGLASGPGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVF
+TGLSGSGKSSLAFDTIFAEGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKS
+TNRNPRSTVGTITEVYDYLRLLWARVGVPHCPQCGEPVSRQTPQQIVDQLEELPERTRFQ
+VLAPVVRGRKGEFVDLFADLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRLAM
+KEGIRQRLTDSVETALKLADGLVVAEFVDVEVVAEKGKKNTAEFGGRDAEGNPRYRSFSE
+KLSCPNGHEQTVDEIEPRSFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVV
+PWSLGKSTSDYWLRVLGGLAKEMGFSLDTPWRELEPAQREAVLHGKDFKVEVTFRNRFGR
+ERRYTTGFEGVVPYVLRKHGETESDGARERYESFMREIPCPVCHGARLNPTVLNVLVGGL
+SIAEATRLPLREARDFLAGLELSARERQIADQVLKEILARLAFLLDVGLEYLNLERPAGT
+LSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEH
+DEDTIAEADWIVDIGPRAGEHGGEVVHSGSLEDLKANTASITGDYLAGRRAITAPQTRRA
+PQEGRTLTVRGARENNLKDVSVDIPLGVLTAVTGVSGSGKSTLINEILYKVLANRLNGAK
+LVPGRHRAVDGLEHLDKVVHVDQSPIGRTPRSNPATYTGVFDAIRKLFAETPEAKVRGYQ
+QGRFSFNIKGGRCEACSGDGTLKIEMNFLPDVYVPCEVCDGARYNRETLEVTYKGKNIAE
+VLDMPIEEAAQFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKR
+SNGRSVYVLDEPTTGLHFDDIRKLLQVLQSLVDKGNTVITIEHNLDVVKCADHVIDLGPE
+GGSGGGTIVATGTPEEVARVEASHTGRFLAELLA
+>PROKKA_01669
+MPKNSSSAAAPARPDAAARGGLASGPARGSAQHERIVVKGAREHNLKNVDVSIPRDSMVV
+FTGLSGSGKSSLAFDTIFAEGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQK
+STNRNPRSTVGTITEIYDYMRLLWARVGVAHCPVCGEVVSKQTPQQIVDQLEQLPERTRF
+QVLAPVVRGRKGEFVDLFSSLSTQGYARALVDGELIQLSDPPALKKQNKHTIAVVVDRLA
+VKEGIRQRLTDSVETALKLADGLVAVEFVDVDVVAQAGKKNQGDLAGEDAEGNPRFRTFS
+EKLSCPHGHPQTVDEIEPRSFSFNNPFGACPECTGIGSRLQVDPDLVVPNDELSLNEGAI
+LPWSLGKSTSDYWLRVLGGLAKEMKFSLDTPFKDLTAQQRDAVLNGKDFKVEVSFRNRFG
+RERRYTTGFEGVLPYVMRKHGETESDNARERYESFMRQIPCPACHGARLNPTVLNVRVGG
+LSIADATRLPLRESLAFLDGLQLTERELAIADQVVREIRARLEFLLDVGLDYLNLERNAG
+TLSGGEAQRIRLATQIGAGLVGVLYVLDEPSIGLHQRDNRRLIDTLIRLRDLGNTLIVVE
+HDEDTIAEADWIVDIGPRAGEHGGEVVHSGSLDELKANTRSVTGDYLAGRRRIEVPAARR
+PVDPKRRLTVKGATENNLKDVTVDIPLGVFTAVTGVSGSGKSTLINEILYKVLADKLNGA
+KMVPGRHRSVAGLEHLDKVVHVDQSPIGRTPRSNPATYTGVFDQIRKLFAETPEAKVRGY
+QQGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTYKGKNIA
+EVLDMPIEEAAEFFGAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQK
+RSTGRTVYVLDEPTTGLHFEDIRKLLQVLQTLVDKGNTVLTIEHNLDVVKCADHVIDLGP
+EGGSGGGTVVATGTPEEVAAVPESHTGRFLAELLG
+>PROKKA_01067
+MPKNSSTTVSSAVEAHPGGLASGPGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVF
+TGLSGSGKSSLAFDTIFAEGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKS
+TNRNPRSTVGTITEIYDYMRLLWARVGVPHCPQCGEPVSRQTPQQIVDQLEELPERTRFQ
+VLAPVVRGRKGEFVDLFQDLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRLAM
+KEGIRQRLTDSVETALKLADGLVVAEFVDVEPVAEKGRKNTAEFGGRDAEGNPRYRSFSE
+KLSCPNGHEQTVDEIEPRSFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVV
+PWSLGKSTSDYWLRVLGGLGKEMGFSLDTPWKDLTEAERDAVLHGKDFKVEVTFRNRFGR
+ERRYTTGFEGVIPYVMRKHGETESDGARERYESFMREIPCPACHGARLNPTVLNVLVGGL
+SIADATRLPMREAMEFFSGLRLTDRERQIADQVLKEILARLAFLLDVGLEYLNLERPAGT
+LSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEH
+DEDTIAEADWIVDIGPRAGEHGGEVVHSGSLADLKANTRSVTGDYLSGRRSIAVPERRRV
+PEKGRVLTVRGAQENNLKDVSVEVPLGVLTAVTGVSGSGKSTLINEILYKVLANRLNGAK
+LVPGRHRSVEGLEHLDKVVHVDQSPIGRTPRSNPATYTGVFDAIRKLFAETPEAKVRGYQ
+QGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTYKGKNIAE
+VLDMPIEEAADFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKR
+SNGRTIYVLDEPTTGLHFDDIRKLLHVLQSLVDKGNTVLTIEHNLDVIKSADHVIDLGPE
+GGSGGGTIVAAGTPEEVAHVAESHTGRFLAELLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000120.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000120.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bcd663b76cafb7edb53ae76d94a231e2fde5b8b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000120.fa
@@ -0,0 +1,31 @@
+>PROKKA_01118
+MATSEPVRRSAAALLRLTCRPEVVGMEHVPARGPFVMASNHLSFVDSVILQALAPRPVHF
+FAKEEYFTGTGLRGRVRRRFFESVGSVPVRRGEQAASVAALESLVGLLESGQGVGIYPEG
+TRSRDGRLYRGRTGAAWLALATGARVVPVGLVGTQHLQPPDTNGFRPHRFSVRVGAPLDF
+GHPGRRHTLPQRRDATAAIMDAIGALSGQERVDAYNAAPGARG
+>PROKKA_00837
+MATSEPVRRSAAALLRLTCRPEVVGMEHVPARGPFVMASNHLSFVDSVILQALAPRPVHF
+FAKEEYFTGTGLRGRVRRRFFESVGSVPVRRGEQAASVAALESLVGLLESGQGVGIYPEG
+TRSRDGRLYRGRTGAAWLALATGAPVVPVGLVGTQHLQPPDTNGFRPHRFSVRVGAPLDF
+GHPGRRHTLPQRRDATAAIMDAIGALSGQERVDAYNAAPGARG
+>PROKKA_00163
+MSALAARARAGLAHAVLAVAGARIHASGPDGAEEAEITRERLAALLPRQAVFYANHTSHL
+DFVTLWAVLPPALQRRVRPVAAADYWGSGLRRRVAEGLFHAYLVERGKTRRRGPGAASGS
+GVSPDGGSQLEGMLEILAGGDSLIIFPEGTRGSGEDVARFQRGLHALAAAFPQVPVVPVS
+LVNLGRILPKGEPIPVPHLSTVRFHPPLDPPEPARPPGPGAPASGTAATDAPEPGRGEDE
+AARTAWLERARAVLVQDLSASLRG
+>PROKKA_01775
+MATSEPVRRSAAALLRLTCRPEVTGMDQVPAEGPFIMASNHLSFFDSVILQALAPRPVHF
+FAKEEYFTGAGVRGRAQRWFFESVGSVPVRRGEQAASVAALESLVGLLDSGQGVGIYPEG
+TRSRDGRLYRGRTGAAWLALTTGAPVVPVGLVDTQHLQPPDTNGFRPHRFAVRVGAPLDF
+GHPGRRHTLPQRRDATAAIMDAIGALSGQERLDAYNAAPGARG
+>PROKKA_01668
+MATSEQLRRAVAGAIRLSCRPHVRGLEHVPPEGPFIVASNHLSFVDSVILQALCPRPVGF
+FAKAEYFEAPGLRGRAQRRFFEAVGSIPVRRGEQAASVAALEDLVALLDGGHGVGIYPEG
+TRSRDGRLYRGRTGAAWLALTTGAPVVPVGLRGTERLQPPGTNGFRPHRFTVEMGEPLDF
+GHPGRRHSLPQRREATATIMAAIAALSGQERVDEYNAAPAARG
+>PROKKA_01068
+MATSEPVRRSAAALLRLTCRPEVVGMEHVPARGPFVMASNHLSFVDSVILQALAPRPVHF
+FAKEEYFTGTGLRGRVRRRFFESVGSVPVRRGEQAASVAALESLVGLLESGQGVGIYPEG
+TRSRDGRLYRGRTGAAWLALATGAPVVPVGLVGTQHLQPPDTNGFRPHRFSVRVGAPLDF
+GHPGRRHTLPQRRDATAAIMDAIGALSGQERVDAYNAAPGARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000121.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000121.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38d4fc4731cb6a6086091729e3fc0f6510962d75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000121.fa
@@ -0,0 +1,36 @@
+>PROKKA_01147
+MADQTTTPTADAQAAGRSVLVTGGNRGIGLAIARAFAANGDRVAITSRSGEGPEGVLAVR
+ADVTDAASVDAAFREVEEVHGPVEVLVANAGITHDQLLLRMSEDDFTSVIDTNLTGAFRV
+VQRATKGMMRLKRGRIVLVSSVVGLLGSPGQVNYAASKSGLVGMARSITRELGARGVTAN
+VVAPGYIDTEMTQSLDDELKAQYKTSIPAGRFAAPEEVAGVVRWLASDEAAYISGAVIPV
+DGGLGMGH
+>PROKKA_00866
+MADQTTTPAADAQAAGRSVLVTGGNRGIGLAIARAFAAHGDRVAITSRSGEGPEGVLAVR
+ADVTDAASVDAAFREVEEVHGPVEVLVANAGITHDQLLLRMSEDDFTSVIDTNLTGAFRV
+VQRATKGMMRLKRGRIVLVSSVVGLLGSPGQVNYAASKSGLVGMARSITRELGARGVTAN
+VVAPGYIDTEMTQSLDDELKAQYKTSIPAGRFAAPEEVAGVVRWLASDEAAYISGAVIPV
+DGGLGMGH
+>PROKKA_00771
+MAEFDGKVALVTGGGSGIGEACAKDLARGGAKVLVTDINLEAAERVAEEIKADGGEAAAY
+RLDSASPDDNEKAVAFAEETFGALHLAVNNAGIGAGTEPAGELKIEDWDRVIDIDLNGVL
+YGMRHQLPAMERAGGGAVVNMASIHGTVATGLGASAYTAAKHGVVGLTKQAGVDYGPRGV
+RVNAVGPGYIETPLLAELPDEVHEALVAKHPIGRLGRAEEVAHLVSFLLSDKASFLTGAY
+YLVDGGYTAP
+>PROKKA_01745
+MADQTTPTAADAKASGRSVLVTGGNRGIGLAIARAFAANGDRVAVTSRSGEGPEGVLAVR
+ADVTDAASVDAAFREVEEAHGPVEVLVANAGITNDQLLLRMSEEDFTSVVDTNLTGAFRV
+VQRATKGMMRLKRGRIVLVSSVVGLLGSPGQVNYAASKSGLVGMARSITRELGARGVTAN
+VVAPGYIDTEMTQSLGEDLKAQYKKSIPAGRFAQPEEVADVVRWLASDEAAYISGAVIPV
+DGGLGMGH
+>PROKKA_01639
+MAEQTEPGGRSVLVTGGNRGIGRAIAEAFLANGDRVAVTSRSGEGGPEGALTVAADVTDA
+ASVDAAFRAVEEAHGPVEVLVANAGVTNDQLLLRMSEDDFTSVVDTNLTGAFRVVQRATK
+GMMRLKRGRIVLVSSVVGLLGSPGQVNYAASKSGLIGMARSITRELGARGITANVVAPGY
+IDTEMTRSLDEELKAQYRKSIPAGRFAEPEEVADVVRWLASPGAGYVSGAVIPVDGGLGM
+GH
+>PROKKA_01097
+MADQTTTPAADAQAAGRSVLVTGGNRGIGLAIARAFAAHGDRVAITSRSGEGPEGVLAVR
+ADVTDAASVDAAFREVEEVHGPVEVLVANAGITHDQLLLRMSEDDFTSVIDTNLTGAFRV
+VQRATKGMMRLKRGRIVLVSSVVGLLGSPGQVNYAASKSGLVGMARSITRELGARGVTAN
+VVAPGYIDTEMTQSLDDELKAQYKTSIPAGRFAAPEEVAGVVRWLASDEAAYISGAVIPV
+DGGLGMGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000124.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000124.fa
new file mode 100644
index 0000000000000000000000000000000000000000..defb44c52ec739ea8dd86f5b5a5b6cd0a63fbb0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000124.fa
@@ -0,0 +1,42 @@
+>PROKKA_01285
+MRHTRLGRSGLTVSVVGLGCNNLGRPGTATLEQAGTDDVVHAALDAGITFFDVADVYGAE
+PGLSEERLGRALGARRDEVVIGTKFGMDMGGVAGDDGGARGSRRYIVRAVEDSLRRLGTD
+WIDLYQFHTPDPATPIEETLRALDDLVRAGKVRYVGHSNRAGWQIAQAEYVARELGVERF
+VSAQNHYNLLDRRAELEVVPAAAEFGLGVLPYFPLANGLLTGKYSQGDAPEGSRLSHVRQ
+HMVADADLEQLAGFGRFARERGITEVQAAIGWLAAQGPVSSVIAGATRAAQVVENAAAAD
+WLATAEDLAELDALFPGPEKVALF
+>PROKKA_01004
+MRHTRLGRSGLTVSVVGLGCNNLGRPGTATLEQAGTDAVVHAALDAGITFFDVADVYGAE
+PGLSEERLGRALGARRDEVVIGTKFGMDMGGVAGDDGGARGSRRYIVRAVEDSLRRLGTD
+WIDLYQFHTPDPATPIEETLRALDDLVRAGKVRYVGHSNRAGWQIAQAEYVARELGVERF
+VSAQNHYNLLDRRAELEVVPAAAEFGLGVLPYFPLANGLLTGKYSQGDAPEGSRLSHVRQ
+HMVADADLEQLAAFGRFARERGITEVQAAIGWLAAQGPVSSVIAGATRAAQVVENAAAAD
+WLATAEDLAELDALFPGPEKVALF
+>PROKKA_01600
+MRHTRLGRSGLTVSVVGLGCNNLGRPGTVTLEQDGTDAVVHAALDAGITFFDVADIYGAQ
+PGLSEERLGRALGARRDDVVIGTKFGMDMAGANGVDHDARGSRRYIVRAVEASLRRLGTD
+WIDLYQFHTPDPATPIDETLRALDDLVRDGKVRYVGHSNRTGWQIAQAEYVARELGTERF
+VSAQNHYNLLDRRAELEVVPAAAEFGLGVLPYFPLANGLLTGKYSQGAAPEGSRLSHVRQ
+HMVADADLEQLAAFGEFARARGITEVQAAIGWLAAQGPVSSVIAGATRTGQVAENARAAD
+WEATEADLAELDALFPGPEKVALF
+>PROKKA_01496
+MRTVRLGRSGLTVSVVGLGCNNLGRPGTATMEQEGTDAVVHAALDAGITLFDVADVYGAR
+PGLSEERLGRALGSRRDEVVLATKFGMDMGGAAGADGGARGSRRYIVRAVEDSLRRLGTD
+WIDLYQFHTPDPATPIEETLRALDDLVRSGKVRYIGHSNRTGWQIAQAEHAAREIGVERF
+VSAQNHYNLLDRRAELEVLPASAEYGLGVLPYFPLANGLLTGKYSDGTAPAGSRLSHVRQ
+HMVEEADRGQLAAFGAFARERGITEVQAAIGWLAAQRPVASVIAGATRPGQIAENARAAD
+WEATPADLAELDALFPAPPPVALF
+>PROKKA_02080
+MSDMIYNRLGSSGLQVSQFSFGSWVTFGNQVDMGLAKDQLAAAKEGGVNFFDNAEVYAGG
+ESESIMGRAIAELGWKRHEYVVSTKLFWGIHGDVVNMKNTLNRKYLMQGIDGSLERLGLD
+FVDLVFCHRPDPHTPIEETVWAMSDMINRGKALYWGTSEWSADEIRAAWNIAERHHLHKP
+VMEQPQYNLLHRTKVEEEYARLYEDIGLGLTTWSPLASGILSGKYVDGVPEGSRGALKGY
+DFVKDSIADQETTAKVRQLVDIAAELDVTPAQLALAWTASNPRVSTVILGASSVAQVQEN
+LKALDVIELVTPEVRERLEAVFA
+>PROKKA_01243
+MRHTRLGRSGLTVSVVGLGCNNLGRPGTATLEQAGTDAVVHAALDAGITFFDVADVYGAE
+PGLSEERLGRALGARRDEVVIGTKFGMDMGGVAGDDGGARGSRRYIVRAVEDSLRRLGTD
+WIDLYQFHTPDPATPIEETLRALDDLVRAGKVRYVGHSNRAGWQIAQAEYVARELGVERF
+VSAQNHYNLLDRRAELEVVPAAAEFGLGVLPYFPLANGLLTGKYSQGDAPEGSRLSHVRQ
+HMVADADLEQLAAFGRFARERGITEVQAAIGWLAAQGPVSSVIAGATRAAQVVENAAAAD
+WLATAEDLAELDALFPGPEKVALF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000129.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000129.fa
new file mode 100644
index 0000000000000000000000000000000000000000..015f689f3c0aa90ab2023f64011d9dcc31058857
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000129.fa
@@ -0,0 +1,51 @@
+>PROKKA_01450
+MPPGPGALLGGRRVRLLPAILALALGSFAIGTTEFAMMGLLPQAVADLGVGLEAGGVLIS
+MYALGVVIGAPLLAASFARVDRRVTSIVLMLLFVVGHVAAFLAPDMGSMMAARFVSGLPH
+GAYFSAAALAAADLAGPARRGQAVAWVMAGLSVANVLGVPGATALGQAVGWRWMFVIVAV
+CAALCVGATAWLVPSVPAPAGASVGRELRGLASGRLWATVAVGVIGFAGMFALYTYIAPL
+LTEVAGLEERWVPAVLALYGVGMVIGTLVSGALTDRDPVGTLRLSFGLSAVSLAAVALTA
+PWAPVMIVFLFCVAVSGSGIAPSLQVLLVDSAPTAPQLAGSLNHSALNMANAMGAWVGAA
+AIGAGASLRTPPLVGAGIALAGLVLAFLLVRRDVAASPGVRADDGGSPR
+>PROKKA_01182
+MPTPTPAADGAHDRSPRAPRPTRPDPSIPPTAPTGPGALLGGRRVRLLPAILALALGSFA
+IGTTEFAMMGLLPQAVADLGIGLEAGGVLISMYALGVVIGAPLLAASFARVDRRVTSIVL
+MLLFVVGHVAAFLAPDAATMMAARFICGLPHGAYFSAAALAAADLAGPARRGQAVAWVMA
+GLSVANVLGVPAATALGQSAGWRWMFVIVATCAALCVAATAWLVPPVPAPEGASVRRELR
+GLASGRLWATVAVGVLGFAGMFALYTYIAPLLTTVSGLDERWVPAVLALYGVGMVVGTLV
+GGALTDRDPVRTLRLSFALSAVFLLGVGLTAQWAPVMVVFLFLVAVSGSGIAPSLQVLLV
+DSAPTAPQLAGSLNHSALNMANAMGAWVGAAAIGAGASLRTPPLIGAAIALGGLVLALLL
+VRRTPAVGAVPHDGPSAATV
+>PROKKA_01449
+MTTPASGDPAASPSVSARPDPADAAGSPAAGAVGPQSLLGGRRVRLLPAILALALGSFAI
+GTTEFAIMGLLPQAVADLGIGLEAGGVLISMYALGVVVGAPLLAAAFARVDRRTTGIVLM
+LLFTVGHTGAFLAPDTATMMAARFVSGLPHGAYFSAAALAAADLAGPARRGQAIAWVMAG
+LSVANVVGVPAATAIGQAAGWRWMFVIVAACALACVAATAWLVPPVPAPEGASVRRELRG
+LASGRLWATVAVGVIGFAGMFALYTYIAPLLTEVAGLDERWVPAVLALYGIGMVVGTLVS
+GALTDRDPVGTLRLSFGLSAVSLLAVGLTAQWAPVMVLLLFCVAVSGSGIAPSLQVLLVD
+SAPGAPQLAGSLNHSALNMANAMGAWVGAAAIGAGASLRTPPLVGAAIALAGLVLAFVLV
+RRASPTSAATAADAR
+>PROKKA_01353
+MRLLPAILALALGSFAIGTTEFTMMGLLPEAVTDLGVGLETGGVLISMYALGVVVGAPVL
+AAALARMDRKLSSILLMGLFVVGHLASLLAPSLGALMAARFVSGLPHGAFFSAAALAAAD
+LAGPARRGQAIGWVMAGLSVANVVGVPAATALGQAAGWRWMFAVVAACALGCIAATALLV
+PRVPAPAGASVAAEIRGLASGRLWATVAIGVVGFAGMFCLYTYIAPLLTEVSGLHPRWVP
+AVLALYGVGMVIGTLVSGALTDRDPIRTLRWSFGVSALGLLAVSLTAPWWPALLVSLLVV
+ALSGSGIAPALQVLLVDAAPTAPQLSGSLNHSALNMANAMGAWVGAAAVGAGASLRMPSL
+IGAGIALVGLLMSVALLRRPASAPPGA
+>PROKKA_01775
+MSAVSNAPRPRLPWGALLALSASGFLAIFTETIPAGLLPELSRGLGVTESAAGQLVTLYA
+MGSVVAAIPLVAATQTVNRKKVLLAAVATLGAFNLVTAAAPWLPVILAARFVAGAAAALV
+WGVLAGFARSLVAPQLQGRALAVTGLGQPIALAGGVPLGSFAASVMDWRWVFVAISVAAG
+GLAVWIAAAVQNVEGSPRRQREPLRRVVMLPGVRLIFAVTGCWILAHNMLYTYAAPLLNR
+TDLRLDVGLGLFGVASMIGISLVGMVIDRALRLVSAICVTAMCLATTVWLLPQVGIALAV
+ASVVAWGLSFGGAPVLLQTALADRAGEHTDAAQSVFVTVFNLAVAGGGFMGGMLLASSGT
+AGIATTSAVLCLVAVGMIVLARAAFPAGHRHKDETDESVVAPSECSA
+>PROKKA_01400
+MPTPTPAADGAHDRSPRAPRPTRPDPSIPPTAPTGPGALLGGRRVRLLPAILALALGSFA
+IGTTEFAMMGLLPQAVADLGIGLEAGGVLISMYALGVVIGAPLLAASFARVDRRVTSIVL
+MLLFVVGHVAAFLAPDMGSMMAARFVSGLPHGAYFSAAALAAADLAGPARRGQAVAWVMA
+GLSVANVLGVPGATALGQAVGWRWMFVIVAVCAALCVGATAWLVPSVPAPAGASVGRELR
+GLASGRLWATVAVGVIGFAGMFALYTYIAPLLTEVAGLEERWVPAVLALYGVGMVIGTLV
+SGALTDRDPVGTLRLSFGLSAVSLAAVALTASWAPVMIVFLFCVAVSGSGIAPSLQVLLV
+DSAPTAPQLAGSLNHSALNMANAMGAWVGAAAIGAGASLRTPPLVGAGIALAGLVLAFLL
+VRRDVAARPGVRADDDGSPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000130.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000130.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7bac96f1a0e1d804b39e060dcc3164ed780900ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000130.fa
@@ -0,0 +1,79 @@
+>PROKKA_01539
+MTQNSEHTPASADLDPTVAAIAEDIVTEDAAPVAPEQTFADFGVHPAIVEALEAKGIVHP
+FPIQAMTLPVALGGHDIIGQAKTGTGKTLGFGIPALQRAIGPGEPGWDGLEAKGTAGAPQ
+ALIVAPTRELAVQVAGDLTAAAARRPLRIATIYGGRAYEPQIEELQRGVEIVVGTPGRLI
+DLMRQRHLRLDLVNTVVLDEADEMLDLGFLPDVETLLAAVPAVRQTMLFSATMPGPVVAM
+ARRYMTQPTHIRAADPEDEGLTKKDIRQLVYRAHHMDKDELVARALQAEGRGRTIIFTRT
+KRTAARVADELTARGFAAGALHGDLGQGAREQALRAFRNGKVDILVATDVAARGIDVDDV
+THVFNFQAPEDEKTYVHRVGRTGRAGNKGVAVTLVDWEDMPRWSLIDKALGLGQPEPVET
+YSSSPHLFSDLGIPKGTKGRLPQAKRVLEGLEGETLEDLGGPEAKQRDGGRGRGREGGRS
+RDGERGGREGGRGGRGGRGRGGRSGEGRDAARGGSRGERSERSGRGRGEAPAEQRAEGRG
+RGRGEGRKRTASRSETPAARTSEPVAGVELTEARRAERAEARAEARRRRGGRSRTRRRNG
+EVVDG
+>PROKKA_01249
+MTQNSEHTPAPADVDPTVAEIAEDIVTEDAAPVAPEQTFADFGVHPKIVEALEAKGIVHP
+FPIQAMTLPVALGGHDIIGQAKTGTGKTLGFGIPALQRAIGPGEPGWDGLEAKGTAGAPQ
+ALIVAPTRELAVQVAGDLTAAAARRPLRIATIYGGRAYEPQIEELQRGVEIVVGTPGRLI
+DLMRQRHLRLDLVNTVVLDEADEMLDLGFLPDVETLLAAVPAVRQTMLFSATMPGTVVAM
+ARRYMTQPTHIRAADPEDEGLTKKDIRQLVYRAHHMDKDELVARALQAEGRGRTIIFTRT
+KRTAARVADELTARGFAAGALHGDLGQGAREQALRAFRNGKVDILVATDVAARGIDVDDV
+THVFNFQAPEDEKTYVHRVGRTGRAGNKGVAVTLVDWEDMPRWSLIDKALGLGQPEPVET
+YSSSPHLFSDLDIPKGTKGRLPQAKRVLEGLEGETLEDLGGPEAKQRDGGRGRGREGGRS
+RDGERGGRGRGGRSGEGRDRARGGGRGERTERSPRGRDEARAEGRGRGEAPAEQRAEGRG
+RGRGEGRERTASRPETPAARTPEPVAGVELTEARRAERAEARAEARRRRGGRTRTRRSNG
+EVVDG
+>PROKKA_01386
+MNRAHGASGPSRPPCRRPNRNASRHDPELRAHPRPGRRRPPQVADIAEEIVTEEAVETAP
+EQTFADFGVHPAIVQALEAKGIVHPFPIQAMTLPVALGGHDIIGQAKTGTGKTLGFGIPA
+LQRAIGPGEPGWDKLEAQGSAGAPQALIVAPTRELAVQVAGDLTAAAAQRPLRIATIYGG
+RAYEPQIEELQRGVEVVVGTPGRLIDLMRQRHLRLDLVNTVVLDEADEMLDLGFLPDVET
+LLGAVPAVRQTMLFSATMPGPVVAMARRYMTQPTHIRAADPEDEGLTKKDIRQLVYRAHH
+MDKDELVARALQAEGRGRTIIFTRTKRTAARVADELTARGFAAGALHGDLGQGAREQALR
+AFRNGKVDILVATDVAARGIDVDDVTHVFNFQAPEDEKTYVHRVGRTGRAGNKGVAVTLV
+DWEDMPRWSLIDKALGLGQPEPQETYSSSPHLFADLGIPKGTKGRLPKEKRVLEGLEGEV
+LEDLGGPESAPRGRGGRSRDGERDGGRGGRGGRGERGGRGGRSRDDERGGREGGRGGRGE
+RAGREGGRGRDAEQSSARGEEAGESKGRGRGGERAGREGGRGESTGRGRGGRSGESRTRG
+ESRTEASEARAAQPVAGVERTEARMAERAEARAEARRRRGGRTRTRRRNGEVVDG
+>PROKKA_00286
+MKSIDNVNVKLGDDLKAEITAGSKVRIAASAFSIYAFEALREELEGLEELQFIFTDPAFS
+ASSIDGTPRREHRRYFIPPLDIESSLTGTEFEVRLRNRLTQRAIARECADWVRRKVRFRS
+NTSGKGMQPIIGVGDDAAYLPVQDFSTSALGYEAGGALSNVVGKFEGPLEAAGLLTVFDQ
+VWNDPSALEDVTSTVLERIEQVYAENSPRHIYFLILNSIFSDFLADLSEDALPNDRTGYR
+ETKVWRALYDFQRDAAESIIQKLETYNGCILADSVGLGKTFTALAVIQYYEKRNKSVLVL
+CPKKLAENWTTYNNNYVTNPFVEDRFNYDVLAHTDLSRTRGESLGVRLDRINWGNYDLVV
+IDESHNFRNATYGEDRDTRYQRLMEKVIREGVRTKVLMLSATPVNNRFNDLKNQLQLAYE
+GEEENLSQHLNLSTTIDGVFRGAQAAFNEWSKLPAEERTPGRILGMLDFDFFELLDAVTI
+ARSRKQIQRFYDTAAIGAFPTRLPPLSLQEPLSEDKSVPSYNDIFEQLQALNLAVYTPLA
+FVHASRRYKYETGPGEENTDNFRSGRGQAGRETGLKRLMTVNLLKRLESSVHAFRKTLVS
+IESQVDALHRRLESEALGPLRVDAPAVEEDILREDDDVAEALFALPGDLELDLNDVDVLS
+WTSALWHDRETLRELIGEMDKITPERDLKLQRLRRLIRDKATSPLNEGNRKVLVFSAFAD
+TADYLYEQLSPALSAAGLETGIITGGSHSARSTLDGAVDFQTLMTLFSPVSKNRSALMPE
+ETREVDVLIGTDVISEGQNLQDCDFLVNYDIHWNPVRIVQRFGRIDRIGSTNERIQLVNF
+WPDMDLDAYIQLKDRVENRMVMVDVTGTADDNVLTPQQEQDAAYRTAQLKRMREEVVELE
+DTQAGVSITDLGLNEFRSALMAYVREHGDLTRAPRGLHAVVPADPDAGLPAGVIFALHNL
+QADPAMHRGNRLHPYYLVYVGEDGATVLEHTKAKPLLDLLRSAAEKQSVPLADAVRAFNT
+ATAEGTDMAAYSALLTRAIESMVEADEEQDVASLFTAGPTTALTSAIRGLEDFELIAFLA
+VVDTAGTDA
+>PROKKA_01277
+MTENTAAAEAVAPTAPEQTFADFGVQEPIVRALSEKGIVHPFPIQAMTLPVALGGHDIIG
+QAKTGTGKTLGFGIPALQRAVGPDEAGWDTRVAAGAAGAPQALVVAPTRELAVQVAGDLV
+AAAKHRPLRIATIYGGRAYEPQIEELQRGVEVVVGTPGRLIDLLRQKHLRLDAVNTVVLD
+EADEMLDLGFLPDVETLLAAVPEVRQTMLFSATMPGPVIAMARRYMTRPTHIRASDPEDE
+GLTKKDIRQLVYRAHHMDKDELVARALQAEGRGRTIIFTRTKRTAARVAEELTNRGFAAG
+PLHGDLGQGAREQALRAFRNGKVDILVATDVAARGIDVDDVTHVINFQAPEDAKTYVHRV
+GRTGRAGHKGTAVTLVDWEDMPRWSLIDKALGLNQPEPVETYSSSPHLFSDLGIPKGTKG
+RLPKEKRVLAGLDAERLEDLGGPEAKEKAARGGRDERSGSRSGGRGERSGGRGGRAGGGS
+RASREDRPPREDRTPRGERAPRPEKTVKAERAPRAERAPRAEKADRPAAAERSEGASGER
+RRRTRTRRRGGDVIDG
+>PROKKA_01466
+MTQNSEHTPASADLDPTVAAIAEDIVTEDAAPVAPEQTFADFGVHPAIVEALEAKGIVHP
+FPIQAMTLPVALGGHDIIGQAKTGTGKTLGFGIPALQRAIGPGEPGWDGLEAKGTAGAPQ
+ALIVAPTRELAVQVAGDLTAAAARRPLRIATIYGGRAYEPQIEELQRGVEIVVGTPGRLI
+DLMRQRHLRLDLVNTVVLDEADEMLDLGFLPDVETLLAAVPAVRQTMLFSATMPGPVVAM
+ARRYMTQPTHIRAADPEDEGLTKKDIRQLVYRAHHMDKDELVARALQAEGRGRTIIFTRT
+KRTAARVADELTARGFAAGALHGDLGQGAREQALRAFRNGKVDILVATDVAARGIDVDDV
+THVFNFQAPEDEKTYVHRVGRTGRAGNKGVAVTLVDWEDMPRWSLIDKALGLGQPEPVET
+YSSSPHLFSDLGIPKGTKGRLPQAKRVLEGLEGETLEDLGGPEAKQRDGGRGRGRDGGRS
+RDGERGGRGRGGRSGEGRDRARGGGRGERNRGGRSGEGRDDARGGGRGERSGRGRGEAPA
+EQRAEGRGRGRGEGRERTASRSETPAARTSEPVAGVELTEARRAERAEARAEARRRRGGR
+SRTRRRNGEVVDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000134.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000134.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de5c1e8bf4801586917ddc1e3e9a51d3820333b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000134.fa
@@ -0,0 +1,49 @@
+>PROKKA_01581
+MSTTLDLDHAATAPVRRSALEAMWPALTGVYGNPSSAHEAGRAAAALLEDARARVACAIG
+ARAGQVVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGADLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFEEAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARR
+LPRHASFALPGVNGESVLEEAARRGVLASAGSACSAHDAEPSPALLALGLSEDEARTALR
+CTFGPDADAPLLDAAADAIVDAVRTVSALR
+>PROKKA_01291
+MSTTLDLDHAATAPVRRSALEAMWPALTGVYGNPSSAHEAGRAAVALLEDARARVARAIG
+ARAGQVVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGADLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFEEAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARR
+LPRHASFVLPGVNGESVLEEAARRGVLASAGSACSAHDAEPSPALLALGLSEDEARTALR
+CTFGPDADAPLLDAAADAIVDAVRTVAALR
+>PROKKA_01342
+MSAALYLDHAATAPVRRVALEAMWPALTGVYGNPSSAHEAGRAAAALLEDARARVARAIG
+ARAGQVVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGSDLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFAEAEAERAAAADAWSGLRDRFAARALDGVQELVPDARLTGHPARR
+LPRHASFVLPGVNGESVLEEAARRGVLASAGSACSAHSTEPSPALLALGLSEDEARTALR
+CTFGPDADEAMLAAAADAIVDAVRTVSALR
+>PROKKA_01235
+MSTILDLDHAATAPVRRSALEAMWPALTGVYGNPSSAHEAGRAAAALLEDARARVARAIG
+ARAGQIVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGADLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFEEAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARR
+LPRHASFVLPGVNGESVLEEAARRGVLASAGSACSAHDAEPSPALLALGLSEDEARTALR
+CTFGPDADAPLLDAAADAIVDAVRTVTALR
+>PROKKA_01767
+MALDVAAVRQDFPILRSTLADGRPLVYLDSGATSQRPRQVIEAEVEFLTISNAAVKRGAH
+QLAEAATDRYESARETVAAFVGATDPRELVFTRNATEALNLVAYALGNGDDATPEHLRVR
+AGDEILVTEMEHHANLVPWQELARRTGATLRHIPLGEDFALDLVDLGSLVTERTKVVAFT
+HQSNVTGTVNPVATLGEAARAVGALTVLDACQSVPHMPVDVAALGVDFLAFSGHKMLGPT
+GIGALWGRYELLAELPPFLLGGSMIEVVHLDRSTYAEPPARFEAGTPPISQAVGLAAACD
+YLSALGMDAVAEHEHALTARALEHLAGMDRVRVIGAPAGPERSGAVSFAVEGIHPHDVGQ
+VLDSLGVQVRVGHHCAWPLHRRYGVPGTTRASFSVYSTLDEVDAFADGLAQTLAFFQGFG
+R
+>PROKKA_01508
+MSTTLDLDHAATAPVRRSALEAMWPALTGVYGNPSSAHEAGRAAAALLEDARARVARAIG
+ARAGQVVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGADLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFEEAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARR
+LPRHASFVLPGVNGESVLEEAARRGVLASAGSACSAHDAEPSPALLALGLSEDEARTALR
+CTFGPDADAPLLDAAADAIVDAVRTVAALR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000135.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000135.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4bb45f7ef94a78b4881a10c5a3c4dfc8de986ca0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000135.fa
@@ -0,0 +1,48 @@
+>PROKKA_01582
+MSLACVPHPGPVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVA
+SRLTLPSGVATGDVTSNSAVLWARSSGRSRLHATLRAVDEDGKVLRGRFARGLTLRSGWV
+DGATDHTAKILADTLPSDTRFEVTYAFEDEAGRLGESAVARFTTAPGARFGRKTSAAQSF
+VWTADTAGQGYGINPEIGGMRGYAAMHATKPDFFLHSGDTIYADNPIPETLEVAGEPTWR
+NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYADVPVIAQWDDHETTNNWWPGEVLED
+PRYTQVRDVDTLAARARRAWQEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDM
+RTHKGENTPGLETHETPILGEEQLQWLIRGLRASTATWKVIANDLPLGLVVPDGTGQESL
+SNGDDGAPLGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWE
+FVAGPINAGSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRL
+INAAGRTVYSRTLTAA
+>PROKKA_01292
+MRLACVPHPGPVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVA
+SRLTLPSGVATGDVTSNSAVLWARSSGRSRLHATLRAVDEDGKVLRGRFARGLTLRSGWV
+DGATDHTAKILADTLPSDTRFEVTYAFEDEAGRLGESAVARFTTAPGARFGRKTSAAQSF
+VWTADTAGQGYGINPEIGGMRGYAAMHATKPDFFLHSGDTIYADNPIPETLEVAGEPTWR
+NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYADVPVIAQWDDHETTNNW
+>PROKKA_01293
+MDTLAARARRAWQEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDMRTHKGENT
+PGLETHETPILGEEQLQWLIRGLRASTATWKVIANDLPLGLVVPDGTGQESLSNGDDGAP
+LGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFESFWEFVAGPINA
+GSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRLINAVGRTV
+YSRTLTAA
+>PROKKA_01340
+MKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWEFVAGPINAGSFGPNTLDGTFGPRLDF
+EAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRLINAVGRTVYSRTLTAA
+>PROKKA_01234
+MSLACVPHPGSVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVA
+SRLTLPSGVATGDVTSNSAVLWARSSGRSRLHATLRAVDEDGKVLRGRFARGLTLRSGWV
+DGATDHTAKILADTLPSGTRFEVTYAFEDEAGRLGESAVARFTTAPGARFGRKTSAAQSF
+VWTADTAGQGYGINPEIGGMRGYAAMHATQPDFFLHSGDTIYADNPIPETLEVAGEPTWR
+NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYADVPVIAQWDDHETTNNWWPGEVLED
+PRYTQVRDVDTLAARARRAWQEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDM
+RTHKGENTPGLETHETPILGEEQLQWLIHGLRASTATWKVIANDLPLGLVVPDGTGQESL
+SNGDDGAPLGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWE
+FVAGPINAGSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRL
+INANGRTVYARTLTAA
+>PROKKA_01509
+MSLACVPHPGPVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVA
+SRLTLPSGVATGDVTSNSAVLWARSSGRSRLHATLRAVDEDGKALRGRFSRGLTLRSGWV
+DGATDHTAKILADTLPSGTRFEVTYAFEDEAGRLGESAVARFTTAPGARFGRKTSAAQSF
+VWTADTAGQGYGINPEIGGMRGYAAMHATQPDFFLHSGDTIYADNPIPETLEVAGEPTWR
+NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYTDVPVIAQWDDHETTNNWWPGEVLED
+PRYTQVRDVDTLAARARRAWQEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDM
+RTHKGENTPGLETHETPILGEEQLQWLIRGLRASTATWKVIANDLPLGLIVPDGTGQESL
+SNGDDGAPLGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWE
+FVAGPINAGSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEGGREFRVRL
+INAAGRTVYSRTLTAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000145.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000145.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa93c3d66fba04e0681ca3454af83519d173ca4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000145.fa
@@ -0,0 +1,30 @@
+>PROKKA_01790
+MDAPASDLTGKARIRHAALRLFAHHGVEGTSMRAIAEEASVTVGLITHHYGSKAGLHREV
+DAAVADDFAAAIASVPAEGTARDVTLRRDAAVAEMLRARPDVLEYVRRHVLLGEPAADSQ
+LVEKLTALAREQVRQLRAAGLISGRRDEVPQVVSMIMRMLGELFFEPLVDRIVDAVDRDA
+ARPAVVVRVQAAEDETARGGRA
+>PROKKA_02051
+MNTPLPFDQDDLSSPARLRLAALELYAERGVEMASVREIAQRAGVAPGLVRHHFGSKAGL
+TRAVDDDVLRLIAATLDEVPLVGTPQEVSAARDAAFADLLADHPVVGAYVRRSLLEAGGE
+TESLLERLVDLTTEQTERLRRSGFAPRRSMPTSVFGTVIRQMGHLMVDPSADRIWRRIAE
+TQEGAAEQASPRVRLVVDPPR
+>PROKKA_01757
+MNTPLPFDQDDLSSPARLRLAALELYAERGVEMASVREIAQRAGVAPGLVRHHFGSKAGL
+TRAVDDDVLRLIAATLDEVPLVGTPQEVSAARDAAFADLLADHPVVGAYVRRSLLEAGGG
+TESLLERLVDLTTEQTERLRRSGFAPRRSMPTSVFGTVIRQMGHLMVDPSADRIWRRIAE
+TQEAAAEQRSPRVRLVVDPPR
+>PROKKA_01086
+MDAPASDLTGKARIRHAALRLFAHHGVEGTSMRAIAEEASVTVGLITHHYGSKAGLHREV
+DAAVADDFAAAIASVPAEGTARDVTLRRDAAVAEMLRARPDVLEYVRRHVLLGEPAADSQ
+LVEKLTALAREQVRQLRAAGLISGRRDEVPQVVSMIMRMLGELFFEPLVDRIVDAVDRDA
+ARPAVVVRVQAAEDETARGGRA
+>PROKKA_00729
+MNTARPLTREDLSSAARLRLSALELYAERGEHAASIRDVGRHAGVAPGLVRHHFGSKDGL
+TRAVDDDIIDLVRATLEAVPLEGTPLEISAARDAAFQELLQERPLIGGYLAQALTASRAS
+GESVLDRLVDLSAEQTRQLIDRGLDPRRGLRTSVFTTVVRQVAVFLVAPVAERAWNRLGH
+TLEGASDVAPMPPVRVVVGPAPEEDRR
+>PROKKA_01985
+MNTPLPFDQDDLSSPARLRLAALELYAERGVEMASVREIAQRAGVAPGLVRHHFGSKAGL
+TRAVDDDVLRLIAATLDEVPLVGTPQVVSAARDAAFADLLADHPVVGAYVRRSLLEAGGE
+TESLLERLVDLTTEQTERLRRSGFAPRRSMPTSVFGTVIRQMGHLLVDPSADRIWRRIAE
+TQEDAAEQASPRVRLVVDPPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000151.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000151.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c3e8fa8916a30ea6a1f98d74d2e2029208987bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000151.fa
@@ -0,0 +1,57 @@
+>PROKKA_01921
+MVLPVLPALATPPLLTALDRLLAGETVPSGVEGDIQDGAAATTRAFGVEWGTLLTVLMAF
+AIGAAVVYLALQVARVVLVRRPAFQHGAARLSLPAAVAAGLLASRIWLGVMAEEQAWYRP
+ASFLLLIAVAAAGAWAAWRLVGVIEAGILGRYQETGVEHRRERRIRTQTILIRRILNAVI
+VVVVVAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDAIRVGD
+VVDMEGVFGTVEEITLSNVVVKLWDGRRVVYPSSHFTTQPFENWTRVGTEVSGVVELDVD
+WRVPMDALRARLAQLLESTDLWDGREHALQVTDATGGVVRIRAVVSARNSGDLWDLRCLV
+REDLVAFLRHEHPEGIVVQRMVVRHPAHDDAAPASEGSDAGARGGDRTGEPGPDGSGVAA
+REPRPRTAPLPRVDGADPRPHTLTTPLTRVGDHSGLYTGSMTAVQRNRELAGPGEEAFAE
+RRAQQAKQAAEAAAADEAGRRSGAGSHADGPLDDAVTRRRQDDED
+>PROKKA_01617
+MVLPVLPALATPPLLTALDRLLAGETVPSGVEGDIQDGAAATTRAFGVEWGTLLTVLMAF
+AIGAAVVYLALQVARVVLVRRPAFQQGAARLSLPAAVAAGLLASRIWLGVMAEEQTWYRP
+ASFLMLIAVAAAGAWAAWRLVGVIEKGILGRYQETSVEHRRERRIRTQTILIRRILNAVI
+VVVAVAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDAIRVGD
+VVDMEGVFGTVEEITLSNVVVKLWDGRRMVYPSSHFTTQPFENWTRVGTEVSGVVELDVD
+WRVPMDALRARLAQLLESTDLWDGREHALQVTDATGGVVRIRAVVSARNSGDLWDLRCLV
+REDLVAFLRHEHPEGIVVQRMVVRHPAHDDAAPASEGSDAGARGGDRTGEPGPDGSGVAA
+REPRPRTAPLPRVDGADPRPHTLTTPLTRVGDHSGLYTGSMTAVQRNRELAGPGEEAFAE
+RRAQQAKQAAEAAAADEAGRRSGAGSHADGPLDDAVTRRRQDDED
+>PROKKA_00786
+MDLPQITPLAVAVGLAVAVVGWLLGRLLGAGVAWLFARRGRSPSSARVFGKLVAAGITVL
+SLGAAVTVVFPSVKPVDLLGGIGVISIAAGIAFQTVLGNMFAGMVILARDRFRVGDQIQV
+GEHAGNVVEMGLSSTAVKTFDGRLVLIPNQMLHSQAVTVQTGFSAVRSSLRVDVETGNDL
+ARTREIAVRAMSELPQVLRDPAPQALLASVGVTTVGMDLRFWSGARQMETKEAMDAVIHA
+VLTAFEKNGVATGDDVRVVDAGPELRRILEGPGAPRGQGGPDYPGGLAGPGEPDRAARPG
+SD
+>PROKKA_00939
+MLLAALSGPASPPVLGSLARLFAGENVPAGVEGNVQDGAAATTAALGVEWGTLLTVLVAF
+AVGATLVYAALQVTRVVLVRRPAFQHGAARLSLPAAVAAGLLASRIWLGVMAEEQTWYRP
+ASFLLLIAVAAAGAWAAWRLVGVIEAGILGRYQETGVEHRRERRIRTQTILIRRILNAVI
+VVVAIAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDAIRVGD
+VVDMEGVFGTVEEITLSNVVLKLWDGRRMVYPSSHFTTQPFENWTRVGTEVSGVVELDVD
+WRVPMPALRERLTQLLDSTDLWDGRESSMQVTDAIGGTVRIRAVVSARNSGDLWDLRCLV
+REDLVTFLRSEHPEAIVVQRVVERHPAHDDAVPASEGSDAGARGGDPTGEPGPDGSGVAA
+REPRPRTAALPRVEGGEPRPDTVTTPLTRVDDHAGLYTGSITAVQRNRELHGPGEDAFAE
+RRAQQAKQAAEAATADEAGRRSGAGSHADGLLDDAVTRRRQDDED
+>PROKKA_00874
+MPVPALLPVLAQTASSDAALSDAVLSAADQVVPGSVEQDVQQGASAASAALGVEWATVAA
+VLGAFLAGGLVVLGVFLVARLALFRRDRLKADAARLTVPVSLFAGFLTARVGLEVMAHGQ
+PWFEAAAFVLLLAVAASAAWAAWRVVDVVESGILARYHQPGVNDRRERKIRTQTMLLRRV
+LNAVIVVVALAVVLLAIPQVRSLGAGLLASAGLISVIAGLAVQSTLTNVIAGFQLAFTDS
+IRVGDVVDMQGVFGTVEEITLSNVVVKLWDGRRMVYPSKHFTSEPFENWTRTGAAVAGVV
+EMDVDWRVPMDPLRARLTELLESTDLWDGRENAMQVIDAVGGMVRIRAVVSAKNSGELWD
+LRCLVREDLVGFLRAEYPEGIYTQRLVERRPSDPAPEAHDDPAPDAHDDAAPAAAPAAPA
+PSDRGSSTRAEPTPQTRPMPTVTGSVPLARAGENASLYTGSIRAVERNQEMDGPGEEAYA
+ERRARAAEREDRAARDAGRGGAHAARS
+>PROKKA_01841
+MVLPVLPALATPPLLTALDRLLAGETVPSGVEGDIQDGAAATTRAFGVEWGTLLTVLMAF
+AIGAAVVYLALQVARVVLVRRPAFQHGAARLSLPAAVAAGLLASRIWLGVMAEEQAWYRP
+ASFLLLIAVAAAGAWAAWRLVGVIEAGILGRYQETGVEHRRERRIRTQTILIRRILNAVI
+VVVVVAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDAIRVGD
+VVDMEGVFGTVEEITLSNVVLKLWDGRRMVYPSSHFTTRPFENWTRVGAEVSGVVELDVD
+WRVPMDALRARLTQLLESTDLWDGREHALQVTDATGGIVRIRAVVSARNSGDLWDLRCLV
+REDLVSFLRHEHPEGIVVQRMVVRHPAHGDASPASEGSDAEARGGDRTGEPGPDGSGVAA
+REPRPRTAPLPRVDGADPRPDTLTTPLTRVGDHSGLYTGSMTAVQRNRELAGPGEEAFAE
+RRAQQAKQAAEAAAADEAGRRSGAGSHTDGLLDDAVTRRRQDDED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000157.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000157.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a57fc5c2ed1509fdf3ed5785bbddf0a920e48c52
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000157.fa
@@ -0,0 +1,36 @@
+>PROKKA_02018
+MTDQQHTPDTVPSSVPAVVGVLGGGRMGGGIAHAFLVSGSSEVVVVERDPQSAEAAKERI
+EADLAASLERGKIDGDLDEWAQRLTVSVDRADFARCDLVVEAVFEDMQVKIDALTDVEAH
+LREDAWLASNTSSLSIGEIATHLQRPERFCGLHYFNPVPASKLVEVVIGEQTGAELQALS
+TEWVRGLGKTPVVVKDAPGFASSRLGVAIALEAIRMVEEGVASPEDIDAAMVLGYKFPVG
+PLALTDIVGLDVRLGIAEYLESQLGERFAPPQLMRDMVARGELGRKSGKGFFDYR
+>PROKKA_00095
+MGQTQKVAVIGAGAMGSQIAMLAAMAGCQTTMVDVDQERLDAARDQVLQTAQRQAERGRL
+EADAVEQAAARLTTEPDLAAAVAEADVVVEAIIEDLEAKRDLFAQLGEHTRPDTILATNS
+SSIVSSRLAQIPHPERVCNMHFFNPALVMRLVEVVGGDHTSQKTIETVKALAERMGKTPV
+VVRQEIFGFIANRIVAAIFDEAISLYEQGIASAEDIDTAVTHGLGHPIGPFALLDLTGID
+VNVGIKRLEAQETGDPSRGPSQTLLDLMAQGRLGRKTGHGFYEYGDR
+>PROKKA_01727
+MTDQQHTPDTAPSSVPAVVGVLGGGRMGGGIAHAFLVSGSSEVVVVERDPRSAEAAQERV
+ESDLAASLDRGKIDGDLDEWAQRLTVTVDRADFARCDLVVEAVFEDMQVKIEALTDVEAH
+LREDAWLASNTSSLSIDEIATHLQRPERFCGLHYFNPVPASKLVEVVIGEQTGAELQALS
+TEWVRGLGKTPVVVKNAPGFASSRLGVAIALEAIRMVEEGVASPEDIDAAMVLGYKFPVG
+PLALTDIVGLDVRLGIAEYLESQLGERFAPPQLMRDMVARGELGRKSGKGFFDYR
+>PROKKA_00803
+MTETPDTSRASVPAVVGVLGGGRMGGGIAHAFLTSGSSEVVVVERDPQSAEAAKERIESD
+LAASLERGKLDGDLDVWAERLTVSVDRADFARCDLVVEAVFEDMQVKIDALTDVESHLRE
+DAWLATNTSSLSVDEIATHLRRPERFCGLHYFNPVPASKLVEVVIGAQTGDELKALTTEW
+VRGLGKTPVVVKDAPGFASSRLGVAIALEAIRMVEEGVASPEDIDAAMVLGYKFPVGPLA
+LTDIVGLDVRLGIAEYLESQLGERFAPPQLMRDMVARGELGRKSGKGFFDYSKG
+>PROKKA_00762
+MTENQQTTGSVPSIVGVLGGGRMGGGIAHAFLVSGSSEVVVVERDPQSAEAAQERIVADL
+AASLERGKIDGDLNVWAQRLTVSVDRTDFARCDLVVEAVFEDMQVKIEALTDVEAHLRED
+AWLASNTSSLSIDEIATHLQRPERFCGLHYFNPVPASKLVEVVIGEQTGAELQALSTEWV
+RGLGKTPVVVKDAPGFASSRLGVAIALEAIRMVEEGVASPEDIDAAMVLGYKFPVGPLAL
+TDIVGLDVRLGIAEYLESQLGERFAPPQLMRDMVARGELGRKSGKGFFDYR
+>PROKKA_01955
+MTDQQRTPDTAPSSVPAVVGVLGGGRMGGGIAHAFLVSGSSEVVVVERDPQSAQAAKERI
+EADLAASLERGKIDGDLDEWAQRLTVSVDRADFARCDLVVEAVFEDMQVKIEALTDVEAH
+LREDAWLASNTSSLSIDEIASHLQRPERFCGLHYFNPVPASKLVEVVIGEQTGAELQALS
+TEWVRGLGKTPVVVKDAPGFASSRLGVAIALEAIRMVEEGVASPEDIDAAMVLGYKFPVG
+PLALTDIVGLDVRLGIAEYLESQLGERFAPPQLMRDMVARGELGRKSGKGFFDYR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000163.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000163.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9fc8af54d28472868b2895fd7a8466c7e8ad6c08
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000163.fa
@@ -0,0 +1,123 @@
+>PROKKA_02098
+MATADSGDVLPHLRTEAIRAVVGPTSADRGFAVAASGAVGRLRYDAATGRLSASVQGTAP
+SPYRVQVQLQEAYDDAAEDGAGALMEPVGGRCTCPVGTDCKHVAAALYQVVRLDADQALD
+DARRKLAEMVTTADALPAPAGRGHDGGGPAGLDAPAADGAAPPPPAGLDWRRVMEPLAGL
+HGPRRVGTPPALAIGVELVAESSRNAFQQWGPATAGEEQVREGRPLYVTVRPLKRGAKGT
+WIKGGLTWKAFQFPRAEFAPAQERAMRLIWRQVQAEDSYPGDAWFGLHVFDSPRIWQLLA
+EAREVGVELVPLGLLTDVVLEAPVAVGLDVTAAPDGGLDVAPSLDPAPPGPGLSGVHAVG
+GIGFYRVELTDEEAVLHLIPAARPVPEAVQQLVLAGGPVRVPAADREEFLGRIYPRLRGA
+LPVTSGDASVELPEFEPPVLRLRADFRPGHELVLRWSWLYFDPPRELGLDAGGDPLRDTR
+HEDAVLRAVAELWPRAGRAEEQVLEGVGAARFSEQVLPLLQRADHVRVDVTGDRPDYREL
+KAAPRIEVGTKATQNDWFDLGVQVSVDGHVLPFVELFTALVQGRTTLILADGSYLGLDHP
+AFDRLRALLSEAATLQEWTPEHTPVSRHQVGFWEDLKELADEVDEDPEWTAAVGRLAAVE
+RLPEAPRPAGLKADLRPYQEEGLRWLAFLWEQDLGGILADDMGLGKTVQTLALFAHARQA
+RPEPPPFLVVAPSSVVSVWAAEAEKFTPDLDVRVLDTTTRKRGTAVADEVAGADVVVTSY
+TLLRIDAGQYGGLDWGGVVFDEAQFLKNRAAKVHTVARDLRAPFRLAITGTPMENSLSDL
+WALLDVVVPGLFPSHRRFRETYVTPIETGGDPERMAALRRRVRPFMLRRSKELVAKDLPS
+KQEQILQVELEPAHRKLYDRVLQRERRKVLGLLGDMDGNRFTIFTSLTLLRMLALAPQIV
+DDQYASVPSSKLERFLDDLTEVIGEGHRVIVFSQFTSFLRVIAEELDHLEIEHAYLDGST
+RGRADVIRGFREGEAPVFLISLKAGGFGLTLTEADYVFLMDPWWNPAAEAQAVDRAHRIG
+QERTVMVYRLVSEGTIEEKVLELQRRKAELFGALMDESDDSGAGAFTDSLTAEDIREMLG
+AEE
+>PROKKA_01805
+MATADSGDVLPHLRTEAIRAVVGPTSADRGFAVAASGAVGRLRYDAATGRLSASVQGTAP
+SPYRVQVQLQEAYDDAAEDGAGALMEPVGGRCTCPVGTDCKHVAAALYQVVRLDADQALD
+DARRKLAEMVTTADALPAPAGRGHDGGGPAGLDAPAADGAAPPPPAGLDWRRVMEPLAGL
+HGPRRVGTPPALAIGVELVAESSRNAFQQWGPATAGEEQVREGRPLYVTVRPLKRGAKGT
+WIKGGLTWKAFQFPRAEFAPAQERAMRLIWRQVQAEDSYPGDAWFGLHVFDSPRIWQLLA
+EAREVGVELVPLGLLTDVVLEAPVAVGLDVTAAPDGGLDVAPSLDPAPPGPGLSGVHAVG
+GIGFYRVELTDEEAVLHLIPAARPVPEAVQQLVLAGGPVRVPAADREEFLGRIYPRLRGA
+LPVTSGDASVELPEFEPPVLRLRADFRPGHELVLRWSWLYFDPPRELGLDAGGDPLRDTR
+HEDAVLRAVAELWPRAGRAEEQVLEGVGAARFSEQVLPLLQRADHVRVDVTGDRPDYREL
+KAAPRIEVGTKATQNDWFDLGVQVSVDGHVLPFVELFTALVQGRTTLILADGSYLGLDHP
+AFDRLRALLSEAATLQEWTPEHTPVSRHQVGFWEDLKELADEVDEDPEWTAAVGRLAAVE
+RLPEAPRPAGLKADLRPYQEEGLRWLAFLWEQDLGGILADDMGLGKTVQTLALFAHARQA
+RPEPPPFLVVAPSSVVSVWAAEAEKFTPDLDVRVLDTTTRKRGTAVADEVAGADVVVTSY
+TLLRIDAGQYGGLDWGGVVFDEAQFLKNRAAKVHTVARDLRAPFRLAITGTPMENSLSDL
+WALLDVVVPGLFPSHRRFRETYVTPIETGGDPERMAALRRRVRPFMLRRSKELVAKDLPS
+KQEQILQVELEPAHRKLYDRVLQRERRKVLGLLGDMDGNRFTIFTSLTLLRMLALAPQIV
+DDQYASVPSSKLERFLDDLTEVIGEGHRVIVFSQFTSFLRVIAEELDHLEIEHAYLDGST
+RGRADVIRGFREGEAPVFLISLKAGGFGLTLTEADYVFLMDPWWNPAAEAQAVDRAHRIG
+QERTVMVYRLVSEGTIEEKVLELQRRKAELFGALMDESDDSGAGAFTDSLTAEDIREMLG
+AEE
+>PROKKA_00681
+MATADSGDVLPHLRTEAIRAVVGPTSADRGFAVAASGAVGRLRYDAATGRLSASVQGTAP
+SPYRVQVQLQEAYDDAAEAGAGALMEPVGGRCTCPVGTDCKHVAAALYQVVRLDAHQALD
+DARRKLAEMVTTADALPAPAGRGHDDAARPDAGPRGAAAGPDGESAAPEAPHSGLDWRRV
+MEPLAGLDAPRRLGAPPALAIGVELVAESSRNAFQQWGPAPAGEDQVREGRPLYVTLRPL
+KRGAKGTWIKGGLTWKNFQFGRAEFAPAQERAMRLIWRQLQAEDSYPTDAWFGLHSFDSP
+RIWQLLAEAREVGVELVPLGLLTDVVLEAPAAVGLDVARAPDGGLDVAPSLDPAPPGRGL
+AGVHAVGGIGFYRVELTDEEAVLHLIPAERPVPEAVQQLVLAGGPVRVPAVDREEFLGRI
+YPRLRGALPVTSGDASVELPEFEPPVLRLRADFRPDHELVLRWSWLYFDPPRELGLDAGG
+DPLRDTRHEDAVLRAVAELWPRAGRAEEQVLEGVAAARFSEQVLPLLQQAEHVRVDVTGH
+RPDYRELKSAPRIEVGTKATKNDWFDLGVQVSVDGHVLPFVELFTALVQGKTTLILADGS
+YLGLDHPAFDRLRALLSEAATLQEWTPENTAVSRHQVGFWEDLKELADEVEEDPEWTAAV
+GRLAAVERLPEAPEVPGLQADLRPYQEDGLRWLAFLWEQDLGGILADDMGLGKTVQTLAL
+SAHARQARPERPPFLVVAPSSVVSVWAAEAQTFTPDLDVRVLDTTVRKRGTDVAAEAAGA
+DVVVTSYTLLRIDAGQFGGIDWGGVVFDEAQFLKNRAAKVHTVARDLRAPFRLAITGTPM
+ENSLTDLWALLGVVVPGLFPSHRRFREAYVTPIETGEDPERMVALRRRVRPFMLRRSKEL
+VAKDLPPKQEQVLNVELEPAHRKLYDRVLQRERRKVLGLLGDMDGNRFTIFKSLTLLRML
+ALAPQIVDEQYASVPSSKLERFLDDLTEVIAEGHRVIVFSQFTSFLRVIAEELDHMEVAH
+AYLDGSTRGRADVIRGFREGQAPVFLISLKAGGFGLTLTEADYVFLMDPWWNPAAEAQAV
+DRAHRIGQERTVMVYRLVSEGTIEEKVLELQRRKAELFGALMDESDDSGAGAFTDSLTAE
+DIRELLGAED
+>PROKKA_01500
+MNLPLTDYQAKYYAHELQRSYANDHVGKLAGLLFDAQVEPKPHQIDAALFALQTPFLPGV
+ILADEVGLGKTIEAGIVISQYWAERRRSILIVAPSSLRQQWQQELYEKFLIPSAILDPKS
+KDSLLAAAGGRSAQVLICSYEFALRHETSLLKAWDLVVADEAHRLRNYWTGKTKAAEAVA
+HVVSGAHKTVLLTATPLQNKLEELYGLVSIFDPNYFYSLDAFRERYVKNRDLGGDDDLVE
+RVATVSKRTLRRDADKYIHFTKRLPLTVEFTPSPDEARLYDLVNDYLQRDELFAFAGSQR
+HLSALIIRKRLGSSTYAVASTLENIANRLAEEVAAGQRRDGRGGLVTADFTVDDEITSEE
+LEEAEEIEGAGPASRPSSSPLDESLLEAMRAEVAELRDYAALARSITENQKAVKLGEALD
+LGFERLRELGAPQKAIIFTDSTKTQEYIARSLREAGRGDGLVLFNGSNNGPEQTAIYQAW
+LKANQDGDLITGIAAVDRRKALVDYFRTEGTIMIATEAAAEGINLQFCSMLVNYDLPWNP
+QRVEQRIGRVHRFGQKHNVVVVNFSNKGNIAEQRILELLTNKFQLFSSVFGASDEVLGAI
+EDGLDFEKTISDILTRCRTADELDAAFRELEGQYASEISREMASAKAKVFDNLDPHVQDR
+LKAYDTQSGEVLNKFERLLLAVTRHELDRFATFEGDGRAFVLNESPVQDVPTGRYFFKSQ
+PLENAHQYRYASSLAQYVVDTSKGHETPARELTFSLGQSERVSSAIRALEGTSGELTVNL
+ATFRMKARDEDVSESYMLAGALTDDGQWLDEEYVADILDLACISVGEQPVAIDESRFTPH
+LDARRAELEKEVQGRNSRYYDQQEELLYRNQQDRKAEHEGKIREYRAKEKEARKLARQAD
+DPMEQLRLKKEARKWEQRAEEADEDFRDTRKKLRAEADKYLELIEQSLQGTQETEHLFTI
+RWRITT
+>PROKKA_00595
+MAPGVSGDPLPHLRTEAIRALVGPTSADRGFDIAAEGGVLRVTYDASRLRLTSAVRGTAP
+QPYRQAVRLQPSGETGPDGEPLLEPTAGRCQCPVGEDCKHVAAALYEITRRHADAARHAA
+REELASRVTTADRLPSPERAGAAPARPDAPAPEAGLPWRGVLESLAGLDGGPRRLAPPPD
+LAIGVELVAESSRNAFAQWGPAPAGEEHLREARLLYVIVRPLKRGAKGTWIKGGLTWKAF
+QFPRAEYDPAQERALRLIWRQLQAEDSYPTEGWFGLHAFDSPRIWQLLAEAQEAGVELVP
+QGILADVVLDAPVEVGLDVASAPDGGLEVAPSLAPAGGAGEGAPADDAAARPDAERLRDT
+HAIGSIGFYRADEEEDGTWTLHLLPAVRRVPEPVQEMVLAGRPVHVPTADREEFLGRIYP
+RLRAALDVGSADASVELPEFEPPVLRLQADFRPGHRLVLRWSWLYFDPPRELGLGHDGLR
+DPRHEEAVLRAAAQVWPRVGRAEEQELEGVGAARFSESVLPQLQRLDHVRVDVTGERPDY
+RELKAAPRIEVSTKAAQNDWFDLGVQVSVDGHVLPFVELFTALVHGKTTLMLQDGTWLGL
+DHPAFDRLRALLSEAAALQEWTPEHTTLSRHQVGFWEDLKELADEAEEDPEWTAAVGRLA
+AVERLPEAPAVPGLKAELRPYQEDGLRWLRFLHDQDLGGILADDMGLGKTVQTLALMAYA
+RAEHPDRPPFLVVAPSSVLSVWASEAAKFTPGLDVRVLDTTTRKRGTSVTEAAEGADVVV
+TSYTLLRIDAAQHADASWAGIVLDEAQFLKNRASKVHQVARDLRAPFRLAITGTPMENSL
+SDLWALLEVVVPGLFPSHRRFRETYVTPIETGEHPERMASLRRRVRPFMLRRSKELVAKD
+LPPKQEQVLRVELDAAHRKVYDRVLARERRKVLGLLGDMDGNRFTIFKSLTLLRMLALAP
+QIVDREYAAVPSSKLERFLDDLEEVLAEGHRVIVFSQFTSFLRVVAEELDAMEVEHAYLD
+GSTRNRAEVIQDFREGDAPVFLISLKAGGFGLTLTEADYVFLMDPWWNPAAENQAVDRAH
+RIGQERTVMVYRMVSEGTIEEKVLELQQRKAELFGALMDESDDSGAGAFTDSLTADDIRE
+LLGAEE
+>PROKKA_02038
+MATADSGDVLPHLRTEAIRAVVGPTSADRGFAVAASGAVGRLRYDAATGRLSASVQGTAP
+SPYRVQVQLQEAYDDAAEDGAGALMEPVGGRCTCPVGTDCKHVAAALYQVVRLDADQALD
+DARRKLAEMVTTADALPAPAGRGHDGGGPAGLDAPAADGAAPPPPAGLDWRRVMEPLAGL
+HGPRRVGTPPALAIGVELVAESSRNAFQQWGPATAGEEQVREGRPLYVTVRPLKRGAKGT
+WIKGGLTWKAFQFPRAEFAPAQERAMRLIWRQVQAEDSYPGDAWFGLHVFDSPRIWQLLA
+EAREVGVELVPLGLLTDVVLEAPVAVGLDVTRAPDGGLDVAPSLDPAPPGLGLSGVHAVG
+GIGFYRVELTDEEAVLHLIPAARPVPEAVQQLVLAGGPVRVPAADREEFLGRIYPRLRGA
+LPVTSGDASVELPEFEPPVLRLRADFRPGHELVLRWSWLYFDPPRELGLDAGGDPLRDTR
+HEDAVLRAVAELWPRAGRAEEQVLEGVGAARFSEQVLPLLQRADHVRVDVTGDRPDYREL
+KAAPRIEVGTKATQNDWFDLGVQVSVDGHVLPFVELFTALVQGRTTLILADGSYLGLDHP
+AFDRLRALLSEAATLQEWTPEHTPVSRHQVGFWEDLKELADEVDEDPEWTAAVGRLAAVE
+RLPEAPRPAGLKADLRPYQEEGLRWLAFLWEQDLGGILADDMGLGKTVQTLALFAHARQA
+RPERPPFLVVAPSSVVSVWAAEAEKFTPDLDVRVLDTTTRKRGTAVADEVAGADVVVTSY
+TLLRIDAGQYGGLDWGGVVFDEAQFLKNRAAKVHTVARDLRAPFRLAITGTPMENSLSDL
+WALLGVVVPGLFPSHRRFRETYVTPIETGGDPERMAALRRRVRPFMLRRSKELVAKDLPS
+KQEQILQVELEPAHRKLYDRVLQRERRKVLGLLGDMDGNRFTIFTSLTLLRMLALAPQIV
+DDQYASVPSSKLERFLDDLTEVIGEGHRVIVFSQFTSFLRVIAEELDHLEIEHAYLDGST
+RGRADVIRGFREGEAPVFLISLKAGGFGLTLTEADYVFLMDPWWNPAAEAQAVDRAHRIG
+QERTVMVYRLVSEGTIEEKVLELQRRKAELFGALMDESDDSGAGAFTDSLTAEDIREMLG
+AEE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000164.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000164.fa
new file mode 100644
index 0000000000000000000000000000000000000000..186e3e7a2d0627d7d453b4efbbb8e8d955a79cdc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000164.fa
@@ -0,0 +1,90 @@
+>PROKKA_02122
+MTHPASSTPAGPQSETTRRVDLDVTGMTCASCVGRVERKLGKLEGVTASVNLPLEQATVT
+APAGVSDEELVAAVEKAGYGATVRRPAPPAGHAGHAGHAHTSEHGEEHAADHDGVDHHDH
+MAHGPSEDVLTPRLIGAAVLTVPLVLISMVPALQFPHWGWVAFALAAPVALWAAWPFHSA
+AFRAARHGSSTMDTLVSLGVLVSFSFSAVELILAPDMTAHVGGTMAEMAHHSLYFETAAV
+ITTFLLLGRWLEARAKREAGAALRALLDLGAAQATLYDPETHDERTVPAESLAPGDVVLI
+RPGEKVPTDAEVLEGTSAVDASLLTGESVPVEVGPGDALTGATLNTSGRLVARATRVGSD
+TTLAQMGRLVSEAQTGKARVARLADRISAVFVPIVLGIAVLTFAVWMIVTGDLPSALRAG
+VAVLVIACPCALGLATPVGLLAGTGRAAQLGILIRGPEVLEDSRTVDTIVLDKTGTVTEG
+RMALADVLVLDPAFVAETGASRSAFVDETAPDQAADVLLTLAAAVERGSEHPIARAIVAG
+AEERGLTVPGVADFASTAGGGVSGLVALPHDDGAPGSGAHGAAGPDPVRVAVGRGSVLET
+ALDGGIPAEHRAAFEAAEQAGATAVWVAVGGRVAGVLSVRDTVKETSADAIARLKELGLR
+PLLVTGDNAAVATQVAAAVGIPAEDVVAGVRPEDKVDVVRRLQSEGHVVAMVGDGVNDAP
+ALAAADMGIAMGSGTDVAREAAQITVMGDDLHQVVQALDLSRRTLGIIRMNLFWAFAYNV
+LGIPVAALGLLNPMIAGGAMAASSVLVVLNSLRLTRYAR
+>PROKKA_01830
+MTHPASSTPAGPQSETTRRVDLDVTGMTCASCVGRVERKLGKLEGVTASVNLPLEQATVT
+APAGVSDEELVAAVEKAGYGATVRRPAPPAGHAGHAGHAHTSEHGEEHGEEHGEEHAADH
+DGVDHHDHMAHGPSEDVLTPRLIGAAVLTVPLVLISMVPALQFPHWGWVAFALAAPVALW
+AAWPFHSAAFRAARHGSSTMDTLVSLGVLVSFSFSAVELILAPDMTAHVGGTMAEMAHHS
+LYFETAAVITTFLLLGRWLEARAKREAGAALRALLDLGAAQATLYDPETHDERTVPAQSL
+APGDVVLIRPGEKVPTDAEVLEGTSAVDASLLTGESVPVEVGPGDALTGATLNTSGRLVA
+RATRVGSDTTLAQMGRLVSEAQTGKARVARLADRISAVFVPIVLGIAVLTFAVWMLVTGD
+LPSALRAGVAVLVIACPCALGLATPVGLLAGTGRAAQLGILIRGPEVLEDSRTVDTIVLD
+KTGTVTEGRMALADVLVLDPAFVAETGASRSAFVAETAPDQAADVLLTLAAAVERGSEHP
+IARAIVAGAEERGLTVPDVADFASTAGGGVSGLVALPHDDGALGSGAHDAAGPAPVRVAV
+GRGSVLETALDGGIPAEHRAAFEAAEQAGATAVWVAVGGRVAGVLSVRDTVKETSADAIA
+RLKELGLRPLLVTGDNAAVATQVAAAVGIPAEDVVAGVRPEDKVDVVTRLQSEGAVVAMV
+GDGVNDAPALAAADMGIAMGSGTDVAREAAQITVMGDDLHQVVQALDLSRRTLGIIRMNL
+FWAFLYNVLGIPVAALGLLNPMIAGGAMAASSVLVVLNSLRLTRYAR
+>PROKKA_00658
+MAASPSPSDRAAEALGRTALQDAEGTRRVDLDVTGMTCASCVGRVERKLGKIEGVEASVN
+LPLERATVTVPASVSDQDLLDAVAKAGYTAAVRPDAQARPARRGRHDDGGTRPGADHAGH
+PDHRDHETPGEDHAGHEGHDDHMAHGPRADVLRPRLIVAAILTVPIVLISMVPALQFPHW
+GWVALALSAPVALWCGWPFHSAAFRAARHGSSTMDSLVSVGVLVAWTYSAVELVLEPGMT
+AHVGGTMAEMMRHSLYFETAAVITTFLLLGRWLEARAKREAGRALRSLLDLGAAQATVLP
+NWDAQTPHPSTSAAATPVAAVSGDFSEVEAASTSDKSPQTHHDGGADALTERVIPAEELE
+PGDVVVIRPGEKVPTDAVVLEGTSAVDASLLTGESVPVEVGPGDEITGATVNTSGRLIAR
+ATRTGADTTLAQMGRLVSDAQTGKARVARLADRISAVFVPIVLVLAVLTFVVWMLVTGGD
+VAPALRAGVAVLVIACPCALGLATPVGLLAGTGRASQLGILIGGPEVLEDTRTVDTIVLD
+KTGTVTEGRMALSDVHAFADDAALTEDRILALAAAVEAGSEHPIARAIVAGARERGLTVP
+RVADFASTAGGGVTGTVALPEAGSVRVAVGRGDLVGEPSPAQQAEFDAAEQAGATAVWVA
+VDGRVAGVLSVKDTVKPSSAAAIARLKELGLRPLLVTGDNAAVAAQVAAAVGIPAEDVVA
+GVRPEDKVDVVTRLQSEGRVVAMVGDGVNDAPALAAADMGIAMGSGTDVAREAAQITVMG
+DDLDQVVQALDLSRRTLGIIRMNLFWAFAYNVLGIPVAALGLLNPMIAGGAMAASSVLVV
+LNSLRLTRYAR
+>PROKKA_00575
+MTHPASSAPAGPQSETTRRVDLDVTGMTCASCVGRVERKLGKLEGVTASVNLPLEQATVT
+APADVSDEELVAAVEKAGYGATVRRPAPPAGHAGHAHTSEHGEGHGEEHAADHDGVDHHD
+HMAHGPGEDVLKPRLIGAAVLTVPLVLISMVPALQFPHWGWVAFALAAPVALWAAWPFHS
+AAFRAARHGSSTMDTLVSLGVLVSFSFSAVELILAPDMTAHVGGTMAEMAHHSLYFEAAA
+VITTFLLLGRWLEARAKREAGAALRALLDLGAAQATLYDPETHDERTVPAESLAPGDVVL
+IRPGEKVPTDAEVLEGTSAVDASLLTGESVPVEVGPGDAVTGATLNTSGRLVARATRVGA
+DTTLAQMGRLVADAQTGKARVARLADRISAVFVPVVLGLAVLTFAVWMLVTGDLPSALRA
+GVAVLVIACPCALGLATPVGLLAGTGRASQLGILIRGPEVLEDSRTVDTIVLDKTGTVTE
+GRMALADVLVLDPAFVTDTGASRSASVAETDAPRSAFVAETAPDRATDLLLTLAAAVERG
+SEHPIARAIVTGAEERGLTVPDVADFASTAGGGVSGLVALPHDDGALASGAHGAAGPAPV
+RVAVGRGSVLETALDGGIPAEHRAAFEAAEQAGATAVWVAVGGRVAGVLSVRDTVKDTSA
+DAIARLKELGLRPLLVTGDNAAVATQVADAVGIPAEDVVAGVRPEDKVDVVRRLQSEGRV
+VAMVGDGVNDAPALAAADMGIAMGSGTDVAREAAQITVMGDDLHQVVQALDLSRRTLGII
+RMNLFWAFLYNVLGIPVAALGLLNPMIAGGAMAASSVLVVLNSLRLTRYAR
+>PROKKA_00718
+MSTSAPPTGGPDIELEIGGMTCASCANRIEKKLNKLDGVAATVNYATEKAKVTVPAGYDP
+SLLVAEVEKTGYTAALPKPKDTTANTSETEAGEEEDSELTSLRHRLIGAIVLTVPVIAMA
+MIPALQFTYWQWASLALAAPVIIWGAWPFHKAAWTNLKHGAATMDTLISMGTSVALLWSL
+YALFLGTAGTPGMTHPFEFTIAPSDGAANIYLEVGAGVTMFILAGRYFEKRSKRQAGAAL
+RALLELGAKEVAVLRDGVEVKIPTSELAVGDEFIVRPGEKIATDGLVTSGSSAVDASMLT
+GESVPVEVREGDSVTGATVNAGGRLVVRATRVGSDTQLAQMAKLVEDAQTGKAEVQRLAD
+RISGIFVPIVIVVAFITLGAWLGGGFPVAAAFTAAVAVLVIACPCALGLATPTALLVGTG
+RGAQMGVLIKGPEVLESTRKVDTVVLDKTGTVTSGKMTLTDVITEPGVDRAELLRFAGAL
+EDSSEHPIAQAIAKGATQEVGQLPTPEDFANVEGKGVQGIVEGTPVVVGRESLLADWSQK
+LSPEVAQAKAQAEGEGKTVVAIGWDGAARGILVVADTVKPTSAEAIRGLKEIGLTPVLLT
+GDNEAVARQIASEVGIDEVIAEVLPKDKVDVVTRLQEEGKIVAMVGDGVNDAPALAQADL
+GLAMGTGTDVAIEASDITLVRGDLRAAVDAIRLSRKTLSTIKTNLFWAFAYNTAAIPVAA
+LGMLNPMLAGAAMAFSSVFVVGNSLRLRGFTSVASK
+>PROKKA_02060
+MTHPASSTPAGPQSETTRRVDLDVTGMTCASCVGRVERKLGKLEGVTASVNLPLEQATVT
+APAGVSDEELVAAVEKAGYGATVRRPAPPAGHAGHAGHAHTSEHGEEHGEEHAADHDGVD
+HHDHMAHGPSEDVLTPRLIGAAVLTVPLVLISMVPALQFPHWGWVAFALAAPVALWAAWP
+FHSAAFRAARHGSSTMDTLVSLGVLVSFSFSAVELILAPDMTAHVGGTMAEMAHHSLYFE
+TAAVITTFLLLGRWLEARAKREAGAALRALLDLGAAQATLYDPETHDERTVPAESLAPGD
+VVLIRPGEKVPTDAEVLEGTSAVDASLLTGESVPVEVGPGDALTGATLNTSGRLVARATR
+VGSDTTLAQMGRLVSEAQTGKARVARLADRISAVFVPIVLGIAVLTFAVWMIVTGDLPSA
+LRAGVAVLVIACPCALGLATPVGLLAGTGRAAQLGILIRGPEVLEDSRTVDTIVLDKTGT
+VTEGRMALADVLVLDPAFVAETGASRSAFVDETAPDQAADVLLTLAAAVERGSEHPIARA
+IVAGAEERGLTVPGVADFASTAGGGVSGLVALPHDDGAPGSGAHGAAGPDPVRVAVGRGS
+VLETALDGGIPAEHRAAFEAAEQAGATAVWVAVGGRVAGVLSVRDTVKDTSADAIARLRQ
+MGLRPLLVTGDNAAVAAQVAEAVGIPAEDVVAGVRPEDKVDVVTRLQSEGAVVAMVGDGV
+NDAPALAAADMGIAMGSGTDVAREAAQITVMGDDLHQVVQALDLSRRTLGIIRMNLFWAF
+LYNVLGIPVAALGLLNPMIAGGAMAASSVLVVLNSLRLTRYAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000171.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000171.fa
new file mode 100644
index 0000000000000000000000000000000000000000..391075362379e8a0ceeb548c8e78e4cae4e92e18
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000171.fa
@@ -0,0 +1,47 @@
+>PROKKA_02305
+MPTVKAPSKRATSATSSRKEPGDSSVESAATEGTVSADIAVLREIPVGDIHPNPRQPREV
+FDEDHMAELVTSIREVGILQPIVVREVDGPTPHELIMGERRWRATQKAGLDTIPAIVRQT
+PDQDLLRDALLENLHRSQLNPLEEAAAYQQLMEDFACTQEELSQRIGRSRPQISNTLRLL
+KLPPLVQRRVAAGTLSAGHARALLGLTDPSDMERLAQRIQSEGLSVRSTEEAVAQLQGGL
+RPGRTPRRSTDDARHERLDHYATALTSRLDTAVKITLGARKGRIAIDFTTVEDLNRIMDL
+IQGGQDGKGKGKKS
+>PROKKA_01998
+MPTVKAPSKRATSATSSRKEPGDSSVESAATEGTVSADIAVLREIPVGDIHPNPRQPREV
+FDEDHMAELVTSIREVGILQPIVVREVDGPTPHELIMGERRWRATQKAGLDTIPAIVRQT
+PDQDLLRDALLENLHRSQLNPLEEAAAYQQLMEDFACTQEELSQRIGRSRPQISNTLRLL
+KLPPLVQRRVAAGTLSAGHARALLGLTDPSDMERLAQRIQSEGLSVRSTEEAVAQLQGGL
+RPGRTPRRSTDDARHERLDHYATALTSRLDTAVKITLGARKGRIAIDFTTVEDLNRIMDL
+IQGGQDGKGKGKKS
+>PROKKA_00432
+MKTSRRGGLGRGLGALIQSTAEPVDEAPQEADATAEDATAPTAAPAEKKAATSTARRLSK
+ETSEAKTPAPRAASASKSSGGAAKEAPADKKAGSAGRAPAAAKKATPTKKASSSAGEAKA
+NSAAAPAAARKTPDRAAQRPVDVFFSPDPEDAPAARRGTKARPAMPTVKAPTKREAASSS
+GEEAAAGASTAAEGTVSTDIAVLREIPVGDIHPNPRQPREVFDEEHMAELVTSIREVGIL
+QPIVVREVDGPTPYELIMGERRWRATQKAGLDAIPAIVRQTPDQDLLRDALLENLHRSQL
+NALEEAAAYQQLMEDFACTQEELAERIGRSRPQISNTLRLLKLPPLVQRRVAAGTLSAGH
+ARALLGLTDPSDMERLAQRIQAEGLSVRATEEAVAQLQGGLRPGRTPRRTADDARHERLD
+HYATALTSRLDTSVKITLGARKGRIAIDFTTVEDLNRIMDVIQGEKGGRGAAS
+>PROKKA_01948
+MVASVKTQGLLQPLVVAPNPTLEGDYTIIAGHRRLDALKRAGRDDAPVIVRTDLDTEEKQ
+VAAMLQENLHRQDLTAVEEADAFAQLSLFEGWDVKRIARETGVAQTRVRSRIKLTYLSEA
+TLASLHDGQVTLERAQALAEFAGSPEEELLEEHLTATATNWDFYLARAKQTRDRRKALSA
+EQKAHEEAGFEVVPMPESLYTPEREWDRQDFESPTAALEAGAVVAFDPDYDAPVYLVKHA
+EQELEKDAAAAERKAEAAERAARNEALERELATAQETVRLWLVDTVFPKAAAGDERILRV
+AARHLAATACEETHFRRAGLAAIFCPDLGAYAPELRTAVAEVLAGKSAQELAVIIAVATR
+WTSTARVHAWRDATREDSSPAVWLAMRQELGRELAAPEQVAFDAAKAGEL
+>PROKKA_00384
+MSTRRGGLGRGLGALIQNTAEIEQPPTREDSSPSAASSNKTTAAPAKRSTRTARTAESSQ
+NGLPASDGATQQDHSSDRAEKTASSGTGSQKTSRSTGSKGAKTPEPTATRSAQEEVPRPA
+DIFFGGGEGTSDEPPESGRHRPTRSARPSMPTVKAPSKPAPKSETEQAAPVRKDEPEGTV
+SADIAVLRELPVGDIHPNPRQPREVFDEDHMAELVASITEVGVLQPIVVREVEGAATPYE
+LIMGERRWRATQRAGLATIPAIVRQTPDQDLLRDALLENLHRSQLNPLEEAAAYQQLMED
+FSCTQEELSQRIGRSRPQISNTLRLLKLPPLVQRRVAAGALTAGHARALLGLTDPAEMER
+LAQRIVSEGLSVRATEDAVAQLQGAVRPAPKSTRSREESTRHERLDYFATALTSRLDTQV
+KITLGARKGKIAIDFASVEDLNRIMDLIQGGGDSTPVKG
+>PROKKA_02246
+MPTVKAPSKRATSATSSRKEPGDSSVESAATEGTVSADIAVLREIPVGDIHPNPRQPREV
+FDEDHMAELVTSIREVGILQPIVVREVDGPTPYELIMGERRWRATQKAGLDTIPAIVRQT
+PDQDLLRDALLENLHRSQLNPLEEAAAYQQLMEDFACTQEELSQRIGRSRPQISNTLRLL
+KLPPLVQRRVAAGTLSAGHARALLGLTDPSDMERLAQRIQSEGLSVRSTEEAVAQLQGGL
+RPGRTPRRSTDDARHERLDHYATALTSRLDTAVKITLGARKGRIAIDFTTVEDLNRIMDL
+IQGGQDGKGKGKKS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000172.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000172.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2546cbd14a919eb9d46753f113c057de81cd0e47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000172.fa
@@ -0,0 +1,65 @@
+>PROKKA_02019
+MKRSPKGRLELTWMGKDSALIPVEDGKYDYSFVDPNDPRALEVKSIEVLEQVGEVEGPTG
+ANENLLIIGDSGDALRSLGTIPEYAEKYGGKVKLVYIDPPFNTEQAFDHYADQLEHSIWL
+TMMRDRIRDFKPLLHPDASIWVHLDDSEVHRMRALMDEEFGAENFIATVVWQKKYSRDNR
+PAIGTVHDYILVYAPAGAQRWKTLRNRIPRISAAQYRNPNNDPNGPWRPVPMDVQGGHAT
+ASQFYDVITPSGKIVRPANGRAWSVTAPVMQAMRDRGEVYFGLDGSGKPNTIRYLKDDEG
+LVPWTWWPHEEVGNNDDAKKEIIALFGEDQVFDTPKPERLLERVIRIATNADDLVLDCFA
+GSGTSAAVAHKLGRRWLTVELSQEVADTFTVPRLRKVQRGTDSIGISVREAEGFADADMD
+GRVKPDDAKALLRAIKEVQKVGLKSLSPEAGAALVQELRERLKPVSARQSVCQDGGFTVA
+KMGPSMYEVDDEHGMVFLSPEATNGAWSKAIAGQLKFTLTPDDPVFCGVRKRQRLAVIDG
+VADETVVRTVVEHLGEKERAVIVAKGVLPEAGDLLQRLSPGSRIKKAPEDMFPKGTVN
+>PROKKA_01501
+MTDEIYETPSTTPNFQTELAAQLADLIPEAIADGKVDVEKLKELLDGDAADSNERFGLFW
+PGKKRALRAAQEPTTATLKPDFEDSKDWDTTQNVFIEGDNLEVLKILQKHYHAKIKLIYI
+DPPYNTGKDFVYPDNYKEGLDTYLEWTRQVNEEGKKVTTNAETEGRYHSNWLNMMYPRLK
+LARNLLTDDGVIFISIDDNEIDNLLRLAKEVFGEPNVSTTFIRQKKKKPSFLHANVGSMT
+EYLVCITRNKAFTFPFSVDTTTAGKKYPINNAGNSLGKLTFPAGAVRFSQKFAEYEPQDM
+SEGNIVTRLLDHVVVSEGVNRNAFTLEGEWRYSQVTLDEFITAGDLITISKAPFRPNHVK
+AGGEIKKMHNLLTPSTYGVGTNEDGTAELEDLMEGSYFDNPKPTSLVRVLAQAVTYDDPS
+AIVLDFFAGSGTTADAVFRLNAQDGGNRRVISVQLPEPLDERSEAWAAGYRTISQLAKER
+IRRAGVRVLDREALLLEGRGVPLDTGFRAYKLSDTNFSKWRLSSDVEEDALQQHLLSLRD
+SATDDANADELLTEILLKQGYSLTEAVSPAEVAGLDVRFVRDRDGDVAVLAYLNEHVKPT
+LEQLRALVDEEPTRIIVLEDAFQGDDELKTNLAQLAKSKGIELWTA
+>PROKKA_00288
+MEMSMDKLRGTSPDLTQDNVARLAELFPTVVTEARDEDGQVTRAVDFDLLRQELSDHVVE
+GPQERYHLDWPGKRAAAFAANAPTTATLRPDREESVDFDTTKNVFIEGDNLEVLKVLQES
+YLGKVKMIYIDPPYNTGNDFVYADDFAESTADYLQRSGEIDDDGARLRANPETNGRFHSD
+WLSMMYPRLKLARNLLTEDGAILASIGEREVSNLRAILNELFGETNFVGELVWEKKKKGA
+FLSSHVTNVKEYILVFCRDRSSFGGLIGEVTHAAETYPVIKSTNSRGIRTIPAGIASNYS
+ERDHEVGAGTRLTSGNMEMILLSDLIIRDGRLAHDVEVESNWIYSQTLIDQFSLSGDLYI
+TRDLYIRRHVREPRTKMLKDLLMMRGESTSGSTFTLEPSLHSDGWGTNEDAFGELHSILG
+EQNLMDFPKPSKLIAKLIRSVTWADSDAIILDFFAGSGTTGQAVTQLNAADGGRRQYLLV
+QLNEAAEESSALRRAGFSSISALSRERLRRSAAAVRETSGTERLDLGFRAFRLDASPFVE
+RNHSADSITPDMLAELENPVLADRSPEDLLTHVLLAWGLDLSATIETVSLAGEEVYDVED
+GALLAALGSTVSDELAHAMAERHPDRALFLDSGFVSDAARINVEQIFREVSPGTDVKVL
+>PROKKA_00347
+MSSLSDLLGQVRATNPDLAANLEREIKNRTRRQRQFGLVFEEHRPEAVELPSREVRKGDK
+VRILPPRGETKKGDQTLWRVQRINRADDIAHLVEVDGEQGAEAALADLVVVAEFRDHMYP
+GLVETGRVERGGDKPFHTVINAENFHALEMLTYTHRHQVHCIYIDPPYNTGAKDWKYNND
+YVASDDDYRHSKWLSFMERRLQVARELLNPEDSVLIVTIDEKEYLRLGMLLEQTFPQARM
+QMVSTVINPKGSHRAGGFARSDEYVFFLFVGASQPAPMPLSSEWKVVQDSRALGLRWADL
+LRTADGSTRAARPNMFYPVFIRLAGDGPVFVSVGEPFYDADLTAVEAPEDAVAIWPIKAD
+GSQGRWQIGADTLRDLITKGYVRIGRWRGSKTTLTYLKAGEQAKVEDGRFPVRGRRADGS
+VLVDASEYSASFVPTSQWRISSHNAEQGGTNLLKSIMGDKRFPFPKSLYAVEDALRFLIK
+KNPDAVVLDFFSGSGTTAHAVMRLNKQDGGRRQCISVTNNEVSAEEQKGLRKQGLRPGDP
+EWEQWGICDYVTKPRVTAAITGRTPTGDPIKGDYKFTDEFPMSDGFEENAAFFTLTYESP
+LMVRQDLAFKRIAPLLWMRAGSRGRVITEVHARGWDVAEAYGVLTKVDRATPFAEAVAEA
+GVGTVYVVTDDERRYQAVCALLPEDVTPVRLYESYLTNFEINTGGRAGA
+>PROKKA_00694
+MSRLTDLLAQARKTDPQLAADLEAEFRQLTQRSQFGLVFERHQPEAVELPGRPVRRGDTV
+RVLPPRGTLTIGDTRHWVVTDLERTPDGKQAHLTEADVDPEVREPATSTAALEDLVVVAR
+FEDPIYPGLVETGRVENGGPDKPFHTVINAENFHALEMLTYTHRHKVDCIYIDPPYNTGA
+KDWKYNNDYVEADDDYRHSKWLSFMERRLQVARELLNPDDSVLIATIDEKEYLRLGMLLE
+QTFPEARIQMISAIINPKGSSRRDQFSRFDEYIFFVMNGSARPAAVAGDMTMRQARSKEK
+VRWAGLMRQGANGRRSARPNLFYPIFVANETGRVHSVGDSLPLDVPRSEVSPPPGTTAIW
+PLSKAGGESTWGRDPESLRKALSAGYVKIGRFTPGSERCGFTHLQSGQIKAIEEGALVVT
+GRDSDGSLQVEFAEGGQTAMPGTAWHRPAHSASEHGSTLLNAILPDRKFPFPKSLYAVED
+AVRFFVHGKPDAVVLDFFSGSGTTAHAVMRLNRQDGGRRQCISVTNNEVSAEEQKGLRKK
+GLRPGDPEWERWGICDYITKPRITAAITGKTPAGDPIKGNYKFTDEFPMADGFEENAAFF
+TLTYEAPRQVRRNRAFARVAPMLWFKAGSRGRIISSLPERGWDVAQAYGVLEDMDHAPEF
+LAALEADPQVGMAFIVTDSEVAFQSVARQLPEHATAVRLYESYLHNFQINRRA
+>PROKKA_00111
+MSSLSDLLGQVRATNPDLAANLEREIKNRTRRQRQFGLVFEGHRPEAVELPSRPVRKGDK
+VRILPPRGETKKGDQTLWHVDHIDRTTGTARLTAVDGEQEAQAAISDLVVVAEFRDHMYP
+GLVETGRVENGGGKPFHTVINAENFHALEMLTYTHHRKVDSCRASDLGHV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000173.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000173.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0c2815c3304755bcbe52ffa6994ada48f84c3203
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000173.fa
@@ -0,0 +1,47 @@
+>PROKKA_00092
+MDLTYKLWEGSWDEGAVLQDKGGSRHADPEKVHKIHHVSERYRVEGPHLPAPSPQRTPVL
+FQAGSSGPGRAFAARNAEAVFLIAPSVEAARQQIEDPRRQAVEFGRRPEDIKFFQGLSFV
+IGDTEEEAQAKLEEYERYVSVDGYLAHAALVDPDGRVYPPDTPLRELETNTQKGFAESLQ
+KAITDREPVVADVAWRSHRDSRVVGTPEQIADELQRWQDAGVDGVNVINWVIPGSFEEFI
+EKVLPVLRERSLAQSDYGEGTLRHRLFGEGDRLPDRHPAAKYRGAFTGTPRSQRAPRTEP
+QGADPAPAA
+>PROKKA_00093
+MTKTARRRPLHLNAFAMNTTSHIHHGQWRRPDARQHEFADLRTWTELARTLEDAAFDAMF
+FADVVGHYGDADADYAVYVEEGLQIPSNDPTVLLGALAAVTERIGLATTSNVFQAHPFQF
+ARQLSTLDHLSRGRIAWNIVTGT
+>PROKKA_00195
+MMTPVHQSPGLWRHPESRIAEFDRLAYWTGLARTVEDGGFSALFLADVLGLYDVYGGGIE
+ATVRGGVQWPVLDPAVAVPAMAAATERIGFGVTASVTYERPYLLARTLATLDHFTGGRVA
+WNIVTSYQDSAARNLGLDRQIPHDARYDLADEALDALYRLWEGSVEPGAVAFDRAAGVVA
+DPDRVHPAAVAGAHVRVPDAALTHPGPQGTPYLFQAGASARGRRFALDHAEAVFAIGPTP
+AHVRRFVDQTRAGLTEAGRSADAIRVLAMVTVVVAETDEAAAQRLAGYAEHVDVAGALAL
+WGGWTGVDVAGLDPDAPLEHVVTDANRSALAAFTEDPSGRTWTLRDVAEFVAIGGRGPVI
+VGSPETVADELQRWQAETGVDGFNVSAAVRPADLERFAALVSPELRRRGVLREPEPGRTL
+RENLSGAGPALPADHRGHAFRTAG
+>PROKKA_00133
+MTGTHPSTPRPRTADRQLILGAHFPGVNNTTVWSDPESGSQIAPESFIRFAEIAERGRLD
+FIFLAEGLRLREQRGLLHDLDVVGRPATLPILAALAAATEHIGLIGTLSTTYNEPYELAR
+QLAGLDALSGGRAGWNVVTSPDAFTGENFRRGGYLPRERRYQHAGEFLATAQQIWDAASG
+RPPHVDVDVEDFSVHGTVDAPAPVHGRPVILQAGDSDEGRDLAAREADAVFTRHGDWEAG
+QEFTADMRRRAAAAGRPDGAVRVLPGVTVVVGDTDEEAAAEAEQIRRAQVSGATAVLTLE
+RIWNRDLSGWDPDGPLPDVEPVLEDTGLSQGRVRHVADPHAEVARLREISQRQGLTLRET
+VIATGQRQDFVGSPETVAQELIRHVEHDVCDGFILIPHLTPGGLEPFVDRVVPLLQERGA
+LRTDYPEDGGGLRGLLGAAVHPTAGRAS
+>PROKKA_00146
+MTATPAPAPFILSAFDMVTPVHQSPGLWRHPESRAHEFDRLSFWTDLARTVEEGGFTAVF
+LADILGLYDVHGGGVDATVRGGVQWPLLDPFTVVSAMAAVTERVGFGVTASVTYEQPYLL
+ARTLTSLDHFTGGRIAWNVVTGYQDSAARNLGLDRQPGHDERYDRADAYLDAMYRQFEGS
+VERDAVVADRESGVFADPAKVHPIDVEGPHVRLPGVALAHPGPQGTPFLFQAGASSRGRR
+FALEHAEAVFYIGPTTAHVRRFVEQTREGLREAGRPEDAIRVLAMVTVVVADTDEEAQAR
+LASYHEHVDVESALALFGGWTGVDLSGLDPDAELEHVESEASRTALAAFTTQSPDRRWTV
+REVAEFVSVGGRGPVIVGSPATVADELERWHRETGVDGFNISAAVRPTDLERFARLVSPE
+LRRRGVLREPEAGRTLRENVAGAGPLLPEDHRGAGFRR
+>PROKKA_00201
+MTATPAPFILSAFDMVTPVHQSPGLWRHPESRAHEFDRLSFWTDLARTVEEGGFTAVFLA
+DILGLYDVHGSGVDATVRGGVQWPLLDPFTVVSAMAAVTERVGFGVTASVTYEQPYLLAR
+TLTSLDHFTEGRIAWNVVTGYQDSAARNLGLDRQPGHDERYDRADAYLDAMYRQFEGSVE
+RDAVVADRESGVFADPAKVHPIGVEGPHVRLPGVALAHPGPQGTPFLFQAGASSRGRRFA
+LEHAEAVFYIGPTTAHVRRFVEQTREGLREAGRPEDAIRVLAMVTVVVADTDEEAQARLA
+EYHEHVDVESALALFGGWTGVDLSGLDPDAELEHVESEASRTALAAFTTQSPDRRWTVRE
+VAEFVSVGGRGPVIVGSPATVADELERWHRETGVDGFNISAAVRPTDLERFARLVSPELR
+RRGLLREPEAGRTLRENVAGGGPLLPEDHRGARFR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000175.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000175.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5b35c0474651c7bcbb5c103ce95240198521d9e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000175.fa
@@ -0,0 +1,39 @@
+>PROKKA_00002
+MQLVKFTVERDILTDAVSWAARSLSPRPPVPVLSGLLITAEAGVVSIASFDYETSARLEI
+EADVETAGQVLVSGRLLNDIVRSLPQAQVTVELDGGKVLVTCRSSRFALATMPVGDYPAL
+PELPAPAGTVDGAAFAHAVAQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMK
+EIRWTPADPSLSTSLLIKARTLTEVAKSLGSGGDLEILLGQTADLVGFASGGRRTTSVLV
+DGEYPKIRSLFPESSPIQAVVDTAALVEASRRVALVAERNTALRMVFTDGQVTLDAGTGD
+DASANESVPCTLEGEDITVAFNPSYLSEGLAVVDQPQVRFAFTSAPKPALLTGVNQEDGV
+VSDYRYLVMPVRIA
+>PROKKA_02007
+MQLVKFTVERDILTDAVSWAARSLSPRPPVPVLSGLLITAEAGVVSIASFDYETSARLEI
+EADVETAGQVLVSGRLLNDIVRSLPQAQVTVELDGGKVLVTCRSSRFALATMPVGDYPAL
+PELPAPAGTVDGAAFAHAVAQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMK
+EIRWTPADPSLSTSLLIKARTLTEVAKSLGSGGDLEILLGQTADLVGFASGGRRTTSVLV
+DGEYPKIRSLFPESSPIQAVVDTAALVEASRRVALVAERNTALRMVFTDGQVTLDAGTGD
+DASANESVPCTLEGEDITVAFNPSYLSEGLAVVDQPQVRFAFTSAPKPALLTGVNQEDGV
+VSDYRYLVMPVRIA
+>PROKKA_00422
+MPVLSGLLITAEAGVVSIASFDYETSARLEIEADVETDGQVLVSGRLLNDIVRALPHAQV
+TVELDGGKVVVTCRSSRFALATMPVGDYPALPELPTPAGTVDGAAFAHAVAQVTVAASKD
+DTLPILTAVKVEIEGDTMTFLATDRYRLAMKEIRWTPADPSISTSLLVKARTLTEVAKSL
+GAGGDLEILLGEGTDLVGFSSGGRRTTSVLVDGEYPKIRSLFPETSPIQAVVDTAALVEA
+SRRVALVAERNTALRMVFTDGQVTLDAGTGDDASANESVPCTLEGEDITVAFNPSYLSEG
+LAVVDQPQVRFAFTSAPKPALLTGVNQEDGVVSDYRYLVMPVRIA
+>PROKKA_00375
+MKFTVARDILSDAVSWAARSLSPRPPVPVLSGLLVTAEAGLVSIASFDYETSARLQIEAD
+VEDEGQVLVSGRLLNDIVRALPNAPVTLELDGGKVLVTCRSSRFQLATMPVADYPALPEL
+PEPAGTVDGAAFAHAVNQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMTEIR
+WNPADPAISTSLLIKARTLTEVAKSLGGGGRLEIMFGSSHDLVGFSSGGRRTTSVLVDGE
+YPKIRSLFPETSPIQAAVDTEELIAASRRVALVAERNTALRMVFTDGQVTLDAGTGDDAT
+ANESVPCTLEGEEITVAFNPAYLSEGLAVVDQPQVRFSFTAAPKPALLTGVHEEDGTVSD
+HRYLVMPVRLT
+>PROKKA_00002
+MQLVKFTVERDILTDAVSWAARSLSPRPPVPVLSGLLITAEAGVVSIASFDYETSARLEI
+EADVETAGQVLVSGRLLNDIVRSLPQAQVTVELDGGKVLVTCRSSRFALATMPVGDYPAL
+PELPAPAGTVDGAAFAHAVAQVTVAASKDDTLPILTAVKVEIEGDTMTFLATDRYRLAMK
+EIRWTPADPSLSTSLLIKARTLTEVAKSLGSGGDLEILLGQTADLVGFASGGRRTTSVLV
+DGEYPKIRSLFPESSPIQAVVDTAALVEASRRVALVAERNTALRMVFTDGQVTLDAGTGD
+DASANESVPCTLEGEDITVAFNPSYLSEGLAVVDQPQVRFAFTSAPKPALLTGVNQEDGV
+VSDYRYLVMPVRIA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000177.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000177.fa
new file mode 100644
index 0000000000000000000000000000000000000000..022609b66cebc4bca0035bc973faf26d40cd32de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000177.fa
@@ -0,0 +1,23 @@
+>PROKKA_00004
+MAETPAPFEPDRPDLALVQLRRVREAARERGEAPLRARGTGAGLAGAMAGTPSAGRERQD
+RRRPFGGADRDPATVSTVFGRLIRDRGWSTPVAVGSVLTRWAELVGPEIALHCRPESFED
+SVVRVRTSSTAWATQLRLMSPVLLQRFDEALGPGVVTRIEVAGPQAPSWRKGPRTVRGGR
+GPRDTYG
+>PROKKA_02009
+MAETPAPFEPDRPDLALVQLRRVREAARERGEAPLRARGTGAGLAGAMAGTPSAGRERQD
+RRRPFGGADRDPATVSTVFGRLIRDRGWSTPVAVGSVLTRWAELVGPEIALHCRPESFED
+SVVRVRTSSTAWATQLRLMSPVLLQRFDEALGPGVVTRIEVAGPQAPSWRKGPRTVRGGR
+GPRDTYG
+>PROKKA_00420
+MSSVFGRLIRDRGWSTPVAVGSVLTRWDELVGPEIALHCRPESFEDSVVRVRTSSTAWAT
+QLRLMTPVLLQRFDDALGPGVVTRLEVAGPQAPSWRKGPRTVRGGRGPRDTYG
+>PROKKA_00373
+MRERSPEPDALAELPPDRPDLALVQLRRVRDAARQRGEAPLNRRGTAAGLAQSMAGSEAA
+AAAGGAVARSGHRRPGAPADRDPAVVSSVFGRLIRDRGWSTPVAVGSVLTRWADLVGPEI
+ALHCRPESFEDSVVRVRTSSTAWATQLRLMSPMLLSRFDEALGPGVVTRIDVAGPAAPSW
+RHGPRTVRGGRGPRDTYG
+>PROKKA_00004
+MAETPAPFEPDRPDLALVQLRRVREAARERGEAPLRARGTGAGLAGAMAGTTSAGRERQD
+RRRPFGGADRDPATVSTVFGRLIRDRGWSTPVAVGSVLTRWAELVGPEIALHCRPESFED
+SVVRVRTSSTAWATQLRLMSPVLLQRFDEALGPGVVTRIEVAGPQAPSWRKGPRTVRGGR
+GPRDTYG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000179.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000179.fa
new file mode 100644
index 0000000000000000000000000000000000000000..288e30942dc76c37602bfd745cc3d631987bdd0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000179.fa
@@ -0,0 +1,82 @@
+>PROKKA_00006
+MSDETTPQTPDEPVEGAPTPQPPQTGLDIEVEHYVLPEGAADKVEPVDLESEMKRSYLDY
+AMAVIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRAFNKSARVVGDVMGNYHPHGDTA
+IYDALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTVD
+MQDNYDGKQQEPVVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEAT
+REELLEALLARVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVT
+ELPYMTNPDNLAAKIAEMVRDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLY
+KHTELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIDVIVRRTAFRKRKAEERAHILR
+GLLKALDMLDEVIATIRRSASAEVAREALKELLDIDDVQAQAILQMQLRQLAALESQKIQ
+DEYDDLMAKIAEYNRILESPQRQREVISEELAEIVAKHGDDRRTEIMAGFDGDMSIEDLI
+PEEEMVVSITRGGYVKRTRIDQYRSQARGGKGVRGATLRGDDVVEHFLTVSTHHWLLFFT
+NFGRVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQIQPLVDYGRAPYLVLATRGGL
+VKKTPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISHKGQSLRFTATDEALR
+PMGRATSGVTGMKFRDDDSLLTMDVVEEDGYVFTVTDGGFAKRTHVDEYRPQNRGGLGIK
+VAKLVDDRGELAGGLVVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDR
+IVAVTLNNEQEMEAKADAEAEAGPDVPLDADIDPTDPVAAPEDALTQDAGEGADGGEQ
+>PROKKA_02011
+MSDETTPQTPDEPVEGAPTPQTGLDIEVEHYVLPEGAADKVEPVDLESEMKRSYLDYAMA
+VIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRAFNKSARVVGDVMGNYHPHGDTAIYD
+ALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTVDMQD
+NYDGKQQEPVVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEATREE
+LLEALLARVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVTELP
+YMTNPDNLAAKIAEMVRDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLYKHT
+ELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIDVIVRRTAFRKRKAEERAHILRGLL
+KALDMLDEVIATIRRSASADVAREALKELLDIDDVQAQAILQMQLRQLAALESQKIQDEY
+DDLMAKIAEYNRILESPQRQREVISEELAEIVAKHGDDRRTEIMAGFDGDMSIEDLIPEE
+EMVVSITRGGYVKRTRIDQYRSQARGGKGVRGATLRGDDVVEHFLTVSTHHWLLFFTNFG
+RVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQIQPLVDYGRAPYLVLATRGGLVKK
+TPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISRKGQSLRFTATDEALRPMG
+RATSGVTGMKFRDDDSLLTMDVVEEDGYVFTVTDGGFAKRTHVDEYRLQNRGGLGIKVAK
+LVDDRGELAGGLVVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDRIVA
+VTLNNEQEMEAKADAEAEAGPDVPLDADIDPTDPVAAPEDALTQDAGEGADGGEQ
+>PROKKA_00418
+MSDETTPQTPDESAEVPETPETGQDVAVEQYVLPEGAADKVEPVDLESEMKRSYLDYAMA
+VIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRSFNKSARVVGDVMGNYHPHGDTAIYD
+ALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTVDMQD
+NYDGKQQEPAVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEATREE
+LLEALLTRVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVTELP
+YMTNPDNLAAKIAEMVRDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLYKHT
+ELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIDVIVRRTVFRKRKAEERAHILRGLL
+KALDMLDEVIATIRRSASADVAREALKELLDIDDVQAQAILQMQLRQLAALESQKIQDEY
+DELMARIAEYDRILESPQRQREVISEELGEIVAKHGDDRRTEIMAGYDGDMSMEDLIPEE
+EMVVSITRGGYVKRTRIDQYRSQGRGGKGVRGATLRGDDIVEHFLTVSTHHWLLFFTNFG
+RVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQIQPLTGYDRAPYLVLATRNGLVKK
+TPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISHKGQSLRFTATDEALRPMG
+RATSGVTGMKFRDDDALLTMDVVEEDGYVFTVTDGGFAKRTHVDEYRLQNRGGLGIKVAK
+LVDDRGELAGGLVVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDRIVA
+VTLNNEHEMEAQADAEAAEDPVSEGSAAAAGVLPEGEPEALVGAEATAGAAADADVRLDA
+DIDPTDPAAAPEGLFEEDADGEGADGGEQ
+>PROKKA_00370
+MSDETTPGTAPGTPQDGHDADQTPQIGQDVAVEHYVLPEGAADKVEPVDLESEMKRSYLD
+YAMAVIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRSFNKSARVVGEVMGNYHPHGDT
+AIYDALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTV
+DMQENYDGKQLEPTVLPARFPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEA
+TREELLAALMQRIKGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVV
+TELPYMTNPDNLAAKIAEMVRDGKIAGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNL
+YKHTELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIEVIVRRTAFRKKKAEARAHIL
+QGLLKALDMLDEVIATIRRSASAEVAREALKTLLDIDDEQAQAILQMQLRQLAALESQKI
+QDEYDELMARIAEYTAILESPQRQREVVSDELGELVAKHGDERRTEIVAGFDGDMSIEDL
+IPEEEMVVTITRGGYVKRTRIDQYRSQARGGKGVRGAALRGDDVVEHFLTVSTHHWLLFF
+TNLGRVYRIKTYELQEAGRDAKGQHVANLLAFQPDERIAQIQPLAGYDGDAPYLVLATRN
+GLVKKTPLEDYDTNRQAGLIAIKLREGDELVSARVVSAQDDLLLISRQGQSVRFTATDEA
+LRPMGRATSGVTGMKFRGDDALLAMDVIRAGDEDSYVFTVTDGGFAKRTHVDEYRTQGRG
+GLGIKVARLVDDRGELAGGLVVGEDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVVFAKP
+DKRDRIVAVTLNNEDEIEATADERAAAEGAAPEAAGAADGAGVPLDAVNDQTDPAAAAEA
+EAAGEDADGGEQ
+>PROKKA_00006
+MSDETTPQTPDEPVEGAPTPQTGLDIEVEHYVLPEGAADKVEPVDLESEMKRSYLDYAMA
+VIVGRALPDVRDGLKPVHRRVLYAMYDGGYRPDRAFNKSARVVGDVMGNYHPHGDTAIYD
+ALVRLIQDWVQRYPLALGQGNFGSPGNDGAAAQRYTETKMAPLAMEMVRDIDEDTVDMQD
+NYDGKQQEPVVLPARYPNLLVNGSSGIAVGMATNIPPHNMREVAAGVQWYLEHPEATREE
+LLEALLARVHGPDFPTGAQILGRKGIEEVYRTGRGPITMRAVVNVEEIQGRTCLVVTELP
+YMTNPDNLAAKIAEMVRDGKINGIADMRDETSGRTGQRLVIVLKRDAVAKVVLNNLYKHT
+ELQSNFSANMLALVDGVPRTLSLDGFVHHWVKHQIDVIVRRTAFRKRKAEERAHILRGLL
+KALDMLDEVIATIRRSASADVAREALKELLDIDDVQAQAILQMQLRQLAALESQKIQDEY
+DDLMAKIAEYNRILESPQRQREVISEELAEIVAKHGDDRRTEIMAGFDGDMSIEDLIPEE
+EMVVSITRGGYVKRTRIDQYRSQARGGKGVRGATLRGDDVVEHFLTVSTHHWLLFFTNFG
+RVYRIKTYELLEAGRDAKGQHVANLLAFQPDERIAQIQPLVDYGRAPYLVLATRGGLVKK
+TPLLDYDTNRTAGLIAIKLREGDELVSARVVSPDDDLILISHKGQSLRFTATDEALRPMG
+RATSGVTGMKFRDDDSLLTMDVVEEDGYVFTVTDGGFAKRTHVDEYRLQNRGGLGIKVAK
+LVDDRGELAGGLVVREDQEVLVVMASGKVVRSAVAGVPAKGRDTMGVIFAKPDKRDRIVA
+VTLNNEQEMEAKADAEAEAGPDVPLDADIDPTDPVAAPEDALTQDAGEGADGGEQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000182.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000182.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45f9b8a022914464831d979a3e163a5cd39ac7c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000182.fa
@@ -0,0 +1,30 @@
+>PROKKA_00011
+MNTTIDTPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYGPTVPVI
+SDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAALTYTVVS
+WTTPVEGFEVWDQALAPMLRITVAGVVAFLVGSLLNASIVVRLKERMKERHVAFRLILST
+VVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRALKRREPT
+YRAPGFEIHRDDDPALAPAASR
+>PROKKA_02029
+MNTTTHAPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYGPTVPVI
+SDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAALTYTVVS
+WTTPVEGFEVWDQALAPMLRITVAGFVAFLVGSLLNASIVVRLKERMKERHVAFRLILST
+VVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRALKRREPT
+YRAPGFEIHRDDDPALAPAASR
+>PROKKA_00386
+MVLDGPVNTTIDTPSPDQPVSGQGTPAYARVPASYYDIFVGVFVALLILSGVTAAKLFYG
+PTVPVFSDVFYGGGPLIFDGGAFLFPFAYIIGDILAEVYGWRRARRAILLGFAMLVLAAL
+TYTVVSWTTPVEGFEVWDQALAPMLRITVAGFVAFLAGSLINATIVVRLKERMRERHVAF
+RLILSTIVGQFFDTLIFCTIAFAGTITLLELANYTFTGFLYKTLVEILIVPITLLVIRRV
+KASEPTYRPASSPARAAADAA
+>PROKKA_02181
+MNTTPASRSEPTSGQGAAASAAAPHSHYDIFVGVFVALLILSGVTAAKLFYGPTVPGVSD
+VFYGGGPLIFDGGAFLFPLSYVVGDILAEVYGLRRARRAIYIGFAMLVVAALTYRLVALT
+TPVEGFEAWDQALAPTLRITLAGLAGYIVGSLLNATVVARMKARMAERAVAWRLIASTLV
+GEFFDTLIFCLVAFAGTITLADLANYTVTGYVYKCLVEICIVPVTLLVIRWLKRHEPTYR
+AQPTPAPVSAPTA
+>PROKKA_00011
+MNTTIDTPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYGPTVPVI
+SDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAALTYTVVS
+WTTPVEGFEVWDQALAPMLRITVAGFVAFLVGSLLNASIVVRLKERMRERHVAFRLILST
+VVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRALKRREPT
+YRAPGFEIHRDDDPALAPAASR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000186.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000186.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e7c2bbb0139cda10ac82a9c2d00fdb099b74dcc5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000186.fa
@@ -0,0 +1,15 @@
+>PROKKA_00017
+MAAPAGKRKDSARRKREELEAARRSRSAVRTDLGDVDPGPKPLSPVYKAVMFGLLILGLL
+WIIVYYLTQGLLPIVQIGGWNILVGFGIALVGFLMMSRWSE
+>PROKKA_02035
+MAAPAGKRKDSARRKREELEAARRSRSAVRTDLGDVDPGPKPLSPVYKAVMFGLLILGLL
+WIIVYYLTQGLFPIVQIGGWNILVGFGLALVGFLMMSRWSE
+>PROKKA_00380
+MAAPSGKRKDSARRKHEELEDARRGARRGSSAVTTDLGDVDPGPKPLSPVYKAVMFGLMI
+VGLLWIVVYYLTQGLFPIVAIGGWNILVGFGIALVGFLMMSRWSE
+>PROKKA_00361
+MATTSGKRKDSARRKRRELEQARSRRGRTASVSTDLGDVDATPAPLPRWYKAVMFGLLIL
+GLLWIVVYYLSQGLFPIPDAGGWNILIGFGIALVGFLMMSRWSE
+>PROKKA_00017
+MAAPAGKRKDSARRKREELEAARRSRSAVRTDLGDVDPGPKPLSPVYKAVMFGLLILGLL
+WIIVYYLTQGLFPIVQIGGWNILVGFGIALVGFLMMSRWSE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000188.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000188.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f43db27f9c3f7617cc0a4a6b03933c0cdb147560
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000188.fa
@@ -0,0 +1,66 @@
+>PROKKA_00019
+MDEQRTLNGRYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRKEA
+RSAASLNHPSIVSVYDTGEVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGPDRAV
+AWTRGVLEALEHAHEEDIVHRDVKPANVMVTDTGTVKVMDFGIAHALADTSATTSQTQAV
+VGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPPAP
+SDVDPDLPPAFDPVVLRALRKDPQDRFPTGAAFLAALEEAAADPHAGPGRHTPPLDAVHP
+ALVGAGGAVLGATPAEHGADVADVPTAAVPLTRPAPSVPAEPDTAQPQAVNHAVAGAGLP
+GAASAAQLAAAAAMDGPRPVTGGQPVTPGAAATPRPEPPPRDTPAPATATPRRVRRRVRR
+RTLLAAGVVLVALALVLAPWLAAALRTTAEVPAVVGLQQDEAVAALEDAGLVAVVSSAYM
+ADAPDGTVTQSDPPTGTEVPRGAEVRIRVSRGEEGIALSDSLHGLSEDAARRELERLGLR
+VSSVQYQDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARRQL
+ALSAPELRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTTSSWIAPTAEPSEPAP
+PSSEAPEPTPSASTSPSPPSSESPEPSESPEPSESAEPSPSPSASATPSPEPTTTATPSP
+TQSPSPPSAAPSTSSEPTEQSPSTSPTATPVDPLPTLTPDPEPSIDPPPST
+>PROKKA_02037
+MSVDEQRTLNGRYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRK
+EARSAASLNHPSIVSVYDTGEVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGTDR
+AVAWTRGVLEALEHAHEEGIVHRDVKPANVMVTETGAVKVMDFGIAHALADTSATTSQTQ
+AVVGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPP
+APSDVDPDLPPAFDPVVLRALRKDPEDRFPTGTAFLAALEEAAADPHAGPGRHTPPLDAF
+PPALVGAVLGAAAAEHGADVPTAAVPLTRPTPSVPAEPDAAQPQAANHAVAGAGLPGAAS
+AAQLAAAAAMDGPRPVTVGQPVMPGAAATPWPEPQGDTPAPATATPRRVRRRLRRRTLPA
+AGVVLVALALVLTPWLAAALRTTVEVPAVVGLQQDEAVVALEDAGLLAVVSSAYMADAPD
+GTVTQSDPPTGTEVPRGAEVRIRVSRGKEGIALSDSLHGLSEDAARRELERLGLRVSSVQ
+YQDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARRQLALSAP
+ELRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTASSWIAPTAEPSEPAPPYSEA
+PEPTPSASASPSPPPSESSEPSESAEPSPSPSASATPSPEPTTTATPSPTQSPSPTSAAP
+SEPTEQPPSTSPTATPVDPLPTLTPDPEPSIDPPPST
+>PROKKA_00377
+MEEQWTLNGRYRIDALIGRGGMADVFRGTDLRLHRPVAVKLMRRDLARDPHFQARFRKEA
+RSVASLNHPSIVSVYDTGEVSLEDGHHPVDCPYLVMELVTGRSLREVLHAEGAVGTERAV
+AWTREVLEALEHAHQEGIVHRDVKPANVMVTDAGSVKVMDFGIAHALADTSATTSQTQAV
+VGTALYLAPEQATGRTVDGRADLYATGCVLFELLTGRPPFTGDTPLAVAYQHVREAPPAP
+SEVDPDLPRAFDPVLLRALEKDPEDRFPTGAAFREALEAAAADPHAAVDADTAALDLVRA
+GAAGAGGAAVAAGREVRRDGARDSADVPTAAVPLTPAPAPAAPAEPAEPPGGEPRRGRGR
+AARRRLRRPAGGRRLRGRPAPGHRLPTPPSRGPRRPAPRPPPGSALPPPLPPPDGAAAGG
+AACRSPGCCWPASSC
+>PROKKA_00359
+MQGQRILHERYRVDELIGRGGMADVFRGHDLRLNRTVAVKMMRPDLARDPAFQARFRTEA
+RHAAALNHPNIVSVYDTGDALLDDGPQSVECPYLVMEHVDGRTLRELLDAGEVAWRDAVE
+WTRGLLHALDHSHRQRIVHRDVKPANVMVTRDGGVKVMDFGIARALSDTSAHTGQTQAVV
+GTALYLPPEQAQGARVDARSDLYAAGCVLFELLTGRPPFTGETPLAIAYQHVREEPPAPS
+AVDPSLSTEFDSVVLRALQKDPGLRHQHAREFLSALDFAAARAARAADDDAPTRVVPASG
+AAPLATGSGALAAAVAGSTAAGPTASGSTALGAGGAPEARPATGPPATTPLGAAAGPTEP
+LIAGHAVAGAAVPGAPSASQLAAAEAVETAPAAASTTGGSAGAGATSGAERAGRRHRLSW
+AVLAAVAAVAAVAAILALGAALLIGSRDPGPVTVPALAGRTEAEAVSALTGLGLRSAISP
+DYHSTEPDGRVLKVHPGAGAAVEPGSTVNLSVARGGEGVVLPTSLRGASEARVRQELARL
+GLNVASVEDTPSGELDRGALVQTDPVLGSRVPPGSAVVLHLADGTARVPSLVGMTGADAR
+TTLAALDPEMTVRFQGAAGADPDTGVVVLQDPAAGTVVDNTAMITLITSAEATPTASAVT
+VAPPDPALPSATTTTAPAEPSPGVPAPTTPAAPAVDTPAPAPATTPAPAPESSSTPGAGT
+DPAPTESAPTPDDGPGSTGTPSTEAPTEAPTDPVGTPAPSPSGEPVPQPSPSVEPLPEPT
+APTEAPTADPAG
+>PROKKA_00019
+MDEQRTLNERYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRKEA
+RSAASLNHPSIVSVYDTGEVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGTDRAV
+AWTRGVLEALEHAHEEGIVHRDVKPANVMVTDTGTVKVMDFGIAHALADTSATTSQTQAV
+VGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPPAP
+SDVDPDLPPAFDPVVLRALRKNPQDRFPTGAAFLAALEEAAADPHAGPGRHPPPLDAVHP
+ALVGAVLGATPAGHGADVPTAAVPLTRPTPSVPAEPDTTQPQAANHAVAGAGLPGAASAA
+QLAAAAAMDGPRPVTAGQPVTAGQPVTPRPEPPPGDTPAPATATPRRVRRRVRRRTLLAA
+GMVLVALALVLAPWLAAALRNTVEVPAVVGLQQDEAVAALEDAGLVAVVSSAYMADAPDG
+AVTQSDPQTGTEVPRGAEVRIRVSRGEEGIALSDSLHGLSEDAARRELERLGLRVSSVQY
+QDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARRQLALSAPE
+LRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTASSWIAPTAEPSEPAPPSSEAP
+EPTPSASAPPSPPPSESPEPSESAEPSPSPSASATPSPDPTSATPSPTQSPSPPSAAPST
+SPEPTAQSPSTSPTGTPVDPLPTLTPDPEPSIDPPPST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000189.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000189.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fab61160b8a48754d71b8125520161cc5967231f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000189.fa
@@ -0,0 +1,64 @@
+>PROKKA_00020
+MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRA
+EAQHTALLNHPGVANVYDYGEEKGSAYLVMELVPGQPLSSILEKEKVLSPERTLRIIAQT
+AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA
+PEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPPLPDTVPAPV
+RALIMCMLSKDPKERPSDATALSEAADALRRKDTRGAVEAVPGLAVFLEEQGVADPSGAE
+TAPLDYDGLRTTHPRTEGIRTDGSPATAALPVTAAQPRTDDAARGPGAAGAAAVGAAGAA
+ASASTRDHEIAAVRDQQTRPGDVVDPGPPAGGGSAPARRRRANPWPLWALLGLVVFALLG
+ALLWPLLTGGRGDGGSAPATSQEESSVNVDPEAYKGRPVSEVRAELEGLGLAVREEDRDA
+QSPQGTVEEINPVGALQRGETVTLAVSTGEGVIPEGLVGQPVDSAIQTLRDRGFTVDRVD
+DPSADGADGEVVRVVPGEGERHRYDTHVQLIVATGGSDAAPTREASQPASEPVPSASEEP
+SSEPSPSASDEPSPSPTAESPTATADPEPTQEPTEEPTTPTGDPTTESSGESTAPTGEPT
+TDPSADARGAEASSADATPSA
+>PROKKA_02038
+MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRNTAVKILKEEYTGDPNFLRRFRA
+EAQHTALLNHPGVANVYDYGEEEGSAYLVMELVPGQPLSSILEKEKVLSPERTLGIIAQT
+AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA
+PEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPPLPDTVPAPV
+RALIMCMLSKDPKERPSDATALSEAADALRRKDTCGAVEAVPGLAVFLEEQGVADPSGAE
+TAPLDYDGMRTTHPRAEGTRADGSPATAALPVTAAQPRTDDAARGPGAAGAAAVGAAGAA
+GAAGAVASTRDHEIAAVRDQQTRPGDVVDPAPPAGGGSAPARRRRANRWPLWALLGLVVF
+ALLGALLWPLLTGGRGIGGSAPATSQDESSVRVDPEAYRGRPVSEVRTELEGLGLAVREE
+DRDAQSPQGTVEEINPVGALRRGETVTLAVSTGEGVIPEGLVGQPVESAIQTLRDRGFTV
+DRVDDPSADGADGEVVRVVPGEGERHRYDTHVQLIVATGGSDAAPTREASQPASEPEPSA
+SEEPSTEPSPSASDEPSPSPTAESPTATADPEPTPEPSEEPTTPTGDPTTESSGESTAPT
+GESTTDPSADARGAEASSADATPSA
+>PROKKA_00376
+MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRA
+EAQHTALLNHPGVANVYDYGEEKGSAYLVMELVPGQPLSAILEKEKVLSPERTLRIIAQT
+AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA
+PEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDAPPPLPSTVPAPV
+RALIMCMLSKDPKERPTDATAASEAADALRRKDTRAAVEAVPGLAAFLAAEGVADPSGAE
+TAPLDYDGMRTAHPRPEGTRADGTPATAALPVTAAQPRTDDGARGSAATAAGAAGAAGLA
+GAAAAGARPANEEIAAVRDPQTRPSDVVQEAPPAGQGSAPVKRRRANRWPVFALLGLVLF
+ALLGALLWPWITGDRTPGGSTPSGTSQASSVSVDPEAYKGRPAAEVRAELERLGLVVREE
+DRDARNPRGTVEEVNPVGSLQRGETVTLAVSTGEGVVPDGLVGQPVDSAIQLLRDRGFTV
+DRVDDPSADGAEGEVVRVVPGEGQRHRYDTHVQLIVAGGAGGDEPAPTPEPSEPAEPTAE
+PSDEPTTEPTSEPTEEPTTEPTAPSEEPTEEPTEEPTTEPTSDPTGEPTGEPTADPTDDA
+GGSASPTAEESPTA
+>PROKKA_00358
+MRPTSGITLGGRYALTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRA
+EAQHTALLNHPGVANVYDYGEEKGSAYLVMELVPGQPLSAILEKDRTLSTDRTLSIIRQT
+AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA
+PEQATGQQATGSSDIYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPALPDTISAPV
+RALIMCMLSKNPKDRPANATALSEAAEALRRKDVAGAVAAVPTLAAFLADQGVHSTGGPG
+DAETTALDAAPRTAPQPTVPLGTTTEPAAPATAALPVAAARPDVAATRSPRAAEPARSVP
+AAAPADPAPRTAKPRRRNRWPLFALLALVAFAVLGALLYPLLSGESGAGAGASSSTGTDA
+QVEVDAAAYRGRPADEVRAELEGRGLAVEEEQRDANDPQGTVVEVTPTGTLRRGDTVTLA
+VSTGQGTIPQDLVGQPADTVVGILRDRGFSVDRVDDPNADGATGQVVRVVPGEGQTHRFD
+TPVQVIVAGGTGSSPVTQSVVTAPTAAPASESPAEPAPASSSSGDPAPSSAQPTPSEAST
+EPSPESPAPTSESAAPSTEPSAGTPSTPDASGPSSQGSDAGSPSTDPAG
+>PROKKA_00020
+MRPTSGITLGGRYQLTDRIAIGGMGEVWKARDKVLGRITAVKILKEEYTGDPNFLRRFRA
+EAQHTALLNHPGVANVYDYGEEEGSAYLVMELVPGQPLSSILEKEKVLSPERTLGIIAQT
+AAALSAAHAQGLVHRDVKPGNLMITPTGRVKVTDFGIARLADQVPLTATGQVMGTAQYLA
+PEQATGQQATGSSDLYSLGIIGYEALAGHRPFTGESQIAIALAQVNDTPPPLPDTVPAPV
+RALIMCMLSKDPKERPSDATALSEAAEALRRKDTCGAVEAVPCLAVFLEEQGVADPSGAE
+TAPLDYDGMRTTHPRAEGIRTDGSPATAALPVTAAQPRTADDARGPGAAGAAAVGAAGAA
+GAAASTRDHEIAAVRDQQTRPGDVVDPGPPAGGGSAPARRRRANRWPLWALLGLVVFALL
+GALLWPLLTGGRGVGGSAPATSQEESSVHVDPEAYRGRPVSEVRTELEGLGLAVREEDRD
+AQSPQGTVEEINPVGALRRGETVTLAVSTGEGVIPEGLVGQPVESAIQTLRDRGFTVDRV
+DDPSADGADGEVVRVVPGEGERHRYDTHVQLIVATGGSDAAPTREASQPASEPEPSASEE
+PSTGPSPSASDEPSPSPTAESPTATADPEPTPEPSEEPTTPTADPTTESSGESTAPTGEP
+TTDPSADARGAGASSADATPSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000190.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000190.fa
new file mode 100644
index 0000000000000000000000000000000000000000..988c3b3dafba064d426e317ecc5fd226eefdeadc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000190.fa
@@ -0,0 +1,50 @@
+>PROKKA_00021
+MNEAIRRTWTVMAAMILVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE
+PIAESVPSDDAYHYQRVYHEPELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA
+MEIITGATPEGDQVELTIDPELQRLAYDALPDGVRASAVVTDPTTGEILAMVSKPSFDSN
+ALSSHSPAEAQAAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT
+VDIPAAWTLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVELGQDRIREVA
+ERFGFNDSFDYPLPVTGSVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM
+EPQLIKAVRRSDLTTVQEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA
+AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGVGHQTIVSGMKAIMEAVVT
+E
+>PROKKA_02039
+MNEAIRRTWTVMAAMILVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE
+PIAESVPSDDAYHYQRVYHEPELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA
+MEIITGATPEGDQVELTIDPELQRLAYDALPDGVRASAVVTDPTTGEILAMVSKPSFDSN
+ALSSHSPAEAQAAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT
+VDIPAAWTLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVELGQDRIREVA
+ERFGFNDSFDYPLPVTGSVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM
+EPQLIKAVRRSDLTTVQEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA
+AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGVGHQTVVSGMKAIMEAVVT
+E
+>PROKKA_00375
+MNEAIRRTWTVMAAMMLVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE
+PIAESVPSDDAYHYQRVYHDPELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA
+MEIITGATPEGDQVELTIDPELQRVAYDALPDGVRASAVVTDPTTGEILAMVSKPGFDSN
+ALSSHSATEAQSAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT
+VDIPAAWPLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVKLGQDRIREVA
+ERFGFNDSFDYPLPVTASVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM
+EPQLIKAVRRPDLTTVEEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA
+AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGIGHQTIVSGIKAITEAVVT
+E
+>PROKKA_00357
+MNEAIRRTWTVMVAMFLVLAVAASVIQVVAADSLKENKLNNRQLFLEFGAPRGPILVDGT
+PVAQSVPSGDAYNYQRVYRDSLLYAPLTGHYSLAYGTAGMEKAMNGELAGTSSSQFLDRA
+LEIVTGSTPEGDQVELTLDSELQKLAYESIPDGVKGSVVATDPKTGRVLAMASKPSYDAN
+TISSHTRSEATAAMSAYEGVPGLTVGQNRPTQQRVAPGSTFKLIDLVAMLESGDYAPDQV
+LDVPAAWTLPGTRTQMSNFDGGRCNGVGRATLTWIVANSCNTPFAQAAVALGQDEIRSVA
+ERFGFNQDGSMPLPVTASVFPEDLDDAALAQSAIGQRDVQATALQMNMVAAGIANDGMVM
+EPNLVQAVRRPDLTTVSEFSPREHGRAMDPDVAHQVRDMMVATVEDGTASAAKSSTLQIA
+AKTGTAEKDGTANVNTWVTGFAPAQDPKVAVTIVYEDQNSSSAHTQAVESMQRIMEAVVA
+E
+>PROKKA_00021
+MNEAIRRTWTVMAAMLLVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE
+PIAESVPSGDAYHYQRVYHETELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA
+MEIITGATPEGDQVELTIDPELQRLAYDALPDGVRASAVVTDPTTGEILAMVSKPGFDSN
+ALSSHSPAEAQSAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT
+VDIPAAWTLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVELGQDRIREAA
+ERFGFNDSFEYPLPVTASVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM
+EPQLIEAVRRSDLTTVQEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA
+AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGVGHQTVVSGMKAIMEAVVT
+E
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000200.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000200.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f231adc37afbb25ba3f29f3aa47333c74c5fa69
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000200.fa
@@ -0,0 +1,45 @@
+>PROKKA_00042
+MSPTPTRPSRGPGWRLHGDGRTITPGTVVAPDERLSWPRTVGIGVQHVMAMFGATVLVPA
+LTGMPATTALLFSGLGTLLFLVITGNRLPSYLGSSFAFIAPLTAATTIGGTGAALGGILV
+TGLLLTVIGVIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQEVPVTTFGTAL
+AVVLTAVAFRGLLGRLSILVGIVVGYVLALAQGQVDFAAVREAAWIGLPPFHGPELRWDL
+LPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTMLSGAGGGVGTTTYA
+ENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAGIILYGMIGMMG
+VRIWVQNRVDFSNTVNLMAAGAGLIIAIADPQLVVGGLVFGGITLGTVAALVVYHLMTAI
+ARARGTEPVPEDEEQFEASEAGRLG
+>PROKKA_02055
+MSPTPTRPSRGPGWRLHGDGRTITPGTVVAPDERLSWPRTVGIGVQHVMAMFGATVLVPA
+LTGMPATTALLFSGLGTLLFLVITGNRLPSYLGSSFAFIAPLTAAAAIGGTGAALGGILV
+TGLLLTVIGAIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQEVPVTTFGTAL
+AVVLTAVTFRGLLGRLSILVGIVVGYVLALAQGQVDFAAVGEAAWIGLPPFHGPELRWDL
+LPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTMLSGAGGGVGTTTYA
+ENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAGIILYGMIGMMG
+VRIWVQNRVDFSNTVNLMTAGAGLIIAIADPQLVVGGLVFGGITLGTVAALVVYHLMTAI
+ARARGTEPVPEDEEQFEASEAGRLG
+>PROKKA_00358
+MSSSPSRPAPGFGWRLHGDGRTITSGTVVAPDERLSWPRTVGIGVQHVMAMFGATVLVPA
+LTGMPATTALLFSGVGTLLFLLLTGNRLPSYLGSSFAFIAPITAATTAGGVGAALGGVLV
+TGVLLAVIGLIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQEVPLTTFGTAL
+AIVLTAVLFRGLLGRLSILVGIVVGYLLALAQGQVDFTAVGEAGWLGLPPFHAPELHWNL
+LPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTTLSGLGGGVGTTTYA
+ENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAGIILYGMIGVMG
+VRIWVQNRVDFSSTINLMTAGAGLIIAIADPQLVLGGLVFGGITLGTIAALVVYHLMTAI
+ARVRGTEPVSEDDEAYEASEAGRLG
+>PROKKA_00300
+MSSSPTPSAPRAGHVPGPGPAVRSWRLHGDGRTITPGTVVAPDERLSWGRTVGIGVQHVM
+AMFGATVLVPAITGMPATTALLFSGLGTLLFLLITGNRLPSYLGSSFAFIAPLTAASASH
+GVGAALGGIAATGVLLMVIGVVVGWAGTGWIHALMPPAVMGTIVALIGLNLAGATTQAMQ
+EVPLTTFGTALAVVLTAVLFKGLLGRLSILVGIVVGYLLALAQGQVDFTAVGQAAWVGLP
+PFHTPELHWSLLPLFLPVVLVLIAENIGHVRTVGLMTKRDLDPLTGRALLADGLATTLSG
+LGGGVGTTTYAENIGVMASSKVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAG
+IILYGMIGVMGVRIWVQNRVDFSNTINLMTAGAGLIVAIANPELVVGGLVFGGITLGTLT
+ALVVYHLMTLVARVRGTEPVDEDTEDPASYRAAEAGRLG
+>PROKKA_00037
+MSPTPTRPSRGPGWRLHGDGRTITPGTVVAPDERLSWPRTVGIGVQHVMAMFGATVLVPA
+LTGMPATTALLFSGLGTLLFLVITGNRLPSYLGSSFAFIAPLTAAAAIGGTGAALGGILV
+TGLLLTVIGAIVHRAGTGWIHALMPPAVMGTIVALIGLNLAGATTTAMQEVPVTTFGTAL
+AVVLTAVTFRGLLGRLSILVGIVVGYVLALAQGQVDFAAVGEAAWIGLPPFHGPELRWDL
+LPLFLPVVLVLVAENIGHVRTVGLMTKRDLDPLTGRALIADGLSTMLSGAGGGVGTTTYA
+ENIGVMASSRVYSTAAYWVAGLTAIALAFLPKFGAAVATIPAGVAGGAGIILYGMIGMMG
+VRIWVQNRVDFSNTVNLMTAGAGLIIAIADPQLVVGGLVFGGITLGTVAALVVYHLMTAI
+ARARGTEPVPEDEEEFEASEAGRLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000204.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000204.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b4cd40a4b335148706edaf75ca34440c41d9775e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000204.fa
@@ -0,0 +1,25 @@
+>PROKKA_00046
+MSERTTYLLIDGENIDATLGTSILQRRPQPDERPRWKRLLGYLEDRWDQPVKGLFFLAID
+GEIPIPFVQALTALGFQPIMLRGEGKVVDIGIQRTAEALLGREDDVVLVSHDADFAPQLT
+DLAATPGRRTGIMGFEEFLSHELRRIPGVEFFDLEHAVGAFDSSLPRLRVIDVEAFDPYE
+FL
+>PROKKA_02059
+MSERTTYLLIDGENIDATLGTSILQRRPQPDERPRWKRLLGYLEDRWDQPVKGLFFLAID
+GEIPIPFVQALTALGFQPIMLRGEGKVVDIGIQRTAEALLGREDDVVLVSHDADFAPQLT
+DLAATPGRRTGIMGFEEFLSHELRRIPGVEFFDLEHAVGAFDSSLPRLRVIDVEAFDPYE
+FL
+>PROKKA_00349
+MGRRADAPAGPGRAVVVPTTTSSPAPASAPVHTPAPAPATSSAPAGSLGQVSESTTYLLV
+DGENIDATLGTSILQRRPQPDERPRWNRLLSFMGEHWDQPVKGLFFLAIDGDIPVPFVQA
+LTAIGYKPIMLRGAGKVVDIGIQKTMEALQEREDDVVLVSHDADFAPQLTDLAATPDRRT
+AIIGFEEFLSHELRRIPDVEFFDLEYGVGAFDTPLRRLRVIDIDEFDPLEFL
+>PROKKA_00294
+MSRRADLPTGPATAVPAAPAAPVSPTAEDRSAATPADTLDTMSARTTYLLVDGENLDATL
+GMSVLNRRPNPEERPRWNRVLRHVERAWGQEVRPLFFLAVDEDGDIPFGFVQALTTMGYQ
+PILLRGAGKVVDIGIQRMAEALIGRDADVVLASHDADFAPQMLDLAAHGHKIAVMGFDEF
+MSAELRAVNGMEVWDLEHDVAAFDVPLPRLRVIDIDDFDPRDFL
+>PROKKA_00041
+MSERTTYLLIDGENIDATLGTSILQRRPQPDERPRWKRLLGYLEDRWDQPVKGLFFLAID
+GEIPIPFVQALTALGFQPIMLRGEGKVVDIGIQRTAEALLGREDDVILVSHDADFAPQLT
+DLAATPGRRTGIMGFEEFLSHELRRIPGVEFFDLEHAVGAFDSSLPRLRVIDVEAFDPNE
+FL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000205.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000205.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5744dd4725f8165fadaa10a7cd5854ab8fc18679
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000205.fa
@@ -0,0 +1,40 @@
+>PROKKA_00047
+MPAPSSHAPAATHTARGRLVWVDVARGLALVAMMVAHTAPAGGPGGVLHLSEHLTAPLFA
+ALVGVGARLEAEWLGRGRAVPRALVRAAALCGAAWLTGHFGAAVVNVLAHLAVLTVIMAL
+LAALPLAAHLVLAVLAGGGGLLLAATPTADVVDRLVPLAQALGLSRATLTPYVSAFLTDG
+PYRLPLFLTWALLGAVLVRTVHGTTTAAPARSARLTGLAWAAGGIALAGVVLALSRTQTG
+AAPVPYTATPAEALLDTGLVLTVLGACAALAPRRAGLLAVPGAMTLSVYVAHLWYLGWVR
+RLGPGPWRSATGTDDTWFNLAVLVAGALLLPLLWRAVVRIGPFRAGPLEGVVRLLTAPFD
+RAR
+>PROKKA_02060
+MPAPSSHAPAATHTARGRLVWVDVARGLALVAMMVAHTAPAGGPGGVLHLSEHLTAPLFA
+ALVGVGARLEAEWLGRGRAVPRALVRAAALCGAAWLTGLFGAAVVNVLAHLAVLTVLMAL
+LAALPLAAHLVLAVLAGGGGLLLAATSTADVVDRLVPLAQALGLSRATLTPWVSAFLTDG
+PYRLPLFLAWALLGAVLVATVHGTTTAAPARRARLTGLAWAAGGIALAGVVLALSRTQTG
+AAPVPYTATPAEALLDTGLVLAVLGACAALAPRRAGLLAVPGAMTLSVYVAHLWYLGWVR
+RLGPGPWRSATGADDTWFNLAVLVVGALLLPLLWRAVVRVGPFRAGPLEGVVRLLTAPFD
+RAR
+>PROKKA_00348
+MPRVSSRPHTGRDRLVWVDVARGVALVSMFVAHVAPSGGPAGVLNLSEHLTAALFAALVG
+VSARLEVQGLGVGRALVRAMVRAAALLGAAWLTSLFDAAVVDVLTHLAVITVLMALLAAL
+PLAVHLVLALLAGGGGILLTASGTLAVADALAPAARALGLDPAELVPAVAGFLTAGPYRL
+TAFLGWALLGAVLVRTVHGTTTALPRSGRLVGLGWGVGGVVLAGLVILLSRVQTGAAPVP
+YTGTAAEILVDTGLVLGVLGLCAAVVPSRPSPATDLLAVPGSMTLSVYVAHQAYLGWVLT
+AGPGPWVDGRGADDTWFNLAVLLAGGILLPLLWRGLVRVRPFRAGPLEGVVRLVTDPIGR
+RSRGEH
+>PROKKA_00295
+MTLAAGHRLTWVDVARGLALVSMFVAHTAPTGGPGGVLNLSEHLTAALFAALVGVSAHLE
+QRRHGFWRAFLRAVVRAAALCGAAWLTSHFGAAVVDVLTHLAVLTVLMSVLALLPGLVQL
+LLVPAAAWAGVRVGALTADDVAARLEPARALVPAQVRPGPAVVAEQAAAFFTVGPYFLLF
+FTAWALLGAVVVRSVQGGGLRAALRLGGHPGPGLGGRAAGGVWAGVGLLVGGAGVALARQ
+RTEDSPVPYEATWDYALLAAGLVLIVLGACAAVVPSHVPWLTAVLAVPGSMTLSVYVAHQ
+AYLGWVLRAGPGPWLSELGTDDTWFNVGALCAAGLLLPLLWRALVRAEPWRRGPLEGPVA
+LVTHGLARR
+>PROKKA_00042
+MPAPSSHAPAATHTARGRLVWVDVARGLALVAMMVAHTAPAGGPGGVLHLSEHLTAPLFA
+ALVGVGARLEVEWLGRGRAVPRALVRAAALFGAAWLTGLFGAAVVNVLAHLAVLTVLMAL
+LAALPLAAHLVLAVLAGGGGLLLAATPTADVVDRLLPAAQALGLSRATLTPWVSAFLTDG
+PYRLPLFLAWALLGAVLVATVHGTTTAAPARRARLTGLAWAAGGIALAGVVLALSRTQTG
+AAPVPYTATPAEALLDTGLVLIVLGACAALAPRRAGLLAVPGAMTLSVYVAHLWYLGWVR
+RLGPGPWRSATGADDTWFTLAVLVAGALLLPLLWRAVVRIGPFRAGPLEGVVRLLTAPFD
+RAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000206.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000206.fa
new file mode 100644
index 0000000000000000000000000000000000000000..25f9b9d92d14a56b68c1e8bcf241999c5c2be86e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000206.fa
@@ -0,0 +1,25 @@
+>PROKKA_00050
+MAALTDRAVLIAGATSASGRAAARTLLDAGAHVVATGRDAAKLAPLAGLGAETATLDLTD
+ETAVRGLVEDLHARGTRIDGLLHLVGGWRGGGGLAGQTEADYRALEASFTALRHVSRALD
+DDLRASSAGRLAIVSSTAVTRPLAGGANYAAVKAASEAWTRAVAQGWAKATRDAETPLRS
+AAVVFRVKSLAGLEERLAEEYARLWKAEAGALNDAVLTLQEKGT
+>PROKKA_02063
+MAALTDRAVLIAGATSASGRAATRTLLDAGAHVVPTGRDAAKLAPLAALGAETAALDLTD
+EAAVRGLVEDLHARGTRIDGLLHLVGGWRGGGGLTGQTEDDYRALEASFTALRHVSRALD
+DDLRASSAGRLAIVSSTAVTRPLAGGANYAAVKAASEAWTRAVAQGWAKAARDAEAPLRS
+AAVVFRVKSLAGLEERLAEEYARLWKAEAGALNDAVLTLQEKGTD
+>PROKKA_00353
+MGTLTGRTVLISGATSASGLAAARALLAAGADVVATGRSPERLAPLAALGADTAALDLSD
+EAAVRGLVEDLHARGVRVDGLLHLVGGWRGGGGLAGQSEEDYRALESSLTALRHVSRALD
+DDLRASSAGRLAIVSSTAVARPLAGGAAYAAVKAASEAWTRAVAQGWDKAARDAGTELRG
+AAVVLRVKSLAGLEDRLAEQFVRLWSADAAQLNDSILAVQEKETA
+>PROKKA_01218
+MSAPAAPDLTGALVLVTGASSGIGSALARGLAAAGADLVLVARRAGRLAALADELRAAHR
+TEVTVLPRDLAAPDAGPALRAELSSRGPRVTGLVNNAGFGSGLPFGREDPARLEAMPAEE
+ERGRERVLCVSPSSTGTEFFDVAGTPGAGGGFARRAAPDDVAAAVLRVLARRGGPAEVVP
+HDRAVTVAARLLPRTVLRGMGAMHRRGAARR
+>PROKKA_00045
+MAALTDRAVLIAGATSASGRAAARTLLDAGAHVVATGRDAAKLAPLAELGAETAALDLTD
+ETAVRGLVEDLHARGTRIDGLLHLVGGWRGGGGLAGQTEEDYRALEASFTALRHVSRALD
+DDLRASSAGRLAIVSSTAVTRPLAGGANYAAVKAASEAWTRAVAQGWAKAARDAEAPLRS
+AAVVFRVRSLAGLEERLAEEYARLWKAEAGALNDAVLTLQEKGTD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000208.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000208.fa
new file mode 100644
index 0000000000000000000000000000000000000000..704a36f023ff8987a9f3c73470a8546ca3b7a538
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000208.fa
@@ -0,0 +1,55 @@
+>PROKKA_00055
+MTENTAALPAAERPGTPALPQDLIDVDALLEAYHTGHPDVTDPAQKVVFGTSGHRGSAFT
+TSFNDDHIAAITQAVVEYRAHHGITGPVLVGRDTHALSGPAQDTAVEVLLGNDVEVLVDS
+RGGYTPTPAVSHAILHLNAGRELSPSGFAVDGDNAGLVDGLVITPSHNPPADGGFKYNPP
+HGGPADTEATTWIADRANELLAAGLAGVHRVASADVAGHAKLGGFDFLDRYVSDLPQVID
+VEAIREAGVRIGADPMGGASVAYWGEIADRHGLDLTVVNPEVDPRFGFMTLDWDGKIRMD
+CSSPNAMASLIERMTPDADGHAPFDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYL
+YRHRQQWPQSAGVGKTLVSSSMIDRVAGDLGRELVEVPVGFKWFVPGLLTGTGVFGGEES
+AGASFVQFDGSPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGDPAYARIDAPA
+TAEQKAKLKTLSPDDVPVTELAGETILATLTNAPGNDAPIGGLKVVTQHAWFAARPSGTE
+DVYKIYAESFRGPEHLKQVQAEAQKLVDAVIG
+>PROKKA_02068
+MTENTAALPAAERPGTPALPQDLIDVDALLEAYRTGHPDVTDPAQKVVFGTSGHRGSAFT
+TSFNDDHIAAITQAVVEYRAHHGITGPVLVGKDTHALSGPAQDTAVEVLLGNDVEVLVDS
+RGGYTPTPAVSHAILHLNAGRELSPSGFAVDGDNAGLVDGLVITPSHNPPADGGFKYNPP
+HGGPADTEATTWIADRANELLAAGLAGVHRVASADVAGHAKLGGFDFLDRYVSDLPQVID
+VEAIREAGVRIGADPMGGASVAYWGEIADRHGLDLTVVNPEVDPRFGFMTLDWDGKIRMD
+CSSPNAMASLIERMTPDADGQAPFDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYL
+YRHREQWPQSAGVGKTLVSSSMIDRVAGDLGRELVEVPVGFKWFVPGLLTGTGVFGGEES
+AGASFVQFDGSPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGDPAYARIDAPA
+TAEQKAKLKTLSPDDVPVTELAGETILATLTNAPGNDAPIGGLKVVTQHAWFAARPSGTE
+DVYKIYAESFRGPEHLTQVQAEAQRLVDAVIG
+>PROKKA_00342
+MTEHTAAPPASERPGTPALPQDLIDVDALLTAYRTGRPDVSDPAQKVVFGTSGHRGSALK
+TSFNDDHIAAITQAVVEYRAEHGITGAVLVGKDTHALSGPAQDTAVEVLLGNDVEVLVDS
+RGGYTPTPAVSHAILHLNAGRDLTPAGFSADGDNAGLVDGLVITPSHNPPADGGFKYNPP
+HGGPADTEATTWIADRANALLAAGLEGVRRVAAADVDGHAKLGGFDFLDRYVTDLPDVID
+VEAIREAGVRIGADPMGGASVAYWGEIARRHGLDLTVVNPDADPRFGFMTLDWDGKIRMD
+CSSPHAMASLIERMTPDADGQAPYDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYL
+YRHRERWPADAGVGKTLVSSSMIDRVAGDLGRELVEVPVGFKWFVPGLLTGTGVFGGEES
+AGASFVKLDGGPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGSPAYARIDAPA
+TAEQKARLKTLSPDDVTVTELAGETILATLTNAPGNDAPIGGLKVVTQNAWFAARPSGTE
+DVYKIYAESFRGPEHLKQVQEEAQRLVDAVIG
+>PROKKA_00281
+MSTPAAGRAGTPALPEDLIDVEALLAAYRDLHPDPADPAQKVVFGTSGHRGSALKSSFND
+DHIAAITQAVVEYRAEHGITGAILVGKDTHALSGPAQDTAVQVLLANDVEVLVDSRGGFT
+PTPAVSHAILHLNAGRDLTAAGFSADGDNAGLVDGLVITPSHNPPADGGFKYNPPHGGPA
+DTDATSWIAARANDLLAARLDGVTRLAPEDVEGHAKLGSFDFLDRYVTDLPQVIDLDAIR
+EAGVRIGADPMGGASVAYWGEIGRRHGLDLTVVNPDVDPQFGFMTLDWDGKIRMDCSSPN
+AMASLIERMTPDADGHAPFDVATGNDADSDRHGIVTPDGGLMNPNHFLAVSIDYLYRNRS
+QWPQNAGVGKTLVSSSMIDRVATDLGRELVEVPVGFKWFVPGLLSGTGVFGGEESAGASF
+VKFDGGAWSTDKDGLLLCLLAAEIQAVTGQSPSERYRDLVALHGDPAYARIDAPATAEQK
+AALKALSPDDVTATELAGETILAALTNAPGNDAPIGGLKVVTKNAWFAARPSGTEDVYKI
+YAESFLGEEHLKQVQQEAQAIVDAVIS
+>PROKKA_00050
+MTENTAALPAAERPGTPALPQDLIDVDALLEAYHTGHPDVTDPAQKVVFGTSGHRGSAFT
+TSFNDDHIAAITQAVVEYRAHHGITGPVLVGKDTHALSGPAQDTAVEVLLGNDVEVLVDS
+RGGYTPTPAVSHAILHLNAGRELSPSGFAVDGDNAGLVDGLVITPSHNPPADGGFKYNPP
+HGGPADTEATTWIADRANELLAAGLAGVHRVASADVAGHAKLGGFDFLDRYVSDLPQVID
+VEAIREAGVRIGADPMGGASVAYWGEIADRHGLDLTVVNPEVDPRFGFMTLDWDGKIRMD
+CSSPNAMASLIERMTPDADGQAPFDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYL
+YRHREQWPQSAGVGKTLVSSSMIDRVAGDLGRELVEVPVGFKWFVPGLLTGTGVFGGEES
+AGASFVQFDGSPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGDPAYARIDAPA
+TAEQKAKLKTLSPDDVPVTELAGETILATLTNAPGNDAPIGGLKVVTQHAWFAARPSGTE
+DVYKIYAESFRGPEHLTQVQAEAQKLVDAVIG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000211.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000211.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a6041f4dc439a1de617d7e4755cfa533b7703d48
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000211.fa
@@ -0,0 +1,65 @@
+>PROKKA_00058
+MVSFSHTDDGTSEAAWAEGGVGELPELRLPVWDAQTLLLVAVAHPDDETLAATGLIRSAL
+RDGARVHVLVATAGEASHPHSPTHTPEDLVRLRRDEMEHALDALAAGLPASAGPGSPARD
+RLTWASLALPDSGVAEHEDAVRDAVAAALDAHPGPAVLASHDPGDGHADHEAVGRAVGAV
+AGECDLPLYAFPIWFWHWADPADLPARRYRRLPLTDDDRAARRAALDAHASQVRPLSAAP
+GDEAILGPAVLAHHERPFEAHRVSGPDDADAHRAAAVFDRLYRAQEDPWRYLSSSYEARK
+RALTLAALPRPRYGTVVEAGASIGVLTADVAARADRVVGLEASSTAVERAAARLAGAPHA
+EVRRAVLPADWPADVAGADLVIASEIGYFLQPEELDALIDDADAALAPGGELLLCHWRHP
+IEGWPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHAVVVVPAKDEQERLP
+AALAALAAALDRWEEHHAQGTAAVVVAADRCDDATVAAALEARAADPRIHVLELGEPTAG
+QAGVGRARLEGARRARALFPDVPAERLWLASTDADSRVPADWLLAQTVAAGHDEVLVLGT
+VDVHQGPLRQAWLRGYRHEEGHPHVHGANLGLPWSLYEAVGGFPPVAEHEDVGLAEAVRA
+LAGERDGGDGRRVRVIATDTTRVLTSSRLEGRTPGGFSGYLKAVGRPG
+>PROKKA_02071
+MVSFSHTDDGTSEAAWAEGGVGELPELRLPVWDAQTLLLVAVAHPDDETLAATGLIRSAL
+RGGARVHVLVATAGEASHPHSPTHTPADLVRLRRDEMEHALDALAAGLPASAGPGSPARD
+RLTWASLALPDSGVAEHEDAVRDAVAAALDAHPGPAVLASHDPGDGHADHEAVGRAVGAV
+AGECDLPLYAFPIWFWHWADPADLPARRYRRLPLTDDDRAARRAALDAHASQVRPLSAAP
+GDEAILGPAVLAHHERPFEAHRVSGPDDADAHRAAAVFDRLYRAQEDPWRYLSSSYEARK
+RALTLAALPRPRYGTVVEAGASIGVLTAAVAARAGRVVGLEASPTAVERAAARLAGAPHA
+EVRRAVLPADWPADVAGADLVIASEIGYFLQPEELDALIDDADAALAPGGELLLCHWRHP
+IEGWPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHAVVVVPAKDEQERLP
+AALAALTAALDRWEEHHAQGTAAVVVAADRCDDATVAAALEARAADPRIHVLELGEPTAG
+QAGVGRARLEGARRARALFPDVPAERLWLASTDADSRVPADWLLAQTVAAGRDEALVLGT
+VDVRQGPLRQAWLRGYRHEEGHAHVHGANLGLPWSLYEAVGGFPPVAEHEDVGLAEAVRA
+LAGERDGGEGRRVRVIATDTTRVLTSSRLEGRTPGGFSGYLKAVGRPG
+>PROKKA_00337
+MVSFSHTDAGTSEEAWAAAGVGALPVLESPAWDADTLLLVAVAHPDDETLGATGLIRSAL
+RGGARVHVLVATAGEASHPDSPTHAPEDLVRLRRAEMEHALDALAADLPGPGEDRRSALT
+WESLGLPDSGVAGREDAVRAAVVAALAAHPGPAVLASHDPGDGHADHEAVGRAVGELAGE
+RDLPLCAFPIWFWHWADPAELPARRYRRLALTDDDRAARRAALDAHASQVRPLSDAPGDE
+AVLGPQVLAHHDRPFEAHRLSGPDDADAHRAAAVFDRLYREHEDPWRYLSSPYEARKRAL
+TLAVLPRPRYGTVVEAGASIGVLTGEVAARADRVVGLEASPTAVERAAARLADTPHAEVR
+RAVLPGHWPDDVAGADLVIASEIGYFLQPEELDALVDDADAALAPGGELLLCHWRHPIEG
+WPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHAVVIVPAKDEQERLPAAL
+AALGAALDRWEEHHAQGSAAVVVAADRCDDATVAAAVAARHADPRVHVLELGEPGPGEAG
+VGRARAEAARRARALFPDVPAQRLWLASTDADSRVPADWLLAQTTAAGPDGALVLGTVDV
+REGALRRAWVRDYRHEEGHPHVHGANLGLPWSLYEAAGGFPPVAEHEDVRLVEAVRALAE
+ARVRATDTTRVLTSSRLTGRTPGGFAGHLQEVGGEAVPRRGAQARP
+>PROKKA_00277
+MVSFDHRDDGTAEAVWMAAGVGELPALPARAWTRADTLLVAVAHPDDETLGAAGLIRAAL
+RGGAAVHVAVATAGEASHPDSPTHTPADLVRLRRAEMDHALAALADGLGPDAGALTWESL
+ALPDGGLTDRPDEVRAALERVLAGRTPAEEGGGAVVLVSHDPDDGHGDHDAVGAAAAALA
+ADHDLELYAFPLWLWHWGAPEDLAPRRYRRLELAAGDDAARLAALDAHASQTRPLSAAPG
+DEAILPERMIAHFTRGFETYRRTAPDDADASRASAVFDRLYREHEDPWRYLTSPYEARKR
+ALTLAVLPRPRYGTVVEAGASIGVLTAALAERAERVVGLEASQVAVERAAAHLAEIPHAE
+VRRAVLPADWPADVGPAEEGAGAPADLVVASEIGYFLQPEELDALVDAADASLGAGGELL
+LCHWRQPITGWPLDGDAVHDRVAADPRWRLLSEHVEADLRLSVHARAAAATHAVAVVPAM
+DEAEHLPAGLDALSAALDLWEAQHTQGSAAVVTVVPADDAPTLEAAHAARARDPRIRVLE
+LAPGAGGVGRARAAAARHARGLFPDVPAEALWLASTDADTRVPADWLVGQPALAARRRAD
+GQVLVLGTVDLPAHADDDLAHRWRADYEHREDHPHVHGANLGLPWGLYERAGGFAEVAEH
+EDVRLAEAVRALGEDRVLATDRVRVHTSSRLEGRTPGGFAGFLRGLLEEGAAEG
+>PROKKA_00053
+MVSFSHTDDGTSEAAWAEGGVGELPELRLPVWDAQTLLLVAVAHPDDETLAATGLIRSAL
+RGGARVHVLVATAGEASHPHSPTHTPEDLVRLRRDEMEHALDALAAGLPASAGPGSPARD
+RLTWASLALPDSGVAEHEDAVRDAVAAALDAHPGPAVLASHDPGDGHADHEAVGRAVGAV
+AGECDLPLYAFPIWFWHWADPADLPARRYRRLRLTDDDRAARRAALDAHASQVRPLSAAP
+GDEAILGPAVLAHHERPFEAHRVSGPDDADAHRAAAVFDRLYRAQEDPWRYLSSSYEARK
+RALTLAALPRPRYGTVVEAGASIGVLTADVAARADRVVGLEASPTAVERAAARLAGAPHA
+EVRRAVLPADWPADVAGADLVIASEIGYFLQPEELDALIDDADAALAPGGELLLCHWRHP
+IEGWPLDGDAVHARVAADPRWRLRTELVEDDFRLSLHVRAAAATHAVVVVPAKDEQERLP
+AALAALTAALDRWEEHHAQGTAAVVVAADRCDDATVAAALEARAADPRIHVLELGEPTAG
+QAGVGRARLEGARRARALFPDVPAERLWLASTDADSRVPADWLLAQTVAAGRDEALVLGT
+VDVRQGPLRQAWLRGYRHEEGHAHVHGANLGLPWSLYEAVGGFPPVAEHEDVGLAEAVRA
+LAGERDGGDGRRVRVIATDTTRVLTSSRLEGRTPGGFSGYLKAVGRPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000214.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000214.fa
new file mode 100644
index 0000000000000000000000000000000000000000..81a5bf3b59d7ab2556ba0b82c66781b031b3265b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000214.fa
@@ -0,0 +1,35 @@
+>PROKKA_00062
+MTGTDSADATPSRLRYAFLGPAGTFTEAALRKVADPAEAEFVPAGSVLSAVAALRRGEVD
+RAVVPIENSVEGGVSATVDEIALGETLQILAEVHVAISFVLVGRPGVAIEDVRRVTTHPH
+AWAQVRGWAETALPGVEFTPAPSTAAGAGLVAQGDFDAAVCAPLVAEQTGLPVLAERIED
+VPGAVTRFVLLSRPTALPAPTGADKTTLVVPLPEDRPGALGQILAEFTTRGVNLSRIESR
+PTGEGIGRYFFSLDLEGHLAEARVGDALAALYREYPDLRFLGSYAQAEPVPTRVPAEFTD
+AAYRSGRAWVESLRSR
+>PROKKA_02075
+MTGTGSADATPSRLRYAFLGPAGTFTEAALRKVADPAEAEFVSAGSVLSAVAALRRGEVD
+RAVVPIENSVEGGVSATVDEIALGETLQILAEVHVPISFVLVGRPGVAMEDVRRVTTHPH
+AWAQVRGWAETALPGVDFTPAPSTAAGAGLVAQGDFDAAVCAPLVAEQTGLPVLAERIED
+VPGAVTRFVLLSRPTALPAPTGADKTTLVVPLPEDRPGALGQILAEFTTRGVNLSRIESR
+PTGEGIGRYFFSLDLEGHLAEARVGDALAALYREYPDLRFLGSYAQAEPVPTRVPAEFTD
+AAYRSGRAWVESLRSR
+>PROKKA_00333
+MTRDDAAPLGRCTFLGPAGTFTEAALRAVPGAEQAELIPATSVPAALAAVRAGEADHAMV
+PIENSVEGGVSATLDDIASGDDLQILREELVQISFVLVGRPGVELADVRRVSTHTHAWAQ
+VRGWVEANLPGVEYTPSGSTAAAARALADAEPGSEPFDAAVCAPLVAEQTGLPVLARAIE
+DVTGAVTRFVLVGRPGPLPAHTGSDKTTLTVPLPDDHPGALREILDQFATRGINLSRIES
+RPTGEGMGKYFFSIDLEGHLAEERVAAAMGALHRIFPGVRFLGSYPRAEHRPVAVRRHTS
+DDAYRAGRAWVDGLLAR
+>PROKKA_00274
+MSPAPRYAFLGPAGTFTEAALRQVASPEDVDLLPASSVLAALAAVRVGEAERAVVPIENS
+VEGGVTATLDDIGADEPLQILAEVLVPISFVLVGRPGVALEDVRRVTTHTHAWAQVRGWM
+EAHLPGVEFTPAGSTAAGARALLPSAGGDGAVASFDAAVCAPLVAEQTGLPVLAEAIEDV
+TGAVTRFVLVSRPGPVPEPTGADKTTLTVPLPDDHPGALREILDQFATRGINLSRIESRP
+TGEGMGRYFFSIDLEGHVAEERVGAALAALHRTFPGVRFLGSYPRAEGRPPTVPEHVTDA
+AYRRGTAWVRGLRSR
+>PROKKA_00057
+MTGTDSADATPSRLRYAFLGPAGTFTEAALRKVADPAKAEFVSAGSVLSAVAALRRGEVD
+RAVVPIENSVEGGVSATVDEIALGETLQILAEVHVPISFVLVGRPGVAIEDVRRVTTHPH
+AWAQVRGWAETALPGVEFTPAPSTAAGAGLVAQGDFDAAVCAPLVAEQTGLPVLAERIED
+VPGAVTRFVLLSRPTALPAPTGADKTTLVVPLPEDRPGALGQILAEFTTRGVNLSRIESR
+PTGEGIGRYFFSLDLEGHLAEARVGDALAALYREYPDLRFLGSYAQAEPVPTRVPAEFTD
+AAYRSGRAWVESLRSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000218.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000218.fa
new file mode 100644
index 0000000000000000000000000000000000000000..80722fcdf276cdcfabe310fe8082823b0663db0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000218.fa
@@ -0,0 +1,46 @@
+>PROKKA_00069
+MGQVDTGRTGRRDRRTERPRSRSLHAVLLAALAAVLVACGPVTAPPAPSSAPASSTTAAP
+TSSSPSAGPTAAEVAAAVEPGLETSPGTASAEFRDLATGEVLYARDADEPVAPASSLKVL
+AAAAIVSALGPETTLQTTVVAQPTADDAATELVLVGGGDVLLGTGASDSTHVSGRAGLRT
+LAQRTVAGLVEDGVTGQVVVSTDLRLFTDRTALNPRWTSDIPESGNIAPVQPLATYGGRE
+APGTGEDRIEDPAQFAALTFQAALDDAVAASGADLEVGLRDTLPATEVPRATVLAAAPVA
+AVESASVGEQVAYLLAHSENQVVEALAHTAAPATDLPATHEGATRLLTATVEDLGVDTAG
+MALVDSSGLSPDNRVSAGQLAGVVAGVARTPALATVLEGLPRPGEDSTLGDRFPDAPARQ
+AVAAKTGTLDQTVSLTGTVTTTSGRVLAFSIICSDLQWKLEPARAAVDEAVSAVAGL
+>PROKKA_02082
+MGQVDTGRAGRRDRRTEHRRSRSLPAVLLAALAAVLVACGPVTAPTAPSSASASTSTAAP
+TSSSPSAGPTAAEVAAAVEPGLETSPGTVSAEFRDLATGEVLYARDADEPVAPASSLKVL
+AAAAIVSALGPETTLQTTVVAQPTADGAATELVLVGGGDVLLGTGASDSKAVSGRAGLRT
+LAERTVAGLVEDGVTGRVVVSTDLRLFADRTALNPRWTSDIPESGNIAPVQPLATYGGRE
+APGTGEDRIEDPAQFAALTFQAALDDAVAASGADLEVGLRDTFPATEVPRATVLAAAPVA
+AVESAPVGQQVAYLLAHSENQVVEALAHTAAPATDLPATHEGATQLLTATAEDLGVDTAG
+MALVDSSGLSPDNRVSAGQLAGVVAGVARTPALGTVLEGLPRPGEDSTLGDRFPDAPARQ
+AVAAKTGTLDQTVSLTGTVTTTSGRVLAFSIICSDLQWKLEPARAAVDEAVSAVAGL
+>PROKKA_00323
+MTPGSPFASLLAALAAALLSAAPVLTPLAGPAALAPGNPVTAEAVAAPSPDARALASAVD
+AALDASPGRVAAQVRDAATGEVLHARDADFLAAPASSLKVLTAAAALRTLGPERTLRTRV
+VAVPAADDGATELVLVGGGDVLLGDGASDPDAVAGRAGLRTLAERTVAGLAEAGVSGDVV
+VSVDLRLFDGAAVNPAWTPDLLEDGHVSAVQPLATWGGREVPGVDEERIEDPAGHAALVF
+QRLLDEEIERTGADLDLGLRDSIPATTAVRDDVVAAEPTAQVESAPVAEVAAYMLAHSEN
+QVAEALGHLSAYAVGRPATHEGAADLLEDVAADLGADTAGMAVLDASGLAEGSLVSPAQL
+AAVVSAASRVPWLAPVLDGLPRPGEDSTLDERFRGTAAEGAVAAKTGTLDHTVSLTGTVT
+TQDGRVLAFSIVASDLDWRLDEAREAVDAAVTAMAGL
+>PROKKA_00265
+MTPSNRAARVAAVTRVLLALAICALLGLLAHDVLLPRLPTPAAPAASAPSAPVPAASPSG
+GATAPSSTALASVAPVDPADVAAAVAPALAQAPGTASAEVRDAATGEVLYARSADQAVAP
+ASALKILTAVTAVDVLGADRALTTSVVALPGGGATELVLVGGGDALLGAGASDPGRVDGR
+AGLRTLARRTVAGLRERGVTGPVAVSTDLRLFTDASPLNPAWSAGLVESGNITAVQPLAT
+YGGRTAPGTGEDRIADPAAFAALAFQRELTAAVADSGADLSVRARDVVPATSAPRGDVLA
+TEPVARVESAPVGQQVAYLLAHSENQVAEVLARVAAAADGRPATHAAVPGLLRDRAAAHG
+VDTAGMRLVDASGLSPQNRVTAHQLAGLVEAVQADPALAPVRDGLPRPGEDSTLAERFPG
+SPAREAVAAKTGTLDQTVSLTGTVTTGSGRVLAFSIVCSGVDWRIAPARAAIDEAVSALA
+AL
+>PROKKA_00063
+MGQVDTGRAGRRDRRTEHRRSRSLPAVLLAALAAVLVACGPVTAPPAPSSAPAASTTAAP
+TSTSPSAGPTAAEVAAAVEPGLATSPGTVSAEFRDLATGEVLYARDADEPVAPASSLKVL
+AAAAIVSALGPETTLQTTVVAQPTADGAATELVLVGGGDVLLGTGASDSTHVSGRAGLRT
+LAERTVAGLVEDGVTGQVVVSTDLRLFTDRTALNPRWTSDIPESGNIAPVQPLATYGGRE
+APGTGEDRIEAPAQFAALTFQAALDDAVAASGADLEVGLRDTLPATEVPRATVLAAAPVA
+AVESASVGEQVAYLLAHSENQVVEALAHTAAPATDLPATHEGATRLLTATAEDLGVDTAG
+MALVDSSGLSPDNRVSAGQLAGVVAGVARTPALATVLEGLPRPGEDSTLGDRFPDAPARQ
+AVAAKTGTLDQTVSLTGTVTATSGRVLAFSIICSDLQWKLEPARAAVDEAVSAVAGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000221.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000221.fa
new file mode 100644
index 0000000000000000000000000000000000000000..02cd2fba391699a79628748ddadd40f6b6221bba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000221.fa
@@ -0,0 +1,25 @@
+>PROKKA_00072
+MDAQDVQNDLTHVLMSREDVQDTITDLARQIDRDYADKDLLIVAVLKGAVMVVADLTRAL
+HSHVELDFMAVSSYGSGTKSSGVVRILKDLDADLTGRHVLIVEDIIDSGLTLSWLKANLE
+SRGPASVEICTLLRKPEAMKVDIDVKYVGRDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH
+VYS
+>PROKKA_02085
+MDAQDVQNDLTHVLMSREDVQDTITDLARQIDRDYADKDLLIVAVLKGAVMVVADLTRAL
+HSHVELDFMAVSSYGSGTKSSGVVRILKDLDADLTGRHVLIVEDIIDSGLTLSWLKANLE
+SRGPASVEICTLLRKPEAMKVDIDVKYVGRDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH
+VYS
+>PROKKA_00320
+MDAQDVQNDLTHVLMRREEVQETVKDLAAQIDRDYEGKDLLIVAVLKGAIMVVADLTRAL
+HSHVQIDFMAVSSYGSGTKSSGVVRILKDLDADLTGRDVLIVEDIIDSGLTLSWLKANLE
+SRGPASVEICTLLRKPDAMKVEIDVKYVGRDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH
+VYS
+>PROKKA_00262
+MDAQDVQNDLTHVLMSKEEVQDTIRDLAAQIDRDYEGKDLLIVAVLKGAVMVVADLTRAL
+HSHVEMDFMAVSSYGSGTKSSGVVRILKDLDADLTGRHVLIVEDIIDSGLTLSWLKANLE
+TRGPASVEICTFLRKPDAMKVDIDVKYVGKDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH
+VYS
+>PROKKA_00066
+MDAQDVQNDLSHVLMSREDVQDTITDLARQIDRDYADKDLLIVAVLKGAVMVVADLTRAL
+HSHVELDFMAVSSYGSGTKSSGVVRILKDLDADLTGRHVLIVEDIIDSGLTLSWLKANLE
+SRGPASVEICTLLRKPEAMKVDIDVKYVGRDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH
+VYS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000222.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000222.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e6a6faeb4cfa27e8c193bf2b88997f11c0437db1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000222.fa
@@ -0,0 +1,65 @@
+>PROKKA_00074
+MKKLFNKPYVWILLGLLVLAVAIPLTTSQSGRTMVDTNVGMALLKDDKAAQARVVDGDQR
+VDLTLREPYKQDDRDLGKEVYFYFATARATDVVTAVDDSALDGYTDEPVRSNWFLSLLGF
+MVPFLLIALLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE
+IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV
+GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD
+ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVDAPDLEGRAKILEVHAQGKPIALDVDL
+RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH
+ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL
+AYAMGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGSSEPFVG
+GAAGGSSREYSEELAYLVDAEVRTLLDQAHAEAHWVLTENRDVLDRLAYELLEKETLTQE
+AIAAIFADVRKRPERGVWLASDDRLPQDIPPVLSPSERRSRHDGGEQTPVGVEGTTVPVR
+PEGAPPSSLGGDAAGPGLPPHGGPSNTPGPGEGPTF
+>PROKKA_02087
+MKKLFNKPYVWILLGLLVLAVAIPLTTSQSGRTMVDTNVGMALLKDDKAAQARVVDGDQR
+VDLTLREPYKQDDRDLGKEVYFYFATARATDVVTAVDDSALDGYTDEPVRSNWFLSLLGF
+MVPFLLIALLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE
+IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV
+GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD
+ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVDAPDLEGRAKILEVHAQGKPIALDVDL
+RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH
+ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL
+AYAMGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGSSEPFVG
+GAAGGSSREYSEELAYLVDAEVRTLLDQAHAEAHWVLTENRDVLDRLAYELLEKETLTQE
+AIAAIFADVRKRPERGVWLASDDRLPQDIPPVLSPSERRSRHDGGQQTPVGVEGTTVPVR
+PEGAPPSSLGGDAAGPGLPPHGGPSNTPGPGEGPTF
+>PROKKA_00319
+MKKLFNKPYIWILLGLLVLAVAIPLATSQTGRTMVDTNVGMAMLQDDKAAQARVVDGDQR
+VDLTLREPYSQDGRDLGKEVYFHFATARASDVVTAVDDSALDGYTDEPVRSNWLLSLLGF
+MIPFLLIALLFWFLLSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE
+IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV
+GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD
+ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVEAPDLEGRAKILEVHAQGKPIALDVDL
+RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH
+ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL
+AYALGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGNSEPFVG
+GGGGGSSREYSEELAYLVDAEVRGLLDGAHAEAHWVLTENRDVLDRLAYELLEKETLTQE
+AIAEIFRDVRKRPERDVWLASDERLPQDIPPVLSPSERRSRHEGGEQTPVGVEGTTVPVH
+PEGAPPSSLGGDAPTPGLPPHGGPSSSPGAGEGPTY
+>PROKKA_00260
+MKKQFNKPYIWILLGLLVLGLVIPLTTAQSGRGMVDTNVGMALLRDDKVAQARVVDGEQR
+VDLTLREPLSQDGRDLGRDVYFQFSAARAQDVVRTVQDSSVDGYQDEPVRDSWLLSLLGL
+MIPFLLISLLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELHE
+IKEFLTEPERFHAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV
+GVGASRVRDLFEQAKANAPAIIFVDEIDAVGRSRGVGIGGGNDEREQTLNQMLVEMDGFD
+ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVEAPDLDGRAKILEVHAQGKPIALDVDL
+RSLAKRTPGYTGADLANVINEAALLTARSRNNVIDNAALDEAVDRVMAGPQKRTRLMNEH
+ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPENDKYSVTRNELLDQL
+AYAMGGRVAEEVVFKDPSSGAANDIQKATETARKMVTDYGMSSKVGAVKLGSANTDPFLG
+GGGAASREYSEELAYLVDAEVRALLDGAHAEAHWVLTENRDVLDRLAAELLEKETLTQEQ
+IAEIFKDVRKRPERPLWLAADDRPPHDVPPVLTARERASRLEGEQPEAVGVEGTTVPDAP
+EGAPPTALGGAGGSAGGPGDLPGQHSPTPGPTY
+>PROKKA_00068
+MKKLFNKPYVWILLGLLVLAVAIPLTTSQSGRTMVDTNVGMALLKDDKAAQARVVDGDQR
+VDLTLREPYKQDDRDLGKEVYFYFASARATDVVTAVDDSALDGYTDEPVRSNWFLSLLGF
+MVPFLLIALLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE
+IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV
+GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD
+ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVDAPDLEGRARILEVHAQGKPIALDVDL
+RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH
+ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL
+AYAMGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGSSEPFVG
+GAPGGSSREYSEELAYLVDAEVRTLLDQAHAEAHWVLTENRDVLDRLAYELLEKETLTQE
+AIAAIFADVRKRPERGVWLASDDRLPQDIPPVLSPSERRSRHDGGEQTPVGVEGTTVPVR
+PEGAPPSSLGGDAAGPGLPPHGGPSNTPGPGEGPTF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000223.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000223.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5c90e0aa7f15c5158eba76c5b0c98940966a244
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000223.fa
@@ -0,0 +1,25 @@
+>PROKKA_00075
+MTAHTPDDAVPGTFDPDSTAVDRPRIEAAVREILLAIGEDPDREGLADTPARVAKAYAEF
+FAGLHQSPDQVLGTTFDIAHEELVLVKDIPFYSTCEHHLVPFHGTAHIGYIPSAEGRVTG
+LSKLARLVELYARRPQVQERLTTQVVEALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAK
+TVTSAVRGQLRDPSTRSEAMSLIMHG
+>PROKKA_02088
+MTAHTPDDAVPGTFDPDSTAVDRPRIEAAVREILLAIGEDPDREGLADTPARVAKAYAEF
+FAGLHQSPDQVLGTTFDIAHEELVLVKDIPFYSTCEHHLVPFHGTAHIGYIPSAEGRVTG
+LSKLARLVELYARRPQVQERLTTQVVEALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAK
+TVTSAVRGQLRDPSTRSEAMSLIMHG
+>PROKKA_00318
+MTEQTHHDDAARGPVPAADGSAAAPTASTPAAAGVPGTFDPDSTAIDRPRIEAAVREILL
+AIGEDPDREGLQDTPKRVAKAYAEFFAGLHQGPEQVLGTTFDIAHEELVLVKDIPFYSTC
+EHHLVPVHGTAHIGYIPSAAGRVTGLSKLARLVELYARRPQVQERLTTQVVEALMEHLAP
+RGAIVVVEAEHMCMSMRGVRKPGAKTVTSAVRGQLRDPSTRSEAMSLIMHG
+>PROKKA_00259
+MTEQHRDAALADAHLHRPHEAAADVAPTTGAGAALAGAVPGVPGTFDPDQDTVDRPRIEA
+AVREILLAIGEDPDREGLQDTPKRVAKAYAEFFAGLHQRPEQVLGTTFDLSHEELVLVKD
+IPFYSTCEHHLVPFHGAAHIGYIPSAEGRVTGLSKLARLVELYARRPQVQERLTTQVVEA
+LMEHLQPKGAIVVVEAEHMCMSMRGVRKPGAKTVTSAVRGQLRDPSTRAEAMSLIMHG
+>PROKKA_00069
+MTAHTPDDAVPGTFDPDSTAVDRPRIEAAVREILLAIGEDPDREGLADTPARVAKAYAEF
+FAGLHQSPDQVLGTTFDIAHEELVLVKDIPFYSTCEHHLVPFHGAAHIGYIPSAEGRVTG
+LSKLARLVELYARRPQVQERLTTQVVEALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAK
+TVTSAVRGQLRDPSTRSEAMSLIMHG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000225.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000225.fa
new file mode 100644
index 0000000000000000000000000000000000000000..952afb1e66c3cc258a6b401da9faee801284a400
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000225.fa
@@ -0,0 +1,25 @@
+>PROKKA_00078
+MSTVDWSHLAEGPAPVPALGARPDAPVAAVLALGANLREPAQTLDAAVAALSALPHITDV
+RASPRAVTAPVGGPPGQPDYLNQVVTLRTDLAPWELLAVAHRLEQDHHRRREVRWGARTL
+DVDVIAYGDVRSDHPDLTLPHPRAAERAFVLLPWLWLDADATLAGTPVADLAAVAADAPG
+VRRQEPERHRLLAGTDDVVPLRPACPDALGREDT
+>PROKKA_02091
+MSTVDWSHPAEGPAPIPELGARPDAPVAAVLALGANLREPAQTLDAAVAALSALPHITDV
+RASPRAVTTPVGGPPGQPDYLNQVVTLRTDLAPWELLAVAHRLEQDHHRRREVRWGARTL
+DVDVIAYGDVRSDHPDLTLPHPRAAERAFVLLPWLWLDADATLAGTPVADLAAVAADAPG
+VRRQEPERHRLLAGTDDVAPLRPARPDALGREAT
+>PROKKA_00315
+MSGVDWRHPAEDPAPTPALGARPAEPVAAVLALGANLREPAQTLDAAVAALSALPHVTDV
+QASPRAVTAPVGGPPGQPDYLNQVLTLRTTLSAWELLAVAHRLEQEHHRRREVRWGARTL
+DVDVIAYGDLVSDHPDLTLPHPRAAERGFVLLPWLWLDPDAVLAGRPVAELAALAADAPG
+VRRAEPERHRLLAGRDDVVPVRPRAVRAPGRDAIDGSGP
+>PROKKA_00256
+MSRPEAAHPAEGPAPTPELAARPSSPVTAVLALGANLGDPSETLDASVAVLTVTPGIEAV
+AASPRALTAPVGGPPGQPDYLNQVVRIRTALSPWELLGVAHRLEQDHHRRRTVRWGARTL
+DVDLIVYGDLTSDHPDLVLPHPRAAERGFVLLPWAWLDPEAELAGESVAELGARAADAPH
+VRREPARTAHLDGPRPDVLRPDSTPGLPSAPLPDGAAIARPWSDPT
+>PROKKA_00072
+MSTVDWSHPAEGPAPIPELGARPDAPVAAVLALGANLREPAQTLDAAVAALSALPHITDV
+RASPRAVTTPVGGPPGQPDYLNQVVTLRTDLAPWELLAVAHRLEQDHHRRREVRWGARTL
+DVDVIAYGDVRSDHPDLTLPHPRAAERAFVLLPWLWLDADATLAGTPVADLAAVAADAPG
+VRRQEPERHRLLAGTDDVAPLRPARPDALGREAT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000227.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000227.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5cf93e8d1407b09939c7e836809e0692f0b9807c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000227.fa
@@ -0,0 +1,20 @@
+>PROKKA_00080
+MPGIDLSGVAFTPASPRLTTVKLIATTIGHLIWLAAFSVPLILKLTGPWAGMAAWVAWGL
+PAVVVVSWIVDLILIPRRVRAMGWAEREDDVLWREGILFRSVHAVPYGRLQYVDVSDGPL
+LRRVGLQTLTLKTAAAGGDVTLEGVPRERAEELREVLMARGQARLAGL
+>PROKKA_02093
+MPGIDLSGVAFTPASPRLATVKLIATTIGHLIWLAAFSVPLILKLTGPWAGMAAWVAWGL
+PAVVVVSWIVDLILIPRRVRAMGWAEREDDVLWREGILFRSVHAVPYGRLQYVDVSDGPL
+LRRVGLQTLTLKTAAAGGDVTLEGVPRERAEELREVLMARGQARLAGL
+>PROKKA_00313
+MPGIDLTGVTFAPASPKLTPVKLISSSIGHLIWLVVFSVPLVLKLLGPWEGLWAWTAWGL
+PAIVVVSWLVDLVLIPRRVRAMGWAEREDDVLWREGLLFRSVHAVPYGRLQYVDVSDGPL
+LRRVGLQTLTLKTAASGSDVTLEGLPRETADELREVLMARGQARLAGL
+>PROKKA_00254
+MPGIDLQGVEFTPVSPALVRVEAVRELIALVIWLAVVSVPLVLKLTGVWPDMWSWTAWGL
+PALVLAWSLVELVLIPRRVVAKGWAEREDDVLWREGILFRRVVAVPYGRLQYVDVTDGPL
+LRWAGLQKLTLKTAGGADVELVGLPRETCDRLREVLMARGQARLAGL
+>PROKKA_00074
+MPGIDLSGVAFTPASPRLATVKLIATTIGHLIWLAAFSVPLILKLTGPWAGMAAWVAWGL
+PAVVVVSWIVDLILIPRRVRAMGWAEREDDVLWREGILFRSVHAVPYGRLQYVDVSDGPL
+LRRVGLQTLTLKTAAAGGDVTLEGVPRERAEELREVLMARGQARLAGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000228.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000228.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de653a4f3ba2200833ba9e977579becc200a61a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000228.fa
@@ -0,0 +1,56 @@
+>PROKKA_00081
+MSAAAPPPADDAGWVRVHPASPWVRGWTFLLLILFFAGRNAVEDFAAGRLSGEDAPGGGD
+GSLLVAGGILLGVTLLISLVFFFSWWFTRFRCGEDRIELRQGWLFRSRRQMRYDRIQAVD
+LQHPLVARLLGLATVKVEAADGGESALELSFLRRAEAEAVRREILDRASGMLGGAGADAS
+APERAAEPGLPDADAADAGELMLQVPAGRLLGSVLLSGGVLGVLAGSLIWLGGLALVVAL
+LPEAVLDEGETLTGIGAAASLPALFSVAGVAWSRLNAGWGFQVRRSTDGLRLRHGLTETT
+HQTVPPGRVQGVTVSQPLFWRPFGWYRVNMAVAGYLQESDGARDVALPVGPWEDVLRVLT
+VVAPDPGLDGDPRAAQGLTPAGLMHLGVHGTGTEGGFQHVPRRGRWWFNWFAWRRTGFTT
+TRSLLVVRSGWLNRRLQTLQHERMQAAELAQGPVQRRLGLATVRVWVAGANAVVRDLDED
+VAVDLYAREARHAAVSRRLADRDQWMRPEELARFEQRTREVAATEVGRRELARAGVVGGA
+VVGEESGAHVPAVRGEEER
+>PROKKA_02094
+MSAAAPPPADDAGWVRVHPASPWVRGWTFLLLILFFAGRNAVEDFAAGRLSGEDAPGGGD
+GSLLVAGGILLGVTLLISLVFFFSWWFTRFRCGEDRIELRQGWLFRSRRQMRYDRIQAVD
+LQHPLVARLLGLATVKVEAADGGESALELSFLRRAEAEAVRREILDRASGVLGGAGADAS
+APERAAEPGLADADPDAVDADAGELLLQVPAGRLLGSVLLSGGVLGVLAGSLIWLGGLAL
+VVALLPEAVLDEGETLTGIGAAASLPALFSVAGVAWSRLNAGWGFQVRRSTDGLRLRHGL
+TETTHQTVPPGRVQGVTVSQPLFWRPFGWYRVNMAVAGYLQESDGARDVALPVGPWEDVL
+RVLTVVAPDPGLDGDPRAAQGLTPAGLMHLGVHGTGTEGGFQHVPRRGRWWFNWFAWRRT
+GFTTTRSLLVVRSGWLNRRLQTLQHERMQAAELAQGPVQRRLGLATVRVWVAGANAVVRD
+LDEDVAVDLYAREARHAAVSRRLADRDQWMRPEELARFEQRTREVAATEVGRRELARAGV
+VGGAVVGEESGAHVPAVRGEEER
+>PROKKA_00312
+MSAAAPVPATRPADDDGWARVHPASPWVRGWTFLLLILFFLGRNAVEDFAAGRFGAGAGG
+GSGEGEGSLLVAGGILLGVTLLVSLAFFFSWWFTRFRIGEDQIELRQGWLFRTRRQMKYD
+RIQAVDLQHPLVARLLGLAVVKVEAADGGESALELSFLPKARAEQVRREILDRASGVLVG
+PASAPRIAEGADAAAGVIPGVMPGVMPGAEAGPGVAPPGADADPTTPRADAPEGAAPSSS
+DPGLARRADDEGELMLRVPSGRLIGSVLLSGGVAGTVAVYLVVVLGTSLFFALAPGTWLE
+GEDTPLTGIVVAWGLPLAFAVVGQAWSGLNGGWGFQVRRSADGLRLRHGLTETTHQTVPP
+GRVQGVTVSQPLFWRPFGWHRVKVSVAGYGEDAAGKRSTALPVGPWEDVLRVLTVVAPDP
+GLDGDPREAEGLTPARLMHLGLHGSGTEGGFHHIPHRGRWWFNWFAWRRRGFTTTRALLV
+VRSGRWNRVLQTLQHERVQTAALDQGPVQRRLRLATVHVRTAGGRAVLPDLDEAVALELF
+AEEARHAAVSRRLADRDRWMRPEELARFEQRTREVAATEVGREELARAGVARPAAPAGGV
+AGTDPEPRTSHEERP
+>PROKKA_00253
+MSAPAPRPEGLASGPSPEDGRIAPAPAADDAGWVRVHPASPWIRGWVMVATFLFFALRDV
+VERWIGGLFGADAGGGPGVDGRGLLIGGGIALGVLLLVGLAFFFSWWFTRFRIGAEEIEL
+KQGWLFRSRRQMHYDRLQAVDLQHPLPARLIGLAVVKVEAADGGGDSALELAYLPKAQAA
+AVRRQILDRASGAAAARPVPSAAPEAAGGPAAAGPVRGLLVDPEEQGPVLLRVPAGRLIG
+SVLLSSTVMGLLGAVVAVPAVLSLLLLLFPDANAGEEAGVWAVTLGSTFPLLFSLAGAVW
+SGLNKGWGFTVRDSSDGLRLRYGFTETVSQTVPPGRVQGVEISQPLFWRPFGWHRVKVSV
+AGYGGLEAEGRRRDVALPVGPWEDVLRVLQVVAPDPGLGGDARAAGELMRTAMTGSGEEG
+GFRHVPRRAAWWWHWLTWRRHGYALTPTLLVVRHGRLSRSVQTVQHERLQAVALTQGPVQ
+RRLRVATLRVHMAGGAARLRGLDEDVLAELFEVESRHAAVSRRLTDRNRWMLPEELERFE
+RRTAEVARTEVGRAEMAAAGVVPMETGPRPGDTPPVATTEHRGEETA
+>PROKKA_00075
+MSAAAPPPADDAGWVRVHPASPWVRGWTFLLLILFFAGRNAVEDFAAGRLSGEDAPGGGD
+GSLLVAGGILLGVTLLISLVFFFSWWFTRFRCGEDRIELRQGWLFRSRRQMRYDRIQAVD
+LQHPLVARLLGLATVKVEAADGGESALELSFLRRAEAEAVRREILDRASGMLGGAGADAS
+APERAAEPGLPDADAADAGELMLQVPAGRLLGSVLLSGGVLGVLAGSLIWLGGLALVVAL
+LPEAVLDEGETLTGIGAAAALPALFSVAGVAWSRLNAGWGFQVRRSTDGLRLRHGLTETT
+HQTVPPGRVQGVTVSQPLFWRPFGWYRVNMAVAGYLQESDGARDVALPVGPWEDVLRVLT
+VVAPDPGLDGDPRAAQGLTPAGLMHLGVHGTGTEGGFQHVPRRGRWWFNWFAWRRTGFTT
+TRSLLVVRSGWLNRRLQTLQHERMQAAELAQGPVQRRLGLATVRVWVAGANAVVRDLDED
+VAVDLYAREARHAAVSRRLADRDQWMRPEELARFEQRTREVAATEVGRRELARAGVVGGA
+VVGEESGAHVPAVRGEEER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000229.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000229.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4c8251758e4df6426a91febfb9d11ced3ff0f8c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000229.fa
@@ -0,0 +1,35 @@
+>PROKKA_00082
+MTGGLDLSLDPHDPAQRPGRLGVGVVSAGRVGAVLGSALRAAGHTITGVHAVSEASRDRA
+EMLLPGVPVLEIPEILRRSEMVVFAVPDDALGELVAGLAAAGHVQTGHLLVHTSGRYGVG
+VMEPVRAHGAIPLAIHPAMTFTGLSLDVARLQDCVFGVTADPVVLPVAQALVVEMGGEPV
+VVKEADRAAYHLALSHGSNHLVTLTAQARQILETIGVADPERVLRSLMTAALENALTDGD
+GALTGPVARGDVDTLRTHRETLGELEAGGLPPDVRAVWETLARATTDRAETRGTLRADTA
+ARLREVLDDSDDPHDD
+>PROKKA_02095
+MTGGLDLSLDPHDPAQRPGRLGVGVVSAGRVGAVLGSALRAAGHTITGVHAVSEASRDRA
+EMLLPGVPVLEIPEILRRSEMVVFAVPDDALGELVAGLAAAGHVQTGHLLVHTSGRYGVG
+VMEPVRAHGAIPLAIHPAMTFTGLSLDVARLQDCVFGVTADPVVLPVAQALVVEMGGEPV
+VVKEADRAAYHLALSHGSNHLVTLTAQARQILETIGVADPERVLRSLMTAALENALTDGD
+GALTGPVARGDVDTLRTHRETLGELEAGGLSADVRAVWETLARATTDRAETRGALRADTA
+ARLREVLDDSDDPHDD
+>PROKKA_00311
+MTGGLDLTLDPTDPTQRPGRLGVGVVGAGRVGAVLGAALRNAGHTITGVHAVSEASRTRA
+EALLPEAPVLEIPEILRRSEMVLFAVPDDVLPELVAGLAAAGHVQTGHLVVHTSGRHGVG
+ALNPVRAHGAIPIALHPAMTFTGLSLDLARLQDCVFGVTADPVVLPVAQALAVEMGGEPV
+VIKEADRGVYHAALSHGSNHLVTLTAQAAQLLRSIGVQDTERLLRPLMHASLENALADGD
+GALTGPVARGDVETVRGHRETLRELVAEGMPADVLAVWETLARATADRAEARGALRPDVA
+ARLREALAPDA
+>PROKKA_00252
+MSRMDMSPELTGADPADRPGRLGVGVIGAGRVGAVLGAALRGAGHTITGVHAVSEASRTR
+AEALLPGVPVLELPEILRRSEMVLFAVPDDALPELIAGLAAAGHIQTGHLLVHTSGRHGV
+RVMDPVRAHGAIPLAVHPAMTFTGLSLDLARLQDCVFGVTADPVVLPVAQALVVEMGGDP
+VVVKEADRAAYHLALSHGSNHLVTVTAQARQILEEIGVAEPERMLRPLMQASLENALTDG
+DGALTGPVARGDVETVRGHRDTLRELVDGGMPADVLAVWESLARATAQRAARRGALRADA
+AERILAVLDGADDGPDATG
+>PROKKA_00076
+MTGGLDLSLDPHDPAQRPGRLGVGVVSAGRVGAVLGSALRAAGHTITGVHAVSEASRDRA
+EMLLPGVPVLEIPEILRRSEMVVFAVPDDALGELVAGLAAAGHVQTGHLLVHTSGRYGVG
+VMEPVRAHGAIPLAIHPAMTFTGLSLDVARLQDCVFGVTADPVVLPVAQALVVEMGGEPV
+VVKEADRAAYHLALSHGSNHLVTLTAQARQILETIGVADPERVLRSLMTAALENALTDGD
+GALTGPVARGDVDTLRTHRETLGELEAGGLSADVRAVWETLARATTDRAETRGALRADTA
+ARLREVLDDSDDPHDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000231.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000231.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6fd4c80a0e70dd907651589bde98e38fef6aa3a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000231.fa
@@ -0,0 +1,41 @@
+>PROKKA_00086
+MTSVRRHAARGLVALAAAVAVSAPLAAPAAAAPAAPTTPAAAQSVTGKPVVRPDVVGHRG
+ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRK
+TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER
+LSARYGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEYGLNKRNAPATVQSFELANLRD
+LNENLGLKAETVFLSSVTGAPYDSVAAGDGLRDYDFYETAAGMREVRAAGVDTLGPAFAQ
+IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDPNARGDMVGMIQ
+PFLDAGIDGFFTDHPDLGVQAVDTWMQGKKEHPGRGVGKTAQRGLKVR
+>PROKKA_02099
+MTSVRRHAARGLVALAAAVAVSAPLAAPAVAAPAATETPAAAQSVTGKPVVRPDVVGHRG
+ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRR
+TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER
+LSARHGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD
+LNENLGLKAETVFLSSVTGAPYDSVAAGDELRDYDFYETAAGMREIRAAGVDTLGPAFAQ
+IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDRNAQGDMVGMIQ
+PFLDAGIDGFFTDHPDLGVQAVDVWMQGKKEHPGRGVGKTAQRGLQGR
+>PROKKA_00305
+MISVRRHAARGLVALAAAVAVSAPLAAPAVAAPAAPTAPAAAQSATGKPVVRPEVVGHRG
+ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRK
+TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYNGRYQVPTFEEVLELRER
+LSDRYGRQIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD
+LNENLGLKAETVFLSSVTGTPYDSVAAGDTVRDYDFYETAAGMREVRAAGVDTLGPAFAQ
+VITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSADSNAQGDMVGMIQ
+PFLDAGIDGFFTDHPDLGVQAVDTWMQGKKEHPGRGVGKSAQRGLQVR
+>PROKKA_00250
+MTALRTTARGLAALTAAVAVAAPLAVPASAAIPAKEPITQAERPDVVAHRGASAYRPEHT
+LAAYELAVAQGADVIEPDLVSTKDGVLVDRHENDITGTTDVSERPEFADRKTTKTVDGVE
+ITGWFTEDFTLAELKTLRAKERLPEARPGSAAYDGMYQVPTFEEDLKLREELSAKYGREI
+GIIPEIKHPSYFDGIGLSQEEEVIELLEEHGLNHADGRAVVQSFEFSNLAEMNTRLGLQA
+DTAYLLWYEGSGYDAVLSGDTARDYAYFSTPAGAAEAAFNGIDIYGPELRQVIALNQDGS
+LGAPTGLVEVAHDAGLTVVPYTFRAENQSLPLQFRSSENPVEHGDLAAYITEVLDAGVDG
+FFTDFPDVGVAARDAWLAEKPAEQPSEQPSDGSHAVPGKVQTGDAAAWLPAGLAAAAAGV
+LVALRRRLTAAR
+>PROKKA_00081
+MTSVRRHAARGLVALAAAVAVSAPLAAPAVAAPAATETPAAAQSVTGKPVVRPDVVGHRG
+ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRR
+TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER
+LSARHGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD
+LNENLGLKAETVFLSSVTGAPYDSVAAGDELRDYDFYETAAGMREIRAAGVDTLGPAFAQ
+IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDRNAQGDMVGMIQ
+PFLDAGIDGFFTDHPDLGVQAVDVWMQGKKEHPGRGVGKTAQRGLKGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000238.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000238.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b4bc6b0cc19e9e627612b837ce7cce4c047446f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000238.fa
@@ -0,0 +1,65 @@
+>PROKKA_00093
+MTATAEPEVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVR
+EVGTGFDPAQARVQATAAAGAHRDVPLAPLDEEDAEGTEHPELKRRIAALYASFMDDETV
+EARGLEPIASDLAAVATVSTPAELLALSGRLQRQGVSGLINTGALNDAGNPDRMLLHLLQ
+GGLGLPDESYYRDEAYAEILEQYTEHTGRLLALAGIGADRDEAAALGVRVVELEKRIAAL
+HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGL
+LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAF
+VNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRSIEELEWMGEETRQRALEKLA
+MFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHITPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGR
+LEDWWTEEDRAAFTERTSRLVAQYNALSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRAL
+EIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVTRIASDPHSPNEFRCNQVVKN
+LDAFHEAFGTREGDPMWLAPEERVTIW
+>PROKKA_02106
+MTATAEPRVPSPREDLYRHVNTGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEGAVR
+EVGAGFDPAQARVQATAAAGAHRDAPLAPLDAEDTEGMEHPELKRRIAALYASFMDDETV
+EARGLEPIASDLAAVATVTTPAELLTLSGRLQRQGVSGLINTGALNDAGNPDRMLLHLLQ
+GGLGLPDESYYRDEAYAEILEQYTEHTGRLLTLAGIGADRDEAAALGVRVVELEKRIAAL
+HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGL
+LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAF
+VNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRSIEELEWMGEETRQRALEKLA
+MFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHMTPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGR
+LEDWWTEEDRAAFTERTSRLVAQYNALSPVEAPDHRVNGEFTLGENIGDLGGLGIAHRAL
+EIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVTRIASDPHSPNEFRCNQVVKN
+IDAFHEAFGTREGDPMWLAPEERVTIW
+>PROKKA_00298
+MTATAEPRVPAPREDLYRHVNAAWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVR
+EVGAGFDPAQARVDATAAAGAEHHTPLEPLDAEETEGMELPEVKRRIAALYASFMDDETV
+EARGLEPVATDMAAVASVQTPAELLELSGRLQRQGVSGLVNTGALNDAGNPDRMLLHLLQ
+GGLGLPDESYYRDEAYAEILEQYTEHAGRLLGLAGIGADSAEAAEAGVRVVELEKRIAAL
+HWDVVRSRDAVARYNLMTHEQLVELFPLAEAWLEGVDAAGERSREVVVWQPDFLSGVQAL
+LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRHRWKRAVAF
+VNGAAGEDVARLYVDRHFPEGHVAAMDELVNLLQEAYRRSIDELEWMSEETRQRALEKLS
+MFRPMVGRPVRWVDYSSLEVHAGDLLGNARAASEFEWERDLRKIEDGPDPEEWHITPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEKSMAANLGAIGAVIGHEIGHGFDDQGSRYDGSGR
+LEDWWTQEDRAAFTELTSRLVAQYNVLSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRAL
+EIWRDEGDGASLDAAAGDREFFSAWAAVWRQLTRPETMVTRIASDPHSPNEFRCNQVVKN
+IDAFHEAFGTQEGDPMWLAPEERVTIW
+>PROKKA_00243
+MTATAEPRVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRRIAEDAAR
+DAAMAAPAPEVEAPAQDEASQDPAAAERAARERIAVLWSAFMDEEAVEAAGILPLAADLE
+AVDAVASPAELLALSGRLQREGVSGLIGTGALNDAGDPERMLLHLIQSGLGLPDESYYRE
+EAYAEILAQYTEHVGRLFALAGVGGDEAGAAALGERVVALEKRIAAHHWDVVRSRDAVAR
+YNLLTRDQLLELLPLAPGWLEGIGAADARADEVVVWQPDFLTGVQALLEGPDAADLADWK
+AWLTLQVLRSRAGFLPDAFVQENFSFYGRRLAGTQEVRPRWKRAVAFVNGGVGEDVGRLY
+VARHFPEGHVAAMDQLVGLLLEAYRRSIDALDWMGEQTRQSALEKLAMFRPMVGFPETWR
+DYSALELTPGDLVGCARAVDRFEWDRDLAKIETGPDPREWHMTPQTVNAYYTPLENAIVF
+PAALLQPPFFDPERSMAANLGGIGAVIGHEIGHGFDDQGSRYDGSGRLHDWWTEQDREAF
+AERTGRLVAQYSALSPAEAPDRQVNGEFTLGENIGDLGGLGIAHQALEIWREEQDGSTED
+ESSGDREFFQAWAAVWRQLTRPETMVTRIASDPHSPNQFRCNQVVKNLDAFHTAYGTREG
+DPMWLAPEERVTIW
+>PROKKA_00088
+MTATAEPEVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVR
+EVGTGFDPAQARVQATAAAGAHRDVPLAPLDEEDAEGTEHPELKRRIAALYASFMDDETV
+EARGLEPIASDLAAVATVSTPAELLALSGRLQRQGVSGLINTGALNDAGNPDRMLLHLLQ
+GGLGLPDESYYRDEAYAEILEQYTEHTGRLLALAGIGADRDEAAALGVRVVELEKRIAAL
+HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGL
+LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAF
+VNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRSIEELEWMGEETRQRALEKLA
+MFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHITPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGR
+LEDWWTEEDRAAFTERTSRLVAQYNALSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRAL
+EIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVTRIASDPHSPNEFRCNQVVKN
+IDAFHEAFGTREGDPMWLAPEERVTIW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000239.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000239.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df21e8ae2d4a77183652cd4de49970612ba90fab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000239.fa
@@ -0,0 +1,21 @@
+>PROKKA_00094
+MADGAPDPGGGGDDAGFEAAVQGLEQAFSRLVLQHRQVMVRYAAALSPALSVGAMKAFMM
+LANEGTMTPSAVAEGLLVDRAQVSRMVRDLEAAGLITREPDPRDRRSALLSASPEGLARL
+DAVRGGPAGRGLRDDLARWDREDIRTLTRLLDRLAAERQTRMQDPAESE
+>PROKKA_02107
+MVDGAPDPGGGGDDAGFEAAVQGLEQAFSRLVLQHRQVMARYAEALSPTLSVGAMKAFMM
+LANEGTMTPSAVAEGMLVDRAQVSRMVRDLEAAGLITREPDPRDRRSALLSASPEGLARL
+DAVRGGPAGRGLRDDLARWDREDIRTLTRLLDRLAAERQTRMQDPAESE
+>PROKKA_00297
+MAERGHGDDRGLDGVGAERGDAGGEIDGFEAAVRGLEDAFARMVRQHRQVVTRQAAALKP
+GLSAGAMKAFITLCNAGTMTPSTLAEHLLLDRAQVSRMVRDLEDEGLITREPDPVDRRSA
+LLTATEEGRARLDAVRGGPAGEGLRADLAHWDRADIHTLVRLLGRLVEEQQARVDRTPDA
+G
+>PROKKA_00242
+MADPADHGSDGRGTGADAFAPEAFDAAVRELEGSFNRLVRQYRATLARQAEAVHPGLPLG
+AMKAFVAICHRGPLTPSDLAEHLMLDRTQISRVLKDLEGDGLIHREPDPRDRRSALLTAT
+DEARARLDAVRQGPAGGGTRARLQRWDLEDVRALSALLRRFVDEREDPAADDACRP
+>PROKKA_00089
+MADGAPDPGRGGDDAGFEAAVQGLEQAFSRLVLQHRQVMVRYAAALSPALSVGAMKAFMM
+LANEGTMTPSAVAEGLLVDRAQVSRMVRDLEAAGLITREPDPRDRRSALLSASPEGLARL
+DAVRGGPAGRGLRDDLARWDREDIRTLTRLLDRLAAERQTRMQDPAESE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000240.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000240.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2dc1b4aca1716fe7a7b20b79001fc1b2e7411023
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000240.fa
@@ -0,0 +1,61 @@
+>PROKKA_00095
+MTPTSPAPEAVAPAGAPSLERAAADAARHRSVLQALTGLLLGMFVSMIANTVVSTSMPVI
+IHDIGGDQTAYTWVITSALLATAIATPIWGKLADLVNRKVLFQVALAIFVAASAAAGFTH
+DPTFLIVCRTVQGLGGGGLVALSQVIMADIISPRERGRYMGLFGAVMAVATVGGPLAGGV
+ITDLWGWRWNFFVAVPFAVVALVMVQRTLHLPHRERQKVSIDYLGIVFLTAATALLLIWV
+TSAGRDFDWASTTSAWMLGGAAVATVLFVVTELRVAEPLIPLTLFRDRTFTLATIASIAT
+GLAMFGSSVYLAQYMQLARGATPTQAGLMTIPMILGLLVSSTVIGGLITRTGVWKRWLVI
+GAVLLIAGTALLGTLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQMGVASS
+GVTFFRTLGGSIGVAVMGAVVSNVVPDRIEERRADLAAALRSLGPDAAEWSESLQSSTLP
+RVAEMPDSLRVIFEDVYAQGIALAFLVAVPLAIVALIAILFLPNLPLGRMTTSERLHATR
+ADLATHATAEAMQTLPATGPIPVVTAAQGQHPAEDPEESRSVSAERPATAVADRPVVPAA
+LAVAGTALLAAVVTALVRARRG
+>PROKKA_02108
+MTPTSPAPEAVAPAGAPSLERAAADAARHRSVLQALTGLLLGMFVSMIANTVVSTSMPVI
+IHDIGGDQTAYTWVITSALLATAIATPIWGKLADLVNRKVLFQVALAIFVAASAAAGFTH
+DPTFLIVCRTVQGLGGGGLVALSQVIMADIISPRERGRYMGLFGAVMAVATVGGPLAGGV
+ITDLWGWRWNFFVAVPFAVVALVMVQRTLHLPHRERQKVSIDYLGIVFLTAATALLLIWV
+TSAGRDFDWASTTTAWMLGGAAVATVLFVVTELRVAEPLIPLTLFRDRTFTLATIASIAT
+GLAMFGSSVYLAQYMQLARGATPTQAGLMTIPMILGLLVSSTVIGGLITRTGVWKRWLVI
+GAVLLIAGTALLGTLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQMGVASS
+GVTFFRTLGGSIGVAVMGAVVSNVVPDRIEERRADLAAALRSLGPDAAEWSESLQSSTLP
+RVAEMPDGLRSIFEDVYATGISHAFLVGVPLAIVALIAILFLPNIPLGRMTTSERLHATR
+ADLATHATAEAMQTLPATGPIPVVTAAQGQHPAEDPEESRSVSAERPATAVADRPVVPAA
+LAVAGTALLAAVVTALVRARRG
+>PROKKA_00296
+MIDHRQSLTAVNHSDDPAEGPHEPHLPAVAGTAPAGAPSLERAAADAARHRAVLQALTGL
+LLGMFVSMIANTVVSTSMPVIISDIGGNQNDYTWVITAALLATAVSTPVWGKLADLMDRK
+MLFQVALVIFVGASAAAGFTNDPTFLIVCRVVQGLGGGGLAALSQVIMADIISPRERGRY
+MGLFGAVMAVATVGGPLAGGVITDLWGWRWNFFVAVPFALVALVMVQRTLHLPAREPRKV
+SIDYLGIVLLGVATSLLLIWVTTAGQQFPWASWTTAWMVGGAVLAAALFVVVELKVTEPL
+IPLTLFRNRTFTLATIASIATGLAMFGAGVYLAQYMQLARGATPTQAGLMTIPMIAGLLI
+TSTVIGRVITRTGVWKRWLIVGAVLLTAGMALLATLHYDTPFVLVSLHMLLLGAGVGMTM
+QNLVLVVQNTTDPRQMGVASSGVTFFRSLGGSVGVAAMGAVVANVVPSRFEARGADLAAA
+LQSLGADGPVWAQRLQSGTLPRVAEMPEPLRVVVEDVYATGISQAFLVGVPLAVVAVVAI
+VFLPNIPLGRMTTSERLDASRADLATVTAPAAMQKVPATGEIPVVAPAAGGAGGTDDACT
+AEDADGTEGVPAAQGPTTAPAEPTAERAERPAVQPAAESVPARVVAPAAAAPSTAAASGR
+SGGARPGARAAAAVALLTAIAVLMRQARRG
+>PROKKA_00241
+MSTTTAPPATAGPAAVGNSPAVPSLERAADDAARHRTVLRALTGLLLGMFVSMIANTVVS
+TSMPVIISDIGGDQTAYTWVITAALLATAIATPIWGKLADLVDRKVLFQVALVLFVAASA
+AAGFTTDPTFLIVCRVIQGLGGGGLAALSQVIMADIISPRERGRYAGLFGAVMAVATVGG
+PLAGGIITDLWGWRWNFFVSLPFALVALVMVQRTLHLPARESRKVSIDYLGIVLLSTATA
+LLLIWVTNAGHQFDWASATTAWMLGGAALAAVLFVVVELTVAEPLIPLTLFRDRTFTLGT
+IASIATGLAMFGASVYLSQYMQLARGATPTQAGLMTIPMIVGLLVSSTVIGGVITRTGVW
+KRWLVIGAVLLIAGAAMLGTLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQ
+MGVASSGVTFFRSLGGTIGVAVMGAVVANVVPDQVEQRRTDIGAALASLGPAGAEWAQRL
+QSGSLPRVAEMPDALRVIFEDVYATGISQAFLVGVPLAVVALAAILFLPNIPLGHMTTTE
+RIDAERADLATVSVPQAMQTLPATGSTPVVAQAQVQEAAPASTTTTPAPAARALRVPAGL
+RERRIAPAGTGRSTAWRATASALAAGAAAAAFVPLLRRSRRG
+>PROKKA_00090
+MTPTSPAPEAVAPAGAPSLERAAADAARHRSVLQALTGLLLGMFVSMIANTVVSTSMPVI
+IHDIGGDQTAYTWVITSALLATAIATPIWGKLADLVNRKVLFQVALAIFVAASAAAGFTH
+DPTFLIVCRTVQGLGGGGLVALSQVIMADIISPRERGRYMGLFGAVMAVATVGGPLAGGV
+ITDLWGWRWNFFVAVPFAVVALVMVQRTLHLPHRERQKVSIDYLGIVFLTAATALLLIWV
+TSAGRDFDWASTTTAWMLGGAAVATVLFVVTELRVAEPLIPLTLFRDRTFTLATIASIAT
+GLAMFGSSVYLAQYMQLARGATPTQAGLMTIPMILGLLVSSTVIGGLITRTGVWKRWLVI
+GAVLLIAGTALLGTLHYDTSFWLVSLYMFLLGAGVGMTMQNLVLVVQNTTDPRQMGVASS
+GVTFFRTLGGSIGVAVMGAVVSNVVPDRIEERRADLAAALRSLGPDAAEWSESLQSSTLP
+RVAEMPDGLRSIFEDVYATGISHAFLVGVPLAIVALIAILFLPNIPLGRMTTSERLHATR
+ADLATHATAEAMQTLPATGPIPVVTAAQGQHPAEDPEESRAVAAERPATASPVAGRPVAP
+AALAVAGTALLAAVVTALVRARRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000245.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000245.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1fb7b117bcbd8070f68d004f963fb253ec0cf28b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000245.fa
@@ -0,0 +1,12 @@
+>PROKKA_00101
+MGIGDLNNLANQHSDKIDEAVDNAQEQHGDKLGEHGDTVNKGVDGAQEKFLSGDEGEQQA
+>PROKKA_02114
+MGIGDLNNLANQHSDKIDEAVDNAQEQHGDKLGEHADTVNKGVDGAQEKFLSGDEGEQQA
+>PROKKA_00289
+MGIGDLNNLANQHSDKINEAVDGAQEQHGDKLGEHADTVNKGVDGAQEKFLSGEKNEGEQ
+QA
+>PROKKA_00235
+MVGFDDVKNLANENSDKINEQVDAAQAQHSDKLGQHADLADKGIDGAQDKFLNGQSAENE
+GEQQA
+>PROKKA_00096
+MGIGDLNNLANQHSDKIDEAVDNAQEQHGDKLGEHGDTVDKGVDGAQEKFLSGDEGEQQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000252.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000252.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c6626d3cc4fc00837c53acab1dddba19d742a6c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000252.fa
@@ -0,0 +1,40 @@
+>PROKKA_00109
+MSTVSTSPRATEDSVTPRRHSLTEGQKPGWTWMAVAAAAAVVAAGLTVLLSGAFNVVGFV
+IIAAILYIAGLYVATRVMENRRRAADGLCRNLVWLAFLVALVPLVSVLWSVLSAGLPTLI
+ANPQIMAYDMKGITGIDDSAWVEDGKPAGGLAGGFGHALIGTVVITIIATLISVPIGMLT
+SIYLVEYSRGGWFSRAIVFFVDVMTGIPSIVAGLFAYAAITWVLTLVTGSKSTALQSVQM
+GLTAAIALSVLMIPVVVRSTEEMLRVVPNELREGAYALGVRKWQTIAKVVLPTAISGIAS
+GVTLAIARVAGETAPILVTAGFATSINWNPFDNWMTALPVYIYRQLVAPTSPTAADPSTA
+RAWAAALLLVTIVMLLNLAARFIAKAFAPKKGR
+>PROKKA_02122
+MSTVSTSPRATEDSVTPRRHSLTEGQKPGWTWMAVAAAAAVVAAGLTVLLSGAFNVVGFV
+IIAAILYIAGLYVATRVMENRRRAADGLCRNLVWLAFLVALVPLVSVLWSVLSAGLPTLI
+ANPQIMAYDMKGITGIDDSAWVEDGKPAGGLAGGFGHALIGTVVITIIATLISVPIGMLT
+SIYLVEYSRGGWFSRAIVFFVDVMTGIPSIVAGLFAYAAITWVLTLVTGSKSTALQSVQM
+GLTAAIALSVLMIPVVVRSTEEMLRVVPNELREGAYALGVRKWQTIAKVVLPTAISGIAS
+GVTLAIARVAGETAPILVTAGFATSINWNPFDNWMTALPVYIYRQLVAPTSPTAADPSTA
+RAWAAALLLVTIVMLLNLAARFIAKAFAPKKGR
+>PROKKA_00281
+MSTAIDDVSTRQDTPPSKHRQNSLTAGQKPGWVWMAIAAAAVLLGLGIEALLSGAAPFSE
+DFSLARFVVLAGVLYIAGMYLVTRVMENRRRASDGLWKNLVWTAFLIALVPLVSVIWTVL
+EGGGPTLLSNPQVLWNDMDGVTGATDAAYDQAGSPAGGLPGGFAHALIGTLVITIIATLI
+AVPIGLLASIYLVEYGRDGWLSRAITFFVDVMTGIPSIVAGLFAYAAMTVLLELIMGPGP
+AALQAVKMGFTAAVALTVLMIPVVVRSTEEMLRVVPNELREGSYALGVRKWRTIFKVVLP
+TAISGIASGVTLAIARVTGETAPILVTAGYAMTTNWNAFDNWMTALPVYIYRQIVSPTSP
+TAADPSMARAWSAALVLIFIVMALNLLARVIAKAFAPKTGR
+>PROKKA_00222
+MSTALNDTPTRENTPASKHTQNSLTAGQKPRWTWMAVAAGAVVLGLGLEALLAGGFADFS
+IARFIILAAILFVAGMYVATRVLENRRQATDGLWRNLVWAAFLIALVPLISVLWSVVADG
+GATLFGNPQLLVNDMQGVTGVTDAQYVQAGEPMGDLPGGFAHALVGTFLITVIATVIAVP
+IGLLTSIYLVEFGRDGWLSRAIIFFVDVMTGIPSIVAGLFAFAAMSVVLEMVMGSGPKAL
+QSVKMGLTAAIALTVLMIPVVVRSTEEMLRVVPNELREGSYALGVRKWRTIFKVVLPTAI
+SGIASGITLAIARVTGETAPILVTAGFASAVNWNPFDNWMTALPVYIYRQLVAPTSPTAM
+DASTSRAWAAALVLIIIVMVLNLLARIVAKAFAPKTGR
+>PROKKA_00104
+MSTVSTSPRATEDSVTPRRHSLTEGQKPGWTWMAVAAAAAVVAAGLTVLLSGAFNVVGFV
+IIAAILYIAGLYVATRVMENRRRAADGLCRNLVWLAFLVALVPLVSVLWSVLSAGLPTLI
+ANPQIMAYDMKGITGIDDSAWVEDGKPAGGLAGGFGHALIGTVVITIIATLISVPIGMLT
+SIYLVEYSRGGWFSRAIVFFVDVMTGIPSIVAGLFAYAAITWVLTLVTGSKSTALQSVQM
+GLTAAIALSVLMIPVVVRSTEEMLRVVPNELREGAYALGVRKWQTIAKVVLPTAISGIAS
+GVTLAIARVAGETAPILVTAGFATSINWNPFDNWMTALPVYIYRQLVAPTSPTAADPSTA
+RAWAAALLLVTIVMLLNLAARFIAKAFAPKKGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000258.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000258.fa
new file mode 100644
index 0000000000000000000000000000000000000000..69b6c8417aa56f3c1f44e0540cc07021fd5c5297
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000258.fa
@@ -0,0 +1,30 @@
+>PROKKA_00116
+MAKNSTIGRYASGKVKDFGLKSALDENGEPTEGFEKALSTVLAVQRPLVLKNIQRMAAKH
+PGESPERLAERLGQQYLTTVTGAGAAVGGTAIVPGIGTVAALGLSGAAVAGFMEATALYA
+QSLAELHGITTQDPQRAQALVMGLMLGDDAKELLREAAAKAGRPYDPQSSLNALAGTASG
+TGISAFVVDRLKRTFMRKMLLRQGAGFVGRAVPFGVGAVIGGVGNRAMGKAVMENAAELF
+GPLPMVIPGEIREGVAQGRAGGESAGAKDDGGVLGAIRRALPGGKDEKDDRQKKGKPAA
+>PROKKA_02129
+MAKNSTIGRYASGKVKDFGLKSALDENGEPTEGFEKALSTVLAVQRPLVLKNIQRMAAKH
+PGESPERLAERLGQQYLTTVTGAGAAVGGTAIVPGIGTVAALGLSGAAVAGFMEATALYA
+QSLAELHGITTQDPQRAQALVMGLMLGDDAKELLREAAAKAGRPYDPQSSLNALAGTASG
+TGISAFVVDRLKRTFMRKMLLRQGAGFVGRAVPFGVGAVIGGVGNRAMGKAVMENAAELF
+GPLPMVIPGEIREGAAQGRAAGESEGTKDYGGVFGAIRRALPGGKDEKDKPAA
+>PROKKA_00271
+MAKNSMIGRYTSGKVKDFALKSALDENGEPTEGFEKVVSKVLGIQRPLVLKHIQNVAAKN
+PELTAEQIAERLGQQYLNTVTGAGAAVGGTAIVPGVGTVAALGLSAAATVGFMEATALYA
+QSLAELHGITMEDPQRAETLVMALMLGDDAKELLREAAAKAGRPFDPNASLNALAGSAAG
+TGGGAGISAFVMDRLKRTFMKKMLVRQGAGFLGRAVPFGVGAVIGGVGNRAMGKAVMENA
+QELFGPLPTVIPGEIREGAARQAQEDDGEGGVFAAIRRALPGGDDKKDAAKA
+>PROKKA_00203
+MAKNSIIGRYASGKAKDFAMKSAFDENGNPTEGFEKLVFTTLDIQRPLVLKNIQRLHESH
+PGETPEQLAERLADQYVTASTGAGAAVGGTAIVPGIGTVAALGLSAAATVAFLEATALYA
+QSLAELHGLTTKDPARSKALVMAVMLGDDTKELLKDISRKSGVKNTGTPDSAAGLAAMMN
+GGAAGQAAGGAGLGAVAIEQLKKQFVKKVLVRQGAGFLGRAVPFGVGAVIGGVGNRAMAK
+AVVKNSRDLFGPLPAQIPGEIVAASAKGQDVGQSAEDGKGGLVSGLIKALPLGKKDEKKA
+>PROKKA_00121
+MAKNSTIGRYASGKVKDFGLKSALDENGEPTEGFEKALSTVLAVQRPLVLKNIQRMAAKH
+PGESPERLAERLGQQYLTTVTGAGAAVGGTAIVPGIGTVAALGLSGAAVAGFMEATALYA
+QSLAELHGITTQDPQRAQALVMGLMLGDDAKELLREAAAKAGRPYDPQSSLNALAGTASG
+TGISAFVVDRLKRTFMRKMRLRQGAGFVGRAVPFGVGAVIGGVGNRAMGKAVMENAAELF
+GPLPMVIPGEIREGAAQGRADGTKDDGGVFGAIRRALPGGKDEKDDRQKKGKPAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000259.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000259.fa
new file mode 100644
index 0000000000000000000000000000000000000000..507e9c5e3da2e51fc2db3664f467a94db1c06b33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000259.fa
@@ -0,0 +1,45 @@
+>PROKKA_00117
+MSLSPDPAQQLLSAGALERAAGLRRMKAVALGLLILLAVVFVVAFPLQDTHPVWGYVRAA
+AEGGMVGALADWFAVTALFRHPMGVPVPHTALIPRKKDQLGAALTEFVQENFLDSEVAHE
+KVDGLKVAEAAGGWLRREENAARTAREIATAARGAMAAADDDAVQELLRQLMERHMVAPD
+WSPTLAGVLEDVVAGRHHERVVDLVVAHTGDWVAAHPELFVETVRRRSPEWSPDLVDRLL
+AERLHAETLKYLAGIRRDREHEARRAVDDWLDRLADEMRNEPATRASVERFKRNLFADER
+LRAWAGRAWVSLRDSLLDALEDPSSDLHRALVAALRDLGARLQEDPELRDRVDGHARRAA
+AYALSSYGPALTGVIEETVARWDGEQTARTLELFVGKDLQFIRINGSVVGALAGLAIHGV
+ATLFL
+>PROKKA_02130
+MSLSPDPAQQLLSAGALERAAGLRRMKAVALGLLILLAVVFVVAFPLQDTHPVWGYVRAA
+AEGGMVGALADWFAVTALFRHPMGVPVPHTALIPRKKDQLGAALTEFVQENFLDSEVAHE
+KVDGLKVAEAAGGWLRREENAARTAREIATAARGAMAAADDDAVQELLRQLMERHMVAPD
+WSPTLAGVLEDVVAGRHHERVVDLVVAHTGDWVAAHPELFVETVRRRSPEWSPDLVDRLL
+AERLHAETLKYLAGIRRDRQHEARRAVDDWLDRLADEMRNEPATRASVERFKRNLFADER
+LRAWAGRAWVSLRDSLLDALEDPSSDLHRALVAALRDLGARLQEDPELRDRVDGHARRAA
+AYALSSYGPALTGVIEETVARWDGEQTARTLELFVGKDLQFIRINGSIVGALAGLAIHGV
+ATLFL
+>PROKKA_00270
+MSLSPDPARQLLSAGTLERERGLRRMKAVALGLLVALAVVFAVAFPLQDVHPVWGYVRAA
+AEGGMVGALADWFAVTALFRHPMGIPVPHTALIPRKKDQLGAALTEFVQENFLDSDVARE
+KVEGLEVAAAAGGWLRRPENAERAAREVATAARGAMAAADDDAVQELLRQLMQRHMVEPE
+WSPTLAGVLQDVVTGRHHERVVDLVVEHTGDWVAAHPEMFVETVRRRSPEWSPDLVDRLL
+AERLHAEALKYLAGIRDDRDHEARRAVDDWLTRLSAEMRDDPHTRASVERFKHSLFADER
+LRAWAGRAWTSLRDSLLDALEDPASDLHRALVAALRDLGARLQEDPVLRDRVDGHARAAA
+AYALSTYGPAVTGVIEETVARWDGDQTARTLELFVGRDLQYIRINGSIVGALAGLTIHAV
+ATLFL
+>PROKKA_00201
+MAPSPVPADSPFPLTPAALERAAGLRRMKAVALGLLIVLAVVFAVAFPLQRVHPAWGFVR
+AAAEGGMVGALADWFAVTALFRRPLGLPIPHTALIPEKKDQLGAALTEFVQENFLDSDVA
+REKVAGLQVARAAGGWLRERPHAVHAAGEIAMAARGAVAATDDDAVQDLLQQLMQRHMVE
+PDWSPTLAGVLEDVLAGRHHEKVVDLVVEHTGDWVATHPEMFLETVRRRSPEWSPDLVDR
+LLAERLHAETLKYLAGVRADRDHEARRSVDDWLARLAGNMRDDPATRASAERFKADLFAD
+EQLRAWAGRAWITLRDSLLAALEDQDSDLHRALVDALVDLGVRLQEDPALQASVDGRARA
+AASYALSSYGPALTGVIEETVARWDGRQTADTLENLVGRDLQFIRINGSVVGALAGLAIH
+TLASLVF
+>PROKKA_00122
+MSLSPDPAQQLLSAGALERAAGLRRMKAVALGLLILLAVVFVVAFPLQDTHPVWGYVRAA
+AEGGMVGALADWFAVTALFRHPMGVPVPHTALIPRKKDQLGAALTEFVQENFLDSEVAHE
+KVDGLKVAEAAGGWLRREENAARTAREIATAARGAMAAADDDAVQELLRQLMERHMVAPD
+WSPTLAGVLEDVVAGRHHERVVDLVVAHTGDWVAAHPELFVETVRRRSPEWSPDLVDRLL
+AERLHAETLKYLAGIRRDRQHEARRAVDDWLDRLADEMRNEPATRASVERFKRNLFADER
+LRAWAGRAWVSLRDSLLDALEDPSSDLHRALVAALRDLGARLQEDPELRDRVDGHARRAA
+AYALSSYGPALTGVIEETVARWDGEQTARTLELFVGKDLQFIRINGSIVGALAGLAIHGV
+ATLFL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000261.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000261.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3816331adbc43a4a1c42e326839e93f5bbc9487
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000261.fa
@@ -0,0 +1,18 @@
+>PROKKA_00123
+MIVAFSVAPSGQPADSAHLPGDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGDWD
+EVMEVVRGAVDAVSSYGSRVSLVLKADIRPGHSGELDGKLERLEAALAEDGNGDAADAR
+>PROKKA_02137
+MIVAFSVAPSGQPADSAHLPGDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGDWD
+EVMEVVRGAVDAVSSYGSRVSLVLKADIRPGHTGELDGKLERLESALAEDEGRRAAPAPH
+DGDAG
+>PROKKA_00262
+MIVAFSVAPSGTPADAAHQPGDEDSASVHRAVAAAVAVVRESGLPHRTSSMFTEIEGDWD
+EVMDVVRGAVDAVAPYGSRVSLVLKADIRPGHTGELDGKLARLEAALASDDVS
+>PROKKA_00196
+MIVAFSVSPSGAPADAAYAPSSDGDSASVHRAVAAAVAVVRASGLPHRTSSMFTEVEGEW
+DEVMGVVKRAVEAVEPYGSRVSLVLKADIRRGRTGELDGKLERLEAALTDGTPATPDRFR
+A
+>PROKKA_00131
+MIVAFSVAPSGQPADAEHLPGDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGEWD
+EVMEVVRAAVDAVSPYGTRVSLVLKADIRPGRTGELDGKLERLESALAEDEGRRAAPAPR
+DGDAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000262.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000262.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da1e1545779bc7dea2914d8c8a104f62bd368bce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000262.fa
@@ -0,0 +1,23 @@
+>PROKKA_00124
+MAVTVRPATSDDVEPLLRVKAQAWREAYGGLLPAAHLDAVDAGVPEQVPGWAALVGSDRE
+LWVADDGGRLLGMALAGPRRSQGGGLPDLELMALYVLAEAYGTGLGALLLDAVVGKRPAV
+LRVLAENPRAVAFYAKHGFAPEGGPEPMTGPWAGLHEQLMVRRG
+>PROKKA_02138
+MPESVTVRPAAPGDVEALLRVKARSWREAYGALLPSAYLDAIEARIPEDVPAWTALIGPD
+RDLWVADDGGRLLGVALAGPRRSAAETGRTGADDAAASPADLPDVELMVLYVLAEAYGTG
+LGARLLDAVVGERPAMLRVLAENPRAVAFYAKHGFAAVGAPEPMTGPWAGLHEQLMVRRR
+PHDGGAA
+>PROKKA_00261
+MAVVVRPARREDAEALLRVKAQSWREAYGAHLPAEVFDRADARVPQDAPAWAALVGSDRD
+LWVAEDDDGGRLVGVALAGPSRIEDEGLPPRELMVLYVLAEAHGTGVGARLLDAVVGDGP
+AVLDVLAENPRARAFYAKHGFEDHGAPAPMDGAWAGLHEQRMVRRG
+>PROKKA_00195
+MRETDGASDAVVRDVNPPSAPAPTVRPAGADDLPAVLAMKNAAWRETYAHLLEPGFLAAQ
+EAELPRAVEAWTRLLGEPGMEVWLAEGAGVVVGMAAAGPADDPALGPEGRELIALYVRAR
+LHGAGLGAALLRAAVGGRPARLDVLVGNERAIAFYERHGFVAVGEPAVLGGPWGDAREQR
+MVRR
+>PROKKA_00132
+MPESVTVRPAAPGDVEALLRVKARSWREAYGALLPSAYLDAIEDRIPEDVPVWTALIGSD
+RDLWVADDGGRLLGVALAGPRRSAAETGRTGADDAAASPADLPDVELMVLYVLAEAYGTG
+LGARLLDAVVGDRPAVLRVLAENPRAVAFYAKHGFASVGAPEPMTGPWAGLHEQLMVRRL
+PHDGGAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000263.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000263.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4f2c76a1794eff07469bd343d2da6a252bb596cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000263.fa
@@ -0,0 +1,34 @@
+>PROKKA_00125
+MSRRSGRSSGRSSAASSSSRGSAARRGRAAEPEGIVPGVHEISHGTAEIREDPYEPGAFV
+LYVNGVESSPLDPDHPERMGFEYMRWAVAAVRAHWPEPTPLRALHLGGAGCALARWVDHA
+HPGSHQTAVEIDAGLAALARERFGLPRAPALRIRVADAAEVLATAHPASRDLIIRDVFAP
+DPTDLTGARHITPPGLTGLDAARAAARVLAPGGLYVLNVGGGPDLTSVRADVAAVVAAFE
+HVEVIADPPMLKGRRRGNVIVAASDAPVARPAADAPPGSDPRDRLARALRMDAFPARLAE
+DPRGFPAGVAPGITGLVPGPEA
+>PROKKA_02139
+MSRRSSARRGRAAGGSAGPAGIEPGVHAITHGTAEIREDAFEPDAFILYVNGVESSPLDP
+ERPERMAFEYMRWAAAAVRAHWPEPTPLRALHLGGAGCALARWVDHAYPGSHQTAVEIDA
+GLAALARERFGLPRAPALRIRVADAAEVLATAHPASRDLIIRDVFAPDPTDLTGARHITP
+PGLTGLDAARAAARVLAPGGLYVLNVGGGPDLTSVRADVAAVVAAFEHVEVIADPPMLKG
+RRRGNVIVAASDAPVARPAADAPPGSDPRDRLARALRMDAFPARLAEDPRGFPAGVAPGI
+TGLVPGPEA
+>PROKKA_00260
+MITPGVFAISSGTAEILPDPWTDGVYLLKVNGVESSQLNPDRPETLGFEYMRWAAAVLAH
+RFAPDAERLRVLHLGGAGCTFARWVTHTWPQAHQLAVELDAGLAELARTHFDLPRAPQLK
+IRVGEAGQVLAGLREATREVVFRDVFAPADPLSLAPDSPHVTPAHLTGADAAAHAARVLV
+PGGVYVLNIGGGPDLASVRREVAALRTAFAHVEVMADPAMLKGRRRGNVIAAASSVPLAA
+EELGGRAALARALRSDALPAQLVDDVARFAGGLAPDPTPLVQASDGTSEGASTQASPGPA
+Q
+>PROKKA_00194
+MITPGTFPISSGTAEIVPDPWTDGVFLLKVNGVESSQLNPDRPETLGFEYMRWAAAVLTH
+RFAPDARLRVLHLGGAGCTFARWVTHTYPASHQLAVELDAGLAAVAREHFDLPRAPQLKI
+RVGEAGEVLAGLRDATREVVFRDVFAPDPADPTGALHVTPAHLTGLDAAAHAARVLTPGG
+VYLLNIGGGPDLTSVRREVAALTETFAHVEVMADPAMLKGRRRGNVIAAASSAPLSADGL
+GGRSALARALRSDALPAQLLDDVVAFTAGLTPDATPLVTPAEG
+>PROKKA_00133
+MSRRSSARRGRAAGGAAGPAGIEPGVHAITHGTAEIRENAFEPGAFILYVNGVESSPLDP
+ERPERMAFEYMRWAAAAVRAHWPEPTPLRALHLGGAGCALARWVDHAYPGSHQTAVEIDA
+GLAALARERFGLPRAPALRIRVADAAEVLATAHPASRDLIIRDVFAPDPTDLTGARHITP
+PGLTGLDAARAAARVLAPGGLYVLNVGGGPDLTSVRADVAAVVAAFEHVEVIADPPMLKG
+RRRGNVIVAASDAPVARPAADAPPGSDPRDRLARALRMDAFPARLAEDPRGFPAGVAPGI
+TGLVPGPEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000267.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000267.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92cd359532f3d7d195763d9c080fa53fd594f9f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000267.fa
@@ -0,0 +1,60 @@
+>PROKKA_00133
+MSDPTPPSTEPMIPEQPGNHPSSATAPDAGVAPATSAAAGRDRVLLPWVFWPSAVIVLSF
+VGATLLAPAQMTVGIGLVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGDITLGKPDEK
+PEFSTLSWFSLLFAAGMGIGLVFFGMTEPLMHFTSPRPDLAAANPTQAEAAQSALATTFL
+HWGLQPWAIYAVVGVAVALAIHRRGRPLALRWAFEPLIGERRVRGGWGHLIDNIALIGTV
+FGVATSLGLGVTQMSAGLRALGIVPEDSPWLEYVMIGAVTCVVLYTVVSGVERGMKWLSN
+TNLILAAGLLLFIAIVGPTAFLFKEMVQSLGSYMQYFFANSLNVSAFYGAEGDAWQAGWS
+AYYWGWWMSWTPFVGIFIARISRGRTVREFIAGVLLVPTLVCVVWFGILGGTAIFLETTR
+PAGYTSVVGADGAIDSNTALFQVLEQLPAGMMLVVGAIILSGIFFITSADSGSLVMGMLA
+TGGDVNPKATVKIFFAIATSLMAAALLAAGGLSAIQVLAITIGLPFSVLMLLICLATFRS
+LGYSVARVEAVRRQAMLASIKDRLGLESDDDEVVDAGPVAASQWWASLSRDHQQRIADAA
+AGVPASEGPRRPRLRRHEH
+>PROKKA_02147
+MSDPTPPSTEPMIPEQPGNHPSSATAPDAGVAPATSAAADRDRVLLPWVFWPSAVIVLSF
+VVATLLAPEQMTVGISLVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGDITLGKPDEK
+PEFSTLSWFSLLFAAGMGIGLVFFGMTEPLMHFTSPRPDLAAANPTQAEAAQSALATTFL
+HWGLQPWAIYAVVGVAVALAIHRRGRPLALRWAFEPLIGERRVRGGWGHLIDNIALIGTV
+FGVATSLGLGVTQMSAGLRALGIVPEDSPWLEYAMIGAVTCVVLYTVVSGVERGMKWLSN
+TNLILAAGLLLFIAIVGPTAFLFKEMVQSLGSYMQYFFANSLNVSAFYGAEGDAWQAGWS
+AYYWGWWMSWTPFVGIFIARISRGRTVREFIAGVLLVPTLVCVVWFGILGGTAIFLETTR
+PAGYTSVVGADGAIDSNTALFQVLEQLPAGMMLVVGAIILSGIFFITSADSGSLVMGMLA
+TGGDVNPKATVKIFFAIATSLMAAALLAAGGLSAIQVLAITIGLPFSVLMLLICLATFRS
+LGYSVARVEAVRRQAMLASIKDRLGLESDDDEVVDAGPVAASQWWASLSRDHQQRIADAA
+AGVPASEGPRRPRLRRHEH
+>PROKKA_00252
+MSESIPPSHPSAPPGPASAHPAAPAAGAADAREASGAVAPASSDAATGARVLLPWVFWPS
+TIVVLLFVGATLLFPEPMTAAIGTVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGAIT
+LGKPDEKPEFSTLSWFALLFAAGMGIGLVFFGMTEPLMHFVSPRPDLAATDPNPAQAAQA
+ALATTFLHWGLQPWAIYAVVGVAVGLAIHRRGRPLALRWAFEPLLGERRVRGGWGHLIDN
+IALIGTVFGVATSLGLGVTQMSAGLRSLGVVPEESAWVEYAMIGLVTLVVLYTVVSGVER
+GMKWLSNVNLVLAAGLLLFIAIVGPTAFLFKEMVQSFGAYLQTFFGASLNVSAFQGAEGD
+AWQAGWSAYYWGWWMSWTPFVGIFIARISRGRTVRQFLAGVLLVPTLIGVVWFGVLGGTA
+IYLETVRPDGYTSVVGADGSIDSNTALFQVVEQLPAGALLVIGAIMLSAIFFVTSADSGA
+LVMGMLATGGDVNPKVPVKIFFAIATALMSAALLAAGGLSAIQTLAITIGLPFSVLMLVM
+CLATFRSLGYSVARVEAVRRQAMLASIKDRFGLDTDDDEVVDGGPVAASQWWASLSRDRQ
+RTIAQAASAGPDDEIRLAGSSAEEPAGSPDARR
+>PROKKA_00188
+MTPAPAGRDADAPAANRPHRTGPDPDVKHPAPATADQADRGHAGLLPWVFWPSTLIVLLF
+VVATLAFPAQMTDVIGDVQAAIIRNFSWWYAIVAFAFVVFCAYLVFSRKGSITLGKPDEK
+PEFSTMSWFALLFAAGMGIGLVFFGMTEPLMHFTSPRPDLAAANPTEAQAAQSALATTFL
+HWGLQPWAIYAVVGVAVGLAIHRRGRPLSLRWAFEPLLGERRVRGGWGHLIDNIALIGTV
+FGVATSLGLGVTQMAAGLRSLGIVPADSPWLEYAMIAAVTCVVMYTVVSGVERGMKWLSN
+INLVLAAGLLLFIALVGPTPFLLKETVQSFGAYLQNFFADSLNVSAFYGAEGDAWQAGWT
+AYYWGWWMSWTPFVGIFIARISRGRTVREFLMGVLLVPTLVCVVWFGILGGTAIWLETVR
+PAGYTSVVGADGAIDSNSALFQVLEQLPAGLLLVIGAIILSGIFFVTSADSGALVMGMLA
+TGGDVNPKTAVKIFFAIATAFMAAALLAAGGLSAIQTLAITIGLPFSVLMLVMCVATFRS
+LGYSAARVEAVRRQAMLASIQDRLGKDTDDDEVVEGGPVAASQWWASLSRDHQRTIARLA
+SPGPDDEIRLHEDATATSARPDTTRGGSTAR
+>PROKKA_00141
+MSDPTPPLKNPLDPERADTRPSSAPTADGAVAPATSAAAARDRVLLPWVFWPSAVIVLSF
+VGATLLAPEQMTVGISLVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGDITLGKPDEK
+PEFSTLSWFSLLFAAGMGIGLVFFGMTEPLMHFTSPRPDVAAANPTQAEAAQSALATTFL
+HWGLQPWAIYAVVGVAVALAIHRRGRPLALRWAFEPLIGERRVRGGWGHLIDNIALIGTV
+FGVATSLGLGVTQMSAGLRALGIVPEDSPWLEYAMIGAVTCVVLYTVVSGVERGMKWLSN
+TNLILAAGLLLFIAIVGPTAFLLKEMVQSLGSYMQYFFANSLNVSAFYGAEGDAWQAGWS
+AYYWGWWMSWTPFVGIFIARISRGRTVREFIAGVLLVPTLVCVVWFGILGGTAIFLETTR
+PAGYTSVVGADGAIDSNTALFQVLEQLPAGMMLVVGAIILSGIFFITSADSGSLVMGMLA
+TGGDVNPKATVKIFFAIATSLMAAALLAAGGLSAIQVLAITIGLPFSVLMLLICLATFRS
+LGYSVARVEAVRRQAMLASIKDRLGLESDDDEVVDAGPVAASQWWASLSRDHQQRIADAA
+AGVPASEGPRRTRLRRHGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000268.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000268.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fac8be1cc954580811c5d9eb5b74fa2463c7f89b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000268.fa
@@ -0,0 +1,59 @@
+>PROKKA_00135
+MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLG
+VDAIWLSPFYLSPQHDAGYDVADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHT
+SSEHAWFQAALAAGPGSPERARYHFAEGRGEHGELPPNNWESTFGGGAWTRVTEADGTPG
+QWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS
+RMGMVTDAGEDADPTFDPDTFEPLTPFMDQDRVHEVYRDWRRVLDSYDHEPMMVAEAWVA
+PLSRMFRYVRPGEMHQTFNFTYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTV
+RHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMVELGLPGSAYIYQGDELGLPE
+HTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA
+PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWSEHHDPTRGVLAF
+TVTSGGGRHLGSGEPIPARTVLVMANLSTEPVDLPANHSRALFSLEEAEAVQDGRLAHDA
+AAWLLMD
+>PROKKA_02149
+MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLG
+VDAIWLSPFYLSPQHDAGYDVADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHT
+SSEHAWFQAALAAGPGSPERARYHFAEGRGEHGELPPNNWESTFGGGAWTRVTEADGTPG
+QWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS
+RMGMVTDAGEDADPTFDPDTFEPLTPFMDQDRVHEVYRDWRRVLDSYDHEPMMVAEAWVA
+PLSRMFRYVRPGEMHQTFNFTYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTV
+RHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMVELGLPGSAYIYQGDELGLPE
+HTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA
+PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWSEHHDPTRGVLAF
+TVTSGGGRHLGSGEPIPARTVLVMANLSTEPVDLPANHSRALFSLEEAEAVQDGRLAHDA
+AAWLLMD
+>PROKKA_00250
+MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLG
+VDAIWLSPFYLSPQHDAGYDVADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHT
+SSEHAWFQAALAAGPDSPERARYHFAEGRGEHGELPPNNWESTFGGGAWTRVTEADGTPG
+QWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS
+RMGMVTDAGEDADPTFDPDTFEPLTPFLDQDRVHEVYRDWRRVLDSYGHEPMMVAEAWVA
+PLSRMFRYVRPGEMHQTFNFTYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTV
+RHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMVELGLPGSAYIYQGDELGLPE
+HTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA
+PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWSEHHDPARGVLAF
+TVTSGGGRHLGSGEPIPARTVLVMANLSTDPVDLPTGHSRALFSLEEAEAVQDGRLAHDA
+AAWLLMD
+>PROKKA_00185
+MTTQRLTTPPSEARNRPETPWWVDAVVYQVYPRSFADGDGNGMGDLPGVTAKIPYLSRLG
+VDAIWLSPFYLSPQHDAGYDVADYRTVDPRFGTLADADALIDAAHAADIRVIVDLVPNHT
+SSEHPWFQAAMAAGPGSRERARYHFTEGRGEHGELPPSNWESTFGGGAWSRVTEADGTPG
+QWYLHLFDTTQPDLNWENPEVREEFESILRFWLDRGVDGFRVDVAHGLVKKPGYPDADHT
+RMGMVTDAGEDQDPDFDVDAFEPAMPFLDQDGVHEVYRQWRRVLDSYPHEPMMVAEAWVS
+PLPRTFRYVRPGEMHQAFNFTYLMAGWDAESLTSAIDRSFTEAEKVGAPNTWVLSNHDTV
+RHTSRYGLSDPTAYPAGITAEDEQPDEALGRRRARAAAMIELALPGSAYIYQGDELGLPE
+HTTLPAELREDPYFFRTGGAEPGRDGCRIPLPWAADEPALGFSGPDADAAPWLPQPDSFR
+VLAADRQVGVEGSHFELYRHLLQIRAELDLGTGTFAWSAEHHRPEQGVLAFTVSSGGGRH
+LGSGVPIPARTVLVMANIGDTPVALPGDHVRAQFSLPESEAVVDDRLAPDAAAWLLLR
+>PROKKA_00143
+MTTQRLSTPPSEARNRPVTPWWVDAVIYQVYPRSFADADGDGMGDLRGVTSRLDYLAQLG
+VDAIWLSPFYLSPQHDAGYDVADYRAVDPRFGTLADADEMIAAAHEAGIRVVVDLVPNHT
+SSEHAWFQAALAAGPGSPERARYHFAEGRGEHGELPPNNWESTFGGGAWTRVTEADGTPG
+QWYLHLFDTTQPDLNWENEEVREEFRSILRFWLDRGVDGFRVDVAHGLIKQPGYPDAEHS
+RMGMVTDAGEDADPTFDPDTFEPLTPFMDQDRVHEVYRDWRRVLDSYDHEPMMVAEAWVA
+PLSRMFRYVRPGEMHQTFNFTYLMAGWDAASLTHAIDRSFEQAGRVGAPNTWVLSNHDTV
+RHASRYGLADPSSYPAGITAEDEQPDEAVGRRRARAAAMVELGLPGSAYIYQGDELGLPE
+HTTLAAEHRQDPYFFRTDGKEPGRDGCRIPLPWAADEPSYGFSTPADDDGPASAAEGVAA
+PWLPQPASFRALAADRQVGVEGSVFELYRRLLQIRGELDLGTGTFAWSEHHDPARGVLAF
+TVTSGGGRHLGSGEPIPARTVLVMANLSTDPVDLPAGHSRALFSLEEAEAVQDGRLAHDA
+AAWLLMD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000274.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000274.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e322ad9bf33892bb19aa8d970a6fdb2318f23f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000274.fa
@@ -0,0 +1,37 @@
+>PROKKA_00141
+MIDNAVYVDGRRVHAPSTLEDTWEECERTGGMAWLGLYRPDVAELQAVAEELRLHPLAVE
+DALAGGERAKLDRYGEDSFMVLHPARYIDRTETVEFGELSVFTGEHYVVTVRHAEEPDLA
+AVRRSLETEGRERLAMGPWQVTLEILDRVVDDYFPVADGLEQDIAEIEDQVFAGDGHVSR
+RIYELSREVLNFQHAIRALPSIVEQLQEEVRTRLHEDTRRLDADGLPRRDDAHAWEDEEL
+SEQARLEVENLRRLRDVHDHAVQINERVMTMRQMLNSALELDSTLASKRLAEQSIAQNEQ
+VKQISSWAAIIFAPQLVGSVYGMNFDGMPELHWAFGYPFALGLMLAVALTLFVLFKRADW
+L
+>PROKKA_02155
+MIDNAVYVDGRRVHAPSTLEDTWEECERTGGMAWLGLYRPDVAELQAVAEELRLHPLAVE
+DALAGGERAKLDRYGEDSFMVLHPARYVDRTETVEFGELSVFTGEHYVVTVRHAEEPDLA
+AVRRSLETEGRERLAMGPWQVTLEILDRVVDDYFPVADGLEQDIAEIEDQVFAGDGHVSR
+RIYELSREVLNFQHAIRALPSIVEQLQEEVRTRLHEDTRRLDADGLPRRDDAHAWEDEEL
+SDQARLEVENLRRLRDVHDHAVQINERVMTMRQMLNNALELDSTLASKRLAEQSIAQNEQ
+VKQISSWAAIIFAPQLVGSVYGMNFDGMPELHWAFGYPFALGLMLAVALTLFVLFKRADW
+L
+>PROKKA_00243
+MIDNAVYVDGRRVHAPSTLEDTWEAAEASGGMAWLGLYRPDADELRAVADELHLHPLAVE
+DALEGGERAKLDRYGEDLFMVLHFQHAIRALPVIVEQLQGGARARLREEEHRREVGAPRT
+GDVHEWDQDELSEEGVFEVENLRRLRDVHDHAVQINERVAAMRQMLANALELDSTLASKR
+LAEQSIEQNEQVKQISSWAAIIFAPQLVGSIYGMNFDGMPELHWAFGYPFALGLMLAVAL
+TLFVLFKRADWL
+>PROKKA_00177
+MTLIDNAVYVDGRRVFAPTSLSDTWDAIERTGGMAWLGLYRPHPDELQEVADELPLHPLA
+VEDALTPGQRAKLERYGDDWFMVLHPARYIDATETVEFGELDVFTGKDYVVTVRHAEEPD
+LADIRAGMEQRHTDRLAQGPSQVAFEILDHVVDAYFPVAEGLEQDIREIEDQIFSGDAAV
+SRRIYELSREIIGFERATRPLPRMIEQLQEDMRARLGDAANGSHASHLEAPEPEPGEEER
+AELVETLRALRDIHDHAVQVTDRVAAMRQMLENALELDSTLASKRLAEQSIAQNEQVKRI
+SSWAAIIFAPQLIGSVYGMNFQHMPELEWPLGYPWALGLMLGVAVALYALFKKADWL
+>PROKKA_00149
+MIDNAVYVDGRRVHAPSTLEDTWEECERTGGMAWLGLYRPDVAELQAVAEELRLHPLAVE
+DALAGGERAKLDRYGEDSFMVLHPARYVDRTETVEFGELSVFTGEHYVVTVRHAEEPDLA
+AVRRSLETEGRERLAMGPWQVTLEILDRVVDDYFPVADGLEQDIAEIEDQVFAGDGHVSR
+RIYELSREVLNFQHAIRALPSIVEQLQEEVRTRLHEDTRRLDADGLPRRDDAHAWEDEEL
+SDQARLEVENLRRLRDVHDHAVQINERVMTMRQMLNNALELDSTLASKRLAEQSIAQNEQ
+VKQISSWAAIIFAPQLVGSVYGMNFDGMPELHWAFGYPFALGLMLAVALTLFVLFKRADW
+L
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000275.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000275.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1eb50beaf460973a64759cbc9c8d8cd6a3be2c68
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000275.fa
@@ -0,0 +1,20 @@
+>PROKKA_00142
+MKTPRHAPPVVRDGKTLLPAHAVSTAPVTAFGLIGGYLTARETGIRPLGGVVLAAAGLYA
+GRTWLAKRGPAVAGGLAALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDRSEA
+GR
+>PROKKA_02156
+MKTPRHAPPVVRDGKTLLPAHAVSTAPVTAFGLIGGYLTARETGIRPLGGVVLAAAGLYA
+GRTWLATRGPAVTGGLAALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDRSEA
+GR
+>PROKKA_00242
+MNSPRHAAPVVRDGRTLLPAHAVTTAPIAAFGLIGGYLTARETGIRPLGGVVLAAAGAYA
+GRTWLAKRGPAVAGGLTALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDREGA
+R
+>PROKKA_00176
+MSKDTSTPVARDGKTLLPADAVTTAPIAALGLVGGYLVARETGIRWLGGVVLGAAGLYAG
+RTWAAKGGPAVAGTLGALYLGGFGASHPLAKKIGAWPSVLSVAAASAGAAYAAVDRKDGR
+R
+>PROKKA_00150
+MKTPRHAPPVVRDGKTLLPAHAVSTAPVTAFGLIGGYLTARETGIRPLGGVVLAAAGLYA
+GRTWLAKRGPAVAGGLAALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDRSEA
+GR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000278.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000278.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cecd077883da5931ef1221628d185a167f650606
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000278.fa
@@ -0,0 +1,35 @@
+>PROKKA_00146
+MPIASPEKYAEMIDAAKNGAFAYPAINVTSSQTLNAAIRGFAEAGSDGIIQVSTGGAAYF
+SGSSVKDMVAGSLAFAAFAREVAKKHSVNIALHTDHCPQDKLEDFVLPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGRELLARTHANKQILEVEIGVVGGEEDGVAHEINEKL
+YTTVADGIATVEALGLGENGRYLTALTFGNVHGVYKPGNVKLRPEILQEIQQAVGEKFGR
+ERPFDLVFHGGSGSAAQEIADSVEYGVVKMNVDTDTQYAFTRPVAGHMFENYDGVLKVDG
+EVGDKKQYDPRVWGAKAEEAMAARVVQACTELNSAGKSIG
+>PROKKA_02160
+MPIASPEKYAEMIDAAKNGAFAYPAINVTSSQTLNAAIRGFAEAGSDGIIQVSTGGAAYF
+SGSSVKDMVAGSLAFAAFAREVAKKYSVNIALHTDHCPQDKLEGFVLPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGRELLARTHANKQILEVEIGVVGGEEDGVAHEINEKL
+YTTVADGIATVEALGLGEHGRYLTALTFGNVHGVYKPGNVKLRPEILQEIQQAVGEKFGK
+ERPFDLVFHGGSGSAAQEIADSVEYGVVKMNVDTDTQYAFTRPVAGHMFENYDGVLKVDG
+EVGDKKQYDPRVWGAKAEEAMAARVVQACTELNSAGKSIG
+>PROKKA_00238
+MPIASPDKYAEMIDAAKNGAFAYPAINVTSSQTLNAAIRGFAEAGSDGIIQVSTGGAAYF
+SGASVKDMVTGSLAMAAFAREVAKNYSVNIALHTDHCPKDKLDAFVMPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGKELLARTHANKQILEVEIGVVGGEEDGVAHEINDKL
+YTTVEDGIATIEALGLGEQGRYLTALTFGNVHGVYKPGNVKLRPQILEDIQKAVGEKFGK
+ERPFDLVFHGGSGSAAQEIADSVSYGVVKMNVDTDTQYAFSRPVAGHMFENYAGVLKVDG
+EVGDKKMYDPRVWGAKAEEAMAARVVQACQELNSAGTSIG
+>PROKKA_00173
+MPIASPDKYAEMIDAAKNGAFAYPAINVTSSQTLNAAVRGFAEAGSDGIIQVSTGGAAYF
+SGSSVKDMVAGSLAMAAFAREVAKKYSVNIALHTDHCPKDKLDGFVKPLLDASEAEVKAG
+RDPLFNSHMWDGSAETLEENLRIAQELLARTHANKQILEVEIGVVGGEEDGVANEINDKL
+YTTVEDGIATIEALGLGENGRYLTALTFGNVHGVYKPGGVKLRPQILQDIQQAVGEKFGR
+QRPFDLVFHGGSGSAAQEIADSVSYGVVKMNVDTDTQYAFSRPVAGHMFENYDGVLKVDG
+EVGNKKMYDPRVWGAKAEDGMAARVVQACQELNAAGKSIG
+>PROKKA_00154
+MPIASPEKYAEMIDAAKNGAFAFPAINVTSSQTLNAAIRGFAEAGSDGIVQVSTGGAAYF
+SGSSVKDMVAGSLAFAAFAREVAKKYSVNIALHTDHCPQDKLEGFVLPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGRELLARTHANKQILEVEIGVVGGEEDGVAHEINEKL
+YTTVQDGIATVEALGLGEHGRYLTALTFGNVHGVYKPGNVKLRPEILQEIQQAVGEKFGK
+ERPFDLVFHGGSGSAAQEIADSVEYGVVKMNVDTDTQYAFTRPVAGHMFENYDGVLKVDG
+EVGDKKQYDPRVWGAKAEEAMAARVVQACTELNSAGKSIG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000279.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000279.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1eb66c73de0b5f7e60eb09dca303207b467dcf7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000279.fa
@@ -0,0 +1,50 @@
+>PROKKA_00147
+MDHGNGPPLVKNVTFFPKHVISSPVPSTVPRMMTRPLPEDSATVDTVALGRRVRHLRKQA
+GLTLDQLAERTGVSGSHLSLVENARREPRLSLVQRIAEVLGVPVEDLLTGRAPTRRAELE
+IEVERFARSEHYASLGLPPLRIGPRTPTEVLEVIAGLEAELRRRLEEQAATPEEARRANA
+QLRARMRAVDNHYPDLEAEAHRLLDAIGHTGGPLGLHAVSELAEHLGFTLRFVPDLPHST
+RSVTDLKHGRIHISGSRSSDHDRRTVVLQALAAAVLGHGEPRDYEDFLAQRVAVNYLAGA
+LLMPQRAASSLLRAAQKRRDLSVDDLKDAFGVSYEAAAHRFTNLATVDLGIRCHFQKVHE
+TGVIHKAYENDGIVFPADHTGAIEGQQACRKWGARQAFSRNDRFRAHAQYTDSPNGTFWC
+TSMIENGPDGLFALSVGTPFEHARYFRGADTRHRVTSTCPDPRCCRRPDPELEAAWGGHV
+WPAARMHAHLLAAMPTQTFPGVDEREVFEFLQAQEEREG
+>PROKKA_02161
+MMTRPLPEDSATVDTVALGRRVRHLRKQAGLTLDQLAERTGVSGSHLSLVENARREPRLS
+LVQRIAEVLGVPVEDLLTGRAPTRRAELEIEVERFARSEHYASLGLPPLRIGPRTPTEVL
+EVIAGLEAELRRRLEEQAATPEEARRANAQLRARMRAVDNHYPDLEAEAHRLLDAIGHTG
+GPLGLHAVSELAEHLGFTLRFVPDLPHSTRSVTDLKHGRIHISGSRSSDHDRRTVVLQAL
+AAAVLGHGEPRDYEDFLAQRVAVNYLAGALLMPQRAASSLLRAAQKRRDLSVDDLKDAFG
+VSYEAAAHRFTNLATVDLGIRCHFQKVHETGVIHKAYENDGIVFPADHTGAIEGQQACRK
+WGARQAFSRNDRFRAHTQYTDSPNGTFWCTSMIENGPDGLFALSVGTPFEHARYFRGADT
+RHRVTSTCPDPRCCRRPDPELEAAWGGHVWPAARMHAHLLAAMPTQTFPGVDEREVFEFL
+QAQEEREG
+>PROKKA_00236
+MMTRPLPEDSATVDAVALGRRVRHLRKQAGLTLDQLADRTGVSGSHLSLVENARREPRLS
+LVQRIAEVLGVPVEDLLTGRAPTRRAELEIEVERFARSEHYASLGLPPLRIGPRTPTEVL
+EVIAGLEAELRRRLEEQAATPEEARRANAQLRARMRAVDNHYPDLEAEAQRLLDAIGHTG
+GPLGLHAVSSLAEHLGFTLSFVANLPHSTRSVTDLKHGRIHVSGGRASDHDRRTVVLQAL
+AAAVLGHGEPRDYEDFLSQRVAVNYLAGALLMPQRPASALLRAAQKRRDLSVDDLKDAFG
+VSYEAAAHRFTNLATVDLGIRCHFQKVHETGVIHKAYENDGLVFPADHTGAIEGQAACRR
+WGARQAFGRSDRFRAHTQYTDAPNGTYWCTSMVEHGPDGLFALSVGTAFEHARHFRGADT
+RHRITSTCPDPRCCRLPDPALEAEWGGHVWPAARMHAHLLAAMPTQAFPGVDEVEVFEFL
+ESQRDRTPGAPGADAPDGAGGVTP
+>PROKKA_00821
+MATPTDPAHEPPRVDPLVLGRRLRHLRRVSGATLSDVAEKVGVTASHLSLVENGHREPRL
+TLLTALADVHGVGVEDLLTPEAPSRRAALEVAVERAQRGPLFQRLGLPALKIGPRTPDEV
+LEVIAGLQAELDRQMAERVSTPEEARRANSALREEMRACGNHYADLERRAQELREAVDVA
+DGPLTHHHVSALAEHLGFAVRFVPDLPHSTRSVTDLKNRRIYLARARRPDHDPRAVLLQA
+VCSSVLGHGEPADYADFLRQRVYTNYLAAAMMMPERGTVRALREAKERRDLSVDDLRDRF
+GVSWESAAHRFTNLATEHLGLTCHFAKVHESGVFHKAYENDGIPFPTDHIGAIEGQTACR
+HWTSRQVFSVADHLGAFPQYTDTPAGTYWSAAVVEPTSTGFYSLTVGVPFDDAKWFRGRE
+TSARTRSTCPDPKCCRLPSAELEAAWGGQAWPAARANAHLLAAMPGGAFPGVEEVQVFEF
+LQTQESRWPPEGSGAA
+>PROKKA_00155
+MMTRPLPEDSATVDTVALGRRVRHLRKQAGLTLDQLAERTGVSGSHLSLVENARREPRLS
+LVQRIAEVLGVPVEDLLTGRAPTRRAELEIEVERFARSEHYASLGLPPLRIGPRTPTEVL
+EVIAGLEAELRRRLEEQAATPEEARRANAQLRARMRAVDNHYPDLEAEAHRLLDAIGHTG
+GPLGLHAVSELAEHLGFTLRFVPDLPHSTRSVTDLKHGRIHISGSRSSDHDRRTVVLQAL
+AAAVLGHGEPRDYEDFLAQRVAVNYLAGALLMPQRAASSLLRAAQKRRDLSVDDLKDAFG
+VSYEAAAHRFTNLATVDLGIRCHFQKVHETGVIHKAYENDGIVFPADHTGAIEGQQACRK
+WGARQAFSRNDRFRAHTQYTDSPNGTFWCTSMIENGPDGLFALSVGTPFEHARYFRGADT
+RHRVTSTCPDPRCCRRPDPELEAAWGGHVWPAARMHAHLLAAMPTQTFPGVDEREVFEFL
+QAQEEREG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000283.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000283.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d96c92d44733283eb0eb20ac8ad712200e72db2f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000283.fa
@@ -0,0 +1,20 @@
+>PROKKA_00151
+MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDIVPVAPESSLVWALMAEDAWAEGR
+TVDSYAYARVGYHRGLDALRRAGWRGAGPVPYAHEPNRGFLRALYALGRAAAGIGESEEV
+ERIRTFLRDSDPTAAEQIEAGQGRARG
+>PROKKA_02165
+MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDIVPVAPESSLVWALMAEDAWAEGR
+TVDSYAYARVGYHRGLDALRRAGWRGAGPVPYAHEPNHGFLRALYALGRAAAGIGESEEV
+ERIRTFLRDSDPTAAEQIEAGQGRAQG
+>PROKKA_00232
+MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDVVPVAPESSLVWALMAEDAWSEGR
+TVDSYAYARVGYHRGLDALRKAGWRGAGPVPYDHEPNRGFLRALYSLGRAAAGIGESEEV
+ERIRTFLKDSDPTAAEKIEATQGRSGS
+>PROKKA_00171
+MSESLIGKNLMEPPATLLPEEPEVLARLDAGDLPEDLVPLAPESSLVWALMAEDAWSEGR
+AVDSYAYSRVGYHRGLDALRRAGWRGAGPVPWSHEPNRGFLRALYALGRAAAGIGESAEV
+DRIRTFLKDSDPTAAQQIEAAQA
+>PROKKA_00159
+MSESLIGKNLMEPPATRLPEEPEVLARLEAGDLPEDIVPVAPESSLVWALMAEDAWAEGR
+TVDSYAYARVGYHRGLDALRRAGWRGAGPVPYAHEPNRGFLRALYALGRAAAGIGESEEV
+ERIRTFLRDSDPTAAEQIEADQGRAQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000284.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000284.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e9beed7b195028219a800c8f31fbcfbdb0bcddc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000284.fa
@@ -0,0 +1,25 @@
+>PROKKA_00152
+MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEGDVVSRLGVTRAVDF
+LVPAGADVRELFRRHATGDDPDALVGHVEAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG
+VPVIAYGLRTDFRTRSFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVDPATGAEHF
+VFEGDQVAIDGVQVTYESLCGTCYLAESGGALG
+>PROKKA_02166
+MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEGDVVSRLGVTRAVDF
+LVPAGADVRELFRRHATGDDPDALVGHVEAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG
+VPVIAYGLRTDFRTRSFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVDPATGAEHF
+VFEGDQVAIDGVQVTYESLCGTCYLAESGGALG
+>PROKKA_00231
+MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEDEVVSRLGVTRTVDF
+LVPAGAGVRELFRRHASGDDPDALVDHVDAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG
+VPVIAYGLRTDFRTRCFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVNPATGAEHF
+VFEGDQVAIDGVEVTYESLCGSCYLAESGGRLG
+>PROKKA_00170
+MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPAVDTKGDAAVVSRLGVTRAVDF
+LVPAGADVLALFRAHAAGDDPDALVDHVDAPPVACLLVDEAQFLEAGQVDDLLRIAVLED
+VPVMAYGLRTDFRTHSFPGSARLLELAHSLEELKTICRCGRKAVLNTRKVVDAATGRSRF
+VFEGDQVAIDGVEVTYESLCAACYLEESGGRLG
+>PROKKA_00160
+MAKLYFRYGAMNSGKSTGLLQAAFNYEERGQRVLLAKPEVDVKGEGDVVSRLGVTRAVDF
+LVPAGADVRELFRRHATGDDPDALVGHVEAPPVACLLVDEAQFLEPAQVDDLLRIAVLDG
+VPVIAYGLRTDFRTRSFPGSARLLELAHSLEELKTICRCGRKAVFNTRKVVDPATGAEHF
+VFEGDQVAIDGVQVTYESLCGTCYLAESGGALG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000285.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000285.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb20b7eae51c6dd3aeb4c2b833e76c6522a32637
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000285.fa
@@ -0,0 +1,25 @@
+>PROKKA_00154
+MATPLLELAASRGVCFPLRARRLTLTPFRGLDAPAVWSFCRLEQVWSWTSGRPESENALR
+ESYLGAGDRLTVRAGDVIVGVGKVAVQDAWSQDGPQEEARDAQAELGWTIDPRQAGQGYG
+TELARALLGFAFDDLGVRRVEAHAFADNAPSLRIMEKVGMRHEGTFKEESLHLTRGWVDG
+ATYAMLASEFHSPLTQE
+>PROKKA_02168
+MATPLLELAASRGVCFPLRTRRLTLTPFRGLDAPAVWSFCRLEQVWSWTSGRPESENALR
+ESYLGAGDRLTVRAGDVIVGVGKVAVRDAWSQGGPREEGRDAQAEIGWTIDPRQAGQGYG
+TELARALLGFAFDDLGVRRVEAHAFADNAPSLRIMEKVGMRHEGTFKEESLHLTRGWVDG
+ATYAMLASEFHSPLTQE
+>PROKKA_00470
+MATPLLDLAARRGVVFPLRTERLTLTSFAADDAPAVFDFCRLEEVWTWTSGRAGSAGELR
+ESYLAAGDRLTVRAGEAIIGVGKLAVQDAWSQGGPREEARDAQAEIGWTIHPTHADQGYA
+TELAGALLKLAFTGLGVHRVEAEAFADNAPTLRVMEKVGLRHEGTFREESLHLTRGWVDG
+VTYAMLASEFLARV
+>PROKKA_00420
+MATPLLDLAARRGVAFPLRTERLTLTPFTAVDAPAVWDFCRLEEVRTWTSGRAGSAAELR
+EEYLATGDRLTVRDGAGDVVGVGKLAVQDAWSQGGPHPDARDAQAELGWTVAPEHAGRGY
+ATEIGRALLDLAFRGLGVRRVEAGAFADNAPSLRVMAKIGLRHEGTFLGESLHLTRGWID
+GVTFALLASEYEGGAAASRA
+>PROKKA_00167
+MAPPLLELAASRGVCFPLRARRLTLTPFRGLDAPAVWGFCRLEQVWSWTSGRPESEGALR
+ESYLAAGDRLTVRVGDVIVGVGKAAVQDAWSQGGPREEARDAQAEIGWTIDPRQAGQGYG
+TELARALLGFAFNDLGVRRVEAHAFADNAPSLRIMEKVGMRHEGTFKEESLHLTRGWVDG
+ATYAMLASEFHSPLTQE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000287.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000287.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a9d3c4c5cd5f0048983682b084f0d68373b6c7a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000287.fa
@@ -0,0 +1,25 @@
+>PROKKA_00178
+MSTAAPHTQHSDFPSPTPTRKGPSVGTWRPWAVLPWALALLALPLIALALRSNFGANGWM
+TVIYMVFGALPHELVLMVLVGSLFLLPRVNPQDEQRGGIRLGRLLHTLLGVSWGSFALAA
+IIFPDGGDHPDSGATTPVLMDLLGKSTAMDVGIVGGLALVAVSALTGLAVIVVCVVRRIR
+AVR
+>PROKKA_02174
+MSTAAPGTQHSDFASPTPTRKGPSVGTWRPWAVLPWALALLALPLIALALRSNFGANGWM
+TVIYMVFGALPHELALVLMVGSLFLLPRVNPQDEQRGGIRLGRLLHTLLGISWGSFALAA
+IIFPDGGDHPDSGATTPVLMDLLGKSTAMDVGLVGGLALVAVSALTGLAVIVVCVVRRIR
+AVR
+>PROKKA_00223
+MSTAAPHTQHSDSASPAPTRKGPSVGTWRPWAVLPWALALLALPLIALALRSNFGANGWM
+TVIYMVFGALPHELFLMLMVGSLFLLPRVNPLDEQRGGIRLGRLLHTLLGVSWGSFALAA
+ILFPDAGDHPDSAATTPVLMDLLGKSTAMDVGSVAGLALAAVSALTGLAVIVVCVVRRIR
+AVR
+>PROKKA_00169
+MAVPHPVMPPPGTPLPHQLRPAGPSVGTPRWLPAVLWIVAFALLPLCVIVGRFATENGGW
+LLFTYIMFGWMVQGGLGVLAAASLFLLPRVNPPVERRAGVRTGVVVHLLLGASWLTGLLG
+MLAFGDYGDAPGSETAPAPLVDLYGMDRAVEIGDAVGPPLVGISLLTGLAAVVLVVVRRL
+AAAVRS
+>PROKKA_00175
+MSTAAPGTQHSEFASPAPARKGPSVGTWRPWAVLPWALALLALPLIALALRSDFGANGWM
+TVIYMVFGALPHELVLMVLVGSLFLLPRVNPQDEQRGGLRLGRLLHTLLGVSWGSFALAA
+IIFPDGGDHPESGATTPVLMGLLGTSTAMDVGIVGGLALVAVSALTGLAVIVVCVVRRIR
+AVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000289.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000289.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d7fbf82338d460134c39d312f21da104919ab52
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000289.fa
@@ -0,0 +1,70 @@
+>PROKKA_00180
+MTTQQPDIPGTPGPITPDLEEHTALTHPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAA
+QGCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGA
+HGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGT
+WDLVGNNIPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTLW
+NMSDRGIPRSYRMMEGFGVHTYRLIAADGSTVLVKFHWKPMLGVHSVTWEEALLTNGMDP
+DFHRRDLADAIEAGAFPEWELGVQVFEDNEEQMFEGIDLLDPTKLVPEELAPVQPLGRMT
+LNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWNQLPIN
+RPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHAFIEHPEPLPASVKER
+AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLA
+QQVADGLGIPVPAPTETPADVQPSPVLSQIGGAWPLDGRQVGVVVGESVDEKELDALVQG
+IHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVVVASPAAPAADAAPGLDQKAG
+AADPEAVDPRVIKVLQEMWRHSKAILALEPAEAVLAAAQVSGKGVESAADGASAVSRLTE
+LLPAHRVWDRFPTTGRLAD
+>PROKKA_02176
+MTTQQPDIPGTPGPITPDLEEHTALTHPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAA
+QGCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGA
+HGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGT
+WDLVGNNIPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTLW
+NMSDRGIPRSYRMMEGFGVHTYRLIAADGSTVLVKFHWKPMLGVHSVTWEEALLTNGMDP
+DFHRRDLADAIEAGAFPEWELGVQVFEDNEEQMFEGIDLLDPTKLVPEELAPVQPLGRMT
+LNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWNQLPIN
+RPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHAFIEHPEPLPASVKER
+AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLA
+QQVADGLGIPVPAPTETPADVQPSPVLSQIGGAWPLDGRQVGVVVGESVDEKELDALVQG
+IHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVVVASPAAPAADAAPSLDQKAG
+AADSEAVDPRVVKVLQEMWRHSKAILALEPAEAVLAAAQVSGKGVESAADGASAVSRLTD
+LLPAHRVWERFPTTGRLAD
+>PROKKA_00221
+MTTQQPDIPGTPGPRTPDLEERTAPTSSDDAAMPAPDQRGPASVSPTGQDTGADPATAAQ
+GCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGAH
+GMFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGTW
+DLVGNNMPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTIWN
+MSDRGIPRSFRMMEGFGVHTYRLIAADGSTVLVKFHWKPKLGVHSVTWEEALITNGADPD
+YHRRDLADAIEAGAFPEWELGVQVFEDTEEQMFEGIDLLDPTKLVPEELVPVQPLGRMTL
+NANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWTQLPINR
+PHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHALIEHPEPLPASVKERA
+HAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLAQ
+QVADGLGIPVPAPTETPADVQPSPVLSQIGGVWPLDGRQVGVVVGESVDEKELDALVQGI
+HGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVVVASPAAPAADAAPGLDEKAGA
+AASEAVDPRVVKVLQEMWRHSKAILALEPAEGVLAAAQVSGKGVESAADGASAVSRLTEL
+LPAHRVWERFGTTGRFAD
+>PROKKA_00166
+MAEQPKIPGTPGPITPDLEEHTALTDPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAAQ
+GCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGAH
+GVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGTW
+DLVGNNMPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTIWN
+MSDRGIPRSFRMMEGFGVHTYRLIAADGSTVLVKFHWKPKLGVHSVTWEEALITNGADPD
+YHRRDLADAIEAGAFPEWELGVQVFEDNEEQMFEGIDLLDPTKLVPEELVPVQTLGLMTL
+NANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWTQLPINR
+PHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHALIEHPEPLPASVKERA
+HAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEETIRVRQLQNLGAIDPRLAQ
+QVADGLGMPVPAPADAPADVQPSAALSQVGGTWPLDGRQVGLVVGPQVDEKELGDAVQGI
+HGAGMVPLVIAPKGGPVAGEVVAQRAYLTAASIELDAVVVLGATPPAGDAQHGLDAKAAA
+DAPDAVDPRVAKLVQEAWRHAKAIVAVGEGTSVLDELGLTGTPGVLTVDAGADAVAQLKE
+LMPAHRVWERFPTTGRLAD
+>PROKKA_00177
+MTTQQPDIPGTPGPITPDLEEHTALTHPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAA
+QGCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGA
+HGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGT
+WDLVGNNIPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTLW
+NMSDRGIPRSYRMMEGFGVHTYRLIAADGSTVLVKFHWKPMLGVHSVTWEEALLTNGMDP
+DFHRRDLADAIEAGAFPEWELGVQVFEDNEEQMFEGIDLLDPTKLVPEELAPVQPLGRMT
+LNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWNQLPIN
+RPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHAFIEHPEPLPASVKER
+AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLA
+QQVADGLGIPVPAPTETPADVQPSPVLSQIGGAWPLDGRQVGVVVGESVDEKELDALVQG
+IHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVVVASPAAPAADAAPGLDQKAG
+AADSEAVDPRVVKVLQEMWRHSKAILALEPAEAVLAAAQVSGKGVESAADGASAVAALKQ
+LLPAHRVWDRFPTTGRLAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000292.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000292.fa
new file mode 100644
index 0000000000000000000000000000000000000000..63c3100076094594ea5a604d61d8c79a61587ca3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000292.fa
@@ -0,0 +1,25 @@
+>PROKKA_00183
+MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD
+DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVATPPDSAVYLAIV
+EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV
+VGALSTLVPAYRCTDELADRCGAALVAATHELAHLLGAADTPRERPADSPGKPKARS
+>PROKKA_02179
+MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD
+DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVTTPPDSAVYLAIV
+EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV
+VGALSTLVPAYRCTDELADRCGAALVAATGELAHLLGAADTPRERPADSPGKPKASS
+>PROKKA_00218
+MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD
+DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVTTPPASAVYLAIV
+EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV
+VGALSTLVPAYRCTDELADRCGAALVAATDELAHLLGAADTPRERPADSPGKPKASS
+>PROKKA_00163
+MPTTPPASTRTVDRALALLAAVVAQPRLSLAEAARATDLPASTALRLLRSLETAGFVDRQ
+EEGEYRPGARLIQLGARAFSREPLVRLARAPMDGVAEATGESVYLSLRNGAQEAVYIAIV
+EGTHSVRHASWVGRTVPLEGTAVGEVYRGEVPPGGYAHGGHSVEQDVTALSSPVVVGGRV
+VAALSALVPDYRCTAEHADRCGRALAGATTRLASALGEEAPPEDAD
+>PROKKA_00180
+MTTTPTASTRTVDRALDLLAAVTEQPRLSLTEAARATELPASTALRLLRSLEGSGFVARD
+DDGAYRPGVRLIQLGARAFSRDSLVQLARGPMDHVVAATGESVYLSVTTPPDSAVYLAIV
+EGTHSVRHTNWVGRTVPLAGTAVGDALRGSVAAGDYTLRTRSVEKDVTSLSAPISVAGTV
+VGALSTLVPAYRCTDELADRCGAALVAATHELAHLLGAADTPRERPADSPGKPKASS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000293.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000293.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4571e7a858dc2f59fc5fa730af9c534b24f40d0e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000293.fa
@@ -0,0 +1,55 @@
+>PROKKA_00184
+MAVGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA
+ARSWEAYDAIVATLKDLEEDETLLVQSGKPVGVFRTNKWAPRVLIANSNLVGDWATWPEF
+RELEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKRYDGSLQGTLTLTGGCGGM
+GGAQPLAVTLNGGVCLIVDVSEDRLRRRMGKRYLDEVETDIDKAVERVMQAKNDGEAVSV
+GLVGNAAEVFPELLERQKAGTVEIDIVTDQTSAHDPLSYLPIEIDEKDWHAEAEADPDTF
+TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC
+EGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY
+GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGVADGTELAAAKLEALLTNDPGMGVIRHVD
+AGYSRAAEVAKERGVRVPMEATIRD
+>PROKKA_02180
+MAEGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA
+ARSWEAYDAIVATLKDLEEDETLLVQSGKPVGVFRTNKWAPRVLIANSNLVGDWATWPEF
+RKLEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKRYDGSLQGTLTLTGGCGGM
+GGAQPLAVTLNGGVCLIVDVSEDRLRRRMGKRYLDEVETDIDKAVERVMQAKRDGEAVSV
+GLVGNAAEVFPELLERQKAGTVEIDIVTDQTSAHDPLSYLPIEIDEKDWHAEAEADPDTF
+TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC
+EGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY
+GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGVADGTELAAAKLEALLTNDPGMGVIRHVD
+AGYSRAVEVAAERGVRVPMEATIRD
+>PROKKA_00217
+MAVGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA
+ARSWEAYDAIVATLKDLEEDETLLVQSGKPVGVFRTNKWAPRVLIANSNLVGDWATWPEF
+RKLEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKRYDGSLKGTLTLTGGCGGM
+GGAQPLAVTLNGGACLIVDVSEGRLRRRMGKRYLDEVVTDIDKAVERVMQAKRDGEAVSV
+GLVGNAAEVFPELLERQKRGEIEIDIVTDQTSAHDPLSYLPIEIDEADWQAEAEGDPETF
+TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC
+EGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY
+GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGLADGTELAAAKLEALLTNDPGMGVIRHVD
+AGYSRAAEIAAERGVRVPMEATIRD
+>PROKKA_00162
+MAAGFTQHDPSRTIRAPRGTELNAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA
+ARSWEAFDAIVETLKDLEEDETLLVQSGKPVGVFRTNVWAPRVLIANSNLVGDWADWKTF
+RELEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKKYDGTLKGTLTLTGGCGGM
+GGAQPLAVTLNGGVCLIVDVSEERLRRRMGKRYLHEVETDIDAAIARVMQAKRDGEAVSV
+GLVGNAAEVFPELLKRQKAGEVEIDIVTDQTSAHDPLSYLPIEIEEKDWHAEAEADPDTF
+TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC
+EGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY
+GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGLADGTELAAAKLTALLTNDPGMGVIRHVD
+AGYSRAVEVAAERGVRIPMEPTVRD
+>PROKKA_00181
+MAVGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA
+ARSWEAYDAIVATLKDLEEDETLLVQSGKPVGVVKTNVWAPRVLIANSNLVGDWADWKTF
+RELEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKRYDGSLKGTLTLTGGCGGM
+GGAQPLAVTLNGGVCLIVDVSEDRLRRRMGKRYLDEVETDIERAVERVMQAKRDGEAVSV
+GLVGNAAEVFPELLERQKAGTVEIDIVTDQTSAHDPLSYLPIEIDEKDWHAEAEADPDTF
+TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC
+EGLGPFRWAALSGDPEDIRVTDAALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY
+GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGVADGTELAAAKLEALLTNDPGMGVIRHVD
+AGYSRAAEVAKERGVRVPMEATIRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000295.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000295.fa
new file mode 100644
index 0000000000000000000000000000000000000000..534fa380ce3afa0f35b7306779e94994204d3f97
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000295.fa
@@ -0,0 +1,40 @@
+>PROKKA_00186
+MRSTLITDIAELTTVDPEGRVLTDAAVVVEDERIAWIGPAADAPEADDRVSVEGRAVLPG
+WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDARLAELVRGRVADAVA
+GGTTYLETKTGYGLTVEEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV
+GPMLAAVREHVGWVDVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE
+FGAASVDHVNHLSDADVEALAGTWADWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL
+LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGALGLRAQDRVG
+SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV
+>PROKKA_02182
+MRSTLITDIAELTTVDPEGRVLTDAAVVVEDERIAWIGPAADAPEADDRVSVEGRAVLPG
+WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDARLAELVRGRVADAVA
+GGTTYLETKTGYGLTVAEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV
+GPMLAAVREHVGWVDVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE
+FGAASVDHVNHLSDADVEALAGTWADWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL
+LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGAIGLRAQDRVG
+SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV
+>PROKKA_00215
+MRSTLITDIAELTTVDPEGRVLTDAAVVVEDERIAWIGPAADAPDADDRVSVEGRAVLPG
+WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDDRLAELVRGRVADAVA
+GGTTYLETKTGYGLTVEEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV
+GPMLEAVREHAGWADVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE
+FGAASVDHVNHLSDTDVEALAGTWTGWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL
+LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGALGLRAQDRVG
+SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV
+>PROKKA_00160
+MASTLITDIAELTTVDPEGRVLRDAAVVLDDEDVAWIGPAAQAPAADERVSVAGRAVLPG
+WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGLTMEATRAASDERLRELVLGRVADAVR
+GGTTYLETKTGYGLTVEEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDVEDYLDDVV
+GPMLEAVREHVGWVDVFCDTGAFDAAQTRRVLAAGVAAGLRARLHGNQIEQGPGVALAVE
+FGAASVDHVNHLSDADVEALAGTWSGWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL
+LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGAIGLRAQDRVG
+SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV
+>PROKKA_00183
+MRSTLITDIAELTTVDPEGRVLQDAAVVVEDERIAWIGAAADAPDADDRVSVGGRAVLPG
+WVDSHTHLVFDGDRSAEFEARMAGESYAAGGIGVTTSATRAASDDRLAELVRGRVADAVA
+GGTTYLETKTGYGLTVAEEARHARLLAGLREEGLVDEVTFLGAHLVPPGRDAEDYLDDVV
+GPMLEAVREHAGWVDVFCDTGAFDAEQTRRVLAAGVAAGLGVRLHGNQIEQGPGVGVAVE
+FGAASVDHVNHLSDADVEALAGTWTGWDRASATGTPGTVAGCLPACDLSTRAPLAPARRL
+LDAGIEVSLASNCNPGTSYTTSMNFNVGTAVLQMHLTLAEAVRAATLGGAIGLRAQDRVG
+SLEVGKRADLHVLDAPAAIHLAYRPGMPLTHAVWRAGRRAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000296.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000296.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ec58d759c2485f86b3dc01d2f6dd7482cf69a4c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000296.fa
@@ -0,0 +1,50 @@
+>PROKKA_00187
+MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV
+STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR
+PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGTDGALRPAGEA
+LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR
+VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR
+DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER
+RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ
+EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV
+PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH
+>PROKKA_02183
+MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV
+STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR
+PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGEDGALRPAGEA
+LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR
+VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR
+DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER
+RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ
+EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV
+PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH
+>PROKKA_00214
+MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV
+STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR
+PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGADGALRPAGEA
+LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR
+VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR
+DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER
+RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ
+EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV
+PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAWKSEGTEAEGH
+>PROKKA_00159
+MTTTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGVSTG
+FGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVRPVV
+VETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGADGALRPAGEALAE
+AGIEPVELREKEGLALVNGTEGMLGMLIMALADLDELVDTVDLTAAMSVEALLGTDRVFV
+PELHLPLRPHPGQAASADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLRDTL
+AYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSERRTD
+RMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQEDH
+VSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGVPGP
+GPDQYMAPQLAAAEQALRDGSVLAAVAEALAGASADAEPQDLAEESAGAEAEGH
+>PROKKA_00184
+MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV
+STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR
+PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGTDGALRPAGEA
+LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR
+VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR
+DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER
+RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ
+EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV
+PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000297.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000297.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b9f9bf0605015fd10eae7d1a39b247bf1a23e78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000297.fa
@@ -0,0 +1,36 @@
+>PROKKA_00192
+MTSELPSSSLSPAWTGRTDGDTPEHLRWHQVVRPADGRGEPTTPQRDPGAGAPTSGARST
+ALIGFASDEGVRRNHGRVGAEDGPEALRGALASLAYLEGTGALVDAGDVSVDRGDDDAPG
+ELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYASITGLTGSTRVAAGTRVGILNLDAH
+FDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGISEANNTRALFDTARERGVTWVTDE
+QAQTADVTGVRRWVRSFINAVDVLYLTIDLDVLPAAVAPGVSAPAGFGVPYEVIHACALE
+ATQSGKLALADVVELNPALDVDGRTAKAAARLIHTIVSRHRTDASLLA
+>PROKKA_02188
+MTSELPSPSLSPAWTGRTDGDTPEHLRWHQVVRPADGRGEPTTTQRHPGAGAPTSGARST
+ALVGFASDEGVRRNHGRVGAEDGPEALRGALASLAYLEGTGALVDAGDVSVDRGDDDAPG
+ELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYASITGLTGSTRVGAGTRVGILNLDAH
+FDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGISEANNTRALFDTARERGVTWVTDE
+QAQTADVTGVRRWVRSFINAVDVLYLTIDLDVLPAAVAPGVSAPAGFGVPYEVIHACALE
+ATQSGKLALADVVELNPALDVDGRTAKAAARLIHTVVSRHRTDASLLA
+>PROKKA_00208
+MTSELPSPSLSSAWAGRTDGDAPEHLRWHQVVRPADGRGEPTTTQRHPGAGAPTSGARST
+ALVGFASDEGVRRNHGRVGAEDGPEALRGALASLAYLEGTGALVDAGDVSVDRGDDDAPG
+ELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYASITGLTGSTRVGEGTRVGILNLDAH
+FDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGISEANNTRVLFDTAREHGVTWVTDE
+QAQIADVTGVRRWVRSFIDAVDVLYLTVDLDVLPAAVAPGVSAPAGFGVPYEVIHACAVE
+AATSGKLALADVVELNPSLDVDGRTAKAAARLIHTIVSRHRTDASLLA
+>PROKKA_00155
+MSGVVRPSLRTRPSMAWNGAMTADRASELPSAALSPAWTGRTDGDAPEHLRWHQVVRSAD
+GGAPAQTVDAAPARSTALVGFASDEGVRRNHGRVGAEDGPDALRGALASLAYLEGTGALV
+DAGDVSVDRGDDDAPGELEAGQAELATVVSGLLNAHDLAVVLGGGHETAYASITGLTGST
+RVAAGTRVGILNLDAHFDLREAPRPSSGTPFLQALRDAEEAEHQLSYAVVGISEANNTRA
+LFDTARERGVTWVTDEQAQTADVTGVRRWVRSFIDAVDVLYLTIDLDVLPAAVAPGVSAP
+AGFGVPYEVIHACTLEATQSGKLALADVVELNPALDVDGRTAKAAARLIHTIVSRHRTDA
+SLLA
+>PROKKA_00192
+MTSELPSSSLSPAWTGRTDGDTPEHLRWHQVVRPADGRGEPTTTQRHPGAGAPTSGARST
+ALIGFASDEGVRRNHGRVGAEDGPEALRGALASLAYLEGTGALVDAGDVSVDRGDDDAPG
+ELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYASITGLTGSTRVGAGTRVGILNLDAH
+FDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGISEANNTRALFDTARERGVTWVTDE
+QAQTADVTGVRRWVRSFINAVDVLYLTIDLDVLPAAVAPGVSAPAGFGVPYEVIHACALE
+ATQSGKLALADVVELNPALDVDGRTAKAAARLIHTIVSRHRTDASLLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000301.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000301.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9512bf968d17e6f3c427de2b1e8a24d3643b6cd5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000301.fa
@@ -0,0 +1,20 @@
+>PROKKA_00196
+MPDDVAVRLLLIADTHIPRRARALPAQVWAEVARADVVLHAGDWVTEDVLDDLDARAARL
+VGVWGNNDGPKLRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS
+HIPWDTVAGPDTANPGLRLLNPGSCTDRRRQPVCTLMRAVVRGGRLEDVELVSVDRTP
+>PROKKA_02192
+MPDDVAVRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDARAARL
+VGVWGNNDGPGPRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS
+HIPWDTVAGPETANPGLRLLNPGSCTDRRRQPVCTLIRAVARDGRLEDVELVPVDRTP
+>PROKKA_00203
+MTTETRLLLLADTHIPPRARAMPAQVWDEVARADVVLHAGDWVEESVLDELEARSRRLVG
+VWGNNDDGALRARLPEVARVEIGGVRIAMVHETGAARGRERRMAEAFPDADVLVFGHSHI
+PWDTVAGPETANPGLRLLNPGSPTDRRRQPVCTLMRAVVRDGGLADVELVPVDRTP
+>PROKKA_00151
+MTTRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDAQAARLVGVW
+GNNDGPRLRARLPEVARVEIGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHSHIPW
+DTVAGPETANPGLRLLNPGSCTDRRRQPVCTLMRAVVRGGRLEDVELVPVDRTP
+>PROKKA_00196
+MPDDVAVRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDARAARL
+VGVWGNNDGPGPRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS
+HIPWDTVAGPETANPGLRLLNPGSCTDRRRQPVCTLIRAVARDGRLEDVELVPVDRTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000306.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000306.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de65e30244a442ac2952ac41c1182a6967879d16
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000306.fa
@@ -0,0 +1,27 @@
+>PROKKA_00208
+MAAAPCLGRQQPQEENMQRRRAVRAAGLGVVGALALAGCASEPQSAGEAWHQARTQLDEA
+ETVRLETAYTTGRQGPHSVRWDIAGRLDGGDAESKGVMQVGRDSHITMESRQVGEDVFVR
+VDVDGSDVPDDVQVMYSDPQWRRVPAGEGQEPPLKALLDQVGFPAADALDGAEVRAEEVD
+WDDGTAYRYAVPEEVADAAMVEGDATRVHSFTVDDDGELVALTVDDGRATQQYALSDWNQ
+IEPAEAPEEVAE
+>PROKKA_02201
+MQRRRAVRAAGLGVVGALALAGCGSEPQSVGEAWHQARTQVDEAETVRLETAYTTGRQGP
+QSVRWDIAGRLDGGDAESKGVMQVGRDSHITMESRQVGEDVFVRVEVDGSDVPDDVQLMY
+ADPQWRRVSAGEGQEPPLKSLLDQVGFPAADALDGAEVRAEEVDWDGGTAYRYAVPEEVA
+DAAMAEGDATRVHSFTVDDDGELVALTVDDGRATQQYALSDWNQIEPAEAPEEVAE
+>PROKKA_00183
+MQRRRAVRAVGLGVAGVLALAGCAAEPQSAGEAWQQARTQLDEAQTVRLETAHTTGRQGP
+NTVRWDIAGRLDGSNGDAKGVIQAGHESHMTMETRTVGEDSYVRVSIDGADFADDVQLAY
+ADPQWRRTPAGQEQERPLKELLEQIGLPSADALEGAEVRAEEVGWAGETAHRYAVPQEVA
+AAAMGQGDSTLLHSFTVDDDGGLLALTVDDGRSLRQYALSDWNEIDPAEAPEEVAE
+>PROKKA_00129
+MQRRRAVHAAGLGVVAALTLAGCGTDQQDVGEAWQHARAQIDGAESVRMTMASVNDSQGP
+SVVAWDVAGPLEGADGTTTGRMQVGRDSWMTVRSVSADGKTWARVDTEGQDVPEQIASMY
+RTDGWTETQQSGQNALRATLDAVGLPAADALDGVDVQPEKVDWSGGTAYRYAMPGDVASA
+ARGDSQFSVRAFTVDEDGDLVGLRVEDGGVIQEFALSDWNEIEPAEAPEEAQH
+>PROKKA_00208
+MAAAPCLGRQQPQEENMQRRRAVRAAGLGVVGALALAGCASEPQSAGEAWHQARTQLDEA
+ETVRLETAYTTGRQGPHSVRWDIAGRLDGGDAESKGVMQVGRDSHITMESRQVGEDVFVR
+VDVDGSDVPDDVQVMYSDPQWRRVPAGEGQEPPLKALLDQVGFPAADALDGAQVRAEEVD
+WDGGTAYRYAVPEEVADAAMAEGDATRVHSFTVDDDGELVALTVDDGRATQQYALSDWNQ
+IEPAEAPEEVAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000307.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000307.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8fa1773af3247fac7a532c5ac5b78c3bfca642f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000307.fa
@@ -0,0 +1,30 @@
+>PROKKA_00209
+MRQRQTQTRRTRRGLSLAALGAAALLLTGCASGDDAPGAWDRARTQLEEADSVRMVTELR
+SEAPSNGRAVPDAVDISGPVDGSSMRYVSVYKDDGLITRDESRIVDGTAYSRFTVERVGA
+SGEDHPAYAERWTATPYEGDPSATGMGAMVSSLLGSLPESGGLDDVEADADGIRRSGQDA
+IRYVLDEPVSGPQEGVELTAFTVSKEDGRLLTVETESAGTKAVVTLSEMGGVDPVQAPPA
+DEVLKQDG
+>PROKKA_02202
+MRQRQTQTRRTRRGLSLAAVGAAALLLTGCASGDDAPGAWDRARTQLEEADSVRMVTELR
+SEAPSNGRAVPDSVDISGPVDGSSMRYVSVYQDDGLITRDESRIVDGTAYSRFTVERAGA
+SGEDRPAYVERWTATPYESDPRATGMGAMVSSLLGSLPESGGLDDVEADADGIRRSGQDA
+IRYVLDEPVSGPQEGVELTAFTVSKEDGRLLTVETESAGTKAVVTLSEMGGVDPVQAPPA
+DEVLKQDG
+>PROKKA_00182
+MPRQNPTGRARRGLPLAALGAAAALVLTGCGASGEDASAAWDRARTQLEETDSVRMVTEL
+RSDAPQAGNRTPESVDLSGPVDGSSMRYVSTYEDGDLITRDESRVVDGTAYSRFTVERRG
+ASGEDRPAYVERWTAAPHTGDPRATGMGAMVSSLLGSLPESGGLEDVAVDADGIRRSGQD
+AVRYVLDEPLSVADDGVAMTAFTVSEEDGRLLTVETESAGTKAVVTVSEMGDVEPLQAPP
+SDEVLPQQQGQGAPGAVPPGGAPQDGTAPGGTPAEPVPPTDG
+>PROKKA_00128
+MRPTTPRTPAPHGGARRRALSLAALGAAAALSLSACGASGEDASAAWDAARTQLQDASSV
+RLTTEARNDSGAAPGTPDGVEIAGDVHSSDLSYTGVFRTDGYITRDESRTVGGQRYERFT
+LEQPGGVSGEGRPAFAEKWKKAEPLPGDASMRSILDGVLTAVPQAGALQGADVRATDIRR
+QGRDATRYVLDTPVKGGTTDSSLTAFTVADDDGTLLTVETTGPGTRGTVTFSDWNAVEPV
+TAPATEDMAQDTATAK
+>PROKKA_00209
+MRQRQTQTRRTRRGLSLAAVGAAALLLTGCASGDDAPGAWDRARTQLEEADSVRMVTELR
+SEAPSNGRAVPDSVDISGPVDGSSMRYVSVYQDDGLITRDESRIVDGTAYSRFTVERAGA
+SGEDRPAYVERWTATPYESDPRATGMGAMVSSLLGSLPESGGLDDVEADADGIRRSGQDA
+IRYVLDEPVSGPQEGVALTAFTVSKEDGRLLTVETESAGTKAVVTLSEMGEVDPVQAPPA
+DEVLKQDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000309.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000309.fa
new file mode 100644
index 0000000000000000000000000000000000000000..862a9828eef8879b693bd271fae41a30f535571b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000309.fa
@@ -0,0 +1,70 @@
+>PROKKA_00211
+MSQQFNIETVADAQATPDVEQPWAELGLKENEYAEIKKILGRRPTAAELAMYSVMWSEHC
+SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ
+GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI
+GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA
+SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS
+NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEYSWL
+GEVTGDGRLIITWDGEVIVDVDPRTVAHDGPVYERPYARPAWQDELQADTFRSSEAGQDL
+PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTALAAPDDAGVVRVDEETGIGVA
+LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPEDPDVMWQFAEA
+VRGLADGCQTLGIPVTGGNVSLYNQTGSTPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG
+QAIYLLGETADELDGSEFARLRGHLGGLPPKVDLKKERLLGELLVNMSRDGMIDAAHDVS
+GGGLAATLSEMVLRFGVGARVVLDEVLRRAGVDLFTALFSETQARAVVAVPRTEEVRFTD
+MTTARGYAAVRIGVVDADSAALEVQDAFTLPIAELREAWEATLPKHFG
+>PROKKA_02204
+MSQQFNIETVADAQATPDVEQPWAELGLKENEYAEIKKILGRRPTAAELAMYSVMWSEHC
+SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ
+GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI
+GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA
+SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS
+NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEYSWL
+GEVTGDGRLIITWDGEVIVDVDPRTVAHDGPVYERPYARPAWQDELQADTFRSSEAGQDL
+PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTALAAPDDAGVVRVDEETGIGVA
+LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPEDPDVMWQFAEA
+VRGLADGCQTLGIPVTGGNVSLYNQTGSTPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG
+QAIYLLGETADELDGSEFARLRGHLGGLPPKVDLKKERLLGELLVNMSRDGMIDAAHDVS
+GGGLAATLSEMVLRFGVGARVVLDEVLRRAGVDLFTALFSETQARAVVAVPRTEEVRFTD
+MTTARGYAAVRIGVVDADSAALEVQDAFTLPIAELREAWEATLPKHFG
+>PROKKA_00175
+MSQQFSIETVADAAANPDIEQPWAELGLKENEYAQIREILGRRPTAAELAMYSVMWSEHC
+SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ
+GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI
+GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGLGNKVVLFGARTGGDGIGGASVLA
+SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFAGSLVEGIQDLGAAGISCATSELAS
+NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPDNVAAFEAVMAKWDVEYSWL
+GEVTGDGRLVITWDGEVIVDVDPRTVAHDGPVYERPYARPGWQDRVQADTFRASEAGADL
+PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTAMAAPDDAGVVRVDEETGMGVA
+LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPENPDVMWQFAEA
+VRGLADGCQVLGIPVTGGNVSLYNQTGATPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG
+QAIYLLGETADELDGSEFARLRGHLGGVPPKVDLAKERLLGELLVNMSRDGMIDAAHDVS
+GGGLAATLSEMVLRHGVGARVVLDEVLRRDGVDLFTALFSETQARAVVAVPRTEEVRFTD
+MTTARGYTVTRIGVVDADSAALEVQDAFTLPIAELREGWEATLPKHFG
+>PROKKA_00124
+MSTQFTIETVEQAAANPDVAQPWAELGLKEDEYARIREILGRRPTAAELAMYSVMWSEHC
+SYKSSKVHLRQFGDTLTEEMKEHMMVGIGENAGVTDLGDGWAVTFKVESHNHPSFVEPYQ
+GAATGIGGIVRDIISMGARPVAVMDPLRFGAVDHPDTARVVHGVVAGIGGYGNSLGLPNI
+GGEVAFDPSYQGNPLVNALAVGVLRHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA
+SESFDDGGKPAKRPSVQAGDPFAEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS
+NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEHSWL
+GEVTGDGRLVITWDGETIVDVDPRTVAHDGPVYERPCHRPSFQDALQADTFRSSAAGQDL
+PATGEELKAAVVELMASPNMADVSWITRQYDRYVRGNTALASPDDAGVVRVDEETGMGVA
+VATDCNDRYAYLDPYAGAQLSLAEAYRNVTTTGAVPLAVTDCLNFGSPEDPEVMWQFAEA
+VRGLADACQVLGVPVTGGNVSLYNQTGGVAIHPTPTVGVLGRFDDVLRRTPSGFGTDADG
+QAVYLLGVTADELDGSEYANLRGHLGGVPPKVDLAQERLLGELLVNMSRDGMVDAAHDVS
+KGGLAATLADMVLRFGVGARIVLDEVVRRDGVDVFTALFSETQGRTVVSVPRTEEVRFTD
+MTTARGYTVTRIGVVDAQSDALEVQGQFTLPIAELREAWEATLPKHFG
+>PROKKA_00211
+MSQQFNIETVADAQATPDVEQPWAELGLKENEYAEIKKILGRRPTAAELAMYSVMWSEHC
+SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ
+GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI
+GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA
+SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS
+NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEYSWL
+GEVTGDGRLIITWDGEVIVDVDPRTVAHDGPVYERPYARPAWQDELQADTFRSSEAGQHL
+PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTALAAPDDAGVVRVDEETGMGVA
+LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPEDPDVMWQFAEA
+VRGLADGCQTLGIPVTGGNVSLYNQTGSTPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG
+QAIYLLGETADELDGSEFARLRGHLGGLPPKVDLKKERLLGELLVNMSRDGMIDAAHDVS
+GGGLAATLSEMVLRFGVGARVVLDEVLRRDGVDLFTALFSETQARAVVAVPRTEEVRFTD
+MTTARGYAAVRIGVVDADSAALEVQDAFTLPITELREAWEATLPKHFG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000310.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000310.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6d25701ebfe6cbefe0b66879dd71804f6709b238
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000310.fa
@@ -0,0 +1,30 @@
+>PROKKA_00212
+MTELPLIGDYSTPATPLSGARIGVITFPGTLDDVDALRAVRLAGAEPVSLWHADADPQRT
+LAGVDAVVIPGGFSYGDYLRAGAIARFAPMMDAVATAAGGPEGEADGLPVLGICNGFQIL
+TESHLLPGSMIKNDHLHFICRDQELVVESTDTVWTRDFEQGQTITVPLKNQDGQYVADET
+TLDALEAEGRVVFRYQGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVETGFGPDTAAGP
+RSGVDGLGFFTSVLTTLASRGGHA
+>PROKKA_02205
+MTELPLIGDYSTPTTPLSGARIGVITFPGTLDDVDALRAVRLAGAEPVSLWHADADPQRT
+LAGVDAVVIPGGFSYGDYLRAGAIARFAPMMDAVATAAGGPEGEADGLPVLGICNGFQIL
+TESHLLPGSMIKNDHLHFICRDQELVVESTDTVWTRDFEQGQTITVPLKNQDGQYVADET
+TLDALEAEGRVVFRYQGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVETGFGPDTAAGP
+RSGVDGLGFFTSVLTTLASRGGHA
+>PROKKA_00174
+MTTDLPLIGDYSTPTTPLNGARIGVITFPGTLDDVDALRAVRLTGAEPVSLWHADEDPQR
+TLAGVDAVVIPGGFSYGDYLRAGAISRFAPMMDAVATAAGGPEGAADGLPVLGICNGFQI
+LTESHLLPGSMIKNDHLHFICRDQELTVENTDTAWTRDYERGQTITVPLKNQDGQYVADD
+ATLDALEAEGRVVFRYRGWNPNGSRRDIAGIANAAGNVVGLMPHPEHAVEPGFGPDTADG
+PRTGTDGLGFFTSVLTTLASRGGHA
+>PROKKA_00123
+MTEIPLIGDYSTPSTPLNGARIGVITFPGTLDDVDALRAVRLTGAEPVSLWHAEADAAAT
+LATVDAVVIPGGFSYGDYLRAGAISRFAPMMGAVAQAAGGPEGSEDGLPVLGICNGFQIL
+TESHLLPGSMIKNDHLHFICRDQQLAVESTDTAWTRDFEQGEVITVPLKNQDGQYVADEK
+TLDALEAEGRVVFRYVGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVEAGFGPDTEAGP
+RSGTDGLGFFTSVLTTLATRGGAA
+>PROKKA_00212
+MTELPLIGDYSTPTTPLSGARIGVITFPGTLDDVDALRAVRLAGAEPVSLWHADADPQRT
+LAGVDAVVIPGGFSYGDYLRAGAIARFAPMMDAVATAAGGPEGEADGLPVLGICNGFQIL
+TESHLLPGSMIKNDHLHFICRDQELVVESADTVWTRDFEQGQTITVPLKNQDGQYVADET
+TLDALEAEGRVVFRYQGWNPNGSRRDIAGIANPAGNVVGLMPHPEHAVEPGFGPDTAAGP
+RSGVDGLGFFTSVLTTLASRGGHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000316.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000316.fa
new file mode 100644
index 0000000000000000000000000000000000000000..01cba00d5aa26f30855adb7332748ac8e8946261
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000316.fa
@@ -0,0 +1,45 @@
+>PROKKA_00222
+MSLIVQKFGGSSVADAAGIQRVARRIADTVRAGNRVCVVVSAMGDTTDELLDLAAELTQD
+APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMLTDTSYGRARIVKVNPHR
+VQEALDAGRVAIVAGFQGMSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY
+SADPRVVPTARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPLHVRSSFSDHEGTW
+IMPDPNDTITLQEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAVSNVNI
+DMIVQNISREGSGRTDISFTLPIVEGKDAMAALRAAQDRIGFQDIVSDPEIGKLSLIGAG
+MRSNPGVSATFFKALADAGVNVDLISTSEIRISVVTAESKLDDAVRAVHAAFGLDAEEEA
+TVYGGTGR
+>PROKKA_02235
+MSLIVQKFGGSSVADAAGIQRVARRIADTVRAGNRVCVVVSAMGDTTDELLDLAAELTQD
+APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMLTDTSYGRARIVKVNPHR
+VQEALDAGRVAIVAGFQGMSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY
+SADPRVVPTARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPLHVRSSFSDHEGTW
+IMPDPNDTITLQEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAVSNVNI
+DMIVQNISREGSGRTDISFTLPIVEGKDAMAALRAAQDRIGFQDIVSDPEIGKLSLIGAG
+MRSNPGVSATFFKALADAGVNVDLISTSEIRISVVTAESKLDDAVRAVHAAFGLDAEEEA
+TVYGGTGR
+>PROKKA_00158
+MSLIVQKFGGSSVADAAGIQRVARRVADTVRAGHRVCVVVSAMGDTTDELLDLAAELTQD
+APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMMTDTSYGRARIVKVNPHR
+VQEALDAGGVAIVAGFQGVSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY
+SADPRVVPSARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPIHVRSSFSDHEGTW
+IMPDPNDTITLKEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAESNVNI
+DMIVQNVSREGSGTTDISFTLPIVEGKDAMAALRAAQERIGFQDIVSDKEIGKLSLIGAG
+MRSNPGVSATFFKALSDAGVNVDLISTSEIRISVVTAEDKLDDAVRAVHTAFGLDAEEEA
+TVYGGTGR
+>PROKKA_00116
+MRLIVQKFGGSSVADAEGIQRVARRIVATQQAGNQVCVVVSAMGDTTDELLDLAAELTAD
+APAREMDILLSAGERISMSLLAMAIDAQGVPARSFTGSQAGMMTDAAYGRARIIEVNPHR
+VRAALDEGAVAIVAGFQGMSRESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY
+SADPRVVSSARKLPQLSSEETLELAASGAKVLHLRSVEYARRFGVPIHVRSSFSDHEGSW
+IMPDPNDTIHLKEGAPMEQPIVAGVAHDRSEAKVTIVGVPDVPGKAAEIFRVIAESNVNI
+DMIVQNVSRQDSGRTDISFTLPIVEGKAAIEALRAAQESIGFEEIVPNKEIGKLSLIGAG
+MRSNPGISATFFKALSDAGVNVDLISTSEIRISVVTSEDKLDDAVRAVHTAFGLDTDVEA
+TVYGGTGR
+>PROKKA_00223
+MSLIVQKFGGSSVADAAGIQRVARRVADTVRAGNRVCVVVSAMGDTTDELLDLAAELTQD
+APAREMDILLSAGERISMSLLAMAIHAEGVEARSYTGSQAGMLTDTSYGRARIVKVNPHR
+VQEALDAGRVAIVAGFQGMSPESKDITTMGRGGSDTTAVALAAALGADVCEIYTDVDGVY
+SADPRVVPTARKLTELSSEETLEMAASGSKVLHLRSVEYARRFGVPLHVRSSFSDHEGTW
+IMPDPNDTITLQEGAPMEQPIVSGVAHDRSEGKVTIVGVPDVPGKAAEIFRVIAVSNVNI
+DMIVQNISREGSGRTDISFTLPIVEGKDAMAALRAAQDRIGFQDIVSDPEIGKLSLIGAG
+MRSNPGVSATFFKALADAGVNVDLISTSEIRISVVTAEDKLDDAVRAVHAAFGLDAEEEA
+TVYGGTGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000317.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000317.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a34d7c7fafb985be9a014f218f02befe844f49bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000317.fa
@@ -0,0 +1,40 @@
+>PROKKA_00224
+MSTAVATSIHDRRPPQPQPGGRLGAAQAVATVVGMELRQRLRSRGWYVLLGVFFVVVGAV
+TLGALGLRGLGVAEMEASGLEPELAEQQMRALGRTLFDGVLLFVLTLSLLVSPALAANAI
+SGDRAGGTLAITQVTLLRTGHLMAGKWLAAWIASAAFPAAALPWLAVAAVVGRVSPWAVL
+VGLVMILVEFGMIAGIGVAVSAIAGRTLFAVVVTYLIVAALTIGTLVAFGLSLQFLQTEV
+RANEADYGSTTAEPFTEAELEKMTPEEAEQAWAEWEAAHPELYDGIADRCVGPVTTRTIP
+DPRRSGWLLAANPYAVLADASPWEGGLLEDGTRAEPGPLNLLSVGLRWTQRDPVRDVECL
+DGELRGLDQSGVPDRQGTWPVWPLGLAMQGVLVAGLGWWGHRRLDTPAGRLPAGTRVA
+>PROKKA_02237
+MSTAVATSIHDRRPPQPQPGGRLGAAQAVATVVGMELRQRLRSRGWYVLLGVFFVVVGAV
+TLGALGLRGLGVAEMEASGLEPELAEQQMRALGRTLFDGVLLFVLTLSLLVSPALAANAI
+SGDRAGGTLAITQVTLLRTGHLMTGKWLAAWIASAAFLAAALPWLAVAAVVGRVSPWAVL
+VGLVMILVEFGMIAGIGVAVSAIAGRTLFAVVVTYLIVAALTIGTLVAFGLSLQFLQTEV
+RANDAEYGSMTAEPFTEAELEKMTPEEAEQAWAEWEAAHPELYDGIADRCVGPVTTRTIP
+DPRRSGWLLAANPYAVLADASPWEGGLLEDGTRAEPGPLNLLSVGLRWTQRDPVRDVECL
+DGELRGLDSTGVPDRQGTWPVWPLGLAMQGVLVAGLGWWGHRRLDTPAGRLPAGTRVA
+>PROKKA_00156
+MSTVVADPTRQGPPPLRPPGGGRLSTASAVRTVVGMELRQRLRSRGWYVLLGVFFLVVGA
+VTLGALGLRATTLGDLQSQGMDPAAAEVQMRSAGQWLFDGVLLFVLTLSLLVSPVLAANA
+ISGDRAGGTLAITQVTLLRTGQLMAGKWIAAWIASAAFLVAALPWLAVAAVVGRVSPLFV
+LVGLLMILVEFGVITGIGVAVSAIAGRTLFAVVVTYLIVAALSIGTLVAFVLSLQFLQTD
+VRANMPEHDGMTMADPLEGQDVENMTQAEIDAAWAEWERQNPDAYDGIADACVGPVGVQS
+VPDPRRVGWLLAANPYAVLADASPWDPTGASMQFTPETGPLNMMSAALRLTQQDPAETTE
+CLDGQLRRIDTTSVPDREGTWPVWPLGLAMQAALTGGLLWWGHRRLDTPAGRLPAGTRVA
+>PROKKA_00114
+MSAVLHTPPPAAAPAGGPTPLGSGRLGVVDALRTLVGMELRQRLRSRGWYILLGVFFLLV
+GGVTLGALGLHAWTGGNSPDSTMVFGRWLYDGVLLFVLTLCLLVSPALSANAISGDRSAG
+TLAITQVTLVSTWQLMLGKWLAAWIAAVAFLVAAAPWLIVAAVVGQVPPLAVLAGLAMIL
+VEFAVVTGIGVAVSAITGRTLFAVVVTYLLVAMMTIGSLIAFTISLQFIETRLQTNQVTY
+GYAEDAGSTKSCAGPLRDTTVPDPRRVAWLLAGNPYVVVADAVPLPELREDSAGEEFGAL
+NLISLGMRVAQIDPREYTDCVDGQVNEGSVTDSPVTLVDRTWPTWPLGMLLQGGFLAALL
+WWGRRRLDTPAGRLPTGTRVA
+>PROKKA_00225
+MSTAVATSIHDRRPPQPQPGGRLGAAQAVATVVGMELRQRLRSRGWYVLLGVFFVVVGAV
+TLGALGLRSLGVTEMEASGLEPELAEQQMRALGRTLFDGVLLFVLTLSLLVSPALAANAI
+SGDRAGGTLAITQVTLLRTGHLMAGKWLAAWIASAAFLAAALPWLAVAAVVGRVSPWAVL
+VGLVMILVEFGMIAGIGVAVSAIAGRTLFAVVVTYLIVAALTIGTLVAFGLSLQFLQTEV
+RANDAEFGSMTAEPFTEAELEKMTPEEADQAWAEWEAANPELFDGIADRCVGPVTTRTIP
+DPRRSGWLLAANPYAVLADASPWEGGLVEDGTWAEPGPLNLLSVGLRWTQRDPVRDVECL
+DGELRGLDQSGVPDRQGTWPVWPLGLAMQGVLVAGLGWWGHRRLDTPAGRLPAGTRVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000320.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000320.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0cf06bcd1be3b7c59f683f8a2d7be13fbd9f8c82
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000320.fa
@@ -0,0 +1,35 @@
+>PROKKA_00228
+MPAGRYAPSPTGSLHLGNLRTALVAWLAARATNRAFLLRVEDLDRVRSGAEADQRADLAA
+VGLDWDAEPVRQSERTALYDAAVAALRAVHGPDAVYECFCSRKDIAEATSAPHPRPDDGA
+PASGGAVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDVAKVAGLPAGETPRATAVD
+VLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAEAL
+CAARGEPTPAVEYLHVPLVLNAEGRRLAKRDGAVTLEDLSAQDPAWTPERVRDRLLESLG
+LPAGPLAAAVPAFDPAALPRVPWVFTGL
+>PROKKA_02241
+MPAGRYAPSPTGSLHLGNLRTALVAWLAARATDRAFLLRIEDLDRVRSGAEAGQRADLAA
+VGLDWDAEPVRQSERTALYDAAVAALRAAHGADAVYECFCSRKDIAEATSAPHPRPDDGA
+PASGGAVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDAAKVAGLPAGEIPRATAVD
+VLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAEAL
+CDGRGEPTPAVEYLHVPLVLNAEGRRLAKRDGAVTLEDLAAQDPAWTPERVRDRLLESLG
+LPAGPLAAAVPAFDPAALPRDPWVFTGL
+>PROKKA_00153
+MPAGRYAPSPTGALHLGNLRTAIVAWLAARATDRTFLLRVEDLDRVRSGAEAAQLSELAA
+VGLDWDAEPVRQSERTGLYDDAVAALRAAHGADAVYECFCSRKDIAEATSAPHPAPADDD
+GAPGPAGAAPLRPPGFYPGTCRGLTAAQRAERRRVRPAALRIDAVQVAGLPEGEIPRAEA
+VDLLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSTPRQRWLAA
+ALCAARGEALPQTSYLHVPLVLNAEGRRLAKRDGAVTLEDLAAADPSWTPERVRDRLLSS
+LGLPPGPPADAVPAFARMLEDGSLPREPWMFDPAAFAGA
+>PROKKA_00110
+MPAGRYAPSPTGTLHLGNLRTALVAWLAARATGRTFLLRIEDLDRVCSGAEAGQLADLAA
+VGLDWDGEPVHQSERTALYDAAVAALRAAHGADAVYECFCSRKDIAEATSAPHPRPDDGA
+PASGGTVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDAAKVAGLPAGEIPRATAVD
+VLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAEAL
+CVARGEPTPAVEYLHVPLVLNAEGRRLAKRDGAVTLGDLAAQDPAWTPARLRDRLLESLG
+LPAGPLAVAVRAFDPAALPRDPWVFTGL
+>PROKKA_00229
+MPAGRYAPSPTGSLHLGNLRTALVAWLAARATDRAFLLRVEDLDRVRSGAEAGQRADLAA
+VGLDWDAEPVRQSERTALYDAAVAALRAAHGADAVYECFCSRKDIAEATSAPHPRPDDGA
+PASGGTVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDVAKVAGLPAGEIPRATAVD
+VLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAEAL
+CSARGEPTPAVEYLHVPLVLNAAGRRLAKRDGAVTLEDLAAQDPAWTPERVRDRLLESLD
+LPPGPLAAAVPAFDPAALPRDPWVFTGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000325.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000325.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a7a9c68d678076d6738cd110b8fbed0dd471b70
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000325.fa
@@ -0,0 +1,39 @@
+>PROKKA_00234
+MPLARLRAALPAAALSLLLLTGCTATDDGVTPASDADTSASVSTMPITSTPSVDAAATSR
+AAASSLAASSSAAQSSRAAASSSSGAAESRAAEGSRSAEPAAPAAPADVEGDVVTVESIS
+DGDTLRVTLGEVSTRVRLLNIDTPETHHPSKPVECMGPEATAALKSMISPGDTVVLRYDR
+RLYDRYDRLLAGVYADGVLLNAEMARLGYGEPAVFDGNDRFLPEVEAAWEQARANGVGRF
+SGECGTAAEPIPEAAPAPAPEAAPAAGDAGPVSGADSVCPDSHPVKANDNSGIYHMPGQQ
+HYGKTNARHCYASASAAQAGGYRAARR
+>PROKKA_02247
+MPLARLRAALPAAALSLLLLTGCTATDDGVTPESAADTSASVSTMPTTPTPSVDAAATSR
+AAASSLAASSSAAQSSRAAASSSSGAAESRAARAAEESRTAEGSRSAEPAAPAAPADVEG
+DVVTVESISDGDTLRVTLGEVSTRVRLLNIDTPETRHPSKPVECMGPEATAALKSMISPG
+DTVVLRYDRRLYDRYDRLLAGVYADGVLVNAEMARLGYGEPAVFDGNDRFLPEVEAAWEQ
+ARANGVGRFSGECGAAAEPIPEAAPAPAPEAAPASGDAGPVRGADSVCPDSHPVKANDNS
+GIYHMPGQQHYGKTNARNCYASAAAAQADGYRAARR
+>PROKKA_00137
+MTPRLFPRAGLVAAAALSLVLTGCTPAASGDDVAAPASAGAPSSGAAATTAAPAVSSTAS
+AEAADRSRAAESSRAAAQASEAEQSRRAEESRAAEARRAEESRAAEASREAERSRRAEES
+RAAAAAAAEEEDLDAAGSAEDAAWGGTAGVEGDVAVVQSVADGDTLRVSLDGVSTPVRLL
+NIDTPETVHPSKPVQCQGPEATAALKSMIGPGDTVVLRYDRRVYDRYDRLLAGVFADGRL
+VNAEMARLGLGEPVVFDGNVRFLPEVEAAWEQARADGVGLFSGECAVEEAPEPVEDEAPT
+AVAEPAPAPAAGSGPVPGADFVCPDDFPVKGNDNSFIYHVPGQQHYGRTNARNCYASAAA
+AEVDGYRAAKR
+>PROKKA_00102
+MPSSRPPAPRVRTRLLVSAALVLLAATGCTASPATSSSTSSTSSAAPAALAASASPPASG
+ASSAAAVEGDAATVVRVVDGDTVDVRRGAEDVRVRLLNIDTPETKHPSRPVECLGPEATR
+KLEELLRPGDEVVLQYDEERFDRYGRTLAGVVEGETLVNAEIVRAGLGVPVVFEPNRRFL
+PPVEAAWAEAQREGAGLNQPGLECSLQTLQESVAQDPAPAAVSELAQALEAVEAEGQEWM
+KVHYAAVIPLAVSLVQQHGGRADVPSAGAASVAPRASTAPAVPAAPQAPAVGAGSDAAER
+DRQRAAEAQAAADRAERKRQAEARAEAQRQAQAQEQVQARERAAQASREAEAAASAREKQ
+KGASSGSSTAKGFADTSARDTSSGSPSSSGGTSQKAPNRCYAPGGETFVYCGEGSTGSSS
+GGSSSSASAGASSSGAGTSSGGAGGPVSGADGVCPAGYPVKVSSSGKYHVPGGQYYDDTS
+AKRCYASTAAAAADGAVASKR
+>PROKKA_00235
+MPLARLRAALPAAALSLLLLTGCTATDDGVTPESDADTSASVSTMPTTPTPSVDAAATSR
+AAASSLAASSAAQSSRAAASSSIEAAQSRAARAAEESRTAEGSRSAEPAAPAAPADVEGD
+VVTVESISDGDTLRVTLGEVSTRVRLLNIDTPETHHPSKPVECMGPEATAALKSMISPGD
