diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000002.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000002.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3be02bd99f9655f24af27472a4eeb0fa265e69c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000002.fa
@@ -0,0 +1,112 @@
+>ACLBLIBL_00757
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>ACLBLIBL_01280
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRIAAEGTWDTVLATLTAAADAQGLVDWSVSVDSTIARAHQHATNTTRHTGGW
+IELQESA
+>ACLBLIBL_01303
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>ACLBLIBL_01313
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRIAAEGTWDTVLATLTAAADAQGLVDWSVSVDSTIARAHQHATNTTRHTGGW
+IELQESA
+>ACLBLIBL_01318
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRIAAEGTWDTVLATLTAAADAQGLVDWSVSVDSTIARAHQHATNTTRHTGGW
+IELQESA
+>ACLBLIBL_02332
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>ACLBLIBL_02348
+MSRFQMLSDAQWELIAPMLPTRTGRPGRPFTGARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>ACLBLIBL_02630
+MSRFQMLSDAQWELIAPMLPTRTGRPGRPFTGARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>MOLHKGIG_01069
+MFRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRGLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>MOLHKGIG_01387
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>NAFOICDF_00316
+MSRFQTLSDAQWELIAPMLPARTGRQGRPFADARTMVEAIIYRYRCGIPWRDLPEVYGPW
+QTVWTWHRRMAEEGTWDTVLATLTAAADAEGLIDWSVAVDSTIARAHQHATNTTRLTGGW
+IELQESA
+>NAFOICDF_00621
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRMAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+IELQESA
+>NAFOICDF_00626
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRMAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+IELQESA
+>NAFOICDF_01795
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>NAFOICDF_01837
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>NAFOICDF_02208
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>NAFOICDF_02231
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFSDARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEEGTWDAVLARLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+VELQESA
+>MHAAABBN_00320
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>MHAAABBN_00332
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFSDARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEEGTWDAVLARLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+VELQESA
+>MHAAABBN_00787
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEEGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>MHAAABBN_01117
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATSITRHTGGW
+IELQESA
+>MHAAABBN_01328
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>MHAAABBN_01659
+MSRFQMLSDTQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEEGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+VELQESA
+>MHAAABBN_02266
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>LFPAFLNI_00113
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+VELQESA
+>LFPAFLNI_01019
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFSDARTMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEEGTWDAVLARLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+IELQESA
+>LFPAFLNI_01540
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRHTGGW
+VELQESA
+>LFPAFLNI_01883
+MSRFQMLSDAQWELIAPMLPTRTGRAGRPFADARAMVEAIIYRYRCGIAWRDLPEVYGPW
+QTVWTWHRRLAEKGTWDTVLATLTAAADAEGLIDWSVSVDSTIARAHQHATNITRLTGGW
+VELQESA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000003.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000003.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b1f3c9187476b260723336a70d4086f93c786619
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000003.fa
@@ -0,0 +1,104 @@
+>ACLBLIBL_00758
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPVSLDADAYKGRNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWS
+KRLSDMP
+>ACLBLIBL_01281
+MLLPLLGQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPVGLDADAYKGRNVIERQYAHLKQWRGLATRYDKYATIYRAAVVLNAVLAWS
+KRLSDMP
+>ACLBLIBL_01304
+MLLPLLEQLRVTRPAGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPVGLDADAYKGRNVIERQYAHLKQWRGLATRYDKYATIYRAAVVLNAVLAWS
+KRLSDMP
+>ACLBLIBL_01312
+MLLPLLGQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPVGLDADAYKGRNVIERQYAHLKQWRGLATRYDKYATIYRAAVVLNAVLAWS
+KRLSDMP
+>ACLBLIBL_01317
+MLLPLLGQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPVGLDADAYKGRNVIERQYAHLKQWRGLATRYDKYAIVYRSAVVLNAVIAWS
+KRLSDMP
+>ACLBLIBL_02331
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPVSLDADAYKGRNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWS
+KRLSDMP
+>ACLBLIBL_02347
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGSAGGRPVGLDADAYKGRNVIERQYAHLKQWRGLATRYDKYATIYRAAVVLNAVLAWS
+KRLSDMP
+>ACLBLIBL_02614
+MTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRRRRGARGGRPV
+SLDADAYKGRNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWSKRLSDMP
+>ACLBLIBL_02631
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGSAGGRPVGLDADAYKGRNVIERQYAHLKQWRGLATRYDKYATIYRAAVVLNAVLAWS
+KALSDTP
+>MOLHKGIG_01068
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPIGLDADAYKGRNVIERQYAHLKPWRGLATRYDKYAIIYRAAVVLNAVIAWS
+KRLSDMP
+>MOLHKGIG_01386
+MDGTGLPLVSLITPGQAGDSPMLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTH
+LRARGIKAVIPEPADQQGHRRRRGARGGRPVSLDADAYKGRNVIERQYAHLKQWRGLATR
+YDKYAIIYRAAVVLNAVLAWSKRLSDMP
+>MOLHKGIG_02280
+MAAEGTWDTVLTKLTAATDAQGLVDWSVSVDSTIARAHQHATNTTGTQGDRSSDTNLREE
+PANHGVGRSRGGLSTKIHQLVDGAGMPLVNLITPGQAGDSPMLLPLLEQLRVARPVGRTR
+TRPEAVLGDKAYSSQPVRAHLRARRIKAVIPEPADPRGHRKRSGPRGGRPVGPDAAAYKG
+RNVIERQYAHLKQWRRLATRYDKYATVYRAAVLLNAVTAWSKLLSDTP
+>NAFOICDF_00317
+MLLPLLEQLRVTRPAGRPRTRPDAVLGDKAYSSRAIRAHLRSRRIRAVIPEPADQRGHRR
+RRGPRGGRPVGLDATAYKGRNVIERRYAHLKQWRGLATRYDKYSIVYRAAVVLNAVLAWS
+KRLSDMP
+>NAFOICDF_00625
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVISEPADQQGHRR
+RRGARGGRPVGLDADAYKGRNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWS
+KRLSDMP
+>NAFOICDF_01796
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARRIKAVIPEPADQQGHRR
+RRGARGGRPVSLDADAYKGRNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWS
+KRLSDMP
+>NAFOICDF_01836
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARRIKAVIPEPADQQGHRR
+RRGARGGRPVSLDADAYKGRNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWS
+KRLSDMP
+>NAFOICDF_02207
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARRIKAVIPEPADQQGHRR
+RRGARGGRPVSLDADAYKGRNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWS
+KRLSDMP
+>MHAAABBN_00319
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPVSLDAAAYKGRNVIERQYAHLKQWRGLATRYDKYAIVYRSAVVLNAVIAWS
+KRLSDMP
+>MHAAABBN_00788
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPVSLDADAYKGRNVIERQYAHLKQWRGLATRYDKYAIVYRSAVVLNAVIAWS
+KRLSDMP
+>MHAAABBN_01116
+MLLPLLAQLRVTRPVGRPRTRPAAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPVSLDADAYKGRNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWS
+KRLSDMP
+>MHAAABBN_01327
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPVSLDADAYKGRNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWS
+KRLSDMP
+>MHAAABBN_01658
+MDGTGLPLVSLITPGQAGDSPMLLPLLEQLRVTRPVGRPRTRPAAVLGDKAYSSRAIRTH
+LRARGIKAVIPEPADQQGHRRRRGARGGRPVGLDADAYKGRNVIERQYAHLKQWRGLATR
+YDKYAIVYRSAVVLNAVIAWSKRLSDMP
+>MHAAABBN_02267
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPVSLDAAAYKGRNVIERQYAHLKQWRGLATRYDKYAIVYRSAVVLNAVIAWS
+KRLSDMP
+>LFPAFLNI_00114
+MDGTGLPLVSLITPGQAGDSPMLLPLLEQLRVTRPVGRPRTRPAAVLGDKAYSSRAIRTH
+LRARGIKAVIPEPADQQGHRRRRGARGGRPVSLDADAYKGRNVIERQYAHLKQWRGLATR
+YDKYAIIYRAAVVLNAVLAWSKRLSDMP
+>LFPAFLNI_01539
+MLLPLLEQLRVTRPVGRPRTRPEAVLGDKAYSSRAIRTHLRARGIKAVIPEPADQQGHRR
+RRGARGGRPVSLDADAYKGRNVIERQYAHLKQWRGLATRYDKYAIIYRAAVVLNAVLAWS
+KRLSDMP
+>LFPAFLNI_01884
+MDGTGLPLVSLITPGQAGDSPMLLPLLAQLRVTRPVGRPRTRPAAVLGDKAYSSRAIRTH
+LRARGIKAVIPEPADQQGHRRRRGARGGRPVSLDAAAYKGRNVIERQYAHLKQWRGLATR
+YDKYAIIYRAAVVLNAVLAWSKRLSDMP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000009.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000009.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e7eeaee1ae9b935ab2c8c067fa1e7f8cffad7ba6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000009.fa
@@ -0,0 +1,140 @@
+>MOLHKGIG_00712
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>MOLHKGIG_01400
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>MOLHKGIG_01503
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVGPRPRGGRGAPALRPRRPGLPAHRRRPPHRDAH
+RHRGTVPDPGHRRLGRPRYLQHRGGSPVSIHTPNTAAPALPADLEALLRQLKMPHARGIA
+AEVLATARAQRWEPAEVLKALLVEETTGRARSMLAARRKAAGFPTGKTFTTWDPGASSIP
+APTQQSLRTLEWLSRRENLVVWGPPAPARPSSSRPWASRPWRRASGWPGSPWRTSGR
+>MOLHKGIG_02228
+MHRPWITEPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDR
+CFRLIGGAPTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGV
+ENAVKLAKADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETS
+ALHRIPATAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVI
+MHAGAQGPVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGA
+RTWLVEAAAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAG
+HRTGMHTATEERSLTQGTAGWAGLGTSNTEGAAR
+>MHAAABBN_00091
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>MHAAABBN_00344
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>MHAAABBN_01014
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>MHAAABBN_01393
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>MHAAABBN_02283
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>LFPAFLNI_00607
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>LFPAFLNI_01017
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>LFPAFLNI_01157
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>LFPAFLNI_01350
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
+>LFPAFLNI_02163
+MKDAAETMKILSAYDLTKSLRGAAELAGCSHHTVARLVRARDAGQTPGSGASRPKVTDVW
+LPKIEEWVEASTGRIRADVVHAKLTAMGYTGSERSTRRAVAEVKAAWRAGKRRVHRPWIT
+EPGAWLQYDFGDGPAIDGAKTVLFVAWLAWSRYRIVIALRDRTAPSVFAALDRCFRLIGG
+APTYVLTDNEKTVTVSHVAGVPVRNQATVAFARHYGVEVLTCQPADPAAKGGVENAVKLA
+KADLVPKDTNLRDQYASFAELEAACAGFMAMVNSREHRVTRRRPDHMLAEETSALHRIPA
+TAHTVAYGVGRKVPENTPMVSFENAQYSVPAHLLGAEVFVRHHGTGPDSMVVIMHAGAQG
+PVEVARHRVARPGSPAIDDAHFPGHETDKVPGDYTPVPRSAAEAEFLAIGAGARTWLVEA
+AAAGTSRIGQKMAEAVTLAKLAGTDQVDRALGVAAVHQRFAHGDLASLLTAAGHRTGMHT
+ATEERSLTQGTAGWAGLGTSNTEGAAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000011.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000011.fa
new file mode 100644
index 0000000000000000000000000000000000000000..13723939b6796585eda9d782c05d7b28b72806c0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000011.fa
@@ -0,0 +1,39 @@
+>ACLBLIBL_00719
+MLTITSRLEVMNRLGRAMADPTRSRIILTLLDHPAYPAELARDLDLTRPNVSNHLACLRD
+CGIVVSEPEGRRTRYEIADSHLAQALTALVDATLAVDEDAPCIDPACSLPGCDAAGEGA
+>ACLBLIBL_00727
+MLTIASRLDVMNRLGRAMADPTRSRILMTLLEGPSYPAVLARDLGLTRSNVSNHLTCLRD
+CGIVVAEPEGRQTRYEIADPHLGAAMTALVEVTLAVDENAPCVDATCTVPGCCPSGTVA
+>ACLBLIBL_02366
+MLTVASRLDVMNRLGRAMADPTRSRILMTLLDGPSYPAVLSRELELTRSNVSNHLTCLRD
+CGIVVAEPEGRQTRYEIADPHLAAALTALVDVTLAVDEHAPCVDSSCTVPGCCGTGAGE
+>MOLHKGIG_00609
+MLTIATRLDVMNRLGRAMADPTRSRILLNLLEGPGYPAELAQALGLTRSNVSNHLACLRD
+CGIVAAEHQGRRTRYAIVDAHLARALSALLEVTLAVDASAPCLDPGCPVPGCCDTGQVAS
+>MOLHKGIG_00616
+MMTIASRLDVMNRLGRALADPTRSRIILTLLDHPAYPAELARDLDLTRPNVSNHLACLRD
+CGIVVSEPEGRRTRYEIADSHLAQALTALVDATLAVDEDAPCIDPACSLPGCDAAGEGA
+>MOLHKGIG_02074
+MADPTRSRILMTLLERPAYPAELARDLGLTRSNVSNHLACLRDCGIAVAVAEGRQTRYEI
+ADAHLARALTALVEVTLAVDESAPCIDPACSLPGCDAAGEGA
+>MHAAABBN_00339
+MMTIASRLDVMNRLGRALADPTRSRIILTLLDHPAYPAELARDLDLTRPNVSNHLACLRD
+CGIVVSEPEGRRTRYEIADSHLAQALTALVDATLAVDEDAPCIDPACSLPGCDAAGEGA
+>MHAAABBN_00350
+MQMCRYQQREPHTRGQQVLYAQRMLTIASRLDVMNRLGRAMADPTRSRILMTLLEGPSYP
+AVLARDLGRV
+>MHAAABBN_00789
+MQMCRYQQREPHTRGQQVLYAQRMLTIASRLDVMNRLGRAMADPTRSRILMTLLEGPSYP
+AVLARDLGHV
+>MHAAABBN_01769
+MLTIATRLDVMNRLGRAMADPTRSRILLSLLEGPGYPAELAQALGLSRSNVSNHLACLRD
+CGIVAVEHQGRRTRYAIVDAHLARALSSLLEVTLAVDASAPCLDPGCPVPRCCDTAEVAS
+>MHAAABBN_01779
+MMTIASRLDVMNRLGRALADPTRSRIILTLLDHPAYPAELARDLDLTRPNVSNHLACLRD
+CGIVVSEPEGRRTRYEIADSHLAQALTALVDATLAVDEDAPCIDPACSLPGCDAAGEGA
+>LFPAFLNI_02002
+MADPTRSRILMTLLERPAYPAELARDLGLTRSNVSNHLACLRDCGIAVAVAEGRQTRYEI
+ADAHLARALTALVEVTLAVDESAPCLDPACSVPGCCEKGVGA
+>LFPAFLNI_02005
+MSTTTLTHVSALSRLGHALSDDTRTRILLALRDGPARPSALAGELGVSKQVMSNQLACLR
+GCGLVTTTAEGRNVWYALADPRLGQTLGELLELTLTIDPDCCSAAGCTCA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000016.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000016.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d325a0c691eab7b35c17a77ca846ca29369f293d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000016.fa
@@ -0,0 +1,105 @@
+>ACLBLIBL_01238
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIAREVE
+LDDPYENMGAQLAKEVATKTNDIAGDGTTTATVLAQALVNEGMRQVAAGAAPGEVKKGIE
+VAVAAVEQRLQENARPVEGKEVAHVAAISAQNDEVGELLARAFDTVGTDGVITIEESSTT
+STELDVTEGMQFDKGFLSPYMVTDAERQEAVLEDPYVLINSGKISNVQELLPVLEKVLQA
+SRPLFVIAEDIEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMLQDIAVLTGAQVVSP
+DLGMKLEQADLDVLGSARRITVTKDETTIVDGGGSAEDVEARVAQIKAESAATDSDWDRE
+KLQERLAKLAGGIGVIRVGAATEVELKERKHRIEDAVSSTRAALEEGIVAGGGTALINAL
+SVLDTDADVQALTGDAASGVDIVRKALKQPLRWIAQNAGEDGYVVVSKVAELEPNHGFNA
+KTGVYGDLIADGVIDPVKVTRSALANAASIAALVLTTETLVADKPEDEDEHQH
+>ACLBLIBL_02606
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPRGRNVVLEKKWGAPTITNDGVSIAKEIE
+LEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQALVREGLRNVAAGADPLSLKRGIE
+KAVDAVTAELLSASREIETKEQIAATASISAADKQIGSLIAEALDKVGKEGVITVEESNT
+FGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISSVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVIS
+SEVGLSLENATLDLLGTARKVVITKDETTIVEGAGDAEQIAGRVAQIRAEIENTDSDYDR
+EKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALIQA
+GAKAFGGLTLEGDEATGANIVKVAIEAPLKQIAFNAGMEPGVVADKVKTLQDGHGLNAAT
+GEYEDLLAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMG
+GMM
+>MOLHKGIG_00355
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPRGRNVVLEKKWGAPTITNDGVSIAKEIE
+LEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQALVREGLRNVAAGADPLSLKRGIE
+KAVEAVTSELLSASREIETKDQIAATASISAADKQIGSLIAEALDKVGKEGVITVEESNT
+FGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISSVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVIS
+SEVGLSLENATLDLLGSARKVVITKDETTIVEGGGDAEQIAGRVAQIRSEIENTDSDYDR
+EKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALIQA
+GAKAFGGLQLEGDEATGANIVKVAIEAPLKQIAFNAGLEPGVVADKVKTLDDGHGLNAAT
+GEYEDLLAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMG
+GMM
+>MOLHKGIG_01656
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIAREVE
+LEDPYENMGAQLAKEVATKTNDIAGDGTTTATVLAQALVNEGMRQVAAGAAPGEVKRGIE
+VAVAAVEQRLQENARPVEGKEVAHVAAISAQNDEVGELLARAFDTVGTDGVITIEESSTT
+STELDVTEGMQFDKGFLSPYMVTDAERQEAVLEDAYVLINSGKISNVQELLPLLEKVVQA
+NKPLFVIAEDIEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMMQDIAILTGAQVVSP
+DLGMKLEQADLDVLGSARRITVTKDETTIVDGGGAPEDVEARIAQIKAEAAATDSDWDRE
+KLQERLAKLSGGIGVIRVGAATEVELKERKHRIEDAVSSTRAALEEGIVAGGGTALINAL
+TVLDTDADVQALTGDAAVGVDIVRKALKQPLRWIAQNAGEDGYVVVSKVAELEPNHGFNA
+KTGVYGDLIADGVIDPVKVTRSALANATSIAALVLTTETLVADKPADEDEAGHQH
+>NAFOICDF_01149
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIARDVE
+LEDPYENMGAQLAKEVATKTNDIAGDGTTTATVLAQALVNEGMRQVAAGAAPNEVKKGIE
+TAVAAVEKRLQENARPVEGKEVAHVAAISAQNDEVGELLARAFDTVGTDGVITIEESSTT
+STELDVTEGMQFDKGYLSPYMVTDAERQEAVLEDAYVLINSGKISNVQELLPLLEKVLQA
+NKPLFVIAEDVEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMMQDIAILTGATVVSP
+DLGMKLEQADLDVLGSARRVTVTKDATTIVDGGGEAADVEARVSQIKAEVAATDSDWDRE
+KLQERLAKLAGGIGVIRVGAATEVELKERKHRIEDAVSSTRAALEEGIVAGGGTALINAL
+SVLDEDAEVTALTGDAATGVEIVRKALKEPLRWIAQNAGEDGYVVVSKVAEMKPNEGFNA
+KTGVYGDLIADGVIDPVKVTRSALANAASIAALVLTTETLVADKVEDEDEHQH
+>NAFOICDF_02465
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPRGRNVVLEKKWGAPTITNDGVSIAKEIE
+LEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQALVREGLRNVAAGADPISLKRGIE
+KAVEAVTSELLSAAREIETKDQIAATASISAADAQIGSLIAEALDKVGKEGVITVEESNT
+FGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISTVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVIS
+SEVGLSLENASLDLLGTARKVVITKDETTIVEGAGDADQIAGRVAQIRSEIANTDSDYDR
+EKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALIQA
+GAKAFEGLQLEGDEATGANIVKVAIEAPLKQIAFNAGLEPGVVADKVKSLESGHGLNAAT
+GEYVDLMAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMG
+GMM
+>MHAAABBN_00071
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPCGRNVVLEKKWGAPTITNDGVSIAKEIE
+LEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQALVREGLRNVAAGADPLSLKRGIE
+KAVEAVTSELLSASREIETKDQIAATASISAADKQIGSLIAEALDKVGKEGVITVEESNT
+FGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISSVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVIS
+SEVGLSLENATLDLLGTARKVVVTKDETTIVEGGGDAEQIAGRVAQIRSEIENTDSDYDR
+EKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALIQA
+GAKAFGGLQLEGDEATGANIVKVAIEAPLKQIAFNAGLEPGVVADKVKTLDDGHGLNAAT
+GEYEDLLAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMG
+GMM
+>MHAAABBN_01361
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIAREVE
+LEDPYENMGAQLAKEVATKTNDIAGDGTTTATVLAQALVNEGMRQVAAGAAPGEVKKGIE
+VAVAAVERRLQENARPVEGQEVAHVAAISAQNDEVGELLARAFDTVGTDGVITIEESSTT
+STELDVTEGMQFDKGFLSPYMVTDAERQEAVLEDAYVLINSGKISNVQELLPLLEKVLQA
+NKPLFVIAEDIEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMMQDIAILTGAQVVSP
+DLGMKLEQADLDVLGSARRITVTKDETTIVDGGGAAEDVEARVAQIKAESAATDSDWDRE
+KLQERLAKLSGGIGVIRVGAATEVELKERKHRIEDAVSSTRAALEEGIVAGGGTALINAL
+TALDTDADVQALTGDAAVGVDIVRKALKQPLRWIAQNAGEDGYVVVSKVAELEPNHGFNA
+KTGVYGDLIADGVIDPVKVTRSALANATSIAALVLTTETLVADKPADEDEAGHQH
+>LFPAFLNI_00362
+MAKTIAFDEEARRGLEKGLNTLADAVKVTLGPRGRNVVLEKKWGAPTITNDGVSIAKEIE
+LEDPYEKIGAELVKEVAKKTDDVAGDGTTTATVLAQALVREGLRNVAAGADPLSLKRGIE
+KAVEAVTSELLSASREIETKDQIAATASISAADKQIGSLIAEALDKVGKEGVITVEESNT
+FGLELELTEGMRFDKGYISGYFVTDADRQEAVLEDPYILIVNSKISSVKDMVAILEKVMQ
+SGKPLLIIAEDVEGEALATLVVNKIRGTFKSVAVKAPGFGDRRKAMLADIAILTGGQVIS
+SEVGLSLENATLDLLGTARKVVVTKDETTIVEGGGDAEQIAGRVAQIRSEIENTDSDYDR
+EKLQERLAKLAGGVAVIKAGAATEVELKERKHRIEDAVRNAKAAVEEGIVAGGGVALIQA
+GAKAFGGLQLEGDEATGANIVKVAIEAPLKQIAFNAGLEPGVVADKVKTLDDGHGLNAAT
+GEYEDLLAAGINDPVKVTRSALQNAASIAGLFLTTEAVVADKPEKAAAGAEGMDPMGGMG
+GMM
+>LFPAFLNI_01586
+MAKQLAFNDDARRALQAGIDKLADTVKVTLGPKGRNVVLDKAWGAPTITNDGVTIAREVE
+LEDPYENMGAQLAKEVATKTNDIAGDGTTTATVLAQALVNEGMRQVAAGAAPGEVKKGIE
+VAVAAVERRLQENARPVEGQEVAHVAAISAQNDEVGELLARAFDTVGTDGVITIEESSTT
+STELDVTEGMQFDKGFLSPYMVTDAERQEAVLEDAYVLINSGKISNVQELLPLLEKVLQA
+NKPLFVIAEDVEGEALSTLVVNKIRGTLNVVAVKAPGFGDRRKAMMQDIAILTGAQVVSP
+DLGMKLEQADLDVLGSARRITVTKDETTIVDGGGAAEDVEARVAQIKAEAAATDSDWDRE
+KLQERLAKLSGGIGVIRVGAATEVELKERKHRIEDAVSSTRAALEEGIVAGGGTALINAL
+TVLDTDADVQALTGDAAVGVDIVRKALKQPLRWIAQNAGEDGYVVVSKVAELEPNHGFNA
+KTGVYGDLIADGVIDPVKVTRSALANAASIAALVLTTETLVADKPADEDEAGHQH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000022.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000022.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8947abbe894a433221b8ecd13b7eb5995d491d76
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000022.fa
@@ -0,0 +1,52 @@
+>ACLBLIBL_00513
+MANDDANTTTTDQLTLQDPVKRYPVISPPEQSLPGTGLDAEMTPKADLGEHSYRGTGRLT
+GRKALITGGDSGIGAATAIAFAREGADVVITYLPEEEKDARNVLAVLEKEGRTAVGIAGD
+LRDRQFCQDVVAQAVEAMGGLDVLVNNGGKQVAQKEFEAIDDEQLEATFDVNILAQFRLV
+RAALPHLKPGASIINTTSVVSYMPPETLIDYASTKAAINNFTKGLGQQLAPKGIRVNAVA
+PGPIWTPLQPSGGQPTEELPDFGQSTPLGRAGQPTELAPAFVFLASAESSYVVGATIAVT
+GGMPTP
+>MOLHKGIG_02238
+MAHDDANTTTTDQLTLQDPTKRYPVISPPEQSLPGTGLDAEMTPKVDLGEKSYRGTGRLE
+GRKALITGGDSGIGAATAIAFAREGADVVITYLPEEEKDAQHVLEVLQAEGRTAVGIPGD
+LRDKTFCVDLVAQAVEKLGGLDVLVNNGGKQVAQDSIEDIDDEQLEATFDINILAQFRLV
+KAALPHLKPGSTIINTTSVVAYMAPEQLVDYSATKAAINTFTKALGQQLAPKGIRVNAVA
+PGPIWTPLQPSGGQKPEALPEFGQSTPLGRAGQPTELAPAYVFLASPESSYVVGATIPVT
+GGMPTP
+>NAFOICDF_00440
+MTDVSTSTDTAVGDSDTRPAAARTDAPAATVLLAGRAALVTGGTLGIGSGIAASLRDAGA
+RVAVTGLTEQECAAAREAGFPAYVLDVRDRAACAEVVGAVVEEFGGLDVLASNAGIYPQA
+RIADMTDEDIDLIFDVNVKGTIHAVQAALPALVASGRGRVVITSSITGNHTGYPAWSHYG
+ATKAAQLGFVRSAAIELARQGVTVNAVLPGNIITPGLEEMGQEYLDSMARSVPAGHLGEP
+ADIGATVAFLASDGARYITGQGIVVDGGQILPETPEALEGL
+>NAFOICDF_00454
+MANDDTNTTTTDQLTLQDPTKRYPVISPPEQSLPGTGLDAEMTPKADLGEKSYRGTGRLE
+GRKALITGGDSGIGAATAIAFAREGADVVLTYLPEEEKDAQHVKEVIEAEGRKAVTVSGD
+LRDKQFCKDLVERAVQELGGLDILVNNGGKQVAQEEFEQIDDEQLEATFDINILAQFRLV
+RAALPHLKPGSTIINTTSVVAYMAPEQLVDYSSTKAAINTFTKALGQQLAPKGIRVNAVA
+PGPIWTPLQPSGGQKPEALPEFGQSTPLGRAGQPTELAPAYVFLASPESSYVVGATIPVT
+GGMPTP
+>NAFOICDF_00650
+MGIHYARDSTAAEAVVERVNEAGASGVLIRADLAEGAAGAAHLATRWRDEVRRHDARGTD
+VLVSNAGINGAQSLSELDEGTVARVVNVNLVAPLMLVHHLSDHINDHGRVIGISSGFARI
+AAPTHVAYTASKAGLEAAFRAIAAELAERDITVNTVRPGVIDTDINADWINEPGARDAVA
+AAAALRRVGQPDDVADIVAFLASHSSRWMTGQSLDATGGTQL
+>NAFOICDF_01865
+MSTHDLPDPLTQFPRFAPERQTQEEPGLSARMDPEPDCGEDTYVGIGRLKGRRALVTGGD
+SGIGRAVALAYAREGADVVFTHLPEEAEDAARTTELLDAEGVRHVAREVDLRDEAATRAL
+VRDAVKFLGGLDLIANVAGEQRYVDDLAELDPRQVRDTFEINVFALIWIVQEALPHLPAG
+AAIVNTASTQATTPLPGLVDYAGTKGAIVSITKALAQQLTPRGIRVNAVVPGAIWTPIQV
+SLGRAPEQVDVLGQDAPLGRPGQPAEMAPAYVFLASTEASYVSGEVLGATGGTLY
+>MHAAABBN_01940
+MAHDDANTTTTDQLTLQDPTKRYPVISPPEETLPGTGLDAEMTPKADLGEKSYRGTGRLE
+GRKALITGGDSGIGAATAIAFAREGADVVITYLPEEEKDAQHVLEVLQAEGRTAVGIPGD
+LRDKTFCVDLVAQAVEKLGGLDVLVNNAGKQVAQDSIEDIDDEQLEATFDVNILAQFRLV
+KAALPHLKPGSTIINTTSVVTYMAPPQLVDYASTKAAINTFTKALGQQLAPKGIRVNAVA
+PGPIWTPLQPSGGQKSEDLPEFGQSTPLGRAGQPTELAPAYVFLASPESSYVVGATIPVT
+GGMPTP
+>LFPAFLNI_02170
+MAHDDANTTTTDQLTLQDPTKRYPVISPPEETLPGTGLDAEMTPKADLGEKSYRGTGRLE
+GRKALITGGDSGIGAATAIAFAREGADVVITYLPEEEKDAQHVLEVLQAEGRTAAGIPGD
+LRDKTFCADLVAQAVEKLGGLDVLVNNGGKQVAQDSIEDIDDEQLEATFDINILAQFRLV
+KAALPHLKPGSTIINTTSVVAYMAPEQLVDYSATKAAINTFTKALGQQLAPKGIRVNAVA
+PGPIWTPLQPSGGQKPEALPEFGQSTPLGRAGQPTELAPAYVFLASPESSYVVGATIPVT
+GGMPTP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000024.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000024.fa
new file mode 100644
index 0000000000000000000000000000000000000000..82f21e0c8c298d723178c741f2ee98ceca28ebc3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000024.fa
@@ -0,0 +1,48 @@
+>ACLBLIBL_02374
+MPSASPSSPAARRARAHPVARRDVVRARWAATLAFLTNGGMLGALIPHYPQAKAAFGLDA
+DAFGLLVVALAAGAAAAGSLPAPVLRRWGSRRVMLAGTVVMAVVVVAAGLVVDLSAPAQG
+RPWAGAVWLFAALLGVAGILDAVVDTAQNAQGLTVQTRLARPVLTSMHAGWSLGAGLGAG
+LGALAVGAGMPAGLHLGLNGAACVAVLVAAGRRFLPDDARPAPDADAPEGTAAPAPGPSP
+RRPARPPPPRPAPPPGWPCSP
+>ACLBLIBL_02375
+MAGFGVEEFGNAWTALFLQSERGLDVAAAGLGASTLLLAQFVGRLVGDRVLHRLGRRRTL
+AGSLAVVVAALVLVLTAPAAPAVFAGLALAGLGCAVVVPTAYALGDEVPGLPPRTGLAVV
+SWLMRVAGIGLSPLVGLLATGLPLPAALAVFPALAVLGLVGTGVVGRRRRRP
+>MOLHKGIG_00570
+MHAGWSLGAAAGAGLGAAVITVGGPAALHLGLNGAVCVAVLLGVRRLFLAEAPVDSASAR
+GAADQSPAPSETSAPPAPAAQALPRRAAVAVLVPAVVIAMAGFGVEEFGNAWATLFLITE
+RGLDPAAAVLGASTLLGAQFVGRLAGDRTLAVLGRRGALTAGLGAVVVGLGLALAPLPGP
+VAVPAAFAGLALAGLGCAVVVPVAYALGDEAPGLRPQTGLAVTSWCMRLAGVGLSPAVGA
+LAGAVGLAPALTVFLGLAAVGTVLAARLPAAP
+>MOLHKGIG_00571
+MSEAPPHLPTADDGVARARRARWAVTAAFATNGALLGALIPHYPEAKAAFGLDPAAFGLL
+VIALAVGGTLAGPLPAPILRRFGARRVMLAGSVAIALLTTAAGLVLDIAGAGAGAGHGAG
+TAAAWLLWVFAGLVLASGVLDAVVDTAQNAQGLQV
+>NAFOICDF_02254
+MTSAPADTPRIDRRAATRSRWAATAAFFTNGALAAAMIPHYPQAKAAFGLDPAGFGLLVT
+VMTLGAACAGPAGAPILRRAGSRATVLWGSLAIAVVLTGAGLALDLGARSDAAGPWLGAY
+AAAVFASGLCDAVVDTAQNAQGLRAQHALGRPVLTSMHAGWSLGAAVGAALGAAAVGAGV
+PAGLHLGLNGAACVLLLALTLPRFLPDTPDHAPAPALLTADDPGPESEATPASHRHPWLL
+LAPIVVISMAGFSVEEFGNSWTSLFLQAERGLDPATAGLGASTLLGAQFLGRLTGDRVLA
+ALGRTRALTGGLAVVLAGLTVTLLVPTPAAMFTGLALAGLGSAVVVPTAFALADEVPGLP
+AQTGLAVVSWLMRLAGLGLSPLVGLLAGVLPLTAALGAFVVLAALGTVLALTLRAPRLAP
+DFR
+>MHAAABBN_00294
+MHAGWSLGAAAGAGLGAAVITVGGPAALHLGLNGAVCVAVLLGVRRLFLAEAPVDSASAR
+GAADQSPAPSETSTPPAPAAQALPRRAAVAVLVPAVVIAMAGFGVEEFGNAWATLFLITE
+RGLDPAAAVLGASTLLGAQFVGRLAGDRTLAALGRRGALTAGLGAVVVGLGLALAPLPEP
+VAVPAAFAGLALAGLGCAVVVPVAYALGDEAPGLRPQTGLAVTSWCMRLAGVGLSPAVGA
+LAGAVGLAPALTVFLGLAAVGAVLAARLPAAP
+>MHAAABBN_00295
+MSEAPPHLPTADDGVARARRARWAVTAAFATNGALLGALIPHYPEAKAAFGLDPAAFGLL
+VIALAVGGTLAGPLPAPILRRFGARRVMLAGSVAIALLTTAAGLVLDIAGAGAGAGHGAG
+TAAAWPLWVFAGLVVASGVLDAVVDTAQNAQGLQV
+>LFPAFLNI_00572
+MSEAPPHLPTADDGFARARRARWAVTAAFATNGALLGALIPHYPEAKAAFGLDPAAFGLL
+VIALAVGGTLAGPLPAPILRRFGARRVMLAGSVAIALLTTAAGLVLDIAGAGAGAGHGAG
+TAAAWPLWVFAGLVLASGVLDAVVDTAQNAQGLQVQTRLARPVLTTMHAGWSLGAAAGAG
+LGAAVITVGGPAALHLGLNGAVCVAVLLGVRRLFLAEAPTDSASARDASDQSPAPSETST
+PPAPAAQALPRRAAVAALLPAVVIAMAGFGVEEFGNAWATLFLITERGLDPAAAVLGAST
+LLGAQFVGRLAGDRTLAALGRRGALTAGLGAVVVGLGLALAPLPGPVAVPAAFVGLALAG
+LGCAVVVPVAYALGDEAPGLRPQTGLAVTSWCMRLAGVGLSPAVGALAGAVGLAPALTVF
+LGLAAVGAVLAARLPAAP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000030.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000030.fa
new file mode 100644
index 0000000000000000000000000000000000000000..140dcdc6d901847122b69ca1811437679f09beb0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000030.fa
@@ -0,0 +1,21 @@
+>ACLBLIBL_00389
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGVTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLVQSPK
+>ACLBLIBL_00393
+MPAAYHREFRQDVIAIARKGQMPIAQVAKDFGIAESRLRRWLAQDDVEAGIRPGVTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLVQSPK
+>ACLBLIBL_00410
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGVTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
+>MOLHKGIG_00627
+MPAAYPREFRQDVVAIARKGQIPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGITKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
+>NAFOICDF_02189
+MPAAYPREFRQDVVAIARNGQMPIAQVAKDLGITASCLRRWLAQDDVEAGIRPGLTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
+>MHAAABBN_00372
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGITKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
+>LFPAFLNI_00604
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGITKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000033.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000033.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f85c1d91b0205d9f87bcc2c42c25013f18916742
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000033.fa
@@ -0,0 +1,58 @@
+>ACLBLIBL_00403
+MTGRRRYQGLAARFFLAQLLVVGASVLAAVVVASLAGPPLFREHLEPAGAGHDAAQMLHV
+EQAYRDANFWTLGVALATALICCLALTWHVARRIQSPINALTQAAKAMAGGRYDTRVPAM
+GAGTEVEELAGSFNTMAARLQRTEDTRRRMLSDLAHELRTPVSVLTVYHEALQDGVSHWD
+EPTGELMGEQLARLTRLVEDINDVSRAEEGRIELDRSPQGVSGLLHAATEAHKEAYATKG
+VALTMDADPGLAVDVDRQRMGQVLGNLLTNALRHTPAGGRVTLEARQSPSGVTLSVTDTG
+EGISPEHLPHVFERFYRGDTARDRDHGGSGVGLAISRALIQAHGGTLSATSTTAGATFTI
+DLPTKQPPDQPTYRRTRSSTVNTGAPPLA
+>ACLBLIBL_01253
+MRTRLSTLLALVLVLSLAVSGITAYAVLRITVNDRIEASLQRAVEQVALLSETGVDPETG
+EPPDSAAAFIRLAMLRVLPHDNEGILGLAPDRAELAASDAVELRLEEDPELVAWALARVG
+DQEARAETVTTASATYRAVVVPVTGWGQDDAGALLLAVDVDAEVGRLDRTFLGFAGGALL
+TTVFALAVGVPLLRRVFAPLESLQEAVGEVTEHDLDRRVEVIGHDDVAALGHSFNAMLER
+LEDSFASQRRLLDDAGHELRTPVTIVQGHLEVMDPDDPADVRETTRLTLDELDRMSRLVD
+DLLVLAKAQHPDFLRPAPVDVAELTRGVLARASGFDGHVWELDGVAEATVSLDAQRITQA
+WLQLAANAVRYSEPGSVVRLGSAVEGDTLRLWVQDHGVGVRPEDRAQIFERFGRGAHGTR
+ADGSGLGLAIVSSIAAAHGGEVSLDSVPGLGSVFRIELPLSTPSRPAGSLTPGKDPA
+>ACLBLIBL_01330
+MTRSKPTGRLSASGRARVVAWILGVSALGMVLMLVSIVLTLRWVERDAIETSLTQESDEV
+AVFAQNGRDPETGEPFATPERFVGHYLERQRVEPTELMFGGTAATPVIAQIHGDAAAPVE
+LLAPATRQAMEQPRSRGTLVDPTHGRISYANLTVTTPADTGHVVVAVFHERYEQRVMTQT
+LLLSALALAALAATAAAAWLVSSRILGHTVEFHRAVDASLKDRGLRRLPENGSEEYAGLA
+RRANDLVRRADRRLEEERRFAEDVTFALRTPLTVIEGGLRNPGGDEQERRTSYRHIGAEA
+TRVRGLLEDLVILSRLQQDDVVLERTPVDVGVLVATAAQAWRERHPDAADEPRLDVEAPA
+EGLTAVTDRARLVQVLEELLDNARHAVRFAPGSDLPRDLTAVTPLERTLSVRVREEERDG
+EPWAVVEVADRGRGIPEEDREEVFERLANASNDPYPGNGLGLPVAALLSTALDGELTLEP
+GPGAAGTVARLAVPLTADQDGEDA
+>MOLHKGIG_00631
+MTGRRRYQGLAARFFLAQLLVVGASVLAAVVVASLAGPPLFHEHLEQAGAGHDAAQMLHV
+EQAYRDANFWTLGVALATALICCLALTWHVARRIQSPINALTQAAKAMAGGRYDTRVPAM
+GAGTEVEELAGSFNTMAARLQRTEDTRRRMLSDLAHELRTPVSVLTVYHEALQDGVSHWD
+EPTGELMGEQLARLTRLVEDINDVSRAEEGRIELDRSPQGVSGLLHAATEAHKEAYATKG
+VALTMDADPGLAVDVDRQRMGQVLGNLLTNALRHTPAGGRVTLEARQSPSGVTLSVTDTG
+EGISPEHLPHVFERFYRGDTARDRDHGGSGVGLAISRALIQTHGGTLSATSTTAGATFTI
+DLPTKQPPTSPPTGAPVYPP
+>NAFOICDF_00451
+MSPTPALRGRPAPGPDAALVARAARRIGLRTALACAALVLGGAGVFFGYLWWQIAHPGVD
+PRDADATVTVQLDLVDLATAAILAGAAAVLITGFASLWFSRSAVQPLADALRRQREFVSN
+ASHELRTPLTVLSARTQVLQARVPAGDPLEPLADELRRDTDVMAGVVEDMLSTARLDSAP
+EGMCDAGEVAAAACADLSLVGAEERGVRLRADLPSLPVALPEAALRRMLAALLDNALGFA
+PPGTEVTVSGERVRGVVELRVADRGAGIQGVEPDHVFDRFARGRPAAVPGSGPGAVPRSS
+HGIGLALVRETAHRYRGEVRVESTGPEGTVMLLTLPAAQEAR
+>NAFOICDF_02198
+MTSRRRYQGLAARFFLAQLLVVGASVLAAVVVASLAGPPLFHEHLEQAGAGHDAAQMLHV
+EQAYRDANFWTLGVALATALICCLALTWHVARRIQSPINALTQAAKAMAGGRYDTRVPAM
+GAGTEVEELAGSFNTMAARLQRTEDTRRRMLSDLAHELRTPVSVLTVYHEALQDGVSHWD
+EPTGELMGGQLARLTRLVEDINDVSRAEEGRIELDRSPQGVSGLLHAATEAHKEAYATKG
+VALTMDADPGLAVDVDRQRMGQVLDNLLTNALRHTPAGGRVTLEARQSPSGVTLSVTDTG
+EGISPEHLPHVFERFYRGDTARDRDHGGSGVGLAISRALIQTHGGTLSVTSTTAGATFTI
+DLPTKQPPDQPTYRRTRLSTVNTGAPPLE
+>LFPAFLNI_00600
+MTGRRRYQGLAARFFLAQLLVVGASVLAAVVVASLAGPPLFHEHLEQAGAGHDAAQMLHV
+EQAYRDANFWTLGVALATALICCLALTWHVARRIQSPINALTQAAKAMAGGRYDTRVPAM
+GAGTEVEELAGSFNTMAARLQRTEDTRRRMLSDLAHELRTPVSVLTVYHEALQDGVSHWD
+EPTGELMGEQLARLTRLVEDINDVSRAEEGRIELDRSPQGVSGLLHAATEAHKEAYATKG
+VALTMDADPGLAVDVDRQRMGQVLGNLLTNALRHTPAGGRVTLEARQSPSGVTLSVTDTG
+EGISPEHLPHVFERFYRGDTARDRDHGGSGVGLAISRALIQTHGGTLSATSTTAGATFTI
+DLPTKQPPTSPPTGAPVYPP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000034.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000034.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed26f7778d4802f555f03ce8fd535498b3e684c0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000034.fa
@@ -0,0 +1,21 @@
+>ACLBLIBL_00412
+MPKEQTAGKPTTRRYSPEEAAAVRMVRTMRAELGTEHGTVQRVATQLGYGVESVRMWVKQ
+ADIDDGVTSGVSSAEAQRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>MOLHKGIG_01397
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRAELGTEHGTVNRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEAQRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>NAFOICDF_00325
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRAELGTEHGTVQRVATQLGYGVESVRMWVK
+HADIDDGVTSGVSSAEAQRVRELEQEVRKLRRANEVLKRAASFFGAELDRHYRK
+>NAFOICDF_00648
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRVELGTEHGTVQRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEARRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>NAFOICDF_02216
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRVELGTEHGTVQRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEARRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>MHAAABBN_01130
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRAELGTEHGTVNRVATQLGYGVESVRMWVK
+QADIDDGVTSDVSSAEAQRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
+>LFPAFLNI_01347
+MPKEQTAGKPTTRRYSPEEKAAAVRMVRTLRAELGTEHGTVNRVATQLGYGVESVRMWVK
+QADIDDGVTSGVSSAEARRVRELEQEVRELRRANEVLKRAASFFGAELDRHYRK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000037.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000037.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b0ace136ffb7f90ea8581011e41f902a6672163
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000037.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00589
+MTTRVLLVDDQPLIRLGFAAILQSQDDIEVVGEAGDGAECLERAAALDPDVICMDVQMPR
+MDGIEATRALAEAGTRAAVLILTTFDRDDFLFETLEAGASGFLLKSAEAEHLIDAVRVLG
+RGDALLDPQVTRRVLRRMASAAPEGVDGPAGVGQPRDDDGAAPGQAEASDAVGKAGLTGR
+EAEILTLMARGLSNGEIAGQLFVGESTVKTHVSNVLMKLGARDRVHAVIWAFEHGVAG
+>ACLBLIBL_00598
+MSTDAENAPVRVALVDDQALIRSGLAMLVDSQPDLTVVAEAGSGREAVASVSVAGADVVL
+MDVRMPEMDGIEATRTLLQRPDAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAPPEELL
+AAIRTVHRGDAVIAPSTTRRLMAHMAPRLRSDHARTAECEHEQAAVESLTPREREVLVLM
+AQGSANLEIAGELVLSEATVKTHVGRVLAKLGARDRVQAVLIAHRAGLVQF
+>ACLBLIBL_02580
+MVLPDAGVRGGVRVRTSRTGVVGDIRLVEGAVSGDLDSADLLLGGVNSLGETRQVARQGR
+DVPPFLLVAEATIVEELSGIDASGAAAVLAYPLDTVELASVAHGIAGSGPFLSPRLPQLS
+VEPLGEGLSAREAEVVVALGEGLSDAEIAQALCVSVKTVHTHVLNLRRKLGARNRAHAVS
+LARSVGPLGDACSEPGLVAAL
+>MOLHKGIG_02160
+MSSEETVPVRVALVDDQALIRSGLAMLVDSQPDLTVVAEAGSGREAVASVSVAGADVVLM
+DVRMPEMDGIEATRALLRRPDAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAPPEELLA
+AIRTVHRGDAVIAPSTTRRLLTHMAPRLRSDQVRSAECEEQQAAVASLTPREHEVLVLMA
+QGAANLEIAAELVLSEATVKTHVGRVLAKLGARDRVQAVLIAHRAGLVQF
+>NAFOICDF_00520
+MSPDDAQPTPIRVALVDDQALIRSGLAMLIDSQPDLTVVAQASDGREAAASVAVAGADVV
+LMDVRMPEMDGIEATRALLRRPDAPRVVVLTTFDLDEHVMDAIEAGASGFLLKDAPPEEL
+LAAIRTVHGGDAVIAPSTTRRLLAHMAPRLRQDAARSAECADEQAAVGSLTPREREVLVL
+MGQGAANPEIAAQLVLSEATVKTHVGRVLAKLSARDRVQAVLIAHRTGLVGF
+>MHAAABBN_01873
+MSSEETVPVRVALVDDQALIRSGLAMLVDSQPDLTVVAEAGSGREAVASVSVAGADVVLM
+DVRMPEMDGIEATRALLRRPDAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAPPEELLA
+AIRTVHRGDAVIAPSTTRRLLTHMAPRLRSDQVRSAECEEQQAAVASLTPREHEVLVLMA
+QGAANLEIAAELVLSEATVKTHVGRVLAKLGARDRVQAVLIAHRAGLVQF
+>LFPAFLNI_02104
+MSSEETAPVRVALVDDQALIRSGLAMLVDSQPDLTVVAEAGSGREAVASVSVAGADVVLM
+DVRMPEMDGIEATRALLRRPDAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAPPEELLA
+AIRTVHRGDAVIAPSTTRRLLTHMAPRLRSDQVRSAECEEQQAAVASLTPREREVLVLMA
+QGAANLEIAAELVLSEATVKTHVGRVLAKLGARDRVQAVLIAHRAGLVQF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000038.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000038.fa
new file mode 100644
index 0000000000000000000000000000000000000000..997ba06567e9ea9f2a1a2837c64812de7d4ee03a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000038.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00620
+MKTRRLTLAAVGILASAGLITGCSTADDAGPSASPSSGQSAATSSSQPASESGSASESAS
+GGGHMDHKMDGGPAPEGIAEAASPAHPVGSEITLTADHMPGMDGATARITGAFDTTAYSV
+DYTPTTGGEPVEDHKWVVHEELQDAGDAPLQVGDTAVMEAEHMAGMKGAEATVASVTDET
+VYMVDYTADGMTMTNHKWVVESEIQPKG
+>MOLHKGIG_01288
+MRKHLKTTVAAGVLGGALVFTGCSTGGDQDQGTPSTTSQHEGHGSSSDSGGMEHPMDGGP
+APEGIETAASPTYPVGTEVTLTADHMEGMDGANAMIAGAYDTYTYAVDFTPSAGGEPVKD
+HKWVVQQEIKDAGDERLADGTEVTLEAEHMEGMKGAKATIASSTEETVYMVDYESDGMTM
+TNHKWVVESELKPAS
+>MOLHKGIG_01627
+MTMRFWTRTVAVTAASLLALTGCATGGEEAATSSSHGGHAGHAMDGGPAPEGIEPAADPA
+HPVGTEVTLMADHMPGMEGAAATVVGAYETTAYSVDYRPTTGGPEVTDHKWVVQEELEDA
+GAERLPDGAAVTLAADHMPGMQGAEGTVHSSTDETVYMVDYESDGMRMRNHKWVVESEIA
+SAG
+>NAFOICDF_00712
+MQRRLRTGLAAGALGVALVLAGCASGADDNQQTDPSATEEHQGHGGNNAESGDEEMEHPM
+DGGPAPEGIAEASEPTYPVGTEVQLTADHMEGMEGATATISGAFDTYTYSVNYTPAGGGD
+PVTDHKWVVQEEIEDAGDARLADGTEVTLLAEHMEGMEGVKAIIASSTDETVYMVDYETD
+GMKMTNHKWVVESEIQPAS
+>MHAAABBN_01007
+MRKHLKTTVAAGVLGGALVFTGCSTGGDQDQGTPSTTSQHEGHGSSSDSGGMEHPMDGGP
+APEGIETAASPTYPVGTEVTLTADHMEGMDGANAMIAGAYDTYTYAVDFTPSAGGEPVKD
+HKWVVQQEIKDAGDERLADGTEVTLEAEHMEGMKGAKATIASSTEETVYMVDYESDGMTM
+TNHKWVVESELKPAS
+>LFPAFLNI_01246
+MRKHLMTTVAAGVLGGALVFTGCSTGGGQDQGTPSTTSQHEGHGSSSDSGGMEHPMDGGP
+APEGIETAASPTYPVGTEVTLTADHMEGMDGANATIAGAYDTYTYAVDFTPSAGGEPVKD
+HKWVVQQEIKDAGDERLADGTEVTLEAEHMEGMKGAKATIASSTEETVYMVDYESDGMTM
+TNHKWVVESELKPAS
+>LFPAFLNI_01556
+MTMRFWTRTVAVTAAGLLALTGCATGGEEVATSSSHGGHAGHAMDGGPAPEGIEPAADPA
+HPVGTEVTLVADHMPGMEGAAATVVGAYETTAYSVDYRPTTGGPEVTDHKWVVQEELEDA
+GAERLPDGAAVTLAADHMPGMQGAEGTVHSSTDETVYMVDYESDGMRMRNHKWVVESEIA
+PAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000041.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000041.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4506352c9605b7ee4d21937778359e2b80d630da
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000041.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00718
+MNLTSVLQAMGLFAATNIDDIIVLSLFFARGAGQRGTTARILAGQYLGFAGILGAAVLVT
+IGAGAFLPSAAIPYFGLIPLGLGLRAAWQAWRGDDDDDDDEAKVAGKKVGVWTVAGVTLA
+NGGDNIGVYTPVFLSVEPLAVVAYCIVFLALVAVLVALAKFVATRPPIAEVLERWEHILF
+PIVLIGLGIVILVSGGAFGL
+>MOLHKGIG_00617
+MSLTSVLQAMGLFAATNIDDIIVLSLFFARGAGQRGTTARILAGQYLGFAGILGAAVLVT
+IGAGAFLPPAAIPYFGLIPLGLGLWAAWQAWRGDDDDDDDEAKVAGKKVGVWTVAGVTLA
+NGGDNIGVYTPVFLSVEPLAVVAYCIVFLALVAVLVALAKFVATRPPIAEVLERWENILF
+PIVLIGLGIVILVSGGAFGL
+>MOLHKGIG_02075
+MSLTSVLQAMGLFAATNIDDIIVLSLFFARGAGQRGTTARILAGQYLGFAGILGAAVLVT
+IGAGAFLPPAAIPYFGLIPLGLGLWAAWQAWRGDDDDDDDEAKVAGKKVGVWTVAGVTLA
+NGGDNIGVYTPVFLSVEPLAVVAYCIVFLALVAVLVALAKFVATRPPIAEVLERWENILF
+PIVLIGLGIVILVSGGAFGL
+>NAFOICDF_02214
+MILTSVLQAMGLFAATNIDDIIVLSLFFARGAGQRGTTARILAGQYLGFAGILGAAVLVT
+IGAGAFLPSAAIPYFGLIPLGLGLWAAWQAWRGDDDDDDDEAKVAGKKVGVWTVAGVTLA
+NGGDNIGVYTPVFLSVKPLAVVAYCIVFLALVAVLVALAKFVATRPPIAEVLERWEHVLF
+PIVLIGLGIVILVSGGAFGL
+>MHAAABBN_00340
+MILTSVLQAMGLFAATNIDDIIVLSLFFARGAGQRGTTARILAGQYLGFAGILGAAVLVT
+IGAGAFLPSAAIPYFGLIPLGLGLWAAWQAWRGDDDDDDDEAKVAGKKVGVWTVAGVTLA
+NGGDNIGVYTPVFLSVKPLAVVAYCIVFLALVAVLVALAKFVATRPPIAEVLERWEHVLF
+PIVLIGLGIVILVSGGAFGL
+>MHAAABBN_01780
+MSLTSVLQAMGLFAATNIDDIIVLSLFFARGAGQRGTTARILAGQYLGFAGILGAAVLVT
+IGAGAFLPSAAIPYFGLIPLGLGLWAAWQAWRGDDDDDDDEAKVAGKKVGVWTVAGVTLA
+NGGDNIGVYTPVFLSVEPLAVVAYCIVFLALVAVLVALAKFVATRPPIAEVLERWENILF
+PIVLIGLGIVILVSGGAFGL
+>LFPAFLNI_02003
+MTLSSALQAIGLFLVTNIDDLIVLSLFFGRGAGQRGTTVRILVGQYLGFAGILGAAVLVS
+LGAGVFLPPEVIPYFGLIPLGLGLWAAWQTWRGDDDDDDDEAKIEGKNVAAWTVAGVTFA
+NGGDNIGVYVPVFLSVGPGAVVAYCVVFLVLVAGLVGLAKFVATRRPIAEVLERWEHILF
+PIVLIGLGVFILISGGAFGL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000042.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000042.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4be4f0cad82b581f38591ad33a80060b3894942f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000042.fa
@@ -0,0 +1,14 @@
+>ACLBLIBL_00724
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>MOLHKGIG_00161
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>MOLHKGIG_01073
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>MHAAABBN_00336
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>MHAAABBN_00347
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>MHAAABBN_00792
+MAAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>LFPAFLNI_01022
+MAAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000045.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000045.fa
new file mode 100644
index 0000000000000000000000000000000000000000..46d06e0afe58ac364a39e721da2265e1d6a8627e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000045.fa
@@ -0,0 +1,63 @@
+>ACLBLIBL_00822
+MSSVLDAAGTPATPHPSPAAPSARVPSSSGGGRLGAGRIGVPALVCMIVAASAPLTAVAG
+GITSNFAVTGLLGVPLSFLVLGVVLLLFSVGYAAMSRHVHNAGAFFAYVARGMGKPAGVG
+AALVALVSYACMQVGIAGMFGFATSSFLEGTFGIAVPWWASALAAWVLVGVLGLYRVDFS
+AKVLMGVVALEFLVVCVYTVLGLRAAPEGVSAAGLLPGQLFTSGVGAALVFSVAAFMGFE
+SGAIYNEEVKDPKRTAGRATLISVVLIAVFYAFSAWAMVMTEGPGGVVAAAQAVGPDVVF
+AFLGAHAPLWFTDLANILFIVSLLAALLAFHNIVARYAFALGREHVLPAFLAHTSTRTGA
+PVGGSLVQSGAALVVLVVFALAGSRSDDPLFPVVTLFTWLTNMGAFGLVLLMALTSVSVI
+GYLRRHRDEFGVFTRVVAPALAAVGLLTLFVLTMVNFPVLLGADGTTPLSWLLPALVVTP
+GALGTAWALWLRARRPATYAGIARGGELS
+>ACLBLIBL_01873
+MSASTPRRRVVDSEGHEHVYPTTSAIEQVNLLNPGGVSNKGLQAGKVGLLGAVVIGVSVV
+APAYTLTSGLGPTISTVGTHVPAILLLGFIPMLLVALGYRALNTRVPDSGTSFTWATHAF
+GPYVGWMGGWGLIAASVIVLSNLAAVAVDFTFLLLAQITGSQAIADLAGNLWVNIPLTLV
+YLALAGWISHRGMETTKHLQYILVAFQILALGAFAVAALTQSSRGAGFDPTPVQLDWFNP
+FTAGDFSVVAAGVSLSIFLFWGWDVTLTMNEETKDPERTPGRAAAVTVLVIIAVYILSAL
+AVISWAGIGSEGLGAGNPDNQESIFAVLAGPILGPFAVIMSSAILVSSLASLQSTMVSPA
+RTLLAMGFYRAVPARFAELSPRFNSPAFATWVCAGFAGLFYVVTRLLSENALWDTITALG
+LMICFYYGITALACVWYFRREWFTSVGNALTTFLFPLIGGLVLLVMFCVTALDSTDPDYG
+SGSSVFGVGTVFVLGMGVLAIGVVLMMWTRLRHPAYFRGETLPQTDSTRPIPIIRPDDDG
+TAVVRDPNERTHS
+>MOLHKGIG_01015
+MSASTPRRRVVDNEGHEHVYPTTSAIEQVNLLNPGGVSNKGLQAGKVGLLGAVVIGVSVV
+APAYTLTSGLGPTISTVGTHVPAILLLGFIPMLLVALGYRALNTRVPDSGTSFTWATHAF
+GPYVGWMGGWGLIAASVIVLSNLAAVAVDFTFLLLAQITGSQAIADLAGNLWVNIPLTLV
+YLALAGWISHRGMETTKHLQYILVAFQILALGAFAVAALTQSSRGAGFDPTPVQLDWFNP
+FTAGDFSVVAAGVSLSIFLFWGWDVTLTMNEETKDPERTPGRAAAVTVFVIIAVYILSAL
+AVISWAGIGSEGLGAGNPDNQESIFAVLAGPILGPFAVIMSSAILVSSLASLQSTMVSPA
+RTLLAMGFYRAVPARFAELSPRFNSPAFATWVCAGFAGLFYVVTRLLSENALWDTITALG
+LMICFYYGITALACVWYFRREWFTSVGNALTTFLFPLIGGLVLLVMFCVTAMDSTDPDYG
+SGSSVFGVGTVFILGMGVLAIGVVLMMWTRLRHPAYFRGETLPQTDSTRPIPIIRPDDDG
+SAVVRDPNERTHS
+>NAFOICDF_02256
+MLSTHQSVSVSTSSVAPVYSAVVTVPLVVGLVGSGAPLAYLLALLPILGVWAGMSANDER
+EPDKGSVYSWAVTGHPVLGWTAGWCLALTGIVATSGLAYVALDAWLPGLGAGVKVLIGAG
+IIAAATALASANVRITAAVQTAGVLVQVAATAYLAWVLARVGLTPLPPAGTVQDWVHAVL
+LAVFAFWGFDAVYALSEESHRGVPRRSAAVSLGLLAAIFLVFSALGASEDPAAVAALTHP
+VVMAGVVVSCVGAIGSTLIPTARGLSAMAERGHLSAVLAPLRAAEVVSALLAIAWLVVSL
+AVPGVFEDSIEMLSVFVGGYFTISSATAAAHASGGARMLHAATAVVMGLITAASLAWMFE
+PDYGATVVGGVGGVGLLAVGFAVLGLILAVGAGHRGRAVHPTSGV
+>MHAAABBN_00729
+MSASTPRRRVVDSEGHEHVYPTTSAIEQVNLLNPGGVSNKGLQAGKVGLLGAVVIGVSVV
+APAYTLTSGLGPTISTVGTHVPAILLLGFIPMLLVALGYRALNTRVPDSGTSFTWATHAF
+GPYVGWMGGWGLIAASVIVLSNLAAVAVDFTFLLLAQITGSQAIADLAGNLWVNIPLTVV
+YLALAGWISHRGMETTKHLQYILVAFQILALGAFAIAALTQSSRGAGFDPTPVQLDWFNP
+FTAGDFSVVAAGVSLSIFLFWGWDVTLTMNEETKDPERTPGRAAAVTVFVIIAVYILSAL
+AVISWAGIGSEGLGAGNPDNQESIFAVLAGPILGPFAVIMSSAILVSSLASLQSTMVSPA
+RTLLAMGFYRAVPARFAELSPRFNSPAFATWVCAGFAGLFYVVTRLLSENALWDTITALG
+LMICFYYGITALACVWYFRREWFTSVGNALTTFLFPLIGGLVLLVMFCVTAMDSTDPDYG
+SGSSVFGVGTVFILGMGVLAIGVVLMMWTRLRHPAYFRGETLPQTDSTRPIPIIRPDDDG
+TAVVRDPNERTHS
+>LFPAFLNI_00958
+MSASTPRRRVVDNEGHEHVYPTTSAIEQVNLLNPGGVSNKGLQAGKVGLLGAVVIGVSVV
+APAYTLTSGLGPTISTVGTHVPAILLLGFIPMLLVALG
+>LFPAFLNI_00959
+MPDSGTSFTWATHAFGPYVGWMGGWGLIAASVIVLSNLAAVAVDFTFLLLAQITGSQAIA
+DLAGNLWVNIPLTLVYLALAGWISHRGMETTKHLQYILVAFQILALGAFAVAALTQSSRG
+AGFDPTPVQLDWFNPFTAGDFSVVAAGVSLSIFLFWGWDVTLTMNEETKDPERTPGRAAA
+VTVFVIIAVYILSALAVISWAGIGSEGLGAGNPDNQESIFAVLAGPILGPFAVIMSSAIL
+VSSLASLQSTMVSPARTLLAMGFYRAVPARFAELSPRFNSPAFATWVCAGFAGLFYVVTR
+LLSENALWDTITALGLMICFYYGITALACVWYFRREWFTSVGNALTTFLFPLIGGLVLLV
+MFCVTAMDSTDPDYGSGSSVFGVGTVFILGMGVLAIGVVLMMWTRLRHPAYFRGETLPQT
+DSTRPIPIIRPDDDGTAVVRDPNERTHS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000051.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000051.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5cc1bb9822a54148c25e950ef8cd7ef20ccc2f3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000051.fa
@@ -0,0 +1,48 @@
+>ACLBLIBL_01707
+MTDGTPEIGDAEGEAPSEMVVQPLIRGEGPEVGPDDSVTVNYVGETWSEGTRFDSSWERG
+APISFSLNQVIPGWKEGLAGQPVGSRVLLSIPAEKAYGEQGSPPDIGPNEPLLFVVDILD
+AQAPSTPPTN
+>ACLBLIBL_01708
+MSSFQTPETTTPRRRRRLLPLVSLGVAGLFLATACASGQDDTPEPQEDAASASQSAAPER
+AAVGEGQGEPDALEGLSFSEGEDGAPSVEVDGELATDQPTTRVLTAGEGDQVKEGDVLKM
+SIAVVDPASGDVLAENFTGDPESVPVDQQLKSMNPEMHDLLVRNGVGSVVAAYSPEREVP
+APPADGASPSASPPPRPSPPSSSCTRSSRSCPRRPRARRSPSATSGCPRSP
+>MOLHKGIG_01181
+MSSFETPQPPTARRRRRLLPLLSLGAAGLMLATACATGDDGADQPHSDTASASTSAAPER
+AAVGEGQGEPDALTGVTFTEGDGGAPTVEIDGEIDTDQPTTRVLTAGEGEQVQEGDVLKM
+SIAVVDPASGEVVAENFSGEPEAVPVDDQLKSMNPEIHEMLVGSGAGTIVAAYSPEYDVS
+VPQTESASPSASPSTQTQPAQLFVYKIDAILPKQAEGEEVTERDERLPDVTVDEQSGRPS
+IAKPDGEAPQELVVQPLIEGEGHEVGADDTVTVQYEGVTWSDGEVFDSSWETGQAITFSL
+NRVIEGWKEGLAGQKVGSRVLLSIPAEKAYGEQGSPPDIGENEPLLFVVDILDAQASATP
+SAN
+>NAFOICDF_00314
+MRPLLPLALTVLMLSAGLTGCAPSSPLDSVQVEEVTGQAQGRSVKFQTPVAVEEVSIRQL
+RAGTGAELDAGDAIVLKMDLFKGSDGTPIEAPFAGGPGQVIALDDQFKAQVPELHEALLQ
+AQEGTMLAYSSPQTAGAAGDESTAVEIYEVAQKIPTTIEGKTSPVPDGLPPITEDETGAP
+VVGPPQGQVPDELVAEYLIQGGGEPVQAGDTVIVHHLGMRWADAQVFDSSYQRGAPARFV
+LDNVIKGWQKGLIGKRTGSRVVLSVPVDQAYGTEAELGDNAPFPAGDLLFVIDILTTQPT
+PPVPTP
+>NAFOICDF_01606
+MNRAPSSAAAPRRRRPRTALSLSLAGLLLATACGAGESSDGSSSPASASSSAAAQGSEAT
+SSSAAPVEYGDPAALDGLTFTVGADGTPSATVGKAIESDKAVVKTLTKGTGATPKAGDVL
+RLSTALLDPATGKVLNENFTTQPEMVAVGSDPASMNPYVHKAVYGAPVGSDVAVYLPAPS
+SSASAPSGTEAAPAQLAVFRVQGVAEQLPQADERLPKVSVDPATGRPSIEKPTGSAPEEL
+VVEPLIQGEGPEVEDTDTVAVQYQGVTWSDGSTFDSSYERGTPATFSLDQVIAGWKEGLA
+GQKVGSRVLISVPSEKAYGAEGTPDGSIGKDEDLLFVVDILAAQPAAASSPAAPSGSTAP
+SGSSSASPSN
+>MHAAABBN_00900
+MSSFETPQPPTARRRRRLLPLLSLGAAGLMLATACATGDDGADQPHSDTASASTSAAPER
+AAVGEGQGEPDALTGVTFTEGDGGAPTVEIDGEIDTDQPTTRVLTAGEGEQVQEGDVLKM
+SIAVVDPASGEVVAENFSGEPEAVPVDDQLKSMNPEIHEMLVGSGAGTIVAAYSPEYDVP
+VPQTESASPSASPSTQTQPAQLFVYKIDAILPKQAEGEEVTERDERLPDVTVDEQSGRPS
+IAKPDGEAPQELVVQSLIEGEGREVGADDTVTVQYEGVTWSDGEVFDSSWETGQAITFSL
+NQVIEGWKEGLAGQKVGSRVLLSIPAEKAYGEQGSPPAIGENEPLLFVVDILDAQAPATE
+SAN
+>LFPAFLNI_01131
+MSSFETPQPPTARRRRRLLPLLSLGAAGLMLATACATGDDGADQPHSDTASASTSAAPER
+AAVGEGQGEPDALTGVTFTEGDGGAPTVEIDGEIDTDQPTTRVLTAGEGEQVQEGDVLKM
+SIAVVDPASGEVVAENFSGEPEAVPVDDQLKSMNPEIHEMLVGNGAGTIVAAYSPEYDVS
+VPQTESASPSASPSTQTQPAQLFVYKIDAILPKQAEGEEVTERDERLPDVTVDEESGRPS
+IAKPDGEAPQELVVQPLIEGEGREVGADDTVTVQYEGVTWSDGEVFDSSWETGQAITFSL
+NQVIEGWKEGLAGQKVGSRVLLSIPAEKAYGEQGSPPDIGENEPLLFVVDILDAQASATP
+SAN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000054.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000054.fa
new file mode 100644
index 0000000000000000000000000000000000000000..767b3bf1a70f5fb3dcf0dc3f7fb3791e519b6fda
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000054.fa
@@ -0,0 +1,66 @@
+>MOLHKGIG_01590
+MPVAPRPSDGAASSVFTPHQQRILAVLLIPIFMSLLAVSSINVALPALQRGLDASDAELQ
+WAISGYTLVFGMVLVPAGRAGDLFGRRRLFMVGLGVFALGALLSGLAPTGVLLVLARLVM
+GVGAGLLNPQVTGFIQSEFSGTSRARAFGALGAVVGVSVAVGPLLSGGLIAWLGGDLGWR
+ATFLVNVPIALGALVVARHWLPRTAPERARRPDLDPVGVVLLAGALVAVMLPFLDRELGP
+WRFVLVPVGIGLAALWTRWEARYARRGRAPMVDLRLFQTRSFACGALLIAIYFTGSTSMF
+VVIAMFMQNGLGYPALHAALIGLPSAVMSSVMSTVAGRVVLRTGRKIVVLGIALALLAVV
+GSIGVAWANREFGLSPWWLLLTLAILGAGQGLVVSPNQTLSLAEVPPRHSGTAGGVLQTG
+QRVGTAVGTAVIVGVFLGVASGADWDGAFMAAFTLVAGCMALALLVALADLRGPRTAAPR
+G
+>NAFOICDF_00643
+MLFASFMDLLDVTIVTVAAPHIAADLNASPAQLQWMLAAYTLALGSGLITGGRIGDDYGR
+RRVFLAALAAFAIASAACALAPTAGALIAVRAVQGLAGGFMVPQVFGIIRSSFEPAAMAK
+AFGAYGAVQGLASVAGPLIGGALADADLWGLGWRTIFWINIPIALVALVLGWRVLPDSRA
+AARSRLDGVGALLAAVGVLLVLLPLVQGRDWGWPTWGWALLAAGVLVLAGFLRYENALAR
+RGGEPVLDPDLLRVRPFVAGLAASVLFFGGLASFFLVVSIYLQAGTGRSAWDTGLVILPY
+AIGSMLTSGAGVALAARAGRALLLTGSLTLAASQALLWWLVRDGSTTPDYWPLAGAMFLG
+GLGLGLGAPILVNVVLAGVPGRRAGAAGGVLSTVNQIGGAVGVAVLGTVFFNAASSAGPA
+TAPAELFGDALAQVMPWQVATYLLAAVAMLALPKTAAPHQD
+>NAFOICDF_00714
+MAGDCIRQIPRWGFVLSLAATILMMAAASAPSLFYPQIAERLGLIPVATTLVFAVYTFTL
+LAALLYLGPLSDHVGRRPVVAAGSLALALSVAMFWFAGSLAALLVARALQGLAAGLLIPA
+LSAMMIDFESPSHRNIAALWNTIGPMIGLGAGALGAALLLDLTSEPTTAVFGSLVLAFLI
+VATVVWSTPELVPKTQIRRGDLRPRFTVPPHLRRMFTVGVPVIIAGWATNGLFLALGADL
+VGSELGGSTHTQAGIVLFALAISGVTASSVLQRRSARTISLYATSALAFGTAVSIGALAL
+GSYPAYVASVAIVGSGFGTAFLGVLRTLMPHTASSERAAVMAVIYTVAYLAFGVPTIVAG
+LLVPVLTLSGTMTILGAIIIALSLVATVLRLRIPHPAAGPAEADDFPEPPTGSHRRSAPD
+REEQP
+>NAFOICDF_01240
+MNPSAGTSGGVFTARQRRVLAVLLVPVFMSLLAVSSINVALPSLQRGLGASDAELQWSIS
+GYTLAFGMVLVPAGRAGDLLGRARLFRIGVLGFGLGALLSGLAPSGLLLVLARVLMGVGA
+GLLNPQVSGFIQAEFEGQARARAFGALGSTVGVSVAAGPLLAGGLIAVLGGDLGWRATFL
+VNVPIALAAVLIARGWLPEESPAPAGRRDFDPVGVALLASALVAVMLPFLDRGLGPWRFA
+LLPLGAALAAGWAVWERGYRARGRAPMVDLSLFGLPGFRNGALMIGVYFTGSTSLFIVVA
+MFMQNGLGYGALQAALVGLPSAVCSSVMATVAGRLVLRAGRRLVVVGVSLVLAAVVGSIG
+VVAAHQAFGLSPWWLLATLGLFGMGQGLTVSPNQTLSLAEVPRPQSGTAGGILQTGQRVG
+TSVGSAVIVGVYLGVAGTGGPDRGFMAALGLIAVSIAAALAVAVADQRRRARQGGR
+>NAFOICDF_01828
+MPRPRLLLAVILLAQFVIPLSISGTAVALPAIASDLGSDPTPLQWVVNGFNVAFAVCTIV
+WGACSDRIGYTRSFRIGIAIAIAGGIVSMFAPNIAVLDAGRIIAGIGSAAVLTSAAPILS
+HLFEGKARAQAFALFGTINGLGLAAGPALSGLLLSAWGWQGIFAAHTIVLIVAFIGAARL
+PQLGRGGTSLREILDFSALKAPKFLAMTLVPIAGAIGFVTFLTYLPSALGAIHGLTAGVT
+GALMLVMTIPVLIAPVAVHRLMERSHLTPTAIVAVSFACLIVGGIGVLLLLRPDLPVALG
+VTPMILLGLGFGLPLGFVDAEALAAVPAERAGAASGVINLFRIGSEAVFVAAYGALLAAV
+ITTTLPGTTGELIASGSPGEPWIYHSGLMAAAGTMIGLVAIAGVTFLALTRAANRSAVTA
+RQVEVAR
+>MHAAABBN_01302
+MPVAPRPSDGAASSVFTPHQQRILAVLLIPIFMSLLAVSSINVALPALQRGLDASDAELQ
+WAISGYTLVFGMVLVPAGRAGDLFGRRRLFMVGLGVFALGALLSGLAPTGVLLVLARLVM
+GVGAGLLNPQVTGFIQGEFSGASRARAFGALGAVVGVSVAVGPLLSGGLIAWLGGDLGWR
+ATFLVNVPIALGALIVARQWLPRTAPERARRPDLDPVGVVLLAGALVAVMLPFLDRGLGP
+WRFVLVPVGIGLAALWTRWEARYARRGRAPMVDLRLFQTRSFACGALLIAIYFTGSTSMF
+VVIAMFMQNGLGYPALHAALIGLPSAVMSSVMSTVAGRVVLRTGRKIVVLGIALALLAVV
+GSIGVAWANREFGLSPWWLLLTLAILGAGQGLVVSPNQTLSLAEVPPRHSGTAGGVLQTG
+QRVGTAVGTAVIVGVFLGVASGADWDGAFMAAFTLVAGCMALALLVALADLRGPRTAAPR
+G
+>LFPAFLNI_01517
+MPVAPRPSDGAASSVFTPHQQRILAVLLIPIFMSLLAVSSINVALPALQRGLDASDAELQ
+WAISGYTLVFGMVLVPAGRAGDLFGRRRLFLVGLGVFALGALLSGLAPTGVLLVLARLVM
+GVGAGLLNPQVTGFIQGEFSGASRARAFGALGAVVGVSVAVGPLLSGGLIAWLGGDLGWR
+ATFLVNVPIALGALIVARQWLPRTVPERARRPDLDPVGVVLLAGALVAVMLPFLDRGLGP
+WRFVLVPVGIGLAALWTRWEARYARRGRAPMVDLRLFQTRSFACGALLIAIYFTGSTSMF
+VVIAMFMQNGLGYPALHAALIGLPSAVMSSVMSTVAGRVVLRTGRKIVVLGIALALLAVV
+GSIGVAWANREFGLSPWWLLLTLAILGAGQGLVVSPNQTLSLAEVPPRHSGTAGGVLQTG
+QRVGTAVGTAVIVGVFLGVASSADWDGAFMAAFALVAGCMALALLVALADLRGPRTAAPR
+G
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000057.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000057.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba433df15f304925c332c43c27120fd90008cf83
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000057.fa
@@ -0,0 +1,43 @@
+>ACLBLIBL_00027
+MSETTRTPGTGRGTMRAVRFTGEGGAGSLAVGQEPIPTPGPGEVLVKVAAAGLNRADVMQ
+REGKYPPPPGASDVPGLEVSGVVVALGEEAGLPGEGRFAPGDEVCALLAGGGYAEHVVVP
+AGQLMAVPPGVDLVTAAALPEVACTVWSTMSERGGVRAGDVVLVHGGSGGIGTFAVQYLA
+AIGARVLATAGGPAKCERVRGLGAEDVFDHRSGEPGAFADWVLERTGGRGADVVLDVVGG
+PYLDANVRCLAEEGRIVVIAVQGGPKADGFNLMRLVSKRGWLTGATLRARSVVDKARIVA
+GTERAVAPLVAAGRIDLAVGARFPLDDAAAAHRRFEAEDRVGRVLLVTDPADALWPQEDR
+T
+>MOLHKGIG_00310
+MDVPAQMRAVRFTGAGDNGVVRVGHEPVPDPGPGEVLVHVAAAGLNRADIAQREGRYPPP
+RGASEIPGLEVSGTVAALGPEAGMPGEGRFAVGDRVCALLAGGGFAEYVAVPAGQLMAVP
+DGVGLVEAAALPEVACTVHSTLVGRAGVQAGDRVLVHGATGGIGSFAVQFLTAVGARVLG