+TVVLRYDRRLYDRYDRLLAGVYAEGVLLNAEMARLGYGEPAVFDGNDRFLPEVEAAWEQA
+RANGVGRFSGECGTAAEPIPEAAPAPAPEAAPAAGDAGPVSGADSVCPDSHPVKANDNSG
+IYHMPGQQHYGKTNARHCYASASAAQAGGYRAARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000329.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000329.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c41825d0ee08dc610a7f8e7c91cf6940ae411860
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000329.fa
@@ -0,0 +1,35 @@
+>PROKKA_00239
+MSANVEETEMTTQTDAANSGQTVLVHAEIGADGALRPVVAELLGAAATVGVPEAVLVTGA
+EGRDAAVARLGEYGATRVHVLVADDAATTLGDAAVQALAAAAARTAPVAVLLSGSPESRA
+VAGRLSVRARGPVCTDAVGLRWADDEVIARHSVFGGDYLSESTGEGGPRIITMRPGAVAD
+RAPAVEAPEVVELAAAELGPVTAGARVLEVNARTQNSARPPLRGAKTVVAGGRGVGSEEG
+FAIVEQLADELGAAVGASRAAVDSGYTAAERQVGQTGVIVSPNLYIALGISGAIQHLAGM
+KTAKTIVAIDKNEDAEIFEHADFGVVGDIFQVVPQVIEQLRTRRG
+>PROKKA_02252
+MSANVEETEMTTQTDAANSGQTVLVHAEIGADGALRPIVAELLGAAATVGVPEAVLVTGA
+EGRDAAVARLGEYGATRVHVLVADDAATTLGDAAVQALAAATARTAPVAVLLSGSPESRA
+VAGRLSVRARGPVCADAVGLRWADDEVIARHSVFGGDYLSESTGEGGPRIITVRPGAVAD
+RAPAVEAPEVVELAAAELGPVTAGARVLEVNARTQNSARPPLRGAKTVVAGGRGVGSEEG
+FAIVEQLADELGAAVGASRAAVDSGYTAAERQVGQTGVIVSPNLYIALGISGAIQHLAGM
+KTAKTIVAIDKNEDAEIFEHADFGVVGDIFQVVPQVIEQLRTRRG
+>PROKKA_00132
+MSANVEESEMTMQNDAANSGQTVLVHAELGADGALRPVVAELLGAAATVGVPEAVLVTGA
+ASQDAAVARLGELGAARVHVLVAEDAAGTLGDAAVQALAAVTARTAPVAVLLSGSPESRA
+VAGRLSVRARGPVCADAVALRWADDEVIARHSVFGGDFLSESTGEGGPRIITMRPGAVSD
+RAPAVASPEVVEVAAAELGAVTAGARVLETTRRVQQADRPALRGAKTVVSGGRGVGSEEG
+FAIVEELADALGAAVGASRAAVDAGYTAADRQVGQTGVIVSPNLYIALGISGAIQHLAGM
+KTAKTIVAIDKNEDAEIFEYADFGVVGDIFKVVPQVIEQLRARRG
+>PROKKA_00097
+MTDLPVTPVLVLAELTAAGDLRPAVAEALGAAARVGVPHAVLVTDADADDALVARLGELG
+AAVVHTAVAQDPAELGTAQVAALAAAVDAVLPEAVVLPNTPESRAVAGRLAVRARGAVTA
+DAVGLHRADGEIVARHSVFGGDVLAESTVEGGPNIVTLRPGAVADRARPVAAPEVRPLDV
+AGRTVTAGARILSSEPAAPSADRPDLRTARAVVAGGRGVGSAEGFTTLVEPLADALGAAV
+GASRVAVDSGFTAPEGQIGQTGVTVAPDLYVALGISGAIQHLVGMKTSGTIVAVDSDEDA
+AIFEHADLGVVGDVNEVVPQLIAALAARRG
+>PROKKA_00240
+MSANVEETEMTTQTDAANSGQTVLVHAEIGADGALRPIVAELLGAAATVGVPEAVLVTGA
+EGRDAAVARLGEYGATRVHVLVADDAATTLGDAAVQALAAATARTAPVAVLLSGSPESRA
+VAGRLSVRARGPVCADAVGLRWADDEVIARHSVFGGDYLSESTGEGGPRIITVRPGAVAD
+RAPAVEAPEVVELAAAELGPVTAGARVLEVNARTQNSARPPLRGAKTVVAGGRGVGSEEG
+FAIVEQLADELGAAVGASRAAVDSGYTAAERQVGQTGVIVSPNLYIALGISGAIQHLAGM
+KTAKTIVAIDKNEDAEIFEHADFGVVGDIFQVVPQVIEQLRTRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000333.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000333.fa
new file mode 100644
index 0000000000000000000000000000000000000000..49a85280494241fce92baf69c3c43946d35a7c5f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000333.fa
@@ -0,0 +1,43 @@
+>PROKKA_00246
+MTTVLFLGLGHMGGPMAANLAAAGHRVLGFDLVPEALEKARAAGVETVTDTAAAAAEADV
+VLTMLPHGRLVLDVYRGEDGDGGLLAAARPGTVFLDCSTIDVAEAREAAAAAEAAGMRAA
+DAPVSGGQVGAEAGTLAFMVGASDEVYAEVLPLLEVMGARIVHCGAAGLGQAAKICNNMV
+LGVTQIAVAEAFVLGERLGLQHQALYDVMSKASGQCWSLTTNCPVPGPVPGSPVNRDFQP
+GFAGALMAKDLGLALAALDEQGVAADLGRLAQAKYAEYAAGEGAARDFSGIIEDIRASHT
+DRSEA
+>PROKKA_02258
+MTTVLFLGLGHMGGPMAANLAAAGHRVLGFDLVPEALEKARAAGVETVTDTAAAAAEADV
+VLTMLPHGRLVLDVYRGEDGDGGLLAAARPGTVFLDCSTIDVAEAREAAAAAEAAGMRAA
+DAPVSGGQVGAEAGTLAFMVGASDEVYAEVLPLLEVMGARIVHCGAAGLGQAAKICNNMV
+LGVTQIAVAEAFVLGERLGLQHQALYDVMSKASGQCWSLTTNCPVPGPVPGSPANRDFQP
+GFAGALMAKDLGLALAALDEQGVAADLGRLAQAKYAEYAAGEGAARDFSGIIEDIRASHT
+DRSEA
+>PROKKA_00123
+MSEKTATTTTAPVIPHFVHGERVDGSSGRHSDVYHPATGQVEGRVPLASVEEIDAALASS
+EKGFAAWSALNPQRRGRILLKWVDLINENVDELATLLSQEHGKTVPDAKGDIQRGVEVVE
+FAAGAPHLLKGEFSSNAGSGIDVHSIRQPLGIAVGITPFNFPAMIPLWKAGIALAAGNAF
+VLKPSERDPSVPVRLAELALEAGMPAGALNVVHGDKTAVDALIEDPRVKAVGFVGSTPIA
+QSIYAHAGRMGKRAQCFGGAKNHAVIMPDADLEMAADALVGAAFGSAGERCMAISVAVPV
+GEETADRLVALLSERIRRLKVGPSLDESSDFGPVVSKDAKERIEGYIAAGAAAARRPGRG
+RPRRRRRGPRGRLLRGRHPLRPRHRGHEHLPRGDLRPGALRGPRRGLRGGAHPRQRARVR
+QRRGHLHPRRRRRPRLRHPRGDRHGGRQRADPRPDRLLHLRRLEGLRLRRPEPARHRRPE
+VLHQDQDHHHALALGRARGRQLRDARRLLTAVHPLPQEDPMTTVLFLGLGHMGGPMAANL
+AAAGHRVLGFDLVPEALEKARMAGIETVTDTAAAAAEADVVLTMLPNGRLVLDVYRGREG
+APGLLDAARPGTVFLDCSTIDVAEAREAAQAAEAAGMRAADAPVSGGQVGAEAGTLAFMV
+GAADEVYAEVLPLLEVMGGRIVHCGGSGLGQAAKICNNMVLGVTQIAVAEAFVLGERLGL
+EHQALYDVMSKASGQCWALTTNCPVPGPVPGSPANRDFQPGFAGALMAKDLGLALAALDE
+QGVAADLGRLAQAKYAEYAAGEGAARDFSGIIEDIRASHTDRSEA
+>PROKKA_00092
+MSQSQTPSASLPGTVAFIGLGNMGGPMAANLVAAGVTVRGFDLVPAAVEAARATGVEIAD
+DAASAVPGADVVITMLPNGALVRGVYEGTADAPGLLGAADPDTLFLDCSTISTSEAQEVA
+ALAEAAGHRAADAPVSGGVVGAQAGTLAFMVGGSVEVFEEIRPLLEVMGSRIVHCGGNGL
+GQAAKVCNNMLLAISQIGVAEAFVLGERLGLEHQVLFDVMSEATGRCWSLTANCPVPGPV
+PTSPANRDFEGGFAGALMAKDLGLALKALDEQHVGAEMGRLAQRTYAAYADGEGARKDFS
+GIIETVREAGKDTAA
+>PROKKA_00246
+MTTVLFLGLGHMGGPMAANLAAAGHRVLGFDLVPEALEKARAAGVETVTDTAAAAAEADV
+VLTMLPHGRLVLDVYRGEDGDGGLLAAARPGTVFLDCSTIDVAEAREAAAAAEAAGMRAA
+DAPVSGGQVGAEAGTLAFMVGASDEVYTEVLPLLEVMGARIVHCGGAGLGQAAKICNNMV
+LGVTQIAVAEAFVLGERLGLQHQALYDVMSKASGQCWSLTTNCPVPGPVPGSPANRDFQP
+GFAGALMAKDLGLALAALDEQGVAADLGRLAQAKYAEYAAGEGAARDFSGIIEDIRASHT
+DRSEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000344.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000344.fa
new file mode 100644
index 0000000000000000000000000000000000000000..75f60299a16d203ad4fbe5e2b6e00665b0f38eb2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000344.fa
@@ -0,0 +1,15 @@
+>PROKKA_00265
+MDGMILINLKFTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYFLLEGF
+TDEGAQAHVASPHFQEGLDAMRPLLASTPQIISEQVGAEGFGPMGELQID
+>PROKKA_02278
+MDGMILINLKFTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYFLLEGF
+TDEGAQAHVASPHFQEGLDAMRPLLASTPQIISEQVGAEGFGPMGELQID
+>PROKKA_00098
+MDRMILINLKYTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYLLIEGF
+TDEGAKAHVESPHFQEGIDAMRPLLASTPQIISEHVDAEGFGPMGELQID
+>PROKKA_00069
+MILINLKFTVKPELADQWMDAVAKYIADVRSEPGNMFFEWYKPVEGGDNEFFLLEGFTDE
+GAQAHVASPHFQEGIDAMRPLLQSTPQIISEQIGAEGFGPMGEIQID
+>PROKKA_00263
+MDGMILINLKFTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYFLLEGF
+TDEGAQAHVASPHFQEGLDAMRPLLASTPQIISEQVGAEGFGPMGELQID
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000349.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000349.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ca17be1ba8a7b67897112f96654f9f2759a8e97
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000349.fa
@@ -0,0 +1,45 @@
+>PROKKA_00270
+MPDTPQPPAVPAHPDHFGFEVTHRLETPGHDGAPLGRTGVITTPHGRIQTPAFIPVATQA
+TVKAVLPESMKDLGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGPTFTDSGGFQVM
+SLGSGFKKVIDMKGPGAPEGQGADDAVAPGKERLANVDDDGVWFKSHLTGDRHRFTPEVS
+VGIQHNLGADIMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARLTGVRAARPYQA
+LFGVIQGAQYEDLRRKACRDLAGMRAEFPAAGELDGVTSGFDGYGVGGALEKENLGTIVG
+WCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFYTRDGRYNLPGA
+KYRRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLLSIHNERFTVSLVDRIRAAM
+QDGTLAELKAETLGRYYAPKG
+>PROKKA_02285
+MPDTPQPPAVPAHPDHFGFEVTHRLETGGADGAPLGRTGVITTPHGRIQTPAFIPVATQA
+SVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGPTFTDSGGFQVM
+SLGSGFKKVIDMKGPGAPEGQGADDAVAPGKERLANVDDDGVWFKSHLTGDRHRFTPEVS
+VGIQHNLGADIMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARLTGVRAARPYQA
+LFGVIQGAQYEDLRRKACRDLAGMRAEFPAAGELDGVTSGFDGYGVGGALEKENLGTIVG
+WCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFYTRDGRYNLPGA
+KYRRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLLSIHNERFTVSLVDRIRAAM
+QDGTLAELKAETLGRYYAPKG
+>PROKKA_00087
+MPDTSPGPAPSSSSSGAPAHPSHFGFEVTHRLEAGGVDGAPLGRTGVISTPHGQIQTPAF
+IPVATQATVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGPTFTD
+SGGFQVMSLGSGFKKVIDMKGPSAPDGQGADDAVAPGKERLANVDDDGVWFKSHLTGDRH
+RFTPEVSVGIQHRLGADVMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARLTGVR
+AARPYQALFGVIQGAQYEDLRRKACRDLAAMRADFPSAGELDGVTSGFDGYGVGGALEKE
+NLGTIVGWCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFYTRDG
+RFNLPGAKYRRDFGPLDPACDCYTCAHYSRAYIRHLFKAKEMVAHTLISIHNERFTVSLV
+DRIRAALQDGTYAELKEETLGRYYAPKG
+>PROKKA_00064
+MPETSAPGTAGPTSSSAVTSDPAHPDHLGFEVRERLDAPGADGIALGRTGVLRTPHGEIQ
+TPAFIPVATQATVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGP
+TFTDSGGFQVMSLGSGFKKVIDMKGPAAPEGQGADDAVAPGKERLANVDDDGVWFKSHLT
+GDRHRFTPERSLQIQHNLGADVMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARL
+TAERAGRPYQGLFGVIQGAQYEDLRRKACRDLSGMTAEFAAAGERPATAHGFDGYGIGGA
+IEKENLGTIVGWCAQELPEDRPRHLLGISEPDDLFRAVENGADTFDCVSPTRVARTGAFY
+TRDGRYNLPGATYKRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLISIHNERFT
+VSLVDRIRASIQAGTFAELKAETLGRYYAPKG
+>PROKKA_00268
+MPDTPQPPAVPAHPDHFGFEVTHRLETGGADGAPLGRTGVITTPHGRIQTPAFIPVATQA
+SVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGPTFTDSGGFQVM
+SLGSGFKKVIDMKGPGAPEGQGADDAVAPGKERLANVDDDGVWFKSHLTGDRHRFTPEVS
+VGIQHNLGADIMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARLTGVRAARPYQA
+LFGVIQGAQYEDLRRKACRDLAGMRAEFPAAGELDGVTSGFDGYGVGGALEKENLGTIVG
+WCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFYTRDGRYNLPGA
+KYRRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLLSIHNERFTVSLVDRIRAAM
+QDGTLAELKAETLGRYYAPKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000354.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000354.fa
new file mode 100644
index 0000000000000000000000000000000000000000..19806a4182a5cecae4222bed84506c486715cc3d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000354.fa
@@ -0,0 +1,74 @@
+>PROKKA_00281
+MQDASSESRAALERLRAASAPRPDDAETRAPAARPRRALAAPGEISRRDLRRHERALRSG
+RSETAAERRVREDHRADVHRAMDRLRTPGAPAEQRPRRDLSEILDRLGSPDLARFADPLV
+GTVERILPAPGRDPEKAAEAARRRTAAEERRRARLRAGRAAEHERPVAEAAAAAQARDAA
+RARDAAALQARLDEEARRAQAARVARRRREEEKQRRRREAERRRRVAAEEKARAAAEAEA
+RRREREERRRREAEVAAERARVQAERRAREEAALAERERLRLEAEAEAERRRQAAEAERR
+RLEAERVEAERRRRAEEAERRRREAEEAARLEAERRRRQAARVRAHTVLHAERALAQARL
+LEDRAREAERRAAEDAARRRREHEERESRALARAARELEGPEVFPAAADRPLLSDPEERL
+TDEELFARARVALPEWRRRQRLSTKAQAVRAEATAHSSAGPVTGALPLIPGYTPAPPEEP
+AGSPTAADRRGQALLTVVWALFVLSGAWGLGLAGRVPGLGALDAGAYPLTADGRHGPGAS
+VFGLSPLHPAIWPVLWLLTGMYVLRQWGRGQGASPRHRRIRGAIAGALLALALWFPLAVL
+APGGFDVVPWLLALVLMLRVVRRLGARPAARRVARVAEDGALGVLLGTLLAGAPTAVGAA
+LHAWGVHVGWFPTELLALLVLVALLLAALRLVLGGRGRMGVALGMAWTLLCLALPRLLPS
+PLGAQQSVWVGLAAAFGALLLVTAAAVRRSWARQIERDAARRPHPAGA
+>PROKKA_02296
+MQDASSESRAALERLRDASAPRPDDDATRAPAERPRRALAAPGEISRRDLRRHERALRSG
+RPETAAERRVREDRRADVHRAMDRLRTPGAPAQQRPRRDLSEILDRLGSPDLARFTDPLV
+GTVERILPAPGRDPEKAAEAARRRTAAEERRRARLRAGRERAAEAARRRAAEHERPVAEA
+AAAAQARDAARARDAAALQARLDEEARRAQAARVARRRREEEKQRRRREAERRRRVAAEE
+KARAAAEAEARRREREERRRREAEVAAERARVQAERRAREEAALAERERLRLEAEAEAER
+RRQAAEAERRRLEAERVEAERRRRAEEAERRRREAEEAARLEAERRRRQAARVRAYTVLH
+AERALAQARLLEDRAREAERRAAEDAARRRREHEERESRALARAARELEGPEVFPAAADR
+PLLSDPEERLTDEELFARARVALPEWRRRQRLSTKAQAVRAEATAHSSAGPVTGALPLIP
+GYTPAPPEEPAGSPTAADRRGQALLTVVWALFVLSGAWGLGLAGRVPGLGALDAGAYPLT
+ADGRHGPGASVFGLSPLHPAIWPVLWLLTGMYVLRQWGRGQGASPRHRRIRGAIAGALLA
+LALWFPLAVLAPGGFDVVPWLLALVLMLRVVRRLGARPAARRVARVAEDGALGVLLGTLL
+AGAPTAVGAALHAWGVHVGWFPTELLALLVLVALLLAALRLVLGGRGRMGVALGMAWTLL
+CLALPRLLPSPLGAQQSAWVGLAAAFGALLLVTAAAVRRSWARQIERDAARRPHPAGA
+>PROKKA_00072
+MQDPSSESHAALERLRGAPKPVPAPEEAAGAPRTPDQDDDGAATAEDPVPAAARTPADDP
+APAPSPSPPQDAETAPAPDASPASDADAPADVEADVEAPRPARRATPPRPRRPRPDLPPR
+PAPPRARPAHRLSPRRPMRGACARAAARTSTRRWSGRAPPAPPRSSAPRRDLSDILDRLG
+SPDLARFTAPLVGTVERILPAPGADPQKAAQAARRREEAEARRRARLQSGRERAAESARR
+RAAEHDRLAAEAAEREAALRDDDARSEARRADEEAAAAKEACRQERLRERRTAGRAAAEE
+RARLAAEAVEADRERERREAEEAAAAAAREEAALQARLQEEARARRERAEQEERLAQERA
+AEEARLAQAARIARRRREEERERQRREAERRRRLAQEAKARAAADQEKRRQQEQERRRRE
+AKVAEERARVQAERRAREEAELAERERRRLEAEAEAERRRQAQEAERRRREAERAEAERR
+ARAEEAERRRREAEEAARRAAEARRLHAERTRAHTVLHAERALAQARLLEDRARDAERRA
+AEEEARRLREHQDRESRALYRAARELEGPEVIPAASQRPLLARPEEGLTDEELVARARQA
+LPEWRHRQRLATKARAVGAETAAGRSAGPPTGPVPLIPGYTPAAPEEPAGPATVRDRRGQ
+LVLTLAWAAFVLAGVWGLGLFRFVPGLDALDAGPYPAAGDGRHGSGATVFSLFPLHPVIW
+PVLWLLTGLHVARQWGPGQGAAPRHRRTRGPMAGTLLALALWFPLTVLVPWGLESVLWLV
+ALALMLGAVRRLGARPAAGRLARLAEDGAPGALLGTLLAGAPTALAATLHAWGVHVGRFP
+TELVAALVLLTLLPGAVRLVLGGRGRMGVAVGMAWTLLCLALPRLLPSPLGAQQSAWVGF
+AAAFGALLLLTAAAVRRSWVRQIERDAARRPPPAVA
+>PROKKA_00058
+MTSQDDDAPRPAPPAPRHAARPRRALAEPGRLAPEQLERHTRRLRGEPLPPETPEEAAAR
+AGRRHDLAAALDRLPAESAPAAPRPRADLSDLLDRIGTPDLARFADPLLGTVGRILPSGP
+SPERAAAAARRRAEHEGRRRAERAAGRARAAEAARRRAEETARREAEAAERARAARTVEE
+SRAEAVRAAEDAAREAERHRAERLRERREAARAAAADKARRVAEAAERARVEEEALLAVE
+ADAQAREVAAAQAEPDALARERRERADQEERRRRAALLARRRRDEERRRRRREAERARRE
+AEEQRERAARAERSAAEAARRRQAEEAAEAERRQMAVEAARARAEAERLAQEAARERRRR
+IAAARALPRTVAARHIAAGTAAEDRRRQAAARASEEAARVLAAHHDRETRALMAAARELD
+GPDVVPPAHLRPLLADPAEGLDDAALLERARAALPQWRRTGRLLTKADAVRAQTAHGAAD
+GTGPATGAFPIVPGYVPPSGPPEPRAPATREDRRHQLELTGAWLLFVLASAWGLGLFRLV
+PGLRVVDQGSYTAAHGGRYAFTTSVLSLFPLHPAVWPVLWLALGVYVAHQWGPGQGAAAR
+QRQTRRSVAGALALTALWFPLAVLVPWGLEFMVWLAALALMIRVMRGLTAVPARTRAAQT
+CTDGVLGGFLGLLLAAAPTTLASPVAATGVFWGWFPSALVAAALLWAVVLTGARLALQDR
+GRLGLALGMAWTLLCLALPRLLPSPLGAWQSAWVGLSAVAGGLGVLLLVVVRRTWVREIE
+EQAAAAPQGVPAGRVNGR
+>PROKKA_00280
+MQDASSESRAALERLRGASAPRPDDDATRAPAARPRRALAAPGEISRRDLRRHERALRSG
+RPETAAERRVREDRRADVHRAMDRLRTPGAPAEQRPRRDLSEILDRLGSPDLARFADPLV
+GTVERILPAPGRDPEKAAEAARRRAAAEERRRARLRAGRERAAEVARRRAAEHERLAAEA
+AAAAQARDAARARDAAALQARLDEEARRAQAARVARRRREEEKQRRRREAERRRRVAAEE
+KARAAAEAEARRREREERRRREAEVAAERARVQAERRAREEAALAERERLRLEAEAEAER
+RRQAAEAERRRLEAERVEAERRRRAEEAERRRREAEEAARLEAERRRRQAARVRAHTVLH
+AERALAQARLLEDRAREAERRAAEDAARRRREHEERESRALARAARELEGPEVFPAAADR
+PLLSDPEERLTDEELFARARVALPEWRRRQRLSTKAQAVQAEATAHSSAGPVTGALPLIP
+GYTPAPPEEPAGSPTRADRRGQTLLTVAWALFVLSGAWGLGLAGRVPGLGALDAGAYPLT
+ADGRHGPGASVFGLSPLHPAIWPVLWLLTGMYVLRQWGPGQGASPRHRRIRGAVAGTLLA
+LALWFPLAVLAPGGLDVVPWLLALVLMLRVVRRLGARPAARRLARVAEDGALGVLLGTLL
+AGAPTAVGAALHAWGVHVDWFPTELLALLVLMALLLAALRLVLGGRGRLGVALGMAWTLL
+CLALPRLLPSPLGAQQSAWVGLAAAFGALLLVTAAAVRRSWARQIERDAARRPHPAGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000356.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000356.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3aece0d0ac32e0c746faeff1be28b0ed29dc9095
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000356.fa
@@ -0,0 +1,47 @@
+>PROKKA_00284
+MADPFPKDPEGAVVALVLAGGTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLR
+DVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQGRAEEGFARGNGHAIAQQLPL
+LEQFGAETVVVLSADHLYQLDLRPVLAEHARSGAELTVVTTETDEDPSRFGVVQVDDDGA
+VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSS
+LGDYGESIIPAFVARGRVREHRLVGYWRDIGTLDAYVRAHREILDGTGLDLAAEGWPLIT
+NPHQAPPAWVAPDARVSGSLLSPGCRIAGEVSDSVVGPGVVVAAGATVRGSLLLGDCEVP
+AGAVLDTVVVDVGGAVPAREVTGRAAPAEEVVVLTPQDRGPAEDETTGSGRPGRSD
+>PROKKA_02306
+MADPFPTDPEGAVVALVLAGGTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLR
+DVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQGRAEEGFARGNGHAIAQQLPL
+LEQFGAETVVVLSADHLYQLDLRPVLAEHARSGAELTVVTTETDEDPSRFGVVQVDDDGA
+VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSS
+LGDYGESIIPAFVARGRVREHRLVGYWRDIGTLDAYVRAHREILDGTGLDVAAEGWPLLT
+NPHAAPPAWVAPEATVTGSLLSPGCRIAGEVTDSVVGPSVVVEAGAVVRGSILLGECTVP
+SGAVLDTVIADVGAAIPAEGATGRAEPADEVVVLEPGERGPASSDETTGSGAPVRD
+>PROKKA_00069
+MPEGDSLVRLAHRLRPVLAGRALTHADLRVPQHATADLTGWTVVEVEPRGKYLLMRLTPP
+AGRPAARPLTLVSHLKMEGRWLVSALDARWGAPAWQVRAVLETADHRVLGAQLGMLTLVP
+TDREDTVLGHLGPDLLDPAWDGSEEAAAALLAEGTRRLTARPERPVGLALLDQRTTCGIG
+NIYRCESLLLAGIDPHRPVGAVPDVPGLLTIARDLLRANVPPAAPFLGWPRTTTGVRANP
+DRPYGIEVVVADRGFPPGLPAAVGSGTAADPAADPGADRTASGPALGRPPARPPADPGAA
+GRRRTGCTGTTAPPACAAAGACARRTSAPPRTTRGSCGGARPASGEPRPNRGPGGGAPYA
+ERRPSPQGRSARPPTPRRTRVADPFPDDPRSAVVALILAGGRGSRLAPLTDARSKPAVPF
+AGQYRLIDVALTTVAHSGLQDAWIVEQYRPFTLNQHVAGGRPWDLDGTRHGLRVLPPAQG
+RDEEGFAQGNGHAIHQQLAPLRRFGAKTVVIMSADHLYRMDLRPVLERHRERDAELTVVT
+TQVAEGASRFGVVSSDADGRVTAYDYKPDEPATDVVATEVFVADVDALTEVIESLLDSAS
+EEQVDDDDPAGAQLGDYGETIIPALVERGRVHEFRHEGYWKDVGTIDAYYQAHMALLRGD
+GLDLDDPRWPLISNFHPRPPAFIHPEAEVNGSMLCPGSRVRGTVTESVIGPGVVVEAGAT
+VHRSVLLGSATVPAGARLDAVIADVGARIPEGATGQTKPGPGNITVLTPDDRSTAEGDET
+TGHA
+>PROKKA_00049
+MADPFPKDPAGSTVALVLAGGRGSRLDPLTAARSKPAVPFAGQYRLIDVVLSNLAHSGLK
+DVWIAEQYRPFTLNQHLAGGRPWDLDGTRHGLRILPPAEGREEEGFSAGNGHALAQQVPI
+LRSFGAERVVVLSADHLYQLDLRPVLAAHADSGAELTMVTTVTDEDPSRFGVVQADEDGA
+VTAYDYKPEDPEGRLVATEVFVFDVAALHEVVAELVAREKAAGEHADGEEDEDGDPVASS
+LGDYGETIIPAFVERGRVREHRLEGYWRDIGTLDAFYRAHMELLDGAGLDLAAPGWPLLT
+NPPAAPPARVGPRAEVSNALLSPGCVVKGTVEDSVLGPGVVVERGAHVRRSVLFGECIVP
+RGARLDAVIADVGAHIPAEEVGRSRPGPGNLTVLTPATRDPDSEDETTGGAAAKDG
+>PROKKA_00290
+MADPFPKDPEGAVVALVLAGGTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLR
+DVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQGRAEEGFARGNGHAIAQQLPL
+LEQFGAETVVVLSADHLYQLDLRPVLAEHTRSGAELTVVTTETDEDPSRFGVVQVDDDGA
+VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSS
+LGDYGESIIPAFVARGRVREHRLVGYWRDIGTLDAYVRAHREILDGTGLDVAAEGWPLLT
+NPHAAPPAWVAPEATVTGSLLSPGCRIAGEVTDSVVGPSVVVEAGAVVRGSILLGECTVP
+SGAVLDTVIADVGAAIPAEGATGRAEPADEVVVLEPGERGPASSDETTGSGAPVRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000359.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000359.fa
new file mode 100644
index 0000000000000000000000000000000000000000..65b7f3d4dc54a4944c953c984f10b557c4b7f172
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000359.fa
@@ -0,0 +1,20 @@
+>PROKKA_00291
+MGLALRAARAAGAAGDVPIGAALVAGDGTVLAVVGNEREQHHDPTAHAEVLALRRGAELR
+AAAGAGDGWRLTDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP
+RFNHQVQVRAGVRSEESAALLRGFFAAQRD
+>PROKKA_02314
+MGLALRAARAAGAAGDVPIGAALVAGDGTVLAVVGNEREQHHDPTAHAEVLALRRGAELR
+AAAGAGDGWRLTDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP
+RFNHRVQVRAGVRSEESAALLRGFFAAQRD
+>PROKKA_00063
+MGLALDAARAAGEAGDVPIGAVLVAGDGTVLAAVGNEREQHHDPTAHAEVLALRRGARAL
+AEAGEADGWRLSDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP
+RFNHAVQVRAGVRAEESAALLRGFFAVQRG
+>PROKKA_00042
+MGLALDAARTAGEAGDVPIGAVLVDGDGRVLAAVGNEREQHHDPTAHAEVLALRRGAAAL
+AARGDADGWRLAECTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVVRDP
+RFNHTVQVRAGVRGDECAALLVDFFAARRPGG
+>PROKKA_00298
+MGLALRAARVAGAAGDVPIGAALVAGDGTVLAVVGNEREQHHDPTAHAEVLALRRGAELR
+AAAGAGDGWRLTDCTLVVTLEPCPMCAGALLLARIPRVVFGAWDPKAGACGSVLDVIRDP
+RFNHQVQVRAGVRAEESAALLRGFFAAQRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000361.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000361.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6242f06c82c1a3714bec3d0131b343f5e32c7e4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000361.fa
@@ -0,0 +1,30 @@
+>PROKKA_00293
+MGQSAGYVHISVRNAQRRADGMSRRGQARAGLRLAGGTDAPDSQTAPTPVLAPNGIPGPQ
+AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGA
+EGRDIEVVRQVLGDPTVQGGTRPDLAQAPAPVSTRQPGVLIDLSRREVQLDGESLNLTFK
+EFELLNYLVENGERTVGREELLDALWRNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR
+GQGYRFYRHPEVVVWAAPEYSI
+>PROKKA_00001
+MGQSAGYVHISVRNAQRRADGMSRRGQARAGLRLAGGTDAPDSQTAPTPVLAPNGIPGPQ
+AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGA
+EGRDIEVVRQVLGDPTVQGGTRPDLAQAPAPVSTRQPGVLIDLSRREVQLDGESLNLTFK
+EFELLNYLVENGERTVGREELLDALWRNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR
+GQGYRFYRHPEVVVWAAPEYSI
+>PROKKA_00061
+MGQSAGYVHISVRNAQRRADGMSRRGQARADLRLAGGTDAPAAQTAPTPVLAPNGIPGPQ
+AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGSESHAAVALAPSGA
+EGRDLEVVRQVLGDPTVQGGAHPDLAQAPAPVSTREPGVLIDLSRREVQLDGESLNLTYK
+EFELLNYLVENGERTVGREELLEALWHNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR
+GQGYRFYRHPEVVVWAAPEYSI
+>PROKKA_00040
+MGETAGYVHISVRNAQRRANVSRARRGDLRLAGGTSHEPTPPQTAPTPVLAPSGIPGPQA
+VARENEARGFVIYVGMDELMASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGAA
+GRDLEVVRQVLGDPTVQGAARPDLAQAPAPVSTRQPGVLIDLSRREVQLDGEALNLTFKE
+FELLNYLVENGERTVGREELLDALWKNSDEVPNERTIDVHIRRLRAKLGRLANTVRTVRG
+QGYRFYRHPEVVVWAAPEYSI
+>PROKKA_00300
+MGQSAGYVHISVRNAQRRADGMSRRGQARAGLRLAGGTDAPDSQTAPTPVLAPNGIPGPQ
+AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGA
+EGRDIEVVRQVLGDPTVQGGTRPDLAQAPAPVSTRQPGVLIDLSRREVQLDGESLNLTFK
+EFELLNYLVENGERTVGREELLDALWRNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR
+GQGYRFYRHPEVVVWAAPEYSI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000362.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000362.fa
new file mode 100644
index 0000000000000000000000000000000000000000..73056925af87e1124c3efa5dc4153cd059e4a933
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000362.fa
@@ -0,0 +1,20 @@
+>PROKKA_00294
+MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPAAGDWLREHGLVPDAVVCSDA
+LRTRQTCVWVCERLGELAPTPYLDPRLYGADAARALAVVNETEETTRRLLVVGHMPWVQE
+LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWAELDGRDAALTHFVVPGR
+>PROKKA_00002
+MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPAAGDWLREHDLVPDAVVCSDA
+LRTRQTCVWVCERLGELAPTPYLDPRLYGADAARALAVVNETEETTRRLLVVGHMPWVQE
+LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWAELDGRDAALTHFVVPGR
+>PROKKA_00060
+MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPAAGDWLRENGLVPDAIVCSDA
+LRTRQTCVWVCERLGELAPTPYLDPRLYHADAAKALAIVNETEETTRSLLVVGHMPWVQN
+LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWVELDGRDAALTHFVVPGR
+>PROKKA_00039
+MSPADAKTLVLLRHAKADWPAGVDDHDRPLAPRGHAQAPAAGDWLLEHGIAPEAAVVSDA
+LRTRQTWVWVAQRLGERAPTAYLDRRLYEADAARALAVVNETEETVRSLIVVGHMPWLQN
+LGMRLMSLDSDQDAALEMAEHLPTLGLQVFRVDTPWAELDGRDAALTHFAVPGR
+>PROKKA_00301
+MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPTAGDWLREHDLVPDAVVCSDA
+LRTRQTCVWVCERLGELAPTPYLDPRLYGADAARALAVVNETEETTRRLLVVGHMPWVQE
+LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWAELDGRDAALTHFVVPGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000365.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000365.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6962a036ebef8cf37924092f18d190d2e4e645af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000365.fa
@@ -0,0 +1,70 @@
+>PROKKA_00299
+MDATSHPDAGPRLPETSVPGGDAALHEEALAVLRRLVDRPDARFKDGQFEAIEALVAHRR
+RALVVQRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSS
+ANATEWDEVRARLAADEVDVLLISPERLTNPRFRDEQLPDLVARMGLLVVDEAHCISDWG
+HDFRPDYRRIRDLIGLLPAEGPRAVPVLATTATANARVVADVVEQLGVASEQDVFVLRGP
+LARASLRLGVLRMPSPAARLAWLLDHLGDLPGSGIVYALTVSAAEDTARALREAGHEVVA
+YTGRTDPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHFGAPGSPVAYYQQVG
+RAGRGTDHADVLLLPGPEDRRIWEYFATASMPDEEQARAVLGALADHGGALSVAALEPAV
+RIKRTALELLLKVLAVDGAVERVGGGWRATGREWTYDAERYARVAEARRAEERLMLDYQT
+TDRCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDGAARERAEAALRRTGVPIEPRRM
+WPSGMDRLGVPVKGRIAPESQAEEGRALARLTDLGWGTVLRDLLDREDAPVPEEVLRGAV
+DVLAGWGWRTRPIAVVAMPSRTRPQLVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGN
+SAYRLGSVYGRFAVPEAMAQMLRTAPDAGRHGPVLLVDDLVDSRWSLAEAARVLREAGAQ
+GVLPLVLAQAG
+>PROKKA_00007
+MDATSHPDAGPRLPETSAPGGDAALHEEALAVLRRLVDRPDARFKDGQFEAIEALVAHRR
+RALVVQRTGWGKSAVYFVASLLLRARDAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSS
+ANATEWDEVRARLAADEVDVLLISPERLTNPRFRDEQLPGLVARMGLLVVDEAHCISDWG
+HDFRPDYRRIRDLIGLLPAEGPRAVPVLATTATANARVVADVVEQLGVASEQDVFVLRGP
+LARASLRLGVLRMPSPAARLAWLLDHLADLPGSGIVYALTVSAAEDTARALREAGHEVVA
+YTGRTDPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHFGAPGSPVAYYQQVG
+RAGRGTDHADVLLLPGPEDRRIWEYFATASMPDEEQARAVLGALADHGGALSVAALEPAV
+RIKRTSLELLLKVLAVDGAVERVGGGWRATGREWTYDAERYARVAEARRAEERLMLDYQT
+TDRCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDGAARERAEAALRRTGVPIEPRRM
+WPSGMDRLGVPVKGRIAPESQAEEGRALARLTDLGWGTVLRDLLDREDAPVPEEVLRGAV
+DVLAGWGWRTRPIAVVAMPSRTRPQLVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGN
+SAYRLGSVYGRFAVPEAMAQMLRTAPDAGRHGPVLLVDDLVDSRWSLAEAARVLREAGAQ
+GVLPLVLAQAG
+>PROKKA_00055
+MDTTQHPDAGPLPSESTAPIGPYGSGAAAPGAAAAREPELHAEALAVLRRLVDRPDAQFK
+DGQFEAIEALVAHRRRALVVQRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQV
+AAAARAGVRAVSVSSANATQWDEVRARLAADEVDVLLISPERLTNPRFREEQLPDLVARM
+GLLVVDEAHCISDWGHDFRPDYRRIRDLIGLLPSTGPRAVPVLATTATANARVVGDVVEQ
+LGVDSAQDVFVLRGSLARASLRLGVLRMPSPAARLAWLLDHLEDLPGSGIVYALTVSAAE
+DTARALREAGHEAVAYTGRTDPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVH
+FGAPSSPVAYYQQVGRAGRGTDHADVLLLPGPEDRRIWEYFATASMPDEEQARAVLQALA
+QHGGALSVAALEPAVRIKRTALELLLKVLAVDGAVERVGGGWRATGREWVYDAQRYARVA
+EARRAEERLMLDYQTTDTCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDTSARERAE
+AALRRTGVPIEPRRMWPSGMDRLGVPVKGRMAPEIQAEEGRALARLTDLGWGTVLRELLD
+KEDAPVPEDVLQGAVGVLAGWGWQTRPIAVVAMPSRTRPLLVGSFAEGIARIGRLPFLGS
+LEHARGGPTAGPGGNSAYRLGSVHGRFEVPEAMAHLLRTASDAGRHGPVLLVDDLVDSRW
+SLAEASRVLREAGAQGVLPLVLAQAG
+>PROKKA_00033
+MSTSPQDPARPAAVADPALYAEALGVLRALVGRPDAEFKDGQYEAVEALVAHRRRALVVQ
+RTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAASLSSANATEW
+EDVRRSLEADEVDVLLISPERLTNPRFRDEQLPDLVSRMGLLVVDEAHCISDWGHDFRPD
+YRRIRDLIRLLPSSGPRAVPVLATTATANARVVQDVVEQLDVESRQDVFVLRGPLARASL
+RLGVLRLPSPAARLAWLLQHLGELPGSGIVYALTVSAAEDTARALREAGHEVVAYTGRTD
+PEQRARIEQDLKDNRVKAVIATSALGMGFDKPDLTFVVHLGAPSSPVAYYQQVGRAGRGT
+DHADVLLLPGQEDRAIWEYFATASMPDEVQARAVLEALEESGGAMSVAALEPVVSVKRTA
+LELLLKVLSVDGAVERVGGGWRATGSPWTYDAERYARVAEARRAEERLMLDYQTTQTCRM
+EFLARTLDDPTAAPCGRCDVCAGPWYPTGWDGAAREQADRALRRTGVPLEPRRMWPSGMD
+RLHVPVKGRISPAEQAEEGRALARLTDLGWGSRLRELLAAPDAPVPEEVLQAAVRVLAEW
+GWQERPIAVVAMPSRGRPQLVDSLARGLAGQGRLPFLGPLELVGGGPTAGPGGNSAYRLA
+SVHGRFAVPEGMARMLATAPDAGRHGPVLLVDDLADSRWSLAEAARVLRGTGAQGVLPFV
+LAQNG
+>PROKKA_00306
+MDATSHPDAGPRLPETSAPGGDAALHEEALAVLRRLVDRPDARFKDGQFEAIEALVAHRR
+RALVVQRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSS
+ANATEWDEVRARLAADEVDVLLISPERLTNPRFRDEQLPDLVARMGLLVVDEAHCISDWG
+HDFRPDYRRIRDLIGLLPAEGPRAVPVLATTATANARVVADVVEQLGVASEQDVFVLRGP
+LARASLRLGVLHLPSPAARLAWLLDHLGDLPGSGIVYALTVSAAEDTARALREAGHEVVA
+YTGRTDPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHLGAPGSPVAYYQQVG
+RAGRGTDHADVLLLPGPEDRRIWEYFATASMPDEEQARAVLGALADHGGALSVAALEPDV
+RIKRTSLELLLKVLAVDGAVERVGGGWRATGREWTYDAERYARVAEARRAEERLMLDYQT
+TDRCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDGAARERAEAALRRTGVPIEPRRM
+WPSGMDRLGVPVKGRIAPESQAEEGRALARLTDLGWGTVLRDLLDREDAPVPEEVLRGAV
+DVLAGWGWRTRPIAVVAMPSRTRPQLVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGN
+SAYRLGSVYGRFAVPEAMAQMLRTAPDAGRHGPVLLVDDLVDSRWSLAEAARVLREAGAQ
+GVLPLVLAQAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000367.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000367.fa
new file mode 100644
index 0000000000000000000000000000000000000000..150fab95e1488f536ee7df3bbf09d03a4426fab5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000367.fa
@@ -0,0 +1,42 @@
+>PROKKA_00301
+MPPTTPPPPAGPPAVPPSGPAPAAPGEAAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSD
+DLGVPADRAALLVSASTLGLALSVVPWSVAGDRWGRRRAMVVSMVSASACALAGVLAPTF
+EAMLRLRLLEGMAHGGVAGLAVALLAEEVAPHAVAAAAGTYIAGTTLGGLSGRLLALPVA
+EASSWRGGMLAVTVVGVLCTVGFLAITPRARRFTPSPTSPATLVRIVRGHLRSPELVAVY
+LQGALLMGGFVALYNFVGYRLLGPPFSWTPTAAGLVFLAYLAGTWSSPRAGRLAARVGRL
+PVLAGATAAMAAGVALTSVPHPAVLVPALVLVTGAFFAAHAVASAWSGTAAPTGRAQSTS
+LYNFAYYAGSSLFGWLGGVFHESHGWPGTVLMVLALVLTALASAVVVLRGRGTAPAR
+>PROKKA_00009
+MPPTTPPPSAGPPAVPPSGPAPAAPGEPAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSD
+DLGVPADRAALLVSASTLGLAVSVVPWSVAGDRWGRRRAMVVSMVSASACALTGVLAPTF
+EAMLGLRLLEGMAHGGVAGLAVALLAEEVVPHAVAAAAGTYIAGTTLGGLSGRLLALPVA
+EASSWRGGMLTVTVVGVLCTVGFLAITPRARRFTPSPTSPATLVRIVRGHLRSPELVAVY
+LQGALLMGGFVALYNFVGYRLLDPPFSWTPTAAGLVFLAYLAGTWSSPRAGRLAARVGRL
+PVLAGATAAMAAGVALTSVPHPAVLVPALVLVTGAFFAAHAVASAWSGTAAPTGRAQSTS
+LYNFAYYAGSSLFGWLGGVFHESHGWPGTVLMVLALVLTALVSAVVVLRGRGTAPAR
+>PROKKA_00053
+MPPQPPPAGPPAVPPSGPAPLAPGDPAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSADL
+GVGAHRAALLVSAGTLGLALSVVPWSMAGDRWGRRRAMVVSMVSASLFALAGVLAPTFEA
+MLGLRLLEGMAHGGVAGLAVALLAEEVAPRAVATAAGTYIAGTTIGGLSGRLIALPVAEA
+FTWRTGMLAVTVVGVACTAAFLAVTPQARRFTPSPTSVARLVRIVRGHLGSAELVAVYLQ
+AALLMGGFVALYNFVGYRLLGPPFSWAPTAAGLVFLAYLAGTWSSPRAGRLAARFGRLPV
+LTGATAAMAAGAALTLVPHPAVLVGALVLTTGAFFAAHSVASAWSGTAAPHGRAQSTSLY
+NLAYYAGSSLFGWLGGVFHESHGWTGTVLMVVALALTALAIAVVVLRGRGTAPARCAGAV
+RGAGRRGIRRISRGRLRRRRWPSGAGRARPRGPRGPAARASRPSAGRSRSRCPARRTPPA
+WSAPRPG
+>PROKKA_00031
+MPPALPAPLEPGTPLYRRLLLGLFLAGVATFAQLYAPQGLLPLVSSDLGVPSHRAALLVS
+AGTLGLALSVVPWSLAGDRWGRRPVMVASLVSASVLALVGVFMPSIELLMGMRLLEGMAH
+GGVAGLAVTLLAEEVAPRVVPVAAGTYVAGTTLGGLSGRLLAMPVGEWAGWRAGMLAVTA
+AGAACTVAFLFVTPPARRSTPVRLSLARLGRIIGGHLRTPGLVALYLQAALLMGGFVALY
+NYIGYTLLAPPFGWPPTAVGLVFLAYLAGTWSSPRAGRLAVRVGRLKVLTGSTALMAVGV
+VLTLVPSPFVLVPALVVATGAFFAAHSVASGWAGTAAPTGRAQSTSLYNLAYYAGSSLFG
+WLGGVFHEGVGWAGTVFMVAGLAAVALVVALVVLRGREDAGPPPPSAVAEGAAA
+>PROKKA_00308
+MPPTTPPPSAGPPAVPPSGPAPAAPGEPAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSD
+DLGVPADRAALLVSASTLGLAVSVVPWSVAGDRWGRRRAMVVSMVSASACALTGVLAPTF
+EAMLGLRLLEGMAHGGVAGLAVALLAEEVAPHAVAAAAGTYIAGTTLGGLSGRLLALPVA
+EASSWRGGMLAVTVVGVLCTVGFLAITPRARRFTPSPTSAAALVRIVRGHLSSPELVVVY
+LQGALLMGGFVALYNFVGYRLLDPPFSWTPTAAGLVFLAYLAGTWSSPRAGRLAARVGRL
+PVLAGATAAMAAGVALTSVPHPAVLVPALVLVTGAFFAAHAVASAWSGTAAPTGRAQSTS
+LYNFAYYAGSSLFGWLGGVFHESHGWPGTVLMVLALVLTALASAVVVLRGRGTAPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000368.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000368.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a2bc322c0feaccb1060d82ff95b388935e2af138
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000368.fa
@@ -0,0 +1,30 @@
+>PROKKA_00303
+MEYLVPVLAVVVIGALAFAAARWMSAGRARQAADQRTPSGRGLDIGPERARLAAGLLDED
+AHRRVYGHIAQSRVMEAVRDYRAHTGRGLKDAVMDVQSLAVHPQVYSEPAQEPDATSAGA
+AGPVPADHEEPHRDDTAPAETPGPERPGQDSSGRGEPDAQTPDREPSDAVAEDDARQDTD
+HASAAPRPTATPADELTTLTVPAEWTAAPAEEELPFEVEVMRGTESVRLSSRDLPPWLRD
+QLSAMVRDGNLESAAVQLSSHSELSVPEAYELLRRMREHRGEG
+>PROKKA_00011
+MEYLVPVLAVVVIGALAFAAARWMSAGRARQAADQRTPSGRGLDIGPERARLAAGLLDED
+AHRRVYGHIAQSRVMEAVRDYRAHTGRGLKDAVMDVQSLAVHPQVYSEPVQEPDATSAGV
+AGPVPGGHGEPHRDDAAPADTPGPKRPGQDSSGRGEPDAQTPDRETSDAVAEDDARQDSD
+HASAAPRPTAPSADELTTLTVPAEWTAAPAEEELPFEVEVMRGTESVRLSSRDLPPWLRD
+QLAAMVRDGNLESAAVQLSSHSELSVPEAYELLRRMRERRGEG
+>PROKKA_00051
+MEYLVPVLAVVLIGALAFAVSRWMSAARDRQTAGPRTPSGRPLEIGPERARQAAALLDED
+AHRRVYGHIAQSRVMEAVRDYRAHTGRSLKDAVMDVQSLAVHPQVYSVPATEQEAPEEAE
+VRDPRTRPTPPEPARDEAADGERQGTERADVVEEGADDPAADDEPRPEAESDLSAEEGRV
+DDGAASGTEPRPGTSEPARADELTALTVPADWSAAPAEEEPPFEVEVMRGMDSVRLSSQD
+LPPWLRDQLSAMVRDGNLESAAVQLSSHSQLSVPEAYELLRRMRERRGED
+>PROKKA_00030
+MEYLVPILAVVVIGGITLLVARRLSGRSQAPTRSATGTGADTVEASPERARTAARRLDEA
+THRAVYGHIAQGRPFEAVRDYRRATGRGVRDAILDIQSLTLHPQVWSLPVQAEPADDASP
+AAADMPSGPPRGPSDGRGRDGESSARPRLRRAEPSEAGPAPDAEPAPGGDAAADPEADGA
+TSRRPGRQAPEELTTLTVPEGWTADPAPEEPPFEVEVMRGEESVRLASQDLPPWLRDQLS
+AMVRDGNLESAAVQLSSHSSLSVPEAFELLRRMKERREGRG
+>PROKKA_00310
+MEYLVPVLAVVVIGALAFAAARWMSAGRARQAADQRTPSGRGLDIGPERARLAAGLLDED
+AHRRVYGHIAQSRVMEAVRDYRAHTGRGLKDAVMDVQSLAVHPQVYSEPVQEPDATSAGV
+AGPVPDDHGEPHRDDAAPAETPGPKRPGQDSSGRGEPDAQTPDREPSDAVAEDDAQQDTD
+HASAAPRPTATPADELTTLTVPAEWTAAPAEEELPFEVEVMRGTDSVRLSSQDLPPWLRD
+QLSAMVRDGNLESAAVQLSSHSELSVPEAYELLRRMRERRGEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000371.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000371.fa
new file mode 100644
index 0000000000000000000000000000000000000000..25189e84130d2daaeeabc023ff4ca7077c5ac582
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000371.fa
@@ -0,0 +1,84 @@
+>PROKKA_00307
+MTPLPRFAARTAVTTAALALLAPAVALPSQASPAGDSLVINEAYTNGGSANAVYTHKFVE
+LYNPTDQPINLDGWSLQYRSAAGTAATQGTVALSGTVPAKGHFLVSGGSNGTAGAALPQA
+DLVAGGAFNPAGTKGTIVLARQAGTVTDLPVGSVVTGQVPGVADVLGYGATNTFETAAAG
+APSANSDPKSLTRTNGVDTDDNSADFTVTGQVTPTNAAATGGEPTPEPEPQPTPSERITI
+AQLQGTGTATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGDTPDATPGASDGVFVY
+SPDTVGSVTLGDHVQVTGEAAEHYGLTQIKVAADGVLPVAEPGAVAPTPVEFPLEEADRE
+ALEGMVLAPQGDWTVTDNYSLNQYGSLGVVPGTKPLDNPTSVARPGAEAQAVAAANAQQL
+IVLDDGASTNFMRSPGNQNPLPYLDADQPVRVGAGLEFSTGVILDWRFDAWSFQPLGHLT
+DATAAAVQPVTIEDTRPAEAAPEAVGGNVTVGSFNVLNYFTTLGQDVAGCGAYRDRAGTP
+VTTNGCLPRGAYTPEAFARQQEKIAAAINGLGTSVVALEEIENSEKFGLDRDHALAHLVE
+ALNAQAGEQRWAYVASPSARPALADEDVIRSAFIYQPAEVTPLGESVILDDQTNFDNARE
+PMAQLFRAADGTAEGAAGTEFVAITNHFKSKGGSGATGDNVDAGDGQGAYNADRVGQAEA
+LVAFAERMKAETGTDRVLLMGDFNAYEKEDPIRVLEAAGYVSQGALTGEYSYAFGGAVGS
+LDGIYASPSAAAAITGQDIWMINANESVALEYSRHNYVAEDLYSADQWRSSDHNPILVGL
+QLDAPVTEPTPEPEPEPTPGETCDGVTDPRGVPGKPANSVREWLRCIGATPGHGGDHPGK
+GHGGDHPGKGRGPVRP
+>PROKKA_00022
+MTPLPRFAARTAVTTAALALLAPAVALPSQASPAGDSLVINEAYTNGGSANAVYTHKFVE
+LYNPTDQPINLDGWSLQYRSAAGTAATQGTVALSGTVPAKGHFLVSGGSNGTAGAALPQA
+DLVAGGAFNPAGTKGTIVLARQAGTVTDLPVGSVVTGQVPGVADVLGYGATNTFETAAAG
+APSANSDPKSLTRTNGVDTDDNSADFTVTDQVTPTNAAATGGEPTPEPEPQPTPAERITI
+AQLQGTGTATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGDTPDATPGASDGVFVY
+SPDTVGSVTLGDHVQVTGEAAEHYGLTQIKVAAGGVLPVAEPGAVAPTPVEFPLEEADRE
+ALEGMVLAPQGDWTVTDNYSLNQYGSLGIVPGTTPLDNPTSVARPGAEAQAVAAANAQQL
+IVLDDGATTNFMRSPGNQNPLPYLDADQPVRVGAGLEFTTGVILDWRFDAWSFQPLGHLT
+DATAAAVQPVTIEDTRPAEAAPEAVGGNVTVGSFNVLNYFTTLGQDVAGCSAYRDRAGTP
+VTTNGCLPRGAYTSEAFARQQEKIAAAINGLGTSVVALEEIENSEKFGLDRDHALAHLVE
+ALNAQAGEQRWAYVASPATRPALADEDVIRSAFIYQPAEVTPVGESVILDDQTNFDNARE
+PMAQLFRAADGTSEGAAGTDFVAITNHFKSKGGSGATGDNVDAGDGQGAYNADRVGQAEA
+LVAFAERMKAETGTDRVLLMGDFNAYEKEDPIRVLEAAGYLSQGALTGEYSYAFGGAVGS
+LDGIYASPSAATAITGQDIWMINANESVALEYSRHNYVAEDLYSADQWRSSDHNPILVGL
+QLDAPVTEPTPEPEPSPGETCDGVTDPRGVPGKPANSVREWLRCVGATPGHGGDHPGKGH
+GPEHPGKGRGPVRP
+>PROKKA_00030
+MTQRTFRLSRPAVALAALTLLAPAVVAGPAHAAPTGDGLVINEVYTNGGSANAVFTHKFV
+ELYNPTDTPISLDGWSLQYRSATGTAAPNGVVALSGTVPAKGHFLIQGGSNGTTGAALPR
+PDLNAGGAFNPAGARGTVVLSDQAGALTALPVGSVTTGQAEGVADLLGYGTSNTFETAAA
+GAPSSNSDPKSLTRTDGVDTDDNAADFTVTAQVTPTSSTGEAPVDPIPDPEPDPEPAPAL
+TIAQIQGDGAATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGSAEDATPGASDGLF
+VYSPDTVGSVALGDHVQVTGEAAEHYGLTQVRVGAAGVTPVAEPAAVAPTAVDFPLSEAD
+REALEGMLLAPTGEWTVTDNYDLNQYGSLGIVPGTEPLPNPTSVAAPGAEAQAVAADNAS
+RLIVLDDGASTNFMRSPGNENPLPYLDADRPVRVGAGLDFTTGVILDYRFDAWSFQPLGH
+LTDATAAAVQPVAVEDTRPEEASPEAVGGNVSVGSFNVLNYFTALGQDFPGCRAYTDRFG
+EPVTTNGCLPRGAYTPEAFARQQEKIAAAIDGLDASVVALEEIENSAKFDLDRDRALAHL
+VDALNAQAGEQKWAYVASPADRPALSEEDVIRNAFVYQPAEVTPVGESVILRDEVNFDNA
+REPLAQHFRAADGTEAGVAGTDFVAVTNHFKSKGGSGAAGDNADSGDGQGAYNGDRTRQA
+QALVAFAEQVADDAGTDRVLLLGDFNAYEKEDPIRVLEEAGYVSQGALTGEYSYTFDGAV
+GSLDGVYASPAASAVVTGQDIWMINANESVALEYSRHDYVAEDLYAPDQWRSSDHNPLLV
+GLQLDAPVVEPEPQPGAGHPGKGKGLDKGAGHPGKGKGLDKGAGHPGHGRVPEAARP
+>PROKKA_00026
+MPTPRLRLVRTAATLAAATLLAPAVLALPAQASPAGDSLVINEAYTNGGSAGALFTHKFV
+ELYNPTDQPISLDGWSLQYRSATGTTAPSTTVALSGTVPAKGHFLIQGGSNGATGAALPT
+PDLTTSFNPAGTKGTIVLADQAGTVAGLPTGSVVTDQVAGVADVLGYGATNTFETAASGA
+PAANSDPKSIARTGGADTDDNAADFTVAADVTPQNAAGGGTAPVDPVDPVDPTPAPAPSV
+TVAEIQGTGATSPLEGRRVSTTGVVTAVYSTGGYDGFYIQTAGTGGAEDATPGASDGVFV
+YAPAEVGSVTLGQTVTVTGDVAEYYGLTQVKAEAGGVRQAAEAGAPVTARELAFPLTEAE
+KEAHEGELLAPAGAWTVTDNYDVNQYGSLGLAPGTSPLPNPTSVALPGADAQAVAADNAQ
+RLIVLDDGASTNFFRSPGNQNALPYIDADAPARVGSAVDFRTPVILDYRYGAWSFQPLGH
+LTDANKAEVQPVDIADTRPAEAVREDLGGNVTVGSFNVLNYFTTLGEDVPGCGYYADKDG
+APVSTKGCLPRGAYTEEAFLEQQAKIATAINGMDTSVVALEEIENSEKFGLDRDHALAHL
+VDALNAQAGYAKWAYVASPTVRPALADEDVIRSAFIYQPAEVTPVGESVILDDQVNFANA
+REPMAQAFRVADGSAGGVVGTEFVAITNHFKSKGGSGATGDNVDTGDGQGAYNGDRTRMA
+QALVAFAEQMKVQAGTDRVLLMGDFNSYEKEDPIRVLEAAGYISQGAKTGEYSYTFDGAV
+GSLDGIYASPAADATVTGQDIWMINANESVAFEYSRDNYVGEEFYAPDQWRSSDHNPVLV
+GLQLDAPAAPVVPTPGTRPTPPADQCALITSPRGAKASAGFSASEWMRCAGVHPGKGRGR
+G
+>PROKKA_00314
+MTPLPRFAARTAVTTAALALLAPAVALPSQASPAGDSLVINEAYTNGGSANAVYTHKFVE
+LYNPTDQPINLDGWSLQYRSAAGTAATQGTVALSGTVPAKGHFLVSGGSNGTAGAALPQA
+DLVAGGAFNPAGTKGTIVLARQAGTVTDLPVGSVVTGQVPGVADVLGYGATNTFETAAAG
+APSANSDPKSLTRTNGVDTDDNSADFTVTDQVTPTNAAATGGEPTPEPEPQPTPAERITI
+AQLQGTGTATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGDTPDATPGASDGVFVY
+SPDTVGSVTLGDHVQVTGEAAEHYGLTQIKVAAGGVLPVAEPGAVAPTPVEFPLEEADRE
+ALEGMVLAPQGDWTVTDNYSLNQYGSLGIVPGTTPLDNPTSVARPGAEAQAVAAANAQQL
+IVLDDGATTNFMRSPGNQNPLPYLDADQPVRVGAGLEFTTGVILDWRFDAWSFQPLGHLT
+DATAAAVQPVTIEDTRPAEAAPEAVGGNVTVGSFNVLNYFTTLGQDVAGCSAYRDRAGNP
+VTTNGCLPRGAYTSEAFARQQEKIAAAINGLGTSVVALEEIENSEKFGLDRDHALAHLVE
+ALNAQAGEQRWAYVASPATRPALADEDVIRSAFIYQPAEVTPVGESVILDDQTNFDNARE
+PMAQLFRAADGTSEGAAGTDFVAITNHFKSKGGSGATGDNVDAGDGQGAYNADRVGQAEA
+LVAFAERMKAETGTDRVLLMGDFNAYEKEDPIRVLEAAGYLSQGALTGEYSYAFGGAVGS
+LDGIYASPSAATAITGQDIWMINANESVALEYSRHNYVAEDLYSADQWRSSDHNPILVGL
+QLDAPVTEPTPEPEPSPGETCDGVTDPRGVPGKPANSVREWLRCVGATPGHGGDHPGKGH
+GPEHPGKGRGPVRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000374.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000374.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd1a2cb5edf85acedfc0c6dc0c66e7d76db653f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000374.fa
@@ -0,0 +1,30 @@
+>PROKKA_00313
+MSLPHAPRTPAPPAAASSAVPLRLAVVDMSGTSIVEHGLQDTAFARSLDQHGVPAGTPEH
+DDAARRFRALRPTSRTAVFPRVFADRAVAAAATRTFEATFDALLAEHGVRAVPGAEEALI
+RLRALGLHVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMILTALLGLD
+LEDVRSVLVVGDTAEDMTAGRRAGAGLVVGVRTGRDADHVLLAAGSDRVVPGLADVPDLV
+VRTR
+>PROKKA_00028
+MSLPHAPRTPAPPAAASSAAPLRLAVVDMSGTSIVEHGLQDTAFARTLDQHGVPAGTPEH
+DDAARRFRALRPTSRTAVFPRVFADRAVAAAATRTFEAAFDALLAEHGVQAVPGAEEALV
+RLRALGLHVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMILTALLGLD
+LDDVRSVLVVGDTAEDMTAGRRAGAGLVVGVRTGRDADDVLLAAGADRVVPGLADVPDLV
+VRTR
+>PROKKA_00024
+MSLPPRPPPRGRAPRADGPPAPPLRLAVVDMSGTSIVERGLQDAAFAHALETHGLAADAP
+AHADAVRVFRARRATSRTAVFAQVFPDRPAAAAAARTFEEAFDSLLAEHGVQPVPGAEEA
+LLRLRALGLRVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPFPDMILTALLG
+LDLDDVRGVLVVGDTAEDMTAGRRAGAGLVAGVRTGRDADAALLAAGAHHVVDGLADVPA
+LVGAGG
+>PROKKA_00020
+MSLSTAVPALSVGTPVPLRLAVVDMSGTSVVEGGLQDRAFAEVVAARGLAEGSPEHERAA
+RLFRERRGTSRTAVFQALFEGRTAALEATRAFEAAFDRLLAEHGVTAVPGAEGALVRLRE
+AGLDLCLITGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMVLTALLALDHDDV
+RSVLTVGDTAADILAGRRAGAGLVVGVRSGQDTGGVLAGAGADQVVDSLAQVPDLVATLR
+G
+>PROKKA_00320
+MSLPHAPRTPAPPAAASSAVPLRLAVVDMSGTSIVEHGLQDTAFARTLDQHGVPAGTPEH
+DDAARRFRALRPTSRTAVFPRVFADRAVAAAATRTFEATFDALLGQHGVQAVPGAEEALV
+RLRALGLHVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMILTALLGLD
+LDDVRSVLVVGDTAEDMTAGRRAGAGLVVGVRTGRDADDVLLAAGADRVVPGLADVPDLV
+VRTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000377.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000377.fa
new file mode 100644
index 0000000000000000000000000000000000000000..faba5b348f985350e38c43a92938d8c2d36faf2f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000377.fa
@@ -0,0 +1,15 @@
+>PROKKA_00316
+MHVALLFDHWLFRVLAIAALVLEVWALVDVVRRRPDDFARIGGRDRSFWLILTGVAAVVG
+LLGVLAGGGMGMFGLVAACVACVYLAGPRQDMGPALRR
+>PROKKA_00031
+MHFALLVDHWLFRVLAIAALVLEVWALVDVVRRRPDDFARIGGRDRSFWLILTGVAAVVG
+LLGVLAGGGMGMFGLVAACVACVYLAGPRQDMGPALRR
+>PROKKA_00021
+MHLALTFDQWLFRILAIVGLVLEVWAFLDALRRSPGDFARIGGRDKSFWMILTGVAAAVG
+VLGVLSGGGMGMFGLLAACVACVYLAGPRQEMGPATRR
+>PROKKA_00017
+MHLAIVAGNWLFYALAVVAFLLELWAFADAARTSQETFLRTGGRTKGFWLALTGAAAAVG
+LVGVLLGPTGGFGILGLAAVCVASVYLAGPRDDLRFYGGRRGR
+>PROKKA_00323
+MHFALLVDHWLFRVLAIAALVLEVWALVDVVRRRPDDFARIGGRDRSFWLILTGVAAVVG
+LLGVLAGGGMGMFGLVAACVACVYLAGPRQDMGPALRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000385.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000385.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1421da20ae6c31f31ec4185e31ecf3759d57d494
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000385.fa
@@ -0,0 +1,50 @@
+>PROKKA_00325
+MAQRFYDTRTAQVRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDILIRWLEATGL
+RVTSVRNVTDIDDKILERSAASHEAGFEASDLYPAREPWWALAYRFEKAFDAAYLALGVR
+RPTYEPRATGHVPEMFALIERLMERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ
+DAPDADPRGKRDPRDFALWKGAKPGEPATAVWESPWGAGRPGWHLECSAMSTKYLGTEFD
+IHGGGLDLRFPHHENELAQSAAAGDGFARLWLHNGLVTYGGEKMSKSVGNTISPEEMLGM
+ARPTAVRYFLGQAHYRSQLDYRPGALDEAEAAVERIEGFTARARAAGAVPPAPDGALADR
+VPAAFRAAMEDDLNVPQALAALHEAVRAGNSALAGQDLDAAAARLAEVEAMTAVLGLDDV
+PEGDDAAAGPVSDALDSLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGADGAT
+WRLAD
+>PROKKA_00040
+MAQRFYDTRTAQVRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDILIRWLEATGL
+RVTSVRNVTDIDDKILERSAASYEAGFEASDLYPAREPWWGLAYRFEKAFDAAYLALGVR
+RPTYEPRATGHVPEMFALIERLMERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ
+DAPDADPRGKRDPRDFALWKGAKPGEPATAVWESPWGAGRPGWHLECSAMSTKYLGTEFD
+IHGGGLDLRFPHHENELAQSAAAGDGFARFWLHNGLVTYGGEKMSKSVGNTISPEEMLGM
+ARPTAVRYFLGQAHYRSQLDYRPGALDEAEAAVERIEGFTARARAAGAVPPAPDGALADR
+VPAAFRAAMEDDLNVPQALAALHEAVRAGNSALAGQDLDAAAARLAEVEAMTAVLGLDDV
+PEGDDAAAGPVSDALDSLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGADGAT
+WRLAD
+>PROKKA_00012
+MAQRFYDTRTAQIRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDVLIRWLEATGL
+RVTSVRNVTDIDDKILDRSAASHEEGFEPSALYPAREPWWALAYRFEKAFDAAYLALGVR
+RPTYEPRATGHVPEMFALIERLVERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ
+DAPDADPRGKRDPRDFALWKGAKEGEPATAVWTSPWGAGRPGWHLECSAMATKYLGAQFD
+IHGGGLDLRFPHHENELAQSAAAGDGFARFWLHNGLVAYGGEKMSKSVGNTISPEEMLGM
+ARPKAVRYFLGQAHYRSQLDYRPGALEEAEAAVERIENFTARARTAGAVPPAVDGALADR
+VPAAFRAAMEDDLNVPQALAALHEAVRAGNSALAAQDLESAAARLTEVEAMTAVLGLDDV
+PEGDGDGTGPAADALDSLVRSQIEARAQARAEKDWAAADRIRDALAAAGVVVEDGADGAT
+WRLAD
+>PROKKA_00008
+MAQRFYDTRSAEIRDFVPLVPGQASVYYCGATVQGMPHVGHVRSAIVFDVLIRWLEATGL
+RVTSVRNVTDIDDKILDRSAASQEPGFEPSEMYPADEPWWALAFRFENAFDAAYLALGVR
+RPTYEPRATGHVPEMLALIERLIERGHAYPAADGSGDVYFDVRSWDRYGELTRQRVEDMQ
+DAPDADPRGKRDPRDFALWKGAKEGEPVTAVWSSPWGAGRPGWHLECSAMSTKYLGGEFD
+VHGGGLDLRFPHHENELAQSAAAGDPFARFWLHNGLVTYQGEKMSKSVGNTISPQEMLAM
+ARPKAVRYFLGQAHYRSQLDYRPGALEEAEAAVERIENFVQRAAAALGAPELTAPLAEHV
+PAAFRAAMEDDLAVPQALAVLHEAVRAGNSALAAGDDAAARARLAEVAAMTAVLGLDDVP
+EASAGGSGPEAAALDSLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGAQGATW
+HLAG
+>PROKKA_00332
+MAQRFYDTRTAQIRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDILIRWLEATGL
+RVTSVRNVTDIDDKILDRSAASHEAGFEASDLYPAREPWWALAYRFERAFDAAYLALGVR
+RPTYEPRATGHVPEMFALIERLIERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ
+DAPDADPRGKRDPRDFALWKGAKPGEPATAVWESPWGAGRPGWHLECSAMSTKYLGAEFD
+IHGGGLDLRFPHHENELAQSAAAGDGFARFWLHNGLVTYGGEKMSKSVGNTISPEEMLGM
+ARPTAVRYFLGQAHYRSQLDYRPGALDEAEAAVERIEGFTARARAAGAVPPAPDGALADR
+VPAAFRTAMEDDLNVPQALAALHEAVRAGNSALAGQDLDAAAARLAEVEAMTAVLGLDDV
+PEGDDAAAGPVSDALDLLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGADGAT
+WRLAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000386.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000386.fa
new file mode 100644
index 0000000000000000000000000000000000000000..783cd68343ad48b7574c9ef9cb3cef71af754d07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000386.fa
@@ -0,0 +1,35 @@
+>PROKKA_00326
+MSTAPRSGGSRKPKGKKGPMKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA
+KRGPVKDQVRGRVKLTDETVSGRNPVLEALRAGIPAKALHVAVRIEMDDRVKEALRLCLE
+QGVPVLENTKPELDRLSGEAVHQGIVLQIPPYEYADATALALDALAKHEKGHLRTPPLLI
+ALDGITDPRNLGAIIRAGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQAGNLN
+TTLVDLHKAGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRMVREHCQQIVSIP
+IDSTMESLNASMAVGISLYEISVQRAGGR
+>PROKKA_00042
+MSTAPRSGGSRKPKGKKGPMKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA
+KRGPVKDQVRGRVKLTDETVSGRNPVLEALRAGIPAKALHVAVRIEMDDRVKEALRLCLE
+QGVPVLENTKPELDRLSGEAVHQGIVLQIPPYEYADATALALDALAKHEKGHLRTPPLLI
+ALDGITDPRNLGAIIRAGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQAGNLN
+TTLVDLHKAGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRMVREHCQQIVSIP
+IDSTMESLNASMAVGISLYEISVQRAGGR
+>PROKKA_00009
+MSTAPRSGGSRKPKGKKGPMKGTGGHGRKALEGKGPTPKAEDRVYHKAYRAKQLSERSAA
+KRGGPVRPSRPKLTDETVSGRNPVVEALRAGIPAKALHVAVRIEMDDRVKEALRLCLEQG
+VPVMENTKPELDRLSGEAIHQGLVLQIPPYEYADAMTLATDALEKHEKGHLRTPPLLIAL
+DGITDPRNLGAIIRSGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQAGNLNTT
+LVELHRAGYFVLGLDGGGDVSLPGLSLATEPLVLVVGAEGKGLSRMVREHCQQIVSIPIN
+SDMESLNASMAVGISLYEISVQRAGGR
+>PROKKA_00007
+MSTAPRSGGSRAPKGKKGPQKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA
+KHGGGRVPVRDQVRGRVKLTDETVSGRNPVVEALRAGIPAKALHVATRIEVDDRVKEALR
+LCAENKVPVMENTRPELDRMSGEAVHQGLVLQIPPYQYADALTLGREAMEAQEKGHLRTP
+PLLIALDGITDPRNLGAIIRSASAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQA
+GNLNTTLVELHRMGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRMVREHCQQI
+VSIPIQSEMESLNASMAVGISLYEIAVGRAGGRPVAS
+>PROKKA_00333
+MSTAPRSGGSRKPKGKKGPVKGTGGHGRKALEGRGPTPKAEDRVYHKAHRAKQLAERSAA
+KRGPVKDQVRGRVKLTDETVSGRNPVLEALRAGIPAKALHVAVRIEMDDRVKEALRLCLE
+QGVPVLENTKPELDRLSGEAVHQGIVLQIPPYEYADATALALDALAKHEKGHLRTPPLLI
+ALDGITDPRNLGAIIRAGSAFDADGVIVPERRSVGVTATAWRTSAGAAARVPVAQAGNLN
+TTLVDLHKAGYFVLGLDGGGDVSLPGLALATEPLVLVVGAEGKGLSRLVREHCQQIVSIP
+IDSTMESLNASMAVGISLYEISVQRAGGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000387.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000387.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f2e2a671eb4e2a9e25d52b2e4876930b4e7d550
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000387.fa
@@ -0,0 +1,65 @@
+>PROKKA_00330
+MKPDTQSATAADVRLQTVTGRIPVTDVQPVVLDGRFPAKAVVGEDIPVRATVFREGHDSV
+RATVRLLDPAGAEVQRVQMRPGRPGLDEVVATLRPAEPGLHQFVVEGWDDPVGTWKHAAT
+VKIAAGIDVELMLAEGAALFRRAAEDAERSAEDRAVFEEVVRGLEDESLIPAQRLASAES
+AEVSAVLHARPVREHLTSSELYPLDVQRELAGRGAWYEFFPRSEGARFDEASGTWSSGTF
+ATAADRLPAVARMGFQVVYLPPIHPIGTTHRKGPNNTLTAGPQDPGSPWAIGGPEGGHDA
+AHPDLGTVEDFEAFVAAAADEGLEVALDLALQCSPDHPWVTAHPEWFTTRVDGTIAYAEN
+PPKKYQDIYPLNFDNDPDGLAQAVLDVVRGWVARGVHIFRVDNPHTKPLWFWEWLIAKVR
+AEEPRVVFLAEAFTRPAMMHALGKVGFQQSYGYFTWRNTAEELAEYLQEISHETPAFYRP
+NLFVNTPDILTEYLQHGGPGAFRIRAVVAATASPLWGVYAGFELFEHVARPGAEEYIDNE
+KYEYRPRDWEGAEAAGASLAPYLTRLNEIRAAHPALGDLQNLTLHASTHPDLLVFSKTRS
+ARPEGAHRDAEAVTDAGPAEDTLIVVVTTNPHDVAEATLDLDLEALRLRPEDRDASGAVE
+VEDLLTGQRWRWGRTPYVRLDPHVEPAHVLRIVRNG
+>PROKKA_00046
+MKPDTQSATAADVRLQTVTGRIPVTDVQPVVLDGRFPAKAVVGEDIPVRATVFREGHDSV
+RATVRLLDPAGAEVQRVQMRPGRPGLDEVVATLRPAEPGLHQFVVEGWDDPVGTWKHAAT
+VKIAAGIDVELMLAEGAALFRRAAEDAERSAEDRAVFEEVVRGLEDESLIPAQRLASSES
+AEVSAVLHARPVREHLTSSELYPLDVQRELAGRGAWYEFFPRSEGARFDEASGTWSSGTF
+GTAADRLPAVARMGFQVVYLPPIHPIGTTHRKGPNNTLTAGPQDPGSPWAIGGPEGGHDA
+VHPDLGTVEDFEAFVAAAADEGLEVALDLALQCSPDHPWVTAHPEWFTTRVDGTIAYAEN
+PPKKYQDIYPLNFDNDPDGLAQAVLDVVRGWVARGVHIFRVDNPHTKPLWFWEWLIAKVR
+AEEPRVVFLAEAFTRPAMMHALGKVGFQQSYGYFTWRNTAEELAEYLQEISHETPAFYRP
+NLFVNTPDILTEYLQHGGPGAFRIRAVVAATASPLWGVYAGFELFEHVARPGAEEYIDNE
+KYEYRPRDWEGAEAAGASLAPYLTRLNEIRAAHPALGDLQNLTLHASTHPDLLVFSKTRS
+ARPEGAHRDAEAVTDAGPAEDTLIVVVTTNPHDVVEATLDLDLEALRLRPEDRDASGAVE
+VEDLLTGQRWRWGRTPYVRLDPNVEPAHVLRVVRNG
+>PROKKA_00005
+MSNSKQAAQSTPVPDVRLQTVTGRIPVTGVQPVVQDGRFPAKAVVGEDIPVRATVFGEGH
+DAVRATVRLLDPSGAEVQRVHMRPGRPGLDEFLATLRPSETGVHHFVVEGWHDPVGTWLH
+AATVKLAAGVDVELMLAEGAALFRAAAEDAERSAQDRAAFEETARVLADEGLVPAQRLAG
+AESAELAAVLGARPLREHVTSSELLPLDVQRELAGRGGWYEFFPRSEGARFDEAAGTWSS
+GTFTTAARRLPAVARMGFQVVYLPPIHPIGTAHRKGPNNTLTAGPQDPGSPWAIGAAEGG
+HDAVHPDLGTIADFEDFVAAAADEGLEVALDLALQCSPDHPWVAEHPEWFTTRVDGTIAY
+AENPPKKYQDIYPLNFDNDPEGLAQAVLEVVQGWVGRGVHIFRVDNPHTKPLWFWEWLIA
+RVRAEEPRVVFLAEAFTRPAMMHALGTVGFQQSYGYFTWRNTAAELAEYLEEISHETPAF
+YRPNFFVNTPDILTEYLQHGGPGAFRIRAVVAALANPLWGVYAGYELFEHVARPGAEESI
+DNEKYEYRPRDWEGAEAAGASLAPYLTRLNEIRAAHPALRDLQNLTLHRSTHQDLLVFSK
+TRTARPEGEHRDAEAVTDAGAHEDTVITVVTVNPHHVAEATLDLDLSALRLRPEDLDESG
+SFEVEDLLTGQRWRWGRTPYVRLDPHVEPAHVLRVVRHG
+>PROKKA_00006
+MSTSKPRPAAHPAPPAPALPDVRRTTLTGRIPVSNVQPTVEEGRFPAKAIVGEDVPVRAN
+VYREGHDAVRATVRLLGPDGAEVQRVHMRPGRPGLDEAVATLRPSEPGVHHFVVEGWDDP
+VGTWRHNASVKLAAGVDVELMLDEGAALFRAAAQDPERGAADRAVFEEAVRGLEDASLAP
+VQRFAVTQSAEVSAVLDARPVRRWVTSSELYPLDVQRPLAGRGAWYEFFPRSEGARYDEA
+AGLWHSGTFRTAAERLPAVAAMGFQVVYLPPIHPIGVAHRKGPNNTLTAGPQDPGSPWAI
+GGEAGGHDAIHPGLGTFEDFDAFQERVRELGMELALDLALQCSPDHPWVTEHPEWFTHRV
+DGSIAYAENPPKKYQDIYPLNFDDDADGLARAVLDVVLGWVRRGVHIFRVDNPHTKPLWF
+WEWLIREVRAVEPEVVFLAEAFTRPAMMHGLGRVGFQQSYGYFTWRNTREELEEYLEEIT
+AETAGFYRPNFFVNTPDILTDYLQHGGPGAFKARAVIAATSNPLYGVYAGFELFEHVARP
+GAEEYIDNEKYEFRPRDWAGEEAAGRSLAPYLTRLNRIRAEHPALQDLQNLTLHSATDPE
+LLVFSKTRSALPEGDHRDAAAVTDAGSAEDTVVVVVACDPHRVAEATLRLDAEALRVRPE
+DRDEEGRFEVEELLTGARWRWDEQPYVRLDPAVEPAHVLRVVRRG
+>PROKKA_00337
+MKPDTQSATAADVRLQTVTGRIPVTDVQPVVLDGRFPAKAVVGEDIPVRATVFREGHDSV
+RATVRLFDPAGAEVQRVQMRPGRPGLDEVVATLRPAEPGLHQFVVEGWDDPVGTWKHAAT
+VKIAAGVDVELMLAEGAALFRRAAEDAERSAEDRAVFEEVVRGLEDESLIPAQRLASAES
+AEVSAVLHARPVREHLTSSELYPLDVQRELAGRGAWYEFFPRSEGARFDEASGTWSSGTF
+ATAAGRLPAVARMGFQVAYLPPIHPIGTTHRKGPNNTLTAGPQDPGSPWAIGGPEGGHDA
+VHPDLGTVEDFEAFVAAAADEGLEVALDLALQCSPDHPWVTAHPEWFTTRVDGTIAYAEN
+PPKKYQDIYPLNFDNDPGGLAQAVLDVVRGWVARGVHIFRVDNPHTKPLWFWEWLIAKVR
+AEEPRVVFLAEAFTRPAMMHALGKVGFQQSYGYYTWRNTAEELAEYLQEISHETPAFYRP
+NLFVNTPDILTEYLQHGGPGAFRIRAVVAATASPLWGVYAGFELFEHVARPGAEEYIDNE
+KYEYRPRDWEGAEAAGASLAPYLTRLNEIRAAHPALGDLQNLTLHASTHPDLLVFSKTRS
+ARPEGAHRDAEAVTDAGPAEDTLIVVVTTNPHDVVEATLDLDLEALRLRPEDRDASGAVE
+VEDLLTGQRWQWGRTPYVRLDPHVEPAHVLRIVRNG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000389.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000389.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a00828e2183df9cc56ef2e99029c6f12ef2af4c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000389.fa
@@ -0,0 +1,21 @@
+>PROKKA_00335
+MSWWPFPRPSASPSPDDDGAPAAAELEEAVAALRQLLRAERHRLRPDSWALAWEMVEQAA
+EYAPAWTRLQRTRPVETQELVLALTGRLEPLLCDFLALPDSEKPTHADAVHARLREQGTE
+HGRLRRRLTRALTARLRAGEEL
+>PROKKA_00051
+MSWWPFLRSSASPSPDDDGAPAAAELEEAVAALRRLLRAERHRLRPDSWALAWEMVEHAA
+EYGPAWTRLQRTRPVETQELVLALTGRLEPLLRDFLALPDSEKPAHADAVHARLREQSTE
+HGRLRRRLTRALTARLRAGEEL
+>PROKKA_02680
+MAWWPFRGPSGAPRDDDASTAGRASLEAAVHSLRALMTAERHRLRPDSRDLAWTITERAA
+EYGPAWDRVSAQRPAEAQELLLLLSHRLEPALRDFLDLPDSQKPRHADELHGRLSELQTE
+AQRLGRRLTRALSSRLRARGEL
+>PROKKA_02492
+MAWWARRRLSSSGPAPLGKPPLVAAEELRRLTDELSEILQRESARIRPDAAAVLRSFLNR
+SRALLPAWDRTAPARSAEALAAYELLRDRVLPGLQDWLCLPDHLKPVHADDLLADAQAWE
+GDLSHHAARLTQVLTARGRAVRELDERQ
+
+>PROKKA_00342
+MSWWPFLHSSASPSPDDDGAPAAAELEEAVAALRRLLRAERHRLRPDSWALAWEMVEHAA
+EYGPAWTRLQRTRPVETQELVLALTGRLEPLLRDFLAIPDSEKPAHADAVHARLREQSTE
+HGRLRRRLTRALTARLRAGEEL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000390.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000390.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9926a64ba10e9de2394d17b119551e53b1284cf1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000390.fa
@@ -0,0 +1,17 @@
+>PROKKA_00337
+MTEQTPSLEHPQVRKNAERYEIVVDEAGTVAGYTVAIDYDTGDGPTQRIFPHTKVDHGYE
+GRGLASTLVREALKDTVAAGRRIVPVCPYVKDWVNEHDDVAGEVDPAGPEHLQFLESRQD
+>PROKKA_00053
+MTEQTPSLEHPQVRKNAERYEIVVDDAGTVAGFTVAIDDDTADGPAQRIFPHTKVDHQYE
+GRGLASTLVREALKDTVAAGRRIVPVCPYVKDWVDEHDDVAGEVDPARPEHMQFLESRQD
+>PROKKA_02676
+MTENTPTLDAPQVRKVGEKYEIVVDGDGTVAGYTLAIDYEGTDGVAQRIFPHTKMAEEYG
+GRGLASVLVREALKDSVAAGFRIVPVCPYVKQWTQKHDDVAGDVDQARPEHLQFLEEHAR
+RRSEG
+>PROKKA_02488
+MTEQTSSLDHPQVRKNAEKYEIVVDADGTVAGYTLAIDYTAEDGTAEDGTEQRIFPHTKL
+EDAYEGKGLASTLVREALRDTEAAGRRIVPVCPYVKQWADKHADEVEGQVDQPRPEHLQF
+LEKHAQERKQG
+>PROKKA_00344
+MTEQTPSLEHPQVRKNGERYEIVVDDAGTVAGFTVAIDDDTADGPAQRIFPHTKVDHEYE
+GRGLASNLVREALKDTVAAGRRIVPVCPYVKDWVDEHDDVAGEVDPARAEHLQFLESRQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000397.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000397.fa
new file mode 100644
index 0000000000000000000000000000000000000000..324602748703ba71701769bd3d8a490850d27824
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000397.fa
@@ -0,0 +1,75 @@
+>PROKKA_00344
+MSTSTVRSAPASTYRLQVSPDLPLESVAGLVPYLRRLGVDWLYLSPLLEAEPGSDHGYDV
+VDPTRLDAARGGAEGLDAVARAAHEAGMGVLVDIVPNHVGVATPQANPAWWDVLTHGPEA
+AHAAWFDVDWAAGGGSLLIPVLGDGPDGDADAELNRLVVDEGRLRYWDNVYPLAPGSLEA
+AEAETGLRAAEVFAEADPAKESTAERARLARAVHDRQHYRLVGWRRGDAELNYRRFFTVT
+TLAGVRVDEPEVFDAVHAEPARWVREGLVDGLRVDHPDGLADPAGYARRLRSHVLPEGYL
+VVEKILEPGEALPADWPVDGTTGYDALGEVERVFMHPEAAGDAAEDARRRREWDEAVVRA
+KHDVATGSLAAETARLVREVRAVHALGAHPDEDVAAAFAAVLARLPVYRTYLPVGLAVLE
+GALADAAEAEPALAAVLGDLRPELTDPDSPVARRFQQTSGMVMAKGVEDRSFYRYTRWAN
+LNEVGGDPSHVALSLADFHAAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEPDR
+WAAELAELRRLHPLGHPDAERLLWESIVGVWPTDGTAPEEERILGFLQKASREAALATSW
+TDQDPEFEARLAALAAAVTSPEGPARGVLQAVADRIAEPGLVVQLGHKLVQLAAPGVPDV
+YQGTEVPFPTLVDPDNRRPVDFAARADLLDRLDAGHTPGLDDPAAAKLAVVAAVLRTRRD
+RPELFTGHRPLDVSGPAAEHAIAFDRGGALAVATRWPVRLAAAGGWGETVVTVPAGRWED
+AVTGHPVHPDARGAVRLDELLSTLPVALLVPAHAPSDRRERTAP
+>PROKKA_00060
+MSTSTVRSAPASTYRLQVSPDLPLESVAGLVPYLRRLGVDWLYLSPLLEAEPGSDHGYDV
+VDPTRLDAARGGAEGLDMVARAAHEAGMGVLVDIVPNHVGVATPRANPAWWDVLTHGPEA
+AHAAWFDVDWAAGGGSLLIPVLGDGPDGDADAELNRLVVDEGRLRYWDNVYPLAPGSLEA
+AEAETGLRAAEVFAEADPASEPTAEQARLARAVHERQHYRLVGWRRGDAELNYRRFFTVT
+TLAGVRVDEPEVFDAVHAEPARWVREGLVDGLRVDHPDGLADPAGYARRLRSHVLPEGYL
+VVEKILEPGEALPADWPVDGTTGYDALGEVERVFMHPEAAGDAAEDARRRREWDEAVVRA
+KHDVATGSLAAETARLVREVRAVHALGAHPDEDVAAAFAAVLARLPVYRTYLPVGLAVLE
+GALADAAAAEPGLADVLGDLRPELTDPDSPVARRFQQTSGMVMAKGVEDRSFYRYTRWAN
+LNEVGGDPSHVALSLADFHSAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEPDR
+WAAELAELRRLHPLGHPDAERLLWESIVGVWPTDGTAPEEERILGFLQKASREAALATSW
+TEQDPEFEARLAALAAAVTSPEGPARGVLQAVADRLAEPGLVVQLGHKLVQLAAPGVPDV
+YQGTEVPFPTLVDPDNRRPVDFAARADLLDRLDAGHTPGLDDPAAAKLAVVAAVLRARRD
+RPELFTGHRPLDVSGPAAEHAIAFDRGGALAVATRWPVRLAAAGGWGETVVTVPAGRWED
+AVTGHPVHPDARGAVRLDELLSTLPVALLVPAHAPSDRRERTAP
+>PROKKA_02625
+MSTSTERPVPSSTYRLQVGPDLPLESVAGLVPYLRRLGVGWLYLSPILEAEPGSDHGYDV
+VDPTRLDAARGGAEGLEAVARAAREAGLGVLVDIVPNHVGVATPEANPAWWDLLAHGSEA
+AHAPWFDVDWTAGEGRVLLPVLGDGPDGEAEAELDRLVVETGDDGGRLRHWDTRYPLAPG
+SLAAAEEETGLRAADVFAGAEPAHEPTPERARLARAVHARQHYRLIGWRRGDAELNYRRF
+FTVTTLAGVRVEDPEVFDAVHAEPARWVREGLVQGLRVDHPDGLADPAGYVRRLRSHVLP
+EGYLVVEKILEPGEELPADWDVDGTTGYDALGEVERVFMHPVAAGGPNEDERRRRDWDEV
+VAEAKRDVATGSLVAETARLVREVRGVHALGAHADEDVAAAFAAVLSRLPVYRTYLPVGL
+AVLERALADAGEAEPALAPVLADLGPELADPDSPVARRFQQTSGMVMAKGVEDRSFYRWT
+RWANLNEVGGDPAHVQLSLDAFHAAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAE
+EPDRWAGELAGLRALHPLGDEGAERLLWESIVGVWPTDGTAPSTERILGFLQKASREAAL
+STTWTDQDPEFEGRLEDLARAVTAPDSPARGAVQAVADRIAEPGLVVQLGHKLVQLAAPG
+VPDVYQGTELPVPSLVDPDNRRPVDFHARADLLDRLDAGHVPGLDDADAAKLAVVAAVLR
+ARRDRPELFTRHRRLDVSGPAAEHAVAFDRGGALAVATRWPVHLAAAGGWGETVVTLPPG
+RWEDAVTGRPVHPDARGAVRLDELLSTLPVALLVPARAEEATP
+>PROKKA_02477
+MSHTDAVSAPASTYRLQVGPDLPLDSVAGLVPYLRRLGVDWLYLSPILAADPGSDHGYDV
+VDPARVDPARGGPEALAALAAAAHEAGMRLLVDVVPNHLGVATPLANPAWADLLAHGPEA
+AHAAWFDVDWEAGDGRVLLPVLGDGPEGDPRGAEAGLDQLIVDPSAGEHGVLRHWDTAYP
+LAPGSLAAAEEETGLRAAEVFAGADPAAPTDDAARLGRAVHDRQHYRLVHWRRGDAELNY
+RRFFTVTTLAGLRVEDPEVFDATHVEIGRWVSEGLVHGLRIDHPDGLTDPGAYLRALRER
+VLPEGYLVVEKILEPGEDLPAAWPVDGTTGYDALGELERVFMPADPDGPAADDAARAAWE
+ALIAEAKRDVATGSLAAETARLVREARAAVVLGAHSDEALTEAFADVLASLDVYRTYLPV
+GAERLAAAVARARAAHPEPADVLDDVARVLADPDSPVARRFQQTSGMVMAKGVEDRSFYR
+WTRWANLNEVGGDPAHLDLPLAGFHALQRARQASWPTTMTALTTHDTKRSEDVRARITAL
+AEEPASWEDALARLRTAHPLDAPGLEELVWESIVGVWPTDGTAPEADRLEEFLLKSAREG
+QEHTSWTAQDDAYEGRLRALAADVVAPDSAARAVVQEIADRIAEPGLTVQLGRKLVQLAA
+PGVPDVYQGTEIPFPTLVDPDNRRAVDFEARADLLDRLDAGHAPTLDEPEAAKLLVVSRA
+LRARRDRPELFHGYRPLDVDGPAAAHLIAFSRGGALALATRLPLTLAAAGGWRETVVSLP
+PGRWRCAVTGRAVTPDARGAVRVDDVLSQLPVALLLPEEETA
+>PROKKA_00351
+MSTSTVRSAPASTYRLQVSPDLPLESVAGLVPYLRRLGVDWLYLSPLLEAEPGSDHGYDV
+VDPTRLDAARGGAEGLDMVARAAHEAGMGVLVDIVPNHVGVATPPANPAWWDVLTHGPEA
+AHAAWFDVDWAAGDGSLLIPVLGDGPDGNADAELDRLVVDAEGGRLRYWDNVYPLAPGSL
+EAAETETGLRAAEVFAAADSAKEPTAEQARLARAVHDRQHYRLVGWRRGDAELNYRRFFT
+VTTLAGVRVEEPEVFDAVHAEPARWVREGLVDGLRVDHPDGLADPAGYARRLRSHVLPEG
+YLVVEKILEPGETLPADWPVDGTTGYDALGEVERVFMHPEAAGDAAEDARRRREWDEAVV
+RAKHDVATGPLAAETARLVREVRAVHALGAHPDEDVAAAFAAVLARLPVYRTYLPVGLAV
+LEGALADAAEAEPGLADVLGDLRPELTDPDSPVARRFQQTSGMVMAKGVEDRSFYRYTRW
+ANLNEVGGDPSHVALSLADFHAAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEP
+DRWAAELAELRRLHPLGHPDAERLLWESIVGVWPTDGTTPEEERILGFLQKASREAALAT
+TWTDQDPEFEARLAALAAAVTSPEGPARGVLQAVADRIAEPGLVVQLGHKLVQLAAPGVP
+DVYQGTEVPFPTLVDPDNRRPVDFAARADLLDRLDAGHTPGLDDPAAAKLAVVAGVLRAR
+RDRPELFTGHRPLDVSGPAAEHAIAFDRGGALAVATRWPVRLAAAGGWGQTVVTVPAGRW
+EDAVTGHPVHPDARGAVRLDELLSTLPVALLVPAHAPSDRRERTAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000402.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000402.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9bfc038ca1b268c50dd4469da93ad207778ab677
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000402.fa
@@ -0,0 +1,25 @@
+>PROKKA_00352
+MEFIAPLDPGWEAALAPQAAAFEQVGERLRARRAGGEQVLPAPEHILRAFRQSFADVRVL
+VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLANIHRELHDDLGITPPAHGDLSAWTDQGV
+LLLNRALSVRAGAPGSHRGLGWEQITEAAVRALCARGTPLVGLLWGADARRMAPLLTAAG
+AGVVESPHPSPLSAHRGFFGSRPFSRVNRLLEAAGAAPVDWRLPD
+>PROKKA_00068
+MEFIAPLDPGWEAALAPQAAAFEQVGEALRARRAAGEQVLPAPEHILRAFRQPFADVRVL
+VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLANIHRELHDDLGITPPAHGDLSAWTDQGV
+LLLNRALSVRAGAPGSHRGLGWEQITEAAVRALCARGTPLVGLLWGADARRMAPLLAAAG
+AGVVESPHPSPLSAHRGFFGSRPFSRVNRLLEAAGAAPVDWRLPD
+>PROKKA_02609
+MELIAPLDPGWEAALAPQAAALEQVGAALTQRRAAGEQVLPAPEHILRVFRRPFEDVRVL
+VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLVNIHRELQDDLGIAPPAHGDLSAWADQGV
+MLLNRALTVRAGAPGSHRGLGWEQITEAAVRALCERGTPLVGLLWGADARRMAPLLTQAG
+AGVVESPHPSPLSAHRGFLGSRPFSRVNRLLEEAGAEPVDWRLPD
+>PROKKA_02468
+MDLISPLDPGWAAALADQEEALVRVGAELTARRAAGEHVLPAPEHILRAFRQPFADVKVL
+IVGQDPYPTPGHPIGLCFACDRHVRPLPRSLANIHRELHDDLGVPPAAHGDLSAWTDQGV
+LLLNRVLTVRAGAAGSHRGIGWEQITEAAVRALVARGTPLVGLLWGNDARRLAPLLTAGG
+AGVVESAHPSPLSASRGFFGSRPFSRVNALLEAAGASPVDWRLPD
+>PROKKA_00359
+MEFIAPLDPGWEAALAPQAAAFEQVGERLRARRAAGEQVLPAPEHILRAFRQPFADVRVV
+VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLANIHRELHDDLGIAPPAHGDLSAWTDQGV
+LLLNRALSVRAGAPGSHRGLGWEQITEAAVRALCARGTPLVGLLWGADARRMAPLLTAAG
+AGVVESPHPSPLSAHRGFFGSRPFSRVNRLLEAAGAAPVDWRLPD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000404.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000404.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8229ca6c43881bb5f57cfa1899861af05f588d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000404.fa
@@ -0,0 +1,35 @@
+>PROKKA_00354
+MAYQPDRFDEVPEYTDQRGAHRESFAVAGATATGGGRRLSPLLWVAGLVLLAGLFVGVVL
+PWLTGDRSEPVAAESSTTAPAAAPSTSASSVSSSASSASASTASATESATPSEDAVEASR
+SAAAAESSRAAQEAAAAEAAESSQAAASSRAAAEAQAAEASRSEAAAQSAEASRAAAEAQ
+AAEASRSEAAAQSAEASRSAAAVQAAESSRAAASRSAAAAEASRSQSAAASSSRAAAQSA
+AASSSRAAAQSAAVRGTHVTVYNATRTQGLAASYAQRLTGAGYTSVDAKNWSGYGIQSST
+VLYNGSANKAAAEAVGKELGFPVMQTPNLQVNGIAVVVTS
+>PROKKA_00070
+MAYQPDRFDEVPEYTDQRGAHRESFAAAGATAAGGGRRLSPLLWVAGLVLLAGLFVGVVL
+PWLTGDRSEPVAAESSTTAPAVEPSPSTSTSASSESSSASSASASTASATESATPSEDTA
+EASRSAAAAAAESSRVAQEAAAAEAAESSRAAESSRAAAEAAESSRAAAEAQAAEASRSE
+AAAQSAEASRSAAAVQAAESSRAAASRSAAAAEASRSQSAAASSSRAAAQSAAASSSRAA
+AQSAAVRGTHVTVYNATRSQGLAASYAQRLTSAGYTSVDAKNWSGYGIQSSTVLYNGSAN
+KAAAEAVGKELGFPVMQTPNLQVNGVAVVVTG
+>PROKKA_02607
+MAYQPDRFDEVPEYTDQRGAHRASFAAPAGAAAAGGGARRFSPLLLVAGLVLLAGLFVGV
+VLPWLTGDRSEPVAAESSASSPAADPSTSSEPASPTEGAATTEPASPSEDAAAAEASRSQ
+AAAQSAAEQSAAEAAAASSRAAEEAAAAEASRSAEAAQAAEASRSAAAAAEASRSAGAAQ
+AAEASRSAEAAQAAEASRSAAAAAEASRSAEAAQAAEASRSAAAAAEASRSAEAAQAAEA
+SRSAAAQAAEASRSAAAQAAAAARSTNVTVYNATRTTGLAASYAQRLRSAGFTSVSAQNW
+GGYGIQSSTVLYNGSGNQAAAEAVAAELGFPVLQTPNLQVNGVAVVVTG
+>PROKKA_02466
+MAYPADRFDDVPEYTDQSGAHRESFAAAPAAAGAAGATAAGTEAAAGGGILKWLLAAAAA
+VLLVGLFLGLVLPRLNGGDDKPVAGAASSSSSSEPAADASSSSSDAPSSDASSSAGPDSA
+APAAPSSDAGAESAAAPSSDAAVESRAAAESSQAAAESSQAAADAQRSRDDAARAASESA
+QAAADASSADAAARERAASESAQAAADASRAAEASRSAEASRSAEASRSAEASRSAEASR
+SAEASRSAAASRSAAAQESADRAVKSTPVNVYNATRRNGLAASYADRLTGAGYTRVTADN
+WPGFRVTSNTVMYNGADKRAAAEAVGRELGMPVQQVPNLQVPGIAVVVVR
+>PROKKA_00361
+MAYQPDRFDEVPEYTDQRGAHRESFAAAGATAAGGGRRLSPLLWVAGLVLLAGLFVGVVL
+PWLTGDRSEPVAAESSTTAPAVEPSTSASSESSSASSASASTASATESATPSEDTAEASR
+SAAAAAAESSRVAQEAAAAEAAESSQAAASSRAAAEAQAAEASRSEAAAQSAEASRSAAA
+VQAAESSRAAASRSAAAAEASRSQSAAASSSRAAAQSAAASSSRAAAQSAAVRGTHVTVY
+NATRTQGLAASYAQRLTGAGYTSVDAKNWSGYGIQSSTVLYNGSANKAAAEAVGKELGFP
+VMQTPNLQVNGIAVVVTS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000407.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000407.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b8d6605a61846f910a45566244dd12d4afd9f346
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000407.fa
@@ -0,0 +1,59 @@
+>PROKKA_00358
+MRARLDAAAARVRHPRAWLRGAWQGQSLRTKLVVMIAALMLALVAVTAVATAVLFRQEAV
+RQLDEDMAANRDTVSMYLANVAQTGEYYMPQLPILRFYGVVWDNEGARVVQTPVMPGADE
+PALPDITPAEALERGSASFEVPGTQPDSSGWRVQLYGLSSGDGTMAVALPLQSVTSSVER
+VTSIVVTIGLLATAGTVIVANLAVQRAFRTLNRVERTAAKIAAGDLSQRVESAAPDTEVG
+RLSRSLNAMLAHIESAFRDKEISEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGLREE
+EDVAAAMQRIESEATRMTRLVEDLLTLARLDEQRPLEHAPVDLLILAMDSMMDASVNAPD
+RKVTLVGPDGDRAAPAPILGDENRMRQVVVNLMANALRYTPAGTPIEIAVGTVDHLGGQA
+GADGAGRSSVIEIRDHGPGVSEEDRARIFERFYRADTSRHRETGGTGLGLAIVAAIVAQH
+GGSVRLLETEGGGATFSVHLPWAPFEDEADEDVEDERLPARDTDDDAAGPPTGPLALAAP
+SGAGASAADAARSSRLLRAAERFRRASAERRRRASAPAQAPQADPPSPGEDDPAAERDAR
+P
+>PROKKA_00074
+MRARLDAAAAHVRHPRAWLRGTWQGQSLRTKLVVMIAALMLALVAVTALATAALFRQEAV
+RQLDEDMAANRDTVSMYLANVAQTGEYYMPQLPILRFYGVVWDNEGARVVQTPVMPGADE
+PALPDITPAEALERGSASFEVPGTQPDSSGWRVQLYGLSSGDGTMAVALPLQSVTSSVER
+VTSIVVTIGLLATAGTVIVANLAVQRAFRTLNRVERTAAKIAAGDLSQRVESAAPDTEVG
+RLSRSLNAMLAHIESAFRDKEISEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGLREE
+EDVAAAMQRIESEATRMTRLVEDLLTLARLDEQRPLEHAPVDLLILAMDSMMDASVNAPD
+RKVTLVGPDGDRAAPAPILGDENRMRQVVVNLMANALRYTPAGTPIEIAVGTVDHLGGQA
+GADGAGRSSVIEIRDHGPGVSEEDRARIFERFYRADTSRHRETGGTGLGLAIVAAIVAQH
+GGSVRLLETEGGGATFSVHLPWAPFEDEADEDVEDERPSARDTDDDAAGPPTGPLAQTAP
+SGAGASAADAARRSRLLRAAERFRRASAERRRRVSAPAQAPQADAPSPGGDDPAAGRDAR
+P
+>PROKKA_02603
+MSGRLDAAAARARLPRAWLSSAWRGQSLRTKLVMMITVLMLALVAVTAIATAALFRQEAV
+RQLDEDMAANRDTVSMYLANVAQTGEYYMPQLPILRYYGVVWDNDGDRVVQTPVVPGSDE
+PDLPSITPERALEIGSASFEVAGTQDESSRWRVQLYGLSSGDGTMAVALPLEGVRSSVER
+VTSLVVTIGLLGTAGTVIVANLAVQRAFRALNRVERTAAKIAAGDLTQRVESAAPDTEVG
+RLSRSLNAMLAHIESAFRDKEVSEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGLREE
+EDVAAAMQRIESEATRMTRLVEDLLTLARLDEQRPLELAPVDLLILAMDSMMDASVNAPD
+RKVTLVGLDGGRAGSAPIVGDENRMRQVVVNLMANALRYTPAGTPIEIAVGTVDPLGGPG
+AAGDGEGRTSVIEIRDHGLGVSEEDAARIFERFYRADTSRHRETGGTGLGLAIVAAIVAQ
+HGGSVRLLETEGGGATFSVHLPWAPFEDDDDLEDEDDAGPVSESENAAEVSHTGPLGLVA
+PSGAGASVVDAARRSRLLRAGERFRRASAERRPRAGTPAQAPAEGAASPGEEEPGPAAPD
+RP
+>PROKKA_02462
+MGPRLGVAAARLRHPRTWLWGWWGARPLRTKLVVMITALMMVLVAVIALVTAVLFRTELL
+RQLDDDLSHNRDEVSIYLTTMSQTGGYYTPQQSILRFYGVVWDTSGRAVVSTPLMPGADG
+PALEGMTPEQVDAQGSASFEVPGTTAGSDGWRVQLYHLRSGEGSLAIALPLHGVRTSVER
+VVTLVVTIGLLGTAVSVVASNLLVERAFRALNRVERTAAKIAAGDLSQRVAYAPPSTEVG
+RLSRSLNAMLAHIETAFRDKEASEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGITRE
+EDVAAAMGRIESEAGRMHRLVEDLLTLARLDEQRPLEHEPVDLLVLGMDSMMDASVNAPD
+RKVSLVGLDGGPAGSAPLMGDENRMRQVVVNLMTNALRYTPEGTPIEIAVGTRDAFGGDS
+GVDGTRHSVIEIRDHGAGVSEEDAARIFERFYRADASRHRETGGTGLGLAIVAAIVAQHG
+GSVRLLETEGGGATFSVHLPWAALEDDADDDLDLEDDDARPGAGVPAGRPPTGGSTAAGS
+AGALETGQRRRLAWAGERFRRASAARRQAQAGTSPAQAARDGA
+>PROKKA_00365
+MRARLDAAAARVRHPRAWLRGAWQGQSLRTKLVVMIAALMLALVAVTAVATAVLFRQEAV
+RQLDEDMAANRDTVSMYLANVAQTGEYYMPQLPILRFYGVVWDNEGARVVQTPVMPGADE
+PALPDITPAEALERGSASFEVPGTQPDSSGWRVQLYGLSSGDGTMAVALPLQSVTSSVER
+VTSIVVTIGLLATAGTVIVANLAVQRAFRTLNRVERTAAKIAAGDLSQRVESAAPDTEVG
+RLSRSLNAMLAHIESAFRDKEISEDKMRRFVQDASHELRTPLVTIRGFSELYRHGGLREE
+EDVAAAMQRIESEATRMTRLVEDLLTLARLDEQRPLEHAPVDLLILAMDSMMDASVNAPD
+RKVTLVGPDGDRAAPAPILGDENRMRQVVVNLMANALRYTPAGTPIEIAVGTVDHLGGQA
+GADGAGRSSVIEIRDHGPGVSEEDRARIFERFYRADTSRHRETGGTGLGLAIVAAIVAQH
+GGSVRLLETEGGGATFSVHLPWAPFEDEADEDVEDERPSARDTDDDAAGPPTGPLAQTAP
+SGAGASAADAARRSRLLRAAERFRRASAERRRRVSAPAQAPQADAPSPGGDDPAAGRDAR
+P
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000408.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000408.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5373bade36824078173626147cc5ac09a09228d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000408.fa
@@ -0,0 +1,14 @@
+>PROKKA_00360
+MTSQDSPTRVAGMPRTSTLPAPAPADHRGGRGVVLVLGVAVTAVSALALVALLVAYFLAW
+PASPALFALALFGLPVGFGLMLLHVVLGAVRRSRP
+>PROKKA_00076
+MTSQDSPTRVAGMPRTSTLPASAPAADPADHRGGRGVVLVLGVAVTAVSALALVALLVAY
+FLAWPASPALFALALFGLPVGFGLMLLHVVLGAVRRSRP
+>PROKKA_02601
+MLGVTVTAVSFVALLGLLAAYFFSWPAVPALYALAMFGLPVGFSLMLLHVVLGAVRRSRL
+>PROKKA_02460
+MPSPRTSPQPRPDAAPAPSGARRALRVLLTAGVVLTVVSGLGLLGALAAYFLHATPAFLP
+ALYAVSLFGLPLGFTLMVLHVVLSAVLRARS
+>PROKKA_00367
+MTSQDSPTRVAGMPRTSTLPASAPAADPADHRGGRGVVLVLGVAVTAVSALALVALLVAY
+FLAWPASPALFALALFGLPVGFGLMLLHVVLGAVRRSRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000413.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000413.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa4d5cf879ac244af9a1b5736da4ad558664e47f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000413.fa
@@ -0,0 +1,20 @@
+>PROKKA_00365
+MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR
+VPHTDAAPVSRKGVLRRDGHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNGAK
+ADRSLEALGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA
+>PROKKA_00081
+MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR
+VPHTDAAPVSRKGVLRRDGHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNGAK
+ADRSLEALGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA
+>PROKKA_02596
+MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR
+VPHTDAAPVSRKGVLRRDAHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNALK
+ADRSLESMGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA
+>PROKKA_02455
+MRTLVLNAGYEPVSVVSDRRALLLVATGKASVLEDGDAPMHSPTRAWGRPLVILLHQYVR
+VPHADAAAVSRKGVLRRDGHRCAYCGAHATTVDHVHPRSRGGQNTWENLVACCLRCNSAK
+ADRSLDALGWRLRVVPTRPCGVQWRLRELERPAPAWEGWLQFAA
+>PROKKA_00372
+MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR
+VPHTDAAPVSRKGVLRRDGHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNGAK
+ADRSLEALGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000422.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000422.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5be29f32a1c4ac51ec265a6a766eacf48702a13
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000422.fa
@@ -0,0 +1,20 @@
+>PROKKA_00380
+MDAAETPDGPETAAHDGGRPAWQHRLLAGGEEPDPRFTLANERTFLAWVRTALALLAGGV
+AVEAFTGALFAPPVRVVLSTVLLVLAALLALGAGARWLRVERAMRRGRPLPLPLIVPVLA
+GGVVLAVVVLLAAVVLPRG
+>PROKKA_00104
+MDAAETPDGPETAAHDGGRPAWQHRLLAGGEEPDPRFTLANERTFLAWVRTALALLAGGV
+AVEAFTGALFAPPVRVVLSTVLLVLAALLALGAGARWLRVERAMRRGRPLPLPLIVPVLA
+GGVVLAVVVLMLAVVLPRG
+>PROKKA_02575
+MDAAETPEGPEATAYDGGRPAWQHRLLAGGDEPDPRFTLANERTFLAWVRTALALLAGGV
+AVEAFTGALFAPPVRVALSTVLLVLAALLAVGAGARWLRVERAMRRGRPLPLPLIVPVLA
+GGVVLAVVVLMLAVVLPRG
+>PROKKA_02447
+MDAAETPDGPEAAAYDGGRPAWQHRLLAGGDEPDPRFTLANERTFLAWVRTALALLAGGV
+AVEAFTGALFAPPVRVALSTVLLVLAALLALGAGARWLRVERAMRRGRPLPLPLIVPVLA
+GGVVLAVVVLMLAVVLPRG
+>PROKKA_00386
+MDAAETPDGPETAAHDGGRPAWQHRLLAGGEEPDPRFTLANERTFLAWVRTALALLAGGV
+AVEAFTGALFAPPVRVVLSTVLLVLAALLALGAGARWLRVERAMRRGRPLPLPLIVPVLA
+GGVVLAVVVLLAAVVLPRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000423.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000423.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a94fd1a5f77462d9aafc442331b1d2a5acb34877
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000423.fa
@@ -0,0 +1,15 @@
+>PROKKA_00381
+MRLHHDPGLQPERTVMSWGRTALALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT
+QRRRYVAHADGIAREQARPALASVACMVALVVGLAALGITATLLHAA
+>PROKKA_00105
+MRLHHDPGLQPERTVMSWGRTVLALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT
+QRRRYVAHADGIARERARPALASVACMVALVVGLAALGITATLLHAA
+>PROKKA_02574
+MRLHHDPGLQPERTVMSWGRTVLALGVLSLMFLRWWPAVGAWAFGPAVVAAVGGAAVLAT
+QRRRYVAQSRGIAGEWARPALASVAGMVALVVGLAALGITATLLHAA
+>PROKKA_02446
+MRLHHDPGLQPERTVMSWGRTVLALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT
+QRRRYVAQADGIAREQARPALASVACMVALVVGLAVLGITATLLHAA
+>PROKKA_00387
+MRLHHDPGLQPERTVMSWGRTVLALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT
+QRRRYVAHADGIAREQARPALASVACMVALVVGLAALGITATLLHAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000424.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000424.fa
new file mode 100644
index 0000000000000000000000000000000000000000..edd13c3c349da5015f4175268d137d81fa29086e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000424.fa
@@ -0,0 +1,40 @@
+>PROKKA_00382
+MTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHGVILKIVATNICGSDLHIYRGSFP
+APEGMVLGHEMTGQVLEVGSDVQFLQEGDLVSVPFNVACGRCRNCRAGRTEICETANPDQ
+ACAAYGFNLGGFQGGQAEYLFVPYADFQLLRFPDQEQAMEKILDLTVLSDILPTAFHGLV
+EAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVGDQDASRLELVRKHGCETIDLSTT
+ENLQDAVSDILGEPMVDCAVDCVGSEAHGLGSASDEMQPIAAVNQVLDITRPGGATGIIG
+IYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQAPVMRYNRQLMMSILWDRMPYLTE
+MVNPRVISLDEAPQAYAEFDQGSLEKFVIDPHGMIAR
+>PROKKA_00106
+MTTENRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHGVILKIVATNICGSDLHIYRGSFP
+APEGMVLGHEMTGQVLEVGSDVQFLQEGDLVSVPFNVACGRCRNCRAGRTEVCETTNPEQ
+ACAAYGFNLGGFQGGQAEYLFVPYADFQLLRFPDQEQAMEKILDLAVLSDILPTAFHGLM
+EAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVGDQDASRLELVRKHGCETIDLSTT
+ENLQDAVNDILGEPMVDCAVDCVGSEAHGLGSASDEMQPIAAVNQVLDVTRPGGATGIIG
+IYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQAPIMRYNRQLMMSILWDRMPYLTE
+LVNPRVITLDEAPQAYAEFDQGSVEKFVIDPHGMIAR
+>PROKKA_02573
+MSPRGRSGSRLTQASLETEGNSFMTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHG
+VILKIVATNICGSDLHIYRGSFPVPEGMVLGHEMTGQVLEVGSDVQFLKEGDLVSVPFNV
+ACGRCRNCRAGRTEVCETANPEQACAAYGFNLGNFQGGQAEYLFVPYADFQLLRFPDQEQ
+AMEKILDLAVLSDILPTAFHGLMAAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVG
+DQDASRLELVRKHGCETIDLSVTENLQDAVNDILGEPMVDCAVDYVGSEAHGLGSESDEM
+QPIAAVNQVLDITRPGGATGIIGIYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQA
+PIMRYNRQLMMSILWDRMPYLTEMVNPRVISLDEAPQAYAEFDQGSVDKFIIDPHGMIAR
+>PROKKA_02445
+MTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHGVILKIVATNICGSDLHIYRGSFP
+VPEGMVLGHEMTGQVLEVGSDVQFLKEGDLVSVPFNVACGRCRNCRAGHTEICETANPEQ
+ACAAYGFNLGNFQGGQAEYLFVPYADFQLLRFPDQEQAMEKILDLAVLSDILPTAFHGLM
+AAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVGDQDASRLELVRKHGCETIDLSVT
+ENLQDAVNDILGEPMVDCAVDYVGSEAHGLGSESDEMQPIAAVNQVLDITRPGGATGIIG
+IYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQAPIMRYNRQLMMSILWDRMPYLTE
+MVNPRVISLDEAPQAYAEFDQGSVDKFIIDPHGMIAR
+>PROKKA_00388
+MTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHGVILKIVATNICGSDLHIYRGSFP
+APEGMVLGHEMTGQVLEVGSDVQFLQEGDLVSVPFNVACGRCRNCRAGRTEICETANPEQ
+ACAAYGFNLGGFQGGQAEYLFVPYADFQLLRFPGQEQAMEKILDLAVLSDILPTAFHGLM
+EAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVGDQDASRLELVRKHGCETIDLSVT
+ENLQDAVNDILGEPMVDCAVDCVGSEAHGLGSASDEMQPIAAVNQVLDITRPGGATGIIG
+IYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQAPIMRYNRQLMMSILWDRMPYLTE
+MVNPRVISLDEAPQAYAEFDQGSLEKFVIDPHGMIAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000434.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000434.fa
new file mode 100644
index 0000000000000000000000000000000000000000..32f890a3df61a0c7e3b509bc7ab672b30f869c50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000434.fa
@@ -0,0 +1,40 @@
+>PROKKA_00396
+MRVVVVAESFLPHMNGVTNSILQVLRHLRERGDEAMVVAPAASWSAGWTQRAGAGEAPRE
+VEGFPVRTLPSVPLTGYTSVRVAAGTVGRLRGMLADFAPDVVHIASPFVLGWRAVQAAEE
+LGIPSVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNMATLTLAPSSFTVRQLHRQGVR
+RVHLWGRGVDSRRFHPAKRDEALRAELAPNGEKLVGFVGRLAHEKQVGDLRVLSDLPGTR
+LVVIGSGPLREQLERELPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS
+GVPVVAVGRGGPLDIVDASRTGWLYPPGELDELRRHVADLVYDDVKRAAFADAAWASVQG
+RTWPVLCEQLMGYYEKAIAVQERRRVELARRLLTAPALLAARVFG
+>PROKKA_00120
+MRVVVVAESFLPHMNGVTNSLLQVLRHLRERGDEAMVVAPAASWSAGWTQRAGAGEAPRE
+VEGFPVRTLPSVPLTGYTSVRVAAGTVGRLRGMLADFAPDVVHIASPFVLGWRAVQAAEE
+LGIPSVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNMATLTLAPSSFTVRQLHRQGVR
+RVHLWGRGVDSRRFHPAKRDEALRAELAPNGEKLVGFVGRLAHEKQVGDLRVLSDLPGTR
+LVVIGSGPLREQLERELPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS
+GVPVVAVGRGGPLDIVDASRTGWLYPPGELDELRRHVADLVYDDVKRAAFADAAWASVQG
+RTWPVLCEQLMGYYEKAIAVQERRRVELARRLLTAPALLAARVFG
+>PROKKA_02561
+MVAESFLPHMNGVTHSILQVLRHLRERGDEAIVIAPAASWSAGWTQRAGEGQAPREVEGF
+PVHALPSVPLSGYSSVRVAAGTVGRLRGILTAFGPDVVHIASPFVLGWRAVQAAEELGIP
+SVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNTATLTLAPSSFTVRQLHAAGLRRVHL
+WGRGVDTRRFHPVKRDDALRAELAPHGERLIGFVGRLAHEKQVEDLRVLSDLPGTRLVVI
+GSGPLREQLERRLPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMASGVPV
+VAVGRGGPLDIVDPSRTGWLYPPGELDELRRHVADLAHDDVKRSAFAQAAWASVQGRTWP
+VLCEQLVGCYEKAVAVQDRRRRELARRLLAMPSQLTARVFG
+>PROKKA_02432
+MRVAVIAESFLPHMNGVTNSILQVLKHLRSRGDEAVVIAPAASWSAGWTQRAGAGQAPSE
+VEGFPVITLPSMPLSGYASVRVAAGTVLRLRSLLADFAPDVVHIASPFVLGWRAVQAAEE
+LGIPSVAVYQTEVPRYAAKYGAPWLEDVLWNHVTRLHNTATLTLAPSSFTLRQLHHVGVR
+RVHLWGRGVDSTRFHPAKRDEALRAELAPNGERLIGFVGRLAHEKQVADLRVLADLPDTR
+LVIIGSGPLRDQLERRLPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS
+GVPVVAVGRGGPLDIVDSSRTGWIYQPGDLGELRARVADLAYDDAKRAAFAEAAWASMQG
+RTWPVLCEQLVGYYEKAIHVQRRRRGELSRRLLGAPGAVASRAYRVFG
+>PROKKA_00402
+MRVVVVAESFLPHMNGVTNSILQVLRHLRERGDEAMVVAPAASWSAGWTQRAGAGEAPRE
+VEGFPVRTLPSVPLTGYTSVRVAAGTVGRLRGMLADFAPDVVHIASPFVLGWRAVQAAEE
+LGIPSVAVYQTEVPGYAARYGAPWLEDVLWSHVARLHNMATLTLAPSSFTVRQLHRQGVR
+RVHLWGRGVDSRRFHPAKRDEALRAELAPNGEKLVGFVGRLAHEKQVGDLRVLSDLPGTR
+LVVIGSGPLREQLERELPGAHFAGFQGGEDLARHVASLDLFVHPGESDTFGQTLQEAMAS
+GVPVVAVGRGGPLDIVDASRTGWLYPPGELDELRRHVADLVYDDVKRAAFADAAWASVQG
+RTWPVLCEQLVGYYEKAIAVQERRRVELARRLLTAPSLLAARVFG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000438.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000438.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e11a7fb7d5ab8f4b082d899b125a4ab84be575c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000438.fa
@@ -0,0 +1,45 @@
+>PROKKA_00400
+MSSATPPRPSADGAHPGPAPDVVAPDAALPTGEAVVQELPWRWSVQGRIFLIGGLGFMFD
+AWDVTLNGVMIPLLREEWALDKADAAWIGTANLIGMAVGAFLWGTIADRIGRKAAFAWTL
+AIFSVFTIAGALTDSLLWFALFRFVAGMGLGGTIPVDYALVGEFTPRRLRGRVLAAMDGW
+WPVGAALCGLVSAWLVGTWGDWRLPLLAMVLPALLVFVVRLGIPESPLFLMSRGREAQAR
+AVIDRMVAATGAPRRPYTMPPAEPARSSGVGAQLAAVWRFSPRITAVAWALFVAIMLVYY
+IALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATALIEVTGRRWLLAVSAVVASA
+LTVWLASVLDVPAAVLPLVLTFGFVVQVAIPVLYTYVSELYPTTLRASGFGWASAASRVG
+AGLGPLLFVGTLVPALGLPGAFAVTGGLVVLACAAMLALAPETRGRALEVSAD
+>PROKKA_00124
+MSSATPPRPSADGAHPGPTPDVVSPDAALPTGEAVVQELPWRWSVQGRIFLIGGLGFMFD
+AWDVTLNGVMIPLLREEWALDKADAAWIGTANLIGMAVGAFLWGTIADRIGRKAAFAWTL
+AIFSVFTIAGALTDSLLWFALFRFVAGVGLGGTIPVDYALVGEFTPRRLRGRVLAAMDGW
+WPVGAALCGLVSAWLVGTWGDWRLPLLAMVLPALLVFVVRLGIPESPLFLMSRGREAQAR
+AVIDRMVAATGAPRRPYTMPPAEPARSGGVGAQLAAVWRFSPRITAVAWALFVAIMLVYY
+IALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATALIEVTGRRWLLAVSAVVASA
+LTVWLASVLDVPAAVLPLVLAFGFVVQVAIPVLYTYVSELYPTTLRASGFGWASAASRVG
+AGLGPLLFVGTLVPALGLPGAFAVTGGLVVLACAAMLALAPETRGRALEVSAD
+>PROKKA_02557
+MQGRIFLIGGLGFMFDAWDVALNGVMIPLLREEWALAPADAAWIGTANLIGMAVGAFLWG
+TIADRIGRKAAFAWTLAIFSVFTLAGALTDSLLWFAVFRFVAGVGLGGTIPVDYALVGEF
+TPRRLRGRVLAAMDGWWPVGAALCGLVSAWLVGTWGDWRLPLLAMVLPALLVFVVRLGIP
+ESPLFLMSRGREAEARKVIDRMVEATGAERREYVMPPVEQERAGGVLAQLAAVWRFSPRI
+TAVTWALFVAIMVVYYIALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATVLIEV
+TGRRWLLGVSAVVASALLVWLASVLGVPSAVLPLVLAFGFVVQIAIPVLYTYVSELYPTT
+LRASGFGWASAASRVGAGLGPLFFVGTLVPAMGLPAAFAVTGGLVLLACVAMLALAPETR
+GRALEVSAD
+>PROKKA_02427
+MPPTGSHAASAAPTGEQVVQELPWRWPVQGRIFLIGGLGFMFDAWDVTLNGVMIPLLTEE
+WGLSKADAAWIGTANLIGMAVGAFLWGTVADQIGRKAAFTWTLLIFSVFTLAGALTDSLL
+WFAVFRFMAGIGLGGTVPVDYALVGEFTPRRLRGHVLTAMDGWWPIGAALCGVVSAWLVG
+TWSDWRLPLLAMVLPALLVFLVRLGIPESPLYLMSRGREREARAVIDRMVERTGAEPRPY
+VMPAADSRAHGGLLAQLAAVWRFSPRITATAWLLFVAVMLIYYIALQWLPTFLIEAGFAQ
+SRAFITTSGMAAAGLVGVAVSAVLVEATGRRRLLAVSGVVASGLLVWLASVLGVPGAALP
+LVLAYGFVIQIAVPVLYTYVSELYPTTLRASGFGWASAASRVGAGLGPLFFVGTLVPALG
+LPGAFGVTAGLVVVAVLVMFAWAPETRGRALEVAED
+>PROKKA_00406
+MSSATPPHPSADGAHPGPTSDVVAPDATLPTGEAVVQELPWRWSVQGRIFLIGGLGFMFD
+AWDVTLNGVMIPLLREEWALDKADAAWIGTANLIGMAVGAFLWGTIADRIGRKAAFAWTL
+AIFSVFTIAGALTDSLLWFALFRFVAGMGLGGTIPVDYALVGEFTPRRLRGRVLAAMDGW
+WPVGAALCGLVSAWLVGTWGDWRLPLMAMVLPALLVFVVRLGIPESPLFLMSRGRETQAR
+AVIDRMVAATGAPRRPYTMPPAEPARSGGVGAQLAAVWRFSPRITAVAWALFVAIMLVYY
+IALQWLPTFLIDAGYAEGRAFIMTSGMAAAGLLGVVVATALIEVTGRRWLLAVSAVVASA
+LTVWLASVLDVPAAVLPLVLTFGFVVQVAIPVLYTYVSELYPTTLRASGFGWASAASRVG
+AGLGPLLFVGTLVPALGLPGAFAVTGGLVVLACAAMLALAPETRGRALEVSAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000444.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000444.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac293a5ff28a2fee7d3fe2258f9eb2534043618d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000444.fa
@@ -0,0 +1,81 @@
+>PROKKA_00410
+MVPMPTPVDPVTVPSALSAALGRLSAGLTFAAALPDLEAALDARGAAVVEAPPGTGKTTV
+VPPALAVRLADHGGGRVLVTQPRRVAVRAAWRRLRTAVLAAAADSHPGADPDARARLADA
+AVGYAVRGDAVGGGASAVEFVTPGLLLRRLLADPGLDGVGAVVLDEVHERDLDTDVLFAL
+LADLRQLRPELALVAMSATVDAAALAARWARGMGEAPLPVVSTPAVLHPLREEHAPFRGH
+RLTAEGRVDRAFLDHVAATAARAHAKALEADPTVDALVFLPGVAEVETVAGRVAALAPDT
+EVRVLHGRQEPADQDAALAGRTDPAVPRVVVATAVAESSLTVPGVRLVVDSGLAREPRRD
+RGRGMAGLVTVQASRAAAGQRAGRAARLGPGTVVRCHTAAALGTAPAAPTPALAVVDLAP
+VALAFAAWGAPGGRGLTLPEDPPADAMAAAERTLASLGAVDADGRITPHGAVLAELPLDP
+PLGHALLRAAPLTGPRPAAEATAALALDLRAPGADLEALVAALRDGRHPEAGRWHREADR
+LERLARRHAHHAPETREPDEPGPEAATAPRHSAGLVAALAFPAWIARRAGEEGAYLLASG
+TRAALPRDAVGGLAGQEWLAVAEVARVAGDAAGTGAAIRAAAPIDRSLVERAGAGLRRTE
+DTAEWRGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRDALAADGLARFDPRGRAERL
+RRRVHLLHRVLGAPWPDLSDTALPDLDTLVDGLAADLAAGRPLARLDAEALLRGALPWPE
+AGRLDELAPERLPVPSGRAVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREPVVL
+HLLSPAGRPLAVTADLPSFWAGPYAQVRAENRGRYPKHPWPEDPAVAEPTARTNRRAL
+>PROKKA_00130
+MDPMPTPVDPVAVPSALSTALGRLSAGLTFAAALPELGSALDARGAAVVEAPPGTGKTTV
+VPPALAVRLADHGGGRVLVTQPRRVAVRAAWRRLRTAVLAAAADAQPGADPDARARLADA
+AVGYAVRGDAAGGGASAVEFVTPGLLLRRLLADPGLDGVDAVVLDEVHERDLDTDVLFAL
+LADLRQLRPELALVAMSATVDAAALAARWARGMGEAPLPVVSTPAVLHPLREEHAPFRGH
+RLTAEGRVDRAFLDHVAATAARAHAEALEADPTVDALVFLPGVAEVEAVAGRVAALAPDT
+EVRVLHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRRD
+RGRGMAGLVTVQASRAAAGQRAGRAARLGPGTVVRCHTAAALGTAPAAPTPALAVVDLAP
+VALAFTAWGAPGGRGLTLPEDPPADAMAAAERTLASLDAVDADGRITPHGAVLAELPLDP
+PLGHALLRAALWTGPRPAAEATAALALDLRAPGADLEALVASVRDGRHPEAGRWRREADR
+LERLARRHAHHSLETRAPGEPGPEATAAARRHPAGLVAALAFPAWIARRAGEAGAYLLAS
+GTRAALPRDAAGGGLAGQEWLAVAEVARVAGDAAGTGAAIRATAPIDRTLAELAGAGLRR
+TEDTADWRGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRAALAADGLARFDPSGRTE
+RLRRRVHLLHRVLGAPWPDLSDAALPGLDALVDGLAADLAAGRSLARLDAEALLRGALPW
+PEAGRLDELAPERLPVPSGRAVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREPV
+VLHLLSPAGRPLAVTADLPSFWAGPYAQVRAENRGRYPKHPWPEDPAAAEPTARTNRRAR
+>PROKKA_02549
+MPAPSPHSSRPASVDTAVAPALSAALERLGSGLTFVAALPDLEAALDARGAAVVEAPPGT
+GKTTVVPPALAVRLADHGGGRVLVTQPRRVAVRAAWRRLRSAVLDAADRTSAPDALADAA
+VGYAVRGDAVGGGASAVEFVTPGLLLRRLLADPGLDGVDAVVLDEVHERDLDTDVLFALL
+ADLRQLRPELALVAMSATVDAAALAARWARGMGEEAPLPVVSTPAVLHPLREEHAPFRGR
+RLTAEGRVDRAFLDHVAATAARAHAAALDADPTVDALVFVPGVAEVEAVAGRVAARAPDT
+EVRVLHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRRD
+RGRGMAGLVTVQASRAAAGQRAGRAARLGPGTVVRCHTAAALGAAPAAPTPALAVVDLAP
+VALAFAAWGAPGGRGLTLPKDPPADAMAAAERTLASLGAVDTDGRITPHGAVLAELPLDP
+PLGHALLRAAPLTGPRPAAEATAALALDLRASGADLEALVAALRDGRHPESRRWRREADR
+LERLARRHAHRAPETREPDGPGPEAATARRHPAGLVAALASPAWIARRAGEAGAYLLASG
+TRAALPRNAVVGGLAGQEWLAVAEVARAAGDAAGTGAAIRAAAPIDRPLAELAGAGLRRT
+EDTADWRGDRLTGRRVDRMGALVLAETPAPVAPDAAAQAVRAALAADGLARFDPSGRAER
+LRRRVHLLHRVLGAPWPDLSDTALPGLDALVDGLAADLAAGRSLAHVDAEALLRGALPWP
+EAGRLDELAPERLPVPSGRGVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGRELVV
+LHLLSPAGRPLAVTADLPSFWAGPYAQVRAENRGRYPKHPWPEDPAAAEPTARTNRRVR
+>PROKKA_02417
+MSTSSASHSTPDLRAALAAASARLGADLAFSASLPALEAALDARAGAVVHAPPGTGKTTA
+VPPAVALWLARRAESGGEGGRVLVTQPRRVAVRAAWRRLHGAVADALGPESGPDTGRLPD
+AVVGYAVRGDAVGRGASAVEFVTPGLLLRRLLGDPGLEGVGAVVLDEVHERDLDTDVLFA
+LLADLRQLRPELALTAMSATLDADALAARWATGMGEDPVPVVRTPSVQHPLTVEHAPFGG
+PRTTADGRVDRDFLDHVAATAARAHAEALDADPTVDALVFVPGVAEVEAVAGRVAALAPD
+TEVRVLHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRR
+DRGRGITGLATVQASRAAADQRAGRAARLGPGTAVRCHTAAALGAAPAAPTPALAVADLA
+SVVLAFAVWGAPGGDGLVLPEDPPADAMAAAERTLASLDAVDTDGRITPHGTVLAELPLD
+PPLGHALLRAAPLTGPRSAAEATAALALDLRAPGADLEALVAALRDGRHPEAGRWRREAD
+RLERLARRHAHRAPETREPDEPGPAATATARRHPAGLVAALAFPAWIARRAGEEGAYLLA
+SGTRAALPRDAVGGGLAGQEWLAVAEVARVAGDAAGTGAAIRAAAPIDRPLAELAGAGLR
+RTEDTAEWRGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRVALAADGLARFDPSGRA
+ERLRRRVHLLHRVLGAPWPDLSDATLPGLDALVDGLAADLAAGRSLTRLDAEALLRGALP
+WPEAGRLDELAPERLPVPSGRGVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREP
+VVLHLLSPAGRPLAVTADLPSFWAGPYAQVRAENRGRYPKHPWPEDPAAAEPTDRTNRRA
+R
+>PROKKA_00413
+MPTPVDPVSVPSALSAALGRLSAGLTFAAALPDLEAALDARGAAVVEAPPGTGKTTVVPP
+ALAVRLADHGGGRVLVTQPRRVAVRAAWRRLRTAVLAAAADAQPGADPDAQARLGDAAVG
+YAVRGDAAGGGASAVEFVTPGLLLRRLLADPGLDGVGAVVLDEVHERDLDTDVLFALLAD
+LRQLRPELALVAMSATVDAAALAARWARGMGEDAPLPVVSTPAVLHPLREEHTPFRGHRL
+TAEGRVDRAFLDHVAATAARAHAEALDADPTVDALVFLPGVAEVEAVAGRVAALAPDTEV
+RVLHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRRDRG
+RGMAGLVTVQASRAAAGQRAGRAARLGPGTVVRCHTAAALGTAPAAPTPALAVVDLAPVA
+LAFAAWGAPGGRGLTLPEDPPADAMAAAERTLASLDAVDADGRITPHGAVLAELPLDPPL
+GHALLRAAPWTGPRPAAEATAALALDLRAPGADLEALVAAVRDGRHPEAGRWRREADRLE
+RLARRHAHHAPGEPGPEAAATVRRHPAGLVAALAFPAWIARRAGEAGAYLLASGTRAALP
+RDAAGGDLTGQEWLAVAEVARVAGDAAGTGAAIRAAAPIDRTLAELAGAGLRRTEDTADW
+RGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRAALAADGLARFDPSGRTERLRRRVH
+LLHRVLGAPWPDLSDAGLPGLDALVDGLAADLAAGRPLTRLDAEALLRGALPWPEAGRLD
+ELAPERLPVPSGRAVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREPVVLHLLSP
+AGRPLAVTADLPSFWAGPYAQVRAENRGRYPKHPWPEDPAAAEPTARTNRRAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000445.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000445.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f5d145edbe5654ee99d72ce94927720ea18245f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000445.fa
@@ -0,0 +1,45 @@
+>PROKKA_00411
+MRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTNPDDGGQAKIAAQCTDAA
+NGRYRVETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFVPELAEPGFLAPVPEEMQ
+AYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAAGLDMSQPVTWDQLIEAA
+RSQDKDLAVQGARAESMTVWLNALIEGGGEQIVPNAEAPTDEVTTNLDSEAGRTAARIIS
+TIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATLGSVEEGSLPEDLPEDIG
+WAVYPRTVEGEDAAPPVGGINLGVGAKSEHQDLAWDAISCITTTEHQSQYFVENGNPPAD
+PAAYDAPEVAEKYPMADTIRESLELGAPRPQTPYYNEVSTAIQQRYAPPSGVSESTPAET
+DDFIQEVLRGERLL
+>PROKKA_00131
+MRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTNPDDGGQAKIAAQCTDAA
+NGRYRVETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFVPELAEPGFLAPVPEEMQ
+AYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAAGLDMSQPVTWDQLIEAA
+RSQDKDLAVQGARAESMTVWLNALIEGGGEQIVPNAEAPTDEVTTNLDSEAGRTAARIIS
+TIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATLGSVEEGSLPEDLPEDIG
+WAVYPRTVEGEDAAPPVGGINLGVGAKSEHQDLAWDAISCITTTEHQSQYFVENGNPPAD
+PAAYDAPEVAEKYPMADTIRESLELGAPRPQTPYYNEVSTAIQQRYAPPSGVSESTPAET
+DDFIQEVLRGERLL
+>PROKKA_02548
+MRHDTRARQRRRATLAGAVVAGALILAGCAPAEQTPTLTWYTNPDDGGQAKIAAQCTDAA
+NGRYRIETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFVPELAEPGFLAPVPEEMQ
+AYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAAGLDMSQPVTWDQLIEVA
+RSQDKDLGVQGARAESMTVWLNALIEGGGEQIIPNAEAPTDEVTTNLDSEAGRTAARIIS
+TIGKEGLGSAGLPTQDENASMLLFQGNNGSFMVNWPFVWPATLGSVEEGSLPEDLPEDIG
+WAVYPRTVEDKDAAPPVGGINLGVGEKSEYQDLAWDAISCITTTEHQSQYFVENGNPPAD
+PAAYDAPEVAEKFPMADTIRESLELGAPRPQTPYYNEVSTAIQQRYAPPSGVSESTPAET
+DDFIQEVLRGERLL
+>PROKKA_02416
+MGDDGRHIRLASNEVPLVRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTN
+PDDGGQAKIAAQCTDAANGRYRIETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFV
+PELAEPGFLAPVPEEMQAYAKDNALEGALAAASWKDELVTVPFWANTQLLWYRKSVAEAA
+GLDMSKPVTWDQLIEVARSQDKDLGVQGARAESMTVWLNALIEGGGEQIIPNAEAPTDQV
+TTNLDSEAGRTAARIISTIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATL
+GSVEEGSLPKDLPEDIGWAVYPRTVEDKDAAPPVGGINLGVGAKSEHQDLAWDAISCITT
+TEHQSQYFVENGNPPADPAAYDAPEVAEKFPMADTIRESLELGAPRPQTPYYNEVSTAIQ
+QRYAPPSGVSESTPAETDDFIQEVLRGERLL
+>PROKKA_00414
+MRDDGRHIRLASIEVPLVRHDTRARQRRRATLAGAVAAGALILAGCAPAEQTPTLTWYTN
+PDDGGQAKIAAQCTDAANGRYRVETSMLPTDAASQREQLTRRLAAGDTSMDIMSLDPPFV
+PELAEPGFLAPVPEEMQAYAKDNALEGALAAASWKDEIVTVPFWANTQLLWYRKSVAEAA
+GLDMSQPVTWDQLIEAARSQDKDLAVQGARAESMTVWLNALIEGGGEQIVPNAEAPTDEV
+TTNLDSEAGRTAARIISTIGKEGLGSAGLPTQDENASMLLFQGKNGSFMVNWPFVWPATL
+GSVEEGSLPEDLPEDIGWAVYPRTVEGKDAAPPVGGINLGVGAKSEHQDLAWDAISCITT
+TEHQSQYFVENGNPPADPAAYDAPEVAEKYPMADTIRESLDLGAPRPQTPYYNEVSTAIQ
+QRYAPPSGVTESTPAETDDFIQEVLRGERLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000448.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000448.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6c9518b2a59161d343ec3901092fe3410daf8b68
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000448.fa
@@ -0,0 +1,20 @@
+>PROKKA_00416
+MAHIITVAGATPRIHESVFLAPTAAITGDVEMAERSSAFYGVSARGDSAPIRVGAGTNLQ
+DNVVLHADEGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA
+LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKKNAATYLRLSAAHRDAVAG
+>PROKKA_00136
+MAHIITVAGATPRIHESVFLAPTAAITGDVEMAERSSAFYGVSARGDSAPIRVGAGTNLQ
+DNVVLHADEGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA
+LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKKNAATYLRLSAAHRDAVAG
+>PROKKA_02544
+MAHIITVAGAGPRIHESVFLAPTAAITGDVEMAERSSAFYGVSARGDSAPIRVGERTNLQ
+DNVVLHADKGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA
+LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKVNAATYLELSAAHREATAER
+>PROKKA_02412
+MGHLVTVLGRTPRVDPSAFVARTAVLSGDVELGPRASAFYGVSARGDSAAIRVGEGSNLQ
+DNVVLHADAGFPCTLGAGVSVGHAAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA
+VVLEGTQVPPGSLVAGVPAKVRRGLTEEERASLTVNARTYLDLAAAHRAAEEAEQAGV
+>PROKKA_00419
+MAHIITVAGATPRIHESVFLAPTAAITGDVEMAEHSSAFYGASARGDSAPIRVGAGTNLQ
+DNVVLHADEGFPCTLGAGVSVGHSAVVHGATVEDDCLIGMSATVMNGAVIGAGSLVAAGA
+LVLEGTQVPAGSLVAGVPAKVRRPLTDEEREGLKKNAATYLRLSAAHRDAVAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000450.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000450.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad257debb28fecb8d4fb8bfc32d15d05beb64300
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000450.fa
@@ -0,0 +1,50 @@
+>PROKKA_00419
+MTEYQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERR
+PHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFAL
+RFYSEEGNYDLVGNNTPIFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAH
+QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA
+GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVG
+TLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLP
+VNRPKNAVHNYAFDGQMWYDHTGDRSTYAPNSNGDSWSDETGPVDDGWEADGTLTREAQA
+LRADDDDFGQAGTLVREVFSAQEREDFVETVAGALKGVRQDVQARAFEYWKNVDTAIGQR
+IEDEVKRHEGDGIPGVEAGGEARI
+>PROKKA_00140
+MTEYQKKTPHATGSTRQNGAPAISDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERR
+PHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFAL
+RFYTEEGNYDIVGNNTPIFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAH
+QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA
+GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVG
+TLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLP
+VNRPKNAVHNYAFEGQMWYDHTGDRSTYVPNSNGDSWSDETGPVDDGWEADGTLTREAQA
+LRADDDDFGQAGTLVREVFSDQERDDFVETVSGALKGVRQDVQARAFEYWKNVDATIGQR
+IEDEVKRHEGDGIPGVEAGGEARI
+>PROKKA_02540
+MTENQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLVETHQHFNRMNIPERR
+PHAKGSGAFGEFEVTEDVSKYTKALVFQPGAKTETLLRFSTVAGELGSPDTWRDVRGFAL
+RFYTDEGNLDVVGNNTPVFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNTPESAH
+QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNFSNEEAEAMA
+GKNADYHRQDLFESIAKGDYPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVG
+TLTLNRNPENHFAQIESAAFNPGNMVPGVGLSPDRMLLGRSFAYHDAQLYRVGAHVNQLP
+VNRPKNEVHNYAFDGQMWYDHTGSRSTYAPNSNGDSWSDETGPVDDGWEADGTLTREAQA
+LRKDDDDFGQAGTLVREVFTDAERDAFVETVAGALDGVREDVQARAFQYWKNVDATIGQR
+IEDEVNKGQGDDIPGAAGGGEARI
+>PROKKA_02409
+MTEYQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERR
+PHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFAL
+RFYSEEGNYDIVGNNTPVFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAH
+QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA
+GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISQKDYPRIKVG
+TLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLP
+VNRPKNAVNNYAFDGQMWYDHTGDRSTYAPNSNGDSWSDETGPVDDGWEADGTLTREAQA
+LRADDDDFGQAGTLVREVFSDQERDDFVETVAGALKGVRQDVQARAFEYWKNVDATIGQR
+IEDEVKRHEGDGIPGVEAGGEARI
+>PROKKA_00422
+MTEYQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERR
+PHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFAL
+RFYSEEGNYDLVGNNTPIFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAH
+QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA
+GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVG
+TLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLP
+VNRPKNAVHNYAFDGQMWYDHTGDRSTYAPNSNGDSWSDETGPVDDGWEADGTLTREAQA
+LRADDDDFGQAGTLVREVFSAQEREDFVETVAGALKGVRQDVQARAFEYWKNVDTAIGQR
+IEDEVKRHEGDGIPGVEAGGEARI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000454.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000454.fa
new file mode 100644
index 0000000000000000000000000000000000000000..42fc6131a8cd18d7a3f44ab0014ceaaf93dc11b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000454.fa
@@ -0,0 +1,49 @@
+>PROKKA_00424
+MTPRPPHPADPASGAFTPDQRRILTALLMPLFLALMSVSVVNVALPAIESGLDATSADLQ
+WVLAGYTLTFGTVLVAAGRAGDLWGRKNLFLAGITLYMLGSLLSGLAGDTLLLNAGRLLT
+GLGAGVFNPQVIGFIQSNFHGRARGRAYGLFGTVVGLGVAVGPLLGGLFLGAFGPEWGWR
+STFLMNVPVGLAAVAMGALWLPPPTRVHGLPPAPGPRGIAALDPVGALLLGAGGVSLMVP
+FIVPGTAWLLVLAAALVTAWWLWEKRVKARASATGVQPMVDPALFRRPSFTIGALESTIY
+LATMPAVFAIVAIFLQRGMGFTPLEAGLVGLPGAVVVASLSPWVGSMVQRRGPVLVLLGA
+LVGLVSLGVLALAFERSAAGAWSPWIVGVGLIVQSASQALLLTSTQVLMMDDVAGHEAGA
+AGGVAQTAQRLGTALGLSVVTGAFFAALAGAAGESAGPPSAAAYAHAASTAMGMVAVCWA
+LTAAVAALDVVRRRRAARAA
+>PROKKA_00145
+MTPRPPHPADPASGAFTPDQRRILTALLMPLFLALMSVSVVNVALPAIESGLDATSADLQ
+WVLAGYTLTFGTVLVAAGRAGDLWGRKNLFLAGITLYMLGSLLSGLAGDTLLLNAGRLLT
+GLGAGVFNPQVIGFIQSNFHGRARGRAYGLFGTVVGLGVAVGPLLGGLFLGAFGPEWGWR
+STFLMNVPVGLAAVAMGALWLPPPTRVHGLPPAPGPRGIAALDPVGALLLGAGGVSLMVP
+FIVPGTAWLLVLAAALVTAWWLWEKRVKARASATGVQPMVDPALFRRPSFTIGALESTIY
+LATMPAVFAIVAIFLQRGMGFTPLEAGLVGLPGAVVVASLSPWVGSMVQRRGPVLVLLGA
+LVGLVSLGVLALAFERSAAGAWSPWIVGVGLIVQSASQALLLTSTQVLMMDDVAGHEAGA
+AGGVAQTAQRLGTALGLSVVTGAFFAALAGAAAESAGPPSAAAYAHAASTAMGMVAVCWA
+LTAVVAALDVVRRRRAVRAA
+>PROKKA_02533
+MGGPVAATARRPANRRAGPVVVRAYPEAVTPRPRSADGDAAPAAFTPEQRRILTALLMPL
+FLALMSVSVVNVALPAIESGLHATSADLQWVLAGYTLTFGTVLVASGRAGDLWGRKSLFL
+VGIGLYVAGALVSGFAADPLMLNAGRLVTGVGAGVFNPQVVGFIQSNFSGRARGRAYGLF
+GTVIGLGVAVGPMLGGLLLGALGPEWGWRSTFLMNAPVGLAAIVMGVLWLPAPTRVHGLP
+AAPGPRGIAALDPVGALLLGLGAVCLMVPFIVPGTAGLLVLAAALVTAWWLWEKRVKARA
+SATGVQPMVDPALFRRLSFTIGALESTIYLATMPAVFAIVAIFLQRGMGFTPLEAGLVGL
+PGAVVVASLSPWVGSMVQRRGPVLVLLGALVGLVSLGVLALAFERSAAGAWSPWIVGVGL
+IVQSASQALLLTSTQVLMMDDVAGHEAGAAGGVAQTAQRLGTALGLSVVTGAFFAALAGA
+AAEGAGPPSAAAYAHAASTAMGMVAVCWALTAVVAALDVVRRRRAVRAA
+>PROKKA_02403
+MTLPSPAAAESGAFTADQRRILTVLLIPLFLALMSVSVVNVALPSIEGGLGASSADLQWV
+LSGYTLTFGMVLVAAGRAGDLWGRRPLFLAGIALYVLGSLLSGLAPDPLWLNAGRLLTGL
+GAGVFNPQTIGFIQSHFTGRARGRAYGLFGMVVGLGVAVGPLLGGLLLGALGPDWGWRST
+FLMNVPVGVLAIVMATAWLSPDTRVKGAAGRSGGPRGIAALDPVGALLLGGASLCLMVPF
+IAPGTWALLAGAAVLGVGWWLWELRVKRRAAATGVEPMVDPALFRRASFSIGAAESTIFL
+SSMPAVFAVTAVFLQQGMGFSPLASGLATLPGAVVQAVASPWAGSKVPSQGARMVFGGGV
+VGLASLAILALAFERSAAGAWSPWIVGAALAVMAVSQALILTTTQVLMMEDVAGHEAGAA
+GGVAQTAQRMGTALGLSVVMGAFYAALAGAAGPGGAPSAAGFAHAASAAVLMVGACWLVT
+TAIAAADLVRRRRTAR
+>PROKKA_00427
+MPLFLALMSVSVVNVALPAIESGLDATSADLQWVLAGYTLTFGTVLVAAGRAGDLWGRKS
+LFLAGITLYMLGSLLSGLAGDTLLLNAGRLLTGLGAGVFNPQVIGFIQSNFHGRARGRAY
+GLFGTVVGLGVAVGPLLGGLFLGAFGPEWGWRSTFLMNVPVGLAAVAMGALWLPPPTRVH
+GLPPAPGPRGIAALDPVGALLLGAGGVSLMVPFIVPGTAWLLVLAAALVTAWWLWEKRVK
+ARAWATGVQPMVDPALFRRPSFTIGALESTIYLATMPAVFAIVAIFLQRGMGFTPLEAGL
+VGLPGAVVVASLSPWVGSMVQRRGPVLVLLGALVGLVSLGVLALAFERSAAGAWSPWIVG
+VGLIVQSASQALLLTSTQVLMMDDVAGHEAGAAGGVAQTAQRLGTALGLSVVTGAFFAAL
+AGAAAESAGSPSAAAYAHAASTAMGMVAVCWALTAVVAALDVVRRRRAARAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000457.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000457.fa
new file mode 100644
index 0000000000000000000000000000000000000000..119f187557d0665cc290ecc286ec5fc80442f362
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000457.fa
@@ -0,0 +1,35 @@
+>PROKKA_00427
+MTMKKNSVQDVLAQDAAATAHLAGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD
+FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV
+LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH
+VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP
+KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAVSGTPIPQLEEEFVGKMYGHLKV
+AVADAVVERLAPVRERALALLDDPAELDRILAAGAEKARAVATPVLEDVYAKVGFLPPLR
+>PROKKA_00148
+MTMKKNSVQDVLAQDAAATAHLPGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD
+FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV
+LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH
+VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP
+KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILAAVSGTPIPQLEEEFVGKMYGHLKV
+AVADAVVERLAPVRERALELLADPAELDRILASGAEKARAVATPVLEDVYAKVGFLPPLR
+>PROKKA_02530
+MKKNSVQDVLAQDVSATAHLAGASDRHRVLSGMQPSADSLHLGNYLGALTNWVRTQDDFE
+AFFFIPDLHAITVPQDPAALAQRTRVAAAQFIAAGIDPERSTLFVQSQVPEHAQLAWVLT
+CMTGMGEAMRMTQFKDKSAKQGAEAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQHVE
+LTRDLAQRFNHRHGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINVMDDPKR
+TAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAMTDVPVAELEGRYVGRMYGHLKVDV
+ADAVVERLAPVKARTEELLADPAELDRILAAGAAKARAVATPVLEDVYAKVGFLPPLR
+>PROKKA_02400
+MTMKKNSVQDVLAQDAAATAHLAGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD
+FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV
+LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH
+VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP
+KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAVSDRPIPELEAEFEGKMYGHLKV
+AVADAVVERLAPVRERALGLLDDPAELDRILAAGAAKAREVATPVLEDVYARVGFLRPLR
+>PROKKA_00430
+MTMKKNSVQDVLAQDAAATAHLAGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD
+FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV
+LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH
+VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP
+KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAVSGTPIPQLEEEFVGKMYGHLKV
+AVADAVVERLVPVRERALALLADPAELDRILAAGAEKARAVATPVLEDVYAKVGFLPPLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000458.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000458.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ee77ee6b6a9a0fb27eb9a55f6346ce83bb727b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000458.fa
@@ -0,0 +1,30 @@
+>PROKKA_00428
+MSTAVPIPAVAEVPPGAEPVLETENLVKVYGRGASRFDALKGITLQIQRGESLAVVGKSG
+SGKSTLMHLLALLDQPSAGVVAMDGRPVSQLKAAEISQLRNERFGFVFQQFFLNPNQTVL
+ENTVLPLKIAGVGRAERARRGMAVLERLELADKAKNKATDLSGGQKQRVCIARALVNNPT
+VLFADEPTGNLDSATSAAVEDILFGLHRDEGITLVVVTHDDDLAAKCDRRVELQDGVVIA
+DERVGTERDGARA
+>PROKKA_00149
+MSTAVPIPAVAEVPPGAEPVLETENLVKVYGRGASRFDALKGITLQIQRGESLAVVGKSG
+SGKSTLMHLLALLDQPSAGVVAMDGRPVSQLKAAEISQLRNERFGFVFQQFFLNPNQTVL
+ENTVLPLKIAGVGRAQRTRRGMAVLERLELADKAKNKATDLSGGQKQRVCIARALVNNPT
+VLFADEPTGNLDSATSAAVEDILFGLHRDEGITLVVVTHDDDLAAKCDRRVELQDGVVIA
+DERVGTERDGARA
+>PROKKA_02529
+MHTVQQAAGAHAPAGREPVLETENLVKVYGRGESRFDALKGVTLQIQAGESVAIVGKSGS
+GKSTLMHLLALLDRPSAGVVAMDGRPVQDVSPAEVARLRNETFGFVFQQFFLNPAQTVLE
+NTVLPLKISGVPRAERRERGMAVLERLELADKAGNKATDLSGGQKQRVCIARALVNRPTV
+LFADEPTGNLDSATSAAVEDILFGLHRDEGITLVVVTHDDDLAARCDRRLVMQDGMIVDE
+TTTAGAQA
+>PROKKA_02399
+MSTVHTHPPETQASRGEEPVLETENLVKVYGRGASRFDALKGVTLQIHRGESVAVVGKSG
+SGKSTLMHLLALLDVPTSGVVAMDGRPVSQLKAAEVAHLRNERFGFVFQQFFLNADQTVL
+ENVVLPLKIAGVPRHEREARGREVLERLEIADKAKNRANDLSGGQKQRVCIARALINRPT
+VLFADEPTGNLDSATSRSVEEILFGLHRDEGITLVVVTHDDDLAAQCDRRLVMQDGVIVA
+AEGAGRAVAAGTGARA
+>PROKKA_00431
+MSTAVPIPAVAEVPPGAEPVLETENLVKVYGRGASRFDALKGITLQIQRGESLAVVGKSG
+SGKSTLMHLLALLDQPSAGVVAMDGRPVSQLKAAEISQLRNERFGFVFQQFFLNPNQTVL
+ENTVLPLKIAGVGRAQRTRRGMAVLERLELADKAKNKATDLSGGQKQRVCIARALVNNPT
+VLFADEPTGNLDSATSAAVEDILFGLHRDDGITLVVVTHDDDLAAKCDRRVELQDGVVID
+DERVGTEQDGARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000459.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000459.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aaf5a693d0cccf1d10d86a7a93231a03a70ceab0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000459.fa
@@ -0,0 +1,45 @@
+>PROKKA_00429
+MKATDVAGTALANTMRSKLRTFLTVVAIVIGAFTLTLTTGLGAGINKYVDNVVEGFGKPG
+ELTVMKQQDMSSAGAASGSPQEYAEQDAAGGEMFGMPLLTQEDLAAIEDTEHVTEVKTYR
+VAEPEYIQGPDDRKWQTGFMGSSGEIDMLTFSAGRAPEAGAAEIVMPESWVEDLGAGDAE
+DLVGTELTVVAATPLQEHKSVTATVVGVTKAAASGAGTAPTPSESLEQEIYDITTEGLPE
+SQRDTYFQATAIVADPEANEDAVKQALADQGLLAQTLEEQLGVIRGIIDAVTWVLTGFAL
+IALLAASFGIINTLLMAVQERTREIGLMKALGMTGGKIFGLFTMEAVVIGLLGSLVGIGL
+GVAVGLIANQVLTTGPLSGVTGLVLFAVNPLALLLILLLIVAIAFIAGTLPALRAARKDP
+IEALRHE
+>PROKKA_00150
+MKATDVAGTALANTMRSKLRTFLTVVAIVIGAFTLTLTTGLGAGINKYVDNVVEGFGKPG
+ELTVMKQQDMSSAGAASGSPQEYTEQDAAGGEMFGMPLLTQEDLAAIEDTEHVTEVKTYR
+VAEPEYIQGPDDRKWQTGFMGSSGEIDMLTFSAGRAPEAGAAEIVMPESWVEDLGAGDAE
+DLVGTELTVVAATPLQEHKSVTATVVGVTKAAASGAGTAPTPSESLEQAIYDITTEGLPE
+SQRNTYFQATAIVEDPEANEDAVKQALADQGLLAQTLEEQLGVIRGIIDAVTWVLTGFAL
+IALLAASFGIINTLLMAVQERTREIGLMKALGMTGGKIFGLFTMEAVVIGLLGSLVGIGL
+GVAVGLIANQVLTTGPLSGVTGLVLFAVNPLALLLILLLIVAIAFIAGTLPALRAARKDP
+IEALRHE
+>PROKKA_02528
+MKATDLAGTALANTMRAKLRTFLTVVAIVIGAFTLTLTSGLGAGINKFVDNMVEGFGSPD
+QLTVMKQVDPTSFAAGGAPQEYEPDEAAAGEMFGLPLLTAADLDRIRDTEHVTEVETARL
+VEPEYIEGEDGRQWQVPFMGSSFEIGALSLAAGREPAADAAEVTVPQDWVEALGGQTPED
+VLGQTVTLVAADPLGKQDGVEAEVVGVTEPMASGSGSGPVPSGEVETRLHEIQTAGLPEA
+QRDTFFSASVTVADMAANEAAVKAALAEEGYSAQTLEDQLGPIRGIIDAVTWVLNGFALI
+ALLAASFGIINTLLMAVQERTREIGLMKALGMTGRKIFGLFTMEAVVIGLLGSLIGVGLG
+VAVGVVANQVLTEGALSGVTGLVLYAVEPLSLALIVLLIVAIAFLAGTLPAARAARKDPI
+EALRYE
+>PROKKA_02398
+MKAPDLIRTALGNTARAKLRTFLTVIAIMIGAFTLTLTSGLGAGINKYVDNMVAGFGAPD
+ELTVSKPAGNQMAGMTGGAPTEYEDSAAAGEMYGMPLLTQEDLDRIGATEHVTGVETVRI
+VEVQDLRGADGRRWSVPMMGGTYEIGKLSVKAGREPAADGGAMELTVPTEWVESLGGTAP
+EDVLGQEVTLTTKTPLQQERTVQAEVVGVTERLPSGVGANPVPSAALEQGLHDIQTEGLP
+EEQRNTYFQATAIVEGMPGNEAAVKAALSEQGYQAQTLEDQLGSIRGIISAVTWVLNGFA
+LIALLAASFGIINTLLMAVQERTREIGLMKALGMTSGRIFGLFTLEAVVIGLLGSLLGVG
+LGVAVGVGVNAWLTTGGPLEDVAGLVLYAVDPLALLLIVLLIVAIAFVAGTLPAARAARK
+DPIEALRHE
+>PROKKA_00432
+MKATDVAGTALANTMRSKLRTFLTVVAIVIGAFTLTLTTGLGAGINKYVDNVVEGFGKPG
+ELTVMKQQDMSSAGAASGSPQEYTEQDAAGGEMFGMPLLTQEDLAAIEDTEHVTEVKTYR
+VAEPEYIQGPDDRKWQTGFMGSSGEIDMLTFSAGRAPEAGAAEIVMPESWVEDLGAGDAE
+DLIGTELTVVAATPLQEHKSVTATVVGVTKAAASGAGTAPTPSESLEQEIYDITTEGLPE
+SQRDTYFQATAIVADPEANEDAVKQALADQGLLAQTLEEQLGVIRGIIDAVTWVLTGFAL
+IALLAASFGIINTLLMAVQERTREIGLMKALGMTGGKIFGLFTMEAVVIGLLGSLIGIGL
+GVAVGLIANQVLTTGPLSGVTGLVLFAVNPLALLLILLLIVAIAFIAGTLPALRAARKDP
+IEALRHE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000460.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000460.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3fb960607358686b68eb7d04f88d49bc6a4d25c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000460.fa
@@ -0,0 +1,26 @@
+>PROKKA_00430
+MTTDRPNPDPNPEQPAVGSRYGTQPYAAPGYGAQPGSPYGIVPEPAAFPALLTLTLTSLA
+LYVLSSLPALFGGEESIERMRDSLRQSGLTPEQVEEIAPVVGASVTVGTIIVLLIGVALY
+ALVYFNLRGAKNWARILGIVVGILGTLSAVGGIFSFVTYPGIGGVLASVLSLALVIVNIL
+WLVKAFNPQVAAYTRQGRRA
+>PROKKA_00151
+MTTDRPNPNPEQPAAGSRYGTQPYAAPGHGAQPGSSYGIVPEPAAFPALLTLTLTSLALY
+VLSSLPALFGGEESIERMRDSLRQSGLTPEQVEEIAPVVGASVTVGTIIVLLIGVALYAL
+VYFNLRGAKNWARILGIVVAILGTLSAVGGIFSFVTYPGIGGVLASVLSLALVIVNILWL
+VKAFNPQVAAYTRQGRRA
+>PROKKA_02527
+MSNQNPDFTNPAYNPANPPFEGESGQAGQAPQQGQPGQAAQYGQPGPYGQAPQYGQPGQY
+PATGTRYGTQPYGVDGRYGTVPEPRGFRTLLTLTLVSAALWVLSSLPAMFTMDDMMDVVM
+RDAASQPGVTAEDMEMVSSFMRTAGITSIVISLIIGLGLYALVYFNLRGVKNWARILGIV
+FAILGALAIFSGIGFLFSGSTMLILSGALTLAYAVVNIIWVITAFRSDVAEWFRQGRPAA
+A
+>PROKKA_02397
+MTDQNTPYPQNPQGGQPAPQYGQPGQAAPQYGQPGEGSRFGTQAYGAPGLQYGAPLAEPA
+KFRTLLKLTLASAVVYVLSALPGLFVDQDALVRDQLRAQGMSAEQIDQAMQNAGMFSAMA
+GIGAVVGLLIALGLYALVYFGLRAGKNWARVLGIVLAILGTLSAVFGLFSLGSFPAGVMI
+ASLVLSVLFIAVNVLWLVNAFNKDVAAYTKQGRLPAA
+>PROKKA_00433
+MTTDRPNPDPNPEQPAAGGPGPYPGQNPAYGQPTAGSRYGTQPYAAPGYGAQPGSPYGIV
+PEPAAFPALLTLTLTSLALYVLSSLPALFGGEESIERMRDSLRQSGLTPEQVEEIAPVVG
+ASVTVGTIIVLLIGVALYALVYFNLRGAKNWARILGIVVAILGTLSAVGGIFSFVTYPGI
+GGVLASVLSLALVIVNILWLVKAFNPQVAAYTRQGRRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000477.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000477.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5bfd75fba271e0f4d0c3c0a22cf83f555c779009
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000477.fa
@@ -0,0 +1,27 @@
+>PROKKA_00449
+MSPRRPRVPRVDPTTGAPRRTAVAAPAAPTTASPKADAPTPTPEATTPTPAATGAEVIDL
+HSVQERRQAGHHGHLDGHPDADRADTAPAAPASPSAPPRRTAPARPAGRRTRPAPRRAAS
+AAATAARRRAPLPEPVPARQITGRSLIVVAVLLVAAVLVAPTLRAFLNQQLEISAAREEI
+ATMQAQREDYERRIQLWDDPAYVTQQARERLELVMPGETLYSVTGRPSETETETDTEAED
+TPAARADEVVNTRLPWAEGLWDSAVRAGLE
+>PROKKA_00170
+MSPRRPRVPRVDPTTGAPRRTAVAAPAAPTTAFPEADTPTPTPAAPTPAPAATDAEVIDL
+QSIQERRQAGHPDVDRADTAPAGDTAAPASPSAPPRRTAPARPAGRRPRPAPRGAASAAA
+TAARRRAPLPEPVPARQITGRSLIVVAVLLVAAVLVAPTLRAFLNQQLEISAAREEIATM
+QAQREDYERRIQLWDDPAYVTQQARERLELVMPGETLYSVTGRPSETDTATETEDTPAAG
+ADEVVNTRLPWAEGLWDSAVRAGLE
+>PROKKA_02507
+MAARRRAPLPDPVPARQITGRSLLVVAVLLVAAVLVAPTLRAFLNQQLEIAAAEEEIAAM
+QAQREDYEERIRLWDDPGYVTQQARERLQLVMPGETLYSVTGVPEEAPRDPRPEAPAGEP
+VNTRLPWAEGLWDSAVRAGPRVSPGPRPDPGSGPARP
+>PROKKA_02379
+MSARRPRVPRVAVPDTAPERATPAVVEPVVVEPAPVAPAAPEAPAPPAPPGPQVIDLQEA
+AQRRRHEATRPSPRPDAERAAAQRVARLREERRRATVREHAAARRRVPLPEPVPARQLTG
+RSLVVLAVLIIAAVLVAPTARLMLNQQLEISAAQQDIAEQQRRKAEYEEQIRRWDDPGYV
+AQQARQRLELVMPGETLYTVTGLPDESGAVPADSVPQEKVNDRLPWVEGLWDSAVRAATE
+>PROKKA_00452
+MSPRRPRVPRVDPTTGAPRRTAVAAPAAPTTAFPEADTPTPTPAAPTPAPAATDAEVIDL
+QSVQERRQAGHPGHLDGHPDADRADTAPAGDTAAPASPSAPPRRTAPARPAGRRPRPAPR
+RAASAAATAARRRAPLPEPVPARQITGRSLIVVAVLLVAAVLVAPTLRAFLNQQLEISAA
+REEIATMQAQREDYERRIQLWDDPAYVTQQARERLELVMPGETLYSVTGRPSETDTATET
+EDTPAAGADEVVNTRLPWAEGLWDSAVRAGLE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000479.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000479.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5b87940aa159b769f7fe2f17b3b052887e94b2b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000479.fa
@@ -0,0 +1,45 @@
+>PROKKA_00451
+MSLTPELSPKPRLLIVGGGYAGFQLAKELQTKVKDRGGVVTVVDPLPYMTYQPFLPEVVG
+GHIVGRNVVVDLATHLKDAEVLRGTVVKVEHARRVATVRGEDGHEFELPYQDIAMTAGAT
+TRVFPIKGLGEHGIGLKTVEEAVTLRNQILERLDAASLMVDAEARRRALTFVVVGGGFAG
+IETVGEMEHLIRTAVARNPRLSQSEVRIVLVEAMGRIMPEVGEDQAVGVVEHLKDRGIEV
+LLNTSLGDATDGIMTLVDMKDKSEKEKFGADTLVWTAGVAANAVAKQTDFPVEERGRIEV
+TPTLQVKDGENGVFEGAWGCGDVCAVPDLTGAGPGGFCVPNAQHAGRQAKQLAANYMAVR
+HGEGEVQEYVHKSLGAVAGLGFFKGVGNPLGVKISGPAAFLAHRGYHAYAMPTLDRRFRI
+LSGWVAETLFGRDSTSVAGLDTPFNPFRRAAGVELEPGRFERQRALESSKG
+>PROKKA_00172
+MSLTPELSPKPRLLIVGGGYAGFHVARELQKKVAERGGVVTVVDPRPYMTYYPFLPEVVG
+GHIEGRHVNVDLQTHLKDAEVVRGAVVSVDHAGRTAVVRGEGGDEFEIPYQDIVMTAGAV
+TRVFPIPGLGEQGIGLRSVEEAVQLRNQILERLDAGSLMTDAEERKRALTFVVVGGGFAG
+IEAIAEMENLIRNAVERNERLSQSEIRIVLVEAMGRIMPEVSEEQAQGVVEHLKDRGIEV
+LLNTSLGDATDGVMKLVAMPSKEEAETFAADTLVWCAGVVANSVVKSTDFPVDDRGRVEA
+TPTLQIKDGEAGALEGAWACGDVSAVPDLTGAGPGGFCVPNAQHAIRQAKRLAANYMAVR
+HGEGEVQEYVHKSLGTVAGLGFGRGVGNPLGTKIAGIPAFLAHRGYHGYAMPTLERKFRI
+LSGWVAETLFGRDSTSVAGLDTPFNPFRRAAGVELEPGRFERQRALESSKG
+>PROKKA_02505
+MSLTPELSPKPRLLIVGGGYAGFHIAKELQKKVKDAGGVVTVVDPLPYMTYQPFLPEVVG
+GHIDGRNVVVDHATHLKDAEVLRGTVVKVEHARRVATVRGEDGHEFEVPYQDVVMTAGAT
+TRVFPIAGLGEHGIGLKTVEEAEALRNQILERLDAASLMVDAEARRRALTFVVVGGGFAG
+VETVGEMEHLIRTAVSRDPRVSQSEVRIALVEAMGRIMPEVSEDQAAGVVEHLKDRGIEV
+LLNTSLGDATDGIMTLVDMKDKSEKEKFGADTLVWTAGVAANSVAKQTDFPVEERGRIEV
+TATLQVKDGQGGVLEGAWGCGDVCAVPDLTGAGPGGFCVPNAQHAGRQAKQLAANYLAVR
+HGEGEVQEYVHKSLGTVAGLGFFKGVGNPLGVKISGPAAFLAHRGYHAYAMPTLDRRFRI
+FAGWVAETLFGRDSTSVEGQDRPFNAFRRAAGVELEPGRFERKRALESSKG
+>PROKKA_02377
+MSITPDLSPKPRLLVVGGGYAGFHIAQTLQSKVKDRGGVVTVVDPRPYMTYQPFLPEVVG
+GHIEGRHVIVDLQTHLKDTEVVRGAVTKVEHARKVAVVRGEDGAEFEVPYQDIVMTAGAN
+TRVFPIPGLAEQGIGLKTVEEAVALRNQILERLDAAALMTDAEQRRAALTFVVVGGGFAG
+IEAIAEMENLIRTAVSRNENLSQTEVRIVLVEAMGRIMPEVSEDQAQAVVAHLKGRGIEV
+LLNTSLGDATGGVMKLVNMADKSEADSFRADTLVWTAGVAANGVAKQTDFPVEDRGRIEV
+TPTLQIKDGEGVLEGAWACGDVAAVPDLTGAGPGGFCVPNAQHAGRQAAQLAKNYMAVRH
+GEGEVQEYVHKSLGAVAGLGFLKGVGNPMGVKLFGVPAFLAHRGYHAYAMPTLERRFRIV
+SGWIAETLFGRDSTSVDGQETPFNAFRVAAGAEPVPSTLEKKRAGELAAK
+>PROKKA_00454
+MSLTPELSPKPRLLIVGGGYAGFHVARELQKKVAERGGVVTVVDPRPYMTYYPFLPEVVG
+GHIEGRHVNVDLQTHLKDAEVVRGAVVSVDHAGRTAVVRGEGGDEFEIPYQDIVMTAGAV
+TRVFPIPGLGEQGIGLRSVEEAVQLRNQILERLDAGSLMTDAEERKRALTFVVVGGGFAG
+IEAIAEMENLIRNAVERNERLSQSEIRIVLVEAMGRIMPEVSEEQAQGVVGHLKDRGIEV
+LLNTSLGDATDGVMKLVAMPSKEEAETFAADTLVWCAGVVANSVVKSTDFPVDDRGRVEA
+TPTLQIKDGEAGALEGAWACGDVSAVPDLTGAGPGGFCVPNAQHAIRQAKRLAANYMAVR
+HGEGEVQEYVHKSLGTVAGLGFGRGVGNPLGTKIAGIPAFLAHRGYHGYAMPTLERKFRI
+LSGWVAETLFGRDSTSVAGLDTPFNPFRRAAGVELEPGRFERQRALESSKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000482.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000482.fa
new file mode 100644
index 0000000000000000000000000000000000000000..528a1e961b210d7582096c2df7f1e91b277ed306
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000482.fa
@@ -0,0 +1,40 @@
+>PROKKA_00458
+MSSTLAAQTKINKDVPYGLTVAAAWSWRLVAVVIGIGVVVYLLGFVSLVVIPILVAALLA
+TLLAPVFQAMRRIKVPGVAAALLCVLLLVVVVVGLMGLAGQQIVQGFAELGDQLGQAVDD
+AIAWLAGVGVEIPRSGAGLEGLWQTLRDNSATVMNSAVSLGSTAVNIGAGLFIALFSLIF
+FLYDGDRIWRFLLIFVPKAHRATVGRAGRSGWQSLGSYVRVQIFVAFIDAVGIGIGALIL
+GVPLAIPLAVLVFLASFIPMIGATLTGAMAVLLALMSNGLVNALLMLGVVLLVQQIESNV
+LQPLVMGKAVALHPLAVFLAVAAGSTVLGLAGAVFAVPVLAFVNSFVRALTADTPEELTE
+RTGHALEPGGAEDETAGSHRYRPSAHDDAALASEADAGTRHGDDA
+>PROKKA_00176
+MSSTLAAQTKIDKDVPYGLTVAAAWSWRLVAVVIGIGVVVYLLGFVSLVVIPILVAALLA
+TLLAPVFQAMRRIKVPGVAAALLCVLLLVVVVVGLMGLAGQQIVQGFAQLGDQLGQAVDD
+TIAWLAGVGVEIPRSGAGLEGLWQTLRDNSATVMNSAVTFGSTAVNIGAGLFIALFSLIF
+FLYDGDRIWRFLLIFVPKAHRATVGRAGRSGWQSLGSYVRVQIFVAFIDAVGIGIGALIL
+GVPLAIPLAVLVFLASFIPMIGATLTGAMAVLLALMSNGLVNALLMLGVVLLVQQIESNV
+LQPLVMGKAVALHPLAVFLAVAAGSTVLGLAGAVFAVPVLAFVNSFVRALTADTPEELTE
+RTGHALEPGGAEDEAAGSHRYRPSAHDDAALASEADAGTRHGDDA
+>PROKKA_02489
+MSSTLAAQTKINKDVPYGLTVAAAWSWRLVAVLVGLGILWWLLSFVSLVLIPVLVAALLA
+TLLAPLFEGMRRIGIPGIAASLLCVVLLIVVVVGLVVVAGQQIAQGFSDLGDKLTQAVDG
+AIAWLASIGVELPTAGGGLEGLWQTLRDNSGTLLDSAMTFGSTAVNIGAGFFIALFSLIF
+FLYDGDRIWRFILVFVPKAHRATVGRAGQTGWRALGNYVRVQIFVAFVDAVGIGLGALIL
+GVPLAIPLAVLVFLASFIPMIGATVTGAIAVLFALMSNGLVNALLMLGVVLLVQQIESNV
+LQPLVMGKAVALHPLAVFLAVAAGSAVLGLAGAVFAVPVLAFVNSFIRALTADPPEQLTD
+RSDQALAPGSAADEAVGSHVFEPTKHDDAALASEDDAGTSGDLR
+>PROKKA_02373
+MSSTLSTDAKLEKDIPYGLTVAAGWSWRVIAVAAMLWVVWHFAGFASLVIIPVLVAALLA
+VLLAPIYRALRRARIPGVLAAVLSIVLLLAAVVLLAWVAGLELVQGFSDLSDQLGASVEH
+LVTWVQGMGVPVSFDAAALDNVWSTVKDNSGVLVDGALAFGSTAANVLTGLFIALFTLIF
+FLFDGERIWRFLLAFVPHTSRSRVDVAGRTGWNALGSFVRVQIVVAFIDAVGIGLGAWLL
+GVPLALPVAVIVFLFSFVPTIGAIASGALACVLALTANGLVNALLMLGVVILVQQIESNL
+LQPLIMGRAVSLHPLAVFLGVAAGGVALGLVGAVFAVPLLAFANAFVQALRAKGPGEEIL
+PGEKVFRPSDEVIAAARRDAKLDPKLDPTSFDDDSGPDGDVEDGRTGSTRTELKP
+>PROKKA_00458
+MSSTLAAQTKIDKDVPYGLTVAAAWSWRLVAVVIGIGVVVYLLGFVSLVVIPILVAALLA
+TLLAPVFQAMRRIKVPGIAAALLCVLLLVVVVVGLMGLAGQQIVQGVAQLGDQLGQAVDD
+AIAWLAGVGVEIPRSGAGLEGLWQTLRDNSATLMNSAVSFGSTAVNIGAGLFIALFSLIF
+FLYDGDRIWRFLLIFVPKAHRATVGRAGRSGWQSLGSYVRVQIFVAFIDAVGIGIGALIL
+GVPLAIPLAVLVFLASFIPMIGATLTGAMAVLLALMSNGLVNALLMLGVVLLVQQIESNV
+LQPLVMGKAVALHPLAVFLAVAAGSTVLGLAGAVFAVPVLAFVNSFVRALTADTPEELTE
+RTDHALEPGGAEDEAAGSHRYRPSTHEDAALASEADAGTRHGDGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000485.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000485.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0b582cfc759a9895b0bbd2a3179a710dfa216c4d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000485.fa
@@ -0,0 +1,20 @@
+>PROKKA_00461
+MTTSQSDAPWLTQEAYDRLSKELEYISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAADDESL
+EVYSERSPLGEAINGAKKGDKVSYTAPNGKDIKVEVKDVQPYSG
+>PROKKA_00179
+MTTSQSDAPWLTQEAYDRLSKELEYISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAADDESL
+EVYSERSPLGEAINGAKKGDKVSYTAPNGKDIKVEVKDVQPYSG
+>PROKKA_02486
+MTTSQSDAPWLTQEAFDRLSKELEHISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAEDDEHL
+EVYSERSPLGEAINGAAKGDKVTYTAPNGKEIKVEIKDVKPYSG
+>PROKKA_02370
+MATTPSDAPWLTQEAFDRLSKELAHISGPGRQEIIERIEAAREEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGETQAADGVVTPGTVVTAVVAGDEMTFLFGNREIAADGEDL
+EVYSERSPMGEAINGAKQGDKVTYTAPNGKDIAVEITDVKPYQA
+>PROKKA_00461
+MTTSQSDAPWLTQEAYDRLSKELEHISGPGRQEIIERIEAARDEGDLKENGGYHAAREEQ
+SKNEGRIAELKHLLETARVGEAAENDGAVHPGTVVTAVVAGDEMTFLFGNREIAADDESL
+EVYSERSPLGEAINGAKKGDKVSYTAPNGKDIKVEVKDVQPYSG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000488.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000488.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b756e39590749e1979c10a5b1dc8ba810421151
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000488.fa
@@ -0,0 +1,26 @@
+>PROKKA_00465
+MTPLRETDAARRLRWRIERIRDPDHPLYKPRLRGWIHAVMAPLTLAAGIVLIVLAPTATL
+RWASAVYAVTGLLLFAVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYTPLSLALLAP
+DRARVLLTLVWVGAVAGVAFRVLWTDAPRWLYTPVYVALGLAALLYLGDFFAADAAAGWL
+IVAGGVAYITGAVCYALQAPTIHREWFGFHELFHAFTVAGFVCHAVAIYRAVLVVA
+>PROKKA_00183
+MTPLRETDAARRLRWRIERIRDPDHPLYKPRLRGWIHAVMAPLTLAAGIVLIVLAPTATL
+RWASAVYAVTGLLLFAVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYTPLSLALLAP
+DRARVLLTLVWVGAVAGVAFRVLWTDAPRWLYTPVYVALGLAALLYLGDFFAADAAAGWL
+IVAGGVAYITGAVCYALQAPTIHREWFGFHELFHAFTVAGFVCHAVAIYRAVLVVT
+>PROKKA_02482
+MDPLTPAREPEAARRLRWRIERIRDPEHPLFKPRLRGWIHAAMAPLTLAAGIVLIVLAPT
+ATLRWASAVYAVTGLLLFGVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYTPLSLAL
+LPPGKAHLLLTLVWAGAVAGVAFRLLWTDAPRWLYTPVYVVLGLAALLYIGDFFAADVAA
+GWLIVAGGAAYIVGAVFYALRAPTIHREWFGFHELFHVFTVGGFVCHAVAIYRAVLVVA
+>PROKKA_02366
+MWEHGGMVTRAPSVENRTGRPLKWRIERIRDPEHPLYKPRLRGWVHAVMAPLVLVAGIVL
+IVLAPGATLTWACVVYVVTGLLLFGVSATYHLVQWNETVSRVLKRLDHTNIMLVIAGTYT
+PLSLAMLPADKAWTLVTAVWVGAALGVAFRLLWTDAPRWLYTPVYVALGLAAVVYLGDFF
+AASVPAAVLICAGGAAYIVGAVFYALKAPTIHREWFGFHELFHVFTVGGFVCHYIAVMMA
+VLAA
+>PROKKA_00465
+MTPLRETDAARRLRWRIERIRDPDHPLYKPRLRGWIHAVMAPLTLAAGIVLIVLAPTATL
+RWASAVYAVTGLLLFGVSATYHLVQWNEVVSRVLKRLDHTNIMLVIAGTYTPLSLALLAP
+DRARVLLTLVWVGAVAGVAFRVLWTDAPRWLYTPVYVALGLAALLYLGDFFAADAAAGWL
+IVAGGVAYITGAVFYALQAPTIHREWFGFHELFHAFTVAGFVCHAVAIYRAVLVVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000492.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000492.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fcaa5fdaf6bb5d74c5818f4b0afcc86548234c90
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000492.fa
@@ -0,0 +1,20 @@
+>PROKKA_00469
+MSGVGWAWTHGAPATAVLWSLGLVWFAVCAGVLVRTDLREHRLPNRWTLRLALGGLTMMT
+GGALLAGRGDLTLCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV
+LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA
+>PROKKA_00187
+MSGVGWAWTHGAPATAVLWTLGLAWFAVCSGVLVRTDLREHRLSNRWTLRLALGGLAMMT
+GGALLAGRGDLALCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV
+LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA
+>PROKKA_02478
+MDGVGWAWAQGLPATAVLWSAGLAWFAVCAAVLVRVDLREHRLPNRWTLRLALGGLAAMA
+GGAALAGRADLVLSSVLGGLGYAAAMLVLHVLSRGSLGMGDVKLAAGLGAYTGVLGGSAV
+VAAGLGAILLGGAVAAVLVAARRASRSTALPFGPPMILAAAAVLAFAPAGG
+>PROKKA_02362
+MTWWTGAWEAGERLTAMLWAAGLVWFLLCSVVLARTDLREHRLPNRWTGRLALGGVVAMG
+GGAVLGGLWSVVASCLLGGLGYALAMLALHVLTRGGLGLGDVKLAAGLGLYCGVAGLAAV
+LAAAVLAVLLGGVVAVVLVLARRADRHTALPFGPAMVAGALGVLLLA
+>PROKKA_00469
+MSGVGWAWTHGAPATAVLWTLGLAWFAVCSGVLVRTDLREHRLSNRWTLRLALGGLAMMT
+GGALLAGRGDLALCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV
+LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000495.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000495.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ed5a47af4c22806b36004813005f3113f2274ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000495.fa
@@ -0,0 +1,25 @@
+>PROKKA_00472
+MLTVSSADPHAPAPRPVLTATQAQRARQPWMAMVLSLAALLAIVAVVLLLNPEPPQRPRE
+DRVDVAAEAATIPHDDGDLPALAPEVPESWYANYARLQKLDGVSTWDVGWVVTDTVFAGL
+QQAEDVDPTWVSLRVDQVPTSETIEIDGIAWDLHADPKKPERRLVAEVDGSTVVLTTTGD
+QAVLEDLAHGVAKETR
+>PROKKA_00190
+MLTVSSADPHAPAPRPVLTATQAQRARQPWMAMVLSLAALLAIVAVVLLLNPEPPQRPRE
+DRVDVAAEAATIPHDDGDLPALAPEVPESWYANYARLQKLDGVSTWDVGWVVTDTVFAGL
+QQAEDVDPTWVSLRVDQVPTSETIEIDGIAWDLHADPKKPERRLVAEVDGSTVVLTTTGD
+QAVLEDLAHGVAKETR
+>PROKKA_02475
+MLTVSSTHPTDPTDPNAPAPRPVLTAKQAQRARQPWIGMVLSVVALLALVAVVLILNPEP
+PQRPREDRVDVAAAAATVPHDDGVLPALAPEVPESWYANFARLQTMDGVSTWDVGWVVTD
+TVFAGMQQAHDVDPTWVTLRVDSVPATETLEIDGLAWDLHADPRAPEKRLVTEVEDTTVV
+LTTTGDRAVLEDLARGVAKETR
+>PROKKA_02359
+MPGMSSPDPAAPPAPRPVLTPKQAQRARAPWIAMVLSTLAVLGIVLVALMVNQPPPAPAQ
+ADRVDVAAAASTVPHDDGALPALAPDVPEPWDSTYARVERLQGVDTWDVGWAVNDAVFAG
+LKQTSRADPTWLALRVGSAPAVGTVDVDGITWDHYAPQDSKDQHLVAEVRGSTLVLTTSG
+DQAVLEDLARAVAKEIR
+>PROKKA_00472
+MLTVSSADPHAPAPRPVLTATQAQRARQPWMAMVLSLAALLAIVAVVLLLNPEPPQRPRE
+DRVDVAAEAATVPHDDGDLPALAPEVPESWYANYARLQKLDGVSTWDVGWVVTDTVFAGL
+QQAEDVDPTWVSLRVDHVPTSETIEIDGIAWDLHADPKKPERRLVAEVDGSTVVLTTTGD
+RAVLEDLAHGVAKETR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000499.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000499.fa
new file mode 100644
index 0000000000000000000000000000000000000000..027e0c1c3c7bd94648bbe97f5c1c264a6c4fdc73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000499.fa
@@ -0,0 +1,43 @@
+>PROKKA_00477
+MMAGAAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPT
+EHLRALQEAGVAVRPDPEALQHAQDKLVMRAAVERLGLPNPAWAPVDDLEAVLAFGDEHG
+WPMILKTARGGYDGKGVLKLDDADDARASAADGTLAAWLGAGITPLLAEALVPFSRELSA
+QVARTPSGEVAVYPVVDSVQVAGVCDLVVAPAQDLDPAVAAAATAAAVRLAEELDVTGML
+AVELFETPGVGPGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGETAPRGAG
+VVMKNVLGGAREDLHAGSVAALAAHPQAKVHLYGKDVRPGRKVGHVNVVADHGLSLEEAV
+RTAESAAALLRDDAPTTGTETEARP
+>PROKKA_00195
+MMAGAAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPT
+EHLRALQEAGVAVRPDPEALQHAQDKLVMRAAVERLGLPNPAWAPVDDLEAVLAFGDEHG
+WPMILKTARGGYDGKGVLTLDDADDARASAADGTLAAWLGAGIAPLLAEALVPFSRELSA
+QVARTPSGEVAVYPIVDSVQVAGVCDLVVAPAQDLDPAVAAAATAAAVRLAEELDVTGML
+AVELFETPGVGPGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGETAPRGAG
+VVMKNVLGGAREDLHAGSVVALAAHPQAKVHLYGKDVRPGRKVGHVNVVADHGLSLEEAV
+RTAESAAALLRDDAPTTGTETEARP
+>PROKKA_02470
+MMAGPAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPT
+EHLRVLQEVGVAVRPGPEALQHAQDKLVMRAAVERLGLPNPAWAAVRDLDEVLAFGDEHG
+WPMILKTPRGGYDGKGVLKLDDADDARASASDGTLGTWLGAGIAPLLAEALVPFTRELSA
+QVARTPSGRVAAYPVVDSVQVAGVCDLVVAPARDLDPAVAEAATAAAVRLAEELDVTGML
+AVELFETPGVGPGFQINELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGDTAPRGAG
+VVMKNLLGGAREDLHAGLADALAAHPQAKVHLYGKAVRPGRKVGHVNVVADHGLTLEQAV
+RAAESAAAVLRDGAAPDAVDASPSSPATPHPAGGPPMTATPQNPAQPLQDDAPVVSVVMG
+SDSDWPVMSAAAEALRELDVPVEVGVVSAHRMPHEMVEFGARAHERGIRVIVAGAGGAAH
+LPGMLASVTPLPVIGVPVKLKSLDGLDSLLSIVQMPAGVPVATVSVDGARNAGLLAARIL
+ASADTEEGERLRAALTEHAAELNAQAQAKGARLRERMAADR
+>PROKKA_02354
+MIGGGQLARMMAGPAAELGVPFRVLAEAPDASAAQVAPHMVGDHASLEDLRAFAATVDVV
+TFDHEHVPTEHLRTLEAAGVAVRPGPDALQYAQDKLLMRGLVERLGLPNPAWAPVSSLEE
+VIAFGDEHGWPMILKTARGGYDGKGVLKVDSADDARSGAADGTLGTWLGAGIAPLLAEAM
+VPFARELSAQVARRPSGEVAAYPVVASLQTQGVCDVVTAPAPDLAPAVAEAASGAAVRIA
+EELDVTGMLAVELFETPGTDAGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDMPL
+GGTAPRGDGTVMKNVLGGAHEDLHSGFSEALAAHPEAKVHVYGKGVRPGRKVGHVNVVAE
+HGLSLADAERIAESTAAVLRDATAPSAPTPKA
+>PROKKA_00477
+MMAGAAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPT
+EHLRALQEAGVAVRPDPEALQHAQDKLVMRAAVERLGLPNPAWAPVDDLEAVLAFGDEHG
+WPMILKTARGGYDGKGVLKLDDADDARASAADGTLAAWLGAGITPLLAEALVPFSRELSA
+QVARTPSGEVAVYPVVDSVQVAGVCDLVVAPAQDLDPAVAAAATAAAVRLAEELDVTGML
+AVELFETPGVGPGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGETAPRGAG
+VVMKNVLGGAREDLHAGSVAALAAHPQAKVHLYGKDVRPGRKVGHVNVVADHGLSLEEAV
+RTAESAAALLRDDAPTTGTETEARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000504.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000504.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6cfebeceb559db386f3c52de46af5b4a1a6d7632
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000504.fa
@@ -0,0 +1,16 @@
+>PROKKA_00482
+MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRRAEPHTYDLCGEHARRTTAPRGWEVLR
+LELPEHYEAVDADGGVRTVPTRPMAVPPARPGLRVVRDGD
+>PROKKA_00200
+MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRRAEPHTYDLCGEHARRTTAPRGWEVLR
+LELPEHYEAVDADGGVRTVPTRPMAVPPARPGLRVVRDGD
+>PROKKA_02465
+MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRLAEPHTYDLCAEHARRTTAPRGWEVLR
+LELPGHYEAVAPDGTVHTVPTAPRAVPAAPPADVASRPSLAAPRPAPAVPPVDADEPEAP
+APPTRPGLRLVRDDDPLPPA
+>PROKKA_02349
+MRRCSKTGCQEPAEATLTYNYAGSQVVIGPLAQRAEPHAYDLCAAHAARTTAPRGWEVLR
+LAPAAPAAPGVAAPTHPALRLVTDPVEGTAG
+>PROKKA_00482
+MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRRAEPHTYDLCGEHARRTTAPRGWEVLR
+LELPEHYEAVDADGGVRTVPTRPMAVPPARPGLRVVRDGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000505.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000505.fa
new file mode 100644
index 0000000000000000000000000000000000000000..358eb74042cd4b6179b41bdc91fd678c62798bb3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000505.fa
@@ -0,0 +1,50 @@
+>PROKKA_00483
+MTETSAEFRTPDVDPAFANRTTVPGASFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLRE
+EYGEAQPLKGARIAGSLHMTVQTAVLIETLIALGAEVRWASCNIFSTQDEAAAAVVVGSG
+TPEDPQGVPVFAWKNESLEDYWWTASQILTWPGADEDPERGPNMILDDGGDATLLVHKGV
+EFEAAGAVPSATEDDPEEYRIILETLRRSLARDPQHWTRTAGTLRGVSEETTTGVLRLYQ
+LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGK
+GAAEALRGQGARVIVTEIDPICALQAAMDGYQVARLEDVVGEGDIFVTTTGGKDIIMAEH
+MAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQVHEWTLGGGTEAERSIIVLSE
+GRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK
+VARLHLDALGVGLTELTKAQAEYLGVDVAGPYKADHYRY
+>PROKKA_00201
+MTETSAEFRTPDVDPAFANRTTVPGASFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLRE
+EYGEAQPLKGARIAGSLHMTVQTAVLIETLIALGAEVRWASCNIFSTQDEAAAAVVVGSG
+TPEDPQGVPVFAWKNESLEDYWWTASQILTWPGADEDPERGPNMILDDGGDATLLVHKGV
+EFEAAGAVPSATEDDPEEYRIILETLRRSLARDPQHWTRTAGTLRGVSEETTTGVLRLYQ
+LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGK
+GAAEALRGQGARVIVTEIDPICALQAAMDGYQVARLEDVVGEGDIFVTTTGGKDIIMAEH
+MAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQVHEWTLDGGTEAERSIIVLSE
+GRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK
+VARLHLDALGVGLTELTKAQAEYLGVDVAGPFKADHYRY
+>PROKKA_02464
+MTETPAESRTPDVDPAYANRATVPGAAFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLRE
+EYGESQPLAGARIAGSLHMTVQTAVLIETLTALGAEVRWASCNIFSTQDEAAAAVVVGSG
+TPEDPQGVPVFAWKNETLEDYWWTASQILTWPGAAEDPERGPNMILDDGGDATLLVHKGV
+EFEAAGAVPSATEDDPEEYRIILETLRRSLAEDPQRWTRTASTLRGVSEETTTGVLRLYQ
+LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGK
+GAAEALRGQGARVIVTEIDPICALQAAMDGYQVARLEDVVGQGDLFVTTTGGKDIIMAEH
+MAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQVHEWTLDAGTDSERSIIVLSE
+GRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK
+VARLHLDALGVGLTELTKSQAEYLGVDVAGPYKADHYRY
+>PROKKA_02348
+MTETSSARPTPDVDPAFANRSTVPGATFDFAVRDLSLAEAGRHQIRLAEHEMPGLMALRE
+EYGESQPLKGARIAGSLHMTVQTAVLIETLTALGAEVRWASCNIFSTQDEAAAAIVVGSG
+TPDAPAGVPVFAWKGESLEEYWWTASQILTWPGAAEDPDRGPNMILDDGGDATLLVHKGV
+EFEAAGAVPSATEDDPEEYRIILETLRRSLAEDPQRWTRTASTLRGVSEETTTGVLRLYQ
+LAQEGTLLFPAINVNDSVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGK
+GAAEALRGQGARVIVTEIDPICALQAAMDGYQVARLEDVVEQGDLFVTTTGGKDIIMAED
+MLRMKDKAIVGNVGHFDNEIDMAGLGRVDGVVKTEIKPQVHEWTFDTGTEDERSIIVLSE
+GRLLNLGNATGHPSFVMSASFTNQVMAQIELYDGSTGQGALTGEHYEKQVYTLPKVLDEK
+VARLHLDALGVGLTELTKAQAEYLGVDVAGPYKADHYRY
+>PROKKA_00483
+MTETSAEFRTPDVDPAFANRTTVPGASFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLRE
+EYGEAQPLKGARIAGSLHMTVQTAVLIETLIALGAEVRWASCNIFSTQDEAAAAVVVGSG
+TPEDPQGVPVFAWKNESLEDYWWTASQILTWPGADEDPERGPNMILDDGGDATLLVHKGV
+EFEAAGAVPSATEDDPEEYRIILETLRRSLARDPQHWTRTAGTLRGVSEETTTGVLRLYQ
+LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGK
+GAAEALRGQGARVIVTEIDPICALQAAMDGYQVARLEDVVGEGDIFVTTTGGKDIIMAEH
+MAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQVHEWTLDGGTEAERSIIVLSE
+GRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK
+VARLHLDALGVGLTELTKAQAEYLGVDVAGPYKADHYRY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000509.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000509.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f27cff3c96b68838bba069695e7ce548d5392dfb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000509.fa
@@ -0,0 +1,30 @@
+>PROKKA_00487
+MPEGRIVLAATPIGNLGDASARLRDLLAEADVIAAEDTRTARRLCAGLGVTPAGRVVAHH
+EHNEAASAQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVTCAPGPSAVT
+TALALSGLPTDRFAFDGFVPRKDGERRRWLTSLLTEARTVVAFESPQRLADALAVVAEVL
+GAERPVCVARELTKLHEEVVRGTAAGVHAWAAERHAGEGIRGEIVLVIGPAAPGAEGEAS
+EADAVAEVAVLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAARG
+>PROKKA_00207
+MTGRIVLAATPIGNLGDASARLRELMAEADVIAAEDTRTARRLCAGLGVTPAGRVVAHHE
+HNEAASTQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVTCAPGPSAVTT
+ALALSGLPTDRFAFDGFVPRKDGDRRRWLTSLLTEARTVVAFESPQRLADALAVVVEVLG
+AERPVCVARELTKLHEEVVRGTAADVHAWAAERHAGEGIRGEIVLVIGPAAPGAEGEASE
+ADAVAEVAVLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAARS
+>PROKKA_02459
+MTPRPTDLPSPSGRIVLAATPIGNLGDASARLRELLAEADVIAAEDTRTARRLCQGLGVT
+PAGRVVAHHEHNEAASTQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVT
+CAPGPSAVTTALALSGLPTDRFAFDGFVPRKDGERRRWLTSLLTEARTVVAFESPQRLAD
+ALAVVVEVLGAERPVCVARELTKLHEEVVRGTAAEVHAWAAERHAGEGIRGEIVLVIGPA
+SPDAASAGGATEADAVAEVGVLVDSGTRLKEAVATVAAAHGLRSRTLYQAVLAARG
+>PROKKA_02343
+MSLPAASGRIVLAATPLGNLGDATGRLRELLATADVIAAEDTRNTRRLCQGLGITPAGRL
+MAHHEHNEAASAAGLLERVRAGETVVMVSDAGMPTVSDPGFRLVEAAVAAGLPVTCAPGA
+SAVTTALALSGLPSDRFAFDGFLPRKDGERRRRLEEIRTDPRTVVYFESPQRTASALAVI
+AEVLGGARPVCVARELTKLHEEVVRGTADELVAWAVEREAGEGIRGEVAIVVGPAAPDAG
+AGADEADVLAEVAALTDSGTRLKEAVAAVAAAHGLRSRELYQAVLDARRG
+>PROKKA_00487
+MPEGRIVLAATPIGNLGDASARLRDLLAEADVIAAEDTRTARRLCAGLGVTPAGRVVAHH
+EHNEAASAQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVTCAPGPSAVT
+TALALSGLPTDRFAFDGFVPRKDGERRRWLTSLLTEARTVVAFESPQRLADALAVVVEVL
+GAERPVCVARELTKLHEEVVRGTAAGVHAWAAERHAGEGIRGEIVLVIGPAAPGAEGEAS
+EADAVAEVAVLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000516.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000516.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e85abe65e5c07fbcdfab67dfb0fec6e2f3340d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000516.fa
@@ -0,0 +1,35 @@
+>PROKKA_00500
+MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADHIRSSVEGEEVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVQILKDAGAKDVIIAATHPVFSDPAAQRLGECGAREVVVTNTLPIPEEKRFETLTVLS
+IAPLIARAIREVFEDGSVTSLFDGVA
+>PROKKA_00221
+MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADHIRSSVEGEEVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVQILKDAGAKDVIIAATHAVFSDPAAQRLGECGAREVVVTNTLPIPEEKRFETLTVLS
+IAPLIARAIREVFEDGSVTSLFDGVA
+>PROKKA_02449
+MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADYIRTRVEGEEVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVQILKEAGAKDVIIAATHAVFSEPAAQRLGECGAREVVVTNTLPILEEKRFETLTVLS
+IAPLIARAIREVFEDGSVTSLFDGDA
+>PROKKA_02333
+MTELSRSEDKRLVLAAGRAHPGLAQEIAEALGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFVIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADYIRGQVEGEKVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVRILKEAGAKDVIIAATHAVFSDPAAQRLGESGAREVVVTNTLPIPEEKRFDNLTVLS
+IAPLIARAIREVFEDGSVTSLFDGDA
+>PROKKA_00499
+MTELSRSEDKRLVLATGRAHPELAQEIAEELGTELLPMSAYDFANGEIYVRSGESVRGKD
+VFIIQSHPAPLNNHLMEQLIMVDSMKRASARRITVVSPFYPYARQDKKGRGREPISARLV
+ADLYKTAGASRVMSVDLHTAQIQGFFDGPVDHLFAIPLLADHIRSSVEGEEVTVVSPDTG
+RVRVAEQWADRLGGVPLGFVHKSRDLTVPNKAESKTVVGDVEGRVCVLIDDMIDTGGTIA
+GAVQILKDAGAKDVIIAATHPVFSDPAAQRLGECGAREVVVTNTLPIPEEKRFETLTVLS
+IAPLIARAIREVFEDGSVTSLFDGVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000519.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000519.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92b1e70b60df6ed3f44ccc5ccd1899cb2f4dc929
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000519.fa
@@ -0,0 +1,35 @@
+>PROKKA_00504
+MAAQSTTAAVTVVIPHYGDPAPTLALVDRLLTDPGDALAAVVVSDDASPTPYPEAHDPRL
+TVVRRERNGGFGANVNTGLAAVTTELALVLNSDAEITGAQIDALVVAAAPYQPAVVSPQV
+VNEDGTPQWSGRHFPTVLHQTVEWLTPLARFRHLDVLHEAVGHDVAATRSASPVAVDWVM
+GAVLLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSIVVPAVRVPHGLHGSSDPL
+RRRGWLVDSRYRYARKFGHPRVLKAALTAATGANFAVNALRQARGVDVDARAVLRDEHAL
+VWKGQRR
+>PROKKA_00224
+MAAQSPTAAVTVVIPHYGDPAPTLALVDRLLTDPGDALAAVVVSDDASPTPYPEAHDPRL
+TVVRRERNGGFGANVNTGLAAVTTELALVLNSDAEITGAQIDALVAAAAPYQPAVVSPQV
+VNEDGTPQWSGRHFPTVLHQTVEWLTPLARFRHLDVLHEAVGHDVAATRSASPVAVDWVM
+GAVLLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSIVVPAVRVPHGLHGSSDPL
+RRRGWLVDSRYRYARKFGHPRVLKAALTAATGANFAVNVLRQARGVDVDARAVLRDEHAL
+VWKGKRR
+>PROKKA_02446
+MAAQSTAAAVTVVIPHYGDPAPTLALVDRLLADPGDALAAVVVSDDASPTPYPEAHDPRL
+TVVRRERNGGFGANVNTGLSEVDTDLALVLNSDALITGEQIDALVAAAAPFQPAVVSPQV
+VNEDGSPQWSGRHFPTVLHQGVEWLTPLARFRHLPLLHEAVGHDVAAARSAAPVAVDWVM
+GAVMLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRDRGVASIVVPSVRVEHGMHGSSDPL
+RRRGWLVDSRFRYARKFGRPRALKAVLTAATGVNYAVNRVRQARGTDVDAAAVLRDEHAL
+IWKGTRR
+>PROKKA_02330
+MPASRIAPSVTVVIPHYGDPEPTRALVDALLAAPGRSVAGVVVSDDASPEPYPQPAPGRE
+GLTVVRREANGGFGANVNTGLAEVRTELALVLNSDAEITGEQIDALVEAARPYQPAVVSP
+QVVNEDGSPQWSGRHFPTVTHQTVEWLTPLARFRHLPALHEAVGHDVRAAEADSPVAVDW
+VMGAVMLLPMAEVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSVVVPSVRVVHGLHGSSD
+PLRRRAWLVDSRFRYARKFGRPRLLRGALTAATGVNWAVNRVRQTRGTDVDANAVFRAER
+DLIWKGTRR
+>PROKKA_00503
+MTAQSPTAAVTVVIPHYGDPAPTLALVDRLLSDPGDALAAVVVSDDASPTPYPEAHDPRL
+TVVRRERNGGFGANVNTGLAAVTTELALVLNSDADITGAQIDALVAAAAPYQPAVVSPQV
+VNEDGSPQWSGRHFPTVLHQTVEWLTPLARFRHLDVLHEAVGHDVAAARSASPVAVDWVM
+GAVLLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSIVVPAVRVPHGLHGSSDPL
+RRRGWLVDSRYRYARKFGHPRVLKAALTAATGANFAVNALRQARGVDVDARAVLRDEHAL
+VWKGRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000526.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000526.fa
new file mode 100644
index 0000000000000000000000000000000000000000..393243d9d2d3c60316af2678c7c67332e1fcfcc1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000526.fa
@@ -0,0 +1,40 @@
+>PROKKA_00513
+MTDMTRGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTFPEFKDARIITS
+PLNRVGVLRKDPRRALPLLPLASSLLHVKEPVAVVSTSGWAHGFRYDGATLVYCHTPARW
+VYLLDDYLGEGGRNSIKGRIARALRPGLRRWDRAAVRRRSRYVANSTVVKERIEDVYGLD
+GVDLVFPPHSVSTDGPQEPIPGAERLAEDGFLLSVARLMPYKHVDVAIEAAARAGRPLVV
+IGKGPEEARLRAMAGEDVVFGQDLTDAQLRWAYAHAIALIAASHEDFGITPLEASAWGVP
+TVALRAGGYLDTIVDGVNGTFVLDASIDAVGEGIKKLQAARWDTAAMRRHVEKFSEREFA
+LRIRALVEGLPGA
+>PROKKA_00233
+MSEQTPATIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTFPEFEDAHIVTS
+PLNRVGVLRKDPRRALPLLPLASSLMHVKEPIAVVSTSGWAHGFRYDGATLVYCHTPARW
+VYLLDDYLGEDGRNSIKGRIARVLRPGLRRWDRAAVRRRSRYVANSTVVKKRIDDVYGLD
+GVDLVFPPHSVSTDGPQGPIPGAEQLAEDGFLLSVARLMPYKHVDVAIEAAARAGRPLVV
+IGKGPEEARLRAMAGEDVVFGQDLTDAQLRWAYAHATALIAASHEDFGITPLEASAWGVP
+TVALRAGGYLDTIVDGVNGVFVEEPTVDAVAGGVERLLAHDWDRAAMQAHAERFSEAQFG
+RRIRALVAESPAGPAHRGRQ
+>PROKKA_02438
+MTDTTRGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTFPEFKDARIITS
+PLNRVGVLRRDPRRALPLLPVASSLMHVKEPVAVVSTSGWAHGFRYHGDTLVYCHTPARW
+VYLLEDYLGEEGQKSMKGRVARVLRPGLRAWDRAAQRRRTRYVANSTVVKERIEEAYGLT
+DVPIVFPPHSVSTDGSQEPIPGAEHLAEGGYLLSVARLMPYKHVDVAIRAAERTGLRLLV
+IGKGPDEARLKAMAGDGVVFAQDLTDAQLRWAYAHATALIAASHEDFGITPLEASAWGVP
+TVALRAGGYLDTITEGVNGVFVEAPTVEAVTDGVEQALARDWDPPAMRAHAERFSEDQIA
+RQVRTQLGQLQNHARNKGAM
+>PROKKA_02321
+MKIHASRPLSARRASQPGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYNPEGTF
+PEFKKARIITSPLNRVGVLRSDPRRALPLLPLASSLMHVKEPLAVVSTSGWAHGFRYEGD
+TLVYCHTPARWVYLLEDYLGEGGQRSLKGRVARALRPALRAWDSAAQLRRTRYVANSTVV
+KRRIEEVYGVANVDLVFPPHSVSTDGPQAPIPGAEDLAEGGYLLSVARLMPYKHVDVAIR
+AAERTGRRLLVIGKGPEEARLRALAGQGVVFAQDLTDAQLRWAYAHAVALIAASHEDFGI
+TPLEASAWGVPTVALRAGGYLDTIVEGVNGVFVPEPTVEAVTDVVEQVLAQDWDRGAMQA
+HAEHFSEVAFRERLARLLDDPHGAV
+>PROKKA_00512
+MTDTTRGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTFPEFKDARIITS
+PLNRVGLLRKDPRRALPLLPLASSLMHVKEPIAVVSTSGWAHGFRYDGATLVYCHTPARW
+VYLLDDYLGEGGRDSIKGRIARVLRPGLRRWDRAAVRRRSRYVANSTVVKERIEEVYGLI
+DVPVVFPPHSVSTDGPQEPIPGAEHLAEGGYLLSVARLMPYKHVDVAIRAAERTGLRLLV
+IGKGPEEARLKAMAGDGVVFAQDLTEAQLRWAYAHATALIAASHEDFGITPLEASAWGVP
+TVALRAGGYLDTIVEGVNGVFVNGTSVAAVAGGIEWVRAHNWDRAAMRSHARRFSEFEFG
+QQVQAQLGWIGISR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000531.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000531.fa
new file mode 100644
index 0000000000000000000000000000000000000000..771b9f6cab59511e61a4db4c3fcf2f67a7644b68
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000531.fa
@@ -0,0 +1,20 @@
+>PROKKA_00529
+MAFSAQQSIPHPPAAVAAALASEDFHRSVVESFGGSLVSFSVEGSPEGPMTVTAVRSLPA
+DRIPDRVPDMARKLIGSALQVEQVERWDAPAADGSRAGTTTITVPSAKATADGALRLTAA
+GEGSQFSVDGTLVCRIPLVGSKLAAKAEPMVGKVVNRQARALSSWLERDGGAARG
+>PROKKA_00250
+MAFSAQQSIPHPPAAVAAALASEDFHRSVVESFGGSLVSFSVEGSPEGPMTVTAVRSLPA
+DRIPDRVPDMARKLIGSALQVEQVERWDAPAADGSRAGTTTITVPSAKATADGSLRLTAA
+GEGSQFSVDGTLVCRIPLVGSKLAAKAEPMVGKVVDRQARALSSWLERDGGAARS
+>PROKKA_02423
+MAFSAQQSIPHPPAAVAAALASEEFHRSVVEQLGGSLVSFRVEGSPEGPMTVTTVRSAPA
+DRLPEMARKFIGSSLQVEQVERWEAPAADGSRVGTTTITVPAAKATAEGAQRLTAAGEGS
+QYSVDGTVTCKIPLVGSKLAAKAEPMVGKVVNRQARALTSWIGRDGGAAGA
+>PROKKA_02305
+MAFSAQQTIPHPPAAVAEALFSEDFHRSVAESLGGGLVSFARQDQADGGVELTIVRSGPT
+DRLPDMVRKVVGENLNIEQVERWSAPAADGSRTGTTTIRVPKAKATAEGTLRLAAAPAGT
+EYGVNGDLQVKIPLVGSKMAQMAEPMVGKVVARAGREVSAWIDRGGRG
+>PROKKA_00529
+MAFSAQQPIPHPPSAVAAALASEDFHRSVVESFGGSLVSFSVEGSPEGPMTVTAVRSLPA
+DRIPDRVPDMARKLIGSALQVEQVERWDAPAADGSRTGTTTITVPSAKATADGSLRLTAA
+GEGSQFSVDGTLVCRIPLVGSKLAAKAEPMVGKVVNRQARALSSWLERDGGAARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000534.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000534.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad0845bcf036d406098f9dc35b2bef535c1f0915
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000534.fa
@@ -0,0 +1,16 @@
+>PROKKA_00532
+MTVETTEGWTLAPNIAWARTAGGQAAVMTLEAGQPLLLGASGDVIWDVLVGGRTPEDDLV
+ADPPASLSTTDVTVQVAEAFGLAPADVAADVHAFLEMLEAHGVLVRVRTA
+>PROKKA_00253
+MTVETTEGWALAPDIAWARTAGGQTAVMTLEAGQPLLLSASGDVIWDVLVGGRTPADDLV
+ADPPAPLSTTDVTVQVAKAFGLYPADVAADVHAFLEMLEAHGVLVRVRTA
+>PROKKA_02420
+MAADRLPAPFGMTSERGSAWAVAPGVAWALTDGGDAAVMHLEHGVPLLLSPTGHAVWDVL
+VGGRTPEDDLTAAPPIPLPEEAVAAETAAAFGLAPEDVAADVGAFLAMLEQHGVVVRVGG
+VLPRP
+>PROKKA_02302
+MSDAEHPPFAQAPAARAWRVAPTTAWVRSGEHQVTVMDLDEGNPQVLSPTGSAVWELLLD
+GRTPEDDLAADPPKPVEEEALCGAVAEAFGVDVEVVAADTRAFLGMLAGHRLVVPAVLP
+>PROKKA_00532
+MTVETTEGWALAPDIAWARTAGGQAAVMTLEAGQPLLLSASGDVIWDVLVGGRTPEDDLI
+ADPPVPLSTTDVTVQVAEAFGLDPADVAADVHAFLEMLEAHGILVRVRTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000537.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000537.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aba08d61ca90a9fb0bf970433d9a3e5f5902489c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000537.fa
@@ -0,0 +1,35 @@
+>PROKKA_00535
+MDALRLVSIAAVVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVWGRFRS
+LMVPYLVWAALMSVAAFAWFADDPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFTTVL
+RRFLERFPSAVAWAVGLAGLAWAHLVPDSAIARTPLGVGLALPCLLFVLSGEMFRRRVQP
+HVRRHRTLIGVGLVLLGMVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFGSTV
+ERLLRSFARRTGTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALALAL
+SWLAGLALLATPLSKPFTGARRRWHPVHRLRHVEPPHPVTSALPRVTTASERTHP
+>PROKKA_00259
+MVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVWGRFRSLMVPYLVWAAL
+MSVAAFAWFADDPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFTTVLRRFLERFPSAV
+AWAVGLAGLAWAHLVPDSAIARTPLGVGLALPCLLFVLSGEMFRRRVQPHVRRHRTLIGV
+GLVLLGMVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFGSTVERLLRSFARRT
+GTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALALALSWLAGLALLAT
+PLSKPFTGARRRWHPVHRLRHVEPPHPVTSALPRVTTASERTHP
+>PROKKA_02414
+MDALRLVSIAAVVLGHAYLADLTFSRYLEIWRMPLFFFLTGYFWTRGRPVARDARGRFKA
+LMVPYLVWAVVMSAAALAWFGDDPERLQRLMAAGWYGGADQEPPWWAFWFISVLFFATVL
+RRFLERFPTAVAWGVGLAGLAWAYLVPESAIARTPLGVGLALPCLLFILSGEAFRRRVQP
+RIRRHRTLLGLALVGLGLAAVALGLEPHNIKFGGFGTPLLTPLVGVLMSAGMVLVFGAAV
+ERILREFARRTGSGQALRRVITALVRTGTVVVLLHGWVLMWVMRQGVEDNLLKFVLALGI
+SWLVGLALLATPLSKPLTGARRRWFPLHRLRGEEPPHPPTSALPRVTTASERTHP
+>PROKKA_02296
+MDALRLVSISAVVLGHAYLADLTFSPYLEIWRMPLFFFLTGYFWTRGRPWAADALSRFRS
+LMVPYLLWSVLMTLVVLSWSRRSQIDGVTLADLVSAGWYGGADQPPPWWAFWFISVLFFV
+ALLRRALERAPSWAGWAVALAGLAAAELVPESAIARTPLGIGLAAPCLFYVLAGEAFRRR
+VQPRIRRHRTLIGVALVAAGVGAVALGLPPHNIKWGGFGLFPWTPLTGIAMAAGMVLVFG
+AFVERRLRAFARDTGTGRAIRAGITALTRTGTVVVLLHGLVLMEAMRVGIEDNLMKFVVA
+LTVSWAVGLALLATPLARPLTGVPQQWFPFGREAGA
+>PROKKA_00538
+MDALRLVSIAAVVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVRGRFRS
+LMVPYLVWAALMSVAAFAWFADDPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFTTVL
+RRFLERFPSAVAWAVGLAGLAWAHFVPDSAIARTPLGVGLALPCLLFVLSGETFRRRVQP
+HVRRHRTLIGVGLVLLGLVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFGSTV
+EGLLRSFARRTGTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALALAL
+SWLAGLALLATPLSKPFTGARRRWHPVHRLRRVEPPHPVTSALPRVPTASERTHP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000538.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000538.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e0e6f9181828b8bf0c114add506a0a5278ac9fd9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000538.fa
@@ -0,0 +1,25 @@
+>PROKKA_00537
+MTVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELAGS
+DVLTCTVIGFPLGANASEVKAFEARQAIDAGADEVDMVLDVAAARAGDRDRLVADVRAVA
+EAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH
+VALMRRTVGERIGVKASGGVRTRADALAMIEAGATRIGASSALAILGSD
+>PROKKA_00261
+MTVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELADS
+DVLTCTVIGFPLGANTSEVKAFEARQAIDAGADEVDMVLDIAAARAGDRARLVADVRAVA
+EAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH
+VALMRRTVGEDIGVKASGGVRTREDALAMIEAGATRIGASSALAILGSD
+>PROKKA_02412
+MTRTLSTAELAQYIDATALKTETSEADVRRLVAEARQAGVKSVCVNPRWVPLVSAELAGS
+DVLTCTVIGFPLGANASEVKTFEARQAIEAGAHEVDMVIDVAAARAGDRARLVEDVRAVA
+EAAHAAGPAGQGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH
+VALMRRTVGEHVGVKASGGVRTREDALAMIEAGATRIGASSALAILGTD
+>PROKKA_02294
+MSETPQLTTAELAKHIDHTLLKPEASREDILRVVAEAREAGVKSVCVNPRWVREVRAGLE
+GSDVLTCTVIGFPLGASSSAVKAFETTQAIADGADEVDMVIDIAAARAGDRARLEEDVRA
+VVAAAHASGPAGRAGTLVKVIIETALLDDAAKVLACEAAVAAGADFVKTSTGFSTGGATV
+EDVALMRRTVGPEIGVKASGGVRSREDALAMITAGATRIGASSALAILGDD
+>PROKKA_00540
+MTVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELAGS
+DVLTCTVIGFPLGANASEVKAFEARQAIDAGADEVDMVLDVAAARAGDRDRLVADVRAVA
+EAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH
+VALMRRTVGERIGVKASGGVRTRADALAMIEAGATRIGASSALAILGSD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000540.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000540.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09684f9c3faf1be83ba0598089c46d3037e6157b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000540.fa
@@ -0,0 +1,30 @@
+>PROKKA_00539
+MTDQTSIPSPDSPLTGDHPGFAEARAAADTIARATGVAEHRVAVVLGSGWGEAAGLIGDE
+VAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTVRTA
+AAAGARTVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLVGATFVDLTDLYSPRLRAI
+AREVDPSLREGVYVQFAGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVFGIS
+LVTNLGAGISETPLSHAEVVEAGQAAGPRIARLLADIVGRL
+>PROKKA_00263
+MTDQTSIPSPDSPLTGDHPGFAEARAAADTIARATGVAEHRVAVVLGSGWGEAAGLIGEE
+VAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTVRTA
+AAAGARTVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLAGATFVDLTDLYSPRLRAI
+AREVDPSLREGVYVQFAGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVFGIS
+LVTNLGAGISETPLSHAEVVEAGQAAGPRIARLLADIVGRL
+>PROKKA_02410
+MSEQTFSPSPASPLAGDHPGFDQARAAAAVIADATGVAEHRIAVVLGSGWGEAAGLIGEE
+VAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTVRTA
+AAAGAKTVVLTNGCGGLDPEIAPGTPVLISDHLNLTGATPLVGATFVDLTDLYSPRIRQI
+AREVDPSLREGVYVQFSGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVFGMS
+LVTNLGAGISETALSHGEVVEAGQAAGPRISRLLADIVWRL
+>PROKKA_02292
+MSEQSTPTPTPASLARLAGDHPGFAEARAAAEAIAEATGCAEHRIAVVLGSGWGEAAELI
+GVERARIDLADVPGFHAPKVPGHNAVIRSVELADGSRALVFGSRTHFYESRDAQAVAHTV
+RTAAAAGAATVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLVGATFVDLTDVYSPRI
+RAIAQEVDPTLTEGVYVQFSGPQYETPAEVRMATALGGDLVGMSTALDAIAARHAGLEVF
+GISLVTNHGAGIQETPLSHQEVVEAGQAAGPRISRLLAEIVGRL
+>PROKKA_00542
+MTDQTSIPSPDSPLTGDHPGFAEARAAADTIARATGVAEHRVAVVLGSGWGEAAGLIGDE
+VAAVPLAEVPGFHAPKVPGHNAVIRSVRLPDGTHALVFGSRTHFYESRDAQAVAHTVRTA
+AAAGARTVVLTNGCGGLDPEIAPGTPVLIADHINLTGATPLVGATFVDLTDLYSPRLRAI
+AREVDPSLREGVYVQFAGPQYETPAEVRMARTLGGDLVGMSTALDAIAARHAGLEVFGIS
+LVTNLGAGISETPLSHAEVVEAGQAAGPRIARLLADIVGRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000542.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000542.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e40afc7fa24ed84777f52637f436481fbf9c192b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000542.fa
@@ -0,0 +1,45 @@
+>PROKKA_00541
+MSHSTPPVNPGAPTDLTSDAVATAEEVPRSRVIIASLVGTSIEFYDFYIYATAAVSVFPL
+IFFAGGDDNTALLASMATFGAAFIARPLGAVVFGHLGDRVGRKTTLIGSLLTMGIATFLI
+GLLPTYFQIGLWAPAMLTLLRFFQGLGLGGEWSGAALLATEYAKDGKRAQAAMWPQLGAP
+IGFLLANGLFLALVLGFDHDSTNPVLDGPFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP
+VFQRALDRDQRVKAPLSEVFRRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKPANGF
+LGVPYAEFLVLQLVGILFFAAFVPVSGLLADRFGRRPTLIVISVLMVLFGLSFGLWLSPE
+NMGVGAELNGPLMVAFLATGMTLMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA
+ALTPFIAAWLVQKFDVSYVGYYLAAASAITVIALVLSPETRHTDLDTVTSARERRAAR
+>PROKKA_00265
+MSHSTPPVNPGAPTDLTSDAVATAEEVPRSRVIIASLVGTSIEFYDFYIYATAAVSVFPL
+IFFAGGDDNTALLASMATFGAAFIARPLGAVVFGHLGDRVGRKTTLIGSLLTMGIATFLI
+GLLPTYFQIGLWAPAMLTLLRFFQGLGLGGEWSGAALLATEYAKDGKRAQAAMWPQLGAP
+IGFLLANGLFLALVLGFDHDSTNPVLDGPFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP
+VFQRALDRDQRVKAPLGEVFRRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKPANGF
+LGVPYAEFLVLQLVGILFFAAFVPVSGLLADRFGRRPTLIVISVLMVLFGLSFGLWLSPE
+NMGVGAELNVPLMLAFLATGMTLMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA
+ALTPFIAAWLVQKFDVAYVGYYLAAASAITVIALALSPETRHTDLDTVTSARERRAAR
+>PROKKA_02408
+MSRTTTPADGTAAGLEAAAEVPRGRVITASLVGTSIEFYDFYVYATAAVSVFPLIFFPGD
+DQTTALLASFAVFGTAFVARPIGSVLFGHFGDIMGRKVTLIGSLLTMGIATFLIGLLPTA
+FQIGLWAPAMLVVLRFCQGLGLGGEWSGAALLATEYAAEGKRARAAMWPQLGAPIGFFLA
+NGLFLALVIGFGHDSTNPDHDGAFLNWVWRLPFLLSIVMVAVGLYVRVKLEETPVFQRAI
+ANDTRVKAPLGEVFKRNWWELILGTFIMYATYVLFYLMTTWILSYAIGKTENGMLGVPYA
+EFLVLQLIGILFFAAFVPASGWLADRFGRKPTLLTVSALMVLFGLSFGLWLSAERMGTGA
+GVNVPLMLAFLAVGMALMGLTFGPMSAVLPELFPTNTRYTGSGISYNVSSILGAALTPFL
+AAWLVKEYGVAYVGYYLAAASVITMIALALAPETRHTDLDGVTSARERRAASV
+>PROKKA_02290
+MSHTTARSAEAPSVEDVPKSRVILASLVGTSIEFYDFYVYATAAVSVFPLIFFPGDDPTT
+ALLASFAVFGTAFVARPIGSILFGHFGDRMGRKVTLIGSLLTMGIATFLIGLLPTAFQIG
+LWAPAMLVVLRFCQGLGLGGEWSGAALLATEYADHGKRARAAMWPQLGAPIGFLLANGLF
+LILVRAFGHDSTNPQLEGSFLTWVWRVPFLLSIVMVAVGLYVRVKLEETPVFQRALEDDT
+RVKAPLGEVFKRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKTQNGMLGVKYADFLV
+LQLVGILFFAAFVPVSGWLADRFGRKPTLLVVSGLMVVFGLSFGAWLSPAAMGQGDALNV
+PSMLAFLAVGMALMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGAALTPFLAGWL
+VKEFGVATVGWYLAIASVITMAALALSPETRHADLHEVTSARERRAAAR
+>PROKKA_00544
+MSHSTPPVNPGAPTDLTSDAVATAEEVPRSRVIIASLVGTSIEFYDFYIYATAAVSVFPL
+IFFAGGDDNTALLASMATFGAAFIARPLGAVVFGHLGDRVGRKTTLIGSLLTMGIATFLI
+GLLPTYFQIGLWAPAMLTLLRFFQGLGLGGEWSGAALLATEYAKDGKRAQAAMWPQLGAP
+IGFLLANGLFLALVLGFDHDSTSPVLDGPFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP
+VFQRALDRDQRVKAPLGEVFRRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKPANGF
+LGVPYAEFLVLQLVGILFFAAFVPVSGLLADRFGRRPTLIVISVLMVLFGLSFGLWLSPE
+NMGVGAELNVPLMLAFLATGMTLMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA
+ALTPFIAAWLVQRFDVSYVGYYLAAASAITVIALALSPETRHADLDTVTSARERRAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000546.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000546.fa
new file mode 100644
index 0000000000000000000000000000000000000000..58b39d220ae8af980786fe5ec51ebd943b369282
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000546.fa
@@ -0,0 +1,50 @@
+>PROKKA_00546
+MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELD
+ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ
+EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA
+YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE
+DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLEVIASIV
+DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAF
+NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS
+KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN
+PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL
+>PROKKA_00271
+MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELD
+ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ
+EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA
+YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE
+DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLAVIASIV
+DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAF
+NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS
+KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN
+PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL
+>PROKKA_02401
+MSDPDLTTTAGRLADLHRRLEATAAPGGEGAVERQHARGKHTARERIDLLLDEGSFVELD
+ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ
+EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA
+YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNSTSGTAHYMASSEE
+DAIAYVQELLELLPSNNLAEAPTFEAADPETTDEDLALDEIVPDSANQPYDMLEVIGAIV
+DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPQQLAGTLDIAASEKAARFVRFCDAF
+NIPILTLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS
+KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATQDAGGDVDARRAEIVADYEAELLN
+PYQAAELGYVDAVVPPHATRGALIRALRATLHKREARPAKKHGNMPL
+>PROKKA_02284
+MSAPELSTTAGRLADLHRRLEATAAPGGEAAVERQHSRGKHTARERIDLLLDEGSFVELD
+ALATHRTTAFGMDAKHPAGDGVVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ
+EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVMASGMIPQISLIMGPSAGGAA
+YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNSTTGTAHYMATSEE
+DAIAYVQDLLEYLPSNNLAEAPVFEAESLEETEQDLALDTIVPDSANQPYDMLEVIAALV
+DDGHLLQLQEMYAPNVITGLARLDGMSVGVVANQPQQLAGTLDIAASEKASRFVRFCDAF
+NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS
+KKLGADLNLAWPSAQIGVMGPQGAVNILYRRELAAAEAAGEDVEARRAQIVADYEAELLN
+PYQAADLGYVDAVVPPRQTRAHLVRALRATFHKREARPAKKHGNMPL
+>PROKKA_00549
+MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELD
+ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ
+EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA
+YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE
+DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLEVIASIV
+DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAF
+NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS
+KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN
+PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000550.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000550.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c09f20338505247bb3144e69ec25c95967f788e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000550.fa
@@ -0,0 +1,35 @@
+>PROKKA_00552
+MSARTTVPGLLVVAKAAARAGADVLARRWTGHHPAVPLGIEEIGAQTKSSGSDWVTDYDR
+RAEQAVREVVAGYRPSDEITGEEYGATRPAEPSGYRWSIDPLDGTTNFVRGLPQFCTSVA
+VTGPVDAETADLLGVAEGTERWLAGVVAAPALGRTWYASAGRGAFSTADATTAGVDLPDR
+DAAPVRLTGPLPGRSGRLLATGFGYDPARRALQVRALAALLPAFGDVRRIGSAALDLCMV
+ADGTLDAYAEFGTQEYDWAAGALVAEEAGVAVTRPASADGTAHPDWMVAGDVDGSALAAM
+TGERA
+>PROKKA_00277
+MSARTTVPGLLVVAKAAARAGADVLARRWTGHHPAVPLGIEEIGAQTKSSGSDWVTDYDR
+RAEQAVREVVAGYRPSDEITGEEYGATRPAEPSGYRWSIDPLDGTTNFVRGLPQFCTSVA
+VTGPVDAETADLLGVAEGTERWLAGVVAAPALGRTWYASAGRGAFSTADATTAGVDLPDR
+DAAPVRLTGPLPGRSGRLLATGFGYDPARRALQVRALAALLPAFGDVRRIGSAALDLCMV
+ADGTLDAYAEFGTQEYDWAAGALVAEEAGVAVTRPASADGTAHPDWMVAGDVDGSALAAM
+TGERA
+>PROKKA_02393
+MSSPTRVAHVPSQPPGISGLLVVAKAAARAGADVLARRWTGHHPAVPLGREEIGAETKTS
+GSDWVTDYDRRAEQAVREVLVAYRPQDEITGEEYGATVPAEPSGLRWSIDPLDGTTNFVR
+GLPQFCTSVAVTGPVDEETAALLGVPAGTRRWLAGVVAAPALGRTWFASAGRGAFSTADA
+TTAGVDVPDRDAAPVRITGPAPGRSGRLLATGFGYDPARRAMQVRALAALLPAFGDVRRI
+GSAALDLCMVADGTLDAYAEFGTQEYDWAAGALIAEEAGVRVRRPASGDGTAHPDWMVAG
+DVDEAALAAAQEETA
+>PROKKA_02278
+MSAAPARPASPAGLLVIAKAAARAGADVLAERWAGHHPAVPLTSDELGADTKSSGSDWVT
+DYDRRAEDAVRAVLTGYRPHDEITGEEHGSTAPVEPSGYRWSIDPLDGTTNFIRGLPQFG
+TSVAVEGPVDEETAALLGVLPGSRRWLAGVVAAPALGRTWFASAGRGAFSTADATTAGVA
+VPDRDAAPVRLTGPVPGRSGRLLATGFGYHPGRRAMQLRALAALLPAFGDVRRIGSAALD
+LCMVADGTLDAYAEFGTQEWDWAAGALIADEAGVPVDRPASGDGTGHPDWMTAGDVDAAA
+LAAAKEATA
+>PROKKA_00555
+MSARTTVPGLLVVAKAAARAGADVLARRWTGHHPAVPLGIEEIGAQTKSSGSDWVTDYDR
+RAEQAVREVVAGYRPSDEITGEEYGATRPAEPSGYRWSIDPLDGTTNFVRGLPQFCTSVA
+VTGPVDAETADLLGVAEGTERWLAGVVAAPALGRTWYASAGRGAFSTADATTAGVDLPDR
+DAAPVRLTGPLPGRSGRLLATGFGYDPARRALQVRALAALLPAFGDVRRIGSAALDLCMV
+ADGTLDAYAEFGTQEYDWAAGALVAEEAGVAVTRPASADGTAHPDWMVAGDVDGSALAAV
+TGERA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000555.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000555.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1e1bacc2d00893a87405635512c1d6881093d446
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000555.fa
@@ -0,0 +1,36 @@
+>PROKKA_00558
+MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL
+RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLASALAERDVSWAVPVALSDPVSAG
+PGAAVLQRFLPGGPYPPHEGDPDVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPAR
+ARHVAALPGAVAARLGAWEGHDVDARLGAEAWPDAVAALTDAVTTWTAAPPVPPSLVHGD
+LAGHNMRWRAVPEDEDPRAPLRWALAGVLDWDLACAWGPALNVAYLALWHGEQKVPDLAR
+DAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLRKTLPRVARALTALDG
+>PROKKA_00283
+MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL
+RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLAAALAERRVPWTVPIALSDPVPAG
+PGAAVLQRFLPGGPHPPHEGDPAVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPER
+ARHVAALPGAVAARLGAWEGHDVDARLGAEAWPDAVAALADAVTTWTAAPPVPPSLVHGD
+LAGHNMRWRAVPEDEDPRAPLRWALAGVLDWDLACAWDPALNVAYLALWHGEEKVPDLAR
+DAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLRKTLPRVARALTALDG
+>PROKKA_02385
+MASDPVDSELELVHRALGRLRPHVSPADARALHEADWSAGTVEEGGQFNRVLVCAGAGVL
+RMTRAHEVGAAPAARWSPERDPARQLGRRMALLDGLDAALAEQGVAWTVPVALSDPVPAG
+TGAAVLQRYLPGGPHPPHEGDPAVLRRLLDEIAAVDVADPRIAPHLGRPFSFRGPWTAQR
+AEHVAGIPGRLAPRLGAWPGDDVDARTGADAWADAVARVTRAVTAWTEEPPVPPSLVHGD
+LAGHNMRWRAMPAADDAPGEVRWELAGVLDWDLACAWDPALNVAYLSLWHGEDQVERLAV
+DAGEAARARVWLGAMALETLDDAAARDELVGGLPNGSWRRLLRKALPRVARALTALG
+>PROKKA_02269
+MASDPARSELDLVAAALQRLRPGLDDGVAARLRGADWSAGRVEEGGQFHRVLVLEDVGVL
+RMTRVHEAGAAPAARWTPERDPAVHLPRRLALLDGLAAVLAEAGVRWSLPTALSAVVEDG
+PGAAVLQRYVPGFPHPPHEGDPAVLRGVLADLAAVDVADPRVAPHLGRPFTFRGPWTPER
+AAHVAGLPARLAPRLGAWPGDALGHAGDETAAGEAAVRLRADAWGESVTALTGVVSAWTR
+EPPVPPALVHGDLAGHNMRWRVVPAAATPDAEVPDAPVRWELAGVLDWDLACAWDPALNV
+AYLGLWHGEDLVEAIAADPAEARRARVWLGAMALETLDDAGARDVLVGGLAESSWRRLLR
+KTLPRVGRALAAAAA
+>PROKKA_00561
+MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL
+RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLAAALAERRVPWTVPIALSDPVPAG
+PGAAVLQRFLPGGPHPPHEGDPAVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPER
+ARHVAALPGAVAARLGAWEGHDVDARLGAEAWPDAVAAVTDAVTAWTAAPPVPPSLVHGD
+LAGHNMRWRAVPEDEDPRAPLRWALAGVLDWDFACAWDPALNVAYLALWHGEEKVPDLAR
+DAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLRKTLPRVARALTALDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000562.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000562.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f78f057c3738a0963e174a1c034542da8758eea0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000562.fa
@@ -0,0 +1,15 @@
+>PROKKA_00565
+MTETNAPDAQPLPIRDESIRLGQALKLASLVEDGAMARDVVTDGLVTVNGAVETRRGAQL
+HDGDVVEFAGEAFVVQAEQA
+>PROKKA_00290
+MMDTMTETNAPDAQPLPIRDESIRLGQALKLASLVEDGAMARDVVTDGLVTVNGAVETRR
+GAQLHDGDVVEFNGEAFVVQAGQA
+>PROKKA_02378
+MMDTMTETNPADARPLPIRDASIRLGQALKLAALVEDGAMARDVVQDGLVTVNGAVETRR
+GAQLKDGDVVEFHGEAVVIEAGSAD
+>PROKKA_02262
+MTSSSDVQPLPIRDESIRLGQALKLASLVEDGAMARDVVQDGMVSVNGEVETRRGRQLHD
+GDVVEFNGEEIVVEAGQS
+>PROKKA_00568
+MTETNAPDAQPLPIRDESIRLGQALKLASLVEDGAMARDVVTDGLVTVNGAVETRRGAQL
+HDGDVVEFAGEAFVVQAEQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000563.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000563.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad741b8e1fbc7cbfc9200f868e8ace6c06acccd1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000563.fa
@@ -0,0 +1,45 @@
+>PROKKA_00566
+MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE
+DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHRRHRQDHLLEAFEAKKGRPAEGMA
+EIVCPDCGTQGAWTEPQLFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGAARK
+KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAGQHFDRWVEDCWDWFID
+LGIDPAHLRKFDVPADERAHYSDATIDLEYDFGFTGGDGWGELMGIANRTDYDLGRHTEH
+SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGVDVRTVLKLD
+PRLAPVKAAVLPLSKKPELQPTTQSLAAELRTLWNIETDDSGAIGRRYRRQDEIGTPFCI
+TVDFDTLEDQAVTIRERDTMAQERVALSQVKSYLLERLVK
+>PROKKA_00291
+MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE
+DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHRRHRQDHLLEAFEAKKGRPAEGMA
+EIVCPDCGTQGAWTEPQLFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGAARK
+KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKQHFDRWVEDCWDWFID
+LGIDPAHLRKFDVPAEDRAHYSDGTIDLEYDFGFTGGDGWGELMGIANRTDYDLGQHTTH
+SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGVDVRTVLKLD
+PRLAPVKAAVLPLSKKPELQPATQSLAAELRGLWNIETDDSGAIGRRYRRQDEIGTPFCI
+TVDFDTLEDQAVTIRERDTMAQERVALSQVKSYLLERLVK
+>PROKKA_02377
+MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE
+DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHKRHRQDHLLEAFEAKKGRPSASMD
+EIVCPDCGTKGAWTEPQMFSGLVKTFLGPVDNEEGLHYMRPETAQGIFVNFLNVLGASRK
+KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKQHFDTWVEACWDWFID
+LGIDPENLRRLDVPEEERAHYSDGTIDLEYRFGFGGGDGWGELMGVANRTDYDLGRHTEH
+SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGTDVRTVLKLD
+PRLAPVKAAVLPLSKKPELQPATQALAAELRALWNIETDDSGAIGRRYRRQDEIGTPFCI
+TVDFDTLEDQAVTIRERDTMSQERVALSQVKSYLLERLVK
+>PROKKA_02261
+MAAKSPLDNVINLAKRRGFVFQAGDIYGGSRSAWDYGPLGVELKENIKAEWWRTFVRSRE
+DMVGLDSSIILPRQVWEASGHVATFTDPLVECQQCHRRHRQDHLLEAFEAKKGRAAAGME
+EITCPDCGTTGKWTEPQMFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGASRK
+KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKEHFDTWVEACWDWFID
+LGIDPANLRKFDVPEEERAHYSDGTIDLEYRFGFAGGDGWGELMGVANRTDYDLTSHANA
+SGAKLQYFDQANDVHYTPYVIEPSFGLTRSMMAFLVDAYTEDEAPNAKGGVDVRTVLKLD
+PRLAPVKAAVLPLSKKLELQEPSQRLAAELRAHWNIETDDSGAIGRRYRRQDEIGTPFCI
+TVDFDTLEDQSVTIRERDTMSQERVALAQVRAYLAERLTK
+>PROKKA_00569
+MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE
+DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHRRHRQDHLLEAFEAKKGRPAEGMA
+EIVCPDCGTQGAWTEPQLFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGAARK
+KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKQHFDRWVEDCWDWFID
+LGIDPAHLRKFDVPADERAHYSDATIDLEYDFGFTGGDGWGELMGIANRTDYDLGRHTEH
+SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGVDVRTVLKLD
+PRLAPVKAAVLPLSKKPELQPATQSLAAELRTLWNIETDDSGAIGRRYRRQDEIGTPYCI
+TVDFDTLEDQAVTIRERDTMAQERVALSQVKSYLLERLVK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000569.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000569.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88f755f63dce0d9b06a6b48f129c42773e44f495
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000569.fa
@@ -0,0 +1,34 @@
+>PROKKA_00579
+MADPHPVLAASAPVLADPHPVLAASAPDLDPDALDAVRALVAAAERPVVLSGAGMSAESG
+IPTFRDARTGLWERFSAEELATEEAFLADPALVWSWYRWRARMVRARRPNPGHDAVAAWQ
+RRTPGLEVVTQNVDDLHERAGARVLAHLHGSLFEHRCAECWAPADVDPGAPADEATAGSE
+ADLEAMLREAPPACTVCGDGLIRPGIVWFGEMLPAEPWDRAFAALEDCDLCVVVGTSGIV
+QPAASLPFVALGAGAAVVEVNPVETELSGAVTHVLRGPAGAVLPALVAGVWPGPSGALST
+ARHVTW
+>PROKKA_00311
+MADPHPVLAASAPVLAASAPVLAASAPDLDPGALDAVRALVAAAERPVVLSGAGMSAESG
+IPTFRDAQTGLWERFSAEQLATEEAFLADPALVWSWYRWRARMVRARRPNPGHDAVAAWQ
+RRTPDLEVVTQNVDDLHERAGARVLAHLHGSLFEHRCAECGAPADVDPGAPSDVDAAGSE
+ADLEAMLREAPPACPACGTGRIRPGVVWFGEMLPQEPWERAYEALERCDLALVVGTSGLI
+QPAASLPFVALGAGVAVVEVNPVKTELSGAVTHALRGSAGAVLPALVAGVWPGPSGALST
+ARHVTW
+>PROKKA_02354
+MPVEPGRDDVGPAGEAGRAVVGAGQRRRVVNPVAATPPSYLGRHYPVPMSHPSPGDLSET
+VPTADLDAVRALVAQARRPVVLTGAGMSAESGIPTFRDAQTGLWERYSPEQLATEDAFLA
+DPDLVWSWYRWRARMVRARRPNPGHDAVAHWQRAVPGLEVVTQNVDDLHERAGARVLAHL
+HGSLFEHRCAECGAPADVDPGAPADAEAAGSEADLEAMLREAPPTCPACGTGRIRPGVVW
+FGEMLPQEPWERAYEALERCDLALVVGTSGLVQPAASLPFVALGAGAAVVEVNPVETELS
+GAVTHALRGSAGAVLPALVAGV
+>PROKKA_02248
+MSPTQPSDPAALGAVRRLILEAERPVVLTGAGVSAESGVPTFRDAQTGLWERYSPEQLAT
+AEAFAADPSLVWSWYLWRARMVRAVEPNAGHRALAAWQARTPALRIVTQNVDDLHERAGA
+DVLSHLHGSLFAFRCAECDTPADVDPSAVVALAESAAPGSEAGLEALMHLEPPLCAACRR
+GRVRPDIVWFGELLPERAWGDAQAALEECDLCVVVGTSGVVQPAASLPFLALGAGAPVVE
+VNPDRTALSDAMTHVLRGPAGTVLPALLG
+>PROKKA_00580
+MADPHPVLAASAPVLADPHPVLAASAPDLDPGALDAVRALVAAAERPVVLSGAGMSAESG
+IPTFRDAQTGLWERFSAEQLATEEAFLADPALVWSWYRWRARMVRARRPNPGHDAVAAWQ
+RRTPDLEVVTQNVDDLHERAGARVLAHLHGSLFEHRCAECGAPADVDPGAPSDVDAAGSE
+ADLEAMLREAPPACPACGTGRIRPGVVWFGEMLPQEPWERAYEALERCDLALVVGTSGLI
+QPAASLPFVALGAGVAVVEVNPVETELSGAVTHALRGSAGAVLPALVAGVWPGPSGALST
+ARHVTW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000571.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000571.fa
new file mode 100644
index 0000000000000000000000000000000000000000..442c90e9e1dc1b7ff0f2a16ffcbb5ac2c7568c14
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000571.fa
@@ -0,0 +1,60 @@
+>PROKKA_00583
+MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY
+HCFGCGAHGDVISFLMELEHTTFTETVERLASRVGVELHYEDGGTGPDKAETGRRRRLFE
+ANKVADEFFRRALGSPEAQAARDFLTQRGFTQEHATQFGLGYAPQGWSHLLDHLRQRGFR
+DEELRASGLVSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP
+LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKVA
+RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTFVAVEPSGMDPCDLRMQKG
+DEAVRALIASRRPLFEFAIRAGLKDYDLDTVEGRAGALRHAVPIVAGIKDAVLRPGYERE
+LAGWLGLDPNAVHRAVAAAGRAPRRGPEPEARPAPADDGQAIGPQGRHGEAAAPAPRIVV
+PVDPRDPVARRERESLEVVLQHPTLLSAEQWTALYAARFTVPQYAAVHQGVKMAGSAGAT
+PQRWVDAVRDAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFALQIVHRKEELL
+GRLQRLGPEGDPAEFTRLNSELMELEARRRALRADD
+>PROKKA_00316
+MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY
+HCFGCGAHGDVISFLMELEHTTFTETVERLASRVGVELHYEDGGTGPDKAETGRRRRLFE
+ANKVADEFFRRALGSPEAQAARDFLTQRGFTQEHAVQFGLGYAPQGWSHLLDHLRQRGFR
+DEELRASGLVSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP
+LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKVA
+RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTFVAVEPSGMDPCDLRMQKG
+DEAVRALIASRRPLFEFAIRAGLKDYDLNTVEGRAGALRHAAPIVAGIKDAVLRPGYERE
+LAGWLGLDPNAVHRAVAAAGRAPRRGPEPEARPAPADDGQAIGPTGRHGEAAAPAPKIVV
+PVDPRDPVARRERESLEVVLQHPTLLSAEQWTALYAARFTVPQYAAVHQGVKMAGSAGAT
+PQRWVDAVRDAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFALQIVHRKEELL
+GRLQRLGPEGDPAEFTRLNSELMELEARRRALRADD
+>PROKKA_02351
+MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY
+HCFGCGEHGDVISFLMELEHTTFTETVERLAARVGVELHYEDGGTGPDKAETGRRRRLLE
+ANKVADEFYRRALGSAEAQTGRDFLTQRGFTQEHAEQFGLGYAPQGWSHLLDHLRQKGFR
+DEELRASGLFSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP
+LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKMA
+RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTYVAVEPSGMDPCDLRMQQG
+DEAVRALIASRRPLFEFAIRAGLKDYDLDTVEGRAGALRHAAPIVAGIKDAVLRPGYERE
+LAGWLGLDPNAVHRAVAAAGRGQRRGGGSEPRREPERGPEPDQAPGQGRGPAPEGPSVGP
+QGRHGEAAAPAPQVLVPVDPRDPVARCERESLEVVLQHPTLLSAEQWTALYAARFTIPQY
+AAVHHGVKVAGSSGATPQRWVDAVRYAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIM
+NRLFALQIVHRKEELLGRLQRLGPDGDPAEFTALNSELMELEARRRALRADD
+>PROKKA_02246
+MVRMAGLIVRKDIDLVRERADLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGV
+GTYHCFGCGEHGDVISFLMEMEHTTFTETVERLAARAGVELHYEDGQGPDRAETSRRRRL
+LEANKLADEFYRARLAAPDAQPGRDFLTGRGFTQEHAEQFGLGYAPQGWSALLDHLRQQG
+FRDDELRASGLFSEGQRGLYDRFRGRLLWPIRDMTGNTIGFGARKLFEDDPGPKYLNTPE
+TPLYKKSQVLYGIDLAKRAIAKERQLVLVEGYTDVMAAHLSGVETAVATCGTAFGADHIK
+IARRLISDDGTGGEVIFTFDGDAAGQKAALKAFDEDHRFLAKTFVAVEPNGLDPCDLRMQ
+QGEEAVRALIASRRPLFEFAISAGLKDYDLNTVEGRAGALRHAAPIVAGIKDSVLRPGYE
+RELAGWLGMDPNVVSRAVAQELRGRRRGGPSGGSAERTPAPERAPEGANAGQAPGEEPAA
+PRPALIVPVDPRDPAARRERESLEVVLQHPTLLSAEQWTAFYQARFTIPQYAAVHHAVKV
+AGTAGATPSRWVDAVRDAAPGEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFSLQIV
+HRKEELLGQLQRLGPEGDHDEFMRLNAELMELETRRRALRADD
+>PROKKA_00584
+MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY
+HCFGCGAHGDVISFLMELEHTTFMETVERLASRVGVELHYEDGGTGPDKAETGRRRRLFE
+ANKVADEFFRRALGSPEAQAARDFLTQRGFTQEHAVQFGLGYAPQGWSHLLDHLRQRGFR
+DEELRASGLVSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP
+LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKVA
+RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTFVAVEPSGMDPCDLRMQKG
+DEAVRALIASRRPLFEFAIRAGLKDYDLNTVEGRAGALRHAAPIVAGIKDAVLRPGYERE
+LAGWLGLGPNAVHRAVAAAGRAPRRGPEPEARPTPASDGQAVGPTGRHGEAAAPAPRIVV
+PVDPRDPVARRERESLEVVLQHPTLLSAEQWTALYAARFTVPQYAAVHQGVKVAGSAGAT
+PQRWVDAVRDAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFALQIVHRKEELL
+GRLQRLGPEGDPAEFTRLNSELMELEARRRALRADD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000572.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000572.fa
new file mode 100644
index 0000000000000000000000000000000000000000..258763a70229158ad1f21a786be267721583ff9c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000572.fa
@@ -0,0 +1,25 @@
+>PROKKA_00584
+MTITTLTRKTALTGTGMLAALALAACGTTSDNGDDGSASPEVDASSSLASTPATDDASGS
+ATSSSASSASASSTAAAAGSDSATGQADDPAYAVIDAVLEKYGDGIIVAVDADDDDTTWE
+VDVVVGEEVKELDVTADGDITETDRESDLEDVQKAKDAEVTAQQALDTAREGRDGVTLDE
+MDLDDDNGTLQWEVGFDREDGSDGPEVEIDATSGEVLTVDEH
+>PROKKA_00317
+MTITTLTRKTALTGTGVLAALALAACGTTADNGDDGSVSPEVDASSAVASTPATDDASTT
+SASASSSASSTSASSTAAAASSGSGTGQADDPAYAVIDAVLEKHGDGIIVEVDANDDDTT
+WEVDVVVGEEVKELDVTADGDITETDRESDLEDVQKAKDAEVTAQQALDTAREGRDGVTL
+DEMDLEDDNGTLQWEVGFDREDGSDGPEVEIDATSGEVLTVDER
+>PROKKA_02350
+MNATSLARKTALTGTGLLAALALAACGTADDDTAANPQETAVQQSPTQAATTAPASASGS
+ASASASGSASASASGSASPAAASGSVERQGDDPAYAAIDAILGLHDDGVIVEMDLDDDDA
+KWEVDVVVGDDVKEYDVTTGGQVSEGVRPQIDDDVRRAGEAQVTAETAISTALQGRTDQT
+VDEVDLDEEGGTLVWKVELDRENGEDGAEVKIDAKTGDVIEVEEG
+>PROKKA_02245
+MTITTLTRKTALTGTGVLAALALAACGTTADNGDDGSASLEVDASSAVASTPATEDASTT
+SASASSASSAPASSTAAAAGRDSATGQADDPASAVIDAVLEKYGDGIIVGVDANDDDTTW
+EVDVVVDKEVKELDVTADGDITETDRESDPEDVQKAKDAEVTAQQALDTARKGRDGVTLD
+EMDLDDDNGTLQWEVEFDREDGSDGPEVEIDATSGEVLTVDEH
+>PROKKA_00585
+MTITTLTRKTALTGTGMLAALALAACGTTSDNGDDGSASPGVDASSAVASTPTTDDASGS
+ASSSASSASASSTAAAAGSGSATGQADEPAYAVIDAVLEKYADGIIVAVDANDDDTTWEV
+DVVVGEGAKELDVTADGDITETDRESDPEDVQKAKEAEVTAQQALDTAREGRDGVTLDEM
+DLEDDNGTLQWEVRFDREDGSDGPEVEIDATSGEVLTVDER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000575.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000575.fa
new file mode 100644
index 0000000000000000000000000000000000000000..063506ef2d188fec65bb55f0ee55e593bb3a2d72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000575.fa
@@ -0,0 +1,25 @@
+>PROKKA_00634
+MKRTMTLTALALASALTLTACGTGAQDENAGAEASATAASSAPAATPAATATATPSTTAT
+GSAEEVSAEHNDADVMFAQMMIPHHQQAVEMSEMLLAKDDVPAEVAAFAQKVIDAQGPEI
+KRMNSMLTAWGQDPVDTDGMDGMEGMDHGGMSGMMSEEDMTALDQAQGTEAARLYLEQMT
+AHHKGAVDMAKDEAKDGQNPQAVQLAEQVIADQEAEITEMQQMLDKL
+>PROKKA_00406
+MKRTMTLTALALASALTLTACGTGAQDENAGAEASATATSSAPAATPAATATATPSTTAT
+GSAEEVSAEHNDADVMFAQMMIPHHQQAVEMSEMLLAKDDVPAEVAAFAQKVIDAQGPEI
+KRMNSMLTAWGQDPVDTDGMDGMEGMDHGGMSGMMSEEDMTALDQAQGTEAARLYLEQMT
+AHHKGAVDMAKDEAKDGQNPQAVQLAEQVIADQEAEITEMQQMLDKL
+>PROKKA_00753
+MSTETSAAGRAGHSVRLVVLATVIVLILGAAGWALGRLTAPVTSFPSAASPEAGFARDMQ
+VHHLQAVEMSFLVRDRTEDPEIRQLAYDIARTQQHQAGQMYGWLSIWGLPQASPEPAMAW
+MDEDAGHSSPHDTGQQSTAMPGMATAAQLEALTDAEGSEAEQLYLELMISHHQAGTTMAQ
+AVLDRTDNEAVRALAQSIATSQQTEIRYLEQLLRTR
+>PROKKA_02195
+MKRTMTLTALALASALTLTACGTGAQDENAGAEASATATSSAPAATPAATATATPSTTAT
+GSAEEVSAEHNDADVMFAQMMIPHHQQAVEMSEMLLAKDDVPAEVAAFAQKVIDAQGPEI
+KRMNSMLTAWGQDPVDTDGMDGMEGMDHGGMSGMMSEEDMTALDQAQGTEAARLYLEQMT
+AHHKGAVDMAKDEAKDGQNPQAVQLAEQVIADQEAEITEMQQMLDKL
+>PROKKA_00597
+MKRTMTLTALTLASALTLTACGTGAQDENAGAEASATATGSAPAATPAATDTATPSATES
+ATSSATGSAEEVSAEHNDADVMFAQMMIPHHQQAVEMSEMLLAKDDVPAEVAAFAQKVID
+AQGPEIERMNAMLTAWGQDPVDTDGMDGMEGMDHGGMSGMMSEEDMTALDQAQGTEAARL
+YLEQMTAHHKGAVDMAKDEAKDGQNPQAVQLAEQVIADQEAEITEMQQMLDKL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000577.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000577.fa
new file mode 100644
index 0000000000000000000000000000000000000000..31a4075fb44ab2fd236b894baf6e0fd0bb4bd49a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000577.fa
@@ -0,0 +1,20 @@
+>PROKKA_00637
+MTHHVSAMLDTYPKNVGNIDRQKLAECIQACFECAQTCTACADACLAEDMVADLRQCIRL
+NLDCADVCAATGRMLSRQTGNNVETTRALLEACRAACKTCGDECESHAQMHEHCKVCAEA
+CRRCEQACADLLVTLG
+>PROKKA_01994
+MTHHVNAMLDTHPKDLGGIDRQKLAECIEACFACAQTCTACADACLSEDMVAELRQCIRL
+NLDCADVCAATGAVLTRQTGEDASTVRALLEACRAACRSCGEECASHAGMHEHCAVCAEA
+CRRCEQACADLLAALG
+>PROKKA_02191
+MTHHVSAMLETYPKEVGNIDRQKLAECIQACFECAQTCTACADACLAEDMVADLRQCIRL
+NLDCAEVCAATGRVLSRQTGTNVETTRALLEACRAACKTCGDECESHAQMHEHCKVCAEA
+CRRCEQACADLLVTLG
+>PROKKA_00594
+MTHHVSAMLDTYPKNVGNIDRQKLAECIQACFECAQTCTACADACLAEDMVADLRQCIRL
+NLDCADVCAATGRMLSRQTGNNVETTRALLEACRAACKTCGDECESHAQMHEHCKVCAEA
+CRRCEQACADLLVTLG
+>PROKKA_00894
+MTHHVSAMLETHPKDLGGVDRRKLAECIEACLACAQTCTACADACLSDDMVAEMRRCIRL
+NLDCADVCGATAAVLTRQTGEDASTVRALLEACRTACRACGDECASHAEMHEHCKVCAES
+CRRCEQACADLLASLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000578.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000578.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2b704e3aca87da538da84e68dd952cef600c9949
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000578.fa
@@ -0,0 +1,36 @@
+>PROKKA_00641
+MDTTRFDDDLRAMLGEVESDRRGEPSDYLEDVAGQHVDGLAVAVCTVDGHQAAAGETEHA
+FALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGAILV
+HSLLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGRLPI
+SAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQTMSVMLTCGM
+YDASGQWVAEVGVPAKSGVSGALLGAVPGALGLAAWSPRLDEQGNSRRGIGLFEGLSARW
+DLHVLQHRGALRGLSGPR
+>PROKKA_00378
+MDTTRFDDDLRAMLDEVESDRRGEPSDYLEDVAGQHVDGLAVAVCTVDGHQAAAGETEHA
+FALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGAILV
+HSLLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGRLPI
+SAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQAMSVMLTCGM
+YDASGQWVAEVGVPAKSGVSGALLGAVPGALGLATWSPRLDEQGNSRRGIGLFEGLSARW
+DLHVLQHRGALRGLSGPR
+>PROKKA_02321
+MDTTRLDDDLRAMLAEVESDRRGEPSDYLEDVAGQHVDGLAAAVCTVDGHQAAAGETDHA
+FALQSVSKALTYAVVLQEVGLDAVLERVGVEPSGEAFNHLSLHDDGRPYNPLINAGAIMA
+HALLPAGDHEERVALLVRRYSALAGAELEVSQDVLDAELTRADRNLGLAHLLADAGQLPV
+SAREAVAGYLAQCSVTVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQTMSVMLTCGM
+YDATGQWVAEVGVPAKSGVSGALLGAVPGALGIATWSPRLDERGNSRRGIGIFEGLSARW
+DLHVLQHRGALRGLRASR
+>PROKKA_02184
+MGIGSLIATMLPSSIAFLPACTGMVIGWRWLGLPLGPNARSSAHRDRPGARPRPGRPSTT
+VTGMDTTRFDDDLRAMLGEVESDRRGEPSDYLEDVAGQHVDGLAVAVCTVDGHQAAAGET
+EHAFALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGA
+ILVHSLLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGR
+LPISAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQTMSVMLT
+CGMYDASGQWVAEVGVPAKSGVSGALLGAVPGALGLAAWSPRLDEQGNSRRGIGLFEGLS
+SRWDLHVLQHRGALRGLSGPR
+>PROKKA_00611
+MDTTRFDDDLRAMLDEVESDRRGEPSDYREDVAGQHVDGLAAAVCTVDGHQAAAGETEHA
+FALQSVSKALTYAVVLQEIGLDHVLEDVGVEPSGESFNHLSLHDDGRPCNPLINAGAILV
+HALLPAGDEDERTALLLRRYSALAGVELEVCEDVLDAERTRADRNLGLAHLLADAGRLPI
+SAREAVAGYLAQCSVLVTAPQLAVMGATLAAGGTNPVTGERVLDEWVAQQAMSVMLTCGM
+YDASGQWVAEVGVPAKSGVSGALLGAVPGALGIATWSPRLDEQGNSRRGIGLFEGLSARW
+DLHVLQHRGALRGLSGPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000584.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000584.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d78da01a1b9e8296c80c792819f46cbc2dac6967
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000584.fa
@@ -0,0 +1,25 @@
+>PROKKA_00651
+MTPRTHLPRPLPRPHIAGCVAAALLAWLVLASGVGGLDAVPRATSAPSGRDALLLVAASP
+AGPGSTAAPVAWHAPVAGAAPDDVLRAFVAPERPWGRGHRGVDLAVPSGAAIRAPAAGRV
+VFAGVVVDRPVLTLEHEDGTRSSLEPVEADVAVGAVVAAGDPVGRLAGAPPHCTRACVHW
+GVREPDGWRVGDAAFDRYLDPLVLIGWSGPSVLWPHAAPHPARP
+>PROKKA_00388
+MTPRTLLPRPLPRPRIAGCVAAALLAWLVLALEMGDLGPASRATPAPSTRDALLLVAASP
+AGPGATAAPVAWHPPVAGAAPDDVLRAFVAPERPWSRGHRGVDLAVQTGAPIQAPAAGRV
+VFAGVVVDRPVLTLEHADGTRSSLEPVEADVAVGAVVDAGDPVGRLAGAPPHCPRACVHW
+GVREPDGWRVGDAAFDRYLDPLVLIGWSGPSVLWPHAAPHPARP
+>PROKKA_02312
+MTARSPAPRRARPAASPHRLLAVLLLCVLGLALAFALGPGIGAATPSSIRAEDGPTADAR
+LAVAATPARAWTAPAAGVRPGDVLRPFAAPERPWGRGHRGVDLAVSPGAAVLAPAAGTVV
+FAGTVVDRPVVTLEHADGTRSSLEPVEAAAPVGARLERGAPLGTVADAPAHCAVPCVHWG
+VRVPDGWRFGDATFDRYLDPLVLIGWSGPSVLWPHAAPPPAGPAPARE
+>PROKKA_02169
+MNEASTPPPRLRAAAVLAVALLATASAARAEDAPAAPPVTGALLAPTPGAGPSDVLRGFA
+GPERPWSRGHRGVDLATSSGLVTAPAAGTVRFVGSVAGRGVLTLAHPDGTLSSFEPVTSD
+LTAGQAVAAGQEVARVQEGAAHCPVRCVHWGVRREDAWAVGAARFDRYLDPLLLLGWSGP
+SVLWPVGDAG
+>PROKKA_00621
+MTPRTLLPRPLPRPRIAGCVAAALLAWLVLALGMGDLGPVSRATPAPSTRDALLLVAASP
+AGPGATAAPVAWHPPVAGAAPDDVLRAFVAPERPWSRGHRGVDLAVQTGAPIQAPAAGRV
+VFAGVVVDRPVLTLEHEDGTRSSLEPVEADVAVGAVVAAGDPVGRLAGAPPHCTRACVHW
+GVREPDGWRVGEAAFDRYLDPLVLIGWSGPSVLWPHAAPHPARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000590.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000590.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f1df45c94665be74c12c2c5cf98417e3c6588930
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000590.fa
@@ -0,0 +1,40 @@
+>PROKKA_00658
+MTLVDHTRPTGGQSAGSPPPAGPAEAVMLQVLDTEGRRRPQPELDPWIEDVDADALAALY
+RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALRPDDFVFPSYRENGVALL
+RGVPALDLLRVWRGSTFSSWDPNETRVATQQIIIGAQALHAVGYAMGVQRDQADVATIVY
+FGDGATSQGDVNEAMVFSASYQSPVVFFCQNNHWAISEPVRLQTRRSIADRPWGFGIPSM
+RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA
+RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALEALEEDGADRLFDEIYAEPH
+QELERQRREHALYLQQFGDEEAGA
+>PROKKA_00395
+MTLVDHTRPTGGQSAGSPLPAGPAEAVMLQVLDTEGRRRPQPELDPWIEDVDADALAALY
+RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALRPDDFVFPSYRENGVALL
+RGVPALDLLRVWRGSTFSSWDPNETRVATQQIIIGAQALHAVGYAMGVQRDQADVATIVY
+FGDGATSQGDVNEAMVFSASYQSPVVFFCQNNHWAISEPVRLQTRRSIADRPWGFGIPSM
+RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA
+RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALEALEEDGADRLFDEIYAEPH
+QELERQRREHALYLQQFDDEEAGA
+>PROKKA_02305
+MTLVDHTRPAGGEAATSPPPGEPAEAPMLQVLDAEGRRHAQPELDPWIEDVDADALAALY
+RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALREDDFVFPSYRENGVALL
+RGVPALDLLRVWRGSTFSGWDPQATGVATQQIIIGAQALHAVGYAMGVQRDQADAATIVY
+FGDGATSQGDVNEAMVFSASYRSPVVFFCQNNHWAISEPVKLQTRRSIADRPWGFGIPSL
+RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA
+RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALESLVEDGAELLFDEIYAEPH
+QELERQRREHALYLQQFDDEEAGA
+>PROKKA_02161
+MTDVHLPEQDAPPRSDRPAEQLQVLTPDGRRSPSPELDPWLTDVDEEMLARLHRELTLVR
+RLDTEATHLQRQGRLALWPPLRGQEASQVGAAAALRPADHVFPSYRENGLCLLRGVEAGE
+LLRVWSGSSFSGWDPAATGVATQQLVIGAQTLHAVGYAMGVQRDAADVSTLVCFGDGATS
+EGDVHEAMVFAASYQAPVVFFCQNNHWAISEPVGLQARRSIADRAWGYGIPALRVDGNDV
+LAVLAAVRRGVDRAAAGAGPMFVEAVTYRMGAHTTADDPTRYQDPAELEAWARRDPLERL
+TAHLRDVGADADAVVDASEAAADDLAARMRADLDALPEEGPEALFAHVYAEPHQELARQQ
+RDLQLHLDGLDAGEEQA
+>PROKKA_00628
+MTLVDHTRPTGGQSAGSPPPAGPAEAVMLQVLDAEGRRRPQPELDPWIEDVDADALAALY
+RQMAVVRRLDVEATHLQRQGELALWPPLLGQEAAQVGSAVALRPDDFVFPSYRENGVALL
+RGVPALDLLRVWRGSTFSSWDPNETRVATQQIIIGAQALHAVGYAMGVQRDQADVATIVY
+FGDGATSQGDVNEAMVFSASYQSPVVFFCQNNHWAISEPVRLQTRRSIADRPWGFGIPSM
+RVDGNDVLAVLAATRAAVERAADGGGPTFIEAVTYRMGPHTTADDPTRYRDDAELEAWKA
+RDPLTRVEAHLRTLDVDVDAVLAQAQAEADELAAEVRRALEALEEDGADRLFDEIYAEPH
+QELERQRREHALYLQQFDDEEAGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000593.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000593.fa
new file mode 100644
index 0000000000000000000000000000000000000000..139d9b5d054f8f2bc5a692f563699f1449d94925
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000593.fa
@@ -0,0 +1,20 @@
+>PROKKA_00661
+MAGTRDGDAVEPRPERSTAVLLRDVRPEDLDEFFLHQQDEQANLMSAFAPRNPRDRGVFD
+YHWAHLLGDEDTVVRTIEHEGRAVGALVCTQQDGVGELSFWTAQDYWGLGLTTAAVDRFL
+EEHTARPLRAHVPEDNVGSVKVLSRRGFETVGEEKVFSNARAEVITELVMELPAAD
+>PROKKA_00398
+MLLRDVRPEDLDEFFLHQQDEQANLMSAFAPRNPRDRGVFDYHWAHLLGDEDTVVRTIEH
+EGRAVGALVCIQQDGVGELSFWTAQDYWGLGLTTAAVDRFLEEHTARPLRAHVPEDNVGS
+VKVLSRRGFETVGEEKVFSNARAEVITELVMELPAAD
+>PROKKA_02302
+MLLRDVRPEDLDEFFLHQQDEQASLMSAFAPRNPRDRGVFDYHWSSLLAAETAVVRTIEH
+EGRAVGAIVCTEHDGVGELSFWTAQDYWGLGLTTAAVDAFLREHTRRPLRAHVPEDNAGS
+VKVLSRRGFETVGQEKVFSNARAEVITELVMELPAGAE
+>PROKKA_02158
+MPLRDVRPDDLDAFFLHQQDERANLMSAFAPRNPSDRGVFDYHWAHLLGDDATEVRTIEH
+EGRPVGALVCTRVDGVDELSFWVAREFWGQGLTTSAVDEFLSTHRERPVRAHVPEDNLGS
+VKVLTRRGFREVGREKVFSNARAEVVEELVLELPGA
+>PROKKA_00631
+MLLRDVRPEDLDEFFLHQQDEQANLMSAFAPRNPRDRGVFDYHWAHLLGDEDTVVRTIEH
+EGRAVGALVCTQQDGVGELSFWTAQDYWGLGLTTAAVDRFLEEHTARPLRAHVPEDNVGS
+VKVLSRRGFETVGEEKVFSNARAEVITELVMELPAAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000594.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000594.fa
new file mode 100644
index 0000000000000000000000000000000000000000..889dace09a8b5be2924d66fe0c64b3cc6a07831c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000594.fa
@@ -0,0 +1,25 @@
+>PROKKA_00662
+MPAADPASPAAPATPPTAREAAKARRRVDLLAAAARLFAARGFDAVRLEDIGAAVGISGP
+AIYRHFAGKAAVLTAILDTASQDLLDGGLAAEAQHAPGAETLRALIGFQADFALAQRDVI
+RVQDRDMSALPDGARTAITRTQRAYIDVWARQLQVVHPREDQATAVFRAQAVLGLLNSTP
+RSVRRTAADRAARRATLVAMAWAAATAPGPLSGED
+>PROKKA_00399
+MPAVDPASPAAPATPPTAREAAKARRRVDLLAAAARLFAARGFDAVRLEDIGAAVGISGP
+AIYRHFAGKAAVLTAILDTASQDLLDGGLAAEAQHAPGAETLRALIGFQADFALAQRDVI
+RVQDRDMSALPDGARTAITRTQRAYIDVWARQLQVVHPHEDQATAVFRAQAVLGLLNSTP
+RSVRRTAADRAARRATLVAMAWAAATAPGPLSGED
+>PROKKA_02301
+MPAAVDPSAPAASAAAPTSRVAAKARRREDLLAAAARLFAARGFDAVRLEDIGAEVGISG
+PAIYRHFAGKAAVLVAILATASQDLLEGALATEREHDAGEDALRALIAFQTDFALAQRDV
+IRVQDRDMSALPEDERAAVTGTQRAYIDVWARQLRVVHPSEDQATAVFRAQAVLGLINST
+PRSVRRTAADRAARRATLVAMAWAAATAPGPAADRP
+>PROKKA_02157
+MPHAPDTAAPGPTGTPRERAKARRRAELLAAAARLFAAHGYEATRLEDIGAAAGISGPGI
+YRHFAGKAAVLVEILSSASLFLLDGAEAVAARGLSGAEAVHDLIAFHTDFALANRDVIRV
+QGRDMSSLPPADGAEITRVQRRYIDLWGAQLRRLHPGEDHATARFRTQALLGLINSTPFS
+VRRSRADRGARRDALIGMAWAAARTPGGTARPEPPVVP
+>PROKKA_00632
+MPAVDPASPAAPATPPTAREAAKARRRVDLLAAAARLFAARGFDAVRLEDIGAAVGISGP
+AIYRHFAGKAAVLTAILDTASQDLLDGGLAAEAQHAPGAETLRALIGFQADFALAQRDVI
+RVQDRDMSALPDGARTAITRTQRAYIDVWARQLQVVHPHEDQATAVFRAQAVLGLLNSTP
+RSVRRTAADRAARRATLVAMAWAAATAPGPLPGGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000598.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000598.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1332221c68bd445a008532174ddd0b0b92698e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000598.fa
@@ -0,0 +1,44 @@
+>PROKKA_00670
+MTHGSLTDYTLPAPAPAHDGGAPRAVALIGSTGSIGTQGLDVIAQDPARLRAVALAGGAN
+TTLLAEQAVRFEVEAVGSAAAGEEELRAALADAAARLGRPAPRPVLFTGPRAAEQIAAWP
+GADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAARPGQLVPVDSEHS
+ALAQALRGGTADEVRRLVLTASGGPFRGLDRAALHAVTPAQALAHPTWDMGRVVTTNSAS
+LVNKALEVIEAHLLFDVPLDRIDVVVHPQSVVHSMVEFVDGSTLAQASPPDMRLPIALGL
+CWPRRLPGAAPACDWTRAATWTFEPLDEEAFPAVRAAKEAAAASPTHMAVFNAANEESVD
+AFHAGALPFDGIVDTVRAVVADYAPEHVLAAAGHDPAPTGLTVDAVLAAEAWARRAARAR
+W
+>PROKKA_00407
+MTHGSLTDYTLPAPAPADDDGAPRAVALIGSTGSIGTQGLDVIAQDPTRLRAVALAGGAN
+TTLLAEQAVRFEVEAVGSAAAGEEELRAALADAAARLGRPSPRPVLFTGPCAAEQIAAWP
+GADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAAAPGQLVPVDSEHS
+ALAQALRGGTADEVRRLVLTASGGPFRGLDRAALHAVTPAQALAHPTWDMGRVVTTNSAS
+LVNKALEVIEAHLLFDVPLDRIDVVVHPQSVVHSMVEFVDGSTLAQASPPDMRLPIALGL
+CWPRRLSGAAPACDWTRAATWTFEPLDEEAFPAVRAAKEAAAASPTHMAVFNAANEESVD
+AFHAGALPFDGIVDTVRAVVADYAPEHVLAAAGHDPAPTGLTVDAVLAAEAWARRAARAR
+W
+>PROKKA_02292
+MTHGSLTDYTLPAAGAPSASNAHDDGAPRAVALIGSTGSIGTQGLDVIAQDPARFRAVAL
+SGGANTGLLAEQAVRFEVQAVGSATATEDELRAAIADAAARLGLKPAPRPALFTGPTAAE
+RIAAWKGADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAAAPGQLVP
+VDSEHSALAQALRGGTADEVRRLVLTASGGPFRGLDRAALAEVTPAQALAHPTWDMGRVV
+TTNSASLVNKALEVIEAHLLFDVPLERIDVVVHPQSVVHSMVEFTDGSTLAQASPPDMRL
+PIALGLAWPARVPGAAAGCDWTRAATWAFEPLDEDAFPAVRAAKEAAAASPTHMAVFNAV
+NEEAVDAFHDGRIRFDAIVDTVRAVVGEYEPARVLGAAGHGHVAQDLTVEAVLAAEDWAR
+TAARARW
+>PROKKA_02154
+MTHGSLTDYTFPADHGPGASDGACRAVALVGSTGSIGTQGLDVIAQAPERFRAVALSGGA
+NTALLAEQAVAHGVEAVGSAAASEEELRAALADAAARLRRPDPRPALFTGPEAAARIAAW
+EGADTVLNGITGSIGLAPTLAALRAGHRLALANKESLIVGGALVKAAAAPGQLVPVDSEH
+SALAQALRGGTAGEVRRLVLTASGGPFRGFSAAQLAEVTPAQALAHPTWDMGRVVTTNSA
+SLVNKALEVIEAHLLFDVPLERIDVVVHSQSVVHSMVEFTDGSTLAQASPPDMRLPIALG
+IGWPHRVLGAAAGCDWTQAAQWTFEPLDEAAFPAVSLAKEAAASSDTHMAVFNAANEEAV
+DAFHGGRIRFDQIVETVRAVLGEYRPDGVLAAAGADPDELTVEAVLAAEDWARAAARGRW
+>PROKKA_00640
+MTHGSLTDYTLPAPAPADDDGAPRAVALIGSTGSIGTQGLDVIAQDPARLRAVALAGGAN
+TTLLAEQAVRFEVEAVGSAAAGEEELRAALADAAARLGRPAPRPVLFTGPRAAEQIAAWP
+GADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAARPGQLVPVDSEHS
+ALAQALRGGTADEVRRLVLTASGGPFRGLDRAALHAVTPAQALAHPTWDMGRVVTTNSAS
+LVNKALEVIEAHLLFDVPLDRIDVVVHPQSVVHSMVEFVDGSTLAQASPPDMRLPIALGL
+CWPRRLPGAAPACDWTRAATWTFEPLDEEAFPAVRAAKEAAAASPTHMAVFNAANEESVD
+AFHAGALPFDGIVDTVRAVVADYAPEHVLAAAGHDPAPTGLTVDAVLAAEAWARRAARAR
+W
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000604.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000604.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2af3aef3ee28f8d59263ff61bfad45e908817995
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000604.fa
@@ -0,0 +1,25 @@
+>PROKKA_00676
+MDSTDRRDDLAELRTRVEEALAADDVVVEQVRATGTAEHRTVEVVLDRASGTQGLSLDDV
+ARLSGRVSAALDALGDHVPGVGAGEYLLEVTTAGVDRPLTEPRHFARNVGRLVEVSVDGA
+APVTARLKDVTDDDVELAVVRPPAKKGMKAKELPAERVALDRLGPAIVQVEWSPAQQAGD
+ADAAAGEDTAEHTEA
+>PROKKA_00413
+MDSTDRRDDLAELRTRVEEALAADDVVVEQVRATGTAEHRTVEVVLDRASGTQGLSLDDV
+ARLSGRVSAALDALGDHVPGVGAGEYLLEVTTAGVDRPLTEPRHFARNVGRLVEVSVDGA
+APVTARLKDVTDDDVELAVVRPPAKKGMKAKELPAERVALDRLGPAIVQVEWSPAQQAGD
+ADAAAGEDTAEHTEA
+>PROKKA_02286
+MDSTDRHDDAASLRARVEEALASADVVVEEVRVAGAAAHPTVEVVVDRASGTEGLSLDEL
+AGLSGRVSAALDALGDHVPGVGAGEYLLELTTAGVDRPLTQPRHFARNVGRLVEVAVDGG
+EPFTARLLAADEDAVELAEVRPGAKKGMKAKELPAQRVELARLGPAVVQVEWTPAQQAAD
+AAAAGEQTAEHTEA
+>PROKKA_02148
+METVPAALTELVEGAVSHRGVVVESVRVAGAADAPTVEVVLDRLEGTEGLSLDEVAELSG
+LVSDALDACGDEVPGVGAGEYLLEVSTAGVDRPLTGPRHWLRNVGRLVEVSIDAALPVTA
+RVLGVEASGVELEVVRPGAKKGMPAKVLPAEHVDFSRLGPGQVQVEWSTAAEQSGAEQTA
+EQTEA
+>PROKKA_00646
+MDSTDRRDDLAELRTRVEEALAADDVVVEQVRATGAAEHRTVEVVLDRASGTQGLSLDDV
+ARLSGRVSAALDALGDHVPGVGAGEYLLEVTTAGVDRPLTEPRHFARNVGRLVEVSIDGA
+APVTARLKDVTDDDVELAVVRPPAKKGMKAKELPAERVALDRLGPAIVQVEWSPAQQAGD
+ADAAAGEDTAEHTEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000610.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000610.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f07a45f8c4d581d5fae49ab49c85c5c8a47b4d3a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000610.fa
@@ -0,0 +1,20 @@
+>PROKKA_00683
+MAPSDGAPARNQGLGRIIVMVYAVFALSASARSLFQILTQFDAAPVAYTLSAVAAVVYIV
+ATFALARSGARAWAVALGAVLVELAGVVGVGLWTVLDPGMFAHDTVWSRFGAGYGYVPLV
+LPVVGLIWLLTHRPARPAEAGAL
+>PROKKA_00420
+MAPSDGAPARNQGLGRIIVMVYAVFALSASARSLFQILTQFDAAPVAYTLSAVAAVVYIV
+ATFALARSGARAWAVALGAVLVELAGVVGVGLWTVLDPGMFAHDTVWSRFGAGYGYVPLV
+LPVVGLIWLLTHRPARPAEAGAL
+>PROKKA_02280
+MARTRTASGAARPGAAAPARNQGLGRIIVMVYAVFALSATARSLFQILTDVEAAPVAYSL
+SAFAATVYIVATLALARSGARAWAVALGAVLVELIGVVGVGLWTVLDPGLFAEETVWSRF
+GAGYGYVPLVLPVVGLAWLLAHRPSRPTAEEMAR
+>PROKKA_02141
+MVEQHPVADDGAPARPRRNQGLGRIIVMVYAVFALSASARSLFQILDHFWVAPFAYVLSA
+FAAVVYIVATLALARSGPTAWKVAVAAVGVELAGVVGVGLLTVLDPQLFADATVWSRFGA
+GYGYVPLVLPMVGLAWLLSHRPSREGRVR
+>PROKKA_00653
+MAPSDGAPARNQGLGRIIVMVYAVFALSASARSLFQILTQFDAAPVAYTLSAVAAVVYIV
+ATFALARSGARAWAVALGAVLVELAGVVGVGLWTVLDPGMFAHDTVWSRFGAGYGYVPLV
+LPVVGLIWLLTHRPARPAEAGAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000618.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000618.fa
new file mode 100644
index 0000000000000000000000000000000000000000..22ff44496d009469625077af3443ae1dcab5593d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000618.fa
@@ -0,0 +1,20 @@
+>PROKKA_00691
+MDWTDTWTLAEPSRTPDDGAVGPPAPAVRARRSTVMSKVWVGFVCLLVLLFAGFALNASV
+ALVRAPQPLAKAIGAGVILVVLVTVAVLAREVWFGRQTERLADQLEAEGGLPEDDLPRSP
+GGRIDREAADAQFELYRVEAEAAPRDWRARYRLALAYDASGDRRRAREAAREAVRLHRAG
+>PROKKA_00428
+MAEPSRTPDDGAVGPTEHAARARRSTVMSKVWVGFVSLLVLLFAGFALNASVALVRAPQP
+LAKAIGAGVILVVLVTVAVLAREVWFGRQTERLADQLEAEGGLPEDDLPRSPGGRIDREA
+ADAQFELYRVEAEAAPRDWRARYRLALAYDASGDRRRAREAAREAVRLHRAG
+>PROKKA_02264
+MADRAPRPAEQTVADPAEHAARARRSTLMSKLWVGFVSLLVLFFASFAVYVAVAFIRAPQ
+LLAKGIGVGVIFVVLVTVAVLAREVWFGQQTERLADLLEAEGGLPEDDLPRSPGGRIDRA
+AADAQFEVYRVEAEAAPRDWRTRYRLALAYDASGDRRRAREAAREAVRLHRQG
+>PROKKA_02132
+MASTDPRPGVDREQAPRAGSSTGAKLWVLFVAALTLFFAFFVVRAAVVFIAAGGVLPAVI
+GVAVILVVLVGLGLLGREMLFGLQTERLARTLEAEGGLPADDLPRSPGGRIDRDAADAAF
+ADAADEVRAAPEDWRARYRLSLAYDAAGDRRRAREAARQAISLASRRG
+>PROKKA_00661
+MAEPSRTPDDGAVGPTEHAARARRSTVMSKVWVGFVSLLVLLFAGFALNASVALVRAPQP
+LAKAIGVGVILVVLVTVAVLAREVWFGRQTERLADQLEAEGGLPEDDLPRSPGGRIDREA
+ADAQFELYRVEAEAAPRDWRARYRLALAYDASGDRRRAREAAREAVRLHRAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000622.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000622.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc9b95a8eec46edaad8f13e32de135c22f640606
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000622.fa
@@ -0,0 +1,25 @@
+>PROKKA_00696
+MSAAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWGGDSLVARWVALALFAAAMY
+TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT
+LMRFVVIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPVVGGWWPWAGWVVIGAATVLTV
+LTGLEYVKDAWVLRRDALAAQRGA
+>PROKKA_00433
+MSTAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWGGDSLVARWVALALFAAAMY
+TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT
+LMRFVVIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPLVGGWWPWAGWVVIGAATVLTV
+LTGLEYVKDAWVLRRDALAAQRGA
+>PROKKA_02258
+MSTGGEAERVSAWNLPNILTSVRILMVPLFAWALWAGGPWGGDSATARWIAVALFAAAMY
+TDKLDGDIARARGLITDFGKIADPIADKLLTGAALVLFSLLGELWWWVTVVILVREWGIT
+LMRFVVIRYGVMPAGRGGKLKTVLQAVGIGLLLMPLAPVVGGWWPWVGWTVIGAATVLTV
+LTGLEYVKDAWILRRDALAAPRGA
+>PROKKA_02129
+MNAQPERVSAWNLPNILTTVRILMVPFFVWAVWAGGPWGQDSLTARWIAVALFAAAMYTD
+KLDGDIARSRGLITDFGKIADPIADKLLTGSALVLFALLGELWWWVVIVILVREWGITAM
+RFVVIRYGVMPAGRGGKLKTVLQAVGIGLLLMPLAPVLGGWWPWLGWTVIGAALALTVVT
+GVEYVRDAVRLRADWLASHPEARR
+>PROKKA_00666
+MSTAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWSGDSLLARWVALALFAAAMY
+TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT
+LMRFVMIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPLVGGWWPWAGWVVIGAATVLTV
+LTGLEYVKDAWVLRRDALAAQRAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000623.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000623.fa
new file mode 100644
index 0000000000000000000000000000000000000000..866c2e1937a252bffbf9d81c75b9af64213fc5ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000623.fa
@@ -0,0 +1,22 @@
+>PROKKA_00697
+MAGAQDVVHALAHAGRTVATGESLTAGLLAARLADVPGASAVLHGGVVAYQNAVKTGLLG
+VPEDLLARVGAVDADVARRMALGARAALGADVGVATTGVAGPEPHQGQPVGTVWLGLAVP
+DADANALDVLGGERDGAATAILLRLDGDRAAIREATVAAALQALTRLLAVRGH
+>PROKKA_00434
+MAAARDVVHALADAGLTVATGESLTAGLVAARLADVPGASAVLHGGVVAYQNAVKTGLLG
+VPEDLLARVGAVDADVARRMALGARAALGADVGVATTGVAGPEPHQGQPVGTVWLGLAVP
+DADASALDVFGGERDGAATAILLRLDGDRAAIREATVAAALQALTRLLAGRGH
+>PROKKA_02257
+MAAQETVRALAGAGLTVATAESLTAGLVAARLADVPGASAVLQGGVVAYQNSVKAGLLGV
+PADLLERVGAVDPEVARRMAEGARAGLGADVGVATTGVAGPEPHQGRPVGTVWLGVAVPE
+RLTAALDGLGGERRGAATAIPLALDGDRRAIREATVAAALAALTRLGAPVGERATGEGAA
+GEPCAGA
+>PROKKA_02128
+MSTGVGAVAAEGEAADPARAAVRALTTAGLTVATAESLTAGLVAARLADVPGASAALQGG
+VVAYQNHVKAGLLGVDAGLLTARGAVDPEVARQMACGARRAAGADVGVATTGVAGPEPHQ
+GKPVGTVFVGVAVPAELAPALAGLDGEPGAGEAAPGEAGSGGSEAGVAAAAFALTLPGNR
+AEIRAATVETVLDLLAALGTTGRGMPDEAPALS
+>PROKKA_00667
+MTTAAARDVVHALADAGLTVATGESLTAGLVAARLADVPGASAVLHGGVVAYQNAVKTGL
+LGVPEDLLARVGAVDADVARRMALGARAALGADVGVATTGVAGPEPHQGQPVGTVWLGLA
+VPDADASALDVLGGERDGAATAILLRLDGDRAAIREATVAAALQALTHLLAGPGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000624.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000624.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51557407c31526e229497b0ca4468031c0775229
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000624.fa
@@ -0,0 +1,17 @@
+>PROKKA_00699
+MPLLRHEIGDVLRDVRQLQGRTLREVSHDARVSLGYLSEVERGQKEASSELLASICQALD
+IPLSYLLREVSDRLVEQEGMVVPDTLPDDLTDPSLGSLAGR
+>PROKKA_00436
+MPLLRHEIGDVLRDVRQLQGRTLREVSHDARVSLGYLSEVERGQKEASSELLASICQALD
+IPLSYLLREVSDRLVEQEGMVVPDTLPDDLTDPSLGSLAGR
+>PROKKA_02255
+MMRHPVQAHGITRWVDDQPRPRATTPDIKERSMPLLRHEIGDVLRDVRQLQGRTLREVSH
+DARVSLGYLSEVERGQKEASSELLASICQALEIPLSYLLREVSDRLVDQEGIQVPDTLPE
+DLTDAADPSLGTLAGR
+>PROKKA_02127
+MMRHPVQAHGITRWVDSQPRPSQPTPELKERSMPILRHEIGDVLRDVRQRQGRTLREVSH
+DARVSLGYLSEVERGQKEASSELLASICDALQIPLSFLLREVSDRLAEQEGVVVPDTVPA
+DMAEDGAADVAPLAVR
+>PROKKA_00669
+MPLLRHEIGDVLRDVRQLQGRTLREVSHDARVSLGYLSEVERGQKEASSELLASICQALD
+IPLSYLLREVSDRLVEQEGMVVPDTLPDDLTDPSLGSLAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000628.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000628.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28c70406c6ce8d0ece55f2c18d0b935cee7728af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000628.fa
@@ -0,0 +1,49 @@
+>PROKKA_00706
+MTLTDPTPRTTPLAQDGAAARPHEGLTYEVRTFGCQMNVHDSERISGLLESTGYAPVAED
+AQADLVVFNTCAVRENADNRLYGNLGNLRAVKDAHPGMQIAVGGCLAQKDQAAIQRRAPW
+VDVVFGTHNIGSLPVLLERSRHNAEAEIEILESLEVFPSTLPTKRDSTHSGWVSISVGCN
+NTCTFCIVPSLRGKEKDRRPGEILAEVQALVDAGAVEVTLLGQNVNTYGVEFGDRGAFAK
+LLRACGEIEGLERVRFTSPHPAAFTDDVIDAMAETPNVMPQLHMPLQSGSDKVLKDMRRS
+YRSAKFLRILEKVRERIPHAAITTDIIVGFPGETEEDFAETMRVVEASRFSSAFTFQYSI
+RPGTPAGEMDHQVPKAVVQERFERLVALQDRISAEEMATLVGTRQELLVTADSGSKAAER
+GRLSGRAPDNRLVHFSVPAGAETPRPGDFVTVTVTEAHPFFAVADPTAQDYVLRRSRAGD
+AWDRAQAESCGAPAPGTAGGSGATSLGMPTLRPRS
+>PROKKA_00440
+MTLTDPTPRTTPLAQDGAAARPHEGLTYEVRTFGCQMNVHDSERISGLLESTGYAPVAED
+AQADLVVFNTCAVRENADNRLYGNLGNLRAVKDAHPGMQIAVGGCLAQKDQAAIQRRAPW
+VDVVFGTHNIGSLPVLLERSRHNAEAEIEILESLEVFPSTLPTKRDSTHSGWVSISVGCN
+NTCTFCIVPSLRGKEKDRRPGEILAEVQALVDAGAVEVTLLGQNVNTYGVEFGDRGAFAK
+LLRACGEIEGLERVRFTSPHPAAFTDDVIDAMAETPNVMPQLHMPLQSGSDRVLKDMRRS
+YRSAKFLRILEKVRERIPHAAITTDIIVGFPGETAEDFAETMRVVEASRFSSAFTFQYSI
+RPGTPAGEMDHQVPKAVVQERFERLVALQDRISAEEMATLVGTRQELLVTADSGSKAAER
+GRLSGRAPDNRLVHFSVPAGAETPRPGDFVTVTVTEAHPFFAVADPTAQDYVLRRSRAGD
+AWDRAQAESCGAPAPGTAGGSGATSLGMPTLRPRS
+>PROKKA_02251
+MNVHDSERISGLLESTGYAPVPQDAQADLVVFNTCAVRENADNRLYGNLGNLRAVKDARP
+GMQIAVGGCLAQKDQATIQRKAPWVDVVFGTHNIGSLPVLLERSRHNAEAEIEILESLEV
+FPSTLPTKRDSTHSGWVSISVGCNNTCTFCIVPSLRGKEKDRRPGEILAEVQALVDAGAV
+EVTLLGQNVNTYGVEFGDRGAFAKLLRACGQIEGLERVRFTSPHPAAFTDDVIDAMAETP
+NVMPQLHMPLQSGSDTVLKAMRRSYRSKRFLGILEKVRERIPHAAITTDIIVGFPGETEE
+DFQDTMRVVEASRFSSAFTFQYSIRPGTPAGEMADQVPKAVVQERFERLVALQDRISAEE
+MATLVGTRQELLVTADSGTKASERGRLSGRARDNRLVHFSVPAGAPTPRPGDFVTVTVTE
+AHPFFAVADPAPEDYSLRRSRAGDAWDRAQAESCGVPTPGASGGAGATSLGMPTLRPRS
+>PROKKA_02123
+MTLTDPTTHLPALGTAPDAHAGLTYEVRTFGCQMNVHDSERISGLLESTGYTPAEDGTQP
+DLVVFNTCAVRENADNRLYGNLGNLRPVKDAHPGMQIAVGGCLAQKDQATIQEKAPWVDV
+VFGTHNIGSLPALLERSRHNAEAEMEILESLEVFPSTLPTKRESTHSGWVSISVGCNNTC
+TFCIVPSLRGKEKDRRPGEILAEVQALVDAGAVEVTLLGQNVNTYGVEFGDRGAFAKLLR
+ACGEIDGLERVRFTSPHPAAFTDDVIDAMAETPNVMPQLHMPLQSGSDKVLKDMRRSYRS
+AKFLRILEKVRERIPHAAITTDIIVGFPGETEEDFAETMRVVEASRFSSAFTFQYSIRPG
+TPAGEMDHQVPKAVVQERFERLVALQDRISAEEMATLVGTRQELLVTADSGSKATERGRL
+SGRAPDNRLVHFSVPAGAETPRPGDFVTVTVTEAHPFFAVADPTAQDYVLRRSRAGDAWD
+RAQAESCGAPAPGAAGGSGATSLGMPTLRPRF
+>PROKKA_00673
+MTLTDPTPRTTPLAQDGAAARPHEGLTYEVRTFGCQMNVHDSERISGLLESTGYAPVAED
+AQADLVVFNTCAVRENADNRLYGNLGNLRAVKDAHPGMQIAVGGCLAQKDQAAIQRRAPW
+VDVVFGTHNIGSLPVLLERSRHNAEAEIEILESLEVFPSTLPTKRDSTHSGWVSISVGCN
+NTCTFCIVPSLRGKEKDRRPGEILAEVQALVDAGAVEVTLLGQNVNTYGVEFGDRGAFAK
+LLRACGEIEGLERVRFTSPHPAAFTDDVIDAMAETPNVMPQLHMPLQSGSDKVLKDMRRS
+YRSAKFLRILEKVRERIPHAAITTDIIVGFPGETEEDFAETMRVVEASRFSSAFTFQYSI
+RPGTPAGEMDHQVPKAVVQERFERLVALQDRISAEEMATLVGTRQELLVTADSGSKAAER
+GRLSGRAPDNRLVHFSVPAGAETPRPGDFVTVTVTEAHPFFAVADPTAQDYVLRRSRAGD
+AWDRAQAESCGAPAPGTAGGSGATSLGMPTLRPRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000631.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000631.fa
new file mode 100644
index 0000000000000000000000000000000000000000..55de8b692d4b265f5a26cf50fd0689609bc8acbc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000631.fa
@@ -0,0 +1,25 @@
+>PROKKA_00709
+MVAVSSASHYFDADPSAPERRRTVRTRLAGRDVEVQTANGIFSPDGLDKGTAALFSAVPA
+PPARGRFLDVGAGWGPIALTLALRSPEAEVTAVEVNDRSLQLTRDNAAALGLDNLVALRP
+EDVPEGAEFDLIWSNPPIRIGKPALHALLERWLPRLAPGGEAWLVVQKNLGADSLLPWIG
+RMLEERAPGRFTAERADSVKGFRILRVARAR
+>PROKKA_00443
+MVAVSSASHYFDADPSAPERRRTLRTRLAGRDVEVQTANGIFSPDGLDKGTAALFSAVPA
+PPATGRFLDVGAGWGPIALTLALRSPEAEVTAVEVNDRSLQLTRDNAAALGLDNVVALRP
+EDVPEDAEFDLIWSNPPIRIGKPALHALLERWLPRLAPGGEAWLVVQKNLGADSLLPWIG
+RMLEERAPGRFTAERADSVKGFRILRVVRAR
+>PROKKA_02246
+MVAVTSPAHYFSPDPGTPERRRSVDVELAGRRVTLQTANGVFSPDGIDKGTAALLSAVPA
+PPARGAFLDVGAGWGPLALTLALASPEAEVTGVEVNERSLALARDNAAAVGASNARFLTP
+EQIPDDARFDLIWSNPPIRIGKAALHDLLAQWLPRLAPGGEAWLVVQKNLGADSLLPWIA
+GMLQEQAPGEFTATRAATVKGFRILRISRAAESSS
+>PROKKA_02119
+MDAVTSPAHYFSPDPGTPERRRRVDVEIAGRRVTLQTANGVFSPDGIDKGTAALLSAVPA
+PPARGAFLDVGAGWGPLALTLALTSPEAEVTGVEVNERSLALARDNAAAVGAQNARFLTP
+EQVPDDARFDLIWSNPPIRIGKAALHDLLAQWLPRLAPGGEAWLVVQKNLGADSLLPWIS
+GMLQERAPGEFTATRAATVKGFRILRISRAAESSS
+>PROKKA_00676
+MVAVSPASHYFDADPSAPERRRTLRTRLAGRDVEVQTANGIFSPDGLDKGTAALFSAVPA
+PPATGRFLDVGAGWGPIALTLALRSPEAEVTAVEVNDRSLQLTRDNAAALGLDNVVALRP
+EDVPEDAEFDLIWSNPPIRIGKPALHALLERWLPRLAPGGEAWLVVQKNLGADSLLPWIG
+RMLEERAPGRFTAERADSVKGFRILRVVRAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000632.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000632.fa
new file mode 100644
index 0000000000000000000000000000000000000000..66b84cd4a27f698b09f8e8c477cfa8a102fc08ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000632.fa
@@ -0,0 +1,37 @@
+>PROKKA_00710
+MGRTQWPLTDEFAGQRVVIVGMGVSATQLLAEISTVADTLWVTRREPRWQDSAAPGALAE
+SVRGVDERTRAGLPPGSVVGATGMHRSSWVREAESRGVLVRHPMFTAVEPDGVRMPDGSF
+EPADVILWATGFRPAIRHLAPLRLRTPAGGIRVAGGRALDEPRLFLLGYGPSQSTVGANR
+AGRDAVRAILADLAGPASG
+>PROKKA_00444
+MGVECTGRRVWATGAPAPGPLTTRTYPAGMTASPSPAPPRPGRTGRATVVVIGAGQAGLS
+AAYHLRRRGFVGLGPNDDGAAGVPDDAPGTFVVLDAETAPGGAWQHRWDSLTMATVNHIH
+ELPGDPVPPADPAAHANTLLPAYFADYEARFALPIRRPVRVRRVERIGEPGRARGFFVRT
+DGAPGTWRADFVVNATGTWTSPRWPSVPGMRSFRGRQLHTRDYVSKDEFAGQRVVIVGMG
+VSATQLLAEISTVADTLWVTRREPQWQDSAAPGALAESVRGVDERTRAGLPPGSVVGATG
+MHRSSWVREAETRGVLVRHPMFMAVEPDGVRMPDGSFEPADVILWATGFRPAIRHLAPLR
+LRTPAGGIRVAGGRALDEPRLFLLGYGPSQSTVGANRAGRDAVRAILADLAGPASG
+>PROKKA_02245
+MRTILAADRRRRHPSPVGEHAPAVPTLGRMTPHPDRHVTVLVVGAGQAGLSAAHHLRRRG
+FQPVGPGEAPRPAPEGSPGTFAVLDAEDRPGGAWLHRWDTLTMGSVNHIHELPGHPVPPA
+DPAARANAVLPAYFAEYEERFDLRVHRPVRVSRVERIGEPGAAEGFRVHTDAGTWTCGFL
+VNATGTWTSPHWPAVPGRREFRGRQLHTHDYRDPEEFARRRVVVVGMGVSATQHLAEVSR
+VADTLWVTRREPRWIDDPDPGHLAESVEGVDERTRLGLAPRSVVSATGMFRSDWVREAQA
+RGVLERHPMFERIEPDGVRMPDGSLERADVILWATGFRPAVRHLAPLRLRTPDGGIRAAH
+GRALDEPRLFLIGYGPSQSTVGANRAGRDAVRAILADLRAAGAA
+>PROKKA_02118
+MTPHPDRHVTVLVVGAGQAGLSAAHHLRRRGFLPVGPGEAPGPAPGGSPGTFAVLDAEDR
+PGGAWLHRWDTLTMGSVNHIHELPGHPVPPADPDAQANAVLPAYFAEYEERFDLRVHRPV
+RVSRVERIGEPGAAEGFRVHTDTGTWTCGFLVNATGTWTSPHWPAVPGRREFRGRQLHTH
+DYRGPQEFAGRRVVVVGMGVSATQHLAEVSRVADTLWVTRREPRWIDDPDPGHLAESVEG
+VDERTRLGLAPRSVVSATGMFRSDWVREAQARGVLERHPMFERIEPDGVRMPDGSLERAD
+VILWATGFRPAVRHLAPLRLRTPDGGIRAAHGRALDEPRLFLIGYGPSQSTVGANRAGRD
+AVRAILADLRAAGAA
+>PROKKA_00677
+MGVECTGRRVWATGAPAPGPLTTRTYPAGMTASPSPAPPRPGRTGRATVVVIGAGQAGLS
+AAYHLRRRGFVGLGPNDDGAAGVPDDAPGTFVVLDAETAPGGAWQHRWDSLTMATVNHIH
+ELPGDPVPPADPAAHANTLLPAYFADYEARFALPIRRPVRVRRVERIGEPGRARGFFVRT
+DGAPGTWRADFVVNATGTWTSPRWPSVPGMRSFRGRQLHTRDYVSKDEFAGQRVVIVGMG
+VSATQLLAEISTVADTLWVTRREPQWQDSAAPGALAESVRGVDERTRAGLPPGSVVGATG
+MHRSSWVREAETRGVLVRHPMFMAVEPDGVRMPDGSFEPADVILWATGFRPAIRHLAPLR
+LRTPAGGIRVAGGRALDEPRLFLLGYGPSQSTVGANRAGRDAVRAILADLAGPASG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000640.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000640.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b73c0c70d4f29e5f0e2351d7fc00e5a08bf86e73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000640.fa
@@ -0,0 +1,10 @@
+>PROKKA_00721
+MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVGA
+>PROKKA_00452
+MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVGA
+>PROKKA_02237
+MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVAR
+>PROKKA_02109
+MPYWSVLYLGLGGILLGAAWSMRTQKAPTWAVVIALVLAAMAVAAAFLTV
+>PROKKA_00685
+MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000641.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000641.fa
new file mode 100644
index 0000000000000000000000000000000000000000..105cac119d56ad6e19ec50cab85617a7a1905352
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000641.fa
@@ -0,0 +1,30 @@
+>PROKKA_00722
+MTPNAPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPVTAALDWQRAGAEWIHLVDLDA
+AFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPDWTAR
+VIERFGDRVAVGLDVRGTTLAARGWTKEGGDLWEVLARLEDAGCARYVVTDVTKDGTLKG
+PNTELLAQVCAKTAKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQAL
+AVAGGATVEQARSEQPGPVAP
+>PROKKA_00453
+MTPNAPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPVTAALDWQRAGAEWIHLVDLDA
+AFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPDWTAR
+VIERFADRVAVGLDVRGTTLAARGWTKEGGDLWEVLARLEDAGCARYVVTDVTKDGTLKG
+PNTELLAQVCAKTAKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQAL
+AVAGGATVEQARSEQPGPVAP
+>PROKKA_02236
+MTPNPAAPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPLTAALDWQRAGAEWIHLVDL
+DAAFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPAWT
+ARVIERFGDKVAVGLDVRGTTLAARGWTQEGGDLWEVLARLEDAGCSRYVVTDVTKDGTL
+KGPNTELLAQVCARTDKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQ
+ALAVAGGATVEQARAEQPGPVAE
+>PROKKA_02108
+MTETTPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPLTAALDWQDAGAEWIHLVDLDA
+AFGRGDNRDVLRRVVDEIGVKIELSGGIRDDASLENALAMGAARVNLGTAALEDPAWTAR
+AIERFGNRVAVGLDVRGTTLAARGWTQDGGDLWEVLARLEEAGCARYVVTDVTKDGTLRG
+PNRELLARMCAATDKPVVASGGISSLEDIAALAAMVPQGVEGAIMGKALYAGRFSLEQAL
+AVAAGATVERAREQHPFQAAP
+>PROKKA_00686
+MTPNAPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPVTAALDWQRAGAEWIHLVDLDA
+AFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPDWTAR
+VIERFADRVAVGLDVRGTTLAARGWTKEGGDLWEVLARLEDAGCARYVVTDVTKDGTLKG
+PNTELLAQVCAKTAKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQAL
+AVAGGATVEQARSEQPGPVAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000647.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000647.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e89616ec5cbcc65bf240f176fe6a77e174f3f1c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000647.fa
@@ -0,0 +1,25 @@
+>PROKKA_00728
+MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD
+VVDGDDGRVLFRLADPATFGRDRFAILDADGLPFANLVRQIAFLRTSVNVEVVDGTCFAV
+TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRSNG
+>PROKKA_00459
+MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD
+VVDGDDGRVLFRLADPATFGRDRFAILDADGLPLAHLVRQFAFLRTSVNVEVVDGTCFAV
+TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRSNG
+>PROKKA_02229
+MNTAFDAGRLGRTDVLTLQQVTSFMSNDMQVTGPDGQTVATVVTTGGGLGRMVLGSRTFD
+VVDGEDGRVLFRLADPATFGRDRYAIVDADGLPLANLVREFALFRTSVSVEVVDGTRFAV
+TGNLWDHDYTMTVGQAPIARATATFGGFMNALAGRSRYELRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRRNN
+>PROKKA_02102
+MTTFDAGRLALVNSLALQQVTSFLSNDMQVLGPDGEVVATVQTQGGGLSRMLMGSRRLLV
+CDGDDGRPLFELQDPATFGRDRFQVLDPAGLPLANLRREVAFFRTAVSVEVVDGTVFRVE
+GDLFDHDYRMIAGEVPIARAVSQWSGFGNALLGRSRYRLELDPAMPPVVRCAVLGTAIAL
+DLLRAKDARRND
+>PROKKA_00692
+MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD
+VVDGDDGRVLFRLADPATFGRDRFAILDADGLPFANLVRQIAFLRTSVNVEVVDGTCFAV
+TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRSNG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000649.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000649.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d4c5a5b7aa4c04b88523e930b3c729029f18d0e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000649.fa
@@ -0,0 +1,25 @@
+>PROKKA_00730
+MAQIVLFHHALGLTDGVRALAEQIASGGHTVHTPDLYDGRTFATVDEGVAHAQHLGFEEI
+GRRGMRACAEHQEASVVAGISMGVMPAWRAAQVVPGFRACIAMAGVLALDAYAPLWQPHT
+ALQIHLGTRDPWALEGDLATARSYAATAEHPDRPADLFEYDTDRHLFMNSSTADFDADLT
+AVLVRRIHELLA
+>PROKKA_00461
+MAQIVLFHHALGLTDGVRALAEQIAGGGHTVHTPDLYDGRTFATVDEGVAHAQHIGFEEI
+GRRGMRACAEHQEASVVAGISMGVMPAWRAAQVVPGFRACIAMAGALALDAYAPLWQPHT
+ALQIHLGTRDPWALEGDLETARSYAATAEHPDRPADLFEYDTDRHLFMDSSTADFDADLT
+AVLVRRIHELLA
+>PROKKA_02223
+MAQILLFHHALGLTDGVRALAAQIEAGGHTVHTPDLYDGALFTDVEEGIAHVESLGGFDV
+IAERGMRAAAQHPQASVVAGISMGVVAAHKAAQAVPAFRACIDIAGIVPLDAFAPLWQPH
+TALQVHLATRDPWVMDEDLPLARSVAATEEDPDKPAVLFEYDTDAHLFMDSSTDGHDPAL
+TEVLVRRIHELLA
+>PROKKA_02099
+MAQIILFHHARGLTEGVLALAEQIEQASGHHVHTPDLFGGAVLPTVEDGLAHLQQIGQDE
+VMTRAMHACAEHKEASVVAGISMGVMPAWKAAQTAPGFRACIAMSSALPLDAYARLWQPH
+TSLQIHLAAQDPWVKDEDLPLARTYAATAEHPDRPADLFEYETASHLFMDSSTDQYDARH
+TEVMVERIRELLA
+>PROKKA_00694
+MAQIVLFHHALGLTDGVRALAEQIASGGHTVHTPDLYDGRTFATVDEGVAHAQHLGFEEI
+GRRGMRACAEHQEASVVAGISMGVMPAWRAAQVVPGFRACIAMAGVLALDAYAPLWQPHT
+ALQIHLGTRDPWALEGDLETARSYAATAEHPDRPADLFEYDTDRHLFMDSSTADFDADLT
+AVLVRRIHELLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000650.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000650.fa
new file mode 100644
index 0000000000000000000000000000000000000000..272d7701b1cd6caa3880ae736f327f25be02ca4d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000650.fa
@@ -0,0 +1,40 @@
+>PROKKA_00732
+MDAVRILEDEIREIVRRQGIDPQREHARVLTLIQDAAADYESRAMVSSLPDLEDPVAARQ
+DLFDRIAGLGPLQRLMDDPSVEEIWLNAPDAVYCARSGRSELTGIVLTEEEVQDLVEVML
+KSSGRRLDLSMPFVDAALPDGSRLHVAIPDITRRHWAVNIRKFIARARRLDDLVRGGSLT
+PTAARFLDAAVDAGMNILVSGATQAGKTTLLNCLASAIGPRERVITVEEIFELQIPVRDV
+VGLQCRQPNLEGHGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI
+HANSAADALTKLCTLPLLAGENISRDFVVPTVATCIDVVVHCERDRQGRRRVREILTVGS
+RVEGGVIETSALFQRDAEGDLRLNEGANLEFEALARRGVDVHELVGLR
+>PROKKA_00463
+MDAVRILEDEIREIVRRQGIDPQREHARVLTLIQDAAADYESRAMVSSLPDLEDPVAARQ
+DLFDRIAGLGPLQRLMDDPSVEEIWLNAPDAVYCARSGRSELTGIVLTEEEVQDLVEVML
+KSSGRRLDLSMPFVDAALPDGSRLHVAIPDITRRHWAVNIRKFIARARRLDDLVRGGSLT
+PTAARFLDAAVDAGMNILVSGATQAGKTTLLNCLASAIGPRERVITVEEIFELQIPVRDV
+VGLQCRQPNLEGHGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI
+HANSAADALTKLCTLPLLAGENISRDFVVPTVATCIDVVVHCERDRQGRRRVREILTVGS
+RVEGGVIETSALFQRDAEGDLRLNEGANLEFEALARRGVDVHELVGLR
+>PROKKA_02221
+MDAVRILEDEIREVVRRQGIDPQREHARVIALIQDAAADYESRAEVSALPDLEDPAAARQ
+DLFDRIAGLGPLQRLMDDPSVEEIWLNAPDAVYCARAGRSELTGIVLTEEEVHDLVEVML
+KSSGRRLDLSMPFVDAALPDGSRLHVAIPDITRRHWAVNIRKFISRARRLEDLVRSGSLT
+PTAARFLDAAVDVGMNVLVSGATQAGKTTLLNCLASSIGARERVITVEEIFELQIPVRDV
+VGLQCRQPNLEGHGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI
+HANSAADALTKLCTLPLLAGENISRSFVVPTVATCIDVVVHCERDWDGRRRVLEVLTVGA
+RVEDGVIETSTLFQRDSAGDLRLNEAASLEFDAFARRGVDVHELVGLR
+>PROKKA_02097
+MDAVRMLEDELRELVRRRGVDPRVEGHRIRTMIAEATLDYESRSLVSSLPPLEDPEAARQ
+ELFDRIAGLGPLQRLMDDPTVEEIWLNAPDQVYCARAGRSELTGIVLSEEQVRDLVELML
+KSSGRRLDLSMPFVDASLPDGSRLHVAIPDITRRHWAVNIRKFISRAHRLDDLVRSESLT
+TPAARFLDAAVDAGMNILVSGATQAGKTTMLNCLSASIGARERVITVEEIFELQIPVRDV
+VGLQCRQPNLEGTGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI
+HANSASDALTKLCTLPLLAGENISRNFVVPTVATCIDVVVHCERDREGRRRVREILTVGS
+RVEGGVIETSTLFRRDAHGDLVLNPSADLEFEAFARRGLDPRDLVEVR
+>PROKKA_00696
+MDAVRILEDEIREIVRRQGIDPQREHARVLTLIQDAAADYESRAMVSSLPDLEDPVAARQ
+DLFDRIAGLGPLQRLMDDPSVEEIWLNAPDAVYCARSGRSELTGIVLTEEEVQDLVEVML
+KSSGRRLDLSMPFVDAALPDGSRLHVAIPDITRRHWAVNIRKFIARARRLDDLVRGGSLT
+PTAARFLDAAVDTGMNILVSGATQAGKTTLLNCLASAIGPRERVITVEEIFELQIPVRDV
+VGLQCRQPNLEGHGEIPLRRLVKEALRMRPDRLIVGEVREAEALDMLVALNSGLAGMCTI
+HANSAADALTKLCTLPLLAGENISRDFVVPTVATCIDVVVHCERDRQGRRRVREILTVGS
+RVEGGVIETSALFQRDAEGDLRLNEGANLEFEALARRGVDVHELVGLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000653.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000653.fa
new file mode 100644
index 0000000000000000000000000000000000000000..77f5f51d582a65e096933be7cfe5e9ff4ba53ac8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000653.fa
@@ -0,0 +1,15 @@
+>PROKKA_00735
+MLHHHAITVLAALRALIHDDVRDERGDVPGWVMITLMSAVLVAGLLALALPALQGLFNQA
+ISQVSQGG
+>PROKKA_00466
+MLHHHAITVLAALRALIHDDVRDERGDVPGWVMITLMSAVLVAGLLALALPALQGLFNQA
+ISQVSQGG
+>PROKKA_02195
+MLHHHVISILTALRGLLHDDVRDDRGDVPGWVMITLMSAVLVAALLTLALPALTDLFDQA
+ISQVTQGE
+>PROKKA_02094
+MLTNAYLTVVSALTSLLHDDARDERGDVPGWVMITLMSAALVVALLGLAMPALKAMFDQA
+ITQVNNAAG
+>PROKKA_00699
+MLHHHAITVLAALRALIHDDVRDERGDVPGWVMITLMSAVLVAGLLALALPALEGLFNQA
+ISQVSQGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000669.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000669.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d119584a7da931a3facf0521c6ba90d457afaea3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000669.fa
@@ -0,0 +1,110 @@
+>PROKKA_00756
+MPELTSDRLAQEFPGNERLVAEIYRKYREDSGSVDRQWAQIFARLEASAPAAEAEPKAAA
+KTEPKTAAKAEPKATAKVTEPKAATAPARGAQPKETSVSTGPKPKKTPAAQAVPSEPADT
+ATTTADEKQEKATVLKGMAKAVATNMDASLSMPTATTVRDLPAKVLIDNRVVINSHLART
+RGGKVSFTHFIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLPRPDGTRA
+LVVPNVKAAETLDFRGFWKAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGTVHSVPRL
+SQGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSGEFLKIVH
+GLLLGEDGFYDEVFHSLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN
+VDPLEYSMAYHPDLDIREHGLTLWDLDRKWPTGGFGGAGSLTLRKILGVLRDAYCRTIGV
+EYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE
+GGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA
+SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRLDLGGQRP
+DSFSVLPILVHGDAAFAGQGVVTEVLQLSQLPGYRTGGTIHVVVNNQVGFTTPPTQARSA
+VYSTDVAKTIQAPIFHVNGDEPESVVHVAQLAFEYRQRFNKDVVIDLVCYRRRGHNEGDD
+PSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADSALKDYQQQLERVFAETHEDAP
+ASGGEGLRPAEDRDAAPEAPASTAISAETLRAIGQAHIDVPEGFTVHPKLAALLERRAKM
+AVDGGIDWGFAELAAFGSLLMERVPVRLAGQDSQRGTFTQRHSVFHDRITGDTWAPLRHL
+SEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFVNGAQTIIDEFISSAD
+QKWSQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSTGANHFHLLREHA
+YARPRRPLIVFTPKQLLRLKAAANSVEDFTEGGFQPVIPDAGVDAKDVTRVLLVSGRLYY
+DLLARRQKSGDTSTAIVRVEQLYPLPLDEIRKALRAYPVADVTWVQDEPANQGPWPFMAL
+NLVPQLDVPVTLVSRPASAATSAGTKGRHDQELSTLLDAAFGR
+>PROKKA_00486
+MPELTSDRLAQEFPGNERLVAEIYRKYREDSGSVDRQWAQIFARLEASAPAAEAEPKAAA
+KTEPKTAAKAEPKATAKVTEPKAATAPARGAQPKETSVSTGPKPKKTPAAQAVPSEPADT
+ATTTADEKQEKATVLKGMAKAVATNMDASLSVPTATTVRDLPAKVLIDNRVVINSHLART
+RGGKVSFTHLIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLPRPDGTRA
+LVVPNVKAAETLDFRGFWKAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGTVHSVPRL
+SQGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSGEFLKIVH
+GLLLGEDGFYDEVFHSLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN
+VDPLEYSMAYHPDLDIREHGLTLWDLDRQWPTGGFGGASSLTLRKILGVLRDAYCRTIGV
+EYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE
+GGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA
+SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRLDLGGQRP
+DSFSVLPILVHGDAAFAGQGVVAEVLQLSQLPGYRTGGTIHVIVNNQVGFTTPPTQARSA
+VYSTDVAKTIQAPILHVNGDEPESVVHVAQLAFEYRQRFNKDVVIDLVCYRRRGHNEGDD
+PSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADSALKDYQQQLERVFAETHEDAP
+ASGGEGLRPAEDRDAAPEAPASTAISAETLRAIGQAHIDVPEGFTVHPKLAALLERRAKM
+AVDGGIDWGFAELAAFGSLLMEGVPVRLAGQDSQRGTFTQRHSVFHDRITDETWAPLKHL
+SEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFVNGAQTIIDEFISSAD
+QKWSQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSTGANHFHLLREQA
+YARPRRPLVVFTPKQLLRLKAAANSVEDFTEGRFQPVIPDAGVDAKDVTRVLLVSGRLYY