+TAGGPEKVALGRGLGAEHMFDHRAAESGAFAPWVKEVTDGHGADVILDVVGAPYLAPNVS
+ALAPEGRIVTLAVQGGAVPEDFNIMKLVVKRGWLTGATLRSRSVTDKAGIVAAAERAVWP
+LVAAGRIDASVGACFPLAEAAEAFDWFDSATRTGKVVLVTDPADARRPSGDRA
+>NAFOICDF_00023
+MDTAPDMLAVRFAGAGGTDVIRVGREPVPEPGPGEVLVRVAAAGLNRADVVQREGHYPVP
+PGASEVPGLEVSGTVVALGPQAGVAGEGRFAVGDRVCALLAGGGYAEHVAVPAGQLMSVP
+DGLDLVSAAGLPEVACTVHSNLEGRAGVRPGEWALVHGATGGIGAFAVQYLSAVGVRVLA
+TAGGPAKVARALELGADAAFDHRAAAPGAFADWVREITGGHGADVVLDVVGGPYLAPNVK
+ALAMDGRIVVIAAQDGPVPEDFHLMRLAARRGWVTGSLLRPRPPDEKAGIVAAAERAVWP
+LVAAGRIDPGVTARFPLREAAAAHAHFEGAARMGKVLLVTDDADALLPGGAA
+>NAFOICDF_00654
+MHPSLPRTMLAAIIPAPGGRPELRQCPVPEPGPGEVLVRVMASSVNPTDVMTWRRGMFVT
+GQTVPFVGGYDMSGIVVKLGRGVTALDVGDAVTGMPRFPAPAAAFAQYSAVPARHLARIP
+TGTEDLSAGAWGRWAGLPLAGLTAYQALVDTAHLQSGQTVLVHAASGGVGSLACQLAVNL
+GAQVTAVTSDRGRTLVEVLGTRHVVDRATVDWQRFAGCFDVVLDTVGGDTTPRSLAMASP
+DGVVVALHPYAHDDLAQRDPRLRRMLVEPDHHALELLIEQAARGRLTVQVGAGYPLSDLG
+DALLHVETNKTPGKTIIHIQGDNA
+>MHAAABBN_00025
+MDVPAQMRAVRFTGAGDNGVVRVGHEPVPDPGPGEVLVHVAAAGLNRADIAQREGRYPPP
+RGASEIPGLEVSGTVAALGPEAGMPGEGRFAVGDRVCALLAGGGFAEYVAVPTGQLMAVP
+DGVGLVEAAALPEVACTVHSALVGRAGVQAGDRVLVHGATGGIGSFAVQFLAALGARVLG
+TAGGPEKVALGRRLGTEHMFDHRAAESGAFAPWVKEVTDGHGADVILDVVGAPYLAPNVS
+ALAPEGRIVTLAVQGGAVPEDFNIMKLVVKRGWLTGATLRSRSVVDKAGIVAAAERAVWP
+LVAAGRIDASVGACFPLAEAAEAFDWFDSATRTGKVVLVTDPADARRPSGDRA
+>LFPAFLNI_00317
+MDVPAQMRAVRFTGAGDNGVVRVGHEPVPDPGPGEVLVHVAAAGLNRADIAQREGRYPPP
+RGASEIPGLEVSGTVAALGPEAGMPGEGRFAVGDRVCALLAGGGFAEYVAVPAGQLMAVP
+DGVGLVEAAALPEVACTVHSALVGRAGVQAGDRVLVHGATGGIGSFAVQFLAALGARVLG
+TAGGPEKVALGRRLGAEHMFDHRAAESGAFAPWVKEVTDGHGADVILDVVGAPYLAPNVS
+ALAPEGRIVTLAVQGGAVPEDFNIMKLVVKRGWLTGATLRSRSVVDKAGIVAAAERAVWP
+LVAAGRIDASVGACFPLAEAAEAFDWFDSATRTGKVVLVTDPADARRPSGDRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000059.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000059.fa
new file mode 100644
index 0000000000000000000000000000000000000000..677b636818e548c3228d4d741778a453c5967f09
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000059.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_00057
+MLSEKSRPVIEATAAVVAEHMPEITPKFYAHMFEAHPELLDGVFSRANQRSGEQAQALAG
+SIVTFAVHLLEHPDTLPEAVLARIAHKHTALGIVPEQYQIVYENLFWAIADVLGEAVTPE
+VAEAWTEVYWLMADALIKIEEGLYAQQANTKMWTDWKVVAKEPTGNAAVTFRFAPADETP
+QTPGRPGGYLSVRLKVEDGLRQCRQYSLSDHAESTDERVITVKLDEGGEVSPVLIQNVEV
+GDVIELSNPYGDITLRDDAETPLVLATAGIGITPAAAILDTLASRGSQREVHFFHGDASW
+DSVALREQVAESLQALENGTGRLWLGVPPQEAPAAFTTTEGLMEFDDVELPADASYLLCG
+PLAFMQATRSKLIDAGVPATSIRYEIFGPDLWLAA
+>MOLHKGIG_00297
+MLSEKSRPVIEATAAAVAEHMPEITPLFYAHMFEAHPELLDGVFSRANQRNGEQAQALAG
+SIVKFAVHLLENPGTLPEAVLSRIAHKHTALGIVEEQYPIVYENLFWAIGEVLGDAVTPE
+VADAWTEVYWLMADALIKIEKGLYAQQANDRMWTDWKVVAKEPTGNAAVTFRFEPADDTP
+QSRGKAGGYVSVRLKVEDGLRQCRQYSLSEKAESATERVITVKLDEGGEVSPMLIQNVEV
+GDVIELSNPYGDITLEDEDSTAPLVLATAGIGITPAAAILDALAQQGSDRQVLLLHGDAS
+WEAVALREQVTESLAALAHGDARLFLGVRPEQDPEGVTTVEGVMHFDDVELPRDGHYILC
+GPLAFMQSTRSKLIDAGVPATSIRYEIFGPDLWLAA
+>NAFOICDF_00035
+MLSEKSRPVIEATAAVVSANMPQITPAFYGHMFEAHPELLDGTFSRANQLNGEQAQALAG
+SIVHFAAHLLEHPDSLPEAVLARIAHKHTALGITEDQYQVVYENLFWAIAQVLGDAVTPE
+VAEAWTEVYWLMADALITLEKDLYAVQANDRMWTDWKVVAKEPTGNAAVTFRLEPADDTP
+QTPGRPGGYVSVRVTVADGLRQARQYSLSESASSTGQRVITVKLDEAGEVSPVLIQEVEV
+GDVVELSNPYGDITLQDSDAPLVLMTAGIGITPAAAILDSLAASGSQREVRVLHGDASWD
+SVALRDQVLEDVASLPHAQADLWFGVAPETAPEGVSVHEGKVDTAAAALPEGADYILCGP
+LAFMKSERSALIEAGVPAPRIRYEIFGPDLWIAAT
+>NAFOICDF_01222
+MPAHGWGARAGRTSFREHPVDVQECLWRGAHASSHDRSALHSRPSRGGSADPAPADRPPP
+PLTPAPGPAGIRDRPAGRIPAWWRDASGSLLWLVLLAVTALWVHGGGVQDLAAVGSGLTS
+LGRLTGLIASALLLAQVFLMARVPLVEQAWGQDRLTRVHRRVGFTSFTLMFAHLALITAG
+YAWDTPAGLWGTLVDFAVDYPGMLLAIAGTAALVMVVVTSFKAARARLRYESWHLIHLYG
+YLGAGLALPHQLWTGQEFLASPVATAFWWTLWAVTAGAVVVFRALLPLWCSARAGLRVQS
+VTAAGPHAVTVTVAGRGAHRLHARGGQFFQWRFLDGPGWTRAHPYSLSAAPDGRTLQFTA
+AVVGDGTGRLWDMRPGTRVLVEGPYGRMHDGVRTGRKALLMGAGIGITPMKALLESLPAD
+AGEITVVHRVSDPDDPTLHADLLAAARTRGARYIRLEGRRRPGADSWLPASAGDVDDVTA
+LRRICPDLAEHDVFVCGAPAWTDLVRQAARRGGVPAERIHDERFSF
+>MHAAABBN_00005
+MLSEKSRPVIEATAAAVAEHMPEITPKFYAHMFEAHPELLDGLFSRANQRNGEQAQALAG
+SIVRFAVHLLENPGTLPEAVLARIAHKHTALGITEDQYQIVYENLFWAIADVLGDAVTPE
+VAEAWTEVYWLMADALIKLEKGLYAKQANDKMWLDWKVVSKEPTGNAAVTFRFEPADDTP
+QTPGEAGGFVSVRVKVADGLRQARQYSLSDHAASTTERVITVKLDEGGEVSPMLIQNVEV
+GDVIELSNPYGDITLEDEDSTAPLVLATAGIGITPAAAILDALAQQGSDRQVLFFHGDAS
+WEAVALREQVTESLAALPHGDARLFLGVRPEQDPEGVTTVEGVMHFDDVELPRDGHYILC
+GPLAFMQSTRSKLIDAGVPATSIRYEIFGPDLWLAA
+>LFPAFLNI_00304
+MLSEKSRPVIEATAAVVAEHMPEITPLFYAHMFEAHPELLDGVFSRANQRNGEQAQALAG
+SIVKFAVHLLENPGTLPEAVLSRIAHKHTALGIVEEQYPIVYENLFWAIGEVLGDAVTPA
+VADAWTEVYWLMADALIKIEKGLYSQQANDRMWTDWRVVAKEPTGNAAVTFRFEPADDTP
+QSRGRAGGYVSVRLKVEDGLRQCRQYSLSEKAESTTERVITVKLDEGGEVSPMLIQNVEV
+GDVIELSNPYGDITLEDEDSTAPLVLATAGIGITPAAAILDALAQQGSDRQVLFFHGDAS
+WEAVALREQVTESLAALPHGDARLFLGVRPEQDPEGVTTVEGVMHFDDVELPRDGHYILC
+GPLAFMQSTRSKLIDAGVPATSIRYEIFGPDLWLAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000063.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000063.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cd0e5bae5b972ccacc89a5188a474be63dfb99dd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000063.fa
@@ -0,0 +1,108 @@
+>ACLBLIBL_00086
+MTPPLSRRHRALGMTSALALVLTGASAAGATSGTGAPAAAEADAVTAVTGAAGTADQGPR
+TAPEVFEDGGYIVLMAEAPVASYDGGTPGYAPTKPGKGLGRDKGFNPKSANAKKYAAHLE
+RGQDRALERAGAEAAPHTRYTTSLNGFAGELTAQEAAALASDPAVLAVVPDEIRQPDTVS
+SPDFLGLTGKKGLWAQVVGKKAPATDAGRGVVVGVVDSGIRPEAASFQDRGHPAAPADWA
+GGCETGDEEAFPADSCNDKLIGAKYFVQGFGAGRLAPVETLSPLDAGGHGTHTASTAAGN
+AGVPAVVDGTPRGEISGMAPGAHVAAYKACWEGVPSGGCATSDTVAAINAAVEDGVDVLN
+YSISGTTSNVVDPVEVAFMHAAAAGVFVAASSGNSGPTVSTTAHPSPWITTVAASTQAVY
+EQTLVTGDGQRFIGSSITAPLEAETPMVHAADLAADGVDAARAALCLPGTLDATAAADML
+VVCDRGENARAEKSQVVADAGGAGMVLVNVADSGLNADLHALPAVHLPHTERDRLLAYVD
+TEEPTGRILPTTEGTTTRVPEVAGFSSRGPSLAAASDLLKPDVSAPGVDVLAAYSPDEAG
+EDFAYASGTSMSSPHVAGLAALVKQGRPDLGPMEIKSSLMTTAGDHASATSPFAEGAGFV
+DPMKILDPGLVFDTDQGDWYDYLAGQGIVFSGSGEPVSETPIDASDLNVPSIAVGELYGS
+QTVTRTLKNVGGNNGVWTARVEGMEGMDVSVSPQVIKPRRGQEQDVEITLTAAGAPAGQW
+ATGHVVWSGPAGKEVRIPVVARPGVADAPASVTVDRDADGLELPVLSGVDGTFTTRVNGL
+TAGTEHIGTTVRRMFFDSTDPALTGHDFAYPRGYPTVRIEAETSAEDVDLDVYVTGSWTS
+YPVARSVTRGTGMEVFQGPIYSSAPQHRIFVVAKTGADGVEHDEPIDYTLRVFFPQAGGG
+DNGVLSFDPASAAVKPGQTHVFHGTLNTDGTSVYTGTVDILHEGKVVDTTQIRVQ
+>ACLBLIBL_00159
+MRKAEAMPHIPTPARRRRALAAAVVGASLVAAPALAASAIAVELPDGSVVTSPQGEAKVE
+QQFEDGRYFVVLKDAPSVTAQEAGAPAPGAAPKAKFDPDHPRVKNYEAKLQRQQEKVARD
+NGVEPKTTFQRAVNAFVAELTAEEAMRLSKDSAVLGVAPDEQVAPDYSSTEFLGLPGKKG
+TWNTTYGKPENAGKGVVVGVIDTGIHPDNPFIDAEPVKPLKGKAKVGEPYRTADGDIAVL
+KADGTTATAECETGPGFPADSCDTKLIGAYAFSDDFERFVPVENRHPAEQLSPLGVFSHG
+THVATTILGNTGVEQTIDGTSFGEGAGVAPAASLISYKICWEDNDPNTGGCYTSASVAAI
+EQAIENNVDVLNYSISGSNTTIVDPVAMAFKSAAEAGIFVAASGGNSGPTPNTVNHSSPW
+LTTVAAETFSNELTGTVEFSDGTKYRGASSAGSDAGPAEVIHASEVAAGDAEAARLCLPG
+SLTAEAADKIVLCERGQNARVEKSAVVAEAGGVGMILANTPTGSLDADIHSVPTVHINDT
+DGVIEKVKSSDLTATIVRGDTTGLPQDPLPQIAGFSSRGPSNAVNQEFLKPDVAAPGVNV
+IAGVSPLDPDYNGNEFGLMSGTSMASPNLAGMAALLIGKEAAWSPMAVKSALMTTAGDVF
+NADGSVNEDNFATGAGSADPKAAARPGLVYEADSTQWDALLLGEIAGREVNVPSVAIPDV
+VGSASVTRTLTATENGRWQFSGSVPGFEVTASPSMLDLKKGQSAEVELTFTRTDAEVNTW
+AHGSMSWSTAKGKAVPTVTSPVTLKALSATATSAVEGSGAEGSATVEIEPGMTGELTPQI
+LGLGKVEAAEVSAVANTSASGAALAGRVVNVEEGTKALVASINAGAEGVDWDLYVITPQG
+RQLNMATAAGDETLTIQNPVPGEYTVIGHLYSAPAGTDTASLETLKLREDVGNLTVDPNP
+VPVTTGEATTAELAWSGLTEGTWKGLVTWDAGVTTDVTVTVP
+>MOLHKGIG_00221
+MRKAEAMPQNPTPARRRRALAAAVAGASLVAAPALAVSATAVELPDGSTVSSPQGEVQVQ
+QQFEDGRYFVVLKDQPSVTAPEAGAVPGAAPKAKFDPSHPRVKNYEAKLQRQQAKVAKAH
+GAKAEISFQRAVNAFVAELTAEEAQSIAKDPAVLGVAPDEQVAPDYSSTEFLGLPGKKGT
+WKSVYGKAENAGKGVVVGVIDSGIHPDNPFIDGQPVQPLKGKAKVGVPYRTADGQIAVLK
+ADGTTATAECETGPDFPASSCDSKLIGAYAFSDDFERFVPVDERAPEERISPLGVFSHGT
+HVATTILGNTGVEQTIDDDSFGEGAGVAPAAHLISYKICWEDTDPDTGGCYTSASVAAIE
+QAIENNVDVLNYSISGSNTSIVDPVAMAFKSAAEAGIFVAASGGNSGPGPNTVNHGSPWL
+TTVAAETFSNELTATVQFSDGTQLRGASSARTGVGPAEVIHASEVAAGDAEAARLCLPGG
+LTEEAADKIVLCERGGNARTEKSQVVEEAGGVGMILVNTPSGSLDADIHAVPTVHMNDNG
+VIEKVKSSDLTATVVPGDTTGLPEDPLPQIAGFSSRGPANAVNQELLKPDLAAPGVNVIA
+GVSPLDPDYHGNTFGLMSGTSMASPNLAGMATLLIGKYPAWSPMAVKSALMTTAGDVYNA
+DGTVNTDNFATGAGSADPAAAARPGLVYDSGKEQWDALLRGDIAGREVNVPSLAIPDVVG
+SATVTRTVTALENGRWQFSASVPGFEVTASPAVLDLKAGQSADVELTVTRTDAAVNTWTH
+GSMSWTTAKGKAVPEVTSPVTVKAKSAAVTSAVEGSGATGSADVEITPGVTGELTPQVLG
+LGKVDSTVAAATASNSLVSSALAVSTVTVEEGTKSLVASINAGAAGADWDLYVITPEGKQ
+LSRATADESETLTIANPTPGAYTVVGHLYAANGGKDTGTLETLKLREDAGNLTVSPNPVP
+VTSGKATEATLSWSGLTSGTWKGLVTWDAGITTDVTVQVP
+>NAFOICDF_00117
+MNRHPQRLRLLGAAVTAVGLMAAPLAAPAFAAPQAEHAVGVQAATPLKAGRYFVILKDAP
+SAVAESQATAPGAAPSAKFDANHPRVKNYEAKLKRQQEKVAAQQGVTPKVTFQRALNGFV
+AELSAEQAQAYAEDPAVLAVTADEQVAPDYTSTDFLGLNGKKGAWNTTFGKAENAGRGVV
+VGVIDSGIYPDSPFLDGTPVGPRTNNGKLKAGDTFRTADGRIAVQKADGTLATAECQSGP
+DFPASTCDSKLIGAYAFSDDFVRGTPVEKRDPAERISPLGVKSHGTHVATTIVGAKDVEQ
+TIDGASFGLGSGVAPAAKLISYKVCWEDTDPDTGGCYSSASVAAVEKAIENNVDVLNYSI
+SGNNTSVVDPVALAFRSAAEAGIFVAASGGNSGPTPSTVNHSSPWVTTVAAETFSNELTG
+TLELSDGTKVRGASSARTGVGPAPVIHAADAAAAGVSADDARLCKPGALDPAKAAGKIVL
+CERGVNARVEKSAVVKDAGGVGMILVNVTPGSLDADIHAVPTVHTNDASLIAKAKAGGLQ
+ATIVPGDTTGQAPDPLPQIAGFSSRGPSNAVNQEFLKPDVAAPGVNVIAGVSEYDSDYHG
+NVFGLMSGTSMASPNLAGMATLLIGKHPEWSPMAVKSALMTTAGDVYNADGTVNQDNFAT
+GAGSADVAAANRPGLVYESDATQWNALILGDLAGREVNVPSVALPDVLGTASVKRTVTAL
+ENGRWTFSGSVPGYTVTASPSVLDLKAGQKAEVTLTFTRTDAALSQWTHGSFSWTTAKGK
+AVPSVTSPVTLKSVPATADASVTGTGASGSAAVAVQPGFTGQLTPSVLGLNKVESQAVTL
+QPGGSKVTPVTVAPGTKSVTFAVDSGVDTADWDMLVQTPSKKQFTSATESSDESVTIQDP
+EPGTYLVLTQLYANPAGADTAALETVQLRSDAGNMTVTPNPIPVTTGQETSATVNWTGLT
+SGTWRGQVTWAEGTATQVEVTVP
+>MHAAABBN_02234
+MRKAEAMPQNPTPARRRRALAAAVAGASLVAAPALAVSATAVELPDGSTVSSPQGEVQVQ
+QQFEDGRYFVVLKDQPSVTAPEAGAVPGAAPKAKFDPSHPRVKNYEAKLQRQQAKVAKTH
+GAKAEISFQRAVNAFVAELTAEEAQAIAKDPAVLGVAPDEQVAPDYSSTEFLGLPGKKGT
+WKSVYGKAENAGKGVVVGVIDSGIHPDNPFIDGQPVQPLKGKAKVGVPYRTADGQIAVLK
+ADGTTATAECETGPDFPASSCDSKLIGAYAFSDDFERFVPVDERAPEERISPLGVFSHGT
+HVATTILGNTGVEQTIDDDSFGEGAGVAPAAHLISYKICWEDTDPNTGGCYTSASVAAIE
+QAIENNVDVLNYSISGSNTSIVDPVAMAFKSAAEAGIFVAASGGNSGPGPNTVNHGSPWL
+TTVAAETFSNELTATVQFSDGTQLRGASSARTGVGPAEVIHASEVAAGDAEAARLCLPGG
+LTEEAAGKIVLCERGGNARTEKSQVVEEAGGVGMILVNTPSGSLDADIHAVPTVHMNDNG
+VIEKVKSSDLTATIVPGDTTGLPEDPLPQIAGFSSRGPANAVNQELLKPDLAAPGVNVIA
+GVSPLDPDYHGNTFGLMSGTSMASPNLAGMATLLIGKYPAWSPMAVKSALMTTAGDVYNA
+DGTVNTDNFATGAGSADPAAAARPGLVYDSGKEQWDALLRGDIAGRDVNVPSLAIPDVVG
+SATVTRTVTALENGRWRFSANVPGFEVTASPAVLDLKAGQSADVELTVTRTDAAVNTWTH
+GSMSWTTAKGKAVPEVTSPVTVKAKSATVTSAVEGSGATGSADVEITPGVTGELTPQVLG
+LGKVDSTVAAATASNSLESSALAVSTVTVEEGTQSLVASINAGAAGADWDLYVITPEGKQ
+LSRATADESETLTIADPAPGAYTVVGHLYAANGGKDTGTLETLKLREDAGNLTVSPNPVP
+VTSGKATEATLSWSGLTSGTWKGLVTWDAGITTDVTVQVP
+>LFPAFLNI_00222
+MRKAEAMPQNPTPARRRRALAAAVAGASLVAAPALAVSATAVELPDGSTVSSPQGEVQVQ
+QQFEDGRYFVVLKDQPSVTAPEAGAVPGAAPKAKFDPSHPRVKNYEAKLQRQQAKVAKAH
+GAKAEISFQRAVNAFVAELTAEEAQAIAKDPAVLGVAPDEQVAPDYSSTEFLGLPGKKGT
+WKSVYGKAENAGKGVVVGVIDSGIHPDNPFIDGQPVQPLKGKAKVGVPYRTADGQIAVLK
+ADGTTATAECETGPDFPASSCDSKLIGAYAFSDDFERFVPVDERAPEERISPLGVFSHGT
+HVATTILGNTGVEQTIDGDSFGEGAGVAPAANLISYKICWEDTDPDTGGCYTSASVAAVE
+QAIENNVDVLNYSISGSNTSIVDPVAMAFKSAAEAGIFVAASGGNSGPGPNTVNHGSPWL
+TTVAAETFSNELTATVQFSDGTQLRGASSARTGVGPAEVIHASEAAAGDAEAARLCLPGG
+LTEEAADKIVLCERGVNARTEKSQVVEEAGGVGMILVNTPSGSLDADIHAVPTVHMNDNG
+VIEKVKSSDLTATIVPGDTTGLPEDPLPQIAGFSSRGPANAVNQELLKPDLAAPGVNVIA
+GVSPLDPDYHGNTFGLMSGTSMASPNLAGMATLLIGKYPAWSPMAVKSALMTTAGDVYNA
+DGTVNTDNFATGAGSADPAAAARPGLVYDSGKEQWDALLRGDIAGRDVNVPSLAIPDVVG
+SATVTRTVTALENGRWRFSANVPGFEVTASPAVLDLKAGQSADVELTVTRTDAAVNTWTH
+GSMSWTTAKGKAVPEVTSPVTVKAKSATVTSAVEGSGATGSADVEITPGVTGELTPQVLG
+LGKVDSTVAAATASNSLESSALAVSTVTVEEGTKSLVASINAGAAGADWDLYVITPEGKQ
+LSRATAAESETLTIANPTPGAYTVVGHLYAANGGKDTGTLETLKLREDAGNLTVSPNPVP
+VTSGEATEATLSWSGLTSGTWKGLVTWDAGITTDVTVQVP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000064.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000064.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b499d3699883285800ea4b885f0fe9b1e5686955
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000064.fa
@@ -0,0 +1,61 @@
+>ACLBLIBL_00088
+MTAALTTRENTAPAAEPAGARIPVAELRNLRVGFDDGAGGTRAVVHGVDLRIEPGQCVAI
+VGESGSGKSVTARTLVGLTGAGSRVSADLARLGEDDVLALDERAWRRRRGVRVGYILQDA
+LVSLDPLRTVGAEIGDVLRLHGVSDRGERRRRAADLLAEVGVPEPQVRLDQRPGELSGGL
+RQRALIASAVALQPELVIADEPTTALDVSVQVQVLELLSRLKSSGTAVLLISHDFAVVSR
+LADHVLVMEGGRIVESGPVRRILDAPEHPYTRRLLAAIPSGDTRGQRLSPEPRAVVTHAP
+LVAAPTAQGGPTLAARGLTKRYRGPDGRDRTVVDDVSFDVFAGQTLGIVGESGSGKSTTA
+AMALGLVQPDAGTVELDGRPWSGVSARARRARRRQVAVVYQDPLSSFDPRWNGERILADA
+AGAGVPPWASPARRRAARDDARARAVDLARLVGLDPRHLTRSPARLSGGQRQRLAITRAL
+AVQPRVLVLDEAVSALDVSVQAQVLDLLGDLKEGLGLTSLFISHDLGVIHHVSDRILVMK
+DGRAVEQGDADQVFHAPRHEYTRGLLASLEQLSIR
+>ACLBLIBL_00265
+MDPKHDDGALGAGSHAAAPEAAPTAGTDPAGVGSAEMPAPGAPLLEIRDLDVEFRTQQGT
+VKAVEGASLTLPAGGTLAIVGESGSGKSTTAMAAIGLLPGNGRVTGGSVKFAGEELVGLS
+DAKMRRIRGRRIGLVPQDPMSNLNPVTRVGQQIGETLLTHGLATKKDVGAKVVEVMERAG
+IPEPARRAKQYPHELSGGLRQRVLIAIGLACRPQLLIADEPTSALDVTVQQVILDQIDEM
+TRELGSSVLLITHDLGLAADRAQQLVVMHRGRVVESGDARAILEDPQHAYTRSLVAAAPS
+VAAARLLPEAFDPAPSALKEDDTAALSTVALAKKDLTPLVEIRDLTKVYPVRGHDDFTAA
+KDVSLKIPRGKTVSIVGESGSGKTTTARMLLKLIEPTSGEITFEGKDVLGMKGEDLKDFR
+QRVQAVFQDPFSSLNPSFTVGRIIEEPLQTYKRGNAKERRARVLELMEQVALPSHFHRRY
+PAELSGGQRQRVAIARALALNPELIVCDEPVSALDVLVQDQILTLLRRLQDELGLSYLFI
+SHDLAVVRLISDYVCVMKDGEVVEAASSEEVFTNPRHPYTRRLLASIPGNELGIAVEADG
+EHV
+>MOLHKGIG_00119
+MLLKLIEPTSGEISFEGRDVLALKGEGLKDFRQRVQAVFQDPFSSLNPSFTVGRIIEEPL
+QTYRRGNATQRRARVLELMDQVALPSHFHRRYPAELSGGQRQRVAIARALALNPELIVCD
+EPVSALDVLVQDQILTLLRRLQDELGLRSYLFISHDLAVVRLISDYVCVMKDGRVVEAAS
+SEEVFTNPRHPYTRRLLASIPGNELGIAVEADGTHV
+>NAFOICDF_00137
+MSIPKSPTSTLPSAVAPAPALSVHGLDVDYAGRHGQAPALRDVRLEVPAGGTLAVVGESG
+SGKSTLARVLLGLSAANARIRSGRIHVAGQTVDAADTDALARLRGRCIGFVPQDPVTGLN
+PVRTIGEQVVAAVRTHTRLRVDDAYGRAEALLAEAGVDRPGHRLGQFPHELSGGLRQRVL
+IALALAGDPEVIVADEPTSALDATVQQQVLDRLGLLQERTGAALVLITHDLAVAAGRAER
+IVVMRQGRIVEAGPAEQIAQSPQDSFTRRLVAASPGRRPTARVLAAPDVEAGPGADPAPV
+VRVRGLRHEYPGVHGSAPHVAVDGVDLDIRAGETLALIGESGSGKTTTGRLVLGLETVRE
+GSVQIRGVETAGVGGRAWRRARRHLQTVHQNPFASLDPRQTVERIVAEPLRAFSVGSRTE
+RRDRVTELLERVSLPAATASRRPGELSGGQRQRVAIARALALDPDVLVCDEPTSALDVSV
+QAQVLELLARLQDEQGLACLFITHDLRVVWDIAHRVAVMRDGRILETAATERLFRAPEHP
+YTAELLAAAGVTAPLTGTQTSAGTMTPAGARALVGRP
+>MHAAABBN_02135
+MDPKHDDGAPGPGAAPAVPAAGAPLLEIRDLDVEFTTQQGTVQAVEGASLTLPAGGTLAI
+VGESGSGKSTTAMAAIGLLPGNGRVTAGSVRFAGEELVGLPESRMRRIRGRRIGLVPQDP
+MSNLNPVTRVGQQIGETLLTHGMATKKDVGAAVVEVMERAGIPEPARRAKQYPHELSGGL
+RQRVLIAIGLACRPQLLIADEPTSALDVTVQQVILDQIGEMTRELGSSVLLITHDLGLAA
+ERAQQLVVMHRGRVVESGDARAILEDPQHAYTRSLVAAAPSVAAARLLPEAFDPAPVALA
+EDDTAALTTVALAKQDLTPLVEIRDLTKVYPVRGHEDFIAVKDVSLKIPRGKTVSIVGES
+GSGKTTTARMLLKLIEPTSGEITFEGRDVLALKGEGLKDFRQRVQAVFQDPFSSLNPSFT
+VGRIIEEPLQTYRRGNATQRRARVLELMDQVALPSHFHRRYPAELSGGQRQRVAIARALA
+LNPELIVCDEPVSALDVLVQDQILTLLRRLQDELGLSYLFISHDLAVVRLISDYVCVMKD
+GEVVEAASSEEVFTNPRHPYTRRLLASIPGNELGIAVEADGTHV
+>LFPAFLNI_00127
+MDPKHDDGAPGPGAAPAVPAAGAPLLEIRDLDVEFTTQQGTVQAVEGASLTLPAGGTLAI
+VGESGSGKSTTAMAAIGLLPGNGRVTAGSVRFAGEELVGLPESRMRRIRGRRIGLVPQDP
+MSNLNPVTRVGQQIGETLLTHGMATKKDVGAAVVEVMERAGIPEPARRAKQYPHELSGGL
+RQRVLIAIGLACRPQLLIADEPTSALDVTVQQVILDQIGEMTRELGSSVLLITHDLGLAA
+ERAQQLVVMHRGRVVESGDARAILEDPQHAYTRSLVAAAPSVAAARLLPEAFDPAPVALA
+EDDTAALTTVALAKQDLTPLVEIRDLTKVYPVRGHEDFIAVKDVSLKIPRGKTVSIVGES
+GSGKTTTARMLLKLIEPTSGEITFEGRDVLALKGEGLKDFRQRVQAVFQDPFSSLNPSFT
+VGRIIEEPLQTYRRGNATQRRARVLELMDQVALPSHFHRRYPAELSGGQRQRVAIARALA
+LNPELIVCDEPVSALDVLVQDQILTLLRRLQDELGLSYLFISHDLAVVRLISDYVCVMKD
+GEVVEAASSEEVFTNPRHPYTRRLLASIPGNELGIAVEADGTHV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000065.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000065.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c3b2c9e270cf33dc61b5b4fb5fd00c4fca58375b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000065.fa
@@ -0,0 +1,47 @@
+>ACLBLIBL_00092
+MDLTYKLWEGSWDEGAVLQDKGGSRHADPEKVHKIHHVSERYRVEGPHLPAPSPQRTPVL
+FQAGSSGPGRAFAARNAEAVFLIAPSVEAARQQIEDPRRQAVEFGRRPEDIKFFQGLSFV
+IGDTEEEAQAKLEEYERYVSVDGYLAHAALVDPDGRVYPPDTPLRELETNTQKGFAESLQ
+KAITDREPVVADVAWRSHRDSRVVGTPEQIADELQRWQDAGVDGVNVINWVIPGSFEEFI
+EKVLPVLRERSLAQSDYGEGTLRHRLFGEGDRLPDRHPAAKYRGAFTGTPRSQRAPRTEP
+QGADPAPAA
+>ACLBLIBL_00093
+MTKTARRRPLHLNAFAMNTTSHIHHGQWRRPDARQHEFADLRTWTELARTLEDAAFDAMF
+FADVVGHYGDADADYAVYVEEGLQIPSNDPTVLLGALAAVTERIGLATTSNVFQAHPFQF
+ARQLSTLDHLSRGRIAWNIVTGT
+>ACLBLIBL_00195
+MMTPVHQSPGLWRHPESRIAEFDRLAYWTGLARTVEDGGFSALFLADVLGLYDVYGGGIE
+ATVRGGVQWPVLDPAVAVPAMAAATERIGFGVTASVTYERPYLLARTLATLDHFTGGRVA
+WNIVTSYQDSAARNLGLDRQIPHDARYDLADEALDALYRLWEGSVEPGAVAFDRAAGVVA
+DPDRVHPAAVAGAHVRVPDAALTHPGPQGTPYLFQAGASARGRRFALDHAEAVFAIGPTP
+AHVRRFVDQTRAGLTEAGRSADAIRVLAMVTVVVAETDEAAAQRLAGYAEHVDVAGALAL
+WGGWTGVDVAGLDPDAPLEHVVTDANRSALAAFTEDPSGRTWTLRDVAEFVAIGGRGPVI
+VGSPETVADELQRWQAETGVDGFNVSAAVRPADLERFAALVSPELRRRGVLREPEPGRTL
+RENLSGAGPALPADHRGHAFRTAG
+>NAFOICDF_00133
+MTGTHPSTPRPRTADRQLILGAHFPGVNNTTVWSDPESGSQIAPESFIRFAEIAERGRLD
+FIFLAEGLRLREQRGLLHDLDVVGRPATLPILAALAAATEHIGLIGTLSTTYNEPYELAR
+QLAGLDALSGGRAGWNVVTSPDAFTGENFRRGGYLPRERRYQHAGEFLATAQQIWDAASG
+RPPHVDVDVEDFSVHGTVDAPAPVHGRPVILQAGDSDEGRDLAAREADAVFTRHGDWEAG
+QEFTADMRRRAAAAGRPDGAVRVLPGVTVVVGDTDEEAAAEAEQIRRAQVSGATAVLTLE
+RIWNRDLSGWDPDGPLPDVEPVLEDTGLSQGRVRHVADPHAEVARLREISQRQGLTLRET
+VIATGQRQDFVGSPETVAQELIRHVEHDVCDGFILIPHLTPGGLEPFVDRVVPLLQERGA
+LRTDYPEDGGGLRGLLGAAVHPTAGRAS
+>NAFOICDF_00146
+MTATPAPAPFILSAFDMVTPVHQSPGLWRHPESRAHEFDRLSFWTDLARTVEEGGFTAVF
+LADILGLYDVHGGGVDATVRGGVQWPLLDPFTVVSAMAAVTERVGFGVTASVTYEQPYLL
+ARTLTSLDHFTGGRIAWNVVTGYQDSAARNLGLDRQPGHDERYDRADAYLDAMYRQFEGS
+VERDAVVADRESGVFADPAKVHPIDVEGPHVRLPGVALAHPGPQGTPFLFQAGASSRGRR
+FALEHAEAVFYIGPTTAHVRRFVEQTREGLREAGRPEDAIRVLAMVTVVVADTDEEAQAR
+LASYHEHVDVESALALFGGWTGVDLSGLDPDAELEHVESEASRTALAAFTTQSPDRRWTV
+REVAEFVSVGGRGPVIVGSPATVADELERWHRETGVDGFNISAAVRPTDLERFARLVSPE
+LRRRGVLREPEAGRTLRENVAGAGPLLPEDHRGAGFRR
+>LFPAFLNI_00201
+MTATPAPFILSAFDMVTPVHQSPGLWRHPESRAHEFDRLSFWTDLARTVEEGGFTAVFLA
+DILGLYDVHGSGVDATVRGGVQWPLLDPFTVVSAMAAVTERVGFGVTASVTYEQPYLLAR
+TLTSLDHFTEGRIAWNVVTGYQDSAARNLGLDRQPGHDERYDRADAYLDAMYRQFEGSVE
+RDAVVADRESGVFADPAKVHPIGVEGPHVRLPGVALAHPGPQGTPFLFQAGASSRGRRFA
+LEHAEAVFYIGPTTAHVRRFVEQTREGLREAGRPEDAIRVLAMVTVVVADTDEEAQARLA
+EYHEHVDVESALALFGGWTGVDLSGLDPDAELEHVESEASRTALAAFTTQSPDRRWTVRE
+VAEFVSVGGRGPVIVGSPATVADELERWHRETGVDGFNISAAVRPTDLERFARLVSPELR
+RRGLLREPEAGRTLRENVAGGGPLLPEDHRGARFR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000069.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000069.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf135b6065f78e1b30026aa84a3eb97c68796970
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000069.fa
@@ -0,0 +1,54 @@
+>ACLBLIBL_00135
+MALSVLDLFSIGIGPSSSHTVGPMRAARRFTQSMDQHGVLERTARVEAELFGSLAATGIG
+HGSDTAVLLGLAGQDPETIDPDACVGLVDEILQGGRMPLDGRHEIAFDRQKDMTLHMRRT
+LPGHPNGMRLTAFDADGEQLHTRDYYSVGGGFVVTSDELEAELDESRDVSRHDDGEGGEP
+YPFATGAELAGRCRTNGLSIAELMLANEATRHDLGELRTQLLAIWDVMQECVHNGVTRTE
+PILPGGLKVRRRAPALRAHLLETTDRTDPMWAMEWVNLFALAVNEENASGGRIVTAPTNG
+AAGIIPAVLHYYMRFVLPQDATQQERDDKVVEFLLTAAAIGILYKRNASISGAEVGCQGE
+VGSACSMAAGALCAVLGGTVDQVENAAEIGIEHNLGLTCDPVGGLVQVPCIERNAIASVK
+AINAARLALLGDGSHRVTLDQAIKTMRDTGADMKSKYKETSRGGLAVNVIEC
+>MOLHKGIG_00236
+MALSVLDLFSIGIGPSSSHTVGPMRAARRFTDSMGQHGVLERTARVHAELFGSLAATGVG
+HGSDTAVLLGLAGQDPETIDPDACTGLVAEIVTGGRLPLDGRHEIAFDRQADLTLHMRES
+LPGHPNGMRLTAYDDAGEQLHTRDYYSVGGGFVVTSDELEAELDATKDVNRTDDGDTGEP
+YPFSTGAELAARCREAGLSIAELMLANEATRHDLDELRTQLLAIWAVMEECVHNGVTRTE
+PILPGGLQVRRRAPALREHLLQTTDRTDPMWAMEWVNLFALAVNEENASGGRIVTAPTNG
+AAGIIPAVMLYYMRFVLPEGATQQERDDKVVEFLLTAAAIGILYKRNASISGAEVGCQGE
+VGSACSMAAGALCAVLGGTVDQVENAAEIGIEHNLGLTCDPVGGLVQVPCIERNAIASVK
+AINAARLALLGDGSHRVTLDQAITTMRDTGADMKSKYKETSRGGLAVNVIEC
+>NAFOICDF_00100
+MALSILDLFSIGIGPSSSHTVGPMRAARRFTYALERDGLVERTARVKGELFGSLSATGVG
+HGSDMAVILGLCGNDPETIDPEAAAPQVQACVEGGTLPLDGTHEIPFDRPKDLVLHMRRS
+LPGHPNGMRLTAFDADGAELLTRDYYSVGGGFVVTGEELEAELDETRDVSRHGEEPEPHP
+FSTGADLIAQCEIHGLSIADVVRANEAARGDLADVEAKVLEIWDVMQECVAHGIHRTEPI
+LPGGLKVKRRAPGLHAQLLEKGTDGAEKDPMWAMEWVNLFALAVNEENASFGRIVTAPTN
+GAAGIIPAVLHYYDRFVLPPGTPAEERRAKILDFLFTAAAIGILFKRNASISGAEVGCQG
+EVGSACSMAAGALCAVLGGTPLQVENAAEIGIEHNLGLTCDPVGGLVQVPCIERNAIASV
+KAINAARLALVGDGDHRVTLDQAIQTMRETGADMKSKYKETSRGGLAVNVIEC
+>MHAAABBN_00102
+MALSVVDLFSVGIGPSSSHTVGPMRAGRRFALGLVERGLVDATERIHVQLFGSLSATGHG
+HGSDRAVLLGLEGEDPETVDTDRANARVESMKAERRLALAAGAEQGGKDLDFDPDADLVM
+HRRRSLPYHPNGMSFTAYDGSGEVVVERVYYSVGGGFVVDDEAAGADRVVEDATEPPLPF
+SSGRELLNHCDREGISIPELMRRNEEAFRPWEAARAALLNTWRVMQECVEAGCEATGTLP
+GGLKVPRRAALLKEQLEVSAPRDGSAPPRDGGAPDALGAMEWVNLYALAVNEQNASGGRI
+VTAPTNGAAGIIPAVLHYWRDFLAREMTAEHIEDGVVDFLLTAAAIGILIKENASISGAE
+MGCQGEVGSACSMAAAGLCQLLGGTPQQVENAAEVGIEHNLGLTCDPVGGLVQIPCIERN
+AIASVKAINAARLCRRGDGRHTVSLDQAIKTMRETGQDMKVKYKETSRGGLAVNVIEC
+>MHAAABBN_02249
+MALSVLDLFSIGIGPSSSHTVGPMRAARRFTDSMGQHGVLERTARVHAELFGSLAATGVG
+HGSDTAVLLGLAGQDPETIDPDACTGLVEEIVTGGRLPLDGRHEIAFDRQGDLTLHMRES
+LPGHPNGMRLTAYDDAGEQLHTRDYYSVGGGFVVTSDELEAELDATKDVNRTDDGDTGEP
+YPFSTGAELAARCHEAGLSIAELMLANEATRHDLDELRTRLLAIWAVMEECVHNGVSRTE
+PILPGGLQVRRRAPALREHLLQTTDRTDPMWAMEWVNLFALAVNEENASGGRIVTAPTNG
+AAGIIPAVMLYYMRFVLPEGATQQERDDKVVEFLLTAAAIGILYKRNASISGAEVGCQGE
+VGSACSMAAGALCAVLGGTVDQVENAAEIGIEHNLGLTCDPVGGLVQVPCIERNAIASVK
+AINAARLALLGDGSHRVTLDQAIKTMRDTGADMKSKYKETSRGGLAVNVIEC
+>LFPAFLNI_00237
+MALSVLDLFSIGIGPSSSHTVGPMRAARRFTDSMGQHGVLERTARVHAELFGSLAATGVG
+HGSDTAVLLGLAGQDPETIDPDACTGLVEEIVTGGRLPLDGRHEIAFDRQGDLTLHMRES
+LPGHPNGMRLTAYDDAGEQLHTRDYYSVGGGFVVTSDELEAELDATKDVNRTDDGDTGEP
+YPFSTGAELAARCHEAGLSIAELMLANEATRHDLDELRTRLLAIWAVMEECVHNGVTRTE
+PILPGGLQVRRRAPALREHLLQTTDRTDPMWAMEWVNLFALAVNEENASGGRIVTAPTNG
+AAGIIPAVMLYYMRFVLPKGATQQERDDKVVEFLLTAAAIGILYKRNASISGAEVGCQGE
+VGSACSMAAGALCAVLGGTVDQVENAAEIGIEHNLGLTCDPVGGLVQVPCIERNAIASVK
+AINAARLALLGDGSHRVTLDQAIKTMRDTGADMKSKYKETSRGGLAVNVIEC
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000070.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000070.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1765ecc643207fe3c8df2a651d6ba184d955f65
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000070.fa
@@ -0,0 +1,41 @@
+>ACLBLIBL_00157
+MAHGLARSFGDVHAVRDVSLTVPSGSVTALVGPNGSGKTTLMLLLATLLRPDAGAVTIGG
+VDAVREPQEARRRLGWMPDTLGVWESLTCRDILTSLGRLYGMGAAEAAARAGEQLERVAL
+TEFADRPARVLSRGQQQRLSLARATVHRPGVLLLDEPANGLDPAARIRLRDDVRAMAAEG
+TAILVSSHVLAELEEMSDRAVFVREGATLSTQEFREDAAQTRPYRIAGPASARPDVLVRA
+LEARGLAVEPAAAHGQPRAGVVVGLRGETAAAELLADLVREGVPVSHFAPEGSRLENAYL
+GLHLDRDTAEGDRP
+>ACLBLIBL_00588
+MITVNEVSKSFGSTPVLQDLTFSIRPGLMTGFVGGNGAGKTTTMRILLGVLDADSGRIEV
+DGAPITRDYRAGIGYMPEERGLYPKMSVLDQLVYLGRLHHMRGADAKARALELLERLNLG
+DRAGSRLEELSLGNQQRAQIAAALVHDPVALVLDEPFSGLDPNAVETTLQVLRETADTGV
+PVLFSSHQLDLVERLCDELVILAGGRVRASGTRDELLAAHADPEWELHADADTGWVRGLP
+GIEVLHFDGGRARFRADTPQAAQRVLADAAARGPVHRFGPVTRSLHEIFTEVTR
+>MOLHKGIG_00223
+MTAPAPPPASPVLGVAAHDGIVAHGLARSFGAVHAVRDVSLTVPAGSVTALVGPNGSGKT
+TLLLILATLLRPDAGAVSVAGVDAVREPVEARRRLGWMPDTLGVWEELTCHDILASLGRL
+YGMGKAEASARADEQLAWVELTEFAHRPARVLSRGQQQRLSLARATVHRPSVLLLDEPAN
+GLDPAARIRLRDDLRAMAAAGTAVLVSSHVLAELEEMSDRAVFLREGATVATQEFRAADD
+LARPYRIAGPDPTARDTLIRALETRGLTVTAATGAGAGQRRDGVVVQLRGEAAAAALLAD
+LVREGVLVSHFAPEGSRLENAYLGLHLEGPRTEGDRP
+>NAFOICDF_00115
+MTSSVLPQPPSGIVAHGLARSFGSVHAVRDVSLTAPAGSVTALVGPNGSGKTTLMLLLAT
+LLRPDRGSVSVAGVDAMADPGQARRLLGWMPDTLGVWDSLTCADILTSLGRLYGMGQAEA
+ATRAREQLAWVQLEPFADRPARVLSRGQQQRLSLARATVHRPAVLMLDEPANGLDPTSRI
+RLRDDVRAMAAAGVAVLVSSHVLAELEEMADRAVFVSEGATVAVRDLSGADDAGRERPYR
+IAGPDPSRRDELVRALQARGVPLAAPLEGHRPGVVVRLRGEDAAAALLADLVAAGVPVSR
+LAPEGSRLENAYLDLALGGPAPHAAGPVTAAGPAPTVEGGRA
+>MHAAABBN_02236
+MTAPAPPPASPVLGVAAHDGIVAHGLARSFGAVHAVRDVSLTVPAGSVTALVGPNGSGKT
+TLLLILATLLRPDAGAVSVAGVDAVREPVEARRRLGWMPDTLGVWEELTCHDILASLGRL
+YGMGKAEASARADEQLAWVELTEFAHRPARVLSRGQQQRLSLARATVHRPSVLLLDEPAN
+GLDPAARIRLRDDLRAMAAAGTAVLVSSHVLAELEEMSDRAVFLREGATVATQEFRAADD
+LARPYRIAGPDPTARDTLIRALETRGLTVTAATGAGAGQRRDGVVVQLRGEAAAAALLAD
+LVREGVLVSHFAPEGSRLENAYLGLHLEGPRTEGDRP
+>LFPAFLNI_00224
+MTAPAPPPASPVLGAAAHDGIVAHGLARSFGAVHAVRDVSLTVPAGSVTALVGPNGSGKT
+TLLLILATLLRPDAGAVSVAGVDAVREPVEARRRLGWMPDTLGVWEELTCHDILASLGRL
+YGMGKAEASARADEQLAWVELTEFAHRPARVLSRGQQQRLSLARATVHRPSVLLLDEPAN
+GLDPAARIRLRDDLRAMAAAGTAVLVSSHVLAELEEMSDRAVFLREGATVATQEFRAADG
+LARPYRIAGPDPTARDTLVRALETRGLTVTAATGAGAGQRRDGVVVQLRGEAAAAALLAD
+LVREGVLVSHFAPEGSRLENAYLGLHLEGPRTEGDRP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000071.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000071.fa
new file mode 100644
index 0000000000000000000000000000000000000000..088f238f946b2088208a77dd0f5b89e1052bc455
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000071.fa
@@ -0,0 +1,37 @@
+>ACLBLIBL_00162
+MVGLLGPTAGGLLLGVVGVLAAASVIAAVLRARMGARNPELIGNLVQRIGAWWAMVAVLA
+AVLALGETATLLLFLVLTWLSLREFLTISPTGRADHRTLVWLFFVVTPLHYWFVWEHWYG
+MFSVFIPVYAFLFLPVRAALAGRTEGFLRRAAAVQWAAMVCVYAVSHIPAVLQLPVAMEH
+GRHMAEGSAPGSGDEAGALLLLFLLLVVQGSDVFQYVWGKTLGRRPIAPSVSPNKTWEGF
+VGGVLTATALGAALSFLTPFPWWVAALFAFVSCLLGFGGGLVMSAIKRDRGIKDFGSLIP
+GHGGIMDRIDSLVFAAPVFFHLVRFFYA
+>ACLBLIBL_02307
+MTTAVSTPAPPRGGRDLKSAVLVGVGLLVLALVGLVWLDWLLVLLVVALLVGAVTEVATA
+VRGIGLQVPRPPLWAAAVALPVSAWLWGVPALFVALAACLALLAVWTALTRHRPTGQFML
+AGVFIVLWAPFLLSFAVAMLDQPRGNLLVAITLLMVVSNDTFGYIVGYRFGRTPIAPRIS
+PKKSWEGLAGSLAGSALVGVVTVPLFVGQPWWVGAILAVTTVAAATSGDFSESMVKRELG
+IKDMSSALPGHGGVMDRLDSLVFAAPVAYTVLALPLT
+>MOLHKGIG_00656
+MTSAVSTSPAPPRGGRDLKSAVLVGVGLLATALVGLFWLDWLLVLLVVALLVGAVSEIAT
+AVRGIGLDVPRPPLWVAAAVLPLTAWRWGVPALFIALVACLALVAVWTALTRRRPAGQFM
+LAGVFIVLWAPFLLSFAAALLDEPLGHRMVAVLLLMVVSNDTFGYIVGYRFGRTPIAPRI
+SPKKSWEGLAGSLAGSVLVGVVAVPLLVGQPWWVGAVLGVTTVAAATSGDFSESMVKREL
+GIKDMSSALPGHGGVMDRLDSLVFAAPVAYTVLALPLT
+>NAFOICDF_02164
+MTPDATAPSPPRGGRDLRSAVLVGVGLLGTALVGLVWLPWLLVLLVVSLLVGAVNEVAVA
+IRQIGLDVPRPPLWVGATVMPLAAWTGGIPALFLALMASLVLMFAWTAVTRRRPTGQFML
+AGTFVLLWAPFLLSFAAALLDQPAGHMMVVCLVLMVVSNDTFGYMVGYRWGRTPIAPRIS
+PKKSWEGALGSLAGSVAVGSVLVPVLVGHPWWAGALLGALTVGAATAGDFSESMVKRELG
+IKDMSSALPGHGGIMDRLDSLVFAAPVAYAVLALPLS
+>MHAAABBN_00393
+MTSAVSTSPAPPRGGRDLKSAVLVGVGLLATALVGLFWLDWLLVLLVVALLVGAVSEIAT
+AVRGIGLDVPRPPLWVAAAVLPLTAWRWGVPALFIALVACLALVAVWTALTRRRPAGQFM
+LAGVFIVLWAPFLLSFAAALLDEPLGHRMVAILLLMVVSNDTFGYIVGYRFGRTPIAPRI
+SPKKSWEGLAGSLAGSVLVGVVAVPLLVGQPWWVGAVLGVTTVAAATSGDFSESMVKREL
+GIKDMSSALPGHGGVMDRLDSLVFAAPVAYTVLALPLT
+>LFPAFLNI_00626
+MTSAVSTSPAPPRGGRDLKSAVLVGVGLLATALVGLFWLDWLLVLLVVALLVGAVSEIAT
+VVRGIGLDVPRPPLWVAAAVLPLTAWRWGVPALFIALVACLALVAVWTALTRRRPAGQFM
+LAGVFIVLWAPFLLSFAAALLDEPLGHRMVAVLLLMVVSNDTFGYIVGYRFGRTPIAPRI
+SPKKSWEGLAGSLAGSVLVGVVAVPLLVGQPWWVGAVLGVTTVAAATSGDFSESMVKREL
+GIKDMSSALPGHGGVMDRLDSLVFAAPVAYTVLALPLT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000074.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000074.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b8c88a84382020ea166ea961b411b0d07bf7d1d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000074.fa
@@ -0,0 +1,53 @@
+>ACLBLIBL_00184
+MAEHPAARPEQDATTSTSAATSTSPASRAGRELLFNAFDMNCVAHQSPGLWRHPEDRARD
+YNTLGYWTHLAQTLEKGLFDGLFIADVLGPYSVYGGTAEAAIRSGAQTPVNDPFLLVSAM
+AAVTGHLGFGVTAGTAYEHPYPFARRLATLDHLTGGRVGWNVVTGYLPSAAQNMGQDDQM
+EHDERYEHADEYLDVVYKLLEGSWEDDAVRYDKETGVFADPAKVHDIGHEGRYFKVPGAA
+VTEPSPQRTPVIYQAGASTRGRAFAGKHAEAVFINSPTKELTAATVKKIRQALVDAGRDP
+YDVKIFAMQTIVTGATDEDARAKYDDLAQYVDPLGGLVLMSGWMGIDLSQYDLDEPIGDV
+KSNAIQSAVEAFQKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDV
+DGYNLAYHITPGTFEDVVEFVVPELQKLGRYKTAYTDGTLRHKLFGRGDHLPEGHHGASF
+ALRRRG
+>MOLHKGIG_00207
+MSTAENAGAGAPTRPDEHRAILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTHLAQ
+TLEKGLFDGLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVT
+AGTAYEHPYPFARRLATLDHLTGGRVGWNVVTGYLPSAAQNMGQDDQMEHDERYEHADEY
+LDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAHEGRYFTVPGHAVTEPSVQRTPVI
+YQAGASTRGRAFAGKHAEAVFINSPTKELAAATVKKIRQALVDAGRDPYDVKIFAMQTIV
+TGATDEDARAKYDDLAQYVDPLGGLVLMSGWMGIDLSQYDLDEPIGDVKSNAIQSAVETF
+QKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPG
+AFEDVVEFVVPALQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFALRRR
+>NAFOICDF_00130
+MSTAENAGAGAPTRPDEHREILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTRLAQ
+TLEKGLFDGLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVT
+AGTAYEHPYPFARRLATLDHLTGGRVGWNVVTGYLPSAAQNMGQDDQMEHDERYEHADEY
+LDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAHEGTWFKVPGHAVTEPSVQRTPVI
+YQAGASTRGRAFAGKHAEAVFINSPTKELAAATVKKIRQALVDAGRDPYDVKIFAMQTIV
+TGATDEDARAKYDDLAQYVDPLGGLVLMSGWMGIDLSQYDLDEPIGDVKSNAIQSAVETF
+QKASGTDEGWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPG
+TFEDIVEFVVPELQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFAFRNRRG
+>NAFOICDF_00132
+MSTPTPTLGIALTTQTPADARGHWTRLSQALEETSLDWAVLTDPLGTAPQAGTHRIDAVL
+AACWTATRTHRIGLVPEVTTTHTEPFHVSIGLATLDHVSHGRAGWLATVSAAPEVSALFG
+RRRHPAERTPGLQASRVDLELWEELQDAVAAVRDLWESWEPDAEIRDIATGRFIDRERVH
+HVDVEAERFSVRGPSITPRPPQGRLPVLVEAAGPAGLEAARRTADVVLLPAAEVGRTDAA
+RLPDRRRRGATPAVPVEPTRIVADVTLEGDGARVADAVRHALQAGADGARLVPNPTADPF
+DALALAADVHDRLDDIRPPDTGTVPLRECLGLAPALSPWRHPEDPTARPTDEEATA
+>MHAAABBN_02200
+MSTAENAGAGAPTRPDEHRAILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTHLAQ
+TLEKGLFDGLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVT
+AGTAYEHPYPFARRLATLDHLTGGRVGWNVVTGYLPSAAQNMGQDDQMEHDERYEHADEY
+LDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAHEGRYFTVPGHAVTEPSVQRTPVI
+YQAGASTRGRAFAGKHAEAVFINSPTKELAAATVKKIRQALVDAGRDPYDVKIFAMQTIV
+TGATDEDARAKYDDLAQYVDPLGGLVLMSGWMGIDLSQYDLDEPIGDVKSNAIQSTVETF
+QKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPG
+TFEDIVEFVVPELQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFALRRR
+>LFPAFLNI_00207
+MSTAENAGAGAPTRPDEHRAILFNAFDMNCVAHQSPGLWRHPDDHARDYNTLGYWTHLAQ
+TLEKGLFDGLFIADVLGPYSVYGGTSEAAIRTGAQTPVNDPFLLVSAMAAVTEHLGFGVT
+AGTAYEHPYPFARRLATLDHLTGGRVGWNVVTGYLPSAAQNMGQDDQMEHDERYEHADEY
+LDVVYKLLEGSWEDDAVVYDKESGVFADPAKVHDIAHEGRYFTVPGHAVTEPSVQRTPVI
+YQAGASTRGRAFAGKHAEAVFINSPTKELAAATVKKIRQALVDAGRDPYDVKIFAMQTIV
+TGATDEDARAKYDDLAQYVDPLGGLVLMSGWMGIDLSQYDLDEPIGDVKSNAIQSAVETF
+QKASGTDEEWTVRKLAEWVGIGGFGPVIVGGGESAARQLVEWADETDVDGFNLAYHITPG
+AFEDVVEFVVPALQKLGRYKTAYTDGTLRHKLFGRGDHLPQNHHGASFALRRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000080.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000080.fa
new file mode 100644
index 0000000000000000000000000000000000000000..31015c2b036e19aea63940e18052f802776933da
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000080.fa
@@ -0,0 +1,47 @@
+>ACLBLIBL_00201
+MTPGSPDDDGAPAVRRRVLVLLNPHAGRRRSLARAQARLRTHPGLALDLVVPDPADHAAQ
+LAAGRTALADGVDAVVVRGGDGMVAAGVGLVGDHAEATGRRVPLGIVPAGTGNDLARAAG
+LHRRDPGAALEAVLRALEDPAAPVRRIDALRLTVTRAGAVVERRWAANSVNIGFDARVNA
+RANALGAVPGPLRYLAALGLEARAFAAVEMGLGLDDGPVRRERVALVSVQNGPTIGGGIP
+LAPGARLDDGRAEATVVGPLPTAGLALLFPLVYVRAHRLLRPLCTERARRVRVAVPDGVP
+VYADGDEVLPASHGGAAVEVEAVPGAVALLG
+>ACLBLIBL_00332
+MALVALVLGAVLAVAVIVLAVRHRGLAERHERTRGQLDAVEHRLDAAQRRLGELPGVDRP
+RQEIALVLNPVKARADEVRRTLEAMADREGLGSVLVLETEEDDPGTQMAKDALEAGVRLV
+IAAGGDGTVRTVAEQLTGTDVALGVVPLGTGNLLARNLDLPINDIEECLRIALTGRQRRI
+DTVDVRFTHEEGEVTRQTFTVIGGAGYDADIMADTKDELKDVAGWLAYSEAGMRHLRGKR
+HDVSISLDGGASRRFKVRTVMVANCGMLTGGVELLPEAKLDDGLLDVLVLSPRHALDWAR
+IAAKTVTRHGANIPVMHTEQAQRVKVEFADPMPSQLDGDATGHIVALDARVQPDSLVVML
+LDEKEASVHDDGRSEAAPVPEPAPHI
+>MOLHKGIG_00063
+MTPEWWMALAALVLLALLVVVVVVLAVRQVRLGVQHERTRLLVDALDARVGGVQRRLEEV
+PGIGTGRHEVALVLNPIKTHADRVRRELERLAEAEGLGEVLVLETQEDDPGTAMARQALD
+AGARLVIAAGGDGTVRTVAEQLAGTDVALGVVPLGTGNLLARNLDLPINDVEQCLRIAVG
+GRQRRIDTVDVRFTHEDGRVTRQTFTVIGGAGYDADIMGDTKDELKSLAGWLAYSEAGMR
+HLRGKRHEVTVALDGGQPRRFKVRTVMVANCGMLTGGVELLPQAKLDDGLLDVMVLSPRH
+ALDWARIAVKTVTRHRSSVPAMHTEQAQRVKVEFAEPMPSQLDGDATGVITALDARVQPD
+SLVVMLVAEDDASVRDDGVSAAAPVPEPAPHI
+>NAFOICDF_00273
+MALAALVLAALFAVAVVVLGLRLRRLDGAHERTRGQLDAVEARLGDLRRRAGRAPGVDLP
+GPQVALVLNPVKARADEVRRAMEALAEKEGLGEVLVLETTEEDPGTAMTREALTAGVRLV
+VAAGGDGTVRTVAEQLAGTDVALGVMPLGTGNLLARNLDLPINDIEECLRIALTGRQRRI
+DTVDVRLTHEDGARTRQTFTVIGGAGYDADIMGDTKDELKDMAGWLAYSEAGMRHLRGRR
+HEVSITLDGGAVQRFKVRSVMVANCGMLTGGMELLPEAKLDDGLLDVLVLSPRHALDWVR
+IAAKTLTRHRASIPVMHTEQAQRVQVRFAEPMSSQLDGDATGDITALDARIQPDSLVVML
+GDEDDASVEDGGRSAEAPVPEPAPHI
+>MHAAABBN_02076
+MTPEWWMALAALVLLALLVVVVVVLAARQVRLGVQHKRMRLRVDALDARVGGVQRRLEKV
+PGIGTGRHEVALVLNPIKTNAGQVRRELERLAEAEGLGEVLVLETQEDDPGTAMARQALG
+AGARLVIAAGGDGTVRTVAEQLAGTDVALGVVPLGTGNLLARNLDLPINDVEQCLRIAVG
+GRQRRIDTVDVRFTHEDGRVTRQTFTVIGGAGYDADIMGDTKDELKDLAGWLAYSEAGIR
+HLRGKRHEVTVALDGGQPRRFKVRTVMVANCGMLTGGVELLPQAKLDDGLLDVMVLSPRH
+ALDWARIAVKTVTRHRSSVPAMHTEQAQRVKVEFAEPMPSQLDGDATGVITALDARVRPD
+SLVVMLVAEDDASVRDDGVSAAAPVPEPAPHI
+>LFPAFLNI_00058
+MALAALVLLAVLAVVVVVLAVRQVRLGVQHQRTRLLVDALDARVGGVQRRLEEVPGIGTG
+RHEVALVLNPIKTHADRVRRELERLAAAEGLGEVLVLETQEDDPGTAMARQALDAGARLV
+IAAGGDGTVRTVAEQLAGTDVALGVVPLGTGNLLARNLDLPINDVEQCLRIAVGGRQRRI
+DTVDVRFTHEDGRVTRQTFTVIGGAGYDADIMGDTKDELKDLAGWLAYSEAGIRHLRGKR
+HEVTVALDGGQPRRFKVRTVMVANCGMLTGGVELLPQAKLDDGLLDVMVLSPRHALDWAR
+IAVKTVTRSRSSIPVMHTEQAQRVKVEFAEPMPSQLDGDATGVITALDARVQPDSLVVML
+VAEDDASVRDDGVSAAAPVPQPAPRI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000082.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000082.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b3c9ab939262edb440b1d71d07129093039c2d5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000082.fa
@@ -0,0 +1,29 @@
+>ACLBLIBL_00326
+MPHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDAMV
+LLPGFDLVPGCVVEARPVGVFNMTDDGGGDAKLLCVPADKRFDHITELEHIEESLKQEIE
+HFFTRYKDLEPGKWVKAEGWQGRADAEAELEASIARFDAAGEHSPTDEPQGRDVETEDPS
+PATEEGEEKDVPQGR
+>MOLHKGIG_00068
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+YLPGFDLVPGCVVEARPIGVFNMTDDGGGDAKLLCVPADKRYDHITELEHVEESLKQEIE
+HFFTRYKDLEPGKWVKAEGWEGRAAAEAELEASIQRFDAEGEESPTDEPQGRAVDTEEAQ
+PATEEGEATDEPQGR
+>NAFOICDF_00266
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+FLPGFDLVPGCIVEARPVGVFNMTDDGGGDAKLLCVPADKRFDHIQELEDVEESLKQEIE
+HFFTRYKDLEPGKWVKADGWEGREAAEKELEASIERFAAEGEHSPSDEPQGRDVDTEEAA
+PAAEQEA
+>NAFOICDF_00684
+MLFDVTIEIPRGSGNKYEVDHTTGRIRLDRAVFTSMVFPQDYGSIDNTLGDDGDPLDALV
+LLPRPTFPGVVITVRPVGMLRMVDENGGDDKILTVPAGDDRFAQLRDITDVPEHTLAEIE
+HFFAHYKEIEHGKHVTTNGWADRAAAEAVIRTAQNAHTRHP
+>MHAAABBN_02081
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+YLPGFDLVPGCVVEARPVGVFNMTDDGGGDAKLLCVPADKRYDHITELEHVEESLKQEIE
+HFFTRYKDLEPGKWVKAEGWEGRAAAEAELEASIQRFNAEGEESPTDEPQGRAVDTEEAQ
+PATEEGEATDEPQGR
+>LFPAFLNI_00062
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+YLPGFDLVPGCVVEARPIGVFNMTDDGGGDAKLLCVPADKRYDHITELEHVEESLKQEIE
+HFFTRYKDLEPGKWVKAEGWEGRAAAEAELEASIQRFDAQGEESPTDEPQGRDVDTEEAQ
+PATEEGEPQGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000083.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000083.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d9f1a881e9baefd0283018334e4ef5db80b1ea6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000083.fa
@@ -0,0 +1,29 @@
+>ACLBLIBL_00331
+MPHQLDNADYGSCLNQDESFCPDGEWVQARTVDITRPDADPLYGRPTCTSDVAAGAGGAR
+SFTLEEVRTLLLLDPTIESDNAGRGVRNAETNFYTDAGVETLSTTINGVPVELRATPVSF
+HWNYGDGTAPRVTHVGGHAQAEFNTPTPTSHVYEETGEYTVTLTTVYIGEYREADGDWVL
+IPGTITLDAAPVTADIWRTVTRNVAEDCAADPSAWGCTGPIEAPDAP
+>ACLBLIBL_00544
+MPHQLDNADYGSCLNQDESFCPDGEWVQARTVDITRPDADPLYGRPTCTSDAAAGADGAR
+SFTLEEVRTLLLLDPTIESDNAGRGVRNAETNFYTDAGVETLSTTINGVPVELRATPVSF
+HWNYGDGTAPRVTHVGGHAQAEFNTPTPTSHVYKETGEYTVTLTTVYIGEYREADGDWVL
+IPGTITLDAAPVTADIWRTVTRNVAEDCAADPSAWGCTGPIEAPDAP
+>MOLHKGIG_01042
+MLEPEIRSDNGGRGIRNAETNFYADAETRTLVTTLNGVEVELRATPVSFHWDYGDGSPTK
+TTSVAGQSQPEFNVPTPTSHVYEDTGQYTVRLTTVYIGEYREAGGEWVLIPGTISLDSAP
+VTANIWRTITRNVADDCSVDSSAWGCTGPIESAPAG
+>NAFOICDF_01735
+MTSRRGDFPACMAVLFALIFLVSAVTLVTPSQAHASSCDTAGRKAQLTDDSLIVGQRCHK
+SSIAEIVGDGLADDQEKSAKATSPTTKVTTLQNACYENLPEPGFENCATQQELICGDQNV
+AWLQPSTKDTARPEDAPVKGDAFCADGSAAPSAPPQPSRPAVSIDDMGEVIAPEPRILAD
+TDGRGVRNAETNFYSPEAVRHETAVIDGVSVEMRLTPVSFIWDYGDGTAPVTTDVGGNPQ
+DGFDVRTPTSHVYDETGTYEVTLTTVYTGEIRYPGQGWEAVPGTIRRTATPVTADIWTTS
+TRNVADDCSADASAWGCAGPVEAPNGG
+>MHAAABBN_00755
+MLKPEIRSDNGGRGIRNAETNFYADAETRTLVTTLNGVEVELRATPVSFRWDYGDGSPTK
+TTSVAGQSQPEFNVPTPTSHVYEDTGQYTVRLTTVYIGEYREAGGEWVLIPGTISLDSAP
+VTADIWRTITRNVADDCSVDSSAWGCTGPIESTPAG
+>LFPAFLNI_00983
+MSIDEVRTLLVLEPEIRSDNGGRGIRNAETNFYADAETRTLVTTLNGVEVELRATPVSFH
+WDYGDGSPTKTTSVAGQSQPEFNVPTPTSHVYEDTGQYTVRLTTVYIGEYREAGGEWVLI
+PGTISLDSAPVTANIWRTITRNVADDCSVDSSAWGCTGPIESAPAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000087.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000087.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef4d41151db584fd7b6b7e094dd14a7bdf982a18
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000087.fa
@@ -0,0 +1,33 @@
+>ACLBLIBL_00392
+MTYPVVKDLARDGIPVRLCCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP
+EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFR
+AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLAVDALQMALARR
+GGKAEVQGCRVHSDRGSQFRARRFVETLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNV
+LNRRRWQSFDQLRLAIVSWIERTYHRRRRQAPLGRLTPVEFEMVQSVQAAAAA
+>ACLBLIBL_00411
+MTYPVVKDLARDGIPVRLCCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP
+EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFR
+AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFLKRPGSDEDS
+>MOLHKGIG_00626
+MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYQWLAEPVSAREWSDAHAANAVLDAHAGDP
+EFGYRFLADELRGRGLAVSDHQVLKACRLVRVRCCHWFRRGSGKRPGPAVHDDLVRREFR
+AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLALDALQMALARR
+GGKAEVQGCRVHSDRGSQGGFNRSSQHPLGITGGMGDGKQGLGEEDQ
+>NAFOICDF_02188
+MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYPWLAEPVSAREWSDAHAANAVFDAHADDP
+EFGYRFLADELRGRGLDVSDHQVLKACRLVRVRCCHSIRRGSGKRPGPAVHDDLVRRQFR
+ADKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSIDRRMSSQLAVDALQMALARR
+GGKAGVQGCRVHSDRGSQFRARRFVETLRVNSLIGSMGRVGAAGDNAAMESFFALLQKNV
+LNRRRWDSFAQLRLAIVSWIERTYHRRRRQARLGKLTPVEFEMVQSVQAAAAA
+>MHAAABBN_00371
+MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP
+EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFR
+AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLAVDALQMALARR
+GGKAEVQGCRVHSDRGSQFRARRFVETLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNV
+LNRRRWQSFDQLRLAIVSWIERTYHRRRRQARLRKLTPVEFEMVQSVQAAAAA
+>LFPAFLNI_00605
+MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP
+EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFA
+AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLAVDALQMALGRR
+GGKAEVQGCRVHSDRGSQFRARRFVETLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNV
+LNRRRWQSFDQLRLAIVSWIERTYHRRRRQARLGKLTPVEFEMVQSVQAAAAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000093.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000093.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dd6cf7038c4ee59459a71e09ec6d1cd1467016a1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000093.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_00469
+MDVTFTPLDPAGADRDALVALLTENAWPFHTRPLVTRPEAEEAVDGGAWEDEDHRTFWIE
+HPEHGRVGVVRLEDLTDPTPLFDLRVAERFRGRGLGAQILTALTRHVFETMPAVDRFEGQ
+TREDNVPMLRTFRRAGWVKEAHYRRGWPVDGGEPLASVAYAMLRQDWASGTTTPVPADVD
+APPPAGRKEGAAAGGRAPDWPLPTARLTLRPHREDDLGWLQEMYTQPEVVRHLLDEPWDE
+ATAREKLAKRITWDDLGGPSGAVSLVVEHAGVPVGDVILWLTDRERGVAEIGWALDPRHA
+GQGFAREAAAALLDLGFETSGLHRVVARMDARNTASARLAETLGMRREAHHRQDWWSKGE
+WTDTLVYAMLASDRG
+>ACLBLIBL_00641
+MAERFRGRGLGAQILAALTRHVFETMPAVDRFEGQTREDNIPMLRAFRRAGWVKEAHYRR
+GWPVEGGEPLASVAYAVLRQDWETGTTTPVPADVDVPSRRKRDVGAESNGHIPDWPMRTE
+RLTLRPHREDDLGWLQEMYAQPEVVRHLLDEPWDEPTARQKLVRRIEWNDLAGPSGVASL
+VIEHAGVPVGDVILWLTNRERGVAEIGWALDPRHAGQGFAREAAAAMLALGFEVHGLHRV
+VAQMDARNTASARLAEAIGLRREAHHRQDWWSKGKWTDTLVYATLSSDRD
+>MOLHKGIG_02265
+MDVTFTPLDPAGADRDALVALLTENAWPFHTRPRVTRPEAEKAVDGGAWEDEDHRTFWIE
+HPEHGRVGVVRLEDLTDPTPLFDLRVAERFRGRGLGAQILTALTRHVFETMPAVDRFEGQ
+TREDNVPMLRTFRRAGWVKEAHYRRGWPVDGGEPLASVAYAMLRQDWASGTTTPVPADVD
+APPPAGRKEGAAAGGRAPDWPLPTARLTLRPHREDDLGWLQEMYMQPVVVRHLLDEPWDE
+ATARAKLAKRITWDDLGGPSGAVSLVVEHAGVPVGDVILWLTDRERGVAEIGWALDPRHA
+GQGFAREAAAALLDLGFETSGLHRVVAQMDARNTASARLAETLGMRREAHHRQDLWSKGE
+WTDTLVYAMLASDRGVRGHL
+>NAFOICDF_00419
+MDVTFTPLDPAGADRDALVALLTENVWPFHMRPRITRSEAEEAVDGGAWEDEDHRTLWIE
+HPEHGRVGVVRLDELTDPTPLFDLRVTERFRGRGLGAPILTALTRLVFETMPAVDRFEGQ
+TREDNVPMLRTFRRAGWVKEAHYRRGWPVEGGEPLASVAYAVLRQDWETGTTTPVPAEVD
+VPPQVEHGEGAAAVGPAPDWPLRTERLTLRPHREDDLGWLRDMYARPEVVRHLLDEPWDE
+ATARQKLAKRIAWDGLAGPSGAVSLVVEHRGVPVGDVILWLTDRERGVAQIGWALHPEHA
+GQGFAREAAAALLTLAFETYDLHRVVAQMDARNTASAQLAEAVGLRREAHHRQDWWSKGE
+WTDTLVYATLASDRG
+>MHAAABBN_01960
+MDVTFTPLDPAGADRDALVALLTENAWPFHTRPRVTRPEAEKAVDGGAWEDEDHRTFWIE
+HPEHGRVGVVRLEDLTDPTPLFDLRVAERFRGRGLGAQILTALTRRVFETMPAVDRFEGQ
+TREDNVPMLRTFRRAGWVKEAHYRRGWPVDGGEPLASVAYAMLRQDWASGTTTPVPADVD
+APPPAGRKEGAAAGGRAPDWPLPTARLTLRPHREDDLGWLQEMYMQPEVVRHLLDEPWDE
+ATARAKLAKRITWDDLGGPSGAVSLVVEHAGVPVGDVILWLTDRERGVAEIGWALDPRHA
+GQGFAREAAAALLDLGFETSGLHRVVAQMDARNTASARLAETLGMRREAHHRQDLWSKGE
+WTDTLVYAMLASDRGGGGPSMTANGLLRSPHAARDREGVDSRGSPGVRTEVLEDLQVEKP
+LVRAGGLGEHRLVGADVDDLPHTEAGGLLRLKDRQVSVAGDAVDLGEPPRGPHLVCRPHH
+GPHTTQRDRPGGAAVVVMGDDPACRGQGPSLTHSPGGQQDQLVDFPHGDRVTAAFLLPVR
+ERGAADGADGDVHGRSVGAGPHPGARGASSPVMLGIGLEARRVKARTTHPHRVHRIDAMT
+RTGAFTIAGLAAFAISTGILVLLLITGSETPRETMAFFALIIGCYALSALCFAAAKRVLL
+ALLSGALAVVSFPLALFIGYVVEMLQSQQ
+>LFPAFLNI_02198
+MVRLEDLTDPTPLFDLRVAERFRGRGLGAQILTAITRHVFETMPAVDRFEGQTREDNVPM
+LRTFRRAGWVKEAHYRRGWPVDGGEPLASVAYAMLRQDWASGTTTPVPADVDAPPPAGRK
+EGAAEGGRAPDWPLPTARLTLRPHREDDLGWLQEMYTQPEVVRHLLDEPWDEATARAKLA
+KRITWDDLGGPSGAVSLVVEHAGVPVGDVILWLTDRERGVAEIGWALDPRHAGQGFAREA
+AAALLDLGFETSGLHRVVAQMDARNTASARLAETLGMRREAHHRQDLWSKGEWTDTLVYA
+MLASDRGVRGHL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000094.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000094.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de35c9badfe38c26e599626dc22155df831e2b2d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000094.fa
@@ -0,0 +1,42 @@
+>ACLBLIBL_00489
+MTAQTPATPAVPETMKAVIMRAPGDVVVEEVDTPRVAKPTDVVLKLAAACVCGSDLWPYR
+GHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVNAG
+EYTGSQAQYMRVELADGSLVKVPGGEPADPDRLADYLAASDVLGTGWYAAVAANAGPGKT
+IAVVGDGAVGLCAVLAAKTLGAEQVIAFSRHEDRAALAREFGADVIIAERGEEGAAKVKE
+LTNGYGAHGVCEAVGTQESMDQALASVRPGGHVGFVGVSHDQTIDGSRLFGLEIHLEGGP
+APVRRFLPELIERIQAGEIQPGRVFTARMPIDDAAEAYKAMDERREIKVLLEV
+>MOLHKGIG_02252
+MTAQTPATPAIPETMKAVVMRAPGDVVVEEVDTPRVAQPTDVVLKLAAACVCGSDLWPYR
+GHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVNAG
+EYTGSQAQYMRVELADGSLVKVPGGEPSDPDRLADYLAASDVLGTGWYAAVAAQAGPGKT
+IAVVGDGAVGLCAVLGAKTLGAEQVIVFSRHEDRAALAREFGADVVIAERGEEGAAQVRE
+LTGGYGAHGVCEAVGTQGSMDQALASVRPGGYVGFVGVSHDQTLDGSDLFGRQIHLEGGP
+APVRRFLPELIERIQSGEIQPGRVFTARRPIDDAAEAYQAMDERREIKVLLEV
+>MOLHKGIG_02276
+MTTETPTLAAPEIPATMKAVVMRAPGDVVVEEVDTPRVAQPTDVVLKLAAACVCGSDLWP
+YRGHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVN
+AGEYTGSQAQYMRVELADGSLVKVPGGEPSDPDRLTDYLAASDVLGTGWYAAVAAQAGPG
+KTIAVVGDGAVGLCAVLAAKTLGAEQVIVFSRHEDRAALAREFGADVVIAERGEEGAAQV
+RELTGGYGAHGVCEAVGTQGSMDQALASVRPGGYVGFVGVSHDQTLDGSDLFGREIHLEG
+GPAPVRRFLPELIERIQSGEIQPGRVFTARRPIDDAAEAYQAMDERREIKVLLEV
+>NAFOICDF_00435
+MTAQTPTTPAIPETMKAVVMRAPGDVVVEEVDTPRVVQPTDVVLKLAAACVCGSDLWPYR
+GHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVNAG
+EYTGSQAQYMRVELADGSLVKVPGGEPSDPDRLADYLAASDVLGTGWYAAVAAQAGPGKT
+IAVVGDGAVGLCAVLAAKTLGAEQVIVFSRHEDRAALAREFGADVVIAERGEEGAAQVRE
+LTGGYGAHGVCEAVGTQGSMDQALASVRPGGYVGFVGVSHDQTLDGSDLFGREIHLEGGP
+APVRRFLPELIERIQSGEIQPGRVFTARMPLDDAAEAYRAMDERREIKVLLEV
+>MHAAABBN_01951
+MTAQTLATPAIPETMKAVVMRAPGDVVVEEVDTPRVAQPTDVVLKLAAACVCGSDLWPYR
+GHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVNAG
+EYTGSRAQYMRVELADGSLVKVPGGEPSDPDRLADYLAASDVLGTGWYAAVAAQAGPGKT
+IAVVGDGAVGLCAVLAAKTLGAEQVIVFSRHEDRAALAREFGADVVIAERGEEGAAQVRE
+LTGGYGAHGVCEAVGTQGSMDQALASVRPGGYVGFVGVSHDQTLDGSDLFAREIHLEGGP
+APVRRFLPELIERIQSGEIQPGRVFTARMPLDDAAEAYRAMDERREIKVLLEV
+>LFPAFLNI_02183
+MTAQTLATPAIPETMKAVVMRAPGDVVVEEVDTPRVAQPTDVVLKLAAACVCGSDLWPYR
+GHNDVDHRRMGHEYVGTIVEKGEDVATLEVGDFVIGSFMLSDNTCEICQAGYQSRCVNAG
+EYTGSQAQYMRVELADGSLVKVPGGEPSDPDRLADYLAASDVLGTGWYAAVAAQAGPGKT
+IAVVGDGAVGLCAVLAAKTLGAEQVIVFSRHEDRAALAREFGADVVIAERGEEGAAQVRE
+LTGGYGAHGVCEAVGTQGSMDQALASVRPGGYVGFVGVSHDQTLDGSDLFAREIHLEGGP
+APVRRFLPELIERIQSGEIQPGRVFTARMPLDDAAEAYQAMDERREIKVLLEV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000097.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000097.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08475e8e23be8fa775092edf64b00090f4e721c5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000097.fa
@@ -0,0 +1,33 @@
+>ACLBLIBL_00578
+MFDAVAERYDLMNTVMTWGQEPRLVRHTVARANVPAHGRVLDLATGTGDLAFEVLRQHPD
+ATVVGADISAEMMEVGRRREGGDRVEWVVADAQDLPFEDASFDSVTHGYLLRNVADIPAA
+LAEQFRVLRPGGWMAALETSPPPANIIRPFSTFYMHQVMPRLARVITDKPEAYEYLSSST
+KAFHAPEEIADMLAHAGFVNIGHETHMFGTLATHWAMKPVA
+>MOLHKGIG_00604
+MPKMSGIETAFCRSALWGRFARDIIVPWSLGGQDLGGDVLELGAGSGQMAAALLQRSPGM
+RLTLTDIDERMVATARRRFPTSPRLTVQQADSTALPFAESSFDVVLSFLMLHHVVNWKAA
+VAEAARVLKPGGMLIGYDLTAWSSPS
+>MOLHKGIG_02174
+MSQNPLPAPRGDAQRGAADHHDRVSAMFDAIAGRYDLMNAVMTWGQEPRLVRRTVARANI
+PAQARVLDLATGTGDLAFEVLKQHPDAQVVGADIAAEMMEVGRARAGGDRIEWVVADATD
+LPFEAGSFDAVTHGYLLRNVADIPATLAEQFRVLRPGGWVAALETSPAPDNVLKPFSSFY
+IHRVMPQLAKLIADRPEAYAYLSSSTKAFHTPDEVADLFAEAGFVNIGHETHMFGTLATH
+WAMKPVD
+>NAFOICDF_00505
+MSETSPSPLPRPASLAHDADHGARVSGMFDAIAGRYDLMNTVMTWGQEPRLVRRTVERAN
+VPAAARVLDLATGTGDLALEILKQHPDAHVVAADFAPEMMEVGRTRPNGDRIEWVEADAL
+ALPFADGEFDSLTHGYLLRNVANIPAALAEQFRVLRPGGWVAALETSPAPDNLIKPFSSF
+YMHRIMPRLARLITDRAEAYEYLSSSTRAFHTPEEIAGMLADAGFVNIGHELHMFGTLAT
+HWAMKPLD
+>MHAAABBN_01888
+MSQNPLPAPRGDAQRGAADHHDRVSAMFDAIAGRYDLMNAVMTWGQEPRLVRRTVARANI
+PAQARVLDLATGTGDLAFEVLKQHPDAQVVGADIAAEMMEVGRARAGGDRIEWVVADATD
+LPFEAGSFDAVTHGYLLRNVADIPATLAEQFRVLRPGGWVAALETSPAPDNVLKPFSSFY
+IHRVMPQLAKLIADRPEAYAYLSSSTKAFHTPDEVADLFAEAGFVNIGHETHMFGTLATH
+WAMKPVD
+>LFPAFLNI_02119
+MSQNPLPAPRGDAQRGAADHHDRVSAMFDAIAGRYDLMNAVMTWGQEPRLVRRTVARANI
+PAQARVLDLATGTGDLAFEVLKQHPDAQVVGADIAAEMMEVGRARAGGDRIEWVVADATD
+LPFEAGSFDAVTHGYLLRNVADIPATLAEQFRVLRPGGWVAALETSPAPDNVLKPFSSFY
+IHRVMPQLAKLIADRPEAYAYLSSSTKAFHTPDEVADLFAEAGFVNIGHETHMFGTLATH
+WAMKPVD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000099.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000099.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3e2d35369e665f9ab798d73df50dfa8c8b592351
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000099.fa
@@ -0,0 +1,24 @@
+>ACLBLIBL_00595
+MRADARANRQDLLAAAGRLLEEQGAAMSLRGVAQEAGVGVGTLYRHFPTRRDLLDAVLED
+VVARVSGILHAFLDGGGSADRRWRRLAEELAAVNLTSLVTAGDDLEAADRPQEALIVEAE
+QVIISLTDRAVTEARRAGLVALGVTGTRYLTGLLAVTRPPAGELLARHADQRDWLLGVYL
+RGLRP
+>MOLHKGIG_02162
+MRADARANRQDLLAAAGRLIATQGAAMSLRGVAQEAGVGVRTLYRHFPTRRDLLDAVLED
+VVARTGGILQAFLDGVGGDGHGGGTEARWRRLAEDLGAVNLASLAAARDDFDPADRPPEA
+LIAEAERVILELADQVVAEARRAGLVGPDVTGADYLFGLLMVTRSPECALLGHGPDQRGW
+LLDTYLRGLRP
+>NAFOICDF_00518
+MQEEDTPPAEAMGRAEDAVMGLADRAVDLAREAGLVGDDVTGRAYMNGLIAVTRPPLPAL
+ESCRDDLEDWLLTVFLRGLRPAA
+>MHAAABBN_01875
+MILELADQVVAEARRAGLVGPDVTGADYLFGLLMVTRSPECALLGHGPDQRGWLLDTYLR
+GLRP
+>MHAAABBN_01876
+MRADARANRQDLLAAAGRLIATQGAAMSLRGVAQEAGVGVGTLYRHFPTRRDLLDAVLED
+VVARTGGILQAFLDGVGGDGHGGGTEARWRRLAEDLGAVNLASLAAARDDFDPADRPPRP
+SSPRPSV
+>LFPAFLNI_02107
+MRADARANRQDLLAAAGRLIATQGAAMSLRGVAQEAGVGVGTLYRHFPTRRDLLDAVLED
+VVARTGGILQAFLDGVGGDGHGGGTEARWRRLAEDLGAVNLASLAAARDDFDPADRPPEA
+LIAEAERVILELADQVVAEARRAGLMGPDVTGADYLLWVMRFLARGPG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000101.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000101.fa
new file mode 100644
index 0000000000000000000000000000000000000000..77092c75333ac3ec68201eadec2cdacac8d15c7e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000101.fa
@@ -0,0 +1,90 @@
+>ACLBLIBL_00658
+MAASPSPSDRAAEALGRTALQDAEGTRRVDLDVTGMTCASCVGRVERKLGKIEGVEASVN
+LPLERATVTVPASVSDQDLLDAVAKAGYTAAVRPDAQARPARRGRHDDGGTRPGADHAGH
+PDHRDHETPGEDHAGHEGHDDHMAHGPRADVLRPRLIVAAILTVPIVLISMVPALQFPHW
+GWVALALSAPVALWCGWPFHSAAFRAARHGSSTMDSLVSVGVLVAWTYSAVELVLEPGMT
+AHVGGTMAEMMRHSLYFETAAVITTFLLLGRWLEARAKREAGRALRSLLDLGAAQATVLP
+NWDAQTPHPSTSAAATPVAAVSGDFSEVEAASTSDKSPQTHHDGGADALTERVIPAEELE
+PGDVVVIRPGEKVPTDAVVLEGTSAVDASLLTGESVPVEVGPGDEITGATVNTSGRLIAR
+ATRTGADTTLAQMGRLVSDAQTGKARVARLADRISAVFVPIVLVLAVLTFVVWMLVTGGD
+VAPALRAGVAVLVIACPCALGLATPVGLLAGTGRASQLGILIGGPEVLEDTRTVDTIVLD
+KTGTVTEGRMALSDVHAFADDAALTEDRILALAAAVEAGSEHPIARAIVAGARERGLTVP
+RVADFASTAGGGVTGTVALPEAGSVRVAVGRGDLVGEPSPAQQAEFDAAEQAGATAVWVA
+VDGRVAGVLSVKDTVKPSSAAAIARLKELGLRPLLVTGDNAAVAAQVAAAVGIPAEDVVA
+GVRPEDKVDVVTRLQSEGRVVAMVGDGVNDAPALAAADMGIAMGSGTDVAREAAQITVMG
+DDLDQVVQALDLSRRTLGIIRMNLFWAFAYNVLGIPVAALGLLNPMIAGGAMAASSVLVV
+LNSLRLTRYAR
+>MOLHKGIG_02122
+MTHPASSTPAGPQSETTRRVDLDVTGMTCASCVGRVERKLGKLEGVTASVNLPLEQATVT
+APAGVSDEELVAAVEKAGYGATVRRPAPPAGHAGHAGHAHTSEHGEEHAADHDGVDHHDH
+MAHGPSEDVLTPRLIGAAVLTVPLVLISMVPALQFPHWGWVAFALAAPVALWAAWPFHSA
+AFRAARHGSSTMDTLVSLGVLVSFSFSAVELILAPDMTAHVGGTMAEMAHHSLYFETAAV
+ITTFLLLGRWLEARAKREAGAALRALLDLGAAQATLYDPETHDERTVPAESLAPGDVVLI
+RPGEKVPTDAEVLEGTSAVDASLLTGESVPVEVGPGDALTGATLNTSGRLVARATRVGSD
+TTLAQMGRLVSEAQTGKARVARLADRISAVFVPIVLGIAVLTFAVWMIVTGDLPSALRAG
+VAVLVIACPCALGLATPVGLLAGTGRAAQLGILIRGPEVLEDSRTVDTIVLDKTGTVTEG
+RMALADVLVLDPAFVAETGASRSAFVDETAPDQAADVLLTLAAAVERGSEHPIARAIVAG
+AEERGLTVPGVADFASTAGGGVSGLVALPHDDGAPGSGAHGAAGPDPVRVAVGRGSVLET
+ALDGGIPAEHRAAFEAAEQAGATAVWVAVGGRVAGVLSVRDTVKETSADAIARLKELGLR
+PLLVTGDNAAVATQVAAAVGIPAEDVVAGVRPEDKVDVVRRLQSEGHVVAMVGDGVNDAP
+ALAAADMGIAMGSGTDVAREAAQITVMGDDLHQVVQALDLSRRTLGIIRMNLFWAFAYNV
+LGIPVAALGLLNPMIAGGAMAASSVLVVLNSLRLTRYAR
+>NAFOICDF_00575
+MTHPASSAPAGPQSETTRRVDLDVTGMTCASCVGRVERKLGKLEGVTASVNLPLEQATVT
+APADVSDEELVAAVEKAGYGATVRRPAPPAGHAGHAHTSEHGEGHGEEHAADHDGVDHHD
+HMAHGPGEDVLKPRLIGAAVLTVPLVLISMVPALQFPHWGWVAFALAAPVALWAAWPFHS
+AAFRAARHGSSTMDTLVSLGVLVSFSFSAVELILAPDMTAHVGGTMAEMAHHSLYFEAAA
+VITTFLLLGRWLEARAKREAGAALRALLDLGAAQATLYDPETHDERTVPAESLAPGDVVL
+IRPGEKVPTDAEVLEGTSAVDASLLTGESVPVEVGPGDAVTGATLNTSGRLVARATRVGA
+DTTLAQMGRLVADAQTGKARVARLADRISAVFVPVVLGLAVLTFAVWMLVTGDLPSALRA
+GVAVLVIACPCALGLATPVGLLAGTGRASQLGILIRGPEVLEDSRTVDTIVLDKTGTVTE
+GRMALADVLVLDPAFVTDTGASRSASVAETDAPRSAFVAETAPDRATDLLLTLAAAVERG
+SEHPIARAIVTGAEERGLTVPDVADFASTAGGGVSGLVALPHDDGALASGAHGAAGPAPV
+RVAVGRGSVLETALDGGIPAEHRAAFEAAEQAGATAVWVAVGGRVAGVLSVRDTVKDTSA
+DAIARLKELGLRPLLVTGDNAAVATQVADAVGIPAEDVVAGVRPEDKVDVVRRLQSEGRV
+VAMVGDGVNDAPALAAADMGIAMGSGTDVAREAAQITVMGDDLHQVVQALDLSRRTLGII
+RMNLFWAFLYNVLGIPVAALGLLNPMIAGGAMAASSVLVVLNSLRLTRYAR
+>NAFOICDF_00718
+MSTSAPPTGGPDIELEIGGMTCASCANRIEKKLNKLDGVAATVNYATEKAKVTVPAGYDP
+SLLVAEVEKTGYTAALPKPKDTTANTSETEAGEEEDSELTSLRHRLIGAIVLTVPVIAMA
+MIPALQFTYWQWASLALAAPVIIWGAWPFHKAAWTNLKHGAATMDTLISMGTSVALLWSL
+YALFLGTAGTPGMTHPFEFTIAPSDGAANIYLEVGAGVTMFILAGRYFEKRSKRQAGAAL
+RALLELGAKEVAVLRDGVEVKIPTSELAVGDEFIVRPGEKIATDGLVTSGSSAVDASMLT
+GESVPVEVREGDSVTGATVNAGGRLVVRATRVGSDTQLAQMAKLVEDAQTGKAEVQRLAD
+RISGIFVPIVIVVAFITLGAWLGGGFPVAAAFTAAVAVLVIACPCALGLATPTALLVGTG
+RGAQMGVLIKGPEVLESTRKVDTVVLDKTGTVTSGKMTLTDVITEPGVDRAELLRFAGAL
+EDSSEHPIAQAIAKGATQEVGQLPTPEDFANVEGKGVQGIVEGTPVVVGRESLLADWSQK
+LSPEVAQAKAQAEGEGKTVVAIGWDGAARGILVVADTVKPTSAEAIRGLKEIGLTPVLLT
+GDNEAVARQIASEVGIDEVIAEVLPKDKVDVVTRLQEEGKIVAMVGDGVNDAPALAQADL
+GLAMGTGTDVAIEASDITLVRGDLRAAVDAIRLSRKTLSTIKTNLFWAFAYNTAAIPVAA
+LGMLNPMLAGAAMAFSSVFVVGNSLRLRGFTSVASK
+>MHAAABBN_01830
+MTHPASSTPAGPQSETTRRVDLDVTGMTCASCVGRVERKLGKLEGVTASVNLPLEQATVT
+APAGVSDEELVAAVEKAGYGATVRRPAPPAGHAGHAGHAHTSEHGEEHGEEHGEEHAADH
+DGVDHHDHMAHGPSEDVLTPRLIGAAVLTVPLVLISMVPALQFPHWGWVAFALAAPVALW
+AAWPFHSAAFRAARHGSSTMDTLVSLGVLVSFSFSAVELILAPDMTAHVGGTMAEMAHHS
+LYFETAAVITTFLLLGRWLEARAKREAGAALRALLDLGAAQATLYDPETHDERTVPAQSL
+APGDVVLIRPGEKVPTDAEVLEGTSAVDASLLTGESVPVEVGPGDALTGATLNTSGRLVA
+RATRVGSDTTLAQMGRLVSEAQTGKARVARLADRISAVFVPIVLGIAVLTFAVWMLVTGD
+LPSALRAGVAVLVIACPCALGLATPVGLLAGTGRAAQLGILIRGPEVLEDSRTVDTIVLD
+KTGTVTEGRMALADVLVLDPAFVAETGASRSAFVAETAPDQAADVLLTLAAAVERGSEHP
+IARAIVAGAEERGLTVPDVADFASTAGGGVSGLVALPHDDGALGSGAHDAAGPAPVRVAV
+GRGSVLETALDGGIPAEHRAAFEAAEQAGATAVWVAVGGRVAGVLSVRDTVKETSADAIA
+RLKELGLRPLLVTGDNAAVATQVAAAVGIPAEDVVAGVRPEDKVDVVTRLQSEGAVVAMV
+GDGVNDAPALAAADMGIAMGSGTDVAREAAQITVMGDDLHQVVQALDLSRRTLGIIRMNL
+FWAFLYNVLGIPVAALGLLNPMIAGGAMAASSVLVVLNSLRLTRYAR
+>LFPAFLNI_02060
+MTHPASSTPAGPQSETTRRVDLDVTGMTCASCVGRVERKLGKLEGVTASVNLPLEQATVT
+APAGVSDEELVAAVEKAGYGATVRRPAPPAGHAGHAGHAHTSEHGEEHGEEHAADHDGVD
+HHDHMAHGPSEDVLTPRLIGAAVLTVPLVLISMVPALQFPHWGWVAFALAAPVALWAAWP
+FHSAAFRAARHGSSTMDTLVSLGVLVSFSFSAVELILAPDMTAHVGGTMAEMAHHSLYFE
+TAAVITTFLLLGRWLEARAKREAGAALRALLDLGAAQATLYDPETHDERTVPAESLAPGD
+VVLIRPGEKVPTDAEVLEGTSAVDASLLTGESVPVEVGPGDALTGATLNTSGRLVARATR
+VGSDTTLAQMGRLVSEAQTGKARVARLADRISAVFVPIVLGIAVLTFAVWMIVTGDLPSA
+LRAGVAVLVIACPCALGLATPVGLLAGTGRAAQLGILIRGPEVLEDSRTVDTIVLDKTGT
+VTEGRMALADVLVLDPAFVAETGASRSAFVDETAPDQAADVLLTLAAAVERGSEHPIARA
+IVAGAEERGLTVPGVADFASTAGGGVSGLVALPHDDGAPGSGAHGAAGPDPVRVAVGRGS
+VLETALDGGIPAEHRAAFEAAEQAGATAVWVAVGGRVAGVLSVRDTVKDTSADAIARLRQ
+MGLRPLLVTGDNAAVAAQVAEAVGIPAEDVVAGVRPEDKVDVVTRLQSEGAVVAMVGDGV
+NDAPALAAADMGIAMGSGTDVAREAAQITVMGDDLHQVVQALDLSRRTLGIIRMNLFWAF
+LYNVLGIPVAALGLLNPMIAGGAMAASSVLVVLNSLRLTRYAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000103.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000103.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a390c1a8c6368584bc217b2eb4597ece27b80b90
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000103.fa
@@ -0,0 +1,22 @@
+>ACLBLIBL_00685
+MSHVTRGGTMTDTTTARPMRPTHHDDDPPVRGIGHLRHPVVSGGLIDGAMAAQGLLASPR
+PD
+>MOLHKGIG_02093
+MTDTTTARPKRPAHRDDGPPVRGIGHLRHPAVSGGLIGVIGGGAFLFGGIAGLPAEHRAT
+LRGIAISLISFTLVVVLLRRRMLPTVPTPARGALRVYGIAVVAMLAFLPVTRLVALALDA
+PTAQIALVAAVVGGHFLPFARAFQAPVFWWIGGAMAALGLAGAALAALGDPVAGPAGAAA
+AGVAMLVIVAAQGLLASPRQD
+>NAFOICDF_00555
+MERDSTHARGIAHPMHPAVLGAVVGMVGGSLFMLLSRPELPFPWPTVTLVAWIALLAAAA
+WAVFLAPRRLRDVGAPSRHAGPIYGLSVLGMVALIIASPHLVRALGIEAAQPAVVVMAVG
+LHFIPFASAFGARVFAWLGGSLTAIGLAGVIAAAVVGAPAGAVAAVLAGAAMLAFLAVDA
+RRGA
+>NAFOICDF_00601
+MSHVMRGGTMTATTTARPMRPTHHDDDPPVRGVGHLRHPVVSGGLIDGAMAAQGLLASPR
+QD
+>MHAAABBN_01800
+MSHVMRGGTMTDTTTARPMRPAHFDDDPPVRGIGHLRHPVVWGGLIGVVGGGAFLFGGIA
+GLPAEHQGTLRGSAIALIGFTLVVVLLRRRVLPAVQAPARGASTGSPSSRCWRSSP
+>MHAAABBN_01801
+MLALLPVTRLVALALDAPTAQIALVAAVVGGHFLPFARAFQAPVFWWIGGAMAVLGLAGA
+VVAVLGDPVAGPAGAAEAGAAMLVIVAAQGLLASPRQD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000107.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000107.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e3134278300357f73075e70640e737dbf9601d01
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000107.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_00771
+MAEFDGKVALVTGGGSGIGEACAKDLARGGAKVLVTDINLEAAERVAEEIKADGGEAAAY
+RLDSASPDDNEKAVAFAEETFGALHLAVNNAGIGAGTEPAGELKIEDWDRVIDIDLNGVL
+YGMRHQLPAMERAGGGAVVNMASIHGTVATGLGASAYTAAKHGVVGLTKQAGVDYGPRGV
+RVNAVGPGYIETPLLAELPDEVHEALVAKHPIGRLGRAEEVAHLVSFLLSDKASFLTGAY
+YLVDGGYTAP
+>ACLBLIBL_01745
+MADQTTPTAADAKASGRSVLVTGGNRGIGLAIARAFAANGDRVAVTSRSGEGPEGVLAVR
+ADVTDAASVDAAFREVEEAHGPVEVLVANAGITNDQLLLRMSEEDFTSVVDTNLTGAFRV
+VQRATKGMMRLKRGRIVLVSSVVGLLGSPGQVNYAASKSGLVGMARSITRELGARGVTAN
+VVAPGYIDTEMTQSLGEDLKAQYKKSIPAGRFAQPEEVADVVRWLASDEAAYISGAVIPV
+DGGLGMGH
+>MOLHKGIG_01147
+MADQTTTPTADAQAAGRSVLVTGGNRGIGLAIARAFAANGDRVAITSRSGEGPEGVLAVR
+ADVTDAASVDAAFREVEEVHGPVEVLVANAGITHDQLLLRMSEDDFTSVIDTNLTGAFRV
+VQRATKGMMRLKRGRIVLVSSVVGLLGSPGQVNYAASKSGLVGMARSITRELGARGVTAN
+VVAPGYIDTEMTQSLDDELKAQYKTSIPAGRFAAPEEVAGVVRWLASDEAAYISGAVIPV
+DGGLGMGH
+>NAFOICDF_01639
+MAEQTEPGGRSVLVTGGNRGIGRAIAEAFLANGDRVAVTSRSGEGGPEGALTVAADVTDA
+ASVDAAFRAVEEAHGPVEVLVANAGVTNDQLLLRMSEDDFTSVVDTNLTGAFRVVQRATK
+GMMRLKRGRIVLVSSVVGLLGSPGQVNYAASKSGLIGMARSITRELGARGITANVVAPGY
+IDTEMTRSLDEELKAQYRKSIPAGRFAEPEEVADVVRWLASPGAGYVSGAVIPVDGGLGM
+GH
+>MHAAABBN_00866
+MADQTTTPAADAQAAGRSVLVTGGNRGIGLAIARAFAAHGDRVAITSRSGEGPEGVLAVR
+ADVTDAASVDAAFREVEEVHGPVEVLVANAGITHDQLLLRMSEDDFTSVIDTNLTGAFRV
+VQRATKGMMRLKRGRIVLVSSVVGLLGSPGQVNYAASKSGLVGMARSITRELGARGVTAN
+VVAPGYIDTEMTQSLDDELKAQYKTSIPAGRFAAPEEVAGVVRWLASDEAAYISGAVIPV
+DGGLGMGH
+>LFPAFLNI_01097
+MADQTTTPAADAQAAGRSVLVTGGNRGIGLAIARAFAAHGDRVAITSRSGEGPEGVLAVR
+ADVTDAASVDAAFREVEEVHGPVEVLVANAGITHDQLLLRMSEDDFTSVIDTNLTGAFRV
+VQRATKGMMRLKRGRIVLVSSVVGLLGSPGQVNYAASKSGLVGMARSITRELGARGVTAN
+VVAPGYIDTEMTQSLDDELKAQYKTSIPAGRFAAPEEVAGVVRWLASDEAAYISGAVIPV
+DGGLGMGH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000111.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000111.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ffe79dd1341ef9675cd6dc91acb48954b7706bdd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000111.fa
@@ -0,0 +1,51 @@
+>ACLBLIBL_00806
+MARYITRNPATGETLEEFAELPASEVESVIERADTAYRAWRERPVAERAAVLARAADLYE
+ERAEQLAQDVTTEMGKPISAARGEMKTVAGIFRYYAEQGPAMLEHERIEVAGGGTAYVRR
+DPVGVLLGVMPWNFPHYQIARFAAPNLLLGNTMILKHAGICARSALNVEQLLLDAGLPEG
+AFVNAFIGHEAVAQIVADERVQGVSLTGSDKAGQIIGEQAGRNVKKAVLELGGSDPFIVA
+GDADVARAAKDAVSGRCVNSGQTCTSSKRFIVVEEHYEQFLSAFVEGMRAVPHGDPTDES
+TVVGPLSSPEAVQEVHELVQDAVAHGATLHVGGEPGEGPGAYYPPTVLTDVDESARAFRE
+EIFGPVAVVHRVKDLDAAIELANDSPYGLSSSVYTTSAEVAEEVSARLETGMVWVNSTSK
+SSAELPFGGVKRSGIGRELGTLGIEEFANHKLVRSPEGLIGA
+>ACLBLIBL_02161
+MTTTSASQGYRTINPATGELLKSFDTATDQQIADALDASQAAYEQWSQKSVAERAAVVKR
+ISELLAERSKDIATLITTEMGKSLGAAVGEVRFGAQIFAYYADNAEELLADQPIKDFSGQ
+EAFVERLPLGPLLGIMPWNFPVYQVARFVAPNLILGNTILLKHSEINPQTAALLEDLFRE
+AGLPEGVYQNLYATHEQVSTIIADPRVQGVSLTGSERAGAAVAEQAGRHLKKVVLELGGS
+DPYIVLSAPDARQAARDALATRMGNWGQACNSNKRMIVMEDLYDDFVDELVQRASAMKAA
+DPTSRDEDVYGPLSSESAADGLAEQIKAAKDAGATVHVGGERVSGPAGEGFYVSPAVITD
+VDQDNPAYTQELFGMAAVVYKVSSPEEAVALANDSQYGLGGAVFSTDLDEARRVADQLEV
+GMANVNLPSAAGANLPFGGVKRSGFGRELGPFAVDEFANKRLYAVKGPLQG
+>MOLHKGIG_00769
+MTTTSASQGYRTINPATGELLKSFDNATDQQIADALDASQAAYEQWSRKSVAERAAVVKR
+ISELLAERSKDIAAVITTEMGKSLGAAVGEVRYGAQIFGYYADEAEELLADQPIKQFSGQ
+EAFVQRLPLGPLLGIMPWNFPVYQVARFVAPNLVLGNTILLKHAEINPQVAQLLEELFTE
+AGLPEGVYQNVFATHDQISTIIADPRVQGVSLTGSERAGAAVAEQAGRHLKKVVLELGGS
+DPYIVLSAPDARAAARDALATRMGNWGQACNSNKRMIVMEDLYDDFVDELVQRSSEMKPG
+DPTSRDADVYGPLSSESAADGLAEQIAEAKQAGATVHVGGERTSGPEGEGFYVSPAVITD
+VDQENPAYTQELFGMASVVYKVSSAEEAVALANDSQYGLGGAVFSTDLDEAKRVADQLEV
+GMANVNLASAAGANLPFGGVKRSGFGRELGPLALDEFANKRLYAVQGPLEG
+>NAFOICDF_02057
+MTTTTSASQGYRTINPATGELIKQYDNATDQQVQDALAASQAAYEQWAATTVAERAGVVK
+RISELLAERSKDIAALITTEMGKSLGGAIGEVRFSAQIFAYYADNAEELLADQPIKDFSG
+QEAFLEKLPLGPLLGVMPWNFPVYQVARFAAPNLVLGNTILLKHSEINPQTAQLLQDLFE
+EAGLPAGVYQNLYATHDQISTIIADPRVQGVSLTGSERAGASIAEQAGRHLKKCVLELGG
+SDPYIVLSAPDARQAAREALQTRMGNWGQACNSNKRMIVMEDLYDEFVDELVKQSTALKP
+GDPTSRDEDVYGPLSSESAADGLAAQIRDAKEAGATVVGGERLSGPSGEGFYVSPAVITD
+VDQENPAYSQELFGMASVVYRVSSAEEAVALANDSQYGLGGAVFSTDLDEAKRVAEQLEV
+GMANVNLPSAQGANLPFGGVKRSGFGRELGPFAVDEFANKRLYAVKGDLQG
+>MHAAABBN_00499
+MQGVSLTGSERAGAAVAEQAGRHLKKVVLELGGSDPYIVLSAPDARAAARDALATRMGNW
+GQACNSNKRMIVMEDLYDDFVDELVQRSSAMKPGDPTSRDADVYGPLSSESAADGLTEQI
+AAAKEAGATVHVGGERVSGPEGEGFYVSPAVITDVDQENPAYTQELFGMAAVVYKVSSAE
+EAVALANDSQYGLGGAVFSTDLDEAKRVADQLEVGMANVNLASAAGANLPFGGVKRSGFG
+RELGPMAVDEFANKRLYAVQGPLEG
+>LFPAFLNI_00733
+MTTTSASQGYRTINPATGELLKSFDNATDQQIADALDASQAAYEQWSRKSVAERAAVVKR
+ISELLAERSKDIAAVITTEMGKSLGAAVGEVRYGAQIFGYYADEAEELLADQPIKQFSGQ
+EAFVQRLPLGPLLGIMPWNFPVYQVARFVAPNLVLGNTILLKHAEINPQVAQLLEELFTE
+AGLPEGVYQNVFATHDQISTIIADPRVQGVSLTGSERAGAAVAEQAGRHLKKVVLELGGS
+DPYIVLSAPDARAAARDALATRMGNWGQACNSNKRMIVMEDLYDDFVDELVQRSSAMKPG
+DPTSRDADVYGPLSSESAADGLTEQIAAAKEAGATVHVGGERVSGPQGEGFYVSPAVITD
+VDQENPAYTQELFGMAAVVYKVSSAEEAVALANDSQYGLGGAVFSTDLDEAKRVADQLEV
+GMANVNLASAAGANLPFGGVKRSGFGRELGPMAVDEFANKRLYAVQGPLEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000113.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000113.fa
new file mode 100644
index 0000000000000000000000000000000000000000..18c18bce58e1926c6f11330d57110af148125463
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000113.fa
@@ -0,0 +1,24 @@
+>ACLBLIBL_00875
+MTLAIVVSVLAVLLLIVGVVGTVYPILPGSMLILVTAVAWAWILGSGASWTFGLLAAGLA
+VAGMSASAVLTGRRLLRERVTRGPIAAGVVGAIVGFFVIPVVGLFIGFAVGLFGSQWART
+KDARAALASSWGALKAMGLGMLVELGCAMLALVSVGVGILVHFVF
+>MOLHKGIG_01983
+MTPALISLVAVLLLLVGLVGTVYPVLPGSLLNLVTALGWAALLGSPASWTFGVIAAGLAV
+AGLSASAVLTGRRLRRERVTRGPILWGVAGAAVGFFVIPVVGLFLGFAVGLFASQWARTR
+DARAALSSSIGALTAMGVGMLVEFCCALGSLTAVGVGALVHGLTA
+>NAFOICDF_00810
+MTPALISLVAVLLLLVGLVGTVYPVLPGSLLNLVTALGWAALLGSPASWTFGLIAAGLAV
+AGLSASAVLTGRRLRRERVTRGPILWGVAGAAVGFFVIPVAGLFLGFAVGLFASQWARTR
+DARTALSSSIGALTAMGVGMLVEFCCALGSLTAVGVGALVHGVTA
+>NAFOICDF_00823
+MTFAILVSLLAVLLLIVGLVGTVYPVLPGSVLNAVVSLAWAWVLGSVASWTFGLIACAFS
+IAGMSASAALTGRRLVKERIPRGPILTGVAAAVVGFFVIPVVGVFVGFAAGLFGAEWARR
+RDARAALTSSWGALKAMGLGMLVEFGCAMVALASVGAGALVHVLSL
+>MHAAABBN_01677
+MTPALISLVAVLLLLVGLVGTVYPVLPGSLLNLVTALGWAALLGSPASWTFGVIAAGLAV
+AGLSASAVLTGRRLRRERVTRGPILWGVAGAAVGFFVIPVVGLFLGFAVGLFASQWARTR
+DARAALSSSIGALTAMGMGMLVEFCCALGSLTAVGVGALVHGLTA
+>LFPAFLNI_01909
+MTPALISLVAVLLLLVGLVGTVYPVLPGSLLNLVTALGWAALLGSPASWTFGVIAAGLAV
+AGLSASAVLTGRRLRRERVTRGPILWGVAGAAVGFFVIPVVGLFLGFAVGLFASQWARTR
+DARAALSSSIGALTAMGVGMLVEFCCALGSLTAVGVGALVHGLTA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000114.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000114.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4aa703eebfd2431f83bb1b5d35ecf86fba9505c0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000114.fa
@@ -0,0 +1,49 @@
+>ACLBLIBL_00882
+MPPSQDGAELVQLGVIGVIVLVVFFYGGTMLMSLAISRRKENADAYMTAGNKIGFGVSAA
+SMTATWIWASSMYASVTAGYTYGVSGPIHYGLWGALMILFIYPFGRRIRKVAPRAHTLAE
+VMYARHGRSSQLMLAGSNVLGSVISLTSNFIAGGALIAILSPLSFGAGILIVAAGVLLYT
+LWSGFRASVLTDFAQVMAMLGATVVIIPAVFFAAGGPGMFEAGVQAGNVTAQQQDFFSSE
+AFMNQGAPYIAAVLAYAIGNQTIAQRLFAVREDLIKPTFITATVGYGGTVIGVGMIGVMA
+LYLGVQPLDGDVNNLLPQMVSSYLPLLVVALAFLMIIGSLSSTADSDLSALSSIVMTDVY
+GQSVGRENANPKTMLLIGRVTMIVATAAALYFATARFNILDLLVFVGALWGCLVFPVIAS
+FYWRKVTNAAFTVGVLAALAVFLPVRFEWIPLTGAWALVVEALAILGVGVVLGIMAFGFF
+GLRAAVVVGALATAATAFVGFGFLRDYATLSGSLVAYAVSFLVCWGMSVRSGQDFDFDRI
+ARVTGDFDPATDDAADRPVAQPAGARAS
+>MOLHKGIG_01975
+MPPSQDAASLTQLGVIGVILLVVLFYGGTMIMSVAISKKKENADAYMTAGNQIGFGVSAA
+SMTATWIWAASMYASVTAGYTYGVSGPLHYGL
+>MOLHKGIG_01976
+MILFIYPFGRRIRAVAPRAHTLAEVMYARHGRSSQLMLAGSNVLGSVISLTSNFIAGGAL
+ISLLSPLSFGAGILIVAAGVLLYTLWSGFRASVLTDFAQVMAMLGATVIIIPAVFFAAGG
+PDMFQAGVEAGHVTAQQQSFFSSDAFMNQGAPYIAAVLAYAIGNQTIAQRLFAVREDLIK
+PTFITATLGYGGTVIGVGMLGVMALYLGVEPLDGDVNNLLPQMVADHLPLALVALAFLMI
+IGSLSSTADSDLSALSSIVMTDVYGQSVGRKNADPKTMLLIGRITMIVATAAALYFATAK
+FDILDLLVFVGALWGCLVFPVIASFYWGRITNVAFTVSVLAALTVFLPVRFEWIPIEGAW
+AFVVETLAILGVGVVLCIMCFGFFGLRPAVVVGAIASVVMLFLGYGFLRDYATLTGSLVA
+YAVSFLVCWGLSVRSGQDFDFDRIARVTGDFDPATEDLPQVERASAPVS
+>NAFOICDF_00817
+MSVLAALAVFLPVRFEWFPLEGAWAFVVETLAILGVGVALGIMCFGFFGLRPAVVVGAIA
+SVVMLFLGYGFLRDYATLTGSLVDYAVSFLVCWGLPVRSGQDFDFDQIARVTGDFDPATE
+DLPQVERVAASVS
+>MHAAABBN_01669
+MPPSQDAASLTQLGVIGVILLVALFYGGTMIMSVAISKKKENADAYMTAGNQIGFGVSAA
+SMTATWIWAASMYASVTAGYTYGVSGPLHYGLWGALMILFIYPFGRRIRAVAPRAHTLAE
+VMYARHGRSSQLMLAGSNVLGSVISLTSNFIAGGALISLLSPLSFGAGILIVAAGVLLYT
+LWSGFRASVLTDFAQVMAMLGATVIIIPAVFFAAGGPGMFQAGVEAGHVTAQQQSFFSSE
+AFMNQGAPYIAAVLAYAIGNQTIAQRLFAVREDLIKPTFITATLGYGGTVIGVGMLGVMA
+LYLGVEPLDGDVNNLLPQMVADHLPLALVALAFLMIIGSLSSTADSDLSALSSIVMTDVY
+GQSVGRQNADPKTMLLIGRITMIVATAAALYFATAKFDILDLLVFVGALWGCLVFPVIAS
+FYWGRITNVAFTASVLAALAVFLPVRFEWIPLEGAWAFVVETLAILGVGVVLGIMCFGFF
+GLRPAVVVGAIASVVMLFLGYGFLRDYATLTGSLVAYAVSFLVCWGLSVRSGQDFDFDRI
+ARVTGDFDPATEDLPQVERASASVS
+>LFPAFLNI_01901
+MPPSQDAASLTQLGVIGVILLVALFYGGTMIMSVAISKKKENADAYMTAGNRIGFGVSAA
+SMTATWIWAASMYASVTAGYTYGVSGPLHYGLWGALMILFIYPFGRRIRAVAPRAHTLAE
+VMYARHGRSSQLMLAGSNVLGSVISLTSNFIAGGALISLLSPLSFGAGILIVAAGVLLYT
+LWSGFRASVLTDFAQVMAMLGATVIIIPAVFFAAGGPDMFQTGVEAGHVTAQQQSFFSSD
+AFMNQGAPYIAAVLAYAIGNQTIAQRLFAVREDLIKPTFITATLGYGGTVIGVGMLGVMA
+LYLGVEPLDGDVNNLLPQMVADHLPLALVALAFLMIIGSLSSTADSDLSALSSIVMTDVY
+GQSVGRQNADPKTMLLIGRITMIVATAAALYFATAKFDILDLLVFVGALWGCLVFPVIAS
+FYWGRITNVAFTASVLAALAVFLPVRFEWIPIEGAWAFVVETLAILGVGVVLGIMCFGFF
+GLRPAVVVGAIASVVMLFLGYGFLRDYATLTGSLVAYAVSFLVCWGLSVRSGQDFDFDRI
+ARVTGDFDPATEDLPQVERASAPAS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000118.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000118.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1b996961577a1654865988d5b5fe612fb4d049af
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000118.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01065
+MQTPATVHLVRHGEVHNPDRVLYGRLPEFGLSELGRQMADGVAAWFLERAEQTGRRPDVV
+AASPLTRAQQTAEPIAAALGRPLATEPDLIEAENDFEGMSQVAASLKRNPRLWPKLRNPL
+RPSWGEPYRQQAARMLAVVDRVRDEAEAAGGPGAEAVLVSHQLPIWVTRLAVEGRPLWHD
+PRRRECSLTSVTSLVFEEGRALPRVEYHEPNQALLKDASSLPGA
+>ACLBLIBL_02644
+MSDKLLHLVRHGEVHNPDRVLYGRLPGFRLSEPGHRMAEAAALELAGSDRVVARLLASPL
+ERTRQSARPIASALGLEVSIEERIVEPANVFEGMVNSGSDSAFRQPRYWYRFVNPFRPSW
+GEPYRQIAARVREAMDEAWETTRDGDIVMVSHQAPIWIAHLDVAGKPLFHNPATRRCELS
+SITSFEKRGERWFEVDYRTPAAGLVDDAVDVGAV
+>MOLHKGIG_01809
+MQTLATVHLVRHGEVHNPDRVLYGRLPEFGLSELGHEMARGVAAWFAERAAQTGRAPAVV
+AASPLTRAQQTAAPLAAAFDLPLVTEPDLIEAENAFEGMSQVAASLKRNPRLWPRLRNPL
+RPSWGEPYRAQAARMLAVVDRLRGEAVAADGPGAESVLVSHQLPIWVTRLAVEGRPLWHD
+PRRRECSLTSVTSLVYEEGRGVPRVEYHEPNQALLKDASSLPGA
+>NAFOICDF_01000
+MQTLATVHIVRHGEVHNPDRVLYGRLDGFGLSELGQRMAVGVAEWFLDRATELQRRPAIV
+AASPLLRAQQTAAPIAGAFATQLRTEQDLIEAENTFEGMSDVAATLRRSPRLWPLLRNPL
+RPSWGEPYRQQAARMLAVVDRVKDEAVDALGPGAEAILVSHQLPIWVTRLAVEGRPLAHD
+PRRRECSLTSVTSLVFEDGRALPRVEYHEPNAALLKDASSLPGA
+>MHAAABBN_01506
+MQTLATVHLVRHGEVHNPDRVLYGRLPEFGLSELGHEMARGVAAWFAERAAQTGRAPAVV
+AASPLTRAQQTAAPLAAAFDLPLVTEPDLIEAENAFEGMSQVAASLKRNPRLWPRLRNPL
+RPSWGEPYRAQAARMLAVVDRLRGEAVAADGPGAESVLVSHQLPIWVTRLAVEGRPLWHD
+PRRRECSLTSVTSLVYEEGRGVPRVEYHEPNQALLKDASSLPGA
+>LFPAFLNI_01730
+MQTLATVHLVRHGEVHNPDRVLYGRLPEFGLSELGHEMARGVAAWFEERAAQTGRAPAVV
+AASPLTRAQQTAAPIAAAFDLPLVTEPDLIEAENAFEGMSQVAASLKRNPRLWPRLRNPL
+RPSWGEPYRAQAARMLAVVDRLRGEAVAAEGPGAESVLVSHQLPIWVTRLAVEGRPLWHD
+PRWRECSLTSVTSLVYEEGRRVPRVEYHEPNQALLKDASSLPGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000123.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000123.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d48ec584b8f49a9ec87b375243f7ae1fb5aee05b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000123.fa
@@ -0,0 +1,42 @@
+>ACLBLIBL_01197
+MPMRVLVTGGAGYLGSHTVVVLLEAGHDVLVLDSLVAGSTAPLERAAELAGVALGGRRLD
+LVVADIRCPADYRAALEAFAPEAMVHFAGLKSPAESLSRPADYYDVNVGGTAAVAAAALA
+AGARTVLFSSSATVYGDRAPVPVDETAPTDPVSPYGRSKLMAEQVLRDVCATTDGVGLAM
+LRYFNPVGAHPSGRLGEDPRGVPANLMPFVARVATGAYPELQVFGADFPTRDGSAVRDFI
+HVMDLAEAHLAALAWLAARRGDGAEPTTRVWNIGRGEGVTVFEMVRAFEEVTGARIPCRV
+TARRAGDIAESCAAVDAVGAEVGWRARRDVTAMVRDLWAWQRAHPHGFGTGAA
+>ACLBLIBL_01209
+MRVLVTGGAGFLGSHTVSVLLDAGHDVLVLDSLVSSTTVPLERIADLAGVTFGGSRLRFH
+RADVREPTSYREAVVAFGPDAVVHFAGLKSPTESLADPASYYTVNVAGTAAVAEVAGGAG
+VRAFLFSSSATVYGDEAPVPVGEDAAVAPVTPYGHSKLMAEQVLRHMHEAGRHMGVAVLR
+YFNPVGAHPSGRLGEDPQGVPANLMPFVARVAGGRYEQLNVFGADFATRDGSAVRDFIHV
+MDLAEAHVATLEWMVAQPGDEVGVRVWNIGRGEGVTVFEMIQAFERVTGRPVPFQVVGRR
+PGDIAASCASVDAIAATVGWRASRDTDAMVRDLWAWQQANPSGYAGDAP
+>MOLHKGIG_01681
+MRVLVTGGAGYLGSHTVLTLLEAGHDVLVLDSLVTATTTSLERVAELAETRLGGSRLRLH
+VADIRRPEDYRGALADFGPAALVHFAGLKSPTESMTRPAAYYDVNVGGTAAVAEAALAAG
+ARTVLFSSSATVYGDRAPVPVAEDAATDPVSPYGHSKLMAEQVLRDVCATVDGGGLAMLR
+YFNPVGAHPSGRLGEDPSGVPANLMPFVARVASGAYPELRVFGADFDTRDGSAVRDFIHV
+MDLAEAHVAGLEWLAARVAAGGGTTTRVWNIGRGEGVTVFEMVRAFEAVTGGRIPYRVVE
+RRPGDIAESCAAVDAIGAEVGWHARRDVTAMVRDLWAWQEANPAGFSPRTE
+>NAFOICDF_01126
+MRALVTGGAGYLGSHTVTTLLDAGHDVLVLDSLAGAGRAGLERAAEVCGVGLGGARLRLV
+VADIRRPEDWADEVVAWAPDTVVHFAGLKSPTESMASPAEYYSVNVGGTAHVAEAAVRAG
+ARTLLFSSSATVYGDRAPVPVAESAPIDPVSPYGRSKAMAEQVLTDVHAASPGLSVASLR
+YFNPVGAHPSGRMGEDPQGTPANLMPFVSRVASGAYPELTVFGADFATRDGSAVRDFIHV
+MDLAEAHVAALEWMAARPSEEAGVRVWNIGRGEGVTVFEMVRAFEEVTGRPVPFTVGGRR
+AGDIAESCADVGAVARDVGWRARRDVREMVRDLWAWQQAEQEGDGGP
+>MHAAABBN_01385
+MRVLVTGGAGYLGSHTVLTLLEAGHDVLVLDSLVTATTTSLERVAELAGTRLGGSRLRLH
+VADIRRPEDYRGALADFGPAALVHFAGLKSPTESMTRPAAYYDVNVGGTAAVAEAALAAG
+VRTVLFSSSATVYGDRAPVPVAEDAATDPVSPYGHSKLMAEQVLRDVCATVDGGGLAMLR
+YFNPVGAHPSGRLGEDPSGVPANLMPFVARVASGAYPELRVFGADFDTRDGSAVRDFIHV
+MDLAEAHVAGLEWLAARVATGGGTTTRVWNIGRGEGVTVFEMVRAFEAVTGGRIPYRVVE
+RRPGDIAESCAAVDAIGAEVGWHARRDVTAMVRDLWAWQEANPAGFSSRAE
+>LFPAFLNI_01610
+MRVLVTGGAGYLGSHTVLTLLEAGHDVLVLDSLVTATTTSLERVAELAGTRLGGSRLRLH
+VADIRRPEDYRGALADFGPAALVHFAGLKSPTESMTRPAAYYDVNVGGTAAVAEAALAAG
+ARTVLFSSSATVYGDRAPVPVAEDAATDPVSPYGHSKLMAEQVLRDVCATVDGGGLAMLR
+YFNPVGAHPSGRLGEDPSGVPANLMPFVARVASGVYPELRVFGADFDTRDGSAVRDFIHV
+MDLAEAHVAGLEWLAARVATGGGTTTRVWNIGRGEGVTVFEMVRAFEAVTGGRIPYRVVE
+RRPGDIAESCAAVDAIGAEVGWHARRDVTAMVRDLWAWQEANPAGFSSRTE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000131.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000131.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8107332b22f54f19a954789e61a50323dd1738b4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000131.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01310
+MVGQTVGYVRVSSAEQNLDRQLEAVGECDRIFRDKISGSSRAKRAGLAELLGYVREGDLV
+KIASMDRLGRDTRDLYAIVDELTGKGCAVQFVSERITVDKSGTSPVDGLMLGILAAFAEF
+ERRRIKERQAEGIALAKARGKYVQAPKLSDTDVEQAKAMVDMGIPKSEVARTLGVSRQTL
+YTSLGRIASS
+>MOLHKGIG_00620
+MVGQTVGYVRVSSAEQNLDRQLEAVGECDRIFQDKISGSSRAKRTGLAELMQYVREGDLV
+KVASMDRLGRDTRDLYAIVDELTGKGCAVQFVSERITVDKSGTSPVDGLMLGILAAFAEF
+ERRRIKERQAEGIALAKARGKYVQAPKLSGTDVEQARVMIEMGIPKAEVARTFGVSRQTL
+YTSLRRFESG
+>NAFOICDF_00689
+MVGQTVGYVRVSSVEQNLDRQLEAVGECDRIFEDKISGSSRAKRTGLAELMRYVREGDLV
+KVASMDRLGRDTRDLYAIVDELTGKGCAVQFVSERITVDKSGTSPVDGLMLGILAGFAEF
+ERRRIKERQAEGIALAKARGKYVQAPKMSDLDVEQARVMISIGIPKAEVARTFGVSRQTL
+YASLRRVAP
+>NAFOICDF_02211
+MVGQAVGYVRVSSAEQNLDRQLEAVGECDRVFEGKISGSSRAKRTGLAELMRYVREGDLV
+KVASMDRLGRDTRDLYAIVDELTDKGCAVQFVSERITVDKSGTSPVDGLMLGILAAFAEF
+ERRRIKERQAEGIALAKARGKYVQAPKLSGTDVEQARVMINMGIPKAEVARTFGVSRQTL
+YTSLARMGL
+>NAFOICDF_02215
+MHVGYARVSTLEQDLSAQREALERLGVENKDIYFDHGLTGTTRARPGLREALAATRDGDT
+LVVTKLDRLARSLPDARDIADELTTKGVALSLGGSVYDPNDAVGRLLFNVLGMVAEFEAD
+LIRLRTREGMAIARSKGKLKGKKPKLSPSQRKHLLTLHAAGEHTQAELAELFNVSRTTIY
+RELRRTTTDT
+>MHAAABBN_00361
+MVGQTVAYVRVSSAEQNLDRQLEAVGECDRIFEDKISGSSRAKRAGLAELIGYVREGDLV
+KVASMDRLGRDTRDLYAIVDELTDKGCAVQFVSERITVDKSGTSPVDGLMLGILAAFAEF
+ERRRIKERQAEGIALAKARGKYVQAPKLSGADVEQARVMIDMGIPKAEVARTFGVSRQTL
+YTSLSRGAGAEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000132.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000132.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85fa8725661d5d4c0bbdd0330f80f6abc325dd97
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000132.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01337
+MSTDRDAGAEIRLESLTKRYPGQDRPAVDALDLLIPAGETVVFVGPSGCGKTTSLKMINR
+LIEPTSGRILIGGEDITRRDPTRLRRQIGYVVQGGGMMPHLSVAENVGLVPRLLKWDRRR
+IADRVDELLDLVGLDPAVYRDRFPRELSGGQQQRVGVARGLAADPPVLLMDEPFGAVDPL
+TRQRLQQEMLDIQARVGKTIVMVTHDVDEAVLLGDRILVLEPGAHVAQYATPEEVLARPA
+TEFVADFVGSGAGLKRLGLRSVDSLPLRPIAHHPTGTLPDGPVLDAATPISEALAALVTA
+PTEEIAVVRDGTVIGLLDYPTLRAHARAGDEQARP
+>MOLHKGIG_01585
+MSTDRDAGAEIRLESLTKLYPGQDRPAVDALDLIIPAGETVVFVGPSGCGKTTSLKMINR
+LIEPTSGRILIGGEDITRRDPTRLRRQIGYVVQGGGMMPHLSVAENVGLVPRLLKWDRRR
+IADRVDELLDLVGLDPAIYRDRFPRELSGGQQQRVGVARGLAADPPVLLMDEPFGAVDPL
+TRQRLQKEMLDIQARVGKTIVMVTHDVDEAVLLGDRILVLEPGAHVAQYATPEEVLARPA
+TEFVADFVGSGAGLKRLGLRSVDSLPLRPIAQHPTGTLPGEPVLDAATPISEALAALVMA
+PTEEIAVVRDGTVIGLLDYPTLRAHARASDEQARP
+>MOLHKGIG_02251
+MIRFEHVEKTFPDGTRAVEDFSLEVPSHTTTVLLGSSGCGKTTLLQMVNRMVDPTGGRVL
+IEGRDVASLDPVKLRRGIGYVMQNAGLLPHRTVLDNVLTVPRLTGRISRQDRDHAHELLE
+LVGLPAAVASRYPSQLSGGQRQRVGAARALAPDPDVLLMDEPFSAVDPVVRADLQAEMLR
+IQRELSKTVLFVTHDVDEAVLLGDEVLVLREGARVAQHGTGEDILLRPADDFVRSFVGGA
+RRELHVEDRTGTPIVVDASGRVAGTLVQP
+>NAFOICDF_00456
+MIRFEHVGKVFDDGTAAVEDFSLEVPSHTTTVLLGSSGCGKTTLLQMVNRMVDPTSGRVW
+IDDADVASVDPVRLRRRIGYVMQQAGLLPHRTVLDNVLTVPRLTGRVSAADRSRAHELLE
+LVGLPADAARRRPDQLSGGQRQRVGVARALASDPDILLMDEPFSAVDPVVRAELQAELLR
+IQRELAKTVLFVTHDVDEAVLLGDEVLVLRTGAQVAQRGRGEEILLHPADGFVDRFVGGD
+RRRLHVEERAGTATVVDAAGRVAGLLETP
+>MHAAABBN_01296
+MSTDRDAGAEIRLESLTKLYPGQDRPAVDALDLIIPAGETVVFVGPSGCGKTTSLKMINR
+LIEPTSGRILIGGEDITRRDPTRLRRQIGYVVQGGGMMPHLSVAENVGLVPRLLKWDRRR
+IADRVDELLDLVGLDPAIYRDRFPRELSGGQQQRVGVARGLAADPPVLLMDEPFGAVDTL
+TRQRLQKEMLDIQARVGKTIVMVIHDVDEAVLLGDRILVLEPGAHVAQYATPEEVLARPA
+TEFVADFVGSGAGLKRLGLRSVDSLPLRPIAQHPTGTLPGGPVLDAATPISEALAALVMA
+PAEEIAVVRDGTVIGLLDYPTLRAHARAGDEQARP
+>LFPAFLNI_01512
+MSTDRDAGAEIRLESLTKLYPGQDRPAVDALDLIIPAGETVVFVGPSGCGKTTSLKMINR
+LIEPTSGRILIGGEDITRRDPTRLRRQIGYVVQGGGMMPHLSVAENVGLVPRLLKWDRRR
+IADRVDELLDLVGLDPAIYRDRFPRELFGGQQQRVGVARGLAADPPVLLMDEPFGAVDPL
+TRQRLQKEMLDIQARVGKTIVMVTHDVDEAVLLGDRILVLEPGAHVAQYATPEEVLARPA
+TEFVADFVGSGAGLKRLGLRSVDSLPLRPIAQHPTGTLPGGPVLDAATPISEALAVLVTA
+PAEEIAVVRDGTVIGLLDYPTLRAHARAGDEQARP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000133.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000133.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9a28acfbe4ab71bb4d937aadb6868b18729ae973
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000133.fa
@@ -0,0 +1,34 @@
+>ACLBLIBL_01338
+MIARLRAASAEDRLLLIGLPLLVAALLIGWTVWVRGAALDDVEARLLTWPTVLRLTAEHL
+ALVGVSTVLVVATAVPLGVLLSRPAARRFTPVAMGLANAGQAAPVIGVIVLLAMAWGFGF
+RVAVLALSLYAFLPVLANTLAGLRGVDPTVVEAARGMGMSPLQTLLRVELPLALPVIMAG
+LRTALVLLVGTGAFATFIDAGGLGLLIQTGIVLFRFPLLVSGAILVAALALMIEWIGRLV
+ETLATPRGLA
+>MOLHKGIG_01584
+MIARLRAASAEDRLLLIGLPLLVAALLIGWTVWVRGAALDDVEARLLTWPTVLRLTAEHL
+ALVGVSTVLVVATAVPLGVLLSRPAARRFTPVAMGLANAGQAAPVIGVIVLLAMAWGFGF
+RVAVLALSLYAFLPVLANTLAGLRGVDPTVVEAARGMGMSPLQTLLRVELPLALPVIMAG
+LRTALVLLVGTGAFATFIDAGGLGLLIQTGIVLFRFPLLVSGAILVAALALMIEWIGRLV
+ETLATPRGLA
+>MOLHKGIG_02249
+MISSLFSWFADPAHWAGPNGVPARVLEHLGYSVLALVIAAAIAFPVGVWIGHTGRGRRVV
+VALSSALRALPTLGLLTFLAIVLDIRLRQALIPTVMVLVILAIPPLLAGTYAGLQAVPRE
+VVHAARANGHSTGQLIGQVELPIALPMAVGGLRSATLQVIATTSVASYLGLGGLGRYLFD
+ALAVQDYVTMLAGAVLIAVLALLCDGLLLLVQRILTPAGLRARG
+>NAFOICDF_00458
+MIADLFAWFADPAHWTGPGGVPARVAEHLGYSLLALAIAAVIALPAGVAIGHTGKGRRVV
+VAVSSALRALPTLGLLTFLAIVLQVGLRQALIPAVIVLVVLAVPPLLAGAYAGVHAVPRD
+VVVAARANGHSTRQLVSQVEVPLALPMIVGGLRSASLQVLATTSVAAYLGLGGLGRYLFD
+ALAVQDYTTMLAGAVLIALLALVSDAVLLLFQRLVTPA
+>MHAAABBN_01295
+MIARLRAASAEDRLLLIGLPLLVATLLIGWTVWVRGAALDDVEARLLTWPTVLRLTAEHL
+ALVGVSTVLVVATAVPLGVLLSRPAARRFTPVAMGLANAGQAAPVIGVIVLLAMAWGFGF
+RVAVLALSLYAFLPVLANTLAGLRGVDPTVVEAARGMGMSPLQTLLRVELPLALPVIMAG
+LRTALVLLVGTGAFATFIDAGGLGLLIQTGIVLFRFPLLVSGAILVAALALMIEWIGRLV
+ETLATPRGLA
+>LFPAFLNI_01511
+MIARLRAASAEDRLLLIGLPLLVAALLIGWTVWVRGAALDDVEARLLTWPTVLRLTAEHL
+ALVGVSTVLVVATAVPLGVLLSRPAARRFTPVAMGLANAGQAAPVIGVIVLLAMAWGFGF
+RVAVLALSLYAFLPVLANTLAGLRGVDPTVVEAARGMGMSPLQTLLRVELPLALPVIMAG
+LRTALVLLVGTGAFATFIDAGGLGLLIQTGIVLFRFPLLVSGAILVAALALMIEWIGRLV
+ETLATPRGLA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000137.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000137.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6dfbd283987dec92695ed3f4010f8cc4092505d8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000137.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01363
+MVGGALLGVVAGALGTAVHLTLSPLPGGWTLPWGAVLALVLAGSVQRWWMRRTAERGGAP
+LPAGAAVVAGAFTAVLALHRLPVHDALGVSWTAGLWAAAPGAVVASVAWNVGQPVLGLVL
+LAAGRRLDRRPAEAADGATRPRRTSVTARETRPGERVPWTAAPQPRAQREVDGQP
+>ACLBLIBL_02268
+MSRRVLLLLTAAVLVYALQFLPPLIFHDLVIAPSLGEHFGWALPYLAPVMVVPPLAWAAV
+AAAPVLRGGSTRRASGLSMTLLFFAPFAYAFATPVTWVAVRGVDAIGGLEDDPLLLGMVL
+PFLSGMILSPVLVGVVLQWWLRRTARRAAAGGAQAEAAPERPAPEAPTHDASGLPLP
+>MOLHKGIG_01563
+MVGGTLLGVVAGALGTAVHLNLASLPGGWTLPWGAVLALVLVGSTQRWWMVRRADRGGRA
+LPAGAAVVAGAFTAVLALQRLPVDDALGVSWTAGLWAAAPGAVVASVAWNVGQPALGLVL
+LAVGRRLDRRPAGAADGATRPRRATVTARETRPGERVPWTAAPQPRAQREVDGQP
+>NAFOICDF_01254
+MLPGLALGVGTGALGTATHLSLLPVGSWLLPWGLVLALVLVGSTQRWWMRRAAAAGGRPV
+RAGAAVVLAAFTMASALRWLPATDRLDLPWTAGVAQAMPVAFAASVGWTLGLPVLGVVLL
+WLGARAGEGRAAGESTLERTPNPVPARKVDGQP
+>MHAAABBN_01273
+MPERPRRRARPADVVGGALLGVVAGALGTAVHLNLASLPGGWTLPWGAVLALVLVGSTQR
+WWMVRRAGRGGRALPAGAAVVAGAFTVVLALQRLPVDDALGLSWTAGLWAAAPGAVVASV
+AWNVGQPALGMVLLAAGRRLDRRPAEAAEAATRPRRATVTARETRPGERVPWTAAPQPRA
+QREVDGQP
+>LFPAFLNI_01490
+MVGGTLLGVVAGALGTAVHLNLASLPGGWTLPWGAVLALVLVGSTQRWWMVRRAGRGGRA
+LPAGAAVVAGAFTAVLALQRLPVDDALGLSWTAGLWAAAPGAVVASVAWNVGQPVLGMVL
+LAAGRRLDRRPAEAAEAATRPRRATVTARETRPGERVPWTAAPQPRAQREVDGQP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000142.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000142.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2fdbc535a994523fd4bfa32d7149324b79506088
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000142.fa
@@ -0,0 +1,65 @@
+>ACLBLIBL_01501
+MTDEIYETPSTTPNFQTELAAQLADLIPEAIADGKVDVEKLKELLDGDAADSNERFGLFW
+PGKKRALRAAQEPTTATLKPDFEDSKDWDTTQNVFIEGDNLEVLKILQKHYHAKIKLIYI
+DPPYNTGKDFVYPDNYKEGLDTYLEWTRQVNEEGKKVTTNAETEGRYHSNWLNMMYPRLK
+LARNLLTDDGVIFISIDDNEIDNLLRLAKEVFGEPNVSTTFIRQKKKKPSFLHANVGSMT
+EYLVCITRNKAFTFPFSVDTTTAGKKYPINNAGNSLGKLTFPAGAVRFSQKFAEYEPQDM
+SEGNIVTRLLDHVVVSEGVNRNAFTLEGEWRYSQVTLDEFITAGDLITISKAPFRPNHVK
+AGGEIKKMHNLLTPSTYGVGTNEDGTAELEDLMEGSYFDNPKPTSLVRVLAQAVTYDDPS
+AIVLDFFAGSGTTADAVFRLNAQDGGNRRVISVQLPEPLDERSEAWAAGYRTISQLAKER
+IRRAGVRVLDREALLLEGRGVPLDTGFRAYKLSDTNFSKWRLSSDVEEDALQQHLLSLRD
+SATDDANADELLTEILLKQGYSLTEAVSPAEVAGLDVRFVRDRDGDVAVLAYLNEHVKPT
+LEQLRALVDEEPTRIIVLEDAFQGDDELKTNLAQLAKSKGIELWTA
+>NAFOICDF_00288
+MEMSMDKLRGTSPDLTQDNVARLAELFPTVVTEARDEDGQVTRAVDFDLLRQELSDHVVE
+GPQERYHLDWPGKRAAAFAANAPTTATLRPDREESVDFDTTKNVFIEGDNLEVLKVLQES
+YLGKVKMIYIDPPYNTGNDFVYADDFAESTADYLQRSGEIDDDGARLRANPETNGRFHSD
+WLSMMYPRLKLARNLLTEDGAILASIGEREVSNLRAILNELFGETNFVGELVWEKKKKGA
+FLSSHVTNVKEYILVFCRDRSSFGGLIGEVTHAAETYPVIKSTNSRGIRTIPAGIASNYS
+ERDHEVGAGTRLTSGNMEMILLSDLIIRDGRLAHDVEVESNWIYSQTLIDQFSLSGDLYI
+TRDLYIRRHVREPRTKMLKDLLMMRGESTSGSTFTLEPSLHSDGWGTNEDAFGELHSILG
+EQNLMDFPKPSKLIAKLIRSVTWADSDAIILDFFAGSGTTGQAVTQLNAADGGRRQYLLV
+QLNEAAEESSALRRAGFSSISALSRERLRRSAAAVRETSGTERLDLGFRAFRLDASPFVE
+RNHSADSITPDMLAELENPVLADRSPEDLLTHVLLAWGLDLSATIETVSLAGEEVYDVED
+GALLAALGSTVSDELAHAMAERHPDRALFLDSGFVSDAARINVEQIFREVSPGTDVKVL
+>NAFOICDF_00347
+MSSLSDLLGQVRATNPDLAANLEREIKNRTRRQRQFGLVFEEHRPEAVELPSREVRKGDK
+VRILPPRGETKKGDQTLWRVQRINRADDIAHLVEVDGEQGAEAALADLVVVAEFRDHMYP
+GLVETGRVERGGDKPFHTVINAENFHALEMLTYTHRHQVHCIYIDPPYNTGAKDWKYNND
+YVASDDDYRHSKWLSFMERRLQVARELLNPEDSVLIVTIDEKEYLRLGMLLEQTFPQARM
+QMVSTVINPKGSHRAGGFARSDEYVFFLFVGASQPAPMPLSSEWKVVQDSRALGLRWADL
+LRTADGSTRAARPNMFYPVFIRLAGDGPVFVSVGEPFYDADLTAVEAPEDAVAIWPIKAD
+GSQGRWQIGADTLRDLITKGYVRIGRWRGSKTTLTYLKAGEQAKVEDGRFPVRGRRADGS
+VLVDASEYSASFVPTSQWRISSHNAEQGGTNLLKSIMGDKRFPFPKSLYAVEDALRFLIK
+KNPDAVVLDFFSGSGTTAHAVMRLNKQDGGRRQCISVTNNEVSAEEQKGLRKQGLRPGDP
+EWEQWGICDYVTKPRVTAAITGRTPTGDPIKGDYKFTDEFPMSDGFEENAAFFTLTYESP
+LMVRQDLAFKRIAPLLWMRAGSRGRVITEVHARGWDVAEAYGVLTKVDRATPFAEAVAEA
+GVGTVYVVTDDERRYQAVCALLPEDVTPVRLYESYLTNFEINTGGRAGA
+>NAFOICDF_00694
+MSRLTDLLAQARKTDPQLAADLEAEFRQLTQRSQFGLVFERHQPEAVELPGRPVRRGDTV
+RVLPPRGTLTIGDTRHWVVTDLERTPDGKQAHLTEADVDPEVREPATSTAALEDLVVVAR
+FEDPIYPGLVETGRVENGGPDKPFHTVINAENFHALEMLTYTHRHKVDCIYIDPPYNTGA
+KDWKYNNDYVEADDDYRHSKWLSFMERRLQVARELLNPDDSVLIATIDEKEYLRLGMLLE
+QTFPEARIQMISAIINPKGSSRRDQFSRFDEYIFFVMNGSARPAAVAGDMTMRQARSKEK
+VRWAGLMRQGANGRRSARPNLFYPIFVANETGRVHSVGDSLPLDVPRSEVSPPPGTTAIW
+PLSKAGGESTWGRDPESLRKALSAGYVKIGRFTPGSERCGFTHLQSGQIKAIEEGALVVT
+GRDSDGSLQVEFAEGGQTAMPGTAWHRPAHSASEHGSTLLNAILPDRKFPFPKSLYAVED
+AVRFFVHGKPDAVVLDFFSGSGTTAHAVMRLNRQDGGRRQCISVTNNEVSAEEQKGLRKK
+GLRPGDPEWERWGICDYITKPRITAAITGKTPAGDPIKGNYKFTDEFPMADGFEENAAFF
+TLTYEAPRQVRRNRAFARVAPMLWFKAGSRGRIISSLPERGWDVAQAYGVLEDMDHAPEF
+LAALEADPQVGMAFIVTDSEVAFQSVARQLPEHATAVRLYESYLHNFQINRRA
+>MHAAABBN_02019
+MKRSPKGRLELTWMGKDSALIPVEDGKYDYSFVDPNDPRALEVKSIEVLEQVGEVEGPTG
+ANENLLIIGDSGDALRSLGTIPEYAEKYGGKVKLVYIDPPFNTEQAFDHYADQLEHSIWL
+TMMRDRIRDFKPLLHPDASIWVHLDDSEVHRMRALMDEEFGAENFIATVVWQKKYSRDNR
+PAIGTVHDYILVYAPAGAQRWKTLRNRIPRISAAQYRNPNNDPNGPWRPVPMDVQGGHAT
+ASQFYDVITPSGKIVRPANGRAWSVTAPVMQAMRDRGEVYFGLDGSGKPNTIRYLKDDEG
+LVPWTWWPHEEVGNNDDAKKEIIALFGEDQVFDTPKPERLLERVIRIATNADDLVLDCFA
+GSGTSAAVAHKLGRRWLTVELSQEVADTFTVPRLRKVQRGTDSIGISVREAEGFADADMD
+GRVKPDDAKALLRAIKEVQKVGLKSLSPEAGAALVQELRERLKPVSARQSVCQDGGFTVA
+KMGPSMYEVDDEHGMVFLSPEATNGAWSKAIAGQLKFTLTPDDPVFCGVRKRQRLAVIDG
+VADETVVRTVVEHLGEKERAVIVAKGVLPEAGDLLQRLSPGSRIKKAPEDMFPKGTVN
+>LFPAFLNI_00111
+MSSLSDLLGQVRATNPDLAANLEREIKNRTRRQRQFGLVFEGHRPEAVELPSRPVRKGDK
+VRILPPRGETKKGDQTLWHVDHIDRTTGTARLTAVDGEQEAQAAISDLVVVAEFRDHMYP
+GLVETGRVENGGGKPFHTVINAENFHALEMLTYTHHRKVDSCRASDLGHV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000147.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000147.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d67516a8bfe09e65d2d0a0ef0a0cc9e7897fac35
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000147.fa
@@ -0,0 +1,56 @@
+>ACLBLIBL_01615
+MSAEPSPLSGLAADPEERRLEAALRPKHLDEFVGQRRVREQLDLMLASARLRDRAADHVL
+LSGPPGLGKTTLAMIVAAEMNAPLRLSSGPAIQHAGDLAAILSSLTEGEVLFLDEIHRMS
+RPAEEMLYMAMEDFRVDIVVGKGAGATSIPLELPPFTLVGATTRAGLLPGPLRDRFGFTG
+HLDFYAEAELERVLRRSALLLDVRLASDGYRQIATRSRGTPRIANRLLRRVRDWALVKGV
+EQVEADHAAAALDMYDVDARGLDRLDRSVLTALCTTFGGGPVGLTTLATAVGEEAETVET
+VAEPFLIREGMVARTPRGRIALPGAWDHLGLASPEAGSGA
+>MOLHKGIG_01272
+MSAESSPLSAAAVDPEERRLEAALRPKHLDEFVGQMRVREQLDLMLASARLRDRAADHVL
+LSGPPGLGKTTLAMIVAAEMNAPLRLSSGPAIQHAGDLAAILSSLTEGEVLFLDEIHRMS
+RPAEEMLYMAMEDFRVDIVVGKGAGATSIPLELPPFTLVGATTRAGLLPGPLRDRFGFTG
+HLDFYTEVELERVLRRSALLLDMRLATEGYRQIARRSRGTPRIANRLLRRVRDWALVKGL
+AEVGAHDAAAALDMYEVDGRGLDRLDRSVLTALCTTFGGGPVGLSTLATAVGEEAETVET
+VAEPFLIREGMVARTPRGRVALPGAWEHLGLAAPEATPGP
+>NAFOICDF_01510
+MSERPVTAFEADAEERRLEAALRPKHLDEFVGQARVREQLDLMLASARLRDRAADHVLLS
+GPPGLGKTTLAMIVAQEMNAPLRLSSGPAIQNAGDLAAILSSLTEGEVLFLDEIHRMSRP
+AEEMLYMAMEDFRVDIVVGKGAGATSIPLELPPFTLVGATTRAGLLPGPLRDRFGFTGHL
+EFYAIEELERVLRRSSALLDMRVETDGYRQIASRSRGTPRIANRLLRRVRDWALVKGLDT
+VDAEAASAALTMYEVDARGLDRLDRSVLTALCTTFGGGPVGLTTLATAVGEEAETVETVA
+EPFLIREGMMARTPRGRVALPGAWDHLGMTPPEAPLG
+>MHAAABBN_00991
+MSAESSPLSAAAVDPEERRLEAALRPKHLDEFVGQMRVREQLDLMLASARLRDRAADHVL
+LSGPPGLGKTTLAMIVAAEMNAPLRLSSGPAIQHAGDLAAILSSLTEGEVLFLDEIHRMS
+RPAEEMLYMAMEDFRVDIVVGKGAGATSIPLELPPFTLVGATTRAGLLPGPLRDRFGFTG
+HLDFYTEVELERVLRRSALLLDMRLATEGYRQIARRSRGTPRIANRLLRRVRDWALVKGL
+AEVGAHDAAAALDMYEVDGRGLDRLDRSVLTALCTTFGGGPVGLSTLATAVGEEAETVET
+VAEPFLIREGMVARTPRGRVALPGAWEHLGLAAPEATPGP
+>LFPAFLNI_01230
+MSAESSPLSAAAVDPEERRLEAALRPKHLDEFVGQMRVREQLDLMLASARLRDRAADHVL
+LSGPPGLGKTTLAMIVAAEMNAPLRLSSGPAIQHAGDLAAILSSLTEGEVLFLDEIHRMS
+RPAEEMLYMAMEDFRVDIVVGKGAGATSIPLELPPFTLVGATTRAGLLPGPLRDRFGFTG
+HLDFYTEVELERVLRRSALLLDMRLATEGYRQIARRSRGTPRIANRLLRRVRDWALVKGL
+AEVGAHDAAAALDMYEVDGRGLDRLDRSVLTALCTTFGGGPVGLSTLATAVGEEAETVET
+VAEPFLIREGMVARTPRGRVALPGAWEHLGLAAPEATPGP
+>LFPAFLNI_01882
+MSILRVHDGLFGLTFQQALDKASPGATIALTPGTYAEFESIPVGNLRIIGAGSRPEDVIL
+VTQLDVHGQISVENLTLQAPHFHNAVRLHGPTASAVFLYTAIQPEPTGQFPAVYSEGGAV
+TVRRSTLDQGPGGCALYVEGQGTATFEDSTTGTVNAVASTVTTVDSTHGAFHLSAASKVH
+ARGTLCLAPAEGMRGLVLTAFSVLKAERLTTDITYLELSLEDSALDVAEVSTSSDVDVHV
+MTSGGSHVQIPPDTVRVTDIDRQKAEQEVAERRQREEAAARRRAEEAAAEAAATGEAARQ
+AAAEAQAEARRQEEAKPRAVMWTAAQGADFTTVQDQLRPGDTLVLEEGDFHLPDPAIMLN
+CHIRGTGRADRIRLHGAVGIPNGATVRLENMLLVTPSTGNAVNVHAGGNATLTGVLVDPT
+KAEVFSPLCSSGGRLTLNEVRVVSEPTSYLADVLGTQGGVIVAEDSTFGIVRLESSARAT
+LTDCTANQLYVLGSGEALSLGTLRIPPTTPHLRALAVEEGGRGTIADLCVEEPCEVFVAG
+SLQIAHVSSAPHALHLITTDTALHSIPEDAIATAEEPSQTATADATLVEHPGENSTGDRE
+PSAGRGHDGADLADTNCDPMAQLSALTGLADVKNQVQTFIAEVRFAEARRQRGFAVRRQT
+LHSQFLGNPGTGKTTVARLLGRALHQAGVLSSDVFVEVTREDLVSEHIGGTGPKTRRILE
+SALGGILFIDEAYTLAEGGPQDFGREAIATLLAFMENHRDEFMVILAGYPEQMHAFFKAN
+PGLRSRVPLRFDFEDYSTAELVQMGLAALADDGFTVDPDAYRRTVAEAHRSSGDRSNGRW
+VRNLNDRLVRHMAHRVMAESGAAEDMVGVEDERLTQVDPADLHALLGRSTEDDTGVDHLL
+VELDEMVGLETVKAWVRGLVAQAEADERLRDAGVDLPRPTYHMVFAGSPGTGKTTVARLV
+GKLFHRLGILSTPQVVEASRERMVGRYIGHTEERTGLLLDEARGGVLFVDEAYQLDMPDS
+SNDFGKVAVETLITRLEDDRHSFIAIFAGYTDRMAQFLSLNPGLASRVPHNIEFPDYSPD
+DIAEIVVRTLRRTWSFDETVLRSAVAQGYAALPPESRANARQARNYADAISQAHKTWITE
+SSTDGDDIRHIRDATIIGVLAAEPTGQDQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000148.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000148.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b13a02fad5f2a62a1190b18fdb361edbf8ca097d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000148.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_01740
+MAEPAATAEPDGREVRLARAEDLADPRLVPYTTLTDAALRRRVDAEHGVFLAESSQVVRR
+ALAAGHTPRSFLLGDRYRGSFADVLAAHPDVPVFTGPDDVLEALTGFHLHRGALAAMDRP
+APRPLADVLAGARRVLIAEDLVDHTNLGAVVRSAVALGWDALLLTPQAADPLYRRAIRVS
+MGTVFRLPWARLEGPVAEAVPALREAGFAVAALEVTERAVGLDSPELEPLRSADRLALVL
+GQEGPGVRTETLEHTDADVVIPMPDGVDSLNVAAAAAVALWELRAR
+>MOLHKGIG_01152
+MGEVGTREVRLERIEDLADPRLAPYTTMTDAALRRRVDAEHGVFLAESSQVVRRALDAGH
+TPRSFLLGDRYRGSFADVLAAHPDVPVFTGPDDVLEALTGFHLHRGALAAMDRPAPRPLA
+DVLAGARRVLIAEDLVDHTNLGAVVRSAVALGWDALLLTPQAADPLYRRAIRVSMGTVFR
+LPWARLPGPVAQSLPALRAAGFAVAALEVTERAVGLDSARIEPLRTAERLALVLGQEGPG
+VRPETLAQTDADVVIPMPAGVDSLNVAAAAAVALWELRAR
+>NAFOICDF_00545
+MSSESPAQPASADQPAEAPAGVIVDPKDARLRKVRELLKGKNKASRAIIVDDEENLLAAL
+AAGVELFTVFHGEDAELPAALAAVLPADQDVQVVSTHAAKELFGVERRSRVFALARRPKP
+LTVAEVLEHPGDVLVLDGVKLMGNIGAITRSARALGAAGLVLVDADLASVTDRRLIRASR
+GMVFSLPVALASADDVAAQLAEAGVPLVSLDLGSEKALDSVAEIPGRVALLLGSEKHGPS
+ARLAETAEHTVSITIHPEVESLNVSVSAALALYERRASNPLPQA
+>NAFOICDF_01634
+MPDDGAPAPFPGEVRLQSAADLADPRLAPYTTLTDAALRRDVDAAHGVFLAESSPVVRRA
+LDAGHAPRSFLLGDRYRETFADVIAAHPGVPVFTGPDEVLTALTGFHLHRGALAAMDRPA
+PRSVAEALDGAHRVLIAEDLVDHTNLGAVVRSAVALGWDALLLTPRAADPLYRRAIRVSM
+GTVFRLPWARADGPLEEALPALRAAGFATAALEVTDRAVGLDSPELEPVRTAERLALVLG
+QEGPGVRPETLAAVDAHVVIPMPAGVDSLNVAAAAAVALWELRPRDTPAA
+>MHAAABBN_00871
+MGEGGAREVRLERIEDLADPRLAPYTTMTDAALRRRVDAEHGVFLAESSQVVRRALDAGH
+TPRSFLLGDRYRGSFADVLAAHPDVPVFTGPDDVLEALTGFHLHRGALAAMDRPAPRPLA
+DVLAGARRVLIAEDLVDHTNLGAVVRSAVALGWDALLLTPQAADPLYRRAIRVSMGTVFR
+LPWARLPGPVAQSLPALRAAGFAVAALEVTERAVGLDSAWIEPLRTAERLALVLGQEGPG
+VRPETLAQTDADVVIPMPAGVDSLNVAAAAAVALWELRAR
+>LFPAFLNI_01102
+MGEGGAREVRLERIEDLADPRLAPYTTMTDAALRRRVDAEHGVFLAESSQVVRRALDAGH
+TPRSFLLGDRYRGSFADVLAAHPDVPVFTGPDDVLEALTGFHLHRGALAAMDRPAPRPLA
+DVLAGARRVLIAEDLVDHTNLGAVVRSAVALGWDALLLTPQAADPLYRRAIRVSMGTVFR
+LPWARLPGPVAQSLPALRAAGFAVAALEVTERAVGLDSAWIEPLRTAERLALVLGQEGPG
+VRPETLAQTDADVVIPMPAGVDSLNVAAAAAVALWELRAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000149.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000149.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c95207ce036f6209af05eb7c405263ca4aadad1e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000149.fa
@@ -0,0 +1,106 @@
+>ACLBLIBL_01776
+MPKNSSTTVSSAVETHAGGLASGPGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVF
+TGLSGSGKSSLAFDTIFAEGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKS
+TNRNPRSTVGTITEVYDYLRLLWARVGVPHCPQCGEPVSRQTPQQIVDQLEELPERTRFQ
+VLAPVVRGRKGEFVDLFADLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRLAM
+KEGIRQRLTDSVETALKLADGLVVAEFVDVEVVAEKGKKNTAEFGGRDAEGNPRYRSFSE
+KLSCPNGHEQTVDEIEPRSFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVV
+PWSLGKSTSDYWLRVLGGLAKEMGFSLDTPWRELEPAQREAVLHGKDFKVEVTFRNRFGR
+ERRYTTGFEGVVPYVLRKHGETESDGARERYESFMREIPCPVCHGARLNPTVLNVLVGGL
+SIAEATRLPLREARDFLAGLELSARERQIADQVLKEILARLAFLLDVGLEYLNLERPAGT
+LSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEH
+DEDTIAEADWIVDIGPRAGEHGGEVVHSGSLEDLKANTASITGDYLAGRRAITAPQTRRA
+PQEGRTLTVRGARENNLKDVSVDIPLGVLTAVTGVSGSGKSTLINEILYKVLANRLNGAK
+LVPGRHRAVDGLEHLDKVVHVDQSPIGRTPRSNPATYTGVFDAIRKLFAETPEAKVRGYQ
+QGRFSFNIKGGRCEACSGDGTLKIEMNFLPDVYVPCEVCDGARYNRETLEVTYKGKNIAE
+VLDMPIEEAAQFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKR
+SNGRSVYVLDEPTTGLHFDDIRKLLQVLQSLVDKGNTVITIEHNLDVVKCADHVIDLGPE
+GGSGGGTIVATGTPEEVARVEASHTGRFLAELLA
+>MOLHKGIG_01117
+MPKNSSTTVSSAVEAHPGGLASGSGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVF
+TGLSGSGKSSLAFDTIFAEGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKS
+TNRNPRSTVGTITEIYDYMRLLWARVGVPHCPQCGEPVSRQTPQQIVDQLEELPERTRFQ
+VLAPVVRGRKGEFVDLFKDLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRLAM
+KEGIRQRLTDSVETALKLADGLVVAEFVDVEPVAEKGRKNTAEFGGRDAEGNPRYRSFSE
+KLSCPNGHEQTVDEIEPRSFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVV
+PWSLGKSTSDYWLRVLGGLGKEMGFSLDTPWKDLTEAERDAVLHGKDFKVEVTFRNRFGR
+ERRYTTGFEGVIPYVMRKHGETESDGARERYESFMREIPCPACHGARLNPTVLNVLVGGL
+SIADATRLPMREAMEFFSGLRLTDRERQIADQVLKEILARLAFLLDVGLEYLNLERPAGT
+LSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEH
+DEDTIAEADWIVDIGPRAGEHGGEVVHSGSLADLKANTRSVTGDYLSGRRSIAVPERRRV
+PEKGRVLTVRGAQENNLKDVSVEVPLGVLTAVTGVSGSGKSTLINEILYKVLANRLNGAK
+LVPGRHRSVEGLEHLDKVVHVDQSPIGRTPRSNPATYTGVFDAIRKLFAETPEAKVRGYQ
+QGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTYKGKNIAE
+VLDMPIEEAADFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKR
+SNGRTIYVLDEPTTGLHFDDIRKLLHVLQSLVDKGNTVLTIEHNLDVIKSADHVIDLGPE
+GGSGGGTIVAAGTPEEVAHVAESHTGRFLAELLA
+>NAFOICDF_01669
+MPKNSSSAAAPARPDAAARGGLASGPARGSAQHERIVVKGAREHNLKNVDVSIPRDSMVV
+FTGLSGSGKSSLAFDTIFAEGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQK
+STNRNPRSTVGTITEIYDYMRLLWARVGVAHCPVCGEVVSKQTPQQIVDQLEQLPERTRF
+QVLAPVVRGRKGEFVDLFSSLSTQGYARALVDGELIQLSDPPALKKQNKHTIAVVVDRLA
+VKEGIRQRLTDSVETALKLADGLVAVEFVDVDVVAQAGKKNQGDLAGEDAEGNPRFRTFS
+EKLSCPHGHPQTVDEIEPRSFSFNNPFGACPECTGIGSRLQVDPDLVVPNDELSLNEGAI
+LPWSLGKSTSDYWLRVLGGLAKEMKFSLDTPFKDLTAQQRDAVLNGKDFKVEVSFRNRFG
+RERRYTTGFEGVLPYVMRKHGETESDNARERYESFMRQIPCPACHGARLNPTVLNVRVGG
+LSIADATRLPLRESLAFLDGLQLTERELAIADQVVREIRARLEFLLDVGLDYLNLERNAG
+TLSGGEAQRIRLATQIGAGLVGVLYVLDEPSIGLHQRDNRRLIDTLIRLRDLGNTLIVVE
+HDEDTIAEADWIVDIGPRAGEHGGEVVHSGSLDELKANTRSVTGDYLAGRRRIEVPAARR
+PVDPKRRLTVKGATENNLKDVTVDIPLGVFTAVTGVSGSGKSTLINEILYKVLADKLNGA
+KMVPGRHRSVAGLEHLDKVVHVDQSPIGRTPRSNPATYTGVFDQIRKLFAETPEAKVRGY
+QQGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTYKGKNIA
+EVLDMPIEEAAEFFGAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQK
+RSTGRTVYVLDEPTTGLHFEDIRKLLQVLQTLVDKGNTVLTIEHNLDVVKCADHVIDLGP
+EGGSGGGTVVATGTPEEVAAVPESHTGRFLAELLG
+>MHAAABBN_00373
+MVESSSFVPPKLSVQPDVRVLGARENNLQDVDLTVPRDATVVFTGVSGSGKSSLAFGTLY
+AESQRRYLESVAPYARRLIDQAGVPDVDSITGMPPAVALQQQRGSGNARSTVGSITTLSS
+LVRMLYSRAGDYPEGQPMLYAEDFSANTVQGACSECHGIGRVYEVNEQQMVPDPSLTIRE
+RAIASWPTAWHGHQLRDVLVALGYDVDVPWRDLPKKDRDWILYTDETPFVPVHSRLTLSE
+SKAAIEAGVEPSYSGTFVGARRYILDTFANTKSASMKRRVAQFLTAAICPTCNGKRLKPE
+ALSVTFEGFDIAEFSQLPLRELATILSGVVAREEDHEAASSDVRPTASRTPEKRAAAVQL
+ASGVLQRLRPLVDLGLGYLSLSRTTPTLSGGELQRLRLATQLSSDLFGVVYVLDEPSAGL
+HPQDVAALLEILDGLKGRGNSLFIVEHSVAVMRHADWLVDIGPGAGEHGGRVLYSGPPDG
+LAGVTESVTRGYLFGGRGLPLRTPREARSWLRLENVTRNNLHDLTVDIPLGVFTAVTGVS
+GSGKSSLVSQALPSLLGDRLGLAARADDEPVSDESLLADAPEHLEGRVAGPVTGVQRLVV
+IDQRPIGRTPRSNVATYTGLFDHVRRRFADTPEARSRGYKPGRFSFNVAGGRCPTCEGEG
+SVMVELLFLPSVYTECPDCHGTRYKASTLEVTWRGRTIADVLSMSVEEANLFFVGDEEIT
+RSLAALSDVGLEYLRLGQPATELSGGEAQRVKLATELQRAQRGDTLYVLDEPTSGLHCAD
+TDRLVAHLQTLVDAGNTVVAAELDMRVVAVADHVIDLGPGAGDAGGTVVAAGTPAHVADQ
+GVGASAGYLAAALQAATNVTPS
+>MHAAABBN_00836
+MPKNSSTTVSSAVEAHPGGLASGSGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVF
+TGLSGSGKSSLAFDTIFAEGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKS
+TNRNPRSTVGTITEIYDYMRLLWARVGVPHCPQCGEPVSRQTPQQIVDQLEELPERTRFQ
+VLAPVVRGRKGEFVDLFQDLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRLAM
+KEGIRQRLTDSVETALKLADGLVVAEFVDVEPVAEKGKKNTAEFGGRDAEGNPRYRSFSE
+KLSCPNGHEQTVDEIEPRSFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVV
+PWSLGKSTSDYWLRVLGGLGKEMGFSLDTPWKDLTEAERDAVLHGKDFKVEVTFRNRFGR
+ERRYTTGFEGVIPYVMRKHGETESDGARERYESFMREIPCPACHGARLNPTVLNVLVGGL
+SIADATRLPMREAMEFFSGLRLTDRERQIADQVLKEILARLAFLLDVGLEYLNLERPAGT
+LSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEH
+DEDTIAEADWIVDIGPRAGEHGGEVVHSGSLADLKANTRSVTGDYLSGRRSIAVPERRRV
+PEKGRVLTVRGAQENNLKDVSVEVPLGVLTAVTGVSGSGKSTLINEILYKVLANRLNGAK
+LVPGRHRSVEGLEHLDKVVHVDQSPIGRTPRSNPATYTGVFDAIRKLFAETPEAKVRGYQ
+QGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTYKGKNIAE
+VLDMPIEEAADFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKR
+SNGRTIYVLDEPTTGLHFDDIRKLLHVLQSLVDKGNTVLTIEHNLDVIKSADHVIDLGPE
+GGSGGGTIVATGTPEEVARAAESHTGRFLAELLA
+>LFPAFLNI_01067
+MPKNSSTTVSSAVEAHPGGLASGPGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVF
+TGLSGSGKSSLAFDTIFAEGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKS
+TNRNPRSTVGTITEIYDYMRLLWARVGVPHCPQCGEPVSRQTPQQIVDQLEELPERTRFQ
+VLAPVVRGRKGEFVDLFQDLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRLAM
+KEGIRQRLTDSVETALKLADGLVVAEFVDVEPVAEKGRKNTAEFGGRDAEGNPRYRSFSE
+KLSCPNGHEQTVDEIEPRSFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVV
+PWSLGKSTSDYWLRVLGGLGKEMGFSLDTPWKDLTEAERDAVLHGKDFKVEVTFRNRFGR
+ERRYTTGFEGVIPYVMRKHGETESDGARERYESFMREIPCPACHGARLNPTVLNVLVGGL
+SIADATRLPMREAMEFFSGLRLTDRERQIADQVLKEILARLAFLLDVGLEYLNLERPAGT
+LSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEH
+DEDTIAEADWIVDIGPRAGEHGGEVVHSGSLADLKANTRSVTGDYLSGRRSIAVPERRRV
+PEKGRVLTVRGAQENNLKDVSVEVPLGVLTAVTGVSGSGKSTLINEILYKVLANRLNGAK
+LVPGRHRSVEGLEHLDKVVHVDQSPIGRTPRSNPATYTGVFDAIRKLFAETPEAKVRGYQ
+QGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTYKGKNIAE
+VLDMPIEEAADFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKR
+SNGRTIYVLDEPTTGLHFDDIRKLLHVLQSLVDKGNTVLTIEHNLDVIKSADHVIDLGPE
+GGSGGGTIVAAGTPEEVAHVAESHTGRFLAELLA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000150.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000150.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ced6c5872ceef169b2630ef78edc9a1bdcd439b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000150.fa
@@ -0,0 +1,90 @@
+>ACLBLIBL_01787
+MTSPLTRLHDALGLRTTPAIFFGSAAVVVLFTLAMGLFPGPVQAGFGVVSSWLRYDAGWI
+YTLSLTVLVAFLLLLAVTRYGRVKLGDDDAVPEYSGLAWFGMMFAAGVGAVLMFWGIAEP
+MNHYANPPLAGTEPFSDQAASQAMAIANFHFGIHMWAILLVPGLCFGYFTYKRKLPPRVS
+SAFQPLLGDRIHGPIGKAIDIVSVVSTVFGLGVSVGLGALQINAGMNYVFGTPVAGWVQA
+LILAVITAVGTASVLAGMDKGVKRLSYANILMAIALLVYVLMWAVSSMDVIRGTVQAVGE
+YLTMLPMLSTFNDTYNSGQWSGDWTVFYWAWTVTWAPFVGMFFAKISRGRTIRSFIAAGL
+GLPTAFVIIWMGIYGYSAFQSDRATAAAPGTGGDLTETIVTEGNVQAALFQHLQGTPLYT
+VAAVLALVVITLFFITSIDSGALVMDAMANGHEDPAPRRQSVIWAVSIGAVCAAIILTAG
+ENGLAALQEVIIVIGLPILLITVTQAGLLLQALREDAGTARPLRTRQWKPVLPAEEYHRR
+AHEEGVDVSDYVIRPEFEVGTEPEHDTHTPNTWHQQRTVAAKALVTVGLTGGIAAGRTVV
+GEELERLGAVVVEFDDLMGEILVPGSPVLEELREVFGDDVVRADGTLDARTLNRLTAEST
+TARTRMYEIVSPAVRDEANRRARAIGEDSVLVVDLALLAETGSAGDFDQVLAVSAPAEQR
+VARLMDSHDLPREQAWAFIDEEALDAERAEIADTVIENDGTLEDLHEAVRAYWEAKIQPQ
+IEAARGVSP
+>ACLBLIBL_01788
+MNSLLTRLHDRLGLRTSPAVFFSAAAVIILFTVAMGVLPGPVQAVFGAAAHWLRYDVGWF
+YTLAATLLLAVCLILAVSRYGRVKLGDDDASPEYSGLAWFGMMFASGIGAVLMFWGIAEP
+MTHYALPPLEGTEPYSDQAAVQALNIANLHFGLHMWAILVVPGLCFGYFTYKRNLPPRVS
+SAFQLLLGDRIHGPIGKTIDVIAIVSTVFGMGVSTGMGALQINAGVNYVVGVPVAGWVQA
+LILAVALMLWVLMWAASSMDVVRGVIESFGRTLGALPLLTTFNDTLGGGTWSGDWTLFYW
+AWTVSWAPSVGMFVARISRGRTIREFVFASLGLPTAFVIVWMGVYGYSAIFADRAAAPEA
+GTGGPLAQTIAVEGNVQVALFQSLQEMPLYLPIAVLALIVIVIFFVTSIDSGALVMDAMA
+NGHEDLAPRRQRVFWGVSVGAVCTAIIVTAGDDGLNALREVIIVIGFPVMVLTVLQALLL
+LQALREDAGAARPLRTRQWKRVLPPEEYHRRAREDATVREEYAIRPEFEVGTEPEYETHT
+PNTWHAQQPAARRATVSVGLTGGVASGKSAVAAEFERLGAVVVDYDDLMREILVPGHPAV
+DELRDVFTAEVVADDGTVDWLALDALTAESPSARTRLHEVVAPVVRAETDRRATDAGESS
+VLVVDLALLVDAADVRDFDQVLEVLAPAEVRVARLMDERGLDREQAWAEVDADEQRRPAL
+GGTHTVLANEGDRAELERSVRDWWDEVVEPARERGRRPGPRLRRLTRTVPPPPPAAGGGG
+RGWRPGAGSPYRRDRVPDGTRPSARPLDRPPRSVGDPVPGDS
+>MOLHKGIG_01106
+MTSPLTRLHDTLGLRTSPAIFFGSAAAVVLFTAAMGLFPGPVQAAFGVVSSWLRYDVGWI
+YTLSLTLLVAFLFILAVTRYGRVKLGDDDAVPEYSGLTWFGMMFAAGVGAVLMFWGIAEP
+MNHYANPPMAGTEPFSDRAASEAMAIANFHFGIHMWAILLVPGLCFGYFTYKRKLPPRVS
+SAFQPLLGDRIHGPIGKTIDIIAVVSTVFGLGVSVGLGALQINAGMNYVLGTPVAGWVQA
+LILAVVTAVGTASVLVGMDKGVKRLSYANILLAIALLVYVLMWAVSSMDVIRGTVQAIGE
+YASMLPVLSTYNDTYNSGQWSGDWTVFYWAWTVTWAPFVGMFFARISRGRTIRSFIMAGL
+GLPTAFVIIWMGIYGYSAFQSDRATAPAPGQGGDLTQTIVTDGNVQAALFQHLQGTPLYT
+VAAVVALVVITLFFITSIDSGALVMDAMANGHEDAAPRRQSVFWAVSIGAVCAAIILTAG
+ENGLAALQEVIIVIGLPILLITVTQAALLLQALREDAGAARPMRTRQWKQVLPVEEYRRR
+ATEDGVDVSDFVIRPEFEVGTEPENDTHTPKTWHQQRIDAAKALVTVGLTGGIAAGRTEV
+GAELERLGAVVVEFDDLMGEILVPGNPVLEELRSVFGEDIVRADGTLDARTLNRLTTESS
+TARTRMYEIVSPAVRDEANRRAREIGEDSVLVVDLALLAETGSGQDFDQVLAVSAPAEVR
+VARLMESHDMTRERAWAFIDEEAADEERAEIADTVIENDGSLEDLQEAVRAYWEAKIQPQ
+LEAARGERV
+>NAFOICDF_01679
+MNSLHTRVHDALGLRTSPAIFFTSAAVIVLFTAAMGLFPGPVQEVFGVVAGWLRYDIGWF
+YTLSATLLALFAVLLACSRYGRIKLGDDDATPEYTGVAWFGMMFAAGVGAVIMFWGIAEP
+MNHYANPPMPGTEPFSDQAALQAMDIANFHFTIHMWAILLVPGLCFGYFTYKRKLPPRVS
+SAFQPLLGDRIHGPIGKAIDVISVVSTVFGLAVSTGLGALQINAGMNYVLGTPVAGWVQA
+LILAVITAAGVCSVLAGMDSGVKRLSYINIVVAVALMLFVLMFSISTNDVLRGTVQSVGS
+FVGHLPVLSTFNDVFGSGRWSGDWTVFYWAWTVTWAPFVGMFVAKISRGRTIREFVTAGL
+GLPSIFTMIWMGIYGYSAFQADRATAAGPGQGGDLTRTIVEEGNVQAALFQHLQGMPLYL
+PVAIVALVVITLFFVTSIDSGALVMDAMANGHEDPAPRRQGAFWAISIGAVCAAIILTAG
+ENGLDALQEVIIVIGFPVMLLTLVQAAMLLQALREDAGAARPIRTRQWKQVLPAEEYHRR
+AQEDGVDIQEYVIRPEFEPGTEPEFDTHTPNTWHQQRTVAQRALLTLGLTGGMASGRTAV
+GEELERLGAVVVEFDDLLDELLVPGAPVLDEVREVFGDDVVRADGTLDARAMNALIDASE
+AARSRFYEIVSPLVRAEADARAKAIGDDAVLVVDLALLAETGSARDFDQVLAVSAPAEVR
+VQRLVDERHVTRERAWALLDEGAQDDERAAIADTVIENGGTREELRAAVEAYWAEKVAPA
+VEAARIAGGVG
+>MHAAABBN_00825
+MTSPLTRLHDTLGLRTSPAIFFGSAAAVVLFTAAMGLFPGPVQAAFGVVSSWLRYDVGWI
+YTLSLTLLVAFLFILAVTRYGRVKLGDDDAVPEYSGLTWFGMMFAAGVGAVLMFWGIAEP
+MNHYANPPMAGTEPFSDRAASEAMAIANFHFGIHMWAILLVPGLCFGYFTYKRKLPPRVS
+SAFQPLLGDRIHGPIGKTIDIIAVVSTVFGLGVSVGLGALQINAGMNYVLGTPVAGWVQA
+LILAVVTAVGTASVLVGMDKGVKRLSYANILLAIALLVYVLMWAVSSMDVIRGTVQAIGE
+YASMLPVLSTYNDTYNSGQWSGDWTVFYWAWTVTWAPFVGMFFARISRGRTIRSFIMAGL
+GLPTAFVIIWMGIYGYSAFQSDRATAPAPGQGGDLTQTIVTDGNVQAALFQHLQGTPLYT
+VAAVVALVVITLFFITSIDSGALVMDAMANGHEDAAPRRQSVFWAVSIGAVCAAIILTAG
+ENGLAALQEVIIVIGLPILLITVTQAALLLQALREDAGAARPMRTRQWKQVLPVEEYRRR
+ATEDGVDVSDFVIRPEFEVGTEPENDTHTPKTWHQQRIDAAKALVTVGLTGGIAAGRTEV
+GAELERLGAVVVEFDDLMGEILVPGNPVLEELRSVFGEDIVRADGTLDARTLNRLTTESS
+TARTRMYEIVSPAVRDEANRRAREIGEDSVLVVDLALLAETGSGQDFDQVLAVSAPAEVR
+VARLMESHDMTRERAWAFIDEEAADEERAEIADTVIENDGSLEDLQEAVRAYWEAKIQPQ
+LEAARGERV
+>LFPAFLNI_01055
+MTSPLTRLHDTLGLRTSPAIFFGSAAAVVLFTAAMGLFPGPVQAAFGVVSSWLRYDVGWI
+YTLSLTLLVAFLFILAVTRYGRVKLGDDDAVPEYSGLTWFGMMFAAGVGAVLMFWGIAEP
+MNHYANPPMAGTEPFSDRAASEAMAIANFHFGIHMWAILLVPGLCFGYFTYKRKLPPRVS
+SAFQPLLGDRIHGPIGKTIDIIAVVSTVFGLGVSVGLGALQINAGMNYVLGTPVAGWVQA
+LILAVVTAVGTASVLVGMDKGVKRLSYANILLAIALLVYVLMWAVSSMDVIRGTVQAIGE
+YASMLPVLSTYNDTYNSGQWSGDWTVFYWAWTVTWAPFVGMFFARISRGRTIRSFIMAGL
+GLPTAFVIIWMGIYGYSAFQSDRATAPAPGQGGDLTQTIVTDGNVQAALFQHLQGTPLYT
+VAAVVALVVITLFFITSIDSGALVMDAMANGHEDAAPRRQSVFWAVSIGAVCAAIILTAG
+ENGLAALQEVIIVIGLPILLITVTQAALLLQALREDAGAARPMRTRQWKQVLPVEEYRRR
+ATEDGVDVSDFVIRPEFEVGTEPENDTHTPKTWHQQRIDAAKALVTVGLTGGIAAGRTEV
+GAELERLGAVVVEFDDLMGEILVPGNPVLEELRSVFGEDIVRADGTLDARTLNRLTTESS
+TARTRMYEIVSPAVRDEANRRAREIGEDSVLVVDLALLAETGSGQDFDQVLAVSAPAEVR
+VARLMESHDMTRERAWAFIDEEAADEERAEIADTVIENDGSLEDLQEAVRAYWEAKIQPQ
+LEAARGERV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000153.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000153.fa