+DLLARREKSGDTSTAIVRVEQLYPLPLEEIRKALRAYPDADVAWVQDEPANQGPWPFMAL
+NLVPQLDVPVTLVSRPASAATSAGTKGRHDQELSTLLDAAFGR
+>PROKKA_02174
+MLRKRRYTVPELTSDRLAQEFPGNERLVAEIYRKYRADSGSVDRQWAQIFARLEASAPAP
+AEKAPAQAAAKAAPKAEPQAEAKVTEPKAKPAPARGAQPKETSTSTGPKVKKTPAAQAVP
+SEPADPSKDAAKEEKQEKATVLKGMAKAVATNMDASLSMPTATTVRDVPAKVLIDNRVVI
+NSHLARTRGGKVSFTHLIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLP
+RPDGSRSLVVPNVKAAETLDFRGFWQAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGT
+VHSVPRLSKGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSG
+EFLKIVHGLLLGEDGFYDEVFHSLRIPYEPVRWAQDLQVNPEEQVGKVARVQQLIHAYRD
+RGHLMANVDPLEYSMPYHPDLDIREHGLTLWDLDRQWPTGGFGGASTLTLRKILGVLRDA
+YCRTIGVEYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIG
+QKRFSLEGGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYGQVFREFE
+GATPGGTSGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRL
+DLGGQRPDSFSVLPILVHGDAAFAGQGVVTEVLQLSQLPGYRTGGTIHVIVNNQVGFTTP
+PTQARSAVYSTDVAKTIQAPILHVNGDEPESVMHVAELAFEYRQRFNKDVVIDLVCYRRR
+GHNEGDDPSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADTALKDYQQQLERVFA
+ETHEGSASSGGEGIRPAEDRDQAPEAPETTAISAETLRAIGQAHIDVPEGFTVHPKLAAL
+LERRAKMAVDGGIDWGFAELAAFGSLLMEGVPVRLAGQDSQRGTFTQRHSVFHDRITGDE
+WAPLKNLSEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFINGAQTIID
+EFISSAEQKWAQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPTTGANHF
+HLLREQAYARPRRPLVVFTPKQLLRLKAAANSVEDFTEGRFQPVIPDAGVDPKKVTRVQL
+VSGRLYYDLLARRNKDGDETTAIVRVEQLYPLPLDELRAALEAYPQAEVVWVQDEPANQG
+PWPFMALNLLPQLDREVRLVSRPASASTSAGTKGRHDQELSTLLDAGFAR
+>PROKKA_02069
+MPELTSDRLSQEFPGNEDLVAQIYRKYREDQGAVDRQWAQIFARLEASQPQPEPAAAAPK
+ATSSATAEPAPAVKPAVKRGAATPADPQAAAKKSGPTDVSAPAQRKRSVSEAVPSEPARD
+AAAGASEKQDKATVLKGMAKAVATNMDASLSMPTATTVRDLPAKLLIDNRTVINSHLART
+RGGKVSFTHLIGYAVVRALKAMPSMNTLYEERDGKPTMVEPAHVNFGLAIDLPKPDGTRA
+LVVPNIKAAETLSFRQFWEAYDDLVKRGRANKLTMDDYAGTTVSLTNPGGIGTVHSVPRL
+SKGQAAIIGVGALTYPAAFQGAAESTLNSLAISKTITLTSTYDHRVIQGAGSGEFLKLIH
+GYLLGEDGFYDDVFHDLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN
+VDPLEYRMPTHPDLDIREHGLTLWDLDREWPTGGFGGADTLTLRRILGVLRDAYCRTVGV
+EYMHIQNPAERAWFQDKLERPYEKPSREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE
+GGESLIPLLDSILGDAADEGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA
+SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVARAKQDRLEAAGESG
+AAFPVLPILVHGDAAFAGQGVVTEVLNLSQLPGYRTGGTIHVVVNNQVGFTTSPAEGRSS
+VYATDVAKTIQAPILHVNGDEPESVLRVARLAYEYRQRFHKDVVIDLVCYRRRGHNEGDD
+PSMTQPRMYTLIEQKRSTRKLYVESLVGRGDITQEEADTALKDYQQQLERVFAETHAAET
+GQAVATTGLEPARDRDAARPAPSTTAISPDTLRRIGDVHLEVPEDFTVHPKLSQLLEKRA
+KMAVDGGIDWGFAELAAFGSLLMEGVPVRLSGQDSQRGTFTQRHSVFHDRVTDETWTPLN
+HLSESEAPFWVYNSLLSEYAVLGFEYGYSVERSDALVLWEAQFGDFINGAQTMIDEFISS
+AEQKWSQNSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSHGANHFHLLRE
+QAYSRPRRPLVVFTPKQLLRLKAAADPVEAFTQGGFRKVIGDASVDAAQVERVILVSGRL
+YYDLLARREKSGDTSTAIVRVEQLYPLPAEEIRAELAKYPGAQVRWVQDEPANQGPWPFM
+ALNLLPQLDREVTLVSRPALAATSAGTKGRHDEELSTLLDTAFGA
+>PROKKA_00720
+MPELTSDRLAQEFPGNERLVAEIYRKYREDSGSVDRQWAQIFARLEASAAAAEAEPKAAA
+EAEPKAAARAEPKATAKVTEPKAATAPARGAQPKETSVSTGPKAKKTPAAQAVPSEPADT
+ATTTADEKQEKATVLKGMAKAVATNMDASLSMPTATTVRDLPAKVLIDNRVVINSHLART
+RGGKVSFTHLIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLPRPDGTRA
+LVVPNVKAAETLDFRGFWKAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGTVHSVPRL
+SQGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSGEFLKIVH
+GLLLGEDGFYDEVFHSLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN
+VDPLEYSMAYHPDLDIREHGLTLWDLDREWPTGGFGGASSLTLRKILGVLRDAYCRTIGV
+EYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE
+GGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA
+SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRLDLGGQRP
+DSFSVLPILVHGDAAFAGQGVVTEVLQLSQLPGYRTGGTIHVIVNNQVGFTTPPTQARSA
+VYSTDVAKTIQAPIFHVNGDEPESVVHVAQLAFEYRQRFNKDVVIDLVCYRRRGHNEGDD
+PSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADSALKDYQQQLERAFAETHEDAP
+TSGDEGIRPAEDRDAAPKAPASTAISAEMLRAIGQAHLDVPEGFTVHPKLAALLERRAKM
+AVDGGIDWGFAELAAFGSLLMEGVPVRLAGQDSQRGTFTQRHSVFHDRITGDTWAPLKHL
+SEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFVNGAQTIIDEFISSAD
+QKWSQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSTGANHFHLLREHA
+YARPRRPLIVFTPKQLLRLKAAANSVEDFTEGRFQPVIPDAGVDAKDATRVLLVSGRLYY
+DLLARRQKSGDTSTAIVRVEQLYPLPLEEIRKALRAYPDADVAWVQDEPANQGPWPFMAL
+NLVPQLDVPVTLVSRPASAATSAGTKGRHDQELSTLLDAAFGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000672.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000672.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71886b7e8026e37be9af9ed72c260bc20941d604
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000672.fa
@@ -0,0 +1,36 @@
+>PROKKA_00759
+MNGDVVGLLWLVVLLAANAFFVAGEFAVMGARRAQIEPRAEAGSRQAQVALYAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLVVPMAALGVPSAAADVTAFVLALLVVTFLHVTL
+GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPVVAALNWTANLVLHALRIEPKDEVASS
+YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHRAGDVMVPLERVVTVPEGITPHDFE
+WTVGRVGFSRFVVEDPDGGYTGYLHLKDVLTVGPSGHDEPIPLTRVRSLANVRLEDEVED
+ALALMQRTGSHLARVITPEGETAGILFLEDVLEELVGEINDVTQSPRRFRPA
+>PROKKA_00489
+MNGDVVGLLWLVVLLAANAFFVAGEFAVMGARRAQIEPRAEAGSRQAQVALYAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLVVPMAALGVPSAAADVTAFVLALLVVTFLHVTL
+GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPVVAALNWTANLVLHALRIEPKDEVASS
+YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHRAGDVMVPLERVVTVPEGITPHDFE
+WTVGRVGFSRFVVEDPDGGYTGYLHLKDVLTVGPSGHDEPIPLTRVRSLANVRLEDEVED
+ALALMQRTGSHLARVITPEGETAGILFLEDVLEELVGEINDVTQSPRRFRPA
+>PROKKA_02171
+MNEDVIGLLWLVVLLVANAFFVAGEFAVMGARRSQIEPKAEAGSRPAQVALYAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLVGPMTALGVPDAAADVTAFVLALLVVTFLHVTF
+GEMVPKNAAVSFADRAVMILARPLVGLSKLLHPIVTVLNWAANVVLRAFRIEPKDEVASS
+YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHTAGDVMVPLEKVVTVPEGITPHDFE
+WTVGRVGYSRFVVEDPDGGYTGYLHLKDVLTVGPSGHEEPIPLTRVRSLANVRLEDEVED
+ALALMQRTGSHLARVITPEGETAGVLFLEDVLEELVGEINDVTQSPRRFRPA
+>PROKKA_02066
+MSQDVVGLLWLAVLLAANAFFVAGEFAVMGARRSQIEPRAEAGSRQAQVALFAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLAAPMEALGLPLAAADVVAFVLALLIVTFLHVTM
+GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPLIVVLNWAANTVLRAFGIEPKDEVASS
+FTLEEVQTIVAESTRSGTLEDESGVLHSALEFSSYTAGDVMVPIEKVVSVPEDVTPQQFE
+WAVGRVGYSRFVVEDSQGGYAGYLHLKDVLAGGPSRYADPVPVTRVRSLANVRVADEVED
+ALGLMQRTGSHLARVISEDGATVGVLFLEDVLEELVGEIHDVTQSPRRFRPTTGSHAAPE
+PTRMRDLPAR
+>PROKKA_00723
+MNGDVVGLLWLVVLLAANAFFVAGEFAVMGARRAQIEPRAEAGSRQAQVALYAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLVVPMGALGVPAAAADVTAFVLALLVVTFLHVTL
+GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPVVAALNWTANLVLHALRIEPKDEVASS
+YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHRAGDVMVPLERVVTVPEGITPHDFE
+WAVGRVGFSRFVVEDPDGGYTGYLHLKDVLTVGPSGHDEPIPLTRVRSLANVRLEDEVED
+ALALMQRTGSHLARVITPEGETAGILFLEDVLEELVGEINDVTQSPRRFRPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000673.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000673.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d0e5765a5cd605fdab0913b7ecc2202590e8230
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000673.fa
@@ -0,0 +1,35 @@
+>PROKKA_00760
+MLRRRRLPALTGALAALTLSLAACGGTSGDSAGAQAAGASADSGSGSAAGAPVAVATTTQ
+LGSVLDRVVACADARSATVMGPGDDPHDFSASSAQVKDMVSSGLVFSNGLGLEGGMESAL
+ANAEADGATVVEVAPQLDPLPFGGHDHAEEGAGHEGHDHGSEDPHVWMDVARMARAAELM
+GDTLAQERGDERFAECGATVRGELEQTDAQVREILAGVPEDRRTLVTDHDAYGYFSDAYD
+FTVSGVVVPGGSTDGEPSSQEIAELARSIRDGGADAVITSVGARNSLVDTVAEEAGNLPV
+IEVYESGVGPKDTPEADYAEAMLANARTLADALEG
+>PROKKA_00490
+MLRRRRLPALTGALTALTLSLAACGGTSGDSAGEQAAGASAAAGSGSAAGAPVAVATTTQ
+LGSVLDRVVACADARSVTVMGPGDDPHDFSASSAQVKDMVSSGLVFSNGLGLEGGMESAL
+ANAEADGATVVEVAPQLDPLPFGGHDHAEEGAGHEGHDHGSEDPHVWMDVARMARAAELM
+GDTLAQERGDERFAECGATVRGELEQTDTQVREILAGVPEDRRTLVTDHDAYGYFSEAYD
+FTVSGVVVPGGSTDGEPSSQEIAELARSIRDGGADAVITSVGARNSLVDTVAEEAGDLPV
+IEVYEGGVGPKDTPEADYAEAMLLNARTLADALEG
+>PROKKA_02170
+MHRTPRRRAAAALTLASALALAGCGADSGGDGQAGSGEPAAVATTTQLGSVLGDVARCAG
+ATTATVMGPGDDPHDFAPSSQQVAQMARAGLVFANGFGLEAGMASALENAAQDGAQVLEV
+APRLDPLPFGAGEGAADGHAGETADEHAAHAEEGSAGAHDGHDHGSQDPHVWMDVARMAR
+AAEVMGDALAEHTGEDRFADCGRQVRGELEATDAEVREILAAVPEDRRRLIADHDAYGYF
+AAAYGFEVAGVVVPGGSTDGEPSSQRIAELTQAVAEAGADALVTSAGGGAPTVETIAADG
+GGSTPVVELYEGGVGPADGEPAGYAEAMLHNARVLADALGE
+>PROKKA_02065
+MSRSSPTPRLAAPAVVAALGVALAGCSVADSSSPSAAEEGAVTASSSAAGPVVAVATTTQ
+LASVADRVARCGGGSVVSVMGPGDDPHDVAASSDQVAQMVHSGLVFTNGLGLEGGMDSAL
+DNARQDGAVVVEVAPRLDPLPFGEHDADHAGHEGADAHAGHEHGSQDPHVWMDVARMAAA
+ARVVGDELAAETGEQKYAECGATVEGELEETDRQVREILAAVPQERRTLVTDHDAYGYFS
+AAYGFTIEGVVVPGGSTDAEPSSRELAALTQQVKDHGAAALLTSTGTPNGLVETVAREAG
+GLPVVQLYEGGVGPVGTPEADYAQAMLHNARTLADALKG
+>PROKKA_00724
+MLRRRRLPALTGALTALTLSLAACGGTSGDSSGAQAAGASADAGSGSAVGEPVAVATTTQ
+LGSVLDRVVACAGARSATVMGPGDDPHDFSASSAQVKDMVSSGLVFSNGLGLEGGMESAL
+ANAEADGATVVEVAPQLDPLPFGGHDHAEEGAGHEGHDHGSEDPHVWMDVARMARAAELM
+GDTLAQERGDEQFAECGATVRGELEQTDTQVREILAGVPEDRRTLVTDHDAYGYFSEAYD
+FTVSGVVVPGGSTDGEPSSQELAELARSIRDGGADAVITSVGARNSLVDTVAEEAGDLPV
+IEVYEGGVGPKDTPEADYAEAMLVNARTLADALEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000674.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000674.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b520e738a1d9f22d413b62b37051746a97c86da4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000674.fa
@@ -0,0 +1,31 @@
+>PROKKA_00761
+MDWLLEPFQMGFQQRALVGGLIAVVMCSVVGTWLVLRGMSFFGDAFVHGVLPGIALAVVT
+GGSPHLGAAVAAVVMMAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISKSDSYTGSLT
+SILFGDVLGVSVDGIVTQAVIAVVVIALALLLYRPLLALSFSEVKARSLGMRPGLTHTLL
+LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRSVPQMMLVSVVIGAACVVTGLTLS
+YRLGTAGSATMALMPILLFFVVLAVRAAVLALLGRHVRSRAQRERETPVVALPGAEVAR
+>PROKKA_00491
+MDWLLEPFQMGFQQRALVGGLIAVVMCSVVGTWLVLRGMSFFGDAFVHGVLPGIALAVVT
+GGSPHLGAAVAAVVMMAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISKSDSYTGSLT
+SILFGDVLGVSVDGIVTQAVIAVVVIALALLLYRPLLALSFSEVKARSLGMRPGLTHTLL
+LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRSVPQMMLVSVVIGAACVVTGLTLS
+YRLGTAGSATMALMPILLFFVVLAVRAAVLALLGRHVRSRAQREQEAPVVALPGAEAPR
+>PROKKA_02169
+MDWLIEPFLLGFQQRALVGGLIAAALCAVVGTWLVLRGMSFFGDAFVHGVMPGIALSVVL
+GFDAHLGAALAALVMLAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISLSDSYTGSLT
+AILFGDALGVTWEGIVRQAVIAALVLVLALVLYRPLMALSFSPAKARSLGMRPRLTHALL
+LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRTVPQMMALAVLLGAAGVTIGLVLS
+YHLGTAASATMALVPIAMFFVVLAGRAGLRALRSRRVRADRRRAVVETPSRRSVSP
+>PROKKA_02064
+MDWLIDPFLLGFQQRALLGGLIAALMCSAVGTWLVLRGMSFFGDAFVHGVLPGIALAVLL
+GGSPHLGAALAAVLMMGGISLVHRTTTLKEDTAIGLLFVGMMALGVVIISLSSSYTGSLT
+AILFGDALGVTPENLLVQAAIGVVVVVLALVLYRPLLALSFSEAKSQALGMRPRLTHTLL
+LVLIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRTVPQMMALSAGIGALSVVAGLVLS
+YHWGTAASATMALVPVVLFFVVLLGRSAVQAAAGRRRRTRGAASAPTPAGDDDAESRRET
+EGSPAR
+>PROKKA_00725
+MDWLLEPFQMGFQQRALVGGLIAVVMCSVVGTWLVLRGMSFFGDAFVHGVLPGIALAVVT
+GGSPHLGAAVAAVVMMAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISKSDSYTGSLT
+SILFGDVLGVSVDGIVTQAVIAVVVIALALLLYRPLLALSFSEVKARSLGMRPGLTHTLL
+LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRSVPQMMLVSVVIGAACVVTGLTLS
+YRLGTAGSATMALMPILLFFVVLAVRAAVLALLGRHVRSRAQREQEAPVVALPGAEAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000678.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000678.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b08e9b29e8a26dee3e1f816b1fa8d631d1a0366f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000678.fa
@@ -0,0 +1,121 @@
+>PROKKA_00766
+MTQTPPPSTPAAQPSATPHDAVAITFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKT
+TQLPKMCLALGLGEAGSIGHTQPRRIAARSVAERIAQELGEEIGQTVGYQVRFTAQTSKA
+TRVKVMTDGILLAEIPHDPQLRRYSVIIVDEAHERSLNIDFLLGYLRNLLPQRPDLKVII
+TSATIDPERFARHFGRPLAEGEDHADAVEADDGGRVVPAPIIEVSGRTYPVEIRYRPLTD
+EPSPDDPEDDADDAAETRDPLDAIGDAVLELASEPPGDILVFLPGEREIREAADHLTGVV
+AGTTRLAGTEILPLFGRLSMAEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDT
+GTARISRYSHRTKVQRLPIERVSQASANQRSGRSGRTSDGIAIRLYSEEDYLSRPEFTDP
+EILRTSLASVILQMLSLGVARTPGDVKEFPFVQPPDGRQVTDGATTLTELGALEAGGARA
+GTITRVGRRLARLPVDPRLGRMILEAGERGCVREVMVIAAALTIQDPRERPTEQREAADE
+LHRRFADENSDFSAILNLWAYLRERQQELSGSQFRKLCRREHINWLRVQEWQDLVRQLRQ
+LAKDVGLTVEAGPVDPVGRHEAVHKSLLTGLLAQIGAYDERRREYAGARGTRFAVFPGSA
+LFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEVAGHLVKRAYNEPHWSRRAGSVVAR
+EKVTLFGVTLIPDRSVRYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDAL
+ETRLRRRDLRIGDEDLFAFYDARIPANVVSERHFDAWWKKARQEQPDLLDLDVAALLTAD
+AEDLDTDAFPTTFSYPMPGGDVELDLEYTFDPTGAAGTDGVTVAVPILLLNQVSPGPFAW
+LVPGLRVELVTALIKALPKAVRKNLVPAPDVAQQLVADLEAHADPLRDELPEALSAAVRR
+VRGVVVEPGLWAPDAVPLHLRMDYRVVDARGAVMGAGQDLPALQARLAQANRSAIAARLA
+GTDDPASARPGPRGTGRGGRAQADARAGAEGRRRPEGPGRSGATPAFEERHRLTSWSIGT
+VPKTVSTAAGARGPAITGYPSLVPETTPDGGPAAGLTVARSAEDQAAWHRAGVIRLLLAT
+LPSPQRYVLDHLDNREKLTFTQNPHGSVDSLVADCTQAAVDRLVGDELPFDEAAFRALFD
+RVRADLIDTVFAVTSLVEQVLSRAAQVRRRLKGSVSLALAPALSDVKAHLEQLVFPGFVA
+ATGWERLQHLPRYLQGMLTRLDRLDAGGHLQRDGQHMAVVQGLEDEFDAAVAAHRARFAG
+TPVPAELERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALARATRA
+>PROKKA_00496
+MTQTPPPSTPAAQPSATPHDAVAITFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKT
+TQLPKMCLALGLGEAGSIGHTQPRRIAARSVAERIAQELGEEIGQTVGYQVRFTAQTSKA
+TRVKVMTDGILLAEIPHDPQLRRYSVIIVDEAHERSLNIDFLLGYLRNLLPQRPDLKVII
+TSATIDPERFARHFGRPLAAGEDHADAVEADDGGRVVPVPIIEVSGRTYPVEIRYRPLTD
+EPSPDDPEDDADDAAETRDPLDAIGDAVLELAAEPPGDILVFLPGEREIREAADHLTGVV
+AGTTRLAGTEILPLFGRLSMAEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDT
+GTARISRYSHRTKVQRLPIERVSQASANQRAGRSGRTSDGIAIRLYSEEDYLSRPEFTDP
+EILRTSLASVILQMLSLGVARTPGDVKEFPFVQPPDGRQVTDGATTLTELGALEAGGARA
+GTITRVGRRLARLPVDPRLGRMILEAGERGCVREVMVIAAALTIQDPRERPTEQREAADE
+LHRRFADENSDFSAILNLWAYLHERQKELSGSQFRKLCRREHINWLRVQEWQDLVRQLRQ
+LAKDVGLTVEAGPVDPVGRHEAVHKSLLTGLLSQIGAYDERRREYAGARGTRFAVFPGSA
+LFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEVAGHLVKRAYNEPHWSRRAGSVVAR
+EKVTLFGVTLIPDRSVRYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDAL
+ETRLRRRDLRIGDEDLFAFYDARIPGNVVSERHFDAWWKKARQDQPDLLDLDVAALLTAD
+AEDLDTDAFPTTFAYPMPGGDVELDLEYTFDPTGAAGTDGVTVAVPILLLNQVSPGPFAW
+LVPGLRVELVTALIKALPKAVRKNLVPAPDVAQQLVADLEAHADPLRDELPDALSAAVRR
+VRGVVVEPGLWAPDAVPLHLRMDYRVVDARGAVMGAGQDLPALQARLAQANRSAIAARLA
+GTDDPASARPGPRGTGRGGRAPADARAGAEGHRRPEGPGRSGATPVFEERHGLTSWSIGT
+VPKTVSTAAGARGPAITGYPSLVPETTPDGGPAAGLTVARSAEDQAAWHRAGVIRLLLAT
+LPSPQRYVLDHLDNREKLTFTQNPHGSVDSLVADCTQAAVDRLVGDELPFDEAAFRALFD
+RVRADLIDTVFAVTSLVEQVLSRAAQVRRRLKDSVSLALAPALSDVKAHLEQLVFPGFVA
+ATGWERLQHLPRYLQGMLTRLDRLDAGGHLQRDGQHMAVVQGLEDEFDAAVAAHRARFAG
+TPVPAELERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALARATRA
+>PROKKA_02163
+MTETPTPPAAASSAPAIVFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKTTQLPKMC
+LALGLGEAGVIGHTQPRRIAARSVAERIAEELGEDIGRTVGYQVRFTAQTSKATRVKVMT
+DGILLAEIPHDPQLRRYSVVIVDEAHERSLNIDFLLGYLRTLLPQRPDLKVIITSATIDP
+ERFARHFGRALAEGEEHEDAVPADDGGLVVPAPVIEVSGRTYPVEVRYRPLTGEPSPDDP
+EDDSDDAAETRDPLDAIGEAVLELAAEPPGDILVFLPGEREIRDAADHLSGVVASSKRLA
+GTEVLPLFGRLSMAEQHRVFGRAAAGVRRRIVLATNVAETSLTVPGIKYVIDTGTARISR
+YSHRTKVQRLPIERVSQASANQRAGRSGRTSPGIAIRLYSEEDYLSRPEFTDPEILRTSL
+ASVILQMLSLGVAATPADVQGFPFVQPPDGRQVSDGATTLTELGALHPPRPSGAKDGHDG
+GRGRGGRAPEPGTITPIGRRLARLPVDPRLGRMILESGERGCVREVMVLAAALTIQDPRE
+RPVEQREAADELHRRFADENSDFSAILNLWAYLQEQQKELSGSQFRKLCRREHINWLRVH
+EWQDLVRQLRQLAKDVGVAVHAGPVDPVGQHEAVHRSLLTGLLSQIGSYDERRREYAGAR
+GTRFAVFPGSALFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEAAGGLVKRTYNEPH
+WSRRAGAVVAREKVTLFGVTLIPDRSVKYGRIDPELSRELFIRHALVEGDWRTRHRFFAR
+NRAALEEVDALETRLRRRDLRIGDEDLFAFYDARVPANVVSERHFDAWWKKARQERPDLL
+DLDVAALLTADAEDLDTDAFPTVFPYPLSGGDVDLDLEYTFDPTGASGTDGVTVSVPVLL
+LNQVSPGPFAWLVPGLRVELVTALIKALPKAVRKQLVPAPDVARQLVADLDAHADPLADE
+LTEALSAAVRRVRGIVVEPGLWAPDAVPAHLRMDYRVVDARGAVMGAGQDLAALQARLAK
+ANRSAIAARLAGTDDPANARPGPGRQGGRRDGGGNDGGAGRRGSGRGVRGRGRDGTGRPE
+AGAQGAGGAAAAFAERHGLTSWSIGTVPRRITTDPGARGPAITGYPALVPETTAEGGPAA
+GLTVARSAEDQAAWHRAGVIRLLLATLPSPQRYVLDHLDNREKLTFTQNPHGSVDSLVAD
+CSQAAVDRLVGDELPFDEAAFRALFDRVRADLIDTVFAVTRLVEQVLSRAAEVRRRLKGS
+VSLAMAPALSDVKAHLEQLVFPGFVAATGWERLQHLPRYLQGILVRLDRLDAGGHLQRDG
+QHMAVVQRLEDEFDAAVQAHRARFSGVPVPADLERVRWLIEELRVSFFAQELGTAVSVSE
+KRVRQALAQAARA
+>PROKKA_02059
+MTDFPQPPAAAPVITFPAHLPVAERREEIMDAVRENQVVIVAGETGSGKTTQLPKMLLAL
+GLGGAGVVGHTQPRRIAARSVAERIAEELGEDVGRTVGYQVRFTAQTSTRTRVKVMTDGI
+LLAEIPHDPDLRKYSAIIVDEAHERSLNIDFLLGYLKRLLPRRPDLKVIITSATIDPERF
+ARHFGTEDEPAPIIEVSGRTYPVEIRYRPLTEEPSPDDPDDDADDHAETRDPIDAVGDAV
+LELAGEAPGDILVFFPGEREIREAADHLAGVVASTPRLAGTEVLPLYGRLSMAEQHRVFG
+RAGAGVRRRIVLATNVAETSLTVPGIKYVIDTGTARISRYSHRTKVQRLPIERISQASAN
+QRSGRSGRTSDGIAIRLYSEEDFLSRPEFTDPEILRTSLASVILQMLSLGVADTPREVMD
+FPFVQPPDSRQVTDGAATLTELGALHADAPTRGGGRGRGKGAGNRSAAGTITDIGRRLAR
+LPVDPRLGRMILESGRRDCTREVMVLAAALTIQDPRERPVEQRQAADELHARFADDRSDF
+SAYLNLWEYLREQQRELSGSQFRKLCRREHINWLRVHEWQDLVRQLRQLSKDVGVSVHPG
+PVDPVGKHDDVHKSLLTGLLSQIGAYDERRREYQGARNTRFAVFPGSALFKKRHPFVMAA
+ELVETSRLWARAVARIEPEWIEEVAGDLVLRSYAEPHWSRKAGAAVAMEKVTLFGVTIVP
+ERSVRYGRIDPVLSRELFLRHALVEGDWRTRHRFFARNRRLLEEVDELETRLRRRDLRVG
+DEELFAFYDARVPANVVSERHFDAWWKKARQETPDLLDLDLDALLTQDADELDTDAFPTA
+FRYPLPGGDADLALDYTYDPTGASGTDGVTVAVPILLLNEVAPGPFAWLVPGLRGELVTA
+LIKALPKAVRKNLVPAPDVARLLVEDLDAHADPLRDELPAALSSAVRRVRGAVVEPELWR
+LDAVPDHLRMDYRVVDARGAVMGAGQDLPALQARLAKANRSAIAARLAGTDDPRNARPGQ
+GAGRGRGKTEPKGGDGGARGPAADTGRPGPSRTADGAPAFRERHGLTSWTVGEVPRQITT
+APGDRGPAITGYPSLIPETTADGSPAAGLVVARSAQDQAAWHRAGVIALLLATLPSTHRY
+VLDHLDNKEKLTFTQNPHGSVESLVRDATHVAVDRLVGTDLPFTEVGFRALFDRVRADLI
+DTVFAVTALVEQVLSRAAEVRRRLKGGVSLAMAPAKSDVQAHLEQLVFPGFLAATGWQQL
+QHLPRYVQGMLARLDKLDAGGHLQRDGQHMAVVQGLEDEFDAAVTAHRSRFPGTPVPAEL
+ERVRWLLEELRVSYFAQELGTAVSVSEKRVRQALAQARQG
+>PROKKA_00730
+MTQTPPPSTPAAQPSATPHDAVAITFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKT
+TQLPKMCLALGLGEAGSIGHTQPRRIAARSVAERIAQELGEEIGQTVGYQVRFTTQTSKA
+TRVKVMTDGILLAEIPHDPQLRRYSVIIVDEAHERSLNIDFLLGYLRNLLPQRPDLKVII
+TSATIDPERFARHFGRPLAAGEDHADAVEADDGGRVVPAPIIEVSGRTYPVEIRYRPLTD
+EPSPDDPEDDADDAAETRDPLDAIGDAVLELAAEPPGDILVFLPGEREIREAADHLTGVV
+AGTTRLAGTEILPLFGRLSMAEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDT
+GTARISRYSHRTKVQRLPIERVSQASANQRAGRSGRTSDGIAIRLYSEEDYLSRPEFTDP
+EILRTSLASVILQMLSLGVARTPGDVKEFPFVQPPDGRQVTDGATTLTELGALEAGGARA
+GTITRVGRRLARLPVDPRLGRMILEAGERGCVREVMVIAAALTIQDPRERPTEQREAADE
+LHRRFADENSDFSAILNLWAYLHERQKELSGSQFRKLCRREHINWLRVQEWQDLVRQLRQ
+LAKDVGLTVEAGPVDPVGRHEAVHKSLLTGLLSQIGAYDERRREYVGARGTRFAVFPGSA
+LFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEVAGHLVKRTYNEPHWSRRAGSVVAR
+EKVTLFGVTLIPDRSVRYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDAL
+ETRLRRRDLRIGDEDLFAFYDARIPGNVVSERHFDAWWKKARQDQPDLLDLDVAALLTAD
+AEDLDTDAFPTTFTYPMPGGDVELDLEYTFDPTGAAGTDGVTVAVPILLLNQVSPGPFAW
+LVPGLRVELVTALIKALPKAVRKNLVPAPDVAQQLVADLEAHADPLRDELPDALSAAVRR
+VRGVVVEPGLWAPDAVPLHLRMDYRVVDARGAVMGAGQDLPALQARLAQANRSAIAARLA
+GTDDPASARPGPRRTGRGGRAQADGRAGAEGRRRPEGPGRSGATPAFEERHGLTSWSIGT
+VPRTVSTAAGARGPAITGYPSLVPETTPDGGPAAGLTVARSADDQAAWHRAGVIRLLLAT
+LPSPQRYVLDHLDNREKLTFTQNPHGSVDSLVADCTQAAVDRLVGDELPFDEAAFRALFD
+RVRADLIDTVFAVTSLVEQVLSRAAQVRRRLKGSVSLALAPALSDVKAHLEQLVFPGFVA
+ATGWERLQHLPRYLQGILTRLDRLDAGGHLQRDGQHMAVVQGLEDEFDAAVAAHRARFAG
+TPVPAELERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALARATRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000682.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000682.fa
new file mode 100644
index 0000000000000000000000000000000000000000..17036e75660e72d01c4818f98d7cd91dfe6f1026
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000682.fa
@@ -0,0 +1,40 @@
+>PROKKA_00772
+MSHVTESSPAHPGRAEESAPLRPTSPLGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG
+TGALVIAGALFFLLAVIVLRLAQKLRTTDIHRIVNPTTSRVPTWFADLSITTSLLGTLVI
+MLAGAGAAVHTAFGLPSLVGSLVMATVCVVSVLAGITGLVRVQAVVVPLIIVVAVGVAVW
+GLANPGAAVDDVAALVTSSPLINQWWLSGVLYVAFNIQLAYAVLAPIGEESSSSGRSLVA
+GAGLGALGLVVMAGAVMAAMTAHAQLIGRAELPMVELAAMIGGWAALLYTVVLLLAQFTT
+AVSCLYGGVERIALLSSMRRVPGWVIAVVTALAATLLSSVGFSDLVGTVYPVLGYAGLVI
+IVMLVVTWIVERSTVRRRAARAARA
+>PROKKA_00503
+MSHVTESSPAHPGRAEESTPLRPTSPLGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG
+TGALVIAGALFFLLAVIVLRLAQKLRTTDIHRIVNPTTSRVPTWFADLCITTSLLGTLVI
+MLAGAGAAVHTAFGLPSLVGSLVMAAVCVVSVLAGITGLVRVQAVVVPLIIVVAVGVAVW
+GLANPGAAVDDVAALVTSSPLINQWWLSGVLYVAFNIQLAYAVLAPIGEESSSSGRSLVA
+GAGLGALGLVVMAGAVMAALTVHAQLIGRAELPMVELAAMIGGWAALLYTVVLLLAQFTT
+AVSCLYGGVERIALLSSMRRVPGWAIAVVTALAATLLSSVGFSDLVGTVYPVLGYAGIVI
+IVMLIVTWIVERTTVRRRAARAARA
+>PROKKA_02158
+MSPVTESSPAHRGRAEESAPLRPTSRLGIAATFIGTTIGAGYASGNEILQYFVSFGFWGG
+TLALVIAGALFFLLSAIVLKMAQKLRTTDIHRLVNPTTSRVPTWFADLCITASLLGTLVI
+MLAGAGAAVNTSFGLPTMVGSLLMAAVCVLSVLAGISGLVRVQAVVVPLIIVVAVGVAWW
+GLANPGAPVEDVASLVTSSPLINQWWMSGILYVAFNFQLAYAVLAPIGRDSSSSGRTLVA
+GAGLGAVGLVVMAGAIMFAMAAHAHLIGRADLPMVELAAMIGGWAALVYTVILLLAQFTT
+AVSCLFGGVERIALLSPLRRVPGWAIAVATALAATLLSSVGFSDLVGTVYPVLGYAGIAI
+IVMLIITWIAERTLVRRRAARAARA
+>PROKKA_02053
+MSHVAQSTHENRPAQDGGNGLRPMSALGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG
+TGALVIAGVLFFLLSAIVLKMAQQLRTTDIHRLVNPTSSRIPTWFADLCITASLLGTLVI
+MFAGAGAALDTWLGLPAWAGAALMAAVCVLTVLGGISGLVKVQGLVVPLIILVAVGVAWW
+GLTHPGAGADDVASLVTSSPLINTWWMSGILYVAFNFQLAYAVLAPIGKGSSSPGTSLVA
+GAGLGAIGLVVMAGAIMAAMGAHATLIGRAELPMVELAGMVAPWVAAVYTVILLLAQFTT
+AVSCLFGGVERIALLSPLRDVPGWLIAVVTAVVAVLLSSVGFSDLVGIVYPVLGYAGIAI
+VAMLIATWILDRTLVRRRAARADRA
+>PROKKA_00739
+MSHVTESSPAHPGRAEESAPLRPTSPLGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG
+TGALVIAGALFFLLAVIVLRLAQKLRTTDIHRIVNPTTSRVPTWFADLCITTSLLGTLVI
+MLAGAGAAVHTAFGLPSLVGSLVMAAVCVVSVLAGITGLVRVQAVVVPLIIVVAVGVAVW
+GLANPGAAVDDVAALVTSSPLINQWWLSGVLYVAFNIQLAYAVLAPIGEESSSSGRSLVA
+GAGLGALGLVVMAGAVMAAMTAHAQLIGRAELPMVELAAMIGGWAALLYTVVLLLAQFTT
+AVSCLYGGVERIALLSSMRRVPGWVIAVVTALAATLLSSVGFSDLVGTVYPVLGYAGIVI
+IVMLVVTWIVERSTVRRRAARAARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000683.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000683.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0fd7fba8d162d597455229e06e147b09898775b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000683.fa
@@ -0,0 +1,31 @@
+>PROKKA_00773
+MTSAVPRVLSIAGSDSGGGAGVQADLKTIAAWGGYGMTAITAITAQNTQGVQAVHPLPVD
+VVRAQLDSVAADIAVDAVKIGMLGTVELMRAVAGWLEETRPAVVVLDPVMVASSGDALTA
+VGDDDGRAAWARLLRVAHLVTPNLPELARLTGRDATDWDAALDAARGLAAEHGVTVLLKG
+GHLDETEAPEAAAAEVPDAVVRVGGAVHEVRGPRVTTRASHGTGCTLSSALATLAGAGLS
+WDDALERAKPWLADAMRAGEALAVGDASRPTWHGPVDHGHAQRG
+>PROKKA_00504
+MTPAVPRVLSIAGSDSGGGAGVQADLKTIAAWGGYGMTAITAITAQNTQGVQAVHPLPVD
+VVRAQLDSVAADIAVDAVKIGMLGTVELMRAVAGWLEETRPAVVVLDPVMVASSGDALTA
+VGDDDGRAAWARLLRVAHLVTPNLPELARLTGRDATDWDAALDAARGLAAEHGVTVLLKG
+GHLDETEAPEAAAAEVPDAVVRVGGAVHEVRGPRVTTRASHGTGCTLSSALATLAGAGLS
+WEDALERAKPWLADAMRAGEALAVGDASRPTWHGPVDHGHAQRG
+>PROKKA_02157
+MLSIAGSDSGGGAGVQADLKTIAVWGGYGMTAITAITAQNTQGVQAVHPLPVDVVRAQLD
+SIAADIAVDAVKIGMLGTAELMGAVAGWLEETRPAVVVLDPVMVASSGDALTAVGDDDGR
+AAWSRLLRAAHLVTPNLPELARLTGRDSTDWEAALDAAGGLAAEHEVTVLLKGGHLDEAA
+AAEVPDAVVRVAGAVHEVRGPRVATRASHGTGCTLSSALATLAGAGLSWEDALERAKPWL
+ADAMRAGEALAVGDASRPTWHGPVDHGHARRG
+>PROKKA_02052
+MAPSPSTPPSSSPAAEGPAVPRVLSIAGSDSGGGAGIQADLKTIAEWGGYGMTAITAITA
+QNTQGVQAVHPLPAEVVRAQLDSVASDIAVDAVKVGMLGTAELMRVVADWLEEARPAVVV
+VDPVMAATSGHALTPVGDAEAHAAWGRLLRAAHLVTPNLPELARLAGRPLDSWAAALDAA
+RELAAAHAVTVLAKGGHLADLTRADPEGAEAGDDPDAEGGVPDALVRPDGSVHEVRGPRV
+ESGATHGTGCTLSAALATLAAGGLGWEDAIERAKPWLAQAMVAGEALAVGDRTRPTWHGP
+VDHGHARRG
+>PROKKA_00740
+MTSAVPRVLSIAGSDSGGGAGVQADLKTIAAWGGYGMTAITAITAQNTQGVQAVHPLPVD
+VVRAQLDSVAADIAVDAVKIGMLGTVELMRAVAGWLEETRPAVVVLDPVMVASSGDALTA
+VGDDDGRAAWARLLRVAHLVTPNLPELARLTGRDATDWDAALDAARGLAAEHGVTVLLKG
+GHLDETEAPEAAAAEVPDAVVRVGGAVHEVRGPRVTTRASHGTGCTLSSALATLAGAGLS
+WEDALERAKPWLADAMRAGEALAVGDASRPTWHGPVDHGHAQRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000684.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000684.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c5fad74733a1d071519a35f3f6e7b1285181b96
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000684.fa
@@ -0,0 +1,30 @@
+>PROKKA_00775
+MHSPDPLLMTAAGRDDGGTGPGARRRARLAASRLYVCTDLQRFLRPDGTLDTAAFADFCA
+AAFRGGVDVIQVRDKAVDVAVELAAFATLVPLAREHGALSAANDRADVAALAGVDVFHTG
+QTDLTTAQCRALLGPDVVLGRSCHTEAQVRGARAEDGLDYFCTGPVWATPTKPGRAAVGL
+ELPTLAARLDAEDPAGARPWFAIGGVDADRLPEVRAAGAERIVVVRAVTQAEDPEAAART
+LRAGLPG
+>PROKKA_00506
+MHSPDPLLMTAAGRDDGGTGPGARRRARLAASRLYVCTDLQRFLRPDGTLDTAAFADFCA
+AAFRGGVDVIQVRDKAVDVAVELAAFATLVPLAREHGALSAANDRADVAALAGVDVFHTG
+QTDLTTAQCRALLGPDVVLGRSCHTEAQVRGARAEDGLDYFCTGPVWATPTKPGRAAVGL
+ELPTLAARLDAEDPAGARPWFAIGGVDADRLPEVRAAGAERIVVVRAVTQAEDPEAAART
+LRAGLPG
+>PROKKA_02155
+MHSPDPLLMAAAGRDDGDTGPGTGRRARLAASRLYVCTDLQRFLRPDGTLDTVAFADFCA
+AAFRGGVDLIQVRDKAVDVAVELAAFAVLVPLARAHEALSAANDRADVAALAGVDVFHTG
+QTDLTTVQCRALLGPDVVLGRSCHTEAQVRAARAEDGLDYFCTGPVWATPTKPGRAAVGL
+ELPSHAARLDAEDPAGARPWFAIGGVDADRLTEVRAAGADRIVVVRAVTQAEDPEAAART
+LRAGLPG
+>PROKKA_02050
+MHSPDPLLMTAAGRDDGDTGPGAGRRARLAASRLYVCTDLQRFLRPDGTLDTAAFGGFCA
+AAFRGGVDLIQVRDKAVDVAVELAAFAVLIPLAREHGALSAANDRADVAALAGVDVFHTG
+QTDLTTAQCRALLGPNVVLGRSCHTPDHVRAARAEDGLDYFCTGPVWATPTKPGRAAVGL
+GLPTLAARLDAEDPAGARPWFAIGGVDAERLPEVRAAGAGRIVVVRAVTQAADPEAAARE
+LRAGLPA
+>PROKKA_00742
+MHSPDPLLMAAAGRDDGGTGPGAGRRARLAASRLYVCTGLQRFLRPDGTLDTAAFADFCA
+AAFRGGVDVIQVRDKAVDVALELAAFAVLVPLAREHGALSAANDRADVAALAGVDVFHTG
+QTDLTTAQCRALLGPNVVLGRSCHTEAQVRAARAEDGLDYFCTGPVWATPTKPGRAAVGL
+GLPSLAARLDAEDPAGARPWFAIGGVDADRLPEVRTAGAERIVVVRAVTQAEDPEAAART
+LRAGLPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000692.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000692.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bfd39fa55c85fb1e0ef53f0ed0731260a8ddba98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000692.fa
@@ -0,0 +1,40 @@
+>PROKKA_00783
+MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS
+FKDRGMTMAITAAVADGAKAVVCASTGNTSASAAAYAAQAGITCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDTLGDAP
+DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDAELPAVATKTPVMWGFQAAGAAPI
+VQGHPVTDPDTIATAIRIGNPASWEQAEAARDESGGMIDSVTDEEILEAHRWLSAKEGVF
+VEPASAAGVAGLLKHHAAGNVPAGKSWVITVTGHGLKDPQWALRGADGADVTPRSVPFDV
+VTVAQALGLS
+>PROKKA_00514
+MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS
+FKDRGMTMAITAAVADGAKAVVCASTGNTSASAAAYAAQAGITCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDTLGDAP
+DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDAELPAVATKTPVMWGFQAAGAAPI
+VQGHPVTDPDTIATAIRIGNPASWEQAEAARDESGGMIDSVTDEEILEAHRWLSAKEGVF
+VEPASAAGVAGLLKHHAAGNVPAGKSWVITVTGHGLKDPQWALRGADGADVTPRSVPFDV
+VTVAQALGLS
+>PROKKA_02147
+MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS
+FKDRGMTMAITAAVDQGAKAVVCASTGNTSASAAAYAAQAGLTCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDALGDAP
+DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDEELPAVSTKTPVMWGFQAAGAAPI
+VLGHPVTEPDTIATAIRIGNPASWEQAEAARDGSGGMIDSVTDEEILAAHRWLSAKEGVF
+VEPASAAGVAGLIKHHAAGNVPAGKSWVITVTGHGLKDPQWALRDADGEDVTPRTVPFDV
+VTVAQALGLA
+>PROKKA_02041
+MAHVWRGVIREYAGRLPVTEDTRVVSLGEGGTPLIRAPHLSELVEGEVYVKFEGMNPTGS
+FKDRGMTMAITAAVENGAKAVVCASTGNTSASAAAFAAQAGLTCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDNCLDIARKLSENYPVFLVNSVNPARIEGQKTAAFEVVDLLGDAP
+DYHLLPVGNAGNITAYWKGYQEYSRPYVNPHPGTSDEELPAVATKTPVMWGFQAAGAAPL
+VLGHPVTEPETIATAIRIGNPASWDQATAARDASGGMIDSVTDEEILAAHRWLSSKEGVF
+VEPASAAGVAGLIKHHAAGNVPAGKTWVITVTGHGLKDPQWALKGADGDDVTPRSVPFDV
+VTVAEALGLT
+>PROKKA_00750
+MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS
+FKDRGMTMAITAAVADGAKAVVCASTGNTSASAAAYAAQAGITCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDTLGDAP
+DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDAELPAVATKTPVMWGFQAAGAAPI
+VQGHPVTDPDTIATAIRIGNPASWEQAEAARDESGGMIDSVTDEEILEAHRWLSAKEGVF
+VEPASAAGVAGLLKHHAAGNVPAGKSWVITVTGHGLKDPQWALRGADGADVTPRSVPFDV
+VTVAQALGLS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000694.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000694.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff093cb7b41b1e4f095ac71173494b62ec42f6e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000694.fa
@@ -0,0 +1,65 @@
+>PROKKA_00785
+MTESTEQTTPTNGGGLASLKLAQLQALASQLGIAGGSRMRKADLVTAISDHQRGGSVADR
+DAAERAAQAPAAPAAEAAPAAASSQDAAPAAERPARRRSRRADADTSAPAAAQDGQPQAE
+AREDQTEQAPRETASDQDRSEGSETRDEGEGRPQSERRSRGRRAGDDDAQQGQDRRSDGA
+QGEDGADRRGDREDRDDNGRENGRGRNGRNGRDRDNGRDRENGRENNRDRENGRDGSREQ
+RGDKSEDGGRGDGGRGDRSRRDDRDDEGGRNRRNRRNRNERGRNRRGRGGPEVDETELTE
+DDVLQPVAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKYGLRKGDAVVGAIRAPRDG
+EKQQHHGGGSNRQKFNALVKISSVNGQPAVEHPQRVEFGKLVPLYPQERLRLETDPKLIG
+PRVIDLVSPIGKGQRGLIVSPPKAGKTMILQSIANAIKTNNPEVHLMMVLVDERPEEVTD
+MQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLDSMTRLGRAYNLAA
+PASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKGT
+GNMELRLSRHLAERRIFPAVDVNASGTRREEALLSQEEVKIMWKLRRVLSGLEQQQALDL
+LTNKIKDTASNAEFLMLVSKTTLGSKGDD
+>PROKKA_00516
+MTESTEQTTPTNGGGLASLKLAQLQALASQLGIAGGSRMRKADLVTAISDHQRGGSVADR
+DAAERAAQAPAAPAAEAAPAAASSQDAAPAAERPARRRSRRADADTSAPAAAAQDGQPQA
+EAREDQTEQAPRETASDQDRSGGSEARDEGEDRPQSERRSRNRRRAGDDDAQQGQDRRSD
+GAQGEDGADRRGDREDRDDNGRENGRGRNGRNGRDRENGRDRENGRENNRDRENGRDGSR
+EQRGDKSEDGGRGDGGRGDRSRRDDRDDEGGRNRRNRRNRNERGRNRRGRGGPEVDETEL
+TEDDVLQPVAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKYGLRKGDAVVGAIRAPR
+DGEKQQHHGGGSNRQKFNALVKISSVNGQPAVEHPQRVEFGKLVPLYPQERLRLETDPKL
+IGPRVIDLVSPIGKGQRGLIVSPPKAGKTMILQSIANAIKTNNPEVHLMMVLVDERPEEV
+TDMQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLDSMTRLGRAYNL
+AAPASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFK
+GTGNMELRLSRHLAERRIFPAVDVNASGTRREEALLSQEEVKIMWKLRRVLSGLDQQQAL
+DLLTNKIKDTASNAEFLMLVSKTTLGSKGDD
+>PROKKA_02145
+MTESTEQTTPTTGGGLAALKLAQLQALASQLGIPGGSRMRKADLVTAISDHQRGGSVADR
+AAAERAAKAAAAPAAEAAPAADKAAEQPAEAAERPARRRSRRADADTSAAAQSAESGKDQ
+AERRAEQPAEGRDAEGSQDSGDRAQDSGDRTQGERRSRGRRRAGDDDARGQDRRRQDGED
+AGQDQAHDSAEDRGGDREDGGRENGRGNRGRNGRDNGRDRENGNGRDRDNGNGRDRDGSR
+EQKQDKSEDGGRDGGRNDRNRRDDRDDEGGRGRRNRRNRNERGRNRRGRGGPDVDETELT
+EDDVLQPVAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKHGLRKGDAVVGAIRAPRE
+GEKPQHQGGGSNRQKFNALVKISSVNGQPAVEHPERVEFAKLVPLYPQERLRLETDPKQV
+GPRVIDLVSPIGKGQRGLIVSPPKAGKTMILQSIANAIKTNNPEVHLMMVLVDERPEEVT
+DMQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLDSMTRLGRAYNLA
+APASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKG
+TGNMELRLSRHLAERRIFPAVDVNASGTRREEALLSPEEVKIMWKLRRVLSGLEQQQALE
+LLTNKIKDTGSNAEFLMLVSKTTLGAKGED
+>PROKKA_02039
+MTESPDQTTAGGGLASLKLAQLQALASQLGITGGSRMRKSDLVAAISDHQRGGSVADRDA
+AAQAAAAPAAQAEAAEAPAAEQAPRSRRRSRRADSDGAVAADQPAEATQAPADEQPAAET
+EDAPARAEASAESGAQEAGSGRSRRRRGDRAARDEQQDGAQDEKQESGRGAGEETRREQD
+GDEERAEGRSRSRRGRGDRDRGERQNADRQNGERANGERANGQGEDRSQGGRREDREEES
+GRGQGGDGQKRSDRGNGRREDRDEDGRRGRNRRNRNDRGRNRRSRGPEVDDVEVTEDDVL
+QPVAGILDVLDNYAFVRTSGYLPGEKDVYVSLAMVKKFGLRKGDAVVGAIRAPREGEKPH
+SGGGRNQKFNALVKVTTVNGQPAEENPQRVEFGKLVPLYPTERLRLESDHKLVGPRVIDL
+ISPIGKGQRGLIVSPPKAGKTMILQSIANAITRNNPEVHLMMVLVDERPEEVTDMQRSVA
+GEVIASTFDRPAEDHTTVAELAIERAKRLVEMGRDVVVLLDSMTRLGRAYNLAAPASGRI
+LSGGVDSAALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKGTGNMELR
+LSRQLAERRIFPAVDVNASGTRREEVLLSPEEVKIMWKLRRVLSGLDTQQALELLTNKIK
+DTASNAEFLMLVSKTTLGSKGDD
+>PROKKA_00752
+MTESTEQTTPTNGGGLASLKLAQLQALASQLGIAGGSRMRKADLVTAISDHQRGGSVADR
+DAAERAAQAPAAPAAEAVPAAASSQDAAPAAERPARRRSRRADADTSAPAAVAQDGQPQA
+EAREAQTEQGPRETASDQDRSGGSETRDEGEDRPQSERRSRGRRRAGDDDAQQGQDRRSD
+GAQGEDGADADRRGDREDRDDNGRENGRGRNGRNGRDRDNGRDRDNGRDRENGRDGSREQ
+RGDKSEDGGRGDGGRGDRSRRDDRDDEGGRNRRNRRNRNERGRNRRGRGGPEVDETELTE
+DDVLQPAAGILDVLDNYAFVRTSGYLPGPNDVYVSLAMVKKYGLRKGDAVVGAIRAPRDG
+EKQQHHGGGSNRQKFNALVKISSVNGQPAVEHPQRVEFGKLVPLYPQERLRLETDPKLIG
+PRVIDLVSPIGKGQRGLIVSPPKAGKTMILQSIANAIKTNNPEVHLMMVLVDERPEEVTD
+MQRSVDGEVIASTFDRPADDHTTLAELAIERAKRLVEMGRDVVVLLDSMTRLGRAYNLAA
+PASGRILSGGVDSSALYPPKKFFGAARNIENGGSLTILATALVETGSRMDEVIFEEFKGT
+GNMELRLSRHLAERRIFPAVDVNASGTRREEALLSQEEVKIMWKLRRVLSGLEQQQALDL
+LTNKIKDTASNAEFLMLVSKTTLGSKGDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000695.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000695.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e6f654baa9e6cab9aebfd81f01c9907d8f10e4fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000695.fa
@@ -0,0 +1,40 @@
+>PROKKA_00786
+MFDSEQRREAVDRLLAEHRELTARLSDPAVHQDPALARRLNRRFAELGAVVTAHRAWSAA
+AEELADARELAAAGDDDAAAFAAEVPGLEAAEAEAAERLRRLLIPRDPDDARDVILEIKG
+GEGGEEAALFAGDLLRMYLRYADSRGWKTEVLSATHSDLGGYKDVHVAVRGSAADPADGV
+YARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVHLDPNDLKVDVFRSSG
+PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAEQDAEDS
+AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVIASCLALDEER
+RLAALGGDA
+>PROKKA_00517
+MFDSEQRREAVDRLLAEHRELTARLSDPAVHQDPALARRLNRRFAELGAVVTAHRAWSAA
+AEELADARELAAAGDDDAAAFAAEVPGLEAAEAEAAERLRRLLIPRDPDDARDVILEIKG
+GEGGEEAALFAGDLLRMYLRYADSRGWKTEVLSATHSDLGGYKDVHVAVRGSAADPADGV
+YARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVHLDPNDLKVDVFRSSG
+PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAEQDAEDS
+AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVIASCLALDEER
+RLAALGGDA
+>PROKKA_02144
+MFDSEERREAVDRLLAEHRELTARLSDPAVHQDPVLARRLNRRFAELGAVVTAHAAWREA
+AAELADARELAAAGDDDAAAFAAEVPCLEEAETAAAERLRRLLIPRDPDDARDVILEIKG
+GEGGEEAALFAGDLLRMYLRYAESRGWKTEVLSATHSDLGGYKDVHVAIRAGATDPAEGV
+FARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVRIDPNEVKTDVFRSSG
+PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAAMRVLRSRLLERRRAEQDAEDS
+AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVVASCLALDEER
+RLAALGGDA
+>PROKKA_02038
+MFESVERLLAEHRELAGQLSDPALHADAARARRVGRRYAELGAVVAAHREWEQAVADRDD
+ARELAAAPGEDAAAFAAEVPALEAAADEAAERLRRLLIPRDPDDGRDVILEIKGGEGGEE
+AALFAGDLLRMYLRYAESRGWRTEVLSATHSDLGGFKDVHVAVRGSAQDPAEGVYARLKH
+EGGVHRVQRVPVTESAGRIHTSAAGVLVLPEADAPDEVQIDPNDLKTDVFRSSGPGGQSV
+NTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAERDAEDSAARSAQ
+VRTMDRSERIRTYNFPENRIADHRTGFKAHNLDAVLDGALDPVIDSCVALDEQRRLARLG
+EEAR
+>PROKKA_00753
+MFDSDQRREAVDRLLAEHRELTARLSDPAVHQDPALARRLNRRFAELGAVVTAHRAWSAA
+AEELADARELAAAGDDDAAAFAAEVPGLEAAEAEAAERLRRLLIPRDPDDARDVILEIKG
+GEGGEEAALFAGDLLRMYLRYAESRGWKTEVLSATHSDLGGYKDVHVAVRGSAADPADGV
+YARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVHLDPNDLKVDVFRSSG
+PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAEQDAEDS
+AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVIASCLALDEER
+RLAALGGDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000697.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000697.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b1d0408d0de6a0021d823439f8e3444110a04111
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000697.fa
@@ -0,0 +1,40 @@
+>PROKKA_00789
+MRAYLVLVMVTAVACGALTPLMRRLGLRARVFTPLRQRDVHRHPVPKLGGVAMAAAVLVG
+FAVGGVVPFLQGIYADDAAMRGLLVAVAVVLVVGIADDMWDLRWWVKMAGQVLAGLAVAL
+GGIRIEAMPVGWIPVGNETTQVILTVFAVVLTMNAINFVDGLDGLAAGVALIGGSAFFVY
+SYLLTRTINQFDYANLATLLMALLVGACVGFLPWNLAPARIFMGEVGAMLIGLLMAAAAV
+AVTADVNALDGMRFRNVPAYMPILLPVAVLALPLADLALAVLRRTAKGTSPFSADRGHLH
+HKLVDGGYTQAQAVGLLWLWAFLVAWGAVSLNFVDHMVVLPVLAVALAGAGYLTLHPIVE
+RRRADRNDAAAHPDERGDA
+>PROKKA_00520
+MRAYLVLVMVTAVACGALTPLMRRLGLRARVFTPLRQRDVHRHPVPKLGGVAMAAAVLVG
+FAVGGVVPFLQGIYADDAAMRGLLVAVAVVLVVGIADDMWDLRWWVKMAGQVLAGLAVAL
+GGIRIEAMPVGWIPVGNETTQVILTVFAVVLTMNAINFVDGLDGLAAGVALIGGSAFFVY
+SYLLTRTINQFDYANLATLLMALLVGACVGFLPWNLAPARIFMGEVGAMLIGLLMAAAAV
+AVTADVNALDGMRFRNVPAYMPILLPVAVLALPLADLALAVLRRTAKGTSPFSADRGHLH
+HKLVDGGYTQAQAVGLLWLWAFLVAWGAVSLNFVDHMVVLPVLAVALAGAGYLTLHPIVE
+RRRADRNDAAAHPDERGDA
+>PROKKA_02142
+MRAYLVLVVVTALACGALTPLMRRIGLRARVFTPVRQRDMHRRPIPKLGGVAMAAAVLVG
+LAVGGTVPFLQGIYADDAAMVGLLVAVAVVFVVGIADDLWDLRWWVKMAGQVCAGLAVAL
+GGIRIEAMPVGWIPVGSEAMQIALTVFAVVLTMNALNFVDGLDGLAAGVALIGGSAFFVY
+SYLLTRTINQFDYANLATLLMALLVGACLGFLPFNRFPARIFMGEVGAMLLGLLMAAAAV
+AVTADVKALDGMRFRNVPAYMPILLPIAVLALPLLDLALAVVRRTARGASPFSADRGHLH
+HKLVDGGYTHAQAVWLLWLWAFLVAWGAVSLNFVDDMIVLPVLGLALLGAGYLTLRTPVR
+RRRAGAPAAGPALDPEEGA
+>PROKKA_02035
+MRAYLLVAAVTALTCLALTPWVRRVGVRARAYTPHRDRDVHRAPVPKLGGVAMVAAVLAG
+LAVAGTVPFLGGIFTDASAMRGLLAALGIILVLGVVDDLVDLRWWAKLGGQSLAALAVAL
+GGIRIAALPVGWIHVGSEAVQVALTVFVVVLTMNAINFIDGLDGLAAGVALIGGSAFFVY
+SYLLTRTIDQFDYSNLATLLMALLIGACAGFLPYNRHPARIFMGESGALLLGLLLSTAAV
+AVTADLDALEGFRFRNVPAYMPVLLPIAVLALPLADLTISVIRRAAHGESPFGADRGHLH
+HRLVDGGFTHAQAVRVLWLWSFIVAWGVLSLNFADDAVVLLLAAAGLAVATWLTVHPLRA
+RAARPASRPDAQPKDQP
+>PROKKA_00756
+MRAYLVLVVVTAVACGALTPLMRRLGLRARVFTPLRQRDVHRHPVPKLGGVAMAAAVLVG
+FAVGGVVPFLQGIYADDAAMRGLLVAVAVVLVVGIADDMWDLRWWVKMAGQVLAGLAVAL
+GGIRIEAMPVGWIPVGNETTQVILTVFAVVLTMNAINFVDGLDGLAAGVALIGGSAFFVY
+SYLLTRTINQFDYANLATLLMALLVGACVGFLPWNLAPARIFMGEVGAMLIGLLMAAAAV
+AVTADVNALDGMRFRNVPAYMPILLPVAVLALPLADLALAVLRRTAKGTSPFSADRGHLH
+HKLVDGGYTQAQAVALLWLWAFLVAWGAVSLNFVDPMIVLPVLAVALAGAGYLTLHPIVE
+RRRAVRNDAAAHPDERGDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000698.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000698.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71e0bab6008bc34441e6ecf920e6e6dad45fdc6f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000698.fa
@@ -0,0 +1,20 @@
+>PROKKA_00790
+MTGAGGRRRRRRWENRRGWWGILGWSLAAAGVALAITCAAWLLSVGGEAAGSALLGGGAV
+LALSALTGVTTALVWDRAREAALPVSVGLFVLKIAVFAVLLGVLPRPGWVRADAAAIAAL
+VTILVWQAAEVLVFARTRRGIYAD
+>PROKKA_00521
+MTGAGGRRRRRRWENRRGWWGILGWSLAAAGVALAITCAAWLLSVGGEAAGSALLGGGAV
+LALSALTGVTTALVWDRAREAALPVSVGLFVLKIAVFAVLLGVLPRPGWVRADAAAIAAL
+VTILVWQAAEVLVFARTRRGIYAD
+>PROKKA_02141
+MSPRTAPDAAPRSARARRRPRRRRWENRRGWWGILAWSLAATAAAVAVVCAVALAAGGPD
+AAASALLGGGAVLVLSALTGATTALVWDRAREAALPVSVGLFVLKIAVFAVLLGTVPRPD
+WILPDAAAIAALVAILVWQGVEVLVFARTRRGIYAD
+>PROKKA_02034
+MTASARPARRRWENRAGWWGILRWCCAATAVGVLACGAVAAVLHGGPAGLSALTGGGAVL
+VLSALTGATTAVAWDRARAAALPLSVGAFVVKLVLYALLLATLRMPEWMSGTAVAVGALV
+GVVVWQAVEVLVFARTRRGIYAD
+>PROKKA_00757
+MTGAGGRRRRRRWENRRGWWGILGWSLAAAGAALAITCAAWLLSAGGEAAGSALLGGGAV
+LALSALTGATTALVWDRAREAALPVSVGLFVLKIAVFAVLLGVLPRPGWVRADAAAIAAL
+VTILVWQAAEVLVFARTRRGIYAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000699.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000699.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a7eed5bdb2236996ffc64583ecc6a95f4ee5a0c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000699.fa
@@ -0,0 +1,30 @@
+>PROKKA_00791
+MLTLVLANASFVPPTISDGHLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP
+RLVPGKAQWLAESGYSFVRNDIAKDILGEKNFKQWVPLLFAIFFFVLLNNLFGAIPVLQL
+PTFSHAGAAYGLALIVYAIWIGVGIKRHGVRYLKLAVVPSGVPGWILPLLVPLEIISNFI
+VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVILGSVALYFLELL
+IMYLQAFVFTLLTAIYIQGAIDANDH
+>PROKKA_00522
+MLTLVLANASFVPPTISDGHLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP
+RLVPGKAQWLAESGYSFVRNDIAKDILGEKNFKQWVPLLFAIFFFVLLNNLFGAIPVLQL
+PTFSHAGAAYGLALIVYAIWIGVGIKRHGVRYLKLAVVPSGVPGWILPLLVPLEIISNFI
+VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVILGSVALYFLELL
+IMYLQAFVFTLLTAIYIQGAIDANDH
+>PROKKA_02140
+MLTLVLANASFVPPTISDGNLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP
+QLVPGKAQWLAESGYSFVRNGIAKDILGEKNFRQWVPLLFAIFFFVLLNNLFGAIPVLQL
+PSFSHAGAAYGIALIVYAIWIGVGLKRHGIRYLKLAVVPSGVPSWILPLLVPLEIISNFI
+VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVIIGSVALYFLELL
+IMYLQAFVFTLLTAIYIQGAIDANDH
+>PROKKA_02033
+MLPLVLANAEFVPPSVSDAHLPDLLPWGAEYGTGFGKQMLLVLLSVVLITGFFAWAMRKP
+KLVPGRAQWIAESGYAFVRNGIGRDVMGEKHFKQWVPLLFAIFFFVLLNNLFGAIPLLQM
+PSFSHAGSAYAIALIVYAIWIGVGVKHHGVKYFKLAVVPSGVPGWILPLLVPLEFISNFI
+VRPLTHSLRLMAVMLAGHMIVMLAGAGAAFLITQTGNPLLAGTGVLVILASVALYLLEIL
+LMYLQAFVFTLLTALYIQGAIDANDH
+>PROKKA_00758
+MLTLVLANASFVPPTISDGHLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP
+RLVPGKAQWLAESGYSFVRNDIAKDILGEKNFKQWVPLLFSIFFFVLLNNLFGAIPVLQL
+PTFSHAGAAYGLALIVYAIWIGVGIKRHGVRYLKLAVVPSGVPGWILPLLVPLEIISNFI
+VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVILGSVALYFLELL
+IMYLQAFVFTLLTAIYIQGAIDANDH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000702.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000702.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc429dc05f00e4e74590eb20c9f7ca2fbe087e8f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000702.fa
@@ -0,0 +1,30 @@
+>PROKKA_00794
+MMTGASRDSLAASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH
+GLVDSLFGARVTPGALQVLKDLAGRRWSAERDLGDALETVAVHAAAAEAARGGHAGLAAL
+LGELLAFNRTVEDSHELQRALTDQHAPLEARAALAGRLLGESASPAGRLLVERAVSAPRG
+LKPSAAIRKAADAVAERQRQWIAEVTVARPLEAEQQERLALGLRRAFGRDLVMDVTVDPH
+VVGGVRVQVGDDVVDGSMASRLHDLQRRMAG
+>PROKKA_00525
+MMTGASRDSLAASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH
+GLVDSLFGARVTPGALQVLKDLAGRRWSAERDLGDALETVAVHAAAAEAARGGHAGLAAL
+LGELLAFNRTVEDSHELQRALTDQHAPLEARAALAGRLLGESASPAGRLLVERAVSAPRG
+LKPSAAIRKAADVVAERQRQWIAEVTVARPLEAEQQERLALGLRRAFGRDLVMDVTVDPH
+VVGGVRVQVGDDVVDGSMASRLHDLQRRMAG
+>PROKKA_02137
+MMTGASRDSLTASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH
+GLVDSLFGARVTPGALQVIKDLAGRRWSAERDLGDALETVAAHAAAAEAGRGGHAGLAAL
+SGELLAFNRTVEDSHEVQRALTDQHAPVEARAALARRLLGESASPAGQLLVERAVAAPRG
+VKPAAAVRQAADVVAERQRQWIAEVTVARPLGAEQQERLALGLRRAFERDLVMDVTVDPH
+VVGGIRVQVGDDVVDGSMASRLNDLQRRMAG
+>PROKKA_02030
+MMTGASGDSLTASLESVRTVLDEGGVALARELFAALDVVDQQGALRRALTDPAWSTERRH
+GVLDSLFGGRVSPGALQVLKDLAGRRWSAERDFGDALEAVAADAAAGEAARGGHAGLAAL
+SGELLGFQRVFQDSHEVERALTDQRAPRESRSGLARRLLGAQASPAAVLLVERAVTDGRG
+VKPATALRSYADVVATRQRQWIAEVTVARPLEDGQRERLAAGLRRAFGRDLVLDVNVDPT
+VVGGIRVQVGDDVIDGSMASRLNDLQRRMAA
+>PROKKA_00761
+MMTGASRDSLAASLEAVGPVLDEGGVALARELFGALDVVDEHGALRRALTDPAWTTERRH
+GLVDSLFGARVTPGALQVLKDLAGRRWSAERDLGDALETVAAHAAAAEAARGGHAGLAAL
+SGELLAFNRTVEDSHEVQRALTDQHAPLEARAALAGRLLGESASPAGRLLVERAVSAPRG
+LKPSAAVRKAADVVAERQRQWIAEVTVARPLEAEQQERLALGLRRAFGRDLVMDVTVDPH
+VVGGIRVQVGDDVVDGSMASRLHDLQRRMAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000707.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000707.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb1112014bd684127d7e2ce069ff6fb9b3989516
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000707.fa
@@ -0,0 +1,20 @@
+>PROKKA_00799
+MQGPVLIASATVAAVIVLSALALVMRRRALARVTAAFPAVLEREGPGRERVIGVYDESRL
+RLTGRWRLSRERWSADRSRLQIDRLPADEAGRTVLELSAGARPVRVVVDPDDAGALRAWS
+EAGPSAASSFWRR
+>PROKKA_00530
+MLIASATVVAVIVLSALALVMRRRALARVTAAFPAVLEREGPGRERVIGVYDESRLRLTG
+GWRLSRERWSADRSRLQIDRLPADEAGRAVLELSAGARPVRVVVDPDDAGALRAWSEAGP
+SAASSFWRR
+>PROKKA_02132
+MLIALAGVLAVFALSASALAVRRRALLRTSAAFPAVLQGHGRPRERVIGVYDETRLLFTG
+RWMIRRERWSVGRCDLQIDRLPVAEDGRAVLELDGGRGSVTVVVDPDDAGALRAWSEAGP
+SAASSFWRR
+>PROKKA_02025
+MRGPVLLLSGALAVFALLALAGWARHRALVRGPGRFAGVLVTDGGRRCRVVGCFRSHELV
+LSHHLLPERRLWSAERWRLEVDRLPAAEAGHTRLRITDASGRSDDAVDLEVEDDVAGAVR
+AWTEAGPSQAGQSWWRPPGAA
+>PROKKA_00766
+MEGPVLIASATVVAVIVLSALALVMRRRALARVTAAFPAVLEREGPGRERVIGVYDESRL
+RLTGGWRLSRERWSADRSRLQIDRLPADEAGRAVLELSAGTRPVRVVVDPDDAGALRAWS
+EAGPSAASSFWRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000712.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000712.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a434fb312271fbf9b958a7b4f47f350a3dbd7cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000712.fa
@@ -0,0 +1,30 @@
+>PROKKA_00804
+MTPHASEPAPTHLAAATRRRAVDAPDPDLALVTRGLTQRFGDKLALDALDLDVPAGSFFG
+VVGPNGAGKTTALSMATGLLRPDHGRAWIHGVDVWEQPLEAKRRVGVLADGVRTFDRLTG
+AQLVTYAGLLHGLDADTVAERTADLLRVMDLEDAGRTLVADYSAGMTKKVSLAAAMVHAP
+DLLVLDEPFEAVDPVSAANIRDILHSYVERGGTVIVSSHVMDLVQRMCTHVAVIAAGTLR
+AAGTLEEVRDGRDLEDRFVELVGGRHGSEGLAWL
+>PROKKA_00535
+MTPHAPEPAPAHLAAAARRRAADAPDPDLALVTRGLTQRFGDKLALDALDLDVPAGSFFG
+VVGPNGAGKTTALSMATGLLRPDHGRAWIHGVDVWEQPLEAKRRVGVLADGVRTFDRLTG
+TQLVTYAGLLHGLDADTVAERTADLLRVMDLEDAGRKLVADYSAGMTKKVSLAAAMVHAP
+DLLVLDEPFEAVDPVSAANIRDILHSYVERGGTVIVSSHVMDLVQRMCTHVAVIAAGTLR
+AAGTLEEVRDGRDLEDRFVDLVGGRHGSEGLAWL
+>PROKKA_02126
+MSEHPAEPHRTAPSSAEAPHAGPAPAEAPAVVPSAAARRRAVDAPDPDLALVTRGLTKRF
+GDKTALDGLDLDVPAGSFYGVVGPNGAGKTTALSMATGLLRPDLGQAWIHGVDVWAQPLE
+AKRRVGVLADGVRTFDRLTGAQLVTYAGLLHGVDADTVAARTEDLLRVMDLADAGRKLVV
+DYSAGMTKKISLAAAMVHAPDVLVLDEPFEAVDPVSAANIRDILHDYVGRGGTVIVSSHV
+MDLVQRMCSHVAVIAGGTLRAAGTLEEVRAGRDLEDRFVDLVGGRHEQEGLAWL
+>PROKKA_02019
+MRAQDAPDPNLALVTRGLAKRFGEKVALAGLDLEVPAGSFFGVVGPNGAGKTTALSMATG
+MLRPDAGRVWIHGVDVWEQPLEAKRRVGVLADGVRTFDRLTGAQLITYAGLLHGLDRDTV
+DVRTADLLRVMDLEEAGRKLVVDYSAGMTKKVNLAAAMVHAPDVLVLDEPFEAVDPVSAA
+NIRDILHDYVGRGGTVIVSSHVMDLVQRMCSHVAVIAGGVLRAAGTLEEVRAGRDLEERF
+VDLVGGRHTGEGLAWL
+>PROKKA_00771
+MTPHAPEPAPAHLAAAARRRAVDAPDPDLAFVTRGLTQRFGDKLALDALDLDVPAGSFFG
+VVGPNGAGKTTALSMATGLLRPDHGRAWIHGVDVWEQPLEAKRRVGVLADGVRTFDRLTG
+AQLVTYAGLLHGLDADTVAERTTDLLRVMDLEDAGRKLVADYSAGMTKKVSLAAAMVHAP
+DLLVLDEPFEAVDPVSAANIRDILHSYVERGGTVIVSSHVMDLVQRMCTHVAVIAAGTLR
+AADTLEEVRDGRDLEDRFVDLVGGRHGSEGLAWL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000720.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000720.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fc7a9b0827a93deb711bfe6c04313463b404fd33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000720.fa
@@ -0,0 +1,35 @@
+>PROKKA_00813
+MSGQRAAVDAAAPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTEHSPYGPRPIAEVRA
+LALAIMDELVARGVKALVIACNSASAAVLRDARERYTGGHGIPVIEVIQPAVRRAVAATR
+TGRIGVIGTEATVGSRAYEDSFSAAPHLEITSVACPRFVEFVEAGITTGPELLETAREYT
+APLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEHPHS
+AAGSGQATRHRFAATGDPDHFQALARRFLGPEVESVRRLETIGAPRPAAAPVPTRSTAFV
+PLGAEQEGVT
+>PROKKA_00545
+MSGQRAAVDAAAPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTEHSPYGPRPIAEVRA
+LALAIMDELVARGVKALVIACNSASAAVLRDARERYTGGHGIPVIEVIQPAVRRAVAATR
+TGRIGVIGTEATVGSRAYEDSFSAAPHLEITSVACPRFVEFVEAGITTGPELLETAREYT
+APLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEHPHS
+AAGSGQATRHRFAATGDPDHFQALARRFLGPEVESVRRLETIGAPRPAAAPVPTRSAASV
+RPGPEQEGVT
+>PROKKA_02117
+MSAPPQARPEVSASSPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTAHAPYGPRPIAQ
+VRALALGIMDELVDAGVKALVIACNSASAAVLRDARERYTGRHGIPVVEVIQPAVRRAVA
+ATRSGRIGVIGTQATVGSRAYDDSFSAAPHLQVTSAACPRFVEFVEAGITTGPELLATAQ
+EYTEPLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEH
+PHSAAGSGQDTRHRFAATGDPEHFQALARRFLGPEVGAVRRLDTVRERYPTAALAQLTPD
+LIARLGAEQERET
+>PROKKA_02008
+MSATADTAQTGAGPSSPIGVFDSGVGGLTVARAIMDQLPHEPIIYVGDTAHSPYGPRPIA
+QVRALALGVMDELVEAGVKALVIACNSASAAVLRDARERYTGRLGIPVVEVIQPAVRRAV
+AATRNGRVGVIGTQATVGSRAYEDSFSAAPHLQITSVACPRFVEFVEAGITTGPELLETA
+EEYVAPLKAAGVDTMVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRALVRHGLE
+HPHSAAGSAAAPEHRFAATGDPEHFAALARRFLGPEVGPVRQIQEIRERYPTAALTALTP
+DVLARLRAEMEEDGAR
+>PROKKA_00782
+MSGQRAAVDAAAPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTEHSPYGPRPIAEVRA
+LALAIMDELVARGVKALVIACNSASAAVLRDARERYTGGHGIPVIEVIQPAVRRAVAATR
+TGRIGVIGTEATVGSRAYEDSFSAAPHLEITSVACPRFVEFVEAGITTGPELLETAREYT
+APLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEHPHS
+AAGSGQATRHRFAATGDPDHFQALARRFLGPEVESVRRLETIGAPRPAAAPVPTRSAASV
+RPGPEQEGVT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000721.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000721.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8ceae5d6be1975b834d7b2d203686562abd9d26
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000721.fa
@@ -0,0 +1,30 @@
+>PROKKA_00814
+MKLTIIGASGSFPGPGSPASCYLLTAEGVAEDGVTPRTWRILLDLGNGALGVLQRYVELE
+DLDGILLSHLHPDHFMDLCGMHVAIRWNPAGWDRGRLPVYGPAGTADRIAEAYGMDPEPG
+MHQDFEFRCWAAGRTERLGPFRFTPVPVRHPIDEAYAIRVEVDRVDDDGDVTTRVLTYSG
+DTDACEGLVEAARDADVFLCEAAFHEGRDDGIDGVHLTGRRAGETAAQAGARKLLLTHLP
+VWNDPQRAVQEARAVYDGPLAVAVSGLSYGV
+>PROKKA_00546
+MKLTIIGASGSFPGPGSPASCYLLTAEGVAEDGVTPRTWRILLDLGNGALGVLQRYVELE
+DLDGILLSHLHPDHFMDLCGMHVAIRWNPAGWGRGRLPVYGPAGTADRIAEAYGMDPEPG
+MHQDFEFRCWAAGRPERLGPFRFTPVPVRHPIDEAYAIRVEVDRVDDDGDVTTRVLTYSG
+DTDACEGLVEAARDADVFLCEAAFHEGRDDGIDGVHLTGRRAGETAAQAGARKLLLTHLP
+VWNDPQRAVQEARAVYDGPLAVAVSGLSYGV
+>PROKKA_02116
+MKLTVIGASGSFPGPGSPASCYLVTAQGVAEDGVTPRTWRILLDLGNGSLGVLQRYIELE
+ELDGILLSHLHPDHCMDLCGMHVAIRWNPEGWHRDRMPVYGPTATADRIAEAYGMDPEPG
+MHEDFDFRVWRPGRTERFGPFRLTPVPVRHPIDEAYAIRVEADEPDGEGGTVTRVLTYSG
+DTDACEGLVEAARDADLFLCEAAFHEGRDDGIDGVHLTGLRAGQTAAQAGAKKLLLTHLP
+VWNDPQRAVLEAREAYEGPMAVAVSGLSYGV
+>PROKKA_02007
+MKLTVIGASGSFPGPGSPASCYLVTADGPDGNGGTRPWRILLDLGNGSLGVLQRHIELEQ
+IDGVLLSHLHPDHCIDLCGLHVAVRWNPEGWDAGRIPVYGPAATATRIAEAYGMDPEPGM
+QEDFDFRAWEAGRTEGLGPFRLTPFAVRHPIDEAYAIRVETTEPGPDGEPVTRVLAYSGD
+SDTCDGLVEAARDADLFLCEAAYHEGRDDHIDGVHLTGRRAGQMAAEAGARKLLLTHLPV
+WNDPQRCAQEAREAYVGPLAVAVSGLSYGL
+>PROKKA_00783
+MKLTIIGASGSFPGPGSPASCYLLTAEGVAEDGVTPRTWRILLDLGNGALGVLQRYVELE
+DLDGILLSHLHPDHFMDLCGMHVAIRWNPAGWGRGRLPVYGPAGTADRIAEAYGMDPEPG
+MHQDFEFRCWAAGRPERLGPFRFTPVPVRHPIDEAYAIRVEVDRVDDDGDVTTRVLTYSG
+DTDACEGLVEAARDADVFLCEAAFHEGRDDGIDGVHLTGRRAGETAAQAGARKLLLTHLP
+VWNDPQRAVQEAREVYDGPLAVAVSGLSYGV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000724.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000724.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bfdf4e4f7cf25ef2c55fcc350f56938b6d457a79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000724.fa
@@ -0,0 +1,39 @@
+>PROKKA_00817
+MSGGRVPVPGLDFTAIDFETANGFRGSPCAVGAVRVRDGVMVDRAEWLIRPPVGFDRFDP
+RNVRIHGITEDRVLDAPRFAQVYDELADFVGTDVLAAHNAGFDVGVIESGLEVSGRDVPG
+LEFVCTLVLARRVYDLPSYALPSAAREAGFTPGRHHDALADAEACAAILVDIGRRVLGAP
+PADADVLPGLTDAPAGRGVDRLMRAQGLGVSVLAPRAAGAGAESKATRQARRTEGVFDAR
+VPLRDERAMPDFMRWPDEGVNPLPNPAADPGHPLFGQTVVFTGGIGMSRQRAKTRAAAHG
+AQTANRVGAATTMLVVGDGFEAADLHRPRAEDGAPQAVTTALAHRKTRDALRRRDRG
+>PROKKA_00549
+MSGGRAPVPGLDFTAIDFETANGFRGSPCAVGAVRVRDGVMVDRAEWLIRPPVGFDRFDP
+RNVRIHGITEDRVLDAPRFAQVYDELADFVGTDVLAAHNAGFDVGVIESGLEVSGRDVPG
+LEFVCTLVLARRVYDLPSYALPSAAREAGFTPGRHHDALADAEACAAILVDIGRRVLGAP
+PADAEILPGLTDAPAGRGVDRLMRAQGLGVSVLAPRAAGSGAESKATRQARRTEGVFDAR
+VPLRDERAMPDFMRWPDEGVNPPPNPTADPGHPLFGQTVVFTGGIGMSRQSAKTRAAAHG
+AQTANRVGAATTMLVVGDGFEAADLHRPRAEDGAPQAVTTALAHRKTRDALRRRDRGQAI
+ALVSEGEFLQMLDGNWPDAAR
+>PROKKA_02113
+MSGVLAPVPGLDFTAIDFETANGFRGSPCALGAVRVRDGVMVERAEWLIRPPVGFDRFDP
+RNVRIHGITEDRVLDAARFADVYDELAGFVGADVLAAHNAGFDVGVIESGLEVSGRDVPR
+LDFVCTLVLARRVYDLASYALPSAAREAGFAPGPHHDALADAEACAAILVDVARRVLGTE
+AGDGAAVAPAGARGLPEPFDVPRLMRAQGLTVNTLAQRAAGEGPESKATRQARRAQGVFD
+ARVPLKDERAMPDFLRWPDEGTNPVPNPDADPGHPLHGQTVVFTGGIGMSRQTAKVRAAR
+LGAQTANRVGAATTMLVVGDGFEAADLDRPAPAPGTREAVTTALAHRKTRDALRRRERGQ
+HISLVSEGEFLQMLDGNWPDAAR
+>PROKKA_02004
+MTAGIAPVRQPGLDFTAIDFETANGFRGSACQLGAVRVRDGLPASRAVWLMRPPAGFDRF
+DPRNVRIHGIHADRVVDAPRFAEVYDAFAAFAGDDVLVAHNAGFDLGVIESGLEVSGRDV
+PAHDYACTLTLARRIYDLPSYSLPSAAREAGFVPGRHHDALADAEACAAILVDLARRVCP
+PGEATVDALLASQGLRRSRLTARAAGTGRESRATRQARTMPGLFDATIPLADDRTLPDLM
+RWPDEGVNPEPAADADPGHPLYGQVVVFTGGIGMSRQEAKNRAAQRGAATANRVNGRTTM
+LVVGDGVDPAELVGAPEVHGVVVDPGATDPAGRGVDPGGAVTHRKTREALQRRAKGQAIA
+LVSEAEFLQMVDGAWPAGAR
+>PROKKA_00786
+MSGGRVPVPGLDFTAIDFETANGFRGSPCAVGAVRVRDGVMVDRAEWLIRPPVGFDRFDP
+RNVRIHGITEDRVLDAPRFAQVYDELADFVGTDVLAAHNAGFDVGVIESGLEVSGRDVPG
+LEFVCTLVLARRVYDLPSYALPSAAREAGFTPGRHHDALADAEACAAILVDIGRRVLGAP
+PADAEILPGLTDAPAGRGVDRLMRAQGLSVSVLAPRAAGSGAESKATRQARRTEGVFDAR
+VPLRDERAMPDFMRWPDEGVNPLPNPAADPGHPLFGQTVVFTGGIGMSRQSAKTRAAAHG
+AQTANRVGAATTMLVVGDGFEAADLHRPRAEDGAPQAVTTALAHRKTRDALRRRDRGQAI
+ALVSEGEFLQMLDGNWPDAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000725.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000725.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5fafa5bdd60fa2aac0a35825a92ac714859a9f69
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000725.fa
@@ -0,0 +1,40 @@
+>PROKKA_00818
+MSATAPEPTASSSTPLPGPEHADRVLALLAAGAAGDALGGVVEFTPASGIAAVHGPAGVT
+DAADLLAQEGAHALPITDDTQLTLYVLDGLLEWIEWQNDGVPADPAACVWLACLRWFATQ
+DGALPEGAPPAPPRWIDAHAELKVRRAPGTACLTGLAEPGMGLPGDPHNPGSKGCGTVMR
+SAPYGMVPGLEDPHVVSLARQGAVLTHGHPTAWVAAAAYALVIAALLRGLDLAAAVAHAR
+AWLDTLGEEAEETRAAVTAAVDLAGTVDADPGAPGALPTALGEGWVAEEALAIALYAALT
+AQAAHPADPAAALALALRIGVNHDGDSDSTASLAGQVLGAAHGTAVFGAHDPADRAAAEA
+SVPGWIAEREVVLEAARRWSAATT
+>PROKKA_00550
+MSATAPEPTASSSTPLPGPEHADRVLALLAAGAAGDALGGVVEFTPASGIAAVHGPAGVT
+DAADLLAQQGAHALPITDDTQLTLYVLDGLLEWIEWQNDGVPADPAACVWLACLRWFATQ
+DGALPEGAPPAPPRWIDAHAELKVRRAPGTACLSGLAEPGMGLPGDPHNPGSKGCGTVMR
+SAPYGMVPGLEDPHVVSLARQGAVLTHGHPTAWVAAAAYALVIAALLRGLDLAAAVAHAR
+AWLDTLGEEAEETRAAVTAAVDLAGTVDADPGAPGALPTALGEGWVAEEALAIALYAALT
+AQAAHPADPAAALALALRIGVNHDGDSDSTASLAGQVLGAAHGTAVFGAHDPADRAAAEA
+SVPGWIAEREVVLEAARRWSAATT
+>PROKKA_02112
+MTETPAAPSLPGPEHATRVAALLAAGAAGDALGYTVEFDADAAVRARHGAEGLTTGEAAL
+AVVGGEALPISDDTQMTLYVLDGLLEWIEWQNDGQAADPAACVWLACLRWWATQHGGALP
+DGAPPVPPRWLEDHPELRARRAPGNACLSGLDSAAMGLPGDPRNPDSKGCGTVMRSAPYG
+MVPGLEDVHVVSFARQGAVLTHGHPTAWVAAAAYSLMIAALLRGAGLEDAVAHARVWVDS
+LDPAEGGETAAALASAVELAASPADDAGRPGTLPAALGEGWVAEEALAIAVHAALVAQAR
+HEDPADMLALALRIGANHAGDSDSTASLAGQLLGAAHGPAVFGADAAADGPAGLVPAWVA
+EREVVAEAARRWSAATT
+>PROKKA_02003
+MTDAAPSPRTDVSYPSRVLGLLAAGAAGDALGYAVEFDSVDRILGRLGAAGVTDGPALAA
+VSGVSALPVSGDTQMTLYVLDGMLEWIEWQNAGQASDPAACVWLACLRWLRTQDGALPDG
+APPAQDRWIDAHTELHAQRAPGMACLSGLRSSGMGVVPDPKNPDSKGCGAVMRSAPYGMV
+PGLEDHHVASFARQGAVLTHGHPTGWTAAAAFALTVSALFDGAELRGALEHPRTWLDSTG
+EDGAETRAALDGALAEAARAVEAGDDVGAPGTLPASLGEGWVAEEALAIAAYAALVAEAR
+AEDPAAALGLALRIGANHDGDSDSTAALAGQLVGARHGMAVFGSRGQDADSVPAWITERE
+VVAEAARRWIAATT
+>PROKKA_00787
+MSATAPEPTASSSTPLPGPEHADRVLALLAAGAAGDALGGVVEFTPASGIAAVHGPAGVT
+DAADLLAQEGAHALPITDDTQLTLYVLDGLLEWIEWQNDGVPADPAACVWLACLRWFATQ
+DGALPEGAPPAPPRWIDAHAELKVRRAPGTACLTGLAEPGMGLPGDPHNPGSKGCGTVMR
+SAPYGMVPGLEDPHVVSLARQGAVLTHGHPTAWVAAGAYALVIAALLRGLDLAAAVAHAR
+AWLDGLGEEAAETRAAVTAAVDLAGTVDADPGAPGALPTALGEGWVAEEALAIALYAALT
+AQAVHPADPAAALALALRIGVNHDGDSDSTASLAGQVLGVAHGTAVFGAHDPADRAAAEA
+SVPGWVAEREVVLEAARRWSAATT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000728.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000728.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24cd7299bea462681c373ddbad58dd0f3d1ec88a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000728.fa
@@ -0,0 +1,98 @@
+>PROKKA_00821
+MGALARFSLGRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVV
+DAQVGEPLETALQAVEGLESSRSTSQSGFNAVQLEFAYGTDLNRARSQVDRVVANLGPQL
+PEEAETSSFAGSVSDFPVVFLALSGDEDLNTLRRRAEDVLAPRLQKIDGVRGADVLGGTD
+ENVSVVPDPAALAAAGLTTSDITDALEENAGLFPVGQVTEGATTYPVQAGAAVEDLEGLR
+GIVVAPSGDGEPRTLDEVADVTLVAAAPTSLTRTDGVPTLSVSVTATPDADLVAVSQAVR
+DALPELASLVGGGADLTVVFDQAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSVRSTLV
+TAVSIPLSLLAALIGVAAFGYSLNTLTLGALTISIGRVVDDAIVVVENIRRHLGLGADRR
+TAILDGTREVATAITASTLVSVAVFLPIAFVGGLAGELFRPFAVTATVALLASLVVALTI
+VPVLCWWFLRSPRRGAETTAAPAVPGDRPVAAGGWLTRAYRPVLRWTQRHTVVTLAAALA
+LLAGTAALVPLIPTNLLGDSGQNSFVVTAEQEPGTSLETTAAAAERIERVLLDTDGVETV
+QWTAGTAAGPMGAFGGSSADRARFTVVTDPDADQVALQDGVRAELTGLDGVGDVSVSTQQ
+GPSGGQDIEVAVSAPDPQALTAAADQVAEALRPVEGAREVTTPASDLRPTFQVDVDTVAA
+ARLGLTEEAVAGQAAAALQAVPVGDVRFGFESFAVQLGDPEPVESLDALRQVPVETAEGP
+VPLADLAEVSRVSVPARVTSSNGERTAVVTVTPDDEDLGAVSRRVTQAVAELDLPEGVTA
+AVGGAAEQQAQTFRDLGLALLAAVATVYVVLVATFNSLRQPLVLLVSIPFAATGVFLALL
+ATGTPLGLSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMPLDEAIEVGALNRVRPVVM
+TALATVLAMTPMALGVTGHAGFISQPLAVAVVGGLVSSTLLTLVLVPVLYRLTEVRGERR
+LQEERRVAAAWEAQRVAAERAAKQERRAEQGSAAPSELDAGRLGRLRQRLRRRWRRA
+>PROKKA_00553
+MGALARFSLGRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVV
+DAQVGEPLETALQAVEGLESSRSTSQSGFNAVQLEFAYGTDLNRARSQVDRVVANLGPQL
+PEEAETSSFAGSVSDFPVVFLALSGDEDLNTLRRRAEDVLAPRLQKIDGVRGADVLGGTD
+ENVSVVPDPAALAAAGLTTSDITDALEENAGLFPVGQVTEGATTYPVQAGAAVEDLEGLR
+GIVVAPSGDGEPRTLDEVADVTLVAAAPTSLTRTDGVPTLSVSVTATPDADLVAVSQAVR
+DALPELASLVGGGADLTVVFDQAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSVRSTLV
+TAVSIPLSLLAALIGVAAFGYSLNTLTLGALTISIGRVVDDAIVVVENIRRHLGLGADRR
+TAILDGTREVATAITASTLVSVAVFLPIAFVGGLAGELFRPFAVTATVALLASLVVALTI
+VPVLCWWFLRSPRRGAETTAAPAVPGDRPVAAGGWLTRAYRPVLRWTQRHTVVTLAAALA
+LLAGTAALVPLIPTNLLGDSGQNSFVVTAEQEPGTSLETTAAAAERIERVLLDTDGVETV
+QWTAGTAAGPMGAFGGSSADRARFTVVTDPDADQVALQDGVRAELTGLDGVGDVSVSTQQ
+GPSGGQDIEVAVSAPDPQALTAAADQVAEALRPVEGAREVTTPASDLRPTFQVDVDTVAA
+ARLGLTEEAVAGQAAAALQAVPVGDVRFGFESFAVQLGDPEPVESLDALRQVPVETAEGP
+VPLGDLAEVSRVPVPARVTSSNGERTAVVTVTPDDEDLGAVSRRVTQAVAELDLPEGVTA
+AVGGAAEQQAQTFRDLGLALLAAVATVYVVMVATFNSLRQPLVLLVSIPFAATGVFLALL
+ATGTPLGLSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMTLDEAIEVGALNRVRPVVM
+TALATILAMTPMALGITGHAGFISQPLAVAVVGGLVSSTLLTLVLVPVLYRLTEVRGERR
+LQEERRVAAEREAQRVAAERAAEQARRAEERWAAPSELDAGRLGRLRQRLRRRWRRA
+>PROKKA_02109
+MGALARFSLRRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVV
+DSLVGEPLETALQAVEGLESSGSTSQASFNSIQLQFAYGTDLNRARSQVDRVVSNLASQL
+PEEAETSSFAGSVSDFPVVFLALSGDEDLNELRRRAEAVLAPRLQKLEGVRGADVLGGTE
+EHVSVVPDPEALAAAGLSTQDITTALEENAGLFPVGQVTEGESTYPVQAGAAVEDLEGLR
+GIVVTPAEGGQGAAPQDRTADGGPVGGGGGPPADAEATPAAPAEPAGDGEPRTLGEVAEV
+SLQAAEPTSVTRTDGADTLSVSVTATPDADLVAVSEAVREALPELESVVGGGADLTVVFD
+QAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSLRSTLVTAVSIPLSLLAALIGVAVFGY
+SLNTLTLGALTISIGRVVDDAIVVVENIRRHLDLGADRRTAILIGTREVATAITASTLVS
+VAVFLPIAFVGGLAGELFRPFAVTATIALLASLVVALTIVPVLCWWFLRTPRRPAGDESP
+ADAAEGGAPAVPAGEHGHDAHPSAAGGWLARAYRPVLRWTQRHTVATLAGAVAVLAGTAA
+LVPLIPTNLIGDTGQNSFVVTADQEPGTSLEATAAAAGVIERTLLETEGVETVQWTAGTA
+GGPAGAFGGSSADRARFTVVTDENADQTALQDGVRADLAALEGVGEVSVSTQQGPGGGQD
+IEVSVSAPDPQALATAADEVAGALRGVEGAREVTTPAADVRPTFQVDVDTEAAARLGLTE
+EAVAGQAAAALQAVPVGDVRFGFEQFQVRLGDPDPVESLEALRQVAVQTGSGPVPLEELA
+SVERVDVPARVTSSNGERTAVVTVTPDDQDLGAVSRRVTEAVDGLALPEGVTATVGGAAE
+QQAATFRELGLALLAAIATVYVVMVATFNSLRQPLVLLVSIPFAATGVFLALLATGTALG
+LSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMGLDEAIEVGALNRVRPVVMTALATIL
+AMVPMALGLTGHSGFISQPLAVAVVGGLLSSTLLTLVLVPVLYRLTEARGERRIQAERAE
+QARRDEEARRRAAEAEQAAAEQAESARAGLLARRRTGGAPAASAAAGMADDGGRRPGPLG
+RLRARLGGLVGRARRA
+>PROKKA_02000
+MGALARFSLSRRALVALVTAFIAVFGVLSAGLLKRELIPSLELPVISVSTTYPGASPEVV
+DAEIGQPLEQALQAVEGLDSSASTSATSFNSVQLRFRYGTDLTRARSQVDRVISNLASQL
+PEEAQTTSFAGSVSDFPVVFLALSGDEDLNALKRRAEDVLVPRLQRIDGVRGAQVLGGTE
+EYVSVVPDAAKLAAAGLTTQDVTTALEENAGLFPIGQATSGTVTYPVQAGAPVGSVADLE
+QVTVTPGGGQSSTGAADQGAGAGAGGGPGAATGTPARLGDVAAVSMQAADPTSVTRTDGA
+PTLSLSVTATPDADLVAVSHAVADALPELESLAGSGAKLTVVFDQAPFIEQSIRTLFVEG
+LLGLAMAILVIAVFLLSARSTMVTAVSIPLSLLTALIGVAVFGYSLNTLTLGALTISIGR
+VVDDAIVVVENIRRHLGLGADKRTAILEGTREVATAITASTLVSVAVFLPIAFVDGLAGE
+LFRPFAVTTSIALLASLVVALTIVPVLCWWFLRAPRAAAAPGGAEGVSSPVEDAAQDTWL
+ARAYRPVLRWTQRHAVATLAGAAALLAGTVALAPLIPTNLLGDSGQNSFVVTAQQAPGTS
+LEATTAIAGRIEAALRDTPGVRTVQFTAGSAGGAMGAFGRGSADRATFTVVTDPDADQTA
+LQDEVRGRLAGLGDVGEVDVSAQQGPAGGQDITVSVTAPDPEALADGIDRVAEALRGLDG
+VLQASTPSSDVRPTFQVDVDTLAAAERGLTEKAVSGQVAAALQAVPAGTVRFGFQEFTVR
+LGDPDPVESLGALRAVPISTPSGPVPLSELADVRRADVPAQVTSSNGQRTAEVTVTPDPA
+DLGGVSRRVSDALEGVALPDGVEATVGGAATEQAKTFRDLGLALLAAIAAVYVVMVATFN
+SLRQPFVLLVSIPFAATGVVLALLASGTALGVATMIGLLMLVGIVVTNAIVLIDLINQYR
+RRHGMALDEAIERGALHRVRPVVMTALATVLAMTPMALGITGHAGFISQPLAVAVVGGLA
+SSTVLTLVLVPVLYRLTEARGERRIQAERAAREAEERELAEREARERELAEREAAARAVA
+GPAAAAHPAPAGRLSRRRGWRGWIRRATS
+>PROKKA_00790
+MGALARFSLGRRALVALVTVFIAVFGVLSAGQLKRELIPPLELPVISVSTLYPGASPEVV
+DAQVGEPLETALQAVEGLESSRSTSQSGFNAVQLEFAYGTDLNRARSQVDRVVANLGPQL
+PEEAETSSFAGSVSDFPVVFLALSGDEDLNTLRRRAEDVLAPRLQKIDGVRGADVLGGTD
+ENVSVVPDPAALAAAGLTTSDITDALEENAGLFPVGQVTEGATTYPVQAGAAVEDLEGLR
+GIVVAPSGDGEPRTLDEVADVTLVAAAPTSLTRTDGVPTLSVSVTATPDADLVAVSQAVR
+DALPELASLVGGGADLTVVFDQAPFIQQSIDTLFQEGLLGLAFAVLVIAVFLLSVRSTLV
+TAVSIPLSLLAALIGVAAFGYSLNTLTLGALTISIGRVVDDAIVVVENIRRHLGLGADRR
+TAILDGTREVATAITASTLVSVAVFLPIAFVGGLAGELFRPFAVTATVALLASLVVALTI
+VPVLCWWFLRAPRRGAETTAAPAVPGDRPVAAGGWLTRAYRPVLRWTQRHTVVTLAAALA
+LLAGTAALVPLIPTNLLGDSGQNSFVVTAEQEPGTSLETTAAAAERIERVLLDTDGVETV
+QWTAGTTAGPMGAFGGSSADRARFTVVTDPDADQVALQDGVRAELTGLDGVGDVSVSTQQ
+GPSGGQDIEVAVSAPDPQALTAAADQVAEALRPVEGAREVTTPASDLRPTFQVDVDTVAA
+ARLGLTEEAVAGQAAAALQAVPVGDVRFGFESFAVQLGDPEPVESLDALRQVPVETAEGP
+VPLGDLAEVSRVPVPARVTSSNGERTAVVTVTPDDEDLGAVSRRVTQAVAELDLPEGVTA
+AVGGAAEQQAQTFRDLGLALLAAVATVYVVMVATFNSLRQPLVLLVSIPFAATGVFLALL
+ATGTPLGLSTMIGLLMLVGIVVTNAIVLIDLINQYRRDRGMTLDEAIEVGALNRVRPVVM
+TALATILAMTPMALGITGHAGFISQPLAVAVVGGLVSSTLLTLVLVPVLYRLTEVRGERR
+LQEERRVAAEREAQRVAAERAAEQARRAEERWAAPSELDAGRLGRLRQRLRRRWRRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000732.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000732.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa1a883c99cdc926d6ad1bde193114bb3069cc71
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000732.fa
@@ -0,0 +1,24 @@
+>PROKKA_00827
+MTRADGSAYVGPMDTPTLHRRLRRVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLE
+MLLCPFDPTSTPDDHDRRAPGVAEDDPHGPVTEASADRADVVEVGLANVATVADTGSGYQ
+VETVTGFRTWFDVPEHTRVPVGDLTEDGTAELDQAEDATDFHAFMTAFMDELDRLYATPE
+TDATDVTPPDLHGV
+>PROKKA_00559
+MDTPTLHRRLRRVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLEMLLCPFDPTSTP
+DDHDRRAPGVAEDDPHGPVTEASADRADVVEVGLANVATVADTGSGYQVETVTGFRTWFD
+VPEHTRVPVGDLTEDGTAELDQAEDATDFHAFMTAFMDELDRLYATPETDATDVTPPDLH
+GV
+>PROKKA_02095
+MDSPTLQRRLRGVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLEMLLCPFDPTSTP
+DDAPADAPAADAPEEDPHGPVAEPSSHGTDVVGVALGNVATVADTGSGYQVETVTGFRTW
+FDVPEHARVPVGDLTEDGTAGLDQAEDAVDFHAFMTAFMDELDRLYAAPEAGGTDVTGPD
+LHAR
+>PROKKA_01994
+MDSPTLARRIRGAFDARVFNHGDYNLVYGQRSGGSLPLVIGYRHSPLEMLLCPLDPVEAV
+AAVPEEVALANVATVADTGSGYQVETVTGFRTWFEVVDRPRVPVGEASEDGLAELDQADD
+AADFHAFMTAFMDELDRLYAEPADPDLHPPQKSV
+>PROKKA_00796
+MDTPTLHRRLRRVFDARVFNHGDYNVVYGQPSGSSSPLVIGYRHQPLEMLLCPFDPTSTP
+DDHDRRAPGVAEDDPHGPVTEASADRADVVEVGLANVATVADTGSGYQVETVTGFRTWFD
+VPEHTRVPVGDLTEDGTAELDQAEDATDFHAFMTAFMDELDRLYATPETDATDVTPPDLR
+GV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000737.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000737.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3370f46626123474e056ace89904108d22be3e09
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000737.fa
@@ -0,0 +1,35 @@
+>PROKKA_00833
+MTVKKFYDDDADLSIIQGRTVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSKSRAKAEA
+EGLRVVDVATAAAEADLIMILTPDQVQADVYDQHIAGNLQKGDALFFAHGFNVRFGYIQA
+PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEKDASGQAHALALSYAKAVGGTRAGV
+IETTFTEETETDLFGEQAVLCGGASQLVQYGFETLTEAGYQPEIAYFEVLHELKLIVDLM
+VEGGIAKQRWSISDTAEYGDYVSGPRVITPDVKENMKAVLADIQSGAFAQRFMDDQKAGA
+PEFKELRARGEAHPIEKTGRELRQMFSWLKDADDDYTEGTAAR
+>PROKKA_00565
+MTVKKFYDDDADLSIIQGRTVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSKSRAKAEA
+EGLRVVDVATAAAEADLIMILTPDQVQADVYDQHIAGNLQEGDALFFAHGFNVRFGYIQA
+PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEKDASGQAHALALSYAKAVGGTRAGV
+IETTFTEETETDLFGEQAVLCGGASQLVQYGFETLTEAGYQPEIAYFEVLHELKLIVDLM
+VEGGIAKQRWSISDTAEYGDYVSGPRVITPDVKENMKAVLADIQSGAFAKRFMDDQKAGA
+PEFKELRARGEAHPIEKTGRELRQMFSWLKDADDDYTEGTAAR
+>PROKKA_02091
+MTVKKFYDDDADLSIIQGRTVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSKSRAKAEA
+EGLRVVDVATAAAEADLIMILTPDQVQADVYDQHIAGNLQEGDALFFAHGFNVRFGYIQA
+PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEKDASGQAHALALSYAKAVGGTRAGV
+IETTFTEETETDLFGEQAVLCGGASQLVQYGFETLTEAGYQPEIAYFEVLHELKLIVDLM
+VEGGIAKQRWSISDTAEYGDYVSGPRVITPDVKENMKAVLADIQSGAFAQRFMDDQKAGA
+PEFKELRAKGEAHPIEKTGRELREMFSWLKDADDDYTEGTAAR
+>PROKKA_01990
+MTAQKFYDDDADLSIIQGRTVAVIGYGSQGHAHSLSLRDSGVDVRIGLAEGSKSRAKAEA
+EGLRVVDVATAAAEADLIMILTPDQVQADVYDEHIAPNLQEGDALFFAHGFNVRFGYIQA
+PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEQDASGQAEALALSYAKAIGGTRAGV
+IKTTFTEETESDLFGEQAVLCGGASQLIQYGFEVLTEAGYQPEIAYFEVLHELKLIVDLM
+VEGGIAKQRWSISDTAEFGDYVSGPRVITPEVKDHMKEVLADIQNGAFAKHFMDDQKAGA
+PEFTELRAKGESHPIEKTGRELRQMFSWLKDTDDDYTEGTAAR
+>PROKKA_00803
+MTVKKFYDDDADLSIIQGRTVAVIGYGSQGHAHALSLRDSGVDVRIGLAEGSRSRAKAEA
+EGLRVVDVATAAAEADLIMILTPDQVQADVYDQHIAGNLQEGDALFFAHGFNVRFGYIQA
+PEGVDVALVAPKGPGHVVRREFEAGRGVPALIAVEKDASGQAHALALSYAKAVGGTRAGV
+IETTFTEETETDLFGEQAVLCGGASQLVQYGFETLTEAGYQPEIAYFEVLHELKLIVDLM
+VEGGIAKQRWSISDTAEYGDYVSGPRVITPDVKENMKAVLADIQSGAFAKRFMDDQKAGA
+PEFKELRARGEAHPIEKTGRELRQMFSWLKDADDDYTEGTAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000739.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000739.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a5e35153e89ec721693c96fa3226f07f8ca15ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000739.fa
@@ -0,0 +1,54 @@
+>PROKKA_00847
+MTDARAPYYLTTAISYPNGEPHIGHAYEYIASDAMARFQRLDGRDVRFLTGTDEHGQKME
+QTAQQQGVSALELATRNAAVFKEMDDDVLDISYDRFIRTTDTDHAEAVREIWRRMEANGD
+IYLGSYAGWYSVRDERYFGEDETEVGQDGVRRAVETGTEVTWTEEESYFFRLSKYQQPLL
+DHYREHPDFAAPRYRFNEVIRFVEAGLEDLSISRTSFQWGIDLPAPADPDAADADRRADH
+VTYVWVDALTNYLTGAGWPAEDPEAFARYWPADLHVIGKDISRFHCIFWPAFLMSAGLEL
+PRRVMIHGFLNNNGAKMSKSLGNVVHPREWVARYGLDAIRFFLLREFPFGADGSYSHEAV
+VSRKNADLANNLGNLAQRSLSMVAKNCGAAVPEPGEFTEADRAVLAQVDALLERSRSAYA
+VQDFHDALEETWRVLGEINAYFADQAPWVLRKTDEPRMRTVLYVTLQAVRRVALLAQPVM
+PGSASRLLDLLGVPAEGDAGRTGASGTGPRSFAAFHEDLVPGTPLPAPQPVFPRHEEPAE
+D
+>PROKKA_00569
+MTDARAPYYLTTAISYPNGEPHIGHAYEYIASDAMARFQRLDGRDVRFLTGTDEHGQKME
+QTAQQQGVSALELATRNAAVFKEMDDDVLDISYDRFIRTTDTDHAEAVREIWRRMEANGD
+IYLGSYAGWYSVRDERYFGEDETEVGQDGVRRAVETGTEVTWTEEESYFFRLSKYQQPLL
+DHYREHPDFAAPRYRFNEVIRFVEAGLEDLSISRTSFQWGIDLPAPADPDAADADRRADH
+VTYVWVDALTNYLTGAGWPADDPEAFARYWPADLHVIGKDISRFHCIFWPAFLMSAGLEL
+PRRVMIHGFLNNNGAKMSKSLGNVVHPREWVARYGLDAIRFFLLREFPFGADGSYSHEAV
+VSRKNADLANNLGNLAQRSLSMVAKNCGAAVPEPGEFTEADRAVLAQVDALLERSRSAYA
+VQDFHDALEETWRVLGEINAYFADQAPWVLRKTDEPRMRTVLYVTLQAVRRVALLAQPVM
+PGSASRLLDLLGVPAEGDAGRTGASGTGPRSFAAFHEDLVPGTPLPAPQPVFPRHEEPAE
+D
+>PROKKA_02088
+MTDARAPYYLTTAISYPNGEPHIGHAYEYIATDAMARFQRLDGRDVRFLTGTDEHGQKME
+QTAQREGVTALELATRNAAVFKEMDDEVLDISYDRFIRTTDADHAEAVQEIWRRMEANGD
+VYLGSYAGWYSVRDERYFGEDETAVGEDGVRRAVETGTEVTWTEEESYFFRLSKYQEPLL
+EHYRRNPEFAAPRYRFNEVIRFVEDGLEDLSISRTSFDWGVPLPAPVDPDAEVADRRADH
+VTYVWVDALTNYLTGAGWPGRDPEAFGRYWPADLHVIGKDISRFHCIFWPAFLMSAGIEL
+PKRVMIHGFLNNNGAKMSKSLGNVVHPRDWVARYGLDAIRFFLLREFPFGADGSYSHEAV
+VGRKNADLANNLGNLAQRSLSMVAKNCEAAVPQPGPLTAEDEAVLAQVDALLERSRTAYA
+VQDFHDALEETWRVLGEVNAYFADQAPWVLRKTDEARMRTVLYVTLQAVRRVALLVQPVM
+PASASRLLDLLGVPAEGDAGRTGASGQGPRSFAAFHEDLVPGTALPKPEGVFPRHEEPAE
+A
+>PROKKA_01988
+MTDTRAPYYVTTAIHYPNGEPHIGHAYEVVGADALARFMRLDGRDVFFLTGTDEHGQKMA
+QTAERLGVTPMELATRNSAAFKAMDDEVLGVSYDRFIRTTDEDHHRASQEIWRRMEANGD
+VYLDRYAGWYSVRDERFFDEDETEVREDGQRYAAETGTEVTWTEEESWFFRLSKYQEPLL
+ALYRDDPEFAAPRSRFNEVIRFVEGGLEDLSISRTSFDWGIDVPAPADGAASDAHHVMYV
+WVDALTNYLTGVGFPDESSESFRRFWPADVHVIGKDISRFHCVFWPAFLMSAGIELPKRV
+MIHGFLNNNGEKMSKSLGNVVAPRDWVARYGLDAVRFFLLREFPFGADGSYSHEAVVGRK
+NADLANNLGNLAQRSLSMVAKNCGGGVPEPGSLTEADTAVLAQVDALLEHSRAAYTVQDF
+HGALEETWRVLGEVNAYFADQAPWVLKKTDEPRMRTVLYVTLQAVRRVALLVQPVMPASS
+SRLLDLLGVPAEGDAGATAASNAGPRSFAAFGEDLMPGTALPRPEGVFPRHEDPAEG
+>PROKKA_00806
+MTDARAPYYLTTAISYPNGEPHIGHAYEYIASDAMARFQRLDGRDVRFLTGTDEHGQKME
+QTAQQQGVSALELATRNAAVFKEMDDDVLDISYDRFIRTTDTDHAEAVREIWRRMEANGD
+IYLGSYAGWYSVRDERYFGEDETEVGQDGVRRAVETGTEVTWTEEESYFFRLSKYQQPLL
+DHYREHPDFAAPRYRFNEVIRFVEAGLEDLSISRTSFQWGIDLPAPADPDAADADRRADH
+VTYVWVDALTNYLTGAGWPAEDPEAFARYWPADLHVIGKDISRFHCIFWPAFLMSAGLEL
+PRRVMIHGFLNNNGAKMSKSLGNVVHPREWVARYGLDAIRFFLLREFPFGADGSYSHEAV
+VSRKNADLANNLGNLAQRSLSMVAKNCGAAVPEPGEFTEADRAVLAQVDALLERSRSAYA
+VQDFHDALEETWRVLGEINAYFADQAPWVLRKTDEPRMRTVLYVTLQAVRRVALLAQPVM
+PGSASRLLDLLGVPAEGDAGRTGASGTGPRSFAAFHEDLVPGTPLPAPQPVFPRHEEPAE
+D
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000747.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000747.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa2f4f19d0b25af99419e0245fee215dee69f966
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000747.fa
@@ -0,0 +1,40 @@
+>PROKKA_00860
+MTVRDPAAAAGATVGDLTEAELLEVVLTGLAPAVRDGHWPAGTVAPGDDAALVPAPRGGT
+LISTDAMGEGTDFLHRWPAGPRTRGHDAGWKAVAQNLSDVNAMGGSASALVTALTLPPTT
+PVAWVRSFAAGIVGAVRHLGAPDCRVAGGDLGTGGRVHAAVTVLGDPHPGGVLCRTPAAA
+DRDRVLAEGADLVHAQAVPDGPRAAAPPGPGWAAAGLAVLLTDRAELERRADALPAADRP
+SPRELARAVRAQLRPRPPLALGPAAVTAGLLTLMDVSDGLGKDAHRMAAATGGAGPAPAP
+WLDEAWLAQAAAPLRRVAALAGTSPEALVTGGGEDYGLLGLAWPETELPRGFTRIGRLVP
+AGARAPAGHRPLPGSGWDPFAG
+>PROKKA_00582
+MTVRDPAAAAGATVGDLTESELLEVVLTGLAPAVRDGHWPAGTVAPGDDAALVPAPRGGT
+LISTDAMGEGTDFLPRWPAGPRTRGHDAGWKAVAQNLSDVNAMGGTASALVTALTLPPTT
+PVAWVRSFAAGIVGAVRHLGAPDCRVAGGDLGTGGRVHAAVTVLGDPHPGGVLCRTPAAA
+DRDRVLVEGADLVHAQAVPDGPRAAAPPGPGWAAAGLTLLLTDRAELERRADALPAADRP
+SPRELARAVRAQLRPRPPLALGPAAVTAGLLTLMDVSDGLGKDAHRMAAATGGAGPAPAP
+WLDEAWLAEAAAPLRRVAALAGTSPEALVTGGGEDYGLLGLAWPETELPRGFTRIGRLVP
+AGARPPAGHRPLSESGWDPFAG
+>PROKKA_02075
+MTPAGGRPADGRTVGEVTEAQLLRVVLDGLAPAVRPGHWPPGTVAPGDDAALVPAPRGGT
+LVSTDAMGEGTDFLHRWPAGVRTRGHDAGWKAVAQNLSDVNAMGGTASALVTALTLPPTT
+PLAWVRSFAAGVVGAVDRLGAPGCRVAGGDLGTGERVHAAVTVLGDPHPAGVLRRAPAPA
+ARERVLAEGADLVHAQDAPGSSGAARSGALRPSAARPGPGWAAAGLALLLTDRDELARRA
+AALPPEDRPGARDLARAVRAQLRPRPPLALGPAAVEAGILTLMDVSDGLGRDAHRMAAAT
+GAAASAEAPPPVPWIDAAWLAEAAAPLRGVAALAGVSAESLVTGGGEDYGLLGLAWPETA
+LPAGFVRIGRLEPAGAPAPAGHRELPEAGWDPFGG
+>PROKKA_01969
+MSTPASTASAGGRPAPARTVGEASEAELLDLIQDALAPVARDVPWPAGTVPPGDDCAVVP
+APRGLVAVSTDAMGEGTDFLRRWPAGVRTRGHDVGWKAAAQNLSDVNAMGATPSALVTAL
+ALPAPTPLDWVASLAGGFTAAVRALGADRCRVAGGDLGAGESVQVAVTALGDPDPAGALR
+RAAGGERGARIARRGADLVLAAGSPRAAAAGEGQDSAWGPAGPGWAAAGLALLLTDRAVL
+TRRWADLAAHERPSARELARAVRGQLRPRPPLAAGPAAARAGLAALMDVSDGLGRDGHRL
+ARASSAPGAPLVPWVDRRWLAEAAEPLRRVASLAGTTPEALVLGGAEDYGLLGLAEPGLA
+LPSGFRRVGRLAPAGETPDGHVRLPEAGWDHFDAGRG
+>PROKKA_00819
+MTMRDPAAAAGATVGDLTEAELLEVVLTGLAPAVRDGHWPAGTVAPGDDAALVPAPRGGT
+LISTDAMGEGTDFLHRWPAGPRTRGHDAGWKAVAQNLSDVNAMGGTASALVTALTLPPTT
+PVAWVRSFAAGIVGAVRHLGAPDCRVAGGDLGTGGRVHAAVTVLGDPHPGGVLRRTPAAA
+DRDRVLAEGADLVHAQAVPDGPRAAAPSGPGWAAAGLTLLLTDRAELERRADALPAADRP
+SPRELARAVRAQLRPRPPLALGPAAVTAGLLTLMDVSDGLGKDAHRMAAATGGAGPAPAP
+WLDEAWLAEAAAPLRRVAALAGTSPEALVTGGGEDYGLLGLAWPETELPRGFTRIGRLVP
+AGARPPAGHRPLSESGWDPFAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000749.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000749.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00afe4944c58fdf4f9f5466c8d08807438f78cb5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000749.fa
@@ -0,0 +1,30 @@
+>PROKKA_00862
+MTTEPVRPPTEDDLIGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVIATGIARPTL
+HRLAAALTHHRMVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV
+FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT
+PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRLHAD
+AVVSAATRLTELIRAGEA
+>PROKKA_00584
+MTTEPVRPPTEDDLIGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVIATGIARPTL
+HRLAAALTHHRMVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV
+FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT
+PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRLHAD
+AVVSAATRLTELIRAGEA
+>PROKKA_02073
+MTAEPARAQADDDVLGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVTATGIARPTL
+HRLAAALTHHRLVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV
+FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT
+PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRNHAD
+AVVAAATRLTELIRAGEA
+>PROKKA_01967
+MTTTPLPDAGADIGPALHVHPSGVGVVDKSVAILDALESGPATLAQLVTATGIARPTLHR
+LAAALTHHRLVAKDLQGRYVLGSRLAELASAAGEDRLTSAAGPVLQWLRDACGESAQVFR
+RQADSRVCVASAERPWGLRDTIPVGTRMSMKAGSAAQVLLAWEDNERLVDGLVGAVFTPT
+VLAAVRRRGWAQSLAEREPGVASVSAPVRGPNGKVIAALSISGPLERLSRQPGRLHAGSV
+VAAADRLTELIRAGEA
+>PROKKA_00821
+MTTEPVRPPTEDDLIGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVTATGIARPTL
+HRLAAALTHHRMVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV
+FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT
+PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRLHAD
+AVVSAATRLTELIRAGEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000750.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000750.fa
new file mode 100644
index 0000000000000000000000000000000000000000..782780af338f6190cc30fc80ecadf55d72b349ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000750.fa
@@ -0,0 +1,50 @@
+>PROKKA_00863
+MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR
+PVRRPDLTIATEDHNTPTLDIDQPIADATSRTQIETLRANCAEFGVRLHPLGDAEQGIVH
+VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAVT
+VDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAGAR
+AGMVAPDETTFAYLKGRPHAPEGDDWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPFVT
+WGTNPGQGVSLNDTVPAPEDFADPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSCTN
+SRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM
+CLGMNPDQLSPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT
+PQEA
+>PROKKA_00585
+MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR
+PVRRPDLTIATEDHNTPTLDIDQPIADPTSRTQIETLRANCAEFGVRLHPLGDAEQGIVH
+VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAVT
+VDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAGAR
+AGMVAPDETTFAYLKGRPHAPEGADWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPFVT
+WGTNPGQGVSLNDTVPAPEDFTDPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSCTN
+SRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM
+CLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT
+LQEA
+>PROKKA_02072
+MTSETTRPRTLAEKVWDEHVVVRGEGEGSSRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR
+PVRRPDLTIATEDHNTPTLEIDKPIADPTSRTQIETLRANAAEFGVRLHPLGDAEQGIVH
+VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAIT
+VDGTLRPGVTAKDVILAVIAKIGTGGGQGFVLEYRGEAIRSLSMEGRMTICNMSIEAGAR
+AGMVAPDETTFAYLKGRPHAPEGADWDAAVEHWRTLATDEGAEFDAEVVIDADELEPFVT
+WGTNPGQGVSLNGAVPAPEDFDDPVAQESARKALGYMDLTPGTPMKEVAVDTVFMGSCTN
+SRIEDLRAFAEVVKGRKKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM
+CLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT
+PQEA
+>PROKKA_01966
+MSTQTQTPRPRTLAEKVWDEHVVVRGEGEGARRTPDLLYIDLHLVHEVTSPQAFDGLRLA
+DRPVARPELTIATEDHNTPTLEIDRPIADETSRVQIETLRANAEEFGVRLHSLGDREQGI
+VHVVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLRLKPFRTMA
+ITVDGTLRPGVTAKDVILAVIAKIGTGGGQGYVLEYRGEAIRSLSMEGRMTLCNMSIEAG
+ARAGMVAPDDTTFEYLKGRPHAPQGADWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPF
+VTWGTNPGQGVSLNDAVPAPEDFSDPAAQEAARKALSYMDLTPGTPMKDVAVDTVFMGSC
+TNSRIEDLRAFAEVVKGRTKADGLRVMVVPGSARVRLQAMDEGLDKVFEDFGAEWRFAGC
+SMCLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPLVAAATAVLGRLASPSDLPA
+LENQEA
+>PROKKA_00822
+MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR
+PVRRPDLTIATEDHNTPTLDIDQPIADATSRTQIETLRANCAEFGVRLHPLGDAEQGIVH
+VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAVT
+VDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAGAR
+AGMVAPDETTFAYLKGRPHAPEGDDWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPFVT
+WGTNPGQGVSLNDTVPAPEDFADPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSCTN
+SRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM
+CLGMNPDQLSPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT
+PQEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000755.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000755.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1629ce77f323786c5275221c943a4b889d28f0cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000755.fa
@@ -0,0 +1,40 @@
+>PROKKA_00868
+MTATPAPEAAADARPRVLLLFGGRSSEHPISCVTAAGVLHAADRQRWDVVPVGVARSGLW
+SHDELDVASFRLDGDALPEVPEPEAPVSLRALPDGTVELTAADGSSLGPVDVVFPLLHGP
+WGEDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITARDWARD
+PEAALARAGALAYPLFVKPARAGSSFGITRVTEPAGLRAAVEEARRFDPKVVVEAGIVGR
+EIECAVLDGHGSAAPRASLPGEIVVAHDEGETQFYDFESKYQDTGTTQLSCPAELPEEEI
+ERLRALAIRAFEAVDGSGLGRCDFFFTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSY
+DDLISELLDLALERGVGLH
+>PROKKA_00590
+MTATPAPEAAADARPRVLLLFGGRSSEHPISCVTAAGVLHAADRQRWDVVPVGVARSGLW
+SHDELDVASFRLDGDALPEVPEPEAPVSLRALPDGTVELTAADGSSLGPVDVVFPLLHGP
+WGEDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITARDWARD
+PEAALARAGALAYPLFVKPARAGSSFGITRVTEPAGLRAAVEEARRFDPKVVVEAGIVGR
+EIECAVLDGHGAAAPRASLPGEIVVAHDEGETQFYDFESKYQDTGSTQLSCPAELPEEEI
+ERLRALAIRAFEAVDGSGLGRCDFFFTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSY
+DDLISELLDLALERGVGLH
+>PROKKA_02067
+MLLLFGGRSSEHPISCVTAAGVLHAADPQRWDVVPVGVARSGLWSHDELDVAAFRLDGET
+LPEVPEPEAPVSLRTLPDGTVELTAEDGSSLGRVDVVFPLLHGPWGEDGTLQGMFESLGL
+PYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITDRDWARDPEAALARAGALAFPLF
+VKPARGGSSFGITRVSDPADLRAAVEEARRFDPKVVVEAGIVGREIECAVLDGHGSDAPR
+ASLPGEIVVKHDEGDLQFYDFQAKYQDDDAAQLSCPAELPEEQTRRLRELAVRAFEAVDG
+SGLGRCDFFHTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSYDALISELLDLALERGV
+GLH
+>PROKKA_01961
+MTQPPETAPGRRPRVLLLFGGRSSEHPISCVTAAGVLHAADRERWDVVPVGVAHSGLWSH
+GEVDAAAYALGDGELPSVPEPERPVSLRARADDAVELVGADGEDLGVVDVVFPLLHGPWG
+EDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAGGLEVGPWETITDRQWRNDPE
+AALERAGALDYPLFVKPARGGSSFGITKVDAPEDLRAAVEEARRFDPKVVVEAGILGREI
+ECAVLDGHGAESPRASLPGEIVVKGAESGHQFYDFEAKYQDASAAQLSCPAELPEEAIER
+LREQAVRAFEAVDGAGLGRCDFFYTPDGRWVVNEINTMPGFTSISMYPAMWERTGLPYGE
+LISELLDLALERGVGLH
+>PROKKA_00827
+MTAIPAPEAAAGARPRVLLLFGGRSSEHPISCVTAAGVLHAADRQRWDVVPVGVARSGLW
+SHDELDVASFRLDGGALPEVPEPEAPVSLRALPDGTVELTAADGSSLGPVDVVFPLLHGP
+WGEDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITARDWARD
+PEAALARAGALAYPLFVKPARAGSSFGITRVTEPAGLRAAVEEARRFDPKVVVEAGIVGR
+EIECAVLDGHGSAAPRASLPGEIVVAHDEGETQFYDFESKYQDTGTTQLSCPAELPEEEI
+ERLRALAIRAFEAVDGSGLGRCDFFFTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSY
+DDLISELLYLALERGVGLH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000756.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000756.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e0daf4ea4818ab23f111233cf4e67125a4e28779
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000756.fa
@@ -0,0 +1,20 @@
+>PROKKA_00869
+MESRRLRRLVPLLTAIALGATACTGRVATVEAAPHAADPACAPAMVAMPDALGDLDLRPT
+DSQATAVWGDPAAVVLRCGAEVPGPTTDRCISVDGIDWVVRDEDENWRITTYGRDPAVEV
+LFGKDQASSDTVMVGLSSAVAQIEPSGGCVGVQDATPVG
+>PROKKA_00591
+MESRRLRRLVPLLTAIALGATACTGRVATVEAAPHAADPACAPAMVAMPDALGDLDLRPT
+DSQATAVWGDPAAVVLRCGAEVPGPTTDRCISVDGIDWVVRDEDENWRITTYGRDPAVEV
+LFGKDQASSDTVMVGLSSAVAQIEPSGGCVSVQDATPVG
+>PROKKA_02066
+MESRPLRPLRRLVPLLTAIALGATACSGRVATVEAAPDAANPECAPAMVAMPDALGDAAL
+RPTDSQATAVWGDPAAVVLRCGAPVPGPTTDRCISVDGVDWVIRDEDENWRIVTYGRDPA
+VEVLFGKDKASSDTVMVGLASAVAQIDADGGCVNLQDATPVG
+>PROKKA_01960
+MPRLPRPVILAPALAAAALGLTACSGPVVSVEAAPGAADPACAPAMVAVPDVLGGQDRRE
+TDSQATAAWGEPAAVVLRCGVPTPGPTTDRCVSVDDIDWVVRDEDDHWRITTYGRTPAVE
+AVFGKSEVSSDSVMTGLGSAVAQIPSQRRCVNIEDATPVG
+>PROKKA_00828
+MESRRLRRLVPLLTAIALGATACTGRVATVEAAPHAADPACAPAMVAMPDALGDLDLRPT
+DSQATAVWGDPAAVVLRCGAEVPGPTTDRCISVDGIDWVIRDEDENWRITTYGRDPAVEV
+LFGKDQASSDTVMVGLSSAVAQIESSGGCVSVQDATPVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000766.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000766.fa
new file mode 100644
index 0000000000000000000000000000000000000000..66eeb25211ed0fe37ac2d23e9944415d2ca32e07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000766.fa
@@ -0,0 +1,26 @@
+>PROKKA_00879
+MHITAGTLERALTHRSFAYEQGGLPTNERLEFLGDSVLGYVVTDHIFTVYPDLAEGDLAR
+RRAAVVSTRALAKVARRIGIGPFVRLGTGERRTGGADKDSILADTLEALIGAVYVDHGAV
+AAAALVHRHVVPLLDEPDLLRESTDWKTVVAEAASRHGLGAVRYAIEGQGPAHDPRYRAT
+LVVGEREYGSAVASSKKQAERDAAAASWPALEADLPAAGR
+>PROKKA_00601
+MHITAGTLERALTHRSFAYEQGGLPTNERLEFLGDSVLGYVVTDHIFTVYPDLAEGDLAR
+RRAAVVSTRALAKVARRIGIGPFVRLGTGERRTGGADKDSILADTLEALIGAVYVDHGAV
+AAAALVHRHVVPLLDEPDLLRESTDWKTVVAEAASRHGLGAVRYAIEGQGPAHDPRYRAT
+LVVGEREYGSAVASSKKQAERDAAAASWPALEAGLPAAGR
+>PROKKA_02056
+MHVTAETLERALTHRSYAYEQGGLPTNERLEFLGDSVLGYVVTDHIFTVHPDLAEGDLAR
+RRAAVVSTRALAKVARRIGIGPFVRLGTGEGRTGGADKDSILADTLEALIGAVHVDHGLV
+AASALVHRHVVPLLDEPDLVRESTDWKTVVAEAANRHGLGAVRYAIEGQGPAHDPRYRAT
+LVVGEREYGSAVASSKKQAERDAAAASWPALEADLPAAGR
+>PROKKA_01950
+MASPQTRTGSVPVPESSALLERLGVHITAGTLERALTHRSYAYEHGGLPTNERLEFLGDS
+VLGFVVTDHLFTAFPDLPEGDLARRRAAIVSTRALAKVARRIGVGPHVRLGTGETRTGGA
+DKDSILADTFEALIGAVYRDHGAVAAAALVHRHVVPLLDEPGLLRESTDWKTVVAEAASR
+HGLGEVRYDIEGQGPAHDPRFRATLTVGGRAFGSAVASSKKQAERDAAAEGWPELSATLP
+AAGS
+>PROKKA_00838
+MHITAGTLERALTHRSFAYEQGGLPTNERLEFLGDSVLGYVVTDHIFTVYPDLAEGDLAR
+RRAAVVSTRALAKVARRIGIGPFVRLGTGERRTGGADKDSILADTLEALIGAVYVDHGAV
+AAAALVHRHVVPLLDEPDLLRESTDWKTVVAEAASRHGLGAVRYAIEGQGPAHDPRYRAT
+LVVGEREYGSAVASSKKQAERDAAAASWPALEAGLPAAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000772.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000772.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5a7c8e00a7dd34845a52d9d69a6368232752595c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000772.fa
@@ -0,0 +1,29 @@
+>PROKKA_00896
+MSDTGDPRVPSGTAVLTVDGATLRRVGARPGLARYLASLWEYRSFILFDSRSRIAGANSV
+NALGRVWMVLNPILDGAAYFLVFGLLLGTGRGVPNFLGYLIIGVFLFRYTSSAITAGSRS
+ISTNLSIVRAFRFPRATLPIATNIRELMLFGPTLVVMLVLVLAIPPMEQITWRWLLLIPL
+LALQTLFNVGASLLLARYVARWSDLSNLIAFGTRIWLYVSAVFFSADRFADFPPMMTAMH
+LNPLFCVLDIARQSLLYASDADPMRWVVLAAWTAALLVVGTVVFWRAEETYGEER
+>PROKKA_00618
+MADTGDPRVPSGTAVLTVDGATLRRVGARPGLARYLASLWEYRSFILFDSRSRIAGANSV
+NALGRVWMVLNPILDGAAYFLVFGLLLGTGRGVPNFLGYLIIGVFLFRYTSSAITAGSRS
+ISTNLSIVRAFRFPRATLPIATNIRELMLFGPTLVVMLVLVLAIPPMEQITWRWLLLIPL
+LALQTLFNVGASLLLARYVARWSDLSNLIAFGTRIWLYVSAVFFSADRFADIPPLMTAMH
+LNPLFCVLDIARQSLLYASDADPMRWIVLAAWTAALLVVGTVVFWRAEETYGEER
+>PROKKA_02043
+MSGTGMAASGPVNTVVVDAAPLGVVGARPSLRDYVLSLFRYRSFILFDSRSRISGANAVN
+TLGRLWMVLNPILDGGAYFLVFGVLLGTGRGIPNFIAYLIIGVFFFRYSSQAITAGSKAV
+SSNLTLVRAFRFPRATLVLATNLRALLEFVPTLAVMVVLILAIPPLEVFTWRWLLLVPLL
+ILQTLFNVGLSLVLARFVAHWPDLANMIAFGMRIWLYLSAVFFSVERFDGQPIVQTAMHL
+NPLYCVLDIARQSLLYGQDAEPHRWLVLAGWAALVAVVGLVVFWRAEETYGEER
+>PROKKA_01941
+MTDRVEATSPPVELRVDESRLERVGRRPSLGDYVTRLWRLRHYVRYDAVAAVQAQNRRHR
+LGNVWLLLNPILNGATYFLVFGVLLRTSLGVENFIGYLTVGVFMFTFTTRAVTALSRSLT
+ARNNVADAFQLPRAVLPLTALAREVLAYGFTLAAMLLAVLILPPHAQVTWWWLLFPVVVA
+LQLMLVAGVGLLLARAVSRVRDLSQIVGFGIRLWMYGSAVFYSFDRFVSQPNVLAVLQLN
+PMYQVLDISRDLLLYGRSPSPVAWGILAAWSVGLLVVGVVVFWLGEERYAKDLNR
+>PROKKA_00847
+MLDAIFYWLIFGLLLRFDHGMDNFVAFVIVGVFMFQMTSAALTSGTRTIASNLSLTRAFR
+FPRMALPLADLVYDVLQRLPAIAVMFILVIAIPPHETPEWSWLVFPGVLGLHVILNFGIM
+LLLARLSTLLPDVSRMVPFVSRLLMYGSGVIFPITRFTDNHPALHAIIQLNPLYVLITMY
+RQVIIEGVTPPASSWAMLAAYAVCLTIVGGIVFWLGEESYGRDQYR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000773.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000773.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5411ae7d5eee7c8fcdb1edbe2ee76215fe7cd0cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000773.fa
@@ -0,0 +1,40 @@
+>PROKKA_00897
+MPKVMPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDLN
+IIQPRQTLNGVFARTLDGLDAVLEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEAG
+LRSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAAEDIYVTGNTVIDALLE
+AVGHQVPFEDERLAELEASGRRVVLVTTHRRENQGDAMRGVGRALARLAADHPEVTFVLP
+AHRNPVVREAILPEIEGRENVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAPSLGKPV
+LVMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLLTDEAAYTAMSQAVNPYGDGRAAER
+TVSAIAELLGVGERLPAFDGGDPA
+>PROKKA_00619
+MPKVMPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDLN
+IIQPRQTLNGVFARTLDGLDAVLEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEAG
+LRSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAPEDVYVTGNTVIDALLE
+AVSHQVPFEDERLAGLEASGRRVVLVTTHRRENQGDAMRGVGRALARLAADHPEVTFVLP
+AHRNPVVREAILPEIEGRENVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAPSLGKPV
+LVMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLLTDEAAYSAMSQAVNPYGDGRAAER
+TVSAIAELLGVGERMPEFAPDDRG
+>PROKKA_02044
+MKVMPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDLNI
+IQPRQTLNGVFARTLDGLDAILEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEAGL
+RSFDILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAPEDVYVTGNTVIDALLEA
+VGHQVPFEDERLAELEASGRRVVLVTTHRRENQGDAMRGVGRALARLAADHPEVTFVLPA
+HRNPVVREAILPEIEGRANVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAPSLGKPVL
+VMRENTERPEAVTAGTVRLIGTDEEVVVTEVTRLLTDEAAYTAMSQAVNPYGDGRAAERT
+VSAIAELLGVGERLPAFDGA
+>PROKKA_01942
+MPLKIMPIYGTRPEAIKMAPIVNALRADDRFECFTTVTGQHREMLDQVNAIFGITPDADL
+DIMRPNQTLNGIMSVMLEGLDELLVRERPDAVVVQGDTTTSTAGAIAAFYRGIPVVHAEA
+GLRSGDLFSPFPEEANRKITSQIASLHLAPTSVSRANLEREAIDSAAITVTGNTVIDALL
+ETVAQQLPFTDPRLAELAERRAADPQSRVLLVTTHRRENQGEAMRGVGRALARLAQSHPN
+LTIVLPAHRNPVVREAVLPTLEGIDSVIVTEPLPYGEFTRMMDLADVVLTDSGGVQEEAP
+SLGKPVLVMRDNTERPEAVHAGTVRLIGTDEERLVEETSLLLTDPDAYAAMAHAVNPYGD
+GRAGLRTVAAIAQLLGVGDRLDEFGA
+>PROKKA_00848
+MPIYGTRPEAIKVAPIVKALQADERFECVVTVTGQHREMLDQVNELFGIVPDHDLNIIQP
+RQTLNGVFARTLDGLDAVLEQERPDAVVVQGDTTTSTAGAVAAFNRGIPVVHAEAGLRSF
+DILSPFPEEANRKITSQISALHLPPTTVSRDNLLREAVAAEDIYVTGNTVIDALLEAVSH
+QVPFEDERLAELEASGRRVVLVTTHRRENQGDAMRGVGRALARLAADHPEVTFVLPAHRN
+PVVREAILPEIEGRENVLVTEPLAYGEFTHLLSVATVVLTDSGGVQEEAPSLGKPVLVMR
+ENTERPEAVTAGTVRLIGTDEEVVVTEVTRLVTDEAAYTAMSQAVNPYGDGRAAERTVSA
+IAELLGVGERLPAFDGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000774.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000774.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f104d2fb248c9be8bc54cd09e0a0ec5f5f64cbba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000774.fa
@@ -0,0 +1,45 @@
+>PROKKA_00900
+MPSSPPAARVPLPTEIKVMVAAAFVIAIGFGIIAPLLPQYAEMFASDFANPATAVAAVVS
+AFGLTRLLFAPVSGRLTNRLGETPVYMTGVLIVAASMFLIAFAQDYTQLLLYRALGGVGS
+TLFTVSAMAFLASKSPPTIRGRVSGAYASAFLIGNIVGPIVGSVLAVFGFRVPFLIYGTS
+LVIAAGIVFVMLRDTRLQDRARGETRPVMPLRAALGHRSYRAALTSMFANGWATFGVRNA
+ITPLFAASAFTGTALLGWGITEENRQLMAGLALSVFAAGNVLAVASSSRLSDLHGRKPLI
+LVGLAVMAVFTGAIGWLESPLLFLVSCALAGAGTGTLNAPQQAAVADLVGQDRKAGPVMS
+AAQMSGDLGAILGPLLVGLVVDAAGYGWGFVVTGAVIAVGALAWARAPETNLPVAPGGPR
+TGSLPKVDPDVDPCRMEGRELG
+>PROKKA_00620
+MAVMPSSSARSSRVPLPREIKVLVAAAFIIAIGFGIIAPLLPQYAATFDASAVGVAAVVS
+AFGLTRLLFAPVSGKLTNRLGETPVYMTGVLIVAASMFLVAFAQTFPQLLLFRALGGVGS
+TLFTVSAMAFLARKSPPTMRGRISGAYASAFLIGNIVGPIVGSALSVFGYRAPFLIYGSS
+LVVAAALVFFLLKDTRLADRAVRDVRPAMPVREALSNPSYRAALVSFFANGWATFGVRNS
+VMPLFAATAFAGTGLLGWQVDGAMMAGLALSVFALGNVVAVSFSSRLSDVHGRKPLILTG
+LLVMAVTTGAIGWVGTPSLFLIACLVSGAGTGILNAPQQAAIADVVGQDRRSGSVMSSAQ
+MSADLGAIVGPLAAGLVVDVAGYGWAFVVTGAVILLGAIAWWRAPETNLPVVPGGPRTGA
+LPKIEPEDARPPHREDG
+>PROKKA_02041
+MPSSSSRTARAPLPREIKVLVAAAFIIAIGFGIIAPLLPQYAASFNASATAVAAVVSVFG
+LTRLLFAPLSGRLTNRLGETPVYMTGVLIVAASMFLIAFAQTFAQLLAFRAIGGVGSTLF
+TVSAMAFLARKAPPSMRGRVSGAYASAFLIGNIVGPIVGSALAVFGYRAPFLIYGTSLVI
+AAALVFFMLKDTRLADRAARDARPAMPVKEALENPSYRAALVSFFANGWATFGVRNSVMP
+LFAASAFAGSGLLGWQVDGALMAGLALSVFALGNVVAVTFSSRLSDMHGRKPLILTGLLV
+MAVTTGVLGWMQSPLLFLLACLVSGAGTGVLNAPQQAAIADVVGQGRRSGAVMSSAQMSA
+DLGAIIGPLLAGLVVDAAGYGWAFVLTGGVILLGALAWWRAPETNLPIVPGGPRTGSLPL
+VRPEDARVTPREDG
+>PROKKA_01939
+MPTTPSAARAPLPREIKVLVAAAFVIAIGFGIIAPLLPQYAERFASDFANPATAVAAVVS
+AFGLTRLLFAPLSGRLTNRLGETPVYMTGVLIVAASMYLIAFAQDYTQLLVFRGLGGVGS
+TLFTVSAMAFLASKSPPSMRGRVSGAYASAFLIGNIVGPIVGSVLSVFGYRVPFLIYGTS
+LVIAAAIVFFMLKDTRLHDRAAADSRPVMRLREALDHPSYRAALVSMFANGWATFGVRNA
+VTPLFAASAFTGTALLGWTVTQENQALMAGLALSVFAAGNVAAVTFSSRLSDVRGRKPLI
+LLGLAVMAVCTGVIGWMTSPLLFLVACLLAGAGTGTLNAPQQAAVSDLVGQGRKAGPVMS
+VAQMAADLGAISGPMLVGLVVDGAGYGWAFAVTGAVLAVGFLAWLRAPETNLPIVPGGPR
+TGSLPKIAPEDVAPPHHREA
+>PROKKA_00849
+MAVMPSSSARSSRVPLPREIKVLVAAAFIIAIGFGIIAPLLPQYASSFNASATAVAAVVS
+AFGLTRLLFAPLSGRLTNRLGETPVYMTGVLIVAASMFLIAFAQTFEQLLLFRALGGVGS
+TLFTVSAMAFLAAKSPPTMRGRVSGAYASAFLIGNIVGPIVGSALAVFGFRAPFLIYGTS
+LVIAAGMVFVLLRDTRRADRGTGDPRPTMPLKEAFGLPSYRAALASFFANGWATFGVRNS
+VMPLFAATAFAGTGLLGWQVDGAFMAGLALSVFALGNVVAVTFSSRLSDVHGRKPLILTG
+LLTMAATTGVIGWMSSPALFLLACLLAGAGTGTLNAPQQAAIADVVGQGRRSGAVMSAAQ
+MSADLGAISGPLLAGLVVDTAGYGWAFVLTGGVILLGALAWWRAPETNLPIVPGGPRTGS
+LPLVRPEDARVTPREDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000776.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000776.fa
new file mode 100644
index 0000000000000000000000000000000000000000..68e4b09084752fb4dc41a4f8dbdeac63bc9a5d52
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000776.fa
@@ -0,0 +1,43 @@
+>PROKKA_00903
+MNEMTLDAGTVWMVVSAGLVLLMTPGLALFYGGMTRSKSALNMMMMSFVSMGLVGVVWIL
+WVSGMTGGEGWLGLVGSPLADPGLTTAMEEGGLIAAGFGATFAIITVALISGAVADRARF
+LTWCVFVPVWVTLVYAPLAYMVWGGGLLAEEGAIGSRLGEALDFAGGLVVHISAGVAALV
+LALMMGKRKGFGVDPGHKPHNVPFTMLGAALLWFGWFGFNGGAAGDTGQLGLIWINTLAA
+AAAGMLGWVVVEWVRRGRPTSIGTASGIVAGLVGITPACAFVSPLGALVIGVASGAASAL
+AVNLKYRLGFDDSLDVVGVHLTAGILGTVLIGFFALPSEGPAGLFYGGDGRLLLAQTVAV
+VVAVVFTAVLTFLIALVLKATLGLRVSEEDEERGVDLTLHDESAYHYDVGFGGVPVPADA
+QAHRGGAAG
+>PROKKA_00622
+MEESNVLDAGTVWMVTSAAMVLLMTPGLAIFYGGMTRAKSSLNMIMMSFVSMGLVGVVWV
+LWVHGMTGGDGWAGVVGNPAGDLGLTGTMAEGGLVAAAYGATFAIIAVALISGAVADRFK
+FVTWCVFVPVWTTVVYAPLAYMVWGGGLLSEDGAIGARLGEALDFAGGLVVHISAGVAAL
+VLALLLGKRHGFGVDPGHRPHNVPFTMLGAALLWFGWFGFNGGAAGGVDELGLIWVDTLA
+AGAAGMLGWVFVEWLRRGRPTSIGTASGIVSGLVAITPACAYVSPLGAVVIGLVSGAASA
+LAVNLKYRLGFDDSLDVVGVHLTSGILGTVLIGFFALPGEGRAGLFYGGDAGLLVAQTVA
+VLVAVVFTAVVTTAIALVLRGTMGLRVSKEDEERGVDLTLHDESAYDVGFGGVPVPAEAR
+>PROKKA_02039
+MNEMTLDAGTVWMVVSAGLVLLMTPGLALFYGGMTRSKSALNMMMMSFVSMGLVGVVWIL
+WVSGMTGGEGWLGLVGSPLADPGLTTAMEEGGLIAAGFGATFAIITVALISGAVADRARF
+LTWCVFVPVWVTLVYAPLAYMVWGGGLLAEEGAIGSRLGEALDFAGGLVVHISAGVAALV
+LALMMGKRKGFGVDPGHKPHNVPFTMLGAALLWFGWFGFNGGAAGDTGQLGLIWINTLAA
+AAAGMLGWVVVEWVRRGRPTSIGTASGIVAGLVGITPACAFVSPLGALVIGVASGAASAL
+AVNLKYRLGFDDSLDVVGVHLTAGILGTVLIGFFALPSEGPAGLFYGGDGRLLLAQTVAV
+VVAVVFTAVLTFLIALVLKATLGLRVSEEDEERGVDLTLHDESAYHYDVGFGGVPVPADA
+QAHRGGAAG
+>PROKKA_01937
+MTETTPLDAGAVWTVTAAALVLLMTPGLALFYGGMTRAKSALNMMMMSFVSMGLIGVAWI
+LWAYGMTSGDGLAGIVGSPLNDLGAVQSMADGDLISVGFSATFAIIAVALISGAVADRAK
+FSTWCVFVPVWVTLVYAPLAYMVWGGGLLSADGAIGARLGEALDFAGGLVVHISAGVAAL
+VLAMMMGKRQGFGVDAAHRPHNVPFTMLGAALLWFGWFGFNSGAASDVEQLGLTWVTTLV
+AAAAGMLGWVLVEWLRRGRPTSIGTASGIVSGLVAITPACAFVSPLGAVVIGLVAGAACA
+LAVNLKYRWGFDDSLDVVGVHLTAGILGTLLIGLFALPETGHAGLFHGGDGSLLLAQTVA
+VVVAVVFTAVVTAVIAFVLRATLGLRVSVEEEERGVDLTLHDETAYDVGFGGVPVPTDAQ
+ARSTAAAE
+>PROKKA_00851
+MEESNVLDAGTVWMVTSAAMVLLMTPGLAIFYGGMTRAKSSLNMIMMSFVSMGLVGVVWV
+LWVHGMTGGDGWAGVVGNPAGDLGLTGTMAEGGLVAAAYGATFAIIAVALISGAVADRFK
+FVTWCVFVPVWTTVVYAPLAYMVWGGGLLSADGAIGARLGEALDFAGGLVVHISAGVAAL
+VLALLLGKRHGFGVDPGHRPHNVPFTMLGAALLWFGWFGFNGGAAGSVDELGLIWVATLA
+AGAAGMLGWVFVEWLRRGRPTSIGTASGIVSGLVAITPACAYVSPLGAVVIGLVSGAASA
+LAVNLKYRLGFDDSLDVVGVHLTAGILGTVLIGFFALPDEGRAGLFYGGDAGLLVAQTVA
+VLVAVVFTAVVTTAIALVLRGTMGLRVSKEDEERGVDLTLHDESAYDVGFGGVPVPAEAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000778.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000778.fa
new file mode 100644
index 0000000000000000000000000000000000000000..112c8007d73014708b1a2b4340c308592d4514f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000778.fa
@@ -0,0 +1,20 @@
+>PROKKA_00905
+MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL
+SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE
+APAESEQAAEAPAAEAPAEDAEKSE
+>PROKKA_00624
+MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL
+SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE
+APAESEQAAEAPAEEAAEAPAEDAEKSE
+>PROKKA_02037
+MAVKIRLKRFGKIRAPYYRIVVADSRTRRDGRAIEEIGKYHPTEEPSYIEVDSERAQYWL
+SVGAQPTEQVAALLKITGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKAEE
+PKAKESAEAETPAEEAPEAPAEDAEKSE
+>PROKKA_01935
+MAVKIRLKRFGKIRAPYYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL
+SVGAQPTEQVAALLKITGDWQKFKGEAGAEGTLKTKGEKEAFVAPAKESVILPEEPKQEE
+APAESAEAEAPVEEAADAEAPAEDAEKAE
+>PROKKA_00853
+MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL
+SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE
+APAESEQAAEAPAEEAAEAPAEDAEKSE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000780.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000780.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3853aae3642355b18619b149c6ae7adbd72b8d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000780.fa
@@ -0,0 +1,25 @@
+>PROKKA_00907
+MSPAAQDDLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGERLVVRDGAPGLPAELTVT
+RARWNKQILVVGFEESPDRNVAETLRGAQLFAVPAAPEESDEWYEEDLVDLEVRVDGERV
+GVVTALTTGAVQDLLHVALDGVEEEALVPFVEEIVPEIDPEAGVLVLTPPPGLLELATGE
+DEGAADGPTDADAED
+>PROKKA_00626
+MSPAAQDDLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGERLVVRDGAPGLPAELTVT
+RARWNKQILVVGFAESPDRNVAETLRGAQLFAVPAVPEESDEWYEEDLVDLEVRVEGERV
+GVVTALTTGAVQDLLHVALDGVEEEALVPFVEEIVPEIDSEAGVLVLTPPPGLLELATGE
+DEGAVDGPADADAED
+>PROKKA_02035
+MSPAPQDGLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGATLTVRDGGPSLPAELTVT
+RARWNKQILVVGFEQSPDRNTAETLRGAQLFAAPAAPEESDEWYEDDLVDLEVRVDGRRV
+GVVTALTTGAVQDLLHVALDGVDEEALVPFVEEIVPEIDPEAGVLVLTPPPGLLELASGE
+AEQDDDAAASDAEADADAGREG
+>PROKKA_01933
+MSPAPQPAETEGQVRVARIGKPHGIRGEVTVQLFTDDPEARFAADSRLEVRQGPPGAPAA
+LTVTRARWNKAILVVGFAEVPDRNAAEALRGAQLYAAPLEKVEDDAWYEDDLLDLEVHVD
+GARVGVVTGLLTGTVQDLLQVRLDATGDDALVPFVEEIVPEVDQEAGVVVVAPPPGLLEL
+ASETTAGEG
+>PROKKA_00855
+MSPAAQDDLVRVARIGKPHGIRGEVTVQVFTDDPDARFAPGERLVVRDGAPGLPAELTVT
+RARWNKQILVVGFAESPDRNVAETLRGAQLFAVPAAPEESDEWYEEDLVDLEVRVEGERV
+GVVTALTTGAVQDLLHVALDGVEEEALVPFVEEIVPEIDSEAGVLVLTPPPGLLELATGE
+DEDAADGPADADAED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000782.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000782.fa
new file mode 100644
index 0000000000000000000000000000000000000000..74e09e00f1121797baf331373b3608cbbbab9f7b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000782.fa
@@ -0,0 +1,15 @@
+>PROKKA_00909
+MHILDSFDKKTLRDDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGHGVRETFRV
+RKVSFGIGVERVFPVHSPVIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRVDAK
+>PROKKA_00628
+MHILDSFDKKTLRDDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGYGVRETFRV
+RKVSFGIGVERVFPVHSPVIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRADAK
+>PROKKA_02033
+MHILDSLDSNSLRSDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRNGYGVRETFRV
+RKVSFGVGVERVFPVHSPVIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRVDAK
+>PROKKA_01931
+MHILDSFDKASLREDIPAFGPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGHGVRETFRV
+RKVSFGVGVERVFPVHSPVIDKIEVLTKGDVRRAKLYYMRDRHGKAARIREKRADAK
+>PROKKA_00857
+MHILDSFDKKTLRDDIPEFAPGDTVKVHVNIIEGKTARVQVFQGYVMGRQGYGVRETFRV
+RKVSFGIGVERVFPVHSPIIDKIEVVTKGDVRRAKLYYMRDRHGKAARIREKRVDAK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000787.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000787.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9a5d2868fa974a97dd59eb6a3904cf6fd4b3d449
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000787.fa
@@ -0,0 +1,20 @@
+>PROKKA_00914
+MTGTAEQVGAQPPGERRASRAHTALGRFGEDAAARWLAERGYVIADRNWRGEAGELDIVA
+HHAGWWVGVEVKTRSGLAFGDPFESIDRRKLTRLHRLTAAWVRAHAADRRGTPWRVDAVA
+VLVPRTGGIRFDLLQDVRP
+>PROKKA_00633
+MTGTAERIGAQPPGDRRASRAHTALGRFGEDAAARWLAERGYVIADRNWRGEAGELDIVA
+HHAGWWVGVEVKTRSGLAFGDPFESIDRRKLTRLHRLTAAWVRAHAADRRGTPWRVDAVA
+VLVPRTGGIRFDLLQDVRP
+>PROKKA_02028
+MTGTAEKVGADSPGGGRGSRAHTALGRFGEDAAARWLADRGYVIADRNWRGEAGELDLVA
+HHAGWWVGVEVKTRSGLAFGDPLESIDRRKLLRLHRLTAAWVRAHGEGRRAERWRVDAVA
+VLVPRTGGIRFDLLQDVRP
+>PROKKA_01926
+MVPLDTTTTTPAARRGSTAHTALGRYGEDAAARWLAERGYQIVARNWRGEDGELDLVARH
+GPWWVGVEVKTRSGLAYGDPLEAIGRRKLLRLHRLTAAWVREAAAREGRPLRSQQWRVDA
+VAVLVPRTGGVHFDLVQDVRP
+>PROKKA_00862
+MTGTAEQVGAQPPGERRASRAHTALGRFGEDAAARWLAERGYVIADRNWRGEAGELDIVA
+HHAGWWVGVEVKTRSGLAFGDPFESIDRRKLTRLHRLTAAWVRAHAADRRGTPWRVDAVA
+VLVPRTGGIRFDLLQDVRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000790.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000790.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec4fa5567a5cd2780518b7137b84250966095933
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000790.fa
@@ -0,0 +1,35 @@
+>PROKKA_00917
+MAPSSSVRPAPAPRAPSPRDTAWLEAFEEHLRHERNRSPQTVRAYLADLHSLIDYVAGTA
+ATAGTPPVDDDAPARHGPSAPDVLPELDIEDLRGWLAAMSGSGLARATLARRVAAVRTFT
+AWLRREGLRSDDPALRLRSPRPEGTLPHVLQEQQATRLLAAAQERVDAAAAGDDPAAHAL
+ALRDAALLELLYATGARVAELSALDVDDLEAGRGVVRLTGKGDRQRTVPYGAPAGRALQA
+WERLGRPRLARPDSGPALFLGARGGRLGVRQARTVVDRALEGLGDTAARGPHALRHTAAT
+HLLDGGADLRSVQELLGHASLRTTQVYTHVSIDRLREGYRQAHPRA
+>PROKKA_00636
+MAPSSSARPAPAPRAPSPRDTAWLEAFEEHLRHERNRSPQTVRAYLADLRALIDHVAGTA
+GTSGSPAADDDAPARHVPSAPDVLAELDIEDLRGWLAAMSGAGLARATLARRVAAVRTFT
+AWLRREGLRSDDPALRLRSPRPEGTLPHVLQEQQATRLLAAAQDRVDAAAAGDDPAAHAL
+ALRDAALLELLYATGARVAELSALDVDDLEAGRGVVRLTGKGDRQRTVPYGAPAGRALQA
+WQRLGRPRLARPDSGPALFLGARGGRLGVRQARTVVDRALEGLGDTAARGPHALRHTAAT
+HLLDGGADLRSVQELLGHASLRTTQVYTHVSIDRLREGYRQAHPRA
+>PROKKA_02024
+MASSSSSARPAAARAFAPSPRDAAWLEAFEEHLRHERNRSPQTVRAYATDLRDLVAHVAS
+GTWGGHPGTATSEAAVEADAVAPDVFAEVDVEDLRGWLAAMTDAGLARTTLARRVAAVRT
+FTGWLRREGLREDDPALRLRSPRPAATLPHVLQEQQAERLLAGAQARVAEAAVGDDPAAH
+ALALRDAALLELLYATGARVAELSALDVDDLEPGRAVARLTGKGDRQRTVPYGAPAARAL
+DAWLRLGRPRLARDGSGPAVFLGVRGGRLGVRQVRAVVDRALEGLGDTAARGPHALRHTA
+ATHLLDGGADLRSVQEVLGHSSLRTTQVYTHVSIDRLREGYRQAHPRA
+>PROKKA_01923
+MHPPHAHHAPGAPLPPASARDEAWLEAFAEHLLHERGRRPRTVRAYLADLRHLAAHVTDD
+GADAFAEVDLEDLRRWLARMRDQGLSRATVARRVAAARTFLGWLHRSGLRPDDPTLRLRA
+PAPDSRLPQVLQAEQAQRLLQAAEERVHEARRADDLHGAALAARDVALFELLYATGARVA
+EVAALDVDDLDLDRRTARLTGKGDRQRTVPFGAPAAAAVERWLRVARPVLATEHSGVALL
+LGARGGRADVRVLRGAVDRALERLGDTAARGPHALRHTAATHLLDGGADLRSVQELLGHS
+SLQTTQRYTHVSVDRLRDGYRRAHPRA
+>PROKKA_00865
+MTPSSSARPAPVPRDPSPRDTAWLEAFEEHLRHERNRSPQTVRAYLADLHSLIDHVAGTA
+GTSDTPAVDDDAPARHASSAPDVLAELDIEDLRGWLADMSGSGLARATLARRVAAVRTFT
+AWLRREGLRSDDPALRLRSPRPEGTLPHVLQEQQATRLLAAAQERVDAAAAGDDPAAHAL
+ALRDAALLELLYATGARVAELSALDVDDLEAGRGVVRLTGKGDRQRTVPYGAPAGRALQA
+WQRLGRPRLARPDSGPALFLGARGGRLGVRQARTVVDRALEGLGDTAARGPHALRHTAAT
+HLLDGGADLRSVQELLGHASLRTTQVYTHVSIDRLREGYRQAHPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000795.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000795.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f4501bfb418e14f1d7573284354fc5546cbab270
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000795.fa
@@ -0,0 +1,35 @@
+>PROKKA_00922
+MLAIVCPGQGSQTPGFLAPWLELDGTRDLLASLSDAAGVDLIRHGTESDEETIKDTAVAQ
+PLIVAAGLVAAAALEADAAAPKSTVVAGHSVGEVTAAAVTGVLSPAEALSLVRVRATGMA
+RAAAATPTGMAAVVGGDQDEVLAAIDAAGLAPANVNGAGQIVAAGTAEALGALAESAPAR
+ARVIPLKVAGAFHTEHMRPAVDDLATHVAGLSPSDPRLPLLSNRDGETVESGTDVLARIV
+DQVTRPVRWDLCMATMAARQVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA
+FLAEHSA
+>PROKKA_00641
+MLAIVCPGQGSQTPGFLAPWLELDGTRDLLASLSDAAGVDLIRHGTESDEETIKDTAVAQ
+PLIVAAGLVAAAALEADAAAPKSTVVAGHSVGEVTAAAVTGVLSPAEALSLVRVRATGMA
+RAAAATPTGMAAVVGGDQDEVLAAIDAAGLTPANVNGAGQIVAAGTAEALGALAESAPAR
+ARVIPLKVAGAFHTEHMRPAVDDLAAHVAGLSPSDPRLPLLSNRDGEAVESGTDVLARIV
+DQVTRPVRWDLCMATMATRQVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA
+FLAEHSA
+>PROKKA_02019
+MLAIVCPGQGSQTPGFLSPWLELDGTRALLESLSDAAGVDLVRHGTESDEETIKDTAVAQ
+PLIVAAGLVAAAALEADAAAPASTLVAGHSVGEITAAAVTGVLSPADALALVRVRATGMA
+RAAAATPTGMAAVVGGDQDEVLAAIEAADLAPANVNGAGQIVAAGTAEALAALGESAPAR
+ARVIPLKVAGAFHTEHMRPAVEELAAHVAGLSPADPRLTLLSNRDGQAVDAGAEVLSRIV
+DQVTRPVRWDLCMEAMAEREVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA
+FLAEHTA
+>PROKKA_01918
+MLAIVCPGQGSQTPGFLAPWRELEGVPSLLDRLSAAAGVDLTAHGTVSDEETIKDTAVAQ
+PLIVAAGLVAADVLGLDALAPDRVLAAGHSVGEITAAAVAGVLSPEDALALVRVRATGMA
+EAAAATPTGMAAVVGGDQDEVLAAVEAAGLTPANVNGGGQIVAAGTQDALDALAAQPPAR
+ARVIPLKVAGAFHTEHMRPAVDALAAHVTGLSPADPRLTLLSNREGAAVASGTEVLERIV
+NQVTRPVRWDLCMEAMAERGVTGIMEVLPGGTLAGLAKRGLKGVPSLAVKAPDDLDAARA
+FIAEHTA
+>PROKKA_00870
+MLAIVCPGQGSQTPGFLAPWLELDGTRDLLASLSDAAGVDLIRHGTESDEETIKDTAVAQ
+PLIVAAGLVAAAALEADAAAPKSTVVAGHSVGEVTAAAVTGVLSPAEALSLVRVRATGMA
+RAAAATPTGMAAVVGGDQDEVLAAIDAAGLAPANVNGAGQIVAAGTAEALGALAESAPAR
+ARVIPLKVAGAFHTEHMRPAVDDLAAHVAGLSPSDPRLPLLSNRDGEAVESGTDVLARIV
+DQVTRPVRWDLCMATMATRQVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA
+FLAEHSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000801.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000801.fa
new file mode 100644
index 0000000000000000000000000000000000000000..95b702e900b9a272709eca69c1145a1cc80c0006
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000801.fa
@@ -0,0 +1,15 @@
+>PROKKA_00929
+MTGAAYLVAAAVVAGLVTFCLRAVPFALLQPLRESVLAARLAVWMPAGVLTILALVMLLD
+AAALAPGEPVDGTRVAHALFAAAVTVVVHLLAGRRTLVSIAAGTLAYVLLVNLA
+>PROKKA_00648
+MTGAAYLVAAAVVAGLVTFCLRALPFALLQPLRESVLAARLAVWMPAGVLTILALVMLLD
+AAALAPGEPVDGTRVAHALIAAAVTVVVHLLAGRRTLVSIAAGTLAYVLLVNLA
+>PROKKA_02011
+MTDAAYLVAVAVVAGAVTFALRALPFALLRPLRESVLAARLAVWMPAGVLTILAVVMLLD
+AAALAPGAPVDPRRVAHALIAAVVTVAVHLLGGRRTLLSIAAGTLAYVLLVNLA
+>PROKKA_01910
+MIDGVVHPGYIVAAALVAGGVTFLLRALPFVLLRPLRESRLVARLAVWMPAGILTILAVV
+MVLDSAALAPGDPVDWPRVGCTLAAGAVTVLVHLLGGRRTLLSIGAGTLAYVLLVNLAL
+>PROKKA_00877
+MTGAAYLVAAAVVAGLVTFCLRALPFALLQPLRESVLAARLAVWMPAGVLTILALVMLLD
+AAALAPGEPVDGARVAHALIAAAVTVVVHLLAGRRTLVSIAAGTLAYVLLVNLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000802.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000802.fa
new file mode 100644
index 0000000000000000000000000000000000000000..131789e932e2d2c8a8e76fd5e4edfd7d75d4f901
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000802.fa
@@ -0,0 +1,25 @@
+>PROKKA_00930
+MGLLRDLLTRRSARDRSSDPPATLGRHLDNAAAIVAAARRADVPLAVAAALAELESGGRN
+VFGHDAGGVHSAPRGTDVLVTRERYEELVARVAQGETSNGVGPAQITWPPYFAQAAERGL
+HLWEPEDNLAFGLEILRGHLRGDLSAEGIARAGTLYNAGTLSDGVTAYGRRLAAASRAWA
+ERLGEPAPPPVRPG
+>PROKKA_00649
+MGLLRDLLTRRSARDRSSDPTATLGRHLDNAAAIVAAARRADVPLAVAAALAELESGGRN
+VFGHDAGGVHSAPRGTDVLVTRERYEELVARVAQGEKSNGVGPAQITWPPYFAQAAERGL
+HLWEPEDNLAFGLEILRGHLRGDLSAEGIARAGTLYNAGTLSDGVTAYGRRLAAATRAWA
+ERLGESAPPPVRPG
+>PROKKA_02010
+MATTPSVGRMSWFPRRRAASAPRALAARLENADAIAAAARRADVPLPVAAALAQLESGGR
+NVFGHDAGGVHAAPRGTDVPVTRELFEELEARVAAGETSNGVGPAQITWPPYFAQARRRG
+LRLWEPEDNMAFGLEILRGHLGGDLTEEGIARAGTLYNAGTLQGGVTDYGRRLARASRDW
+ARRLGEPAPPSSSPGRGAGRDGDRGRARSGAPGRTHVIEPGDTLWAIARANGTDVATLRR
+LNPDLVPEALAVGAPVRLP
+>PROKKA_01908
+MDPVTVLSASLAHPEAIVAAAGRARVPVSVAAALAELESGGRNVFGNDVGGVFSSPGAPD
+VEVTPERVAELRRRVADGERSNGVGPAQITWPPLFDRADAEGLDLADPEDNMTLGLSLLR
+DSARGDFSVAGLERAGTLYNAGTLAGGVTDYGRRLAAAAAAWERRLTARG
+>PROKKA_00878
+MGLLRDLLTRRSARDRPSDPTATLGRHLDNAATIVAAARRADVPLPVAAALAELESGGRN
+VFGHDAGGVHSAPRGTDVPVTRERYEELVARVAQGETSNGVGPAQITWPPYFAQAAERGF
+RLWEPEDNLAFGLEILRGHLRGDLSAEGIARAGTLYNAGTLTHGVTAYGRRLAAATRVWA
+ERLGELAPPPVRPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000803.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000803.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37957d82c5fb02e2172de4e5973b3a0134543b93
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000803.fa
@@ -0,0 +1,20 @@
+>PROKKA_00931
+MSATPLGFWKLPARPDGAARHLAVITGGEAQQTMLFLQDGQWSILALFQDELAGKAAART
+LDALLQSVTCLRMGGRDVLDGADTPRPGIEWAGYDREFEEADVAEQRDVEPRGRIWILPA
+TDGASVGLKLPGHRRYDDAVAQFADVDAARAAVAAIDELLGVGPRG
+>PROKKA_00650
+MSATPLGFWKLPARPDGAARHLAVITGGEAQQTMLFLQDGQWSILALFQDELAGKAAART
+LDALLQSVTCLRMGGRDVLDGADTPRPGIEWAGYDREFEEADVAEQRDVEPRGRIWILPA
+TDGASVGLKLPGHRRYDDAVAQFADVDAARAAVAAIDELLGVGPRG
+>PROKKA_02009
+MLFLQDGQWSILGLFQDELAGKATARTLDALLQSVTCLRMGGRDVLDGADTPRPGVEWAG
+YDREFEEADVAESRDVEPHGRIWILPATDGATVGLKLPGHRRYHDAVAQFADVDAARAAV
+AAIDELLGVGPRG
+>PROKKA_01907
+MPATPHGFWKLPAPSDAGPRHLAVITGGEAEQTMLFLQDAAGWHVLALFQDELAGRTTAR
+TLDRLLQSVTYLRMGGADLMDGADTERPGVEWAGYDREFEEQDAADETAADPAARLWILP
+ATDGASVGLKLPGHPRYADAVAQFVDAGTARAAVDAVDALIGARRPGAARPAAD
+>PROKKA_00880
+MSATPLGFWKLPARPDGAARHLAVITGGEAQQTMLFLQDGQWSILALFQDELAGKAAART
+LDALLQSVTCLRMGGRDVLDGADTPRPGIEWAGYDREFEEADVAEQRDVEPRGRIWILPA
+TDGASVGLKLPGHRRYDDAVAQFADVDAARAAVAAIDELLGVGPRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000812.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000812.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5b7dddc2f5c3afce833762518c03c9aef0c17cdf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000812.fa
@@ -0,0 +1,30 @@
+>PROKKA_00940
+MLILLPPSEGKTAPRSGAPLDLDALALADDAAVTGARADLLTRLAAVSAAPDALAALGVG
+ASLTGEVEANTRLASAPAAPGHRVFTGVLFDALDHASLSAAAKRRARASVLVFSALFGAT
+ALADRIPAFRLPVGAKLPGLPGLAAHWRPVLTPALDALAARDGGPVVDCRSGGYAAQWRA
+PAERTLAVDVFQLRDGERTVVSHFAKHTRGLVARALLEAGARETSTLERVADVVARAGDG
+HGWEVELARPSGAKPGALRVILPEG
+>PROKKA_00659
+MLILLPPSEGKTAPRSGAPLDLDSLALADDAAVTGARADLLTRLAAVSAAPDALTTLGVG
+ASLAGEVEANTRLAVAPAAPGHRVFTGVLFDALDHASLSAAAKRRARLSVLVFSALFGAT
+ALADRIPAFRLPVGAKLPGLPGLAAHWRPVLTPALDALAARDGGPVVDCRSGGYAAQWRA
+PAEQTLAVDVFQLRDGERTVVSHFAKHTRGLVARALLEAGARETSTLDRVADVVARAGDG
+PGWEVELARPSGGKPGALRVILPEG
+>PROKKA_01999
+MLILLPPSEGKTAPRSGAPLRLEDLALAEHDAVTAARRDLLARLAEASAAPDALETLGVG
+ASLAGEVAANTSLATAPAAPGHRVFTGVLFDALDHASLSPGAKRRARDAVLVFSALFGAT
+SLADRIPAHRLSVGARLPGLPGLAAHWRPVLAPALDAVAQADGGPIVDCRSGGYAAMWKA
+PAERTATVDVFQLRGGEPTVVSHFAKHTRGLVARALLEAGARATGALDRAAEVVAAAGAG
+DVEGRRWDVELVAPSGAKPGSLRVVLPEA
+>PROKKA_01896
+MLILLPPSEGKTGPRSGRPLDLSSLTLADDDAVTAARAELLPRLAEASARPDALDILGVG
+ASLADEVAANTRLATAPSAPARKVYTGVLFEALDLTSLSPAAKRRAASDVLVFSALFGAT
+TPGDRIPAYRLPVGARLPGMPGLAAWWRPRLAPALDGYAEARGGVVVDCRSGGYAAQWKA
+PAERSLAVDVFQLRAGRRTVVSHFAKHTRGLVARALLEAGSRAAGTPATAADVVARAGDG
+GVPGQRWEVELVPPTGRKAGSLQVILPEE
+>PROKKA_00889
+MLILLPPSEGKTAPRSGAPLDLESLALADDAAVTGARADLLTRLAAVSAAPDALTALGVG
+ASLAGEVEANTCLASAPAAPGHRVFTGVLFDALDHVSLSSAAKRRARASVLVFSALFGAT
+ALADRIPAFRLSVGAKLPGLPGLAAHWRPVLTPALDALAARDGGPVVDCRSGGYAAQWRA
+PAERTLAVDVFQLRDGERTVVSHFAKHTRGLVARALLEAGARETSTLERVADVVARAGDG
+HGWEVELARPSGAKPGALRVILPEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000817.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000817.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98aeacaf85e91cf32fd2bf88a89fab9741e48d54
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000817.fa
@@ -0,0 +1,25 @@
+>PROKKA_00956
+MSETSTPTPESAPLVWIDCEMTGLHPQVDELVEVAVLITDAELNILDEGIDLVIRPSAAA
+LEQMDPFVRDMHTTSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNTVGQDKLF
+LARYMPAVVDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIKDSITELRYY
+RAAVMAPAPGPTTEEARAIAEVVSGAQA
+>PROKKA_00669
+MSETSTPAPESAPLVWIDCEMTGLHPQVDELVEVAVLITDAELNTLDEGIDLVIRPSAAA
+LEQMDPFVRDMHTTSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNTVGQDKLF
+LARYMPAVVDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIKDSITELRYY
+RAAVMAPAPGPTTEEARAIAEVVSGAQA
+>PROKKA_01931
+MSETSTPAPENAPLVWIDCEMTGLHPHVDELVEVAVLITDAELNILDEGIDLVIRPSEAA
+LAQMDPFVRDMHTTSGLLPELEHGLTLENATARVMEYLTARVPAGKALLAGNTVGQDKLF
+LSAYMPAVVEHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIRDSITELRYY
+RAAVMAPSPGPTSEEAQAIARVVAEAQA
+>PROKKA_01883
+MSETSTPAPESAPLVWIDCEMTGLDPDVDVLVEVAVLITDSELNVLDEGLDLVIRPTPEA
+LAQMDPFVRDMHTSSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNSVGQDKLF
+LARYMPAVIDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIRDSITELRYY
+REAVMVPAPGPTSEEARAIAEVVSGAQA
+>PROKKA_00902
+MSETSTPTPESAPLVWIDCEMTGLHPQVDELVEVAVLITDAELNILDEGIDLVIRPSEAA
+LEQMDPFVRDMHTTSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNTVGQDKLF
+LARYMPAVVDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIKDSITELRYY
+RAAVMAPAPGPTTEEARAIAQVVSGAQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000819.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000819.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1e658d355dc7a097cf86106d0b454865a32f5856
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000819.fa
@@ -0,0 +1,55 @@
+>PROKKA_00959
+MTSHPRSPAPSRPSGRWVGLLVGLTVVAAAVGVLTKQWCRVNGWAAPGVHAHMCYSDFAQ
+LFPTRGLSDGHFPFYTPLPPEQWMEYPALLAVVAGVTMWLVPASGDLHERTVTYFDVNAI
+GVVLCWIVLVVATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAGR
+PTLAGLLIGLGTATKLYPLFFFGAIFVLALRTGRWAGFVKAALAGAAAWLAVNLPFMLTA
+FDQWSRFYTFSGDRAVSFSSTWLALAWTGWSGETFTTLQNGLFLVCCVGIAYLALAARHR
+PRMAQLCFLIVASFILWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGVWME
+SARITSDGAFAGGAWWITAWYASGIVAHIVALVWLMTTVVKDILDPVRDPVRRTALDQGA
+PEIAPGVAEDPHAGVFTGARDRLLLPPAGLGLQPLGESAGR
+>PROKKA_00672
+MTSHPRSPAPSRPSGRWVGLLVGLTVVAAAVGVLTKQWCRVNGWAAPGVHAHMCYSDFAQ
+LFPTRGLSDGHFPFYTPLPPEQWMEYPALLAVVAGVTMWLVPASGDLHERTVTYFDVNAI
+GVVLCWIVLVVATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAGR
+PTLAGLLIGLGTATKLYPLFFFGAIFVLALRTGRWAGFVKAALAGAAAWLAVNLPFMLTA
+FDQWSRFYTFSGDRAVSFSSTWLALAWTGWSGETFTTLQNGLFLVCCVGIAYLALAARHR
+PRMAQLCFLIVASFILWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGVWME
+SARITSDGAFAGGAWWITAWYASGIVAHIVALVWLMTTVVKDILDPVRDPVRRTALDQGA
+PEIAPGVAEDPHAGVFTGAPDRLLLPPAGRGLQPLGGSADR
+>PROKKA_01929
+MRRAGLAPTPAPPGLPERETAPPEPAVAVRQGTWAAVLIMVGSWGVGWLPMTPDSVFSGS
+TLLNPLRVNLPGVLASTLLLASGSLLLVRAWLVLGRSLRGRWEGHGRLVSRAAWQWSAPL
+MLALPIFSRDVFSYLQQGRLFALGLDPYTQGVSALPGWFMQGADSIWAESPSPYGPLFLL
+CAEAIWRVTGGQIELSVTAFRLLALAGLALCLWAVPRLAEAAGRCGAWAAWVCVANPLFL
+LYMIAGVHNDALMSGLMLAGIVLMVRVPRRRLHALWGIVLIALSVAIKPLTALVLPFVGL
+LLPTGWDRFRRADPGLRRRDRLGPWITTAAIALAVLTILGAGSRLWFGWVPAMLTSGDAA
+FPYAPVGVLGLLLGAAADGLAGLPARAVAGGFYTLMTLAALGFGAWLALRRRAPEPVSAA
+AAVLFVAVVTAPIVQPWYLLWVLPLLACALRPLPWGADHPRWLGWVTALAVLLLTGVGVV
+DQISVAQWLPVAAVRALTAVVVLAGIAWIVVRDPATAPLFPGRRRPPREVVEPREAVGPR
+EPGAPPGPPTAAPDAEFPPDALAADPDRRRRPAPDRRPARPGETVTSQPRRPADTRTGSA
+AAPPSPAALRPGPRWIGILVGLTAVAAVVGLLTKQWCRVNGWAAPGVHVHMCYSDFAQLF
+PTRGLSDGYFPFYTPLPPEQWMEYPALLAVVAGVTMWLVPDSGDLHERTVMYFDVNALGV
+VLCWVVLVIATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAHRPT
+LAGLLIGLGTALKLYPLFFFGAILVLALRTGRWRGLITSLAAGVAAWLAVNVPFMLTAFD
+QWSRFYTFSGDRAVSFSSTWLSLAWTGWSGETFSTLQNGMFALFCAGIAWLGLSARHRPR
+MAQLCFLIVASFLLWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGVWMESA
+RITSGGAFADGAWWITAWYASGIVAHIVALVWLMVTVVKDILDPSRDPVRRTALAQGAPT
+IAPGVAEDPHAGVYAGAPDRLVLPPAGRGLQPAEGATSGS
+>PROKKA_01880
+MSSHPRAADAAPRPAAGLRPAGRPSPRWIGVLIAVTAAAAVVGLLTKQWCRLNGWATPGV
+HVHMCYSDFAQLFPTRGLSDGYFPFYTPLPEEQWMEYPALLAVVAGASSWLVPSTGTLAE
+RTVTYFDVNAAGVVLCWMAVVVATAFTARGRSKDALLVAVAPGIILTSMLNWDLWAVMLA
+ALALWAWSEDRPVLSGLLLGLGAAMKLYPLFFFGALLVLALRTGRWRGFLGALAAGAAAW
+LAVNVPFMLTAFDQWSRFYTFSGDREVSFSSMWLAFTWTGLSGSAFSVISNGLFALCCVG
+VAYLGLSSRHRPRLAQLCLLIVAAFLLLGKVYSPQFVMWLIPLVVLATPRRKQFWIWQAA
+EFFHWAGVWMESARITSGGEFGGTWVTVWYASGIVLHMATLIWICVTVIRDIRDPERDPV
+RRSALEQGVEPLAPGVAEDPNAGVFTGAADRFLLPPAGHGLQPTR
+>PROKKA_00905
+MTSHPRSPAPTRPSARWVGLLVGLTVVAAAVGVLTKQWCRVNGWAAPGVHAHMCYSDFAQ
+LFPTRGLSDGHFPFYTPLPPEQWMEYPALLAVVAGVTMWFVPASGDLHERTVTYFDVNAI
+GVVLCWIVLVVATAYTARGRSRDALLVALAPGIILTSMLNWDLWAVMLAALALWAWTAGR
+PTLAGMLIGLGTATKLYPLFFFGAIFVLALRTGRWAGFVKAAVAGAAAWLAVNLPFMLTA
+FDQWSRFYTFSGDRAVSFSSTWLALAWTGWSGETFTTLQNGLFLVCCVGIAYLALAARHR
+PRMAQLCFLIVASFILWGKVYSPQFVMWLIPLVVLATPRWRAFWIWQAVEVYHWGGVWME
+SARITSDGAFAGGAWWITAWYASGIVAHVVALVWLMTTVVKDVLDPVRDPVRRTALDQGA
+PEIAPGVAEDPHAGVFTGARDRLLLPPAGRGLQPLGESAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000824.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000824.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2665f8f04372f64b697231f19e4d377cfe108578
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000824.fa
@@ -0,0 +1,37 @@
+>PROKKA_00966
+MKHTFSLRTEWTGDRGSGTSGVRDYDRSVVIQDAAVGEIQASAARPFRGDDSKWNPETLL
+LGALAECHVLSYLHVAATSGVVVTGMTCGVEGELEVDGDGAGRFTAITLRPEVTLQDEAD
+RERAEALHAEAHRLCFIANSLSAPVAVEPVRPEALPTGAPTLPDHSARLGAPLAVLRPRV
+AKGPSRVTGLAERPTEVEPVMQEGTPAPVEQVRARDAAAGPAGATPGTPAAPGQAASFYD
+AVGGRPTFDRLTAEFYARVREDEILAPMYPQDDFEGAQRRLLMFLEQYWGGPRTYSEERG
+HPRLRMRHAPYRIDPAARNAWLRHMRAAVDTLELSPLHEAELWDYLERAAHSLQNSA
+>PROKKA_00679
+MKHTFSLRTEWTGDRGSGTSGVRDYDRSVVIQDAAVGEIQASAARPFRGDDSKWNPETLL
+LGALAECHVLSYLHVAATSGVVVTGMTCGVEGELEVDGDGAGRFTAITLRPEVTLQDEAD
+RERAEALHAEAHRLCFIANSLSAPVAVEPVRPEALPTGTSTLPDHSARLGAPLAVLRPRV
+AKGPSRVTGLAERPTEVEPVMQEGTPAPVEQVRARDAAAGPTGATPGTPAVPGQATSFYD
+AVGGRPTFDRLTAEFYARVREDEILAPMYPQDDFEGAQRRLLMFLEQYWGGPRTYSEERG
+HPRLRMRHAPYRIDPAARDAWLRHMRAAVDTLELSPLHEAELWDYLERAAHSLQNSA
+>PROKKA_01921
+MKHTFALRTEWTGNRGTGTSGVRDYDRSVVIQDAAVGEIHASAARPFRGDDSKWNPETLL
+LGALAECHVLSYLHVAATSGLVVTGMACAAEGVLEVDGDGAGRFAAVTLRPEVALQDEAD
+RERADALHAEAHRLCFIANSLSAPVSVEPAVAGSGAAASGGPALPDHSSRLGAPLAVLRP
+RVAKRPSQVTGLAERPTEVEPVMKAGAPAPVDQMQARDAAAGRAASPATPAPAAETAAPG
+QAASFYEAVGGRETFDRLTAEFYARVREDELLSPMYPQDDFEGAQRRLLMFLEQYWGGPR
+TYSEERGHPRLRMRHAPYRIDPAARDAWLTHMRAAVDTLGLSPLHEAELWDYLERAAHSL
+QNSA
+>PROKKA_01869
+MKHTFSLRAEWTGDRGTGTTGVRDFDRSVVIQESEVGEIHASAARPFRGDAAKWNPETLL
+LGALAECHVLSYLHAAATGGLVVTGMTCAAEGTLEVDSDGAGRFASITLRPEVALRDEAD
+RARADELHAEAHRMCFIANSISAPITVEAGPGSSPTRGDGAALPDHSARLGAPLAVLRPR
+VANRPTRVTGLADRPTEAEPVVRADAPSGAEQARARDEATARGERPPSATPIATPAPGAT
+PAASPATAAPGQATSFYEAVGGHPTFEKLVHVFYQGVREDPLLAPMYPHQDWDGAEERLR
+MFLEQYWGGPRTYSERRGHPRLRMRHMPFTVDPAARDAWLRHMRAAVDAVELSPLHEAEL
+WDYLERAAHSLQNSA
+>PROKKA_00912
+MKHTFSLRTEWTGDRGSGTSGVRDYDRSVVIQDAAVGEIQASAARPFRGDDSKWNPETLL
+LGALAECHVLSYLHVAATSGVVVTGMTCGVEGELEVDGDGAGRFIAITLRPEVTLQDEAD
+RERAEALHAEAHRLCFIANSLSAPVTVEPVRPEALPTGTPTLPDHSARLGAPLAVLRPRV
+AKGPSRVTGLAERPTEVEPVMQEGTPAPVEQVRARDAAAGPAGATPGTPAAPGQATSFYD
+AVGGRPTFDRLTAEFYARVREDEILAPMYPQDDFEGAQRRLLMFLEQYWGGPRTYSEERG
+HPRLRMRHASYRIDPAARDAWLRHMRAAVDTLELSPLHEAELWDYLERAAHSLQNSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000833.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000833.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a985ace8786db10fb6b11ea5c878db07227a2169
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000833.fa
@@ -0,0 +1,20 @@
+>PROKKA_00981
+MRPTPDPAPAGRRACDSSARRMSAALAAMGVLHFVRPEPFDGLIPPFLPGSARAWTHGSG
+VAELAVAGLLAVPRTRRAGGRAAQALFLGVWPGNAWMAWRWRRRPWPAQLVSLGRLPLQV
+PLIRAAGRVARS
+>PROKKA_00695
+MRPTPDPAPAGRRACDSSARRMSAALAAMGVLHFVRPEPFDGLIPPFLPGSARAWTHGSG
+VAELAVAGLLAVPRTRRAGGRAAQALFLGVWPGNAWMAWRWRRRPWPAQLVSLGRLPLQV
+PLIRAAGRVARS
+>PROKKA_01908
+MRRASAPRTDTAGATGTGARRMAAALAGMGVLHFARPKPFDGLIPPALPGPARAWTVGSG
+VAELAVAGMLAAPRTRRAGGRAAQALFLGVWPGNAWMAWRWRGRSWPWRALALGRLPLQV
+PMIRAAGRIARG
+>PROKKA_01856
+MKPTPDPAPAGRRASDGSARRMSAALAAMGVLHFVRPEPFDGLIPPFLPGSARAWTHGSG
+VAELAVAGLLAVPHTRRAGGRAAQALFLGVWPGNAWMAWRWRRRPWPAQLVSLGRLPLQV
+PLIRAAGRVARR
+>PROKKA_00924
+MRPTPDPAPAGRRACDSSARRMSAALAAMGVLHFVRPEPFDGLIPPFLPGSARAWTHGSG
+VAELAVAGLLAVPRTRRAGGRAAQALFLGVWPGNAWMAWRWRRRPWPAQLVSLGRLPLQV
+PLIRAAGRVARS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000836.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000836.fa
new file mode 100644
index 0000000000000000000000000000000000000000..330a26ca30cea8468f7e262d768d505c9cd04f39
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000836.fa
@@ -0,0 +1,30 @@
+>PROKKA_00984
+MSAPVLHVIACAHGTHDAAGRDVIDGLRADLAALLAAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPGTIAAAPLAGAGDDVEPRLVTVLAER
+VARAVPAGEAATSDVILAAAGTRAADGQAQVHALAGALARATGLPVTAAFGAAATPRVPD
+AVARVHAAGRRAVVAAHLLAPGYFHDRLGEAGADAVTDPLLPHPLVARIALDRLRSALVE
+APRGAAGGR
+>PROKKA_00698
+MSAPVLHVIACAHGTHDAAGRDVIDGLRADLAALLAAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPGTIAAAPLAGAGDDVEPRLVTVLAER
+VAQAVPAGEAATSDIILAAAGTRAADGQAQVHALAGALARATGLPVTAAFGAAATPRVPD
+AVSRVRAAGRRAVVAAHLLAPGHFHDRLGESGADAVTDPLLPHPLVARIALDRLRSALAE
+APRGAAGGR
+>PROKKA_01905
+MSAPVLHVIACAHGTHDAAGRVVIDGLRADLAALLDAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPDTIAAAPLAGAGDDVEPRLVAVLAER
+VAQAVPAGEAATSEVILAAAGTRAADGQAQVHALAAALARATGLPVTAAFGAAATPPVPD
+AVSRVRATGRRAVAAAHLLAPGYFHDRLGESGADAVTDPLLPHPLVARIALDRLRSALAE
+APRGAAGGR
+>PROKKA_01852
+MSAPVLHVIACAHGTHDAAGRVVIDGLRADLAALLDAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPDTIAAAPLAGAEDDVEPRLVTVLAER
+VAQAVPAGEAATSDIILAAAGTRAADGQAQVHALAAALARATGLPVTAAFGAAATPRVPD
+AVARVRATGRRAVVAAHLLAPGYFHDRLGESGADAVTDPLLPHPLVARIALDRLRSALAE
+APRGAAGGR
+>PROKKA_00927
+MSAPVLHVIACAHGTHDAAGRDVIDGLRADLAALLAAEGPGAQVHEAYVDVQSPSLDEVV
+AALPPGEPAVIVPLLLSLGHHVHHDIHHAAAARPGTIAAAPLAGAGDDVEPRLVTVLAER
+VARAVPAGEAATSDVILAAAGTRAADGQAQVHALAGALARATGLPVTAAFGAAATPRVPD
+AVARVHAAGRRAVVAAHLLAPGYFHDRLGEAGADAVTDPLLPHPLVARIALDRLRSALVE
+APRGAAGGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000838.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000838.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7260b08007126bcf181785a60891cc73ce7cf231
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000838.fa
@@ -0,0 +1,30 @@
+>PROKKA_00986
+MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL
+PHLVAQRMPGVDVLFLDTGYHFTETLATRDEVARRLAVTVVDVLPELTVAEQDERHGKDL
+FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA
+PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH
+V
+>PROKKA_00700
+MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL
+PHLVAQRMPGVDVLFLETGYHFTETLATRDEVARRLDVTVVDVLPELTVAEQDERHGKDL
+FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA
+PWSLDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH
+V
+>PROKKA_01903
+MSTVPPTRPTEELERLQALAESGAAELGWDAPAAAVVDWAARHVDLRRAAVACSMADAVL
+PHLVAQRMPGVDVLFLETGYHFTETLATRDEVARRLDVTVVDVLPELTVAEQDERHGKDL
+FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA
+PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWTGTAKTECGIH
+V
+>PROKKA_01850
+MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL
+PHLVAQRMPGVDVLFLETGYHFTETLATRDEVARRLDVTVVDVLPELTVAEQDERHGKDL
+FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA
+PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH
+V
+>PROKKA_00929
+MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL
+PHLVAQRMPGVDVLFLDTGYHFTETLATRDEVARRLAVTVVDVLPELTVAEQDERHGKDL
+FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHSMVKVNPVA
+PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH
+V
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000840.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000840.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2944c71e0ff7d6307d83f3d1792d4d8dfd7fdeb1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000840.fa
@@ -0,0 +1,45 @@
+>PROKKA_00988
+MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARKGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYAEEVFTAIAEDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPHDGATLAAGMVRGGDEA
+>PROKKA_00702
+MSTALLDRRAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARKGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYAEEVFTAIAEDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPVRTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPHDGATLAAGMVRGGDEA
+>PROKKA_01901
+MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARSGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYSEEVFTAIADDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVLRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPQDGATLAAGMVRGGDEA
+>PROKKA_01848
+MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARKGVVEQTRRHLSVVALLRVPQVIVAVNKIDLVDYSEEVFTAIAEDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPQDGATLAAGMVRGGDEA
+>PROKKA_00931
+MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARKGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYAEEVFTAIAEDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPHDGATLAAGMVRGGDEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000845.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000845.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7522f0e6a6225976424fc743b266d726ff8a26da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000845.fa
@@ -0,0 +1,53 @@
+>PROKKA_00995
+MRGDAPGTVEEVYRDLLARAPENKMQPRLEPMRRVLALLGDPQHAAPVIHLTGTNGKTST
+ARMVEAVLRAYGLRTGRYTSPHLQRVTERISIDGAPVADETFVRVWGEILPIVQTVDAEL
+EAAGEVPLTYFEAVTTLGFAVFADEPVEVVVLEVGLGGVTDATNVADAVVSVVTPISLDH
+TDLLGETEAEIAEEKAGIIKPGGALVSAAQERDAAQVLLEAAQAADVPFRFEGVEFGVLE
+RSLAVGGQQVSVRGLAAEYRDLFLPLLGEHQAQNLAVAVAALEMFLGGGERPLDEELLRE
+GLSQVTSPGRLEVLRTAPTLIVDAAHNPDGVRATARAVQEAFGFTRLSLVVGILQEKDAP
+GMLAALYRAFGDDVEDLAVTQSSSARAIPAGELARMAVDAGWPEDDVYATESVPDALEWA
+VGRAEALETSADELASGTGGGVLVLGSITLAAEVRTLVGEPRHAGPVTVAARGLDPADLL
+DAVGLADADEDDLDPEILELLEDRDDAGARRRPEEDR
+>PROKKA_00709
+MRGDVPGTVEEVYRDLLARAPENKMQPRLEPMRRVLALLGDPQHAAPVIHLTGTNGKTST
+ARMVEAVLRAYGLRTGRYTSPHLQRVTERISIDGAPVADETFVRVWGEILPIVQTVDAEL
+EAAGEVPLTYFEAVTTLGFAVFADEPVEVVVLEVGLGGVTDATNVADAVVSVVTPISLDH
+TDLLGETEAEIAEEKAGIIKPGGALVSAAQERDAAQVLLEAARAADVPFRFEGVEFGVLE
+RSLAVGGQQVSVRGLAAEYRDLFLPLLGEHQAQNLAVAVAALEMFLGGGERPLDEELLRE
+GLSQVTSPGRLEVLRTAPTLIVDAAHNPDGVRATARAVQEAFGFTRLSLVVGILQEKDAP
+GMLAALYRAFGDDVEDLAVTQSSSARAIPAGELARMAVDAGWPEDDVYATESVPDALEWA
+VGRAEALETSADELASGTGGGVLVLGSITLAAEVRTLVGEPRHAGPVTVAARGLDPADLL
+DAVGLADADEDDLDPEILELLEDRDDAGARRRPEEDR
+>PROKKA_01894
+MSGAPAPQTVEQVYADLLARAPENAMEPRLEPMRRVLALLGDPQHAAPVIHLTGTNGKTS
+TARMIEAVLRSYGLRTGRYTSPHLQSVTERISIDGAPVSDETFVRVWGEILPIVQAVDAE
+LEAEGRPRLTYFEAVTTLGFAVFADEPVEVVVLEVGLGGITDATNVADGAVSVVTPISLD
+HTDLLGETEAEIAEEKAGIVKPGGALVSAVQERDAAQVLLEAARAADVPFRFEGVEFGVL
+ERSLAVGGQQVSVRGLAAEYRDLFLPLHGEHQAQNLAVAVAALEMFLGGGDRPLDEELLR
+EGLAQVASPGRLEVLRTAPTLIVDAAHNPDGVRATARAVQEAFGFTRLALVVGILREKDA
+PAMLEALFRAFGDDVEDLALTQSSSPRAIPAGDLARMAVDAGWPEADVFAAESVPDALEW
+AVGRAEALETSADELASGTGGGVLVLGSVTLAAEVRALVGEPRHAGPVTVAARGLDPADL
+PRRRRPGRGGRGRPGPRDPRAARGPRRRRLPPPHRGGPMSTPQPGTGRTPEEDERFGDES
+WRPERETRAQRAWRPGTRRRRRSVRALFTSTVLMLEAVVIFFLGMMLFGMNRDQPGAVWF
+IAGYTLLAAVAVLTCALVRRPVGIAIGWAIQAVLVLSGFWEYSMFVVGALFALTWAYAVI
+KGGGMDVENAERDRLQAEWEAEHGQ
+>PROKKA_01841
+MSAPAEGRVPGTVEEVYADLLARAPEHRMEPRLDPVRRVLALLGDPQHAAPVIHLTGTNG
+KTSTARMIEAVLRAYGLRTGRYTSPHLERVTERISVDGEPVADEDFVRVWGEILPMVHTV
+DAELEAAGEPRLTYFEAVTVLGFAVFADAPVEVVVLEVGLGGITDATNVADGAVSVVTPI
+SLDHTDLLGDTEAEIAEEKAGIIKPGGFLVSAAQDADAAQVLLEAARAADVPFRFEGVEF
+GVLERRLAVGGQQVDVRGLADEYRELFLPLHGAHQAENLAVAVAALEAFLGGGQRPLDVE
+LLREGLAQVTSPGRLEVLRTAPTVVVDAAHNPDGVAVTARAVQEVFSFTRLALVVGVLQE
+KDARTMLEVLHREFGDLISDVALTQSASPRAIPAGDLAALAVDAGWPEDDLFITESVPDA
+LEWAVGRAEAVETSADALASGTAGGVLVLGSITLAAEVRSLLGAPAHAGPVTVAARGMDP
+ADLLAAVGLEDDDADAVDPEVLELLDDREEHTR
+>PROKKA_00938
+MRGDVPGTVEEVYRDLLARAPENKMQPRLEPMRRVLALLGDPQHAAPVIHLTGTNGKTST
+ARMVEAVLRAYGLRTGRYTSPHLQRVTERISIDGAPVADETFVRVWGEILPIVQTVDAEL
+EAAGEVPLTYFEAVTTLGFAVFADEPVEVVVLEVGLGGVTDATNVADAVVSVVTPISLDH
+TDLLGETEAEIAEEKAGIIKPGGALVSAAQERDAAQALLEAARAADVPFRFEGVEFGVLE
+RSLAVGGQQVSVRGLAAEYRDLFLPLLGEHQAQNLAVAVAALEMFLGGGERPLDEELLRE
+GLSQVTSPGRLEVLRTAPTLIVDAAHNPDGVRATARAVQEAFGFTRLSLVVGILQEKDAP
+AMLAALYRAFGDDVEDLAVTQSSSARAIPAGELVRMAVDAGWPEDDVYATESVPDALEWA
+VGRAEALETSADELASGTGGGVLVLGSITLAAEVRTLVGEPRHAGPVTVAARGLDPADLL
+DAVGLADADEDDLDPEILELLEDRDDAGARRRPEEDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000847.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000847.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1b42a4f96726196f7b8cf0320154b572d729e78a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000847.fa
@@ -0,0 +1,25 @@
+>PROKKA_00998
+MPATPLTDDIRLSPADDIPAEEARLTWYARPAGTAALLLITSLVALTATIIIIVERTLLT
+ADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLLAGARFARW
+YWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNLQTGTLPA
+PAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID
+>PROKKA_00712
+MPATPLTDDIRLSPADDIPAEEARLTWYARPAGTAALLLITSLVALTATIIIIVERTLLT
+ADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLLAGARFARW
+YWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNLQTGTLPA
+PAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID
+>PROKKA_01892
+MPSTPTADRVRPAQPAETPASDGTLSWYARPAGMAWTLLVTSLVALTATIVIIVERSILA
+ADPGHRTSCDLNPWVSCGRVMQSWQAMTFGFPNTYIGIVAFSVLITVAVSLFAGARFARW
+YWLLMNVGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNIQTGTLPA
+SPGAARLARELAWPVILILYVLVFATILLELGFGVIGLD
+>PROKKA_01838
+MDVTETAENPPAPRAHHAAHALPEDRSLSWYARPLGTAWMLLITSIVAVTATIIIIVERS
+ILAENPNYRTSCDINPWLSCGTVMQSWQAHTFGFPNTFVGIVAFPVLITVAVSLFAGARF
+ARWYWVLMNVGILAGFAFAAWLWYSAVYSIGTLCLYCMIVWAMVILQLVLVTSRNLQTGA
+LPSSPGLARLAQDFAWPVIVLLYALVFASILLQLGLGVIGIR
+>PROKKA_00941
+MSMPTTPPTDDVRLSPADDVPAEEARLTWYARPAGTAALLLITSLVALTATIVIIVERAL
+LTADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLLAGARFA
+RWYWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNLQTGTL
+PAPAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000852.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000852.fa
new file mode 100644
index 0000000000000000000000000000000000000000..19e50003413ba4a86e0a4626a357c74c5e95bbd3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000852.fa
@@ -0,0 +1,40 @@
+>PROKKA_01003
+MSVRRTVVTRYPTPATRGSEDPQANPVTSRETMQAARRVVVKIGSSSLTTPDGLDVAAID
+RLVDVLAAERQKGTQVVLVSSGAIAAGFPHLGLSRRPKDTATQQASAAVGQSKLMAHYTT
+SFGRHDTEVAQVLLTAEELMRRTQYTNAHRALARLLTLDVMPIVNENDAVATREIRFGDN
+DRLAALTANLCKADLLVLLSDVDALYTGHPSNPDARRIPEVTSDDDLSGVDVRVPGSAGV
+GTGGMVTKVDAAGIAATTGIPTLLTSAANAGAAFAGEDVGTWFSATGRRRSARAAWLGLT
+AEVRGRLIIDDGAVAGAIDRGRSLLAAGITGCTGAFTPGDVVEIVDAHGRVRARGLVQYS
+SSQLPAMLGRTTADLREDLGAGYDGVVVHADDWVRLAPPQR
+>PROKKA_00717
+MSVRRTVVTRYPTPATRGSEDPQANPVTSRETMQAARRVVVKIGSSSLTTPDGLDVAAID
+RLVDVLAAERQKGTQVVLVSSGAIAAGFPHLGLGRRPKDTATQQASAAVGQSKLMAHYTT
+SFGRHDTEVAQVLLTAEELMRRTQYTNAHRALSRLLTLDVMPIVNENDAVATREIRFGDN
+DRLAALTANLCKADLLVLLSDVDALYTGHPSHPDARRIPEVTSDDDLAGVDVRVPGSAGV
+GTGGMVTKVDAAGIAATTGIPTLLTSAANAGAAFAGEDVGTWFSATGRRRSARAAWLGLT
+AEVRGRLIIDDGAVAGAIDRGRSLLAAGITGCTGAFTPGDVVEIVDAHGRVRARGLVQYS
+SSQLPAMLGRTTADLREDLGAGYDGVVVHADDWVRLAPPQR
+>PROKKA_01887
+MSARRTVVTRYPTPATRGAEDPRANPVTTRDTMAAARRVVIKIGSSSLTTATGLDVAAID
+RLVDVIAELRGRGTQVVLVSSGAIAAGFPHLGLDRRPKDTATQQAAAAVGQGRLLAHYTH
+SFGRHETEVAQVLLTAEELMRRTQYTNAHRALARLLTLDVMPIVNENDAVATREIRFGDN
+DRLAALTANLVKADLLVLLSDVDALYTGHPSLPDSRRIPVVATDADLEGVDVHVPGSAGV
+GTGGMVTKVDAAGIAATTGIPTLLTSAPNAGSAFAGEDVGTWFEATGRRRSARAAWLGLT
+AEVRGQLVIDDGAVAGAIDRGRSLLAAGIIGLSGRFTPGDVVEILDATGRVLARGLVQYS
+SSQLPRMLGRSTSDLKEDLGAGYDGVVVHADDWVRLAPPRR
+>PROKKA_01815
+MARRPSTVHRHATPSSRGAEDPKANPVHTRADIGAARRVVIKVGSSSLTTGTGLNTDAID
+ALVELVARLRGRGTQVVLVSSGAIAAGFPALGLSRRPKDTATQQAAAAVGQNRLVAYYSQ
+SFARFDTTVAQVLLTAEELMRRGQYINAHRALARLLTLDVLPIVNENDAVATREIRFGDN
+DRLAALTANLVKADLLVLLSDVDALYTGHPSRPGSRRIDTVTAETDLGGVDVRTPGSAGV
+GTGGMVTKVDAAGIAATTGIPTLLTSAALASAALDGEDVGTWFSAAGRRRTARAAWLGLT
+AQVRGRLTIDDGAVAGAIDRGRSLLAAGITAAEGDFTAGDVVEIADAQGTVLARGLAAYS
+SSQLPRMLGRQTAQLKEEIGAGYDGVVVHADDWVRLAPTHSAFR
+>PROKKA_00946
+MSVRRTVVTRYPTPATRGSEDPQANPVTSRETMQAARRVVVKIGSSSLTTPDGLDVAAID
+RLVDVLAAERQKGTQVVLVSSGAVAAGFPHLGLGRRPKDTATQQASAAVGQSKLMAHYTT
+SFGRHDTEVAQVLLTAEELMRRTQYTNAHRALSRLLTLDVMPIVNENDAVATREIRFGDN
+DRLAALTANLCKADLLVLLSDVDALYTGHPSNPDARRIPEVTSDDDLAGVDVRVPGSAGV
+GTGGMVTKVDAAGIAATTGIPTLLTSAANAGAAFAGQDVGTWFSATGRRRSARAAWLGLT
+AEVRGRLVIDDGAVAGAIDRGRSLLAAGITGCTGDFTPGDVVEIVDTHGRVRARGLVQYS
+SSQLPAMLGRTTADLREDLGAGYDGVVVHADDWVRLAPPQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000860.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000860.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6d676b1f5b4c03ea9369e228964f8422300d0a78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000860.fa
@@ -0,0 +1,45 @@
+>PROKKA_01018
+MTATPDLEQTRHLATELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGNR
+LIDLASGIAVTSVGASHPRVVAAVQDQVAQFTHTSFMITPYEGYVAVAEQLDRTSPIPGE
+TRTALFNSGAEAVENAVKVARAYTGKQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGPF
+APEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEGF
+LPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVTG
+RAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIREHFEQNADD
+RIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRATGVILLTCGTYGNVVRFLPPLT
+IGEDLLKEGLSEVTKALQSA
+>PROKKA_00732
+MTATPDLEQTRHLATELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGNR
+LIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTSPIPGE
+TRTALFNSGAEAVENAVKVARAYTGKQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGPF
+APEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEGF
+LPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVTG
+RAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIREHFAQNADD
+RIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRAAGVILLTCGTYGNVVRFLPPLT
+IGEDLLKEGLSEVTNALQSA
+>PROKKA_01869
+MSSTPDLEQSRHLATALPGPRSQALAERQKAAVPAGVATTMPVYAARAAGGILEDVDGNR
+LIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTAPISGQ
+TRTALFNSGAEAVENAVKVARSYTGKQAVAAFDHAYHGRTTLTMALTAKNMPYKHHFGPF
+APEVYRVPGSYPLRDGLSGAEAARRAIGALETQIGAENLAAVIMEPIQGEGGFIVPAEGF
+LPAVVEWCRANDVLFIADEVQSGVARTGSWFACEAEGVEPDLMTTAKGIAGGMPLSGVTG
+RAEVMDSVHPGGLGGTYGGNPVAAAAALAVFEAIEDEDLLAKATRIEEVIREHFAAHADD
+RIAEVRGRGAMMAIELVEPGTGEPDAALTAAVAAAVRATGVILLTCGTYGNVIRFLPPLT
+IGEDLLKEGLSEVTKALQSA
+>PROKKA_01761
+MTSPVTAPEQSRHIATELPGPKSRELAARQAGAVPAGVATTMPVFASRAGGGIIEDVDGN
+RLIDLGSGIAVTSVGASHPKVVEAVQEQVADFTHTCFMITPYEGYVAVAEKLGEKAPISG
+ETRTALFNSGSEAVENAVKVARAYTRKQAVVAFDHAYHGRTTLTMSLTAKSMPYKHSFGP
+FAPEVYRVAGSYPLRDGLNGAAAAKKAISAMEKQIGADNLAAVIMEPLQGEGGFIVPAEG
+FLQAIVEWCTANDVLFIADEVQSGFARTGAWSASELEGIEPDLMCTAKGIAGGMPLSAVT
+GRAEVMDAVHPGGLGGTYGGNPVATAASLAVFEAIEEDGLLQEAQMIERVIREHFEQNAD
+ERIAEVRGRGGMMAIEFVDPASGEPDAALTGKLAAAVRAAGVVLLTCGTYGNVVRFLPPL
+TIGEELLREGLAEVTTALQSA
+>PROKKA_00962
+MTATPDLEQTRHLVTELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGNR
+LIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTCPIPGE
+TRTALFNSGAEAVENAVKVARAYTGRQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGPF
+APEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEGF
+LPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVTG
+RAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIRDHFEQNADD
+RIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRATGVILLTCGTYGNVVRFLPPLT
+IGEDLLKEGLSEVTKALQSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000864.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000864.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc940f1e9ede5cd397d818096789c6b3dc9d9aa2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000864.fa
@@ -0,0 +1,31 @@
+>PROKKA_01022
+MRTARPTRLAVALGAGVLLTGVGATPALASPAHPAGWTAEHGLPGGSFLVAGAEGETGAS
+FGTEFEVDESDVRLTVAPAMEGEARGAETEVPFTYDDELERGDFDVAAARRSLGESGTGP
+VVYTLYVLGGEVAALTYGPDADLTDADPGEPLRADQRHELGFHMLPTAWDTTLLAAPGER
+HVFISSYTGDEAAPLTLVAGPAEGRVVEVTEEETGGPRGYVYQAPEGFTGSDTVTLRATR
+DGVTTTRTVTVRFGDPRVDLYDWENGRIPGFVTFPVAGLFDDAPGQPADPDTPTSPAEPE
+TPADPADGEHTVPDTVETGRGPAAWPVAVAVLAAGVLAVVRRHRVAA
+>PROKKA_00736
+MRTARPTRLAAALGAGVLLTGLGATPVLASPAHPAGWTAEHDLPGGSFLVASAEGETGAS
+FGTEFEVDESDVRLTVAPVLEGEARGAETEVPFTYDDELERGDFDVAAARRSLGESGTGP
+VVYTLYR
+>PROKKA_00737
+MLPTAWDTTLLAAPGERHVFISSYTGDEAAPLTLVAGPAEGRVVEVAEEETGGPRGYVYQ
+APEGFTGSDTVTLRATRDGVTTTRTVTVRFGDPRVDLYDWENGRIPGFVTFPVAGLFDDA
+PAPGQPADPDTPTSPAEPETPADPADGEHTVPDTVETGRGPAAWPVAVAVLAAGVLAVVR
+RHRVAA
+>PROKKA_00782
+MSARRTTRPLSTALAAAVLAGGLAASTAAPALAAPAETTDGWQNGHFVGGTFGSTELSPR
+TGSFYTQHAVKDVRVTVAPFYPAFTDLEEISYKVPGEMGPETDVEFTYDAELEAGYVDVL
+EQRRVLDEEGTAGAVFTLYVDGKATATLVFGEDRNLGDDVPGMFLDATGPQAYDFSARPT
+VDHQTRLAAPGSRLVHLQGNSTGDAPVEDSTRTVVEQPEHGTLVELPRIGDPTNWTSDGA
+NGSFASTVYVADEGFTGTDQAVFTLTDGSTGEQKTLVVTFSIGDPRAADPHLGVQGTGLP
+FDEARVWEALEAQGEDDASEAPAPESPATPAPDSTDAPEASEPSEPADEHTVPETVETGS
+GQAWWLAAVAAAGTGALVAGRRRFGLAR
+>PROKKA_00966
+MRTARPTRLAAALGAGVLLTGLGATPALASPAHPAGWTAEHGLPGGSFLVAGAEGETGAS
+FGTEFEVDESDVRLTVAPVLEGEARGAETEVPFTYDDELERGDFDVAAARRSLGESGTGP
+VVYTLYVLGGEVAALTYGPDADLTDADPGEPLRADQRHELGFHMLPTAWDTTLLAAPGER
+HVFISSYTGDEAAPLTLVAGPAEGRVVEVTEEETGGPGGYVYQAPEGFTGSDTVTLRATR
+DGVTTTRTVTVRFGDPRVDLYDWENGRIPGFVTFPVAGPFDDAPGQPADPDTPTSPAEPE
+TPADPADGEHTVPDTVETGRGPAAWPVAVAVLAAGVLAVVRRHRVAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000867.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000867.fa
new file mode 100644
index 0000000000000000000000000000000000000000..090170c7b77547280e6643d9c3882cd6bbf4ae4d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000867.fa
@@ -0,0 +1,20 @@
+>PROKKA_01025
+MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREPT
+LGATAPYVLMTPTYGGGSGPGAVPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLAGY
+IISRKCQVPLMYKFELMGTPDDVERVRGGLEGMWT
+>PROKKA_00740
+MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREPT
+LGATAPYVLMTPTYGGGSGPGAVPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLAGY
+IISRKCQVPLMYKFELMGTPDDVERVRGGLEGLWT
+>PROKKA_01860
+MTVAADPGHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVQKLELPEDRVARLPLITREPT
+LGATAPYVLLTPTYGGGDGPGAVPKQVIKFLNVPGNRTWIRGVIASGNTNFHEAYCLAGY
+IIARKCQVPLMYKFELMGTPEDVDSVRGGLEGLWT
+>PROKKA_01750
+MTTATAGPNHMRDAEAQGLVPTDARLIYFSSASGYTHRFVEKLGLPLGQAARLPLLTREP
+TLGATAPYVLLTPTYGGGGDTGGEVPKQVIKFLNVPGNRALIRGVIASGNTNFSGAYAAA
+GYIISRKCQVPLMYKFELMGTPEDVVAVREGLERLEEGQHA
+>PROKKA_00969
+MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREPT
+LGATAPYVLMTPTYGGGSGPGAVPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLAGY
+IISRKCQVPLMYKFELMGTPDDVERVRGGLEGLWT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000869.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000869.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2163c138f508f47e45d014e4057b66aca505d59c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000869.fa
@@ -0,0 +1,35 @@
+>PROKKA_01027
+MCPAVTETQQSHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDEE
+RLLSMRVFTGLTLLDTIQGTVGAVSLIPDAMTPHEEAVLTNIAFMESVHAKSYSSIFSTL
+ASTPEIDEAFRWSRENRNLQAKARLIVERYDGQDPYKKKIASTLLESFLFYSGFYWPMYL
+SGHARLTNTADLIRLIIRDEAVHGYYIGYKYQRSIETLPEEKREELKAFTFELLFELYEN
+EVEYTHDLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSDE
+NHDFFSGSGSSYVIGKAENTEDEDWDF
+>PROKKA_00742
+MCPAVTETQQSHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDEE
+RLLSMRVFTGLTLLDTIQGTVGAVSLIPDAMTPHEEAVLTNIAFMESVHAKSYSSIFSTL
+ASTPEIDEAFRWSRENRNLQAKAGLIVERYDGQDPYKKKIASTLLESFLFYSGFYWPMYL
+SAHARLTNTADLIRLIIRDEAVHGYYIGYKYQRSIETLPEEKREELKAFTFELLFELYEN
+EVEYTHDLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSDE
+NHDFFSGSGSSYVIGKAENTEDEDWDF
+>PROKKA_01858
+MTEVTDTVKTNHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDEE
+RLLSMRVFTGLTLLDTIQGTVGAVSLIPDAITPHEEAVLTNIAFMESVHAKSYSSIFSTL
+ASTKEIDEAFRWSRENENLQRKASLIVERYDGEDPYKRKIASTLLESFLFYSGFYWPMYL
+SAHARLTNTADLIRLIIRDEAVHGYYIGYKYQRNIETLPEEKREELKAFTFELLFELYEN
+EVEYTHDLYDAVGLSEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSDE
+NHDFFSGSGSSYVIGKAENTEDADWDF
+>PROKKA_01745
+MTEPHHGPSVHDHLVEAINWNRIQDEKDNEVWQRLVNNFWLPEKVPLSNDVQSWNQLTDD
+ERLLSMRVFTGLTLLDTIQGTVGAVSLIPDAITPHEEAVYTNIAFMESVHAKSYSSIFST
+LASTKEIDEAFRWSRENPNLQRKAQLILERYDGEDPYKKKIASTLLESFLFYSGFYWPMY
+LSSHARLTNTADLIRLIIRDEAVHGYYIGYKYQRNIETLPEERREELKAFTFELMFELYE
+NEVEYTHSLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTDVNPAILSALSPNSD
+ENHDFFSGSGSSYVIGKAEATEDEDWDF
+>PROKKA_00971
+MCPAVTETQQSHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDEE
+RLLSMRVFTGLTLLDTIQGTVGAVSLIPDAMTPHEEAVLTNIAFMESVHAKSYSSIFSTL
+ASTPEIDEAFRWSRENPNLQAKARLIVERYDGQDPYKKKIASTLLESFLFYSGFYWPMYL
+SAHARLTNTADLIRLIIRDEAVHGYYIGYKYQRSIETLPEEKREELKAFTFELLFELYEN
+EVEYTHDLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSDE
+NHDFFSGSGSSYVIGKAENTEDEDWDF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000876.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000876.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6d4e63285fb9b9062e74878c7d1a03576d29f51d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000876.fa
@@ -0,0 +1,28 @@
+>PROKKA_01043
+MSLTAPGRALRRHRFAQAGTLSVALALALTACGGQSEPAESSTTSPSSAKPAVETSAPAS
+TSETAGVSSSPTATESGSGEYVPASADGPARSVPKPEMPADMKEETKEGAEAAIRYFWDV
+HYYAEQTGDTELLDSLYSEYCEFCQFSSNDLQMIYKDGGWYTGTEVQIDSILTHRSETGY
+VSTLLVTTGTGTGYTKGGVVPENGDVEAASKQPWIAEVSFNPESSHWIVDEMSYEGSIGS
+N
+>PROKKA_00756
+MSLTAPGRALRRHRFAQAGTLSVALALTLTACGGQSEPAESSTTSPSSAKPAVETSAPAS
+TSATAGVSSSPTATESGSGEYVPASADGPARNVPKPEMPAAMKEETKEGAEAAIRYFWEA
+IYYTDQTGETADFDSTYSEYCELCQAVSDSTAQHYKEGGWSTGEHTSIKSLTLTPSEFGY
+TATLVRDASAVDVFDSQGVRDDSASGAETHDETWLADVVYEPSKGHWVIDEMQNQQDAQ
+>PROKKA_00543
+MSFTAPRRVLRRHRLTQVGALGAGLALLLTACGGGSEPAESSSPAPTGSSSSPAEATTAS
+PSAESSPTTSPSGSVGSTAAAGSSGSGGAYVPASAEGPARNVPKPEMPAVTKEETQEGAE
+AAVEYFWEAAYYLQQTGDSEYQESVSSPTCKFCDLQRTSMEGHYRDGGWMKVEAVNIASM
+VTRPSANGYMSTLLLDMPKEEAFASQGGKAESIGTQPALEESPWIAETSFSEEAGHWVIE
+AMIAGGS
+>PROKKA_01734
+MTLPAPRRTLRRRRLARTGALSGALLLALTACAGGGADSGASSASTTTTAPAASSTSAAA
+SSSTGGASASESDATTSGAAGEYVPASSKGPAQNVPKPVMPAAVKENTPEGAEAAVKYWW
+EAVNYLQQTNDPEPLKSISMEECNLCSAHIKTIKRIYGDGGWATGENFAVNSVSMEKKKD
+FTLATVAISTDDSATFNADGVKVDQAPADAGTDAPWGVLLKFDSNKGQWVVREAEYDFQE
+G
+>PROKKA_00984
+MSLTAPGRALRRHRFAQAGTLSVALALALTACGGQSEPAESSTTSPSSAKPAVETSAPAS
+TSETAGVSSSPTATESGSGEYVPASADGPARNVPKPEMPAAMKEETKEGAEAAIRYFWEA
+IYYTDQTGETADFDSTYSEYCELCQAVSDSTAQHYKEGGWSTGEHTSIKSLTLTPSEFGY
+TATLVRDASAVEVFDSQGVRDDSASGVETHDETWLADVVYEPSKGHWVIDEMQNHQDAQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000879.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000879.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cfcbb11d7299d837ebcec62e3c2b24a6980ab723
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000879.fa
@@ -0,0 +1,65 @@
+>PROKKA_01046
+MSEPKNILLTVDGELREVTHGTTGLDLFREKPTTAVMRVDGLLWDLAREIPAGASVESVD
+ITEPEGLEVLRHSTAHVMAQAVQQLRPGAKLGIGPYITDGFYFDFDVDEPFTPEDLKQIS
+SLMQKIVKSGQTFRRRVVDEETARAEMAEEPYKLELLGKKDAADTAGEGASVEVGAGEIT
+IYDNVDRKTGDAVWCDLCRGPHLPSTKLIGNGFALTRSAAAYWLGNEKNKQLQRIYGTAW
+ASKDDLKAYQERLAEAERRDHRKLGAELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSR
+RRHTEAGYEFVYTPHITKQHLYEVSGHLDWYADGMFPPMHIDEVRDPETGEITRQGQNYY
+LKPMNCPMHNLIYRSRGRSYRELPLRLFEFGSVYRYEKSGVVHGLTRVRGMTQDDAHIYC
+TREQMKEELTTTLNFVLDLLKDYGLNDFYLELSTKDPEKFVGSDEIWEEATRTLAEVAEA
+SGLQLVPDPGGAAFYGPKISVQARDAIGRTWQMSTIQLDFNLPERFDLEYQAADGTRQRP
+VMIHRALFGSIERFLGVLTEHYAGAFPAWLAPEQVVAIPVAEAFNDYLDDVVAKLRAEGI
+RARLDDSSDRFPKKIRTAAKEKAPFVLIAGGEDREANAVSFRFRDGTQDNGVPVEEAIER
+IVKAVREREVTP
+>PROKKA_00759
+MSEPKNILLTVDGELREVTHGTTGLDLFREKPTTAVMRVDGLLWDLAREIPAGASVESVD
+ITEPEGLEVLRHSTAHVMAQAVQQLRPGAKLGIGPYITDGFYFDFDVDEPFTPEDLKQIS
+SLMQKIVKSGQTFRRRVVDEETARAEMADEPYKLELLGKKDAADTAGEGASVEVGAGEIT
+IYDNVDRKTGDAVWCDLCRGPHLPSTKLIGNGFALTRSAAAYWLGNEKNKQLQRIYGTAW
+ASKDDLKAYQERLAEAERRDHRKLGAELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSR
+RRHTEAGYEFVYTPHITKQHLYEVSGHLDWYADGMFPPMHIDEVRDPETGEITRQGQNYY
+LKPMNCPMHNLIYRSRGRSYRELPLRLFEFGSVYRYEKSGVVHGLTRVRGMTQDDAHIYC
+TREQMKEELTTTLNFVLDLLKDYGLNDFYLELSTKDPEKFVGSDEIWEEATRTLAEVAEA
+SGLQLVPDPGGAAFYGPKISVQARDAIGRTWQMSTIQLDFNLPERFDLEYQAADGTRQRP
+VMIHRALFGSIERFLGVLTEHYAGAFPAWLAPEQVVAIPVAEAFNDYLDDVVAKLRAEGI
+RARLDDSSDRFPKKIRTAAKEKAPFVLIAGGEDREAGAVSFRFRDGTQDNGVPVEEAIER
+IVKAVREREVTP
+>PROKKA_01842
+MSEPNNILLTVDGQMREVAHGITGLELFRDQSTTVVMRVDGVLWDLSREIPGGASVESVD
+ITEQDGLDVLRHSTAHVMAQAVQQLRPDAKLGIGPYITDGFYFDFDVAEPFTPEDLRTLE
+KMMQKIINSGQAFRRRVVTEDEARAEMADEPYKLELLGKKNDAATAGEGASVEVGAGEIT
+IYDNVDRKSGDAVWCDLCRGPHLPQTKLISNAFALTRSAAAYWLGNQDNKQLQRIYGTAW
+PTKADLKAYQERLAEAERRDHRRLGSELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSR
+RRHTEAGYEFVYTPHITKQHLYETSGHLDWYADGMFPPMQIDEQRDPETGEVTRQGQNYY
+LKPMNCPMHNLVFRSRGRSYRELPLRLFEFGAVYRYEKSGVVHGLTRVRGMTQDDAHIYC
+TREQMKDELTTTLNFVLDLLKDYGLDDFYLELSTRDPEKSVGSDEIWEEATRTLDEVARA
+SGLDLVPDPGGAAFYGPKISVQAKDAIGRTWQMSTIQLDFNLPERFDLEYQAPDGSRQRP
+VMIHRALFGSIERFLGVLTEHYAGAFPAWLAPEQVVAIPVAEAFADYLGDVVKRLRAEGI
+RARLDDSSDRFPKKIRTASKEKVPFVLIAGGEDAEAGAVSFRFRDGSQDNGVPVDEAIER
+IVRAVREREATP
+>PROKKA_01730
+MSESNPILLTVDGEMREVTHAITGAELFKDQPTTVVMRVDGQLWDLSRELHGGEAVESVD
+ITEQDGLNVLRHSTAHVMAQAVQELRPDAKLGIGPFITDGFYFDFDVAEPFTPEDLKQLE
+KMMQRIVKSGQTFRRRVVTEDEARAEMADEPYKLELLGKKDDAEAAGEGATVEVGAGEIT
+IYDNVDRKSGDAVWCDLCRGPHLPTTKLIGNGFALTRSAAAYWLGNEKNKQLQRIYGTAW
+PTKEDLKAYQERLAEAERRDHRKLGAELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSR
+KRHAAAGYEFVYTPHITKQHLYEVSGHLDWYADGMFPPMQIDEVRDPETGQITKQGQNYY
+LKPMNCPMHNLIYRSRGRSYRELPLRLFEFGSVYRYEKSGVVHGLTRVRGMTQDDAHIYC
+TREQMKDELTTTLNFVLDLLKDYGLDDFYLELSTKDPEKFVGSDEIWEEATRTLAEVAEA
+SGLELVPDPAGAAFYGPKISVQARDAIGRTWQMSTIQLDFNLPERFDLEYQAADGSRQRP
+VMIHRALFGSIERFLGVLTEHYAGAFPAWLAPEQVVAIPVAEAFNDYLADVVATLKAEGI
+RVRLDESSDRFPKKIRTASKEKVPFVLIAGGEDAEAGAVSFRYRDGSQDNGVPVDEAVAR
+IVKAVREREVTP
+>PROKKA_00987
+MSEPKNILLTVDGELREVTHGTTGLDLFREKPTTAVMRVDGLLWDLAREIPAGASVEAVD
+ITEPEGLEVLRHSTAHVMAQAVQQLRPGAKLGIGPYITDGFYFDFDVDEPFTPEDLKQIS
+SLMQKIVKSGQTFRRRVVDEETARAEMADEPYKLELLGKKDAADTAGEGASVEVGAGEIT
+IYDNVDRKTGDAVWCDLCRGPHLPSTKLIGNGFALTRSAAAYWLGNEKNKQLQRIYGTAW
+ASKDDLKAYQERLAEAERRDHRKLGAELDLFSFPDELGSGLPVFHPRGGIIRKEMEDYSR
+RRHTEAGYEFVYTPHITKQHLYEVSGHLDWYADGMFPPMHIDEVRDPETGEITRQGQNYY
+LKPMNCPMHNLIYRSRGRSYRELPLRLFEFGSVYRYEKSGVVHGLTRVRGMTQDDAHIYC
+TREQMKEELTTTLNFVLDLLKDYGLNDFYLELSTKDPEKFVGSDEIWEEATRTLAEVAEA
+SGLQLVPDPGGAAFYGPKISVQARDAIGRTWQMSTIQLDFNLPERFDLEYQAADGTRQRP
+VMIHRALFGSIERFLGVLTEHYAGAFPAWLAPEQVVAIPVAEAFNDYLDDVVAKLRAEGI
+RARLDDSSDRFPKKIRTAAKEKAPFVLIAGGEDREANAVSFRFRDGTQDNGVPVEEAIER
+IVKAVREREVTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000881.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000881.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c50ed604e872126722f023168dff9ced304c96ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000881.fa
@@ -0,0 +1,25 @@
+>PROKKA_01048
+MLDRHARDLTTRLFTPVAHTLLRAGVSPDTVTVVGTLGVSLGALVLFPLGHLFWGTLFIT
+AFVFSDLVDGIMAREAGSTGRWGAFLDSTLDRVQDAAVFLGLCLWGFGVGAAPAVGALSG
+ACLALGMLVSYVRAKAEALGWSAHVGIAERAERLVAALVVAGLTGLGLPPVVLAVTLGLL
+AAASLVTVGQRMAAVRRQARDDA
+>PROKKA_00761
+MLDRHARGVTTRLFTPVARTLLRAGVSPDTVTVVGTLGVSLGALVLFPLGHLFWGTLFIT
+AFVFSDLVDGIMAREAGSTGRWGAFLDSTLDRVQDAAVFLGLCLWGFGVGAAPAVGALSG
+ACLALGMLVSYVRAKAEALGWDAHVGIAERAERLVATLVVAGLTGLGLPPVVLAVTLGLL
+AAASLVTVGQRMVAVRRQARDDA
+>PROKKA_01840
+MLDRHARGATTRVFTPVARALLRAGVSPDAVTVVGTLGVSLGALVLFPLGELFWGTLFIT
+AFVFSDLVDGIMAREAGTTGRWGAFLDSTLDRVQDAAVFLGLSLWGFGVGGEPAVGTLAA
+VCLALGMLVSYVRAKAEALGLTANVGIAERAERLVAALVLAGLTGLGLPPAFLAATLGLL
+AAASLVTVGQRVAAVRSQTRRAA
+>PROKKA_01728
+MLDRRARGTTTALFTPLARRLLRAGVTPDAVTVAGTVGVSAAALLLYPAGHLFWGTIVIT
+LFVFSDVLDGVMAREAGTTGPWGSFLDSTLDRVQDAAIFLALSWWGFGVGAHPAVGVLAG
+VCLALGMLVSYARAKAESLGFTAAGGIAERAERLIVTLVFAGLTGLGLPSAVLTAVLGLL
+ALASLITVAQRVAGVRRQSRTA
+>PROKKA_00989
+MLDRHARGVTTRLFTPVARTLLRAGVSPDTVTVVGTLGVSLGALVLFPLGHLFWGTLFIT
+AFVFSDLVDGIMAREAGSTGRWGAFLDSTLDRVQDAAVFLGLCLWGFGVGAAPAVGALSG
+ACLALGMLVSYVRAKAEALGWDAHVGIAERAERLVATLVVAGLTGLGLPPVVLAVTLGLL
+AAASLVTVGQRMAVVRRQARDDV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000884.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000884.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5c18039f49e3b10900d613002f6e4b0a5dbc38c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000884.fa
@@ -0,0 +1,30 @@
+>PROKKA_01051
+MTDTAAKFSEYAHPEKLVSTQWVADHVGDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE
+LNDPVTRDFVGPEAFAEFAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD
+GGRDKWIAEGRETTREVPTVARAEYPVIERDDHTERAAREDVLQAIGTTPLIDVRSRPEY
+TGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRAGAGLQEGDD
+VIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR
+>PROKKA_00764
+MTDTAAKFSEYAHPEKLVSTQWVADHVDDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE
+LNDPVTRDFVGPEAFAEVAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD
+GGRDKWIAEGRETTREVPTVARAEYPVIERDDHTERAAREDVLQAIGTTPLIDVRSRPEY
+TGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRTDAGLREGDD
+VIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR
+>PROKKA_01835
+MTETATEFSQYAHPEKLVSTQWVADHVGEEGVVVLESNEDALLYATGHIPGAQRIDWHTE
+LNDPVTRDFIGPEAFAEMAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDVRLMN
+GGRDKWIAEGRETTREVPTVARGEYPVVPRDDTTERAAREDVLQAVGTTPLIDVRSRPEY
+TGETTHMDGYPQEGTLRGGHIPTAASVPWAQAANEDGTFKSREELEAVYRDGAGLKDGDD
+VIAYCRIGERSSHTWFVLKHLLGHENVRNYDGSWTEWGNSVRLPIVVGEEPGAAPAR
+>PROKKA_01725
+MTETPAEFAEYAHPEKLVSTQWVADHIDDEGVVVLESNEDTLLYSTGHIPGAVKIDWHTE
+LNDPVSRDFVGPEAFAELVASKGIGPDTTVVFYGDKSNWWAAYALWVFTLYGHRDVRLMN
+GGRDKWIAEGRPTTREVPEVTPAPSYPVSQRDDATDRAAREDVLAAIGSTPLVDVRSPKE
+YTGETTHMDGYPQEGTLRGGHIPTAASVPWAKAANEDGTFKSRAELEEIYKEGAGLGESD
+SVIAYCRIGERSSHTWFVLKQLLGYENVRNYDGSWTEWGNGVRLPIALGDEPGEAPAR
+>PROKKA_00992
+MTDTAAKFSEYAHPEKLVSTQWVADHVGDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE
+LNDPVTRDFVGPEAFAEFAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD
+GGRDKWIAEGRETTREVPTVARAEYPVIERDDHTDRAAREDVLQAIGTTPLIDVRSRPEY
+TGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRAGAGLQEGDD
+VIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000886.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000886.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85891a965916c7da490448084cc35a1b1fae1ee8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000886.fa
@@ -0,0 +1,34 @@
+>PROKKA_01057
+MYARSLSGLPEVPSITTVIGMEKTDLDGWVGWMAAQSVTQDPRLAESVGSAARLKQVARQ
+SADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTMAEARARLIEHGEGAYADRFDEWW
+DLYDVRPIAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTGRDGRVKALDPKVVM
+QLTAGLKAEESLVDPEAGTWEEWRHGQAEMLLGVALGETEVAVHQANPGVLPRHWHKFWA
+LRQVWKHAQAVDDAGPALRVIGPPPPSVPVSAATGLQAVRAAAFGGGSHAAPAVAPDGLS
+SRPASAEGGDRVTA
+>PROKKA_00776
+MYARSLSGLPEVPSITTVIGMEKTDLDGWVGWMAAQSVTQDPRLAESVGSAARLKQVARQ
+SADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTMAEARARLIEHGEGAYADRFDEWW
+DLYDVRPIAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTGRDGRVKALDPKVVM
+QLTAGLKAEESLVDPEAGTWEEWRHGQAEMLLGVALGETEVAVHQANPGVLPRHWHKFWA
+LRQVWKHAQAVDDAGPALRVIGPPPPSVPVSAATGLQAVRAAAFGGGSHAAPAVAPDGSS
+SRPASAEGGDRVTA
+>PROKKA_01829
+MTQPRLAHQTPLGRMYARSLTGLPEVPSITTVIGMERTDLDGWIGWMAAQSVTQDPRLAE
+SVGSAARLKQVARQSADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTLAETRAKLIE
+HGEGAYADRFDEWWDLYDVRPLAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTG
+RDGRVKALDPKVVMQLTAGLKAEESLVDAEAGTWEEWRHGQAEMLLGVALGETEVAVHQA
+NPGVLPRHWHKFWALRQVWKHAQAADDAGPALRVIGPPPPSVPLHRG
+>PROKKA_01719
+MYARSLSGLPEVPSITTVIGMERTDLDGWVGWMAANAVAQDPRLGESLGSPARLRQVAKQ
+SADAAARYRDAAAERGDRVHDYAEQVALRALGRPHTMAASREELQRHGEGAYADRFDEWW
+DLYDVQPVAAEITVWNHSVGYAGTLDLVARIGGRLCLIDYKTKGTGRDGRVKALDPKVVM
+QLTAGLKAEESLVDAEAGTWEPWAHGGAEMLLGVALGETEVAVHQANNAALPRHWHKFWA
+LRQVWKHALAVDDAGPALRVIGPPPVSVPGAAGGLSAARAAAFGAPPAVAHDPGTSAPAD
+RLQP
+>PROKKA_01004
+MYARSLSGLPEVPSITTVIGMEKTDLDGWVGWMAAQSVTQDPRLAESVGSAARLKQVARQ
+SADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTMAEARARLIEHGEGAYADRFDEWW
+DLYDVRPIAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTGRDGRVKALDPKVVM
+QLTAGLKAEESLVDPEAGTWEEWRHGQAEMLLGVALGETEVAVHQANPGVLPRHWHKFWA
+LRQVWKHAQAVDDAGPALRVIGPPPPSVPASAATGLQAVRAAAFGGGSHAAPDVAPDGSS
+SRPASAAEGGDRVTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000887.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000887.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dfcb05db608c0e1d29c6513479d74bf2ac713fe5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000887.fa
@@ -0,0 +1,25 @@
+>PROKKA_01058
+MTVLPVRTIPDPVLRTAASPVPAGADVRALVADMIETMHAVGGVGLAAPQVGVGLRVFVF
+DVAGVAGHVVNPVLETAGQALREPGEGCLSVPGLRYHPARAAEAVVRGTDVDGNPVEHRG
+TGLLARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRAARRIGAARAAAVSSVF
+GAPGAPAAGTGAAR
+>PROKKA_00777
+MTVLPVRTIPDPVLRTAASPVPAGADVRALVADMIETMHAVGGVGLAAPQVGVGLRVFVF
+DVAGVAGHVVNPVLETAGQALREPGEGCLSVPGLRYHPARAAEAVVRGTDVDGNPVEHRG
+TGLLARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRAARRIGAARAAAVSSVF
+GAPAVPAAGTGAAR
+>PROKKA_01828
+MSVLPVRTVPDPVLRTPARPVPAGMDVRALVADMVETMHAVGGVGLAAPQVGVGLRVFVF
+DVQGVAGHVVNPVLETGEETVREPGEGCLSVPGLRYHPARAAEAVVRGVNVDGHPVEHRG
+TGLVARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRTARRVGAERAAAVGSVF
+AAPAAPPTPARAPRGGTR
+>PROKKA_01718
+MTVLTLRTVPDPVLRTPAAPVAAGQDVRALVEDMVETMHAVGGVGLAAPQVGVGLRVFVF
+DCAGASGHVLNPVLETFGSPVREPGEGCLSVPGLRYHPARAERAVVRGVDVDGNPVEHRG
+EGLLARCLQHETDHLDGILYVDRLDGDDRREARRRLRADAPDPEAERIRARRDALAGSVF
+GARPSVSPSAARTTPRRGAQ
+>PROKKA_01005
+MTVLPVRTVPDPVLRTAASPVPAGADVRALVADMIATMHAVGGVGLAAPQVGVGLRVFVF
+DVAGVAGHVVNPVLETAGQALREPGEGCLSVPGLRYHPTRAAEAVVRGTDVDGNPVEHRG
+TGLLARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRAARRIGAARAAAVSSVF
+GAPAVPAAGTGAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000891.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000891.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c58977c6d29003f013e287e0884938c01d887418
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000891.fa
@@ -0,0 +1,25 @@
+>PROKKA_01062
+MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARRVWAWPVGILGNLILLTVFL
+ASLFTGADHATLLGQAGRQVMFIAVSVYGWARWRQARRGHAEDAPAITPEWAGWRGRVFL
+VTAMAVGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV
+PLLWSTGYYASAVMYAFYGAFTLIGFFVWLRATDRDKPAVETLLPDGPEGDVAR
+>PROKKA_00781
+MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARRVWAWPVGILGNLILLTVFL
+ASLFTGADHATLLGQAGRQVMFIAVSVYGWARWRRARRGHAEDAPAITPEWAGWRGRVFL
+VTAMAVGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV
+PLLWSTGYYASAVMYAFYGAFTLIGFFVWLRATDRDKPAVETLLPDGPEGDVAR
+>PROKKA_01824
+MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARKVWAWPVGILGNLILLTVFL
+ASLFTGADHATLLGQAGRQVMFIAVSVYGWVRWNEARRGRSEHATAITPEWAGLGGRAFL
+VLGMLIGTLALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLVWVAVDVVGV
+PLLWSTGYYASAVMYAFYGAFTLVGFFVWLRAKDRDKPAVETLLPDGPEEHAAR
+>PROKKA_01714
+MQWLVDVFNWTIPVAGGGLLMREVVGNVFGLASALGGMARKVWAWPVGILGNLLLLTVFL
+ASLFNDAPHATLLGQAGRQVMFIAVSVYGWKRWRDAQRGRADHAPAITPEWAGWGNRAFL
+AVALVLGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV
+PLLWSSGYYASAVMYAFYGVFTLTGFFVWMRARDRDKPAVETLLPDGPAPEEAAR
+>PROKKA_01009
+MDWLVDAFNWTIPVAGGGLLMREVLGNVFGLASALGGMARRVWAWPVGILGNLILLTVFL
+ASLFTGADHATLLGQAGRQVMFIAVSVYGWVRWRQARRGHAEDAPAITPEWAGWRGRVFL
+VTAMAVGTVALTPVFRALGSWEPVWADAWTFVGSLLATYGMARGWVEFWLIWVAVDVVGV
+PLLWSTGYYASAVMYAFYGAFTLIGFFVWLRATDRDKPAVETLLPDGPEGDVAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000892.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000892.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a606efe931ff35edd52d95ac50cf9c039ed95011
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000892.fa
@@ -0,0 +1,43 @@
+>PROKKA_01063
+MNAAETPSADPMDLAVGAALRGVRGANPLVGAVLTDAAGRILAVGHHRGRGTAHAEVDAL
+TRWRAARAADPALATLDPAGLTLHVTLEPCDHTGSTGPCSQAVLDAGIGALRYAVADPTG
+HDGGGAARLAAHGVHVTGPTGEAAALTLTARWREVRDAGRPWVTGHLAQSLDGHAAAADG
+TSQWITGPDSRVHAHEVRSRVDAIVVGTGTVLADDPRLTARDAAGAELAHQPVPVVQGHR
+PVPDGAALRTHPVLLHVPDHDPHAVLAALAAHPGPWPHGRRAEHVLIEGGPRVLGAWLRA
+GLVDELMVYTAPLLLGPGRAAVAGLDVATLSEGPRWHPDPAEGGPARALGVDVWTHLSPV
+PAPRLPTAPAPTRFQED
+>PROKKA_00782
+MSAAETPSADPMDLAVRAALRGVRGANPLVGAVLTDEAGRVLAVGHHRGRGTAHAEVDAL
+TRWRAARATDPALAALDPAGLTLHVTLEPCNHTGSTGPCSQAVLDAGVGALRYAVADPTG
+HDGGGAARLAAHGVRVTGPTGEVAALALTARWREARDAGRPWVTGHLAQSLDGHAAAADG
+TSQWITGPDSRVHAHEVRSRVDAIVVGTGTVLADDPRLTARDAAGAELAHQPVPVVQGHR
+PVPDGAALRAHPVLLHVPDHDPHAVLAALAAHPGPWPHGRRAEHVLIEGGPRVLGAWLRA
+GLVDELMVYTAPLLLGPGRAAVAGLDVATLSEGPRWHPDPAEGGPARALGDDVWTHLSPV
+PAPRLPTAPAPTRFQED
+>PROKKA_01823
+MSGAPDPMALAVGAALRGVRGANPLVGAVLTDDAGRVLAAGHHRGRGTAHAEVDALARWE
+AARAADPALAALDPAGLTLHVTLEPCDHTGSTGPCSGAILASGVGAVRYAVADPTGVDGG
+GAARLAAHGVRVSGPTGEPAALALTERWRRARDAGRPWITGHLAQSLDGHAAAADGTSRW
+ITGAASRAHAHRVRARVDAIVVGTGTVLADDPRLTVRDAAGAETGPQPVPVVQGRTPIPA
+GAALRARPETLHVPAHEPEAVLAALAARPGPWPHGGARPGHVLIEGGPRVLGAWIRAGLV
+DELMVYTAPLLLGAGRPAVAGLDVGTLADGLRWHPDPAEDGPVRALGEDVWTHLAPVPAP
+APEGPDPQEDCMFTGIVTHLGTVLALEPDPAADTARLVLDAGGALEGLPAGGSLAVDGVC
+LTALDGPGAEPGVFRADLMGQTLRMTSLGGRTPGDRVNLERCLRPTDHLDGHVVQGHVDG
+VGEVLSVTPQGAWTTVRIGLPAALARYVPAQGAIALQGVSLTVSAVSEPGADAHWFEVGL
+IPATLEATTLGALRPGDRVNLETDVLARYAERLALLPAAPAASPSAAPAEEVRP
+>PROKKA_01713
+MSAPAARHDDAGRPAEPLDLAAAAALAGVRGANPLVGAVITGPDGAVLAVGHHRGRGTAH
+AEVDALNRWAAARAADPSLHVDPAACTIHVTLEPCDHTGSTGPCAGAILDAGLGAVRYAV
+ADATGTAGGGAARLTRAGLRVEGPTGHAASAALTARWRRVRDAGRPWITVHLAQSLDGRA
+AAADGTSRWITGPASRAHAHAVRARVDAVVCGTGTVAADDPRLTARDAAGEQLPVQPVPV
+VMGERDLPAGAALAARADLIHVRSHDPRAVLAALASRPGPWPHGGSRPGHVLIEGGPHVL
+GAWLAAGLVDEVFAYTAPVLLGDGLPGVAGLDVPTLAAGHRWAPDPAEDGPVRALGDDVL
+THLAPVTDPAD
+>PROKKA_01010
+MNAAETPSADPMDLAVRAALRGVRGANPLVGAVLTDEAGRVLAVGHHRGRGTAHAEVDAL
+TRWRAARATDPALAALDPAGLTLHVTLEPCDHTGSTGPCSQAVLDAGIGALRYAVADPTG
+HDGGGAARLAAHGVHVTGPTGEAAALTLTARWREVRDAGRPWVTGHLAQSLDGHAAAADG
+TSQWITGPDSRVHAHEVRSRVDAIVVGTGTVLADDPRLTARDAVGAELAHQPVPVVQGHR
+PVPDGAVLRTHPVVLEVLDHDPHAVLAALAAHPGPWPHGRRAEHVLIEGGPRVLGAWLRA
+GLVDELMVYTAPLLLGPGRAAVAGLDVATLSEGLRWHPDPAEGGPVRALGVDVWTHLSPV
+PAPRLPTAPAPTRFQED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000893.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000893.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1aa205a9ce78a116f447bf1bcaf35f85332c6415
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000893.fa
@@ -0,0 +1,20 @@
+>PROKKA_01066
+MSGAGAPTFTPDPAAASGLNVAIVAAQWHTEIMDGLIAGAQAAAADLGLEPVLVRVPGTV
+ELTVAAARLAERFDVVVVLGVVVRGDTPHFDYVCQSVTQGVTEVSVRTGVPVGFGVLTVD
+TEQQARDRAGLPGSREDKGREALEAAVLTELALRSVTPRD
+>PROKKA_00785
+MSGAGAPTFTPDPAAASGLNVAIVAAQWHTEIMDGLIAGAQAAAADLGLEPVLVRVPGTV
+ELTVAAARLAERFDVVVVLGVVVRGDTPHFDYVCQSVTQGVTEVSVRTGVPVGFGVLTVD
+TDQQARDRAGLPGSREDKGREALEAAVLTELALRSVTPRD
+>PROKKA_01821
+MAVVAAQWHTEIMDGLIAGARAAAADLGLEPVLVRVPGTVELSVAAARLAEDFDAVVVLG
+VVVRGDTPHFDYVCQAVTQGVTEVSVRTGTPVGFGVLTVDTEQQARDRAGLPGSREDKGR
+ESLEAAVLTELALRDVQA
+>PROKKA_01710
+MSGAGAPTLALTTLTDADRAAAGSLRVAVVAAQWHTEIMDGLIAGSRAAAADLGIDVDLV
+RVPGTVELSVAAARLAATHDVVVVLGVVVRGGTPHFDYVCQSVTQGVTEVSVRTGVPVGF
+GVLTVDTVEQARDRAGLPGSQEDKGREALEAAVLTELALRAALG
+>PROKKA_01013
+MSGAGAPTFTPDPAAASGLNVAIVAAQWHTEIMDGLIAGAQAAAADLGLEPVLVRVPGTV
+ELTVAAARLAERFDVVVVLGVVVRGDTPHFDYVCQSVTQGVTEVSVRTGVPVGFGVLTVD
+TDQQARDRAGLPGSREDKGREALEAAVLTELALRSVTPRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000895.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000895.fa
new file mode 100644
index 0000000000000000000000000000000000000000..471e6bd358676e35e3998259e0cbd0b39698ad8e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000895.fa
@@ -0,0 +1,30 @@
+>PROKKA_01079
+MLRIAVPNKGALSESAREILTEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG
+TLDVGLTGRDLFCDAQVGDTAEEIMALGFGRSVFRLAAPVGSFTSAEQLAGKRIATSYDG
+LLSDYLARTGLDATVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMEVFGEPILDSE
+AVLIGRAGERPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEAATAVTPGLESPTVSPL
+RDETMVAVRSMVRKPDANRVMDELYALGARGILISAIHAIRL
+>PROKKA_00798
+MLRIAVPNKGALSESAREILTEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG
+TLDVGLTGRDLFCDAQVGDTAEEIMALGFGRSVFRLAAPVGSFTSAEQLAGKRIATSYDG
+LLSDYLARTGLDATVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMEVFGEPILDSE
+AVLIGRAGERPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEAATAVTPGLESPTVSPL
+RDETMVAVRSMVRKPDANRVMDELYALGARGILISAIHAIRL
+>PROKKA_01819
+MLRIAVPNKGALAEAAREILQEAGYRQRRDSRELVLVDPENQVEFFYLRPRDIAVYVGQG
+TLDVGLTGRDLFRDAQVDGGAEEIMALGFGRSVFRLAAPVGAFSSEAELSGKRIATSYDG
+LLSAYLERTGLDAEVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMETFGESILDSE
+AVMIARVGARPEGLDVLLRRLKGVLVARRWVMIDYDVRRELLEQATAVTPGLESPTISPL
+RDESMVAVRSMVRKADANRAMDDLYALGARGILISAIHAIRL
+>PROKKA_01706
+MLRIAVPNKGALSESAREILIEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG
+TLDVGLTGRDLFRDARVGETAEEIMALGFGKSVFRLAAPVGSFTSAEELAGRRIATSYDG
+LLTEYLAESGLDARVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMETFGEPILDSE
+AIMIARVGARPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEQATAVTPGLESPTVSPL
+RDESMVAVRSMVRKADANRAMDDLYDLGARGILISAIHAIRL
+>PROKKA_01028
+MLRIAVPNKGALSESAREILTEAGYRQRRDSRELVLVDPENNVEFFYLRPRDIAVYVGQG
+TLDVGLTGRDLFCDAQVGDTAEEIMALGFGRSVFRLAAPVGSFTSAEQLAGKRIATSYDG
+LLSDYLARTGLDATVVHLDGAVESSVKLGVADAIADVVETGSTLRAAGMEVFGEPILDSE
+AVLIGRAGERPEGLDVLLRRLKGVLVARRWVMIDYDIRRDLLEAATAVTPGLESPTVSPL
+RDETMVAVRSMVRKPDANRVMDELYALGARGILISAIHAIRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000897.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000897.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6d8f3727ea4ecb1fc5415a0c70fa08baf8d2bf71
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000897.fa
@@ -0,0 +1,20 @@
+>PROKKA_01081
+MSISPPDDLVASVTFDDRGLVPAIAQQEGTGEVLMMAWMNEESLRATLETGWATYWSRSR
+GELWRKGETSGHLQRVRAVHADCDGDTLLLTVDQTGPACHTGTRTCFTGRELVMPPAAVD
+PEEAAR
+>PROKKA_00800
+MSISPPDDLVASVTFDDRGLVPAIAQQEGTGEVLMMAWMNAESLRATLETGWATYWSRSR
+GELWRKGETSGHLQRVRAVHADCDGDTLLLTVDQTGPACHTGTRTCFTGRELVMPPAAVD
+PEEAAR
+>PROKKA_01816
+MSISSHHDLVASLAFDDRGLVPAIAQQEGTGEVLMMAWMNAESLRLTLETGWATYWSRSR
+GELWRKGETSGHLQRVLAVHADCDADTLLLTVDQTGPACHTGTRSCFTDRLLAEPAAPAG
+DQAEGAGR
+>PROKKA_01704
+MSPSDVVADLPPLIFDERGLIPAIAQQHDSGEVLMMAWMNEESLRRTLEDGWATYWSRSR
+QEYWRKGETSGHLQRVLAVAADCDGDTLLLTVDQTGPACHTGTTSCFTDRRFAAPTAADE
+DPQTEDAEAVR
+>PROKKA_01030
+MSISPPDDLVASVTFDDRGLVPAIAQQEGTGEVLMMAWMNAESLRATLETGWATYWSRSR
+GELWRKGETSGHLQRVRAVHADCDGDTLLLTVDQTGPACHTGTRTCFTGRELVMPPAAVD
+PEEAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000899.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000899.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0e809f272ba4f1ab2c40a12af04f1f36623514de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000899.fa
@@ -0,0 +1,25 @@
+>PROKKA_01083
+MRRRTVVLAALAAGALVLLTAGRTWVTATGLSGGIASEATTSGGAAAPVATAMALVVMAG
+ALALTTARRLGAVIVGVLMALAGVVIASTSVTAALDPATTAAAAVADATGTTALAQDYAV
+TAWPWVAAAGGVLAALCGVVAALAGRGWRSSRRYEKAPAASEPGPAAAGEQPAQSAREAA
+QRRRVDQMDAWDELSRGNDPT
+>PROKKA_00802
+MRRRTVVLAALAAGGLVLLTAGRTWVTATGLSGGIASEATTSGGAAAPVATAMALVVMAG
+ALALTTARRLGAVIVGVLMALAGVVIASTSVTAALDPATTAAAAVADATGTTALAQDYAV
+TAWPWVAAAGGVLAALCGVVAALAGRGWRSSRRYEKAPAASEPGPAAAGEQPAQSAREAA
+QRRRVDQMDAWDELSRGNDPT
+>PROKKA_01814
+MRRRTVVLAALAAGSLVLLAAGQTWVVGSGLTGGLSEEATTSGGAAAPGATAMALVVLAG
+ALALTTARRVGVVVVGALLVLAGIVIVTGAAGAALDPAGTAASAVAEATGTTAAAGSYAV
+TAWPWVAVTGGVLAALCGAVAALAGRGWVSVRRYEKAEATDAAEPAAPGRAAAPGRTEAE
+RRRTEQMDAWDELSRGNDPT
+>PROKKA_01702
+MRRRWIVLAALLAGVLVLAATGQTWVTASGLEGSPVPQATAGGGRVAPVATALALVVMAG
+ALALTTARRVGVVLVGVLMTLAGVVIASTAVTAALDPVAAAAGAVSELTGTTAPAAAYAV
+SAWPWVSAAGGVMAAVLGVATLVVGPRWAASRRFESPATADEPAAAAPPSRHVDRMDAWD
+ELSRGEDPT
+>PROKKA_01032
+MRRRTVVLAALAAGGLVLLTAGRTWVTATGLSGGIASEATTSGGAAAPVATAMALVVMAG
+ALALTTARRLGAVIVGVLMALAGVVIASTSVTAALDPATTAAAAVADATGTTALAQDYAV
+TAWPWVAAAGGVLAALCGVVAALAGRGWRSSRRYEKAPAASEPGPAAAGEQPAQSAREAA
+QRRRVDQMDAWDELSRGNDPT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000906.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000906.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c06556dfcb1d5a110762b87b2d31c0fd810e33b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000906.fa
@@ -0,0 +1,50 @@
+>PROKKA_01090
+MADPRGFLKNRERVDRPTRPVPVRIMDFKDVYVRQDEAIVRTQAGRCMDCGIPFCHSGCP
+LGNLIPEWNDLVRRRRWDEAAARLHSTNNFPEVTGRICPAPCEDSCTLGINQPAVTIKQT
+EVAIAEQIFDNDWLEPVVPARLNGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDERLG
+GLLRLGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGVDLPWDQLKARFDAVIVATGAP
+VARELPVPGRGLDGIHLAMDYLVQSNRAVAGDEVPDQISAEGRHVVILGGGDTGADCIGT
+AHRQGAASVTTLAIGQQLPVERPVHQPWPTIPKVHQQTTADAEGGARAHLASTVEFLGDE
+HGRVRALRVAETEYREDGTRGPKAGTEREVQADLVLLALGFTGIEEGLLTQQLGVHVTRG
+LVARKDGYETDEPGVFACGDAGRGASLVVWAIAEGRACAQEVDESLERWSRLPHPVDPDD
+RGLVLG
+>PROKKA_00809
+MADPRGFLKNRERVERPTRPVPVRIMDFKDVYVRQDEAIVRTQAGRCMDCGIPFCHSGCP
+LGNLIPEWNDLVRRRRWDEAAARLHSTNNFPEVTGRICPAPCEDSCTLGINQPAVTIKQT
+EVAIAEQIFDNDWLEPVVPARLNGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDERLG
+GLLRLGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGVDLPWDQLKARFDAVIVATGAP
+VARELPVPGRGLDGIHLAMDYLVQSNRAVAGDEVPDQISAEGRHVVILGGGDTGADCIGT
+AHRQGAASVTTLAIGQQLPVERPVHQPWPTIPKVHQQTTADAEGGARAHLASTVEFLGDE
+HGRVRALRVAETEYREDGTRGPKAGTEREVQADLVLLALGFTGIEEGLLTQQLGVHVTRG
+LVARKDGYETDEPGVFACGDAGRGASLVVWAIAEGRACAQEVDESLERWSRLPHPVDPDD
+RGLVLG
+>PROKKA_01806
+MADPRGFLKHRERVARPSRPVPVRIMDFKDVHVRQDEAIVRTEASRCMDCGVPFCHAGCP
+LGNLIPEFNDLVYRDDWDEAGARLEATNNFPEFTGRICPAPCEASCVLGINQPAVSIKQV
+EQSIADHLFDAPSLTPHPPQRQNGLTVAVVGSGPAGLAAAQQLTRSGYTVVVYEKDEALG
+GLLRFGIPDFKLEKHLIDRRIAQMTEEGTRFRTGVRIGTDMSWEALQRRYDAVVLATGAP
+VGRELPLPGRGLDGIHLAMDYLVPVNRRVAGGEPEPISAQGRHVVILGGGDTGADCIGTA
+HRQGAASVTTLAIGRRPPEQRPEHQPWPTVPTLFEVASAHAEGGERTYLASTVEFLGDAE
+GRVRALKVAETEIRADGTRGPRAGTEHEIPADLVLLALGFTGADLDELVDRSAVSLERGL
+VVRDETYATQAPGVFACGDVSRGASLVVWAIAEGRAVAAEVDRFLTGDTMLPAPVRPSDH
+GFVLR
+>PROKKA_01695
+MADPRGFLKNRERVERPTRPVPVRIMDFKDVYVRQDEAVVRTQASRCMDCGIPFCHSGCP
+LGNLIPEWNDLVRRGRWEDAAARLHSTNNFPEVTGRICPAPCEDACTLGINQPAVTIKQT
+EVAIAEQIFDHDWLEPVVPTRINGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDDRPG
+GLLRYGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGRDLAWDALKARFDAVIVATGAP
+VGRELPVPGRGLDGIHLAMDYLVQSNHATAGDDVPGQITAEGRHVVVLGGGDTGADCIGT
+AHRQGAASVTTLAIGQQLPVDRPVHQPWPTVPKVHQMTTADAEGGQREHLASTVEFLGDE
+NGRVRALRVAETEYRADGTRGPKAGTEREVKADLVLLALGFTGVEEEALTAQLAVRTERG
+LVARAGTYETDEPGVFVCGDAGRGASLVVWAIAEGRACAQAVDESLESWSRLPHPVDPTD
+RGLVLG
+>PROKKA_01039
+MADPRGFLKNRERVERPTRPVPVRIMDFKDVYVRQDEAIVRTQAGRCMDCGIPFCHSGCP
+LGNLIPEWNDLVRRGRWDEAAARLHSTNNFPEVTGRICPAPCEDSCTLGINQPAVTIKQT
+EVAIAEQIFDNDWLEPVVPARLNGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDERLG
+GLLRLGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGVDLPWDQLKARFDAVIVATGAP
+VARELPVPGRGLDGIHLAMDYLVQSNRAVAGDEVPDQISAEGRHVVILGGGDTGADCIGT
+AHRQGAASVTTLAIGQQLPVERPVHQPWPTIPKVHQQTTADAEGGARAHLASTVEFLGDE
+HGRVRALRVAETEYREDGTRGPKAGTEREVQADLVLLALGFTGIEEGLLTQQLGVHVTRG
+LVARKDGYETDEPGVFACGDAGRGASLVVWAIAEGRACAQEVDESLERWSRLPHPVDPDD
+RGLVLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000908.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000908.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28cff291b87f7800cad4465e9f9ebeda8d7775ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000908.fa
@@ -0,0 +1,25 @@
+>PROKKA_01092
+MSTLTPPEETGLRAVVAEDETLIRLDLVEVLTGAGYRVVAEAGDGRAAVEAVREHRPDIV
+VMDVKMPVMDGIAAAGEIAGERLAPVVMLTAFSQRELVERARTAGAMAYVVKPFTEADLV
+PAIELAVARFDELRSLEAEVRDLGDRLETRKIVDRAKALLQERMRLTEAESFRWIQKTSM
+DRRLTMREVAQAVIDQVG
+>PROKKA_00811
+MSTLTPPEETGLRAVVAEDETLIRLDLVEVLTGAGYRVVAEAGDGRAAVEAVREHRPDIV
+VMDVKMPVMDGIAAAGEIAGERLAPVVMLTAFSQRELVERARTAGAMAYVVKPFTEADLV
+PAIELAVARFDELRSLEAEVRDLGDRLETRKIVDRAKALLQERMRLTEAESFRWIQKTSM
+DRRLTMREVAQAVIDQVG
+>PROKKA_01804
+MPMTTPAEGTGLRAVVAEDETLIRLDLVEVLTGAGYEVVAEAGDGAAAVAAVREQRPDIV
+VMDVQMPVMDGIAAASEIAQDRLAPVVMLTAFSQRDLVERARTAGAMAYVVKPFTEHDLV
+PAVELAVARFEELRSLESEVRDLGDRLETRKLVDRAKSVLQDRLRLSEAESFRWIQKTSM
+DRRLTMREVAQAVIDQVR
+>PROKKA_01693
+MTIPAESADPTAGLRVVVAEDEALIRLDVVETLTHAGHTVVAEVGDGQAAVAAVREHRPD
+IVVMDVMMPVMDGIAAAGEIAAERLAPVVMLTAFSQRDLVERASQVGAMAYVVKPFTEKD
+LLPAMELAVARFDQLRGLEEEVRGLEDRLATRKLVDRAKSLLQAHMGLSEAESFRWIQKT
+SMDRRLTMREVAQTVVDQIGA
+>PROKKA_01041
+MSTLTPPEETGLRAVVAEDETLIRLDLVEVLTGAGYRVVAEAGDGRAAVEAVREHRPDIV
+VMDVKMPVMDGIAAAGEIAGERLAPVVMLTAFSQRELVERARTAGAMAYVVKPFTEADLV
+PAIELAVARFDELRSLEAEVRDLGDRLETRKIVDRAKALLQERMRLTEAESFRWIQKTSM
+DRRLTMREVAQAVIDQVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000909.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000909.fa
new file mode 100644
index 0000000000000000000000000000000000000000..314532499e0093f1cac0b88abf812998e50709ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000909.fa
@@ -0,0 +1,77 @@
+>PROKKA_01094
+MLLTSLLLTLLSVVAAVPASRALGRDAGWVLAAPLLAAAGVLIAAWTGDVRTEHHPWIPA
+VGVDLDLRLNGLALVFAMIVLVIGAAILAYSSRYLSRDRTESRPGSFYLLMTAFAASMLL
+LVLADNIVVLFVAWEFTSFTSFFLIGRSGDHARDPAIRTLLVTVGGGLALLAAVALMAVR
+TGTASLSGVLASDVWSEAGFTTTVAVLLAVAAFTKSAQFPFQAWLPDSMVAISPVSAYLH
+AAAMVKAGIFLLLVFSPVLAGNPVWSALLIGSGLITALLGAVSAIRRHDLKGLLAYSTMS
+QLGLLVTAIGIGTPVALTAAIVHTVAHALFKSALFMLIGVVDHEAGTRDLRELAARHVRM
+PVTGTAIAVAALSMAGIPPLFGFISKEGLVEAALGTPGPAWLPVLVTAGIALTSVFTVAY
+SGRLVLGALGLWGPSPDGAAHSWPTGREDEVHEASATFWGVPVLAAAAGVALGLLPGVLD
+TPVSYAAEAASGAEVHAHLALWHGVNTALLVSAAIIVLGLLLVALRRPVERVASHAALPF
+SALDAVDEVRHRLIGVGAVVSRASGTLAPRPHLLIPALVLGLLAVAGVATIEDLPAVVGQ
+PSRWHDWVLVVLVGAGVIATIRAKTRIAAMVVVGVVGFGMTLWFLTLGAVDVALTQLMVE
+VLTVCVMVLLLRRLPARFSDEPTPRRMQAVLAASVAGVAATLGVLAFTGRSSMSEIAHFY
+LTQSYAQAGGTNVVNVILVDFRAVDTWGEMTVLGATALTIAALLLNRRPTPPQPSAVDMR
+SPLAHVRENLVHIRVFGRVFGVLIILLSAFLLLRGHYEPGGGFIAALVAGAGYALLYLAA
+DSDTAPELRWPYLAFIGSGIAVGTATGIVGYLTGKGFLGAAGVKVLDYGLSTTLAFDMGV
+YLAVIGLIVAAFSLLGPERPGEDPLRASSRDPGVAPAAPSSDPSAPTTTTAREEVTR
+>PROKKA_00813
+MLLTSLLLTLLSVVAAVPASRVLGRDAGWVLAAPLLAAAGVLIAAWTGDVRTEHHPWIPA
+VGVDLDLRLNGLALVFAMIVLVIGAAILAYSSRYLSRDRTESRPGSFYLLMTAFAASMLL
+LVLADNIVVLFVAWEFTSFTSFFLIGRSGDHARDPAIRTLLVTVGGGLALLAAVALMAVR
+TGTASLSGVLASDVWSEAGFTTTVAVLLAVAAFTKSAQFPFQAWLPDSMVAISPVSAYLH
+AAAMVKAGIFLLLVFSPVLAGNPVWSALLIGSGLITALLGAVSAIRRHDLKGLLAYSTMS
+QLGLLVTAIGIGTPVALTAAIVHTVAHALFKSALFMLIGVVDHEAGTRDLRELAARHVRM
+PVTGTAIAVAALSMAGIPPLFGFISKEGLVEAALGTPGPAWLPVLVTAGIALTSVFTVAY
+SGRLVLGALGLWGPSPDGAAHSWPTGREDEVHEAPATFWGVPVLAAAAGVALGLLPGVLD
+TPVSYAAEAASGAEVHAHLALWHGVNTALLVSAAIIVLGLLLVALRRPVERVASHAALPF
+SALDAVDEVRHRLIGVGAVVSRASGTLAPRPHLLIPALVLGLLAVAGVATIEDLPAVVGQ
+PSRWHDWVLVVLVGAGVIATIRAKTRIAAMVVVGVVGFGMTLWFLTLGAVDVALTQLMVE
+VLTVCVMVLLLRRLPARFSDEPTPRRMQAVLAASVAGVAATLGVLAFTGRSSMSEIAHFY
+LTQSYAQAGGTNVVNVILVDFRAVDTWGEMTVLGATALTIAALLLNRRPTPPQPSAVDMR
+SPLAHVRENLVHIRVFGRVFGVLIILLSAFLLLRGHYEPGGGFIAALVAGAGYALLYLAA
+DSDTAPELRWPYLAFIGSGIAVGTATGIVGYLTGKGFLGAAGVKVLDYGLSTTLAFDMGV
+YLAVIGLIVAAFSLLGPERPGEDPLRASSRDPGVAPAAPSSDPSAPTTTTAREEVTR
+>PROKKA_01801
+MDEARHGLVRLGALVDRASGSVAPRVHLLIPACVLGAFALAGVFTVDDLPAVVGTPSRWH
+DWALVVLVGAGVVATIRAKTRISAMVVVGVVGFGVTLWFFTLGAVDVALTQLLVEVLTVC
+VMVLLLRRLPGRFRDEEAPRRVQAVVAATIAGVAATVGVLAFTGRSEMSEIAHFYLTQTY
+AQAGGVNVVNVILVDFRALDTLGEMTVLGATGLTVAALLLNRRPAPPQRSAVDLRSPLAH
+VRENLVHIRVFGRVFGVLIIALSVLLLLRGHYEPGGGFIAALVAGAGYALLYLAADHDTD
+RRLQWPYLTLIGGGIALGALTGVAGYLTGKGFLGAAGVKILGYGLSTTLAFDLGVYLAVL
+GLIVAAFSLLGPERSETEAGAEPDPTSPIADPAAEQTTGQTTEPTTAPGTAPTPAAAREE
+TSR
+>PROKKA_01691
+MLLTSLLLTLLAVVLAAPLGRTLGRDAGWVLALPLLTSAGALVSARAGGGGETVVERRPW
+IPSLGAHLDLRLDGLAFVFALLVLVVGAGILAYSSRYLPRDRDEARAGSFYTLMTAFAAS
+MLLLVLADNLVVLFVAWEFTSFASFLLIARSGDHARRPAIRTLLVTVGGGLCLLAAVALT
+AARTGTASLSGALASDAWADPGFAAPVAALLAVAAFTKSAQFPFQSWLPDSMVAISPVSA
+YLHAAAMVKAGIYLLLVFSPVLAGTPVWSALLIGSGLTTALLGAVSAIRRHDLKGLLAYS
+TMSQLGLLVTAIGVGTPTALAAAVVHTVAHALFKSTLFMLIGVVDHEAGTRDLRDLAARH
+VRMPVTGAAIAVAAASMAGLPPLLGFVSKEGLLDAALGAQGPAWLPGLVTAGIALTSVFT
+VAYSGRLVLGALGVWGTAPAGAADMWSAGRGEDVHEAPAAFWAVPVLGVVVTLVLGLVPG
+VLDEAVAAAATAAAGAPVHAHLALWHGVTPALLVSAGVIAAGLALVAARRPVERVASHAG
+LPFSGLGVVDGILRGAVSLGAAVSRVSGGIAPRAHLLMPALVLGAFAVAGVVASPDLPAV
+VGQPSRWHDWALVALVGVGVAATLRARTRIAAMVVVGTVGFGVTLWFFTLGAVDVALTQL
+MVEVLTVCVMVLLLRRLPARFSAESTPHRAGAVAAAVIAGVASTLSVLAFTGRREISDIA
+QYYLDRTYPDAGGHNVVNVILVDFRALDTLGEMTVLGVTGLTVAALLMNRRPAPPQPSAV
+DVRSPLAAVHENLVYARTFGRALGPIILVLSVLLLLRGHYEPGGGFIAALVGGAGYALLH
+LSADTDDEPRLRWPYLALIGGGVTLGTVAGLAGYLTGKGFLGSASVKVLGYSLGTTLAFD
+MGVYLAVLGLIVAAFRLLGPDNATADDAAPAPTTGGESAREEAAR
+>PROKKA_01043
+MLLTSLLLTLLSVVAAVPASRVLGRDAGWVLAAPLLAAAGVLIAAWTGDVRTEHHPWIPA
+VGVDLDLRLNGLALVFAMIVLVIGAAILAYSSRYLSRDRTESRPGSFYLLMTAFAASMLL
+LVLADNIVVLFVAWEFTSFTSFFLIGRSGDHARDPAIRTLLVTVGGGLALLAAVALMAVR
+TGTASLSGVLASDVWSEAGFTTTVAVLLAVAAFTKSAQFPFQAWLPDSMVAISPVSAYLH
+AAAMVKAGIFLLLVFSPVLAGNPVWSALLIGSGLITALLGAVSAIRRHDLKGLLAYSTMS
+QLGLLVTAIGIGTPVALTAAIVHTVAHALFKSALFMLIGVVDHEAGTRDLRELAARHVRM
+PVTGTAIAVAALSMAGIPPLFGFISKEGLVEAALGTPGPAWLPVLVTAGIALTSVFTVAY
+SGRLVLGALGLWGPSPDGAAHSWPTGREDEVHEAPATFWGVPVLAAAAGVALGLLPGVLD
+TPVSYAAEAASGAEVHAHLALLHGVNTALLVSAAIIVLGLLLVALRRPVERVASHAALPF
+SALDAVDEVRHRLIGVGAVVSRASGTLAPRPHLLIPALVLGLLAVAGVATIEDLPAVVGQ
+PSRWHDWVLVVLVGAGVIATIRAKTRIAAMVVVGVVGFGMTLWFLTLGAVDVALTQLMVE
+VLTVCVMVLLLRRLPARFSDEPTPRRMQAVLAASVAGVAATLGVLAFTGRSSMSEIAHFY
+LTQSYAQAGGTNVVNVILVDFRAVDTWGEMTVLGATALTIAALLLNRRPTPPQPSAVDMR
+SPLAHVRENLVHIRVFGRVFGVLIILLSAFLLLRGHYEPGGGFIAALVAGAGYALLYLAA
+DSDTAPELRWPYLAFIGSGIAVGTATGIVGYLTGKGFLGAAGVKVLDYGLSTTLAFDMGV
+YLAVIGLIVAAFSLLGPERPGEDPLRASSRDPGVAPAAPSSDPSAPTTTTAREEVTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000914.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000914.fa
new file mode 100644
index 0000000000000000000000000000000000000000..63a98b40332e564e5ba7adedcb7100aa6b4f1cae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000914.fa
@@ -0,0 +1,20 @@
+>PROKKA_01099
+MDVVLTAAGSVLVVIGALAFVTAGLGLIRFPDPYTRVSAVGTAGGVGMILIVVGALLLAP
+GVAAFVKVALIVVLQLGSASVATMALGRSAYLTGVPMNPGHYDELAEDTPGREHGEPAPR
+APDEV
+>PROKKA_00818
+MDVVLTAAGSVLVVIGALAFVTAGLGLIRFPDPYTRVSAVGTAGGVGMILIVVGALLLAP
+GVAAFVKVALIVVLQLGSASVATMALGRSAYLTGVPMNPGHYDELAEDTPGREHGEPAPR
+APDEV
+>PROKKA_01796
+MDLVLTVIGSVLVVAGALVFVTAGLGLIRFPDPYTRISATGTAGGVGMILIVVGGLVLAP
+SVANVVKVALIVVLQLGSAAVATMALGRSAYLTGVPMNPGHYDELAEDTPGREHGEPAPR
+TPDAS
+>PROKKA_01686
+MDLVMTVAGSVLAVAGAVVFLGAAVGLIRFPDPYTRISATGTAGGVGMILIVTGGLLLMP
+SVANLVKVVLIVVLQLGTAAIATMALGRSAYLTGVPMNLAHYDELAEDTPGREHGEPAPR
+HPED
+>PROKKA_01048
+MDVVLTAAGSVLVVIGALAFVTAGLGLIRFPDPYTRVSAVGTAGGVGMILIVVGALLLAP
+GVAAFVKVALIVVLQLGSASVATMALGRSAYLTGVPMNPGHYDELAEDTPGREGGRAAPR
+LPDMD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000916.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000916.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3560fe90e15f95ccb4965aadcbb569e078ee52c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000916.fa
@@ -0,0 +1,85 @@
+>PROKKA_01101
+MAADPTPEAPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR
+PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTLEGYEA
+DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVKAKYG
+VAPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLKQYGDLDGVLAHAHEITGKKGEALR
+EHLEDVRRNRRLNALVRDLDLPIGLETMRLEMPEREPVEELFDALQFHRIRERVFEVFGE
+RVGEDAPPPEVEAAPEFTEATTAEDVRAFLAAEAGNLLGVHVDVEGPALLPRRKVPVPGT
+FGTPVGVALVGEHAGLHVTLDGDAPDPALVAAVREALGEGGLAKAVHDLKRTLKALAAPT
+EGDGLGPDAALDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLTAPRESAQQRAQGS
+FDLDGGQAAAERADRAADAVRAAWVVRRLSTQFTPQVLDRGAQRLLQELEIPLSRLLARM
+ELTGIAVDVDALTGLREDFTDAADAAKESAWASVAEETGGMQVNLGSPKQLQEVLFERLN
+MPRTRKTKTGYSTDVDSLQDLLEQTRHPFLENLMAHRDATKLRQTVEGLLETVAPDGRIH
+TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIREVFVADEVAGEQAVLLSADYSQIEMR
+IMAHLSEDEGLIQAFREGEDLHSFVGSQVFGVDPDDVTAEQRAKVKAMSYGLAYGLSSFG
+LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARQDGYTSTIEGRRRYLPDLSSDN
+RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLEEHGLASRLLLQVHDELILEVPAAE
+LEKATALLKERMGRAAELSVPLDVHVGQGRSWHDAAH
+>PROKKA_00820
+MAADPTPEAPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR
+PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTLEGYEA
+DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVMAKYG
+VAPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLKQYGDLDGVLAHAHEITGKKGEALR
+EHLEDVRRNRRLNALVRDLDLPIGLEAMRLEMPEREPVEELFDALQFNRIRERVFEVFGE
+RVGEDAPPPEAEAAPEFTEATTAEDVRSFLAAEAGNLLGVHVDVEGPALLPRRKVPVPGT
+FGTPVGVALVGEHAGLHVTLDGDAPDPALVAAVREALGEGGLAKAVHDLKRTLKALAAPT
+EGDGLGRDAALDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLTAPREPAQQRAQGT
+FDLDGGQAAAERADRAADAVRAAWVVRRLSTQFTPQVLDRGAQRLLQELEIPLSRLLARM
+ELTGIAVDVDALTGLREDFTDAADAAKESAWASVAEETGGMQVNLGSPKQLQEVLFERLN
+MPRTRKTKTGYSTDVDSLQDLLEQTRHPFLENLMAHRDATKLRQTVEGLLETVAPDGRIH
+TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIREVFVADEVAGEQAVLLSADYSQIEMR
+IMAHLSEDEGLIQAFREGEDLHSFVGSQVFGVDPDDVTAEQRAKVKAMSYGLAYGLSSFG
+LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARQDGYTSTIEGRRRYLPDLSSDN
+RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLEEHGLASRLLLQVHDELILEVPAAE
+LEQATALLKERMGRAAELSVPLDVHVGRGRSWHDAAH
+>PROKKA_01794
+MAADPTPEDPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR
+PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTITLEGYEA
+DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVMAKYG
+VSPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLTQYGDLDGVLAHADEIKGKKGEALR
+AHLDDVRRNRRLNALVRDLDLPIGLEAMALEMPEREPVEELFDALQFNRIRERVFEVFSE
+RIGETAPAAQVEEAPEFTEAATAQDVADFLAAEAGNLLGVHVDVEGPALLPKRKVPVPGT
+FGTAVGVALVGEHAGLHVSLDADAPDPALLAALREALGEGGLSKAVHDLKRVLKAIAEPA
+EATALEAGTPLDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLAAPREPAEADAQGA
+FDLDGGAAAAERAARAADAVRAAWVVRRLSVLFTPQVLERGAQRLLQELEIPLARLLARI
+ELTGIAVDAQALETLRADFSEAAAAAQESAWASVAEETGGMKVNLGSPKQLQEVLFEHLD
+MPRTRKTKTGWSTDVDSLQDLLEQTRHPFLENLMRHRDATKLRQTVEGLLETVAPDGRIH
+TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIREVFVADRVAGEDAVLLSADYSQIEMR
+IMAHLSEDAGLIQAFREGEDLHSFVGSQVFGVAPDEVSSEQRAKVKAMSYGLAYGLSSFG
+LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARRDGYTSTIEGRRRYLPDLSSDN
+RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLAEHGMASRLLLQVHDELILEVPAAE
+LEQATALLQERMGRAAELAVPLDVHVGQGRSWHDAAH
+>PROKKA_01684
+MGENSTEARPRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTSMLLTMIRQQAP
+THVAVAFDLSGPTFRSAEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTKEDFEAD
+DIVATLSAQAEAQGWDVCVVSGDRDAFQLISERTQVLYPKKGVSDIPPMTAADVEAKYGV
+RPEQYPELAALVGESADNLPGVPGVGPGFAAKWLQKYGDLDGVLAHADEITGKKGEALRA
+HLDDVRRNRRLNALVRDLDLDVSLDAMELTMPEREVVEELFDALQFQRIRERVFEVFAER
+LGSAAPAAPVAEAPAAVLAATADDVHAFVSAHAGTLLGLHVEIDGPDLLPKRKVPVPGTF
+GTPVGLALAAEDAALYVDLTDADADPGLVAALGDLLAEDGAAKAVHDLKRTLKAIAVPTG
+PTALPADTSLHGVVDDVALSAYLIQPDRRDTDLATLSQAHLQEPLEAPESAAAGAQGAFD
+LDGAQEEAERTARAARAARSAWVVRRLSQAFTPQVLERGAQRLLQEMEIPLARLLARMEL
+AGIAVDGDALSALLADFTDRAEAAKESAWASVAEETGGMKVNLGSPKQLQEVLFEHLDMP
+KTRKTKTGWSTDVDSLQDLLEQTQHPFLENLMAHRDATKLRQTVEGLRETVAPDGRIHTT
+YSQTVAATGRLSSLHPNLQNIPVRTEAGRRIREAFVAAPVDGEPAELLSADYSQIEMRIM
+AHLSEDAGLIEAFNSGEDLHSFVGSQVFGVDPDDVTSEQRSKVKAMSYGLAYGLSSFGLS
+KQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARRDGFTSTIEGRRRYLPDLTSDNRQ
+LRDMAERAALNAPIQGSAADIIKRAMLDVQAGLVEQGLRSRLLLQVHDELILEVPASELD
+AATALLQERMGRAADLSVPLDVHVGHGGTWHAAAH
+>PROKKA_01050
+MAADPTPEAPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR
+PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTLEGYEA
+DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVKAKYG
+VAPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLKQYGDLDGVLAHAHEITGKKGEALR
+EHLEDVRRNRRLNALVRDLDLPIGLEAMRLEMPEREPVEELFDALQFNRIRERVFEVFGE
+RVGEDAPPPEVEAAPEFTEATTAEDVRAFLAAEAGTLLGVHVDVEGPALLPRRKVPVPGT
+FGTPVGVALVGEHAGLHVSLDGDAPDPALVGAVREALGEGGLAKAVHDLKRTLKALAAPT
+EGDGLGRDAALDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLTAPREPAQQRAQGT
+FDLDGGQAAAERADRAADAVRAAWVVRRLSTQFTPQVLDRGAQRLLQELEIPLSRLLARM
+ELTGIAVDVDALTGLREDFTVAADAAKESAWASVAEETGGMQVNLGSPKQLQDVLFERLN
+MPRTRKTKTGYSTDVDSLQDLLEQTRHPFLENLMAHRDATKLRQTVEGLLETVAPDGRIH
+TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIRGVFVADEVAGEQAVLLSADYSQIEMR
+IMAHLSEDEGLIQAFREGEDLHSFVGSQVFGVDPDDVTAEQRAKVKAMSYGLAYGLSSFG
+LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARQDGYTSTIEGRRRYLPDLSSDN
+RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLEEHGLASRLLLQVHDELILEVPAAE
+LEQATALLKERMGRAAELSVPLDVHVGRGRSWHDAAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000918.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000918.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca5970e429c184698cebe24d301a9e78b50ae2b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000918.fa
@@ -0,0 +1,37 @@
+>PROKKA_01104
+MSEPLPRGVTPDVAHGGLPDDLTAGVDFAALDRWPLPPEPDRQAHDAADLLLLDTLAGWI
+ASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDANLAAWRAAGRLGGEA
+GELERTATPEDAARGARTVLLPLPRSLDELDRLSRIVAAAADPGVVLLAGGRDKHMSPRM
+NAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTPRPPEEADRDVPGVGSLHLVAHAGAFG
+GAAADPGSRLLLASLADDPRPPGRLVDLGCGNGLLSVGAARLWPHVTVLATDQSAVAVAS
+TLATARANRVADRVRAVRDDALATWPDGTEECVLLNPPFHDGNAVDPSVAHRLVAAAARV
+LEPGGRLWCVWNSHLRYRPVLEDLVGPTRQTARDRTFTVTVSERR
+>PROKKA_00823
+MSEPLPRGVTPDVARGGLPDDLTAGVDFAALDRWPLPTEPDRQAHDTADLLLLDTLAGWI
+ASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDANLAAWRAAGRLGGET
+GELERTATPEEAARGARTVLLPLPRSLDELDRLSRIVSAAADPGVVLLAGGRDKHMSPRM
+NAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTARPPEEADRDVPGVGRLHLVAHAGTFG
+GAAADPGSRLLLASLADDPRPPGRVVDLGCGNGLLSVGAARLWPHVTVVATDQSAVAVAS
+TLATARANRVADRVRAVRDDALATWPDGEEECVLLNPPFHDGNAVDPSVAHRLVAAAARV
+LEPGGRLWCVWNSHLRYRSVLEDLVGPTRQTARDRTFTVTVSERR
+>PROKKA_01790
+MDLGCGNGLLGVGAARLWPHVRVLATDQSAVAVASTLATARANGVADRLEAVRDDALAGR
+PDASEECILLNPPFHDGNAVDPAVAHRLVAEAARVLAPGGRLWCVWNSHLRHRPVLEAEV
+GPTRQVARDRTFTVTVSTRR
+>PROKKA_01681
+MDAIAQTPPRDPGPARLTATELVTPDAAGRGLPRDWTAEFPFERLGRWPLPESRERQAHD
+AADLLLVDTLAGWTADGRVPGPVAVLHDQHGAVSLPLLARGLNVRLGLDEASAARSVERN
+LDLFRDADGALPAGWGRLTVGGVDAATLADARTVLLLLPRALDALHLTAARIAVHAAPDV
+LVLGAGRDKHMTPSMNDVLARSFAAVVPGRGRSKSRVITAARPVDDATEPAPRRAQHRLG
+RLGAVTLVGGWATFGGAAADPGSLLLAGTLADRAPALPVPAPHRMRTDSGLGVDIPWATR
+AGAPDVVDAGSGNGMLSVVAARVWPEAAVLASDQSADAVASSAATAEANGLAERITAVQD
+DALGALPDASVRAVLLNPPFHDGTAVDPTVAHRMIEAAGRILAPGGELWCVWNSHLRHRP
+VLETAVGPTRQVARNRTFTVTVSTRR
+>PROKKA_01053
+MSEPLPRGVTPDVARGGLPDDLTAGVDFAALDRWPLPTEPDRQAHDAADLLLLDTLAGWI
+ASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDANLAAWRAAGRLGGET
+GELERTATPEEAARGARTVLLPLPRSLDELDRLSRIVSAAADPGVVLLAGGRDKHMSPRM
+NAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTARPPEEADRDVPGVGRLHLVAHAGTFG
+GAAADPGSRLLLASLADDPRPPGRVVDLGCGNGLLSVGAARLWPHVTVVATDQSAVAVAS
+TLATARANRVADRVRAVRDDALATWPDGEEECVLLNPPFHDGNAVDPSVAHRLVAAAARV
+LEPGGRLWCVWNSHLRYRSVLEDLVGPTRQTARDRTFTVTVSERR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000921.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000921.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ae026bd87451234cf419e9ce74da26bd32371756
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000921.fa
@@ -0,0 +1,65 @@
+>PROKKA_01108
+MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW
+LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK
+DSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGAEMDRDV
+LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG
+QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDRLLEAQRLRMRTTY
+DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE
+GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII
+RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT
+SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRI
+ADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSLDRAPATGEGAEAPAVDPASL
+PAKDLADLIEQMSQQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ
+>PROKKA_00827
+MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW
+LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK
+DSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGAEMDRDV
+LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG
+QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDKLLEAQRLRMRTTY
+DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE
+GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII
+RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT
+SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRI
+ADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSLDRDATTGEGTEAPAVDPASL
+PAKDLADLIEQMSKQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ
+>PROKKA_01785
+MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW
+LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK
+DSSVNEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGEEMDRDV
+LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG
+QVVREETEMYIFPASHYVAGDERMGRAVTAIEDELRERLQELESQDRLLEAQRLRMRTTY
+DLEMMQQMGYCNGIENYSRHIDGRPDGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE
+GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII
+RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLDAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT
+SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIEETERRRAVQIAYNEEHGIDPQPLRKRI
+ADITDQLAREDADTADFLKGMGGVKSGFDYGMGHRGLSSLDREEGQERAGGGPAVDAASL
+PAKDLADLIEQMSLQMHQAAADLQFELAARLRDEVGELKKELRQMRREQ
+>PROKKA_01677
+MSLAKQINRVVAPFEVVSPYQPSGDQPTAIAEIAERVQAGEKDVVLMGATGTGKSATTAW
+VIEQLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK
+DSSINEEVERLRHSATNALLTRRDVVVVATVSCIYGLGTPEEYIAQMVTLRRGQEMDRDA
+LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEVESIQTLHPLTG
+QVVREEEEMYIFPASHYVAGDERMGRAIATIEDELRERLQELESQDKLLEAQRLRMRTTY
+DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE
+GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGQYELSQADGVVEQII
+RPTGLVDPTVVVKPTQGQIDDLLEQIRTRTEKDERVLVTTLTKRMAEDLTEYLLEAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVSILDADKEGFLRSTT
+SLIQTIGRAARNVSGEVHMYADRVTDSMRRAIEETERRREVQIRYNAEHGIDPQPLRKKI
+ADITDALAREDADSADFLKGMGGVKAGFDYGMGHRGLGSLDHEPPAGEVPSGSPAVDPAA
+LPAKDLAQLIEQMSAQMHQAAADLQFELAARLRDEIGDLKKELRQMKREQ
+>PROKKA_01057
+MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW
+LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK
+DSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGAEMDRDV
+LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG
+QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDKLLEAQRLRMRTTY
+DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE
+GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII
+RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT
+SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRI
+ADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSLDRDATTGEGTEAPAVDPASL
+PAKDLADLIEQMSKQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000922.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000922.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc8b8bf7e621d74e84c082dfb17b3595fed56812
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000922.fa
@@ -0,0 +1,25 @@
+>PROKKA_01109
+MSAAPPVAAVIADIVGSRALPDRDRAQEQILAAFAAAEQDVPPLRPAWASVGDEFQALHR
+TWPDALRLTVRVTLALPPGLDLRFGIGLGQRRALDAGGDGIEDGPAWYRAREAVERAHER
+AVGAATAFRAADPSLTAAVDGLVLLRDHVLGRLKARERRIAAALLGGATQAEAARAERIT
+QSAVSQAVARSGIDRLLELDAELAAAATEVAP
+>PROKKA_00828
+MSAAPPVAAVIADIVGSRALPDRERAQEQILAAFAAAEQDVPPLRPAWASVGDEFQALHR
+TWPDALRLTVRVTLALPPGLDLRFGIGLGQRRALDAGGDGIEDGTAWYRAREAVEHAHER
+AAGAATAFRAADPSLTAAVDGLALLRDHVLGRLKARERRIAAALLGGATQAEAARAERIT
+QSAVSQTVARSGIGRLLELDAELAAAATEVAP
+>PROKKA_01783
+MTRAPQAAAVIADIVGSRRLPDREAAQEQILAAFAVAEKDVPPLRAAWATVGDEFQALHG
+VWPQAVRAVVRVSLALPPGLELRFGIGVGERRSLDDGAGDRIEDGTAWYRARAAVERAHA
+RADGAATAFVAADPSLTAAVDGVLLLRDHVLGRLKARERRLAAALLGGATQTQAARAERI
+TQSAVSQAVTRSGIDRLLELDAALAEAAAGRPGHAGAAGEGAGDEGDAG
+>PROKKA_01676
+MSLTDEGPVRGTAVIADIVGSRGLRDRAAAQEAILAAFAAAEEAVPARIPAWATVGDEFQ
+ALHADWAAAVRATLRVAVALPEGVELRFGLGDGVHREVTGAADDDGRPILDGSAWHRARE
+ALEAAEHRTRGLAGAYRGPDADLTAAVDGQLLVRDHVLRRLKARERRIAAALLAGRTQAE
+TATAERITQGAVSQAVARSGVRELLALDAALGALPGAGRGAKATAEEDRP
+>PROKKA_01058
+MSAAPPVAAVIADIVGSRALPDRERAQEQILAAFAAAEQDVPPLRPAWASVGDEFQALHR
+TWPDALRLTVRVTLALPPGLDLRFGIGLGQRRALDAGGDGIEDGTAWYRAREAVEHAHER
+AAGAATAFRAADPSLTAAVDGLALLRDHVLGRLKARERRIAAALLGGATQAEAARAERIT
+QSAVSQTVARSGIGRLLELDAELAAAATEVAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000924.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000924.fa
new file mode 100644
index 0000000000000000000000000000000000000000..794c4a82e496cf1f1f9a67cbd210a2ab5339ff16
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000924.fa
@@ -0,0 +1,50 @@
+>PROKKA_01113
+MAGDPRGFAPLEPARHRVGERTELYDGTVTVDHWFSVPIDHALGLAEAEAQDAAGTGVGP
+HGRGTLTVFAREIRAKDDPEGERPWALYLQGGPGSAGPRPARLSGWLGALAESHRVLLLD
+QRGTGRSTPATVATLTAPGAFATDEARAEHLVHLRAPSIVRDAEMLRLALGAGPWTTLGQ
+SFGGFCTLSYLSFHPEGLQRSLVTGGLAPLTGHADRVYRATYARMRARTEEFFDRHPADR
+DAWSEAVGLIRAAEAAGAPIPLPGGGPLTVGRAQGLGMLLGGNTRVDRLHWVLAEAVDRT
+GPAPRLSETFLAAVADQDDRLVNPLYTVLHEAIYAQPADLAGGRADTGWSASRMLAEHPD
+FDPEATTVPLPTGEHVMPWSVEVDPRLRPLAGTARLLAERTQWGPLYDVAALAQNTVPVA
+AAVYADDVYVDRDLSLETARRVRGLQVWETDAFHHDGIADDGPAILERLLAMTAPDGAGT
+TTAPDPVD
+>PROKKA_00832
+MAGDPRGFAPLEPARHRVGERTELYDGTVTVDHWFSVPIDHALGLAEAEAQDAAGTGVGP
+HGRGTLTVFAREIRAKDDPEGERPWALYLQGGPGSAGPRPARLSGWLGALAESHRVLLLD
+QRATGRSTPATVATLTAPGAFATDEARAEHLVHLRAPSIVRDAEMLRLALGAGPWTTLGQ
+SFGGFCTLSYLSFHPEGLQRSLVTGGLAPLTGHADRVYRATYARMRARTEEFFDRHPADR
+DAWSEAVGLIRAAEAAGAPIPLPGGGPLTVGRAQGLGMLLGGNTRVDRLHWVLAEAVDRT
+GPAPRLSETFLAAVADQDDRLVNPLYTVLHEAIYAQPADLAGGRADTGWSASRMLAEHPD
+FDPEATTVPLPTGEHVMPWSVEVDPRLRPLAGTARLLAERTQWGPLYDVAALAQNTVPVA
+AAVYADDVYVDRDLSLETARRVRGLQVWETDAFHHDGIADDGPAILERLLAMTAPDGAGT
+TTASDPVN
+>PROKKA_01780
+MSAPAPRVPGDPRGFAPLEPARHRVGERTELYDGTVAVDHWFTVPVDHALTLAEAEAQDA
+AGTGVGPHGRGTLTVFAREIRAAGDADGARPWALYLQGGPGGAGPRPARGGGWIGALASE
+HRVLLLDQRGTGRSTAASVAALTAPGAFASDEALAEHLVHLRAPSIVRDAEMVRLALGAA
+PWTTLGQSFGGFCTLTYLSFHPEGLRRCLVTGGLAPLTGHADRVYQATYARMRDRAHEFF
+ARHTGDRAAWAEAVALIRAAEQAGEPVRLPDGGLLTVARAQALGMLLGGNTRVDRLHWIL
+AEAVDRSGPAPRLSETFLAAVAEQNDRHVNPLYTVLHESIYAQPAELAGGRAATDWSAAR
+VLAEHPDFDPDAADAPLPTGEHVMPASLELDPHLRPLRGAARLLAERTDWGPLYDVEALA
+RNIVPVAAAVYTDDVYVDRDLSLETAGRVRGLRVWETDAFHHDGLADDGPAIVRRLLEMT
+GEGAAPAAAEGAERSDSAPAASETTTAPGPVD
+>PROKKA_01673
+MTRTGTGDAAFVPGDPRGFAPVGPAAHREGERTVLFDGTVAVDHWFTVPVDHALTLAEAL
+AQDAAGTGLGPGGRGTLEVFAREVRHPEDPEGERPWLLYLQGGPGSGGPRPARLGGWQCE
+LAQHHRLLLLDQRGTARSTPVTAATLAGLPDDAARAAYLTHLRAPQIVQDAEMIRVALGA
+PPWTTLGQSFGGFCTLSYLSWRAEGLERCLVTGGLAPLTGHADRVYRATTARMHARWQEF
+LERHPQDAGHWAEAVALIRAAQDDGDPYVLPDGTALTVGRAQQLGMLLGGNTRVDGLHWV
+LAEAVDRSGGEPRLSPGFLAAVAAQTTRAVNPLYAVLHEAIYAQPAALTDGRGATAWSAQ
+RVLAEHPDSSPAADPAPVPTGEHVLPWSFETEPELRALAGVAALLAAKDDWGALYDLDAL
+AANEVPVAAAVYTDDVYVDRDLSLETAARVRGLQVWETDAFHHDGLADDGPGIVRRLRGM
+LGA
+>PROKKA_01063
+MAGDPRGFAPLEPARHRVGERTELYDGTVTVDHWFSVPIDHALGLAEAEAQDAAGTGVGP
+HGRGTLTVFAREIRAKDDPEGERPWALYLQGGPGSAGPRPARLSGWLGALAESHRVLLLD
+QRGTGRSTPATVATLTAPGAFATDEARAEHLVHLRAPSIVRDAEMLRLALGAGPWTTLGQ
+SFGGFCTLSYLSFHPEGLQRSLVTGGLAPLTGHADRVYRATYARMRARTEEFFDRHPADR
+DAWSEAVGLIRAAEAAGAPIPLPGGGPLTVGRAQGLGMLLGGNTRVDRLHWVLAEAVDRT
+GPAPRLSETFLAAVADQDDRLVNPLYTVLHEAIYAQPADLAGGRADTGWSASRMLAEHPD
+FDPEATTVPLPTGEHVMPWSVEVDPRLRPLAGTARLLAERTQWGPLYDVAALAQNTVPVA
+AAVYADDVYVDRDLSLETARRVRGLQVWETDAFHHDGIADDGPAILERLLAMTAPDGAGT
+TTAPDPVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000925.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000925.fa
new file mode 100644
index 0000000000000000000000000000000000000000..be8ec912e79bd821677dc3a34b2bfdc052978662
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000925.fa
@@ -0,0 +1,80 @@
+>PROKKA_01114
+MTSAATNPPSLTDRIDALPPAPDADDVFGAFAAWTEDRGISLYPAQEEAALELVQGRHVI
+LATPTGSGKSLVALAAHADALAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS
+TVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQVPLLELPQAR
+FLLMSATLGDTTRLEADLTERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEEFVSTHQA
+PVYIVHFSQLDAVETAQGLSSISVTSREEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGV
+HHAGMLPKYRRLVEKLAQDGLLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQA
+REFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAAAKFANVKDEAERAKRMKQSV
+KSGKRKTPPAGFVSWGPATFERLVSAEPEPLVSRMRITHSMLLNILDRPGDPVIAVRRLL
+RGTHETPARQAVLMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLS
+PFALAALDLLDPADPDHALDVVSVIEATLDPPRQVLSAQVKHAKGEAVAAMKAEGMDYND
+RMRALDEITHPRPLAELLEQQFELYRQDAPWLAEFELTPKSVVRDMFERAMGFGDYVRFY
+GIARSEGVLLRYLTDAVKALRHTVPEAARTEELQVLLDWLDEMVKQTDSSLLEEWEDLVA
+GDIDELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEALARLSGELSA
+DDWADALDAYFDDHEDIDDGPAARGPELFRVAAAPDVAAPLELAGPRWWAVRQVLKDPDG
+DLDHGINAVVDLDASDEAGHPVIRVVSVGAPESGWGL
+>PROKKA_00833
+MTSAATNPPSLTDRIDALPPTPDADDVFGAFAAWTEDRGISLYPAQEEAVLELVQGKHVI
+LATPTGSGKSLVALAAHADALAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS
+TVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQVPLLELPQAR
+FLLMSATLGDTTRLEADLTERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEELVSTHQA
+PVYIVHFSQLDAVETAQGLSSISVTSREEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGV
+HHAGMLPKYRRLVEKLAQDGLLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQA
+REFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAAAKFANVKDEAERAKRMKQSV
+KSGKRKTPPAGFVSWGPATFERLVSAEPEPLVSRMRITHSMLLNILDRPGDPVIAVRRLL
+RGTHETPARQAVLMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLS
+PFALAALDLLDPADPDHALDVVSVIEATLDPPRQVLSAQVKHAKGEAVAAMKAEGMDYND
+RMRALDEITHPRPLAELLEQQFELYRQDAPWLAEFELTPKSVVRDMFERAMGFGDYVRFY
+GIARSEGVLLRYLTDAVKALRHTVPEAARTEDLQVLLDWLDEMVKQTDSSLLEEWEDLVA
+GDIDELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEALARLSGELSA
+DDWADALDAYFDDHEDIDDGPAARGPELFRVAAAPDVAAPLELAGPRWWAVRQVLKDPDG
+DLDHGINAVVDLDASDEAGHPVIRVVSVGAPESGWGL
+>PROKKA_01779
+MTSPATNPPSLTDRIDALPPTPDADDVFGAFAAWTEVRGISLYPAQEEAALELVQGRHVI
+LATPTGSGKSLVALAAHADALAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS
+TVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQVPLLELPQAR
+FLLMSATLGDTTRLEADLIERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEELVSTHQA
+PVYIVHFSQLDAVETAQGLSSISVTSKEEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGV
+HHAGMLPKYRRLVEKLAQDGLLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQA
+REFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAAAKFANVKDEAERAKRMKQSV
+KSGKRKSPPAGFVSWGPATFERLVAAEPEPLVSRMQITHSMLLNILDRPGDPVVAVRRLL
+RGTHETPARQAILMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLS
+PFALAALELLDPAEPDHALDVVSVIEATLDPPRQVLSAQVKKAKGEAVAAMKAEGMDYND
+RMRALDEVTHPQPLADLLEQQFEVYRASAPWLAEFELTPKSVVRDMFERAMGFGDYVRFY
+GIARSEGVLLRYLTDAVKALRQTVPEASRTEELQVLLDWLDEMVKQTDSSLLEEWEDLVA
+GDIEELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEELARLSGDLSA
+DDWADALDAYFGDHEDIDDGPAARGTELFRVAESPDVAPPVELAGSRWWAVRQVLKDPDG
+VHDHGVNAVVDLDASDEAGHPVIRVVSVGAPESGWGL
+>PROKKA_01672
+MTPSATNPPSLTDRLDALPASPDADDVFGAFAAWTEDRGISLYPAQEEAVLELVQGRHVI
+LATPTGSGKSLVALGAHADALAHGKVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS
+SVNADAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQLPLLELPQAR
+FLLMSATLGDTSMLERDLAERTGREVAVVAHAERPIPLSFEWSEVPLQEKVEELVSTHQA
+PVYIVHFSQLDAVETAVGLASISVTTKEEKEAIAERIAGFRFSAGFGKTLNRLVRAGIGV
+HHAGMLPKYRRLVEKLAQEGRLKVISGTDTLGVGINVPIRTVLLTALSKFDGEKTRILQS
+REFHQIAGRAGRAGFDTQGYVVVQAPEHVIENKAAERKAAAKFAGIKDEAERAKRMKQSV
+KGSKRKTPPQGFVSWGPATFDKLVASEPEPLVSRMRITHSMLLNILDRPGDPVLAVRRLL
+RATHETPARQAQLMRRALGIFRELLATGVVEVLPEPDAEGRTVDLTVDLQPDFALNQPLS
+PFALAALDLLDPAAPDHHLDVVSVIEATLDAPRQVLSAQVKKAKGEAVAAMKAEGMDYSD
+RMRALDEVTHPQPLAELLEQAFERYRQDAPWLAEFELSPKSVVRDMFERAMGFGDYVRFY
+GLARSEGVLLRYLTDAVKALRQTVPQEDRTEDLQVLLDWLDEMVKQTDSSLLEEWEDLMS
+GDIAELRRDLESLEPTPPPRLTDNAAVFRVMVRNAMFHRVRLFGDEQDARLAELSGDLSA
+NDWADALDAYFDEHEDIDDGPDARGQEFFRVATAPGARCPVELEGSRWWAVRQVLKDHDG
+DHDHGINAVVDLEASDEAGHPAIRVVSVGAPVPGWDL
+>PROKKA_01064
+MTSAATNPPSLTDRIDALPPTPDADDVFGAFAAWTEDRGISLYPAQEEAVLELVQGKHVI
+LATPTGSGKSLVALAAHADALAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS
+TVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQVPLLELPQAR
+FLLMSATLGDTTRLEADLTERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEELVSTHQA
+PVYIVHFSQLDAVETAQGLSSISVTSKEEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGV
+HHAGMLPKYRRLVEKLAQDGLLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQA
+REFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAAAKFANVKDEAERAKRMKQSV
+KSGKRKTPPAGFVSWGPATFERLVSAEPEPLVSRMRITHSMLLNILDRPGDPVIAVRRLL
+RGTHETPARQAVLMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLS
+PFALAALDLLDPADPDHALDVVSVIEATLDPPRQVLSAQVKHAKGEAVAAMKAEGMDYND
+RMRALDEITHPRPLAELLEQQFELYRQDAPWLAEFELTPKSVVRDMFERAMGFGDYVRFY
+GIARSEGVLLRYLTDAVKALRHTVPEAARTEDLQVLLDWLDEMVKQTDSSLLEEWEDLVA
+GDIDELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEALARLSGELSA
+DDWADALDAYFDDHEDIDDGPAARGPELFRVTAAPDVAAPLELAGPRWWAVRQVLKDPDG
+DLDHGINAVVDLDASDEAGHPVIRVVSVGAPESGWGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000926.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000926.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6a3151ad8ce5a15b8d265b08efdad44e111e0ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000926.fa
@@ -0,0 +1,34 @@
+>PROKKA_01115
+MSQIAPESPHPDTDAVVGDVTGRQGGGFTWDPAQYEGFAEHRARPFHDLVGRVRAEAPRV
+VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLERAREQAARTGAPANLRFEAVDASQW
+RPSGATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED
+PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR
+PSLQALARWDAEEGAAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF
+MAGQKPA
+>PROKKA_00834
+MSQIAPESPHPDTDAVVGDVTGRQGGGFTWDPAQYEGFAEHRARPFHDLVGRVRAEAPRV
+VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLERAREQAARTGTPANLRFEAVDASQW
+RPSRATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED
+PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR
+PSLQALARWDAEEGSAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF
+MVGQKPA
+>PROKKA_01778
+MSQIAPESPHPDTDAVAGDVTGRQGGGFTWDPAQYESFAEHRARPFHDLVGRVRAEAPRV
+VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLKRAREQAARTGAPANLRFEAVDASQW
+RPSRATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED
+PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR
+PSLQALARWDAEECSAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF
+MVGQKPA
+>PROKKA_01671
+MSTVPAVTGRETAGFTWDPAQYEGFAEHRARPFHDLVARVEAEAPRVVVDLGCGPGTLTR
+TLAERWPAAEVIGLDDSPAMLERAREGAADADLPNLRFDRVDASQWRPGPEVDVIVSNAM
+LQWIPTHRRLIRRWLGDLHPGAWFGAQLPRPYQQASHATIVALADEPVFSEALHGVETTR
+TVAPPEEYTRLFLEAGWTPSVWETEYQQVLTGPDPVLRWTSGAALRPSLQALAAWDAEEG
+AAEGAGLLELFVARYRQAMREAYPPVPGVSDADGGPLTVFPVRRMFLVGRKPGE
+>PROKKA_01065
+MSQIAPESPHPDTDAVVGDVTGRQGGGFTWDPAQYEGFAEHRARPFHDLVGRVRAEAPRV
+VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLERAREQAARTGTPANLRFEAVDASQW
+RPSRATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED
+PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR
+PSLQALARWDAEEGSAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF
+MVGQKPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000935.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000935.fa
new file mode 100644
index 0000000000000000000000000000000000000000..616a2cb9c262eb8186810e93a1a64153e58b61de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000935.fa
@@ -0,0 +1,30 @@
+>PROKKA_01126
+MAEQTTRVPLIAGNWKMNLDHLEAVTLVQRLTWLLSDADHDQEAVEVAVFPPFTGLRSVQ
+TLVTGDRLDLVYGAQDLSPEDAGAYTGDVSGAFLAALGCRYAIVGHSERRTLHGEDDALV
+ARKAAAALRHGLTPVICVGEGLEVRQAGRHVEHTLAQLEGSIAGLSAQDVAGVVVAYEPV
+WAIGTGEVAGPEDAQQMCAALRARVAALHGDDVAAGLRILYGGSVKSSSAPALLAQPDVD
+GALVGGASLDADEFAKIVRFDQA
+>PROKKA_00845
+MAEQTTRVPLIAGNWKMNLDHLEAVTLVQRLTWLLTDADHDQEAVEVAVFPPFTGLRSVQ
+TLVTGDRLDLVYGAQDLSPEDAGAYTGDVSGAFLAALGCRYAIVGHSERRTLHGEDDALV
+ARKAAAALRHGLTPVICVGEGLEVRQAGRHVEHTLAQLEGSIAGLSAQDVAGVVVAYEPV
+WAIGTGEVAGPEDAQQMCAALRARVAALHGDDVAAGLRILYGGSVKSSSAPALLAQPDVD
+GALVGGASLDADEFAKIVRFDQA
+>PROKKA_01766
+MAETAARVPLIAGNWKMNLDHREAVTLVQRLAWLLTDADHDHEDVEVAVFPPFTDLRAVQ
+VLVTGDRLDVAYGAQDLSPEDSGAYTGDVSGAFLAALGCRYAIVGHSERRTIHGEDDALV
+ARKAAAALRHGLSPVVCVGEGLDVRQAGRHVAHTVAQLEGSLVGLSAEDVARTVVAYEPV
+WAIGTGEVAGAGDAQEMCAALRARVGELHGDDVAAGLRILYGGSVKSTSAPELLAQPDVD
+GALVGGASLDAEEFARIVRFDQA
+>PROKKA_01660
+MSVVQPVRVPLIAGNWKMNLDHQEAVTLVQRLGWLLGDADHEQGNVEAAVFPPFTDLRSV
+QTLVAADRIGVAYGAQDVSAEDSGAFTGEVSGAFLAKLGCAYAIVGHSERRTLHHEDDAL
+VARKAAAALRHGLVPVVCVGEGLDVRQAGRHVEHTVAQLRGSLDGLSSEDVARVVVAYEP
+VWAIGTGEVASAADAQEMCAALRADLAERHGAEVAERVRVLYGGSVKSSSAPELLAQPDV
+DGALVGGASLDADEFARIVRSDAAH
+>PROKKA_01076
+MAEQTTRVPLIAGNWKMNLDHLEAVTLVQRLTWLLTDADHDQEAVEVAVFPPFTGLRAVQ
+TLVTGDRLDLAYGAQDLSPEDAGAYTGDVSGAFLAALGCRYAIVGHSERRTLHGEDDALV
+ARKAAAALRHGLTPVICVGEGLEVRQAGRHVEHTLAQLEGSIAGLSAQDVAGVVVAYEPV
+WAIGTGEVAGPEDAQQMCAALRARVAALHGDDVAAGLRILYGGSVKSSSAPALLAQPDVD
+GALVGGASLDADEFAKIVRFDQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000936.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000936.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed28899a924ff7034cd47c7e9ebfcac07ed38898
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000936.fa
@@ -0,0 +1,15 @@
+>PROKKA_01127
+MDVLTLALQILVVVLSVVIVLLILLHKGRGGGVSDMFGGGVTSSMSSSGSAQRLLTRLTV
+GSVVAWGVVIALLGVLPRLTMES
+>PROKKA_00846
+MDVLTLALQILVVVLSVVIVLLILLHKGRGGGVSDMFGGGVTSSMSSSGSAQRLLTRLTV
+GSVVAWGVVIALLGVLPRLTMES
+>PROKKA_01765
+MDMLTLILQILVVVLSVVIVLLVLLHKGRGGGVSDMFGGGVTTSMSSSGSAQRLLTRLTV
+GTVAAWALLIVTLGVLPRLAMES
+>PROKKA_01659
+MDILTLLLQIAVVALSVVIIMLVLLHKGRGGGVSDMFGGGVTTSMSSSGSAQRLLTRVTV
+SATVLWGLAIVALALIARFSVES
+>PROKKA_01077
+MDVLTLALQILVVVLSVVIVLLILLHKGRGGGVSDMFGGGVTSSMSSSGSAQRLLTRLTV
+GSVVAWGVVIALLGVLPRLTLES
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000938.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000938.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a7954c549d4c1e4a9bef198cafc5899a150bf45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000938.fa
@@ -0,0 +1,50 @@
+>PROKKA_01129
+MAGESRTAPRNPLRDPRDRRLTRIAGPSALVLFGVTGDLAKKKLLPAMYDLAQRGLLPPA
+FSLVGFGRRSWSDEEFADYVRAAVEASSRTTFDETVWDQFQGGLRFVSGAFDDEAAYVRL
+DEVLAELETSRGTRGNTAFYLSIPPDWFEAVSRHLADQGLADRSQPAEGPWRRVVIEKPF
+GHDLASAQELNAVIERVFPSDAVFRIDHYLGKETVQNILAFRFANRMFEPLWNAEHVDHV
+QITMAEDIGIGGRASYYDGVGAARDVIQNHLLQLLAFTAMEEPISFDADHLRAEKEKVLE
+AVTVPDTPEGLAAASARGQYTSGWQGGERVTGFLDEEGFNPASVTETYAALKVGIRTRRW
+QGVPFYLRAGKRLGRRVTEIAVVFKKPPHLLFPVHDGDEFGQNIIVIRVQPDEGVTIRFA
+SKVPGTQTEIRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQAEVELSWRIVD
+PFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRSWRRP
+>PROKKA_00848
+MAGESRTAPRNPLRDPRDRRLTRIAGPSALVLFGVTGDLAKKKLLPAMYDLAQRGLLPPA
+FSLVGFGRRSWSDEEFADYVRAAVEASSRTTFDETVWDQFQGGLRFVSGAFDDEAAYVRL
+DEVLAELETSRGTRGNTAFYLSIPPDWFEAVSRHLADQGLADRSQPAEGPWRRVVIEKPF
+GHDLASAQELNAVIERVFPSDAVFRIDHYLGKETVQNILAFRFANRMFEPLWNAEHVDHV
+QITMAEDIGIGGRASYYDGVGAARDVIQNHLLQLLAFTAMEEPISFDADHLRAEKEKVLE
+AVTVPDTPEGLAAASARGQYTSGWQGGERVTGFLDEEGFNPASVTETYAALKVGIRTRRW
+QGVPFYLRAGKRLGRRVTEIAVVFKKPPHLLFPVHDGDEFGQNIIVIRVQPDEGVTIRFA
+SKVPGTQTEIRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQAEVELSWRIVD
+PFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRSWRRP
+>PROKKA_01763
+MPGESKAAARNPLRDPRDRRLTRIAGPSALVLFGVTGDLAKKKLLPAMYDLAQRGLLPPS
+FSLVGFGRRDWSDEEFAEYVRAAVEASARTTFDETVWDQFRGGLRFVSGAFDDEAAYVRL
+GEVLGELESSRGTRGNTAFYLSIPPDWFEDVSRHLADQGLADRSQPADGPWRRVVIEKPF
+GHDLASAQELNAVIERVFPPDAVFRIDHYLGKETVQNILAFRFANRMFEPIWNAEHVDHV
+QITMAEDIGIGGRAGYYDGVGAARDVIQNHLLQLLAFTAMEEPISFDADHLRTEKEKILE
+AVQVPDTPAGLEAASARGQYTSGWQGGERITGFLDEEGFNPESVTETYAALKVGIRTRRW
+QGVPFYLRAGKRLGRRVTEIAVVFKKPPHLLFPVHEGDEFGQNVIVIRVQPDEGVTIRFA
+SKVPGTQSEVRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQAEVELSWRIVD
+PFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRAWRRP
+>PROKKA_01657
+MRPEPGGPARRNPLRDPRDRRLTRIAGPSALVLFGVTGDLARKKLLPAMYDLAHRGLLPP
+SFSLVGFGRRDWSEAEFADYVRAAVEAGSRTAFNETVWDQFRGGLRFVSGAFGDADAYAR
+LDEVLTELESSRGTGGNTAFYLSIPPDWFEDVSRHLADQGLADRSQPADGPWRRVVIEKP
+FGHDLASAHELNAVIERVFPPDAVFRIDHYLGKETVQNILAFRFANRIFEPLWSAEHVDH
+VQITMAEDIGIGGRAGYYDGVGAARDVIQNHLLQLLALTAMEEPISFDAAHLRAEKEKVL
+AAVRVPCTPEGLEAASARGQYTSGWQGGEQVTGFLDEEGFNPASVTETFAALKVDIGTRR
+WQGVPFYLRAGKRLGRRVTEIAVVFKSPPHLLFPVHPGDEFGQNVIVIRVQPDEGVTIRF
+ASKVPGTQHEVRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQEEVELSWAIV
+DPFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRTWRRP
+>PROKKA_01079
+MAGESRTAPRNPLRDPRDRRLTRIAGPSALVLFGVTGDLAKKKLLPAMYDLAQRGLLPPA
+FSLVGFGRRSWSDEEFADYVRAAVEASSRTTFDETVWDQFQGGLRFVSGAFDDEAAYVRL
+DEVLAELETSRGTRGNTAFYLSIPPDWFEAVSRHLADQGLADRSQPAEGPWRRVVIEKPF
+GHDLASAQELNAVIERVFPSDAVFRIDHYLGKETVQNILAFRFANRMFEPLWNAEHVDHV
+QITMAEDIGIGGRASYYDGVGAARDVIQNHLLQLLAFTAMEEPISFDADHLRAEKEKVLE
+AVTVPDTPEGLAAASARGQYTSGWQGGERVTGFLDEEGFNPASVTETYAALKVGIRTRRW
+QGVPFYLRAGKRLGRRVTEIAVVFKKPPHLLFPVHDGDEFGQNIIVIRVQPDEGVTIRFA
+SKVPGTQTEIRDVTMDFGYGHAFTEDSPEAYERLILDVLLGEPPLFPRQAEVELSWRIVD
+PFEEHWASLGTQPEPYAPGTWGPPSADALMARDGRSWRRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000941.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000941.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba1ab461bd71484ffebf82f98ee719dec0d9fbae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000941.fa
@@ -0,0 +1,69 @@
+>PROKKA_01132
+MTDAAQPSTPPTLDRVAPARGFVYSEQDRRMVDTLKALSADAVEKAGHGHPGTAISLAPV
+AWQLYQNVMHLDPTDDRWEGRDRFILSAGHASLIQYLQLFAAGAGLEIEDIQGLRTEGSR
+TPGHPEYGHTHGVEVTTGPLGQGLAMGVGFAYEQRRVRGLMDPDAAPGTSPFDHHVFVLA
+SDGDIQEGVAAEASSLAGHQELGNLVVVYDANRISIEDDTDIAFTEDVVRRYEAYGWHVQ
+EVDWTNGAQGHAVTEYTEDVEALYDALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGIH
+GSKLGTDEVAGLKESLGLDPTKTFDVDPELLARARSIAERSAEYRRGWEVAFQAWREANP
+ENARLYDRLAGRELPAGFADAFPSWDADEKGLATRAASGEVLTALAPVMPELWGGSADLA
+GSNNTTMKGEPSFIPARRSTATWQGHEYGRTLHFGVREFAAGAIVNGITIGGLTRAYVGT
+FLTFSDYMRPAVRLAALMGTPSTYVWTHDSIGLGEDGPTHQPVEHLAALRAIPGLDVVRP
+ADANETAWAWRTVLEHRDRPAGLVLSRQSLPVLPRDTDGFAPASGVARGAYVLIDATDAD
+GAPTPARALLIATGSEVSVAVRARALLQADGVPTRVVSAPCLEWFAEQDEAYRAEVLPDG
+PDAPVRVSVEAGIAMPWFEHTVTASSPGARVSLEHYGESADGARLMEKYGFTGEHVAEVT
+RGLL
+>PROKKA_00851
+MTDAAQPSTPPTLDRVAPARGFVYSEQDRRMVDTLKALSADAVEKAGHGHPGTAISLAPV
+AWQLYQNVMHLDPTDDRWEGRDRFILSAGHASLIQYLQLFAAGAGLEIEDIQGLRTEGSR
+TPGHPEYGHTHGVEVTTGPLGQGLAMGVGFAYEQRRVRGLMDPDAAPGTSPFDHHVFVLA
+SDGDIQEGVAAEASSLAGHQELGNLVVVYDANRISIEDDTDIAFTEDVVRRYEAYGWHVQ
+EVDWTNGAQGHAVTEYTEDVEALYDALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGIH
+GSKLGTDEVAGLKESLGLDPTKTFDVDPELLARARSIAERSAEYRRGWEVAFQAWREANP
+ENARLYDRLAGRELPAGFADAFPSWDADEKGLATRAASGEVLTALAPVMPELWGGSADLA
+GSNNTTMKGEPSFIPARRSTATWQGHEYGRTLHFGVREFAAGAIVNGITIGGLTRAYVGT
+FLTFSDYMRPAVRLAALMGTPSTYVWTHDSIGLGEDGPTHQPVEHLAALRAIPGLDVVRP
+ADANETAWAWRTVLEHRDRPAGLVLSRQSLPVLPRDTDGFAPASGVARGAYVLIDATDAD
+GAPTPARALLIATGSEVSVAVRARALLQADGVPTRVVSAPCLEWFAEQDEAYRAEVLPDG