new file mode 100644
index 0000000000000000000000000000000000000000..142cb02ccf3bd8c2fd9d11588be7f93ed61a54f1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000153.fa
@@ -0,0 +1,54 @@
+>ACLBLIBL_01822
+MSDSIPLDAVPAAIAAFAAGRPVVVVDDADRENEGDLVYAAALATDAVTAFTVRHTSGVI
+CAPMPADLADRLALPPMTARNEDPKGTAYTVSVDAATEVSTGISAADRTRTLRILADPAA
+GPADLTRPGHVFPLRAVPGGVRARRGHTEAGVELCRLADVAPVAAIAELVHDDGTMMRLP
+ALREFADEHGLVLISIEDLVRHLEEEGPTPVPVPAEATLPTRHGVFRVSVHADAVTGAEH
+VLLVAKKAGEAGEADPERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALSRAGSEGGAVL
+YLRGHEGRGIGLANKVRAYRLQEQGLDTVEANIALGLPTEARDWAGAAAVLAAAGHTRVR
+LVTNNPAKVAGLQAAGIDVVERVPAPTPVTEHNLGYLRTKRDRMAHALADRVLEHPVAPG
+HEDPRHETPTHQEDTP
+>MOLHKGIG_00838
+MSLEFRTSEESPDVTRVVATHLPTRHGDFALLGYRDGRGTDHVALTLGDVAADDGELPLV
+RLHSECLTGDALGSYRCDCGEQLDAALQAIGAAGRGVLIYIRGHEGRGIGLLDKLRAYAL
+QDSGIDTVDANTHLGLPADARDYDQSAQILRELGVGKIRLLSSNPAKQEALEALGIHVEA
+RVRLNVADRPENSRYLSTKRARMRHDLPPERNAWDLLAGARVPTGPLTPQEEALVLRYGP
+LVEAGPRLVIGQLGQSLDGFIASRTGDACFVTGEADREHLHRLRALVDAVLVGAQTVAAD
+DCQLTVRAVNGADPARVVVDPHARIPLTAKVLTDPRSRTLWLVGSDASVPASLAPHVSVH
+RLETSTGFEPAAILQYLADQGLGRVLIEGGGLTVSGFLHAGVLDRLYLTSAPLLVGDGVP
+GIRFDGADALSGALSAPVRRFVLGDDVCTEFDFSAAKPASPAALHRADQENQPTGQD
+>MOLHKGIG_01065
+MSEHIRLDPVPVAIAAIAAGRPVVVVDDADRENEGDLIYAAALATDEVTAFTVRHTSGVI
+CAPLPAGLADRLALPPMTTVNEDPKGTAYTVSVDAAAGVTTGISAADRTRTLRLLADPGA
+APGDLTRPGHVFPLRAVPGGVRARRGHTEAGVELCRLAGVAPVAAIAELVHDDGTMMRLP
+ALREFSDEHGLVLISIEDLVAHLEETTPALTAVPAEATLPTRHGLFRVSVHVDAETGAEH
+LLLVAGETDSERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALARAAAEGGAVLYLRGHE
+GRGIGLANKIRAYRLQEEGMDTVEANLALGLPAEARDWAGAAAVLTAAGHRRIRLVTNNP
+AKVAGLRAAGIDVVERVPAPTPVTEHNVVYLRTKRDRMAHALADRVLEPPTATGGPATPA
+DDPTTDPTHPTHQEDTP
+>NAFOICDF_01711
+MSIDTAVEPAAPVDIRLDPVADAVAAIAQGRPVVVVDDADRENEGDLIYAAALATDAVTA
+FTVRHTSGVICAPLPAELADRLNLPPMTARNEDPKGTAYTVSVDAVAGVTTGISAADRTV
+TLRVLAGEESTAADLTRPGHVFPLRAVPGGVRARRGHTEAGVELCELADLPPVAAIAELV
+HDDGTMMRLPALREFADEHSLVLISIEDLVAHLHEHRPEQRVVPAEAALPTAHGDFRISV
+HPDTATGAEHVLLVADRPGSATGGDADAPVTVRVHSECLTGDVFGSLRCDCGPQLQAALD
+AAARDGGAVLYLRGHEGRGIGLTNKIRAYRLQEEGLDTVEANLALGLPAEGRAYAGAADL
+LREAGLTRIRLVTNNPAKVDALRAAGIDVVERVPAPTPVTEHNAAYLRTKRDRMHHELAD
+RDLGDA
+>MHAAABBN_00784
+MSEHIRLDPVPAAIAAIAAGRPVVVVDDADRENEGDLIYAAALATDEVTAFTVRHTSGVI
+CAPLPAGLADRLALPPMTTVNEDPKGTAYTVSVDAAAGVTTGISAADRTRTLRVLADPGA
+APGDLTRPGHVFPLRAVPGGVRARRGHTEAGVELCRLAGVAPVAAIAELVHDDGTMMRLP
+ALREFSDEHGLVLISIEDLVAHLEETTPTLTAVPAEATLPTRHGLFRVSVHVDAETGAEH
+LLLVAGETDPERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALARAAAEGGAVLYLRGHE
+GRGIGLANKIRAYRLQEEGMDTVEANLALGLPAEARDWAGAAAVLTAAGHRRIRLVTNNP
+AKVAGLRAAGIDVVERVPAPTPVTEHNVVYLRTKRDRMAHALADRVLEPPTATGGPATPA
+DDPTTDPTHPTHQEDTP
+>LFPAFLNI_01012
+MSEHIRLDPVPAAIAAIAAGRPVVVVDDADRENEGDLIYAAALATDEVTAFTVRHTSGVI
+CAPLPAGLADRLALPPMTTVNEDPKGTAYTVSVDAAAGVTTGISAADRTRTLRVLADPGA
+APGDLTRPGHVFPLRAVPGGVRARRGHTEAGVELCRLAGVAPVAAIAELVHDDGTMMRLP
+ALREFSDEHGLVLISIEDLVAHLEETTPTLTAVPAEATLPTRHGLFRVSVHVDAETGAEH
+LLLVAGETDPERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALARAAAEGGAVLYLRGHE
+GRGIGLANKIRAYRLQEEGMDTVEANLALGLPAEARDWAGAAAVLTAAGHRRIRLVTNNP
+AKVAGLRAAGIDVVERVPAPTPVTEHNVVYLRTKRDRMAHALADRVLEPPTATGGPATPA
+DDPTTDPTHPTHQEDTP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000158.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000158.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9837bc2e4c0447cae838022e2222085c87bfa3e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000158.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02168
+MSRSAAVVPEAAPAPLAVAEHLELRHGDHLAVEASSFTLPAGCVVAVIGPNGSGKSTLLQ
+ALAGVLDPAAGRLEVRGESPSRHGRLTSFVMQSLQFPQGVPLTVRDVVTMGRYTTAGWFR
+RLGATDRAAVAAAMERVRVTDLADRHLDQLSGGQRQRVYVAQGLAQEHDVLMLDEPVTGL
+DIVSARTIDEIIHEQPERGVSVVYTTHDLDEAAAADHVVLMDGRVVASGPPAQVLTAANL
+DAVYGRGALHAPLLVHLDDPADCSPDRG
+>MOLHKGIG_00762
+MNASFPAGAAAATPPLAVARALELRHGSHVAVRPSDFTLPARRLIAVIGPNGSGKSTLLT
+ALAGLSDPASGALEVLGEDPRRRSQRTSFVMQSIGVPQGVPVTVRDVVGMGRYPTLGWFR
+RFRREDRDIVRAAMERMQVADLARRHLDQLSGGQRQRAYVAQGLAQDHDVLLLDEPMTGL
+DIVSARTIDDLLHEEPTRGVSVVYTTHDLDEAAEADHVVLMGGRVVASGSPRDVLTVENL
+DIAYGRGALHGPSTAVEDAADFLDDPAGGRRH
+>NAFOICDF_00528
+MNPAAPAPAIRLADVSAAYDRRRPVFTGADLVIDGPGLVRVHGRNGGGKSTLIELVSGYL
+RPSDGQVRIGGLPAHDPRAHERRRVCRTEPALYPLMDVHDHVVFASRWAGADPAEGLARA
+ERYGLGPWMHAPAQTLSTGNRRRLWIVQCTVGAFDTVVLDEPFNGLDDESSAVLAAELAA
+WARTRCVVLICHLPPPGLAFDRVVRWPPGQAAADPAPPADPGVRP
+>NAFOICDF_02063
+MTRTVPTAPTPGAGVLAEARGLELRRAAHVAVAPSDLTLPAGVLVAVIGPNGSGKSTLLH
+ALAGTLEPAAGSLTVRGESPSRHARRTAFVMQTIPVPQGVPLTVRDVVRMGRYPRVGWFG
+RFGAADREAVDAAMERMSVTDLARRHLDELSGGQRQRVYVAQALAQEHDVLMLDEPLTGL
+DLVSARTIDRLLHEEPARGVSVVHTTHDLDEAAAADFVVLMSGRVVAAGTPRQVLTEANL
+EAAYGHGVLHGPRLPFLDDPVDGVR
+>MHAAABBN_00492
+MNASFPAGAAATPPPLAVARALELRHGSHVAVRPSDFTLPARRLIAVIGPNGSGKSTLLT
+ALAGLSDPASGALEVLGEDPRRRSQRTSFVMQSIGVPQGVPVTVRDVVGMGRYPTLGWFR
+RFRREDRDIVRAAMERMQVADLARRHLDQLSGGQRQRAYVAQGLAQDHDVLLLDEPMTGL
+DIVSARTIDDLLHEEPTRGVSVVYTTHDLDEAAEADHVVLMGGRVVASGPPRDVLTVENL
+DIAYGRGALHGPSTAVEDAADFLDDPAGGRRH
+>LFPAFLNI_00726
+MNASFPAGAAAAPPPLAVARALELRHGSHVAVRPSDFTLPARRLIAVIGPNGSGKSTLLT
+ALAGLSDPASGALEVLGEDPRRRSQRTSFVMQSIGVPQGVPVTVRDVVGMGRYPTLGWFR
+RFRREDRDIVGAAMERMQVADLARRHLDQLSGGQRQRAYVAQGLAQDHDVLLLDEPMTGL
+DIVSARTIDDLLHEEPTRGVSVVYTTHDLDEAAEADHVVLMSGRVVASGPPRDVLTVENL
+DIAYGRGALHGPSTAVEDAAEFLDDPAGGIRH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000166.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000166.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08f6c8f6a04eef6787df9635c3d8c12a860ac994
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000166.fa
@@ -0,0 +1,60 @@
+>ACLBLIBL_02458
+MTVTAEREKALLESVPTGLLIDGEWRDASSGKTFDVKDPATGKVIASLQDANSDDAMAAF
+DAACAAQADWARTPAKERADILRRAYDLINERAEDFALLMTLEMGKPLAEARGEVTYGNG
+FLRWFSEEAGRHYGRTLTVPEGTLRMQVHHRPVGPCLLITPWNFPLAMATRKVGPAVAAG
+CTMVIKAAKLTPLTTQLFAQVMQEAGLPKGVLNVVAGSSASSISSPILQDRRLRKVSFTG
+STPVGVRLMKDAADNVLRTSMELGGNAPLIVFEDADLDAAVEGAFAAKMRNMGEACTAAN
+RFLVHEDVAEEFTQKFVAKLEALKPLRGTDPESTLGPIVDEGARDDIDQLVQDAVAAGGE
+VLTGGHKIEGDGYFYAPTAIKVEKGNPILQQEIFGPVAPIVTFSSEEEAIEMANDTEYGL
+ASYVFTKDQARMYRVAESIEFGLMGYNVGVISNPAAPFGGVKQSGLGREGGAEGIEEYTT
+VQYIGIADPWAAVKA
+>MOLHKGIG_00489
+MTVTAEREKALLESVPTGLLIDGEWRDASSGKTFDVKDPATGKVIASLQDANSDDAMAAF
+DAACAAQADWARTPAKERADILRRAYDLINERAEDFALLMTLEMGKPLAEARGEVTYGNG
+FLRWFSEEAGRHYGRTLTVPEGTLRMQVHHRPVGPCLLITPWNFPLAMATRKVGPAVAAG
+CTMVLKAAKLTPLTTQLFAQVMQEAGLPKGVLNVVAGSSASSISSPILQDRRLRKVSFTG
+STPVGVRLMKDAADNVLRTSMELGGNAPLIVFEDADLDAAVEGAFAAKMRNMGEACTAAN
+RFLVHEDVAEEFTQKFVAKLEALKPLRGTDPESTLGPIVDEGARDDIDQLVQDAVAAGGE
+VLTGGHKIEGDGYFYAPTAIKVEKGNPILQQEIFGPVAPIVTFSSEEEAIEMANDTEYGL
+ASYVFTKDQARMYRVAESIEFGLMGYNVGVISNPAAPFGGVKQSGLGREGGAEGIEEYTS
+VQYIGIADPWAATKA
+>NAFOICDF_02342
+MTVTAEREKALLESVPTGLLIDGEWRDASSGKTFDVKDPATGKVIASLQDANSDDAMAAF
+EAAVAAQADWARTPAQERADILRRAYDLINERAEDFALLMTLEMGKPLAEARGEVVYGNG
+FLRWFSEEATRHYGRTMIMPDGKLRMQVHHKPVGPSLLITPWNFPLAMATRKVGPAVAAG
+CTMVLKAAKLTPLTTQLFAQVMLEAGLPKGVLNVVSGSSASAISGPILEDPRLRKVSFTG
+STPVGVRLMQDAAKNVLRSSMELGGNAPLIVFEDADMDKAVDGAFAAKLRNMGEACTAAN
+RFLVHESVAEEFTRRFVERLEALKPLRGTDPESTLGPIVDEGARDDIHALIEEAVAAGGE
+ILTGGHKIEGDGYFYAPTALKVGKDNPILKKEIFGPVAPIVTFSTEEEAIQMANDTEYGL
+ASYVFTEDNARMHRVTEQIDFGIVGYNVGVVSNPAAPFGGVKQSGLGREGGAEGIAEYTT
+VQYIGIEDPFAGR
+>MHAAABBN_00210
+MTVTAEREKALLESVPTGLLIDGEWRDASSGKTFDVKDPATGKVIASLQDANSDDAMAAF
+DAACAAQADWARTPAKERADILRRAYDLINERAEDFALLMTLEMGKPLAEARGEVTYGNG
+FLRWFSEEAGRHYGRTLTVPEGTLRMQVHHRPVGPCLLITPWNFPLAMATRKVGPAVAAG
+CTMVLKAAKLTPLTTQLFAQVMQEAGLPKGVLNVVAGSSASSISSPILQDRRLRKVSFTG
+STPVGVRLMKDAADNVLRTSMELGGNAPLIVFEDADLDAAVEGAFAAKMRNMGEACTAAN
+RFLVHEDVAEEFTQKFVAKLEALKPLRGTDPESTLGPIVDEGARDDIDQLVQDAVAAGGE
+VLTGGHKIEGDGYFYAPTAIKVEKGNPILQQEIFGPVAPIVTFSSEEEAIEMANDTEYGL
+ASYVFTKDQARMYRVAESIEFGLMGYNVGVISNPAAPFGGVKQSGLGREGGAEGIEEYTS
+VQYIGIADPWAATKA
+>LFPAFLNI_00488
+MTVTAEREKALLESVPTGLLIDGEWRDASSGKTFDVKDPATGKVIASLQDANSDDAMAAF
+DAACAAQADWARTPAKERADILRRAYDLINERAEDFALLMTLEMGKPLAEARGEVTYGNG
+FLRWFSEEAGRHYGRTLTVPEGTLRMQVHHRPVGPCLLITPWNFPLAMATRKVGPAVAAG
+CTMVLKAAKLTPLTTQLFAQVMQEAGLPKGVLNVVAGSSASSISSPILQDRRLRKVSFTG
+STPVGVRLMKDAADNVLRTSMELGGNAPLIVFEDADLDAAVEGAFAAKMRNMGEACTAAN
+RFLVHEDVAEEFTQKFVAKLEALKPLRGTDPESTLGPIVDEGARDDIDQLVQDAVAAGGE
+VLTGGHKIEGDGYFYAPTAIKVEKGNPILQQEIFGPVAPIVTFSSEEEAIEMANDTEYGL
+ASYVFTKDQARMYRVAESIEFGLMGYNVGVISNPAAPFGGVKQSGLGREGGAEGIEEYTS
+VQYIGIADPWAAAKA
+>LFPAFLNI_01553
+MTPTPDPTATQYIDGAWVPSSDGGTRTIHCPADGSEVGVVAEGTREDALAAIAAARRAFD
+SGEWSSTPAAERGDLLIRLADHILEHRDEFARAEALDTGKRLVEAEGDMADIAACFRYFG
+KIADQNPGRLVDAGDPTVLSRVVTEPVGVCGMITPWNFPLLQAAWKIAPALAAGCTFVLK
+PAEQTPHTAILTMRALESLGLPAGVANLVLGPGATVGEPLSSHPDVDLVSFTGGLATGKT
+IAQAAAGTVKKVALELGGKNPNVIFPDAHYEAALDNALNAAFTDSGLVCSAGTRLIVHES
+IAERFVDDLVERAGHIVMGGPFDEHAETGPLISAAHRDKVTDYVRRGVEAGARLRVGGHW
+GGEEHKDGFFYAPTVLDRCDRDNPAVIEEGFGPVITVETFSTEAEAIEIANHTEYGLAGA
+VWSSDAGTCQRVSRALRHGTVWINDYHPYLPQAEWGGFKASGIGRELGPTGLGEYVEHKH
+IYQNTEPAVTGWFADRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000167.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000167.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fca61b2eb7805d3631070d2a1f48d371c1069cb1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000167.fa
@@ -0,0 +1,54 @@
+>ACLBLIBL_02509
+MALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAAVPSGASTGEFEAVERRDGDTKRYL
+GKGVLDAVAAVEEIADELEDEFAVDQRAVDRLMLDLDGTPNKGKLGANAILGVSMAVAAA
+AAQSSDLMLYKYLGGPNAHVLPVPMMNILNGGAHADSNVDIQEFMIAPIGAPSFREALRW
+GTEVYHSLKKVLQEKGLSTGLGDEGGFAPSLESNRAALDLIAEAVEKAGYTLGEDIALAL
+DVASSEFCEKGAYTFEGQKRSAEDMVAYYTELADNYPIVSIEDPLDENDWDGWRLLTEKL
+GDRVQLVGDDLFVTNVERLQRGIDDKAGNALLVKVNQIGSLTETFDAIALAQRHMFHCMI
+SHRSGETEDTFIADLAVATNAGQIKTGAPARSDRVAKYNQLLRIEEDLADAAVYAGRSAF
+PRYRG
+>MOLHKGIG_00448
+MALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAAVPSGASTGEFEAVERRDGDKKRYG
+GKGVLDAVAAVEGIAEELEGEFAADQRAVDRAMRDLDGTPNKGKLGANAILGVSMAVAVA
+AAQASDLMLYKYLGGPNAHVLPVPMMNILNGGAHADSNVDIQEFMIAPIGAPSFREALRW
+GTEVYHALKTVLQEKGLSTGLGDEGGFAPSLESNRAALDLIAEAVTKAGYRLGEDIALAL
+DVASSEFFDNGSYTFEGQQRSAEEMAAYYTELVDNYPIVSIEDPLDEDDWDGWQHLTAQL
+GDRVQLVGDDLFVTNVERLQRGIDEKAGNALLVKVNQIGSLTETFDAIALAQRHMFHCMI
+SHRSGETEDTFIADLAVATNAGQIKTGAPARSDRVAKYNQLLRIEEDLADAAVYAGRSAF
+PRFRG
+>NAFOICDF_00683
+MNDYISGIHHHGAHQGEYVTHHDHPVTIDAVHGARILDSRGYPTVRVSLELDDGRTVTGD
+APAGASTGAHEAVELRDGGSAFGGRDVTQALHLIDTDISGLLTGRSWSAIGQIDAALAEL
+DGTTGYRRLGANSVVATSIAASRALAHAADLPLWQWIAEITGSTPRMPVPHFNVLNGGAH
+AANELDFQEFMIAPVNAGSMADAVRIGADVYHALAALVRDRFGSLGLGDEGGFAPSIAAP
+EEALDLLVDAIRTAGYEPGVDQVAIALDPAANEFSQGDGSYRVLNDSLDRDGLVDYYRHL
+IDTYPIRSIEDAFAEDDHEGFRRMQAALGDRIQIVGDDLYVTDPQRIRDGGEQQLTNAAL
+IKPNQIGTVSQTLGAIATAKSIGMASMVSHRSGETTDTFIADLVVGTGTGQIKSGAPGRG
+ERVAKYNRLTEIAEQHPELPYGLI
+>NAFOICDF_02380
+MAQIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAAVPSGASTGEFEAVERRDGDTERYL
+GKGVQDAVNAVFEIAEELEDELATDQRAVDQMMLDMDGTENKGKLGANAILGVSMAVAVA
+AADSADLPLYKYLGGPNAHVLPVPMMNILNGGAHADSNVDIQEFMIAPIGAPSFREALRM
+GAEVYHSLKKVLQEKGLSTGLGDEGGFAPNLESNRAALDLIAEAVQKAGYTLGEDVALAL
+DVASSEFCENGSYTFEGRQRSAEEMSAYYAELVDAYPIVSIEDPLDENDWEGWEHLTEQL
+GDRVQLVGDDLFVTNVARLQRGIDEKAGNALLVKVNQIGSLTETFDAIALAQRHMFHCMI
+SHRSGETEDTFIADLAVATNAGQIKTGAPARSDRVAKYNQLLRIEEDLADAAVYAGRSAF
+PRFQG
+>MHAAABBN_00169
+MALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAAVPSGASTGEFEAVERRDGDKKRYG
+GKGVLDAVAAVEGIAEELEGEFAADQRAVDRAMRDLDGTPNKGKLGANAILGVSMAVAVA
+AAQASDLMLYKYLGGPNAHVLPVPMMNILNGGAHADSNVDIQEFMIAPIGAPSFREALRW
+GTEVYHALKTVLQEKGLSTGLGDEGGFAPSLESNRAALDLIAEAVTKAGYRLGEDIALAL
+DVASSEFFDNGSYTFEGQQRSAEEMAAYYTELVDNYPIVSIEDPLDEDDWDGWQHLTAQL
+GDRVQLVGDDLFVTNVERLQRGIDEKAGNALLVKVNQIGSLTETFDAISLAQRHMFHCMI
+SHRSGETEDTFIADLAVATNAGQIKTGAPARSDRVAKYNQLLRIEEDLADAAVYAGRSAF
+PRFRG
+>LFPAFLNI_00451
+MALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAAVPSGASTGEFEAVERRDGDKKRYG
+GKGVLDAVAAVEGIAEELEGEFAADQRAVDRAMRDLDGTPNKGKLGANAILGVSMAVAVA
+AAQASDLMLYKYLGGPNAHVLPVPMMNILNGGAHADSNVDIQEFMIAPIGAPSFREALRW
+GTEVYHALKTVLQEKGLSTGLGDEGGFAPSLESNRAALDLIAEAVTKAGYRLGEDIALAL
+DVASSEFFDNGSYTFEGQQRSAEEMAAYYTELVDNYPIVSIEDPLDEDDWDGWQHLTAQL
+GDRVQLVGDDLFVTNVERLQRGIDEKAGNALLVKVNQIGSLTETFDAIALAQRHMFHCMI
+SHRSGETEDTFIADLAVATNAGQIKTGAPARSDRVAKYNQLLRIEEDLDDAAVYAGRSAF
+PRFRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000169.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000169.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aba29dff97e06e53130fdc030b3361f93cde785f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000169.fa
@@ -0,0 +1,54 @@
+>ACLBLIBL_02541
+MPTDAEPAADDTEGAALPVQDATRADAVRPGTARTDASAGDSKLAQAGAAAGTVLETVRD
+KVAIPLRDNVAIPAKDKAVKVLKAKLAEAQERRRNKR
+>ACLBLIBL_02542
+MGESTLYWIIGAIIVVLLILIILSVVASRRRRAAEAEAAEAQLERRRVTPTAAGVGASHE
+DALEETHDADARPHTVASTGGDVAPAAAAGAAAGTTRLSQLDDVAPVAAAAADADAESLP
+ADGVAAGSGVTVDQQDASDQSVRPAAPAAPAGADTRGPNASVKSAGAAAAAVGLGAAGVA
+GGRGVTVDQQDAAADVPSTPASPSPVAQTPAAPSSAGATTAQDDRADRTAQDAADAEPVK
+GTVPLSEDAHAVPPAADPPSGGDAVADDAHLEAHTVATTEHGSVVVVTAEQDEDDQATAA
+SRETETETDDSRGDDAGQDRDAERAVAEGVAGGTGVTVDQKAVAEAAATQGAPASAAGAA
+SAAGAAARRRDRGRRLDPACGGARLLQDRRHAGHARPRRLRGAGRGRGGDRPARPPRRRP
+GDARLHHPRDAPGRRAGAGPGRRRRGLPQGRGRDPAAPPRGRRPGAKPRRRPTSTRPRPR
+PPRRTAPAR
+>MOLHKGIG_00418
+MPESTLYWIIAAIIVVLLILIILSVIASRRRREAEAEAAETRLERRGTTADTADTAGEQA
+AAPAAPTRLSRLDEVAAEQDARPAAAVKPAGGPAASETAAAGRETDESVAGVAGGAGVTV
+DQQDAPRTDATAETSRPTAAPTTRGTLRPAAAAPSTAREADTVGLGAAGVAGGSGITLDE
+QTPAADVAAAPASPSPVTETPAPAAPAAEAPQHRSHLTPAPEHVHGTVPAEEVAAEHTPT
+KEFATDAIPVAQGEHLETNTVATTAHGSVTVVAAESDQTQQNDADGAERSAAGSLRIDGT
+PGVPGRVAEAGREPARTEDHRADAAQPAAVEPAAERPSLEAAAERPSLEATPATRRAEAP
+ETHAGTTPATPLGGAPELDPTAASSGRAEDATPATRREARAAQSAAAAGTAATAGTAGTA
+APTSSTPTTVAPDTSTSSAPTNEEPAEDDTEGAALPDLRADRDETRGSDAEGESKLAQAG
+AVAASAFETVRDKVAIPLRDNVAVPAKDKAVKVVKDKLAQAQERRWGKR
+>NAFOICDF_02410
+MPQSTLYWIIGIIIVVLVIILIVSSLRAKRGREEEAAAAGRHADSAPAPLAATAARGGTV
+GASTVPATGDAPADRTDGRAAGATALPSFDVDEVDRRAAEQREQDVVERRRATGAEAGAA
+GHAAVPGVTGGSGVSVDEAEGVAKDATGQDVTPVADAQRRNGSSAAPAATGAGLGLAAAG
+VAGGTGVTVDDAGTGADLPAPKGSPAGVVEVAETQAEAAQADAAPAEHTVVPGVAGGDAV
+TVDTADVQSSSAPQGAQAAAGRSDLTDAEARTYPVTGLPGVPSAVDPEQVAAARVQDAAE
+LKAAEGQGAEHERGASQPADPESVPGTVPLTGEEAVIEAPVHTHEMPEPVLGTPAYIQDS
+TTGQDPTEDLPEGQVYGTTPLSGEDAIVEPADQLPAEAAETEDRAASDAGTASAETAVVP
+VEETETAVVPVAETRSADAGPSEDSVALTGQGVETADRVEPAAPVAGTPARDEARTHDEH
+RSRLEIVKDAVAETAGTVATTAGTAAEKAAPVVRSAARTVGKAAGSAASTLKDKLAQAQE
+RRWGKR
+>MHAAABBN_00139
+MPQSTLYWIIAAIIVVLLILIIVSVIASRRRREAEAEAAETRLERRGVSADTAGEQAAAP
+AAPTRLSRLDEVAAEKDARPAPAVRPAGGLAAFDTAAADRETDESGAGVAGGAGVTVDQQ
+DAPSTEATAQTHRRDAAAPATRGTLRPAPAVPSTVREADTVGLGAAGVAGGSGVTLDEQT
+PAADVPATPASPSPVTETPAPAAPVAEAPQQRSHLTPAPEHVHGTVPADEVAAEHTPTKE
+FATDGIPVPQGEHLETHTVATTAHGSVTVVATESDQAQQTGVDGTERSAAGSLRIDGTPG
+VPGRVAEADREPARTDDHGADVAQPAAVEPAAERPPLEAAPATRRAEAPETHAGTTPATP
+LGGAPELDPTAASSGRAEDATPATRREARAAQSAAAAGTAGTAAPTSSTPTTVAPDTSTS
+SAPTDEEPAEDDTEGAALPDLRADRDETRASDAEGESKLAQAGAVAASAFETVRDKVAVP
+LRDNVAVPAKDKVVKVVKDKLSQAQERRWGKR
+>LFPAFLNI_00421
+MPESTLYWIIAAIIVVLLILIILSVIASRRRREAEAEAAETRLERRGTTADTADTAGEQA
+AAPAAPTRLSRLDEVAAEQDARPAAAVKPAGGPAASETAAAGRETDESVAGVAGGAGVTV
+DQQDAPRTDATAETSRPTAAPTTRGTLRPAAAAPSTAREADTVGLGAAGVAGGSGITLDE
+QTPAADVAAAPASPSPVTETPAPAAPAAEAPQHRSHLTPAPEHVHGTVPAEEVAAEHTPT
+KEFATDAIPVAQGEHLETNTVATTAHGSVTVVAAESDQTRQNDADGAERSAAGSLRIDGT
+PGVPGRVAEAGREPARTEDHRADAAQPAAVEPAAERPSLEAAAERPSLEATPATRRAEAP
+ETHAGTTPATPLGGAPELDPTAASSGRAEDATPATRREARAAQSAAAAGTAATAGTAGTA
+APTSSTPTTVAPDTSTSSAPTNEEPAEDDTEGAALPDLRADRDETRGSDAEGESKLAQAG
+AVAASAFETVRDKVAIPLRDNVAVPAKDKAVKVVKDKLAQAQERRWGKR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000170.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000170.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b8f81576b02468b0ddc3aee190b9d7a5ed824103
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000170.fa
@@ -0,0 +1,42 @@
+>ACLBLIBL_02547
+MSHVDTAPAASTPRTAEGRRPRRVKSQRAKSEARLGWLLAGPAFFVMLFVVMYPILQALY
+DSLFKYRLTAPDDREFVGLGNYGVILSDPVFWKDLGVTLLITVVTVVVELILGFLLALAM
+HHAIKQTRGLIRTIILVPYGIITVVSAFAWFYMFSIDSGYINAWFEWLPGVDADLNWFAQ
+SNTALSVIMLSEIWKTTPFISLLLLAGLAQVPGDLTEAAAVDGASWWQRMKLVILPNMKA
+SIMVAVLFRAMDAFRIFDSIYIMTNGAYGTEVLSLLAYRTSIGRLEIGMGSAVSVILFLC
+VALMAVIAVKGFKVDLADRGGSK
+>ACLBLIBL_02646
+MFTEVLPQQQVAPRPEAATAEPGIAESGIAESRTATDAPRPAKQKSRRTGRSFSIVPYLY
+VLPAVALLLLWTYLPLAQTFELSFYDWNLLPTKAKEPVGLENYATVLTLPEMQQALGNTV
+LYIGAFFLLSVALPVIFALLSKRVSGRAKTIYQALIFVPYLVTPVATSAIWRWLFAEEGG
+TIPAVAHFFGIDMGNVFREPGASMIAVMVIVGWQLLGFGVLVVSAGLSGISPDYEHAAGV
+DGARRWQITSRITLPLLSPSLVFLSLMTILLSAQWTFPMIDIITQGGPSGSSTNIYYLLY
+EFGFKNFDAGISAAAGVLFFIGFGLIALVFVELSEKLSFHDN
+>MOLHKGIG_00412
+MSHVDTAPAASTPRAAEGRRPRRVKSQRAKSEARLGWLLAGPAFFVMLFVVLYPILQALY
+DSLFKYRLTAPGDREFVGLGNYGVILTDPVFWKGLGVTLLITVVTVVVELILGFLLALAM
+HHAIKQTRGLIRTIILVPYGIITVVSAFAWFYMFSIDSGYINAWFEWLPGVDADLNWFAQ
+GSTALFVIMLSEIWKTTPFISLLLLAGLAQVPGDLTEAASVDGASWWQRMKLVILPNMKA
+SIMVAVLFRAMDAFRIFDSIYIMTNGAYGTEVLSLLAYRTSIGRLEIGMGSAVSVILFLC
+VALMAVIAVKGFKVDLADRGGSK
+>NAFOICDF_02415
+MSHVDTAPAASTPRAAEGRRPRRVKSARAKSEARLGWLLAGPAFFIMLFVVLYPTVQAFY
+DSLFKYRLTAPQDREFVGLGNYGVILSDPVFWKDLGVTVLITLVTVLVELVLGFLLALAM
+HHAIKQTRGLIRTIILVPYGIITVVSAFAWFYMFSIDSGFVNNWFDWVPGITSDLNWFAQ
+SGTALSVIMLSEIWKTTPFISLLLLAGLAQVPGDLTEAAAVDGASWWQRMKLVILPNMKA
+SIMVAVLFRAMDAFRIFDSIYIMTNGAYGTEVLSLLAYRTSIGRLEIGMGSAISVILFLC
+VALMAFTAVKVFKVDLADRGGSK
+>MHAAABBN_00132
+MSHVDTAPAASTPRAAEGRRPRRVKSQRAKSEARLGWLLAGPAFFVMLFVVLYPILQALY
+DSLFTYRLTAPGDREFVGLGNYGVILTDPVFWKGLGVTLLITVVTVVVELILGFLLALAM
+HHAIKQTRGLIRTIILVPYGIITVVSAFAWFYMFSIDSGYINAWFEWLPGVDADLNWFAQ
+GSTALFVIMLSEIWKTTPFISLLLLAGLAQVPGDLTEAASVDGASWWQRMKLVILPNMKA
+SIMVAVLFRAMDAFRIFDSIYIMTNGAYGTEVLSLLAYRTSIGRLEIGMGSAVSVILFLC
+VALMAVIAVKGFKVDLADRGGSK
+>LFPAFLNI_00415
+MSHVDTAPAASTPRAAEGRRPRRVKSQRAKSEARLGWLLAGPAFFVMLFVVLYPILQALY
+DSLFKYRLTAPGDREFVGLGNYGVILTDPVFWKGLGVTLLITVVTVVVELILGFLLALAM
+HHAIKQTRGLIRTIILVPYGIITVVSAFAWFYMFSIDSGYINAWFEWLPGVDADLNWFAQ
+GSTALFVIMLSEIWKTTPFISLLLLAGLAQVPGDLTEAASVDGASWWQRMKLVILPNMKA
+SIMVAVLFRAMDAFRIFDSIYIMTNGAYGTEVLSLLAYRTSIGRLEIGMGSAVSVILFLC
+VALMAVIAVKGFKVDLADRGGSK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000174.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000174.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd24b4f15222e84ce27d08d8cb123370ad6aa66f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000174.fa
@@ -0,0 +1,69 @@
+>ACLBLIBL_00004
+MLGAHPHPDGAAVTYRVLRPLARTVTVVRTGDGERVELAHEHDGVFAGVARMPRVAGAAA
+GDYRLEVAYETADGQTGPAQEQDDAYRHLPTLGELDLHLIGEGRHERLWEVLGARVVRTP
+AGEAVGTAFAVWAPNARAVRVVGEHNGWDGRGHAMRSLGSSGVWELLVPGVGHGHRYKFE
+ILGRDGRWRQKADPMARWTEVPPATASRVLESEYEFGDRTWMERRRTVDPHERPLSIYEV
+HLGSWRPGLDYRELAEQLVEYVQWLGFTHVEFLPVAEHPFGGSWGYQVTGYYAPTSRFGS
+PDEFKHLVDALHRAGIGVIVDWVPAHFPKDEWALARFDGTPLYEHADPRRGEHPDWGTYV
+FDFGRTEVRNFLVANALYWLAEFHIDGLRVDAVASMLYLDYSREDGQWEPNVHGGNHNLE
+AIDFLREVNATVYRVHPGVHMIAEESTAFSGVSAPVDAGGLGFGKKWNMGWMHDTLAYLS
+QDPVNRRWHHGQWTFSMVYAYSENYVLPLSHDEVVHGKGSLLTRIPGDRRHQLATLRAYY
+GYMWAHPGKQLLFMGGEYGQPSEWSEAEGLDWPVSWDESHRGVQLTVRELNALYRSKPAL
+WSQDHSPAGFEWVDGGDADGNTLVFLRHPAERVVPEARIDDDGAAVSAAEPGGAPLLCIT
+NLSGSPRQGLRVGVPGAGSGPWSWTPTPPTSTGTAGGSRPGSPRC
+>MOLHKGIG_00331
+MTPSAAPRPAVAPLAVDPEVLAAVAQGRHHDPHTVLGAHPHPDGAAVTYRVLRPLARTVT
+VVRAGDGQRVELTHEHDGVFAGVAPTPRVAGAAAGDYRVEVAYETEDGTTGPVQEQDDAY
+RHLPTLGELDLHLIGEGRHERLWEVLGARVVRTSADEAVGTAFAVWAPNARAVRVVGDHN
+GWDGRTHAMRSLGSSGVWELLAPGVGHGDRYKFEILGRDGLWRQKADPMARWTEVPPATA
+SRVLESDYAFGDRTWMERRRVTDPHERPLSIYEVHLGSWRPGLDYRELAEQLVEYVQWLG
+FTHVEFLPVAEHPFGGSWGYQVTGYYAPTSRFGSPDEFKHLVDALHQAGIGVIVDWVPAH
+FPKDEWALARFDGTALYEHPDPRRGEHPDWGTLVFDFGRTEVRNFLVANALYWLGEFHID
+GLRVDAVASMLYLDYSREDGQWEPNVHGGNHNLEAIDFLREVNMTVYRLHPGVHMIAEES
+TAFSGVTAPVDAGGLGFGKKWNMGWMHDTLAYLSQDPVNRRWHHGQWTFSMVYAYSENYV
+LPLSHDEVVHGKGSLLSRIPGDRRQQLATLRAYYGYMWAHPGKQLLFMGGEYAQPSEWSE
+GEGLDWPVSWDEAHRGVQLTIRELNALYRSKPALWSLDHSPEGFAWVDGGDADGNTLVFL
+RMPAAQVVPEPRIDDDGDAVPAAEPGGAPLLCITNLSGSPRQGLRVGVPSAGEWTVVLDT
+DSTDFHGDGWREQTGQSEVIAAHEGQWQGQPAHVTVNVPALTTLWLQPHPDSTVTP
+>NAFOICDF_00005
+MTSPTLSPQSVDPAVLAAVAEGLHHDPHAVLGAHPHPDGAAVTYRALRPFARAVTVVREG
+DAARIELAHEADGVFAGVGALPRKAGVAAGDYRLEVVYPGADGEDVVELHDDAYRHLPTL
+GELDLHLIGEGRHERLWEVLGARVRRAADGALVGTSFAVWAPNARAVRVVGDFNGWTGRT
+HAMRSLGSSGVWELLVPGVEHGAAYKFEILGADGQWQQNADPMARWTEVPPATASRVMES
+EFAFTDRDWMERRRAEDPHERPLSIYEVHLGSWRPGLSYVDLAEQLVEYVQWLGFTHVEF
+LPVAEHPFGGSWGYQVTGYYAPTSRFGSPDEFKHLVNALHEAGIGVIVDWVPAHFPKDAW
+ALGRFDGTALYEHPDPRRGEHPDWGTYVFNFGRTEVRNFLVANALYWLGEFHVDGLRVDA
+VASMLYLDYSREDGQWTPNALGGNHDLEAISFLQDVNATVYRVHPGILMIAEESTAFSGV
+SAPVSAGGLGFGKKWNMGWMHDTLAYLSEDPVNRRWHHDQWTFSMAYAYSENYVLPLSHD
+EVVHGKGSLLARIPGDHRQKLATLRAYFAYMWAHPGKQLLFMGGEYGQPSEWSEERGLDW
+AASWDESHRGVQLTVRELNALYRAKPALWSADHSPQGFTWVDGGDADGNTLVFLRRPGAG
+VEGAPLLCITNLSGGTRQGLRVGVPSSGEWTVVLDTDSTDFHGDGRREQAGQLEVIEAED
+GQWQGQPAYLTLNVPPLTTLWLQPDED
+>MHAAABBN_00047
+MTPSAAPRPAVAPLAVDPEVLAAVAQGRHHDPHTVLGAHPHPDGAAVTYRVLRPLARTVT
+VVRAGDGQRVELTHEHDGVFAGVAPTPRVAGAAAGDYRVEVAYETEDGTTGPVQEQDDAY
+RHLPTLGELDLHLIGEGRHERLWEVLGARVVRTSAGEAVGTAFAVWAPNARAVRVVGDHN
+GWDGRTHAMRSLGSSGVWELLVPGVGHGDRYKFEILGRDGLWRQKADPMARWTEVPPATA
+SRVLESDYAFGDRTWMERRRLTDPHERPLSIYEVHLGSWRPGLDYRELAEQLVEYVQWLG
+FTHVEFLPVAEHPFGGSWGYQVTGYYAPTSRFGSPDEFKHLVDALHRAGIGVIVDWVPAH
+FPKDEWALARFDGTALYEHPDPRRGEHPDWGTLVFDFGRTEVRNFLVANALYWLGEFHID
+GLRVDAVASMLYLDYSREDGQWEPNVHGGNHNLEAIDFLREVNATVYRLHPGVHMIAEES
+TAFSGVSAPVDAGGLGFGKKWNMGWMHDTLAYLSQDPVNRRWHHEQWTFSLVYAYSENYV
+LPLSHDEVVHGKGSLLGRIPGDRRQQLATLRAYYGYMWAHPGKQLLFMGGEYAQPSEWSE
+GEGLDWPVSWDEAHRGVQLTIRELNALYRSKPALWSLDHSPEGFAWVDGGDADGNTLVFL
+RMPAAQVVPETRIDDDGAAVPAAEPGGAPLLCITNLSGSPRQGLRVGVPSAGEWTVVLDT
+DATDFHGDGWREQTGQSEVIAAHEGQWQGQPAHVTVNVPALTTLWLQPTLDTTATP
+>LFPAFLNI_00338
+MTPSAAPRPAVAPLAVDPEVLAAVAQGRHHDPHTVLGAHPHPDGAAVTYRVLRPLARTVT
+VVRAGDGQRVELMHEHDGVFAGVAPTPRVAGAAAGDYRVEVAYETEDGTTGPVQEQDDAY
+RHLPTLGELDLHLIGEGRHERLWEVLGARVVRTSADEAVGTAFAVWAPNARAVRVVGDHN
+GWDGRTHAMRSLGSSGVWELLAPGVGHGDRYKFEILGRDGLWRQKADPMARWTEVPPATA
+SRVLESDYAFGDRTWMERRRVTDPHERPLSIYEVHLGSWRPGLDYRELAEQLVEYVQWLG
+FTHVEFLPVAEHPFGGSWGYQVTGYYAPTSRFGSPDEFKHLVDALHRAGIGVIVDWVPAH
+FPKDEWALARFDGTALYEHPDPRRGEHPDWGTLVFDFGRTEVRNFLVANALYWLGEFHID
+GLRVDAVASMLYLDYSREDGQWEPNVHGGNHNLEAIDFLREVNATVYRLHPGVHMIAEES
+TAFSGVSAPVDAGGLGFGKKWNMGWMHDTLAYLSQDPVNRRWHHGQWTFSMAYAYSENYV
+LPLSHDEVVHGKGSLLGRIPGDRRQQLATLRAYYGYMWAHPGKQLLFMGGEYAQPSEWSE
+GEGLDWPVSWDEAHRGVQLTIRELNALYRSKPALWSLDHSPEGFSWVDGGDADGNTLVFL
+RMPAAQVVPEPRIDDDGAAVPAAEPGGAPLLCITNLSGSPRQGLRVGVPSAGEWTVVLDT
+DATDFHGDGWREQTGQSEVIAAHEGQWQGQPAHVTVNVPALTTLWLQPTLDTASTP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000178.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000178.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ea70f0a50f87db30570711216fa8a10758f50d4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000178.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_00012
+MAQRFYDTRTAQIRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDVLIRWLEATGL
+RVTSVRNVTDIDDKILDRSAASHEEGFEPSALYPAREPWWALAYRFEKAFDAAYLALGVR
+RPTYEPRATGHVPEMFALIERLVERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ
+DAPDADPRGKRDPRDFALWKGAKEGEPATAVWTSPWGAGRPGWHLECSAMATKYLGAQFD
+IHGGGLDLRFPHHENELAQSAAAGDGFARFWLHNGLVAYGGEKMSKSVGNTISPEEMLGM
+ARPKAVRYFLGQAHYRSQLDYRPGALEEAEAAVERIENFTARARTAGAVPPAVDGALADR
+VPAAFRAAMEDDLNVPQALAALHEAVRAGNSALAAQDLESAAARLTEVEAMTAVLGLDDV
+PEGDGDGTGPAADALDSLVRSQIEARAQARAEKDWAAADRIRDALAAAGVVVEDGADGAT
+WRLAD
+>MOLHKGIG_00325
+MAQRFYDTRTAQVRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDILIRWLEATGL
+RVTSVRNVTDIDDKILERSAASHEAGFEASDLYPAREPWWALAYRFEKAFDAAYLALGVR
+RPTYEPRATGHVPEMFALIERLMERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ
+DAPDADPRGKRDPRDFALWKGAKPGEPATAVWESPWGAGRPGWHLECSAMSTKYLGTEFD
+IHGGGLDLRFPHHENELAQSAAAGDGFARLWLHNGLVTYGGEKMSKSVGNTISPEEMLGM
+ARPTAVRYFLGQAHYRSQLDYRPGALDEAEAAVERIEGFTARARAAGAVPPAPDGALADR
+VPAAFRAAMEDDLNVPQALAALHEAVRAGNSALAGQDLDAAAARLAEVEAMTAVLGLDDV
+PEGDDAAAGPVSDALDSLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGADGAT
+WRLAD
+>NAFOICDF_00008
+MAQRFYDTRSAEIRDFVPLVPGQASVYYCGATVQGMPHVGHVRSAIVFDVLIRWLEATGL
+RVTSVRNVTDIDDKILDRSAASQEPGFEPSEMYPADEPWWALAFRFENAFDAAYLALGVR
+RPTYEPRATGHVPEMLALIERLIERGHAYPAADGSGDVYFDVRSWDRYGELTRQRVEDMQ
+DAPDADPRGKRDPRDFALWKGAKEGEPVTAVWSSPWGAGRPGWHLECSAMSTKYLGGEFD
+VHGGGLDLRFPHHENELAQSAAAGDPFARFWLHNGLVTYQGEKMSKSVGNTISPQEMLAM
+ARPKAVRYFLGQAHYRSQLDYRPGALEEAEAAVERIENFVQRAAAALGAPELTAPLAEHV
+PAAFRAAMEDDLAVPQALAVLHEAVRAGNSALAAGDDAAARARLAEVAAMTAVLGLDDVP
+EASAGGSGPEAAALDSLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGAQGATW
+HLAG
+>MHAAABBN_00040
+MAQRFYDTRTAQVRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDILIRWLEATGL
+RVTSVRNVTDIDDKILERSAASYEAGFEASDLYPAREPWWGLAYRFEKAFDAAYLALGVR
+RPTYEPRATGHVPEMFALIERLMERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ
+DAPDADPRGKRDPRDFALWKGAKPGEPATAVWESPWGAGRPGWHLECSAMSTKYLGTEFD
+IHGGGLDLRFPHHENELAQSAAAGDGFARFWLHNGLVTYGGEKMSKSVGNTISPEEMLGM
+ARPTAVRYFLGQAHYRSQLDYRPGALDEAEAAVERIEGFTARARAAGAVPPAPDGALADR
+VPAAFRAAMEDDLNVPQALAALHEAVRAGNSALAGQDLDAAAARLAEVEAMTAVLGLDDV
+PEGDDAAAGPVSDALDSLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGADGAT
+WRLAD
+>LFPAFLNI_00332
+MAQRFYDTRTAQIRDFEPLVPGEASVYYCGATVQGMPHVGHVRSAIVFDILIRWLEATGL
+RVTSVRNVTDIDDKILDRSAASHEAGFEASDLYPAREPWWALAYRFERAFDAAYLALGVR
+RPTYEPRATGHVPEMFALIERLIERGHAYPAQDGSGDVYFDVRSWERYGELTRQRVEDMQ
+DAPDADPRGKRDPRDFALWKGAKPGEPATAVWESPWGAGRPGWHLECSAMSTKYLGAEFD
+IHGGGLDLRFPHHENELAQSAAAGDGFARFWLHNGLVTYGGEKMSKSVGNTISPEEMLGM
+ARPTAVRYFLGQAHYRSQLDYRPGALDEAEAAVERIEGFTARARAAGAVPPAPDGALADR
+VPAAFRTAMEDDLNVPQALAALHEAVRAGNSALAGQDLDAAAARLAEVEAMTAVLGLDDV
+PEGDDAAAGPVSDALDLLVRSQIEARAQARADKDWATADRIRDALAAAGVVVEDGADGAT
+WRLAD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000180.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000180.fa
new file mode 100644
index 0000000000000000000000000000000000000000..caab701df11c3c21491f18077aee64db14b2f238
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000180.fa
@@ -0,0 +1,21 @@
+>ACLBLIBL_00014
+MVFEVGETVVYPHHGAARIEEIKMRTIKGEEKMYLKLKVAQGDLTIEVPAENVDLVGVRD
+VVDSEGLEEVVEVLQAEQVEEPTNWSRRYKANLEKLASGDVKKVAEVVRDLWRRDQDRGL
+SAGEKRMLSKARQVLVSELALAKKVTEEEAEGMLDQVLEG
+>MOLHKGIG_00323
+MVFEVGETVVYPHHGAARIEEIKMRTIKGEEKMYLKLKVAQGDLTIEVPAENVDLVGVRD
+VVDAEGLEHVMEVLRAEHVEEPTNWSRRYKANLEKLASGDVNKVAEVVRDLWRRDQDRGL
+SAGEKRMLAKARQVLVSELALAKKVTEEEAEGRLDKVLEG
+>NAFOICDF_00010
+MPDTRGVFRVSVVESTDRKGAFHMVFEVGETVVYPHHGAARIEEIKTRTIKGEEKMYLKL
+KVAQGDLTIEVPAENVDLVGVRDVVDDKGLEHVVEVLQAEHVEEPTNWSRRYKANLEKLA
+SGDVNKVSEVVRDLWRRDHDRGLSAGEKRMLSKARQVLVSELALAKKVSEEEAEGMLDKV
+LEG
+>MHAAABBN_00038
+MVFEVGETVVYPHHGAARIEEIKMRTIKGEEKMYLKLKVAQGDLTIEVPAENVDLVGVRD
+VVDAEGLEHVMEVLRAEHVEEPTNWSRRYKANLEKLASGDVNKVAEVVRDLWRRDQDRGL
+SAGEKRMLAKARQVLVSELALAKKVTEEEAEGRLDKVLEG
+>LFPAFLNI_00330
+MVFEVGETVVYPHHGAARIEEIKMRTIKGEEKMYLKLKVAQGDLTIEVPAENVDLVGVRD
+VVDAEGLEHVMEVLRAEHVEEPTNWSRRYKANLEKLASGDVNKVAEVVRDLWRRDQDRGL
+SAGEKRMLSKARQVLVSELALAKKVTEEEAEGRLDKVLEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000183.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000183.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a9f230794863115b2d221cecaaa3b0099baf102c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000183.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00017
+MDPVIIGLLCGAVGLFIGVASMLAFRASERSRTVDLAVGEPTLAPGAAEVLAVVGRAYAV
+VDDVDGVVRANPSAYALGLVRGHSLVQQQVKDLTRSVRAEGVIVERRLELPRGPLGQSSL
+VVELRVAPLDEEYILILADDRTDVTRTEAMRHDFVVNVSHELKTPVGAISLLAEAIGDAA
+EDEEAVRRFASRLGIESRRLTALVQDIIEFSRLQAKDVVQDGRAVDLNAVVADAVDRLRL
+TAEDRGITLRVGGRVDAVVHGDADQLMTAVRNLVDNAVRYSPEGTTVGIGLSSADGLAQV
+TVTDQGIGISPEEQERVFERFYRVDSARSRQTGGTGLGLSIVKHVVINHGGEVSLWSQPG
+RGSTFTIRLPEWEDDGAAVDGPPAASHVTERRGHRVTASAASPPRKESSA
+>MOLHKGIG_00320
+MDPVIIGLLCGAVGLFTGVASMLAFRASERSRTVDLTVGEPTLAPGAAEVLSVVGRAYAV
+VDDVDGVVRANPAAYALGLVRGHSLVQDQLRELTRTVRADGVIVERRMELPRGPLGQSSL
+VVELRVAPLDEEYILILADDRTDVTRTEAMRHDFVVNVSHELKTPVGAISLLSEAIGDAA
+EDEEAVRRFAARLGVESRRLSALVQDIIEFSRLQAKDVVQDGGPVDLNAVVADAVDRLRL
+TAEDRGIALRVGGRVDAVVHGDQDQLMTAVRNLVDNAVRYSPEGTTVGIGLSSVDGLAQV
+TVTDQGIGISPEEQERVFERFYRVDAARSRQTGGTGLGLSIVKHVVINHGGEVTLWSQPG
+RGSTFTIRLPEWGDGVAVDGAPGAAHVTERRGHRVTASAAPPTRKETSA
+>NAFOICDF_00013
+MDPVIIGLLCGAVGLLIGVASMLAFRASERSRTVDLSVEEPTLSPGAAEVLSVIGRSYIV
+VDAVDGVVRANPSAYAMGLVRGHTLVPDALRELTGAVRADGVVRERQVDLPRDPRHQSSL
+VVELRVAPLDDEYILVLAEDRTGAMRTEAMRHDFVVNVSHELKTPVGAISLLSEAIADAA
+DDDDAVRRFARRLGVESTRLTALVQDIIEFSRLQAKDVVREGRSVDLNLVVAEAVDRVRL
+TAEARGISIRAGGHVDTVVHGDPDQLMTAVRNLVDNAVRYSPDGTTVGVGLTSKDGLAQI
+TVTDQGIGISPEEQERVFERFYRVDAARSRQTGGTGLGLSIVKHVVINHGGEVTLWSQPG
+RGSTFTIRLPEWAQAPQTPDAGAPATVATLPERRGHRVAAAAAPARKEHSA
+>MHAAABBN_00035
+MDPVIIGLLCGAVGLFTGVASMLAFRASERSRTVDLTVGEPTLAPGAAEVLSVVGRAYAV
+VDDVDGVVRANPAAYALGLVRGHSLVQDQLRELTRTVRADGVIVERRMELPRGPLGQSSL
+VVELRVAPLDEEYILILADDRTDVTRTEAMRHDFVVNVSHELKTPVGAISLLSEAIGDAA
+EDEEAVRRFAARLGVESRRLSALVQDIIEFSRLQAKDVVQDGGPVDLNAVVADAVDRLRL
+TAEDRGIALRVGGRVDAVVHGDQDQLMTAVRNLVDNAVRYSPEGTTVGIGLSSVDGLAQV
+TVTDQGIGISPEEQERVFERFYRVDAARSRQTGGTGLGLSIVKHVVINHGGEVTLWSQPG
+RGSTFTIRLPEWGDGVAVDGAPGAAHVTERRGHRVTASAAPPTRKETSA
+>LFPAFLNI_00327
+MDPVIIGLLCGAVGLFTGVASMLAFRASERSRTVDLTVGEPTLAPGAAEVLSVVGRAYAV
+VDDVDGVVRANPAAYALGLVRGHSLVQDQLRELTRTVRADGVIVERRMELPRGPLGQSSL
+VVELRVAPLDEEYILILADDRTDVTRTEAMRHDFVVNVSHELKTPVGAISLLSEAIGDAA
+EDEEAVRRFAARLGVESRRLSALVQDIIEFSRLQAKDVVQDGGPVDLNAVVADAVDRLRL
+TAEDRGIALRVGGRVDAVVHGDQDQLMTAVRNLVDNAVRYSPEGTTVGIGLSSVDGLAQV
+TVTDQGIGISPEEQERVFERFYRVDAARSRQTGGTGLGLSIVKHVVINHGGEVTLWSQPG
+RGSTFTIRLPEWGDSVAVDGAPGAAHVTERRGHRVTASAAPPTRKETSA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000191.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000191.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cdd0a022cbc84a8c34ea106164c81e8e5389c086
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000191.fa
@@ -0,0 +1,72 @@
+>ACLBLIBL_00029
+MSSLFRRHAVATAACTVLVLAPASAAPALAVETVAADETTISLLSFNDFHGALSSDFSGT
+QFADTVEDYRTAFEAQHGERSVLLTSAGDLIGGSASVSNVQQDDPTIDVMNALGLSALAA
+GNHEFDRGLDDLQDRVIPRAEFPVLAANFVDPDTLEPILASHAIFDVNGVSVAVIGAVPN
+ELYATTTGAGLQGNTVLDMVEAVNGVAAELEASGAADVIVASYHEGAAGAGDLAAELGKR
+EVFRSMVEDTHPAVDVIFNGHTHQLYQYETAGDGVARPVLQAGASGSNLAAVELTVDAAG
+EVTAVASRLLDRSTQDPAEAAAESAVTAEVYAIEQEAVAVFEDMQSQVVADLDGSLTTDY
+QKRLDEGGTWRAGGTRSAETTLGNWVADATKQTALNADPEVDLGVVNPGGLRSEILVDAF
+TGGGTFSPKPADLIGKLTLGELLDVAPFGNSISYFDIPGSSIELALEQNWRDDVRTFTLG
+WSENLTWTYDESRPQGEKVTGVWIDGEPLEQDAIYTVATQSFLADDTWVALGDPTAAPDG
+YTAFATGREDFVDLGVLDTQAISDYARLQASAEGAVGPDFAKKGVPVSGAPETVAAGEEI
+VLTLGDLVIDSDDAPAAAEVAVAFEAADGTVTELGSVTVPAGSEEVTLSGIAAPAEAGAG
+ELRMTVRYADGTETIVRHALEVTASEAPVEPTEPTDPTVPADPSEPADPADPTVPADPSE
+PADPADPSDPTDPAAPVEGDDDGDDRDEEHTVPSTVETGDASAWWLAGFGALLGAALLRG
+RRALGLTASSTPAGR
+>MOLHKGIG_00308
+MPSLFRRRAVTTAACTVLVLAPASAAPALAVETAAADETTISILSFNDFHGALSADYIGT
+QFADTVEDYRTAFEAEHGAGSTLLTSAGDLIGGSKSVSNVQQDNPTIDVMNALGLASLTA
+GNHEFDKGLDDLQGRVESRAQFPVLSANLVDPTSKEPVLTSHAVFDVDGVRVAVIGASPN
+ELYATTTGAGLKGNEVLDEVAAVNAVADELEAQDAADVIVASYHDGAAGAGELAAERAAR
+AEFDRIVGETSSAVDVIFNAHTHQLYQYDTTAGGAHRPVIQAGASGSHLAAVELTVGADG
+EVTGLTPRLLARSTQAPAEAAAESPVTAQVYAIEQEAVAVFEDLQGEVVADLSASITTDY
+QKLIDAGGSWKAGGTRAAETTLGTWVGDAVKHAAEQANPEVDLGVTNPGGLRSELLTDRF
+TDGGAFPAKPADLVGRLTLGELLDMAPFGNTITYFDIPGSSIKLALEENWRNDVRKFTLG
+WSEELTWTYDESRPQGDKVTGVWIDGEPLQADRMYTVASQSFLADDTWTTLGDPTKAPDG
+YTAFATGRQNFVNMGLLDSQAITDYARAQDAAHGAVAPDFGKNGVPVTDAPASVEAGQAV
+GLTLGDLVVDSDGAPAATAVDVAFRTADGTETALGTVAVPAGSETVTLSGITAPAAAGTG
+ELVMTVRYADGSTTVVRHALEVTAAPSPTEPEQPAPTHPGKGHGKGHDKDADHPGKGRVK
+GEDHPGKGRGVQRGAATHPVFSAQAWLTAAGLPR
+>NAFOICDF_00025
+MSSIFSRRTAATLACTTLVLAPAAAPALAADASGERTISVLSFNDFHGALSEDFKGTQFA
+DTVEDYRTAFEAQHGEGSTLLTSAGDLIGGSASVSNVQQDNPTIDVMNALGLASLTAGNH
+EFDRGLDDLQGRVADRADFPVLSANFVDPNTKAPVLTSHKVFDVDGVRVAVIGASPNELY
+ATTTGAGLQGNLVVDMVDAVNAVATGIEAADEADVIIASYHDGAAGAAADLSAELGNRAT
+FDAMVERTVPAVDVIFNGHTHQLYQYQTDNGGVPRPIMQAAASGADLAAVELTVDAAGEV
+TAVTPRMLPRSTQDPAEAAAESPVTARVYEIEQQAVDVFTDMQSQVIADLSGSITTDYAT
+RIAAGMGWKAGGTRTAETTLGNWVADSLKHSVSAAEPGVDLGVVNPGGIRSELLVDQTNA
+GGVFSPKPEQLVGKLTMGEVMDVAPFGNTLTYFDLPGSSIKEALEQNWRDGERTFTLGWS
+SNLTWTYDDARAQGDKVTGVWIDGEPLQADRMYTVAAQSFLADDTWVKLGDPSKAPDGYT
+AFATGRQGFVDLGVLDTTAVLSWARAQDAADGAAHPDYAKKGVPVTGAPASVEGGQDVVL
+TLGDLVIDSDGAPAATAVDVAFQGADGAVTELGTVEVPAGQESVTLSGITAPQTAGAGEL
+VMTVRYADGTTAVVRHALEVTASAAPVDPSTPAEPTQPGEPSDPAEPTTPGEPTPSAQPT
+APVEPTAPVEPSAPAEPTAPVEPTAPAESPEPTPTAQPSTPAEPTAPTPSAPAEDGGEHA
+VPGKVQTGDQAIWLVAALGALGAGALVAVRRRAAAR
+>MHAAABBN_00023
+MPSLFRRRAVTTAACTVLVLAPASAAPALAVETAAADETTISILSFNDFHGALSADYIGT
+QFADTVEDYRTAFEAEHGAGSTLLTSAGDLIGGSKSVSNVQQDNPTIDVMNALGLASLTA
+GNHEFDKGLDDLQGRVESRAQFPVLSANLVDPTSKEPVLTSHAVFDVDGVRVAVIGASPN
+ELYATTTGAGLKGNEVLDEVAAVNAVADELEAQDAADVIVASYHDGAAGAGELAAERAAR
+AEFDRIVGETSSAVDVIFNAHTHQLYQYDTTAGGAHRPVIQAGASGSHLAAVELTVGADG
+EVTGLTPRLLARSTQAPAEAAAESPVTAQVYAIEQEAVAVFEDLQGEVVADLSASITTDY
+QKLIDAGGSWKAGGTRAAETTLGTWVGDAVKHAAEQANPEVDLGVTNPGGLRSELLTDRF
+TDGGAFPAKPADLVGRLTLGELLDMAPFGNTITYFDIPGSSIKLALEENWRNDVRKFTLG
+WSEELTWTYDESRPQGDKVTGVWIDGEPLQADRMYTVASQSFLADDTWTTLGDPTKAPDG
+YTAFATGRQNFVNMGLLDSQAITDYARAQDAAHGAVAPDFGKNGVPVTDAPASVEAGQAV
+GLTLGDLVVDSDGAPAATAVDVAFRTADGTETALGTVAVPAGSETVTLSGITAPAAAGTG
+ELVMTVRYADGSTTVVRHALEVTAAPSPTEPEQPAPTHPGKGHGKGHDKGADHPGKGRVK
+GEDHPGKGRGVQRGAATHPVFSAHAWLTAAGLPR
+>LFPAFLNI_00315
+MPSLFRRRAVTTAACTVLVLAPASAAPALAVETAAADETTISILSFNDFHGALSGDYIGT
+QFADTVEDYRTAFEAEHGAGSTLLTSAGDLIGGSKSVSNVQQDNPTIDVMNALGLASLTA
+GNHEFDKGLDDLQGRVESRAQFPVLSANLVDPTSKEPVLTSHAVFDVDGVRVAVIGASPN
+ELYATTTGAGLKGNEVLDEVAAVNAVADELAAQDAADVIVASYHDGAAGAGELAAERAAR
+AEFDRIVGETSSAVDVIFNAHTHQLYQYDTTAGGAHRPVIQAGASGSHLAAVELTVGADG
+EVTGLTPRLLTRSTQAPAEAAAESPVTAQVYAIEQEAVAVFEDLQGEVVADLSASITTDY
+QKLIDAGGSWKAGGTRAAETTLGTWVGDAVKHAAEQANPEVDLGVTNPGGLRSELLTDRF
+TDGGAFPAKPADLVGRLTLGELLDMAPFGNTITYFDIPGSSIKLALEENWRNDVRKFTLG
+WSEELTWTYDESRPQGDKVTGVWIDGEPLQADRMYTVASQSFLADDTWTTLGDPTKAPDG
+YTAFATGRQNFVNMGLLDSQAITDYARAQDAAHGAVAPDFGKNGVPVTDAPASVEAGQAV
+GLTLGDLVVDSDGAPAATAVDVAFRTADGTETALGTVAVPAGSETVTLSGITAPAAAGTG
+ELVMTVRYADGSTTVVRHALEVTAAPSPTEPEQPAPTHPGKGHGKGHDKGADHPGKGRVK
+GEDHPGKGRGVQRGAATHPVFSAHAWLTAAGLPR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000194.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000194.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d5c53c2c8311244bd058942308f57b668f3ca33
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000194.fa
@@ -0,0 +1,31 @@
+>ACLBLIBL_00032
+MDRNMLDQLQNANVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ
+TTADGITVPFDKAFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSNVDHDRDVRHDDGLRA
+DAGTAGVAGTAGVAGVADRREDTVVDGDRRDVVDGDRRDLVDADRRDVVDGDRDSMVVKD
+EHLQVGTERQATGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDI
+EVTTYEETPVVNKTVEAEKVSLGKRQVQDTETVSEELRHEDVKIDGDATDRDLDGRTDRK
+DRI
+>MOLHKGIG_00305
+MDRNALDQLQNSTVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ
+ITADGITVPFEKSFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSYSVEHPAADHDGDVRR
+DDVRTDAGTAGVAGTAGVAGVADRRDEAVVDGDRRDVADRDRRDVTDADSVVVKDEHLNV
+GTERRASGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDVEVTTY
+EETPVVNKTVDAEKVSLGKRQVQDTETVTEEVRHEDVKVDGDATDRDLDGRNDRKDRI
+>NAFOICDF_00028
+MDRNALDQLQNGHVFSTDGEKIGSVGQVYLDDVTNEPTFVTVKTGLFGAKETFVPLQQAQ
+TTTDGITVPFTKDFVKDAPNVDADGSLTPEEEQRIYEYYSMDYSAVDTHDRRDVRDAAAA
+GTAGGVVTDRERRDVVDADRRDVVDNDRRDLVDGDADSVVVKDEKLNVGTERRATGRVRL
+RKQSYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDIEVTTYEETPVVNKTVEA
+EKVSLGKRTVQDTETVSEELTHEDVKIDGDDVDGRRR
+>MHAAABBN_00020
+MDRNALDQLQNSTVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ
+TTADGITVPFEKSFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSAADHDGDVRRDDVRTD
+AGAAGVAGTAGVAGVADRRDEAVVDGDRRDVADRDRREVTDADSVVVKDEHLNVGTERRA
+SGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDVEVTTYEETPVV
+NKTVDAEKVSLGKRQVQDTETVTEEVRHEDVKVDGDATDRDLDGRNDRKDRI
+>LFPAFLNI_00312
+MDRNALDQLQNSTVFATDGDKIGSVGQVYLDDVTNEPTFVTVKTGLFGARETFVPLQQAQ
+TTADGITVPFEKSFVKDAPNVDADGSLTPEEEQRIYEYYSMEYSAADHDGDVRRDDVRTD
+AGAAGVAGTAGVAGVADRRDEAVVDGDRRDVADRDRREVTDADSVVVKDEHLNVGTERRA
+SGRVRLRKQAYTTTETVEVPVTREEVVVERESVDPNSAEARTAGRDGDVEVTTYEETPVV
+NKTVDAEKVSLGKRQVQDTETVTEEVRHEDVKVDGDATDRDLDGRNDRKDRI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000195.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000195.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d82f5885f0960981cdbc7a1252e4bdd05e9b837
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000195.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00051
+MEYLVPVLAVVLIGALAFAVSRWMSAARDRQTAGPRTPSGRPLEIGPERARQAAALLDED
+AHRRVYGHIAQSRVMEAVRDYRAHTGRSLKDAVMDVQSLAVHPQVYSVPATEQEAPEEAE
+VRDPRTRPTPPEPARDEAADGERQGTERADVVEEGADDPAADDEPRPEAESDLSAEEGRV
+DDGAASGTEPRPGTSEPARADELTALTVPADWSAAPAEEEPPFEVEVMRGMDSVRLSSQD
+LPPWLRDQLSAMVRDGNLESAAVQLSSHSQLSVPEAYELLRRMRERRGED
+>MOLHKGIG_00303
+MEYLVPVLAVVVIGALAFAAARWMSAGRARQAADQRTPSGRGLDIGPERARLAAGLLDED
+AHRRVYGHIAQSRVMEAVRDYRAHTGRGLKDAVMDVQSLAVHPQVYSEPAQEPDATSAGA
+AGPVPADHEEPHRDDTAPAETPGPERPGQDSSGRGEPDAQTPDREPSDAVAEDDARQDTD
+HASAAPRPTATPADELTTLTVPAEWTAAPAEEELPFEVEVMRGTESVRLSSRDLPPWLRD
+QLSAMVRDGNLESAAVQLSSHSELSVPEAYELLRRMREHRGEG
+>NAFOICDF_00030
+MEYLVPILAVVVIGGITLLVARRLSGRSQAPTRSATGTGADTVEASPERARTAARRLDEA
+THRAVYGHIAQGRPFEAVRDYRRATGRGVRDAILDIQSLTLHPQVWSLPVQAEPADDASP
+AAADMPSGPPRGPSDGRGRDGESSARPRLRRAEPSEAGPAPDAEPAPGGDAAADPEADGA
+TSRRPGRQAPEELTTLTVPEGWTADPAPEEPPFEVEVMRGEESVRLASQDLPPWLRDQLS
+AMVRDGNLESAAVQLSSHSSLSVPEAFELLRRMKERREGRG
+>MHAAABBN_00011
+MEYLVPVLAVVVIGALAFAAARWMSAGRARQAADQRTPSGRGLDIGPERARLAAGLLDED
+AHRRVYGHIAQSRVMEAVRDYRAHTGRGLKDAVMDVQSLAVHPQVYSEPVQEPDATSAGV
+AGPVPGGHGEPHRDDAAPADTPGPKRPGQDSSGRGEPDAQTPDRETSDAVAEDDARQDSD
+HASAAPRPTAPSADELTTLTVPAEWTAAPAEEELPFEVEVMRGTESVRLSSRDLPPWLRD
+QLAAMVRDGNLESAAVQLSSHSELSVPEAYELLRRMRERRGEG
+>LFPAFLNI_00310
+MEYLVPVLAVVVIGALAFAAARWMSAGRARQAADQRTPSGRGLDIGPERARLAAGLLDED
+AHRRVYGHIAQSRVMEAVRDYRAHTGRGLKDAVMDVQSLAVHPQVYSEPVQEPDATSAGV
+AGPVPDDHGEPHRDDAAPAETPGPKRPGQDSSGRGEPDAQTPDREPSDAVAEDDAQQDTD
+HASAAPRPTATPADELTTLTVPAEWTAAPAEEELPFEVEVMRGTDSVRLSSQDLPPWLRD
+QLSAMVRDGNLESAAVQLSSHSELSVPEAYELLRRMRERRGEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000196.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000196.fa
new file mode 100644
index 0000000000000000000000000000000000000000..06b0faca6b2511774324e21742f582c765a7de2a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000196.fa
@@ -0,0 +1,42 @@
+>ACLBLIBL_00053
+MPPQPPPAGPPAVPPSGPAPLAPGDPAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSADL
+GVGAHRAALLVSAGTLGLALSVVPWSMAGDRWGRRRAMVVSMVSASLFALAGVLAPTFEA
+MLGLRLLEGMAHGGVAGLAVALLAEEVAPRAVATAAGTYIAGTTIGGLSGRLIALPVAEA
+FTWRTGMLAVTVVGVACTAAFLAVTPQARRFTPSPTSVARLVRIVRGHLGSAELVAVYLQ
+AALLMGGFVALYNFVGYRLLGPPFSWAPTAAGLVFLAYLAGTWSSPRAGRLAARFGRLPV
+LTGATAAMAAGAALTLVPHPAVLVGALVLTTGAFFAAHSVASAWSGTAAPHGRAQSTSLY
+NLAYYAGSSLFGWLGGVFHESHGWTGTVLMVVALALTALAIAVVVLRGRGTAPARCAGAV
+RGAGRRGIRRISRGRLRRRRWPSGAGRARPRGPRGPAARASRPSAGRSRSRCPARRTPPA
+WSAPRPG
+>MOLHKGIG_00301
+MPPTTPPPPAGPPAVPPSGPAPAAPGEAAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSD
+DLGVPADRAALLVSASTLGLALSVVPWSVAGDRWGRRRAMVVSMVSASACALAGVLAPTF
+EAMLRLRLLEGMAHGGVAGLAVALLAEEVAPHAVAAAAGTYIAGTTLGGLSGRLLALPVA
+EASSWRGGMLAVTVVGVLCTVGFLAITPRARRFTPSPTSPATLVRIVRGHLRSPELVAVY
+LQGALLMGGFVALYNFVGYRLLGPPFSWTPTAAGLVFLAYLAGTWSSPRAGRLAARVGRL
+PVLAGATAAMAAGVALTSVPHPAVLVPALVLVTGAFFAAHAVASAWSGTAAPTGRAQSTS
+LYNFAYYAGSSLFGWLGGVFHESHGWPGTVLMVLALVLTALASAVVVLRGRGTAPAR
+>NAFOICDF_00031
+MPPALPAPLEPGTPLYRRLLLGLFLAGVATFAQLYAPQGLLPLVSSDLGVPSHRAALLVS
+AGTLGLALSVVPWSLAGDRWGRRPVMVASLVSASVLALVGVFMPSIELLMGMRLLEGMAH
+GGVAGLAVTLLAEEVAPRVVPVAAGTYVAGTTLGGLSGRLLAMPVGEWAGWRAGMLAVTA
+AGAACTVAFLFVTPPARRSTPVRLSLARLGRIIGGHLRTPGLVALYLQAALLMGGFVALY
+NYIGYTLLAPPFGWPPTAVGLVFLAYLAGTWSSPRAGRLAVRVGRLKVLTGSTALMAVGV
+VLTLVPSPFVLVPALVVATGAFFAAHSVASGWAGTAAPTGRAQSTSLYNLAYYAGSSLFG
+WLGGVFHEGVGWAGTVFMVAGLAAVALVVALVVLRGREDAGPPPPSAVAEGAAA
+>MHAAABBN_00009
+MPPTTPPPSAGPPAVPPSGPAPAAPGEPAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSD
+DLGVPADRAALLVSASTLGLAVSVVPWSVAGDRWGRRRAMVVSMVSASACALTGVLAPTF
+EAMLGLRLLEGMAHGGVAGLAVALLAEEVVPHAVAAAAGTYIAGTTLGGLSGRLLALPVA
+EASSWRGGMLTVTVVGVLCTVGFLAITPRARRFTPSPTSPATLVRIVRGHLRSPELVAVY
+LQGALLMGGFVALYNFVGYRLLDPPFSWTPTAAGLVFLAYLAGTWSSPRAGRLAARVGRL
+PVLAGATAAMAAGVALTSVPHPAVLVPALVLVTGAFFAAHAVASAWSGTAAPTGRAQSTS
+LYNFAYYAGSSLFGWLGGVFHESHGWPGTVLMVLALVLTALVSAVVVLRGRGTAPAR
+>LFPAFLNI_00308
+MPPTTPPPSAGPPAVPPSGPAPAAPGEPAYRRLLIGLFLAGVATFAQLYSPQGLLPLVSD
+DLGVPADRAALLVSASTLGLAVSVVPWSVAGDRWGRRRAMVVSMVSASACALTGVLAPTF
+EAMLGLRLLEGMAHGGVAGLAVALLAEEVAPHAVAAAAGTYIAGTTLGGLSGRLLALPVA
+EASSWRGGMLAVTVVGVLCTVGFLAITPRARRFTPSPTSAAALVRIVRGHLSSPELVVVY
+LQGALLMGGFVALYNFVGYRLLDPPFSWTPTAAGLVFLAYLAGTWSSPRAGRLAARVGRL
+PVLAGATAAMAAGVALTSVPHPAVLVPALVLVTGAFFAAHAVASAWSGTAAPTGRAQSTS
+LYNFAYYAGSSLFGWLGGVFHESHGWPGTVLMVLALVLTALASAVVVLRGRGTAPAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000197.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000197.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a87a21140b220b66e11510183c369750909dd0f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000197.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_00054
+MTTSTSSLDLHESFKAYDVRGIVGETITADSVRAVGAAFVDVLGLAGETVLVGGDMRPSS
+PAFMAAFAEGATRRGADVVDLGLISTDMLYYAAGVKQAAGVVFTASHNPAEYNGMKMAKA
+GAVPVSSDTGLYEIRDAAQALLDAGEIPAAEAVGTVTQQDILPAYAEYLRSLVDLSGVRP
+LTVVVDAGNGMAGKTTPAVLGDAALDALPLRIEPLYFELDGTFPNHPANPLEPENLRDLQ
+AAVVEHGADIGLAFDGDADRCFVVDEKGAPVSPSAITALVARREIARAKGEGEETPVVIH
+NLITSRAVPELVAADGGRAVVTRVGHSFIKAVMAEESAVFGGEHSAHYYFRDFFNADTGM
+LAAMHVLAALGEQDQPLSELAEEYEPYVASGEINSQVADKDAAVAAVVAQFAPTVGEGAG
+EGRAVHEDFAGVDTAVTRMDGTTVAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEAIR
+DAVLAIVRAER
+>MOLHKGIG_00300
+MTTSTPSLDLHDSFKAYDVRGIVGESITAESVRAVGAAFVDVLGLAGQTVLVGGDMRPSS
+PAFMTAFAEGATRRGADVVTLGLISTDMLYYAAGVKQAAGVVFTASHNPAEYNGMKMAQA
+GAVPVSSDTGLFEIRDAAQAYLDAGEIPAAETAGTVTEEDILPGYAAYLRSLVDLTGVRR
+LKVVVDAGNGMAGKTTPAVLGDAELAALPLEIEPLYFELDGTFPNHPANPLEPENLRDLQ
+AAVVEHGADIGLAFDGDADRCFVIDEQGAPVSPSAITALVARREIARAKADGEQTPVVIH
+NLITSRAVPELVAADGGRAVETRVGHSFIKAVMAAESAVFGGEHSAHYYFRDFFNADTGM
+LAAMHVLAALGGQEQPLSELAEEYEPYVASGEINSQVADKDAAVAAVVAQFAPAVGEGVG
+EGQAVHEDFAGVATTVTRMDGTTVAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEALR
+DAVLAIVRAER
+>NAFOICDF_00032
+MVTLRPGRIIDRVTTAADAINLRDSFKAYDVRGIVGETITAETVRAVGAAFVDVLGLAGQ
+TVLVGGDMRPSSPEFIEAFAEGATRRGGNVQRIGLISTDMLYYAAGVEQAAGVMFTASHN
+PAAYNGMKMAKAGAVPVSSDTGLYEIRDVAQGYLDAGEIPAADAQGSVTESDILTGYAEY
+LRSLVDLSGIRPLKVVVDAGNGMAGKTTPAVLGGEVLEALPLEITPLFFELDGTFPNHPA
+NPLEPENLRDLQRAVVEHGADIGLAFDGDADRCFVIDEQGEPVSPSAVTALVARREIARA
+KASGEETPVIIHNLITSRAVPELVSADGGRAVQTRVGHSFIKAVMASEGAVFGGEHSAHY
+YFRDFFNADTGMLAAMHVLAALGEQDGPLSTLGAEYEPYVASGEINSQVEDKDAAVAAVL
+ARFAPQAADGGESGTAVEDAVAGTSTSVLRMDGTTVSAADGSWWFNLRPSNTEPFLRYNG
+EAKDRATMETVRDAVLAIVRAPR
+>MHAAABBN_00008
+MTTSTPSLDLHDSFKAYDVRGIVGESITAESVRAVGAAFVDVLGLAGQTVLVGGDMRPSS
+PAFMTAFAEGATRRGADVVTLGLISTDMLYYAAGVKQAAGVVFTASHNPAEYNGMKMAQA
+GAVPVSSDTGLFEIRDAAQAYLDAGEIPAAETAGTVTEEDILPGYAAYLRSLVDLTGVRR
+LKVVVDAGNGMAGKTTPAVLGDAELAALPLEIEPLYFELDGTFPNHPANPLEPENLRDLQ
+AAVVEHGADIGLAFDGDADRCFVIDEQGAPVSPSAITALVARREIARAKADGEQTPVVIH
+NLITSRAVPELVAADGGRAVETRVGHSFIKAVMAAESAVFGGEHSAHYYFRDFFNADTGM
+LAAMHVLAALGGQEQPLSELAEEYEPYVASGEINSQVADKDAAVAAVVAQFAPAVGEGAG
+EGRAVHEDFAGVATTVTRMDGTTIAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEALR
+DAVLAIVRAER
+>LFPAFLNI_00307
+MTTSTPSLDLHDSFKAYDVRGIVGESITAESVRAVGAAFVDVLGLAGQTVLVGGDMRPSS
+PAFMTAFAEGATRRGADVVTLGLISTDMLYYAAGVKQASGVVFTASHNPAEYNGMKMAQA
+GAVPVSSDTGLFEIRDAAQAYLDAGEIPAAETTGTVTEEDILPGYAAYLRSLVDLTGVRR
+LKVVVDAGNGMAGKTTPAVLGDAELAALPLEIEPLYFELDGTFPNHPANPLEPENLRDLQ
+AAVVEHGADIGLAFDGDADRCFVIDEQGAPVSPSAVTALVARREIARAKADGEQTPVVIH
+NLITSRAVPELVAADGGRAVETRVGHSFIKAVMAAESAVFGGEHSAHYYFRDFFNADTGM
+LAAMHVLAALGGQEQPLSELAEEYEPYVASGEINSQVEDKDAAVAAVVAQFAPAVGEGVG
+EGQAVHEDFAGVATTVTRMDGTTVAAQDGTWWFNLRPSNTEPFLRYNGEARTAATMEALR
+DAVLAIVRAER
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000198.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000198.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c2c42822813b8eeb7c073177195440a23b6facfe
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000198.fa
@@ -0,0 +1,70 @@
+>ACLBLIBL_00055
+MDTTQHPDAGPLPSESTAPIGPYGSGAAAPGAAAAREPELHAEALAVLRRLVDRPDAQFK
+DGQFEAIEALVAHRRRALVVQRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQV
+AAAARAGVRAVSVSSANATQWDEVRARLAADEVDVLLISPERLTNPRFREEQLPDLVARM
+GLLVVDEAHCISDWGHDFRPDYRRIRDLIGLLPSTGPRAVPVLATTATANARVVGDVVEQ
+LGVDSAQDVFVLRGSLARASLRLGVLRMPSPAARLAWLLDHLEDLPGSGIVYALTVSAAE
+DTARALREAGHEAVAYTGRTDPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVH
+FGAPSSPVAYYQQVGRAGRGTDHADVLLLPGPEDRRIWEYFATASMPDEEQARAVLQALA
+QHGGALSVAALEPAVRIKRTALELLLKVLAVDGAVERVGGGWRATGREWVYDAQRYARVA
+EARRAEERLMLDYQTTDTCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDTSARERAE
+AALRRTGVPIEPRRMWPSGMDRLGVPVKGRMAPEIQAEEGRALARLTDLGWGTVLRELLD
+KEDAPVPEDVLQGAVGVLAGWGWQTRPIAVVAMPSRTRPLLVGSFAEGIARIGRLPFLGS
+LEHARGGPTAGPGGNSAYRLGSVHGRFEVPEAMAHLLRTASDAGRHGPVLLVDDLVDSRW
+SLAEASRVLREAGAQGVLPLVLAQAG
+>MOLHKGIG_00299
+MDATSHPDAGPRLPETSVPGGDAALHEEALAVLRRLVDRPDARFKDGQFEAIEALVAHRR
+RALVVQRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSS
+ANATEWDEVRARLAADEVDVLLISPERLTNPRFRDEQLPDLVARMGLLVVDEAHCISDWG
+HDFRPDYRRIRDLIGLLPAEGPRAVPVLATTATANARVVADVVEQLGVASEQDVFVLRGP
+LARASLRLGVLRMPSPAARLAWLLDHLGDLPGSGIVYALTVSAAEDTARALREAGHEVVA
+YTGRTDPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHFGAPGSPVAYYQQVG
+RAGRGTDHADVLLLPGPEDRRIWEYFATASMPDEEQARAVLGALADHGGALSVAALEPAV
+RIKRTALELLLKVLAVDGAVERVGGGWRATGREWTYDAERYARVAEARRAEERLMLDYQT
+TDRCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDGAARERAEAALRRTGVPIEPRRM
+WPSGMDRLGVPVKGRIAPESQAEEGRALARLTDLGWGTVLRDLLDREDAPVPEEVLRGAV
+DVLAGWGWRTRPIAVVAMPSRTRPQLVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGN
+SAYRLGSVYGRFAVPEAMAQMLRTAPDAGRHGPVLLVDDLVDSRWSLAEAARVLREAGAQ
+GVLPLVLAQAG
+>NAFOICDF_00033
+MSTSPQDPARPAAVADPALYAEALGVLRALVGRPDAEFKDGQYEAVEALVAHRRRALVVQ
+RTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAASLSSANATEW
+EDVRRSLEADEVDVLLISPERLTNPRFRDEQLPDLVSRMGLLVVDEAHCISDWGHDFRPD
+YRRIRDLIRLLPSSGPRAVPVLATTATANARVVQDVVEQLDVESRQDVFVLRGPLARASL
+RLGVLRLPSPAARLAWLLQHLGELPGSGIVYALTVSAAEDTARALREAGHEVVAYTGRTD
+PEQRARIEQDLKDNRVKAVIATSALGMGFDKPDLTFVVHLGAPSSPVAYYQQVGRAGRGT
+DHADVLLLPGQEDRAIWEYFATASMPDEVQARAVLEALEESGGAMSVAALEPVVSVKRTA
+LELLLKVLSVDGAVERVGGGWRATGSPWTYDAERYARVAEARRAEERLMLDYQTTQTCRM
+EFLARTLDDPTAAPCGRCDVCAGPWYPTGWDGAAREQADRALRRTGVPLEPRRMWPSGMD
+RLHVPVKGRISPAEQAEEGRALARLTDLGWGSRLRELLAAPDAPVPEEVLQAAVRVLAEW
+GWQERPIAVVAMPSRGRPQLVDSLARGLAGQGRLPFLGPLELVGGGPTAGPGGNSAYRLA
+SVHGRFAVPEGMARMLATAPDAGRHGPVLLVDDLADSRWSLAEAARVLRGTGAQGVLPFV
+LAQNG
+>MHAAABBN_00007
+MDATSHPDAGPRLPETSAPGGDAALHEEALAVLRRLVDRPDARFKDGQFEAIEALVAHRR
+RALVVQRTGWGKSAVYFVASLLLRARDAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSS
+ANATEWDEVRARLAADEVDVLLISPERLTNPRFRDEQLPGLVARMGLLVVDEAHCISDWG
+HDFRPDYRRIRDLIGLLPAEGPRAVPVLATTATANARVVADVVEQLGVASEQDVFVLRGP
+LARASLRLGVLRMPSPAARLAWLLDHLADLPGSGIVYALTVSAAEDTARALREAGHEVVA
+YTGRTDPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHFGAPGSPVAYYQQVG
+RAGRGTDHADVLLLPGPEDRRIWEYFATASMPDEEQARAVLGALADHGGALSVAALEPAV
+RIKRTSLELLLKVLAVDGAVERVGGGWRATGREWTYDAERYARVAEARRAEERLMLDYQT
+TDRCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDGAARERAEAALRRTGVPIEPRRM
+WPSGMDRLGVPVKGRIAPESQAEEGRALARLTDLGWGTVLRDLLDREDAPVPEEVLRGAV
+DVLAGWGWRTRPIAVVAMPSRTRPQLVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGN
+SAYRLGSVYGRFAVPEAMAQMLRTAPDAGRHGPVLLVDDLVDSRWSLAEAARVLREAGAQ
+GVLPLVLAQAG
+>LFPAFLNI_00306
+MDATSHPDAGPRLPETSAPGGDAALHEEALAVLRRLVDRPDARFKDGQFEAIEALVAHRR
+RALVVQRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSS
+ANATEWDEVRARLAADEVDVLLISPERLTNPRFRDEQLPDLVARMGLLVVDEAHCISDWG
+HDFRPDYRRIRDLIGLLPAEGPRAVPVLATTATANARVVADVVEQLGVASEQDVFVLRGP
+LARASLRLGVLHLPSPAARLAWLLDHLGDLPGSGIVYALTVSAAEDTARALREAGHEVVA
+YTGRTDPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHLGAPGSPVAYYQQVG
+RAGRGTDHADVLLLPGPEDRRIWEYFATASMPDEEQARAVLGALADHGGALSVAALEPDV
+RIKRTSLELLLKVLAVDGAVERVGGGWRATGREWTYDAERYARVAEARRAEERLMLDYQT
+TDRCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDGAARERAEAALRRTGVPIEPRRM
+WPSGMDRLGVPVKGRIAPESQAEEGRALARLTDLGWGTVLRDLLDREDAPVPEEVLRGAV
+DVLAGWGWRTRPIAVVAMPSRTRPQLVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGN
+SAYRLGSVYGRFAVPEAMAQMLRTAPDAGRHGPVLLVDDLVDSRWSLAEAARVLREAGAQ
+GVLPLVLAQAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000201.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000201.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f93057340cd9fcb0c0ea9735618dc7d373bb11c0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000201.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00060
+MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPAAGDWLRENGLVPDAIVCSDA
+LRTRQTCVWVCERLGELAPTPYLDPRLYHADAAKALAIVNETEETTRSLLVVGHMPWVQN
+LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWVELDGRDAALTHFVVPGR
+>MOLHKGIG_00294
+MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPAAGDWLREHGLVPDAVVCSDA
+LRTRQTCVWVCERLGELAPTPYLDPRLYGADAARALAVVNETEETTRRLLVVGHMPWVQE
+LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWAELDGRDAALTHFVVPGR
+>NAFOICDF_00039
+MSPADAKTLVLLRHAKADWPAGVDDHDRPLAPRGHAQAPAAGDWLLEHGIAPEAAVVSDA
+LRTRQTWVWVAQRLGERAPTAYLDRRLYEADAARALAVVNETEETVRSLIVVGHMPWLQN
+LGMRLMSLDSDQDAALEMAEHLPTLGLQVFRVDTPWAELDGRDAALTHFAVPGR
+>MHAAABBN_00002
+MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPAAGDWLREHDLVPDAVVCSDA
+LRTRQTCVWVCERLGELAPTPYLDPRLYGADAARALAVVNETEETTRRLLVVGHMPWVQE
+LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWAELDGRDAALTHFVVPGR
+>LFPAFLNI_00301
+MSTADAKTLIVLRHAKAGWPDAADDHARPLAERGHAQAPTAGDWLREHDLVPDAVVCSDA
+LRTRQTCVWVCERLGELAPTPYLDPRLYGADAARALAVVNETEETTRRLLVVGHMPWVQE
+LGMRLMSLDSDQDAALRMSEHYPTLGMQVFRVEKPWAELDGRDAALTHFVVPGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000202.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000202.fa
new file mode 100644
index 0000000000000000000000000000000000000000..687b74db8edabb2ae6ea5a76034e348bca3e5e58
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000202.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00061
+MGQSAGYVHISVRNAQRRADGMSRRGQARADLRLAGGTDAPAAQTAPTPVLAPNGIPGPQ
+AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGSESHAAVALAPSGA
+EGRDLEVVRQVLGDPTVQGGAHPDLAQAPAPVSTREPGVLIDLSRREVQLDGESLNLTYK
+EFELLNYLVENGERTVGREELLEALWHNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR
+GQGYRFYRHPEVVVWAAPEYSI
+>MOLHKGIG_00293
+MGQSAGYVHISVRNAQRRADGMSRRGQARAGLRLAGGTDAPDSQTAPTPVLAPNGIPGPQ
+AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGA
+EGRDIEVVRQVLGDPTVQGGTRPDLAQAPAPVSTRQPGVLIDLSRREVQLDGESLNLTFK
+EFELLNYLVENGERTVGREELLDALWRNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR
+GQGYRFYRHPEVVVWAAPEYSI
+>NAFOICDF_00040
+MGETAGYVHISVRNAQRRANVSRARRGDLRLAGGTSHEPTPPQTAPTPVLAPSGIPGPQA
+VARENEARGFVIYVGMDELMASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGAA
+GRDLEVVRQVLGDPTVQGAARPDLAQAPAPVSTRQPGVLIDLSRREVQLDGEALNLTFKE
+FELLNYLVENGERTVGREELLDALWKNSDEVPNERTIDVHIRRLRAKLGRLANTVRTVRG
+QGYRFYRHPEVVVWAAPEYSI
+>MHAAABBN_00001
+MGQSAGYVHISVRNAQRRADGMSRRGQARAGLRLAGGTDAPDSQTAPTPVLAPNGIPGPQ
+AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGA
+EGRDIEVVRQVLGDPTVQGGTRPDLAQAPAPVSTRQPGVLIDLSRREVQLDGESLNLTFK
+EFELLNYLVENGERTVGREELLDALWRNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR
+GQGYRFYRHPEVVVWAAPEYSI
+>LFPAFLNI_00300
+MGQSAGYVHISVRNAQRRADGMSRRGQARAGLRLAGGTDAPDSQTAPTPVLAPNGIPGPQ
+AVARENEARGFVIYVGMDELAASAAGTSLTRLANELRHYVESLVPGAESHAAVALAPAGA
+EGRDIEVVRQVLGDPTVQGGTRPDLAQAPAPVSTRQPGVLIDLSRREVQLDGESLNLTFK
+EFELLNYLVENGERTVGREELLDALWRNADEVPNERTIDVHIRRLRAKLGRLANTVRTVR
+GQGYRFYRHPEVVVWAAPEYSI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000203.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000203.fa
new file mode 100644
index 0000000000000000000000000000000000000000..91a355bfc5d721ffed91a70ffba58563085930f4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000203.fa
@@ -0,0 +1,26 @@
+>ACLBLIBL_00062
+MRVHLVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVEIQTPVAT
+TTGLRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTYAERLPAD
+LSGRHVFVLDPMLATGGTLIESIRFLYERGAARVTCICLLGAPEGIARLEESLGDVEVDL
+YLAAQDERLDENAYIVPGLGDAGDRLYGLAE
+>MOLHKGIG_00292
+MDGTVGAMRVHIVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVR
+IETPVTETTGFRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY
+AERLPADLSGRHVFVLDPMLATGGTLIEAIRFLYQRGAARVTCLCLLGAPEGIERLEASL
+GDVEVDLYLAAVDERLDERSYIVPGLGDAGDRLYGLAE
+>NAFOICDF_00041
+MRLHVVDHPLVAHKLTVLRDERTPSMIFRQLTEELVMLLAYEATRGVAVTEVEVKTPVAT
+TVGTTLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTYAERLPAD
+LTGRHVFVLDPMLATGGTLIEAIRFLYERGAERVTCLCLLGAPEGVARLEEALGDVDVEL
+YLAAVDERLNEKSYIVPGLGDAGDRLYGLAE
+>MHAAABBN_02315
+MGGTVGAMRVHIVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVR
+IETPVTETTGFRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY
+AERLPADLSGRHVFVLDPMLATGGTLIEAIRFLYQRGAARVTCLCLLGAPEGIERLEASL
+GDVEVDLYLAAVDERLDERSYIVPGLGDAGDRLYGLAE
+
+>LFPAFLNI_00299
+MGGTVGAMRVHIVDHPLVAHKLSVLRDKKTPSMIFRQLTEELVMLLAYEATRDVAMEEVR
+IETPVTETTGFRLARPRPLVVPILRAGLGMLEGMTKMAPSAEVGFLGMARNEETLDIVTY
+AERLPADLSGRHVFVLDPMLATGGTLIEAIRFLYQRGAARVTCLCLLGAPEGIERLEASL
+GDVEVDLYLAAVDERLDERSYIVPGLGDAGDRLYGLAE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000207.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000207.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38116c293aafea5a9c581b6e1f5efed70adf631b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000207.fa
@@ -0,0 +1,47 @@
+>ACLBLIBL_00069
+MPEGDSLVRLAHRLRPVLAGRALTHADLRVPQHATADLTGWTVVEVEPRGKYLLMRLTPP
+AGRPAARPLTLVSHLKMEGRWLVSALDARWGAPAWQVRAVLETADHRVLGAQLGMLTLVP
+TDREDTVLGHLGPDLLDPAWDGSEEAAAALLAEGTRRLTARPERPVGLALLDQRTTCGIG
+NIYRCESLLLAGIDPHRPVGAVPDVPGLLTIARDLLRANVPPAAPFLGWPRTTTGVRANP
+DRPYGIEVVVADRGFPPGLPAAVGSGTAADPAADPGADRTASGPALGRPPARPPADPGAA
+GRRRTGCTGTTAPPACAAAGACARRTSAPPRTTRGSCGGARPASGEPRPNRGPGGGAPYA
+ERRPSPQGRSARPPTPRRTRVADPFPDDPRSAVVALILAGGRGSRLAPLTDARSKPAVPF
+AGQYRLIDVALTTVAHSGLQDAWIVEQYRPFTLNQHVAGGRPWDLDGTRHGLRVLPPAQG
+RDEEGFAQGNGHAIHQQLAPLRRFGAKTVVIMSADHLYRMDLRPVLERHRERDAELTVVT
+TQVAEGASRFGVVSSDADGRVTAYDYKPDEPATDVVATEVFVADVDALTEVIESLLDSAS
+EEQVDDDDPAGAQLGDYGETIIPALVERGRVHEFRHEGYWKDVGTIDAYYQAHMALLRGD
+GLDLDDPRWPLISNFHPRPPAFIHPEAEVNGSMLCPGSRVRGTVTESVIGPGVVVEAGAT
+VHRSVLLGSATVPAGARLDAVIADVGARIPEGATGQTKPGPGNITVLTPDDRSTAEGDET
+TGHA
+>MOLHKGIG_00284
+MADPFPKDPEGAVVALVLAGGTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLR
+DVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQGRAEEGFARGNGHAIAQQLPL
+LEQFGAETVVVLSADHLYQLDLRPVLAEHARSGAELTVVTTETDEDPSRFGVVQVDDDGA
+VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSS
+LGDYGESIIPAFVARGRVREHRLVGYWRDIGTLDAYVRAHREILDGTGLDLAAEGWPLIT
+NPHQAPPAWVAPDARVSGSLLSPGCRIAGEVSDSVVGPGVVVAAGATVRGSLLLGDCEVP
+AGAVLDTVVVDVGGAVPAREVTGRAAPAEEVVVLTPQDRGPAEDETTGSGRPGRSD
+>NAFOICDF_00049
+MADPFPKDPAGSTVALVLAGGRGSRLDPLTAARSKPAVPFAGQYRLIDVVLSNLAHSGLK
+DVWIAEQYRPFTLNQHLAGGRPWDLDGTRHGLRILPPAEGREEEGFSAGNGHALAQQVPI
+LRSFGAERVVVLSADHLYQLDLRPVLAAHADSGAELTMVTTVTDEDPSRFGVVQADEDGA
+VTAYDYKPEDPEGRLVATEVFVFDVAALHEVVAELVAREKAAGEHADGEEDEDGDPVASS
+LGDYGETIIPAFVERGRVREHRLEGYWRDIGTLDAFYRAHMELLDGAGLDLAAPGWPLLT
+NPPAAPPARVGPRAEVSNALLSPGCVVKGTVEDSVLGPGVVVERGAHVRRSVLFGECIVP
+RGARLDAVIADVGAHIPAEEVGRSRPGPGNLTVLTPATRDPDSEDETTGGAAAKDG
+>MHAAABBN_02306
+MADPFPTDPEGAVVALVLAGGTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLR
+DVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQGRAEEGFARGNGHAIAQQLPL
+LEQFGAETVVVLSADHLYQLDLRPVLAEHARSGAELTVVTTETDEDPSRFGVVQVDDDGA
+VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSS
+LGDYGESIIPAFVARGRVREHRLVGYWRDIGTLDAYVRAHREILDGTGLDVAAEGWPLLT
+NPHAAPPAWVAPEATVTGSLLSPGCRIAGEVTDSVVGPSVVVEAGAVVRGSILLGECTVP
+SGAVLDTVIADVGAAIPAEGATGRAEPADEVVVLEPGERGPASSDETTGSGAPVRD
+>LFPAFLNI_00290
+MADPFPKDPEGAVVALVLAGGTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLR
+DVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQGRAEEGFARGNGHAIAQQLPL
+LEQFGAETVVVLSADHLYQLDLRPVLAEHTRSGAELTVVTTETDEDPSRFGVVQVDDDGA
+VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSS
+LGDYGESIIPAFVARGRVREHRLVGYWRDIGTLDAYVRAHREILDGTGLDVAAEGWPLLT
+NPHAAPPAWVAPEATVTGSLLSPGCRIAGEVTDSVVGPSVVVEAGAVVRGSILLGECTVP
+SGAVLDTVIADVGAAIPAEGATGRAEPADEVVVLEPGERGPASSDETTGSGAPVRD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000209.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000209.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34c148b45945ebecef2b70c17784567226b39f3d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000209.fa
@@ -0,0 +1,74 @@
+>ACLBLIBL_00072
+MQDPSSESHAALERLRGAPKPVPAPEEAAGAPRTPDQDDDGAATAEDPVPAAARTPADDP
+APAPSPSPPQDAETAPAPDASPASDADAPADVEADVEAPRPARRATPPRPRRPRPDLPPR
+PAPPRARPAHRLSPRRPMRGACARAAARTSTRRWSGRAPPAPPRSSAPRRDLSDILDRLG
+SPDLARFTAPLVGTVERILPAPGADPQKAAQAARRREEAEARRRARLQSGRERAAESARR
+RAAEHDRLAAEAAEREAALRDDDARSEARRADEEAAAAKEACRQERLRERRTAGRAAAEE
+RARLAAEAVEADRERERREAEEAAAAAAREEAALQARLQEEARARRERAEQEERLAQERA
+AEEARLAQAARIARRRREEERERQRREAERRRRLAQEAKARAAADQEKRRQQEQERRRRE
+AKVAEERARVQAERRAREEAELAERERRRLEAEAEAERRRQAQEAERRRREAERAEAERR
+ARAEEAERRRREAEEAARRAAEARRLHAERTRAHTVLHAERALAQARLLEDRARDAERRA
+AEEEARRLREHQDRESRALYRAARELEGPEVIPAASQRPLLARPEEGLTDEELVARARQA
+LPEWRHRQRLATKARAVGAETAAGRSAGPPTGPVPLIPGYTPAAPEEPAGPATVRDRRGQ
+LVLTLAWAAFVLAGVWGLGLFRFVPGLDALDAGPYPAAGDGRHGSGATVFSLFPLHPVIW
+PVLWLLTGLHVARQWGPGQGAAPRHRRTRGPMAGTLLALALWFPLTVLVPWGLESVLWLV
+ALALMLGAVRRLGARPAAGRLARLAEDGAPGALLGTLLAGAPTALAATLHAWGVHVGRFP
+TELVAALVLLTLLPGAVRLVLGGRGRMGVAVGMAWTLLCLALPRLLPSPLGAQQSAWVGF
+AAAFGALLLLTAAAVRRSWVRQIERDAARRPPPAVA
+>MOLHKGIG_00281
+MQDASSESRAALERLRAASAPRPDDAETRAPAARPRRALAAPGEISRRDLRRHERALRSG
+RSETAAERRVREDHRADVHRAMDRLRTPGAPAEQRPRRDLSEILDRLGSPDLARFADPLV
+GTVERILPAPGRDPEKAAEAARRRTAAEERRRARLRAGRAAEHERPVAEAAAAAQARDAA
+RARDAAALQARLDEEARRAQAARVARRRREEEKQRRRREAERRRRVAAEEKARAAAEAEA
+RRREREERRRREAEVAAERARVQAERRAREEAALAERERLRLEAEAEAERRRQAAEAERR
+RLEAERVEAERRRRAEEAERRRREAEEAARLEAERRRRQAARVRAHTVLHAERALAQARL
+LEDRAREAERRAAEDAARRRREHEERESRALARAARELEGPEVFPAAADRPLLSDPEERL
+TDEELFARARVALPEWRRRQRLSTKAQAVRAEATAHSSAGPVTGALPLIPGYTPAPPEEP
+AGSPTAADRRGQALLTVVWALFVLSGAWGLGLAGRVPGLGALDAGAYPLTADGRHGPGAS
+VFGLSPLHPAIWPVLWLLTGMYVLRQWGRGQGASPRHRRIRGAIAGALLALALWFPLAVL
+APGGFDVVPWLLALVLMLRVVRRLGARPAARRVARVAEDGALGVLLGTLLAGAPTAVGAA
+LHAWGVHVGWFPTELLALLVLVALLLAALRLVLGGRGRMGVALGMAWTLLCLALPRLLPS
+PLGAQQSVWVGLAAAFGALLLVTAAAVRRSWARQIERDAARRPHPAGA
+>NAFOICDF_00058
+MTSQDDDAPRPAPPAPRHAARPRRALAEPGRLAPEQLERHTRRLRGEPLPPETPEEAAAR
+AGRRHDLAAALDRLPAESAPAAPRPRADLSDLLDRIGTPDLARFADPLLGTVGRILPSGP
+SPERAAAAARRRAEHEGRRRAERAAGRARAAEAARRRAEETARREAEAAERARAARTVEE
+SRAEAVRAAEDAAREAERHRAERLRERREAARAAAADKARRVAEAAERARVEEEALLAVE
+ADAQAREVAAAQAEPDALARERRERADQEERRRRAALLARRRRDEERRRRRREAERARRE
+AEEQRERAARAERSAAEAARRRQAEEAAEAERRQMAVEAARARAEAERLAQEAARERRRR
+IAAARALPRTVAARHIAAGTAAEDRRRQAAARASEEAARVLAAHHDRETRALMAAARELD
+GPDVVPPAHLRPLLADPAEGLDDAALLERARAALPQWRRTGRLLTKADAVRAQTAHGAAD
+GTGPATGAFPIVPGYVPPSGPPEPRAPATREDRRHQLELTGAWLLFVLASAWGLGLFRLV
+PGLRVVDQGSYTAAHGGRYAFTTSVLSLFPLHPAVWPVLWLALGVYVAHQWGPGQGAAAR
+QRQTRRSVAGALALTALWFPLAVLVPWGLEFMVWLAALALMIRVMRGLTAVPARTRAAQT
+CTDGVLGGFLGLLLAAAPTTLASPVAATGVFWGWFPSALVAAALLWAVVLTGARLALQDR
+GRLGLALGMAWTLLCLALPRLLPSPLGAWQSAWVGLSAVAGGLGVLLLVVVRRTWVREIE
+EQAAAAPQGVPAGRVNGR
+>MHAAABBN_02296
+MQDASSESRAALERLRDASAPRPDDDATRAPAERPRRALAAPGEISRRDLRRHERALRSG
+RPETAAERRVREDRRADVHRAMDRLRTPGAPAQQRPRRDLSEILDRLGSPDLARFTDPLV
+GTVERILPAPGRDPEKAAEAARRRTAAEERRRARLRAGRERAAEAARRRAAEHERPVAEA
+AAAAQARDAARARDAAALQARLDEEARRAQAARVARRRREEEKQRRRREAERRRRVAAEE
+KARAAAEAEARRREREERRRREAEVAAERARVQAERRAREEAALAERERLRLEAEAEAER
+RRQAAEAERRRLEAERVEAERRRRAEEAERRRREAEEAARLEAERRRRQAARVRAYTVLH
+AERALAQARLLEDRAREAERRAAEDAARRRREHEERESRALARAARELEGPEVFPAAADR
+PLLSDPEERLTDEELFARARVALPEWRRRQRLSTKAQAVRAEATAHSSAGPVTGALPLIP
+GYTPAPPEEPAGSPTAADRRGQALLTVVWALFVLSGAWGLGLAGRVPGLGALDAGAYPLT
+ADGRHGPGASVFGLSPLHPAIWPVLWLLTGMYVLRQWGRGQGASPRHRRIRGAIAGALLA
+LALWFPLAVLAPGGFDVVPWLLALVLMLRVVRRLGARPAARRVARVAEDGALGVLLGTLL
+AGAPTAVGAALHAWGVHVGWFPTELLALLVLVALLLAALRLVLGGRGRMGVALGMAWTLL
+CLALPRLLPSPLGAQQSAWVGLAAAFGALLLVTAAAVRRSWARQIERDAARRPHPAGA
+>LFPAFLNI_00280
+MQDASSESRAALERLRGASAPRPDDDATRAPAARPRRALAAPGEISRRDLRRHERALRSG
+RPETAAERRVREDRRADVHRAMDRLRTPGAPAEQRPRRDLSEILDRLGSPDLARFADPLV
+GTVERILPAPGRDPEKAAEAARRRAAAEERRRARLRAGRERAAEVARRRAAEHERLAAEA
+AAAAQARDAARARDAAALQARLDEEARRAQAARVARRRREEEKQRRRREAERRRRVAAEE
+KARAAAEAEARRREREERRRREAEVAAERARVQAERRAREEAALAERERLRLEAEAEAER
+RRQAAEAERRRLEAERVEAERRRRAEEAERRRREAEEAARLEAERRRRQAARVRAHTVLH
+AERALAQARLLEDRAREAERRAAEDAARRRREHEERESRALARAARELEGPEVFPAAADR
+PLLSDPEERLTDEELFARARVALPEWRRRQRLSTKAQAVQAEATAHSSAGPVTGALPLIP
+GYTPAPPEEPAGSPTRADRRGQTLLTVAWALFVLSGAWGLGLAGRVPGLGALDAGAYPLT
+ADGRHGPGASVFGLSPLHPAIWPVLWLLTGMYVLRQWGPGQGASPRHRRIRGAVAGTLLA
+LALWFPLAVLAPGGLDVVPWLLALVLMLRVVRRLGARPAARRLARVAEDGALGVLLGTLL
+AGAPTAVGAALHAWGVHVDWFPTELLALLVLMALLLAALRLVLGGRGRLGVALGMAWTLL
+CLALPRLLPSPLGAQQSAWVGLAAAFGALLLVTAAAVRRSWARQIERDAARRPHPAGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000210.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000210.fa
new file mode 100644
index 0000000000000000000000000000000000000000..585627924efda4d6aca3c4431a55a1367005292b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000210.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_00073
+MPSYRARLQIGDLLPGHRPEEVMDLAEAAVQATHVLAAKDIEVVARVPRIVLRFTVPGSH
+RAGEDAEAAEVARRMAEAVSGVAATGRLDVLRRDGGRWVPVPAGPGR
+>MOLHKGIG_00280
+MPSYRARLQIGDLLPGHRPEEVMDLAEAAVQATHVLAAKDIEVVARVPRIVLRFTVPGSH
+RAGEDAEAAEVARRMAEAVSGVAVTGRLDVLRRDGGRWVPVPAGLGR
+>NAFOICDF_00059
+MPSYRARLQIGDVLPGHRPEEVLDTAEAAIGATHEVAAKDVEVVARVPRIVLRFTVPAAH
+RAAEDAEAAAVAGRMAEAVADVATVGRLDVLRREGGRWLPVSAR
+>MHAAABBN_02295
+MPSYRARLQIGDLLPGHRPDEVMDLAEAAVQATHVLAAKDIEVVARVPRIVLRFTVPGSH
+RAGEDAEAAEVARRMAEAVSGVAVTGRLDVLRRDGGRWVPVPAGLGR
+>LFPAFLNI_00279
+MPSYRARLQIGDLLPGHRPDEVMDLAEAAVQASHVLAAKDIEVVARVPRIVLRFTVHGSH
+RAGEDAEAAEVARRMAEAVSGVAVTGRLDVLRRDGGRWVPVPAGPGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000212.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000212.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d45c80a5ae28d9d841c08e11fcb7c7e5bc3ca423
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000212.fa
@@ -0,0 +1,31 @@
+>ACLBLIBL_00076
+MAPMTGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV
+KIAHGSVIRVRTDRQEERRAVPDTTFSPVDAGSPEERIVAVGKRHLEDTELTATAARLSH
+GLNLRSGSQLEDLFGMAERLYLLHEDVEGTLAALGLLTNLPWDGAVGRWKSIQAGLALAS
+QILRDEGEHIVAANLGKRLHEADEVPSEPGRAARVLEVRQRQLNEPQLYDREISRALQAR
+DAEAEYRWRRARFAQLLYLRGRGGSETLTDADLDSRIARELGTLRGLARDLDAKAAARS
+>MOLHKGIG_00277
+MAPVVGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV
+KIAHGSVIRVRTDRPEERRAVPDTTFSPVDAGSPEERIVAVGKRHLDDTELTATAARLSH
+GLNLRSGSQLEDVFGMAERLYLLHEDTEGTLATLGLLTNLPWDGAVGRWKSIQAALSLAS
+LILREEGEHIAAANLGRRLLEADEVPSEPGRASRVLEVRQRQLNEPPLYDREISRALQAR
+DAEAEYQWRRARFGQLLYLRARGGSETLTDADLDSRIARELGALRTLADELEAKAATRR
+>NAFOICDF_00061
+MSDGGAEVAPIAGGYLRHLKAQDVRPGDSFLTRRGEPAPAVASTRVVRDDFGTPALVIAT
+LVGGREVKIAHGSVIRVRTDRPEEVKAAADTAFSPVDAGSPESRIVAVGQRHLDDAELTA
+TAARLSHGLNLRSGAQLEDVFGMAERMYLLHEDVEGTLTTLGLLTNLPWDGAVGRWKSIQ
+AALGLAALILREDGDHITAANLGSRLKEADEVPSEPGRAARVLEVRQRQLDEPQLYDREI
+SRALQARDAEAEFRWRRARFAQLLYLRGRGGSQTLTDQDLDSRIHRELGTLRQLAKRLAA
+QAARA
+>MHAAABBN_02292
+MAPVVGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV
+KIAHGSVIRVRTDRPEERRAVPDTTFSPVDAGSPEERIVAVGKRHLDDTELTATAARLSH
+GLNLRSGSQLEDVFGMAERLYLLHEDTEGTLATLGLLTNLPWDGAVGRWKSIQAALSLAS
+LILREEGEHIAAANLGRRLLEADEVPSEPGRASRVLEVRQRQLNEPPLYDREISRALQAR
+DAEAEYQWRRARFDQLLYLRARGGSETLTDADLDSRIARELGTLRTLADELEAKAATRR
+>LFPAFLNI_00276
+MAPVVGGYLRHLKSQDVQPGDSFLTRRGEPAPPVASTRVMRDDFGTPALVIATLEGGREV
+KIAHGSVIRVRTDRPEERRAVPDTTFSPVDAGSPEERIVAVGKRHLEDTELTATAARLSH
+GLNLRSGSQLEDVFGMAERLYLLHEDTEGTLATLGLLTNLPWDGAVGRWKSIQAALSLAS
+LILREEGEHIAAANLGRRLLEADEVPSEPGRAARVLEVRQRQLNEPPLYDREISRALQAR
+DAEAEYQWRRARFDQLLYLRARGGSETLTDADLDSRIARELGTLRTLADELEAKAATRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000216.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000216.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5db0f19f31346c8b731c516a4b9f5ab67c703cd7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000216.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00090
+MTALASRPGAASRASRSAPVSPASRSTRRTHRRRTLVGAGTVLRRLAGAVGVVWATATLT
+FLMQFLLPGDRATLVFNLRAGQAQPRTAEELAPLNALFGFQDPVLVQYLHFLGGLLRGDL
+GTSYVTFEPVTTVIGDQLAPTLLLTGASIAIAWAVALVLLVATVRRARWVSGLASAVEAL
+LAALPHYWLGVILLVVFALGLGLFPVVGGTGPAALVLPALTMGLPLAGYLAQTMRSEYAS
+VLDQPFILTARTRGQSDAGIRVRHALRHALLPGLSLTGWAVGAQFSAAVIAEGVFSRPGI
+GGVLVDAANGRDLPVVCGVVVLIAIVYVLANLAVDVLYTVVDPRLRSAR
+>ACLBLIBL_00267
+MLRLIGKRLLLLIPTLFGLSVLLFLWVRSLPGGPATALLGDRATPEAVARVNAAYGFDKP
+LLEQYTTYMGRLLRGDFGTSTMTNRPVLEEFADRFPATLELSLFAIVFAVAIGIPLGYWA
+ARHVGRWQDNIAVVLSLIGVVVPVFFLAFILKWVFAVKLGWLPTDGRQDPRLDATHYTNF
+YVWDGISTGEWDAALNALTHLVLPGIALGTIPLAIIARITRASVLDVQNADFVRTARAKG
+LAPRLIRDRFIMRNALLPVSTTLGLQLGLLISGAVLTETVFAFNGIGRFLAQAIFQLDFP
+VLQGFIIFIALIYSLINLVVDVSYGLIDPRVRVS
+>NAFOICDF_00135
+MARRILLRLALALAVLLGAYTAAFLILYVMPGDPVTAMAAGGLEAGAISDADLQALRAEH
+GLDRPLPVQYLSQLAAAVTGDLGTSVQTGQPVTEAILDRLPTTLRLAWAALLVAVVAGPA
+IALVAAGTRRRWVRATASAIPALGAALPTFWTGLLLVQVFSFGLGWLPALGDDGLAGLVM
+PALTLGLPLSALIAQVMLRALDESGTQEYVETALASGQSRRRVLITHMLPNAALPTLAML
+GVITGNVVAGAVVVETVFSRPGVGQLTVQAVTAQDLPVVLGVVLLSSLVFVLVTLTVDLL
+SPLLDPRVGPAGAV
+>MHAAABBN_02133
+MLRLIGKRLLLLIPTLFGLSVLLFVWVRSLPGGPATALLGDRATPEAVARVNAAYGFDKP
+LLEQYVTYMGRLLRGDFGTSIMTNRPVVEEFADRFPATLELSIFAIVFAVVIGIPLGYWA
+ARHVGRWQDDVAVVLSLIGVVVPVFFLAFILKWVFAVKLGWLPTDGRQDPRIDATHYTNF
+YVWDGIITAEWDAALNALTHLVLPGIALGTIPLAIIARITRASVLDVQDADFVRTARAKG
+LAPRLIRDRFIMRNALLPVSTTLGLQLGLLISGAVLTETVFAFNGIGRFLAQAIFQLDFP
+VLQGFIIFIALLYSLINLVVDVSYGLIDPRVRVS
+>LFPAFLNI_00125
+MLRLIGKRLLLLIPTLFGLSVLLFVWVRSLPGGPATALLGDRATPEAVARVNAAYGFDKP
+LLEQYVTYMGRLLRGDFGTSIMTNRPVVEEFADRFPATLELSIFAIVFAVVIGIPLGYWA
+ARHVGRWQDDVAVVLSLIGVVVPVFFLAFILKWVFAVKLGWLPTDGRQDPRIDATHYTNF
+YVWDGIITAEWDAALNALTHLVLPGIALGTIPLAIIARITRASVLDVQDADFVRTARAKG
+LAPRLIRDRFIMRNALLPVSTTLGLQLGLLISGAVLTETVFAFNGIGRFLAQAIFQLDFP
+VLQGFIIFIALLYSLINLVVDVSYGLIDPRVRVS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000217.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000217.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d1dd6e5ca7091a3334ecbb3a06c5b6b5bde93c5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000217.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00095
+MTENLPTAEPEYDVAAPLDTDFYLALGDVSDDEKEVWRRARAFALEPDVLPRIREAWDRH
+EYPLDLVARLGAADLLRDGVPVDGLPEVSRVAAGLAMMELSRLDGSIATVAGVQGGLAMR
+SIQLCGSDEQRAELLPAMSRGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLRGHKKW
+IGNGAAGGVSVVWARSAEDEQVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVFV
+PDADVLPEARSFKDTSRVLFATRVGVAWSALGQAVGCYEAAVQYAGQRIQFGRPLAAAQT
+VQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASLAKYSATRAARSIAANARDLLGG
+NGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV
+>MOLHKGIG_00268
+MTETLPTVEPEYDVATPLDTDFYLALADVSDAEKDVWRRARAFALEPDVLPRIREAWDRH
+EYPLDLVARLGQADLLRDGVPVDGLPEISRVAAGLAMMELSRLDGSIATMTGVQGGLAMR
+SIQLCGSEEQRAEHLPAMARGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLHGHKKW
+IGNGAAGGVTVVWARSAEDEKVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVFV
+PDADVLPEARSFKDTSRVLFATRVGVAWSALGKAVGCYEAAVHYAGQRVQFGRPLAAAQS
+VQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASMAKYSATRAARSIAANARDLLGG
+NGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV
+>NAFOICDF_00066
+MTETLPTAEPDYSTITGPLDTDAYAVFAELPDEDLALARAARAFLTPEVQKRLQEAWDTG
+EYPTELIAGLAEADLLRDGVAVEGKPAQSRLACGLAAMETSRIDGSLATVVGVQGGLAMR
+SIEMCGSDEQKAKYLPAMDRGELFGAFALTEPTHGSDSVSLQTTATKVEGGWRISGHKKW
+IGNGAAGGITVTWARSAEDGQVKGFIVQQDAEGYSAEVIRGKMSLRAIHQAHITYDDVFV
+PDEDVMPGAQSFKNTAAVLFATRLGVAWAAVGHALGCYEAAVQYAKQRVQFGRPLAESQI
+VQERLARMLSELTQVQLLVLRAARLEDAGKLTGPQASLAKYSATRTARSIAANARDLLGG
+NGILLENEVGKHFADIEAIHTYEGTETVQALIVGRDITGVGAFA
+>MHAAABBN_02281
+MTETLPTVEPEYDVATPLDTDFYLALADVSDAEKDVWRRARAFALEPDVLPRIREAWDRH
+EYPLDLVARLGQADLLRDGVPVDGLPDVSRVAAGLAMMELSRLDGSIATMTGVQGGLAMR
+SIQLCGSEEQRAEHLPAMARGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLHGHKKW
+IGNGAAGGVTVVWARSAEDEKVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVFV
+PDADVLPEARSFKDTSRVLFATRVGVAWSALGKAVGCYEAAVHYAGQRVQFGRPLAAAQS
+VQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASMAKYSATRAARSIAANARDLLGG
+NGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV
+>LFPAFLNI_00266
+MTETLPTVEPEYDVATPLDTDFYLALADVSDAEKDVWRRARAFALEPDVLPRIREAWDRH
+EYPLDLVARLGQADLLRDGVPVDGLPDVSRVAAGLAMMELSRLDGSIATMTGVQGGLAMR
+SIQLCGSEEQRAEHLPAMARGELYGAFALTEPTHGSDSVSLETRAERVDGGWRLHGHKKW
+IGNGAAGGVTVVWARSAEDEKVRGFIVRQESEGYTAEVIKGKVALRAIDQAHITLDGVFV
+PDADVLPEARSFKDTSRVLFATRVGVAWSALGKAVGCYEAAVHYAGQRVQFGRPLAAAQS
+VQTRLAEMLSQLTQVQLLVLRATRLEDEGRLTGPMASMAKYSATRAARSIAANARDLLGG
+NGILIQNEVARHFADIEAIHTYEGTETVQGLIIGREITGVGAFV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000219.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000219.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24e7d9acfc33ac4bffc258cdf266d2d034754fdd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000219.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00097
+MSTEQNSTQTPAYRAAHVPAGQDLGHRWSTRVADHEDPADRRAIRQIAELTFESSAEADL
+VEELAGGGEGWLPQYSLVAMTASIPGTDLQSDPMGYGTLVRAHVGEAEVLALAPHGVLPE
+HQGEGAGTAIVNALLQKAQGDGEKVVVVYGWPEYYAKFGFRPGVEHGVTAAFADQPEALQ
+VLTLQDDAEVPSGEFRYPPAFGAENAQVAGRA
+>MOLHKGIG_00266
+MSAEQNSTQTPGHRTAHVPAGQDLGHRWSTREADHDDPADRRAVRQIAELAFASTAEADL
+VEALADGAEGWLPQYSLVAMTAAIPGTDLQSDPMGYGTLVRAHIDDAEVLALAPHGVLPE
+HQGEGAGTALVNALLQKAQADGEEVVVVYGWPEYYAKFGFHQASEHGVHAAFARQPEALQ
+ILTLQDGAEVPAGEFRYPPAFGAENAQVAGR
+>NAFOICDF_00068
+MSTEKGSTATPTYRAAHVPEGQDLGHRWSTRLAHHDDPADRRAVRQIAELTFESSAEADL
+VEELVASGEGWLPQYSLMAMTASIPGTDLYSDPMGYGTLVRAHIDDAEVLALAPHGVLPE
+HQGEGAGTALVNALLEKAQKDGEQAVVVYGWPEYYAKFGFRPAAEHGVTAAFATQPEALQ
+VIALQEGAEIPSGEFRYPPAFGAENAQVAGR
+>MHAAABBN_02279
+MSAEQNSIQTPGYRAAHVPAGQDLGHRWSTREADHDDPADRRAVRQIAELAFASTAEADL
+VEELAGGAEGWLPQYSLVAMTAAIPGTDLQSDPMGYGTLVRAHIDDAEVLALAPHGVLPE
+HQGEGAGTALVNALLQKAQADGEEVVVVYGWPEYYAKFGFHRASEHGVHAAFARQPEALQ
+VLTLQDGAEVPAGEFRYPPAFGAENAQVAGR
+>LFPAFLNI_00264
+MSAEQNSTQTPGHRAAHVPAGQDLGHRWSTREADHDDPADRRAVRQIAELAFASTAEADL
+VEELAGGAEGWLPQYSLVAMTAAIPGTDLQSDPMGYGTLVRAHIDDAQVLALAPHGVLPE
+HQGEGAGTALVNALLQKAQADGEEVVVVYGWPEYYAKFGFHRASEHGVHAAFARQPDALQ
+VLTLQDGAEVPAGEFRYPPAFGAENAQVAGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000220.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000220.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37374f658bdbfb1c6a23f4747c55cab5d4ae13c0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000220.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_00098
+MDRMILINLKYTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYLLIEGF
+TDEGAKAHVESPHFQEGIDAMRPLLASTPQIISEHVDAEGFGPMGELQID
+>MOLHKGIG_00265
+MDGMILINLKFTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYFLLEGF
+TDEGAQAHVASPHFQEGLDAMRPLLASTPQIISEQVGAEGFGPMGELQID
+>NAFOICDF_00069
+MILINLKFTVKPELADQWMDAVAKYIADVRSEPGNMFFEWYKPVEGGDNEFFLLEGFTDE
+GAQAHVASPHFQEGIDAMRPLLQSTPQIISEQIGAEGFGPMGEIQID
+>MHAAABBN_02278
+MDGMILINLKFTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYFLLEGF
+TDEGAQAHVASPHFQEGLDAMRPLLASTPQIISEQVGAEGFGPMGELQID
+>LFPAFLNI_00263
+MDGMILINLKFTVQPERADEWMDAVAKYTADVRSEPGNLFFEWYRPVEGGPNEYFLLEGF
+TDEGAQAHVASPHFQEGLDAMRPLLASTPQIISEQVGAEGFGPMGELQID
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000226.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000226.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb6ae5b4684a490ca41114804a5affa6f9497103
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000226.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00113
+MSDSTRNSPLHPVHEAAGATFTDFGGWNMPLKHGSELAEHKAVRTAAGLFDLSHMGEVRV
+TGPQAGAMLDYALSSVLSTLKPGRAKYALCLTDAGTILDDTIVYRMDDGEDGSEPDFMVV
+PNAGNIAAVHTALNQRASGWDATVEDQSSTTSLVAVQGPKAEAILAQAMPEAAEQLAALK
+YYGHLTLTVPTEAGDVTAVVARTGYTGEDGFELFLPASSTQEAGDRGSAVWNAVLKAAEA
+ADVELTLCGLASRDSLRLEAGMPLYGNELDTAHQPHASGVGFAVPASKEADFVGKAALVG
+KDDAEEVLVGLRGEGRRAARHGYAVLDESGERVGEVTSGAPSPTLGHPIALARVRRDVAA
+EGTSLQVDLRGRGEPFTVVATPFYRRER
+>MOLHKGIG_00256
+MSDSTRNSPLHPVHEAAGATFTDFGGWNMPLKYGSELAEHKAVRTSAGLFDLSHMGEIRV
+TGPEAGAMLDHALSSVLSTLKPGRAKYALCLTDAGTILDDTIVYRMDDGEAGSEPDYLVV
+PNAGNIAAVHTALNQRASGWDAVVEDESSTTALVAVQGPQAERILARAMPEAAAQLAELK
+YYGHLTLTVPTDAGDVTAVVARTGYTGEDGFELFLPAASTAEAGDRGSAVWNTMLSAADE
+AGVELTLCGLASRDSLRLEAGMPLYGNELDTGHQPHASGVGFAVPASKEADFVGRSALVG
+RDDVEEVLVGLQGAGRRAARHGYAVLDESGERVGEVTSGAPSPTLGHPIALARVRRDLAA
+EGTSLQVDLRGRGEPFTVVATPFYRRER
+>NAFOICDF_00081
+MTESTRNSPLHPVHEAAGASFTDFGGWNMPLKYGSELAEHKAVRESAGLFDLSHMGEVRV
+SGPESGAMLDHALSSSISVLKPGRAKYALCLTDAGTVLDDLIVYRTDSGAEGEDQEFLVV
+PNAGNISAVVTALTQRASGWDVEVHDESSTTALVAVQGPQSEAILARLMPASAQELAELK
+YYGHVTLTVPTAAGDVQAVVARTGYTGEDGFELFLPASSTAEAGDRGSAVWSAVVKAAEE
+AGIALTPCGLASRDSLRLEAGMPLYGNELDTAHQPHASGVSFAVPASKEGDFVGKAALVG
+KDEVEEVLVGLKGEGRRAARHGYSVLDADGAVIGEVTSGAPSPTLGHPVAMARIRREHAA
+EGTSVQVDLRGRGEPFTVVPLPFYTRAR
+>MHAAABBN_02270
+MSDSTRNSPLHPVHEAAGATFTDFGGWNMPLKYGSELAEHKAVRTSAGLFDLSHMGEIRV
+TGPEAGAMLDHALSSVLSTLKPGRAKYALCLTDAGTILDDTIVYRMDDGEAGSEPDYLVV
+PNAGNIAAVHTALNQRASGWDAAVEDESSTTALVAVQGPQAERILARAMPEAAAQLAELK
+YYGHLTLTVPTDAGDVIAVVARTGYTGEDGFELFLPAASTAEAGDRGSAVWNTMLSAADE
+AGVELTLCGLASRDSLRLEAGMPLYGNELDTGHQPHASGVGFAVPASKEADFVGRSALVG
+RDDVEEVLVGLQGAGRRAARHGYAVLDESGERVGEVTSGAPSPTLGHPIALARVRRDLAA
+EGTSLQVDLRGRGEPFTVVATPFYRRER
+>LFPAFLNI_00255
+MSDSTRNSPLHPVHEAAGATFTDFGGWNMPLKYGSELAEHKAVRTSAGLFDLSHMGEIRV
+TGPEAGAMLDHALSSVLSTLKPGRAKYALCLTDAGTILDDTIVYRMDDGEAGSEPDYLVV
+PNAGNIAAVHTALNQRASGWDAVVEDESSTTALVAVQGPQAEKILARAMPEAAAQLAELK
+YYGHLTLTVPTDAGDVIAVVARTGYTGEDGFELFLPAASTAEAGDRGSAVWNTMLSAADE
+AGVELTLCGLASRDSLRLEAGMPLYGNELDTGHQPHASGVGFAVPASKEADFVGRSALVG
+RDDVEEVLVGLQGAGRRAARHGYAVLDESGERVGEVTSGAPSPTLGHPIALARVRRDVAA
+EGTSLQVDLRGRGEPFTVVATPFYRRER
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000233.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000233.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5a98d47c5db89a8d0db19043ec8c3815513c1d6d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000233.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00128
+MRWHGDRAAASGVTALTNILGHPIICDAAGRGRSASVLTVQNSLRPAADSPTGPRAHASG
+RTEQLFGIRRHAAMPERDGALNPAAFEAGPWCLDLDGRPTGAAATVIMDNATAVAVHHAA
+PGVETVVTTELQINVLAPLPAFDAAAITEGRAEGPLLECWTRPLSWDAGGGVGRAWLEDA
+EGRRIVEATGWFQAVPTGAPEHRAAFTAAADLPRGPETRVPMPGLLAARPETLPPAARAG
+RPAVTAAVAPGARFAPKPELANPSGAVHGGAMTLRAVVAAQAAMPDRELYDVQAVRVVFT
+RPGHGEMVALTRVRHAGRSLRLVDVDLVPVGEDGAPVAEKPMVQVQVTFRAAR
+>MOLHKGIG_00241
+MICRVATGPWASVLPVQTTTSPTADSPTGPRSHPSGRTEQLFGIRRHALMTERDGALNPA
+AFEVGPWCLDLDGRPTGAAATVIMDNATAVAVHHAARDIETVVTTELQVNVLGPLPAFDA
+AAVTAGDEDGPLLECWTRPLAWDAAGGVARAWLEDADGRRVVEATGWFQSVPAGAPERMA
+EFVAAGRLPRGAETRVPMPGLLAARPESLPTADPDVRPAVDAAATAGARFAPKPELANPS
+GAVHGGAMTLRAVTAAQAAMPDRERYDVQAVRVVFVRPGHGEMVALTRVRHAGRSLRLVD
+VDLVPVGADGVPVADKPMVQVQVTFRAARS
+>NAFOICDF_00095
+MDEITLNPDADARWRGPRRLLLGRPEQLAGLRRRETAEIQGDTLHPGDWEVGPWVRDLDG
+RPTGAAACVAADNLTAVALHWAAAEAYDAMVTTQLQVNVLRPLPVFDPADPADRPRLRML
+GTPLSTDALGGCARGVIVDDDGTAYVEATGWFQATPGPMSLALEAFREHAALPVAEADRA
+DLPAVTAVVADSVPAPRPGERPAVSQEMTAGLRFRAEPLLDNPGGMTHGGIQCLRAVLAA
+QAALPDRLEYDVQAVQVVFARPGLGEQVALTRVRHAGRSLRIVEVELVGVDPETGAPQAG
+RPSILAQVSFRAAQG
+>MHAAABBN_02254
+MISRVAAGPWASVLPVQTTTSPTADSPTGPRSHPSGRTEQLFGIRRHALMTERDGALNPA
+AFEVGPWCLDLDGRPTGAAATVIMDNATAVAVHHAARDIETVVTTELQVNVLGPLPAFDA
+AVAAGDEDGPLLECWTRPLSWDAAGGVARAWLEDADGRRVVEATGWFQSVPAGAPERMAE
+FVAAGRLPRGAETRVPMPELLAARPESLPTADPDTRPAVAAAPTAGARFAPKPELANPSG
+AVHGGAMTLRAVTAAQAAMPDRERYDVQAVRVVFVRPGHGEMVALTRVRHAGRSLRLVDV
+DLVPVGADGVPVADKPMVQVQVTFRATRS
+>LFPAFLNI_00242
+MISRVAAGPWASVLPVQTTTSPTADSPTGPRSHPSGRTEQLFGIRRHALMTERDGALNPA
+AFEVGPWCLDLDGRPTGAAATVIMDNATAVAVHHAARDIETVVTTELQVNVLGPLPAFDA
+AAVTAGDEDGPLLECWTRPLAWDAGGGVARAWLEDADGRRVVEATGWFQSVPAGAPERMA
+EFVAAGRLPRGAETRVPMPELLAARPESLPTADPDTRPAVAAAPTAGARFAPKPELANPS
+GAVHGGAMTLRAVTAAQAAMPDRERYDVQAVHVVFVRPGHGEMVALTRVRHAGRSLRLVD
+VDLVPAGADGVPVADKPMVQVQVTFRAARS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000234.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000234.fa
new file mode 100644
index 0000000000000000000000000000000000000000..52e8ac31fbc75345d13998570ec24a313d760083
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000234.fa
@@ -0,0 +1,52 @@
+>ACLBLIBL_00131
+MARRRRRPGGRSGLGHPAGAPAAAPAPIAASASPTQSPRPAEPAAAQPRLAEQDVAAAVA
+RPAAAAPVAVESDLVPLGQRRRMGGYVPLAREGEWFAELAAADAAPAGETAEPTVLEAAH
+DDAAPAAEAAVTEPAAPTTTAAAAAATTAAAQAPAAPAQPAAAAAAPTAPDTRSAPPASA
+AQPPRAEPAAASGRPARATKKTDAAEEAPAPSRLRKALPLVAGVVVLALVAVLAARWLRT
+LDPVADFIAAYDGHPALAEGTPVGMPPWLGWQHFLNMFLMVLIIRTGLQIRNETRPPANF
+TPKKDGAFSARGNTPKKFSLTIWTHQALDALWLLNGVVFVVLLFVTGQWARIVPTDPYVF
+HHAFSAGIQYLSLDWPTENGWVHYNALQMLSYTLVVFVAAPLAALTGWRMSSWFPTEAKG
+LNRAFPMEAARKVHFPVMLFFVLFILTHVFLVFFTGALKNLNHMYTSRGDATDAWGLVVF
+LVSVAVTAAAWFLLRPSFTAPAASKFGTVGR
+>MOLHKGIG_00240
+MPKQRMAGYVPLKGAPAETEPAPAPAQDTTTAAPASAAAAVPVAPTAPTSGLTPLSARRR
+MAGYVPFAREAEWLGGAPAPAAGSIPAAAPARSVAPEPIAASASPTRAPAPAETEPVVPD
+VAAVVASATGAPAAAGVGAPVESDLVPLAKRRRMAGYVPFAREGEWFTELAAVGGPTAPE
+MVAQEVDAPEQATAEPTAEPAAAAPARPVVAELADVEPADAEPAVAAPVAAASAPEPAPT
+APDTRSAPPASAVQPPRAATGTPARTAETDAAESAVPSRLRKALPAVAGVVVLALLAVLA
+ARWLRSLDPVADFIATYDGHPVLPEGTPEGMPWWMGWQHFLNMFLMVLIIRTGLQIRHET
+RPPANFTPTKDGLFSARGNTPKKFSLTIWMHQALDALWLLNGLIFVVLLIATGHWARIVP
+TDPHVFQHALSAGIQYLSLDWPTENGWVHYNALQMLSYALVVFVAAPLAALTGWRMSSWF
+PTEAKGLNKAFPMEVARKVHFPVMVFFVAFIVVHVFLVAFTGLLTNLNHMYTSRGGATDA
+WGLVVFLVSVAVTAAAWFFLKPAFTAPVASRFGTVGR
+>NAFOICDF_00096
+MPQRMQGYTEFRGEPWPPRDRVPQAPAPTTTPAVAADERRPGRRMVGYTAFRGEPWPPVR
+EAAQPAPAPAAAASPAEVTEAAAAAVPLEATAPAGIAVPGRRMAGYTAFRGEPWPPARVG
+AAPQAPEPAPMATVEPAVATGPTPTVEPVAAGAPETTPKPAPSTGRRVAAAVGGVVVLGL
+LAVLGARWLLTLPEVAAFVARYPGVPRHPEVTPVGIPAWLAWQHFLNLFLLVLVVRTGLQ
+VRHETRPPATFTPHQPGPFAPRSATGGTYSLTVWIHQALDALWLLNGLVFVVLLFATGHW
+MRLIPTDPQTPQHMVSTALQYLSLQWPEHDGWLHYNALQMVTYAGVVFVLAPLAALTGFR
+MSSWWPSRNTALSRGFPMELARRLHYPTMLAFVLFVVVHVVLVLFSGVLHELNAMFLARN
+AADAWGLAAFLVGCAVIAAGWVLLKPAIVAPVAERFGRVSR
+>MHAAABBN_02253
+MPKQRMAGYVPLKGAPAETEPAPAPGQDTTTAAPASAAAAVPVAPTAPTSGLTPLSARRR
+MAGYVPFAREAEWLGGAPAPAAGSIPAAAPARSVAPEPIAASASPTRAPAPAETEPVVPD
+VAAVVASATGAPAAAGVGAPVESDLVPLAKRRRMVGYVPFAREGEWFTELAAVGGPTAPE
+TAAQEVVAEPATAEPAAAEPADAEPAVAAPVAAAPAAEPAPTAPDTRSAPPASTAQPPRA
+APGAATGTPARAAETDAAESAAPSRLRKALPAVAGVVVLALLAVLAGRGLRSLDPVADFI
+ATYDGHPVLPEGTPEGMPWWMGWQHFLNMFLMVLIIRTGLQIRHETRPPANFTPTKDGLF
+SARGNTPKKFSLTIWMHQALDALWLLNGVIFVVLLIVTGHWARIVPTDPHVFQHAVSAGI
+QYLSLDWPTENGWVHYNALQMLSYSLVVFVAAPLAALTGWRMSSWFPTKATGLNKAFPME
+VARKVHFPVMVFFVAFILVHVFLVAFTGLLTNLNHMYTSRGGATDAWGLVVFLVSVAVTA
+AAWFFLKPAFTAPVASRFGTVGR
+>LFPAFLNI_00241
+MPKQRMAGYVPLKGAPAETEPAPAPAQDTTTAAPASAAAAVPVAPTAPTSGLTPLSARRR
+MAGYVPFAREAEWLGGAPAPAAGSIPAAAPARSVAPEPIAASASPTRAPAPAETEPVVPD
+VAAVVASATGAPAAAGVGAPVESDLVPLAKRRRMAGYVPFAREGEWFTELAAVGGPTAPE
+MVAQEVVAEPATAEPAAAEPADAEPAVAAPVAAAPAAEPAPTAPDTRSAPPASTAQPPRA
+VPGAATGTPARAAETDAAESAAPSRLRKALPAVAGVVVLALLAVLAGRWLRSLDPVADFI
+ATYDGHPVLPEGTPEGMPWWMGWQHFLNMFLMVLIIRTGLQIRHETRPPANFTPTKDGLF
+SARGNTPKKFSLTIWTHQALDALWLLNGVIFVVLLIVTGHWARIVPTDPHVFQHALSAGI
+QYLSLDWPTENGWVHYNALQMLSYALVVFVAAPLAALTGWRMSSWFPTEAKGLNKAFPME
+VARKVHFPVMVFFVAFIVVHVFLVAFTGLLTNLNHMYTSRGGATDAWGLVVFLVSVAVTA
+AAWFFLKPAFTAPVASRFGTVGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000237.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000237.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1368cdd94b37ae409b2155089ab74256b7a19c51
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000237.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00134
+MSPAAPSADPADGDRPDVPAVPASSLMLVRPEQDGDTSVFALRRAGSMAFSAHATAFPGG
+RVDPADDLPDALWEGTDLAAWGRRLGLPHEPVDALGTLAALDPAEGAGRVLAAAVRETFE
+ETGVLLARDTATGAPVDPDRVAALPEDLRDAVERHEVDFGDLLRDEGLRPDAGALVPWSR
+WITPHGGPRRYDTFFFAVHLPAGQSPERMSSEAAEHGWASPAELLRRFRAGEVNLMAPTW
+WQLRTLDDAGEDVHAGRSRFEPLEGVMLVAGQGPAFSHADEYLRDLAAFRAAAHVEESKD
+NIL
+>MOLHKGIG_00237
+MSPAAPPTAPPAAEDRPRVPAVPASSLVLVRPGAGGEISVFTVRRAGTMAFSAHATAFPG
+GRVDPADDLSDRLWEGTDLADWGRRLGLPHEPADAHGTLAELDPAEGAGRVLAAAVRETF
+EETGVLLARDAVTGTPVDPARVAAFPDELRDAVERHEVDFGELLDREGLRPDAGALVPWS
+RWITPHGGPRRYDTFFFAVHLPQGQSPERMSSEAASHGWASPAELLRRFRVGKVNLMAPT
+WWQLRTLVDAGEDVHAGRSRFEPLEGVMLVAGQGPVFPHADEYLRDLTAFRAAAQVEESK
+DNIL
+>NAFOICDF_00099
+MDAAQTSSSETLPVEATPARAAASLLLLRDGAAGLEVFHVHRAGTMAFSAHATAFPGGRV
+DPSDDALPVPGADLAAWARRLGLEDRPVETQPEDDPARVAARFLAAVVRETFEETGVLLA
+RAADGGPVPPEAAAALAGRREDVEAHAADLGALLAEHGLAADVSGLRAWQRWITPLSVPR
+RYDTAFFLVAVPAGQDPDRLTTEATEHGWARPADLITAFQAGDVNLMAPQWAQLRALMDL
+PDVEAALRAGAAAEPVPVVQLASEASPEERTREFSHAAEYREHLRSFRTHDRVQDTPDNV
+L
+>MHAAABBN_02250
+MSPAAPPTAPPAAEDRPRVPAVPASSLVLVRPGAGGETSVFTVRRAGTMAFSAHATAFPG
+GRVDPADDLPDRLWEGTDLADWGRRLGLPHEPVDAHGTLTELDPAEGAGRVLAAAVRETF
+EETGVLLARDAVTGTPVDPARVAAFPDELRDAVERHEVDFGELLDREGLRPDAGALVPWS
+RWITPHGGPRRYDTFFFAVHLPHGQSPERMSSEAASHGWASPAELLRRFRAGEVNLMAPT
+WWQLRTLVDAGEDIHAGRSRFEPLEGVMLVAGQGPVFPHADEYLRDLMAFRAAAQVEESK
+DNIL
+>LFPAFLNI_00238
+MSPAAPPAEPSAAEDRPRVPAVPASSLVLVRPGAGGEISVFTVRRAGTMAFSAHATAFPG
+GRVDPADDLPDRLWEGTDLAEWGRRLGLPHEPVDAHGTLTELDPAEGAGRVLAAAVRETF
+EETGVLLARDAVTGTPVDPARVAAFPDELRDAVERHEVDFGELLDREGLRPDAGALVPWS
+RWITPHGGPRRYDTFFFAVHLPQGQSPERMSSEAASHGWASPAELLRRFRAGKVNLMAPT
+WWQLRTLVDAGEDIHAGRSRFEPLEGVMLVAGQGPVFPHADEYLRDLTAFRAAAQVEESK
+DNIL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000242.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000242.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d77d8486be707308bd7e6605adf901292d5fecee
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000242.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00147
+MSTPSPIGLLLDVDGPVASTQTRTVPDGIVATLVRLAGRGVPVGFNTGRSADFLLHSVIG
+PLRAAGLPADAPFFAVCEKGAVWFPFSAVPAGTLPEVTVDAPAPAWVRTDPAMALDPGLR
+ERIWELNRERAGDLQFVDRTKLAMVSLEMRVGADQAAYEAVRDDVAAGVEEMLAERGLAD
+EVRVDPTVISVDVEHRSSGKDLGVDRCRALMAEAGVPVPGRWFTAGDSRTDYAMADRLHA
+IGLAVEHLDVRPADGIPATPYPVLTAADLAGRGVGNAEDVHERAGESLLRWVERDLLD
+>MOLHKGIG_00232
+MRTSSPIGLLLDVDAPVASTETRTVPEGIIDVLVRLARRGVPVGFNTGRSTDFLLHNLIA
+PLRDAGLPDDAPFHAICEKGAVWFPFSAVPSGDLPDVTVDGTAPDWLRTDPDMAIDADTR
+DAIWALNDERAGDLQFTDRTKLAMVSLEKTVGADQTEYERVRDDVAAGVEDLLAERGLAE
+EVRVAPSVISVDVEHRSSGKDLGVERCFDLLAEAGTPVPERWLTAGDSRSDYAMADRLHE
+RGLAVEHMDVRPADGVPEKPYGVVTAAILAERGIGDADDVHERAGESLLRWVERDLLR
+>NAFOICDF_00105
+MTSPSPIGLLLDVDGPVASTETRAVPEGIVTTLVRLAAARVPVGFNTGRSADFLLHSVIG
+PLRAAGLPEDAPFFAICEKGAVWFPFSDVPAGDLPAVTVDAPTPGWVRTDPAMAVDADVR
+DAIWEINGERAGDLQFVDRTKLLMVSLEKTVGADQDAYVQVRDDVAAGIEDLLRERGLAE
+DVRVDPTVISIDVEHRTSGKDLGVDRCLGMLAEVGVAVPERWFTAGDSRTDYAMADALHA
+MGAPVEHMDVRPADGIPERPYRVLTAADLAERGVGQAEDVHERAGESLLRWVERDLLA
+>MHAAABBN_02245
+MRTSSPIGLLLDVDAPVASTETRTVPEGIIDVLVRLARRGVPVGFNTGRSTDFLLHNLIA
+PLRDAGLPDDAPFHAICEKGAVWFPFSAVPSGDLPDVTVDGTAPDWLRTDPDMAIDADTR
+DAIWALNDERAGDLQFTDHTKLAMVSLEKTVGADQTEYERVRDDVAARVEDLLAERGLAE
+EVRVAPSVISVDVEHRSSGKDLGVERCFDLLAEAGTPVPERWLTAGDSRSDYAMADRLHE
+RGLAVEHMDVRPADGVPEKPYGVVTAAILAERGIGDADDVHERAGESLLRWVERDLLR
+>LFPAFLNI_00233
+MRTPSPIGLLLDVDGPVASTETRTVPEGIIDVLVRLARRGVPVGFNTGRSTDFLLHSVIA
+PLRDAGLPDDAPFHAVCEKGAVWFPFSAVPSGDLPDVTVDGTAPDWLRTDPDMAIDADTR
+DAIWALNDERAGDLQFTDHTKLAMVSLEKTVGADQTEYERVRDDVAAGVEGLLAERGLAE
+EVRVAPSVISVDVEHRSSGKDLGVERCFDLLAEAGTPVPERWLTAGDSRSDYAMADRLHE
+RGLTVEHMDVRPADGVPEKPYGVVTAAILAERGIGDAEDVHERAGESLLRWVERDLLR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000246.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000246.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fc5ecf969db079266a4dfaf2c39a6a6353833565
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000246.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00153
+MPAGRYAPSPTGALHLGNLRTAIVAWLAARATDRTFLLRVEDLDRVRSGAEAAQLSELAA
+VGLDWDAEPVRQSERTGLYDDAVAALRAAHGADAVYECFCSRKDIAEATSAPHPAPADDD
+GAPGPAGAAPLRPPGFYPGTCRGLTAAQRAERRRVRPAALRIDAVQVAGLPEGEIPRAEA
+VDLLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSTPRQRWLAA
+ALCAARGEALPQTSYLHVPLVLNAEGRRLAKRDGAVTLEDLAAADPSWTPERVRDRLLSS
+LGLPPGPPADAVPAFARMLEDGSLPREPWMFDPAAFAGA
+>MOLHKGIG_00228
+MPAGRYAPSPTGSLHLGNLRTALVAWLAARATNRAFLLRVEDLDRVRSGAEADQRADLAA
+VGLDWDAEPVRQSERTALYDAAVAALRAVHGPDAVYECFCSRKDIAEATSAPHPRPDDGA
+PASGGAVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDVAKVAGLPAGETPRATAVD
+VLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAEAL
+CAARGEPTPAVEYLHVPLVLNAEGRRLAKRDGAVTLEDLSAQDPAWTPERVRDRLLESLG
+LPAGPLAAAVPAFDPAALPRVPWVFTGL
+>NAFOICDF_00110
+MPAGRYAPSPTGTLHLGNLRTALVAWLAARATGRTFLLRIEDLDRVCSGAEAGQLADLAA
+VGLDWDGEPVHQSERTALYDAAVAALRAAHGADAVYECFCSRKDIAEATSAPHPRPDDGA
+PASGGTVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDAAKVAGLPAGEIPRATAVD
+VLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAEAL
+CVARGEPTPAVEYLHVPLVLNAEGRRLAKRDGAVTLGDLAAQDPAWTPARLRDRLLESLG
+LPAGPLAVAVRAFDPAALPRDPWVFTGL
+>MHAAABBN_02241
+MPAGRYAPSPTGSLHLGNLRTALVAWLAARATDRAFLLRIEDLDRVRSGAEAGQRADLAA
+VGLDWDAEPVRQSERTALYDAAVAALRAAHGADAVYECFCSRKDIAEATSAPHPRPDDGA
+PASGGAVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDAAKVAGLPAGEIPRATAVD
+VLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAEAL
+CDGRGEPTPAVEYLHVPLVLNAEGRRLAKRDGAVTLEDLAAQDPAWTPERVRDRLLESLG
+LPAGPLAAAVPAFDPAALPRDPWVFTGL
+>LFPAFLNI_00229
+MPAGRYAPSPTGSLHLGNLRTALVAWLAARATDRAFLLRVEDLDRVRSGAEAGQRADLAA
+VGLDWDAEPVRQSERTALYDAAVAALRAAHGADAVYECFCSRKDIAEATSAPHPRPDDGA
+PASGGTVPLRPPGFYPGTCRGLTEAERAERRRVRPAALRIDVAKVAGLPAGEIPRATAVD
+VLHGEVTGLVDDLVLRRNDGAYAYNLAVVVDDLAQGVDQVVRGDDLLDSAPRQRWLAEAL
+CSARGEPTPAVEYLHVPLVLNAAGRRLAKRDGAVTLEDLAAQDPAWTPERVRDRLLESLD
+LPPGPLAAAVPAFDPAALPRDPWVFTGL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000253.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000253.fa
new file mode 100644
index 0000000000000000000000000000000000000000..57897b46bd6736f73415a3dcae3e920ae2cb7f38
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000253.fa
@@ -0,0 +1,17 @@
+>ACLBLIBL_00169
+MTDPCPCGAGLPLAECCGRLHARFAADGALTAPTAEALMRSRYAAFALLGEAGADDDGTQ
+GTDGASGPGGTGPGHAGPGHAGPDRARAMAAYLAATWAPEHRPAVEDLLPEAGERAPRFT
+RLAVTDVRDGGPFQDRGIVEFTALGHGEEGRFRLRERSRFRREDGAWLYVDGDVA
+>MOLHKGIG_00214
+MRSRYTAFARLGEAGPAEAQAMADYLAATWAPEHRPPAAELLPAAGEQAPRFTRLAVLDV
+RDGGPFQDAGTVEFVAVGAGAEGRFRLHEVSRFRREDGVWRYVDGDVR
+>NAFOICDF_00120
+MTEAPCPCGLGLPYPECCGRLHAAHAADGSLTAPTAEALMRSRYTAFARLGEVEGAGATG
+AADVAATVAYLRATWAPEHRPSTAELTPGPGDPAPAFTRLAVLAVEGGGPFQDVGEVEFA
+AVGRGPEGRFRLHERSRFRRESGVWLYVDGDVTA
+>MHAAABBN_02207
+MRSRYTAFARLGEAGPAEARAMADYLAATWVPEHRPTAAELLPTEGEQAPRFTRLAVLDV
+RDGGPFQDAGTVEFVAVGTGAEGRFRLHEVSRFRREDGIWRYVDGDVR
+>LFPAFLNI_00214
+MRSRYTAFARLGEAGPAEVRAMADYLAATWAPEHRPTAAELLPAAGEPAPRFTRLAVLDV
+RDGGPFQDAGTVEFVAVGTGAEGRFRLHEVSRFRREDGIWRYVNGDVR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000257.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000257.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5ea779bd65afed8fc0145b9c520bb82b86616842
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000257.fa
@@ -0,0 +1,70 @@
+>ACLBLIBL_00175
+MSQQFSIETVADAAANPDIEQPWAELGLKENEYAQIREILGRRPTAAELAMYSVMWSEHC
+SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ
+GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI
+GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGLGNKVVLFGARTGGDGIGGASVLA
+SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFAGSLVEGIQDLGAAGISCATSELAS
+NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPDNVAAFEAVMAKWDVEYSWL
+GEVTGDGRLVITWDGEVIVDVDPRTVAHDGPVYERPYARPGWQDRVQADTFRASEAGADL
+PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTAMAAPDDAGVVRVDEETGMGVA
+LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPENPDVMWQFAEA
+VRGLADGCQVLGIPVTGGNVSLYNQTGATPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG
+QAIYLLGETADELDGSEFARLRGHLGGVPPKVDLAKERLLGELLVNMSRDGMIDAAHDVS
+GGGLAATLSEMVLRHGVGARVVLDEVLRRDGVDLFTALFSETQARAVVAVPRTEEVRFTD
+MTTARGYTVTRIGVVDADSAALEVQDAFTLPIAELREGWEATLPKHFG
+>MOLHKGIG_00211
+MSQQFNIETVADAQATPDVEQPWAELGLKENEYAEIKKILGRRPTAAELAMYSVMWSEHC
+SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ
+GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI
+GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA
+SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS
+NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEYSWL
+GEVTGDGRLIITWDGEVIVDVDPRTVAHDGPVYERPYARPAWQDELQADTFRSSEAGQDL
+PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTALAAPDDAGVVRVDEETGIGVA
+LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPEDPDVMWQFAEA
+VRGLADGCQTLGIPVTGGNVSLYNQTGSTPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG
+QAIYLLGETADELDGSEFARLRGHLGGLPPKVDLKKERLLGELLVNMSRDGMIDAAHDVS
+GGGLAATLSEMVLRFGVGARVVLDEVLRRAGVDLFTALFSETQARAVVAVPRTEEVRFTD
+MTTARGYAAVRIGVVDADSAALEVQDAFTLPIAELREAWEATLPKHFG
+>NAFOICDF_00124
+MSTQFTIETVEQAAANPDVAQPWAELGLKEDEYARIREILGRRPTAAELAMYSVMWSEHC
+SYKSSKVHLRQFGDTLTEEMKEHMMVGIGENAGVTDLGDGWAVTFKVESHNHPSFVEPYQ
+GAATGIGGIVRDIISMGARPVAVMDPLRFGAVDHPDTARVVHGVVAGIGGYGNSLGLPNI
+GGEVAFDPSYQGNPLVNALAVGVLRHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA
+SESFDDGGKPAKRPSVQAGDPFAEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS
+NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEHSWL
+GEVTGDGRLVITWDGETIVDVDPRTVAHDGPVYERPCHRPSFQDALQADTFRSSAAGQDL
+PATGEELKAAVVELMASPNMADVSWITRQYDRYVRGNTALASPDDAGVVRVDEETGMGVA
+VATDCNDRYAYLDPYAGAQLSLAEAYRNVTTTGAVPLAVTDCLNFGSPEDPEVMWQFAEA
+VRGLADACQVLGVPVTGGNVSLYNQTGGVAIHPTPTVGVLGRFDDVLRRTPSGFGTDADG
+QAVYLLGVTADELDGSEYANLRGHLGGVPPKVDLAQERLLGELLVNMSRDGMVDAAHDVS
+KGGLAATLADMVLRFGVGARIVLDEVVRRDGVDVFTALFSETQGRTVVSVPRTEEVRFTD
+MTTARGYTVTRIGVVDAQSDALEVQGQFTLPIAELREAWEATLPKHFG
+>MHAAABBN_02204
+MSQQFNIETVADAQATPDVEQPWAELGLKENEYAEIKKILGRRPTAAELAMYSVMWSEHC
+SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ
+GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI
+GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA
+SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS
+NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEYSWL
+GEVTGDGRLIITWDGEVIVDVDPRTVAHDGPVYERPYARPAWQDELQADTFRSSEAGQDL
+PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTALAAPDDAGVVRVDEETGIGVA
+LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPEDPDVMWQFAEA
+VRGLADGCQTLGIPVTGGNVSLYNQTGSTPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG
+QAIYLLGETADELDGSEFARLRGHLGGLPPKVDLKKERLLGELLVNMSRDGMIDAAHDVS
+GGGLAATLSEMVLRFGVGARVVLDEVLRRAGVDLFTALFSETQARAVVAVPRTEEVRFTD
+MTTARGYAAVRIGVVDADSAALEVQDAFTLPIAELREAWEATLPKHFG
+>LFPAFLNI_00211
+MSQQFNIETVADAQATPDVEQPWAELGLKENEYAEIKKILGRRPTAAELAMYSVMWSEHC
+SYKSSKVHLRQFGEKLTDEMKQHMMVGIGENAGVTDLGDGWAVTFKVESHNSPSYVEPYQ
+GAATGIGGIVRDIISMGARPVAVMDPLRFGAIDHPDTARVFHGVVAGIGGYGNSLGLPNI
+GGETRFDPIYQGNPLVNALAVGVLKHEDLRLANASGVGNKVVLFGARTGGDGIGGASVLA
+SESFDGDGKPAKRPSVQVGDPFSEKVLIECCLELFRDSLVEGIQDLGAAGISCATSELAS
+NGEGGMRVELTDVLLRDSTLTPGEILMSESQERMMAVVTPENVAAFEAVMAKWDVEYSWL
+GEVTGDGRLIITWDGEVIVDVDPRTVAHDGPVYERPYARPAWQDELQADTFRSSEAGQHL
+PATGEELRAAVVELMSSPNLADTSWITRQYDRYVRGNTALAAPDDAGVVRVDEETGMGVA
+LATDCNDRFTYLDPYTGAQASLAEAYRNVTTAGAVPLAVSDCLNFGSPEDPDVMWQFAEA
+VRGLADGCQTLGIPVTGGNVSLYNQTGSTPIHPTPTVAVLGQLDDVLRRTPSGFAPDADG
+QAIYLLGETADELDGSEFARLRGHLGGLPPKVDLKKERLLGELLVNMSRDGMIDAAHDVS
+GGGLAATLSEMVLRFGVGARVVLDEVLRRDGVDLFTALFSETQARAVVAVPRTEEVRFTD
+MTTARGYAAVRIGVVDADSAALEVQDAFTLPITELREAWEATLPKHFG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000264.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000264.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a316434cf3425e5322cefa595cf58449913a575d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000264.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00202
+MARYVPAPAPEPVPAAEEAALRQGRARPWWPYLLTAAVSVALLVWTVVAYPGLPEQVPVR
+WGIDGRPDRWEDTTFGTVAFGPIFGLGMTAFLALIAAMIPAMTGVHGATSAWRRVRQEGV
+NRGVREGMGWIALLSLLMTAPTTAEVLSAGAWRMPWWLMPLLLTALMVGVFGALRATLGR
+WTRWADGVAADLGHRPTPEELAEDKTWTPLGMKDDPEDPTVFPAKRPGYGVGTTINIGTR
+AGRLLVYGFVAVFMVALPLATWIGAYLAR
+>MOLHKGIG_00197
+MPHPPRPTPDDVPAAERAALRRGRLRPWLPFLLAAALCLALLGWALVALPGLPERVPTHW
+GVDGRPDAWEDASFGTVATGPLIGLGVTGFLALVSAMVTVLVPTDPGLSPWRRVRQAGVH
+RGVQECLGWSCVLIVLVLAPTTAEVLAAGAWTMPWWILPLTLTVLMVGVFPAMRASTRRW
+TRWSDRVAAELGYRPTAAERAEDEVWTPLGLKRDPDDPAVFPTKRPGYGVGVTVNLATPA
+GRWLVRGFVVVVIVGLPLALWLGAFAAR
+>NAFOICDF_00150
+MPHPPRPTPDDVPAAERAALRRGRWIPWLPYLLTAAVSAGLLVWAIVALPGLPDRVPVHW
+GIDGRPDAWEEKSFGTVAFGPLLGLGMTALLAFCAALTPAMTATPQDASPWRRVRQEGVN
+RGVREALGWLTLLIALATAPSTVEVLSNGAWRPAWWLMPLVLTLVMLGTVGVFGPALRRW
+TGWADRTAQDLGYRADFAELAEDAKWTPLGLKNDPEDPSAFPAKREGYGVGATVNLATTT
+GRLLVYGFVALFVIGLPAALWIGAFLNR
+>MHAAABBN_02193
+MPHPSRPTPDDVPAAERAALRRGRLRPWLPFLLAAALCLALLGWALVALPGLPERVPTHW
+GVDGRPDAWEDTSFGTVATGPLIGLGMTGFLALVSAMVTALVPTDPGLSPWRRVRQAGVH
+RGVQECLGWPCVLIVLVLAPMTAEVLAAGAWTMPWWLLPLTLTVLMVGVFPAMRVSTRRW
+TRWSDRVAAELGYRPTAAELAEDEVWTPLGLKRDPDDPAVFPAKRPGYGVGVTVNLATPA
+GRWLVRGFVAVFIVGLPLALWLGAFAAR
+>LFPAFLNI_00197
+MTHPPHPVPADVPAAERAALRRGRLRPWLPFLLAAALCLALLGWALVALPGLPERVPTHW
+GVDGRPDAWEDASFGTVATGPLIGLGMTGFLALVSAMVTALVPMDPGLSPWRRVRQPGVH
+RGVQACLGWSCVLIVLVLAPTTAEVLAAGAWTMAWWLLPLTLTVLMVGIFPAMRAGTRRW
+TRWADRVAADLGHRPTAAELAEDEVWTPLGLKRDPEDPAVFPAKRPGYGVGVTVNLATPA
+GRWLVRGFVAVFIVGLPLALWLGAFAAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000265.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000265.fa
new file mode 100644
index 0000000000000000000000000000000000000000..63cc0060053a5d7b447a10594fc5643112d1da1e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000265.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00203
+MTTETRLLLLADTHIPPRARAMPAQVWDEVARADVVLHAGDWVEESVLDELEARSRRLVG
+VWGNNDDGALRARLPEVARVEIGGVRIAMVHETGAARGRERRMAEAFPDADVLVFGHSHI
+PWDTVAGPETANPGLRLLNPGSPTDRRRQPVCTLMRAVVRDGGLADVELVPVDRTP
+>MOLHKGIG_00196
+MPDDVAVRLLLIADTHIPRRARALPAQVWAEVARADVVLHAGDWVTEDVLDDLDARAARL
+VGVWGNNDGPKLRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS
+HIPWDTVAGPDTANPGLRLLNPGSCTDRRRQPVCTLMRAVVRGGRLEDVELVSVDRTP
+>NAFOICDF_00151
+MTTRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDAQAARLVGVW
+GNNDGPRLRARLPEVARVEIGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHSHIPW
+DTVAGPETANPGLRLLNPGSCTDRRRQPVCTLMRAVVRGGRLEDVELVPVDRTP
+>MHAAABBN_02192
+MPDDVAVRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDARAARL
+VGVWGNNDGPGPRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS
+HIPWDTVAGPETANPGLRLLNPGSCTDRRRQPVCTLIRAVARDGRLEDVELVPVDRTP
+>LFPAFLNI_00196
+MPDDVAVRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDARAARL
+VGVWGNNDGPGPRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS
+HIPWDTVAGPETANPGLRLLNPGSCTDRRRQPVCTLIRAVARDGRLEDVELVPVDRTP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000270.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000270.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de054af6f001192bc17ec4c6e14c34601796932b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000270.fa
@@ -0,0 +1,88 @@
+>ACLBLIBL_00209
+MSSNFDFLAPVWPRVHENAVRAESYLHADPRSACFYARRTVELVVEGIYRLRNLPEPYKA
+DLAARINADAFLHEADPRIVQKLNVIRQRGNDAVHKLPDIDPRTAAFVLTELHHVLLWAA
+FRHSAAGPALDMQARFAPALAPQAAPLTREEVVQLNDLIEKKDAEAAAALAASEQAREQL
+EADLAAARAELTAAKEAAGAVVDPRDYTENDTRDLFIDQLLNEAGWPLTAARDREFPVTG
+MPTPTGDGFVDYVLWGADGKPVALVEAKRTTASVQLGQDQAARYADALEARFGRRPVIFY
+TNGVEHYLWDDAAGYPPRQVRGFYTPAQLDTLIQRRAGRRPLAQTPVKAEIAGRPYQERA
+IRAIGEAFENKRRATLLVMATGTGKTRTAVALVDQMARAGWVKRVLFLADRQALVKQAAD
+AFVEHGFAGTTVNLLKNRHGEGRVYASTYPTMLGLIQESTGQGARFDPGYFDLVIVDEAH
+RSVYAKYGEIFRHFDALLVGLTATPKDEIDRNTYGLFGLEPGVPTDAYTLDEAVADGFLV
+PPRGVSVGTAFLRRGIRYDQLPAEEQEAWDALDWGEDEAPEEVSSEEINRFLFNADTVDR
+VLSTLMEHGHKVADGERLGKTIVFAKNQPHAEFILQRFDAQWPELGGRYAQIITHASRYP
+EAMLDDFKTPGKAPHIAISVDMLDTGVDVPDVVNLVFFKLVRSKTKFWQMIGRGTRLRPD
+LYGPGRDKEDFLVFDWCQNLEFFNQDLPESDGSTQKSLTQRLFEDRLALVVALDALDDDG
+GAPAAVGPEERAVRRTAAEELQAAIARLTLENVLVRPHRREVEEFQRPEAWTSLSAQAAE
+RARALAGVVTGLPGEDVDAKRFDLLIVRRQLADLSGEGGTAERIRATVQSLAENLLSKDA
+IPAVKEQIILLEAVAGEDWWEGVTLGMLEHARKKLRGLVQFIEKVRRSRVYTDFADTLTQ
+LEEVDVVRPTPGVDIERFWAKVSEPLRRNESSLALQKLRHGKQLTKQDLESLEQLLRSIG
+AEDVHLAAAKSEGEGQLGLFVRMLVGMDRAAAQGVVADFVQDRTLTQAQIRFLGHMVEEL
+TANGVLDAGRLFESPYTDDAPEGPFGLFEEAQVYSLRERLDLVRASAMVPGPEANADGDE
+ARGVVA
+>MOLHKGIG_00035
+MRRIPRTGPLDEGPGLLTLFSAFMDTPSDAARVAAEERARALIDEQFRRAGWSVQDGAQK
+NLMASAGVAVREVTMRAGHGRVDYLLYVDRRPVGVIEAKPVGTTLAGVEWQSGMYADGLP
+DDALKRAVVVDGRLPFVFESTGSESYLTNGYDPNPRARRVFSIPRPEYFSQLMRDAEADP
+DAPTWRGKVRAMPPLQTEGLRPAQIDAVRGLERSLAEQRHDRSLIQMATGAGKTFTAITA
+AYRLLAHGGFRRILFLVDRNNLADQTLAEFENYRLPGDGRRFTEVYPVDKLRRAGMRDSA
+NVVISTIQRVYAGLQGKEVPDSDDPMLDEFVPDRPVTVDYSADLPPESFDLVIVDEAHRS
+IYGVWRGVLEYFDAHVVGLTATPGKQTLGFFRQNLVSEYTYPQSVADGVNVDFDLYRIRT
+QISEEGSTIEAGTVVPVQDKSTRIERFETLDEDLDYTRTQLDRAVVSTNQIRLVLEVFRD
+RLFTEIFPGRTEVPKTLIFAKDDNHAESIVRTVREVFGRGNEFAAKITYSARDPKGQLQA
+FRNSPALRVAVTVDMIATGTDVKPLECVLFMRDVRSAQYFEQMKGRGARTIPDADFQAVT
+PDAATKTRFVIVDAVGVTEHDFVDPPLNRQKAVPLKKLLEKAASLTITEDEAATLASRLA
+KLELELSDSERQELDDVAGGSVRQMVKDLVAAVDADEQASVRAEAAARGEDEDRALEEHI
+ERAVTPLAANPDLRMRILELRRAHDRVIDEVSADVLLDAYGVVDADKARSVVESWSAYLE
+EHRDEITAVQVMFEAGEGRLQYAQVAELAERIKRPPYSWTPEILWKAYESLDAGRVRRSD
+HHTLTDLVSLLRFATGTDDELVPFADRVRENYAGWLLAQEQAGAEFSDTQRWWLDRMVEV
+IGASAELTVDDLEGAPFTDRGGIDGAVRDLGPRAGLLIEELNEELTA
+>MOLHKGIG_00190
+MATGTGKTCTAVALVDQMARAGWVKRVLFLADRQALVKQAADAFVEHGFVGTTVNLLKNR
+HGEGRVYASTYPTMLGLIQESTGQGARFDPGYFDLVIVDEAHRSVYAKYGEIFRHFDALL
+VGLTATPKDEIDRNTYGLFGLEPGVPTDAYTLDEAVADGFLVPPRGVSVGTTFLRRGTRY
+DQLPAEEQEAWDALDWGEDEAPEEVSSEEINRFLFNADTVDRVLSTLREHGHKVAGSERL
+GKTIVFAKNQPHAEFILQRFDAQWPELGGRYAQIITHASRYPDALLDDFKTPGKAPHIAI
+SVDMLDTGVDVPDVVNLVFFKLIRSKTKFWQMIGRGTRLRPDLYGPGRDKEDFLVFDWCQ
+NLEFFNQDLPESDGFTQRSLTQRLFEDRLALVVALDALDDDAGAPAAVGPEERAVRELRR
+TAAEELQAAIARLTLENVLARPLRREVEEFQRPEAWTSLSAQAAERARALAGVVTGLPGE