+PDAPVRVSVEAGIAMPWFEHTVTASSPGARVSLEHYGESADGARLMEKYGFTGEHVAEVT
+RGLL
+>PROKKA_01760
+MTDAQHPSTAPALDRTAPARDFVYSEQDRRMVDTLKVLSADAVEQAGHGHPGTAISLAPV
+AWQMYQNVMHLDPQDDRWEGRDRFILSAGHASLIQYLQLFAAGAGLELEDIRALRTEGSK
+TPGHPEYGHTHGVEVTTGPLGQGLAMGVGFAYEQRRLRGLMDPDAAPGTSPFDHHVFVLA
+SDGDIQEGVAAEASSLAGHQELGNLVVVYDANRISIEDDTDIAFTEDVSARYEAYGWHVQ
+EVDWTNGALGHAVTEYTEDVEALYEALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGVH
+GSKLGAEELAGLKEGLGFDPAESFDVDPEVLANSRSIAERSAAYRRTWEGAFQAWREAHP
+ENARLYDRLAGRELPEGFAEAFPSWDADEKGLATRAASGEVLTALAPVMPELWGGSADLA
+RSNNTTMKGEPSFIPARRSTATWQGDEHGRTLHFGIREFAAGAIVNGITIGGLTRAYMGT
+FLTFSDYMRPAVRLAALMGTPSVYVWTHDSIGLGEDGPTHQPVEHLAALRAIPGLDVVRP
+ADANETAWAWRTVLENRDRPAGMVLSRQNLPVLPRDTDGFASAEGVARGAYVLVDAVGGS
+GAPAPARVLLIATGSEVSVAVHARELLQAEGVPTRVVSAPCLEWFAEQDEAYRAEVLPDG
+PDAPVRVSVEAGIAMPWFEHTVTAVSRGARVSLEHYGESADGARLMEKYGFTGEAVAQAA
+RGLL
+>PROKKA_01654
+MTDTASTALDRTLPARDFVYDEQDRRMVDTLKVLAADAVEKAGHGHPGTAISLSPVAWQL
+YQNVMHLDPSDDRWEGRDRFILSAGHASLIQYLQLFAAGAGLELEDIAALRTEGSLTPGH
+PEYGHTHGVEVTTGPLGQGLAMAVGFAYEQRRLRGLMDPDAAPGTSPFDHHVFVLASDGD
+IQEGVSSEASSLAGHQELGNLVVVYDANRISIEDDTDISFTEDVAKRYKAYGWHVQEVDW
+SNGAQGHEVTEYTEGVQDLYEALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGIHGSKL
+GGDEVVGLKEALGFDPQKSFDVDPEVLAHARSISERSAAYRETWEAAFAAWREAHPENAR
+LYDRLASRELPAGFEDAFPSWDADEKGVATRAASGKVLTALAPVMPELWGGSADLAGSNN
+TTMEGEPSFIPAHRSTAAWQGDPFGRTLHFGIREFAAGAIVNGITIGGLTRAYMGTFLTF
+SDYMRGAVRLAALMGTPAVYVWTHDSVGLGEDGPTHQPVEHLAALRAIPGLDVVRPADAN
+ETAWAWRTILQHRDRPAGLVLTRQNVPVLPRGTEGFAPADGVARGAYVLVDGADASGAAA
+PARVVLIATGSEVSVAVGARELLQAEGVPTRVVSAPCLEWFAEQDEAYRAEVLPDGPGAP
+VRVSVEAGIAMPWHELTVTQSSRGARVSLEHYGESADGPHLLKKYGFSPENVADTARGLL
+>PROKKA_01082
+MTDAAQPSTPPTLDRVAPARGFVYSEQDRRMVDTLKALSADAVEKAGHGHPGTAISLAPV
+AWQLYQNVMHLDPTDDRWEGRDRFILSAGHASLIQYLQLFAAGAGLEIEDIQGLRTEGSR
+TPGHPEYGHTHGVEVTTGPLGQGLAMGVGFAYEQRRVRGLMDPDAAPGTSPFDHHVFVLA
+SDGDIQEGVAAEASSLAGHQELGNLVVVYDANRISIEDDTDIAFTEDVVRRYEAYGWHVQ
+EVDWTNGAQGHAVTEYTEDVEALYDALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGIH
+GSKLGTDEVAGLKESLGLDPTKTFDVDPELLARARSIAERSAEYRRGWEAAFQAWREANP
+ENARLYDRLAGRELPAGFADAFPSWDADEKGLATRAASGEVLTALAPVMPELWGGSADLA
+GSNNTTMKGEPSFIPARRSTATWQGHEYGRTLHFGVREFAAGAIVNGITIGGLTRAYMGT
+FLTFSDYMRPAVRLAALMGTPSTYVWTHDSIGLGEDGPTHQPVEHLAALRAIPGLDVVRP
+ADANETAWAWRTVLEHRDRPAGLVLSRQSLPVLPRDTDGFAPASGVARGAYVLIDATDAD
+GAPTPARALLIATGSEVSVAVRARALLQADGVPTRVVSAPCLEWFAEQDEAYRAEVLPDG
+PDAPVRVSVEAGIAMPWFEHTVTASSPGARVSLEHYGESADGARLMEKYGFTGEHVAEVT
+RGLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000944.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000944.fa
new file mode 100644
index 0000000000000000000000000000000000000000..23241a81462bd499d280bf52846d3229d9f7ce03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000944.fa
@@ -0,0 +1,30 @@
+>PROKKA_01135
+MSTPVVDHRAPAGTGAHAGAAPLAARVLRQAGYETGTALRNGEQLLVTVVLPLLALVGVH
+VTGLLDAPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALATTPLGTLGLV
+AGKALAVVALLLVQVSVIGGVGLALGWRPDPEGILPALVALALGAAAFTALGLLLAGTAR
+PEATLAVANLLWVLFGAVGGTVFPARVPGVDLLPSGALGTALRAALLDGAWSPVPLLVLT
+LWGAVAVAAALRWFRWRP
+>PROKKA_00854
+MSTPVVDHRAPAGTGAHAGAAPLAARVLRQAGYETGTALRNGEQLLVTVVLPLLALVGVH
+VTGLLDAPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALATTPLGTLGLV
+AGKALAVVALLLVQVSVIGGVGLALGWRPDPEGILPALVALALGAAAFTALGLLLAGTAR
+PEATLAVANLLWVLFGAVGGTVFPARVPGVDLLPSGALGTALRAALLDGAWSPVPLLVLT
+LWGAVAVAAALRWFRWRP
+>PROKKA_01757
+MSAPIAPGSAEPRTAGQVPEPGTAPHAGAAPLATRVLRQAAYETGTALRNGEQLLVTVVL
+PLLALVGVHVTGLLDEPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALAT
+TPLGTLGLVAGKALSVVALLLVQVAVIGGVGLALGWRPEAAGILPAVVALALGAAAFTAL
+GLLLAGTARPEATLAAANLLWVLFGAVGGTVFPSRVPGVDLLPSGALGSALRAALVDGAG
+APIPLLVLALWCAVAVAAALRWFRWRP
+>PROKKA_01651
+MSAPAAPIPASHAGAAPLGARILAQARYETVTALRNGEQLLVTLVLPLLALVGVHVTGLL
+DAPGRNGLDLAVPGVLALAVISAAFTATAISTGFERRYDVLAALATTPLGTGGLVAGKAA
+AVAAVLLLQTIVIGGVGLALGWSPDPAGIPPAVVALLLGAAAFTALGLLLAGTARPEATL
+AVANLVWVLLGALGGTVFPSRWAWMDLLPSGALGTALRSALQDGAWAPSALAVLAAWTVM
+AVAAALRWFRWRP
+>PROKKA_01085
+MSTPVVDHRAPAGTGAHAGAAPLAARVLRQAGYETGTALRNGEQLLVTVVLPLLALVGVH
+VTGLLDAPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALATTPLGTLGLV
+AGKALAVVALLLVQVSVIGGVGLALGWRPDPEGILPALVALALGAAAFTALGLLLAGTAR
+PEATLAVANLLWVLFGAVGGTVFPARVPGVGLLPSGALGTALRAALLDGAWSPVPLLVLT
+LWGAVAVAAALRWFRWRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000945.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000945.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e0ec07b66d76985b4709b5893bec08f56019997c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000945.fa
@@ -0,0 +1,35 @@
+>PROKKA_01136
+MPRDEPVLRLSDVHRSLGRGRSRTPVLRGVDLTARAGAVTVLLGPNGAGKSTTLGLCHGM
+DRPDAGTVRVFGADPWRASADLRARIGVMWQEGGLPPAIPARRFVGHVASLYRDPLPVEP
+LLERLLIAEVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLDPETRPVVHDVV
+REQTDRGAAVLLTTHLLDDAERLADDVAILRAGRVVRSGSLAELTRVAEGDVVDVDFGDA
+SPDAVRAWADTLPAPLRAAGLDESARLRVAGVRGPDDLAVLAASWREHALMPTRFERAGL
+RLEQILRETAA
+>PROKKA_00855
+MPRDEPVLRLSDVHRSLGRGRSRTPVLRGVDLTARAGAVTVLLGPNGAGKSTTLGLCHGM
+DRPDAGTVRVFGADPWRASADLRARIGVMWQEGGLPPAIPARRFVGHVASLYRDPLPVEP
+LLERLLIAEVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLDPETRPVVHDVV
+REQTDRGAAVLLTTHLLDDAERLADDVAILRAGRVVRSGSLAELTRVAEGDVVDVDFGDA
+SPDAVRAWADTLPAPLRAAGLDESARLRVAGVRGPDDLAVLAASWREHALMPTRFERAGL
+RLEQILRETAA
+>PROKKA_01756
+MVPRPVLTPDPAPRDEPVLRLRDVHRSLGRGRARTPVLRGVDLTARAGAVTVLLGPNGAG
+KSTTLGLCHGMDRPDAGAVRVFGADPWRAPADLRARIGVMWQEGGLPPSVPARRFVGHVA
+SLYRDPMPVEPLLERLLIADVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLD
+PETRPVVHEVVREQTARGAAVLLTTHLLDDAERLADDVAILRAGRVVRAGSLADLTRVAE
+GDVVDVDFGDAAPEAVRAWADALPEPLRAAGLAEPARLRVAGVHGPAELAALAASWHRHA
+LMPTRFERAGLRLEQILRETAA
+>PROKKA_01650
+MPETSPHPDAPALRLHEVRRTLGRGAARTEVLRGVDLEARRGAVTVLLGPNGAGKSTTLA
+LCHGSDRPDSGTVRVFGRDPWRADADLRARLGVMWQEGGLPPSVTARRFVRHVASLHGDP
+LDPDALLGRLRIDRVADRPIRRLSGGQRQRVALAAAVVGRPDLLFLDEPTAGLDPETRPV
+VHDVVREHTARGAAVLLTTHLLDDAERLADDVAILRAGRVVRAGTLAELTRVQDGDVVDV
+RFDEARAADVRAWVAAAPASFRAVASAGAPAARVAGVRSPADLEALAASWTRAGLFPTRL
+ERAVLRLEELLQSPDADTPSPERSR
+>PROKKA_01086
+MPRDEPVLRLSDVHRSLGRGRSRTPVLRGVDLTARAGAVTVLLGPNGAGKSTTLGLCHGM
+DRPDAGTVRVFGADPWRASADLRARIGVMWQEGGLPPAIPARRFVGHVASLYRDPLPVEP
+LLERLLIAEVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLDPETRPVVHDVV
+REQTDRGAAVLLTTHLLDDAERLADDVAILRAGRVVRSGPLSELTRVAEGDVVDVDFGDA
+SPDAVRAWADTLPAPLRAAGLGESARLRVAGVRGPDDLAVLAASWREHALMPTRFERAGL
+RLEQILRETAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000950.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000950.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ef07985907ba503ac8bac6bbe866ecb35d54654
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000950.fa
@@ -0,0 +1,15 @@
+>PROKKA_01141
+MTETANQVPTEDIREALKDVIDPELGVNVVDLGLLYGLHYADDGALLVDMTLTTAACPLT
+DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI
+>PROKKA_00860
+MTETTNQAPTEDIREALKDVIDPELGVNVVDLGLLYGLHYADDGALLVDMTLTTAACPLT
+DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI
+>PROKKA_01751
+MTETANQVPTEDVREALKDVIDPELGVNVVDLGLLYGLHYAEDGALLVDMTLTTAACPLT
+DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI
+>PROKKA_01645
+MTDTAAQTPVEDIREALKDVIDPELGVNVVDLGLLYGLHYAEDGALLVDMTLTTAACPLT
+DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGKDQMRALGFNI
+>PROKKA_01091
+MTETTNQAPTEDIREALKDVIDPELGVNVVDLGLLYGLHYADDGALLVDMTLTTAACPLT
+DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000953.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000953.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af873860073fc21af2dfe44fa1adfdb1607462cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000953.fa
@@ -0,0 +1,35 @@
+>PROKKA_01144
+MSIPAPMTDPTARDAERLPALRFGFLATGPWILGFVVCVLFAFLCHALAQWQWDRRVEVQ
+HRVNRVLENYDDDPVPFAEASRLFTAFQTDDEWTPVTLTGEYLVDETLIVRNRPRAGQPG
+YEVLVPFRTDEGPVVVVDRGWLPVGNSPGQPDAVPAPPAGHAEVVVRVKPGEPALDRDAP
+DGQVPSIDLAEIADTVGGPVAGTAYGIMVTEDPAVEPMPQKLVEPTLDEGPHLSYAIQWY
+LFAAMGFGVWGYSAWMRARNDRADALDDAADDGLLSAHRVPRAKPARRRRDGRLTDEEAE
+DALFD
+>PROKKA_00863
+MSTPAPMSAPTARDAERLPPLRFGFLATGPWILGFVLCILFAFLCHALAQWQWDRRVEVQ
+HRVNRVLENYDDDPVPFAEASRLFTAFQTEDEWTPVTLTGEYLVDETLIVRNRPRAGQPG
+YEVLVPFRTDEGPVVVVDRGWLPVGNSPGQPDAVPAPPAGHAEVVVRVKPGEPALDRDAP
+DGQVPSIDLAEIADTVGGPVAGTAYGIMVTEDPAVESMPQKLVEPTLDEGPHLSYAIQWY
+LFAAMGFGVWGYSAWMRARNDRADALDDAADDGLLSAHRVPRAKPARRRRDGRLTDEEAE
+DALFD
+>PROKKA_01747
+MTAPAPATGFRRDPGSARPPRLRFDFLATPPWILGFVLCILFAFACHYLAQWQWERRVQV
+QHQVNRVLENYDDAPVPFAQASRMFTDFDAQDEWTPVTLSGEYLAEETLVVRNRPRAGRP
+GYEVLVPFRTDEGPVVVVDRGWLPVGNTPGRPDAVPAPPAGPAEVVVRVKPGEPALDRDA
+PEGQVPSIDLAEIRGHVGGPVADTAYGIMVEEDPAVQDLPQKLVEPTLDEGPHLSYAIQW
+YLFAAMGFGVWGYSAWMRARNDRADALEGVRDDGMLTARRAPRPKPVRRRRDGRPTDEEA
+EDALFD
+>PROKKA_01642
+MTPAPAPTDTPDAPGAERLPPLRFGFLASGPWILGFVVCILFAFLCHGLAQWQWDRRVQV
+MHDVNRVLANYDDDPVPFAEAPRLFTDFDSEDEWTPVTLTGRYETDETLVVRNRPRAGAP
+GYEVLVPFVTEEGVTVIVDRGWLPIGSQPGRPDAIPAPDPAAGEVVVRVKPGEPALDRDA
+PEGQVPSIDLAAIERILGRPIADTAYGLMVSESPAAATVPNQLVAPTLDEGPHLSYAIQW
+YIFAAMGFAVWGYSAWMKARNDRADALEDAEDDGLLAARRAPRPKARRRRRGGRPSDEEV
+EDALQEDVLRDRPGQASEIRSR
+>PROKKA_01094
+MSTPAPMSAPTARDAERLPPLRFGFLATGPWILGFVLCILFAFLCHALAQWQWDRRVEVQ
+HRVNRVLENYDDDPVPFAEASRLFTAFQTEDEWTPVTLTGEYLVDETLIVRNRPRAGQPG
+YEVLVPFRTDEGPVVVVDRGWLPVGNSPGQPDAVPAPPAGHAEVVVRVKPGEPALDRDAP
+DGQVPSIDLAEIADTVGGPVAGTAYGIMVTEDPAVESMPQKLVEPTLDEGPHLSYAIQWY
+LFAAMGFGVWGYSAWMRARNDRADALDDAADDGLLSAHRVPRAKPARRRRDGRLTDEEAE
+DALFD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000965.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000965.fa
new file mode 100644
index 0000000000000000000000000000000000000000..351c8ca05d74a944cd3553f6da630e77e6ea5ca0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000965.fa
@@ -0,0 +1,45 @@
+>PROKKA_01161
+MTHHETPASETASRPAVAGGALRPAVILGGNRIPFARANTAYAEVGNQEMLTATLDGLVA
+RFGLQGERLGQVTAGAVLKHPRNFNLTREAVLGSALSAATPAADVQVACATGMEALGTLA
+NKIRLGQLDSAIGGGVDSISDAPVSLSDGARRVLLQLNTAKTMKDRLRALAQLRPGQLVP
+EPAGAGEPRTGMSMGEHQALTTHKWGITRQTQDELAAASHRNLGAAYAAGYMDDLVTPFH
+GLARDNNLRPDSTPEKLAGLKPAFGRQLGDEATMTAANSTPLTDGASAVLLSSEEWAAER
+GLPVLAEFVDMENAAVDFVDGHEGLLMAPAYAVPRLLARHGLTLDDLDFVEIHEAFAGTV
+LSTLAAWEDEEYCRERLGLPGALGSVDRARLNVHGSSLAAGHPFAATGGRIVALLAKMLH
+EKGEGSLGLISVCAAGGQGIVALLRGR
+>PROKKA_00880
+MTHHETPASETASRPAVAGGALRPAVILGGNRIPFARANTAYAEVGNQEMLTATLDGLVA
+RFGLQGERLGQVTAGAVLKHPRNFNLTREAVLGSALSAATPAADVQVACATGMEAVGTLA
+NKIRLGQLDSAIGGGVDSISDAPVSLSDGARRVLLQLTTAKTMKDRLRALAQLRPGQLVP
+EPAGAGEPRTGMSMGEHQALTTHKWGITRQAQDELAAASHRNLGAAYAAGYMDDLVTPFH
+GLARDNNLRPDSTPEKLAGLKPVFGRQLGDEATMTAGNSTPLTDGASAVLLSSEEWAAER
+GLPVLAEFVDMENAAVDFVDGHEGLLMAPAYAVPRLLARHGLTLDDLDFVEIHEAFAGTV
+LSTLAAWEDEEYCRERLGLPGALGSVDRARLNVHGSSLAAGHPFAATGGRIVALLAKMLH
+EKGEGSLGLISVCAAGGQGIVALLRGR
+>PROKKA_01729
+MTQPETTARPAVAGGALRPAVVVGGNRIPFARANTAYAEVGNQEMLTAALEGLVARFGLQ
+GERVGQVSAGAVLKHPRNFNLTREAVLGSALASDTPAADLQVACATGMEAIGTLADKIRL
+GRIDSAIGGGVDSISDAPVSLSDGARRALLRLNAAKTMKDRLAALKDLRPGHLAPEPAGA
+GEPRTGMSMGDHQALTTHRWGITRQAQDELAAASHRNLGAAYAAGYMDDLVTPFRGLDRD
+NNLRPDSTPEKLAGLKPAFGRHLGEEATMTAGNSTPLTDGASAVLLSSEDWAAERGLPVL
+AEFVDVENAAVDFVDGDEGLLMSPAYAVPRLLARHGLTLQDLDFVEIHEAFAGTVLSTLA
+AWEDEEYCRERLGLPGALGSVDRAKLNVHGSSLAAGHPFAATGGRIVALLSKMLHEKGEG
+SLGLVSVCAAGGQGIVALLRGR
+>PROKKA_01626
+MSTESPRVPAETARPAIAGGELRPAVVVGSNRIPFARAFTAYAEVGEQEMLTAAIDGLVA
+RLGLQGERLGQVSAGAVMKHPKDFNLTREAVMGSALSSETPAADIQVACATGMEAIGTLA
+DKIRLGRIDSAIGGGVDSISASPMTVSESARRVLLQLNSAKTVKDRLKALSSLRPGQLVP
+EPAAAGEPRTGMSMGEHQALTTHQWGITRQAQDELAAASHRNLGASYASGYQDDLVTPFR
+GLAKDNNLRPDSTVEKLAGLKPAFGRHLGDEATMTAGNSTPLTDGASAVLLSSEDWAVQR
+NLPVLAEIVDMENAAVDFVDGEDGLLMSPVYAVPRLLARHGLTLDDLDFVEIHEAFAGTV
+LATLAAWEDEEFGRTRLGLPGAYGSVDRAKLNVNGSSLAAGHPFAATGGRIVGLLSKMLH
+EKGEGSLGLVSVCAAGGQGIVALLRGR
+>PROKKA_01111
+MTHHETPASETASRPAVAGGALRPAVILGGNRIPFARANTAYAEVGNQEMLTATLDGLIA
+RFGLQGERLGQVTAGAVLKHPRNFNLTREAVLGSALSAATPAADVQVACATGMEALGTLA
+NKIRLGQLDSAIGGGVDSISDAPVSLSDGARRVLLQLNTAKTTKDRLRALAQLRPGQLVP
+EPAGAGEPRTGMSMGEHQALTTHKWGITRQAQDELAAASHRNLGAAYAAGYMDDLVTPFH
+GLARDNNLRPDSTPEKLAGLKPAFGRQLGDEATMTAANSTPLTDGASAVLLSSEEWAAER
+GLPVLAEFVDMENAAVDFVDGHEGLLMAPAYAVPRLLARHGLTLDDLDFVEIHEAFAGTV
+LSTLAAWEDEEYCRERLGLPGALGSVDRARLNVHGSSLAAGHPFAATGGRIVALLAKMLH
+EKGEGSLGLISVCAAGGQGIVALLRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000966.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000966.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c5d5b712de2bb38bb7b218b6c8d3158b2d31c618
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000966.fa
@@ -0,0 +1,45 @@
+>PROKKA_01162
+MTDRYGTFVASPLGRRLTGALGLPQPVELRRHTPGDPVLPGSVLVLGATPAAADARTLLA
+SWGLEVADAPREGARHAAIVACFDGVATPADLGAVALEIGGALRSLGSSSRVVTVFEDPE
+AATDPTLRAARQGVTGLTRSIAHEMRRGGTANGLVLGEGVPLTAPGAAGALAFLLSGRAA
+YVSGQFVPVATADGAVPADAARPLAGKVAVVTGAARGIGAAIVRTLARDGAVVVGVDVPA
+AGEALAEVVNEVGGTALALDITAPDAGARILEHCRTRHGRMDAVVHNAGITRDRMLANMD
+AARWDSVLAVNTTAQLAMNEAFLAEDARDVAGQGLRIVGLASISGIAGNRGQTNYAASKA
+GVIGLTAASAPVLAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNALQQGGLPQDVA
+ETVAWLASDAAGGTNGATLRVCGQSKLGA
+>PROKKA_00881
+MTDRYGTFVASPLGRRLTGALGLPQPVELRRHTPGDPVLPGSVLVLGATPAAADARTLLA
+SWGLEVADAPREGARHAAIVACFDGVATPADLGAVALEIGGALRSLGSSSRVVTVFEDPE
+AATDPALRAARQGVTGLTRSIAHEMRRGGTANGLVLGEGVPLTAPGAAGALAFLLSGRAA
+YVSGQFVPVSTADGAVPADAARPLAGKVAVVTGAARGIGAAIVRTLARDGAVVVGVDVPA
+AGETLAKVVNEVGGTALALDITAPDAGARILEHCRTRHGRMDVVVHNAGITRDRMLANMD
+AARWDSVLAVNTTAQLAMNEAFLAEDARDVAGHGLRIVGLASISGIAGNRGQTNYAASKA
+GVIGLTAASAPVLAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNALQQGGLPQDVA
+ETVAWLASDAAGGTNGATLRVCGQSKLGA
+>PROKKA_01728
+MTDRYGAFAASALGRRLTGALGLPQPVELRRHAPGEPVLHGSVLVLGAGPAAADARTLLA
+SWGLEVADAPREGARLAGVVACFDDAAAPGDLGETVLQIGGALRSLGASSRVVTVSVDPE
+AAAEPAVRAARQGVQGLTRSLAQEMRRGGTANGIVLGEGVPLTAPGAAGALAFLLSGRSA
+YVSGQFLPVTTRDGATPADAARPLADKVAVVTGAARGIGAAIVRTLARDGATVVGVDVPV
+AGESLAAVVNEVGGTALALDITAPEAGARILEHCRARHGRMDVVVHNAGITRDRMLANMD
+AARWDSVIAVNTASQLAMNEAFLADDAREVTGEGLRIIGLASISGIAGNRGQTNYAASKA
+GVIGLTAASAPALAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNSLQQGGLPQDVA
+EAVAWFASDAAGGTNGATLRVCGQSKLGA
+>PROKKA_01625
+MPANDPYGDLVRTRLGRRLTGALGLPQPAELRRHTAGDPAVRGTVLVLGATSAADAARAL
+VTAEGARAVAHPAEGERLAAVIACFDGVAAPGDLSDTALALGGALRSLEPSAHVVTVVED
+PEEAEVPAVRAARAGVMGLTRSLAHEMRRGGVANGLLLRGGARLGDAGPAGALRFLLSGR
+AAFVSGQFLPAAAGAGSAPASADARPLEGRVAVVTGAARGIGAAILRTLARDGATVVGVD
+LPAAGEDLVRIVNELGGTALPLDITAPDAGARIVEHARARHGRLDVVVHNAGITKDKLLA
+NMDAARWDAVLAVNTASQLAINEVLLSAEAADVVSPDIRIVGLASISGIAGNRGQTNYAA
+SKAGVIGLTAATAPDLAARGGGITAVAPGFIETEMTAKIPLVTRELGRRVNSLQQGGRPE
+DVAEAVAFLSSPAASGINGTTLRVCGQSMLGA
+>PROKKA_01112
+MTDRYGTFVASPLGRRLTGALGLPQPVELRRHTPGDPVLPGSVLVLGATPAAADARTLLA
+SWGLEVADAPREGARHAAIVACFDGVATPADLGAVALEIGGALRSLGSSSRVVTVFEDPE
+SATDPTLRAARQGVTGLTRSIAHEMRRGGTANGLVLGEGVPLTAPGAAGALAFLLSGRAA
+YVSGQFVPVATADGAVPADAARPLAGKVAVVTGAARGIGAAIVRTLARDGAVVVGVDVPA
+AGEALAEVVNEVGGTALALDITAPDAGARILEHCRTRHGRMDVVVHNAGITRDRMLANMD
+AARWDSVLAVNTTAQLAMNEAFLAEDARDVAGQGLRIVGLASISGIAGNRGQTNYAASKA
+GVIGLTAASAPVLAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNALQQGGLPQDVA
+ETVAWLASDAAGGTNGATLRVCGQSKLGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000969.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000969.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f546955d07b6e55815820a120f749dfbbf2a9b4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000969.fa
@@ -0,0 +1,45 @@
+>PROKKA_01166
+MVENIVNPARSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAEYCARLMAEAGMTPRF
+FESAPGRVSVVGHLPGWDPEAPGLVIHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV
+DMKGMDAMVLAVLLHLARTGRRPRRPLTVAFFADEEAGGVYGARWVVDHHPEVFDGCTEA
+ISEVGGFSTEVHGSRAYLVQTAEKGLAWLNLTAEGAPGHGSAPHPDNAVTRLAGAMTRIG
+GHEWPLVYTKTTRALLEQVAEIMGVDFDEADPTPQLDALGQARSWVAGTLRTSSNPTGLT
+AGYKHNVIPSSATGTVDVRLIPGEEESALATIAELAGPEVTIAPEHRDVALETPFSGDLV
+ELMIASLQAEDPEAQVLPFMLGGGTDNKSLSRLGITGYGFAPMRLPADLAFTSLFHAIDE
+RVPVDALEFGCRVLERMLEPR
+>PROKKA_00885
+MVENIVNPARSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAEYCARLMAEAGMTPRF
+FESAPGRVSVVGHLPGWDPEAPGLVIHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV
+DMKGMDAMVLAVLLHLARTGRRPRRPLTVAFFADEEAGGVYGARWVVDHHPEVFDGCTEA
+ISEVGGFSTEVHGSRAYLVQTAEKGLAWLNLTAEGAPGHGSAPHPDNAVTRLAGAMTRIG
+GHEWPLVYTKTTRALLEQVAEIMGVDFDETDPTPQLDALGQARSWVAGTLRTSSNPTGLT
+AGYKHNVIPSSATGTVDVRLIPGEEESALATIAELAGPDVTIAPEHRDVALETPFSGDLV
+ELMIASLQAEDSEAQVLPFMLGGGTDNKSLSRLGITGYGFAPMRLPADLAFTSLFHAIDE
+RVPVDALEFGCRVLERMLEPR
+>PROKKA_01723
+MIQNAHDTPVSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAALCARLMEEAGMRPRL
+FESSPGRVSVVGHLPGWDEDAPGLVVHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV
+DMKGMDAMVLSVLLHLTRTGRRPRRPLTVAFFADEEAGGVYGARWLVEHHPELFDGCTEA
+ISEVGGFSTEVHGSRAYLVQTAEKGIAWLNLRAEGAPGHGSAPHPDNAVTRLAGAMTRIG
+GHEWPLVYTKTTRALLEQVAEIMGVDFDEQDPTPQLDALGQARSWVAGTLRTSSNPTGMT
+SGYKHNVIPSTATGTVDARLLPGEEEAALATLQELAGPGVSIEPEHRDVALETPFSGDLV
+ELMVASLQAEDPGAEVLPFMLGGGTDNKSLARLGITGYGFAPMRLPADLAFTSLFHGIDE
+RVPVDALEFGCRVLERMLEPR
+>PROKKA_01621
+MDASTPSTAPSTADADVVEICRDLIRIDTTNHGGGRSVGEPEAAELCAAWMRKAGMEPEL
+IESAPGRVSVVGRLEGWDPEAPGLVLHGHTDVVPAEPDEWTVDPFGAEFRDGMIWGRGAV
+DMKGMDAMILSVLVHLARTGRRPRRPVVVAFFSDEEAGGVFGAQWLVAHRPELFAGCTEA
+ISEVGGFSTDVAGTRAYLVQTGEKGLAWLNLRAQGAPGHGSAPHTDNAVTRLAGAMERIG
+RHPWPLTYTKTTRQLLEEVAEITGTPFDERDPTPQLQALGHARDWVAGTLRTSSNPTGLT
+AGYKHNVIPSTATGTVDVRLIPGEEEQTLAELADLAGDGIEISPEHQDTGLEVPFSGDLV
+ERMASALDAEDPGAHVLPFMLGAGTDNKSLHRLGIAGYGFSPLQLPSGLEFTRLFHGIDE
+RVPVESLRFGCRVLEHVLEPRA
+>PROKKA_01116
+MVENIENPARSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAEYCARLMTEAGMTPRF
+FESAPGRVSVVGHLPGWDPEAPGLVIHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV
+DMKGMDAMVLAVLLHLARTGRRPRRPLTVAFFADEEAGGVYGARWVVDHHPEVFDGCTEA
+ISEVGGFSTEVHGSRAYLVQTAEKGLAWLNLTAEGAPGHGSAPHPDNAVTRLAGAMTRIG
+GHEWPLVYTKTTRALLEQVAEIMGVDFDETDPTPQLDALGQARSWVAGTLRTSSNPTGLT
+AGYKHNVIPSSATGTVDVRLIPGEEESALATIAELAGPDVTIAPEHRDVALETPFSGDLV
+ELMIASLQAEDPEAQVLPFMLGGGTDNKSLSRLGITGYGFAPMRLPADLAFTSLFHGIDE
+RVPVDALEFGCRVLERMLEPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000977.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000977.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2e413dd77f3d9015bcb80a1168b6c48f7ddb02ca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000977.fa
@@ -0,0 +1,36 @@
+>PROKKA_01174
+MTEPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGEFHSYQGVLRHDDLIGGFEGVV
+VENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIVQQADIFPGAVVVEAGVGSGAL
+SMSLLRAVGDHGRLHSYERRPEFADVARANVEAFFGAEHPAWSVHLGDAQEEMPKVHEPG
+SVDRVVLDMLAPWECLDAVAEVLAPGGVWLNYVATATQLSRVAEAIRDSGRFTQVEANET
+LVRGWHLDGLAVRPDHRMVAHTGFLLTARRLASGEEALRLKKRSKVSEFRAEDVEAWQPA
+DEARWTPEALGERPITDKKARKAAKEARLMAARSRAAEQGVDAYGGRTPTGEQD
+>PROKKA_00893
+MTEPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGEFHSYQGVLRHDDLIGGFEGVV
+VENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIVQQADIFPGAVVVEAGVGSGAL
+SMSLLRAVGDHGRLHSYERRPEFADVARANVEAFFGAEHPAWSVHLGDAQEEMPKVHEPG
+SVDRVVLDMLAPWECLDTVAEVLAPGGVWLNYVATATQLSRVAEAIRDSGRFTQVEANET
+LVRGWHLDGLAVRPDHRMVAHTGFLLTARRLASGEEALRLKKRSKVSEFKAEDVEAWQPA
+DEARWTPEALGERPVTDKKARKAAKEARLMAARSRAAEQGVDAYGGRTPTGEQD
+>PROKKA_01715
+MTEPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGEFHSYQGVLRHDDLIGGFEGVV
+VENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIVQQADIFPGAVVVEAGVGSGAL
+SMSLLRAVGDHGRLHSYERREEFADVARANVEAFFGAEHPAWSIHLGDAQEQMTRVHEPG
+SVDRVVLDMLAPWECLDAVAEVLAPGGVWLNYVATATQLSRVAEAIRDSGRFTQVEANET
+LVRGWHLDGLAVRPDHRMVAHTGFLLTARRLATGEEALRLKKRSKVSEFKAEDVEAWQPA
+DEARWTPEALGERPVTDKKARKAAKEARLMAARSRAAERGVDAYGGSIQEQDQD
+>PROKKA_01613
+MSDATAPETPAAPTTPDTAAPAGRPAGVTARRGPLRAGQRVQIKDAKGRLNTITLLPGGE
+FHSYQGVLRHDDLIGGPEGIVVQNSSGHAYQVLRPLLNDFVLSMPRGATVVYPKDAGQIV
+QQADIFPGAVVVEAGVGSGALSMSLLRAVGDAGRLHSYERRAEFAEIARGNVESFFGGVH
+PAWSIHLGDAQEEMPKVHEPHSVDRVVLDMLAPWECLDAVATVLAPGGVWLNYVATATQL
+SRVAEAIRASGKFTQIEATETLVRGWHLDGLAVRPDHRMVAHTGFLLTARRLAAGEDALV
+MKKRLKVSEFTTEDVEAWTPSDGARWTPQALGERTVTDKKARKAAKEARLTARRARAALE
+GRDPRTVGQDKD
+>PROKKA_01124
+MTEPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGEFHSYQGVLRHDDLIGGFEGVV
+VENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIVQQADIFPGAVVVEAGVGSGAL
+SMSLLRAVGDHGRLHSYERRPEFADVARANVEAFFGAEHPAWSVHLGDAQEEMPKVHEPG
+SVDRVVLDMLAPWECLDAVAEVLAPGGVWLNYVATATQLSRVAEAIRDSGRFTQVEANET
+LVRGWHLDGLAVRPDHRMVAHTGFLLTARRLASGEEALRLKKRSKVSEFKAEDVEAWQPA
+DEARWTPEALGERPVTDKKARKAAKEARLMAARSRAAEQGVDAYGGRTPTGEQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000982.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000982.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb45e28012655aae7973418085523f6e4cbd751d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000982.fa
@@ -0,0 +1,15 @@
+>PROKKA_01179
+MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQRLDSLLDEIDSVLESNAEEFVKGFVQK
+GGQ
+>PROKKA_00898
+MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQRLDSLLDEIDSVLESNAEEFVKGFVQK
+GGQ
+>PROKKA_01710
+MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQGLDSLLDEIDSVLESNAEEFVKGFVQK
+GGQ
+>PROKKA_01608
+MAQEQIRPRPAGGPEDEGAAAQAQAKAAPQDTGLDGLLDEIDSVLESNAEEFVKGFVQKG
+GQ
+>PROKKA_01129
+MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQGLDSLLDEIDSVLVSNAEEFVKGFVQK
+GGQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000993.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000993.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f62a5092f529ff73e3428c247e61ad29afe2b52d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000993.fa
@@ -0,0 +1,20 @@
+>PROKKA_01191
+MEWIEANAGWLWLVLAAGLAGVELLTLDLVFLMIAAGAGAAGVVALVGGPLALQLAAFAA
+VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITGDAGTLAVDGDTWSARV
+EPGAPEVAPGDEVTVLRIDGATLVVRPLPRIDWEADGA
+>PROKKA_00910
+MEWIEANAGWLWLVLAAGLAGVELLTLDLVFLMIAAGAGAAGVVALVGGPLALQLAAFAA
+VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITGDAGTLAVDGDTWSARV
+EPGAPDVAPGDEVTVLRIDGATLVVRPLPRIDWQADGA
+>PROKKA_01697
+MDWIEANAGWLWLVAAAGLIGVELLTLDLVFLMIAAGAGAAGVVALAGGPLPLQLAAFAV
+VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITAEAGTLTVDGDTWSARV
+EDGAPDAAPGAEVTVLRVEGATLVVRPLPQIDWEDGRS
+>PROKKA_01596
+MEWIEANADWLWLVLALGLVGAELLSLDLVLAMLAAGALSAGVAALAGAPLGLQLGVFVV
+VSLLTLVAVRPAAMRRLHPDPAVGASWLDGLSGRRLTATGPVTDEGGRIDVDGETWSARV
+EPGAAPAAHGQGVTVLRVEGAHLILRPDPVIDWDAPAHD
+>PROKKA_01141
+MEWIEANAGWLWLVLAAGLAGVELLTLDLVFLMIAAGAGAAGVVALVGGPLALQLAAFAA
+VALLMLAAVRPVALRHLRKDTGAGASYLDTLPGRRVAAQGAITGDAGTLAVDGDTWSARV
+EPGAPEVAPGDEVTVLRIDGATLVVRPLPRIDWEADGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000998.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000998.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e97ddae27a7934f4858c9d67154ea7d880bfc5ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0000998.fa
@@ -0,0 +1,15 @@
+>PROKKA_01196
+MVTAIVLIKTDKSSIPETAETLAALEGVGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL
+SKVDGIQDTETMLAFRAYSSEDLGEGWALGFDS
+>PROKKA_00916
+MVTAIVLIKTDKSSIPETAETLAALEGVGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL
+SKVDGIQDTETMLAFRTYSSEDLGEGWALGFDS
+>PROKKA_01691
+MVTAIVMIKTDKSSIPETAETLAALEGIGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL
+SKVEGIQDTETMLAFRTYSSEDLGEGWALGFED
+>PROKKA_01589
+MVTAIVMITTDKSTIPETAQAIASLEGVSSVYSVTGAWDLVAMVKLKRYEDLADVIADQL
+SKVDGIEDTETMLAFRTYSTEDLEEGWALGFDG
+>PROKKA_01150
+MVTAIVLIKTDKSSIPETAEALAALEGVGSVYSVTGAWDLVAMVKVRRYEDLADVIADHL
+SKVDGIQDTETMLAFRTYSSEDLGEGWALGFDS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001001.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001001.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a0b621cc87042435486b22f11aaa4ac82fba6d2c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001001.fa
@@ -0,0 +1,30 @@
+>PROKKA_01199
+MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDISEGEKLF
+NANCASCHGTGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAQVKPNQFNDEQTA
+QLAAYVASLGAGPAVPEDEYLDVNHEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKYA
+PSLQGVEEKHIYEAMETGPQNMPVFSDSNIKPEDKRDIIAYLKTIENQGSPGGLALGSLG
+PVSEGLFIWTAGLALIIGFMVWLTSRSS
+>PROKKA_00919
+MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDITEGEKLF
+NANCASCHGMGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAPAKPNQFNEEQTA
+QLAAYVASLGAGPAIPEDEYLDVNHEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKYA
+PSLQGVDEKHIYEAMETGPQNMPVFSDSNIKPEDKRDIIAYLKTIENQGSPGGLTLGSLG
+PVSEGLFIWTAGLALIIGFMVWLTSRSS
+>PROKKA_01688
+MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDITEGEKLF
+NANCATCHGMGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAPAKPNQFNEEQTA
+QLAAYVASLGAGPAIPEDEYLDINNEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKFA
+PSLQGVEEKYIYEAMETGPQNMPVFSDANIKPEDKRDIIAYLKTIENQGSPGGLSLGSLG
+PVSEGLFIWTAGLALIIGFMVWLTSRSS
+>PROKKA_01585
+MKALSQNRRHPLVGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAAAADDITAGEKLF
+NANCASCHNMGATGTADGPSLVGVGAAAVDFQVGTGRMPMQMNGPQAQRKPNQFSEEQTA
+QLAAYVASLGAGPAVPADEDLDPNAEGVNIAKGGDLFRINCAMCHNAAAAGGALTRGKFA
+PSLEGVSEKHIYEAMETGPQNMPVFSDANLKPEDKRDIIAYLKTIEANGSPGGLQLGSLG
+PVAEGLFIWTAGLALIVGFMVWLTSRSS
+>PROKKA_01153
+MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDISEGEKLF
+NANCASCHGTGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAQVKPNQFNDEQTA
+QLAAYVASLGAGPAVPEDEYLDVNHEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKYA
+PSLQGVEEKHIYEAMETGPQNMPVFSDSNIKPEDKRDIIAYLKTIENQGSPGGLALGSLG
+PVSEGLFIWTAGLALIIGFMVWLTSRSS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001003.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001003.fa
new file mode 100644
index 0000000000000000000000000000000000000000..74c937c7e0489788f295035d03bef69c52ead942
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001003.fa
@@ -0,0 +1,55 @@
+>PROKKA_01201
+MSTTVNEFQPATSTGRIANFVDTRTGMSPIVKFFARKIFPDHWTFMFGEVALYSFVILLL
+SGAFLTFFFDPSMSEVVYNGAYAPLRGIEMSAAYASTLDISFDVRGGLFMRQLHHWAALM
+FVAAMSVHMLRVFFTGAFRRPRELNWLVGCFLLMAGWAAGFTGYSLPDEVLSGNGLRIID
+GILKSLPLVGTYLSAFFFGGEFPGHSVIGRLYALHIMIVPAAILLLIGIHLFMVVVHKHT
+QYPGPGRTEDNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINANWNYGPYDPSPVQ
+AGTQPDWYIGVFDGALRLMPGMIGDYSFLWNIPMPWGSSVSLPMGVLVPLIPVGVLLVGM
+CAWPWIERWITKDDTEHHLLDRPRNAPARTGIGVAAVVWYCVMWAAASSDLIATHFHLSL
+NDVLYVLRALFFLGPVIAFIVTRRICLSLQRKDRELVLHGHEAGVIEMSPEGGFHERHRP
+LTDYELYRLVAFEDRRPVPAIPGRNGKVGALEKARAGLNRMFYQERVAPVSREELVEART
+HGQHGHEEHPVELGHGSDAPRLER
+>PROKKA_00921
+MSTTVNEFQPATTTGRIANFVDTRMGMSPIVKFFGRKIFPDHWTFMFGEVALYSFVILLL
+SGAFLTLFFDPSMSEVVYDGAYAPLRGIEMSAAYASTLDISFDVRGGLFMRQLHHWAALM
+FVAAMSVHMLRVFFTGAFRRPRELNWLVGCFLLMAGWAAGFTGYSLPDEVLSGNGLRIID
+GILKSLPLVGTYLSAFFFGGEFPGHSVIGRLYALHIMIVPAAILLLIGIHLFMVVVHKHT
+QYPGPGRTEDNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINANWNYGPYDPSPVQ
+AGTQPDWYIGVFDGALRLMPGMIGDYSFLWNIPMPWGSSVSLPMGVLVPLIPVGVLLVGM
+CTWPWIERWITKDNTEHHLLDRPRNAPARTGIGVAAVVWYCVMWAAASSDLIATHFRLSL
+NDVLYVLRALFFLGPVIAFIVTRRICLSLQRKDRELVLHGHEAGVIEMSPEGGFHERHRQ
+LTDYELYRLVSFEDRRPVPAIPGRNGKVGMLEKARAGLNRMFYQDRVAPVSREELVEART
+HGQHGHEEHPVELEHGSHAPHLDR
+>PROKKA_01686
+MSTTVNEFQPATSTGRIANFVDTRMGMSPIVKFFARKIFPDHWTFMFGEVALYSFVILLL
+SGAFLTFFFDPSMSEVVYNGAYAPLRGIEMSAAYASTLDISFDVRGGLFMRQLHHWAALL
+FVAAMSVHMLRVFFTGAFRRPRELNWLVGCFLLMAGWAAGFTGYSLPDEVLSGNGLRIID
+GILKSLPIVGTYLSAFFFGGEFPGHSIIGRLYALHIMVVPAAILLLIGIHLFMVVVHKHT
+QYPGPGRTENNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINANWNYGPYDPSPVQ
+AGTQPDWYIGVFDGALRLMPGMIGDFSFLWNIPMPWGSSVSLPMGVLVPLIPIGVLIVGM
+CAWPWIERWITKDDTEHHLLDRPRNAPTRTGIGVAAVIWYCVMWAAASSDLIATHFRLSL
+NDVLYALRTLFFLGPVIGFIVTRRICLSLQRKDRELVLHGHEAGVIEMSPDGGFHERHRQ
+LTDHELYRLVSFEDRRPVPALPNRSGKVGMIEKARAGLNRMFYQDRVAPVTREELVEARA
+HGHHGVEDGGHHELGADPSSHNPKIDG
+>PROKKA_01583
+MSTATHEYQPATGTGRLANFLDTRVGLSPIVKFFGRKTFPDHWTFMFGEVALYSFVILLL
+SGAFLTFFFDPSMSHVTYDGAYAPLRGIEMSAAMASALDISFDIRGGLFMRQLHHWSALL
+FVASMSVHMLRIFFTGAFRRPRELNWVVGCFLLMAGWAAGFTGYSLPDDVLSGNGLRIID
+GILKAMPLVGSYLSAFLFGGEFPGYSVIGRLYALHIMIVPAIILLLIAVHLFMVVVHKHT
+QYPGPGRTENNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINSIWIYGPYDPSPVS
+AGTQPDWYIGPFDGALRLMPGMIGDFSFLWNIPMPWGSRVSLPMGVLTPLIPVGVILVGM
+ISWPWIERWITKDDREHHLLDRPRNAPARTGIGVGMMIMWCTMWAAASSDLIATHFHLSL
+NDVLYFLRALFILGPILGFIVTRRICISLQRRDRETVLHGHESGVVEMSPEGGFSERHRQ
+LTDYEMYRLVSFEDRRPVPATPGRNGKVSGAERMRAGLNRMFYQERVAPVSREELVEART
+HGHGEHVGAVQGGSHSAELGH
+>PROKKA_01155
+MSTTVNEFQPATTTGRIANFVDTRMGMSPIVKFFGRKIFPDHWTFMFGEVALYSFVILLL
+SGAFLTLFFDPSMSEVVYDGAYAPLRGIEMSAAYASTLDISFDVRGGLFMRQLHHWAALM
+FVAAMSVHMLRVFFTGAFRRPRELNWLVGCFLLMAGWAAGFTGYSLPDEVLSGNGLRIID
+GILKSLPLVGTYLSAFFFGGEFPGHSVIGRLYALHIMIVPAAILLLIGIHLFMVVVHKHT
+QYPGPGRTEDNVVGYPVGPVYAAKAGGFFFIVFGVLALIASTVTINANWNYGPYDPSPVQ
+AGTQPDWYIGVFDGALRLMPGMIGDYSFLWNIPMPWGSSVSLPMGVLVPLIPVGVLLVGM
+CTWPWIERWITKDNTEHHLLDRPRNAPARTGIGVAAVVWYCVMWAAASSDLIATHFHLSL
+NDVLYVLRALFFLGPVIAFIVTRRICLSLQRKDRELVLHGHEAGVIEMSPEGGFHERHRQ
+LTDYELYRLVSFEDRRPVPAMPGRNGKVGALEKARAGLNRMFYQDRVAPVSREELVEART
+HGQHGHEDGGHHELGADPSSHNPKIDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001007.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001007.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b95b9ce5e09bb47ca9668da5cdcfe4ce5687d1ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001007.fa
@@ -0,0 +1,20 @@
+>PROKKA_01206
+MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAG
+GSCACGDSFH
+>PROKKA_00925
+MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAG
+GSCACGDSFH
+>PROKKA_01681
+MALSADETGVEIGATQDSEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVQVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAV
+GSCACGDSFH
+>PROKKA_01579
+MALSAEETGVEIGATEDATGLPPHEVELTDVAAAKVRALLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAV
+GSCACGDSFH
+>PROKKA_01163
+MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYIMGATIDFEDTISKQGFTIDNPNAG
+GSCACGDSFH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001008.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001008.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3dc828cc4cb321cfeafa6b6182a7161ee07c3ace
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001008.fa
@@ -0,0 +1,45 @@
+>PROKKA_01207
+MTDITSRAPQDAALVSAVREAVEARFPTTLQTLTDLVAIPGIAWDSADRAQLERSAEAVA
+GLLREAGLQDVEIVSEIRDDGRPGGPAVIGEKPGTSDKPTVLFYAHHDVQPIGDEDLWDT
+PPLVATERGGRLYGRGAADDKAGIMVHLAALAALRDVLPDAGVGVRVFIEGEEEAGSPTF
+RTFLEKHRARLDADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP
+VLDAVVLLSRLIATLHDADGAVAVPGLEPRQTAGLDYPEDVFRADAGVLDGVTLAGRGPV
+ADRLWNAPALSIIGIDAPSVAESSNTIQPAARAKFSMRLGPGMEPAEAFEALRTHLEAQS
+AAVLGAEITVTAGEFGQPFTTDTSAPAAAAMMAALEDAWGVEPRAIGMGGSIPFTADLAE
+VFPEATLLITGVEDPDTRAHSANESLHIDDFQRAVVAEALWLARLSA
+>PROKKA_00926
+MTDITSRAPQDAALVSAVREAVEARFPTTLQTLTDLVAIPGIAWDSADRTQLERSAEAVA
+GLLRAAGLQHVEIVTETRDDGRPGGPAVIGEKPGASDKPTVLLYAHHDVQPIGDEDLWDT
+PPLVATERGGRLYGRGAADDKAGIMVHLAALAALRDVLPDAGVGVRVFIEGEEEAGSPTF
+RTFLEKHRARLDADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP
+VLDAVVLLSRLIATLHDADGAVAVPGLEPRQTAGLDYPEDVFRADAGVLDGVTLAGRGPV
+ADRLWNAPALSIIGIDAPSVAESSNTIQPAARAKFSLRLGPGMDPAEAFEALRTHLEAQS
+AAVLGAEITVTAGEFGQPFTTDTSATAAAAMMAALEDAWDVEPRAIGMGGSIPFTADLAQ
+VFPEATLLITGVEDPDTRAHSANESLHIDDFQRAVVAEALWLARLSA
+>PROKKA_01680
+MTETTPPVRDDAALVAAVRDAVDARFPQTLQTLTDLVAIPGIAWDSADRAQLERSSEAVA
+ALLRQAGLQGVEIVTETREDGRPGGPAVIGEKPGASDKPTVLLYAHHDVQPIGDEALWDT
+EPLVATEKGGRLYGRGAADDKAGIMVHLAALAALKDVLPDAGVGVRVFIEGEEEAGSPTF
+RTFLENHRARLEADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP
+VLDAVVLLSRLIATLHDADGAVAVPGLEPRRSASLDYPEDVFRADAGVLDSVTLAGRGPV
+ADRLWNAPALSVIGIDVPSVAESSNTIQPQARAKFSLRLGPGMDPAEAFEALKAHLEAQS
+AAVLGAEITVEAGEFGQPFDTDTSDPLAAAMMGALGDAWGVAPKEAGMGGSIPFTADLAE
+VFPDATILITGVEDPDSRAHSANESLHIEDFRRAVVAEALWFARLAG
+>PROKKA_01578
+MTQSTQNTPVGAAPDPELVSAIRAAVDRRFPETLQSLKDLVSIPGIAWDSMDREPLERSA
+AAVADLLRTAGLEGVETAVEERADGRPGGPAVIGGRPAVGDKPTVLLYAHHDVQPLGEEG
+LWDTPPLVATERDGRLYGRGAADDKAGIMVHLAALAALDEVCPDAGVGVRVFIEGEEEAG
+SPTFRPFLERHRDRLAADAIVVADSSNWAVGEPALTTSLRGVVSATVTVRALDHAVHSGM
+FGGPVLDAVVLMSRLIATLHDADGAVAVPGLEPRHHADVDYPEDAFRADSGILPGTRLAG
+RGALADRLWNGPALSVIGLDAPSVDTSSNTIQPAARAKISLRLGPGMDPAASLDALRAHL
+EAQSDAVLGAEITVEPGELGQPFSTDTSAPAAAAMMGALGAAFATPARETGLGGSIPFTA
+DLKELFPEATILITGVEDPDSRAHSANESLHLEDFRRAIVAEALWLAAMGA
+>PROKKA_01164
+MTDITSRAPQDAALVSAVREAVEARFPTTLQTLTDLVAIPGIAWDSADRTQLERSAEAVA
+GLLREAGLQEVEIVTETRDDDRPGGPAVIGEKPGASDKPTVLLYAHHDVQPIGDEDLWDT
+PPLEATERGGRLYGRGAADDKAGIMVHLAALAALRDVLPDAGVGVRVFIEGEEEAGSPTF
+RTFLEKHRARLDADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP
+VLDAVVLLSRLIATLHDADGAVAVPGLEPRQTAGLDYPEDVFRADAGVLDGVTLAGRGPV
+ADRLWNAPALSIIGIDAPSVAESSNTIQPAARAKFSLRLGPGMEPAEAFEALRTHLEAQS
+AAVLGAEITVTAGEFGQPFTTDTSAPAAAGMMAALEDAWGVEPRAIGMGGSIPFTADLAE
+VFPEATLLITGVEDPDTRAHSANESLHIDDFQRAVVAEALWLARLSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001014.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001014.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d4d8ee962d6713bab1d2184f81a1bc015ba7a8ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001014.fa
@@ -0,0 +1,35 @@
+>PROKKA_01214
+MTDLVDPARAADGFRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH
+REDFQLVLVDTPGLHRPRTLLGERLNDLVAETLNEVDAVGMCLPADEAIGPGDRFIAQQL
+SYLHRTPVVAVVTKTDKVGPEQLMAQLVAVTALGDEVLGPENGGEGFAAVVPVSAVAGRQ
+VDDVLGVFAGLLPAGPPLYPDGELTDEPEAVMVAELIREAALEGVRDELPHSVAVMVEEM
+SLREDRPADRPLMDVWANVFVERDSQKGIIIGKGGSRLREIGAQARAGIERMLGTKVHLD
+LRVKVAKEWQRDPKQLGRLGF
+>PROKKA_00933
+MTDLVDPARAADGFRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH
+REDFQLVLVDTPGLHRPRTLLGERLNDLVAETLNEVDAVGMCLPADEAIGPGDRFIAQQL
+SYLHRTPVVAVVTKTDKVGPEQLMAQLVAVTALGDEVLGPENGGEGFAAVVPVSAVAGRQ
+VDDVLGVFAGLLPAGPPLYPDGELTDEPEAVMVAELIREAALEGVRDELPHSVAVVVEEM
+SLREDRPADRPLMDVWANVFVERDSQKGIIIGKGGSRLREIGAQARAGIERMLGTKVHLD
+LRVKVAKEWQRDPKQLGRLGF
+>PROKKA_01674
+MTDLVDPARAADGHRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH
+REDFQLVLVDTPGLHRPRTLLGQRLNDLVAETLGEVDAVGFCLPADEAIGPGDRFIAQQL
+AHLHRTPVVAVVTKTDKVGPEQLMAQLLAVTALGEEVLGPENGGEGFAAVVPVSAVAGRQ
+VDDVLEVLRGLLPEGPPLYPDGELTDEPEAVMIAELIREAALEGVRDELPHSVAVVVEEM
+ALREGRPDDRPLMDVWANLFVERDSQKGIIIGKGGSRLREIGARARAGIERMLGTKVHLD
+LRVKVAKEWQRDPKQLGRLGF
+>PROKKA_01571
+MTSLLDPAVPEGHRSGFACLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVHR
+PDFQLVLVDTPGLHRPRTLLGERLNALVQETLSEVDVVGFCLPADEKIGPGDRFIAQQLA
+ALRRTPVVAIVTKTDKTDPQRVAEQLLAVTALGDEVLGPENGGRGFAAVVPVSAVAGRQV
+EDVESVLAQLLPDGPPLYPDGELTDEPEAIMVAELIREAALEDVRDELPHSVAVVVEEMN
+PREGRPEERPLLDVYANVFVERDSQKGIIIGKGGSRLRAIGTQARTGIERMLGTPVHLDL
+RVKVAKDWQRDPKHLNRLGM
+>PROKKA_01171
+MTDLVDPARAADGFRSGFVSLVGRPNAGKSTLTNALVGEKVAITSSKPQTTRHTIRGIVH
+REDFQLVLVDTPGLHRPRTLLGERLNDLVAETLNEVDAVGMCLPADEAIGPGDRFIAQQL
+SYLHRTPVVAVVTKTDKVGPEQLMAQLVAVTALGDEVLGPENGGEGFAAVVPVSAVAGRQ
+VDDVLGVFAGLLPAGPPLYLDGELTDEPEAVMVAELIREAALEGVRDELPHSVAVVVEEM
+SLREDRPADRPLMDVWANVFVERDSQKGIIIGKGGSRLREIGAQARAGIERMLGTKVHLD
+LRVKVAKEWQRDPKQLGRLGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001019.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001019.fa
new file mode 100644
index 0000000000000000000000000000000000000000..47b3cd0dc13b398c927ffcf4879b9bbad818c642
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001019.fa
@@ -0,0 +1,40 @@
+>PROKKA_01219
+MTDHYETLGVSRDASTEEIRRAYRKLARTHHPDVNPDPEAAEQFKRISHAYEVLSDEGRR
+RAYDTTGNENGQAGFPGGFGGAGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT
+ARIDLRDAVFGGEQTIELDTAVRCDRCEGSCCEPGTQPETCQTCHGHGMIQRPVRSLLGT
+VMATEACPACQGFGTVIPTPCHECDGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP
+GGGPNGDLYVEIAVRPDETFRREGDHLATTVTVPMAAAALGTTVTLDTLDGKQSLSLDPG
+VQSGHVEVLHGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRQLLERLAEVRGEEVVHGA
+PQAKGMFARLRENLRNL
+>PROKKA_00938
+MTDHYETLGVSRDASTEEIRRAYRKLARTHHPDVNPDPEAAEQFKRISHAYEVLSDEGRR
+RAYDTTGNENGQAGFPGGFGGAGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT
+ARIDLRDAVFGGEQTIELDTAVRCDRCEGSCCEPGTQPETCQTCHGHGMIQRPVRSLLGT
+VMATEACPACQGFGTVIPTPCHECDGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP
+GGGPNGDLYVEIAVRPDETFRREGDHLATTVTVPMAAAALGTTVTLDTLDGKQSLSLDPG
+VQSGHVEVLHGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRQLLERLAEVRGEEVVHGA
+PQAKGMFARLRENLRNL
+>PROKKA_01669
+MTDHYATLGVSRDASTEEIRRAYRKLARTHHPDVNPDPESAEQFKRISHAYEVLSDEGRR
+RAYDTTGNENGQSGFPGGFGGGGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT
+APIDLEDAVFGGEQTITLDTAVRCKRCEGSCCEPGTEPETCQTCQGHGMIQRPMRSLLGT
+VMATEACPACQGFGTVIPDPCHECAGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP
+GGGPNGDLYVEIAVRPHETFRREGDHLATTVTVPMAAAALGTTVTLATLDGEQTVRLEPG
+VQSGHVETLAGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRELLERLAELRGEEVVHGT
+PPARGMFARLRENLRNL
+>PROKKA_01566
+MADHYATLGVSRDASAEEIKRAYRKLARQHHPDVNPSEEAAEEFKRISHAYEVLSDEDKR
+RVYDQTGNENGTAGGFGGGGFGGAGFGGFADIFETFMNAAGTPGGGRGPMPRARRGQDAL
+VTARIELRDAVFGGEATLQLDTAVTCERCSGTCCEPGTHPETCSTCQGQGMTQRPVRSML
+GTIMAAETCPVCRGFGTVIPHPCTECSGQGRVRVQQPLTIRIPAGVDDGTRIHLAGRGEA
+GPGGGPNGDLYVEVQVRPDEVFRREGDHLATTVTVPMAAAALGTSVTLETLDGPQEVDIE
+PGTQSGHVETLRGLGVGRLRGAGRGDLKVDVVVTTPTDVTDEQRALLEQLAGLRGEEVVH
+GAPPQSKGMFARLRENLKNL
+>PROKKA_01177
+MTDHYETLGVSRDASTEEIRRAYRKLARTHHPDVNPGPEAAEQFKRISHAYEVLSDEGRR
+RAYDTTGNENGQAGFPGGFGGAGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT
+ARIDLRDAVFGGEQTIELDTAVRCDRCEGSCCEPGTQPETCQTCHGHGMIQRPVRSLLGT
+VMATEACPACQGFGTVIPTPCHECDGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP
+GGGPNGDLYVEIAVRPDETFRREGDHLATTVTVPMAAAALGTTVTLDTLDGKQSLSLDPG
+VQSGHVEVLHGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRQLLERLAEVRGEEVVHGA
+PQAKGMFARLRENLRNL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001025.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001025.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f6348772c1328145a3975d63c92beb4c58765967
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001025.fa
@@ -0,0 +1,15 @@
+>PROKKA_01226
+MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEPEAAAAALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG
+>PROKKA_00945
+MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG
+>PROKKA_01662
+MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG
+>PROKKA_01559
+MANIKSQKKRILTNEKARQRNIAVKSELKTAIRAVDKAVAAGEQDAAVEALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG
+>PROKKA_01184
+MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001029.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001029.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d76aa96a8961dad92f7391132da311ca0c729797
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001029.fa
@@ -0,0 +1,35 @@
+>PROKKA_01230
+MASIEQWRDDALVRLRSRRSQLAGRARYGLRPPRRDRTAVVTDSAAALPGAVLGHGLAAG
+IRQVALPVMVGEQIHTEGTDELALELPLALAAGTPVRTSRPSPGAFRTVYAELARAGYAR
+ILSVHLSGELSGTVEAARLAAADAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMPVARI
+RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLLGTLLQVRPVMAVDDGAIGLVDRPR
+SAARAVDRLVELAVERAGEDPVRIAVHEYGDPETAMQLAERLQPISTTPVPVVELPAVLA
+AHLGLGALGVVICPLESPTGGSGD
+>PROKKA_00949
+MASIEQWRDDALVRLRSRRSQLAGRARYGLRPPRRDRTAVVTDSAAALPGAVLGHGLAAG
+IRQVALPVMVGEQIHTEGTDELALELPLALAAGTPVRTSRPSPGAFRTAYAELARAGYAR
+ILSVHLSGELSGTVEAARLAAAEAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMPVARI
+RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLLGTLLQVRPVMAVDDGAIGLVDRPR
+SAARAVDRLVELATERAGEDPVRIAVHEYGDPETAVQLAERLQPVSTTPVPVVELPAVLA
+AHLGLGALGVVICPLESPTGGSGD
+>PROKKA_01658
+MATIEQWRDDALVRLRSRRSQLVGRARYGLKPPRRDRTAVVTDSAAALPAAALGHSLAAG
+IRQVPLPVMVGDQIHAEGTDDLALELPLALAAGTAVRTSRPSPGAFRSVYAQLAREGYAR
+ILSVHLSGELSGTAEAARLAAVDAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMTVARI
+RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLIGTLLHVRPVLAVDDGAISLVDRPR
+SAARAVDRLVELATERAGDVPVRIAVHEYGDPETAAALAERLTPVSTTPVPVVELPAVLA
+AHLGLGALGVVVCPLESPTGGSGD
+>PROKKA_01555
+MASTSQWLEDAVERLRARRGQLVGRARYGLKPARRDRTGIVTDSAAALPVEVFAHPFAAG
+IRQVALPVMVGEQIHVEGDADLDLELQLALAAGTPVRTSRPAPGAFRAAYADLAQAGCAR
+ILSVHLSGELSGTVEAARLAAADAPVPVVVLDSRTAGLALGHAVLDAAVEAGFGRPLDQV
+AAIAQACADQSSVLFTVPHLEQLRRGGRIGAVPSLLGALLQVRPVLGLQDGSVHLVDRAR
+TSPRALERMVDLARERAAGGPARIAVHEYGDPAGATALAERLQSASATPVPVVPLPAVLA
+AHLGLGTLAVVLSPLEPVPSTSSSPAQAN
+>PROKKA_01188
+MASIEQWRDDALVRLRSRRSQLAGRARYGLRPPRRDRTAVVTDSAAALPGAVLGHGLAAG
+IRQVALPVMVGEQIHTEGTDELALELPLALAAGTPVRTSRPSPGAFRTAYAELARAGYAR
+ILSVHLSGELSGTVEAARLAAAEAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMPVARI
+RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLLGTLLQVRPVMAVDDGAIGLVDRPR
+SAARAVDRLVELATERAGEDPVRIAVHEYGDPETAVQLAERLQPVSTTPVPVVELPAVLA
+AHLGLGALGVVICPLESPTGGSGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001039.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001039.fa
new file mode 100644
index 0000000000000000000000000000000000000000..61479259b6ecf4f554c32507c168de081c66cebc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001039.fa
@@ -0,0 +1,31 @@
+>PROKKA_01240
+MTTTATGGAGPRAPFGRRLAHAMETAGPLCLGVDPHPGLLRQWGLSDTPAGLEAFSLTAL
+EAAVGPEGPRVAAIKPQVALYERHGSAGLAALERLLAAARDAGVLTIADAKRGDIGSTMD
+GYAAAWIADASPLAADAVTLSPYLGFGTLVPTIRAAHEVGRGVFVLALTSNPEGREVQHV
+GEGSAEGSVARRIAAAAAAENAALRGDDAWGPVGLVLGATVAAEADRLGLDLPALGGPLL
+APGFGAQGATARGMRADFGTAWPQVLATSSRGILSAGPSVASLVDTIEENRAALR
+>PROKKA_00959
+MTTTATGGAGPRAPFGRRLAQAMETAGPLCLGVDPHPGLLRQWGLSDTPAGLEAFSLTAL
+EAAVGPEGPRVAAIKPQVALYERHGSAGLAALERLLAAARDAGVLTIADAKRGDIGSTMD
+GYAAAWIADASPLAADAVTLSPYLGFGTLVPTIRAAHEAGRGVFVLALTSNPEGREVQHV
+GEGSAEGSVARRIAAAAAAENAALRGDDAWGPVGLVLGATVAAEADRLGLDLPALGGPLL
+APGFGAQGATARGMRADFGTAWPQVLATSSRGILSAGPSVASLVDTIEENRAALR
+>PROKKA_01648
+MAQAGPLCLGVDPHPSLLRQWGLPDTPAGLEAFSLTGLEAAVGPDGPRVAAIKPQVALYE
+RHGSAGLAALERLLAEARDAGVLTIADAKRGDIGSTMDGYAAAWTSDASPLAADAVTLSP
+YLGFGTLVPTIEAAHAAGRGVFVLALTSNPEGREVQHVGRDAGEGAVARRIAAAAADLNA
+ALRAEDEWGPVGLVLGATVAEDAERLGLDLPGLAGPLLAPGFGAQGATAAGMREGFGRAW
+PQVLATSSRGILAGGPTVAALVERIERDRADLG
+>PROKKA_01545
+MSVPAASMTREPFGRRLAAAMAAAGPLCLGIDPHPSLLQAWGLPDTAAGLESFGLTALEA
+AAGDGAARVAAVKPQVALFERHGSAGLAVLERLLAEARDAGVLTIADAKRGDIGSTMDGY
+AAAWLDDASPLAADAVTLSPYLGYGTLTASIERAAAAGRGVFVLALTSNPEGASVQHVGA
+SEGQGAVAARIVTSAAADDARLAGLDGWGPVGLVVGATVAGHARELGIDLAALRGPLLAP
+GFGAQGATGAGMREAFGAAWPQVLATSSRGILAAGPTVTSLTRAIDAARADLGVEGPDPR
+HAAGRDA
+>PROKKA_01198
+MTTTATGGAGPRAPFGRRLAHAMETAGPLCLGVDPHPGLLRQWGLSDTPAGLEAFSLTAL
+EAAVGPEGPRVAAIKPQVALYERHGSAGLAALERLLAAARDAGVLTIADAKRGDIGSTMD
+GYAAAWIADASPLAADAVTLSPYLGFGTLVPTIRAAHEAGRGVFVLALTSNPEGREVQHV
+GEGSAEGSVARRIAAAAAAENAALRGDDAWGPVGLVLGATVAAEADRLGLDLPALGGPLL
+APGFGAQGATARGMRADFGTAWPQVLATSSRGILSAGPSVASLVDTIEENRAALR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001040.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001040.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b38d2d94899ce4bf92559a4aab2765315a61fe93
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001040.fa
@@ -0,0 +1,100 @@
+>PROKKA_01241
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPEL
+ADATYVEPITPAVVAKIIEKERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANI
+EAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVEDLKYPVVVRPSFTMGGLGSG
+MAYDEADLYRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPVDGRVVVIEM
+NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR
+FAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRSLEQKGSELAFPQDADPQALL
+AAASTATTDRLSQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADEIRDAEVLDEA
+LLRRAKRHGFSDAQIGSLRHMDAAVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY
+DLETEVAPHEGESVIILGSGPNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVST
+DYDISDRLYFEPLTLEDVLEVIAAEEASGGVRGVFVQLGGQTPLKLAQQLADAGVPILGT
+SPAAIDLAEHRGEFALVLERAGLVAPKNGTAVSFDDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVEHATEITPDQPMLVDRFLEDAIEIDVDALYDGTELYLGGVMEHIEE
+AGIHSGDSACVLPPVTLGPDVLERVHRATERIAAGVGVRGLINIQFALASDVLYVIEANP
+RASRTVPFVSKATGVQLAKAAARIGVGESIADLRAAGMLPTAYDGGTLPIGAPVAVKEAV
+LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDKHFDTAFAKSQSAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQVVSTGGTAEVLRRNGIPAEVVAKIADAGHEDGAGTVLEQ
+LHAGTVDLVLNTPSGGDARTDGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRSYEWSV
+TSLQEHDARLQQAVAGPEAAA
+>PROKKA_00960
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPEL
+ADATYVEPITPAVVAKIIEKERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANI
+EAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVEDLKYPVVVRPSFTMGGLGSG
+MAYDEADLYRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPVDGRVVVIEM
+NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR
+FAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRSLEQKGSELAFPQDADPQALL
+AAASTATTDRLSQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADEIRDAEVLDEA
+LLRRAKRHGFSDAQIGSLRHMDAAVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY
+DLETEVAPHEGESVIILGSGPNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVST
+DYDISDRLYFEPLTLEDVLEVIAAEEASGGVRGVFVQLGGQTPLKLAQQLADAGVPILGT
+SPAAIDLAEHRGEFALVLERAGLVAPKNGTAVSFDDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVAHATEITPDQPMLVDRFLEDAIEIDVDALYDGTELYLGGVMEHIEE
+AGIHSGDSACVLPPVTLGPDVLERVHRATERIAAGVGVRGLINIQFALASDVLYVIEANP
+RASRTVPFVSKATGVQLAKAAARIGVGESIADLRAAGMLPTAYDGGTLPIGAPVAVKEAV
+LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDKHFDTAFAKSQSAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQVVSTGGTAEVLRRNGIPAEVVAKIADAGHEDGAGTVLEQ
+LHAGTVDLVLNTPSGGDARTDGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRSYEWSV
+TSLQEHDARLQQAVAGPEAAA
+>PROKKA_01647
+MPKRPDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPEL
+ADATYVEPITPAVVAKIIEKERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANI
+EAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVEDLKYPVVVRPSFTMGGLGSG
+MAYDEADLHRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPADGRVVVIEM
+NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR
+FAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRSLEQKGSELAFPQDADPRELL
+RRARTATTDRLAQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADQIRDAEVLDES
+LLRHAKRHGFSDAQIGSLRHMGADVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY
+DLETEVAPHEGRSVIILGSGPNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVST
+DYDISDRLYFEPLTLEDVLEVIAAEEASGGVLGVYVQLGGQTPLKLAQQLADAGVPILGT
+SPEAIDLAEHRGEFARVLDRAGLVAPKNGTAVSFEDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVEHATEITPDQPMLVDRFLEDAIEIDVDALYDGERMYLGGVMEHIEE
+AGIHSGDSACVLPPVTLGPDVLERVHRATEQIAAGVGVRGLINIQFALASDVLYVIEANP
+RASRTVPFVSKATGVQLAKAAAMIGVGKSIADLQAEGVLPTAYDGATLPLGAPVAVKEAV
+LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDRHYDTAFAKSQAAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQIVSTGGTAEVLRRNGIPAETVAKIAEAGGEDGAGTVLEQ
+LHAGTVDLVLNTPSGGDARTDGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRAYEWSV
+TSLQEHDARLQQAVEASA
+>PROKKA_01544
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVILVNSNPATIMTDPEL
+ADATYVEPITPEVVAKIIEKERPDAVLPTLGGQTALNTAIALDKDGVLEKFGVELIGANI
+AAIELGENRELFKGVVERAGGESARSHIVHTMEEAFAAVEDLKYPVVVRPSFTMGGLGSG
+MAYDEADLRRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPEDGRVVVIEM
+NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR
+FAFEKFPAADATLTTTMKSVGEAMAIGRSFSEALQKALRSLEQKGSELSFDRDADPASLL
+ASARTATTQRLAQTQRALYAGATLEEAFEATAIDPWFLDQLMLINEVADEVREAPQLDEA
+VLRRAKRHGFSDAQIGSLRHMDPAVVRGLRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY
+DLESEVDEHAAPSVVILGSGPNRIGQGIEFDYSCVHATLALREAGYETVMVNCNPETVST
+DYDISDRLYFEPLTLEDVLEVIAAEEATGGVAGVFVQLGGQTPLKLAQQLADAGVPILGT
+SPEAIDLAEHRGEFARVLDEAGLIAPKNGTAVSFEDARRVADEIGYPVLVRPSYVLGGRG
+MEIVYTEEALAHYVTNATEITPTQPMLVDRFLEDAIEIDVDALYDGHELYLGGVMEHIEE
+AGIHSGDSACVLPPVTLGPDVLERVRTATEKIAAGVGVRGLINIQFALASDVLYVIEANP
+RASRTVPFVSKATGVQLAKAAAMIGMGRTIAELRAAGTLPTAFDGASLPMGASVAVKEAV
+LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDRHFDTAFAKSQAGAGGPLPTEGRVFVSV
+ANRDKRAVVGQAKRLVDLGFEIVSTGGTAEVLRRNGVPAEVVAKIADASDADGAGTVLEQ
+LHEGRVDLVLNTPSGGEARTDGYEIRAAATSLGVPVITTTAEFAACLQAIEAMRTYEWSV
+TSLQEHEERLAQAVAAEASA
+>PROKKA_01199
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPEL
+ADATYVEPITPAVVAKIIEKERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANI
+EAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVEDLKYPVVVRPSFTMGGLGSG
+MAYDEADLYRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPVDGRVVVIEM
+NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR
+FAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRSLEQKGSELAFPQDADPQALL
+AAASTATTDRLSQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADEIRDAEVLDEA
+LLRRAKRHGFSDAQIGSLRHMDAAVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY
+DLETEVAPHEGESVIILGSGPNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVST
+DYDISDRLYFEPLTLEDVLEVIAAEEASGGVRGVFVQLGGQTPLKLAQQLADAGVPILGT
+SPAAIDLAEHRGEFALVLERAGLVAPKNGTAVSFDDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVEHATEITPDQPMLVDRFLEDAIEIDVDALYDGTELYLGGVMEHIEE
+AGIHSGDSACVLPPVTLGPDVLERVHRATERIAAGVGVRGLINIQFALASDVLYVIEANP
+RASRTVPFVSKATGVQLAKAAARIGVGESIADLRAAGMLPTAYDGGTLPIGAPVAVKEAV
+LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDKHFDTAFAKSQSAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQVVSTGGTAEVLRRNGIPAEVVAKIADAGHEDGAGTVLEQ
+LHAGTVDLVLNTPSGGDARTDGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRSYEWSV
+TSLQEHDARLQQAVAGPEAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001041.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001041.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e5de797b64bb0d6a761d61f5132317b85a7564a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001041.fa
@@ -0,0 +1,40 @@
+>PROKKA_01242
+MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT
+SPHIGNTGVNDADRESRAIFAAGYVVRDAARRPSNWRAERTLDEELEAFGVVGIREVDTR
+AITRRLRTEGSMRAGVFSGEHAARPEAELLAEVRAQPSMAGARLAESVTTEQPYVIEPAE
+HGWEGEPIAEIAALDLGIKAATPRHLASRGIRVHVLPAATDLAGIRAVDPDGVFLSNGPG
+DPATADAQVELLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVLDKATG
+RVAITSQNHGFAVAAPLGEPIEAPESRFGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP
+ESAAGPNDTLDLFDRFVQLLTEHRAATTPATEGA
+>PROKKA_00961
+MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT
+SPHIGNTGVNDADRESRAIFAAGYVVRDAARRPSNWRAERTLDEELETFGVVGIREVDTR
+AITRRLRTEGSMRAGVFSGEHAARPEAELLAEVRAQPSMAGARLAESVTTEQPYVIEPAE
+HGWEGEPIAEIAALDLGIKAATPRHLASRGIRVHVLPAATDLAGIRAVDPDGVFLSNGPG
+DPATADAQVELLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVLDKATG
+RVAITSQNHGFAVDAPLGEPIEAPESRFGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP
+ESAAGPNDTLDLFDRFVQLLTEHRAATTPATEGA
+>PROKKA_01646
+MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT
+SPHIGNTGVNDTDRESRAIFAAGYVVRDAARRPSNWRAERTLDEELEAFGVVGIREVDTR
+AITRRLRTEGSMRAGVYSGEHAGRPEAELLAEVREQPSMAGARLAETVTTEQPYVIEPAA
+HGWEGEPLAEIAALDLGIKAATPRHLASRGIRVHVLPATAGLEEIRAVSPDGVFLSNGPG
+DPATADAQVALLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVMDNATG
+RVAITSQNHGFAVDAPLGEPVEAPETRYGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP
+ESAAGPNDTLDLFDRFVRMLTEHRDAAAPAATEGA
+>PROKKA_01543
+MSTPTPETALLVLEDGTVHRGRAYGARGSTLGEAVFTTGMTGYQETLTDPSYARQIVVQT
+APHIGNTGVNDEDAESRAIWVAGYVVRDAARRPSNWRSQRTLDEELAAHGVVGIQDVDTR
+AITRALRTEGSMKAGIFSGEAAQRPEAELLAEVREQPSMAGARLAETVSAPSAYVVEPSD
+HGWDGEPIADVAALDLGIKAATPHHLAARGIRVHVLPADSDFAAIQAVRPDGVFMSNGPG
+DPATADAQVAVLREVLDAGLPYFGICFGNQIFGRALGFGTYKLPFGHRGPNQPVMDKATG
+RVEITSQNHGFAVDAPIGEVVEAPEARYGRVEVSHWSLNDDVVEGLRLLDRPAFSVQFHP
+EAAAGPHDSLGLFDRFAHTLTERRAAAPSATPEGA
+>PROKKA_01200
+MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT
+SPHIGNTGVNDADRESRAIFAAGYVVRDAARRPSNWRAERTLDEELEAFGVVGIREVDTR
+AITRRLRTEGSMRAGVFSGEHAARPEAELLAEVRAQPSMAGARLAESVTTEQPYVIEPAE
+HGWEGEPIAEIAALDLGIKAATPRHLASRGIRVHVLPAATDLAGIRAVDPDGVFLSNGPG
+DPATADAQVELLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVLDKATG
+RVAITSQNHGFAVAAPLGEPIEAPESRFGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP
+ESAAGPNDTLDLFDRFVQLLTEHRAATTPATEGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001048.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001048.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6cd602f5603bc9fe86bc2d14e122f862d3941f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001048.fa
@@ -0,0 +1,25 @@
+>PROKKA_01250
+MTDTPGTAPAPGPDPSTRPVPGPVTVCPWEGMTGALEARLTAAATVAAAADEDPAARPAR
+RVVLVGPMGAGKTTVGRALAAVTGLPFVDSDELFTQVHGPIPEFFAEHGEAAFRAEEARV
+IGHVLGRPTPCVLSCGGGAVLHPGTRRALAGPDSDVVYLAVGEEEALRRVGGGAGRPVLA
+GDPAGTWRRILAEREGLYREVADLVLDTTGLTAAEAAWRIVGDAHRPRRSESHP
+>PROKKA_00969
+MTDTPGTAPAPGPDPSTRPVPGPVTVCPWEGMIGALEARLTAAATVAAAADEDPAARPAR
+RIVLVGPMGAGKTTVGRALAAVTGLPFVDSDELFTQVHGPIPEFFAEHGEAAFRAEEARV
+IGHVLGRPAPCVLSCGGGAVLHPGTRRALAGPDSDVVYLAVGEEEALRRVGGGAGRPVLA
+GDPAGTWRRILAEREGLYREVADLVLDTTGLTAAEAAWRIVGDAHRPRRSESHP
+>PROKKA_01638
+MPGPVSLCAWEAMTGALEARLATAAAAADGAPAPRIVLVGPMGAGKTTVGRALAATTGLP
+FVDADELFVQVHGPIPEFFAARGEAAFREEEARVIAHVLGRPSPCVLSCGGGAVLHPATR
+RALRGPGSDVVHLAVDEAVALRRVGGGAGRPVLAGDPAGTWRRILAEREPFYREVADLVV
+DTTGLTAAEAAWRIVEGVHRPRRSESHP
+>PROKKA_01535
+MSAQPAPTDGVPSWEAMVRGLDGRLAETSRDPGPVVVLVGPMGAGKTTVGRALAEATGRV
+FVDSDALFEDAFGSIPAYFTSRGEPEFRRQEERVIAHVLAHPAPCVLACGGGAVLSAATR
+ARLADPRAVVVSLQVAEPEALRRLGGGAGRPVLAGDPAGRWKAVLAERAPLYAEVADLTL
+DGTGHRPGDIASRIVEAIPTLPRRHTRP
+>PROKKA_01208
+MTDTPGTAPAPGPDPSTRPVPGPVTVCPWEGMIGALEARLTAAATVAAAADEDPAARPAR
+RIVLVGPMGAGKTTVGRALAAVTGLPFVDSDELFTQVHGPIPEFFAEHGEAAFRAEEARV
+IGHVLGRPAPCVLSCGGGAVLHPGTRRALAGPDSDVVYLAVGEEEALRRVGGGAGRPVLA
+GDPAGTWRRILAEREGLYREVADLVLDTTGLTAAEAAWRIVGDAHRPRRSESHP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001052.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001052.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a15bb90ef59140b01ee46cefbba11953f659820
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001052.fa
@@ -0,0 +1,85 @@
+>PROKKA_01255
+MKSQEIARRWTAFFESRGHRVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRVV
+SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKETAIPMAWELLTSSVEDGGFGLD
+PERLWVTVYREDDEAERIWREDVGVRPERIQRMGKEDNYWHTGQPGPGGPCSEIFYDRGP
+AYGVDGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDVAGELEHKNIDTGLGLERLAMI
+LQGVENMYETDQVRPVLDRAAQLAGRSYTSTEDPADPHYDDDVRLRMVADHVRSALMLIS
+DGVRPGNEGRGYVLRRLIRRVVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERI
+ARIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPDAFELHDTYGFPIELTLEIAE
+EAGVAVDEAGFRALMAEQRDRARADAKAKKSGHTDTAVYQRLRAEGQTHFTGYTEHTTES
+VVRGLLQNGEEVPSAGAGTELELVLDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPV
+KGLSVHRVKVLDGEVAAGAQALGAIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGS
+FNKEGYLRFDFRWAESLSAGARSEVEDVVNIAIRDDHTVLTQEMSLEEARALGAMSLFGE
+KYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH
+LAAERTLVSELSEMFKAPAEELKDRIGATLDRLKAAEKQVAELRAQALQAQAGQLAAQAR
+DVTTSGGTSVRVLAHHAGDVAGDQLRSLALDLRARIESAGGNAAGTPVFVALTAEAKGRP
+LVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQGGGQDVTRVGDALDAVVAAV
+RAA
+>PROKKA_00974
+MKSQEIARRWTAFFESRGHRVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRVV
+SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKETAIPMAWELLTSSVEDGGFGLD
+PERLWVTVYREDDEAERIWREDVGVRPERIQRMGKDDNYWNTGQPGPGGPCSEIFYDRGP
+AYGVDGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDIAGELEHKNIDTGLGLERLAMI
+LQGVENMYETDQVRPVLDRAAQLAGRSYTSTEDPADPHYDDDVRLRMVADHVRSALMLIS
+DGVRPGNEGRGYVLRRLIRRVVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERI
+SRIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPDAFELHDTYGFPIELTLEIAE
+EAGVAVDEAGFRALMAEQRDRARADAKAKKAGHTDTAVYQRLRAEGQTHFTGYTEHTTES
+VVRGLLQNGEEVASAGAGTELELVLDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPV
+KGLSVHRVKVLDGEVAAGAQALGAIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGS
+FNKEGYLRFDFRWAEALSAGARSEVEDVVNIAIRDDHAVLTQEMSLEEARALGAMSLFGE
+KYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH
+LAAERTLVSELSEMFKAPAEELKDRIGATLDRLKAAEKQVAELRAQALQAQAGQLAGQAQ
+DVTTSAGTSVRVLAHHVGDVAGDQLRSLVLDLRARIESAGGNAAGTPVLVALTAEAKGRP
+LVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQGGGQDVTRVGDALEAVVAAV
+RAA
+>PROKKA_01633
+MKSQEIARRWIAFFESKGHQHVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRAV
+SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKEKAIPMAWELLTTSVEDGGYGLD
+PERLWVTVYEEDDEAARIWEESVGVRPERIQRMGKDDNYWNTGQPGPGGPCSEIFYDRGP
+EYGADGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDVAGELENKNIDTGLGLERLAML
+LQGVENMYETDQVRPVLDRAAELSGREYTSTEDPTDPHYEDDVRLRMVADHVRSALMLIG
+DGVRPGNEGRGYVLRRLIRRVIRALRLMGVTEPVLPELLPVSRDAMKGSYPVVADEFERI
+SRIAYAEEKAFLRTIAAGTARLDAAVGQARTAGGGIAGADAFELHDTYGFPIELTLEIAE
+ESGVAVDEAGFRALMAEQRDRARADAKAKKSGHTDTALYQRLRAEGQTHFTGYTEHTTES
+VVRGLLLDGEEVASASAGTELEVILDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPV
+RGLSVHRVKVLDGEVPAGAEALGAIDLQRRLDGEKAHSGTHLVHAALHQVLGPEATQSGS
+FNKEGYLRFDFRWAESLSAGARSEVEDVVNIAIRDDHTVLTQEMSLEEARALGAMSLFGE
+KYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH
+LAAERTLVSELSEMFKAPAEELKDRIAASMDRLKAAEKQIAELQAKALQAQAGELAAQAQ
+DVTTASGVSVRVLARHVGEVAGDQLRGLVLDLRSRIESAGGNAAGTPVLVALTGEAKGRP
+LVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQGGGQDVTRVGDALDAVVAAA
+RAA
+>PROKKA_01530
+MKSHEIARRWTAYFEKQGHLVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRAT
+SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKEKAIPMAWELLTTSVEDGGYGLD
+PERLWVTVYEEDDEAARIWREDVGVRPERIQRMGKADNYWNTGQPGPGGPCSEIFYDRGP
+EYGVEGGPEADDTRYIEIWNLVFMQYRLSQVRSKYDFDVAGELEHKNIDTGLGLERLAMI
+LQGVENMYETDQVRPVLDRAAELAGKSYTSTEDPADPHYDDDVRLRMVADHVRSALMLIS
+DGVRPGNEGRGYVLRRLIRRVVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERI
+SRIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPDAFELHDTYGFPIELTLEIAE
+EAGVAVDEAGFHALMAEQRDRARADAKAKKSGHTDTAVYQRLRAEGQTHFTGYTEHTTES
+VVRGLLQNGEEVASAGAGTELELVLDATPFYAESGGQAADTGVITGDGFSLEVLDVQAPV
+KGLSVHRVKVLDGEVPVGAEAVGRIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGS
+FNKEGYLRFDFRWAEAVSAMARSEIEDVVNIAIRDDHQVLTQEMSLDEARAMGAMSLFGE
+KYGDRVRVVEINGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH
+LAAERTLVSDLSEMFKAPADQLKDRITATMDRLKAAEKQVADLQAKALQAQAGTLAAQAQ
+DVTTTSGASVKVLAHHAGEVAGDQLRSLVLGLRSRIESAGGNAAGTPVLVALTGEAKGRP
+LVVVATNEAARGAGLKAGAMVKLATAALGGGGGGKDDVAQGGGQDVTAVAAALDAVLDAV
+RDA
+>PROKKA_01213
+MKSQEIARRWTAFFESRGHRVVPSASLVSPDPSLLFTVAGMVPFIPYFLGEQTPPSPRVV
+SVQKCIRTADIEEVGKTVRHGTFFQMCGNFSFGDYFKETAIPMAWELLTSSVEDGGFGLD
+PERLWVTVYREDDEAERIWREDVGVRPERIQRMGKDDNYWNTGQPGPGGPCSEIFYDRGP
+AYGVDGGPAADDTRYIEIWNLVFMQYRLSAVRSKDDFDIAGELEHKNIDTGLGLERLAMI
+LQGVENMYETDQVRPVLDRAAQLAGRSYTSTEDPADPHYDDDVRLRMVADHVRSALMLIS
+DGVRPGNEGRGYVLRRLIRRVVRALRLMGVTEPVFPELLPVSRDAMKGTYPVVADEFERI
+SRIAYAEEKAFLRTIAAGTARLDAAVGQARSAGGGIAGPDAFELHDTYGFPIELTLEIAE
+EAGVAVDEAGFRALMAEQRDRARADAKAKKAGHTDTAVYQRLRAEGQTHFTGYTEHTTES
+VVRGLLQNGEEVASAGAGTELELVLDATPFYAESGGQAADTGLITGDGFRLEVLDVQAPV
+KGLSVHRVKVLDGEVAAGAQALGAIDLQRRLDGEKAHSGTHLVHAALHQILGPEATQSGS
+FNKEGYLRFDFRWAEALSAGARSEVEDVVNIAIRDDHAVLTQEMSLEEARALGAMSLFGE
+KYGDRVRVVEIDGAWSRELCGGTHVGRTAQIGSLTLLGEQSVGSGNRRVEALVGLDSFRH
+LAAERTLVSELSEMFKAPAEELKDRIGATLDRLKAAEKQVAELRAQALQAQAGQLVGQAQ
+DVTTSAGTSVRVLAHHVGDVAGDQLRSLVLDLRARIESAGGNAAGTPVLVALTAEAKGRP
+LVVVATNEAARAAGLKAGAMVKTATGVLGGGGGGKDDVAQGGGQDVTRVGDALEAVVAAV
+RAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001054.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001054.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b72fae447aaabb91a9b220842b2521197daaa920
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001054.fa
@@ -0,0 +1,25 @@
+>PROKKA_01257
+MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL
+RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEQRLDALVLRAGFARTIQQARQLVVHR
+HIMVDGKRVDVPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIDKL
+RATLTRRPKRSEVPVTCEEQLVVEYYAR
+>PROKKA_00976
+MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL
+RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEQRLDALVLRAGFARTIQQARQLVVHR
+HILVDGKRVDVPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIDKL
+RATLTRRPKRSEVPVTCEEQLVVEYYAR
+>PROKKA_01630
+MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL
+RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEMRLDALVLRAGFARTIQQARQLVVHR
+HIMVDGKRVDIPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIDKL
+RATLTRRPKRSEVPVTCEEQLVVEYYAR
+>PROKKA_01528
+MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL
+RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEMRLDALVLRAGFARTIQQARQLVVHR
+HIMVDGKRVDIPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIEKL
+RATLTRRPKRSEVPVTCEEQLVVEYYAR
+>PROKKA_01215
+MSGNLRTRRTVRHSRALGIALTPKAEKYMERRPYGPGQHGRARRKQDSDYAVRLKEKQRL
+RAQYNIREAQMRRYFEEAKRTAGLTGENLVELLEQRLDALVLRAGFARTIQQARQLVVHR
+HILVDGKRVDVPSFRVKEGQMIHVHERSEKMVPFQLAAAGAHQQVLPATPGYLTVEIDKL
+RATLTRRPKRSEVPVTCEEQLVVEYYAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001058.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001058.fa
new file mode 100644
index 0000000000000000000000000000000000000000..981ef350fe479b9775114d676909fdc1777fe01c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001058.fa
@@ -0,0 +1,55 @@
+>PROKKA_01261
+MPRLARLATAVTAAALSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHET
+GVFGESAAEIPAFDAVSGRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVT
+DKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTTTLRYLGGVRVGALPDSLAFSPNG
+AYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTALPAG
+VRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLED
+LWALTPTDWSTEGVLDASDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGR
+EWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLKVLTDLGYDSERECHSSLTTLGGR
+SFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPEPES
+VVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGA
+EGLTFVPADESPSGTALLIVANEVSGSTTVYEVNPTRRQ
+>PROKKA_00980
+MPRLARLATAVTAATLSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHET
+GVFGESAAEIPAFDAVSGRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVT
+DKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTTTLRYLGGVRVGALPDSLAFSPNG
+AYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTALPAG
+VRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLED
+LWALTPTDWSTEGVLDASDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGR
+EWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLKVLTDLGYDSERECHSSLTTLGGR
+SFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPEPES
+VVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGA
+EGLTFVPADESPSGTALLIVANEVSGSTTVYEVNPTRRQ
+>PROKKA_01627
+MRTLSRLAAATSMVALSAAVVAPLTVAAPAANPSGRSIELTAAGTHATGVFDASAAEIPA
+FDKTTGRLFVVNAQKGAIDVLTVGEDAEPAAESVLSVAGLPAADGSVTGAGAVVNSVAVA
+GAVMAATVEAEDKTGHGWLVFFDTRTLGFLGGVRVGALPDSVALAPNGAYAVVANEGEPA
+DDFSSDPEGTISVVSVPKNARQFARLGQDAVRTVDFRAYDEGAALPEGVRVFGPDVAVPS
+GHEEAGRIARNLEPEYASIDPTGRTAYVSVQEANAVVAVDLASASLADFWALHLTDWSTE
+GVLDVSDKDGAISPAYQPVLGVPMPDGLATYKHRGQTLVVTANQGDSREWGDFVDAERVK
+DLELCGDVFPHAKALQKNEALGRLNVLTDLGYDAERGCHTELHALGGRGFSIYTADGQRL
+FDSSGMLEEQIARLIAAGELPAHAFNANNDETPSFDSRSDDKGVEPESVVVGEVQGRQYA
+FVGLERIGGVMVFDITDPTDARYVDYINERAWDAVGEDGDAGLGDMGAEGLAFVPASDSP
+SGTALLIVATEVSGSTTVYEVDPVKGGKRT
+>PROKKA_01524
+MSRIVRLTRLGAAAGALALSAAVVAPSAVSAPVTATAAAANPSGKTVELSLAGTHETGVF
+GESAAEIPAFDAATGRLFVVNAEKGAVDVLRVGADGAPAAETVLSAEGLRTADGSVTDGG
+ATVNSVAVSGGVLAVAVEAADKTGLGWVAFFDTTTLSYLGGVRVGALPDSIAFSPDGAYA
+VVANEGEPADDFSADPEGTISVISVPKNVRQFARLTQAAVRTVDFRAYDAGTALPEGVRV
+FGPDVQVPEGQEPAGRIARNLEPEYVTIDDTGRTAYVSVQEANAVVAVDLKSATLKDFWA
+LQLTDWSKEGVLDASNEDKAITLRNQPVLGVPMPDGVDTYRYRGQDLVVTANEGDSREWG
+DFVDAARVKDLELCTAEYPDAKALQKKPALGRLNVVTDLGYDADRDCFSQLHAFGGRSFS
+IYTADGTRLFDSAGMIEEQIAQLIADGELPESAFNANNDETPSFDSRSDDKGPEPEAVVV
+GRVQGRTYAFVGLERIGGVMVFDITDPTKATYVDYVNERNWDAEGDDAAAGLGDMGAEGL
+TFVPANESPSGTALLVVANEVSGSTTVYEVNPVRR
+>PROKKA_01219
+MPRLARLATAVTAATLSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHET
+GVFGESAAEIPAFDAVSGRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVT
+DKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTTTLRYLGGVRVGALPDSLAFSPNG
+AYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTALPAG
+VRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLED
+LWALTPTDWSTEGVLDASDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGR
+EWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLKVLTDLGYDSERECHSSLTTLGGR
+SFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPEPES
+VVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGA
+EGLTFVPADESPSGTALLIVANEVSGSTTVYEVNPTRRQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001060.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001060.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa80663b0ac6c9c67b961fd9e41c8a93c1188787
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001060.fa
@@ -0,0 +1,60 @@
+>PROKKA_01263
+MLRTHSLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVRDEADFDPLR
+NEWVLQVTGTVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARL
+RHRYLDLRRPQPSRIMRLRSEVNRTARELLHGEGFVEVETPTLTRSTPEGARDFLVPARL
+APGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADRQPEFTQLDIEASFVEQD
+DVIALGEKIVKALWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKDT
+PFRVFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGELTGPVSKNI
+SEEEKAGLAAAVGANPGDCVFFAAGKPKESRALLGAARVEIGRRCGLFTDAGDGVAAKDA
+DWAFVWVVDAPMFEPAADAVASGDVAVGAGAWTAVHHAFTSPKPEFADTFDTDPGAALAY
+AYDIVCNGNEIGGGSIRIHRQDVQERVFEVMGLSPEEANEKFGFLLEGFKYGAPPHGGIA
+FGWDRVVALLAGTDSIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAQPEPKQAEA
+EPEA
+>PROKKA_00982
+MLRTHSLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVREEADFDPLR
+NEWVLQVTGTVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARL
+RHRYLDLRRPQPSRIMRLRSEVNRTARELLHGEGFVEVETPTLTRSTPEGARDFLVPARL
+APGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADRQPEFTQLDIEASFVEQD
+DVIALGEKIVKALWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKHT
+PFRVFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGELTGPVSKNI
+SEEEKAGLAAAVGANPGDCVFFAAGKPKESRALLGAARVEIGRRCGLFTDAGDGVAAKDA
+DWAFVWVVDAPMFEPAADAVASGDVAVGAGAWTAVHHAFTSPKPEFADTFDTDPGAALAY
+AYDIVCNGNEIGGGSIRIHRQDVQERVFEVMGLSPEEANEKFGFLLEGFKYGAPPHGGIA
+FGWDRVVALLAGTDSIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAQPEPKQAEA
+EPEA
+>PROKKA_01624
+MNPTISSGRSPDGEDAFVLRTHQLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDAS
+GFAQVVVRDEADFDPLRNEWVLQVSGVVERRPEGNENPNLPSGEIELIAETVTVLNTAAA
+LPFQVDEHVEVGEEARLRHRYLDLRRPEPSRIMRLRSEVNRTAREMLHGEGFTEVETPTL
+TRSTPEGARDFLVPARLAPGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADR
+QPEFTQLDIEASFVEQDDVIALGEKIVKAVWALVGVDVPTPIRRMTYAEAMEKYGSDKPD
+LRFGLELTDLTAYFKDTPFRVFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAY
+VLIQEDGSLTGPVSKNISDEEKAGLAAAVGANPGDCVFFAAGKPKESRALLGAARVEIGR
+RCELFTDAGNGVEAKDADWAFVWVVDAPMFEPAADAVASGDVAVGSGAWTAVHHAFTSPK
+PEFADTFDTDPGSALAYAYDIVCNGNEIGGGSIRIHRQDMQERVFSVMGLSQEDAQEKFG
+FLLEGFKYGAPPHGGIAFGWDRVVALLAGTESIREVIAFPKTGGGFDPLTAAPAPITAQQ
+RKEAGVDAKPEPKKAEGEKAEAAGQPQA
+>PROKKA_01521
+MLRTHHLGELNASLIGQTVTVTGWVAKRRDHGGVAFVDLRDASGRAQVVVRDEADFDPLR
+NEWVLQVTGTVERRPEGNENPNLPTGEVELIADDVVVLNTAAALPFQIDEHVEVGEEARL
+RHRYLDLRRPQPARIMRLRSEANRVARELLNEQGFVEVETPTLTRSTPEGARDFLVPARL
+APGSWYALPQSPQLFKQLLQVGGLEKYYQIARCYRDEDFRADRQPEFTQLDIEASFVEQD
+DVIALGEQIVKALWGLVGVEVQTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKDT
+PFRVFQNEYVGAVVMPGGASQPRRTLDAWQEWAKQRGAKGLAHVLIQEDGTLTGPVSKNI
+TDEEKAGLAAAVGANPGDCVFFAAGKAKESRALLGAARVEIGRRCELFTDAGDGVEAKDA
+DWAFVWVVDAPLFEPAADAVASGDVAVGAGQWTAVHHAFTSPKPEFMDTFDTDPGSALAY
+AYDIVCNGNEIGGGSIRIHRQDVQKRVFSVMGLSEEDANEKFGFLLEGFKYGAPPHGGIA
+FGWDRVVALLAGTESIREVIAFPKTGGGYDPLTAAPAPITPQQRKEAGVDAKPEAKKAEG
+AASEGAEAQAKANDEKTAADEAQLR
+>PROKKA_01221
+MLRTHSLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVRDEADFDPLR
+NEWVLQVTGTVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARL
+RHRYLDLRRPQPSRIMRLRSEVNRTARELLHGEGFVEVETPTLTRSTPEGARDFLVPARL
+APGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADRQPEFTQLDIEASFVEQD
+DVIALGEKIVKALWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKDT
+PFRVFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGELTGPVSKNI
+SEEEKAGLAAAVGANPGDCVFFAAGKPKESRALLGAARVEIGRRCGLFTDAGDGVAAKDA
+DWAFVWVVDAPMFEPAADAVASGDVAVGAGAWTAVHHAFTSPKPEFADTFDTDPGSALAY
+AYDIVCNGNEIGGGSIRIHRQDVQERVFEVMGLSPEEANEKFGFLLEGFKYGAPPHGGIA
+FGWDRVVALLAGTDSIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAQPEPKQAEA
+EPGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001061.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001061.fa
new file mode 100644
index 0000000000000000000000000000000000000000..594526213538af72db148725e8756c6ca124352c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001061.fa
@@ -0,0 +1,45 @@
+>PROKKA_01264
+MTAALQRRLTLLHAVAIGLGSMIGAGVFTAIGLAAALTGGHPGLLYGALAVAAVAALCNA
+LSTAQLATVHPESGGAYVYGRRQLHPWAGFVAGWGFVTGKTASVAAVAATLGLYLVPDDA
+AAARWTGVAAVVVLTGVAMAGVTRTAQATLAILVPVLAVLVLAIGAGLAREAPGGSAAAL
+GVDSPVQGVLMGAGVLFFAFAGYARVATMGEEVIDPARTIPRAILIALAVTVALYLLLAT
+ALISGLGTSGLARSPAPVRELLETALGSGWGWVAVAGAALAAAGAMLTLLTGISRTALAM
+AREADLPRPLARVHAGTGTPWTAQLTVAAAVVLLLLTTDILTVVGFSSFGVLVYYAVANL
+SALTLRGDDHGHRPARPRPLRVPRAVNVLGLALCLLLAFSLPPMSVAAMAGVFLIGVGGR
+AFVRAGRRGG
+>PROKKA_00983
+MTAALQRRLTLLHAVAIGLGSMIGAGVFTAIGLAAALTGGHPGLLYGALAVAAVAALCNA
+LSTAQLATVHPESGGAYVYGRRQLHPWAGFVAGWGFVTGKTASVAAMAATLGLYLFPDDD
+AAARWTGVAAVVVLTGVAMAGVTRTAQATLAILVPVLAVLVLAIGAGLAREAPGGSAAAL
+GVDSPVQGVLMGAGVLFFAFAGYARVATMGEEVIDPARTIPRAILIALAVTVALYLLLAT
+ALISGLGTSGLARSPAPVRDLLETALGSGWGWVAVAGAALAAAGAMLNLLTGISRTALAM
+ARESDLPRPLARVHAGTGTPWTAQLTLAAAVILLLLTTDILTVVGFSSFGVLVYYAVANL
+SALTLRGDDDGRRPARPRPLRPLRVPRAVNVLGLALCLLLALSLPPMSVAAMAGVFLIGV
+GGRAFVRAGRRGR
+>PROKKA_01623
+MLQRRLTLTHAVVIGLGSMIGAGVFTAIGLAAALTGGHPGLLYAALALALLTALCNALST
+AQLATVHPESGGAYVYGRRQLHPLAGFVAGWGFVTGKTASVAAMAATIGLYLFPDDAAAA
+RLTGVAAVVVLTAVAMAGVTRTAQATMAILVPVAAVLALAIGAGLALGAPSEADAFAGVA
+DSPVTGVLMGAGILFFAFAGYARVATMGEEVIDPRRSIPRAILIALGLTAGLYVLLTAAL
+FAGLGPTGLALSPAPVRELLETTLGATWGWAALAGAALAAAGAALNLLTGISRTALAMAR
+ESDLPRPLARVNARTGTPWVGQLTIAVAVILLLLTTDILTVVGFSSFGVLVYYAVANLAA
+ATLRGGEDGRDPALPRPLRVPRAVNVLGLVLCAVLAATLPPMAVVAMLAVFLVGVGGRAF
+VLAGRGRPGRRGAVAP
+>PROKKA_01520
+MTATSPAPRGLPLRGALAIGVGSMVGAGAFTSLGLAALLTGGHVGALAAALGLAVAVATC
+NALSTAQLAAVHPASGGTYVYGRRQIGPTAGFVAGWGFVTGKTASVAAMATTAGLYLFPD
+SPLAARLAGAAAVVILTAVALRGITRTAQATVAILVPVLAVLGLTIVAGLAGGRAAADTP
+VSAADPAGVLAAAGVLFFAFAGYARVATMGEEVEDPRRTIPRAVLGALAFTVVLYALLAA
+ALVAALGGTGLAASEAPVRATLEASLGAGWGWAAVVGAVLACAGAMLNLLAGISRTGMAM
+AREGDLPRPLARVDERTAVPWAGQVTVAVAVILLVLTTDVLTVVGFSSFGVLVYYAVANL
+SALTLRPEQRTLRVPRAVNVLGLGLCLVIAFTLPPASVAAMVGVFLIGLGGRWFVRSRRP
+DRIG
+>PROKKA_01222
+MTAALQRRLTLLHAVAIGLGSMIGAGVFTAIGLAAALTGGHPGLLYGALAVAAVAALCNA
+LSTAQLATVHPESGGAYVYGRRQLHPWAGFVAGWGFVTGKTASVAAMAATLGLYLFPDDA
+AAARWTGVAAVVVLTGVAMAGVTRTAQATLAILVPVLAVLVLAIGAGLAREAPGGSAAAL
+GVDSPVQGVLMGAGVLFFAFAGYARVATMGEEVIDPARTIPRAILIALAVTVALYLLLAT
+ALISGLGTSGLARSPAPVRDLLETALGSGWGWVAVAGAALAAAGAMLNLLTGISRTALAM
+ARESDLPRPLARVHAGTGTPWTAQLTVAAAVILLLLTTDILTVVGFSSFGVLVYYAVANL
+SALTLRGDDDGRRPARPRPLRVPRAVNVLGLALCLLLALSLPPMSVAAMAGVFLIGVGGR
+AFVRAGRRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001062.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001062.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f1b2cbb192072604e457ab4fecfe4dcf9c63ca0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001062.fa
@@ -0,0 +1,45 @@
+>PROKKA_01265
+MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE
+VYAVSRLAEDEEVAAGRREPKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ
+KVWRGERPQEGRAREFTQADIDVVGDGALSPRYDADVALVMAEALGALPIGDFLIRVNNR
+KLAEGFYRGIGLEDTAGVLRSIDKLEKVGPEEVARLLQEEVGASPEQAAQALALADIRTS
+DTSFVERVRALGVTHELLEEGLTELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET
+VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQQMAVASRSVPTAV
+YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFMGRDDAG
+ARVHEVKDIRSGEQHAVDPADWTPPTEDLLPQITRTQD
+>PROKKA_00984
+MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE
+VYAVSRLAEDEEVAAGLRDPKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ
+KVWRGERPQEGRAREFTQADIDVVGDGALSPRYDADVALVMAEALGALPIGDFLIRVNNR
+KLAEGFYRGIGLEDTAGVLRSIDKLEKVGPEEVARLLQEEVGASPEQAAQALALADIRTS
+DTSFVERVRALGVTHELLEEGLTELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET
+VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQQMAVASRSVPTAV
+YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFMGRDDAG
+ARVHEVKDIRSGEQHAADPADWTPPAEDLLPQVARAQD
+>PROKKA_01622
+MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE
+VYAVSRLAEDEEVAAGRREAKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ
+KVWRGERPQEGRAREFTQADIDVVGDGELSPRHDADVALVMAEALGALPIGDFLIRVNNR
+KLAEGFYRGIGLTDAAGVLRSIDKLEKIGADEVARLLQEEVGASPEQARQALALAAIRTE
+DVSFVEQVRALGVSDPLLEEGLAELADVVETLHRRAPGRAVADLSIARGLDYYTGTVYET
+VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQEMAQASRSVPTAV
+YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFLGRDDAG
+ARVHEVKDIRSGDQHPADPADWTPPSEDLLPQVTRTESTEG
+>PROKKA_01517
+MSRKQSLSGFHEWLPAERIVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE
+VYAVSRLAEDQEVAEGVREAKDPSDPKRLALHFDLTVPFARYVTENAGHLAFPFRRHQIQ
+KVWRGERPQEGRAREFTQADIDVVGDGELSPRYDADVALVMAEALGALPIGDFRIRVNNR
+KLAEGFYRGIGLEDAAGVLRSIDKLEKVGAEEVARLLQEEVGATAEQAAQALKLAEIRTP
+DTAFVEQVRALGVEDPLLEEGLAELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET
+VLVGHEQLGSICSGGRYDALATKGNRAFPGVGLSIGVTRLVMRMLSQEMAVASRAVPTVV
+YVALTHDDDWSRAQDVAAGLRGRGIAAEVAVSAEKFGKQIKYADRRGIPFVWFLGAEGAS
+DEVKDIRSGEQVPADAATWAPPAEDLVPQVTESPRAED
+>PROKKA_01223
+MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE
+VYAVSRLAEDEEVAAGLRDPKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ
+KVWRGERPQEGRAREFTQADIDVVGDGALSPRYDADVALVMAEALGALPIGDFLIRVNNR
+KLAEGFYRGIGLEDTAGVLRSIDKLEKVGPEEVARLLQEEVGASPEQAAQALALADIRTS
+DTSFVERVRALGVTHELLEEGLTELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET
+VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQQMAVASRSVPTAV
+YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFMGRDDAG
+ARVHEVKDIRSGEQHAADPADWTPPAEDLLPQVARAQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001064.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001064.fa
new file mode 100644
index 0000000000000000000000000000000000000000..83df129dc8ab857937cf6b74498d7dcd9a1bd659
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001064.fa
@@ -0,0 +1,25 @@
+>PROKKA_01267
+MTTVTIEETAPAGALMLAGDPFTEPELQALGARGAVRPLLPGVWARPDAADDPAVRAAAL
+WTLGGPLLAAGWTAIGPSAAWILAGGAAPGRLHAAVPHFHRRPAGGGQLPWTLTQSDVAA
+DATGVAPAEQDVLRFGPVRVTTPARTVEDLLLSADPDAARRAAAVIGAHGAAGLRERLAR
+RTRRAGVVAARRRLGALLTALDVPD
+>PROKKA_00986
+MTTVTIEETAPTGALVLAGDPFTEPELQALGARGAVRPLLPGVWARPDAADDPAVRAAAL
+WTLGGPLLAAGWTAIGPSAAWILAGGAAPGRLHAAVPHFHRRPAGGGLLPWTLTQSDVAA
+DATGVAPAEHDVLRFGPVRVTTPARTVEDLLLSADPDAARRAAAVIGAHGAAGLRERLAR
+RTRRAGVVAARRRLGALLAALDVPD
+>PROKKA_01620
+MEGLILAGEPFTPAELQALGSRGVVVPLVPGVWARPEAARRPGVRAEALWMLGGPVLAGG
+WTAIGSSAAWVLTGGAVPERLHAAVPHFHRLPAGGSPLPWTLTQSDVAAGPDGRAPAEED
+VLRIGPLRVTTPERTVEDLLLSPDPDAARTAAAVIAAHGAAGLRERLARHSRRSGVVAAR
+RRLDVLLGALEAAG
+>PROKKA_01515
+MHQGHGSRGGAAWELAGMTFTEPELRLLAARGTLEAVLPGVYRPVDVPSEPAGRAAALGL
+LGGPVLASGWTAVGPSAAWVHVGGPAPHRLHAAVPHFHRLPAGGAAPAWRLVQSDVAAGP
+TGAAPAEEDVQVLEGVRVTVPARTVEDLLLTGDPDDARRAARVIAAHGAEGLRDRLDRPS
+RRPGSVGARRRLRMLLDALGADG
+>PROKKA_01225
+MTTVTIEETAPTGALVLAGDPFTEPELQALGARGAVRPLLPGVWARPDAADDPAVRAAAL
+WTLGGPLLAAGWTAIGPSAAWILAGGAAPGRLHAAVPHFHRRPAGGGLLPWTLTQSDVAA
+DATGVAPAEHDVLRFGPVRVTTPARTVEDLLLSADPDAARRAAAVIGAHGAAGLRERLAR
+RTRRAGVVAARRRLGALLAALDVPD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001073.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001073.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fe158ca8d3d67b4b082e42f4311be25599c80de0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001073.fa
@@ -0,0 +1,44 @@
+>PROKKA_01277
+MAARPRRPRPHPADLPPALAAAVTVAARRAGSRESRVRRAGRLVRRGVTGSVRGGVAVAS
+PVARWAPPVLSVAAAYAFVLAGASSALAGVFARTVVTPVRRHAESTPILAVVDTPAGQDV
+ILQADEYTTVPGQYSLTFDDGAGCARIGEITSFDPRDGTVQRAVEEVFSGDLTTATRGRF
+TGFVYPTPADAGLDAEDVQVPVPGGHARAWRIAPYPSEDGEPRPAEGLWAVMVHGRGARR
+NEGIRAVPTARRLGMTSLLISYRNDGDAPDAADARYGLGTTEWEDVEAAIRYALDHGARD
+VVLFGWSMGGAVVLQTVDRSALAPHVRGVVLTGPVIDWVDVLRHQARLNRIPEAVGLLGQ
+WLLANRAGRFITGLAAPVDLKALDWVTRADHVRVPTLILHSEDDEYVPVGPSQDLAERNP
+DLVRFVRFHQARHTREQNVDPRKWDTAVRGWLRAVLSAPRPGGRGR
+>PROKKA_00996
+MAARPRRPRPHPADLPPALAAAVTVAARRAGGRDSRVRRAGRLVRRGVTGSVRGGVAVAS
+PVARWAPPVLSVAAASAFVLAGASSALAGVFARTVVTPVRRHAESTPILAVVDTPAGQDV
+ILQADEYTTVPGQYSLTFDDGAGCARIGEITSFDPRDGTVQRAVEEVFSGDLTTATRGRF
+TGFVYPTPADAGLDAEDVQVPVPGGHARAWRIEPDPSEDGEPRPAEGLWAVMVHGRGARR
+NEGIRAVPTARRLGMTSLLISYRNDGDAPDAADARYGLGTTEWEDVEAAIRYALDHGARD
+VVLFGWSMGGAVVLQTVDRSPLAPHVRGVVLTGPVIDWVDVLRHQARLNRIPEAVGLLGQ
+WLLANRAGRFITGLAAPVDLKALDWVTRADHVRVPTLILHSEDDEYVPVGPSQDLAERNP
+DLVRFVRFHQARHTREQNVDPRKWDTTVRGWLRAVLSAPRPGGRGR
+>PROKKA_01610
+MRTGVKAASPLARWTPPVLSVLASSAFVLAGASSALAGVFARTVVTPVRRHTETTAVLAV
+VDTPTGPEVILKADEYTTVPGVYSLTFDGGAGCARIGRISSFDPRDGTVQRVVEEVYFGD
+LAAATRGRLTGFVYPTPADAGLDAEEVLVPVPGGHAPAWLVGPDPDDDGAARPAAGIWAI
+MVHGRGARRNEGIRTVPTAQRLGMTSLLISYRNDGDAPDAADSRYGLGTTEWEDVEAAIR
+YALDNGASDVVLFGWSMGGAVVLQAVDRSDLAPQVRGVVLTGPVVDWVDVLQHQARLNRI
+PEAVGVLGQWLLSNRAGRFITGLAAPVDLKSLDWVTRAEHVRVPTLIIHSEDDEYVPVGP
+SQDLAERNPGLVRFVRFHQARHTREQNVDPKRWDTTVRGWLRAVLNADRPGAAER
+>PROKKA_01505
+MACPRRHSPRLRARPDLRDALLGSLRGSAAVARPAARLAPAAASVAASAAFVLAGASAGL
+AGVFARTVVTPVRSRPEHTAVLAVLDTGDGMDVILPADEHTTVPGTYSLTFHGGEGCARI
+GAIRSYDPRDGTVQRVVEEVYSGDLRSAVRGRFTAFIWPGPAEAGLEAADVEVPVPGGAA
+PAWRIDPPPAEDGEERAGEGMWAVMVHGRGAVRNEGLRAVPTAARLGMTSLLVSYRNDGD
+APDAEDARYGLGTTEWEDVEAAVRYALDHGARDVVLFGWSMGGAVVLQTADRSDLTSRVR
+GIVLTGPVVDWMDVLRHQARLNRIPEGIGLLGQWLLSNRAGRLVTGLAAPVDLKALDWVT
+RADHVRVPTLILHSEDDEYVPVGPSQDLAERNPALVRFVRFHQARHTREQNVDPVKWDRS
+VRGFLRAVLTAPRPGAVSPPGAPQAPSGSSPRRRSSGSSSASRPRNAR
+>PROKKA_01235
+MAARPRRPRPHPADLPPALAAAVTVAARRAGGRDSRVRRAGRLVRRGVTGSVRGGVAVAS
+PVARWAPPVLSVAAASAFVLAGASSALAGVFARTVVTPVRRHAESTPILAVVDTPAGQDV
+ILQADEYTTVPGQYSLTFDDGAGCARIGEITSFDPRDGTVQRAVEEVFSGDLTTATRGRF
+TGFVYPTPADAGLDAEDVQVPVPGGHARAWRIEPDPSEDGEPRPAEGLWAVMVHGRGARR
+NEGIRAVPTARRLGMTSLLISYRNDGDAPDAADARYGLGTTEWEDVEAAIRYALDHGARD
+VVLFGWSMGGAVVLQTVDRSPLAPHVRGVVLTGPVIDWVDVLRHQARLNRIPEAVGLLGQ
+WLLANRAGRFITGLAAPVDLKALDWVTRADHVRVPTLILHSEDDEYVPVGPSQDLAERNP
+DLVRFVRFHQARHTREQNVDPRKWDTTVRGWLRAVLSAPRPGGRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001075.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001075.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad183fdf89bb48471d8f71fdf9cf02f015002316
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001075.fa
@@ -0,0 +1,25 @@
+>PROKKA_01279
+MSVIGPRRLSAAPGAVEAPVPPGVFRRALADLRDARPRTEVRLREIPAPEGQAPFAVALA
+ADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLAGAVAW
+TWLVEALERHHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLGSHLEA
+WSDMICAFAGLPPEHAADVHTAGP
+>PROKKA_00998
+MSVIGPRRLSAAPGAVEAPVPPGVFRRALADLRDARPRTEVRLREIPAPEGQAPFAVALA
+ADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLAGAVAW
+TWLVEALERRHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLGSHLEA
+WSDMICAFAGLPPEHAADVHTAGP
+>PROKKA_01607
+MTVIGPRRLAPVTGPRGAVAPAPAPLPAAFRRALADLRTARPRPEVRLREIAAPAGQAPH
+AVALAAEVCGSPGADDVLATGRFVLLHDPSPAARWPGGFRAVTWIRASLEPDVALDQLAG
+AVAWTWLVEALERRHAEHTQAGGTATRSIAEGFGTLGTAPDATDIELRASWTPAPRDLGA
+HLEAWSDMIGAFAGLPPR
+>PROKKA_01502
+MTESGPRAPAPAAGGASGAFADALADLRAAHPRPEVRLRPIPDPPGLAPFAVTLAADVLD
+PHGAEADPLATGRFVLLHDPAGSPVWRGDFRVVTYIRASLEPDVATDHLAGAVAWDWLAE
+ALERRHAAHTEAGGTATRQLAEHFGTLALEPGWTDIELRASWTPGPRDLGAHLEAWSDMI
+CAFAGLPPLADDDVPAAVPLRP
+>PROKKA_01237
+MSVIGPRRLSAAPGAVEAPVPPGVFRRALADLRDARPRTEVRLREIPAPEGQAPFAVALA
+ADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLAGAVAW
+TWLVEALERRHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLGSHLEA
+WSDMICAFAGLPPEHAADVHTAGP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001077.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001077.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3611b4cfd927d33addaefe374239545b3328088d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001077.fa
@@ -0,0 +1,69 @@
+>PROKKA_01281
+MTSVSLASFDHLPALAPDEVVTTVTVTDHALPEGAGTLALLTLDNGQGPRRPATLGPATL
+LGLGRVLDEQAARAAAGEIQALAVTGVEGTFAAGADLSLIASITDDVGRDLALLGHAVYD
+RLAALEIPTVALVNGLALGGGLELALAAGHRVVAADAKGFGLPEVRLGLIPGWSGVWRVP
+HLIGPEAAVDVVLKNPLDDNRMLDARAAHGLGLMDRIVEGDLLDAGLELAAALVTGDESV
+AAELAAHRDRDVSDAAWDRALAALERLQAARPGRHLPARRHLEALFTGARTRTRAESAQA
+EADALGTLLHSPEFRRTVYAFLGLVQGRAKRPAGDPGRELAREVRKVGIVGAGLMAGQLA
+LVFARHLRVPVVMTDIDAERVERGLAGVRAQVEKMVSRGRLSAEDGQALAGLITADTDKA
+VYADADIVIEAVFEELEVKRTVFRELEGIVREDAILMTNTSSLSVAAMAEVLERPERLVG
+FHFFNPVAVMPLVEIVRTEATTDEVVATAFELTRRLRKTGVLVHDATAFVVNRVLLRMMG
+EVQNSFDEGTDAHEADHALDPLALPMTPFTLLAMVGIPVAQHVSESLSASFGAERFPVSA
+NLQRLIDAGKTAIWAKDVRPDRRDEEAAGATGEQIPEATAALLEQGSTPQTSEELLRRVE
+DALAEEIGLLLDERVVAAPEDVDLCMILGANWPLHLGGITPYLDDCGAAERVNGRRFHPA
+AQA
+>PROKKA_01000
+MTSVSLASFDHLPALAPDEVVTTVTVTDHALPDGAGTLALLTLDNGQGPRRPATLGPATL
+LGLGRVLDEQAARAAAGAIQALAVTGVEGTFAAGADLSLIAGLTDDVGRDLALLGHAVYD
+RLAALEIPTVALVNGLALGGGLELALAAGHRVVAADAKGFGLPEVRLGLIPGWSGVWRVP
+HLIGPEAAVDVVLKNPLDDNRMLDARAAHGLGLMDRIVEGDLLDAGLELAAALVAGDESV
+AAELAAHRDRDVSDAAWDRALAALERLQAARPGRHLPARRHLEDLFTGARTRTRAESAQA
+EADALGTLLHSPEFRRTVYAFLGLVQGRAKRPAGDPGRELAREVRKVGIVGAGLMAGQLA
+LVFARHLRVPVVMTDIDAERVERGLAGVRAQVEKMVSRGRLSAEDGEALAGLITADTDKA
+VYADADIVIEAVFEELEVKRTVFRELEGIVREDAILMTNTSSLSVAAMAEVLEHPERLVG
+FHFFNPVAVMPLVEIVRTEATTDEVVATAFELTRRLRKTGVLVHDATAFVVNRVLLRMMG
+EVQNSFDEGTDAHEADHALDPLALPMTPFTLLAMVGIPVAQHVSESLSASFGAERFPVSA
+NLQRLIDAGKTAIWAKDVRPDRRDEEAAGATGEQIPEATAALLEQGSTPQTSEELLRRVE
+DALAEEIGLLLDERVVAAPEDVDLCMILGANWPLHLGGITPYLDDCGAAERVNGRRFHPA
+AQA
+>PROKKA_01605
+MTFTPAPLAPFESLLPLVPDEVLTHVAATDHVLPGGAGTLVLLTLDNGQGPRRPATLGPA
+SLLELGRAVDAQAERARAGEVQALALTGVEGTFAAGADLSLIAGIEDRTVGRDLARLGHA
+VHDRIDAFPAPTLALVNGTALGGGLELALAADHRVVAADARGFGLPEVRLGLIPGWSGVW
+RVPHLIGPEAAVEVVLKNPLDNNRMLDARTAHGLGLMDEVAEGDLLEAGLAFAARIVAGD
+DAALAAVRDHRDRDVSDAAWDRALEAMEALQAGRPGRDLPARRALQELFAGARTRTREES
+AEAEAEALHGLIGSDEFRRTVYAFLDLLQRRAKRPVGDPGKELAREVTKVGVVGAGLMAG
+QLALVFAQHLRVPVVMTDMDQERVDRGLAGVRGQVEKMVSRGRITAEQGEALAGLITAST
+DKSVYADADVVIEAVFEELEVKRTVFRELEPIVREDAVLMTNTSSLSVAAMAEVLEHPER
+LVGFHFFNPVAQMPLIEVVRVAETSDEAVATAFELSRRLRKTGVLVHDAAAFVVNRVLLR
+MMGEVQASFDEGTDAHTADHALDPLALPMTPFTLLAMVGIPVAQHVSESLQAAFGAERFP
+VSANLQRLIDAGKTAIWAKDVRRDKVEEEAAGATGETIPAGTAALIERGSSPQTAEELRR
+RVEDALAEEIGLLLAEGVVAAPEDVDLCMILGAGWPLHLGGITPYLDDCGAAERVNGTRF
+HG
+>PROKKA_01500
+MSHTPAPLDQFEHLSTIAPDEILTRATATDHALPDGAGTLALITLDNGQGPRRPATLGSA
+SLLELARAVDEQAARASAGEIQALGITGVEGVFAAGADLALVASLPADAETGRALGRLGH
+AVYDRIDAFPVPTVALVNGTALGGGLELALACDRRVIAPEVKALGLPEVRLGLIPGWSGV
+WRAPHLVGPEAAVALLLTNPLDNGRMIGAADAVRLGLMDSLAEGDLLAAGLTAAADAVAG
+RTVQRTADVSDAAWDRALQAFGAAQSARPGRDLPARRHLEELFAGARTRTRAESAEAEAD
+ALADLIGSAEFRRTVYAFLGLVQGRAKRPAGDPGVEQAHTVHRVGVVGAGLMAGQLALLF
+ATALRVPVVMTDLDQERVDRGLAYVRSQLERSVTKGRMKAEDAEAVAGLITGATDVSAHA
+EAEFVIEAVFEELEVKRTVFRQLEQVVSPTAILATNTSSLSVAGMAEVLEHPERLVGFHF
+FNPVAQMPLVEIVRVAETTDAAVATAFELARRLRKTAVLVNDAAAFVVNRVLLRMMGEIQ
+NSFDQGTDAHTADHALDPLAFPMTPFTLAAMVGLPVAQHVSESLQAAFGAERFPVSENLQ
+RLIEAKKTAIWAKDVKSPEEAGGATGETIPADTAALIEQGDTPQTADELRVRVEDALAEE
+IGLLLDEGVVAAPDDVDLCMILGAGWPLHLGGITPYLDDCGASERVRGARFHQA
+>PROKKA_01239
+MTSVSLASFDHLPALAPDEVVTTVTVTDHALPEGAGTLALLTLDNGQGPRRPATLGPATL
+LGLGRVLDEQAARAAAGEIQALAVTGVEGTFAAGADLSLIAGLTDDVGRDLALLGHAVYD
+RLAALEIPTVALVNGLALGGGLELALAAGHRVVAADAKGFGLPEVRLGLIPGWSGVWRVP
+HLIGPEAAVDVVLKNPLDDNRMLDARAAHGLGLMDRIVEGDLLDAGLELAAALVAGDESV
+AAELAAHRDRDVSDAAWDRALAALERLQAARPGRHLPARRHLEDLFTGARTRTRAESAQA
+EADALGTLLHSPEFRRTVYAFLGLVQGRAKRPAGDPGRELAREVRKVGIVGAGLMAGQLA
+LVFARHLRVPVVMTDIDAERVERGLAGVRAQVEKMVSRGRLSAEDGEALAGLITADTDKA
+VYADADIVIEAVFEELEVKRTVFRELEGIVREDAILMTNTSSLSVAAMAEVLEHPERLVG
+FHFFNPVAVMPLVEIVRTEATTDEVVATAFELTRRLRKTGVLVHDATAFVVNRVLLRMMG
+EVQNSFDEGTDAHEADHALDPLALPMTPFTLLAMVGIPVAQHVSESLSASFGAERFPVSA
+NLQRLIDAGKTAIWAKDVRPDRRDEEAAGATGEQIPEATAALLEQGSTPQTSEELLRRVE
+DALAEEIGLLLDERVVAAPEDVDLCMILGANWPLHLGGITPYLDDCGAAERVNGRRFHPA
+AQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001078.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001078.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ca855dd7510f2ba3e0936b14385b35d3696e1f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001078.fa
@@ -0,0 +1,25 @@
+>PROKKA_01282
+MTDPAPRPTGAARFDLTPFERWEAVTLDDVHVGFLHRVLEDGVLTTRTGFAPTTAQRAAR
+DGLPERYLAQTQVGFTPDGDGWAWTTHEDSAGAQRVRIDRERAGIDAAVLPSYAEYLLLA
+RVAAEGPLAVDRLEEASPLQGGLRVPRAELRPADAGGSDVRVAVVADGVELGAHLVREGA
+VVASDWGGGTASTPVADQAAATAGLDAHVVTFAGLPIA
+>PROKKA_01001
+MTHPAPRPTGAARFDLTPFERWEAVTLDDVHVGFLHRVLEDGVLTTRMGFAPTPAQRAAR
+GGLPERYLAQTQVGFTPDGDGWAWTTHEDSAGAQRVRIDRERAGIDAAVLPSYAEYLLLA
+RVAAEGPLAVDRLEEASPLQGGLRVPRAELRPADAGGSDVRVAVVADGVELGAHLVREGA
+VVASDWGGGTASTPVADQAAATAGLDAHVVTFAGLPIA
+>PROKKA_01603
+MTDPAPVRPSLDLTPFERWEAVTLDGEHVGFLHRVLDGTLLTTRMGFAPTPAQRRARPEL
+PERYLAQSQVSFTADGTSWDWTSHEDSAGAQRVRIDRERAGLDADVLPSYAEYLLLAVAA
+ADGPVVVAARLEESSPLQGGLRMPRAELRPADAGDGDVSVTVVADGAALGAHLVRDGAVV
+ASDWGGGTASTPVAGRAEATEGLDEHVVTFSGMPLV
+>PROKKA_01499
+MSARYDLTPFETWEAVALDGVHAGFLHRRLADGILTTRMAFQPTGAQRRERADLPQRYLA
+QARVRFSADGSTWEVCDFEDSLTTQNVRIARERAGLGAEVVPSWAEHLLITAQRTPEHDG
+APYLRLEESSPLQGPVRMPPAVLRIGAREAVPAAGPAGSEAGQARPEGLRVEVVSEGHVL
+AVHWLGEPATEGRRPLVASDWGGGTVSVPVATAAEALEGLPADLHTFAQLPTD
+>PROKKA_01240
+MTHPAPRPTGAARFDLTPFERWEAVTLDDVHVGFLHRVLEDGVLTTRMGFAPTPAQRAAR
+GGLPERYLAQTQVGFTPDGDGWAWTTHEDSAGAQRVRIDRERAGIDAAVLPSYAEYLLLA
+RVAAEGPLAVDRLEEASPLQGGLRVPRAELRPADAGGSDVRVAVVADGVELGAHLVREGA
+VVASDWGGGTASTPVADQAAATAGLDAHVVTFAGLPIA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001079.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001079.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9006ca0d2b3129413b1a9434d397239d429fa640
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001079.fa
@@ -0,0 +1,21 @@
+>PROKKA_01283
+MTTQDSPLTPNSSRSACCGGHARPDTSRRTVLGRGAAVAAAGAGALALTGCTDQLREKDT
+AQDHYTGSDAVDALPAAELPVGASREVQVQGRTLMMHRVDETTVTAFTNVCTHQGCLLQV
+VDRQEGPAYACPCHGSHFDVTSGKPFGGPARQALMDYDAAVVDDRIVVKL
+>PROKKA_01002
+MTTQDSPLTPNSSRSGCCDDHARPDTSRRTVLGRGAAVAAAGAGTLALAGCTDRLREKDT
+AQDHYTGSDAVDALPAAELPVGASREVQVQGRTLMMHRVDETTVTAFTNVCTHQGCLLQV
+VDRQEGPAYACPCHGSHFDVTSGKPFGGPARKALMDYDAAVVDDRIVVKL
+>PROKKA_01602
+MTAQDSTPTPDPSAVAPPSAPAGCCGGRAAADAARPEASRRTVLGRGAAVAAAGAGALAL
+SGCTEQLREKENAQDHFAGADAVEALPAADLPVGAAREVEVEGRTLMMHRVDETTVTAFT
+NVCTHQGCLLQVVDRAEGPSFACPCHGSHFDVQTGKPFGGPARQPLMDYEAVVDGDRIVV
+KL
+>PROKKA_01498
+MTSQDPAPHTSASPCCSGCSAEPAGSSRRSVLGAGSLVALAGAGSVVLSGCTQQLKDEAA
+AGDHHVGSETTDAMALAELPVGGTTSVQVQGRTLLLHRADESTVTAFSNVCTHQGCLVQV
+VDRPEGTAYACPCHGSNFDVATGEPFGGPAKAPLTDYQAAIEGDRIVVKL
+>PROKKA_01241
+MTTQDSPLTPNSSRSGCCDDHARPDTSRRTVLGRGAAVAAAGAGTLALAGCTDRLREKDT
+AQDHYTGSDAVDALPAAELPVGASREVQVQGRTLMMHRVDETTVTAFTNVCTHQGCLLQV
+VDRQEGPAYACPCHGSHFDVTSGKPFGGPARKALMDYDAAVVDDRIVVKL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001081.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001081.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37b1a58ce494f4d7a036f20ac77860e06d1bfd47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001081.fa
@@ -0,0 +1,21 @@
+>PROKKA_01286
+MSIVRLYRESVGDDGARLFEYREAWADAEAGEFVVHHGRVGQPGTVGEQPLADQAEGDQL
+LAAFVAQGAEEGFAEADPATFAVLPVAYRLRGREATAIERRTVERLRVEMTHQLAWRGLG
+EVEDVVEEVGALVLRVRTPHARKAAAEIPAAAKRADGVQPNKVDVRTAEQEG
+>PROKKA_01005
+MSIVRLYRETVGDDGTRLFEYREAWADAEAGEFVVHHGRVGQPGTVGEQPLADQVEGDQL
+LAAFVAQGAEEGFAEADPATFAVLPVAYRLRGREATVIERRTVERLRVEVTHQLAWRGLG
+EVEDVVEEAGALVLRVRTPHARKAAAEIPAAAKRADGVQPNKVDVRTAEQEG
+>PROKKA_01599
+MSIVRLYRETTNEDGSRLFEYREAWADVEGGEFVVHHGRVGHPGTVGEQPLADEAEGEEL
+LAAFLAQGAEEGFAEADPAGFALLPVAFRLRGREASDIERRNVEHLRVEVTHQLAWRGLG
+EVEDVTEEPGALVLAVRTPHARKAAAEIPVAARRADGVQPNKVEVRSAVQED
+>PROKKA_01495
+MSISRLYRDRTEEDGRRSFEYREAWIDPSGELFTVHHGRVGHPGTVGDQPLTSEAEGAEL
+MDAFLAQGEADGFAPADEDAFDVLEVAYRLRGRAITEIERRHGRTLREEVTHQLAWRGLG
+EVTDVVDGDGELVLVVRTPHAPKAAAEVPAAAKRAHGIQPNKVEVRRVDAPRTPAGAAPD
+ADGEG
+>PROKKA_01244
+MSIVRLYRETVGDDGTRLFEYREAWADAEAGEFVVHHGRVGQPGTVGEQPLADQVEGDQL
+LAAFVAQGAEEGFAEADPATFAVLPVAYRLRGREATVIERRTVERLRVEVTHQLAWRGLG
+EVEDVVEEAGALVLRVRTPHARKAAAEIPAAAKRADGVQPNKVDVRTAEQEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001083.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001083.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ffb2303ca0a68c08d2af35364d3e69d8ce9d2b2d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001083.fa
@@ -0,0 +1,80 @@
+>PROKKA_01295
+MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAQKLPYSLKVLLENLLRTEDGANVTADQIK
+ALAAWDPNAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE
+LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN
+IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM
+LIPRVVGFKLTGSIPSGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG
+NMSPEFGSTAAIFPIDEVTLDYLRLTGRSEEQVALVEAYTKEQGMWHDPSSEVAYSEYLE
+LDLSTVVPSISGPKRPQDRIELTDSKDQFRKDLHNYATQDEAGEGRPSKLVDVAMPDGRQ
+FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY
+YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR
+INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDTEGNDVFLKDIWPDPTEVQQIID
+ASIDTEMFTSQYATIFDGDERWQSLETPSGSTFEWDEKSTYVRKPPYFEGMTMQPDPVSD
+ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGRYLLENGVQRKDFNSYGSRRGNHEVMIR
+GTFANIRIKNQLLDGVEGGFTRDFTQEGAPQAYVYDAAQNYAEQGTPLVVLGGKEYGSGS
+SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS
+GITALNEGTTPKTVKVTATGEDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA
+>PROKKA_01018
+MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAQKLPYSLKVLLENLLRTEDGANVTADQIK
+ALAAWDPNAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE
+LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN
+IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM
+LIPRVVGFKLTGSIPSGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG
+NMSPEFGSTAAIFPIDEVTLDYLRLTGRSEEQVALVEAYTKEQGMWHDPSSEVAYSEYLE
+LDLSTVVPSISGPKRPQDRIELTDSKDQFRKDLHNYATQDEAGEGRPSKLVDVAMPDGRQ
+FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY
+YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR
+INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDTEGNDVFLKDIWPDPTEVQQIID
+ASIDTEMFTSQYATIFDGDERWQSLETPSGSTFEWDEKSTYVRKPPYFEGMTMQPDPVSD
+ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGRYLLENGVQRKDFNSYGSRRGNHEVMIR
+GTFANIRIKNQLLDGVEGGFTRDFTQEGAPQAYVYDAAQNYAEQGTPLVVLGGKEYGSGS
+SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS
+GITALNEGTTPKTVKVTATGEDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA
+>PROKKA_01597
+MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAEKLPYSLKVLLENLLRTEDGANVTAEQIK
+ALASWNPDAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE
+LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN
+IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM
+LIPRVVGFKLTGSIPAGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG
+NMSPEFGSTAAMFPIDEVTLDYLRLTGRTAEQVDLVEAYTKEQGMWHDPSSEVKYSEYLE
+LDLSTVVPSISGPKRPQDRIELSDSKDQFRKDLHNYATQDEAGEGRPSKLVDVSMEDGRQ
+FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY
+YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR
+INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDSEGNDVFLKDIWPDPTEVQKIID
+ESIDTEMFTSQYGTIFDGDERWQSLETPSGSTFEWDEQSTYVRKPPYFEGMTMQPDAVSD
+ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGKYLLENGVERKDFNSYGSRRGNHEVMIR
+GTFANIRIKNQLLDGVEGGFTRDFTQDGAPQAYVYDAAQNYAAAGTPLVVLGGKEYGSGS
+SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS
+GITALNEGTTPKTVKVTATGGDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA
+>PROKKA_01493
+MTTVDSFGSKGVLDVNGSEYEIFRLNAVEGAQKLPYALKVLLENLLRTEDGANVTAEQIK
+ALASWDPTAEPDTEIQFTPARVIMQDFTGVPCIVDLATMREAIADLGGDPSRVNPLSPAE
+LVIDHSVQIDSFGNDAAVERNMDIEYQRNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN
+IENLARAVMVRDVDGVKRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM
+LIPRVVGFKLTGQIPAGATATDVVLTITEQLREHGVVGKFVEFYGEGVGAVPLANRATIG
+NMSPEFGSTAAMFPIDDVTLDYLRLTGRSEEQVALVEAYTKEQGLWHDPSAEVQYSEYLE
+LDLSTVVPSISGPKRPQDRIVLSDSKDQFRKDLHNYATQDEAGEGRPSKLVDVHMEDGRE
+FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLTAKPWVKTSVAPGSRVVTDY
+YEKSGLNASLDALGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR
+INPDVKMNYLASPPLVVAYALAGTMDCDFENEALGTDQDGNDVFLKDIWPDPAEVQRIID
+ESIDTEMFTSQYGTIFDGDERWQSLETPTGKTFEWDEASTYVRKPPYFEGMPAQPEPVQD
+IAGARVLLKLGDSVTTDHISPAGSFKSDTPAGQYLLANGVERKDFNSYGSRRGNHEVMIR
+GTFANIRIKNQLLDGVEGGFTRDFTQDGAPQAYVYDAAQNYAAAGTPLVVLGGKEYGTGS
+SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPAGESADSLGLTGTETFAIS
+GIAELNEGRTPKTVKVTATAEDGKVTEFDAVVRIDTPGEADYYRNGGILQYVLRQIAAKA
+>PROKKA_01253
+MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAQKLPYSLKVLLENLLRTEDGANVTADQIK
+ALAAWDPNAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE
+LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN
+IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM
+LIPRVVGFKLTGSIPSGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG
+NMSPEFGSTAAIFPIDEVTLDYLRLTGRSEEQVALVEAYTKEQGMWHDPSSEVAYSEYLE
+LDLSTVVPSISGPKRPQDRIELTDSKDQFRKDLHNYATQDEAGEGRPSKLVDVAMADGRQ
+FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY
+YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR
+INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDTEGNDVFLKDIWPDPTEVQQIID
+ASIDTEMFTSQYATIFDGDERWQSLETPSGSTFEWDEKSTYVRKPPYFEGMTMQPDPVSD
+ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGRYLLENGVQRKDFNSYGSRRGNHEVMIR
+GTFANIRIKNQLLDGVEGGFTRDFTQEGAPQAYVYDAAQNYAEQGTPLVVLGGKEYGSGS
+SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS
+GITALNEGTTPKTVKVTATGEDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001084.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001084.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a6cf0c40387ab7da61949a74920342f242afb798
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001084.fa
@@ -0,0 +1,50 @@
+>PROKKA_01296
+MAVVDTSTDVTGIGRTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEDG
+ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF
+RDTVHRIADLAVEPEVCFAGSEDEPTGQRWRTRNAFAVTPQGHIAMHAYRSATLLPVRNM
+PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEVKLGRLRTRIRQ
+AANACGVDVSTGLALPGPKQFQPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH
+QHAPATLVDAVLEDARVEPGQVVADLYGGAGLFSAYLADAVGPEGRVYSVEASRQASKDA
+RRNLHDQPQASVLNGPTDKVLGSWLKYPERPVADGGLGGAALDTVVLDPPRAGAGRRAIE
+RILALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPAAQ
+SAPAAAVVEI
+>PROKKA_01019
+MAVVDTSTDVTGIGRTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEDG
+ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF
+RDTVHRIADLAVEPEVCFAGSEDEPTGQRWRTRNAFAVTPQGHIAMHAYRSATLLPVRNM
+PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEVKLGRLRTRIRQ
+AANACGVDVSTGLALPGPKQFQPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH
+QHAPATLVDAVLEDARVEPGQVVADLYGGAGLFSAYLADAVGPEGRVYSVEASRQASKDA
+RRNLHDQPQASVLNGPTDKVLGSWLKYPERPVADGGLGGAALDTVVLDPPRAGAGRRAIE
+RILALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPAAQ
+SAPAAAVVEI
+>PROKKA_01596
+MAVIDTSTGVTGIGGTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEEG
+ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF
+RDTVHRIAGLTVEPEVCFAGPEDEPTGQRWRTRNAFTVTPQGHIAMHAYRSATLLPVRNM
+PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEAKLGRLRTRIRQ
+AANACGVDVSTGLALPGPKRHSPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH
+RHAPATLVDAVLEDARIEPGQTVADLYGGAGLFSAYLADAVGPEGRVFSVEAAGQASKDA
+RRNLHGQPQATVLNGPTDKALGSWIKYPERTVADGGLEGASLDTVVLDPPRAGAGRRAIE
+RLLALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPATQ
+LAAVPAIVEI
+>PROKKA_01492
+MDTSTEVVAPGGVIEVEAGAMAHGGHCVARHEGRVVFVRHAIPGEIVRVALTEAEPGARF
+WRGDVVEVVRPSEFRRIHQWKLADSLRAHASGRLPVGGAEYGHIVVHHQRRLKAQVFRDT
+VARIAGVTIEPEALHAGHEDEPTGQHWRTRTAFAVTPQGRIAMHAHRSAVLLPVRNMPLG
+VHALDALALWDWDFTGAARVDVATPADGTQPLVLATPTPQTLADEARLGKLRTRIRQAAN
+ACPVDVSTGFAVPGPKKFSPTGIQRITGRTWVHETVSSERGGERTFRVTGDGFWQVHQHA
+PATLVDAVLEDVDPQPGEVIADLYAGAGLFSAFLSDAVGEEGRVYSVEASRQASKDARRN
+LLSLPQAGVLNGPTDKVLGSWIKEPERTTRDGGLDGDRLDAVVLDPPRAGAGRRAIERIL
+ALAPGRICYVSCDPASFARDLAWLREGGYEVERARVFDLYPDTHHLESVTLLRPAGEVEQ
+TTL
+>PROKKA_01254
+MAVVDTSTDVTGIGRTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEDG
+ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF
+RDTVHRIADLAVEPEVCFAGSEDEPTGQRWRTRNAFAVTPQGHIAMHAYRSATLLPVRNM
+PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEVKLGRLRTRIRQ
+AANACGVDVSTGLALPGPKQFQPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH
+QHAPATLVDAVLEDARVEPGQVVADLYGGAGLFSAYLADAVGPEGRVYSVEASRQASKDA
+RRNLHDQPQASVLNGPTDKVLGSWLKYPERPVADGGLGGAALDTVVLDPPRAGAGRRAIE
+RILALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPAAQ
+SAPAAAVVEI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001085.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001085.fa
new file mode 100644
index 0000000000000000000000000000000000000000..efe39f087b1bfb06fd28a790de58606c460a77f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001085.fa
@@ -0,0 +1,61 @@
+>PROKKA_01297
+MATLSSLLRRGLLGRPVTSHAADEPRMNRWRALPVTSSNALSSLAYAPDEVILTLVAAGT
+SALALGPAVGWAVVAVMLLIVVSFRAAVAAVPHGGIYHMAGMKLGPRAGVVASAALLLDF
+VFTAAVSVAAFAHFVAALAPGLTVGSRVLVASAALVGVLLAALRGVRLSRWVLPVLVSVF
+VALTALLVLAGLWQEGRGLLGAAPTAGWTQEGAGVGGTVGTVATALLALRAFSAGSVLLT
+GVEVPVSSTRLMARPAVPTVRWVLTVMALTLGALTVGVMHLAQRTGVVVGLELENLRDAA
+GAEVTPDRAPAPVLAQLADTVYGPGSILSVATIAATALLLLFAAKSAFRSFPALAARVAE
+DGYLPRQLRVRSDRLVHTWSVLGMGAVALSLVLFFEARTALLVQLYVIGVLLAFTLAQAG
+MLRLWRRRLVHTPGARARAAVRLRLIITAVAWVVTALAGVVVLVTRFTQGAWVALLAIVL
+GSLVMGRIRRHYADVDRELAPDPQDDARALPSRVHVVVVVTTLDRPALRALAYARASRPS
+SLEAVVVDAERAATLEVIDAWERAGLPMSLTVIASPYRDTVAPLVRHVREHRRRSPRDLT
+MVFIPEYVVRPGWRTLLHNRTATRQTRRLQREPGVMVGSVPWQVHEGQGS
+>PROKKA_01020
+MATLSSLLRRGLLGRPVTSHAADEPRMNRWRALPVTSSNALSSLAYAPDEVILTLVAAGT
+SALALGPAVGWAVVAVMLLIVVSFRAAVAAVPHGGIYHMAGMKLGPRAGVVASAALLLDF
+VFTAAVSVAAFAHFVAALAPGLTVGSRVLVASAALVGVLLAALRGVRLSRWVLPVLVSVF
+VALTALLVLAGLWQEGRGLLGAAPTAGWTQEGAGVGGTVGTVATALLALRAFSAGSVLLT
+GVEVPVSSTRLMARPAVPTVRWVLTVMALTLGALTVGVMHLAQRTGVVVGLELENLRDAA
+GAEVTPDRAPAPVLAQLADTVYGPGSILSVATIAATALLLLFAAKSAFRSFPALAARVAE
+DGYLPRQLRVRSDRLVHTWSVLGMGAVALSLVLFFEARTALLVQLYVIGVLLAFTLAQAG
+MLRLWRRRLVHTPGARARAAVRLRLIITAVAWVVTALAGVVVLVTRFTQGAWVALLAIVL
+GSLVMGRIRRHYADVDRELAPDPQDDARALPSRVHVVVVVTTLDRPALRALAYARASRPS
+SLEAVVVDAERAATLEVIDAWERAGLPMSLTVIASPYRDTVAPLVRHVREHRRRSPRDLT
+MVFIPEYVVRPGWRTLLHNRTATRQTRRLQREPGVMVGSVPWQVHEGQGS
+>PROKKA_01595
+MATLSSLLRRGLLGRPVASHDVAEPRMSRWQALPVTSSNALSSLAYAPDEIVLTLVAAGT
+AALALGPLVGWGVVVVMLLIVASFRAAVAAVPQGGIYQMARTKLGPRAGVVASAALLLDF
+VFTAAVSVAAFAHFAAALLPGLGLESRVLVACAALVGVLLTSLRSARLSRWALPVLVSAF
+VALTALLVAAGLWQEGQGLLGRAATSGWTQEGAGIGGTVGAVATALLALRAFSAGSVLLT
+GVEVPVSSSSAMARPAVATVRWVLAVMALTLGALTLGVMHLAQRTGVVVALDPARLRDAA
+GRPVAEADTPAPVIAQLADTVFGPGSVLSLATIAATALLLLFAARSAFRSFPALASRLAE
+DGYLPRQLRVRGDRLVHTWGVLALGAAALALVLLFRAQTALLVQLYVIGVLLAFTLAQAG
+MLRLWRRRLAQTPGARARAAVRLRLTITAVAWVVTALAGVVVLVTRFAQGAWVALLAIVL
+GSLVMGRIRRHYEDVGRELAPDPEDDARALPSRVHVVVVVSTLNRPALRALAYARATRPS
+SLEAVVVDAERAVTEDVIDAWSRAGLPVPLTVVAAPYRDTVVPLVRHLRERRRRSPRDLT
+MVFIPEYVVRPGWRTLMHNRTATRQKRRLQREAGVMIGSVPWQIHEGQGDGQRSTTV
+>PROKKA_01491
+MSTPPSTLRRLLLGRPVASGARPAPRRGRWLALPATASNALSSLAYAPDEVILTLVASGT
+GALALGPLVGWAVVAVMVLIVLAFRAAVVAVPRGGIYRMARTKLGPRSGVVAAAALLLDF
+VFTAAVSVAAFAHHASALVPALRGHVGIVSAVALVLVLVSALRGERGSGALVTVLVAAFV
+GLLGTLVAVGLWQSGQGTLAAAPSAGLHVDGAGLGPVGDAATALLALRAFSAGSVLLSGV
+EVPLSATDRMARPAVRTARWVLTVLAVVVGTLTVGVMHLAQRTGVVVALHPDRLRTADGA
+PLAPDTAPAPVVAQLAETVFGAGSPGAVATVAVTSLLLLVAARGAFRSFPTLTARLAEDG
+WLPRQLRVRGDRMVHTGGTLALATATLLLLVLFRGRTALLVQLYVIGVLLAFALALVGML
+RLWRLKLAHTPGARARASVRVKLVVTAVGLGATALAGVVVLVTRFAQGAWVALLAIGVSA
+VVMGRIRRHYRAVEAELAPDPQDDARALPSRVHAVVVVSTLNRPALRALAYARATRPATL
+EAVVVDADRRQTERVVEDFARAGLPVPLTVIAAPYRDTVVPLVRHVRGRRLRSPRDLTMV
+FIPEHVVRGGWRRLLHNRTASRQKARLQREAGVMVGSVPWQIREGDPHRPVEGGIVACAA
+PGDVPEGVESS
+>PROKKA_01255
+MATLSSLLRRGLLGRPVTSHAADEPRMNRWRALPVTSSNALSSLAYAPDEVILTLVAAGT
+SALALGPAVGWAVVAVMLLIVVSFRAAVAAVPHGGIYHMAGMKLGPRAGVVASAALLLDF
+VFTAAVSVAAFAHFVAALAPGLTVGSRVLVASAALVGVLLAALRGVRLSRWVLPVLVSVF
+VALTALLVLAGLWQEGRGLLGAAPTAGWTQEGAGVGGTVGTVATALLALRAFSAGSVLLT
+GVEVPVSSTRLMARPAVPTVRWVLTVMALTLGALTVGVMHLAQRTGVVVGLELENLRDAA
+GAEVTPDRAPAPVLAQLADTVYGPGSILSVATIAATALLLLFAAKSAFRSFPALAARVAE
+DGYLPRQLRVRSDRLVHTWSVLGMGAVALSLVLFFEARTALLVQLYVIGVLLAFTLAQAG
+MLRLWRRRLVHTPGARARAAVRLRLIITAVAWVVTALAGVVVLVTRFTQGAWVALLAIVL
+GSLVMGRIRRHYADVDRELAPDPQDDARALPSRVHVVVVVTTLDRPALRALAYARASRPS
+SLEAVVVDAERAATLEVIDAWERAGLPMSLTVIASPYRDTVAPLVRHVREHRRRSPRDLT
+MVFIPEYVVRPGWRTLLHNRTATRQTRRLQREPGVMVGSVPWQVHEGQGS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001086.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001086.fa
new file mode 100644
index 0000000000000000000000000000000000000000..beb40baa20e743f010789b31625da9b13ffa04e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001086.fa
@@ -0,0 +1,25 @@
+>PROKKA_01298
+MAHYVIVGGGRVGTRLAAALDAAGHGVALVDRDPRTVEGLAPGFSGELVAGVGFDRSALL
+AAGIDRAQGLAAVTADDNTNIIAARVARETFHVDHVVARIYDADRARLYQRLGIPTVASI
+QWTADQVLHRLLPAGTADAEHRDASGRLLVTELVPHSSWWGRRLTDVESTVGMRIAYLTR
+LGDGQLPRPGDRLQEGDVLHAVYPVDRRDRVEAALQGEARVPDGTDEDEEGRA
+>PROKKA_01021
+MAHYVIVGGGRVGTRLAAALDAAGHGVALVDRDPRTVEGLAPGFSGELVAGVGFDRSALL
+AAGIDRAQGLAAVTADDNTNIIAARVARETFHVDHVVARIYDADRARLYQRLGIPTVASI
+QWTADQVLHRLLPAGTADAEHRDASGRLLVTELVPHSSWWGRRLTDVESTVGMRIAYLTR
+LGDGQLPRPGDRLQEGDVLHAVYPVDRRDQVEAALQGEARVPDGTDEDEEGRA
+>PROKKA_01594
+MAHYVIVGGGRVGTRLACALDAAGHSVALVDRDPRTVDGLVPGFSGELVAGVGFDRAALL
+AAGVDRAQGLAAVTAEDNTNIIAARVARETFHVEHVVARIYDADQAKVYQRLGIPTVASI
+QWTADQVLHRLLPAGTADVERRDASGRLLVTGLVPHPSWWGRRLTDVESGAGLRIAYLTR
+RGEGLLPRPGDRLQEGDLLHAVYPVDRRDQVEAALQGEAVRSDRDAEDEDEEGRA
+>PROKKA_01490
+MAHYVIVGAGRVGTRLAGALDTAGHSVAVIERSPELTAGLGPDFGGTVVAGIGFDRDALR
+RAGIEQAQGLAAVTTEDTTNVIAARVARETFGVQHVVARIYDAQRARVFQRLGIPTVASV
+EWTADQVLHRLLPAGTAEPSRRDASGRLAMGDYMPHRSWWGSPLHAVEAAVGARIAYLTR
+YGEGVLPSPDGVLQEGDVLHVAYPAARRDRVEAALQGEAGDVRAGEDEDQEEDA
+>PROKKA_01256
+MAHYVIVGGGRVGTRLAAALDAAGHGVALVDRDPRTVEGLAPGFSGELVAGVGFDRSALL
+AAGIDRAQGLAAVTADDNTNIIAARVARETFHVDHVVARIYDADRARLYQRLGIPTVASI
+QWTADQVLHRLLPAGTADAEHRDASGRLLVTELVPHSSWWGRRLTDVESTVGMRIAYLTR
+LGDGQLPRPGDRLQEGDVLHAVYPVDRRDQVEAALQGEARVPDGTDEDEEGRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001090.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001090.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2874fb2e40f18689a8de8dd1abb73de7e672b1fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001090.fa
@@ -0,0 +1,30 @@
+>PROKKA_01302
+MIFGRNRTVRHEQVSLPAELLEERDLEIAAAPEAADVGPHDVATRPDPAGMIDLGSLRLR
+AVQGMKLRLDVEDATKRIVAATVSLGRSALQVQAFSAPRRTGLWDDLRAELHDSLSTTAH
+ATVQEQTGRFGIEILTRVPAALPDGSPGWNVARFVGVDGPRWFVRGVFHGEAAFQPEAAE
+PLEQVFSDLVVVRGDEPLPPRELLPLRPPPNARPLQRRRPAPDEGRDVLADTATGPGDGA
+APEATALPERGPEITETR
+>PROKKA_01025
+MIFGRNRTVRHEQVSLPAELLEERDLEIAAAPEAADVGPHDVATRPDPAGMIDLGSLRLR
+AVQGMKLRLDVEDATKRIVAATVSLGRSALQVQAFSAPRRTGLWDDLRAELHDSLSTTAH
+ATVQEQTGRFGIEILTRVPAALPDGSPGWNVARFVGVDGPRWFVRGVFHGEAAFQPEAAE
+PLEQVFSDLVVVRGDEPLPPRELLPLRPPPNARPLQRRRPAPDEGRDVLADTATGPGDGA
+APEATALPERGPEITETR
+>PROKKA_01590
+MIFGRNRKVRHEQVSLPEELLEERDHEVAALPEAAETGPHDVATRPDPAGAIDLGSLRMR
+AVQGMKLRLDVEDSTKRIVAATITLGRSALQVQAFSAPRRAGLWDEVREELRDSLDTTPN
+ATVQEQAGRFGTEILTRVPAALPDGSPGWNVARFVGVDGPRWFVRGVFHGEAAFQPEAAA
+QLEQVFSDIVVVRGDEPMPPRELLPLRPPANARPVQRRRPGAARDAGRDVLADTERGPQE
+APALPERGPEITEIR
+>PROKKA_01486
+MIFGRNRNVRHEQVAVPEQLKDERDRLVEARPAPAAEGDRGPFDVEAAPSGRPSVDLGAL
+RVPAVQGMQLRLDVEDATQRIVAVTVTLERSALQIQAFSAPRAAGVWDDLRAEIKEALVG
+TPGAQVQEQSGGFGPEVLTRIPATLPDGSPGWNVARFVGVDGPRWFVRGVFHGEAAYLPD
+AARALEDVFAGVVVVRGDAPLPPRELLPLRPPADAQPVRRRPRPHAGGEPDVHARRPDDA
+PETGAETLPERGPEITEIR
+>PROKKA_01260
+MIFGRNRTVRHEQVSLPAELLEERDLEIAAAPEAADVGPHDVATRPDPAGMIDLGSLRLR
+AVQGMKLRLDVEDATKRIVAATVSLGRSALQVQAFSAPRRTGLWDDLRAELHDSLSTTAH
+ATVQEQTGRFGIEILTRVPAALPDGSPGWNVARFVGVDGPRWFVRGVFHGEAAFQPEAAE
+PLEQVFSDLVVVRGDEPLPPRELLPLRPPPNARPLQRRRPAPDEGRDVLADTATGPGDGA
+APEATALPERGPEITETR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001092.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001092.fa
new file mode 100644
index 0000000000000000000000000000000000000000..86cefc90262c1c4b44999abf4f5c4201273dabb1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001092.fa
@@ -0,0 +1,20 @@
+>PROKKA_01304
+MRDPQQHPVADASRRAPGGAAAGPDPVLFEERLTPSPGVWAVALMLAALTILVFAPIDLG
+VGIAAAVAFFAVEVLILVATTPRIVVRERTLQVGRASIERHHVGQVTGYRGEDARAQRGP
+LLHGLAFVNVRGWIAPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMARQEGTAEGR
+>PROKKA_01027
+MRDPQQHPVADASRRAPGGAAAGPDPVLFEERLTPSPGVWAVALMLAALTILVFAPIDLG
+VGIAAAVAFFAVEVLILVATTPRIVVRERTLQVGRASIERHHVGQVTGYRGEDARAQRGP
+LLHGLAFVNVRGWIAPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMARQEGTAEGR
+>PROKKA_01588
+MREPQQHPVSDAPVDRPQDPAQGSDRVLFEERLTPSAGVWVVALMLASLTILVFAPIDLW
+FGVAAAVVFFGLEALLLLTTTPRIVVRERTLQVGRASIERRHVGEVTGHRGEDARRQRGP
+LLHGLAYVVVRGWISPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMVQEDPADEDR
+>PROKKA_01484
+MQDASATPDHHAPRTVAASADPVQYEERLSPSVGVWLVALLLAGLCIFVLAPVALWAGFL
+AAAVFFVVEAVVLLASTPRIVVRERTLQVGRAQIERRHLGAVTGHRGEAARAQRGPLLHG
+LAYVCVRGWISPVVRIQIEDERDATPYWLASTRHPEDLVAALGGRMAGEG
+>PROKKA_01262
+MRDPQQHPVADASRRAPGGAAAGPDPVLFEERLTPSPGVWAVALMLAALTILVFAPIDLG
+VGIAAAVAFFAVEVLILVATTPRIVVRERTLQVGRASIERHHVGQVTGYRGEDARAQRGP
+LLHGLAFVNVRGWIAPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMARQEGTAEGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001100.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001100.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de5f84a9b526ddea4ccc73f337df20f532aabbd4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001100.fa
@@ -0,0 +1,50 @@
+>PROKKA_01313
+MDPLDLARWQFGITTVYHFLMVPLTIGLGLVVAVMQTLWVRTGREQYLRMTKFWGKLFLI
+NFIMGVATGIVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGVWIFGWGRV
+PRRLHLAAIWCAVIGAHLSAYFIMTANAFMQHPVGYEVVDGRPVLNDIGAVLANPIVLTH
+FPHTIAGSWAVAGGFLLGISWYHLWKRRRDGIDTVDEHGRVVVGTTGSKARDRLDHRVWI
+TSLRAGAAVAIVGFLGTAFTGHAQAQQMIEFQPTKMASAEAACHDGTAFSVLTLGDLGAG
+DRTTCTDVTTVIELPGLLSYLAYEDFTTPVPGLNSLLPDFEERYGTHLPDDPLYGERAGA
+PIDYQPLMEVTYWGFRLMITFGGLGALAGALTLWMTRRGTVPDSRGWTATAVASIGAPFA
+ANVAGWVFTEMGRQPFVVYPNPAMGVDEVYMFTAAAVSPGVSAQEVLASLIVLVGIYAVL
+LVVEVVLMVRYVRGGVPAGMPELTADEHRDPDEDRHDRDDVLAFAY
+>PROKKA_01036
+MDPLELARWQFGITTVYHFLMVPLTIGLGLVVAVLQTLWVATGKDHYLRMTKFWGKLFLI
+NFIMGVATGLVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGIWIFGWDRI
+PRRLHLAALWCAVLGINLSAYFIMVANGFMQHPVGYEVVDGRPVLNDLGAVLTNPIVLTH
+YPHTIFGSWAVAGGFLVGIAWYHLWKRRRDGIDVVDEAGRVVVGDAGTAARDRTDHRVWL
+TSLRAGAAVALIGFVGTAFSGHAQAQQMIHFQPTKMAAAEAACHDGTAFSVLTLGDVRSG
+GATTCEDVQGVIEVPGLLSYLAYEDFTTPVRGINTLLPEFEQKYGTHLPDSELYGDRAGS
+EISYLPLMEVTYWGFRLMILFGGLGALAALGALWFSRRGTVPASRGWMRLAVASIGAPFA
+ANMTGWVFTEMGRQPFVVYPNPAMGVDQVYMFTAAAVSPGVTGEEVLVSLIVLVGIYAVL
+LGVEVFLLTRFVRGGVPAAMPELTAAEHSDEQKRDRDDVLAFAY
+>PROKKA_01579
+MDPLDLARWQFGITTVYHFLMVPLTIGLGLVVAVMQTLWVRTGREQYLRMTKFWGKLFLI
+NFIMGVATGIVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGVWIFGWGRV
+PRRLHLAAIWCAVIGAHLSAYFILTANAFMQHPVGYEVVDGRPVLNDIGAVLANPIVLTH
+FPHTIAGSWAVAGGFLLGISWYHLWKRRRDGIDTVDEHGRVVVGTTDSKARDRLDHRVWI
+TSLRAGAAVAIVGFLGTAFTGHAQAQQMIEFQPTKMASAEAACHDGTAFSVLTLGDLGAG
+DRTTCTDVTTVIELPGLLSYLAYEDFTTPVPGLNSLLPDFEERYGTHLPDDPLYGERAGA
+PIDYQPLMEVTYWGFRLMITFGGLGALAGALTLWMTRRGTVPDSRGWTATAVASIGAPFA
+ANVAGWVFTEMGRQPFVVYPNPAMGVDEVYMFTAAAVSPGVSAQEVLASLIVLVGIYAVL
+LVVEVVLMVRYVRGGVPAGMPELTADEHRDPDEDRHDRDDVLAFAY
+>PROKKA_01475
+MDPLELARWQFGITTVYHFLMVPLTIGLGLVVAVLQTLWVRTGREHYLRMTKFWGKLFLI
+NFIMGVATGLVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGMWIFGWDRL
+PRRLHLAAIWCAVIGAHLSAYFIMAANAFMQHPVGYEVVDGRPVLNDIVAVLTNPIVLTH
+FPHTIAGSWAVAGGFLLGISWYHLWKRRRDGIDTVDAEGRVVVGTTGSKARDALDHRVWI
+TSLRAGAAVVIVGFLGTAFTGHAQAQQMIHYQPTKMASAEAACHDGTAFSVLTLGDVNTP
+GATTCDDVTGVIEIPGLLSFLAYSDFTTPVPGITTLLPQFEARYGTQLPDDPMYGERAGQ
+EISYLPLMEVTYWGFRLMITFGGLAALAGALTLWMTRKGTVPDSKPWMITAVASIGASFA
+ANVAGWVFTEMGRQPFVVYPNPAMGVDEVYMFTAAAVSPGVSGEEVLTSLIVFVVLYAVL
+LVVEVALLARYVRGGVPAGMPELTADEHRDPDDDRHDRDDVLAFAY
+>PROKKA_01271
+MDPLELARWQFGITTVYHFLMVPLTIGLGLVVAVLQTLWVATGKDHYLRMTKFWGKLFLI
+NFIMGVATGLVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGIWIFGWDRI
+PRRLHLAALWCAVLGINLSAYFIMVANGFMQHPVGYEVVDGRPVLNDLGAVLTNPIVLTH
+YPHTIFGSWAVAGGFLVGIAWYHLWKRRRDGIDVVDEAGRVVVGDAGTAARDRTDHRVWL
+TSLRAGAAVALIGFVGTAFSGHAQAQQMIHFQPTKMAAAEAACHDGTAFSVLTLGDVRSG
+GATTCEDVQGVIEVPGLLSYLAYEDFTTPVRGINTLLPEFEQKYGTHLPDSELYGDRAGS
+EISYLPLMEVTYWGFRLMILFGGLGALAALGALWFSRRGTVPASRGWMRLAVASIGAPFA
+ANMTGWVFTEMGRQPFVVYPNPAMGVDQVYMFTAAAVSPGVTGEEVLVSLIVLVGIYAVL
+LGVEVFLLTRFVRGGVPAAMPELTAAEHSDEQKRDRDDVLAFAY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001103.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001103.fa
new file mode 100644
index 0000000000000000000000000000000000000000..286d3fafe2f149a816b971cc1f1f2197222b6e8c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001103.fa
@@ -0,0 +1,35 @@
+>PROKKA_01318
+MSGFGYDVGLDEAGMPELVERLESRRVLVTGASGLLGAGVARVLADAGNDVVTLQRRPSG
+VAGARDVQGSVTDPAAVEEALTGADTVVHVAAKVSVSGPEHEYEAVNVEGTRILLHAAQR
+HGVRRFVHVSSPSVAHAGDSIVGEGAGAASPEHARGPYARTKAAGERLALAADRDDFRVL
+VLRPHLMWGPGDLQLTDRIVQRARAGRMPVLGTGAPLVDTLYTANAVEAVVAAVSAADVH
+HGEALVVTNGEPRPVGELIRQIALAGGAAEPERRVPAGLARRAGALIERAWERDLFGLRS
+RGVGSDDGEPPLTEFLAEQLSTAHWFDQRRTREVLSWTPTVSIDEGLHRVAAYYRDR
+>PROKKA_01039
+MSGFGYDVGLDAAGMPDLVERLESRRVLVTGASGLLGAGVARVLADAGNDVTTLQRRPSG
+VPGARDVRGSVTDPAAVEEALTGADTVVHVAAKVSVSGPEHEYEAVNVEGTRILLHAAQR
+HGVRRFVHVSSPSVAHAGDSIVGEGAGAASPEHARGPYARTKAAGERLALAADRDDFRVL
+VLRPHLMWGPGDLQLTDRIVQRARAGRMPVLGTGAPLVDTLYTANAVEAVVAALSAADVH
+HGEALVVTNGEPRPVGELIRQIALAGGAAEPERRVPAGLARRAGALIERAWERDLFGLRS
+RGVGSDDGEPPLTEFLAEQLSTAHWFDQRRTREVLAWTPTVSIDEGLHRVAAYYRDR
+>PROKKA_01574
+MSGFGYDVGLDEAGMPELVERLESRRVLVTGASGLLGAGVARVLADAGNDVVTLQRRPSG
+VAGARDVQGSVTDPAAVERAVAGVDTVVHVAAKVSVSGPEHEFEAVNVEGTRILLHAAQR
+HGARRFVHISSPSVAHAGDSIVGEGAGPASPEHARGPYARTKAAGERLALAADRDDFRVL
+VLRPHLMWGPGDMQLTDRIVQRARAGRMPVLGTGAPLIDTLYTGNAVEAVVAAVSAADHH
+HGEALVVTNGEPRPVGELVRQIALAGGAEEPERHVPAGLARRAGALIERAWERDLFGLRS
+RGVGSDDGEPPLTEFLAEQLSTAHWFDQRRTREVLDWTPSVSIGEGLHRLAAYYRAR
+>PROKKA_01470
+MGFEVHLGDDGLLQLAERVEHRRVLVTGASGLLGSGVARVLAEAGNPVTTLQRRPSGVPG
+AVDVLGSVTDPAAVERALEGVDTVVHVAAKVSVSGPEEEFAAVNVEGTRILVHAARRRGV
+HRFVHVSSPSVAHAGASIVGEGAGPADPEHARGPYARTKAAGELIALGADADDFRVLALR
+PHLMWGPGDLQLTDRIVQRAREGRMPVLGSGAALVDTLYTGNAVEAVVAAVSAVDHTHGE
+ALVVTNGEPRPVGELIRRIALAGGAPEPERTVPAGVARRAGALIERAWERDLFGVRSSGR
+GSADGEPPLTEFLAEQLSTSHWFDQRRTREVLDWTPSVSMDEGLLRLAAYYRDR
+>PROKKA_01274
+MSGFGYDVGLDAAGMPDLVERLESRRVLVTGASGLLGAGVARVLADADNDVTTLQRRPSG
+VPGARDVRGSVTDPAAVEEALTGADTVVHVAAKVSVSGPKHEYEAVNVEGTRILLHAAQR
+HGVRRFVHVSSPSVAHAGDSIVGEGAGAASPEHARGPYARTKAAGERLALAADRDDFRVL
+VLRPHLMWGPGDLQLTDRIVQRARAGRMPVLGTGAPLVDTLYTANAVEAVVAAVSAADVH
+HGEALVVTNGEPRPVGELIRQIALAGGATEPERRVPAGLARRAGALIERAWERDLFGLRS
+RGVGSDDGEPPLTEFLAEQLSTAHWFDQRRTREVLAWTPTVSIDEGLHRVAAYYRDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001105.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001105.fa
new file mode 100644
index 0000000000000000000000000000000000000000..27837f3a4aea30ea6669b57a0bde643660e8124c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001105.fa
@@ -0,0 +1,15 @@
+>PROKKA_01320
+MSITAVAEPAALTRSDRCDRCGAQAYVRAVLHSGGALQFCAHHARAVEDALRPQAALWQD
+ETDRLTAGA
+>PROKKA_01041
+MSITAVAEPAALTRSDRCDRCGAQAYVRAVLHSGGALQFCAHHARAVEDALRPQAALWQD
+ETDRLTAGA
+>PROKKA_01571
+MSITAVAEPAALTRSDRCDRCGAQAYVRAVLPSGGALQFCGHHARAVEDALRPQAAHWQD
+ETDRLTAGA
+>PROKKA_01467
+MSITAVAEPAALTRADRCDRCGAQAYVRAVLPSGGELLFCGHHARGVEASLRPQAALWQD
+QTEELDGSTAA
+>PROKKA_01276
+MSITAVAEPAALTRSDRCDRCGAQAYVRAVLHSGGALQFCAHHARAVEDALRPQTALWQD
+ETDRLTAGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001111.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001111.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d72b4f7f0412c48e2feafa3ad91dcc92f35d9c13
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001111.fa
@@ -0,0 +1,60 @@
+>PROKKA_01326
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEIL
+VEEDDTVEVGAPLATIGDGSGGGSADASEDDAAAEEPAVEEAQQDDAQQEPAGEPAPEER
+ASTDQGSDGAPSAGGEASEVTLPALGESVTEGTVTRWLKSVGDEVEVDEPLLEVSTDKVD
+TEIPSPVAGTLLEIRAEEDDTVEVGAVLALVGSGSAGGGSAPSEGSSGQDEASAEEIEDK
+ATEAEAPEETEEAAEAAGAEKSEKTPEASPSEEASRRESAERDSAQAESAEAPSATEPGQ
+GYVTPLVRRLAHQNNVDLSTVRGTGVGGRIRKQDVLAAALASQAAAGGSEAPAEQASEAA
+APSSAPAAASAPAASSSVDPSVRGEVEKAPRIRQVIAQRMRESLDLSAQLTQVHEVDVTR
+IVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEITYHASEDIA
+IAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVG
+ALFDTPIINQPQVAILGIGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAG
+RFLRTLRQRLEGGEFANELGL
+>PROKKA_01047
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEIL
+VEEDDTVEVGAPLATIGDGSGGGSADASEDDAAAEEPAVEEAQQDDAQQEPAGEPAPEER
+ASTDQGSDGAPSAGGEASEVTLPALGESVTEGTVTRWLKSVGDEVEVDEPLLEVSTDKVD
+TEIPSPVAGTLLEIRAEEDDTVEVGAVLALVGSGSAGGGSAPSEGSSGQDEASAEEIEDK
+ATEAEAPEETEEAAEAAGAEKSEKTPEASPSEEASRRESAERDSAQAESAEAPSATEPGQ
+GYVTPLVRRLAHQNNVDLSTVRGTGVGGRIRKQDVLAAALASQAAAGGSEAPAEQASEAA
+APSSAPAAASAPAASSSVDPSVRGEVEKAPRIRQVIAQRMRESLDLSAQLTQVHEVDVTR
+IVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEITYHASEDIA
+IAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVG
+ALFDTPIINQPQVAILGIGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAG
+RFLTTLRQRLEGGEFANELGL
+>PROKKA_01565
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLQEIL
+ADEDETVEVGAPLATIGDGDGGGSSESDDDAQAEESEEPAAEEAQEDEEQQEPEGEPAPE
+ERSSTQDSEEKSSGGASGGDASEVTLPALGESVTEGTVTRWLKAVGDEVEVDEPLLEVST
+DKVDTEIPSPVAGTLLEIRAEEDETVEVGAVLALVGSGSAGGSSDSSDDSAKDDSAPDEA
+SAEEIEDKATEAETGEETEEAAQDAGEEKEEKAPEASASENASREESAEQEKAAAADAPE
+ATSPGQGYVTPLVRRLAHQNDVDLSTVRGTGVGGRIRKQDVLAAALAQQAGSAESAPAQE
+QGSKEQAAAASSAPAVASSVDPSVRGEVEKAPRIRQVIAQRMRESLDLSTQLTQVHEVDV
+TRIVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEITYHASED
+IAIAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGS
+VGALFDTPIINQPQVAILGTGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGAD
+AGRFLTTLRQRLEGGEFANELGL
+>PROKKA_01461
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEIL
+VEEDDTVEVGAPLATIGDGSGGGSADASEDDAAAEEPAVEEAQQDDAQQEPAGEPAPEER
+ASTDQGSDEAPSAGGEDSEVTLPALGESVTEGTVTRWLKSVGDEVEVDEPLLEVSTDKVD
+TEIPSPVAGTLVEILANEDDTVEVGAVLARVGSGAAPAASQDPAPAADTASPEEIEDKAT
+EAPTGEQTEEAAEQAGDVKQEQAPAASPAETASAAPAASAPAAETSASEPGPGYVTPLVR
+RLAKQNGVDLSTVRGTGVGGRIRKQDVLAASLANQASSGSASPAAAEEQQTPAAASAPAP
+AAVRGETEKAPRIRQVIAQRMRESLDLSTQLTQVHEVDMTRIVQLRGKAKASFQEKNGVK
+LTYLPFITQAVTEALKQHPKLNASFSEDNKEITYHASEDIAIAVDTDRGLLVPVVKDAGT
+LNLAGLAQKIADVAERTRTNKINPDELSGGTFSITNIGSVGALFDTPIINQPQVAILGTG
+AIVKRPMVVADADGNDTIAIRHMMYLSLTYDHRLVDGADAGRFLQTLKARLEGGEFAAEL
+GL
+>PROKKA_01282
+MSETVNLPALGESVTEGTVTRWLKAVGDEVAVDEPLVEVSTDKVDTEIPSPVAGVLEEIL
+VEEDDTVEVGAPLATIGDGSGGGSADASEDDAAAEEPAVEEAQQDDAQQEPAGEPAPEER
+ASTDQGSDEAPSAGGEASEVTLPALGESVTEGTVTRWLKSVGDEVEVDEPLLEVSTDKVD
+TEIPSPVAGTLLEIRAEEDDTVEVGAILALVGSGSAGGGSAPSEGSSGQDEASADEIEDK
+ATEAEAPEETEEAAEAAGAEKSEETPEASPSEEASRRESAERDSAQGESAEAPAATEPGQ
+GYVTPLVRRLAHQNNVDLSTVRGTGVGGRIRKQDVLAAALASQAAAGGSEAPAEQASEAA
+APSSAPAAASAPAASSSVDPSVRGEVEKAPRIRQVIAQRMRESLDLSTQLTQVHEVDVTR
+IVQLRKKAKASFQQQAGVNLTYLPFITKAVAEALKQHPKLNASFSEDNKEITYHASEDIA
+IAVDTEKGLLVPVIKDAGSLNLTGLAQKIADVAERTRTNKISPDELSGGTFSITNIGSVG
+ALFDTPIINQPQVAILGTGAIVKRPMVVTDADGNDSIAIRHMMYLSLTYDHRLVDGADAG
+RFLTTLRQRLEGGQFADELGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001113.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001113.fa
new file mode 100644
index 0000000000000000000000000000000000000000..25ed1090c5e448359937c9d9a2d7a9813185ffdf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001113.fa
@@ -0,0 +1,55 @@
+>PROKKA_01328
+MRDWDEADGGAAGRVGGGPETEPERSSEPGTAAPRAPGWEPVRLLGAGAQAEVWLVEDGR
+GVRAALKVPRAGAAPDALAAEAQAGRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDM
+VQRVGPLSPGQAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVV
+GGASGAGATPGFAAPEALAAVEGAGAEPGASPAVGAPSDVHAWAALGWYALTGRAPGAAG
+HRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATARPEPVPLGEAAPAEV
+AHLLPTVLPGSGPTRRRRGRRAAPRRRALARRRGAAPRRGVLVAAGLATALAVGGGTAGL
+WWPASLGDATEGAPEPAGAVPAGTSVDAARPADGTPESGTPARVPDAGAPGEDAAGEDAV
+DVGEALAAVGHARTAALIDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGLEVTV
+EQAGPARRAGDDALRVDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGEGPEGR
+DGGAAGRTWRVETVDPR
+>PROKKA_01049
+MRDWDEADGGAAGRVGGGPETEPERSSEPGTAAPRAPGWEPVRLLGAGAQAEVWLVEDGR
+GVRAALKVPRAGAAPDALAAEAQAGRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDM
+VQRVGPLSPGQAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVV
+GGASGAGATPGFAAPEALAAVEGAGAEPGASPAVGAPSDVHAWAALGWYALTGRAPGAAG
+HRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATARPEPVPLGEAAPAEV
+AHLLPTVLPGSGPTRRRRRRAAPRRRALALRRGAAPRRGVLVAAGLATALAVGGGTAGLW
+WPASLGDATEGAPEPAGAVPAGTSVDAARPADGTPESGTPARVPDAGAPGEDAAGEDAVD
+VGEALAAVGHARTAALIDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGLEVTVE
+QAGPARRAGDDALRVDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGEGPEGRD
+GGAAGRTWRVETVDPR
+>PROKKA_01563
+MRDWDEADDGAVGRVGGGPETEPERTSELGTAAPRAPGWAPVRLLGAGAQAEVWLVEDGR
+GVRAALKVPRAGAAPDALAAEAQAGRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDM
+VQRVGPLSPGHAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVV
+GGASGAGATPGFAAPEALAAVQGAGAEPEASPAVGAPSDVHAWAALGWYALTGRAPGAAG
+HRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATARPEPVPLGEAAPAEV
+AHLLPTVLPGSGPTRRRRRRAGPGRRALVGRRGAAPRRGVLLAAGLATALAVGGGTAGLW
+WPAAPGSAAEGAPAEGAPEPAGTEPTGTPVDAARPADGTPESGTPARATDTGAPGEDAAG
+ADAVDVGEALAAVGQARTAALTDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGL
+EVTVEQAGPARRAGDDALRVDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGED
+PEARDGGAAGRTWRVETVDPR
+>PROKKA_01459
+MEAEDAERSGGVPPVGRPATDDWFADGGRDVSAWADPPRGGEGPAAVEPGVGDVGSPAEL
+GPADRPPQAPGLRVVSRIGMGGQAEAWLVRREDGTECVLKVPRADGDPDAVAKEAAVYGH
+LRHPHLLRVLGTVDTDRGTGVLSERLPAGSLASMVHDAGPLRPGQAVTVLVPVAQALAHL
+HEHGVVHGDVSPGNVLFGVDGRPALADLGVARVVGGPRGRGGTPGFTAPEDEAGVGEGGA
+AADVYAWGALGWFALTGRAPGPREHRAPLPVLVPDVPVELALLLSAALDPDPAGRPGAAE
+AAVAAYDAAPPEPVPLHESAPAEVAHLLPTVVPPARPGGSGDARRSRPRAGGRRDAGRGR
+GGRKRRNRSPRSRGWHPVMLVGAAVLAGTVVSAAVGGLTDRPEDQGEGAGSRAVAAPPTS
+PTAAPANPRASVTPTGAADPKDAITPTRDGGVPSAAGTGPAAVLPAEDAAAALAAVAEGR
+TAALTDPDPARVDAYAVPDGPAWRRDRAIQDQLREGGSAFSGLVVTLEAVGRPRPAEAGG
+SGGAEAGWVVVPAVLRMSAHTVLDDAGSVVGEVPASEEDVSVTLVPGGEGRWRAAAVDPR
+>PROKKA_01284
+MRDWDEADGGAAGRVGGGPETEPERSSEPGTAAPRAPGWAPVRLLGAGAQAEVWLVEDGR
+GVRAALKVPRAGAAPDALAAEAQAGRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDM
+VQRVGPLSPGQAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVV
+GGASGAGATPGFAAPEALAAVQGAGAEPGASPAVGAPSDVHAWAALGWYALTGRAPGAAG
+HRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATARPEPVPLGEAAPAEV
+AHLLPTVLPGSGPTRRRRRRAGPGRRALARRRGAAPRRGVLVAAGLATALAVGGGTAGLW
+WPASLGDATEGAPEPAGAVPAGTSVDAARPADGTRESGAPARVPDTGAPGEDAAGEDAVD
+VGETLAAVGHARTAALTDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGLEVTVE
+QAGPARRAGDDALRVDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGEGPEGRD
+GGAAGRTWRVETVDPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001114.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001114.fa
new file mode 100644
index 0000000000000000000000000000000000000000..150b790a46edcca509b1a22e7817e78522bff8e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001114.fa
@@ -0,0 +1,25 @@
+>PROKKA_01329
+MPETLLPPLRLLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE
+DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF
+GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG
+IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA
+>PROKKA_01050
+MPETPLPPLRVLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE
+DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF
+GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG
+IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA
+>PROKKA_01562
+MPETLLPPLRVLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE
+DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF
+GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG
+IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA
+>PROKKA_01458
+MPHALLPPVRVLGLAPDLIDYEEGWALQRTLHADVVAGRSDGEILLLEHEAVYTAGRRTE
+DADRPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEEVLIRTAAEF
+GVTAVRVDGRAGIWITAREGDPRPDRKLGAIGLSIHDGVSMHGFSFNCSNSLTPYETIIA
+CGIADASTTTLSVETGREVTPVDVLPVLVRHLEDLGPEHIALTPTEGTPA
+>PROKKA_01285
+MPETLLPPLRVLGLAPDLVDYHAAWDAQRALHADVVAGRSDGEFLLLEHEAVYTAGRRTE
+DAERPTDGAPVVDVDRGGKITWHGPGQLVGYPVVRLRDRAHVKDYVWFLEELLIRTAAEF
+GVTAVRVDGRAGIWVLADRDDDGTARPDRKVGAIGLSIHDGVSMHGFALNCSNSLAPYEG
+IIACGITDAATTTLSVETGRTITPADVVPVLTRHLDELGPAYIAVTPTEGIPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001116.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001116.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b6d8f44db2c9ee2924573b3f255f0cd78396b828
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001116.fa
@@ -0,0 +1,30 @@
+>PROKKA_01331
+MTKNSQPPASSSGSTSATLKEVKAMQRERRLREKEQAKAQRRDKRATKGPGVISQLKQAY
+AMTKAHDPKVGLWMLLAFLGALVVGLVIGLLLDNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVSEQPAAVNPKTQDLVYRAVGRPGVVLVTEGPSPR
+VAALVVKEEKAMRRFLPGVPVTVVESGNGQGQVPLHELPGTLKGMKKALTAQEVQAVDKR
+LTALNTNRLPIPKGVDPNKVRPSRRAMRGR
+>PROKKA_01052
+MTKNSQPPASSSGSTSATLKEVKAMQRERRLREKEQAKAQRRDKRATKGPGVISQLKQAY
+AMTKAHDPKVGLWMLLAFLGALVVGLVIGLLLDNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVSEQPAAVNPKTQDLVYRAVGRPGVVLVTEGPSPR
+VAALVVKEEKAMRRFLPGVPVTVVESGNGQGQVPLHELPGTLKGMKKALTAQEVQAVDKR
+LTALNTNRLPIPKGVDPNKVRPGRRAMRGR
+>PROKKA_01560
+MTKNSQPPASSSGSTSADLKQVKAMQRDRRRRVKEETRAQRRDKRANRGPGIISQLKQAY
+AMTKANDPKVGLWMLLAFVGVLVLGLVIGLLLNNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVPEQPVAVNPKTQDVVYRAVGRPGVVLVTEGPSNR
+IAALVGKEEKAMRRFLPGVPVTVVEAGNGQGQVPLHELPRTLKSMKKALTAQEVQAVDKR
+VNALNVNRLPIPKGVDPMKARPSRRAMRGR
+>PROKKA_01456
+MAKNPSTSPSSSGSSSLKEVKAMQRDRRAQLKADAKAERAQKRANAGPGIISQLKQVFAI
+TRQQNPRLVLWMVLAFASVLVLGLVVGLLLHNWITWLLLAIPFGVLAAVIVMNRLGERAM
+FDRLEGQTGAAGATLSSLGRGWIVGEQPSAVNPKTHDLVYRAIGKPGVVLVTEGPASRVG
+KLVSKEQKAMERFLPGVPVHVVETGRGEGQIPLREVPKTLKALPKKLTAQEVSAVDKRLS
+ALGTQKPPIPKGVDPMRARPDRRGMRGR
+>PROKKA_01287
+MTKNSQPPASSSGSTSATLKEVKAMQRERRLREKEQAKAQRRDKRATKGPGVISQLKQAY
+AMTKAHDPKVGLWMLLAFLGALIVGLVIGLLLDNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVSEQPAAVNPKTQDLVYRAVGRPGVVLVTEGPSPR
+VAALVVKEEKAMRRFLPGVPVTVVESGNGQGQVPLHELPGTLKGMKKALTAQEVQAVDKR
+LTALNTNRLPIPKGVDPNKVRPSRRAMRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001117.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001117.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4bb5bb6d28cc9bb4df4c281649772526dec26476
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001117.fa
@@ -0,0 +1,21 @@
+>PROKKA_01332
+MARRAPDPAQEPEPTRRDEPLITRRDLAGWVDGPGGGLAGGRWPGDLLGLPEHGPTSMAT
+AARRAVALVIDWFLALGVSWLLFDSDAIATLMVFATMHILGITLLATTVGKAVCRTQVVR
+LGGRTAPVHRVVVRTALLCLVLPAVVVGPDGRGMHDKVAGTVEIRM
+>PROKKA_01053
+MARRAPDPAQEPEPTRRDEPLITRRDLAGWVDGPGGGLAGGRWPGDLLGLPEHGPTSMAT
+AARRAVALVIDWFLALGVSWLLFDSDAIATLMVFATMHILGITLLATTVGKAVCRTQVVR
+LGGRTAPVHRVVVRTALLCLVLPAVVVGPDGRGMHDKVAGTVEIRM
+>PROKKA_01559
+MARRAPDPAQEPEPTRRDEPLITRRDLAGWVDGPGGGLAGGRWPGDLLGLPEHGPTSMAT
+AARRAVALVIDWFLALGVSWLLFDSDAIATLMVFATMHILGITLLATTVGKAVCRTQVVR
+LGGRTAPVHRVVVRTALLCLVLPAVVVGPDGRGMHDKVAGTVEIRM
+>PROKKA_01455
+MSCVFPACNASSGPDYPGGVAHRASDPAPRDRSERDAAGRAEPLISRADLAGWIDGPGGG
+RAGGRWPGDLLGLPEHGPASMATAARRAGALMIDWALALVVSNLAFGGDAIATLLVFAAM
+HVVGLTLLATTVGKALCRIQVVREGTGGTAPVHRVLIRTALLCLVLPAVVVGPDGRGMHD
+RVAGTVELHM
+>PROKKA_01288
+MVAHYAGGVARRAPDPQDRTETTGRAEPLITRRDLAGWVDGPGGGRAGGRWPGDLLGLPE
+RGPASMATAARRMGALVLDWFIALGISWLAFDADAIATLLVFAAMHVIGLTLLATTVGKA
+VCRIQVVRVGGRPAGLLRILLRTALLCLVLPAVVVGPDGRGMHDKLADTVEIRM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001118.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001118.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a338ef802bed75016da6d16f6136da9f1c291581
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001118.fa
@@ -0,0 +1,45 @@
+>PROKKA_01333
+MFTSPADVLAYIKDEGIEFVDVRFTDLPGMQHHFNVPASSVDEDFFVTGQLFDGSSIRGF
+AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS
+SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG
+GYFPVSPTDKQADLRDEICSVLAEVGLEVERSHHEVGAAGQAEINYRFNTLTHSADDLQK
+FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW
+YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR
+IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD
+EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV
+>PROKKA_01054
+MFTSPADVLAYIKDEGIEFVDVRFTDLPGMQHHFNVPASSVDEDFFVTGQLFDGSSIRGF
+AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS
+SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG
+GYFPVSPTDKQADLRDEICSVLAEVGLEVERSHHEVGAAGQAEINYRFNTLTHSADDLQK
+FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW
+YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR
+IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD
+EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV
+>PROKKA_01558
+MFTSPADVLAYIKEEGIEFVDIRFTDLPGMQHHFNVPASTVDEDFFTTGQLFDGSSIRGF
+AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS
+SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG
+GYFPVSPTDKQADLRDEICSVLAEVGLEVERSHHEVAAAGQAEINYRFNTLTHSADDLQK
+FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW
+YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR
+IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD
+EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV
+>PROKKA_01454
+MFTSVEDVLAYIKDEGVEFVDIRFTDLPGMQHHFNVPASTVDEDFFVTGQLFDGSSIRGF
+AGLAESDMQLIPDVTTAFVDPFRVRKTLAMNFSIVNPRTGEDYRRDPRGVAQRAEAYLAS
+TGIADTAFFAPEAEFYVFDDVRYESSARSSFYRVDSTEAHWNTSRDEEGGNLGHKTPRQG
+GYFPVTPVDKQADLRDEICAVLAEVGLEVERSHHEVGSAGQAEINYRFNTLTHSADDLQK
+FKYVVKNVAEMFGKSVTFMPKPVFGEAGSGMHCHQSLWLGGEPLFYDEKGYANLSDTARW
+YIGGLLQHASAVLAFTNPTVNSYRRLVPGFEAPVSMVYSQGNRSAGVRIPVTGSNPKAKR
+LEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPPEEAADIQKAPTSLE
+EALNALEEDHEFLLAGDVFTEELIRTWIDYKREMELTPLAARPNPYEFELYYSC
+>PROKKA_01289
+MFTSPQEVLTYIREEGVEFVDVRFTDLPGLQHHFNVPASSVDEDFFVTGQLFDGSSIRGF
+AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS
+SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG
+GYFPVSPTDKQADLRDEICAVLAEVGLTVERSHHEVGAPGQAEINYRFNTLTHSADDLQK
+FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW
+YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR
+IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD
+EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001119.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001119.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f043e72e37cdaf34b0598ba640e0024e1285f18a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001119.fa
@@ -0,0 +1,95 @@
+>PROKKA_01335
+MSSLSTTGALPAVPDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRA
+LLLWVRLAEREPRVHHALRDPETTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAAT
+APALAQPDPADGEPWGDASATLRRLLLDSVGADPDTDRPVAAVTGKDAAVALRRAYRRQL
+AAIALRDLDSAEPTAAMPSVGRWLADLAGATVDAALAVSRAVLTEREGPVVDRVDLAVIG
+MGKCGAGELNYVSDVDVVFAHAVREAADGADPDAEVPDGPRAAALAAELAAGIGRVIQGA
+APEPGLWEVDANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGER
+YIAEIWPRVWESSSRDGFVESVRAMRARVLDTLAPAEREREIKLGPGGLRDVEFTAQLLQ
+LVHGRADESLRVRGTLDAVRALHAASYITTRDARAFDEHYRWLRTLEHRIQLVHLRRTHL
+MPVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALS
+AEDVRLSAEAVRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGAD
+PDGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLSGSRFVGDLLEHSPEAVAWVG
+DDRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVALADISGLLDLE
+AVTGALSDIDQVTVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVH
+RPRPGVDEGRAREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGRQGPLVRTLD
+SYREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAGDLTTADAREIRRIKA
+RVEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGTLPALRAIARH
+GLLPEAEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTAGGELE
+ERYLRVTRLARQVFETRFYGL
+>PROKKA_01056
+MSALPDAATADAPDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRAL
+LLWVRLAEREPRVHHALRDPGTTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAATA
+PALAQPDPTAGEPWGDASAALRRLLLDSVGADPDADRPLAAVTGKDAAVALRRAYRRQLA
+AIALRDLDSAEPTAAMPSVGRWLADLAGATVDAALAVSRAVLTEREGPVVDRVDLAVIGM
+GKCGAGELNYVSDVDVVFAHAVREAADGADPDAQVPDGPRAAALAAELAAGIGRVIQGAA
+PEPGLWEVDANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGERY
+IAEIWPRVWESSARDGFVESVRAMRARVLDTLAPAEREREIKLGPGGLRDVEFTAQLLQL
+VHGRADESLRVRGTLDAVRALHAASYVTTRDARAFDEHYRWLRTLEHRIQLVHLRRTHLM
+PVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALSA
+EDVRLSAEAVRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGADP
+DGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLSGSRFVGDLLEHSPEAVAWVGD
+DRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVALADISGLLDLEA
+VTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVHR
+PRPGVDEGRAREQAEEVVRTLMALLQKPVAPPLPGERRLEVDADLRPEGRQGPLVRTLDS
+YREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAQDLSAADAREIRRIKAR
+VEAERLPRGADPARHVKLGRGGLSDVEWLVQSMQLKHAGQIEDLRVTGTLPALRAIARHD
+LLPESEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTTGGELEE
+RYLRVTRLARQVFETRFYGL
+>PROKKA_01556
+MSALPDAATADAPDRRALAQAGVADARRVQSLLASPEFEGADVAPLVKRLGHAADPDRAL
+LLWVRLAEREPRVHRALRDPETTARLLRLLGASEALGEFLIRRPEHLDLVLEPESAAATA
+PALAQPDPADGEEWADEPAALRRLLLEAVEADPDADRPRAGLTGADAAVALRRAYRRQLA
+AIALRDLDSADPAAVMPSVGRWLADLAGAAVDAALAVSRATLAEREGPAVDRVDLAVIGM
+GKCGARELNYISDVDVVFVHELLDPGPDAAGEAGADGADGEASDAVDGTRAAVLAAELAA
+GIGRVIQAAAPEPGLWEVDANLRPEGKDGALSRTLDSHAEYYRRWAHGWEFQALLKARPI
+AGSADLGARYLERIWPRVWESSAREGFVDSVRAMRSRVLETIAPAEREREIKLGSGGLRD
+VEFTAQLLQLVHGRADESIRVRGTLDAVRALHEASYISTRDAAAFDEHYRWLRTLEHRIQ
+LVHLRRTHLMPVKDEALRIVARSLRGAQETGPATGEDLQAAFTRVRRAVRGLHETVFYRP
+LLSTTAALSDDEVRLSAEAVRERLAALGYRDPKGALRHIEALTQGVSRRAAIQRQLLPAM
+LGWFAEGADPDGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLAASRFVGDLLEH
+SPEAVAWVGDDRELEPRGTVQLWRQADARLDRRIEAQETPAAVRHVRQVRRSETLRVALA
+DISGLLDLEAVTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYG
+SDLDALFVHRPRPGVDEGRAREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGR
+QGPLVRTLDSYREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAGDLTTAD
+AREIRRIKARVEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGTL
+PALRAIARHGLLPEAEVAVLEEAWLLASRIRAAVLLWTGKVGDVLPTNMRDLEAIARLSG
+VGTAGGELEERYLRVTRLARQVFEARFYGL
+>PROKKA_01452
+MAPTPDSHVPGPRRALVHAGVADLTRAERLLSSPELAEQDADAALAALAHAADPDSALLL
+YIRLAERDPQVHRVLAEADRARDLLRLLGASEALGEFLIRRPEHLDLVLDPARAAATAPA
+LAQQDPTDGGDWHDEPAALRALLLEAVGADPAADQPVAGLTGADASVALRRAYRRQLTAI
+ALADLASREPTLVMPAVGRWLADLAGAALEAALAVSRAELRAREGAAVDCVELAVIGMGK
+CGARELNYVSDVDVVFVHDVLEPGAPDAPSAQEAARLAAELAAGISRVLSGPAPEPGLWE
+VDANLRPEGRDGALSRTLDSHVEYYRRWAHGWEFQALLKARPVAGSPALGERYVAAVWPR
+VWESSAREGFVENVRAMRTRVLDTIARDERDREIKLGAGGLRDVEFTAQLVQLVHGRADE
+SVRVRGTLDALRVLHAASYISSRDMRAFDAAYRWLRLLEHRIQLVHLRRTHLMPVKEGPR
+RVVARSMRGAGDVHPVAGDDLQDRFSRVRREVRALHETVFYRPLLSTTAALSDEDVRLSA
+DAVQARLSALGYRDPRRALAHIEALTRGVSRRAAVQRQLLPAMLGWFADGADPDAGLLAF
+RRLSESLGSSPWFLRMLRDSTDAARRLCLVLAGSRRVGDLLEHAPESVAWIGETRELAPR
+GLSALTSEVTARLDRRSPEESAAQVIRHVRQIRQREILRTALADITGVVGLEEVGHALAD
+VDQAAVQGALRVAGQAVLDGADPLTEVVVVAMGRQGGREIAYGSDLDAMFVHRPLAGADE
+TAAAAQAEAVARQLMALLQQPAAPPLPSEQPLDVDADLRPEGRQGPLVRTLDSYREYYAR
+WAEVWERQALLRARVVAGPAGLAEEFTAWADGVRYGDELSAGDAREIRRIKARVEAERLP
+RGADPARHVKLGRGGLSDVEWLVQSLQLRHAHDEPELRVTGTLPALRALARLDLLPPSEA
+ALLEEAWLLATRVRSALVLWTGKGSDVLPTNARDLGALARLAGDACGGGVAFEERYLRVT
+RQARQVFEQRFYGL
+>PROKKA_01291
+MSALPDAATADAPDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRAL
+LLWVRLAEREPRVHHALRDPGTTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAATA
+PALAQPDPTAGEPWGDASAALRRLLLDSVGADPDADRPLAAVTGKDAAVALRRAYRRQLA
+AIALRDLDSAEPTAAMPSVGRWLADLAGAAVDAALAVSRAVLTEREGPVVDRVDLAVIGM
+GKCGAGELNYVSDVDVVFAHAVREAADGADPDAQVPDGPRAAALAAELAAGIGRVIQGAA
+PEPGLWEVDANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGERY
+IAEIWPRVWESSARDGFVESVRAMRARVLDTLAPAEREREIKLGPGGLRDVEFTAQLLQL
+VHGRADESLRVRGTLDAVRALHAASYVTTRDARAFDEHYRWLRTLEHRIQLVHLRRTHLM
+PVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALSA
+EDVRLSAEAVRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGADP
+DGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLSGSRFVGDLLEHSPEAVAWVGD
+DRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVALADISGLLDLEA
+VTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVHR
+PRPGVDEGRAREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGRQGPLVRTLDS
+YREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAGDLTTADAREIRRIKAR
+VEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGTLPALRAIARHG
+LLPEAEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTAGGELEE
+RYLRVTRLARQVFETRFYGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001120.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001120.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a5b52d5e9105e300cd8ea8d0deaf1bace65fe5b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001120.fa
@@ -0,0 +1,45 @@
+>PROKKA_01336
+MDRQQDYVLRTIEDRDVRFVRLWFTDVIGTLKSVALSPAEVENAFTEGLGFDGSSIDGYT
+RISESDMLLQPDPSTFQILPWRGDQGQSSRMFCDVLTPDGRPAPADPRHVLRRVLDRAAD
+RGFTCFTHPEIEFYLLQSDQPGPDGEPVPVDRAGYFDNVPGSDAADFRRDAVSLLEGMGI
+SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSHHPG
+SGMHTHFSLFEGDANAFYDPADEFRLSVTGRRFIAGLLRHSVEITAVTHQFVNSYKRLWG
+GGEAPSYTSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLIAAGLKGI
+EEGYEVPEAAAEDISALTTHERRVLGHVPLPGTLHDALRTAEESEFVASVLGEHVFDALL
+RNKRQEWDDYRVEVTPYELRRYLSGL
+>PROKKA_01057
+MDRQQDYVLRTIEDRDVRFVRLWFTDVIGTLKSVALSPAEVENAFTEGLGFDGSSIDGYT
+RISESDMLLQPDPSTFQILPWRGDQGQSSRMFCDVLTPDGRPAPADPRHVLRRVLDRAAD
+QGFTCFTHPEIEFYLLQSDQPGPDGEPVPVDRAGYFDNVPGSDAADFRRDAVSLLEGMGI
+SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSEHPG
+SGMHTHISLFEGDSNAFYDPADEFRLSVTGRRFIAGLLRHSVEISAVTHQFVNSYKRLWG
+GGEAPSYVSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLIAAGLKGI
+EEGYELPESAAEDVSALTTHERRVLGHVPLPGTLHDALRAAEESEFVASVLGEHVFDALL
+RNKRQEWDDYRVEVTPYELRRYLSGL
+>PROKKA_01555
+MDRQQDYVLRTIEDRDVRFVRLWFTDVVGTLKSVALSPAEVENAFAEGLGFDGSSIDGYT
+RISESDMLLQPDPATFQILPWRGDGGQSSRMFCDVLTPDGRPAPADPRHVLRRVLEKASD
+MGFSCFMHPEIEFYLLTSDQPGPDGRPVPVDRAGYFDNVPGSDAADFRRDAVTLLESMGI
+SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSEHPG
+SGMHTHISLFEGDSNAFYDPADEFRLSVTGRRFIAGLLRHSVEISAVTHQFVNSYKRLWG
+GGEAPSYVSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLLAAGLKGI
+EEGYELPESAAEDVSALTTHERRVLGHDPLPGTLHDALRAAEESEFVASVLGEHVFDALL
+RNKRQEWDDYRVEVTPYELRRYLSGL
+>PROKKA_01451
+MDRQQDFVLRTIEDRDVRFVRLWFTDVIGTLKSVALAPAEVEAAFTEGLGFDGSSIDGYT
+RISESDMLLQPDPATFQILPWRGEAGQTSRMFCDVLTPDGRPAPADPRNVLRRVLDKASD
+MGFSCYTHPEIEFYLLASDRPGPDGRPVPVDSAGYFDHVPGGAAQDFRRDAVTLLEDMGI
+SVEFSHHENGPGQNEIDLRAADALTTADNVQTFRTIMKEVAARQGHYATFMPKPFGDQPG
+SGMHTHFSLFEGDSNAFYDPADEFRLSVTGRRFIAGLLKHSVEISLVTHQFVNSYKRLWG
+ADEAPAYVSWGHNNRSALVRVPLYKPDKAGSARIEYRGLDASANPYLAYALLLAAGLKGV
+EENYDLPEPASEDVGALTPQERRVLGHVSLPGTLHDAVRAAEESEFVADVLGEHVYEALL
+RNKRQEWDDYRVEITPYELRRYMTGL
+>PROKKA_01292
+MDRQQDYVLRTIEDRDVRFVRLWFTDVIGTLKSVALSPAEVENAFTEGLGFDGSSIDGYT
+RISESDMLLQPDPSTFQILPWRGDQEQSSRMFCDVLTPDGRPAPADPRHVLRRVLDRAAD
+RGFTCFTHPEIEFYLLQSDQPGPDGEPVPVDRAGYFDNVPGSDAADFRRDAVSLLEGMGI
+SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSHHPG
+SGMHTHFSLFEGDANAFYDPADEFRLSVTGRRFIAGLLRHSVEITAVTHQFVNSYKRLWG
+GGEAPSYTSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLLAAGLKGI
+EEGYELPESAAEDVSALTTHERRVLGHVPLPGTLHDALRAAEESEFVASVLGEHVFDALL
+RNKRQEWDDYRVEVTPYELRRYLSGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001121.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001121.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3cb736af15e79cf65282bd15009fcd9ee1db3da0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001121.fa
@@ -0,0 +1,31 @@
+>PROKKA_01338
+MSAPQSPRQPDDTAPYGPPAPSRYRTVHLQRAKDEGRRFAMLTTYDAMTAALFDEAGVEV
+LLVGDSVGNTVLGHPTTLPVTLDQMILFTQAVVRGAERALVVADLPFGSYEASPRQAVES
+AVRLVKESGAHAVKVEGDERFAEHVAAMTAAGVAVMAHIGFTPQSEHVLGGYRVQGRGAG
+AVERMTASARALEAAGAFAVLMEMVPSDVAAAVDAALRVPTVGIGAGPGTTGQVLVWQDM
+LGLREGRVPRFVRQYARLHEVVGDAVRAYRADVLDGAFPAPEHGFQG
+>PROKKA_01058
+MSAPQSPRQPDDTAPYGPPAPSRYRTVHLQRAKDEGRRFAMLTTYDAMTAALFDEAGVEV
+LLVGDSVGNTVLGHPTTLPVTLDQMILFTQAVVRGAERALVVADLPFGSYEASPRQAVES
+AVRLVKESGAHAVKVEGDERFAEHVAAMTAAGVAVMAHIGFTPQSEHVLGGYRVQGRGAG
+AAERMTASARALEAAGAFAVLMEMVPSDVAAAVDAALRVPTVGIGAGPGTTGQVLVWQDM
+LGLREGRVPRFVRQYARLHEVVGEAVRAYRADVLDGAFPAPEHGFEG
+>PROKKA_01554
+MLTAYDAMTAALFDEAGIEVLLVGDSVGNTVLGHSSTLPVTLDQMILFSQAVVRGAQRAL
+VVADLPFGSYEASPQQAVESAVRLVKESGAHAVKVEGDERFAEHVAAMTAAGVAVIAHIG
+FTPQSEHVIGGYRVQGRGEGAVEAMTASARALEAAGAFAVLMEMVPSDVAAAVDAALRVP
+TVGIGAGPGTTGQVLVWQDMLGLREGRTPRFVRQYARLHEVIGAGVRAYRRDVLDGAFPA
+PEHGFEA
+>PROKKA_01450
+MDSRTVTPPASSPAASEAAAPYGGAATAAAAAPVEAPARYRTVHLQRAKDEGRRFAMLTT
+YDAMTAALFDEAGVEVLLVGDSLGNTVLGHGSTLPVTLEDMIVFSAAVARGARRAFVLAD
+LPFGSYEASPEQAVRAGVRLMKEAGVHGVKVEGDERFAPHIAAMVAAGVPVMGHIGFTPQ
+SEHVLGGYRVQGRGEGAAERLIASARALEDAGAFAVLMEMVPSDVAAAVDAALRVPTVGI
+GAGPKTTGQVLVWQDMLGLGAGRTPRFVKRYADLRAVMGDAVRAYRADVLSGAFPDPAHA
+FES
+>PROKKA_01293
+MSAPQSPRQPDDTAPYGPPAPSRYRTVHLQRAKDEGRRFAMLTTYDAMTAALFDEAGVEV
+LLVGDSVGNTVLGHPTTLPVTLDQMILFTQAVVRGAERALVVADLPFGSYEASPRQAVES
+AVRLVKESGAHAVKVEGDERFAEHVAAMTAAGVAVMAHIGFTPQSEHVLGGYRVQGRGAG
+AAERMTVSARALEAAGAFAVLMEMVPSDVAAAVDAALRVPTVGIGAGPGTTGQVLVWQDM
+LGLREGRVPRFVRQYARLHEVVGEAVRAYRADVLDGAFPAPEHGFEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001123.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001123.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28d189bf475c658ab86fa6a8e5c8f780ed3343b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001123.fa
@@ -0,0 +1,35 @@
+>PROKKA_01340
+MSQRQNPVAPSSHNGPRPAGPTAPEPGSFAPVGTLTPGAPSPAPPVPAAIPRPEYVGKAT
+PDEGKASDVYDAAGVERIRAAGRLAAQAMEHTAAHIRPGVTTDELDRIAHAFLVERGAYP
+SCLGYRGFPRSICTSINEVICHGIPDGTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHDRLLVPGMVFTIEPMLTLGTIEWDQWDDGWTVVTRDRRRTAQFEHT
+IVVTDDGAEILTLP
+>PROKKA_01060
+MSQRQNPAVPSSHNGPRPAGPTAPEPGSLAPVGTLTPGAPSPAPPVPAAIPRPEYVGKAT
+PDEGNASDVYDAAGIERIRAAGRLAAQAMEHTAAHIRPGVTTDELDRIAHAFLVERGAYP
+SCLGYRGFPRSICTSINEVICHGIPDGTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHDRLLVPGMVFTIEPMLTLGTIEWDQWDDGWTVVTRDRRRTAQFEHT
+IVVTDDGAEILTLP
+>PROKKA_01552
+MSHRQSTASPSSHNGPRPEGPAAPQPGSLAPVGTLTPGAPSPAPPVPASIPRPEYVGRAT
+ADEGNASDVYDAAGIERIRAAGRLAARAMEHTAAYIRPGVTTDELDRIAHAYLVEHGAYP
+SCLGYRGFPRSICTSMNEVICHGIPDSTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHDRLLEPGMVFTIEPMLTLGTIDWDQWDDGWTVVTRDRRRTAQFEHT
+LVVTDDGAEILTLP
+>PROKKA_01448
+MSTTARPTSQPSHNGPRPEGPPAPEPGSRAPLGTLTPGAPSPAPAVPASIVRPEYVGRAT
+ADEGNASDVYDTEGIGRIREAGRIAAQAMEHTAEHIRPGITTDELDRIAHEFIVAAGAYP
+SCLGYRGFPRSICTSVNEVICHGIPDGTVLEDGDIVNLDITAYKDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIKAVKPGREINVIGRAIESYARRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHNRLMVPGMVFTIEPMITLGGIDWEQWDDGWTVVTKDRRRTAQFEHT
+LVVTEDGAEILTLP
+>PROKKA_01295
+MSQRQNPAVPSSHNGPRPAGPTAPEPGSLAPVGTLTPGAPSPAPPVPAAIPRPEYVGKAT
+PDEGKASDVYDAAGIERIRAAGRLAAQAMEHTAAHIRPGVTTDELDRIAHAFLVERGAYP
+SCLGYRGFPRSICTSINEVICHGIPDGTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHDRLLVPGMVFTIEPMLTLGTIEWDQWDDGWTVVTRDRRRTAQFEHT
+IVVTDDGAEILTLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001124.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001124.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca2c4a5e8832f50714185fe5d2725ea7b3291921
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001124.fa
@@ -0,0 +1,20 @@
+>PROKKA_01342
+MHCPFCRHEDSRVVDSRSLDDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRATGNAEVDAHDVGLAILDPLRRLDQVA
+FLRFASVYRDFESLDDFEEAIAELRAGDGDDRGRPAVQPRLFTR
+>PROKKA_01062
+MHCPFCRHEDSRVVDSRSLDDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRATGNAEVDAHDVGLAILDPLRRLDQVA
+FLRFASVYRDFESLDDFEEAIAELRAGDGDDRGRPAVQPRLFTR
+>PROKKA_01550
+MHCPFCRHEDSRVVDSRSLEDGSAIRRRRQCQSCGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRASGNAEVDAHDVGLAILDPLRRLDQVA
+FLRFASVYRDFESLDDFADAIAELRAGTDERGRPAVQPRLFSR
+>PROKKA_01446
+MHCPYCRHEDSRVVDSRSLEDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVSSDDLAVLAQEVEEAVRASGNAEVDAHEVGLAILGPLRRLDQVA
+YLRFASVYRDFESLSDFEDAIAELRAQEGEAPGRPAVQPRLFSR
+>PROKKA_01297
+MHCPFCRHEDSRVVDSRSLDDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRATGNAEVDAHDVGLAILDPLRRLDQVA
+FLRFASVYRDFESLDDFEEAIAELRAGDGDDRGRPAVQPRLFTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001126.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001126.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bad322cd3045195299b37d06ac9d89c3e73ddf52
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001126.fa
@@ -0,0 +1,35 @@
+>PROKKA_01344
+MGMRPGLTERLEVTEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA
+KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG
+PTVVGALAALGYDITTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK
+VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLEDGRPSVTHYETLEVFGRATLLEVHL
+ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLAFPHPVTGEPVTI
+TSPYPDDLAHALAALRGDED
+>PROKKA_01064
+MGMRPGLTERLQVAEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA
+KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG
+PTVVGALAALGYDITTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK
+VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDDGRPSVTHYATLEVFGRATLLEVHL
+ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLAFPHPVTGEPVTI
+TSPYPDDLAHALAALRGDED
+>PROKKA_01548
+MEPIPGATARIEVTPDRAGRRADAVLAEVLGLSRSALADWFSRGLVRAESRTGRRDRVLA
+KSAKAVAGEVLAVDVPDDPDPLEVRAERVDALRILHEDEHLIAVDKPTGVAAHPSPGWAG
+PTVVGALAALGHDISTSGAPERQGIVHRLDVGTTGVMVVAKTEQAYAALKDQFRRRVPEK
+VYHALVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDGGRPSVTHYETLEVFGRATLLEVHL
+ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLSFPHPVTGEPVSV
+TSEHPDDLAHALARLRRDGS
+>PROKKA_01444
+MGLRPGLTERLAVTEDDAGRRADAVLADAFGVSRASLADLFSRGLVRAESRTGRRDRVLA
+KSAKAVAGETLAVDVPVDPDPLEVRAERVDAMTVLYEDDDLLAVDKPTGVAAHPSPGWFG
+PTVVGGLAGLGRRISTSGAPERQGIVHRLDVGTTGVMVVAKSERAYTALKDQFRERVPEK
+VYHAVVQGMPDPLEGTIDAPIGRDPNHHWRFAVLEGGRPSVTHYETVEAFGRATLLEIHL
+ETGRTHQIRVHTSALRHPCAGDLTYGADPRLAAELGLTRQWLHAHRLALPHPATGERLEI
+VSPYPDDLAHALRVLRGEDRGAAPDA
+>PROKKA_01299
+MGMRPGLTERLEVTEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA
+KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG
+PTVVGALAALGRDISTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK
+VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDDGRPSVTHYETLEVFGRATLLEVHL
+ETGRTHQIRVHTSALRHPCVGDLTYGADPRMAAELGLTRQWLHAHRLAFPHPVTGEPVTI
+TSPYPDDLAHALAALRGDAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001128.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001128.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88296ad82181260f54d9c867804c77fc787bd45d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001128.fa
@@ -0,0 +1,25 @@
+>PROKKA_01346
+MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA
+APAAGPAADTPEAAATPASAEESAPAAAPESADAAATSAAGVLAMAQRLHDEHVAAGEQR
+STELVAEAEATAARLVSDAEEQKARTLEALAEEKAGLEGEVEQLRSFETDYRSRLTSYIE
+GQLREIRAQKRVEPPTPTA
+>PROKKA_01066
+MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA
+APVADTPEAAETPSPVEEPAPAAAPEAADAAATSAAGVLAMAQRLHDEHVAAGEQRSTEL
+VAEAEATAARLVSDAEEQKARTLEALAEERAGLEGEVEQLRSFETDYRSRLTSYIEGQLR
+EIRAQKRVEPPTPTA
+>PROKKA_01546
+MALSWEDVVNKQFQPTKFREGYDQGEVDDFLDEIVGELKRLQGLNEQLTAENEALRAGGA
+VPDADAAVDAPVADADAAAVVDAGQSPAPAALADAEPGLEVEPTPSSADPASASAAGVLA
+MAQRVHDEHVAAGEQRRDELISEAEARAEALVAEAEETRTRTLEELAADKAGLEAEVEQL
+RGFETDYRSRLTAYIEGQLREIRSQERVEPAQRPA
+>PROKKA_01442
+MVLSWEDVVNKEFQLTKFREGYDREEVEDFLDEVVEELKRLTEENDRLRSDLDACREGAP
+AQAEASAPAAGEAAPALQAPAPVAPVEPSAPGEPVAPTDSATSAAGVLAMAQRLHDEYVA
+EGEQRRDRIIADAEAEATTVVRQAEETRTRTLSDLESRRKGLEADVERLRAFETDYRSRL
+TAYIEGQLREITAQERLEPAKGTV
+>PROKKA_01301
+MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA
+APAAAPAADTPEAAATPASVEEAAPAAAPESADAAATSAAGVLAMAQRLHDEHVAAGEQR
+STELVAEAEATAARLVSDAEEQKARTLEALAEEKAGLEGEVEQLRSFETDYRSRLTSYIE
+GQLREIRAQKRVEPPTPTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001133.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001133.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d680670d714b07d1145097376b745cf89361356
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001133.fa
@@ -0,0 +1,41 @@
+>PROKKA_01351
+MAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLDVGR
+ELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARIARS
+LGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVMDAF
+RQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKAAEL
+AIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDDALG
+DEVRVTVIAAGFDKVDVTSAPAAPQAVQQQAAPQRAAAPAQPQPAAQPQPAAPAQPQQAE
+RPAVRGTVPLAPQEQQPRRQQDLPTVVEPDLGAGSSDLDVPDFLK
+>PROKKA_01071
+MAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLDVGR
+ELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARIARS
+LGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVMDAF
+RQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKAAEL
+AIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDDALG
+DEVRVTVIAAGFDKVDVTSAPAAPQAAQQQAAPQRAAAPAQPQPVPAQPQQAERPAVRGT
+VPLAPQEQQPRRQQDLPTVVEPDLGAGSSDLDVPDFLK
+>PROKKA_01541
+MDTVAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLD
+VGRELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARI
+ARSLGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVM
+DAFRQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKA
+AELAIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDD
+ALGDEVRVTVIAAGFDKVDATSAPASPQAGQFQQAPQRPAQQAQPQQQAPAPQQHQAQPA
+QQEQPQQVQPQSVRGTVPLAPQQPQQTEQRRQQDLPTVVEPDLGAGSSDLDVPDFLK
+>PROKKA_01437
+MDTVAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLD
+VGRELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARI
+ARSLGALTIGVVTRPFTFEGRRRAGSAENGIDALRDEVDTLIVIPNDRLLSISDRNVSVM
+DAFRQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKA
+AELAIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDD
+ALGDEVRVTVIAAGFDKVDATSAPAAPFQQQAAPQRAAAPQQPAQQAQQAPVSQQAAPQR
+PSVPGTMPLNSSSAFGGAPAQPAATQQPAAPQQPAAPQRAQQDLPTVVEPEFGSSDLDVP
+DFLK
+>PROKKA_01306
+MAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLDVGR
+ELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARIARS
+LGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVMDAF
+RQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKAAEL
+AIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDDALG
+DEVRVTVIAAGFDKVDVTSAPAAPQAVQQQAAPQRAAAPTQPHPVPAQPQPAPAQPQPAP
+AQPQQAERPAVRGTVPLAPQEQQPRRQQDLPTVVEPDLGAGSSDLDVPDFLK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001137.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001137.fa
new file mode 100644
index 0000000000000000000000000000000000000000..845b00b1918282ac9e4379722d97e52b7f56bbea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001137.fa
@@ -0,0 +1,45 @@
+>PROKKA_01355
+MSPIELRPVRPRAADDAPEHRERILRRMWRVLEGRRALDLSVLLISGCTALLTVLGLVMV
+LSSSSVEAIGTGGGSYALFLRQSAWAVAGVAALLVFSRLPVRVLKALAWPAFGVAVILLA
+LVAFSPLGVTVGGNRNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALIPV
+LPGGLLLLVLVMAGSDLGTAIILAIVLATVLYVAGTHWGVFLTFLALSVLGILALTLLAP
+HRMVRVQAWMGDCSDATDPCFQPAHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT
+ILGEELGLVGTLVVLLAYLGLAIGIYRVAAGTTSTFIRLSTWGILAWLVGQAAVNIAMVS
+GVIPVVGVPLPFISYGGSALTLSLSAVGIVLAFARHERRRAAQPDARPQADEPDTDPLPV
+IPTPALQEPR
+>PROKKA_01075
+MSPIELRPVRPRADDDAPEHRERLLHRMWRVLEGRRALDLSVLLISGCTALLTVLGLVMV
+LSSSSVEAIGTGGGSYALFLRQSAWAVAGVAALLVFSRLPVRVFKALAWPAFGVAVILLA
+LVAFSPLGVTVGGNRNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALIPV
+LPGGLLLLGLVMAGSDLGTAIILAIVLATVLYVAGTHWGVFLTFLALSVLGILALTLLAP
+HRMVRVQAWMGDCSDATDPCFQPAHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT
+ILGEELGLVGTLVVLLAYLGLAIGIYRVAAGTTSTFIRLSTWGILAWLVGQASVNIAMVS
+GVIPVVGVPLPFISYGGSALTLSLSAVGIVLAFARHERRRAAQPDARPQADEPDTDPLPV
+IPTPALQEPR
+>PROKKA_01537
+MSPTELHPVRTPADEEETEARSRPLQRLWRLVEGRRALDLSVLLIGGSTFLLTALGLVMV
+LSSSSVEAIGTGGGSYGLFLRQTMWAVAGLAALLLFSRLPIGWIKALAWPAFGLAVVLLS
+LVAFTPLGVTVGGNTNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALVPV
+LPGGLLLIGLVMAGSDLGTAIILALVLAAVLFVAGTHHGVFIAFSAVTVVGAIALTLLAP
+HRMVRVQAWLGDCSDASDPCFQPDHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT
+ILGEELGLVGTLGVLLAYLALAVGMYRVAAGTTSPFIRLATWGIMAWLVGQAFVNIAMVS
+GVIPVVGVPLPFISYGGSALTLSLTAVGIVLAFARHERRRAEEPDARPDADDPDTDPLPV
+IPAPASQES
+>PROKKA_01433
+MPSTATRPEASSRASARTAVRPRLAGFWGALEGRRALDWAALLIGLCTAVLTVLGLVMVL
+SASSVEAISSSGGSYGLFLRQGGWALGGAVLLAVLRRLPVDLYRRLAWAAYLFAFLLLAL
+VAFTPLGKEVNGNTNWLQLGPVTFQPSEAAKLAMALWAAAVLQRKERLVHLVSHALVPVL
+PFGVALILLVLKGRDLGTALILAFILAVILFVAGTPGRVFAVLAGIGVVAALGMTVFAAN
+RMERVQAWLFGCEGLQGDPCMQPDHGIYALASGGWWGVGLGQSRQKWNYIPEAENDFIFT
+ILGEELGLVGTLLVLACFVGLAVGMYRVAAGASSTFVRLATWGILAWIVGQAAMNIAMVT
+GLLPVVGVPLPFISYGGSALTLSLAAVGVVLSFARHERDLLPAAEASAADPASSASPQES
+R
+>PROKKA_01310
+MSPIELRPVRPRADDDAPEHRERLLPRMWRVLEGRRALDLSVLLISGCTALLTVLGLVMV
+LSSSSVEAIGTGGGSYALFLRQSAWAVAGVAALLVFSRLPVRVFKALAWPAFGVAVILLA
+LVAFSPLGVTVGGNRNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALIPV
+LPGGLLLLILVMAGSDLGTAIILAIVLATVLYVAGTHWGVFLTFLALSMLGILALTLLAP
+HRMVRVQAWMGDCSDATDPCFQPAHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT
+ILGEELGLVGTLVVLLAYLGLAIGIYRVAAGTTSTFIRLSTWGILAWLVGQAAVNIAMVS
+GVIPVVGVPLPFISYGGSALTLSLSAVGIVLAFARHERRRAAQPDARPQADEPDTDPLPV
+IPTPALQEPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001142.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001142.fa
new file mode 100644
index 0000000000000000000000000000000000000000..31f1fc2620257b842ff3968540b37c42963df123
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001142.fa
@@ -0,0 +1,25 @@
+>PROKKA_01361
+MTLHEEMSMAAHARIAESLRPGSTPVAPARPTPQERTPLSVVPAPLPRSRSGVTVLCVLV
+VLAALAAVLVMNITMSNRQYALLDLRQEQQAVTETNERLAEQVGHLEAPQNLAARADALG
+MVAPAGTASVDAGTGQFSGEAQAAQDGDISATYVAPPADADAVRQGTAGDGQDEIEGPRT
+LGGEDASAAPDQDAADR
+>PROKKA_01081
+MTLHEEMSMAAHARIAESLRPGSTPVAPARPAPQERTPLSVVPAPLPRSRSGVTVLCVLV
+VLAALAAVLVMNITMSNRQYALLDLRQEQQAVIETNERLAEQVGNLEAPQNLAARADALG
+MVAPAGTASVDAGTGEFGGEAQAAQDGDVSATYVAPPADADVVRQGASAEGQDEIEGPRT
+LGGEDASAAADQDAADR
+>PROKKA_01532
+MTLHEEMSMAAHARIAEPLRHTGAPARPAPQERTPLSVVPAPLPRSRSGMTVLCVVVLLA
+ALAAVLVMNITMSNRQYALLDLRQEQQAVTEVNERLAEQVGYLEAPQNVAARADALGMVA
+PAGTASVDAATGEFRGEAQPAREGEISATFVAPPVNADAVRQGSAGSADADRGDIEGPRT
+LGAPAAAPGAAASDDRDASDR
+>PROKKA_01427
+MTAYEETGMSAQAWRDEARTAWPRTGATPEREHRQRTPLSVVPTPLPRSGSGVAVLCGLV
+LLVALGLVLVMNITMSNRQFTLLDLRAQQTTLTETNERLAEQAGYLDAPQNLAARAGAMG
+MVSPGATSTVDVASGAVAGPSTGAGSTTLPEGRIAPPADADLARQGEAQGQIPGPRTVDP
+AAPTAAPSGETAPTPAPTDAPAGR
+>PROKKA_01316
+MTLHEEMSMAAHARIAESLRPGSTPVAPARPTPQERTPLSVVPAPLPRSRSGVTVLCVLV
+VLAALAAVLVMNITMSNRQYALLDLRQEQQAVTETNERLAERVGHLEAPQNLAARADALG
+MVAPAGTASVDAGTGQFSGEAQAAQDGDISATYVAPPADADAVRQGTAGDGQDEIEGPRT
+LGGEDASAAPDQDAADR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001145.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001145.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b88370a7de1d80ea5b021f925075fc51c09fdd99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001145.fa
@@ -0,0 +1,20 @@
+>PROKKA_01364
+MPLSEHEQRMLDQLEQQLRTEDPRLATQMADTGRHRLPVGRVVAGAVLAVVGLLVVVLGV
+ANHAILLGVLGVVVIGAGIFLLTTRPRAVASGASGPEARRSGAPRRQGGGDFMGRLERRW
+DERRAGGD
+>PROKKA_01084
+MPLSEHEQRMLDQLEQQLRTEDPRLATQMADTGRHRLPVGRVVAGAVLAVVGLLVVVLGV
+ANHAILLGVLGVVVIGAGIFLLTTRPRAVASGASGPEARRSGAPRRQGGGDFMGRLERRW
+DERRAGGD
+>PROKKA_01529
+MPLSEHEQRMLDQLEHQLRTEDPRLATQMADTRRDPVPVKRVVLGAVLAVVGLLVIVMGV
+ANQLVPVGVLGALVVGAGIFLVTTRPRGGRAAGADRPGPGRGGRPGGGRPEGGRPGGDFM
+GRLERRWDARREQGD
+>PROKKA_01424
+MPLSDHEQRVLDELERQLHADDPSLASQLSTPRGPAPVRRIVLGAAMMLAGLAVVLVGVS
+THLVVVGVLGAVLLGGGILVLTSRRVSASRAPGAPVAGDGGPHAGRRRGGLMDRLDREWD
+SRGRADT
+>PROKKA_01319
+MPLSEHEQRMLDQLEQQLRTEDPRLATQMADTGRHRLPVGRVVAGAVLAVVGLLVVVLGV
+ANHAILLGVLGVVVIGAGIFLLTTRPRAVASGASGPEARRSGAPRRQGGGDFMGRLERRW
+DERRAGGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001146.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001146.fa
new file mode 100644
index 0000000000000000000000000000000000000000..02f76255a5a1f79acade50fa24611eaab015eb67
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001146.fa
@@ -0,0 +1,44 @@
+>PROKKA_01365
+MSETAPAAPRDEATILHVDMDAFFLSVELRERPDLEGRPAAVAAPSGRSVVLSASYAARA
+YGVRSAMPLAHARALCPPLVVIPPRQQLYRAVSAEVMAVLADVTPVMEQLSVDEAFLDVA
+GARRRLGPPEHIGHLIRERVRSALGLPCTVGGSAVKFVAKTASTAAKPDGLLIVPPERTL
+DFLHPLPVGRLWGVGPKAAERLARRGVATIGDLARVDPARLEASFGAAGREWASLARGID
+PRPVAPRPAARSIGADHTFDVDPVDVAGVDPEVLRLCHRVAARLRAEQATAGAVTVRLKA
+PDGSVRSRTARLARPTATGHDLLGPARRLVRELHAERPHPVRLVGVRAERLGDEADQPPA
+QEALFGGPAWGTEGEASEAGDWAGAEAALDAVARRFPTAAVRPASLLGRREARADARRDA
+PRPGPGGPDRE
+>PROKKA_01085
+MSESAPAAPRDEATILHVDMDAFFLSVELREQPDLEGRPAAVAAPSGRSVVLSASYAARA
+YGVRSAMPLAHARALCPPLVVIPPRQQLYRAVSAEVMAVLADVTPVMEQLSVDEAFLDVA
+GARRRLGPPEHIGHLIRERVRSALGLPCTVGGSAVKFVAKTASTAAKPDGLLIVPPQRTL
+DFLHPLPVGRLWGVGPKAAERLARRGVATIGDLARVDPARLEASFGAAGREWASLARGID
+PRPVAPRPAARSIGADHTFDVDPVDVAGVDPEVLRLCHRVAARLRAEQVTAGAVTVRLKA
+PDGSVRSRTARLARPTATGHDLLGPARRLVRELHAERPHPVRLVGVRAERLGDEADQPPA
+QEALFGGPAWGTEGEASEAGDWAGAEAALDAVARRFPTAAVRPASLLGRREARADARRDA
+PRPGPGGPDRE
+>PROKKA_01528
+MSDTAAAQARPEASILHVDMDAFFLSVELRERPDLTGRPAAVAAPSGRSVVLSASYEARA
+YGVRSAMPLAHARALCPPLVVVPPRQDVYRSVSADVMALLGQVTPVLEQLSVDEAFLDVA
+GARRRLGPPARIGGLIRRRVREELGLPCTVGAAGVKFVAKMASTAAKPDGLLVVPPERTL
+EFLHPLPVGRLWGVGPKAAEALRRRGMATIRDLAAADPEQLERAFGAAGRSWAQLSRGID
+PRPVAPRPAARSIGADHTFDVDPLDVAGVDLEVLRLCHRVAARLRAEEVAAGAVTVRLKD
+PDGRVRSRTARLARPTTTAHGLLGPARRLVAELHAQRPHPVRLVGVRAERLTDADEPAPE
+QEALFGGSGFGDDDAAEGGAGDWAGAEAAADAVARRFPTAAVRPASLLRRAAGRPDTRRD
+VPGP
+>PROKKA_01423
+MSAPDPGPAPSSPPPPRREPSILHVDMDAFFLSVERRERPELRGVPAAVAHPEGRSVVLS
+ASYEARAYGVRSAMPLAQARALCPPLRVTPPRQELYRSTSARVMDLFGRVTPVVEQLSVD
+EAFLDVAGARRLLGPPERIAALIRERVRAELGLPCTVGGAGVKFVAKMASTAAKPDGMLL
+VPPQCTLAFLHPRPVGALWGVGPQAARRLRERGVETIGDLAARDPRWLREAFGAAGAAWA
+ELAAGRDPRPVAPREPARSVGADHTFDVDARDPAALDREVLSLCHRVAARLRSGGHTAAA
+VTVRVKDPALATRARTVRLPAPTASGRVLHAHAGPAVAGLLTERPHPVRLVGVRAERLSD
+AEAHGAVQEALFAPEGHEGPTDDAGWRRAEEAADAVARRFPGAGVRPASLLGPPEGS
+>PROKKA_01320
+MSETAPAAPRDEATILHVDMDAFFLSVELREQPDLEGRPAAVAAPSGRSVVLSASYAARA
+YGVRSAMPLAHARALCPPLVVIPPRQQLYRAVSAEVMAVLADVTPVMEQLSVDEAFLDVA
+GARRRLGPPEHIGHLIRERVRSELGLPCTVGGSAVKFVAKTASTAAKPDGLLIVPPERTL
+DFLHPLPVGRLWGVGPKAAERLARRGVATIGDLARVDPARLEASFGAAGREWASLARGID
+PRPVAPRPAARSIGADHTFDVDPVDVAGVDPEVLRLCHRVAARLRAEGVTAGAVTVRLKA
+PDGSVRSRTARLARPTATGHDLLGPARRLVRELHAERPHPIRLVGVRAERLGGEADQPPA
+QEALFGGPAWGTEGEASEAGDWAGAEAALDAVARRFPTAAVRPASLLGRREARADARRDA
+PRPGPGGPDRE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001152.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001152.fa
new file mode 100644
index 0000000000000000000000000000000000000000..239e5c6d177bfd77f0b1795ff9b0f0b9901c20f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001152.fa
@@ -0,0 +1,30 @@
+>PROKKA_01372
+MPRPVAVAPEDLPLRLMPAAPARRDHCVVLLHGFTSTPASVRAWAEGLAAGGSPVSVPLL
+PGHGTRWEDLAATGADEIRAAVRAVVDLELARHGRVVMAGISMGGALALDAAAHRPVAGV
+LVVNPALRFASPLAPFAPLLAPFVPTVAPIADDIADPTARERAYPRTPVAGVAALGRIQR
+AARRALPRITAPVTVYRSARDAVVPASSHRTLVRGLRQAPVEVVGLPRSRHVATLDYDLP
+LLIDHGRSAVAAMTTH
+>PROKKA_01092
+MPRPVAVAPEDLPLRLMPAAPARRDHCVVLLHGFTSTPASVRAWAEGLAAGGSPVSVPLL
+PGHGTRWEDLAATGADEIRAAVRAVVDLELARHGRVVMAGISMGGALALDAAAHRPVAGV
+LVVNPALRFASPLAPFAPLLAPFVPTVAPIADDIADPTARERAYPRTPVAGVAAVGRIQR
+AARRALPRITAPVTVYRSARDAVVPASSHRTLVRGLRQAPVEVVGLPRSRHVATLDHDLP
+LLIDHGRSAVAAMTTH
+>PROKKA_01520
+MDRPVPPVEPAPPAVPAPAVDPVHLPLRLAPGSGAGADRCVVVLHGFTSGPDSVRAWAEG
+IAAGGSHVSVPLLPGHGTRWQDLAATGADEIRGAVRETVDRELSRHRHVVVAGISMGGAL
+ALDAAAHRPVSAAIVVNPALRFASPLAPLAPALAPFVPSVAPIANDIADPDARELAYPRT
+PVAGVAAVGRIQRAARRALPRITAPVTVFRSARDAVVPAASHRTLLRGLRRAPVDVVPLP
+RSRHVATLDYDLPLLIERSRAAVEAATRA
+>PROKKA_01416
+MTRLRPAAPDRRPAPGVDPAQRPFRLPATSLPGVAVVMLHGFTSGPDSVRAWAEGVAAGG
+AAVHVPLLPGHGTRWEDLGTTDADELRAAVRDAVDAALATHRRVVVAGISMGGALALDAA
+AHRDVAGVLVVNPALRFGSPLAVAAPLLRHVVPSVPSIAGDIADPDARELAYERAPVAGV
+AQVGRIQTAARRGLGRITAPVTVFRSAEDAVVPERSHHTLLRGLTAAPVEVVRLLHSRHV
+ATLDRDLPLLVARSRDAVAAAAR
+>PROKKA_01327
+MPRPVAVAPEDLPLRLMPAAPARRDHCVVLLHGFTSTPASVRAWAEGLAAGGSPVSVPLL
+PGHGTRWEDLAATGADEIRAAVRAVVDLELARHGRVVMAGISMGGALALDAAAHRPVAGV
+LVVNPALRFASPLAPFAPLLAPFVPTVAPIADDIADPTARERAYPRTPVAGVAALGRIQR
+AARRALPRITAPVTVYRSARDAVVPASSHRTLVRGLRQAPVEVVGLPRSRHVATLDYDLP
+LLIDHGRSAVAAMTTH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001158.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001158.fa
new file mode 100644
index 0000000000000000000000000000000000000000..58b94e345307110e06bc0404d0c6a241b928fdb0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001158.fa
@@ -0,0 +1,30 @@
+>PROKKA_01378
+MIDPRPLPDAVPTARPAGRLGIGEVVAALEAEFPGVTASKVRFLEDRGLVLPERTPAGYR
+RFRPEDVDRLRFVLALQRDHFLPLKVIADHLAALDRGERPTGLPGTAAVPASSDAARLGR
+EVAGGRRSWTRAELAAESGAGEELLAELDQYSLLPVDPDGGYPSHAMDVARAAVVLAGHG
+LEPRHLRPLRAAADRELGLVERAVAPLQARRDAGTRPRVARSAREIAQASLRLHAALVAV
+GLEQWDD
+>PROKKA_01098
+MTDPRPRPDAVPTARPAGRLGIGEVVASLEVEFPGVTASKVRFLEDRGLVLPERTSAGYR
+RFRPEDVDRLRFVLALQRDHFLPLKVIADHLAALDRGERPTGLPGTAAAPASSDAERLGR
+EVAGGRRSWTRAELAAESGAGEELLAELDQYSLLPVDPDGGYPSHAMDVARAAVVLAGHG
+LEPRHLRPLRAAADRELGLVERAVAPLQARRDAGTRPRVARSAREIAQASLRLHAALVAV
+GLEQWDD
+>PROKKA_01514
+MTEPQHADAGPRTRPAGRLGIGEVVAALKSDFPGVSASKVRFLEDRGLVLPERTPAGYRR
+YRPEDVDRLRFVLTVQRDHFLPLKVIAAQLAALDRGEVPADLPGGVVAPGASDASRLGRE
+VAAGRRGWTRSELAEESGAGEELLAELDQYSLLPADEDGAYSSHAMEVARAAVVLAGHGL
+EPRHLRPFRAAADRELGLVERAVAPLQARRDANMRPRVARSAQEIAQASLRLHSALVAEG
+LEQWDDGAVG
+>PROKKA_01409
+MSAPHEPSAAPPPAGAALGIGDLVAALEPSFPGVSASKVRFLEDRGLVRPERTAAGYRRY
+RPADVDRIRLVLTLQRDRFLPLKVIREHLDALDRGERPEDLGEAPAAAQEAVRLGHGIAD
+PDRRWTRAELAREAEVPAPLVDELDQYALLPRAEDGLHPPAALGVVRAAGRLAAHGIEPR
+HLRPFRAAADRELGLVQSAVAPLATRRDAGTRERAARTAEEIATACLALHAALVRAGLES
+LDG
+>PROKKA_01333
+MTDPRPRPDAVPTARPAGRLGIGEVVASLEVEFPGVTASKVRFLEERGLVLPERTSAGYR
+RFRPEDVDRLRFVLALQRDHFLPLKVIAEHLAALDRGERPTGLPGTAAAPASSDAERLGR
+EVAGGRRSWTRAELAAESGAGEELLAELDQYSLLPVDPDGGYPSHAMDVARAAVVLAGHG
+LEPRHLRPLRAAADRELGLVERAVAPLQARRDAGTRPRVARSAREIAQASLRLHAALVAV
+GLEQWDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001159.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001159.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dec85a8512aa6193672571401495ea800b8fc105
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001159.fa
@@ -0,0 +1,20 @@
+>PROKKA_01379
+MNQPGREPDLSTSAINLTELAPLVSADLTREESDAIRALPAGSALLLAHEGPDQSARFLL
+DKDVVSVGRHPDADIFLDDVTVSRRHAEFRAEDGGHRLVDLNSLNGTFVNHDRVDEILLR
+SGMHVQIGKYRLTYYAAPARG
+>PROKKA_01099
+MNQPGREPDLSTSAINLTELAPLVSADLTREESDAIRALPAGSALLLAHEGPDQSARFLL
+DEDVVSVGRHPDADIFLDDVTVSRRHAEFRAEDGGHRLVDLNSLNGTFVNHDRVDEILLR
+SGMHVQIGKYRLTYYAGPARG
+>PROKKA_01513
+MNQPGREPDLSTSSINLTELAPLVAADLSAEESDAIRALPAGSALLLADGGPEKAARFLL
+DQDVVTVGRHPDADIFLDDVTVSRRHAEFRAEAGGHRLVDMNSLNGTFVNHDRVDDVLLR
+SGTHVQIGKYRLTYFTSTQRG
+>PROKKA_01408
+MTQQEPSLHTSSISLTDLAPVAETGLSPEETAAVRALPAGAALLVAHEGPDAGARFLLDT
+PVVTVGRHPESDILLDDVTVSRRHAEFRAVDGGHELVDLSSLNGTYVNNDRVDQVRLRTG
+MQLQIGRYRLSYHAAEPA
+>PROKKA_01334
+MNQPGREPDLSTSAINLTELAPLVSADLTREESDAIRALPAGSALLLAHEGPDQSARFLL
+DEDVVSVGRHPDADIFLDDVTVSRRHAEFRAEDGGHRLVDLNSLNGTFVNHDRVDEILLR
+SGMHVQIGKYRLTYYAGPARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001160.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001160.fa
new file mode 100644
index 0000000000000000000000000000000000000000..754909c6424780875f75934e7e3c17d9795f7536
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001160.fa
@@ -0,0 +1,20 @@
+>PROKKA_01380
+MSSIPEGLKYSAEHEWIAEAGAAGTVRVGITDFAQDALGDVVYVDLPEVGTEVTAGTAVG
+EVESTKSVSDIYAPVSGTVAAVNDELDGEPGLVNSAPYEGGWLFEITLADEAQLEGLMDA
+EGYASHTS
+>PROKKA_01100
+MSSIPEGLKYSAEHEWIAKAGAAGTVRVGITDFAQDALGDVVYVDLPEVGTEVTAGTAVG
+EVESTKSVSDIYAPVSGTVAAVNDELDGEPGLVNSAPYEGGWLFEITLADEAQLEGLMDA
+EGYASHTS
+>PROKKA_01512
+MSSIPEGLKYSAEHEWIAEAGQAGTVRIGITDFAQDALGDVVYVDLPEVGSEVTAGTAVG
+EVESTKSVSDIYAPVTGTVAAVNEDLDGEPGLVNSAPYEGGWLFEVTLADEAQLEGLLDA
+EGYASHTS
+>PROKKA_01407
+MSSIPEGLKYSTDHEWAQDAAEPGVVRVGITDFAQDALGDVVYVDLPSVGDEVTAGAAIG
+EVESTKSVSDIMAPVSGTVTAVNEELDGEPALVNSAPYEGGWLVEIKLSDPAEVDGLLDA
+AGYAAHVG
+>PROKKA_01335
+MSSIPEGLKYSAEHEWIAEAGAAGTVRVGITDFAQDALGDVVYVDLPEVGTEVTAGTAVG
+EVESTKSVSDIYAPVSGTVAAVNDELDGEPGLVNSAPYEGGWLFEITLADEAQLEGLMDA
+EGYASHTS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001164.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001164.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac72de05181e4cfdb5d6f4392b04f4e8d3f7928a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001164.fa
@@ -0,0 +1,40 @@
+>PROKKA_01406
+MSAPAESAAKLGDGPAGIPQPVLVRGTGLLGASIGIGLSAAGVDVRLHDPSPAALAVAAD
+IRAGRPARLDAEGDDLDVAPGLVVVAAPPDVTADVVVDSLRRWPAAVVVDIASVKEAVAA
+GVRAAVDDGRLAPQDADRYLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTHPGALA
+AGRALARTLQATPYRMAARAHDESVALISHLPQIAASLVASRLQDTPDQALALAGNGLRD
+TTRIAASDPQLWVQILSGNAGRIVPALHGLRADLDRLIRTLEDPSAPGARLDMAQLIAEG
+NAGRARVPGKHGAPPQAFAVVTVIVDDAPGQIAALLDEVGRTDVNVEDLRLEHASGHRVG
+MVEISVLPGRRDELVAALTAAGWKVV
+>PROKKA_01136
+MSAPAESAAKLGDGPAGIPQPVLVRGTGLLGASIGIGLSAAGVDVRLHDPSPAALAVAAD
+IRAGRPARLDAEGDDLDVAPGLVVVAAPPDVTADVVVDSLRRWPAAVVVDIASVKEAVAA
+GVRAAVDDGRLAPQDADRYLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTHPGALA
+AGRALARTLQATPYRMAARAHDESVALISHLPQIAASLVASRLQDTPDQALALAGNGLRD
+TTRIAASDPQLWVQILSGNAGRIVPALHGLRADLDRLIRTLEDPSAPGARLDMAQLIAEG
+NAGRARVPGKHGAPPQAFAVVTVIVDDAPGQIAALLDEVGRTDVNVEDLRLEHASGHRVG
+MVEISVPPGRRDELVAALTAAGWKVV
+>PROKKA_01490
+MSAAAETAAAVPGALPAGIPQPVLVRGTGLLGASIGIGLSAAGADVLLHDLSPAALAVAA
+DIGAGRPMRIDDDGADAGPAPALVVVAAPPDVTADVVVDSLRRWPEALVLDIASVKEAIA
+AGVRAAVDDGRLGPSDPDRHLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTLPAAV
+QAGRALALALRATPYRMDARAHDESVAMISHLPQIAASLVAARLQDTPDQALALAGNGLR
+DTTRIAASDPQLWVQILSGNAERIVPALHGLRDDLDRLIRTLEAPGAPGSRLDMARLIAE
+GNAGRARVPGKHGAPPQAFAVVTVIVDDTPGQIAAVLDEVGRTDVNVEDLRLEHASGHRA
+GMVDISVLPGRRDELVAALSAAGWKVV
+>PROKKA_01401
+MIPAEGGAGPAGLSGPVLVRGTGLLGASIGLGLRAAGADVLLDDPSPTALAVARDIGAGA
+VVDLDDPALAPGLVVVGAPPDVTPAVVVDSLRRWPHAVVTDIASIKGAILAEVREAATRG
+DIAPGDVARYLPGHPMAGSERSGPVAARGTLFTASPWVLCPAAETDPAALAAGEALARTL
+QATVHRMSAADHDASVALISHLPQIAASLVASRLQDAPDPSLALAGNGLRDTTRIAASDP
+HLWVQILAGNAPQIVPTLHGLREDLDRLIGTLEAPSAPGARLDVARLIAEGNAGRARIPG
+KHGAPPQAFALVTVIVDDTPGQLAALFEEIGRAGVNVEDIRLDHASGYRVGMVDVSVLPG
+RKDELVSALTDAGWKVV
+>PROKKA_01356
+MSAPAESAAKLGDGPAGIPQPVLVRGTGLLGASIGIGLSAAGVDVRLHDPSPAALAVAAD
+IRAGRPARLDAEGDDLDVAPGLVVVAAPPDVTADVVVDSLRRWPAAVVVDIASVKEAVAA
+GVRAAVDDGRLAPQDADRYLGTHPMAGSERSGPVAARGTLFTQAPWVLCPTDTTHPGALA
+AGRALARTLQATPYRMAARAHDESVALISHLPQIAASLVASRLQDTPDQALALAGNGLRD
+TTRIAASDPQLWVQILSGNAGRIVPALHGLRADLDRLIRTLEDPSAPGARLDMAQLIAEG
+NAGRARVPGKHGAPPQAFAVVTVIVDDAPGQIAALLDEVGRTDVNVEDLRLEHASGHRVG
+MVEISVLPGRRDELVAALTAAGWKVV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001170.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001170.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b705a9fbeca3a9fa4e49f41706aa73e33fcaacbc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001170.fa
@@ -0,0 +1,40 @@
+>PROKKA_01416
+MTETEIKKGLAGVVVDTTAISKVNPETNSLLYRGYPVQDLAAQLSFEAVALLLWTGELPT
+DEELAAFEHFERAHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAQALFAAFPAVVAYDQRRRRGQDVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESRQDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLQSAMDEAKQIKPNLDYPAGPTYHLMGFDTEMFTPLFIASRITGWTAHIMEQRAA
+NALIRPLSAYDGPEQRELPAG
+>PROKKA_01147
+MTETEIKKGLAGVVVDTTAISKVNPETNSLLYRGYPVQDLAAQLPFEAVALLLWTGELPT
+DEELTAFERFERTHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAQALFAAFPAVVAYDQRRRRGQEVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLEQAMDEAKQIKPNLDYPAGPTYHLMGFDTELFTPIFIASRITGWTAHIMEQRAA
+NALIRPLSAYDGPEQRELPAG
+>PROKKA_01483
+MTETEIKKGLAGVVVDTTAISKVNPDTNSLLYRGYPVQDLAAKLPFESVALLLWNGELPT
+DEELAEFQRFERAHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAKALFAAFPAAVAYDQRRRRGQDVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLQSAMDEAKQIKPNLDYPAGPTYHLMGFDTEMFTPLFIASRITGWTAHIMEQRAA
+NALIRPLSSYDGPEQRELPAG
+>PROKKA_01390
+MTETEIKKGLAGVVVDTTAVSKVNPETNSLLYRGYPVQDLAAQLPFEAVALLLWNGELPT
+DAELEEFQRFERAHRALDPEVKAAVDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAKALFAAFPAVVAYDQRRRRGQEVVEPRADLDYAQNFLWMSFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLEQAMDEAKQIKPNLDYPAGPTYHLMGFDTEMFTPIFIAARITGWTAHIMEQRAA
+NALIRPLSAYNGPEQRELPGK
+>PROKKA_01366
+MTETEIKKGLAGVVVDTTAISKVNPETNSLLYRGYPVQDLAAQLSFEAVALLLWTGELPT
+DEELAAFERFERAHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAQALFAAFPAVVAYDQRRRRGQDVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLEQAMDEAKQIKPNLDYPAGPTYHLMGFDTELFTPIFIASRITGWTAHIMEQRAA
+NALIRPLSAYDGPEQRELPAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001171.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001171.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6dd0b0ccb5068e5e2699541256290283bbacff52
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001171.fa
@@ -0,0 +1,35 @@
+>PROKKA_01418
+MSADPAPRGSRGGRGAESALAAPFRRHLEHLAVERGLAANTLAAYRRDLERYRRWLEAQG
+VRAPADVDPGHVSGFLRALGTGEDGGRPLAVRSAARVLAAVRGLHRFWALEGLTPADPAL
+DVHPPKPGARLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARISEVVGLDVD
+DVVGLAQTGDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGRPTIMAGAARSTPA
+LFVNACGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLAGGADVRVVQELLG
+HASVTTTQVYTLVTVDSLREVYSAAHPRAR
+>PROKKA_01149
+MSTDPAARGSGEAEARGGRGAESALAAPFRRHLEHLAVERGLAANTLAAYRRDLERYRRW
+LEAHGVRAPADVDPGHVSGFLRALGTGEDGGRPLAVRSAARVLAAVRGLHRFWALEGLTP
+ADPARDVHPPKPGDRLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARISEVV
+GLDVDDVVGLAQTGDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGRPTIMTGVT
+RSTPALFVNARGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLAGGADVRVV
+QELLGHASVTTTQVYTLVTVDSLREVYSAAHPRAR
+>PROKKA_01481
+MSTDPAARGSGEAEARGSRGGRGAESALAAPFRRHLEHLAVERGLAANTLAAYRRDLERY
+RRWLEAHGVRAPADVDPGHVSGFLRALGTGEDGGRPFAVRSAARVLAAVRGLHRFWALEG
+LTPADPARDVHPPKPGDRLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARIS
+EVVGLDVDDVVGLAQTGDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGRPTIMT
+GAARSTPALFVNARGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLAGGADV
+RVVQELLGHASVTTTQVYTLVTVDSLREVYAAAHPRAR
+>PROKKA_01389
+MSASPELHRALDRHLDHLAVERGLASATLAAYRRDLGRYLAWLEASRVDRPADVDPGHVA
+GFLSALGTGDDGGRPLGARSAARVLSAVRGMHRFWALEGLTPTDPAADVAPPRPPERLPK
+ALPVETVTRILEAVPTAEPADLRDRALLEFLYGTGARVSEAVGLDVDDVVGVAGDRGAGR
+GDDDRLPVVRLFGKGSKERLVPVGSHAADALAAWLVRGRPALAAAATRPVPALFLNLRGG
+RLSRQSAWSILKAAAERAGVAQDVSPHTLRHSFATHLMQGGADVRVVQELLGHASVTTTQ
+VYTRVTAEALREVYASAHPRARWTT
+>PROKKA_01368
+MSPHAPQTSALAAPFRRHLDHLAVERGLAENTLAAYRCDLARYRRWLEAAGVRAPGDVDP
+GHVAGFLQALATGDDGGRPLAVRSAARVLAAVRGLHRFWALEGLTPADPARDVHPPKPGD
+RLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARISEVVGLDVDDVVGLAQTG
+DDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGRPTIMTGVTRSTPALFVNARGGR
+LSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLAGGADVRVVQELLGHASVTTTQV
+YTLVTVDSLREVYSAAHPRAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001173.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001173.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d0b4b22125c678c81171e1688c7f8ed37ddf5c96
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001173.fa
@@ -0,0 +1,55 @@
+>PROKKA_01420
+MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSS
+RAVVDAGVRVTADHAALRLAQEAGAVVDEGDNGTHDLVLSRSVTASGDGTRSRATAGGRS
+VPVGLLSEIGATLVAVHGQNDQVRLQGADAQRHALDAFGGAELAAALRAYRADHAAWTAA
+RREREELTAHRQERAREAEALQRSLEEIDLAEPREGEDEELRALIRRLEDVEELRAASGE
+AHARLAGPDVDAMDETPGAVSLVEAARQAVLAAPGDDPDLAAAAARLAEAAVVLTDIAGD
+LARYTADLDADAASDLDAAQSRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGR
+LEELEAEVDRLDAALRERAATLTALRTAAAERLETAVTEELHALFMPDASFHVGLTPVAG
+DGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV
+DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV
+TLTADERVEELARMLAGHGDSAAAREHARELLESSARERG
+>PROKKA_01151
+MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSS
+RAVVDAGVRLPEAHAALALAEDAGAVLDEADEGVRELVLSRSVTASGEGTRSRAAAGGRT
+VPVGLLAEIGATLVAVHGQNDQVRLQGADAQRHALDAFGGAELAAALRAYRADHAAWTAA
+RREREELTAHRQERAREAEALQRSLEEIDLAEPQEGEDEELRALIRRLEDVEELRAASGE
+AHARLAGPDVDTMDETPGAVSLVEAAQQAVLAAPGDDPELAAAAARLAEAAVVLTDIAGD
+LARYTADLDADAASDLDAAQSRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGR
+LEELEAEVDRLDAALRERAATLTALRTAAAERLETAVTEELHALFMPDASFHVGLTPVAG
+DGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV
+DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV
+TLTADERVEELARMLAGHGDSAAAREHARELLESSARERG
+>PROKKA_01479
+MIEHLRISGLGVIGEATVDLDPGLTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGAA
+RAVVDAGVRLPEAHAALALAEDAGAVLDEADDGVRELVLSRSVTASGEGTRSRAAAGGRT
+VPVGLLAEIGATLVAVHGQNDQVRLQGAEAQRRALDAFGGAELAASLRAYRADHAAVSAA
+RRERDELTAHRQERAREAEALQRSLEEIDLAEPLAGEDAELRELIRRLEDVEELRAASGE
+AHARLAGAEMDALEETPGAVSLVEGARQAVLAAPGDDPALAAAAERLAEAAVVLTDIAAD
+LARYTADLDTDAASDLDAAQSRLAELTRLQRLYGPELEDVIGWAETQRPRLDELQGDSGR
+LEELEGELERLESALRERAAALTALRTAAAGRLEEAVTQELHALFMPDASFHVDLAPVGG
+DGLGPHGAEDVALALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV
+DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV
+TLSAEERVEELARMLAGHGDSAAAREHARELLEASARERG
+>PROKKA_01387
+MIDWMQITGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGRRADAGAVRRGSR
+RAAVDAGVRLPADHPALSLAVEAGAVLDDAGDGSADLVLSRSVTASGDGTRSRAGLGGRA
+VPVGVLAEVGSALVAVHGQNDQVRLQSAAAQRHALDAFGGPQLVAAAAAYRADHTAYVAA
+RRERDLLVERQQERAREAEALQRGLEEIDRAEPEAGEDETLRALIRRLEDVEELRAAADG
+GHAHLAGPDIESGDDLPGAITLVESARAAVQAAPGDDPELAAAAGRLAEASVILGDIAAD
+LARFSADLDGDAVSDLDAAQTRLAELSRLQRLYGPELTDVLAWAEAQRPRLEELQGDSGR
+IDELEADLARLDASRRERAAELTTLRTAAAGRLEQAVTAELHALFMPDASFHVSLVPLDD
+GDPGPHGAEDVALALRPHAGAEPRPLGRGASGGELSRVMLALEVVLAETDPVPTFVFDEV
+DAGVGGEAAVSIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPEAGVTTSDVV
+TLGQQERVDELARMLAGHGDSAAARAHARELLEASAAERA
+>PROKKA_01370
+MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSS
+RAVVDAGVRLPEAHAALALAEDAGAVLDEADEGVRELVLSRSVTASGEGTRSRAAAGGRT
+VPVGLLAEIGATLVAVHGQNDQVRLQGADAQRHALDAFGGAELAAALRAYRADHAAWTAA
+RREREELTAHRQERAREAEALQRSLEEIDLAEPQEGEDEELRALIRRLEDVEELRAASGE
+AHARLAGPDVDAMDETPGAVSLVEAARQAVLAAPGDDPELAAAAARLAEAAVVLSDIAGD
+LARYTADLDADAASDLDAAQSRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGR
+LEELEAEVDRLDAALRERAATLTALRTEAAERLETAVTEELHALFMPDASFHVGLTPVAG
+DGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV
+DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV
+TLTADERVEELARMLAGHGDSAAAREHARELLESSARERG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001175.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001175.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1eb9944ac0b6d1a703b645cea6f9bb26bbcf47d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001175.fa
@@ -0,0 +1,30 @@
+>PROKKA_01422
+MAETARADVALAARGLARSRTEGAALIRAGQVLLDGRPVRRPADRVAADATLRLRDPGPR
+YVSRAAHKLVSALEAFPDVGVAGRRALDAGASTGGFTQVLLERGAERVAAVDVGHNQLAP
+PVRADPRVLVREGLNIRDLTAEDIDGPVDLVVSDLSFISLRLVLAPLASVCRPGAELLLM
+VKPQFEVGRRALPRSGVVTDPDARRHAVVGVTAAALGAGLAPRGLARSGLAGQDGNAEFF
+LRLRRPDATAADNPAGGTSPAPPAGERAAGWVRGAHIDWS
+>PROKKA_01153
+MAETARADVALAARGLARSRTEGAALIRAGQVLLDGRPVRRPSDRVAADATLRLRDPGPR
+YVSRAAHKLVSALEAFPDVAVAGRRALDAGASTGGFTQVLLERGAERVAAVDVGHDQLAP
+PVQADPRVLVREGLNVRDLRAEDIDGPVDLVVSDLSFISLRLVLAPLAGVCRPGAELLLM
+VKPQFEVGRRALPRSGVVTDPDARRDAVAGVAAAALGAGLAPRGLTRSGLAGQDGNAEFF
+LRLHRPDATAADDPAGRTSPATPADERAAGWVRGAHIDWS
+>PROKKA_01477
+MAEAVRADVALAARGLARSRTEASALIRAGQVLVDGRPVRRASERVAPTASLTLADDGPR
+WVSRAAHKLVSALEAFPDVAVRGRRALDAGASTGGFTQVLLEGGAARVAAVDVGHGQLVD
+LVRTDPRVLVREGLNVRDLTVQDVEGEVDLVVSDLSFISLRLVMDALAGVCRPGADLLLM
+VKPQFEVGRAALPRTGVVTDPAARRDVVAAVAAAALDSGLELRGLARSGLPGQDGNVEFF
+LRLRRPAADAAGAPGTGLDDDAPAAEAVAAAWTAAAEVDWA
+>PROKKA_01385
+MGEARRADVALAADGLARSRTEAAALVKEGVVLVDGTPVRRPSQPVASGAVLSLLDQGPR
+WVSRAAHKLVSALEAFPVPVAGRRALDAGASTGGFTQVLLERGAARVAAVDVGHGQLVQE
+LRADPRVLVREGLNVRDLTATDVEGSVDLVVSDLSFISLRLVLDALAGVCRPDADLLLMV
+KPQFEVGRAALPRTGVVTDPRARRSAVEGVVAAALGTGLAARGVARSGLPGQDGNVEFFL
+HLRAPAAPRDGGAVAGDADEDERRRRAAALVAAADVDWS
+>PROKKA_01372
+MAETARADVALAARGLARSRTEGAALIRAGQVLLDGRPVRRPSDRVAADATLRLRDPGPR
+YVSRAAHKLVSALEAFPDVAVAGRQALDAGASTGGFTQVLLERGAERVAAVDVGHDQLAP
+PVRADPRVLVREGLNVRDLRAEDIDGPVDLVVSDLSFISLRLVLAPLAGVCRPGAELLLM
+VKPQFEVGRRALPRSGVVTDPDARRDAVAGVAAAALGAGLAPRGLTRSDLAGQDGNAEFF
+LRLHRPDATAADDPAGRTSPATPADERAAGWVRGAHIDWS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001177.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001177.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f53e3b13b8c21b76b7d21482474bd3282b3605fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001177.fa
@@ -0,0 +1,36 @@
+>PROKKA_01424
+MTGKELDRGTLKEINGLDERAASWVAKHLVMAGRYLDVDPTLAFQHALAASRKGGRLSRV
+REAVALTAYAAGEYADALREFRTYRRMTGDDTHIAAQVDSERALGRTEKALQLAAEVDAS
+RLDRAARAELAMVVSGIREDAGDLQGAHEALQIPELDRRRGYPFSPRLFQRQADVLLALG
+RRDEARLWARAVRVAEKALGVGGFADPEIIDVDTEPVEDPRNRRPSPRERRHERYAAEAG
+AEPTADGSPAEEPEAAAEPTLVPRQEAVAQPPAAVDTPDEVDPNQLSLFDALEAPEADER
+>PROKKA_01155
+MTGQELDRGTLKEINGLDERPASWVAKHLVMAGRYLDVDPALAFQHALAASRKGGRLSRV
+REAVALTAYAAGEYADALREFRTYRRMTGDDTHIAAQVDSERALGRTEKALQLAAEVDAS
+RLDRAARAELAMVVSGIREDAGDLQGAHEALQIPELDRRRGYPFSPRLFQRQADVLLALG
+RRDEARLWARAVRVAEKALGVGGFADPEIIDVDTEPVEDPRDRRPSPRERRHERYAAEAG
+AEPTADGSPAEEPEAATEPTEAPRPEAAAEPPAAVDAPDEVDPNQLSLFDALEAPEADER
+>PROKKA_01475
+MAEDTPRGRRDDRRSPGDGAGRSRGGSGDARRFGGPRDGRRSGGSGEGRSGQDRRDRSSE
+GFRGGRSGDGPRRERSSDGPRRERSSDGFRRDRSSDGPRGERSGDGPRGPRAGGDRRQSG
+AGSARGGFEGRRGGERREGAGGERRDRRSASSSPRWEGRGQDRTERTERRERPAHNPRDL
+RAANRVDQERSPDIDADVTGQELDRGTLKEVNGLDERPASWVAKHLVMAGRYIDVDPALA
+FQHALAASRKGGRLSRVREAVALTAYAAGEYADALREFRTYRRMTGDDTHVAAQVDSERA
+LGRPAKALQLAAEIDTARLDRAARVELAMVVSGIREDAGDLQGAHDALQIPELDRRRGYP
+FSPRLFQRQADVLLLLGRADEARLWARAVRVAEKALGIGGFAEPEIVDVDTEPVDDRRER
+GPSPRERRYAENAAPAAEEVPDTPEADDEVAADADTEAPASTESELDAPPAAVAQADEVD
+PNQMSLFDELDGGEGEGR
+>PROKKA_01383
+MAERSAREPRDDRRGDGHDGTRSGTPRGRRDGDGGRRQGEGRPFRPHRDGEGVGRSRNVG
+GRDGAAPRPGRPERAQRERPAHSPSDLRAANRVDQQRSPDIDGDVTGKELDRGTLKEIGG
+LDERPATWVAKHLVMAGRYIDEDPELAFQHALAASRKGGRLARVREAVALTAYAAGEYHE
+ALREFRTYRRMTGDDTHIAAQVDSERALGRHEKALQLAGEVDTSRLDRAARVELAMVVSG
+VREDLGDLEGALAALKIPELDRRRGYPFSPRLFQRQADVLTALGRTQEAAVWQRSVHVAE
+RALGIGGFAEPEIVDVEVEPAEDDRPVRGHRERHTGPRVSDASQSSAESAPVGEGSAEEH
+GQAAPAERES
+>PROKKA_01374
+MTGQELDRGTLKEINGLDERPASWVAKHLVMAGRYLDVDPALAFQHALAASRKGGRLSRV
+REAVALTAYAAGEYADALREFRTYRRMTGDDTHIAAQVDSERALGRTEKALQLAAEVDAS
+RLDRAARAELAMVVSGIREDAGDLQGAHEALQIPELDRRRGYPFSPRLFQRQADVLLALG
+RRDEARLWARAVRVAEKALGVGGFADPEIIDVDTEPVEDPRDRRPSPRERRHERYAAEAG
+AEPTADGSPAEEPEAATEPTEAPRPEAAAEPPAAVDAPDEVDPNQLSLFDALEAPEADER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001178.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001178.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab633632ccdc4c25005ac9722ca8dac97407cc07
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001178.fa
@@ -0,0 +1,45 @@
+>PROKKA_01428
+MAPQNEERAARLRAQANDPSFENVWQELRWRGLVHVSTDEAALEQALAGEPVSYYCGFDP
+TAPSLHLGHLVQLLTLRRLQLAGHRPYALVGGATGLIGDPRQTSERVLNSQETVAAWVES
+LRAQIEPYLSFEGENAATMVNNLDWTAGMSALDFLRDVGKNFRVGTMVKKEIVAKRLNSD
+EGISYTEFSYQVLQGNDFLELHRRHGVTLQTGGSDQWGNLTAGTELIRKVEGTHAHALGT
+PLITNADGTKFGKSEGNAVWLDAEMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE
+YAQKVADEPFRREAQRRLAWEVTALAHGEETTTKVIEASQAVFGGGDLTTVDPDTLTAVL
+AELPQADRTQWEGEPGTVTAVELLVSTGLVASRSEARRTVRDGGASVNNVRVTDADQVFT
+RDDALAGRHLLVRRGKKNMAGADLGEA
+>PROKKA_01159
+MAPQNEERAARLRAQANDPSFENVWQELRWRGLVHVSTDEAALEQALAGEPVSYYCGFDP
+TAPSLHLGHLVQLLTLRRLQLAGHRPYALVGGATGLIGDPRQTSERVLNSQETVAAWVES
+LRAQIEPYLSFEGENAATMVNNLDWTAGMSALDFLRDVGKNFRVGTMVKKEIVAKRLNSD
+EGISYTEFSYQVLQGNDFLELHRRHGVTLQTGGSDQWGNLTAGTELIRKVEGTHAHALGT
+PLITNADGTKFGKSEGNAVWLDAKMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE
+YAQKVADEPFRREAQKRLAWEVTALAHGEETTTKVIEASHAVFGGGDLTTVDPDTLTAVL
+AELPQADRTQWEGEPGTVTAVELLVSTGLVASRSEARRTVRDGGASVNNVRVTDADQVFT
+RDDALAGRHLLVRRGKKSMAGADLGEG
+>PROKKA_01471
+MAPDNEERAARLRAQANDPSFENVWQELLWRGLVHVSTDEAALEEALAGEPISYYCGFDP
+TAASLHLGHLVQLLTLRRLQLAGHRPMALVGGATGLIGDPRQTSERVLNSQETVAGWVES
+LREQIQPYLSFEGENAATMVNNLDWTAGMSALDFLREVGKNFRVGTMMKKEIVAKRLNSE
+EGISYTEFSYQVLQGNDFLELYRRHGVSLQTGGSDQWGNLTAGTELIRKVEGVPAHALGT
+PLITNADGTKFGKSEGNAIWLDAAMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE
+YAQKVADEPFRREAQKRLAWEVTSLAHGEEATTKVIEASQAVFGGGDLGEVDAETLGAIL
+SELPQADRTQWEGEPGTVTAVELLVSTGLVGSKSEARRTVKEGGASVNNERVSDADRVYT
+REDALAGRHLLVRRGKKNMAGADFGSQDADRG
+>PROKKA_01378
+MAETTVTRAERLRQQANDPSFENVWQELTWRGLVHVSTDEAALEEALAGEPISYYCGFDP
+TAPSLHLGHLVQLLLMRRLQLAGHRPVALVGGATGLIGDPRQTSERVLNTREVVQEWVES
+LRAQIEPYLAFEGDNGARMVNNLDWTASMSALDFLREVGKNFRVGTMVKKEIVAKRLHSE
+EGISYTEFSYQVLQGNDFLELYRQHGVTLQSGGSDQWGNLTSGTELIRKVEGAHVHALGT
+PLITNSDGTKFGKSEGNAIWLDADMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE
+YAAKVDAEPFRREAQKRLAWEVTALAHGEEAARTVIDASAAVFGGGDLSEVDVDVLSAVL
+AELPQADAAQWGAAGKPTAVELLVSTGLVSSNSEARRTIKEGGASVNNVKVADAEQVFGA
+DEALAGRYLLVRRGKKNMAAADLRSGE
+>PROKKA_01378
+MAPQNEERAARLRAQANDPSFENVWQELRWRGLVHVSTDEAALEQALAGEPVSYYCGFDP
+TAPSLHLGHLVQLLTLRRLQLAGHRPYALVGGATGLIGDPRQTSERVLNSQETVAAWVES
+LRAQIEPYLSFEGENAATMVNNLDWTAGMSALDFLRDVGKNFRVGTMVKKEIVAKRLNSD
+EGISYTEFSYQVLQGNDFLELHRRHGVTLQTGGSDQWGNLTAGTELIRKVEGTHAHALGT
+PLITNADGTKFGKSEGNAVWLDAEMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE
+YAQKVADEPFRREAQRRLAWEVTALAHGEETTTKVIEASQAVFGGGDLTTVDPDTLTAVL
+AELPQADRTQWEGEPGTVTAVELLVSTGLVASRSEARRTVRDGGASVNNVRVTDADQVFT
+RDDAFAGRHLLVRRGKKNMAGADLGEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001179.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001179.fa
new file mode 100644
index 0000000000000000000000000000000000000000..632ea8b7a33453966512fc417b28d4082f5e108c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001179.fa
@@ -0,0 +1,70 @@
+>PROKKA_01429
+MTDTVSVRQSELDLERGRVAERYARLDALREEKERQLAAVRRTGPQGSLQNHSERDAFAS
+LYEDRLAQLYAVDDRLVFGRLDLDAEREGGADEQRYIGRIGLTTEDHERLLVDWRAAEAG
+AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDILDPTLLGEDGVRADAQGALLAAVTARR
+TGRMGDIVATIQAEQDEVIRAPLPGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG
+VLIVGPSTAFMRYIERVLPSLGETGVVMSSLGTLMPGVRAVPERDLDAAAVKGRLDMVDA
+VAHAVAQRQRLLVEPRRLMIDGTAVKLKPAMVRRARDKARATRKPHNEARVTFVKILVRE
+LAEKLRKKLEKSSGTPVQRDLLLEDVRTSRDVRIALNLCWMPLTPEKLIGDLLTREDLLR
+AAAPWLSDAEVGALLRPADAPWTEADVPLLDEAAELLGRLDTPGRGGESAAQHERNLENA
+RASLENMHQTLADLGVDGVVDAEQLAAANEARGVRRTTAETAAHDRTWTYGHVVVDEAQE
+LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLAPEFGDRWRLEELTVNYRSP
+ARVMRWAAQVARAAGLEVSHPRAVREGDHRPRLVTEPGGDVAALALDAVEAERDRVPEAL
+TAVIAPAERTGELLTALRERWGEAAVDTAPLPGVEIVVATPWETKGLEFDTVVLVLPERI
+VADARGVVGDLYVAMTRATQSLSVVAGTDAAALPAGLADVPE
+>PROKKA_01161
+MTDTVSVRQSELDLERGRVAERYARLDALREEKERQLAAVRRTGPQGSLQNHSERDAFAS
+LYEDRLAQLYAVDDRLVFGRLDLDAEREGGADEQRYIGRIGLTTEDHERLLVDWRAAEAG
+AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDILDPTLLGEDGVRADAQGALLAAVTARR
+TGRMGDIVATIQAEQDEVIRAPLPGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG
+VLIVGPSTAFMRYIERVLPSLGETGVVMSSLGTLMPGVRAVPERDLDAAAVKGRLDMVDA
+VAHAVAQRQRLLVEPRRLMIDGTAVKLKPAMVRRARDKARATRKPHNEARVTFVKILVRE
+LAEKLRKKLEKSSGTPVQRDLLLEDVRTSRDVRIALNLCWMPLTPEKLIGDLLTREDLLR
+AAAPWLSDVEVGALLRPADAPWTEADVPLLDEAAELLGRLETPGRGGESAAQHERNLENA
+RASLENMHQTLADLGVDGVVDAEQLAAANETRGVRRTTAETAAHDRTWTYGHVVVDEAQE
+LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLAPEFGDRWRLEELTVNYRSP
+ARVMRWAAQVARAAGLEVSHPRAVREGDHRPRLVTEPGGDVAALALEAVEVERDRVPEAL
+TAVIAPAGRTGELLTVLRERWGEAAVDTAPLPGVEIVVATPWETKGLEFDTVVLVSPERI
+VADARGVVGDLYVAMTRATQSLSVVAGTDAAALPAGLADVPE
+>PROKKA_01470
+MTDAVSVRQSELELERARVAERYARLDALREEKERQLAAVRRTGLEGSLQNHSERDAFAS
+LYEDRLAQLLAVDDRLVFGRLDLDPERAGDPDEERYIGRIGLTTEEHERLLVDWRAAEAG
+AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDVLDPDLLGQEGVRADAQGALLAAVTARR
+TGRMGDIVATIQAEQDEVIRAPLAGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG
+VLIVGPSTAFMRYIERVLPSLGETGVVMASLGTLMPGVQAGPERDLDAAAVKGRLEMAQV
+IAHAVAQRQRLLAQPRRLMIEGTAVKLKPAAVRRARDRARATGKPHNEARVTFVKILVRE
+LAEKLSKKLEKSSGAPVQRDLLLEDVRTSRDVRVALNLCWMPLTPQKLVGDLLTREHLLR
+AAAPWLSDGEVGALLRPADAPWTEADVPLLDEAAELLGRLEAPAKGGESAAQHERNLENA
+RASLENMHQTLADMGVDGVVDAEQLAAANEARAVRRTTAETAAHDRTWTYGHVVVDEAQE
+LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLEPEFGDRWRLEELTVNYRSP
+ARVMRWASQVAQAAGLEVSRPRAVREGEHAPRLTVRPGADLVALTLDAVAGERDRVPEGL
+VAVITAAAHAPELLAALRERWGRARVDTAPLPGVEIVVATPWETKGLEFDAVVLAAPERL
+VDDARGVVGDLYVAMTRATQSLSVVSTAAVAALPAGLADPPA
+>PROKKA_01377
+MTDTVSSRQAELELERERVAVRYARLDALRAEKEEQLARVRRSGLQGSVQNHSERDAFAS
+LYEDRLAQLYAVDERLVFGRLDLDADDAGDVEQRYIGRIGLTDEGQERLLVDWRAQEAGA
+FYQATAARRLGVGRRRHLLLRGREVRDFEDDVLDPSLIAEGAAGAQSQGALLAAVTARRT
+GRMGDIVATIQAEQDEVIRADTSGALVVQGGPGTGKTAVALHRAAYLLYTHRDRLAKSGV
+LVVGPSNAFMRYIERVLPSLGETGVVMASLGTLMPGVQAGPDRSARAAELKGRLEMADVV
+AAAVAQRQRLIPETRRLEIEGTVVKLKPAMVRRARDRARATGKPHNEARTTFVKILVREL
+AEKLRKKLEKSSGVPVQRDLLLEDVRTARDVRVALNLCWMPLTPQKLVGDLLTKEHLLRA
+AAPGLSDGDVAALLRTDPDAWVESDVPLLDEAAELLGELEEPHRPGESEAQHRRNVENAQ
+ASLENMHQTLAELGVDGVVDAEQLAAANEVRAVRRTTAEQAAHDRTWTFGHVVVDEAQEL
+SPMQWRLLARRCPLKSFTVVGDIAQASRRGGARSWKDVLGPEFGDRMRLEELTVNYRSPA
+RITRWAAQVAQAAGLEISSPEAVREGEHEPLLTVEPGADPTRLAQRVVEAERGRVGDGLV
+AVIVPADDAAEHLTHLQDRWGSLVDRAPAPGVEVVVVTARETKGLEFDAVVLVSPERIVA
+DADGVVGDLYVAMTRCTQSISVVSGAAEEELPAGLMPVPA
+>PROKKA_01379
+MTDTVSVRQSELDLERGRVAERYARLDALREEKERQLAAVRRTGPQGSLQNHSERDAFAS
+LYEDRLAQLYAVDDRLVFGRLDLDAEREGGADEQRYIGRIGLTTEDHERLLVDWRAAEAG
+AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDILDPTLLGEDGVRADAQGALLAAVTARR
+TGRMGDIVATIQAEQDEVIRAPLPGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG
+VLIVGPSTAFMRYIERVLPSLGETGVVMSSLGTLMPGVRAVPERDLDAAAVKGRLDMVDA
+VAHAVAQRQRLLVEPRRLMIDGTAVKLKPAMVRRARDKARATRKPHNEARVTFVKILVRE
+LAEKLRKKLEKSSGTPVQRDLLLEDVRTSRDVRIALNLCWMPLTPEKLIGDLLTREDLLR
+AAAPWLSDAEVGTLLRPADAPWTEADVPLLDEAAELLGRLETPGRGGEFAAQHERNLENA
+RASLENMHQTLADLGVDGVVDAEQLAAANEARGVRRTTAETAAHDRTWTYGHVVVDEAQE
+LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLAPEFGDRWRLEELTVNYRSP
+ARVMRWAAQVARAAGLEVSHPRAVREGDHRPRLVTEPGGDVAALALDAVEVERDRVPEAL
+TAVIAPAGRTGELLTVLRERWGEAAVDTAPLPGVEIVVATPWETKGLEFDTVVLVSPERI
+VADARGVVGDLYVAMTRATQSLSVVAGTDAAALPAGLADVPE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001180.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001180.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8810e7db05d5ef3cd3adc5eecd0f745f52390b2d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001180.fa
@@ -0,0 +1,50 @@
+>PROKKA_01430
+MTENTDARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA
+GLLSADDLDGMIAALDRLEADVRSGAYTPAASDEDVHGSLERGLIERAGPELGGRLRAGR
+SRNDQVATLGRMFLRDHARIIARGVIATVDALLDQARAHPHAPMPGRTHLQHAQPVLLSH
+HLLAHAWAFARDLQRLVDWDARAAVSPYGSGALAGSSLGLDPNAVATELGFESAVWNSID
+GTAARDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVTLHDAYSTGSSIMPQKKNPD
+VAELARGKSGRLIGDLTGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA
+TLEFQTERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVKAAEARGVELWDLTD
+DEYAAISPALTPQVREVLSTEGSLASRDAQGGTAPTAVAAQIGALEDALEPLRRWADTPG
+SVVDAR
+>PROKKA_01162
+MTENTDARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA
+GLLSADDLDGMIAALDRLEADVRSGAYTPAASDEDVHGSLERGLIERAGPELGGRLRAGR
+SRNDQVATLGRMFLRDHARIIARGVIATVDALLDQARAHPYAPMPGRTHLQHAQPVLLSH
+HLLAHAWAFARDLQRLVDWDARAAVSPYGSGALAGSSLGLDPNAVAAELGFESAVWNSID
+GTAARDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVRLHDAYSTGSSIMPQKKNPD
+VAELARGKSGRLIGDLTGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA
+TLEFQTERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVMAAEARGVELWDLTD
+DEYAAISPALTPQVREVLSTEGSLASRDAQGGTAPTAVAAQIGALEDALAPLRRWADTPG
+SVVDAR
+>PROKKA_01469
+MTENPEARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHAA
+GLLGAEDLEGMIAALDRLETDVRSGAYAPADSDEDVHGSLERGLIERAGPELGGRLRAGR
+SRNDQVATLGRMFLRDHARIIARGLVATVDALLSQVQAHPYAPMPGRTHLQHAQPVLLSH
+HLLAHAWAFARDLQRLVDWDARTAVSPYGSGALAGSSLGLDPEAVAAELGFDSAVWNSID
+GTASRDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVKLHDAYSTGSSIMPQKKNPD
+VAELARGKSGRLIGDLAGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA
+TLEFETERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVKAAEARGVELWDLTD
+EEYAAISPALTPQVREVLSTEGSLNSRDAQGGTAPAAVAAQVEALERTLEPLRRWAQTPG
+SVVDAR
+>PROKKA_01376
+MSENSTPRHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA
+GLLTADELAGMIDALDRLEADVRSGAYAPAESDEDVHGSLERGLIERAGAELGGKLRAGR
+SRNDQVATLGRMFLRDHARVVARGVLATVDALVEQAEAHPFAPMPGRTHLQHAQPVLLSH
+HLLAHAWAFTRDLQRLVDWDARAAVSPYGSGALAGSTLGLDPNAVAAELGFDSAVWNSID
+GTAARDVYAEFAWVAGMIGVDLSRISEEVIFWATKEAGFVRLHDSYSTGSSIMPQKKNPD
+VAELARGKAGRLIGDLAGLMATLKGLPLAYNRDLQEDKEPVFDAVDTLELLLPAVSGMIA
+TLSFNTERMAALAPQGFALATDIAEWLVRQGVPFRVAHELSGEAVQVAESRGVELWDLTD
+EEYAGISAHLTPAVREVLSTEGSLNARRGQGGTAPEAVAEQLAALKAALEPLRAFAASAG
+SVVDAR
+>PROKKA_01380
+MTENTDARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA
+GLLSADDLDGMIAALDRLEADVRSGAYTPAASDEDVHGSLERGLIERAGPELGGRLRAGR
+SRNDQVATLGRMFLRDHARIIARGVIATVDALLDQARAHPYAPMPGRTHLQHAQPVLLSH
+HLLAHAWAFARDLQRLVDWDARAAVSPYGSGALAGSSLGLDPNAVATELGFESAVWNSID
+GTAARDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVTLHDAYSTGSSIMPQKKNPD
+VAELARGKSGRLIGDLTGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA
+TLEFQTERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVKAAEARGVELWDLTD
+DEYAAISPALTPQVREVLSTEGSLASRDAQGGTAPTAVAAQIGALEDALAPLRRWADTPG
+SVVDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001182.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001182.fa
new file mode 100644
index 0000000000000000000000000000000000000000..44f06ebce07428c5666458b9b83fb38b56f090aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001182.fa
@@ -0,0 +1,33 @@
+>PROKKA_01432
+MDTMTLFTTSATRSRRATASIVAGMTLAGAAAVGFSAPAQAATVDTWDRLAECESSGTWD
+INTGNGFYGGVQFTLSSWQAVGGEGYPHQASKAEQIKRAEILQDLQGWGAWPLCSQKLGL
+TQADADAGDVDAAPVAVERTATVQRQSAADETAADQAAAEQAAADQAAAEQAAADQAAAE
+RWAAKQAAADQAAAERWAAKQAAAEQAAADKAAAQRAAAAEKAAAQKAAAAEKAAAQKAA
+AAEKAAAQKAAAAEQAAAAEQAVVAEAETIVVKSGDSLWKLANEYEVEGGWTALYEANKG
+AVSDAAVIYVGQELVLPQA
+>PROKKA_01164
+MDTMTLFTTSATRSRRATASIVAGMTLAGAAAVGFSAPAQAATVDTWDRLAECESNGTWD
+INTGNGFYGGVQFTLSSWQAVGGEGYPHQASKAEQIKRAEILQDLQGWGAWPLCSQKLGL
+TQADADAGDVDATEAAPVAVERTATVQRQSAADEAAAEQAAAEQAAADQAAAERWAAEQA
+AADQAAAERWAAEQAAAEQAAAERWAAKQAAAEQAAADKAAAQRAAAAEKAAAQKAAAAE
+KPAAQKAAAAEKAAAQKAAAAEQAAAAEQAVVAEAETIVVKSGDSLWKLANEYEVEGGWT
+ALYEANKGAVSDAAVIYVGQELVLPQA
+>PROKKA_01467
+MDTMTLFTSTRTRRTTASVAAGMTLMGAAAVGFSAPAQAATEETWDAIAFCESTNRWDIN
+TGNGFYGGLQFTLSSWQGVGGQGYPHQASKAEQIKRAEMLQDLQGWGAWPKCAAGLTQAD
+ADATDAAPVAVERTSSVQRQAAAEQAAAEEAAAEQAAAEEAAAEQAAAEQWAAEQAAAEQ
+AAAERAEAKRAAAAEKAAAKKAAAAERAAAHQAAAEQAVVAEAETIVVKAGDSLWKLAAE
+HEVEGGWTALYEANKDTVSDAAMIYVGQELVLPQA
+>PROKKA_01374
+MTFFTTSSRRATATALTGMTLVGAAAAFAAPAQAASVETWDKIAACESNGNWAINTGNGY
+YGGLQFSLTSWRGVGGTGYPHEASKAEQIKRAEILQDMQGWRAWPVCSVKAGLSGADTAP
+DAYSTTPVQRQSTQASASAAQDWAAEQSAAEQRAAEKAAAQRAAAAAHTPKSVLKAAEKA
+NTENATELAAAEDTVFVKPGDSLWKIAKTHKVAGGWKALHEANKDIIEDASVIYVGQELV
+LPTA
+>PROKKA_01382
+MDTMTLFTTSATRSRRATASIVAGMTLAGAAAVGFSALAQAATVDTWDRLAECESNGTWD
+INTGNGFYGGVQFTLSSWQAVGGEGYPHQASKAEQIKRAEILQDLQGWGAWPLCSQKLGL
+TQADADAGDVDATEAAPVAVERTATVQRQSAADEAAAEQAAAEQAAADQAAAERWAAEQA
+AADQAAAERWAAEQAAADQAAAERWAAEQAAAEQAAADKAAAQRAAAAEKAAAQKAAAAE
+KAAAQKAAAAEQAAAAEQAVVAEAETIVVKSGDSLWKLANEYEVEGGWTALYEANKGAVS
+DAAVIYVGQELVLPQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001184.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001184.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8db7a3bda434481af6c41c68812c41d087009a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001184.fa
@@ -0,0 +1,35 @@
+>PROKKA_01434
+MTPAAAVRHFLVDTDLTPAEQAEVLDLAAQMKADRFRHRPLAGPRTGIVFFDKTSTRTRV
+SFAAGIAELGGTPLIVNPGESQLGHKESVADTARVLERMVGVIVWRTFAQAGLEEMAAHS
+SVPVVNALSDDYHPCQILADLLTVREHLGGTAGRTLTYLGDAANNMAHSYLLGCATAGMH
+VRVAGPEGHLPAEDVVAAARQRAAETGGSVLVTTDAAEALAGADVVVTDTWVSMGQEEEK
+EARLALFRDYQVDAAAMARAADDAIFLHCLPAYRGYEVTAEVIDGPRSVVFDEAENRLHA
+QKALIAWLLYRSGLAEEPR
+>PROKKA_01166
+MTPAAAVRHFLVDTDLTPAEQAEVLDLAAQMKADRFRHRPLAGPRTGIVFFDKTSTRTRV
+SFAAGIAELGGTPLIVNPGESQLGHKESVADTARVLERMVGVIVWRTFAQAGLEEMAAHS
+SVPVVNALSDDYHPCQILADLLTVREHLGGTAGRNLTYLGDAANNMAHSYLLGCATAGMH
+VRVAGPEGHLPAEDVVAAARQRAAETGGSVLVTTDAVEALAGADVVVTDTWVSMGQEEEK
+EARLALFRDYQVDAAAMARAADDAIFLHCLPAYRGYEVTAEVIDGPRSVVFDEAENRLHA
+QKALIAWLLYRSGLAEEPR
+>PROKKA_01464
+MTPAPTPAPAAVRHFLVDTDLTPGEQAEVLDLAAQMKTDRFAHRPLAGPRTGVVFFDKTS
+TRTRVSFAAGIAELGGSPLIVNPGESQLGHKESVADTARVLERMVGIIVWRTFAQSGLEE
+MAAHSRVPVVNALSDDYHPCQILADLLTVREHLGGTQGRVLAYLGDAANNMAHSYLLGCA
+TAGMHVRIAGPAGHLPAEHVVAAARERAAETGGSVLVTTDAAEALDGADVVVTDTWVSMG
+QEDEKEARLALFRDYQVDAAAMARAGSDAIFLHCLPAYRGYEVSAEVIDGPQSVVFDEAE
+NRLHAQKALMAWLLYRSGLAEDPR
+>PROKKA_01372
+MTAAPGTDVPVRHFLVDTDLSPAEQAEVLDLALEMKADRFRHRPLAGPQTGIVFFDKTST
+RTRVSFAAGIADLGGTPLIVNPGESQLGHKESIADTARVLERMVGVIVWRTYAQSGLEEM
+AAHSRVPVVNALSDDYHPCQLLADLLTVREHKGRTRGLTMAYLGDAANNMANSYLLGGVT
+AGMHVRVAGPEGFLPDPAVVRAAEERAGETGGSVLVTTDAAAALDGADVVVTDTWVSMGQ
+EDEKEERLRLFADYRVDAAAMARAASDAVFLHCLPAYRGYEVTEDVIDGPQSVVFDEAEN
+RLHAQKALMAWLLYRSGLAQDPR
+>PROKKA_01384
+MTPAAAVRHFLVDTDLTPAEQAEVLDLAAQMKADRFRHRPLAGPRTGIVFFDKTSTRTRV
+SFAAGIAELGGTPLIVNPGESQLGHKESVADTARVLERMVGVIVWRTFAQAGLEEMAAHS
+SVPVVNALSDDYHPCQILADLLTVREHLGGTAGRNLTYLGDAANNMAHSYLLGCATAGMH
+VRVAGPEGHLPAEDVVAAARQRAAETGGSVLVTTDAVEALAGADVVVTDTWVSMGQEEEK
+EARLALFRDYQVDAAAMARAADDAIFLHCLPAYRGYEVTAEVIDGPRSVVFDEAENRLHA
+QKALIAWLLYRSGLAEEPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001189.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001189.fa
new file mode 100644
index 0000000000000000000000000000000000000000..76ea2d25f85e318f79fe3b89d19015f4c4fe6804
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001189.fa
@@ -0,0 +1,35 @@
+>PROKKA_01439
+MTTANTPAVPRTHHAVVVSATGGPEVLQWTETEVPSPAPGHVLVRTAAAGLNFIETYQRS
+GVYTMDLPFTPGTEGSGEVVALGEGVDAGLLGARVATATATGAYAEHFTAPADRLLTVPE
+GIDLAEAAALPLQGMTAHYLCRSTFPVEEGHTVVVTAGAGGVGLLLTQLATARGARVVTT
+ASTEEKRELSRGAGAVAAVDYPDLAATVAELTDGEGAHVVYDGVGKDTFDTSLEVLRVRG
+TLVLFGGASGQVPPFDLQRLNAAGSLYVTRPSLVHYTRTGEETRWRGGEVFGAWASGELD
+VRIGERFPLADAAAAHAALESRSTTGKVLLTLS
+>PROKKA_01171
+MTTANTPAVPRTHHAVVVSATGGPEVLQWTETEVPSPAPGHVLVRTAAAGLNFIETYQRS
+GTYAMDLPFTPGTEGSGEVVALGEGVDAALLGARVATATATGAYAEHFTAPADRLLAVPE
+GIDLAEAAALPLQGMTAHYLCRSTFPVEEGHTVVVTAGAGGVGLLLTQLATARGARVVTT
+ASTEEKRELSRGAGAVAAVDYPDLAATVAELTDGEGAHVVYDGVGKDTFDTSLEVLRVRG
+TLVLFGGASGQVPPFDLQRLNAAGSLYVTRPSLVHYTRTGEETRWRGGEVFGAWASGELD
+VRIGERFPLADAAAAHAALESRSTTGKVLLTLS
+>PROKKA_01459
+MPHASSPAVPRTHHAVVVAETGGPEVLRWTQADVPAPGPGRVLVRTAAVGLNYIETYQRA
+GVYPMDLPFVPGTEASGTVVGLGEGVDPTLLGARVATATAQGAYAEHFTAPADRLLTVPE
+GVDLADAAALPLQGMTAHYLCRSTFPVEEGQTVVVTAGAGGVGLLLTQLAAARGARVITT
+ASTEAKRELSRAAGAAAAVDYPELAATVDRLTDGHGAHAVFDGVGKDTFETSLRVLRVRG
+TLVLFGGASGQVPPFDLQRLNAAGGLYVTRPSLVHYTRTEEETRGRSDELFAAWAAGELD
+VRIGERIPLAEAAAAHAALESRATTGKVLLTLG
+>PROKKA_01367
+MSTHAEIPARHHAIIAEEVGGPEVLRWTETAVPTPGAGEVLVRTAAAGLNFIETYQRSGV
+YAVPHPFTPGSEGSGVVVALGPGVDEALRGARVATAAGRGTYAEHFTAPADQLLHVPAGV
+DLADAAALPLQGMTAHYLCRSTFPVEPGHVVALTAGAGGVGLLLTQLAAARGATVITAAS
+TEDKRALSAAAGASAAVPYAELRQTVLDATGGEGAHAVFDGVGADTFEDSLASLRVRGTL
+VLFGGASGQVPPFDLQRLNSGGGLYVTRPSLAHYTRTAEETAWRGRELFDAWSAGALDVR
+IGARVPLAEAGRAHTLLASRATTGKVLLPLS
+>PROKKA_01389
+MTTANTPAVPRTHHAVVVSATGGPEVLQWTETEVPSPAPGHVLVRTAAAGLNFIETYQRS
+GVYTMDLPFTPGTEGSGEVVALGEGVDAGLLGARVATATATGAYAEHFTAPADRLLTVPE
+GIDLAEAAALPLQGMTAHYLCRSTFPVEEGHTVVVTAGAGGVGLLLTQLATARGARVVTT
+ASTEEKRELSRGAGAVAAVDYPDLAATVAELTDGEGAHAVYDGVGKDTFDTSLEVLRVRG
+TLVLFGGASGQVPPFDLQRLNAAGSLYVTRPSLVHYTRTGEETRWRGGEVFGAWASGELD
+VRIGERFPLADAAAAHAALESRSTTGKVLLTLS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001190.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001190.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d3a83aa98e20fbe4f1003ca133e08f5db18f408
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001190.fa
@@ -0,0 +1,45 @@
+>PROKKA_01441
+MSTDPYVPGVGTDAATVEHIALDLDVRLAANRVSGTAVLRVRLTKQSRRIELDLYRLRVS
+RVDAVVDGRAVASSFTQPGRAPSRLVVDLDESRPEGTLVELTVVYAGTPTLRRSPWGTIG
+WEELTDGVLVAGQPHGASTWLPCVDSPTSRSTAEITLTCDAGYLPVANGVGAPVRTRGSR
+VTWRWRLHQRVPAYLLSVQIGRYRLVDAAPPAEGLPPLRLVVSPRTEQRALRALAPQPAM
+MATFIDAYGPYPFEDYTAVVADEELEIPLEAASMSLFGTNHLDGSWESERLIAHEMSHQW
+FGNAVTLGRWSDLWLHEGFACWSEWLWAEASGRSSITSMARRAWQKLAAHPVEQALAEPG
+PEEMFEDWVYKRGALTVEALRHLLGTDLFGSMLRAWVREHRFGTVDSLGLRTHVHAWAPH
+AGVSRAQVDELFDAWTLRPELPPFPG
+>PROKKA_01173
+MSTDPYVPGVGTDAATVEHIALDLDVRLAANRVSGTAVLRVRLTKQSRRIELDLYRLRVS
+RVDAVVDGRAVASSFTQPGRAPSRLVVDLDESRPEGTLVELTVVYAGTPTLRRSPWGTIG
+WEELTDGVLVAGQPHGASTWLPCVDSPTSRSTAEITLTCDAGYLPVANGVGAPVRTRGSR
+VTWRWRLDQPVPAYLLSVQIGRYRLVDAAPPAEGLPPLRLVVSPRTEQRALRALAPQPAM
+MATFIDAYGPYPFEDYTAVVADEELEIPLEAASMSLFGTNHLDGSWESERLIAHEMSHQW
+FGNAVTLGRWSDLWLHEGFACWSEWLWAEASGRSSITSMARRAWQKLAAHPVEQALAEPG
+PEEMFEDWVYKRGALTVEALRHLLGTDLFGSMLRAWVREHRFGTVDSLGLRTHVHAWAPH
+AGVSRAQVDELFDAWTLRPELPPFPG
+>PROKKA_01457
+MSTDPYVPGVGTDAAVIEHVVLDLDVRLAANRVSGTAVLSVRLTRQSRRIELDLHRLRVS
+KVGAAVDGRALPASFSQPRRWPSRLVVDLGESRPEGTLVELTVAYAGTPTPRRSPWGTIG
+WEELTDGVLVAGQPHGASTWLPCVDSPVSRSTADITLTCDAGYLPVANGVGAPVRTRGSR
+VTWRWRLTQPVPAYLLTVQIGRYRLVDAAAPADGLPPLRLVASTRTEQRARAALATQPAM
+MAAFIAAYGPYPFEEYTAVVADDVLEIPLEAAGMSLFGTNHLDGSWESERLIAHEMAHQW
+FGNAVTLGRWADLWLHEGFACWSEWLWAEASGRSSIASMARRAWQRLAEDPVEHVLTEPG
+AAEMFEDWVYKRGALTVEALRVLLGREVFGSMLRAWVDEHRFGTVDTAGLRAHVHAWAPR
+AQVTPEQVDELFEAWTRRPELPPFPG
+>PROKKA_01365
+MSTDPYIPGVGSDTATIEHLRVELDVRLASNRVAGVAELHVRLCRQSDTVELDLHRLAVD
+GAAGTHDGRPLKVRATTPRNRPHRVVVHLGASLPEGSLVVLRLSYSGHPRPRRSPWGTIG
+WEELTDGVLVAGQPHGASTWVPCIDSPAVRQTADITVTCDAGYLPVANGRGTRLRSRGSR
+ETWRWVMDRPVPAYLLTLQIGRYRQVTAPGSGTPESAAAGGVPPLRLVVSPRLQARAEAA
+MAGQGRMMEAFTAAYGPYPFDDYAAVVADDVLEIPLEAAGLSLFGVNHLDGSWESERLIA
+HEMAHQWFGNAVTLGRWSDLWLHEGFACYSEWLWAEASGRAALRHEAKQAWHGLKRQGED
+LVLAAPGAADMFDDRVYKRGALTVLAVRTLLGDAVFGEMLRDWVARHRFATVDTPGFRAH
+VLAWAPRADVAPEDVDALFDAWTLRPELPAFPG
+>PROKKA_01391
+MSTDPYVPGVGTDAATVEHIALDLDVRLAANRVSGTAVLRVRLTKQSRRIELDLYRLRVS
+RVDAVVDGRAVASSFTQPGRAPSRLVVDLDESRPEGTLVELTVVYAGTPTLRRSPWGTIG
+WEELTDGVLVAGQPHGASTWLPCVDSPTSRSTAEITLTCDAGYLPVANGVGAPVRTRGSR
+VTWRWRLDQPVPAYLLSVQIGRYRLVDAAPPAEGLPPLRLVVSPRTEQRALRALAPQPAM
+MATFIDAYGPYPFEDYTAVVADEELEIPLEAASMSLFGTNHLDGSWESERLIAHEMSHQW
+FGNAVTLGRWSDLWLHEGFACWSEWLWAEASGRSSITSMARRAWQKLAAHPVEQALAEPG
+PEEMFEDWVYKRGALTVEALRHLLGTDLFGSMLRAWVREHRFGTVDSLGLRTHVHAWAPH
+AGVSRAQVDELFDAWTLRPELPPFPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001203.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001203.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3d254f1393a490a16b5eb31b959f53e13877c4e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001203.fa
@@ -0,0 +1,20 @@
+>PROKKA_01457
+MAQSRRPDPVAPSESSGADATTVPPRPGRGLPVAVLVVAAALVLEAGALLWLAVDAVVHA
+ADGVLPAGARVMLVVIYALLTLWILATAVALLRGRAWSRGAAVAIQLFGVLLSSWLFSVD
+AAALGGPLLAVSGVALLTLFTTPVTRHLTPAPEASTDA
+>PROKKA_01189
+MAQSRRPDPVAPSESSGADATTVPPRPGRGLPVAVLVVAAALVLEAGALLWLAVDAVVHA
+ADGVLPAGARVMLVVIYALLTLWILATAVALLRGRAWSRGAVVAIQLFGVLLSSWLFSVD
+AAALGGPLLAVSGVALLTLFTTPVTRHLTPAPEASTDA
+>PROKKA_01443
+MAQSRRPDPVDPREAPAAPAPEGPRTGGRAPVAALVVAAALALQAAALLWLAGDAIAHLG
+DGVLPAGARVMLIVIYVLLGLWILVTSVALLRGRAWSRGAATAVQLFGVLLSSRLLSVGE
+PVVGGVLLAVSGIALVTLFSRPVTAHLSQAAREPSAE
+>PROKKA_01346
+MSSSIPASPSGRRRMPAQAVVVAGVLGLEALTLVWLAVDGVAHLGAGALPTAAGVFLVVV
+YVLLAAWVGAVCGGMVRGRRFSRGAAVAIQLFAVILSTWLMSIGAPIAGGLLLVGSGAAL
+LCLFSGAVQAHLAGPDAGRPDAGRPDVG
+>PROKKA_01407
+MAQSRRPDPVAPSESSGADATTVPPRPGRGLPVAVLVVAAALVLEAGALLWLAVDAVVHA
+ADGVLPAGARVMLVVIYALLTLWILATAVALLRGRAWSRGAVVAIQLFGVLLSSWLFSVD
+AAALGGPLLAVSGVALLTLFTTPVTRHLTPAPEASTDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001210.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001210.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88c97c35fdf11ce2468d3344b660aaafaf25fca2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001210.fa
@@ -0,0 +1,31 @@
+>PROKKA_01464
+MERSTSPAGPAPTRPVDAADAVGLTVLLLAGPGLLACAAALLQTGTSAPGAELTRVLGLG
+AGLAGLGLLAWWAVGLIGLALVALGRRAGRPAWARLGRSLTPALLGRVAGAVVGAQLLAA
+PAAWADAAHPVPDASWTVAAVPAHATGVEAPAPDAAWTPRPPAPAPPGAGTGRADPDHPT
+VTVRRGDCLWHLAAAELGPDATPREIDARWRRWYEANRRVIGDDPHLLLPGTVLTSPVFT
+PHAGVDGPRP
+>PROKKA_01196
+MERSTSPAGPAPTRPVDAADAVGLTVLLLAGPGLLACAAALLQTGTSAPAAELTRVLGLG
+AGLAGLGLLAWWAVGLTGLALVALGRRAGRPAWARLGRSLTPALLGRVAGAVVGAQLLAA
+PAAWADAAHPVPDASWTVAASPTHATGVEAPAPDAAWTPRPPAPAPPGAGTGRADPDHPT
+VTVRRGDCLWHLAAAELGPDATPREIDARWRRWYEANRRVIGDDPHLLLPGTVLTSPVFA
+PHAGVDGPRP
+>PROKKA_01436
+MQRITEPARRGRAALSEADGHRADGHRVDTVDAVGLVVLALAAPALLIGAAALLEPGEGA
+ASSELVRLLGLGAGIAGLGLVAWWAVGLLGLVLATVGRRTGRLGFARLGARLTPALLGRV
+AGAVLGAHMLAAPAAWAEQPAVGPVPDAGQTVSHAAPASTTASAPAAVPEAAWTPRTPVP
+APPGATAARNLSDRPTVTVRRGDCLWDIAAAELGPDATPREIDARWRRWHEANRRVIGDD
+PHLLLPGTVLTAPVFSPHAAPQEGLAMTPRPRTTPTTTRPQEPAMTALAARPPSPPSTAA
+PAVSPGTPTVAPTVPPPRCCTVPPTARPCCPAARRSPAGPPSSRAGRSCVGSAPWPR
+>PROKKA_01339
+MSFVASQPPAAGVHAPRASALDVAALAVLAAAVPALGWAAATLLGPAAPTPDAALGRALG
+LGAAGLGLALAAWWALGLLGLAALALGRRTGHRGWSRLGERMTPALLRRAGAAVLGAQLL
+AAPAAWADAPPAPSAAVVDASWTSAAASPTLPDAAWTPGAPPTPQPGSPAAPRDTGDRPT
+VTVRAGDCLWDIAADELGPDATPREVDRRWREWHRHNRDLIGEDPNLILPGTVLTAPDFT
+PHVQRGGTP
+>PROKKA_01414
+MERSTSPAGPAPTRPVDAADAVGLTVLLLAGPGLLACAAALLQTGTSAPGAELTRVLGLG
+AGLAGLGLLAWWAVGLIGLALVALGRRAGRPAWARLGRSLTPALLGRVAGAVVGAQLLAA
+PAAWADAAHPVPDASWTVAAVPAHATGVEAPAPDAAWTPRPPAPAPPGAGTGRADPDHPT
+VTVRRGDCLWHLAAAELGPDATPREIDARWRRWYEANRRVIGDDPHLLLPGTVLTSPVFT
+PHAGVDGPRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001212.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001212.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bbb17b5793afe803122133822a293b712863350a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001212.fa
@@ -0,0 +1,85 @@
+>PROKKA_01466
+MPSIIDRVLKISDNRVLKRMQATVDAVNLLEDDFRALSDAELRAETDTLRARHADGESLD
+LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL
+SGRGVHVVTVNDFLASYQADLMGRVFRFLGMQTGVIVAGQTPAVRREQYAADITYGTNNE
+FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA
+RLVRRLEADTDYEVDHKKRTVGILGPGIEKVEDHLGITNLYETQNTTLIQFLNNAVKAKE
+LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ
+NYFRGYEKLAGMTGTAETEAAEFTSTYGLGVVVIPPNRERQRVDRNDVVYKNEKVKFDAV
+VDDIAERHAKGQPVLVGTTSVEKSEYLSTLLAKRGVRHEVLNAKNHAREAAIVAQAGRPG
+AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLAQAEAAVED
+AHRAVIEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA
+QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLKYDDVMNRQREAIYTDR
+RSILEGEDLQDRVRRFVEDAVGNIVDAATEEGHATDWDLDQLWRDLAELYPVGISQEDVL
+DEVGGRGRLKAEVLKRELVSDALLAYEDREAQVGSEALREAERRVVLATIGRRWQEHLYE
+MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAAIREDAVRTLFQAQISAAPASTSLP