+DVDAKRFDLLIVRRQLADLTGEAGTAERIRATVQSLGENLLSKDAIPAVKEQIILLEAVA
+GEEWWEGVTLGMLEHARKKLRGLVQFIEKVRRSRVYTDFADTLTQLEEVDVVRPTPGVDI
+ERFWAKVSEPLRHNESSLALQKLRHGKQLTEPDLESLEQLLRSIGAEDAHLAAAKSEGEG
+QLGLFVRMLVGMDRAAAQGVVADFVQDRTLTQARIRFLGHMVEELTANGVLDAGRLFESP
+YTDDAPEGPFGLFEEAQVYSLRERLDFVRTSAMVPGPEANAGGDEARGVVA
+>MHAAABBN_02020
+MAVDITYDEALIEEIAARFDLRDPNKNALTEIVQRIADGGIGYQEMVADLATGVGKTFLM
+SSLIEYLAQQGVRHVLVVTPGSTIQRKTLANFDAASAKYVAGADIAPFVVTPDNFQAANV
+GSVLRNPQRLKVFVFNVQQLIRPTDKVSRKVRSEDENLGDALYSHLENADDLFVIADEHH
+VYREKAKAFSAAIRDLNPVALVGLTATPDKDDYGKVVFQYTLGEAIADGYVKVPVIVYRK
+DGTKDERTQLRDACQLLGHKEKSYAVYRETNRDAPTVKPVLFVVCQTIEHATEVGQLLAQ
+SGMIGDGSQVLEITSQSSDVALEALAKVEEPDSPIRAIVSVNMLREGWDVKNIAVIVALR
+RLASQTLTEQILGRGLRLPFGARTGIADVDQVDLVAHDSYQQLLAQKDVLRQRIQLPSTA
+VEVDDQGFATTTEVDPNQPVPVEPLAGSSQHDQIGGSGGSSSLAPAPGQWTLFDWEEDDS
+AQGEDYQPNPGLIFEETEQRVESQVPEPQYRVKDAPQIIFPRREPRLVHSPFSLSDIPDG
+DAQKAGAAFVKEVPTFIFRDALEAKRKGDQVEIISTPQGTSEAQQTLAGLDVVQAELTEA
+IMQQPEVPAERPSKNAAKRLVKAFMKGAGVTNDEETAQWGTKRRQQAVEGMRTMIRDKIT
+SRPRQEKFEFVKIELPLEPVTVAADAVKAHNVVKFKKGLQYVGWEKNVMPVATFDAGTTE
+WELARLMDRDPNIKWWVRVYVGGQAFIPTPEGRYFPDFIALDVDGVHWLIEGKADDHAKD
+DSVLRKKKAAENWARAVRDDGDFGTWRYMFATESNIKNSAGSWNALLMSTKPE
+>LFPAFLNI_00190
+MSSNFDFLAPVWPRVHENAVRAESYLHTDPRSACFYARRTMELVVEGIYRLRGLPEPYKA
+DLAARINADAFLHEADPRIVQKLNVIRQRGNDAVHKLLDIDPRTAAFVLTELHHVLLWAA
+FRHSAAGPALDMQARFDPALAPQAAPLTREEVVQLNDLIEKRDAEAAAALGASEQARAQL
+EADLAAARAELTAVKEAAGAVVDPRDYTENDTRDLFIDQLLNEAGWPLTDTRGREFPVTG
+MPTPTGDGFVDYVLWGADGKPVALVEAKRTTASVQLGQDQAARYADALEARFGRRPVIFY
+TNGVEHYLWDDAAGYPPRQVRGFYTPAQLDTLIQRRAGRRPLAQTPVKAEIAGRPYQERA
+IRAIGEAFENKRRAALLVMATGTGKTRTAVALVDQMARAGWVKRVLFLADRQALVKQAAD
+AFVEHGFAGTTVNLLKNRHGEGRIYASTYPTMLGLIQESTGQGARFDPGYFDLVIVDEAH
+RSVYAKYGEIFRHFDALLVGLTATPKDEIDRNTYGLFGLEPGVPTDAYTLDEAVADGFLV
+PPRGVSVGTTFLRRGIRYDQLPAEEQEAWDALDWGEDEAPEEVSSEEINRFLFNADTVDR
+VLSTLMEHGHKVADGERLGKTIVFAKNQPHAEFILQRFDAQWPELGGRYAQIITHASRYP
+DALLDDFKTPGKAPHIAISVDMLDTGVDVPDVVNLVFFKLVRSKTKFWQMIGRGTRLRPD
+LYGPGRDKEDFLVFDWCQNLEFFNQDLPESDGSTQKSLTQRLFEDRLALVVALDALDDDA
+GAPATAGPEERAVRELRRTAAEELQAAIARLTLENVLARPLRREVEEFQRPEAWTSLSAQ
+AAERARALAGVVTGLPGEDVDAKRFDLLIVRRQLADLTGEAGTSERIRATVQSLAENLLS
+KDAIPAVKEQIILLEAVAGEEWWEGVTLGMLEHARKKLRGLVQFIEKVRRSRVYTDFADT
+LTQLEEVDVVRPTPGVDIERFWAKVSEPLRRNESSLALQKLRHGKQLTEQDLESLEQLLR
+SIGAEDVHLAAAKSEGEGQLGLFVRMLVGMDRAAAQGVVADFVQDRTLTQAQIRFLGHMV
+EELTANGVLDAGRLFESPYTDDAPEGPFGLFEEAQVYSLRERLDFVRTSAMVPGPEANAG
+GDEARGVVA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000271.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000271.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da93ea90352a481e6ae467e8586e60d68b2aab86
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000271.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_00214
+MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV
+STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR
+PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGADGALRPAGEA
+LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR
+VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR
+DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER
+RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ
+EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV
+PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAWKSEGTEAEGH
+>MOLHKGIG_00187
+MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV
+STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR
+PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGTDGALRPAGEA
+LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR
+VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR
+DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER
+RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ
+EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV
+PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH
+>NAFOICDF_00159
+MTTTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGVSTG
+FGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVRPVV
+VETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGADGALRPAGEALAE
+AGIEPVELREKEGLALVNGTEGMLGMLIMALADLDELVDTVDLTAAMSVEALLGTDRVFV
+PELHLPLRPHPGQAASADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLRDTL
+AYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSERRTD
+RMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQEDH
+VSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGVPGP
+GPDQYMAPQLAAAEQALRDGSVLAAVAEALAGASADAEPQDLAEESAGAEAEGH
+>MHAAABBN_02183
+MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV
+STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR
+PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGEDGALRPAGEA
+LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR
+VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR
+DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER
+RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ
+EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV
+PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH
+>LFPAFLNI_00184
+MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV
+STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR
+PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGTDGALRPAGEA
+LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR
+VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR
+DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER
+RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ
+EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV
+PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000273.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000273.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce42e5efbae5e53e539a0c000d8f60256554193c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000273.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_00216
+MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPVTINGASSIPLD
+HLVTWVRGLLGPADRWVGLAIIATGAVYPFASGRWRTSTTRTVFALLAVLGLVASAMVVF
+GVGPSWILDESIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL
+GLMDIWLWYFFSALVVTFVVTAITVCIPPLSRIPDEVYPGAVHSPEQAVTRDRFRVALRA
+AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGMIFYPL
+FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLVARFVIGVVCVSAIIFFSAVVPAI
+LATDIPVKMWHLLVIWVERVALTIVLATPLAHLVAALT
+>MOLHKGIG_00185
+MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPITINGASSIPLD
+HLVTWVRGLLGPADRWVGLAIIAAGAVYPFASGRWRTSTTRAVFAFLAVLGLVASAMVVF
+GVGPSWILDESIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL
+GLMDIWLWYFFGTLAVTFAVTAITVRIPPLSRIPDECYPGVTHSPEQAVTRDRFRVARRA
+AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGVIFYPL
+FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLGARFVIGVVCVSAIIFFSAVVPAI
+LATDIPVKMWHLLVIWVERVALTIVLATPLAHLVAALT
+>NAFOICDF_00161
+MTHAHPADGELHTDTTAMAAIEADSPRPPARWRMVVYSLIGIVMFFVPVTINGASSIPLD
+HLVTWVRGLLGPADRYVALALIAAGAVFPFATGRWRQSVTTTVFAFLGVVGLLTACMVVF
+GFGPSWVLDKGIGPFLLDKLVIPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL
+DLMDHWLWYFFGTLVVTFVVTAITVRIPPLSRIPDEPFPGAVHVPEEAVTQDRFRVARRA
+AEQTLAEAPSLGRNVWLNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWVGLIFQPV
+FWALGFSDPALMASASATSIAEMFIPATMLAGHEDFVARFVIGVVCVSAIIFFSALVPAI
+LATDIPVKLWHLVVIWVERVVLTVLLATPLGHLVAALTS
+>MHAAABBN_02181
+MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPVTINGASSIPLD
+HLVTWVRGLLGPADRWVGLAIIAAGAVYPFASGRWRTSTTRTVFALLAVLGLVASAMVVF
+GVGPSWILDKSIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAAGFSTVSATFMVIVAKTL
+GLMDIWLWYFFGTLVVTFAVTAITVRIPPLSRIPDEVYPGAVHSPELAVTRDRFRVARRA
+AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGVIFYPL
+FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLVARFVIGVVCVSAIIFFSAVVPAI
+LATDIPIPLWKLVVIWAERVALTILLAMPVAHLVAALT
+>LFPAFLNI_00182
+MDSSRPADHELHTDTTAMAAIEADAPRPPARWRMIVYSAIGIVMFFVPITINGASSIPLD
+HLVTWVRGLLGPADRWVGLAIIAAGAVYPFASGRWRTSTTRAVFAFLAVLGLVASAMVVF
+GVGPSWILDKSIGPFLMDKLVVPVGLIVPIGGVFLALVIGYGLMEFVGVYLRPAMRPIWR
+VPGRAAVDAVASFVGSYALGLLLTNRMYTGGRYTAREAAIIAVGFSTVSATFMVIVAKTL
+GLMDIWLWYFFGTLAVTFAVTAITVRIPPLSRIPDECYPGVTHSPELAVTRDRFRVARRA
+AEQTLAEAPSLPKNIWVNFRDGLVMVLQILPSIMSVGLIALVLATYTPVFEWIGVIFYPL
+FWALGYSDPGLLASASATSIAEMFIPATMAAGHEDLVARFVIGVVCVSAIIFFSAVVPAI
+LATDIPIPLWKLVVIWAERVALTILLATPVAHLVAALT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000277.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000277.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ebec26014968e42f0247c0f2e1c289b6adc02c24
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000277.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00220
+MRISVGQFGPVGDVEANLAVMARLAARAAGEGAELLVLPEEAMLGAREVGEEFPDAIAAA
+WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH
+RESDRISPGDGGVAAIELDGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK
+VEHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVVELADEREAVVTAEVTR
+ERIDEVRKFLPSLANRRTDVL
+>MOLHKGIG_00181
+MRISVGQFGPVGDVEENLAVMARLAARAAGEGADLLVLPEEAMLGAREVGEEFPDAVAAA
+WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH
+RESDRITPGDGGVAAIELGGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK
+VEHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVAELADEREAVATAEVTR
+ERIDEVREFLPSLANRRTDVL
+>NAFOICDF_00165
+MRIAVGQFGPTGRVEDNLEAMGRLAARAAAEGAGLLVLPEEAMLTFREVEDEFAHAVAGS
+WEPFTEGLARLARQHGLAIVAGGYEPSATDRPYNTLVAVDADGAVAGAYRKLHLYDAFEH
+RESELITPGDRGLVTVEVGGLTVGLQTCYDLRFPEVSRALALAGAQVLAIPAAWFAGEHK
+VDHWRTLLRARAVENTVWVAAADTASAATVGHSAIIDPLALTLAEADDDAAPETLLCADV
+TAERVEEVRRTVPVLANRRTDVLTPPVDVEPGG
+>MHAAABBN_02177
+MRISVGQFGPVGDVEANLAVMARLAARAAGEGADLLVLPEEAMLGAREVGEEFPDAVAAA
+WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH
+RESDRITPGDGGVAAIELGGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK
+VDHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVAELADEREAVVTAEVTR
+ERIDEVREFLPSLANRRTDVL
+>LFPAFLNI_00178
+MRISVGQFGPVGDVEANLAVMARLAARAAGEGADLLVLPEEAMLGAREVGEEFPDAVAAA
+WEPFAAGLAALAREHGIAVVAGGYEPGPDRRPYNTLLAVGADGARLGAYRKLHLYDAFAH
+RESDRITPGDGGVAAIELGGLRLGLLTCYDLRFPELSRRLAVEGADVLVIPAAWFSGEHK
+VDHWRTLLKARAVENTVWVAAADTCSDGTVGHSMIVDPLALPVAELADEREAVVTAEVTR
+ERIDEVREFLPSLANRRTDVL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000280.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000280.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea070d709042478a45564f6e9fc588431385ca89
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000280.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00223
+MSTAAPHTQHSDSASPAPTRKGPSVGTWRPWAVLPWALALLALPLIALALRSNFGANGWM
+TVIYMVFGALPHELFLMLMVGSLFLLPRVNPLDEQRGGIRLGRLLHTLLGVSWGSFALAA
+ILFPDAGDHPDSAATTPVLMDLLGKSTAMDVGSVAGLALAAVSALTGLAVIVVCVVRRIR
+AVR
+>MOLHKGIG_00178
+MSTAAPHTQHSDFPSPTPTRKGPSVGTWRPWAVLPWALALLALPLIALALRSNFGANGWM
+TVIYMVFGALPHELVLMVLVGSLFLLPRVNPQDEQRGGIRLGRLLHTLLGVSWGSFALAA
+IIFPDGGDHPDSGATTPVLMDLLGKSTAMDVGIVGGLALVAVSALTGLAVIVVCVVRRIR
+AVR
+>NAFOICDF_00169
+MAVPHPVMPPPGTPLPHQLRPAGPSVGTPRWLPAVLWIVAFALLPLCVIVGRFATENGGW
+LLFTYIMFGWMVQGGLGVLAAASLFLLPRVNPPVERRAGVRTGVVVHLLLGASWLTGLLG
+MLAFGDYGDAPGSETAPAPLVDLYGMDRAVEIGDAVGPPLVGISLLTGLAAVVLVVVRRL
+AAAVRS
+>MHAAABBN_02174
+MSTAAPGTQHSDFASPTPTRKGPSVGTWRPWAVLPWALALLALPLIALALRSNFGANGWM
+TVIYMVFGALPHELALVLMVGSLFLLPRVNPQDEQRGGIRLGRLLHTLLGISWGSFALAA
+IIFPDGGDHPDSGATTPVLMDLLGKSTAMDVGLVGGLALVAVSALTGLAVIVVCVVRRIR
+AVR
+>LFPAFLNI_00175
+MSTAAPGTQHSEFASPAPARKGPSVGTWRPWAVLPWALALLALPLIALALRSDFGANGWM
+TVIYMVFGALPHELVLMVLVGSLFLLPRVNPQDEQRGGLRLGRLLHTLLGVSWGSFALAA
+IIFPDGGDHPESGATTPVLMGLLGTSTAMDVGIVGGLALVAVSALTGLAVIVVCVVRRIR
+AVR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000286.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000286.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8bc443cd052da2ea293462c90776abf249916e80
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000286.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_00236
+MMTRPLPEDSATVDAVALGRRVRHLRKQAGLTLDQLADRTGVSGSHLSLVENARREPRLS
+LVQRIAEVLGVPVEDLLTGRAPTRRAELEIEVERFARSEHYASLGLPPLRIGPRTPTEVL
+EVIAGLEAELRRRLEEQAATPEEARRANAQLRARMRAVDNHYPDLEAEAQRLLDAIGHTG
+GPLGLHAVSSLAEHLGFTLSFVANLPHSTRSVTDLKHGRIHVSGGRASDHDRRTVVLQAL
+AAAVLGHGEPRDYEDFLSQRVAVNYLAGALLMPQRPASALLRAAQKRRDLSVDDLKDAFG
+VSYEAAAHRFTNLATVDLGIRCHFQKVHETGVIHKAYENDGLVFPADHTGAIEGQAACRR
+WGARQAFGRSDRFRAHTQYTDAPNGTYWCTSMVEHGPDGLFALSVGTAFEHARHFRGADT
+RHRITSTCPDPRCCRLPDPALEAEWGGHVWPAARMHAHLLAAMPTQAFPGVDEVEVFEFL
+ESQRDRTPGAPGADAPDGAGGVTP
+>MOLHKGIG_00147
+MDHGNGPPLVKNVTFFPKHVISSPVPSTVPRMMTRPLPEDSATVDTVALGRRVRHLRKQA
+GLTLDQLAERTGVSGSHLSLVENARREPRLSLVQRIAEVLGVPVEDLLTGRAPTRRAELE
+IEVERFARSEHYASLGLPPLRIGPRTPTEVLEVIAGLEAELRRRLEEQAATPEEARRANA
+QLRARMRAVDNHYPDLEAEAHRLLDAIGHTGGPLGLHAVSELAEHLGFTLRFVPDLPHST
+RSVTDLKHGRIHISGSRSSDHDRRTVVLQALAAAVLGHGEPRDYEDFLAQRVAVNYLAGA
+LLMPQRAASSLLRAAQKRRDLSVDDLKDAFGVSYEAAAHRFTNLATVDLGIRCHFQKVHE
+TGVIHKAYENDGIVFPADHTGAIEGQQACRKWGARQAFSRNDRFRAHAQYTDSPNGTFWC
+TSMIENGPDGLFALSVGTPFEHARYFRGADTRHRVTSTCPDPRCCRRPDPELEAAWGGHV
+WPAARMHAHLLAAMPTQTFPGVDEREVFEFLQAQEEREG
+>NAFOICDF_00821
+MATPTDPAHEPPRVDPLVLGRRLRHLRRVSGATLSDVAEKVGVTASHLSLVENGHREPRL
+TLLTALADVHGVGVEDLLTPEAPSRRAALEVAVERAQRGPLFQRLGLPALKIGPRTPDEV
+LEVIAGLQAELDRQMAERVSTPEEARRANSALREEMRACGNHYADLERRAQELREAVDVA
+DGPLTHHHVSALAEHLGFAVRFVPDLPHSTRSVTDLKNRRIYLARARRPDHDPRAVLLQA
+VCSSVLGHGEPADYADFLRQRVYTNYLAAAMMMPERGTVRALREAKERRDLSVDDLRDRF
+GVSWESAAHRFTNLATEHLGLTCHFAKVHESGVFHKAYENDGIPFPTDHIGAIEGQTACR
+HWTSRQVFSVADHLGAFPQYTDTPAGTYWSAAVVEPTSTGFYSLTVGVPFDDAKWFRGRE
+TSARTRSTCPDPKCCRLPSAELEAAWGGQAWPAARANAHLLAAMPGGAFPGVEEVQVFEF
+LQTQESRWPPEGSGAA
+>MHAAABBN_02161
+MMTRPLPEDSATVDTVALGRRVRHLRKQAGLTLDQLAERTGVSGSHLSLVENARREPRLS
+LVQRIAEVLGVPVEDLLTGRAPTRRAELEIEVERFARSEHYASLGLPPLRIGPRTPTEVL
+EVIAGLEAELRRRLEEQAATPEEARRANAQLRARMRAVDNHYPDLEAEAHRLLDAIGHTG
+GPLGLHAVSELAEHLGFTLRFVPDLPHSTRSVTDLKHGRIHISGSRSSDHDRRTVVLQAL
+AAAVLGHGEPRDYEDFLAQRVAVNYLAGALLMPQRAASSLLRAAQKRRDLSVDDLKDAFG
+VSYEAAAHRFTNLATVDLGIRCHFQKVHETGVIHKAYENDGIVFPADHTGAIEGQQACRK
+WGARQAFSRNDRFRAHTQYTDSPNGTFWCTSMIENGPDGLFALSVGTPFEHARYFRGADT
+RHRVTSTCPDPRCCRRPDPELEAAWGGHVWPAARMHAHLLAAMPTQTFPGVDEREVFEFL
+QAQEEREG
+>LFPAFLNI_00155
+MMTRPLPEDSATVDTVALGRRVRHLRKQAGLTLDQLAERTGVSGSHLSLVENARREPRLS
+LVQRIAEVLGVPVEDLLTGRAPTRRAELEIEVERFARSEHYASLGLPPLRIGPRTPTEVL
+EVIAGLEAELRRRLEEQAATPEEARRANAQLRARMRAVDNHYPDLEAEAHRLLDAIGHTG
+GPLGLHAVSELAEHLGFTLRFVPDLPHSTRSVTDLKHGRIHISGSRSSDHDRRTVVLQAL
+AAAVLGHGEPRDYEDFLAQRVAVNYLAGALLMPQRAASSLLRAAQKRRDLSVDDLKDAFG
+VSYEAAAHRFTNLATVDLGIRCHFQKVHETGVIHKAYENDGIVFPADHTGAIEGQQACRK
+WGARQAFSRNDRFRAHTQYTDSPNGTFWCTSMIENGPDGLFALSVGTPFEHARYFRGADT
+RHRVTSTCPDPRCCRRPDPELEAAWGGHVWPAARMHAHLLAAMPTQTFPGVDEREVFEFL
+QAQEEREG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000288.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000288.fa
new file mode 100644
index 0000000000000000000000000000000000000000..979aebe880c4e5f2f04fb6b69e4f2606862e93a2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000288.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00240
+MRAEQVTDPITYHGEGPVWAEHWGTAASGLAAGGGLRWVDMLAGDVLSLRADGAVERTHV
+GDVAAVVRPRAGGGAVLAVERGFALMSPEGELTTLPELWGPEAGLRMNEGGCDPDGRFHA
+GTMAYAKTPGAASLHRLSPGPDGGAGEVDVVLTGATTSNGLEWSPGGSLAYYNDTPTRQV
+AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV
+VEVPVQKTTACTFGGEDLGTLYITTSWENMERGEDPLAGALFAVRPGVTGLPARPFAS
+>MOLHKGIG_00144
+MRAEQVTDPIAYHGEGPVWAASWGAAAEGVTAGGGLRWVDMLAGDVLSLRADGTVDRTHV
+GDVAAALRPRAGGGAVVAVERGFALISPEGELTTLPELWGADAGIRMNEGGCDPDGRFHC
+GTMAYAKTPGAANLYRLAPGPDGGAGEVDVVLTGATTSNGLEWSPDGTLAYYNDTPTRQV
+AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV
+VEVPVQKTTACTFGGDDLGTLYITTSWENLERGEDPLAGALFAVRPGVTGLPARPFAG
+>NAFOICDF_00174
+MRADQVTDPLCYHGEGPVWAESWGGLRWVDMLAGDVLSLGADGGVTRRNVDPKVCAVVRP
+RVGGGAVFAVERGFALEDPDGTLHRLPPLWDDAAGLRMNEGGCDPDGRFYAGSMAYAKTP
+GAASLHRLSPAPEGGAGEVDVVLEGVTTSNGLAWSPDGSLAYYDDTPTRQVAVFDYSREE
+GLTNRRVLVDVLDGEGKPDGLCVDAEGGIWVAVISHGRIHRYTPEGVLDEVVEVPVQKTT
+ACTFGGDDLGTLYITTSWEGMERGEDPLAGALFSVRPGVAGLPTLPFAG
+>MHAAABBN_02158
+MRAEQVTDPITYHGEGPVWAASWGSAAEGVTAGGGLRWVDMLAGDVLSLRADGTVDRTHV
+GDVAAALRPRAGGGAVVAVERGFALISPEGELTTLPELWGADAGIRMNEGGCDPDGRFHC
+GTMAYAKTPGAANLYRLAPGPDGGAGEVDVVLTGATTSNGLEWSPDGTRAYYNDTPTRQV
+AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV
+VEVPVQKTTACTFGGDDLGTLYITTSWENLERGEDPLAGALFAVRPGVTGLPARPFAG
+>LFPAFLNI_00152
+MRAEQVTDPIAYHGEGPVWAASWGSAAEGVTAGGGLRWVDMLAGDVLSLRTDGTVDRTHV
+GDVAAALRPRAGGGAVVAVERGFALISPEGELTTLPELWGADAGIRMNEGGCDPDGRFHC
+GTMAYAKTPGAANLYRLAPGPDGGAGEVDVVLTGATTSNGLEWSPDGTRAYYNDTPTRQV
+AVFDYSREEGLTNRRVLVDVLDGEGKPDGLTVDAEGGIWVAVISHGQIHRYTPEGTLDEV
+VEVPVQKTTACTFGGDDLGTLYITTSWENLERGEDPLAGALFAVRPGVTGLPARPFAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000294.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000294.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9a45d47cf89da789e3d27badacfac440e88f0566
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000294.fa
@@ -0,0 +1,33 @@
+>ACLBLIBL_00246
+MRELQQQIIAEQGVRPQIDPAQEIERRVEFLVDYLEATGAAGFVLGISGGVDSTVGGRLA
+QLAVERRRARLGAPDAVALGGPEAPRGAPAADEAPSPQRPQFTAVRLPYRQQKDEADARA
+AMDFVDADREITLDIAAGVEGIASAFVEATGDEIADFDKGNVKARMRMVAQYALAGAHRQ
+LVIGTDHAAEAVTGFYTKFGDGGADVLPLSGLNKRQVRALGRELGAPEHLWNKVPTADLL
+DGNPGRTDEDELGMTYEHIDDYLEGGDIPEEAAEKLEGIWLRSRHKRTMPVTVHDDWWR
+>MOLHKGIG_00138
+MRELQQRIIAQQGVLPEIDPAAEVERRVAFLADYLAATGASGFVLGISGGVDSTVGGRLA
+QLAVERRRAQLGVTDAVALGGPDTTPPGEAGVGADVVPSRENPRFTAVRLPYKVQHDEAD
+ARAAMDFVGADQDVTLNIAEAVQGLAAAFAEAVGEPISDYNQGNVKARIRMTAQYAVAGA
+HGQLVIGTDHAAEAVTGFYTKFGDGGADVLPLAGLNKRQVRALGRELGAPEPLWNKVPTA
+DLLDGTPGQTDEAELGMTYEDIDDYLEGKDVPTEVAEKLEGIWLRSRHKRTTPVTIHDDW
+WR
+>NAFOICDF_00180
+MPEPYAGAMRELQQQIIAEMGVRPEVDPAAEVEARVRFLVDYLEATGASGFVLGISGGVD
+STTAGRLAQLAVERRRAELGTEAGDDAAPSRENPRFTAVRLPYRVQADEADATAAMDFVG
+ADGRVTLNIAEAVAGMASAFQEATGEPISDYNQGNVKARMRMVAQYAIAGAHGQLVIGTD
+HAAESITGFFTKFGDGGADVLPLAGLDKRQVRAVAKELGAPEHLWAKVPTADLLDGSPGR
+ADEDELGLSYEHIDDYLEGREIPEEAAEKLEGVWRRSRHKRTTPVTIHDDWWR
+>MHAAABBN_02152
+MRELQQRIIAQQGVLPEIDPAAEVERRVAFLADYLAATGASGFVLGISGGVDSTVGGRLA
+QLAVERRRAQLGVPDAVALGGPGTTPPGEAGVGADVVPSRENPRFTAVRLPYKVQHDEAD
+ARAAMDFVGADQDVTLNIAEAVQGLAAAFAEAVGEPISDYNQGNVKARIRMTAQYAVAGA
+HGQLVIGTDQAAEAITGFYTKFGDGGADVLPLAGLNKRQVRALGRELGAPEPLWNKVPTA
+DLLDGTPGQTDEAELGMTYEDIDDYLEGKDVPTEVAEKLEGIWLRSRHKRTTPVTIHDDW
+WR
+>LFPAFLNI_00146
+MRELQQRIIAQQGVLPEIDPAAEVERRVAFLVDYLAATGASGFVLGISGGVDSTVGGRLA
+QLAVERRRAQLGVTDAVALGGPGTTPPGEAGVGADVVPSRENPRFTAVRLPYKVQHDEAD
+ARAALDFVGADQDVTLNIAEAVQGLAAAFAEAVGEPISDYNQGNVKARIRMTAQYAVAGA
+HGQLVIGTDQAAEAITGFYTKFGDGGADVLPLAGLNKRQVRALGRELGAPEPLWNKVPTA
+DLLDGTPGQTDEAELGMTYEDIDDYLEGKDVPTEVAEKLEGIWLRSRHKRTTPVTIHDDW
+WR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000302.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000302.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de12f6e92b0414158e23bc57a603ef8a0686759c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000302.fa
@@ -0,0 +1,34 @@
+>ACLBLIBL_00260
+MITPGVFAISSGTAEILPDPWTDGVYLLKVNGVESSQLNPDRPETLGFEYMRWAAAVLAH
+RFAPDAERLRVLHLGGAGCTFARWVTHTWPQAHQLAVELDAGLAELARTHFDLPRAPQLK
+IRVGEAGQVLAGLREATREVVFRDVFAPADPLSLAPDSPHVTPAHLTGADAAAHAARVLV
+PGGVYVLNIGGGPDLASVRREVAALRTAFAHVEVMADPAMLKGRRRGNVIAAASSVPLAA
+EELGGRAALARALRSDALPAQLVDDVARFAGGLAPDPTPLVQASDGTSEGASTQASPGPA
+Q
+>MOLHKGIG_00125
+MSRRSGRSSGRSSAASSSSRGSAARRGRAAEPEGIVPGVHEISHGTAEIREDPYEPGAFV
+LYVNGVESSPLDPDHPERMGFEYMRWAVAAVRAHWPEPTPLRALHLGGAGCALARWVDHA
+HPGSHQTAVEIDAGLAALARERFGLPRAPALRIRVADAAEVLATAHPASRDLIIRDVFAP
+DPTDLTGARHITPPGLTGLDAARAAARVLAPGGLYVLNVGGGPDLTSVRADVAAVVAAFE
+HVEVIADPPMLKGRRRGNVIVAASDAPVARPAADAPPGSDPRDRLARALRMDAFPARLAE
+DPRGFPAGVAPGITGLVPGPEA
+>NAFOICDF_00194
+MITPGTFPISSGTAEIVPDPWTDGVFLLKVNGVESSQLNPDRPETLGFEYMRWAAAVLTH
+RFAPDARLRVLHLGGAGCTFARWVTHTYPASHQLAVELDAGLAAVAREHFDLPRAPQLKI
+RVGEAGEVLAGLRDATREVVFRDVFAPDPADPTGALHVTPAHLTGLDAAAHAARVLTPGG
+VYLLNIGGGPDLTSVRREVAALTETFAHVEVMADPAMLKGRRRGNVIAAASSAPLSADGL
+GGRSALARALRSDALPAQLLDDVVAFTAGLTPDATPLVTPAEG
+>MHAAABBN_02139
+MSRRSSARRGRAAGGSAGPAGIEPGVHAITHGTAEIREDAFEPDAFILYVNGVESSPLDP
+ERPERMAFEYMRWAAAAVRAHWPEPTPLRALHLGGAGCALARWVDHAYPGSHQTAVEIDA
+GLAALARERFGLPRAPALRIRVADAAEVLATAHPASRDLIIRDVFAPDPTDLTGARHITP
+PGLTGLDAARAAARVLAPGGLYVLNVGGGPDLTSVRADVAAVVAAFEHVEVIADPPMLKG
+RRRGNVIVAASDAPVARPAADAPPGSDPRDRLARALRMDAFPARLAEDPRGFPAGVAPGI
+TGLVPGPEA
+>LFPAFLNI_00133
+MSRRSSARRGRAAGGAAGPAGIEPGVHAITHGTAEIRENAFEPGAFILYVNGVESSPLDP
+ERPERMAFEYMRWAAAAVRAHWPEPTPLRALHLGGAGCALARWVDHAYPGSHQTAVEIDA
+GLAALARERFGLPRAPALRIRVADAAEVLATAHPASRDLIIRDVFAPDPTDLTGARHITP
+PGLTGLDAARAAARVLAPGGLYVLNVGGGPDLTSVRADVAAVVAAFEHVEVIADPPMLKG
+RRRGNVIVAASDAPVARPAADAPPGSDPRDRLARALRMDAFPARLAEDPRGFPAGVAPGI
+TGLVPGPEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000304.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000304.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd8b6d91d0a277e8e0a5aa935bb28eae79d99c2c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000304.fa
@@ -0,0 +1,18 @@
+>ACLBLIBL_00262
+MIVAFSVAPSGTPADAAHQPGDEDSASVHRAVAAAVAVVRESGLPHRTSSMFTEIEGDWD
+EVMDVVRGAVDAVAPYGSRVSLVLKADIRPGHTGELDGKLARLEAALASDDVS
+>MOLHKGIG_00123
+MIVAFSVAPSGQPADSAHLPGDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGDWD
+EVMEVVRGAVDAVSSYGSRVSLVLKADIRPGHSGELDGKLERLEAALAEDGNGDAADAR
+>NAFOICDF_00196
+MIVAFSVSPSGAPADAAYAPSSDGDSASVHRAVAAAVAVVRASGLPHRTSSMFTEVEGEW
+DEVMGVVKRAVEAVEPYGSRVSLVLKADIRRGRTGELDGKLERLEAALTDGTPATPDRFR
+A
+>MHAAABBN_02137
+MIVAFSVAPSGQPADSAHLPGDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGDWD
+EVMEVVRGAVDAVSSYGSRVSLVLKADIRPGHTGELDGKLERLESALAEDEGRRAAPAPH
+DGDAG
+>LFPAFLNI_00131
+MIVAFSVAPSGQPADAEHLPGDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGEWD
+EVMEVVRAAVDAVSPYGTRVSLVLKADIRPGRTGELDGKLERLESALAEDEGRRAAPAPR
+DGDAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000305.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000305.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b8ef8d36fbf03a08ca8599c512123c2d3c198b6a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000305.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_00263
+MPHTADRGHPVHNPDIVGFTEAELNETPIKPRWNSLGPGIVAAATGVGAADLVATLTAGS
+RYGYMLLWAVVLGVIFKIVLVEGVGRWYLSTGKTIFQGWRQLGSWTSWYFGPYILIWGFV
+YGATAMSSTAIPLAALFPAVDAKVFAIAAGLIGLALVWLNKYGLIEKLMTALIGVMFVTV
+LISAALTAPNVGEILSGLVPRIPSGDPQVMFYVLGLAGGVGGTITLGAYAYWLREKGWNV
+PKYMKVMKFDNATSYVLTGIFVIATMIMGVELLHSAGLAISSGDKGLLDVGNVLAERYGQ
+VWSYVFLIGFFAASFSSLLGVWHGVSLMFADFWTNFRRPADELDQDDAPSLASKPARFYL
+LWLTILPMSLLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNRKDVPVQHRNGWIRNIL
+LGLTAAVFVAIGVNELIKALQSVLGG
+>MOLHKGIG_00122
+MATRADRGRPVHNPDIIGFTDAELNETPIRPKWNSLGPGIVAAATGVGAADLVATLTAGS
+RYGYMLLWAVILGVIFKIVLVEGVGRWYLSTGKTIFQGWRSLGSWTSWYFGPYILIWGFV
+YGATAMSSAALPLAALFPGVDMKVYAIGLGLVGLGLVWLNRYGLIEKLMAVLIGVMFLTV
+LLSAALTAPNVGDILAGLVPRIPSGDPDVMFYVLGLAGGVGGTITLGAYAYWLREKGWNV
+PKYMRVMKFDNATSYILTGIFVIATMIMGVELLHSAGLAISSGDRGLLDVGNVLAERYGQ
+AYSVVFLVGFFAASFSSLLGVWHGVSLMFADFWTNFRRPADELDQDDAPSLASKPGRFFL
+LWLTFPPMTLLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNKKEVPAQFRNGWIRNTL
+LGLTAAVFVAIGVNELWKALQPLIGG
+>NAFOICDF_00197
+MSHTTPPGHGLVDRHHPVHDPDIVGFTEAELNETPIKPKWNSLGPGIVAAATGVGAADLV
+ATLTAGSRYGYMLLWAVVLGVVFKIVLVEGVGRYYLSTGKTIFQGWRGLGSWTSWYFGPY
+ILIWGFVYGATAMSSTALPLAALFPGVDSKVFAIASGLVGLGLVWLNRYGLVEKVMTVLI
+GVMFVTVLISAALTVPNLGDILGGLVPRIPSGDPDVMFYVLGLAGGVGGTITLGAYGYWL
+REKGWNTPKYMRVMRFDNTVSYVLTGVFVIATMIMGVELLHSAGIAISSGDKGLLDVGDV
+LAQRYGDVWATVFLIGFFAASFSSVIGVWHGVSLMFADFWTNFRRPADELDQDDAPSLAS
+KPGRFYLLWLTFPPMVLLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNSRRVPGKFRN
+GWVRNVLLALTTAVFLVIGGNELLKALKPLIGG
+>MHAAABBN_02136
+MAHAVDPGRPVHNPDIVGFTDAELNETPIRPRWNSLGPGIVAAATGVGAADLVATLTAGS
+RYGYMLLWAVVLGVIFKIVLVEGVGRYYLSTGKTIFQGWRTLGAWTSWYFGPYILIWGIV
+YGATAMSSTALPLAALFPGVDSKVFAIASGLIGLGLVWLDRYRLIEWLMTVLIGVMFVTV
+LLSAALTVPNLGAILAGLVPRLPSGDPQAMFYVLGLAGGVGGTITLAAYGYWLREKGWNV
+PKYLKVMRFDNATSYILTGIFVIATMVMGVELLHSAGLAISSGDKGLLDVGDVLAERYGS
+AWSTVFLIGFFAASFSSLLGVWHGVSLMFADFWTNFRRPAEELDQDDAPSLSSKPGRFFL
+LWLTLPPMALLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNTKDVPRQFRNGWVRNTL
+LGLTAAVFVAIGVNELIKALQPVLGG
+>LFPAFLNI_00130
+MATRADRGRPVHNPDIIGFTDAELNETPIRPKWNSLGPGIVAAATGVGAADLVATLTAGS
+RYGYMLLWAVVLGVIFKIVLVEGVGRYYLSTGKTIFQGWRTLGAWTSWYFGPYILIWGIV
+YGATAMSSTALPLAALFPGVDSKVFAIAAGLIGLGLVWLDKYRLIEWLMTVLIGVMFVTV
+LLSAALTAPNLGEILAGLVPRLPSGDPQAMFYVLGLAGGVGGTITLAAYGYWLREKGWNV
+PKYLKVMRFDNATSYILTGIFVIATMVMGVELLHSAGLAISSGDKGLLDVGDVLAERYGS
+AWSTVFLIGFFAASFSSLLGVWHGVSLMFADFWTNFRRPAEELDQDDAPSLSSKPGRFFL
+LWLTLPPMALLFLDRPIFLILLYGTLGALFMPFLAVTLLFLNNTKDVPRQFRNGWVRNTL
+LGLTAAVFVAIGVNELIKALQPVLGG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000312.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000312.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e80fef06710d09cb7600493f980768e0514c3c9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000312.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00280
+MSKRIQAKDVDVYYGKFKAVEGVNIDIAPRTVTAFIGPSGCGKTTFLRAINRMHEVLPGA
+HVEGQLLLDGEDVYGPGVDPVTVRSQIGMVFQRPNPFPTMSIRDNVLAGYKLNGTRLSRS
+RADEIVEKSLRGANLWNEVKDRLDKPGSGLSGGQQQRLCIARSVAVSPDVILMDEPCSAL
+DPISTLAVEDLINELKEQYTVIIVTHNMQQAARVADKTAFFNIQGIGQPGKLIEFDDTNV
+IFNNPSNQQTEDYVSGRFG
+>MOLHKGIG_00110
+MSKRIQAIDVDVFYGKFKAVEGVNIDIAPRSVTAFIGPSGCGKTTFLRSINRMHEVLPGA
+TVDGQLLLDGEDIYGPGVDPVRVRSQIGMVFQRPNPFPTMSIRDNVLAGYKLNGTRLNKS
+RADELVEKSLRGANLWNEVKDRLDKPGSGLSGGQQQRLCIARSIAVQPDVILMDEPCSAL
+DPISTLAVEDLINELKEEYTVIIVTHNMQQAARVADKTAFFNIQGVGKPGKLIEYDDTNV
+IFNNPSSQQTEDYVSGRFG
+>NAFOICDF_00221
+MSKRIQAKDVDVYYGKFKAVEGVSIDIAPRTVTAFIGPSGCGKTTFLRAINRMHEVLPGA
+HVEGQLLLDGEDVYGPGVDPVTVRSQIGMVFQRPNPFPTMSIRDNVLAGYKLNGTRLTKS
+RADEIVEKSLRGANLWNEVKDRLDKPGSGLSGGQQQRLCIARSVAVEPDVILMDEPCSAL
+DPISTLAVEDLINELKEDYTVIIVTHNMQQAARVADKTAFFNIQGIGQPGKLIEYAETNT
+IFNNPSNQQTEDYVSGRFG
+>MHAAABBN_02123
+MSKRIQAIDVDVFYGKFKAVEGVNIDIAPRSVTAFIGPSGCGKTTFLRSINRMHEVLPGA
+TVDGQLLLDGEDIYGPGVDPVRVRSQIGMVFQRPNPFPTMSIRDNVLAGYKLNGTRLNKS
+RADELVEKSLRGANLWNEVKDRLDKPGSGLSGGQQQRLCIARSIAVQPDVILMDEPCSAL
+DPISTLAVEDLINELKEEYTVIIVTHNMQQAARVADKTAFFNIQGVGKPGKLIEYDDTNV
+IFNNPSSQQTEDYVSGRFG
+>LFPAFLNI_00105
+MSKRIQAVDVDVFYGKFKAVEGVNIDIAPRSVTAFIGPSGCGKTTFLRSINRMHEVLPGA
+TVDGQLLLDGEDIYGPGVDPVRVRSQIGMVFQRPNPFPTMSIRDNVLAGYKLNGTRLNKS
+RADELVEKSLRGANLWNEVKDRLDKPGSGLSGGQQQRLCIARSIAVQPDVILMDEPCSAL
+DPISTLAVEDLINELKEEYTVIIVTHNMQQAARVADKTAFFNIQGVGKPGKLIEYDDTDV
+IFNNPSSQQTEDYVSGRFG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000313.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000313.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3092bcef616adc88177d0dfbca3067cf28690c77
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000313.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00281
+MSTAIDDVSTRQDTPPSKHRQNSLTAGQKPGWVWMAIAAAAVLLGLGIEALLSGAAPFSE
+DFSLARFVVLAGVLYIAGMYLVTRVMENRRRASDGLWKNLVWTAFLIALVPLVSVIWTVL
+EGGGPTLLSNPQVLWNDMDGVTGATDAAYDQAGSPAGGLPGGFAHALIGTLVITIIATLI
+AVPIGLLASIYLVEYGRDGWLSRAITFFVDVMTGIPSIVAGLFAYAAMTVLLELIMGPGP
+AALQAVKMGFTAAVALTVLMIPVVVRSTEEMLRVVPNELREGSYALGVRKWRTIFKVVLP
+TAISGIASGVTLAIARVTGETAPILVTAGYAMTTNWNAFDNWMTALPVYIYRQIVSPTSP
+TAADPSMARAWSAALVLIFIVMALNLLARVIAKAFAPKTGR
+>MOLHKGIG_00109
+MSTVSTSPRATEDSVTPRRHSLTEGQKPGWTWMAVAAAAAVVAAGLTVLLSGAFNVVGFV
+IIAAILYIAGLYVATRVMENRRRAADGLCRNLVWLAFLVALVPLVSVLWSVLSAGLPTLI
+ANPQIMAYDMKGITGIDDSAWVEDGKPAGGLAGGFGHALIGTVVITIIATLISVPIGMLT
+SIYLVEYSRGGWFSRAIVFFVDVMTGIPSIVAGLFAYAAITWVLTLVTGSKSTALQSVQM
+GLTAAIALSVLMIPVVVRSTEEMLRVVPNELREGAYALGVRKWQTIAKVVLPTAISGIAS
+GVTLAIARVAGETAPILVTAGFATSINWNPFDNWMTALPVYIYRQLVAPTSPTAADPSTA
+RAWAAALLLVTIVMLLNLAARFIAKAFAPKKGR
+>NAFOICDF_00222
+MSTALNDTPTRENTPASKHTQNSLTAGQKPRWTWMAVAAGAVVLGLGLEALLAGGFADFS
+IARFIILAAILFVAGMYVATRVLENRRQATDGLWRNLVWAAFLIALVPLISVLWSVVADG
+GATLFGNPQLLVNDMQGVTGVTDAQYVQAGEPMGDLPGGFAHALVGTFLITVIATVIAVP
+IGLLTSIYLVEFGRDGWLSRAIIFFVDVMTGIPSIVAGLFAFAAMSVVLEMVMGSGPKAL
+QSVKMGLTAAIALTVLMIPVVVRSTEEMLRVVPNELREGSYALGVRKWRTIFKVVLPTAI
+SGIASGITLAIARVTGETAPILVTAGFASAVNWNPFDNWMTALPVYIYRQLVAPTSPTAM
+DASTSRAWAAALVLIIIVMVLNLLARIVAKAFAPKTGR
+>MHAAABBN_02122
+MSTVSTSPRATEDSVTPRRHSLTEGQKPGWTWMAVAAAAAVVAAGLTVLLSGAFNVVGFV
+IIAAILYIAGLYVATRVMENRRRAADGLCRNLVWLAFLVALVPLVSVLWSVLSAGLPTLI
+ANPQIMAYDMKGITGIDDSAWVEDGKPAGGLAGGFGHALIGTVVITIIATLISVPIGMLT
+SIYLVEYSRGGWFSRAIVFFVDVMTGIPSIVAGLFAYAAITWVLTLVTGSKSTALQSVQM
+GLTAAIALSVLMIPVVVRSTEEMLRVVPNELREGAYALGVRKWQTIAKVVLPTAISGIAS
+GVTLAIARVAGETAPILVTAGFATSINWNPFDNWMTALPVYIYRQLVAPTSPTAADPSTA
+RAWAAALLLVTIVMLLNLAARFIAKAFAPKKGR
+>LFPAFLNI_00104
+MSTVSTSPRATEDSVTPRRHSLTEGQKPGWTWMAVAAAAAVVAAGLTVLLSGAFNVVGFV
+IIAAILYIAGLYVATRVMENRRRAADGLCRNLVWLAFLVALVPLVSVLWSVLSAGLPTLI
+ANPQIMAYDMKGITGIDDSAWVEDGKPAGGLAGGFGHALIGTVVITIIATLISVPIGMLT
+SIYLVEYSRGGWFSRAIVFFVDVMTGIPSIVAGLFAYAAITWVLTLVTGSKSTALQSVQM
+GLTAAIALSVLMIPVVVRSTEEMLRVVPNELREGAYALGVRKWQTIAKVVLPTAISGIAS
+GVTLAIARVAGETAPILVTAGFATSINWNPFDNWMTALPVYIYRQLVAPTSPTAADPSTA
+RAWAAALLLVTIVMLLNLAARFIAKAFAPKKGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000315.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000315.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5e096ccf67060c2a72d2ee959858069b301de06
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000315.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00283
+MKALRFGRSAALLSVAALALTACGGNGGGDASSSAPAGGSSSAAAEGSGAAAASGTLIGG
+GASSQEAAMTAWSEGVKATSPELTVQYSPDGSGAGREGFLGGAFSFAGSDAALKEDEAEQ
+AKQICGDNGAFHVPAYISPIAIAYNLEGVDEVKMDAETIAKVFSKEITTWNDPAIAEQNE
+GVELPDTPITVVHRSDDSGTTENFTAYLTEAAGDAWKYDEVETWPSEITAESAQGTRGVV
+GQAAQTDGAITYADASAVGELGTVAVKVGEEYVPYSSDAAAKTVSASVQNEDGSIELDRA
+TTEAGVYPIVLVSYHIYCNQYQNQETADQVKAFASYVVSEDGQKAAEEAAGNAPIGAETR
+DAAVERIEAITAG
+>MOLHKGIG_00107
+MKALRFGRSAALLSVAAIALTACSSADSGNGGSDASGSAGGEQGTTSEVQGNLVGAGASS
+QEAAMTAWTQGVTETAPNLTVQYSPDGSGAGREKFLAGATSFAGSDAALKEEEAESAKEN
+CGDEGAFHVPAYISPIAVAYNLPGVDDVKMDAETIAKVFSGEIKNWNDEAIAAQNEGVEL
+PDTPITVVHRSDDSGTTENFTAYLTEAAGDAWSYDEVETWPSDITAESAQGTKGVVGLAS
+QTEGAITYADASAVGELGTVSVKVGEEYVKYSAEAAAATVEKSEAKEDGSIELDRATDES
+GVYPVVLVSYHIYCNQYESQETVDQVKAFAEYVVSEDGQKTAEESAGNAPISEDTRKKAM
+ERIEAISVKG
+>NAFOICDF_00224
+MKALRFGRSAALLSVAALALTACGGGNDSASSSSSAASSSAAGSSSASSSAAGSSSASSS
+AAESSSASGSSSAAQGGYAIDVPTASGTLMGSGASSQEAAMTAWTEGVKATSPELQVQYS
+PDGSGAGRKAFLSGAATFAGSDAALKDEEKTQAQEVCGPDGAFHVPAYVSPIAVAYNLEG
+VDSLNLDADTIAKIFSKKITKWNAPEIAALNEGVELPDTAITVVHRADESGTTENFTAYL
+DQVAPEAWTYGKVKEWPGDITAESAQGTKGVVSQAAATNGAITYADESGVGSLKTAKVGK
+DGKFAEISPEAAAKIVADGKKQDDGSIELDRANAGEGVYPIVLVSYHIFCNQYGDQETVD
+QVKAFASYVISEDGQKAAQEASKSAPLDAELAKEAKTRIDAIKVG
+>MHAAABBN_02120
+MKALRFGRSAALLSVAAIALTACSSADSGNGGSDASGSAGGEQGTTSEVQGNLVGAGASS
+QEAAMTAWTQGVTETAPNLTVQYSPDGSGAGREKFLAGATSFAGSDAALKEEEAESAKKN
+CGDEGAFHVPAYISPIAVAYNLPGVDDVKMDAETIAKVFSGEIKNWNDEAIAAQNEGVEL
+PDTPITVVHRSDDSGTTENFTAYLTEAAGDAWSYDEVETWPSDITAESAQGTKGVVGLAS
+QTEGAITYADASAVGELGTVSVKVGEEYVKYSAEAAAATVEKSEAKEDGSIELDRATDES
+GVYPVVLVSYHIYCNQYESQETVDQVKAFAEYVVSEDGQKTAEESAGNAPISEDTRKKAM
+ERIEAISVKG
+>LFPAFLNI_00102
+MKAHRFGRSAALLSVAAIALTACSSADSGNGGSDASGSAGGEHASGSAGGEQGTTSEVQG
+NLVGAGASSQEAAMTAWTQGVTEIAPNLTVQYSPDGSGAGREKFLAGATSFAGSDAALKE
+EEAESAKENCGDEGAFHVPAYISPIAVAYNLPGVDEVKMDAETIAKVFSGEIKNWNDEAI
+AAQNEGVELPDTPITVVHRSDDSGTTENFTAYLTEAAGDAWSYDEVETWPSDITAESAQG
+TKGVVGLASQTEGAITYADASAVGELGTVSVKVGEEYVKYSAEAAAATVEKSEAKEDGSI
+ELDRATDESGVYPVVLVSYHIYCNQYESQETVDQVKAFAEYVVSEDGQKTAEESAGNAPI
+SEDTRKKAMERIEAISVKG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000321.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000321.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c15d44e17da7fd67020e35d1028ea0bb8a326941
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000321.fa
@@ -0,0 +1,80 @@
+>ACLBLIBL_00291
+MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR
+EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA
+AQVLVKLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR
+NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG
+DVPETLKDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG
+AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVPEPSVEDAT
+EILRGLRDRYEAHHRVSITDGALKAAATLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT
+VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLEDERRQKEEAWRTGADSDV
+ATVDEELIAEVLSKSTGIPVFKLTAEETDRLRTMEDELHKRVIGQDEAIKSLSRAIRRTR
+AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG
+APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD
+FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD
+VIVFPQLQKHEIVEIVDLFVSRLGKRLAEQDLSIELTQAAKDLLADRGYDPAMGARPLRR
+TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFGFSGGREALEGAELPELEPG
+SGETVEAGRSA
+>MOLHKGIG_00100
+MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR
+EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA
+AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR
+NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG
+DVPETLRDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG
+AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVAEPSVEDAT
+EILRGLRDRYEAHHKVSITDGALKAAAGLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT
+VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLGDERREKEQAWRTGADADV
+ATVDEDLIAEVLSKSTGIPVFKLTEEETDRLRNMEDELHRRVIGQDEAIKSLSRAIRRTR
+AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG
+APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD
+FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD
+VIVFPQLQKHEIVEIVDLFVSRLGKRLAEQDLSIELTQSAKDLLADRGYDPAMGARPLRR
+TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFAFSGGREALEGADLAELESG
+AGDPVDADRSV
+>NAFOICDF_00237
+MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLAAVR
+EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA
+AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGSEGQNAGSVVLDQFGR
+NLTAAAHDGKLDPVIGRAQEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIERG
+DVPETLKGKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG
+AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVPEPSVEDAT
+QILRGLRDRYEAHHKVSITDGALSAAASLADRYISDRHLPDKAIDLIDEAGARLRIRRMT
+VPPEVKAYEERIAEVKAQKEAAIDGQDFEGAARLRDQEKQLEEEREQKEQAWRAGQDAAV
+ATVDEDLIAEVLSLSTGIPVFKLTEEETDRLRNMEAELHQRVIGQDEAIKSLSRAIRRTR
+AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG
+APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHADLFNSLLQILEDGRLTDSQGRVVD
+FKNTVIIMTTNLGTRDISKGVMTGFQSSTDTSTGYERMKGKVREELRQHFRPEFLNRVDD
+VIVFPQLQKHEIVEIVDLFVSRLAKRLAEQDLSIELTPAAKDLLADRGYDPAMGARPLRR
+TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFAFAGGRAALEGDDAAEPAAL
+PAAADAPVEGREAPGADVPRGDDAGQDGPEAGGALGARLD
+>MHAAABBN_02113
+MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR
+EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA
+AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR
+NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG
+DVPETLRDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG
+AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVAEPSVEDAT
+EILRGLRDRYEAHHKVSITDGALKAAAGLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT
+VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLGDERREKEQAWRTGADADV
+ATVDEDLIAEVLSKSTGIPVFKLTEEETDRLRNMEDELHRRVIGQDEAIKSLSRAIRRTR
+AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG
+APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD
+FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD
+VIVFPQLQKHEIVQIVDLFVSRLGKRLAEQDLSIELTQSAKDLLADRGYDPAMGARPLRR
+TIQQMVEDQLSEKILFGEIPAGSLITVDTTGEGEGAELTFAFSGGREALEGADLAELEPG
+AGDPVDADRSA
+>LFPAFLNI_00095
+MFERFTDRARRVVVLAQEEARMLNHSYIGTEHILLGLIHEGEGVAAKALESMDISLGAVR
+EKVQEDIGQGQQNPPGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVA
+AQVLVQLGADLNRVRQTVIQLLSGYQGGAQGGKETAGAGVGQGGEAGQNAGSVVLDQFGR
+NLTAAAHDGKLDPVIGRAGEMERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQAIDRG
+DVPETLRDKQLYSLDLGSLVAGSRYRGDFEERLKKVLKEIRTRGDIILFIDEIHTLVGAG
+AAEGAIDAASILKPMLARGELQTIGATTLDEYRKHIEKDAALERRFQPIQVAEPSVEDAT
+EILRGLRDRYEAHHKVSITDGALKAAAGLADRYVSDRHLPDKAIDLIDEAGARLRIRRMT
+VPPEIKAYESRIAEVRTQKEAAIDGQDFEGAARLRDQEQQLGDERREKEQAWRTGADADV
+ATVDEDLIAEVLSKSTGIPVFKLTEEETDRLRNMEDELHRRVIGQDEAIKSLSRAIRRTR
+AGLKDPNRPSGSFIFAGPTGVGKTELAKSLAEFLFGDEDALITLDMSEFQEKHTVSRLFG
+APPGYVGYEEGGQLTEKVRRRPFSVVLFDEVEKAHQDLFNSLLQILEDGRLTDSQGRVVD
+FKNTVIIMTTNLGTRDISKGVMTGFQSATDTTTGYERMKGKVKEELRQHFRPEFLNRVDD
+VIVFPQLQKHEIVEIVDLFVSRLGKRLAEQDLSIELTQSAKDLLADRGYDPAMGARPLRR
+TIQQMVEDQLSEKILFGEIPAGSLITVDATGEGEGAELTFAFSGGREALEGADLAELEPG
+AGDPVDADRSV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000322.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000322.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea80d1d75c979c307c692eba2d25ea222bdf36be
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000322.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_00293
+MATFWEYFSVLAPSIGLGLIFWLVMRSLLRSDTAERESMGRRSTGEDARAAREEADAREW
+ARRRGGDDVPRRGDDSR
+>MOLHKGIG_00098
+MAAFWDYFSVLAPSIGLGLIFWLVMRSLLRSDTGERESQARRLSGADARAAREEAEAREW
+AARRRAEGGPGADPEDRAR
+>NAFOICDF_00238
+MAAFWEYFSVLAPSVGIGLVFWLVMRSLLRSDTAEREARQRRGEDARAAREEAEAREWAA
+RRRGDAPAGPGGAERP
+>MHAAABBN_02111
+MADFWDYFSVLAPSIGLGLIFWLVMRSLLRSDTGERESQARRLSGADARAAREEAEAREW
+AARRRAEGGPGADPEDRAR
+>LFPAFLNI_00093
+MAAFWDYFSVLAPSIGLGLIFWLVMRSLLRSDTGERESQARRLSGADARAAREEAEAREW
+AARRRAEGGPGADPEDRAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000323.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000323.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2dcf1188c86658f32a9dbbb55d5f90c960f1109
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000323.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_00294
+MTSQNSANPQTSAVDHHDQQAVRAAKREQLLAAGREAYPVQVPRTHTLTEVREQFDGHEP
+DWASGETVSVTGRVVFLRNTGKLCFATLQESGVDGEAVRLQVMVSLAAVGEDSLAQWKKA
+VDLGDFLSVTGEVIVSRRGELSIMASAWEMASKALRPLPVLHADLNEETRVRQRYADLIV
+RDEARRMVYTRAKVTSAVRRTLEGHGYVEVETPMLQLIHGGALARPFETHLNAFDQPMTL
+RIATELYLKRAVVGGIDRVYEIGRVFRNEGVDSTHSPEFTTLESYEAWADMHVMAERMQE
+IILAAADAVGAGRRIETDRGVIDLDGEWAWVSVYPGLSEAVGREITPDTDAETLRAIAAE
+HEVKVDPAWDAQKLVIELFGEIVEPTLMNPTFVHDYPPAAQPLARPHREDGRVIEAWDLI
+IGGMERGTAFSELIDPVIQRERLTAQSAMAAAGDDEAMQLDEDFLRALEYGAPPMGGIGL
+GIDRLVMLFTDAGIRETILFPLLKPEA
+>MOLHKGIG_00097
+MTTQNSASAAVDHHDQQAVRAAKREQLLASGREAYPVQVPRTHALAEVRERFDGHEPDWT
+SGETVSVTGRVVFLRNTGKLCFATLQESGADGEAVRLQVMVSLAAVGEESLAEWKKVVDL
+GDFLSVTGEVIVSRRGELSIMASAWEMASKALRPLPVLHADLNEETRVRQRYADLIVREE
+ARRMVYTRAKVTSAVRRTLEGHGYVEVETPMLQLVHGGALARPFETHLNAFDQPMTLRIA
+TELYLKRAVVGGIDRVFEIGRVFRNEGVDSTHSPEFTTLESYEAWADMHVMAERMQEIIL
+NAADAVGAGRRLETAKGVIDLDGEWAWVAVYPGLSEAVGREITPETDAETLRAIAAEHEV
+KVDPAWDAEKLVIELFGEIVEPTLMNPTFVYDYPPAAQPLARPHRSDDRVIEAWDLIIGG
+MERGTAFSELIDPVIQRERLTAQSAMAAAGDDEAMQLDEDFLRALEYGAPPMGGIGLGID
+RLVMLFTDAGIRETILFPLLKPEA
+>NAFOICDF_00239
+MTPENPAPAAVDHHDQQAVRAAKREQLLTSGRQAYPVQVPRTHSLAAVRAKFDGKHEAGW
+EEGPEVSVTGRVVFLRNTGKLCFATLQESGAAGEAVRLQVMVSLAEVGEESLGEWKKSVD
+LGDFLSVTGRVIVSRRGELSIQAAAWEMASKALRPLPVLHADLNEETRVRQRYTDLIVRD
+EAREMVYKRAKITSAVRRTLESHGYVEVETPILQLVHGGAQARPFETHLNAFDQDMTLRI
+ATELYLKRAVVGGIERVYELGRVFRNEGVDSTHSPEFTTLESYEAWADMHVMADRIKEII
+LNAADAIGAGRRIETSRGVIDLDGEWAWVSVYPGLSEAVGREVTPDTDAETLRAIAAEHD
+VKVDPKWDAQKLVIELFGEIVEPTLMNPTFVYDYPPAAQPLARPNRDDDRVIEAWDLIIG
+GMERGTAFSELIDPVIQRERLTEQSLKAADGDDEAMQLDEDFLRALEYGAPPMGGIGLGI
+DRLVMLFTDAGIRETILFPLLKPEA
+>MHAAABBN_02110
+MTTQNSASAAVDHHDQQAVRAAKREQLLASGREAYPVQVPRTHALAEVRERFDGHEPDWT
+SGETVSVTGRVVFLRNTGKLCFATLQESGADGEAVRLQVMVSLAAVGEESLAEWKKVVDL
+GDFLSVTGEVIVSRRGELSIMASAWEMASKALRPLPVLHADLNEETRVRQRYADLIVRDE
+ARRMVYTRAKVTSAVRRTLEGHGYVEVETPMLQLVHGGALARPFETHLNAFDQPMTLRIA
+TELYLKRAVVGGIDRVFEIGRVFRNEGVDSTHSPEFTTLESYEAWADMHVMAERMQEIIL
+NAADAVGAGRRLETAKGVIDLDGEWAWVAVYPGLSEAVGREITPDTDAGTLRAIAAEHEV
+KVDPAWDAEKLVIELFGEIVEPTLMNPTFVYDYPPAAQPLARPHRSDDRVIEAWDLIIGG
+MERGTAFSELIDPVIQRERLTAQSAMAAAGDDEAMQLDEDFLRALEYGAPPMGGIGLGID
+RLVMLFTDAGIRETILFPLLKPEA
+>LFPAFLNI_00092
+MTTQNSASAAVDHHDQQAVRAAKREQLLASGREAYPVQVPRTHALAEVRERFDGHEPDWA
+SGETVSVTGRVVFLRNTGKLCFATLQESGADGEAVRLQVMVSLAAVGEESLADWKKVVDL
+GDFLSVTGEVIVSRRGELSIMASAWEMASKALRPLPVLHADLNEETRVRQRYADLIVREE
+ARRMVYTRAKVTSAVRRTLEGHGYVEVETPMLQLVHGGALARPFETHLNAFDQPMTLRIA
+TELYLKRAVVGGIDRVFEIGRVFRNEGVDSTHSPEFTTLESYEAWADMHVMAERMQEIIL
+NAADAVGAGRRLETAKGVIDLDGEWAWVAVYPGLSEAVGREITPETDAETLRAIAAEHEV
+KVDPAWDAEKLVIELFGEIVEPTLMNPTFVYDYPPAAQPLARPHRSEDRVIEAWDLIIGG
+MERGTAFSELIDPVIQRERLTAQSAMAAAGDDEAMQLDEDFLRALEYGAPPMGGIGLGID
+RLVMLFTDAGIRETILFPLLKPEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000324.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000324.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee850e3d4304817f6aa5bdcd2ea24943956e95ed
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000324.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00295
+MSPRFLLMTEIPEPGLGMLREAGEVTLGSEVGGNDALPALAASGDYDVVVCALAQKFDAD
+VLAQARLKGIANYAVGYNNVDVAAATEAGIAVGNTPDVLTDATADIALLLILGVSRRAHE
+GEAMMRAGEFTGWRADLLVGKDVKGATLGLAGFGRIGKAVAERALAFGMDVVFAPRPPAH
+REVAPEELGELAGRVEQVRWEELVERSDFLSLHVPLTADTEHLVDADVLARMKDDAVLIN
+TARGPVVDEAALVEALRAGRLFGAGLDVYEDEPAMAPGLAELDNVMLLPHLGSATRDTRA
+AMAELTARNAIAMATGGEVPALVNPDVRR
+>MOLHKGIG_00096
+MTPRFLLMTRLPEPGLGMLREAGEVVDGADVGGDAALARLVASGDYDVVVAALDQKFTAD
+VLADARIRGIANYAVGYNNVDVAAATRRGIAVGNTPDVLTDATADIAMLLILGVTRRAPE
+GERMVREGRFHGWAPDLLVGRDVRGATLGLAGFGRIGKAVAERALAFGMEVVFAPRPPAH
+REVAAAELGDLAGRVRQVRWEELVEVADVLSLHVPLTDDTHHLVDADVIAKMKDDAVLVN
+TARGPVVDEAALVTALREGRLFGAGLDVYEDEPALAPGLAELENVMLLPHLGSATRDTRA
+AMAELAARNAIAMATGAEAPALVNPEVRG
+>NAFOICDF_00240
+MSPRFLLMADLPEPGLGMLREAGEVVRGGDVGGNAALADLCASGEYDVVVGALDQRYDAD
+LLARARVKGIANYAVGFDNVDVPAATEHGILVGNTPDVLTAATADIALLLILGVTRRAVE
+GERMMREGRFEGWRADMLVGKDVVGATLGLAGFGRIGRAVAERALAFGMEVVFAPRPPAH
+REVPAEELGDLAGRVRQVRWEELVETADVLSLHVPLTEDTRHLVDEDVIARMKDDAVLVN
+TARGPVVDEAALVTALREGRLFGAGFDVYEDEPAMAEGLAELPNVMLLPHLGSATRDARA
+AMAELTARNAIGMATDGEAPALVNPEARG
+>MHAAABBN_02109
+MTPRFLLMTRLPEPGLGMLREAGEVVDGADVGGDAALARLVASGDYDVVVAALDQKFTAD
+VLADARIRGIANYAVGYNNVDVAAATRRGIAVGNTPDVLTDATADIAMLLILGVTRRAPE
+GERMVREGRFHGWAPDLLVGRDVRGATLGLAGFGRIGKAVAERALAFGMDVVFAPRPPAH
+REVAAEELGDLAGRVRQVRWEELVEVADVLSLHVPLTDDTHHLVDAEVIAKMKDDAVLVN
+TARGPVVDEVALVTALREGRLFGAGLDVYEDEPALAPGLAELENVMLLPHLGSATRDTRA
+AMAELAARNAIAMATGAEVPALVNPEVRG
+>LFPAFLNI_00091
+MTPRFLLMTRLPEPGLGMLREAGEVVDGADVGGDAALARLVASGDYDVVVAALDQKFTAD
+VLADARIRGIANYAVGYNNVDVAAATRRGIAVGNTPDVLTDATADIAMLLILGVTRRAPE
+GERMVREGRFHGWAPDLLVGRDVRGATLGLAGFGRIGKAVAERALAFGMDVVFAPRPPAH
+REVAAEELGDLAGRVRQVRWEELVEVADVLSLHVPLTDDTHHLVDAEVIAKMKDDAVLVN
+TARGPVVDEVALVTALREGRLFGAGLDVYEDEPALAPGLAELENVMLLPHLGSATRDTRA
+AMAELAARNAIAMATGAEVPALVNPGVRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000326.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000326.fa
new file mode 100644
index 0000000000000000000000000000000000000000..035d3545102324315c0b0792467ce5412240c488
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000326.fa
@@ -0,0 +1,21 @@
+>ACLBLIBL_00297
+MAERGHGDDRGLDGVGAERGDAGGEIDGFEAAVRGLEDAFARMVRQHRQVVTRQAAALKP
+GLSAGAMKAFITLCNAGTMTPSTLAEHLLLDRAQVSRMVRDLEDEGLITREPDPVDRRSA
+LLTATEEGRARLDAVRGGPAGEGLRADLAHWDRADIHTLVRLLGRLVEEQQARVDRTPDA
+G
+>MOLHKGIG_00094
+MADGAPDPGGGGDDAGFEAAVQGLEQAFSRLVLQHRQVMVRYAAALSPALSVGAMKAFMM
+LANEGTMTPSAVAEGLLVDRAQVSRMVRDLEAAGLITREPDPRDRRSALLSASPEGLARL
+DAVRGGPAGRGLRDDLARWDREDIRTLTRLLDRLAAERQTRMQDPAESE
+>NAFOICDF_00242
+MADPADHGSDGRGTGADAFAPEAFDAAVRELEGSFNRLVRQYRATLARQAEAVHPGLPLG
+AMKAFVAICHRGPLTPSDLAEHLMLDRTQISRVLKDLEGDGLIHREPDPRDRRSALLTAT
+DEARARLDAVRQGPAGGGTRARLQRWDLEDVRALSALLRRFVDEREDPAADDACRP
+>MHAAABBN_02107
+MVDGAPDPGGGGDDAGFEAAVQGLEQAFSRLVLQHRQVMARYAEALSPTLSVGAMKAFMM
+LANEGTMTPSAVAEGMLVDRAQVSRMVRDLEAAGLITREPDPRDRRSALLSASPEGLARL
+DAVRGGPAGRGLRDDLARWDREDIRTLTRLLDRLAAERQTRMQDPAESE
+>LFPAFLNI_00089
+MADGAPDPGRGGDDAGFEAAVQGLEQAFSRLVLQHRQVMVRYAAALSPALSVGAMKAFMM
+LANEGTMTPSAVAEGLLVDRAQVSRMVRDLEAAGLITREPDPRDRRSALLSASPEGLARL
+DAVRGGPAGRGLRDDLARWDREDIRTLTRLLDRLAAERQTRMQDPAESE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000327.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000327.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f56015ffba1fb6c200f7b1e3fd118de1695075c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000327.fa
@@ -0,0 +1,65 @@
+>ACLBLIBL_00298
+MTATAEPRVPAPREDLYRHVNAAWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVR
+EVGAGFDPAQARVDATAAAGAEHHTPLEPLDAEETEGMELPEVKRRIAALYASFMDDETV
+EARGLEPVATDMAAVASVQTPAELLELSGRLQRQGVSGLVNTGALNDAGNPDRMLLHLLQ
+GGLGLPDESYYRDEAYAEILEQYTEHAGRLLGLAGIGADSAEAAEAGVRVVELEKRIAAL
+HWDVVRSRDAVARYNLMTHEQLVELFPLAEAWLEGVDAAGERSREVVVWQPDFLSGVQAL
+LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRHRWKRAVAF
+VNGAAGEDVARLYVDRHFPEGHVAAMDELVNLLQEAYRRSIDELEWMSEETRQRALEKLS
+MFRPMVGRPVRWVDYSSLEVHAGDLLGNARAASEFEWERDLRKIEDGPDPEEWHITPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEKSMAANLGAIGAVIGHEIGHGFDDQGSRYDGSGR
+LEDWWTQEDRAAFTELTSRLVAQYNVLSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRAL
+EIWRDEGDGASLDAAAGDREFFSAWAAVWRQLTRPETMVTRIASDPHSPNEFRCNQVVKN
+IDAFHEAFGTQEGDPMWLAPEERVTIW
+>MOLHKGIG_00093
+MTATAEPEVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVR
+EVGTGFDPAQARVQATAAAGAHRDVPLAPLDEEDAEGTEHPELKRRIAALYASFMDDETV
+EARGLEPIASDLAAVATVSTPAELLALSGRLQRQGVSGLINTGALNDAGNPDRMLLHLLQ
+GGLGLPDESYYRDEAYAEILEQYTEHTGRLLALAGIGADRDEAAALGVRVVELEKRIAAL
+HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGL
+LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAF
+VNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRSIEELEWMGEETRQRALEKLA
+MFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHITPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGR
+LEDWWTEEDRAAFTERTSRLVAQYNALSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRAL
+EIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVTRIASDPHSPNEFRCNQVVKN
+LDAFHEAFGTREGDPMWLAPEERVTIW
+>NAFOICDF_00243
+MTATAEPRVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRRIAEDAAR
+DAAMAAPAPEVEAPAQDEASQDPAAAERAARERIAVLWSAFMDEEAVEAAGILPLAADLE
+AVDAVASPAELLALSGRLQREGVSGLIGTGALNDAGDPERMLLHLIQSGLGLPDESYYRE
+EAYAEILAQYTEHVGRLFALAGVGGDEAGAAALGERVVALEKRIAAHHWDVVRSRDAVAR
+YNLLTRDQLLELLPLAPGWLEGIGAADARADEVVVWQPDFLTGVQALLEGPDAADLADWK
+AWLTLQVLRSRAGFLPDAFVQENFSFYGRRLAGTQEVRPRWKRAVAFVNGGVGEDVGRLY
+VARHFPEGHVAAMDQLVGLLLEAYRRSIDALDWMGEQTRQSALEKLAMFRPMVGFPETWR
+DYSALELTPGDLVGCARAVDRFEWDRDLAKIETGPDPREWHMTPQTVNAYYTPLENAIVF
+PAALLQPPFFDPERSMAANLGGIGAVIGHEIGHGFDDQGSRYDGSGRLHDWWTEQDREAF
+AERTGRLVAQYSALSPAEAPDRQVNGEFTLGENIGDLGGLGIAHQALEIWREEQDGSTED
+ESSGDREFFQAWAAVWRQLTRPETMVTRIASDPHSPNQFRCNQVVKNLDAFHTAYGTREG
+DPMWLAPEERVTIW
+>MHAAABBN_02106
+MTATAEPRVPSPREDLYRHVNTGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEGAVR
+EVGAGFDPAQARVQATAAAGAHRDAPLAPLDAEDTEGMEHPELKRRIAALYASFMDDETV
+EARGLEPIASDLAAVATVTTPAELLTLSGRLQRQGVSGLINTGALNDAGNPDRMLLHLLQ
+GGLGLPDESYYRDEAYAEILEQYTEHTGRLLTLAGIGADRDEAAALGVRVVELEKRIAAL
+HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGL
+LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAF
+VNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRSIEELEWMGEETRQRALEKLA
+MFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHMTPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGR
+LEDWWTEEDRAAFTERTSRLVAQYNALSPVEAPDHRVNGEFTLGENIGDLGGLGIAHRAL
+EIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVTRIASDPHSPNEFRCNQVVKN
+IDAFHEAFGTREGDPMWLAPEERVTIW
+>LFPAFLNI_00088
+MTATAEPEVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVR
+EVGTGFDPAQARVQATAAAGAHRDVPLAPLDEEDAEGTEHPELKRRIAALYASFMDDETV
+EARGLEPIASDLAAVATVSTPAELLALSGRLQRQGVSGLINTGALNDAGNPDRMLLHLLQ
+GGLGLPDESYYRDEAYAEILEQYTEHTGRLLALAGIGADRDEAAALGVRVVELEKRIAAL
+HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGL
+LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAF
+VNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRSIEELEWMGEETRQRALEKLA
+MFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHITPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGR
+LEDWWTEEDRAAFTERTSRLVAQYNALSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRAL
+EIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVTRIASDPHSPNEFRCNQVVKN
+IDAFHEAFGTREGDPMWLAPEERVTIW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000334.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000334.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d875c28ae37146b8169390c3782708f5799ef9b3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000334.fa
@@ -0,0 +1,41 @@
+>ACLBLIBL_00305
+MISVRRHAARGLVALAAAVAVSAPLAAPAVAAPAAPTAPAAAQSATGKPVVRPEVVGHRG
+ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRK
+TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYNGRYQVPTFEEVLELRER
+LSDRYGRQIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD
+LNENLGLKAETVFLSSVTGTPYDSVAAGDTVRDYDFYETAAGMREVRAAGVDTLGPAFAQ
+VITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSADSNAQGDMVGMIQ
+PFLDAGIDGFFTDHPDLGVQAVDTWMQGKKEHPGRGVGKSAQRGLQVR
+>MOLHKGIG_00086