+GVQDARAVTMAPQISVEGIDAPQQPAQLRFTGPSEDGQSAVTRSGTDSGATVAAGTNRRS
+RRQAERRGRRG
+>PROKKA_01198
+MPSIIDRVLKISDNRVLKRMQATVDAVNLLEDDFRALSDAELRAETDTLRARHADGESLD
+LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL
+SGRGVHVVTVNDFLASYQADLMGRVFRFLGMQTGVIVAGQTPAVRREQYAADITYGTNNE
+FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA
+RLVRRLEANTDYEVDHKKRTVGILGPGIEKVEDHLGITNLYETQNTTLIQFLNNAVKAKE
+LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ
+NYFRGYEKLAGMTGTAETEAAEFTSTYGLGVVVIPPNREPQRVDRNDVVYKNEKVKFDAV
+VDDIAERHAKGQPVLVGTTSVEKSEYLSTLLAKRGIRHEVLNAKNHAREAAIVAQAGRPG
+AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLAEAEAAVED
+AHRAVIEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA
+QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLKYDDVLNRQREAIYTDR
+RSILEGEDLQDRVRRFVEDAVGNIVDAATEEGQATDWDLDQLWRDLAEIYPVGVSQEDVL
+DEVGGRGRLTAEVLKRELVSDALLAYEDREAQVGSEALREAERRVVLATIGRHWQEHLYE
+MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAAIREDAVRTLFQAQISAAPAPTSLP
+GVKDARAVTMAPQISVEGIDAPQQPAQLRFTGPSEDGQSAVTRSGTDSGATVAAGTNRRS
+RRQAERRGRRG
+>PROKKA_01434
+MPSIIDRVLKISDNRVLRRMQGTVDAVNLLEEDFRALSDAELRAETDTLKARHADGESLD
+LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL
+TGRGVHVITVNDFLASYQAELMGRVFRFLGMETGVVVAGQLPAVRREQYAADITYGTNNE
+FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA
+RLVRRLEEGSDYEVDHKKRTVGVLGPGIEKVEDHLGIANLYETQNTTLIQFLNNAVKAKE
+LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ
+NYFRGYDKLAGMTGTAETEAAEFTSTYGLGVVVIPPNRERQRVDRNDVVYKNEKVKFDAV
+VEDIAERHERRQPVLVGTTSVEKSEYLSTLLAKRGIRHEVLNAKNHAREAAIVAQAGRPG
+AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPQVLAEAEAAVED
+ANREVLEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA
+QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLKYDDVMNRQREAIYADR
+RSILEGEDLKDRVRRFVEDAVGNIVDATTEEGHAADWDLDQLWRDLSELYPVGITQEDVL
+EEVGGRGRLKAEDLRRELVSDALLAYEDREAQVGSEALREAERRVVLSAIGRRWQEHLYE
+MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAGIREDSVSTLFKAQITAAPAPTSLP
+GIKDARGLTMTPQISVEGVEAPQRPSQLRFTGPSEDGQGAVTRAGTETGATVEAGTNRRS
+RREAERRERRS
+>PROKKA_01337
+MPSIIDRVLKISDNRVLKRMRGTVDAVNLLEDDFRALSDAELRAETDSFKKRLADGETLD
+LLLPEAFAAVREAAGRTLGQRHYDVQLLGGLALHQGNIAEMKTGEGKTLVATAPAYLNAL
+TGKGVHVVTVNDFLASYQADLMGRVYRFLGMETGVIVSGQDPATRRAQYAADITYGTNNE
+FGFDFLRDNMAWSKEELVQRGHHFAIVDEVDSILIDEARTPLIISGPAQGDISRWYGEFA
+RLVRSLERGTDYEVDEKKRTVGVLEPGIEKVEDHLGIANLYESQNTTLVQFLNNAVKAKE
+LFKRDKDYVVLDGEVQIVDEHTGRVLAGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ
+NYFRGYEKLSGMTGTAETEAAEFTSTYGLGVVVIPPNREKQRVDRNDLVYKNEKVKFDAV
+VKDIAERHATGQPVLVGTTSVEKSEYLSTLLTKAGVRHEVLNAKNHAREAAIVAQAGRPG
+AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLEQAEAAVQD
+AREKVREAGGLYVLGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDDLMRNFNPGAA
+QRIMNSASIPDDMALEFKMVSSAIQNAQSQVEGRNAEQRKNVLKYDDVMNRQREAIYADR
+RAILEGDSLGERVRGFVEDAVGAVVDAATEEGAPVDWDLEKLWETLREVYPVGISPEDVL
+EQVGGRGRLKAADLKRELVSDALLAYDDREAQVGSEALREAERRVVLAMIGRHWQEHLYE
+MDYLKEGIGLRAMAQREPLVEYQREGFTMFQAMLAAIKEDSARTLFHAQIAAAPAPTQLP
+GVKDARAMTMVPQISVEGVETPRQPARLHLSGPSEDGEGVEEKDLAADGAQTPAGANRAS
+RRAEARRRRRGED
+>PROKKA_01416
+MPSIIDRVLKISDHRVLKRMQATVDAVNLLEDDFRALSDAELRAETDALRARHADGESLD
+LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL
+SGRGVHVVTVNDFLASYQADLMGRVFRFLGMQTGVIVAGQTPAVRREQYAADITYGTNNE
+FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA
+RLVRRLEADTDYEVDHKKRTVGILGPGIEKVEDHLGITNLYETQNTTLIQFLNNAVKAKE
+LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ
+NYFRGYEKLAGMTGTAETEAAEFTSTYGLGVVVIPPNRERQRVDRNDVVYKNEKVKFDAV
+VDDIAERHAKGQPVLVGTTSVEKSEYLSTLLAKRGVRHEVLNAKNHAREAAIVAQAGRPG
+AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLAEAEAAVED
+AHRAVIEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA
+QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLQYDDVMNRQREAIYTDR
+RSILEGEDLQDRVRRFVEDAVGNIVDAATEEGHATDWDLDQLWRDLAELYPVGISQEDVL
+DEVGGRGRLKAEVLKRELVSDALLAYEDREAQVGSEALREAERRVVLATIGRRWQEHLYE
+MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAAIREDAVRTLFQAQISAAPAPTSLP
+GVKDARAVTMAPQISVEGIDAPQQPAQLRFTGPSEDGQSAVTRSGTDSGATVAAGTNRRS
+RRQAERRGRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001215.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001215.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec40f47c0b13f5d6131cccec8a0239f03152f941
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001215.fa
@@ -0,0 +1,55 @@
+>PROKKA_01469
+MTTVDPQPPRPPRVAVVAVIVALVLALSGCTQIPQSSEVRSADPVDGASAAADAPQFHPP
+GPAESDTAEEAIRGFLLAGTSPQDDYAVAREFLDGPAATQWTPGQRTLVYSAEPRITRGD
+GDGDYQIQVEVDSEIDEYGLRTVAPPGTTRAWAVTVQERPQGMRITSTENGTLLSQAQFG
+QLFAPHELAFYDTAKRYIVPDVRWFVNRGTTVTAVTRALLRGPAPYLAGAVETAFPLRTG
+TDLAAPTVPVDDDGVAHVDLTQAAAEGADAERRHRMREQLELTLRGLQSVKEVEVTVAGA
+QLSTSGDDGPAPVQTDPAVRSVQVGIDAATGGLVYVQGSSVTPVGGAPDVTALDPVRPTM
+SGDRSRFAFVTGDRTAVHVAGTDGSLREVLRGTGLTVPSLDLLGWVWAADRGTTSRIRAV
+SAQPGGQERIVTATWLRPGERIVDLRLARSGARAAMLVDDGQRTTLRVSGVVRGSDGVPN
+ALTEPILLPSSGSEDSVEWAGDTNLLVSAYAEKPDERVVPRIVSIDGTVRELNPLGGLRG
+ISAGDDGAYYAETEELVFLLVGSSWRAQELDRGVRDLSFPD
+>PROKKA_01201
+MTTVDPQSPRPPRLAVVGVIVALMLALSGCTQIPQSSEVRSADPVDGATADADAPQFHPP
+GPAESDTAEEAIRGFLLAGTSPQDDYAVAREFLDGPAATQWTPGQRTLVYSAEPRITRGD
+GAGDYQIQVEVDSEIDEYGLRTIAPPGTTRAWAVTVQERPQGMRITSTENGTLLSQAQFG
+QLFAPHELAFYDTAKRYVVPDVRWFVNRGTTVTAVTRALLRGPAPYLAGAVDTAFPLRTG
+TDLAAPTVPVDDDGVAHVDLTQAAAEGADAERRHRMREQLELTLRGLQSVKEVEVTVAGA
+QLSTSGDDGPAPVQTDPAVRSVQVGIDAATGGLVYVQGSSVTPVGGAPDVTALDPVRPTM
+SGDRSRFAFVTGDRTAVHVAGTDGSLREVLRGTGLTVPSLDLLGWVWAADRGTTSRIRAV
+SAQPGGQERIVTATWLRPGERIVDLRLARSGARAAMLVDDGQRTTLRVSGVVRGSDGVPN
+ALTEPILLPSSGSEDSVEWAGDTNLLVSAYAAKPDERVVPRIVSVDGTVRELNPLGGLRG
+ISAGDDGAYYAETEEFVFLLVGSSWRAQELDRGVRDLSFPD
+>PROKKA_01431
+MSPTRPTGPRRARRLAGVGLAAALALALGGCTQIPQSSDVRSAEPLDGATAAPEAPQFRP
+PGPSADDTAEDVIRGFLLAGTSPQDDYAVAREFLDGPAAARWAPGQRTLVYSAQPRITRG
+EGTGNYQVQVEVDSEIDEFGLRTIAPEGTTRAWQVSVQERPEGMRITATENGTLLSQSQF
+GQLFAPHELAFYDTAQRYAVPDVRWFVNRGTTVTAVTRALLRGPAPYLTGAVETAFPLRT
+GADLAGPTVPVDEDGVAHVDLTEAAAEGADADRRHRMREQLEITLLGLQSVSDVRVTVDG
+AELSASGENPPPPVQDEPTTGSVQVGIDSATGDLAYFQGMSVGPVGGAPDVSALDPVDPT
+MSRDRSRFAFVTRDRTAVHVAGTDGSLREAMRGTGLTSPSIDGLGWVWAADGAETSRVRA
+VPAEPGQEARIVTATWLRPAERIVDLRVSRSGARAALLVDDGDRRTVRVAGIVRGSDGVP
+SALTEPILLPSTGRAASVEWAGDTNLLVSPRAATPDERVVPRIVSIDGTVRELNPLGGLT
+GVSAGDGGALYAETDELVFLLVGSSWRAQELERGVRDLSFPG
+>PROKKA_01333
+MRPSGPARPRRRLCAAALAGALALAGCAQIPQSSPVRSGAPLDVGSRAADAPQFRPPGPA
+EDATAEQLVRGFAQAGIAPEDGYAIARQYLSAEASDGWEPDRGVVVYSGEPTVTRGLGEG
+TYEVQLEVESEVDEFGQRTMAPPNTTQAREVTVEEVDGVLRITGVQDGVLLSRSQFAQLY
+APHPLYFFDQSQAFAVPDVRWFVNRGTAVTALTRALLRGPAPYLTGAVATAFPLRTGADL
+TGPSVPVAEDGTAAVDLTGATVDGADPARLSRMREQLERTLTGVSGVERVEVTVEGRSLT
+SSAPSGSVPSARIGEDPGTVQVGVSDAGELVFFQGLDAVPVGGLPSVADLGPEDPAMDRE
+RRRFVFLDRTRTVLHGVGTDGGEHRLLDGGRLTAPSLDSSGWAWTVDRARSSRISVVRAD
+GSEPARVVTTPWLAEGESIVALHIGPAGARAALIVDDGQQRTLRVAGVVRGGDGVPTALT
+PPVYIPTLDPPDDVEWMGDGSLVSTPLAPDAETRVRPEVVSLDGTSRQLNPLAGLTGISA
+REEGTLYAETAEDVFLLVGSSWRAQDVATPVHDLAFPD
+>PROKKA_01419
+MTTVDPQPPRPLRVAVFAVIVALVLALSGCTQIPQSSEVRSADPVDGATAAADAPQFHPP
+GPAESDTAEEAIRGFLLAGTSPQDDYAVAREFLDGPAATQWTPGQRTLVYSAEPRITRGD
+GAGDYQIQVEVDSEIDEYGLRTVAPPGTTQAWAVTVQERPQGMRITSTENGTLLSQAQFG
+QLFAPHELAFYDTAKRYVVPDVRWFVNRGTTVTAVTRALLRGPAPYLAGAVDTAFPLRTG
+TDLAAPTVPVDDDGVAHVDLTQAAAEGADADRRHRMREQLELTLTGLQSVKEVEVTVAGA
+QLSTSGDDGPAPVQTDPAVGSVQVGIDTATGGLVYVQGTSVTPVGGAPDVTALDPVRPTM
+SGDRSRFVFVTRDRTAVHVAGTDGTLREVLRGTGLTVPSLDLLGWVWAADRETTSRIRAV
+PAQPGGQERIVTATWLRPGERIVDLRLSRSGAQAAMLVDDGQRTTLRVSGVVRGSDGVPN
+ALTEPILLPSSGSEDSVEWAGDTNLLVSAYAEKPDERVVPRIVSIDGTVRELNPLGGLRG
+ISVGDDGAYYAETEELVFLLVGSSWRAQELDRGVRDLSFPD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001217.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001217.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5893c332d31223ae65dba9a487531489391c5742
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001217.fa
@@ -0,0 +1,40 @@
+>PROKKA_01472
+MTEAAHDDGATGPVALGGTPWRGTDVAEAQRVTLGELGADHWPVLPELPDRGPGADATGR
+SAALLQQLAVDLQPHGWRVSPPGAAGSGRDRRRAVSLWREDAHRWADTAGAEGAVVERLA
+VRVRGPLSLLACLWLPGGERVLGDHGARRDVAESYLEGLQDALPRLRRATGAGRLGVVVD
+EPWAAAVLAGTLPTASGYRTVRSLPREEARGLWRAALDGLTALPDVARVWLAPGRRAASP
+GAELPGPAALSTLTGESLPRPDAAADAPAPAPVSLVVGVGALDDGADGTPGTREAWEAAA
+GWADIGRGLTLAPEPGVRPVEVVRTWERLGVDPGRVGDVGLTAAGLHDPVVLHTLRRDAE
+ELTARLAELRG
+>PROKKA_01204
+MTEAAHDDGATGPVALGGTPWRGTDVAEAQRVTLGELGADHWPVLPELPDRGPGADATGR
+SAALLQELAVDLQPHGWRVSPPGAAGSGRDRRRAVSLWHEDAHRWADTAGAEGAVVERLA
+VRVRGPLSLLAGLWLPGGERVLGDHGARRDVAESYLEGLQDALPRLRRATGAGRLGVVVD
+EPWAAAVLAGTLPTASGYRTVRSLPREEARGLWRAALDGLTALPDVARVWLAPGRRAASP
+GAELPGPAALATLTGESLPRPDAAADAPVPAPVSLVVGVGALDDGADGTPGTREAWEAAA
+GWADIGRGLTLAPEPGVRPVDVVRTWERLGVDPGRVGDVGLTAAGSHDPAVLRTLRRDAE
+ELTARLAELRG
+>PROKKA_01428
+MPEAHDDGARPVALGGSPWAGTDAAEAQRVTLGELGAEHWPVLPELPSRGPGADATGRSA
+ALLSELAVDLQPHGWRVSPPGAAGSGMDRRRAASFWREDAHRWADTAGAEGAVVERLAVR
+VRGPLSLLGGLWLPGGERVLADHGARRDVAASYLEGLLEAVPRLRAATGAAGLGLLVDEP
+WAAAVLAGALPTASGYRTVRSLPRDEARGLWRELLAGLTALPGVASVWLAPGRRTASAAD
+VPATAELAALAGECLPAAGGEDDDAGAPVRLVVPVGDLDDGPDGTAGTRAAWESAAGWAD
+AGRGLTLSPAAHLRPADVVTTWERLGADPAHLRGTGLTAPGRHDATVLRRLRTDAAELAA
+RLDDALG
+>PROKKA_01330
+MPEASDDVGAVRVAALGGAPWRGTDAAEAQLATLGELGAEHWPVLPELPDRGPGADATGR
+SAALLHELAVDLQPHGWRVSPPGVVGSGMDRRRAASFWREDAHRWADTAGAEGAVVERLG
+VRLRGPLSLLGSLWLPGGERVLVDHGARRDVAASYVEGLRDAVPRLAAATGARTLGVVLD
+EPWAAAVLAGALPTASGYRTVRSVPRDEVRALWRDALAALADLPGVGRVWLAPGRRSAGV
+DVPLPDVSALAALAGESLPAAAPSADDDAPAPTRVDLVVPVGALDPGPDGTGGTRAGWET
+AAGWTDAGRGLTLSTATGVRPADVARTWERLGADPGHLAGVGLTVPGPHDAAVLGRLRAD
+AEELAARVGELLG
+>PROKKA_01422
+MTEAAHDDGATGPVALGGTPWRGTDVAEAQRVTLGELGADHWPVLPELPERGPGADATGR
+SAALLQELAVDLQPHGWRVSPPGAAGSGRDRRRAVSLWREDAHRWADTAGAEGAVVERLA
+VRVRGPLSLLAGLWLPGGERVLGDHGARRDVAESYLEGLQDALPRLRRATGAARLGVVVD
+EPWAGAVLAGTLPTASGYRTVRSLPREEARGLWRAALARLTALPDVARVWLAPGRRAASP
+GAELPGPAALATLTGESLPRPDAAADAPARAPVSLVVGVGPLDDGADGSPGTREAWEAAA
+GWADVGRGLTLAPEPGVRPVDVVRTWERLGVDPGRVGDVGLTAAGPHDPAVLRTLRRDAE
+ELAARLAELRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001220.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001220.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f9d10b62f6d923fe0f2240b61ddc17798b80b6f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001220.fa
@@ -0,0 +1,41 @@
+>PROKKA_01475
+MTTPDRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLRLEEARERIAAAL
+GAHPTEVILTSGGTEADNLAIQGLYRARRAAAPERTRIVLTGIEHHAVLDVVDWLAAHEG
+AEPVLVPVDDDGRVDLAAWGAALATAPERTALATLMWANNEIGTVQPVAEAARLAADHGV
+PLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALLVRRDVTLEAVVHGGGQER
+RLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLTGPRDLDP
+ATGQALSPGTRRLPGNVHITVPGRTADALLFSFDMAGLDTSSGSACTAGVAEPSHVVAAL
+PGRTEADARATQRFTLGRTTTPAEAAALIDALRTLLGPGV
+>PROKKA_01207
+MTTPDRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLHLEEARERIAAAL
+GAHPPEVILTSGGTEADNLAVQGLYRARRAVAPERTRIVLTGIEHHAVLDVVDWLAAHEG
+AEPVLVPVDDDGRVDLAAWGAALAAAPERTALATLMWANNEIGTVQPVAEAARLAADHGI
+PLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALFVRRDVTLEAVVHGGGQER
+RLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLTGPRDLDP
+ATGEPLPPGTRRLPGNVHITVPGRTADALLFSFDMAGLDTSSGSACTAGVAEPSHVVAAL
+PGRTEADARATQRFALGRTTTPAEAAALIDALRTLLGPGV
+>PROKKA_01425
+MPSAATPRPLGERVHLDHAATTAVRPSALAALAEAAALPGNPASLHASGRRAKLALEQAR
+EAVAAALGAHPSEVVLTSGGTEADNLAVQGLFRARRAADPQRLRIVLTGAEHHAVLDAVD
+WLAAHEGAEPVIVPVDADGVVDLAAWEAALAAAPERTALAALMWANNEIGTVQPVAEAAR
+IAAAHGVPLHTDAVQAVGAVPVDFAASGAATLAVSGHKAGAPVGVGALLVRRDVALTPVV
+HGGGQERRLRSGTVSVALAAALAAALTEAVAEQPAEAVRLGVLRDRVIEAVEALETVVLT
+GPRDADPATGEPLPPGTRRLPGNVHVTVPGRTADALLFTFDTAGLDTSSGSACTAGVAEP
+SHVVAALPGRTEADARATQRFTLGRTSTSADVDALIAALRALAPAPRRGAPTPKGAPTTK
+EESR
+>PROKKA_01327
+MTTPDRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLHLEEARERIAAAL
+GAHPTEVILTSGGTEADNLAVQGLYRARRAAAPERTRIVLTGIEHHAVLDVVGWLAAHEG
+AEPVLVPVDDDGRVDLAAWGAALAAAPERTALATLMWANNEIGTVQPVAEAARLAADHGV
+PLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALLVRRDVTLEAVVHGGGQER
+RLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLTGPRDLDP
+ATGEPLPPGTRRLPGNVHITVPGRTADALLFFFDMAGLDTSSGSACTAGVAEPSHVVAAL
+PGRTEADARATQRFTLGRTTTPAEAAALIDGLRTLLGPASRLDRPSVVERGVRP
+>PROKKA_01425
+MTTPDRVHLDHAATTTVRPTALAALAEAAALPGNPASLHASGRRAKLHLEEARERIAAAL
+GAHPSEVILTSGGTEADNLAVQGLYRARRAVAPERTRIVLTGIEHHAVLDVVDWLAAHEG
+AEPVLVPVDDDGRVDLAAWGAALAAAPERTALATLMWANNEIGTVQPVAEAARLAADHGI
+PLHTDAVQALGAVPVDFAASGAATLAVSGHKVGAPVGVGALFVRRDVTLEAVVHGGGQER
+RLRSGTVSVALAAALAAAVAEAVAEQPAEAARLGGLRDEVIAAVDALDGVRLTGPRDLDP
+ATGEPLPPGTRRLPGNVHITVPGRTADALLFSFDMAGLDTSSGSACTAGVAEPSHVVAAL
+PGRTEADARATQRFALGRTTTPAEAAALIDALRTLLGPGV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001221.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001221.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec38cfba4da0d4717ae969d969e84ce2816d7ec6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001221.fa
@@ -0,0 +1,35 @@
+>PROKKA_01478
+MSREGNIVLPGRTVTVRRRWLNGRVPTPSVPLVHPVHRFAHHEIDFRRRIVTMAVVNRTP
+DSFYDDGAGAVLEDALAQAHAAADAGAEWVDVGGVPFAPGAELDPTEEAARVVPLIAALR
+SGDGAGSSEASRRLILSADTFQPAVAEAALAAGADVVNDTTGLFHADLGRVVAAAGAHLV
+VTHSLAHVRGPRAVVPRPTYGDVVREVRDHLRRTVDRAVALGVPEERIIVDPGHDLNKNT
+RHTLEITRRLDEIATLGLPVLAAVSNKDFIGESLDRHRHERLPGSLAAAAACVYGGARIL
+RMHDADASVSAARMLECVFGWRQPARLVHNMGAENPPPDRSTLAGHRAHRGGRA
+>PROKKA_01210
+MSREGNIVLPGRTVTVRRRWLNGRVPTPSVPLVHPVHRFAHHEIDFRRRIVTMAVVNRTP
+DSFYDDGAGAVLEDALAQAHAAADAGAEWVDVGGVPFAPGAELDPTEEAARVVPLIAALR
+SGDGAGSSEASRRLILSADTFQPAVAEAALAAGADVVNDTTGLFHADLGRVVAAAGAHLV
+VTHSLAHVRGPRAVVPRPTYGDVVREVRDHLRRTVDRAVALGVPEERIIVDPGHDLNKNT
+RHTLEITRRLDEIATLGLPVLAAVSNKDFIGESLDRHRHERLPGSLAAAAACVYGGARIL
+RMHDADASVSAARMLECVFGWRQPARLVHNMGAENPPPDRSTLAGHRAHRGGRA
+>PROKKA_01424
+MRQNVAMALTELALRHPVRRFARREVDFRRRILTMAVVNRTPDSFYDDGAAFALEAAVDQ
+ARAAAEAGAEWVDVGGVPFAPGPALDPGEEARRVVPLIAALRGEAAEHSEAVAGLILSAD
+TFEPAVAEAAIAAGADVVNDTSGLVHADLGRVVAASQAHLVLTHSLAHVHGPRAVVPRPR
+YGDVVAEVREHLLRTVERAVALGVPEERIIVDPGHDLNKNTLHTLEITRRLDEIAGLGLP
+VLAAVSNKDFIGESLDQHRHERLAGSLAAAVACVHGGARILRMHDAAASVSAARLLECVF
+GWREPARLVHNMGEANPAPDRTSLAEHRAGRVRAGGTR
+>PROKKA_01324
+MPTPSVPLAHPVHRFAHHEIDFRRRIVTMAVVNRTPDSFFDDGAGFAFDAALAQVHTAAD
+AGAEWVDVGGVPFAPGRELDPAEEAARVAPFVAAVRAGRGEGASEAARRLILSADTFQPA
+VAEAAIDAGADVVNDTTGLYYPDLGRVVAASNAHLVVTHSLAHVSGPRTVVPRPRYDDVV
+AEVREHLLRTVDRAVALGVPEERIIVDPGHDLNKTTVHTLEVTRRLDEIADLGFPVLAAV
+SNKDFIGESLDRHRHDRLAGTLASAAFCALAGARILRMHDADASVSTAHMLECILGWREP
+LLAVHNTGDVNPAADRTTPADRVPADRPPAAVPAPTHDPEEARP
+>PROKKA_01428
+MSREGNIVLPGRTVTVRRRWLNGRVPTPSVPLVHPVHRFAHHEIDFRRRIVTMAVVNRTP
+DSFYDDGAGAVLEDALAQAHAAADAGAEWVDVGGVPFAPGAELDPTEEAARVVPLIAALR
+SGDGAGSSEASRRLILSADTFQPAVAEAALAAGADVVNDTTGLFHADLGRVVAAAGAHLV
+VTHSLAHVRGPRAVVPRPTYGDVVREVRDHLRRTVDRAVALGVPEERIIVDPGHDLNKNT
+RHTLEITRRLDEIATLGLPVLAAVSNKDFIGESLDRHRHERLPGSLAAAAACVYGGARIL
+RMHDADASVSAARMLECVFGWRQPARLVHNMGAENPPPDRSTLAGHRAHRGGRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001222.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001222.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5478cd40623294d4fa249d223e8a1a1d310b37e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001222.fa
@@ -0,0 +1,30 @@
+>PROKKA_01479
+MRRLTETGPGLDDDALRTALAAPAAEDTGPGPWVRVVFIASADGAATLDGRAGGLGSPAD
+QRLLSLSRHDADVVLVGAGTIRAEGYEGALLSEEDRRRRAEAGGPADPPVAVVSGSLDLD
+PASAFFTAAPVRPWILTSRAALAAEPERAAALAARADVLAVGEEHVDPQTVVATLHARGA
+RVVHCEGGPRLFGSLAAAGLVDEVHLTVAPLLAGPAAGRVLTGEDGPGLPARLQLVQVLH
+DDGMLFLRLHHERHASPGPDPTP
+>PROKKA_01211
+MRRLTETGPGLDDDALRTALAAPAAEDTGPGPWVRVVFIASADGAATLDGRAGGLGSPAD
+QRLLSLSRHDADVVLVGAGTIRAEGYEGALLSEEDRRRRAEAGGPADPPVAVVSGSLDLD
+PASAFFTAAPVRPWILTSRAALAAEPERAAALAARADVLAVGEEHVDPQTVVATLHARGA
+RVVHCEGGPRLFGSLAAAGLVDEVHLTVAPLLAGPAAGRVLTGEDGPGLPARLQLVQVLH
+DDGMLFLRLHHERHASPGPDPTP
+>PROKKA_01423
+MRRLAAVGPELSDEDLLALRRAPSTQDAPGPWVRAVFVSSLDGATALDGRSGTLGSPADR
+RQFALARTDADVILVGAGTVRAEGYAGPLVDAAARARRAARGLPEHPAVAVVTGSLDLDP
+DGEFFRAAPVRPWVIASERAVAAQPERAAALAEVADVLTAGVRDVEPRELLALLAGRGAR
+VVHCEGGPTLLGALAAAGAVDELLLTLSSLLAGGAGPRLIPAVEGIGLPARMLPHHVLTQ
+DGDLYLRLLHERHAALLADAPGLDGRAGTGR
+>PROKKA_01323
+MRLLTATGPEIDDDALLALRRAPAPDLVPGPWVRAVFVSSLDGAATLDGRAGGLGSPADQ
+RQFTLARTDADVVLVGAGTVRAEGYEGPLVGPAARARREEAGLPAHPGIAVVSGALGLDP
+DGDFLRQAPVRPLILTTQTALERCPDRAEALAARADVVASGAEVVEAPALVDALTARGHR
+VLHCEGGPRLFGTLAAADLVDELLLTISPLLAGGDGPRVLSGGDGPGLPTRLRPHHVLTE
+DGELYLRLVHERHAAVLAEAPGLEADPADADPAPGAP
+>PROKKA_01429
+MRRLTETGPGLDDDALRTALAAPAAEDTGPGPWVRVVFIASADGAATLDGRAGGLGSPAD
+QRLLSLSRHDADVVLVGAGTIRAEGYEGALLSEEDRRRRAEAGGPADPPVAVVSGSLDLD
+PASAFFTAAPVRPWILTSRAALAAEPERAAALAARADVLAVGEEHVDPQTVVATLHARGA
+RVVHCEGGPRLFGSLAAAGLVDEVHLTVAPLLAGPAAGRVLTGEDGPGLPARLQLVQVLH
+DDGMLFLRLHHERHASPGPDPTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001225.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001225.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1100038143c9e0f902c42dde45dda821f405f0cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001225.fa
@@ -0,0 +1,47 @@
+>PROKKA_01482
+MQTPDASEPHADRPDDAGQPALDTLLRRSAEGDRAAFSAFYDATVPWVHGLAEAMFGPGD
+DAAAATVRTYLTAWEEASEAGLDLSEQDDATHRERQVFTWLEVLAHRVMTSLRRAGGSAA
+ERGRRPGPAGPAALPEDLMDRVDPDAFEAVRLAWLGGCTDREVADRLDLPADRARTLLRD
+GVRQVVAARRDITQDAARPSAPAPATGPALGADVREDVDAGRALELADLSAVHALDTAGH
+TAAFSAVQRRGGELARWRSRVDGARQAVAWAFRSVTAEPPSALLDEVLRRLPAQDVGMDL
+IGDESTPAGPPRDRLRWLKVTALLLLAALVLGIGGWTVWSQFTRPGIVHRIDQSKDLFTT
+SEYPAQDGGTVQAFLSREQNSGYLTISGMPQLPEGQSYQLWLYPSDGTAPASLGTYDANG
+FGEPVTFRGLDRFAAMGISVEPSSGSEVPTSEPIVGVDLDPTAQTGPRYGGRPSTN
+>PROKKA_01214
+MQTPDASEPHVDRPDDAGQPALDTLLRRSAEGDRAAFSAFYDATVPWVHGLAEAMFGPGD
+DAAAATVRTYLTAWEEASEAGLDLSERDDATHRERQVFTWLEVLAHRVMTSLRRAGGSAA
+ERGRRPGPAGPAPLPEDLVGRVAPDAYEAVRLAWLGGCTDREVADRLGLPADEARTLLRD
+GVRQVVAARRDLTQDAARPSAPAPATGPALGADVREDVDAGRALELADLSAVHALDTAGH
+TAAFSAVQRRGGELARWRSRVDGARQAVAWAFRSVTAEPPSALLDEVLRRLPAQDVGMDL
+IGDESAPAGPPRDRLRWLKVTALLLLAALVLGVGGWTVWSQFTRPGIVHRIDQSKDLFTT
+SEYPAQDGGTVQAFLSREQNSGYLTISGMPQLPEGQSYQLWLYPSDGTAPASLGTYDANG
+FGEPITFRGLDRFAAMGISVEPSSGSEVPTSEPVVGVDLDPTAQTGPRYGGRPSTN
+>PROKKA_01420
+MQTPDASEPRADRSAAAGAPALDTLLRRSAEGDRAAFSAFYDATVPWVHGLASAMFRSAD
+DAAEATTLTYLTAWEEASEAGLDLSEHDAASHRERQVFTWLEVLAHRVMTTLLRSDGLPE
+AGHGLLPDRAGPGSAGPAERPEDLDSRVDPAAFEAVRLAWLGGLSDRQVAARMGRPVAES
+RTLLRDGVRQVVEAHRALTRDAADRSPETSARPALATSVREDVEAGHALELADLSAVHAL
+ETAGHTAAVSAVQRRGGDLPRWRSRVDGARQAVAWAFRSVTAEPPSAVLDDVLRRLPAQD
+VGMDLIGEEAAPARPPKDRLRWLKITVMVLLAALVLGVGAWTVWSQFTRPGIVHRVDQSE
+DLFTTSENPARDGGTAQAFLSRDQNSGYVTVSGMPQLPDGQAYQVWLYPDDGTAPASLGT
+FDANGFGEPVTFRGLDRFAAVGITVEPSSGSEVPTTDTLVGVDLDPTAHTGPRYGGRPST
+N
+>PROKKA_01320
+MQTPQHPETPGADASTAPQQPSRRGVDELLHASARGDRAAFSAFYDATVPWVHGMATAMF
+RSRRDAAEATAQTYLAAWSEAPEAELDLSDRDAAAARERRVFAWLEVLAHRVMTGLLRTD
+ALPEQGRRLLPERAGLGTGGPTALPATLEGSVSPETHRAVRLAWLGGRTDAQVAEALDVP
+VDRARTLLRDGVQELVAAHRADQGLPAPVAGARPALAATTREDVDAGRGAELADLSALHA
+LDAAGHTAAAAAAQQRGAGELALWRTRVDAGRRAVAWAFRDVVAEPPSDLLDGVLRRLPA
+QDMGLELVEETAAPRGAAERRRGLKTVLLGLLALVVLALGVYAGWSQFSRDGITHRVHGA
+KDLYTTSEYPAAGGGTMQGFLSDSENSGYVTVSGMPQLEDGQTYQVWLYPKDGSAPSSLG
+TYDADGFDDPISFRGLDRFAAVSMTVEPSGGSPEPTADDVLLGLDLDPSNQSGPQYGGMP
+SNN
+>PROKKA_01432
+MQTPDASEPHADRPDDAGQPALDTLLRRSAEGDRAAFSAFYDATVPWVHGLAEAMFGPGD
+DAAAATVRTYLTAWEEASEAGLDLSERDDATHRERQVFTWLEVLAHRVMTSLRRAGGSAA
+ERGRRPGPAGPAPLPEDLVDRVAPDAYEAVRLAWLGGCTDREVADRLGLPADQARTLLRD
+GVRQVVAARRDLTQDAARPSAPAPATGPALGADVREDVDAGRALELADLSAVHALDTAGH
+TAAFSAVQRRGGELALWRSRVDGARQAVAWAFRSVTAEPPSALLDEVLRRLPAQDVGMDL
+IGDESAPAGPPRDRLRWLKVTALLLLAALVLGVGGWTVWSQFTRPGIVHRIDQSKDLFTT
+SEYPAQDGGTVQAFLSREQNSGYLTISGMPQLPEGQSYQLWLYPSDGTAPASLGTFDANG
+FGEPVTFRGLDRFAAMGISVEPSSGSEVPTSEPVVGVDLDPTAQTGPRYGGRPSTN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001226.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001226.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd39035955744a8f8b9ccb0f1e4fb5163ab9b231
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001226.fa
@@ -0,0 +1,29 @@
+>PROKKA_01483
+MAVGAHPDDLDFGAAATLAGFSAAGLHIELCIVTDGDAGGFDSEGAEAMTARRHAEQRAA
+AAVVGAAEVHFLGERDGHLEPDHGVRRKLVALMRRVRPDVVLSTHPERDWERMQAAHPDH
+LACGEAVVRAAYPAVENPYAYPELAAEGLEAFKIRNLLLYAAPAARRNTVVDVTGLAEQK
+LRALDAHLSQHPDVDAMRRHVLAQMAEHHRHAAGPAAGPGHAEAFHLVTVNGPGTIAGF
+>PROKKA_01215
+MTTTLTTPAALAAHHGWRRVLAVGAHPDDLDFGAAATLAGFSAAGLHIELCIVTDGDAGG
+FDSEGPEAMTARRHAEQRAAAAVVGAAEVHFLGERDGHLEPDHGVRRKLVALMRRVRPDV
+VLSTHPERDWERMQAAHPDHLACGEAVVRAAYPAVENPYAYPELAAEGLEAFKVRNLLLY
+AAPAARRNTVVDVTGLAEQKLRALDAHLSQHPDVDAMRRHVLAQMAEHHRRAAGPAAAPG
+HAEAFHLVTVNGPGTIAGF
+>PROKKA_01419
+MTTPITPAALAAEHGWRTVLAVGAHPDDLDFGAAATLAGLSAAGLRVELCVVTDGDAGGF
+DSEGPEAMTARRHAEQRAAAAVVGAHEVHFLGERDGHLEPDHGVRRKLVALMRRVRPDVV
+LSTHPERDWELMQAAHPDHLACGEAVVRAAYPAVENPYAYPELAAEGLEAFKIRHLLLYS
+APAARRNTVVDVTGLEDVKLRALDAHISQHPDVAAMRRHVLAQMTEHHRRAAGPAAAPGL
+AEAFHLVTVNGPGTISGF
+>PROKKA_01319
+MSAVPESLPTPADLAVRHGWRTVLAFGAHPDDLDFDASATLAGLAAAGVRVELCVVTDGD
+AGGFDSDGPEAMTARRHAEQRAAAAVIGAADVHFLGERDGHLEPTHEVRRRIVELMRRVR
+PDVVLCPHPERDWESMQASHPDHLACGEAVVRAAYPAVENPYAYPELADAGLDAFRIRHL
+MLYTAPAARRNLTVDVTGLEDVKLRALDAHVSQHPDAPAMREAVRAKLTRRHREAAGPDA
+PAGSGEAYHLVTVNGDGVIAGF
+>PROKKA_01433
+MTTTLTTPAALAAHHGWRRVLAVGAHPDDLDFGAAATLAGFRAAGLHIELCIVTDGDAGG
+FDSEGPEAMTARRHAEQRAAAAVVGAAEVHFLGERDGHLEPDHGVRRKLVALMRRVRPDV
+VLSTHPERDWERMQAAHPDHLACGEAVVRAAYPAAENPYAYPELAAEGLEAFKVRNLLLY
+AAPAARRNTVVDVTGLAEQKLRALDAHLSQHPDVDAMRRHVLAQMAEHHRRAAGPAAAPG
+HAEAFHLVTVNGPSTIAGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001230.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001230.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bdffeb6f4f1f49c089d3678c6c3e78921b94e372
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001230.fa
@@ -0,0 +1,41 @@
+>PROKKA_01487
+MQEQFTAWSVLVDAGLIGALLAVGTLARAVITPLQTLMIPASVIAGILGLVLGPNGLGWL
+PFSSQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGAFASYGVLIYASQVAIGALVTLV
+LLQPLFDAPDSFAALLFAGWAGGFGSAAAVGQAYAANGDATVTSLAYTSATVGMIVGVVG
+GIIQAKIGAQRGHAREFAGLTSIPEELRTGVLNQVEERPVIGRHTFSAASVESLAFQVGV
+VAMIAAAAHGVVSWITSVWPSVVGEDGPQLIIPAFAIAFLLGLIARVLFQATKTAKFLDP
+GSLNSVSGTATDILIVCGIAAIAPTVVVDYWQPLLLLFVIGLALALFLGIVVAPRVMTDA
+WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL
+LAGLSWAVVGIWGAIAVIAIIAAVWLRRTDPGRRTPAQQAVRASSR
+>PROKKA_01219
+MQEQFTAWSVLVDAGLIGALLAVGTLARAVITPLQTLMIPASVIAGILGLALGPNGLGWL
+PFSSQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGAFASYGVLIYSSQVAIGALVTLV
+LLQPLFDAPDSFAALLFAGWAGGFGSAAAVGQAYAANGDATVTSLAYTSATVGMIVGVVG
+GIIQAKIGAQRGHAREFAGLTSIPEELRTGVLNQVEERPVIGRHTFSAASVESLAFQVGV
+VAMIAAAAHGVVSWITAVWPSVVGEDGPQLIIPAFAIAFLLGLIARVLFQATKTAKFLDP
+GSLNSVSGTATDILIVCGIAAIAPTVVVDYWQPLLLLFVIGLALALFLGIVVAPRVMTDA
+WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL
+LAGLSWAVVGIWGAIAVIAIIAAVWLRRTDPGRRTPAQQAVRASSR
+>PROKKA_01415
+MQEQFTAWSVLVDAGLIGALLAVGTLARAVIKPLQTLMIPASVIAGILGLVLGPNVLGWL
+PFSTQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGSFASYGVLIYASQVAIGALVALL
+VLQPLFSTPDSFAALLFAGWAGGFGSAAAVGQAYAANGDMTVTSLAYTSATVGMIVGVVG
+GIIQAKIGARRGHAKEFAGLTSIPDELRTGVLDQVQERPVIGRHTFSAASVESLAFQVGV
+VAMIAAAAHGVVTWITAVWPNIVGEDGPKLIIPAFAVAFILGLIGRVVFQATKTAKFLDP
+GSLNSVSGTATDILIVCGIASIAPTVVVDYWQPLLVLFVIGLALALFLGLVVAPRVMTDA
+WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL
+IAGLSWAVVGIWGAIAIAAILAAIWLRRTDPGVRSPAQQAVRAASR
+>PROKKA_01314
+MTWFQGVWPSIVGPEGPKLMIPAFAVAFVLGIIGRLLLQVTKTATFLDSASLNSVSGTAT
+DILIVCGIASIAPKVVLDYWQPLLILFVVGLALAVLLGLVVAPHVMTESWFEKQLFTWGW
+ATGAVATGVAMLRIVDPKLKSGTMEQFGVAYITVVPVEIAAVSFVPLLIIAGLSWAVVGI
+WDAIAEAAIIAAVFLVRSDPARKSAVPA
+>PROKKA_01437
+MQEQFTAWSVLVDAGLIGALLAVGTLARAVITPLQTLMIPASVIAGILGLALGPNGLGWL
+PFSSQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGAFASYGVLIYSSQVAIGALVTLV
+LLQPLFDAPDSFAALLFAGWAGGFGSAAAVGQAYAANGDATVTSLAYTSATVGMIVGVVG
+GIIQAKIGAQRGHAREFAGLTSIPEELRTGVLNQVEERPVIGRHTFSAASVESLAFQVGV
+VAMIAAAAHGVVSWITAVWPSVVGEDGPQLIIPAFAIAFLLGLIARVLFQATKTAKFLDP
+GSLNSVSGTATDILIVCGIAAIAPTVVVDYWQPLLLLFVIGLALALFLGIVVAPRVMTDA
+WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL
+IAGLSWAVVGIWGAIAIIAIIAAVWLRRTDPGRRTPAQQAVRASSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001236.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001236.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa09f52026ebdf034becdbfbf69416adb64e9c46
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001236.fa
@@ -0,0 +1,35 @@
+>PROKKA_01518
+MASCPPSSSDPTVAPPLALPLAREELDRGAVARLDPGHLAASWAREGTEVLWLQGGRAPV
+ADGRLVFTAPSGPVPAEAAYLGRGTAADRGPHGREREVVSVAVEPPAALPEDAATALADA
+VWVGLRDAAAALSDADTGLFVAAVANANWHATHRFCAFCGGVTDVEAAGWVRRCRDCSRE
+QFPRTDPAVIVAVIDPAGRILLGRNAAWPEGLYSCLAGFVEPGESLEHAVVREIAEESGV
+TVTQPRYRGSQPWPFPRSLMLGFTALAPAGAEPVPDGEEILSVRWFEREELARLAREGDV
+TLPGAVSIARALIEDWYGGTLPDAQTLIT
+>PROKKA_01227
+MASCPPSSSDPTAAPPLALPLAREELDRGAVARLDPGHLAASWAREGTEVLWLQGGRAPV
+ADGRLVFTAPSGPVPAEAAYLGRGTAADRGPHGREREVVSVAVEPPAALPEDAATALADA
+VWVGLRDAAAALSDADTGLFVAAVANANWHATHRFCAFCGGVTDVEAAGWVRRCRDCSRE
+QFPRTDPAVIVAVIDPAGRILLGRNAAWPEGLYSCLAGFVEPGESLEHAVVREIAEESGV
+TVTQPRYRGSQPWPFPRSLMLGFTALAPAGAEPVPDGEEILSVRWFEREELARLAREGDV
+TLPGAVSIARALIEDWYGGTLPDAQTLIT
+>PROKKA_01407
+MPVPDPAAPAPEPRHDPAPAPAPAAPLALPLAREEVDRGAVARLDPGHLAAAWEREGTEV
+LWLQGGRAPVADGRLRFTTPSGPVPPQAAYLGRGTAADLGPGGRERAVVAVALEPPAVLP
+PDAAAALGDAAWVGLRDAAAALSDADAGLFVAAVANANWHAAHRFCSFCGGATAVEAAGW
+VRRCEACGREHFPRTDPAVIVAVTDPDGRILLGRNAAWPAGRYSCLAGFVEPGESLEHAV
+VREVAEESGVTVADPRYRGSQPWPFPRSLMLGFTAQAPAGAEPVADGTEILSVRWFEREE
+LAALAREGEITLPGAVSIARALIEDWYGGTLPDAQTLIT
+>PROKKA_01306
+MPVPSAPDAVPAALPHLTLAREALDRSGAEREDPGLLGRLAADPATGVLHLVGGRAPVRD
+GALVLVPPAGPFPPEAVFLGRRLTDAAAPSAAGRPLVLVARESAPGSSGDGGPTRPAEPT
+DAPTRDPLAGAAWLGLRDVAAGLSDADTGLFVEAVAIANWHAGHGFCSRCGGRTDTESAG
+WVRRCRDCSARHFPRTDPAVIMAVMDDQDRILLGSNAAWPAGRHSCLAGFVEPGESLEHA
+VAREVLEEAGIVVVDAAYRGSQPWPFPRSLMVGYRAHALPGQEPVADGHEIRSVRWFTRD
+ELAAEVRAGAVTLPGAVSIARALIEDWYGGTLPDPTTLIS
+>PROKKA_01445
+MASCPPSSSDLTAAPPLALPLAREELDRGAVARLDPGHLAAVWAREGTEVLWLQGGRAPV
+ADGRLVFTAPSGPVPAEAAYLGRGTAADRGPHGREREVVSVAVEPPAALPEDAATALADA
+VWVGLRDAAAALSDADTGLFVAAVANANWHATHRFCAFCGGVTDVEAAGWVRRCRDCSRE
+QFPRTDPAVIVAVTDPAGRILLGRNAAWPEGLYSCLAGFVEPGESLEHAVVREIAEESGI
+TVTQPRYRGSQPWPFPRSLMLGFTALAPAGAEPVPDGEEILSVRWFEREELAHLAREGDV
+TLPGAVSIARALIEDWYGGTLPDAQTLIT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001240.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001240.fa
new file mode 100644
index 0000000000000000000000000000000000000000..250fa87d596ba1aee5381ebce5dee35f42b52e7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001240.fa
@@ -0,0 +1,20 @@
+>PROKKA_01522
+MTDHPVLPGARHRDDGPLTLGEGLEALARLVPPGRAVSYGGLAGLLGVGGPRQAGRAMAE
+SSPGTPWWRVVRADGSLPPELAARAAVEHEREAMPRTPAGRVDLPRARWEPDDGAARAIR
+AIADRIVSGPGARMRP
+>PROKKA_01231
+MTDHPVLPGARHRDDGPLTLGEGLEALARLVPPGHAVSYGGLAGLLGVGGPRQAGRAMAE
+SSPGTPWWRVVRADGSLPPELAARAAVEHEREATPRTPAGRVDLPRARWEPDDGAARAIR
+AIADRIVSGPGARMRP
+>PROKKA_01403
+MTTPPADPRPVPDGPLTLGEGLEAVARLVPAGRAVSYGDLAGLLGVGGPRQAGRAMAKSA
+PGTPWWRVVSADGSLPGELARRAAVEHAREGTPVRPGGRVDLPRARWEPDEAALGAVAAI
+AARIVSGPGARMQA
+>PROKKA_01302
+MSPVPSTPPDPDPHLPTDGPVTLGEALAAAARLIPSGRAASYGALAGLLGRGGPRQAGRA
+MAESEPGTPWWRVVRADGSLPEPLRRQARERWAAEGTPVRGSGTVRDQRVDLAQAGWEPD
+AAARAALADLAARVG
+>PROKKA_01449
+MTDHPVLPGARHRDDGPLTLGEGLEALARLVPPGRAVSYGGLAGLLGVGGPRQAGRAMAE
+SSPGTPWWRVVRADGSLPPELAARAAVEHEREGTPRTPAGRVDLRRARWEPDDGAARAIR
+AIADRIVSGPGARMGP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001241.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001241.fa
new file mode 100644
index 0000000000000000000000000000000000000000..32223393192172f0f4bbe385641722c112ff92e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001241.fa
@@ -0,0 +1,25 @@
+>PROKKA_01523
+MTWHESIRAGFDLETTGRDPRTALIVTATLVMVDEQGRAASSAEWLVDPGVPIPAEAAEV
+HGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARHHGLTPL
+EARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALAARY
+EQLRVAPVDLHERQVRWKAEQAESFEQYLRRKDPQATVSRHWPVEAER
+>PROKKA_01232
+MTWHESIRAGFDLETTGRDPRTALIVTATLVMVDEQGRAASSAEWLVDPGVPIPAEAAEV
+HGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGLTPL
+EARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALAAQY
+EQLRVAPADLHERQVRWKAEQAESFEQYLRRKDPQATVSRHWPVDAER
+>PROKKA_01402
+MSPVNWHQSIRAGFDLETTGRDPRSALIVTATLVMVDAQGRATASAEWLLDPGVPIPAEA
+AEVHGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGL
+APVEARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALA
+ERHEQLRVDPAELHERQVRWKAEQAESFEEYLRRKDPQATVSRDWPVESGR
+>PROKKA_01301
+MSWNEQIRAGFDLETTGRDPRQARIVTATIVMVDAAGKAVSSAEWLLDPGVPIPEEAAAV
+HGVTTERARAEGLEARRGVSEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGVAPL
+EPRPVVDPYVVDKQVDRFRKGKRTLGAVSEHYDVVLEDAHTSAADALAAVQVMDELVRRH
+PKADLPLDELHAAQARWKAEQAESFEEYLRRKDPQATVSRAWPVEPDV
+>PROKKA_01450
+MTWHESIRAGFDLETTGRDPRTALIVTATLVMVDEHGRAASSAEWLVDPGVPIPAEAAEV
+HGVTTERAQAEGMPAAQGVTEITETLRDLFAAGIPVVAFNGVYDFTVMDREARRHGLTPL
+EARPVIDPFVLDKQVDRFRKGKRTLSAVSEHYGVTLENAHTSAADALAAVQVADALAARY
+EQLRVAPTDLHERQVRWKAEQAESFEQYLRRKDPQATVSRHWPVEAER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001243.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001243.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5b1df0dfd8020ead734eb8336c36d80e68d00b9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001243.fa
@@ -0,0 +1,35 @@
+>PROKKA_01525
+MSFPLHRPRRLRRSAAMRRLAAETRLHPAELILPAFIKEGAAEPVPIASMPGVVQHTADS
+LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRDVKAEVGDGLVVMSDL
+CLDEFTDHGHCGVLTAEGAVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA
+LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALLEVALDLE
+EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV
+LSIRRAGADSVLTYWAAELGRWMKEGSL
+>PROKKA_01234
+MSFPLHRPRRLRRSAAMRRLVAETRLHPAELILPAFIKEGAAEPVPIASMPGVVQHTADS
+LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRDVKAEVGDGLVVMSDL
+CLDEFTDHGHCGVLTAEGTVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA
+LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALLEVALDLE
+EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV
+LSIRRAGADSVLTYWAAELGRWMKEGSL
+>PROKKA_01400
+MSFPLHRPRRLRRSAAMRRLVAETRLHPAELILPAFIKEGAPEPIAIASMPGVVQHTSDT
+LKAAAAEAAELGLGGIMLFGVPETRDAVGSISLDPEGVLNQAIRDVKSEVGDALVVMSDL
+CLDEFTDHGHCGVLTEDGAVDNDATLEIYAQMGVAQAEAGADVLGPSGMMDGQVRVIREA
+LDAAGHVDTGILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRTEALHEVALDLE
+EGADMVMVKPAMSYLDIVRDVAELADVPVSAYQISGEYAMIEAAAANGWIDRKASIVESV
+LSIRRAGADTVLTYWATELGRWMKEGSL
+>PROKKA_01299
+MSFPLNRPRRLRQSAAMRRLVAETRLHPNELILPAFIKEGAAEPVPIASMPGVVQHTTDT
+LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRDVKAEVGDGLVVMSDL
+CLDEFTDHGHCGVLTAEGTVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA
+LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALREVALDLE
+EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV
+LSIRRAGADSVLTYWAAELGRWMKEGSL
+>PROKKA_01452
+MSFPLHRPRRLRRSAAMRRLVAETRLHPAELILPAFIKEGAAEPVPIASMPGVVQHTADS
+LKAAAAEAAELGLGGIMLFGVPTTRDAVGSAALDPDGVLNRAIRGVKAEVGDGLVVMSDL
+CLDEFTDHGHCGVLTAEGTVDNDATLEIYARMGVAQAEAGADVLGPSGMMDGQVRVIREA
+LEGAGHHETAILAYAAKYSSAFYGPFRDAVDSQLTGDRKTYQMDAANRSEALLEVALDLE
+EGADMVMVKPAMSYLDIVRDVADMADVPVSAYQISGEYAMIEAAAAHGWIDRKASIVESV
+LSIRRAGADSVLTYWAAELGRWMKEGSL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001249.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001249.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8af1983ec0a340366812f5b81c63b74f990c5480
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001249.fa
@@ -0,0 +1,45 @@
+>PROKKA_01531
+MTTAPEPRADAPVHTGPDAGVAPALRTPEKAAAGVDYDVCGVMAPKDYDALLLASFGGPE
+GQDDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALKAAIEAELAARGLD
+LPVYWGNRNWEPYFPDTLARMHADGHRRILTVTTSAYSCYSSCRQYREDMGMAMEQTGLT
+GKVDLDKTRQYFNHPGFIEPFRDGLRADLASLRAELGDDARIHVLFATHSIPTSDAAAAG
+PRGLAADLRAQAGAEPGDEGADVYSAQHLDVAREILAGVPEAADVPWSLVYQSRSGPPSV
+PWLEPDINDAMEHLAGEGAETDAQGRAVAGFVVVPLGFVSDHMEVVWDLDTEAKETAEGL
+GVGFRRSPTPGTDPRFVAGLVDIVEERLGRREGRAAVGCFPAWYDVCRPDCCVKVMRDGS
+TRPTTSAVDAAVRGLAEHEAGAAAPAEEA
+>PROKKA_01241
+MTTAPEPRADAPVHTGPDAGVAPALRTPEKAAAGVDYDVCGVMAPKDYDALLLASFGGPE
+GQDDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALKAAIEAELAARGLD
+LPVYWGNRNWEPYFPDTLARMHADGHRRILTVTTSAYSCYSSCRQYREDMGMALEQTGLT
+GKVDLDKTRQYFNHPGFIEPFRDGLRADLASLRAELGDDARIHVLFATHSIPTSDAAAAG
+PRGLAADLRAQAGAEPGDEGADVYSAQHLDVAREILAGVPEAADVPWSLVYQSRSGPPSV
+PWLEPDINDAMEHLAGEGAETDAQGRAVAGFIVVPLGFVSDHMEVVWDLDTEAKETAEGL
+GVGFRRSPTPGTDPRFVAGLVDIVEERLGRREGRAAVGCFPAWYDVCRPDCCVKVMRDGS
+TRPTTSAVDAAVRGLAEHEAGAAAPAEEA
+>PROKKA_01394
+MSTAPENAAAASPAPEPRADAPVHAGPRAGVAPTLRAPEEAAAGVDFDVCGVMAPKEYDA
+LLLASFGGPEGQDDVIPFLRNVTRGRGIPDERLEEVATHYRANDGVSPINAQNRALKAAI
+EAELAARGLALPVYWGNRNWEPYVPDTLERMHADGHRRILTVTTSAYSCYSSCRQYREDM
+GMALRRTGLEGVVDLDKTRQYFNHPGFIEPFRDGLRADLASLREELGEDARIHVLFATHS
+IPTSDAAAAGPRGLAADLRAQAGAEPGEEGADVYSAQHLDVAREILAGVPEAADVPWSLV
+YQSRSGPPSVPWLEPDINDAMEHLAGEDAEADAAGRAVAGFVVVPLGFVSDHMEVLWDLD
+TEARQTAADLGVAFRRSPTPGTDPRFVSGLVDIVEERMGRREGRASLGCFGAWYDVCRPD
+CCSKVMRDGTVRPTTSAVDADVRGLAEHEAGTAPAGRTEES
+>PROKKA_01285
+MTAVPTHRVPEDARRPVHEPERAAAGVDYDACGAMAPKAYDALILASFGGPEGQEDVIPF
+LRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALISAIEAELVRRGLELPVYFGNR
+NWEPYFPDALQRAYDDGHRRILTVTTSAYSCYSSCRQYREDMGLAMERTGLEGKVDLDKT
+RQYFNHPGFVEPFAEGLRADLASLREEVGEDARVHLLFATHSIPTADAAAAGPRGLAAAL
+REQAGGEPGDVEGADAYSAQHLDVIREVLARVPEAEGVDWSLVYQSRSGAPHVPWLEPDI
+NDALEALAGPDAPADADGRALAGVVVVPVGFVSDHMEVVWDLDTEAKDTAAELGVAFRRT
+PTPGTDPRFVSGLVDIVEERLGRREGREAVGCFPAWYDVCRPDCCVKVMRDGSVRPTTSA
+VDAPVRGLAEHRGEQDGADDAGAQDS
+>PROKKA_01458
+MTTAPEPRADAPVHTGPDAGVAPALRTPEKAAAGVDYDVCGVMAPKDYDALLLASFGGPE
+GQDDVIPFLRNVTRGRGIPDERLEEVATHYRANGGVSPINAQNRALKAAIEAELAARGLD
+LPVYWGNRNWEPYFPDTLARMHADGHRRILTVTTSAYSCYSSCRQYREDMGMAMEQTGLT
+GKVDLDKTRQYFNHPGFIEPFRDGLRADLASLRAELGDDARIHVLFATHSIPTSDAAAAG
+PRGLAADLRAQAGAEPGDEGADVYSAQHLDVAREILAGVPEAADVPWSLVYQSRSGPPSV
+PWLEPDINDAMEHLAGEGAETDAQGRAVAGFVVVPLGFVSDHMEVVWDLDTEAKETAEGL
+GVGFRRSPTPGTDPRFVAGLVDIVEERLGRREGRAAVGCFPAWYDVCRPDCCVKVMRDGS
+TRPTTSAVDAAVRGLAEHEAGAAAPAEEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001252.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001252.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e8d6db5441d15760538e0e2ec664249b426e1de5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001252.fa
@@ -0,0 +1,40 @@
+>PROKKA_01534
+MSALSQTPETPAAVPALPAEHPLRTEDPSRSTVASPLLRALRGQRPDRHPVWFMRQAGRS
+LPEYRRVREGIGMLDSCLMPDLVREITMQPVRRHDVDAAIFFSDIVVPLRLAGVDVEIQP
+GVGPVLGQAVRTADDVAALPVLEDAALDVIREAVAATVAELGPRPLIGFAGAPFTLAAYM
+VEGRPSRDHFGPRRMMHADPETWAALAGWAATVSGQFLRAQLESGASAAQLFDSWAGSLS
+ADDYLEHVQPHSTAALAHVADLAGPGVPDGAPLLHFGTGTGEFLHHMRDAGATAVGVDHR
+LTLAEAHRRLSANPGPDGRGAVPLQGNIDPALLAAPWEVLEAHVRDVVASGAVAPGHVVN
+LAHGVPPETDAAVLTRVVELIHSLPVPEREGQDPAPGAETAEREERA
+>PROKKA_01244
+MSALSQTPETPAAVPALPAEHPLRTEDPSRSTVASPLLRALRGQRPDRHPVWFMRQAGRS
+LPEYRRVREGIGMLDSCLMPDLVREITMQPVRRHDVDAAIFFSDIVVPLRLAGVDVEIQP
+GVGPVLGQAVRTADDVAALPVLEDAALDVIREAVAATVAELGPRPLIGFAGAPFTLAAYM
+VEGRPSRDHFGPRRMMHADPETWAALAGWAATVSGQFLRAQLESGASAAQLFDSWAGSLS
+ADDYLEHVQPHSTAALAHVADLAGPGVPDGAPLLHFGTGTGEFLHHMRDAGATAVGVDHR
+LTLAEAHRRLSANPGPDGRGAVPLQGNIDPALLAAPWEVLEAHVRDVVASGAVAPGHVVN
+LAHGVPPETDAAVLTRVVELIHSLPVPEREGQDPAPGVETAEREERA
+>PROKKA_01391
+MSDLSQTSEIRAGAPALPADHPLRTQDPARSTAASPLVRALRGQRPDRHPVWFMRQAGRS
+LPEYREARAGIGMLESCLMPDLVREITLQPVRRHDVDAAIFFSDIVVPLRLAGVDVEIQP
+GVGPVLGRAVRTAEDVAALPVLEDSALDVIREAVSSTVAELGPRPLIGFAGAPFTLAAYM
+VEGRPSRDHFGPRRMMHGDPEAWAALAGWAATVSGQFLRAQLEAGASAAQLFDSWAGSLA
+AEDYLEHVQPHSRAALAHVDDLAGPGVDGGAPLLHFGTGTGEFLHHLRDAGASAVGVDHR
+LTLSEAHRRLSERPGPDGRTVVPLQGNIDPALLAAPWPVVEAHVRDVVASGAAAPGHVVN
+LAHGVPPETDPTVLTRVVELIHSLPVPEREGQDPAPPAGAAAGEGRA
+>PROKKA_01282
+MSAMTTPPGLPAEHPLSTADPARSTADAPLVCALRGRRPHRHPVWFMRQAGRSLPEYRKA
+REGVGMLESCLRPELAAEITLQPVRRHDVDAAIFFSDIVVPLKLAGVGVEIVPGVGPVLD
+HPVRTAEDAAALPELEDSALDVIREAVSRTVAELGPTPLIGFAGAPFTLAAYMVEGRPSR
+DHLGPRRMMHGDPQTWAALAAWAATVSGQFLRAQLEAGASAAQLFDSWAGSLSAADYRKH
+VQPHSAAALSAVSDLAGPGVEGGAPLLHFGTGTGEFLDLMRDAGASAVGVDHRITLAEAH
+RRLSSRPGPDGRAAVPLQGNIDPALLGAPWEVLEAHVREVVASGAAAPGHVVNLAHGVPP
+ETDPEVLTRVVELIHSIPVADGAEK
+>PROKKA_01461
+MSALSQTPETPAAVPALPAEHPLRTEDPSRSTVASPLLRALRGQRPDRHPVWFMRQAGRS
+LPEYRRVREGIGMLDSCLMPDLVREITMQPVRRHDVDAAIFFSDIVVPLRLAGVDVEIQP
+GVGPVLGQAVRTADDVAALPVLEDAALDVIREAVAATVAELGPRPLIGFAGAPFTLAAYM
+VEGRPSRDHFGPRRMMHADPETWAALAGWAATVSGQFLRAQLESGASAAQLFDSWAGSLS
+ADDYLEHVQPHSTAALAHVADLAGPGVPDGAPLLHFGTGTGEFLHHMRDAGATAVGVDHR
+LTLAEAHRRLSANPGPDGRGAVPLQGNIDPALLAAPWEVLEAHVRDVVASGAVAPGHVVN
+LAHGVPPETDAAVLTRVVELIHSLPVPEREGQDPAPGAETAEREERA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001253.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001253.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c2e2f44676a5c81fd1de09bba41ac575971bf02b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001253.fa
@@ -0,0 +1,45 @@
+>PROKKA_01535
+MTVFSLVASHHDLDLDTVARLSAGATGVGPALPGSGAAGAVVLATCNRVEIYAEADAAGV
+EAARAGLLSAVAASTSLPDEDVHAAFRTLDADATARHLFEVGAGLDSAVVGEREIAGQVR
+RALTAAQEAGTASGPLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLAEELRGLTDA
+AAQRDFWAGATILLIGTGAYAGTTLAQLADRGATTVGVHSASGRAEQFVADRGGWALALG
+GEAVAGAVAEADVIIGSSGGERQISPERLQELRKGGRRPLTVVDLALSRDFDPAVADLPD
+VDLITLESVRLAAPEQAQVAVAEARALVDDAVEEYRAAQRGRSADAAIKALRRHTLGVLD
+RELERVRARHGCTAAAEEVEFALRRMVNQLLHEPSVRAKRLAAEGRLDRYEDALEAVFGI
+EAPGRPAPAVGTVEAVCPAHEDEGGAARIA
+>PROKKA_01245
+MTVFSLVASHHDLDLDTVARLSAGATGVGPALPGSGAAGAVVLATCNRVEIYAEADAAGV
+EAARAGLLSAVAASTSLPDEDVHTAFRTLDADATARHLFEVGAGLDSAVVGEREIAGQVR
+RALTAAQEAGTASGPLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLAEELRGLTDA
+AAQRDFWAGATILLIGTGAYAGTTLAQLADRGATTVGVHSASGRAEQFVADRGGWALALG
+GEAVAGAVAEADVIIGSSGGERQISPERLQELRKGGRRPLTVVDLALSRDFDPAVADLPD
+VDLITLESVRLAAPEQAQVAVAEARALVDDAVEEYRAAQRGRSADAAIKALRRHTLGVLD
+RELERVRARHGCTAAAEEVEFALRRMVNQLLHEPSVRAKRLAAEGRLDRYEDALEAVFGI
+EAPGRPAPAVGTVEAACPAHEDDGGAARIA
+>PROKKA_01390
+MADVVTVFSLVASHQHLDLDTVARLSAGATGVGPALPGSGAAGAVVLATCNRVEIYAEAD
+ESGVEAAREGLVAAVAAHSSLPDEAVRSAFRVLDSEATARHLFEVGAGLDSAVVGEREIA
+GQVRRALSMARESGTASGSLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLTEELRG
+LADDDAKAAFWADASVLLIGTGAYAGTTLAQLAERGATAVAVHSASGRAEQFVEDRGGWA
+LALGGGAVAGAVAEADVIIGSSGGERQISPERLQELREDVDRPLTVVDLALSRDFDPAVG
+DLPDVDLITLESVRLAAPEQARAAVAEARVLVDGAVAEYRAAQRGRSADASIKALRRHTL
+AALDREMERVRARHGCTAAAEEVEFALRRMVNQLLHEPIVRAKRLAAEGRLDRYEDGLEA
+VFGIEPPGSTSSPAERPDAGCPAHEDEAGTARIA
+>PROKKA_01281
+MDVAVTVFSLVASHKDLSLDTVARLSAGSAGVGSALASSTDDGAVVLATCNRVEVYADAR
+DADAARERIVAAIAEQSGLPEDAVRSAFRVLDDDASARHLFEVGAGLDSAVVGEREIAGQ
+VRRALVDARDAGTATGSLTRLFESATRTAKDVGSHTALGATGRSVVSVALDLAEELRGLT
+DAMARRTFWQEANVLLIGTGAYAGTTLAQLADRGAQAVGVHSASGRAAQFVADRGGWALA
+LGGADVAGAVAEADVIIGSSGGDRQISPERMAGLRRGAERPVTVVDLALSRDFDPAVGEL
+EGVDLITLESVRLAAPEQAQAAVAEARGLVETALEEYTSARRGRTADAAIKALRGHTMAA
+LDREMERVRARHGCTAAADEVQFALRRMVNQLLHTPSVRARELAAQGRLDEFEHALEVLF
+DIPVPGTRPADAPGDACPATEADDARRTA
+>PROKKA_01462
+MTVFSLVASHHDLDLDTVARLSAGATGVGPALPGSGAAGAIVLATCNRVEIYAEADGAGV
+EAARTGLLSAVAASTSLPDEDVHTAFRTLDADATARHLFEVGAGLDSAVVGEREIAGQVR
+RALTAAQEAGTASGPLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLAEELRGLTDA
+AAQRDFWAGATILLIGTGAYAGTTLAQLADRGATTVGVHSASGRAEQFVADRGGWALALG
+GEAVAGAVAEADVIIGSSGGERQISPERLQELREGGRRPLTVVDLALSRDFDPAVADLPD
+VDLITLESVRLAAPEQAQVAVAEARALVDDAVEEYRAAQRGRSADAAIKALRRHTLGVLD
+RELERVRARHGCTAAAEEVEFALRRMVNQLLHEPSVRAKRLAAEGRLDRYEDALEAVFGI
+EAPGRPAPAVGTVEAACPAHEDDGGAARIA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001257.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001257.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38e0e81e22146da6fd977fe9030dbc3cc0338664
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001257.fa
@@ -0,0 +1,30 @@
+>PROKKA_01540
+MAAMARYDLHTHSTESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWAEAAQAARETGL
+TLVPGMEMSCTSADGVSVHVLSYLHDPEDPALLREVGRARDARLTRAQEMVRRLGADFSI
+TWELVQEHAAENATIGRPHLADALVTIGAVPDRSAAFREILAGRSKYYVPHFAPDPAEAV
+ALIRAAGGVPVFAHPRARMRGRVVGDEVFEQMAEAGLAGVEVEHRDNPAEERTWLRAFAD
+RHGLFVTGSSDYHGTGKPNPIGEHTTGAEVLAEIERQGTGTAIIRG
+>PROKKA_01250
+MAAMARYDLHTHSTESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWAEAAHAARETGL
+TLVPGMEMSCTSADGVSVHVLSYLHDPEDPALLREVGLARDARLIRAQEMVRRLGADFPI
+TWELVQEHAAENATIGRPHLADALVTIGAVPDRSAAFREILAGRSKYYVPHFAPDPAEAV
+ALIRAAGGVPVFAHPRARMRGRVVGDEVFEQMAEAGLAGVEVEHRDNPAEERTWLRAFAD
+RHGLFVTGSSDYHGTGKPNPIGEHTTGAEVLAEIERQGTGTAIIRG
+>PROKKA_01385
+MSRYDLHTHSVESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWEAAAEAALAEGIAFV
+PGMEMSCMAADGTSVHVLSYLHDPADPSLLREIGTARSARLTRAQEMVHRLARDYPITWE
+LVQEHAAEGATIGRPHLADTLVTLGVVEDRSAAFAHILTGRSKYYVPHYAPDPAIAVELI
+RSAGGVPVFAHPRAVTRGRVVGVEVIEEMIDAGLAGLEADHRDNPEEERSWLREVAARHD
+LFVTGSSDYHGTGKPNLLGEFSTGEDVLAEIERQGTGAAVVRG
+>PROKKA_01276
+MSTARYDLHTHSTESDGTEPAADVVHAAALAGLDGLALTDHDTTAGWAAAADAARETGLL
+LVPGMEMSCMAADGTSVHLLSYLHDPADPSLLAELGASRDARLTRAQSMTDRLAEDFPIT
+WDLVREHASENATIGRPHIADALVTIGAVPDRSAAFSSILRGGSKYYVPHYAVDPVEAVR
+LVRAAGGVPVFAHPRARLRGRIVGDDVLEAMIEAGLAGLEADHRDNPEQERTWLRETATR
+HGLFVTGSSDYHGAGKPNLIGEFTTGPEVLAEIEHQGTGAAVVRG
+>PROKKA_01467
+MAAMARYDLHTHSTESDGTEPPADVVRAAARAGLDGLALTDHDTTAGWAEAAHAARETGL
+TLVPGMEMSCTSADGVSVHVLSYLHDPEDPALLREVGLARDARLIRAQEMVRRLGADFPI
+TWELVQEHAAENATIGRPHLADALVTIGAVPDRSAAFREILAGRSKYYVPHFAPDPAEAV
+ALIRAAGGVPVFAHPRARMRGRVVGDEVFEQMAEAGLAGVEVEHRDNPAEERTWLRAFAD
+RHGLFVTGSSDYHGTGKPNPIGEHTTGAEVLAEIERQGTGTAIIRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001259.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001259.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5d6fbbf2ac01d59bfdeaceb7d58e58378d2bfe1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001259.fa
@@ -0,0 +1,59 @@
+>PROKKA_01542
+MGIDLTTELTALRDRLLSAEAEHADLISRVRDRHRASARNLVHYVALRGTDLRPLQEALS
+DAGLSSLGRMEAGVLGHVDAVLAAARALDGDLATAPEDDALTSAEGRAILARNAASLLGP
+ARGDRDARIMVTMPSEAATDPELVARIAEAGMDLARVNCAHDDEQAWAAMIAAVRRCAGA
+GRPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPARDPSGIVTEPSRVWLAAGPHDAVAVAD
+RPDGAVVVPLAAPDGKTLAGLQRGDEIELTDARGAHRRLEVERVSGEGVLVRADKTVYWA
+TGTALTTPHGPLEVGPLPPLEQSMRVHEGEQIVLTRSLEPVPAVDTPPYRIGLTLAQAFA
+DATVGDRVSLDDGRIGTRITGVSDDEITLEVTQAGPRGAKLKAEKGVNFPDTHLDIPALT
+DEDLAHIPFAARHADMVNMSFVRSAEDVAQLIDALEAEDAPDVDITLKIETVEAFRQLPR
+MLLEAMRWRDVGVMIARGDLAVEAGFARMAELQEEILWLCEAAHVPAIWATQVLESLAKT
+GLPSRAEITDAAMAQRAEAAMLNKGPYIDRAVTVLGDILGRMHGHASKKRDMLRRLESWS
+L
+>PROKKA_01252
+MGIDLTTELTALRDRLLSAEAEHADLISRVRERHRASARNLVHYVALRGTDLRPLQEALS
+DAGLSSLGRMEAGVLGHVDAVLAAARALDGDPAPAPEDDALTSAEGRAILARNAASLLGP
+ARGDRDARIMVTMPSEAATDPELVARIAEAGMDLARVNCAHDDEQAWAAMIAAVRRCAGA
+GLPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPARDPSGIVTEPSRVWLAAGPHDAVATAD
+RPDGAVVVPLADPEGTTLAVLQRGDEIELTDARGAHRRLEVEQVDGEGVLVRAEKTVYWA
+TGTALTTPHGPLEVGPLPPLEQSMRVHEGEEIVLARSLEPVPAVDTPPYRIGLTLAQAFA
+DAAVGDRVSLDDGRIGARITAVSADEITLEVTQAGPRGAKLKAEKGVNFPDTHLAIPALT
+DEDLAHIPFAARHADMVNMSFVRSAEDVAQLIDALEAEDAPDVDITLKIETVEAFRQLPR
+MLLEAMRWRDVGVMIARGDLAVEAGFARMAELQEEILWLCEAAHVPAIWATQVLESLAKT
+GLPSRAEITDAAMAQRAEAAMLNKGPYIDRAVTVLGDILGRMHGHASKKRDMLRRLESWS
+L
+>PROKKA_01383
+MDIDLTTELTALRDRLLSAEAEHADLISRVRDRHRASARNLVHYVALRGTDLRPLQDALS
+DVGLSSLGRMEAGVLGHVDAVLAAARALDGEDAPSPDDDALTPARGREILARDADRLLGP
+ARPDRAARIMVTLPSEAAQDPDLVARMAEAGMDLARVNCAHDDEAAWAAMIEAVRACATP
+ERPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPARTPAGLVTEPSRVWLAAAGAADAPAGA
+VVVPVTEAGAEVLAGLAAGDEVELTDARGSHHVLTVEQAGAAGALVRADKTVYWGTGLAV
+DTPRGTLTVGELAPLEQSMRVRRRDQVVLTRSLDPVPAASAPPYRIGLTLAQAFEDVAVG
+DRVSIDDGKIDAVVRAANADEITLEVTEAGPNGTKLKAEKGVNFPDTALSIPALTDEDLA
+HIPFVARHADMVNLSFVRSAEDVAQLIDALAAEDATDVDITLKIETVGAFEQLPRMLLEA
+MRWRDVGVMIARGDLAVEAGFERMAELQEEILWLCEAAHVPAIWATQILESLAKTGLPSR
+AEITDAAMAQRAEAAMLNKGPYIEEAITALGDILGRMGGHARKKRDMLRRLESWSL
+>PROKKA_01274
+MSTLPENAPDSRPTAESPVVAPGAAVTELIEAIDALRARIVAAEQAHAERLDRVADRHRA
+SARNLVHYVTLRGEDLRPLQDALSAVGLSSLGRMEAGVLGHLDAVRTALHPLGGRPAPDP
+ADDDPLSPAEGRALLAANAESLLGPSRPGRETRIMVTMPSEAATNAALVQGMADAGMDLA
+RVNAAHDGEAAWAAMVANIRGVARDGGRPAPRICMDLAGPKLRTGPLEPGPGVVKVKPRR
+DVDGTVLERSRVWLGEADAPEAADAVVLPLDPAGSGHSPVLSALRPGDHAMLTDARDSDR
+TLHVLAATEAGVLLACRKTVYWHTGLEVDTPRGTLVVGALPSVPQAMRVHAGDEIVLTRS
+MDPRPAVSEGPFTIGCSLPQAFQDVRPGERVLIDDGKITGEVVSNDGEAITLTVTEAGPT
+GAKLRAEKGVNFPDTDLRLPALTDEDRSHLPFAAAHADVVNMSFVRSPADVAALIDALDA
+EDARGVGVSLKIETVGAFERLPAMLLEAMRWNDVGVMIARGDLAVEAGFERMAELQEEIL
+WLCEAAHVPAVWATQILETLAKQGLPSRAEITDAAMAQRAEAAMLNKGPYIDEAIGALSD
+ILTRMGGHADKKRDMLRRLRSWSL
+>PROKKA_01469
+MGIDLTTELTALRDRLLSAEAEHADLISRVRERHRASARNLVHYVALRGTDLRPLQEALS
+DAGLSSLGRMEAGVLGHVDAVLAAARALDGDPAPAPEDDALTSAEGRAILARNAASLLGP
+ARGDRDARIMVTMPSEAATDPELVARIAEAGMDLARVNCAHDDEQAWAAMIAAVRRCAGA
+GRPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPTRDPSGTVTEPSRVWLAAGPHDAVAAAD
+RPDGAVVVPLADPEGTTLAVLQRGDEIELTDARGAHRRLEVEQVDGEGVLVRAEKTVYWA
+TGTALTTPHGPLEVGPLPPLEQSMRVHEGEQIVLTRSLEPVPAVDTPPYRIGLTLAQAFA
+DATVGDRVSLDDGRIGTRITGVSDDEITLEVTQAGPRGAKLKAEKGVNFPDTHLDIPALT
+DEDLAHIPFAARHADMVNMSFVRSAEDVAQLIDALEAEDAPDVDITLKIETVEAFRQLPR
+MLLEAMRWRDVGVMIARGDLAVEAGFARMAELQEEILWLCEAAHVPAIWATQVLESLAKT
+GLPSRAEITDAAMAQRAEAAMLNKGPYIDRAVTVLGDILGRMHGHASKKRDMLRRLESWS
+L
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001266.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001266.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0515c4b0fc64967634777b5831bedce2029fa0bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001266.fa
@@ -0,0 +1,10 @@
+>PROKKA_01550
+MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQA
+>PROKKA_01260
+MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQA
+>PROKKA_01375
+MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQG
+>PROKKA_01266
+MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEAKELQQCLEGVTQA
+>PROKKA_01477
+MAAMKPRTGDGPMEVTKEGRSLIMRVPIDGGGRLVLEINADEARELKECLEGVIQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001267.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001267.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a11f2460ae06b94930562d12e6ee28c4a1e92bfa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001267.fa
@@ -0,0 +1,18 @@
+>PROKKA_01551
+MRAPLGGEGRRVSGPQWIVLVAVLVVVLAALAAALAGRLTLRADDPAGRTPGHPVLLPER
+PRAADVDLLRLAVAVPGYQRDQVDAVLLRLRDALAQCEDEVTALRARVAELEAADPSRSD
+PAGRA
+>PROKKA_01261
+MRAPLGGEGRRVSGPQGIVLVAVLVVVLAALAAALAGRLTLRADDPAGRTPGHPVLLPER
+PRAADVDLLRLAVAVPGYQRDQVDAVLLRLRDALAQREDEVTALRARVAELEAADPSRSD
+PAGRA
+>PROKKA_01374
+MSTPLWIAVIAALVVVVAALAAAAAGRLTLRAGEPAGQAPVHPVALPERPRADDVAFVRL
+AVAVPGYQRDQVDAVLLRLRDALADHEDEVAALRARLAELEADAARDAERTGPR
+>PROKKA_01265
+MTQPIWIAVLVVAVVAVAALAAAALGRALPRPADPAGQAPPHPVLLPEHPRAADVDRLRL
+ATAVPGYQRDQVDEVLARLRAALAADEERIAALEARLGEGDGVGR
+>PROKKA_01478
+MRAPLGGEGRRVSGPQGIVLVAVLVVVLGALAASLAGRLTLRADDPAGRTPGHPVLLPER
+PRAADVDLLRLAVAVPGYQRDQVDAVLLRLRDALAQREDEAAALRARLAELEAADPSRSD
+PAARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001268.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001268.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a2f55b44224f2cfc257160e48f54c8468772cc63
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001268.fa
@@ -0,0 +1,30 @@
+>PROKKA_01552
+MAPHEHPSGGDVAAKPQRVRRGGQVLRGDAAHTPTFDQLLLDGRRPGDAARPAADVASTT
+SEAWRVLRIQAEFVEGFGTLAGLGPAVSVFGSARTPEGSAEYALAHEVGTRLARAGYTVI
+TGGGPGTMAAANRGAHEAGGESVGLGIDLPFETGLNPWVHVGVDFRYFFVRKVMFLKYAQ
+GFIVLPGGLGTLDELFEALTLVQTGTVTRFPVVLVDRGFWSPLVDWIRGTLVERGMISPE
+DPDLFHLVDTAEEAVACVLRSAGRADA
+>PROKKA_01262
+MAPDEHPLDGDVAEPEHVRRGGQVLRGEAERTPTFDQLLLDGRQPGDATQPAADIASTTS
+EAWRVLRIQAEFVEGFGTLAGLGPAVSVFGSARTPEGSAEYALAHEVGTRLARAGYTVIT
+GGGPGTMAAANRGAHEAGGESVGLGIELPFETGLNPWVHVGVDFRYFFVRKVMFLKYAQG
+FIVLPGGLGTLDELFEALTLVQTGTVTRFPVVLVDRGFWGPLVDWIRGTLVERGMISPED
+PDLVQLVDTAEEAVACVLRSAGRADA
+>PROKKA_01373
+MDPDQHPRTDAVPAPERVRRGGQVLRGEAARRPTSDQLLLDARRPGDALPPAADLASTTS
+EAWRVLRIQAEFVEGFGTLAGIGPAVSVFGSARTPEASPEYALAREVGARLAEAGFTVIT
+GGGPGSMAAANRGAHEAGGESVGLGIELPFEAGLNEWVHVGVDFRYFFARKVMFLKYAQG
+FVVLPGGFGTLDELFEALTLVQTGTVTRFPVVLVDSTFWGPVVDWIRGTLVERGMISPGD
+PEIFHVVETAEEAVDCVQRVCGPGAP
+>PROKKA_01264
+MTDKPDPARADRVDRHRVHRGGQILRGDAAASPTFDQLLLDARRAPAGKTRTPSTSSTSD
+AWRVLRIQSEFVEGFGTLADLGPAISVFGSARTGEGTDEYALGVEIGRRLAEEGWAVITG
+GGPGAMESANRGADEAGGVSVGLGIELPFETGLNPWVGIGVDFRYFFARKVMFLRYAQGF
+VVLPGGFGTLDELFEALTLVQTGTVTRFPVVLVGTEFWGPLVDWIRGTLTARGMISPGDA
+DLITVVDTAEEAVAHVSATCGGARA
+>PROKKA_01479
+MAPHEHPSGGDVAAKPQRVRRGGQVLRGEAARTPTFDQLLLDGRRPGDATQPAADIASTT
+SEAWRVLRIQAEFVEGFGTLAGLGPAVSVFGSARTPEGSAEYALAHEVGTRLARAGYTVI
+TGGGPGTMAAANRGAHEAGGESVGLGIELPFETGLNPWVHVGVDFRYFFVRKVMFLKYAQ
+GFIVLPGGLGTLDELFEALTLVQTGTVTRFPVVLVDRGFWGPLVDWIRGTLVERGMISPE
+DPDLVQLVDTAEEAVACVLRSAGRADA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001269.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001269.fa
new file mode 100644
index 0000000000000000000000000000000000000000..74082d437e3711a6e9169dfacabde6317bb2f441
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001269.fa
@@ -0,0 +1,30 @@
+>PROKKA_01553
+MTQITPEQPHGAHLPDEAGVRRRRGAAGDDLIVLEGVNKHFGDFHALRQIDLRIPRGQVA
+IVLGPSGSGKSTLCRTINRLETIDDDGGRILIDGRPLPTEGRQLAQLRAEIGMVFQSFNL
+FAHKSILENVTLGPIKVKGKRRADAERHAMELLERVGVAQQARKMPAQLSGGQQQRVAIA
+RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF
+MADGAILEDTDPDTFFTNPRHERAQDFLGKILAH
+>PROKKA_01263
+MTQITPEQPHGAHLPDEAGVRRRRGAAGDDLIVLEGVNKHFGDFHALRQIDLRIPRGQVA
+IVLGPSGSGKSTLCRTINRLETIDDDGGRILIDGRPLPTEGRQLAQLRAEIGMVFQSFNL
+FAHKSILENVTLGPIKVKGKRRADAERHAMELLERVGVAAQARKMPAQLSGGQQQRVAIA
+RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF
+MADGAILEDTDPDTFFTNPRHERAQDFLGKILAH
+>PROKKA_01372
+MTQITPEEPHGAHARDEAAPRRPRAAPGDDLIVLENVNKHFGDFHALKDIDLRIPRGQVA
+IVVGPSGSGKSTLCRTINRLETIDDDGGRILLDGQPLPAEGKQLAQLRAEVGMVFQSFNL
+FAHKSILENVTLGPIKVKGKRKADAERHAMELLERVGVAQQAKKMPAQLSGGQQQRVAIA
+RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF
+MADGAILEDTDPESFFTAPQHERARDFLGKILAH
+>PROKKA_01263
+MSEITSGTVHGSTAASGPAPAAASDALIRLEHVNKHFGEFHALKDIDLAIPRGQVAIVLG
+PSGSGKSTLCRTINRLETIDDDGGRILIDGRPLPSEGRELARLRAEVGMVFQSFNLFAHK
+SILENVTLGPIRVKGRKKAEAERHALELLERVGVAHQAKKMPAQLSGGQQQRVAIARALA
+MEPQALLFDEPTSALDPEMVQEVLDVMVGLAREGMTMVVVTHEMGFARKAGDRVVFMADG
+EILEDTDPESFFTRPQHPRAQEFLGKILVH
+>PROKKA_01480
+MTQITPEQPHGAHLPDEAGVRRRRGAAGDDLIVLEGVNKHFGDFHALRQIDLRIPRGQVA
+IVLGPSGSGKSTLCRTINRLETIDDDGGRILVDGRPLPTEGRQLAQLRAEIGMVFQSFNL
+FAHKSILENVTLGPIKVKGKRRADAERHAMELLERVGVAQQARKMPAQLSGGQQQRVAIA
+RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF
+MADGAILEDTDPDTFFTNPRHERAQDFLGKILAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001275.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001275.fa
new file mode 100644
index 0000000000000000000000000000000000000000..824d6bd415fdb723503bdcca9c87b33dcb99d9b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001275.fa
@@ -0,0 +1,45 @@
+>PROKKA_01560
+MTHHESVRLTVGEQSLDLGVEHATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTF
+IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL
+KLFFNGFPRDAHPMPVLSSSVSALSTFYPDSLDPHDQEQVHISTVRLLGKLPVLASYAFK
+KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYDIDPDVVKALDLLLMLHADHEQNASTST
+VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRKIKSEGITPEDFMEKVKNKED
+GVRLMGFGHRVYKNYDPRAKIIKKTAEDILGKMGGNDELLEIAQRLEEKALADDYFVERK
+LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPAAKIGRPRQIYVGE
+QLRQYPQR
+>PROKKA_01270
+MTHHESVRLTVGEQSLDLGVEHATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTY
+IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL
+KLFFNGFPRDAHPMPVLSSSVSALSTFYPDSLDPHDPEQVHISTVRLLGKLPVLASYAFK
+KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYDIDPDVVKALDLLLMLHADHEQNASTST
+VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRKIKSEGITPEDFMEKVKNKED
+GVRLMGFGHRVYKNYDPRAKIIKKTAEDILGKMGGNDELLEIAQRLEEKALADDYFVERK
+LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPATKIGRPRQIYVGE
+QLRQYPQR
+>PROKKA_01366
+MTQNESVRLTVGEQSLDLGVERATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTF
+IDGDEGILRYRGYAIEDLAANSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL
+KLFFNGFPRDAHPMPVLSSSVSGLSTFYPDSLDPHDPEQVHISTVRLLGKLPVLASYAFK
+KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYEIDPDVVKALDLLLMLHADHEQNASTST
+VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRTIQSDGIKPEDFMEKVKNKED
+GVRLMGFGHRVYKNYDPRAKIIKKTAEDILSKMGGNDELLEIAQRLEEKALADDYFVERK
+LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPATKIGRPRQIYVGE
+PLRQYPQR
+>PROKKA_01257
+MSEIESARLTVGEKTLDLGVEKAAEGNDGIVVAPLLKETGKVTYDPGFMNTANAKSAITY
+IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKEALEAWETNILRHNMVHEDL
+KMFFNGFPRDAHPMPVLSSSVSALSTFYADSLDPKDPEQVHISTVRLLGKLPVLASYAFK
+KSLGQPFMYPHNNLNYVENFLRLCFGVPAEEYEIDPDMVKALDLLLMLHADHEQNASTST
+VRLVGSTDANLFASVSAGINALYGPLHGGANEAVLNMLRRIQAEGIKPEDFMEKVKHKED
+GVRLMGFGHRVYKNYDPRAKIVKKTAEDILAKLGGNDELLEIAMRLEEKALADDYFVERR
+LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELTEDPATKIGRPRQIYVGE
+QLRQYPQR
+>PROKKA_01487
+MTHHESVRLTVGEQSLDLGVEHATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTF
+IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL
+KLFFNGFPRDAHPMPVLSSSVSGLSTFYPDSLDPHDPEQVHISTVRLLGKLPVLASYAFK
+KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYDIDPDVVKALDLLLMLHADHEQNASTST
+VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRKIKSEGITPEDFMEKVKNKED
+GVRLMGFGHRVYKNYDPRAKIIKKTAEDILGKMGGNDELLEIAQRLEEKALADDYFVERK
+LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPATKIGRPRQIYVGE
+QLRQYPQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001276.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001276.fa
new file mode 100644
index 0000000000000000000000000000000000000000..719466d6a5a48210a2708a5f7dae11c62b29b278
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001276.fa
@@ -0,0 +1,40 @@
+>PROKKA_01561
+MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPALIRRALTEAADAHGYPTTHG
+TDDLRRAVVDWYARRRGVSGLDPAAVVPTVGSKEFIAWLPTLLGLGAGDVVVHPEAAYPT
+YAVGALLAGAEAVAADDLDALAPEVRERVRLVWTNSPANPTGAVLDAAALRRTVDAARDV
+GAVVCGDECYAELGWDAWDGAVVPCILSDEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA
+GDPQLVATLINTRKHAGMIVPAPVQHAMAVALADDAHVAEQKDRYRRRRDALRTALEASG
+HTVDHSEAGLYLWTRRADLDPADATAQDSWDLLGELADLGIIAGPGVFYGAGGDGYVRVA
+ITATDEAVARAAARLTARGPRTG
+>PROKKA_01271
+MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPALIRRALTEAADAHGYPTTHG
+TDALRRAVVDWYARRRGVSGLDPAAVVPTVGSKEFIAWLPTLLGLGAGDVVVHPEAAYPT
+YAVGALLAGAEAVAADGLDALAPEVRERVRLVWTNSPANPTGAVLDAAALRRTVDAARGV
+GAVVCGDECYAELGWDAWDGAVVPCILSDEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA
+GDPELVATLVNTRKHAGMIVPAPVQHAMAVALADDAHVAEQKDRYRRRRDALRTALEASG
+HTVDHSEAGLYLWTRRADLDPADATAQDSWDLLGDLADLGIIAGPGVFYGAGGDGYVRVA
+ITATDEAVARAAARLTARGPRTG
+>PROKKA_01365
+MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPELIRRALTEAADAHGYPTTHG
+TADLRRAVVDWYARRRGVAGLDPEAVVPTVGSKEFIAWLPTLMGLGAGDVVVHPEAAYPT
+YAMGALIAGAEAVAADDLASLAPEVRERVRLVWTNSPANPTGAVLDAAALKRVVDDARAL
+GAVVCGDECYAELGWDEWDGELVPCILSEEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA
+GDPGLVATLVNTRKHAGMIVPAPVQHAMAVALADEGHVAQQKDRYRRRRDALRAALEASG
+HAVDHSEAGLYLWTRRADTDPAAATEQDSWDLLGELADLGIIAGPGVFYGAGGHGYVRVA
+ITASDEAVEQAARRLAARGPLRR
+>PROKKA_01256
+MLTLPDYPWDTLAPYRERAAAHPEGTVDLSIGTPVDPTPALIRDALTAAADAHGYPTTHG
+TAELRQAVVDWFARRRGVPGLDPEAVLPTVGSKELIAWLPTLLGLGAGDVVVFPATAYPT
+YAIGAQIAGAEAVAADTLAELDDDVRSRVRLVWTNSPANPTGAVLDAAELRAIVDDARAL
+GAVVCGDECYAELGWDEWEDRVVPCILAPEVSGGDLTGLLSVYSLSKQSNLAGYRAAFVG
+GDPELIAPLTNTRKHAGMIVPGPVQHAMAVALRDDAHVAAQRDLYRERRAALKAALESAG
+YAVDHSEAGLYLWTRRADLAPGQGTAQDSWDLLGELAELGIVAGPGVFYGAAGHGHVRVA
+ITASDEAVAAGAARLTARGPLPR
+>PROKKA_01488
+MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPALIRRALTEAADAHGYPTTHG
+TDALRRAVVDWYARRRGVSGLDPAAVVPTVGSKEFIAWLPTLLGLGAGDVVVHPEAAYPT
+YAVGALLAGAEAVAADDLDALAPEVRERVRLVWTNSPANPTGAVLDAAALRRTVDAARGV
+GAVVCGDECYAELGWDAWDGAVVPCILSDEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA
+GDPELVATLVNTRKHAGMIVPAPVQHAMAVALADDAHVAEQKDRYRRRRDALRTALEASG
+HTVDHSEAGLYLWTRRADLDPADATAQDSWDLLGDLADLGIIAGPGVFYGGDGYVRVAIT
+ATDEAVARAAARLTARGPRTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001277.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001277.fa
new file mode 100644
index 0000000000000000000000000000000000000000..639b1499bca1132fe18d573f946867770828da47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001277.fa
@@ -0,0 +1,15 @@
+>PROKKA_01562
+MTYVIALPCVDVKDKACIDECPVDCIYEGERMLYIHPDECVDCGACEPVCPVEAIYYEDD
+TPEEWAEYYKANVEFFDDLGSPGGAAKLGMIAKDHPIISALPLQNADA
+>PROKKA_01272
+MTYVIALPCVDVKDKACIDECPVDCIYEGERMLYIHPDECVDCGACEPVCPVEAIYYEDD
+TPEEWAEYYKANVEFFDDLGSPGGAAKLGMIAKDHPIISALPLQNADA
+>PROKKA_01364
+MTYVIALPCVDVKDKACIDECPVDCIYEGERSLYIHPDECVDCGACEPVCPVEAIYYEDD
+TPEEWADYYKANVEFFDDLGSPGGAAKLGMIAKDHPIIAALPPQNADA
+>PROKKA_01255
+MTYVIALPCVDVKDKACIDECPVDCIYEGERSLYIHPDECVDCGACEPVCPVEAIYYEDD
+VPEEWADYYKANVEFFDDLGSPGGAAKLGQIAKDHPLISALPPQGEGA
+>PROKKA_01489
+MTYVIALPCVDVKDKACIDECPVDCIYEGERMLYIHPDECVDCGACEPVCPVEAIYYEDD
+TPDEWAEYYKANVEFFDDLGSPGGAAKLGMIAKDHPIISALPLQNADA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001280.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001280.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f51f9cecab7fd9c5b58d82064b86ff66e3c7824c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001280.fa
@@ -0,0 +1,40 @@
+>PROKKA_01566
+MTTNNSSMTGAQLDEKQIFDLAEAEDAKLRAKAGKSYSQGALVRKRFFRHRAAMISLIVL
+VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD
+TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSLLMRLTDLIIVI
+PLLVLAAVLGQMASGMKMGILPLAVVLGLVSWTSLARLVRGEVLSLREKEFVAAAVAMGA
+KPGRLIFKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISDYQNA
+FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGGGAHRRLRFFGRRAAATEAGAT
+TAGGLAAAPTAGRIEAPVEEAGGSARISDADEDGQR
+>PROKKA_01276
+MTTNNSSMTGAQLDEKQIFDLAEAEDAKLRAKAGKSYSQGALVRKRFFRHRAAMISLIVL
+VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD
+TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSVLMRLTDLIIVI
+PLLVLAAVLGQMASGMKMGILPLAVVLGLVSWTSLARLVRGEVLSLREKEFVAAAVAMGA
+KPGRLIFKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISDYQNA
+FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGAGAHRRPRFFGRRAAATEAGAT
+TAGGLAAAPTAGRIEAPVEAAGGSARISDADEDGQR
+>PROKKA_01360
+MTTNNSSTTGAQLDEKQIFDLAEAEDAKLRVKAGKSYSQGALVRKRFFRHKAAMISLIVL
+VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD
+TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSVLMRLTDLIIVI
+PLLVLAAVLGQMASGANMGILPLALVLGLVTWTSLARLVRGEVLSLREKEFVAAAVAMGA
+KPGRVIGKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISLYQNS
+FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGAAAGRKRGLFSRRAAKTDAGAT
+TAGGLGTAPTARDGEADDLIADPDAPEHRRGGAGGPAGGVGQ
+>PROKKA_01251
+MTMSHSAQQNPRSTSPAVVDLAEAEDLKLQQKTGKSYSQGALIRMRFFRHKAAMVSLVVL
+AFIALMAFTSIGFAGIPGWWDESYSAASTVVDGGRPTLSVVPQFLGGEGLRWGAHPFGQT
+STGTDFFALVMRGTQQSLIIAFIVGLISTAIGALVGAASAYFGGWVDSVLMRLTDLIIVI
+PLLVLAAVLGKMAGGLQLGILPLAFVLGIVSWTSLARLVRGEILSLREKEFVAAAVAMGA
+KPGRIIGKHLLPNTIGVIVVNATFAIAGAVLLETSLSYLGFGVKSPDSSLGLLISDYQTA
+FTTRPWLFWWPGMTILAIALSVNFLGDGLRDAFDPRQSGSGRRKRGLFSRRAAVTEATPT
+TAGGLQASPASAPAGHADVVTDSRGLDAPAAWTVTDADGTSRPAGDDVDTTEGDAR
+>PROKKA_01493
+MTTNNSSTTGAQLDEKQIFDLAEAEDAKLRAKAGKSYSQGALVRKRFFRHKAAMISLIVL
+VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD
+TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSVLMRLTDLIIVI
+PLLVLAAVLGQMASGMKMGILPLAVVLGLVSWTSLARLVRGEVLSLREKEFVAAAVAMGA
+KPGRLIFKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISDYQNA
+FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGAGAHRRPRFFGRRAAATEAGAT
+TAGGLAAAPTAGRIEAPVEEAGGSARISDADEDGQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001284.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001284.fa
new file mode 100644
index 0000000000000000000000000000000000000000..74f4b3635a1710786199c9e6c7724976f057d640
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001284.fa
@@ -0,0 +1,40 @@
+>PROKKA_01571
+MTPPGWPPRARRSPLAFVIALFGVLGALVLAGGLTALLAGRMVDVAADSAPTVPAAEAPA
+REAGELAAGLTHIHDGVAVDWSASAHDGSSLDPGQPVADAPGILLVETALGARTGTGTGM
+VLSPDGLAVTNYHVVEDSSEVHVVVADTGARHTATVLGRDAEHDIAVLDVEGVSDLPVAS
+VSLDPVRRGDQVAAVGNGGGQGHLTAVRGTVLGTDRSIMAAAEGTDQYARLSGLIQTDAD
+VVPGYSGGPVVDDAGQVVGVTVAASDGTTADEVDGFAIPLEVAFDVVDQVLTGEETDTVS
+IGADGALGIMVGADPDVGVVVMQVDAGSAAEQIGLVEGDVILEIEGRAVGDDASRMSRLV
+NDHNVGDRITVQWRTADGEVREAEAVLQPALVN
+>PROKKA_01281
+MTPPGWPPRARRAPLAFVIALFGVLGALVLAGGLTALLAGRMVDVAADSAPTVPAAEAPA
+REAGELAAGLTHVHDGVAVDWSASAHDGSSLDPGQPVADAPGILLVETALGARTGTGTGM
+VLSPDGLAVTNYHVVEDSSEVHVVVADTGARHTATVLGRDAEHDIAVLDVEGVSDLPVAS
+VSLDPVRRGETVAAVGNGGGQGHLTAVRGTVLGTDRSIMAAAEGTDQYARLSGLIQTDAD
+VVPGYSGGPVVDDAGQVVGVTVAASDGTTAEEVDGFAIPLDVAFDVVDQVLSGEETDTVS
+IGADGALGIMVGADPDVGVVVMQVDAGSAAEQIGLVEGDVILEIEGRPVGDDAFRMSRLV
+NDHNVGDRITVQWRTASGEVREAEAVLQPALVN
+>PROKKA_01353
+MSVPPGWPPRRRRSPLALAISFFGVLGALVLAVGVTLLVAGRMVDVVGAPDPVVSARESA
+PPDAGALAQELAGAHEGVAVDWDAPAHAGSELDPGLAVDHAPGILLVETVLGQRMGTGTG
+MVLTPEGLALTNYHVVEDSSEVFVVEADTGERHTATVLGRDAEHDVAVLDVHGVTDLPVA
+SVSLDPVRRGDEVAAVGNGRGQGHLTAVRGTVLGTDRSIMAASQGSDEYARLTGLIQTDA
+DVVPGYSGGPVVDDDGQVVGVTVAASDGTGAQEVDGFAIPLGVALGVVDQVLSGEETDTV
+SIGADGALGIMVAADPEAGVVVMQVDADSAAEAIGLVPGDVVLAVDGQAVEGNASRMSRL
+VNDHNVGDRITVTWRTASGEVREAEAVLQEAVVN
+>PROKKA_01246
+MAIAVFGVLGAVVLAVGLTLLAGGRLIAAVGAGSSSSAAAPSGPQVTTRSLDALAASLDH
+AHAGIAVPAADAPPADGSLDPGERVRRAPGVLLVETRLEAMQGTGTGMVLTSDGLALTNY
+HVVEDSTAVSVVVADTGARHAATVLGRDAKNDVAVLQIDGVSGLTTTSVSRDPVRPGEAV
+AAVGNGGGQGYLTSVGGEVLRVDQSILAATEGTDDFERLTGLIQTDADVVPGYSGGPLVD
+GEGQVVGVTVAASEGRTAAQVDGYAIPLSTAFDVVAQVLSGEETDSVSIGADGSLGISVA
+GSRDGVEVLSVDRGSAGEELGLRPGDVITAIDGRTLDGNATAMSRLVNDHEVGDRLSVQW
+RTADGEARQGEAVLQKARHN
+>PROKKA_01498
+MTPPGWPPRARRSPLAFVIALFGVLGALVLAGGLTALLAGRMVDVAADSAPTVPAAEAPA
+REAGELAAGLTHIHDGVAVDWSASAHDGSSLDPGQPVADAPGILLVETALGARTGTGTGM
+VLSPDGLAVTNYHVVEDSSEVHVVVADTGARHTATVLGRDAEHDIAVLDVEGVSDLPVAS
+VSLDPVRRGDQVAAVGNGGGQGYLTAVRGTVLGTDRSIMAAAEGTDQYARLSGLIQTDAD
+VVPGYSGGPVVDDAGQVVGVTVAASDGTTADEVDGFAIPLEVAFDVVDQVLSGEETDTVS
+IGADGALGIMVGADPDVGVVVMQVDAGSAAEQIGLVEGDVILEIEGRAVGDDASRMSRLV
+NDHNVGDRITVQWRTADGEVREAEAVLQPALVN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001285.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001285.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f253eb1f6cfdcc14d37c51916affce4d78ccb19d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001285.fa
@@ -0,0 +1,20 @@
+>PROKKA_01572
+MATTHMKSTPVHTVGELPQVGSPAPDFTLTGADLSPVTLRELRGRRVILNIFPSLDTGVC
+AASVREFDSRVADLGDTTVVAVSADLPFAAARFCSVEGIDHVRSGSVFRSSFGGDYGVRM
+TDGPLEGLLARAVVMVDADGVVRHAQLVPEISEEPDYEAALAAARG
+>PROKKA_01282
+MATTHMKSTPVHTVGELPPVGAPAPDFTLTGADLSPVTLRELRGRRVILNIFPSLDTGVC
+AASVREFDSRVADLEDTTVVAVSADLPFAAARFCSVEGIDHVRSGSVFRSSFGDDYGVRM
+TDGPLEGLLARAVVVVDADGVVRHAQLVPEISEEPDYEAALAAARG
+>PROKKA_01352
+MATTHMKSTPVQTVGDLPEVGAPAPDFTLTGADLSPVTLQELRGRRVILNVFPSLDTGVC
+AASVREFNSRATDLEDTTVLAVSADLPFAAARFCSAEGIENVRSGSVFRSSFGDDYGVTM
+VDGPLEGLLARAVVVVDAEGVVRHAQLVPEITEEPDYEAALAAAQA
+>PROKKA_01245
+MATTHFKGTSVHTVGELPEVGSAAPEFTLTGSDLSSVTLADLKGRTVVLNIFPSLDTGVC
+AASVRRFNQEAAGLEDTTVLAVSADLPFAAGRFCSAEGIENVVTGSVFRSDFGTAYGAEL
+ADGPMRGLLARAVVVVDAEGTVAYTELVPEITTEPDYEAALAVVRG
+>PROKKA_01499
+MATTHMKSTPVHTVGGLPQVGAPAPDFTLTGADLSPVTLRELRGRRVILNIFPSLDTGVC
+AASVREFDSRVADLGDTTVVAVSADLPFAAARFCSVEGIDHVRSGSVFRSSFGDDYGVRM
+TDGPLEGLLARAVVVVDADGVVRHAQLVPEISEEPDYEAALAAARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001288.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001288.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3d8ea72c10a9c518efc71f5ac889899d5b4e6c5a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001288.fa
@@ -0,0 +1,19 @@
+>PROKKA_01575
+MKLTDDLLQKFNDQITLEFEASMVYRQLAIAADDLDLSGMAAWLRHQADEEIVHANKFID
+HVADRDSFPTIGAIPAPPVQAGLSALEIFRAALAHEQKVSEAIRELYRATESAGDLNSRP
+LLNWFLDEQIEEEATVSEIVGQLELVGDDGSGLLRIDGRLGSRPVETTENDA
+>PROKKA_01285
+MKLTDDLLQKFNDQITLEFEASMVYRQLAIAADDLDLSGMAAWLRHQADEEIVHANKFID
+HVADRDSFPTIGAIPAPPVQAGLSALEIFRAALAHEQKVSEAIRELYRATESAGDLNSRP
+LLNWFLDEQIEEEATVSEIVGQLELVGDDGSGLLRIDGRLGSRPVETTENDA
+>PROKKA_01349
+MTGVTAADGLDLSGMAAWLRHQADEEIVHANKFIDHVTDRGSDAAGDLSSRPLLNWFLEE
+QIEGEATPPL
+>PROKKA_01242
+MSIDKDLTRKFNEQITLEFEASMVYRQLAIAADMQDLSGMAAWLRHQADEEIVHANKFID
+HVVDREASAVIGAIPAPDVPEHITPVQIFEAALAHERKVSEAIRELYRAAEAAGDLSSRP
+LLNWFLEEQIEEEATVGEIVGQLKLVGEDGSGLLRIDSALGARPVETTENAG
+>PROKKA_01502
+MKLTDDLLQKFNDQITLEFEASMVYRQLAIAADDLDLSGMASWLRHQADEEIVHANKFID
+HVADRDSFPTIGAIPAPPVQAGLSALEIFRAALAHEQKVSEAIRELYRATESAGDLNSRP
+LLNWFLDEQIEEEATVSEIVGQLELVGDDGSGLLRIDGRLGSRPVETTENDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001290.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001290.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2698d0d9ff076c0d2bb8328210b30207e90d24c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001290.fa
@@ -0,0 +1,30 @@
+>PROKKA_01577
+MNTTAAASDPSDAPLASTRIGEGPRGVAFLHGLMGRGRNFTGPAKELGDDFTVELIDLPD
+HGASPWTDRVDYREIADRVAAHLRAGLAADGPVHLLGHSMGGKVAMVLALRHPELVDRLI
+VEDISPRLSPQATDEFVHLLGTMLRMDLDAYDSRAEADAAMAEHVHDARVRGFLLQNLRR
+TAGHFAWQPNVAMLFEHLREIGSFPDPVVPEDPERVFDHPVLWLAGAESDYVQDEDVPRM
+KELFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD
+>PROKKA_01287
+MNTTAAASDPSDAPLASTRIGEGPRRVAFLHGLLGRGRNFTGPAKELGDDFTVELIDLPD
+HGASPWTDRVDYREIADRVAAHLRAGLAADGPVHLLGHSMGGKVAMVLALRHPDLVDRLI
+VEDISPRVSPQATDEFVHLLGTMLRMDLDAYDSRAEADAAMAEHVHDARVRGFLLQNLRR
+TAGHFAWQPNVAMLFEHLREIGSFPDPVVPEDPERVFDHPVLWLAGAESDYVQDEDVPRM
+KELFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD
+>PROKKA_01346
+MTISDQGSPRRLPDSLERVSTPDPSASAAPSDAALASDVIGDGPHRVAFLHGLMGRGRNF
+TGPAKALADDFTVELLDLPDHGRSPWTDRVDYQEIADRVAEHLRAGLAADGPVHVLGHSM
+GGKVAMVLALRHPDLVDRLIVEDISPRLLPQATDEFVHLLGTMLRMDLDSYESRAEADAV
+MAKHVHDARVRGFLLQNLRREGGRFAWQPNVAMLFEHLEAVGSFPDPAAPEDPDRVFDRP
+VLWLAGANSDYVRDEDVPRMKDLFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD
+>PROKKA_01239
+MPTWSRASLSRVNTTAASAPSDAPLASTRIGEGSRRVAFLHGLMGRGRNFTGVATALADD
+FTVELIDLPDHGQSPWTDAVDYQDMADRVADHLRAGLAADGPVHLLGHSMGGKVAMVLAL
+RHPELVERLVVVDISPRMSPSATGEFVHLLGTMLRMDLASYTSRAEADAAMAEHVHDARV
+RGFLLQNLRREDGHFAWQPNVRMLFEHLDEIGAFPDPVVPEDPDRVFDRPVLWLGGADSD
+YIRDGDAPEMKALFPRVVRVTVRGASHWVHADQPEAFVSAVRTFLTAD
+>PROKKA_01504
+MNTTAASAPSDAPLASTRIGEGPRRVAFLHGLMGRGRNFTGPAKELGDDFTVELIDLPDH
+GASPWTDRVDYREIADRVAAHLRAGLAADGPVHLLGHSMGGKVAMVLALRHPELVDRLIV
+EDISPRLSPQATDEFVHLLGTMLRMDLDAYDSRAEADAAMAEHVHDARVRGFLLQNLRRT
+AGHFAWQPNVAMLFEHLREIGSFPDPVVPEDPERVVDHPVLWLAGAESDYVQDEDVPRMK
+ELFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001291.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001291.fa
new file mode 100644
index 0000000000000000000000000000000000000000..87e141ebb0443f05cace3bec26f63afed2113fb7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001291.fa
@@ -0,0 +1,30 @@
+>PROKKA_01578
+MPVAEARVSVAVSTAVFGVRPDPHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD
+VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPVLDDDGAAPASRPDPD
+VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR
+AVHEAVLGRGLDAANFRRATLAAGTLEETGEVRGGTPHRPPKLYRYRPAGPGTDPDPAGP
+DARR
+>PROKKA_01288
+MPVAEARVSVAVSTAVFGVRPDPHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD
+VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPALDDDGAAPASSPDPD
+VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR
+AVHEAVLGRGLDAANFRRATLAAGALEETGEVRGGTPHRPPKLYRYRPAGPGTDPDPAGP
+DARR
+>PROKKA_01345
+MPAPEARVTVAVSTAVFGVRPDPSGAPRLHVALVPRMREPFLDRWALPGTWLAADEELAD
+AAARVAAETVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPALDDDGAAPSHGGGLD
+VAGLPAGVHVRWQRADAPPAMAFDHAEILTAAVARLRADLPRAGVAHALLGPSFTLAELR
+AVHEAVLGRTLDAANFRRATLATGVLEETGEVRAGTRHRPPKLYRYRPADGAPPPAAPDD
+PGDLS
+>PROKKA_01238
+MPVAEARVSVAVSTAVFGVRPDAHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD
+VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPTLDDDGAAPASRPDPD
+VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR
+AVHEAVLGRGLDAANFRRATLAAGTLEETGEVRDGTPHRPPKLYRYRPAGPGTDPNPAGP
+DASR
+>PROKKA_01505
+MPVAEARVSVAVSTAVFGVRPDPHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD
+VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPALDDDGAAPASSPDPD
+VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR
+AVHEAVLGRGLDAANFRRATLAAGTLEETGEVRGGTPHRPPKLYRYRPAGPGTDPDPAGP
+DARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001292.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001292.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac14649f2829cda4ba1f33fbb1e44de16f64e1c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001292.fa
@@ -0,0 +1,45 @@
+>PROKKA_01579
+MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA
+PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR
+ASQGRPEAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL
+EAVYGTEPDDDGRVPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL
+FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALRDAKVLLWHGFCSVHRRFTVA
+QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ
+RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPASVAEPART
+ALERMLAVAPKQSAAQSAGAGT
+>PROKKA_01289
+MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA
+PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR
+ASQGRPEAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL
+EAVYGTEPDDDGRVPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL
+FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALRDAKVLLWHGFCSVHRRFTVA
+QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ
+RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPASVADPART
+ALERMLAVAPKQSAAQSAGAGT
+>PROKKA_01344
+MTATPETTASVARTLTLVARDPARGSACSSDLTTGPWAFDAGLPAYGPGASQDDAIPADA
+PVQGRIPEEYQQASDEELHARIAAAKAALGDRAVVLGHFYQRDEVVRHADFVGDSFQLAR
+ASQGRPEAEAIVFCGVHFMAETADLLSTPEQAVILPNLAAGCSMADMADLDSVQDAWEQL
+EEVYGTEPDADGRVPLLPVTYMNCSAALKGFVGERGGIVCTSSNASAVLEWAFERAQRVL
+FFPDQHLGRNTGRAMGIELERMPMWNPRLPLGGNTEETLRDARVLLWHGFCSVHRRFTVA
+QIEQARAEHPDVRVIVHPECPLPVVEAADESGSTDHIVKAIQAAPAGSTFAIGTEINLVQ
+RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPDAVADPARA
+ALERMLAVAPRQSVAQGAGA
+>PROKKA_01237
+MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA
+PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR
+ASQGRPAAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL
+EAVYGTEPDDDGRMPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL
+FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALREAKVLLWHGFCSVHRRFTVA
+QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ
+RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPVSVADPART
+ALERMLAVAPKQSAAQSAAQSAGAGT
+>PROKKA_01506
+MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA
+PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR
+ASQGRPEAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL
+EAVYGTEPDDDGRVPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL
+FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALRDAKVLLWHGFCSVHRRFTVA
+QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ
+RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPASVADPART
+ALERMLAVAPKQSAAQSAGAGT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001294.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001294.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d509e046992ceb75b76f16bde8d95111912ab1e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001294.fa
@@ -0,0 +1,43 @@
+>PROKKA_01587
+MSRSHSDALDASGPDSGGAVAVPRRRFGLLPRILVAIVAGVLVGLVAPTWLVQAFATFNG
+LFSNFLGFIVPVLILALVAPAIGDIGRGAGKLLALTGGIAYGSTLVGGFGALLVCLLVFP
+LILTPGSFEGMANPEDALLGPLFEVQMDPPFGVMTALLLAFVLGIGLTMLPRGALHESFD
+QLRSIIERVVMGLIVPLLPVYIFGVFLNMTAAGEVFKVITTFLGVILLVFGLTVVLLLLQ
+YVVAGTIAGRNPFTALKTMLPAYATALGTSSSAATIPVTLRQTLLLGVRRPIASFVVPLC
+ATIHLAGSTVKIVSFSIAVLFLSGQSIDVPVFVGFIFMLGVTMIAAPGVPGGAIVAASGL
+LTSMLGFTEPQVALMVATYIAIDSFGTATNVTGDAAIAMIVDKIAGDRLIEDSEDEGLER
+LDDEGAATGADAG
+>PROKKA_01298
+MSRSHSDALDASGPDSGGAVAVPRRRVGLLPRILVAIVAGVLVGLVAPTWLVQAFATFNG
+LFSNFLGFIVPVLILALVAPAIGDIGRGAGKLLALTGGIAYGSTLVGGFGALLVCLLVFP
+LILTPGSFEGMANPEDALLGPLFEVQMDPPFGVMTALLLAFVLGIGLTMLPRGALHESFD
+QLRSIIERVVMGLIVPLLPVYIFGVFLNMTAAGEVFKVITTFLGVILLVFGLTVVLLLLQ
+YVVAGAIAGRNPFTALKTMLPAYATALGTSSSAATIPVTLRQTLLLGVRRPIASFVVPLC
+ATIHLAGSTVKIVSFSIAVLFLSGQSIDVPVFVGFIFMLGVTMVAAPGVPGGAIVAASGL
+LTSMLGFTEPQVALMVATYIAIDSFGTATNVTGDAAIAMIVDKIAGDRLIEDSEDEGLER
+LDDEGAATGADAG
+>PROKKA_01335
+MSHASSGAAAPSDRAPQGAVSESCRRRRFGLLPRILVAIVAGVLVGLVAPTWLVQAFATF
+NGLFSNVLGFIVPVLILALVAPAIGDIGRGAGKLLALTGGIAYGSTLFGGFGALLVCLLV
+FPLILTPGSFEAMANPEDALLGPLFEVQMDPPFGVMTALLLAFVLGIGLTMLRRGALHEG
+FDQLRSIIERVVMGLIVPLCATIHLAGSTVKIVSFSIAVLFLSGQSIDVPVFVGFIFMLG
+VTMVAAPGVPGGAIVAASGLLSSMLGFTEPQVALMVATYIAIDSFGTATNVTGDAAIAMI
+VDKIAGDRLIEDSEDEGLERLDDEEAATGADAG
+>PROKKA_01233
+MSHAAPSSSVPPAPPSSSATDGTAAPEKAPRRGLRRLGLLPRVLLGIVLGVVVGLVSPEW
+LTRTAVTGTSLFSAFLGFIVPVLIVALVAPAIAELGRGAGRWLSVTAAIAYGSTLFGGFL
+SLGVALALFPRILTPGSISGVTDPSEGGATPFFEIAMDPPFGVMTALLLSFVLGIGMTLI
+PRGVLQQGFEELRTIIERVVTGIVVPLLPFYIFGIFLAMAASGGVFEVIGTFLGVILIVF
+ALTVVLLLVQYAVAGVIAHRNPLTALKAMMPAYATALGTSSSAATIPVTLRQVVSLGVRQ
+PIAAFVVPLAATIHLAGSTVKIVAFSTAVIILTGGQVDVGLMVGFIFMLGITMVAAPGVP
+GGAIVAASGLLSSMLGFTEPQVALMVATYIAIDSFGTATNVTGDGAIALIMDRIAGDRIA
+ADPGVAEESPAA
+>PROKKA_01514
+MSRSHSDALDASGPDSGGAVAVPRRRFGLLPRILVAIVAGVLVGLVAPTWLVQAFATFNG
+LFSNFLGFIVPVLILALVAPAIGDIGRGAGKLLALTGGIAYGSTLVGGFGALLVCLLVFP
+LILTPGSFEGMANPEDALLGPLFEVQMDPPFGVMTALLLAFVLGIGLTMLPRGALHESFD
+QLRSIIERVVMGLIVPLLPVYIFGVFLNMTAAGEVFKVITTFLGVILLVFGLTVVLLLLQ
+YVVAGAIAGRNPFTALKTMLPAYATALGTSSSAATIPVTLRQTLLLGVRRPIASFVVPLC
+ATIHLAGSTVKIVSFSIAVLFLSGQSIDVPVFVGFIFMLGVTMVAAPGVPGGAIVAASGL
+LTSMLGFTEPQVALMVATYIAIDSFGTATNVTGDAAIAMIVDKIAGDRLIEDSEDEGLER
+LDDEGAATGADAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001296.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001296.fa
new file mode 100644
index 0000000000000000000000000000000000000000..82627b9d588e8986f8dfa62aeca6e7c3a079cf32
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001296.fa
@@ -0,0 +1,20 @@
+>PROKKA_01591
+MAEPRPGDVRVTPGPGAPRGLVIPAGELVERFSHASGPGGQGVNTADSRVQLSLDLAATS
+ALDDVQRARVLARLAPRLAGTVLTVSVAEHRAQRRNRVAARERLAALLREALAPPTPRRA
+TKPTRGSRRRRLEAKHRRSEVKRTRRRPGLD
+>PROKKA_01303
+MAEPRPGDVRVTPGPGAPRGLVIPAGELVERFSHASGPGGQGVNTADSRVQLSLDLAATS
+ALDDVQRARVLARLAPRLAGTVLTVSVAEHRAQRRNRVAARERLAALLREALAPPTPRRA
+TKPTRGSRRRRLEAKHRRSEVKRTRRRPGLD
+>PROKKA_01300
+MADLRVEPGPGAPRGLVIPAAELMERFSHASGPGGQGVNTADSRVQLSLDLATTTALDES
+QRARALAVLGPRLAGTVLTVAAEEHRAQRRNRVAARERLAAMLREALIPETPRRATRPTR
+GSRRRRLEAKRQRSETKQLRRRPGV
+>PROKKA_01219
+MDDLRVPPGPGVPRGLRIPAAELSERFSHGSGPGGQGVNTADSRVQLSLDLAATTALTDA
+QRIRLLEGLAPRLAGTVLTVDAAEHRAQRRNRTAARERLAALLREALVPETPRRATKPTR
+GSQRRRLQAKARRSEVKQSRRRPRMD
+>PROKKA_01518
+MAEPRPGDVRVTPGPGAPRGLIIPAGELVERFSHASGPGGQGVNTADSRVQLSLDLAATS
+ALDDVQRARVLARLAPRLAGTVLTVSVAEHRAQWRNRVAARERLAALLREALAPPTPRRA
+TTPTRGSRRRRLEAKRRRSEVKRTRRRPGLD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001308.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001308.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3bd233bf753acf1c2c79c9440b255ff9bbc2110b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001308.fa
@@ -0,0 +1,61 @@
+>PROKKA_01620
+MARRAAKAKPAKTLEQTLWDAADKLRGNQEPSEYKHVVLGLVFLKYVSDRFEERREQLKD
+ELAAEGIKPERIESFLEDRDEYASQNVFWVPSLARWGYVQSVAKQPEIGQQIDQAMDLIE
+KENPSLRGVLPRNYGRDGLDKRRLGELVDLIGSIGFTETDDHGADDVLGRVYEYFLGQFA
+GKETGKDAGAFYTPRSVVKTLVEMLEPFKGRVYDPAVGSGGMFVQSAEFVKAHGGKRTDI
+SVYGQEFTDTTWKLAKMNLALRGVEADMGSHSADSFTEDLHLDLRADYVIANPPFNVSDW
+WDAKLADDPRWKYGTPPKGNANFAWVQHFLHHLAPHGTAGFVLANGSLSSKSSGEGEIRQ
+RLVEAGLVDCIVAMPDKLFFNTGIPVSLWFISKGRDGNGHRARKGEVLFIDARKLGAMQS
+RRLRVLSDDDIAQIADTYHEWRNHDGCYEDVPGFAKSATIGEIEKHEFVLTPGRYVGAAE
+AEVDDEPIDEKIERLTNELLAEFERGRELENEVRLRMGSLS
+>PROKKA_01648
+MTIPATRGAASAPHRSPQNLSNFVWGIADQLRGVFKPNQYGTLVLPLTILRRMEAVMAPH
+REFFAELAAKGHPDFVLDNLVESRTGLTFYNLSPFTLDRILQEPDLLRTNLLAYVDGFSQ
+NVADLFTYYEFDKTVAKLDEHDRLFLVLQQFASIDLSPETVSNAEMGTLFEDLIRRFAAA
+SNETAGEHFTPRDAVKLLVDLLTANDDDVLTGYPVRTVYDPTAGTGGMLSVLDERLRRMN
+PNAEVRLFGQELNDQSYAICKSELLGKGQAADGIARGDTLKNDAHMTERFDYVLSNPPYG
+GDWKASRAAVEKEIAAGGATNRFPGGTPAISDGQMLFLQLVASKLRPVSEGGGRAGIVLN
+GSPLFTGGAGSGPSEIRRWLLESDLVDVIVALPTDMFYNTGIATYVWVLDNNKPADRRGR
+AQLIDARTFFTKLRRNVGSKNKELSKADRQRVLDIYRDFDAQSEANAEFSKVLTAQDFGY
+REITVERPLQLRFEVEDATIAAALATKPADKLPDDGRSALEAALASLRGRVWDHQPTFVL
+DLKKALKEHGVTAGAPLVKALTGAIGVHDPKAEVVTNKKGEPEPDTSLRDTELVPFGRDI
+HEYFEAEVAPHVPGAWIDESKTKIGYEIPFTRLFYTYVPPRPLEEIDADLKQLTAEIIEL
+LQEVER
+>PROKKA_00900
+MTTPATPGAASAARRSPQNLSNFVWGIADQLRGVFKPNQYGTLVLPLTILRRMEAVMAPH
+REFFAELAAKGHPDFVLDNLVESRTGLTFYNLSPFTLDRILQEPDLLRTNLLAYVDGFSQ
+NVADLFTYYEFDKTVAKLDEHDRLFLVLQQFASIDLSPDTVSNAEMGTLFEDLIRRFAAA
+SNETAGEHFTPRDAVKLLVDLLTANDDDVLTGYPVRTVYDPTAGTGGMLSLLDERLRRMN
+PNAEVRLFGQELNDQSYAICKSELLGKGQDADGIARGDTLKNDVHLTERFDYVLSNPPYG
+GDWKASRTAVEKEIAAGGATNRFPGGTPAISDGQMLFLQLVASKLRPVSEGGGRAGIVLN
+GSPLFTGGAGSGPSEIRRWLLESDLVDAIVALPTDMFYNTGIATYVWVLDNNKSAERRGR
+VQLIDARTFFTKLRRNVGSKNKELSKADRQRVLDIYRDFDAQSEANAEFSKVLTAQDFGY
+REITVERPLQLRFEVEDATIAAALATKPVDKLPDDGRSALETALASLRGRVWDHQPTFVL
+DLKKALKEHGVTAGAPLVKALTGAIGVHDPEAQIVTNKKGEPEPDTSLRDTELVPFGRDI
+HEYFAAEVAPHVPGAWIDESKTKIGYEIPFTRLFYTYVPPRPLDEIDAELKQLTAEIIEL
+LQEVER
+>PROKKA_00838
+MPSPQNLSNFVWGIADQLRGVFKPNQYGTLVLPLTILRRMEAVMAQHREFFAELAAKGHP
+DFVLDNLVQSRTGLTFYNLSPFTLDRILQEPDLLRTNLLAYVDGFSQNVADLFTYYEFDK
+TVAKLDEHDRLFLVLQQFASIDLSPETVSNAEMGTLFEDLIRRFAAASNETAGEHFTPRD
+AVKLLVDLLTANDDDVLTGYPVRTVYDPTAGTGGMLSLLDERLRRMNPNAEVRLFGQELN
+DQSYAICKSELLGKGQDADGIARGDTLKNDAHLTERFDYVLSNPPYGGDWKASRTAVEKE
+IAAGGATNRFPGGTPAISDGQMLFLQLVASKLRPVSEGGGRAGIVLNGSPLFTGGAGSGP
+SEIRRWLLESDLVDAIVALPTDMFYNTGIATYVWVLDNNKSAERRGKVQLIDARTFFTKL
+RRNVGSKNKELSTADRQRVLDIYRDFDAQSEANAEFSKVLTAQDFGYREITVERPLQLRF
+EVEDATIAAALATKPADKLPVDGRSALGAALASLRGRVWDHQPTFVLDLKKALKEHGVTA
+GAPLVKALTGAIGVHDPKAEVVMNKKGEPEPDASLRDTELVPFGRDIHEYFEAEVVPHVS
+GAWIDESKTKIGYEIPFTRLFYTYVPPRPLEEIDAELKQLTAEIIELLQEVER
+>PROKKA_01879
+MTTPATRGAASAPHRSPQNLSNFVWGIADQLRGVFKPNQYGTLVLPLTILRRMEAVMDPH
+REFFAELAEKGHPDFVLDNLVQSRTGLTFYNLSPFTLDRILQEPDLLRTNLLAYVDGFSQ
+NVADLFTYYEFDKTVAKLDEHDRLFLVLQQFASIDLSPDTVSNAEMGTLFEDLIRRFAAA
+SNETAGEHFTPRDAVKLLVDLLTANDDDVLTGYPVRTVYDPTAGTGGMLSLLDERLRRMN
+PNAEVRLFGQELNDQSYAICKSELLGKGQDADGIARGDTLKNDAHLTERFDYVLSNPPYG
+GDWKASRTAVEKEIAAGGATNRFPGGTPAISDGQMLFLQLVASKLRPVSEGGGRAGIVLN
+GSPLFTGGAGSGPSEIRRWLLESDLVDAIVALPTDMFYNTGIATYVWVLDNNKPADRRGR
+VQLIDARSFFTKLRRNVGSKNKELSTADRQRVLDIYRDFDAQSEDNAEFSKVLTAQDFGY
+REITVERPLQLRFEVEDATIAAALATKPVDKLPDDGRSALESALASLRGRVWDHQPTFVL
+ELKKALKKHGVTAGAPLAKALTGAIGVHDPDAEVVKDKKGEPEPDTSLRDTELVPFGRDI
+HEYFEAEVAPHVPGAWIDESKTKIGYEIPFTRLFYTYVPPRPLEEIDAELKQLTAEIIEL
+LQEVER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001309.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001309.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2353c9fd704f983a0231e37614eca662f1496e18
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001309.fa
@@ -0,0 +1,20 @@
+>PROKKA_01626
+MARPIDPFREMERLVNGLTPRATGTVSMPMNLYREGDVFVAEVELPGVDPASIDVDVEER
+TLTVRAERKEDPAREDRRWLTRERSAGTFARQLTLGEGLALDRIQADYSDGVLTLTIPVA
+EQAKPRKISVTHGGAAPVAGQTVEGETAETTGE
+>PROKKA_01332
+MARPIDPFREMERLMTGFARTSGAASMPMNLYREGDVFVAEVELPGVDPSSIDVDVEERT
+LTVRAERKEAPAGEDRRWLTKERPAGTFARQLNLGQGLALDKIEADYSDGVLLLTIPVAE
+QAKPRKIQVKHTGSAAQVEGEAVEGEAVEGSAAEASGE
+>PROKKA_01271
+MARPIDPFREMERPFREMERLVNGLTRTSGTASMPMNLFREGDRFVAEVELPGVDPASID
+VDVEERTLTVRAERKESPAGEDRRWLTRERSAGTFARQLTLGEGLALDRIEADYEDGVLT
+LTIPVAEQAKPRKISVKHSGAGAGAGQTVPGETAEVEERSAEQEAAQNGGAPQA
+>PROKKA_01181
+MARPIDPFREMERPFREMERLVNGLTTRATGTASMPMNLYREGDAFVAEVELPGVDPASI
+DVDVEERTLTIRAERKEAAASEGRQWLTRERSSGTFARQLTLGQGLALDRIEADYRDGVL
+VLSIPVAEQAKPRKIQVKHSAADQVEGQEVAGQESVQDSAAVEAPQQPSGE
+>PROKKA_01555
+MARPIDPFREMERLVNGLTPRATGTVSMPMNLYREGDVFVAEVELPGVDPASIDVDVEER
+TLTVRAERKEDPAREDRRWLTRERSAGTFARQLTLGEGLALDRIQADYSDGVLTLTIPVA
+EQAKPRKISVTHGGTAPVAGQTVEGETAETTGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001310.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001310.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d70c0ff153434a6fb39c41fb7ff29633681e23be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001310.fa
@@ -0,0 +1,23 @@
+>PROKKA_01628
+MQLTIAPGDITATHADAVVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPEGL
+PAGQAVATTAGRLPARWVIHTVGPVWAKTIDKSDTLASCYRESLKVAAGLGARTVAFPAI
+SAGIYGWPMEDAARIAVETCHAMADEVGDTVDEVLFVPYGETAEAAFRAALGHLEAPQTT
+DDEGDTGR
+>PROKKA_01333
+MQLTIAPGDITATHADAVVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPEGL
+PAGQAVATTAGRLPARWVIHTVGPVWAKTIDKSDTLASCYRESLKVAAGLGARTVAFPAI
+SAGIYGWPMEDAARIAVETCHAMADEVGGTVEEVLFVPYGDTAEAAFRTALDRVERG
+>PROKKA_01268
+MELLIAPGDITATTADVVVNAANSTLLGGGGVDGAIHRRGGPEILAACRRLRETELPDGL
+PVGQAVATTAGRLPARWVVHTVGPVWAKTIDKSATLASCYRESLRVAAELGARSVAFPAI
+SAGVYGWPMDDAARIAVTTCREVAAQGAGSVERVLFVPFGERAEAAFRAALDAPDETGAP
+AAS
+>PROKKA_01176
+MKLSIAPGDITATHADAIVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPDGL
+PAGQAVATTAGRLPARWVIHTVGPVWAKTIDKSDTLASCYRESLRVARELGARTVAFPAI
+SAGVYGWPMDDAARIAVETSHAMADEVGDVVEEVLFVPFGDRAEAAFRAALEHLT
+>PROKKA_01557
+MQLTIAPGDITATRADAVVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPEGL
+PAGQAVATTAGRLPARWVIHTVGPVWAETIDKSDTLASCYRESLKVAAGLGARTVAFPAI
+SAGIYGWPMEDAARIAVETCHAMADEVGGTVDEVLFVPYGETAEAAFRAALGHLEDPQAT
+DDEGDTGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001312.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001312.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3860231b055874a62ef778a8ed1f43a51a7427b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001312.fa
@@ -0,0 +1,42 @@
+>PROKKA_01630
+MEILSLLLALTLGLVLGALLGAWLMWRRAADGGEEARRAQAELAALRTEHQGAREALAAA
+RAEQRALTAARAEDAERQRAESQVMSTLAPLGQRLAALQEQVSVLERDRASQFGRLGEQL
+RAAAATDRDLLNQTTSLMATLKSTSARGHWGEAQLRRVVEAAGMLHHVDFTEQATLSGRD
+GERLRPDLVVSLPGGKAMAVDAKAPIGDALAAEALADEPGEEAYERRQALAAQHAAAVRR
+HVDQLSAKSYWDGLEHSPELVLCFLPAESLLAAALDADPGLLDHAFSRNVALVAPVSLLT
+ALKSVAYAWRQDTLAENAHTVVASAKDLYERLGTLGTHLDRMGGSLKTAVDRYNQLVGSV
+ESRVLPAARRLRDADPGLAPTPDIRTLESAPRPLAAPELVAGVEEDELRRRRAESAREA
+>PROKKA_01335
+MEILSLLLALILGLVLGALVGAWLMWRRAAGGGEEARRAQAELAALRTEHQGAREELAAA
+RAEQRALTAARAEDAERQRAESQVMSTLAPLGQRLAALQEQVGVLERDRASQFGRLGEQL
+RAAAATDRDLLNQTTSLMATLKSTSARGHWGEAQLRRVVEAAGMLHHVDFTEQATLSGKD
+GERLRPDLVVSLPGGKAMAVDAKAPIGDALAAEALADEPGEEAYERRQALAGQHAAAVRR
+HVDQLSAKSYWAGLEHSPELVLCFLPAESLLAAALDADPGLLDHAFSRNVALVAPVSLLT
+ALKSVAYAWRQDTLAENAHTVVASAKDLYERLGTLGTHLDRMGGSLKTAVDRYNQLVGNV
+ESRVLPAARRLRDADPGLAPTPDIRTLESAPRPLAAPELVAGVEEDELRRRRAESAREA
+>PROKKA_01266
+MDILSLLLALALGLVVGALTGAWLMWRRAAGGGEEARRAEQELAALRVEHQGAREELAAA
+RAEHRAVAAARAEDVERQRSEARVLSTLTPLGQQLTALQEQVGVLERDRAAQFGRLGEQL
+RAAAATDRDLLNQTTSLMATLRSTSARGHWGEAQLRRVVEAAGMLHHVDFSEQSTLSGRD
+GERLRPDLLVSLPGGKSMAVDAKAPIGDALAAEALADEPGEEAWERRQALAAQHAAAVRR
+HVDQLSAKAYWAGLEHSPELVLCFLPAESLLAAALDADGGLLDHAFSRNVALVAPVSLLT
+ALKSVAYAWRQDTLAENAHTVVASAKDLYERLGTLGTHLDRMGGSLKTTVDRYNQLVGNV
+ESRVLPAARKLREADPGLAPTPDIRTLESAPRVLSAPELVEGVEQDELRRRREDPAREEA
+VREDPAREA
+>PROKKA_01174
+MDFLTLVITLALGLLVGAAVGAWLMWRRMDGAADGSAGAELDALRREHAAVREELAGARA
+ESRALTQQRAEDAERARTDARVLETLAPLGRQLGALQEQVGVLERDRAAQFGRLGEQLRT
+AAANDRDLLNQTASLMATLKSTSARGHWGEAQLRRVVEAAGMLHHVDFSEQTTMTGRDGE
+RLRPDLLVSLPGGKTLAVDAKAPIGDALAAGALAEEPGEEAAERRAALNARHAAAVRRHV
+DALSAKAYWTGLERSPELVLCFLPAESLLAAALDADGALLDHAFSRNVALVAPVSLLTAL
+KSVAYAWRQERLAENAQLIVSGARELYDRLGTMGSHLDRMGGSLRAAVDGYNRLVGNVES
+RVLPAARTLREADPGLPALADVRSVDNAPRPLTAPELVDGDGPVDEGWTPAGSAAAEDRP
+EPAPAFEESPLWEDDEWTEDAAWDTDRRTA
+>PROKKA_01559
+MEILNLLLALILGLVLGALVGAWLMWRRAAGGGEEARRAQAELAALRTEHQGAREELAAA
+RAEQRALTAARAEDAERRRAESQVMSTLAPLGQRLAALQEQVSVLERDRASQFGRLGEQL
+RAAAATDRDLLNQTTSLMATLKSTSARGHWGEAQLRRVVEAAGMLHHVDFTEQATLSGRD
+GERLRPDLVVSLPGGKAMAVDAKAPIGDALAAEALADEPGEEAYERRQALAAQHAAAVRR
+HVDQLSAKSYWDGLEHSPELVLCFLPAESLLAAALDADPGLLDHAFSRNVALVAPVSLLT
+ALKSVAYAWRQDTLAENAHTVVASAKELYERLGTLGTHLDRMGGSLKTAVDRYNQLVGNV
+ESRVLPAARRLRDADPGLAPTPDIRTLESAPRPLAAPELVAGVEEDELRRRRAESAREA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001313.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001313.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40b2634b3b0074ca6b6d4bf1f75aecca3a54cc43
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001313.fa
@@ -0,0 +1,51 @@
+>PROKKA_01631
+MESRPLPPPSNVNEHVSRFDPRAAAQEFEHELSPGMRDEPLPGGENVKRIIGLVVGPLLA
+VALFLLMPGDLGVWPRLVAATAVLMAVWWMTEALPIPATALLPLVVFPLGVPAEESDGGI
+TFDAVGASYGNNIIFLFMGGFMLALAMQRWNLHRRIALGVLKFMGARTVNLILGFMIATG
+FISMWVSNTATAVMMLPIGVSILVLVQRYGTDGALTADEGADQVDRPAAPASAAGEAPTQ
+AEIRSLTKSNFGTALMLGIAYAASIGSLGTIIGTPPNTLLAGHMAAEHGVQIGFGQWMLV
+GVPIAVVLLFACWFLLTRVLFRPEIDEVPGGRDLIATELARLGRMSAPEAKVLAVFVLAA
+LAWITVPLISEYVLDLESPLLSDAAIAIVVGLILFLLPAGGGAGRGVRLLDWEAAKDLPW
+GVLLLFGGGLALSGQFSKSGLSTWLGEQVKGFGDIPVWVLVVIASVGILLLTEMTSNTAT
+AATFLPVASGVALGTGVAPLMLAAPVALAATCAFMLPVATPPNAIAYGSGYVTIGQMVKG
+GVWLNIIAAVLISIASMTLLVWVFGL
+>PROKKA_01336
+MESRSIPPPSNVNEHVSRFDPRAAAQEFEHELSPGMRDEPLTGGENVKRIIGLVAGPLLA
+VALFLLMPGDLGVWPRLVAATAVLMAVWWMTEALPIPATALLPLVIFPLGVPAEESDGGI
+TFDSIGASYGNNIIFLFMGGFMLALAMQRWNLHRRIALGVLKFMGARTVNLVLGFMIATG
+FISMWVSNTATAVMMLPIGVSILVLVQRYGTDDALTGDEAAGQVDRPAAPASAPGEAPTQ
+AEIRSLTKSNFGTALMLGIAYAASIGSLGTIIGTPPNTLLAGHMAAEHGVEIGFGQWMLV
+GVPIAVVLLFACWFLLTRVLFRPEIDEVPGGRDLIATELARLGRMSAPEAKVLAVFVLAA
+LAWITVPLISEYVLDLKSPLLSDAAIAMVVGLILFLLPAGGGAGRGVRLLDWEAAKELPW
+GVLLLFGGGLALSGQFSKSGLSTWLGEQVKGFGDIPVWVLVVIAAVGILLLTEMTSNTAT
+AATFLPVASGVALGTGVAPLMLAAPVALAATCAFMLPVATPPNAIAYGSGYVTIGQMVKG
+GVWLNIIAAVLISLASMTLLVWVFGL
+>PROKKA_00143
+MSSSLAFEGRAVAGAAVWMAVWWMTEAVPIPVTSLLPIVRFPLFGMGTMAEVASPYANSV
+VFLVMGGVILGLATEKAYLLENHDDDMQFGRWMLVGVPWAIVMLLIAWVVLTKLVFRAEV
+DRIPGGAEMIRGELAKLGPMTTPERRIALIFATAIFFWVAVPFIADIPAVADVAPWLGTI
+DDTQVAIAAAIACFIVPARRRGEDASQTALLQWSASKEIPWGLLLLFGVVVGLALTELTS
+NTATEAAFFPIFGAVALGLGMDPIFMTIAVTLAVCSAYMLPVATPSNAVAFGSGEVSIKQ
+MVRAGVGLNVVSIGLIMLVMYTLVPAVFG
+>PROKKA_01265
+MASRPVPPPSNVNEHVSRFAPQAAAQEFEHETSPGMRDQPLTGGEHTKRIIGLVAGPLLA
+IGLFLLMPGDLGVWPRLVAATAVLMAVWWMTEALPIPATALLPLVVFPLGVPAAESDGGV
+TFDSIGASYGNNIIFLFMGGFMLALAMQRWNLHRRIALGVLKLMGAKTVNLVLGFMIATG
+FISMWVSNTATAVMMLPIGVSILVLVQRYGTEDALAADAVPAAEQSAPGEAPTQAEIRSL
+TKSNFGTALMLGIAYAASIGSLGTIIGTPPNTLLAGHMATEHGIEIGFGQWMLVGVPIAV
+VLLLACWLLLTRVMFRPEIDEVPGGRDLIAAELARLGRMSAPEAKVLVIFVLAALAWITV
+PLLSEYVLGLDSPLLSDAAIAMVVGLVLFLLPAGGGAGRGVRLLDWEAAKELPWGVLLLF
+GGGLALSGQFSKSGLSTWLGEQVRSLGEIPVWVLVVIAAIGILLLTEMTSNTATAATFLP
+VASGVALGTGVEPLMLAAPVALAATCAFMLPVATPPNAIAYGSGYVTIGQMVKGGVWLNI
+TAAVLISVASMTLLVWVFGL
+>PROKKA_01560
+MESRPLPPPSNVNEHVSRFDPRAAAQEFEHELSPGMRDEPLPGGENVKRIIGLVVGPLLA
+VALFLLMPGDLGVWPRLVAATAVLMAVWWMTEALPIPATALLPLVVFPLGVPAEESDGGI
+TFDAVGASYGNNIIFLFMGGFMLALAMQRWNLHRRIALGVLKFMGARTVNLILGFMIATG
+FISMWVSNTATAVMMLPIGVSILVLVQRYGTDGALTADEGADQVDRPAAPASAAGEAPTQ
+AEIRSLTKSNFGTALMLGIAYAASIGSLGTIIGTPPNTLLAGHMAAEHGVEIGFGQWMLV
+GVPIAVVLLFACWFLLTRVLFRPEIDVVPGGRDLIATELARLGRMSAPEAKVLAVFILAA
+LAWITVPLISEYVLDLTSPLLSDAAIAMVVGLILFLLPAGGGAGRGVRLLDWEAAKELPW
+GVLLLFGGGLALSGQFSKSGLSTWLGEQVKGLGDIPVWVLVVIAAVGILLLTEMTSNTAT
+AATFLPVASGVALGTGVAPLMLAAPVALAATCAFMLPVATPPNAIAYGSGYVTIGQMVKG
+GVWLNIIAAVLISLASMTLLVWVFGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001316.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001316.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ee65f5db3fc29d094d99980c183fc25038bd701
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001316.fa
@@ -0,0 +1,45 @@
+>PROKKA_01634
+MDQPVTEGASAASDVPVSAPARAGETSAERPWPLRRLSENLKAHIERAPATWIEGQLIEF
+KNNRGNVYMTMRDLEEEVSLPLTAWRNVAMTLDGTVQQGSRVVARVKPNFWLKAGRLSMN
+VQEMRPVGLGDLLARVELLRRALAEEGLTSPARKRPLPLLPRRIGLITGRDSDAKKDVLR
+NTLLRWPAAEFEIREVAVQGAEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS
+DEALVRAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQEAAGLADA
+RLRLAAAVERRVRAEAEGLAALRSRPVLARPHVMVDTRQEETDRWRERGRSALGHRLVRE
+EDALTQLRARVRALSPQRTLDRGYAVVQHAGQVVRDADQVAPDDRLDILVAAGRIAADVV
+ATHRTTPTPSHERTRQA
+>PROKKA_01339
+MDQPVTEGASAASDVPVSAPARAGETSAERPWPLRRLSENLKAHIERAPATWIEGQLIEF
+KNNRGNVYMTMRDLEEEVSLPLTAWRNVATTLDGTVQQGSRVVARVKPNFWLKAGRLSMN
+VQEMRPVGLGDLLARVELLRRALAEEGLTSPARKRPLPLLPHRIGLITGRDSDAKKDVLR
+NTLLRWPAAEFETREVAVQGAEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS
+DEALVRAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQEAAGLADA
+RLRLAAAVERRVRAEAEGLAALRSRPVLARPHVMVDIRQEETDRWRERGRSALGHRLVRE
+EDALTQLRARVRALSPQRTLDRGYAVVQHAGQVVRDADQVAPDDRLDILVAVGRIAADVV
+ATHRPTPTPSHERTRQA
+>PROKKA_01261
+MDPSSTAHVEADALLDAGVPATASQTSAERPWPLRRLSENLKLHIERAPATWIEGQLIEY
+KTNRGNVYMTMRDLEEEYSLPVTAWRNVAVTFEGTVQQGSRVVARVKPNFWTKAGRLSMV
+VQEMRPVGLGDLLARVELLRRRLGEEGLLDPARKRPLPLLPGLVGLITGRDSDAKKDVLR
+NAQLRWPAVRFEVREVAVQGPEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS
+DEALVRAVAAARTPVVSAIGHEADRPVLDDVADVRASTPTDAAKRIVPDAAQEAAGIAEA
+RRRLAAAVERRVQREGEGLAQLRSRPVLADPVVMVDGREQDLHAWRERARRATAHRLTRE
+RDAVEHLVARVRALSPQQTLDRGYAVVQQEGRLIRDAAQVAPGEDVDILVASGRISAEVT
+AVRPGRVGGVGTVQDEDEQAGTKEQA
+>PROKKA_01170
+MEESAAREEGTVVVPATASETSPERPWPLHRLSENLKLHIERAPATWIEGQLIEHKNNRG
+NLYMTMRDLEEEVSLPLTAWRAVAAGIDPSVQQGSRVVARVKPNFWVKGGRLSMVVQEMR
+PVGLGDLLARVELLRRRLAEEGLTSPARKRQLPVLPGVIGLITGRDSDALKDVVRNTHLR
+WPAAVFEVREVAVQGPDAPRQVAAALAELDARPEVEVIVIARGGGALEEVVLPFSDEALV
+RAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQESVGIREARLRLA
+GAVERRVRGEADALAALRSRPVLAHPHVMVDTRTEDLGRWQERGRVALGHRLAREADAVS
+ALRAQVRALSPQQTLDRGYAVVQHAGHVVRRAEDVTPGDDLDVLVAAGRIEAYVTDVTPV
+ETPSPTQEDA
+>PROKKA_01563
+MDQPVTEGASAAPDVPVSAPARAGETSAERPWPLRRLSENLKAHIERAPATWIEGQLIEF
+KNNRGNVYMTMRDLEEEVSLPLTAWRNVAMTLDGTVQQGSRVVARVKPNFWLKAGRLSMN
+VQEMRPVGLGDLLARVELLRRALAEEGLTSPARKRPLPLLPHRIGLITGRDSDAKKDVLR
+NTLLRWPAAEFEIREVAVQGAEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS
+DEALVRAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQEAAGLADA
+RLRLAAAVERRVRAEAEGLAALRSRPVLARPHVMVDTRQEETDRWRERGRSALGHRLVRE
+EDALTQLRARVRALSPQRTLDRGYAVVQHAGQVVREADQVATDDRLDILVAAGRIAADVV
+ATHRTTPTPSHERTRQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001320.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001320.fa
new file mode 100644
index 0000000000000000000000000000000000000000..789e933d722565241de35f2afe7ba63dbff8c6bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001320.fa
@@ -0,0 +1,38 @@
+>PROKKA_01639
+MSRPAHRRPTALAASALALSLALGACARQADAPPTPSASGTPITVVHGGEGLEGAVAAVL
+ARHLRLHGHAVADEDGVAVEQPAWSAAGGDTVAVVDTLALAVAADPAVALPSPPPPTSTP
+SSTPTGTEAGPSADAVPTPSATASTAVPSPTALPVGDPAADAQAAGRVLETLLAEETAAA
+GTPQDEAPAVLSSSAGVLRLTAVVTQTTAARLELESITDLNGWCESLTAVAPPPLTAAAD
+PDAATALRARLDRLAGCRPETWLADTEDPSAALVADEAQVALLTDTDPEIDANTLVPLED
+DGRVLPEGRLTAVGSAATLDDDAERRIAEVMSALDGDGLRELERLTTGADPLPAAEAAQY
+WLVDHGLEDAPEDWFVPRGSWF
+>PROKKA_01344
+MSRPAHRRPTALAASALALSLALGACARQADAPPTPSASGAPITVVHGGEGLEAAVAAVL
+ARHLRLHGHAVADEDGVAVEQPAWSAAGGDTVAVVDTLALAAAADPAAALPSPPTPTPTP
+TPTGTEAGTSTGTVPTPSATASTAAPSPTALPVGDPAADAPAAGRVLETLLAGQTAAAGT
+PQDEAPAALSSSAGVLRLTAVVTQTTAARLELESITDLNGRCESLTAVAPPALTSAADAA
+TALRARLDRLAGCRPETWLADTEDPTAAVVADEAQVALLTGTDPEIDANTLIPLEDDGRV
+LPEGRLTAVGSAATLDDDAERRIAEVMSALDGDGLRELERLTTGADPLPVAEAAQYWLVD
+QGLEDAPEDWFVPRGSWF
+>PROKKA_01256
+MPTASESSDAADASATPEPTPLPDGEPAADAAEAGRVVERLLQGDAEAGASPEPGDAVAV
+LGSSAGVLRLSAVVTATTAARLELDALEDLNGRCEGLTAALPAGLAGDPQANAALHARLD
+RLAGCRPGTWREEDASAAAVVVADQAQLGLLSATDPEIPASMLVPLEDPERVLPEGRLAA
+VGAPDALDDDAQRRIEEVLSALDEDGLRELERITTGADALPPAEAARYWLVDQGLEDVPE
+GWFMPRDSWF
+>PROKKA_01165
+MTRPAERPRTSRVRAAAGASALSLALALSGCGAPRAGAPADPTGAPVTVVHTSDPLDSAV
+AAVVARHLRHRGHPVTLEDAGDATPWSAAAGDTVAVVDTLRLALQADPAAVLPPEPEDAA
+ASRAAAAPTPSESSLEPIDPSAPARVPATGSATPSPTPLASGLPAADADAAQAVVDAALS
+RVAAGADAAAPTPAASRSAATPTGPSPRVLADSAGTLRLAAVVTATTASREGLDSIDDLD
+GRCGDLTLAVPAALAAAVSDGLLAHRLDDFAGCRPADWRTDAADVGPAVVADAAQVGLTY
+RTDPDIPPNGLVLLEDPDRVLPEGRIAVVGERETLDDDAQSALGEVMDRLDDDGIAELAR
+LTEGGDALPADEAAQYWLVSQRLEDAPEDWVVPADPWF
+>PROKKA_01568
+MSRPAHRRPTALAASALALSLALGACARQADAPPTPSASGTPITVVHGGEGLEGAVAAVL
+ARHLRLHGHAVADEDGVAVEQPAWSAAGGDTVAVVDTLALAAAADPAAALPSPPSPTSTP
+SSTPTGTEAGTSADAVPTASTAAPSPTALPVGDPAADAPAAGRVLETLLAEETAAAGTPQ
+AEAPAVLSSSAGVLRLTAVVTQTTAARLELESITDLNGRCESLTAVAPPTLTAAADADAA
+TALRTRLDRLAGCRPETWLADTEDPTAAVVADEAQVALLTGTDPEIDANTLVLLEDDGRV
+LPEGRLTAVGSAATLDDDAERRIAEVMSALDGDGLRELERLTTGDDPLPVAEAAQYWLVD
+HGLEDAPEDWFVPRGSWF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001321.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001321.fa
new file mode 100644
index 0000000000000000000000000000000000000000..11664f255a0ebc189ea60be8e1b6684039678982
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001321.fa
@@ -0,0 +1,20 @@
+>PROKKA_01640
+MSTTPAAPDAAGAHPAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIELGES
+PEEACLREVWEETGHTAELTGLLGVTTGTIPVEKRLRGEPLPLLTVQVLYTARITGGVLR
+PEVGGSSTDARWFDLAELSELRTASWVTEALARAGVDT
+>PROKKA_01345
+MSTTPAAPDAAGAHPAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIELGES
+PEEACLREVWEETGHTAELTGLLGVTTGTIPVERRLRGEPLPLLTVQVLYTARITGGVLR
+PEVGGSSTDARWFDLAELSGLRTASWVTEALARAGVAT
+>PROKKA_01255
+MSPTPVPDAEPARADAPAGPFQTRAGAYALIVDGGRVLLSSWQGPEHLVWTLPGGGIELG
+ESPEEACRREVWEETGHTAELTGLLGVTTGVIPAERRLRGEALPLLTVQVLYTARITGGV
+LRPEVGGSSTDARWFDLAGLDAVRTAPWVREALARAGAAA
+>PROKKA_01164
+MSAASPTAASTAPGPFETRAGAYALIVEDGRVLMSAWAGPTGIVWTLPGGGIELGESPEE
+ACVREVEEETGHTAELTGLLGVTTGTIPVERRLRGEPLPLLTVQVLYTARLTGGVLRPEA
+DGSSVDAAWFALDGLADVRTSAWVDRALALAGLAADDAAGTAR
+>PROKKA_01569
+MSTTPAAPDAAGAHPAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIELGES
+PEEACLREVWEETGHTAELTGLLGVTTGTIPVEKRLRGEPLPLLTVQVVYTARITGGVLR
+PEVGGSSTDARWFDLAELSELRTASWVTEALARAGVDT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001325.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001325.fa
new file mode 100644
index 0000000000000000000000000000000000000000..83c99c4c58678e763e064569b2e755af0b1e9e95
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001325.fa
@@ -0,0 +1,25 @@
+>PROKKA_01644
+MSWQRSPWPVTLRHGTLALRPLRRRDREAWEEQRAHNREWLTPWDATSPVPGAGPASFGQ
+MVRWHGRQGRDGSAYTWGMALDDDRPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREAG
+RGLTPTAVAMATDWAFRSAGLHRVEVNIRPENAASLRVVAKLGLRDEGLRRAYLHVDGAW
+RDHRTFAVTAEEVPDGLLAGWLATRPRP
+>PROKKA_01349
+MSWQRSPWPVTLRHGTLALRPLRRRDREAWEEQRAHNREWLTPWDATSPVPGAGPASFGQ
+MVRWHGRQGRDGSAYTWGMVLDDDDRPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREA
+GRGLTPTAVAMATDWAFRSAGLHRVEVNIRPENAASLRVVAKLGLRDEGLRRAYLHVDGA
+WRDHRTFAVTAEEVPDGLLARWLASRPRA
+>PROKKA_01249
+MSWQRSPWPVTLRHGTLSLRPLRRRDRDAWEAQRAHNHAWLTPWDATSPVPGAGPSSFGQ
+MVRWHGRQGREGSSFTWGVALDDDAPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREAG
+RGLTPTAVAMAADWAFRSAGLHRVEVNIRPENAASLRVVEKLGLRDEGVRRSYLHVDGDW
+RDHRTFAITAEEVPEGLLARWLASRPRA
+>PROKKA_01160
+MDVSGSLWPVALRHGTLTLRPLRRGDRRAWEEQRAANRDWLTPWDATSPVPGAAPASFAQ
+MVRWQHRQARAGTSYTWGMALDDDAPGRDRLIGLLSLGGVQHGSVMSGAVGYWIDRRQAG
+RGLTPTAVAMATDWAFHGLGLHRVEVNIRPENTASLRVAEKLGLREEGLRRAYLHVDGAW
+RDHLSFAVTAEEVPEGLLPRWLARREAAAGTAEPRDTAHTPGVAGDVPGPSGR
+>PROKKA_01574
+MSWQRSPWPVTLRHGTLALRPLRRRDREAWEEQRAHNREWLTPWDATSPVPGVGPASFGQ
+MVRWHGRQGRDGSAYTWGMVLDDDRPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREAG
+RGLTPTAVAMATDWAFRSAGLHRVEVNIRPENAASLRVVAKLGLRDEGLRRAYLHVDGAW
+RDHRTFAVTAEEVPDGLLARWLATRPRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001328.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001328.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bd1d9e16cd645859594f0dba5fa92efa3c210f3e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001328.fa
@@ -0,0 +1,15 @@
+>PROKKA_01647
+MPADGAPRRRGPRRADAPGTGPASADGREPRLPGMPRLIGQAGTSPATAPTGDVAGVESG
+PAEAERDRWLREQRPPHWG
+>PROKKA_01352
+MSADGAPRRRGPRRADAPGTGPAAADGREPRLPGMPRLAGQAGTSPVTAPTGDVAGVESG
+AAEAERDRWLREQRPPHWG
+>PROKKA_01246
+MGAEVPDPAPRRRGPRRADAPGTGPASADAPEPRLPGVGAGTDGARGAEGVRGAGGVRGA
+VGVRGAAGEPTADERDRWLLEQRPPHWG
+>PROKKA_01157
+MRTTPTASPEPGRRRGHRRADAAGTGPASADGPEPTLPEPTLPGPALPGAQTAGDATPSR
+PAVSRGRAVTSAAGADRPQPADELGRWLLEQRPPHWG
+>PROKKA_01577
+MSADGAPRRRGPRRADAPGIGPAAADGREPRLPGMPRLAGTSPATAPTGDAAGVESGPAE
+AERDRWLREQRPPHWG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001330.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001330.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c8da3067ebda1883b5d7322d619e4bcd714b6b5e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001330.fa
@@ -0,0 +1,50 @@
+>PROKKA_01649
+MTQNAPHPDTPAPLSDVMPTVLVLDFGAQYAQLIARRVREANVYSEVVPASTPAAQILER
+KPAALILSGGPSSVYEPGAPQLDPALLEAGVPVLGLCYGFQSIAHALGGTVAQTGTREYG
+STRLDSVDADSVLFAGQDLEQVVWMSHGDAVTQAPEGFAVTASTAGAPVAAFEDRERRIY
+GVQWHPEVGHSSHGQRVLEQFLHVGAGLGADWTVSNVIEEQVERIREQIGDKRAICGLSG
+GVDSAVAAALVQRAIGDRLTCVYVDHGLMREGESAEIEQAFGEAHGGARLVMVDAREDFL
+SALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESEHDPDATEVRFLVQGTLYPDVVESG
+GGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG
+LGIRIIGEVTQERLDLLRRADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY
+GHPVVLRPVTSEDAMTADWARIPDDVLSRISNRITNEVDGVNRVVLDVTSKPPGTIEWE
+>PROKKA_01354
+MTQNAPHPDTPAPLSDVMPTVLVLDFGAQYAQLIARRVREANVYSEVVPASTPAAQILER
+KPAALILSGGPSSVYEPGAPQLDPALLEAGVPVLGLCYGFQSIAHALGGTVAQTGTREYG
+STRLDSVDADSVLFADQDLEQVVWMSHGDAVTQAPEGFAVTASTAGAPVAAFEDRERRIF
+GVQWHPEVGHSSHGQRVLEQFLHVGAGLGADWTASGVIEEQVERIREQIGDKRAICGLSG
+GVDSAVAAALVQRAIGDRLTCVYVDHGLMREGESAEIEQAFGEAHGGARLVMVDAREDFL
+SALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESEHDPDATEVRFLVQGTLYPDVVESG
+GGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG
+LGIRIIGEVTQERLDLLRRADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY
+GHPVVLRPVISEDAMTADWARIPDDVLSRISNRITNEVDGVNRVVLDVTSKPPGTIEWE
+>PROKKA_01244
+MTENAPHSDAPAPLSDVMPTVLVLDFGAQYAQLIARRVREANVYSEVVPASTPAAQILER
+RPAALILSGGPSSVYEPGAPTLDPALLEAGVPVLGLCYGFQSIAHALGGTVAKTGTREYG
+STRLDSVDADSVLFAGQDLEQVVWMSHGDAVTQAPEGFAVTASTAGAPVAAFEDAERRIY
+GVQWHPEVGHSSHGQQVLEHFLHQGAGLGSDWTASNVIEEQVERIREQIGDKRAICGLSG
+GVDSAVAAALVQRAIGDRLTCVYVDHGLMRQGESAEIEQAFGEAHGGARLVMVDAREDFL
+SALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESEHDPEATEVRFLVQGTLYPDVVESG
+GGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG
+LGIRIIGEVTQERLDLLRSADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY
+GHPIVLRPVTSEDAMTADWARIPDDVLSRISNRITNEVDGVNRVVLDVTSKPPGTIEWE
+>PROKKA_01155
+MTQNEPTRDQPAPLHDVLPTVLVMDFGAQYAQLIARRVREANVYSEVVPSSTPAQEILDR
+RPAALILSGGPSSVYEAGAPQLDPALLEAGVPVLGLCYGFQSIAHALGGTVARTGTREYG
+STRLESADGGSVLLAGQDAAQVVWMSHGDAVTEAPEGFAVTAVTAGAPVAAFEDRERRIF
+GVQWHPEVGHSERGQEILANFLTEGAGLSQDWTAENVIEEQVARIREQIGDARAICGLSG
+GVDSAVAAALVQRAIGDRLTCVYVDHGLMRQGESDEIERAFGEAHGGAKLVMVDAREDFL
+AALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESAHDPNAPEVRFLVQGTLYPDVVESG
+GGDGTANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG
+LGIRIIGEVTQERLDLLRQADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY
+GHPVVLRPVTSEDAMTADWARIPSEVLSRISNRITNEVDGINRVVLDVTSKPPGTIEWE
+>PROKKA_01579
+MTQNAPHPDTPTPLSDVMPTVLVLDYGAQYAQLIARRVREANVYSEVVPASTPAAQILER
+EPAALILSGGPSSVYEPGAPQLDPALLEAGVPVLGLCYGFQSIAHALGGTVAKTGTREYG
+STRLDSVDADSVLFADQDLEQVVWMSHGDAVTQAPEGFAVTASTAGAPVAAFEDRERRIY
+GVQWHPEVGHSSRGQRVLEQFLHVGAGLGADWTASGVIEEQVERIREQIGDKRAICGLSG
+GVDSAVAAALVQRAIGDRLTCVYVDHGLMREGESAEIEQAFGEAHGGARLVMVDAREDFL
+SALAGVTDPEAKRKIIGERFIRTFEKAQADIVLESEHDPDATEVRFLVQGTLYPDVVESG
+GGDGAANIKSHHNVGGLPDDIEFELCEPLRELFKDEVRAVGAELGLPEGIVHRQPFPGPG
+LGIRIIGEVTQERLDLLRRADAIVRAELTAAGLDRQIWQCPVVLLADVRSVGVQGDGRTY
+GHPVVLRPVTSEDAMTADWARIPDDVLSRISNRITNEVDGINRVVLDVTSKPPGTIEWE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001334.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001334.fa
new file mode 100644
index 0000000000000000000000000000000000000000..400b74f7ee49425e05ba52f10722cb457616cd8e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001334.fa
@@ -0,0 +1,50 @@
+>PROKKA_01653
+MARTRVAGLTPGHRIAETPVPKGVFVTTTSTGPSPEPVHSSSDPFGFFGLTYDDVLLLPN
+ATDVIPADADPGTRLTRNIRLNIPIVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQ
+ARHVDTVKRSESGMIKDPVTIGPDATLADLDELCAQYRVSGLPVVAEDMTLLGIITNRDT
+RFIPREEWATRTVDTAMTRMPLVTAQEGVSRAETIRLFSQNRVEKLPLVDDAGRLTGLIT
+IKDFDKAEQYPDAAKDDEGRLRVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGV
+LDMIARLKKEKAAAHVDVIGGQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGV
+PQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGADSVMLGSLLAGTAESPGDLV
+FYQGKQFKTYRGMGSLGAMQTRNGTRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPVA
+SVVHQLVGGLRQTMFYTGASTVTDLKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR
+>PROKKA_01358
+MARTRVAGLTPGHRIAETPVPKGAFVTNTSTGPSPEPVHSSSDPFGFFGLTYDDVLLLPN
+ATDVIPADADTGTRLTRNIRLNIPIVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQ
+ARHVDTVKRSESGMIKDPVTIGPDATLADLDELCAQYRVSGLPVVAEDMTLLGIITNRDT
+RFIPREEWATRTVDTAMTRMPLVTAQEGISRAETIRLFSQNRVEKLPLVDDAGRLTGLIT
+IKDFDKAEQYPDAAKDDEGRLLVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGV
+LDMIARLKKEKAAAHVDVIGGQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGV
+PQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGADSVMLGSLLAGTAESPGDLV
+FYQGKQFKTYRGMGSLGAMQTRNGTRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPIA
+SVVHQLVGGLRQTMFYTGASTVADLKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR
+>PROKKA_01240
+MARTRVAGLTPGHRIAETPVPKGAFVTTTSTGPSSEPVHSSADPFGFFGLTYDDVLLLPS
+ATDVIPAEADTSTQLTRNIRLNIPVVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQ
+ARHVDTVKRSESGMIKDPVTIGPKATLADLDELCAQYRVSGLPVVAEDMTLLGIITNRDT
+RFIPHEEWETRTVDTAMTRMPLITAREGISREETIRLFSQNRVEKLPLVDEAGRLTGLIT
+IKDFDKAEKYPDAAKDDEGRLRVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGV
+LDMIARLKKEKAAAHVDVIGGQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGV
+PQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGAESVMLGSLLAGTAESPGDLV
+FYQGKQFKAYRGMGSLGAMQTRNGKRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPIA
+SVVHQLVGGLRQTMFYTGASTVDELKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR
+>PROKKA_01151
+MSTSTGPSSDPVYASEDPFGFFGLTYDDVLLLPNATDVIPADADTSTQLTRNIRLNIPVV
+SAAMDTVTEAPLAIAIARQGGMGIIHRNLSIEDQAKHVDTVKRSESGMISDPVTIGPKAT
+LAELDELCAQYRVSGLPVVAEDMTLLGIITNRDTRFIPHEEWDTRTVDTAMTRMPLITAQ
+DGISREEVLHLFSQNRVEKLPLVDDAGRLTGLITIKDFDKAEKYPDAAKDDEGRLRVGGA
+VGFFGDGWERAMTLVEAGVDALVVDTANGHTHGVLDMIARLKKEKAAAHVDVIGGQAATY
+AGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGVPQITAIYEAAKATRPAGVPLIADGGL
+QHSGDIGKALVAGADSVMLGSLLAGTAESPGDLVFYQGKQFKAYRGMGSLGAMQTRNGTR
+SFSKDRYFQADVPDEDKLIPEGIEGQVPYRGPIASVVHQLVGGLRQTMFYTGAPTIVDLK
+ENGRFVRITTAGLKESHPHDIMMTVEAPNYRSK
+>PROKKA_01583
+MARTRVAGLTPGHRIAETPVPKGAFVTNTSTGPSPEPVHSSSDPFGFFGLTYDDVLLLPN
+ATDVIPADADTGTRLTRNIRLNIPIVSAAMDTVTEAPLAIAMARQGGMGIIHRNLSIEDQ
+ARHVDTVKRSESGMIKDPVTIGPDATLADLDELCAQYRVSGLPVVAEDMTLLGIITNRDT
+RFIPREEWATRTVDTAMTRMPLVTAQEGISRAETIRLFSQNRVEKLPLVDDAGRLTGLIT
+IKDFDKAEQYPDAAKDDEGRLLVGGAVGFFGDGWERAMALVEAGVDALVVDTANGHTHGV
+LDMIARLKKEKAAAHVDVIGGQAATYAGAKAIVDAGADAVKVGVGPGSICTTRVVAGVGV
+PQITAIYEAAKATRPAGVPLIADGGLQHSGDIGKALVAGADSVMLGSLLAGTAESPGDLV
+FYQGKQFKTYRGMGSLGAMQTRNGTRSFSKDRYFQADVPDEDKLIPEGIEGQVPFRGPVA
+SVVHQLVGGLRQTMFYTGASTVADLKENGRFVRITAAGLKESHPHDIMMTVEAPNYRSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001339.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001339.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb05bc27dec79451e16d41b03b234b422c708eee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001339.fa
@@ -0,0 +1,35 @@
+>PROKKA_01661
+MTLDVRHHVADAPPRLEEPGRGDRVCWVPPAVLRPERTRWQRTWPLLVGVVVTAALIVVS
+LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE
+WAGLGLLVTMVLVPGAGLVTRMAGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA
+VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFVIADRFTVAGL
+GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRMNL
+PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG
+>PROKKA_01366
+MILDVRHHVADAPPRLEEPGRGDRVCWVPPAVLRPERTRWQRTWPLLAGIVVTAVLVVVS
+LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE
+WAGLGLLVTMVLVPGAGLVTRMAGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA
+VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFVIADRFTVAGL
+GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRTNL
+PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG
+>PROKKA_01233
+MTDLHPGVADARTRLPEPGPGERVCWVPPTVLRPQRSRWQRTWPLLAGVAVTVLLAVVSL
+FVGVYDVGAEGGREMFAITRVPRTVALVLAGAAMAMCGLIMQLMTQNRFVEPSTTGTTEW
+AGLGLLVTMILIPGASIVTRMTGAVLFAFVGTMVFFLFLRRVRLQSSLIVPIVGIMLGAV
+VGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLVVCVAVFVIADRFTVAGLG
+KDVATNVGLNYNAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNIVSMVRGDNLRTNLP
+WVVMVGIWVVIVCDLIGRTVIAPFEVPISLILGLVGAVVFLGLLIRQAKHG
+>PROKKA_01144
+MTLDVRHHVADAPPRLEEPGRGDRVCWVPPAVLRPERTRWQRTWPLLVGVLVTAALIVVS
+LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE
+WAGLGLLVTMVLVPGSGLVTRMVGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA
+VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFVIADRFTVAGL
+GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRTNL
+PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG
+>PROKKA_01591
+MILDVRHHVADAPPRLEELGRGDRVCWVPPAVLRPERTRWQRTWPLLVGVVVTAALIVVS
+LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE
+WAGLGLLVTMVLVPGAGLVTRMVGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA
+VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFLIADRFTVAGL
+GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRTNL
+PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001340.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001340.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a679e72df83f80b2638abd0a8b14d0fc94a147e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001340.fa
@@ -0,0 +1,36 @@
+>PROKKA_01662
+MPRSVSAPRLARLALTSVAALALVGCSAGGAATGSSSASASGESSASASAAGGSSAASGG
+IAAGVTVTDMSGAEVTLPEEVDSVIATDNRAFRTLDDWGVELSAAPKQIMYKGEGGPSYL
+QDDSVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAAVVDTDFDVTQTP
+MDEGLKELTTLLGEATGHEADAEKLIADFDAATQRAKDAYDPEQTVMGLIASGGELSYVA
+PSTGRAIGPFFDMLELTPALEQSGTDNHQGDDISVEAIAKSNPDWLIVMDRDAAIGEENA
+TAAELIERSEALQDVTAVKEGNIVYLPADFYVAEDIQNHTTVMEDLAKAFEGAQ
+>PROKKA_01367
+MPSSARAPRLARLALTSVAALALVGCSAGGAATGSSSASASGESSASASASGESSASASA
+AGGSSAASGGIATGVTVTDMSGAEVTLPEEVDSVIATDNRTFRTLDDWGVELSAAPKQIM
+YKGEGGPSYLQDDSVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAAVV
+DTDFDVTQTPMDEGLKELTTLLGEATGHEADAEKLIADFDAATQRAKDAYDPEQTVMGLI
+ASGGELSYVAPSTGRAIGPFFDMLELTPALEQSGTDNHQGDDISVEAIAKSNPDWLIVMD
+RDAAVGEENATAAELIERSEALQDVTAVKEGNIVYLPTDFYVAEDIQNHTTVMEDLAKAF
+EGAQ
+>PROKKA_01232
+MQRSPRTPRLKALALASVAALALVGCSAGGAAEGPASGSADTGSAAGSGSASAPAGDGVA
+AGATVTDMSGAEITLPEEIDSVITTDNRTFRTLDEWGVELSAAPKQLMFKGEGGPGYLQD
+DEVADIGNHREPDMEVFVTAEPDVVFNGQRFNERKAEIDELTGDAAVIDTDFDPKQKPMD
+EGLKELTTLLGEATGHQDDAAALNKEFDDAVAKAKGAYDSEQTVMGLISTGGELSYVAPG
+TGRSIGPMFDILGLTPALEQAGSDNHQGDDISVEAIAQSNPDWLIVMDRDAATGEANATA
+AELIERSEALKDVTAVKEGNIVYLPQDFYVAEDIQNYTTVMDDLAKAFEGAR
+>PROKKA_01143
+MRTARLSTAAALASLAALTLAGCGAGGPAAEGSSPASSAASSSPASSAASSSATAGGVAA
+GVTVTDMSGTEVTLPEEVDSVIATDNRIFRTLDDWGVELSAAPKQIMYKGEGGPSYLQDD
+SVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAAVVDTNFDVTQTPMDE
+GLKKLTTLLGEATGHEADAEKLIADFDAATQLAKDAYDPEQTVMGLIASGGELSYAAPST
+GRSIGPFFDMLDLTPALDQSGTDNHQGDDISVEAIAKSNPDWLIVMDRDAAVGEENATAA
+ELIERSEALQDVTAVKEGNIVYLPADFYVSEDIQNHTTVMEDLAKAFEGAQ
+>PROKKA_01592
+MPRSARAPRLARLALTSVAALALVGCSAGGAATGSSSASASGESSASASASGGSSAASGG
+IATGVTVTDMSGAEVTLPEEVDSVIATDNRIFRTLDDWGVELSAAPKQIMYKGEGGPSYL
+QDDSVADIGNHREPDMELFVTAEPDVVFNGQRFNERKAEIDELTGDAAVVDTNFDVTQTP
+MDEGLKELTTLLGEATGHEADAEKLIADFDAATQRAKDAYDPEQTVMGLIASGGELSYVA
+PSTGRAVGPFFDMLELTPALEQSGTDNHQGDDISVEAIAKSNPDWLIVMDRDAAIGEENA
+TAAELIERSEALQDVTAVKEGNIVYLPADFYVAEDIQNHTTVMEDLAKAFEGAQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001341.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001341.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa2382ed158d9397190068c3735648bf5bbc796c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001341.fa
@@ -0,0 +1,43 @@
+>PROKKA_01663
+MARPRPAARPSRPSAAASEEDDTALAPVLESEGRALLDSLAGYREADALAVSSRLRAAGH
+PPERVAAALTQAALRSRAEARLGPEARRMLFTRDGLEQATRPLVAGLHADRLAAAGARRV
+ADLGCGLGLDARAFADRGLDVVAVERDAVVAAAAEVNLAGHRGARVVHGDAVAWARAHVP
+AEADAVWLDPARRQVGGGGSARVFDPEAFSPPLSVVTDIAATGVPVGVKLGPGLPHEAVP
+AGAEAEWVSVDGDVVEAALWFNAAARPGVRRAARVMTVHGGKTTTAQLVSGADFGDSPEV
+EAVGEEGMAGLVGAVLHEPDGAVIRAGLVTDLAVSWPVPTRQLDPHLAYLVAPEPVHDGL
+ARAHRIEAVHGFHLASLRRWAKETGVGRLDVKKRGIRETPEEVRRAVLGGAKPGRRGGAG
+RHATLVLARVGRSRFALEVTPLD
+>PROKKA_01368
+MARPRPASRSPRPTAAASEADDTALAPVLEPEGRALLDSLAGYREADALAVSSRLRAAGH
+PPERVAAALTQAALRSRAEARLGPEARRMLFTRDGLEQATRPLVAGLHADRLAAAGARRV
+ADLGCGLGLDARAFADRGLDVVAVERDAVVAAAAEVNLAGHRGARVVHGDAVAWARAHVP
+AEADAVWLDPARRQVGGGGSARVFDPEAFSPPLSVVTDIAATGVPVGVKLGPGLPHEAVP
+EGAEAEWVSVDGDVVEAALWFNAAARPGVRRAARVMTVRGGETTTAQLVSGADFGDSPEV
+EAVGEEGMAGLVGAVLHEPDGAVIRAGLVTDLAASWPVPTRQLDPHLAYLVAPEPVRDGL
+ARAHRIEAVHGFHLASLRRWAKETGVGRLDVKKRGIRETPEEVRRAVLGGAKPGRRGGAG
+RHATLVLARVGRSRFALEVTPLD
+>PROKKA_01231
+MLTQADLRARAVPRLGPDARGMLFTRDGLEQATRPVVAALHAQRMAAAGARTVADLGCGL
+GLDARAFADAGLGVVAVERDAVVAAAAEVNLTDRPGARVVHGDAVPWAREHVPAQADAVW
+LDPARRQVGGGGSARVFDPEAFSPPLSVVEELAATGVPVGVKLGPGLPHEAVPAGAEAEW
+VSVDGDVVEAALWFNAAARPGVRRAARVIDTRGGQATTAELVSGADFGDSPGVEAVGEEG
+MPGLVGRCSTSRTAPSSGPGSSRTWRSPGRRRPASWTRTWPIWWPPSTRPTRWPGRTGST
+RSTISTSSLCAGGRRRRGSAAWT
+>PROKKA_01142
+MARSQRPARPSRPRPRPADRPGRPRAAESAADATRLEPVLDPAGRVLLDGLGDVSGQDPL
+ALSSRLRAAGHDADTVAAALTQAGLRHAGRAKLGALADGMLLTRDGLEQATRAVVAEHRA
+RRLQEAGVRSLADLGCGIGADALVYARAGLDVTAVERDPTVAAAAAANLATLAPAGAASV
+VTGDAEAWAAAHADEVDALWLDPARRRLGSSGTARVFDPEAFSPPLSFVLGLADGGRPVG
+VKLGPGLPHEHVPAAAEAEWVSVDGDVVEVTLWFGPLAQAPGRRTATLLDTRGSAVHRLV
+PAAASSPAVEAVGEEGVDGLVGQVLLEPDGAVIRAGLVTDLAVELGPAVRLLDPHLAYLV
+APDAAPHPLARGYRVLAVHEFRTKALARWARETGVGRLDVKKRGVRETPEQVRAAVLGRG
+TPGGRHATLVLARVGERRVAFEVEPLPAG
+>PROKKA_01593
+MARPRPASRSPRPTAAASEADATALTPVLEPEGRALLDSLAWYREADALAVSSRLRAAGH
+PPERVAAALTQAALRSRAEARLGRQARRMLFTRDGLEQATRPLVAGLHADRLAAAGARCV
+ADLGCGLGLDARAFADRGLDVVAVERDAVVAAAAEVNLAGHRGARVVHGDAVAWARAHVP
+AEADAVWLDPARRQVGGGGSARVFDPEAFSPPLSVVTDIAATGVPVGVKLGPGLPHEAVP
+AGAEAEWVSVDGDVVEAALWFNAAARPGVRRAARVMTVRGGETTTAQLVSGADFGDSPEV
+EAVGEEGMAGLVGAVLHEPDGAVIRAGLVTDLAASWPVPTRQLDPHLAYLVAPEPVHDGL
+ARAHRIEAVHGFHLASLRRWAKETGVGRLDVKKRGIRETPEEVRRAVLGGAKPGRRGGAG
+RHATLVLARVGRSRFALEVTPLD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001342.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001342.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4771ccc19b404eab9a39f5d79e02823e5b642710
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001342.fa
@@ -0,0 +1,40 @@
+>PROKKA_01664
+MTLPFADSAQSTLGIEWELALVDAVSGELRSEAPDLLRALHVTEGLAEDDVNPHMTSELL
+QNTVELVTGVHERVDAATADLGRIAARVADAAAERGISLFCQGTHPFADAIAQPSTPSER
+YDRMLDLTQYWGRQLLIFGVHVHVGLDDVSKAMPVVNGLVNRVPHLLALSASSPFWAGTD
+TGYQSQRTLLFQQLPTAGLPFQFQEWEGFERCVAQMEQVGMIADVTECRWDVRAVPRLGT
+VEMRACDGLATLEEIAAVTAYTQCLVDDLSASLERGETVEVLPPWHVQENKWRAARYGMD
+ATVIVDARGTQVPLAEHLPAEIERLTPVAERLGCAAELAGVQAMIDDGGAARQRRVEAQA
+LAGPPAAGEDADDAVAPLRAVVLDAAARTRASLDGRAG
+>PROKKA_01369
+MTLPFADSAQSTLGIEWELALVDAVSGELRSEAPDLLRTLHATEGLAEDDVNPHMTSELL
+QNTVELVTGVHERVDAATADLGRIAARVADAAAARGISLFCQGTHPFADAIAQPSTPSER
+YDRMLDLTQYWGRQLLIFGVHVHVGLDDVSKAMPVVNGLVNRVPHLLALSASSPFWAGTD
+TGYQSQRTLLFQQLPTAGLPFQFQEWEGFERCVAQMEQVGMIADVTECRWDVRAVPRLGT
+VEMRACDGLATLEEIAAVTAYTQCLVDDLSASLERGETVEVLPPWHVQENKWRAARYGMD
+ATVIVDARGTQVPLAEHLPAEIERLTPVAERLGCAAELAGVQAMIDDGGAARQRRVEAQA
+LAGPPAAGEDTDDAVAPLRAVVLDAAARTRASLDGRTG
+>PROKKA_01230
+MNLPFADSTQSTLGIEWEVALVDAATGDLRSEAPAILHELHKEAGLAEGEDHPHVTGELL
+QNTVELVTGVHEAVPTAVAELGTIAARVARAAADRGLALYCQGTHPFGEAMTQPITPKER
+YGRMVDLTQYWGRQMLIFGVHVHVGLDDPAKAMPAVNRLISRFPHLLALSASSPFWVGAD
+TGYQSQRTQLFQQLPTAGLPFQFETWAEFEACVQQMTDVGMVEDVTECRWDVRAVPRLGT
+VEMRACDGMATLEEIAAVAAYTQCLVHELSADVERGRHMEILPPWYTQENKWRASRYGMD
+ATVIVDAAGTQVPLAEHLGADLERLAPIAEELGCAAELAHARVLMEHSPADRQRAVEAEA
+LAGPPAEGESAHDAAAPLRAVVLDAAARTRESLERVGG
+>PROKKA_01141
+MSLPFADSAQSTLGIEWELALVDPLTGDLRSEAPGILEELRAEAGLDADADHPHVTGELL
+QNTVELVTGVHGSVPDAVADLGGIAARVQRAAADRGLALFCQGTHPFGEAMTQPITPKAR
+YGRMVDLTQYWGRQMLIFGVHVHIGLDDRAKAMPAVNRLISRLPHLLALSASSPFWVGAD
+TGYQSQRTQLFQQLPTAGLPFQFETWEGFEHCVEQMTGVGMVEDVTECRWDVRAVPRLGT
+VEMRVCDGMATLEEIGAVAAYAQCLVHELSAQVEDDEPVAILPPWYTQENKWRAARYGLE
+ATVITDDAGTQVPLAEHLAADLERLAPVAEELGCAAELAHARVLMEHSPADRQRRVAAEA
+AAGPPRTGEDPADPVAPLRAVVRDAADRTRESLRAFQG
+>PROKKA_01594
+MTLPFADSAQSTLGIEWELALVDAVSGELRSEAPDLLRALHVTEGLAEDDVNPHMTSELL
+QNTVELVTGVHERVDAATADLGRIAARVADAAAERGISLFCQGTHPFAEAIAQPSTPSER
+YDRMLDLTQYWGRQLLIFGVHVHVGLDDVSKAMPVVNGLVNRVPHLLALSASSPFWAGTD
+TGYQSQRTLLFQQLPTAGLPFQFQEWEDFERCVAQMEQVGMIADVTECRWDVRAVPRLGT
+VEMRACDGLATLEEIAAVTAYTQCLVDDLSASLERGETVEVLPPWHVQENKWRAARYGMD
+ATVIVDARGTQVPLAEHLPAEIERLTPVAERLGCAAELAGVQAMIDDGGAARQRRVEAQA
+LAGPPAAGEDADDAVAPLRAVVLDAAARTRTSLDGRTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001343.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001343.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6cd472497897d1f2ca19bbea9797edd7ff8bb798
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001343.fa
@@ -0,0 +1,40 @@
+>PROKKA_01665
+MRALTWQGKRNVVVEDVPDPRIQEPTDAIIEVTSTGICGSDLHLYEVLGPFMDAGDVIGH
+EPMGIVREVGSEVTHIRPGDRVVVPFTISCGRCWMCQRGLQSQCETTQVREQGCGAALFG
+YSRLYGSVPGGQAELLRVPHADYGPVKVPHTGPDEQWLFLSDVVPTAWQGVQYANVPDGG
+TLAVLGLGPIGQLAARIGVHLGYRVIGVDPVPERRAMAARHGIEVLDADGGEAEVLRERT
+GGRGPDAVLDAVGMEAHASPVGHAAHTAVGLLPDALGRAAMKTAGVDRLSALHTAIDAVR
+RGGTVSISGVYGGMKDPMPMLTLFDKQVTLTMGQCNVRRWVDDLLPLLDDPSDPLGVLDL
+TTHTAPLEDAPALYETFQKKEDGCVKVVLKP
+>PROKKA_01370
+MRALTWQGKRNVAVEDVPDPRIQEPTDAIIEVTSTGICGSDLHLYEVLGPFMDAGDVIGH
+EPMGIVREVGSEVTHIRPGDRVVVPFTISCGRCWMCQRGLQSQCETTQVREQGSGAALFG
+YSRLYGSVPGGQAELLRVPHADYGPVKVPHTGPDEQWLFLSDVVPTAWQGVQYANVPDGG
+TLAVLGLGPIGQLAARIGVHLGYRVIGVDPVPERRAMAARHGIEVLDADGGEAEVLRERT
+GGRGPDGVVDAVGMEAHASPAGHAAHTAVGLLPDALGRAAMKTAGVDRLSALHTAIDAVR
+RGGTVSLSGVYGGMKDPMPMLTLFDKQVTLTMGQCNVRRWVDDLLPLLDDPSDPLGVLDL
+ATHTAPLEDAPALYETFQKKEDGCIKVVLKP
+>PROKKA_01229
+MRALTWQGKRNVAVEDVPDPRIQEPTDAIVEITSTGICGSDLHLYEVLGPFMDAGDVIGH
+EPMGIVREVGAEVTHIKPGDRVVVPFNIACGRCWMCERGLQSQCETTQVREQGSGAALLG
+YSRLYGSVPGGQAEYLRVPHADYGPVKVPHTGPDEQWLFLSDVVPTAWQGVQYAQVPRGG
+TLAVIGLGPIGQLAARIGVHQGLRVIGVDPVPERRAMAARHGVEVLDSSDGGVAELLREC
+TQGRGPDGVVDAVGMEAHGSPVAKAAHTVVGLLPDALGRAAMKTAGVDRLDALHTAIDAV
+RRGGTVSLSGVYGGMQSPMPLLTMFDKQVTLAMGQCNVRRWVDDLLPLLDDPSDPLGVLD
+LTTHTAPLEDAPALYETFQKKEDGCIKVVLKP
+>PROKKA_01140
+MRALTWQGKRSVSVEDVPDPRIQEPTDAIIKVTSTGICGSDLHLYEVLGPFMDKGDVIGH
+EPMGIVEEVGSAVTNLSPGDRVVIPFNISCGHCWMCQHGLQSQCETTQVKEQGSGAALLG
+YSRLYGSVPGGQAEYLRVPHADYGPIKVPHTGPDTQWLFLSDVVPTAWQAVQYANVSKGD
+TLAVLGLGPIGQMSARIGVHLGCRVIAVDPVPERRHMAARHGVEVLDMEGSGTGVPDLLR
+QATGGRGPDGVVDAVGMEAHGAPVAAAAQTAAGMLPGPLARAAVKTSGIDRLTALHTAIE
+SVRRGGTVSLSGVYGGMQDPMPLLTMFDKQIQFTMGQCNVRRWVDDLLPLMDDPSDPLGV
+LDLVTHTAPLEDAPAMYEKFQKKQDGCIKVVLTP
+>PROKKA_01595
+MRALTWQGKRNVTVEDVPDPRIQEPTDAIIEVTSTGICGSDLHLYEVLGPFMDAGDVIGH
+EPMGIVREVGSEVTHIRPGDRVVVPFTISCGRCWMCQRGLQSQCETTQVREQGSGAALFG
+YSRLYGSVPGGQAELLRVPHADYGPVKVPHTGPDEQWLFLSDVVPTAWQGVQYANVPDGG
+TLAVLGLGPIGQLAARIGVHLGYRVIGVDPVPERRAMAARHGIEVLDADGGEAEVLRERT
+SGRGPDGVVDAVGMEAHASPAGHAAHTAVGLLPDALGRAAMKTAGVDRLSALHTAIDAVR
+RGGTVSLSGVYGGMKDPMPMLTLFDKQVTLTMGQCNVRRWVDDLLPLLDDPSDPLGVLDL
+TTHTAPLEDAPALYETFQKKEDGCIKVVLKP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001345.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001345.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9871e720806b2e110f4f8a2e6c260589932e7374
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001345.fa
@@ -0,0 +1,20 @@
+>PROKKA_01667
+MRTRTLTRRAALTGLLGSAALGFTACTSSGYPADPDGTLDRVTGGVLRVGVVHHPPHVDV
+SGAEPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHA
+SITRDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR
+>PROKKA_01372
+MTITRRAALAGLLGGAALGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDASGA
+EPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHASIT
+RDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR
+>PROKKA_01227
+MTITRRAALTGLLGGAVLGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDASGA
+EPVGPEPDLIRGFAAAHDAEIAWTVSGEEALLTALEKGDVDLVAGGLTSDSPWTTHASLT
+RDYAEAAGPDGEPVKLVMAVPPGENQMLAALEAHLDAQAREAGR
+>PROKKA_01138
+MQTPRRTLLTGALAAAGVVLTGCTSSGYPADPDGTLDRITGGTLRVGASHHPPHVDAAGA
+EPQGPEPDLVRAFAAERDARVEWTVSGEEALMTALKQGDLDLVVGGLTKKSPWTTDAGLT
+RPYAETTGPDGEKAELVMAVPLGENQFQSALERFLDAHGEEAGA
+>PROKKA_01597
+MTITRRAALAGLLGGAALGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDASGA
+EPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHASIT
+RDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001346.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001346.fa
new file mode 100644
index 0000000000000000000000000000000000000000..587ce0700fa41fa10d14b467101c7ffb23e6f471
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001346.fa
@@ -0,0 +1,35 @@
+>PROKKA_01668
+MTRRDTRETGPSGRRFGATELPPEIERVVQQAKRLEWATLGVIVVTIVLVAFVMGSSQAM
+RAAWIEDLLSLIPPIAFLVALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLVG
+DSLLGLVTAEHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLKLAEQLHDRVL
+YADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAILVGVSIVLDGWKNLKEAVTNLAD
+RRAATIDGARPHPLIDRAERVAWAEPWVRHAGARVRDEGHVFHVEMFVVPHEGADVTVAR
+CCALRDAIAALDWKLQDVVVAPVDELPAEVHGGRSGEHQTGEE
+>PROKKA_01373
+MTRQDTRETGPSGRRFGATELPPEIERVVQQAKRLEWVTLGVIVVTIVLVAIVMGSSQAM
+RAAWIEDLLSLIPPIAFLIALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLVG
+DSLLGLVTAEHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLTLAEQLHDRVL
+YADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAIFVGVSIVLDGWKNLKEAVTNLAD
+RRATTIDGARPHPLIDRAERVAWAEPWVRHAGARVRDEGHVFHVEMFVVPHEGADVTVAR
+CCALRDAIAALDWKLQDVVVAPVDELPAEVHGGRSGEHQTGEE
+>PROKKA_01226
+MTHHASTTHRSPGGRRFGATELPPEIERALRRAVRLEWATLAVLAVTIALVAVVMGSSQA
+MRAAWIEDLLSLVPPIAFLVAVRVTRRHPTRARPYGSHRSVGVGHLVAAVALSVMGVILV
+ADSALGLVTGEHPPIGTLDLFGHTVWQGWFMMAVMALSIPGPVLLGRAKLKLAEQLHDRV
+LYADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAIFVGVSIVLDGWRNLREAVGNLA
+DRRATTIDGDRPHPLIDRAERVAWAQPWVRHAGTRVRDEGHVLHVEMFVVPHEGAGATVG
+RCAQLREEIVALDWKLEDVVVVPVAELPAEVHGGASGDEQSGEE
+>PROKKA_01137
+MSEKRTIGRAELPDDVARAAHQAVVLEWVSLGWLVLTVSLVAVVMGSSQAMRAAWIEDLL
+SLIPPIAFLVALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLVGDSLLGLLTA
+EHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLKLAEQLHDRVLYADADMNKA
+DWQTGVATIVGVAGIGLGWWWADAAAAIFVGVSIVLDGWKNLKEAVTNLADRRATTIDGA
+RPHPIIDRAERVAWAQPWVRHAGARVRDEGHVFHLEMFVVPRHGADVTVGRCADLRERIE
+ELDWKLEDVVVVPVAELPEEVHGGRSGDEQSKGSE
+>PROKKA_01598
+MTRRDTRETGPSGRRFGATELPPEIERVVQQAKRLEWATLGVIVVTIVLVAIVMGSSQAM
+RAAWIEDLLSLIPPIAFLVALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLVG
+DSLLGLVTAEHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLKLAEQLHDRVL
+YADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAIFVGVSIVLDGWKNLKEAVTNLAD
+RRAATIDGARPHPLIDRVERVAWAEPWVRQAGARVRDEGHVFHVEMFVVPHEGADVTVGR
+CCALRDAIAALDWKLQDVVVAPVDELPAEVHGGRSGEHQTGEE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001349.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001349.fa
new file mode 100644
index 0000000000000000000000000000000000000000..615828763c415e359de0b0d3ef6c6c9d4ae47399
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001349.fa
@@ -0,0 +1,25 @@
+>PROKKA_01672
+MALLLAIDSSAAASVAVLRDGEELARWATDDTHAHAEVLAPAVQTVLGEAGVTGTALDAL
+AVGVGPGPFTGLRAGLATAAALGLAWDVPVHGVRSLDALAHEAGVDAFRHGIEEFVVATD
+ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPVYGAGAGLYPEALRAVPDWESATP
+SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRAGA
+>PROKKA_01377
+MALLLAIDSSAAASVAVLRDGEELAHWATDDTHAHAEVLAPAVQTVLGEAGVTGTALDAL
+AVGVGPGPFTGLRAGLATAAALGLAWDVPVHGVRSLDALAHAAGVDAFRHGIEEFVVATD
+ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPVYGAGAGLYPEALRAVPDWETATP
+SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRAGA
+>PROKKA_01206
+MALLLALDSSAAASVAVLRDGEALARWATEDTHAHAEVLAPAVRAVLAEAGVAGAGLDAV
+AVGVGPGPFTGLRAGLATAAALGLAWDVPVRGVRSLDALAHDAAVDAFRHGAEEFVVATD
+ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPAYGAGAGLYPEALRAVPGWETATP
+SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRAGA
+>PROKKA_01134
+MPLLLALDSSSAASVALLRDGEPLAAWSTADTTSHAEVLAPAVRQVLAEAGVAGGDLDGI
+AAGVGPGPFTGLRAGLATAEALGFAWDVPVHGIRSLDALAHRAGTDAFAHAVEEFVVVTD
+ARRREVYWAHYAQVGGQPTLLHGPFVTPAAEVTPLPAYGAGAGLYPEALHAVDGWEGAVP
+DAVSLGRVDELALRRGRGVLPPTPLYLRESDATVPAPRTPARPAGA
+>PROKKA_01602
+MALLIAIDSSAAASVAVLQDGEELARWATDDTHAHAEVLAPAVQAVLGEAGVTGTALDAL
+AVGVGPGPFTGLRAGLATAAALGLAWDVPVHGVRSLDALAHEAGVDAFRHGIEEFVIATD
+ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPVYGAGAGLYPEALRAVPDWETATP
+SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRAGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001353.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001353.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20db8abf68a91dfd25f5d8a5993ed6eb4811bbb7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001353.fa
@@ -0,0 +1,19 @@
+>PROKKA_01676
+MIVGVGVDVVDVPRFRAQLERTPALRARLFTEDERDLPLRSLAARFAAKEAIAKAMGAPP
+GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEALGITHWHLSLSHDGDVATAYVVAERRA
+AEEESA
+>PROKKA_01381
+MIVGVGVDVVDVPRFRAQLERTPALRARLFTEDERDLPLRSLAARFAAKEAIAKAMGAPP
+GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEALGITHWHLSLSHDGDVATAYVVAERRA
+AEEESA
+>PROKKA_01202
+MIVGVGMDVVDVPRFRAQLERTPALRERLFTEDERDLPLRSLAARFAAKEAIAKAMGAPP
+GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEAQGITHWHLSLSHDGDVAAAYVVAERRA
+GEDGA
+>PROKKA_01130
+MIVGIGVDVVDVPRFERQLARTPALRERLFTEEERDLSLRSLAARFAAKEAIAKALGAPP
+GMMWHHCSIPRPAHGDGRPEVRLTDSVRDRADELGVTHWHLSLSHDGDVAVAYVVAERHD
+>PROKKA_01606
+MIVGVGVDVVDVPRFRAQLERTPALRARLFTEDERDLPLRSLAARFAAKEAVAKAMGAPP
+GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEALGITHWHLSLSHDGDVATAYVVAERRA
+AEEESA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001355.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001355.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34bac03608e0523ff5468eca0758b549f188d45e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001355.fa
@@ -0,0 +1,65 @@
+>PROKKA_01678
+MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHA
+HVAGIGHGQRYGYRVHGPWDPARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPD
+RIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYETHVKGMTKLHPAVPEELRGT
+YAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS
+SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEG
+DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD
+MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGLWSEWNGMYRDAVRDFWRGEP
+GTLGEFATRLTGSADLYEGDGRGPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG
+EAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNV
+YCQDNEISWIDWSAMDDSLVAFTRDLIALRRDHAVFRRRHHFDGRPAARDVEAPLPDIVW
+LEPDATAKTEDDWGAEARSIGFYLNGHMLTRGDEEGEEPYRDFYVLMNAWWEPVPYTLPG
+PTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQVPEGA
+>PROKKA_01383
+MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHA
+HVAGIGHGQRYGYRVHGPWDPARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPD
+RIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYETHVKGMTKLHPAVPEELRGT
+YAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS
+SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEG
+DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD
+MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGLWSEWNGMYRDAVRDFWRGEP
+GTLGEFATRLTGSADLYEGDGRGPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG
+EAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNV
+YCQDNEISWIDWSAMDDSLVAFTRDLIALRRDHAVFRRRHHFDGRPAARDVEAPLPDIVW
+LEPDATAKTEDDWGAEARSIGFYLNGHMLTRGDEEGEEPYRDFYVLMNAWWEPVPYTLPG
+PTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQVPEGA
+>PROKKA_01200
+MHTVDIGQPYPLGATVDETGTNFAVALAREAESVELCLVDEDGVETRLPVVERHGTTWHV
+HVAGVGHGQRYGYRVTGPWDPSRGLWHNPAKILVDPYARAFAGEHEWGQQHHSYDFDEPD
+RMDTSDNLGTTMLGVVTDDDFDWGEDAPPNIEMTDTVVYETHVKGMTMRHPAVPEELRGT
+YAGMAHPEVVRHLTDLGVTAVELMPVHQFVDDATLQEKGLSNYWGYNTLGFFAPHAAYAA
+SQEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSMRGLDNAGYYHLVEA
+DERHYMDYTGTGNSVDLSSPKALQLVMDSLRHWVTEMHVDGFRFDLATTLTRVEGEQGPD
+MFSAFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGIWSEWNGMYRDTVRDFWRGEP
+GTLGEFATRLTGSADLYEGDGRSPGASVNFVTAHDGFTLRDLVSYNEKHNAANGEDNNDG
+ESHNRSWNCGVEGETDDPEVLTLRARQQRNFLATLLISQGVPMISHGDELGRTQGGNNNV
+YCQDNEISWIDWSAVDDSLVAFTRDLIALRHDHAVFRRRHHFDGRPAARDVEAPLPDIVW
+LEPDATAKTEDDWGAEARSIGFYLNGHTLTRGDEDEEGPYRDFYVLMNAWWEPVPYTLPG
+PLFPETWEVVVDTSSHVAPSGSRPRVRAGEVLEVPARSTVILRQVPEGA
+>PROKKA_01128
+MHTVDIGQPYPLGATVDEAGTNFAVAVGREVEAVELCLIAEDGSEERIPVTERHDTTWHV
+HVAGIGGGQRYGWRVHGPWDPARGLWHNPHKLLADPYARAFTGDYAWGQQHFSYAFDEPD
+RMDTADSRGTSMVGVVVDDDFDWGDDAPPQRLLTDTVVYETHVKGLTALHPDVPEELRGT
+YAGVAHPSVLEHLTSLGVTAVELMPVHQFVNDSILQEKGLSNYWGYNSLGYLAPHAAYSS
+ADTVGGQVHEFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPLLSFRGFDNAGYYHLVEG
+DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD
+MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGIWSEWNGMYRDTVRDFWRGEP
+GTLGEFATRLTGSADLYEGDGRNPGASVNFVTAHDGFTLRDLVSYNEKHNHANGEDNNDG
+DSHNRSWNCGVEGETDDPEVLTLRARQQRNFLTTLMVSEGVPMLSHGDELGRTQKGNNNV
+YCQDNELSWIDWSTRDDALIAFTRDVIALRRDHAVFRRRQHFDGRPAERDVEAPLPDIVW
+LEPDATAKTEADWGAEARSIAFYLNGHDLQRREGEPDEAFRDFYVLMNAWWEPVPYTLPG
+PLFPGEWEIVVDTSSHVAPAGTRPHVVAGEVIEVPGRSTMILREVVRQEQG
+>PROKKA_01608
+MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHA
+HVAGIGHGQRYGYRVHGPWDPARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPD
+RIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYETHVKGMTKLHPAVPEELRGT
+YAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS
+SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEG
+DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD
+MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGLWSEWNGMYRDTVRDFWRGEP
+GTLGEFATRLTGSADLYEGDGRSPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG
+DAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNV
+YCQDNEISWIDWSAMDDSLVAFTRDLIALRRDHAVFRRRHHFDGRPAARDIEAPLPDIVW
+LEPDATAKTEDDWGAEARSLGFYLNGHTLPRGDEEGEEPYRDFYVLMNAWWEPVPYTLPG
+PTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQVPEGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001359.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001359.fa
new file mode 100644
index 0000000000000000000000000000000000000000..edfada3ff62ca0fde179a8d77211fea19f2afcca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001359.fa
@@ -0,0 +1,14 @@
+>PROKKA_01685
+MTSDAAPRPRRWTLFAGLLAGLAVLWSAAFLAVDAPVCARQSAPVEWLPCLDPDRQDSEV
+APDAGSSADRTTSRP
+>PROKKA_01389
+MTSDAAPRPRRWTLFAGLLAGLAVLWSAAFLAVDAPVCARQSAPVEWLPCLDPDRQDSEV
+APDAGSSADRTTSRP
+>PROKKA_01193
+MSSEAVPRPPRWSPFGALLAGLAVLWGAAFLAVDAPVCERHGAPVEWLPCLDRDRGDPDV
+APQR
+>PROKKA_01123
+MSPRRDPGRLRPLAGPAALLAALWVAAWLAVSVPVCDRGGPADWLPCVDPGRSVPAPGAP
+>PROKKA_01614
+MTSDAAPRPRRWTLFAGLLAGLAVLWSAAFLAVDAPVCARQSAPVEWLPCLDPDRQDSEV
+APDAGSSADRTTSRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001360.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001360.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a88f409eb9b1360fdf9d3a48d10c4415a466621
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001360.fa
@@ -0,0 +1,45 @@
+>PROKKA_01686
+MSRLFGTDGVRGLANETLTVELSVQLAQAASPVLGAEAFDAGRRPVAVVARDPRISGEFI
+TAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLDADFGVMISASHNPAPDNGIKFLARGG
+EKLTDAQEDEIIRHLEGVTPRRPQGADVGRVRVFADAEDRYVLHLLQTLPHRLDGLKVVL
+DCAHGAAAGCSPEAFRAAGAEVVVIGASPDGLNINDGYGSTHLEKLQAAVREHGADLGIA
+HDGDADRCLAVDERGEVVDGDQIMGVMAVALKDRGVLRDDTLVVTVMSNLGLKLAMGREG
+VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLASRVAETGTP
+LSELAAVMDRLPQVLVNVRGVDKSRAAEDEAVQAAVAEAEARLGETGRVLLRPSGTEPVV
+RVMVEAPDEETAGREAQVLADVVQRELRLHD
+>PROKKA_01390
+MSRLFGTDGVRGLANETLTVELSVQLAQAASPVLGAEAFDAGRRPVAVVARDPRISGEFI
+TAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLDADFGVMISASHNPAPDNGIKFLARGG
+EKLTDAQEDEIIRHLEGVTPRRPQGADVGRVRVFADAEDRYVLHLLQTLPHRLDGLKVVL
+DCAHGAAAGCSPEAFRAAGAEVVVIGASPDGLNINDGYGSTHLEKLQAAVREHGADLGIA
+HDGDADRCLAVDEHGEVVDGDQIMGVMAVALKDRGVLRDDTLVVTVMSNLGLKLAMGREG
+VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLASRVAETGTP
+LSELAAVMDRLPQVLVNVRGVDKSRAAEDEAVQAAVAEAEARLGETGRVLLRPSGTEPVV
+RVMVEAPDEETAGREAQVLADVVQRELRLHD
+>PROKKA_01192
+MSRLFGTDGVRGLANETLTVELSVQLAQAAAPVLGAEALEAGRRPVAVVARDPRISGEFI
+AAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLGADFGVMISASHNPAPDNGIKFLARGG
+EKLTDAQEDEIIRHLEGVEPRRPQGADVGRVKVFSDAEDRYVVHLLQALPHRLEGLKVVL
+DCAHGAAAGCSPEAFRDAGAEVVVIGASPDGLNINEGYGSTHLEKLQAAVLEHGADLGIA
+HDGDADRCLAVDERGEVVDGDQIMGVMAVAMKDRGVLRDDTLVVTVMSNLGLKLAMGREG
+VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLAARVAETGRP
+LSALAAVMDRLPQVLVNVRGVDKSRAAEDVAVQAAVAEAEARLGETGRVLLRPSGTEPVV
+RVMVEAPDEETAGREAEALADVVQRELRLHV
+>PROKKA_01122
+MSRLFGTDGVRGLANDVLTVELSVQLAQAAAPVLGADALAAGRRPVAVVARDPRISGQFI
+AAAVIAGLASSGVDVHDAGVVPTPAAAFLVGDLDADFGVMISASHNPAPDNGIKFLARGG
+EKLTDEQEDEIIQHLESEHPLRPTGAEVGRVRTFSDAEDRYVVHLLQTLPHRLDGLTVVL
+DCAHGAASGCSPDAFRDAGAQVIVIGAEPDGLNINEGVGSTHLEKLQAAVKEHGADLGIA
+HDGDADRCLAVDELGEVVDGDQIMGIMALALKDRGQLKEDTLVVTVMSNLGLKLAMRGAG
+IELVETQVGDRYVLAGMRLGEYSLGGEQSGHVIFADHATTGDGVLTGLQIAARVAETGTP
+LSQLAAVMTRLPQVLVNVRGVDKSRAAEDAAVQSAVREAEARLGETGRVLLRPSGTEPVV
+RVMVEAPDEETARREAEALAEVVQRELRLHD
+>PROKKA_01615
+MSRLFGTDGVRGLANETLTVELSVQLAQAASPVLGAEAFDAGRRPVAVVARDPRISGEFI
+AAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLDADFGVMISASHNPAPDNGIKFLARGG
+EKLTDAQEDEIIRHLEGVTPRRPQGADVGRVRVFADAEDRYVLHLLQTLPHRLDGLKVVL
+DCAHGAAAGCSPEAFRAAGAEVVVIGASPDGLNINDGYGSTHLEKLQAAVREHGADLGIA
+HDGDADRCLAVDERGEVVDGDQIMGVMAVALKDRGVLRDDTLVVTVMSNLGLKLAMGREG
+VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLASRVAETGTP
+LSELAAVMDRLPQVLVNVRGVDKSRAAEDEAVQAAVAEAEARLGETGRVLLRPSGTEPVV
+RVMVEAPDEETAGREAQVLADVVQRELRLHD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001365.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001365.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb88e76235edb1b3e591d4ca1a4641e753efeb7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001365.fa
@@ -0,0 +1,30 @@
+>PROKKA_01692
+MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPYAERLITFAKKGDL
+PARRKVQGLIAAKNRTNKAVVHELFTVIGPAMAERNGGYTRITKIGNRHGDNAPMAVIEL
+IMDPISGKQAVVREAEQAAASAPAAPAESTPVEAVDPAATEEVTVAESQETAAEIDGAVP
+TTEDGSAPAEATIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGEAAQK
+MA
+>PROKKA_01399
+MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPYAERLITFAKKGDL
+PARRKVQGLIAAKNRTNKAVVHELFTVIGPAMAERNGGYTRITKIGNRQGDNAPMAVIEL
+IMDPISGKQAVVREAEQAAASAPAAPAESTPVEAVDPAATEEVTVAESQETAAEIDGAVP
+TTEDGSAPAEATIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGEAAQK
+MA
+>PROKKA_01186
+MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPYAERLITFAKKGDL
+PARRKVQGLIAAKNRTNKSIVHELFTVIGPAMAERNGGYTRITKIGNRQGDNAPMAVIEL
+IMEPISGKQAVVREAEQAAASAPAAETAPVQETAPVEAVDPAAAEDVTVAESQEAAAEID
+GAVATTEDGSAPEGASIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGE
+AAQKMAD
+>PROKKA_01116
+MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPHAERLITIAKKGDL
+PARRKVQGIIAAKSRTNKSIVHELFTVIAPAMAERNGGYTRITKIGNRQGDNAPMAVIEL
+VMEPVSGKQAVVREAEQAAASAPAAAPVEETPVEVVDPAATEEVTVAESEETAAEIDGAV
+ATTEDGSAPEGATIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGEAAQ
+KMA
+>PROKKA_01621
+MPTPTKGPRLGGSPAHERIMLANMSAQLFEHKSITTTLTRAKRLRPYAERLITFAKKGDL
+PARRKVQGLIAAKNRTNKAVVHELFTVIGPAMAERNGGYTRITKIGNRHGDNAPMAVIEL
+IMDPISGKQAVVREAEQAAASAPAAPAESTPVEAVDPAATEEVTVAESQETAAEIDGAVP
+TTEDGSAPAEATIKGNASSKKYHVPGSRWYDQTTAEVWFSTVEEAKAAGFEPAGGEAAQK
+MA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001367.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001367.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1e4104508292a5b2ab476c3e4a6e6524118c05f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001367.fa
@@ -0,0 +1,20 @@
+>PROKKA_01694
+MPPKTRASAARKPRRKANKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS
+RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP
+MAHNGARPAKRRRV
+>PROKKA_01401
+MPPKTRASAARKPRRKANKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS
+RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP
+MAHNGARPAKRRRV
+>PROKKA_01184
+MPPKTRASAARKPRRKDKKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS
+RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP
+MAHNGARPAKRRRV
+>PROKKA_01114
+MPPKTRSAVRKPRRKDKKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGSR
+KSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTPQ
+AHNGARPAKRRRV
+>PROKKA_01623
+MPPKTRASAARKPRRKANKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS
+RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP
+MAHNGARPAKRRRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001370.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001370.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a16678e2bd386d28c8f5ca7dcaa7aad7d5683bde
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001370.fa
@@ -0,0 +1,15 @@
+>PROKKA_01697
+MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV
+VVELSPYDLNRGRIVYRYK
+>PROKKA_01404
+MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV
+VVELSPYDLNRGRIVYRYK
+>PROKKA_01181
+MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV
+VVELSPYDLNRGRIVYRYK
+>PROKKA_01111
+MAKKEGVIEVEGTVTEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRVVVELSP
+YDLNRGRIVYRYK
+>PROKKA_01626
+MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV
+VVELSPYDLNRGRIVYRYK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001371.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001371.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9eccdc859de49f31b1dcab7cf79d9de536936e67
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001371.fa
@@ -0,0 +1,30 @@
+>PROKKA_01698
+MIGRRSLELKTAPQLQAMQRAGVVLSEALDATLAAAAPGVTTAELDAVFAGVLAERGATS
+NFLGYYDFPASICTSVNDEVVHGIPGDRVLQTGDVLKVDGGAIVDGWHADSARTVILGSS
+EAGTAGPADERLSAITREALWVGIAAFASATHVGDIGDAIDDFVSAQPGEELGILEEYVG
+HGIGSAMHLPPDVFNYRTGHRGPKIRPGLALAIEPMLVRGSIDTKVLADDWTVVTLDGAR
+ASQWEHSVCRHDGGVWVLTAPDGGASELARFGVVPVPPGE
+>PROKKA_01405
+MIGRRSLELKTAPQLQAMQRAGVVLSEALDATLTAAAPGVTTAELDAVFAGVLAERGATS
+NFLGYYDFPASICTSVNDEVVHGIPGDRVLQTGDVLKVDGGAIVDGWHADSARTVILGSS
+AAGTADPADERLSAITREALWVGIAAFASATHVGDIGDAIDDFVSAQPGEELGILEEYVG
+HGIGSAMHLPPDVFNYRTGHRGPKIRPGLALAIEPMLVRGSIDTKVLADDWTVVTLDGAR
+ASQWEHSVCRHDGGVWVLTAPDGGASELARFGVVPVPPGE
+>PROKKA_01180
+MVGRRSLELKTTPQLQTMRRAGVVLSEALDATLAAAAPGVTTAELDAVFAGVLAEHGATS
+NFLGYYDFPATICASVNEEVVHGIPGDRVLQAGDVLKVDGGAIVDGWHADSARTLVLGSS
+EAGTADEGDERLSAITREALWVGIAAFATAKHVGDIGDAIDDFVSAQPGEPLGILEEYVG
+HGIGSSMHMPPDVFNYRTGHRGPKVRPGLALAVEPMLVRGGIETRVLEDDWTVVTVDGAR
+ASQWEHSVCRHAGGLWVLTAPDGGASELERFGVVPVPPGE
+>PROKKA_01110
+MFSRRSIELKTTPQLQTMQRAGVVLSEALDAAVAAAAPGVTTAEVDAVFADVLAQHGATS
+NFLGYYGYPATVCASVNEEVVHGIPGERVLQQGDVLKIDGGAIVDGWHSDSARTLILGSS
+EAGTADPEDERLSEITRQALWVGIAAFAQARHVGEIGDAVDDFVTSQPGAPLGILEDYVG
+HGIGSAMHLAPDVFNYRTGHRGPKVQHGMALAIEPMLVRGGIETRTLEDEWTVVTTDGAR
+ASQWEHTVCRHPGGVWVLTAPDGGAAELAAHGVVPVPPGE
+>PROKKA_01627
+MIGRRSLELKTAPQLQAMQHAGVVLSEALDATLTAAAPGVTTAELDAVFAGVLAERGATS
+NFLGYYDFPASICTSVNDEVVHGIPGDRVLQTGDVLKVDGGAIVDGWHADSARTVILGSS
+AAGTADPADERLSAITREALWVGIAAFASATHVGDIGDAIDDFVTAQPGEELGILEEYVG
+HGIGSAMHLPPDVFNYRTGHRGPKIRPGLALAIEPMLVRGSIDTKVLADDWTVVTLDGAR
+ASQWEHSVCRHDGGVWVLTAPDGGASELARFGVVPVPPGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001380.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001380.fa
new file mode 100644
index 0000000000000000000000000000000000000000..712074d7de3e1c0c5a6173913c284e594c6d1c03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001380.fa
@@ -0,0 +1,25 @@
+>PROKKA_01707
+MTEVQQTEKVTPRLKTKYRDEIRGALQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII
+DGAVADLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR
+IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL
+KALGFPFKTDQ
+>PROKKA_01414
+MTEVQQTEKVTPRLKTKYRDEIRGALQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII
+DGAVADLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR
+IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL
+KALGFPFKTDQ
+>PROKKA_01171
+MTEVQQTEKVAPRLKTKYREEIRATLQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII
+DGAVTDLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR
+IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL
+KALGFPFKTDQ
+>PROKKA_01101
+MTEVQQTEKVTPRLKTKYREEIRASLQEQFEYANVMQVPGLVKVVVNMGVGEAAKDSKII
+DGAIADLTAITGQKPMVTKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR
+IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL
+KALGFPFKTDK
+>PROKKA_01636
+MTEVQQTEKVTPRLKTKYRDEIRGALQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII
+DGAVADLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR
+IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL
+KALGFPFKTDQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001381.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001381.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a2ac9d906e84af18262421bedf399d3b86359b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001381.fa
@@ -0,0 +1,15 @@
+>PROKKA_01708
+MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGL
+QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKDGVSKTVKVRFAKASGKEL
+>PROKKA_01415
+MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGL
+QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKDGVSKTVKVRFAKASGKEL
+>PROKKA_01170
+MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGR
+QVAEAPIHISNVAVVDPETKKPTRVGYRFETVEKNGESKTVKVRFAKASGKEL
+>PROKKA_01100
+MAKIKKDDLVQVLSGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQNNNGSTEGGL
+QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKNGEQVTVKVRFAKASGKEL
+>PROKKA_01637
+MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGL
+QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKDGVSKTVKVRFAKASGKEL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001390.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001390.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ffa3edf05b8e2bd9b16caa51c894da015d3366a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001390.fa
@@ -0,0 +1,15 @@
+>PROKKA_01717
+MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKSEIKQAVERIFNVDVASVN
+TLNRSGKRRRTRFGWGQRKSTKRAIVTLKDGTIDIFGGPLA
+>PROKKA_01424
+MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKSEIKQAVERIFNVDVASVN
+TLNRSGKRRRTRFGWGQRKSTKRAIVTLKDGTIDIFGGPLA
+>PROKKA_01161
+MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKSEIKQAVERIFNVDVASVN
+TLNRSGKRRRTRFGWGQRKSTKRAIVTLKDGTIDIFGGPLA
+>PROKKA_01091
+MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKTEIKQAIERIFDVSVASVN
+TLNRPGKRRRTRFGWGQRKSTKRAIVSLKDGATIDIFGGPLAS
+>PROKKA_01646
+MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKSEIKQAVERIFNVDVASVN
+TLNRSGKRRRTRFGWGQRKSTKRAIVTLKDGTIDIFGGPLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001391.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001391.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4bc5b1923837cc5b19a41480884ff77a6b07d1cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001391.fa
@@ -0,0 +1,25 @@
+>PROKKA_01718
+MAENSVKTVQVDLPAELFDVQSNVPLMHQVVVAQLAAARQGTHKTKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGVVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ
+>PROKKA_01425
+MAENSVKTVQVDLPAELFDVQSNVPLMHQVVVAQLAAARQGTHKTKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGVVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ
+>PROKKA_01160
+MAENSVKTVQVDLPAEIFDVQSNVPLMHQVVVAQLAAARQGTHKVKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGIVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ
+>PROKKA_01090
+MAENTVKTVQVELPAEIFDVQANVPLMHQVVVAQLAAARQGTHKVKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGIVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLESLNTGRKNVLLVIDRADDLTALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTKVAYEAYVAQASGAKKEDAQ
+>PROKKA_01647
+MAENSVKTVQVDLPAELFDVQSNVPLMHQVVVAQLAAARQGTHKTKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGVVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001393.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001393.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3547e3bd65debb5f6905aba6f0826a2a01dbf102
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001393.fa
@@ -0,0 +1,15 @@
+>PROKKA_01720
+MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD
+SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL
+>PROKKA_01427
+MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD
+SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL
+>PROKKA_01158
+MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD
+SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL
+>PROKKA_01088
+MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD
+SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL
+>PROKKA_01649
+MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD
+SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001395.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001395.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b3b0deab07e4a4aaa4d6467cb6479d21689582db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001395.fa
@@ -0,0 +1,10 @@
+>PROKKA_01722
+MSDDGAAAAARLGSMPELILLIAVLAVVVVAVRWALRTFRPEIDRARRIRRANRGGELER
+>PROKKA_01429
+MSDDGAAAAARLGSMPELLILIVVLAVAVVAVRWALRTFRPEIDRARRIRRANRGGELER
+>PROKKA_01156
+MPELLITLLVLAAAVVAVVWALRTFRPEIDRARRIRRANRNGELRR
+>PROKKA_01086
+MEWLIALVVIAAVVAGGLWARRAFAPEIERARRIRRAERGGRLER
+>PROKKA_01651
+MSDDGAAAAARLGSMPELILLIAVLAVVVVAVRWALRTFRPEIDRARRIRRANRGGELER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001403.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001403.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af0646621ad58b3137b0deb5478dc44023c484b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001403.fa
@@ -0,0 +1,20 @@
+>PROKKA_01730
+MATSAKESAVAELTDLFRESSAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA
+AKDAGLEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI
+KQLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAAQGEAA
+>PROKKA_01437
+MATSAKESAVAELTDLFRESSAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA
+AKDAGLEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI
+KKLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAAQGEAA
+>PROKKA_01148
+MATSAKESAVAELTDLFRESNAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA
+AKEAGVEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI
+KKIADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAQQGEAA
+>PROKKA_01077
+MATSAKESAVAELTDLFRSSSAAVLTEYRGLTVSELKQLRDSIRQDATYSVAKNTLTEIA
+AKEAGVEGLDAHLAGPTAIAFVTGDPVTVAKALRDFAKDHDKLVLKGGYMDGQPLDEAGI
+EKLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTARTVEALRAQQDQAA
+>PROKKA_01659
+MATSAKESAVAELTDLFRESSAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA
+AKDAGLEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI
+KKLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAAQGEAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001406.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001406.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a34ee9404b84bc76525735e9129c0b588f90048
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001406.fa
@@ -0,0 +1,30 @@
+>PROKKA_01733
+MSEQELDRQPAEESVPMSEDAVAEETAETAQDAGTPVEDALDEVAGSGDETAEATVQEAD
+LAVAEGEDAPTPVEEQSDDEPAVDPAEELRTRLRRQPGDWYVVHTYAGYEKRVKTNLEAR
+ILTQDMEDSIYEIEVPMEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTPGV
+TGFVGNDAHHPQPLSLDEVYDMLAPSVIQEAARAAEKAGLAVPAAAESGAPAAPAIHVDF
+EVGESVTVNDGPFETLPATISEIKPEAQQLVVLVSIFERETPVTLSFNQVTKAI
+>PROKKA_01440
+MSEDAVAEETAETAQDAGTPVEDALDEAAGSGDETAEATVQEADLAVAEGEDAPTPVEEQ
+ADDEPAVDPAEELRTRLRRQPGDWYVVHTYAGYEKRVKTNLEARILTQDMEDSIYEIEVP
+MEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTPGVTGFVGNDAHHPQPLSL
+DEVYDMLAPSVIQEAARAAEKAGLAVPALVESGAPAAPAIHVDFEVGESVTVNDGPFETL
+PATISEIKPEAQQLVVLVSIFERETPVTLSFNQVTKAI
+>PROKKA_01145
+MSEQELDRQAAEESVSVQEDGAVEETVETAQDAPAPAEDAAGETAVDGEEAAEATEATAQ
+EADPAAVEQAEEEPAVDPGEELRTRLRRQPGDWYVVHTYAGYEKRVKTNLEARILSQDME
+DAIYEIEVPMEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTPGVTGFVGND
+AHHPQPLSLDEVYDMLAPSVIQEAARAAEKAGLAVPASAESGAAAAPAIHVDFEVGESVT
+VNDGPFETLPATISEIKPEAQQLVVLVSIFERETPVTLSFNQVTKVI
+>PROKKA_01074
+MSEQELDRQDVEETAVAEDSTALEAPVEDTAAEEAEQTVQEADLAIAEGDQDAAEAPSAE
+ELDAAGQAPAQPDVEAAEQLRTRLRRQPGDWYVVHTYAGYEKRVKTNLEARIQTQDMEDS
+IYEIEVPMEEVVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTSGVTGFVGNDAH
+HPQPLTLDEVYDMLAPSVVQEAVREAEKAGLVPVAVAESGAAGAPAIHVDFEVGESVTVD
+DGPFETLPATISEIKPETQQLVVLVSIFERETPVTLSFNQVTKVI
+>PROKKA_01662
+MSEDAVAEETAQDAGTPVEDALDEPAGSGDETAEATVQEADLAVAEGEDAPTPVEEQSDD
+EPAVDPAEELRTRLRRQPGDWYVVHTYAGYEKRVKTNLEARILTQDMEDSIYEIEVPMEE
+VVEIKNTTRKIVSRVRIPGYVLVRMDLDDASWGVVRHTPGVTGFVGNDAHHPQPLSLDEV
+YDMLAPSVIQEAARAAEKAGLAVPAAAESGAPAAPAIHVDFEVGESVTVNDGPFETLPAT
+ISEIKPEAQQLVVLVSIFERETPVTLSFNQVTKAI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001410.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001410.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5aa027f0ecdbba03b600de33ee069f1953f3bc08
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001410.fa
@@ -0,0 +1,42 @@
+>PROKKA_01738
+MPTPSAPAPAPRPPLMRHGADRPVSGVAAGLARHLGMPAGRVRAALALLSLLGGAGLALY
+VWLWLLVPEEGPDGAPAADAPTLRGRAPEVLERVREGGWPVLLAAVVLGVGVLTVADGLG
+LAVDWALVGPVAVLVIGLGLAWMQLDLAGGPRAGRSGRLVRLVLGTALVLLAVLAIVLGA
+VSSGELWRALLAAVAMLAGAALVAMPYVLAWLRRRDAERTAFAVQAQRAEIAAHLHDSVL
+QSLALIQRRAQDADAVARVARAQERELRQFLALDSRGGPHSLAEALEQHAAAVEDAHGAR
+VEVVAVGRAAGAWLEPLAAAAREAMQNAARHAGDAQVFAEAGEDDRGRTVAEVFVRDRGP
+GFDLPTVPADRLGVRESILGRMGRAGGTARIRSGPGGTEVHLTLAEPEGARARTGQEHP
+>PROKKA_01445
+MPTPSAPAQAPRPPLMRHGADRPVSGVAAGLARHLGVPVGRVRAALALLSLMGGAGLALY
+VWLWLLMPEEGPDGAPAADAPTLRGRAPEVLERVREGGWPVLLAAVVLGVGVLTVADGLG
+LAVDWALVGPVAVLVIGLGLAWMQLDLAGGPRAGRSGRLVRLVLGTALVLLAVLAIVLGA
+VSSGELWRALLAAVAMLAGAALVAMPYVLAWLRRRDAERTAFAVQVQRAEIAAHLHDSVL
+QSLALIQRRAHDADAVARVARAQERELRQFLALDSRGGPRSLAEALEEHAAAVEDAHGSR
+VEVVAVGRAAGAWLEPLAAAAREAMQNAARHAGDAQVFAEAGEDDHGRTVAEVFVRDRGP
+GFDLHTVPADRLGVRESILGRMERAGGAARIRSGPGGTEVHLTLTEPEGARARAGQEHP
+>PROKKA_01140
+MPASAVPPSAPSGRAGPRRAAADDARTRPIGADPRTSEARASGTRAPLMRHRADRPVSGV
+AAGAARHLGLSPRTARAGFAVLALAGGAGLALYVWLWLLMPEEGADGAPTGEAPSLRGRA
+PEVLERVREGGWPVLLAAVVLGVGVITIADGLGLAVDWALVGPVAVLVIGLGLAWMQLDL
+AGGPPAGRVGRVVRLALGTALVLLAVLAIVLGGVTSGDLWLGLLVAVALIAGVAMVAMPY
+ALSWLRRRDAERTAFAVQAQRAEIAAHLHDSVLQSLALIQRRAHDPEAVARAARAQEREL
+RRFLALDDRGGHDSLAATLREHAAAVEDAHGRRVEVVAVGEASGAWLEPLTAAAREAMLN
+AARHAGDAQVFAEVAEDDDGRTVAEVFVRDRGPGFDPGAVPADRLGVRESVVGRMERAGG
+AARIRSGPGGTEVHLTLTRPDRVPPHAAQERP
+>PROKKA_01069
+MPAPAIPPPADLSARPALLRHAADRPVSGVAGGVARHLGLDPRLARAGFAVLALAGGAGI
+ALYAWLWLLMPEEGPDGAPAGPAPTLRGRAPEVLERLREGGWPILLAVVVLGVGVLTVAD
+GLGVPVDWALVGPVAVLVIGLGLAWMQLGAADGPEGGRWARRARLGLGTALVLLGVLAIV
+VGAVTAGDLWLGLLVAVALLAGGALVAMPFVLARRRRRDEERTGAAVRAQRDEIAAHLHD
+SVLQSLALIQRRADDPETVARVARAQERELRQFLALDSARAHGTLAEAVEDHAAAVEDAF
+GRRVEVVSVGEASGPWLEPLASAAREAMVNAARHAGDVQVFVEVSEDDGGRTLAEVFIRD
+RGTGFDLADVPADRLGVRESILGRMRRAGGTARIRSGPSGTEVQLSLADPGAPGVGLREG
+RGRA
+>PROKKA_01667
+MPTPSAPAPAPRPPLMRHGADRPVSGVAAGLARHLGMPAGRVRAALALLSLLGGAGLALY
+VWLWLLMPEERPDGAPAADAPTLRGRAPEVLERVREGGWPVLLAAVVLGVGVLTVADGLG
+LAVDWALVGPVAVLVIGLGLAWMQLDLAGGSRAGRSGRLVRLVLGTALVLLAVLAIVLGA
+VSSGELWRALLAAVAMLAGAALVAMPYVLAWLRRRDAERTAFAVQAQRAEIAAHLHDSVL
+QSLALIQRRAQDADAVARVARAQERELRQFLALDSRGGPHSLAEALEQHAAAVEDAHGAR
+VEVVAVGRAAGAWLEPLAAAAREAMQNAVRHAGDAQVFAEAGEDERGRTVAEVFVRDRGP
+GFDLHTVPADRLGVRESIVGRMERAGGTARIRSGPGGTEVHLTLTEPEGARARTGQEHP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001415.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001415.fa
new file mode 100644
index 0000000000000000000000000000000000000000..75c630abddd737d79c4bdb5df13c13f1f3fd5cdf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001415.fa
@@ -0,0 +1,25 @@
+>PROKKA_01743
+MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSAGTEIFYQRVDFTEHGLPFVEYRAESW
+LCEADGTLLRPLTVESGFWQVDRARRDGDVGPGMRPADIVPAFRSAEDVERLRAGDEGFG
+LTATITHPGSLSELYYGRIKGPQLQLATDAVLRGSAAGPYHRATRMAGLVNGQLFWRWDV
+ADAAGAELEAHASAILDRMPSAAEGRLAPGAERPRGARGEQS
+>PROKKA_01450
+MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSAGTEIFYQRVDFTEHGLPFVEYRAESW
+LCEADGTLLRPLTVESGFWQVDRARRDGDVGPGMRPADIVPAFRSAEDVERLRAGDEGFG
+LTATITHPGSLSELYYGRIKGPQLQLATDAVLRGSAAGPYHRATRMAGLVNGQLFWRWDV
+ADAAGAELEAHASAILDRMPSAAEGRLAPGAERPRGARGEQS
+>PROKKA_01134
+MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSDGTEIFYQRVDFTEHGLPFVEYRAESW
+LCEADGTLLRPLTVESGFWQVDRERRDGDVGPGMRPADIVPAFRSAEDVESLRAGDEGFG
+ITATITHPGSLAELYYGRIKGPQLQLVTDAVLRGSAAGDYHRATRMAGLVNGQLFWRWDS
+SGSEGAELEAHASAILDRMPSESEGRLAPGAPRPRGAGGAEPGERP
+>PROKKA_01063
+MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSEGTDIFYQRVDFVEHGLPFVEYRAESW
+LCEADGTLLRPLTVESGFWQVDRARQDGDVGPGMVPADIVPAYRSAEDVEALRSEDGAFR
+ITATITHPGSLAELYYGRIKGPQVQIVMDSLLRGAAAGEYARATRMAGLVNGQLFWRWDS
+SPAVEGPMEVHASAILDRMPDPSEGRLAPGAPRPRGERGRAPEQGA
+>PROKKA_01672
+MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSAGTEIFYQRVDFTEHGLPFVEYRAESW
+LCEADGTLLRPLTVESGFWQVDRARRDGDVGPGMRPADIVPAFRSAEDVERLRAGDEGFG
+LTATITHPGSLSELYYGRIKGPQLQLATDAVLRGSAAGPYHRATRMAGLVNGQLFWRWDV
+ADAAGAELEAHASAILDRMPSAAEGRLAPGAERPRGARGEQS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001416.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001416.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a10dca7635c0b783a964a23aa6729a2665f0493e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001416.fa
@@ -0,0 +1,10 @@
+>PROKKA_01744
+MDTLLALEIFFLALVVLAGLGMAAVAAVVISGLFKGQR
+>PROKKA_01451
+MDTLLALEIFFLALVVLAGLGMAAVAAVVISGLFKGQR
+>PROKKA_01133
+MDTLLALEIFFLALVVLAGLGMAAVAAVVVGGLFKGQR
+>PROKKA_01062
+MDSIVALEIFFLVLVVLAGLGMAAVAALVVGGLFKGQR
+>PROKKA_01673
+MDTLLALEIFFLALVVLAGLGMAAVAAVVISGLFKGQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001417.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001417.fa
new file mode 100644
index 0000000000000000000000000000000000000000..93590f7d83c55e45621a11dfdf923a6a0be11d30
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001417.fa
@@ -0,0 +1,30 @@
+>PROKKA_01745
+MAREVRPAVARPGPSRCAPGRMGQVMRLSMALSAAVAALVLGGAALLGPVPAALAAAVVI
+LVIAWGWPRQMGAPARLSLSVTLAVAGGAAVLLMLLWPPLEDGHSGAWTLFEPLAVVVAW
+STMASFVVQLVRGTGRPLRLESTVATMGGAFMAVVTACWVAVSRWTDTPAVAGLVITLAV
+TVAAVSLVGLTPWMQGRPGVLALVVIPLGTVLAWPVSALAGVGARDRPAVTAAALAVAVL
+VSLTAATAPSSRPRPEDRPVGTTLRPRRAGYALALAPVGAAGVVAHVMVGFLA
+>PROKKA_01452
+MAREVRPAVARPGPSRCAPGRMGQVMRLSMALSAAVAALVLGGAALLGPVPAALAAAVVI
+LVIAWGWPRQMGAPARLSLSVTLAVAGGAAVLLMLLWPPLEDGHSGAWTLFEPLAVVVAW
+STMASFVVQLVRGTGRPLRLESTVATMGGAFMAVVTACWVAVSRWTDTPAVAGLVITLAV
+TVAAVSLVGLTPWMQGRPGVLALVVIPLGTVLAWPVSALAGVGARDRPAVTAAALAVAVL
+VSLTAATAPSSRPRPEDRPVGTTLRPRRAGYALALAPVGAAGVVAHVMVGFLA
+>PROKKA_01132
+MMRLSMALSAAVAALVLGGATLLGPVPAAVAAMAVILVIAWGWPRQMGAPARLSLSVTLA
+AVGLVAVLLMLLWPPIEDGRSGAWTLFEPLAVALAWSTMASFVVQLVRGTGRPLRLESTV
+ATMGGGLIAVMTACWVAVSRWTDAPAVAGLVLTLAISVAAFSLIGLIPGVQGRPGVLALV
+VVPLGALLAWPVSALLGVGPQDRAAVVAAVVAVATLVSLTAATAPSARPRPEDRPVGTTL
+RPRRAGYALALAPVGAAGVVAHVMVGFLA
+>PROKKA_01061
+MMRLSMALSAALAALVLGGAALLGPVPAAVAACLVIAVIAFGWPRQMGAPARLSLTLTML
+VAGVLGVLVMVLWPRGDAGPRGAWALFEPLAVVLAFGTMASFIVQLVRGTGRPLRLESTV
+TTMGGVLVCLLAASWVPLAHHREAPGATGLVVTLAATLIVTSLIGLTPFMQGRPRVLALV
+MVPASGVVAALVSLLLGAPAHTAWVYAAAALGTAGLVSLTAAAAPSSRPLPEDRVVGTTL
+SPRRAGYALAMAPVGAAGVVGHVMLGFLA
+>PROKKA_01674
+MMRLSMALSAAVAALVLGGAALLGPVPAALAAAVVILVIAWGWPRQMGAPARLSLSVTLA
+VAGGIAVLLMLLWPPLEDGHSGAWTLFEPLAVVVAWSTMASFVVQLVRGTGRPLRLESTV
+ATMGGAFMAVVTACWVAVSRWSDTPAVAGLVITLAVTVAAVSLVGLTPWMQGRPGVLALV
+VIPLGTVLAWPVSALAGVGARDRPAVTAAALAVAVLVSLTAATAPSSRPRPEDRPVGTTL
+RPRRAGYALALAPVGAAGVVAHVMVGFLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001422.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001422.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad3f67d2efa0be981cfea7b1e2f85dd637abe577
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001422.fa
@@ -0,0 +1,25 @@
+>PROKKA_01750
+MRSDPMSRATRPTEPVIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR
+TWESFPARFRPLPGRTNIVVSRTLTATEEAGAELRAAGAVVVPNFGAALAAAAEADGCDT
+VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPPLDARWRRTAVDPAPDAWLDSASG
+PRHRFERWERD
+>PROKKA_01457
+MRSDPMSRATRPTEPVIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR
+TWESFPARFRPLPGRTNIVVSRTLTATEEAGAELRAAGAVVVPNFGAALAAAAEADGCDT
+VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPPLDARWRRTAVDPAPDAWLDSASG
+PRHRFERWERD
+>PROKKA_01127
+MRSDPMSRATRPTEPAIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR
+TWESFPARFRPLPGRTNIVVSRTLTASEEAGAELRAAGAVVVPDFGAALAAAAEADGCDT
+VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPVLDPRWRRTAVDPAPDAWLDSASG
+PRHRFERWERD
+>PROKKA_01052
+MARHHDDGARPRQTIAMIWAQTPDGVIGADGTMPWHLPEDLARFKALTLGHPVIMGRRTW
+DSFPARVRPLPGRTNIVVSRTLTATPEAGEAVRAAGAVVVPDFGAALTAADEADGLDLVW
+VIGGATLYEQALDVATRAEITVVDVDAPGDTHAPALDSRWRLVAADPSPDGWLDSAAGPR
+RRDERWERD
+>PROKKA_01679
+MRSDPMSRATRPTEPVIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR
+TWESFPARFRPLPGRTNIVVSRTLTATEEAGAELRAAGAVVVPDFGAALAAAAEADGCDT
+VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPLLDARWRRTAVEPAPDAWLDSASG
+PRHRFERWERD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001423.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001423.fa
new file mode 100644
index 0000000000000000000000000000000000000000..807b716d02ab115bec4418eeca50aaad3633def0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001423.fa
@@ -0,0 +1,15 @@
+>PROKKA_01751
+MAPTDSDQRLLSPQAVSFLALVALPVLAFVCAVFGLILVLQGKTIAGLVFLLVLTQVFAV
+GGLIAWNRRKRAQQGR
+>PROKKA_01458
+MAPTDSDQRLLSPQAVSFLALVALPVLAFVCAVFGLILVLQGKTIAGLVFLLVLTQVFAV
+GGLIAWNRRKRAQQGR
+>PROKKA_01126
+MAPTDPQDRLFTPQAVTFLALVACPVLAFVCAVMGLILVLQGKTIAGLVFLIVLTQVFAV
+GGLIAWNKRKRAQQGR
+>PROKKA_01051
+MADLPSDEKAPLLDAQAVTFLTLIAFPVLAFVCAVMGLILVLQGKVVAGVVFLVVLTQVF
+AAGGLITWNRRRRDRSGR
+>PROKKA_01680
+MAPTDSDQRLLSPQAVSFLALVVLPVLAFVCAVFGLILVLQGKTIAGLVFLLVLTQVFAV
+GGFIAWNKRKRAQQGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001427.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001427.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1798210c1579d2e1387858d43aef34924142def3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001427.fa
@@ -0,0 +1,20 @@
+>PROKKA_01755
+MSVNPDVAGRSYPPAPPFQVGREAVRGFAEAVQAQHPAHHDVAAARALGHADLVAPPTFA
+VVIAQRAEAAVVADPELGIDFSRVVHADERFVHHRPLVAGDEVVATVRVEAVKSLGGNRM
+VTTVTEIADLDGAAVSTVTSTLLVRGEES
+>PROKKA_01462
+MSVNPDVAGRSYPPAPPFQVGREAVRGFAEAVQAQHPAHHDVAAARALGHADLVAPPTFA
+VVIAQRAEAAVVADPELGIDFSRVVHADERFVHHRPLVAGDEVVATVRVEAVKSLGGNRM
+VTTVTEIADLDGAAVSTVTSTLLVRGEES
+>PROKKA_01122
+MSVNPDVAGRSYPPAPPFQVGREAVRAFASAVQAQHPAHHDVEAARALGHADLLAPPTFA
+VVIAQRAEAAAVNDPEVGIDFSRVVHADERFVHHRPLVAGDEVVATVRIASVKSLGGNDM
+VTTVTEIADADGAPVSTVTSTLLVRGEES
+>PROKKA_01047
+MSETESLVGRTYPPAPPYQVGREAVRAFADAVQAAHPAHTDVDAARALGYADVVAPPTFA
+VVVAQRAEAAVVADPEAGIDFSRVVHADERFTHHRPIVAGDELTATVLIEAVKELGGNRM
+VTTVTEIVDAAGAPVSDVASTLLVRGEES
+>PROKKA_01684
+MSVNPDVAGRSYPPAPPFQVGREAVRGFAEAVQAQHPAHHDVAAARALGHADLVAPPTFA
+VVIAQRAEAAVVADPELGIDFSRVVHADERFVHHRPLVAGDEVVATVRVEAVKSLGGNRM
+VTTVTEIADLDGAPVSTVTSTLLVRGEES
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001429.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001429.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de7cb6da785d6c5f75e9dc8a21d927056c0db032
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001429.fa
@@ -0,0 +1,66 @@
+>PROKKA_01759
+MSDILDPQTTAEVAPELAEAEQEATGTVPQVDAAPEAPAEPAAPEAPAEPAGPTFLDLGL
+DARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETTD
+VTGRADTPQVLVLAPTRELALQVADAFDSYAKHLDDVSVLAVYGGSPYGPQLAGLRRGAQ
+VVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRMGFAEEVDRILASTPDTKQTALFS
+ATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKFEALSRILETEEHDG
+VIAFVRTRAGTEELAQKLTRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAAR
+GLDVERISHVVNYDIPQDAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQ
+VEEMAVPSVADVNAARKRRFADGITRTLERASEEELAVFGEIVAAYVDEHEAEPARVAAA
+LGMMAQGGRPLLAREQEIPFGGARGRKDRDGGREGGRDGGRERGTSDGRGSRGPAREPAA
+GNVTYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTSAQLEA
+AANAEINGRRLGLRKDTGRPTRAERDGEDRGERRGGFRKDRGERGERGGFRGDRDGGQRG
+GYRKDRDDRGSREDRGGFRKDRDDRSFRGDRRGRPGGRKPRWGAQERSDRGARR
+>PROKKA_01466
+MSDILDPQTTAEVAPELAEAEQEATGTVPQVDAAPEAPAEPAAPEAPAEPAGPTFLDLGL
+DARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETTD
+VTGRADTPQVLVLAPTRELALQVADAFDSYAKHLDDVSVLAVYGGSPYGPQLAGLRRGAQ
+VVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRMGFAEEVDRILASTPDTKQTALFS
+ATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKFEALSRILETEEHDG
+VIAFVRTRAGTEELAQKLTRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAAR
+GLDVERISHVVNYDIPQDAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQ
+VEEMAVPSVADVNAARKRRFADGITRTLERASEEELAVFGEIVAAYVDEHEAEPARVAAA
+LGMMAQGGRPLLAREQEIPFGGARGRKDRDGGREGGRDGGRERGTSDGRGSRGPAREPAA
+GNVTYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTSAQLEA
+AANAEINGRRLGLRKDTGRPTRAERDGEDRGERRGGFRKDRGERGERGGFRGDRDGGQRG
+GYRKDRDDRGSREDRGGFRKDRDDRSFRGDRRGRPGGRKPRWGAQERSDRGARR
+>PROKKA_01118
+MSDALDPQTTPEAQVDAAELAEARQEAAEAAAPKAETPETAAAATETDSAPEAETAEEPE
+APAEPAGPTFLDLGLDARVLAAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTG
+AFALPALARLAETADVNGRADTPQVLVLAPTRELALQVADAFDSYAKHLEDVSVLAVYGG
+SPYGPQLAGLRRGAQVVVGTPGRVIDHLERGSLDLSDLQTLVLDEADEMLRMGFAEEVDR
+ILASTPDTKQTALFSATMPPAIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWK
+LEAFTRILETEDHDGVIAFVRTRAGTEELAQKLNRAGFKAVAISGDIAQKQREKTVEDLK
+AGRVDILVATDVAARGLDVERISLVVNYDIPQDAESYVHRIGRTGRAGRQGDAVLFMTPR
+ERFLLKQIERTTRQQVEEMAVPAVKDVNAARKRRFADGITRTLERASEEELAVFGEIVAA
+YVEEHDAEPSRVAAALGMMAQGGRPLLAKEQEIPTGPRGRKERDGGRDGGREHGTADGRG
+SRGPAREPAAGNATYWIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELP
+ADLTPAQLEAAANIEISGRRLGLRKDTGRPTRAERDGDERRGGFRKDRGERGGHGGHRGG
+FRKDRDERGFRGDREERGGFRGDRDDRGDRGGFRKDREDRGGFRKDREDRGDRGGFRKDR
+EDRGGFRKDRDERGGFRGGKAGGRKPRWGAQERSDRGPRR
+>PROKKA_01043
+MTPHETIPADDQAPVDLTEFDPELAETTAEAPAAEQDADDAEADAEPAGPTFLSLGLDAR
+VLAAVEDLGYQRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETQDVNG
+RSQAPQILALAPTRELALQVAEAFESYAKHLDDVSVLAVYGGAPYGPQLAGLRRGAQVVV
+GTPGRVIDHLERGNLDLSQLQTLVLDEADEMLRMGFAEEVDRILAETPDSKQTALFSATM
+PPAIRRISAQYLNDPEEVAVARQSTTGTNIRQRYLQIAHQWKFEAMTRILETEDHEGVIA
+FVRTRAGTDELAQRLNQAGFSAVAISGDVAQKQREKTVDDLKAGRVDILVATDVAARGLD
+VERISLVVNYDIPQDAESYVHRIGRTGRAGRSGDAVLFMTPRERFLLKQIERTTRQEVEE
+MQVPTVAQVNEARTRGVVAGIGRTLETASEADLDTYARMVAEYVEANDVDPARAAAALAL
+MAQGGRPLLTEADEVPAGGRVRRDRDRDDRRERGDRSERGDRDGRGSRGPRREPAAGNAT
+YWIGVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHALVELPADLTAAQLDAAANT
+EINGRRLNLRKDTGRPTRAERDGDGERGHRGPREDRGGFRRDRGDRGGFRRDRGERPERG
+GFRKDRDDRGPREDRGGFRHDRDDRGGRPGARKPRWGSDDRRDRGPRR
+>PROKKA_01688
+MSDILDPQTTAEAAPELAEAEQEATGTVPQVDAAEPAAPEAPAGPAGPTFLDLGLDARVL
+AAVEDLGYTRPSPIQEATIPLLLDGRDVVGLAQTGTGKTGAFALPALSRLAETTDVTGRA
+DTPQVLALAPTRELALQVADAFDSYAKHLDDVSVLAVYGGSPYGPQLAGLRRGAQVVVGT
+PGRVIDHLERGSLDLSDLQTLVLDEADEMLRMGFAEEVDRILASTPDTKQTALFSATMPP
+AIRRISAQYLNAPEEVAVARQSTTSATIRQRYLQVGHQWKFEALSRILETEEHDGVIAFV
+RTRAGTEELAQKLTRAGFKAVAISGDIAQKQREKTVEDLKAGRVDILVATDVAARGLDVE
+RISHVVNYDIPQDAESYVHRIGRTGRAGRQGDAVLFMTPRERFLLKQIERTTRQQVEEMA
+VPSVADVNAARKRRFADGITRTLERASEEELAVFGEIVAAYVDEHEAEPARVAAALGMMA
+QGGRPLLAREQEIPFGGARGRKDRDGGREGGRDGGRERGTSDGRGSRGPAREPAAGNATY
+WIAVGHQDRVRPGNIVGALANEVGLPASAIGAIDLRGNHSLVELPADLTSAQLEAAANAE
+INGRRLGLRKDTGRPTRAERDGEDRGGFRKDRGERGERGGFRGDRDGGQRGGYRKDRDDR
+GSREDRGGFRKDRDDRSFRGDRRGRPGGRKPRWGAQERSDRGARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001433.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001433.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7f2e6e3bbd508574cb37cf115ff3f98fae1abb1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001433.fa
@@ -0,0 +1,50 @@
+>PROKKA_01763
+MQYAENVLELIGHTPLVKLHSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEEAEREGL
+LGPGGTVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLSAYGAELVVTPTAV
+DPTSEESYYGVADRLVREIPGAYQPNQFFNPAAPASHYETTGPEIWEDTAGRVTHVVMGA
+GTGGTITGTGRYLKEVSADRPSGAVRVIGADPSGSVYSGGAGRPYFVEGVGEDMWVDNYD
+PAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARELGPEDVMVIVLPD
+SGRGYLAKIFNDPWMDERGFDYDVRETVLPAWARGRTRSAVPQTDDDGATGAAGGAGTPV
+EALEHADAEPATRAGAPAEADRWSATAGELLTEKADLFPGSVPTLVTAAPTTSVADAVAT
+MNRYGVDALPVILEPRHDLRIGEVRGTVSSAALADALAEGRATAQTPVADVMGPVLPCLG
+ARTPLRAVARRLAQDPVLLVLEAGRVQGVVTLHDVLAHVTA
+>PROKKA_01470
+MQYAENVLELIGHTPLVKLHSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEEAEREGL
+LGPGGTVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLSAYGAELVVTPTAV
+DPTSEESYYGVADRLVREIPGAYQPNQFFNPAAPASHYETTGPEIWEDTAGRVTHVVMGA
+GTGGTITGTGRYLKEVSADRPSGPVRVIGADPSGSVYSGGAGRPYFVEGVGEDMWVDNYD
+PAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARELGPEDVMVIVLPD
+SGRGYLAKIFNDPWMDERGFDYDVRETVLPAWARGRTRSAVPQMDDDGATGAAGGAGTPV
+EVLEHADAEPATRAGAPAEADRWSATAGELLTEKADLFPGSVPTLVTAAPTTSVADAVAT
+MNRYGVDALPVILEPRHDLRIGEVRGTVSSAALADALAEGRATAQTPVADVMGPVLPCLG
+ARTPLRAVARRLAQDPVLLVLEAGRVQGVVTLHDVLAHVTA
+>PROKKA_01114
+MQYAENVLELIGHTPLVKLNSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEDAEKAGK
+LAPGGTVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLTAYGAEIVVTPTSV
+APESEESYYGVANRLERDIPGAYQPNQFFNPAAPASHYETTGPEIWEDTAHRVTHVVIGA
+GTGGTITGTGRYLKEVSADRESGPVRVIGADPSGSVYSGGTGRPYFVEGVGEDMWVDNYD
+PAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARDLGPKDVMVIVLPD
+SGRGYLAKIFNDPWMDERGFDYDVQDTVLPEWARGRTRSAAPEADDDGAQGAAGGAGTPV
+EALEQADAAAGADAGQVADAPAEADRWAATAGELLAEKADLFPGSVPTLVTASPTTSVAD
+AVATMNRYGVDALPVVAEPRHDLRIGEVRGTVSAAALGEALAAGRVHPGTPVAEAMGPVL
+PCIGARTPLRAVARRLAQDPTLLVLSAGRVAGVVTLHDVLAHVTA
+>PROKKA_01039
+MGAVNEINPAPAHGQPRWAENVLDLIGRTPLVKLNRVTEGVEATVLVKVEYLNPGGSVKD
+RIALRMLEEAERDGKLAPGGTVVEPTSGNTGVGLALVAQQKGYRAVFVTPDKVGQEKRDV
+LTAYGAEIVVTPTSVEPSSDESYYGVANRLEKEIPGAFQPNQFFNPAAPASHYETTGPEI
+WEDTAGTVTHVVIGAGTGGTITGTGRYLKEVSADRASSPVRVIGADPEGSVYSGGTGRPY
+FVEGVGEDMWPGNYDPSVPDEVIAVSDDAAFEMTRRLAAEEGLLVGGSSGMAVVAGLQAA
+RELGPDDVMVIVLPDSGRGYLAKIFNDDWMDERGFHYAQEETVLPAWAQGRTRSAVATAP
+SDSREGARGGVGTPVEAPGEGSPQDGAATATPAPGSRWDASLADVLADKEDLFPGSVPTL
+VTASPDTTVADAVATLARYGVDALPVIAEPRHDLRINEVRGTVSAPALAAALAAGRVQPG
+SAVSDVMEPALPSVGAAMTLRAAARRLQEDPILLVMDAGIVQGVVTLHDVLVYATA
+>PROKKA_01692
+MQYAENVLELIGRTPLVKLHSVTEGIEATVLVKVEYLNPGGSVKDRIALKMIEEAEREGL
+LGPGGTVVEPTSGNTGVGLALVSQLKGYRTVFVTPDKVGQEKRDVLSAYGAELVVTPTAV
+DPTSEESYYGVADRLVREIPGAYQPNQFFNPAAPASHYETTGPEIWEDTAGRVTHVVMGA
+GTGGTITGTGRYLKEVSADRPSGPVRVIGADPSGSVYSGGAGRPYFVEGVGEDMWVDNYD
+PAVPDEVIAVEDAEALAMTRRLAAEEGLLVGGSSGLAVVAGLRAARELGPEDVMVIVLPD
+SGRGYLAKIFNDPWMDERGFDYDVRETVLPAWARGRTRSAVPQTDDDGATGAAGGAGTPV
+EVLEHADAELATRAGAPAETDRWSATAGELLTEKADLFPGSVPTLVTAAPTTSVADAVAT
+MNRYGVDALPVILEPRHDLRIGEVRGTVSTAALADALAEGRATAQTPVADVMGPVLPCLG
+ARTPLRAVARRLAQDPVLLVLEAGRVQGVVTLHDVLAHVTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001436.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001436.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f0663768dc207670f35909423f3ac837dad8245
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001436.fa
@@ -0,0 +1,20 @@
+>PROKKA_01768
+MASDSTFDVVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMRASSEERVK
+AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEATMKEGIDQPTAKKITKLIRDEGPK
+SVKAQIQGDELRVSSKSRDDLQSVIAMLKDFEDADLQFVNFR
+>PROKKA_01475
+MASDSTFDIVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKASSEERVK
+AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEATMKEGIDQPTAKKITKLIRDEGPK
+SVKAQIQGDELRVSSKSRDDLQSVIAMLKDFEDADLQFVNFR
+>PROKKA_01109
+MASDSTFDVVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKASSEERVK
+AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEASMKEGIDQPTAKKITKLIRDEGPK
+SVKAQIQGDELRVSSKSRDDLQEVIAMLKDFEDADLQFVNFR
+>PROKKA_01035
+MASDSTFDVVSKVDKQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKANSEERVK
+AVLDVFESKLVKRGISLKSLDCGEPFASGKETRMEASIKEGIDQPTAKKITKLIRDEAPK
+SVKAVIQGDELRVSSKSRDDLQETIALLKTFEDADLQFINFR
+>PROKKA_01697
+MASDSTFDVVSKVDSQEVSNALNQAQKEIAQRYDFKGVGAEIDFSGEKILMKASSEERVK
+AVKDVFESKLVKRGISLKSLDAGAPFASGKEYRIEATMKEGIDQPTAKKITKLIRDEGPK
+SVKAQIQGDELRVSSKSRDDLQSVIAMLKDFEDADLQFVNFR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001439.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001439.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b68622e74f0afc90e1491830770f6aa9ac990e02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001439.fa
@@ -0,0 +1,35 @@
+>PROKKA_01772
+MVRVSPSSPAVRPGVTPDGAAPDTGALPTVSPAPADDPRGLALGFTAYFVWGLLPLYMAV
+LAPAGALEIVVVRIGFALIFCLLLLTVMRRLRELGTALATPGRWGTTGLAAGIIAVNWLL
+YAVSVTTGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWVAVGIAVAAVVVMSAAMGQ
+VPWIALGLATSFGLYGFVKKRFPSPVHAVTAMTAETVVLIPVFVVGSVLLAQAGLLTTVT
+EGPGHFWLMAGLGVLTAVPLILFSAAARSLTLTTLGMLQYTAPILQFLVAVTVLGEQMPA
+ARWAGFGLIWLSLAVFTLDQLNASRLQRRAVRAGQGAHA
+>PROKKA_01479
+MVRVSPSSPAVRPGVTPDGAAPDTGALPTVSPAPADDPRGLALGFTAYFVWGLLPLYMAV
+LAPAGALEIVVVRIGFALIFCLLLLTVMRRLRELGTALATPGRWGTTGLAAGIIAVNWLL
+YAVSVTTGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWVAVGIAVAAVVVMSAAMGQ
+VPWIALGLATSFGLYGFVKKRFPSPVHAVTAMTAETVVLIPVFVVGSVLLAQAGLLTTVT
+EGPGHFWLMAGLGVLTAVPLILFSAAARSLTLTTLGMLQYTAPILQFLVAVTVLGEQMPA
+ARWAGFGLIWLSLAVFTLDQLNASRLQRRAVRAGQGAHA
+>PROKKA_01105
+MARVSPSPASRRPGVPPDAAAPDTGALPAVSPAPANDPRGLALGFTAYFLWGLLPLYMAR
+LAPAGAVEIVVVRVGFALVFCLVLLALMRRLRELRTSLATPARWGATALAAGFIGTNWLL
+YAVSVTTGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWAAVGIAVAAVVVMSVAMGQ
+VPWIALGLAFSFGLYGFVKKRFPTPVHAVTTMTAETVVLLPAFAVGMVWLGQAGLLTTFT
+EGPAHFWLMAGLGVLTAVPLILFSAAAKALTLTTLGMLQYTAPILQFIVAVTVLGEQMPV
+ARWAGFGLIWVSLLVFTLDQVRVSRLHRRAARAGHGARA
+>PROKKA_01031
+MAQVSHSPSPSGPDAPRDGVPVEAAAPDTGALPTITPAPANDPRGLALGFAAYVIWGLLP
+LYMAATAPAGAVEIVVVRVVFALIFCLLLLAVMRRLPELRTALATRARWGSITLAAAFIA
+VNWLLYAHSVTSGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWIAVGIAVVAVVVMS
+VAMGQVPWIALGLAFTFGMYGFVKKRFPVPVHAVTTMTAETVVLLPAFAVGMVFLVQAGL
+LTTVSEGPGHFWMMAGLGVLTAVPLILFSAATQSLTLTTLGMLQYIAPIMQFLVAVAVLG
+EHMPAARWAGFALIWLSLVVFTLDQANASRVQRRAARAAGRART
+>PROKKA_01701
+MVRVSPSSPAVRPGVTPDGAAPDTGALPTVSPAPADDPRGLALGFTAYFVWGLLPLYMAM
+LAPAGALEIVVVRIGFALIFCLLLLTVMRRLRELGTALATPGRWGTTGLAAGIIAVNWLL
+YAVSVTTGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWVAVGIAVAAVVVMSAAMGQ
+VPWIALGLATSFGLYGFVKKRFPSPVHAVTAMTAETVVLIPVFVVGSVLLAQAGLLTTVT
+EGPGHFWLMAGLGVFTAVPLILFSAAARSLTLTTLGMLQYTAPILQFLVAVTVLGEQMPA
+ARWAGFGLIWLSLAVFTVDQLNASRLQRRPVRVRRGAHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001443.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001443.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c9f652cf93bed4e9ff3cb4abd68d107b4003c30
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001443.fa
@@ -0,0 +1,45 @@
+>PROKKA_01776
+MTDTPTSPAPDSTSAVVRRADVLISGCGPAGATAAAHLAAAGLDVVVLEKTAHPREKVCG
+DGLTPQAVRELQLLGVPHRGEPGDDGGWRVIRGLRLRAGERSVDVPWAPTQTWPDYALTR
+TRRDFDALLADLARTRGAEVRERHAVTGVVRDEAGRVVGLDAELIAPNGRKTGETARFTA
+PIVLACDGVSARAAVSAGLHRREDRPMGVAVRAYYTAGAAVDGAIPAPPGDRGEWMESWL
+RLPDAEGNPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLKSWTGALTADWGIA
+EQTRTSRILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARLAADLAV
+QAHAAGTDGAADAILSRYPVITQHLWGRHFALGARFARLIGDPRVMKAALGAGMAAPPLL
+RAAVKVMGNTVDARGGDAVDRAVRVLEALTPALTTAGGAPLGRLAR
+>PROKKA_01483
+MTGTPTSPAPASTPAVVRRADVLISGCGPAGATAAAHLAAAGLDVVVLEKTAHPREKVCG
+DGLTPQAVRELQLLGVPHRGEPGDDGGWRVIRGLRLRAGERSVDVPWAPTQTWPDYALTR
+TRRDFDALLADLARTRGAEVRERHAVTGVVRDEAGRVVGLDAELIAPNGRKTGETARFTA
+PIVLACDGVSARAAVSAGLHRREDRPMGVAVRAYYTAGAAVDGAIPAPPGDRGEWMESWL
+RLPDAEGNPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLKSWTGALTADWGIA
+EQTRTSRILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARLAAELAV
+QAHAAGTDGAADAILSRYPVITQHLWGRHFALGARFARLIGDPRVMKAALGAGMAAPPLL
+RAAVKVMGNTVDARGGDAVDRAVRVLEALTPALTTAGGAPLGRLAR
+>PROKKA_01101
+MTAAPSSSPSESAPPPVVRRADVLISGGGPAGATAAAHLAAAGLDVVVLEKTAHPREKVC
+GDGLTPQAVRELQLLGVPHRGEPGDDGGWQVIRGLRLRAGERSVDVPWPETRSWPDYALT
+RTRRDFDALLADLARERGAEVRERHAVTSVVRDDAGRVCGLDAELIAPNGRKTGETARFE
+APVVLSCDGVSARAAVSAGIHRREDRPMGVAVRAYYTAGPAADGAVPAPPGDRGEWMESW
+LRLPDAQGRPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLKSWSGALTPDWGI
+SEQTRVSKILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARIAADLA
+VQAHAAGSDAAADTVLSRYPVITQHLWGRHFALGARFARLIGDPRVMRASLGAGMAVPPL
+LRAVVKVMGNTVDPERGDAVDRAVRVLEALTPALTTADSAPLGRLAR
+>PROKKA_01025
+MTEHPTPAAAPVVRRADVLISGAGPAGATAAAHLAAAGLDVVVLEKSAFPREKVCGDGLT
+PQAVQEIRNLGIEHQGGPGDDGGWHAVRGLRLRAGERSVDVPWPATQSWPDYALTRTRKD
+LDALLADTARARGAEVRERHAVTGVTRDDAGRVDGLEAELIAENGRKTGERVRFAAPLVL
+ACDGVSARAAVSMDVHRRTDRPMGVAVRAYYTAGPVGADGAVPRPPGDRVDWMESWLRLP
+DEHGNPLPGYGWLFPLADGTVNVGLGILDTSPLFGKLDYRALLKQWSGALSEDWGISEET
+RTSKILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARIAADLAVQAH
+AAPNTPAADAVLARYPVITQHLWGRHFRLGTVFARLIGEPRVMRAALATGMAVPPLLRTV
+ARVMGNVVDPSGGDAVDRAVRILESVTPSLTTADAPGVGRLAR
+>PROKKA_01705
+MTGTPTSPAPASTPAVVRRADVLISGCGPAGATAAAHLAAAGLDVVVLEKTAHPREKVCG
+DGLTPQAVRELQLLGVPHRGEPGDDGGWRVIRGLRLRAGERSVDVPWAPTQTWPDYALTR
+TRRDFDALLADLARTRGAEVRERHAVTGVVRDEAGRVIGLDAELIAPNGRKTGETARFTA
+PIVLACDGVSARAAVSAGLHRREDRPMGVAVRAYYTAGAAVDGAIPAPPGDRGEWMESWL
+RLPDAEGNPLPGYGWLFPLADGTVNVGLGILDTSPQFGKLDYRGLLRSWTGALTADWGIA
+EQTRTSRILGAALPMAFNRTPQHVPGMLLVGDAAGMVSPFNGEGIGFAMEAARLAADLAV
+QAHAAGTDGAADAILSRYPVITQHLWGRHFALGARFARLIGDPRVMKAALGAGMAAPPLL
+RAAVKVMGNTVDARGGDAVDRAVRVLEALTPALTTAGGAPLGRLAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001446.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001446.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c74aca496140341f266702743de39f77f6cd5dcc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001446.fa
@@ -0,0 +1,50 @@
+>PROKKA_01782
+MSNTFLLPDLGEGLTEADIVRWLVAEGDTVAVDQPMVEVETAKALVEVPSPYAGTVLTLH
+GAEGETMDVGSPLITIGAAGESGEGSAPAAGTEALAVPPATGAAAAEAARPGALSYREEE
+MAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHRATSRSRPSKRGRGAARPTPAP
+TAGAGAPRVTSPIVRKLAREKGVDVAALTGTGPDGLITRADVLAAAEGSAPQAAPAQAPL
+VAAVPAAEAAAQPGAVDGRTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVT
+ALLELRASLKAKDSENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDGVHL
+GLAVQTDRGLMVPSVEHAEKLSADELTAAVNDTVSRARAGRAAPAELTRGTFTLNNYGPL
+GTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTFDHRVTDGATASAFLT
+FVADCLHDPTAALARI
+>PROKKA_01489
+MSNTFLLPDLGEGLTEADIVRWLVAEGDTVAVDQPMVEVETAKALVEVPSPYAGTVLTLH
+GAEGETMDVGSPLITIGAAGESGEGSAPAAGTEALAVPPATGAAAAEAARPGALSYREEE
+MAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHRATSRSRPSKRGRGAARPTPAP
+TAGAGAPRVTSPIVRKLAREKGVDVAALTGTGPDGLITRADVLAAAEGSAPQAAPAQAPL
+VAAVPAAEAAAQPGAVDGRTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVT
+ALLELRAALKAKDPENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGQDEIVEVDGVHL
+GLAVQTDRGLMVPSVEHAEKLSADELTAAINDTVSRARAGRAAPAELTRGTFTLNNYGPL
+GTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTFDHRVTDGATASAFLT
+FVADCLHDPTAALARI
+>PROKKA_01096
+MSNTFLLPDLGEGLTEADIVRWLVAEGDEVVVDQPIVEVETAKALVEVPSPYAGTVLTLH
+GAEGQTMEVGRPLITVGAAGESGEGSAPVAGTEAQAVPPATGEDAAEADRPGALSYREEE
+MAGVQPKPDKARGGDGDVAGSDEEASGAVLIGYGTSGHSATSRTRPSKRGRRGAGTTTAG
+GSGAASGQGEQAGQARAPRVTSPIVRKLAREQGVDVAALTGTGPDGLITRADVLSAAQGG
+DAPQAAAAPAAQPAATAGAASTVGAGSADARTGLAVVARTPISGVRKVIADQLSRSRREV
+PEVTAWLDVDVTALLELRAALKAKDAENAPSLLGLIARFTLAGLRRYPVMNARIEAGADG
+KDEIVEVDGVHLGLAVQTDRGLMVPSVEHAERLSADELTAAINETVTRAREGKAAPAELT
+RGTFTLNNYGPLGTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTFDHR
+VTDGATASAFLTFVADCLNDPQSALARI
+>PROKKA_01019
+MSNTFLLPDLGEGLTEADIVRWLVAEGDEVAVDQPMVEVETAKALVEVPSPFAGTVLTLH
+GAEGETMEVGAPLITVGAVGESAGDAPPPSSAADAGTAPAADGAVPGALSYREEERAGVQ
+PKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHTATSRSRPSKRARGGAGTTQAAAGAAP
+AASGRAPRVTSPIVRKLARERGVDVATLTGTGPDGLITRADVLGAAGGASAPQDAQAPAP
+VQTAPSAAAQAPAVAAGATDARTGLAVVARTPISGVRKVIADQLSRSRREVPDVTAWLDV
+DVTALLELRAQLKAKDPENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDG
+VHLGLAVQTDRGLMVPSVEHAEKMSADELTRAINDTVSRAREGRAAPAELTRGTFTLNNY
+GPLGTDGATPILNIPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTFDHRVTDGATASA
+FLTFVADCLNDPQAALARI
+>PROKKA_01711
+MSNTFLLPDLGEGLTEADIVRWLVAEGDTVAVDQPMVEVETAKALVEVPSPYAGTVLTLH
+GAEGETMDVGSPLITIGAAGESGEGSAPVAGTEALAVPPSTGADAAEAARPGALSYREEE
+MAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHRATSRSRPSKRGRGATRPTPAP
+TAWAGAPRVTSPIVRKLAREKGVDVAALTGTGPDGLITRADVLAAAEGSAPQAAPAQAPS
+VAAVPAAEAAAQPGAVDGRTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVT
+ALLELRAALKAKDPENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDGVHL
+GLAVQTDRGLMVPSVEHAEKLSADELTAAVNDTVSRARAGRAAPAELTRGTFTLNNYGPL
+GTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIMVRKVTEMTVTFDHRVTDGATASAFLT
+FVADCLHDPTAALARI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001447.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001447.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0e41c0299c123c9878370e14001207bec3980ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001447.fa
@@ -0,0 +1,35 @@
+>PROKKA_01783
+MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTARFGEERCFDTPLAE
+SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPITIRIPYG
+GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRSAIRLDDPVVFMEPKKMYWTK
+AELDLDQLRAEFEEGWARVEDKKEHGEAWARAAVVREGTDVTLVSYGPSVPTCLAAAHAA
+AEEGLSVEVVDLRTVNPLDEDTMAASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS
+LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLDAEEARA
+>PROKKA_01490
+MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTARFGEERCFDTPLAE
+SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPITLRIPYG
+GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRSAIRLDDPVVFMEPKKMYWTK
+AELDLDQLRAEFEEGWARVEDKKEHGEAWARAAVVREGTDVTLVSYGPSVPTCLAAAHAA
+AEEGLSVEVVDLRTVNPLDEDTMAASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS
+LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLDAEEARA
+>PROKKA_01095
+MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTKRFGEERCFDTPLAE
+SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPMTIRIPYG
+GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRAAIRLDDPVVFMEPKKMYWTK
+AELDLEDLRAEFEERWGRVEEKKEHGEAWARAAVVRAGSDVTLVSYGPSVPTCLAAARAA
+EEEGLSVEVVDLRTVNPLDEDTMVASVSKTGRAVVVAEPQGFASVASELVARIQQRCFHS
+LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLDAEEARA
+>PROKKA_01018
+MANLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTQRFGDERCFDTPLAE
+SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQVASHVAKMRNRTKGGAPMPIVIRIPYG
+GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYLMLRSAIRLDDPVVFMEPKKMYWTK
+ADLDLDELRAEFDEQWARAQEKTAQGEAWARAAVVRQGADVTLVSYGPSVPTCLAAAQAA
+AEEGLSVEVVDLRTVNPLDEDTMAASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS
+LAAPVGRVTGFDIPFPAPKLEEHHLPNVDRILDAIDDLNWDLDAEEARA
+>PROKKA_01712
+MATLTFAAALNAALADEMAADDMVVVFGEDVGTLGGVFRITDGLTARFGEERCFDTPLAE
+SGIAGMAVGMALGGARPVIEMQFDAFAYPAFEQIASHVAKMRNRTKGATPMPITIRIPYG
+GGIGGVEHHCDSSESYYAHTPGLKVYTPASVKDAYMMLRSAIRLDDPVVFMEPKKMYWTK
+AELDLDQLREEFEEGWARVEDKKEHGEAWARAAVVREGTDVTLVSYGPSVPTCLAAAHAA
+AEEGLSVEVVDLRTVNPLDEDTMTASVAKTGRAVVVAEPQGFASVASELVARIQQRCFHS
+LAAPVGRVTGFDIPFPAPKLEEHHLPNIDRILDAIDDLNWDLGAEEARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001448.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001448.fa
new file mode 100644
index 0000000000000000000000000000000000000000..101c425ffef3c29fcf70ac3cbeccd13ba22c0635
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001448.fa
@@ -0,0 +1,40 @@
+>PROKKA_01784
+MSDPTPAVPGAARTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQGTE
+PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLG
+EDDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHAVG
+MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ
+SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAHTN
+TDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQIARDAEDVAQQLRDAMNA
+ETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA
+>PROKKA_01491
+MSDPTPAVPGAVRTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQGTE
+PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLG
+EHDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHAVG
+MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ
+SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAHTN
+TDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQITRDAEDVAQQLRDAMNA
+ETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA
+>PROKKA_01094
+MSDPTPAVSGSARTDQAEARPNAGAAFGISLEEYLLPATRRIQLIGEDGTLLSPEEQGAE
+PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLG
+KQDWLFPTYRDTVAVIARGVPPLEVMVSYQGTWHQGYDPNEHHVSVQSTPLTTQLLHAVG
+MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ
+SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVDLCRQGQGPFLVEADTYRMQAHTN
+TDDPTRYREDAEVQEWEARDPLRRMTAYLESTGALTEEVSAEIAQAAEDVAKDLRDAMNA
+EAELDPLELFDHVYSVQTPQLAAQRAQLTEELSRSENQEA
+>PROKKA_01017
+MTSTRPGPATPDTRTEAAAAFGITLEEYLLPAARRIQLISPEGELLPAEEQGTAPGHEYP
+LPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLGQDDWLF
+PTYRDTVAVIARGVAPLDVMVSFQGTWHQGYDPKEHRVSVQSTPLTTQLLHAVGMAKAAR
+LRGEDVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFLVQNNKFAISVPFAKQSAAPSL
+AHKAVGYGLAGERVDGNDLAALLAVLGRAVDLCREGKGPFLVEADTYRMQAHTNTDDPTR
+YREDSEVKEWEVRDPLRRMTAYLESTGALTAEVSTSIAKDAEDVAQQLRDAMNADVELDP
+LELFDHVYSVQTPQLAAQRAQLAEELSRSENKEA
+>PROKKA_01713
+MSDPTPAVPGAVRTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQGTE
+PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVSLG
+EDDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHAVG
+MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ
+SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAHTN
+TDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQIARDAEDVAQQLRDAMNA
+ETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001451.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001451.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a3a56f5025045e6adf3c12d718a347bf13a82abe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001451.fa
@@ -0,0 +1,70 @@
+>PROKKA_01798
+MPQTTSHAPVPPSASAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD
+QAPLREAIVGEIKARTVETDRSVPARRDGWWYFVRTREGAEYPIHCRVPARDTGDLEADW
+TPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPDATRVAYAVDHTGDERFTLRV
+REIATGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVRAHVLGTDPAEDVLLHE
+EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLAD
+VEPVTDADGVRRLLVVHDRALDDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVK
+VDGVMVTLTHAALAVRRETTPRVVVAELDAVLAGQAAHWREPAFDEELYACHLSATAAES
+PFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPSSVTGE
+DVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGG
+GELGRRWYEDGKKLAKRHSFTDFVDATRHLVGLGWADPARVACMGGSAGGLLMGAVLNLA
+PELYRACLAVVPFVDALTTILDPELPLSALEWEEWGNPIEDAAVYAAMRAYTPYENVRAV
+DYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQATPLAEGGAPILLRTEMDGGHGGA
+SGRYQGWEDTAWEYAFLLTALGATARIV
+>PROKKA_01495
+MPQTTSHAPVPPSASAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD
+QAPLREAIVGEIKARTVETDRSVPARRDGWWYFVRTREGAEYPIHCRVPARDTGDLEADW
+TPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPDATRVAYAVDHTGDERFTLRV
+REISTGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVKAHVLGTDPAEDVLLHE
+EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLAD
+VEPVTDADGVRRLLVVHDRALDDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVK
+VDGVMVTLTHAALAVRRETTPRVVVAELDAVLAGQAAHWREPAFEEELYACHLSATAAQS
+PFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPSSVTGE
+DVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGG
+GELGRRWYEDGKKLAKRHSFTDFVDATRHLVDLGWADPARVACMGGSAGGLLMGAVLNLA
+PELYRACLAVVPFVDALTTILDPELPLSALEWEEWGNPIEDAAVYEAMRAYTPYENVRAV
+DYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQATPLAEGGAPILLRTEMDGGHGGA
+SGRYQGWEDTAWEYAFLLTALGATARID
+>PROKKA_01078
+MPQTTSHAPVPPSVSAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD
+QAPLRAAIFGEIKARTVETDRSVPSRRDGWWYFARTKEGAEYPVHCRVPAADTGDLEADW
+TPPVVTPDAPLEGEQVILDGNAEAEGHPFFALGGLHISPDSTRVAYAVDHTGDERFTLRV
+REIATGEDLPDVVENIAHGVRFDRSGARVLYTVWDDSWRPYQVKAHVLGTDPAQDQLLYE
+ESDPGMWTGFTGTADRTQLLIGVGNSEVSETHVVDLPESPDAPLPAPRLLIPRAWGMLAD
+VEPVTGADGVRRLLVVHDRTVARQDAADAGADAPAPNGMLSLVAEADVADRGAWRTVVPH
+REDVKVDGVMVTLTHAALAVRRETTPRVVVAPLDSVLAGEAADWREPAFEEELYACHLAS
+TAAESPFLRLAYTSWISPARVLDVSAATGEVHLRRETEVPGYDPSLYVAERVWAPASEPS
+SVTGEPVRIPVTVIRRKDVAADGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVYAVA
+HVRGGGELGRRWYEDGKKLAKRHSFTDFVDATRHLVDLGWADPARVACTGGSAGGLLMGA
+VLNLAPELYRACLAVVPFVDALTSILDPELPLSALEWEEWGNPIEDPEVYAAMRDYTPYE
+NVRAVDYPTIAAVTSLHDTRVLYVEPAKWVARLRRTVTSDQATPLAEGGAPVLLRTEMDG
+GHGGASGRYQGWEDTAWEYAFLLTALGATQRVD
+>PROKKA_01013
+MYETSLPTPPRAAARPTARTVHGETFTDDFEWMRAKTEQEVLDHLQAENAYTEAATADQA
+DLRAAIYGEIKAHTVETDQSVPARRDGWWYFVRTVEGKDYAVHCRVPAQDTGDALADWTP
+PVVPADAALPGEQVILDGNAEAAGHPFFSLGGMHISPDGALAAYAVDLAGDERYTLRVRE
+IATGTDLPDVVRNIAPGVRFDRSGTRLIYTVWDETWRPYQVRVHTLGTDAAEDAVLYEES
+DPGMWTGFDASADRTQLLIGVGNSEVSETWAVDLPVDASPLPAPRVLVPRTARMLADVEP
+FDMDGRRRLLIVHDRLADGTTAPNGMLSIVDEADVADRDAWRPVVPHADDVRVDGVLVTR
+THVGLAVRRDTTPRVLIAPLEGLREGSAPAWTEPSFDEELYMCRLAGVNLDSPFLRLSYA
+SWTTPARVLDVVAATGEVRLRREVEVPGFDREDYVAERWWAPASEPSSLTGEQVRIPLTV
+IRRRDVAQDGTAPAVVYGYGSYEMSMDPVFGVARLSLLDRGVVYVVAHVRGGGELGRAWY
+EDGKKAAKRHSFTDFVDATRFVADSGWVDPARIACTGGSAGGLLMGAVLNLAPELYRACL
+AVVPFVDALTSILDPDLPLSALEWEEWGNPIEDPEVYATMKAYTPYENVRAVDYPAIAAV
+TSLNDTRVLYVEPAKWVAQLRRTVTSDQTTPIAAGGSPILLRTEMDGGHGGASGRYQGWE
+DTAWEYAFLLTALGATARVD
+>PROKKA_01717
+MPQTTTHAPVPPSVAAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD
+QAPLREAIVGEIKARTVETDRSVPARRDGWWYFVRTREGAEYPIHCRVPARETGDLEADW
+TPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPDATRVAYAVDHTGDERFTLRV
+REIATGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVKAHVLGTDPAEDVLLHE
+EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLAD
+VEPVTDADGVRRLLVVHDRALDDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVK
+VDGVMVTLTHAALAVRRETTPRVVVTELDAVLAGQAAHWREPAFDEELYACHLSATAAES
+PFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPSSVTGE
+DVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGG
+GELGRRWYEDGKKLAKRHSFTDFVDATRHLVDLGWADPARVACMGGSAGGLLMGAVLNLA
+PELYRACLAVVPFVDALTTILDPELPLSALEWEEWGNPIEDAAVYAAMRAYTPYENVRAV
+DYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQARPLADGGAPVLLRTEMDGGHGGA
+SGRYQGWEDTAWEYAFLLTALGATRRVV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001456.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001456.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08206b1c2d6364c89b9dfd9f206b278b3a594b51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001456.fa
@@ -0,0 +1,15 @@
+>PROKKA_01803
+MRIFFYGLVRVVLFVALWALFYYVMDLWMIFAVIAAAILAFAVSYLFLDRLRTGATEDLS
+AAWEGRPGRRGRTETADADAEDAYTEGRFRE
+>PROKKA_01500
+MRILYYGLLRVALFFVLWWVGLQLGLGMVMATLAAAILTFAVSYLFLGRLRRGATQDLSA
+AWEGRPGRRGRTEAADAEAEDAYTQGRFRE
+>PROKKA_01070
+MRILYYGLLRVALFFVLWWVGLQLGLGMVMATLAAAILTFAVSYLFLGRLRRGATQDLSA
+AWEGRPGRRGRTEAADAEAEDAYTEGRFRE
+>PROKKA_01006
+MRLFLYGLVRVVLFFVIWALCYYVFGLGMLFSTLAAVILTFAVSYLFLTRLRLDASTDLQ
+NAWEGRPSRRGRTEAADAAAEDAYTDGRFPG
+>PROKKA_01724
+MRIFFYGLVRVVVFVALWALFYYVMDLGMIFGVIAATILTFAVSYLFLGRLRAGATEDLS
+AAWEGRPGRRGRTETADADAEDAYTEGRFRE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001461.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001461.fa
new file mode 100644
index 0000000000000000000000000000000000000000..892f17e866b8316bf5191bd357c33a58ee8ab4ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001461.fa
@@ -0,0 +1,10 @@
+>PROKKA_01812
+MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK
+>PROKKA_01509
+MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK
+>PROKKA_01062
+MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK
+>PROKKA_00997
+MGSVIKKRRKRMAKKKHRKLLRKTRHQRRNKK
+>PROKKA_01733
+MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001462.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001462.fa
new file mode 100644
index 0000000000000000000000000000000000000000..221ffdf686258cefe66face827f1f3d8b51dd98e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001462.fa
@@ -0,0 +1,40 @@
+>PROKKA_01813
+MSTTSTPPAPTPAAVVWDSSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVRIVEP
+PVATDEQLALVHDPEYVAAVRRAAATSSAEDGRFGLGTEDCPVFPDLHESAARIAGGSLV
+AAEAIWSGEVDRAVNFAGGMHHAARSSASGFCIYNDCAVAIQRLLDLGAERVAYVDVDAH
+HGDGTQSIFYDDPRVLTISLHETGISLFPGTGFANEIGGSAAQGTAVNVALPPRTGDAGF
+LRAAHAVVPPLLEAFAPDVLVSQHGCDGHLTDPLADLRLSVDGQRQLAFDVGDWADRFAY
+GRWLATGGGGYNPLRVVPRAWAHLTAAVLQTPIPVRSEIPAAWIEHVRALTADELTGDMS
+VHEGDDAERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRREVFPLHGLDPWFD
+>PROKKA_01510
+MSTTSTPPAPTPAAVVWDSSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVRIVEP
+PVATDEQLALVHDPEYVAAVRRAAATSSAEDGRFGLGTEDCPVFPDLHESAARIAGGSLV
+AAEAIWSGEVDRAVNFAGGMHHAARSSASGFCIYNDCAVAIQRLLDLGAERVAYVDVDAH
+HGDGTQSIFYDDPRVLTISLHETGISLFPGTGFANEIGGSAAQGTAVNVALPPRTGDAGF
+LRAAHAVVPPLLQAFAPDVLVSQHGCDGHRTDPLADLRLSVDGQRQLAFDVGDWADRFAH
+GRWLATGGGGYNPLRVVPRAWAHLTAAVLQTPIPVKSEIPAAWIEHVRTLTADELTGDMS
+VHEGDDAERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRREVFPLHGLDPWFD
+>PROKKA_01061
+MSTTSQRPAPTPAAVVWDPSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVSIIEP
+PVATDAQLALVHDPDYIAAVRRASEAASDEDAPFGLGTEDCPVFPDLHEASARIAGGTLA
+AAEAVWSGQVRRAVNFAGGMHHAARAKASGFCIYNDCALAIQRLLDLGAERVVYLDVDAH
+HGDGTQAIFYDDPRVMTISVHETGISLFPGTGFANEIGGPDAQGTAVNVAVPPRTGDAGF
+LRAVHAVVPQLLQGFDPDVIVSQHGCDGHHADPLADLRLSVDGQRQLAFDIGDWAEKFAD
+GRWVATGGGGYNPLRVVPRVWTHLTAAVLQTPIPVKAEIPQSWIEHARTLTAEELTGDMS
+LHEGDESERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRRELFPLHGLDPWFD
+>PROKKA_00996
+MTSATSDCSQPAPSAVVWDPSLLKYRFSAQHPMAPLRLDLTHRLASSLGLLDAEHVRILQ
+PPVATDEQLATVHDPAFIAAVRAASREDAEADEPHGLGSEDCPTFPDLHESAARIAGGSL
+VAAEAVWSGEVSRAVNVAGGMHHAARAKASGFCIYNDCAVAIQRLLDLGAERVAYVDVDA
+HHGDGTQSIFYDDPRVLTISLHETGISLFPGTGFANETGGPGAEGTAVNVALPPGTGDAG
+FLRAVHAVVPQLLGAFQPDVLVTQHGADAHRGDPLADLRLSVDGQRQLAFDLGDWADRYA
+HGRWLATGGGGYNHVRVVPRAWTHLIGAVTGQPVPSSTPVPESWLEHVRSLTPDDLEGDM
+SLFEGAEEDRYPLTMTEDADVWWRSWEVGYDPADPVDQTIMATRREVFPIHGLDPWFD
+>PROKKA_01734
+MSTTSTPPAPTPAAVVWDSSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVRIVEP
+PVATDEQLALVHDPEYVAAVRRAAATSSAEDGRFGLGTEDCPVFPDLHESAARIAGGSLA
+AAEAIWSGEVDRAVNFAGGMHHAARSSASGFCIYNDCAVAIQRLLDLGAERVAYVDVDAH
+HGDGTQSVFYDDPRVLTISLHETGISLFPGTGFANEIGGAAAQGTAVNVALPPRTGDAGF
+LRAAHAVVPPLLEAFAPDVLVSQHGCDGHRTDPLADLRLTVDGQRQLAFDVGDWADRFAH
+GRWLATGGGGYNPLRVVPRAWAHLTAAVLQTPIPVKSEIPAAWIEHVRALTADELTGDMS
+VHVGDDAERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRREVFPLHGLDPWFD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001465.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001465.fa
new file mode 100644
index 0000000000000000000000000000000000000000..22a1df7f88bd9b64ff3ca05afe0cebfc5c812924
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001465.fa
@@ -0,0 +1,30 @@
+>PROKKA_01816
+MKLTILGLGTMTGAILAGALDAGAVRAEDVTATTRSAASAEKAAAQHGVTVTSQERDERA
+NHAAVAEADIVLVGVKPKDMVATLTDLASSLRPETVVVSVAAGVTAATMAAVLPAGQPIV
+RTMPNTPLTVGSGVVGVAPGPGVTEEQATAVRALFEGSGLVVPVAEEQLSAVVATAGSAP
+AYVFLLAELIAAHGAEMGLDAASAEAMAAATVKGAGIMLQQEGARAGALRKAVMSPNGTT
+EKAVEAFLDGGMGDLVNRAMDAAAQRDREMAEEFGA
+>PROKKA_01513
+MKLTILGLGTMTGAILAGALEAGAVRAEDVTATTRSAASAEKAAAQHGVTVTSQERDERA
+NHAAVAEADIVLVGVKPKGMVATLTDLAPSLRPETVVVSVAAGVTAATMAAVLPAGQPIV
+RTMPNTPLTVGSGVVGVAPGPGVTEEQTTAVRALFEGSGLVVPVAEEQLSAVVATAGSAP
+AYVFLLAELIAAHGAEMGLDAASAEAMAAATVKGAGIMLQQEGARAEALRKAVMSPNGTT
+EKAVEAFLDGGMGDLVNRAMDAAAQRDKEMAEEFGA
+>PROKKA_01054
+MKLTILGLGTMTGAILTGAIEAGAVRAEDVRATTRSAASAERARGRHPGVEVLAAEEDAH
+ANKRAVEGADVVLLGVKPKDIAATAAEVAQALGTDTTVVSVAAGVRAETIAAALREGQPL
+VRTMPNTPLTVGSGVVGVAPARGVTDAQTQAVEALFAGSGLVVRVAEEQLAAVVAAAGSA
+PAYVFLLAESIAKHAEQLGLDRANAEAMAAATVKGAGLMLQNGIREGDQTAEDLRRGVMS
+PGGTTEQAIRTFQEGGFERLVADAMDAAARRDEEMGRELAG
+>PROKKA_00992
+MTAQPRIAILGLGSMTGAILTGLLAASVTTPERVVATTRTAASAQAKGNRFPGVRVLSGE
+QDVDANLTAVAEADVVLLGVKPKDIVVTARQIAPALRPEAVVVSVAAGVRAETLAGALPE
+GQPLVRTMPNTPLTVGSGVVGVAPAAGVTADQRALVESLFSGSGVVVPVSEEQLPAVVAA
+SGSAPAYVFLLAEAIAAHAVELGLSAEAAEAMAAATVKGAGAMLVDAVTSGEQTAEGLRR
+AVMSPNGTTERAIAAFEDGGFAGLVADAMDAAARRDEEMGREFGA
+>PROKKA_01737
+MKLTILGLGTMTGAILAGALDAGAVRAEDVTATTRSAASAEKAAAQHGVTVTSQERDERA
+NHAAVAEADIVLVGVKPKDMVATLTDLAPSLRPETVVVSVAAGVTAATMAAVLPAGQPIV
+RTMPNTPLTVGSGVVGVAPGPGVTEEQATAVRALFEGSGLVVPVAEEQLSAVVATAGSAP
+AYVFLLAELIAAHGAEMGLDAASAEAMAAATVKGAGIMLQQEGARAEALRKAVMSPNGTT
+EKAVEAFLDGGMGDLVNRAMDAAAQRDKEMAEEFGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001467.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001467.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2e33f6e14db62d6b988a2149be58fa303f371d3b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001467.fa
@@ -0,0 +1,35 @@
+>PROKKA_01818
+MRLGVLDIGSNTVHLLLVDAHPGARPVAYAEHKRSLPLIRYQDADGAITEEGQRELVDFV
+REAAAFAEEHRAEDMISFCTSAIRESANGAAVLARVQAETGVHLSELTGDQESAMTYFAV
+RRWQGWDAGSILNFDIGGGSFEIAYGQDELPSHALSLPLGAGRLTRDWVPEDPPSPKAVK
+KLRKHVEKRLEEAYTVFPRIESPVVVTATSKTFRSLARITGAAPSAAGPFVKRHLRADDL
+HLWVNRLAAMTIAERAELPGVSDVRAHQVFAGAIVALTAMRTFGIAQLEICPWALREGLI
+LNRLDALMLEGHLTRDGLPGVGHVNLNPDTLLPGLSLGVR
+>PROKKA_01515
+MRLGVLDIGSNTVHLLLVDAHPGARPVAYAEHKRSLPLIRYQDADGAITEEGQRELVDFV
+REAAAFAEEHRAEDMISFCTSAIRESANGAAVLARVQAETGVHLSELTGDQESAMTYFAV
+RRWQGWGAGSILNFDIGGGSFEIAYGQDELPSHALSLPLGAGRLTRDWVLEDPPSPKAVK
+KLRKHVEKRLEEAYTAFPRIESPVVVTATSKTFRSLARITGAAPSAAGPFVKRHLRADDL
+HLWVNRLAAMTVAERAELPGVSDVRAHQVFAGAIVALTAMRTFGIAQLEICPWALREGLI
+LNRLDALMLEGHLTRDGRPGVGHVNLNPDTLLPGLSLGVR
+>PROKKA_01052
+MRLGVLDIGSNTVHLLLVDAHPGARPSAYAEHKRSLPLIRYQDAEGAITEEGQHELVDFI
+REAVAFAEEHRAEDMISFCTSAIRESANGAEVLARVDREAGVHLAELSGDQESAMTYFAV
+RRWQGWDAGSILNFDIGGGSFEIAYGQDELPSHALSLPLGAGRLTRDWLPEDPPSPKAVK
+KLRKHVEKRLEEAFAAFPPVEAPVAVTATSKTFRSLARLTGAAPSAAGPYVKRHLRADDL
+HLWVNRLAAMTAAERADLPGVSEVRAPQVLAGAIVALAAMRTFGIAQLEICPWALREGLI
+LNRLDALMLEGHLTHDGLPGVGHVNLNTDTLLPGLRLGVR
+>PROKKA_00990
+MRLGVLDIGSNTVHLLLVEARAGARPTPYAEHKRSLPLIRYLDESGAINEEGQDELVGFI
+GEAVAFAEEHRAEDMISFCTSAIREAENGPAVLARVEAETGVHLSELSGEQEASMTYFAV
+RRWQGWGVGSILNFDIGGGSFEIAYGQDELPSHAVSLPLGAGRLTRERLPDDPPSPKAVK
+KLHKHVSREIEAVFADFPPLEAPYVVTATSKTFRSLARLTGAAPSAAGPYVKRHLRADDL
+QLWVNRLAAMTWEQRAELPGVSEVRAPQVLAGALVALAAMRTFGVAQLEICPWALREGLI
+LNRLDALMLEGHLTREDGLGVGHVNLNTDSLLPGLSLGVR
+>PROKKA_01739
+MRLGVLDIGSNTVHLLLVDAHPGARPVAYAEHKRSLPLIRYQDADGAITEEGQRELVDFV
+REAAAFAEEHRAEDMISFCTSAIRESANGAAVLARVQAETGVHLSELTGDQESAMTYFAV
+RRWQGWGAGSILNFDIGGGSFEIAYGQDELPSHALSLPLGAGRLTRDWVLEDPPSPKAVN
+KLRKHVEKRLEEAYTAFPRIESPVVVTATSKTFRSLARITGAAPSAAGPFVKRHLRADDL
+HLWVNRLAAMTVAERAELPGVSDVRAHQVFAGAIVALTAMRTFGIAQLEICPWALREGLI
+LNRLDALMLEGHLTRDGRPGVGHVNLNPDTLLPGLSLGVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001468.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001468.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c8e9f7274443727ec9a428d70c36bd655b9f2ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001468.fa
@@ -0,0 +1,85 @@
+>PROKKA_01819
+MSTSSASVTAPVPEGKKLVIVESPAKSKSIAKYLNAVGSGWVVDSSVGHIRDLPKPSDLP
+ADMKKGPFGKFAVDTEHGFTPYYVVHPDKKKKVAELKRELKDAEALYLATDADREGEAIA
+WHLLDTLKPTVPVYRMTFGEITQEGVRRGLENIRELDTALVDAQETRRILDRLFGYELSP
+VLWRKVSRGLSAGRVQSVATRLVVERERERMAFVSAHYWGVEGTFTVAEGAQAADAVGSS
+FTARLSTVDGERVATGRDFDDAGRLKASAGKKVTHLDEAGARSLAEGLRGADFTVDSVED
+KPYTRRPAAPFTTSTLQQEAARKLRMSSRVSMQVAQRLYENGYITYMRTDSVNLSQEAVQ
+AARRQATELYGADAVPAQPRVYAKRNETAQEAHEAIRPAGDSFRTPAQVKAELRPDEFRL
+YELIWKRTVASQMADAKGYTATLRLSATAQDGRLAQFSASGTVITFKGFLDAYEEGRDAE
+VDGENAEAKDRRLPQVAQGERLTGDPIEATGHETSPPARYTEASIVAELERREIGRPSTY
+APTISTIMDRGYVSKRGTALVPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGE
+LGREAWLQTFYFGAPAAETEKGVEGLKHVVDNLGEIDARAVNSLPITEDITLRVGQYGPY
+LERSLPADAEAGATPPRANVPEDLAPDELTPAKAEELFATAQPSERELGTDPETGRTIVA
+KDGRYGPYVTEVIPEMTEEELQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFTSMSV
+DTVTLEQALQLMSLPRVVGADAEGEVITAQNGRFGPYLKKGSDSRSLESEDQIFSITQEQ
+ALEIYAQPKQRGRGAAKPPLAEFGEDPVSGKKVTVKEGRFGPYITDGVTNITVPRGRRPE
+ELTAEEAYQLLADKRAKGPATRGGAKKPAARKAPAKKTTARKKA
+>PROKKA_01516
+MSTSSASVTAPVPEGKKLVIVESPAKSKSIAKYLNAVGSGWVVDSSVGHIRDLPKPSDLP
+ADMKKGPFGKFAVDTEHGFTPYYVVHPDKKKKVAELKRELKDAEALYLATDADREGEAIA
+WHLLDTLKPTVPVYRMTFGEITQEGVRRGLENIRELDTALVDAQETRRILDRLFGYELSP
+VLWRKVSRGLSAGRVQSVATRLVVERERERMAFVSAHYWGVEGTFTVAEGAQAADAVGSS
+FTARLSTVDGERVATGRDFDDAGRLKASAGKKVTHLDEAGARSLAEGLRGADFTVDSVED
+KPYTRRPAAPFTTSTLQQEAARKLRMSSRVSMQVAQRLYENGYITYMRTDSVNLSQEAVQ
+AARRQATELYGADAVPAQPRVYAKRNETAQEAHEAIRPAGDSFRTPAQVKAELRPDEFRL
+YELIWKRTVASQMADAKGYTATLRLSATAQDGRLAQFSASGTVITFKGFLDAYEEGRDAE
+VDGENAEAKDRRLPQVAQGERLTGDPIEATGHETSPPARYTEASIVAELERREIGRPSTY
+APTISTIMDRGYVSKRGTALVPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGE
+LGREAWLQTFYFGAPAAETEKGVEGLKHVVDNLGEIDARAVNSLPITEDITLRVGQYGPY
+LERSLPADAEAGATPPRANVPEDLAPDELTPAKAEELFATAQPSERELGTDPETGRTVVA
+RDGRYGPYVTEVIPEMTEEELQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFTSMSV
+DTVTLEQALQLMSLPRVVGADAEGEVITAQNGRFGPYLKKGSDSRSLESEDQIFSITQEQ
+ALEIYAQPKQRGRGAAKPPLAEFGEDPVSGKKVTVKEGRFGPYVTDGVTNITVPRGRQPE
+ELTAEEAYQLLADKRAKGPATRGGAKKPAARKAPAKKTTARKKA
+>PROKKA_01051
+MPTTPASVTASVPEGKKLVIVESPAKSKSIAKYLNAVGEGWVVDSSVGHIRDLPKPSDLP
+ADMKKGPFGKFAVDTENGFAPYYVVHPDKKKKVTELKRELKDAVALYLATDADREGEAIA
+WHLLDTLKPKVPVYRMTFGEITKEGVRRGLENIRELDTHLVDAQETRRILDRLFGYELSP
+VLWRKVSRGLSAGRVQSVATRLVVERERERMAFVSAAYWGVEGTFTVAPGAQAADAVGSS
+FTARLSTVDGERVATGRDFDDAGALKASAGKKVTHLDEAAASSLAQGLRGADFTVDAVED
+KPYTRRPAAPFTTSTLQQEASRKLRMSSRVSMQVAQRLYENGYITYMRTDSVNLSQEAVQ
+AARRQATELYGQDAVPAQPRVYAKRNESAQEAHEAIRPAGDSFRTPAQVKAELRPDEFRL
+YELIWKRTVASQMADAKGYTATLRFSATAQDGRAAQFSASGTVITFKGFLDAYEEGKDAE
+TEDEKAEAKDRRLPQVAEGERLVGEPIEATGHETSPPARYTEASIVAELERREIGRPSTY
+APTISTIMDRGYVSKRGNALVPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGE
+LGREAWLQTFYFGAPASETGKGVEGLQQVVENLGEIDARAVNSLPITDEITLRVGQYGPY
+LEKPLPADAEAGSTPPRANVPEELAPDELTPAKAEELFATAKPSERELGTDPETGRAVVA
+KDGRYGPYVTEVIPEMTEEQLQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFSSMSV
+DTVTLEEALRLMSLPRVVGADAEGEVITAQNGRFGPYLKKGTDSRSLESEDQIFTITQEQ
+ALEIYAQPKQRGRGAAKPPLAEFGEDPVSGKKVTVKEGRFGPYVTDGVTNITVPRGRQPE
+ELTAEEAYQLLADKRAKGPATRKAPARKPAARKAPAKKSAPKKKA
+>PROKKA_00989
+MPTASASTSSSVPQGKKLVIVESPAKSKSIAKYLNAVGEGWVVDSSVGHIRDLPKPSDLP
+ADMKKGPYGKFAVDTEHGFTPYYVVHPDKKKKVTELKRELKDAEALYLATDADREGEAIA
+WHLLDTLKPKVPVYRMTFGEITKEGVRRGLENIRELDTHLVDAQETRRILDRLFGYELSP
+VLWRKVSRGLSAGRVQSVATRLVVERERERMAFVAAQYWGVEGTFTVGPDAKADGAAGSS
+FTARLSTVDGARVATGRDFDDAGRLKESAGKKVAHLDEAAAASLAEGLDGKDFTVDSVED
+KPYTRRPAAPFTTSTLQQEASRKLRMSARVTMQVAQRLYENGYITYMRTDSVNLSQEAVQ
+AARRQATELYGQESVPTQPRVYAKRTENAQEAHEAIRPAGDSFRTPAQVKAELRPDEFRL
+YELIWKRTVASQMADAKGYTATLRFSAQAEDGRTAQFAASGTVITFKGFLDAYEEGRDAE
+PEEEKDAKDRRLPQVAEGETLTGAPIQPTGHETTPPARYTEASIVAELERREIGRPSTYA
+PTISTIMDRGYVSKRGSALVPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGEL
+AREAWLQTFYFGADSADTQKGVEGLKHVVENLGEIDARQVNSLPVTEDITLRVGQYGPYL
+ERRLPEGAAEGTAPERANVPEDLAPDELTPAKAEELMAAGGADERELGVDPETGRTVVAK
+DGRYGPYVTEVIPEMGEEELQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFKTMSVD
+TVTLEQALQLMSLPRIVGADAEGEVITAQNGRFGPYLKKGTDSRSLESEDQIFTVTQEQA
+LEIYAQPKQRGRGTAKPPLAEFGEDPVSGKKVTVKEGRFGPYVTDGVTNITVPRGRAPEE
+LTAEEAYQLLADKRAKGSAKKPAAKKPAARKPAAKKTTTSTTTRKKA
+>PROKKA_01740
+MSTSSASVTAPVPEGKKLVIVESPAKSKSIAKYLNAVGSGWVVDSSVGHIRDLPKPSDLP
+ADMKKGPFGKFAVDTEHGFTPYYVVHPDKKKKVAELKRELKDAEALYLATDADREGEAIA
+WHLLDTLKPTVPVYRMTFGEITQEGVRRGLENIRELDTALVDAQETRRILDRLFGYELSP
+VLWRKVSRGLSAGRVQSVATRLVVERERERMAFVSAHYWGVEGTFTVAEGAQAADAVGSS
+FTARLSTVDGERVATGRDFDDAGRLKASAGKKVTHLDEAGARSLAEGLRGADFTVDSVED
+KPYTRRPAAPFTTSTLQQEAARKLRMSSRVSMQVAQRLYENGYITYMRTDSVNLSQEAVQ
+AARRQATELYGADAVPAQPRVYAKRNETAQEAHEAIRPAGDSFRTPAQVKAELRPDEFRL
+YELIWKRTVASQMADAKGYTATLRLSATAQDGRLAQFSASGTVITFKGFLDAYEEGRDAE
+VDGENAEAKDRRLPQVAQGERLTGDPIEATGHETSPPARYTEASIVAELERREIGRPSTY
+APTISTIMDRGYVSKRGTALVPSWTAFAVIGLLEDYFAKYVDYDFTARMEDDLDRIAAGE
+LGREAWLQTFYFGAPAAETEKGVEGLKHVVDNLGEIDARAVNSLPITEDITLRVGQYGPY
+LERSLPADAEAGATPPRANVPEDLAPDELTPAKAEELFATAQPSERELGTDPETGRTVVA
+RDGRYGPYVTEVIPEMTEEELQAWLDAQPTEYYKNGKPKPKKKPAKEKPRTGSLFTSMSV
+DTVTLEQALQLMSLPRVVGADAEGEVITAQNGRFGPYLKKGSDSRSLESEDQIFSITQEQ
+ALEIYAQPKQRGRGAAKPPLAEFGEDPVSGKKVTVKEGRFGPYVTDGVTNITVPRDRQPE
+ELTAEEAYQLLADKRAKGPATRGGAKKPATRKAPAKKTTARKKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001469.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001469.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e94d48ff831213d97b8a2a1ac29d7cf54ff9c3d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001469.fa
@@ -0,0 +1,55 @@
+>PROKKA_01820
+MSPVPTPPSPPAPRLTPATAVALAADLAALPFTTAAVEGLLGPVATLALDREHAEAARRV
+VAGHLAGPGRHDDAAGPGDRPGTRGLAAAVGAWLLGDPVPAADLDAALPSLGLAGAVAAG
+LVVEGPDGRVRGAVDLSPYEADEPGRMWIASDLTALQRRGPLPPEHVLGVGRASLTLAGA
+TQRRPVARALDVGVGCGIQTLHLLAHADHVTATDLSERALAFTRFNLLLNADVLGLDRER
+LEDRVRLAAGDLLAPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGREGDRIVAELI
+AALPDVLAEGGTAQLLANWEIPAGDTADADTAPWDARPRSWVASGMQAWFIQRDRQDPAG
+YAETWLQDSSLELDPPAYEAAYRGYLDDFAARGVAGVGFGHVWLRRPAADGSQGRGWVVA
+EELTQAVDEALGTAWAAAVARRDRLTAGAGAGDAVGDPALAALRGLHLRVAADVTEERHQ
+RFGAEHPEVILARQGSGFRRVARLDTATAGVLSASDGELSVGQLVGAVAALLELDDVGRA
+GLLAALRELYEDGFLVEG
+>PROKKA_01517
+MSPVPTPPSPPAPRLTPATAVALAADLAALPFTTAAVEGLLGPVATRALDREHAEAARRV
+VAGHLAGPGRHDDAAGPGDRHGTRGLAAAVGAWLLGDSVPAADLDAALPRLGLAGAVAAG
+LVVEGPDGRVRGAVDLSPYEADEPGRMWIASDLTALQRRGPLPPEHVLGVGRASLTLAGA
+TQRRPVARALDVGVGCGIQTLHLLAHADHVTATDLSERALAFTRFNLLLNADVLGLDRDR
+LEDRVRLAAGDLLAPVTGERFDLVVSNPPFVITPRTDPGAPVLIYRDGGREGDRIVAELI
+AALPDVLAEGGTAQLLANWEIPAGDTANADTAPWDARPRSWVAPGMQAWFLQRDRQDPAG
+YAETWLQDSSLELDPPAYEAAYRGYLDDFAARGVAGVGFGHVWLRRPAADGSQGRGWVVA
+EELTQPVDEALGAAWAAAVARRDRLAAGAGAGDAVGDPALAALRGLHLRVAADVTEERHQ
+RFGAEHPEVILARQGSGFRRVARLDTATAGVLSASDGELSVGQLVGAVAALLELDDVGRA
+GLLAALRELYEDGFLVEG
+>PROKKA_01049
+MKPPAPSPSSPSLPAPRLTPATAAALDADLAALPYTTAAVEELLGPVATAALDREHAEPA
+RRVVARVLTAAPGDHTQALYDDGALGSGARPLEAGIGSPAARRALAALVSVWMLGDAADA
+ADVAAALPALGLDGAREAGLVAEEGGGTVRGTVDLSPYEADEPGRMWVASDQTALQRRGP
+LPEDHVLGIGRASLTLAGATQRRPVACALDVGVGCGIQTLHLLAHAEHVTATDLSERALE
+FTRFNLLLNADVLGLDRERLEDRVRLAAGDMLAPVAGERFDLVVSNPPFVITPRTDPDAP
+VLTYRDGGREGDRIVAELVAALPAHLTEGGTAQLLANWEIPAGAAAIPAAAAASADGDLA
+DTAGPAPWDARPRSWIAPGMQGWIIQRDAQDPAGYAETWLQDSSLELDPHRYEAAYRGYL
+EDFAARGVAGVGFGHVWLRRPVDDGAQGRAWTVAEELTQPVDEALGAAWAAAVARRDRLA
+AGAPDGAGDPALAALRGLHLRVAEDVSEERHGRFGAEHPEVILARQGAGFRRTARLDTAT
+AGVLSASDGELSVGQLVGAVAALLELDDAGRAGLLAAIRELYEDGFLVERAED
+>PROKKA_00988
+MSLPAPHLSPAAAAALAADLTALPYTTDVVETLLGPVATAALDREHAVAARRVVAGVLAA
+PAARDAAAASRPLAAVVGAFMLGEPVPAADLAAALPALGLDGAVEAGLVVLDGADTGAER
+ARATVDLSPYAADEPGPMWVASDQTALQRRGPLPEDHVLGIGRASLTLAGATQRRPVARA
+LDLGVGCGVQTLHLLAHAEHVTATDLSERALDFTRFNLLLNADVLRLDRERLEDRVRLAA
+GDLLGPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGREGDRLVAELIAALPEHLVE
+GGTAQLLANWEIPAGAAEIPAGAAEVPAGDDAPPAWDARPRSWVGPGMQAWFVQRDRQDP
+AGYAETWLQDSSLELDPAAYEAAYRGYLDDFAARGVTGVGFGHVWLRRPAADRSQGRAWT