+MTSVRRHAARGLVALAAAVAVSAPLAAPAAAAPAAPTTPAAAQSVTGKPVVRPDVVGHRG
+ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRK
+TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER
+LSARYGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEYGLNKRNAPATVQSFELANLRD
+LNENLGLKAETVFLSSVTGAPYDSVAAGDGLRDYDFYETAAGMREVRAAGVDTLGPAFAQ
+IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDPNARGDMVGMIQ
+PFLDAGIDGFFTDHPDLGVQAVDTWMQGKKEHPGRGVGKTAQRGLKVR
+>NAFOICDF_00250
+MTALRTTARGLAALTAAVAVAAPLAVPASAAIPAKEPITQAERPDVVAHRGASAYRPEHT
+LAAYELAVAQGADVIEPDLVSTKDGVLVDRHENDITGTTDVSERPEFADRKTTKTVDGVE
+ITGWFTEDFTLAELKTLRAKERLPEARPGSAAYDGMYQVPTFEEDLKLREELSAKYGREI
+GIIPEIKHPSYFDGIGLSQEEEVIELLEEHGLNHADGRAVVQSFEFSNLAEMNTRLGLQA
+DTAYLLWYEGSGYDAVLSGDTARDYAYFSTPAGAAEAAFNGIDIYGPELRQVIALNQDGS
+LGAPTGLVEVAHDAGLTVVPYTFRAENQSLPLQFRSSENPVEHGDLAAYITEVLDAGVDG
+FFTDFPDVGVAARDAWLAEKPAEQPSEQPSDGSHAVPGKVQTGDAAAWLPAGLAAAAAGV
+LVALRRRLTAAR
+>MHAAABBN_02099
+MTSVRRHAARGLVALAAAVAVSAPLAAPAVAAPAATETPAAAQSVTGKPVVRPDVVGHRG
+ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRR
+TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER
+LSARHGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD
+LNENLGLKAETVFLSSVTGAPYDSVAAGDELRDYDFYETAAGMREIRAAGVDTLGPAFAQ
+IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDRNAQGDMVGMIQ
+PFLDAGIDGFFTDHPDLGVQAVDVWMQGKKEHPGRGVGKTAQRGLQGR
+>LFPAFLNI_00081
+MTSVRRHAARGLVALAAAVAVSAPLAAPAVAAPAATETPAAAQSVTGKPVVRPDVVGHRG
+ASGYRPEHTLAAYELAAAQGADVIEPDLVSTKDGVLVVRHENLIDGTTDVAQRPEFADRR
+TTKVVDGVALTGWFTEDFTLAELKTLRAKERLPQVRPESASYDGRYQVPTFEEVLELRER
+LSARHGREIGVIPEIKHPTYFDSIGLSMEERVVELLDEHGLNKRNAPATVQSFELANLRD
+LNENLGLKAETVFLSSVTGAPYDSVAAGDELRDYDFYETAAGMREIRAAGVDTLGPAFAQ
+IITKEKDGSMGEETAFVSLAHRAGLEVVPYTFRAENQFLYTEFRSSTDRNAQGDMVGMIQ
+PFLDAGIDGFFTDHPDLGVQAVDVWMQGKKEHPGRGVGKTAQRGLKGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000337.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000337.fa
new file mode 100644
index 0000000000000000000000000000000000000000..15e45f3dca4b15251c91566b3242748154ad5dd4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000337.fa
@@ -0,0 +1,56 @@
+>ACLBLIBL_00312
+MSAAAPVPATRPADDDGWARVHPASPWVRGWTFLLLILFFLGRNAVEDFAAGRFGAGAGG
+GSGEGEGSLLVAGGILLGVTLLVSLAFFFSWWFTRFRIGEDQIELRQGWLFRTRRQMKYD
+RIQAVDLQHPLVARLLGLAVVKVEAADGGESALELSFLPKARAEQVRREILDRASGVLVG
+PASAPRIAEGADAAAGVIPGVMPGVMPGAEAGPGVAPPGADADPTTPRADAPEGAAPSSS
+DPGLARRADDEGELMLRVPSGRLIGSVLLSGGVAGTVAVYLVVVLGTSLFFALAPGTWLE
+GEDTPLTGIVVAWGLPLAFAVVGQAWSGLNGGWGFQVRRSADGLRLRHGLTETTHQTVPP
+GRVQGVTVSQPLFWRPFGWHRVKVSVAGYGEDAAGKRSTALPVGPWEDVLRVLTVVAPDP
+GLDGDPREAEGLTPARLMHLGLHGSGTEGGFHHIPHRGRWWFNWFAWRRRGFTTTRALLV
+VRSGRWNRVLQTLQHERVQTAALDQGPVQRRLRLATVHVRTAGGRAVLPDLDEAVALELF
+AEEARHAAVSRRLADRDRWMRPEELARFEQRTREVAATEVGREELARAGVARPAAPAGGV
+AGTDPEPRTSHEERP
+>MOLHKGIG_00081
+MSAAAPPPADDAGWVRVHPASPWVRGWTFLLLILFFAGRNAVEDFAAGRLSGEDAPGGGD
+GSLLVAGGILLGVTLLISLVFFFSWWFTRFRCGEDRIELRQGWLFRSRRQMRYDRIQAVD
+LQHPLVARLLGLATVKVEAADGGESALELSFLRRAEAEAVRREILDRASGMLGGAGADAS
+APERAAEPGLPDADAADAGELMLQVPAGRLLGSVLLSGGVLGVLAGSLIWLGGLALVVAL
+LPEAVLDEGETLTGIGAAASLPALFSVAGVAWSRLNAGWGFQVRRSTDGLRLRHGLTETT
+HQTVPPGRVQGVTVSQPLFWRPFGWYRVNMAVAGYLQESDGARDVALPVGPWEDVLRVLT
+VVAPDPGLDGDPRAAQGLTPAGLMHLGVHGTGTEGGFQHVPRRGRWWFNWFAWRRTGFTT
+TRSLLVVRSGWLNRRLQTLQHERMQAAELAQGPVQRRLGLATVRVWVAGANAVVRDLDED
+VAVDLYAREARHAAVSRRLADRDQWMRPEELARFEQRTREVAATEVGRRELARAGVVGGA
+VVGEESGAHVPAVRGEEER
+>NAFOICDF_00253
+MSAPAPRPEGLASGPSPEDGRIAPAPAADDAGWVRVHPASPWIRGWVMVATFLFFALRDV
+VERWIGGLFGADAGGGPGVDGRGLLIGGGIALGVLLLVGLAFFFSWWFTRFRIGAEEIEL
+KQGWLFRSRRQMHYDRLQAVDLQHPLPARLIGLAVVKVEAADGGGDSALELAYLPKAQAA
+AVRRQILDRASGAAAARPVPSAAPEAAGGPAAAGPVRGLLVDPEEQGPVLLRVPAGRLIG
+SVLLSSTVMGLLGAVVAVPAVLSLLLLLFPDANAGEEAGVWAVTLGSTFPLLFSLAGAVW
+SGLNKGWGFTVRDSSDGLRLRYGFTETVSQTVPPGRVQGVEISQPLFWRPFGWHRVKVSV
+AGYGGLEAEGRRRDVALPVGPWEDVLRVLQVVAPDPGLGGDARAAGELMRTAMTGSGEEG
+GFRHVPRRAAWWWHWLTWRRHGYALTPTLLVVRHGRLSRSVQTVQHERLQAVALTQGPVQ
+RRLRVATLRVHMAGGAARLRGLDEDVLAELFEVESRHAAVSRRLTDRNRWMLPEELERFE
+RRTAEVARTEVGRAEMAAAGVVPMETGPRPGDTPPVATTEHRGEETA
+>MHAAABBN_02094
+MSAAAPPPADDAGWVRVHPASPWVRGWTFLLLILFFAGRNAVEDFAAGRLSGEDAPGGGD
+GSLLVAGGILLGVTLLISLVFFFSWWFTRFRCGEDRIELRQGWLFRSRRQMRYDRIQAVD
+LQHPLVARLLGLATVKVEAADGGESALELSFLRRAEAEAVRREILDRASGVLGGAGADAS
+APERAAEPGLADADPDAVDADAGELLLQVPAGRLLGSVLLSGGVLGVLAGSLIWLGGLAL
+VVALLPEAVLDEGETLTGIGAAASLPALFSVAGVAWSRLNAGWGFQVRRSTDGLRLRHGL
+TETTHQTVPPGRVQGVTVSQPLFWRPFGWYRVNMAVAGYLQESDGARDVALPVGPWEDVL
+RVLTVVAPDPGLDGDPRAAQGLTPAGLMHLGVHGTGTEGGFQHVPRRGRWWFNWFAWRRT
+GFTTTRSLLVVRSGWLNRRLQTLQHERMQAAELAQGPVQRRLGLATVRVWVAGANAVVRD
+LDEDVAVDLYAREARHAAVSRRLADRDQWMRPEELARFEQRTREVAATEVGRRELARAGV
+VGGAVVGEESGAHVPAVRGEEER
+>LFPAFLNI_00075
+MSAAAPPPADDAGWVRVHPASPWVRGWTFLLLILFFAGRNAVEDFAAGRLSGEDAPGGGD
+GSLLVAGGILLGVTLLISLVFFFSWWFTRFRCGEDRIELRQGWLFRSRRQMRYDRIQAVD
+LQHPLVARLLGLATVKVEAADGGESALELSFLRRAEAEAVRREILDRASGMLGGAGADAS
+APERAAEPGLPDADAADAGELMLQVPAGRLLGSVLLSGGVLGVLAGSLIWLGGLALVVAL
+LPEAVLDEGETLTGIGAAAALPALFSVAGVAWSRLNAGWGFQVRRSTDGLRLRHGLTETT
+HQTVPPGRVQGVTVSQPLFWRPFGWYRVNMAVAGYLQESDGARDVALPVGPWEDVLRVLT
+VVAPDPGLDGDPRAAQGLTPAGLMHLGVHGTGTEGGFQHVPRRGRWWFNWFAWRRTGFTT
+TRSLLVVRSGWLNRRLQTLQHERMQAAELAQGPVQRRLGLATVRVWVAGANAVVRDLDED
+VAVDLYAREARHAAVSRRLADRDQWMRPEELARFEQRTREVAATEVGRRELARAGVVGGA
+VVGEESGAHVPAVRGEEER
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000338.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000338.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7983bd17b341726ba8001184166ba46a84e941ca
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000338.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00313
+MPGIDLTGVTFAPASPKLTPVKLISSSIGHLIWLVVFSVPLVLKLLGPWEGLWAWTAWGL
+PAIVVVSWLVDLVLIPRRVRAMGWAEREDDVLWREGLLFRSVHAVPYGRLQYVDVSDGPL
+LRRVGLQTLTLKTAASGSDVTLEGLPRETADELREVLMARGQARLAGL
+>MOLHKGIG_00080
+MPGIDLSGVAFTPASPRLTTVKLIATTIGHLIWLAAFSVPLILKLTGPWAGMAAWVAWGL
+PAVVVVSWIVDLILIPRRVRAMGWAEREDDVLWREGILFRSVHAVPYGRLQYVDVSDGPL
+LRRVGLQTLTLKTAAAGGDVTLEGVPRERAEELREVLMARGQARLAGL
+>NAFOICDF_00254
+MPGIDLQGVEFTPVSPALVRVEAVRELIALVIWLAVVSVPLVLKLTGVWPDMWSWTAWGL
+PALVLAWSLVELVLIPRRVVAKGWAEREDDVLWREGILFRRVVAVPYGRLQYVDVTDGPL
+LRWAGLQKLTLKTAGGADVELVGLPRETCDRLREVLMARGQARLAGL
+>MHAAABBN_02093
+MPGIDLSGVAFTPASPRLATVKLIATTIGHLIWLAAFSVPLILKLTGPWAGMAAWVAWGL
+PAVVVVSWIVDLILIPRRVRAMGWAEREDDVLWREGILFRSVHAVPYGRLQYVDVSDGPL
+LRRVGLQTLTLKTAAAGGDVTLEGVPRERAEELREVLMARGQARLAGL
+>LFPAFLNI_00074
+MPGIDLSGVAFTPASPRLATVKLIATTIGHLIWLAAFSVPLILKLTGPWAGMAAWVAWGL
+PAVVVVSWIVDLILIPRRVRAMGWAEREDDVLWREGILFRSVHAVPYGRLQYVDVSDGPL
+LRRVGLQTLTLKTAAAGGDVTLEGVPRERAEELREVLMARGQARLAGL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000339.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000339.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1687bc3ef83c82273a4299eb5bdf676d0dc2099
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000339.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00314
+MIALRSWWTVVAVAVAVLLGWLAGLAAPSLGWGAPVVGRSGLITVTAVSVLCLVLGWRVR
+RDREKPPAARMDPIAAARTLVLGQAAGFAGAALAGWHAGVALQVAARAGAGAPTVREAAL
+QAAGGLVLLAVGLVVERWCRIPPEGDAAEGGRGEDGTAGRGRAPRPETEGGYARARD
+>MOLHKGIG_00079
+MIALRSGWTLLVVLAAAVLGWLAGLAAPSLGWPAPVVGRGGLITVAAVSVLCIGLGWRVR
+RDREKPAAARMDPLAAARTLVLGQASGFAGAALGGWHAGVAVQVLLRAGVGAPTVREAAL
+QAAGGLVLLVVGLIVERWCRIPPEEDAPEGGRGQDGSPGRGRPVRPETEGGYARARH
+>NAFOICDF_00255
+MISLVSGRTALLAFAAAVLGWLAALTAPSLGLAAPVMHLAALVTVVAVGVLCLVLGWRVR
+RDRDRPLAQRMDPLAAARTLVLGQASGLTGAGLAGWHAGVGLEVASRAGIEAPAVLTAGL
+LALGGAALLTVGVVVERWCRIPPEGDGAEPGAGQDGGGSGGHGARRPEAEGGFARARD
+>MHAAABBN_02092
+MIALRSGWTLLVVLVAAVLGWLAGLAAPSLGWPAPVVGRGGLITVAAVSVLCLALGWRVR
+RDREKPAAARMDPLAAARTLVLGQASGFAGAALGGWHAGVAVQVLLRAGVEAPTVREAAL
+QAVGGLVLLVVGLIVERWCRIPPEEDAPEGGRGQDGSPGRPARPETEGGYARARH
+>LFPAFLNI_00073
+MIALRSGWTLLVVLVAAVLGWLAGLAAPSLGWPAPVVGRGGLITVAAVSVLCLALGWRVR
+RDREKPAAARMDPLAAARTLVLGQASGFAGAALGGWHAGVAVQVLLRAGVEAPTVREAAL
+QAVGGLVLLVVGLIVERWCRIPPEEDAPEGGRGQDGSPGRPARPETEGGYARARH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000342.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000342.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7179fc7d7c8d02a8acdfb73a9a5361be9cdfd352
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000342.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00318
+MTEQTHHDDAARGPVPAADGSAAAPTASTPAAAGVPGTFDPDSTAIDRPRIEAAVREILL
+AIGEDPDREGLQDTPKRVAKAYAEFFAGLHQGPEQVLGTTFDIAHEELVLVKDIPFYSTC
+EHHLVPVHGTAHIGYIPSAAGRVTGLSKLARLVELYARRPQVQERLTTQVVEALMEHLAP
+RGAIVVVEAEHMCMSMRGVRKPGAKTVTSAVRGQLRDPSTRSEAMSLIMHG
+>MOLHKGIG_00075
+MTAHTPDDAVPGTFDPDSTAVDRPRIEAAVREILLAIGEDPDREGLADTPARVAKAYAEF
+FAGLHQSPDQVLGTTFDIAHEELVLVKDIPFYSTCEHHLVPFHGTAHIGYIPSAEGRVTG
+LSKLARLVELYARRPQVQERLTTQVVEALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAK
+TVTSAVRGQLRDPSTRSEAMSLIMHG
+>NAFOICDF_00259
+MTEQHRDAALADAHLHRPHEAAADVAPTTGAGAALAGAVPGVPGTFDPDQDTVDRPRIEA
+AVREILLAIGEDPDREGLQDTPKRVAKAYAEFFAGLHQRPEQVLGTTFDLSHEELVLVKD
+IPFYSTCEHHLVPFHGAAHIGYIPSAEGRVTGLSKLARLVELYARRPQVQERLTTQVVEA
+LMEHLQPKGAIVVVEAEHMCMSMRGVRKPGAKTVTSAVRGQLRDPSTRAEAMSLIMHG
+>MHAAABBN_02088
+MTAHTPDDAVPGTFDPDSTAVDRPRIEAAVREILLAIGEDPDREGLADTPARVAKAYAEF
+FAGLHQSPDQVLGTTFDIAHEELVLVKDIPFYSTCEHHLVPFHGTAHIGYIPSAEGRVTG
+LSKLARLVELYARRPQVQERLTTQVVEALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAK
+TVTSAVRGQLRDPSTRSEAMSLIMHG
+>LFPAFLNI_00069
+MTAHTPDDAVPGTFDPDSTAVDRPRIEAAVREILLAIGEDPDREGLADTPARVAKAYAEF
+FAGLHQSPDQVLGTTFDIAHEELVLVKDIPFYSTCEHHLVPFHGAAHIGYIPSAEGRVTG
+LSKLARLVELYARRPQVQERLTTQVVEALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAK
+TVTSAVRGQLRDPSTRSEAMSLIMHG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000343.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000343.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4013196a129f701032006a19c382419ff8188383
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000343.fa
@@ -0,0 +1,65 @@
+>ACLBLIBL_00319
+MKKLFNKPYIWILLGLLVLAVAIPLATSQTGRTMVDTNVGMAMLQDDKAAQARVVDGDQR
+VDLTLREPYSQDGRDLGKEVYFHFATARASDVVTAVDDSALDGYTDEPVRSNWLLSLLGF
+MIPFLLIALLFWFLLSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE
+IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV
+GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD
+ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVEAPDLEGRAKILEVHAQGKPIALDVDL
+RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH
+ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL
+AYALGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGNSEPFVG
+GGGGGSSREYSEELAYLVDAEVRGLLDGAHAEAHWVLTENRDVLDRLAYELLEKETLTQE
+AIAEIFRDVRKRPERDVWLASDERLPQDIPPVLSPSERRSRHEGGEQTPVGVEGTTVPVH
+PEGAPPSSLGGDAPTPGLPPHGGPSSSPGAGEGPTY
+>MOLHKGIG_00074
+MKKLFNKPYVWILLGLLVLAVAIPLTTSQSGRTMVDTNVGMALLKDDKAAQARVVDGDQR
+VDLTLREPYKQDDRDLGKEVYFYFATARATDVVTAVDDSALDGYTDEPVRSNWFLSLLGF
+MVPFLLIALLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE
+IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV
+GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD
+ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVDAPDLEGRAKILEVHAQGKPIALDVDL
+RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH
+ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL
+AYAMGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGSSEPFVG
+GAAGGSSREYSEELAYLVDAEVRTLLDQAHAEAHWVLTENRDVLDRLAYELLEKETLTQE
+AIAAIFADVRKRPERGVWLASDDRLPQDIPPVLSPSERRSRHDGGEQTPVGVEGTTVPVR
+PEGAPPSSLGGDAAGPGLPPHGGPSNTPGPGEGPTF
+>NAFOICDF_00260
+MKKQFNKPYIWILLGLLVLGLVIPLTTAQSGRGMVDTNVGMALLRDDKVAQARVVDGEQR
+VDLTLREPLSQDGRDLGRDVYFQFSAARAQDVVRTVQDSSVDGYQDEPVRDSWLLSLLGL
+MIPFLLISLLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELHE
+IKEFLTEPERFHAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV
+GVGASRVRDLFEQAKANAPAIIFVDEIDAVGRSRGVGIGGGNDEREQTLNQMLVEMDGFD
+ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVEAPDLDGRAKILEVHAQGKPIALDVDL
+RSLAKRTPGYTGADLANVINEAALLTARSRNNVIDNAALDEAVDRVMAGPQKRTRLMNEH
+ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPENDKYSVTRNELLDQL
+AYAMGGRVAEEVVFKDPSSGAANDIQKATETARKMVTDYGMSSKVGAVKLGSANTDPFLG
+GGGAASREYSEELAYLVDAEVRALLDGAHAEAHWVLTENRDVLDRLAAELLEKETLTQEQ
+IAEIFKDVRKRPERPLWLAADDRPPHDVPPVLTARERASRLEGEQPEAVGVEGTTVPDAP
+EGAPPTALGGAGGSAGGPGDLPGQHSPTPGPTY
+>MHAAABBN_02087
+MKKLFNKPYVWILLGLLVLAVAIPLTTSQSGRTMVDTNVGMALLKDDKAAQARVVDGDQR
+VDLTLREPYKQDDRDLGKEVYFYFATARATDVVTAVDDSALDGYTDEPVRSNWFLSLLGF
+MVPFLLIALLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE
+IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV
+GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD
+ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVDAPDLEGRAKILEVHAQGKPIALDVDL
+RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH
+ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL
+AYAMGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGSSEPFVG
+GAAGGSSREYSEELAYLVDAEVRTLLDQAHAEAHWVLTENRDVLDRLAYELLEKETLTQE
+AIAAIFADVRKRPERGVWLASDDRLPQDIPPVLSPSERRSRHDGGQQTPVGVEGTTVPVR
+PEGAPPSSLGGDAAGPGLPPHGGPSNTPGPGEGPTF
+>LFPAFLNI_00068
+MKKLFNKPYVWILLGLLVLAVAIPLTTSQSGRTMVDTNVGMALLKDDKAAQARVVDGDQR
+VDLTLREPYKQDDRDLGKEVYFYFASARATDVVTAVDDSALDGYTDEPVRSNWFLSLLGF
+MVPFLLIALLFWFLMSRMQGGGGKVMQFGKSRAKLINKDNPDVLFKDVAGADEAVEELQE
+IKEFLTVPDRFRAVGAKIPKGVLLYGPPGTGKTLLAKAVAGEAGVPFYSISGSDFVEMFV
+GVGASRVRDLFEQAKSNAPAIIFVDEIDAVGRHRGAGIGGGNDEREQTLNQMLVEMDGFD
+ASTNVIMIAATNRPDVLDPALLRPGRFDRQIPVDAPDLEGRARILEVHAQGKPIALDVDL
+RSLAKRTPGYTGADLANVINEAALLTARSNNNVIDNHALDEAVDRVMAGPQKRTRLMNEH
+ERKVTAYHEGGHALVAAGLRNSAPVTKITILPRGRALGYTMVVPEDDKYSVTRNELLDQL
+AYAMGGRVAEEIVFKDPSTGAANDIQKATDTARKMVTEYGMSAKVGAVKLGGGSSEPFVG
+GAPGGSSREYSEELAYLVDAEVRTLLDQAHAEAHWVLTENRDVLDRLAYELLEKETLTQE
+AIAAIFADVRKRPERGVWLASDDRLPQDIPPVLSPSERRSRHDGGEQTPVGVEGTTVPVR
+PEGAPPSSLGGDAAGPGLPPHGGPSNTPGPGEGPTF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000345.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000345.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a662797cb66c3be785e54818eb0ba378a51b364
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000345.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00321
+MPSGSAAPPALESWPPRGRWPEPLHRAVAALRPVLAAHDGGALIGLSGGADSCALAVAAA
+ALRGTRAGAALGPVGAVVVDHGLQAGSADVAEAAARVARTLGLEPVLVRRVAVREAGDGP
+EAAARRARRGAFADAAREAGAGLVLTAHTADDQAEQVLLGLARGSGTRSLAGIPAGGALP
+GGTALARPLLGLTRADAEAICRWAGVRWWEDPHNADPALLRSRVRTRVLPALEDLADGLG
+PGVREGLVRTAAIAAEDAAALEQWAACALAECRVRGEAGPGPGAEPGDDPGAGTGRSEAP
+GRGDVVVRLDLAAFAALPPAVRHRVLGLAVVEAGGPRPTRERTLAVDALAVPADPGAGGP
+RGPWSCPAGWK
+>MOLHKGIG_00071
+MPRPEARDPGPTPAGGVGGLPAVGAWPPRTRWPEPLHRAVAAVREALAGDGPRRADVVPG
+RAGSRPRGLVALSGGADSLALAVACAVLVGTREGARLGPIGAAVVDHGLQSGSDAVAAAA
+ADVARILGLTPVTVTRVEVARTGDGPEADARRARRVALAAAAREAGQGGAAPGAGTAVVL
+TAHTADDQAEQVLLGLARGSGTRSLAGIPARGTLPGGAAVARPLLGLTRADTETICRWAG
+LTWFEDPHNRDPALLRSRVRTRVLPALEDPDAGLGPGVRAGLVRTAAIAAEDAAALEAWA
+GDEFTRLRVDPPGRDPRVVSLDLDTLAALPAAVRHRVIARAARAAGGQAPPRERILAVDT
+LVTGARAGGTSAGPVELPGGVAAHRACARLDLIPCLPGP
+>NAFOICDF_00263
+MSSPFVRDVVAVPGAPTLPALAGPWPPRSRWPEPLHRAVESVRAVRAEHPGPVLVALSGG
+ADSLALAVACAVLAGTRAGERLGPAGAVVVDHGLQDGSAAVAAAAARTARALGLAPVTVE
+AVTVTPAGDGPEASARSARRTALARAAEGVGEGTPALVLTAHTADDQAEQVLLGLARGSG
+TRSLAGIPAHGALPGGVALARPLLGLSRADTEAICRWAGLTWFTDPHNADPALLRSRVRT
+RILPALEDPDTGLGPGLRAALVRTAAIAAEDAAALDAWADDALARLRLPAPETDRPAPVL
+LDLDALAALPAAVRHRVHARAARAAGAGTPSRERILAADALVAAAHAGGGSAGPVELGHG
+VTVRRVAAGEGGVGGRKEGGPSGCARLAYIPRPADR
+>MHAAABBN_02084
+MPRPEARDPGPTPAGGAGGLPAVGAWPPRTRWPEPLHRAVAAVREALAGDGSCRADAGPG
+RAGNRPRGLVALSGGADSLALAVACAVLVGTRDGARLGPIGAAVVDHGLQSGSDAVAAAA
+ADVARILGLTPVTVTRVEVARTGDGPEADARRARREALAAAARDAGQGRAAVVLTAHTAD
+DQAEQVLLGLARGSGTRSLAGIPARGTLPGGAAVARPLLGLTRADTETICRWAGLTWFED
+PHNRDPALLRSRVRTRVLPALEDPDAGLGPGVRAGLVRTAAIAAEDAAALEAWAGAEVTR
+LRVDPPARDPRVVSLDLDALAALPAAVRHRVIARAARAAGGQAPPRERILAVDALVTGAR
+AGCTSAGPVELPGGVAAHRACARLDLIPCLPGP
+>LFPAFLNI_00065
+MPRPEARDPGPTPAGGVGGLPAVGAWPPRTRWPEPLHRAVAAVREALAGDGPRRADVVPG
+RAGSRPRGLVALSGGADSLALAVACAVLVGTREGRRFGPIGAAVVDHGLQSGSDAVAAAA
+ADVARILGLAPVTVTRVEVARTGDGPEADARRARRKALAAAAREAGQGDAVPGAGAAVVL
+TAHTADDQAEQVLLGLARGSGTRSLAGIPARGTLPGGAAVVRPLLGLTRADTETICRWAG
+LTWFEDPHNRDPALLRSRVRTRVLPALEDPDVGLGPGVRAGLVRTAAIAAEDAAALDAWA
+GDEVARLRVDPPARDPRVVSLDLDALAALPAAVRHRVIARAARAAGGQAPPRERILAADA
+LVTGARAGGTSAGPVELPGGVAAHRACARLDLIPCLPGP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000346.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000346.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8778ed0945048e859b79c45fa3ed3f1b1a9043be
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000346.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00322
+MDTAPADRVPQPVDWAFAARTAAALAPAGPRFTAREAAREAAGLRAAAEASVPHVHRLTG
+LAAAEDLRDSQVLVVDRPTWSASATQSFATMLEPTFAHLQATRPQEYQAALTPVARHATA
+LEMGGILAWLSGKVLGQYDPFAGPSGGRLLLNAPSVAQVRTEINVDPEDFRLWVCLHEQT
+HRVQFAAAPWLRGHLQEQITALASGLFDKAESLPERLRSALAAANPLGRGSGAGAASTGP
+ASGPDDGRPGPAQAGGDVVPARGAGLLGALQDEEDRARLSHVTAVMSLLEGHANVVMDGV
+DADVVSSVKTIRRRFEDRADRRSPLDRMLRRLLGMDAKMAQYRDGQRFVSAAVAELGMDG
+FNVVWDAPELLPTEDELHRPERWTARVRAQA
+>MOLHKGIG_00070
+MSDDHATDRPRTAADAEPGAPAEPGPAVAHPVDWAFAARTARSLAAAGPRFTPREATREA
+EGLRAAAEAAVPHVHRLTGLEAARDLRDSQVLVVDRPTWSRAATQSFATLLDPTFAHLRD
+TRPREHAATTRVTRHATALEMGGILAWMSGKILGQYDPFIALPGPGGTAAGPAGGRLLLV
+APNVAQVRAEINVDPADFRLWVCLHEQTHRVQFAAAPWLREHLRGEITALTVGLFDKAES
+LPERLRTALAAANPLGREADAGRTGTRDGHDAQDAVAARPAPGLLGAIQDEEDRERLSRL
+TAVMSLLEGHANVVMDGVDSSVVSSVKTIRRRFDERGDRRSPLDRMLRRLLGMDAKMAQY
+RDGQRFVAAAVAELGMAGFNVVWDAPELLPSEAELHAPETWVARIRAQA
+>NAFOICDF_00264
+MTADQPVPSPAHPVDWDAAARAAGSLAAAGPRIGTREARREAEGLRAAAAASVAHVHRLT
+GLAAAEDLRDSQVLVVDRPTWSLANTQSFAGLLEPSFAHLRATRPQEYALTTAPLTRRAA
+ALEMGGILAWLSSKVLGQYDPFSALPGPDGVPAGPAGGRLLLVAPNVAQVRREIHVDPAD
+FRLWVCLHEQTHRVQFAAAPWLRGHLQGEITALTGGLFDKAESLPERLRSALAAANPLGA
+STSPGAGRAGQDDGAAGPGGRPALGLLGAIQDEEDRARLSRLTAVMSLLEGHANVVMDAV
+DSSVVSSVKTIRRRFDARGDRRSGLDRLLRRLLGMDAKMAQYRDGQRFVDAAVAELGRDG
+FNVVWDAPELLPSEEEIHAPDRWVARIRAQA
+>MHAAABBN_02083
+MSDDHATDRPRAAADAEPGAPAEPGPAVAHPVDWAFAARTARSLAAAGPRFTPREATREA
+EGLRAAAEAAVPHVHRLTGLEAARDLRDSQVLVVDRPTWSRAATQSFATLLDPTFAHLRD
+TRPREHAAATTRVTRHATALEMGGILAWMSGRILGQYDPFIALPGPGGTAGGPAGGRLLL
+VAPNVAQVRAEINVDPADFRLWVCLHEQTHRVQFAAAPWLREHLRAEITALTVGLFDKAE
+SLPERLRTALAAANPLGREADAGRTGARDGHDAQDAAPARPTPGLLGAIQDEEDRERLSR
+LTAVMSLLEGHANVVMDGVDSSVVSSVKTIRRRFDERGDRRSPLDRMLRRVLGMDAKMAQ
+YRDGQRFVAAAVAQLGMAGFNVVWDAPELLPSEAELHAPETWVARIRAQA
+>LFPAFLNI_00064
+MSDDHATDRPRTAADAEPGAPAEPGPAVAHPVDWAFAARTARSLAAAGPRFTPREATREA
+EGLRAAAEAAVPHVHRLTGLEAARDLRDSQVLVVDRPTWSRAATQSFATLLDPTFAHLRD
+TRPREHAAATTRVTRHATALEMGGILAWMSGRILGQYDPFIALPGPGGTAAGPAGGRLLL
+VAPNVAQVRAEINVEPADFRLWVCLHEQTHRVQFAAAPWLREHLRAEITALTVGLFDKAE
+SLPERLRTALAAANPLGREADAGRIGTRDGHDAQDAAAARPAPGLLGAIQDEEDRERLSR
+LTAVMSLLEGHANVVMDGVDSSVVSSVKTIRRRFDERGDRRSPLDRMLRRLLGMDAKMAQ
+YRDGQRFVAAAVAELGMAGFNVVWDAPELLPSEAELHAPETWGARIRAQA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000348.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000348.fa
new file mode 100644
index 0000000000000000000000000000000000000000..82f11f154a0e8ecb8fa29c80bcea5f584a9cb60b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000348.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00327
+MLVLTINQRDTLDAGDRVDAFLRSLGDAPGLAGAVALPFQRAVGDELIGAVTDPAAAVEV
+ALRALRERRWNVGIGVGALRGADGTEGAPSSGSLDDAAGPALAHARRAVEAAAVSTARIP
+LAVRGADAQASAEAEAVLRLVGQLVWSRTDAEWAVLDLLVPGVRGQQKPAADALGITAQA
+VSQAVQRAYWNEEHACRPAASRLLALAEEG
+>MOLHKGIG_00067
+MFVLTINQRDTLDAGDRVDTFLRALQDVPGLDDAVVLPFQRAVGDELIGAVEDPRVAVDV
+ALRALRQRRWNVGVGVGTVTHADGAAGAPASGDLHDAGGPGLAAARRAVEAAAVSTARIP
+LAVRGRDEEAAAEAEAVLRLVGQLVWSRTDAEWAVLDLLVPGVRGQQKPAAAALGITAQA
+VSQAVQRSYWNEEHACRPAAARLLTLAGG
+>NAFOICDF_00267
+MFVLTLNQRDTPDAGDRVDALLRELTDAAAAVPGLRSPALPFQRSVGDELVGVLEDPHAA
+VDVALRALRQRRWNVGIGVGTVCHADGSAGIPASGDLHHAGGPGLAAARRAVEAAALSTA
+RIPLAVRGRDAEAAAEAEAVLKLIGQLVWTRTAAEWSVLDLLVPGVRGQQKPAAQALGIT
+TQAVSQAVQRSFWNEEHACRPAAARLLALAAG
+>MHAAABBN_02080
+MFVLTINQRDTLDAGDRVDTFLRALQDVPGLDDAVVLPFQRAVGDELIGAVEDPRVAVDV
+ALRALRQRRWNVGVGVGTVTHADGAAGAPASGDLHDAGGPGLAAARRAVEAAAVSTARIP
+LAVRGRDEEAAAEAEAVLRLVGQLVWSRTDAEWAVLDLLVPGVRGQQKPAAAALGITAQA
+VSQAVQRSYWNEEHACRPAAARLLTLAGG
+>LFPAFLNI_00061
+MFVLTINQRDTLDAGDRVDTFLRALQDVPGLGDAVVLPFQRAVGDELIGAVEDPRVAVDV
+ALRALRQRRWNVGVGVGTVTHADGAAGAPASGDLHDAGGPGLAAARRAVEAAAVSTARIP
+LAVRGRDEEAAAEAEAVLRLVGQLVWSRTDAEWAVLDLLVPGVRGQQKPAAAALGITAQA
+VSQAVQRSYWNEEHACRPAAARLLTLAGG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000351.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000351.fa
new file mode 100644
index 0000000000000000000000000000000000000000..53af795f74d51aebb4da48b71db6b148699f1ffe
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000351.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00333
+MTRDDAAPLGRCTFLGPAGTFTEAALRAVPGAEQAELIPATSVPAALAAVRAGEADHAMV
+PIENSVEGGVSATLDDIASGDDLQILREELVQISFVLVGRPGVELADVRRVSTHTHAWAQ
+VRGWVEANLPGVEYTPSGSTAAAARALADAEPGSEPFDAAVCAPLVAEQTGLPVLARAIE
+DVTGAVTRFVLVGRPGPLPAHTGSDKTTLTVPLPDDHPGALREILDQFATRGINLSRIES
+RPTGEGMGKYFFSIDLEGHLAEERVAAAMGALHRIFPGVRFLGSYPRAEHRPVAVRRHTS
+DDAYRAGRAWVDGLLAR
+>MOLHKGIG_00062
+MTGTDSADATPSRLRYAFLGPAGTFTEAALRKVADPAEAEFVPAGSVLSAVAALRRGEVD
+RAVVPIENSVEGGVSATVDEIALGETLQILAEVHVAISFVLVGRPGVAIEDVRRVTTHPH
+AWAQVRGWAETALPGVEFTPAPSTAAGAGLVAQGDFDAAVCAPLVAEQTGLPVLAERIED
+VPGAVTRFVLLSRPTALPAPTGADKTTLVVPLPEDRPGALGQILAEFTTRGVNLSRIESR
+PTGEGIGRYFFSLDLEGHLAEARVGDALAALYREYPDLRFLGSYAQAEPVPTRVPAEFTD
+AAYRSGRAWVESLRSR
+>NAFOICDF_00274
+MSPAPRYAFLGPAGTFTEAALRQVASPEDVDLLPASSVLAALAAVRVGEAERAVVPIENS
+VEGGVTATLDDIGADEPLQILAEVLVPISFVLVGRPGVALEDVRRVTTHTHAWAQVRGWM
+EAHLPGVEFTPAGSTAAGARALLPSAGGDGAVASFDAAVCAPLVAEQTGLPVLAEAIEDV
+TGAVTRFVLVSRPGPVPEPTGADKTTLTVPLPDDHPGALREILDQFATRGINLSRIESRP
+TGEGMGRYFFSIDLEGHVAEERVGAALAALHRTFPGVRFLGSYPRAEGRPPTVPEHVTDA
+AYRRGTAWVRGLRSR
+>MHAAABBN_02075
+MTGTGSADATPSRLRYAFLGPAGTFTEAALRKVADPAEAEFVSAGSVLSAVAALRRGEVD
+RAVVPIENSVEGGVSATVDEIALGETLQILAEVHVPISFVLVGRPGVAMEDVRRVTTHPH
+AWAQVRGWAETALPGVDFTPAPSTAAGAGLVAQGDFDAAVCAPLVAEQTGLPVLAERIED
+VPGAVTRFVLLSRPTALPAPTGADKTTLVVPLPEDRPGALGQILAEFTTRGVNLSRIESR
+PTGEGIGRYFFSLDLEGHLAEARVGDALAALYREYPDLRFLGSYAQAEPVPTRVPAEFTD
+AAYRSGRAWVESLRSR
+>LFPAFLNI_00057
+MTGTDSADATPSRLRYAFLGPAGTFTEAALRKVADPAKAEFVSAGSVLSAVAALRRGEVD
+RAVVPIENSVEGGVSATVDEIALGETLQILAEVHVPISFVLVGRPGVAIEDVRRVTTHPH
+AWAQVRGWAETALPGVEFTPAPSTAAGAGLVAQGDFDAAVCAPLVAEQTGLPVLAERIED
+VPGAVTRFVLLSRPTALPAPTGADKTTLVVPLPEDRPGALGQILAEFTTRGVNLSRIESR
+PTGEGIGRYFFSLDLEGHLAEARVGDALAALYREYPDLRFLGSYAQAEPVPTRVPAEFTD
+AAYRSGRAWVESLRSR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000355.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000355.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d7ddbf2aa9a763ed0db360756110d9435eb32c2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000355.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00338
+MAQPEPVRLAPPGRTAEPDAARPAERALLAAASACDGDVAPMLALLGAGRAPDTEASAPD
+AAAPLELPLTGEGRTRQQWELLASVAAQDLSAARVLEPHLDALSILSQASVPAPAGLLGV
+YASESGGRTPRLTPAPHDDDAGSASDGRPDAGPDAWLLDGEKPWCSLADECAAAVITGRE
+ADGTRRAVLVDLDHPGVAETSSAWPALGLAPIRTVGLGFDAVPGTAVGGPEWYLRRPGFA
+WGGIGVAAVWFGGAVGIARTLRDATRSRAAAEAEGRGPGPDQVAQAALGRVDRLLHAMAA
+LLARAAEDVDAGRLDHGRGMVEADRIRGTVAQLCTEVVDVVGQATGPGPLTGSAAHARAV
+ADLQVYLRQHHAHRDDARLGRALLDGDADGGWTW
+>MOLHKGIG_00057
+MAQPEPVRLVPGGAVDRPAEQALLAAAAACDGDVDAMVELLRAASGAPSGEDAAPLDLPL
+TGAGRTREQWELLASVAAQDLSAARVLEPHLDALSILSQAGVPAPAGLLGVYASESGGRT
+PALRPAPDGPDTAWLLDGEKPWCSLADRCAAAVVTGREADGTRRAVLVDLSHPGVAETDS
+AWPALGLAPIRTVGLAFDAVPGSAVGGAEWYLRRPGFAWGGIGVAAVWFGGAVGIARTLR
+NATAARAAAEAEGRGPGPDQIGQAALGRVDRLLHAMAALLARAADDVDAGRLDHGRGMVE
+ADRIRGTVAQLCTEVMDVVGQATGPGPLTGSAAHARAVADLQVYLRQHHGHRDDARLGAA
+LLTGETDGGWTW
+>NAFOICDF_00278
+MSETPWVHLPGAEGDGRPAAPTEAEAALLAAARDGEDGEAGIEPILALLSGDDAAASLDL
+PLTGAGRTRRQWELLASVGAVSLPAARVLEPHLDALSILDQAGVPAPRGVLGVYASESGG
+VSPSARPAPGAAVGDEDAVWRLDGDKPWCSLADRCTAAVVTARQEDGLRRAFLVDLGEPG
+MEVADPRWPSLGLAPITTVGLRFADVPAVPVGGPEWYLRRPGFAWGGIGVAAVWFGGAVH
+VARTLRTSLERRTAAASDGSGPGPDQVGLAALGRVDRHLHAMASLLGRAADDVDAGRLDH
+AHGLVEADRIRGTVAQLCTEVLDVVGQATGPGPLTGDAAHARAVADLQVYLRQHHGPRDD
+ARLAESLLAADPAERAELQPW
+>MHAAABBN_02070
+MAQPEPVRLVPGGAVDRPAEQALLAAAAACDGDVDAMVELLRAASGAASGEDAAPLDLPL
+TGAGRTREQWELLASVAAQDLSAARVLEPHLDALSILSQAGVPAPAGLLGVYASESGGRT
+PALRPAPDGPDTAWLLDGEKPWCSLAGRCAAAVVTGREADGTRRAVLVDLSHPGVAETDS
+AWPALGLAPIRTVGLAFDAVPGIAVGGAEWYLRRPGFAWGGIGVAAVWFGGAVGIARTLR
+NATAARAAAEAEGRGPGPDQIGQAALGRVDRLLHAMAALLARAADDVDAGRLDHGRGMVE
+ADRIRGTVAQLCTEVMDVVGQATGPGPLTGSAAHARAVADLQVYLRQHHGHRDDARLGAA
+LLTGETDGGWTW
+>LFPAFLNI_00052
+MAQPEPVRLVPGGAVDRPAEQALLAAAAACDGDVDAMVELLRAASGAASGEDAAPLDLPL
+TGAGRTREQWELLASVAAQDLSAARVLEPHLDALSILSQAGVPAPAGLLGVYASESGGRT
+PALRPVPDGPDTAWLLDGEKPWCSLADRCAAAVVTGREADGTRRAVLVDLSHPGVAETDS
+AWPALGLAPIRTVGLAFDAVPGSAVGGAEWYLRRPGFAWGGIGVAAVWFGGAVGIARTLR
+NATAARAAAEAEGRGPGPDQIGQAALGRVDRLLHAMAALLARAADDVDAGRLDHGRGMVE
+ADRIRGTVAQLCTEVMDVVGQATGPGPLTGSAAHARAVADLQVYLRQHHGHRDDARLGAA
+LLTGETDGGWTW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000363.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000363.fa
new file mode 100644
index 0000000000000000000000000000000000000000..23c9619b0b7e2ecccf59046657200fb3d8f71248
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000363.fa
@@ -0,0 +1,39 @@
+>ACLBLIBL_00356
+MRARRRAGLFSAGVRGYDGRVSTVSAPSRAPRTVTVTGAAGNIGYALLFRIAAGGMLGPD
+TPVRLRLLEIPAALRAAEGTAMELADAAFPLLADVEVTDDPAVAFDGVQHAMLVGARPRT
+KGMERGDLLEANGGIFGPQGRAINDHAADDVRVVVVGNPANTNALIAAAHAPDVPAERFT
+ALTRLDHNRAVAQLAARAGVAVTDVDGVTIWGNHSATQFPDLTHARVRVAGAWRPALEVV
+DPAWAAEEFVPRVAKRGAEIIEVRGASSAASAASAAVDHMRDWTLGTGAGAGGAGTDAGP
+RWTSAAVVSDGSYGVPEGLVSSFPVTSDGGAAWRIVPGLAPDESLLPGTGGRLAATVAEL
+EAERDAVHGLGLL
+>MOLHKGIG_00044
+MGGVDTAQQTTAQDTAQDPASTTPRTVTVTGAAGNIGYALLFRIAAGGMLGPDTSVRLRL
+LEIPAALGAAEGTAMELADAAFPLLADVEVTDEPARAFDGVQHALLVGARPRTKGMERSD
+LLEANGGIFGPQGRAINDHAAQDVRVVVVGNPANTNALIAAAHAPDVPAERFTALTRLDH
+NRAVAQLAARAGVAVTDVAGVTIWGNHSATQFPDLTHARVRVDGTWRPALEVVDPVWAGE
+EFVPRVARRGAEIIEVRGASSAASAASAAIDHMCDWTLGTGVDADGASRRTSAAVVSDGS
+YGVPEGLISSFPVTSDGGTAWRIVPGLEPDESVLPGEGGRLAATVAELEAERDAVRGLGL
+L
+>NAFOICDF_00298
+MTQDTLRTPATVTVTGAAGNIGYALLFRIASGQLLGPDTPVRLRLLEIPAAVRAAEGVAM
+ELADSAFPLLASVDVTDSADAAFDGTTHALLVGARPRTAGMERADLLRANGGIFGPQGAA
+INASADASVRVVVVGNPANTNALIASAHAPDVPAERFTALTRLDHNRAVSQLAARAGVGV
+ADVDGITIWGNHSATQFPDLTHARVRMSGDDGAPVWRPALEVVDPAWAAEEYIPRVAKRG
+AEIIEVRGASSQGSAASAAIDHMRDWSLGTGVDADGAPRRTSAAVVSDGSYGVPEGLISS
+FPVTSDGSGAWTIVPGLEPDESLLPGDGGRLAATVAELEAERDAVRALGLI
+>MHAAABBN_02057
+MRRAGVSSAGERGHDGGVDTALQTTAQDTAPDPVSTTPRTVTVTGAAGNIGYALLFRIAA
+GGMLGPDTPVRLRLLEIPAALGAAEGTAMELADAAFPLLADVEVTDDPARAFDGVQHALL
+VGARPRTKGMERGDLLEANGGIFGPQGRAINDHAAQDVRVVVVGNPANTNALIAAAHAPD
+VPAARFTALTRLDHNRAVAQLAARAGVAVTDVSGVTIWGNHSATQFPDLTHARVRVDGTW
+RPALEVVDPVWASEEFVPRVARRGAEIIEVRGASSAASAASAAIDHMRDWTLGTGVDADG
+APRRTSAAVVSDGSYGVPEGLISSFPVTSDGGTAWRIVPGLEPDESVLPGEGGRLAATVA
+ELEAERDAVRGLGLL
+>LFPAFLNI_00039
+MRRAGVSSAGERGHDGGVDTAQQTTAQDTAPDPASTTPRTVTVTGAAGNIGYALLFRIAA
+GGMLGPDTPVRLRLLEIPAALGAAEGTAMELADAAFPLLADVEVTDDPARAFDGVQHALL
+VGARPRTKGMERGDLLEANGGIFGPQGRAINDHAAQDVRVVVVGNPANTNALIAAAHAPD
+VQAARFTALTRLDHNRAVAQLAARAGVAVTDVSGVTIWGNHSATQFPDLTHARVRVDGTW
+RPALEVVDPVWASEEFVPRVARRGAEIIEVRGASSAASAASAAIDHMRDWTLGTGVDADG
+APRRTSAAVVSDGSYGVPEGLISSFPVTSDGGTAWRIVPGLEPDESVLPGEGGRLAATVA
+ELEAERDAVRGLGLL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000366.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000366.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a2e874a1272b38177cf7b5d75ded0eba716b9a60
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000366.fa
@@ -0,0 +1,33 @@
+>ACLBLIBL_00360
+MGPRRGLPEGEGPLSGARGGRGAGRQRASRGGPARSTRTGGRAGAKGGGPQRAGSGSRAG
+GEGRRRAPSAPADLAAPPETLFLATIPGATPSTWVDRFTTRQRVVQLVNHDEASQLAHLA
+HDDAGMPRHPLPQLGYVRRRRDVEAEEMLRAAGVDPRRVHLVGVYAELPVVCVGRDHLLA
+AWDAEADGPVPLAELDSHEELDPARFAAAPVEDPLDSAELPGAGERMALEIAASGAGHVV
+LPMSVARMFGRKDVVVLPLASALDDTVGMSRADREAAATRAEVEADAGDAGTAAAGPGEA
+DDDAARHPGWDVALAWLKEADSELVQSFVGVARGRRGNSSR
+>MOLHKGIG_00040
+MAKGVKPAGRAGGEGRRRPAPAPPADLPVPPETLFLATIPGATPSTWVERFTTRQRTVQL
+VNHDDAAQLAHLAHDDAGQPRHFLPQLGYVRRRRDVSAEEFLRAGDVDPRHVHLVGVYSE
+LPVVCVGRDHLLAAWDVDADGPVPPAELDPDEELDPARFAPAPSPEPMDAAELPGAGERM
+ALEIAASGAGHVVLPMSVARMFGRKDVIVLPLASTLDDTVGLSRADREAAATRSALADEQ
+ARAEAEAGAAVVDGADPAGHGDDDARHPVWDVALAWLKAADSELVQAFVGVARGRRGASS
+R
+>NAFOICDF_00301
+MPAAPADLPTPPETLFLATIPGATPSTWVQRFSSRARTVQLVNHEEAQQAAHLAHDAAGA
+PLHPLPQLGYVRWLRDAGVESVLRESGVDPRFVHVVGVYSELPVVCVGKEHLLAAWDLEA
+DGPVPLAELDPAEHMDPARFAPEPGAASNPLDSAELPGAGERMALEIVASGVGHVVLPQS
+VARVFGRKDVVVLPVACELDDVVGLSRADREAAATRAEVAEEGDGVVPDGADAPATTAPR
+HPGWDVGLAWLKEQDSELVQSFVGVARGRRGGTSR
+>MHAAABBN_02053
+MAKGVKPAGRAGGEGRRRPAPAPPADLPVPPETLFLATIPGATPSTWVERFTTRQRTVQL
+VNHDDAAQLAHLAHDDAGQPRHFLPQLGYVRRRRDVSAEEFLRAGGVDPRHVHLVGVYSE
+LPVVCVGRDHLLAAWDVDADGPVPPAELDPDEELDPARFAPAPSAEPMDAAELPGAGERM
+ALEIAASGAGHVVLPMSVARMFGRKDVIVLPLASTLDDTVGLSRADREAAATRSALADEQ
+ARAQAEAGAAVVDGADPAGQGDDDARHPGWDVALAWLKAADSELVQAFVGVARGRRGASS
+R
+>LFPAFLNI_00035
+MKPAGRAGGEGRRRPAPAPPADLPVPPETLFLATIPGATPSTWVERFTTRQRTVQLVNHD
+DAAQLAHLAHDDAGQPRHFLPQLGYVRRRRDVSAEEFLRAGDIDPRHVHLVGVYSELPVV
+CVGRDHLLAAWDVDADGPVPPAELDPDEELDPARFAPAPSPEPMDAAELPGAGERMALEI
+AASGAGHVVLPMSVARMFGRKDVIVLPLASTLDDTVGLSRADREAAATRSALADEQARAE
+AEAGAAVVDGADPAGQGDDEARHPGWDVALAWLKAADSELVQAFVGVARGRRGASSR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000376.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000376.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c55b7cedbb624d256a5a6953bc4a16e7e3c50f1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000376.fa
@@ -0,0 +1,66 @@
+>ACLBLIBL_00377
+MEEQWTLNGRYRIDALIGRGGMADVFRGTDLRLHRPVAVKLMRRDLARDPHFQARFRKEA
+RSVASLNHPSIVSVYDTGEVSLEDGHHPVDCPYLVMELVTGRSLREVLHAEGAVGTERAV
+AWTREVLEALEHAHQEGIVHRDVKPANVMVTDAGSVKVMDFGIAHALADTSATTSQTQAV
+VGTALYLAPEQATGRTVDGRADLYATGCVLFELLTGRPPFTGDTPLAVAYQHVREAPPAP
+SEVDPDLPRAFDPVLLRALEKDPEDRFPTGAAFREALEAAAADPHAAVDADTAALDLVRA
+GAAGAGGAAVAAGREVRRDGARDSADVPTAAVPLTPAPAPAAPAEPAEPPGGEPRRGRGR
+AARRRLRRPAGGRRLRGRPAPGHRLPTPPSRGPRRPAPRPPPGSALPPPLPPPDGAAAGG
+AACRSPGCCWPASSC
+>MOLHKGIG_00019
+MDEQRTLNGRYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRKEA
+RSAASLNHPSIVSVYDTGEVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGPDRAV
+AWTRGVLEALEHAHEEDIVHRDVKPANVMVTDTGTVKVMDFGIAHALADTSATTSQTQAV
+VGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPPAP
+SDVDPDLPPAFDPVVLRALRKDPQDRFPTGAAFLAALEEAAADPHAGPGRHTPPLDAVHP
+ALVGAGGAVLGATPAEHGADVADVPTAAVPLTRPAPSVPAEPDTAQPQAVNHAVAGAGLP
+GAASAAQLAAAAAMDGPRPVTGGQPVTPGAAATPRPEPPPRDTPAPATATPRRVRRRVRR
+RTLLAAGVVLVALALVLAPWLAAALRTTAEVPAVVGLQQDEAVAALEDAGLVAVVSSAYM
+ADAPDGTVTQSDPPTGTEVPRGAEVRIRVSRGEEGIALSDSLHGLSEDAARRELERLGLR
+VSSVQYQDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARRQL
+ALSAPELRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTTSSWIAPTAEPSEPAP
+PSSEAPEPTPSASTSPSPPSSESPEPSESPEPSESAEPSPSPSASATPSPEPTTTATPSP
+TQSPSPPSAAPSTSSEPTEQSPSTSPTATPVDPLPTLTPDPEPSIDPPPST
+>NAFOICDF_00359
+MQGQRILHERYRVDELIGRGGMADVFRGHDLRLNRTVAVKMMRPDLARDPAFQARFRTEA
+RHAAALNHPNIVSVYDTGDALLDDGPQSVECPYLVMEHVDGRTLRELLDAGEVAWRDAVE
+WTRGLLHALDHSHRQRIVHRDVKPANVMVTRDGGVKVMDFGIARALSDTSAHTGQTQAVV
+GTALYLPPEQAQGARVDARSDLYAAGCVLFELLTGRPPFTGETPLAIAYQHVREEPPAPS
+AVDPSLSTEFDSVVLRALQKDPGLRHQHAREFLSALDFAAARAARAADDDAPTRVVPASG
+AAPLATGSGALAAAVAGSTAAGPTASGSTALGAGGAPEARPATGPPATTPLGAAAGPTEP
+LIAGHAVAGAAVPGAPSASQLAAAEAVETAPAAASTTGGSAGAGATSGAERAGRRHRLSW
+AVLAAVAAVAAVAAILALGAALLIGSRDPGPVTVPALAGRTEAEAVSALTGLGLRSAISP
+DYHSTEPDGRVLKVHPGAGAAVEPGSTVNLSVARGGEGVVLPTSLRGASEARVRQELARL
+GLNVASVEDTPSGELDRGALVQTDPVLGSRVPPGSAVVLHLADGTARVPSLVGMTGADAR
+TTLAALDPEMTVRFQGAAGADPDTGVVVLQDPAAGTVVDNTAMITLITSAEATPTASAVT
+VAPPDPALPSATTTTAPAEPSPGVPAPTTPAAPAVDTPAPAPATTPAPAPESSSTPGAGT
+DPAPTESAPTPDDGPGSTGTPSTEAPTEAPTDPVGTPAPSPSGEPVPQPSPSVEPLPEPT
+APTEAPTADPAG
+>MHAAABBN_02037
+MSVDEQRTLNGRYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRK
+EARSAASLNHPSIVSVYDTGEVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGTDR
+AVAWTRGVLEALEHAHEEGIVHRDVKPANVMVTETGAVKVMDFGIAHALADTSATTSQTQ
+AVVGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPP
+APSDVDPDLPPAFDPVVLRALRKDPEDRFPTGTAFLAALEEAAADPHAGPGRHTPPLDAF
+PPALVGAVLGAAAAEHGADVPTAAVPLTRPTPSVPAEPDAAQPQAANHAVAGAGLPGAAS
+AAQLAAAAAMDGPRPVTVGQPVMPGAAATPWPEPQGDTPAPATATPRRVRRRLRRRTLPA
+AGVVLVALALVLTPWLAAALRTTVEVPAVVGLQQDEAVVALEDAGLLAVVSSAYMADAPD
+GTVTQSDPPTGTEVPRGAEVRIRVSRGKEGIALSDSLHGLSEDAARRELERLGLRVSSVQ
+YQDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARRQLALSAP
+ELRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTASSWIAPTAEPSEPAPPYSEA
+PEPTPSASASPSPPPSESSEPSESAEPSPSPSASATPSPEPTTTATPSPTQSPSPTSAAP
+SEPTEQPPSTSPTATPVDPLPTLTPDPEPSIDPPPST
+>LFPAFLNI_00019
+MDEQRTLNERYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRKEA
+RSAASLNHPSIVSVYDTGEVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGTDRAV
+AWTRGVLEALEHAHEEGIVHRDVKPANVMVTDTGTVKVMDFGIAHALADTSATTSQTQAV
+VGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPPAP
+SDVDPDLPPAFDPVVLRALRKNPQDRFPTGAAFLAALEEAAADPHAGPGRHPPPLDAVHP
+ALVGAVLGATPAGHGADVPTAAVPLTRPTPSVPAEPDTTQPQAANHAVAGAGLPGAASAA
+QLAAAAAMDGPRPVTAGQPVTAGQPVTPRPEPPPGDTPAPATATPRRVRRRVRRRTLLAA
+GMVLVALALVLAPWLAAALRNTVEVPAVVGLQQDEAVAALEDAGLVAVVSSAYMADAPDG
+AVTQSDPQTGTEVPRGAEVRIRVSRGEEGIALSDSLHGLSEDAARRELERLGLRVSSVQY
+QDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARRQLALSAPE
+LRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTASSWIAPTAEPSEPAPPSSEAP
+EPTPSASAPPSPPPSESPEPSESAEPSPSPSASATPSPDPTSATPSPTQSPSPPSAAPST
+SPEPTAQSPSTSPTGTPVDPLPTLTPDPEPSIDPPPST
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000378.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000378.fa
new file mode 100644
index 0000000000000000000000000000000000000000..97236eb55c46fc830884129ff17a7f5b35c9396c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000378.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_00380
+MAAPSGKRKDSARRKHEELEDARRGARRGSSAVTTDLGDVDPGPKPLSPVYKAVMFGLMI
+VGLLWIVVYYLTQGLFPIVAIGGWNILVGFGIALVGFLMMSRWSE
+>MOLHKGIG_00017
+MAAPAGKRKDSARRKREELEAARRSRSAVRTDLGDVDPGPKPLSPVYKAVMFGLLILGLL
+WIIVYYLTQGLLPIVQIGGWNILVGFGIALVGFLMMSRWSE
+>NAFOICDF_00361
+MATTSGKRKDSARRKRRELEQARSRRGRTASVSTDLGDVDATPAPLPRWYKAVMFGLLIL
+GLLWIVVYYLSQGLFPIPDAGGWNILIGFGIALVGFLMMSRWSE
+>MHAAABBN_02035
+MAAPAGKRKDSARRKREELEAARRSRSAVRTDLGDVDPGPKPLSPVYKAVMFGLLILGLL
+WIIVYYLTQGLFPIVQIGGWNILVGFGLALVGFLMMSRWSE
+>LFPAFLNI_00017
+MAAPAGKRKDSARRKREELEAARRSRSAVRTDLGDVDPGPKPLSPVYKAVMFGLLILGLL
+WIIVYYLTQGLFPIVQIGGWNILVGFGIALVGFLMMSRWSE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000379.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000379.fa
new file mode 100644
index 0000000000000000000000000000000000000000..80d48d5496bef7b151599e656547f66d9867524f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000379.fa
@@ -0,0 +1,34 @@
+>ACLBLIBL_00381
+MDCAAQGGAPAGTTTSPAAVGSPGPGGVGMAGAAGRGAPARRRTGLAAAPVTWTLIAVTV
+AAYVAQWATRDTVPGVTEALWYAGLYTSPFGLEPWRMATYALVHDLSGPTHLILNMLALW
+VIGRVLEPALGWWRFAALYVLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLVTRV
+RGGQVRSIAVLIGLNLVISFLLPGISWQVHVGGLITGAVVALVYSLAGGLRPGRASAPSA
+GAQAAGLVLVAAVLAVLTVLGADRIGLDAVLR
+>MOLHKGIG_00016
+MSTTPSDPHGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS
+GVVAGPAPTVAPAGAAASVPARRRTGFTASPVTWILLAVTTVVYAAQWMTRDQASGVTEA
+LWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGWWRFLALY
+VLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLIGLNLVFS
+FLLPGVAWQVHMGGLLTGAVVAVVFSLAGGLRPGRARVPSVGAQVAGLVVVAAALAALTV
+LGAARVTVAGLLG
+>NAFOICDF_00362
+MSTTPSDPHGPDVAEGTPPVCPRHPGRAAYVRCASCADPVCLDCQRPAAGGLTLCPDCAA
+RLAAGVPGPASGTTTSPAPASAGAGRGGVGAALRAAPVTWTLLAVTLLVYAGQWLTRGSR
+TGVTESLWYAGAYTSAIGMEPWRMLTYALVHDVSGPTHVALNMVALWVIGRVLELALGWW
+RFLALYLVSALGGAVFALWTADPLQPVVGASGAVYGLFAALFAVTRFRGGQVTSIAVLIG
+LNLVFSFLMPGISWQVHVGGLLTGAVAGALLVSAGGPPGRSAAADGTARRSSAGVHVAGL
+VLLAAVLAVLTLVGAARLSPAALLG
+>MHAAABBN_02034
+MSTTPSDPYGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS
+GVVAGPAPTSPPAAGAAATVPARRRTGFAASPVTWILLAVTTVVYAAQWMTRDQASGVTE
+ALWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGWWRFLAL
+YVLSAVGGAVFALWASDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLIGLNLVF
+SFLLPGVAWQVHVGGLLTGAVVAVVFSLAGGLRPGRARLPSVGAQVAGLVVVAAALAALT
+VLGAARVTVAGLLG
+>LFPAFLNI_00016
+MSTTPSDPHGPDSADGTPPVCPRHPGRAAYVRCAVCRRPACLDCQRPGSAAGPVCVDCAS
+GVVAGPAPTVAPAGAAASVPVRRRTGFAASPVTWILLAVTAVVYAAQWMTRDQASGVTEA
+LWYAGLYTSPYGMEPWRMASYALVHDVSGPTHLLLNMLALWVIGRVLEPALGWWRFLALY
+VLSAVGGAVFALWVSDPLQPVVGASGAVYGMFAALFLLTRVRGGQVRSIAVLIGLNLVFS
+FLLPGVAWQVHVGGLLTGAVVAVVFSLAGGLRPGRARVPSVGAQAAGLVVVAAALAALTV
+LGAARVTVAGLLG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000380.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000380.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c27a16fd3f053f672c7068ac8de28bd35f219389
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000380.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00382
+MARMANATHIATIKTNQGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGVGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEESQQVVDRLNAVATDPRDRPLEDVVIESVEIAEA
+>MOLHKGIG_00015
+MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA
+>NAFOICDF_00363
+MTRMTNATQIATIHTNQGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDQLNSVATDPRDRPLEDVVIESVEISEA
+>MHAAABBN_02033
+MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA
+>LFPAFLNI_00015
+MGRMANKTHTATIHTNHGDIVVELFGNHAPKTVKNFVGLATGEQEWTHPQTGEKNNGAPL
+YSGTVFHRIIKDFMIQGGDPLGMGIGGPGYQFGDEIHPELQFDRPYLLAMANAGPGTNGS
+QFFITSVPTGWLNGKHTIFGEVKDEASQKVVDELNAVATDPRDRPLEDVVIESIDIDEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000381.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000381.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c31a1b314f081ffba7a56a3b352e7b98b27ff231
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000381.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00383
+MARTTLNDEIQHDGGADTFVTRQTENLRHWAAPKLEAARTWGEYGAAFTGVGASVAAEEG
+RRAAHDAKQEYGPRVEKQAKRAGDAVADRYAKLAPAVATGAGVLQDVLHRLQEQAQEAGH
+EAQKQFADARKDAEKAAEKGRKRGAKKAKQVRRAGRGARKDVTKAARGARKDARQAGSFL
+ADRAGQAGSAAAAGGLTLAGALAAAVNALQEQGEKLAPQVQARLSDAGDYAQRRKEEVVP
+LAAARLADGAAHARKTAHDVQVPDAVEQALIALTGDKAIVRKLRKGAEQYAGSAEKDLNR
+AAGRKARSGGRGWILGGMALAAAGAGYALWRLTKPVQDPWTAPVPGPITANIPVVEANNP
+YAQQQKVVAESGSAAAGEGVRVDTAAPVTTAVPAQDPVAEANAKVLGTDR
+>MOLHKGIG_00014
+MARKTLHDEIQHDGGANAFVARQAENLRHWAAPKVESTRAWSEVAAAYGLIGGSAAAEEG
+RRKAQDAKKEYGPVVERGARKAGEAVAHQYGLLAPAVAKGVDTVQDFLEHLQAQAQDAGH
+EVQQQFAAARKDAEKAAKKGRRRGGRKAKQLRRDGRQAAKGLRKDAKKAAKGARKDAQRS
+AALFSDRAGQAKDAAAAGGLTLAGLLATGLSALQEQGGKVAPQVQARLADAGDYAQRRKE
+EVLPVAAARLADGAAHARKTAHDVEVPDALEQALIKLTGDKAIVQRLRQGAEQYAGAAEK
+DLNRAAGRRASRSGGRAWIVAGMAAAAAGAGFALWRLTKPVQDPWTAPVPGPITANIPVV
+EANNPYAQQQKVVAEAGSAAAGQGVRVDTATPDPVAAANAKVLGVQPGQQR
+>NAFOICDF_00364
+MARTTLSNEIEHNGSADTFFARQAENLRHWAAPQLENARAWAEVTTGFGQVGGKVAAAEG
+RRLAEEEVAPRVKDSAERVNAAAKGRYEKAAPVVATGLGAAGTVLQQLLEAAQDKAQQAG
+QQVQDLAEQAQKDAKKSAKRTRKDAKKAGKRVSKKADKAQSLFASKAGDAKGAAAAGGLN
+VAGLLAAAVAAAQDRGQELAPQVKGRVEQAAQYAQDRRAEYAPKAAASLAGVAGRAEKAA
+GDVTVPASVEQLLVKLTGDKNAVKHLRQDVQSRARETQKGLKKQARQESRRGGATGWIIA
+GMAAAAAGAGLAVWKLTKPVQDPWAAPVPGPITANIPVVQADGTVNPYAKQEQAVAEARA
+AQGGMVNVRPQVG
+>MHAAABBN_02032
+MARTTLHDEIQHDGGANAFVARQAENLRHWAAPKVESTRAWSEVAAAYGLIGGSAAAEEG
+RRKAQDAKQEYGPVVERGARKAGEAVAHQYGLLAPAVAKGVDTVQDFLEHLQAQAQDAGH
+EVQQQFAAARKDAEKAAKKGRHRGGRKAKQLRRDGRQAAKGARKDAQRSAALFSDRAGQA
+KDAAAAGGLTLAGLLATGLSALQEQGGKVGPQVQARLADAGDYAQRRKEEVLPVAAARLA
+DGAAHARKTAHDVEVPDALEQALIRLTGDKAIVQRLRKGAEQYAGAAEKDLNRAAGRRTS
+RSGGRAWIVAGMAAAAAGAGYALWRLTKPVQDPWTAPVPGPIAANIPVVEANNPYAQQQK
+VVAEAGSAAAGEGVRVDTAAPDPVAAANAKVLGVQPGQQR
+>LFPAFLNI_00014
+MARTTLHDEIQHDGGANAFVARQAENLRHWAAPKVESTRAWSEVAAAYGLIGGSAAAEEG
+RRKAQDAKKEYGPVVERGARKAGEAVAHQYGLLAPAVAKGVDTVQDFLEHLQAQAQDAGH
+EVQQQFAAARKDAEKAAKKGRRRGGRKAKQLRRDGRQAAKGLRKDAKKAAKGARKDAQRS
+AALFSDRAGQAKDAAAAGGLTLAGLLATGLSALQEQGGKVAPQVQARLADAGDYAQRRKE
+EVLPVAAARLADGAAHARKTAHDVEVPDALEQALIKLTGDKAIVKRLRQGAEQYAGAAEK
+DLNRAAGRRASRSGGRAWIVAGMAAAAAGAGFALWRLTKPVQDPWTAPVPGPITANIPVV
+EANNPYAQQQKVVAEAGSAAAGQGVRVDTATPDPVAAANAKVLGVQPGQQR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000383.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000383.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a6576b074f67d8092a90a369f90d6c39771d7ae
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000383.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00386
+MVLDGPVNTTIDTPSPDQPVSGQGTPAYARVPASYYDIFVGVFVALLILSGVTAAKLFYG
+PTVPVFSDVFYGGGPLIFDGGAFLFPFAYIIGDILAEVYGWRRARRAILLGFAMLVLAAL
+TYTVVSWTTPVEGFEVWDQALAPMLRITVAGFVAFLAGSLINATIVVRLKERMRERHVAF
+RLILSTIVGQFFDTLIFCTIAFAGTITLLELANYTFTGFLYKTLVEILIVPITLLVIRRV
+KASEPTYRPASSPARAAADAA
+>MOLHKGIG_00011
+MNTTIDTPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYGPTVPVI
+SDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAALTYTVVS
+WTTPVEGFEVWDQALAPMLRITVAGVVAFLVGSLLNASIVVRLKERMKERHVAFRLILST
+VVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRALKRREPT
+YRAPGFEIHRDDDPALAPAASR
+>NAFOICDF_02181
+MNTTPASRSEPTSGQGAAASAAAPHSHYDIFVGVFVALLILSGVTAAKLFYGPTVPGVSD
+VFYGGGPLIFDGGAFLFPLSYVVGDILAEVYGLRRARRAIYIGFAMLVVAALTYRLVALT
+TPVEGFEAWDQALAPTLRITLAGLAGYIVGSLLNATVVARMKARMAERAVAWRLIASTLV
+GEFFDTLIFCLVAFAGTITLADLANYTVTGYVYKCLVEICIVPVTLLVIRWLKRHEPTYR
+AQPTPAPVSAPTA
+>MHAAABBN_02029
+MNTTTHAPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYGPTVPVI
+SDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAALTYTVVS
+WTTPVEGFEVWDQALAPMLRITVAGFVAFLVGSLLNASIVVRLKERMKERHVAFRLILST
+VVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRALKRREPT
+YRAPGFEIHRDDDPALAPAASR
+>LFPAFLNI_00011
+MNTTIDTPSPDRPASGQGTPAYARVPASYYDIFVGVFIALLILSGVTAAKLFYGPTVPVI
+SDLFYDGGPLIFDGGAFLFPFAYIVGDILAEVYGWRRARRAIVLGFAMLVLAALTYTVVS
+WTTPVEGFEVWDQALAPMLRITVAGFVAFLVGSLLNASIVVRLKERMRERHVAFRLILST
+VVGQFFDTLIFCTIAYAGTISLLELANYTVTGFAYKTLVEILIVPVTLLVIRALKRREPT
+YRAPGFEIHRDDDPALAPAASR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000388.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000388.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b3730bf31aec5dedf995800165c98af95dea0a3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000388.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00417
+MSTSASSRPGKAAGAGRTAERSGRPVRKASGSSQENLVRAVPKAKVRRARLMLNRVDPWS
+VLKLAFLLSVALGILTVVAAVALYSLSDALGLFQRINDALGTVLGAESGRYTVQSLAPLS
+TVVSLATVLAVLNVILLTALATVAALLYNVCAALVGGVGVTLTDD
+>MOLHKGIG_00007
+MSTSASSRPGQGRSTGKAAEPRSGRPVRKASGSSQEDLVRAVPKAKVRRARLVLTRVDPW
+SVLKLAFLLSVALGILTVVAAVALYSLSDVLGIFDRVNDVIGTVLGSEAGRYTVASLAPL
+STVTSLATVLAVVNVILLTALATVAALLYNLCASLVGGIGVTLTDD
+>NAFOICDF_00369
+MSTSASSRPAGAKGASASRPARRSSSRDSQEDLVRAVPKAKVRRARLQLTKVDPWSVLKL
+AFLLSVALGIILVVATVGFYTLAELTGVFGKINDVLGTVLGTESGTYTVENLAPLSTVVS
+LATVVAVLNVILLTALGVVGALLYNVCASLVGGVGVTLADD
+>MHAAABBN_02012
+MSTSASSRPGQGRSTGKAAEPRSGRPVRKASGSSQEDLVRAVPKAKVRRARLVLTRVDPW
+SVLKLAFLLSVALGILTVVAAVALYSLSDVLGIFDRVNDVIGTVLGSEAGRYTVASLAPL
+STVTSLATVLAVVNVILLTALATVAALLYNLCASLVGGLGVTLTDD
+>LFPAFLNI_00007
+MSTSASSRPGQGRSTGKAAEPRSGRPVRKASGSSQEDLVRAVPKAKVRRARLVLTRVDPW
+SVLKLAFLLSVALGILTVVAAVALYSLSDVLGIFDRVNDVIGTVLGSEAGRYTVASLAPL
+STVTSLATVLAVVNVILLTALATVAALLYNLCASLVGGLGVTLTDD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000392.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000392.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f11e45a487237b8007b3e15799d4a5a7dd65f5fb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000392.fa
@@ -0,0 +1,41 @@
+>ACLBLIBL_00421
+MHLSHLTVADFRSYRWADLELGPGSTVLLGANGVGKTNLVEAVGYLGSHQSHRVSSDAQL
+VRFGQDRARIAGRVHRGSRTVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE
+DLNLVTGEPGGRRRLLDQLMVQLRPALGEAAADFERVLRQRNALLKSARKARRWGPEEEA
+TLEVWDEHLCAAGARLLHGRLHVLRLLAHPLREMYGALTNGSKAATYAYESTVPLARGTH
+AEVPPVAELAADMRRALVAQRDEEQARALTLVGPHRDELALFLGPAPARGYASHGETWSL
+ALALRLAAYDVLVADDPDPDGRPVLILDDVFAELDAARRRRLAALVGRAEQVIVTAAALE
+DVPAELAGPRVLIRQDAEGSEAVPAAAPVEGDIRAPRGAGGTEGEAPGARRGRRRRRRHA
+PADPAEDDPDG
+>MOLHKGIG_00003
+MYLSHLTVADFRSYRWADLELTPGSTVLLGANGVGKTNLVEAIGYLGAQQSHRVSSDAQL
+VRFGRDRARIAGRVHRGSRAVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE
+DLSLVTGEPGGRRRLLDQLMVQLRPALGEAAADYERVLRQRNALLKSSRGSRRWGPEEDA
+TLAVWDEHLCAAGARLLHGRLHVLRLLARPLQEMYAALTNGSKAAAYAYESTVPLARGTH
+AEVPAVADLAVDMRRTLETQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL
+ALALRMAAYDVLVADDPDPDARPVLILDDVFAELDAARRRRLAALVHRAEQVIVTAAALE
+DVPEELTAHRVLIRQDAEGSEAVAAAAPVEGDIREPRREGGADG
+>NAFOICDF_00374
+MHLSHLTVQDFRSYRWADLELSPGSTVLLGANGVGKTNLVEAIGYLGSHQSHRVSQDAQL
+VRFGQDRARIAGRVHRGARSVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE
+DLGLVTQDPGGRRRFLDQLMVQLRPALGQAAADYERVLRQRNALLKSARKARRWGAEEDA
+TLAVWDEHLCAAGARLLHGRLHVLRLLAHPLQEDYAALTNGSKTATYSYESTVPAARGTH
+VQAPPVAELAASMHAALVEQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL
+ALALRLAAYDVLVADDSDPEGRPVLILDDVFAELDAARRERLAGLVGRAEQVIVTAAALA
+DIPASLAGHRVLIRQDAEGSEAVAAAEPVEGDIRAPRPGAAPGAAASEAEEPEDGDARA
+>MHAAABBN_02008
+MYLSHLTVADFRSYRWADLELTPGSTVLLGANGVGKTNLVEAIGYLGAQQSHRVSSDAQL
+VRFGRDRARIAGRVHRGSRAVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE
+DLGLVTGEPGGRRRLLDQLMVQLRPALGEAAADYERVLRQRNALLKAGRGSRRWGPEEDA
+TLAVWDEHLCAAGARLLHGRLHVLRLLARPLQEMYAALTNGSKAAAYAYESTVPLARGTH
+AEVPAVADLAVDMRRTLETQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL
+ALALRMAAYDVLVADDPDPDARPVLILDDVFAELDAARRRRLAALVHRAEQVIVTAAALE
+DVPEELTAHRVLIRQDAEGSEAVAAAAPVEGDIREPRREGGADG
+>LFPAFLNI_00003
+MYLSHLTVADFRSYRWADLELTPGSTVLLGANGVGKTNLVEAIGYLGAQQSHRVSSDAQL
+VRFGRDRARIAGRVHRGSRTVALELEILPGRSNRVAINRGAPVRAKEGLGILRTVVFAPE
+DLSLVTGEPGGRRRLLDQLMVQLRPALGEAAADYERVLRQRNALLKSSRGSRRWGPEEDA
+TLAVWDEHLCAAGARLLHGRLHVLRLLARPLQEMYAALTNGSKAAAYAYESTVPLARGTH
+AEVPAVADLAADMHRTLEAQREEERARALTLVGPHRDELALFLGPAPARGYASHGETWSL
+ALALRMAAYDVLVADDPDPDARPVLILDDVFAELDAARRRRLAALVHRAEQVIVTAAALE
+DVPEELTAHRVLIRQDAEGSEAVAAAAPVEGDIREPRREGGADG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000396.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000396.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b627767c67af0e76a6877f56963e26d3b454c0e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000396.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00425
+MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDHTRSTSPSVPRPRAGFVVSKAV
+GNAVTRNRVKRRLRAVVAEQMRAAPLRELPVLVQVRALPPAAEADHALLRRETVGALAKA
+LRPHLPAVPRDEA
+>MOLHKGIG_02311
+MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDQTRSTPPSAPRPRAGFVVSKAV
+GNAVTRNRVRRRLRAVVADQMRTAPLRELPVLVQVRALPAAAEADFALLRRETVGALGKA
+LKPHLPAASEHA
+>NAFOICDF_00378
+MLPRDRRVRTPEEFRRIRRTGSRAGRSTVVVSVAADTDPARPGATSQPRRPRAGFVVSKA
+VGNSVVRHRVTRRLRALLRAELDSPALRDRALLIQVKALPAAVDADHATLRRDVHGALGA
+AVRKLDQADRSR
+>MHAAABBN_02004
+MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDQTRSTSPSAPRPRAGFVVSKAV
+GNAVTRNRVKRRLRAVVADQMRLPPLRDLPVLVQVRALPAAAEADYALLRRETVGALGKA
+LKPHLPAASEHA
+>LFPAFLNI_02252
+MLPRDRRVRTPAEFRHLGRTGTRAGRRTVVVSVATDPDQTRSTSPSAPRPRAGFVVSKAV
+GNAVTRNRVKRRLRAVVADQMRLPPLRDLPVLVQVRALPAAAEADYALLRRETVGALGKA
+LKPHLPAASEHA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000405.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000405.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d4489aec9850e54815306be5eb54bb428aa41880
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000405.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_00437
+MDLTTATLALPAGFPADAALPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRVSGDLDFT
+TDAGPDAAEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG
+DSLEEDLLRRDFTVNAMALRLPGLELVDPYGGVQDLAAGVLRTPGAPEDSFSDDPLRMLR
+AARFASQLGFTVADEVEAAMTAMAERIGIISAERVREELVKLVCGAHPRRGLDLLVRTGL
+AEHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEAEYSPSAPDPVLRLAALLHDV
+GKPATRRFEKGGAVSFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGEA
+GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNKRKAERLAHAYDDLERRIAEIAEQEEL
+AAVRPDLDGEQIMALLGIRPGPVVGRAYRHLLEWRLDEGPHEPAEAEAELRRWWAEQPEA
+AEG
+>MOLHKGIG_02299
+MDLTTATHALPPGFPADATLPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRPSPDLDFT
+TDADPDASEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG
+DSLEDDLLRRDFTVNAMALRLPALELVDPFGGMRDLHAGVLRTPGTPEDSFSDDPLRMMR
+AARFASQLGFAVAPEVEQAMTAMAERITIISAERVREELVKLVCGAHPRAGLDLLVRTGL
+ADHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEGEYAPSTPDPVLRLAALLHDV
+GKPATRRFEKGGAVTFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGDA
+GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIAEITEAEEL
+AAVRPDLDGQQIMALLGIRPGPVVGRAYTHLLEWRLDEGPHEPAEAEAELRRWWAEQPEA
+QQD
+>NAFOICDF_00390
+MEPRTDTRPLPAGFPADAALPAVVVELGRRFEAAGHELSLVGGPVRDLLLGRPVVDLDFT
+TDADPDATERIGAGWAEAAWDVGRHFGTIGFQKGGWQLEVTTYRAEQYDPTSRKPQVAFG
+DSLEDDLLRRDFTVNAMALRLPAMELVDPHGGVRDLAAGVLRTPGAPEDSFSDDPLRMMR
+AARFASQLGFGVADEVEAAMTDMAERIGIISAERVRDELVKLVRGDRPRAGLDLLVRTGL