+VAEELTQPLDEALGTAWAAAVARRDRLAAGPEAGATDAVVTGDPALAALRGLHLRVAEDV
+TEERHSRFGAEHPEVILARQGAGFRRTARLDTATAGVLSASDGELSVGQLVGAVAALLEL
+DDAGRAGLLAAVRELHEDGFLLEA
+>PROKKA_01741
+MSPVPTPPSPPAPRLTPATAVALAADLAALPFTTAAVEGLLGPVATLALDREHAEAARRV
+VAGHLAGPGRHDDAAGPGDRPGTRGLAAAVGAWLLGDPVPAADLDAALPSLGLAGAVAAG
+LVVEGPDGRVRGAVDLSPYEADEPGRMWIASDLTALQRRGPLPPEHVLGVGRASLTLAGA
+TQRRPVARALDVGVGCGIQTLHLLAHADHVTATDLSERALAFTRFNLLLNADVLGLDRER
+LEDRVRLAAGDLLAPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGGEGDRIVAELI
+AALPDVLAEGGTAQLLANWEIPAGDTADADTAPWDARPRSWVAPGMQAWLLQRDRQDPAG
+YAETWLQDSSLELDPPAYEAAYRGYLDDFAARGVAGVGFGHVWLRRPAADGSQGRAWVVA
+EELTQPVDEALGTAWAAAVARRDRLAAGAGAGDAVGDPALAALRGLHLRVAADVTEERHQ
+RFGAEHPEVILARQGSGFRRVARLDTATAGVLSASDGELSVGQLVGAVAALLELDDVGRA
+GLLAALRELYEDGFLVEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001470.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001470.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a706a9b545ee4d969b3dfacddf5b7603e884523
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001470.fa
@@ -0,0 +1,35 @@
+>PROKKA_01821
+MSTAALSRIALYYRFTPLADPEAVRLWQRTLAASLGLTGRIIVSPQGINGTVGGPVDAVK
+RYVRGTREHPAFRDLEVKWSDGSAADFPRLSVKLKPELVAFGAPERVTVDADGVVGTGER
+LTPAQVDALVAERAGSANPVRFLDGRNTVEAAIGRFDGAVVPDAHTTRDLLAAVDSGALD
+HLKDAPLITYCTGGVRCEVLSALLKDRGFAEVYQLDGGIVRYGEARGDAGLWRGELAVFD
+RRLSTRFTADAETIGRCVTCEAPTSALRNCADPACTTLEVRCAACAVDDPERRCPVCVHH
+PHPAERTEA
+>PROKKA_01518
+MSTAPLSRIALYYRFTPLADPEAVRLWQRTLAASLGLTGRIIVSPQGINGTVGGPVDAVK
+RYMRGTREHPAFRDLEVKWSDGSAADFPRLSVKVKPELVAFGAPERVTVDADGIVGTGER
+LTPVQVDALVAERAGTANPVRFLDGRNTVEAAIGRFDGAVVPDAHTTRDLLAAVDSGALD
+HLKDAPLITYCTGGVRCEVLSALLKDRGFAEVYQLDGGIVRYGEARGDAGLWRGELAVFD
+RRLSTRFTADAETIGRCVTCHAPTSALRNCADPACTTLEVRCAACAVDDLEHRCPFCAHR
+PHPAERTEA
+>PROKKA_01048
+MSPAPVSRIALYYRFAPLADPEAVRLWQRTLAASLGLTGRIIVSPQGINGTVGGPVDAVK
+QYVKGTREHPALKDLEVKWSDGSAADFPRLSVKVRPELVAFGVPERITVDEHGVVGTGER
+LTPERLEALVAERAGTENPVRFLDGRNTVEAQIGRFDGAVVPAAHTTRDLLAAVDSGSLD
+HLRDAPLVTYCTGGVRCEVLSALLKDRGFREVYQLDGGIVRYGEAFGDAGLWRGELAVFD
+RRIALRFSEDAETIGRCVTCEAPTSALRNCSDPACTTLEVRCAACAAADPDRRCPVCTER
+SAA
+>PROKKA_00987
+MTAAAPAAPTPLPAPGGPGRIALYYRFTPLADPEAVRLWQRTLAVSLGLAGRIIVSPQGI
+NGTVGGPAEAVKRYVRGTREHPAFRGLEVTWSDGSAADFPRLSVKVRPELVAFGAPERIR
+VDEHGVVGTGEHLPADQLHALVAERAAQGRPVRFLDGRNSVEAAIGRFEDAVIPAAHTTR
+DLLEAVDSGSLDHLKDQPVVTYCTGGVRCEVLSALLKDRGFSEVYQLDGGIVRYGEAHGD
+AGLWHGRLAVFDRRLSLAFTDGAETLGRCVTCGGATSHLANCADPACTTLQVRCPDCVAA
+HPDHVCPRCLERTPA
+>PROKKA_01742
+MSTAALSRIALYYRFTPLADPEAVRLWQRTLAASLGLTGRIIVSPQGINGTVGGPVDAVK
+RYVRGTREHPAFRDLEVKWSDGSAADFPRLSVKLKPELVAFGAPERVTVDADGVVGTGER
+LTPAQVDALVAERAGSANPVRFLDGRNTVEAAIGRFDGAVVPDAHTTRDLLAAVDSGALD
+HLKDAPLITYCTGGVRCEVLSALLKDRGFAEVYQLDGGIVRYGEARGDAGLWRGELAVFD
+RRLSTRFTADAETIGRCVTCEAPTSALRNCADPACTTLEVRCAACAVDDPERRCPVCVHH
+PHPAERTEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001473.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001473.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1866dddc02381a214c0a96a0b8f5b65f657bc806
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001473.fa
@@ -0,0 +1,20 @@
+>PROKKA_01824
+MTRGRAPARGERGSGTVSVLGTAALGAGLLLAVAALGQASATGSRAAGAADLAALAASDA
+RRGLSDHEPCVLAGRTAERNGAAVVACEVREDGTVRVAVELARAPLPAATADAVAGPPRS
+QAPGAASVAPPEDPPEAPPPEPSVEASAGTR
+>PROKKA_01521
+MTRGRAPVRGERGSGTVSVLGTAALGAGLLLAVAALGQASVTGARAAGAADLAALAASDA
+RRGLSDHEPCVLAGRTAERNGAAVVACEAREDGTVRVAVELARAPLPAATADAVAGPPRS
+QAPGAGSADPPEAPPPEPSVEASAGTR
+>PROKKA_01045
+MTGRAPGGVPRGAASETGSGTVSVLGTAALGAGLLLAVAALGQASVAGAQAAGAADLAAL
+AASDARRGLSAGEPCLVAGQTAARNRAVVVECEVRENGTVRVSVERGRAPLPPALAAAVA
+GPPRLQAPQAVPEDPLPDASSPSTPTPSSVPPSVSPDPSATTGTR
+>PROKKA_00984
+MSGTATALGTALLGAGLLTGVLAVGHASATAARASGAADLAALAASDARRGLGAVPDAGV
+LEPCPLAEESARRNGAEVTECVLLPDGSVRVAVVIAADPLPASTAVAVAGPPVGPRGPVA
+GPGRDDAPEDAPDTPGAPPEAATP
+>PROKKA_01745
+MTRGRAPARGERGSGTVSVLGTAALGAGLLLAVAALGQASVTGSRAAGAADLAALAASDA
+RRGLSDHEPCVLAGRTAERNGAAVVACEVREDGTVRVAVELARAPLPAATADAVAGPPRS
+QAPGAASVAPPEAPPEPSLEASAGTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001476.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001476.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6206e39978f4ad098bb213475220a5d115bd184c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001476.fa
@@ -0,0 +1,37 @@
+>PROKKA_01827
+MLVGALRRWAALVAAGLTEEQAWRETACTLPACGSGPGEAGAACCAHHRARRRAEALAWD
+VPASHAPTGEAARGGGTLPWRTPARDPGWALVDAALAAGARAGAAPAAVARRLAHSLEAD
+VDAARARRSAAAGPGATSRLLQWLPLGGLGLAWLLGTSPWDLARSPFGAVVAAVGLLFWL
+AGRSWTRLLLRAAAREPAAVGAAVVLDVLAALLSAGRSLPAALDDLGRTLPGARGLRATA
+ALLLWGRDWDEAWAGLDTDPVWIETAARLRPLHRSGMAGARTLAETAAAVRQQTRRADER
+AAEELAVRLVMPLGLCLLPAFVCWGVVPVVMALLGAGPG
+>PROKKA_01524
+MSPTTATGPARRSHAGRAVALLPWRAGRVPPEEETEVLIGVLRRWAALVAAGLTEEQAWR
+ETACTLPACGSEPSEAGTACCAHHHARRRAEALAWDVPAAHAPTGEAARRGGTLPWRTPA
+RDPGWALVDAALAAGARAGAAPAAVARRLAHSLEADVDAARARRSAAAGPGATSRLLQWL
+PLGGLGLAWLLGTSPGDLVRSPFGAVVAAVGLLFWLAGRSWTRLLLRAAAREPAAVGAAV
+VLDVLAALLSAGRSLPAALDDLGRTLPGARGLRATAALLLWGRDWDEAWVGLDTDPVWAE
+TAARLRPLHRSGMAGARTLAETAAAVRQQTRRADERAAEELAVRLVMPLGLCLLPAFVCW
+GVVPVVMALLGAGPG
+>PROKKA_01042
+MSTAAPEDATEELVVVLRRWAALVSAGLTEEAAWRETVRMLPDDDGHARHAARLRAERLA
+WDAAGDLSTGRDAPDVRGLRRDEHPPGDTHDASPDRSRRRWCPPWRTPPPDPGWALVDAA
+LAAGARAGAAPAVVVRRLAESLEADVDAARARRSAAAGPAATARLLQWLPLGGVGLAWLL
+GSSPWETVSTPFGAVVAAVGLLFWLAGRSWTRLLLRSAAREPAALTAPVVLDVLAALLGA
+GRSLPAALDDLARTLPGARGLRVTSALLLWGRGWDEAWAGIGEETVWAEAAARLRPLHRS
+GMAGARTLAESAAAARQQGRRADERAAEELAVRLVMPLGLCLLPAFVCWGVIPVVMALLG
+AGA
+>PROKKA_00981
+MIALPGRAEERAEERAQEVVEALRRWAGLTAAGMTPAEAWTAVAQASSPCGRPTPGCCPR
+HEALRRAALARWGGPGRGAEGGQPRPGERSPWDLADAALAAAARAGASFSRTAARLADAL
+EADVDASRARRTAAAGPRATARLLSWLPVGGLGLAWLLGMGPADLLATGFGWVLLVLGGV
+LTAAGRAWTRLALRRGARPLGEASPGVVVDVAAVLLGAGRSLPAALDDVSAHLPGAADLR
+VVAVLLRWGADWDEAWAPVTEEPRWAALGERLRPLHRTGMAGEAVLHQTAAALRQETRRA
+DERGAEELAVRLVVPLGLCQLPAFVCWGVAPMALALLGAR
+>PROKKA_01748
+MLVGVLRRWAALVSAGLTEEQAWRETACTLPACGPGPSEAGTACCAHHRARRRAEALAWD
+VPASHAPTGEAARGGGTLPWRTPARDPGWALVDAALAAGARAGAAPAAVARRLAHSLEAD
+VDAARARRSAAAGPGATSRLLQWLPLGGLGLAWLLGTSPWDLARSPFGAVVAAVGLLFWL
+AGRSWTRLLLRAAAREPAAVGAAVVLDVLAALLSAGRSLPAALDDLGRTLPGARGLRTTA
+TLLLWGRDWDEAWAGLDTDPVWIETAARLRPLHRSGMAGARTLAETAAAVRQQTRRADER
+AAEELAVRLVMPLGLCLLPAFVCWGVVPVVMALLGAGPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001477.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001477.fa
new file mode 100644
index 0000000000000000000000000000000000000000..99b3b61803bc0eb239f4457fd294ef73d948b544
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001477.fa
@@ -0,0 +1,44 @@
+>PROKKA_01828
+MRPFVPAAPARPPRGRRRRPAPPEGGRRFPWPRTGPAEPERTQVAAPPLAAPAAGPDGLD
+AAVVRRRVAEARASAADGAEPPLAPLIAEALDVPIDDPRVAALVDELDGFGPLAPWVRTP
+GVTDVLVDGAGAVWTDGDGGLVRRPDRLDPETARALAVRLLHRAGRRLDAAVPLADARVG
+GVRVHAVLPPVSGGGTLLSLRIPAAATPSLAALADGWPDGALWADALEALVRDRATVLVS
+GATGAGKTTLLSAALGRVPGDERIVVVEDTAEAAPDHPHVVALQCRAANAEGAGEVGLAE
+LVRHALRMRPDRLVVGECRGAEVADVLTALNTGHQGAWGTLHANAAAEVPARLTAMASLA
+GWRPETVAAQARAGVDAVLHIARDGHGRHPVELAVPDLRADGFALLPALTWRPGTEATGG
+RTVEGPGMPALAARLAGRSGR
+>PROKKA_01525
+MRPFVPAAPARPPRGRRRRPAPPEGSRRFPWPRTDPAEPERTQVAAPPLAAPAAGPGGLD
+AAVVRRRVAEARASAADGAEPPLAPLIAEALDAPIDDPRVAALVDELDGFGPLAPWVRTP
+GVTDVLVDGAGAVWTDGDEGLVRRPGRLDPETARALAVRMLHRAGRRLDAAVPLADARVG
+GVRVHAVLPPVSGGGTLLSLRIPAATTPSLAALADGWPDGALWADALEALVRDRATVLVS
+GATGAGKTTLLSAALGRVPGDERIVVVEDTAEAAPDHPHVIALQCRAANAEGAGEVGLAE
+LVRHALRMRPDRLVVGECRGAEVADVLTALNTGHQGAWGTLHANAAAEVPARLTAMASLA
+GWRPETVAAQARAGVDAVLHVARDGHGRHPVELAVPDPRADGFALLPALTWRPGTEATGG
+RTVEGPGVPALAARLAGRSGR
+>PROKKA_01041
+MRRRVAEARAAAAEGQEPALAPLVAEAIGVSATDPRVAALVDELDGFGPLAGWVRAPGVT
+DVLVDGSGAVWTDGAEGLLRRPQRLDPHAAQALAMRLVHRAGRRLDAAVPLADARVDGVR
+VHAVLPPVSGGGTLLSLRIPAARTPSLAELAAGWPDGDLWGEALEALVRDRASVLVSGAT
+GTGKTTLLAAALGCVPGDERILTVEDTAEAAPEHPHVVALQCRAANAEGAGAVGLAELIR
+HALRMRPDRLVVGECRGAEVADFLTALNTGHQGAWGTLHANGAADVPARLTAMGSLAGWG
+PDTVAAQARAGVDAVVHLVRDRHGRHPVELAVPDPDARGFALLPALTWTPGPGPGDGSTA
+EGPGLRALAARLAGRGSR
+>PROKKA_00980
+MPAWVPDAPRPARRPALLPAGLSLPAPLLPDLRRVGRRRPGSDRGEPAHVGPDPDARLRR
+AVAEAQARADPHAPPPLRETVSRALADLAAEDGDTPPSGCPRPAGLRDPDAVLEELVGFG
+PLAPWVRRTGVTDVLVDAAGSVWTDGVEGLVRRPLILPEPTARALAVRLIGLAGRRLDPA
+CPVADARVDGVRVHAVLPPVSGGGTVLSLRVPAAEPPSLDALAADWPDGERWRDAVVALV
+RGRASVLVSGATGTGKTTLLAAALGLAGADERIVLVEDTAEAAPAHPHVISLQARAPTAD
+GAGEVTLAELIRQALRMRPDRLVVGECRGPEVADLLTALNTGHQGAWGTLHANAAADVPA
+RLAAMGALAGWSASAVAAQARAGVDAVLHVRRDGRGRHPVELAVPAPAAHPDAPLSVLPA
+LTWDGGGTRAGPGLEVLEARLSGRGHG
+>PROKKA_01749
+MRPFVPAAPARPPRGRRSRLAPPEVGRRFPWPRTGAAEPERTQVAAPPLAAPAAGPCGLD
+VAAVRRRVAEARASAADGAEPPLAPLIAEALDAPIDDPRVAALVDELDGFGPLAPWVRTP
+GVTDVLVDGVGAVWTDGDEGLVRRPGRLDPETAGALAVRLLHRAGRRLDAAVPLADARVG
+GVRVHAVLPPVSGGGTLLSLRIPAATTPSLAALADGWPDGALWADALEALVRDRATVLVS
+GATGAGKTTLLSAALGRVPGDERIVVVEDTAEAAPDHPHVVALQCRAANAEGAGEVGLAE
+LVRHALRMRPDRLVVGECRGAEVADVLTALNTGHQGAWGTLHANAAAEVPARLTAMASLA
+GWRPETVAAQARAGVDAVLHLARDGHGRHPVELAVPDPRADGFALLPALTWRPGTEAAGG
+RTIEGPGVPALAARLAGRSGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001478.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001478.fa
new file mode 100644
index 0000000000000000000000000000000000000000..25f836b5c193312687c3991f1ec59d36dcaff07d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001478.fa
@@ -0,0 +1,30 @@
+>PROKKA_01829
+MPETPASPRPTSRDAVGTSDASLAGARDQLADLVARWGAAPADAPGHHDPVSLTTVPPEA
+VPMWGFDWPRSGDPRPSAVLILFGALDDVPARHDAERVHPHVDVLLTQRAATLRQHAGQI
+AFPGGRVDPEDGDVVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGHVVHPVLGWWRD
+PSRVAVVDQAEAAAVFRMPVADLVDPANRCRVARPGGRRGETPGFLVGERLVWGFTAALL
+DRVLGLLGWDVPWDDSRVRDARTHEILRD
+>PROKKA_01526
+MPETPASPHPTSRDAAGTSDASLAGAREQLADLVARWGAPPAEAPGHHDPASLTTVPPEA
+VPMWGFDWPRSGDPRPSAVLILFGALDDVPARHDAGRVHPHVDVLLTQRAATLRQHAGQI
+AFPGGRVDPEDGDVVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGHVVHPVLGWWRD
+PSRVAVVDQAEAAAVFRMPVADLVDPANRCRVARPGGRRGETPGFLVGERLVWGFTAALL
+DRVLALLGWDVPWDDSRVRDARTHRILRD
+>PROKKA_01040
+MAAVRDRLAALVERHGVPADQAPRDALTEIPASAVSTWGFDWPRAQRARPSAVLILFGSL
+DDVPAHHADDRVHPDVDVLLTQRAATLRTHAGQIAFPGGRVDPEDADVVATALREAEEET
+DLDPDGVEVLGVLPPVPVVVSGHVVHPVIGWWRDPSRVAVVDQAEAAAVFRMPVGDLVDP
+ANRCRVARPGGRRGETPGFLVGERLVWGFTAALLDRILTLLDWDTPWDSGRVIDAHTHAP
+LRG
+>PROKKA_00979
+MSIPPLPPSSPSSARADLQRIVAEHGVAPVAGDDEAGLTTIPASSVRVWGFDWPQAARPR
+ASAVLILVGELDDVPAAHDGRACGVSPAVDVLLTQRAAGLRTHAGQVAFPGGGVEAQDAD
+VVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGYVVHPVIGWWRDPSRVAVVDHNEAT
+AVFRVPVADLAAPANRVRVRRPGGRRGETPGFLAGDRLVWGFTAALLSRVLELAGWDEPW
+AGAPLIDAGSRAVLEG
+>PROKKA_01750
+MPETPASPRPTSRDAAGTSEASLTGARDQLADLVARWGTAPADAPGHHDPASLTTIPPEA
+VPMWGFEWPRSGDPRPSAVLILFGALDDVPARHDAERVHPHVDVLLTQRAATLRQHAGQI
+AFPGGRVDPEDADVVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGHVVHPVLGWWRD
+PSRVAVVDQAEAAAVFRMPVADLVDPANRCRVARPGGRRGETPGFLVGERLVWGFTAALL
+DRVLALLGWDVPWDDSRVRDARTHEILRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001483.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001483.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dce359ecb0af1b6b8d7f993524e881c99ef4d331
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001483.fa
@@ -0,0 +1,54 @@
+>PROKKA_01835
+MSSTVSAPATAPKRTREEFAGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI
+ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTETVGWWQVLICVVIGIYYAAIIGWA
+IMYTWFSVDQRWGDDPETFLMGDYLQVADDPSPSFDVVSGVFWPMLAVWVITLLIMGFGV
+RRGVALASMVGIPLLIVMFLVLVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI
+FFSLSVGFGIMITYASYLNRRTNLTGSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS
+VSEVAGSGIGLAFIAFPTLISQAPLGALIGVLFFGSLVVAGFTSLISILEVVISAVKDKL
+GWGRWTATIVVIGLSGVVSLALFSTTTGLQMLDTMDAFANNFGIVGAALLSVLLVTGALG
+SARRITAHLNAVSSFKVGRGYVLLIGVLMPIVLAYIWLSWIMKVIAEGYEGYPGDFLGVF
+GWGIALGSVALAVLLSLIPWSRKSNLYAEDLDSEIHGDLIPHNAVPEGTVPTGALPVVPV
+ATTRKEL
+>PROKKA_01532
+MSSTVSAPATAPKRTREEFTGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI
+ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTETVGWWQVLICVVIGIYYAAIIGWA
+IMYTWFSVDQRWGEDPETFLMGDYLRVADDPSPSFDFVSGVFWPMLAVWVITLLIMGFGV
+RRGVALASMVGIPLLIVMFLILVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI
+FFSLSVGFGIMITYASYLNRRTNLTGSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS
+VSEVAGSGIGLAFIAFPTLISQAPLGALIGVLFFGSLVVAGFTSLISILEVVISAVKDKL
+GWGRWTATIVVIGLSGVVSLALFSTTTGLQMLDTMDAFANNFGIVGAALLSVLLVTGALG
+SARRITAHLNAVSSFKVGRGYVLLIGVLMPIVLAYIWLSWIMKVIAEGYEGYPGDFLGVF
+GWGIALGSVALAVLLSLIPWSRKSNLYAEDLDSEIHGDLIPHNAVPEGTVPTGALPVVPT
+AATRKEL
+>PROKKA_01033
+MSSTVSAPAAAPTRTREEFAGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI
+ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTESVGWWQVLICVVIAVYYAAIIGWA
+IMYTWFSVDQRWGADPETFMMGEFLQVSETPNPTFDVVSGVFWPMLAVWVITLLIMGFGV
+RRGVAMASMIGIPLLVVMFLVLVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI
+FFSLSVGFGIMITYASYLKKRTNLTSSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS
+VADVAGSGIGLAFIAFPTLISQAPVGALIGVLFFGSLVLAGFTSLISILEVVISAVKDKL
+GWGRWTATIIVVGLAGVVSMALFSTTSGLHMLDTMDAFANNFGIVGAALVSVLLVTGVLG
+SARRVTAHLNAVSSFKLGRGYVLLIGVLMPIVLAYIWLSWIMKVISEGYGGYPGDFLGVY
+GWGVAIGSVVLAVVLSLIPWSRKSNLYAEEMETEIHGDLIPHNAVPEGTTPTGAIPLVPA
+DHTRKEL
+>PROKKA_00974
+MSTSTGATAAPSRTREEFTGRWAFILAAIGSAVGLGNIWRFPYVAYEHGGGAFVIPYLVA
+LLTAGIPLLFLDYAIGHRFRGSAPMAFRRMSRWTEAIGWWQVLICAVIGVYYAAIIAWSI
+MYTWFSLDQRWGDDPEGFLFSTYLQQVKDPNPSFDIVPGVFWPMVAVWGVLLLIMGLGIR
+RGVALASMIGIPLLVVMFVVLVIISLTLPGAMQGLDALFTPNWAALKEPGVWIAAYGQIF
+FSLSVGFGIMITYASYLKKRTNLTASGLVVGFSNSGFEILAGIGVFSALGFMAQASGVQV
+SEVAGSGIGLAFIAFPTLITQAPAGALIGVLFFASLVIAGFTSLISILEVVVSAVKDKLG
+WGRWTAVLVVVGISAVISISLFSTTTGVAMLDTMDAFANNFGIVGAALVAVIAVMWIARR
+GGELVAHLNSVSSFRVGRVYRILVGVVMPVLLGWMWIEWIRENAATPYGGYPTDFLAVYG
+WGLAIGSVVLAVLLSLIPWSHKSSLHAEESVNEIDHTAPVASKES
+>PROKKA_01756
+MSSTVSAPATAPKRTREEFTGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI
+ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTETVGWWQVLICVVIGIYYAAIIGWA
+IMYTWFSVDQRWGEDPETFLMGDYLRVADDPSPSFDFVSGVFWPMLAVWVITLLIMGFGV
+RRGVALASMVGIPLLIVMFLILVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI
+FFSLSVGFGIMITYASYLNRRTNLTGSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS
+VSEVAGSGIGLAFIAFPTLISQAPLGALIGVLFFGSLVVAGFTSLISILEVVISAVKDKL
+GWGRWTATIVVIGLSGVVSLALFSTTTGLQMLDTMDAFANNFGIVGAALLSVLLVTGALG
+SARRITAHLNAVSSFKVGRGYVLLIGVLMPIVLAYIWLSWIMKVIAEGYEGYPGDFLGVF
+GWGIALGSVALAVLLSLIPWSRKSNLYAEDLDSEIHGDLIPHNAVPEGTVPTGALPVVPA
+ATTRKEL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001485.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001485.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d08e438b56b67bb44aed8e92078a0093d1e6174
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001485.fa
@@ -0,0 +1,31 @@
+>PROKKA_01838
+MSADPAGLLLPVPGQEEDLTRQWLDRRFRQVRPARPGSSVVLVRDGDDGPEVFLRHRAGR
+TPLGRVGLPGGALIESDADSCPWYGPEPSQWARTFGTTDRRRARQHVVAAVRELHDEAGV
+LLAGRSDTDVVSTARIETWGGGRSSLEEGSESLPHLLAARGLGVRADLLRPVMRWRSAPH
+VHRRFDTAVFATMTPPLQSAPASEEPGPELQAWVSARRALAGPLRLPGPAGAEGTAPFDQ
+VATPLTQVIVRRVAAHRTAAAFLLSVTPCARRGPVPEYHLVTEAGDDGTPRMRVKRATRD
+>PROKKA_01535
+MSADPAGLLLPVPEQEEDLTRQWLDRRFRQVRPARPGSAVVLVRDGDDGPEVFLRHRAGR
+TPLGRVGLPGGALIESDADLCPWYGPEPSQWAHTFGTTDRRRARQHVVAAVRQLHDEAGV
+LLAGRSDTDVVSTARVETWGGGRSSLEEGSESLPHLLASRGLGLRADLLRPVMRWHSAPH
+VHRRFDTAVFATTTPPVQSAPASEEPGPELQAWVPACRALAGPLRLPGPAGAEGTAPFDQ
+VATPLTQVIVRRVAAHRTAAAFLLSVTPCARRGPVPEYHLVTEAGDDGTPRMRVERATRD
+>PROKKA_01030
+MVLVRDGEDGPEVFLRHRPGRTPLGRVGLPGGALSEADADACAWFGPDPAHWARVLGTTD
+RRCARQQVVAAVRELHDEAGVLLAGRTDADVVLDARGETWGGGGSSLEEGAESLPRMLAA
+RGLGLRTDLLRPVARWHSAPHAHRRFDTAVFAAAVPPLQRPLERPETAPALQAWVSARRA
+VAGPVPLPGPAGEEGVAPLDQVATPLTQVLVRRVAAHRTAAAFLLSLTQGAGHGPVPEYR
+LVTEAGDDGAPRMRVERVTRD
+>PROKKA_00971
+MSAEPDAPRVRVPGHEEELTRQWLAQRHRQVRPARPASAVVLVRDGADGVEVLLRHRSGR
+TPLGRIGLPGGSLVDSDADPCTWYGPAPDEWARALGLADRRRVRQHVVAAVRELFEESGV
+LLAGPADMDLVQDARGETWGASRSSLEEGDESLPRLLGDRGLGLRTDLLRGVGRWLSAPH
+SPRRFDTVVFAAALPPQQELVHRPEGPVLQGWFSARRLLSEPAALPGPDGWLGESGVVAL
+EEVSTPMTQLVLRRVAEHRTAAGFLLSPAGCRGPVPVVKLRTEAEHDDLATGTLYTVAER
+VDPVG
+>PROKKA_01759
+MSADPAGLLLPVPEQEEDLTRQWLDRRFRQVRPARPGSAVVLVRDGDDGPEVFLRHRAGR
+TPLGRVGLPGGALIESDADLCPWYGPEPSQWAHTFGTTDRRRARQHVVAAVRQLHDEAGV
+LLAGRSDTDVVSTARVETWGGGRSSLEEGSESLPHLLASRGLGLRADLLRPVMRWHSAPH
+VHRRFDTAVFATTTPPVQSAPASEEPGPELQAWVPACRALAGPLRLPGPAGAEGTAPFDQ
+VATPLTQVIVRRVAAHRTAAAFLLSVTPCARRGPVPEYHLVTEAGDDGTPRMRVERATRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001489.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001489.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1be90490e50815c45239c49ff7fba0feb50aeea3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001489.fa
@@ -0,0 +1,35 @@
+>PROKKA_01842
+MPPAASPTRRMLRSAAPAAVGMAATAGLGLAWGLAEAEARTVRTHRLAVLPAGSAPLRVL
+HLSDIHLLPRHRAKRAWLRGLDALEPDLVVNTGDNVSAAASVPLVLDALGPLLARPGVFV
+PGSNDYYAPKAANPLRYFAGPSRMDEDRPRLPSDVLFGAFRAAGWADLTNRGAALAVPTR
+AGTTLEVLAAGTDDPHLGLDAWAGFPGAAPDENAGRPGDDGRFRLGVTHAPYRRVLDAMT
+ADGADLLLAGHTHGGQVCVPFLGALVTNCDLPRRQASGVSTWTAAGRTVPLEVSAGLGTA
+PSAPVRFACRPEAVVLDLVPRG
+>PROKKA_01539
+MPPAASPTRRMLRSAAPAAVGMAATAGLGLAWGLAEAEARTVRTHRLAVLPAGSAPLRVL
+HLSDIHLLPRHRAKRAWLRGLDALEPDLVVNTGDNVSAAASVPLVLDALGPLLARPGVFV
+PGSNDYYAPKAANPLRYFAGPSRMDEDRPRLPSDVLFGAFRAAGWADLTNRGAALAVPTR
+AGTTLEVLAAGTDDPHLGLDAWAGFPGAAPDENAGRPGDDGRFRLGVTHAPYRRVLDAMT
+ADGADLLLAGHTHGGQVCVPFLGALVTNCDLPRRQASGVSTWTAAGRTVPLEVSAGLGTA
+PSAPVRFACRPEAVVLDLVPRG
+>PROKKA_01026
+MRPSATAPRRLVRAGSRAAVGMGTAAALGLAWGLVEAEARVVRTHRLAVLPAGADPVRVL
+HLSDIHLLPRNRSRMAWLRGLDALEPDLVVNTGDNISAAASVPLVLDALGPLLRRPGVFV
+PGSNDYYEPKPANPFRYFAGPSRMDEDRARLPTEALFGAFRAAGWADLTNRGSVLSVPTR
+AGTVLEVLAAGTDDPHLGLDAWGGFPAPAPAPAPAPGDAAASGPASAHDDGAARPGGDGR
+FRLGVTHAPYRRVLDAMTVDGADLLLAGHTHGGQVCLPGFGALVTNCDLPRAQASGVSTW
+TAAGRTVPLEVSAGLGTAPSAPVRFACRPEAVVLELLPCA
+>PROKKA_00967
+MTDAPGPRLRRLTHTAAWAAGGASALGAGALVWGRVEAEARVVRTHTVPVLPAGARPLRV
+LHLSDIHLLPRHRRRLEWLCSLADLEPDLVVDTGDNISSAASIPLLLDALAPLLAVPGVF
+VPGSNDYFTPKPANPLRYLRGPSELEASRSRLPTEDLFSAFRAAGWTDLTDRAADVVVGS
+GPDAVRIRAAGTDDPHLGLDRWPGFDLADEGAAGDAPLLRLGVTHAPYRRVLDAMTADGA
+DLLLAGHTHGGQVCLPFAGALVTNCDLPRSQASGLSSWTAAGRTVPLEVSAGIGTAPSAP
+VRTFCRPEAVVLDLVPRA
+>PROKKA_01763
+MRPAASPARRMFCAAAPAAAGLAATAGLGLAWGLAEAEARTVRTHRLAVLPAGSAPLRVL
+HLSDIHLLPRHRAKRAWLRGLDALEPDLVVNTGDNVSAAASVPLVLDALGPLLARPGVFV
+PGSNDYYAPKAANPLRYFAGPSRMDADRPRLPSDVLFGAFRAAGWADLTNRGAALAVPTR
+AGTTLEVLAAGTDDPHLGLDAWAGFPGSAPDGGAGRPGDDGRFRLGVTHAPYRRVLDAMT
+ADGADLLLAGHTHGGQVCVPFLGALVTNCDLPRRQASGVSTWMAAGRTVPLEVSAGLGTA
+PSAPVRFACRPEAVVLDLVPRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001490.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001490.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0506de95d9a07c95b7f0537c1a822c3a1eece396
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001490.fa
@@ -0,0 +1,61 @@
+>PROKKA_01843
+MTRATSPDASSLRDALGGIAPYLEGVRARWVLGLASATAAGLVALAIPQVIHLLVDTVFT
+QTVLAGPSSPDSRADVWRAAGLLTVLGLAEAAFIGLRRYFILPPAAGVENRARIALFERL
+QRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVMLVVDVVTIAVGLVLLFLLSWQLA
+LLYLAAAVPIMWASFGFRNDFRAASRLSQDQAGDLATSVEESVHGIRVLKAFGRGAHALD
+GFRGRARTLQGTEVHKASVLARFIALIVALPETVLGLGLALGLWLVATGELTVGALAAYF
+ATAAVLAGPVESVGQLMGMTLSARTAIDRHVDVLATPVDIASPTGEAAVVPPATGALAFR
+GVRFRWPDADPGRGERDLLDGVDLELVPGETMALVGATGAGKSTLLQLVPRLLDVTAGSV
+CVDGVDVRRMPLEELRRRVSVAFEDATLFSATIRQNVLLGAPADVLADGLHSPAADALLD
+LALETAQAGFVADLADGVETEIGEEGLSLSGGQRQRIALARAIAARPDVLVLDDPLSALD
+VRTEETVTARLREVLDGTTTLIVAHRPSTVALADRVAVLADGRIEDVGTHPELLARSAVY
+RHIISSRPEEQA
+>PROKKA_01540
+MTRATSPDASSLRDALGGIAPYLEGVRARWVLGLASATAAGLVALAIPQVIHLLVDTVFT
+QTVLAGPSSPDSRADVWRAAGLLTVLGLAEAAFIGLRRYFILPPAAGVENRARIALFERL
+QRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVMLVVDVVTIAVGLVLLFLLSWQLA
+LLYLAAAVPIMWASFGFRNDFRAASRLSQDQAGDLATSVEESVHGIRVLKAFGRGAHALD
+GFRGRARTLQGTEVHKASVLARFIALIVALPETVLGLGLALGLWLVATGELTVGALAAYF
+ATAAVLAGPVESVGQLMGMTLSARTAIDRHVDVLATPVDIASPTGEAAVVPPATGALAFR
+GVRFRWPDADPGRGERDLLDGVDLELVPGETMALVGATGAGKSTLLQLVPRLLDVTAGSV
+CVDGVDVRRMPLEELRRRVSVAFEDATLFSATIRQNVLLGAPADVLADGLHSPAADALLD
+LALETAQAGFVADLADGVETEIGEEGLSLSGGQRQRIALARAIAARPDVLVLDDPLSALD
+VRTEETVTARLREVLDGTTTLIVAHRPSTVALADRVAVLADGRIEDVGTHPELLARSAVY
+RHIISSRPEEQA
+>PROKKA_01025
+MTRTATRPLPLREALQVVAPYLQGVRGRWVLGLLSAMAAGLVALAIPQVVQVLVNTVFAE
+AAPGTAGTADPAAGVWWAAGALALFGLAEALFIWLRRFFILPPAADVENRARISIYRRLQ
+RLPVAFHDAWASGQLLSRAQGDLALLRRWIAFGSVMLVVETVTIVVGLVLLFVMSWQLAL
+LYLVAAVPIMIRSFRFRTDFRAASRLSQDQAGDLATTVEESVHGIRVLKAFGRGPDALDG
+FRGEAETLQGTEVHKASVLAKFISLTVSLPELVLGVALGLGLYLVAVGDLTVGALAAYFA
+TTAVLARPVEGVGQLMGMTLSAKTAIDRHLEVMRVPVAVASPAGTDAAEEEATSRAVASS
+AAEDSPVVTDGLPPSSGRLAFRDVVFRYPDAPEDSRPLLAGVDLELTPGETMALVGVTGS
+GKSTLVQLVPRLLDVTAGVVEVDGTDVRAYPLDELRRRVSIAFEDATLFSDTVRANVLLG
+APAEVTADGLDSPRAQALLDLALDTAQAGFARDLPAGVDTEIGEEGLSLSGGQRQRIALA
+RAIAARPDVLVLDDPLSALDVRTEEAVTGRLREVLAGTTTLIVAHRPSTVALADRVAVLQ
+DGAIHDVGTHAELLARSAAYREIITTGAAEDRSLAGLADAAHDDAALAAATDAARPPAGA
+ARPPAGRTAGREETR
+>PROKKA_00966
+MTRTTTAAAPLPLRDAVRGIAPYLEGVRTRWVLGLLSALAAGLVALAIPQVIRLLVNTVF
+AAPTTPGAPAAEDATASVWWAVGGLALLGAAEALFIWLRRFFILPPAADVENRARIAVYR
+RLQRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVMLVVETVTLVVGVGLLFWLSWP
+LALVYLAAALPIMWRSYGFRNDFRTASRLSQDQAGDLATTVEESVHGIRVLKAFGRGPHA
+LEGFRGEAQTLQGTEVHKAGVLASFIAFTVSLAEVMLGVALALGVWLVATGQMTVGALAA
+YFATTAVLARPVEGIGQLLGMTLSAKTAIDRHLEVMRQPVSIASPPGTDPAEEAATGASV
+GEDPDPAVADAPVDVSALPPSRGGLAFRGARFRHPDTPDDAPDLLAGVDLELVPGETMAL
+VGLTGSGKSTLLQLVPRLRDVTGGVVEVDGVDVRDYPLEELRRRVSIAFEDATLFSDTVR
+ANVLLGAPAAEVADGPDSPAAEALLELALDTAQAGFVADLPQGVDTPIGEEGLSLSGGQR
+QRLALARAIAARPDVLVLDDPLSALDVRTEEAVTARLREVLAGTTTLIVAHRPSTVALAD
+RVAVLQDGRIADVGTHADLLARSGAYRQIITTDREDAR
+>PROKKA_01764
+MTRATSPAASSLRDALGGIAPYLEGVRARWVLGLASATAAGLVALAIPQVIHLLVDTVFT
+QTVLAGPSSPDSRADVWRAAGLLTVLGLAEAAFIGLRRYFILPPAAGVENRARIALFERL
+QRLPVAFHDAWPSGQLLSRAQGDLSLLRRWIAFGSVMLVVDVVTIAVGLVLLFLLSWQLA
+LLYLAAAVPIMWASFGFRNDFRAASRLSQDQAGDLATSVEESVHGIRVLKAFGRGAHALD
+GFRGRARTLQGTEVHKASVLARFIALIVALPETVLGLGLALGLWLVATGELTVGALAAYF
+ATAAVLAGPVESVGQLMGMTLSARTAIDRHVDVLATPVDIASPTGEAAVVPPATGALAFR
+GVRFRWPDADPGRGERDLLDGVDLELVPGETMALVGATGAGKSTLLQLVPRLLDVTAGSV
+CVDGVDVRRMPLEELRRRVSVAFEDATLFSATIRQNVLLGAPADVLADGLHSPAADALLD
+LALETAQAGFVADLADGVETEIGEEGLSLSGGQRQRIALARAIAARPDVLVLDDPLSALD
+VRTEEAVTARLREVLDGTTTLIVAHRPSTVALADRVAVLADGRIEDVGTHPELLARSAVY
+RHIISSRPEEQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001494.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001494.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a3d411689391cc9eb4d1a74f80be53fe1e9bf78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001494.fa
@@ -0,0 +1,45 @@
+>PROKKA_01850
+MSVAPRAAVPPAPTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPEASSGPFPAT
+TLVLLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVAHHGDFAWVA
+FPLFFVVLHVVDRVARQAWVRHVVGPALVVAMAVVVVAGMAAGAGGVRVPAVIGPLVGAA
+VAVVLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLTQG
+LASIVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGTGAPSLIEAL
+ERAVAGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLANVGAHAGARRAR
+VTLGYLGDELTVDVADDGAGFDPAVVAARPRAGAAGADPGAGTGVGLASVRERLAAVGGE
+ATVESAPGEGTVVALRVPLVAAGAGRSADPEQTESEETA
+>PROKKA_01546
+MSVAPRAAVPPAPTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPDASGPFPATT
+LVLLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVGHHGDFAWVAF
+PLFFVVLHVVDRVARQAWVRHVVGPALVVAMAAVVVAGMAAGAGGVRVPAVIGPLVGAAV
+AVVLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLTQGL
+ASIVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGTGAPSLVEALE
+RAVTGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLANVGAHAGARRARV
+TLGYLGDELTVDVADDGAGFDPAVVVARARAGAAGADPGAGTGVGLASVRERLAAVGGEA
+TVESAPGEGTVVALRVPLAAAGAGRSADPEQTESEETA
+>PROKKA_01018
+MPTTRPSADTAGAPAETGAAAVLAGLRVALHVAFAVLLAVGLGRALADLSRTGAPAPAVL
+ALTGCTALLAGVYLAGTLVERRRWGRGEDVGRGPALLWLALVLALWGLLVAQHRDFAWVA
+FPLFFVALHVVARTARTAMARRIAGPVLVAAMAAVVVAGMAAGVDEGVRPAAVIGPLVGA
+AVAVVLSGAYRALHQESERQRDVAEQLRAAQAELARTQHRAGVGEERERLAREIHDTLTQ
+GLASIVLVSRAAQDALDAQDPALARTRMETVRTTAAENLDESRRFVRDLRATGGASLVAA
+VERAVAGFAERQAAAGTPVAADVEVVGTPVPLAEAVEAALLRAVQASLANVAAHARATRA
+RVTLAWMPGELAVDVADDGVGFRPEAVVTGDAGTQGTGAGTQGARAGRASRPGAGTGVGL
+ASVRERLAGVGGHASVESAPGEGTVVALRVPLPAAAGRAEEDEGRERG
+>PROKKA_00960
+MRTSDPADGPRGANGTAALLSGLRVAVHVGFAVLLALALVRALAGPDAGARLTGRPALAL
+VGLTVVLAGVYLTGTVAERRLHAAGRAPGRTAAGTWLAVLLGVWALAVLRHPDMMWVAFP
+LFFVALHAVHVILGRPRLALACVAAMTVVVVVASLERGTAPGAVLGPAVGAAVAVVVFHA
+CRLLVVESERQRSVAEQLRATRAELAASERHAGVLAERERLAREIHDTLTQGLASIVLVS
+RAAQDAVRAGDAALADERLETVRTTAAENLAESRAFVRGLRAPVDGVQGGADRAGSALEA
+ALGAAVRGFRARRQALGRPVEAELAVVGEPVAVGEAVETVLVRAAQSSLANVDQHARTDR
+CRVTLTWMDGEVALDVADDGVGFDPEAARARASRAAVSDPAAPRPAEEGTGVGLAGLAER
+VAGVGGRVDVESAPGQGCVVAVRIPVPRQHERRGA
+>PROKKA_01770
+MSVAPRAAAPTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPEASSGPFPVTTLV
+LLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVAHHGDFAWVAFPL
+FFVVLHVVDRVARQAWVRHVVGPALVVAMAVVVVAGMAAGAGGVRVPAVIGPLVGAAVAV
+VLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLTQGLAS
+IVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGTGAPSLIEALERA
+VTGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLANVGAHAGAHRARVTL
+GYLGDELTVDVADDGAGFDPAVVAARPRAGAAGADPGAGTGVGLASVRERLAAVGGEATV
+ESAPGEGTVVALRVPLVAAGAGRSADPEQTESEETA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001501.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001501.fa
new file mode 100644
index 0000000000000000000000000000000000000000..61ba4255daa4aa6516018b8ac10266ef49fdce9e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001501.fa
@@ -0,0 +1,35 @@
+>PROKKA_01858
+MATSSLPLSDIVETGRPFTRGDLRAAGVSERLVRGGDVRRVTHGVHRLRSDHLGSWADLG
+YVEAPAPFAPEETAAIVEASGGVASHLTALLLHRVPLPPFLAEDGTVHVSRPHPRGASVR
+PEITSHARLVPAADVTALHGIRLTSLERSWADLAALLRPGMLEPVVAAGDALIHRPWSPE
+GRRSPRTTTAALRSALLRAGRFKGVRTARAALELVRVGADSPQETALRLALLHAGLPEPE
+LQLVLHPGRARSPDADLGWRQWRLVVHYDGGHHLDPAQLAVDSWRDEGWARAGWTQIWAT
+VDDARDDFRRVVAEVQTHRARLGGRVFAS
+>PROKKA_01554
+MVTSSLPLSDIAEAGRPFTRGDLRAAGVSERLVRGADVRRVTHGVHRLRSDHLGSWADLG
+YVEAPAPFAPEETAAIVEASGGVASHLTALLLHRVPLPPFLAEDGTVHVSRPHPRGASVR
+PEITSHARLVPAADVTALHGIRLTSLERSWADLAALLRPGMLEPVVAAGDALIHRPWSPE
+GRRSPRTTTAALRSALLRAGRFKGVRTARAALELVRVGADSPQETALRLALLHAGLPEPE
+LQLVLHPGRARSPDADLGWRQWRLVVHYDGGHHLDPAQLAVDSWRDEGWARAGWTQIWAT
+VDDARDDFRRVVAEVQTHRARLGGRIFAS
+>PROKKA_01006
+MSMSTSTSTSLPCPQDRRPPVPARPLDVVAAGGPLFTRADLSAAGLPADRLRAADVRRVT
+HGVHRRADDVPGDWGALGYAEPPVAFAPEETAAIVTASRGVASHLSALLLHGIPVPPFLV
+DDGRVHVSRPHSRGASERPEVRSHARSVPEADAVVLHGIRVTSVERTWADLAALVRPGHL
+DPVVAAGDAVVTGIWTPQGRLPPRATILRLRAGLARSGRFKGARTARAALELIRAGADSP
+PETALRLALLHAGLPEPELQLVLHRGRRRSPDADLGWRAWRLVVHYDGDPHLDPAQQAVD
+AWRNGGWARAGWSQIVATVDDARDDFRRVVAEVLAHRARLGGRAYVA
+>PROKKA_00950
+MALESLADVLGSAPLPIRAEGPPPLGLFTRSDLRAAGLGGHRVHGRDVRRVTHGVHRLAT
+DPAGDWAVLGHRCPPAPFAPEETAAIVEAAGGVASHLTALLLHGVPLPPFLAEDGTVHVS
+RPHARGASGRLEVTSHARSVPAADVTSLHGIRVTSLERTWADLASLVPPGLVDPVVAAGD
+AVVRHPWTPQGRSAPRTTPARLAAALDRAGRFKGVRTARRALEAVRVGSDSPQETALRLA
+LVHAGIPEPELQLVLHPGRERSPDADLGWRMWRLVVHYDGASHLEPAQRAVDARRHEGWE
+RAGWAQIVATVDDARDDFRRVVAEVQAHRRRLGGRVYVC
+>PROKKA_01778
+MATSSLPLPDIVETGRPFTRGDLRAAGVSERLVRGGDVRRVTHGVHRLRTDHLGSWADLG
+YAEAPAPFAPEETAAVVEASGGVASHLTALLLHRVPLPPFLAEDGTVHVSRPHPRGASVR
+PEITSHARLVPAADVTALHGIRLTSLERSWADLAALLRPGMLEPVVAAGDALIHRPWSPE
+GRRSPRTTTAALRSALLRAGRFKGVRTARAALELVRVGADSPQETALRLALLHAGLPEPE
+LQLVLHPGRARSPDADLGWRQWRLVVHYDGGHHLDPAQLAVDSWRDEGWARAGWTQIWAT
+VDDARDDFRRVVAEVQTHRARLGGRIFAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001510.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001510.fa
new file mode 100644
index 0000000000000000000000000000000000000000..be36896dd9fff3c9e11e9bcd009329399f3d1c92
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001510.fa
@@ -0,0 +1,30 @@
+>PROKKA_01867
+MAQQNPITGSFGAVAAADAAGVHVAGLNKSFGANHVLRGIDLDVAPGEVVCLIGPSGSGK
+STLLRCVNLLEKPDSGVVTVGEFTVTDEDVDLDVLRRHVGMVFQQFNLFPHLSVLENCTV
+AQLKVLKRGKAEAVDIARRQLARVGLAELEDRYPDQLSGGQQQRVAIARALAMDPQLMLF
+DEPTSALDPETVGDVLAIMRQLARDGMTMLVVTHEMGFAREVADRVVFMDGGVVVEAGPA
+AAVISDPQQPRTQDFLRRVLHPTEIDL
+>PROKKA_01563
+MAQQNPITGSFGAVAAADAAGVHVAGLNKSFGANHVLRGIDLDVAPGEVVCLIGPSGSGK
+STLLRCVNLLEKPDSGVVTVGEFTVTDEDVDLDVLRRHVGMVFQQFNLFPHLSVLENCTV
+AQLKVLKRGKAEAVDVARRQLARVGLAELEDRYPDQLSGGQQQRVAIARALAMDPQLMLF
+DEPTSALDPETVGDVLAIMRQLARDGMTMLVVTHEMGFAREVADRVVFMDGGVVVEAGPA
+AAVISDPQQPRTQDFLRRVLHPTEIDL
+>PROKKA_00993
+MAQQTPQPAASAVDAAGVHVADLNKSYGSNHVLRGIDLDVAPGEVVCLIGPSGSGKSTLL
+RCVNLLEKPDSGRITVGEFDVTDEDVDLDALRRHVGMVFQQFNLFPHLSVLENCTVAQVK
+VLKRSKAEAAEVARRQLARVGLAELEDRFPDQLSGGQQQRVAIARALAMDPQLMLFDEPT
+SALDPETVGEVLAIMRQLARDGMTMLVVTHEMGFAREVADRVVSMDAGVVVETGPAAALI
+ADPQQPRTQDFLRRVLHPTEIDL
+>PROKKA_00931
+MTEQTASPRPSDAGTAAGVHIAGLHKSYGSNHVLRGIDLDVAPGEVVCLIGPSGSGKSTL
+LRCVNLLEVPDSGGVQVGEFTVTDPDVDLDRLRQHVGMVFQQFNLFPHLTVLENCTVAQV
+KVLKRSAAEAADTARRQLARVGLGELEGRYPDQLSGGQQQRVAIARALSMDPRLMLFDEP
+TSALDPETVGDVLAIMRKLAREGMTMLVVTHEMGFAREVADRVVFMDGGVVVEQGPASAV
+ITDPQEPRTQDFLRRVLNPAGVDI
+>PROKKA_01787
+MAQQNPITGSFGAVAAADAAGVHVAGLNKSFGANHVLRGIDLDVAPGEVVCLIGPSGSGK
+STLLRCVNLLEKPDSGVVTVGEFTVTDEDVDLDVLRRHVGMVFQQFNLFPHLSVLENCTV
+AQLKVLKRGKAEAVDVARRQLARVGLAELEDRYPDQLSGGQQQRVAIARALAMDPQLMLF
+DEPTSALDPETVGDVLGIMRQLARDGMTMLVVTHEMGFAREVADRVVFMDGGVVVEAGPA
+AAVISDPQQPRTQDFLRRVLHPTEIDL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001512.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001512.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b3cbd901883909f396d43e1916f17afe31a12c1a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001512.fa
@@ -0,0 +1,30 @@
+>PROKKA_01869
+MLPLVAPLTVAAAAPTDYGWLGNIVVDIMEAVGPIGVGLAVFAENIFPPIPSEVILPLAG
+FTAAGGAFSPHAALVWATVGSIVGALALYGLGAWLGRHRMYRLADRMPLVDMEDVAKTER
+WFIRYGYWTVFLGRMVPVFRSLISIPAGIERMNLAKFTLFTALGSLIWNAIFVYGGYALG
+ERFHVVSEYADVFSNIVLVLILAFLAIWVVLRLRRDARRRNDPDWRPPTADEMAARVEAI
+LESSDHRK
+>PROKKA_01565
+MLPLVAPLTVAAAAPTDYGWLGNIVVDIMEAVGPIGVGLAVFAENIFPPIPSEVILPLAG
+FTAAGGAFSPHAALVWATVGSIVGALALYGLGAWLGRHRMYRLADRMPLVDMEDVAKTER
+WFIRYGYWTVFLGRMVPVFRSLISIPAGIERMNLAKFTLFTALGSLIWNAIFVYGGYALG
+ERFHVVSEYADVFSNIVLVLILAFLAIWVVLRLRRDARRRNDPDWRPPTADEMAARVEAI
+LESSDHRK
+>PROKKA_00991
+MLPAVTPLTLAASTVTADTDYGWLGNVVVDIMEAVGPVGVALAVFAENIFPPIPSELILP
+LAGFTAAGGAFSPLAALLWATVGSVTGALALYGIGALLGRRRMYRIADRMPLVDVEDVAK
+TERWFARYGYWTVFLGRMVPVFRSLISIPAGIERMHLGMFTLFTTLGSLIWNAIFVYGGY
+ALGERFHLVSDYADVFSNVVVVLVLAFLVVWVVLRLRRNARRAKDPDWHQPTADEMAARV
+DALLESSDHRK
+>PROKKA_00929
+MIRRGRTTSDAAAVVVVENGGMSALSTLPLLAAAGTPDYGWLGNTIVAIMEAIGPVGVGL
+AVFAENIFPPIPSEVILPLAGFTAAGGAFSPHAALIWATVGSVVGALALYGLGAWLGRRR
+LYRIAAWMPLVDVSDVERTEKWFARYGYWTVFVGRMVPVFRSLISIPAGIERMNVAKFTL
+FTALGSLLWNAIFVYGGYALGENFHVISDYADMFSNIVMVLILVFLAVWVVLRLRRNRGR
+AADPAVDHEDPEAAAARVEAEIKALQHRK
+>PROKKA_01789
+MLPLVAPLTVAAAAPTDYGWLGNIVVDIMEAVGPIGVGLAVFAENIFPPIPSEVILPLAG
+FTAAGGAFSPHAALVWATVGSILGALALYGLGAWLGRHRMYRLADRMPLVDMEDVAKTER
+WFIRYGYWTVFLGRMVPVFRSLISIPAGIERMNLAKFTLFTALGSLIWNAIFVYGGYALG
+ERFHVVSEYADVFSNIVLVLILAFLAIWVVLRLRRDARRRNDPDWRPPTADEMAARVEAI
+LESSDHRK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001518.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001518.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f4ae8b570cd5f343b1c7d2ec9d1edd75c75a9692
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001518.fa
@@ -0,0 +1,25 @@
+>PROKKA_01875
+MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETGEPRVSAESAAEQAEDGDALAQAER
+ILDEAGAQAGTEAPQPEASDREAELEADLRRLQAEYVNYKRRVDRDRDLARDAGVLKAVT
+ALLPVLDDIDAARAAGDLTDGPFAAIATKLDTALAGLGLERHDQEALAGVEFDPAVHEAV
+MRQPHAEVPADHVVQVFRNGYVRDGRVLRAAQVMVSAGDE
+>PROKKA_01571
+MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETGEPRVSAESAAEQAEDGDALAQAER
+ILDEAGAEAGTQAPQPAASDREAELETDLRRLQAEFVNYKRRVDRDRDLARDAGVLKAVT
+ALLPVLDDIDAARAAGDLTDGPFAAIATKLDTVLAGLGLERHDQAALAGVEFDPALHEAV
+MRQPHAEVPADHVVQVFRNGYVRDGRVLRAAQVMVSAGDE
+>PROKKA_00984
+MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETGEPRVSAESAAEQAEDGDALTQAER
+ILDEAGAQAGTEAPQPAASDREAELETDLRRLQAEYVNYKRRVDRDRALAQDLGVLKAVT
+ALLPVLDDLDAARAAGDLTDGPFAAIATKLDTALAGLGLERHDQEALAGVEFDPSVHEAV
+MRQPHAEVPADHVVQVFRNGYVRDGRVLRAAQVMVSAGDE
+>PROKKA_00922
+MSENQNETPSPEEPVIRDRRRIDPETGQARTPGAGEDTVPAQEQGQAPQDSGDALSQAEQ
+ILDEAGAAAEAEALPAAGSDREAELLEDLRRLQAEYVNYKRRVDRDRDVAKEQGVLKAVT
+ALLPVLDDLDAARAAGDLEDGPFAAIAAKLMTALEGLGLEREDQEALAGVEFDPVRHEAV
+MRQPHAEVPADHVVQVFRNGYARDGRVLRAAQVMVSAGQD
+>PROKKA_01795
+MSADQQRPHGSSDAERGSEEEPIVFNDRRRIDPETDEPRVSAESAAEQAEDGDALAQAER
+ILDEAGAQAGTEAPQPEASDREAELEADLRRLQAEFVNYKRRVDRDRDLARDAGVVKAVT
+ALLPVLDDIDAARAAGDLTDGPFAAIATKLDTALAGLGLERHDQEALAGVEFDPAVHEAV
+MRQPHAEVPADHVVQVFRNGYLRDGRVLRAAQVMVSAGDE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001521.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001521.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb49e9eeb14964daa88c4df1d14e0448bd605d4a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001521.fa
@@ -0,0 +1,99 @@
+>PROKKA_01881
+MATLLYRLGLGAARRPLLVILAWVLALALAVGGFLAFGGTLSSTVTIPGTPTAQVTDRLK
+EEFPEASRGRGQVVFTTEDGSPLTDAQREQITALLDDVAEQPAVEGVVNPFEAQAQQDDA
+RTRLDEGRTELADGEQRLADGRQEIEDGRAELERRTAEADAAEQRLAEAAAQLEEGQAKL
+DAARADLEERGLDALPAEALAPLREAEQQVAEGQEQLDAGRAELEEQAERLEAGQAKLDA
+QRQELEAAQAELDARWAELEAGQAELDARAEQLAAGRAELEQARDAALAEAEAAGIPAEQ
+VTEQFADQEAQLAAAEAQLAAGQDQADAARAQLEAAQAEADAGAEQLAAAQAEADDGAAR
+LAAGRQQLQESEAELEAGREQVAAGRQQALDAAEAELDAQQQKIDEGRAEYERGVAELED
+GRAQLAAGAERLDQAEADLADGRAELEDGRVEAERGERTLALAEDFRTVSEDGSTAVGIV
+TFTTPTLDVTAEDKEAVTGALTGADIDGVAVHPSQELNATAPSLLGPGEVVGLVVAAIVL
+VVMLGTLVGAGLPLVNALVGVGVGAAGALAFSSAVEMISVTPVLGVMLGLAVGIDYALFI
+VNRHRQELRRGTGLHESIALANGTSGNAVVFAGITVIVALVGLNVTGIPFLGLMGTVGAV
+CVAVAVLVAVTLTPALLSLAGMRILSKKERARLADEGPASVAEGSAAVRRAGRRSTMSTP
+AAIASALAAVALLVLVALPVGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVV
+TVDLPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVST
+EELVRDLRATEPAGEASNLGVAGMTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRS
+ILVPLIATGGFVLSMFAAMGGVVAIYQWGWLGSVFGVHNPGPVLSFLPTIMIGVLFGLAM
+DYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPM
+GFGLAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERAHAPAQ
+PSVPAPDGGAHRA
+>PROKKA_01577
+MATLLYRLGLGAARRPLLVILAWVLALALAVGGFLAFGGTLSSTVTIPGTPTAQVTDRLK
+EEFPEASRGRGQVVFTTEDGSPLTDAQREQITALLDDVAEQPAVEGVVNPFEAQAQQDDA
+RTRLDEGRTELADGEQRLADGRQEIEDGRAELERRTAEADAAEQRLAEAAAQLEEGQAKL
+DAARADLEERGLDALPAEALAPLREAEQQVAEGQEQLDAGRAELEEQAERLEAGQAKLDA
+QRQELEAAQAELDARWAELEAGQAELDARAEQLAAGRAELEQARDAALAEAEAAGIPAEQ
+VTEQFADQEAQLAAAEAQLAAGQDQADAARAQLEAAQAEADAGAEQLAAAQAEADDGAAR
+LAAGRQQLQESEAELEAGREQVAAGRQQALDAAEAELDAQQQKIDEGRAEYERGVAELED
+GRAQLAAGAERLDQAEADLADGRAELEDGRVEAERGERTLALAEDFRTVSEDGSTAVGIV
+TFTTPTLDVTAEDKEAVTGALTGADIDGVAVHPSQELNATVSSLLGPGEVVGLVVAAIVL
+VVMLGTLVGAGLPLVNALVGVGVGAAGALAFSSAVEMISVTPVLGVMLGLAVGIDYALFI
+VNRHRHELRRGTSLHESIALATGTSGNAVVFAGITVIVALVGLNVTGIPFLGLMGTVGAV
+CVAVAVLVAVTLTPALLSLAGMRILSKKERARLADEGPASVAEGSAAVRRAGRRSTMSTP
+AAIASALAAVALLVLVALPVGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVV
+TVDLPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVST
+EELVRELRATEPAGEASNLGVAGMTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRS
+ILVPLIATGGFVLSMFAAMGGVVAIYQWGWLGSVFGVHNPGPVLSFLPTIMIGVLFGLAM
+DYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPM
+GFGLAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERGHAPAA
+EAASAPAPEAGRTPAVDGGAHRA
+>PROKKA_00977
+MAKLLYRLGLGAARRPLTVILAWVLALALAVGGFLAFGGTLSTNVTIPGTPTAQVTDRLQ
+DEFPEASRGMGQVVFTTEDGQPFTDAQRDAVAALLDEVAGQDAVDAVVDPFEVQAQQDDA
+RTALADGRQEIADGEQALVDGREQVDAGRAEIEEGRAQADAGEQELADAAAQLEDGQVQL
+DAARADIEARGLDALPAEALAPLREAEQQIADGQAELDAGRAEIEEQAARLAAGQAEIDA
+NREQLEAGQAELDARWGELDAAQAQLDAQREELEAGRAQLEQALAAALEQAEAAGIPAEQ
+VTAQFAEQQAQLEAGQAQLDAAQEQADAGREQLVAAQAEADAGAEQLAEAQAQADAGAEQ
+LAAGREQLEAAEAELESGREQLAAGRQQALDAAAAELDAQQARIDEGRAQHEQGVADLEA
+GRAELAAGAERLDQAEADLATGRTELEDGRVAAERGERSLALVGGYRSVSEDGSTAVGIV
+SFSQPSLDVTAEEKEAVTGALTGADIDGVAVHPSQELNATVPSILGPGEVVGLIVAAIVL
+VVMLGTLVGAGLPLVNALVGVGVGAAGALAFSSVVEMISVTPVLGVMLGLAVGIDYALFI
+VNRHRQELKRGTALHEAIALANGTSGNAVVFAGITVIIALVALNVTGIGFLGLMGTVGAV
+CVAVAVLVAVTLTPALLSLAGTRILSRKERARLADEGPASAAEGSAAVRRAGRRSTMSTP
+AAIASALAAIALLVLVALPFGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVV
+TVDLPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVST
+EELVRELRATEPAGEASNLGVAGMTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRS
+ILVPLIATGGFVLSVFAAMGGVVAIYQWGWLGSVFGVHNPGPVLSFLPTIMIGVLFGLAM
+DYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPI
+GFGLAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERGHAPAA
+EAASAPAPEAGRTPAVDGGAHRA
+>PROKKA_00915
+MATLLHRLGLASARRPWAAILAWLIALALAVGAFLAFSGTLTTAVTIPGTPTAQVTDRLK
+EQFPDAAKGTGQVVFATEDGSAFTEAQRRAVSDALRGVEGQDAVDSVVDPFDVARQQDEA
+RTALEDGRRQIAEGEQKIAENEKALEDGRAQLAEAKDKAEAGQKELDAAAAQLDAGQEKL
+DAARADLEARGLDALPAEATAPLTEAQQKLDAGQAEYDAGVAALEEQRPALEAAEAEIAK
+QEAALEQAQARFEAGRAQAIAQAEAAGATPEQAAAAVDARLAPEREKLDAGAAQLEEARA
+RTEAGRAEFDAGEEKLAAAAAELEQGRAQLAAGREKALTAARAELDAQQQKIDAGRAEHE
+QGVRELEAGRAEIAQNEAKLADGPAQLEQARKDLAAGREKADRGQRMLTLTDGYRVVSED
+GSAALGTVAFDRPSLDVTTEQKTAVIDALADADIPGVRAIPTQALNATMPSLIGPGEVVG
+LAVAALVLVLMLGTLVGAGLPLVNALIGVGVGAAGALAFSGVVEMMSVTPVLGIMLGLAV
+GIDYALFIVNRHRLELKRGTPLHASIALANGTSGNAVVFAGITVVIALVALNVTGIPFLG
+LMGTVGAVCVAVAVLVAVTLTPALLSLAGMRILSRKERARRAAEAAPVADDAAAPSGSHA
+AAPVSRSAARAVRDARRRRRMSTPAAVATVLASAAALIVVAIPFGSMRLGLPDGASEPVG
+SDSQVSYELIADEFGEGYNGPLVVTVDLPSGLDETTAEDAQVQVGEQLKGLEHVAAVVPA
+GFNQDRTTAMFQVLPEEGPNAISTGDLVHTLRDTEPAGEASNLGVAGVTSGFIDVSEKLS
+AALPLYLGVVVGLSLLIMILVFRSILVPLIATGGFVLSVFAAMGGVVAIYQWGWLGGLFN
+VHAPGPVLSFLPTIMIGVLFGLAMDYQLFIASGMREAYAHGQPARDAVMTGLRAGRAVVT
+AAAIIMISVLGGFVFSHDAMIRPIGFGLAFGVLLDAFVVRLLLMPALMHLLGDAAWWLPK
+WLDRILPDVDVEGAGLERHGAAGEAADAAPVGADRA
+>PROKKA_01801
+MATLLYRLGLGAARRPLLVILAWVLALALAVGGFLAFGGTLSSTVTIPGTPTAQVTDRLK
+EEFPEASRGRGQVVFTTEDGSPLTDAQREQITALLDDVAEQPAVEGVVDPFEAQAQRDDA
+RTRLDEGRAELADGEQRLADGRQEIEDGRAELERRTAEADAGEQRLAEAAAQLDEGQAAL
+DAARADLEERGLEALPADALAPLREAEQKVADGQEQLDAGRAELEEQAERLEAGQAEIDA
+QRQELEAGQAELGDRWTELEAGQAELDAQAEQLAAGRAELEQARDAALAEAEAAGIPAEQ
+VAAQFADQEAQLAAGEAQLAAGQDQADAARAQLEAAQAEADAGAEQLAAAQAEADDGAAR
+LAAGRQQLQESEAELEAGREQVAAGRQQALDAAEAELDAQQQKIDEGRAEYERGVAELED
+GRAQLAAGAERLDQAEADLADGRAELDDGRVEAERGERTLALAEDFRTVSEDGSTAVGIV
+TFTTPTLDVTAEDKEAVTGALTGADIDGVAVHPSQELNATAPSLLGPGEVVGLVVAAIVL
+VVMLGTLVGAGLPLVNALVGVGVGAAGALAFSSAVEMISVTPVLGVMLGLAVGIDYALFI
+VNRHRQELRRGTGLHESIALANGTSGNAVVFAGITVIVALVGLNVTGIPFLGLMGTVGAV
+CVAVAVLVAVTLTPALLSLAGMRILSKKERARLADEGPASVAEGSAAVRRAGRRSTMSTP
+AAIASALAAVALLVLVALPVGSMRLGLPDGGSEPEGSDSQVAYELTAEKFGEGYNGPLVV
+TVDLPAGLDEDAAEDARLAVGEQLAGLEHAHAVVPAGFNEDRTVTMFQVLPEEGPNAVST
+EELVRDLRATEPAGEASNLGVAGMTSGFIDVSEKLSDALPLYLGVVVGLSLLIMVLVFRS
+ILVPLIATGGFVLSMFAAMGGVVAIYQWGWLGSVFGVHNPGPVLSFLPTIMIGVLFGLAM
+DYQLFIASGMREAYAHGLPARQAVLTGLRSGRAVVIAAAIIMISVFGGFIFAHDAMIRPM
+GFGLAFGVLLDAFVVRLLLMPALMHLLGEKAWWLPRWLDRIMPDVDVEGAQLERAHAPAQ
+PSVPAPDGGAHRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001525.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001525.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa52fbb8184ff832245c77ddbe9cdbb3db114afb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001525.fa
@@ -0,0 +1,15 @@
+>PROKKA_01885
+MDPMDLATWAGGALLVVGAVGALYRIVRGPSLLDRAVATDVLLVVFSGMLVLEMAVHRHT
+HHVVLVVLAATVGFVGSVTVARFAEDRRPDHSLEDQARVPGTTDVPGGEEGR
+>PROKKA_01581
+MTDPFHLAAWIAGTLLFVGALGALYRIVRGPSLLDRAVATDVLLVVFSGMLVLEMAAHRH
+THHVVLVVLAATVGFVGSVTVARFAEDRRPDHSLEDQARVPGTTDVPGGEEGR
+>PROKKA_00973
+MTDPFHLAAWIAGTLLFVGALGALYRIVRGPSLLDRAIATDVLLVVLSSGLILDMAVRRH
+TDNVVLVVLAATVGFVGSVTVARFVEDRRPDHSMEDQARVPGTSDVPGGEEGR
+>PROKKA_00911
+MSLPLTLAAWIGGAMLFVGAVGALYRIARGPSLLDRAAATDVLLVVLSGALLLDMGVHRR
+TDTVVLVLLAAAVGFMGSVMVSRFVEDRRPEHPQEHEALVPGTSDVPAPREDA
+>PROKKA_01805
+MDPMDLATWAGGALLVVGAVGALYRIVRGPSLLDRAVATDVLLVVFSGMLVLEMAVHRHT
+HHVVLVVLAATVGFVGSVTVARFAEDRRPDHSLEDQARVPGTTDVPGGEEGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001526.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001526.fa
new file mode 100644
index 0000000000000000000000000000000000000000..03f1df51d693ee0a0542654d7dca95bfd02c61fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001526.fa
@@ -0,0 +1,26 @@
+>PROKKA_01886
+MPGSDSARRGVVRPDRIRGIVAQWPLILVMVAVWCALWQDFAPHVALTGLAFALLIIGLF
+PMPSIPFSGRLNPWWSLVFTVRFLVDVVRASVNVAGTVLLRGRRARGSIVGVPLRSHDDL
+IITLVSHALALVPGSIVLDVDRVRSVLYLHVLDATTDEDVAGFRAKALDVEAGIIRAVGT
+REDLELVRRFPSSAPPAARPPKEEA
+>PROKKA_01582
+MPGSDSARRDVVRPDRVRGIVAQWPLILVMVAVWCALWQDFAPHVALAGLAFALLILGLF
+PMPSIPFSGRLNPWWSLVFTVRFLVDVVRASVNVTGVVLLRGRRARGSIVGVPLRSHDDL
+IITLVSHALVLVPGSIVLDVDRVRSVLYLHVLDATTDEDVEGFRAKALDVEAGIIRAVGT
+REDLELVHRYPDTAPPEEESAERRRPAAPRPGGTAPIGSTADHAKEGT
+>PROKKA_00972
+MPGTDPARDAAGAERPARPHRVRDMVGQWPLIAVLVLLWCAVWEDYSLHVALAGLAFSLL
+VMVLFPMPRIPFSGRLNPWWFLVFTAQFLGDVVRSSVEVSKVVLLRGRAARSSIVGVRLR
+SHDDLVITLVSHALALVPGSIVLDVDRARSILYLHVLDATTDEDIEDFRAKALRVEAGII
+KAVGTREDLELVHRYPDTAPPEEESAERRRPAAPRPGGTAPIGSTADHAKEGT
+>PROKKA_00910
+MPAAETTSPASAPTRPAPGGVRSVLRQWPLLLALVLMWCAVWQDFSAHVALTGLLFSLLV
+VVLFPMPPIPFGGRFHPGHALVFTGRFLADVVASSLSVTRVILTRGRTVRSSVVRVPLRS
+HDDIVLTLVSHALALVPGSIVLDMDRANGVLYLHVLDATTDADVADYRAKALRVEADIIR
+AVGTRADVAVLRDHPDSAPDPEGVEERRRHPAYRAELLPDTPGPVAPAPVDARPEPDAPG
+GDR
+>PROKKA_01806
+MPGSDSARRGVVRPDRIRGIVAQWPLILVMVAVWCALWQDFAPHVALTGLAFALLIIGLF
+PMPSIPFSGRLNPWWSLVFTVRFLVDVVRASVNVAGTVLLRGRRARGSIVGVPLRSHDDL
+IITLVSHALALVPGSIVLDVDRVRSVLYLHVLDATTDEDVAGFRAKALDVEAGIIRAVGT
+REDLELVRRFPSSAPPAARPPKEEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001530.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001530.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9501ab4870d2d93d810b146b67723100f6e24e31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001530.fa
@@ -0,0 +1,45 @@
+>PROKKA_01890
+MTDVALPPVASAAPRRQVAAWALWDWGSAAFNAVMVTFVFGTYLASDAFGPDERGTAWLS
+TAMAVAGVVIAVTAPVLGRRADGAGRRRLWLALTTGAVIACTAACFWVTPEESSLLLGVT
+LIALGTVFFEFAEVQVNAILVHISTPATIGRISGIGWGAGYLGGILLLLIVFVGFVSGDA
+HWFGVTEDAALNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPAADGGPRRESVLGSYREL
+GATLARMWREDRNTLWFLVASAVFRDGVGAVFVYGAILGTTVYGLAASDVILFAIAANVV
+AALGAFVGGRLDDAVGPRRVILGSLAAMVLVAGALFFASGTLAFWVGGLALCLFVGPVQS
+ASRAFLGRLTTPRTAGEVFGLYATTGRAVGFITPALVTLALALHPDNRVVIPVIAVVLVA
+GGLLFARVTEPITRSAESVR
+>PROKKA_01586
+MTDVALPPVASAAPRRQVAAWALWDWGSAAFNAVMVTFVFGTYLASDAFGPDERGTAWLS
+TAMAVAGVVIAVTAPVLGRRADGAGRRRRGLGLTTGAVIACTAACFWVTPEESSLLLGVT
+LIALGAVFFEFAEVQVNAILVHISTPATIGRISGIGWGAGYLGGILLLLIVFVGFVSGDA
+HWFGVTEDEGLNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPSPGGGPRRESLAASYRAL
+GSTLARMWREDRNTLWFLLSSAVFRDGVGAVFVYGAILGTTVYGLAASDVILFAIAANVV
+AALGAFVGGRLDDAVGPRRVILGSLAAMVLVAGALFFASGTLAFWVGGLALCLFVGPVQS
+ASRAFLGRLTTPRTAGEVFGLYATTGRAVGFITPALVTLALALHPDNRVVIPVIAVVLVA
+GGLLFARVTEPITRSAESVR
+>PROKKA_00968
+MPGMDPAASAVPDAALPRLATAAPRRQVVAWALWDWGSAAFNAVMVTFVFGTYLASDAFG
+PDERGTAWLSTALAVAGVVIALTAPVMGRRADGAGRRRLWLGVMTAAVIACTTACFLVTP
+QESSLLLGVTMIALGTVFFEFAEVQVNAILVQISTPATIGRISGIGWGAGYLGGILLLLI
+VFVGFVSGDAHWFGITGDEALNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPTPGGGPRR
+ESLAASYRALGSTLARMWRQDRNTLWFLVSSAVFRDGVGAVFVYGAILGTTVYGLAASDV
+ILFAIVANVVAAAGAFAGGRLDDAIGPRRVILGSLAAMVLVAAGLALASGTLAFWIGGLA
+LCLFVGPVQSASRAFLGRLTTERTAGEVFGLYATTGRAVGFITPMLVTLALAAVPDNRVV
+IPVIVLVLIVGGVLFARVTDPVTRSAEPAP
+>PROKKA_00906
+MPRMSSPAPHAAPQPCPAPHGGAGPAPARVPRGRVVAWAAWDWGSAAFNAVMVTFVFGTY
+LASDAFGPDDRGTQWLSAANALAGVVIALTAPALGRLADGTGRRRLWIALTTGAVIACTA
+ACFLVTPEESMLGLGVTLIALGTVFFEIASVHINAILLQISTPATIGRVSGFGWGAGYLG
+GIVLLLIVFVGFVSGDDHWFGVGEERALNIRVVALVAAAWFLVFALPVLAASPEPPAARG
+ADGSPRRESLVESYRGLGRTLARMWRQDRLTLRFLAASAVFRDGVGAVFVYGAILGTTLY
+GLAAQDVVLFAIVANVVAALGAFAGGRLDDALGPRRVILGSLAAMVVVAAALVLAEGTAA
+FWAGGLALCLFVGPVQSASRAFLGRLTVPETAGEAYGLYATTGRAIGFITPALVSAALAV
+WGDSRVIIPVIALVLLAGGALLLGVREPEGPTVAGARPGTGPRAAR
+>PROKKA_01810
+MTDVALPPVASAAPRRQVAAWALWDWGSAAFNAVMVTFVFGTYLASDAFGPDERGTAWLS
+TAMAVAGVVIAVTAPVLGRRADGAGRRRRGLALTTGAVIACTAACFWVTPEESSLLLGVT
+LIALGTVFFEFAEVQVNAILVHISTPATIGRISGIGWGAGYLGGILLLLIVFVGFVSGDA
+HWFGVTEDAALNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPAADGGPRRESVLGSYREL
+GATLARMWREDRNTLWFLVASAVFRDGVGAVFVYGAILGTTVYGLATSDVILFAIAANVV
+AALGAFVGGRLDDAVGPRRVILGSLAAMVLVAGALFFASGTLAFWVGGLALCLFVGPVQS
+ASRAFLGRLTTPRTAGEVFGLYATTGRAVGFITPALVTLALALHPDNRVVIPVIAVVLVA
+GGLLFARVTEPITRSAESVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001531.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001531.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f1b8ea14681b874e5e41eac02ca7e00f62f58a73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001531.fa
@@ -0,0 +1,25 @@
+>PROKKA_01891
+MLLSDRDIRAELDSGRVGLDPLDPAMVQPASVDVRLDRFFRLFDNHRYAHIDPRQKQDEL
+TRLVEVDPDEAFILHPGEFVLGSTYEQVTLPDDLAARLEGKSSLGRLGLLTHSTAGFIDP
+GFSGHVTLELSNVATLPITLWPGMKIGQLCFFRLSSSAQSPYGTGANQNRYQGQRGPTAS
+RAHRDFHLTRIER
+>PROKKA_01587
+MLLSDRDIRAELDSGRVGLDPLDPAMVQPASVDVRLDRFFRLFDNHRYAHIDPRQEQDEL
+TRLVEVDPDEAFILHPGEFVLGSTYEQVTLPDDLAARLEGKSSLGRLGLLTHSTAGFIDP
+GFSGHVTLELSNVATLPITLWPGMKIGQLCFFRLSSAAQSPYGTGANQNRYQGQRGPTAS
+RAHRDFHLTRIE
+>PROKKA_00967
+MLLSDQDIRAELASGRVGLDPLDEAMVQPASVDVRLDRFFRLFDNHRYAHIDPRQEQDEL
+TRLVEVDPDEAFILHPGEFVLGSTYEQVTLPDDLAARLEGKSSLGRLGLLTHSTAGFIDP
+GFTGHVTLELSNVATLPITLWPGMKIGQLCFFRLSSPAASPYGTGANQNRYQGQRGPTAS
+RAHLDFHLTRIDR
+>PROKKA_00905
+MASVLLSDRDIRAELSSGRIGLDPLELSMVQPASVDVRLDRFFRLFDNHRYAHIDPAQPQ
+EELTRLVEVEPDQPFVLHPGEFVLGATYEQITLPDDVAARLEGKSSLGRLGLLTHSTAGF
+VDPGFTGHVTLELSNVATLPITLWPGMKIGQLCFFRMSSPAESPYGSGGNLNRYQGQRGP
+TASRSHQDFHLTRIPR
+>PROKKA_01811
+MLLSDRDIRAELDSGRVGLDPLDPAMVQPASVDVRLDRFFRLFDNHRYAHIDPRQEQDEL
+TRLVEVDPDEAFILHPGEFVLGSTYEQVTLPDDLAARLEGKSSLGRLGLLTHSTAGFIDP
+GFSGHVTLELSNVATLPITLWPGMKIGQLCFFRLSSSAQSPYGTGANQNRYQGQRGPTAS
+RAHRDFHLTRIER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001533.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001533.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c3634e1b187923b1fb51ea55bd932e35d29690b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001533.fa
@@ -0,0 +1,20 @@
+>PROKKA_01899
+MTTLIVTSSAHGSTREIAERVAEVLRTSQAVPTVVEDVEGAAAWLATADAVIVAAPVYTG
+SFAADARAFLDTRRAELTDLPLVILASGGAPELARPVREKLESYGPREVAYFRGALFEER
+LGRLEKLKLKLSRNEHYGDFRDWDAIEAWAKTLPGAGVR
+>PROKKA_01595
+MTTLIVTSSAHGSTREIAERVAEVLRTSQAVPTVVEDVEGAAAWLATADAVIVAAPVYTG
+SLAADARAFLDTRRAELADLPLVILASGGAPELAPPVREKLESYGPREVAYFRGALVEER
+LGRLEKLKLKLSRNEHYGDFRDWDAIEAWAKTLSGAGVR
+>PROKKA_00959
+MTTLIVTSSAHGSTREIAERVAEVLRTSQSVETVVEDVAGAAAWLATADAVIVAAPVYEG
+SLAAEARHFLDSRRAELADKPLLFLASGGGYELDPKVREKLESYGPREIAFFRGALVEER
+LGWLEKLKLKVSRNENYGDYRDWDAIEAWAKSLSGHGVR
+>PROKKA_00899
+MTALIVTASRHGSTREIAERVAEVLRTTAQTDTVVEDVAGAAAWLDTADAVVVAAPVYGD
+KLEKSAKAFLDSRRAELSQKSLVILYSGASPVPNRALADQLGTYGARDVKYLRGALVEER
+LGALEKLQIKLVKGRYGDFRDWNAVEHWAKGLSAHGVN
+>PROKKA_01819
+MTTLIVTSSAHGSTREIAERVAEVLRTSQAVPTVVEDVKGAAAWLATADAVIVAAPVYTG
+SLAADARAFLDTRRAELADLPLVILASGGAPELARPVREKLESYGPREVAYFRGALVEER
+LGRLEKLKLKLSRNEHYGDFRDWDAIEAWAKTLSGAGVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001535.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001535.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3e54b06fa7f582780ffa8a6b222204a876ce54e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001535.fa
@@ -0,0 +1,30 @@
+>PROKKA_01901
+MSADRVRPLRRPAAPRRGRLRLVAAVAAGLLALTGCGAGDNDPAAASVPADGVHDDAGTA
+VHTESAAPEGLGLGDRQDERMAEAAAERAATFGFVRQRAATAEEIDAAREDSRDRRADAD
+RTTVQPAQCKAPLTALDFSPIALDGAEATRVDVGADTFTGTGTVEVARLTGQGRQDVERH
+IQTVNALRADCREMTMTVQEGDATVDYRLEVSDAPLSDGTPAQSALVWERTVASESEPQL
+TAQVLTAVTSDAVVMVSFVGRPEAGRKEFTLIAEEMLAAALAAD
+>PROKKA_01597
+MSADRLPPLGRPAAPRRGRLRLAAAVAAGLLALTGCGAGDGDPAAASASADGVHGDAGTA
+APTESAAPEGLGLGDRQDERMAEAAAERAATFGFVRQRAATAEEIDAAREDSRDRRADAD
+RTTVQPAQCKAPLTALDFSPIALDEAEATRVDVGADTFTGTGTVEVARLTGQGRQDVERH
+IQTVNALRADCREMTMTVQEGDATVDYRLEVSDAPLSDGTPAQSALVWERTVASESEPQL
+TAQVLTAVTSDAVVMVSFVGRPEAGRKEFTLIAEEMLAAALAAD
+>PROKKA_00957
+MLALTGCGAGDEPAPEQPSAPADALHGDVGGAAPAPEEGAEGLGLGDRQDERMAAAAAER
+AVGFGFVRQRAAAPEEIDAAREDSRARRSDADRTTVQPAACKAPLTALDFSPISLDEGEA
+TRVDVGADTFTGTGTVEVARLTGSGRQEVERHLQTVNGLLADCREMTMTVQDGDASVDYR
+LAVSEAPLSEGTPAQSALVWERSLASADGPQLTAQVLTAVTADAVVMVSFVGQPEAGRKE
+FTLIAEEMLAAALAAG
+>PROKKA_00897
+MSADRTRPRPAVRRLAVASSGAALAAVLLAGCASGGDAAASSGAQAAGPSSSAATGGLDL
+GDRVDQRRAEAAAARAASFGFTRQDAVGADQIAAARGDAADRAADDGRTTVEPARCQAPL
+AALDFSPILLDQEEVSRVDVGTDSFAGTGTVEVATLDGPGRQRVEEHLQTVNTLLADCRD
+MTVTTRDADGARTYRLQMSAAGLSDGSPAQSGLVWTQTPAGRDEPATAAQILTAVGPEDV
+VMVSFTGQPQAAERQFTVMAEEMLAAAGTVTR
+>PROKKA_01821
+MSADRVRPLRRPAAPRRGRLRLVAAVAAGLLALTGCGAGDNDPAAASVPADGVHDDAGTA
+VHTESAAPEGLGLGDRQDERMAEAAAERAATFGFVRQRAATAEEIDAAREDSRDRRADAD
+RTTVQPAQCKAPLTALDFSPIALDGAEATRVDVGADTFTGTGTVEVARLTGQGRQDVERH
+IQTVNALRADCREMTMTVQEGDATVDYRLEVSDAPLSDGTPAQSALVWERTVASESEPQL
+TAQVLTAVTSDAVVMVSFVGRPEAGRKEFTLIAEEMLAAALAAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001542.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001542.fa
new file mode 100644
index 0000000000000000000000000000000000000000..86fcafab5a4425ab8e172fa91ec737d8d259e29a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001542.fa
@@ -0,0 +1,15 @@
+>PROKKA_01908
+MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV
+RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW
+>PROKKA_01604
+MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV
+RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW
+>PROKKA_00950
+MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV
+RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW
+>PROKKA_00890
+MAKKSKIAKNEQRKVMVARNAEKRLELKKTLIDPNASDEAREAARVGLQKLPRDASPVRV
+RNRDAIDGRPRGTFQRFGISRVRFREMAHRGELPGVTKSSW
+>PROKKA_01828
+MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV
+RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001545.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001545.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e3e6eeb3c72bf746c36c01f05404a35873653792
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001545.fa
@@ -0,0 +1,30 @@
+>PROKKA_01911
+MSHTSEQSSPLADQVPPGGPDEPHAAEGVHARLNWLRAGVLGANDGIVSVAATVVGVAGA
+TTALTPVLLAGAAAVVGGAFSMALGEYVSVSSSSDSQKSLIAKERRELEEDPEGELEELV
+QLYEADGLSRATAEAAARELTEKDALAAHLRMELGMAEEDVVSPWAAAGASFLSFLVGAL
+LPFLTVVLAPVDFRIPLTFGVTLVALAVTGWVGARLGDAPALRAAVRVVLGGALALGLTL
+AVGSLLGASVA
+>PROKKA_01607
+MSHTSEQSSPLADQLPPGGPDEPHAAGGVHARLNWLRAGVLGANDGIVSVAATVVGVAGA
+TTALTPILLAGAAAVVGGAFSMALGEYVSVSSSSDSQKSLIAKERRELEEDPEGELEELV
+QLYEADGLSRATAEAAARELTEKDALAAHLRMELGMAEEDVVSPWAAAGASFLAFLVGAL
+LPFLTVVLAPVGLRVPFTFGVTLVALAVTGWVGARLGDAPALRAAVRVVLGGALALGLTF
+AVGSLLGASVA
+>PROKKA_00943
+MNESTAPSEPTVRDDVAASSGHDRPEPHAGGGLHERLNWLRAGVLGANDGIVSVAATVVG
+VAGATTAVAPVAIAGVAAVVGGAVSMALGEYVSVSSSSDSQKALIAKERRELAEDPEGEL
+EELVGLYEAEGLSRATAENVARELTEKDALKAHLRAELGMDETGVVSPWSAAGASFVAFL
+LGALLPFLTIILAPVDIRVALTFVTTLVALAGTGYAGAWLGGAPPVRAMLRVVIGGALAL
+ALTFAVGAWLGTTVA
+>PROKKA_00884
+MSHSTAPAAPSSYPDEPHAQTGVHARLNWLRAGVLGANDGIVSVAATVVGVAGATTAVTP
+VLLAGTAAVVGGAVSMALGEYVSVSSSSDSQKAMIAKERRELAEDPEGELEELVGLYEAE
+GLSRDTAEQVARELTANDPVTAHLRMELGMAEEDVVSPLAAAGASFIAFLVGALLPFLAI
+LLSPVGVRVPVTFGVTLVALAVTGYLGAWLGNAPAVRAMVRVVVGGALALALTFGVGTWL
+GVGVA
+>PROKKA_01831
+MSHTSEQSSPLTDQVPPGGPDEPHAAGGVHARLNWLRAGVLGANDGIVSVAATVVGVAGA
+TTALTPILLAGAAAVVGGAFSMALGEYVSVSSSSDSQKSLIAKERRELEEDPEGELEELV
+QLYEADGLSRATAEAAARELTEKDALAAHLRMELGMAEEDVVSPWAAAGASFLAFLVGAL
+LPFLTVVLAPVGLRVPFTFGVTLVALAVTGWVGARLGDAPALRAAVRVVLGGALALGLTF
+AVGSLLGASVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001551.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001551.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f33e16b569b5259cf378e4100be8b6bb71c1dd4c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001551.fa
@@ -0,0 +1,17 @@
+>PROKKA_01924
+MTLVEYTRRHPDADHLDPEKESVLEEAVGTGTQQITVDAQQGAVLRVIVLCPSDATGETE
+ILTSRGGGGTKTWMAGSEALCGGWSAATPPVDEAGPMTFTVTVDNDKPFRMVLTAPSA
+>PROKKA_01620
+MTLVEYTRQHPDADYLDPEKESVLEEAVGTGTQQITVDAQQGAVLRVIVMCPSDATGETE
+ILTSRGGGGTKTWMAGSEALCGGWSAATPPVDEAGPMTFTVTVDNDKPFRMVLTAPSA
+>PROKKA_00936
+MPHRRRRPCVPVALSVAAALGLSLSACASTTTAGVGSQSPAPSSAAGAASSAAGTSSAAP
+TTSAALTTSGTAAEIAGDEAAAQAQDDAATRTALNRAVAEDGIPYAELDPSLTPVPDGAS
+ILWEGLAVGAQSLRVDARAGEEYTVVLLCAEQDGSRRSLVMATVPGEDFSDVMAESPGCG
+HWSAGLPAREADGPLTLTGVVPDGGPFRMVVYRSEG
+>PROKKA_00868
+MTLEEYTRQNPDSDYLHPETESVLQEKVGTGTQQITVDAQEGAVLRVILLCPSDATGKTD
+IHTSRGAEGEKTWMAGSEALCGGWSAATPPVEKAGPMTFSATVDNDKPFRMVLTAPAA
+>PROKKA_01844
+MTLVEYTRRHPDADHLDPEKESVLEEAVGTGTQQITVDAQQGAVLRVIVLCPSDATGETE
+ILTSRSGGGTKTWMAGSEALCGGWSAATPPPVDEAGPMTFTATVDNDKPFRMVLTAPSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001557.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001557.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e7170c393139eb535f19a5ac2c9769448e59af8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001557.fa
@@ -0,0 +1,36 @@
+>PROKKA_01932
+MAAVDPAPTDARERRDLVVPVPGPEDPPERAWLVLPHRHPVPTLLEETRDAVVGLAETLA
+AVLPVTVLAHPRDAGAARLVPPEVDLLRAPVGSPLLGRTGPSFVRRPEGLAAVAWRSAAG
+LTGTGPLDGAAATAVAEAAGLPLLTPLLCAPRGAWVSDGEGTAVVAADPVLDGRINGAWT
+PGQVAAEFAALLGITRVLWVPPAPRPDTGPWGGPGHLASWVRLQGDGEAAVHWRGDRFNP
+EHPYAAAALRFLQGADDAAGRPLRVRTVTGAAQPAEYDPAERGPRSLLDTLPLGAAVLRP
+AFEDAAGEEAAAAACAALHPGRPQLSFPAPPLLRLAGALNDLVLLQPRP
+>PROKKA_01628
+MAAVDPAPTDARERRDVVVPVPGPEDPPERAWLVLPHRHPVPTLLDETRDAVVGLAETLA
+AVLPVTVLAHPRDAGAARLVPPEVDLLRAPVGSPLLGRTGPSFIRRPEGLAAVAWRSAAG
+LTGTGPLDGAAATAVAEAAGLPLLTPLLCAPRGAWVSDGEGTAVVAADPVLDGRINGAWT
+PGQVAAEFAALLGITRVLWVPPAPRPGTGPWGGPGHLASWVRLRGDGEAAVHWRGDRFHP
+EHPYAAAALRFLQGADDAAGRPLRVRTVTGAAQPAAYDPAERGPRSLLDTLPLGAAVLRP
+AFEDAAGEEAAAAACAALHPGLPQLSFPAPPLLRLAGALNDLVLLQPRP
+>PROKKA_00927
+MPAAETVPADAAGRPDARPRVPGPREQPERAWLALPRRHPVPALLDEARDAVAGLAETLA
+EVLPVTVLTDPADHAVRSLIPPEVDLLAAPVDSPLLGRTGPGFVRRPEGLAAIAWRPAAG
+AGGPGPRDAGVAAAVAAAAGLPLLTPMLRAPRDAWVADGEGTAVVAADPVLDGRTNPAWT
+PEQVEAEFAALLGITRVAWLPPVPRIPTGPWGGAGHLGAWVRLLGGGEAAVHWRADRFHP
+EHLHGAAALRILQDAPDAAGRPLRVRTVPGGALPPEHDPAEIGPRSLVDTVPLGSAVLRP
+AFEDAATEEAAAAACAALHPGLRPVPFPGPPLLRLAGSLSDLVLVQPHP
+>PROKKA_00861
+MSTPAVPEPPRAPAPWEVPERLWLALPAVHPVPGLLAEARDAVAGLAETLGAHAPVAVLT
+DPDDADAARLLPGVVERVPVRGASPLPGREGPTFVHAAGTRGSVEAVHWRLPSDAAGTAG
+RAAATADAVARSAGLPLRTPLFSAPAGTWAADGDGTAVVSAALLDPAVNEGWTRAQAEDA
+LAGLLGAERVLWLPPVAGHAAGPWDGGGAAQPHPHPWLRFVAPGEVAVHWQPGRLHPDHA
+ASAAALHALTGARDARGRALSVRTVRALPPGPDADLEARGPLSALDLLPLAPGVVLRPAH
+ADPEADAATAEAAAALFPGAEQVPFPGPPLLRLLGTLSDLVLPQPPGARTRRPSPAPAHP
+EGPRAAP
+>PROKKA_01851
+MAAADPVPTDARERRDVVVPVPGPEDPPERAWLVLPHRHPVPTLLDETRDAVVGLAETLA
+AVLPVTVLAHPRDAGAARLVPPEVDLLRAPVGSPLLGRTGPSFIRRPEGLAAVAWRSAAG
+LTGTGPLDGAAATAVAEAAGLPLLTPLLCAPRGAWVTDGEGTAVVAADPVLDGRINGAWT
+PGQVAAEFAALLGITRVLWVPPAPRPGTGPWGGPGHLASWVRLRGDGEAAVHWRGDRFHP
+EHPYAAAALRFLQGADDAAGRPLRVRTVTGAVQPAEYDPAERGPRSLLDTLPLGAAVLRP
+AFEDAAGEEAAAAACAALHPGLAQLSFPAPPLLRLAGALNDLVLLQPRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001559.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001559.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2089edec77fb1e79f48073dda794d4c2ceea94f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001559.fa
@@ -0,0 +1,36 @@
+>PROKKA_01934
+MSRTPHRALAALSVAALALTGCSVSGSSGDGASSSAAGAGGEPTTVTIMTHDSFNLPQEL
+VQKFEQESGYTLKTTAPGDAGSVVNQLLLAKDEPTVDGVYGVEDHSAHRLVREGVVAEYT
+PQDLPASAQDRMVEDRMTPVDQGQVCFNTDPAWFEAHDVEAPTSIDQLDDPEYAKLTVAT
+SPVASSPGLALLAATTEKYGDDGWQDWWRGLKENGGKVADSWSDAYNSDFSGGEGKGRFP
+VVLSYSSSPAFAPETEVIEDSCTPQVEYAGVLEGAKNPEGAQAFVDFMLTEEVQSALPES
+MYMYPIDESVQLPEEWAQNAPLVEDAITPDPARIDERREDLLKEWTALAEASRR
+>PROKKA_01630
+MSRTPHRALAALSVAALALTGCSVSGSSGDGASSSASGAGGGEPTTVTIMTHDSFNLPQE
+LVQKFEQESGYTLKTTAPGDAGSVVNQLLLAKDEPTVDGVYGVEDHSAHRLVREGVVAEY
+TPQDLPASAQDRMVEDRMTPVDQGQVCFNTDPAWFEAHDVEAPTSIDQLDDPEYAKLTVA
+TSPVASSPGLALLAATTEKYGDDGWQDWWRGLMENGGKVADSWSDAYNSDFSGGEGKGRF
+PVVLSYSSSPAFAPETEVIEDSCTPQVEYAGVLEGAKNPEGAQAFVDFMLTEEVQSALPE
+SMYMYPIDESVQLPEEWAQNAPLVEDAITPDPARIDERREDLLKEWTALAEASRR
+>PROKKA_00925
+MTTAPHRVRTRPRRHGALAALSVAALALTGCSVADRGGSGDQGSSSAEARTVTIMTHDSF
+SLPDELIARFEQESGHTLVTTAPGDAGSVVNQLLLAKDAPTVDGVYGIEDHSAHRLVSEG
+VIAEHVPADLPDSARDLVVDGRMTPVDQGQVCLNVDTPWFQEQGLAAPTTLEQVAAPEYA
+ELTVVTSPVSSSPGLALLAATVAEFGEDGWQDWWRTALQGGMQVDASWSDAYNTSFSGGE
+GTGTRPIVLSYSSSPAFAPDTDVVAASCTPQVEYAGVVEGAENPEGARAFVDFLLTEDVQ
+AAIPDAMYMYPVDSSVPLPEAWAEHAPLVEDPIVPDAGLLDSRREDLLKEWTALHEEAAS
+>PROKKA_00859
+MSVHRTATTRRGVLAAACLSALALTGCSVSAPSTGSSSSAASSSAAPSSASGSSSTSASG
+TAAAGSKGTVTIMTHDSFALPKELIAQFEAESGYRLVTTAPGDAGAVVSQVLLSKDAPVA
+DGVYGVENHSAHRLVDQGAVQDVAPADLPASAEDLVVDGKMIPVDQGQVCFNTDPAWFTE
+HGVAEPTSIDQLRDPEYAKLTAVTSPVTSSPGLALLAATTEKYGDDGWQGWWEDLLKGGA
+KVDSTWSDAYSTDFSGGEGKGEFPVVLSYSSSPAFAPQTAVIEDSCTPQVEYAGVLTGAE
+NPEGAKAFVEFLLSKDVQAAIPENMYMYPVDDTVELPAEWAANGPLVEDPITPDPAEIDT
+EREGLLKEWTALSESAGSR
+>PROKKA_01853
+MSRTPHRALAALSVAALALTGCSVSGSSGDGASSSAAGAGGEPTTVTIMTHDSFNLPQEL
+VQKFEQESGYTLKTTAPGDAGSVVNQLLLAKDEPTVDGVYGVEDHSAHRLVREGVVAEYT
+PQDLPASAQDRMVEDRMTPVDQGQVCFNTDPAWFEAHDVEAPTSIDQLDDPEYAKLTVAT
+SPVASSPGLALLAATTEKYGDDGWQDWWQGLMENGGKIADSWSDAYNSDFSGGEGKGQFP
+VVLSYSSSPAFAPETEVIEDSCTPQVEYAGVLEGAKNPEGAQAFVDFLLTEEVQSALPES
+MYMYPIDESVQLPEEWAQNAPLVEDAITPDPARIDERREDLLKEWTALAEASRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001562.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001562.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ead2cc0a4b24b5d9ef211e91fe0ddcf98b2f14c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001562.fa
@@ -0,0 +1,20 @@
+>PROKKA_01937
+MTPPAPRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAGVLGVQASALYWHVPDKQSLLAR
+VADRIVAEAEETVRARRVTDLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLHRLLT
+EAADTPEDGERALALLLGTVSLRQQRAQAQALGVATGPDVQRHRTDPL
+>PROKKA_01633
+MTPPAPRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAAVLGVQASALYWHVPDKQSLLAR
+VADRIVAEAEETVRARRITDLAGRAEAAEAALLRHRDGADLVLSALALGLGGLGLHRLLT
+EAADTPEDGERALALLLGTVSLRQQRAQAQALGVPTGPDVQRHRTDPL
+>PROKKA_00922
+MSSPPRAGSSRGRLSATDVVDAAVGILQDFGMGDLSMRRVASVLGVQASALYWHVPDKQT
+LLARVADRIVAEAEEAVRHRGIADLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLH
+ALLTEAAPTPEEGERALALLLGGVSLRQQRAQAEALGVRVGPDVQRHRTDPL
+>PROKKA_00856
+MSTSSARGRLSAEDVVDAAVGILQDFGMGDLSMRRVASMLGVQASALYWHVPDKQTLLAR
+VADRIVADVERACAARRVEDLAGRAEEAEAVLLRHRDGADVVLSALALGLGGLGLHRLLV
+DAAHTPEEGERALAALLGTAALRQQRNQAAALGLRLGPDVQARRTGAL
+>PROKKA_01856
+MTPPAPRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAGVLGVQASALYWHVPDKQSLLAR
+VADRIVAEAEETVRARRVTDLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLHRLLT
+EAADTPEDGERALALLLGTVSLRQQRAQAQALGVATGPDVQRHRTDPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001563.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001563.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c2ea2449d506935779479159b82bfeb0d84b2750
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001563.fa
@@ -0,0 +1,45 @@
+>PROKKA_01938
+MGARINHPRTVVDRTLHHDVEPAHPAALVDVGWDFRGPGAKAEEQHRPLRVVRARRPRGT
+PRDRNGVDLTRTGPVVPRPSPPRTRIRRDGVRVVASPLAMLPGVDHGPALRLDLHPTTGG
+IVYVARELELRELGDDVRGHVYTGMVGTAHLSVFWSTVTVDLPPERPVIVRLRSDRDAEL
+LSLLEVLAPVDTRVVSYRLDESPVGTQRSSYLLPDVDPETVAQTGAARIPLEAIEAAQEE
+EDALRRSSGVFLSRRRTDRFLRRNLPGVTHSLTFADEADVTDVYVDGSVLRGSRIGGAAA
+VAGPSMWAVQAVAGATMPLEVELEALVLGHVICAWAGTPGGRVTIHSDSRAALALLNAAR
+RERLTLGGARGERIRRTLRRLLAAVDLAQAADVQVDTTWVKGHVGVHGNELADDLARAAA
+RHASVGTPEGDLPERMGQLIQLRVEDDAAG
+>PROKKA_01634
+MGARINHPRTVVDRTLHHDVEPAHPAALVDVGWEFRGPGAKAEEQHRPLRVVRARRPRGT
+PRDRNGVDLTRTGPVVPRPSPPRTRIRRDGVRVVASPLAMLPGVDHGPALRLDLHPTTGG
+IVYVARELELRELGDDVRGHVYTGMVGTAHLSAFWSTVTVDLPPERPVIVRLGSDRDAEL
+LSLLEVLAPVDTRVVSYRLDESPVGTQRSSYLLPDVDPETVAQTGAARIPLEAIEAAQEE
+EDALRRSSGVFLSRRRTDRFLRRNLPGVTHSLTFADEADVTDVYVDGSVLRGSRIGGAAA
+VAGPSMWAVQAVAGATMPLEVELEALVLGHVICAWAGTPGGRVTIHSDSRAALALLNAAR
+RERLTLGGARGERIRRTLRRLLAAVDLAQAADVQVDTTWVKGHVGVHGNELADDLARAAA
+RHASVGTPEGDLPERMGQLIRLRVEDDAAAG
+>PROKKA_00921
+MRVVAAPLAMLPGVDHGPALRMDLHPVPGGIVYVARDLVLRELGDDVRGHVHAGMVGTAQ
+LHAFWSTVTVDLPPDRPVIVRLRSDRDAELLSLLEVLAPVEMRVVSYRLDESPVGTQRSS
+YLLPDVDPEIVARAESPRVPLEAIEATQEEEDALRRSSGVFLSRRRTDRFLRRTLPTVTH
+SLSFSDEADVADVYVDGSVLRSSRIGGAAAVGGPSMWAVQAVNGATTPLEVELEALVLGH
+VVSAWAGVPGERVTIHSDSRAALALLNAARRERLTLGGARGERVRRTLRRLLAAVDLAQA
+ADVRVETTWVKGHVGVQGNELADDLARAAARHAGVGTSEEDLRRRLDRLIDLHEEAEAEA
+GQTPARAVAAEGHRPMPPGRRPGPRL
+>PROKKA_00855
+MDNSSTHPREGQVRSLHFDTDASSPDALLDPMWAFTGPRASRAGAPAPDGADVLARRARP
+AHPGAALVRAATSLFTLPGPPGMPHRSRSAALEAARAPAGYLSPVPHRLALPRPARPRPA
+PPRMRVRQDGVRVVARPLAMLPGVDHGRALRLDLHPVRDGIVFVSRHLELRELGDDVKGL
+VLTGVVPAARLGYFWDTVAGDLPEGRPVIVRLRSNDDAELLTLLRAIAPPWLRVVSYRLD
+ESPVGSQRSSYLLPDVDGEAVAASGAERVPLETLREAHQASAEVERASRVFLARRRVDRF
+VRRSVPDLMHSLSYTDPAEVRHVYVDGSVLRGTRTGGAAAVTRSGPWAAHALPGATIPLE
+AELEALTLGHLMAAWSGTPDERVLIHSDSRAALALLREAHRERLTLGDARGERIRRALRR
+LLAAVDLAGSAGVEVSTLWVKGHAGTHGNELADDLARSAARNTAAGVSADEMRRRMRHVV
+QLWDATTHPQA
+>PROKKA_01857
+MGARINHPRTVVDRTLHHDVEPAHPAALVDVGWDFRGPGAKAEEQHRPLRVVRARRPRGT
+PRDRNGVDLTRTGPVVPRPSPPRTRIRRDGVRVVASPLAMLPGVDHGPALRLDLHPTTGG
+IVYVARELELRELGDDVRGHVYTGMVGTAHLSVFWSTVTVDLPPERPVIVRLRSDRDAEL
+LSLLEVLAPVDTRVVSYRLDESPVGTQRSSYLLPDVDPETVAQTGAARIPLEAIEAAQEE
+EDALRRSSGVFLSRRRTDRFLRRNLPGVTHSLTFADEADVTDVYVDGSVLRGSRIGGAAA
+VAGPSMWAVQAVAGATMPLEVELEALVLGHVICAWAGTPGGRVTIHSDSRAALALLNAAR
+RERLTLGGARGERIRRTLRRLLAAVDLAQAADVQVDTTWVKGHVGVHGNELADDLARAAA
+RHASVGTPEGDLPERMGQLIQLRVEDDAAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001569.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001569.fa
new file mode 100644
index 0000000000000000000000000000000000000000..14ee19856fdb38618a98dcefc24be63df7b16000
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001569.fa
@@ -0,0 +1,15 @@
+>PROKKA_01948
+MKIGLRKPSLKKSIKARTTGRAKRAIKRKVIPGYGRKGMGWLRDPKRAAYNAVYRRTTVG
+LGDVLKMFK
+>PROKKA_01642
+MKIGLRKPSLKKSIKARTTGRAKRAIKRKVIPGYGRKGMGWLRDPKRAAYNAVYRRTTVG
+LGDVLKMFK
+>PROKKA_00907
+MKIGLRKPSLKKSIKARTTGRAKRAIKRKVIPGYGRKGMGWLRDPKRAAYNAVYRRTTVG
+LGDVLKMFR
+>PROKKA_00846
+MKIGLRKPSLKKSIKARTTGRAKRAIKRKVIPGYGRKGMGWLRDPKRAAYNAVYRRTTVG
+LGDVLKMFK
+>PROKKA_01871
+MKIGLRKPSLKKSIKARTTGRAKRAIKRKVIPGYGRKGMGWLRDPKRAARNAVYKRTTFG
+LGDVLRMFR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001570.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001570.fa
new file mode 100644
index 0000000000000000000000000000000000000000..946485125697565e2e23da80db43932e7b43f221
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001570.fa
@@ -0,0 +1,68 @@
+>PROKKA_01951
+MINSAEPRHVHELFSSQTKAHYVVPPYQREYSWHRAQWEALFADLVESEDEHFLGTIITL
+SRTKDSLSGPVLEVIDGQQRLTTLTILLAAVHSHLQDAEDLDEDARFERMTLRRELVRDE
+AKAPRLTPQVQGANRADYQAMLADAGLPVKSEKKAYYPSRKVAKAFWFFRAAITELAEER
+GESLSTTALSVLAAARRALIVNIEVASAADAFVLFESLNNRGVPLTPVDLIKNSFLARAE
+HRAGMEVEEAFELWSDTLAHLGDSYATHERFLRHFYNAFRGDLPPVKLAPVATRKNLIRI
+YETLLDQDLEGTVRSLERAAQVYGRIAGGGDVDEPTSLDQELTALRRAQAAPSYVLVMWL
+LVRQEKAGWSEEDLAAVARLLVSFFVRRNLTGFPATYALPRLFMDVIDQVAAGEPDRLLT
+IVRGSLVAASASDATFRERLEGPVYEENRDVTRFLLATLAEDAMTKETRVDLWAQSGKTF
+VWTIEHILPQGENLPQEWVDALGGPEAAAETQNRFVHTLGNLTITGFNSTLGNQTFLRKR
+DRIDHQGRAIGYRNGLALNAELAEKEAWSSADIEARTVRLVERALERFAL
+>PROKKA_00906
+MVAAREVTLQELLGGSYQYTVPLYQRTYSWGRPQWQRLWEDVVDVADHRRDNPSATHFIG
+SLVLAGFRDNGPGGVQRWLVVDGQQRLTTLTLLLAAVRDHRAEHEGPMHADRVNEKYLVN
+KWEDGDLRYKVLPTQADRAAYRGRIEHAPDAAEGSRISEAHQFFLTKLFGLSQPSADGEE
+EQLTLAEVESAVVAGLSIVSVTTGENDNAHRIFESLNNTGLKLTQGDLLRNYLFMQLPTR
+ADEVYTTLWLPLQNLLSNEELETLFWLDLVQQDPKVRQTEIYAGQQRRMRGLQDESQVRA
+EVERFLALGRLYDVMLRPEKEKDAAVRFRLARLRAWRTTTTFPITLHLMERRSLGDIDSD
+ELARALLYLESYLVRRLVFGRYSDGLNTTLLAATADIQGQDDPADALQRFLSSGRKHFAS
+DDQIRQAVITAPFYTTGRAAHRKLILRWIEESYGSKEPVDLDSATIEHVMPQTLTEEWER
+ALAGQLEAHQDLREVHTELLHTLGNLTLTGYNSELSNGPFAVKRAELAKSGIRMNQEIST
+VPVWGPAQIRARAERLADRIVGIWPGPSAEAASGVAHTAWQTLTDAVEAIPAGSWTSYGE
+LARLIGSHPVPVGTYLARTALPHAHRVLQAGGTVSPSFRWTDVHRKDDPHDVLAAEGVRF
+SEDGRAYGGQRLVAEQLAELIDVDVDLTDPRSLAAPGNDPALRDRWVDRLHDHNDPESAR
+ALIEVQRGWVERGGRAEFADNAAGGCFLVVPRASARAIWPVILYPTYGVEVVFYHLAKWP
+PFTDEALLDDFRGRLNLIPGVEFGPEALRRRPSIRPQILQPAAAQEAFLDALEWFLHTIQ
+EDDRSA
+>PROKKA_00292
+MSHERVYRIGSPGAEPLVPVSFAEAGLRERQDLQEWVIAHPEILGEDIRIVAFEFDRWED
+ADGGRQRDRLDVLGLDQSGCLVLAELKRDAAPDTVEMQAIKYAAMASRFTEEKLVAWHAA
+MLGRLENRPVSEEEAREALTDHAGELDVEQLRRPRIVLVAGAFTRSTTAAVVWLTEMGLD
+ITLQRVQAYRMGGDDVVITVSQLFPVPDVEEFTVSPMRMESTARRTSSTRSPSTVRRLVK
+AGTLPDGTVLTLVPTTEVNAETREAIADWISDDPRRGRATWWNDPTKPMEWELDGNRYRP
+SRIVQQALREATGITRSPRGPAWWVTESGMSLTELAGDVENGAFDWTQLHRLLCELPAGR
+WTTYGEVARLIGTAPQPLGGHFRTCTLCRNAYRVLDANGAVSSGFTWGDPQETRTQQEVL
+EAEGISFDGGRAAPSQRLQPSELESVWKVAQAALGE
+>PROKKA_00845
+MVAAREVTLQELLGGSYQYTVPLYQRTYSWGRPQWQRLWEDVVDVADHRRDNPSATHFIG
+SLVLAGFRDNGPGGVQRWLVVDGQQRLTTLTLLLAAVRDHRAEHEGPMHADRVNEKYLVN
+KWEDGDLRYKVLPTQADRAAYRGRIEHAPDAAEGSRISEAHQFFLTKLLGLSQPSAAGEE
+EPLTLAEVESAVVAGLSIVSVTTGENDNAHRIFESLNNTGLKLTQGDLLRNYLFMQLPTR
+ADEVYTTLWLPLQNLLSNEELETLFWLDLVQQDPKVRQTEIYAGQQRRMRDLQDESQVRA
+EVGRFLALGRLYDVMLRPEKEKDAAVRFRLARLRAWRTTTTFPITLHLMERRSLGDIDSD
+ELARAFLYLESYLVRRLVFGRYSDGLNTTLLAATADVQGQDDPADALQRFLSTGRKHFAS
+DDQIRQAVMTAPFYTTGRAAHRKLILRWIEESYGSKEPVDLDSATIEHVMPQTLTEEWER
+ALAGQLEAHQDLREVHTELLHTLGNLTLTGYNSELSNGPFAVKRAELAKSGIRMNQEISA
+EPVWGPAQIRARAERLADRIVDIWPGPSAEAASGVAHTAWQTLTDAVEAIPAGSWTSYGE
+LARLIGSHPVPVGTYLARTALPHAHRVLQAGGTVSPSFRWTDVHRTDDPHDVLAAEGVRF
+SEDGRADGGQRLVAEQLAELIDVDVDLIDPRSLAAPGNDPALRDRWVDRLHDHNDPESAR
+ALIEVQRGWVERGGRAEFADNAAGGCFLVVPRTSARAIWPVILYPTYGVEVVFYHLAKWP
+PFTDEALLDDFRGRLNLIPGLEFGPEALRRRPSIRPQTLQPAAAQEAFLDALEWFLHTVQ
+EDDRSA
+>PROKKA_01872
+MVAAREVTLQELLGGSYQYTVPLYQRTYSWGRPQWQRLWEDVVDVADHRRDNPSATHFIG
+SLVLAGFRDNGPGGVQRWLVVDGQQRLTTLTLLLAAVRDHRAEHEGPMHADRVNEKYLVN
+KWEDGDLRYKVLPTQADRGAYRGRIEHAPDAAEGSRISEAHQFFLTKLLGLSQPSADGEE
+EPLTLAEVESAVVAGLSIVSVTTGENDNAHRIFESLNNTGLKLTQGDLLRNYLFMQLPTR
+ADEVYTTLWLPLQNLLSNEELETLFWLDLVQQDPKIRQTEIYAGQQRRMRGLQDESQVRA
+EVERFLALGRLYDVMLRPEKEKDAAVRFRLARLRAWRTTTTFPITLHLMERRSLGDIDSD
+ELARALLYLESYLVRRLVFGRYSDGLNTTLLAATADIQGQDDPADALQRFLSSGRKHFAS
+DDQIRQAVMTAPFYTTGRAAHRKLILRWIEESYGSKEPVDLDSATIEHVLPQTLTEEWER
+ALAGQLEAHQDLREVHTELLHTLGNLTLTGYNSELSNGPFAVKRAELAKSGIRMNQEISA
+EPVWGPAQIRARAERLADRIVGIWPGPSAEAASGVAHTAWQTLTDAVEAIPDGSWTSYGE
+LARLIGSHPVPVGTYLARTALPHAHRVLQAGGTVSPSFRWSDVHRTDDPHDVLAAEGVRF
+SEDGRADGGQRLLAEQLAELIDVDVDLTDPRSLAAPGNDPALRDRWVDRLHDHNDPETAR
+ALIEVQRGWVERGGRAEFADNAAGGCFLVVPRTSARAIWPVILYPTYGVEVVFYHLAKWA
+PFTDETLLDEFRGRLNLIPEVEFGPESLRRRPSIKPQTLQPAAAQEAFLDALEWFLRTVQ
+EDDRTS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001572.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001572.fa
new file mode 100644
index 0000000000000000000000000000000000000000..630f85c058b21d455039044dd0f3c7f5ed23c706
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001572.fa
@@ -0,0 +1,36 @@
+>PROKKA_01966
+MHEDEGRRRHYGHFYGLEDLPEDDLLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVP
+PAFEAQPDEVAHLERLLPRVKALVTQPIPHDYRGMPIGTDQLVARLPEDAAVVRIPVVYD
+VSRFPWQVTLRNWKFAPGAAERPGEDPPVVPYHDLRVLAEAATGRRREVAPAAIREAAAA
+SVQALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTLLTRVAERVAERLPGDVAVQPV
+PASRVLLGGVRAPLEAPVVEALDLDAAPTEDWTVAGQTVPAEQLRQTHLDWYAQNPQAVE
+VGMRKYADQLRLLGLTG
+>PROKKA_01660
+MNEDEGRRRHYGHFYGLEDLPEGDLLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVP
+PAFEAQPDEVEHLERLLPRVKALVTQPIPHDYRGMPIGTDQLVARLPKDAAVVRIPVVYD
+VSRFPWQVTLRNWKVAPGAAERPGEDPPVLPYHDLRVLAEAATGRRRQVAPAAIREAAAA
+SVQALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTLLTRVAERVAGHLPGDVAVQPV
+PASRVLLGGVRAPLEAVVVEALDLDAEPTEDWTVAGQTIPAEQLRQTHLDWYAQNPQAVE
+VGMRKYADQLRLLGLAA
+>PROKKA_00893
+MHEDEGRRRHYGHFYGLEDLPEGDLLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVP
+PAFEVQPDEVEHLERLLPRVKALVTQPIPHDYRGMPIGTDQLVARLPEDAAVVRIPVVYD
+VSRFPWQVTLRNWKFAPGAAERPGEDPPVVPYHDLRVLAEAATGRRREVAPAAIREAAAA
+SVQALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTVLTRVAERVAEHLPGDVAAQPV
+PAARVLLGGVRAPLEAVVVEALDLDAEPTEDWTVGGETIPAEQLRQTHLDWYAQNPQAVE
+VGMRKYADQLRLLGLAA
+>PROKKA_00833
+MSEETPMDDQTRTAGAEPGDEGVQVRGAAERAPSSDLPADEGRRRHYAHFYGLEPLPEGE
+LLTVMGGCQAEATRLLLCGEPGRAEGGTPASVRVPPMFELGPDDLPHLLALLKRTTVLVV
+KPVRDDYQGLPLGLGQLESLLPAGARSIRVPALYDSSRFPWLVTLRHPTRPWEDPPVVPY
+HDLRTVAEAAAEAGLIPWPAALGGPGEAGAYDAGPRLPLSAEALRGLAAESVARLRAREE
+HFGTVRVSDAVADERGVGFHTVNHPDNPLLEALARTVLAELGVDKEVHAPDRLLLGHVLA
+PIEEQVVDALGLQTAPRAAWRVGGAEVSDAEVRRAHLGWFRANPEALAPGLERHGALMRE
+LGLLA
+>PROKKA_01892
+MNEDEGRRRHYGHFYGLEDLPEGDLLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVP
+PAFEVQPDEVAHLERLLPRVKALVTQPIPHDYRGMPIGTDQLVARLPEDAAVVRIPVVYD
+VSRFPWQVTLRNWKFAPGAAERPGEDPPVVPYHDLRVLAEAATGRRREVAPAAIREAAAA
+SVQALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTLLTRVAERVAERLPGDVAVQPV
+PASRVLLGGVRAPLEAVVVEALDLDAEPTEDWTVAGQTVPAEQLRQTHLDWYAQNPQAVE
+VGLRKYADQLRLLGLTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001573.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001573.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8476e0107985405c17524460ee6393e433b95e9b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001573.fa
@@ -0,0 +1,45 @@
+>PROKKA_01968
+MSAAVSVVVPYYRAQADLDRLTAALAAQRGVTGGLQLVVADDGSPVPPRVDPGLPFDVVT
+VRQQDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLAAALAAVAEAPRDAAVVGRR
+RHLAEAWLERAWADGWRPGHEVPADALLAEPAWLRDGYRATDDLRRADSTGYRYVISAVL
+TVAREVYEDAGGFDPAFVGYGGEDWELAHRLWRVGAALRHAPDAVAWQAGADFGGRGDAA
+EAARVKAREALVLVSRIPATTSRGHGLSLAGPLRAEARVRVPEGADGAAAAVVAVDAVLR
+AAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAAPEDLPPTPARGDLDAVRSVPDW
+SVDVQVPLRPAAAGARPDTDAVAAWLLRLERAGVERVEVLGEPGERAERDVLAVLTCARA
+RWRPRRGGTARVWRVPASRLGWAPVAAVPDLEAWWGGWG
+>PROKKA_01662
+MSAAVSVVVPYYRAQADLDRLTAALAAQRGLTGGLQLVVADDGSPVPPRVGPGLPFDVVT
+VRQQDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLAAALAAVAEAPRDAAVVGRR
+RHLAEAWLERAWVDGWRPGDEVPADARLAEPAWLREGYRATDDLRRADSTGYRYVISAVL
+TVAREVYADAGGFDPAFVGYGGEDWELAHRLWRVGAALRHAPDAVAWQAGADFGGRGDAA
+EAARVKAREALVLASRIPATTARGHGLSLAGPLRVEARVRVPEGADGAAAAVVAVDAVLC
+AAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAASQDLPPTPARGDLDAVRSVPDW
+SVDVHVPLRPAAAGARPDADAVAAWLLRLERAGVERVEVLGEPGERAERAVLAVLTCARA
+RWRRRRGGTARVWRVPASRLGWAPVATVPDLEAWWGGWG
+>PROKKA_00891
+MSAAVSVVVPYYRAQADLDRLTAALAAQRGVTGGLQLVVADDGSPVPPMVGPDLPFDVVT
+VRQQDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLAAAVAAVAEAPRDAAVVGRR
+RHLAEAWLERAWADGWRPGHEVPADARLADPAWLREGYRTTDELRRADSTGYRYVISAVL
+TVAREVYEDAGGFDPAFVGYGGEDWELAHRLWRVGAALRHAPDAVAWQAGADFGGRGDAA
+EAARVKAREALALASRIPATTARGHGLSLAGPLRVEARVRVPERADGAAAAVVAVDAVLR
+AAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAASQDLPPTPARGDLDAVRSVPDW
+SVDVRVPLRPAAAGARPDADAVAAWLLRLERAGVERVEVLGEPGERAERAVLAVLTCARA
+RWRRRRGGTSRVWRVPASRLGWAPVAAVPDLEAWWGGWG
+>PROKKA_00832
+MTAPVAGREAAAETAGPEASVPEVSVVVPHYRAPADLERVVAALAAQDHPASRLQLVVAD
+DGSPEPPVLPAGLPFEAVVVAQEDHGFRASAARALGASAAEGRILAFLDGDMLPEPGYLT
+AACAAPAASVDAVVVGRRRHLDPALLESGWRPGEPVPEAARLPEPAWLAEAYQRSGDLAA
+ADSTSYRYVISAVLTVAREVYADAGGFDPAFVGYGGEDWELAHRLWRVGGAFRHQPAAVA
+WQAGEDFGGRGDAAERTAVKQREALRLAARITATTARGHGLSLPGPLRVGARVRAEASGD
+AAAVVGVDALLAAAPGARVGVTGLGSGAARAALADPRVWIMDGGGEAARADLPPAPARGD
+LGAVRGIPDWSCDVRTPLRPAAPGARPDAARAADWLLRLERAGVERVEVLGEPQAAEEPG
+EAGRGERPVLAVLTCSRALWRSRRGGDSRVWRVPAARLGWAPVARDVDLEAWWGGWG
+>PROKKA_01894
+MSAAVSVVVPYYRAQADLDRLTAALAAQRGLTGGLQLVVADDGSPVPPRVDPGLPFDVVT
+VRQPDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLAAALAAVAEAPRDAAVVGRR
+RHLAEAWLERAWAHGWQPGHEVPADARLAEPAWLREGYRATDDLRRADSTGYRYVISAVF
+TVAREVYEDAGGFDPAFVGYGGEDWELAHRLWRVGAALRHAPDAVAWQAGADFGGRGDAA
+EAARVKAREALVLASRIPATTARGHGLSLAGPLRVEARVRVPEGADGAAAAVVAVDAVLC
+AAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAADEDLPPTPARGDLDAVRSVPDW
+SVDVHVPLRPAAAGARPDADAVAAWLLRLERAGVERVEVLGEPAEPGERAVLAVLTCARA
+RWRHRRGGTARVWRVPASRLGWAPVATVPDLEAWWGGWG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001574.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001574.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e4eb561ad50d276813434e98b4fb823ad9337be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001574.fa
@@ -0,0 +1,40 @@
+>PROKKA_01969
+MKGIVDVDSQPQGRVLYVTVGAPEHGVVRHGRQTAAALQRVGAEVELLTAEDVAAFRGLV
+PLLEEARALGAAVHLDVTDALFGPTATAAADLLVDVLPAGTTLTLHDIPQPAEGDGRYRR
+RGEAYARLAQAVAGVVVSSQHERALLADLVDVAADVVPLPVQDRRAAAARAEPVVPESMA
+GLDQDLVLFGFVYPGKGHALALEALTELHRQWGPDSGAPRRLTALGPVSAGHDDLVAELT
+RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRAIASAGR
+YTEEMERLRPGTLRLVHPNGSPAFAMAEAIAEAVEDPERTWLDPAVDLSPGAEGCARMLF
+DVLRRVHRWT
+>PROKKA_01663
+MKGIVDVDSQPQGRVLYVTVGAPEHGVVRHGRQTAAALRRVGAEVELLTAEDVAAFRGLV
+PVLEEARALGAAVHLDVTDALFGPTATAAADLLVDVLPEGTTLTLHDIPQPAEGDGRYRR
+RGEAYARLAQAVDGVVVSSQHERALLADLVDVAADVVPLPVEDRRAAAARAEPVVPESMA
+GLDRDLVLFGFVYPGKGHALALEALTELHRQWGPDSGAPRRLTALGPVSAGHDDLVAELT
+RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRAIASAGR
+YTEEMERLRPGTLRLVHPNGSPAFAMAEAIAEAVEDPERTWLGPGVDLSPGAEDCARMLF
+DVLRRVHRWT
+>PROKKA_00890
+MESQPQGRVLYVIVGPPEHGVVRHARQTAAALRRVGAEVELLTAEDVAAFHGLVPLMAEA
+RSLGAAVHLDVTDALFGPTAAAAADLLVDVLPEGTTLTLHDIPQPAEGDGRYRRRGEAYA
+RLARHAAGVVVSSQHERALLAELVDADADVVPLPVEDRRAEAARAESVVPENMAGLDQDV
+VLFGFVYPGKGHALALEALTELHRQWGPNSGAPRRLTALGPVSAGHDDLVAELTRDAEAR
+GLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRAIASAGRYTEEME
+RLRPGTLRLVHPNGSPAFAMAEAIAEAVEDPEHTWLDPAVDLSPGAEDCARMLFDVLRRV
+HRWT
+>PROKKA_00831
+MTSHAQGRVLYLSVGSRGHGVVHHGLLTAEELAQVGLDVESLHTEDATGFVGLAPVLARA
+REARRAVHVDVTDSLFGPSPAAAADTLSRILPDGATVTLHDVPQPAEGEARFLERAEAYV
+RIAQAAAGVVVSSEHERALLHAIVDVDAHVVPLPVEDRRAAREAVRLPEALEGLDRDVVI
+FGHLYPGKGHAEAIDALAELDRQWGPSPHRPRRVTALGAVAARHEFLVDELTARAEVSGL
+QFRVTGFVPDEVLDPALRAAAVPLAAHHNVSASGSLASWMSVGRRPIVPAGRYTQEMARL
+RPGTLRIVQVGTSGPEYALAEAVAEAVEEPSRTWQARGTSLAPGPRACARMLAAALADVH
+GWAWPR
+>PROKKA_01895
+MKGIVDVDSQPQGRVLYVTVGAPEHGVVRHGRQTAAALRRVGAEVELLTAEDVAAFRGLV
+PVLEEARALGAAVHLDVTDALFGPTATAAADLLVDVLPEGTTLTLHDIPQPAEGDGRYRR
+RGEAYARLAQAVDGVVVSSQHERALLADLVDVAADVVPLPVEDRRAAAARAEPVVPESMA
+GLDRDLVLFGFVYPGKGHALALEALTELHRQWGPDSGAPRRLTALGPVSIGHDDLVAELT
+RDAEARGLEFRVTGFVPDEFADAALLSAGIPFAAHRNVSASGSLAAWTSVGRRTIASAGR
+YTEEMERLRPGTLRLVHPNGSPAFAMAEAIAEAVEDPERTWLDPAVDLSPGAEDCARMLF
+DVLRRVHRWT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001575.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001575.fa
new file mode 100644
index 0000000000000000000000000000000000000000..abfb33d93ae909e4a8b07438dd5f8613d56c9525
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001575.fa
@@ -0,0 +1,64 @@
+>PROKKA_01970
+MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPGAPAHQWWPPRALHAEWLAEHR
+PDVLHVHFGFEHFSPAQLAAALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGR
+ADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVAQGDDDAPGAEPGLLPPDASDD
+GDGAAAPARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQDTVQDEDAL
+AALRAGCAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAV
+ADIGHIADQSGAWLTPDSLAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVA
+AAHVAVYREALARARGALPGVSVLVITGHRDEHLARVIAGLERSHRRPDQVVVVFMGQPD
+GRVPATDLPVTVGHVAAEAGLPLAQARNRAAELATGEILVFLDVDCIPAAETVGVLATEV
+AAHPGSVVMGRPRYLRPGWTRDVGEADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHL
+VWTLILALRRADLARIGGFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMT
+PPLHHLEDILVNARRFRQVHGRWAMEGWLRAFADAGLIAWDPEGERLELLRHPTEAELTA
+ARRDDAAY
+>PROKKA_01664
+MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPDAPAHQWWPPRALHAEWLAEHR
+PDVLHVHFGFEHFSPAQLAAALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGR
+ADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVAQGDDDAPGLLPPDASDDGDGA
+PVPARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQDTVQDEDALAALR
+AGCAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAVADIG
+HIADQSGAWLSPDSLAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVAAAHV
+AVYREALARARGALPSVSVLVITGHRDEHLARVIAGLERSHRRPDQVVVVFMGQPDGRVP
+ATDLPVTVGHVAADAGLPLAQARNRAAELAIGEILVFLDVDCIPAAETVGVLATEVAAHP
+GSVVMGRPRYLRPGWTRDVGEADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHLVWTL
+ILALRRADLARIGCFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMTPPLH
+HLEDILVNARRFRQVHGRWAMEGWLRAFADAGLIAWDPEGERLELLRHPTEAELTAARRD
+DAAY
+>PROKKA_00889
+MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPGAPAHQWWPPRALHAEWLAEHR
+PDVLHVHFGFEHFNPAQLAAALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGR
+ADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVSQGDDDAPGLLPPDASDDGAAA
+PARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQATVQDEDALAALRAG
+CAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAVADIGHI
+ADQSGAWLAPDSLAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVAAAHVAV
+YREALARARGALPSVSVLVITGHRDEHLARVIAGLERSHRRPDQVVVVFMGQPDGRVPAT
+GLPVTVGHVAAEAGLPLAQARNRAAELATGEILVFLDVDCIPAAETVGVLATEVAAHPGS
+VVMGRPRYLRPGWTRAVEEADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHLVWTLIL
+ALRRADLARIGGFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMTPPLHHL
+EDILVNARRFRQVHGRWAMEGWLRAFADAGLIAWDPEGERLELLRTPTADELAVARRDDA
+AY
+>PROKKA_00830
+MSLTVQHVPAGHPYARSVRPLDGAAAPDVEFWPDPPVPGAAEGVWWPPRALDPAWIAEHR
+PDVLHVHFGFEHFTPEQLRAALDAQHAHGGAVVVTVHDLQNPHLQDQDPHRARLRVLLDA
+ADAVITLTPGAAAAVEAASGRAPLVLPHPHVVPLDALPDDGAADGERPGVDRPARLLMHA
+KDLRAQVDPVGLLPVLAAARDALAARGLAVEVTVDVQDGVRDEAALAELEAGAEAHGFAL
+WRHARLDDAELHAALRDADVSVLPYRVGTHSGWVEMCRDLGVPVAVAEVGHIADQARAWT
+TPELLAAFDPDDPASLADALAALLTAAPDARAAAPAARAAQRRRVAAAHVAVYRQALAVR
+RGTAATVSVLVITGHRDAHLARVLAGLERSHRRPDQVVVVFMGQPDGAVPATDLPVTVGH
+VAADHGLPLATARNRAAELATGEVLVFLDVDCIPAADTVGVLAAEVAAHPGSLVMGAPRY
+LAPDWTAALAAEGVDADAAPTDGDLRRHAVPHRARTHLRPGPSEEWALVWTLVMAIGAAD
+LARIDGFDEGFAGYGAEDTDLAFRARDAGLTLRISPAEAFHQHHGVHRPPLHHVADIVVN
+ARRFRTLHGTWPMGGWLAAFAERGLIRWDPDGDLLELVREPTPDDVAAARVDDAAY
+>PROKKA_01896
+MSITVQHVPAQHPYTRAIRPLDPGAAPDVEFLPDPPVPGAPAHQWWPPRALHAEWLAEHR
+PDVLHVHFGFEHFSPAQLAAALDAQHAHGGAVVVTVHDLENPHLTDQGPHRDRLAVLLGR
+ADAVLTLTPGAAATLARDYGVRALVVPHPHIVPLEDLVAQGDDDAPGALPPDASDDGDGA
+AAPARLLVHAKDLRAQVAPVALLPVLAAAVGTLAERGVDARVTVEVQDTVQDEDALAALR
+AGCAHHGFELWQHDRLDDPALHALLRDVDVSVLPYRIGTHSGWVEMCRDLGVPVAVADIG
+HIADQSGAWLSPDSLAAFDPEDPDSLADALETLVRARARTAPADPAARARQRRRVAAAHV
+AVYREALARARGALPGVSVLVITGHRDEHLARVIAGLERSHRRPDQVVVVFMGQPDGRVP
+ATDLPITVGHVSAEAGLPLAQARNRAAELATGEILVFLDVDCIPAAETVGVLATEVAAHP
+GSVVMGRPRYLRPGWTRDVGEADLTSHRADALLRRLSVPHRARAHLTAGPSDEWHLVWTL
+ILALRRADLARIGGFDAGFTGYGAEDTDLAFRARDAGLTLRFSPAEAFHQHHGVMVPPLH
+HLEDILVNARRFRQVHGRWAMEGWLRAFADAGLIAWDPEGERLELLRHPTEAELTAARRG
+DAAY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001580.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001580.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6d9420c042e2dc7db6d461cd1a5de4c9d4da3b42
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001580.fa
@@ -0,0 +1,54 @@
+>PROKKA_01979
+MSTAPTRVRLGMPTVRPVHGEGEILLNTPFPESAREQLGNGQMRANIRRATHTIRAKRAG
+VVEELPDWQELRAAGSALKQSVMADLPALLERLESEVTARGGVVHWARDAAEANRIITEL
+VTAKGVDEVIKVKSMATQEIGLDAALEHAGVAAVETDLAELIVQLGHDRPSHILVPAIHR
+NRREIRDIFRREMPDTDESLTSEPADLAEAARRHLREKFLSTKVAISGANFGVAETGTLS
+VVESEGNGRMCLTLPETLITVMGIEKLVPTFEDLEVFLQLLPRSSTGERMNPYTSMWTGV
+TEGDGPQEFHLVLLDNGRSAVLSDPKGRSALHCIRCSACMNVCPVYEQTGGHAYGSVYPG
+PIGAILSPQLTGVDAGENGTLPYASTLCGACYDVCPVAIDIPSILIHLRDEDVQATHAAR
+KALRTEKDAAAGPLARAKAAVESVTPSQMDVAMKGASVVMSSGRRMSLAERGLGLGRVAA
+GPDRVLGWLPGIAGGWTDERDVPAPPRESFRNWWARHKDETEHRTALDGVAGLDRQEDEH
+VEEDGR
+>PROKKA_01673
+MSTAPTRVRLGMPTVRPVHGEGEVLLKTPFPESAREQLGNDQMRANIRRATHTIRAKRAG
+VVEELPDWQELRAAGSALKQSVMADLPALLERLESEVTARGGVVHWARDAAEANRIITEL
+VTAKGVDEVIKVKSMATQEIGLDAALEHAGVAAVETDLAELIVQLGHDRPSHILVPAIHR
+NRREIRDIFLREMPETDESLTSEPADLAEAARRHLREKFLSTKVAISGANFGVAETGTLS
+VVESEGNGRMCLTLPETLITVMGIEKLVPTFEDLEVFLQLLPRSSTGERMNPYTSMWTGV
+TEGDGPQEFHLVLLDNGRSAVLSDPKGRSALHCIRCSACMNVCPVYEQTGGHAYGSVYPG
+PIGAILSPQLTGVDAGENGTLPYASTLCGACYDVCPVAIDIPSILIHLRDEDVQATHAAR
+KALRTEKDAAGGPLARAKTAVESVTPSQMDVAMKGASVVMSSGRRMSLAERGLGLGRVAA
+GPDRVLGWLPGIAGGWTDERDVPAPPRESFRNWWARHKDETEHRTALDGVAGLDRQEDEH
+VEEDGR
+>PROKKA_00879
+MTRTALGMPAVRPAHGHGNIVLDEPFPSAARTQLGNAQMRANIHHATHTIRGKRARVVGE
+LPDWAELRQAGSALKQQVMADLPALLEQFEQRVTERGGVVHWARDAEEANRIITGLVKAK
+GVDEVIKVKSMATQEIDLEHALQAEGIAAVETDLAELIVQLGHDKPSHILVPAIHRNREE
+IREIFVREMPETDESLTSDPSALADVARVHLREKFLTTSVAISGANFGVAETGTLTVVES
+EGNGRMCLTLPETLITVMGIEKIVPTFQDLEVFLQLLPRSSTGERMNPYTSMWTGVTPGD
+GPQEFHLVLLDNGRSAVLSDPEGRPALHCIRCSACMNVCPVYEQTGGHAYGSVYPGPIGA
+ILSPQLTGVQEGANGSLPYASSLCGACYDVCPVAIDIPSILVHLRDQDVRATHARKKEET
+RVPLPSQMDLMMKGARTVMSSGTAMSLAERGLPLGRLAAGRDATLGWLPGIAGGWTDQRD
+VPSPPRQSFRNWWRGNAEHTEERVARDGGRRDVAAEDETTTTDGQEQR
+>PROKKA_00814
+MSTAPTRVRLGMPTLRPVHGEGEILLKTPFPESAREQLGNGQMRANIRRATHTIRAKRAG
+VVGELPDWQELRAAGSALKQSVMADLPALLERLESEVTARGGVVHWARDAAEANRIITEL
+VTAKGVDEVIKVKSMATQEIGLDAALAQAGVAAVETDLAELIVQLGHDRPSHILVPAIHR
+NRREIRDIFLREMPETDESLTSEPADLAEASRRHLREKFLSTKVAISGANFGVAETGTLA
+VVESEGNGRMCLTLPETLITVMGIEKLVPTFEDLEVFLQLLPRSSTGERMNPYTSMWTGV
+TEGDGPQEFHLVLLDNGRSAVLSDPKGRSALHCIRCSACMNVCPVYEQTGGHAYGSVYPG
+PIGAILSPQLTGVDAGENGTLPYASSLCGACYDVCPVAIDIPSILIHLRDEDVQATHAAR
+KALRTEGDGDAGPLARAKAAVESVTPSQMDVAMKGASVVMSSGRRMSLAERGLGLGRVAA
+GPDRVLGWLPGIAGGWTDERDVPAPPRESFRNWWARHKDETEHRTALDGVAGLDRQEDEH
+VEEDGR
+>PROKKA_01905
+MSTAPTRVRLGMPTVRPVHGEGEILLNTPFPESAREQLGNGQMRANIRRATHTIRAKRAG
+VVEELPDWQELRAAGSALKQSVMADLPALLERLESEVTARGGVVHWARDAAEANRIITEL
+VTAKGVDEVIKVKSMATQEIGLDAALEHAGVAAVETDLAELIVQLGHDRPSHILVPAIHR
+NRREIRDIFLREMPETDESLTSEPADLAEAARRHLREKFLSTKVAISGANFGVAETGTLS
+VVESEGNGRMCLTLPETLITVMGIEKLVPTFEDLEVFLQLLPRSSTGERMNPYTSMWTGV
+TEGDGPQEFHLVLLDNGRSAVLSDPKGRSALHCIRCSACMNVCPVYEQTGGHAYGSVYPG
+PIGAILSPQLTGVDAGENGTLPYASTLCGACYDVCPVAIDIPSILIHLRDEDVQATHAAR
+KALRTDEDAAAGPLARAKAAVESVTPSQMDVAMKGASVVMSSGRRMSLAERGLGLGRVAA
+GPDRVLGWLPGIAGGWTDERDVPAPPRESFRNWWARHKDETEHRVAMDGVAGLDRPEDEH
+VEEDGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001581.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001581.fa
new file mode 100644
index 0000000000000000000000000000000000000000..83d18beb1a820bd66b3de3597472bfcbd8c63b1f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001581.fa
@@ -0,0 +1,30 @@
+>PROKKA_01980
+MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYMEDALPVVR
+NHVRTFMKADYDLAVAPSASCVASLGHQQPDVARSGGDEGLARDAEVVASRTLELSQLLT
+DVLGVTDAGAQLGSWFPHTVTYHPSCHGMRLLRLGSRQEDLLRTVADIDLRPLPDAEECC
+GFGGTFSLKNPDVSAAIAEEKIEKVTASGASLCTGGDASCLLHLDGAMHRREARGQDGRP
+LRTVHLAEILAATRENPLEVDGPVELSIPASAGARRGPSARVEEARR
+>PROKKA_01674
+MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYMEDALPVVR
+NHVRTFMKADYDLAVAPSASCVASLGHQQPDVARSGGDEGLARDAEVVASRTLELSQLLT
+DVLGVTDAAAQLGSWFPHTVTYHPSCHGMRLLRLGSRQEDLLRTVADIDLRPLPDAEECC
+GFGGTFSLKNPDVSAAIAEEKIEKVTASGASLCTGGDASCLLHLDGAMHRREARGQDGRP
+LRTVHLAEILAATRENPLEVDGPVELSIPTSAGVRRGPSARVEEARR
+>PROKKA_00878
+MRVALFATCIVDAMYPKVALATVRILERLGHEVVFPRGQGCCAQMHVNSGYLDDALPVVK
+NHVRTFQGADYDVAVAPSGSCVASLGHQQPMVARAAGDEALARDAEEVAANTYELAALLT
+DVLGVTDAAAQLGSWFPHTVTYHPSCHGMRLLRLGDRQERLLRSVADIDYRALPDAEECC
+GFGGTFSLKNPDVSGAMAEEKIGNIERTQARLCTGGDASCLLHLGGVMSRRGTTAPDGSP
+VTTLHFAEILAATRENPLDVSGPVDLSIPAQGPARRRRQKEATR
+>PROKKA_00813
+MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYVEDALPVVR
+NHVRTFMKADYDLAVAPSGSCVASLGHQQPDVARSCGDEGLARDAEVVASRTLELSQLLT
+DVLGVTDAAAQLGSWFPHTVTYHPSCHGMRLLRLGTRQEDLLRTVADIDLRPLPDAEECC
+GFGGTFSLKNPDVSAAIAEEKIEKVTASGASICTGGDASCLLHLGGAMHRREARGQDGRP
+LRTVHLAEILAATRENPLEVDGPVELSIPASAGARRGPSARVEEAHR
+>PROKKA_01906
+MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYMEDALPVVR
+NHVRTFMKADYDLAVAPSASCVASLGHQQPDVARSGGDEGLARDAEVVASRTLELSQLLT
+DVLGVTDAGAQLGSWFPHTVTYHPSCHGMRLLRLGSRQEDLLRTVADIDLRPLPDAEECC
+GFGGTFSLKNPDVSAAIAEEKIEKVTASGASLCTGGDASCLLHLDGAMHRREARGQDGRP
+LRTVHLAEILAATRENPLEVDGPVELSIPASAGARRGPSARVEEARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001588.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001588.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4555f970fd228077fb02c2f74e29606046c241cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001588.fa
@@ -0,0 +1,40 @@
+>PROKKA_01990
+MRNLRDHLSQRAVGVKQSAVRDVFDIAMDPNLVSLAGGNPWLADLPLDELGRIASDLMTR
+FGTESLQYGPGQGTEEMRAAAATVMAADGIPDADPDLVVITPGSQAAIDTACRAFANPGD
+VVVVEDPTFVGALTTFATWQLEAVATGTDDQGLVPAALDETLTRLAAEGRRVAFLYTIPS
+FANPSGALLPPGRRAEVGAICEKHGVLIVEDNPYGQIAFDGEPVAPIAADHRDNVVHLGT
+MSKIFSPGVRIGWALVPAALKREFYLCAESAYIHASTYSQMLSTAFVTQLDWQGHVRHVT
+GLYRERAGALVDAVREHWDPGVEFITPQGGFFLWATLPAGVDTLEVMHRGIEAGAVFVPG
+AAFTPVEGTHSTLRLAYSFVDAEKLVEGVRRLAPAVNESIARAR
+>PROKKA_01684
+MRNLRDHLSQRAVGVKQSAVRDVFDIAMDPNLISLAGGNPWLADLPLDELGRIASDLMTR
+FGTESLQYGPGQGTEAMRAAATAVMAADGIPDADPDLVVITPGSQAAIDTACRAFANPGD
+VVVVEDPTFVGALTTFTTWQLEAVATGTDDHGLVPAALDETLTRLAAEGRRVAFLYTIPS
+FANPSGALLPPGRRAEVGAICEKHGVLIVEDNPYGQIAFDGEPVAPIAADHRDNVVHLGT
+MSKIFSPGVRIGWALVPAALKREFYLCAESAYIHASTYSQMLSTAFVTQLDWQGHVRHVT
+GLYRERAAALVDAVREHWDPAVEFITPQGGFFLWATLPVGVDTLEVMHRGIEAGAVFVPG
+AAFTPVEGTHSTLRLAYSFVAAEKLVEGVRRLAPAVNESIARAR
+>PROKKA_00867
+MRHLRDHLSHRAVGVKQSAVRDVFDIAMDPNLVSLAGGNPWLADLPLDELGRIASDLMTR
+FGTESLQYGPGQGTEEMRAAAAAVMAADGIPDADPELVVITPGSQAAIDTACRAFGNPGD
+VVVVEDPTFVGALTTFNTWELDAVATGTDEHGLVPAALDETLTRLAAEGRRVAFLYTIPS
+FANPSGALLPADRRAEVAAICERHGVLIVEDNPYGQIAFDGDPVAPIAAEHRDGVVYLGT
+MSKIFSPGVRIGWALVPAELKREFYLSAESAFIHASTYSQMLSTAFVTQLDWQGHVRHVT
+GLYRERAGVLVDAVREHWDPGVEFITPRGGFFLWATLPGGVDTIELMHRGIEAGAVFVPG
+GAFTPVEGVHSTLRLAYPFVEAERLVEGVRRLAPVVNDAVARAR
+>PROKKA_01757
+MSTLDPAGARAHLARRATTVQQSAVRDVFDIAMDPDLVSLAGGNPWLAGLPLEELGATAA
+RLVAEQGTASLQYGPGQGLECMRVAACAVMAADGIPDADPELVVITPGSQAAIDTACRAF
+ADPGDVVVVEDPTFVGALTSFQTWELEAVATPTDEHGLVPADLDATLARLEAEGRRVAFL
+YTIPSFANPSGLLLPADRRDDVAAVCERHGVLIVEDNPYGQIAFDGAPVAPIAAAHRERT
+VYLGTMSKIFSPGVRVGWALVPEALHREFYLCAESAFIHASTTSQMLSTAFVTEYDWQDH
+VRGVTGLYRSRAQALQAAIAEHWDPGFTFTPPAGGFFLWGSLPAGVDAVELMHRGIAAGA
+VFVPGAAFTPVPGTHSTLRLAYSFVDEETLAEGVRRLAPVVNTAVEGAR
+>PROKKA_01916
+MRNLRDHLSQRAVGVKQSAVRDVFDIAMDPNLVSLAGGNPWLADLPLDELGRIASDLMTR
+FGTESLQYGPGQGTEEMRAAATAVMAADGIPDADPDLVVITPGSQAAIDTACRAFANPGD
+VVVVEDPTFVGALTTFTTWQLEAVATGTDDHGLVPAALDETLTRLAAEGRRVAFLYTIPS
+FANPSGALLPPGRRAEVGAICEKHGVLIVEDNPYGQIAFDGEPVAPIAADHRDNVVHLGT
+MSKIFSPGVRIGWALVPAALKREFYLCAESAYIHASTYSQMLSTAFVTQLDWQGHVRHVT
+GLYRERAGALVDAVREHWDPGVEFITPQGGFFLWATLPAGVDTLEVMHRGIEAGAVFVPG
+AAFTPVEGTHSTLRLAYSFVDAEKLVEGVRRLAPAVNESIARAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001591.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001591.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5b4eebec438ce92c20ccc137593d242509b11066
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001591.fa
@@ -0,0 +1,50 @@
+>PROKKA_01993
+MTEKTSIEARKPAGLPDVLRHYIDGEFVDSIDGDTFEVLDPVTNEPYLTAASGKAADIDR
+AVAAAKRAFESGEWSQALPRQRSRVLHAIADIMETRGNQLAEMECFDTGLPIKQARGQAA
+RAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAI
+ATGNSVVLKPAEFTPLSASLWGGIFEEAGLPKGVFNMVHGFGEEGYAGDPLVKHPDVPLI
+SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERC
+TAGSRILVQRSVYDEFVERYAAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKT
+EARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDTEEEALQLAN
+NTKYGLAAYIWTNDLKRAHNVAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS
+IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG
+>PROKKA_01687
+MTEKTSIEARKPEGLPDVLRHYIDGEFVDSIDGDTFEVLDPVTNEPYLTAASGKAADIDR
+AVAAAKRAFESGEWSQALPRQRSRVLHRIADIMETRGDQLAEMECFDTGLPIKQARGQAA
+RAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAI
+ATGNSVVLKPAEFTPLSASLWGGIFEEAGLPQGVFNMVHGFGEEGYAGDPLVKHPDVPLI
+SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERC
+TAGSRILVQRSVYDEFVERYAAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKT
+EARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDTEEEALQLAN
+NTKYGLAAYIWTNDLKRAHNVAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS
+IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG
+>PROKKA_00864
+MTEINDRKPEGLPDLIRHYIDGQSVDSVDGDTFDVLDPVTNQPYIKAASGKTADVDKAVA
+AAKAAFESGVWSQALPRERSRVLHKIADIMETRGDQLAAMECFDTGLPIKQAKGQAARAA
+ENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAIATG
+NSVVLKPAEFTPLSASLWPGIFEEAGLPKGVFNMVHGFGEEGFAGDPLVKHPDVPLISFT
+GESRTGQIIFGNAAPHLKGLSMELGGKSPAVVFADADLDAAIDATIFGVFSLNGERCTAG
+SRILVAREVYDEFVERYAAQASRVKVGMPNDETTEVGAIVHPEHFEKVMSYVEIGKSEAH
+LVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDSDEEALELANNTK
+YGLAAYIWTNDLKRAHNFAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRSIDF
+YTDQQAVHINLGEVHNPVFGKQEQAAAKIDG
+>PROKKA_00802
+MTEKTSIAARTPEGMPDVIRHYIDGEFVDSIDGDTFDVLDPVTNEPYIKAASGKSADVDA
+AVAAAKRAFESGEWSQALPRQRSRVLHRIADIMETRGDQLAEMECFDTGLPIKQAKGQAA
+RAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAI
+ATGNSVVLKPAEFTPLSASLWGGIFEEAGLPTGVFNMVHGFGEEGYAGDPLVKHPDVPLI
+SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERC
+TAGSRILVQRSVYDEFVERYAAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKA
+EARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDTEEEALQLAN
+NTKYGLAAYIWTNDLKRAHNFAQDVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS
+IDFYTDQQAVHINLGEVHNPVFGKQESKETGDA
+>PROKKA_01919
+MTEKTSIEARKPQGLPDVLRHYIDGEFVDSIDGDTFEVLDPVTNEPYLTAASGKAADIDR
+AVAAAKRAFESGEWSQALPRQRSRVLHRIADIMETRGDQLAEMECFDTGLPIKQARGQAA
+RAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAI
+ATGNSVVLKPAEFTPLSASLWGGIFEEAGLPKGVFNMVHGFGEEGYAGDPLVKHPDVPLI
+SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERC
+TAGSRILVQRSVYDEFVERYAAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKT
+EARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDTEEEALELAN
+NTKYGLAAYIWTNDLKRAHNVAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS
+IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001592.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001592.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9f86acc23735d3eb67be4fd2873bc2c049d9c3cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001592.fa
@@ -0,0 +1,40 @@
+>PROKKA_01994
+MTNLESRQKTSSGFFVTKEVPIDPENPLPTPTSEAPDILRSASMELVVTDLAQSREFYVD
+VLGLVVTEEDEETVYLRSMEEFIHHNLVLRQGETAAVAAFSYRVRTPEDLDKAVAFYEEL
+GCRVERRKDGFVKGVGDSVRVEDPLGFPYEFFHDVEHVERLAWRYDLYTPGALVRLDHFN
+QVTPDVPRAARYMQDLGFRVTEDIQDENGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVCF
+ATHEKHNILAICDKLGALRMSDHIERGPGRHGVSNAFYLYLRDPDGHRVEVYTQDYYTGD
+PDNPVVTWDVHDNQRRDWWGTPVVPSWYTDASRVLDLDGNLQPLVSRTDDSEMAVTIGAD
+GFSYTREGQGEESLPEWKQGEYKLGNQL
+>PROKKA_01688
+MTNLESRQKTSSGFFVTKEAPIDPENPLPTPTSEAPDILRCASMELVVTDLAASREFYVD
+VLGLVVTEEDEETVYLRSMEEFIHHNLVLRQGETAAVAAFSYRVRTPEDLDKAVAFYEEL
+GCRVERRKDGFVKGVGDSVRVEDPLGFPYEFFHDVEHVERLAWRYDLYTPGALVRLDHFN
+QVTPDVPRAARYMQDLGFRVTEDIQDENGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVCF
+ATHEKHNILAICDKLGALRMSDHIERGPGRHGVSNAFYLYLRDPDGHRVEVYTQDYYTGD
+PDNPVVTWDVHDNQRRDWWGTPVVPSWYTDASRVLDLDGNLQPLVSRTDDSEMAVTIGAD
+GFSYTREGQGEESMPEWKQGEYKLGNQL
+>PROKKA_00863
+MSNYAGRTRTSVGTYVGQEGPVKTDNPIPTPKAEAPDVLRCASMELVVTDLEKSRQFYVD
+VLDLVVTEEDEDTVYLRSMEEFIHHNLILRKGEIAAVAAFSYRVRTPEDLDKAVAFYTEL
+GCRVERNKDGFVKGVGDSVRVEDPLGFPYEFFYEVDHVERLAWRYDLYSPGALVRLDHFN
+QVTPDVPRAARYMQDLGFRVTEDIQDENGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVAF
+ATHEKHNILAICDKLGSLRMSDAIERGPGRHGVSNAFYLYLRDPDGHRVEIYTQDYYTGD
+PDNPVVTWDVHDNQRRDWWGTPVVPSWYTDASLVLDLDGNVKEVVARTDDSEMAVTIGAD
+GFSYTRAEEGEDSMPEYKKGEYKLGNQL
+>PROKKA_00801
+MSNLESRKKTSSGFFVTEEAPITPANPLPTPKAEAPDILRCASMELVVTDLAASRHFYVD
+VLGLVVTEEDEETVYLRSMEEFIHHNLILRKGETAAVAAFSYRVRTPEDLDKAVAFYTEL
+GCRVERNKDGFVKGVGDSVRVEDPLGFPYEFFFETEHVERLAWRYDLYTPGALVRLDHFN
+QVTPDVPRAAKFMQDLGFRVTEDIQDEQGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVCF
+ATHEKHNILAICDKLGALRMSDHIERGPGRHGVSNAFYLYLRDPDGHRVEVYTQDYYTGD
+PDNPVVTWDVHDNQRRDWWGTPVVPSWYTDASRVLDLDGNLQPLVARTDDSEMAVTIGAD
+GFSYTREDEGEESMPEYKQGEYKLGNQL
+>PROKKA_01920
+MTNLESRQKTSSGFFVTKEVPIDPENPLPTPTSEAPDILRCASMELVVTDLAASREFYVD
+VLGLVVTEEDEETVYLRSMEEFIHHNLVLRQGETAAVAAFSYRVRTPEDLDKAVAFYEEL
+GCRVERRKDGFVKGVGDSVRVEDPLGFPYEFFHDVEHVERLAWRYDLYTPGALVRLDHFN
+QVTPDVPRAARYMQDLGFRVTEDIQDENGTVYAAWMRRKPTVHDTAMTGGDGPRMHHVCF
+ATHEKHNILAICDKLGALRMSDHIERGPGRHGVSNAFYLYLRDPDGHRVEVYTQDYYTGD
+PDNPVVTWDVHDNQRRDWWGTPIVPSWYTDASRVLDLDGNLQPLVSRTDDSEMAVTIGAD
+GFSYTREGQGEESMPEWKQGEYKLGNQL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001600.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001600.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b67525a6918de05fd0dd0371ed5e662510eb730b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001600.fa
@@ -0,0 +1,20 @@
+>PROKKA_02007
+MPPLIGPQQIATALRAVGLDDDAARLVAWADPARREREAAEQALADLAVAQTQLRAALGG
+LVSAATDVRSAIQTGWRGEAAGAYGEAVRRAAALAAELEREAGEWLALRATAERDAEDAR
+RNAEARQRAAEETALAVLRSLAVAA
+>PROKKA_01717
+MSPLIGPQQIATALRAVGLDDDAARLAAWADPARREREAAEQALADLAAAQTQLRTALGG
+LVSAATDVRSAMHTAWRGEAAGAYGEAVRRAATLAAELEREAGEWLALRATAERDAEDAR
+RNAEARQRAAEETALAVLRSLAVAA
+>PROKKA_00835
+MLQLIGPQHLAAALQAAGLDDDAARLLAWADPARRDRDAAQAALDELAVAQESLRGALAG
+LVAAARDVRAGAAVAWRGPAAGEYADAVAEAVGAAEGLEREAGEWLALRATAEREAEDAR
+QDAEARLRAAEETARAALRALAVAA
+>PROKKA_00772
+MLLPPTAQALLRTLVAAGLDDDAARLAVGLTDAHADLQAARAAQDALADAAEDLRDLLAL
+LEELTRGVAAALDVDWRSEAGAEYGERTDGLHRTATDRQDEAREWAGLLGRARSEAEQAE
+RDAELRVRRAEEGASALLRAMAAA
+>PROKKA_01945
+MSPLIGPQQIATALRAVGLDDDAARLVAWADPARREREAAEQALADLAVAQTQLRTALGG
+LVSAATDVRSAMHTAWRGEAAGAYGEAVRRAATLAAELEREAGEWLALRATAERDAEDAR
+RDAEARQRAAEETALAVLRSLAVAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001607.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001607.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88169a0f03cd5b46d0f5bddde852ff7c98167c4e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001607.fa
@@ -0,0 +1,40 @@
+>PROKKA_02016
+MSAQSQALLVGGRRTPVGKYGGALSSVRPDDLAALTVKAVIEDAGIDPSVVDDVILGNAN
+GAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAGGVE
+SMSRAPWVMEKPTTAFAKPGAAFDTAIGWRFVNPRFADGEFGEKFTFSMPETAEEVGEVD
+GITREDADAFAARSHERALAAIEAGRFADEIVPVVVTGRKGAETVVDTDEGPRPGSTPEV
+LASLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLAPEI
+MGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPETVNADGGAIALG
+HPLGSSGSRLVVTLLGRMEREGADRGLATMCVGVGQGSAMLVERV
+>PROKKA_01725
+MSAQSQALLVGGRRTPVGKYGGALSSVRPDDLAALTIKAVIEDAGIDPSVVDEVILGNAN
+GAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAGGVE
+SMSRAPWVMEKPTTAFAKPGAAFDTAIGWRFVNPRFADGEFGEKFTFSMPETAEEVGEVD
+GITREDADAFAARSHERALAAIEAGRFADEIVPVVVTGRKGAETVVDTDEGPRPGSTPEV
+LASLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLAPEI
+MGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPETVNADGGAIALG
+HPLGSSGSRLVVTLLGRMEREGADRGLATMCVGVGQGSAMLVEKV
+>PROKKA_00805
+MTTPSPQPQALLVGGKRTAVGRYGGALSAVRPDDLAALTIKQVIEDAGIDPAAVDEVILG
+NANGAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAG
+GVESMSRAPWVMEKPTTAFAKPGAAFDTSIGWRFVNPRFADGEFGEKFTFSMPETAEEVG
+EVDGITREDADAFAARSHGRAIAAIEAGRFKDEIVPVTVKGRKGAETVVDTDEGPRPGST
+PEVLAGLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLA
+PEIMGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPEIVNADGGAI
+ALGHPLGSSGSRLVVTLLGRMEREGADRGLATMCVGVGQGSAMLVEKV
+>PROKKA_00764
+MSAQSQALLVGGRRTPVGKYGGALSSVRPDDLAALTVKAVIEDAGIDPSVVDDVILGNAN
+GAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAGGVE
+SMSRAPWVMEKPTTAFAKPGAAFDTSIGWRFVNPRFADGEFGEKFTFSMPETAEEVGEVD
+GITREDADAFAARSHERALAAIEAGRFADEIVPVVVTGRKGAETIVDTDEGPRPGSTPEV
+LAGLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLAPEI
+MGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPETVNADGGAIALG
+HPLGSSGSRLVVTLLGRMEREGADKGLATMCVGVGQGSAMLVEKV
+>PROKKA_01953
+MSAQSQALLVGGRRTPVGKYGGALSSVRPDDLAALTIKAVIEDAGIDPSVVDEVILGNAN
+GAGEENRNVARMAWLLAGFPDTVPGITVNRLCASGMSAIGIATAMVRSGMADVVVAGGVE
+SMSRAPWVMEKPTTAFAKPGAAFDTAIGWRFVNPRFADGEFGEKFTFSMPETAEEVGEVD
+GITREDADAFAARSHARALAAIEAGRFADEIVPVVVTGRKGAETIVDTDEGPRPGSTPEV
+LAGLRPIIKKDGVVTAGNSSSLNDGASAILVVSERAAQKYGLTPRARVVESTSAGLAPEI
+MGLGPVPATEKALERSGWSVADLGAVELNEAFATQSLASMRRLGLDPETVNADGGAIALG
+HPLGSSGSRLVVTLLGRMEREGADRGLATMCVGVGQGSAMLVERV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001613.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001613.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f442e4cf554b2622fa1beb2e3ba20fcb83faff40
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001613.fa
@@ -0,0 +1,65 @@
+>PROKKA_02023
+MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGARLTGVSTDGLDTAAAIEHART
+VGQQALGALTIHERALKLKELALYLNSRVQELYDVSFATGATQRDHAFDVDGGIGTLFTF
+SGKGRRELPNSNVIIDGDVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP
+AFVAGVPTVVKPATPTGYVAQKCVELMLESGVLPEGSIQLISGSARDLLDHLDYRDHVAF
+TGSAATAATLKKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVK
+AGQKCTAIRRVIVPQDRVEAVTAALTERLAAKVVLGDPRVEGTTMGALASKEQQGEVRGA
+VQRLVDAGGQVRLGGPEGSTGDADAESGAFFAPTVLTFEDARTPEVHSVEAFGPVTSVIG
+YTDVADAVALAALGSGSLVATVATNDGETARAFAAGIGAHHGRVHVLNRQTATTTTGHGA
+PVPVLIHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTRE
+DVEAGTAVHPFYKSLAELTVGDQFASGLRTVTLEDITAFAEETGDRFYAHTDEEAAMANP
+FFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFITPVTYDDAIRVTLTAKRITP
+RVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG
+>PROKKA_01732
+MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGARLTGVSTDGLDTAAAIEHART
+VGQQALGELTIHERALKLKELALFLNSRVQELYDVSFATGATQRDHAFDVDGGIGTLFTF
+SGKGRRELPNSTVIIDGDVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP
+AFVAGVPTVVKPATPTGYVTQKCVELMLESGVLPEGSIQLISGSARDLLDHLDYRDHVAF
+TGSAATAATLKKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVK
+AGQKCTAIRRVIVPQDRVEAVTAALTERLAAKVVLGDPRVEGTTMGALASKDQQGEVRGA
+VQRLVDAGGQVRLGGPEGSTGDADAESGAFFAPTVLTFEDARTPEVHSVEAFGPVTSVIG
+YTDVADAVALAALGSGSLVATVATNDGETARAFAAGIGAHHGRVHVLNRQTAATTTGHGA
+PVPVLIHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTRE
+DVEAGTAVHPFYKSLAELTVGDQFASGLRTITLEDITAFAEETGDRFYAHTDEEAAMANP
+FFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFITPVTYDDAIRVTLTAKRITP
+RVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG
+>PROKKA_00796
+MTVTLPSLPEILPSYVNGAWWTPQSPSKVTDVTDANTGERLTGVSTDGLDTAAAIEHART
+VGRKSLGELTIHERALKLKELALYLNSRIQELYDVSFATGATQRDHAFDVDGGIGTLFTF
+SGKGRRELPNSNVITDGPVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP
+SFVAGVPTVVKPATPTGYVTQKCVELMLESGVLPEGSLQLISGSARDLLDHLDYRDHVSF
+TGSAATAQTLRKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVK
+AGQKCTAIRRVIVPQDRVDAVVEALSARLGKVVLGDPRVEGTTMGALASKEQQGEVRGAV
+QRLVDAGGQVRLGGPDASTGDADAESGAFFAPTVLSFEDARTPEVHAVEAFGPVTSVVGY
+TDVEDAVALAALGSGSLVATVATDDGETARAFAAGIGAHHGRVHFLNRQTATTTTGHGAP
+VPVLVHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTRED
+VEAGTAVHPFYKSLAELTVGDQFASGLRTVTLQDITDFAEETGDKFYAHTDEEAAMANPF
+FPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFITPVTYDDAIRVTLTAKRITPR
+VSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG
+>PROKKA_00757
+MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGELMARVSTDGIDTAGAIEHART
+VGQRNLGELTIHERALKLKELALYLNSRIQELYDLSFATGSTQRDHAFDVDGGIGTLFTF
+SGKGRRELPNSNVIIDGDVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP
+AFVAGVPTVVKPATPTGYVTEACVRMMVESGVLPEGSIQLISGSARDLLDHLDYRDHVAF
+TGSAGTAQTLRQHENVLNGGVRFTAETDSLNAAILGPDAGVDTPEFEAFVKVVFQEMTVK
+AGQKCTAIRRVIVPEAMVEDVTAALTERLSSTVVLGDPRAEGTTMGALASKEQQSEVRKA
+VQTLVDAGGQVRLGGPEGSTGDADAEAGAFFAPTVLTFADADTPQVHSVEAFGPVTSVIG
+YTDVADAVRLAALGSGSLVATLATNDGATASEFIAGIGAHHGRVHVLNRQTAKTTTGHGA
+PVPVLIHGGPGRAGGGEELGGVRAVKHYMQRTAVQGSPDMLTAITGVWHQGAAAQTATRE
+DVEAGKAKHPFYKALDELQIGDQFASGLRTVTIEDITAFAESTGDKFYAHTDEEAAMANP
+FFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLDDLRFITPVTYDDAIRVTLTAKRITP
+RVTDEYGEVAWDCRLHNQKDELVAQYDVLTLVAKTWPMPEAEPKA
+>PROKKA_01960
+MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGARLTGVSTDGLDTAAAIEHART
+VGQQALGALTIHERALKLKELALYLNSRVQELYDVSFATGATQRDHAFDVDGGIGTLFTF
+SGKGRRELPNSTVIIDGDVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP
+AFVAGVPTVVKPATPTGYVTQKCVELMLESGVLPEGSIQLISGSARDLLDHLDYRDHVAF
+TGSAATAATLKKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVK
+AGQKCTAIRRVIVPQDRVEAVTAALTERLAAKVVLGDPRVEGTTMGALASKEQQSEVRGA
+VQRLVDAGGQVRLGGPEGSTGDADAESGAFFAPTVLTFEDARTPEVHSVEAFGPVTSVIG
+YTDVADAVALAALGSGSLVATVATNDGETARAFTAGIGAHHGRVHVLNRQTATTTTGHGA
+PVPVLVHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTRE
+DVEAGTAVHPFYKSLAELTVGDQFASGLRTVTLEDITAFAEETGDRFYAHTDEEAAMANP
+FFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFITPVTYDDAIRVTLTAKRITP
+RVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001618.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001618.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c35c887085c59a2c50f2a9bb707286cb71843de7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001618.fa
@@ -0,0 +1,19 @@
+>PROKKA_02028
+MTETAHHPMLAEDRVARWLGVTLEAAEKDHARIRMTLTEDQHNGFGLAHGGAVFAFADTC
+FALTCNDPASDGSTLTVASGVDVNFLAATRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG
+TPVAAFRGRSRTIPAPGR
+>PROKKA_01737
+MTETAHHPMLAEDRVARWLGVTLEAAEKDHARIRMTLTEDQHNGFGLAHGGAVFAFADTC
+FALTCNDPASDGSTLTVASGVDVNFLAATRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG
+TPVAAFRGRSRTIPAPGR
+>PROKKA_00791
+MTLTEDHHNGFGMAHGGAVFAFADSCFALTCNDPGGDGSTITVASGVDVNFLAGTRAGQT
+LVAEGRLVAAAGRSAVYDITVTTDDGTPVAAFRGRSRTIPAPGR
+>PROKKA_00752
+MTETPHHPALVGDRVARWLGVTLEAAEKDHARIRMTLGEEHHNAFGMAHGGVVFAFADCC
+FALTCNDPASDGSTLTVASGVDVNFLSGTRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG
+TLVAAFRGRSRTVAVKGA
+>PROKKA_01965
+MTETAHHPMLAEDRVARWLGVTLEAAEKDHARIRMTLTEDQHNGFGLAHGGAVFAFADTC
+FALTCNDPASDGSTLTVASGVDVNFLAATRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG
+TPVAAFRGRSRTIPAPGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001624.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001624.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9e3d58ffdb424b2cd2f17c5956688bdc9ffff612
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001624.fa
@@ -0,0 +1,50 @@
+>PROKKA_02045
+MTTSETTSETTSETPDTSATTHGRPTERRGHVAELLSATVARQPDAVALRIGEARMTYRE
+LDQVTAATAGWLRHRGVGPGDRVAVMLPNVPAFVAVYEALMRLGAVMVPLNPLFTARELG
+YFLEDSGARMLWAMPGLPAVDEVAGNVDVEVVTLDLEAVGRECAAEGIAPVTEITPRDPD
+DDAVLLYTSGTTGRPKGARLTHTNLRSNAMATATGLGRLGPDDVVFAALPMFHVFGLSVV
+LNGAVFAGSTLSLMPRFVPEAAYDQLQDHGITFLPGVPTMHGAFLSVARARREAGAEPAD
+FSRLRMPLSGGASLPVETLRAAEKLFGVPVLEGYGLSENAGACFFNPVDAPTRPGTVGRP
+VDGFEFRIVAMDGTEVPEEDLETSGELRIRGEGIMAGYWGRPEDTEAAFDEDGWFRTGDI
+ARRDEAGYVMIVDRLKDVIIRGGMNVYPREVEEVLYEHPDVVEAAVVGVPDERLGEEIAA
+FVSLAPGSTATGEELQAFAAERLARYKQPREVTIMDGLPKNATGKILRRELRQG
+>PROKKA_01751
+MTTSETPDTSATTHGRPTERRGHVAELLSATVARQPDAVALRIGEARMTYRELDQVTAAT
+AGWLRHRGVGPGDRVAVLLPNVPAFVAVYEALMRLGAVMVPLNPLFTARELEYFLEDSGA
+RVLWAMPGLPAVDEVAGNVDVEVVTLDLEAVGRECAAEGIAPVTEITLRDPDDDAVLLYT
+SGTTGRPKGARLTHTNLRSNAMATATGLGRLGPDDVVFAALPMFHVFGLSVVLNGAVFAG
+STLSLMPRFVPEAAYDQLQDHGVTFLPGVPTMHGAFLSVARARREAGAEPEDFSRLRMPL
+SGGASLPVETLRAAEKLFGVPVLEGYGLSENAGACFFNPVDAPTRPGTVGRPVDGFEFRI
+VAMDGTEVPEEDLETSGELRIRGEGIMAGYWGRPEDTAAAFDQDGWFRTGDIARRDEAGY
+VMIVDRLKDVIIRGGMNVYPREVEEVLYEHPDVVEAAVVGVPDERLGEEIAAFVSLAPGS
+AVTGEQLQAFAAERLARYKQPREVTVLDGLPKNATGKILRRELRQG
+>PROKKA_00735
+MTTSETPDTSTTTHGRPTERRGHVAELLSATVARQPDAVALRIGEARMTYRELDQVTAAT
+AGWLRHRGVGPGDRVAVLLPNVPAFVAVYEALMRLGAVMVPLNPLFTARELGYFLADSGA
+RMLWAMPGLQAVDEVAGNVDVEVVTLDLEAVGRECAAEGIAPVTEITPRDPDDDAVLLYT
+SGTTGRPKGARLTHTNLRSNAMATATGLGRLGPDDVVFAALPMFHVFGLSVVLNGAVFSG
+STLSLMPRFEPEAAYDQLQDHGVTFLPGVPTMHGAFLTVARARREAGAEPADFSRLRMPL
+SGGASLPVDTLHAAEKLYGVPVFEGYGLSENAGACFFNPVDAPTRPGTVGRPVDGFEFRI
+VAMDGTEVPEEDLETSGELRIRGEGIMAGYWGHPEDTVAAFDADGWFRTGDIARRDEAGY
+VLIVDRLKDVIIRGGMNVYPREVEEVLYEHPDVVEAAVVGVPDERLGEEIAAFVSLAPGS
+TVTGEELQAFAAERLARYKQPREVTVLDGLPKNATGKILRRELRG
+>PROKKA_00741
+MNSALPATDPHRGDVCALLEAGHDRDPRAVAWREDGVDTTYAELLELVQATAGVLRRQGV
+GPGDRVALLMPNTLAFPAVYYGALWLGAVVVPLNPLSTDRELEYFLTDSQAVLLWSMRGT
+SAAAEAAQAVGVPHLQSSPADLRDVVAGAEPVRERTPRTSEEADAVVIYTSGTTGQSKGA
+RLSHRTVASSAVLTSEALDWLQAGHTVLGVLPFFHVFGMSAALNMPLYTGCRNSVVTRFA
+PHTALEQVVRDEVRALPAVPTMIGALLRALRSARAKGDDVDLSALRYILSGGAPLPVETL
+HEAEEEFGVPVREGYGLTESCGPVSFNPMLRPSRAGTVGQPLPGVEFRLVTTDGVEVPAG
+DTETPGELRIHGPVLMTGYLGEPQADAASFDDEGWLRTGDVATRDEEDYYRIVGRLKDII
+IHGGYNVYPREVEEAFYEHPAVSEAAVLGVPDERFGEKVVAYVALQDGPEVEVAELNAFV
+RERLASYKWPSQVTVMDALPKNTTGKIVKDLLR
+>PROKKA_01979
+MTNSETPDTSATTVGRPTERRGHVAELLSATVARQPDAVALRIGEASMTYRELDQVTAAT
+AGWLRHRGVGPGDRVAMMLPNIPAFVAVYEALMRLGAVMVPLNPLFTARELEYFLEDSGA
+RMLWAMPGLPAVDGVAGNVDVEVVTLDLEAVGRECDAEGITPVTEITPRDPDDDAVLLYT
+SGTTGRPKGARLTHTNLRSNAMATATGLGRLGPDDVVFAALPMFHVFGLSVVLNGAVFAG
+STLSLMPRFVPEAAYDQLQDHGITFLPGVPTMHGAFLSVARARREAGTEPADFSRLRMPL
+SGGASLPVETLRAAETLFGVPVLEGYGLSENAGACFFNPVDAPTRPGTVGRPVDGFEFRI
+VAMDGTEVPEEDLETSGELRIRGEGIMAGYWGRPEDTEAAFDEDGWFRTGDIARRDEAGY
+VMIVDRLKDVIIRGGMNVYPREVEEVLYEHPDVVEAAVVGVPDERLGEEIAAFVSLAPGS
+AVTGEELQAFAAERLARYKQPREVTILDGLPKNATGKILRRELRQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001628.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001628.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d8801e2b519483f01f78c0b42f3cf6cb66199d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001628.fa
@@ -0,0 +1,25 @@
+>PROKKA_02056
+MLSLYIHGDSPLHHARAGLKTGLFAVWVLALTLLPLSRWTAGAAVVGAVTAYLVGFGLRR
+GAAMIASDLHALWLFYVVLFAAQWIFTDAFAAGLMVARVLGLVLTAQVLTRTTRIADMAG
+VAEAMLRPVERIPWAGPRLARAGFRADRVGLAMGLVLSSIGHLRALAEQIRHAQAARGVR
+MAPWAWALPLLVLSFKHADDVGDALAARGID
+>PROKKA_01762
+MLSLYIHGDSPLHHARAGLKTGLFAVWVLALTLLPLSLWTAGAAVVGAVTAYLVGFGLRR
+GAAMIASDLRALWLFYVVLFAAQWIFTDAFAAGLMVARVLGLVLTAQVLTRTTRIADMTG
+VAEAVLRPVERIPWAGPRLARAGFRADRVGLAMGLVLSSIGHLRALAEQIRHAQAARGVR
+MAPWAWALPLLVLSFKHADDVGDALAARGID
+>PROKKA_00764
+MISLYVPGDSPLHRAPAGLKLALFAAWALAVTLAPPTPWTAGAAVGMALAAYLTGFGPRR
+GAAMLGRDLRALWVFYAFLFAAQWLFADLTAAALMVGRVLGLVLAAQVLTRTTRIAELVG
+VAEAVLAPVERIPWLGPRLARVGLRPERVGLAMGLVLASIGHLRSVAEQVRQAQASRGVR
+MAPWAWVLPLLVLSVKHADDVGDALAARGIE
+>PROKKA_00728
+MLSLHVPGDSPLHRCPAGAKVAALAVWALVVTLAPVSALTAGASVVVGVGAYLLGFGLRR
+GVRLLAADLRGLWVFYAVLFAAQWLFTDLPTAALTTARVLGLVLAAQVLTRTTRIAEMAG
+VAEAVLGPVTRIPWLGPRLARAGVRPDRVGLAMGLVLASVGHLRGLAEQIRAAQAARGVR
+MAPWAWVLPLLVLSLKHADDVGDALAARGID
+>PROKKA_01990
+MLSLYIHGDSPLHHARAGLKTGLFAVWVLALTLLPLSLWTAGAAVVGAVTAYLVGFGLRR
+GAAMIASDLRALWLFYVVLFAAQWIFTDAFAAGLMVARVLGLVLTAQVLTRTTRIADMTG
+VAEAVLRPVERIPWAGPRLARAGFRADRVGLAMGLVLSSIGHLRALAEQIRHAQAARGVR
+MAPWAWALPLLVLSFKHADDVGDALAARGID
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001629.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001629.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e001403f39d69a964910443be22fb15c581b48a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001629.fa
@@ -0,0 +1,29 @@
+>PROKKA_02057
+MSPDRSVTLTGVRVEADGPEGAVVLLDGVDLTLAAPRVAVIGENGSGKSTLARAIAGLAD
+VVAGEVTVHGVDAVRDVKALRRTVGFVFANPAAQMVMPTVREDVELTVKSLRDDAGRRLT
+KDDVAARVAAALQEHRLTALADRACLSLSSGQAQRLAMCSVMTAGPSLVIADEPTSLLDG
+RHRRIVADRLLAADPSAPDGFQLLLVTHDLELARACDEAVWIHSGRVERTGPAEEVVEAY
+ERFLDHAVAAELR
+>PROKKA_01763
+MSPDRSVTLTGVRVEADGPEGVVVLLDGVDLTLTAPRVAVIGENGSGKSTLARAIAGLAD
+VVAGEVTVHGVDAVRDVKALRRTVGFVFANPAAQMVMPTVREDVELTVKSLRDDAGRRLT
+KDDVAARVAAALQEHRLTALADRACLSLSSGQAQRLAMCSVMTTGPSLVIADEPTSLLDG
+RHRRIVADRLLAADPSAPDGFQLLLVTHDLELARACDEAVWVHGGRVERTGPAEDVVEAY
+EHFLDHAVAAELR
+>PROKKA_00763
+MEQTTGVRLRGARVEADGPEGVVALLQDVDLDLTAPRVAVVGENGSGKSTLARAVAGLVD
+VVAGEVTVHGVDAVRDVKALRRVVGMVFANPAAQAVMPTVREDVELTVKSLRDDDGRRLS
+KDDVAARVAAALAEHRLTELAERPCLALSSGQAQRLAMCSVMAGRPRLVIADEPTSLLDG
+RHRRIIADRLLAADGFQLLLVTHDLELARACDDAVWVHEGRVRAVGPAGEVVDAYAAFLD
+EAVAAESAEAAAGDPAAVNPAGASAEARP
+>PROKKA_00727
+MTGRTPPTRAPHDDDAAVRLAGVQVAAPGGPVLLDGVDLHLTAPRVAVVGENGSGKSTLA
+RAVAGLAEVTAGEVAVHGVDAVRDVKALRRTVGMVFANPAAQMVMPTVREDVELTVKALT
+DDAGRRLSRAEVAARVDAALAEHRLTDLAERPCLSLSSGQAQRLAMCSVLVGAPRLVIAD
+EPTSLLDGRHRRIVADRLLGGAERGEFQLLLVTHDLDLARACDAAVWVHSGRVERHGPAA
+ETVAAYEAFLDDAVARELA
+>PROKKA_01991
+MLLDGVDLTLTAPRVAVIGENGSGKSTLARAIAGLADVVAGEVSVHGVDAVRDVKALRRT
+VGFVFANPAAQMVMPTVREDVELTVKSLRDDAGRRLAKDDVAARVAAALEEHRLTALADR
+ACLSLSSGQAQRLAMCSVMTAGPSLVIADEPTSLLDGRHRRIVADRLLAADPSAPDGFQL
+LLVTHDLELARACDEAVWIHGGHVERTGPAEDVVEAYERFLDHAVAAELR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001630.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001630.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34f66bbd9ec4f6d0975ae1a9de647526906fd63e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001630.fa
@@ -0,0 +1,25 @@
+>PROKKA_02058
+MSTSVPSSHDGHVRPAATTTADRPTDAGRPRRGSAGGSLARIAVMTALMAVLGLVPPIAV
+AGVPAPIVLQNIAVILAGVILGPWRGAASMALFAGLVALGLPLLSGGRGGLGVFAGPTAG
+FILGWIPSALIVGLIFWALTSRARPGLDAGRVALGAAVAGLIGGVVMVYFFGVLGFVGIA
+GMEFGAAVLSMAPFVPGDLIKLVVSVILIVGLWKAYPRAFR
+>PROKKA_01764
+MSTSVPSSHDGHVRPAATTTADRPTDAGRPRRGSAGGSLARIAVMTALMAVLGLVPPIAV
+AGVPAPIVLQNIAVILAGVILGPWRGAASMALFAGLVALGLPLLSGGRGGLGVFAGPTAG
+FILGWIPSALIVGLIFWALTSRARPGLGAGRVALGAAVAGLIGGVVMVYFFGVLGFVGIA
+GMEFGAAVLSMAPFVPGDLLKLVVSVILVVGLWKAYPRAFR
+>PROKKA_00760
+MPTSDTLASGRPAHSTDDRRPRRSSAGSGLARVAVFAALMAVLGLVPPVPVAGIPAPIVL
+QNLAVTLAGVILGPWRGAAAILLFNVLVALGLPLLTGGRGGLGVFVGPSSGFILGYVVAA
+AAVGLVFWALTGRARPGLRPGRVLAAALVAGLVGMVVLYAAGAVGFIVAAHMEPGAAVLA
+MGAFVPGDTVKVVLAALLVTGLWKAYPRAFR
+>PROKKA_00723
+MTSPSAPQTAVVDAPATHRPRRSPGADLARIAVMAALIAVLGAMPGIPVPGIPTPITLQT
+LGVMLAGLVLGAWRGAASVALFHLLVALGLPLLAGGRGGAAVFVGPSAGFLWGWIPGAFV
+VGLLFHLYLRGRRDGRNTGGLVAAALTACVVGGIAVIYLFGIPGMNLFGGVPLDKAAIGS
+LAFIPGDLLKAVVAALLAAGLWKAYPRAFA
+>PROKKA_01994
+MSTSVPSSHDGHVRPAATTTADRPADAGRPRHGSAGGSLARIAVMTALMAVLGLVPPIAV
+AGVPAPIVLQNIAVILAGVILGPWRGAASMALFNALVALGLPLLTGGRGGLGVFVGPSVG
+FILGWIPSAMIVGLIFWALTSRSRPGLSAGRIALAAAVAGLIGGVIMVYVFGAFGFVGVQ
+GMEFGAAMLSMAVFVPGDLTKLVIAVLLCAGLWKAYPRAFR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001631.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001631.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5a62c70c65a73ebe0e7d84d3b25979235d1d49ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001631.fa
@@ -0,0 +1,42 @@
+>PROKKA_02071
+MSTTTKDVEQPRVMKEMSFLDRWLPVWILAAMAVGLLMGRFIPGLNTALEAVKIGSVSLP
+IAIGLLVMMYPVLAKVRYDETRRIGADRRLLVTSLVLNWIVGPALMFALAWIFLADLPEY
+RTGLIIVGLARCIAMVLIWNDLACGDREAAAVLVAINSVFQVIAFGALGWFYLQALPSWL
+GLPTTSAEFSIGAIVLSVLIFLGIPLVAGFLTRILGERAKGRTWYEERFLPKIGPWALYG
+LLFTIVLLFALQGDAIISAPGDVARIALPLLVYFVVMFLGSFLLGRAIGLDYAKSTTVAF
+TASGNNFELAIAVAIGTFGVTSGQALAGVVGPLIEVPVLVALVYVALAMGRRLFPGDTTA
+PTR
+>PROKKA_00559
+MPSRAVAPSPATGPAARPAERPVLQEMSFLDRWLPVWILAAMAAGLLLGRLVPGLAEALD
+AFTVAGVSVPIALGLLVMMYPVLAKVRYDETHRIAADRRLMGTSLVLNWIVGPALMFALA
+WLFLADLPEYRTGLIIVGLARCIAMVLIWNDLACGDREAAVVLVAVNSVFQVVAFGALGW
+FYMQVLTGWLGLPTTTAGFSVGAIVLSVLVFLGVPLLAGFLTRVLGERARGRAWYEGRFL
+PRIGPWALYGLLFTIVLLFALQGEAITTSPGDVARIALPLLVYFTVMFLLGLVASRAVGL
+DYARSTTVAFTASGNNFELAIAVAIATFGVHSGQALAGVVGPLIEVPVLVGLVYVARWLA
+PRLFPGDPTVPPPRPRPHRQEHPVTEHAPTDRRPSVLFVCVHNAGRSQMAAGWLEHLSGG
+RVEVRSAGSAPKDRINPSAVAVMAEAGIDLSANTPKVLTTEAVRESDVVITMGCGDTCPV
+FPGKRYEDWAVEDPAGQGVNAVRPIRDEIRGRVEALLADLLPEG
+>PROKKA_00742
+MSVSTTAPAPHQPVLKEMSFLDRWLPAWILLAMAAGLLLGRFVPGLNTALEAVKIGEVSL
+PIAIGLLVMMYPVLAKVRYDEAHRVAGDKWLMITSLVLNWIVGPALMFALAWMLLPDLPE
+YRTGLIIVGLARCIAMVFIWNDLACGDREAAAVLVAINSVFQVVAFGALGWFYLQVLPSW
+LGLPTTSADFSVWAIVLSVLVFLGVPLLAGFLTRLLGERAKGRTWYEERFLPRIGPWALY
+GLLFTIVLLFALQGEAITSNPWDVARIALPLLAYFVLMFGIALLASKAVGLNYAKSTTVA
+FTAAGNNFELAIAVAIGTFGVTSGQALAGVVGPLIEVPVLVGLVYVSLWAGRKLFPGDPT
+VPARPQAAAAHRA
+>PROKKA_00487
+MSSTPRTTAEAAPVAARLSSLDRLLPVWIGAAMLVGLLLGRLVPGLGGVLAAVEVDGVSL
+PIALGLLVMMYPVLAKVRYDRLDSVTGDRRLLVASLVLNWVFGPLLMFALAWIFLADLPE
+YRTGLIIVGLARCIAMVIIWNDLACGDREAAAVLVALNSIFQVIAFAALGWFYLSVLPGW
+LGLPQTGLDVSPWDIARSVLIFLGIPLLAGFLSRVIGERRWGRAAYEGSFLPTIGPWALY
+GLLFTIVVLFALQGEQIAARPWDVARIALPLLVYFAVMWGLGYTVGRRLGLGYERTTTLA
+FTAAGNNFELAIAVAIATFGATSGQALAGVVGPLIEVPVLVGLVYVSLWLRRRFPPAADA
+GTPASAMTVPATTAQENR
+>PROKKA_01999
+MSTTTKDVEQPRVMKEMSFLDRWLPVWILAAMAVGLLLGRLIPGLNTALEAVKIGSVSLP
+IAIGLLVMMYPVLAKVRYDETRRIGADRRLLVTSLVLNWIVGPALMFALAWIFLADLPEY
+RTGLIIVGLARCIAMVLIWNDLACGDREAAAVLVAINSVFQVIAFGALGWFYLQALPSWL
+GLPTTSAEFSIGAIVLSVLIFLGIPLVAGFLTRILGERAKGRTWYEERFLPKIGPWALYG
+LLFTIVLLFALQGDAIISAPVDVARIALPLLVYFVVMFLGSFLLGRAIGLDYAKSTTVAF
+TASGNNFELAIAVAIGTFGVTSGQALAGVVGPLIEVPVLVALVYVALAMGRRLFPGDTTA
+PTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001633.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001633.fa
new file mode 100644
index 0000000000000000000000000000000000000000..655e478b88c2b65651b05f3ae7ddad1e44089f55
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001633.fa
@@ -0,0 +1,25 @@
+>PROKKA_02081
+MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA
+LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVVATTLALTWLN
+PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPKAWRV
+VDVVIAVVMAVLAVRLIAGSGVWG
+>PROKKA_01785
+MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA
+LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVIATTLALTWLN
+PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPKAWRV
+VDVVIAVVMAVLAVRLIAGSGVWG
+>PROKKA_00703
+MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA
+LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALHPQGLVAEQAPRTAGSVIATTLALTWLN
+PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPTAWRV
+VDVVIAVVMAVLAVRLIAGSGVWG
+>PROKKA_00613
+MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA
+LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVIATTLALTWLN
+PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASILWFTALGYGARLLARVLADPKAWRV
+VDLVIAVVMAVLAVRLIAGSGVWG
+>PROKKA_02019
+MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA
+LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVVATTLALTWLN
+PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPKAWRV
+VDVVIAVVMAVLAVRLIAGSGVWG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001638.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001638.fa
new file mode 100644
index 0000000000000000000000000000000000000000..22e13c88d42f98cc75b0ac58d809c18d7b4a6e1a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001638.fa
@@ -0,0 +1,45 @@
+>PROKKA_02086
+MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE
+YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH
+RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH
+DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA
+EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG
+LPDHPGHALAARQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE
+MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGAPPSSAVPRPA
+PAHHRTTRARTPERTR
+>PROKKA_01791
+MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE
+YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH
+RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH
+DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA
+EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG
+LPDHPGHALAARQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE
+MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGAPPSSAVPRPA
+PAHHRTTRARTPERTR
+>PROKKA_00697
+MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE
+YSRGSNPTRNGFETQLAALEHGERAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH
+RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH
+DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA
+EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG
+LPDHPGHDLAARQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE
+MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAVGRGTPSSSAVPRPA
+PAHHRTTRVRTPERTR
+>PROKKA_00607
+MTAVHHPTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE
+YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH
+RLITTVLEPWGVSNTPVDITDTTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH
+DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA
+EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG
+LPDHPGHDLATRQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE
+MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGTPSSSAVPRPA
+PAHHRTTRVRTPERTR
+>PROKKA_02025
+MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE
+YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH
+RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH
+DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA
+EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG
+LPDHPGHALAARQMDGFGGIVSIRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE
+MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGAPSSSAVPRPA
+PAHHRTTHARTPERTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001642.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001642.fa
new file mode 100644
index 0000000000000000000000000000000000000000..717bb8754eb40f2144ed6eb35be67d8e6252da9f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001642.fa
@@ -0,0 +1,43 @@
+>PROKKA_02095
+MSPSAPQRRAARAATFAATLAAAAIALTACGADAAPFSPASAPASASDGAESPAGEATAA
+SSVSEEDRVDPTQTTEVSAVTPRILLSHEDGLTLLDAESGEVVKEQDVTGFTRLSNAGNG
+KDVLVTTGNGWEVFSTGIQAKAHGDHVHHYESAPGMTGVTFPGEHPGHVVTHNGRTTLFA
+DGTGAIRTFDSTHLDKATPDLMPVMTEAETEDPHHGVALELSDGALFTTQGTEDSRDALQ
+VIDPKTGEVTAETDDCPGSHGEAAAQPTEAGDVVVMGCENGPVVYRDGEFHKVDVETEYQ
+RSGNLFGLHDSPIVLGDHKVEEEPKEAVERPTEIALIDTRTDELTTVDLGSSYWFRSLGR
+AEDGSAVVLTYDGEANVIDEETGEVTAEYPVIEPWKEKDEWQEPGPILKVAGNTAYVTDA
+EAQKLVAVDLETGETVLEKDLEFAPVEMAVVTGQPESVKPDEAADAASGHDEHTDHDH
+>PROKKA_01803
+MSHSAPQRRSARTAALSATLAAAAIALTACGADAAPSGPTSAPAPAADGAESPSGEARAA
+SSVSEGDRVDPTRTTEVSAVTPRILLSHEGGLTLLDAESGEVVREQDVPGFTRLSNAGNG
+KDVLVTTGNGWEVFSTGIQAKAHGDHVHHYESAPGMTGVTFPGEHPGHVVTHNGRTTLFG
+DGTGAIRTFDSAHLDKATPDLMPVMTEAETEDPHHGVALELSDGTLFTTQGTEDSRNTLQ
+VIDPKTSEVTAETDDCPGSHGEAAAQPTEAGDVVVMGCENGPVVYRDGEFHKVDVETEYQ
+RSGNLFGLHDSPIVLGDHKVEEEPEEAVERPTAIALIDTRTDELTTVDLGSSYWFRSLGR
+AEDGSAVVLTYDGEVTVIDEETGEVTAEYPVIEPWKEKDEWQEPGPILKVAGNTAYVTDA
+EAQKLVAVDLETGETVLEKDLEFAPVEMAVVTGEPESVKPEEGADAESGHDEHADHDHGH
+ESDEHTDHDH
+>PROKKA_00683
+MSHSAPQCRSTRTAASDGAESTSGETTAASSVSEEERVDPTRTTEVSAVTPRILLSHEDG
+LTLLDAESGEVVKEQDVPGFTRLSDAGNGKDVLVTTGNGWEVFSTGIQAKAHGDHVHNDE
+SAPGMTGVTFPGEDPGHVVTHNGRTTLFADGTGAIRTFDATHLDKATPDLMPVMTEAETE
+DPHHGVALELYDGTLFTTQGTEDSRDTLQVIDSTTGEVTAETDDCPGSHGEAAAQPTEAG
+DVVVTGCENGPVVYRDGEFHKVEVETEYQRSGNLFGLHDSPIVLGDHKVEEEPTEAVERP
+TAIALIDTRTDELTTVDLGSSYWFRSLGRAEDGSAVVLTYDGEVNVIDEETGEVTAEYAV
+IEPWKEKDEWQEPGPILKVAGNTAYVTDAEAQKLVVVDLETGETVLEKDLDFAPVEMAVV
+TGQPESVKPEEAADAESGHDEHTDHDH
+>PROKKA_00598
+MTPRILLSHEDGLTLLDAESGEVVKEQDVAGFTRLSNAGNGKDVLVTTGNGWEVFSTGIQ
+AKAHGDHFHNYESAPGMTGVTFPGEHPGHVVTHNGRTTLFADGTGAIRTFDSAHLDKATP
+DLMPVMTEAETEDPHHGVALELSDGTLFTTQGTEDSRNTLQVIDPTAGEVKAETDDCPGS
+HGEAAAQPTEAGDVVVMGCENGPVVYRDGEFHKVDVETEYQRSGNLFGLHDSPIVLGDYK
+VEEEPKEAVERPTEIALIDTRTDELTTVDLGSSYWFRSLGRAEDGSAVVLTYDGEVNVID
+EETGEVTAEYPVIEPWKEKDEWQEPGPILKVAGNTAHVTDAEAQKLVAVDLETGETVLEK
+DLEFAPVEMAVVTGQRESVKPEEAADAESGHDEHTDHDH
+>PROKKA_02034
+MTGVTFPGEHPGHVVTHNGKTTLFADGTGAIRTFDSAHLDKATPDLMPVMTEAETEDPHH
+GVALELSDGALFTTQGTEDSRNTLQVIDPKTGEVTAETDDCPGSHGEAAAQPTEAGDVVV
+MGCENGPVVYRDGEFHKVDVETEYQRSGKLFGLHDSPIVLGDHKVEEEPKEAVERPTEIA
+LIDTRTDELTTVDLGSSYWFRSLGRAEDGSAVVLTYDGEVNVIDEETGEVTAEYPVIEPW
+KEKDEWQEPGPILKVAGNTAYVTDAEAHKLVAVDLETGETVLEKDLEFAPVEMAVVTGQP
+ESVKPEEGAHGDEDHDDDGHEGHDHGAEPSEGHEGHDH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001643.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001643.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dafbd9a1780520d8bbedbf84e6f2fda4b4b3ed33
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001643.fa
@@ -0,0 +1,54 @@
+>PROKKA_02099
+MASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRA
+GARNPSDLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRI
+ADIVGTAADTAGVAQLVYLSGLHPDTVPVAELSDHMRSRALVAERLERAATPALTFEAGV
+IIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQACALPEPVQLRAQI
+GNGHPQSFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLA
+EEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPS
+DPEWAGTTVYTDERERESDLPAQEVWPVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGL
+TRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQLSTEPREGGGSVYRQ
+RAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRL
+PLRRNPLDRRARGAGGAQSRD
+>PROKKA_01806
+MASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRA
+GARNPSDLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRI
+ADIVGTAADTAGVAQLVYLSGLHPDTVPVAELSDHMRSRALVAERLERAATPALTFEAGV
+IIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQACALPEPVQLRAQI
+GNGHPQSFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLA
+EEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPS
+DPEWAGTTVYTDERERESDLPAQEVWPVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGL
+TRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQLSTEPREGGGSVYRQ
+RAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRL
+PLRRNPLDRRARGAGGAQSRD
+>PROKKA_00680
+MGGRLIPELLAAGFDVRAGARNPSDLADRPWSEGVEAVELDLTEADLVEAAMQDVHTVLY
+LVHSMGGGGDFVTQEQRIADIVGTAADTAGVAQLVYLSGLHPDTIPVAELSDHMRSRALV
+AERLEQAATPALTFEAGVIIGSGSTSFEMIRHLAERLPVMPGPSWLKNRVEPLAIRDVLY
+YLLQACALPEPVQLRAQIGNGHPQSFASVLVDYAKAAGLSRRIVIPTPFPLQTLAGFWIG
+TVTPIPVAVALPLAASLAEEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDV
+TFDADVHAAADPADPLPSDPAWSGTTVYTDERERESDLPPQDVWPVIESVGGANGWYSTP
+MLWKVRGLADKLVGGPGLIRGRRDQDRLRRGDAVDWWRVEDVEHGRRLTLRAEMKAGGRA
+WLQMSTEPRDGGGSVYRQRAIFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEAQRRTT
+GGERRRPRSLARALVDRLPLRRNPLDRGASA
+>PROKKA_00594
+MSTPSTSRGSGLTSAAASGDTPAGTGATTASLSPLGLALPDGHDRRVLVTGATGYVGGRL
+IPELLAAGFRVRAGARTPRDLEDRPWSDRVEVVELDLEKPDLVKAAMQDVHTALYLVHSM
+GAGGDFVEQEQKIADIVATAADEAGITQLVYLSGLHPAGKPVEELSDHMRSRALVAERLE
+AAATPALTFEAGVVIGSGSASFEMIRHLSERLPIMPGPSLLKNRVEPIAVRDVLHYLVQA
+CALEEPVQLHAQIGNGRPQSFASVLVDYAEVAGLSKRIVIPTPLPLSRLAGLWVGVVTPI
+PVKVALPLAASLAEDAVVEDHAIRDVIPAPEGGLTSYKEAVRRALAAEKNGPLDVTFEAD
+VYDSSDPAAPLPSDPEWAGHTVYTDDRERESDLAPEDVWPVIESIGGRNGWYSTPLLWKV
+RGYMDKVVGGPGLMRGRRDQDHLRRGDAVDWWRVEEVDPGHRLTLRAEMKAGGRAWLQLT
+TEPREQGGSVYRQRAIFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEAERRRTGGARR
+RTRGLVRALADRLPLRRSPLDRRAG
+>PROKKA_02039
+MASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRA
+GARNPSDLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRI
+ADIVGTAADTAGVAQLVYLSGLHPDTVPVAELSDHMRSRALVAERLERAATPALTFEAGV
+IIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQACALPEPVQLRAQI
+GNGHPQPFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLA
+EEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPS
+DPEWAGTTVYTDERERESDLPAQEVWPVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGL
+TRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQLSTEPREGGGSVYRQ
+RAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRL
+PLRRNPLDRRARGAGGAQSRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001649.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001649.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a64a81da57e31316ffb5ee8a5a328c82859ac31d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001649.fa
@@ -0,0 +1,36 @@
+>PROKKA_02107
+MGEARTGGEAALSGVTAELDAALRHAAAQAPGSAAFAELLDSLHVHVGAGKLIRPRLVEL
+GWRLATADPVPPSGRAAVDRLGAAFELLHTALLVHDDVIDRDVLRRGQPAVHASARHRLE
+ARGVPAADAAHAGVAVALIAGDVLLTQAFRLAATCAADTARAAEAAAVVFDAAAVTAAGE
+LEDVLLGLSRHTGEEPDPDRILAMQRLKTAHYTVGAPLRAGALLAGADPDLARAMGEAGA
+DLGAAYQVIDDVLGVFGDPGETGKSADGDLREGKATVLTAHGRRIPAVRALLDAGPATPA
+DIEAARRALEAAGAREHALDVAAELTVRARERIAALPLDETVRAEFADACHAVLTRRS
+>PROKKA_01814
+MGEARTGGEAALSGVTAELDAALRHAAAQAPGSAAFAELLDSLHVHVGAGKLIRPRLVEL
+GWRLATADPVPPSGRAAVDRLGAAFELLHTALLVHDDVIDRDVLRRGQPAVHASARHRLE
+ARGVPAADAAHAGVAVALIAGDVLLTQAFRLAATCAADTARAAEAAAVVFDAAAVTAAGE
+LEDVLLGLSRHTGEEPDPDRILAMQRLKTAHYTVGAPLRAGALLAGADPDLARAMGEAGA
+DLGAAYQVIDDVLGVFGDPGETGKSADGDLREGKATVLTAHGRRIPAVRALLDAGPATPA
+DIEAARRALEAAGAREHALDVAAELTVRARERIAALPLDETVRAEFADACHAVLTRRS
+>PROKKA_00672
+MSAGREGVVAELEAALSRAAGLAPESAAFAELLAGLRTHAGAGKLIRPRLVELGWRAAAD
+GPVPAAERPAVDRLGAAFELLHTGLLVHDDVIDRDVVRRGERTVHEATRRRLAARGVPEA
+EAAHAGTAVALIGGDVLLVEALRLAMTCTPDPGRAAPVAAVVLDAATASAAGELEDVLLG
+LARHTGEEPEPERILAMQRLKTAHYTVSAPLRVGGAAGGGGSRRRRGAGEAAAPTWAWPT
+RWWTTCSGCSAPRSRPASPPTATCARARPPCSPRTAAATPPSAPCSTPAPATPEELEAAR
+RALEAAGAREHALQVAEELTRRAAEHLAVLPLGEAACAEFADACHAVLTRSS
+>PROKKA_00588
+MNPLAAGIGGAAPWSASAATPGLDDAGRARAAVRAELDRVFAETPLCADAPDSFHLLWAR
+LREAVSGGKLVRPRLVDLGWRTVRRAPASSGVPRGGTGEEEAADLRAVARVGAAFELLHA
+ALIVHDDVIDRDDLRRGRPTVAEQYRRDAVRDGVPAGEAEHVGRSAGIIAGDLLLTAAFR
+LAAASGARVRAAEAAESVFRAASAAAAGELEDVLLALHRHTGHHPEAGRILTMERLKTAG
+YSFEEPLRAGALLAGADPAHAEALAEAGALLGVAYQVVDDVLGTAGDPAVTGKPHDADLR
+EGKATLLTAHGRRDPRARAALDRVARAERHGEDLGELAAAVAEARAALVDAGSVEHALGV
+AEELVDQARALLDALPMAPAERAEFAATCGQILQREA
+>PROKKA_02047
+MGEARTGGEAALSGVTAELDAALRHAAAQAPGSAAFAELLDSLHVHVGAGKLIRPRLVEL
+GWRLATADPVPPSGRAAVDRLGAAFELLHTALLVHDDVIDRDVLRRGQPAVHASARHRLE
+ARGVPAADAAHAGVAVALIAGDVLLTQAFRLAATCAADTVRAAEAAAVVFDAAAVTAAGE
+LEDVLLGLSRHTGEEPDPDRILAMQRLKTAHYTVGAPLRAGALLAGADPDLARAMGEAGA
+DLGAAYQVIDDVLGVFGDPGETGKSADGDLREGKATVLTAHGRRIPAVRALLDAGPATPA
+DIEAARRALEAAGAREHALDVAAELTVRARERIAALPLDETVRAEFADACHAVLTRRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001653.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001653.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c3fe02c625ef77c71cb75a3ebab36ab1fa7d494
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001653.fa
@@ -0,0 +1,20 @@
+>PROKKA_02114
+MGTQDPRARLLEKLAKVNVCMLTTAEPDGTLVTRPMGLQQAEDGGTLWFLTRATSDVAAD
+APQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNPATEAFFGEGSSPEDPQIVLVRV
+DVQTAQFWESPGAVATAVELVKAKVTGGEAHPGDSETVRF
+>PROKKA_01822
+MGTQDPRTHLLEKLAKVHVCMLTTAEADGTLVTRPMGLQQAEDGGTLWFMTRSTSDVAAD
+APQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNSATEAFFGEGSSPEDPQIVLVRV
+DVNTAQFWESPGAVATAVEMVKAKVTGGTAEPGDSETVRF
+>PROKKA_00666
+MGHKDPRTHLLEKLEKSNVCMLTTSETDGTLTTRPMGLQKAEETGTLWFMTRAASDVASD
+ASQRPVNVSVQDKDFWASVAGHGQVVRDDARKKEFWNPATEAFFGEGAKPEDPQIVLVRV
+DVESAQYWESPGAVGTVVELIKAKVTGGEAHPGESTTVQF
+>PROKKA_00582
+MTEQDPRTALLEKIEKAGVVMLTTAEEDGTLASRPMAVQEVEQEPGVLWFITRATGDAAQ
+DSAGRPVNVAVQEKGFWASVAGHGEIVRDEARKTEYWNSATEAFFGEGARPEDPQIVLVR
+VQADSAEYWDGGGAASVVEIVKAKVTGGEARPGDHDTVEF
+>PROKKA_02052
+MGTQDPRARLLEKLAKVNVCMLTTAEQDGTLVTRPMGLQQAEDGGTLWFLTRATSDVAAD
+APQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNPATEAFFGEGSSPEDPQIVLVRV
+DVDTAQFWESPGAVATAVELVKAKVTGGTAEPGDSETVRF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001658.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001658.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4297fcdeae47a9d8c406bedf1d63842cf6df2ba2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001658.fa
@@ -0,0 +1,18 @@
+>PROKKA_02120
+MSTDSTTTAPAAASPLPSAAADACDGHRPPHEVHRDKAKHLARLRRIEGQVRGLHRMVDE
+DVYCIDVLTQVAAVTKALQSLSLNLTSEHLRHCVAEAAVQAEAEGRTELIDEKVAEATAA
+LGRLLR
+>PROKKA_01828
+MSTDSTTTAPAAASPLPSAAADACDGHRPPHEVHRDKAKHLARLRRIEGQVRGLHRMVDE
+DVYCIDVLTQVAAVTKALQSLSLNLTSEHLRHCVAEAAVQAEAEGRTELIDEKVAEATAA
+LGRLLR
+>PROKKA_00660
+MSTLPTTTDAHDGADPCAGAHPPHAAHRDKDAHLTRLRRIEGQVRGIHRMVDEDVYCIDI
+LTQVAAVTKALQAMSLNLTSEHLRHCVAEAAVEAEASGRTELIDEKVAEATAAIGRLLR
+>PROKKA_00577
+MEHDRHAGPGYSPQREAYLKRLKRIEGQVRGIHRMVEEDVYCIDVLTQVAAATKALHAVS
+LGLVEDHLRHCVAEAAVQAEAEGRTELIDEKVAEATAALGRLLR
+>PROKKA_02058
+MSTDSTTTAPAAASPLPSAAADACDGHRPPHEVHRDKAKHLARLRRIEGQVRGLHRMVDE
+DVYCIDVLTQVAAVTKALQSLSLNLTSEHLRHCVAEAAVQAEAEGRTELIDEKVAEATAA
+LGRLLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001661.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001661.fa
new file mode 100644
index 0000000000000000000000000000000000000000..82bedbfcb7f796236ad36d451844f659c765fbb0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001661.fa
@@ -0,0 +1,14 @@
+>PROKKA_02125
+MSAGQGATTAGPVIESVELHVAAGAEAAFEAAVAEAEPLFRDGGATSFALSRQVEDPARY
+RLLIGWRTLEDHTVAFRESDSFLAWRALVTPHLAQLPAATHWSAV
+>PROKKA_01833
+MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAEPLFRDKGATSFALSRQVEDPARY
+RLLIGWRTLEDHTVAFRESDAFLAWRALVTPHLAQPPAATHWSAV
+>PROKKA_00655
+MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAAELFRGARATSFALTRQVEDPARY
+RLLIGWRTLEDHTVGFRESEAFGQWRALVTPHLAQPPAATHWESVAAAF
+>PROKKA_00572
+MEDPARYRLLIGWRTLEDHTVGFRESDAFLAWRALVTPHLAQPPAATHWSAV
+>PROKKA_02063
+MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAEPLFRDGGATSFALSRQVEDPAHY
+RLLIGWRTLEDHTVAFRESDAFLAWRALVTPHLAQPPAATHWSAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001662.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001662.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38ea0b9ac205ceafff68df89332656ed782b6b38
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001662.fa
@@ -0,0 +1,20 @@
+>PROKKA_02126
+MTETPQSSSGQSRDEILARLEEIYANDPAVREHGVTLGEVAEGRVVLHRDVTADMVNSHE
+ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPARLGAHLVATARQSVEFGRDRM
+IEVGIEADGQLAAWFTGHSTSPRVHA
+>PROKKA_01834
+MTETPQSSSGQSRDEILARLEEIYANDPAVREHGVTLGEVAEGRVVLHRDVTADMVNSHE
+ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPARLGAHLVATARQSVEFGRDRM
+IEVGIEADGQLVAWFTGHSTSPRVHA
+>PROKKA_00654
+MTETPQSSSGQSRDEILARLEEIYANDPAVREHGVTLGEVAEGRVVLHRDVTADMVNSHG
+ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPARLGAHLVATARQSVEFGRDRM
+IEVGIEADGQLVAWFTGHSTSPRVHA
+>PROKKA_00570
+MTDTPQSSSGQSRDEILARLEEIYANDPAVREHDVTLGEVAEGRVVLHRDVTAGMVNSHE
+ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPAKLGAHLVATARQSVEFGRDRM
+IEVGIEADGQLVAWFTGHSTSPRVHA
+>PROKKA_02064
+MTETPQSSSGQSRDEILARLEEIYANDPAVREHGVTLGEVAEGRVVLHRDVTADMVNSHE
+ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPARLGAHLVATARQSVEFGRDRM
+IEVGIEADGQLVAWFTGHSTSPRARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001665.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001665.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0bf834ebdf00a88ac9ddbe8562b37d7f245d901f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001665.fa
@@ -0,0 +1,50 @@
+>PROKKA_02129
+MTVYAFPGTEGAKVEFKSRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID
+AALDAAWKAAPAWGATSPAERALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADVP
+LAIDHFRYFAGAIRAQEGRLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL
+AAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT
+GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMANDDAYWDKAQEGFTLFALNQGE
+VCTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIG
+RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA
+MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE
+NHLMMLDHYQQTKNLLVSYSEDKLGFF
+>PROKKA_01837
+MTVYAFPGTEGAKVEFKSRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID
+VALDAAWKAAPAWGATSAAERALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADVP
+LAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL
+AAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT
+GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMAADDAYWDKAQEGFTLFALNQGE
+VCTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIG
+RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA
+MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE
+NHLMMLDHYQQTKNLLVSYSEDKLGFF
+>PROKKA_00651
+MTVYAFPGTEGAKVEFKPRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID
+VALDAAWKAAPAWGATSAAERALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADVP
+LAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL
+AAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT
+GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMANDDAYWDKAQEGFTLFALNQGE
+VCTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKIISYLDIG
+RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA
+MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE
+NHLMMLDHYQQTKNLLVSYSEDKLGFF
+>PROKKA_00567
+MTVYAFPGTEGAKVEFKPRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID
+VALDAAWKAAPAWGATSAAERALVLHRIADRMEENLEMLAVAETWDNGKAIRETLNADLP
+LAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL
+AAGNAVVIKPAEQTPASIMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT
+GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMANDDAYWDKAQEGFTLFALNQGE
+ICTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIG
+RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA
+MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE
+NHLMMLDHYQQTKNLLVSYSEDKLGFF
+>PROKKA_02067
+MTVYAFPGTEGAKVEFKSRYEHFIGGEWTPPVKGQYFENVTPVTGKVFCEVARGTAEDID
+VALDAAWKAAPAWGATSAAERALVLHRIADRMEENLEMLAVAETWDNGKAVRETLNADLP
+LAIDHFRYFAGAIRAQEGGLSQVDEDTVAYHFHEPLGVVGQIIPWNFPLLMGVWKLAPAL
+AAGNAVVIKPAEQTPASVMVFIELIADLLPAGVVNVVNGFGLEAGKPLAQSPRIRKIAFT
+GETTTGRLIMQYASENIIPVTLELGGKSPNVFFEDVMAADDAYWDKAQEGFTLFALNQGE
+VCTCPSRALVQESIAEKFLDAVVERTSRIVTGNPLDTDVMMGAQASNDQLEKITSYLDIG
+RQEGAEVLIGGARAEMEGELAGGYYVQPTIFRGDNSMRIFQEEIFGPVVSTTTFTDFDDA
+MRIANDTLYGLGAGVWSRNGNTAYRAGRAIQAGRVWVNNYHAYPAHAAFGGYKSSGIGRE
+NHLMMLDHYQQTKNLLVSYSEDKLGFF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001673.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001673.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d72fbd213076bfb2629ffdbcb449f97f04f1ab2a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001673.fa
@@ -0,0 +1,45 @@
+>PROKKA_02138
+MAGPSGSTAAPAPQDARALTRRILALAVPAFGALIAEPLFLLADTAIIGHLGTAQLAGVG
+IGTTILHTLTGLMIFLAYATTPAVARLIGAGNLAAAMDRGRDGIWLGLLLGAVLAVLGWL
+AAPALTAALGATGEVQAHAVAYLRWSMPGLPALLAVLAATGVLRGLQDTVTPLVVAGVGF
+GANIGLNVALVYGLGWGVAGSAVGTSVVQWAMLVTYLFVLAPRFRRSGTAWAPRASGMRA
+TAQVGSWLLLRTASLRAAILITVMAAAGAGDLTLAAHQLVFTLFSTLAFALDALAIAAQA
+LIGAELGAARPDAARRLTRTMVRWGLGFGVVTGAVLALAAPVLPGLFTTDPTVQAAATVG
+LWVLAAGQPVAGYVFVLDGVLIGAGDARYLALAGLVNLVVYAPALWVLAQLATGGFGWTA
+AWPGPNAAVPDAGVQLGLLWLGFAGVYMGMRALTLGWRARRDDWMRLGVV
+>PROKKA_01846
+MAGPSGSTAAPAPQDARALTRRILALAVPAFGALIAEPLFLLADTAIIGHLGTAQLAGVG
+IGTTILHTLTGLMIFLAYATTPAVARLIGAGNPAAAMDRGRDGIWLGLLLGAVLAVLGWL
+AAPALTAALGATGEVQAHAVAYLRWSMPGLPALLAVLAATGVLRGLQDTVTPLVVAGVGF
+GANIGLNVALVYGLGWGVAGSAVGTSVVQWAMLVTYLFVLAPRFRRSGTVWAPRASGMRA
+TAQVGSWLLLRTASLRAAILITVMAAAGAGDLTLAAHQLVFTLFSTLAFALDALAIAAQA
+LIGAELGAARPDAARRLTRTMVRWGLGFGVVTGAVLALAAPVLPGLFTTDPTVQAAATVG
+LWVLAAGQPVAGYVFVLDGVLIGAGDARYLALAGLVNLVVYAPALWVLAQLATGGFGWTA
+AWPGPNAAVPDAGVQLGLLWLGFAGVYMGMRALTLGWRARRDDWMRLGVG
+>PROKKA_00634
+MAEPQGSTAAPAPQDGRALTRRILALAVPAFGALLAEPLFLLADTAIVGRLGTPELAGVG
+IGTTVLHTATGLMIFLAYATTPAVARLIGAGDHAAAMDRGRDGVWLGLLLGAALAVLGWI
+AAPWLTGALGATGEVQEHAVAYLRWSMPGIPALLAVLAATGVLRGLQDTVTPLVVAGAGF
+AVNIGLNFALVYGAGLGVAGSAIGTSAVQWGMLLTYLAVLAPRFRRAGTSLAPRASGMRA
+TAQVGSWLLLRTASLRAAILITVMAAAGAGDMTLAAHQLVFTLFSTLAFALDALAIAAQA
+LIGAELGASRPATARRLTDVMVRWGLGFGVVTGGLLALAAPWLPALFTTDPQVQAAATVG
+LWVLAAGQPIAGYVFVLDGVLIGAGDARYLALAGLVNLAVYAPVLWVLAQVAAGGLGWTV
+DWSDPAAHVPDAGEQLGLLWLGFAGVYMGMRALTLGWRARRDDWMRVGAH
+>PROKKA_00558
+MPSRPPHDDAAPAPEDRRALARQVLGLAVPAFGALIAEPLFLLADTAIVGHLGTAQLAGV
+GVGTTVLHTVTGLLVFLAYATTPAVARMVGAGNPAGALDRGRDGMWLGLMLGFVLGAAGW
+LAAPWLTGALGAAGEVHSHATEYLRWSMPGLPALLAVLAATGVLRGLQDTVTPLVVAGGG
+FAVNIGLNWALVYGAGLGVAGSAIGTAAVQWAMLAVYLAVLAPRFRAAGTRPGPRADGLR
+ATAQVGSWLMLRTASLRAAILITVAAATGLGDVTLAAHQLVFTLYSTLAFALDALAIAAQ
+ALIGAELGASRPRTARRLTDLMVRWGLGFGVVTGAGLAAAAWALPPLFTPDPGVHAAATA
+GLLVLALSQPVAGYVFVLDGVLIGAGDARYLALAGVVNLAVYAPVLWGLARLAAGGADAG
+AQVALLWLGFAGVYLGMRAATLGLRARRDAWMRLG
+>PROKKA_02076
+MAGPSGSTAAPAPQDARALTRRILALAVPAFGALIAEPLFLLADTAIIGHLGTAQLAGVG
+IGTTILHTLTGLMIFLAYATTPAVARLIGAGNPAAAMDRGRDGIWLGLLLGAVLAVLGWL
+AAPALTAALGATGEVQAHAVAYLRWSMPGLPALLAVLAATGVLRGLQDTVTPLVVAGVGF
+GANIGLNVALVYGLGWGVAGSAVGTSVVQWAMLVTYLFVLAPRFRRSGTVWAPRASGMRA
+TAQVGSWLLLRTASLRAAILITVMAAAGAGDLTLAAHQLVFTLFSTLAFALDALAIAAQA
+LIGAELGAARPDAARRLTRTMVRWGLGFGVVTGAVLALAAPVLPGLFTTDPTVQAAATVG
+LWVLAAGQPVAGYVFVLDGVLIGAGDARYLALAGLVNLVVYAPALWVLAQLATGGFGWTA
+AWPGPNAAVPDAGVQLGLLWLGFAGVYMGMRALTLGWRARRDDWMRLGVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001674.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001674.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51370655a88204d44b70d0eb5945419caccc1077
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001674.fa
@@ -0,0 +1,34 @@
+>PROKKA_02139
+MSVPPSGPPAGPPAGWPPSGRPSARRAAVAPSLHGHPGAPGGVPAGWPGRRPAARPAPDW
+TPGRFHWGDAVVVLVYVALMVLGLGLWLAVSLGLVPGDLEAFDLVRDGFTVNIVSYAILV
+VLVLAVAWRPLVTSLRVFRTGTWWKLLLLPATWLACIVVNVIVLSLIGEAQTSANQAALE
+EMTTQAPPVLMILMTVVAAPLVEEYLFRHLLIGKLSRWINVWVCAVVSVLAFTLLHFLGT
+GGDFRLVETVPYLTLAVAITVSYILMGRSFGYAVLLHMVNNGIAIAMLYLVAPLLPDTLP
+GPTAPTTALAPLLALLG
+>PROKKA_01847
+MSVPPSGPPAGPPAGWPPSGRPSARRAAVAPSLHGHPGAPGGVPAGWPGRRPAARPAPDW
+TPGRFHWGDAVVVLVYVALMVLGLGLWLAVSLGLVPGDLEAFDLVRDGFTVNIVSYAILV
+VLVLAVAWRPLVTSLRVFRTGTWWKLLLLPATWLACIVVNVIVLSLIGEAQTSANQAALE
+EMTTQAPPVLMILMTVVAAPLVEEYLFRHLLIGKLSRWINVWVCAVVSVLAFTLLHFLGT
+GGDFRLVETVPYLTLAVAITVSYILMGRSFGYAVLLHMVNNGIAIAMLYLVAPLLPDTLP
+GPTAPTTALAPLLALLG
+>PROKKA_00633
+MPAGWPGRTPGPRTAPDWEPGRFHWGDAVVVLAYAGLMLFGLGLPLAMLLGLVPGDLAAF
+DLVRDGFTVNMVSYAILTALVLIVAWRPLVTSLRVFRTGTWWKILLLPAVWFTCILVNVL
+VLSLIGEAQTSANQAALEEMSAQAPPVLMILMTVVGAPLVEEYLFRHLLVGKLSRWVNVW
+VCAVVSMLAFTLLHFLGTGGQFDLVETVPYLTLAIAITVTYILMGRSFGYAVLLHMVNNG
+IAIAMLYLVAPLLPDVLPEPTAPAAALSPLLALLG
+>PROKKA_00557
+MSVPPPGPHDAGALPPPGSTAPTSAAGEAPEGWPPAGWPGRASAGGAPQGWPPSGWPGRT
+ASARTAPSWEPGRLHWGDAAVVVLYVLMMVVGLGYLLAVLLGLAPRDPAAMDVMDGFRVN
+LVSYAVLVVAVLAVSWRPLVASLRVFATHTWLKILLLPALWLVTVLVNALLLSLIGQAQT
+SANQAALEEMTTQAPALGMVLMTVVGAPIVEEYLFRHLLVGKLSRWINVWVCAAISVAAF
+TLLHFLGTGGDFQWVETVPYLTLAVTITVTYVLIGRSFGYAVLLHMVNNGIAIAMLYLVA
+PLLPSAPAPVGPGALLSPLLALLG
+>PROKKA_02077
+MSVPPSGPPAGPPAGWPPSGRPSARRAAVAPSLHGHPGAPGGVPAGWPGRRPAARPAPDW
+TPGRFHWGDAVVVLVYVALMVLGLGLWLAVSLGLVPGDLEAFDLVRDGFTVNIVSYAILV
+VLVLAVAWRPLVTSLRVFRTGTWWKLLLLPATWLACIVVNVIVLSLIGEAQTSANQAALE
+EMTTQAPPVLMILMTVVAAPLVEEYLFRHLLIGKLSRWINVWVCAVVSVLAFTLLHFLGT
+GGDFRLVETVPYLTLAVAITVSYILMGRSFGYAVLLHMVNNGIAIAMLYLVAPLLPDTLP
+GPTAPTTALAPLLALLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001675.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001675.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c91c7731a3ee0f0ea0b82b44020ab94b5810c93d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001675.fa
@@ -0,0 +1,20 @@
+>PROKKA_02140
+MALFSQPVFINLPTTDTERIREFWTTLGATAMDDYSDEHSVCIELTESTYAMYLSPGYYT
+DFIGNREIADCLTTNSALMALTVGDAAAVDALADRAIELGAAEVPLPEDLREEMADSGMH
+SREIVDPDGHQWEFVTA
+>PROKKA_01848
+MALFSQPVFINLPTTDTERIREFWTTLGATAMDDYSDEHSVCIELTESTYAMYLSPGYYT
+DFIGNREIADCLTTNSALMALTVGDAAAVDALADRAIELGAAEVPLPEDLREEMADSGMH
+SREIVDPDGHQWEFVTA
+>PROKKA_00632
+MALFSQPVFINLPTTDTERIREFWTSLGAQAIEDFSDENSVCIELTESTFAMYLSPGYYT
+DFIGDREIADCMTTNSALMALTVGDAAAVDALADRAIEAGAAEVPLPVDLREEMVDSGMH
+SREIVDPDGHQWEFVTA
+>PROKKA_00556
+MRTRWSTVLVMALFSQPVYINLPSTDTERIREFWTSMGADIDEDFSDENSVCVQLTESTF
+AMYLSPGFYTDFIGDREIADCLTTNSVLLQLTAPDRGAVDALVRAAVEAGGSEVPLPDEL
+QEDMTATGVHSRQVVDPDGHQWEFMAA
+>PROKKA_02078
+MALFSQPVFINLPTTDTERIREFWTTLGATAMDDYSDEHSVCIELTESTYAMYLSPGYYT
+DFIGNREIADCLTTNSALMALTVGDAAAVDALADRAIELGAAEVPLPEDLREEMADSGMH
+SREIVDPDGHQWEFITA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001676.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001676.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d6640d333b6afb58cd8577b2bc6ca5a1c034319
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001676.fa
@@ -0,0 +1,50 @@
+>PROKKA_02141
+MPAPAATTTTTPPATPRERQSVLRTLRTPRWLGTEVLAAVVVALALIPEAIAFSIIAGVD
+PRVGLFASFTMAVTTAIVGGRPAMISAATGAVALVVAPLSHAYGVGHLLAAIILGGVIQI
+LLGVFGVARLMRFVPRSVMVGFVNALAILVFTSQLPELIGVPWLVYPLTALALAIVVLLP
+RLTTAVPATLVAVVVVTALVMAAGLAVPRVGDRGALPDALPVLGLPDVPLTWETLRLILP
+FSVGIAFVGLLESLLTAKLVDDITDTRSDKTRESWGQGVANVVSGLFGGMGGCAVVGQTM
+MNVKANGARTRISTFLAGVFLLVLVVAFGGFVAQIPMAALVGVMMFVAAATFDWHSVRPA
+TLRAMPRSETAVMVVTVAATVLTHNLAIGVGVGVLAALVLFAQRVSRLVTVVREVHDDGD
+AVTYRVHGALFFASSNDLYSQFEYALDPPRVVIDMSAAHVWDASTVAALDSVLTKYARHG
+IHAEVTGLNEASAAMHARLTGRLGA
+>PROKKA_01849
+MPALPAAPPPALTPLQRQSVLRTLRSPRLLGTEVLAAVVVALALIPEAIAFSIIAGVDPR
+VGLFASFTMAVTTAIVGGRPAMISAATGAVALVVAPLSHAYGVGHLLAAIILGGVIQILL
+GVFGVARLMRFVPRSVMVGFVNALAILVFTSQLPELIGVPWLVYPLTALALAIVVLLPRL
+TTAVPATLVAVVVVTALVMAAGLAVPRVGDRGALPDALPVLGLPDVPLTWETLRLILPFS
+VGIAFVGLLESLLTAKLVDDITDTRSDKTRESWGQGVANVVSGLFGGMGGCAVVGQTMMN
+VKANGARTRISTFLAGVFLLVLVVAFGGFVAQIPMAALVGVMMFVAAATFDWHSVRPATL
+RAMPRSETAVMVVTVAATVLTHNLAIGVGVGVLAALVLFAQRVSRLVTVVREVHDDGDAV
+TYRVHGALFFASSNDLYSQFEYALDPPRVVIDMSAAHVWDASTVAALDSVLTKYARHGIH
+AEVTGLNEASAAMHARLTGRLGA
+>PROKKA_00716
+MTPASTASARVAAPPNSREPSPEQLQSVRLTLRSPGRLKTEVLAGLVVALALIPEAIAFA
+LIAGVDPQVGLFAAATMAMTIAFVGGRPAMVSAATAATALVVAPLVASHGLDHLIAAVIL
+AGGLQVVLGLLGVAKLMRFVPRSVMVGFVNALAILIFTSQLPDLMGVPWLVYPLTALGLA
+IILLLPRVTTAVPAPLVAIVVVTVIVLLAGADVPTVGDKGRLPDSLPALLVPDVPFTLET
+LQLLFPYALGMAVVGLLESLMTAKLVDDITDTRSSKTRESWGQGVANVVSGLFGGMGGCA
+MVGQTMINVKASGARTRISTFMAGVFVLILSVTLGDVVALVPMAALVAVMIFVSLATFDW
+HSIRPSTLAFMPKSETAVMLVTVAATVLTHNLAIGVGLGVLAAMVMFAQRVSHLATVTRT
+LEGQGRDAVARYRVQGELFFASSNDLYTQFDYAGDPARVVIDFSQAHLWDASTIAALDAV
+EEKYRRHGATVEITGLNVASRAMRARMSGRLGGGH
+>PROKKA_00554
+MPASPAAPPPALTPLQRQSVLRTLRTPRWLGTEVLAAVVVALALIPEAIAFSIIAGVDPR
+VGLFASFTMAVTTAVVGGRPAMISAATGAVALVVAPLSHAHGLDHLIAAIILGGLIQVAL
+GLLGVARLIRFIPRSVMVGFVNALAILVFTSQLPELIGVPWLVYPLTALALGIVLLLPRL
+TTAVPSTLVAIVVVTALVMAAGWSVPRVGDRGELPDALPGLFVPDVPLTWETLRLILPFS
+VGMAVVGLLESLLTAKLVDDVTDTRSDKTRESWGQGVANIVSGLFGGMGGCAVVGQTMMN
+VKANGARTRISTFLAGVLLLVLVVALGDLVGQIPMAALVGVMVFVAGAAFDWHSVRPATL
+RAMPRSETAVMLLTVLATVVTHNLAIGVGVGVLTAMVLFAQRVSRLARVERVVTDDNGGT
+AVYRVHGELFFASSNDLYSQFEYALDPPRVVIDLSAAHVWDASTVAALDAVVTKYAQHGI
+AAEVTGLNEASAAMHARLTGRTGA
+>PROKKA_02079
+MPALPAAPPPALTPPATPRERQSVLRTLRTPRWLGTEVLAAVVVALALIPEAIAFSIIAG
+VDPRVGLFASFTMAVTTAIVGGRPAMISAATGAVALVVAPLSHAYGVGHLLAAIILGGVI
+QILLGVLGVARLMRFVPRSVMVGFVNALAILVFTSQLPELIGVPWLVYPLTALALVIVVL
+LPRLTTAVPATLVAVVVVTSLVMAAGLTVPRVGDRGALPDALPALGLPDVPLTWETLWLI
+LPFSIGMAFVGLLESLLTAKLVDDITDTRSDKTRESWGQGVANVVSGLFGGMGGCAVVGQ
+TMMNVKANGARTRISTFLAGVFLLVLVVAFGGFVAQIPMAALVGVMMFVAAATFDWHSVR
+PATLRAMPRSETAVMVVTVAATVLTHNLAIGVGVGVLAALVLFAQRVSRLVTVVREVHDD
+GDAVTYRVHGALFFASSNDLYSQFEYALDPPRVVIDMSAAHVWDASTVAALDSVLTKYAR
+HGIHAEVTGLNEASAAMHARLTGRLGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001680.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001680.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1bd5b6faf1f8b10457aca0900b1a864affee7fc4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001680.fa
@@ -0,0 +1,29 @@
+>PROKKA_02146
+MVGLVGALLLAGCASGADAGASAHAETGSTPSKVWDAATWKPTEVIEPVLATEPEKEAAY
+REQMDRLAESGGTPEILQVQRKDWSTTPLESDQKVASCMRADGFPVEVSPTGGLRYSTPP
+AAQARAWALAMNTCIAQHPVDPSYTQDWSEPQLRLVYDYWDQYLIPCLEAQGFTVDTSTR
+PSKESFVTAFFTPGRHDWWPLQATMRGVPEERQTQVVQTCPELPPQDVFWGTSG
+>PROKKA_01853
+MTSLRIPATAALVAAVALTLTGCVGRESAGLGGSSTVAAPPTATAEKTWDASQWVPTERI
+EPLLTTEAEKERAYREQVARHAQGAGMPAPPQVERSGWYATSLESDRMVSTCLAEAGWPN
+SVGPTGGIQIDTPPESQRSAFEAAYVTCYAQHPVDPSYTQDWTDPQLRLVYDYWDQYLIP
+CLEAYGYTVDTSARPSKEAFVSAFYTPGRHQWWPFADSMRGVSAERQAEVAQTCPELPPQ
+DVFWGSSG
+>PROKKA_00626
+MKTKFAAVTAAAVTAVLTLSGCATTAPSTSAAATGSPTEKVWDPETWTPTEKIERRMTEA
+DERERWYESQLARNAAFLGIRNPPAVTRRGWATSRQEQARWSAQCMTERGVPATYNEVMV
+GVTYDTPPPSQEAAVKLVSWTCDALFPIDPSLDQEFSDAQLRLLYDYWDQYAIPCLEDHG
+ITVDTSQRPSKETWLAAFNTPERISWWPVQDSIMGLTDARSAEVSEACPVQPPDSMLFGY
+SE
+>PROKKA_00550
+MTSLRIPATAALVAAVALTLTGCVGRESAGLGGSSTVAAPPTATAEKTWDASQWVPTERI
+EPLLTTEAEKEAAQREQVERMAREAGTPELLQVRRMDWSSTTLESSQKIGECMAAAGFPV
+EVTPTGGLRYPTPPESQKRAWNLAENTCAVKHPVDPAYAHDWTEPQLRLVYDYWDQYLIP
+CLEAQGLHVDTSSRPSKESFVTSFFTQDRHDWWPFSTTMVGVSEERKAHIAQTCPELPPP
+DVFWGTAP
+>PROKKA_02083
+MTSLRIPATAALVAAVALTLTGCVGRESAGLGGSSTVAAPPTATAEKTWDASQWVPTERI
+EPLLTTEAEKERAYREQVARHAQGAGMPAPPQVERSGWYATSLESDRMVSTCLAEAGWPN
+SVGPTGGIQIDTPPESQRSAFEAAYVTCYAQHPVDPSYTQDWTDPQLRLVYDYWDQYLIP
+CLEAYGYTVDTSARPSKEAFVSAFYTPGRHQWWPFADSMRGVSAERQAEVAQTCPELPPQ
+DVFWGSSG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001681.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001681.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7458080c6bb7056cec7c0a467924c01b86dd0b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001681.fa
@@ -0,0 +1,65 @@
+>PROKKA_02147
+MSEHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLVVVALMVLV
+AVVLNVWAPHVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTP
+GEGIDFTELGRLILIVLGMYLVAQTFMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSY
+FDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMMFWLSWQLALIALIAL
+PVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNE
+ELYEAAFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN
+QPLGQIAGMSNMLISGVASAERIFELLDEPEETPDGTPARTPARTFVRETAPSEGTFVRE
+TAPSAASGPDVVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNLVAEPGQTVAIVGPTGA
+GKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRSELRAATGMVLQDAVLFGGTIRENIRYG
+RLDATDEEVVAAAKATYVDRFVHTLPEGYDTVIEHDASNVSAGERQLITIARAFLAQPSL
+LILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVMEHGDIVEQGS
+HAELLAAKGAYHRLYMSQFKGGEDDDGAASRDDAR
+>PROKKA_01855
+MSEHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLVVVALMVLV
+AVVLNVWAPHVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTP
+GEGIDFTELGRLILIVLGMYLVAQTFMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSY
+FDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMMFWLSWQLALIALVAL
+PVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNE
+ELYEAAFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN
+QPLGQIAGMSNMLISGVASAERIFELLDEPEETPDGTPARTPDGTFVWETAPSESAFVRE
+TAPSAIPGPDGVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNFVAEPGQTVAIVGPTGA
+GKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRGELRAATGMVLQDAVLFGGTIRENIRYG
+RLDATDEEVVAAAKATYVDRFVHTLPDGYDTVIEQDAANVSAGERQLITIARAFLAQPSL
+LILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVMEDGDIVEQGS
+HDQLLAARGAYFRLYRSQFQGGEQAEEQDDDGAPAAREDAR
+>PROKKA_00622
+MSGTEKHGSTAAPQGEVGELTDAEIAAFQEAGVTDEWGEGPPRKAKAFWPSAMRLLGLFA
+PERTGLILVSLMVLVAVVLNVWAPHVLGQAMDVIFGGLISRDMPAGLTREQVIEGLRGQG
+QGQAADMLSGMAFVPGQGIDFAELARLILIVLGMYVVAQLFMWLQGRVLNDLVMRIVFRL
+REDIEAKLNRLPLSYFDTRQRGDLLSRTTNDVDNVQQAMQQAFATLVYSVLTIIGIVGMM
+FWLSWQLALIALIALPVAGVMVGVIGSKSQKLFTAQWRETGRLNGHIEESFTGHELVTVF
+GRQADMAERFDERNEAMYEASFKAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMT
+LGAVTAFIQYSREFNQPLGQVAGMSNMLISGVASAERIFELLDEDEQDSDAEVARRASDD
+DVAEPADASVRETGASADDDVAHLPQPVAGRVEFEHVRFSYTEAKPLITDLNLVAEPGQT
+IAIVGPTGAGKTTLVNLIMRFYEVDGGRILVDGVDTRTVSREELRSHTGMVLQDAVLFGG
+TIRENIRYGRQDATDEEVVAAAKATFVDRFVHTLPEGYDTVIEQDASNVSAGERQLITIA
+RAFLAQPSLLILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVME
+HGDIVEQGNHAELLAARGAYHRLYMSQFKGGEDDGGGAASGEDAR
+>PROKKA_00547
+MSEQLTDQEIVELQESGATDEWGGGPGRKAKAFWPSAKRLLGLFRTEKAGLALVAAMVLV
+AVVFNVWAPHVLGRAMDVLFGGVISKGMPAGVSREQVIEGLRGQGQGQAADMLSGMDFTP
+GQGIDFDALARLILTVLGMYVVAQGFMWLQGRVLNDVVMRIVFRLREQIEAKLNRLPLSH
+FDTRQRGDLLSRATNDVDNVQQAMQQAFATLVYSVLTIFGIVGMMFWLSWELALIALIAL
+PVAGVVVGVVGKKSQALFTAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAERFDERND
+AMYEASFKAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN
+QPLGQVAGMSNMLISGVASAERIFELLDEPEEEPDDVVAARADDDVAHLPQPVAGRVEFE
+HVRFSYTEAKPLITDLNLVAEPGQTIAIVGPTGAGKTTLVNLIMRFYEVDGGRILLDGVD
+TRRVPRQELRAATGMVLQDAVLFGGTIRENIRYGRLEATDEEVLAAAKATYVDRFVHTLP
+DGYDTVIEQDASNISAGERQLITIARAFLAQPSLLILDEATSSVDTRTEVLVQQAMAALR
+NDRTSFVIAHRLSTIRDADVILVMEHGDIVEQGSHEELLAARGAYHRLYTSQFRGGEDEH
+HDDGAPASR
+>PROKKA_02085
+MSEHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLAVVAVMVLV
+AVVFNVWAPRVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTP
+GEGIDFTELGRLILIVLGMYLVAQTFMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSY
+FDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMMFWLSWQLALIALVAL
+PVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNE
+ELYEAAFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN
+QPLGQIAGMSNMLISGVASAERIFELLDEPEETPDGTPARTPDGTFVWETAPSESAFVRE
+TAPSAIPGPDGVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNFVAEPGQTVAIVGPTGA
+GKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRGELRAATGMVLQDAVLFGGTIRENIRYG
+RLDATDEEVVAAAKATYVDRFVHTLPDGYDTVIEQDAANVSAGERQLITIARAFLAQPSL
+LILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVMEDGDIVEQGS
+HDQLLAARGAYFRLYRSQFQGGEQAEEQDDDGAPAAREDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001686.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001686.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6ffb8342852e44a39ce56a76cdc20f4686b81491
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001686.fa
@@ -0,0 +1,41 @@
+>PROKKA_02152
+MQCPHFDVGECRSCPLMGVPYARQLADKQAAVLAALADALDADTVVAEPFASAEAGFRNK
+AKLVVTGSAAAPRLGILDPRQHPRHHDGAGVDLRDCGLYEAGMEGVFEACAAAVTAAGLE
+PYDVAARTGELKNVIVTLSPDREAMVRFVLRSADRLDALRAAVPGLLDDLAARGTPAAVV
+SANLLPEHVALPEGDEEIVLAGGPTLRMELNGIGLRLRPQGFFQTNTAVTEGLYATAAAW
+VAEGGVPASAWDLYCGVGGFAFHLARAGVRDVWGMESSAEAVAAARETAAELGLADRARF
+SAGDATSALSFEKRRAPEALSFEKRRSRPDAVVVNPPRRGIGAELADALEDSGAPTVLYS
+SCNPTTLAQDLARMPSYRVARVQLFDMFPQTLHAEVLTLLTRR
+>PROKKA_01865
+MQCPHFDVGECRSCPLMGVPYARQLADKQAAVLAALADAVDADTVVAEPFASAEAGFRNK
+AKLVVTGSAAAPRLGILDPRQHPRHHDGAGVDLRDCGLYEAGMEGVFDACAAAVTAAGLE
+PYDVAARTGELKNVIVTLSPDREAMVRFVLRSADRLDALRAAVPGLLDDLAARGTPAAVV
+SANLLPEHVALPEGDEEIVLAGGPTLRMELNGIGLRLRPQGFFQTNTAVTEGLYATAAAW
+VAEGGVPASAWDLYCGVGGFAFHLARAGVRDVWGMESSAEAVAAARETAAELGLADRARF
+SDGDATSALSFEKRRAPEALSSKKRRPRPDAVVVNPPRRGIGAELADALEDSGVPTVLYS
+SCNPATLAQDLARMPSYRVARVQVFDMFPQTRHAEVLTLLTRR
+>PROKKA_00610
+MQCHHYDAGRCRSCALMGVPYGVQLTDKDAAVCARLDAAVPAEAWLPPQASAESGFRNKA
+KLVATGTAAAPRLGILDPEQHPRHHDGTGHDLRDCGLYEDGMEAAFHAIAETIPAAGLEP
+YDVAARTGELKSVIVTLSPDRELMVRFVLRSAARLDALRAAVPGLRSALAGLGTPAAVVT
+ANLHPEHVALPEGPDEVHLAGDPTLRMELNGIGLRLRPQGFFQTNTDVTRRLYATAAAWL
+AEAAAADGTPVHSAWDLYCGVGGFAFHLARPVAEGGAGVAEVWGLETSEDAVAAARDTAA
+ELGLAGAVRFTAGDATRALSPGRREPSEALSSGKREAWDALSSGSREPSDAGAHPDDDAA
+PAAMPDAVVVNPPRRGIGPELAARLQDSGVPHVLYSSCNAASLAKDLAAMPAYRARRAQV
+FDMFPQTGHAETLVLLSRA
+>PROKKA_00534
+MQCPHFDAGECRSCALMGVPYGAQLADKDAAVRARLAEATDARTRWEAPAASAESGFRNK
+AKLVVTGTAAAPRLGILDPRQHPRHHDGTGVDLRDCGLYEDGMEAAFHAIAGAVTAAGLE
+PYDVAARTGELKNVIVTRSPDRELMVRFVLRSADRLEALRPEVPALREALAALGTPAAVV
+TANLHPEHVALPEGPEEVHLAGDATLRMELNGIGLRLRPQGFFQTNTDITQRLYATAAAW
+LAEAAAEGGTPVERAWDLYCGVGGFAFHLARPVAEGGAGVAEAWGLEVSAEAIEAAREAA
+AELGVAERVRFTAGDATTALAAPGGTRPDAVVVNPPRRGIGAELAGRFEESGVPFVLYSS
+CNAATLATDLTAMPSYRVARAQVFDMFPQTGHAETLVLLARR
+>PROKKA_02095
+MQCPHFDVGECRSCPLMGVPYARQLADKQAAVLAALADAVDADTVVAEPFASAEAGFRNK
+AKLVVTGSAAAPRLGILDPRQHPRHHDGAGVDLRDCGLYEAGMEGVFDACAAAVTAAGLE
+PYDVAARTGELKNVIVTLSPDREAMVRFVLRSADRLDALRAAVPGLLDDLAARGTPAAVV
+SANLLPEHVALPEGDEEIVLAGGPTLTMRLNGVGLRLRPQGFFQTNTAVTEGLYATAAAW
+VAEAGLPAAAWDLYCGVGGFAFHLARAGVRDVWGMESSAEAVAAARETAAELGLADRARF
+SAGDATSALSFEKRRAPEALSSKKRRPRPDAVVVNPPRRGIGAELADALEDSGVPTVLYS
+SCNPATLAQDLARMPSYRVARVQVFDMFPQTRHAEVLTLLTRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001688.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001688.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a4b5828cbb86c4cc54de7c325674e36f49dd005
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001688.fa
@@ -0,0 +1,50 @@
+>PROKKA_02157
+MEVLLALSPILLTLVLLLTRLPAWVAPAAGTAVAVLLALTAFGVAPGDLGGAIGAGVPTL
+LEILAIIAGGITLSRVMEYSGGHARLAAWLSAGNGPTIATALLMVHGVIPFLETVTGFGV
+SLIVGVPLLLGLGYTAFRSALISVLALTIGPWGSMAPGTLMGARLFGLDFREIGVTAAVF
+NLPACLVAGVATVLLLRGARGMRVDVGPARTLPWLGVAVLSGVAQWALILGANLVVGTAP
+AGAVATFVLTVAWLLVIRGGRLLPGPGRDVVPYLTLMAGTVLGTTVKGAFGLEGAAALVG
+TPALWAFVAVGVGVQLLHLDAAARRRVPREAGKLWVGTAIPNALYVAFGLILSAGGVSQA
+LAGALSGMGESYLVAMPFLGAFAGFITASNTGAMALIGPLQMDTGAALGVPPPWSNGLHN
+AAAGWGIVAGPARIQVAHGMAAGAQSPHMPGWAVTRRNLFVVLLPAMLAGILGMAVMGWF
+LLPR
+>PROKKA_01870
+MEVLLALSPILLTLVLLLTRLPAWVAPAAGTAVAVLLALTVFGVAPGDLGGAVGAGVPTL
+LEILAIIAGGITLSRVMEYSGGHARLAAWLSAGNGPTIATALLMVHGVIPFLETVTGFGV
+SLIVGVPLLLGLGYTAFRSALISVLALTIGPWGSMAPGTLMGARLFGLDFREIGVTAAVF
+NLPACLVAGVATVLLLRGARGMRVDVGPARTLPWLGVAVLSGVAQWALILGANLVVGTAP
+AGAVATFVLTVAWLLVIRGGRLLPGPGRDVVPYLTLMAGTVLGTTVKGAFGLEGAAALVG
+TPALWAFVAVGVGVQLLHLDAAARRRVPREAGKLWVGTAIPNALYVAFGLILSAGGVSQA
+LAGALSGMGESYLVAMPFLGAFAGFITASNTGAMALIGPLQMDTGAALGVPPPWSNGLHN
+AAAGWGIVAGPARIQVAHGMAAGAQSPQMPGWAVTRRNLFVVLLPAMLAGILGMAVMGWF
+LLPR
+>PROKKA_00601
+MQVLLALTPILLTLALLLTRLPAWVAPAAGGVLAAALAPTVFGVDPGVLAAEVGRGVPTV
+VEILAIIAGGITLSRVMEHSGAHARLALWLSAGNGPTLATALLMVHGIIPFLETVTGFGV
+SLIVGVPLLLGLGFTAFRSALLAVLALTIGPWGSMAPGTLMGARLYDLDFQAVGVTAALF
+NLPASLVAGAATVLLLRGAQGMRGDGEPARTVPWLAVGLLSGAAQWALILGANLSVGTAP
+AGAVGTFVLTVAWLLVIRRGRLTPGPGRDVVPYVTLMAGTVFGTTVEDALGLTGVLSVVG
+TPALWSFVAVGAGVALLGLGPHARRTVPGEAARLWVGTAIPNALYVAFGLTLSAGGVSQA
+LAGALSGMGPAYLAAIPVIGAFSGFVTASNTGAMALMGPLQMDTGAALGVPPTWTNGLHN
+AAAGWGIIAGPARIQVAHAMAVGAQTPEMPGWAVSRRALLAVLLPAMVVGIALMSLLGLA
+VLPRV
+>PROKKA_00523
+MQVLLALAPILLTLGLLMTRLPAWAAPAAGSVAAVVLGLTVFGVDPAVLGAAVGHGVPTV
+LEILAIIAGGITLSRVMEHSGAHARLGGWLSAGNGPTLATALLMVHGVIPFLETVTGFGV
+SLVVGVPLLLGLGFTAYRAALLSVLSLTIGVWGSMAPGTLMGARLAGLDVQEVGVTAAVF
+NLPASLVAGVATVLAVRGARGLRDDSAPARLAPWLGVALASGTAQWALILGANLLVGTAP
+AGAVATFALTLAWLLVIRRGRLTPGPGRDVVPYVTLMAGTVLGTTAEDALGLTGPLSVVG
+TPALWSFVAVGVGLRLLDLDAAARRTVPRESLRLWRGTAVPNALYVAFGLVLSAGGASPA
+LAGALSGLGESYLAAMPFIGAFAGFVTASNTGAMALVGPLQMDTGAALGVPPAWSNGLHN
+AAAGWGIIAGPARIQVAHGMAAPAQTPDMPGRAVSPRGLVAALLPASLAGVAGMSLMGWL
+LLPR
+>PROKKA_02100
+MEVLLALSPILLTLVLLLTRLPAWVAPAAGTAVAVLLALTAFGVAPGDLGGAIGAGVPTL
+LEILAIIAGGITLSRVMEYSGGHARLAAWLSAGNGPTIATALLMVHGVIPFLETVTGFGV
+SLIVGVPLLLGLGYTAFRSALISVLALTIGPWGSMAPGTLMGARLFGLDFREIGVTAAVF
+NLPACLVAGVATVLLLRGARGMRVDVGPARTLPWLGVAVLSGVAQWALILGANLVVGTAP
+AGAVATFVLTVAWLLVIRGGRLLPGPGRDVVPYLTLMAGTVLGTTVKGAFGLEGAAALVG
+TPALWAFVAVGVGVQLLHLDAAARRRVPREAGKLWVGTAIPNALYVAFGLILSAGGVSQA
+LAGALSGMGESYLVAMPFLGAFAGFITASNTGAMALIGPLQMDTGAALGVPPPWSNGLHN
+AAAGWGIVAGPARIQVAHGMAAGAQSPQMPGWAVTRRNLFVVLLPAMLAGILGMAVMGWF
+LLPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001689.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001689.fa
new file mode 100644
index 0000000000000000000000000000000000000000..497d185a3a010c11f43398c8aab294004496a974
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001689.fa
@@ -0,0 +1,40 @@
+>PROKKA_02158
+MTQPSHPDDVTRARLIPPVPVAVAPMAGGPSTPELVAAVVGAGGGGFLAGGMRTAAQMRA
+QVDALRALLGAERPDRWGVNLFVPDAVNTAIPAAARTEAARSARAAAVAAYRAGLTADGA
+ADLPAVADVVPDPDAERADFEAMLVAAEEQAWPLVSFTFGLPAADVFARLAAAGVPAGAT
+VTDAAEARAALEHGAAFLVVQGHRAGGHRGTSDPAAEPTRAELPTVLAAVRDVVGTGAAS
+AAPVVAAGGVGTAEDVRALLTAGADAVSAGTAFLLTPEAGTSAAHRAAVAACAAGTRFSA
+DDGRARTALTRAYTGRWARSLATAFMAEHPDAPAAYPEVNVLTKGLRAAAAAVGDLERVH
+LWAGTEAHRVREAPAADVLASLTP
+>PROKKA_01871
+MTQPSHPDDVTRARLIPPVPVAVAPMAGGPSTPELVAAVVGAGGGGFLAGGMRTAAQMRA
+QVDALRALLGAEGPDRWGVNLFVPDAVNTAIPDAARTEAARSARAAAVAAYRADLTADGA
+ADLPTAADVVPDPDAERADFDALLTAAEEQAWPLVSFTFGLPAADVFARLAAAGIPAGAT
+VTDATEARAALEHGAAFLVVQGHRAGGHRGTSDPAAEPPRAELPAVLPAVRDVVGTGATS
+AVPVVAAGGVGTAEDVRALLTAGADAVSAGTAFLLTPEAGTSAAHRAAVAACAAGTRFSA
+DDGRARTGLTRAYTGRWARSLATAFMAEHPDAPAAYPEVNVLTKGLRAAAAAAGDLERVH
+LWAGTEAHRVREAPAVDVLASLTP
+>PROKKA_00600
+MSAAQLPDDVVRARLIPPARVLAAPMAGGPSTPELVAAVVRAGGSGFLAGGMRTAAQVRE
+QVDALRGLLGGGDGSVDGSDAARRWGVNLFVPDAVNTAIPAADRTERARAERRAAVAAYR
+ERLAAEGERAAGGAAAEGAGGAPTLPSPDDVTPDPARERAEFAAMLTAAEEQAWPLVSFT
+FGLPEPAVFARLAAAGIPAGVTVTDADEARSARAHGAAFLVVQGHRAGGHRGTLDPAADP
+VERELPSVLAQVRAVVGTRVPVVAAGGVGAAAHVRSLLAAGADAVAAGTAFLLAAEAGTS
+VAHRAGIRRCAAGEGFVGPDGAARTVLTRAYTGRWARTLATDFAAAHPDAPAAYPELNAL
+TTGLRAAAATAGDLERVHLWAGTQAHTAREAGAADVVAGLTP
+>PROKKA_00522
+MSSTTVPSVPAPVPAPLDPPVPVLAAPMAGGPSTPELAAAVIRAGGGAFLAGGMRSAAQV
+REQVDGLRALLTAPEEAGRFGVNLFVPDAVNTAVAASARGGAARIARAQAVASYRERLAP
+LAADLGAELPSVLTVTPDPDAERAAFEDMLAAAEEQSWPAVSFTFGLPAPDVFARLDAAG
+IPAGVTVTSPAEAMAAVASGARFLVVQGPKAGGHRATLDPQGRPGITDLRTLVFAVRHAL
+GPAAVPLVAAGGITDGAQVRPLLEAGAVAVAAGTAFLLTPEAGTSAAHRTALRQASAGVA
+FAHPDDGAASTALTRAYTGRWARGLVTPFMDEHHDAPAAYPEVNGLTGPLRRAAAEEGDL
+EHVHLWAGTGAHRVEEVGAAEVLASLAPRAEP
+>PROKKA_02101
+MTQPSHPDDVTRARLIPPVPVAVAPMAGGPSTPELVAAVVGAGGGGFLAGGMRTAAQMRA
+QVDALRALLGAEGPDRWGVNLFVPDAVNTAIPDAARTEAARSARTAAVAAYRAGLTADGA
+AGLPTAADVVPDPDAERADFDALLTAAEEQAWPLVSFTFGLPAADVFARLAAAGIPAGAT
+VTDATEARAALDHGAAFLVVQGHRAGGHRGTSDPAAEPTRAEMPTVLAAVRDVVGTGAAS
+AAPVVAAGGVGTAEDVRALLTAGADAVSAGTAFLLTPEAGTSAAHRAAVAACAAGTRFSA
+DDGRARTGLTRAYTGRWARSLATAFMAEHPDAPAAYPEVNVLTKGLRAAAAAAGDLERVH
+LWAGTEAHRVREAPAADVLASLAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001694.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001694.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab8746dbcbf28327486545c79849922bb88be258
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001694.fa
@@ -0,0 +1,60 @@
+>PROKKA_02167
+MTSLLRILRFAPQLNRLYLGIAVSSVLAAVLALATPFLIGAATDRIVAAVAGETDVAEAV
+TAVTWLAVAFLAVEVATTLVVSVGGYWGDVMAARMRTILSTRYFEQLLHLPQRYFDTAIT
+GRVVNRLNRTINELTQFLQFFANNAFTMLITTAAVLVITAFYWWPLAILLAVVFPVYMWL
+TARTSTKWQVWEGEKNTEVDIASGRFAEVVSQMSVVRAYNRQDHELSGFRDRFLRTVGIT
+RQQSRFWHGMDAGRRLALNVAFGAMYLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSM
+SFLVDSAQRAVAGSKDYFEVLAEERERAGGAALAVAGASAESAGADAPRVPAEPRADVVP
+GAPDVPADVPAVRFDEVSFAYDADASRPVLDRVSFDIPRGARVALVGESGGGKSTIAHLL
+LGLYPVTSGRIEVFGQDVAGLDLAVLRGRIATVFQEPSLFSGTVRENIAYADPDASDERV
+RAAAEAAYAHRFVEAFDDGYEQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEATSA
+LDTKSERLVQAALEELMVGRSSLIVAHRLSTIASVDRIVTLRGGQVQEIGTPAELAESGG
+IYAQLLELQRAGTQEARKMLKEYGLSG
+>PROKKA_01881
+MTSLLRILRFAPQLHRLYLGIAVSSVLAAVLALATPFLIGAATDRIVAAVAGETDVAEAV
+TAVTWLAVAFLAVEVATTLVVSVGGYWGDVMAARMRTILSTRYFEQLLHLPQRYFDTAIT
+GRVVNRLNRTINEITQFLQFFANNAFTMLVTTAAMLVITAFYWWPLAILLAVVFPVYMWL
+TARTSAKWQVWEGEKNTEVDVASGRFAEVVSQMSVVRAYNRQDHELTGFRDRFLRTVEIT
+RQQSRFWHGMDAGRRLALNVAFGAMYLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSM
+SFLVDSAQRAVAGSKDYFEVLAEERERAGGAALAAASASAESAGADAPRVPAEPRADVVP
+GAPDVPADVPAVRFDEVSFAYDADASRPVLDRVSFDIPRGARVALVGESGGGKSTIAHLL
+LGLYPVTSGRIEVFGQDVAGLDLAVLRGRIATVFQEPSLFSGTVRENIAYADPDASDERV
+RAAAEAAYAHRFVEAFDDGYEQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEATSA
+LDTKSERLVQAALEELMVGRSSLIVAHRLSTIASVDRIVTLRGGQVQEIGTPAELAESGG
+IYAQLLELQRAGTQEARKMLKEYGLSG
+>PROKKA_00585
+MLAAVLTLATPFLIGAATDRIVAAIAGETTVEDAVVAVTWLAVAFLAVEVTTTLVVSVGG
+YWGDVMAARMRTILSTRYFDQLLHLPQRYFDTAITGRVTNRLNRTINELTQFLQFFANNA
+FTMLITTTAVLVITAFYWWPLAILLAIVFPVYMWLTAKTSAKWQVWEGEKNIEVDMASGR
+FAEVVSQMSVVRAYNRQDHELAGFRERFTRTVGITRKQSRFWHGMDAWRRLALNVVFGAM
+YLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSMSFLVDSAQRAVAGSRDYFEVLAEER
+ERAGGAGPQGRGAAAVAAGQPRADDDGGTDVRWGGAAPSRPAQPRADVVPGDGTGGMPAG
+PSADVVPAVRFDEVSFAYDPDASRPVLDRVSFEIPQGQRVALVGESGGGKSTIAHLLMGL
+YPVTGGRIEVFGQDVAELDLAELRERIAAVFQEPSLFSGTVRENIAYADPAASDERVRAA
+AEAAYAHRFVEAFDDGYEQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEATSALDT
+KSERLVQGALEELMVGRSSLIVAHRLSTIASVDRIVTLRGGRVQEVGTPAELAESGGIYA
+QLLRLQKAGTKEARKMLKEYGLSG
+>PROKKA_00512
+MRALLRILRFAPQLNPLYLGIAVCSVLAAALSLATPFLIGAATNRIVDAIAGRSTLDDAV
+AAVTWLALAFLAVEVATTAVVSVGGYWGDVMAARMRAALSGRYYDHLLHLPQRYFDTAIT
+GRIVNRLNRSITELTQFLQFFSNNAFTMLITTAAVLVITAFYWWPLAVLLAVVFPVYMWL
+TAKTSAKWQGWEGEKNTEVDIASGRFAETVAQMNVVRAYNRQDHELAGFTERFRRTVGIT
+RKQSRFWHGMDAGRRLALNLVFGVMYLIVFVRTARGLFSVGDMVILLQLMNMARQPIFSM
+SYLVDSAQRAVAGSKDYFGVLAEERERSGGAALPAGLGSAEAPTTTTATGVVVRDRAEAP
+TGAPVRAGADVPAVRFADVTFAYDPEAERPVLDGVTFDIPQGAKVALVGESGGGKSTLAH
+LLMGLYPVGSGRVEVFGRDVAGLDLAVLRGQVAAVFQEPFLFSGTIRENIAYADPDASGE
+RVRAAAKAAFADGFVEEFEHGCEQLIGERGLRLSGGQKQRIAVARAVLKDAPVLVLDEAT
+SALDTKSERLVQSALDDLMVGRSSLIVAHRLSTIASVDRIVTLRGGRVQEVGTPAELAQS
+GGIYAQLLRLQKAGTKEARKLLKEYGLSG
+>PROKKA_02112
+MTSLLRILRFAPQLHRLYLGIAVSSVLAAVLALATPFLIGAATDRIVAAIAGETGVAEAV
+TAVTWLAVAFLAVEVATTLVVSVGGYWGDVMAARMRTILSTRYFEQLLHLPQRYFDTAIT
+GRVVNRLNRTINELTQFLQFFANNAFTMLITTAAVLVITAFYWWPLAVLLAVVFPVYMWL
+TARTSAKWQVWEGEKNTEVDIASGRFAEVVSQMGVVRAYNRQEQELSGFRDRFLRTVGIT
+RQQSRFWHGMDAGRRLALNAAFGAMYLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSM
+SFLVDSAQRAVAGSKDYFEVLAEERERAGGAVLAVASADAPRVPAEPRADVVAGAPDVPA
+DVPAVRFDEVSFAYDADASRPVLDRVSFDIPRGAKVALVGESGGGKSTIAHLLLGLYPVT
+SGRIEVFGQDIAGLDLAALRGRIATVFQEPSLFSGTVRENIAYADADASDERVRAAAQAA
+YAHRFVAAFDDGYDQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEATSALDTKSER
+LVQAALDELMVGRSSLIVAHRLSTIASVDRIVTLRAGRVEEVGSPAELAESGGIYAQLLE
+LQRAGTQEARKMLKEYGLSG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001695.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001695.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac4ba4bcd229c38926b351541f5f5c2f01cb3803
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001695.fa
@@ -0,0 +1,31 @@
+>PROKKA_02169
+MARTWDGSYPRSVTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLTVCFVADVA
+LLVLGAGGVGVVAERWPWLVPALTVAGVVYLLGFAAGALRSAWRGDRTLSTAAADVEGTG
+HGPDRIDLAVLTGELPLIDPVTGRLAEREPAGAGVGHHDDGAPGFGAPSGGGSVTVRQRV
+QPRRVALDRPQTPLPRIILLALSVSLVNPHAILDTVVMMGTFAQTFGAAKWAYVGGAVAA
+SLVWFTALGWGGTKLAPSMDSARTWRIVDAVVGVLMLGIAVKVGLTLL
+>PROKKA_01883
+MARTWGDSYPRSVTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLTVCFVADVA
+LLVLGAGGVGVVAERWPWLVPALTVAGVVYLLAFAVGALRSAWRGDRTLTTAAADAAGTG
+HGPDRIDLAVLTGELPLIDPATGRLAEREPAGAGVGQHDDGAPGVGAPSGGGSVAARQRV
+QPRRVALDRPQTPLPRIILLALSVSLVNPHAILDTVVMMGTFAQTFGAAKWTYVGGAVAA
+SLVWFTALGWGGTKLAPSMDSARTWRIVDAVVGVLMLGIAVKVGLTLL
+>PROKKA_00583
+MTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLIVCFLGDVALLALGAAGIGVV
+AERWPWLVTALTVAGVVYLVWFAAGALRSAVRGQRTLAAAAEAEGPAVGLTDGEIAALTG
+ELPLIDPATGRLSADFTGRTAEGRAVPVGAGVGMGRGHDPLGDESRTVGGIPVGNPRLCG
+TRPGERGADGRSGGVAVKQRVQPRRVVLSAPQTPLPRIVLLALSVSFLNPHAVLDTVVMM
+GTFAQTYGPGKWVYVGGAVAASLVWFTALGWGGTRLAPYMNTPRTWRIVDAAVGVLMLVI
+AAKVGLTLL
+>PROKKA_00509
+MTVFSAGFLTYLALIVAIGAQTLFLLRQVVRGDRAWTAIGVCFLSDIVLLLAGAAGVGAA
+AERAPWLVPALTVAGVAYLVWFGVSALRSAHRGDRTLAGAAAEVEDDAWAPTAEEVAAMT
+GSLPVVAAGPDAGADAATAPAGTGGGVALRTRPVSTTAPASAAPRPALTPLPRLVLLCLS
+VSLLNPHAILDAVVMMGTFAQGYGADKWLYVAGAVASSALWFLVLGWGGAKLAPLMNTPR
+TWRIVDGAVGVVVLGIAGKVALTLF
+>PROKKA_02114
+MARTWDGSYPRSVTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLTVCFVADVA
+LLVLGVGGVGVVAERWPWLVPALTVAGVVYLLAFAVGALRSAWRGDRTLTTAAADGAGTG
+HGPDRIDLAVLTGELPLIDPATGRLADREPAGAGVGRHDDGAPGVGAPSGGGSVAVRQRV
+QPRRVALDRPQTPLPRIILLALSVSLVNPHAILDTVVMMGTFAQTFGAAKWVYVGGAVAA
+SLVWFTALGWGGTKLAPSMDSARTWRIVDAVVGVLMLGIAVKVGLTLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001696.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001696.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de851d3b6bdf87ae228c799e3d127a862752efd1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001696.fa
@@ -0,0 +1,33 @@
+>PROKKA_02170
+MATPTLDRMNSDHLRALVAAVDHGTFDAAADSLRISGSAFSQRIKALERQVGQVLLARTV
+PVRPTAAGERMLRLARQTLALEDETLAALGRGDGGRVPLRVALNADSLDTWWEPVLREAA
+TWDDVVLQMQSEDQEHTAVLLRDGAVVAAVTDDPTPVAGCTSTPLGTMRYHAVCASFLLE
+LHRDARGRVDFGSLPIVDYGPRDGLQHTVLRRVTRGRPVADPPTHLVPSVHAYLRAVELG
+LGWGMLPSVQIPPGVLEGRHPDLETIPALGAADVHLHWQRWTAGTAALDRLTDAVLRAAP
+SAGDTAD
+>PROKKA_01884
+MATPTLDRMNSDHLRALVAAVDHGTFDAAADSLRISGSAFSQRIKALERQVGQVLLARTV
+PVRPTAAGERMLRLARQTLVLEDETLAALGRGDGGRVPLRVALNADSLDTWWEPVLREAA
+TWDDVVLQMQSEDQEHTAVLLRDGAVVAAVTDDPTPVAGCTSTPLGTMRYHAVCASFLLE
+LHRDARGRVDFGTLPIVDYGPRDGLQHTVLRRVTRGRPVADPPTHLVPSVHAYLRAVELG
+LGWGMLPSVQIPPGVLEGRHPDLEPIPALGAADVHLHWQRWTAGTAALDRLTDAVLRAAP
+SAGDTAD
+>PROKKA_00582
+MNSDHLRALVSAVDHGTFDAAADALRISGSAFSQRVKALERQVGQVLLARTVPVRPTPAG
+ERMLRLARHTLALEEEALASLGRGDGGRVPVRVAINADSLDTWWELVLREAATWDDVVLQ
+LRTEDQEHTAALLRDGTVVAAVTDDPTPVSGCTSTPLGTMRYHAVCASFLLEMHRDERGR
+LDLATLPRVDYGLRDGLQRTVLRRAARGRAAFDPPHHLVPSVQSYLRAVELGLGWGMLPS
+AQLPPGVLEGRHPDLEPVPSLGTVDLTLHWQRWSAGTAALDRLTDAVLRAAPSVADAAD
+>PROKKA_00508
+MNSDHLRALAAAVDEGTFDAAAAWLGISGSALSQRIKALEGQTGQVLLTRTVPVRPTEAG
+ERMLRLARQTLPLEEEALAALGRGTGRRAPLRVGVNADSLETWWTPVLREAATWDDVVLH
+LHAEDQGHTPELLRQGTVVAVVTDDPTPVTGCTVTRIGTMRYHAVAASFLLDLHRDAHGR
+VDVATMPVVDYGPRDGLQRTMLERAARGRVSVPRPPHHLVPSVGAYASAVGMGLGWGMLP
+TGQVPPELAAGSHPDLELVPELGTAEVPLYWQRWSAGTPALDRLTAAVTAAAPAG
+>PROKKA_02115
+MTTPTLDRMNSDHLRALVAAVDHGTFDAAADSLRISGSAFSQRIKALERQVGQVLLARTV
+PVRPTAAGERLLRLARQTLALEDEALAALGRGDGGRVPLRVALNADSLDTWWEPVLREAA
+TWDDVVLQMQSEDQEHTAVLLRDGAVVAAVTDDPTPVAGCTSTPLGTMRYHAVCASFLLE
+LHRDARGRVDFGSLPIVDYGPRDGLQHTVLRRVTRGRPVADPPTHLVPSVHAYLRAVELG
+LGWGMLPSVQIPPGVLEGRHPDLEPIPALGAADVHLHWQRWTAGTAALDRLTDAVLRAAP
+SAGDTAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001699.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001699.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2425674b5fa18fbfe8460eba37886399b647ff18
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001699.fa
@@ -0,0 +1,35 @@
+>PROKKA_02176
+MPSTALASPARVRAGVLMGALPAALLLAALVAGVALGARTVPATTALDTLGAILTGHPVP
+EGIEAAAVASRVPRVVTGALVGAALAVAGAALQGATRNPLGDPGLLGLSAGAGLAVAAGM
+ALGVAGSTFGVLALAAVGTLVAAALGYAVAAAATRSGRTPGAPSPMALVLAGAALTAGAT
+AGTTALLVLSPTVQDRLRFWAVGTVARADLGEALALAPVIAVGLLAAVAVAPGLDALALG
+DDLAHGLGGRPERVRAVLLGAVVLLTAAAVALAGPVGFVGLLVPHALRRLRPPSTRALMV
+GCALWGAVLVILADLAGRLVVAPGEIHLGVTTVLLGVPVLLALLRRPGVAA
+>PROKKA_01890
+MPSTALASPARVRAGVLMGALPAALLLAALVAGVALGARTVPATTALDTLGAVLTGHPVP
+EGIEAAAVASRVPRVVTGALVGAALAVAGAALQGATRNPLGDPGLLGLSAGAGLAVAAGM
+ALGVAGSTFGVLALAAVGTLVAAALGYAVAAAATRRGRTTPGAPSPMALVLAGAAITAGA
+TAGTTALLVLSPTVQDRLRFWAVGTVARADLGEALALAPVIAVGLLAAVAVAPGLDALAL
+GDDLAHGLGGRPERVRAVLLGAVVLLTAAAVALAGPVGFVGLLVPHALRRLRPPSTRALM
+AGCALWGAVLVILADLAGRLVVAPGEIHLGVTTVLLGVPVLLALLRRPGVAA
+>PROKKA_00576
+MPRALLLIAPAVLAVLAALASLALGARPVPVDAAVGALTEAALHGPAAVTGMDGAAVLSR
+VPRTLAAILVGAGLAVAGAALQGATRNPLGDPGLLGLTAGAVLAFALGIALGVAGSLPAV
+MALAILGTLAAAALVTAVAAGAARVSGVPGPPSPLSLVLAGAATTAGATAVTSALVVLHP
+AVRDRLRLWTVGSVARADLGDALWLAPVVLAAVAAVVVLGPGMDALALGTDLAHGLGARP
+ERVRALLLAAAVVLTAAAVALAGTVGFLGLVIPHAVRRLRPPDARTLVLACALWGAVLVL
+VADTLGRLVIAPAEVHLGVTTAVLGVPVLLALLRRRGVAA
+>PROKKA_00503
+MPSSPTRGALLFGLLPLALLLTAGLAALALGARPVPLTTTATTLQAMLAGEGVPAGVDAA
+AVASRVPRTLTAALVGAALAVAGAALQGATRNPLGDPGLLGLSAGASLATAIGLALGVSG
+STFWVLALAAAGTLAAALLVYAVAAAASRGAGAGGAPTPIGLVLAGAAVTAGAGAVTTAL
+LVLSPVVRDRFRFWAVGTVARADLGEAALLTPVIGLGIVLALAAARGLDALALGDDLAHG
+LGARPGRTRALLLAAVVLLTAAAVALAGPVGFVGLVVPHALRRLRPGGTRTLLIGSALWG
+AVLLVAADLLGRLVIAPAEIHLGVTTVLLGVPVLLVLLRRTGLGS
+>PROKKA_02121
+MPSTALASPARVRAGVLMGALPAALLLAALVAGVALGARTVPATTALDTLGAVLTGHPVP
+EGIEAAAVASRVPRVVTGALVGAALAVAGAALQGATRNPLGDPGLLGLSAGAGLAVAAGM
+ALGVAGSTFGVLALAAVGTLVAAALGYAVAAAATRRGRTPGAPSPMALVLAGAAITAGAT
+AGTTALLVLSPTVQDRLRFWAVGTVARADLGEALALAPVIAVGLLAAVAVAPGLDALALG
+DDLAHGLGGRPERVRAVLLGAVVLLTAAAVALAGPVGFVGLLVPHALRRLRPPSTRALMV
+GCALWGAVLVILADLAGRLVVAPGEIHLGVTTVLLGVPVLLALLRRPGVAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001700.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001700.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51ea37aa70d783a62cf9c7de06c7c3d569cce61b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001700.fa
@@ -0,0 +1,36 @@
+>PROKKA_02177
+MSLQCTAPDDVVARLRRADRRRLGGACAGLAVAVLVLALLRVVWGTYQVTVPDLVRILGG
+ETIPGASFIVLEEKLPRAVAAVLTGAALGAAGALYRRTLRNPLASPDILGVTQGAAAAVV
+LGMLATAGQTGGGSDLMRAATALIGGLAAVVAVFATARSVGGERFVVAGIAVAAAGQAVV
+AGAMLSLAQHDLQSATVWIAGSLNGVTWGRIALLAGVLVVALPLAGVLHARLAPADVGPD
+LAHALGARPRPTSAAALGLGAVLAAVATAVVGPLAFVALLATPVARGLTRGLPSLPAAAL
+TGAALVLLADLVAGEAVPLLTGAALPTGVLTGAAGAPLMLWLLLCQGRTPGGVRSA
+>PROKKA_01891
+MNLQHTAPDDVVARLRRSDRRRLGRACAGLAVAVLVLALLRVVWGTYQVTVPDLVRILGG
+ETIPGASFIVLEEKLPRAVAAVLTGAALGAAGALYRRTLRNPLASPDILGVTQGAAAAVV
+LGMLATAGQTGGGSDLMRAATALIGGLVAVAAVFATARSVGGERFVVAGIAVAAAGQAVV
+AGAMLSLAQHDLQSATVWIAGSLNGVTWGRIALLAGVLAAALPLAGALHTQLAPADVGPD
+LAHALGARARPTSAAALGLGAVLAAVATAVVGPLAFVALLATPVARGLTRGLPSLPAAAL
+TGAALVLLADLVAGEAVPLLTGAALPTGVLTGAAGAPLMLWLLLRQGRTPGGVRPA
+>PROKKA_00575
+MSGRGSATLEHAVARVRAARRRDARRVGTALAVLTAAVLALVLLRLTWGAYMVAVPDLVR
+ILTGTTIPGASFIVTEEKLPRAAAAVLAGAALGAAGALYRRGLGNPLASPDVLGVTSGAA
+AGAVLWQAAATGTGGTTDAARAAAALAGGLIAALAVLLAARGTGGERFVVAGIAVAAGAQ
+AVVAGTMVTLAEHDLQAAALWVSGSLTGVTWGRIGLLAAAVALALPLAAWLHGRLEPADT
+GEDLAHALGARPRRTRPAALLLGAVLAAAATAAVGPLAFVALLATPLARGLAGGRPSLAA
+AALAGAVLVLAADLLAAEAVALLADGTRLPTGVLTGAAGAPLMMTLLIRAGRRGERTA
+>PROKKA_00502
+MSARRETTTPGRRDAAPGGDAPETVRALRRADARRVAGVVLGLAVLTAGLMLLRVTWGTY
+QVTVPDLVRILGGERIAGASFIVWEEKLPRAVAATLTGAALGAAGALYRRTLRNPLASPD
+VLGTTAGAAAGVVLTLTASAGQAGGSSDLARAGAALLGALAAGAAVLLAARSVGGQRFVV
+AGVGVAAAGQAIVSGAMLSLSEHDLASATRWIAGSLNGVTWGRIGLLAAVLALALPAAGW
+LHRRLAPADVGDDLAHALGARPRTTAALALTVGAVLAAAATATVGPLSFVALLATPLALG
+LTRGRPSLPAAALTGAGIVLLADVLGTEALGLIADGAALPTGVLTGAAGAPLMLALLLRA
+GRSSEGTR
+>PROKKA_02122
+MSVQRTASDDVVARLRRSDRRRLGGACTGLAVAVLVLALLRVVWGTYQVTVPDLVRILAG
+ETIPGASFIVLEEKLPRAVAAVLTGAALGAAGALYRRTLRNPLASPDILGVTQGAAATVV
+LGMLATAGQTGGGSDLMRAATALIGGLVAVAAVFATARSVGGERFVVAGIAVAAAGQAVV
+AGAMLSLAQHDLQSATVWIAGSLNGVTWGRIALLAGVLAAALPLAGALHTQLAPADVGPD
+LAHALGARARPTSAAALGLGAVLAAVATAVVGPLAFVALLATPVARGLTRGLPSLPAAAL
+TGAALVLLADLVAGEAVPLLTGAALPTGVLTGAAGAPLMLWLLLRQGRTPGGVRPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001707.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001707.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8144f732a51c2abc5b3c52135751d66aef9a00a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001707.fa
@@ -0,0 +1,20 @@
+>PROKKA_02185
+MTQPTTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLAEEARVRALAAWATTT
+ASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRCVLCDAV
+FVQVDPAAGRPVAVSDEERAAFERVLIPAED
+>PROKKA_01899
+MTQPTTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLAEEARVRALAAWATTT
+ASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRCVLCDAV
+FVQVDPAAGRPVAVSDEERAAFERVLIPAED
+>PROKKA_00565
+MNGQDGGQGRTTTDGATGREAPVPFETEIQVRWSDEDRYGHVNNARLLTLTEEARVRATR
+AWSGVTPGRDVHRVVRAMEVQYEAPVVYGPELTAKVWIARIGTSSYTLRHELWQDGRRCV
+LCDAVFVHVDPETGRSVALAEDERVTLERVLIPAEADAT
+>PROKKA_00490
+MSDSQPRPYEGVLDLRWSDMDLYGHVNNVRILTLTEEARVRALKAWDEGDVGRDVMRVVR
+AMTTEYERPVEYGPELTAKVWVRALGRTSYTLHHELWQEGVRCVTCDAVMVHLDPETGAP
+LPHDDARRARLQAVLVPAEG
+>PROKKA_02130
+MTQPTTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLTEEARVRALAAWATTT
+ASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRCVLCDAV
+FVQVDPAAGRPVAVSDEERAAFERVLIPAED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001708.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001708.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a0c5bfac0290ae97e19f4374dc252c9174717492
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001708.fa
@@ -0,0 +1,30 @@
+>PROKKA_02186
+MEQDPSPDAPAPSADVEALRGTPVSELTQLTPAASGALERLRRDVERFDLEYRSALLQVE
+ARLEVLRDEFTHLHDYNPIEHIVTRVKSPESILRKASARGLSLDLDALRTNVTDIAGARV
+IVSFARDVYRVFRQFTQQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPIHLSTGTIPVTV
+EMQFRTSAMDFWATLEHKINYKFDGGVPPDIATELVAAARVAADLDTRMERLHDQVQETD
+RDDDAAAAWEDDGGPAFEDEPTVEPGEARPGDAPGASTA
+>PROKKA_01900
+MEQDPSPDAPAPSADVEALRGTPVSELTQLTPAASGALERLRRDVERFDLEYRSALLQVE
+ARLEVLRDEFTHLHDYNPIEHIVTRVKSPESILRKASARGLSLDLDALRTNVTDIAGARV
+IVSFARDVYRVFRQFTQQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPIHLSTGTIPVTV
+EMQFRTSAMDFWATLEHKINYKFDGGVPPDIATELVAAARVAADLDTRMERLHDQVQETD
+RDDDAAAAWEDDGGPVFEDEPAAGPGEARPGDDAPGASTV
+>PROKKA_00563
+MEQDRDPEESSQSTAIETLRGTPVSELTHLPPAMAGALDRLRRDVERFDLEYRSALLQVE
+ARLEVLRDEFTHLHDYNPIEHIVTRVKTPESILRKAASRGLSMDLDALRSNVTDIAGARV
+IVSFARDVYEVFRLFTRQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPVHLSTGSIPVTV
+EMQFRTSAMDFWATLEHKINYKFDGAVPPDITTELIAAARVAADLDTRMERLSDQVRQTD
+KDDDAAASWEDDGGPAFEDEGDDDGPDGDAPGTSTG
+>PROKKA_00489
+MPRDVDHPPPADDPAPVERPAPGGRGVTSASTALEALRATPLTDLTQLPGEVADALASLR
+TDFERFDLEYRSALLQVETRLETLQDEFTHLHEYNPIEHIATRVKSPESLLRKAASRGLS
+LDLDALRSGVTDIAGARVIVSFTEDVYRVFRQFTSQPDIRVLEVEDYIRDPKPSGYRSLH
+CLVQVPVHLTTGTVPVTVELQFRTIAMDFWASLEHKINYKFAGHVPPAITTELAAAARVA
+HDLDARMERLHQAVHDAGAGPDEHDDEDDWVGHA
+>PROKKA_02131
+MEQDPSPDAPAPSADVEALRGTPVSELTQLTPAASGALERLRRDVERFDLEYRSALLQVE
+ARLEVLRDEFTHLHDYNPIEHIVTRVKSPESILRKASARGLSLDLDALRTNVTDIAGARV
+IVSFARDVYRVFRQFTQQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPIHLSTGTIQVTV
+EMQFRTSAMDFWATLEHKINYKFDGGVPPDIATELVAAARVAADLDTRMERLHDQVQETD
+RDDDAAAAWEDDGGPAFEDEPAAGPDGTDPGEARPGDDAPGASTV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001709.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001709.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6802491a3a401d4c9b547737108f29714e1f1f6e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001709.fa
@@ -0,0 +1,25 @@
+>PROKKA_02189
+MSIPATEVEARWNAAAEPFTAVVREVRDWDAATPCEGWDALDLLDHVIAGQRDFAARQGR
+EVPLFDGSRQQLATQWAKHAAAMSALAGDEEFIMRPMKTALGEMPVGEALIRFHAFDVIV
+HRWDLARSQGVDARFTDAEIDCVEESLELFGDAAYTPGILGEPVPVADDADRQTRLLGRL
+GRRG
+>PROKKA_01903
+MSIPATEVEARWNAAAEPFTAVVREVRDWDAATPCEGWDALDLLDHVIAGQRDFAARQGR
+EVPLFDGSRQQLATQWAKHAAAMSALAGDEEFIMRPMKTALGEMPVGEALIRFHAFDVIV
+HRWDLARSQGVDARFTDAEIDCVEESLELFGDAAYTPGILGEPVPVADDADRQTRLLGRL
+GRRG
+>PROKKA_00557
+MSIPATEVEARWNEASEPFTAVVRAVRDWDAATPCEGWDALDLLDHVVGAERDFAARQGR
+EVPLFDGSRQQTANQWTKHSAALSALAGDEEFIMKPMHTALGEMTVGEAMIRFHAFDLIV
+HRWDLARSQGVDERFTDAEMDCIEESLDLFGDAAYTPGILAQPVPVADDADRQARLLGRL
+GRRA
+>PROKKA_00484
+MSTQTDVEQYWMDCVEPFTDVVRAVEDWDASTPCKGWSAQDLLDHVVVAERDFAARQGRE
+IPVFDGSRNELWTQWVKHASAVTALAGDETFIMQSLHTATGDMTVGEALLHFHGFDLLVH
+RWDLARSQGRDEQWTDEEMDRIERALDSFGEQAYQPGILADPVPVADDAPRQVRLLGRLG
+RRA
+>PROKKA_02134
+MSIPATEVEARWNAAAEPFTAVVREVRDWDAATPCEGWDALDLLDHVIAGQRDFAARQGR
+EVPLFDGSRQQLATQWAKHAAALSALAGDEEFIMRPMKTALGEMPVGEALIRFHAFDVIV
+HRWDLARSQGVDARFTDAEIDCVEESLELFGDAAYTPGILGEPVPVADDADRQTRLLGRL
+GRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001720.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001720.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0986141a40e2ec844434823258a77122457bfc59
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001720.fa
@@ -0,0 +1,40 @@
+>PROKKA_02208
+MTQTPTAPDRTGATAPDDLALAIPGTTVRGRAARVLPQDRPDTTSWAPRTAESRAAATTP
+GLPGVVGSPAVRPPGAAHLTDAQVAELGRELDAIRDDVLARRGTSDAAYIRRVIRWQRRL
+ELGGRALLLNARHPAAFVAGTAMLTVAKIVENMEIGHNVLHGQWDWMRDPDIHSTTWEWD
+FVTPSRAWQNTHNDLHHRWTNVVGKDRDVGYNVLRMDESEPWRPRHLLNPVINAGLAPIF
+EWGIALYDLELDRVQSGEKSREELMTDLRSVGVKAARQFAKDYVATPAVAEVLTGSGKAA
+LVGTLLANGLRNIWAHAVIFCGHFPEGAETFSEEMVDGETRGDWYVRQMIGSANISGSKL
+MHFMTGNLSHQVEHHLFPDLPSSRYAEVAPRVREICARYGLPYTTGPLLRQVGSAWKKVF
+RLALP
+>PROKKA_01921
+MTQTPTTPSRTGATAPDDLALAIPGTTVRGRAARVLPQDRPDTTSWAPHTAESRAATSRS
+TAAATTPGLPGVVGSPAVRPPGAAHLTDAQVAELGRELDAIRDDVLARRGTSDAAYIRRV
+IRWQRRLELGGRALLLNARHPAAFVAGTAMLTVAKIVENMEIGHNVLHGQWDWMRDPDIH
+STTWEWDFVTPSRAWQNTHNDLHHRWTNVVGKDRDVGYNVLRMDESEPWQPRHLLNPVIN
+AGLAPIFEWGIALYDLELDRVQSGEKSREELMTDLRSVGVKAARQFAKDYVATPAVAEVL
+TGSGKATLAGTLLANGLRNIWAHSVIFCGHFPEGAETFSEEMVDGETRGDWYVRQMIGSA
+NISGSKLMHFMTGNLSHQVEHHLFPDLPSSRYAEVAPQVREICARYGLPYTTGPLLRQVG
+SAWKKVFRLALP
+>PROKKA_00537
+MTQTLPATERTGATAPDDLSLAIPGTTVRGRTARVLPEDRPDTTSWAPQTADAGTDAAAP
+AASETPEAPTADAATRPAANAKPGLLGVVGSPAVRPPGAAHLTDEQVAELGRELDAIRDD
+VLSRRGASDAAYIRRVIRLQRWLEIGGRAALLNARHPAAFVAGTTMLTVAKIVENMEIGH
+NVLHGQWDWMRDPDIHSTTWEWDFVTPSRAWQNTHNDLHHRWTNVIGKDRDVGYNVLRMD
+ESEPWRPRHLLNPVINAGLAPIFEWGIALYDLELDRVHAGEKSRKELMTDLRSVGVKASR
+QFAKDYVATPAVAEFLTGSGKAALVAGLLANGLRNIWAHSVIFCGHFPEGAETFSEEMVD
+GETRGDWYVRQMIGSANISGSKLMHFMTGNLSHQVEHHLFPDLPSNRYAEVAPKVREICA
+RYGLPYTTGPLLKQVGSAWKKVFRLALP
+>PROKKA_00468
+MIRSATAGKIIENMEIGHNVLHGQWDWMRDPDIHSTTWEWDFVTPSSAWQHTHNDAHHRW
+TNVTGLDEDLGYNVLRMDEAEPWEPRHLLNPVINAILAPFFEWGIAIYDLELAKVRAGEK
+PVADLRRDLASVAVKAVRQLAKDSLATPIAAELVSRSGSAWRKVFRLALP
+>PROKKA_02152
+MTQTPTTPSRTGATAPDDLALAIPGTTVRGRAARVLPQDRPDTTSWAPHTAESRAATSRS
+TAAATTPGLPGVVGSPAVRPPGAAHLTDAQVAELGRELDAIRDDVLARRGTSDAAYIRRV
+IRWQRRLELGGRALLLNARHPAAFVAGTAMLTVAKIVENMEIGHNVLHGQWDWMRDPDIH
+STTWEWDFVTPSRAWQNTHNDLHHRWTNVVGKDRDVGYNVLRMDESEPWQPRHLLNPVIN
+AGLAPIFEWGIALYDLELDRVQSGEKSREELMTDLRSVGVKAARQFAKDYVATPAVAEVL
+TGSGKATLAGTLLANGLRNIWAHSVIFCGHFPEGAETFSEEMVDGETRGDWYVRQMIGSA
+NISGSKLMHFMTGNLSHQVEHHLFPDLPSSRYAEVAPQVREICARYGLPYTTGPLLRQVG
+SAWKKVFRLALP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001721.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001721.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4538f7f4c71c5cc97eb01d663e8d3ed7f364c0c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001721.fa
@@ -0,0 +1,30 @@
+>PROKKA_02216
+MPAQPSPSGHTVHLSTSGVDARITPDEFGGFVLEIGGAVQSHVDLADPARIRYEYLRRMA
+HVLDAASPAGAPVRVLHLGAGALTLPRYLQATRPGSEQTVVDLDRELVSFVLAELPLPAG
+TDLVSVVADARLAAVDLALDGERFDAVVLDIGTGEEGAEHLRGAVFYGELLELLTAGGVL
+LVNIGDDAGLRFLGAELGALEEAAAEAGVPGPWTLADQGMLERLDWGNVVLAAGAPLGEA
+GCTERLAAAGPHPAAVLDPAESAALADRIRRA
+>PROKKA_01929
+MPAQPSPSGHTVHLSTSGVDARIAPDEFGGFVLEIGGAVQSHVDLADPARIRYEYLRRMA
+HVLDAASPTGAPVRVLHLGAGALTLPRYLQATRPGSEQTVVDLDRELVSFVLAELPLPAG
+TDLVSVVADARLAAVDLALDGERFDAVVLDIGTGEEGAEHLRGAVFYGELLELLTAGGVL
+LVNIGDDAGLHFLGAELGALEEAAAEAGVPGPWTLADQGMLERLDWGNVVLAAGAPLGEA
+GCTERLAAAGPHPAAVLDPAESAALAARIRRA
+>PROKKA_00525
+MRAHPSPTGRTVHLSATGEDARILADELGGSVLEIGGAVQSHVDPADPTALRYEYLRRMA
+NVLDGVAPAGAPLRVLHLGAGALTLPRYVQATRPGSEQTAVDLDRELVSFVLAELPLPAG
+TDLVSVVADARLAAVDLLMDGERFDAVVLDIGTGEDGAAHLTGAEFYGELLGLLTAAGVL
+LVNIGDDDGLRFLGAQLRHMEAACAEAGVPGPWTLASAAMLERLELGNAVLAAGPALRGD
+GAAAGGDAGPEEDGGPLTPAALLARGPHPGAVLDEAASADLARRVAGR
+>PROKKA_00467
+MPTQPQDDASSPAPSPTARTVHLAASGVDARILPDPHAGGWMLEVGGAVQSHVDLADPTQ
+VRYEYLRRIANVLDALAPAGEPLRVLHLGGGALTLPRYVAATRPGSVQTVVDLDRELMGL
+VLEELPLPADADVYVVVADARAVVDDLLDPLEGESQAGAWDAVVLDIDTDAGAVAHLTGA
+AFHAELLELLAPGGVLCVNIGDDDGLAYLATQLTALEAACADAAEGAGVPGPWTLGPNSV
+LERRELGNAVLVAGPGLAGMDAAALHAAGPHPAVVLDAHESAALAERITAAP
+>PROKKA_02155
+MPAQPSPSGRTVHLSTSGVDARIAPDEFGGFVLEIGGAVQSHVDLADPARIRYEYLRRMA
+HVLDGVAPAGAPVRVLHLGAGALTLPRYLQATRPGSEQTVVDLDRELVSFVLAELPLPAG
+TDLVSVVADARLAAVDLAMDGERFDAVVLDIGTGEEGAEHLRGAVFYGELLELLTAGGVL
+LVNIGDDAGLRFLGAELGALEKAAAEAGVPGPWTLADQGMLERLDWGNVVLAAGAPLREA
+GCTERLAAAGPHPAAVLDPAESAALAARIRRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001722.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001722.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3d0dee4895531442ed924a8eccb3c7b7c71725d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001722.fa
@@ -0,0 +1,35 @@
+>PROKKA_02219
+MPPEPSAPSGERGPARPHPADVAARPDAPSPRATALLFALAVAAGSVMPLQGRINSRLAH
+LTGDPVLAALCSFAAGLVVMVLVSVLTPRGRRGLARIRPALAAGSVRPWYAVAGVIGGLL
+VLTQSATIGPLGVAVFTVAVVTGQVVGGMVVDRLGLSPAGVQRLTPRRLTGAALALAAVA
+LVVWPSLGEAGGGPGWALLALLPLLAGLATAGQQVFNARQTTAYGTAIPATLVNFTAGVL
+FLGIVWGGIALASGHGLPALPHDWRLYLGGPLGCVFIGVGAMVVPRLGVFAATLGLVSGN
+LLGSLVVDLVAPTDGSTVTTTTVLGTLGALAAVALASWPARRR
+>PROKKA_01932
+MPPESSVPSAERGPSRPRPAAVAARPEAPSPRATALLFALAVAAGSVMPLQGRINSRLAH
+LTGDPVLAALCSFAAGLAVMVLVSVLTPRGRRGLARIRPALAAGSVRPWYAVAGMIGGLL
+VLTQSATIGPLGVAVFTVAVVTGQVVGGMVVDRLGLSPAGVQRLTPRRLTGAALALAAVA
+LVVWPSLGEAGGGPGWALLALLPLLAGLATAGQQVFNARQTTAYGTAIPATLVNFTAGVL
+FLGIVWGGIALASGHGLPALPHDWRLYLGGPLGCVFIGVGAMVVPRLGVFAATLGLVSGN
+LLGSLVVDLVAPTDGSTVTTTTVLGTLGALAAVALASWPARRR
+>PROKKA_00527
+MSARAARAARAGEGRQGSDAPAGADARPGAAGSALLFAMAIVAGSTIPVQARLNSALAER
+SGDPTLAAVASFAAGLVLVAAVTVLTPAGRRGLRAVRPALAAGRVRWWYLLAGTIGGAMV
+FSQATTVGLIGVAVFTVAVVTGQLIGGMVVDRLGLTPAGVRRMTPRRLAGAALALACVVL
+VVAPQLGARGDGGPPLWLLVALAPLAVGLATSIQQTLNARQAAAYGSVLPVTTVNFVAGT
+GILALVHLGGRLGGGVGGTLPGDWWLYLGGPMGVVFIAFSAYLVPRVGAFLTMLGLVSGK
+LLGSLAVDALAPVGEVAASPWTVVGTLGALAAVVLASGAARPARKG
+>PROKKA_00465
+MPASSPALTPAPRSGATTALLFLLALVAGLAMPVQGRVNSALSLAVGSPALAACASFATG
+LAVLVLATLLLPSGRRGAARIPAAVRNGDVRWWQLLAGTIGAAFVLTQAWTIPLIGVAVF
+TVAVVTGQMLGGMLWDRLGWTPAGVQRISRRRLFGALLAFCAVTAVVWPRLQESGSPGAW
+LALAVLPLAAGVATSGQQAMNGHQTAHFGTPLPPTLVNFAAGTAVLAAATAVAAGTGAGM
+GPLPAAWWMYLGGPLGTVFVGLGAFLIPRVGAFLTTLGMVAGQLVGSLLLDVVAPAPGAQ
+VTWLTVVGTLGALAAMVVASSPQVPAGLRASRRRARRG
+>PROKKA_02158
+MPPEPSAPSGERGPARPHPADVAARPDAPSPRATALLFALAVAAGSVMPLQGRINSRLAH
+LTGDPVLAALCSFAAGLVVMVLVSVLTPRGRRGLARIRPALAAGSVRPWYAVAGVIGGLL
+VLTQSATIGPLGVAVFTVAVVTGQVVGGMVVDRLGLSPAGVQRLTPRRLTGAALALAAVA
+LVVWPSLGEVGGGPGWALLALLPLLAGLATAGQQVFNARQTTAYGTAIPATLVNFTAGVL
+FLGIVWGGIALASGHGMPALPHDWRLYLGGPLGCVFIGVGAMVVPRLGVFAATLGLVSGN
+LLGSLVVDLVAPTDGSTVTTTTVLGTLGALAAVTLASWPARRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001723.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001723.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f49de14bcb275cce1ce349642c5e7cb5d148a2f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001723.fa
@@ -0,0 +1,25 @@
+>PROKKA_02220
+MKHEIVLTRGDLTLRPLTPDDGPALRELVDAAMWAGNSAPLPVDGAAMSAHLAELSEREG
+TFAFAVEQGGELVGRTSLYDLVPGLRVEVGHTVYARRVWGTSVNPGCKLLLFGHAFEEWA
+LERVALRCDHRNARSHAAIARLGATFEGTLRRFRPAADGTIADVDYFSVVREEWPAVRGG
+LEARLAA
+>PROKKA_01933
+MKHEIVLTRGDLTLRPLSPTDGPALRELVDAAMWAGNSAPLPVDGAAMSAHLAELIEREG
+AFAFAVEQGGELVGRTSLYDLVPGLRVEVGHTVYARRVWGTSVNPGCKLLLFGHAFEEWA
+LERVALRCDHRNARSHAAIARLGATFEGTLRRFRPAADGTIADVDYFSVVREEWPAVRAG
+LEARLTA
+>PROKKA_00515
+MSHDLHLTHGPIRLRPLTPDDAPRLRAIVDEASWAGMSTPLPETDAAMAEHLRELMGRPG
+LQAFAVERDGEFVGRTALYDPVPTVRVDVGHTVYARPVWGTEVNPACKLLLLGHAFEELG
+VARVGLRCDHRNTRSHRAILRLGATFEGTLRAFRRAADGTVADADHFSVTAPEWPAVRAG
+LETRLGA
+>PROKKA_00462
+MPAAQLPADLLLEHGAVRLRPLTLDDAPRLRALVDAGSWAGMSSPLPTSDEAMAAHLAQL
+MAREDLTAFAVERDGEFVGRTAYYEHVPGVRVDVGHTIYAREVWGTEVNPACKLLLLRHA
+FEALGVERVGLRCDHRNTRSHRAILRLGATFEGTLRAFRPAADGTVADVDYFSVLAAEWP
+AVRAGLEARLAGSAPAD
+>PROKKA_02159
+MKHEIVLTRGDLTLRPLSPTDGPALRELVDAVMWAGNSTPLPVDGAAMSAHLAELIEREG
+TFAFAVEQGGELVGRTSLYDLVPGLRVEVGHTVYARRVWGTSVNPGCKLLLFGHAFEEWA
+LERVALRCDHRNARSHAAIARLGATFEGTLRRFRPAADGTIADVDYFSVVREEWPAVRAG
+LEARLAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001724.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001724.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1b2c1b6ab00aa6a1ddf2b7dcb817c97d7b3b98c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001724.fa
@@ -0,0 +1,55 @@
+>PROKKA_02239
+MQLDLIVENARLITGDPARPSASRLGVWRGVVVGVDEELDGLAARERLDARGRTVLAGFN
+DAHAHSVWFGQSRLDVDLEGARTAEEVHRRVRARAAELDPGAWVTCTGFDPGHLTGPQPD
+RDGLDAAASGRPVLIRHNTGHAVTVSGAVLVLAGVGEQVLQQPEGGRILTDAEGRPTGLL
+EETAMSLVTRLLQSESHEHIGACLARASQGYAAEGITSVTDAGVAGGWIGHSPLEFGAYQ
+RARDAGLLRTRFQTMVTLDALHSVDGHPDDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDG
+SMLGQTAAMTEDYCGHGHGRGYLQQDAGEMRRACLGAAAAGWALALHAIGDAALDFALDV
+IAEARGRFGRPVMPHRVEHGGVVRDDQVARMAELEVVMATQPNFISAFGGSVRERIGPER
+AALSYPAGRLLRAGLVLPGSSDRPVAGGRPLEVIQDFVLRRTETGEQYGPDAERLTVAEA
+LHAYTVGSAEATGWGGRKGRLVAGQLADFTVLSEDPRVVPSDQIAAIDVVATAVGGEFVH
+GGL
+>PROKKA_01941
+MQLDLIVENARLITGDPARPSASRLGVWRGVVVGVDEELDGLTARERLDARGRTVLAGFN
+DAHAHSVWFGQSRLDVDLEGARTAEEVHRRVRARAAELGPGAWVTCTGFDPGHLTGPQPD
+RDSLDAAASGRPVLIRHNTGHAVTVSGAVLVLAGVGEQVLQQPEGGRILTDAAGRPTGLL
+EETAMSLVTRLLQPESHEHIGACLARASQEYAAEGITSVTDAGVAGGWIGHSPLEFGAYQ
+RARDAGLLRTRFQTMVTLDALRPVDGHPDDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDG
+SMLGQTAAMTEDYCGHGHGRGYLQQDAGEMRRACLGAAAAGWALALHAIGDAALDFALDV
+IAEARGRFGRPVMPHRVEHGGVVRDDQVARMAELEVVMATQPNFISAFGGSVRERIGPER
+AALSYPAGRLLRAGLVLPGSSDRPVAGGRPLEVIQDFVLRRTETGEQYGPDAERLTVAEA
+LHAYTVGSAEATGWGGRKGRLVAGQLADFTVLSEDPRAVPSDQIAAIDVVATAVGGEFVH
+GGL
+>PROKKA_00506
+MQLDLIVENAHLLTGDPARPEATRLGVWRGAVVGVDEELDGLGARERLDARGRTVLAGFN
+DAHAHSVWFGQSRLDVDLEGAHTAQEVYDRIRARAAELTPGAWVTCTGFDPGHLTGPQPD
+RDGLDAAAAGRPVLIRHNTGHAFTVSGAVLFLAGVGEQVMQQPEGGRIITDAADRPTGLL
+EETAMNLVTRLLQPESHEHIGACLARASQEYAAEGITSVTDAGIAGGWIGHSPLEFGAYQ
+RARDAGLLRTRFQAMVTLDALRPVDGHADDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDG
+SMLGQTAAMTADYCGHGHGRGYLQQDAGEMRRECLGAAAAGWSLALHAIGDAALDFALDV
+IAEARARFGRPVMPHRVEHGGVVRDDQVARLAELEVVMATQPNFISAFGGSVRERIGPER
+AALSYPAGRLLRAGLVLPGSSDRPVAGGRPLDVIQDFVLRRTETGEQYGPDLERLTVAQA
+LQAYTVGSAEATGWGGRKGRLVAGQLADFTVLSADPRAVPSEEIAAIDVVATAVGGEFVH
+GGL
+>PROKKA_00442
+MQLDLIVENARLITGDPARPSASRLGVWRGVVVGVDEELDGLAAGERLDARGRTVLAGFN
+DAHAHSVWFGQSRLDVDLEGARTAEEVHRRVRARAAELDPGAWVTCTGFDPGHLTGPQPD
+RDSLDAAASGRPVLIRHNTGHAVTVSGAVLVLAGVGEQVLQQPEGGRILTDAAGRPTGLL
+EETAMSLATRLLQPESHEHIGACLARASQEYAAEGITSVTDAGVAGGWIGHSPLEFGAYQ
+RARDAGLLRTRFQTMVTLDALRPVDGHPDDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDG
+SMLGQTAAMTEDYCGHGHGRGYLQQDAGEMRRACLGAAAAGWALALHAIGDAALDFALDV
+IAEARGRFGRPVMPHRVEHGGVVRDDQVARMAELEVVMATQPNFISAFGGSVRERIGPER
+AALSYPAGRLLRAGLVLPGSSDRPVAGGRPLEVIQDFVLRRTETGEQYGPDAERLTVAEA
+LHAYTVGSAEATGWGGRKGRLAAGQLADFTVLSEDPRAVPSDQIAAIDVVATAVGGEFVH
+GGL
+>PROKKA_02171
+MQLDLIVENARLITGDPARPSASRLGVWRGVVVGVDEQLDGLATRERLDARGRTVLAGFN
+DAHAHSVWFGQSRLDVDLEGARTAEEVHRRVRARAAELDPGAWVTCTGFDPGHLTGPQPD
+RDSLDAAASGRPVLIRHNTGHAVTVSGAVLVLAGVGEQVLQQPEGGRILTDAAGRPTGLL
+EETAMSLVTRLLQPESHEHIGACLARASQEYAAEGITSVTDAGVAGGWIGHSPLEFGAYQ
+RARDAGLLRTRFQTMVTLDALHPVDGHPDDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDG
+SMLGQTAAMTEDYCGHGHGRGYLQQDAGEMRRACLGAAAAGWALALHAIGDAALDFALDV
+IAEARGRFGRPVMPHRVEHGGVVRDDQVARMAELEVVMATQPNFISAFGGSVRERIGPER
+AVLSYPAGRLLRAGLVLPGSSDRPVAGGRPLEVIQDFVLRRTETGEQYGPDAERLTVAEA
+LHAYTVGSAEATGWGGRKGRLVAGQLADFTVLSEDPRAVPSDQIAAIDVVATAVGGEFVH
+GGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001729.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001729.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37f271b42af8b88dd05225f2b8d68efb2b858199
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001729.fa
@@ -0,0 +1,50 @@
+>PROKKA_02247
+MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLTDMVGQLARGGSSSAGISSF
+QSFAMALGGRIGVGNIAGVAAAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVR
+GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQIQANAVTAATTEAWGWDPLW
+VGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQVPAMFGLIFSS
+ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVD
+TLFVCTMTGLMILATNSFNVLGPDGESLLAEHVPGVEEGPAWVQIAIDEALPAFGPSFVA
+IAVFLFSFTTLLSFAFYAETNVAYLIPNKTAQRAVIAIARLLLAGSMVFGSVQTSAFVWS
+LADFGVGLYTWVNIVALILLSPVAIRLFKDYDRQRRAGQDPVLDPAAIGVRNARLWEQIH
+AAYQQTGDLDRAMEHVADTAPDTRAITVVPRREG
+>PROKKA_01949
+MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLRDMVGQLVRGGSSSAGISSF
+QSFAMALGGRIGVGNIAGVAAAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVR
+GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQIQANAVTAATTEAWGWDPLW
+VGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQVPAMFGLIFSS
+ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVD
+TLFVCTMTGLMILATNSFNVLGTGEGPPIVEHLPGVEEGPAWVQIGIDVVLPSFGPSFVA
+VAVFLFAFTTLLSFAFYAETNLAYLIPNKKAQRICIAAARLLLAASMVIGSVQTSAFVWS
+LADFGVGLYTWVNILALVLLSPVAIRLLKDYDRQRRAGQDPVLDPAAIGVRNAHLWEQIH
+AAYQQTGDLDRAMEHVADTAPDTRAITVVPRREG
+>PROKKA_00499
+MEQFLAGANAIMWSLPMVFGLLALGLYFTIRMGAPQLRRIPDMIGQLVRGGSSSAGISSF
+QAFAMALGGRIGVGNIAGVATAISLGGPGALFWMWVTALLGAPVALAESSLAQLYKHKVR
+GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVITGPQIQANAVTAATTQAWGWDPLW
+VGLAMAVLFCVIVFGGMHRLGRTVGLVVPFMAAAYIIVGVVVVALMWQQVPAMFGLIFTS
+AFAADSLYAGMLGAAISWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAFVD
+TLFVCTVTGLMILSTNSFNVLGPDEETVLVEHVPGIEAGPAWVQTAIDSVIPAFGPAFVA
+VAVFLFSFTTLLSFAFYAETNLAYLIPNKSVQRACIAVARLGLAASMVFGAVQTSTLVWS
+FADFGVGLYTWVNILALVLLSPVAIRLMKDYDRQRRAGQDPVLDPRAIGVRNATLWEQIH
+DEYERTGDVTAALDHVADTAPDTRAISVVRSHGERGQG
+>PROKKA_00437
+MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLKDMVGQLVRGGSSSAGISSF
+QSFAMALGGRIGVGNIAGVAAAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVR
+GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQIQANAVTAATTEAWGWDPLW
+VGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQVPAMFGLIFSS
+ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVD
+TLFVCTMTGLMILATNSFNVLGPDGESLLAENVPGVEEGPAWVQIAIDAALPAFGPSFVA
+IAVFLFSFTTLLSFAFYAETNVAYLIPNKTAQRAVIAIARLLLAGSMVFGSVQSSALVWA
+FADFGVGLYTWVNIVALILLSPVAIRLFKDYDRQRRAGQDPVLDPAAIGVRNARLWEQIH
+AAYQQTGDLDRAMEHVADTAPDTRAITVVRGGPERGEG
+>PROKKA_02179
+MEQFVTAANSIMWSLPMVVGLLALGLYFTIRMAAPQVRLLTDMVGQLARGGSSSAGISSF
+QSFAMALGGRIGVGNIAGVAAAIYLGGPGALFWMWVTAILGAPVALVESSLAQLYKHKVR
+GEYRGGPAYYILEGLGRNWRWLAVAYAAATVFATVFTGPQIQANAVTAATTEAWGWDPLW
+VGLGMAVLFCVIVFGGMHRLGRTVGLVVPFMAGAYILVGLLVVGLMWQQIPAMFGLIFSS
+ALGLDSVYGGILGAAVAWGVRRAVYSTEIGTGSGAQASAAAHVSHPVKQGLAQAFSAYVD
+TLFVCTMTGLMILATNSFNVLGPDEESLLAEHVPGVEEGPAWVQIAIDEALPAFGPSFVA
+IAVFLFSFTTLLSFAFYAETNVAYLIPNKTAQRAVIAIARLLLAGSMVFGSVQTSAFVWS
+LADFGVGLYTWVNIVALILLSPVAIRLLKDYDRQRRAGQEPVLDPHAIGVRNARLWEQIH
+AAYQQTGDLDRAMEHVADTAPDTRAITVVPRREG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001730.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001730.fa
new file mode 100644
index 0000000000000000000000000000000000000000..48d6b104e5ce5be40002b2e70b4566783db56daa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001730.fa
@@ -0,0 +1,29 @@
+>PROKKA_02254
+MMGPSHAATGAAAWLALTHWQSPIAVLHLPAELQLLGAVTTAGAAMISDWDHPRATVVHA
+LPPLTEWLSRGIRHVAGGHRRGTHSLVGVAAFTAIATAAASIQVPIAGHVYTPGQGVIAA
+FLAAVAAKALRLLPNRGWRAAWALGILVAVSATVLSDGLWWIPASVAVGVSVHILGDALT
+NNGVALLWPLSPEPPARLWWWQSSGRFRLPLLGRTGSWREWALVSVVTAFTVVRAVRLVP
+LAARGVAALF
+>PROKKA_01954
+MMGPSHAATGAAAWLALTHWQSPIAALHLPAELQLLGAVTTAGAAMISDWDHPRATVVHA
+LPPLTEWLSRGIRHVAGGHRRGTHSLVGIAAFTAVATAAASIQVPIAGHVYTPGQGVIAA
+FLAAVAAKALRLLPNRGWRAAWALGILVAVSATVLSDGLWWIPASVAVGVSVHILGDALT
+NNGVALLWPLSPEPPTRLWWWQSSGRFRLPLLGRTGSWREWALVSVVTAFTVVRAVRLIP
+LAARGVAALF
+>PROKKA_00477
+MGPSHAATGAAAWLALTHWQSPIAVLHLPAELQLLGAVTTAGAAMISDWDHPRATVVHAL
+PPLTEWMSRGIRHVAGGHRRGTHSLVGIAAFTAIATAAASIQVPIAGHVYTPGQGVIAAF
+LAAVAAKALRLLPNRGWRAAWALGILVAGAATVLSDGLWWIPASVAVGVSVHILGDALTN
+NGVALLWPLSPEPPARLWWWQSSGRFRLPLLGRTGSWREWAFVSVVTAFTVVRAVRLVPL
+AARGVAGLLGAGAPS
+>PROKKA_00432
+MSTPPAALALFLPRGPPAGPRGCGDAAWLALTHGQSPVGVRHLPAELQLLGAVTTAGAAM
+ISDWDYPRATAIATAAASIHVPIAGHVYTPGQGVIAAFVAAVAAKALRLLPNRGWRAAWP
+LGILVAVSATVFSDGLRWIPVSVAVGVSVHILGDALTNNGVALLWPLSPEPPARLWWWQS
+SGRFRLPLLGRTGSWREWALVSVVTAFTVVRAVRLVPLAARGAALF
+>PROKKA_02185
+MMGPSHAATGAAAWLALTHWQSPIAVLHLPAELQLLGAVTTAGAAMISDWDHPRATVVHA
+LPPLTEWLSRGIRHVAGGHRRGTHSLVGIAAFTAIATAAASIQVPIAGHVYTPGQGVIAA
+FLAAVAAKALRLLPNRGWRAAWALGILVAVSATVLSDGLWWIPASVAVGVSVHILGDALT
+NNGVALLWPLSPEPPARLWWWQSSGRFRLPLLGRTGSWREWALVSVVTAFTVVRAVRLLP
+LAARGVAALF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001731.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001731.fa
new file mode 100644
index 0000000000000000000000000000000000000000..893cca3d70dea201be1bb42d2d3d75d8836bfda5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001731.fa
@@ -0,0 +1,30 @@
+>PROKKA_02255
+MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLSRRLWLAARQTALLTPVLVTIVLVAA
+FLALTGIDYETYMNGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTVGSLTAM
+VSAVLIVRAMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP
+WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL
+AMTG
+>PROKKA_01955
+MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLSRRLWLAARQTALLTPVLVTIVLVAA
+FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTVGSLTAM
+VSAVLIVRAMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP
+WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL
+AMTG
+>PROKKA_00476
+MNGAELADSLAEAWDALLHTPLFGIALTLAVAVLARRLWLAARQTALLTPVLVTIVLVAA
+FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPIAVGVTVGSLTAM
+VSAVLIVRLMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVFAP
+WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL
+AMTG
+>PROKKA_00431
+MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLARRLWLAARQTALLTPVLVTIVLVAA
+FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTAGSLTAM
+VSAVLIVRVMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP
+WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL
+AMTG
+>PROKKA_02186
+MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLSRRLWLAARQTALLTPVLVTIVLVAA
+FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTVGSLTAM
+VSAVLIVRAMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP
+WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL
+AMTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001732.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001732.fa
new file mode 100644
index 0000000000000000000000000000000000000000..68ca3dea7c377eca7c85b24316c6ba23082a743b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001732.fa
@@ -0,0 +1,17 @@
+>PROKKA_02256
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTASHHLLQ
+HLPLLFVPAGVGVVAVLGLIEEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTDKEDAQ
+>PROKKA_01956
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTASHHLLQ
+HLPLLFVPAGVGVVAVLGLIEEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTDKEDAQ
+>PROKKA_00475
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTTSHHLLQ
+HLPLLFVPAGVGVVAVLGLIGEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTNKKENA
+Q
+>PROKKA_00430
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVITASHQLLQ
+HLPLLFVPAGVGVVAVLGLIQEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTNKKEDA
+Q
+>PROKKA_02187
+MIEGLLILLLCQLAGTLVADTLHLPIPGAVLGMLLLLGLLAWRRPAEDAPVMTASHHLLQ
+HLPLLFVPAGVGVVAVLGLIEEHRALMLVGFVVPWLLGLVVTAGVAAPLARRLTDKEDAQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001734.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001734.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c02ce2c33e621d4024be4e28956bdd30c6ccd633
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001734.fa
@@ -0,0 +1,55 @@
+>PROKKA_02268
+MPTLRTVPLSAATREDHLARLRATSPEAPLDILVVGGGSTGVGAAFDAATRGLDVGIVEA
+RDWASGTSSRSSRLMHGGLRYLEMLDVKLVYEALRERDLLLTQTAPHLVRPLRFVFPFFH
+KVIDRGFIGAGVTMYDAMQSLGRRRAMGAHRHLSRRSMAATFPSLDDEKIVGAVEYADAQ
+FDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGDDGRVQGVRVREETSGEEFDVHARAVI
+LAGGVWTQEQQELAGADGGLEVLASKGAHITVPRDRIRADAATGVITKTEKSVLFLIPWD
+EYWVIGTTDTPWAEDVAHPATTADDIDYILEHANAVLKEDLTRDDVVATYAGLRPLLQPV
+TGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTYRAMAEDVVDFVVRETHPTRPSLTERI
+PVLGGLGYSEIEAEADRIAADYGLDEARVDRLLFRYGTVLRHVLDLIDADPSLSVPLAEA
+PRYLRAEIVYAARAEGVVHLDDVIERRTRLSTEVRDRGVAAAEEIASLVAPELGWDEERI
+AGEIRAYKNLVAARLRGETAHDDVTAAAALAAADADAAPTP
+>PROKKA_01961
+MPTLRTVSLSAATREDHLARLRATSPEAPLDILIVGGGSTGVGAAFDAATRGLDVGIVEA
+RDWASGTSSRSSRLMHGGLRYLEMLDVKLVYEALRERDLLLTQTAPHLVRPLRFVFPFFH
+KVIDRGFIGAGVTMYDAMQSLGRRRAMGAHRHLSRRSMAATFPSLDDEKIVGAVEYADAQ
+FDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGDDGRVQGVRVREETSGEEFDVHARAVI
+LAGGVWTQEQQELAGADGGLEVLASKGAHITVPRDRIRADAATGVITKTEKSVLFLIPWD
+EYWVIGTTDTPWAEDVAHPATTADDIDYILEHANAVLKEDLTRDDVIATYAGLRPLLQPV
+TGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTYRAMAEDVVDFVVRETHPTRPSLTEHI
+PVLGGLGYSEIEAEADRIAADYGLDEARVDRLLFRYGTVLRHVLDLIDGDPSLSVPLAEA
+PRYLRAEIVYAARAEGVVHLDDVIERRTRLSTEVRDRGVAAAEEIASLVAPELGWDEERI
+AGEIRAYKNLVAARLRGETAHDDVTAAAALAAADAAPVHGKEPVHGHDLPA
+>PROKKA_00462
+MGGGSTGVGAAFDAATRGLDVGIVEARDWASGTSSRSSRLMHGGLRYLEMLDVKLVYEAL
+RERDLLLTQTAPHLVRPLRFVFPFFHKVIDRGFIGAGVTMYDAMQSLGRRRAMSAHRHLS
+RRSMAATFPSLDDEKIVGAVEYADAQFDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGD
+DGRVQGVRVREETSGEEFDVHARAVILAGGVWTQEQQELAEADGGLEVLASKGAHITVPR
+DRIRADAATGVITKTEKSVLFLIPWDEYWVIGTTDTPWAEDVAHPAATADDIDYILEHAN
+AVLKEDLTRDDVIATYAGLRPLLQPVTGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTY
+RAMAEDVVDFVVRETHPTRPSLTERIPVLGGLGYSEIEAEADRIAADYGLDEARVDRLLF
+RYGTVLRHVLDLIDADPSLSVPLAEAPRYLRAEIVHAARAEGVVHLDDVIERRTRLSTEV
+RDRGVAAAEEIASLVAPELGWDEERIAGEIRAYKSLVAARLRGETAHDDVTAAAALAAAD
+AASTH
+>PROKKA_00493
+MPTLRTVELSPATRADHLARLRAADADHPLDVLVVGGGSAGVGAAFDAATRGLDVGIVDA
+GDWAGGTSSRSSRLMHGGLRYLEMLDVKLVYEALRERDLLLTRTAPHVVRPLRFVFPLEH
+ARDRGWIGAGVGVYDAMQSVGRRRAVGGHRHLGRKALAETFPGLDPEAAVGAVEYADAQF
+DDARLALLLVRSAVDLGAAALNHAPVVGYLKDGAGAVVGARVRESLTGEELQVHARAVIL
+AGGVWTQEQQELAGVDGGLEVLASKGVHVTVPRERIAAEPGVGVITRTEKSVLFVIPSDE
+HWIIGTTDTPWRQDVDHPAATAADVDYVLEHANAVLSEDLTRADVVAVYAGLRPLLQPAA
+GADDASTKVSREHTVTELAPGLTAVAGGKWTTYRAMAEDTVDFAVRDLFPTRPSLTAHTP
+VLGGLGYAEIAARAAEIAAERGFDAARVDRLLRRYGTLLPHVLALVDADPALGEPLPGGE
+AYLRAEVVYAARAEGAVHLDDVLERRLRLSTEVPDRGADAASEAAALVADVLGWDAARRD
+AEVAAYRALVAARRRAEGLDDDAAAAAELAAAGERAGVVPVTSRETVTPEEKGGAR
+>PROKKA_02200
+MPTLRTVSLSAATREDHLARLRATSPEAPLDILIVGGGSTGVGAAFDAATRGLDVGIVEA
+RDWASGTSSRSSRLMHGGLRYLEMLDVKLVYEALRERDLLLTQTAPHLVRPLRFVFPFFH
+KVIDRGFIGAGVTMYDAMQSLGRRRAMGAHRHLSRRSMAATFPSLDDEKIVGAVEYADAQ
+FDDARLAMMLVRSAVDHGAVAANYTAVTGYLRGDDGRVQGVRVREETSGEEFDVHARAVI
+LAGGVWTQEQQELAEADGGLEVLASKGAHITVPRDRIRADAATGVITKTEKSVLFLIPWD
+EYWVIGTTDTPWAEDVAHPATTADDIDYILEHANAVLKEDLTRDDVVATYAGLRPLLQPV
+TGSDGGSTKISREHTVTEVAPGLTAVAGGKWTTYRAMAEDVVDFVVRETHPTRPSLTEHI
+PVLGGLGYSEIEAEADRIAADYGLDEARVDRLLFRYGTVLRHVLDLIDADPSLSVPLAEA
+PRYLRAEIVYAARAEGVVHLDDVIERRTRLSTEVRDRGVAAAEEIASLVAPELGWDEERI
+ADEIRAYKNLVAARLRGETAHDDVTAAAALAAADAAPTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001737.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001737.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b32d2ce4f50b07567f8f0b6d9da1eafe9c06b45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001737.fa
@@ -0,0 +1,40 @@
+>PROKKA_02285
+MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA
+VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV
+RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV
+EESKGTDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM
+GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR
+LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTCVFPNPADTKVLEEGD
+RLLCFGKTENMRALIPARARRPKRVRRLPATPILASVAEEAPAPEAPADDA
+>PROKKA_01976
+MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA
+VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV
+RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV
+EESKGTDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM
+GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR
+LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTSVFPNPADTKVLEEGD
+RLLCFGKTENMRALIPARARRPKRVRKLPATPILASVAEEAPAPEAPADDA
+>PROKKA_00452
+MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA
+ILPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV
+RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV
+EESKGKDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM
+GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR
+LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTSVFPNPADTKVLEEGD
+RLLCFGKTENMRALIPARARRPKRVRKLPATPILASVAEEAPAPEAPADDA
+>PROKKA_00405
+MKLAILSRSLRAYSTQRLKSAALDRGHDVKVLDTLRFGIDLAGDEPDMMFRGKPLSSYDA
+VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRASQILSRHGIAQPATVFV
+RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV
+EESKGKDVRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVEQVELSEEYAETAVRAAHIM
+GLRVAGVDMLEGEDGPLVMEVNSSPGLEGIERATTLDVAGAIVDYIADQAGFPEVDVRQR
+LAVSTGYGVAEIAVLAGSDMAGQSIEDSGLLEKDLQVLTLHRGASVFPNPADSKVLEEGD
+RLLCFGKTENMRALIPARSQRPKRVKKLPKNPIIEAPPAEPAVRPDAESGES
+>PROKKA_02224
+MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA
+VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV
+RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV
+EESKGTDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM
+GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR
+LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTSVFPNPADTKVLEEGD
+RLLCFGKTENMRALIPARARRPKRVRKLPATPILASVAEEAPAPEAPADDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001741.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001741.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5839abf10a123cade7cbbce31ce76628c5977f95
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001741.fa
@@ -0,0 +1,15 @@
+>PROKKA_02290
+MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ
+AVKNAREVALLPYAGAGRG
+>PROKKA_01982
+MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ
+AVKNAREVALLPYAGAGRG
+>PROKKA_00448
+MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ
+AVKNAREVALLPYAGAGRG
+>PROKKA_00400
+MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ
+AIKNAREVALLPYAGAGRG
+>PROKKA_02230
+MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ
+AVKNAREVALLPYAGAGRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001742.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001742.fa
new file mode 100644
index 0000000000000000000000000000000000000000..75fce4a72a072afc86e9fa4ef28fc234cb1a33b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001742.fa
@@ -0,0 +1,25 @@
+>PROKKA_02291
+MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW
+REAAENVAESLTKGMRVIVQGRLRARSYDDRDGNRRTSWELDVDEVGPALRFATAKVTRA
+QRGGGGGGGFGGGQQGGGFGGAPAGGGFGGNSDGGFGGAQQGGGWGGQQQGGGQAAPQDP
+WSGGGGGGWDTPSSNEPPF
+>PROKKA_01983
+MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW
+REAAENVAESLTKGMRVIVQGRLRARSYDDRDGNRRTSWELDVDEVGPALRFATAKVTRA
+QRGGGGGGGFGGGQQGGGFGGAPAGGGFGGNNDGGFGGAQQGGGWGGQQQGGGQAAPQDP
+WSGGGGGGWDTPSSNEPPF
+>PROKKA_00447
+MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW
+REAAENVAESLTKGMRVIVQGRLKARSYDDRDGNRRTSWELDVDEVGPALKFATAKVTRA
+QRSGGGGGGGFGGGQQGGGFGGAPAGGGFGGNNDGGFGGAPQGGGWGGQQQGGGQAAPQD
+PWSGGGGGGGWDTPSSNEPPF
+>PROKKA_00399
+MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDEEALFVRCSVW
+REAAENVAESLTKGMRVIVQGRLKANSYQDREGNKRTSWELQVDEVGPALKFATAKVTRS
+QRGGGGGGGFGGGQQGGGFGGSPQGGGGFGGGQQQSGGWGQPSGGGQSAPAQDPWSGSGG
+GGWDTPSNGEPPF
+>PROKKA_02231
+MAGETVITVVGNLTADPELRFTPNGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSVW
+REAAENVAESLTKGMRVIVQGRLRARSYDDRDGNRRTSWELDVDEVGPALRFATAKVTRA
+QRGGGGGGGFGGGQQGGGVGGAPAGGGFGGNNDGGFGGAQQGGGWGGQQQGGGQAAPQDP
+WSGGGGGGWDTPSSNEPPF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001745.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001745.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b5d846a65c4aeb2c8456e980085a5aac98ac3ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001745.fa
@@ -0,0 +1,16 @@
+>PROKKA_02294
+MDIMIAVAVGVFLLVAWTVGGWAIVRMGFTRDGDAARTPAHDDGAARPAHPGAAADPATD
+PHVIWREQMKAATAASGAPCVCPPPPREGGAAEAGTSAPPSSPDCPIHRWDYA
+>PROKKA_01987
+MDIMIAVAVGVFLLVAWTVGGWAIVRLGFTRDGDAARAPAHDDGAARPAHRGPAADPATD
+PHVIWREQMKAATAASGAQCVCPPPREGGAAEAGTSAPPSSPDCPIHRWDYA
+>PROKKA_00442
+MEIMIVVAVGVFLMVAWTVGGWVIVRMGFTRDSDAASRAGSQDDDGTRPVPDGPVPVDPA
+SDPNAIWREQMKAATAASGAACTCPRRPVGTPSESPAGSGEQGAAVDSAVDRALDPAADH
+AAVDPSPDCPIHRWDYA
+>PROKKA_00395
+MPNEVLLVAGVGAALFVLWAVGGWLIVRMGFTRDRDRLPDGPGHASALPDGDGAPSPGRL
+PADPAQDPHAAWREQMKAATVASGARCTCEDGAVPDPDCPVHRWDYA
+>PROKKA_02235
+MDIMIAVAVGVFLLVAWTVGGWAIVRMGFTRDGDAARTPAHDAHDDGAARPAHPGAAADP
+ATDPHVIWREQMKAATAASGAQCVCPPPREGGAAEAGTSTPPSSPDCPIHRWDYA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001747.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001747.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d68b8b2552ed1a244db30d74ae1ea8116aff7a8c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001747.fa
@@ -0,0 +1,40 @@
+>PROKKA_02296
+MATNPIRVAIAGVGNCATSLIQGVEYYREAKATDTVPGLMHVQFGDYHVSDLEFVAAFDV
+DAKKVGLDLSEAITASENNTIKIADVPHADVTVQRGPTLDGLGKYYAETIEESDVEPVDV
+AQALRDAKVDVLVCYLPVGSQRATEHYAQAAIDAGVAFVNALPVFIAGTPEWAEKFTAAG
+VPIVGDDIKSQIGATITHRVMAKLFQDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI
+SKTQAVTSNTSAQLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD
+SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHNDDAAHELVEAFIRGDIE
+R
+>PROKKA_01989
+MATNPIRVAIAGVGNCATSLIQGVEYYREAKATDTVPGLMHVQFGVYHVSDLEFVAAFDV
+DAKKVGLDLSEAITASENNTIKIADVPHADVTVQRGPTLDGLGKYYAETIEESEAEPVDV
+AQALRDAEVDVLVCYLPVGSQRATEHYAQAAIDAGVAFVNALPVFIAGTPEWAEKFTAAG
+VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI
+SKTQAVTSNTSAQLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD
+SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHNDDAAHELVEAFIRGDIE
+R
+>PROKKA_00440
+MATTPIRVAIAGVGNCATSLIQGVEYYRDAKATDTVPGLMHVQFGDYHVSDLQFVAAFDV
+DAKKVGLDLSEAILASENNTIKLADVPHADVTVQRGPTLDGLGKYYAETIEESDAEPVDV
+AQALRDAQVDVLVCYLPVGSQLATEHYAQTAIDAGVAFVNALPVFIAGTPEWADKFTAAG
+VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI
+SKTQAVTSNTSAKLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD
+SPNSAGVIIDAVRAAKIALDRGTGGPILSASSYFMKSPPVQHNDDEARELVEAFIRGDIE
+R
+>PROKKA_00393
+MAENPIRVAIAGVGNCATSLIQGVEYYKDAQASDTVPGLMHVQFGDYHVSDLEFVAAFDV
+DAKKVGLDLSEAILASENNTIKISDVPATGVTVQRGPTLDGLGKYYRETIEESSAEPVDV
+VQALKDAKVDVLVSYLPVGSEEADKFYAQCAIDAKVAFVNALPVFIAGTQEWADKFTEAG
+VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI
+SKTQAVTSNTSAELAEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD
+SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHADDEAHELVEAFIRGDIE
+R
+>PROKKA_02237
+MATNPIRVAIAGVGNCATSLIQGVEYYREAKATDTVPGLMHVQFGDYHVSDLEFVAAFDV
+DAKKVGLDLSEAITASENNTIKIADVPHADVTVQRGPTLDGLGKYYAETIEESEAEPVDV
+AQALRDAKVDVLVCYLPVGSQRATEHYAQAAIDAGVAFVNALPVFIAGTPEWAEKFTAAG
+VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI
+SKTQAVTSNTSAQLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD
+SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHNDDAAHELVEAFIRGDIE
+R
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001748.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001748.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc0c4f8da08749916599ce1fa6a3d911de80fd0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001748.fa
@@ -0,0 +1,50 @@
+>PROKKA_02299
+MDLTTATHALPPGFPADATLPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRPSPDLDFT
+TDADPDASEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG
+DSLEDDLLRRDFTVNAMALRLPALELVDPFGGMRDLHAGVLRTPGTPEDSFSDDPLRMMR
+AARFASQLGFAVAPEVEQAMTAMAERITIISAERVREELVKLVCGAHPRAGLDLLVRTGL
+ADHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEGEYAPSTPDPVLRLAALLHDV
+GKPATRRFEKGGAVTFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGDA
+GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIAEITEAEEL
+AAVRPDLDGQQIMALLGIRPGPVVGRAYTHLLEWRLDEGPHEPAEAEAELRRWWAEQPEA
+QQD
+>PROKKA_01992
+MDLTTATHALPPGFPADATLPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRTSPDLDFT
+TDADPDASEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG
+DSLEDDLLRRDFTVNAMALRLPALELVDPFGGMRDLHAGVLRTPGTPEDSFSDDPLRMMR
+AARFASQLGFAVAPEVEEAMAAMAERITIISAERVREELVKLVCGAHPRAGLDLLVRTGL
+ADHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEGEYAPSTPDPVLRLAALLHDV
+GKPATRRFEKGGAVTFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGDA
+GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIAEIAEAEEL
+AAVRPDLDGQQIMALLGIRPGPVVGRAYNHLLEWRLDEGPHEQAEAEAELRRWWAEQPEA
+QQD
+>PROKKA_00437
+MDLTTATLALPAGFPADAALPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRVSGDLDFT
+TDAGPDAAEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG
+DSLEEDLLRRDFTVNAMALRLPGLELVDPYGGVQDLAAGVLRTPGAPEDSFSDDPLRMLR
+AARFASQLGFTVADEVEAAMTAMAERIGIISAERVREELVKLVCGAHPRRGLDLLVRTGL
+AEHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEAEYSPSAPDPVLRLAALLHDV
+GKPATRRFEKGGAVSFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGEA
+GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNKRKAERLAHAYDDLERRIAEIAEQEEL
+AAVRPDLDGEQIMALLGIRPGPVVGRAYRHLLEWRLDEGPHEPAEAEAELRRWWAEQPEA
+AEG
+>PROKKA_00390
+MEPRTDTRPLPAGFPADAALPAVVVELGRRFEAAGHELSLVGGPVRDLLLGRPVVDLDFT
+TDADPDATERIGAGWAEAAWDVGRHFGTIGFQKGGWQLEVTTYRAEQYDPTSRKPQVAFG
+DSLEDDLLRRDFTVNAMALRLPAMELVDPHGGVRDLAAGVLRTPGAPEDSFSDDPLRMMR
+AARFASQLGFGVADEVEAAMTDMAERIGIISAERVRDELVKLVRGDRPRAGLDLLVRTGL
+AQIVLPELPALQLETDEHHRHKDVYAHSLQVLEQAMGEEERYSPERPDVVLRLAALLHDV
+GKPATRRFEPSGAVSFRHHENVGAKLVRRRLKALRFDNDTIKAVARLVELHMRFYGYGEA
+GWTDSAVRRYVHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIEEISAAEEL
+AAVRPDLDGQQIMALLGIRPGPVVGRAYAHLLEWRLDEGPHEQAAAEAELRRWWAEQPEA
+AGASSGGGARD
+>PROKKA_02240
+MDLTTATHALPPGFPADATLPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRPSPDLDFT
+TDADPDASEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG
+DSLEDDLLRRDFTVNAMALRLPALELVDPFGGMRDLHAGVLRTPGTPEDSFSDDPLRMMR
+AARFASQLGFAVAPEVEQAMTAMAERITIISAERVREELVKLVCGAHPRAGLDLLVRTGL
+ADHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEGEYAPSTPDPVLRLAALLHDV
+GKPATRRFEKGGAVTFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGDA
+GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIAEIAEAEEL
+AAVRPDLDGQQIMALLGIRPGPVVGRAYTHLLEWRLDEGPHEPAEAEAELRRWWAEQPEA
+QQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001750.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001750.fa
new file mode 100644
index 0000000000000000000000000000000000000000..077b07f5a3b5925cecbfed3f168e9612e1b1e9c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001750.fa
@@ -0,0 +1,61 @@
+>PROKKA_02302
+MPQPIAVGAVLGGRYRITQHVVTSADQDMVFLGTDQVLNRRVTVLVASRENATQVASSAR
+ELATGERTDDVQVLDLGLSEGRTYLIAGGDPDPDVLLGLAYPQELYVEPFQTDSLGSELF
+GESRTGDPHAYDDDEAYYTDLDRRLRADEDEAQRRPGFLNRLSERLAERVRPSDGTAAKA
+AAGASALAAADAATRKQQEERERAEREAAERAERERKEAAERAERERKEAAERAERERKE
+AEEKARAEREAAERAERERKEAAERAERERREAEERAEEERRAEAERARRQAEQEAEERA
+AREREAEQARLAAEREEAERRELERRAEARRRAEEERAREAAEREAEKRAAQEREAAERE
+AQAGTAALPAVAAGAAAAQAPDADADGATPPTEPVESVAAEKTDPPEPVAPDTEAIPVRR
+QRPVPRRAIVAESAPTAHEESRGTAAPVAAGAGVATAAGAAAAGSTAAAAAPDAQAAPAT
+TGGGDGATVADPGDGHGRTRGGGPLALLLVLGLLAALVVGGVLLAQNLRGGPAPQAASSE
+SESASSESASDTPSPSESTSPSPTPSSESAAAAPQPVQALRSVPDLPEHEAEHDADLSNL
+IDGDPTTVWRTFAYARPNFGGYVESMNLVVQLEERTEVNEVTLQSTGATGGAWFAYIADS
+PEGANAKEIGNGTFDQDTVSIPVPFEGTEAEAEYVIVSLTSLPQLEGTTSDLPFGLRLGE
+IAVR
+>PROKKA_01995
+MPQPIAVGAVLGGRYRITQHVVTSADQDMVFLGTDQVLNRRVTVLVASRENATQVASSAR
+ELATGERNDDVQVLDLGLSEGRTYLIAGGDPDPDVLLGLAYPQELYVEPFQTDSLGSELF
+GESRTGDPHAYDDDEAYYTDLDRRLRADEDEAQRRPGFLNRLSERLAERVRPSDGTAAKA
+AAGASALAAADAATRKQQEERERAEREAAERAERERKEAEEKARAEREAAERAERERKEA
+AERAERERREAEERAEEERRAEAERARRQAEQEAEERAAREREAEQARLAAEREEAERRE
+LERRAEARRRAEEERAREAERREAEKREAQEREAAEREAQEREAAEREAQAGTAALPAVA
+AGAAAAQATDADADGATPPTEPVEPVESVAAEKTDPPEPVAPDTEAIPVRRQRPVPRRAI
+VAESAPPVHEESRSTAAPVAAGTATGATAAAAGSTSAAAAPDALAAPATTGGDDGATVAD
+PGDGNGRTRGGGPLALLLVLGLLAALVVGGVLLAQNLRGGPAPQAAAASSESASSESASD
+TPSPSESTSPSPTPTSESAAAAPQPVQALRSVPDLPEHEAEHDADLSNLIDGDPTTVWRT
+FAYARPNFGGYVESMNLVVQLEERTEVNEVTLQSTGATGGAWFAYIADSPEGANAKEIGN
+GTFDQDTVSIPVPFEGTEAEAEYVIVSLTSLPQLEGTTSDLPFGLRLGEIAVR
+>PROKKA_00435
+MAPGAAETDTVETRADEPAAAEPESTATAPAEDVDPEPTAPAPVVPASTAPDSAPDTEAI
+PVRRQRPVPRRAMVVEPTTPDADRSPDAQRSRGAGAPLAAAGAGAVAAAGATAASAAAAG
+AAPSATSAPSTASAAPEATAAGTSPADGDGGAPVDPDQGGSRRGGWPLALLLLAVLVGAL
+VLGGVLLAQNLRGAPHRAGRPARLPHRDRRGARTRRQPPPTQSDEASPTEASPTESSPAA
+STSASPTESETAAAAPQPARALRMVPDLPAHESEHDGELPNLIDGDPSTAWRTFAYARPN
+FGGYVESMNLVVELEDRAEVNEVTLQSTGATGGAWFAYIADSPEGENAREIGNGTFDQDS
+VTVPVPFDGAEAEAEYVIVSLTSLPRLDGTTPDLPFGLRLGEIGVR
+>PROKKA_00387
+MPQPLAVGSVLGGRYRITDHVVTSADQNMVFQGADQVLNRRVTVLVASPENATQVAASAR
+ELATGERQDDVQVLDLGLSEGRTYLIAGGNPDPDVLLGLAYAQELYVEPFQTDSLGSEIF
+GESRTEQAHEYDDDDAYYADLDRRLRADQKQSQRRPGFLNRISEKLNERVRPADGTAAKA
+AAGASALAAADAATKAQLAEQERAEREAREAQERAEREEAQEAERREREAQERAERERLE
+RAAAAQAEKDRAAREAAEAEAAARREREAQRHAEAETRRREEEAAAAAALAAAAPAADAD
+PADAPTQAVPVTEPASTPEAVPAPVRRPRPAPRRALPAVASAAAVAASVSAEEGASAAEA
+APAESVAPEAVPTATATSSAAIAVAEAEPAVTEHREEAHAAPVAGGAGAGAPAAGATAAP
+ARSTSGKGWLMVLGLLALLALAGLAGLFLLGQNTRSVEPAPSASASSAAPSTAQASSAPP
+AASSSAAPTASSSAAPSTEPAPSTSAAAPAPTAAPQAVAVTRQVPEMPELEAPNDATLAN
+LIDGDPNTAWQSYTYARPNFGGYVGSMNLVVQLQERTTISEVQLENRGATGGKWIAYVAN
+TAQGGEGDARVIGQGTFDEDSITIPVDIAENQGQYVILSITGLPQLEGAGQRPYGLQLTE
+IGVR
+>PROKKA_02243
+MPQPIAVGAVLGGRYRITQHVVTSADQDMVFLGTDQVLNRRVTVLVASRENATQVASSAR
+ELATGERTDDVQVLDLGLSEGRTYLIAGGDPDPDVLLGLAYPQELYVEPFQTDSLGSELF
+GESRTQDPHAYDDDEAYYTDLDRRLRADEDEAQRRPGFLNRLSERLAERVRPSDGTAAKA
+AAGASALAAADAATRKQQEERERAEREAAERAERERKEAEERARAEREAAERAERERKEA
+AERAERERREAEERAEEERRAEAERARRQAEQEAEDRAAREREAEQARLAAEREEAERRE
+LERRTEARRRAEEERAREAERREAEKRAAQEREAAEREAEKREAQAGTAALPAVAAGAAA
+AQTTDADADGATPPVEPVEPVEPVAAEKTDAPEPVAPDTEAIPVRRQRPVPRRAIVAESA
+PPVHEESRSTAAPVAAGAATGATAAAAGSTSAAAAPDALAAPATTEGDDGATVADPGDGN
+GRTRGGGPLALLLVLGLLAALVVGGVLLAQNLRGGPAPQAAAASSESESASSESASDTPS
+PSESTSPSPTPTSESAAAAPQPVQALRSVPDLPEHEAEHDADLSNLIDGDPTTVWRTFAY
+ARPNFGGYVESMNLVVQLEERTEVNEVTLQSTGATGGAWFAYIADSPEGANAQEIGNGTF
+DQDTVSIPVPFEGTEAEAEYVIVSLTSLPQLEGTTSDLPFGLRLGEIAVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001751.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001751.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7880d914cb74795b7f2e5eee4245f3da709b6004
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001751.fa
@@ -0,0 +1,15 @@
+>PROKKA_02304
+MSTITVTDADFDQKVLQSELPVLVDFWAEWCGPCRMLGPVLEDMAVEHEGKAVIAKLNVD
+ENPAIAARYGVTSIPLVVGFQNGEKVAESVGAKPKAALEKEFSALLG
+>PROKKA_01997
+MSTITVTDADFDQKVLQSELPVLVDFWAEWCGPCRMLGPVLEDMAVEHEGKAVIAKLNVD
+ENPAIAARYGVTSIPLVVGFQNGEKVAESVGAKPKAALEKEFSALLG
+>PROKKA_00433
+MSTINVTDTDFDQKVLQSELPVLVDFWAEWCGPCRMLGPVLDEMAVEHEGKAVIAKLNVD
+ENPATAARFGVTSIPLVLGFQGGEKVAESVGAKPKAALEKEFSALLG
+>PROKKA_00385
+MSTINVTDADFQAKVLDSELPVLVDFWAEWCGPCRMLGPVLDELAAEHEGEVLVAKLNVD
+ENPASAARYGVTSIPLVLGFQGGEKVAESVGAKPKAQLEKEFAALLG
+>PROKKA_02245
+MSTITVTDADFDQKVLQSELPVLVDFWAEWCGPCRMLGPVLEDMAVEHEGKAVIAKLNVD
+ENPAIAARYGVTSIPLVVGFQNGEKVAESVGAKPKAALEKEFSALLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001753.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001753.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1214dc1af9cfb2ced29eb6d436dba4dc99904782
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001753.fa
@@ -0,0 +1,29 @@
+>PROKKA_02307
+MTERGSAYERRPGLDPQDRGDRPAPVGQPAPPLTDALRPAAVELFGEALPRAEAYVAHLA
+DTGIEWGLIGPREAPRLWERHVLNCAVVEELLPQGALVADVGSGAGLPGLCLALARPDCQ
+FLLIEPLERRVEWLDMVVADLGLENVDVIRGRAEQVSGNLDVDVVAARAVSALKTLVPLT
+MPMLQGAGELLAIKGRSAADEIAAARKVLRKYGGAEPEILTVGEGLLPETTTVVRVSARP
+R
+>PROKKA_02000
+MTEQGSAYERRPGLDPRDRGDRPAPVGQPAPPLTDALRPAAVELFGEALPRAEAYVAHLA
+DTGIEWGLIGPREAPRLWERHVLNCAVVEELLPQGALVADVGSGAGLPGLCLALARPDCQ
+FLLIEPLERRVEWLDMVVADLGLENVDVIRGRAEQVSGNLDVDVVTARAVSALKTLVPLT
+MPMLQGAGELLAIKGRSAADEIAAARKVLRKYGGAEPEILTVGEGLLPETTTVVRVSARP
+R
+>PROKKA_00429
+MPEQASPYERRPGLDPKERGDRPAPVGQPAPPLIDALRPAAVELFGEDLPRAERYVAHLA
+DTGIEWGLIGPREAPRLWERHVLNCAVVEELIPEGALVADVGSGAGLPGLCLALARPDCR
+FLLIEPLERRVEWLDMVVEDLGLENVDVIRGRAEQVSGNLDVDVVTARAVSALKTLVPLT
+MPMLQGDGQLLAIKGRAAADEIAAARKVLRKYGGDEPEILTVGEGLLPETTTVVRVSARA
+R
+>PROKKA_00382
+MSAPQLTAELRPAAEDLFGEALPLAERYVDHLATTGIEWGLLGPREVPRLWGRHVLNCAV
+VARLLPEGSLVADVGSGAGLPGLCLALARPDCRFTLIEPLERRVAWLEMVIADLGLTNVE
+VVRGRSEQVADEIQVDIVTARAVSALKTLLPLTMPLLRSSGHLLAIKGRSAAEEITAAQK
+PLRKYGGGDPEIVTVGEGLLPEPTTVVRVPARRAR
+>PROKKA_02248
+MTERGSAYERRPGLDPRDRGDRPAPVGQPAPPLTDALRPAAVELFGEALPRAEAYVAHLA
+DTGIEWGLIGPREAPRLWERHVLNCAVVEELLPQGALVADVGSGAGLPGLCLALARPDCQ
+FLLIEPLERRVEWLDMVVADLGLENVDVIRGRAEQVSGNLDVDVVTARAVSALKTLVPLT
+MPMLQGAGELLAIKGRSAADEIAAARKVLRKYGGAEPEILTVGEGLLPETTTVVRVSARP
+R
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001754.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001754.fa
new file mode 100644
index 0000000000000000000000000000000000000000..57ce0bb2323a8eefe455c5a42d965b0c4c6da853
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001754.fa
@@ -0,0 +1,25 @@
+>PROKKA_02308
+MSAENVTPAPEAEDAVVETPAGQGSRVAEQDGAAVSEAVRRLEEEGDVAADYVEELLDIA
+DLDGDIDIEVRDGRTYVSVVSEDHDERLDGLVGPDGRTLEALQELVRLAVLAATGHRSRL
+ILDVCGHRERRNVALRTAAQAAVERVRVGEGPVHLEPMGAYERKIVHDVVADAGLTSESE
+GEGARRHVVISADD
+>PROKKA_02001
+MSAENVTPASEAEDAVVETPVGQGSRVAEQDGAAVSEAVRRLEEEGDVAADYVEELLDIA
+DLDGDIDIEVRDGRTYVSVVSEDHDERLDGLVGPDGRTLEALQELVRLAVLAATGHRSRL
+ILDVCGHRERRNVALRTAAQAAVERVRAGEGPVHLEPMGAYERKIVHDVVADAGLTSESE
+GEGARRHVVISADD
+>PROKKA_00428
+MSAENVNPAAEAEDAVVETTPAPDAPQAPAAEERTGSDAAVAAGEGAESSAAESASDGVR
+RLEEEGDVAADYVEELLDIADLDGDIDIEVRDGRTYVSVVSEDHDERLNALVGRDGKTLE
+ALQELVRLAVLAATGHRSRLILDICGHRERRDADLRETAQDAVERVRAGEGPVHLSPMGA
+YERKIVHDVVADAGLASASEGEGARRHVVISADA
+>PROKKA_00381
+MTAEHEGPLADAAEDSPAVEAPVEATAPDAAVDEQAEAVRRLEEEGDVAADYVEELLDIA
+DLDGDIDIEVRDGRTYVSVVPGEDDEDDRLADLVGPDGKALEALQELVRLAVLTATGHRS
+RLILDIAGHRRRRDAELRTLAGEAVERVRSGAGEVHLDPMGAYERKIVHDVVAEAGLASE
+SEGEGPRRHVVISG
+>PROKKA_02249
+MSAENVTPAPEAEDAVVETPAGQGSRVAEQDDAAVSEAVRRLEQEGDVAADYVEELLDIA
+DLDGDIDIEVRDGRTYVSVVSEDHDERLDGLVGPDGRTLEALQELVRLAVLAATGHRSRL
+ILDVCGHRERRNVALRTAAQAAVERVRAGEGPVHLEPMGAYERKIVHDVVADAGLTSESE
+GEGARRHVVISADD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001759.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001759.fa
new file mode 100644
index 0000000000000000000000000000000000000000..409debdbd619107ae1ae0c5410008ea059a7f0c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001759.fa
@@ -0,0 +1,43 @@
+>PROKKA_00206
+MTVESVDVSVIIPMHNGGELIHEQLDALAAQRTDLNWEVIVGDNRSTDGSPDAVRARADS
+FPVPLAVVDAFRVQGASHARNAAAAAARGEVLAMCDADDRVAPDWVEQAFRGVREIAPMV
+AGANRLLSHPQRPDAPLLNPRILHGRGAQTCNAAVRRDVFLASGGFDESLPPYGVEDSDL
+SARVLAAGHTIAPHPGLVLYFRETTGLKAKLRKIHSSGQAEAVLWSRGHEAQGTPLAESQ
+FVVALAALPADAVRTARARELRSLPKWTLREAAVRTGRWRGYRRWVKTGKAGEPRLPFLD
+GRGGAA
+>PROKKA_00237
+MFADADDVVSRWWVRNGARAFESSDLWSGGAPFMTDEQMREGVEGARRAFDDSDEWHAPV
+PGDLRNAFPVLMGGDFGVTREVFERVGGFDHSLGAVYEDNDFAVRAHLKGIRVDEAAAVR
+IAFRGKWDMRFRTRLVRRSAKAHSLVTTRYELGRQSHFPNPWVEFVRTGASAALMTLGCK
+TPDWEGVRLRAQTAAGAAAGRVEYRWMRRGPQPQIGLGYRRADSSPFSQADAAGAGENSE
+EVLAASVVIPARNAEGWIGEQLDSLAAQCDAPLFEVVVADNGSYDRTAQIALSHPTPFQV
+RVVDASGVPSASHARNVGARLARGHVLLFCDADDFVGDRWAGELYRAVTSGPQLVARGVL
+EHSRFNDVDVLAAYRIDPAQDLHDTEDSPRIERVSDGFAGYLATVPGNNFAIRRDDYLKL
+GGMDPAYPGGSEETDFVWRAQEAGFTVVQAAGAVVYYRLRTTPAAIFRQQRNQQRGRMYL
+WTRYRGRGMSGPSVKASVFAISRHMPMWPFLRRDRGRALAWAYTVGAHVGALEGMARYRR
+PALLRSRRPGSDGGTAA
+>PROKKA_02432
+MSTRARSSSTPTAPSVSVVIPVYNGAPTLPLQLEALHTQVGAPAFEVVVVDNRSTDDLDG
+AVRPFMESGPPLRVVRADGHQGSSYARNRGIAAARAPYVMFCDADDVVSRHWVATGAAAF
+ATAPIWTGSVTHLPAAVFEQGLEAVRDLLGDGPRPQDGPGREVPGPFPVLMGGDFGASRE
+LLVAVGGFDQSFPHAGDDNDLAFRVLRAGHRLVEMPQVRVASRGKTSLQTAHRIAFRSAR
+AHALLADRYGLWERSRATTWASEPVRCLGAAVKMAAHPTRADWRGLACRTAMASGTLAGA
+VEYHLLRRRPAPQVGLGLDPDDTALPGEEPQGAGGPGHPELVSVIIPAYNAEAYIAEQIE
+SLAVQVDAPEFEVIVADNGSTDRTASTAREAAERWGLTLTVVDARGPASASHARNVGAMA
+AAGGVLLFCDADDFVGPEWVRELAAAVRSREDALAVGTLLHRRFNDAAVLAAYGIPPEAG
+EPRTDAAGYPVVHGGFAGHLPTVAGNDFGVRRSLYLAVGGMDSSFPGGSEETDFSWRAQR
+RGAVVVHAPRAIVHYRLRSTPQTVFRQQRIQQVGRMLLWMRHRGDGMSGPSWRVSVTEVA
+RHLPAYLLVRERAARLRHARIAGGHLGALQGMVRYRLLKRIPPRRLVDGSSVPRA
+>PROKKA_02316
+MNQAVSVVIPCHNAAGSMQRQVDALLPQLEETDELLLVENRSADGTRRIAEEAALRDARV
+RVLNAPDKAGANHARNIGAARAHNPIILFCDADDVVHSGWVRSLRQVLGTDGIAGGSATP
+VDEEGRRLGPDLGLHETFGGPAYPLGATMGVRREVLETIGGFDESYAGGHDETDLAWRAA
+RAGWPTHFVPEARIDYVQRPDARSALQQRRLYARTSIQVWVQNPDLVDQSAVSLRGALNG
+VRLGLPLGIKMIRGTATARDAARWGWALGVLEGHLRYRVLGRPPARVAPPIPPAPHPAEP
+NRPCA
+>PROKKA_00516
+MSRPVSVIIPCHNAAAWVDRQISAVLAQLRADDELVLVDNRSTDTTYERLEAAAAGDRRV
+RTVSAPERPGANHARNVGIAAARNPLLLFCDADDLVTGGWVEAFRAALQNAGITGGAATP
+VDADGCRIGSDLGLHEIFGGPAYPLGACMAIRKDVVNAVGGFDESFAGGHDETDLAWRAE
+RAGWPTAFVPDARIDYLQRPDAAATVRQRRAYARTSIQLWARHPETVNPHGVSVKGAVRG
+VLRGLPNAVRVLRGRASADQAAQWGWSLGLLEGHLRYRILGKPPAAHTPRPDASA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001765.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001765.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e308e1df350f08869480da1524a70899a2319be2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001765.fa
@@ -0,0 +1,34 @@
+>PROKKA_02134
+MSVNLPPSPGGGPTEHAVEHALAPVEAGATQATTEAAADTRGTSVWGAAFQRLRRNPAAI
+AGAVIVLLFVLVAVLAPVLAPYAGTATPGMREIRPTHVPGPGEVAGYPLGLDRFGGDVLS
+KLIWGAQASLLIGVVSTAFGLAGGMLLGLLAGTFGGWVDSVVMRVVDILLSVPNLLLAVS
+IAAILGQTPFAVMIAIGVAQVPVFARLLRSSMLTQKGSDYVLAAQTLGLSRGRITMSHVL
+PNSLGPVIVQATLTLATAVIDAAALSFLGLGGGRPETAEWGRMLTYAQAELGINPWLAFL
+PGLCIAITALGFTLLGESLREALDPTSRRR
+>PROKKA_00089
+MTAVLTSSQTPPPPSDSSAAASPVSLVPATRRPRRADLGLAFALTGAAVLLVAALWPQLL
+ATHDPRALDLAAPLQAPSLDHWFGTDQNGRDLYSRIVHGTGPSLLIGLGAAAVGVGLGML
+LGIVAAFGGRWADAAVSRTVEVLFAFPSLLLALMLITVYGPSVSTLILAVGVGTAPGYAR
+LVRGQVLAVRGSAYVQAAEVIGHPPMTILLQHIVPNAVRPLVAVFMLGVGQAIVWASGLA
+FLGFGVAPPSPEWGALLEAGRPYITAAWWLEIFPGLAVLATALTATALGRHLEARLQGET
+R
+>PROKKA_00266
+MSVNLPPSPGSGPAEHAVDHALAPVEAGATQETTEAAADARGTSVWGAAFQRLRRNPAAI
+AGAVIVALFVLVAVLAPVLAPYAGTDTPGMREIRPTHVPGPGEVDGYPLGLDRFGGDVLS
+KLIWGAQASLIIGVVSTAFGLVGGMLLGLLAGTFGGWVDSVVMRTVDILLSVPNLLLAVS
+IAAILGQTPFAVMIAIGVAQVPIFARLLRSSMLTQKGSDYVLAAQTLGLSRGRITMSHVL
+PNSLGPVIVQATLTLATAVIDAAALSFLGLGGGRPETAEWGRMLTYAQAELGINPWLAFL
+PGLCIAIAALGFTLLGESLREALDPTSRRR
+>PROKKA_00136
+MTSAPAVAAEPTPAASATPSDPAGARRRARPRLGLLLSAGFLVVVLLAALFPSLLAPGDP
+FAGASGATLEPPGPGHWLGTDHLGRDLYTRVVHGTGLTVATAAAAVAGALVVGGTLGLAS
+GYVGGVADTLLMRVVDVLLSIPSLLLSLAVVAGLGFGPVQVAVAVGIGSVASFARIGRAQ
+ALRISQAPFVEAAPSFGTRRILVLLHHVVPNAVGPLVSLAVLEFGSALLAVSALSFLGYG
+EPRPAAEWGGLISDGRSYLAVAPWLTALPGLVIAATVLALQQVATSPAPADAPR
+>PROKKA_00126
+MSVNLPPSPGGGPTEHAVEHALAPVEAGATQATTEAAADTRGTSVWGAAFQRLRRNPAAI
+AGAVIVLLFVLVAVLAPVLAPYAGTATPGMREIRPTHVPGPGEVAGYPLGLDRFGGDVLS
+KLIWGAQASLLIGVVSTAFGLAGGMLLGLLAGTFGGWVDSVVMRVVDILLSVPNLLLAVS
+IAAILGQTPFAVMIAIGVAQVPVFARLLRSSMLTQKGSDYVLAAQTLGLSRGRITMSHVL
+PNSLGPVIVQATLTLATAVIDAAALSFLGLGGGRPETAEWGRMLTYAQAELGINPWLAFL
+PGLCIAITALGFTLLGESLREALDPTSRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001766.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001766.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c8a0a9c98dfaf1421442d9a3100f09d949be0152
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001766.fa
@@ -0,0 +1,17 @@
+>PROKKA_02211
+MSLRLSHTTWDALDPHAIAEFWRALLGWEVDEPHLYRPGSDECSLVGPDGQVVLFFRVPD
+AKRVKNRAHMDLRAAAGSTRDAEIERALALGAAMVDDRRVDLGWAVLADPEGNEFCILDG
+>PROKKA_00514
+MSLRLSHTTWDALDPHAVAEFWRELMGWEVTEPEAYELGSDECYLVTPHGYTILFYRVPD
+AKRVKNRAHMDLAVDDGTRDEEVERALGMGATMVDDRRGDLGWAVLADPEGNEFCILDI
+>PROKKA_00528
+MALKWYTLVVDCRDPQAQAHWWARALDWEVVHDTPEEAVAVPKGVGEEPVADPDEWRARG
+QGLVFVPVPEGKTVKNRLHIDLAPHTSQDRDAEIARLEELGATRVDVGQDEEEVTWTVLA
+DPEGNEFCVLSSRDS
+>PROKKA_00455
+MSLRLSHTTWDALDPYAVAEFWRELMGWDVAEPDSYAPGSDECYLATAEGYTVLFYRVPD
+AKRVKNRAHMDLMTAGTTRDEEVERALGLGASMVDDRRGDLGWAVLADPEGNEFCILDTG
+D
+>PROKKA_00218
+MSLRLSHTTWDALDPHAIAEFWRALLGWEVDEPHLYRPGSDECSLVGPDGQVVLFFRVPD
+AKRVKNRAHMDLRAAAGSTRDAEIERALALGAAMVDDRRVDLGWAVLADPEGNEFCILDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001772.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001772.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4997f64b57c00797b7c12f2ef7d8dd293340ae31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001772.fa
@@ -0,0 +1,40 @@
+>PROKKA_00048
+MDTSAPRTSPSTPPASAAHITPEGGSLRRTLKSRHLTMIAMGGAIGTGLFVASGNTIATA
+GPGGALAAYVAIGFMVFLLMQSLGEMSTYLPVSGAFEEYSTRFVSPSFGFAIGWNYWYNW
+AITVAAELVAAALIMRYWLPDVPSWIWSATFLALLFGLNALSTRAYGESEFWFSLIKVAT
+VVIFLVLGVLMIVGILGGSSPGFHNWTDGEAPFVGGGAGILAIFMVAGFSFQGTELVGVA
+AGEAEDPEKNVPKAIRTVFVRILLFYVGAITVVGFLIPYTSPHLLGSDVEDISISPFTLV
+FENAGVLAAASVMNAVILTAILSAGNSGLYASTRMLWALADSGKAPRFLAKVNRRGVPMN
+ALYATTAVGAACFLTTFIGDGAAYVWLVSASGLAGFIVWMGIAWSHYRFRRAYVAQGHDP
+KDLPYRAFLFPLGPIVALVMCAVVILGQNYQAFMGDVDLVAVASAYIGLPLFLALWLGHK
+LVTGSKPVRYEDADLTRVLD
+>PROKKA_02061
+MDTSAPRTSPSTPAASAAHATHEGGSLQRTLKSRHLTMIAMGGAIGTGLFVASGNTIATA
+GPGGALVAYVAIGFMVFLLMQSLGEMSTYLPVSGAFEEYSTRFVSPSFGFAIGWNYWYNW
+AITVAAELVAAALIMRYWLPDVPSWIWSAIFLALLFGLNALSTRAYGESEFWFSLIKVAT
+VVIFLVLGVLMIVGILGGSSPGFHNWTDGEAPFVGGGAGILAIFMVAGFSFQGTELVGVA
+AGEAEDPEKNVPKAIRTVFVRILLFYVGAITVVGFLIPYTSPHLLGSDVEDISISPFTLV
+FENAGVLAAASVMNAVILTAILSAGNSGLYASTRMLWALADSGKAPRFLAKVNRRGVPMN
+ALYATTAVGAACFLTTFIGDGAAYVWLVSASGLAGFIVWMGIAWSHYRFRRAYVAQGHDP
+KDLPYRAFLFPLGPIVALVMCAVVILGQNYQAFMGDVDLVAVASAYIGLPLFLALWLGHK
+LVTGSKPVRYEDADLTRVLD
+>PROKKA_00296
+MNPTDSPRTAGPAGSTAAAASPEPHTGLKRTLAARHLMMIAMGGAIGTGLFVASGNSIAT
+AGPGGALLAYVVIGFMVFLLMQSLGEMATYLPVSGAFEEYATRFVSPSFGFAIGWNYWYN
+WAITVAAELVAAALVMRYWFPDVPSWAWSALFLALLFGLNALSTRAYGESEFWFSLIKVV
+TVVVFLVLGVLMIVGVLGDAAVGTDNWTTGEAPFVGGAPGILAIFLVAGFSFQGTELVGV
+AAGEAEDPERTVPKAIRTVFWRILLFYVGAITVIGFLIPYTSPNLLGSDIEDIAISPFTL
+VFENAGVLAAAAVMNAVILTAILSAGNSGLYASTRMLWALADSGKAPRFLAKVNRRGVPM
+NALVVTTAVGALCFLTTFIGDGAAYVWLVSASGLAGFIVWMGIAWSHYRFRKAYVAQGND
+ITDLPYRAALFPLGPIVALLLCTVVILGQNYEAFLNGVDLVAVASAYIGLPLFLALWIGH
+KLVTGSKGVRPEEADLTRGRA
+>PROKKA_00043
+MDTSAPRTSPSTPAASAAHATHEGGSLQRTLKSRHLTMIAMGGAIGTGLFVASGNTIATA
+GPGGALVAYVAIGFMVFLLMQSLGEMSTYLPVSGAFEEYSTRFVSPSFGFAIGWNYWYNW
+AITVAAELVAAALIMRYWLPDVPSWIWSAIFLALLFGLNALSTRAYGESEFWFSLIKVAT
+VVIFLVLGVLMIVGILGGSSPGFHNWTDGEAPFVGGGAGILAIFMVAGFSFQGTELVGVA
+AGEAEDPEKNVPKAIRTVFVRILLFYVGAITVVGFLIPYTSPHLLGSDVEDISISPFTLV
+FENAGVLAAASVMNAVILTAILSAGNSGLYASTRMLWALADSGKAPRFLAKVNRRGVPMN
+ALYATTAVGAACFLTTFIGDGAAYVWLVSASGLAGFIVWMGIAWSHYRFRQAYVAQGHDP
+KDLPYRAFLFPLGPIVALVMCAVVILGQNYQAFMGDVDLVAVASAYIGLPLFLALWLGHK
+LVTGSKPVRYEDADLTRVLD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001780.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001780.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bd583c8c7d4220edcd07a3a2fc05b2a76706ba3a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001780.fa
@@ -0,0 +1,29 @@
+>PROKKA_00120
+MLVLVINSGSSSLKYQLRELADDGTDAPVPVLAQGLVERIGVPGSGVPDHAAALEQVEAE
+LAEATGGRTIDAAGHRVVHGGERFTAPARVTNEVIRAIERLAPLAPLHNPAAAQGLRAMA
+ERWPDMPQVVVFDTSFHQTMPREAWQYALPDEVYTEHGIRRYGFHGTSDDLVTGLAAEHL
+GIPRGEFRAVVLHLGNGASATAIRDGVSVDTSMGYTPLAGLVMGTRSGDLDPSVVTHLMR
+NHGYDAEELDTLMNRRSGLLGLAGEADMRQVLENAASGDGRARNALDVASYRLAKYVGGY
+HVAVGGAQAIVFTAGIGENSAPFRARVLDRLEALGVAYDAEANRARVAGPHTISAPESAI
+PVLVVPTDEEQAIARLTWELAR
+>PROKKA_00264
+MLHLGNGASATAIRDGASVDTSMGFTPLAGLVMGTRTGDLDPSVVTHLMRTQGHSAEEMD
+TLMNKESGLLGLAGHADMRQVVEAADAGDRRARTAPDVASYRLAKYVGGYHVAVGGAQAI
+VFTAGIGENSAPFRARVVERLGALGVELDAAANEAGLSAAGDDGVAVISAPGSAIPVLVI
+PTDEEQAIARLTWELTRG
+>PROKKA_00199
+MTASPATMTLPTVSARQLPEDALLVLVVNSGSSSLKYQVRELTPDGRDTDQPVVLKGLVE
+RIGVAGSDVPDHAAALERVEAEITAVVGSRRLAAAGHRVVHGGERFQRPELVTNEVIRAI
+ERLAPLAPLHNPAAAQGLRAVAQRWPDLPQVVVFDTSFHQSMPREAWQYAIPDELYTEHG
+IRRYGFHGTSHDLVTGLAAEHLGLERSEFDGVVLHLGNGASATAIRGGRSIDTSMGYTPL
+AGLVMGTRSGDLDPSIVTHLITAHGMSAEDVDAMLNKESGLLGLSGNADMRQVLEAAEAG
+HRASRDALRIASYRLAKYVGGYHVAVGGAKAIVFTAGIGENSAPFRARVLDRLEPLGVRY
+DHARNMVRGDEPRTISTDDSAIPVLVVPTDEEMAIAQLTHHVVEQAEAWTLG
+>PROKKA_00128
+MLVLVINSGSSSLKYQLRELADDGTDAPVPVLAQGLVERIGVPGSGVPDHAAALEQVEAE
+LAEATGGRTIDAAGHRVVHGGERFTAPARVTNEVIRAIERLAPLAPLHNHAAAQGLRAMA
+ERWPDMPQVVVFDTSFHQTMPREAWQYALPDEVYTEHGIRRYGFHGTSHDLVTGLAAEHL
+GIPRGEFRAVVLHLGNGASATAIRDGVSVDTSMGYTPLAGLVMGTRSGDLDPSVVTHLMR
+NHGYDAEELDTLMNRRSGLLGLAGEADMRQVLENAASGDGRARNALDVASYRLAKYVGGY
+HVAVGGAQAIVFTAGIGENSAPFRARVLDRLEALGVAYEAEANRARVAGPHTISAPESAI
+PVLVVPTDEEQAIARLTWELAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001781.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001781.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cdcbed88a63b10d687c92d00ea5b2a70ccd5daf1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001781.fa
@@ -0,0 +1,12 @@
+>PROKKA_00132
+MTDVPFEDREDERELETDLLADPNAAGDPEPEDGRDGQPVRGGSDDPQHWAGEGRAPDSL
+RNAESAAMHIEEDAQDRTRADEGDVEIL
+>PROKKA_02146
+MTDVPFEDREDERELETDLLADPNAAGDPEPEDGRDGQPVRGGSDDPQHRAGEGRAPDSL
+RNAESAAMHIEEDAQDRTRADEGDVEIL
+>PROKKA_00253
+MTSTPYEDGIDQRELQEDLLAEPDSATDPGPQDGRDGQPVRGSSDDPQHWAGDGRAEDSL
+RNAESEAMHIQQDAEDRTRADEGDVEIL
+>PROKKA_00140
+MTDVPFEDREDERELETDLLADPNAAGDPEPEDGRDGQPVRGGSDDPQHRAGEGRAPDSL
+RNAESAAMHIEEDAQDRTRADEGDVEIL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001784.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001784.fa
new file mode 100644
index 0000000000000000000000000000000000000000..47a3d6ba02fceda080d30fcfb58aa5d6d4473850
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001784.fa
@@ -0,0 +1,18 @@
+>PROKKA_00155
+MSGVGNEREWRWRIGVASPLVGSAGVFAGLRQDLGLGWGLTLVAVTALGAMLALRGVHHR
+VEAEQARRNVFDAGAGSTAWVMLLMGAAVIPGLVLNAIDDAGVRAVVAGLLGAVVEMQRR
+VHTTRGELFAYQAGSGRRENWVSRWAPPRAPGIARNVGAVAALAGWLWRVMWRADRAGGS
+AHDAWRDPSPQTTDKGSGPSPSLAGARLSVWLAPLYGGVLSELSGGLQARGQEGAASEAH
+VPQADPSPGQRPTAGRRNRRRDRVHPAQQNRCERSNTPTQQSGPPCAATGP
+>PROKKA_02169
+MSRVGNEREWRWRIGVAPALVGSAGVFAGLRQDLGLGWGLTLVAVTALGAMLALRGVHHR
+VEAEQARRNVFDAGAGSTAWVMLLMGAAVIPGLVLNAIDDAGVRAVVAGLLGAVLAAAAH
+GILAATTTLEEQPRPEPVPLDRRRR
+>PROKKA_01469
+MDAVAQNTGRRVGEPLTERSDAGTGHTAASQGRDGTLRGDAPAWRAAGVGAAFGLASVVC
+SLQDHLAEWSAIGGAAAFMALGLLSMTGLRFVVDQEKARRTVFYAGERQGAWFLLNFLGI
+FQIPRFLISGIADPTGLVLAAAGLGIVVAVANQALVSRYMTGRRQPDPEPVPLG
+>PROKKA_00168
+MCQHGAVSRVGNEREWRWRIGVASALVGSAGVFAGLRQDLGLGWGLTLVASTALGAMLAL
+RGVHHRVEAERARRNVFYAGAGSTAWVMLLMGAAVIPGLVLNVIDDAGVRAVGAGVLGAT
+LAAAAHGILAATTTLEEQPRPEPVPLDRRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001797.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001797.fa
new file mode 100644
index 0000000000000000000000000000000000000000..692440555eced630426d0550324d5b5f7cbacddb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001797.fa
@@ -0,0 +1,80 @@
+>PROKKA_00273
+MIDAPLAQLAETYARDVRLASTSGVSAEPEAQLTVPVSEFLRAFSSVTGIGDLSLLREAQ
+LDGVRPDFAALIDGRPCGWVELKAPGHTVIGEKWRGREKGQWDLLSQLDALLVSNGDEIA
+LYVSGSPVDTAFLPVDGVAGWDADRLRTVLEQFTLAQPRPITRVSQLADRLAPLARFLRE
+RLQEGLSNNYRSVREAKAAWDHTVHHTTTDAQFAGDVAQVVAYSMAIAGLSGQADRNADG
+VVTLEEAKHALETAHRNVLAASLGPIIGIPALMEYIAPEVGAIMRLVSSMDVAAIERSTD
+SRGEPWLWFYEDFLQRYDPAARNRAGVYYTPISVVQCQVRVVDALLRERFGQTLGFGAPS
+VVTLDPATGSGTYPLAVIDRAEAAAREERGPAGVAQVAKNLTKNLLAFELLPGPYSVAHL
+RIGQRLAEAQGHAFQAEEIGVYLTDTLEDPSAGMAEGLFGDARVLAEAAEAARRIKRDRR
+ITVAIGNPPYDRVTSGTGGWVEHGDGEDALFDDVIGPAQEQGVIFSAQASLYNLYVYFWR
+WAIWKAFQQDPGDQAIISFITASSWLTGPAFVGLRDLARRTASEIWVMDLGGEGRGARQE
+ENVFDIQTPVAIVTLVRTGKAAREASVYYRRFRGTRAEKFAALDEVARLDPDDGTWECLP
+GGAGDPLAPASGGEDWAAMPALADLFPWQQPGIKYNRAWPVAPDQDTLQRRWRELLADPS
+ADARAEKYVTGHSGRTIHTAVSGLTPLAALPADAEHRPITRVAWRSFDRQWTFDDPRLIN
+LERPALWQALSDRQLFFVSPKTARISGGPAVTVATAVPDLHYFVGSYGGKDVIPLYRDAE
+AAQPNVTGGLLPLLGERYGREVTPEDLAAYVMGIAGHDAYVQRFDEALEGSPVRVPLTVD
+PALFARAVELGKRLLWLQTYGERFTGVDRPAGRVPRIPGLGWEAPVTALPASPRAVSYDP
+ATQRLKVGDGVVTGVSPEVRAFAVSGMNILDKWLGARTATGIGRAAGKAATPLDRIRPTE
+WADEWNDELLDLLRVLTETVSLGGDQADLLDEILARDLIPANELPEPTPAERKVPKTIKR
+DFSTAQEEMF
+>PROKKA_02288
+MIDAPLAQLAETYARDVRLASTSGVSAEPEAQLTVPVSEFLRAFSSVTGIGDLSLLREAQ
+LDGVRPDFAALIDGRPCGWVELKAPGHTVIGEKWRGREKGQWDLLSQLDALLVSNGDEIA
+LYVSGSLVDTAFLPVDGVAGWDADRLRTVLEQFTLAQPRPITRVSQLADRLAPLARFLRE
+RLQEGLSNNYRSVREAKAAWDHTVHHTTTDAQFAGDVAQVVAYSMAIAGLSGQADRNADG
+VVTLEEAKHALETAHRNVLAASLGPIIGIPALMEYIAPEVGAIMRLVSSMDVAAIERSTD
+SRGEPWLWFYEDFLQRYDPAARNRAGVYYTPISVVQCQVRVVDALLRERFGQTLGFGAPS
+VVTLDPATGSGTYPLAVIDRAEAAAREERGPAGVAQVAKNLTKNLLAFELLPGPYSVAHL
+RIGQRLAEAQGHAFQAEEIGVYLTDTLEDPSAGMAEGLFGDARVLAEAAEAARQIKRDRR
+ITVAIGNPPYDRVTSGTGGWVEHGDGEDALFDDVIGPAQEQGVIFSAQASLYNLYVYFWR
+WAIWKAFQQDPGDQAIISFITASSWLTGPAFVGLRDLARRTASEIWVMDLGGEGRGARQE
+ENVFDIQTPVAIVTLVRTGKAAREASVYYRRFRGTRAEKFAALDEVARLDPDDGTWECLP
+GGAGDPLAPASGGEDWAAMPALADLFPWQQPGIKYNRAWPVAPDQDTLQRRWRELLADPS
+ADARAEKYVTGHSGRTIHTAVSGLTPLAALPADAEHRPITRVAWRSFDRQWTFDDPRLIN
+LERPALWQALSDRQLFFVSPKTARISGGPAVTVATAVPDLHYFVGSYGGKDVIPLYRDAE
+AAQPNVTGGLLPLLGERYGREVTPEDLAAYVMGIAGHDAYVQRFDEALEGSPVRVPLTVD
+PALFARAVELGKRLLWLQTYGERFTGVDRPAGRVPRIPGLGWEAPVTALPASPRAVSYDP
+ATQRLKVGDGVVTGVSPEVRAFAVSGMNILDKWLGARTATGIGRAAGKAATPLDRIRPTE
+WADEWNDELLDLLRVLTETVSLGGDQADLLDEILAGDLIPANELPEPTPAERKVPKTIKR
+DFSTAQEEMF
+>PROKKA_00083
+MDRDAVNALAEEYSRGIGQALSMGVAAEPEAQLTVPFAAFLSRFAQEVELGRLDLLREAQ
+LDGVRPDFAAALDGRPCGWIELKAPGHTVVGERWRGREKSQWALLSQLDALLVSNGELLA
+LYVAGAPVETCALPVDGAAGWDPDRLRRVLEQFTLAQPRPITRVSQLADRLAPLARFLRE
+RLAEGLEHSYDSVVEAKAAWDHTMQHTTSPEEFSGDVAQVVAYSMAIAGLSGQADRNADG
+VVSLEEAKHALETAHRNVLAASLGPILGIPALMQHIAPEVGAITRLVAGMDVAAIERSTD
+SRGEPWLWFYEDFLQRYDPEARSRAGVYYTPISVVECQVRVVDALLRERFGQNLGFGAPS
+VVTLDPATGSGTYPLAIIDRAESVAREERGDAGAKQVAMNLTKNLLAFELLPGPYSVAHL
+RIGQRLAEAQGHAFQAEEIGVYLTDTLEDPSAGMPTGLFGDARVLAEAAESARRVKRDQQ
+ITVAIGNPPYDRVTSGTGGWVEQGSGSGDALFDDVIKPAQDSGVIFSAQASLYNLYVYFW
+RWAIWKAFQQDPKDHAVISFITASSWLTGPAFVGLRRLAQATASEIWVMDLGGEGRGARK
+EENVFDIQSPVAIVTLVRTGKASREAKVFYRRFRGSRAEKFTALDRIQRLDAADGWEQIA
+APGGAPFMPASGGEDWTAMPQLADLFPWQQPGIMYNRAWPVASDQNTLRRRWQELLSDDD
+ADARAGKYVTGNSGRTIHTAVAGLPTLASLPADAEPRPIVRVAWRSFDRQWTFDDPRLIN
+LERPALWQALSDRQLFLVSPKTARINGGPAVTVSTAVPDKHHYVGSFGGKDVIPLYRDAA
+AAEPNVTVGLLELLADRLGHDVTPEDLAAYVMAVAAHDGYAQTFDEALETSPVRIPFTAD
+ASLWDAAVALGERLLWLQTYGERFTSADRPRGRVPRVPGLGWSEAVTHIPADTASLSYDA
+ASRELRVGDGVVTGVSPEVRAFSVSGMNIVDKWLGARTAKGIGRAAGKAATPLDRIRPTE
+WADEWNDELLDLLRVLTETVALGDQQAELLAAILAGELITAADLPVPTAAERKVPKTIKR
+GVSPHQEGLL
+>PROKKA_00271
+MIDAPLAQLAETYARDVRLASTSGVSAEPEAQLTVPVSEFLRAFSSVTGIGDLSLLREAQ
+LDGVRPDFAALIDGRPCGWVELKAPGHTVIGEKWRGREKGQWDLLSQLDALLVSNGDEIA
+LYVSGSLVDTAFLPVDGVAGWDADRLRTVLEQFTLAQPRPITRVSQLADRLAPLARFLRE
+RLQEGLSNNYRSVREAKAAWDHTVHHTTTDAQFAGDVAQVVAYSMAIAGLSGQADRNADG
+VVTLEEAKHALETAHRNVLAASLGPIIGIPALMEYIAPEVGAIMRLVSSMDVAAIERSTD
+SRGEPWLWFYEDFLQRYDPAARNRAGVYYTPISVVQCQVRVVDALLRERFGQTLGFGAPS
+VVTLDPATGSGTYPLAVIDRAEAAAREERGPAGVAQVAKNLTKNLLAFELLPGPYSVAHL
+RIGQRLAEAQGHAFQAEEIGVYLTDTLEDPSAGMAEGLFGDARVLAEAAEAARQIKRDRR
+ITVAIGNPPYDRVTSGTGGWVEHGDGEDALFDDVIGPAQEQGVIFSAQASLYNLYVYFWR
+WAIWKAFQQDPGDQAIISFITASSWLTGPAFVGLRDLARRTASEIWVMDLGGEGRGARQE
+ENVFDIQTPVAIVTLVRTGKAAREASVYYRRFRGTRAEKFAALDEVARLDPDDGTWECLP
+GGAGDPLAPASGGEDWAAMPALADLFPWQQPGIKYNRAWPVAPDQDTLQRRWRELLADPS
+ADARAEKYVTGHSGRTIHTAVSGLTPLAALPADAEHRPITRVAWRSFDRQWTFDDPRLIN
+LERPALWQALSDRQLFFVSPKTARISGGPAVTVATAVPDLHYFVGSYGGKDVIPLYRDAE
+AAQPNVTGGLLPLLGERYGREVTPEDLAAYVMGIAGHDAYVQRFDEALEGSPVRVPLTVD
+PALFARAVELGKRLLWLQTYGERFTGVDRPAGRVPRIPGLGWEAPVTALPASPRAVSYDP
+ATQRLKVGDGVVTGVSPEVRAFAVSGMNILDKWLGARTATGIGRAAGKAATPLDRIRPTE
+WADEWNDELLDLLRVLTETVSLGGDQADLLDEILAGDLIPANELPEPTPAERKVPKTIKR
+DFSTAQEEMF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001798.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001798.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cad3893edd241ef4e669aed67b5d6c2549703cc0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001798.fa
@@ -0,0 +1,20 @@
+>PROKKA_00276
+MTGSAPAQLRPLRATDAPAVLAAFHAGTVGMADPAEVTDDASARAYVDGLVQAEGTDAVA
+VVERGTDTLIGLVAVVRDEAHGTGALTAWLHQGWRGDAIMSRAATTVADAELAEGGLERI
+ELAHRADSPTAGAVARAAGLRHEGTQRGRLRTGGRRLDVHLYGRLAADPLPEERVRPLPW
+ASDARPWADR
+>PROKKA_02291
+MTGSAPAQLRPLRPTDVPAVLAAFHAGTVGMADPAEVTDEASARAYVDGLVQAAETDAVA
+VVERGTDTLIGLVAVARDEAHGTGALTAWLHQGWRGDAIMSRAATTVTDAELAEGGLERI
+ELAHRADSPTAGAVARAAGLRHEGTQRGRLRAGGRRLDVHLYGRLAADPLPEERVRPLPW
+ASDARPWADR
+>PROKKA_00079
+MTGTARAQLRPLHSDDADAVFEGFRSDPVGMARQGDVSDEASARFYVDRMLESEATDAVA
+VVDPATDRLIGLVSVVRDEENRSGWFSYWLNSAWRGDAIMARAAATVADAELAEGGLERL
+ELGHRANNPTSGSVARAAGFLHEGTQRGHFLIDGRRQDVHLYGRLPSDPQPAEKVRPLPW
+ASDERPWSGR
+>PROKKA_00275
+MTGSAPAQLRPLRPTDVPAVLAAFHAGTVGMADPAEVTDEASARAYVDGLVQAAETDAVA
+VVERGTDTLIGLVAVARDEAHGTGALTAWLHQGWRGDAIMSRAATTVTDAELAEGGLERI
+ELAHRADSPTAGAVARAAGLRHEGTQRGRLRAGGRRLDVHRYGRLAADPLPEERVRPLPW
+AADARPWADR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001799.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001799.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e089c013ac56e9c83fa49683d95460381a95f7e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001799.fa
@@ -0,0 +1,28 @@
+>PROKKA_00285
+MPEGDSLVRVAHRLRPVLEGRVLTHADLRVPRHATADLTGWTVAEVLPRAKYLLMRLTPP
+AARPGARPLTLISHLKMEGRWLVSALDARWGAPAWQVRAVLETAEHRVLGAQLGLLTLVP
+TADETTVLGHLGPDLLDPAWDTPDDGAALLAEGMRRLTARPERPVGLALLDQRLVSGIGN
+IYRCETLLLAGIDPHRPIGEVEDVAGLVLLARDLLRANVPPAAPATGARRRTTGVRPNPG
+RPFGVEVLVPAGPPLGTAPGRTPGARGGGAPSYWVYGHDRAPCLRCRGPVRQEDYGSAED
+DARRLWWCPHCQG
+>PROKKA_02307
+MPEGDSLVRVAHRLRLVLEGRVLTHADLRVPRHATADLTGWTVAEVLPRAKYLLMRLTPP
+AARPGARPLTLISHLKMEGRWLVSAVDARWGAPAWQVRAVLETAEHRVLGAQLGLLTLVP
+TADEATVLGHLGPDLLDPAWDTPDDGAALLAEGVRRLTARPERPVGLALLDQRLVSGIGN
+IYRCETLLLAGIDPHRPIGEVEDVAGLVLLARDLLRANVPPAAPAAGARRRTTGVRPNPA
+RPFGVEVLVPAGPSPGTAPGRTPGARGGGAPSYWVYGHDRAPCLRCRGPVRQEDYGSPED
+DARRLWWCPHCQR
+>PROKKA_00048
+MPEGDSLVRAAHRLRPVLAGRVLTHADLRVPQLATARLTGWTVSEVEPRGKWLLMRLTPP
+ADRPDAAPHTLVSHLKMEGRWMVTGRDARWPAPAWQVRAVLETAEHRAVGAQLGRLELAP
+TAEEDRLLGHLGPDLLDPAWDDPARGAELLAEGVRRLTARPERPVGLALLDQRTTCGIGN
+IYRCESLLLAGLDPHRPVAAVPDVSGLLTLARDLLRANVPPAAPFIGWPRTTTRVRPDPS
+GPYGLRVVVEDRGFPGGLPGGPVPDDAPHASATSTSGAGLGRRGDLPRGPHYWVYGHRTT
+PCGRCGGPVTFEEYGSPEDDERQLWWCRTCQR
+>PROKKA_00291
+MPEGDSLVRVAHRLRPVLEGRVLTHTDLRVPRHATADLTGWTVAEVLPRAKYLLMRLTPP
+TARPGARPLTLISHLKMEGRWLVSAIDARWGAPAWQVRAVLETAEHRVLGAQLGLLTLVP
+TADEAAVLGHLGPDLLDPAWDTPDDGAALLAEGVRRLTARPERPVGLALLDQRLVSGIGN
+IYRCETLLLAGIDPHRPIGEVEDVAGLVLLARDLLRANVPPAAPAAGARRRTTGVRPNPA
+RPFGVEVLVPAGPSPDTAPGRTPGARGGGTPSYWVYGHDRTPCLRCRGPVRQEDYGSPED
+DARRLWWCPHCQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001800.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001800.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c370c951b213c77dac1fd6c079434584f93fe02e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001800.fa
@@ -0,0 +1,16 @@
+>PROKKA_00286
+MSIDAAPPEDGGTAPTGTSPAPEALEDALPHPSDPSVTPFLLFEGDAGAAMDAYLTAFVE
+YLPVTEVRRDLFDDSSPRGAEWAGKVLHGELEIAGQRLRFFDSFTPHGFTFTPAISLFVE
+LPDATAVDAIHDTLLAGGGRDYMPPDDYGFSRRFAWVGDRFGVTWQLNAA
+>PROKKA_02308
+MSIDAAPPEDVGTAPTGTSPAPEALEDSLPHPSDPSVTPFLMFEGDAGAAMDAYLTAFVE
+HLPVTEVRRDLFDDSSPRGAAWAGKVLHGELEIAGQRLRFFDSFTPHGFTFTPAISLFVE
+LPDATAVDAVHDALLAGGGRDYMPPDDDGFSRRFAWVGDRFGVTWQLNAA
+>PROKKA_00068
+MSETTTDPGLPDDVGVDAGADPTGTAPAPAALEESMPHPSDPSVTPFLMFEGDAGAAMDA
+YLSVFVEHLPVTEVRRDLFDGSSPRGAEWAGKVLHGELEVAGQRLRFFDSFTSHGFTFTP
+AISLFVELPDPTAVDAVHDALIAGGGQDYMPPGDYGFSRRFAWVGDRFGVTWQLNAA
+>PROKKA_00292
+MSIDAAPPEDVGTAPTGTSPAPEALEDSLPHPSDPSVTPFLLFEGDAGAAMDAYLTAFVE
+HLPVTEVRRDLFDESSPRGAAWAGKVLHGELEIAGQRLRFFDSFTPHGFTFTPAISLFVE
+LPDATAVDAIHDALLAGGGRDCMPPDDDGFSRRFAWVGDRFGVTWQLNAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001804.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001804.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3237010c7114f6463d0041268d0018607252570d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001804.fa
@@ -0,0 +1,24 @@
+>PROKKA_00329
+MLEISQVSKTFFPNTVNERRALQGIDLHLAEGDFVTVIGSNGAGKSTILNTIAGKLLPDT
+GTVAVGGKDVTRMPDHRRAASIGRVFQDPTAGTAPNLTIEENMALAWRRGHARGLSRGVS
+RARRAMFRDELTKLELGLENRLTAKVGLLSGGQRQALSLLMATFSGPKILLLDEHTAALD
+PSRAELVTRLTRQVVAEHRLTTLMVTHNMSQALEVGNRLIMMHDGRIILELDEQEKAGRT
+PADLLAEFAKIKGAVVDDKTMLS
+>PROKKA_00045
+MLEISQVSKTFFPNTVNERRALQGIDLHLAEGDFVTVIGSNGAGKSTILNTIAGKLLPDT
+GTVAVGGKDVTRMPDHRRAASIGRVFQDPTAGTAPNLTIEENMALAWRRGHARGLSRGVS
+RARRAMFRDELTKLELGLENRLTAKVGLLSGGQRQALSLLMATFSGPKILLLDEHTAALD
+PSRAELVTRLTRQVVAEHRLTTLMVTHNMSQALEVGNRLIMMHDGRIILELDEQEKAGRT
+PADLLAEFGKIKGAVVDDKTMLS
+>PROKKA_00006
+MLEISQVSKTFFPNTVNERRALQGIDLHLAEGDFVTVIGSNGAGKSTILNTIAGKLLPDT
+GTVKVSGKDVTRMADHRRAAWIGRVFQDPTAGTAPNLTIEENMALAWRRGHTRGLARGVS
+RSRRGLFREELTKLELGLEDRLTAKVGLLSGGQRQALSLLMATFSGPKILLLDEHTAALD
+PSRAELVTRLTQQVVAEHRLTTLMVTHNMSQALEVGNRLIMMHDGRIILELDEAQKAGRT
+PADLLAEFAKIKGAVVDDKTMLS
+>PROKKA_00336
+MLEISQVSKTFFPNTVNERRALQGIDLHLAEGDFVTVIGSNGAGKSTILNTIAGKLLPDT
+GTVAVGGKDVTRMPDHRRAASIGRVFQDPTAGTAPNLTIEENMALAWRRGHARGLSRGVS
+RARRAMFRDELTKLELGLENRLTAKVGLLSGGQRQALSLLMATFSGPKILLLDEHTAALD
+PSRAELVTRLTRQVVAEHRLTTLMVTHNMSQALEVGNRLIMMHDGRIILELDEQEKAGRT
+PADLLAEFGKIKGAVVDDKTMLS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001806.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001806.fa
new file mode 100644
index 0000000000000000000000000000000000000000..180900accf15cebb71c010ecd9881097e8046d31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001806.fa
@@ -0,0 +1,31 @@
+>PROKKA_00369
+MSTTPTPPVSHGSAPSRMTWMDAMRGFAVLLVMFTHTYTMPQGLDATFSSVAFANVVQVF
+QSWRMPMLVFLSGVLLPRSVSKPLGTYYRGKAERILWPFLVWMVVLALATGKPGSLLSVE
+FWRGGAWHLWFLWVLMLCYLIGPVIRRVPALVVAAVLFVLLLEFVSGPRDWVRPLYWGVY
+FFLGAASARLLPRIRTAPAALGVIAVILMVLTVTATRTGALVVAERQPWSVFAALPGILV
+VLWLGPRLPRLPFLEFCGRRSMVLYVAHMPVLILAVAAFRDLAAVRPVDFYVAIASFTFL
+VPLALALGYRRVRWLFELPTAGRVRARPRTRATVPGAADAVPAQTAEPASTTAPLPVVEP
+ASPPQPAAGPTPAAEPAAGAPARVRAPRPRPRHAD
+>PROKKA_00085
+MSTTPTPPMSHGSTPSRMTWMDAMRGFAVLLVMFTHTYTMPQGLDATFSSVAFANVVQVF
+QSWRMPMLVFLSGVLLPRSVSKPLGTYYRGKAERILWPFLVWMVVLALATGRPGSLLSGE
+FWRGGAWHLWFLWVLMLCYLIGPVIRRVPALVVAAVLFVLLLEFVSGPRDWVRPLYWGVY
+FFLGAASARLLPRIRTAPAALGVIAVILMVLTVTATRTGALVVAERQPWSVFAALPGILV
+VLWLGPRLPRLPFLEFCGRRSMVLYVAHMPVLILAVAAFRDLAAVRPVDFYVAIASFTFL
+VPLALALGYRRVRWLFEFPTAGRGRERPRTRAAVPEAADAVPAQTAEPAPTTAPLPVVEP
+ASEPQSTAGPAPATEPASDAPAQVPRPRPRHAD
+>PROKKA_02394
+MDAIRGTAILLMLLLHATMIPAVVGGMEPVPWLVAITDATAPFRMPVLMFLSGMLLDRAL
+AKPAKRYLSGKFRVLLWSYVVWAVVYFMVMGRPGELFRPWTWVQTLYLWFLAFLLAYYVL
+ALVLRRIPAIVVAVAALVPHVVLVGAERGFLARFFLYMTVFFAGAAFTRFLAARPGILEP
+RRRDGHLLVGLPLLVVGVVAIRSGGALPHPAGAVVGAVAAVAVAMGLVLVVQALVPRPRG
+PLVRVGQQSLVYYCVHYPVMVLVVRLGERLSWDVVVVSLVSLVAAVVVCAVIAEGRDRVP
+VLDALFRAPAPPRRRRPVTH
+>PROKKA_00376
+MSTTPTPPMSHGSTPSRMTWMDAMRGFAVLLVMFTHTYTMPQGLDATFSSVAFANVVQVF
+QSWRMPMLVFLSGVLLPRSVSKPLGTYYRGKAERILWPFLVWMVVLALATGRPGSLLSGE
+FWRGGAWHLWFLWVLMLCYLIGPVIRRVPALVVAAVLFVLLLEFVSGPRDWVRPLYWGVY
+FFLGAASARLLPRIRTAPAALGVIAVILMVLTVTATRTGALVVAERQPWSVFAALPGILV
+VLWLGPRLPRLPFLEFCGRRSMVLYVAHMPVLILAVAAFRDLAAVRPVDFYVAIASFTFL
+VPLALALGYRRVRWLFEFPTAGRGRERPRTRAAVPEAADAVPAQTAEPAPTTAPLPVVEP
+ASEPQSTAGPAPATEPASDAPAQVPRPRPRHAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001807.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001807.fa
new file mode 100644
index 0000000000000000000000000000000000000000..889a3efcb3582d648ca96e1626e570e05d3667e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001807.fa
@@ -0,0 +1,28 @@
+>PROKKA_00387
+MAPWLPTRSRRPFPQVTEAGEVPAVTPTFEGRASHPPAEDVEDQGAAFDVGTLVSRRNAL
+GIFGAGAGALVLAACGVQEGASSSSSSTSASAGSSSPAASSSSAASASPSATLTEMVTET
+AGPYPGDGSNGPDVLDASGIERSDLTTSIDTGTVAEGVPLTVTMNVIDMANGDAAMTGAA
+VYLWHADAQGRYSMYSDGITEETYLRGVQVVGDDGTVTFTTVWPGCYDGRWPHLHFEVFP
+DKASITDATNNVLTSQIAMPEEQSSQVYATSAYDGSTANFAKVSLETDNVFSDGYETQLP
+QITGSVEKGFAITIDVPIDTTTEQEQGGMGGPGGGQPPAGGEGGQPPAQP
+>PROKKA_00111
+MAPWPPTRSRRPFPQVTEGGGAPAVTPTFEGRAFHRPAEDVEDQGAAFDVGTLVSRRNAL
+GIFGAGAGALVLAACGVQEGASSSSGSTSASAGSSSPEASSSSAASASPSATLTEMVTET
+AGPYPGDGSNGPDVLDASGIERSDLTTSIDTGTVAEGVPLTVTMNVIDMANGDAAMTGAA
+VYLWHADAQGRYSMYSDGITEETYLRGVQVVGDDGTVTFTTVWPGCYAGRWPHLHFEVFP
+DKASITDATNNVLTSQIAMPAEQSAQVYATSAYDGSTENFAQVSLETDNVLSDGYETQLP
+QITGSVEKGFAITIDVPIDTTTEQEQGGMGGPGGGQPPARP
+>PROKKA_02441
+MAPWLPTRSRRPFPQVTEGGEAPAVTPTFEGRAFHRPAEDVEDQGAAFDVGTLVSRRNAL
+GIFGAGAGALVLAACGVQEGASSSSSSTSASAGSSSPAASSSAASASPSATLTEMVTETA
+GPYPGDGSNGPDVLDASGIERSDLTTSIDTGTVAEGVPLTVTMNVIDMANGDAAMTGAAV
+YLWHADALGRYSMYSDGITEETYLRGVQVVGDDGTVTFTTVWPGCYDGRWPHLHFEVFPD
+KASITDATNNVLTSQIAMPEEQSSQVYATSAYDGSTANFAKVSLETDNVFSDGYETQLPQ
+ITGSVEKGFAITIDVPIDTTTEQEQGGMGGPGGGQPPAGGEGGQPPARP
+>PROKKA_00393
+MAPWLPTRSRRPFPQVTEAGEVPAVTPTFEGRAFHHPAEDVEDQGAALDVGTLVSRRNAL
+GIFGAGAGALVLAACGVQEGASSSSGSTSASAGSSSPAASSSSAASASPSATLTEMVTET
+AGPYPGDGSNGPDVLDASGIERSDLTTSIDTGTAAEGVPLTVTMNVIDMANGDAAMTGAA
+VYLWHADAQGRYSMYSDGITEETYLRGVQVVGDDGTVTFTTVWPGCYDGRWPHLHFEVFP
+DKASITDATNNVPTSQIAMPEEQSAQVYATSAYDGSTENFADVSLETDNVFSDGNETQLP
+QITGSVEKGFAITIDVPIDTTTEQEQGGMGGPGGGQPPAGGEGGQPPAQP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001809.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001809.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12dcc2ca2511e89ca3f9e46f5607b53d1c28339f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001809.fa
@@ -0,0 +1,28 @@
+>PROKKA_00395
+MDATPHARPAEPGPLPDPAEPRRLAGKDVHPVGLGCMNIVHGYSGFLDDDAAVDLLTRVL
+EDGTDHLDTATLYGGGRSEELVGRALARAGSGVRERVLLASKGGLVRDGQRRIDGRPETL
+RAHVDASLSRLGQDRIDLYYLHRLDPEVPVEESVGALAEAVTEGKIGAIGLSEVSAVTLT
+RAVAVHPIAAVQSEYSLATRNPEWGVLEACRRHGTAFVAFSPVSRGLLTDAPPRLGGLDA
+GDLRHRLPRFAEGHYEANLTLREALSAEAVRLGTSTAGLAVAWVLAQGKDVLAIPGTTSW
+EHWLEDRGAHEVRLTPADVARLDDLVNDATVAGPRYSESQQASIDTEAAPPR
+>PROKKA_00119
+MDATPHARPAEPGPLPDPAEPRRLAGKDVHPVGLGCMNIVHGYSGFLDDDAAVDLLTRVL
+EDGTDHLDTATLYGGGRSEELVGRALARAGSDVRERVLLASKGGLVRDGQRRIDGRPETL
+RAHVDASLSRLGQDRIDLYYLHRLDPEVPVEESVGALAEAVTEGKIGAIGLSEVSAVTLT
+RAVAVHPIAAVQSEYSLATRNPEWGVLEACRRHGTAFVAFSPVSRGLLTDAPPRLGGLDA
+GDLRHRLPRFAEGHYEANLTLREALSAEAVRLGTSTAGLAVAWVLAQGKDVLAIPGTTSW
+EHWLEDRGAHEVRLTPADVARLDDLVNDATVAGPRYSESQQASIDTEAAPPR
+>PROKKA_02433
+MDTAANPALTTDLRSPRRVAGKDVRPVGLGCMNLVHGYSGFLSEREAVDLVVGVLADGTD
+HLDTATLYGGGLSEEYVGKALTRVGADVRDRVLLASKCGLSRDADRPIDGRPETLRAQVD
+ASLRRLGQDRIDLYYLHRLDPRVPVEESVGALAEAVAAGKIGAIGLSEVSGATLDRAATE
+HPVAAVQNEYSLATRNPEWGLLEACRRHGAALVAFSPVCRGLLTDAPPVVADLPDGDMRH
+AMPRFQGPAWEANLRLREEFASEAARLGVPAASLAVAWVLAQGADVVAIPGTTDPAHWRE
+DRGAEEVSLTLEDLARLDALVNHATVQGRRYSDAQQASVDTEDAPQQG
+>PROKKA_00401
+MDATPHPRPAEPGPLPDPAAPRRLAGKDVHPVGLGCMNIVHGYSGFLDDDAAVDLLTRVL
+EDGTDHLDTATLYGGGRSEELVGRALARAGSDVRERVLLASKGGLVRDGQRRIDGRPETL
+RAHVDASLSRLGQDRIDLYYLHRLDPEVPVEESVGALAEAVTEGKIGAIGLSEVSAVTLT
+RAVAVHPIAAVQSEYSLATRNPEWGVLEACRRHGTAFVAFSPVSRGLLTDAPPRLGGLDA
+GDLRHRLPRFAEGHYEANLTLREALSAEAVRLGTSTAGLAVAWVLAQGKDVLAIPGTTSW
+EHWLEDRGAHEVRLTPADVARLDDLVNDATVAGPRYSESQQASIDTEAAPPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001815.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001815.fa
new file mode 100644
index 0000000000000000000000000000000000000000..60a9e598099ee583ac9caffc525802be398e6f14
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001815.fa
@@ -0,0 +1,12 @@
+>PROKKA_00536
+MIRNGKAIDHSNVGGVWGSLIAFIVAFGAFLGCLYAMGFWSLESVWIPGLIALALATVAF
+MIPKAFLGRSDTVDTTAIHTRPVVEHAASGAAHR
+>PROKKA_00260
+MIRNGKAIDHSNVGGVWGSLIAFIVAFGAFLGCLYAMGFWSLESVWIPGLIALALATVAF
+MIPKAFLGRSDTVDTTAIHTRPVVEHAASGAHAVETGAAHR
+>PROKKA_02413
+MIRNGKAIDHSNVGGVWGSLIAFLVAYVAFLGSLYAMGFWTLENAWVPGLIALALAMVTF
+MIPQVFLGRSDTVDTAAIHTRPVAVEHPVSGAHAVETGAARRH
+>PROKKA_00539
+MIRNGKAIDHSNVGGVWGSLIAFIVAFGAFLGCLYAMGFWSLESVWIPGLIALALATVAF
+MIPKAFLGRSDTVDTTAIHTRPVVEHAASGAHAVETGAAHR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001822.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001822.fa
new file mode 100644
index 0000000000000000000000000000000000000000..16f5a4f4f721f8304566ef73656d514ff4aad1e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001822.fa
@@ -0,0 +1,29 @@
+>PROKKA_00625
+MASKDWARKISDVPEGTRRQWRADRALRAPMRSPGRPQPSREVQRQFWRVIATGVTTVEA
+SLTVGVSWPVGARWFRHAGGMTPLSLAEPTGRYLSFAEREEIAILHAQGQGVRQIARTLG
+RDPGTISRELRRNCATRSGKQEYRATVAQWKAQEAARRPKPAKLATNQRLHDYVQARLNG
+VVLGPDGVAVPGPVGPGFKGRKMKPRRADRRWSTAWSPEQISHRLRLEFPDDVSMRISHE
+AIYQSLFIQGRGALKRELVACLRTGRALREPRARTRNKPQGHVTEDVVFSKRPPEAADRA
+VPGHWEGDLIIGTERSAIGTLAERKSRATILVHLPRLEGWGERPPVKNGPSLGGYGAEAM
+TAALIKAMATVPEQLRQSLTWDRGKELAGHVQFTMATGTKVFFADPHSPWQRPTNENTNG
+VLRQYFPKGTDLSRWSAEDLAAVAYTLNNRPRKVLDWKTPAEVFAEQLRSLSTHGVATTG
+>PROKKA_00734
+MASKDWARKISDAPEGARRQWRADRALRAPMRSPGRPQPSREVQRQFWRVIATGVTTVEA
+SLSVGVSWPVGARWFRHAGGMTPLPLAEPTGRYLSFAEREEIAILHAQGHGVRQIGRALG
+RDPGTISRELRRNCATRSGGKEYRATVAQWKAQQAARRPKPAKLATNQRLHDYVQARLNG
+VVLGPDGVAVQGPVGPGFKGRKMKPRRADRRWSTAWSPEQISHRLRLEFPDDVSMRISHE
+AIYQSLFVEGRGALKRELVGCLRTGRALREPRARTRNKPQGHVTEDVVFSKRPPEAADRA
+VPGHWEGDLIIGLQRSAIGTLAERKSRATILVHLPRLQGWGEQPPVKNGPSLGGYGAAAM
+SAALTKAMTGLPQQLRQTLTWDRGGELAGHAQFTMATGTRVFFADPHSPWQRPTNENMNG
+LLRQYFPKGTDLSRWSADDLAAVAYTLNNRPRKVLGWKTPAEVFAEQLSSLETSGVATTT
+>PROKKA_00746
+MRISHEAIYQSLFVEGRGALKRELVGCLRTGRALREPRARTRNKPQGHVTEDVVFSKRPP
+EAADRAVPGHWEGDLIIGLQRSAIGTLAERKSRATILVHLPRLQGWGEQPPVKNGPSLGG
+YGAAAMSAALTKAMTGLPQQLRQTLTWDRGGELAGHAQFTMATGTRVFFADPHSPWQRPT
+NENMNGLLRQYFPKGTDLSRWSADDLAAVAYTLNNRPRKVLGWKTPAEVFAEQLSSLETS
+GVATTT
+>PROKKA_00749
+MASKDWARKISDAPEGARRQWRADRALRAPMRSPGRPQPSREVQRQFWRVIATGVTTVEA
+SLSVGVSWPVGARWFRHAGGMTPLPLAEPTGRYLSFAEREEIAILHAQGHGVRQIGRALG
+RDPGTISRELRRNCATRSGGKEYRATVAQWKAQQAARRPKPAKLATNQRLHDYVQARLNG
+VVLGPDGVAVQGPVGPGFKGRKMKPRRAEVKSLEVV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001824.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001824.fa
new file mode 100644
index 0000000000000000000000000000000000000000..22701ffc2abb09a1b1127d44c5c7056e882ea044
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001824.fa
@@ -0,0 +1,24 @@
+>PROKKA_00629
+MTPLTRRTLIAGGLTLLGAGTLTACAAPNPATSPAAGTGTQGTGTAITHVHALTRDPESG
+EVLLATHQGLFRLQDGELTQVGPVVDFMGFTLTPEGRYLASGHPAPRTDLPEPLGLAEST
+DRGQSWTVLSRGGASDFHALAAGPNGVLGFDGQLRASTDGLTWQSLEIPVAPASLAISPK
+TGTVLATTETGMLRSTDHGATWTTLDTPQLMHLVAWADDTTAVGAGTEGHLLTSTDAGDT
+WTASDRPVGTATALGTGITDDGQTEALLVVGSTVLSTTDGGNTTESLL
+>PROKKA_00401
+MTPLTRRTLIAGGLTLLGAGTLTACAAPNPATSPAAGTGTQGTGTAITHVHALTRDPESG
+EVLLATHQGLFRLQDGELTQVGPVVDFMGFTLTPEGRYLASGHPAPNTDLPEPLGLAEST
+DRGQSWTVLSRGGQSDFHALAAGPNGVLGFDGQLRASTDGLTWQSLEIPVAPASLAISPQ
+TGTVLATTETGMLRSTDHGATWTTLDTPQLMHLVAWADDTTAVGAGTEGHLLTSTDAGDT
+WTASDRPVGTATALGAGITDDGQTEALLVVGSTVLSTTDGGNTTESLL
+>PROKKA_02200
+MTPLTRRTLIAGGLTLLGAGTLTACAAPNPATSPAAGTGTQGTGTAITHVHALTRDPEYG
+EVLLATHQGLFRLQDGELTQVGPVVDFMGFTLTPEGRYLASGHPAPRTDLPEPLGLAEST
+DRGQSWTVLSRGGASDFHALAAGPNGVLGFDGQLRASTDGLTWQSLEIPVAPASLAISPQ
+TGTVLATTETGMLRSTDHGATWTTLDTPQLMHLVAWADDTTAVGAGTEGHLLTSTDAGDT
+WTASDRPVGTATALGTGITDDGQTEALLVVGSTVLSTTDGGNTTESLL
+>PROKKA_00602
+MTPLTRRTLIAGGLTLLGAGTLTACAAPNPATSPAAGTGTQGTGTAITHVHALTRDPESG
+EVLLATHQGLFRLQDGELTQVGPVVDFMGFTLTPEGRYLASGHPAPRTDLPEPLGLAEST
+DRGQSWTVLSRGGASDFHALAAGPNGVLGFDGQLRASTDGLTWQSLEIPVAPASLAISPQ
+TGTVLATTETGMLRSTDHGATWTTLDTPQLMHLVAWADDTTAVGAGTEGHLLTSTDAGDT
+WTASDRPVGTATALGTGITDDGQTEALLVVGSTVLSTTDGGNTTESLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001826.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001826.fa
new file mode 100644
index 0000000000000000000000000000000000000000..829b7eccc87f875b096999755febda4048766e74
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001826.fa
@@ -0,0 +1,28 @@
+>PROKKA_00635
+MQDKIKVAVNGYGVIGKRVADAVRAQEDMALVGVSDVIADYRIATAAGKGIPVYASTEQA
+LPVMADAGLPVVGGLHDLLENVDVVVDCTPAQVGAGNLELYRAHGVKSVFQGGEKHDLTG
+HSFVAHANYATALGRDSTRVVSCNTTATVRALTALKDVGLLSKARGVLIRRATDPWESDH
+SGIMNTIVPEGRIPSHQGPDAQSVVPDLDVVTMAAKGAHTQNHLHYWTIELTRPAEKQEV
+LETFRAMPRIAFVRRSDGVVAVNSTVELMEDLGRPRGDMYEVALWEDILTVDGNELYYTY
+TVDNQAIVIPENIDAIRALTGTVDDGGESIRCTDRALGVRQDFVRSSVAAR
+>PROKKA_00407
+MQDKIKVAVNGYGVIGKRVADAVRAQEDMALVGVSDVIADYRIATAAGKGIPVYASTEQA
+LPVMADAGLPVVGGLHDLLENVDVVVDCTPAQVGAGNLELYRAHGVKSVFQGGEKHDLTG
+HSFVAHANYATALGRDSTRVVSCNTTATVRALTALKDVGLLSKARGVLIRRATDPWESDH
+SGIMNTIVPEGRIPSHQGPDAQSVVPDLDVVTMAAKGAHTQNHLHYWTIELTRPAEKQEV
+LEAFRAMPRIAFVRRSDGVVAVNSTVELMEDLGRPRGDMYEVALWEDILTVDGNELYYTY
+TVDNQAIVVPENIDAIRALTGTVDDGGESIRRTDRALGVRQDFVRSSVAAR
+>PROKKA_02194
+MQDKIKVAVNGYGVIGKRVADAVRAQEDMALVGVSDVIADYRIATAAGKGIPVYASTEQA
+LPVMADAGLPVVGGLHDLLENVDVVVDCTPAQVGAGNLELYRAHGVKSVFQGGEKHDLTG
+HSFVAHANYATALGRDSTRVVSCNTTATVRALTALKDVGLLSKARGVLIRRATDPWESDH
+SGIMNTIVPEGRIPSHQGPDAQSVVPDLDVVTMAAKGAHTQNHLHNWTIELTRPAEKQEV
+LEAFRAMPRIAFVRRSDGVVAVNSTVELMEDLGRPRGDMYEVVLWEDILTVDGNELYYTY
+TVDNQAIVVPENIDAIRALTGTVDDGGESIRRTDRALGVRQDFVRSSVAAR
+>PROKKA_00596
+MQDKIKVAVNGYGVIGKRVADAVRAQEDMALVGVSDVIADYRIATAAGKGIPVYASTEQA
+LPVMADAGLPVVGGLHDLLENVDVVVDCTPAQVGAGNLELYRAHGVKSVFQGGEKHDLTG
+HSFVAHANYATALGRDSTRVVSCNTTATVRALTALKDVGLLSKARGVLIRRATDPWESDH
+SGIMNTIVPEGRIPSHQGPDAQSVVPDLDVVTMAAKGAHTQNHLHYWTIELIRPAEKQEV
+LEAFRAMPRIAFVRRSDGVVAVNSTVELMEDLGRPRGDMYEVALWEDILTVDGNELYYTY
+TVDNQAIVVPENIDAIRALTGTVDDGGESIRRTDRALGVRQDFVRSSVAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001828.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001828.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b3b2826327bbddf1c6d661f860b71c406100cf5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001828.fa
@@ -0,0 +1,22 @@
+>PROKKA_00640
+MARPGDPGRECRRGLDVRIGTSGWIYKHGRGTFYPQGLRIADQLDHCTERDRVSRLRALP
+QRGPGPALRRIVLRRRARPWVGRLRELTGADAAGARPAHVSFYNDNHGHAAFNALTLRRM
+AEAEA
+>PROKKA_00377
+MISGTLRLPRRVKARPGDPGRGYRRGMDVRIGTSGWTYRHWRGTFYPQGLRIADQLDHYT
+ERFRTVELNGSHYRWPADSTVEAWRERLPAGFEMAVKASRYLTHYRKLNEPQDWVERIVH
+TLDLLGDHAGPLLLQLPAHLHRDDGRLAGFLGLLPERVRVAVEVQHESWLDEDVFDLLDR
+HGAGFVVSVIAGREPVLRATGRLAYVRFHNADPDWRYGGSFSDAELAPWVGRLRELTGAD
+DGGPAGDAAGARPAYVYFNNDNHGHAAFNALTLRRMAETEA
+>PROKKA_02185
+MDVRIGTSGWTYKHWRGTFYPQGLRIADQLDHYTERFRTVELNGSHYRWPADSTVEAWRE
+RLPAGFEMAVKASRYLTHYRKLNEPQDWVERIVHTLDLLGDHAGPLLLQLPANLHRDDDR
+LAGFLGLLPERVRVAVEVQHESWLDEDVFDLLDRHGAGFVVSVIAGREPVLRATGRLAYV
+RFHNADPDWRYGGSFSDAELAPWVGRLRVLTGADNGGPAGDAAGARPAYVYFNNDNHGHA
+GFNALTLRRMAETGA
+>PROKKA_00609
+MISGTLRLPRRIKARPGDPGRGYRRGMDVRIGTSGWTYKHWRGTFYPQGLRIADQLDHYT
+ERFGTVELNGSHYRWPADSTVEAWRERLPAGFEMAVKASRYLTHYRKLDEPQDWVQRIVH
+TLDLLGDHAGPLLLQLPAHLHRDDDRLAGFLGLLPERVRVAVEVQHESWLDKDVFDLLDR
+HGAGFVVSVIAGREPVLRATGRLAYVRFHNADPDWRYGGSFSDAELAPWVGRLRELTGAD
+AAGVRPTYVYFNNDNHGHAAFNALTLRRMAEAEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001836.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001836.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf55a494308a5bba631d5c1e11fd5c10fce17714
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001836.fa
@@ -0,0 +1,24 @@
+>PROKKA_00739
+MIRFLHGIGGRPAHFEPLADALGAVADLAASPALPGHPGTDAGGQGRPRAARPATDADPV
+LDAARTWAAQAGPVPGLLIGHSTGGVIALRAVADGLVRPRALVVIDSNVPVTDTALAARA
+AKARLAARPDWRSVLRASLARDLLVPEPWRERILTDLDATPDHPMRELWAAVLAADTRAL
+WAGITVPTLYVRSTRDVHQRDLDAVTQHATVVDVSTGHWPHVTEPEAVAAAIRRWHTTGV
+HPTR
+>PROKKA_00470
+MIRFLHGIGGRPAHFQPLADALDAAADLAASPALPGHPGTDAGGQDRPRSARPAIEADPV
+LDAARTWAAQAGPVPGLLIGHSTGGVIALRAVADGLVRPRALVVIDSNVPVTDIALAARA
+AKARLAARPDWRSVLRASLARDLLVPEPWHERILADVDATPDHPMRELWAAVLAADTRTL
+WAGITVPTLYVRSTRDVHQRDLDAVTQHTTVVDVGPGHWPHVAEPGAVAAAIRRWHTTGV
+HPTR
+>PROKKA_02191
+MIRVLHGIGGRPGHLAPLLDALGHGSTEDAADASPALLGHGDAVPAAPAPTGGAADPAAG
+ADHDWILAAARDWAARAREGAGPDLLIGHSTGGVIALRALAEGLVRPRGLVVIDSNVPVD
+AAALAARADKARLAAAPDWRDRLRASLARDLVAPKPWPARILADLDATADHPMRALWSAV
+LTADPRPLWAAASVPVLYVRSTRQVHQADLDKLTDRARVVDVSAHAGGHWPHLADPAGVA
+RAIRDWRAETGA
+>PROKKA_00703
+MIRFLHGIGGRPAHFQPLADALGAAADLAASPALPGHPGTDAGGQDRPRAARPAIEADPV
+LDAAHTWAAQAGPVPGLLIGHSTGGVIALRAVADGLVRPRALVVIDSNVPVTDPALAARA
+AKARLAARPDWRSVLRASLARDLLVPEPWHERILADLDATPDHSMRELWAAVLAADTRAL
+WSSLTVPTLYVRSTRDVHQRDLDAVTQHATVVDVGPGHWPHVAEPEAVAAAIRRWHATVA
+AQPSHH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001837.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001837.fa
new file mode 100644
index 0000000000000000000000000000000000000000..554cd373fe1e52de315ea5f282a9eaff52ba977a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001837.fa
@@ -0,0 +1,25 @@
+>PROKKA_00787
+MSAPAWSALLRDAAARLTTVGIDSPRVDAELLLAHVLGLDRGALLARVFAGAVAEPAQAA
+AFEALIGRRAAREPVQHLTGVAHFHGLDLAVGPGVFVPRPETELLVETVVADLAARPTAG
+VVVDLCTGSGAIAAAVAAWGEARGRPLAVTAVELDPTAADWARRNLAPRGVDLRQGDALV
+ACPDLEGRVDVVVSNPPYVPEAEVPAQPEARLDPARALYGGDAPGLRIPQAIVHRAAELL
+VPGGLFAMEHHETQGPALLAALGADPRFMGVRVHRDLTGRDRFLTARRSGEAAAGAEVEE
+>PROKKA_00518
+MSAPAWSALLRDAAARLTTVGIDSPRVDAELLLAHVLGLDRGALLARVFAGAVAEPAQAA
+AFEALIGRRAAREPVQHLTGVAHFHGLDLAVGPGVFVPRPETELLVETVVADLAARPTAG
+VVVDLCTGSGAIAAAVAAWGEARGRPLAVTAVELDPTAADWARRNLAPRGVDLRQGDALV
+ACPDLEGRVDVVVSNPPYVPEAEVPAQPEARLDPARALYGGDAPGLRIPQAIVHRAAELL
+VPGGLFAMEHHETQGPALLAALGADPRFMGVRVHRDLTGRDRFLTARRSGEAAAGAEVEE
+>PROKKA_02037
+MTSSGPATPPADWSALLRQAAATLRAAGVDSPRADAELLLSHLLGGDRGTLLARVLAGAA
+PGPGQAEAFGALVERRAVREPLQHITGAAAFHGLTLEVGPGVFVPRPETELLVEEGIRAL
+AVLDGPARVVDLCTGSGAIAAAVAAWAEERHRDVAVTAVEREDAALAWARRNLEPRGVDL
+RQGDALVACADLDGTVDVVLSNPPYVPDAELPVQAEALADPPTALYGGDAAGLRIPRGII
+ARAAGLLRPGGRLVMEHHEAQGEALAAEARLGGRFEDVRVLPDHTGRERFLAAVRTGALV
+APPSDGRMEP
+>PROKKA_00754
+MSAPAWSALLRDAAARLTAVGIDSPRVDAELLLAHVLGLDRGALLARVFAGAVAEPAQAA
+AFEALVGRRAAREPVQHLTGVAHFHGLDLAVGPGVFVPRPETELLVETVVADLAARPAAG
+AVVDLCTGSGAIAAAVAAWGEARGRPLAVTAVELDPTAADWARRNLAPRGVDLRQGDALV
+ACPDLEGRVDVVVSNPPYVPEAEVPAQPEARLDPARALYGGDTPGLRIPRAIAHRAADLL
+APGGLFAMEHHETQGPALLSALGADRRFTGERVHQDLTGRDRFLTARRSGEAAAGAEVEE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001844.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001844.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7eba6ecc9c9ffd9634a4dc9f683865df00219d14
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001844.fa
@@ -0,0 +1,20 @@
+>PROKKA_01013
+MDETTEPPRARRRRGRPLSPALSREAIADAALAVARTEGYEGLTMAAVGRRLGVAPSALY
+NHISGKHELLVLLQDAVMGEVSLVELEAAIRGEVPVVAALRAWARSYRDVFAAHPPLIPL
+IATLPIEGAPSTQRVYETVCAVLARTGLAPEQVLARVIALESFIYGSAYDVDAPADIFEV
+AGAQERLPALGAAAEAFRAGGGTRATGARNPYADAPFEEGLDLLLAGLGD
+>PROKKA_00727
+MAAVGRRLGVAPSALYNHISGKHELLVLLQDAVMGEVSLVELEAAIRGEVPVVAALRAWA
+RSYRDVFAAHPPLIPLIATLPIEGAPSTQRVYETVCAVLARTGLAPEQVLARVIALESFI
+YGSAYDVDAPADIFEVAGAQERLPALGAAAEAFRAGGGTRATGARNPYADAPFEEGLDLL
+LAGLGD
+>PROKKA_01875
+MDETPEPPRTRRRRGRPLSPALSREAIADAALAVARTEGYEGLTMAAVGRRLGVAPSALY
+NHISGKHELLVLLQDAVMGEVSLVELEAAIRGEAPVVAALRAWARSYRDVFAAHPPLIPL
+IATLPIEGAPSTQRVYETVCAVLARTGLAPGQVLARVIALESFIYGSAYDVDAPADIFEV
+AGAQERLPAFGAAAEAFREGGGTRATGARNPYADAPFEEGLDLLLAGLDD
+>PROKKA_00956
+MDETTEPPRARRRRGRPLSPALSREAIADAALAVARTEGYEGLTMAAVGRRLGVAPSALY
+NHISGKHELLVLLQDAVMGEVSLVELEAAIRGEVPVVAALRAWARSYRDVFAAHPPLIPL
+IATLPIEGAPSTQRVYETVCAVLARTGLAPEQVLARVIALESFIYGSAYDVDAPADIFEV
+AGAQERLPALGAAAEAFRAGGGTRATGARNPYADAPFEEGLDLLLAGLGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001854.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001854.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c96d6d1443f7ee6b694cede18c2db12a2dfd34b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001854.fa
@@ -0,0 +1,20 @@
+>PROKKA_01160
+MNPVTSTARDGRSVRWDRHRAERRLELVRAARSAVHALGAHASMEEIASHAGTSKTVYYR
+YFGDREGLRLAVSERVTAHMERRLLEVADEPVSEPEALRRMVEVYLTVAATSPEVYAFAV
+APSPAAAEAPVLGPFLERVYAMLESGLARGMAARGHAPAPADPLALWPRAAVGLVRAAAE
+TWLRTPAAGRIPVEAMARAIADWLLTGLIGAAPGAALEPAAADAVRARPHSRTGASS
+>PROKKA_00879
+MNPVTSTARDGRSVRWDRHRAERRLELVRAARSAVHALGAHASMEEIASHAGTSKTVYYR
+YFGDREGLRLAVSERVTAHMERRLLEVADEPVSEPEALRRMVEVYLTVAATSPEVYAFAV
+APSPAAAEAPVLGPFLERVYAMLESGLARGMAARGHAPAPADPLALWPRAAVGLVRAAAE
+TWLRTPAAGRIPVEAMARAIADWLLTGLIGAAPGAALEPAAADADRARPHSRTGASS
+>PROKKA_01627
+MLVRAARAAVHELGPTASMDEIAAHAGTSKSVFYRYFGDRAGLRQAVAERVTASMERRLR
+EAAVDAPDGVSALHRMVAECLSVAASSPAVYAFAVTQGGAADGTGPDLGPFFERIAALLA
+EGLARTLPAADAGPGTTLVLWPRVAVGTVRAAVEAWLATEESVRPDPVRTAHDVAGWLLA
+GLRSADPSASPAADTHTPTQQGEPS
+>PROKKA_01110
+MNPVTSTARDGRSVRWDRHRAERRLELVRAARSAVHALGAHASMEEIASHAGTSKTVYYR
+YFGDREGLRLAVSERVTAHMERRLLEVADEPVSEPEALRRMVEVYLTVAATSPEVYAFAV
+APSPAAAEAPVLGPFLERVYAMLESGLARGMAARGHAPAPADPLALWPRAAVGLVRAAAE
+TWLRTPAAGRIPVEAMARAIADWLLTGLIGAAPGAALEPAAADADRARPHSRTGASS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001855.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001855.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0e51d5c3ce60d36e1acf15035ad1567f8c2cea97
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001855.fa
@@ -0,0 +1,24 @@
+>PROKKA_01212
+MSGSGSSRRGARHGGYAANSFRTEAIVLRTHRLGEADRIIEALTPEHGLVRAVAKGVRKT
+SSRLGSVVEPFMHSTLQLARGRGELHIVSQAQLLHPYATMLAADYDAYTVAGALAEAVER
+VPAVDDDGRRAQYRLFHGALAALARGAHDPRLILHSFLLRALAQAGWAPTFDRCARCGAP
+GPHTALHVGLGGAVCPACRPPGAAHPAPETFDLLSALAAGGWATADASGAPARREAAGIV
+AAYLQFHAERRLVSLSVLDQDLGLPAPRVERRP
+>PROKKA_00931
+MSGSGSSRRGARHGGYAANSFRTEAIVLRTHRLGEADRIIEALTPEHGLVRAMAKGVRKT
+SSRLGSVVEPFMHSTLQLARGRGELHTVSQAQLLHPYATMLAADYDAYTVAGALAEAVER
+VPAVDDDGRRAQYRLFHGALAALARGAHNPRLILHSFLLRALAQAGWAPTFDRCARCGAP
+GPHTALHVGLGGAVCPECRPPGAAHPAPETFDLLSALAAGDWATADTSGAPARREAAGIV
+AAYLQFHAERRLVSLSVLDQDLGLPAPRVERRP
+>PROKKA_01573
+MSGARHGGYSANSFRTEAIVLRTHRLGEADRIVEAITPEHGVLRCVAKGVRKSSSRFGSV
+VEPFMHSTLQVARGRGELHTITQAQLLHPYATAVAADYEAFAVAAALAEGVERIPALDAD
+GRRAQYLLFHGALAALARRAHDPRMILHSFLLRTLTQAGWAPTFDRCARCGAPGPHTAVN
+VALGGAVCAEHRPPGSASPAPETFALLTALTAGDWAVVDTAGPLARREAAGIVSAYLQFH
+AERRLVALSVLDQEIAPPAPRAERSA
+>PROKKA_01169
+MSASGSSRRGARHGGYAANSFRTEAIVLRTHRLGEADRIIEALTPEHGLVRAVAKGVRKT
+SSRLGSVVEPFMHSTLQLARGRGELHTVSQAQLLHPYATMLAADYDAYTVAGALAEAVER
+VPAVDDDGRRAQYRLFHGALAALARGAHDPRLILHSFLLRALAQAGWAPTFDRCARCGAP
+GPHTALHVGLGGAVCPECRPPGAAHPAPETFDLLSALAAGDWATADASGAPARREAAGIV
+AAYLQFHAERRLVSLSVLDQDLGLPAPRVERRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001861.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001861.fa
new file mode 100644
index 0000000000000000000000000000000000000000..86579ec946dae3a291d3cdb180c6ac052efd4be5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001861.fa
@@ -0,0 +1,32 @@
+>PROKKA_01357
+MIGLLIGGVLGLVLSAVGTPLFIRFLVKRGYGQFVRDDGPTTHKTKRGTPTMGGAVIIGS
+MVLAYLITHGLLAVFGVDFGGPTASGLILLLLTVGMAFVGFVDDFTKITKQRSLGLTPRG
+KIILQALIGTAFAVLALNFPDERGLTPASTAISFARDIPWLDLAFAGPAIGVILFVIWSN
+LITTATTNAVNLTDGLDGLATGATAMITGAYVLISLFQSSQSCALEGTRGCYEVRDPMDL
+ALLAAILTGSLLGFLWWNTSPAKIFMGDTGSLGLGGALAGFAIFTRTEILVAVLAGLMVA
+ITLSVIIQVGWFKVSGGKRVFLMAPLQHHFELKGWAEVTVVVRFWLLSLMCVTVGLAIFY
+GDWLIRQGGLAGVTP
+>PROKKA_01077
+MIGLLIGGVLGLVLSAAGTPLFIRFLVKRGYGQFVRDDGPTTHKTKRGTPTMGGAVIIGS
+LVLAYLITHGLLAVLGVDFGGPTASGLILLLLTVGMAFVGFVDDFTKITKQRSLGLTPRG
+KIILQALIGTAFAVLALNFPDERGLTPASTAISFARDIPWLDLAFAGPASGVILFVIWSN
+LITTATTNAVNLTDGLDGLATGATAMITGAYVLISLFQSSQSCALEGTRGCYEVRDPMDL
+ALLAAILTGSLLGFLWWNTSPAKIFMGDTGSLGLGGALAGFAIFTRTEILVAVLAGLMVA
+ITLSVIIQVGWFKVSGGKRVFLMAPLQHHFELKGWAEVTVVVRFWLLSLMCVTVGLAIFY
+GDWLIRQGGLAGVTP
+>PROKKA_01431
+MIGLLIGGVLGLILSGLGTPLFIRYLVKRGYGQQVRDDGPQTHKSKRGTPTMGGFVIISA
+LVLGYLLTHGILALLGSELAGPTASGWIVLLLTVGMAFVGWIDDYTKIAKQRSLGLTPKG
+KIILQGLIGTAFAVLALLFPNADGVTPASTAVSFVRDIPWLELAFAGPVVGVVLFVIWSN
+IITTATTNAVNLTDGLDGLAAGATAMVTGAYVLVSLFQASQSCGLTEGAEACYVVRDPMD
+LGLLAAVLTGALLGFLWWNTSPAKIFMGDTGSLGLGGALAGLAILSRTEILVVILAGLMV
+AITLSVIIQVGWFKISGGKRVFLMAPLQHHFELKGWAEVTVVVRFWLISLVCVIIGLALF
+YGEWLLQHGALQAVAR
+>PROKKA_01312
+MIGLLIGGVLGLVLSAVGTPLFIRFLVKRGYGQFVRDDGPTTHKTKRGTPTMGGAVIIGS
+MVLAYLITHGLLAVFGVDFGGPTASGLILLLLTVGMAFVGFVDDFTKITKQRSLGLTPRG
+KIILQALIGTAFAVLALNFPDERGLTPASTAISFARDIPWLDLAFAGPAIGVILFVIWSN
+LITTATTNAVNLTDGLDGLATGATAMITGAYVLISLFQSSQSCALEGTRGCYEVRDPMDL
+ALLAAILTGSLLGFLWWNTSPAKIFMGDTGSLGLGGALAGFAIFTRTEILVAVLAGLMVA
+ITLSVIIQVGWFKVSGGKRVFLMAPLQHHFELKGWAEVTVVVRFWLLSLMCVTVGLAIFY
+GDWLIRQGGLAGVTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001865.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001865.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b1ed646b3e734f722785cab4917c0cd2b41d1c09
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001865.fa
@@ -0,0 +1,37 @@
+>PROKKA_01410
+MVQQRVVRAPGRSDPGGSVPPTALAAAAREGVTTAPAGSRVLVLHDRTDLQRLGDELTVA
+HTLTTALRAQTHEHANQLHTALALVESGRLEAARAVLSRRAADEEASDDVLAALLDAKAA
+QARERGVALTWSAELTAPAPLRPLDLLTVLGNLVDNDLDAAAAPDLSAVDRWVDVEVVSD
+ATGLVVQVADGGPGPSDADRRRLFDRGWSTKPVGAAGRGMGLWLTRRIAEEAGGVVDVAT
+DSGTVFTVEVPREPTPQEET
+>PROKKA_01140
+MRHPWSIARRIAVVHVALVAAIALFSVWSAYLQAREVAQRVEERHVQGVTTLVARDPALV
+SALRAGDAPALQAGIDGWIAEAQVSWLTVMDPDGMRLASWRPEQVGVRYPRPVDAVVAGD
+TVVELSSTGAAGRSVRALAPVVDPEDGTVLGVVTTGVQISDVAIMAQAQIPGILLGSAAV
+AAVGLLVAWLVGRYLNRVTLGRGPEQIAEQFLLAETAMDSLEAGVVVLAPDGRARLHNDA
+AARLLGWEGAGEPRLPTELSAALPGAVSGEASLAAGGRVLVVQQRVVRSPGRSDPGGSVP
+PTALAAAAREGVTTAPAGSRVLVLHDRTDLQRLGDELTVAHTLTTALRAQTHEHANQLHT
+ALALVESGRLEAARAVLSRRAADEEASDDVLAALLDAKAAQARERGVALTWSAELTAPAP
+LRPLDLLTVLGNLVDNALDAAAAPDLSAADRWVDVEVVSDAAGLVVQVADGGPGPSDADR
+GRLFDRGWSTKPVGAAGRGMGLWLTRRIAEEAGGVVDVATDSGTVFTVEVPREPTPQEET
+>PROKKA_01396
+MRHPWSIARRVAASLVLLLSVIAVFSGWAGWRQARDATFVVEERHVLGVARLAAREEVVV
+DALGSPAGAAALQARIPSVVDDAGVSWLTLLDARGTRVASWRPEQVGTAYPAPVDRALAG
+ESWTEVSATGPAGISVRALVPVRDAEGAVVGVLTMGVRVSELEVAASAQLPRLAVTFALT
+LAAGLGAALLVARYLHRVTLGRGPEDLAESFLLSAAAMDSLEASLVVLAPDGSIRQHNAA
+AVHALGLPARTEDGTVPAAARLPEELARALEEHADADFPARVGDRLFVVRQRVLGAARPR
+RGGAVDDAAREGISPAPAGTRVLMLHDRTDLQRLTDDLALSRTLTAALRSQTHEHANQLH
+TALALLDSGRTDAARDVLTRHRRPDQDAEDVVSALLEAKAAQAAERGVELTYAVRLSAPA
+PLAALDLVSVVGNLVDNALDAAADAAEPAGRWVDADVTCDADGLLVQVADGGPGLDPDGD
+RVFEPGWSTKPAGIAGRGMGLALVRSIASQAGGVVEVATDSGTVFTVEVPPAGPEQDGEA
+A
+>PROKKA_01360
+MRHPWSIARRIAVVHVALVAAIALFSVWSAYLQAREVAQRVEERHVQGVTTLVARDPALV
+SALRAGDAPALQAGIDGWIAEAQVSWLTVMDPDGMRLASWRPEQVGVRYPRPVDAVVAGD
+TVVELSSTGAAGRSVRALAPVVDPEDGTVLGVVTTGVQISDVAIMAQAQIPGILLGSAAV
+AAVGLLVAWLVGRYLNRVTLGRGPEQIAEQFLLAETAMDSLEAGVVVLAPDGRVRLHNDA
+AARLLGWEGAGEPRLPTELSAALPGAVGGEASLAVGGRVLVVQERVVRAPGRSDPGGSVP
+PTALAAAAREGVTTAPAGSRVLVLHDRTDLQRLGDELTVAHTLTTALRAQTHEHANQLHT
+ALALVESGRLETARAVLSRRAADEEASDDVLAALLDAKAAQARERGVALTWSAELTAPAP
+LRPLDLLTVLATWWTTPSTPPPHRTCPRQTGGSTSKWSRTPRAWWCRWPTAAPDPPTRTA
+AGSSTGAGRRSPSAPPDAAWGCG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001866.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001866.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fc9192392494e0bef140ab6a4cf634b9d2c5a8a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001866.fa
@@ -0,0 +1,19 @@
+>PROKKA_01411
+MTARPYRVLVVEDEQLTAETYVAHLDRLPGFEVAAVAGSLLAARQVAAAGLHANGRFPFD
+VVLLDMNLPDGHGLDFLRQLRAAGFHGGVLALTAATDLPVVRRAVAYGVTQYLVKPFGFD
+EFADRLGGFRAASAMLAGDGALDGQEQVDAVFRVSRERRAEALPKGLTESTLREVVELLG
+ADPETALSAAEVGERLGISRVTARRYLEHLERIRRVRRSARHGGRGRPEQEYRWAGRT
+>PROKKA_01141
+MTARPYRVLVVEDEQLTAETYVAHLDRLPGFEVAAVAGSLLAARQVAAAGLHADGRFPFD
+VVLLDMNLPDGHGLDFLHQLRAAGFHGGVLALTAATDLPVVRRAVAYGVTQYLVKPFGFD
+>PROKKA_01395
+MSAERPYRVLIVEDEELTAQTCADHVTRLPGFTVVGAVGTVDAARRLVAAALDRDGRFPF
+DVLLLDMNLPDGHGLDLLQQLRAAGFQGGVLALTAATELSVVRRAIALGVVQYLVKPFGF
+EAFAQRMTGFRSAAALLAGPGRLSGQEHVDDVFRAGQRRGVEELPKGLSAGTLQAVLDLV
+HDADGGRSASEAAAGLGLSRVTARRYLEHLERIGRVRRRARHGGRGRPEQEYVWAPGAPS
+A
+>PROKKA_01361
+MTARPYRVLVVEDEQLTAETYVAHLDRLPGFEVAAVAGSLLAARQVAAAGLHANGRFPFD
+VVLLDMNLPDGHGLDFLRQLRAAGFHGGVLALTAATDLPVVRRAVAYGVTQYLVKPFGFD
+EFADRLGGFRAASAMLAGDGALDGQEQVDAVFRVSRERRAEALPKGLTEGTLREVVELLG
+ADPETALSAAEVGERLGISRVTARRYLEHLERIRRVRRSARHGGRGRPEQEYRWAGRT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001867.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001867.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b2aec5cfa9eb63f874f03553f6277001ffe085ba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001867.fa
@@ -0,0 +1,44 @@
+>PROKKA_01417
+MFVTGGVASSLGKGLTASSLGHLLKARGLRVVMQKLDPYLNVDPGTMNPFQHGEVFVTED
+GAETDLDIGHYERFLDEDLDGLDNVTTGQVYSTVIARERRGEYLGDTVQVIPHITDEICR
+RMRLPAEPRGDRPAPDVIITEIGGTVGDIESQPFLEAARQVRQDVGRDDVFFLHVSLVPY
+IGPSQELKTKPTQHSVAALRSIGIQPDAIVLRSDRAVPDDVRGKIARMCDVPQDAVVNCA
+DAPSIYDIPRVIHDQGLDAHVVQSLDLKFKDVDWTAWDALMDAVHHPEHELTVALVGKYV
+DLPDAYLSVTEALRAGGFAHRAKVGIRWVAADECATPEGAAVALADVDAVCVPGGFGVRG
+LEGKLGALRHAREQRIPTLGLCLGLQSMVIEYARNVLGLEDADSTEFDPETASPVIATMA
+EQEQIVAGEGDLGGTMRLGAFPATLRPGSVVAEAYGTTEVTERHRHRYEVNNAYRDRLEE
+AGLAICGTSPDGALVEFVELPRDVHPYYVSTQAHPEFSSRPTRPHPLFAGLVAAGLARRA
+DAAARR
+>PROKKA_01148
+MFVTGGVASSLGKGLTASSLGHLLKARGLRVVMQKLDPYLNVDPGTMNPFQHGEVFVTED
+GAETDLDIGHYERFLDEDLDGLDNVTTGQVYSTVIARERRGEYLGDTVQVIPHITDEICR
+RMRLPAEPRGDRPAPDVIITEIGGTVGDIESQPFLEAARQVRQDVGRDDVFFLHVSLVPY
+IGPSQELKTKPTQHSVAALRSIGIQPDAIVLRSDRAVPDDVRGKIARMCDVPQDAVVNCA
+DAPSIYDIPRVIHDQGLDAHVVQSLDLKFKDVDWTAWDALMDAVHHPEHELTVALVGKYV
+DLPDAYLSVTEALRAGGFAHRAKVGIRWVAADECATPEGAAVALADVDAVCVPGGFGVRG
+LEGKLGALRHAREQRIPTLGLCLGLQSMVIEYARNVLGLEDADSTEFDPETASPVIATMA
+EQEQIVAGEGDLGGTMRLGAFPATLRPGSVVAEAYGTTEVTERHRHRYEVNNAYRDRLEE
+AGLAICGTSPDGALVEFVELPRDVHPYYVSTQAHPEFSSRPTRPHPLFAGLVAAGLARRA
+DAAARR
+>PROKKA_01482
+MFVTGGVASSLGKGLTASSLGHLLKARGLRVVMQKLDPYLNVDPGTMNPFQHGEVFVTED
+GAETDLDIGHYERFLDEDLDGLDNVTTGQVYSTVIARERRGEYLGDTVQVIPHITDEICR
+RMRLPAEPRGDRPAPDVIITEIGGTVGDIESQPFLEAARQVRQDVGRDDVFFLHVSLVPY
+IGPSQELKTKPTQHSVAALRSIGIQPDAIVLRSDRAVPDDVRGKIARMCDVPQDAVVNCA
+DAPSIYDIPRVIHDQGLDAHVVQSLDLKFKDVDWTAWDALMDAVHHPEHELTVALVGKYV
+DLPDAYLSVTEALRAGGFAHRAKVGIRWVAADECATPEGAAAALADVDAVCVPGGFGVRG
+LEGKLDALRHAREQRIPTLGLCLGLQSMVIEYARNVLGLEDADSTEFDPETASPVIATMA
+EQEQIVAGEGDLGGTMRLGAFPATLRPGSVVAEAYGTTEVTERHRHRYEVNNAYRDRLEE
+AGLAICGTSPDGALVEFVELPRDVHPYYVSTQAHPEFSSRPTRPHPLFAGLVAAGLARRA
+DAAARR
+>PROKKA_01367
+MFVTGGVASSLGKGLTASSLGHLLKARGLRVVMQKLDPYLNVDPGTMNPFQHGEVFVTED
+GAETDLDIGHYERFLDEDLDGLDNVTTGQVYSTVIARERRGEYLGDTVQVIPHITDEICR
+RMRLPAEPRGDRPAPDVIITEIGGTVGDIESQPFLEAARQVRQDVGRDDVFFLHVSLVPY
+IGPSQELKTKPTQHSVAALRSIGIQPDAIVLRSDRAVPDDVRGKIARMCDVPQDAVVNCA
+DAPSIYDIPRVIHDQGLDAHVVQSLDLKFKDVDWTAWDALMDAVHHPEHELTVALVGKYV
+DLPDAYLSVTEALRAGGFAHRAKVGIRWVAADECATPEGAAVALADVDAVCVPGGFGVRG
+LEGKLGALRHAREQRIPTLGLCLGLQSMVIEYARNVLGLEDADSTEFDPETASPVIATMA
+EQEQIVAGEGDLGGTMRLGAFPATLRPGSVVAEAYGTTEVTERHRHRYEVNNAYRDRLEE
+AGLAICGTSPDGALVEFVELPRDVHPYYVSTQAHPEFSSRPTRPHPLFAGLVAAGLARRA
+DAAARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001873.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001873.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b9aa968bcdc237cd560ef3395f30ac9827f9fffe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001873.fa
@@ -0,0 +1,16 @@
+>PROKKA_01506
+MLATTLEQISVAGARGRPRIRPDRLIADKGYPSKANRAWLRRHGIAATIPERADQITHRR
+RRPGRPIDFGEDQRQRYRGRNVVERCFNRLKQWRGIAMRSDKYARNYHAGLSLAATLHWL
+TTLL
+>PROKKA_00640
+MTTKIHLVCDGKGRTLAFVLTGGQVADTSMFPDTIDEIRVVGVKGRPRTRPERVIADKGY
+PSKKNRAWLRQRGIATTIPERDDQIAHRRKKPGRPIDFGRDQKRRYKGRNAVERCFNKLK
+QWRGIAARSDKTPRNFHAGLSLAATLQWV
+>PROKKA_01746
+MNYKKSGDEPADHAIGRSRGGLTTKSHLVCDGKGRVLAFVVTGGQVADTSMLATTLELIS
+VAGARGRPRARPDRLIADKGYPSKANRSWLRRHGIAATIPERADQIAHRRRRPGRPIDFG
+EDQRQRYRGRNVVERCFNRLKQWRGIAMRSDKYARSYHAGLCLAATLHWLTTTL
+>PROKKA_02236
+MNYKKSGDEPADHAIGRSRGGLTTKSHLVCDGKGRVLAFVVTGGQVADTSMLATTLELIS
+VAGARGRPRARPDRLIADKGYPSKANRSWLRRHGIAATIPERADQIAHRRRRPGRPIDFG
+EDQRQRYRGRNVVERCFNRLKQWRGIAMRSDKYARSYHAGLCLAATLHWLTTTL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001875.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001875.fa
new file mode 100644
index 0000000000000000000000000000000000000000..461cdc0a339d4c4d569b546d0ac1428f6552ce88
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001875.fa
@@ -0,0 +1,28 @@
+>PROKKA_01583
+MTTPRATLPSRRRGRTPARAALAALGLAASLVLSGCGLSTAGGYLPSGTPAGDVAGIDLE
+GAHVAVGSKNFNEGVVLGKITAILLRSAGADVEDLTNMPGSLSARQAQVAGVVDVEWDYT
+GTAWITYLGHTDPIPDAQAQWAAVRDEDAQQGLVWLPPAELDNTYTLSVRQDRAEELGLE
+TLADIKDLPTEEQSFCVSAEFAARNDGFLPMLEAYGIERPTGSRLRQMDIGAVFAAVADG
+SCTFGEAYSTDGRIAALDLTTLQDPLSFFPKYNAAPIVREEVLAQHPEIADLLAPVTARL
+DNATAARLNARVDVDGEEPTQVAWDWLREEGLITD
+>PROKKA_01294
+MTTPRATIPSRRRGRTPARAVLAVLGLAASLVLSGCGLSTAGGYLPSGTPAGDVAGIDLE
+GAHVAVGSKNFNEGVVLGKITAILLRSAGADVEDLTNMPGSLSARQAQVADVVDVEWDYT
+GTAWITYLGHTDPIPDPQAQWAAVRDEDAQQGLVWLPPAELDNTYTLSVRQDRAEELGVE
+TLADIKDLPTEDQSFCVSAEFAARNDGFLPMLEAYGIERPTGSRLRQMDIGAVFAAVADG
+TCTFGEAYSTDGRIAALDLTTLQDPLSFFPKYNAAPIVREEVLAQHPEIADLLAPVTARL
+DNATTARLNARVDVDGEEPTQVAWDWLREEGLITD
+>PROKKA_01339
+MTTPRATLPSRRRGRTPARVALAALGLAASLVLSGCGLSTAGGYLPSGTPAGDVAGIDLE
+GAHVAVGSKNFNEGVVLGKITAILLRSAGADVEDLTNMPGSLSARQAQVAGVVDVEWDYT
+GTAWITYLGHTDPIPDAQAQWAAVRDEDAQQGLVWLPPAELDNTYTFSVRQDRAEELGLE
+TLADIKDLPTQDQSFCVSAEFAARNDGFLPMLEAYGIERPTGSRLRQMDIGAVFAAVADG
+SCTFGEAYSTDGRIAALDLTTLQDPLSFFPKYSAAPIVREEVLAQHPEIADLLAPVTARL
+DNATAARLNARVDVDGEEPTQVAWDWLREEGLITD
+>PROKKA_01510
+MTTPRATLPSRRRGRTPARAALAALGLAASLVLSGCGLSTAGGYLPSGTPAGDVAGIDLE
+GAHVAVGSKNFNEGVVLGKITAILLRSAGADVEDLTNMPGSLSARQAQVAGVVDVEWDYT
+GTAWITYLGHTDPIPDAQAQWAAVRDEDAQQGLVWLSPAELDNTYTFSVRQDRAEELGLE
+TLADIKDLPTEDQSFCVSAEFAARNDGFLPMLEAYGIERPTGSRLRQMDIGAVFAAVADG
+SCTFGEAYSTDGRIAALDLTTLQDPLSFFPKYNAAPIVREEVLAQHPEIADLLAPVTARL
+DNATAARLNARVDVDGEEPTQVAWDWLREEGLITD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001877.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001877.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24795226d434f89af9e147601a7878e66a8eb593
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001877.fa
@@ -0,0 +1,40 @@
+>PROKKA_01588
+MTATRSGGAATSRLNAKVVGISVAAALGGFLFGFDTSVINGAVDALAGEFGLGAGLTGFA
+VSSALIGCALGAWFAGPIANRRGRVPVMVIAAILFLVSAIGSGLAFGVVDLIFWRVVGGL
+GVGAASVIAPAYIAEVSPAHVRGRLGSLQQLAIVLGIFAALLTDALFATMAGGAAQPFWL
+GVDAWRWMFLAEAVPAVLYGLFALKLPESPRYLVARGRTDEAAEVLHEFTGVDRVNLMIE
+DIRRSLDSERRESLADLRGPSAGLQPIVWIGILLSVFQQAVGINVIFYYSTTLWRSVGFG
+ESDALTVTVITSVTNIAVTLIAIALVDRVGRRPMLIAGSAGMTVSLGLMALAFSFAQTGG
+AESVSLPQPWSTVALVAANAFVVFFGATWGPLVWVLLGEMFPNRIRAGALAVAAAAQWAA
+NFTVSTTFPWLADIGLTLAYGLYAVMAALSLAFVAAFVPETKGKTLEEMSDVVVRSPGQR
+RAVRAEAERDLRG
+>PROKKA_01299
+MTATRSGGAATSRLNAKVVGISVAAALGGFLFGFDTSVINGAVDALAGEFGLGAGLTGFA
+VSSALIGCALGAWFAGPVANRRGRVPVMVIAAILFLVSAIGSGLAFGVVDLIFWRMVGGL
+GVGAASVIAPAYIAEVSPAHVRGRLGSLQQLAIVLGIFAALLTDALFATMAGGAAQPFWL
+GVDAWRWMFLAEAVPAVLYGLFALKLPESPRYLVARGRTDEAAEVLHEFTGVDRVNLMIE
+DIRRSLDSERRESLADLRGPSAGLQPIVWIGILLSVFQQAVGINVIFYYSTTLWRSVGFG
+ESDALTVTVITSVTNIAVTLIAIALVDRVGRRPMLIAGSAGMTVSLGLMALAFSFAQTGG
+AESVSLPQPWSTVALVAANAFVVFFGATWGPLVWVLLGEMFPNRIRAGALAVAAAAQWAA
+NFTVSTTFPWLADIGLTLAYGLYAVMAALSLAFVAAFVPETKGKTLEEMSDVVVRSPGQR
+RAVRAEAERDLRG
+>PROKKA_01334
+MTATRSGGAATSRLNAKVVGISVAAALGGFLFGFDTSVINGAVDALAGEFGLGPGLTGFT
+VSSALIGCALGAWFAGPIANRRGRVPVMVIAAILFLVSAIGSGLAFGVVDLIFWRMVGGL
+GVGAASVIAPAYIAEVSPAHVRGRLGSLQQLAIVLGIFAALLSDALFATMAGGAAQPFWL
+GVDAWRWMFLAEAVPAVLYGLFALKLPESPRYLVARGRTDEAAEVLHEFTGVDRVNLMIE
+DIRRSLDSEHRESLADLRGPAAGLQPIVWIGILLSVFQQAVGINVIFYYSTTLWRSVGFG
+ESDALTVTVITSVTNIAVTFIAIALVDRVGRRPMLIAGSAGMAVSLGLMALAFSFAETGG
+AESVSLPQPWSTVALVAANAFVVFFGATWGPLVWVLLGEMFPNRIRAGALAVAAAAQWAA
+NFTVSTTFPWLADIGLTLAYGLYALMAALSLAFVAAFVPETKGKTLEQMSDIVVRSPGQR
+RAGRAEAERDLRG
+>PROKKA_01515
+MTATRSGGAATSRLNAKVVGISVAAALGGFLFGFDTSVINGAVDALAGEFGLGAGLTGFA
+VSSALIGCALGAWFAGPIANRRGRVPVMVIAAILFLVSAIGSGLAFGVVDLIFWRVVGGL
+GVGAASVIAPAYIAEVSPAHVRGRLGSLQQLAIVLGIFAALLTDALFATMAGGAAQPFWL
+GVDAWRWMFLAEAVPAVLYGLFALKLPESPRYLVARGRTDEAAEVLHEFTGVDRVNLMIE
+DIRRSLDSERRESLADLRGPSAGLQPIVWIGILLSVFQQAVGINVIFYYSTTLWRSVGFG
+ESDALTVTVITSVTNIAVTLIAIALVDRVGRRPMLIAGSAGMTVSLGLMALAFSFAQTGG
+AESVSLPQPWSTVALVAANAFVVFFGATWGPLVWVLLGEMFPNRIRAGALAVAAAAQWAA
+NFTVSTTFPWLADIGLTLAYGLYAVMAALSLAFVAAFVPETKGKTLEEMSDVVVRSPGQR
+RAVRAEAERDLRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001884.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001884.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0327109195c3d331132e7a733fa4a925d3066797
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001884.fa
@@ -0,0 +1,24 @@
+>PROKKA_01683
+MRRTLPLAALAALALLVAGCGTPAAGPSSTPTTPTSGSASAAASSGAASSTAPSSGTHAD
+PATLDVVVNKTRPVAPPDWAPSDLVAVPGSELPLRAEAATAAGDLLDAAAAAGHRLTTLS
+AYRSYDYQVRTYGHWVDELGRAEADRVSARPGYSEHQTGLAWDVGDAATPACDLEACFGD
+TAAGRWVAAHAAEYGFVIRYPVGAEDVTGFAHEPWHLRYVGSAEAARVEAAGGVLETAWG
+LPPAPDYAD
+>PROKKA_01387
+MRRTLPLAALAALALLAAGCGTPAAGPSSTPTTPTSGSASAAASSRAASSTAPSSGTHAD
+PATLDVVVNKTRPVAPPDWAPSDLVAVPGSELPLRAEAATAAADLLDAAAAAGHRLTTLS
+AYRSYDYQVRTYGHWVDELGRAEADRVSARPGYSEHQTGLAWDVGDAATPACDLEACFGD
+TAAGRWVAAHAAEYGFVIRYPAGAEDVTGFDHEPWHLRYVGSAEAARVEAAGGVLETAWG
+LPPAPDYAD
+>PROKKA_01195
+MARRALPAAGLAVLAALAAGCSLSDGQPAPSETTSAPAASSASPSGTATGPAPSSAAPAG
+AHSDPAALDVVVNKARPLSPVDWAPQDLVPVPGSDLPLRAEAARAAGGLIEAAARSGHAL
+STLSAYRSHAYQAQTYGHWVDELGRQEADRVSARPGHSEHQTGLAWDVGDPESPQCHLEA
+CFGDTAAGRWVAEHAAEHGFVVRYPAGAEHVTGYAPEPWHLRFVGREAAAAVEAAGGVLE
+TAWGLPAAPDYPG
+>PROKKA_01612
+MRRTLPLAALAALALLVAGCGTPAAGPSSTPTTPTSGSASAAASSGAASSTAPSSGTHAD
+PAALDVVVNKTRPVAPPDWAPSDLVAVPGSELPLRAEAATAAGDLLDAAAAAGHRLTTLS
+AYRSYDYQVRTYGHWVDELGRAEADRVSARPGYSEHQTGLAWDVGDAATPACDLEACFGD
+TAAGRWVAAHAAEYGFVIRYPAGAEDVTGFDHEPWHLRYVGSAEAARVEAAGGVLETAWG
+LPPARDYAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001886.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001886.fa
new file mode 100644
index 0000000000000000000000000000000000000000..afeaf22a18d6d00dcf7870542a09534c62b85f5b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001886.fa
@@ -0,0 +1,20 @@
+>PROKKA_01780
+MTRVPPAHGHRPALRDSTGSAHGPGVEPGARPRLSAEDLLAARDALAPFGRLSRQEPIEW
+AAEEPLAPDLADFYRYVGPEWLEIDTLGLPVMFFPLDRLWDEQAGYRWNPRTGALLVDWN
+DDWTVVAKQGADPFIHAASTGQVLMAPGDEGWEDRLDEPRPVFRDLTEMTRALAAVGTAW
+ARFDDPFTADWHLTEEVTAAVVAGLEGVLGAHDRAVDLARALGYLGAV
+>PROKKA_01487
+MTRVPPAHGHRPALRDSTGSAHGPGVEPGARPRLSAEDLLAARDALAPFGRLSRQEPIEW
+AAEEPLAPDLADFYRYVGPEWLEIDTLGLPVMFFPLDRLWDEQAGYRWNPRTGALLVDWN
+DDWTVVAKQGADPFIHAASTGQVLMAPGDEGWEDRLDEPRPVFRDLTEMTRALAAVGTAW
+ARFDDPFTADWHLTEEVTAAVVAGLEGVLGAHDRAVDLARALGYLRAV
+>PROKKA_01021
+MDRHLLPAGPGEVTPRPRIALDPARLHAARAALSVFGPVHRQEPIEWAAEEPLAPDLAEF
+YREVGPDWVEIDTLGLPLLMFPLERLWDEQAGYRWNHRTGAMLADWNEDWTVVAKQGAEP
+FIHEAATGHVLMAHGEEGWEDRLGEPVPVFRDVAEMTLALCAAGAAWAGSDDPFTADWHV
+RPEVTSAVVDGLEQVLGDRARAVDVARRLGHLRAA
+>PROKKA_01709
+MTRVPPAHGHRPALRDSTGSAPGPGVEPGARPQLSAEDLLAARDALAPFGRLSRQEPIEW
+AAEEPLAPDLADFYRYVGPEWLEIDTLGLPVMFFPLDRLWDEQAGYRWNHRTGALLVDWN
+EDWTVVAKQGADPFIHAASTGQVLMAPGDEGWEDRLDEPEPVFRDLAEMTRALAAVGTAW
+ARFDDPFTVDWHLTEEVTTAVVAGLEAVLGAHDRAVDLARALGYLRAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001891.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001891.fa
new file mode 100644
index 0000000000000000000000000000000000000000..93726f8622c7fccbce521fe22d11412faaae2954
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001891.fa
@@ -0,0 +1,57 @@
+>PROKKA_01878
+MPTPPDLSAFRTPAATGRPPRGLRLGLAAALAVVWFAVLGLGGPVFGRIGDVSSNDQATF
+LPASAESTRAGQEAAAFQDGEAVPAVVVGPASTADPAAAFPALADLAGRLGEVPGVTDVA
+GPIPSDDGAAVQFLAFVDSSAGAERPVADVVADLREVVADPAAADPALAGTVAADTEWHV
+GGPAGLVAELGGAFAGIDGLLLLVALAVVFVILVAVYRSVLLPVLVLLTAVAALCGAIVA
+VYGMALAGWIQLNGQAQGILSILVIGAATDYCLLLVARHREELLVRADVGEALRAAVRGS
+FGAITASASTVALALLILMASDLNSTRSLGPVAATGVAFAWLAALTLLPALLRLTGRAAF
+WPTIPSPERARRRAQRRAARGRAFTPPLDGAGRPVAGLEEDHGVWTRVGAVVARRPRLVW
+VATTVVLLALCGGLLQLRADGVAQEDVLLGDSDARQAQALLSEHFDAGAGAPAQILAPAG
+DAEAVLAAVAEDPGVAEAEVTTDAPEAAAGPPPGVTDAEGGAGAASAPEPQPRVVDGRVL
+VSATLADPGESLAAQQTVARLRDRLADLPATGEILVGGPAAQALDTNVTTQRDLRVVIPL
+ILAMLLVILAVLLRSLLAPVLLVAATVVSFGAALGVSALVFRHVFGFEDADPTVPLYGFV
+FLVALGIDYTIFLMTRAREETPRHGTRAGVLRALTVTGGVITSAGVVLAATFAALAVIPL
+MFMVQLAFIVAFGVLLDTLIVRSLLIPALVRDIGPKVWWPAKVD
+>PROKKA_01574
+MPTPPDLSAFRTPAATGRPPRGLRLGLAAALTVVWFAVLGLGGPVFGRIGDVSSNDQATF
+LPASAESTRAGQEAAAFQDGEAVPAVVVGPASTADPAAAFPALADLAGRLGEVPGVTDVA
+GPIPSDDGAAVQFLAFVDSSAGAERPVADVVADLREVVADPAAADPALAGTVAADTEWHV
+GGPAGLVAELGGAFAGIDGLLLLVALAVVFVILVAVYRSVLLPVLVLLTAVAALCGAIVA
+VYGMALAGWIQLNGQAQGILSILVIGAATDYCLLLVARHREELLVRADVGEALRAAVRGS
+FGAITASASTVALALLILMASDLNSTRSLGPVAATGVAFAWLAALTLLPALLRLTGRAAF
+WPTIPSPERARRRAERRAARGRAFTPPRDGAGRPVAGLEEDHGVWTRVGAVVARRPRLVW
+VATTVVLLALCGGLLQLRADGVAQEDVLLGDSDARQAQALLSEHFDAGAGAPAQILAPAE
+DAEAVLAAVAEDPGVAEAEVTTDAPEAAAGPPPGALDAEGGAGAASAPEPQPRVVDGRVL
+VSATLADPGESLAAQQTVARLRDRLADLPTSGEILVGGPAAQALDTNVTTQRDLRVVIPL
+ILAMLLVVLAVLLRSLLAPVLLVAATVVSFGAALGVSALVFRHVFGFEDADPTVPLYGFV
+FLVALGIDYTIFLMTRAREETPRHGTRAGVLRALTVTGGVITSAGVVLAATFAALAVIPL
+MFMVQLAFIVAFGVLLDTLVVRTLLIPALVRDIGPKVWWPAKVD
+>PROKKA_00981
+MRTPPDLSALRSPDARRAAGSADPDSAAGRPEGLGASAAGRDGERTDGRTGDRTGERTAG
+RPSAWLRFGLAAALFVVWFAVMGLGGPTFGKIGDVSSNDQSTFLPASAESTRAGEEAAAF
+RDGEAVPAVIVAEADLSDPAQAFPALGGLAETLRGVDGVTDVAGPIPAEDGEAVQFLAFV
+DSSDGAEREVADVVEDLKGILADPAAADADLADTVAADADWHLGGPAGLATELGGAFAGI
+DGLLLLVALVVVFVILVIVYRSVLLPILVLLTAVGALCAAILAVYGMAVAGWIQLNGQAQ
+GILSILVIGAATDYCLLLVARHREELLVREEVTASLLAAVRGSFGAITASASTVALALLI
+LLVSDLNSNSSLGPIAATGILFAWLAALTLLPALLQLAGRAAFWPTVPSPENARRRATRR
+AERGRAFVQPEDAAGRPLAGLEEDHGVWTKVGAAVARRPRPVWLATLAVLLVMSAGLLQL
+QASGVAQEDVLLGESDSRQAQALLTEHFDAGSGAPAQIVAPAEDADAVLAAVEADPGVAE
+ASVTTDEAPAPAGPPPGVTGGGEGTPAEGGAGRPEAAPQPDPEPKVVDGTVLISATLADP
+GESLAAQATVERLRAELADVGSGGEVLVGGPAAQALDTNTTSQRDLVVVIPLILAMLLVI
+LSMLLRSILAPVLLVAATVISFGAAMGVSALVFRHVFGFENADPTVPLYGFVFLVALGID
+YTIFLMTRAREETPRHGTRAGVLRALTVTGGVITSAGVVLAATFAALAVIPLMFMLQLAF
+IVAFGVLLDTLVVRTLLIPALVRDIGPKVWWPARAE
+>PROKKA_01798
+MPTAPDLSAFRTPAAPGRPSRGLRLGLAAALAVVWFAVLGLGGPVFGAIGDVSSNDQATF
+LPASAESTRAGEEAAAFQDGEAVPAVVVGPASTADPAAAFPALADLAGLLGEVPGVVDVA
+GPIPSEDGAAVQFLAFVDSSAGAERPVADVVADLREVVADPAAAAPALAGTVAADTEWHV
+GGPAGLVAELGGAFAGIDGLLLLVALVVVFVILVAVYRSVLLPVLVLLTAVAALCGAIVA
+VYGMALAGWIQLNGQAQGILSILVIGAATDYCLLLVARHREELLVRAEVGEALRAAVRGS
+FGAITASASTVALALLILMASDLNSTRSLGPVAATGVAFAWLAALTLLPALLRLTGRAAF
+WPTIPSPERARRRTERRAARGRAFTPPRDGAGRPIAGLEEDHGVWTRVGTVVARRPRPVW
+VATTVGLLALCGGLLQLRADGVAQEDVLLGDSDARQAQALLSEHFDAGAGAPAQILAPAG
+DAEAVLAAVAEDPGVAEAEVTADAPEAAAGPPPGVTDAEGGAGAASAPEPQPRVVDGRVL
+VSATLADPGESLAAQQTVARLRDRLADLPTSGEILVGGPAAQALDTNVTTQRDLRVVIPL
+ILAMLLVILAVLLRSLLAPVLLVAATVVSFGAALGVSALVFRHVFGFEDADPTVPLYGFV
+FLVALGIDYTIFLMTRAREETPRHGTRAGVLRALTVTGGVITSAGVVLAATFAALAVIPL
+MFMVQLAFIVAFGVLLDTLVVRTLLIPALVWDIGPKVWWPAKAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001893.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001893.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad7e590b36b064b234ff571e7fb9156b1c464f42
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001893.fa
@@ -0,0 +1,33 @@
+>PROKKA_01892
+MRDTTADAAQVPARPDDAAVYRYLAFGEADRPFLVGGPRPAPPAPAATPSPVADLESVRA
+AIRAHGGPLASTAHVCGRPAPTPSAADASRGLRGAARTLTATRRDVAARLADSRERADVP
+VEALLNSAFVDAHADERPADRGVPRGRLAGLVDAVLPPARPAGDDAAAGLLLALREPVRE
+VFASDSFAARPYADAPTVRALFEDFLAHPRRHDPERFWRLLNLELWLRDAVDADAAPAGP
+ATAVDEAPTAPAPVKPDHEPNPGKELDLVSAEDGRRYRRFPVQTGLVDRDTDLQAYLRGE
+IEDFFRDLPADAMPQDAPWHFSVSEKIVAITQGRSYYTWEVRPSVAARVLSRLVTRTPAG
+IGLGDPTTMQLAIQEAGLPRIVLSAAAGAAGKVAGKRGVFYNVVGGNVRAIDGPTTYSTF
+PANVSAKLPPAEPDRVAAEVSAMIRAADIPAWAKASFAGTVVMDANDIGRNALGKDTAAS
+AAVLEAAFADNPLGQGRERTPLAVVVRMD
+>PROKKA_01588
+MRDTTADAAQVPARPDDAAVYRYLAFGEADRPFLVGGPRPAPLAPAATPSPVADLESVRA
+AIRAHGGPLASTAHVCGRPAPTPSAADASRGLRGAARTLTATRRDVAARLADSRERADVP
+VEALLNSAFVDAHADERPADRGVPRWRLAGLVDAVLPPARPADDDAAAGLLLALREPVRE
+VFASDSFAARPYADAPTVRALFEDFLAHPRRHDPERFWRLLNLELWLRDAVDPDAAPASP
+AAAVDEAAGAPAPAKPDHEPNPGKELDLVSAEDGRRYRRFPVQTGLVDRDTDLQAYLRGE
+IEDFFRDLPAEAMPQDAPWHFSVSEKIVAITQGRSYYTWEVRPSVAARALSRLVTRTPAG
+IGLGDPTTMQLAIQEAGLPRIVLAAAAGAAGKVAGKRGVFYNVVGGNVRAIDGPTTYSTF
+PANVSAKLPPAEPDRVAAEVSAMIRAADIPAWAKASFAGTVVMDANDIGRNALGKDTAAS
+AAVLEAAFADNPLGQGRERTPLAVVVRMD
+>PROKKA_00966
+MFYNVVGGNVRAIDGPTTYSAFPANVSAKLPPADPDGVAREVSAMIRAADIPEWARRSFA
+GTVVMDANDIGRNALGRDTAASAAVLEAAFADNPLGQGRERTPLAVVVRMD
+>PROKKA_01812
+MRDTTADAAQVPARPDDAAVYRYLAFGEADRPFLVGGPRPAPLAPAATPSPVADLESVRA
+AIRAHGGPLASTAHVCGRPAPTPSAADAPRGLRGAARTLTATRRDVAARLADSRERADVP
+VEALLNSAFVDAHADERPADRGVPRGRLAGLVDAVLPPARHADDDAAAGLLLALREPVRE
+VFASDSFAARPYADAPTVRALFEDFLAHPRRHDPERFWRLLNLELWLRDAVDADAAPAGP
+ATAVDEAPTAPAPAKPDHEPNPGKELDLVSAEDGRRYRRFPVQTGLVDRDTDLQAYLRGE
+IEDFFRDLPADAMPQDAPWHFSVSEKIVAITQGRSYYTWEVRPSVAARALSRLVTRTPAG
+IGLGDPTTMQLAIQEAGLPRIVLSAAAGAAGKVAGKRGVFYNVVGGNVRAIDGPTTYSTF
+PANVSAKLPPAEPDRVAAEVSAMIRAADIPAWAKASFAGTVVMDANDIGRNALGKDTAAS
+AAVLEAAFADNPLGQGRERTPLAVVVRMD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001905.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001905.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d536a6e6624c0e0b7ad7637548ebc17049dee0d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001905.fa
@@ -0,0 +1,13 @@
+>PROKKA_01967
+MSELDELDFAALSAFLAWWFGKTGVDWIRREDG
+>PROKKA_01661
+MSELDELDFAALSAFLAWWFGKTGVDWIRREDG
+>PROKKA_00892
+MSELDELDFVAVEIHTAGTDPASVCAVDMALVRGGEIVAAERWPVRPPTGPTSFSRLHTQ
+LHGVDEAAVADAPEWPEVAAQLDLLGEHLPFVASGADRDRGAYEAATRATGGTPQAHEWR
+DALALVGRLRPDVDPPRIATAAQALGVPDGARPAGAGSEAVRTAEVVLALARQSGRGTVR
+RLWSEAAPPTPDEPIIPESLRRRHATEPSVPPAGAHRWAPPAPAPAPASAAPAGRGGGVG
+WKLAGTAMVGIALGAALFFVASVAVIMEYLEDGRGSDATVGMGIAALSAFLAWWFGKTGV
+DWIRRQDG
+>PROKKA_01893
+MSELDELDFAALSAFLAWWFGKTGVDWIRREDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001910.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001910.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98e19060e38c358288b4435cd3891eb5e7ff9582
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001910.fa
@@ -0,0 +1,52 @@
+>PROKKA_02001
+MKILPPRSAASPRPLAPAVAVAALSILVGGLLPQSPSATTEGAPDARPRDDAARATTVGA
+AATPASAAPVEGAGVATVPQEGENLVPAEEAPAGVVLGEPVVDRPFTVAAAVWDAAADDA
+VKRVEIRVRQDGAWGPWQVLDRPVLPEDAAPARTGTDPFVAFGADGAQLRVTTVDGAAPA
+GLELSLIDPGTAATDETVASAHPAVAAEQAAETAGLPRGVKSSAVVGGEEPAEARTVATV
+SDARAKILPDVITRAQWGADESWAEDSPQFDQVRALTIHHTAGTNDYTRAQAVEQMRGIY
+AYYTKTLGWGDFPYHLITDRFGNIYEGRRGALDSNPLGTHAGGFNRGTMGVSTMGNYDVV
+APSEEVVDAMARATAYYLYRDGIDARGRVTLTSGGSTKYAAGTPVTVDTIFPHRATSATA
+CPGQHLMARFDDLRDRAEAIATAAGQPPAAVTPAPTPAPTTERSTAGTYTVQPNDGWWTI
+ARRTGVPAATLQELNGMTESTVLHPGMVLRTVADPTAPEPTPITTGTYTVQPNDGWWVIA
+RRTGVSAAELQRLNGMTASTVLHPGMVLITAATAPASPPAPAPAPGTYTVREGDGWWIIA
+HRTGVTMETLQRLNGMTATTVLHPGMVLRTGQTASAPAPSPATYVVQANDGWWLIAQRTG
+VSMERLQRLNGMTVSTMLHPGMVLRTA
+>PROKKA_01695
+MKILLPGSAASPRPLAPAVAVAALSVLVGGLLPQQPSATTEGAPDARPLDDAARATTAGT
+ATTPASAAPVEGAGVATVPQEGENLVPAEEAPAGVVLGEPVVDRPFTVAAAVWDAAADDA
+VERVEIRVRQDGAWGPWQVLERPVLPEDAAPARTGTDPFVAFGADGAQLRVTTVDGAAPA
+GLELSLIDPGTAATDETVASAHPAVAAEQAAETAGLPRGVKSSAVVGGAAPAEAHTVATA
+SDARAKILPDVITRAQWGADESWAEDSPQFDQVRALTIHHTAGTNDYTRAQAVEQMRGIY
+AYYTKTLGWGDFPYHLITDRFGNIYEGRRGALNSNPLGTHAGGFNRGTMGISTMGDYDVV
+APSEEVVDAMARATAYYLYRDGIDARGRVTLTSGGSTKYAAGTPVTVDTIFPHRATSATA
+CPGQHLMARFDDLRDRAEAIATAAGQPPTPATPAPTPAPTTEPSTAGTYTVQPNDGWWII
+ARRTGVPAATLQELNGMTESTVLHPGMVLRTVADPTAPEPTPITTGTYTVQPNDGWWVIA
+RRTGVSAAELQRLNGMTASTVLHPGMVLITAATAPTSPPAPAPAPAPAPDTYTVREGDGW
+WIIAHRTGVTMETLQRLNGMTATTVLHPGMVLRTGQTASAPAPSPATYVVQANDGWWLIA
+QRTGVSMERLQRLNGMTVSTLLHPGMVLRTA
+>PROKKA_00856
+MKLSAPRSAAPARSPPAVVVAALSVLVGGLLPQQPVPTTAVPPPPPRLADAAALRTLAPA
+GSGRAPAAASEVRGAAVAAVPQEGEALADAPAGVVLGEPVVDRPFTVAAAVWDAAADHAV
+ERVEIRVRQDGAWGPWQVLERAVLPEGAAVTRTGTDPFVAFGADGAQLRLTTADGAAPAG
+LELSLIDPGTAATDEAVASAHPAVSADQAAQDAALPRGVKSSAVVGGAEPAPARTVSTAS
+EARARILPDVITRAQWGADESWAQASPQFEQVRALTIHHSAGTNDYTRAQAVEQMRAIYA
+YYTKTLDWGDFPYHLITDRFGNIYEGRRGALDANPLGTHAGGFNTGTMGISTMGNYDVVA
+PSEEVVDAMARATAYYLYRDGLDPYGRVTLTSGGSTKYAAGTPVTVDTIFPHRTTSNTAC
+PGRHLMARFDDVRDRAATIAAAAGQEAPAPEPEPIPTPEPEPTPRPEPEPIPMPEPTTPT
+TYTVQDGDGWWVIARRTGVPAATIQELNGMTESTVLHPGMVLRLVADVSAPAPTPVTTGT
+YTVQPNDGWWVIARRTGVPAEELQRLNGMTADSLLHPGMVLITAATAPAPAPAPAPAPAP
+APGTYTVRDGDGWWVIAHRTGVTMETLQRLNGMTADTLLHPGMVLVTGQNATAAAPAPAP
+ATYTVRPNDGWWIIADRTGISMAELQRLNRMTASTLLHPGMVLRIA
+>PROKKA_01927
+MKILLPGSAASPRPLAPAVAVAALSVLVGGLLPQQPSATTEGAPDARPLDDAARATTAGT
+ATTPASAAPVEGAGVATVPQEGENLVPAEEAPAGVVLGEPVVDRPFTVAAAVWDAAADDA
+VERVEIRVRQDGAWGPWQVLERPVLPEDAAPARTGTDPFVAFGADGAQLRVTTVDGAAPA
+GLELSLIDPGTAATDETVASAHPAVAAEQAAETAGLPRGVKSSAVVGGAAPAEAHTVATA
+SDARAKILPDVITRAQWGADESWAEDSPQFDQVRALTIHHTAGTNDYTRAQAVEQMRGIY
+AYYTKTLGWGDFPYHLITDRFGNIYEGRRGALDSNPLGTHAGGFNRGTMGISTMGDYDVV
+APSEEVVDAMARATAYYLYRDGIDARGRVTLTSGGSTKYAAGTPVTVDTIFPHRATSATA
+CPGQHLMARFDDLRDRAEAIATAAGQPPTPATPAPTPAPTTEPSTAGTYTVQPNDGWWII
+ARRTGVPAATLQELNGMTESTVLHPGMVLRTVADPTAPEPTPITTGTYTVQPDDGWWVIA
+RRTGVCAAELQRLNGMTASTVLHPGMVLITAATAPASTPAPAPAPAPGTYTVREGDGWWI
+IAHRTGVTMETLQRLNGMTATTVLHPGMVLRTGQTASAPAPSPATYVVQANDGWWLIAQR
+TGVSMERLQRLNGMTVSTLLHPGMVLRTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001916.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001916.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bbb762a9ac778acc0056c25c20ccc42113d76a28
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001916.fa
@@ -0,0 +1,32 @@
+>PROKKA_02049
+MTQDAFLYDALRTPRGAGKPSGSLHEVKPIDLVVGLTHALRDRHEGLDPADIEDMILGCV
+SPVGDQGAVLPRVAALKAGLPQTVAGVQLNRFCASGLEAMNQAAARIRSGWESLLVAGGV
+ESMSRVPMGSDGGAWAMDPATSLATDFVPQGVSADLIATREGFSRAELDRFAAQSHRRAA
+AAWQEGRFARSVVPVTDMNGMTVLDRDETIRPDSSVETLATLKPSFEALGREAGFDAVAL
+EKYSSLAGIEHLHHPGNSSGIVDGAALTLIGSEEAGRRAGMSPRARIVSAAVVGSEPTIM
+LTGPTPACRKALEVAGMTAADIDLVEINEAFAAVPLLLMKEMGWTEEQTNVNGGAIAMGH
+PLGATGAMILGTLVDELERRDLRTGIATLCIGAGMGVATIVERV
+>PROKKA_01755
+MTQDAFLYDALRTPRGAGKPSGSLHEVKPIDLVVGLTHALRDRHEGLDPADIEDMILGCV
+SPVGDQGAVLPRVAALKAGLPQTVAGVQLNRFCASGLEAVNQAAARIRSGWESLLVAGGV
+ESMSRVPMGSDGGAWAMDPATSLATDFIPQGVSADLIATREGFSRAELDSFAAQSHRRAA
+AAWQEGRFARSVVPVTDMNGMTVLDRDETIRPDSTVETLAKLKPSFEALGREAGFDAVAL
+EKYSSLAEIEHLHHPGNSSGIVDGAALTLIGSEEAGRRAGMSPRARIVSAAVVGSEPTIM
+LTGPTPACRKALEVAGMTAADIDLVEINEAFAAVPLLLMKEMGWTEEQTNVNGGAIAMGH
+PLGATGAMILGTLVDELERRDLRTGIATLCIGAGMGVATIVERV
+>PROKKA_00731
+MTRDAYLFDAVRTPRGLGKPTGSLHEVKPVGLLGGLFDALRERHPEWDPAGVDDVVLGVV
+TPVGDQGGDIARVAALKAGMPESVAGVQLNRFCGSGLEAVNQVAARIRSGWEDMLIAGGV
+EAMSRVPMGSDGSAWAMDPATALDLHFVPQGISADLIATRQGFSREDLDRFAVQSHHRAA
+QAWSEGRFEGSVIPVTDMNGLTVLDRDETIRPDASLETLAGLRPSFAAMGEQAGFDAVAL
+NRYTDVDEIHHVHHAGNSSGIVDGAALTLIGGEEAGRRAGLTPRARIVSAAVVGSEPTIM
+LTGPTPACRKALDVAGMTASDIDLVEINEAFAAVPLQLMRDLGWNEEQTNVNGGAIAMGH
+PLGATGAMILGTLVDELERRDLQTGIATLCIGAGMGVATIVERV
+>PROKKA_01983
+MTQDAFLYDALRTPRGAGKPSGSLHEVKPIDLVVGLTHALRDRHEGLDPADIEDMILGCV
+SPVGDQGAVLPRVAALKAGLPQTVAGVQLNRFCASGLEAVNQAAARIRSGWESLLVAGGV
+ESMSRVPMGSDGGAWAMDPATSLATDFIPQGVSADLIATREGFSRAELDRFAAQSHRRAA
+AAWQEGRFARSVVPVTDMNGMTVLDRDETIRPDSTVETLATLKPSFEALGREAGFDAVAL
+EKYSSLAGIEHLHHPGNSSGIVDGAALTLIGSEEAGRRAGMSPRARIVSAAVVGSEPTIM
+LTGPTPACRKALEVAGMTAADIDLVEINEAFAAVPLLLMKEMGWTEEQTNVNGGAIAMGH
+PLGATGAMILGTLVDELERRDLRTGIATLCIGAGMGVATIVERV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001918.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001918.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fe07b18ca53c52fbb509f2d0ec2327bc2b3906ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001918.fa
@@ -0,0 +1,39 @@
+>PROKKA_02062
+MSEHFDVAVLGLGPGGEVAADRLLKAGKNVVVFERELIGGECAYWACIPSKTVLRPPEAR
+TEVQRAAGVSGAELDWAATAKYRDYMIRNLDDQAQVDGYIKEGAVVIKDEARITGPGRIQ
+AGDREITAEHIIIATGSDAVIPPLDGIDQITAWTNRETYTTSTLPERAVIIGGSAVGVET
+ATFLARFGVAITLIHCGERLLDREGPRVGELAHQYLQEAGIDIRLATSAVQARREGADSI
+IELQTRDGDPAGEVAADVVIFGTGRTPRTEGLGFEHAGVTLGDHGEIQIDDHCRAGENTW
+AIGDVTGIMPFTHVAKYQGRIAADAILGRPHPATYDGIPRVVFTDPEIAGAGLTQEQATK
+QGIRTIATELDLADAIARPWTYEQDSRGHLGLLADADRKILIGAWAVGPMAGEWIHHASL
+AIRTQLPIDTLLDQVAQFPTYHEAYQVALEQLDLTP
+>PROKKA_02222
+MSEHFDVAVLGLGPGGEVAADRLLKAGKNVVVFERELIGGECAYWACIPSKTVLRPPEAR
+TEVQRAAGVSGAELDWAATAKYRDYMIRNLDDQAQVDGYIKEGAVVIKDEARITGPGRIQ
+AGDREITAENIIIATGSDAVIPPLDGIDQITAWTNRETYTTSTLPERAVIIGGSAVGVET
+ATFLARFGVAITLIHCGERLLDREGPRVGELAHQYLQEAGIDIRLATSAVQARREGADSI
+IKLQTRDGDPAGEVAADVVIFGTGRTPRTEGLGFEHAGVTLGDHGEIQIDDHCRAGENTW
+AIGDVTGIMPFTHVAKYQGRIAADAILGRPHPATYDGIPRVVFTDPEIAGAGLTQEQATK
+QGIRTIATELDLADAIARPWTYEQDPRGHLGLLADADRKILIGAWAVGPMAGEWIHHASL
+AIRTQLPIDTLLDQVAQFPTYHEAYQVALEQLDLTP
+>PROKKA_02426
+MTEDLAPTTGPDDATPGAPDEEAVDVVVIGAGPVGENAAQYAHTAGGLEVALVEADLLGG
+ECSYWACMPSKALLRPLEVAGAAAHLGGLTDPDIDLPGLLARRDEWRSHLDDAGQVEWAE
+DAGLRVVRGHGRLAGPRRVEVLGDDGAPARVLRARHAVVVATGSTAVVPGELRGVSPWTS
+RDATGVREVPGRLAIVGGGVVAVEAATWMAALGSDVQLLVRGDRLLSGQEPVASRLVLEG
+LVDAGVRVRFGTSVERAERADVHAESDVGVPHGGPVRLTLAGSGETLEVDELLVAAGRRP
+ALDGLGLEALGLSAEDLQDESGTAVVPASDGAAPWLYAVGDVTGGPALTHWGKHRARLLG
+ERIAALATGRPAPSGEEAGEGVPEAVPQVVFTSPQVARVGVTEAQAREEGGEGELRVVDV
+PLTSAAGAALLRDDAAGRAVLVLRGDRVVGATFVGFEVAELLHAATVAIVGEVPLDRLRH
+AVAAYPTASEVWLRLVEEALGRG
+>PROKKA_02440
+MSSVIPDTARPSSGHAGVHRADVVVLGHGLAGLVAACELLEAGRSVVLVDQERAADLGGQ
+AWWSFGGLFLVDSPEQRRLRVRDSVDLAWSDWRETAGFTGGDDALPRAWAEAYVHFAAGE
+KRAWLRERGHRLFPVVGWAERKVPAPGVGGNSVPRFHITWGTGPGIVEPFAAVVEQAAFD
+GRLTYLPRHRVTELVTQNGAVCGVRGDRLADDDGARGTSSSRTVTGAFEVRAQAVLIASG
+GIGADHDAVRAAWPDRLGTPPERMLSGVPAYVDGSGVAAARAVGAHMLHPDRMWHYTEGV
+ANWDPVWPGHGIRILPGPSSLWLDAAGRRLPHPRWPGFDTLGALGEICRPGGARRAEGAD
+HTWFVLNERIIGREFALSGSEQNPDLTGRSLGHVLGRATQGVPAPVRAFLDHGEDFVQAA
+TVEELVDQMNELQDRTGGGGPRVELHAVRQAVAEHEDGAARAGVDPQLDAVRRARQYLGD
+RLIRTAAPHRLTDPAAGPLIAVRLRTLTRKTLGGLHTDLRGRVLDELGGPVPGLYAAGEA
+AGFGGGGMHGFRALEGTFLGGCLFSGRTAGRALAEDVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001919.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001919.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1abef60f0d9964d65530c8d419f51c75b6553f75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001919.fa
@@ -0,0 +1,16 @@
+>PROKKA_02090
+MVTRPVLQQPVVDAVDIRSVAEFYRELLGLHYRTGDELADGREPDSADWLVLLDDDGRRV
+LTFQRTEELKPSTWPSPEVPMQLHLDFTVPDRESLDAAHDHALRLGGRLVLDRSDDEDEP
+LYVFADPAGHPFCVFVG
+>PROKKA_01798
+MVTRPVLQQPVIDAVDIRSVAEFYRELLGLHYRAGDELADGREPDSADWLVLLDDDGRRV
+LTFQRTDELKPSTWPSPEVPMQLHLDFTVPDRDSLDAAHDHALRLGGRLVQDRSDDEDEP
+LYVFADPAGHPFCVFVG
+>PROKKA_00688
+MITHPALQQPVIDAVDIRSVAEFYRELLGLHYRAGDELADGREPDSADWLVLLDDDGRRV
+LTFQRTEELKPSTWPSPEVPMQLHLDFTVPDRDSLDAAHDHALRLGGRLVQDRSDDEDEP
+LYVFADPAGHPFCVFVG
+>PROKKA_00604
+MVSRPVLQQPVIDAVDIRSVADFYRELLGLHYRTGDELADGREPDSADWLVLLDDDGRRV
+LTFQRTEELKPSTWPSPEVPMQLHLDFTVPDRDSLDAAHDHALRLGGRLVLDRSDDEEEP
+LYVFADPAGHPFCVFVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001920.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001920.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a7582914a148a9a0b44cda5c71551f64f9077adc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001920.fa
@@ -0,0 +1,16 @@
+>PROKKA_02091
+MTDADLDDMFRLLGDAEVMRYYPRAKSRNEVRRWINWSKDNYATHGFGLWVIEHRTTGDF
+IGDCGLTWQNVDGQEVLEVGYHVLPEHQGQGLATEGASACLRHGFETLDATMVTAIINPD
+NMASRRVAERIGMTVWKSTRDPRGAPIVVYSSHGHEA
+>PROKKA_01799
+MTDADLDDMCRLRGDAEVMRYYPRAKSRNEVQRWINWSKDNYAKHGFGLWVIEHRTTGDF
+IGDCGLTWQNVDGQEVLEVGYHVLPERQGQGLATEGASACLRHGFETLDATMVTAIINPD
+NMASRRVAERIGMTVWKRTRDPSRAPIVVYSSHGQEA
+>PROKKA_00687
+MTDADLDDMCRLLGDAEAMRYYPRAKSRNEVQRWINWSKDNYAKHGFGLWVIEHRTTGDF
+IGDCGLTWQNVDGQEVLEVGYHVLPERQGQGLATEGASACLRHGFETLDATMVTAIINPD
+NMASRRVAERIGMTVWKSTRDPSGAPIVVYSSHGQEA
+>PROKKA_00603
+MTDADLDDMCRLLGDAEVMRYYPRAKSRNEVQRWINWSKDNYAEHGFGLWVIEHRATGDF
+IGDCGLTWQNVDGQEVLEVGYHVLPERQGQGLATEGASACLRYGFETLCATMVTAIINPD
+NMASRRVAERIGMTVWKSTRDPSGAPIVVYSSHGQEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001923.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001923.fa
new file mode 100644
index 0000000000000000000000000000000000000000..db28b2e1c96d6b8dab3cb90327da270ebc0b7f4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001923.fa
@@ -0,0 +1,20 @@
+>PROKKA_02101
+MPVGAAGGRDAAPTRAIADMLPLIPADLLRALGLILVPVAAVHAGWPSAAAMLLVFGSQW
+LTRWLAPGGVLDWAAQAVLLLAGWLSVIGLYPRVPSLDLLVHAAASAVVACLTALVVGAW
+LRRRGTEAGQAVALLGPGLAGLGIAAAAVALGVVWELAEWWGHTAVTPEIGVGYTDTIGD
+LAADLVGAGIGAALAVRRGRTR
+>PROKKA_01808
+MPVGAAGGRDAAPTRAIADMLPLIPADLLRALGLILVPVAAVHAGWPSAAAMLLVFGSQW
+LTRWLAPGGVLDWAAQAVLLLAGWLSVIGLYPRVPSLDLLVHAAASAVVACLTALVVGAW
+LRRRGTEAGQAVALLGPGLAGLGIAAAAVALGVVWELAEWWGHTAVTPEIGVGYTDTIGD
+LAADLVGAGIGAALAVRRGRTR
+>PROKKA_00678
+MLPLIPADLLRALGLVLIPAAWAVAGWPSAAVMLLVFGAQWLTRWLVPGSALDWGAQAVL
+LAAGWFSVTGLYHRVEALDLVMHAAASAAVVGLVAVAARARLRRRGEDPGALVRRLGPVL
+SAAALTGAGVGLGVLWELAEWWGHTVVTAEIGVGYDDTIGDLAADLLGAGAGAALAVRGQ
+LRAAGSAR
+>PROKKA_02041
+MPVGAAGGRDAAPTRAIADMLPLIPADLLRALGLILVPVAAVHAGWPSAAAMLLVFGSQW
+LTRWLAPGGALDWAAQAVLLLAGWLSVIGLYPRVPWLDLLVHAAASAVVACLTALVVGAW
+LRRRGTEAGQAVALLGPGLAGLGIAAAAVALGVVWELAEWWGHTAVTPEIGVGYTDTIGD
+LAADLVGAGIGAALAVRRERTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001926.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001926.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f49b6211a24c1a593cc0741d5a740b6aaf9279d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001926.fa
@@ -0,0 +1,20 @@
+>PROKKA_02124
+MSTEPTPSSATPETESAAPSSSGLPQAAPQAAWPERVETGEHQVSYRATVAAPAHELWAM
+LADPHRHHEADGSGTVRPKVSGPHRLAVGDRFRVAMRKYGVPYTMTLTATAVDEDELVEW
+AHPGGHRWRWAFQDNGDGTTEVTETFDYSWARPAVRRAYELLRVPADNGRGIQSSLTRLA
+GRHL
+>PROKKA_01832
+MSTEPTPSSATPETESAAAPSSSGLPQAAPQAAWPERVETGEHQVSYRVTVAAPAHELWA
+MLADPHRHHEADGSGTVRPKVSGPHRLAVGDRFRVAMRKYGVPYTMTLTATAVDEDELVE
+WAHPGGHRWRWAFRDNGDGTTEVTETFDYSWARPAVRRAYELLRVPADNGRGIQSSLTRL
+AGRHL
+>PROKKA_00573
+MSTEPTPSPATPETEPAAPSSSGLPQSAPQAAWPERVETGEHQVSYRATVAAPAQELWAM
+LADPHRHHEADGSGTVRPKVSGPHRLAVGDRFRVAMRKYGVPYTMTLTATAVDEDELVEW
+AHPGGHRWRWAFQDNGDGTTEVTETFDYSWARPAVRRAYELLRVPADNGRGIQSSLTRLA
+GRHL
+>PROKKA_02062
+MGDMSTEPTPSSATPETESAAAPSSSGLPQAAPQAAWPERVETGEHQVSYRVTVAAPAHE
+LWAMLADPHRHHEADGSGTVRPKVSGPHRLAVGDRFRVAMRKYGVPYTMTLTATAVDEDE
+LVEWAHPGGHRWRWAFQDNGDGTTEVTETFDYSWARPAVRRAYELLRVPADNGRGIQSSL
+TRLAGRHL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001927.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001927.fa
new file mode 100644
index 0000000000000000000000000000000000000000..195e8c39773f57cbb6d044cd0fef8bdefc17126b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001927.fa
@@ -0,0 +1,28 @@
+>PROKKA_02135
+MSEHTPAHTPASLGPAHRKVGVVGAGGVGTAICYAALIRGVAREVALYDIDEPKVRAEVL
+DLAHGTPFTSASAMTGGADPDVLAGCEVVVITAGAKQKPGQTRLDLGAHNVEILRGLLPQ
+VQAHAPDALIVLVTNPVDVLTLVAQRLTGLPAGRVIGSGTLLDTSRLRWLLASRAQVHAS
+SVHAAILGEHGDTEFPAWSSARIGPTPLLEWPTPADPLFTRADLDEVADTVVNAAYEVIQ
+GKGATTYAVGVATTRLLEAILRDQHAILPVSTVLDGVHGLSDVALSMPSVVGRDGVTRVI
+QPELDAAEMRALHASADALRREARSLGF
+>PROKKA_01843
+MSEHTPAHSPAAPASLGPAHRKVGVVGAGGVGTAICYAALIRGVAREVALYDIDEPKVRA
+EVLDLAHGTPFTSASAMTGGADPDVLAGCEVVVITAGAKQKPGQTRLDLGAHNVEILRGL
+LPQVQAHAPEALIVLVTNPVDVLTLVAQRLTGLPAGRVIGSGTLLDTSRLRWLLASRAQV
+HPSSVHAAILGEHGDTEFPAWSSARIGPTPILEWPTPVDPLFTRADLDEVADTVVHAAYE
+VIQGKGATTYAVGVATTRLLEAILRDQHAILPVSTVLDGVHGLSDVALSMPSVVGRDGVT
+RVIQPELDDAEMRALHASADALRREARSLGF
+>PROKKA_00637
+MSEHTPAAPASLGPAHRKVGVVGAGGVGTAICYAALIRGVAREVALYDIDEPKVRAEVLD
+LAHGTPFTSASAMTGGADPDVLADCEVVVITAGAKQRPGQTRLDLGAHNVEILRGLLPQV
+QAHAPDALIVLVTNPVDVLTLVAQRLTGLPAGRVIGSGTLLDTSRLRWLLASRAQVHASS
+VHAAILGEHGDTEFPAWSSARIGPTPILEWPTPAAPLFTRADLDEVADTVVHAAYEVIRG
+KGATTYAVGVATTRLLEAILRDQHAILPVSTVLDGVHGLSDVALSMPSVVGRDGVTRVIQ
+PELDAAEMRALHSSADALRREARSLGF
+>PROKKA_02073
+MSEHTPAHSPAAPASLGPAHRKVGVVGAGGVGTAICYAALIRGVAREVALYDIDEPKVRA
+EVLDLAHGTPFTSASAMTGGADPDVLAGCEVVVITAGAKQKPGQTRLDLGAHNVEILRGL
+LPQVQAHAPEALIVLVTNPVDVLTLVAQRLTGLPAGRVIGSGTLLDTSRLRWLLASRAQV
+HPSSVHAAILGEHGDTEFPAWSSARIGPTPILEWPTPVDPLFTRADLDEVADTVVHAAYE
+VIQGKGATTYAVGVATTRLLEAILRDQHAILPVSTVLDGVHGLSDVALSMPSVVGRDGVT
+RVIQPELDDAEMRALHASADALRREARSLGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001929.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001929.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4286e5fdb843d6b1acf44e41985b9c16ec418ba5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001929.fa
@@ -0,0 +1,20 @@
+>PROKKA_02156
+MIRVVVADDQALMRTALEHFVAQAEDLEVVGSAEDGVQALEAARTLAPDVVLMDMQMPRM
+DGVEATARISAEAPGVRVLAITTFSSEQYLVPALRAGAAGYLVKDAPPAEVVDAIRRVHA
+GDAVFSARVAADLVEAVTAAPEHTAPCPAEPLAPHERLTERELDVVRELAKGASNAEIAG
+APFLAEATVKSHIGKVLDKWQVRDRVQILIRAARAGLVDIG
+>PROKKA_01869
+MIRVVVADDQALMRTALEHFVAQAEDLEVVGSAEDGVQALEAARTLAPDVVLMDMQMPRM
+DGVEATARISAEAPGVRVLAITTFSSEQYLVPALRAGAAGYLVKDAPPAEVVDAIRRVHA
+GDAVFSARVAADLVEAVTAAPEHTAPCPAEPLAPHERLTERELDVVRELAKGASNAEIAG
+ALFLAEATVKSHIGKVLDKWQVRDRVQILIRAARAGLVDIG
+>PROKKA_00604
+MLVADDQQLMRTALAHFVSTAEDLEVVGTAADGVEAVEMAKDLRPDVVLMDMQMPRMDGI
+EATTAIMAEAPEVRVLAITTFSSEAYLVPALRAGASGYLVKDAPPEEVVEAVRQVHRGDA
+VFSPRVARELIETVTQQSERRESAAAHALTELEELTPRELEVVTELAKGSSNAEIAQALF
+LAEATVKSHLGKIMDKWQARDRVQVLIRASRAGLVSFDD
+>PROKKA_02099
+MIRVVVADDQALMRTALEHFVAQAEDLEVVGSAEDGVQALEAARTLAPDVVLMDMQMPRM
+DGVEATARISAEAPGVRVLAITTFSSEQYLVPALRAGAAGYLVKDAPPAEVVDAIRRVHA
+GDAVFSARVAADLVEAVTAAPEHAAPCPAEPLAPHERLTERELDVVRELAKGASNAEIAG
+ALFLAEATVKSHIGKVLDKWQVRDRVQILIRAARAGLVDIG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001932.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001932.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c127ca2d6fe83167fb82fa49d53d3f8684caad73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001932.fa
@@ -0,0 +1,24 @@
+>PROKKA_02187
+MPSTAVPPRDSGAASTLPARTGHRGVSILRTAALVLVVAAFVWLALTVRLPGVDELRAQL
+DGFGWWSWLAFTVLYAAVALTPIPVTIMAVTAGVLFGAIEGTVLSVVGALLGSLGAYGIA
+RAVGREVVLRWLGRHAETVERRLEDTGFLALLTLRVAPGLPYWPVNYGAGALAVPLGIFA
+GSTAVGVIPGQLSLVAMGAFAVRPGVVNGVLLGVGWLTVGGLTLWAVRHWRRAARSAEEP
+ENPQSGHDTPSPRRRRGVS
+>PROKKA_01901
+MPSTAVPPRDSGAASTLPARTGHRGVSILRTAALVLVVAAFVWLALTVRLPGVDELRAQL
+DGFGWWSWLAFTVLYAAVALTPIPVTIMAVTAGVLFGAIEGTVLSVVGALLGSLGAYGIA
+RAVGREVVLRGLGRHAETVERRLEDTGFLALLALRVAPGLPYWPVNYGAGALAVPLGIFA
+GSTAVGVIPGQLSLVAMGAFAVRPGVVNGVLLGVGWLAVGGLTLWAVRRWRRAARAAEGP
+AGSEGPESPRSGQDTPSPRARRGVS
+>PROKKA_00562
+MPSSAAPPSDAASSRPDRRGSSGSVGTASRTLLLVVVMALFIWLATSVRLPDIDTLRDRL
+ASFGFWSWLVFVLAYAGVALTPVPVTLMALTGGVLFGAVQGSVLSVAGALLGSIGAYWIA
+RALGRDVILRGLGRHADTVEEHLEDAGFLALLTLRVAPGLPYWPVNYGAGALGVPSGMFV
+GSTAVGVIPGQVSLVALGAFAVHPGVLNGVILGAGWLAVGVLTVWAARHWRRAANHDDGE
+GGED
+>PROKKA_02132
+MPSTAVPPRDSGAASTLPARTGHRGVSILRTAALVLVVAAFVWLALTVRLPGVDELRAQL
+DGFGWWSWLAFTVLYAAVALTPIPVTIMAVTAGVLFGAIEGTVLSVVGALLGSLGAYGIA
+RAVGREVVLRWLGRHAATVERRLEDTGFLALLTLRVAPGLPYWPVNYGAGALAVPLGIFA
+GSTAVGVIPGQLSLVAMGAFAVRPGVVNGVLLGVGWLAVGGLTLWAVRRWRRAARAAEGP
+AGSEGPESPRSGQDTPSPRARRGVS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001935.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001935.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0bdc3ffea6e6cbf3f57e2fc993064a695dcc7d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001935.fa
@@ -0,0 +1,17 @@
+>PROKKA_02193
+MSPADPTADVAAGPAGPAAVAEAFAAAWNAADADALADLFAEDADFVNVVGVWWTRRRQI
+RVNHALGFRWMFPASRLVLGQVRVRELGDVAVVHAPWTMTGQTAPDGDEAGERTGVLLLV
+VRRTEAGAWEAVAGQNTDSVPEAQTHLADDDGLAAVHYHPSAWIDPDDDPDGPEAC
+>PROKKA_01906
+MSPADPTADVAARPTGPAAVAEAFAAAWNAADADALAELFAEDADFVNVVGVWWRRRRQI
+RVNHALGFRWMFPHSRLELGRVRVRELGDVAVVHAPWTMTGQTAPDGDEAGERTGVLLLV
+VRRTETGAWEAVAGQNTDSVPGAQTHLADDEGLAAVHYHPSAWFDPDEDPDGPEAC
+>PROKKA_00553
+MSPADPSPRLLARPPASPAAVAEAFEAAWNAADADALADLFAEDADFVTVLGVWWTRRRQ
+IRLDHARAFRWMFPESRLEMDEVRVRDLGDVAVVHAPWTMTGPGVGGEVGEATGTVGVRE
+AGGDGSGGGDGERTGVLLLVVRRDEAGAWEVVAAQNTDRSPEPRPRPADEDDLLAEVHPH
+PSAWLHPDDDGPASRLSARPRLGWAVHEPVPPLPLPNSPSPPLPLPQGELSCRWPV
+>PROKKA_02137
+MPPADPTADVAARPAGPAAVAEAFAAAWNAADADALAELFAEDADFVNVVGVWWTRRRQI
+RVNHALGFRWMFPASRLVLGQVRVRELGDVAVVHAPWTMTGQTAPDGDEAGERTGVLLLV
+VRRTEAGAWEAVAGQNTDSVPEAQTHLADDDGLAAVHYHPSAWIDPDDDPDGPEAC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001939.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001939.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a58ad0c27fe80fd80472bdcb74de83b30d853f75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001939.fa
@@ -0,0 +1,30 @@
+>PROKKA_02213
+MASVTFRSASRQYPGSPRPAVDSLDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEELSHG
+SILIGDRDVTDVDPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPADERRRRVEDAA
+KLLDLTEYLDRKPKALSGGQRQRVAMGRAIVRDPQVFLMDEPLSNLDAKLRVQTRAQIAN
+LTRRLGTTTVYVTHDQTEAMTMGDRVAVLKEGRLQQVDTPRNLYERPMNVFVAGFIGSPA
+MNIFRMPATHEGVHWGETVIPVPREDLADAGTAVDLGVRPENLVVSDDAAGLPVEVDTVE
+ELGADAYVYGHATIGGEERLITLRTVGYTAPEKGSVVHVVPDPERVHLFHAETGERLNR
+>PROKKA_01926
+MASVTFRSASRQYPGSPRPAVDSLDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEELSHG
+SILIGDRDVTDVDPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPADERRRRVEDAA
+KLLDLTEYLDRKPKALSGGQRQRVAMGRAIVRDPQVFLMDEPLSNLDAKLRVQTRAQIAN
+LTRRLGTTTVYVTHDQTEAMTMGDRVAVLKEGRLQQVDTPRNLYERPMNVFVAGFIGSPA
+MNIFRMPATHEGVHWGETVIPVPREDLADAGTTVDLGVRPENLVISDDAAGLPVEVDTVE
+ELGADAYVYGHATIGGEERLITLRTVGYTAPEKGSVVHVVPDPERVHLFHADTGERLNR
+>PROKKA_00531
+MASVSFRSATRQYPNAPRPAVNRLDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEELSSG
+SIHIGDRDVTDVDPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPADERRRRVEDAA
+KLLDLTEYLDRKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRAQIAQ
+LTRRLGTTTVYVTHDQTEAMTMGDRVAVLKDGTLQQVDTPRSLYEKPVNVFVAGFIGSPA
+MNIFRMPVAADGVHWGESVIPVDRATLADAGQSVDLGVRPENLEITDRGGLAVEVDTVEE
+LGADAYVYGHATIGGEERLITLRTVGYTAPEKGSVVHVVPDPERVHLFHAETGERLNR
+>PROKKA_02650
+MARLVLNQITREFGDFVATDRVSLEVDDGDFLVLLGPSGCGKTTLLRMIAGLLEPSSGSI
+EVDGDDITALPARKRDLAMVFQSYALYPHLTVEKNLAFPLRVRKLPKAEIAARVRAAAEA
+VEIDHLLSRKPKELSGGQRQRVALARALVREPKAFLMDEPLSNLDAKLRTATRRELAALH
+RRLGATFVYVTHDQVEAMTMATKIALLNGGRIEQYGTPEQLYDTPSSVFAAGFLGSPAMN
+LLDATLTTTDGRITAFAPGVEAVLWEGATPERDVVLGVRPEHLSVFAGGAPEAVPTAGAA
+LRGTVELVENLGREQLVHCRVGDERVTVSCAREEAWQAGELVVIAAPLTRLHLFDRRSGR
+RLEWRPAAQSEAPLRAAMAPSAGRPQENASRFRAARGGATAPASRSADVRSTEEAAQSEA
+SLRTATR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001940.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001940.fa
new file mode 100644
index 0000000000000000000000000000000000000000..060938460e07cb5de185aa0ab764f0919884d3af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001940.fa
@@ -0,0 +1,16 @@
+>PROKKA_02214
+MEHIDETALPAPEDRVVSATRHVDAPAGVVFELIADPSRQPEWDGNDNLAEAAPGQRVTA
+VGDVFVMTLQKGVDRANHVVEFEEGRRIAWKPSEVGGEPFGQLWRWEVEGDDEGGCRVTH
+TYDWTALTDPKRVQKALRTGEGQLRASIDRLAELAERQG
+>PROKKA_01927
+MEHIDETALPAPEDRVVSATHHVDAPAGVVFELIADPSRQPEWDGNDNLAEAAPGQRVTA
+VGDVFVMTLQKGVDRANHVVEFEEGRRIAWKPSEVGGEPFGQLWRWEVEGDDEGGCRVTH
+TYDWTALTDPKRIQKALRTGEEQLRASIDRLAELAERQD
+>PROKKA_00530
+MEHIDETALPAPQDRVATASREVDAPAGVVFELIADPARQPEWDGNDNLAGAEPGQRVTA
+AGDVFVMTLRKGVDRANHVVEFEEGRRIAWKPSEVGGEPFGQLWRWEVEGIRDEPRCRVT
+HTYDWTELTDPGRIRRALRTGPEQLRASIDRLAELARTQPQA
+>PROKKA_02153
+MEHFDETALPAPEDRVVSATRHVDAPAGVVFELIADPSRQPEWDGNDNLAEAAPGQRVTA
+VGDVFVMTLQKGVDRANHVVEFEEGRRIAWKPSEVGGEPFGQLWRWEVEGDDEGGCRVTH
+TYDWTALTDPKRIQKALRTGEEQLRASIDRLADLAERQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001947.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001947.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6046758883366c267a8bcbd8b5931d554543cb8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001947.fa
@@ -0,0 +1,32 @@
+>PROKKA_02272
+MGVNGLPGTGKTTTLRDILASNVVERARRLSACENPFDALTERTHEWTGEGRMRRRAREL
+RPEVAGFEMVVASANNAAGESISEEIPQVESRIVV
+>PROKKA_01964
+MPAPSLGEEDKRAIPALQPSLSSSNVTAHEHTGHPQAARIDVVARADVVEAGGPGLMGVN
+GLPGTGKTTTLGDILASNVVERARRLSACENPFDALTERTHEWTGEGRMRRRVRELRPEV
+VGFEMVVASANNAAVENLSEEIPQRSAIKDSRNVDADYFAELAAALGGSRGEEDALGEDS
+LTSEQPGTSGLATAPMATAPTPPRSARRRPTRG
+>PROKKA_00460
+MPAPSLGEEDKRAIPALQPSLSSSNVTAHEHTGHLQAACIDVVARSEVVEVGGPGLMGVN
+GLPGTGKTTMLRDILASNVVERARRLSACENPFDALTERTHEWTGEGRMRRRARELRPEV
+VGFEMVVASANNAAVENLSEEIPQRSAIKDGRHVDADYFACLATAAVGGSGGGRGRPG
+>PROKKA_00410
+MGDTRGRTQQDIVRFWQLQELFDPQPLPKLTPRTSPPFGKRVITWRAEDGDVALPWNRLA
+PPPPTTKGAAREWRHTLYLRIYALEDAYQTLHSAFPADADAYDERPGGRSAAAGALVDAD
+GRLIGGTGVLSSALWGIGRLCRGEGFDDSLVDGFEAAGEAFVDAADRAAGVPDDDAFGEQ
+PVLTAGMLVALIRLAQHSAGVEGMPALAGHEVRIASQVVSASSGDETPDIDFLNSFYLSD
+LHRVGEAIARGDVGPALDAYLTPDGDVDTQRRVDVVARPDIVDAGVEPARVPAGRWPAKT
+SYALARSQQFAVNRALNELGAEPGLMGVNGPPGTGKTTMLRDILAANVVERARKLAGFAD
+PSGAFTGRTLAWTGEGRRHRTVHELRPELTGFEMVVASANNAAVENISEEIPHRDAIKDS
+GRADADYFADLATAALGLGVENADEDGAPGACDGPAAEQPAAASSGAWGLVAARLGNKVN
+RARFRDAVLFGGASGGRGARGRGLDTLLKDWAASPSAPAQWTAAREAFHRALHEVDRGLT
+ERRDAAQRTVRTAAAREAVRAAERRLAELSRQRTAKWAGAEAIRRELSAAQAEAGRIRDA
+LDLHRDAKPGFWETITSFGVAGQQWRETYQPLLEAWSTADAGRAALAADTEAAERRLSEL
+EAQIVHLDGECARRRGDLADLEAAVRADEERFGGRHPSAVVDAQTRETTTPWLDEEMEKA
+RTELFLAALELHRAFIAAAARDLRPSFQAAMEVMAGAAPRDLEAEKRRAAWQVFFLLVPL
+VSTTFASFDRMFTGMGRESLGWLFVDEAGQASPQYAAGAIWRANRAVVVGDPLQLEPVVT
+IPVTVSRSLAKAHGVSSTWIAPEASVQRLADRVSRYGTTLPQGEDDVWVSSPLRVHRRCD
+DPMFALSNDLAYGGLMVSGVQRKGPEEDPFERTGDGEIFASSWMDTPARTPGTHLQPNQI
+ERVRRGIEACRRWGIPCTEIIAISPFREVADALRVLSDEFPGLTAGTIHTAQGREADVVF
+FVLGGAPDKPGARNWASSRVNLANVAVSRAKRRLYVIGDREAWSRHNYFRQIAEALPRAA
+EPDAGRER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001951.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001951.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b9dea2bb8ebdf2670d82e1d55a16163f66a538fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001951.fa
@@ -0,0 +1,12 @@
+>PROKKA_02298
+MAEKKTEKNGAPMGPGTSNIKDPEVYEALRREGASEEKAARIANASARDGRDEVAERGGE
+AGSYEDWTKDELAKRARELDIEGRSTMTKDELIEALRNH
+>PROKKA_01991
+MAEKKAEKNGAPMGPGTSSIKDPEVYEALRREGASEEKAARIANASARDGRDEVAERGGE
+AGSYEDWTKDELEKRARELDIEGRSTMTKDELIEALRDH
+>PROKKA_00945
+MATQKKSESDTPQIKDPEMYEALRRDGASKEKAARISNAAARDGREEVAERGGESESYEE
+WTVDELEDRAKELDLTGYSDKRKDELIAMLREH
+>PROKKA_02239
+MAEKKTEKNGAPMGPGTSNIKDPEVYEALRREGASEEKAARIANASARDGRDEVAKRARE
+LDIEGRSTMTKDELIEALRDH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001952.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001952.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09512c389e5a9b3a790da2a5bbad10795d23b7bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001952.fa
@@ -0,0 +1,20 @@
+>PROKKA_02300
+MTRPDPSAHRGAPLPSALGAWRRRPQPPLRPVTPAPAGPRSAAAASLPTVEEVSAGGVIV
+REHDGGLEVAVIARYNRGGRLEWCLPKGHPEGEEDHRQAAVREVEEETGIAGHILEPLGA
+IDYWFTVARHRVHKTVHHFLLRATGGELTTENDPDHEAVDVAWVRLEDVARRLSFANERR
+IVDLARQVVDQHFPPGGARGPRP
+>PROKKA_01993
+MTRPDPSAHRGAPLPSALGAWRRRPQPPLRPVTPAPAGPRSAAAASLPTVEEVSAGGVIV
+REHDGGLEVAVIARYNRGGRLEWCLPKGHPEGEEDHRQAAVREVEEETGIAGHILEPLGA
+IDYWFTVARHRVHKTVHHFLLRATGGELTTENDPDHEAVDVAWVRLEDVARRLSFANERR
+IVDLARQVVDQHFPPGGARGPRP
+>PROKKA_00389
+MSSPDPTAHRGAPLPSALGAWRRRPPQPPRPLAPGAPAARPQSGAGLPTVEEVSAGGIVI
+REHAGDLEVAVIARYNRGGRLEWCLPKGHPEGAEDHRQAAVREVEEETGIAGCILEPLGS
+IDYWFTVSRHRVHKTVHHFLLRATGGELTTENDPDHEAVDVAWVSIDDVARRLSFANERR
+IVDLARQVIPQHFPTGRPPGRP
+>PROKKA_02241
+MTRPDPSAHRGAPLPSALGAWRRRPQPPLRPVTPAPAGPRSAAAASLPTVEEVSAGGVIV
+REHDGGLEVAVIARYNRGGRLEWCLPKGHPEGEEDHRQAAVREVEEETGIAGHILEPLGA
+IDYWFTVARHRVHKTVHHFLLRATGGELTTENDPDHEAVDVAWVRLEDVARRLSFANERR
+IVDLARQVVDQHFPPGGARGPRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001953.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001953.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a7c6f258d3ae5b745d2766cb2f0b03a7f019b13
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001953.fa
@@ -0,0 +1,32 @@
+>PROKKA_00094
+MTRSTSTRIQGAVLQTLSATAPYAQSRPLEVQDLQLAPPQGREVLVRIEAASVCHSDLSV
+VQGLRPRPVPMLLGHESAGIVESTGPEVASVAVGDRVIMTFLPRCGECPACRTEGRLPCS
+EGTAANERGDLLSGGRRLSTEDGPVAHHLGVSGFATHAVVDARSVVRVEHDVPADIAAVL
+GCAVLTGGGAVMNAVSVPKGSTVVVVGLGGVGMAAAIVARALGHEVIGVDGISTKRDLAV
+ELGAQQVYAPQEALDAEVRGDLVVDATGNPRGFETAVELTGPGGATVTVGLPPADAMSSV
+SPMALVAQARTIVGSYLGSAVPQRDIPRFVELWRAGRLPIERLISSHISLEDINQAMDRL
+DSGAEMRQVILFDQEQPSQGQE
+>PROKKA_01796
+MRAALAMKVGGKFEIHDVVIDDPVGREVLVDVKASGLCHSDLHLIDHDFGLPLPAAGGHE
+ISGVVAAVGPSVTSLKPGDRVVACLIAYCGACARCLAGQTTLCLNQEAVVRGPEEKPRLT
+LQDGTPVAQSVNVGGFAEQVLVHENQLAVVNEDIPFPQAALIGCSVVTGAGAAINTAHVR
+PGDTVAVVGVGGIGLNAVSGARLCGAKRVIAIDLDDSKLEAARRFGATDVVNSGSGDAVE
+AVLGITGTGVDHAFEAIGLPVTQQLAQDVLGPGGTAYLIGIAPPGTTAQFGASLDSLFAQ
+RRLQAVAMGSSNIQRDIPLYADLYVQGRMDLDHMVSQEISLDEINTGYERLLNGEVIRSV
+ITSF
+>PROKKA_00690
+MRAALAMKVGGKFEIHDVVIDDPVGREVLVDVKASGLCHSDLHLIDHDFGLPLPAAGGHE
+ISGIVAAVGPSVTSLKPGDRVVACLISYCGACARCLSGQTTLCLNQEALVRGPEEKPRLT
+LEDGTPVAQSVNVGGFAEQVLVHENQLAVVNEDIPFPHAALIGCSVVTGAGAAINTAHVR
+PGDTVAVVGVGGIGLNAVSGARLCGAKRVIAIDLDDSKLEAARRFGATDVVNSGSGDAVG
+AVLGITGTGVDHAFEAIGLPVTQQLTQDVLGPGGTAYLIGIAPPGTTAQFGASLDSLFAQ
+RRLQAVLMGSSNIQRDIPLYADLYVQGRMELDHMVSQEISLDEINAGYERLLNGEVIRSV
+ITSF
+>PROKKA_00775
+MKTTAAVATAAETPLTITEVEIDDLRADELRIRMVASGVCHTDAIVRDQWYPTPLPAVLG
+HEGAGVVEEVGDGVHGFSAGDRVLLSFSSCGHCRACHEGQPAYCADMFALNFGGRRLEDG
+STSYTLDGEQVSSHFFGQSSFAALANVPARCAVKVDDDAPLELLAPLGCGIQTGAGAVLN
+VLRPEPGASLVVFGAGAVGLSAVMAAKVARCGTIIAVDMHPDRLRLAEELGATHTLQAGE
+PVAERIRELTDGGTEYAVDTTGVAAIFGDNVDALAPRGVLGVVGAAALGTEASFDIGTNL
+PKGITIRTIVEGESIPQVFVPRLMALHAAGEFPFDRLVKSYPFAQINQAFEDSKSGETLK
+PVVVFDQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001958.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001958.fa
new file mode 100644
index 0000000000000000000000000000000000000000..643ec61f979a123cf698a470117e4bec27f32899
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001958.fa
@@ -0,0 +1,52 @@
+>PROKKA_01643
+MQTEKHVPEALTIEEVFTAARHYRVPVYQRAYAWTQVEISTLLADVRRARLRSEKPDTQG
+ASSDYYLGSLVVNRATTPEGVPIDEVVDGQQRLTTLTVLAAVAERVIRAGVLDPRALAVL
+DYEGRPEAGEDLATLRRRGAPAGTSFQVDAIGVAVETIAAACRRALERQTPADDQEVMFD
+GDDLAYLWKHVRLLRTELPKGTDLNHYFEVMNTRGEQLAKHEILKATLMRPLQDATDRKV
+FAHVWDACAVLDRHIQLQFSTERPKDGGEAARDAVFGGSWSALLTRDFASLRAALAPSQT
+AMASGARTIIGVLLAAGQTAVESGPSSDQCQDDADTGAYGTIVDFPNLLLHVLRVMQEKG
+EGAEPGLPRWGQDSTGAVRLEDGSLLEQFAQHGQGDAAWSQRFLVTLLRMRLLLDTYVIR
+TLATTGTQADEENWVLSRAQKLETESGERSPRRRLGVKNTFQDPQVQDAVRNLQAMFQVT
+DTRRTSKYFLYRILRWLDAQPEDGVDGVAFQHMLEDLARERLRAYEADKTWDAGVNVPNF
+VFNALDYILWDAGRTSPMEREHLREPLSDVEQEVLRRRADAFRFRYRTSVEHFYPVVPGE
+EQEALTAEDVNRFGNLCIMGRRENSQRNNLMPVSKVKQYSSDEQSLKFQLMAGILHAEGD
+WDVPQIKEHGNSMRRVIQEWQGKRP
+>PROKKA_00905
+MQTEKHVPEALTIEEVFTAARHYRVPVYQRAYAWTQVEISTLLTDVRRARLRSEKPDTQG
+ALSDYYLGSLVVNRATTPEDVPIDEVVDGQQRLTTLTVLAAVAERVIRAGVLDPRALAVL
+DYEGRPEAGEDLATLRHRGAPAGTSFQVDAIGVAVETIAAACRRAMDRQTPADDQEVMFD
+GDDLAYLWKHVRLLRTELPKGTDLNHYFEVMNTRGEQLAKHEILKATLMRPLQDATDRKV
+FAHVWDACAVLDRHIQLQFSTERPKDGVEAARDAVFGASWSALLTRDFASLRAALAPSLT
+ATVSGARTIIGALRAAGQTAVESGSSSDQRQDDADTGAYGTIVDFPNLLLHVLRVMQEKG
+EGAEPGLPRWSQDSTGAVRLEDGSLLEQFAQHGQDDAAWSQRFLVALLRMRLLLDTYVIR
+TLATTGTQADEENWVLSRAQKLETESGERSPRRRLGVKNTFQDPQVQDAVRNLQAMFQVT
+DTRRTSKYFLYRILRWLDAQPVDSVDGVAFQHMLENLARERLRAYEADKTWDAGVNVPNF
+VFNALDYILWDAGRTSPMEREHLREPLSDVEQEVLRRRADAFRFRYRTSVEHFYPVVPGE
+EQEVLTAEDVNRFGNLCIMGRRENSQRNNLMPVSKVKQYSSDEQSLKFQLMAGILHAEGD
+WDVPQIKEHGNRMRRVIQEWQGKRP
+>PROKKA_00844
+MQTEKHVPEALTIEEVFTAARHYRVPVYQRAYAWTQVEISTLLTDVRRARLGSEKPDTQG
+ALSDYYLGSLVVNRATTPEDVPIDEVVDGQQRLTTLTVLAAVAEHVIRAGVLDPRALAVL
+DYEGRPEAGEDLATLRHRGAPAGTSFQVDAIGVAVETIAAACRRAMDRQTPADDQEVMFD
+GDDLAYLWKHVRLLRTELPKGTDLNHYFEVMNTRGEQLAKHEILKATLMRPLQDATDRKV
+FAHVWDACAVLDRHIQLQFSTERPKDGGEAARDAVFGASWSALLTRDFASLRAALAPSLT
+ATVSGARTIIGALRAAGQTAVESGSSSDQRQDDADTGAYGTIVDFPNLLLHVLRVMQEKG
+EGAEPGLPRWGQDSTGAVRLEDGSLLEQFAQHGQDDAAWSQRFLVALLRMRLLLDTYVIR
+TLATTGTQADEENWVLSRAQKLETESGERSPRRRLGVKNTFQDPQVQDAVRNLQAMFQVT
+DTRRTSKYFLYRILRWLHAQPVDSVDGVAFQHMLENLARERLRAYEADKTWDAGVNVPNF
+VFNALDYILWDAGRTSPMEREHLREPLSDVEQEVLRRRADAFRFRYRTSVEHFYPVVPGE
+EQEVLTAEDVNRFGNLCIMGRRENSQRNNLMPVSKVKQYSSDEQSLKFQLMAGILHAEGD
+WDVPQIKEHGNRMRRVIQEWQGKRP
+>PROKKA_01873
+MSERNAPETLTIGEVFAAGRHYRVPVYQRSYAWTEVEVSTLLADVRRARLRSKALESRGN
+VSDYYLGAMVVNRTQTPAGDQIDEVVDGQQRLTTLTVLAAVAEQITQAGVLDPVALAVLD
+YEGRAEAGEDLATLRRRGGHRHGAFQVEAIGIAAQTVRGACERATDRQATADGQTVVFDA
+DDLAYLWNHVRLLRTELPEGTDLNHYFEVMNTRGEQLAKHEVLKAMLMRPLRDESERQVF
+AQVWDACAVLDRPVQLQFASEQLDPDISPARDAVFGDTWSTLVTTDFESLRAALEPSLAE
+TELGGRTSLDSLLSSRGAGEGTSASAEKRSDETGSYGTIIDFPNLLLHVLRVMEESGMAS
+GSGRPAWGQEPKNAVRLEDNSLLEQCAERRQDDARWSKRFLVMLLRIRFLLDTYVIRTLS
+TTGTRADEENWVLVGALKVESGAEEGSSRRRRLGVKNTFEDPAVQEAVRNLQAMFQVTDT
+RRASKYFLYRILRWLAERPVDRVDGEAFQRMLEDLARERLRAYDADEGLDLGVKVPNFVF
+NVLDYILWDLGRNPSAEAGALGAALGDVERSVLSQRAGSFRFRYRTSVEHFYPVVPGEGQ
+KVLTSTEVNRFGNLCIMGRRENSQRNNLMPVSKVKQYSSDEQSLKFQLMAGILHAEGDWD
+VPQIKEHGNSMRRVIQEWQGKRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001959.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001959.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9e51c038a6b20bec2754e07f50490b10a549a860
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001959.fa
@@ -0,0 +1,40 @@
+>PROKKA_01644
+MRTRPTALDAAVDHPRGAQSDARGPGTGRSGSLTANVMTVADALRDPRLRIPEYQRPYTW
+STTNTGQLVEDIRRFRAAASYRIGTMIVHAEDGWLDIVDGQQRYMTFALIALALQEVLGD
+TAERAEHQRAALDRAAAIELPPGRRDVSERHIVENHRLILQTFRSWDSTEVEDFADYFLD
+HCTLVRLVVSDLDAAFQMFDSQNTRGRALLPTDLLKAYHLRAYGEATSDRAAILAAVREW
+EATPPFEIHHLFSRLLYPILRWSAGESLPRDGFTASRIGAFKGISAGPTGLGRLPWAHGL
+LMAKAHVDDYNGRNAALIAHGALPPLEFPFQLTQPVIDGEMFFRLVRHYTRLARDLGVSA
+TDAEQTAGDDARRGRENRQFQTITRLVRATGTGAGYRYTQELYGALLLAYADRFGDHDIE
+RAALVFARHAFALRTRLTRVYPRSVELHALGQHGAPDLEDRVNLFRLMRSSVDPAVVTGR
+VAALPGPYVDEASPVERLYSDTPWDTEEAHDAD
+>PROKKA_00904
+MEMHSTAADAAVDHPWGAQNDAQGPGTGRSGSLTANVMTVADALRDPRLRVPEYQRPYTW
+STKNAVQLVEDIRRFRAAASYRIGTMIVHAEDGWLDIVDGQQRYMTFALIALALQEVLGD
+TAERAEHQRAALDRAAAIELPPGRRDVSERHVVENHRLILQTFRSWKSSEVEDFADYFLD
+HCTLVRLVVNDLDAAFQMFDSQNTRGRALLPTDLLKAYHLRAYGEATSDRAAILAAVREW
+EATPPFEIHHLFSRLLYPILRWSAGESLPRDGFTASRIGAFKGISAGPTGLGRLPWAHGL
+LMAKAHVDDYNGRNATLIAHGALPPLEFPFQLTQPVIDGEMFFRLVRHYTRLARDLGVSA
+TDAEQTAGDDARRGRENGRFQTITRLVRATGTGAGYRYTQELYGALLLAYADRFGDHDIE
+RAALVLARHAFALRTRLTRVYPRSVELHALGQHGAPDLEDRVNLFRLIRSSLDPAAVTGR
+VAALPGPYVDEASPVERLYSDTPWDTEEAHDAD
+>PROKKA_00843
+MEMHSTAADAAVDHPWGAQNDAQGPGTGRSGSLTANVMTVADALRDPRLRVPEYQRPYTW
+STKNAVQLVEDIRRFRAAASYRIGTMIVHAEDGWLDIVDGQQRYMTFALIALALQEVLGD
+TAERAEHQRAALDRAAAIELPPGRRDVSERHVVENHRLILQTFRSWKSSEVEDFADYFLD
+HCTLVRLVVNDLDAAFQMFDSQNTRGRALLPTDLLKAYHLRAYGEATSDRAAILAAVREW
+EATPPFEIHHLFSRLLYPILRWSAGESLPRDGFTASRIGAFKGISAGPTGLGRLPWAHGL
+LMAKAHVDDYNGRNATLIAHGALPPLEFPFQLTQPVIDGEMFFRLVRHYTRLARDLGVSA
+TDAEQTAGDDARRGRENGRFQTITRLVRATGTGAGYRYTQELYGALLLAYADRFGDHDIE
+RAALVLARHAFALRTRLTRVYPRSVELHALGQHGAPDLEDRVNLFRLMRSSLDPAAVTGR
+VAALPGPYVDEASPVERLYSDTPWDTEEAHDAD
+>PROKKA_01874
+MRTRPTALDAAVDHPRGAQSDAQEPGTGRSGSLTANVMTVADALRDPRLRIPEYQRPYTW
+STTNTGQLVEDIRRFRAAASYRIGTMIVHAEDGWLDIVDGQQRYMTFALIALALQEVLGN
+TAERAEHQRAALDSAAAIELPPGRRDVSERHVIENHRLILQTFRSWDSTEVEDFADYFLD
+RCTLVRLTVTDLDAAFQMFDSQNTRGRPLLPTDLLKAYHLRAYGETTTDRGAIMAAVKDW
+EFTPPDEINHLFSRLLYPVVRWSAGESSPRDGFTSAQIGAFKGISAGAASFGRLPWAHGL
+LMAKAHVDDYNTRNAALIAHGALAPLEFPFQLSQPIIDGEMFFRFVRHYTSLARTLGVSA
+TEADQTVQDDARRHREIRRVHAITGLVRSSGNGAGYRYTQELYGALLLAYADRFGAEDLE
+RAALVLARHAFALRTRLRRVYPRSTELHALGLNKAVDSAEQVNLFRLMMGTMDPAAITGR
+VPARPGDVDNAPEPVRRLYSDRPWDPEEESHHV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001961.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001961.fa
new file mode 100644
index 0000000000000000000000000000000000000000..621c4839ca0d4c6b29f23d05d54da983ee76fe79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001961.fa
@@ -0,0 +1,80 @@
+>PROKKA_01646
+MAIHNESELETYICEYLEQHDWLYSPNDAGYDRKNAIFPEDVHAWLAENQPEDYGRIVKA
+DAPASAQQAQRDQITTRLIDVLNKPQDTGVGGTLNVLRKGFKVGTSATLRMAEPRPATNL
+NPAAVASYERMRLRVMRQVHFNPATNQSVDLVLFVNGLPVATIELKTDSTQSIGHAKKQY
+RDRNPKATPLFGFGTRAVVHFAVSNREVWMTTKLAGKDTFFLPFNQGDDGHAGNPLNPNG
+SSTAYLWERILQRDTWLEILQKFVFLKKETVEDEHGRSRRKSTLIFPRFHQWEAVTTMLA
+AVREEGAGASYLIEHSAGSGKTNTIAWTAHRLLSTYGVDEQRVFDSVIVVTDRTVLDDQL
+QEAVRQIERTSGTVVAVDRKNLGGEATSKSALVKQTLLQGNRIIVVTLQTFPAVLELLKG
+DSTLAGRTYAVIADEAHSSQTGSAAAKLKRVLTPDEQADLDDGGEADTESILAAEVAATG
+RPQNISFFAFTATPKDKTLQMFGRPSGEYDEKGQEIPASFHRYTMQQAIEEEFILDVLKN
+FTNYDTAFKLALAGQQGEFRPEGDRAAVGKPTTEVDQTEASKKLMRWVKLHPTNIAQKVK
+IIVEHFRANVAGLLDGQAKAMVVTDSRAAAVRYKRQMDQYIQDMGYTDVGTLVAFSGEIT
+DDEFGLEKVTERSMNPSVTGDLAKAFDGDGYQVMIVANKYQTGFDQPKLCALYVDKKLSG
+VLAVQTLSRLNRAAPGKDTTYVLDFVNSEDDIQAAFEPYYAGAKLEAVTDPNLIHDLGTK
+LDAAGVYDWDEVDAFAEVWVAWKPGSGQEGLQAALEPVAYRFRKELAHARMNQDETRVNE
+LVLVRKDMRSFVSLYDFLSQIYEFGDTEHYKRALFLRHLVQLVGDQPGGEELIDLSDVQL
+VSIRQKKTSSGDIGLTGGAALKGTTAVGGGQVREEQRGPLEEVIEKINEIFAGEGVDASP
+SQQEAWVSALVAPLMEDEKLLGQAGANSLEQFLASPNLERSAMGAVYANEDAFAKMTDIV
+GRGGDPSKMIVAAIGEYLYWKVRSEGTGPVDVAHGRSAVFADETAPSQGTSVDERARATP
+SRVRKGS
+>PROKKA_00902
+MAIHNESELETYICEYLQSHGWLYSANDEGYDRKNAIFPEDVHAWLVENQPEDYGRIVKA
+DAPASAQQAQRDQITTRLVDVLNKPQDTGVGGTLNVLRKGFKVGTSATLRMAEPRPATNL
+NPAAVASYERMRLRVMRQVHFTGAHESESVDLVLFVNGLPVATIELKTDSTQSIGHAKKQ
+YRDRNPKATPLFGFGTRAVVHFAVSNREVWMTTKLAGKDTFFLPFNQGDDGHAGNPLNPN
+GGSSTAYLWERILQRDTWLEILQKFVFLKKETVEDEYGRSRRKSTLIFPRFHQWEAVTKM
+LAAVREEGVGKSYLIEHSAGSGKTNTIAWTAHRLLSTYGVDEQRVFDSVIVVTDRTVLDD
+QLQEAVRQIERTSGTVVAVDRKNLGGEPTSKSALVKQTLLQGNRIIVVTLQTFPAVLELL
+KGDSTLAGRTYAVIADEAHSSQTGSAAAKLKRVLTPDEQADLEDGGEADTESILAAEVAA
+TGRPQNISFFAFTATPKDKTLQMFGRPSGEYDEKGQEIPASFHRYTMQQAIEEEFILDVL
+KNFTNYDTAFKLALAGQQGEFRPEGDRAAVGKPTTEVDQTEASKKLMRWVKLHPTNIAQK
+VRIIVEHFRANVAGLLDGQAKAMVVTDSRAAAVRYKRQMDQYIQDMGYTDVGTLVAFSGE
+ITDDDFGLEKVTERSMNPPVTGDLAKAFDGDGYQVMIVANKYQTGFDQPKLCALYVDKKL
+SGVLAVQTLSRLNRAAPGKDTTYVLDFVNSEDDIQAAFEPYYAGAKLETVTDPNLIHDLG
+TKLDAAGVYDWAEVDAFAEVWVVWKPGSGQEGLQAALEPVAYRFRKELAHARMNQDETRV
+NELVLVRKDMRSFVSLYDFLSQIYEFGDTEHYKRALFLRHLVQLVGDQPGGEELIDLSDV
+QLVSIRQNKTSSGDIGLTGGTALKGTTAVGGGQVHEKQRGPLEDVIEKINEIFAGEGVDA
+SPSQQEAWVSALVAPLMEDEKLLGQAGANSLEQFLASPNLERSAMGAVYANEDAFAKMTD
+IVGRGGDPSKMIVAAIGEYLYLTVRGEGAGPVDVAHGRSAVFADETAPSQGTSVDERASA
+TPSRVRKGN
+>PROKKA_00841
+MAIHNESELETYICEYLERHGWLYSANDDGYDRKNAIFPEDVHAWLAENQPEDYGRLVKA
+DAPASAQQAQRDQITTRLIDVLNKPQDTGVGGTLNVLRKGFKVGTSATLRMAEPRPATNL
+NPAAVASYEHMRLRVMRQVHFNPATNQSVDLVLFVNGLPVATIELKTDSTQSIGHAKKQY
+RERNSKATPLFGFGTRAVVHFAVSNREVWMTTKLAGKDTFFLPFNQGDDGHAGNPLNPNG
+GSSTAYLWERILQRDTWLEILQKFVFLKKETVEDEYGRSRRKSTLIFPRFHQWEAVTTML
+AAVREEGAGKSYLIEHSAGSGKTNTIAWTAHRLLSTYGADEQRVFDSVIVVTDRTVLDDQ
+LQEAVRQIERTSGTVVAVDRKNLGGEATSKSALVKQTLLQGNRIIVVTLQTFPAVLELLK
+GDSTLAGRTYAVIADEAHSSQTGSAAAKLKRVLTPDEQADLEDGGEADTESILAAEVAAT
+GRPENISFFAFTATPKDKTLQMFGRPSGEYDEKGQEIPASFHRYTMQQAIEEEFILDVLK
+NFTNYDTAFKLALAGQQGEFRPEGDRAAVGKPTTEVDQTEASKKLMRWVKLHPTNIAQKV
+KIIVEHFRANVAHLLDGQAKAMVVTDSRAAAVRYKRQMDQYIHDMGYTDVGTLVAFSGEI
+TDDDFGLEKVTERSMNPSVTGDLAKAFDGDGYQVMIVANKYQTGFDQPKLCALYVDKKLS
+GVLAVQTLSRLNRAAPGKDTTYVLDFVNSENDIQAAFEPYYAGAKLETVTDPNLIHDLGT
+KLDAAGVYDWDEVDAFADVWVAWKPGSGQEGLQAALEPVAYRFRKELAHARMNHDETRVN
+ELVLVRKDMRSFVSLYDFLSQIYEFGDTEHYKRALFLRHLVQLVGDQPGGEELIDLSDVQ
+LVSIRQKKTSSGDIGLTGGAALKGTTAVGGGQAREKQRGPLEEVIEKINEIFAGEGVDAS
+PSQQEAWVSALVAPLMEDEKLLGQAGANSLEQFLASPNLERSAMGAVYANEDAFAKMTDI
+VGRGGDPSKMIVAAIGEYLYWKVRGEGAGPVDVAHGRSAVFADETAPSQGTSVDERASAT
+PSRVRKGN
+>PROKKA_01876
+MAIHNESELETYICEYLEQHGWLYSPNDDGYDRKNAIFPEDVHAWLAENQPEDYGRLVKA
+DAPASAQQAQREQITTRLVDVLNKPQDTGVGGTLNVLRKGFKVGTSATLRMAEPRPATNL
+NPAAVASYERMRLRVMRQVHFNPATNQSVDLVLFVNGLPVATIELKTDSTQSIGHAKKQY
+RDRNPKATPLFGFGTRAVVHFAVSNREVWMTTKLAGKDTFFLPFNQGDDGHAGNPLNPYG
+GSSTAYLWERILQRDTWLEILQKFVFLKKETVEDEHGRSRRKSTLIFPRFHQWEAVTTML
+AAVREEGAGKSYLIEHSAGSGKTNTIAWTAHRLLSTYGADEQRVFDSVIVVTDRTVLDDQ
+LQEAVRQIERTSGTVVAVDRKNLGGEATSKSALVKQTLLQGNRIIVVTLQTFPAVLELLK
+GDSTLAGRTYAVIADEAHSSQTGSAAAKLKRVLTPDEQADLEDGGEADTESILAAEVAAT
+GRPQNISFFAFTATPKDKTLQMFGRPSGEYDEKGQEIPASFHRYTMQQAIEEEFILDVLK
+NFTNYDTAFKLALAGQKGEFRPEGDRAAVGKQTTEVDQTEASKKLMRWVKLHPTNIAQKV
+KIIVEHFRANVAGLLDGQAKAMVVTDSRAAAVRYKRQMDQYIQDMGYTDVDTLVAFSGEI
+TDDEFGLEKVTERSMNPSVTGDLAKAFDGDGYQVMIVANKYQTGFDQPKLCALYVDKKLS
+GVLAVQTLSRLNRAAPGKDTTYVLDFVNSEDDIQAAFEPYYAGAKLETVTDPNLIHDLGT
+KLDAAGVYNGDEVDVFADVWVAWKPGSGQEGLQAALEPVAYRFRKELAHARMNQDETRVN
+ELVLVRKDMRSFVSLYDFLSQIYEFGDTEHYKRALFLRHLVQLVGDQPGGEELIDLSDVQ
+LVSIRQKKTSSGEIGLTGGAALKGTTAVGGGQVREKQRGPLEEVIEKINEIFAGEGVDAS
+PSQQEAWVSALVAPLMEDEKLLGQAGANSLEQFLASPNLERSAMGAVYANEDAFVKMTDI
+VGRGGDPSKMIVAAIGEYLYWKVRSEGAGPVDVAHGRSAVFVDETAPSQGTSVDERASAT
+PSRVRKGN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001962.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001962.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ecc828be76b6ba635cd87c3cb321c9399cb521ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001962.fa
@@ -0,0 +1,14 @@
+>PROKKA_01647
+MARIVEVMTRETAKIDALIAKAERFIELAQERRAALITAAVTGQIEIPTED
+>PROKKA_00901
+MAGLNQRIISVLALPKPSLKEQREIAEHLDRETAKIDALISKAERFIELAQERRAALITA
+AVTGQIEIPTED
+>PROKKA_00840
+MCSRYLGYLVLSSFFLEQVNASTYGTKMPRANWDFIKTIEVWAPDFDTQRCIADYLDRET
+ATIDALIAKQVELMNRLRERRQAVIDRAFVSTSEIVILRRHLVLNDSGAWGEDPTGADDV
+AVLRSTEQTVDGYWAISDPALRTLSQTERQNTRLREGDLIVTKTSGSFKHVGKTTLVDNE
+VAEGGYGFGNFMQRLRLKSTMIPKFLWWFMRTDQARSWINLVATTSTGLMNLNGSTLGRM
+EVPLPSLVEQREIADHLDRETAKIDALIAKAERFIELAQERRAALITAAVTGQIEIPTED
+>PROKKA_01878
+MAGLNQRIISVLALPKPSLKEQREIAEHLDRETAKIDALIAKAERFIELAQERRAALITA
+AVTGQIETTSELHRRW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001968.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001968.fa
new file mode 100644
index 0000000000000000000000000000000000000000..99a26d00f108028d3132a855994527f436ba953f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001968.fa
@@ -0,0 +1,24 @@
+>PROKKA_01703
+MTDDVDAPGARPASGGDVVRALASGLAVLRAFTPDTPTLSVSEAATAAGVTRATARRMLL
+TLTELGYAVQDGRRFALTPRVLELGHGYWSGRSVSEILRPILTQASQRLHQSCSAGVLHG
+AHLMYIARVHTERILRVNLDVGTRLPAFTTSMGRVLLADLPEDEACALLAGAPRTPATEH
+TLTDVDALMAELARVREQGHAVVTAELDAHLSSVAVPVRDAEGRVAVAINTALSLGPDHR
+DPGARRAALRTGARVPAPRTPEVAAAVVQALPVLRAAADDAEAALAALQR
+>PROKKA_00848
+MLRSFTPGRPSLTVSDAAAAAGTTRATARRVLHTLVHEGYAVQEGRDFRLTPRVLELGHG
+YWTGTSLAEILSPVLTRASQELEQSCSAAVLDGPFLLYIARVHTERIIRVNLDVGTRMPA
+FLTSMGRVLLADLPPATVRRVLEAAPRTPRTPRTVTDVEALLEEIAQVRRQDHAVVTAEL
+DDHLSSVAVPVRGPDGAVVAAINTALPHRTPGAAEPSADEQTRAAVAQALPVLRAAARDA
+EDALVALRR
+>PROKKA_00785
+MSLPSTEITSPAPGDGYVRALATGLAVLRAFTPDVPRLTLTEAADAAGVSRATARRSLLT
+LVELGYAVQDGRAFELTPKVLELGHGYWSGRSTSEVLRPVLTRASQRLHQSCSAGVLHGA
+HLMYIARVHTERILRVNLDVGTLLPAFSTSMGRVLLAGLDDAEVRRVLEGAPRTPATAQT
+LTDVDALLEEVRRVRERGHALVHGELDPNLSSVAVPVRDRDGRVVLAVNTALSTRRGRLG
+EALSPAAAEAAAAEALPVLREAADDAEAALELLGR
+>PROKKA_01931
+MTDDVDAPGARPASGGDVVRALASGLAVLRAFTPDTPTLSVSEAATAAGVTRATARRMLL
+TLTELGYAVQDGRRFALTPRVLELGHGYWSGRSVSEILRPILTQASQRLHQSCSAGVLHG
+AHLMYIARVHTERILRVSLDVGTRLPAFTTSMGRVLLADLPEDEACALLAGAPRTPATEH
+TLTDVDALMAELARVREQGHAVVTAELDAHLSSVAVPVRDAEGRVAVAINTALSLGPDHR
+DPGARRAALRTGARVPAPRTPEVAAAVVQALPVLRAAADDAEAALAALQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001969.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001969.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e69069ebbb1d2a9647311049e4de4324ef05ee04
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001969.fa
@@ -0,0 +1,16 @@
+>PROKKA_01706
+MSAEQPIGHDMDRTSQEVLDAGMAVRREVLGDAHVDRAEARKDATTEDFQNLITRYAWGT
+IWTRPGLDRRMRSAVTISAMVAGGYWDECAMHPRAALRNGLTREEIQEILLQTAVYASVP
+AANIAFKLAQEDADLAEGRPL
+>PROKKA_00846
+MSGGRTEHAGGADAGQTPLGHQMERTSQEILDAGMAVRREVLGDAHVDRAEATKDATTDD
+FQNLISRYAWGTIWTRPGLDRRMRSAVTITAMVSGGYWEECAMHLRAALRNGLSRDEIKE
+ILLQAAIYSSVPAANVAFKLAQEVFAQVDEDLAAGRPL
+>PROKKA_00779
+MGEQPIGHDMDRTSREVHDAGMAVRREALEDAHVDRAEANKDAATEDFQNLITRYAWGTV
+WTRPGLDRRMRSAVTITAMVAGGYWDECAMHLRAALRNGLSREEVQEILLQTAVYCSVPA
+ANIAFTLAQRVFAEVDADLAAGRPL
+>PROKKA_01934
+MSAEQPIGHDMDRTSQEVLDAGRAVRREVLGDAHVDRAEARKDATTEDFQNLITRYAWGT
+IWTRPGLDRRMRSAVTISAMVAGGYWDECAMHPRAALRNGLTREEIQEILLQTAVYASVP
+AANIAFKLAQEDADLAEGRPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001971.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001971.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed520b2f09ced1a594bd5c517947e2871a12b861
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001971.fa
@@ -0,0 +1,32 @@
+>PROKKA_01708
+MTSAAADLAAVADVGLLDPAWAGSRAEAATADRTFLGHLLDVEAAWVRVLARHGLATEAE
+AAAAAAAGDPDAYDLAALARAAQGGGTPLIPALKALRAQLPAGSRAVHLGATSQDVVDSA
+LMVMVGRVGAILAEDLAAAQDALAELARAHRSTPMVARSLAQHSLPSTFGLRAANWLDGL
+GQAADRLAAAVADLPVQWGGAAGTLASLSGHVDRAHRAGTLGPEVTAFTLVEDLAAELGL
+AAPAGPWDTNRMAVTGVAAALADVVAACGKIANDVLTSARIENGELGEPLAAGRGGSSPM
+PHKQNPVLSVLIRSAALSAPGLAARVYTAAGAADDERPDGAWHAEWPALRRLLRVAGGTA
+ALTRELVSGLRVHEDRMRRNLELTGPLLVSEPIMAELAPELDEASGEPGSGKRLIQDVVD
+RSLACEGNFRALLRAAVPESVPDARLDDLLDPAAYTGEAEALVDRLLAARRGTTTPPRT
+>PROKKA_00844
+MTDLDALDLSADAGLLNPAWAGRPVARATADRAFLQRMLEVEAAWVAVLAAHGLATDEQA
+RQAEEACDPAGYDLVALARAAQGGGNPLIPALKALRERLPAGSTAVHMGATSQDVIDTAL
+MAMAAEVGRGLGEDLRGLAAALAGLAREHRGTPMVARSLAQHSLPSTFGLRAANWLDAVG
+QAAQRLERATAALPVQWGGAAGTMASLAGHVDRAHRAGRLDESVTVFTLVEDLAARLGLS
+APAGPWDTNRMAVTGVAAALADVTAACGKIANDVLLSSRIENGELGEPLAAGRGGSSAMP
+HKQNPVLSVLVHSAALSAPGMLAQVYTAAGAANDERPDGAWHAEWPALRQLLRVAGGAAS
+LTRELAEGLRVNADRMAENLAQTGPVLVSERLMAELAPAIDEACGEPGAGKAAIQGAVDD
+SLAGRGEFRALLREAVPDTVSDDRLDELLDPAGYTGEAGALVDRILAAHAELIDT
+>PROKKA_00777
+MTRPRVGIVGAAPAGPWDTNRMAVTGVAAALADVVAACGKVANDVLTSARIENGELGEPL
+AAGRGGSSAMPHKQNPVLSVLIHSAALSTPGLLAQVYTAAGAANDERPDGSWHAEWPALR
+QLLCVAGGAAALTRELVSGLRVHTGRMAANLALTGPLLVSERIMAELAPELDALFGGPGS
+GKAVIQGAVDASLAGEGDFAELLRAAVPAEVSDARLADLLDPVAYTGEAETLVDRILAAH
+APRLRASA
+>PROKKA_01936
+MHLGATSQDVVDSALMVMVGRVGAILAEDLAAAQDALAELARAHRSTPMVARSLAQHSLP
+STFGLRAANWLDGLGQAADRLAAAVADLPVQWGGAAGTLASLSGHVDRAHRAGTLGPEVT
+AFTLVEDLAAELGLAAPAGPWDTNRMAVTGVAAALADVVAACGKIANDVLTSARIENGEL
+GEPLAAGRGGSSAMPHKQNPVLSVLIRSAALSAPGLAARVYTAAGAADDERPDGAWHAEW
+PALRRLLRVAGGTAALTRELVSGLRVHEDRMRRNLELTGPLLVSERIMAELAPELDEASG
+EPGSGKRLIQDVVDRSLACEGNSRALLRAAVPESVPDARLDDLLDPAAYTGEAEALVDRL
+LAARRGTTTPPRT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001972.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001972.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b67ca9b10cbebdb872412016e0b0a6fba3b1a385
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001972.fa
@@ -0,0 +1,20 @@
+>PROKKA_01786
+MARFSAVLDACVLVPIAQADTLLHLAEAGLYRPVWSGRILDETVRALEAMHPDMRASGAA
+RHRAGVMDAAFDDARVEGWEQLVPGIDLPDPDDRHVVAAAIQGRADLIVTANLKDFPREV
+VESFDIEVQSPDEFFMNQLDLDPARVMTALAAQAGATRNPPLTVRDVLERLVPCGAPLFA
+EAARAQLWRVDVERP
+>PROKKA_00702
+MARFSAVLDACVLVPIAQADTLLHLAEAGLYRPVWSGRILDETVRTLEAMHPDMRASGAA
+RHRAGVMDAAFDDARVEGWEQLVPGIDLPDPDDRHVVAAAIQGRADLIVTANLKDFPREV
+VGSFDIEVQSPDEFFMNQLDLDPARVMTALAAQASATRNPPLTVRDVLERLVPCGAPLFA
+EAARAQLWRVDVERP
+>PROKKA_00612
+MARFSAVLDACVLVPIAQADTLLHLAEAGLYRPVWSGRILDETVRTLETMHPDMRASGAA
+RHRAEVMDAAFDDARVEGWEQLVLGIDLPDPDDRHVVAAAIQGRADLIVTANLKDFPREV
+VESFDIEVQSPDEFFMNQLDLDPARVMTALAAQAGATRNPPLTVSDVLERLVPCGAPLFA
+EAARAQLWRVDAERP
+>PROKKA_02020
+MARFSAVLDACVLVPIAQADTLLHLAEAGLYRPVWSGRILDETVRALEAMHPDMRASGAA
+RHRAGVMDAAFDDARVEGWEQLVPGIDLPDPDDRHVVAAAIQGRADLIVTANLKDFPREV
+VESFDIEVQSPDEFFMNQLDLDPARVMTALAAQAGATRNPPLTVRDVLERLVPCGAPLFA
+EAARAQLWRVDVERP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001973.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001973.fa
new file mode 100644
index 0000000000000000000000000000000000000000..445dd66ebfdc4b01b59d4ddd357769f91c4329af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001973.fa
@@ -0,0 +1,12 @@
+>PROKKA_01857
+MRTADAETQRKILNRLKRARGQLDAVIREVEGEGRCKDVVTQLSAVSTALDRAGFAIVSA
+AMQYCLADPEKAEDEEKLTVAELEKLFMTLA
+>PROKKA_00617
+MRSADPETQRKILNRLKRARGQLDAVIREVEGEGSCRDVVTQLSAVSTALDRAGFAIVSS
+AMKNCVADPERAREDESLTVEELEKLFLSLA
+>PROKKA_00541
+MRTADAETQRKILNRLKRARGQLDAVIREVEGEGSCRDVVTQLSAVSTALDRAGFAIVSS
+AMKNCVADPEKAREDEGLTVEELEKLFLSLA
+>PROKKA_02087
+MIPLPATVTKEVAVRTADAETQRKILNRLKRARGQLDAVIREVEGEGRCKDVVTQLSAVS
+TALDRAGFAVVSSAMQYCLADPEKAEDEEKLTVAELEKLFMTLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001976.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001976.fa
new file mode 100644
index 0000000000000000000000000000000000000000..684bf480962826fc581a2b3e973a7f4015e4aef2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001976.fa
@@ -0,0 +1,36 @@
+>PROKKA_00196
+MTASRLIPPAVDPASLPRDLPGLRAHFRPVVEEIARGALERDRARLLPFEAVRALGCAGF
+SVLRVPREAGGPDVDVRTVTALLVDLAAADSNVAHLYRSHLGFLDALRFQPQPVRDRWHA
+LVLAGATVGNASTERGGNALGTLNTRLTAPAGGDDDGAPGAAWTLTGTKYYATGSIFSSH
+TRVSAAVVRADGSLAPGRGFAVVPVDAPGVCLEDDWDGFGQRLTGTGTAVFEDVAVDPRD
+VLERIPGSPEAVHEAAWFQLILLAVLAGIARAARDDAAARVAARVRTFNTGLGVPFREDP
+LIQEAVGRIAAKASAAEAVVLAAADALDASLAAGAATGADRWGFTGPVPPAFAEAELAVE
+HAQITVPELALGAAQELFLTGGASDTSVAKGLDRHWRNAQTVATHNPIAFRARAVGDYWI
+NGTLPEGLNAIGDAPAAPSSSAVDAAQPAPEPAEAGAR
+>PROKKA_00148
+MPLTDPTDAPTPLGTVPPLVRPADLPRDLAGLRRHFAPVFARVAEGSRERDRRRILPFAE
+VRALNEAGFATLRVPAEAGGPGVDVRTAVALLIDLAEADANVAHLYRSHLGFLDSLRFQP
+AAVRERWHARILAGATVGNASTEKGGNALGTLNTVLTPPAAGDGPWTLTGTKFYATGSIF
+SSHTRVSAAQTDADGHPAPGRRFAVVPVEAPGVRLDDDWDGFGQRLTGTGTAVFDGVAVP
+PQDVLDRVPGSAEAVYEAAWFQLILLAVLAGIARAARRDAADAVAARVRTFNTGLGLPFR
+EDPLIQEAVGRIAAKAFTAEAAVLSAADALDAALADHDAGRTGSGAPEEVPASFTWAELA
+VEHAQVTVPELALGAAQELFLTGGASATSTAKGLDRHWRNAQTVATHNPIAFRARAIGDY
+WINGTVPEGLNAIGDAPAASAPLGDAPAPGEAAR
+>PROKKA_00597
+MTTPVLDRPAPTSAADAPDTAELRARFAPVFARIAANEARRRDAAVPPHAAVRLLAETGF
+TALRLPRERGGSDATLTQLLDLLVDLAAADANLPQALHGHFMFTEQVARDVHPRLTDWWL
+DEVAAGKVFANALVDPPAATGLPGVTARRDPRDPEAFLLTGTKQYSTGTLLADWTLVAAH
+DDAGALQPLVVEVAGPGVEARDDWDGIGQRGTASGTTVYTDAPAPAWRRVDLERPAAAPG
+YPFLWLILAATQAGIAQRALDDFAEILRRRSRSYQHAASASPAHDPVLQHQLGAAAAQVR
+ALRSVVLGAVPALEAAYTAAAGAAPAIGAAATESPDDGAAEAFEAAHTEAWVAAASASSV
+AADLTLRLTSDLFETAGASAVVAGPGLDRHWRNARVLASHTPLPHRRRQIGECLLHGTPA
+PHSADAVETASSTDADPSRDSVSPSPSTPAATKEQ
+>PROKKA_00199
+MPLTDPTDASAPPAATPVPLGAVPPLERPADLPRDLAGLRRHFAPVFARIAEGSRERDRR
+RILPFEEVRALNEAGFATLRVPAEAGGPGVDVRTAVALLIDLAEADANVAHLYRSHLGFL
+DSLRFQPEAVRERWHARILAGATVGNASTEKGGNALGTLNTVLTPAPAGDGPWTLTGTKF
+YATGSIFSSHTRVSAAQTDADGRPAPGRRFAVVPVEAPGVRLDDDWDGFGQRLTGTGTAV
+FDGVAVPPQDVLDRAPGSAEAVYEAAWFQLILLAVLAGIARAARRDAADAVAVRVRTFNT
+GLGLPFREDPLIQEAVGRIAAKAFTAEAAVLSAADALDAALADHEAGRTGSGAPEEVPAS
+FTWAELAVEHAQVTVPELALGAAQELFLTGGASATSTAKGLDRHWRNAQTVATHNPIAFR
+ARAIGDFWINGTVPEGLNAIGDAPAASAPLGADAPASGEAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001979.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001979.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12980362290bb8572d0121d2f3c17bb2e2378dce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001979.fa
@@ -0,0 +1,23 @@
+>PROKKA_02190
+MSTHQHDHGHPRPEASEQTGREHGAPAPQVDPDEDPRAFWEGRYGGERVWSGKVNATTAA
+LVAGLGVTPGRALDLGCGEGGDVLHLAEAGWDVTGIDLSEAAVARARDAARERGVTQRTR
+FLAADLSDPAADWGAHEAGAAGYDLVTASFLQSPVALDRRRILRRAADSLAPGGHLVLVS
+HGAPPPWAPPQLAERGDFPSPAAELAALGVPADGDARWEVLTAELRERDTTGPDGRSTRL
+KDTVVVVRRR
+>PROKKA_02581
+MHSTTDQHAASGRYGDEHAELYDLMYGSLPDWKQLPALCRRVRPAARTVLEFGIGNGRLA
+LPLAEEGFEVTGLEASGVLAGQLAARARDLPVDVVVGDFRERLTQDRFDLCLLMTNTLFM
+TEGVADQRRVLRRAAEALAPDGMLIVETYDPQVYLEKPAVSNFSMPLGDDALLTDTVIVD
+RLNCSVHIHHTVVRRGEVTVLRERSSWLTPRELDLVCEEVGLKRTLRFADLAGSPITDST
+RNVVSCYERR
+>PROKKA_02669
+MTGATRHDSPSQNPQEFWEGRYRYAERVWSGRPNPSLVNAVQHLAPGKALDLGCGEGADA
+IWLATQGWLVTGVDISATAIARARREAQRQQASAATRFVTADLARWEPDDGPYDLMTASF
+LHSPVPLPRIAILQRAATTVRAGGHLVVLSHAALPPWVDAADHPAHSFPSPARQFVELNL
+NEHDWLVLSIQTHTRHATAPSGEAAELTDGVLLLQRR
+>PROKKA_02089
+MSDQHSPGHEHRHGGAAPQIDPGMDPREFWENRYGGEQVWSGKVNATTAALVAGLDLPDG
+PGRALDLGCGEGGDVVHLAEAGWHATGVDISEAAVARGREAAAARGVAERTRFLAADLTD
+TSADWGARDDGAAGYDLVTGSFFQSPVALDRARILRHAASLVAPGGHVVLVSHAAPPSWA
+PPEVAARGDFPTPAGDLEALGIMTEGDEDWEVLVAEVRGRESTGPNGEAGHLDDGVVVVR
+RQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001990.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001990.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d0d1ea964de4e07c13a56603270a09354b661859
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001990.fa
@@ -0,0 +1,30 @@
+>PROKKA_00031
+METLGLLMEGFAGALTPMNLLWVVLGCLLGTAVGVMPGLGSSMAVALLLPMTFALDPTAA
+FIMFSGVYFGGLFGDSTMAILMNTPGQASAIASTFEGHRMAQDGRAAQALATAALGAFIG
+GMAASVCVVFLAPVLAEFSTSFGPAEYFALALFAFVATSSVVADSVLRGLASLVLGLGIA
+VVGIDAVTGTERFTMGSPQLFDGIPLVTVTVAILALGEVFHVASRVRREHEDLRIRRTGR
+PWLSGAEFREAAPAWLRGTAIGLPFGIVPVGGSEVPTFLAYSVKRRLDRRRAHPQFGRGA
+IRGLAAPEAAGNSTTGMAMGALLTLGLPVSATAAIMLAAFRQYGLQPGPLLFDRSPDLVW
+ALLASFFIAMIVLLAINLPFAQLWAKLLLIPKHYLYAGITLFCGLGIYATTGAVFDLLML
+LGIGVLGFLMRRYGYPLAPLMIGMVLGPLAETSLRDALLSSVGDPAVLVSTPITWVIYGI
+LAIVLAFSVRAAVVRRTRQDV
+>PROKKA_02048
+METLGLLMEGFAGALTPMNLLWVVLGCLLGTAVGVMPGLGSSMAVALLLPMTFALEPTAA
+FIMFSGVYFGGLFGDSTMAILMNTPGQASAIASTFEGHRMAQDGRAAQALATAALGAFIG
+GMVASVCVVFLAPVLAEFSTRFGPAEYFALALFAFVATSSVVADSVLRGLASLVLGLGIA
+VVGIDAVTGAERFTMGSPQLFDGIPLVTVTVAILALGEVFHVASRVRREHEDLRIRRTGR
+PWLSGAEFREAAPAWLRGTAIGLPFGIVPVGGSEVPTFLAYSAERRLDRRRAHPQFGRGA
+IRGLAAPEAAGNSTTGMAMGALLTLGLPVSATAAIMLAAFRQYGLQPGPLLFDRSPDLVW
+ALLASFFIAMVVLLAINLPFAQLWAKLLLIPKHYLYAGITLFCGLGIYATTGAVFDLLML
+LGIGVLGFLMRRYGYPLAPLMIGMVLGPLAETSLRDALLSSVGDPAVLVSTPITWVIYGI
+LAIVLAFSVRAAVVRRTRQDV
+>PROKKA_00030
+METLGLLMEGFAGALTPMNLLWVVLGCLLGTAVGVMPGLGSSMAVALLLPMTFALEPTAA
+FIMFSGVYFGGLFGDSTMAILMNTPGQASAIASTFEGHRMAQDGRAAQALATAALGAFIG
+GMVASVCVVFLAPVLAEFSTSFGPAEYFALALFAFVATSSVVADSVLRGLASLVLGLGIA
+VVGIDAVTGTERFTMGSPQLFDGIPLVTVTVAILALGEVFHVASRVRREHEDLRIRRTGR
+PWLSGAEFREAAPAWLRGTAIGLPFGIVPVGGSEVPTFLAYSAERRLDRRRAHPQFGRGA
+IRGLAAPEAAGNSTTGMAMGALLTLGLPVSATAAIMLAAFRQYGLQPGPLLFDRSPDLVW
+ALLASFFIAMIVLLAINLPFAQLWAKLLLIPKHYLYAGITLFCGLGIYATTGAVFDLLML
+LGIGVLGFLMRRYGYPLAPLMIGMVLGPLAETSLRDALLSSVGDPAVLVSTPITWVIYGI
+LAIVLAFSVRAAVVRRTRQDV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001992.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001992.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa1298177ee52741bfe54d937fc15879b7f829b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001992.fa
@@ -0,0 +1,39 @@
+>PROKKA_00121
+MPQGIFVSTTSTGAGKSLVSLGLADSLYRRSGTVGYFRPVVPGDDVETDPMVLLMREQYG
+LSPEQARGGLTAAEARTLMAEGRGDEVQQRCVEQYDAMRAAGGVVVVEGTDLISPDPAAD
+LDLNAQLARNLGTPVVAVVSGADLTPEQAADVVDLARRTLDDAGVELLAVMVNRADPRDL
+DAVGAAVRPGRHAWPVYVLPELTELAHPSVAEVADALGLEQMAGQETLDRDVAEVKAVSM
+EGGNFLEVLREGALVIVSGDRSDAILATVASSLTPDFPTPSGMILTNGILPNRQLQRLYL
+GAAFPVFVTHDDTFTTAAKVSRVRSELSSAQPRKTAAALGTWHQRVDGDELLARFDLPRT
+DVVTPLRFLHELISRARADRRRIVLPEGEDARVLRAAEILQRRDVCDLVVLGPAAAVREL
+ASREGVDLSGIELVDPADSPDLERYAQEYARLRAHKGVDAERAREVMQEGAYFGTMMVHL
+GDVDGMVSGAAHTTANTIRPALEFVKTKPGVSIVSSVFFMLLPDRALVYGDCAVNPDPDA
+QQLADIAVASAATAAQFGVDPRVAMLSYSTGASGSGQSVDKVRAATELVRERAPELKVEG
+PLQYDAAVNASVAASKMPGSEVAGQATVFVFPDLNTGNNTYKAVQQSSGAVAVGPVLQGL
+NKPVNDLSRGTTVEDIVNTVAITAIQAQAQG
+>PROKKA_00198
+MPQGILVTTTTAGAGKSLVSLGLADSLYRRSGTVGYFRPVVPGDDVEADPMVLLMREQFG
+LTAEQARGGITAAEARSLMAEGRGDELQERCVEVYDRMARECGVVVVEGTDLTGADAAAD
+LELNAGLALNLSTPVVAVVSGAGLGAQEAADAVDLTRHALAEAGADLLAVMVNRADAGRL
+DEIAEAIRPGRRSWPVYVLPELPELAHPSVAEVAAALDLEQVAGRPTQDRDVTEVKAVSM
+EGGNFLEVLREGALVIVSGDRSDAILATLASSLTPDFPTPSGMILTNGILPNAQLQRLYQ
+DAAFPVLATDDDTFGTAADVSRVRSELSSAQPRKTAAALGTWHQRVDGDELLQRIDLPRT
+DVVTPLRFLHDLIERARADRRTVVLPEGEDARVLRAAEILQRRDVCDLVVLGGEAEVREL
+ASREGVDLTGITLVDPATSEDRERYAAEYRRLRSHKGVDLERAREVMLEGAYYGTMMVHL
+GDADGMVSGAAHTTANTIRPALEFVKTKPGVSIVSSVFFMLLPDRALVYGDCAVNPDPDA
+RQLADIAAASAETAAQFGVDPRVAMLSYSTGASGSGDAVDKVRAATELVRAAHPELKVEG
+PLQYDAAVNASVAASKMPGSEVAGQATVFVFPDLNTGNNTYKAVQQSSGAVAVGPVLQGL
+NRPVNDLSRGTTVEDIVNTVAITVIQAQTGSPQPTPKDAP
+>PROKKA_00129
+MPQGIFVSTTSTGAGKSLVSLGLADSLYRRSGTVGYFRPVVPGDDVETDPMVLLMREQYG
+LSPEQARGGLTAAEARTLMAEGRGDEVQQRCVEQYDAMRAAGGVVVVEGTDLISPDPAAD
+LDLNAQLARNLGTPVVAVVSGADLTPEQAADVVDLARRTLDDAGVELLAVMVNRADPRDL
+DAVGAAVRPGRHAWPVYVLPELTELAHPSVAEVADALGLEQMAGQETLDRDVAEVKAVSM
+EGGNFLEVLREGALVIVSGDRSDAILATVASSLTPDFPTPSGMILTNGILPNRQLQRLYL
+GAAFPVFVTHDDTFTTAAKVSRVRSELSSAQPRKTAAALGTWHQRVDGDELLARFDLPRT
+DVVTPLRFLHELISRARADRRRIVLPEGEDARVLRAAEILQRRDVCDLVVLGPAAAVREL
+ASREGVDLTGIELVDPADSPDLERYAQEYARLRVHKGVDAERAREVMQEGAYFGTMMVHL
+GDVDGMVSGAAHTTANTIRPALEFVKTKPGVSIVSSVFFMLLPDRALVYGDCAVNPDPDA
+QQLADIAVASAATAAQFGVDPRVAMLSYSTGASGSGQSVDKVRAATELVRERAPELKVEG
+PLQYDAAVNASVAASKMPGSEVAGQATVFVFPDLNTGNNTYKAVQQSSGAVAVGPVLQGL
+NKPVNDLSRGTTVEDIVNTVAITAIQAQAQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001995.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001995.fa
new file mode 100644
index 0000000000000000000000000000000000000000..168dbf4ea9fb89adc4913da08c370407e960dbf0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001995.fa
@@ -0,0 +1,15 @@
+>PROKKA_00176
+MTRTLEEIWPPYGLVVEAGDLRMTALREADVPEVLDVVAGGIHDPSWTPFLFPWTDAPAE
+EMPANYLRFYASTLTRTVDGDVSLELVVRRNGQVIGMQGMNGPDVAGTRRLETGSWLGLP
+FQGQGLGTRMRRMMCALAFDGLGLDAVTSSAWEDNAASRRVSEKVGYLETGRGQAERRGV
+PTGEVFFELRPEGFVRGDEPVRITGAEELRRFLGLG
+>PROKKA_00642
+MTRTLEEIWPPYGLVVEAGDLRMTALREADVPEVLDVVAGGIHDPSWTPFLFPWTDAPAE
+EMPANYLRFYASTLTRTVDGDVSLELVVRRNGQVIGMQGMNGPDVAGTRRLETGSWLGLP
+FQGQGLGTRMRRMMCALAFDGLGLDAVTSSAWEDNAASRRVSEKVGYLETGRGQAERRGV
+PTGEVFFELRPEGFVRGDEPVRIMGAEELRRFLGLG
+>PROKKA_00050
+MTRTLEEIWPPSGLVVEAGDLRMTALREADVPEVLDVVAGGIHDPSWTPFLFPWTDAPAE
+EMPANYLRFYASTLTRTVDGDVSLELVVRRNGQVIGMRGMNGPDVAGTRRLETGSWLGLP
+FQGQGLGTRMRRMMCALAFDGLGLDAVTSSAWEDNAASRRVSEKVGYLETGRGQAERRGV
+PTPEVYFELLPEGFVHGDEPVRITGADELRRFLGLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001996.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001996.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0b2e64a8b227ae36b214356af9f12dde6c26a9f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0001996.fa
@@ -0,0 +1,21 @@
+>PROKKA_00205
+MSGAGSARLTRRTALGLLAASLPLGLSGCVLQGEATTGPVNGPDTLSIDYATYNPLSLVI
+RHQGWLEETLAPRGVRVNWVFSAGSNKANELLRSNSVDIGSTAGSAALLNRANGAPTRIV
+GVASRPEWSALMVPPGSDITDVAQLAGRTVAATRGTDPYFFAVQALEAAGVDPADVEIQN
+LQHADGRAALAGGSVAAWSGLDPIMAKAEAEGARFLYRDLALNTFSVLNATESFLEADPE
+TAQTVLDTYERARAWALEHPDETVGILAEAAKISPDVARTVILERTNADVSPVPGQELLD
+ALTGVGRILVGTGSVDYQHQVDAALASILDTRFAEEAIR
+>PROKKA_00199
+MRRPVVARPGARTLGRRALLAGGLGLGAAAAAGCVVPGEQTRPGPVDGGDWAWTLNIDYA
+TYNPLSLVIRAKGWLDEALNPDDVGVHWVFSAGSNKANENLRAEAIEVGSTAGSAALLSR
+ANGTPIRTIAVANRPEWAALVRAPGSDVDDVAALAGSVAAATRGTDPYFFLVQALREFDV
+PRERVEILNLQHADGRTALFGGSVQAWSGLDPIMADAQRDGAELFYRNLAFNTFDVLNAT
+QRFLDERPEVAQTVVDVYQQARAWVLASDANLAETARILAEEAGLDAAVARTVLAERTNL
+DVSPVPGADFTTALNGVGPIMAESGDARSLDAVQQAIEQIVEPAFAQRAAARPTPAGGNA
+>PROKKA_00139
+MSGAGSARLTRRTALGLLAASLPLGLSGCVLQGEAGAGPVNDRDTLSIDYATYNPLSLVI
+RHQGWLEETLAPRGVRVNWVFSAGSNKANELLRSNSVDIGSTAGSAALLNRANGAPTRIV
+GIASRPEWSALMVPPGSDITDVAQLAGRTVAATRGTDPYFFAVQALEAAGVDPADVEIQN
+LQHADGRAALAGGSVAAWSGLDPIMAKAEAEGARFLYRDLALNTFSVLNATESFLEEDPE
+TAQTVLDTYERARAWALEHPDETVGILAEAAKISPDVARTVILERTNADVSPVPGQELLD
+ALTGVGRILVDTGSVDYQHQVDAALASILDTRFAEEAIR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002003.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002003.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b7021b37bad022c8b0c8a338bc4f597afbb2cbd9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002003.fa
@@ -0,0 +1,15 @@
+>PROKKA_00453
+MTAITVVGGTGYAGAAIVAEAARRGHTVTAISRTAPGTQAESVRYVTGDLTRSVPDIAGA
+EVVVAALSPRGDNAGKLRDAYRSLAQAAATNGARFVGIGGFSSLRPAQGAPRFVEGDDLP
+PEFAAEAREMNDILTDLATGSVDVDWLFVSPAAEFGSHAPGEALGRYRVSGEVALFDQDG
+KSAISGADFARAVLDEIETPTRHRAQIHFAY
+>PROKKA_02503
+MTAITVVGGTGYAGAAIVTEAARRGHTVTAISRTAPGTQAEGVDYVTGDLTQSVPDIAGA
+EVVVAALSPRGDNAGRLRDAYRSLAQAAATNGARFVAIGGFSSLRPAEGAPRFVEGDGLP
+PEFAAEAREMNDILADLATGSVDVDWLFVSPAAEFGSHVPGEALGRYRVSGEVALFDQDG
+KSAISGADFARAVLDEIETPTHHRAQIHFAY
+>PROKKA_02490
+MKIAVIGATGMVGSRVVAEARARGHEVAAGSRSGSRQDGWFDVDVADTAAVARVIEDNDI
+TVLAVPPVRTGDGDVTAIRRSHQALIAAAPQGRFIVVGGAGALQLPDGSLLKDSAEFPAE
+YKAESDVFGDILEDYRASQGLAWTMLAPAPMIAPGERTGAYKTETDIPAGETVSAEDFAV
+ALVDEAESGAHRGTRFTVAN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002004.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002004.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea48be812a90e8e50ceb73eab4263a291cfb3e30
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002004.fa
@@ -0,0 +1,10 @@
+>PROKKA_00455
+MVTMRQAGAKRGNPYEQGCPTRHILDRIGDKWTVLIVGALGEESLRFSELRRRIEGISQK
+MLTQTLRALEEDGLVTRTVYAEVPARVEYRLTEAGHSLRAPLQALEEWSITHLADVLHAR
+NHYQT
+>PROKKA_02502
+MKRGNPYEQGCPTRHILDRIGDKWTVLIVGALGEESLRFSELRRRIEGISQKMLTQTLRA
+LEEDGLVMRTVYAEVPARVEYRLTEAGHSLRAPLEALEKWSITHLADVLHARTHYQT
+>PROKKA_00141
+MNRSWNPLLASCPSRTSLARIANKWTALIVIALAEGPLRFGGLHDGVDGISRKVLTDTLR
+DLERDGIVARTDHGGVPRRVEYELTALGRTLETPLAALVDWAAEHHDAVEAARVDYDERR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002006.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002006.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4fb7afd999c5fe05edca95affd1eb82252355973
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002006.fa
@@ -0,0 +1,21 @@
+>PROKKA_00499
+MGVPVDRARRLLGAVIVAQMLPEGVVVKGGNGVRLRHGATGTRATRDLDLLARDPQQALK
+DLTGFVDRGWGAAPGSKRELKADPAATRVAFFGTVHEDDPAEPLGVPDPYVLSRAKVTLH
+FLSARTSWVSVPIEIGRDEFEGSTLAQPVEVVAPQVAEAVTALGCGTPRSVAVMAVEQQL
+AQKIHAVTDPHQTRGHDLVDIQLLWHGAEAEGGVDIPLLADLVSRTFMFRSPGRTAAGHT
+PHEWPPPVAHVRTLEQGYLDALEETRVGAEGQARLLQPRVSDAADWLESLITRIARAAGA
+EGSGAQG
+>PROKKA_00220
+MGVPVDRARRLLGAVIVAQMLPEGVVVKGGNGVRLRHGATGTRATRDLDLLARDPQQALK
+DLTGFVDRGWGAAPGSKRELKADPAATRVAFFGTVHEDDPAEPLGVPDPYVLSRAKVTLH
+FLSARTSWVSVPIEIGRDEFEGSTLAQPVEVVAPQVAEAVTALGCGTPRSVAVMAVEQQL
+AQKIHAVTDPHQTRGHDLVDIQLLWHGAEAEGGVDIPLLADLVSRTFMFRSPGRTAAGHT
+PHEWPPPVAHVRTLEQGYLDALEETRVGAEGQARLLQPRVSDAADWLESLITRIARAAGA
+EGSGAQG
+>PROKKA_00498
+MGVPVDRARRLLGAVIVAQMLPEGVVVKGGNGVRLRHGATGTRATRDLDLLARDPQQALK
+DLTGFVDRGWGAAPGSKRELKADPAATRVAFFGTVHEDDPAEPLGVPDPYVLSRAKVTLH
+FLSARTSWVSVPIEIGRDEFEGSTLAQPVEVVAPQVAEAVTALGCGTPRSVAVMAVEQQL
+AQKIHAVTDPHQTRGHDLVDIQLLWHGAEAEGGVDIPLLADLVSRTFMFRSPGRTAAGHT
+PHEWPPPVAHVRTLEQGYLDALEETRVGAEGQARLLQPRVSDAADWLESLITRIARAAGA
+EGSGAQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002007.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002007.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9690d136397bc05c369a2d39cd540b56b89b021c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002007.fa
@@ -0,0 +1,21 @@
+>PROKKA_00515
+MASFDILYIRPAGSGWGPVHELVQLTRRLFDARLIEVDDTGDVNRLQRASALLPRGPRVR
+DRHLLVMGPQPAAIAHVAHPRLWLPGYRSVAVWIIDSFWTDRTPRLLRDRPHVDRLFITD
+PQLVSEWSGQTGLPVGVLPWGSDTTRFTSAQEGTDRPVDVLRVGRQPRAWSDDARTSRDA
+AAHGLHFAGRPPFSDDPARNQMLVREAMGRARVVLAFSNLVSPAPYTHPTRDYLTGRWTD
+ALAAGCLVAGTAPASAASLLWPGATVEISPTSRDDAWPVLAQLASEWTPQAAADRQSEAR
+RRLDWRYRLRDLCMAMDWAVPDRLTAELATL
+>PROKKA_00240
+MSVDVLYVRPGGSGWGPVDVLARLAARLLEGRLVEVEDRGAASWAQRASVLLPRGRRARG
+RRLLVLAGNPAALALAARRDLWWPGHESTAAWIVDSFWTDRIAGIARHRPHFDRLFVTDP
+DLVDEWSALTGRPVDALPWGSDTLAVAADDGPRPVDLLRLGRQPEAWDDDARTAREAQDH
+GLVFRGRPPSSPDPLQNQEAVRAALAQARLVLAFSNLVSPAPYTHPTRDYLTGRWTDALA
+AGCRVAGVAPRSAATLLWPEATLEVSPNSRAEAWPVLAEAAAAWTPERAAEQRRRARREL
+DWRLRLQRLCTAMGWPLPPTLDAELAALG
+>PROKKA_02436
+MTLDILYVRPRGSGWGPVAELVALAARLFDARVAVVDDHGEVSLFRKTAASLPRGRRRPG
+HHLLVVAPHAGMAAYAARPRLWFPGYDSTAVWVIDSFWTDRTPRLLRGTAHVDRVFITDP
+QLVEEWEQITGTPVSVLPWGADTALYPSAAHHRDIDLLRLGRQPKAWADDDATAADARRR
+GLRFAGRPPMNDDPGQNQHNVREALMGAKLVLAFSNLVSPAPYTHPTRDYLTGRWMDALA
+AGCLVAGTAPAAATSTLWDGATLEISPTSREDAWPVLTAAAEGWSPERAAEQQERARRTL
+DWRWRLRQMSSVMGWPEPPRLTQELERLISSPQQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002010.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002010.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b50607dc0a4283ef4d0c552ac893b8acf389d076
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002010.fa
@@ -0,0 +1,9 @@
+>PROKKA_00582
+MVGDMSLSFVSSARRRHGGLASAALFHPLVEAATGALPVIDPATGRPASEGAGAARTEAP
+RTAGTGPAQAAAEAEPSTEAGSARG
+>PROKKA_00315
+MSLSFVSSARRRHGGLASAALFHPLVEAATGALPVIDPATGRPASEGVDAARTEASRAAG
+TGPAQAAAETEPSTQAGSARG
+>PROKKA_00583
+MSLSFVSSARRRHGGLASAALFHPLVEAATGALPVIDPATGRPASEGVDAARTEASRAAG
+TGPAQAAAETEPSTQGGSARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002011.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002011.fa
new file mode 100644
index 0000000000000000000000000000000000000000..44f3e181cd090cfbbd861dca845bfa6d98226402
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002011.fa
@@ -0,0 +1,18 @@
+>PROKKA_00588
+MSAQQMWEARTSGPKRAEAPASGQAVGASENAQSETVHIPKNTLVEHSKDSTGARPTDSG
+IRTLPRRVNPNDGRFIRAVVAGTAVAGLVAFSISFAALYEVAAWLGLPPFMHWAVPVFID
+LAILVYAGSVLVHESRGESARASWWALGAFTGLSMIANGAHAWSAENASVWQSVVGALIA
+VMVPVAVFVATDQLARVAVENPDSRRAERASQVSEEAEQLKAQAELDRQRAELEAELAAS
+RWQIEAQRREAEREAEVAEARHRQELERMERQAKLETEREAREVPQAVVEESQVAQGIEV
+VETVASSEPVAAETKTVEKASGADITAWIVSRAQEGQVPSAAEVAEKFGCSERTGRRRLV
+KSLEVV
+>PROKKA_00322
+MSAQQMWEARTSGPKRAEAPSSGQAVGASENAQSETVHIPKNTLVEHSQDSTGTRPTGSG
+IRSLPRRVNPNDGRFIRAVVAGTAVAGLVAFSISFAALYEVAAWLGLPPFMHWAVPVFID
+LAILVYAGSVLVHESRGE
+>PROKKA_01780
+MRARRWAVRTAVAGTVFIAIGAFWLSFTALADLAARSGIGAGQAWAWPLIVDGIIVVATV
+AVVALAGQKAAWYPWALLIGGAVVSVTANALHAIVAADADVPALLAAAIAAVPPVVLLAI
+THLTVILTRATSPETQTVIWQTIAQQNDQPTPAPRPGIEAEPPPAALLQHDVSDTVGLGD
+ERPTTPESGPSPMKHAEAKPAPEASTPTAPNGETVRGVSEMAGVGRRERAAGLRSEGWSN
+KQIASELGVHPSTVGRWLTSTPTRSSEPDTNPSIKEES
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002015.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002015.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8cd25f7dc3b841cf3b7593d14c2b99852b630933
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002015.fa
@@ -0,0 +1,38 @@
+>PROKKA_00702
+MHRLGPELQGILAWCRSRGVPTAFWNKEDPVHFNTFLTAAGEFDAVFTTDLDCVPRYKRE
+LGHENVHFLPFAAQTAQSNPVEVFDRVEGCAFAGAYYAKYPERLADLRELSAELSADGRR
+FDIYDRNHGRATSGYTFPEDYQRYIVGGALTPGLLDVPYKGYTVNLNLNSVKQSQSMFAR
+RVFELLASNTLTVSNFSRGLRLMFGDLVVSTDSGRQMRRRLEAIEAQPNGNERLRAVALR
+KVLREHTYTERLEFVASRSGVTLPDAAVERPLMVVPSTLGRDAAAVVELVRRWAGQTWND
+WVLAVQGKVEEFAPMPLELQDPRVVLFDELADLDGLARTRGCTLAGMLDPNDWYGPHYLE
+DMVLTLRWADVKTCGHVEHYAVDSVDGSLERRELGTAWRLQDKILPCRSLSRLDWAQVAD
+CNGVARQLDAAQLSGLAVSPLEYCAGGATSEEPALAPASSLDVYEGLTLTEIRQHADDLV
+FAESSDDMPVMDLGTIFEGMKSFDEMTLTWEDGVPRVTSSLGAGRHQYWINSLARPVEFH
+QNGNDQPVYFDVSVGLDIMLVAYWLDADGQRFGHAMIPARQYTTVKIPEQARAMRWGLRV
+SGSGSAVVHRVVNGPYVAPSVPMLAGSSDVLITNIYPAYDNLYRNGFVHSRLRRYREMGH
+RLETILVGEGDGPRFREFEDVDVAVLRVQDLIATLATGEVKTLVVHCLLPETWNVLKATS
+DLPPTTVWVHGFEIQPWWRRRFNYATEEELDAAKMLTEQRLAMWREVFDSSPDNMHFIFV
+SRWFAETVFEDVGIRLPDHRYSVIHNPIDDTVFPYQEKTAQHRLRVLSIRPYHSHVYAND
+LAVAAVLELSNEPWFNELDFTFIGDGPLFEETLAPLWDFENVLIRKGFLTHAEIASEHAR
+HGVLLVPTRSDTQGVSRDEAMSSGLVPITSAVAAIPEFVDEEVAFLAPPEDHRALADAVR
+TLRAEPARYLRMSAAAARRVRRQSGADHVLDAELRLAFRTDGDHSAPSVRPHPEREAHRP
+>PROKKA_00891
+MLRAVFDTLPQDSDAVRRLRAAAAPPRRRRTSPPRPAAPAGAHGDTPGYRGYLHLADVGD
+TYTAQEASTLLQLENAALKRRLFAEPAPPLPPTGHEDEDLAAAPRRVADHLARADAADQL
+GDDAPRHLVVVGVYPTLENPYGNGFVHRRVKYFQAAGVRVDVAVIDRSAEPRSYEYDGVH
+VLVGRGAEAAEMLRTRHYESVAAHFLVRSLWEPIQDALAGHRFFVFMHGFESRRWIRTVR
+NHRTQGQVDDAIVDTLERQRFWREVLEHPHGPERFVFVSRWWRRAAQEDMELVFPGQRTA
+IVHNVIDTDLFRFVPKDPEQRFRVLWVRSAANLNYGADLAVRALERLRDTPLWDRMQVTV
+IGDGKHFGLFEAAFADDANVTVERRYAVQEEIAALHREHGVFLVPTRLDSQGVSRDEAMA
+SGLVPVTNDAGAVREFVDEDCAMIAGVEDVAGLADGLRRLMEDPDLFLRMSQAAAARVRA
+QTSPEHTVDHEMALMGLAAGPGGRGEENA
+>PROKKA_00613
+MLRAVFDTLPQDSDAVRRLRAAAAPPRRRRTSPPRPAAPAGAHGDTPGYRGYLHLADVGD
+TYTAQEASTLLQLENAALKRRLFAEPAPPLPPTGHEDEDLAAAPRRVADHLARADAADQL
+GDDAPRHLVVVGVYPTLENPYGNGFVHRRVKYFQAAGVRVDVAVIDRSAEPRSYEYDGVH
+VLVGRGAEAAEMLRTRHYESVAAHFLVRSLWEPIQDALAGHRFFVFMHGFESRRWIRTVR
+NHRTQGQVDDAIVDTLERQRFWREVLEHPHGPERFVFVSRWWRRAAQEDMELVFPGQRTA
+IVHNVIDTDLFRFVPKDPEQRFRVLWVRSAANLNYGADLAVRALERLRDTPLWDRMQVTV
+IGDGKHFGLFEAAFADDANVTVERRYAVQEEIAALHREHGVFLVPTRLDSQGVSRDEAMA
+SGLVPVTNDAGAVREFVDEDCAMIAGVEDVAGLADGLRRLMEDPDLFLRMSQAAAARVRA
+QTSPEHTVDHEMALMGLAAGPGGRGEENA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002020.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002020.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cbb58b0de4d9152e3a7c136dcc8115c37078bfd9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002020.fa
@@ -0,0 +1,24 @@
+>PROKKA_00889
+MAEFIPAAKPLIGDEERAAVDRVLRSGMVAQGPEVAAFEEEFGAAMVDGRACVAVNSGTA
+GLHLGLLASGIGPGDEVIVPAFTFAATGNAVALTGATPVFADVDLDTYTLDPQDVRAKVT
+ERTAAVMPVHLYGHPARMDELEAICREHGLQLFEDAAQAHGARWKGRPVGTFGAWGMFSL
+YPTKNMTSGEGGMVSVGEADVARRLRLLRNQGMEVQYRNELVGFNNRMTDIHAAIGRVQL
+TKVGAWTRRRQEIAARFDAELRGVTVPTVLEGAEHVYHQYTVRLPEELAGTRADVLARLK
+DEFGVGTGVYYPVPTNELPSFGVEADLPNTRVAASTVFSIPVHPSLTDADVTRVVEAVNT
+VVAEAAA
+>PROKKA_00611
+MAEFIPAAKPLIGDEERAAVDRVLRSGMVAQGPEVAAFEEEFGAAMVDGRACVAVNSGTA
+GLHLGLLASGIGPGDEVIVPAFTFAATGNAVALTGATPVFADVDLDTYTLDPQDVRAKVT
+ERTAAVMPVHLYGHPARMDELEAICREHGLQLFEDAAQAHGARWKGRPVGTFGAWGMFSL
+YPTKNMTSGEGGMVSVGEADVARRLRLLRNQGMEVQYRNELVGFNNRMTDIHAAIGRVQL
+TKVGAWTRRRQEIAARFDAELRGVTVPTVLEGAEHVYHQYTVRLPEELAGTRADVLARLK
+DEFGVGTGVYYPVPTNELPSFGVEADLPNTRVAASTVFSIPVHPSLTDADVTRVVEAVNT
+VVAEAAA
+>PROKKA_01223
+MTDRIFLSSPDVTQAEEDALVRAFRSNWIAPLGPEVDAFEAELAEYTGRAHAVVLSSGTA
+ALHLGLLNLGVGPGDLVPTSSLTFAATANAIAYTGAEPVFVDADESGNMNPALLEQALAT
+LRGEGHEVKAIVPVDLLGKTADHAAIGRIAAEHGAVVLSDAAESLGATRDGKQSAAYGVA
+AAVSFNGNKIMTTSGGGALLTDDEEMATRTRYLATQARQPVVHYEHTDIGYNYRLSNILA
+ALGRAQLNRLEEMIERRRALRIRYRELFAAVPGVEMFGEPSGADGGPTRDNFWLSSVLVD
+PDAAGFTAEDLRAHLAGQDIEARPLWKPMHLQPVFAGRRAFTDGTGERLFTTGLSLPSGS
+VLDESRISRVLDSITAFLESRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002022.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002022.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2327b6681724204c51e66bfa1d3c516995779c72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002022.fa
@@ -0,0 +1,9 @@
+>PROKKA_00945
+MTATTHILLRAEGFSCPSCVRKIEKALDALPGVTGAQVHFETQRIEVDHDPQTTTAQDLV
+EAVAKVGYTARPSAF
+>PROKKA_00664
+MTPTTRTLLRAEGFSCPSCVRKIEKALDALPGVTGAQVHFETQRIEVDHDPQTTTAQDLV
+EAVAKVGYTARPSAF
+>PROKKA_01992
+MTATTHTLLRAEGFSCPSCVRKIEKAVDALPGVTGSKVHFETQRIEVDHDAERTSVQDLV
+DAVDRVGYRARPSVF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002024.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002024.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6eac3ce368dbfd54b04fd43a214835836f2215c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002024.fa
@@ -0,0 +1,31 @@
+>PROKKA_00970
+MTTAMTTTTDVRPAPRDESAEILIIGSGFAGLGMGAQLRRHGREDFLILDRAQQVGGTWR
+DNTYPGAACDVPSHLYSFSFAPNPQWSGFYTPGPEIQDYLVRFSEDEGLTPHLRLGADML
+EAHWDPETERWTVRTPRGTYTGRWLIMGTGHLADPRLPDVPGLDAFEGEVIHSARWDHTV
+DLKGKRVAVVGTGASAIQVIPELAATAAELVVFQRTPAWVTPRVVKPYSAAVRRMFERAP
+HTMQRERDDIFWFAESNYAQRRGVPAALDQVRAQALGHLAAAVSDPELRERLTPRYLPGC
+KRVLVSNDYYPAMARDNVTLEDSALDRVEGSRLFGVSGHGYEVDVVVLCTGFEAAQPPFA
+ERVHDGEGRSLADHWSSGMAAFDSTAVAGFPNLFAINGPNTSLGHNSIVYIIESQIAYIL
+EALDRVEHEGIRTMVPETLAQEEYVDRLQERAATSVWLVDGGCHSWYVDPRSGKLTLIWP
+DYAYDFRARNGHFTGEGFLSSASGEPEPMPVREPERSVALI
+>PROKKA_00683
+MTTTTTTTDVRPALRDESAEILIIGSGFAGLGMGAQLRRHGREDFLILDRAQQVGGTWRD
+NTYPGAACDVPSHLYSFSFAPNPQWSGFYTPGPEIQDYLVRFSEDEGLTPHLRLGADMLE
+AHWDPETERWTVRTPRGTYTARWLIMGTGHLADPRLPDVPGLDAFEGEVIHSARWDHTVH
+LKGKRVAVVGTGASAIQIIPELAATAAELVVFQRTPAWVTPRVVKPYSAAARRMFERAPH
+TMQRERDDIFWFAESSYAQRRGVPAALDQVRAQALGHLAAAVSDPELRERLTPRYLPGCK
+RVLVSNDYYPAMARDNVTLEDSALDRVEGSRLFGVSGHGYEVDVVVLCTGFEAAQPPFAD
+RVHDGEGRSLADHWSSGMAAFDSTAVAGFPNLFAINGPNTSLGHNSIVYIIESQIAYIVE
+ALDRADHEGIRTMVPEALAQEDYVDRLQERAATSVWLVDGGCHSWYVDPRSGKLTLIWPD
+YAYDFRARNGHFTGEGFLSSASEDPEPMPVREPKRSVALI
+>PROKKA_00813
+MTTQTTETTAPTTDAAPGAAAGGDVQTVDAVVIGAGFGGCYLVHRFADEMGMSVIGLEKG
+DDIGGTWYWNRYPGALSDTQSHLYRYSFHKGLLEKGDWSHTYVNQKDILEYFELVDRELD
+VRRHFRFGEEVASATWLEDEQRWELVTKSGLTLRATYVVNAVGLLSAVNMPTIKGIDSFQ
+GEILHTGAYPEGKDLSGKRVGVIGSGSTGTQVVTALGPQVKQLTHFVRSPQYSVPVGRRE
+VTDEEKARIKANYDEIWEQVKNSSVAFGFEESSTPAMSVSAEERERVYEKAWNEGGGFKF
+MFGTFSDIATDEEANETAAAFIRNKIGEIIEDPEKARKLTPHDLYARRPLCDDGFYATFN
+LPHVDVVALKETPIKEITAEGIVTAPESGVEGGEQLHELDVIIFATGFDAVDGNYRRMDI
+RGRDGVEINEHWEGQPTSYLGVATDNFPNWFMILGPNGPFTNLPPSIETQVEWITDFIDY
+ARQNGIATVEPKAQTIEEWTQTCTEIANATVFTKVDSWIFGANVEGKKPSVLFYLGGLGN
+YRGVLDGERDAGYPGFELTRADGTQAAASPQPADVSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002027.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002027.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54dd9575c807b46f1a56aa686bbd39fcbbd0e59c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002027.fa
@@ -0,0 +1,14 @@
+>PROKKA_01291
+MPLAIVAPIQSSRSRLRICAALTGLATSAVLLLSGFADAGPSADAGSDHSLVVEHNLDGL
+NAREIIKRLDSTKVTDRSSEFIASIEPDQLVLTDDQNNQTTVPMPEDEFYVSIAPYRSQT
+HECYFHSLTTCTGELANTDVHVTVVEATSGETLLDETLTTYDNGFVGVWLPRGIDATLTV
+SAEGRTAKKAISTRPDDPTCLTGLQLA
+>PROKKA_01010
+MVEHNLDGLNAREIIKRLDSTKVTDRSSEFIASIEPDQLVLTDDQNNQTTVPMPEDEFYV
+SIAPYRSQTHECYFHSLTTCTGELANTDVHVTVVEATSGETLLDETLTTYDNGFVGVWLP
+RGIDATLTVSAEGRTAKKAISTRPDDPTCLTGLQLA
+>PROKKA_01249
+MPLAIVAPIQSSRSRLRICAALTGLATSAVLLLSGCADAGPSADAGSDHSLVVEHNLDGL
+NAREIIKRLDSTKVTDRSSEFIASIEPDQLVLTDDQNNQTTLPMPEDEFYVSIAPYRSQT
+HECYFHSLTTCTGELANTDVHVTVVEATSGETLLDETLTTYDNGFVGVWLPRGIDATLTV
+SAEGRTAKKAISTRPDDPTCLTGLQLV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002028.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002028.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a01c4cc40e3b206605e263573adc537ccaa076a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002028.fa
@@ -0,0 +1,20 @@
+>PROKKA_01294
+MGAGAEAGAGPLFIPQCRDRPTLGPDGPRACLTMKPGEGRHPRRHGPGSRCSPTPPQAGR
+AGLSPMPSRWSTPSSTGTGASIPWRDLPEIYGPWLSRVDLARPHGRRGHVGHGAGNTDRR
+SGCRNRDRLVGLGGLHDRPRPSAREEHHPAHRGLDRTTRNPREEPADHGLGRSRSGLSTK
+THQLVDGAGREGVLLAGDRHPSARRWHQGRPPQPADQQGHRRRRGSAGGRPVGLDSEAYT
+GRNVIERQDAHLKQWPGLASRYDEYAIVYWAAVVLNAVLAWSTALSDTPEWRVRTDRRSR
+SSAREARRGSAPAGMSVRTWTERIPRNAHRETE
+>PROKKA_01017
+MGAGAEAGAGPLFIPQCRDRPTLGPDGPRACLTMKPGEGRHPRRHGPGSRCSPTPPQAGR
+AGLSPMPSRWSTPSSTGTGASIPWRDLPEIYGPWLSRVDLARPHGRRGHVGHGAGNTDRR
+SGCRNRDRLVGLGGLHDRPRPSAREEHHPAHRGLDRTTRNPREEPADHGLGRSRSGLSTK
+THQLVDGAGREGVLLAGDRHPSARRWHQGRPPQPADQQGHRRRRGSAGGRPVGLDSEAYT
+GRNVIERQDAHLKQWPGLASRYDEYAIVYWAAVVLNAVLAWSTALSDTPEWRVRTDRRSR
+SSAREARRGSAPAGMSVRTWTERIPRNAHRETE
+>PROKKA_01252
+MKPGEGRHPRRHGPGSRCSPTPPQAGRAGLSPMPSRWSTPSSTGTGASIPWRDLPEIYGP
+WLSRVDLARPHGRRGHVGHGAGNTDRRSGCRNRDRLVGLGGLHDRPRPSAREEHHPAHRG
+LDRTTRNPREEPADHGLGRSRSGLSTKTHQLVDGAGREGVLLAGDRHPSARRWHQGRPPQ
+PADQQGHRRRRGSAGGRPVGLDSEAYTGRNVIERQDAHLKQWPGLASRYDEYAIVYWAAV
+VLNAVLAWSTALSDTPEWRVRTDRRSRSSAREARRGSAPAGMSVRTWTERIPRNAHRETE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002034.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002034.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c6741ced36562af958b22a5baa616a5a5a7f6a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002034.fa
@@ -0,0 +1,9 @@
+>PROKKA_01396
+MSEEQWDEAAFRASIPAAREKVEFAARFCEIGPSQPRWDSHRPVVELIFYLCKLDYDIKV
+LLLPS
+>PROKKA_01129
+MSEEQWDEAAFRASIPAAREKVEFAARFCEIGPSQPRWDSHRPVVELIFYLCKLDYDIKV
+LLLPS
+>PROKKA_01346
+MSEEQWDEAAFRASIPAAREKVEFAARFCEIGPSQPRWDSHRPVVELIFYLCKLDYDIKV
+LLLPS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002038.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002038.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6c2e89aed521e91d51ecc03124d54b3a49241a1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002038.fa
@@ -0,0 +1,8 @@
+>PROKKA_01615
+MRLVWDRSAWEDYTHWQTTDRKVLNRINTLIDAALRDPFEGIGKPEQLKYGAAGAWSRRI
+TEEHRLVYLVDGEDLIILQARYHY
+>PROKKA_01325
+MRLVWDRSAWEDYTHWQTTDRKVLTRVNTLIDAALRDPFEGIGKPEQLKYGAAGAWSRRI
+TEEHRLVYLVDGEDLIILQARYHY
+>PROKKA_01188
+MTRKPSGPFGPPLAPASAAAIARRAAGAWSRRITAEHRLVYLVDGEDLIILQARYHY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002041.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002041.fa
new file mode 100644
index 0000000000000000000000000000000000000000..64d032e0a268b1c50955eb3f802556dcdc84c38c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002041.fa
@@ -0,0 +1,21 @@
+>PROKKA_01621
+MTLPANSIRIIEANNWVSAETAARMKLKLTPPGAVAFAKIGEGLKAERLRRITVPTAMDN
+NMMAAIPKPAVVDSGFLIYLIESVHIAEWAQGSALPYLSQKLLADIPVHVPSLPEQRAIA
+ATLGAFDDKIESNRQAMATGESLIRAVVESTLDASEGEDGTLGDYCALVKAPVEIDKIDP
+DDNYIGLEHMPRGSIFLTEWKKAKGLGSNKTAFKRGDLLFGKLRPYFKKVGIAPIDGVCS
+TDILVVRPKSPRDIALVTAVAASDALIDSLSASSTGTRMPRASWKDLAAWRVPVLTATER
+IELSARVDPLVERLTQLTFESHRLVALRDALLPELLSGGLRVPVTS
+>PROKKA_00210
+MKPGWTTVALGDVAEVRRTSVHPAHMRPDDPYLGLENIERGGRLLSVSTVAGEGVKSTKF
+RFSPGDVLYGKLRPNLAKILKVDFEGLCSTDILPIAVNSGTLSADFLAYYLSQPQVVAQA
+ASRASGANLPRLAPAEFLALRIPLPPLDEQRRIAAALDRATVVIGGIGDLRRRTRSIGES
+VVQQSSTGAGRWSTIGKSLTLRSGSTLPATRRRPGGVPVYGANGAIGEHDEATHEQPHVT
+IGRVGAVGAVNVTAGRAWISDNALIVVKAPEHLSNGYLAIALAMADLGRFASQSAQPLIT
+QRKVADVPLWIPSQAEALRIDAILDRLAEVERANVERVARADALFASLQSRAFRGEL
+>PROKKA_00189
+MKPGWTTVALGELCELKYGKSLPAKARSGEGFPVFGSSGLVGAHEKAIQRGPGIIVGRKG
+SIGEVHWSEDDFWPIDTTYFALPRRANVDLRWLYLALRWLPLKTLNKAAAVPGLNREDAY
+RLTLALPPLDEQRRIAAILGTSLHSIGCRVRACIWIDDFLDNVYNSTLRSGDIPRRPIRS
+LGEVSTGKTPATSKADYFGGVIPFVAPGDLGGLVSAKRTLTDLGAQESRLVRAGATMVCC
+IGATIGKVGIVAEQSAFNQQINAIEWGPDMDDLYGYFTMRAQSDVVAARGSSTTMPILAK
+SKFEELLIPVAPFEVQEEFARVASIVSRVRSNLVAAWEAERQLFASLQSRAFRGEL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002043.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002043.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f8a85827a7897f42f04328464c7c3dbff300b12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002043.fa
@@ -0,0 +1,33 @@
+>PROKKA_01623
+MSTFNENVVELAALEHFAELGYRRVHAPEIAPGEPDAERDSYEDVVLWGRLRDALRRINT
+SADAALIAEAVKTVQRAGSQSAVDENARLHKLITEGVPVEHRGDDGLLRTTRLWLVDFDE
+PANNDWVAVNQFTIVENGKNRRPDVLVMVNGLPLALLELKNPAAGHATLKSAWNQVQTYR
+HDIPSVFVPNAVTVISDGTSAAMSSYSGAFEHYAPWKTIEGREVVSNRPALEVLIKGVFE
+PKRFLDLLKNFVVFSDETVTDKSTGQPTRALLKRVAKYHQYWAVNAAVESTVQASSPDGD
+RRGGVVWHTQGSGKSFEMVFYAAKIMRDPRMANPTLVFITDRNDLDDQLFGETFAPARIL
+PETPVQAATRSDLRAKLKRASGGIVFTTLQKFAPGEDGDANPVLTDRRNVIVIADEAHRS
+QYGFSETLDRHGRLKSGLAKHMRDALPGATYLGFTGTPIESNDKSTRAVFGDYVDVYDLT
+RAVEDGATVRIFYESRLAKIELSEADLAALDDLADEITESVEKDTATAAKSRWSRLEAVV
+GAEARLDLVARDIVEHWEKRRESLFGKGMIVTMSRRIAVRLYEKIIALRPDWHSDDPAQG
+KIKVVMTGSASDPAEFQPHIHSKDVRKDLKLRAKNADDPLELVIVRDMWLTGFDAPSMHT
+MYVDKTMQGAGLMQAIARVNRTFRDKPGGLIVDYIGVFANLQNALSEYSPSDRDQAGVPI
+DEMVQVMLEKHDIVRGLLHGVQFDSSPELTAAQRLNEYAKVLDFVMADPDRTSRFNDQVL
+ALAKAFALAGARDEAAAIRNDVRLFTDVRAAILKIQNPDSGRGGSGAVEVDTALSQLLNE
+AVTANQVVDVYMLAGIETPEISILSEEFLDSFAEKDRPNLQMGLLRRLLNDQIRTVQRTN
+VVQGRKYSEMLEETVNRYTNRSLTTAEIIAELVKLAKQMRDAQKRHEELGLREDEVAFYD
+AVVQNDSAVMELGDETLKAIAQELVTSVRQSATIDWNLKESVLAAMRSKVRRILAKYDYP
+PDAEAKAIELVIEQAELFARGVSA
+>PROKKA_02203
+MTHANAPLTPTGRLRMVHRHLRDLLTQSNSGGIYFTTLQKFGLTQAERDAGADHPVLSDR
+RNIIVMADEAHRSHYDTLDGYAAHLKNALPNASLIAFTGTPIAEGERDTRRVFGDDIDVY
+DLHRAVEDGATVPVSFEPRLITLSRVDGVDDESLDAAADELTAGLDEADRDRIQRGVATL
+EAVYGAPHRLQTLAEDFVRHWEDRRDAMQPTMGVPGKAMIVCATRSIAARLYERIVALRP
+EWHDDADDKGRIKVVYDANPSDTGEIKKHMRRPSALAAVKKRLKNPADELEIVIVKDMLL
+TGFDAPALHTLYVDRPLKGALLMQTLARVNRTFRGKEDGLLVAYAPLAENLQQALAEFTR
+DTRTAGTKTLAQNTEEAAEIIETMVGMLADTVGVDWKATYQSDPKNGWRKALLEVTSRLR
+SPGTPGNTDPEDPTVRPVADTFRSQASRLHRAWALAGRVAAVERFRLDVKFYEEVRTWLA
+KLDAQDRIARGEPIPEEIARLLGEMVVDSTEATGVMDIYAAAVG
+>PROKKA_02206
+MEEAAAPSKAELAIEGLRTDLLKEATRVTGGNEIRRAQFSERINAVMAKYTNQQLTAAEV
+IAELVEMAKEVVAEADRGRRFTPPLHDDELMFYDVVAQNEAALDVMGDDVLAQIARDLVA
+TMRRDIKTDWTVREDVKAKLRASIKRLLRKYGYPPDQQPEAIVEVMRQMEAVAPRMAEGQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002047.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002047.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4f67b881bc293b8d0f5d449cbf91d65d69d81a0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002047.fa
@@ -0,0 +1,9 @@
+>PROKKA_01962
+MTTAVRTCAASACAFNAETSCSALAITVAGSDRTPGCGTFVQLDVRRPVTEGASTVGACH
+RLECTYNADLACTAEGIEVTDVATCATYTID
+>PROKKA_01655
+MTTAVRTCAASACAFNAETSCNALAITVAGSDRTPGCGTFVQLDVRRPVTEGASTVGACH
+RLECTYNVDLACTAEGIEVTDVATCATYTID
+>PROKKA_01888
+MTTAVRTCAASACAFNAETSCNALAITVAGSDRTPGCGTFVQLDVRRPVTEGASTVGACH
+RLECTYNADLACTAEGIEVTDVATCATYTID
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002051.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002051.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac60200211e97804f76bf4d659305fb85bf80d35
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002051.fa
@@ -0,0 +1,30 @@
+>PROKKA_02042
+MTPTTSTPATFHDTRVDQQFIAGQWRDGASGDRASDINPYTDDVVAEFALATAEDLDEAY
+RAAAAAQEEWAAMPPKDRAAVLRRAAEILEERRDEVIDWLVKEAGSTRIKADSEVSLAIA
+ITQEAASFPTRVHGKIFDSNTPNRETRVYRKPIGVVGVISPWNFPLHLSQRSVAPALALG
+NAVVLKPASDTAVTGGTLIARVFEEAGLPAGVLSVVVGSGSEIGDAFVTHPVPRLISFTG
+STVVGKQVAANAVTGDTIKKVALELGGNAPLVVLDDADLDAAVDQAVLGGYLHSGQICMS
+VQRVIVDESVYDEFLPKYEGAVKALKVGDPAEEGVLVGPIINDSQVESLRKKIASAEADG
+ARALVGGEIQGRVVPPFVWVDATADMDIAREEIFGPMTVVLKAHDEAHALELANDHEYGL
+SSAVFTQDLDRGLRFANGLAAGMSFINEMTVQDEAHVAFGGARNSGLGRFNGEWALEEFT
+TDHTIGVTRVG
+>PROKKA_00776
+MSPTTHAAATFHSNDVSKQFIAGQWRDGAAGSTKQDLNPYDDAVVAEFALASEADLDEAY
+RAAADAQKEWAAVAPAKRAAVLRRAAELLEERRAEIVDWLVKESGSTVIKANIEVSLAVG
+ITQEAASFPTRVHGTIHPSNTPDREMRVYRKPIGVVGVISPWNFPLHLSQRSVAPALALG
+NAVVIKPASDTPVTGGTLIARLFEEAGLPAGVLSVVVGAGSEIGDAFVKHPVPRLISFTG
+STPVGKQVGANAVSGDHIKKVTLELGGNAPVVVLDDADLDAAVEQSVTGGYLHSGQICMS
+VQRVIVDEKVYDEFLPKYEGAVKSLKFGDPREEGVLVGPVVNDQQLETLKKKIASAEADG
+ARALVSGEIEGRVVPPFLWVGAEPDMEIARDEIFGPMTVVLKARDEAHALELANDHEFGL
+SSAVFTQDLDRGLRFADGLAAGMSFINEMTVQDEAHVAFGGARNSGLGRFNGEWAIEEFT
+TAHTIGVKRLG
+>PROKKA_00744
+MTPTTHASGTFLGNDVGKQFIAGQWRDGAAGSTKQDVNPYDDSVVAEFALASEADLDEAY
+RSAAEAQKGWAETGPKERAAVMRRAAELLEEHRDEVVDWLVQEAGSTVIKANIEVSLAIA
+ITEEAATFPTRVHGKIFDSNTSNRESRVYRSPIGVVGVISPWNFPLHLSQRSVAPALALG
+NAVVIKPASDTPVTGGTLIARLFEQAGLPAGVLSVVVGAGSEIGDAFVKHPVPRLISFTG
+STPVGKQVAANAVLGENIKKVALELGGNAPLVVLDDADLDTAVEQAVTGGYLHSGQICMS
+TQRVIVDAKVYDEFLPKYEQAVKALKVGDPRGEGVLVGPIINDSQVEGLQKKIASAEADG
+ARALVGGEVEGRVVPPFVWVDVDPDMEIAKEEIFGPMTVVLKARDEEHALELANHHEFGL
+SSSVFTQDTGRGVRFAQRVAAGMTFVNEMTVQDEAHVAFGGARNSGLGRFNGEWAVEEFT
+TDHTIGVTTVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002052.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002052.fa
new file mode 100644
index 0000000000000000000000000000000000000000..01bfe2c3be2a492d734b9f7f0214a52cc8595a11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002052.fa
@@ -0,0 +1,21 @@
+>PROKKA_02043
+MSEPIGLRDAAIEWLKMRSLDGQVPLTREDIGDFRWNGEPFPLISTQNGIRKPAGFDAAL
+SFYTVYRPKGHARPYEDEIGDDGLMRYKWQGTNPRLPANQGLFRAYERGLPLIWFVGVGM
+SPARFQVVAPVYVVGREDERHQIVFAPMEPEDYSPELMHESVLEASLKRYLRREVKIRVH
+QPHFRSTVLAAYDNHCAVCNFAHPELLDAAHIVPDREVHGLPTVVNGLAMCRIHHGAFDN
+HFLGITPDFTVEIRQDLLDEVDGPMLRHGLQDLHGRKLMKLPTRRADRPCRENLAWAYER
+FREATVADVA
+>PROKKA_00774
+MVEPAGLRNDAIRWLAERTLDGQLSVTREDLADYRWDGEKFPLISTMQGIRRPAGWSATL
+SIRTAFRRSGETRPYEDEIGDDGLIRYKWRGDNPQQPENVGLRNAMHQRLPIIWFIGISM
+NPAQYQVISPVYILGEEPERQQFVMAPFAEEDYVPDLMTGSVMESSLKRYLKRETTVRLH
+QPLFRSTVLAAYGNHCSVCNFAHPELLDAAHIVPDREVHGLPTVTNGIALCKIHHAAFDR
+RFLGLRPTQGRPVVEIQQDLLDEVDGPMLRHGLQDLHGKPVMTMPKRRVDYPSNENLAWA
+YAEFTRAGRAA
+>PROKKA_00742
+MVEPDGLRETAIQWLIERTLDRQVSLTREDIADFRFQGEPFRLIPSYQGIWKPARFEATL
+SIVTTYRAPGQERPYNDALGEDGLHRYKWRGDNPNHPENVGLRRAMERQLPIMWFTGVGG
+KPPQYQVTAPVYIVNEERDRQQFVLAPLEDASEIPERGEGSEMVTALRRYMKRETVVRLH
+QPVFRSTVLVAYEDHCAVCNFAHSELLDAAHIVPDSEEEGVPDVTNGMALCKIHHAAFDR
+RFLGIRPTKDVPVVEIRQDLLDEVDGPMLRHGLQELHGKPLMKVPSRRADRPGTDKLVWA
+YERFLNATAADVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002054.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002054.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5bb460e54559d2c21ab4049177c0859f5ee93ae6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002054.fa
@@ -0,0 +1,14 @@
+>PROKKA_02096
+MGGASATLRTRGLGRHGRNARVLASHNPLIYRARLLGDRAVNGTPLERHYRLGG
+>PROKKA_00596
+MTTTTDRTDTISRPADVGTADSGVPTTAHPADRPQFLAARARLAPVFAWLAETAAERDRE
+RVTDREATDRLAAAGFPGLRVPEDAGGAGLTFPEAARLYVELAEADSNVLQALRVHVVNV
+ETVLGSPDGPRRERWLHRFATGETVANATTEIGNRTGHYETRLTTRPDGSAVVNGRKAYS
+TGTLYADWTIVVVEDEDGAERAATVRSDAPGVTLHDDWDGFGQRLSASGTTEFTDVVVDP
+EELTPVGQSLDDGSSIFASQAIFQFVHLVGLTGIARAVVRDAAAYVAGRTRGFSHGAAPR
+PGDDPQVLQVVGELEAAAFGAQAALDAVVGPLDRALRAEAAGAPLAEAEVDAVYTAVYAA
+QQVIARAALDAATRLFEVGGASATLRTRGLDRHWRNARVLASHNPLIYRARLLGDRAVNG
+TPLERHYRLGG
+>PROKKA_02036
+MRLIHNKDCCGWFAIRRGASARHTGGADGAPPSREPARDALERAATRLFEVGGASATLRT
+RGLDRHGRNARVLASHNPLIYRARLLGDRAVNDTPLERHYRLGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002057.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002057.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2231e50e937cb9525cbd601ee948cc7ceaf1925b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002057.fa
@@ -0,0 +1,21 @@
+>PROKKA_02166
+MRVPGPFPAHLQDAPFTRAQALAAGVSGSRLRSRDVERVAHGHYRWIGPVTGATPPARPL
+ATELSRLQDLAAMRPDVVVTGESVARLLGWPLPDDVKARVRPTVLRSRTRRVLREPGVRT
+RLVDLDRVLVRRDRLHGLRWTSHADTWFHLATVLDRDALVAVGDRLAREDERRGKVALAT
+RRELGAALERHTGEAGIVRAREALALVRTGSDSPAETELRLALMAAGLPEPDLQIELWDP
+DYSLWHPASADLGYRRWRIAIHYEGKTHDGAAQVGKDTRRDAVFLRQGWLNIRVAGTDRW
+RGFVETAGLVRAAIAERGGLDAGGAEDRLRN
+>PROKKA_01880
+MRVPGPFPAHLQDAPFTRAQALAAGVSGSRLRSRDVERVAHGHYRWIGPVTGATPPARPL
+ATELSRLQDLAAMRPDVVVTGESVARLLGWPLPDDVKARVRPTVLRSRTRRVLREPGVRT
+RLVDLDRVLVRRDRLHGLRWTSHADTWFHLATVLDRDALVAVGDRLAREDERRGKVALAT
+RRELGAALERHTGEAGIVRAREALALVRTGSDSPAETELRLALMAAGLPEPDLQIELWDP
+DYSLWHPASADLGYRRWRIAIHYEGKTHDGAAQVGKDTRRDAVFLRQGWLNIRVAGTDRW
+RGFVETAGLVRAAIAERGGLDAGGAEDRLRN
+>PROKKA_02111
+MRVPGPFPAHLQDAPFTRAQALAAGVSGSRLRSRDVERVAHGHYRWIGPVTGATPPARPL
+ATELSRLQDLAAMRPDVVVTGESVARLLGWPLPDDVKARVRPTVLRSRTRRVLREPGVRT
+RLVDLDRVLVRRDRLHGLRWTSHADTWFHLATVLDRDALVAVGDRLAREDERRGKVALAT
+RRELGAALERHTGEAGIVRAREALALVRTGSDSPAETELRLALMAAGLPEPDLQIELWDP
+DYSLWHPASADLGYRRWRIAIHYEGKTHDGAAQVGKDTRRDAVFLRQGWLNIRVAGTDRW
+RGFVETAGLVRAAIAERGGLDAGGAEDRLRN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002058.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002058.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e3ef3754b0800f546df72bba820d42aff1020338
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002058.fa
@@ -0,0 +1,14 @@
+>PROKKA_02191
+MGGRPAAGLDPPQTAQSGHADDPSSARTVFDRFVFGNHIRSFSVD
+>PROKKA_00551
+MTTTIQDPWAQPTPAGAYDDLLVRALPVTRAQRRWEPADGPMPSLFVSHGAPPTLDDPQW
+LADLFDWAQSMPKPRAIVIVSAHWEDAPVAISSAAAGTPLVYDFGGFHPRYYELQYATPD
+ATDLAARVAGVLGQGRPGSVHQTGRGLDHGAYIPLMAMYPDADVPVVQVSMPSMDPSALL
+DLGVKLRSLREEGVLVIGSGFMTHSFAAMRDPRLFGHVDAFDKWAAEMTHAGDVDSLIGY
+LDKAPGARIAHPTADHYVPLLLTMGAANDPSSARTVFDRFVFSNHIRSFSVD
+>PROKKA_00474
+MTLADPWAQPTPAGAYDDLLARALPLTRRQKLWEPSDGRMPALFISHGAPPTLDEPQWLN
+DLFEWAQTMPKPRAIVIVSAHWENAPAAISASAAGTPLVYDFGGFHPRYYTLRYDTPDAT
+DLARRLAGVLGAQGQEVHQHTDRGLDHGAYIPLMAMYPDADVPVLQVSMPSQDPADLLRL
+GERLRELRDEGVLVIGSGFMTHSFAAMRDPRLFGHVDAFDTWAAEMAHAGDVDALMGYLD
+RAPGARIAHPTADHYVPLLLTMGAAHDPSTTRTVFNRFVFSNHIRSFTVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002059.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002059.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f07bf944b0900f1eae1c6a21d267e4032df80f0c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002059.fa
@@ -0,0 +1,24 @@
+>PROKKA_02199
+MAQHSSTPYPLVIVGSGPAGVSAARAYVDAGGPGPVLMLTSDVDHPYERPPLSKELLRGT
+AEPDPTVLDELPDAVELRRGVTVTHADLGARTLWAAEEPVRFERLILALGAHPKPLPVAD
+DDAEVHLLRSLDHARRLVASAGHARSAVVVGSGFIGCEAAASLALRGVATTLVTPDEVPQ
+QKRLGREAGDRIAQWLIGAGVELRTGVRVGQVRAPRTVHLDDGATLAPDLILAAVGVEPG
+GGWLEDSELTMHEGRIVADEHLAAAPGVWVAGDVARAHHAVAGRPIPVEHWGDALGMGEV
+AGHNAARTEVGVPGGAGQASVLAHAATADPESLRRWEAVPGFWSTIGEHTLKHAAWGDGH
+EQARMVERTGGFTLWYTDAQDRVVGVLTYNADEDYERGRELVAGRDAVGEGRGRPDPA
+>PROKKA_01912
+MAQHSSTPFPLVIVGSGPAGVSAARAYVDAGGPGPVLMLTSDVDHPYERPPLSKELLRGT
+AEPEPTVLEDLPDAVELRRGVTVTHADLGARTLRVGEEPVRFERLILALGAHPKPLPVAD
+DDAEVHLLRSLDHARRLVASAGHARSAVVIGSGFIGCEAAASLALRGVATTLVTPDEVPQ
+QKRLGREAGDRIAQWLIGAGVELRTGVRVGQVRAPRTVHLDDGATLAPDLILAAVGVEPG
+GGWLEDSELTMHEGRIVADEHLAAAPGVWVAGDVARAHHAVAGRPIPVEHWGDALGMGEV
+AGHNAARTEVGVPGGAGQASVLAHAATADPESLRRWEAVPGFWSTIGEHTLKHAAWGDGH
+EQARMVERTGGFTLWYMDAQDRVVGVLTYNADEDYERGRELVAGRDAVGEGRGRPDPA
+>PROKKA_02143
+MAQHSSTPYPLVIVGSGPAGVSAARAYVDAGGPGPVLMLTSDVDHPYERPPLSKELLRGT
+AEPDPTVLDELPDAVELRRGVTVTHADLGARTLWAAEEPIRFERLILALGARPVPLPDVE
+ADAEVHLLRSFADARRLVTSAGHARSAVVVGSGFIGCEAAASLALRGVETTLVTPDEVPQ
+QKRLGREAGDRIAQWLIGAGVELRTGVRVGQVRAPRTVHLDDGATLAPDLILAAVGVEPG
+GGWLEDSELTMHEGRIVADEHLAAAPGVWVAGDVARAHHAVAGRPIPVEHWGDALGMGEV
+AGHNAARTEVGVPGGAGQASVLAHAATADPESLRRWEAVPGFWSTIGEHTLKHAAWGDGH
+EQARMVERTGGFTLWYTDAQDRVVGVLTYNADEDYERGRELVAGRDAVGEGRGRPDPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002064.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002064.fa
new file mode 100644
index 0000000000000000000000000000000000000000..04fdb29b65c119608aaa70053bfc0172fe668246
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002064.fa
@@ -0,0 +1,22 @@
+>PROKKA_02212
+MVGIKDVARMAGVSTATASRALTGSGPVAAATRTRVQEAVATLGYVADSAASSLASGRTR
+NIGLVTPSVHRWFFAAVLEGAADELVRHGYDLTLYDVGQDPERRSTVISDLLPRRRLDAL
+ITLSFRLSVFEFAGLERLGRPVIAIGGRLPAGETLPDWFTAVQVDHARAARMATEHLLEL
+GHRDIAYVGRVDEDIEFQVSTERTRGFLHALAATGVRTPADWMVPADFTIGGTYHQARAL
+LADPRRRPTAVMCISDEMAMGTWMAAHSLGLRVPEDVSVMGLDGHPEAARLGISTVDQNP
+LEQGRRAVRLALGALDGAAHPHRIMHHLALRPRASTAPP
+>PROKKA_01925
+MVGIKDVARMAGVSTATASRALTGSGPVAVATRTRVQEAVATLGYVADSAASSLASGRTR
+NIGLVTPSAHRWFFAAVLEGAADELVRHGYDLTLYDVGQDPERRSTVISDLLPRRRLDAL
+ITLSFRLSMFELAGLERLGLPVIAVGGRLPAGETLPDWFTAVQVDHARAARMATEHLLEL
+GHRDIAYVGRVDEDIEFQVSTERTRGFLHALAATGVRTPADWMVPADFTIGGTYHQARAL
+LADPRRRPTAVMCISDEMAMGTWMAAHSLGLRVPEDVSVMGLDGHPEAARLGISTVDQNP
+LEQGRRAVRLALGALDGAAHPHRIMHHLALRPRASTAPP
+>PROKKA_00532
+MVGIKDVARMAGVSAATASRALTGSGPVASSTRTRVQEAVAALGYVPDAAASSLASGRTR
+NIGLVTPSVHRWFFAAVLEGAADELVRRRYDLTLYDVGQDHDRRSAVLTDLLPRRRLDAL
+VTLSFRLSPFELDGLARLGRPVVAVGGRLPSGEALPEWFTAVQVDDARAARMATGHLIEL
+GHREIAYMGRVADDIEFQVSTERTRSFLDALAAAGLRTPADWMLPADFTIGDAYHRARAL
+LADPEHRPTAVLCISDEMAMGTLMAAQSLGLRVPEDVSVMGLDGHPDAARLGISTVDQTP
+VDQGRRAVRLALGALDGTPTRPASSTTWPCNPGRAPRRRERRAGSRPRRRRPPSTPPSPR
+IVGHVPARERTPPWPP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002065.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002065.fa
new file mode 100644
index 0000000000000000000000000000000000000000..27c393e3f50d9a6dfd0a304a0deba88efe39ad75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002065.fa
@@ -0,0 +1,12 @@
+>PROKKA_02217
+MMQSSEGAWVDPVEGIMYEHMLLLRVATQGVAPYGRSSALERSATVLLARLEAGGAMSIA
+ELAEAFDLDVSTVHRQVAAAMKAGLVERVVDPDGGSARLHRPTEEGRARLAAELSSRADN
+VAQIVSSWPAEDVVEFSRLLRRFNEGAEERRGHPWPRPQTGPGAEDPRL
+>PROKKA_01930
+MMQTSEGAWADPVRGIMYEHMLLLRVATQGVAPYGRSSALERSATVLLARLEAGGAMSVA
+ELAEAFDLDVSTVHRQVAAAMKAGLVERVADPDGGSARLHRPTEEGRARLAAELSSRADN
+VAQIVASWPAEDVVEFSRLLRRFNEGAEERRGHPWPRPQTGPGAEDPRP
+>PROKKA_02156
+MMQSSEGAWVDPVEGIMYEHMLLLRVATQGVAPYGRSSALERSATVLLARLEAGGAMSIA
+ELAEAFDLDVSTVHRQVAAAMKAGLVERVADPDGGSARLHRPTEEGRARLAAELSSRADN
+VAQIVSSWPAEDVVEFSRLLRRFNEGAEARRGHPWPRPQTGPGAEDPRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002066.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002066.fa
new file mode 100644
index 0000000000000000000000000000000000000000..76b2978342ae1e283ae099ff3e1a6de701221cd4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002066.fa
@@ -0,0 +1,12 @@
+>PROKKA_02242
+MIRTPWTRTPAGARRARRPRQFRRVTTTGPAAVDVAWARYADLRLWPRWAPQIRAVEAPR
+RRLRAGLRGVVHAPLGLRVPFVVEEVDDDARTWRWTVRVAGTAVSMTHDLTATPRGTRAG
+LTVHGPAVVALAYRLPARVALRRLCRAHL
+>PROKKA_01944
+MIRTPWTRTPAGARRARRPRQFRRVTTTGPAAVDVAWARYADLRLWPRWAPQIRAVEAPR
+RRLRAGLRGVVHAPLGLRVPFVVEEVDDDARTWRWTVRVAGTAVSMTHDLTATPRGTRAG
+LTVHGPAVVALAYRLPARVALRRLCRAHL
+>PROKKA_02174
+MIRTPWTRTPAGARRARRPRQFRRVTTTGPAAVDVAWARYADLRLWPRWAPQIRAVEAPR
+RRLRAGLRGVVHAPLGLRVPFVVEEVDDDARTWRWTVRVAGTAVSMTHDLTATPRGTRAG
+LTVHGPAVVALAYRLPARVALRRLCRAHL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002069.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002069.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c97ac617a2a5776b5bca708f7a1243ecc541288
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002069.fa
@@ -0,0 +1,12 @@
+>PROKKA_02262
+MRNGQSGAGPPATAPSPRSTRDVDVGWVPRFDVDVLEAALRPVHERPRWEEWGQIAAPTL
+LITGENGYVPAGELDEMRRRRPDVRHVQVPGAGRDVHLDAPERVAELVRGFAA
+>PROKKA_00417
+MSGLGRRSAGPVTREDGTRLHVLDSGGSGPALLLLHGLAGYAREWAQVAERLAAACRVVA
+FDQRGHGSSTRRPADLSRTAHVGDVVAVADALGLQRFTLVGQSMGAHTALLAAAAHPARV
+GRLVLIEGGVGGEGPEATAGVIDWFRAWPIPFATVDDAVAHLGGGPAARVWAEGLEETDA
+GGVPRFDVDVLEAALRPVHERPRWEEWGQIAAPTLLITGENGYVPAGELDEMRRRRPDVR
+HVQMPGAGHDVHLDAPERVAELVRGFAA
+>PROKKA_02193
+MRNGQSGARPPAIAPSPRSTRDVDAGWVPRFDVDVLEAALRPVHERPRWEEWGQIAAPTL
+LITGENGYVPAGELDEMRRRRPEVRHVQVPGAGHDVHLDAPDRVAELVRGFAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002070.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002070.fa
new file mode 100644
index 0000000000000000000000000000000000000000..17fb96bdd5639ee4565dd174328fb7a792284296
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002070.fa
@@ -0,0 +1,9 @@
+>PROKKA_02264
+MEAHAFADNAPILRVMEKVGLRHEGTFKEESLHRTRGWVDGVTYAMLASEHRARGRRLST
+SRRPEVRNSLDITLRKVAA
+>PROKKA_01959
+MEAHAFADNAPILRVMEKVGLRHEGTFKEESLHRTRGWVDGVTYAMLASEHRARGRRLST
+SRRPEVRNSLDITLRKVAA
+>PROKKA_02195
+MEAHAFADNAPILRVMEKVGLRHEGTFKEESLHRTRGWVDGVTYAMLASEHRARGRRLST
+SRRPEVRNALDITLRKVVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002071.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002071.fa
new file mode 100644
index 0000000000000000000000000000000000000000..90c7ae587c6ff83c0ea08e5ad1e261140e474c3d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002071.fa
@@ -0,0 +1,12 @@
+>PROKKA_02267
+MDITVGAVGRASLSDWEQECCGDPIAVGEVHELILLPSRGVSQAGPLASAGWVVTHHDDG
+SPAGSIPLRRVRAVVRAAHEVWPSGRLAEIDRVPGHADLTILEPEEATGLGLGEVVYVGA
+YEPVLPETPRPDEWLLDLEILEDLGPHTW
+>PROKKA_00468
+MDITVGAVGRASLSDWEQECCGDPIAVGEVHELIVLPSRGMSQAGPLASAGWVVTYHDDG
+SPAGSIPLRRVRAVVRAAHEVWPSGRLAEIDRVPGHADLTILEPEEATGLGLGEVVYVGA
+CEPVLPETPRPDEWLLDLEILEDLGPHTW
+>PROKKA_02199
+MDITVGAVGRASLSDWEQECCGDPIAVGEVHELILLPSRGVSQAGPLASAGWVVTHHDDG
+SPAGSIPLRRVRAVVRAAHEVWPSGRLAEIDRVPGHADLTILEPEEATGLGLGEVVYVGA
+YEPVLPETPRPDEWLLDLEILEDLGPRTW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002076.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002076.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b52b39ce13cb7f1890f94c2ab5509bcddce6db2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002076.fa
@@ -0,0 +1,18 @@
+>PROKKA_00242
+MRAVGAVKASILRTVRRGAPVSWAPEWMGLGNLLYQGLWAYEGASLGEPRFVLLPENRVG
+VIELFPRLREKRFLRRSHVPFTAQRVRPWENEERSTGRFAPPLLEDFIRDDLLPGSAVSP
+ATDSYDDAIVVNVRRGDYYSVERHRAQFGMDQEKYLRSALAEAVRTQGPVGRIVVISDGL
+DWCRDHVNDLLSEFAPVEYEDGDIAHDLKAIIHAKRLIITNSTFSYWGGYIGDVLNPGRQ
+VIAPWFFSRTENGGRSHLLAPSWTVIEGDF
+>PROKKA_02430
+MKFLDKSKSRALKAIRRGDPVSWVPDWMGLGNILYQGLWAFEGDDRQEGRRVLLHPKREA
+AVALFPTLRGRYFVTRDRVPFTARRVMPWREESPEPIPYQPAELPGFIREVLLPGSPVAA
+VPDGLSEDDVVINVRRGDYYSVPQHEAEFGMDQVAYVRAAISRAAAVSGPIGRILVISDG
+LDWCRENLGPVLEPHGPVIYEDGDLFHDLRTIVHARRLVITNSTFSYWGGYIGDELHPGR
+LVIAPALFSHNLNGGRAHQLKPSWTVLEDGCWDRAR
+>PROKKA_00514
+MNRLLDMKSNALSAIRRGRPIAWVPEWMGLGNLLYLGHWAYEGSAEDEDRRVLLHADRGA
+AVGIFPRLRERLFVRREDVRFTDRRVMPWSGAATRQRPDHIPAQAHEAFIRDLLLPDSPV
+ATPPHCLKGMLVVNVRRGDYYSVKDHQDDFGMDQVEYIKAALKTSVAAHGSPDGIAVVSD
+GLDWCKEALGGVLEAVAPTTYVDGDLTHDLGTIVHAERLIITNSTFSYWGGYIGDVLSPG
+REVIAPWFFSRSQDGGRATQLRPHWTALEGDFY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002077.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002077.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bedddba8dceb43ffcf90e8a76b9f2ac047422650
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002077.fa
@@ -0,0 +1,9 @@
+>PROKKA_00324
+MPKKFDPEVKDRAVRMVLDRVEEAGSVTKAVALVSPKVDVGRETLRRWVCQHRVDAGLKD
+GPTSDDLAELKRLRGEVKRLREDNEILRKASIFFAGELDPRNR
+>PROKKA_02272
+MPKKFDPEVKDRAVRMVLDRVEEAGSVTKAVALVSPKVDVGRETLRRWVCQHRVDAGLKD
+GPTSDDLAELKRLRGEVKRLREDNEILRKASIFFAGELDPRNR
+>PROKKA_01826
+MPLPFEFERMLFMPKKFDPEVKDRAVRMVLDRVEEAGSVTKAVALVSPKVDVGRETLRRW
+VCQHRVDAGLKDGPTSDDLAELKRLRGEVKRLREDNEILRKASIFFAGELDPRNR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002079.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002079.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4df697ffe0f7121b321f378f5783199a82a1729b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002079.fa
@@ -0,0 +1,15 @@
+>PROKKA_00358
+MQAMSLDEITPVAQDYLKAIWSATEWGDAPLSTKSLAARMGTTAPNVTETVKRLAAQGLV
+EYQPYKPVTLTGKGCEHAIAMVRRHRLLESFLAASLGYSWDEVHAEAERLEHAASDELIE
+RIDQMLGHPTHDPHGDPIPTPVGQRERPAHAVRLDAAEPGFYRVLRISDADPQRLIRFQQ
+AGIVPDSVVEVAEAGHFRLRVVAVGPVELIETDAAAIWLVPSSTRG
+>PROKKA_00672
+MQAMSLDEITPVAQDYLKAIWSATEWGDAPLSTNSLAARMGTTAPNVTETVKRLAAQGLV
+EYQPYKPVTLTGKGREHAIAMVRRHRLLESFLAATLGYSWDEVHAEAERLEHAASDELIE
+RIDQMLGRPTRDPHGDPIPTPEGQRAQPAHAVRLDVAEPGFYRVLRISDADPQRLVRFQQ
+AGLVPGTVVEVTEAGHSRLRVVAVGPVELIETDAAAIWLVPSATRG
+>PROKKA_02012
+MQAMSLDEITPVAQDYLKAIWSATEWGDAPLSTNSLAARMGTTAPNVTETVKRLAAQGLV
+EYQPYKPVTLTGKGREHAIAMVRRHRLLESFLAATLGYSWDEVHAEAERLEHAASDELIE
+RIDQMLGRPTRDPHGDPIPTPEGQRAQPAHAVRLDVAEPGFYRVLRISDADPQRLVRFQQ
+AGLVPGTVVEVTEAGHSRLRVVAVGPVELIETDAAAIWLVPSATRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002080.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002080.fa
new file mode 100644
index 0000000000000000000000000000000000000000..efa58c75a56a90f95c934d17764890df02b022a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002080.fa
@@ -0,0 +1,20 @@
+>PROKKA_00366
+MTRISPLSAAGTDFDGTRLTVARRLRRKTKATLAREVGVTPTAIAQFEKNLSKPTQSVLA
+RLCLQLGLPREFFGAGRPLALLPASGAHFRSLRSTSATSREQALAYGELCLELVDLIGAY
+VDLPPVSLPELELPEELTDEAIVEAARLTRSTWGIAPGPLPSVVQTLEAHGIIALRLPVE
+TDAAVDAFSTYSGARPLVFLSPTKDDKARSRFDAAHELGHLVLHPDTEPGSKLVEQQAHQ
+FAAEFLMPRDEIIEDLPRRINWPAFHELKRHWGVSLRALVYRAHSLGRLSEASYRRANQQ
+LSAWGHPEPGPLGPAESPQVLGIARQLITDGGYDFEGIMAAGRIAPEVAEAVMDAASTVR
+PKLRFVI
+>PROKKA_00320
+MTMMHELGHVIYDRDVSTPWRSTKSPEEERAFRFAGAMLIPANVMKKRVTESLTLHGYLA
+IKADYGVSVGALVKRAESLGIISKSRARSLYIQISSQGWRYNEPVPVAAERSLLIQQATA
+RAFGENLEGVAQSTGVPHRLVEHWTGFKRDLRAPMADVIPLRR
+>PROKKA_00171
+MSLEPSRIVRARRRAGISKKRLADLIGATPRTISNYETRGAPDALAATLADVLNVDPTFF
+SMPATSPLEEDRVFFRARRRTSAAVRHAASEAGRTGVEFYSLIAEHFKLPEVDLPDLVGM
+GPAIAARQLRAHWKVGAGPLPNLIQLAESRGLRVMSLPGTTDEVDAFSVWEKGVPYIFLS
+QRKTAERSRFDLAHEIGHLVLHSGLGNGDSVERDAEREADAFASEFLLPGEVLRGAMPRQ
+PSTEAVLKAKVSFGVSAMAMAYALFRNGLLSEWAHRQMCIDLTRRGYRSSEPGGIHRETS
+RVFGLTLSLARQRLGLGTEEIAQALGVCPQEIHELTFGHAVTPVASVGGSSAAPEPGPRP
+SLRVV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002082.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002082.fa
new file mode 100644
index 0000000000000000000000000000000000000000..13a971ae14283ff2c6b51d49b768e23f1b594c2e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002082.fa
@@ -0,0 +1,36 @@
+>PROKKA_00539
+MPVSAPSPSSSRPAVLGFAARYPWVLATLVVVALTLGLHLAGAEDPARWIASAYALVVAA
+WTSVGMVRDLMRGHWGVDILAVTAIVATVLVGEHLAAVLVCLMLTGGEALEDYAAGRARR
+DLSALLDRAPQRAHRLGPDGSVEDVPVEEVRAGDRLLVRPAEVLPVDGTVASAEDGGEVA
+VDLDESSLTGESLPVTHRTGSAVMSGALNGTRAFVLEATASAADSQYAAIVSLVQQAAES
+RAPMVRLADRYAVPFTAVAYLIAGLAWWLSQDPVRFAEVLVVATPCPLLIAAPVAFLGGM
+SRAATSGVIVKSGGTIEALGSVQTVGFDKTGTLTAGRPELVGVRPAAGFAQDELLRLAAS
+AEQYSVHVLADAIRAAAEERGLSLATAQDATEEATHGVVAVLEGRRVVVGKRAYVTQAAP
+DTVTADLAPGQSAVYVAVDGAFAGVLLLADRIRPESAATVQALHRLGARQVLMLTGDAEA
+TGRHIAREAGIDEVHADLLPADKVRLLSERPERPVMMVGDGVNDVPVLAAADVGVAMGAR
+GSTAASESADVVVLADDVSKVAVAVAAGQRTLQVATQSIWVGIALSLVLMVIAATGAIPA
+LVGALFQELVDVVAIVNALRAMKPGPHEAERLGDLAAAPARGERQAVSA
+>PROKKA_00799
+MTRLSRFARSYPLVAVTLAVLALVLGLHAAGLDAAAAVIATVYVAGHIAWAAVGMVREVL
+RGHFGLDILAVVAMTASLLVGEHLAALIIVLMLTGGEALEDFAAARARRELTALLEKAPQ
+TAHLLGADGEAREVPAAQVRPGDELLVKPNEVVPVDAELLSAEAAFDESSLTGESLPSAK
+AAGDAVLSGSVNGTAAVRVRATAAAADSQYQRIVELVEQAHEQKAPVVRLADRFALPFTA
+VSLAIAGVAWWASGDPVRFAEVLVLATPCPLLIAAPVAFLGGMSQASRRGVIVKGGGVLE
+SLAHARAVAFDKTGTLTHGRPRLQRVEPAEGFTADAVLAAAAAAEAYSTHVMAEAVVRAA
+DDAGLARLSARGGTEEGTRGVRALVRGTDGGAGAGTGTDTHEPGAAVEVRVGKLAFVREV
+APDAPEARFAPGETAAYVSVDGRHAGTLVLADALRENAGETVAALRAEGFERAVMLTGDN
+EHTARSLAAEAGLDDVAHSLLPEDKVRLLAELQPRPVIMVGDGVNDAPVLAAADVGIAMG
+ARGSSAAGESADVVITRDDIGRTVEAVRIGRHTYRIALQAVLLGVALSVGLMLVAAFGHI
+PAVAGALTQELVDLACILYALRARTSPRGTPQGAAARARGRAPQEAARA
+>PROKKA_00776
+MPVSAPSPSRPAVLGFAARYPWVLATLVVVALTLGLHLAGAEDPARWIASAYALVVAAWT
+SVGMVRDLMRGHWGVDILAVTAIVATVLVGEHLAAVLVCLMLTGGEALEDYAAGRARRDL
+SALLDRAPQRAHRLGPDGSVEDVPVEEVRAGDRLLVRPAEVLPVDGTVASAEDGGEVAVD
+LDESSLTGESLPVTRRTGSAVMSGALNGTRAFVLEATASAADSQYAAIVSLVQQAAESRA
+PMVRLADRYAVPFTAVAYLIAGLAWWLSQDPVRFAEVLVVATPCPLLIAAPVAFLGGMSR
+AATSGVIVKSGGTIEALGSVQTVGFDKTGTLTAGRPELVGVRPAAGFAQDELLRLAASAE
+QYSVHVLADAIRAAAEERGLSLATAQDATEEATHGVVAVLEGRRVVVGKRAYVTQAAPDT
+VTADLAPGQSAVYVAVDGAFAGVLLLADRIRPESAATVQALHRLGARQVLMLTGDAEATG
+RHIAREAGIDEVHADLLPADKVRLLSERPERPVMMVGDGVNDVPVLAAADVGVAMGARGS
+TAASESADVVVLADDVSKVAVAVAAGQRTLQVATQSIWVGIALSLVLMVIAATGAIPALV
+GALFQELVDVVAIVNALRAMKPGPHEAERLGDLAAAPARGERQAVSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002084.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002084.fa
new file mode 100644
index 0000000000000000000000000000000000000000..90e706466b03b7a3a77c59a214c50a92f1c4a1b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002084.fa
@@ -0,0 +1,46 @@
+>PROKKA_01105
+MTVSMRVMSAGDGYKYLLRSVAAADGDRSLSTPLTRYYAEEGTPPGRWLGSGLTGLGDGQ
+LAVGDQVSEAQLQLLIGMGRDPITGEPLGRAFPQYAPVADRIERRVDELPDELGPAGRAE
+AVAQIEAEEASRGTRRAVAGFDYTFSVPKSVSVLWAVADAGTQALIAEAHHDAVAEVVD
+>PROKKA_02653
+MTVSMRVMSAGDGYKYLLKSIAAGDGDRSLSTPLTRYYAEAGTPPGFWMGSGLGRLGHGD
+LVEGGQVSEAQLALLVGMGHDPITGEPLGRAYQQFASITERIKQRVDALDPELGPATRAQ
+EVAAIEAEEAERGTRRAVAGYDFTFSVPKSVSTIWAVADAGTQALIADAHHAAVAELVAF
+LEREVAATRVGATGPDGAVAHVDVAGVVAAAFDHYDSRAGDPQLHTHVVVSNKVLTVQDG
+RWRTLAGRPMHSVVVAVSELYNAALADQLTRVLGVEWEARERGRDRNPAWEIEGVPDELV
+TEFSTRSRHIEAEKDRLIAGYVAKHGRQPSARTVLKLRAQATLATRPEKQVRSLADLTAE
+WRQRAGRVLRRDANGWARTFTASTADAPRRVLRADDVPLDVVREVGQTVMETVGEKRSTW
+TRWNLHAEASRQLMGWRFASIQDREAITGLVVDAAEHASLRLTPPELASSPLQFRRVDGT
+SRFRPHASTLFSSEVLLAAEDRLLARAATTAGPVVPLETVERIARKPDARGRVLGEDQAA
+ALAAIAVSGRVVDVLVGPAGAGETTAMNGLRRAWEKEHGTGSVIGLAPSAVAAQVLADDL
+GIATENTAKWWQNHLMYGTTFTAGQLVIIDEASLAGTMSLDRLTHEAEKAGAKVLLVGDW
+GQLQSPGAGGSFAMLVHARDDAPELTDLHRFTNEWEKTTSLQLRHGRAEAIDALIEHGRI
+TGGDEEAMIDAAYTEWRADLAAGRASILVTETHATVTELNARARADRIIDGTVNPTRELP
+LRDGTAVSEGDLVITRENDRRLRNGRTWVRNGSRWTVTGVREDGSVIIRPAGRRFGGGIV
+LPADYVAEHLDLGYAITAHRAQGVTTDTAHAVVTATTTRENFYVSMTRGAHSNHAYVTVD
+REDAEHAVPHPGDNPNVTARSILYGVLQHIGAELSAHETVAAEQDRWGSIAQLAAEYDTI
+AQAAQHDRWATLLAASGITAEQIEDVLGSDAYGALSAELRHAEANHHDLDALLPRLVAAR
+SLDDADDIASVLHARVARATARPAGSGRTRKAPRLIVGLIPHAGGQMADDMRRALDERRE
+LIEGRADAVLRGYLTDEEPWTADLGAAPRGDKQKAAWWRAARTVAAYRDRYGITDDRTPL
+GPTPESTSQKIDAIRARAALNRAQAIAHEGTTADAVRPATTSRPAPSL
+>PROKKA_01772
+MVWVTVSMRVMSAGDGYKYLLRTVAAGDGDRSLSTPLTRYYAEAGTPPGRWLGSGVTALG
+NGEIAPGAQVSEAQLQLLVGMGRDPITGVPLGRAYPVYSSTADRVADRVNQLDPALGAVE
+RGRRVAQIEAEEAARGSRRAVAGFDFTFSVPKSASVLWAVADAGTQALIAQAHHEAVAAV
+VAFMEREVAATRTGATAGDGAVAQVDVTGLIATAFDHFDSRAGDPHLHTHVVISNKARTV
+LDGKWRSLDGRPMHAAVVALSELHEAVFADHMTRTLGVSWEPREMGRDRNPSWAITDVPE
+ELAAEFSTRARQIEVEKDRLVAEYVATHGRQPSDATVIRLRAQATLGTRPDKQLRSLAEL
+TAEWRTRASQQLGVDATVWARTITVGERQMLLRADDVPLDLIGQVGRSVVEVVGEKRSTW
+RRWNLMAEAARQTMGWRFATVEDREAITAMVADAAEHASLRLTPPELTTSPVEFRRLDGT
+SVFRPKHSTVFSSDTLLAAEDRLLQRTRATTGQSVDLATVEAITGRPDAEGRVLGRDQAA
+ALASVAVSGRVVDVLVGPAGAGKTTAMNALRRAWETEHGAGSVVGLAPSAVAAQVLADDL
+RIATENTAKWWTTHQHTGATFHAGQLVIIDEASLAGTLSLDRITQAAEEAGAKVLLVGDY
+AQLQSVDAGGAFSLLIHDRDDAPELVDVHRFTHDWEKTASLELRHGRAPVIDTYLAHDRI
+HDGDAEAMTDAAYTAWRHDRQAGLVSVLIAETRENVTALNVRARADLILDGTLKPGPEIT
+LSDGSAAGVGDTIITRRNDRRLRNRHGWVRNGQTWTITAVHDDGSITIRPPGTRFGNSIV
+LPADYVAEHVDLGYAVTAHRAQGITTDTAHVLVEPTTTRENLYVAMTRGRESNKAYVILD
+RPDDHATAHPGDSPDATARTVLYGVLQHSGAELSAHETITAEQDRWGSIAQLAAEYETIA
+AAAQHDRWTTLVRGSGLTGDQAQAVIDSDAFSALTAELRRAEANHHNVDTLLPRLIRARG
+FADADDIASVIHHRLANATTRPAGSGRTRQAPRLIAGLIPEATGPMTPDMQQALTERRHL
+IETRAEAVLDTALHTHEPWVTALGPIPTSGRERQQWRRRAVVVAAYRDRYQITDPTPLGA
+QPEDTAQRIDRARAETAVRTLTRPTMEDERGRPAAQATRHLDL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002085.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002085.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dcbec34444ec9fe53071fff10a6ad93dc03a53ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002085.fa
@@ -0,0 +1,12 @@
+>PROKKA_01119
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISAY
+GT
+>PROKKA_01966
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGLSRL
+RDLTPGQVPGSGVTVFEAVGA
+>PROKKA_00145
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGRIP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002091.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002091.fa
new file mode 100644
index 0000000000000000000000000000000000000000..896b880a511978a598881d7007c2f7bb571a021e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002091.fa
@@ -0,0 +1,18 @@
+>PROKKA_01710
+MSIAAQAKDDDTFDSAHVLDPAATRDSQGQISEEIAAVHAQAQGETQPRLDFPPYRSSVF
+RHPTKSLVHADPETVELWSPAFGHRDVHPLEADLTVGQNGEPIGERIKVRGRVLDDDGRP
+VRHQLVEIWQANAAGRYVHKRDQHPAPLDPNFTGIGRTLTGADGTYEFTTIKPAPYPWKN
+HRNAWRPAHIHFSLFGTDFTQRMITQMYFPGDPLFPLDPIYQGITDQAARDRLVATYDHS
+VTSHEWNTGYWWDIVLTGSHRTWMEDEEGDH
+>PROKKA_00842
+MSDPVQKQDDDTFDNARVLDPAATQDSQEQISEEMAAVHGQASGETQPRLDFPPYRSSVF
+RHPTKSMAHADPESIELWSPAFGHRDVHQLESDLTVGQNGEPIGERIKVRGRVLDGQGRP
+VRGQLVEIWQANAAGRYVHKRDQHPAPLDPNFTGVGRTITDDRGFYEFTTIKPAPYPWKN
+HHNAWRPAHIHFSLFGTDFTQRMITQMYFPGDPLFSLDPIYQGITDQKARDRLVATYDHS
+VSEHEWNTGYYWDIVLTGSHRTWTEDEEGDH
+>PROKKA_01938
+MSIAAQAKDDDTFDSAHVLDPAATRDSQGQISEEIAAVHAQAQGETQPRLDFPPYRSSVF
+RHPTKSLVHADPETVELWSPAFGHRDVHPLEADLTVGQNGEPIGERIKVRGRVLDDDGRP
+VRHQLVEIWQANAAGRYVHKRDQHPAPLDPNFTGIGRTLTGADGTYEFTTIKPAPYPWKN
+HRNAWRPAHIHFSLFGTDFTQRMITQMYFPGDPLFPLDPIYQGITDQAARDRLVATYDHS
+VTSHEWNTGYWWDIVLTGSHRTWMEDEEGDH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002095.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002095.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51b8bd8df1e43c4bc7bd2993ab5bedb04e8c51f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002095.fa
@@ -0,0 +1,14 @@
+>PROKKA_01775
+MRVSKADGSQATDLQRDALLEAGVEPEALYEDKASGKSDDRPHLAACLKALRAGDTLLVW
+KLDRLGRDLRHLVNIVHELTERGVGLKVLTGQGAAIDTTTASGKLVFGIFAALAEFEREL
+ISERTKAGLASARARGRKGGRPYKMTPAKIRLAMASMGNKDTNVGALCKELGITRQTLYR
+HVSPTGELREAGQKVLAQRR
+>PROKKA_00731
+MEPEALYEDKASGKSDDRPHLAACLKALRAGDTLLVWKLDRLGRDLRHLVNIVHELTERG
+VGLKVLTGQGAAIDTTTASGKLVFGIFAALAEFERELISERTKAGLASARARGRKGGRPY
+KMTPAKIRLAMASMGNKDTNVGALCKELGITRQTLYRHVSPTGELREAGQKVLAQRR
+>PROKKA_00679
+MGHLLGYARVSTTDQDASLQIDALGAAGCYRVFVDTMSGSLQHRPELDKLLDQLRPGDTL
+VVWRLDRLGRSIRHLIDQLHALAERGIGFRSLQETIDTTSPGGRLVFHVFAALAEFERDL
+IKERTNAGLAAARARGRTGGRPSRLSADQVRTARRLYEQQDMTVAQIGDVLGVSRTTIYR
+TLAKHAEPVARRRAKPSPTM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002098.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002098.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea2ebb5bd4020ebbb877442825685f256cb8101f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002098.fa
@@ -0,0 +1,29 @@
+>PROKKA_01797
+MTETSNSPMTARVRAFLDRPHRLLIGGEWVDAASGKTFETRDPATGEVLATVAHAEQADI
+DAAVAAARAAFDEGSWVRMRPNVREDLLWRISNLITERLEDFALLESLDQGKGVGIASAF
+DVRAAADCFRYYAGWPSKLQGAVNAPSMLLAPPEAEFHSYTRREPVGVCGQIIPWNFPLL
+MAAWKIAPALATGNTVVLKPAEQTPLTALMLGELLTEAGVPAGVVNIVTGHGDAGAALTA
+HPDVDKVAFTGSTEVGKKIVGAAAENLKKVSLELGGKSPNIVFADANIDAAVDGALMGFT
+LNSGQACESGTRVFVHADVYDRFNEALAAKMRQMSIGPGTEDAAITPLVSQEQLDRVMGF
+VEEGKRDGAVALTGGQRHGDAGFYVEPTLFTETTPEMSIVREEIFGPVAVSVKFTDEDEV
+IRAANDSVYGLAAALWTRDVSRAHRVAARLKAGTVWVNTFHALDSQLPFGGFRQSGWGRE
+LGAESLELYTQVKSVTIAL
+>PROKKA_00689
+MTETSNSPMTARVRAFLDRPHRLLIGGEWVDAASGKTFETRDPATGEVLATVAHAEQADI
+DAAVAAARAAFDEGSWVRMRPNVREDLLWRISNLITERLEDFALLESLDQGKGVGIASAF
+DVRAAADCFRYYAGWPSKLQGAVNAPSMLLAPPEAEFHSYTRREPVGVCGQIIPWNFPLL
+MAAWKIAPALATGNTVVLKPAEQTPLTALMLGELLTEAGVPAGVVNIVTGHGDAGAALTA
+HPDVDKVAFTGSTEVGKKIVGAAAENLKKVSLELGGKSPNIVFADADIDAAVDGSLMGFT
+LNSGQACESGTRVFVHADVYDRFNEALAAKMRQMSIGPGTEDAAITPLVSQEQLDRVMGF
+VEEGKRDGAVALTGGQRYGDAGFYVEPTLFTETTPEMSIVREEIFGPVAVSVKFTDEDEV
+IRAANDSVYGLAAALWTRDVSRAHRVAARLKAGTVWVNTFHALDSQLPFGGFRQSGWGRE
+LGAESLELYTQVKSVTIAL
+>PROKKA_00823
+MTETLTYADLLAAVVAPEGAGTEIKDPATGDLIGYAPQSTTADLDAAVELARTAQRDWAK
+LSHAERSAALNRAADAIEANSAALAELLSREQGKPVKNGPNAAFEVGGCVAWTRATAGFE
+VQPETIVDDETGRAELHWMPIGVVGGIGPWNWPMMISVWQIAPALRMGNTVVLKPSEYTP
+LSVLGLVHVMNQALPEGVLQVLAGDGELGRAFTSHDGIDKITFTGSTATGKAIMKGAADD
+LKRLTLELGGNDAGIVLDDADPKAIAEGLFWGAFINTGQTCAALKRLYVPDSLYDAVCEE
+LVAVARRMPMGPGLEEENVLGPLQNRAQYEIVERLVQAAKDGGGRVLLGGDPDPERPGLF
+YPTTIVADIDNDNPLVAEEQFGPALPIVRYTDLEQAIEWANGLDVGLGASVWSADPERAK
+EVAMRLEAGSVWINKHGTIDPRVPFGGVKHSGMGREFGVLGLKEMAEAKSISV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002103.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002103.fa
new file mode 100644
index 0000000000000000000000000000000000000000..762c394ea5b92fcd97b16a5b7c5e75b007cae880
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002103.fa
@@ -0,0 +1,15 @@
+>PROKKA_02186
+MKYRPQHEANPLPFSPFKSSTVPRPIGWLSSVSTDGRENIAPYSQWQNLTFDPPMVMFSA
+NQYPDGRRKDTVLNAEQTGWFVWNMATYDLREAVNVSAMALEPGESEWDRIAEHGVTKVY
+ADNHPIPMVAESPVRFECRYHSTHRIKGDSNVGTIDVVFAHVDTIHIDDDVITADGRLDI
+PRIQPIARLGYFDYTVVRETFEMRVPGADGDAQAGLEGRS
+>PROKKA_00824
+MSARTEFDPAALGDRETTLLVKSLLIPRPIAWVGTLSADGVPNLAPHSFFTVASSEPPIV
+LIGSAGRKDTLRNAEATGEFTVSLVTRALAEAANRTSAPFAPEVDEFAAASLTPEPSVVV
+GPPRVAASPAALECRLHEVHPVGDSFLLMGRVVHVSVDTDVLTTDARGRTLPDPAALGPV
+SRLGRMEWGGLGEVFELERPSAG
+>PROKKA_00157
+MKYRPQHEANPLPFSPFKSSTVPRPIGWLSSVSTDGRENIAPYSQWQNLTFDPPMVMFSA
+NQYPDGRRKDTVLNAEQTGWFVWNMATYDLREAVNVSAMALEPSESEWDRIAEHGVTKVY
+ADNHPIPMVAESPVRFECRYHSTHRIKGDSNVGTIDVVFAHVDTIHIDDDVITADGRIDI
+PRIQPIARLGYFDYTVVRETFEMRVPGADGDAQAGLEGRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002104.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002104.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e99e1b21b386a5463da4e110e9b9c919411cf4f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002104.fa
@@ -0,0 +1,24 @@
+>PROKKA_02304
+MSETRSGVLPDHDIYLLDDELTEEQREVRDRVRAFVDAELMPVINDYWERAEFPFELVPK
+LAELNVAGTVIEGYGCPGMSRMAGALVSMELARGDGSFNTFFGVHSGLAMGSINAFGSDE
+QKERWLPRMARMEMIGAFALTEPDHGSDSVALETTARREGDTWVLDGAKRWIGNASYAHV
+IVIYARDVADGQVKAFVLEREPDTEFPAGFEPTVITGKIGKRAILQPDIVISGLRIPEAD
+RLPGCSSFKDVNRVLSTTRGGVAVETLGHAVAAYEAAVAYAGQRVQFGKPIAGHQLVQGQ
+LATMLADVTNIKLTCFRLLELQDQGRLTGPMASLAKMSAARQARRVTSMARDILGGNGLL
+LENHVARHLTDMEVVYTYEGTDSMQSLIVGRAITGVSAFA
+>PROKKA_00809
+MADRPAVIDHPDYFLLDSDLTDAQRALRDRVRDFGREQVLPIINEWWEKAEFPEPLLPGL
+ADLGIIGTYIEGYGCPGMSRIEAGLVAREMGRIDGSVNTFLGVHSNLCMGSIYILGSDEQ
+RQRWLPAMAKLEKTGAFALTEPKHGSDSVSLETSARRDGDEWVITGHKRWIGNGHAADVV
+VLYARDEADGEVKAFVVEKQEDGSFPAGYNPTVITGKVGKRAILQADIVIENLRVKEENR
+LVNCESFAGVNRVLKATRGGASWEAVGHGMAAFEIAAAYALEREQFGAQIGGYQLVQERL
+ATMLTDLTTMQLMCVRMAELQERDELTLAMASMVKMHTSRKALDMTRTARDIVAGNGLLL
+ERHIGRHLTDMEVVSTYEGTDSMQALIVGRDITGISAFTRSRRKS
+>PROKKA_00288
+MSETRSGVLPDHDIYLLDDELTEEQREVRDRVRAFVDAELMPVINDYWERAEFPFELVPK
+LAELNVAGTVIEGYGCPGMSRMAGALVSMELARGDGSFNTFFGVHSGLAMGSINAFGSDE
+QKERWLPRMARMEMIGAFALTEPDHGSDSVALETTARREGDTWVLDGAKRWIGNASYAHV
+IVIYARDVADGQVKAFVLEREPDTEFPAGFEPTVITGKIGKRAILQPDIVISGLRIPEAD
+RLPGCSSFKDVNRVLSTTRGGVAVETLGHAVAAYEAAVAYAGQRVQFGKPIAGHQLVQGQ
+LATMLADVTNIKLTCFRLLELQDQGRLTGPMASLAKMSAARQARRVTSMARDILGGNGLL
+LENHVARHLTDMEVVYTYEGTDSMQSLIVGRAITGVSAFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002108.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002108.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fadadb876dd5aa4c88445a0499a59f84481b7d65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002108.fa
@@ -0,0 +1,26 @@
+>PROKKA_00761
+MTLAHPASRPMPATSPATPGATPPDPAARLVPLRGADHAAVLAEAVRVRASGGIPVVGDE
+RWPAALMAAQVEHAAATLRDLAVRDPRAAAEIAWAAFTSGSTSRPRVVLRTEASWRAGHR
+VAADWLGLRPGEELLVAVHPVSSMAVHAASLCGALGARLRVTARARLSAADLAGPVVLDA
+TPSQLVDALDLLDDGAPSTLRVALIGGDRLPAGARDRAAAHGIRVAHFYGSAEASFVAVD
+LDGAGLRPLPDVRLRIADGADDAGPAGPNTPDPNTPRARTGLLELRSDQLAAPDDSRLSS
+GAPRWREDGWLTTGDRATWDPDAGVLEVHGRADDVILTAGATVAAADVEAELAAARDGSG
+RPVASGVLVVGVPDRRLGERVCAVVEPARGQDPEAALQMLKTAARAGLSPAARPRRWVLV
+DRLERTGSGKIRRALPAATRHAAGRQDHA
+>PROKKA_00724
+MSPLAPVPDPAARLAFLADADHAAVLAEAVAVRARGGVPVVGDERWPADLRAAQREHAVV
+QLRRLAARDPDLAARVGWAAFTSGSTSRPRVVLRTDDSWRAGHPHVAAWLGLAPGEAMLT
+AVHPVSSMALHAAAWCAATGHRLAVSPHARLTAADLTGPAALTATPSQLTDALDLLDDGA
+PSTLRVALVGGDRLPAGARERAAAHGLRTVHYYGAAEASFVAVDLDGSGLRPLPGVELEV
+AEPDVLADADGPRTGVLRVASPQLAVPDDSRLASGAPRWDAEGRLTTGDRVTWDPAAGIL
+TVHGRADEVVLTAGATVSAADVEAELAAVAGPDGRPVAAGVLVLGVPDPRLGQRVAAAVE
+PAPGVAPEDALAALQGVARARLSPAARPRRWVAVGRLERTGSGKIRRVTPPELRP
+>PROKKA_01993
+MIPPVRLPPSDDDVAPAVSRLAPLRGADHEAVLRRALEARTAGLVPLVGDERWSVAQWQA
+GVGHAEALLAELTARAPDRAARIGWAAFTSGTTGRPRVILRTADSWRTGHRLVEDWLGLE
+PGESLLVPVHPVSSMAVNAADLCAHVGARLLVPSRARLRAADVTGGAAAVHCTPAQLADL
+CDLLAAVRAASAPAGPRVVLVGGDRLPGQLRERAAALGLRVVHYYGSAEASFVAVDPDGS
+GLRALPGVRLEIREGVLHVRSDQLAEPDGTRLTDGTPRWGADGWLCTGDRAQIDDDGVLH
+LRGRADDAILTGGATVIPAEVEAELLRATVRRESTASGGDSAPHAVPVCTAVLVQGEPAP
+RLGSLVVAHVEPAPGLPADVVLAALKEHARTHLPPAARPRRWQVVDRLERTGSGKIRRMA
+PDVAAIPDPPGGSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002109.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002109.fa
new file mode 100644
index 0000000000000000000000000000000000000000..096daf34ec74cf5810da18950fc896a461b68817
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002109.fa
@@ -0,0 +1,20 @@
+>PROKKA_00762
+MVASALTGGDPALPGIGPVAAVREVLDAAGIALAEVAVVEVVEAYAAQVWAVLDELGLSA
+EAGAARADDWGVDPRVNAEGGALAFGHPWGASGAVAATHAVRRLQSCPPGSSALVTCAVG
+GGMGVALVLDVA
+>PROKKA_00725
+MSAVGLDAAPVWITAVSRTPVTARSRAQAHLGAGELAAGPVGEVAAGTHPAAVVLGNGAG
+PGGNVARIAALAAGLGVATPGWTVDAQCGAGLVAVAQAAGHAVATGRACVGGGVESPSTA
+PERSIDGVSYAQAPMVPAGWDDPGMTAAADALAAARGIGRARQESFAARSHVLALAGGLR
+LPDDDGPRRLDAAALARFRAVTPGADPATAVTGATAARIADGAAAVLVTPHSAVVRETDG
+VSTASVRGVDVLRPCRVLSWSLTGVDPALPGLGPVSAVRDALDAAGRTLEGVAVVELVEA
+YAAQVLAALDDLGLTGASGTSAPGASGPATAHDPWGVDPRVNAAGGALALGHPWGASGAV
+AVVHAVRRLQAEPPGAVGLAACAVGGGMGAAMVLEVA
+>PROKKA_01992
+MTTTPGLWITAAARTAFTARSRGQAGLDAGALSAQAVAAVTGPAAADVAAVVLGNCTGPG
+GNLGRIAALAAGLGEHTPGWSVDAQCGAGLAGVLQAAQHAAFTGRPCVGGGVESPSTAPQ
+RSRDGVPYTQAPMVPSGWPDPGMTAAADALAAADAMPRARQEAFAARSHALALAAAGLRR
+IERVPGAPDDDGPRRLDARALARFTPVHPDADPAAAVTGGTAARIADGAAAVLVVPCERS
+PVGRDEPAGGLRPVRIVGAEIRGGDPALPGIAPVAAVERALAAADWRLGEVAVVEVVEAY
+AVQALATLDRLGLTDHARPGPASLGSDRQGLDDWGVDRRVNAAGGALALGHPWGASGAAA
+VVRAVHRLQGQPPGARAVVACAVAGGLGITMLLEVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002112.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002112.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8fa51c81ff99192bbee1b6f2e5186f26b22748cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002112.fa
@@ -0,0 +1,36 @@
+>PROKKA_01077
+MTTATPRQPLIEDHAYLSNQHSGALLTREGDVTWLCLPRFDAPSVFTSLLGEPEHGRWSL
+RIADGEVRERAYLPGTLVLRTRWRGPDGEAEVLDFMPLTSHRGSGRAHDDDAGALADEGE
+AARADLVRLVRCTSGSVSVDQCLQFRMDYGEVVPWVSRQTDPADESFLAVVAGGDALAVH
+GPDLRPDSTAHRGRTRLEAGQSAAWTLAWYPSWSMAPAAPDPERALEATVTDWVEWLGEP
+LATGPRADRVARSLLVLKGLTHRDTGGIVAAPTASLPEDFGGVRNWDYRYVWLRDTALTL
+EALMAHNHTDDACAWRDWLLRAIAGDPRDVQIMYTLSGERRMPERDLEHLPGYEGSRPVH
+VGNGAADQWQADVIGTVMLALGRLRDAGVDEDRWSWTLQKRLVERVLEHRDTKEHGLWEM
+RGEPAYFTHGRVMMWAALDQALHAARDHGLPAEDEELAAWEQARDELREEILTEGVGPSG
+GFRQTYGSEETDASLLQIPHTGFLPHDDPRMLATVADVERDLVTETGLVMRYRASGMDGL
+PGEEAPFMMCGFWLVEQYARSGRLADAERLMARLDECSNDLFLMAEEYDDGRDRMAGNFP
+QAFSHLGLIRAVDALEEARGAAGGEG
+>PROKKA_01012
+MTAQTAPASPLIEDHAYLSNQHSGALVTRAGDVTWLCLPRFDGPSVFTSLLGAPEHGQWS
+LGIADGEVVERAYLPGTLVLRTRWRGPEGEADVLDFMPLADHAGSGVVDADDVGILMGEG
+EGPLRRADLVRLVRCTSGTVEVDQWIRARLDYGEVTPWVSRQEDPAGEEFLAVVAGGDAL
+AVHGPDLRPDGMRHRGSTRLEEGRSQAWTLAWYPAWTTAPAAPDAEHALEKTVTGWVEWL
+GDPRARGPRAERVARSLLVLKGLTHENTGGIVAAPTASLPEDIGGVRNWDYRYVWLRDTS
+LTLEALMAHNHTDDAAQWRDWLLRAIAGEPKDNIQIMYTLSGERRMPERELGHLPGYEGS
+TPVNVGNGAADQWQADVIGTVMLALDRLRDAGVDEDQWSWPLQKRLVERVLAHRDTKEHG
+LWEMRGEPAYFTHGRVMMWAALDRALHGVREHGLDATEEETAEWERVRDELREEILTEGV
+QEDGAFRQTYGSDETDASLLQIPHTGFLPHDDPHMLATVAQVERDLTTETGLVRRYRATG
+MDGLPGEEAPFMMCAFWLVEQYARSGRVEDAERLMARLDDCANDLFLMAEEYDDDRGRMA
+GNFPQAFSHLGLIRAVDALEECAEDARAAE
+>PROKKA_01718
+MSAQPRIDDHAFLSHQLSGALVSREGAITWLCLPRFDSASVFTSLLGTREHGEWSLGIED
+GEVAERAYLPGTLVLRTLWRSPSGVAEVLDFMPLLDADGVGDAQGDDGGPDGTGASEAAP
+RADVMRLVRCLAGRVRVTQSVFARLDYGEVEPWVSRQEDADGESFLAVVAGGDALAVHGP
+DLEPVDGHHEGTTELVAGESAQWCLTWYPAWGMAPSAPRAEDVLEATVRRWRGWLEESTR
+QAPRADDPLADRVQRSLLVLKGLTHRATGGIVAAPTTSLPEDIGGVRNWDYRYVWLRDTA
+LALEALLAYGHVEVATAWRDWLLRAIAGEPHEVQVMYTLSGERYMPERELEHLPGHADSR
+PVVVGNGAADQWQADVIGTVMMALCALRDAGVPEDEWSWPLQKRLVERVVAHREDPDHGL
+WEMRGEPAFFTHSRVKMWAALDRALHAVATHGVPATEAETAAWERHRDELREEILTRGVH
+ADGHFTQAYGSDAVDASLLQIPHTGFLPPDDPRMLATVRRIEEELVTDTGLVLRYRPDGS
+DGLPGEEAPFLACAFWLVEQYARTGRLDDADALMERLDACANDLDLMAEEYDDGQDRMAG
+NFPQAFSHLALLRAADALALVRAGDGAGEAGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002113.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002113.fa
new file mode 100644
index 0000000000000000000000000000000000000000..74f41950837ae426bcb99f0a0d4e73893b677fd3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002113.fa
@@ -0,0 +1,16 @@
+>PROKKA_01297
+MSSPTGGSTAADASPRNRAPGGLLNRFLNVIEWSGNKLPDPIIIFAALCALTLAASAVAG
+LSGWSAVHPGTGETLVATNLLSTEGMRVVIGDAAKTFGAFAPLGQVLIIMLGIGVAERSG
+WFEVGLTQSMTSAPKGLIIPAIALIGLLGNIAGDAAPIVLPPLAALIFLKLGWHPIAGIA
+LAYAAATGGFAANLMIGMSDALVQGFTQEAAVIIDPDIETTVPMNWWFIAASVVVLLPVL
+WLVTSKIAIPRLGSYQATDDVEAGDMEVTDVQRRANRWALVALALFAALVVAACIPQGSF
+LRNAETGSLTTDAPLMNGIGLILAVAFFLPGLVYGVRAKTITGSSDVARMMVESMATMAS
+FIVVVFFASQLLSYVSASNMGAILAIRGAELLQGQDGIVLILGIIAISAVVNLFVGSASA
+KWAILAPIFIPMMMLLGYHPAFTQMVYRIGDAVTNPITPMFPYFALVLTYAQRYDKKLGI
+GTFISTLVPYSLAMGLVWTVMMVVWYLLGWPMGPDGPIHLPTP
+>PROKKA_01206
+MTSPTGGSTAADASPRKHTPGGLLNRFLNVIEWSGNKLPDPIIIFAALCALTLAASAVAG
+LSGWSAVHPGTGETLVATDLLSTEGMRVVIGDAAKTFGAFAPLGQVLIIMLGIGVAERSG
+WTICAATTWCGTTRPAPRWSRSCARTCSRAR
+>PROKKA_00610
+MGIGSLIATMLPSSIAFLLAWTGMVIGWMWLALPLGPNAPVQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002116.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002116.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ef0b70dd4ce7e6b299900db1efc5e89cdd1aa7f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002116.fa
@@ -0,0 +1,17 @@
+>PROKKA_02431
+MSQPTAAGFRFYDAFNGSAADPSPHFNVARYRAHYPGPPTPGQAGCAISHFRVLESFASS
+LGHEDGVALVSEDDVLMPPETEAVLEGILKDDSFEIAVLADRGPTNPSLAFQRLLMTEAE
+LSLLSRPIVCGGRIRRLGRFEGNPYMAALYLVTRSGARKLASGLVDDAGGPWTIADDWPL
+FRDRYGLDIRVLRPGLVTYMGGSTTRDAESLARDALSAAGDGRPLTRLKTAVGLRSRSRA
+ARLVVRATLRDIATR
+>PROKKA_02276
+MPDIVDYRVIALADSTRLEGFLAQPLGRRFRPFEAVDARKGYGPEDFDAEGFEVRFGRPP
+LNGEVGCTLSHMSVLREFAVEDGAVTDVLVVAEDDARFSRFTSEVLNRLLETSAVRGLVV
+LADPYGPVDMRGRLGAPTLEDKLQQSLLRRRLRPLAGAPRFAVGRWSRGLVGTGFYLVSR
+DAAKYDIAWRLRHRRGGAR
+>PROKKA_02312
+MGQITDRYVISLEGSPRREAFFSQPGVADFVVWDAFDGRTGAGRDRFDVVAFERRAGRPP
+EGGEIGCTLSHAGLLADFAAGLGRPDDLMLVAEDDVVFTPDFEAVLGRVARTRGWGWTLL
+AQGLEDPFRDPFWAKSRDRAPQSLLAKPVGPPSSPWRYRLGNWDGELWGTGLYLVTREAA
+RALTDHATREGLSWAADDYVTWHAAAGVKVWILLPTIAGWVGESEINATTRPHLQIQSYA
+AHPMGRQAWSRRVSRFRAGARIAWKEMRGDTRPWAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002117.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002117.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28395519ce92c2c5babf79e6ecd56afe071fe958
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002117.fa
@@ -0,0 +1,9 @@
+>PROKKA_00329
+MPQKYTPEFKAKALKLIEERVRAEQCSAWVACTAVGEALGGISPHTLRNWWKQDRVDHGE
+APGLSTAEAEEIKKLRRENLELRRANEILRKASAFFAAELDRPTTR
+>PROKKA_00416
+MQLIEERIRAKQCSGWAACAAVGEALGGISPHTLRNWWKQSHVDRGETPGVSTDEFEEMR
+RLRRENLELRRANEILRKASAFFAAEHDRPTTR
+>PROKKA_00665
+MPQKYTPEFKARALELIEERIRAEQCSGWGACVAVGEALGGISPHTMRNWWRQGRIDRGG
+APGVSTDESEEMRRLRRENLELRRANEILRKASAFFAAELDRPTTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002120.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002120.fa
new file mode 100644
index 0000000000000000000000000000000000000000..851fbbef87276d4fc4798e681e219dc30f1c7684
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002120.fa
@@ -0,0 +1,8 @@
+>PROKKA_00171
+MDRLGRDTRDLYAIVDELTDKGCAVQFVSERITVDKSGTSPVDGLMLGILAAFAEFERRR
+IKERQAEGIALAKARGKYVQAPKLSDTDVEQARVMIEMGIPKAEVARTFEVSRQTLYTSL
+RRVVSS
+>PROKKA_02330
+MKYVREGDLVKVASMDRLGRDTRDLYAIVDELTDKGCAVQFVSERITVDKSGTSPVDGLM
+LGILAAFAEFERRRIKERQAEGIALAKARGKYVQAPKLSDTDVEQARVMIQMGIPKAEVA
+RTFGVSRQTLYTSLRRQASD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002122.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002122.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5d599c480fa5ef37a106153b4c6b35bbe1a635c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002122.fa
@@ -0,0 +1,14 @@
+>PROKKA_00189
+MSQQDLATAVGLERTMVNRIEGGQRKVTALELASIADALGTRMQSFFTEPAPALVSHRSA
+QGLDTTESAVDHLLAELLADVEFLHGLHPIEGFGVRDPWEQPKSVHEADDMAARAREHVG
+YTATEPVKDLQAHLATAGLLLFSRNFGVDAADAGTVLLAEGGISLVNSTPKVGRRRLSAV
+HELGHYLLADEYTVDWRTAHTGPDIEGRLDRFARAFLLPAAVLLQEWPAAAHSGDVRTAA
+VKIAGTYLVDMSTLARRLHDLELVDASTANDIRAVQTTQTDIITHDLYPSDEMAGTTQPR
+VYQKHVIALFEAEKLSRERTLDLLDGTFDDDDLPDLPPRQEQEIWEYVS
+>PROKKA_00212
+MVNRIEGGQRKVTALELAAIADALQARMQSFFTDPAPSIVSHRSAQGLDATESAVDHLLT
+ELAAAVEFLHGLRPIQGLATREPWEPPTSTEAVEDMAARARAEAGYGPDEPAKNLQDHLA
+TAGLLLFSQDFGADAADAGSVLLEEGGVAIVNSAPKVGRRRLSAVHEFGHYLLADEYTVD
+WRTAHTGPDIEGRIDRFARAFLLPATAMASVWPRAVTANGTRTAAVTIAGSYLVDMSTLA
+RRLRDLDLVDASTANDIRAVQTTQTDIVTHDLYPSHELEGLTQPRTYQKHVLALFEAEKI
+SRDRALGLLGGTFTDADLPELPPRQEQEIWEYVS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002124.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002124.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cd9a5a6d0fb27999ec723a17ebfd09d90059c74d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002124.fa
@@ -0,0 +1,16 @@
+>PROKKA_00254
+MATQARDGRFSNEVLPQDERPSRFGPGLIIAASFIGPGTITTSIVTGAEQGFVLAWAVVF
+SILATIVLQEMSGRLGLATRMSLGHALREVFSSVPARLVMAILVVAAIGIGGASYAGGDT
+VGTALALTSVTGLSQPVVVIGIVLTIGILLWTGSYKLIERVLTVMVGLLGLLFIVTAVLV
+QPPIGDLLMGMFIPRLPPGTALLAVALIGTTVVPYNLFLHASLVQEKWGPGLDSRESLRA
+ARTDTAVSISVGGVITLAVMATAFGGMYVKGMQAETGRDLASALEPLLGDAAGWVFAAGM
+FAAGFTSAVAGPLGAAYAIAGTLGQDTDLRSVPARIVWGAVLAIGAVIALTGTNPTEVIV
+IAQAANGLLLPIVAVFLMVVMNSRRLMGSHRNGPLANALGGLVCLVVIGLAVYQLGGLAG
+LWD
+>PROKKA_02268
+MAILVVAAIGIGGASYAGGDTVGTALALTSVTGLSQPVVVIGIVLTIGILLWTGSYKLIE
+RVLTVMVGLLGLLFIVTAVLVQPPIGDLLMGMFIPRLPPGTALLAVALIGTTVVPYNLFL
+HASLVQEKWGPGLDSRESLRAARTDTAVSISVGGVITLAVMATAFGGMYVKGMQAETGRD
+LASALEPLLGDAAGWVFAAGMFAAGFTSAVAGPLGAAYAIAGTLGQDTDLRSVPARIVWG
+AVLAIGALIALTGTNPTEVIVIAQAANGLLLPIVAVFLMVVMNSRRLMGSHRNGPLANAL
+GGLVCLVVIGLAVYQLGGLAGLWD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002132.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002132.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bd1c8c51de31d89d5ee39643543f12a57f6ae5c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002132.fa
@@ -0,0 +1,20 @@
+>PROKKA_00596
+MATMIQESMDSEYDDVRFPQERTQGLILGLTLEQVIVVLAGVLIGMAFILRGGPAMFVGI
+GLMAVIGAFGATRFRGRSLPGWVWVAAQYLRRGATDQLEYRQGMAPAHVLELVDGEPQAP
+VSEAGPQAQRDAKGRIKPGEPARFRLPGVAGELMVYAMPNGAGFVWDPRAREAVVCAKVM
+TTRGFDLESFDAQEERSLSWGSSLAALSRLPGVVRIQASDQTTLISGAAVEDFYESKQEG
+AGRTGASIDPFLDQAFRELMKEAQSMPVHEQWLTLVVSPSKITSQVKALGGGTPALMEHM
+LKLMTTVESTLPRSGTQVTAWHSPRTLAGLSRSAFDPDASVMVSTMKADGKTAGTAPSSA
+GPMAVEVHAGHMVTDGNYHRTYKVSELPQNLARLGFLDELVFAGDFRHTVSVFLAPVERG
+AAVRSVQRRKTDWHTNSRLMNKLGRIGSLEHDQSLEDVEREEAELRRRHTGVEVVVLVTV
+TGASRSELESAAAEVVASGITAECELRPVWMEQDAAFVAGALPFGRMKL
+>PROKKA_01792
+MSSRKKNNSHEPEATGSELVPVKFSRLTRRGILLGLSAAQLVTVGIAIATIITALYAGGG
+MWLAYTAPVWATAVLLTWVPVAGRPVIEWVPVAGWWVYRTTIGQLLYRRRIVTPRPAGTL
+ALPGDQARLREYEDPTTGAGMIHDPHQNTLTVVCEITHPAFVLLDPAEQERRVTAWGRVL
+ATVCRSGRIATLQILERTLPDSGTGLAEWWTTHGQPDDTSWAATTYAELINRAGPAGERH
+ATTLSLSLDMRNAARQIRTAGGGIRGAAAVLRQEMNTLTAALRSADLTPSGWLTPGQIAV
+ILRSAYDPAIAATLERHGEIGHDLATAGPVAVNETWSRIRTDSAHHAVLWISEWPRSMVY
+PGFLSPILLSSGIQRSFSLICTPMRSDQAARDIRKKKVEHISDQAQRAKIGQIEDASQTA
+EYHDVLQQEADLTAGHGILRYTGLITVTATTIEDLDAHVAALEQAAIQANCETRLLAGQQ
+AKAFTAAALPLCRQV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002133.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002133.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6342b4a6539c603c3c43536289374ca34529258
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002133.fa
@@ -0,0 +1,18 @@
+>PROKKA_00597
+MREEPKVDLFQIIEPGKMSLREARVAQRKMKMAQAQAQRLRNREAREERFPQPQWGKAGP
+RGARQLRGLRTLAPRPVRTTTHTAATAYPFVAGPGLGARGLMIGKDMHGGGAFCFDPWAL
+YEAGIISGMSMMLFGQVGTGKSSLAKSLAVRQVLAGRKLSVASDKKGEWTRVVKGLGGSV
+IQVGPGLDTRLNPLDPGTRPSTDVQGEPMTDRAWASMVRTRRMSILVALVKILTDREMTS
+PEHHVLSAGLDAAVAVADAEGRPPIIPDVIRALDAARTDPDAMKAEAASVTMMTLGRVSS
+GDLAGMFDGETTVVLDEQACATSIDTSALLGASPEAVRVVNACAGAWTEAMVTTRDGGQR
+IVIYEEGWDNISSEADLRRMVEQWKLSRAYGIFNVLVLHKIADLDMAGDQSSKMAAMARS
+LLADADVKVIYRQDRSALKITTSEMELSDRERSLVRSLPKGTGLWRLGDSSFEVQNVLTR
+AELPLFDTDERMDKAKEAVA
+>PROKKA_01798
+MAEGGLGSDGVFVGQDLYSGGSFVYDPWVLYARGIITAPNLVLAGIVGSGKSSLAKSLYT
+RSLPFGRRVYVPGDPKGEHTAVAEAVGGKAIVLGHGLHTRLNPLDEGHRPGGLTDQEWAS
+TVASRRRDLIGALAETVLARGLTPLEHTAIDLALTATVAENEVPILPMVVDHILTPSHDP
+GGRLAEDGRLVGHALRRLVAGDLAGLFDGPSTVAFDPDLPMISLDLSRVTENSTLISVLM
+TCSSAWMESALLDPNGGQRWVIYDEAWRLMSHPALLKRMDAHWRLARHYGIANMLIFHKL
+SDLDNVGDEGSAMRSLANSLLANAETRIVYRQESDQLGPTATALGLTGTEQTLLPNLGVG
+QGLWRIKNRSFVIQHQLHPGELELFDTSSRLTAGVK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002134.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002134.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c9d9853e6d8ebe2481852f02047293c3d09d90c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002134.fa
@@ -0,0 +1,15 @@
+>PROKKA_00598
+MRRERGNNSVLEGDNPAETALIWLIGPAVLLYGAYLLAGFLAGRIHCGAATKPDSLFAPL
+GFLVGEHDPAAFGATAQGCTATTGGVIGWLIGLGVLALVLIGVAVTAWSRYQQSDKKFIK
+ELREREGLARSAEITKTVGRKSVLSRVKKVRPSIKKPAITDGAMRLGKAEGVDVFASYEE
+SVVLIGPPRSGKGVHLLIGAILDAPGPVITTSSRADNLGATAELRKKKGPVALFDPQGLT
+GQPSTLKWSPITGCEEPRVANQRAASLIGASGLGSSSSNAEWQAPAITIMECLLHAAALG
+ERTVDDLMRWGNNPAEAKEAVKILTEHPKAALNWNLVLKGIIEGDPKLLQSKWFGVEGAV
+KGLSVPEVRDVLRPNRFEETLDIDKFLTECGTLYIVGTKTGGSSAGPFLIAMMDAITERA
+RELAAKSPGNRLDPPLSLVLDEIANISGAWPGLTQLMADGGGVGISPFAVFQSMAQARNE
+WGEQQAQALFDAATVKVQLGGASNVSDLEQFAKLAGQRKIMRTSKSRGKDHTSVSEQIHD
+TEVVSVAELRRLPFGWGVLLNRNGRPILMQMTRWWDRKDGKQIKEAAGRYSKALLAELES
+KDPAPSTPTDADRAEDSVAALDPVPETAPAIPVR
+>PROKKA_02243
+MLEAIARTSKSCGKDHTSVSEQIHDTEVVSVAELRRLPFGWGILLNRNGRPILMRMTRWW
+DRKDGKQIKEAAGRYSKALLAELESKDPAPSSTPTDADRAEESVAASDPVPEAAPAIPVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002136.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002136.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7278e3c197b72292d6b08e118d33d13b0186f845
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002136.fa
@@ -0,0 +1,18 @@
+>PROKKA_00601
+MIPVKDLIKAREDWDFEREVALDEQSSVERELASANGHLSRLKEALIERGLASLLWGAQH
+EDVASVPDLVQDTSEAVLAAQMYLADWLVLPDSAVRHLEDIDTAPEAYNWGNKAWRGFRA
+LAAYAQDRASGWDKGGFWEWCASGPVLGWPATSKKLSMTESEGVQTSGKFKGTRDFKVDP
+AVDSSGEITMLAHLKISEGGGNLAPRVYFYDDTNGATKKVHIGLVGPHYLVPNKSTN
+>PROKKA_00187
+MAVGYRAIFAVSPREDALAIARESVHSWLVDKLNRARPEVRQQALELDFNAPFAVQLSDE
+IHVSNTRAHGDNGQLQQLIRLDESSAPGETWRVNITADRNDVGGVRQQTIMVELDPLHLD
+AETAVMRAAPPRFVREMLTQHVLRSGTTVLTATPKALRGSEGGREAYRAVIDPLRQAQAV
+IAAQPPGSDMTIWQAAVASLTRQAMGITTALTLDKDALDQFNRRLPRNLQLQPGEVRTFA
+PHVDLDDPADSLRHRSLGPGTFARHIKPRVKDGVTVPEVDPTFASVHARRARMYALEQPL
+PDSIRSMRQQVRTGELREERDRAAGLVTGFSTVRVRPAAPAPAASPHRPGAGKRPSPTPT
+SGRLGASGAIPVPRPLPPSQEKVAEASSATPVAPAEAPQASAPSSITPVPAWQKTLVQLV
+WSTLGTEEITKEAIELLAEQLAASGRREQVADEQIANAVREAEIAAAQHDDLRARLEDAE
+LAAAAEQEERESLAREVEHLRRKAIEAERYEDLVVPEATDEEAKPSTFDDLIERIQSERF
+TTHEYVVFTGDMKKVNEVEAIDIVGRHLSSCWEFVLTLEGYARAKKDGFNGGVHQYLTSG
+EVDGKRCSPGKHASLESESVKSNAAQRRERLLPVPKNVDRSGAVHMWAHFKCSKDGTKSP
+RMHYYDDTDNTGKIYIGYIGPHLTNRQTSSM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002140.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002140.fa
new file mode 100644
index 0000000000000000000000000000000000000000..155db5152197f074f1880687864787d8b3641c80
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002140.fa
@@ -0,0 +1,14 @@
+>PROKKA_00890
+MSVLRTGLIGLGMMGRHHARVMRSIEGTELVAVADAMGDPHGVAGDLPLYDSVQGLIDHG
+VDAVMCAVPTGLHEEVGLALAEAGVHVMVEKPIAHSTEAGTRLVHAFDEAGLVGAVGHIE
+RFNPALQEMRRRIQAGELGRVLQITTVRQGGFPARIADVGVVKDLGTHDIDLTAWLADSP
+FTRVAAETMTNSGREHEDMVVANGRLECGAITSHVVNWLSPVKIRQTVVTGELGAFVADT
+VHADLTFQANGSVRTRWDAVSAFRGVSEGDVTRLAIEKPEPLHTEHEAFRDAILGVRQEH
+VSMAEGLATLRVAEAMIASAHTGESIRL
+>PROKKA_00612
+MSVLRTGLIGLGMMGRHHARVMRSIEGTELVAVADAMGDPHGVAGDLPLYDSVQGLIDHG
+VDAVMCAVPTGLHEEVGLALAEAGVHVMVEKPIAHSTEAGTRLVHAFDEAGLVGAVGHIE
+RFNPALQEMRRRIQAGELGRVLQITTVRQGGFPARIADVGVVKDLGTHDIDLTAWLADSP
+FTRVAAETMTNSGREHEDMVVANGRLECGAITSHVVNWLSPVKIRQTVVTGELGAFVADT
+VHADLTFQANGSVRTRWDAVSAFRGVSEGDVTRLAIEKPEPLHTEHEAFRDAILGVRQEH
+VSMAEGLATLRVAEAMIASAHTGESIRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002141.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002141.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f25aa424e990b67802c147981f5821398d233d97
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002141.fa
@@ -0,0 +1,26 @@
+>PROKKA_00892
+MSTVLLLTTGTGPAEGLLLQDLRDSGHVVDVLDVASHAWLRRRPGLAPAPLYPWTGTHAL
+RAAGAQIAREMRRVTAAGAYDAILASGLGAAGFAARHVEEEFIPLLRRGDLDFSAARRHA
+EEDFAALTRAVDRLFLADEWEFDKALSKGSRSAHLRHPRVGLAPQTLAPLAAEAETPRVV
+VLHPEHVDADRLAAQMEALQTAVDTVPGASLRSLSASALYRTRDLAAGRAFDAVAATRLG
+GATHVVLVGSSRDHAAVGELLVGTGFAERLVVEDTIGSGAWAAGHPGVRTGRGLRLVTEL
+AAALHGGPETHSAVDTVDGGTTDLLSAYRAAMTGRVDRTFEDLAVLRHDGPLDVFFSTSP
+LEDRTDGARPQRVRNMNDALSEPAAALRLSSVPGVFDRRLRVLDEALAAGRPLGLLYGEN
+STSPIPVDRVTAALADVMARFSAGGGTSVWFVRDLHWLDEIDGYLEDADARRDVQERGLA
+EFDAMAEAAYRLAAPSAESGAGFDALLARHGRGPVDWLPLPPAVSPANTVPADAPAIGEE
+GVTLLYAGGVGGIYGLGQYLTAVGTLDPQVRLDFVVRAGERSVLEDMLAEHGLADRPGLR
+ITTVPLEWYVPATRTVVGVVLLGGKYARFSFPYKTMSLIERGYPVLCFADMGIADFLERN
+RVGLGVARSSEAIRAGIVTLVRDGAPGMAEAQRSQSWAVRVATARAALED
+>PROKKA_00614
+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/Orthogroup_Sequences/OG0002152.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002152.fa
new file mode 100644
index 0000000000000000000000000000000000000000..221679118584e792bf83b00b88049d5a59c658d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002152.fa
@@ -0,0 +1,13 @@
+>PROKKA_01389
+MIRVEAGMSTARFCQLFDMPERTWRRWQAKARTGTAVKGPWPQPGRQAARELVVKHALAH
+PAWGHRKIWAMVRHDGHVVSEATVLRILRDEGLILPAQYQRERRKLAERRKAAFATEPSG
+PNQVWQLDFSEFETTTGGTWRLAGCRDYWSKYEHPFHVSPTGNQHDAIDAIELALADYEA
+MFGHPLVEACPVDPETGELLPVVTIVTDNGGPFRSFRFESFIAAHPELHHVRTRVKTPGQ
+NGSRERGFGTLKYERLYLDEIDDAIVLAERAEDYRIEYNELRPHEAISWNRPKEVHLGLA
+DPTTPTFKTKEILPTT
+>PROKKA_01121
+MVKHALAHPAWGHRKIWAMVRHDGHVVSEATVLRILRDEGLILPAQYQRERRKLAERRKA
+AFATEPSGPNQVWQLDFSEFETTTGGTWRLAGCRDYWSKYEHPFHVSPTGNQHDAIDAIE
+LALADYEAMFGHPLVEACPVDPETGELLPVVTIVTDNGGPFRSFRFESFIAAHPELHHVR
+TRVKTPGQNGSRERGFGTLKYERLYLDEIDDAIVLAERAEDYRIEYNELRPHEAISWNRP
+KEVHLGLADPTTPTFKTKEILPTT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002163.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002163.fa
new file mode 100644
index 0000000000000000000000000000000000000000..33d1f0adab9960b18531cc552de8740981a840a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002163.fa
@@ -0,0 +1,8 @@
+>PROKKA_01608
+MSFLIPSVPVSCGCRREVREETGLEVTAGRLVAVDTRPSKADGRIGLRFLFRAVHPLTAA
+DVAAIRLQEDEASEHSFVTCQEARKLLRPAIARRVDAAWDAAHCVYLEDGRPAAGVDQPA
+G
+>PROKKA_01320
+MVNLLLSVTFACGVAIAGLHVVNRRFIAPMYDVVLNLAAFLAAVASSVLLGHVLPAVFAA
+LAVLAWLILAVRTVRARRAGHKLEVTAGRLVAVDTRPSKADGRIGLRFLFRAVHPLTAAD
+VAAIRLQEDEASEHRFVTCQEARKLLRPAIARRVDAAWDAAHCVYLEDGRPAAGVDQPAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002164.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002164.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e68f054e8215fac1570234de6db56dfb332ec734
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002164.fa
@@ -0,0 +1,6 @@
+>PROKKA_01613
+MSGNAFQDLPFPVSGPILGSVGERFRLETASDEGTATFSAGGTEGGTYSCGAGQTLLIGD
+SALLCRAVGENSLDFTISRPR
+>PROKKA_01276
+MRTRVTTSLLGLGLTAAALVGCQTQTWISMCFTDATLRSCEVSVSGNAFQDLPFPVSGPI
+LGGVGDRFRLETASVEGTATFSAGGTYSCGAGQTLLIGDSALLCRAVGENSLDFTISRTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002167.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002167.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6439f3dbb19a3341a2cf3b0bfb15fb6c88a97455
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002167.fa
@@ -0,0 +1,8 @@
+>PROKKA_01789
+MTAQATDGRHAEDFTVGEECDLGTYEVTEQEVIAFASHWDPQDIHIDPGHAETGGRYGGL
+IASGLHTLAILQRLQVLGRREHWNVIAGQGIDRLRFRRPVRPGDVLSGHSRVIDVRLEPE
+WRRGLVVFDVRALNQEGKEVLTMEMAAYLEMRSEATAGRRA
+>PROKKA_01087
+MTAQATDGRHAEDFTVGEECDLGTYEVTEQEVIAFASHWDPQDIHIDPGHAETGGRYGGL
+IASGLHTLAILQRLQVLGRREHWNVIAGQGIDRLRFRRPVRPGDVLSGHSRVIDVRLEPE
+WRRGLVVFDVRALNQEGKEVLTMEMAAYLEMRSEAPAGRRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002168.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002168.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92af38a2b48075f3abd03b9e40a5a0c05dc6464a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002168.fa
@@ -0,0 +1,20 @@
+>PROKKA_01792
+MATLPSVLATTARRVPQHPALKWGDSSLTYADLDATVDRLAGELISRGLRPGDRVVLVAG
+NTPEFVIGLYGALRAGAIVAPVNPRSARPELEHFLADTEARMLLVDPTVGEGVQALAAAD
+SGSAQLLALGALDGFDDVLAAADGRPEGAVAHPDLAEDDDALIIYTSGTTGRPKGALFDH
+HRVLWVGQNMIMGLGMRVGETMVHVAPLYHSAALNLLLFSGVMLGATHVLLPAFDPDEVI
+ATLERERATIFFGVPTMLAYMLRSPRLAASDLSHLRGILYGAAPMPASTAEALVAALPHV
+HIIQACGQTEGGPGGILLTHEEVMAKPHTSGRMAMPNTEVRVVDADGRDVGPGEVGEMIM
+RGETMMKGYWRNPEATAVTVVDGWVHTGDLTRVDEEGFLTVVDRLKDLIITGGRNVYSAE
+VENALAGCPGVAELAIIGRPHPDYGESIVAVVAPMPGATVSLEALRDYGEGRLSHYKLPH
+ELVLREIPRNLSGKILKHRLRADLTEPGVPA
+>PROKKA_01084
+MATLPSVLATTARRVPQHPALKWGDSSLTYADLDATVDRLAGELISRGLRPGDRVVLVAG
+NTPEFVIGLYGALRAGAIVAPVNPRSARPELEHFLADTEARMLLVDPTVGEGVQALAAAD
+SGPAQLLALGALDGFDDVLAAADGRPEGAVAHPDLAEDDDALNIYTSGTTGRPKGALFDH
+HRVLWVGQNMIMGLGMRVGETMVHVAPLYHSAALNLLLFSGVMLGATHVLLPAFDPDEVI
+ATLERERATIFFGVPTMLAYMLRSPRMAASDLSHLRGILYGAAPMPASTAEALVAALPHV
+HIIQACGQTEGGPGGILLTHEEVMAKPHTSGRMAMPNTEVRVVDADGRDVGPGEVGEMIM
+RGETMMKGYWRNPEATAVTVVDGWVHTGDLTRVDEEGFLTVVDRLKDLIITGGRNVYSAE
+VENSLAGCPGVAELAIIGRPHPDYGESIVAVVAPMPGATVSLEALRDYGEGRLSHYKLPH
+ELVVREIPRNLSGKILKHRLRADLTEPGDPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002171.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002171.fa
new file mode 100644
index 0000000000000000000000000000000000000000..be6976ff4e5b8295cfc54e2c021f69f568484e2b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002171.fa
@@ -0,0 +1,12 @@
+>PROKKA_01796
+MTRDIIRTERIGPVTVIHLQDDRALNALGSALVAGLADALEHAQQDPEVRAVVITGSDRA
+FCAGAHIPEVLALREALTADPDAEVYLDRLFDLLAASPQPVIAAVRGLALGGGCELALAC
+DLVVAGESASFGLPEVRLGVIPGAGGTQRLVHAIGKAKATRMLMTGESVDAAWAESAGLV
+AEVAADEDVVARAVDIARRAADNAPGAVRLAVGCARRAQDLSLTDGLAHERRAFLEALAS
+DDAAEGMSAFAQKRRPVFGSR
+>PROKKA_01080
+MTRDIIRTERIGPVTVIHLQDDRALNALGSALVAGLADALEHAQQDPEVRAVVITGSDRA
+FCAGAHIPEVLALREALTADPDAEVYLDRLFDLLAASPQPVIAAVRGLALGGGCELALAC
+DLVVAGESASFGLPEVRLGVIPGAGGTQRLVHAIGKAKATRMLMTGESVDAAWAESAGLV
+AEVAADEDVVARAVDIARRAADNAPGAVRLAVGCARRAQDLSLTDGLAHERRAFLEALAS
+DDAAEGMSAFAQKRRPVFGSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002172.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002172.fa
new file mode 100644
index 0000000000000000000000000000000000000000..996fea404c01dea381ba73fe77cabd72031c863e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002172.fa
@@ -0,0 +1,16 @@
+>PROKKA_01797
+MILDSYRSPWLTEDAEALLEHCRDFLAREVVPHEERWAEQHGVDRDLWTKAGEAGLLCPS
+LPEEYGGAGGTFALEAAILTEQGRCFDDAWGFSIHSPIVAHYILAYGTEEQKQRWLPGLA
+SGELVGAIAMTEPNTGSDLQAVRTRATRDGDHYVINGSKTFISNATHCGLLLIVARTGDE
+PGGRGLSLIVAETDGLEGFERGRVLKKIGQHGQDTRELSFSDMRVPVSHLLGPDEGQGFV
+QLMAQLPQERLTLAVLAAGVCEAAVRETIRYTKERHAFGEPLMSFQNTQFVLAECVADTL
+ATRTLVDQCIVAHVDGTLTAADASMVKFFASDMQNKVVDRCLQLFGGYGYMEEYPIARAF
+TGARVQKIYGGTNEIMKMLVARAL
+>PROKKA_01079
+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/Orthogroup_Sequences/OG0002177.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002177.fa
new file mode 100644
index 0000000000000000000000000000000000000000..acf6b6359c76370a1b8380541db463b2952c3ff9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002177.fa
@@ -0,0 +1,10 @@
+>PROKKA_02061
+MNNISEVTDRLASNETGMEPWLWMPLLKLLALGDPVDVSDLAAATGRAGEEVRTALKAMG
+DTEYDGSGRIIGQGLTQRPTQHRFEVNGEQLYTWCALDTLIFPTLLGASARIESSHQATG
+TPVRVAVTAMGVTSVEPATAVVSLVNPEDISSVRSSFCNQVHFFASPDDAAPWLETHPGG
+TIMPVKEAYELGSSMAEKMLTHTPGPATDQVSNGVQSCAC
+>PROKKA_02221
+MNNISEVTDRLASNETGMEPWLWMPLLKLLALGDPVDVSDLAAATGRAGEEVRTALKAMG
+DTEYDGSGRIIGQGLTQRPTQHRFEVNGEQLYTWCALDTLIFPTLLGASARIESSHQATG
+TPVRVAVTAMGVTSVEPATAVVSLVNPEDISSVRSSFCNQVHFFASPDDAAPWLETHPGG
+TIMPVKEAYELGSSMAEKMLTHTPGPATDQVSNGVQSCAC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002179.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002179.fa
new file mode 100644
index 0000000000000000000000000000000000000000..204f920d4e8cf1b688e30a7a1f402ee0c695141e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002179.fa
@@ -0,0 +1,12 @@
+>PROKKA_02215
+MLRPRLARPTALLTAGLAALALLTGCSVDGDAAAGSSAGSPSAASSSSGASSSGRVSDGA
+APSSSRAAGSSSAVASASRAVESSQAAEASRAAAASREAEKSAAAAAAEASRSAEAEAEA
+VAEAEREAEASAEVEVGAAEEESAASAGGDGLSAEGQQAVRQAQSYLSFTAFSRSGLIDQ
+LEFEGFSNADATAAVDSLDVDYAAQAVKQAQSYLTHTAFSRTGLIDQLEFEGYSNADATA
+AVDGLGIDYNEQAAKQAQSYLSHSAFSRAGLIDQLMFEGYSASQAEYGVDAAGL
+>PROKKA_00529
+MLRPRHTRPALLLTAGLTSLALLTGCADGDPAPGAAATTAAATTAAATSSAPTTQAASSS
+PASSPRTSSAAASSSAKASDAAAAASSSAAAASASEAAESSRAAEAEAEASREAEAEAEA
+ARAREAEESAAAEAEREAEAAATVEEDSSTTAGEGTVSSGQAVRAAKNYLEVLPFSRDGL
+VHQLVAGDGYSDADAAAAVDSLTVDYEAQARRAAQNYLDVLPFSRDGLVHQLIAGDEYSD
+ADAAAAVDSLTVDYQEQAARAAQNYLDVMPFSRDGLIRQLMDGDDYSASQAEYGVDAVGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002180.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002180.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b9c3e36b08733effd5b889ce73c548a64ed9a40f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002180.fa
@@ -0,0 +1,16 @@
+>PROKKA_02230
+MSAGRITVVKGDERLASIPLERVSAVVVHGNVDLSGALLRELMWRGLPCVWCTGAGRVVG
+WTNGVKPPNGGARFRQFAASAEGRVDIAREFVVAKVANQATILRRFGGMPAVVKRLRSAT
+RLASTATSTGQLFGIEGRAAAEYFAGFPGLLAPGVDAGVAESFPGRVGRGATDPLNIALN
+YGYGMLLSEVIRAVLACGLDPHAGVLHSSGRNKPALALDLMEEFRPPVVDSAILAAFNNG
+ELGRLSFTHVLGGARLTQS
+>PROKKA_02165
+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/Orthogroup_Sequences/OG0002183.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002183.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c64c32c258ef00f68e1b767a822177679f98339
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002183.fa
@@ -0,0 +1,20 @@
+>PROKKA_02236
+MGGLVISADFPLGVYTGHGPDGGAERFPDVARLFSALVQAAAAGTLSTGDPEAPFTAESL
+AALDWLEEHPPDALVLPGHTPVAPGVRRFAYRKEGVFLKEVGKTNYKVTGRPVSDGTALG
+GPVQWVWDDGPSGTDTQVCSTLEQLCADVPHLGEASSPVRLTVHEGEGLPAPTHRRDRNA
+SLRAVPGAVRQAMPSPGRRAELDRAHAATTLGRKPSASGDKHTTSAVPHATLPPRDHLRS
+GIFAPVEHHEPDVPWTQVLAVPVIGANSTVPEERYVSVCVALHRALVSRLGPDAPPEITG
+RYAPSVAPPANRVALHLAPGDLPNLPFSDGRDRFLVLVPRGMPGPALGMLASALAGVRRV
+VTSEHQLTVAPEEIEVYDGTEFWKAPTEGAVRTWDAQPAVVVERRLKSKPPIRDVDLAAA
+WSLGNVLRDVEPAFATKDPVARHAAVVESGAQLRGRAFRTLTPTAYVHRTDRRSPIEPFR
+LTLTLSTAVPDRAILALGQSRHLGCGLLVPTDIPGSTQERS
+>PROKKA_02168
+MGGLVISADFPLGVYTGHGSDGGAERFPDVARLFSALVQAAAAGTLSTGDPEAPFTAESL
+AALDWLEEHPPDALVLPGHTPVAPGVRRFAYRKEGVFLKEVGKTNYKVTGRPVSDGTALG
+GPVQWVWDDGPSGTDTQVCSTLEQLCADVPHLGEASSPVRLTVHEGEGLPAPTHRCDRNA
+SLRAVPGAVRQAMPNPGRRAELDRAHAATTLGRKPSASGDKHTTSAVPHAALPPRDHLRS
+GIFASVEQHEPDVPWTQVLAVPVIGANSTVPEERYVSVCVALHRALVSRLGPDAPPEITG
+RYAPSDAPPANRVALHLVPGDLPALPFSDGRDRFLVLVPRGMPGPALGMLASAVAGVRRV
+VTSEHQLTVAPEEIEVYDGAQFWKAPPEGAVRTWDAQPAVVVERRLKSKPPIRDVDLAAA
+WSLGNVLRDLEPAFTTKDPVARHAAVVESGAQLRGRAFRTLTPTAYVHRTDRRSPIEPFR
+LTLTLSTAVPDRAILALGQSRHLGCGLLVPTDIPGSTQERS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002186.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002186.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f24e18779de18569009b6d1fb6ec8571a1c5ee28
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002186.fa
@@ -0,0 +1,12 @@
+>PROKKA_02250
+MTWISANLDFILSLTWRHIAIASPVVLLSLLISVPLGRLANATGWGRRLIVGGSSLLYAI
+PSLAVFVILPGLVGTKILDPLNVVIALTLYGVALLTRSASEAFDAVDDELLTAATAQGHS
+AWQRFWRVELPLAGESLLAGTRVVSASTLSLVSVGALIGVQSLGTLFTEGYARSFVTEIV
+VGIVGTVILAVVFDLVLVALAALLMPWTRRAKVRKASGRRRSSQDTTTTALATVPDLAVQ
+EGRR
+>PROKKA_00457
+MTWIAENLDLILDLTLRHVALAVPAILLSVLIAVPLGRAANVSRWGRRLAVGGSSLLYAI
+PSLAVFVILPGLIGTRILDPLNVVIALTLYGAALLTRSASEAFDALDPDVLHAATAQGHS
+PSQRFWGVELPLAGESLLAGTRVVSASTLSLVSVGALIGVPSLGTLFTEGYARAFLTEIL
+VGIAGTVLLAVLFDAALVALAAALMPWTRRGRRTVPAPEDARHDAALTDAVTDPVTAPAE
+GVTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002190.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002190.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc296c88da689db0aa03ffd0f32eaf1edc713e03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002190.fa
@@ -0,0 +1,16 @@
+>PROKKA_00018
+MATPRKLPRGITLNPSGRYRVKLYAQDREFSLGTFAALADAKAALAVAQGEVARGTFIPP
+AERRRALKAEAEAASARAAAESRTVRQLADAFLAWKEGAGLAWGSVYTYRRHLEGHFLPE
+FGDRAVGAVTTVDLNAWLDRLESDHGASVAPEVHGTVTALFKFAAGQARDLPRGFTPWIT
+ASPVPALTRTRRREHRQVTILAPSELARLSELMTYPEDRALILTAGWCALRIGEALALRR
+RHVVTDDAGRLMLRIETQVQARGRGLYEAPPKSEAGRRTIYVPALAREALTAHLAQHVGA
+TAEALLFSRRGGGNRLNNPNTIGKRLKSAVDLLNREREDAGAEPLGRFTFHGLRHTGLTR
+MGQQGATEAELMAFAGHSDPKAVRIYQHAERNRLAALADRMTGEDA
+>PROKKA_00034
+MPKPQRLPRGVDRLPGGGYRARLTVDGYQHTIGSFATLGDARAALDIARGEKARGTFVPP
+AVTRARLKAEKEARRAQAAADSRTVRDMAEAWLSWQTERGLKLGSVYTYRRHLEAHFLPT
+FGDRPVGEVTALDLNAWLDALEESKGHAGAAQIHRVVAALFKWATGDAAELPRTFTPWLL
+TSPVPPLAARRLRRPNLPQRNRETLTDAELSALADLMPEADRLAVLLSGWCALRIGEVLA
+LRRRHVTTDPDGTAWVRVESQVQARGSGVREESPKSDAGRREVPVPPVIAADLAAHLDTH
+AAPGPDGLLFPRVGGGNGLNNPNTVRKRFNAALAALNAQRAEAGENPVENFTWHGLRHTA
+LTRLGQAGATTAELKAYAGHSDGKSVEVYQHAERRRLAALIQDV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002193.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002193.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c2adf1bf5a57cb5d5a5f7f31b78afc998cf7626e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002193.fa
@@ -0,0 +1,12 @@
+>PROKKA_00241
+MRSLMRMRTPRDIAAGVLATVRRADPPVIWGAEPMNGGNFLYLWATAWARRRETGRPWLV
+RYKPKMEPWLTEFPALRDLTVREEDVSFRQERTVEWGQQTYQDWFFRDLLDFARERLLTS
+SGFQVRLKQVDRGAVVVNVRRGDYYSDPVHRANFGFDVAGYVRAAVARVPRDEAGRIILV
+SDDVDWCRENLGFLSAWGEVGTIPGEHDMFNDLAQLAGGRHLVLANSTFSYWGGYLASAM
+PVNDRPQSVQAPLHFNRLYARGESPLLLPQWQAIPDDAFI
+>PROKKA_02433
+MARCDLAAARGRALSLVRTQQPFVIWGAEPMNGGNYLYLWATAWARQRHTGEQWLVRHKP
+KMDPWLEEFPLLRALTVDEADVGWRQRRTVEWGQQAGQDFRFKDLRDFARELLLASESFR
+SRMAARPGDAMVVNVRRGDYYADAGLRAVFGFDIPGYVHAALRRIPAERQERVVVVSDDP
+DWCAANLGFLGRERSVVFMPTPHDMFEDLAQLAVARDLILANSTFSYWGGYLASARSAQE
+RPRTVFAPLHFNRLYSDGESPLLLPEWTAIPDDEFSTPDRIQGEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002194.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002194.fa
new file mode 100644
index 0000000000000000000000000000000000000000..06b4b3574e8bb6d44fa54040a4e2b5223f0a3624
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002194.fa
@@ -0,0 +1,12 @@
+>PROKKA_00299
+MSAALDRLKQQNAQSGSQQQLDSPETMEALTSILAAVEAQNARLDRLAEQQKKLAGFVKV
+MDEETTRRLERITASASTSSPSSDASARIASIESRLNEIASTLGEFAQSLNGESLNAASQ
+SLVAEAQRNHAATASAIEGLKAQAAANQKLVSQVGGAVQRIEKRTEERVVKAVEQVAGEA
+SATIAANLDASNERAERIIAATAKLEARQLWSAAAAMCLALLPVVVVVAGLWMGIAGLIT
+GAQWALDVDGSVWLGIGRWLVIAAGLAAAGYGVFASVRWVAGLVETWKGRGMPTWPNWRR
+>PROKKA_02367
+MSAALDRLKQQNAHEQPPQQLGSPATMEVLTSILTAVEAQNARLDRLAEQQKKLAGFVKV
+MDEETTRRLERIAAPASTSSPSSDVSARIASIESRQNEIASTLGEFARSLNGESLNAASR
+SLVAEAQKNHAATASAIEGLKAQAAANQKLVSQVGGAVQRIEKRTEERVEKAVEQVTGEA
+SATMTANLDASNERAERIIAATAKLETRQLWSAAAAMCLALLPVVVVIAGLWMGIAGLIT
+GAQWALDVNGSVWLGIGRWLVVGVGLAGASYGLFASVRWVAGLVETWKDRGLPKWPRWRK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002196.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002196.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40cd27428df721891887ccb75f8cf809c353e1b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002196.fa
@@ -0,0 +1,18 @@
+>PROKKA_00301
+MAKQENNPTSIGLTQYLDPSYWAWAAEDPNGAALLQQGAEAILAYVVQRLEATGCQVVEA
+YGIVHDKDEREVWSDTEKALVVEPKPEHLHAVIKFASRAKSAPLDRLAFGIGVEPQYVEK
+PGRGRYAFDNMLSYLTHVKYADKHQYAPSEVATVRGPDYLGIDAQRRETWLKGRAHVKKK
+IVAENFEDMRERVLQGEITRDQIMLTDELFDIYSRHQREIDDALSAYGQRRAYRAAAKLR
+AGEFSTHVVFVHGDAGIGKTRFATDFITEAINAANAHGERWQVYRAATGNPLDDWRGEEV
+LLLDDLRASAMDANDWLLLLDPYNASPAKARYKNKGEVAPRLIVITATIEPVEFFYYARQ
+KGNVDEALDQFIRRLASVVKVYRADDINRYLVQHIGKIEPYEWHQCSVPTAAHTPGMYGN
+AYHQNVGSRELTYGPETSAEHDAEGAVAELLGGLAVRSPDVPLALIGGAA
+>PROKKA_02369
+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/Orthogroup_Sequences/OG0002198.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002198.fa
new file mode 100644
index 0000000000000000000000000000000000000000..44cfa6de82f65db4948df54e74a98d00ae765814
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002198.fa
@@ -0,0 +1,6 @@
+>PROKKA_00304
+MTRKHLGFLNFGHWIHRPGAEPDARQALDDVVAMAVAAEDAGLDGAWLRVHHFQRMFSSP
+FPILAAMAARTERISLGTGVIDLR
+>PROKKA_02362
+MTKKHLGFLNFGHWIHRDPVGGRPAEPDATAALDDVVQMAVDAEAAGLDGAWIRIHHFQR
+MFSSPFPILTAMAARTQRIHLGTGVIDLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002201.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002201.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4268b24fe0a8a753279b580151f40c7601e1d1fd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002201.fa
@@ -0,0 +1,8 @@
+>PROKKA_00331
+MLLPLLGRLRVARPVGRPRTRPEAVLGDKAYSSRAIRTHLRARRIKAVIPEPADQQGHRR
+RRGSAGGRPVGLDSQAYKGRNVIERQYAHLKQWRGLATRYDKYAIVYRAAVVLNAVLAWS
+KRLSDMP
+>PROKKA_02232
+MLLPLLGRLRVARPVGRPRTRPEAVLGDKAYSSRAIRTHLRARRIKAVIPEPADQQGHRR
+RRGSAGGRPVGLDSQAYKGRNVIERQYAHLKQWRGLATRYDKYAIVYRAAVVLNAVLAWS
+KRLSDMP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002202.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002202.fa
new file mode 100644
index 0000000000000000000000000000000000000000..29bb970310ce3e693cd0df321d584a9d3f07995e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002202.fa
@@ -0,0 +1,25 @@
+>PROKKA_00367
+MVMSLSRVLWKVRSKAPTVTASVQGTVSVTGEGYTTIRDSTCGAGNFLNLAYAKLREIET
+DLLADQRRRTGSQDLSLDVSLDQRIHIDRFYGIEINWWPAKIAETAMFLVDHQANRQLAA
+ALGQAPVRLPIKITATIYQHDALTLDWSQALPKPAGRTFVFGNPPFLGDHTRTAAQLALM
+QAAWGEGKQLSRLDFVTSWHALTLRLLAERDGEWAFVTTNSIVQGDQPARLFAPIFAAGW
+RIKFAHRTFAWDSQAPGKAAVHCVIIGFTRDPGTKARLFKYEHARGEAREVPGVKTINAY
+LVDGPNVLVDKRSTPLAPDLPEVTYGSKPADAGNLVVTAEQYQAVMADPVMAPYVRPYVG
+AVELIRGQQRWCLWLADMDPDAPSHSPELKRRLEGVAAERAKSKAASTRDWARFPHLFRQ
+RGLVSDVPFVGIPEVSSEARAYLPVAHFEPDVIISNKVYGALDPDGIVFAVASSSMFITW
+MKTVGGRMKSDLSFSSTITWNGFPLPALTDKDRAALARAAEKVLEARALHPRRSLAQHYA
+PLGMDPALVKAHDGLDAVMDKIMGAPRRCRTELERQELLFARYAQLTS
+>PROKKA_02209
+MTKTEEQEASIAAAQLMASMFTALVGDEVDVPVGEEAPEDAEEEEFATQQASILLTRLLF
+LLYGDDAGLWEADLFQRWVEWDTTADNLGPQLDALFRVLNTPENRRRGVPDSLARFPYVN
+GGIFDGTSTAGFLTRDFRDALVAACRFRWTQISPAVFGSMFQLVKSKQARRGDGEHYTSE
+ENILKTIGPLFLDEYRARADRLIQNKTTTRREVIGLIEEIASNIYVDPACGAGNFLNLAY
+AKLREIETDLLADQRRRTGSQDLSLDVSLDQRIHIDRFYGIEINWWPAKIAETAMFLVDH
+QANRQLAAALGQAPVRLPIKITATIYQHDALTLDWAQALPVPAGRTFVFGNPPFLGDHTR
+TAAQLALMQAAWGEGKQLSRLDFVTSWHALTLRLLAERDGEWAFVTTNSIVQGDQPARLF
+APIFAAGWRIKFAHRTFAWDSQAPGKAAVHCVIIGFTRDRDAKARLFKYEHARGEAREVP
+GVKTINAYLVDGPDVLVQKRSTPLAPDMPEVVYGSKPTDDGNLIVTAEQYQAVMADPVMA
+PYVRPYVGAVELIRGQRRWCLWLTDMDPDAPSRSPELKRRLEGVATERAKSKAASTRDWA
+RFPHLFRQRGLVSDVPFVGIPEVSSEGRAYLPVAHFEPDVIISNKVYGAVDPYGIVFAVA
+SSSMFITWMKTVGGRLESRISFSSTITWNGFPLPALTDKDRASLAKAGQKVLEARALHPE
+RSLAQHYAPLSMDPVLVRAHDGLDTVMDKIMGAPRRCRTELERQELLFTRYAELTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002203.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002203.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a76b0dde09368f23201ddaf92b185cbf5e3998e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002203.fa
@@ -0,0 +1,6 @@
+>PROKKA_00374
+MSVTKGLLVRLEALPGKEDEVQEFLGIGRGLVEEEPATVAWFAIRLGPSSFGIFDVFPDD
+AGRDAHLSGAVAKALGEQTGKLFSEPTIEKLDVLASKLPA
+>PROKKA_01211
+MSVTKGLLVRFDALPGKEDDVKDFLDSGRALVAEEPATIAWFAIRLGPSSFGIFDVLPED
+AGRDAHLSGPVAVALGGQTGAGALFSEPTIEKLDVLGSKLPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002205.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002205.fa
new file mode 100644
index 0000000000000000000000000000000000000000..224ca86119e6fe8540c2bf3a1c6868c69d051b2a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002205.fa
@@ -0,0 +1,34 @@
+>PROKKA_00766
+MSADAWTGTATGDVAGRCHRDAHGVPTLVAASLPELAYLQGWHVATERAWQVDCEHRRVT
+GMGAEVFGPPAVANDVAARQMDLDGAARRAFDALDDAEDRAWFTRFADGVNAGLDAGARR
+APEFAAHGVKPLPFDPHTALALHLGYNVWLTNAPAALFRTLLAERFPALAAALISPRPDA
+DGSNAWAVRVGAEGAPLVAADPHRLLELPGVYQQVRLVVEAERPRDRVDVVGLAFPGVPG
+VPHVGQSEHVAWVTTSAMVSSLEMVLEDAPEGPEVLDARTERVHVRGGDPVDVRVAHTPR
+GRLVDVPGAGPVSMRFPAWDRADTGLPSARRLLTAASAAEACAVLDGHVEPVNRVIVADR
+RTVLTRHAGAVRRRDRRSAWGAARASALGRGSADGSLDQRWVRWPAPAAADDVVVAANEP
+HPDTACLTVDACAPWRSRRIREALEALAPQERTVDAMAALQTDTRTPGAPRAWLADAVDA
+LVADGVLAAESVPAWAGDAAAGSAAARWWLLVEHEVAAALIAHLPPASRALLGGPWAPWG
+DAAAWVGAALAERGPEPLRAALGITASTRDLVRAAVAAVDDAAEPPGPDGAARTWGEAHA
+LTPFLFTHEHPGGPDEPGLADVLDTIGSVRVGGTADAVCATSHAPGLAVGTHRGPVARVV
+FDLGDRTRSRWVVPFGASGLGGGHVTDQLDAWAAGRLLPVPSRPVPPSAGSGVAPARSVP
+GGAPPGRIVAEVGVGALGLTMTRVRPALDAPLIHALVTEPRAEFYGMRGHSVQDVEEVYD
+FLEFQPTHANHLVWHGGTLVALVQTYDPRAEEVGGAYEVRDGDLGFHFITAPGGLQGRAR
+ATAYRSIVDWLGARPGTRRLVIEPDVRNTRAVKTARALGFTVDREVELPGKRAALCFRDV
+R
+>PROKKA_00994
+MSADAWTGTATGDVAGRCHRDAHGVPTLVAASLPELAYLQGWHVATERAWQVDCEHRRVT
+GMSAEVFGPPAVANDVAARQMDLDGAARQAFNALDDAEDRAWFTRFADGVNAGLDAGARR
+APEFAAHGVKPLPFDPHTALALHLGYNVWLTNAPAALFRTLLAERFPALAAALISPRPDA
+DGSNAWAVRVGAEGAPLVAADPHRLLELPGVYQQVRLVVEAERPRDRVDVVGLAFPGVPG
+VPHVGQSEHVAWVTTSAMVSSLEMVLEDAPEGPEVLDARTERVHVRGGDPVDLRVAHTPR
+GRLVDVPGAGPVSMRFPAWDRADTGLPSARRLLTAASAAEACAVLDGHVEPVNRVIVADR
+RTVLTRHAGAVRRRDRRSAWGAARASALGRGSADGSLDQRWVRWPAPAAADDVVVAANEP
+HPDTACLTVDACAPWRSRRIREALEALAPQERTVDAMAALQTDTRTPGAPRAWLADAVDA
+LVADGVLAAESVPAWAGDAAAGSAAARWWLLVEHEVAAALIAHLPPASRALLGGPWAPWG
+DAAAWVGAALAERGPEPLRAALGVAASTRDLVRAAVAAVGDAAEPPGPDDTARTWGAAHA
+LTPFLFTHEHPGGPDVPGLADVLDTIGSVRVGGTADAVCATSHAPGLAVGTHRGPVARVV
+FDLGDRTRSRWVVPFGASSLGGGHVTDQLDAWAAGRLLPVPSGPVPPSAGSGVAPARSVP
+GGAPPGRIVAEVGVGALGLTMTRVRPALDAPLIHALVTEPRAEFYGMRGHSVQDVEEVYD
+FLEFQPTHANHLVWHGGTLVALVQTYDPRAEEVGGAYEVRDGDLGFHFITAPGGLQGRAR
+ATAYRSIVDWLGARPGTRRLVIEPDVRNTRAVKTARALGFTVDREVELPGKRAALCFRAV
+H
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002207.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002207.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34d38f7f4c19a6ba7f13bce8a261e688d1dfdd63
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002207.fa
@@ -0,0 +1,10 @@
+>PROKKA_00768
+MSAVTPPQTTVDGAAASAARRVELRPVGAQDHPLLHRWVTSPHAVYWEMTEAGLADVVAE
+YEAIAAHPHHHAHVGLVDGTATFLVEVYDPAHSELAGRYAGAPGDVGLHVLVAPTDTPVP
+GTTDLVMAAVVRWCLAQPGARRVVVEPDERNAAIRAKNLAAGFTELGPVALGSKTAMLSI
+ATPESFTASRIGVLAAGLDLTLPEPPLLLTPDRQVSA
+>PROKKA_00996
+MSAVTPPQTTVDGAAASAARRVELRPVGAQDHPLLHRWVTSPHAVYWEMTEAGLADVVAE
+YEAIAAHPHHHAHVGLVDGTATFLVEVYDPAHSELAGRYAGAPGDIGLHVLVAPTDTPVP
+GTTDLVMAAVVRWCLAQPGARRVVVEPDERNAAIRAKNLAAGFTELGPVALGSKTAMLSI
+ATPESFTASRIGVLAAGLDLTLPEPPLLLTPDRQVSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002210.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002210.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b1becedcb5ad765f1a412017e7a10a170d1b3e45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002210.fa
@@ -0,0 +1,12 @@
+>PROKKA_00771
+MKAYRGLAALGQAMPVDRDEYPQWTMTVRATWLLAPRLRRLTFAAEEFRTFTPQGCDEYF
+GLLTPPPGRALVMPDPAALNARRAVGRIPEDVRPDLRWYTVAEHRPSVGEIDVDVVVHDH
+AGPAGTWARTARPGDVAGFRTGTGAYRLPAAGESHLVVGDETAVPSIAAALAAQRRTPRG
+GRMDVVLEVPGRDHVPALEVPEGATLTVLHRGDAVPGALLTPHLEDLPAAPRDHVWACGE
+QSLATAARRVIVRRGIAPKRAIMFSGYWRVDGPRL
+>PROKKA_00999
+MKAYRGLAALGQAMPVDRDEYPQWTMTVRATWLLAPRLRRLTFAAEEFRTFTPQGCDEYF
+GLLTPPPGRALVMPDPAALNARRAVGRIPEDVRPDLRWYTVAEHRPSVGEIDVDVVVHDH
+AGPAGTWARTARPGDVAGFRTGTGAYRLPAAGESHLVVGDETAVPSIAAALAAQRRTPRG
+GRMDVVLEVPGRDHVPALEVPEGATLTVLHRGDAVPGALLTPHLEDLPAAPRDHVWACGE
+QSLATAARRVIVRRGIAPKRAIMFSGYWRVDGPRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002219.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002219.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a51db15d2daea34555c5a247b1756124a386bd91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002219.fa
@@ -0,0 +1,10 @@
+>PROKKA_01953
+MTTLQRLRAEVARRYAALGLPAWPDPHPDGAPPREEEYSRVTDPQRYRIAAARARVWAEV
+LAEAGAVVVPDPVRGIPLDEAGRADLAAPVDRALRVAPPAGVDGASPWWLLETDVPQDDD
+GGVLPVIRVAVGAPRQVHALLPDCGCDACDPGSDELLEAVDQAVVRADGTAEALGRVPGW
+SFEALTDACRDLAAGGRPRLPRGTRRWCGRAK
+>PROKKA_00433
+MTARARVWAEVLAETGAVVVPDPVRGIPLDEAGRADLTVPVDRALRVAPPAGVDGASPWW
+LLETDVPQDDDGGVLPVIRVAVGAPGQVHALLPDCGCDACGPGSDELLEAVDQAVASAVG
+TGVNLRGRHGLRRRDWHVHWRSDGTAEGQGRVPGWPFEALKDACRDLAAGGRPRLPRGTE
+ATVRAGWFPEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002221.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002221.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e89f0d03f69f944467e94f5acdcadf4e2a2457c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002221.fa
@@ -0,0 +1,12 @@
+>PROKKA_01979
+MTARPVAPGIHLVQHANVNCYLIEDTDGLTLVDAGLPAVWRPLGHAVRALGRRPEDIKAL
+VLTHAHFDHVGAARRLVERLGVPVYAHRAEHYLAAHPYSYAHENPRALYPLRHPAALPIL
+GSMVAAGVFTVKGVRATAELTPGETVPVPGRPVVVPSPGHTHGHCALHLPDRDVLISGDA
+LVTLDPYTGRRGPRIIAGAATADSGLALRSLDALAATGAGTVLPGHGEPWHSGVASAVEE
+ARRHGPA
+>PROKKA_02227
+MTARPVAPGIHLVQHANVNCYLIEDTDGLTLVDAGLPAVWRPLGHAVRALGHRPEDIKAL
+VLTHAHFDHVGAARRLVERLGVPVYAHRAEHYLAAHPYSYAHENPRALYPLRHPAALPIL
+GSMVAAGVLAVKGVRATAELTPGETVPVPGRPVVVPSPGHTHGHCALHLPDRDVLISGDA
+LVTLDPYTGRRGPRIIAGAATADSGLALRSLDALAATGAGTVLPGHGEPWHSGVASAVEE
+ARRHGPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002223.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002223.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eaa69d63c939b341a9b94f9a93d7e9ef8461da0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002223.fa
@@ -0,0 +1,4 @@
+>PROKKA_02024
+MRVTSPQTLISAVFEAAERATNDLTHLIPDLDRDRAEYAVASVLLEEAWLSNR
+>PROKKA_01147
+MRATNQQALITAVFEAAERATDSITHLVPDLDRDRAEYALVSVLLEEAWVAQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002231.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002231.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d932aaf0c9360f935d1f22fc48e5056b1a0bad0f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002231.fa
@@ -0,0 +1,6 @@
+>PROKKA_02300
+MITAVSSAWVGAMSTEGPGASSSAKSRVPAGRSPAPVETTYTVGPPSDPPAWAAPLTAAS
+AAVSTVMSTAVSESDR
+>PROKKA_00284
+MITAVSSAWVGAMSTEGPGASSSAKSRVPAGRSPAPVETTYTVGPPSDPPAWAAPLTAAS
+AAVSTVMSTAVSESDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002234.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002234.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b468ee922553ce81097a45b030fc918714337ab8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002234.fa
@@ -0,0 +1,16 @@
+>PROKKA_02303
+MPEAVIVSAVRSPIGRARKGSLRDLRADDMAAQMVTAALDRVPELDRAEVEDLILGCGAP
+GGEQGGNLGRVVAVLAGLPSVPGTTITRFCSSSLQSTRMAFHAIRAGEGDVFVSAGVESA
+SRLDRGASDEDTRNPAFRSAWERSARRAEGDAPVWTDPAEEGELPDVYIAMGQTAENVAQ
+LRGVSRQAQDEYAVRSQQLTEKSQASGFWDREISPLVLPDGIRVTRDDSPRAGTTLEAVS
+QLNPVFRPDGTVTAGNACPLNDGAAALVVMSDTRAAELGLTPLARIVSTGLSALSPEIMG
+LGPVEASRQALARAGMSIDDVDLVEINEAFAAQVLPSAEDLGIPLDKLNVNGGAIALGHP
+WGMTGARITATLLNSLREHDKHIGLETMCVGGGQGMAMVIERLS
+>PROKKA_00287
+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/Orthogroup_Sequences/OG0002241.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002241.fa
new file mode 100644
index 0000000000000000000000000000000000000000..77556c9d6462b0a037ddb6f8851a5523564bbfe1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002241.fa
@@ -0,0 +1,20 @@
+>PROKKA_00094
+MADIDLTAAPATPEAATGQLTPLASLGRAAAVFGDREAVVYGALRWDYAQFAAHVQSFAR
+ALRGRIEPGQTVAAILPNVPAMLAAHFAVPLAGGVLCALNPRLTPRELEYILEHAEARVV
+LADADVAEDVRGVVERIGTGAAVAEVVDPEAGHAQPDDGRLTYEALVAEGADGADLPWTV
+PDERLPITLNYTSGTTGRPKGVRYTHRSAQLTAVANVLSQEFDAQTRYLWTLPMFHCNGW
+TRPWSVTAAGGTHVCLRAVRQDPIWDAFEREGITHLCGAPIVAASIIEAERAHPVEQKIR
+MAAAGAAPPPSVIAALEGLNITPVHVYGLTETHGPFTICEPQPGWAELSRPDRAQVMARQ
+GVALPLVGEVAVVDMDMNPVPADGQTLGEVVMRGDGVMLGYFKNPEATEEAFRGGWFHSG
+DLGVMHPDGYIQLRDRAKDIIISGGENISSIEVEGVVAAHPAVADVAVVGVQDDRWGERP
+VAYVVFRSGVERPDDAALRAHCREHLAGFKVPDRFVPVEEMPRTATGKIRKNELRQG
+>PROKKA_00065
+MDVTQDTLAPELAVARTEPLTPLAFLGRAAAVFGDREAVVYGDMRWSYAELAAHVQSLAR
+ALTARIEPGQTVAAILPNVPAMLAAHYAVPLAGGVLTALNPRLTPRELEYILEHAEARVV
+LADGDVAAEVRGVVEQIGTGAAVAEVVDAAAGHAAPDAGLLTYDALLAEGAEGEDLPWAV
+ADETAPITLNYTSGTTGRPKGVRYTHRSAHQTAVANVITQGYDGATRYLWTLPMFHCNGW
+TRPWAVTAAAGTHVCLRAVRMDPIWDALDDEGVTHLCGAPIVAAMIIESERAHPVDREIR
+MAAAGAAPPPSVIAALEGLNITPVHVYGLTETHGPFTICEPQPGWAELDRAARAQVMARQ
+GVAMPMVGQVAVVDMDMNPVPADGRTMGEVVMRGEGVMLGYYKNPEATAEAFRGGWFHSG
+DLGVMHPDGYIQLRDRAKDIIISGGENISSIEVEGVLHAHPAVTDVAVVGVSDERWGERP
+VAYLVLDPASGPLDVEALRAHCREHLAGFKVPDRFEVVEEMPRTATGKIRKNELRRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002244.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002244.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc530b3dad6c77baabe66a875e069a8293479ce5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002244.fa
@@ -0,0 +1,24 @@
+>PROKKA_00117
+MNPTFSRRTGLRTLAAAVVAGTVTIQAPAVLARTAASTPAAGADGFRVLPYLMEPTATSM
+DLVWFSEREVPGTVVVSGPGLGDNHRGGRTRPAGTRVSTPEFQPLLAYTEKERAQSIKGL
+AQGSWLLGPASYKHRVSLTGLKAGKEYRYTVTQGGQRHTAAFRTADDGANWSDLRLIAFS
+DTETEPYGRIENREWELSMVTPYTEGSLPRPGEGSVWHQTFGSTTRYGQFTLKYPLTQDV
+ALRENIRHIDAAAPDLLLVAGDLGQGGGYQPGWDEFFRHFAGEHSDIASRVPLITSLGNW
+ETFAALNDGYGTAADRSPVVRSRNKYHAYFERTSAGTDRENPRFRGSYYRTDHGPLTILT
+LDSTNGVPDESVGAGLLSGAPFSGDDRNLTAATMPSDTQGSFTQAEYEAAFPTVFPGSTP
+ADADLPVLNPGHEQWAWTERQLADARAAGRIVIVEFHHAAYSVGVHGTPPNHEFPDDQSG
+VAMRVYTPLFEKYGVAVVISGHDEMFQRSWVDEDGDGVGFHSYDVGVAADGLRGEQYAKD
+ASGQWKPVRFNTHMEWTANTHEPETWADVDGVRQLVDGGMHYGHLQIDLKRRGREAEMTL
+TPMYVFPILDDEYRLVRTERRAYDDVQTVRFDRRGVPKPRR
+>PROKKA_00085
+MNPAFSRRTGLRALAAAVVTGTVATTAPAALAKTAQHAPAVPAGADGFRVLPYLMEPTAT
+SMDLVWFSERPVAGTVVVSGPGLGNNHGNGRTRPAGTRVSAPELQPLLAYTQKELTQTLT
+GLPQGSWLLGAENWKHRVSLAGLKPGKEYTYTVTQGGRRHTASFRTADDGRDWSDLRLIA
+FSDTETEPYGRIENREWELSQVTPYTEGSLPRPGEGSLWQQTFGSTVRYGAFTLKYPLTQ
+DVGLRENIAHIDAADPDLLLVAGDLGQGSAYQPGWDEFFRHVAGEHSDIASRVPLITALG
+NWETFAALNGGYGTPADRSPVVRSRNKYHAYFERTGAGTDRQNPRFRGSYYRTDHGPLTI
+ITLDSTNGVPDESVNGPLSGAPISGDDRGLTAATMPTDTQGSFTQAEYEAAFPKVFPGST
+PADADLPVFNPGHAQWAWAEEQLADARAKGQIILVEFHHVPLSIGEHGTPPNHAVPDDQS
+GVAMRVYAPLLEKHGVAVVISGHDEMFQRSWVDADGDGVGFHSYDVGVASDGLRGEKYAK
+NAAGEYEPVRFNTHMEWTANTHEPETWADVDGVRQLVDGGMHYGHLQIDLKRRGQSAEMT
+LTPMYVFPILDSQYRLVRTERRAYGDVQLIRFDRNGVPLPRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002247.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002247.fa
new file mode 100644
index 0000000000000000000000000000000000000000..383dd00cde92fb071c48b3b141519126d304bb4d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002247.fa
@@ -0,0 +1,6 @@
+>PROKKA_00224
+MTDEQDAVDGRAGVPSWRVIADRISAEHRAADDGPIDEVDPADFDLDEDCCLGGCCAKGI
+AYLDAVEQAAARRARRTRA
+>PROKKA_00172
+MTDEQDAADGRAGVPSWRAIADRISAEHRAGDDGPIDEVDPADFDLDEDCCLGGCCAKGL
+AYLDAVERAAARRARRTRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002249.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002249.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec65a9acfe9e00222c90d4e79f6ddf97de1ebffb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002249.fa
@@ -0,0 +1,6 @@
+>PROKKA_00290
+MADMGNKFDKLKGDAKEGLGKATGDDRLRAEGKTESTAAGAKDAVQNAGDKVKDAAAGIK
+DGLSKDR
+>PROKKA_00236
+MADMGNTFDKLKGDAKGAVGEATGDSHLEAEGRTESAAASAKDAARSAGDAVKGAAEGVK
+NAVSRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002251.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002251.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da164a4b141b063a2fc54e81f61d386a9fd5f826
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002251.fa
@@ -0,0 +1,11 @@
+>PROKKA_00343
+MQRIVPNIWCDGTADAAAEFYLRAFAGLPGTAHVRTDRYPTEGLLDFQRPLAGKTLTQEL
+DLAGHRFILVNAGDEFAPNPSISFFVNADPSRMDDPRGTLDALWAELTDGGRVLMDLGPY
+PHSEHYGWVEDRHGVSWQLMLTDPAGDPRPVIIPQLMFCGPAQNRAAEALDHYLAVFDDA
+TPGQRVTYGDMGHVPEGGPVEAGSIVFADARLRGEWVAAMDSAVAQDFTFTEGVSLMVQC
+RDQAEIDRLWEALSAVPEAEQCGWLKDRWGVSWQIVPEDMGELMERPGAFEALLGMKKLV
+IADF
+>PROKKA_00477
+MSDAAAGAPQLISPFLWFHDGAEEALRYYVDVFPDSEIEEIQRYPDESLDPHYAGMAGKV
+ISAWVRLGGVRFGALDGGPAFTLSEAVSFVVACRDQEEIDRYWAALSHVPEAEQCGWCKD
+RFGVSWQIIPADMGRLLQSPAQIQAMMAMRKIEVAALEALA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002254.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002254.fa
new file mode 100644
index 0000000000000000000000000000000000000000..832cab49f8ac67064de7dde9b79d0f819fd8a091
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002254.fa
@@ -0,0 +1,8 @@
+>PROKKA_00350
+MAPRPTPIRSVLQVFALDCPDPPALAAFYAGLLGWRVVEDRPDDEWVNVLPPEHEPQTMK
+LAFQLVPDHREPTWPEGDVPQQAHLDFHVPALAEAVPLAEAAGARRHPVQPAEDGSWVVF
+TDPAGHLFCLCQA
+>PROKKA_02481
+MDTQNAPVARLAMITLDAPDAAALGTFYQAVLGWPVAYEGDGVVMLAGPGGVNLGIGTVE
+DYTAPRWPDTGRKQYHLDLAAEDVAAAAARCVALGATRPDHQPGETWTVLLDPAGHPFCV
+TDAANWG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002260.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002260.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bd52e8b98142e06ea13f37bba9e215ef25b454d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002260.fa
@@ -0,0 +1,4 @@
+>PROKKA_00473
+MTVAITRLDPVGADRAEPIALLTGSAWPFPVRPHVTRPVAKEAIEDGGRHHTLSGHQLPM
+>PROKKA_02196
+MDVTFTPLDPAGADRDALVALLTENAWPFHTRPRVTRPEAEKAVDDGS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002261.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002261.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5e3bfb5d63bd0df9ba5e7ac315158ea849debf2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002261.fa
@@ -0,0 +1,12 @@
+>PROKKA_00484
+MVTHTDLMTIGEFSSLSRLSVRMLRHYDAHGVLVPEHVDAHSGYRRYAPAQLRDAADIRN
+LRDVGLGVSAITALLAARGTSTWTDALALQRCTLVEELHAARERLSLIDRMLTPGEIPMT
+IQLNRTAVPAMTVVALRGTVPSYSDEGRLWERLMPALQQQGIRPVGPCGVIEHDDEYREA
+DVDLSVYCPVAPGTRAEGPLVVLQLPERDCLVAHVIGPYTQISQAHDLIVQRMEAEGLAA
+RQDGTLASNVFNRYLVTPDQAAPEDLVTEVCRPLA
+>PROKKA_02684
+MSRRMLRHWEQEGLLSPALVDPVTGYRRFQATQLGRIRAIAELRDLGFSLSEIRQLLDPQ
+IAHSSLERILMQQADRLRDQITEASARLAQVQHRVDTIQKKAQEISMNLSLTPLPELSLQ
+GASTTVLDETDIGSAVARLRDLVPHDQGDLILLFDGTSPDQITVTAATADGATTPGLQPV
+SAPLAPQGATVTFPTPPSSVADAWVLIDAELEKRGLASGGVYRQIISPDGSTTLQAAVHA
+RD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002262.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002262.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2fd656172ef6dac3079b03887c716fba178197d0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002262.fa
@@ -0,0 +1,7 @@
+>PROKKA_00491
+MDEDQGKILATHRQELRRGTLVVACLLACRTPRYGYALLEHLADARLDAEANTLYPLLRR
+LEGQGLLQAEWNTDEPRPRKYYRTTPEGEAIVAELRGDWLRLTDSMTRLGKDPS
+>PROKKA_00765
+MNEPTDRPPSGTAPEAWPSAWVRAALEPAILGSLAGGPLHGYGIAHALADHGFGRLRGGS
+LYPVLGRLEEAGHITARWAPGDAGPGRKDYELTDAGRAAYRDAVANWRRLGDALADLGAT
+PRLTAQEGTAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002265.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002265.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a408961126aaf06eedf7ad72702a8366e9b0ab0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002265.fa
@@ -0,0 +1,12 @@
+>PROKKA_00510
+MTATPRPAARRFLEVDVFATGPLTGNPLAVVVDAEGLPAERMQALAAWTGFSETAFLLPP
+TDPEADYRVRIFTPREEFDFAGHPTLGSALAWLHAGGTPRTPGRLVQECGVGLVPVTVAD
+DGVLAFATPPLRRSGPLNEADVVRIAAGLGVEREAIVDHAWGENGPAWQLVRLTDADAVR
+ALRPRGHAELKVGVVGLEAAGAETACEVRAFAYGSEDPVTGSLNGALAQWLRGAGLVSPR
+YVAAQGSQVGRRGRIHVHDDGARIWVGGRAAVLVDGTIAL
+>PROKKA_00444
+MTESHAPFPDSSPARPRRFLEVDVFATGPLTGNPLAVVVDAEGLTDGQMQAVAAWTGFSE
+TTFLLPPTDPAADYRVRIFTPREEFDFAGHPTLGTALAWLHTGGTPRTPGRGGGSTALVQ
+ECGAGLVPVTLAGDGLLAFATPPLRRSGPLGEEDVRAIAAGLRIDRDAILDHGWGDNGPG
+WQLVRVADAEAVRALEPRGHEELKVGVVGLEPEGAETAYEVRAFAYGGEDPVTGSLNGAL
+AQWLRGAGLVPPRYAAAQGSQVGRRGRIHVHDDGARIWVGGRAAVLVDGTLTL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002271.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002271.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0758a26af28c2d16489a2a718981be786d79152
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002271.fa
@@ -0,0 +1,10 @@
+>PROKKA_00558
+MSETIERAYPHAPTADDAPLDTAALAVCTTVLQQGAADLRRRFGPVLGEAVVDRQIEDSL
+EELRRSGVPRTHRESTAIHFAESRLLALAETTGVVEPSVPRVLFVCLQNAGRSQLAAALL
+AERAGDAVRVSSAGSRPTPEVHDDVAPVLSEIGADPAAAYPKPVTPELLAAADYVISLGC
+SDECRERTGVEVRDWPVGDPAEADWERLQEIVADIERRVDALWAEIQGRFAA
+>PROKKA_00485
+MAEAHPAVAGTGPSPSTGPLPRIGEHVGILAHGAAELRRVFGPALGEETVDRIVEESAAG
+LSPAAADPAHRESIAVRFAHDRLASLADARGVTRSGVPHVLFVCVQNAGRSQLAAALLAE
+RAGDAVRVSSAGSQPAGRIHGNVQPVLTAHGADPARIFPKPITEEVLASADYVITMGCGD
+DCPVRLGQDARDWPVGDPAEVDWDRLQEIVADIEVRVDALWREISGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002277.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002277.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e2c72d7c4e04fa27a0087402e0281ff60612b368
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002277.fa
@@ -0,0 +1,8 @@
+>PROKKA_00644
+MSGGAQSVSVRVHGDSILGQECLKSMMWPWSVERLGLPCVGLSWGVPGETFKVQGAYARE
+PVRYEDLNFQEIGLVGEDFGRGRPAWPDRCFSLELFPEYSPEVAWLRLRVVEEAGAQVFR
+AQVTLRPRSEGRGCEADLDWWESRLGALPAQMREWARS
+>PROKKA_02224
+MSGGAQSVSVRVHGDSILGQECLKSMMWPWSVERLGLPCVGLSWGVPGETFKVQGAYAQE
+PVRYEDLNFQEIGLVGEDFGRGRPAWPDRCFSLELFPEYSPEVAWLRLRVVEEAGAQEFR
+AQVTLRPRSQGRGCQADLDWWESRLGALPAQMREWARS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002281.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002281.fa
new file mode 100644
index 0000000000000000000000000000000000000000..86cc60c84ca16584185b3dc28baa2274314bfb7f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002281.fa
@@ -0,0 +1,10 @@
+>PROKKA_00713
+MTQRRTRWRSAASQDAEYRAHWKAAASADVGTPDALTWAVLGDSAAVGVGAARVEESYVA
+QVAAGVAERTGRPVRVLNLAVSGATAAHVLADQLPLLPADGVDAVTCVVGGNDVAWPVRF
+RVDRFAAPLEKIAQRLPAGATLGTVPVFRIPPYESRVECANAAVRVIAARHGLGVADVHA
+ATRRTSLRHQVSMLSHDLFHPNGAGYRDWARAVLPEVLRQVRGEAPTR
+>PROKKA_02032
+MPSPSGWQAQHDADYRAHWHALAARADPDALTWVVLGDSAAVGIGAESVERTYVAQVAER
+VAAETGRPVRVVNLAVSGAMAKDVLADQLPLMPASGVDAVTCVVGGNDVTWAWRFREAAF
+EEPLEAIARALPAGATLGLVPTFRIPPFEARVRRANTVVRRVAARHGLGVADVHAATWRR
+NLRHQVSRLARDLFHPNGAGYEDWAAAVAPEVLRQVRGQAPAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002285.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002285.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2c2ae3e168f092964d3030eb310b92ef3ff4028
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002285.fa
@@ -0,0 +1,14 @@
+>PROKKA_00773
+MAGGEAAVAWILGALRRELGAANLGEEDLEIVVERDRVWGSLWTVTAQGRRFWFKRPHAC
+LRREVPLRRVLSARAPGELLSTVAACAETGWQLTADQGPVLAQRAREDGPSHYVELARSL
+ARVQKSLTAADVAELRNIGLPVFETGDAVARLDEQLGWFSGLPAGHPAQCTAAERERAIE
+GMSVLVERWAVDARMLEGVVPELSVDHNDLHGGNAFVTAEGVRLSDWGDTVLAHPFASLR
+ALLVPVRNVFETEAMEQIRGAYLAEWGLGEDVGDVLDLAMMLAVPQRLSCWSALADADAW
+AEYAEYIAPLWREIGTPVAEVEVP
+>PROKKA_02404
+MTGTGVLDVAGRTAARDWIAGVLDLPAAALTVRVVRERSWGDVWRLSSPAGVHWFKAPHP
+RLRGEVPLRALLESRAAERVLPLVAADHERGWQLTADAGRTLAALARDDAGAPRPGEVAR
+LYAGLAGALAAMQEAVGEDDLRGRGLTEFDPAKAELSLLRELAPFRALPAAHPAHCTAEE
+EARAVAVRAALAMRWEDCGGPADPLGLDHNDLHGGNAFLGADGRVLVSDVGDAVLGHPGA
+SLRALLVPVRAEHGADAAETVRTAWLAARGQDHAAGRERLELAMLLAVPQRLRAWGALRS
+PETWAAYAEWITALWRDIGTPVDQLTTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002289.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002289.fa
new file mode 100644
index 0000000000000000000000000000000000000000..01a6f65df2934502d2c7a60140f1a2c5aae646fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002289.fa
@@ -0,0 +1,14 @@
+>PROKKA_00883
+MPDSPAPPGAAPSELVPRAFAERIARRPADPLLAAAGGEAVSGEAWLARLPHLVEERLAA
+WNLTLDPDAPGAPWTGHGALVLPVRRHTLRPAVLKLTWPHLEARHEHLALRLWDGAGAVR
+LHAASPPDGALLLERLDADWPLTLEPVLDACVAVGGLLRALDRPATPQFDAVAVKAERWD
+GTLAAPVAAVPRRLQVQARSHLRRLVDSAPEPRLVHEDLHDGNVLAPLPDDGPSGAAPDA
+RRGHVARRGRWLAIDPKPVAGEGAYAVAPIVWNRPEVTAAAHNARIHVRLRADVVAEAAG
+LDEERVRAWTFVRLVLNAVDAAHEGPSADEWRARMIALAGHFAS
+>PROKKA_00825
+MPASPPEILVPIPPEFAADIADRPADPLLAAAPDAAAQPLSGEQWLARLPRILAGRLTAW
+DLTLDPDVPGAPWAGTSALVVPVRLPTRRPAVLKVTWPHLEARHEHLALRLWDGAGAVRL
+HAADPRDGALLLERLDAGRPLSAEPILDACEVVGGLLRTLARSATPQFDAVADRGARWLD
+TLAAPVAQVPRRLQVQARSHLRDLLDSAPPPRLLHEDLHDGNVLAAPSPADGGEAARGPW
+LAIDPKLVAGEPAYAVAPIVWSRPEATARAHHARVHVRMRADVVAEAAGLDGERVRAWTF
+VRLVLRAVDAAGRGEAGDEVRARMITLAGHFAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002303.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002303.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d31de96e09d3ac774fb299a72e40a33710300641
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002303.fa
@@ -0,0 +1,10 @@
+>PROKKA_01039
+MTKIAIITGSTRPNRLNRQVADWVLERANGRGDAAEYELVDIADFDLPLLDEPMPAAWQQ
+YANEHTKAWSAKIAEFDGFVFVTPEYNHSLAPALANALSYLNAEWANKAAGIVGYGSAMG
+VRATEHLRAILSELQVAHVQKHGMFSLFTDFKDFAEFQPTELQAASVDPMFDQLLSWTEA
+MKTVRQG
+>PROKKA_01321
+MRLGIVIGSVREGRFGAQVGAWVEEVARGLDTGGRDAEWDVLDVAAFDLPIMTDEGWAQD
+EDGPAEVHRWRDAVAACDGFVFISPEYNRNIPGAFKNAFDLLSAQWKDKALALVAYGGLG
+GVRATEAWRFTVAAYNMHVVGDSVQLVRRADFPDETFARTEHHDKTLSRVLTRLVDLTEA
+TAALRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002305.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002305.fa
new file mode 100644
index 0000000000000000000000000000000000000000..83d5cfa0bb90241acb94d1a31e0efb2f12312e47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002305.fa
@@ -0,0 +1,15 @@
+>PROKKA_01212
+MVLGFGGSTVLILVVGLVYATAIRALPRTGGGVLFAVLSAGRIPGFIAGWSLALGYIGII
+AMNASAVSLIFRVTFPGLLSHGKLLEVAGWEVYLAEVLVSILFIWVFALLNMKGVEFSGR
+FQFWAVVTMLTCIAVLGVSAVYAFLTKNIELPAAVPSGQSPLTSVVVILAIAPWALSSKV
+PLVRAWAAILRSPDLMDNPPLHGAGVGPPAGCRGRRTRMGGGLHLSDSTGSIRRCATPGR
+R
+>PROKKA_01871
+MSHVTSSPPATGPGLKKTLSSLDAYAMGFGAMIGFGWVVLVGGWLKDAGTLGSIIAIVSG
+GLIMTVVALVYAELVAAIPKAGGEHHYLLRGMGARWSFLGSWGITGGYISIVAFEAVALP
+RTAAYIWPEIESIPLWNAFGSDVYLVWALVGAGAAVVITWINYIGVKLAGIVQTIVVATL
+LVIGALLVFGAGTGGSVANFEPLFTDARGLFTVMIVVPFLFVGFDVIPQSAEELNMPPRR
+MGVMIIVSVAAATLWYIMVILTNASSMPREQLVNADLVTADAMAALFHSPAMANVLLVGG
+MAGILTSWIALLMGAARLLYAMGVSGMLPRWFGHIHPKYRTPSNAVLFIGVLSIAAPFFG
+AGALGWFVDSGSPSIVFTYMMVCIVFLLLRRREPEMDRPFRAGGATAGRVLGVTGVILTA
+GLLSLYIPGMPASIAPMAYAFFGLWWLLGLVFLFRIPRGITPGEDAEERLLERLARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002307.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002307.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f378455ee9e22c76c5667ecd1ec4a383f0821a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002307.fa
@@ -0,0 +1,10 @@
+>PROKKA_01272
+MVKKLEQNMGADAMRAATGRDHAGWRAVLQDAGAQQWSHPRIAAYLVEEHGVDGWWAQGI
+TVDYEQAHQGRLPGQQADGTFSVGLTRTVPGERLEALARVEAAVSAVHGEPHGRNLTASQ
+PVVRWRLPDGGRLAAAAQAPNKTGTPVNLTMQRLPDAAAVEPTRRALEELLEAARSGEGP
+VATPGR
+>PROKKA_02055
+MSTSPARGANLNAIAEATGLTFEDWAAWLDARGARDLTVHAEIVGLVLERMRSGETAEVG
+SPEWWAQGVTVAYEQHIGRRRPGQRADGTFAVTASRILEGTREEVHARAVGAVRAALSDG
+GALRGVGLAKEPTESATATRLFWRAVLADGTRAELATEPRPQTAGKPAKAAVVATHSRAA
+SAEEAAAWKAFWRNLPAAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002310.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002310.fa
new file mode 100644
index 0000000000000000000000000000000000000000..366222c5a2195c6037795b77e588e95591711bea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002310.fa
@@ -0,0 +1,12 @@
+>PROKKA_01311
+MTVQKFPVFPAGTLEHVCKLIAELYTGNELTRIMSEIPLRDDLGEGNTKWRRLACAVSKN
+QAHTQSGNAVIALVSASMRPERTLDRADAARLTRDQLNQVLSLVGYRVRDDGRVARASRA
+RSTDEAEKRTEHLRGLLERGGAHREVLTYCRPELLRKDYYEAVFEAIKGLGSRLRQLTGV
+DGDGYALVEDAMAGSTPRIRLNALQTRTQRDEQRGVANLTKGLFSAFRNPAAHEPRIEWT
+LSEQDALDVLGTLSMIHRRLDMATVEAL
+>PROKKA_02210
+MQRAGLTPVTIIKNRGSANEERIEVQAQLQNSSLAMFAIEDPLFEGDHVEMPDPRGGQMV
+KVVRKLVQHPMPANMARAFGGSNGYAEVTWGESAAVRQAPVRRLELEGLHPEVVRVSSAL
+FADEQFDSAVTEAMKSLEIRVRRLAASTLSGAPLMQEAFRPKEPKLDVAVEEGRSGEDER
+EGFFHLFRGAMVGIRNPKAHELAHGDNPFEALEALALASMLHRRLDIAAGRLECADDSVT
+VLDQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002317.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002317.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ffdeaa04ec87f643b565c1e563a58f7aa853c39e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002317.fa
@@ -0,0 +1,10 @@
+>PROKKA_02013
+MTTPAPTSRSDWAEYNAAQAGRGRIRPLTARAVDALAADADLGARHAVELGCGAGVEARH
+LLALGLTVSTIDADPSIAPAMAALAAGGALDHRTGRIEDWDPLPAADLVLANAALPFVPR
+HAFDAVWSRIRAALAPGGVLAVDLFGAEDDWSSNAGTYLTRPEVEDLVRGLEVVELTERS
+ERGPAFSGPKHWHVFTVIARARRRPSDRSPV
+>PROKKA_01290
+MGDTALMIATPTSSSDWNSYNAARAGTSAVRPLTERALTALRATHQNLSGLRAVELGSGA
+GIEARRLLQEGLTVHTIDVDASVEERMHELTSLGVLEHRTGLIEEWDPLPLADLILANAS
+LPFIPRAHFAPVWERLRQALLPGGILAVDLFGCEDTWASDQGTYLTLQEVERLLDALEVI
+ELNERNEEGRSFDGIKHWHTFTVIARRTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002319.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002319.fa
new file mode 100644
index 0000000000000000000000000000000000000000..14de5578abfdb66a36185d4ad91abc17d32a000a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002319.fa
@@ -0,0 +1,13 @@
+>PROKKA_02277
+MADAVQVCAFNSTYTASQGPAVPCSSSAREREDALLDALDVDPPGSWWSRAAELARPRTV
+VAGDPPREDWLAVPLRRDGPLATTGDLGRAAAVGLVIREDGPLWDEDLVRTLTPPPICPK
+VLEVRTPADWLRLVEAWPEAASKATAEILARHTGLDGRWLVPRWTAVAEQWDAVHLSIGA
+WARSAGVVQPVGEGSAWTMCAGWDPDATFWLTAQPTVASEQVLPTLTPAEALDGLAG
+>PROKKA_01291
+MKASVQDLLPGPRGRRLCLEAARMLSHRVADLVFWLGYELDPDRGISSLVMWPPGGGALE
+AGARPAVSIDQVAQALADLDLSGLTDGVVQAALVGSVMSARYWQEPDGEDVLAGHPDIHA
+ALEAVAAGVLGSAAARHWGSPRAAAQWVIDWRAFEDPAPVPRDARRVLAAWAREERRQEV
+RAAAEHPVDPTANFSGTWWSIPQGAVVSVGQIPTGLDLVEDDIGAEAATVIPVRGAGRTY
+EVRGPGDWIRLCRRFPLEVSASRRHDWYRVTGRSGRWVIPDWEQVASEWDAVHLTTLGYL
+SAATRALPVEAGVATVLAGWDPDTTVWLADAVRESEEPRQCWQRVSGDDGWARCVPVRDV
+GSEGPARGRGASPPVEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002320.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002320.fa
new file mode 100644
index 0000000000000000000000000000000000000000..70840d5ed5f5edb2e1ee7867ef93046948b6eca9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002320.fa
@@ -0,0 +1,6 @@
+>PROKKA_02324
+MTAFGIIWLIAVTLVSAVAVRGILRQSTGVHAADRNGSTSFLWFLVALAFLLTNLPSGID
+PFRAVGLHLGAAALLGFLLHVLTRGAPAARD
+>PROKKA_02187
+MTVIGIIWLSELTLVSGVAVRGLLLTHLPSGIDPFRAVGLHLGAAALSGFILHVLTRGSA
+SRAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002328.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002328.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ea7b11a54c914783578b34c847d1877a79a59c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002328.fa
@@ -0,0 +1,10 @@
+>PROKKA_02675
+MSNTERDPKEQVCENGPGAAPTGQEESLREARFTDGLSAGVAEAAGDAGAVVEILEPREV
+PLGGPRAMPVQRTLPQRARSLIGAWCFLDFYGPDDVSATGGMDVPRHPHTGLATVSWLFE
+GRIDHADSAGNWATVRPGEVNLMNAGTGITHTEYSTDDTSGLHGAQLWYALPDAHRFSAP
+ALHSHRPEPVAGEGWTARVFLGDLLGESSPVPTYIPLTGAELRLEPGATARIAVPQDHEH
+GLLTVSGAVTLQGADVPAAHLGYVGTGTAELTVTAGEEPVIALLIGGEPLGEQIIMWWNF
+VGRSHEEVVRWRSAYQQEMGFEAPEDGSPLASAAARALRGGDGALGSPVQGALLDALVGT
+AYDDGRAFPQFGDFPPDPKPPIPAPPLPNTRMRLRG
+>PROKKA_02487
+MDALRGAAYDDGRAFPQFGDFPPDPKPPIRAPPLPHTRMRPRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002330.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002330.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51fafcd38362217e3392e2caef7d28dfe781cae2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002330.fa
@@ -0,0 +1,10 @@
+>PROKKA_00051
+MAAVPDSLKLEGARFVGRSLRGARFIDSDLSHVRARGVMLDGADFDSPWLLDGEGSLVVN
+GVDVAPLVEVELNRRFPGRAQRRAEDAEGLRGAWGAVEASWRQATDRASALPDGAVDVSV
+EGEWSFSQTLRHLVFATDAWLSRGIQGAEEPFHPLGQPRAGAEDDGVDLAFFASTPPPYE
+QVLAVRSERLAQVREFLASVDDAGLDEERRHPWSPEYPETVRSCLHVILEEEWEHLRYAL
+RDLDALDDAAAQGR
+>PROKKA_01208
+MPALSAGACGTQRRAEDAEGLRGAWGAVEASWRQATDRASALPDGAVDVSVEGEWSFSQT
+LRHLVFATDAWLSRGIQGAEEPFHPLGQPRAGAEDDGVDLAFFASTPPPYEQVLAVRSER
+LAQVREFLESVDDAAAQGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002331.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002331.fa
new file mode 100644
index 0000000000000000000000000000000000000000..346e0a39bf2885071c955bb5b5edfe98fa048e72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002331.fa
@@ -0,0 +1,12 @@
+>PROKKA_00053
+MRLIALPSGESIPVLGQGTWGWGEDPGRRGDEVAALHAGLELGMTLVDTAEMYADGGAEE
+VAGEALAGRRDEAFVVSKVMPSHASRSGTIAACERSLKRLGTDRIDLYLLHSQGRYPLED
+TVSAFHQLVEDGKIRYWGVSNFDHRDLADLQDVPGSSGLATDQVLYNLSRRGPEYDLLPW
+CADHQLPVMAYSPIEQGRILHDTTLNDVAARHSVSPAAAALAWVLRRDSLCTIPKASSPQ
+HVRDNATALDVELTRDDLDALDRAFPPPSGPRPLEML
+>PROKKA_01995
+MTLPSGESIPVLGQGTWGWGEDPGRRGDEVAALHAGLELGMTLVDTAEMYADGGAEEVVG
+EALAGRRDEAFVVSKVMPSHASRSGTIAACERSLKRLGTDRIDLYLLHWQGRYPLQDTVA
+AFHQLVEDGKIRYWGVSNFDHRALAELQDVPGSSGLATDQVLYNLSRRGPEYDLLPWCTD
+HQLPVMAYSPIEQGRILDDTTLNDVAARHSVSPAAAALAWVLRRDSLCTIPKASSPQHVR
+DNATALDVQLTREDLDALDRAFPPPSGPVKSF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002332.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002332.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ccee810fa71c4ac54b7d8ded3f326897ec345d79
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002332.fa
@@ -0,0 +1,18 @@
+>PROKKA_00147
+MSTLRTHRRRAALGSFIGTTIEWYDFYLYGLAAALVFNVQFFPGQTAFGATLASFATLAV
+GVVLRPLGGIVAGHFGDRVGRKALLVISLLLMGGASMLIGVLPTFAQAGWWAVAGLVLLR
+CLQGVSAGMEWGGAALMSVEHAPAGRRGLFGSFTQVGSSAGMLLATGAFSLVKLVTTDEQ
+FAAFGWRLPFLASGLLVVVGLAIRLGVEDSAEFRVHRDVGTVSRAPVVELLRHHARPVLV
+TAGLRLGQNGLYYLVTAYLVSYLVLRGADDGVLVSAIMVASAIGLLSTPFWGAVSDRVGR
+ARVSRVGYALTAVAGWVLFAVVDAGALAVLPLVVVLVINVAHDSVYGPQAAWFSEQFPVR
+VRYSGVNLGYQLGTVVGGGFAPFIAALLYEAGGHTPWLIAAYLTLLATLSLIATRFARDP
+VARPETDLVADDAAILAPQADGPAAVVPADRAPVTLETR
+>PROKKA_00200
+MSTLRTHRRRAVLGSFIGTTIEWYDFYLYGLAAALVFNVQFFPGQTAFGATLASFATLAV
+GVVLRPLGGIVAGHFGDRVGRKALLVISLLLMGGASMLIGVLPTFAQAGWWAVAGLVLLR
+CLQGLSAGMEWGGAALMSVEHAPADRRGLFGSFTQVGSSAGMLLATGAFSLVKLATTDEQ
+FAAFGWRLPFLASGLLVVVGLAIRLGVEDSAEFRVHRDAGTVSRAPVVELLRHHARPVLV
+TAGLRLGQNGLYYLVTAYLVSYLVLRGADDGVLVSAIMVASAIGLVSTPFWGAVSDRVGR
+ARVSRVGYALTAVAGWVLFAVVDAGALAVLPLVVVLVINVAHDSVYGPQAAWFAEQFPVR
+VRYSGVNLGYQLGTVVGGGFAPFIAALLYEVGGHTPWLIAAYLTLLATLSLIASRFARDP
+VARPETDLVADDAAILAAQADGPAVDAAPGAAAVTARPDRAPVTLETR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002334.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002334.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bce6cafcbabc587753ef9aa98e1cee3d014e8266
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002334.fa
@@ -0,0 +1,12 @@
+>PROKKA_00307
+MRQDAGAQTVGNVVSTIAVSAGTGALAGSVLPGLGNVVGFAAGVVSGVAMAVPVADTDGD
+GQKDSVAEMAGDVAEGAWNWIRGK
+>PROKKA_00335
+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/Orthogroup_Sequences/OG0002335.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002335.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8edaa1574631ea706b4ab611ad8b32e2e98dd08f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002335.fa
@@ -0,0 +1,5 @@
+>PROKKA_00323
+MTQTPTPHLAGPSPVKVGLLVLAICAVGGVIIGAVAGLTDGGSVENMFIGAVYAGFIGFF
+LPGLPAALIAGLVAAARGRRRG
+>PROKKA_00343
+MDQDVATEAEQTVSEDGAVYAGVIGLFLPAALIAALVAAARGRRRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002336.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002336.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eff01f468d69dac052216f560020c258a870c6c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002336.fa
@@ -0,0 +1,8 @@
+>PROKKA_00324
+MPEYDFETYPTTPDAMAKYLQEREAAGNPMTGEEALAYSDWSRERGRAIQAKIDARKTPE
+EREEFRRFAEEFERQCLEDEKRFAEEAAREAAEDAERAAQGKRPIKRERDIVTPKGFSGI
+GVTPRGW
+>PROKKA_00344
+MTKYNFEAYPTEPESMAKYLHEREAAGKPITRAEGEAYIEWSLAKEQEITERKERMSPAE
+RAGHEGFQREEEPMGAIFDLEDARSEVEALVEAAEDAERAAAGKRPLKRERDIVTPEGFS
+GMGVTPRGW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002337.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002337.fa
new file mode 100644
index 0000000000000000000000000000000000000000..57d608ca88ab024900676a302cfd082b0f2ad39a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002337.fa
@@ -0,0 +1,14 @@
+>PROKKA_00327
+MGAPRELFAEHALRGEIVVLDYAAGRTRSGLPVRRHHVVVRAGDRLVHSFRWYVGAAREV
+FEVTLTFDEEWLPHRLWEPVAEAVRSARAPLAGEVDVPAVVPGAWDERPETVVVESGPGL
+DVAESLVEGLEVISASRKRWRSWSEADEVEQAVVRSMAPTLSARGGLRGRRTEVDVYAVL
+DEAVVVRRRWWGDQGTEIIEREVLRVPGRVAPWAMFVGMDVRAGWMREVSARRPVDAEAR
+SSDAEWEVIAGGERALGLLHGPRDVWAVSTGGGGLVAEWWQLPGEGLLGVFRDADSAQMM
+VGPVDGWTIYLLVLEAWLA
+>PROKKA_00333
+MHPTVALRHFTEPADGNVASASFREAFLGGQEVVEGFLLLSYEAFFTGRGLPGRRHHVIG
+WEEDLVWHSVRWYVGSGAEIVELTLTAEAGADLEIWGGQCDRMIRNVVCQGAPEPASNLC
+WPEVPADVRAQDSWEVVTEQGLNPPWLESLRAGYDAVQEQAPWSAWAREPSLEQRRVLEQ
+ELPILSGVGERSGQGFRIEACLDGRGGAVVVVVPEGEGDGTNVRRGVRTVPVSLVVPVLL
+TWAGLRADWLRDEVMEAPGDVAPTEMAELWRGRRGADGVGSEASADWWRWWNQEGEVVAE
+WVQPLHRAPLAVFRDESRCVGVPVMPGVLYSVLQATVQEIAGSPHM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002339.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002339.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8066cf4db547c65eaa3abf7fe5a33a8f0aa59714
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002339.fa
@@ -0,0 +1,12 @@
+>PROKKA_00345
+METFWGLTTPAWTAIYTLLTAGLLVAAIVAGLYAKRQWETARDAQVEATRPYVLVTLEPG
+ERSMAMVDFVIRNIGVRPAYNVTISIEPHLLRAREEGGNEMAAMRLLHEPTAMIPPGQVT
+RMFYDRMSDRSGRDDLPVHHTAVVSYVDSSGREWTDTFDLDLRVLEGGMFHSYDDLHTVS
+QTLKKMARTLDRSRVLKEGEMDVVAVTENRADHQVRTLLEEYHRQVEIANLHRGKPGYVD
+RVRSFDARAESIAEQLRALGVSVQGAPQD
+>PROKKA_01145
+MDDTFWGMSATGWTAYYTLLTAGLLLVAIAAALYARNQVQIARAAQREATRPYIIVTAEP
+SPIGWRVMDLVIRNIGQRPAYNVKVSLTPEPVRANETPGAPISEVQWLREPIPMLAPGQE
+LRTFYDAMEERLNSGRSDLPTSHDYSVEYDEGTVAAKKGKRDHRDSGVVDLNAMAGAMQP
+DVYNIHHVASALRDIKKEVAKMNRSGTYIQPASEVRDILDQRGPRTKPRSTVPGPLPAER
+SALRRLYDRFTGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002340.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002340.fa
new file mode 100644
index 0000000000000000000000000000000000000000..06fb6145069b1f8ebf253169c86dd763b97fe88e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002340.fa
@@ -0,0 +1,20 @@
+>PROKKA_00425
+MGKVRGDQAVQSLQPHKVLDSDSSHGRLIRQQGERVPTDGDFTLSDRAQKEIVKLFIASE
+SSLEGRTIGEWFSEDFFESNFWTYWATMFAFETWHSLAEMRRYLLRFVHAIDGLADFSAL
+KFNRYDQYDSMVKPLLAYLEPHGVDFRYSTTVRDVRVETADGKVRAERLLLTVDGVQQEQ
+EVGEDDLVSVTNGSITESTTYGDHHTPAPSTTEPGGSWTLWENLAEQSPLFGRPGVFYRG
+LPERSWFVSATATVESREVEEHIERLTQRPLHDGKVNTGGIVTATDSPWMLSFTVHRQPH
+FPTQRPDQTIVWIHALYSDTEGAYVKKPVTECTGEEITQEWLYHLGVPEDRIPEPAAQES
+VNTVLVYMPFITSYFMPRRAGDRPAVMPEGSMNLAFIGNFAESPTRDTVFTTEYSVRTAM
+EAVYTLFDVERGVPEVFASATDLRELI
+>PROKKA_01186
+MQYTAGNYEAFARPRPAQHAQETKAYIVGSGLAGLAAAVFLIRDAGVPGANVTILEKGEI
+AGGALDGLDVPEKGFVIRGGRELENHMECLWDMMRSIPSLELEDASVLDEFYWLNKDDPN
+YSLRRATVRRGEDAGHEGRFDLPKRAQKDLLKIFLAERAEMEGKRIDEVMGREFLDSPFW
+MYWRTMFAFEEWHSALEFKLYLHRFIHHIGGLPDFTALKFTKYNQYESFVLPLMHYLTEH
+GVVFRSGTEVLDVDFAHRNGEIRATAIRCRRDGAEETIELGEHDLALMTIGSLVDNSDEG
+DHHTPAALNEGPAPAWDLWKRIAKKDPAFGRPEVFCSSIEETKWESATVTTLDERIPAYI
+ERIAQRDPFSGRVVTGGIVTAEDSSWLLSWTVNRQPHFKKQPKDQIVVWVYGLFVDVDGD
+YVKKPLAQCTGEEITQEWLYHLGVPVEEIPELAATGARCVPVMMPYVTSFFMPRRAGDRP
+QVVPEGAANFAFLGQFAETGRDTIFTTEYSVRTGMEAVYELLDVERGVPETWGSTYDVRD
+LLEASARMRDGKKVEMPGPAALRGYLRGKLEHGEIGQLLEEHGLI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002341.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002341.fa
new file mode 100644
index 0000000000000000000000000000000000000000..687d42bc9e6c8d32223f2a377c5bc961e2abecbd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002341.fa
@@ -0,0 +1,4 @@
+>PROKKA_00620
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVISEPADQ
+>PROKKA_01018
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002342.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002342.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2dac01f898e307249adbf6935a0e41f9b835668b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002342.fa
@@ -0,0 +1,12 @@
+>PROKKA_00628
+MAINWRRAQYLLAEDLTDIPVRYIDELFGSNGIALGPENPQDVDTSVRRARMRRYLTTLD
+LDTNRADQQRFADVMAERYRKIALVHQHGNTDETQWKLERWTTLLRAAGFQVDTTALSVT
+WPPGPQMGTLAPDVLAHLNDPSAIEDHLERIHTTIDSDPRLAVATARSLMESTAKIVLTS
+RDKTYTATESLTKLVSRAQASLGMSPKDLGGEQPEVRRLLQSLQGIAAPISTLRNDTNVH
+HGAEVVPQWVRPRHARLVLGAAQLWCQTVLETLSDPTAPWRVTDAAAQR
+>PROKKA_00696
+MAINWRRAQYLLAEDLTDFPVRYIDELFDGNGIALGPENPQDVDTSVRRARMRRYLTTLD
+LDINRADQQRFADVLAERYREIALVHQHGNTGETQWNLDRWTTTLQAAGFRVDTTALSVT
+WPPDPQMGTLAPDVLAHLNDPSAIEDHLERIHTTIDSDPRLAVATARSLMESTAKIVLTS
+RGETYTATESLTKLVSRAQTSLGMSPKGLGGEQPEVRQLLQSLQGIAVPISTLRNDTNVH
+HGAEVVPQWVRPRHARLVVGAAQLWCQTVLETLSDPTAPWRVVDAAAQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002346.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002346.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6290ddc009612573a4eaaef9a956d9913f5038c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002346.fa
@@ -0,0 +1,10 @@
+>PROKKA_00637
+MSQLMGDAGGGPATPWSHLEFSTPEGPVLCHPTDPLPDLGTIMSVRTPRSHALSRHVPVQ
+TFSATNTDVVAVESGLEQELVLVLDRDPAQDRLVGQPLTVTWARQSGGTRRHTPDLLTLT
+HEGAVTVWDVRPEGRRDPKFWEAARCTRAVCEHNGWTYELFGGLPEVHAINLRWLSSYRH
+SMPWYADLRDTLERLACTNSATIGTLLGADDGSGELISAMWHWAWDGRLQLDLTRPLKTS
+TPVRWEPR
+>PROKKA_02219
+MLSLDRDGQVCLWDARPSRRQDEEFLEAARTTEACARLLGWDYRVHAGHGPAYEANLRWL
+SAFRALKPWYPEAEQRLGQLLAHGERSVQEVFAVDDGTGELISGLWHHVWAGRVETDLDS
+PLCGASILRWVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002349.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002349.fa
new file mode 100644
index 0000000000000000000000000000000000000000..686cb7355290b110dddcda707735da8403d21522
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002349.fa
@@ -0,0 +1,10 @@
+>PROKKA_00667
+MDLAPSSSPTIELSWHADLTPGQLDDLNRLFAAEYLEDFGEWDPDQPYGYAPHDMHVIAT
+LDAQTVGHIGWARRSITVGDHHVTIAGVGGVLVTPSGRGHHLGQRLMRAAVDSMRAHSDA
+EFGYLGCHESVVPFYVSCGWRRIVAAERYIGLNGQPSESAQGDPLLVMPLRNAKQPWSAG
+EIDLQGRPW
+>PROKKA_00699
+MDLVPSSSLKIELTWHTDLTPGQLDDLNRLFAAEYREDYGEWDPDQPYGYAPHDMHVIAT
+LDAQTVGHIGWARRSIAVGARPVTIAGVGGVLVAPSGRGHHVGQRLMRSAVDSMRVHSDA
+EFGYLGCDESVVPFYVSCGWQRIVAAERSIGRGGQPTQSTQGEPLLVMPLRGTEQLWPAG
+EIDLRGRPW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002350.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002350.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c1bc9e917efb72cb0d49224660c4fa6bcbcd956
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002350.fa
@@ -0,0 +1,6 @@
+>PROKKA_00668
+MHAPFYSRAIPVHQIATITCGPDDGMNHGLLNWFVTGLATSPDGLRINNGGQAHIDMSTT
+EGLRSVVVVDDLSQTEQLICAVRTTCSR
+>PROKKA_02016
+MHAPFYSRAIPVHQIATITCGPDDGMNHGLLNWFVTGLATSPDGLRINNGGQAHIDMSTT
+EGLRSVVVVDDLSQTEQLICAVRTTCSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002351.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002351.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c4e7941d6152f1ab9e22ae598968147ec1a8adf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002351.fa
@@ -0,0 +1,4 @@
+>PROKKA_00669
+MPRRDSHQDLRQKLEAVETKISHHLFQSPGIAESLRIVDQSTGKEADAVDAVLTSRGPA
+>PROKKA_02015
+MPRRDSHQDLRQKLEAVETKISHHLFQSPGIAESLRIVDQSTGKEADAVDAVLTSRGPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002353.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002353.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3d4df76726eafdd1daca2b9265391d4a1c3b3c7f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002353.fa
@@ -0,0 +1,13 @@
+>PROKKA_00695
+MSRRSLASLATAAAFVVTAVLGGAGPAAAGTTYSAPLRTAVASLPVAAENNAGYDRAAQF
+GDWKDANRDCQNTRAEVLIAESKTTPKFTTARKCTVATGKWVSSWDLRTHTSASTVQIDH
+MVPVHEAWGSGARYWTKAKRVAFYNDLGDARSLNAQTSALNSAKQARGPEQWLPPKNQCQ
+YIADWTAVKIRWGLKADATEKAFLVKKAASCANTTLKVTRY
+>PROKKA_02179
+MLGCSGCLGLVALGLLLLSLLVGGFTGSPSPSAASQAPDGRSAAPSAPDAPGDPAGSAPA
+PAPTPDRAEAPVSDRAEAPAPAPAPASAPAPAPGDAGEAAPSSPAAEAPAADGTALAALQ
+SLPVKGRAPKTGYSREQFGPAWADVDRNGCDTRNDVLRRDLADVVLKAGTNGCVVLSGTL
+HGPYTGEVIAFQRGPGTSTAVQIDHVVSLSDAWQKGAQGLSAGRRAAFGNDPLNLLAVQG
+SVNQSKSDGDAATWLPPLRSARCPMVARQIAVKARYGLWVTPAERDAMARVLRECPGQGL
+PAEGGPVDPSPETAAEPTPQAPAPTVQAPAPAPAAPAGGADPSFSSCRKAKAAGYGPYVQ
+GVDPEYAWYRDGDGDGMNCE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002355.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002355.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40acfb68a8037de678ab2c512d3706e58d8ea90b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002355.fa
@@ -0,0 +1,7 @@
+>PROKKA_00939
+MHGEERSTRAALERAGHVGLASRIGLDGTLVPPDGRAGPGAPDAAGVGYASRVPEQRIIA
+RRSLGNAPTRPDGLRLASLAALGEEQFSTHMLAASGGDPFDTSTEESALEDLLEIIEGAG
+DHFDPHAWYVVGDGEGEIGVVLPQPLPDKPGTGTVFYVAVLPSRRGRGKGRQLHQFGLSE
+LARRGCTEYVGSTSVDNAPMVAVFQANGCELEH
+>PROKKA_01294
+MAVLPSRRGQGMGRRLHALGLAELARRGARKYIGSTGRKKAAMVAVSRANDCIVEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002356.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002356.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff522d2dd84276de3cbb550883b6f1d35f949b13
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002356.fa
@@ -0,0 +1,11 @@
+>PROKKA_01187
+MDTRDDTELAPSATLGRRERAKAEKRARILAAARALFEERGFERTSMSEVARAADVAEGT
+VFQYAATKVELLMMVVDALWGAHERATTTPSLSAFAAPGAATAGGETADRIAELISPLVT
+AMWRWSELATWVAREILFGADMPHRRRVLDHVDRLEEEIAARLQDGRADASGAIGAARDG
+ATGTAGEEPGAAAAAGARLIVAGVLAELNRSRQRRIDGEDVDVVLRRLIDLVVAGAGAAR
+>PROKKA_02289
+MPVTLVSPRARGGEFATNVHMVDARPPLPSRSIDCAVVSHSRLAPESEPEPEPEPEPATP
+TRVPGLRERNKAAQRERILAAVRERLGRQGYRAMTTAQIAQDAGVAAGTVFTYAATKPEM
+LMMATHDRWKDSVPSALAGSLPEDRTEAVRALVDPIVATAVAEPENSAAIARELLFGQPG
+AHHDAVLVLVRRLEEAIARIIADGDPGPRERTAADLVVMGVVLELHRDRTEGGRVEGLEE
+RIERVIGLFID
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002359.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002359.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8cf3d48dec99df9cbd3a80e4e4e2fb99716d95d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002359.fa
@@ -0,0 +1,10 @@
+>PROKKA_01196
+MTDRSDPRLQDESRLDAVKRAVEDVAQDAPTLAKIALEAMIRKHNPNLSGTAESAGRVGM
+RSGKVSELTAIARLKPGGAERLQRIFDLTRGNMDGAQRVSTLHDMRFVFFDDNTRILFAT
+AYDGDWDAYINDFATKIPELMDLLFQNVEGWPGIDSPTVKDFIADHQITASGWFVANPQV
+TVVDTRRLQRTEDAVNTFLDQMAGRTDLDEDTAAALKQLTDAISTPEAVDY
+>PROKKA_01533
+MTDRSDPRLQDESRLDAVKRAVEDVAQDAPTLAKIALEAMIREHNPDLSGTADSAGRVGM
+RSGKVSELTAIARLKPGGAERLQRIFDLTRGNMDGAQRVSTLHDMRFVFFDDNTRILFAT
+AYDGDWDAYINDFATKIPELMDLLFQNVEGWPGIDSPTVKDFIADHQITASGWFVANPQV
+TVVDTRRLQRTEDAVNTFLDQMAGRTDLDEDTAAALKQLTDTISTPEAVDY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002362.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002362.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e5d35779281f5f68b19c77ffeaf0eff52e6dea05
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002362.fa
@@ -0,0 +1,6 @@
+>PROKKA_01788
+MNIYPDFGAFGDNTTLHTVIGALLTFVLVTAVLTMLISGITWAIATANGNHTTATKARTG
+LLVALGTATLAGAGITWLNWLINLGDQL
+>PROKKA_01790
+MLDLMTSVLPTLPMMLPMEVDITPNDDGLPGIAQLRNIVAAVMTIGLILSVLALIISAIV
+WGFGANSSNPHLAGRGKVGVLVSCGAAIICGAAVTLINFFWNVGQSV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002363.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002363.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c28d7f9e0ce05f4723716ede73d6d260fc948e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002363.fa
@@ -0,0 +1,14 @@
+>PROKKA_01823
+MEGLERVGSVLGMMLQVCVNGARDIAEHPALSADPVRVAAECAEAVAAGADAVHVHPKDA
+HGQDSLQNPDVGRWVREVRARCAGVPVGVTTGAWALPSVEDRRQAIVGWQTLPDFASVNW
+HEPGADQIAATLLDRGIGVEAGIWHQEGLTAWLASPLRSRCLRVLIEVQDIPAEEVESEA
+LVLVQGVRRAEPAMPLLLHGEERSAWPALKLAGRLGLDTRAGLEDMVTFADGRPAPGNAE
+LITVASHLRGRSLEEEPTVMKPYSVPLAEARTAFLAALDAFEEGASSLDDLTLLGVSHVH
+GWSRLDCLVHVRLGLQEMLAGLAARTDDTPDVDAASYWTTYEPEKDPVPGILMTRRTASA
+YARPRNALEHLNQVSAGLRHAADTLIEESIAFQGHVLTAGDMLATWAVELAVHHHDLALP
+AGAPAPAPAAVHIGRLTAEALGSTSGARAGAEDDLAVMLAGFGRR
+>PROKKA_01870
+MSVAGEAERFAQQAHQFAEAASGLDDLALLDPSLCRGWSRLDLVVHVRLGLEEMAAGLGV
+RADDAPDHDDVTYWSSFAADEQDPVPGHMWLRRTASAYARPTDATAHLRDAAERACAASA
+LQDPRPVRFQGKVLSVMDFLRTWSVELALHLVQLDVGVVPSAAGLARRTLEALTGAPLPV
+RLTDHSALRVALGADPWPADEPGGGAYPLGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002364.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002364.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c779e9dc73ed1bb0a9b8a5c364a3f7c80527ba9a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002364.fa
@@ -0,0 +1,16 @@
+>PROKKA_01885
+MAVEMGLWRADGDRLSRITPTAIGLESQLETYIESDPGMLGETLLVLGPQVATAFAGFID
+LLALDETACVHVIELKRDRTPRDVTAQALDYGSWVSGLGRAEIQSIFEAYKPGVALEEAF
+TECFNETLPEELNSAQTFTIVAASVDAATERIVRFLNEDFGVPINVVFFRHFADNGAKYL
+VRTWLVEHEGQQQSAATPARQTKTREAWNGSDWYVSFGEDSGTRQWSDGRKYGFVSGGGG
+KWFSQTLKNLPVGARVFVHIPKTGYVGVGTVTGEARRFDQLQVEVDGVDRLVKELPLSGS
+YAHEGDIEDVNAEWAVPVAWTHTVPRERAIWKNGMFANQNTAAKLRQKFTIEHVLEEFDI
+AD
+>PROKKA_00900
+MAVEMGLWRADGDRLSRITPTAIGLESQLETYIESDPGMLDETLLILGRQVATAFGGFID
+LLALDETACVHVIELKRDRTPRDVTAQALDYGSWVSGLGRAEIQSIFEAYKPGVALEEAF
+AECFNETLPEEVNSAQTFTIVAASVDAATERIVRFLNEDFGVPINVVFFRHFADNGAKYL
+ARTWLVEHEGQQQSAATPARQTKTREVWNGSDWYVSFGEDSGTRQWSDGRKYGFVSGGGG
+KWFSQTLKNLPVGARVFVHIPKTGYVGVGTVTGVARRFDQLQVEVDGVDRLVKELPLSGS
+YAHEGDIEDVNAEWAVPVAWTHTVPRERAIWKNGMFANQNTAAKLRQKFTIEHVLEEFDI
+AD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002368.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002368.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f1bef70869c03b84f98554de9823de635488fa6f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002368.fa
@@ -0,0 +1,28 @@
+>PROKKA_02315
+MALHVGLYSPWNTTDPRAWSGVISPMAEALRDVFDVTVIPPVGQRDARGERIRTRLRGMT
+GRRSLPTHTMATARLRSAVLAHQLRRHTGAPLDALVTIAASTDVLSLPDDLPIVQVTDAT
+FPAIRGFYPLATGLGRRNEREGMRVEEAGAQATDRYLVASEWAALSLTDVVGVAPHRVTV
+APFGPGTPPPADARRREPGSSLRVLAVIADWERKRGDDIVAAVARAREFRDLTLTIVGRA
+PEGLPSWVNAPGVVDRARLAELYRGHDVLVDLALANAAGVVMTDALASGLPVIATHVGGV
+DTIVRDGKTGWLVQPSGAVDATARVLTTLDAAAVTRASAAALADARARLSWRAWAATADE
+VVRAAVAERRGQASPEAQRRRALMVTPILPSTGGQESAGEHLVNDIAQVIAERSELTMLS
+SDGPANRRALERGVAFAHRLLTSAPLRCDRLPRLLGVAPALNARTVEQVRGLVASADLVD
+LQWEESALLLGPLRRMNADARIVVTLHDVLSQRFARQRELQSSRLRKGVWAARQAAATML
+EAHIVREADAVVVLSQKDADLLPKRGRRARIHVVPPAITGPLRPLRDGTGAPFLLFVAYM
+ARWENEDAMHWFVTEILPRVRAEAPDVRVAVAGGGLRDHVVAELEANDVEVLGFVHDLEP
+LYEEASAVVVPLRYGAGVKFKVVDALVRGVPVVTTTVGNEGIHPADAAIVADEPAAFAEA
+VTAVLANLPCAERYARSRATDVAREFGPNRFRARLQEVYR
+>PROKKA_00517
+MTPRIGLYSPWDLTDPRAWSGAAHQMAEALAAVADVEIVPPVQVDDAPLERARTRARGAR
+GRRSLPRHTMATARRRSQALSQALEARVGPSLDALVAIAGSTDVLRIPANLPLVQVTDAT
+FPAICGFYPMATGLGRRGEREGQRVEHASAVRTDRWAVASQWAADSLVADVGVPASAVRV
+APFGPGVTPTSAPRVRRPQRPMRVLAVIADWQRKRGDAVVDAVQQARRHADIELTIVGHA
+PDDLPIWVHLEGVVQSDRLSDIYADHDVLLDLASANAAGVVMTDALASGLPVIATRVGGV
+ASIVQDGRTGWLVDADRAAEQAANQLRLLGESGGADQVAAASKAAAEDAARRLTWRSWAA
+AVMESVEEAVAAHAATERRIVMISPLLPSAAHQETAGEKLVRQTVDTLTADGARVTLVST
+PGPANRRAILRGGVPDHRLLSPARRITGRAARLLDLAPVLSPADLAPVRGLLRTADVVDL
+QWEESGILLPALRLTAPGARTVVTLHDVLSQRFARQRDLQLRPARRAVWEARRRAALAVE
+RLVLAMADDVVVLSDKDAALLSSRGRARVHVVPPPIPGSLRPERRDLQPTAEPQLLFVGF
+MARWANEEGMHWFVTEVLPRIRAELPGARVAVAGGGHRDHVVEELENSEIEVLGFVEDLE
+ALYNAADIVVVPLLSGAGVKFKVVEALVRGVPVVTTSVGNEGIHPADAALVADDPQDFAD
+AVLDVARYPQIAESHARAHASAVAEEFGVAGFRQRIKEIYR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002372.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002372.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d7957a1c87c97b3c619e5b5cc147c06067f2a856
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002372.fa
@@ -0,0 +1,2 @@
+>PROKKA_00170
+MVGQTVAYVRVSSAEQNLDRQLEAVGECDRIFEDKISGSSRAKRTGLAELMTYVRAGGTW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002376.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002376.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b48cc721227a4838301aaddcc6904010f3ea748e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002376.fa
@@ -0,0 +1,7 @@
+>PROKKA_00408
+MRKLIFYPNLSKGGVSAVIRGRAQAEPDVQFDAVFLHDRGGSDAFSDMANVHVRLIQESR
+SGPYLTHLAHQFDYESVSVLSHPATANVLSALDHVAVTYEFHSSSIPVIEKELGALELDR
+LAAVVVPSQIMAREIQPLLPRRLRFRLAVEPNLVDVETFGEQGSAQFLADSGFGDGPGTI
+PLLWVGRFDQGKAYAHFLRVIAALPQEYVGHVVVSLEDDPHRAERFFAEAAGLGVLERVR
+LYLNLTPQALGEFYRSVRDADGWLVSTSLKESFGYAVAEATNAGLRVAASDLPVWDLFAG
+TGLVHRVPSGSIADLVRVIREGAPVSAGAATAW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002380.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002380.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e40c785472483c07f8cbbd5b3ea9829ec92213b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002380.fa
@@ -0,0 +1,6 @@
+>PROKKA_00519
+MRITTREEALAAAGSRYAPVSAGGRSADDAGVMVGKPCEVAGRRQLDAANGVDSPVLLSF
+FCAGTPSQDATEVLLEREGIQRDEPLMDLWYRGRGWPGDFTALTRDGRRATVDYASSWGG
+ALGPTVQWRCRLCVDGVGEFSDITAGDFWDADERGYPVFDDAAGMSALIARTPRGLQIVQ
+DAVAAGRLHVEPMDLQALLRVQRYQVERRKYMLGRLVGNRLSGGHNPRYRGFGLLTLVSR
+SPRRVLHEVRGTIERAAKRRGGRGPS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002382.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002382.fa
new file mode 100644
index 0000000000000000000000000000000000000000..03a19793bfff1e168d322e8cfc0f5173ed918310
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002382.fa
@@ -0,0 +1,3 @@
+>PROKKA_00586
+MSNHTRCVRSNLAAEISRRDLTQARAAALAGLTPDGLSKRMSGQVEFRLGELLELARVLG
+VPFATLVAGIDAADEQLAEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002391.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002391.fa
new file mode 100644
index 0000000000000000000000000000000000000000..942e3ed15c0f66f77207320a3c421475c545cec2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002391.fa
@@ -0,0 +1,3 @@
+>PROKKA_00619
+MGKTVHRSASTGRFVKTSTAKRNPRTTTTETIPSPGGATRSVGRSAITGRFVTTSTVARH
+PGTTITQQVSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002393.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002393.fa
new file mode 100644
index 0000000000000000000000000000000000000000..735894a889dc2e6f42076354aab8b09e8d1c23e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002393.fa
@@ -0,0 +1,3 @@
+>PROKKA_00622
+MMSSQKDTATLKVQDVHQLQAIAEAAARIAEQLAGEGAAESVRDAIRAVDDQLGDYAGHW
+DEYAAVNDWSSTIKGGLGNHVKAVPATDLF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002396.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002396.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5d32d70badb82186035ef739726ce994599e82c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002396.fa
@@ -0,0 +1,7 @@
+>PROKKA_00839
+MNRRALLLALLQVAVAAGILGWVVLLFGTGPFVAAVRVLTWPGVVGALVLGSIGVLVQAQ
+RWRLIARRHGIELGWRAAAERCWQAAFINSVLPGGLAGDVVRAAEQRPVGAGRRRDMVKR
+SLGVVAAERLAGTSVVFLAAGFALLAVRPGLGGLGLLVAAVAATAAWPWLRRLGVRDIGL
+VWGLSAVGWCSFAGLFLLACLAVSPDLPPAQIPYLAAVTLAGMSIPLNVAGWGPREGAAA
+LGFMAWGHAAQQGVEVSVAYGILALVSVLPGGLVLLVRTVQGSRRRRLGGGEIELGAHVI
+AQDEAAHGGGEGSGKSVGPVETNPGDPVSHQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002400.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002400.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b6242d331cd9e9ec30df1deece47e1c72121eb8e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002400.fa
@@ -0,0 +1,6 @@
+>PROKKA_00844
+MRHPTTPFRRQAMVDVLCTVVGSVGLGVTLVHFGKTSAWGSVAAIASGLTLVSVAVVTMV
+RRNPLFSTLADRVTLSRAVLGGGCATIVMLAALDTAPHRSWWLVLLAAPAVLLDAVDGRV
+ARHTGTASAQGSRLDMETDAALLLVLTVPLAFTIGPWVLAIGLMRYAFVVLSWFRPAWRE
+PLDFSQFRRVVAAIQAVVLVVALVPVVPLTGACIILALSLALLLTSFLRDIITLERGTSS
+RGDREPTRVGRTCSSHADLSDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002401.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002401.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5bfc19c9d6741ece348700d27e3172281ef344ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002401.fa
@@ -0,0 +1,8 @@
+>PROKKA_00898
+MLREQLGGRAGLDAAQRLRTRVGEALGHAALEQRPLPQHDALPRRGRVGSPVAGRLGLGE
+RLTAGLPEGGEHVLAWPRPVQDGRLRDLVRHPEGLGHHARHHGVGLVLLTEGDGPCVDVA
+TLQQGEQGAGVLPAGEPQLHRAAGEHVLDPIHGRGEGGGRRLGPLLRRVVLRQRRAQARG
+DLPERGGAPHDLQRPVDRQSRDALERGDVLEAVPRVQVVGQVALVPAHARPVSGGQGERH
+QERPVGDVHVLRVLRPVETVESGHGGPRGHPVHVAFHHHGRVLTPYRAVVPETGADPADI
+PDQLIPHGMAAGDGPPVPLGSGKRGATSALEHEGDGRDGGLHDHRLLVVGRAHERCVTVS
+DRAQAAPGEVEGETPAGPTRDGEEELGHAGSPPSKAGSRSPTPSSSAIAETVRSAARPSP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002403.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002403.fa
new file mode 100644
index 0000000000000000000000000000000000000000..534489f6e3f59309aef03557f43297a2653d9cd9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002403.fa
@@ -0,0 +1,13 @@
+>PROKKA_00901
+MSRPRGFRVLPRARARSAALAVTLGAGLVLTGCTAPDGVEEPREPPTVTASPAPPSAAPT
+ASGAAAPADPASASASTAELARAELYPCQGYGRVPRHNTVESNARDVYAWHVFEPVAVGD
+GHGDVDWDADPYEDEGWRLWLASLRWIGPSIEAAREGDEEAFAVAERLIADWAADHEQGW
+AEDHDDLEANTHRLNVLLCFRSVVLQREGGTVPEEYAWVDELIGRHADQNMARYSARHNH
+GSMENRGLLGAGCVLDRPKWMRHAMQRVEADLPYQIDEEGLSNEAAPHYAQFNYTLFHAI
+DTTSTACGVPSEAFEGRVEAMGEALPHMVDSTGSYWQYGDSAEYPVKPFTGISEGLRYAA
+TQGAEGVAPADRVRAFENGPVFGRSSWGTPEEGFRQAASWMLRSGTGTEKKAHRGDLLQF
+LYTARGRQVIEDGGHPGIVTDDWRPWGLGPTAHNVIHLPTLEEFPGDGAAERTSLTVSPD
+GSADGASARQALTAGGERGRSVLVLTEPDAAVVVDRTRIEDGRAGHVVESLWNLPTEFTA
+ERIAPDTVRAVESASGEATTLVQVRLDGASVGEDDLAIHRGRMDPEGHLHRGWHYPAEQV
+REEATQVAFRSAGPEAGLVSVLIPAGSEDEVGVEVEQHDDGTLTLVVRGAEGTARVGIDA
+DGTPTRLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002411.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002411.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c19212b3cbc91af13215658333ada8220397ea5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002411.fa
@@ -0,0 +1,2 @@
+>PROKKA_01501
+MSGQKGQLVGYERVSSVDQNLAWQLEALAGADRIFEEKASAKDRERPVLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002414.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002414.fa
new file mode 100644
index 0000000000000000000000000000000000000000..258684bfec8f48a27fa9ea5df28f2623352a93e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002414.fa
@@ -0,0 +1,3 @@
+>PROKKA_01609
+MTFACGVAIAGLHVVNRRFITPMYDVVLNLAAFLAAVASSVLLGHVLPAVFAALAVLAWL
+ILAVRTVRARRAGHKSAGQRPAGAGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002415.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002415.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cd51d3366e5e531fb2911998ea2f1a6737823cfb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002415.fa
@@ -0,0 +1,3 @@
+>PROKKA_01619
+MDTDTLDNTPRVWIGCLHCYNSGGLVGEWFDAVDAEEVTLTHVHRGAGGTAPVARSCGAS
+TTRICPCAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002416.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002416.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bfee028188bc27577c44887d6920cf6ff386ca78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002416.fa
@@ -0,0 +1,3 @@
+>PROKKA_01925
+MAEADRVAEGAADVGVTEDAAAVEETLPGDAEHPEMAVPRRAATTTAADNAARFFSMSIR
+MIRSLSENRLRGRGLRSRAPLSSGLILAGDARCVKHHIGQLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002419.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002419.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38d8fd08dbb19eb0653624cc1bdae67053489d5d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002419.fa
@@ -0,0 +1,17 @@
+>PROKKA_01956
+MTRSTRRGTAGRITGAAVRSVIADAQRQGYAPSEDTPAVVGIYADPAGVAELGDVVVDGA
+AVTVLPAASTLAALDQVHHAPRGSWSALVTNRPEEDLGVGVLSALVGGVLRTPDLWETVR
+TDFAATGLEPALYGVPESMSVALGILQVTPDGGWPVVPGGALTRDHALGAVARAHLGLPQ
+RSLDLAGLLSWSVRPGLTTSIARLRETGTQALADVVLTWISDQAGDPRLAQLVRRLLLDG
+TPDLLVPLGLVLDVLVPRADRAGTTSAGDVDRLNAVLAVRGVPSRSLTRWADAALDEIER
+LLGSEDASTASEALLAAEALLDRIGATDAALQSAVLPTGLRHRQRLVAEAVAAATTVPAG
+YDGTPAELHAAASAGLDAVERAWSWLGSHRLVGVASAHVPAVRHLPVLESAVRLTRWLAA
+ERPEPTGLAALALRQAGESAWVDAAVARAHRGVTDTALSHALDSVLAAVRTVRDAEDRAF
+ALAWAAQTPHDLATDTGYGTAPDAVGLIEHTVRDHVVPLARHAPVLVLLVDGMSTGVATV
+LIDALLAEAGASWDEALLPGLTRRHAAVAALPTLTEVSRTAFFTGTVQRGGQAQEKAGFA
+ALMDAAGLGATELFHKAELQSAPDARTFSDEVAFALQDVDGHRVVAAVLNSIDDALDKSD
+PGGTDWTPDAVRHLRDLLDAARMAGRAVLLTSDHGHVVERRAGTLRSTPDATSARSRGPV
+PPPHEDEVLVTGPRVAGGSAVLPSSERLRYTALKAGYHGGATPAEAVVPVAVLVPDSAKH
+LLTAGSDSGLRVAPPQHPAWWAGSTHVPVPPPEAVTGPVPPAVHEPTPAAPPATAGAVSP
+EAGTTPVSAPASAAVEDAGLGAAVVASPVFQDQRETAGAVLLADAAVAAAVSALDAAPGQ
+RLPLAELGAVMGVPRSMAGGAFAQLTMLLNVEGYPVVSTVPGAVRLDRALLREQFELD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002430.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002430.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a44fe54065fdf7dbdb1c51b3ef5cb639f7d47101
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002430.fa
@@ -0,0 +1,3 @@
+>PROKKA_00013
+MVTLDTEHTIHLGAVALESPGTSTLTVYGKIVTTEAPGRPRVAWADVRVEDSELSTGGAF
+LPDARQARALADYFLRLADLMDVETGQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002432.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002432.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5dbebc39e8f33992d1ccb0685fac27aed3d6a920
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002432.fa
@@ -0,0 +1,4 @@
+>PROKKA_00015
+MTLPQTRERRPHAVGAAPWKSYDGDETRIPTASAPEGLATPLFVADLLGRLAEAEHAPSC
+TCGDWGRALALVLALASEHECTAHPAIVESVARTFAGWDGADAAEDRSVTRFRVWHAAAR
+ADINEGMAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002433.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002433.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7483a80611b6dfe65026d62792c38ea4b4d4cabf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002433.fa
@@ -0,0 +1,4 @@
+>PROKKA_00017
+MSTPSRQGHFITVVCAHPRHRGERRWIVTRFMGTADGSPVDWIEIPGTSRAWRAERKHPS
+PDRNAAELGWVSDKPGHRFYYQHGQSRPLFELLNEYGEPRDVSAPIENRVILWCERCARA
+GRTPELRCPEPELWRLLDLLLAAGRESVTVRELIQARQQVRPE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002435.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002435.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b50e39f7ab01c1271b06301c2e3397c5e9cba398
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002435.fa
@@ -0,0 +1,3 @@
+>PROKKA_00090
+MAGGPLGVFLAAHLRRAKRRFGLRWILTLALWCLFWVLGLLMGEARPWAGAVTAVGIMTV
+TVGGAVWELRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002436.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002436.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eea70f0fb2ef1b71295fbb4ebebd9c6d48c87fcb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002436.fa
@@ -0,0 +1,3 @@
+>PROKKA_00097
+MSSSPQTMLSGSFFPISRFRLISATVLLIMSIVALTPWSFETRIGGMALINILLTAVMLY
+GLVVLIIDLMVTRETAAARTVSTEERHD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002437.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002437.fa
new file mode 100644
index 0000000000000000000000000000000000000000..33dbc43d247e5cdd981a11e3e0aa83071530fc4e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002437.fa
@@ -0,0 +1,4 @@
+>PROKKA_00099
+MYTTVITPRVSETDGVGHINNTVLPAWFEAGRAELFRLFNPTDSFEDWPMIVKTYTVTFD
+REIRYGADVTVECAVSRIGGTSIRLAERIVQDGTVCATGEVVYVLVGGDRRPMAIPADLR
+RELERHLIEENHD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002439.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002439.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e59496ea9728cc63a3bebdc7110b633803dcf45d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002439.fa
@@ -0,0 +1,4 @@
+>PROKKA_00234
+MDILHSARRLKHRLWLAQKHGAHVVTEGRDLIYRMSSAVSPARYDAARYELDFTALTGRN
+TSWKPDRPIPRVVWCVWSGTNAMSANRAACLQSIREVQHDLDVRLVTPDTLHEVVVNGHP
+LHPSYEHLSDVHR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002440.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002440.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f80091cff2d291a757c70292c3e4e9ee8ad9db8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002440.fa
@@ -0,0 +1,4 @@
+>PROKKA_00266
+MTVEVNGKRVDVTLPTWGEALHTISGAAQRAGAGRRRPRGKRGAPVAAAVSTDALTAPMQ
+GTVVKVAAENGQTVAEGDLIVVVEAMKMEQPLAAHRAGVVSGLEVEPGQTVTAGTVIATI
+ADAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002441.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002441.fa
new file mode 100644
index 0000000000000000000000000000000000000000..780f822f530aed03c1d448b7e1183e2160ff0c2d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002441.fa
@@ -0,0 +1,3 @@
+>PROKKA_00354
+MRTGSVSSTSNGGTSRIALNNGKTYNATNGLAVPANGSVGRTDGTCRLGLDRTEACGTTG
+QSPYSVAGSTGASSTAVTAISLYRSITVSGYGTTVVYLNATGVGTNLSVSAAPLI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002443.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002443.fa
new file mode 100644
index 0000000000000000000000000000000000000000..819ff0e90851bcb6cc55be018c9970d87acddf93
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002443.fa
@@ -0,0 +1,5 @@
+>PROKKA_00362
+MVLELRGEPDRTGLRFFRLKSHTACMETKPNATRTVLPPADLEEMLDLSRFLGALTQPAA
+LLGPDGQTVPLPLEAFNVLREVVEAMQVGKAITVAPVDQMLTTQEAANFLGISRPTLVKL
+LEGGELAHELTSGGRHRRVRLQDVVQYQEAKRRDRRAALEDLTGSASEAGLYDEDADRYR
+QALRQARRDLGRQAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002444.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002444.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e55469a4120561bb121ea3f5233488c94478e701
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002444.fa
@@ -0,0 +1,3 @@
+>PROKKA_00363
+MARFSAVLDACVLVPIAQADTLLYMAEAGLYRPLWSERILEETIRALETIHPDMRETGAA
+RRRAAVMNQAFDDACV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002445.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002445.fa
new file mode 100644
index 0000000000000000000000000000000000000000..db261f2540c4b153a06c6f0e2ac449316fa4dd65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002445.fa
@@ -0,0 +1,3 @@
+>PROKKA_00364
+MVAAAVQGRADLIVTANLKDFPAEVLGRFNLQAQDPDEFFMNQLDLDPAQVMRSVQVQAA
+ATRNPPLTVAAVLASLERCGAGMFAEAARGQTWRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002446.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002446.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e253fe204371c32f2e611d7207b9529b1d3590ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002446.fa
@@ -0,0 +1,3 @@
+>PROKKA_00365
+MLLWGGEAKTPLTAGWLAVPVLGERPFIAHERLWWDADRDAQVTQTPMPDRGPNFDERPA
+AALSMALKQRPQEGQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002447.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002447.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d7c7dfd45adcae83aa86673b3dd64ca56d9b547
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002447.fa
@@ -0,0 +1,3 @@
+>PROKKA_00375
+MVARCLVDADQGSQFRSGLLQDALTRHGLIGTMGQVGPAGDNAAMESFFALLQKSVIDRG
+RWATRDESIMDPTPAHAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002449.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002449.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3540ce9c6ad9e6703abd267643d0c61b47c5627e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002449.fa
@@ -0,0 +1,2 @@
+>PROKKA_00667
+MPGGVVPVALAVAALALALFEGLERHREKVRRSAWT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002450.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002450.fa
new file mode 100644
index 0000000000000000000000000000000000000000..208bb9d41f9c0bd77dcf1aebf9df4927405dbf1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002450.fa
@@ -0,0 +1,7 @@
+>PROKKA_01106
+MLHLLVDTSTWLDLSKRRDGQRWIVALRVLVHQGEVELIVPPLVIDEYERNRERVEASMT
+ASVAQRFKLIRQDLDDYGGTDTEQALSTIEDLARHAPLIGAMTTRNFDEVLELLRGGRTV
+EPTESERHAVVERGLVKQAPFHRSRNSIADALLIELYASAVAGVDLAREPHAFVTSNSED
+FSLPHGDKRQPHPDIAATFALGGSTYALGVDGLNEVLLAHFGPEIEALFADTDFVEEPRR
+LDEIVEAETRLFDRVWYHRSLQHEYRLQDANNHVEIEQLRAIAGPGRKRVEETCNLPGEL
+GPYTDFELGMLNGKLSALRWVLGSEWDFLDT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002454.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002454.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f9353f4361075b3afe40bfd25c8408ad3552af78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002454.fa
@@ -0,0 +1,10 @@
+>PROKKA_01329
+MGQKQKTKSFQLGEIPSSSDAWWNLFNFAAEAQWEIPGVSLESFANPESIFLRSAAEISL
+NQPTRLRLEHGGFHFAVRLADNSSVPIDIDADIIPNEYILSSYEYEYSTKNFTYRGYKAQ
+RTSPADLTVILGHELTIDLKEVGSDNGKCDIKYPLSRYLAHRVRDLELYIDILEYGFLTI
+GSYGIQVDTTAVSDVHIQEDKEYLETLRNLLQNIEYFGGNAEKVLVDSINDDQVRAIQAA
+VESSRSHQRPPGYRGSTGRVRFGVGDKSLELFVYARDDEGQIDVTNLFGDDNGFWLASTE
+TVDGGESSRLVTPYEFIDDEDLVGLININLSSISRHYERIKGYDGVEQIADSMIIRLWRV
+AVKQEDRREEFRSAALSLALWVSCAYVNSTQRLRYLTNIHLLRFWANGFAWSDDSQRLAC
+RRLQQDVMRANLSDISLYHVCLTFLLGSEVDLGDTIQGLNENEMKQLQSWPVWDLIGEAY
+PKLTAT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002455.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002455.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a61dd42ab5c02ac08f24726df045774bf6787b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002455.fa
@@ -0,0 +1,4 @@
+>PROKKA_01395
+MAENTSPTPDPRTRGEHGTEHAAQAPFAVTRDYAAEVDEIRELGRKLGGEKKTPTPDPQA
+WREGYPYKTKLSRKSYERRKRELQIELLKMQLWVKETGQKVLIIFEGRDAAGKGGAICQG
+PLSSAHRRPVFLPAGGHQNCPLVASWFARLGGGAGHRDGISSVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002457.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002457.fa
new file mode 100644
index 0000000000000000000000000000000000000000..11e39458d5238612248730b7cbdac01564578759
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002457.fa
@@ -0,0 +1,6 @@
+>PROKKA_01651
+MGNRRRLRIRASRGRSKRCRPPHPKNSSGPGSQASGVRLLSARMRPTATPPCSERLRHHA
+LSPEPLELRVGDRGSAPGRVQAESVRHARPSAHHPAPHGGGHGPAPARSRGIPRSDRTGL
+AGWSRRRRAPTRHRPGWGCEKSRDDPLRRAASSTPPAAGCEVRLWQVKWPFTLPTRKRDM
+SIPARLSHVLGVSLNGCVAVHNMQLRAFSPFLDRLSLAPIPAARALGSRLAHQSRRVFSC
+ALSDSSSSCPSCSWPPAVPVRRDRGRLAPNPHCPRLLRRCRRRPPPRRAPCS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002458.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002458.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2797b37208f04945d6144394ac5159f7f542893a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002458.fa
@@ -0,0 +1,6 @@
+>PROKKA_01653
+MTFRPTHYRLTTAALGVALALTLTSCGTAQDAGSSSEPATATVVDSALTRIKEAGTLRVC
+STGDYPPFTEQTESGDWKGIDVDMARDLAETMGVEPEFVKTSWKTLMDDYTSGACDVAVG
+GISLNPERAEQVYFTVPTQEDGKTPITRCEDVEKYDTVAEINQPGVRSIFPEGGTNEKFA
+REHYPQGELLTHDNLTVFDALAAGEADVMTTDRSEVLYIDHEYPELCAANPDEPFDYFQK
+GYMLPQGDEVFKHYVDQWLAIALKDGTYEGFAEPWVGDVELSLED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002461.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002461.fa
new file mode 100644
index 0000000000000000000000000000000000000000..41e653214dccccd50d9069d3ec0771c89a78579e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002461.fa
@@ -0,0 +1,2 @@
+>PROKKA_01934
+MTLAELEEGQVLVTSTVMSVGPCMGGHMNDVASDVAPFEVDAPSTAAGSAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002464.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002464.fa
new file mode 100644
index 0000000000000000000000000000000000000000..232173df42b3565f861f4e037d86e9176c44a556
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002464.fa
@@ -0,0 +1,2 @@
+>PROKKA_01970
+MKYGLCAYKWVICRAIAIRSIFFTKLNPTAAIRGFLVIFGMGFAARPVGAFRLSILDDL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002465.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002465.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d60c6856cad33a24f3bb7c2c5e7ccffb9655aff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002465.fa
@@ -0,0 +1,11 @@
+>PROKKA_01972
+MSKFHVDQIATRIRELYSTDYWDANLSDVNNLSRLLARYAVDLTIPESSDSGNQRIVEVI
+DGGEDRGIDAIGIDFVSQLVVLVQSKWRQDGSGTMDLAGLLKFRRGVETLLGIRTDNVPV
+SASPEMRMAVSDILKKPGTRMRFIAVTTAQEELPTQQQESMNELLSSVNEGGASEPIASF
+VHLGQGALFDSIVEREPMDLDLNMQIFNWGKIDEPRRMVYGRVDAAQIAQWYRDHEHKLF
+AENIRLVIPRSDINDGIRKTLTSEPENFAYFNNGITMVVRDMQVAPAGSATREAGYFTAK
+GVSIVNGAQTVSTIGRISKSEGSLDFLEAASVMIRCIVVSDEEAEFGRLVTRYANTQNDV
+STQDFAFLDAEQHRLKSEIKVMGFEYLLRSGEDVLTESSDKRIDVRSAAIALACAHRDVE
+LSVLVKREISQLFSDRYRTIFNPSTDPRLLVSSVLVNQVVENKLGELEPLTEGVKNGVII
+HGKRVISHLILRGIGTTNLSSSEFAIENYDSWIEDECERIVAALVENFPDNSYPGNVFKN
+TIRVRALLNESSLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002468.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002468.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab112662e306ae4d995c1f76d962cb2376cb41be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002468.fa
@@ -0,0 +1,5 @@
+>PROKKA_02028
+MDTVTTTTPARQRLLDAVARLFYAEGMVATGIDTITAEAGVARKRLYNNFASKQDLMLAY
+IRGRHEEWLELFQDRLDRAGSPRERVLAVFDAYLDHAEAAYAHGFRGCGLLNAAEFRAGS
+AGREAVREHKEQVEAILTDHLTEAGCADPAGTAEHFSFLLEGAMSRAGLEGRSDRLLRAR
+RIAETLLDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002469.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002469.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a581c924ced99f7ad70f33f357f94263c5a43d12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002469.fa
@@ -0,0 +1,5 @@
+>PROKKA_02173
+MRIEVVTGTDTDVGKTWGTAALAARALVAGLRVHVDKPVQTGVAPGEAGDVETVRDLVAA
+AAASGALDAAAPARLTVSEGARVGPAMAPVDAVAHAGEGTPPLPPLGEQLGRWRGLAAGV
+DHLLIEGAGGITVAWTEADEGPVDAVRALRAAGLDAGLTVVARPGLGTQNHARLTVEHAA
+ARGVAPERILVSGVAADPDPVERANLVFLARLAGAHGAVLETVPRGTPPRVMSVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002470.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002470.fa
new file mode 100644
index 0000000000000000000000000000000000000000..69a75955cf9e42ce2424fb6e2443364ebdd24d70
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002470.fa
@@ -0,0 +1,4 @@
+>PROKKA_02185
+MFGAYADRVGRKRSLFAAMMITALGSLIIAFTPTYGTVGVLASVILVIARLLQGLAHGGE
+MGTSVTYLVERAPQGRRGLFGATSWVSVVVGTILATLVGLAVNTLLSHEQVASWGWRVAF
+GIGGVLGLYALYLRRSLTESEHFTAAQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002473.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002473.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d10524a4ea12f264d414f917dae58684ba59da06
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002473.fa
@@ -0,0 +1,4 @@
+>PROKKA_02217
+MLTSRRIVASTLALSALLLTGCQGDPESTRSSTFPSDDYVTVTVRGQWLPPNGTTVRREK
+GKVLLNVDRETVDSNLNALLPSSPSGKWYEASYMLTRGSLVEAYVSLPGAVPGMTTACEL
+EVDGVTLDRSELVAGSGNTAICSARLPAK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002474.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002474.fa
new file mode 100644
index 0000000000000000000000000000000000000000..afe83be3a181f77c68c5757bf67791ec986c485f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002474.fa
@@ -0,0 +1,3 @@
+>PROKKA_02218
+MTGVESPEAGRVEVSTDLTDPRTENSTEADQAKAICEAAADVEGVDYVNVTESDGTSWVL
+FGHPRYPAGECTEV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002475.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002475.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b94e6db0434cf7e8a4b4c0bea54774efc38dcf1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002475.fa
@@ -0,0 +1,6 @@
+>PROKKA_02219
+MPAPKVHLPLETRCSTYFVDEAGAKGSQGEYFVTAAVKTDDPDRVLRGFEAVRQESNYTN
+ADELKFGRVNKGSLPVLRRVIDDAVGAGARFGIFVLDKRHFDPWVDVEQWEGHLFATERL
+LRGMTTRRELGVALLDHISVPKEVSYGAELLARINGRMGNRRFLTAVSLDSKTCPGLQIA
+DIVASSAYHYRRGVEEMGQTQYLQQQSPKAQLARHVAETIGLGDFSDHKSDIASVRTSHP
+QSLTELRDGVASLVSEEP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002479.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002479.fa
new file mode 100644
index 0000000000000000000000000000000000000000..591df53dd66eacd4523e902493bf341868df5f06
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002479.fa
@@ -0,0 +1,4 @@
+>PROKKA_02223
+MKHPHITHAEAEAQAHPLPLEDQITYWKARGRALERAAQRAQTHPRPEDAAPETAPTPTG
+PDPVQLEMLEARMEAAAARRGIDPDPLLPYLRAEPFMNEDGRVERAAVETFFQQLADARD
+ARMVRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002482.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002482.fa
new file mode 100644
index 0000000000000000000000000000000000000000..18311988c3e43422fb267dd09d605d5b21774819
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002482.fa
@@ -0,0 +1,3 @@
+>PROKKA_02230
+MPGFGPYGGQNYVMTDMKKGRPATDGAAPTTKLATPILLDPETMLEGVLVLVVAHTEAGE
+TRYRRRVFYTVAAAQRAADRAVERGHAASVTLCRLAPVTTLAGGWKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002484.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002484.fa
new file mode 100644
index 0000000000000000000000000000000000000000..525fd90b45cb8a21809e26f0552a2bcef13ed717
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002484.fa
@@ -0,0 +1,5 @@
+>PROKKA_00010
+MGRRLASAWALPALLVLSEPGRLPLVLALGVAVAAVLATRAVGAGAEEVGRSPELERLLP
+IGRDAAWSVHTVAPALVLVPWGAGLGLVLALGTHGVGPSLGPVVLCGALAGVGLAGAVVR
+TATPDPVDWGAVMQPAQTTRAAGPLVRDAVRGADAAVLAVAPLALTPLLSAVPLGFAGVA
+GVVALIAWGIGRHVRPAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002485.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002485.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f08486bbce05fa7acbe8b87f284e6e5fb20bd202
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002485.fa
@@ -0,0 +1,3 @@
+>PROKKA_00036
+MSAAADLQARVTRGNGRGITLFAFQHELSTRDKRGAVDLICETFPRLSRSWAKRHLARIQ
+DMDGARLGEFIAAADPVVYMRRLRTLDPTGDTAARNVDRERREVVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002486.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002486.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bcaa0eb7dcddade23996280c80fd6cdb87dbff32
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002486.fa
@@ -0,0 +1,2 @@
+>PROKKA_00039
+MSTTTATPLTVPELIAAIRSISDEIRAIQAGLAADNAQERHP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002490.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002490.fa
new file mode 100644
index 0000000000000000000000000000000000000000..282f3622f462e4c98718590954b13922e95a7803
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002490.fa
@@ -0,0 +1,3 @@
+>PROKKA_00046
+MTVMTPIGDSVREVRATSAGDLPLHAYELRNRDFLVVQLPTGAVLAVPSDSVPPIERDLW
+EDAELRRSLWRGFDDAVCGRVTPLEDVLAELDFDLSSED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002491.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002491.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00e6e7c3446a1805992835cf88b226261652761f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002491.fa
@@ -0,0 +1,3 @@
+>PROKKA_00047
+MPGGFKVDLTDEARRVLLELKKSDLKRAKKVAKALQTLREFGPDYPGFKTHKNDSVPGPF
+GETWQAYLENHTPSAWRMFFCYGPGRGVITVFLFAPHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002495.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002495.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd0e5bb8da6eaf611978b57c0a6acba63140e18e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002495.fa
@@ -0,0 +1,7 @@
+>PROKKA_00085
+MTSTGSAGLDPADVAAFRALLARPETPAEELDDDAVARLAELGLVRRGGDGSLAVMPPHR
+PLLAEAHRAQARADALREAAEVLRGEFRRRPGAGREAIEVVVGGTEIVGAAVQLTRQARR
+IVRGFDRGPYFHAEALPEAAQSRSWERGVHWHVIFEGRSLQSEPPERWELLGSTPGETGR
+ILPRLPFKLLIADDAVALIGLAGVAGQGEGLVVRGSLLVDALVRLFELQWEMAVPIADVA
+GPDDDAAALTEQERRLLAMLSSGMTDEAMARAVGLSHRTVQRRLAELARRVGAEGRFQLG
+VQAARRGWV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002499.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002499.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c887070b5e32c63a34121f45ed6e99c31d79092d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002499.fa
@@ -0,0 +1,4 @@
+>PROKKA_00107
+MSQEPVIRRDRLEAPSRILPMTDVAAPPRSAVAPWAPIVAAGVVAAMHIWKLPGVMDQVR
+ADLGMSLVDVGVLMGIVQVASLLLGLAAGGWGSSWVLTVGASLLGLALTPLALRAPRARG
+PRGMRSARRSGPRPPGRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002503.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002503.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc27a76e3e322e58d7d011eca98ba32493f67c8b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002503.fa
@@ -0,0 +1,8 @@
+>PROKKA_00141
+MKITRIEAIPYAIPYTRPLKFASGEVQTADHVLVRVHTEDGIVGEADAPPRPYTYGETQV
+SIKNVLEEVFAPHVVGLSVFDRSQIHAVMRRTIHNQVAKGALDIALWDAMGKALKTPVTT
+LLGGWTDSMRVSHMLGFKPAQELLDEARRFGEEHGITTFKLKTGRRPLSLDIEACHVLRE
+GLGDDVDLYLDANRGWTANEAMEVLRRTEGLGLSLLEEPCDAKEAMSRRRLVEKSPIPVV
+GDESVPTAGDASRELLSGGCNAICIKTARSGFTEAQEILGLCTGLGVDVTMGNQIDTQVG
+SLATVTFGAAFEATSRRAGELSNFLDMADDLLAEPLQIRDGRIAVRHVPGVGAAIDEDKL
+TRYRTDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002505.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002505.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2c5fb766b18582d41c2b88033d110b6704b469f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002505.fa
@@ -0,0 +1,6 @@
+>PROKKA_00164
+MPGPQGTDRRAIPQRSTRWAARLADLMHAAGLTPNRVSVGSVLFAAVGAAALVAAGHAAT
+GDGARAGWFVLAAACIPLRLNMLDGMLAVEKGLHSPTGDLFNEVPDRVADMLLLAGAGYA
+AAGAWLVPGWGAGLDVGVLLGWTAAAAAVLTAYVRSLGAANGVGNFFEGVLPKPHRMWVL
+AAACLLSLLEPLLPVPRGTVLALALAVIAAGSVLTVARRLRLIAAALRERADAAPARPAG
+ERTAGLPTDGGERA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002506.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002506.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d54c3f0cb27975deffc04f9fa1077f876279bc8f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002506.fa
@@ -0,0 +1,5 @@
+>PROKKA_00165
+MPRRQPAADRSALLDHALAAAAGFAEATFFVVVPDVWTSRVAFERPRRGLATAASALAGA
+LAGGAVTHAVSRRAGAARTRSWLTALPGISDGMVDTVEARVGAGGHLALITGPSRGIPYK
+VFARCYGVDAARPGRGLGALLLASVPARLPRFLLVTGGVGLLGARLRRRAPGLGRRGRGV
+LFWTGWGAFYAWYLPAVTRAYRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002509.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002509.fa
new file mode 100644
index 0000000000000000000000000000000000000000..78fdaa5c0d231755e7782c3e982bbb4ea73b3911
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002509.fa
@@ -0,0 +1,3 @@
+>PROKKA_00178
+MSTDLSELAHRFAAGHADAMADVYAEHARMVFSLCMVGLRHREDAEDAAQQVFTRAWRSR
+DTYDPRRPLGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002511.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002511.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f4646c3c58f327b606a10938f8df203df718dd63
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002511.fa
@@ -0,0 +1,6 @@
+>PROKKA_00180
+MPDMDSTRGALSDDAFDALVSALAEGGVRPEDLDEALHARGVTSLTPRERADLRDTLRVI
+EALRADPLLVEPPHGLWEKVAAAIEAEGDLAATPATVADLDAHRSRRRGGAGARWWVPAA
+AAVAGLLVGGGAVWLNLQPSEAPETGPVAEPQVIGDAEMDPVAATGTTASAKMTREPDGS
+LELTVDVPEVPDAAAGYYEVWLRDADASRLISLGTISSTSTTLRVPEGIDFSRYPVVDVS
+HEHFDGDPTHSGTTLWAGAMTERS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002513.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002513.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d79312038602d986c63660a9ac2e91764d4aa884
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002513.fa
@@ -0,0 +1,3 @@
+>PROKKA_00226
+MKDTTGLSIGYRLIWRLQYIALFFLGPAQRPAHQDPRRLLRRERAQKVLDAHAARGTEAD
+QTVHDEAAGRF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002516.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002516.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc5f9531caeb46c51bc18437b9bb7675c33e1fe2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002516.fa
@@ -0,0 +1,10 @@
+>PROKKA_00274
+MTASSSPASPSRRALGALRGAVPPPRLVRLPRAAREGGAGREGGGVRGHDDGAPGPGAGR
+RTTWSGSASWTPAETARPGSVAEVADVVRRAAAAGRRVKPIGAGHSFSPIAVTDGVQLEL
+DALSGLTGVDRAAGRVRVLAGTPLHRLGPLLGAHGLALANMGDIDRQSLAGALSTSTHGT
+GLGFTGYGGMVTGLRLVTADGAVRWLDVRTEPELFQAARVGLGALGVVVEAEIQAVPAFL
+LRAEERSEPLEDVVASFVERSRAADHLEFYWFPGTSVALTKENTRLPLGSGLDPVPPLRA
+AVMDRILANGLFEATCRLGARVPRLVPALNAAAARGVDRRTYTDVSHRVFVADRAVRFRE
+MEYAPPLERFTEAFTGLRALLADRARGGGPVSFPVEVRTAAADDVWLSTAHGRESVYLAV
+HRYHREDPADCFRAVEELFLGLGGRPHWGKEHTRDAAWAAEAYPRFGDFLAQRDAVDPGR
+VFANDHLDRVLGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002529.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002529.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eaedf5726c6bd4bdcef997b2749832b7a162761d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002529.fa
@@ -0,0 +1,3 @@
+>PROKKA_00409
+MLETPTALIVDYIDEHKHEFGVEPICATLSAAGTQIAPSTYYAAKTRPPSVRSLRDEQVL
+GLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002532.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002532.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eeafed39f53ff2ffffd038facad442bcf4885d9e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002532.fa
@@ -0,0 +1,3 @@
+>PROKKA_00456
+MHVIIGAGSGIRAAAILQEKWETVVGVDLNDTGLTAGLTQEGCAGAVKDALAATDGRVEA
+VIALR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002533.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002533.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1b4186825e91b4f97a223c34923a331ab0ce8272
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002533.fa
@@ -0,0 +1,3 @@
+>PROKKA_00457
+MDAMLTGAEVQATASADQLASGLLRNDESTKFLDGVVPMLLNFRLPPEAIASLVIGQTFV
+GNTHYGRQTIYCDGGHEVVLRERTRRAGPMSAKASTSRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002540.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002540.fa
new file mode 100644
index 0000000000000000000000000000000000000000..81122cfa6a9f05eaecd5142a57375106f581bb01
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002540.fa
@@ -0,0 +1,5 @@
+>PROKKA_00480
+MTPDSDDAATPPATDAAHTAGAAPTLWEGDLGTLGEQSRRALLELLQGPYLSGRRRPQLW
+QALIADEAAIRSRLHDLFLDVVIDQHDEFAFTRRVATDEIAVPAALRSKSMTFLDTAMLL
+VLRQHLLTAAGERRVIVGRDEVFEQLAVYQQGDDSGWARRLNSSWTKMLNSFSVLQQLED
+DRAEVSPVLKVMIGPEEARAFTELYREIAAGQNDDDADVTTQEDDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002543.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002543.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f16692958c33dc8dcbe6a4538b6b16f78a077c7e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002543.fa
@@ -0,0 +1,4 @@
+>PROKKA_00483
+MTHAHAPLTPTGEELRQPPQKITARAPGHMVHLDVKKIGKIPDGGGPRAHGRGTEAARAV
+RTAKHGPGAKVGYTSLHSAIDGHTRLAYTEALEDERPAAVNAAIPINECVPCRRPPARTR
+P
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002546.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002546.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5410172c047fcd1e49b6f84c4c520436eb71baef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002546.fa
@@ -0,0 +1,3 @@
+>PROKKA_00487
+MCGACGRGVASPTTALLNEHGLKRRALARLRGELAPGCRLTLEGDAWTLIRRSGRGEHHA
+DVEGLIASLEGGAAGDWVGAEPPREVVAAVTAGMVARARRRSD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002552.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002552.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3fb5c58fb32bef10807806925a19ccc13e0531fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002552.fa
@@ -0,0 +1,7 @@
+>PROKKA_00501
+MSDDLLPELTAAFGLVDVHPESLSWWSLVHRARVVPRGHAEPVGVVVKLTGRTAERAAGM
+AGWTRALAAGGFPVVAPVDLDGPNPRQVGEHWYAVYPFVAGRPYDAERDVAALGDLLGRL
+HATPLEPAVRDALRSYAWPESGRDDADADLASLADKFPRVLGEEAGAAALEAVRGLVERW
+WTVSFPALRAAEEAGELPRAGVTSDYKSANVVIAEDGPVIVDPDNGGWEPRLFDLAMAVV
+LLHNDTDSAPGRMMTAAEWEAFHAAYARHVTLTDRERALWPAALDHMLWEEGTWALEDND
+DDAYAQPRQGGYLRDLATMPVERYRLPGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002554.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002554.fa
new file mode 100644
index 0000000000000000000000000000000000000000..756fc254bdb9eea9db6c0184dac34752313d87c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002554.fa
@@ -0,0 +1,6 @@
+>PROKKA_00504
+MGVYVAGGGLGIVVSGLALPWALNSFPDDVGWRVGWGLLGAVGLVAWAVAARAARRVPAP
+APRAAGSRAPVRGMVPLLVGYTLFGMGYIAYMTFIVALLRGDGATDQQVAVFWVVLGLAA
+VAGGFAWAPVVERLQGGRAPALLMVVVALGAGLPLLWAGPVPALASAVLFGGTFLALVGS
+VTHSAQRVLPAAQVADGIGLLTTVFALGQSVGPVLSGVLADSADGVRAGIALSVAIVVLG
+AVAFLPQRRVLPEAATTAGGAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002555.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002555.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df5e5bc6acc37f33d0c55178211b0ba1ecb5dd95
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002555.fa
@@ -0,0 +1,5 @@
+>PROKKA_00511
+MPAATLDDLRRARRVLFHGVTGAGKSTAAVRLGAVLDLPVTLVDEELGWLPGWVIRTPEA
+QVALAEPILAGERWVLDSAYRFYREAAVARADVVVGLDYSRAATFARLLRRTVRRAATAE
+PVCNGNTETWGRALGPESILRWHAQTFEAKRAWIRAREADDAGTPVLRLTHPRQWERTLA
+ALAAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002558.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002558.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1e3312668a0d431240509b4d0fd39f5721c5c59e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002558.fa
@@ -0,0 +1,5 @@
+>PROKKA_00522
+MSENAPDPRRRLSTAEIDAAGLTDWRLLAGRLQARFAPADYAAGLDLVARIGAAAEDADH
+HPETTLTYGHVVLTLSSHDVGGVTSRDVRMARRISALAAELGAGADVAGLTRAEFGLDTD
+RGDEHARYYAALLGAEVTAGGEVTDPALQAPTLWWQGSAGEGSASETPLPAPEVEQRWHL
+DVWVAPEEAPARLRAVLDAGGRLVSDAAAPSFWVVEDVEGNRSCICTSQDRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002559.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002559.fa
new file mode 100644
index 0000000000000000000000000000000000000000..487d6c7433384d0cc94dad21b5d148c37b45e149
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002559.fa
@@ -0,0 +1,2 @@
+>PROKKA_00524
+MDTQETQDLPAFTFLAADPADGDAEGAVEDTDAAFCRLDGSC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002562.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002562.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5d067c16757bae67bfcf793c03662302ba0265fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002562.fa
@@ -0,0 +1,4 @@
+>PROKKA_00564
+MLAERLGEITVEPEDAAQAPTEEPGVIDVDDWTARRRAGSAHLTGRFCVVTAFETIAALR
+PRFAGIATGGLGRADFDAAALTDGRPRLLTQAVSPHLWEMRQKDGAVRCDGVEFLSRHGD
+DLPLWAVFERPGDGEISPHLTDTAEHALTRDTPDLVRAFELHGLRMRPRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002567.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002567.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fcff9863258b26159d151ec85f73a92ea50b8112
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002567.fa
@@ -0,0 +1,10 @@
+>PROKKA_00606
+MNAAPRTGEAAVARPDAWPAPASFSDSPRYVLARWITDLPAMAIGLVGSLTWIAQWPAPW
+GPLVQALMLLWVASLVLGPVVRWRTARFHVSADGVQVDSGLLSRRSESLPWDLVTSVDHR
+QPWAFQLLGITEVTCTQTGEDGSRVRLDGLAPADLAAFQRHADAAAALGRSAPAAPSRVE
+DVAASRVDDDGAPADRASTGQVDAPTGQAAAAPAAVVHRTTLADLLVLSLVYGQVLLLVP
+PVAFGLMELTDVLDLTERLESLLFSGLGSWPTALLIVALAVVVGLVATVVKFHGFTVLAT
+PEGRLRIRYGLVSTHERVITPGAVQGVVWHRNAAEQLLGRARLSVLTLDSAAQLGGNLVL
+PSMPVERARAIVAEHLPEFAGTDRRLSTGLATPAVNLVSLLALAAAFAGTWVLTAQTWGW
+PWPLAAGACLAAAAVVAGIIAVAPARLYADPAAGLFLTRRITVGERVTAVRATRLHGISA
+HHLHHARTPRGRRTAWLPTVFYFAGAPRRAMALVAAPEAVEALQAMVRHSSVPLRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002576.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002576.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e94811dbeda0067861870d28076efedf1522b939
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002576.fa
@@ -0,0 +1,4 @@
+>PROKKA_00646
+MIESTPAGRVSERSAPRVVLGLVLLVLIVPVVIAVFMAVYAVAEFVQGGHAPVGAPPLLV
+SVGQILAVACASVCGIRFARSRTTRARWGWTAAVVALLVLAAWPVLVGGIGLVGREACEV
+RPAPFWCE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002577.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002577.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09a944cef7086c119098bba1757fef8042e32e65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002577.fa
@@ -0,0 +1,5 @@
+>PROKKA_00657
+MIRGMSVSLRHPTPDDVPALVDFVVRNRDHFRTGEPARSEAYYTPAGQADLVAAADRARE
+TGTGLLFLVEEDGVLVGRAQLNSVIRGAFDSASVGYGVDRACTGRGIATAALRLLVGVGF
+DVLGLHRLQGETLVDNVASQRVLAACGFKHYGTAPDYLRIDGRWRAHELFQRINPGWRPR
+GA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002578.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002578.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e193ae393197e687b599b10801515ef4b80d3287
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002578.fa
@@ -0,0 +1,2 @@
+>PROKKA_00707
+MPAPYPREFRDDVVRVAQNREPGTRLRRIAQDFGI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002582.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002582.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bbd602e51ec2728a7261d0f15ed5ce5fe524a89a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002582.fa
@@ -0,0 +1,4 @@
+>PROKKA_00717
+MVADSEAAMPGHAMKIGEVAGRTGLSLRSIRHYDDVGLVPPSARSEGGFRLYTEDDVTRL
+LRVMRITPLGFSLEETALLLEVLEGPAAEAPREDIAAYLERARKGRATLARKLRQADELL
+AELEALGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002583.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002583.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5732e06ac197d08c17e8e43ec5e49f2aa17ae85b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002583.fa
@@ -0,0 +1,5 @@
+>PROKKA_00730
+MELLTPILQAIGLFVATNIDDIIVLSLFYARGAGQRGTTRKILLGQYLGFGGILLAAVVI
+SLGARSFLPEDALPYFGLIPLALGLYAAWRAWRNRGDDDDDEAKVADKQVGVLTVAAVTF
+ANGGDNIGVYVPVFATASTTAIIAYCLVFLALVGLLVLAAKYVATRRPIAEILERWEHIL
+FPLVLIGLGIVILLEGGAFGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002586.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002586.fa
new file mode 100644
index 0000000000000000000000000000000000000000..062632f3805eab6523a57e1a168124cf4ff36a7f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002586.fa
@@ -0,0 +1,3 @@
+>PROKKA_00747
+MKVREGGRVVNAVVLLATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLV
+TSDAHTRDCARRLPRTCPARPGSAAAPTTQRI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002590.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002590.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a82d6bfbd6c1f19b53720e86042f3cd91a8e2de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002590.fa
@@ -0,0 +1,3 @@
+>PROKKA_00756
+MMHVPSMLKAYPKDLGEVDKVKLAACIAASVECAQACTACADACLSEDMVGQLATCIRTN
+LDCADICVTTGNVLSRHTGYDPNVTPAVLEACRIAAKTCADECEAHAEMHEHCGLSPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002591.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002591.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d75d74b8b498af600d64226b740503d12a698ed5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002591.fa
@@ -0,0 +1,7 @@
+>PROKKA_00767
+MVPSLGILTESIHFAVLNPEEPYVDQNTLIMLARSLPLEGRIVMLTVDVADPGADEAAMR
+ADAEATARAMVLEYRTGMPEDPPSTGPDGFPLLDPPWLMMTVMLPPADDDGALAPVVHLA
+TGTGVTPAPDLVSRLEADLRDARPGTEHTGALEALVRTAVEHSTPSEQVRAAAAEDSLFA
+DRPAWQWALVGALLLALAAVVATALRRRRRRADPARDAHAADPARFAHAGEDPALRLRAL
+TELLALAADAPGARALPQARDATAAVVEHTLALDALAPGSRQGRPDAFRRSVRPELEDRV
+GRAGATLRVLVAAGRDARPAVRFPDAVLEAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002592.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002592.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5049737a6bac7fb44ce11932a0e1f31fd018a38
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002592.fa
@@ -0,0 +1,4 @@
+>PROKKA_00784
+MLLPPLDEFLRILIVTPLAYVAVVVLLRISGKRSLAKLNAFDMIVTVALGSVLASTVTAS
+GTVLVAGLTGFTVLLLLQVIVSWLTSRRRVQTSLVRSEPTLLVRHGRLLTDAVAEARLTE
+DEVRQAVRSQGIGGLDQVAAVCLESDGTLSVIPTSSLGDESALADVGAW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002598.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002598.fa
new file mode 100644
index 0000000000000000000000000000000000000000..36de5060dcbef6e24e703bd22c712327e5eafab0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002598.fa
@@ -0,0 +1,9 @@
+>PROKKA_00814
+MLVAAPIAALVAVVFAGGPLLASYTQVFMPALGKFIVGFFPLFLAGAVFGKLMASTGYAM
+AIARWITGLIGARRAILATVLTGTVLTYGGISVFVVAFGLFPIAYELFRQADIPRRLIPA
+AIAMGAFTYAMSALPGSPQVQNTIPTRYFGTDAFAAPLLGVFAAVVMFAVGMAWLSFRAR
+QAARRGEGFETTWTGGGMAGELRGEEDHLTEDTAHLEQESARAARTRHGRPDPPVALAAV
+PLLIVILVNLALSRWILPTLDFGYLAEEQWGATTLTSVIGLWSVFVALVTAVAFVLLVNL
+RRVRVLVEDLHQGAKDAVLPVFSTASEVGFGAVIASLPAYALVRDALLGVSSNPLVTASL
+ATTSLAGITASASGGLSIALETLGADMLASAQAAGISPEALHRVASIASGGLDTLPHSGA
+VITLLLITGMSHRESYKDVAMVTVVGPLLATALVVVAAAAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002602.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002602.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6645dd03fbdfb704e156a66cc131293ba9c26688
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002602.fa
@@ -0,0 +1,12 @@
+>PROKKA_00819
+MTTETAGDFRLQTPEEIEAVVAVLGDAGMLGENARIAYLGLLDPPRGAERAAVSRDRRFR
+VFVLDVAGGLPVEAVVSATRRELLSSRELDSTVDGEFPVMEEEFAVVEEVLAQDPRWQEA
+MRARGIPVEEVRVAPLSAGVFEYEEERGHRILRGLAFHQQHEADSPWAHPIDGIVGYVDV
+TAKEVTQVIDLGAMPVPQEHGNYTDPELTGDLRTTQKPIEITQPEGPSFTVDGGNHVEWE
+RWSLDIGFDMREGLVLQNIAFDDPHTSRRRTILDRASIAEMVVHYGDPSPIRSWQNYFDT
+GEYLVGQWANSLELGCDCLGDITYLSPWVVNNAGEPRQIKNGICMHEEDWSILSKHTEMW
+TGISYTRRNRRLVISFFTTIGNYDYGFYWYLYLDGTIGFEAKATGIVFTSAVPEGSTDFA
+SEIAPGLGAPFHQHLFSARLDFALDDGTCRVLEEDGVRLPFSEENPRGNAFTRRRTVLAT
+EQQAQRDADMAVGRTWVVESSEHTNRLGAPVGYKLHPEGLPTLMAAEGSSIHRRATFASK
+ALWVSQYHEDERYPTGDFPNQHGGGAGLPEWTAADRNVDGEDLVVWHTFGLTHFPRVEDW
+PIMPVDQVGFRLRPEGFFDRSPVLDVPGPRKGACHSGGAPGAGDGGSDDACGCGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002606.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002606.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20741e58370388dc40586f71dde6f658147ee2f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002606.fa
@@ -0,0 +1,4 @@
+>PROKKA_00862
+MDETTPRILADVAELTADPAGAAPGAAWRLEQEPRDLDANVVRLPPGGRNEPFDGPALDI
+LVHVVAGSGLLHTADQDVPIRAGQVLWLPRQSRRGFTAGPEGLAWLTVHRRKPGLGIGRR
+LEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002607.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002607.fa
new file mode 100644
index 0000000000000000000000000000000000000000..16c3ed2e5e19753158b698408447bc6950181b31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002607.fa
@@ -0,0 +1,4 @@
+>PROKKA_00874
+MNLLHGLDGMDRRLLELLRQDARRTNASLAEELGIAASTCLARLKALRASGAVRGFTVDV
+DPAALGHGLVALISVRIRPGARHRMEELFDRLRGLSGVQQVFFLGGEDDFLLHVAVADSE
+EVSRFVLKNLSADPAVAATRTSLVFRHEGGERPW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002611.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002611.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad734f3aa2d20123d13fd40a3d367acd02432e18
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002611.fa
@@ -0,0 +1,6 @@
+>PROKKA_00932
+MGGRGSRGRGPEGDRASLAWLWALVAGAALTQTALNLARPVTSYRLLALDAPEAAVGWAT
+AAYALLPLLGALWMGRATDRLPSAVPLVAAGALTMGAGGAGLALATSAPAVYAASAVLGV
+GHLAFTIAGQAAIARRAGPGLLDAGFGWFTAAFSAGQMAGPLIAGPLLADGATAEATALA
+LWASAGIAAAGMLPVLLVPGARPRPGERDGTVEPDARSGDAAETAHASAPRGGETADAAA
+SPGEATTPEPAAGRHGGGRASRASCGCRAWPRSCSPGWRCWPWWTSSPRSCRWWGNTTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002613.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002613.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a1fbe99748a34f4e19b5c15560d3f9843fbecfc2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002613.fa
@@ -0,0 +1,5 @@
+>PROKKA_00985
+MASQDWMDKDFYATLGVSKDASEADVKKAYRKLARTHHPDQNPGDEAAEKKFKEISEAYA
+VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRTTQSGPDLSDL
+FGGMFGGAARQTGGFGPGGFGDAGYARRAPRRARTAPPPPRSPSAARSRAPRCPCALRTA
+RRSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002614.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002614.fa
new file mode 100644
index 0000000000000000000000000000000000000000..689722c9a2bf49a96d8795de81fc4560bb405f75
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002614.fa
@@ -0,0 +1,5 @@
+>PROKKA_01000
+MDTARDFVSGLPEALQGLGVFLVSFIPWVEGEGAALIGVLVGVSPWLAIPVAVVGNVLAV
+AALVYAVGGTREAVLRRRRSAVAAGVGPVDADLHDDVAPPAADARMRERFERWGVPGVSM
+LGPWVFLPGHVAGPAMVGLGATKGYVMLWQVVSIVVYTVFTGLLAAGLIGWAARAGVEAS
+LPGAF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002615.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002615.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b6b57301c66dfe056e291e5b9e93c08e064dde9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002615.fa
@@ -0,0 +1,3 @@
+>PROKKA_01013
+MRRFTAFTSALLMASGMLAAAPVAMAASIYEHRDYSGAAQGGENVNKLGTMNDKTSSIRV
+YGKTVTFYEHAYLSGNALRLWSDASNLREYQYPFAPTLSWNDRISSWYTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002619.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002619.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3679e0fba8037b7581dc5824a2e71d772aa5e1d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002619.fa
@@ -0,0 +1,10 @@
+>PROKKA_01057
+MRFAREAWHAAISWPSILLAVVLTALTLHGVSEAASDPGVNGWDVAVVQVSNLQLVPLVI
+AVVWAPVFLARHRALQREDELLRRGSWRKAVAAVVISDAAIIIGALTLSTAAVLAVSASL
+GLDGGWSDRVVGIVSSGGLDSEVSAAAAAAWVGQWHGAPWLFLAIQTAWTAAGLLAWAAL
+HAALMIGIGPRTAAAVVISGALWGVLSGAGLLVGRPFPDMSAWTNSLWAVSNPPSVAVTV
+ALWTLAGVGVVGAAAARDGVREDGRLRLTFPHLAVSLALSVVLLYSWYGAGTEGGTGLAD
+VAFGGQYSSLLGHLLGALPAVVMAGLLAVQLSDLEGGGAEQILLRHGAPHRWVGGLLGRF
+LVGSVAMTGLLVGTFAAADFLWHSEGTTRSAGEWTLLAAAYVSFCCLLGVIALVLFWVRG
+HVQEWIFVVLAILVLGYPTLFPPSPANPLVPYSLEPGTPFTATPLVASLSLLALFVLGLG
+VLLSRLPAPRSS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002620.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002620.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e18373622c304b721ca97ccab5745d92fad6c90c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002620.fa
@@ -0,0 +1,4 @@
+>PROKKA_01075
+MLLVAEAEGRPLGVAAWAAPGQAVAQRRRSLLAAPALLRAAWPHRAALRVLGERGPRVDQ
+ALEARHAAEPHWYLGLLTVAPDAQVGGVGSALVRAGLARADADGLPACLECDRHLEAYYA
+RFGFARTHTVEIDDGAPAHLGMGRPAGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002621.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002621.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a468177c6e626c7617bcae5239fe4b4846ee5ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002621.fa
@@ -0,0 +1,5 @@
+>PROKKA_01210
+MTRFQWQPGGGDRHALEREGPFKVLFVCTANICRSAYADVTSRARGIQGVEFGSAGTRAL
+VEHPIDPPMAAEVHAAGDPSQHVARQLTRDLLEKADLVLAMGPDHRRWILDAWPQHGRKV
+LLLGQAARIMSDLPADLELDRLVAHLWARRSTDPSDEVQDPYRRGPEAMAIAARQIDAAM
+DVIAPTLEHVAQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002622.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002622.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dd1ffbac706b194e3da59344183961e198f9e828
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002622.fa
@@ -0,0 +1,10 @@
+>PROKKA_01216
+MKSVRKPPATATPGGAGPLVVPVVVTLLVLAAVMLIDPQMRAWSMPVSLWIAAVGFAAAR
+IHDRIMLLALLATYAFFLLGKPIMMGYFGYDGLGWYAEVEDHLILTLSLGLLGIVAGYLL
+YPRAIIALLDRRRRRARSAAREEARRQFSARFASAAELAYWATLPFALAHVITNIRTASQ
+AGYTGLYVSGQSGFASVTAYGNFANTVALCVFLAALASTRRTWVVLITAFTAQALVMVTG
+DRGNFGTFLLMVFAYLVYRARHQDAALIPLRPLMLIGGAAVTALVPVFLLVGANRDGAEG
+SDTLSGFLYGQGSSLNVIEYGLRYESRLPDGHYLMSFASQGILRLILGGDGGLAGNTVAY
+AQSGTSLSHSLSYITLGDLYLTGRGVGSSFLAEGFADYGYGGVLLVAVAYGLLVAWIDAF
+APGSVLANAVRLLSIPAIVFAPRGSASGFLADVLSPVTVAVLLGTWFVALLLKDRRREGA
+PRITPRVVSTTHVGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002627.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002627.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12bff7f70ef6546849a8820eb0bc536e4f16d0b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002627.fa
@@ -0,0 +1,6 @@
+>PROKKA_01274
+MEFSRVGLTDMPRTLVHYTNAPAFMSILEGHALWASSIGYMNDSQEYHYLYVQARHFLEI
+GYGALRHYGDAHPEDLETFINGVGWPYANSPSVYVIALSTDDDDLNLWRAYTAPGEGYCI
+SFDSQKIRELAEKSGWRLAQVEYGASCIPVLEDLWVRAFTKVEEGESSQEVLTWVNSRLA
+EIAPFYKHESFASEREWRLVKVQANFDQEDLRFRPGVSFIVPFVVFDFGAPDQHSIVQVR
+CGPGPNQKLAFDSMDWMVDKIGWNPSRGVSNAPFRPW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002631.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002631.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1843659b345305e751e2b01364408d8b5536cff4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002631.fa
@@ -0,0 +1,5 @@
+>PROKKA_01299
+MIITVAGEHRAAHPPELGTLTVRIAVEDADAAAGMAALTREADRLTAEVDALRQAEPSPV
+VASAVQAPGTRSWRPWNERGEALPPRHEASVRASVTFDDVGALAGCASRWGERDGWSLDE
+VAWSLTDAVRARLEAAALRAAVADARRRAEAIAAECGTGRVTVLDVADAGLLPGGGAPEP
+RVEAMVRAFGKDAGEGVAVAPEDVEVLVRLHARFEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002633.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002633.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0b425b129e9ba31e3e1a658da109cf9c931cba74
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002633.fa
@@ -0,0 +1,6 @@
+>PROKKA_01305
+MESPLTPHPIGATLLPRLPGAVPVLLEFEDVQLGGYAWWRERQAPAILLLHGWGEDASTM
+APVAHQVLERGRHAVSISLRGWHGSTGVDDYGLSASLDISRVLAWIRRQPDVAGIVLVGF
+SMGGLMAALAAADQPAGALDGVVLVNAPAELRSFARDTAFGGARRYLEKTLQPRQWQDSS
+PLNHADRLSHPLLVVVGTEDTMTPPDQGRRLADAAPASALFEVAGMGHHPTHGEWAQILE
+AADTQFDLRRGLPSPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002634.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002634.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5eb3d86438f771a6da7cc61f8ef8a6a5e2ad0864
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002634.fa
@@ -0,0 +1,3 @@
+>PROKKA_01306
+MGKRETSKRRFLMMAVLLCLAGAAIITFTDLPWRGLIGAGLSLTGIALLMAGVIAGTRAK
+ETHSPEGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002642.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002642.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ce763452e13732e0a39861163b40073ab038447
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002642.fa
@@ -0,0 +1,8 @@
+>PROKKA_01332
+MQTETADLIASLSFELEKKYRHLSDHPAEGHSVDGVEEVELSPRRLRRAKTSYTARAFRQ
+RARGEEHQGYGLRRGRGVTPKAGDLVLARIATIGHHKRLESYNSRRRNLFVGDEVIVAYG
+DRYAPDQFLAEVPRNLNYTNLVAAGGMASRVIEKHENIDPATVLEPLGLITRGGEVVSLS
+DTAPHEITPWAQARKTLGEDGPTVVVVFGSSMNSGKSTTVGCLVNGLVNAGLTVHAGKAT
+GTGAGNDAGLFRDAGAEKVVDFTDFGLPSTFRLSFECIKDIMFSMTSVLSQGDPDVVVIE
+IADGIYQGETAALVADPEFGELADKVLFACGEALSAAAGVGLLQRAGLPLVAVSGLLTSA
+PLIAREASAVVDVPVIPTYDLCEADVTLRTLGLDAETVGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002645.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002645.fa
new file mode 100644
index 0000000000000000000000000000000000000000..762dfc4f8099e94cb163b1cf8869f89a6d23f5fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002645.fa
@@ -0,0 +1,4 @@
+>PROKKA_01356
+MSLWPLRAYAGSHLSGTDAPKFRLDSFPLSTYPMFSEHRGRSTHVPHVIGLTAEGERVIP
+HHRHFGTGGLNQTRKQVARAFRRGDAAVVVQDYADALARQHEALGGAVPTGSGPGSTRRR
+REAAIVTVEAVRSRFRFDEYMAGQRLPQREQVLARCAVGGRAEAVQGRRDAAQLGREAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002646.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002646.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb86ca47c05bdbc0ca8b2b319490ed9f5383e926
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002646.fa
@@ -0,0 +1,7 @@
+>PROKKA_01357
+MSTGRPLRASVWRHAVDVLRPAATPARPAVVRLGVGAFAAWNGHRRRDLVRGLHRQDPRR
+FEPVGVVKVLKRPLPPRVADGLFDAAQAVNALATLGVAHRVTGPLNAALQLWTLSYRNSW
+GMLYHNDNMLLMHQMVLGVSPSADALSVDAAVAGRGLAPAVLERRYGGVLPMVNAATCVV
+YLISGVAKVRSELGVKWAGGDVLRGQIAIDGLRKELLGSEMPAAGRALYRQEHLFTLMAT
+VALAVELGAPLSLVDRRLGRAFAVAAWGMHVGIRVIMGIKFTYNTSGVSYLGYFPVGPAL
+PR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002647.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002647.fa
new file mode 100644
index 0000000000000000000000000000000000000000..05fec6dcfeee42f4ca887f2463e5a6d25061ec72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002647.fa
@@ -0,0 +1,12 @@
+>PROKKA_01430
+MDPGPRLARAAPPLGPVPAAAHRRAGRAAHPPGRAGVLRTAHPADHAGPLRLPLRAGPGR
+GPPRPEPGAGHVRPDLRHGRPEHGRARHPDAARPRGRLRHHHPPPLPPGAAAGLGVRLRG
+HDLLDRPGPRRDPGGSAGGRRLRPRRLRRQRGPARRLRRHAARPRLRCPGGAPAGRRLRP
+LPRLRPLRRAGVPRLRAAGAARVRRRVPAGQRARVLVGLAARGAARAAGRPGRRVHLRRQ
+PGRAHAGARRGRDGPPGHLVQPDGGQHPGPDRPARAALPDAAAVRLGRLPRAAHPADHRA
+DGRGRALRLPRRLRPRQPPLHRAALPPGRPLPGHARRPARDHPVRRRRRHPGPRGDRHAR
+ARPRRRSHRPAAGGPDRRARLPGADGPGSPGRLRGVRGPAPHRAHPAQPGEQRDRARRGP
+ARGRARGRRRRGRQPGRGGPRHRHEPRGGAARVRPVLARRPLAQAHHGRLRARPGDRHRG
+HPPARRTARGLGRAGGGLHLHGDPAAAAARDRPGRRGARADRPVGAAHAPAVQHRGPSVR
+RGPHPARAAGPRRRRVRRRRPRRRGGDGRRRRARGGRGAASAARHAEQALLPPSRLLGTP
+AAQGDDGGRSGRDPGEDDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002651.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002651.fa
new file mode 100644
index 0000000000000000000000000000000000000000..36a7174f9f5d568400e535804314c8399a60fbd6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002651.fa
@@ -0,0 +1,9 @@
+>PROKKA_01496
+MADENVPVPVWTLATEAVAVPDLVGDADMTPERLADLRTALATFAQAPIATLEMHPIERR
+RDTAGGIMLHASSPLAQQLSQLVTQTARSAPAKVDIAASGEVLYRMVVPAKVASQVSKGL
+VKPMASKAVSGGVYSALRDSTGIVSKATFVPVAGTGATTGAAATAGVGIAGAGALTVAAP
+LVLMAVAVGASAYADHQRQKAIERITDLLEQLHDDKLEHERNRLDGCRDAIDKATSVLLD
+QGKIGQSLGLDSASHEISTAIAAVRTRLKKWQDALDELPEGPVELATLTEAFPGITNENG
+AFSAHLETARLALALKRRVLVLQAVEHAQLDGTGNPFNSFLSELRSDEQRLNDLEASING
+VLLRLASLELKRPGGLLKKVHYAPSDVDKLLTAAYRLRGLSSGVDAAGNHADVVIEIERG
+HDGSVVVFPAAAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002652.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002652.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f710836b6ba378a08963a2275ddec2f0393c2575
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002652.fa
@@ -0,0 +1,5 @@
+>PROKKA_01497
+MSSYQQQRESRSRIIFTVLIIAVSVAITYGFIRLTLPSITGQNPTTNDSSNQTTQKQEEK
+KDLPRGDAKRVADLDRLATALKTYKERHGGYPMSTGTCAGGTFDSDADLGFLADLEREAV
+IDAIPRDPAGIAKSTKTGQGANATTTADDRDTMYGAKHYLYYSNGTKFALIASVDDADAI
+PDDAAGVYLAEGDREWFDGSGLIADWHWSRNVYVVSNQKLAEAAGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002653.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002653.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e20529e909da38747f491aa490d1328688e5c5ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002653.fa
@@ -0,0 +1,10 @@
+>PROKKA_01498
+MRLAPDLTPVGWFLFGAMVLLILTYLYFWWMVIKASAHKHVSREKVTNRKLTASLAHAKR
+KGNTHRFLIQITTKGGALSVVQRGIDNVLAGVARYPVLQKVVWVEIITEDANEVAALQTR
+YRNAVIPVTPYLLPTDYRTPKDTHLKAPALEYMVEQHRASPTESYVVHYDEESVFTPDNL
+ARLVHRLSRHPVGISEGMISYGLDWNETTLLNKTMESNRPFGCHECYSVMTSPPPMHLHG
+SNLVVRQDLENQIGWDIGNLDGSALIAEDLVFGLAAYLKFGKDVFGWHHTEMIEQPPFTL
+KAAYKQRERWVFGAMQALAHIRQQPDWMRLSRKDRWHINVIIRLRVLTYALGFPVSLLAL
+GSNVVILLILAAEAVREGTITVVAPELTVYGIVTSIGLVLWLAGTQLGLFYNLRYTGMTR
+LQRLRDHVLVLLVTPFAGVIDTAGPLVAVLKWLAGIREVAWKPTPKLAVPSRETTPKRVA
+AAEVAAGEKAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002654.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002654.fa
new file mode 100644
index 0000000000000000000000000000000000000000..13055b744145c488692193df86a0dca6a038f2ed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002654.fa
@@ -0,0 +1,11 @@
+>PROKKA_01503
+MRAVEVQIHNFRSIHDARIRLEPLSLIAGANNAGKSNIIDAIRLFYGDLKWDDARDKPKV
+ASGDAEAWVEVEFKPTENELAQLKDDYKSADGTFRVRNYVSPSTGADGKARSGYYAYEND
+NLSNNLFYGAKNVGSGKVGHIVYIPAVSKIDENTKLTGPSALRELVAEVLNKVVADSPAY
+KHLTEAFGTFEGSIKAQASADGQSLESLEKEVTDEITSWEASFSLAVQSIQPEEILKTLI
+KPQLIDETHGGEIDQARFGAGFQRHLIYTLIKLAAKHANPPKVLSSEKKEFTPQLTWILF
+EEPEAFLHPSQEEVLHDSLLKLVRDGTTQVLLTTHSSRFVSRSMDDLTRLIRLRRDAGVT
+TSYQLTQPELDQLFSDALVADDSILPHGTSSADVNKAAMMASLKTELWMQSTRTTAFFSQ
+RVVLVEGPSETAIYSYLTSRGIMEPPVRGLAIIDCMGKYNIHRFVAILSAFGIDHSVLYD
+GDNGGAYDAEVTQAISGAKTTFTKRITRFVNDLETELGIAPLPRNQSSRKPQYALYNLES
+GLVDQVKLEALKQEFVDLATAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002655.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002655.fa
new file mode 100644
index 0000000000000000000000000000000000000000..102421402ab8e93b986265648e29112c9e83855b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002655.fa
@@ -0,0 +1,9 @@
+>PROKKA_01504
+MHEIKCPHCGKTFTVDEAGYADIVKQVRDSEFEKQLHERLELADQDKQKALELAETKAAS
+ELQKAAAAKDTEIQELKAKLETGDVQQKLAVTEALAAIEKDRDSLATELAQVKQEKQSAV
+ELAEAKALAELQKAAASKDSEIQELKSKLDSIETAKKLELAEAVSAVEKERDALRTGLEK
+AELEKQLAEKSLKDKYETQLKDRDDAIERLKDLKAKLSTKMVGETLEQHCEIEFNKIRAT
+AFPRAYFEKDNDARTGSKGDFIFRDFNDAETEIVSIMFEMKNESDGTATKHKNEDFFKEL
+DKDRNEKGCEYAILVSLLEPENEYYNTGIIDVSHRYPKMYVIRPQFFIQMITLLRNAAIN
+SLKYKTELALVKAQNIDITNFENELDAFKTAFGKNFDLASRRFHTAINEIDKSIDRLQKA
+KEALLGSERNLRLANDKAQDVTIKKLTRRNPTMAAKFAELEGPAHSGSE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002659.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002659.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d0c896534593b7c7c12a4d3436aa1f7ed331edb2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002659.fa
@@ -0,0 +1,3 @@
+>PROKKA_01573
+MPSHRNARDAPMTRRAWRLRIVLASTAFGGAAGALALRTQLPPAWLLAAAVVAVVLGVVA
+LPDPALQSPAAAVLAAAVASAVHGVLSLSTTPTPQPVPDVVRPGPSTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002660.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002660.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7438fd5e2dff3ec6e4a5c05f7b1cdeda9ebb81f9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002660.fa
@@ -0,0 +1,12 @@
+>PROKKA_01586
+MAGRSRAAGASAFRASSSSASSAASEGVPAGDVVVGGVGGVGRSGLGGVGDLGRGVRGRL
+RRLVRPVDDGLDLGGGRGIGVDTGRALVRGILSGAGLVRGGQAALRVHGGEAARGLVLAG
+LAVGVLAGDEVGEGVVGLHVRAHALAAAHPQDLQQVGVPVRPRGGGARRGDGLRGVGRDL
+ALVVLGLQRGVGGGAGLGAGEHVPGLGLGEDAGPRVPGLQVAAGRAEGPQGGRLLAGGQA
+GQSRHGETGGHGPAALLAAPGVPLQGGAVHADLGEAVAGEEAEGAGPAVLDDVRVEVRTA
+DPDLHGLGLLGHPAALSQHRVAVGADAGERVAALPGHLLHGGAGADALLDLTGERGSASW
+VAAAFTDSWSVSAAGEAAAGAASSSSASAAGCGVCVGGWLGVDARGQGQLLVRTGGAGGV
+LARAGRVIVVRRFLARGRVLLGGLVHLRQVVPGGGCGGGVVVARPLGVLEHEAAQVGGQG
+QRVLGAVGIQQAQGVAVLGGSGQSQLCHGGGPSHVVFSSPGARTPGRAFPDPSGRAARRT
+PTGARRDPRVRRRRDGRSSFGRAGAMVHNLRATAQAGPVCSGHGPVPSLPGTGPGAVPHQ
+RSVRTPWPPTTTPLGRTRKS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002678.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002678.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e92110e0601e3433dc701e60d1ff2fe6d119a77
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002678.fa
@@ -0,0 +1,5 @@
+>PROKKA_01936
+MFERFDLRPLARPHFQSLIDPGRRRISFGTTAIIFLLPLAVGILGGWAVPIPGAAPADAS
+GGAPAPASSAASAVFTALPGAAGTLVAGFLAAFVLLMNLRIKLDDSPQLPRTPAQLRSIS
+TAAMSSLYLTTVSGSALIVSLCLAIFGAPLAAIAPLAFRALVGLVLGLFTHILVNAITVL
+RRVAGAYYVLYKGEIRRVPVRGVPEHDKRAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002679.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002679.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12a65c009e0ee28415628fff1496defb6f5c53ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002679.fa
@@ -0,0 +1,7 @@
+>PROKKA_01937
+MSVRRRYPYGFRVWTFSLEQARERDSEAGPETVPLLPLQTESAKGMLLGALQVLQTEGLK
+IHDQKQHRIVEIHDATAQGFILLKIEGGRAGSKFTVKDERGQERGEVREEDSLVWPGRVL
+IAFSSNDARQGFMVHETYSGRTHSEVTRLRLYAHLLARHNVSLHTAHDLADNMAWDQVLK
+DDAARIEEIEFTVKAPDDVTIGEDTRPRKMSVAYQVEPAPVDRFLRKGSRTSVTDLVNSV
+GSLPHPDSFEEGEAVVEIATAHGTRRLQIGRRPYPFTRLIKSPYQVDDVEFLHEVTPDLL
+ELAARLDMALPQPFLPTDSLRPNP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002681.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002681.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1f6f4b09e2192b9a42e7e15462119fcc664ee10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002681.fa
@@ -0,0 +1,6 @@
+>PROKKA_01940
+MTALTPFQYGATAVRTAVVDGEPHFVAADLCAVLEIGRQQDATRYLDADEKRGCLVDTPS
+GPQTMVVVTEAGMYSLVLRSRKPEAKAFKRWLTHEVLPAIRKTGAYSVQRELTEDEIIHR
+ALTLTVAKVEALEAKVAEDAPKVAAWESIVSSAGSWSYNDAAKVLCESGQIEIGEKRLVK
+ALVDWGYLYRDARGRPHVYQRYVEQGLFVVKARTYRDLVSGEVRESAAPQVRLTGKGLGV
+VRSRLTNQPAFELLGIRVVKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002682.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002682.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b808e3b1fcd46ea28a6f973bf277bbbffe4e8d2d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002682.fa
@@ -0,0 +1,3 @@
+>PROKKA_01941
+MSTPLIEDLLPSAPGSGVYDVEVRGGVVHESVWLDEAGFWRSADDVLVMPAQIERFAVVD
+GPDVIRWVRDTDHRWSSIVERDLEAGPAVAGGVVTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002688.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002688.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8843551a65ca9c417e8c845dfbb38eb3257ec17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002688.fa
@@ -0,0 +1,3 @@
+>PROKKA_01947
+MSTRQSHPLVFARPGGKPLSRPYPVVSYTDATSLKTAVALAARHYFPALRSVFVDLAGPW
+RQCRGRAYIVAPSHPPVDLEFHPAATRPQAPEATQEGLLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002689.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002689.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5b6a15411f749fafc1f84cd502429495630d39c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002689.fa
@@ -0,0 +1,3 @@
+>PROKKA_01949
+MRALVTDGLGATSVEESGEWPCRRADPDAWFSTNPYRQAEAAQACHQCPAQELCLRAALD
+LEGSTGKSYRFGVWGGHTPEDRARIARARRRLVRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002691.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002691.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b3ba7fad60015e2e852728daf0f7b5eaef71f2fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002691.fa
@@ -0,0 +1,2 @@
+>PROKKA_01951
+MGDCECGRRGVLLDRELDLCILCRNRLDSAPAKEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002694.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002694.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf309abecb0852521090a234ecb88a0d16ec907d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002694.fa
@@ -0,0 +1,3 @@
+>PROKKA_01954
+MSARRPRTYPAGSPERAVADAVAAVYAEADLKLEALQLDLLEPRPDGTRWTPQQVQARRI
+TEALDALRDGFQEFGRGITAVAAAASKAVAALSAALTTTTRDDYTLAGPSKGAAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002702.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002702.fa
new file mode 100644
index 0000000000000000000000000000000000000000..06b5a6779e668bc4b176c9e3a8d35cbf9e910085
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002702.fa
@@ -0,0 +1,4 @@
+>PROKKA_01962
+MPLKFTLTTVRGRQVDVVVYGTRRQMRRAAQRWNGAELAPDVRGVTQGFTKPCNPQAVVR
+INQQDLSRRVIDHELVHAAQAIYGHDYGEAIEAHPLEHWTHFNETFAFTVTELQAAIYTA
+LAAHGLEPGISYEEGQPYG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002703.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002703.fa
new file mode 100644
index 0000000000000000000000000000000000000000..849ca0496b782ef76024d77ef6df510b690107bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002703.fa
@@ -0,0 +1,4 @@
+>PROKKA_01963
+MADAPAGLGDRGLTIWERYAGVDAGVDALALEAARAADRLDELDNVIQGKGVLKLMQFRL
+RDLPDLDADEPTWRVEVQFQSVLAEARQQQAGFSAMIGRLAAMEAPKGAAAPTAAHAAAV
+QAGGNVTPLQAARSAATR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002704.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002704.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ca63b811ec380016fa3c7176184a89033ccb5ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002704.fa
@@ -0,0 +1,10 @@
+>PROKKA_01964
+MSVNPRYLLTPPADDVDETHADGAIALAAGYGLVLDDWQQQAVRAWLRCGPDGRFLASTW
+GLSAARQNGKNAALEAVELYLMTVLGWKIIHTSHKLGSARKAFKRLTKFFGRFKGDPSAP
+YPELSALIQEFRRTNSQEAIELTNGGLIELSARTSGGARGTSYDLLVVDEAQEYEELEQE
+ALEPTISASAHGQPIVIYLGTPPKTIGERGEPFIRVRSKAVSGQMERTAWVEYGASLEID
+RMTDVELQAAVRDDHHVRDANPAVGARVTWETVNGERGRWSARTFARERLNCFPLPRTSS
+EKAIEEDVWAARHDPDPDPHARLAAVGLDMDPARTKVTITMAYWAEAGVHVEVAAAAPYA
+DAGVASLVAWLWERCKARVPVVIDSFSPARAIEVHLLQKRMKVRVLSAREWADACMGLYD
+AVSAGAVTHFDQTQLSLAVLAATKAPVGTQGAWRMQWPKDDVDRAPAVAGVCAHFGAMKF
+GRRPREGAASQKQTGHSFV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002711.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002711.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a7e44c4169516b6255c380465dc732129179298f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002711.fa
@@ -0,0 +1,4 @@
+>PROKKA_01971
+MSGFATVQDLEERWPGITTGAVTRAETLIEDAELLIEGDYPAVGEWVASGLLRADVVTFV
+VCRMVKRALGPDADDAPGGQFESMSRTTGPFLTTLNFREPAGDGEELFLRRAERNLLTAH
+LRARARAGRAFTIQPGAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002714.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002714.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a9f62485777495bfdad9fb6e781bc1cd9bcb3d69
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002714.fa
@@ -0,0 +1,4 @@
+>PROKKA_01974
+MQGQRFPQPREVLRELTDGREFAGHVVTTVFQEQADAYGAHDPVPQLLVFETSVVEGFLD
+RVTQVQLALYAEGPSAALQVLEAILAEVCGVGITTSAGYIDSISVVQGATEAPYTERLNR
+GSALLQVVSRPI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002715.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002715.fa
new file mode 100644
index 0000000000000000000000000000000000000000..740631cfceb900b5d9ce5360073247a65654eed4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002715.fa
@@ -0,0 +1,5 @@
+>PROKKA_01975
+MVTFHELQTQSDERKLVRKIQKAVALIAPRNVDLPESLFAGAGQLVNLKEEGWLPLGIVT
+PDGYEFTRDVETEDIDGLGYASPVRTDVTRVPRAITTTLIESGRKHVQEMLYGTDLSTVT
+QDPVTGEVVFDEPDMPANREYRLLLLGKDGPADEEWVLGKGYGTVSLTAGGGATWGQEGA
+VSTEVTLSVYADDELGTPVRHYMGGTGALKYKDVLGYTAGTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002717.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002717.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ad6b1896df191e430665afe3e50e5fc0364fab2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002717.fa
@@ -0,0 +1,3 @@
+>PROKKA_01977
+MATQKKTDSPKVHASLAKLRKESPAAAEPFQIALEDSHVITFPDPFAMDVDAAERMFALP
+DTQVKAALREWLSEEDFTALFRVKRSLRDLMLISQAAQAHFEATYGPVGEDSASRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002718.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002718.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e3d1d21f8d05b8be190f603e5982b6efbe343f1b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002718.fa
@@ -0,0 +1,4 @@
+>PROKKA_01978
+MFGVDLAAWVAAGRWLGVLELIHSLPRSSRLREAQLNDPDVAADLLELQEAQDEPEEWAP
+ALAETSLITDLLSALIGEVRSLRSEQTAIASGKKPRPVKPIPGPRTALETAKALRAEKYA
+AETLSRFGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002720.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002720.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a0829c745432aae29438ad2fbbcccfee92d3aa97
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002720.fa
@@ -0,0 +1,14 @@
+>PROKKA_01980
+MAWSGAGSWASVSGRRMRLIWSATMSPTTVTAATSSVSVTVTHTLQTSAAIDDPSTAFVL
+SGGLGASTTSPYVRIGSLSGGSQVVSTRTVSVPLAYGKAQTLSWSASMSGLAYIPTTAKV
+SGSVPVPARPLAAPAAPSGVGVTRSSDTRHVITWTRNSPGSASAPYQNQVIQRSADNAAT
+WKTVATVGNVSSWTDTTTTAGRRYQWRVAAKNTGGTSAFASSPVVYTTPAAPTAVKAVRQ
+GMDVLVSWVKSVSPHSRSEIAWRQEGGAWQYPGWTSTGTSYVITSPDPSKPLQYAVRAEV
+ESQGVTLGSPYLWSSWVQLLALPAAPTNLSPALADAALPITLSWRYNSTDSSEQSAREIR
+WRPLGADAWKGIPKATAADSTHVVPAGLWEPGTVEWQVRTWGAHADPSPWSTPQLTRVAQ
+APSVTITSLQDGPLAASQAKIVYSFFDPEGDEQTAGSVQILDDEGSIVYQRTWTSASRGL
+TPPVRLQDGRSYTIRVRARAASGLWSEWDQVTVAVDYPEPPVGVLTAEWLPDSAAVMLTV
+AVPPPAEGEVEATSAEIWRSVDGGDWLRIAAGLPLDTALVDPTPHTSRTTAYRLTTVSDL
+PSTAEAAPVLVAPDPQGWIWLNSGPGWSRQVRMRDNARTGPSWSRASERHHMAGAKLPIA
+VRGEQRERSVSVSVRLAPNPDGGCTYAELEQFLDDADLPILYRDAKGRRWFADVSEVSGS
+EERILEEASFTVYEIDHVEAEAEAVEQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002721.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002721.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9e551a066f7140e19d4e29a18b1f6d520650db7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002721.fa
@@ -0,0 +1,8 @@
+>PROKKA_01981
+MTDQLHLIDAPEWGPAAVDLLAGSRDVEWIYELVHARTNRFIRTLRGVRNFRFENNLHAT
+IRSGGSCIWQGAEDIDWMEHRLRAHQRISHRGQSLQWTVGTFIVESPTRVLTDKTRGAQD
+LQLFDAMYRLDVQTSTVSEWVAHKGSNIIGTVRHLLDRQGIKHALEDSDAVFASQMSWEA
+GTTYLRMVNDMLAAANFTAVYADPQGVLRAGPARAATSRGVAWTFRDDSTAMRYAPEVTH
+NRDTYSIPNEVVLIARSDDPDTLPMSASARDTSSPYGTMRRGMVITKVEEVDAASQAILQ
+ARADLRLKEVQRPASTFTFQHLPLPLEMSQVVRFVRTRHDVDVLAVVEKTGFDDGTGLAE
+TTVREVVS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002722.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002722.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a1f6c496f856af60d1ef3896b976dd3b017d3ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002722.fa
@@ -0,0 +1,3 @@
+>PROKKA_01982
+MAGLVQALAGPQEAAKTPGLRVSDGVVVSTNPVRVRQAGADPSTDPLAPLSLVPAADLSV
+GARVLLLHRGTQKILLGRTYPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002723.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002723.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa6149948ad1ccb4b5ecae1d4c2d22f800a3f87a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002723.fa
@@ -0,0 +1,12 @@
+>PROKKA_01983
+MHTYAARVIADQATGRPLAGVRVAVEDAETGAPVQPCRDGQPVTLVTGAHGLITEWQTED
+TTRRVALTAGPVRLTQWCEELQGTAADAVSLMDDRLADAASAVSQAATIRDGLEPRVQTV
+EARQTALESAEGFGPSTPEDGTTASYLSQATSLTAKAATVMFSRGTATVSDRYAPSLQAL
+VDEARPGDTVLVSRAWSLAEPLTISTPLRLRTLDAGEIYAPDRTKDGVVVTSDDVELAAR
+IRGAGATTAGAQRLVRVAGASLASPVRRFALTGSTITDAARDGVQLEWCDDWTIEDCDLS
+HLAYSAITTLSASRGVVRKSRVANVLQPTGFVNSYGFTASRRTDQPLSTHPRSSQIRVDD
+LTVDGVPKWEGIDTHAGENITIRDSTVRNCRVGIALVPGVDASGVDDIAPKGIRVINNDI
+DSGVSDGTRGIGIQAVGALNADGTMREALTGTIEGNTIRGHGTDGTATSGAIMTQATSGL
+SVRGNTIVEPAMNGVIATTRNEGLRVEGNTVVDAWTDKLGYTSVLRVTSHNNSIRLTGND
+AVRGSRTAAVVHGRGLYVSSSLSGVSVRAEGNDFTSASLPMVDGGLSYAREGATKLSFHP
+TAEPVTRPTLRGAATDELTARALVNQLRTALIGYGLAN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002724.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002724.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee80493f4879a132e67028ed92a44d321db2080d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002724.fa
@@ -0,0 +1,6 @@
+>PROKKA_01984
+MVFLFTLALAAVGAGVVTLARGDAAAAEAGLSRAALVLEGANTIGTSRILGTGAVILLVV
+ALAATTTRRWQRVVCLAVGSGLAATMLATGSRGPLLGVALGIAVVLLVSPSLRGRRVRGL
+LAVALAAAAAYWWSASRSAESVDRALGWITGDRDTSTQARQQLWDIAFDHAKRDPFGVGW
+GGFADLDSVPSDLPYPHNFVLEVLVEGGWLVGGAAVIFVIASLWRLTRQATTPAGAAVLA
+LGIFTVTNAMASGDINDNRLMWTILSSAWVSTRLSQPQSQFASPYPISAVRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002726.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002726.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a737f9eac40efa66baca8d9c92061e750aef1f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002726.fa
@@ -0,0 +1,4 @@
+>PROKKA_01986
+MSIPETIILALIAAAASVAAAAAGRGYTRRSKQLEAETARLAAEREREAARLAAEEARWT
+RLEADVERLAAEVQALRQENEQLRRENAAERAARGDAEDTIRDHEELIEDLLVHLIVRQD
+WEDSGSTPPPPVLSWRILAALRKRRAAMTGPIPLAHDQTTPTSQED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002729.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002729.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2b372184129c1f90c66bc49426099675f50a664e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002729.fa
@@ -0,0 +1,3 @@
+>PROKKA_01989
+MQTRRTPIIDTLTLWTGSVQAALAAGAGAAILSDLPGWVAFSLAVGLFVVGMVQAGLRWA
+AQNATVPVGDVVEVREGSDVVAGPANDQVAEGAFVRELGRSPRHRVAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002732.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002732.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3fb8bff06039886233caed883fb8fc04ab35776d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002732.fa
@@ -0,0 +1,5 @@
+>PROKKA_02046
+MTTTGRGSHRAYDSDRDRLLDVIGRAGTPPVDETTFRVDPLALTGHDQTTGPLSGAVVAE
+TVLVVACDALTAEIEQHHRVMHGAPGMTEAQDRRALVDRMVIDFDAFAGGVWSGTDSPHR
+HGVLLDLHTTAVRIRKRGGVVYVVPPADGSADQTRLPGLRVDHDLWLPDTEGAPVSRLLV
+AVRRHAGLMPREDDDQIGELHG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002735.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002735.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b06069244700c42f9a702b15a21470eaa6df135a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002735.fa
@@ -0,0 +1,7 @@
+>PROKKA_02049
+MNPYQQLLYRGMAAQDIVTTPVLSVDGFNPLLAVRAETSGVGVHLHWLNPVLAGARNGAD
+ARARVDRFLERVDEFIDADGRVVWTVHNVLPHDAVHLEQERRLQQGVADRAHLVHVMHPD
+TADVLGESLRWDSARTVVAPHPSYAGAYPDTVRRDEARGVLGIHEDEVVYVALGAIKAYK
+GIDTLLDAFDQLCREDATPRRLVVAGPVDTSPHTRALVKRLRTNPRVLVQAGPVPGDRVQ
+YLLRSADMAVLPHLRALNSGGALLGPTYGLPVLAARVGVLPAVLQPEFTEFFQDHTVPGM
+TAGLRAADRLLGAEARDAASDFARQHDPDLIGERFAQVLRARLWAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002737.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002737.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ae92d443d63e44b6899904a7f796601bdf60cb6c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002737.fa
@@ -0,0 +1,3 @@
+>PROKKA_02099
+MASIEPRRNGDGVVTSYRVVWRDLGAKRSQAVASLEQAQQWKAVLEAAGHDTGACQLVCV
+SGVVTGRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002740.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002740.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a4ff345003108c958ad24466f947d01690cc0466
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002740.fa
@@ -0,0 +1,3 @@
+>PROKKA_02106
+MPDRERGTGLSVRDHLVLQLWGRRWRHGAARDRAAVELVGLRPTELALRVAVLAEEHAAI
+AAYPVVPRRAREARQTRHRVVGGRAASAAEVVAGGS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002742.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002742.fa
new file mode 100644
index 0000000000000000000000000000000000000000..605ecfef9e291acbafa790323edfa96d219b78bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002742.fa
@@ -0,0 +1,3 @@
+>PROKKA_02197
+MPASNLAPAHSDTLTVLEAAREYESFSPEYLRAQIRKGLLPAEKGRRGYLIRRADLDSHP
+GPAPGRPSDRDRLEAFARALVAQAPRFTEEQRQQIVIALEPYADGST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002747.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002747.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e82874a6fa734e2d21153ab032d1fd0855abcf78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002747.fa
@@ -0,0 +1,7 @@
+>PROKKA_02212
+MEPSATAPETVSTAAVCSRDERPPKKGHPPVEPLPPHEPMAPERDQELQAVLAWLQARPI
+QDELTEAVLQSVHYILDGASTGRVYLHDPEVDSDERSAVGVNLQYRVLHVLGLPKEAPLD
+TTIEGIPVDIKCTTGTGYGWMIPPEAQCELCLLVKIDAEHDRFAAYLMRTHRVWLNEGGN
+QDKKRTITAAARKQYAVQLFEGEWAPLPRNPLRDLTSDQRELVLNLHPDRQRGQETRIKA
+MFSYLPSTVVPRHVLETIGAGRTDPARRARAIRSQLRAEHGLILLCGKWKPERDAARSAG
+FDLTGRDWVAVPEADVDPHQLDLVLAQRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002754.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002754.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a27490b45a89834f9da348825a82054d0f9da3d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002754.fa
@@ -0,0 +1,4 @@
+>PROKKA_02227
+MADPRVLQQPSVRSEVHRRTLCEPVTPWGPARARAPAADWDAVTAALAEPSPEEWYCYDT
+DNRDTPLAGPQVIEDWSVLTAVLRETAELSTADGWVEGFEPPQGGGWTTDQAAATLRLWV
+TRRFRRGDARLTDVPRHPDS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002757.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002757.fa
new file mode 100644
index 0000000000000000000000000000000000000000..364090e7fea25a216d0c5ceac3a29eb2664066f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002757.fa
@@ -0,0 +1,3 @@
+>PROKKA_02248
+MTAEQAREAGHQVKVASKPVATIAAMPRPKIEEDAHGVIEVVVDAATDLVLGARPHCVEA
+QGLVNLVALAMRADVMASALRDGIWTHPSATEALNEVLGELG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002761.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002761.fa
new file mode 100644
index 0000000000000000000000000000000000000000..56bc1cd0720d2b6caea041d4193492bb5de37eb0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002761.fa
@@ -0,0 +1,3 @@
+>PROKKA_02326
+MSNQRHTTADVAAFESWLSVFRRPQTVNNRVHYATRLETWATAHGCTPWTLDTTQISAWL
+STVGK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002773.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002773.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f4d5a7d570f6c7f06aefcee048bda1f15a1fb571
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002773.fa
@@ -0,0 +1,8 @@
+>PROKKA_02498
+MKTNIFAHGFSDNHAVSFGASRKGRVWSNEQARDIHDWVRWASQVGPTITDTSISLDSVM
+SGFLLPEPARERPPLVPLSIEWPYQLVSTFSDRRKVSHEDQAFSLLDTELSLTDHTADQP
+LRFEVKTPSWSLEFEFEFHEDGPPTIRPVSDDGQVVTPSGVGSLAAFLTGHGLLVTFEDE
+VVLVEQGFLLKPERERRLFPIDAVETIDWSGVNIRRESQGAERDPATIQHRAIQALSAED
+EWEVVLDDDGTGELADIALLRRTDDVLEVLLVHCKYSSSDTPAARINDLYDVCGQSMKMN
+RAKSMSELLTKRLFRREQERQNAGKSGLIVGDIETLAAIVFEARYRLLKVTVAIVQPGMS
+KSAASEDMRSLLGATDRFLAETYGMKLRVIASA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002779.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002779.fa
new file mode 100644
index 0000000000000000000000000000000000000000..169730bf02125a4cf71f58e0370f02d37c2cf63c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002779.fa
@@ -0,0 +1,5 @@
+>PROKKA_02582
+MIVTTEIRRRPARRGPDLGDVLMAAPFALWGAATLALQFNRGHRFIRALDPTGLIVPDWR
+FFAPRPASHEYHLLYRDARPDGTMSGWNEIDLGADRRLRHIVWAPHRRLEKGLFDATTEL
+MRVITDVRDPAVVRMSAAYLALLTVVTHSASHQDGAVRTQFMLVRAAAHEPDVIPSIDYI
+SDWHRLEGEH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002780.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002780.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4f06e5732d2054d0675e3c2093cc6ab55d5c6db9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002780.fa
@@ -0,0 +1,6 @@
+>PROKKA_02583
+MSEPSPGGEVVAVAGHPIHVRRCSEPGRPWVLLESALGCPCTEWAWVQSHLACRGINSLA
+WDRPGIGATRPAGRTADATARHVARLEALMQQEGIDDAVLVGHSVGALLVRAFAASRPER
+VRGLVLVEGTHPRQRERSPREADLITAMERGLAIGAPTCFQDAREASAGLPTGLHDWTAR
+AASGRSADTAALRELRRVGEWSRRVASAGVGAAIPVHVLSAGRAVEADSAHRVLQQELAA
+LGAGPAEPIVVPDVGHQDIVMEEQPASAVAAVAERAVRSAEGHGAPPPDERSQENT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002781.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002781.fa
new file mode 100644
index 0000000000000000000000000000000000000000..384677744e0c8a7e03483e147448ae1af9ca7289
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002781.fa
@@ -0,0 +1,6 @@
+>PROKKA_02584
+MFTLIDAATNTIRPMTAKQPLDREVDGAATAGRLTAVGALVGSLEELSRREDGGDRSLFS
+WPVRQTALRAFRRRSLAPLWSLIEPRRYPILLAGRVLCAGVVLLAPDTSRVRGPALVGLT
+VSGLLKSYRNSYGSDGSDQLSFITFASLATAHLPGLTAGQRAVPLHFVGFQSVLSYTVAG
+VAKLLSTQWRDGSAIEGIFRTRTYGDAGFYRMIKDRPAAARALSWTVIVAETMTPIVLVL
+PPAGRRAVLGLAGLFHLGNARYMGLNRFFWAFTGTYPLVDRSARSIRRVLGLVEGRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002782.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002782.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bd58e8745dfa57c7ef0fe33b3b2dddb5c9ba9f1f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002782.fa
@@ -0,0 +1,2 @@
+>PROKKA_02617
+MATEQGYQRIVDKNTKPFIRLNDLIASLEQKAQEFGIHDAAAEADAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002787.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002787.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c2e5b138a44cfa982ab179e008171e635f5b5cee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002787.fa
@@ -0,0 +1,2 @@
+>PROKKA_02635
+MMYPLVSELAADGVPVAVSLRVLKLARQPYYRCPSPFLRWSRPTGPTPCTPLT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002795.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002795.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b76137e26c17540507f3a790c238437e13145b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002795.fa
@@ -0,0 +1,3 @@
+>PROKKA_02659
+MRFTAGLIVLVSLLVAEFLWPESRFIAFALSAGLVVAALTGSCLMGRILSRMPWNKVTAS
+PTARSAIASIPVATQEL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002799.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002799.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb83d010cca0af9e42df0be7a6755a2d9b9f361c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002799.fa
@@ -0,0 +1,5 @@
+>PROKKA_02664
+MGSMTSPTTRSRQGIGESFRLAVQALRGWTGRQVLAAIAASAVVAVVIGVATVLIPNPLF
+GRDIPPVWWNYPVWLVTSVLSGMLVATYIRPYRAAADEQQANAVSEDGAATDAADEAQAR
+RSSRMGMAGGILAWFAVGCPVCNKLALLALGYSGAITWFTPVQPFLALGALILTGVALVW
+RLRGQVACPVRPEPVAAVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002801.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002801.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d607d7e64b612b9a1135d1fbea302c2853f37e1d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002801.fa
@@ -0,0 +1,3 @@
+>PROKKA_02667
+MNENTREVILHVADDPADVQRALDAAAGLHAAGLGVRVRVIVNGPALAGLTGTDAVQVPE
+HTEVAACSVGLGRRGIDPGELRPEVGTVPSAVTAIVHAQLADAAYIRI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002802.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002802.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d96c9305afcb766205b039a8063b24906591fb22
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002802.fa
@@ -0,0 +1,5 @@
+>PROKKA_02668
+MRTIGLLHGMSSVATVDYYRRINDRVNELRGGHERAELVLSSVNFGVIERCVRAEAWDEA
+GQYLAGKARGLQRAGADFIACGSNTMHRVAPVIEAAITVPFLHIADVVATTATDIGVTRL
+GLLGTAPTMEQDFYRRRLERAGFTVLPPEPVDRTTVDQIIFDELTRHVFRPESRETYIRV
+MTDLHAAGAEAIVLGCTEIILLVGPDDVPGLPLLDSTTLHVEAIVQTAMSRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002814.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002814.fa
new file mode 100644
index 0000000000000000000000000000000000000000..58e765078af581c40910d026eec346aef1471fe3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002814.fa
@@ -0,0 +1,4 @@
+>PROKKA_00142
+MNNLTPAEVVGAYFQNLADGNVEQAMSALDPNIEWHQPGENRFAGVHRGPEAVGALIGGM
+MEVSQGTFAVAPAGPLMTNGDVVAAPVRFTGRRDGEVLDQDGIDLLTVTDGRISQVRLFS
+SDGPAEDRFWGQS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002818.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002818.fa
new file mode 100644
index 0000000000000000000000000000000000000000..99fd770c8678b012d8e95000cae948e94f7d8730
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002818.fa
@@ -0,0 +1,5 @@
+>PROKKA_00205
+MYLPRVRAPHTKTLPTLALVASITAALATGCSANTSQDAPASSAPAPTATASASSLSPDE
+AARSLASLESEAAQAKVDAAQRNFDAAVASASARALEYSQSKAAGQDLGQVTLETLDIGD
+TRPEWARPIKDVKAVGTDGIYVTYSETLTTAQAVEVATSIARRLAMFSVDSLNRVTLSDA
+SGTEHVVDITRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002819.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002819.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ede7075dc4c55fd305e2f5a3dd0805971cc0dfa7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002819.fa
@@ -0,0 +1,5 @@
+>PROKKA_00206
+MTTAQTITANLTAARHAYYAAVQTARTYQDPDLTPEALTRQRQDREAAARTAYAQELRPI
+REDYERAARLNAKALAKVPAPTGSTADVWRRVEMRLGAGATLDQIVATADVPTLQAVREW
+APTYLAVNGGDPAAAPALGDRLERATLARYATVTKDADMAAALAEAPTLAGLAVTLDDAE
+AEAQGIPGAGGLNGAVAAALAVQAAGSTTVDPDTTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002821.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002821.fa
new file mode 100644
index 0000000000000000000000000000000000000000..457919bbbbf6a4025dc3b4b5cdfceb84ae0cf64b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002821.fa
@@ -0,0 +1,3 @@
+>PROKKA_00209
+MTRTHPAENQHASGRYLDTTARDAEDLAAVADAAAKDADAMARIAADIVAQHAEDLAGIT
+ATTADDSQAHT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002823.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002823.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ba10ef93def3e261534a88b3a8619b84e7189f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002823.fa
@@ -0,0 +1,5 @@
+>PROKKA_00211
+MGASNVIAAYTYWRDRLSHRDLHALVFMAVTALDSDRPPVYYGGWEAVARALGLDLEGNP
+ASAKRTTVKALTALTEAGAITSSGTARAGIRAEYALNLAPGTTYVPSGRGRNVTWTARPT
+TARGTAMDPQVGTVVDPQRGTVVDPLQGDRGGPRRGTAMDPPKRTQEPHGGTREEPPEEP
+PITSQPNPGTRVRESDAMNDDRTPSKAEQEARLLAWAAEHYTEDPNALTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002828.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002828.fa
new file mode 100644
index 0000000000000000000000000000000000000000..131bb70d051d9c0bbf8cdc43234d2355e2d6d91e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002828.fa
@@ -0,0 +1,5 @@
+>PROKKA_00228
+MRLPESLDDIEAYADALSSEVADLGDYVLVGDSFGANIALALGARQPEGLSGLVLSGGFA
+ANPITSPAWKAAMRLMGRLRGPAYRQMVLRAHAHRLASPHDTEGQVPWSESQSRQLFLDH
+TPATSFGARVTAVLNADYTDELDRIQVPTLILTPSHDTLIGDDAARVLRDGIPHARERVL
+ERTGHMFRFTHPETYSQAVAEFLADESL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002830.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002830.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2e2e228e954816d823c0fec66e22948e37986604
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002830.fa
@@ -0,0 +1,4 @@
+>PROKKA_00230
+MGTKTSGVAPRDHPPFANSDDGYAWQSNWCDRCIHDQPAREGRYEDACGIWYIAECGQTP
+GEWLRQPGQRYGDQYHCIEFRSEDDGPEPPTDPEPTPPGQGELLPMEPYLGVKMFADVAA
+EVATVSTTS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002832.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002832.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bcfedb605b968d5273547a134944da26ef604395
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002832.fa
@@ -0,0 +1,15 @@
+>PROKKA_00270
+MATAATRESGTVGGTSPGPAGRVLAGALRWLRGVPATWTLLLFTALGPLLPLVDPARPGS
+LPHAPHEVATSLLFAPHPLAWALALVGVAVLGPPAEREAGSGPFAARVVLGHTASVLAVL
+GLLWAVRQVDPAWGAVLRSDAIAGPWAGLIVAFLASSGSWDSRWRRRLLTLALPVTAATV
+LFSGAPEDASLLTAVLLGGWLGRRRARRLGTDAAPVGSRSERRVLVATAVAAVVLGTFLA
+AGSPHLVGPLAGTRALFAASTVSPDMVAAACADDDRIRECARGTYILTATGPGAVLLAAL
+PLVLQLVLADGLRRGRRAALQGTLVLQSVLAALAAAHLGLAAWAVAAGPRDYPTDPSLIT
+RLILPVLVPLGVLALVLAHRGLFQARAPHGAYRRLRAVPILALAVVAMIVAVGLAVPEQF
+SPRPGVGALLADGLIALLPSTALTVLTPAALPSGPVARFLLEWLPLVPWLAGIWLLWRAQ
+HPLGGPVAQPGEAAEAARALAAEDATMAWMGTWEGCRLWRSPTHAGAVAYRVHQDVALTV
+GDPYSSARDRAVVTRQFAEFCVAHSLVPALYSVHPVTAQAVESRGWFGVQVAEEAVIRLG
+GVTFGGKRFQDLRTARNRAKKEGITARWTTWAEAGDDLRAQIRAISAAWVADKELPEMGF
+TLGGLAELDDPAVRLLLAEDEDGRLHGVTSWLPVHDAGRLVGLTLDFMRRAEGGFRPVVE
+FLLAQAVLDAQEEGLALVSLSGAPLARSQPDPSADVAPAQTGALDRLLDQLGHGLEPVYG
+FRSLHAFKEKFGPESVPLRLCVPDPAELPRVGAALTRAYLPTLTLGDLVRAGQDLRRREG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002833.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002833.fa
new file mode 100644
index 0000000000000000000000000000000000000000..61a48b735667ee0151635b1d9bccc2354f07169e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002833.fa
@@ -0,0 +1,5 @@
+>PROKKA_00287
+MPDVLYAWPSAARVGRRVPKESLYGAGHVSPAVRELFVSSVDRITWDYKLAGGTIGISGT
+PEVPEIQVFRVRAKGDDVPDQVLAAIDRAVQQPVFFEVTRGLDDAEVRLGATYKIAGSAP
+AAEYARTAWLPACAPRRPIPTGVDMAQVYAQVLRPLLGVRMEPGERPQAIAARLVALREL
+ERRHAAVASRHRRERQFNRKVELRKELKGIEQEMEQWR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002835.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002835.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a05558a4c58e6a7c86ac4e1925a38ae03dabfa51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002835.fa
@@ -0,0 +1,8 @@
+>PROKKA_00291
+MPLTLTPNESAQRALHLMAARLEPIIARTLAPHLGGLEWTAFLDVMDDVKGKPSYPYNRM
+DPQPQLRILTERLGNLGYPFGAGRSRMVSALGSQLRIARNMVAHNAEIEPLDAWRVADAA
+SLLLGELGDAEGAQELAAWRDQILRLDAPADDEPDHESGEDLHDGEGGAQEAAKEVTAPD
+AEVFRIQTNEPSPTVGAGLRHERQPYDPWIPGAAGEKSVLDGVRSQHNKDLLRSVLEEIV
+EHEGPIHIDRLATLAGRSFGFGRLETKRKDLLKRHVRKCPGLQVRGEWVWGDSVDPDQWT
+EFRPNDSTSERKFVEIAPQELRNASAFLRTLHPKDDQATHERRVLQTFGRRNKSKAIREH
+LARALD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002845.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002845.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cd880dfa316bc4770720c8fa9bb84c953617180d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002845.fa
@@ -0,0 +1,3 @@
+>PROKKA_00338
+MGFSLEMTDINVFQKANTESAVSGEELMQEIENLRTGVEALKETFKGQGATSYNNFMVAV
+NDAQNQLAEALGKINVGQADVFQAYVTQEDEQVSTNEPAVSEAQSFSFPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002847.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002847.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff087a86b73e058c0549c618fbea622ce7d839f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002847.fa
@@ -0,0 +1,9 @@
+>PROKKA_00340
+MATKYSRVTLLGERRHADVLLPSDTPVGVLMPQILSLLAEQPGREPAVRALYRDTGAQLA
+PETTLGLAGVLDGETLRVAATTTAPDAPIVYDLHDTVAAQTDARGRWGKRARLTVLGLVA
+VFLGWWAAVQLTVGLPDEASALARLGIGAGLLLASLGVSVWSRRRAVALTLLGAGAVIAL
+NGHWWLMAVRAMPLAPAVLIGLCGGVALLLLAAQVSGQRRPLVLAAGVLAVLTGAWAAGP
+TAAGWLIGERTASVPVTVGALTAVVALLVLSVLAQAAVSHAGLAGLDDQESAGARLLRTD
+VAAAVATAHRSMVLGVLLCAASIAVSFWWISDDIVQPAFSVPFSAVLTIAVWLRAQAFPL
+TLQRAPLLLTAAWGLWCTVRLTSTAFPALAVPLLVALAVIAVLLVALQVVTVPPHVQARA
+RRLSTTLETLAVVALIPLLVGYVGLYAAMLETF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002852.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002852.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b138d920f819cfac5f79963bab84c1104b9d21bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002852.fa
@@ -0,0 +1,12 @@
+>PROKKA_00351
+MARTFPNSAPTRDNQSLAGLYDMDFAPNEGAVRGEFTMLRNAQTAARIMEHAGLADLIAT
+WQAEDGQGNRPGPKPWLTEVNVLALLLLLALSRRAPLFQEVGEVLIEASDETLAALGIDP
+ARRTYSEKAAYHRAYHSYRRLLPLIDPEPAPLYRRLTVQECDEVKAAWVLEENAVKRERA
+HTMANALLYGTWMLLPRQVRRAYKGDIAMDATFVKSPAYNGNTKPKSSASEVVHYRSSDP
+FAGWYKRDGNHAGPNELPASRAKYQRTQDYVGWGREAHTAVSYGKDVPGIVLAVSLDTPS
+ARLPENALRMVEHLKRNNMPVGHVVTDRAYLPGTKPAELARPLRARGYRLVFDYRAEEHG
+MGQTASHGGAIQVEGRWYCPSMPAPLVNATKDHMLRKESDPEYIDEATYRTRIEQRKQYE
+LHLKERPDAEGVARYACPAVGPSATVSCPRRKEHPKAADKPKGRIMLPLLVKPAPQVCEQ
+QSMKISPLTGEKYAQEYPYKSEKWREHYTGGRQMVESLNASLKNGAHMPIDDTQMRPRRG
+FAAQIVSLAVMVAATNTRKIIAWLHEQVGVTSLSSAPVKRARRRERTAGFTRADEFGPAY
+SPPGGLPPERRETA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002854.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002854.fa
new file mode 100644
index 0000000000000000000000000000000000000000..abeed18372670394ea2e284bbd9148f85948831b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002854.fa
@@ -0,0 +1,3 @@
+>PROKKA_00372
+MIAAFASRKEHPSLPFWPMLFENHVIRFVGSDDVPAPSKAAAVREVTVAAAHLVIPVAEV
+LPLGETARAHDLGDAGPGGRVLVDACR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002858.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002858.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d12c887f41e44b541cb4475f2a91620c051abe49
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002858.fa
@@ -0,0 +1,4 @@
+>PROKKA_00424
+MREFGETRGDAMRALAARDVAPGVVGYADGEPVAWCSISPRPQIPRLEASQLMPRTDDVD
+VWSVICSGHRRQGHTTRLLEAAVAFAREHGAPAVEAHPVDNRPDGGGAASGTDAPDRIDT
+TMAFAGTWSMFDRAGFEVVGETAAKGSGRPRLVMRRDC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002861.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002861.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b95bbb592b992ad0a9afe499658be8c5cefc76b1
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002861.fa
@@ -0,0 +1,4 @@
+>PROKKA_00445
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002862.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002862.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d279a2fa90bb4e2870793c348256025190be4d47
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@@ -0,0 +1,4 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002864.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002864.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aca1b2cc3d31de1d8761e545b54b4c87f3a7159f
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@@ -0,0 +1,5 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002868.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002868.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f70fcac6f2f60f48b6ede4e8c4bc7b8b902fbf2f
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002868.fa
@@ -0,0 +1,6 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002870.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002870.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f12ee63c5dddb6dd28f8b4125866c60eb904a21
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002870.fa
@@ -0,0 +1,3 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002872.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002872.fa
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/Orthogroup_Sequences/OG0002877.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002877.fa
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/Orthogroup_Sequences/OG0002880.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002880.fa
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/Orthogroup_Sequences/OG0002885.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002885.fa
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002886.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002886.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7f85952d0977b4a9cdcc94503ced7712c02dd706
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002898.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002898.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1c3a47311edcd72628dcde2ff6bf4d907d8668a1
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@@ -0,0 +1,3 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002902.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002902.fa
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002904.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002904.fa
new file mode 100644
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@@ -0,0 +1,3 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002905.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002905.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5612b65d60ddac6f97269e834b85b8cebce4e2ce
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@@ -0,0 +1,3 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002911.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002911.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a57539a621ce380e4ed2c7824690b1830cd292c0
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002913.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002913.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1841246c657340446267ee47d31cd4e8f66f83b0
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@@ -0,0 +1,3 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002914.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002914.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1f31462a141a1841c4acbfdedb04d01d89ec2536
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002914.fa
@@ -0,0 +1,3 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002921.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002921.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2e86d2f19d35526405b68f7fd42e29d266df9561
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002921.fa
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002922.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002922.fa
new file mode 100644
index 0000000000000000000000000000000000000000..78abd8956a694097045ca43d5486721cd3286ac9
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002922.fa
@@ -0,0 +1,4 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002924.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002924.fa
new file mode 100644
index 0000000000000000000000000000000000000000..599c46949077035c0a175c5cb763734b001dd5d6
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002924.fa
@@ -0,0 +1,9 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002928.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002928.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7192d5fb43cd4893c54bf443cf34cc35430785ca
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@@ -0,0 +1,9 @@
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002931.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002931.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98e3962fd129b762114c82e78491261fb7abebe9
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002931.fa
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002932.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002932.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d4b3617c2c124c2a77abe4de7b515107058d9844
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002932.fa
@@ -0,0 +1,5 @@
+>PROKKA_00993
+MLLLIFGPPAVGKMTVGRAVAAASDFRLFHNHMTIEPLLEVFGHGTEPFNVLTDEFRIRV
+IEEAARAGVDLAFTLVWDVTDPDDAEYVARCVAAAGDDAAFVELRADLATRLERNRTEER
+LLHKPSKRNLEWSDGNVREMEATWTMTTADGPGAAEVLLGAHPHLGLQTDDLTAEETAER
+ILAWLADVRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002934.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002934.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1181a64d5cf30fd5aca919da521b39cf1292d4c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002934.fa
@@ -0,0 +1,8 @@
+>PROKKA_01027
+MRSASRRTLIAGLGATAALALTGASAAPALAAGTATATATMDVYLRATPSWTAGRLLVVP
+RGAAVSVTGVVSSGWQQVGYAGQTGWIVPDYLTPVAAVAVTDLTSVATCLRSTPSWSGGQ
+LAYLAAGTGVARTGATSGSWAQVTTGGRTGWLHTGCLTPVVERTVAVVARPVTRLNSTFA
+YGAQSSAYHVWAEGIDWSRPTGVLWYLDGDYTNPAWSRVMNLTGAEMTSIAAEANRRNLV
+CVAVNTPDVYRADVGYSWWYDRPSTAPYFRAFADWFNRTYGMDAGRQWLMGYSGGAQMIT
+GSIMAQQQSTWGFSGGGAIIVGGGGRPWTYDEVGMGSTYKQMSATWVVGSLDVAGATVPA
+TWSALDSARGGQAYFAAQGFVNTAYTELAQVAHRYVLADVMQAPLEAAGVARLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002935.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002935.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7bb42bcd679919f7de9061379a70badf42ba988
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002935.fa
@@ -0,0 +1,5 @@
+>PROKKA_01030
+MTIERSSAPSGGPLPRGIQHIGVTVPDLDAATRFLADGLGAKVAYDGLRPEDEPRSGPEV
+ERQLGLPAGAEIRRQRMLVIGEGPGLEMFEVSGEQRPASGLSDLGLNHISLYCDDIDGSL
+ARLVAAGGEALSEVHGNSRHEDTPGNGSVYVRAPWGMLIELQTIPGGHTYPADAEAEVWM
+PRPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002936.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002936.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12fa4c32c1b81449d8a96020803c76bf986ec788
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002936.fa
@@ -0,0 +1,8 @@
+>PROKKA_01054
+MTLDIPLWPVLLLGLTVVGVLALAARRGPRRSARTTARQHLGLWALLALVLTGALLGPWA
+YVGLWAGDGGLSWVQADGAPTRGTVELVESAVPAELLTPGIAAVALLPALWLVGLAALAQ
+VTWPRETGPRRRAALRSRSWRHLLSRRVLVILGGATVLAAAGIAAMAGLPAVDGVQLSVH
+TGPESTQFRASADSQPAGADVAPWFAAAAATVLAAVAGVVLVVHRRGALGGLSPREDLAA
+RRIAVDRSARIGAALLAWNGLAGLLAAGAHAQARDAAGLLGDLAGRWAEGGIDVAGVTAA
+VRAQDTPDAGVSAAVLAATALIAAVLIFARPRAEERILQDGPDADPVATGGDSASGGDSA
+SGGLDRLPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002939.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002939.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5ff31cf41c8e3d9cef50a1071b9eb5bbf2694de
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002939.fa
@@ -0,0 +1,6 @@
+>PROKKA_01179
+MSTTTTAPGRLFGYARREFVRNVRMIEGSFFIVVLPVALYLMFGALSDWGDLPVGHGNAS
+AYTMTGMAVYGAVMATTSIAGSAAVERQSGWGRQLSLTALTPGAYLAGKCLVALAMAALP
+VLAVLAAGALTGAELDGPLRWLTTGALALVSSLPFALFGLAAALLFRSEAAVSAASGILV
+VFGFLGNLFVPLSGIMLDIGRFTPVYGAGALARWPQMEGERAPMGTEPAAADPLWLPIVN
+LLAWTAVFAVVCLLASRSRTARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002942.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002942.fa
new file mode 100644
index 0000000000000000000000000000000000000000..41bc5e2874f9dafebda76eed5c25fa085e9c3e9b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002942.fa
@@ -0,0 +1,8 @@
+>PROKKA_01212
+MTGTDDVAPTRSPEVAVIGGGIVGLSTAYALREQGVPVRLYEAGLPGAGQSAGESRIFRH
+AHDDPRLVAFARESRGVWDEWAEHFDVELVSSDGVVALGDSALARLRVLDEVGGVEAHEI
+DAAELAQRMPLLAGYSGPAVLDESGGAIRTRAAITALAGALGDAVTTAEVISIDPRADGT
+VEVRSVTDRAVYSKVVVCAGRETARLARTVGLSLPVRLAAHVRLTFDVKDAAPARVACLQ
+DSSGVFGEVGVYATPLPGNSSYSVGLSDTVGVRDDGTFIDPAAIRSLDERAREYVTRALP
+GLHPEPRDFLHCWVTDLPWSEDGVAVWEAGSVLFVAGHNLFKQAPALGRALARAATGGGL
+AADLTPAARLGEALR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002947.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002947.fa
new file mode 100644
index 0000000000000000000000000000000000000000..047c33e3a1f0381c3bb80d2fa76a84fa4e64f25f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002947.fa
@@ -0,0 +1,6 @@
+>PROKKA_01224
+MDAAQLPAFLTSGTVEDLMADAAAPAWGTRAFVEQVMGGPVSVHVRAEDPRRADIAAAVR
+RVWDLLHRIDAVLSPWRTDSDLLRMRRGELDAAAAHPWLAEVRALTDESERVTGGLFTTD
+LPAPDGSRGWDPTGLVKGWAGDLAAQVLAGVPGISYAVNAAGDVRVGVTPGGPRDPWEVG
+VEDPARPGQMAVVVSLVEGALATSGTAARGAHVMDPRVVVDGHPAPATPQLTSVSVLGPT
+LTWADAWATASLLDPGALAAAGPAWAAYRVVSRTV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002951.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002951.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8d0f25791cb5f7f559c63623eff932e6054284a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002951.fa
@@ -0,0 +1,5 @@
+>PROKKA_01315
+MLVDAGLIGALLAIGTLARAVFTPLQTLIIPASVIAGILGLALGPNGAGWLPFSDQVGTY
+GSIVIVFVFVCLALTDDFDVRKIGRPVGSFAAYGVLIYASQVAIGALAALLILHPLFHTP
+DSFGLLLFAGWAGGFGSAAAVGAARGQRPRVCRPDLHPRGPAHGRARPGRRVPRDRPPHL
+LRRLRGVPGLPGGHRRHVRRRRLRPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002952.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002952.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d602b86900e190928d5851d51136c1b0e60ebb0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002952.fa
@@ -0,0 +1,9 @@
+>PROKKA_01336
+MSSRRAATAPPGSAPGGAVPVWSASRARRVVLGAQGLAGPRPAASARRVAGVAARLGVVQ
+VDSVDVLARAHLMPFHSRLEDVDPAHVAALTEGRGRRFTEAWAHEASIVPATSRAALTLL
+QGRRWPLATALPEDRRTAAAADIRALLAAHGPLTAREVRDRRASPCGPGTSWGWNWSEDK
+RVLEHLFAEGSLASAGRTASFERRYALPELLWPQGESGRAPVPPEPAAGGDARLAAALQL
+TRIALRAQGVGVADEIADHHRAPVTLTRRALEVLADRGEALEVRLDLGGTRPVPAWADPT
+ARTPRRAGACTLLNPFDPAVFHRPRVERLFGVRYRLGIYTPVDRRVRGYYPLLLLQGERL
+TAQADLGAVRRGPDPRLELRGAWSEDPAAHPGPAGPAPTPDEVADALAEEALRAARWRGL
+PRVVVPEGAPGDLTPRVRRALLERDGGRVPPGP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002956.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002956.fa
new file mode 100644
index 0000000000000000000000000000000000000000..399b967a7557ccd537ffa384399b5552a6676f21
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002956.fa
@@ -0,0 +1,3 @@
+>PROKKA_01523
+MSLVKGAQMKLKAVGVSVKPGGEVEELVIGGTVSTRGEGIDAVEIDGVVKQARVGGVEAH
+GADARRVRVGDDATCPAGLEAFRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002962.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002962.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c4add8097b795482d077dedbabad820e777c806
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002962.fa
@@ -0,0 +1,4 @@
+>PROKKA_01748
+MHDSLRPTRSFVALLRNPRIRRALGALLTGSEVAASDRGALKAAESVGLTRADDDDTPVL
+QEAFLADAVAALDRALGPLAVLDGGRIRVGDLPHGEVDAAVGAVVERVLSPGERVPEATL
+NDRLALFVVDVAFFRRHAYDLGLVDRELDGSAYWRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002963.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002963.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5020cad89be7b69729b68fc859c6d7edfc21c80
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002963.fa
@@ -0,0 +1,3 @@
+>PROKKA_01753
+MSGSWPERAGRPRRSPNEQDGRATLLAVLDYRDNGTAVSLTRAFTVPTFRGQGHAPTLTA
+GAVQDIAECGGAAGGTHVVPMCWYVAQWFDEHPERQAMLARV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002966.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002966.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e70444859a19904629626e7963c11c35e0233275
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002966.fa
@@ -0,0 +1,5 @@
+>PROKKA_01774
+MVLSVLADDAAVREVFLDSPALEVMNQGSVHVNLATISPSLASEAAGRHTGAGVGYVAAP
+MFGGVPVAQAGRLNIVTAGQTEVVERVRPYLDAFSAALWPVGEDPAQANVLKVAGQILIA
+SAIQAMSEAVSVVERSGGDVNRAVEVFTSTITPGPVYSMYGAMIAESRYEPARFTPILGR
+KDVDLARSQAAAEGLRLPFGDLLSGLLREALAAGHESRDWAVLGEMQRHRNGGEGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002967.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002967.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ae28cf4ab9a6ebdfa7f83156727f326612ddf0e9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002967.fa
@@ -0,0 +1,7 @@
+>PROKKA_01776
+MMRGGEGEKGLGGRAGVEVVPREVLHPARGVANLHGNQIITVGDHMRGEQGDGESVANQP
+EDEIHGHRFESHVSLKIGGLKCQVRLSSTCGATGEINEPFAGDLLKSHVGPPRQPMRSRK
+HCNQTLTGELLGRHLRWWGALGQAQESGIKAAGMNVSQELLATPSAQGDADLRVRLVIAR
+QERRHIDRGHGGDHSEAERATNISRGGRSLGNRTVGRSQTLASGLDKHHTRRSGLHSPRR
+AGKQLDSDLSFQRLDLMTERRLHHKAAFRGPSEAPLLSDRDHVSQLLQFHRPMMHLHPSS
+PKYAARSLTVSGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002973.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002973.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1b234dad2bfd477e113643324b8a507d8f670836
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002973.fa
@@ -0,0 +1,7 @@
+>PROKKA_01783
+MSTPGHIELDRAVDSLHVGRRHRADLGDIDALAASIERDGLLQPLTVSPDGVLICGARRL
+AAIKQLGWRTVNVWVRSGISDRLGHLLAEQDDNVLHKPLTALEAAALYRELKSLMAEDAA
+RRKAATQFRSDNQPGTHGPGKFPEPSGATGEAREQAAGMIPGGASYKTLDKIGYLEHAAT
+DETLPEHVRAAAQRGLEQIDAGSPVHPIYETIRNHTANPDAGDEALHQAAADALARVQSA
+GRPKPAPAKKPNSTPESGPVQYPVRAFVVTWTELDQWWTHYDPAVLAVELTDEHVATFLR
+VIEHTIAFADALQAALTNHDDTTTASGTVTESDDGHAGGRPQLRAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002975.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002975.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5867adcfbac03ad9b6b332b496e0ead87ab1cc1a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002975.fa
@@ -0,0 +1,6 @@
+>PROKKA_01789
+MSPADRLNEGPDRPRALALLNAVLEREGFHAFYAEDNHCYLRHMGTQSVTVLAANPHRPF
+SKAEQERRKLLAAYLDSCSEDDLIEKILLPMFRQLGYHRITAAGHKDKSLEYGKDVWMRY
+TLPTQHVLYFGLQAKKGKLDASGVTKAGNANMAEIHNQALMMLAHEIFDPEVNRRVLVDH
+AFIVAGGEITKSARNWLGNALDASKRSQIMFLDRDDILNLYVVSTLPLPDEAQPSSPPNP
+WLKTDEPPF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002976.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002976.fa
new file mode 100644
index 0000000000000000000000000000000000000000..36ec965ec32a755e17cf63a07be0d5b28a346916
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002976.fa
@@ -0,0 +1,10 @@
+>PROKKA_01791
+MGVCDLPVISGVCETAGEAAASLVSAPFDWLAQAMGSAAGWLFEAVWNVFDATTLVDITS
+DGYLSVYNLLFGIAVFVMLLFFCLQLITGLIRRDPTALTRAALGLAKSVLGSFVVITLTG
+LLLEVVDQLCVGIVQAAGETTESMGEKITILAGGLTAINIAAPGVGAIITIFLAGLAITS
+AAIVWLSLLVRKALLLVAIVFAPLALSGSSWDATRGWISKWAMFVVALICSKLVLVVMFL
+VAITQVAAPIDGDLSSISDPLAGVVLMAMAAFAPYLTYRFISFVGFDMYHAIGAEQDAKN
+SLNRPIPLPDRQPGNPQQVLDGNNSGNGGGGGKQPPKPSSPNPSASQGGTEAGAGTGGAA
+GSGASGSGAASGGSAAAAGPAAAAVIGVQVAKDAATAGPKAGAELGQQAETAADAADHTP
+TPNGGAGNGGNTPPAPAPGGTPPQPGTPPASTQPTPPSTPSSQPPGSSSHGGGEQVSPSA
+PVPNPPPADNPPPPSSAWKEPQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002977.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002977.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b65e20f2e883c24c6d534a9f8f56f23bb4b8521d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002977.fa
@@ -0,0 +1,6 @@
+>PROKKA_01793
+MYNLLIGLTRGEVGADRLLEHTADDVREYLAPEVGQVRIERLLNLPTLLMPETGFDDEPQ
+IARVGHVTNVNKSRYGYTFSFVPNPAIAPIPSPRIEAAAGVLDITDWEFHRTHWAVKDVD
+LYRVLDQELSARVKPKVFQFPTSEPFDPDLVAVMMPFSPAFSAVYESLKEGIEAAGMRCL
+RADDIWERDHILDDVLSLIWRARVVIADLSEKNPNVFYETGIAHTLGRDTILVAQSMSDI
+PFDLQGIRALKYLNNGEGRAALSRGITSRLNTITTS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002979.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002979.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7314b52769748b6d812f276ec4e5605e13445538
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002979.fa
@@ -0,0 +1,4 @@
+>PROKKA_01799
+MPKLPALRHRRNDPSEAVPVVLRHVVITVDITGTLTVTVDQQPHLPQAGEVWGRGDFGAI
+LDDLTEQRRIPVRVDVYESDGSHFTDIIHAHRPRRAPEPEPDDPAAADEEAAADTPAPPT
+DDPGRLVGFLPGETVFLGQIVEEVAADENGTITPPDTALGPVVVVGRASGTVIVQETR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002985.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002985.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e527831d93e4252442b714e05b114c2939f7f20f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002985.fa
@@ -0,0 +1,5 @@
+>PROKKA_01811
+MTTPHESHRPDPDEELLRAVLAEEEAALTEEHGRRDPISPAARTRLRGGTAGAPVPQDRP
+SVEDVYGPVDRPSVGLPGDATADGSVTGAPGAASVPAAGDGSPEVFIGADAETPADVQAG
+RRGARPQRPGPGAAAHRAGHRGAAGRRGVVPVGPPPLARDHGDREHRPVGRPPVGRRGDA
+RRGRDLGGRGAIALTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002986.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002986.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cfe542ef5e4d3485f70f707f364aa8fa4ccb2bdc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002986.fa
@@ -0,0 +1,3 @@
+>PROKKA_01827
+MAGRTDGVEPDEIELGAVLSALADPHRRRVIHDLVNDADGSERSCTSFGLDLSKSTRSHH
+FKVLREAGLVHQVDRGNRSEVTLRRRDLDARFPGLLDLIGSDSGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002993.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002993.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0c968a6e9121ba1ac999632fe1337a444067e828
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002993.fa
@@ -0,0 +1,4 @@
+>PROKKA_01905
+MRRIDRIAGGRQAHLRIAPAALHHPRTRRDFRWITWILTAELVIGAAAVGIAVWLTVQGH
+PVAMSAWMRAVVVLGMTATLFYFFYFALRAAAGWRWAYQRLRLFAQVFPVITLVLAAVPG
+LYPVWMVTEQIVFSLLMIGVGDILTSDHMREAYRHPDRPVPRFE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002994.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002994.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d232dfe51e19db293b3dc460bd4c214b74300e6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0002994.fa
@@ -0,0 +1,9 @@
+>PROKKA_01909
+MPRLHSAHDTADNAPGARALSGVGAARHRALRPAAVLFTAGLLLTGCAGPDGAPAGGSPE
+AGASTTEDAGASSGTAGGSAGGQSGASESRAEGSPPVDPADFPASNTTKLTRVETIKDPG
+LTPKSIVSNQHGLAIANNMMYRHNVMLFDTRSREVVQTLEDTVDTDAMGIDGLSGVVNGS
+PVEAAWTQDGRYAYVSNYQLTGGEGTGVKPDDNCTAGSAISPSLVYRYSVEEKKWDAAYR
+VGRVPKYLALSPDDSRLLVSNWCDATLSVLDAETGELQHTIPLDTMPRGIVVLPDNKTAY
+VVAMWADKLYRVDLDAGTAELVMNTGPQPRHLSLSPDGKTLYMTVAGADRIVKLDAATGK
+VLASASAGDEPRSMDVSRDGTALYVVNYEASTLTKIDAETLEILDTAPAGENTVGVTYDD
+PTGQVWVANYGGTVDVYDDTDGVGPGAAGSAQPTADAPGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003001.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003001.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9697be5738602ee922e86e292e6f2c1bfd1c608
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003001.fa
@@ -0,0 +1,3 @@
+>PROKKA_02014
+MRGGVFAEIAPREVTDEVCPPVNCLSAWETEVGRFVGFRHEGDAEYWHVVLGDEARRNDR
+VLVDFSGGKYDRDQVRHAVDVLFHDRDWT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003003.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003003.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0c11a65dfe048429ab6acd31e11b47248f0c2a7f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003003.fa
@@ -0,0 +1,6 @@
+>PROKKA_02045
+MMGPSHAVTGAAGWLALTGPLADLAGVYVGPQVQLVGALTTAGAALISDWDHPRATIATA
+LPPLSTVLARFIRRAAGGHRRGTHSFVGLAAFTAVTWVLTPLTVTVGSVTFSAGQGVVAA
+FLAAVAARILRVAPGPVTGWAVGLAAGALAGTTAPGATWLTVSVALGVGLHIVGDMLTTR
+GVALLWPALPDPPVPTPFWLPGGRFRLPLLGRAGSWREWVVATACTVYVVGAVSAVVRAL
+LAAADPAAWPLPGPFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003004.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003004.fa
new file mode 100644
index 0000000000000000000000000000000000000000..48169b60f87e34b293f15d41ea8abf08357d4bf0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003004.fa
@@ -0,0 +1,5 @@
+>PROKKA_02078
+MDAAFGPRVRFLGLQGSRARGEASATSDIDAVLVLDALTPRDVDAYRELLDGLPHRELAC
+GFLSGRDELLTWDAADLVQFVHDTTPIRGSLAELLPRLDAAAVARAVTAGAGNVYHGAVH
+TLVHTRSPETIAGLAKAAAFVVQARHLQRTGTHVRRQTDLLDVVDPADRDVLALALAVRG
+GAAVDVDRDGRLLFGWAQRVLVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003005.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003005.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37a762b2a03f91df9bf7dbafa5994464159ed5d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003005.fa
@@ -0,0 +1,9 @@
+>PROKKA_02079
+MEAALFRETLIGDAGLIGGLLLVAVVLRAKVRVLQWLLLPAPVIAGLLGFLLGPQVAGAW
+GLRVGAWEFTGLPFSPYVGSYTTLLIAVVFACLALSQSFSFRKATGPLAGFTGYGVLMSA
+GQVVAGMLLVLLVLGPVMGSSDAIGMVLFASWSGGFGTSAALGDVFADAGRPEITSIAFT
+SATVGMLSGIVGGVILAKIGSSRGHTRAFSTQAAFTPSLRTGVLEHDDRPVAARHTMSGS
+SIETLTLHMALVGAVVALGWLFMTTTGEVLDDFALPLFASAFLAGLLARWVVVRSGASRV
+MEPQTLKALSGAASDVLIVCGIVSIEPAFVADHLAELAVVFALGLAFCLFLGLVVAPRYL
+GESWFEKQIFTWGWATGSVATGIALLRIVDPDLESGTVEDFGYAYLPLIPVEGAAVAIAP
+LLIVAGAPWSVVAIWGVIAVVGAVVMVRQGGPDPRRTTTAARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003010.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003010.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a0353e53e28275c0a87708cbf59b6fedc675d0b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003010.fa
@@ -0,0 +1,3 @@
+>PROKKA_02210
+MRLPRPSDYIAMMIPYITLHKPAEVAALAAKDLCLVDVGNHTASEVEESVIFHPGARISV
+AIKQSFHMSMLQEH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003011.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003011.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e332b42d4d6d516e6c6f47ce2c69ca74647b45ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003011.fa
@@ -0,0 +1,3 @@
+>PROKKA_02212
+MVEGIVYRYRTGIAWRDLPEVFGPWQTVWTWHYRMASDGTWDRVLAKLTAAADAAGLVDW
+SLSVDSTIARAHQHATNTTRLTGGWIELQESAGRAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003012.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003012.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6ae18f777ecbe7e8a8f580913144e18d93ceb03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003012.fa
@@ -0,0 +1,4 @@
+>PROKKA_02213
+MFLPLMGQLRVGRDRGRPRTRPNAVRADKAYSSRAIRGHLRSRGIKAVIPEPDDQKGHRR
+RRGSRGGRPIGLDAIDYKNRNVIERQYCHLKQWRGLATRYDKHAIVYRAAVVLNAVIAWA
+KTLSDTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003013.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003013.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85e5f59cb4334520a22822ce468b1faa5ce589fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003013.fa
@@ -0,0 +1,5 @@
+>PROKKA_02218
+MLSKPAANSWSESNSASLHQTQGASLQREKERLGQAIAAAKGRLAEASEAAESGARRLLT
+KNGEDLELAVEEALSALGFEVTLMDSDGVAKLEDLRVSTSSGTWTALVEVKGYSKAGKSN
+DFQKFARYSSEYSRQTNMQPDAYWYVVNAYMGQPPAARPGPFESVQDHVQTFSEEGGLVI
+PTAELFRLVRSVEAGVLTTGAAQASLTSQRGLYSTDSLTHEASDGGTAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003015.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003015.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d247703509811d292c1b1312f5b19d2ba195351b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003015.fa
@@ -0,0 +1,2 @@
+>PROKKA_02228
+MHTLDQLTAQRPPHARTPMNSSSARPDVM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003020.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003020.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d7e7f7d56546ac796eb237d5d71ae80ee0fa961f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003020.fa
@@ -0,0 +1,2 @@
+>PROKKA_02255
+MFDPEAIESARERLDAKQIAPEERAGQTPDVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003021.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003021.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8552e8684664d16331662fa6f0738211f793c224
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003021.fa
@@ -0,0 +1,8 @@
+>PROKKA_02257
+MERRVMAPRPGWERTIASQGLVFDETVHPDGTVTHYWNESACYALTMAEVEHLEQASERL
+HAMSLEAARFLADEQSVPGSPWRALGIPREAAQLAVDSLNAGEPSLYGRFDLVYSGPDAP
+TKLLEYNADTPTGLVEAAVCQWFWKEDVFGDAVDQWNGIFEALTDRWRRIAPPEADGTPA
+RVHFAHTELDETGEDAMTVAVLRDAAEQAGVRGESLLMSQIGFDTERLRFVGADLRYLRR
+IFKLYPWEDMVTERFGPRLKLDDEVRWIEPPWKMLLSTKALTAALWHLYPGHELLLPTFL
+NDRGGLREWVRKPLHGREGAGIEIRSRAGDVSSAAGRWGAEGHVYQQFHGLPDFPAPDGA
+PNRPVLGTWMVGDECFGVGIRESDGPVTDALCRFVPNIIDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003023.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003023.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2fd00e329bf19d69ce8b824965c779772455bd01
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003023.fa
@@ -0,0 +1,5 @@
+>PROKKA_02270
+MRPLTLTVKNTFQGSHIRFGSQFGTENTNLAVQSGIIGGAANPLSLHQSPLSNSATSDSR
+VDANKTVTTFTFDRPVTSLAFSITDIDSTRNDFADAVAVTSAAAFTSSKADSSSSGLQGV
+GTVADPWRPWTTDNPVNNSATNGNVTVRFTSQVTSFQIHYWNQTAASYASVDGDQKIFIS
+NLSLTYNACA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003028.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003028.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45debc6ac43875be4f793d1cb68bd9a161c14df2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003028.fa
@@ -0,0 +1,2 @@
+>PROKKA_02320
+MWIIRQGKDFQEEVLVFITAKIFIESPHRLCICPPHHLAYLKKALVEELP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003035.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003035.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9666331020c06d87888c54c0f7408966538605cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003035.fa
@@ -0,0 +1,4 @@
+>PROKKA_00112
+MDFWSTIWDAIWWFFTIFVFVAYLIALFSIISDLFRDRELSGVYKAIWLLFLIFLPFLTA
+LVYLIFRGRGMGDRAERQTREAKATADDYIRTVAGGPASEIAQAKQLLDSGTISEAEFQS
+LKQSALDGSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003036.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003036.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb9af3d8bedd3c0b9a654c37a3a0408d4f6cad97
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003036.fa
@@ -0,0 +1,4 @@
+>PROKKA_00115
+MTSKPSIDDVAAAIFEHFDRPITTMKLQKLAYLAQGWNLAFRGDPMFDGKFEAWVNGPVS
+RELYRKHRGEFARSRWPEGNPKALSDEDRIILDAVIDNYGGLSGAELSDLTHVAGTPWHR
+ARAVSNAGPSEPSRQPLDEALIRTHFRQLLGLDDPEYESNTNGEPPPNTGHYHAFSY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003038.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003038.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b1d62c8ede2c351d61c7591c5b8744ebff56bf4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003038.fa
@@ -0,0 +1,7 @@
+>PROKKA_00118
+MMSAEGPKRRELFRWWEWALIALAVISIPAGPGALIFLMPVLPRIVLLIRKHRYFNSEEF
+QEKKAEIRAFVAEHNELKEYIDEIRARGSFSLGESSTGQHAHLAYSENTSRHNYIRDRNV
+ATLGAPNVHNCSLQVVRKAQMDPIRYLMKYFHINAEEDRLAEVEEMGSSLAQLEEALSNL
+QNREASITEAIQPPSFIQKHFLDEFMEQVGVEISPITIPYEIYTFEYVSAGGNSSERTNV
+VLNSQALDALIDTMSARIKFRKSAAGQRALMTSKLRHHIKDRDNFTCQNCGVSTYAEPHL
+LLEVDHIIPVSRGGLTTEENLQALCWKCNRSKSNKI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003042.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003042.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2b2b3f6f12f6fb887b5854358e2822b3019562b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003042.fa
@@ -0,0 +1,3 @@
+>PROKKA_00165
+MIFIVVKFTVKPDWSDRWLDLTSSFTRDTRHEPGNLWFEWSRSVENPNEFILVEAFEDDA
+AEAHVNSEHFQNAMQQMRQALVETPRIISRQIEGNTWDRMGELAID
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003043.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003043.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c460b75e7cac9f94e92d3e8d24a673281743afa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003043.fa
@@ -0,0 +1,3 @@
+>PROKKA_00170
+MLLYRWSRAEPVIRAELSLPSRMDRGDVVAWKERILLPEISLDQFDLSDFDVIAEDDVYF
+GISQTS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003050.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003050.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aff38c8f974fe33e12cb266f990462200714f3c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003050.fa
@@ -0,0 +1,3 @@
+>PROKKA_01146
+MTQQHPKDPLQADWEALAEVFEAEDREDRRAEAQRRREGLPEPKRDIRTFDGFASGGAAP
+RA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003053.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003053.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e52996e74842e047d2c78ff18f0e882065cb6fec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003053.fa
@@ -0,0 +1,9 @@
+>PROKKA_01545
+MSEGLALKCLAALLGSDAAHANLKYFRANPGIAVSELGPDAKDINSIAEQTEADGLFIIE
+DVAICVEVKAKSISSHARRGHVQRLSADLRETVGSATEQALRLENHIRTNHGLWLENREW
+LDLSEIREIRSVTVYLDDFGPLSTALDELVRAKVVGSDRFPWLVTLHDLIVIAEVIDRPA
+EFLLYLRRRTESEVSLKFSAVDELDLFMLFLSGGLWVEPDPDRVSEEFLGVAPPTVKERR
+RYQESAVPTRVMTQTDELDAWVYFNEGASDVEAEKPSFGVLPGIARIVDFLQDGRKPGWF
+RFSADLLNLDEESQESLGDMVEHLVSITRQDGLHHNSIMAFAGSWGYPTLFMGSKPRKMS
+IQEASTRLAAYGCAKKHQIRSDRALMVVFDEEQRIRSIRYDNSPPVENRELDGFVAEMGL
+IPPSVMGRPIPPSARRTTVRLNPSRKRKKRGKRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003056.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003056.fa
new file mode 100644
index 0000000000000000000000000000000000000000..29515f165f10c35ca122e643f3dc3787683b192f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003056.fa
@@ -0,0 +1,10 @@
+>PROKKA_01797
+MLILSSRMRPKEQFEGYAFVGTDYVHGPAGMTAYRARTGRTVGPGEDGCYVVARRAGRLF
+GRRFEVGTDASGLGRLFLYRSGDDWALGSSYSGLVEHLRTEGMTLTPRLGRLRPFALRQT
+LTMQLSIFQTPFDEIRLLPVGTVVVIRGSVLSLERAPELQPLEYEAALQEYLDVWRGRTR
+ALLADPRVTFTADLSGGVDSRTVFAFLLESGLFRTDSDRFWLHSGVNQKEDLAVAKGIAE
+AHGLTVNGPKPPTRTLVSGSRAYRHWRENSLGVYTPVYMSSTFQNPFEVHAHGGGGGTIK
+QYYRHAEPLRLLEPFKEKMPAADFALWQEEMATTQEQLKQTAPGVVPSIQHYLEFRNRFH
+FGHIPKARPLFMPLNSKYAIRALTSLPQDVRRRFYFDVMESLAPGLKDVDYDNARKAPTA
+QELESLLVLPASDRLAAGTAYGDDTVETADPDDPLSAGFQRWLQDIDRAAARPEVRRFIM
+GRAMARTDRTVEALRALGKPFHSHSGHSVALSHLLMVDFTLGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003062.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003062.fa
new file mode 100644
index 0000000000000000000000000000000000000000..665f57d7114681846f11ee33c60ca86bf7ebbb4c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003062.fa
@@ -0,0 +1,8 @@
+>PROKKA_02181
+MAGMIITGLLLGLVLGFVFQRGRFCVTGAFRDLFTIRSTRWLTAFMVIVAVQSVGVFALD
+ALGVITLEAETFPWLGTIIGGLIFGFSIVLAGGCATGTYYRAGEGLVGSWFALIFYIVGA
+TAFRKGPLAGTTEAVRSVETQTGSFQQLTGLSPWVFVALLVAGVGLAVRHHLRREAAMTR
+FRLPAAKTGLAHVLTEKAWHPFVTAAIIGVLAILAWPLSWATGRESGLGITGPSANIGAF
+IGTGELELVDWGVLMVTGLLIGSFIAAKASGEFRVRVPDAQTTVRSIIGGLGMGWGAAWA
+GGCTIGNAMVNTATFSFQGWTALVFMVLGTGLAAKLFILNHRGKGTTPAPTSGSGLTSAE
+GAAADAGAARPVKLTPIG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003063.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003063.fa
new file mode 100644
index 0000000000000000000000000000000000000000..225083b7129fe0943db79cd46d2907ad501ca80c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003063.fa
@@ -0,0 +1,3 @@
+>PROKKA_02182
+MAKHLLETDGQVCPFPLVEANQAMQQIPSGDELVIDFDCTQATDSLPRWAAENGHEVTDF
+VKRGAAEWTITVKKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003065.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003065.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2d2599f1e201ecc71d08e54adee4ed4f34e5c4e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003065.fa
@@ -0,0 +1,6 @@
+>PROKKA_02209
+MTTPSGAPDVSADPEVRLLTARLNRARTHYLDFAELWAAYLEGRPHSIAREILTDGTVTI
+RLDRVAPIPAELSILLGEFLYEMRAALDNCLYAAAVIASGQNPPPGAERLEWPIRTDQTQ
+WKSQANRYKHLPAELTEALEAIQPYNAELPAWNCLAILHGLARFDRHRRPWPLALFLVKT
+QLQVRPDVVEPLDVACNRVIHPGEKLATLRLSPGHVLSPTNFDFHVEFDVDLADIEPSEG
+PEGLHVRPWGSLAHRLQSVHRAVTEYCDDLLLLAASCRKH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003067.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003067.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a32359bc570fdc588cb9d8566940cdfbe6cd771
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003067.fa
@@ -0,0 +1,5 @@
+>PROKKA_02211
+MRDLVYYIATSLDGYIAAPDGDFSAFPQDPVTLKTLFDRYPETCPAHARAALGVDGPARR
+FDTVIMGYRTYEPALTVGLPGGAYPHLNQIVVTHRPLPKAPNLTAISGDVSEHIAHLKTL
+PGRDIWLCGGADVAAQLIEHIDELQLKVNPIALGTGIPVLPFDGKPHSFHLAECEQQPGE
+VLLLTYRAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003068.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003068.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4054ccad661b7a0b7670550f9f57f59fbbe6750d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003068.fa
@@ -0,0 +1,8 @@
+>PROKKA_02212
+MNPLRPLTIPTYRWLFAAMVLTIFAQGAWALYLAMQTLDLGATPATLSGVVVWSGIGLLA
+GSLPAGVLADRMPNKSVIVGVLSLNLAIATATSTVAVFGMVAFWMLAASAFFIGVSTAFF
+FPAYTALVPVLVESDDLMAVNGLEGATRPLVGQALAPAAVGAVIGVSMPAAGGYLIAAAL
+AVALLAALQLPAPTPAESEADASAASPIGDLLDGFGYAARTRWVRTSVLFAAVMGLVVTG
+PLEVLLPALMRSSHENGPALYGAVLAALGVGGLVGSLLAGSWCTPERFLPAMIGAWALGC
+LPLTIPALTSNPWAIGVGLAIYGALIGIGMVIWGTVLQEHVPLEMLGRVASLDFFISIAF
+MPLSIALTGLLSRHIDTHTLFISAGLVPLVTAVLLATLGQLRMPRTTVGVAGGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003069.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003069.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b0a2d6dd9590d23a09122641049a7bf8d30b01b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Orthogroup_Sequences/OG0003069.fa
@@ -0,0 +1,3 @@
+>PROKKA_02220
+MNPECVSLCAWPSKDQRGRPSNYCSRACRELTKRTRQRLSWECDVLEEALAEKELSWNQE
+RILQRALGHRKWALGRYPARDE