+AQIVLPELPALQLETDEHHRHKDVYAHSLQVLEQAMGEEERYSPERPDVVLRLAALLHDV
+GKPATRRFEPSGAVSFRHHENVGAKLVRRRLKALRFDNDTIKAVARLVELHMRFYGYGEA
+GWTDSAVRRYVHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIEEISAAEEL
+AAVRPDLDGQQIMALLGIRPGPVVGRAYAHLLEWRLDEGPHEQAAAEAELRRWWAEQPEA
+AGASSGGGARD
+>MHAAABBN_01992
+MDLTTATHALPPGFPADATLPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRTSPDLDFT
+TDADPDASEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG
+DSLEDDLLRRDFTVNAMALRLPALELVDPFGGMRDLHAGVLRTPGTPEDSFSDDPLRMMR
+AARFASQLGFAVAPEVEEAMAAMAERITIISAERVREELVKLVCGAHPRAGLDLLVRTGL
+ADHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEGEYAPSTPDPVLRLAALLHDV
+GKPATRRFEKGGAVTFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGDA
+GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIAEIAEAEEL
+AAVRPDLDGQQIMALLGIRPGPVVGRAYNHLLEWRLDEGPHEQAEAEAELRRWWAEQPEA
+QQD
+>LFPAFLNI_02240
+MDLTTATHALPPGFPADATLPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRPSPDLDFT
+TDADPDASEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG
+DSLEDDLLRRDFTVNAMALRLPALELVDPFGGMRDLHAGVLRTPGTPEDSFSDDPLRMMR
+AARFASQLGFAVAPEVEQAMTAMAERITIISAERVREELVKLVCGAHPRAGLDLLVRTGL
+ADHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEGEYAPSTPDPVLRLAALLHDV
+GKPATRRFEKGGAVTFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGDA
+GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIAEIAEAEEL
+AAVRPDLDGQQIMALLGIRPGPVVGRAYTHLLEWRLDEGPHEPAEAEAELRRWWAEQPEA
+QQD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000406.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000406.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0dad90c5969043cd1179d5f54b3946cee281c37e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000406.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00440
+MATTPIRVAIAGVGNCATSLIQGVEYYRDAKATDTVPGLMHVQFGDYHVSDLQFVAAFDV
+DAKKVGLDLSEAILASENNTIKLADVPHADVTVQRGPTLDGLGKYYAETIEESDAEPVDV
+AQALRDAQVDVLVCYLPVGSQLATEHYAQTAIDAGVAFVNALPVFIAGTPEWADKFTAAG
+VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI
+SKTQAVTSNTSAKLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD
+SPNSAGVIIDAVRAAKIALDRGTGGPILSASSYFMKSPPVQHNDDEARELVEAFIRGDIE
+R
+>MOLHKGIG_02296
+MATNPIRVAIAGVGNCATSLIQGVEYYREAKATDTVPGLMHVQFGDYHVSDLEFVAAFDV
+DAKKVGLDLSEAITASENNTIKIADVPHADVTVQRGPTLDGLGKYYAETIEESDVEPVDV
+AQALRDAKVDVLVCYLPVGSQRATEHYAQAAIDAGVAFVNALPVFIAGTPEWAEKFTAAG
+VPIVGDDIKSQIGATITHRVMAKLFQDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI
+SKTQAVTSNTSAQLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD
+SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHNDDAAHELVEAFIRGDIE
+R
+>NAFOICDF_00393
+MAENPIRVAIAGVGNCATSLIQGVEYYKDAQASDTVPGLMHVQFGDYHVSDLEFVAAFDV
+DAKKVGLDLSEAILASENNTIKISDVPATGVTVQRGPTLDGLGKYYRETIEESSAEPVDV
+VQALKDAKVDVLVSYLPVGSEEADKFYAQCAIDAKVAFVNALPVFIAGTQEWADKFTEAG
+VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI
+SKTQAVTSNTSAELAEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD
+SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHADDEAHELVEAFIRGDIE
+R
+>MHAAABBN_01989
+MATNPIRVAIAGVGNCATSLIQGVEYYREAKATDTVPGLMHVQFGVYHVSDLEFVAAFDV
+DAKKVGLDLSEAITASENNTIKIADVPHADVTVQRGPTLDGLGKYYAETIEESEAEPVDV
+AQALRDAEVDVLVCYLPVGSQRATEHYAQAAIDAGVAFVNALPVFIAGTPEWAEKFTAAG
+VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI
+SKTQAVTSNTSAQLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD
+SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHNDDAAHELVEAFIRGDIE
+R
+>LFPAFLNI_02237
+MATNPIRVAIAGVGNCATSLIQGVEYYREAKATDTVPGLMHVQFGDYHVSDLEFVAAFDV
+DAKKVGLDLSEAITASENNTIKIADVPHADVTVQRGPTLDGLGKYYAETIEESEAEPVDV
+AQALRDAKVDVLVCYLPVGSQRATEHYAQAAIDAGVAFVNALPVFIAGTPEWAEKFTAAG
+VPIVGDDIKSQIGATITHRVMAKLFEDRGVTLDRTYQLNVGGNMDFKNMLERERLESKKI
+SKTQAVTSNTSAQLGEKDVHIGPSDYVAWLDDRKWAFVRLEGRNFGDAPVSLEYKLEVWD
+SPNSAGVIIDAVRAAKIALDRGIGGPILSASSYFMKSPPVQHNDDAAHELVEAFIRGDIE
+R
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000409.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000409.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e82e511cc771d710dd98c105734bc76524b6f9a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000409.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_00443
+MTAVTRDTAPAPEMSAHVQDLAAFVTASPSSYHAAAEVARRLVAVGFTCLDEAADFPAAP
+GGYVVVRDGAALAWVVPTGAGSDVSDGAGAAGGSGAGAAVPVFRVLGAHTDSPGFKLKPN
+PATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQLAIH
+LDREVNDGLKLQRQRHTNPVVGALAPRGEGAGEAVADVSEGVDGRSAPLEQAAGAGAGVG
+AGAGEGAGAREGDGAGLEARAPGDVLSALAAAAGVDPAAVRGHDVMVADAQAPGLFGLAG
+EFFASGRLDNLSSVHAGLVALEELARANGGASGAIAYAGTVAEGVAGEAAGAPVIPVLAA
+FDHEELGSASRSGAAGPLLEEVMGRVLEALGVAGQGRARAIAGSWLLSADAGHLVHPNYA
+ERHDPVNHPRVNHGPLLKINANQRYATDAGGEAAFARWCGVAGVPFQEFVSNNDMPCGST
+IGPISATRLGIRTVDVGLGLLSMHSAREMCGVRDVEHLTAAVREFFRGV
+>MOLHKGIG_02293
+MTPVTRDTVAELHAHLRDLAEFVTASPSSYHAAEEVARRLEAVGFTRLDETADFPAAPGG
+YVVVRDGAAVAWIVPMGARALGRHEGAEARAAGPDEAGQSAGVVPVFRVLGAHTDSPGFK
+LKPNPATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQ
+LAIHLDREVNEGLTLKRQRHTNPVVGALVPRGEGAGEAEADGLAARVPGDVLTALAAAAG
+VDPAAVRGHDVVVADAQAPGLFGLAGEFFASGRLDNLSSVHAGLVALEELAREHGGAEGA
+IAYEGTVAGGVAGVAAGAPVIPLLAAFDHEELGSASRSGAAGPLLEEVMGRVLEALGVAG
+QGRARAIAGSWLLSADAGHLVHPNYAERHDPVNHPRVNHGPLLKINANQRYATDAGGEAA
+FARWCGVAGVPFQEFVSNNDVPCGSTIGPISATRLGIRTVDVGLGLLSMHSAREMCGVRD
+VEHLTAAVREFFRGV
+>NAFOICDF_00396
+MSTVTSESTVTAAVPGAPALSAHLQDLAAFVQASPSSFHAAAEVARRLEAVGFTRVDPAQ
+DLPAAPGGYVSVTDGAVLAWILPEALAERAADAVPVFRLLGAHTDSPGFKLKPQHLTVTA
+DGWVQAGVEVYGGPLLNSWLDRELRFAGRLALADGRQVLAATGPVGRIPQLAIHLDRSAN
+DDLTLGRQRHTQPIVAAVAGAPDAAGTDAADGASADPVVRLTGDILELLAAQAGVDPAEV
+RGADVVVADAQQGGAFGANGEFFACGRLDNLSSVHAGLRALESLAADADRAGRGVVVAEG
+VAGEAAGAPVIPVLAAFDHEEVGSATRTGAGGPLLEELMGRLLSACGVTGQGAARSRAGS
+WLLSADAGHLVHPNYTERHDPVNHPRVNHGPLLKINANQRYSTDAAGEAAFARWCAAAGV
+PFQRFVSNNDVPCGSTIGPISATRLGVRTVDVGIGLLSMHSAREMCGADDPARLAAVARA
+FFAGV
+>MHAAABBN_01986
+MTPVTRDTAAELPAHLRDLAEFVTASPSSYHAAEEVARRLEAVGFTRLDETADFPAAPGG
+YVVVRDGAAVAWIVPMGAGALGRHEGAEARAAGPDEAGPSAGVVPVFRVLGAHTDSPGFK
+LKPNPATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQ
+LAIHLDREVNEGLTLKRQRHTNPVVGALAPRGEGAGEAEADGLAARVPGDVLTALAAAAG
+VDPAAVRGHDVVVADAQAPGLFGLAGEFFASGRLDNLSSVHAGLAALEELAREHGGAEGA
+IAYEGTVAGGVAGEAADAPVIPLLAAFDHEELGSASRSGAAGPLLEEVMGRVLEALGVAG
+QGRARAIAGSWLLSADAGHLVHPNYAERHDPVNHPRVNHGPLLKINANQRYATDAGGEAA
+FARWCGVAGVPFQEFVSNNDVPCGSTIGPISATRLGIRTVDVGLGLLSMHSAREMCGVRD
+VEHLAAAVREFFRGV
+>LFPAFLNI_02234
+MTPVTRDTAAELPAHLRDLAEFVTASPSSYHAAEEVARRLEAVGFTRLDETADFPAAPGG
+YVVVRDGAAVAWIVPMGAGALGRHEGAEARAAGPDEAGQSAGVVPVFRVLGAHTDSPGFK
+LKPNPATVTADGWVQAGVEVYGGPLLNSWLDRELRFAGRLALDDGTQVLAATGPVGRIPQ
+LAIHLDREVNEGLTLKRQRHTNPVVGALAPRGEGAGEAEADGLAARVPGDVLTALAAAAG
+VDPAAVRGHDVVVADAQAPGLFGLAGEFFASGRLDNLSSVHAGLVALEELAREHGGAEGA
+IAYEGTVAGGVAGEAAGAPVIPLLAAFDHEELGSASRSGAAGPLLEEVMGRVLEALGVAG
+QGRARAIAGSWLLSADAGHLVHPNYAERHDPVNHPRVNHGPLLKINANQRYATDAGGEAA
+FARWCGVAGVPFQEFVSNNDVPCGSTIGPISATRLGIRTVDVGLGLLSMHSAREMCGVRD
+VEHLAAAVREFFRGV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000411.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000411.fa
new file mode 100644
index 0000000000000000000000000000000000000000..67d583a48caa5f768ad732e44473feef5720d7df
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000411.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00445
+MSEHPASPTHVLLLRAVNVGGRNRVPKADLAELAAEAGLADVAVHLNSGNVLGTPDTGDH
+VDDVAARLRALLAERLGVDTSVHAAARTELSALVDGLLASDLLAPGETLDSVDPKTVHLV
+LLDTVPHPEAGEALAAVDAGDDRAVVVGRGVWVRYAGPSHSSHLGLPRIERAASGDAPPA
+QRRVGTARNLATVRVLAGR
+>MOLHKGIG_01260
+MSPAAPRADHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRASSD
+AAAEGVRQGFARRAREEGGLDVPVVLVDVGTLRRALELHDALPWAGGEPKRTQLTVLEDD
+PAPESAAALAALDHGDGRPAGPDRTALEGRLLWTRCATGVADSPLTPARLDRALGVRGTA
+RNLTTVRVLAGLPAGDRPRRTARGASGDVDIRGTPRAGRDVTVRSHPCDGVTPSSASLP
+>NAFOICDF_01525
+MSRAAPRTDHTHVLLLRGINVGRSNRVSNARLAAWAEAARARDVTTHLASGNVLFRLPDA
+DDDAGPAFLRAFRDAALADDGPDVPLILTTPAELRGALAMHDRLPWSGGEAKLTQLTVLA
+ESPRDGAAEALAGLDHGSGRAAGPDRSALEGRFLWIRSPGRISDSPLTPARLEKALGVTG
+TARNLATVRVLAGMA
+>MHAAABBN_00979
+MSPAAPRTDHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRASSD
+AAAEGVRQGFARRAREEGGLDVPVVLVDVGTLRRALELHDALPWAGGEPKRTQLTVLEDD
+PAPEAAAALAALDHGDDRPAGPDRTALEGRLLWMRCAAGVADSPLTPARLDRALGVRGTA
+RNLTTVRVLAGLPSED
+>LFPAFLNI_01218
+MSPAAPRTDHTHVLLLRGINVGRSNRVGKDTLIRWAQAAGGEAVTTHLASGNVLFRASSD
+AAAEGVRQGFARRAREEGGLDVPVVLVDVGTLRRALELHDALPWAGGEPKRTQLTVLEDD
+PAPEAAAALAALDHGDDRPAGPDRTALEGRLLWMRCAAGVADSPLTPARLDRALGVRGTA
+RNLTTVRVLAGLPSED
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000420.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000420.fa
new file mode 100644
index 0000000000000000000000000000000000000000..150fe9862fc2089912cf573d76fef3a926fbd50a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000420.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_00461
+MTTPRYVMAIDQGTTSTRAILFDHSGAIVSTGQREHEQIFPRAGWVEHDPVEIWTNTREV
+IGEALARAEVTRHDVAAVGITNQRETTVVWDRNTGKPVHNAIVWQDTRTDRLCERLAGDV
+GADRYKERVGLPLATYFSGPKVAWILENVDGAREAAENGDLIFGTTDSWLVWNLTGGGAG
+GRHVTDVTNASRTMLMNLDTLDWNEEICADMGIPMSMLPEIVSSSAEVGTVSGQQLLRET
+PITGILGDQHAATFGQACFEVGQAKNTYGTGNFMLINTGEKPVHSDNGLLTTVAYRIGDQ
+KPVYALEGSIAVTGSLIQWLRDNLGMIGSAPEVETLAASVEDNGGVYFVPAFSGLFAPHW
+DATARGAMVGMTRYVNKGHIARAALEATAFQSREVLDAMNADSGVDLTELKVDGGMVANE
+LLMQFQADLLRVPVVRPKVTETTALGAAYAAGLAVGFWSSQDELVANWEEDKRWEPTMDE
+EEAERALRLWKKAVERSRDWVDEDVESAQG
+>MOLHKGIG_02270
+MTTPRYVMAIDQGTTSTRAILFDHSGAIVSTGQREHEQIFPRAGWVEHDPVEIWTNTREV
+IGEALARAEVTRHDVAAVGITNQRETTVVWDRNTGKPVYNAIVWQDTRTDRLCERLAGDV
+GADRYKERVGLPLATYFSGPKVAWILENVDGAREAAENGDLIFGTTDSWLVWNLTGGGEG
+GRHVTDVTNASRTMLMNLDTLDWNEEICADMGIPMSMLPEIVSSSAEVGTVSGQQLLRET
+PITGILGDQHAATFGQACFEVGQAKNTYGTGNFMLINTGEEPVHSDNGLLTTVAYRIGDQ
+KPVYALEGSIAVTGSLIQWLRDNLGMIASAPEVETLAAGVEDNGGVYFVPAFSGLFAPHW
+DAAARGVMVGMTRYVNKGHIARAALEATAFQSREVLDAMNADSGVDLTELKVDGGMVANE
+LLMQFQADLLRVPVVRPKVIETTALGAAYAAGLAVGFWASQDELVANWEEDKRWEPTTDE
+EEVERTLRLWKKAVERSRDWVDEDVESAQG
+>NAFOICDF_00494
+MSAPRYVMAIDQGTTSTRAILFDHAGDAVATGQLEHAQHFPRAGWVEHDPLEIWRNTREA
+IGQALSRADATRDDVAAIGVTNQRETAVVWDRTTGRPVHPAIVWQDTRTQHLCERLGGDA
+GPDRWRERTGLPLATYFAGPKVAWILEHVDGAREAAERGDLLFGTTDSWTVWNLTGGVLG
+GQHVTDVTNASRTLLMDLETLEWDAEIAAEMGIPGGMLPRIVSSSAEVGHAAPTSLLGGV
+PIAGILGDQQAALFGQACFEAGQAKNTYGTGNFLLVNTGARPVRSRHGLLTTVAHRIGDE
+PPAYALEGSVAVTGSLVQWLRDNLGLIRDAAEVEELAAGAPDNGGVFVVPAFSGLFAPHW
+DPTARGTIVGLTRYADRRHLARAVLEATAFQSREVLDAVLADVAEAEEGAGVVGGLTELK
+VDGGMVANDLLMQFQADVLGVPVVRPEVTETTALGAAYAAGLAVGFWASTAELAAHWSED
+RRWEPAMDPERAARLLRLWARAVARSRGWIDDDVEALAAETRTAPDATPAGRTP
+>MHAAABBN_01963
+MTTPRYVMAIDQGTTSTRAILFDHSGAIVSTGQREHEQIFPRAGWVEHDPVEIWTNTREV
+IGEALARAEVTRHDVAAVGITNQRETTVVWDRNTGKPVYNAIVWQDTRTDHLCERLAGDV
+GADRYKERVGLPLATYFSGPKVAWILENVDGAREAAENGDLIFGTTDSWLVWNLTGGGEG
+GRHVTDVTNASRTMLMNLDTLDWNEEICADMGIPMSMLPEIVSSSAEVGTVSGQQLLRET
+PITGILGDQHAATFGQACFEVGQAKNTYGTGNFMLINTGEEPVHSDNGLLTTVAYRIGDQ
+KPVYALEGSIAVTGSLIQWLRDNLGMIGSAPEVETLAAGVEDNGGVYFVPAFSGLFAPHW
+DAAARGAMVGMTRYVNKGHIARAALEATAFQSREVLDAMNADSGVDLTELKVDGGMVANE
+LLMQFQADLLRVPVVRPKVIETTALGAAYAAGLAVGFWASQDELVANWEEDKRWEPTMDE
+EEVERALRLWKKAVERSRDWVDEDVESAQG
+>LFPAFLNI_02202
+MTTPRYVMAIDQGTTSTRAILFDHSGAIVSTGQREHEQIFPRAGWVEHDPVEIWTNTREV
+IGEALARAEVTRHDVAAVGITNQRETTVVWDRNTGKPVYNAIVWQDTRTDHLCERLAGDV
+GADRYKERVGLPLATYFSGPKVAWILENVDGAREAAENGDLIFGTTDSWLVWNLTGGGEG
+GRHVTDVTNASRTMLMNLDTLDWNEEICADMGIPMSMLPEIVSSSAEVGTVSGQQLLRET
+PITGILGDQHAATFGQACFEVGQAKNTYGTGNFMLINTGEEPVHSDNGLLTTVAYRIGDQ
+KPVYALEGSIAVTGSLIQWLRDNLGMIGSAPEVETLAAGVEDNGGVYFVPAFSGLFAPHW
+DATARGAMVGMTRYVNKGHIARAALEATAFQSREVLDAMNADSGVDLTELKVDGGMVANE
+LLMQFQADLLRVPVVRPKVIETTALGAAYAAGLAVGFWASQDELVANWEEDKRWEPTMDE
+EEVERTLRLWKKAVERSRDWVDEDVESAQG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000425.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000425.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f57eb6be95c05721c41e06614bb3869780fb53b4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000425.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00476
+MNGAELADSLAEAWDALLHTPLFGIALTLAVAVLARRLWLAARQTALLTPVLVTIVLVAA
+FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPIAVGVTVGSLTAM
+VSAVLIVRLMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVFAP
+WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL
+AMTG
+>MOLHKGIG_02255
+MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLSRRLWLAARQTALLTPVLVTIVLVAA
+FLALTGIDYETYMNGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTVGSLTAM
+VSAVLIVRAMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP
+WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL
+AMTG
+>NAFOICDF_00431
+MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLARRLWLAARQTALLTPVLVTIVLVAA
+FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTAGSLTAM
+VSAVLIVRVMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP
+WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL
+AMTG
+>MHAAABBN_01955
+MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLSRRLWLAARQTALLTPVLVTIVLVAA
+FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTVGSLTAM
+VSAVLIVRAMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP
+WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL
+AMTG
+>LFPAFLNI_02186
+MNAAELTDSLAEAWDALLHTPLFGIALTLAVAVLSRRLWLAARQTALLTPVLVTIVLVAA
+FLALTGIDYETYMIGGSYLTFLLGPATVALAVPLYRAGPDIRKLLLPVAVGVTVGSLTAM
+VSAVLIVRAMGGDAALAATFAPKSATTPIAMAVADAGGGIVSLAAVLPVLTGVLGAVLAP
+WVLDRLRVRDPRVRGLAIGVSSHGIGTARALAEGPKTGAFSALAMACSGVLTALLAPLVL
+AMTG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000426.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000426.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e043c45be700d513200502da8da06cebeb3ffcf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000426.fa
@@ -0,0 +1,29 @@
+>ACLBLIBL_00477
+MGPSHAATGAAAWLALTHWQSPIAVLHLPAELQLLGAVTTAGAAMISDWDHPRATVVHAL
+PPLTEWMSRGIRHVAGGHRRGTHSLVGIAAFTAIATAAASIQVPIAGHVYTPGQGVIAAF
+LAAVAAKALRLLPNRGWRAAWALGILVAGAATVLSDGLWWIPASVAVGVSVHILGDALTN
+NGVALLWPLSPEPPARLWWWQSSGRFRLPLLGRTGSWREWAFVSVVTAFTVVRAVRLVPL
+AARGVAGLLGAGAPS
+>MOLHKGIG_02254
+MMGPSHAATGAAAWLALTHWQSPIAVLHLPAELQLLGAVTTAGAAMISDWDHPRATVVHA
+LPPLTEWLSRGIRHVAGGHRRGTHSLVGVAAFTAIATAAASIQVPIAGHVYTPGQGVIAA
+FLAAVAAKALRLLPNRGWRAAWALGILVAVSATVLSDGLWWIPASVAVGVSVHILGDALT
+NNGVALLWPLSPEPPARLWWWQSSGRFRLPLLGRTGSWREWALVSVVTAFTVVRAVRLVP
+LAARGVAALF
+>NAFOICDF_00432
+MSTPPAALALFLPRGPPAGPRGCGDAAWLALTHGQSPVGVRHLPAELQLLGAVTTAGAAM
+ISDWDYPRATAIATAAASIHVPIAGHVYTPGQGVIAAFVAAVAAKALRLLPNRGWRAAWP
+LGILVAVSATVFSDGLRWIPVSVAVGVSVHILGDALTNNGVALLWPLSPEPPARLWWWQS
+SGRFRLPLLGRTGSWREWALVSVVTAFTVVRAVRLVPLAARGAALF
+>MHAAABBN_01954
+MMGPSHAATGAAAWLALTHWQSPIAALHLPAELQLLGAVTTAGAAMISDWDHPRATVVHA
+LPPLTEWLSRGIRHVAGGHRRGTHSLVGIAAFTAVATAAASIQVPIAGHVYTPGQGVIAA
+FLAAVAAKALRLLPNRGWRAAWALGILVAVSATVLSDGLWWIPASVAVGVSVHILGDALT
+NNGVALLWPLSPEPPTRLWWWQSSGRFRLPLLGRTGSWREWALVSVVTAFTVVRAVRLIP
+LAARGVAALF
+>LFPAFLNI_02185
+MMGPSHAATGAAAWLALTHWQSPIAVLHLPAELQLLGAVTTAGAAMISDWDHPRATVVHA
+LPPLTEWLSRGIRHVAGGHRRGTHSLVGIAAFTAIATAAASIQVPIAGHVYTPGQGVIAA
+FLAAVAAKALRLLPNRGWRAAWALGILVAVSATVLSDGLWWIPASVAVGVSVHILGDALT
+NNGVALLWPLSPEPPARLWWWQSSGRFRLPLLGRTGSWREWALVSVVTAFTVVRAVRLLP
+LAARGVAALF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000429.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000429.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9835543a801d5f2e7fdc30aa7466cff22403b5bf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000429.fa
@@ -0,0 +1,21 @@
+>ACLBLIBL_00500
+MTPRSLAGLALAVAALAAAFALMAPTAPGLFVGVLTAGTLGFGPFYGEPTRHLVDRPWRR
+DRRWHELARRVRTDWLSRQLGAAGWNAAIRRRITGRADLRRIRTAAVGSLVSHAASVGLH
+GIAALALAVVGHPGWGLLAVLLGLVVHAWPALLQVAVLGRIDGLQAQLRGDRLLW
+>MOLHKGIG_02245
+MTPRSLAGLALTVAALMSAFVLMAPTAPGLFVGVLTVGTFGFGPFYGEPSRQLVDRPWRR
+DTRWRDLARRVRTDWLSRQLGAVGWNAAISRRITGRADLRRIRTAAVGSLVSHAASAGLH
+AVAGVALAAVGHPVWGVVAVALGLVVHAWPALLQVSVLGRIDGLQTQIRGDQLLW
+>NAFOICDF_00511
+MRIPAVCAAVAVVTLLAWGFRQVVPASPGAYVAVLTAATVGFGPFYGVPTRAVVDLPWRR
+LRRLRALAARAHTWWLARQLRVAGSDARIRRRIRSRADVLAFRREAVGRLLNHGLSAVLH
+AAAGVALAAAGHPLWGVVAVVAGLLVHGWPGLLQVGVLGRVDELQATVQARRGVGGAASA
+GR
+>MHAAABBN_01947
+MTPRSLAGLALTVAALMSAFVLMAPTAPGLFVGVLTVGTFGFGPFYGEPSRQLVDRPWRR
+DTRWRDLARRVRTDWLSRQLGAVGWNAAISRRITGRADLRRIRTAAVGSLVSHAASAGLH
+AVAGVALAAVGHPVWGVVAVALGLVVHAWPALLQVSVLGRIDGLQTQIRGDQLLW
+>LFPAFLNI_02177
+MTPRSLAGLALTVAALMSAFVLMAPTAPGLFVGVLTVGTFGFGPFYGEPSRQLVDRPWRR
+DTRWRDLARRVRTDWLSRQLGAVGWNAAISRRITGRADLRRIRTAAVGSLVSHAASAGLH
+AVAGVALAAVGHPVWGVVAVALGLVVHAWPALLQVSVLGRIDGLQTQIRGDQLLW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000431.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000431.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6997b13bc70c2785957f0c31894f4a97f29cdd8c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000431.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00505
+MPDSAARHSAARHDVPAPPPFGPVLHHRAHGMAPGDAISPPLVHASAFHLPGAGPDGAPA
+EPAAQGGFQYARWGTPTWAALEAALGVLEDADVAVVPSGMAAIASVLLSHLRPGDRALLP
+SDGYGATRALAAEHLSPIGVHVDLVPTPALASADLSAYDLVFVETPSNPGLRVADLADVA
+ARAHANGRRGGAGALVVVDNTSLTPLGQRPLDLGADVVVASDTKALNGHSDALGGHVASR
+DADVLARVRGWRTLTGAILGTHEAWLIHRGLETLEVRFARMCASALAVAELAAGHSAVRA
+VAYPGLPDHPDAEVVARQTTAAGSVVGLEFADAAAAERFLAAARLVVPQTSFGGTHTSAE
+RRARWGDDVPAGFVRLSVGVEPTAELLADVERALEAAG
+>MOLHKGIG_02240
+MSAAPPPPAFGTVLHHRAHGMAPGESISPPLVHASAFHLPGADPDGAPTAPGADVPFQYA
+RWATPTWSALEAALGALEDADVAVVPSGMAAIAAVLLPLLHPGDRALLPADGYGPTRALA
+AEHLTPRGVHVDLVATQGLAHADLSGYDLVLVETPSNPGLRVADLADVAARAHANGRRDG
+AGALVVVDNTLLTPLGQRPLELGADVVVASDTKAVNGHTDALGGHVASRDPQVMARVRGW
+RTLAGGILGTHEAWLIHRGLETLEVRFARMCASAQAVAELAAGHPAVRAVVYPGLADHPD
+AEVVARQMTAAGGLVGLRFADAAAAERFIAAAQYVVPQTSFGGTHTAAERRARWGDDVPD
+GFVRLSVGVEPTAELLADLERAMTAAGGGPTA
+>NAFOICDF_00441
+MASPQPPAFGPVLHHRAHGMAPGDAISPPLVHASAFHLPGAGPDGAPVAPGADVAFQYAR
+WGTPTWAALEAALGVLEDADVAVVPSGMAAIAAALLPVLRPGGRALLPSDGYGATRALAA
+EHLVPAGVHVDFVSTPGLADAGFSAYDLVFVETPSNPGLRVADLADVAARAHANGRRDGK
+GALVVVDNTSLTPLGQRPLDLGADVVVASDTKALNGHTDALGGHVASRDPELMTRVRGWR
+TLAGGILGTHEAWLIHRGLETLEVRFARMCASALAVAELAAGHPAVRAVAYPGLPDHPDA
+AIVARQMTAAGGVVGLEFADAAAAERFIGAAAYVVAQTSFGGTHTAAERRARWGDDVPAG
+FVRLSVGVEPTAELLTDLARALDAAAGPA
+>MHAAABBN_01942
+MSAAPPPPAFGTVLHHRAHGMAPGESISPPLVHASAFHLPGADPDGAPTAPGADVPFQYA
+RWATPTWSALEAALGALEDADVAVVPSGMAAIAAVLLPLLHPGDRALLPADGYGATRALA
+AEHLTPRGVHVDLVATQGLAHADLSGYDLVLVETPSNPGLRVADLADVAARAHANGRRDG
+AGALVVVDNTLLTPLGQRPLELGADVVVASDTKAVNGHTDALGGHVASRDPQVMARVRGW
+RTLAGGILGTHEAWLIHRGLETLEVRFARMCASAQAVAELAAGHPAVRAVVYPGLADHPD
+AEVVARQMTAAGGLVGLRFADAAAAERFIAAAQYVVPQTSFGGTHTAAERRARWGDDVPD
+GFVRLSVGVEPTAELLADLERAMTAAGGGPTA
+>LFPAFLNI_02172
+MSAAPPPPAFGTVLHHRAHGMAPGESISPPLVHASAFHLPGADPDGAPTAPGADVPFQYA
+RWATPTWSALEAALGALEDADVAVVPSGMAAIAAVLLPLLHPGDRALLPADGYGPTRALA
+AEHLTPRGVHVDLVATQGLAHADLSGYDLVLVETPSNPGLRVADLADVAARAHANGRRDG
+AGALVVVDNTLLTPLGQRPLELGADVVVASDTKAVNGHTDALGGHVASRDPQVMARVRGW
+RTLAGGILGTHEAWLIHRGLETLEVRFARMCASAQAVAELAAGHPAVRAVVYPGLADHPD
+AEVVARQMTAAGGLVGLRFADAAAAERFIAAAQYVVPQTSFGGTHTAAERRARWGDDVPD
+GFVRLSVGVEPTAELLADLERAMTAAGGGPTA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000433.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000433.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e36f9b3cf1b127dfe0c1f4e4136ffbb74821250
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000433.fa
@@ -0,0 +1,17 @@
+>ACLBLIBL_00514
+MSLRLSHTTWDALDPHAVAEFWRELMGWEVTEPEAYELGSDECYLVTPHGYTILFYRVPD
+AKRVKNRAHMDLAVDDGTRDEEVERALGMGATMVDDRRGDLGWAVLADPEGNEFCILDI
+>ACLBLIBL_00528
+MALKWYTLVVDCRDPQAQAHWWARALDWEVVHDTPEEAVAVPKGVGEEPVADPDEWRARG
+QGLVFVPVPEGKTVKNRLHIDLAPHTSQDRDAEIARLEELGATRVDVGQDEEEVTWTVLA
+DPEGNEFCVLSSRDS
+>NAFOICDF_00455
+MSLRLSHTTWDALDPYAVAEFWRELMGWDVAEPDSYAPGSDECYLATAEGYTVLFYRVPD
+AKRVKNRAHMDLMTAGTTRDEEVERALGLGASMVDDRRGDLGWAVLADPEGNEFCILDTG
+D
+>MHAAABBN_02211
+MSLRLSHTTWDALDPHAIAEFWRALLGWEVDEPHLYRPGSDECSLVGPDGQVVLFFRVPD
+AKRVKNRAHMDLRAAAGSTRDAEIERALALGAAMVDDRRVDLGWAVLADPEGNEFCILDG
+>LFPAFLNI_00218
+MSLRLSHTTWDALDPHAIAEFWRALLGWEVDEPHLYRPGSDECSLVGPDGQVVLFFRVPD
+AKRVKNRAHMDLRAAAGSTRDAEIERALALGAAMVDDRRVDLGWAVLADPEGNEFCILDG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000437.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000437.fa
new file mode 100644
index 0000000000000000000000000000000000000000..87fd1bfcb964f67c6f4d8768993194772d7bdae1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000437.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00527
+MSARAARAARAGEGRQGSDAPAGADARPGAAGSALLFAMAIVAGSTIPVQARLNSALAER
+SGDPTLAAVASFAAGLVLVAAVTVLTPAGRRGLRAVRPALAAGRVRWWYLLAGTIGGAMV
+FSQATTVGLIGVAVFTVAVVTGQLIGGMVVDRLGLTPAGVRRMTPRRLAGAALALACVVL
+VVAPQLGARGDGGPPLWLLVALAPLAVGLATSIQQTLNARQAAAYGSVLPVTTVNFVAGT
+GILALVHLGGRLGGGVGGTLPGDWWLYLGGPMGVVFIAFSAYLVPRVGAFLTMLGLVSGK
+LLGSLAVDALAPVGEVAASPWTVVGTLGALAAVVLASGAARPARKG
+>MOLHKGIG_02219
+MPPEPSAPSGERGPARPHPADVAARPDAPSPRATALLFALAVAAGSVMPLQGRINSRLAH
+LTGDPVLAALCSFAAGLVVMVLVSVLTPRGRRGLARIRPALAAGSVRPWYAVAGVIGGLL
+VLTQSATIGPLGVAVFTVAVVTGQVVGGMVVDRLGLSPAGVQRLTPRRLTGAALALAAVA
+LVVWPSLGEAGGGPGWALLALLPLLAGLATAGQQVFNARQTTAYGTAIPATLVNFTAGVL
+FLGIVWGGIALASGHGLPALPHDWRLYLGGPLGCVFIGVGAMVVPRLGVFAATLGLVSGN
+LLGSLVVDLVAPTDGSTVTTTTVLGTLGALAAVALASWPARRR
+>NAFOICDF_00465
+MPASSPALTPAPRSGATTALLFLLALVAGLAMPVQGRVNSALSLAVGSPALAACASFATG
+LAVLVLATLLLPSGRRGAARIPAAVRNGDVRWWQLLAGTIGAAFVLTQAWTIPLIGVAVF
+TVAVVTGQMLGGMLWDRLGWTPAGVQRISRRRLFGALLAFCAVTAVVWPRLQESGSPGAW
+LALAVLPLAAGVATSGQQAMNGHQTAHFGTPLPPTLVNFAAGTAVLAAATAVAAGTGAGM
+GPLPAAWWMYLGGPLGTVFVGLGAFLIPRVGAFLTTLGMVAGQLVGSLLLDVVAPAPGAQ
+VTWLTVVGTLGALAAMVVASSPQVPAGLRASRRRARRG
+>MHAAABBN_01932
+MPPESSVPSAERGPSRPRPAAVAARPEAPSPRATALLFALAVAAGSVMPLQGRINSRLAH
+LTGDPVLAALCSFAAGLAVMVLVSVLTPRGRRGLARIRPALAAGSVRPWYAVAGMIGGLL
+VLTQSATIGPLGVAVFTVAVVTGQVVGGMVVDRLGLSPAGVQRLTPRRLTGAALALAAVA
+LVVWPSLGEAGGGPGWALLALLPLLAGLATAGQQVFNARQTTAYGTAIPATLVNFTAGVL
+FLGIVWGGIALASGHGLPALPHDWRLYLGGPLGCVFIGVGAMVVPRLGVFAATLGLVSGN
+LLGSLVVDLVAPTDGSTVTTTTVLGTLGALAAVALASWPARRR
+>LFPAFLNI_02158
+MPPEPSAPSGERGPARPHPADVAARPDAPSPRATALLFALAVAAGSVMPLQGRINSRLAH
+LTGDPVLAALCSFAAGLVVMVLVSVLTPRGRRGLARIRPALAAGSVRPWYAVAGVIGGLL
+VLTQSATIGPLGVAVFTVAVVTGQVVGGMVVDRLGLSPAGVQRLTPRRLTGAALALAAVA
+LVVWPSLGEVGGGPGWALLALLPLLAGLATAGQQVFNARQTTAYGTAIPATLVNFTAGVL
+FLGIVWGGIALASGHGMPALPHDWRLYLGGPLGCVFIGVGAMVVPRLGVFAATLGLVSGN
+LLGSLVVDLVAPTDGSTVTTTTVLGTLGALAAVTLASWPARRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000440.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000440.fa
new file mode 100644
index 0000000000000000000000000000000000000000..83805285c09d84d8b0aab7386fba64fce5873e64
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000440.fa
@@ -0,0 +1,27 @@
+>ACLBLIBL_00541
+MLPAPTARLRFREMTEADLDAMAALLGDPAVMRFYPAPRTREQAAEWIAGNRRRYAQDGH
+GLWVIETLPEHSDDGEPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACR
+DHARDALGHHELVAIIHPENSVSRRVAEKIGLREAEQDFTGAAEARETMGLASRTVMAMR
+F
+>MOLHKGIG_02202
+MPPAPTARLRFREMADADLDHLAGLLADPVVMRFYPAPRTRAEAAAWIAGNRRRYAQDGH
+GLWIIETHDDGGPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACRDHAR
+DVLGHHELVAIIHPENTASRRVAERIGMTVVGEDRTGAPEARAALGLEARTVLGMRLRPG
+A
+>NAFOICDF_00472
+MTQPIPRHPDPGNTGTDALDDVVREHMLLLRRAVHGLGAYRRPEALDRSAVLLLARLEAQ
+GPMTMAELAAAFGLDVSTLQRQIGAAQRAGFVERFRDPAGGQARLHRATDAGRAALEGEL
+AARRAAVAEVTRSWPAPDVAALARLLRRFNEGSEELREQPWPRERPEAPGAAAVPAGTAR
+LRFREMTEADLDVLVGLLGDPEVMEFYPAPKTRAEVADWIAWNRRSYAEHGHGLWIVETH
+AGAFVGECGLTWQRVNGERRLEVGYHVAPVLQGRGYATEAAAACRDHARDVLGAPELVAI
+VHPENTASRRVAEKIGMEVLEEDRTGVDASYLEAIGAEARTVLGMRLA
+>MHAAABBN_01915
+MPPAPTARLRFREMADADLDHLAGLLADPVVMRFYPAPRTRAEAAAWIAGNRRRYAQDGH
+GLWIIETHDDGGPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACRDHAR
+DVLGHHELVAIIHPENTASRRVAERIGMTVVGEDRTGAPEARAALGLEARTVLGMRLRPG
+A
+>LFPAFLNI_02146
+MPPAPTARLRFREMADADLDHLAGLLADPVVMRFYPAPRTRAEAAAWIAGNRRRYAQDGH
+GLWIIETHDDGGPGFVGDCGLTWQEVNGEPRLEVGYHVRADLWGRGYATEAAAACRDHAR
+DVLGHHELVAIIHPENTASRRVAERIGMTVVGEDRTGAPEARAALGLEARTVLGMRLRPG
+A
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000441.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000441.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9e569528c050b7b14913ca86f3f56fb4faebbc5c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000441.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00542
+MLAAVLAFALIGAVLWAALALGPDGVPGQQGSRRPAASTPAPPTVSAEGFAEPVRGRVTS
+RFGPRPNPFGEGSAPPSTDTDALTDHTGVDLGGVPEGTPFHSVSDGRVLFVEAGEDAGGN
+LLAVDSGDGHVWRYLHAAPDSTVVNAGQRVSAGDALAGVGQTGTATGVHLHLELRVDGTP
+VDPEPYLRERGVELGSSWERPRRR
+>MOLHKGIG_02200
+MTTPTPGAGSPGSGVAGGVLAAVGALALIATVLALVLAFGPAGRDDAGAGAERRRWNGGF
+TPAPPTVNTQGYAEPVQGRVTSRFGPRPNPFGEGVVPSGVSEEALTRHDGVDLGGVPEGT
+PFHSVSDGRVLFVEAGGDAGGNLLAVDAGDGHVWRYLHAAPDSTVVDAGQRVSAGDHLAG
+VGQTGAATGVHLHLELRVDGEPVDPEAYLAERGVELGGSYPERRRGLSR
+>NAFOICDF_01787
+MKKLAVIAAVLVLFSPALLLLGVGMIFSPGANASCTTSTTGPSVVGPVPDSLDVTTADGQ
+TFTLNTTQLTHAATIIQTGSQIEGVTRDGLQIALMAALTESNLRMLANTSVYPDSGNHPN
+DGDASDHDSLGLFQMRPQAGWGTVPDLMDPGYQARAFFGGPTGPNHPSPRGLLDIPGWQT
+LSKGEAAQAVEVSAYPDRYANYEPVAEQILTTLTTPTADSPQLPETGRVVFPLPEGTWVA
+TSPFGMRVHPITGENKLHTGADYSAPDGTPVLAAADGIVTHASMSGGYGGLIIIEHTTGG
+QKIATAYAHLWETGIHVNVGDQVTAGQHIGDVGSAGYSTGAHLHFELRQGGSDGEFTDPQ
+PWLDQHTSGNLPAPTTPVEQEGCNPVATQPAPPQGPDAGDPDRKVDDPTTDGQITARMLH
+VYTQALTAYPDSSWACYSPRPGTKSEHPLGRACDVTFGNAIGSRPTPQQLEAGWALTNWL
+QDNAETLGVEYLIWQGQIWSLARDAEGWRPYNGGGMHDPTDVTGGHYDHVHITVKEGS
+>MHAAABBN_01913
+MTTPTPGAGSPGSGVAGGVLAAVGALALIATVLALVLAFGPAGRDDAGAGAERRRWNGGF
+TPAPPTVNTQGYAEPVQGRVTSRFGPRPNPFGEGVVPSGVSEEALTRHDGVDLGGVPEGT
+PFHSVSDGRVLFVEAGGDAGGNLLAVDAGDGHVWRYLHAAPDSTVVDAGQRVSAGDHLAG
+VGQTGAATGVHLHLELRVDGEPVDPEAYLAERGVELGGSYPERRRGLSR
+>LFPAFLNI_02144
+MTTPTPGAGSPGSGVAGGVLAAVGALALIATVLALVLAFGPAGRDDAGAGAERRRWNGGF
+TPAPPTVNTQGYAEPVQGRVTSRFGPRPNPFGEGVVPSGVSEEALTRHDGVDLGGVPEGT
+PFHSVSDGRVLFVEAGGDAGGNLLAVDAGDGHVWRYLHAAPDSTVVDAGQRVSAGDHLAG
+VGQTGAATGVHLHLELRVDGEPVDPEAYLAERGVELGGSYPERRRGLSR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000442.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000442.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c23d54c75fb1562672c0838a30f54a9b28435cb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000442.fa
@@ -0,0 +1,28 @@
+>ACLBLIBL_00543
+MSFTAPRRVLRRHRLTQVGALGAGLALLLTACGGGSEPAESSSPAPTGSSSSPAEATTAS
+PSAESSPTTSPSGSVGSTAAAGSSGSGGAYVPASAEGPARNVPKPEMPAVTKEETQEGAE
+AAVEYFWEAAYYLQQTGDSEYQESVSSPTCKFCDLQRTSMEGHYRDGGWMKVEAVNIASM
+VTRPSANGYMSTLLLDMPKEEAFASQGGKAESIGTQPALEESPWIAETSFSEEAGHWVIE
+AMIAGGS
+>MOLHKGIG_01043
+MSLTAPGRALRRHRFAQAGTLSVALALALTACGGQSEPAESSTTSPSSAKPAVETSAPAS
+TSETAGVSSSPTATESGSGEYVPASADGPARSVPKPEMPADMKEETKEGAEAAIRYFWDV
+HYYAEQTGDTELLDSLYSEYCEFCQFSSNDLQMIYKDGGWYTGTEVQIDSILTHRSETGY
+VSTLLVTTGTGTGYTKGGVVPENGDVEAASKQPWIAEVSFNPESSHWIVDEMSYEGSIGS
+N
+>NAFOICDF_01734
+MTLPAPRRTLRRRRLARTGALSGALLLALTACAGGGADSGASSASTTTTAPAASSTSAAA
+SSSTGGASASESDATTSGAAGEYVPASSKGPAQNVPKPVMPAAVKENTPEGAEAAVKYWW
+EAVNYLQQTNDPEPLKSISMEECNLCSAHIKTIKRIYGDGGWATGENFAVNSVSMEKKKD
+FTLATVAISTDDSATFNADGVKVDQAPADAGTDAPWGVLLKFDSNKGQWVVREAEYDFQE
+G
+>MHAAABBN_00756
+MSLTAPGRALRRHRFAQAGTLSVALALTLTACGGQSEPAESSTTSPSSAKPAVETSAPAS
+TSATAGVSSSPTATESGSGEYVPASADGPARNVPKPEMPAAMKEETKEGAEAAIRYFWEA
+IYYTDQTGETADFDSTYSEYCELCQAVSDSTAQHYKEGGWSTGEHTSIKSLTLTPSEFGY
+TATLVRDASAVDVFDSQGVRDDSASGAETHDETWLADVVYEPSKGHWVIDEMQNQQDAQ
+>LFPAFLNI_00984
+MSLTAPGRALRRHRFAQAGTLSVALALALTACGGQSEPAESSTTSPSSAKPAVETSAPAS
+TSETAGVSSSPTATESGSGEYVPASADGPARNVPKPEMPAAMKEETKEGAEAAIRYFWEA
+IYYTDQTGETADFDSTYSEYCELCQAVSDSTAQHYKEGGWSTGEHTSIKSLTLTPSEFGY
+TATLVRDASAVEVFDSQGVRDDSASGVETHDETWLADVVYEPSKGHWVIDEMQNHQDAQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000446.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000446.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c2ae77de97ecb6d7d234c1a9f62b832e00befd20
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000446.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00548
+MSSTPTDADHHGPGPVSVPAHLDDLPPATLVARGLTLRGGRGPVFGPLDLVLPPQTHLAV
+LGTQGSGRSALLLALTGRLRGVRGELVLTGGPVDVALDGPERPAARAYRPLIDATRHPYA
+LRARTAIAHTTDVVELEPALTAAEVVDERCLADGVRRRAGRARFALLADAVRLTVAPEAV
+VGELSAPDRALLAAVVACLRPARLVTFDDVDATLTLDELVALHAALDVLKDHGHPFAVSA
+VASAPVPRDAVVLTLPPVREN
+>MOLHKGIG_02196
+MSSTPTDADHHGPGPAPVPAHLDDLPPATLVARGLTLRGGRGPVFGPLDLVLPPQTHLAV
+LGTQGSGRSALLLALTGRLQGVRGELVLTGGPVDVALDGPERPAARAYRPPIDAARHPHA
+LRARTAVAHTTDVVELEPALTAAEVVDERCLADGVRRRAGRARFALLADAVRLSVAPEAV
+VGELPAPERALLAAVVACLRPARLVTFDDVDATLTIDELVALHAALDVLKDHGHPFAVSA
+VASAPVPRDAVVLTLPPVREN
+>NAFOICDF_00479
+MTEDQTPAPIETDDVVAERAPEPAPGGSHQVGRALTARGLTLRSIRGTVFGPVDVDLPPG
+VPGAVLGTQGSGRSALLLALVGRLQGVGGELTLGDMDGIRHPHRLRRATTVARITDYVEL
+EPLLTIRECIDEHCLAEGISRRTGRKRFARLEAAVGFHPDHGDQVSSLPVEDRTILTCML
+ACLRPADVIVYDDIDSSLTRPQLEHVYRVLETLGRLGHRFVVSALTSAPVPRGAVVVELP
+TPGHDDLPAALPTRPSLED
+>MHAAABBN_01909
+MSSTPTDADHHGPGPAPDPAHLDDLPPATLVARGLTLRGSRGPVFGSLDLVLPPQTHLAV
+LGTQGSGRSALLLALTGRLQGVRGELVLTGGPVDVALDGPERPAARAYRPPIDAARHPHA
+LRARTAVAHTTDVVELEPALTAAEVVDERCLTDGVRRRAGRARFALLADAVRLTVAPEAV
+VRELSAPDRALLAAVVACLRPARLVTFDDVDATLTIDELVALHAALDVLKDHGHPFAVSA
+VASAPVPRDAVVLTLPPVREN
+>LFPAFLNI_02140
+MSSTPTDADHHGPGPAPVPAHLDDLPPATLVARGLTLRGGRGPVFGPLDLVLPPQTHLAV
+LGTQGSGRSALLLALTGRLQGVRGELVLTGGPVDVALDGPERPAARAYRPPIDAARHPHA
+LRARTAVAHTTDVVELEPALTAAEVVDERCLADGVRRRAGRARFALLADAVRLSVAPEAV
+VGELPAPERALLAAVVACLRPARLVTFDDVDATLTIDELVALHAALDVLKDHGHPFAVSA
+VASAPVPRDAVVLTLPPVREN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000449.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000449.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ac65c644a0a8a3708bcf21c80d6a581bc2d5b81
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000449.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00557
+MSIPATEVEARWNEASEPFTAVVRAVRDWDAATPCEGWDALDLLDHVVGAERDFAARQGR
+EVPLFDGSRQQTANQWTKHSAALSALAGDEEFIMKPMHTALGEMTVGEAMIRFHAFDLIV
+HRWDLARSQGVDERFTDAEMDCIEESLDLFGDAAYTPGILAQPVPVADDADRQARLLGRL
+GRRA
+>MOLHKGIG_02189
+MSIPATEVEARWNAAAEPFTAVVREVRDWDAATPCEGWDALDLLDHVIAGQRDFAARQGR
+EVPLFDGSRQQLATQWAKHAAAMSALAGDEEFIMRPMKTALGEMPVGEALIRFHAFDVIV
+HRWDLARSQGVDARFTDAEIDCVEESLELFGDAAYTPGILGEPVPVADDADRQTRLLGRL
+GRRG
+>NAFOICDF_00484
+MSTQTDVEQYWMDCVEPFTDVVRAVEDWDASTPCKGWSAQDLLDHVVVAERDFAARQGRE
+IPVFDGSRNELWTQWVKHASAVTALAGDETFIMQSLHTATGDMTVGEALLHFHGFDLLVH
+RWDLARSQGRDEQWTDEEMDRIERALDSFGEQAYQPGILADPVPVADDAPRQVRLLGRLG
+RRA
+>MHAAABBN_01903
+MSIPATEVEARWNAAAEPFTAVVREVRDWDAATPCEGWDALDLLDHVIAGQRDFAARQGR
+EVPLFDGSRQQLATQWAKHAAAMSALAGDEEFIMRPMKTALGEMPVGEALIRFHAFDVIV
+HRWDLARSQGVDARFTDAEIDCVEESLELFGDAAYTPGILGEPVPVADDADRQTRLLGRL
+GRRG
+>LFPAFLNI_02134
+MSIPATEVEARWNAAAEPFTAVVREVRDWDAATPCEGWDALDLLDHVIAGQRDFAARQGR
+EVPLFDGSRQQLATQWAKHAAALSALAGDEEFIMRPMKTALGEMPVGEALIRFHAFDVIV
+HRWDLARSQGVDARFTDAEIDCVEESLELFGDAAYTPGILGEPVPVADDADRQTRLLGRL
+GRRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000451.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000451.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1561a7c305052ffad7456142fb9b031c1fdf37c4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000451.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00563
+MEQDRDPEESSQSTAIETLRGTPVSELTHLPPAMAGALDRLRRDVERFDLEYRSALLQVE
+ARLEVLRDEFTHLHDYNPIEHIVTRVKTPESILRKAASRGLSMDLDALRSNVTDIAGARV
+IVSFARDVYEVFRLFTRQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPVHLSTGSIPVTV
+EMQFRTSAMDFWATLEHKINYKFDGAVPPDITTELIAAARVAADLDTRMERLSDQVRQTD
+KDDDAAASWEDDGGPAFEDEGDDDGPDGDAPGTSTG
+>MOLHKGIG_02186
+MEQDPSPDAPAPSADVEALRGTPVSELTQLTPAASGALERLRRDVERFDLEYRSALLQVE
+ARLEVLRDEFTHLHDYNPIEHIVTRVKSPESILRKASARGLSLDLDALRTNVTDIAGARV
+IVSFARDVYRVFRQFTQQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPIHLSTGTIPVTV
+EMQFRTSAMDFWATLEHKINYKFDGGVPPDIATELVAAARVAADLDTRMERLHDQVQETD
+RDDDAAAAWEDDGGPAFEDEPTVEPGEARPGDAPGASTA
+>NAFOICDF_00489
+MPRDVDHPPPADDPAPVERPAPGGRGVTSASTALEALRATPLTDLTQLPGEVADALASLR
+TDFERFDLEYRSALLQVETRLETLQDEFTHLHEYNPIEHIATRVKSPESLLRKAASRGLS
+LDLDALRSGVTDIAGARVIVSFTEDVYRVFRQFTSQPDIRVLEVEDYIRDPKPSGYRSLH
+CLVQVPVHLTTGTVPVTVELQFRTIAMDFWASLEHKINYKFAGHVPPAITTELAAAARVA
+HDLDARMERLHQAVHDAGAGPDEHDDEDDWVGHA
+>MHAAABBN_01900
+MEQDPSPDAPAPSADVEALRGTPVSELTQLTPAASGALERLRRDVERFDLEYRSALLQVE
+ARLEVLRDEFTHLHDYNPIEHIVTRVKSPESILRKASARGLSLDLDALRTNVTDIAGARV
+IVSFARDVYRVFRQFTQQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPIHLSTGTIPVTV
+EMQFRTSAMDFWATLEHKINYKFDGGVPPDIATELVAAARVAADLDTRMERLHDQVQETD
+RDDDAAAAWEDDGGPVFEDEPAAGPGEARPGDDAPGASTV
+>LFPAFLNI_02131
+MEQDPSPDAPAPSADVEALRGTPVSELTQLTPAASGALERLRRDVERFDLEYRSALLQVE
+ARLEVLRDEFTHLHDYNPIEHIVTRVKSPESILRKASARGLSLDLDALRTNVTDIAGARV
+IVSFARDVYRVFRQFTQQPDIRVLEVEDYISRPKPSGYRSLHCLVQVPIHLSTGTIQVTV
+EMQFRTSAMDFWATLEHKINYKFDGGVPPDIATELVAAARVAADLDTRMERLHDQVQETD
+RDDDAAAAWEDDGGPAFEDEPAAGPDGTDPGEARPGDDAPGASTV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000452.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000452.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07eae2ab4f105a23ab2fafa0a914f4798f90deeb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000452.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00565
+MNGQDGGQGRTTTDGATGREAPVPFETEIQVRWSDEDRYGHVNNARLLTLTEEARVRATR
+AWSGVTPGRDVHRVVRAMEVQYEAPVVYGPELTAKVWIARIGTSSYTLRHELWQDGRRCV
+LCDAVFVHVDPETGRSVALAEDERVTLERVLIPAEADAT
+>MOLHKGIG_02185
+MTQPTTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLAEEARVRALAAWATTT
+ASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRCVLCDAV
+FVQVDPAAGRPVAVSDEERAAFERVLIPAED
+>NAFOICDF_00490
+MSDSQPRPYEGVLDLRWSDMDLYGHVNNVRILTLTEEARVRALKAWDEGDVGRDVMRVVR
+AMTTEYERPVEYGPELTAKVWVRALGRTSYTLHHELWQEGVRCVTCDAVMVHLDPETGAP
+LPHDDARRARLQAVLVPAEG
+>MHAAABBN_01899
+MTQPTTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLAEEARVRALAAWATTT
+ASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRCVLCDAV
+FVQVDPAAGRPVAVSDEERAAFERVLIPAED
+>LFPAFLNI_02130
+MTQPTTPETPADAGTPTPFEVGLQLRWSDEDRYGHVNNARLLTLTEEARVRALAAWATTT
+ASPDVQRVVRSMEVQYEAPVVYAGPEVTARVWILRIGRTSFTLRHELWQDGRRCVLCDAV
+FVQVDPAAGRPVAVSDEERAAFERVLIPAED
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000456.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000456.fa
new file mode 100644
index 0000000000000000000000000000000000000000..90d63bd13b08d11c1a114741a8a0c304f6638d3d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000456.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00572
+MTRTVIIGGHGKVALLAAPLLAEAGHDVTSIIRNPEHAAEVEAAGAAPLVLDVERAGEED
+LVQAFRDADNVVFSAGAGGGDPARTRAVDHDAALATMRAAEAAGVRRYVMVSYLGASLHH
+GVPEDDSFHAYAQAKAEADEALRDSGLAWTILGPAALTLEEPTGRITVDPDLDTPDAPKG
+EVSRGNVARALVAVLADPTTVGRKIDFVDGDTPVAEAIRGA
+>MOLHKGIG_02180
+MTRTVIIGGHGKVALLAAPLLAEAGHDVVSIIRNPDHAEDVRAAGAEPLVLDIEKADQEE
+LLHALRDADNVVFSAGAGGGDAQRTRAVDHDAAVASMRAAEAAGVRRYVMVSYLGASLHH
+DVPEDDPFYTYAQAKAEADEALRDSGLAWTILGPGALTDEEPSGRITVDPDLSDSDAPQR
+GASRGNVARAIVAVLSEPGTVGRKIDFVDGDVPVAEAVRGD
+>NAFOICDF_00499
+MDILIIGGHGKIALLTAPLLADAGHTVTSAIRNPEHADDVRTAGAEPLVLDVEHSSPAEL
+EAAMRGRDVVVWSAGAGGGDPERTYAVDRDAAIASMDAARAAGVRRYVMVSYRGASVHHG
+VPEDSSFFAYAEAKAAADEHLRGSHLDWTILGPGALTLDEPTGRVQVDPQGPSEELPGTS
+RGNVARMIAAAVDSGASIGRQVEFVDGDTPVDDVFRR
+>MHAAABBN_01894
+MTRTVIIGGHGKVALLAAPLLAEAGHDVVSIIRNPDHAEDVRAAGAEPLVLDIEKADQEE
+LLHALRDADNVVFSAGAGGGDAQRTRAVDHDAAVASMRAAEAAGVRRYVMVSYLGASLHH
+DVPEDDPFYAYAQAKAEADEALRDSGLAWTILGPGTLTDEEPSGRITVDPDLSDSDAPQR
+GASRGNVARAIVAVLNEPGTVGRKIDFVDGDVPVAEAVRGD
+>LFPAFLNI_02125
+MTRTVIIGGHGKVALLAAPLLAEAGHDVVSLIRNPDHAEDVRAAGAEPLVLDIEKADQEE
+LVHALRDADNVVFSAGAGGGDAQRTRAVDHDAAVASMRAAEAAGVRRYVMVSYLGASLHH
+DVPEDDPFYTYAQAKAEADEALRDSGLAWTILGPGALTEEEASGRITVDPDLSGSDASQR
+EASRGNVARAIVAVLSEPGTVGRKIDFVDGDVPVAEAVRGD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000464.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000464.fa
new file mode 100644
index 0000000000000000000000000000000000000000..17346e7513ca51015981c03dcfda9009a6a301e6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000464.fa
@@ -0,0 +1,31 @@
+>ACLBLIBL_00583
+MTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLIVCFLGDVALLALGAAGIGVV
+AERWPWLVTALTVAGVVYLVWFAAGALRSAVRGQRTLAAAAEAEGPAVGLTDGEIAALTG
+ELPLIDPATGRLSADFTGRTAEGRAVPVGAGVGMGRGHDPLGDESRTVGGIPVGNPRLCG
+TRPGERGADGRSGGVAVKQRVQPRRVVLSAPQTPLPRIVLLALSVSFLNPHAVLDTVVMM
+GTFAQTYGPGKWVYVGGAVAASLVWFTALGWGGTRLAPYMNTPRTWRIVDAAVGVLMLVI
+AAKVGLTLL
+>MOLHKGIG_02169
+MARTWDGSYPRSVTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLTVCFVADVA
+LLVLGAGGVGVVAERWPWLVPALTVAGVVYLLGFAAGALRSAWRGDRTLSTAAADVEGTG
+HGPDRIDLAVLTGELPLIDPVTGRLAEREPAGAGVGHHDDGAPGFGAPSGGGSVTVRQRV
+QPRRVALDRPQTPLPRIILLALSVSLVNPHAILDTVVMMGTFAQTFGAAKWAYVGGAVAA
+SLVWFTALGWGGTKLAPSMDSARTWRIVDAVVGVLMLGIAVKVGLTLL
+>NAFOICDF_00509
+MTVFSAGFLTYLALIVAIGAQTLFLLRQVVRGDRAWTAIGVCFLSDIVLLLAGAAGVGAA
+AERAPWLVPALTVAGVAYLVWFGVSALRSAHRGDRTLAGAAAEVEDDAWAPTAEEVAAMT
+GSLPVVAAGPDAGADAATAPAGTGGGVALRTRPVSTTAPASAAPRPALTPLPRLVLLCLS
+VSLLNPHAILDAVVMMGTFAQGYGADKWLYVAGAVASSALWFLVLGWGGAKLAPLMNTPR
+TWRIVDGAVGVVVLGIAGKVALTLF
+>MHAAABBN_01883
+MARTWGDSYPRSVTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLTVCFVADVA
+LLVLGAGGVGVVAERWPWLVPALTVAGVVYLLAFAVGALRSAWRGDRTLTTAAADAAGTG
+HGPDRIDLAVLTGELPLIDPATGRLAEREPAGAGVGQHDDGAPGVGAPSGGGSVAARQRV
+QPRRVALDRPQTPLPRIILLALSVSLVNPHAILDTVVMMGTFAQTFGAAKWTYVGGAVAA
+SLVWFTALGWGGTKLAPSMDSARTWRIVDAVVGVLMLGIAVKVGLTLL
+>LFPAFLNI_02114
+MARTWDGSYPRSVTIFATGFLTYLALIVAIGAQTLFLLRQIVRRDRVWTVLTVCFVADVA
+LLVLGVGGVGVVAERWPWLVPALTVAGVVYLLAFAVGALRSAWRGDRTLTTAAADGAGTG
+HGPDRIDLAVLTGELPLIDPATGRLADREPAGAGVGRHDDGAPGVGAPSGGGSVAVRQRV
+QPRRVALDRPQTPLPRIILLALSVSLVNPHAILDTVVMMGTFAQTFGAAKWVYVGGAVAA
+SLVWFTALGWGGTKLAPSMDSARTWRIVDAVVGVLMLGIAVKVGLTLL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000465.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000465.fa
new file mode 100644
index 0000000000000000000000000000000000000000..66d4bef1b1072d522373cbff1824c1e14dc38d97
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000465.fa
@@ -0,0 +1,60 @@
+>ACLBLIBL_00585
+MLAAVLTLATPFLIGAATDRIVAAIAGETTVEDAVVAVTWLAVAFLAVEVTTTLVVSVGG
+YWGDVMAARMRTILSTRYFDQLLHLPQRYFDTAITGRVTNRLNRTINELTQFLQFFANNA
+FTMLITTTAVLVITAFYWWPLAILLAIVFPVYMWLTAKTSAKWQVWEGEKNIEVDMASGR
+FAEVVSQMSVVRAYNRQDHELAGFRERFTRTVGITRKQSRFWHGMDAWRRLALNVVFGAM
+YLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSMSFLVDSAQRAVAGSRDYFEVLAEER
+ERAGGAGPQGRGAAAVAAGQPRADDDGGTDVRWGGAAPSRPAQPRADVVPGDGTGGMPAG
+PSADVVPAVRFDEVSFAYDPDASRPVLDRVSFEIPQGQRVALVGESGGGKSTIAHLLMGL
+YPVTGGRIEVFGQDVAELDLAELRERIAAVFQEPSLFSGTVRENIAYADPAASDERVRAA
+AEAAYAHRFVEAFDDGYEQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEATSALDT
+KSERLVQGALEELMVGRSSLIVAHRLSTIASVDRIVTLRGGRVQEVGTPAELAESGGIYA
+QLLRLQKAGTKEARKMLKEYGLSG
+>MOLHKGIG_02167
+MTSLLRILRFAPQLNRLYLGIAVSSVLAAVLALATPFLIGAATDRIVAAVAGETDVAEAV
+TAVTWLAVAFLAVEVATTLVVSVGGYWGDVMAARMRTILSTRYFEQLLHLPQRYFDTAIT
+GRVVNRLNRTINELTQFLQFFANNAFTMLITTAAVLVITAFYWWPLAILLAVVFPVYMWL
+TARTSTKWQVWEGEKNTEVDIASGRFAEVVSQMSVVRAYNRQDHELSGFRDRFLRTVGIT
+RQQSRFWHGMDAGRRLALNVAFGAMYLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSM
+SFLVDSAQRAVAGSKDYFEVLAEERERAGGAALAVAGASAESAGADAPRVPAEPRADVVP
+GAPDVPADVPAVRFDEVSFAYDADASRPVLDRVSFDIPRGARVALVGESGGGKSTIAHLL
+LGLYPVTSGRIEVFGQDVAGLDLAVLRGRIATVFQEPSLFSGTVRENIAYADPDASDERV
+RAAAEAAYAHRFVEAFDDGYEQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEATSA
+LDTKSERLVQAALEELMVGRSSLIVAHRLSTIASVDRIVTLRGGQVQEIGTPAELAESGG
+IYAQLLELQRAGTQEARKMLKEYGLSG
+>NAFOICDF_00512
+MRALLRILRFAPQLNPLYLGIAVCSVLAAALSLATPFLIGAATNRIVDAIAGRSTLDDAV
+AAVTWLALAFLAVEVATTAVVSVGGYWGDVMAARMRAALSGRYYDHLLHLPQRYFDTAIT
+GRIVNRLNRSITELTQFLQFFSNNAFTMLITTAAVLVITAFYWWPLAVLLAVVFPVYMWL
+TAKTSAKWQGWEGEKNTEVDIASGRFAETVAQMNVVRAYNRQDHELAGFTERFRRTVGIT
+RKQSRFWHGMDAGRRLALNLVFGVMYLIVFVRTARGLFSVGDMVILLQLMNMARQPIFSM
+SYLVDSAQRAVAGSKDYFGVLAEERERSGGAALPAGLGSAEAPTTTTATGVVVRDRAEAP
+TGAPVRAGADVPAVRFADVTFAYDPEAERPVLDGVTFDIPQGAKVALVGESGGGKSTLAH
+LLMGLYPVGSGRVEVFGRDVAGLDLAVLRGQVAAVFQEPFLFSGTIRENIAYADPDASGE
+RVRAAAKAAFADGFVEEFEHGCEQLIGERGLRLSGGQKQRIAVARAVLKDAPVLVLDEAT
+SALDTKSERLVQSALDDLMVGRSSLIVAHRLSTIASVDRIVTLRGGRVQEVGTPAELAQS
+GGIYAQLLRLQKAGTKEARKLLKEYGLSG
+>MHAAABBN_01881
+MTSLLRILRFAPQLHRLYLGIAVSSVLAAVLALATPFLIGAATDRIVAAVAGETDVAEAV
+TAVTWLAVAFLAVEVATTLVVSVGGYWGDVMAARMRTILSTRYFEQLLHLPQRYFDTAIT
+GRVVNRLNRTINEITQFLQFFANNAFTMLVTTAAMLVITAFYWWPLAILLAVVFPVYMWL
+TARTSAKWQVWEGEKNTEVDVASGRFAEVVSQMSVVRAYNRQDHELTGFRDRFLRTVEIT
+RQQSRFWHGMDAGRRLALNVAFGAMYLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSM
+SFLVDSAQRAVAGSKDYFEVLAEERERAGGAALAAASASAESAGADAPRVPAEPRADVVP
+GAPDVPADVPAVRFDEVSFAYDADASRPVLDRVSFDIPRGARVALVGESGGGKSTIAHLL
+LGLYPVTSGRIEVFGQDVAGLDLAVLRGRIATVFQEPSLFSGTVRENIAYADPDASDERV
+RAAAEAAYAHRFVEAFDDGYEQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEATSA
+LDTKSERLVQAALEELMVGRSSLIVAHRLSTIASVDRIVTLRGGQVQEIGTPAELAESGG
+IYAQLLELQRAGTQEARKMLKEYGLSG
+>LFPAFLNI_02112
+MTSLLRILRFAPQLHRLYLGIAVSSVLAAVLALATPFLIGAATDRIVAAIAGETGVAEAV
+TAVTWLAVAFLAVEVATTLVVSVGGYWGDVMAARMRTILSTRYFEQLLHLPQRYFDTAIT
+GRVVNRLNRTINELTQFLQFFANNAFTMLITTAAVLVITAFYWWPLAVLLAVVFPVYMWL
+TARTSAKWQVWEGEKNTEVDIASGRFAEVVSQMGVVRAYNRQEQELSGFRDRFLRTVGIT
+RQQSRFWHGMDAGRRLALNAAFGAMYLIVFVRTAQGLFSVGDMVILLQLMNMARQPIFSM
+SFLVDSAQRAVAGSKDYFEVLAEERERAGGAVLAVASADAPRVPAEPRADVVAGAPDVPA
+DVPAVRFDEVSFAYDADASRPVLDRVSFDIPRGAKVALVGESGGGKSTIAHLLLGLYPVT
+SGRIEVFGQDIAGLDLAALRGRIATVFQEPSLFSGTVRENIAYADADASDERVRAAAQAA
+YAHRFVAAFDDGYDQVIGERGLRLSGGQKQRIAVARAVLKDAPILVLDEATSALDTKSER
+LVQAALDELMVGRSSLIVAHRLSTIASVDRIVTLRAGRVEEVGSPAELAESGGIYAQLLE
+LQRAGTQEARKMLKEYGLSG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000466.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000466.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b4aa0200e5ca37aec95605f301f12abbeeb0c96e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000466.fa
@@ -0,0 +1,28 @@
+>ACLBLIBL_00586
+MTATPELPDFVPASNQGGDPAVYEVENAALDREGTLWAALQEAAPWAGRTLLDLGAGTGF
+WLPRYADAAEVIAVEPDTRLLDAARARPGGARVRRGSAERIPLAEASVDVVHARFAYFFP
+HPQWDVRPGLEEVARVLRPDGALVVIDNDTERGEFAELLVRSDAAADQGQDTYARRWWAD
+VGAETREVMSSWTFDTRADLEAVLRLEFPAELAEEWLAAHPEATSLTYGYLLHVWRPRG
+>ACLBLIBL_00695
+MELPDFRPSGNQGVDPALYEIENAAMDREGALWAALQEAAPWAGRTLLDLGAGTGFWLPR
+YADAAETIAVEPDARLLGAARARPGGARVLYGSAEQIPLPEASVDVVHARFAYFFPHPHW
+DVRPGLDEVTRVLRPGGALVVIDNDTERGQFAELLRASTNAAAQGQDTYAREWWAGVGAE
+TREVMSSWTFDSRADLEAVLRLEFERGVADAWLAEHPAATSLSYGYLFHVWR
+>MOLHKGIG_02088
+MCVRLPDMTQSTPGGPATDLPDFRPSGNQGVDPALYEIENAAMDREGALWAALQEAAPWT
+GRTLLDLGAGTGFWLPRYADAAETIAVEPDARLLGAARARPGGARVLYGSAEQIPLPEAS
+VDVVHARFAYFFPHPRWDVRPGLDEVTRVLRPGGALVVIDNDTERGQFAELLRASTNAAA
+QGQDTYAREWWAGIGAETREVMSSWTFDSRADLEAVLRLEFERGVADAWLAEHPAATSLS
+YGYLLHVWR
+>MHAAABBN_01793
+MCVRLPDMTQSTPGGPATDLPDFRPSGNQGVDPALYEIENAAMDREGALWAALQEAAPWT
+GRTLLDLGAGTGFWLPRYADAAETIAVEPDARLLGAARARPGGARVLYGSAEQIPLPEAS
+VDVVHARFAYFFPHPRWDVRPGLDEVTRVLRPGGALVVIDNDTERGQFAELLRASTNAAA
+QGQDTYAREWWAGIGAETREVMSSWTFDSRADLEAVLRLEFERGVADAWLAEHPAATSLS
+YGYLLHVWR
+>LFPAFLNI_02027
+MEGGCVRLPGMTQSTPGGPATGLPDFRPSGNQGVDPALYEIENAAMDREGALWAALQEAA
+PWAGRTLLDLGAGTGFWLPRYADAAETIAVEPDVRLLGAARARPGGARVLYGSAEQIPLP
+EASVDVVHARFAYFFPHPRWDVRPGLDEVTRVLRPGGALVVIDNDTERGQFAELLRASTN
+AAAQGQDTYAREWWAGVGAETREVMSSWTFDSRADLEAVLRLEFERGVADAWLAEHPAAT
+SLSYGYLLHVWR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000467.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000467.fa
new file mode 100644
index 0000000000000000000000000000000000000000..94b027d0145ae55aba9e949e3fc7a7b524e5c544
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000467.fa
@@ -0,0 +1,80 @@
+>ACLBLIBL_00593
+MWTVALSQLRAQPRRYVSLVLAILIGTMFLAASFLVSASAQATLRTTLGNTYSAADLVVL
+PEPSDHADEDPTAAFPGLAGTPAEPGALGRVDGVEEAYATQFTWAGGSAGGTEFTATLLP
+VPGDVSLLPVTLTEGAFPAADDARGVTLDTGTAERTGVAVGDEIALTGAPGAGGETATVV
+GLTTRSPDPTLSSGAQIWAAAPVIAAVNPPQDGEAGGSGAYSPHVLLRLTDGADRDAVAD
+AAAAVLAQEGVAASVTTPDEAVRDTLAEAGGGTDVFGWVLGGFAALALLVTALVIGNTFQ
+VLVAQRTRDLALQRTLGSTAGQVRGSVLTEAVVVGLVGSVLGVALAVVGLLAGVAFVRSA
+FDLPTLTFGMDPAGLAITVVVGVLVTLVAALSPAVAATRVSPLQALRPREEVTVASRVGV
+VRTVVGAVLAVGGTALMLWGAFRPEPLTAVGGGALSFIGVLLLATLFVPAAVRGAAVLAR
+PAGVPGRLAGLNATRHRSRTAATAAALLVGTTLVALFLTGGRTAQEQTALALDTAYPVDL
+VLSLPADGDAARAAEAVAARDDVAAVALALPVGATENGSPVLATPGADLRKVVAELPDGE
+DGLGDPGTAFVPGWVDEDTVTATVAGTEQTFSAVRAGDLSSGVYVEADSLRAAGWDGSPL
+ATDGVEVPGQLLVALAGDVPVDRLQALSEDITAAAGEGASIIDGGAPTRAVYAQVIDVML
+WIVVGLLAVSVLIALIGVANTLSLSVIERTRENALLRALGLPRGGLRGMIAIESVLIAAV
+AALLGCVLGVFYGWAGSQLILGELVETVGRGGTVLPTIPWLELALVVGVAAVAGLAASLL
+PARRAARLSPVAGLATV
+>MOLHKGIG_02164
+MWTVALSQLRTQPRRYVSLVLAILIGTLFLAASFLVSSTAQATLRATLGSTYAGADLVVL
+PGGSEDVSDLAGTGAEPGPLARLDGVEEAYALRMAWATARAADAEFGTTVMPLPRDPALA
+GLTVTAGTLPAADDARGVTLDAQTADRHGVAVGDVVTLAGESGPAPATTPLDAVVTGLTQ
+PSPDPMLSGQAQVWASSAALTAVQGQDGEAGFTPHLLLRLADGADVPAVAEAARAEAAAA
+GVDVDVATPDEAVRSAVTQLSGGTDLLGWVLGGFAALALLVTALVIANTFQVLVAQRTRD
+LALLRTIGSTTAQVRASVLTEAAVVGVVGSVLGAGLAVAIVAGVAAAARAMLDLPFLTFG
+LHPAGLAVSVAVGVAVTVLAALAPAVAATRVAPLEALRPKDEVTAGSRGGRVRAAIGLVL
+AVGGTALMLGGVSVREPVSAIGGGALCFVGVLLLARLFVPAAVRGAAVLARPAGVPGHLA
+GLNAVRHRSRTAATAAALLVGTTLVALFLTGGRTAQEQTALALDTAYPVDLVVQLPADAD
+PARAAEAVAATEDVQAVALATPVGTTENGSPVLATPAADLRAVVARLPEGVTGLGDPGTA
+LVPDWVEADPVRAEVAGAAQTFAPVRAGSLSSGVYVAAEPLREAGWDGAADAAVPGQLLV
+ALDPGVPVDRLQGLSEDVTRAAGDGAAVIDGGAGERALYARIIDAMLGIVVALLAVSVLI
+ALIGVANTLSLSVIERTRENALLRALGLTRGGLRGAIAIEAVLIAAVAAVLGCALGVCYG
+WAGAQLVLADLSATAGAGTAVRPVVPWLELGLVVAVAALAGLAASLLPARRAARLSPVAG
+LAAV
+>NAFOICDF_00516
+MWTVALSQLRARRRRYASVVLAVLIGTMFLAASFLVASTAQATLRTTLGSVYAGADLVIQ
+PEDDPETSADASGPPPGQRLAALAGTPETPGALARLDDVAEAWAPTPGFAEAAAPGGGTP
+RPAAVIPAPAHPDLLGVRAVAGALPDPADARGVAVDEETARALGVGVGDELPLTGEPTRA
+PVRATVTGLTSVSPDPMLSSQAQVWASRPVAQDLAPDGQVPYTTAVLLRLAPGADREAVA
+EAAARALHDDGVPAAVQTPDQAVRDQLASLSGGTDLLGWVLGGFALLALVVTALVIANTF
+QVPVAQRTRELALLRAVGAEARQVRGAVLLEAVATGLTGAVAGVVLAVGLTAAVVAVARG
+ALGADALTLGVDWLPLAGAVALGTAVAAVAALGPARAATRVAPVQALRPVDEAPVRSRVG
+LVRAGLGLLLAVGGAALMWWGAWGSAFAAALGGGVLSFLGVLLLARLFVPGAVRAAAVLA
+RPAGVPGRLAGLNAVRHRRRTAATASALLIGTTLVALVLTGGRTAQIRLDALLDEEYPVD
+LVVSVPAGGDLAAATRALGAVDGVGSVAAASPVGATVNGSPAYAVEADALRSVVAALPDG
+QDRALGDGASVLVPAWAGATTEVVVDGRVSGLASVRGSGLTTGVFLTPETAEWVRRHGVA
+ADAGTASDAAGPAAEDQAVAGLVLVAAADDVSVNRLQEMSAALTAAAGAGASIVDGGAAE
+RAVYAQIIDALLWIVVGLLAVSVLIALIGVANTLSLSVIERTRENALLRALGLTRGGLRG
+MIAVEAVLVAGVAAVLGCGLGVLYGWAGSQLVLGQLVAQLGEDRALVWPEVPWAELALVV
+AVAAVAGLLASLAPAGRAARLSPVEGLATV
+>MHAAABBN_01878
+MWTVALSQLRTQPRRYVSLVLAILIGTLFLAASFLVSSTAQATLRATLGSTYAGADLVVL
+PGGSEDVSDLAGTSAEPGPLARLDGVEEAYALRMAWAAARAADAEFGAAVMPLPRDPALA
+GLTVTAGALPAADDARGVTLDAQTADRHGVAVGDVVALASESGPDSTTTPVDAVVTGLTQ
+PSPDPMLSGQAQVWASPAALTAVQGQDGEAGFTPHLLLRLADGADVPAVAEAARAEAAAA
+GVDVDVAAPDEAVRSVVTQLSGGTDLLGWVLGGFAALALLVTALVIANTFQVLVAQRTRD
+LALLRTIGSTTAQVRASVLTEAAVVGVVGSVLGAGLAVAIVAGVAAAARAMLDLPFLTFG
+LHPAGLAVSVAVGVAVTVVAALAPAVAATRVAPLKALRPRDEVTAASRGGRVRTAIGLAL
+AVGGTALMLGGVSVREPVSAIGGGALSFVGVLLLARLFVPAAVRGAAVLARPAGVPGRLA
+GLNAVRHRSRTAATAAALLVGTTLVALFLTGGRTAQEQTALALDTAYPVDLVVQLPADAD
+PARAAEAVAATADVQAVALATSVGATEDGSPVLATPAADLRAVVARLPEGVTGLGDPGTA
+LVPDWVDTDQVRGQVAGAERTFVPVRAGSLSSGVYVAAEPLREAGWDGAAGAAVPGQLLV
+ALDPGVPVDRLQGLSEDVTRAAGTGAAVIDGGAGERALYARIIDAMLGIVVALLAVSVLI
+ALIGVANTLSLSVIERTRENALLRALGLTRGGLRGTIAIEAVLIAAVAAVLGCALGVFYG
+WAGAQLVLADLSATAGAGTAVRPAVPWLELVLVVAVAALAGLAASLLPARRAARLSPVAG
+LAAV
+>LFPAFLNI_02109
+MWTVALSQLRTQPRRYVSLVLAILIGTLFLAASFLVSSTAQATLRATLGSTYAGADLVVL
+PGGSEDVSDLAGTSAEPGPLARLDGVEEAYALRMAWAAARAADAEFGAAVMPLPRDPALA
+GLTVTAGALPAADDARGVTLDAQTADRHGVAVGDVVALASESGPDSTTTPVDAVVTGLTQ
+PSPDPMLSGQAQVWASPAALTAVQGQDGEAGFTPHLLLRLADGADVPAVAEAARAEAAAA
+GVDVDVAAPDEAVRSVVTQLSGGTDLLGWVLGGFAALALLVTALVIANTFQVLVAQRTRD
+LALLRTIGSTTAQVRASVLTEAAVVGVVGSVLGAGLAVAIVAGVAAAARAMLDLPFLTFG
+LHPAGLAVSVAVGVAVTVVAALAPAVAATRVAPLKALRPRDEVTAASRGGRVRTAIGLAL
+AVGGTALMLGGVSVREPVSAIGGGALSFVGVLLLARLFVPAAVRGAAVLARPAGVPGRLA
+GLNAVRHRSRTAATAAALLVGTTLVALFLTGGRTAQEQTALALDTAYPVDLVVQLPADAD
+PARAAEAVAATADVQAVALATSVGATEDGSPVLATPAADLRAVVARLPEGVTGLGDPGTA
+LVPDWVDTDQVRGQVAGAERTFVPVRAGSLSSGVYVAAEPLREAGWDGAAGAAVPGQLLV
+ALDPGVPVDRLQGLSEDVTRAAGTGAAVIDGGAGERALYARIIDAMLGIVVALLAVSVLI
+ALIGVANTLSLSVIERTRENALLRALGLTRGGLRGTIAIEAVLIAAVAAVLGCALGVFYG
+WAGAQLVLADLSATAGAGTAVRPAVPWLELVLVVAVAALAGLAASLLPARRAARLSPVAG
+LAAV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000470.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000470.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7692a5082ff477c41cc2bcdf828137d52ea77fa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000470.fa
@@ -0,0 +1,46 @@
+>ACLBLIBL_00599
+MNPLHRIDQWMRAHPVRTDVLVSVLLFAVLGLTPWVMLGSLAGPTPGSIVASILIALALI
+APWAFRRVRPVASAAAVAAAAVAHLVAGPEFSLALVLVPMTVYNLAANAPRWASFTGLVA
+ALLGGVANGIRVGLFPDPAMRPDGVYEPVDPSLEALLVMVFGCAAVVLTAWAFGDVVRHR
+RLAVRALEDRNRRLETMALQERRLAASDERNHIAREMHDIVAHSLQVIISQADGARYAAA
+AKPELAVATLDTIGLTGRAALADMRQLLGVLRETGETVAGVPGVAPDDGAPGPAAGASDE
+GAAGAADEGAAGAADEGAAGAGTAGAGTTPGAGRTRLPADVASRDGRGARQPPGHRPQPT
+LADVPALIETMRLSGLEVSLLETGAPRRPLPPGGELAAYRIVQEALTNTLRHGGPQASAF
+LTLAWTGRGLDVQSDDDGRGADADPGTRGSGHGLRGVAERVALFGGTVETGPRAGAGYRV
+SAHLPYSAV
+>MOLHKGIG_02159
+MNPLRRLDQWTRLHPVRTDVMAAAALFTVLVALPWIALGPMVAPDPQGRQTAVSLLAGAG
+MVLPWAVRRVRPVASAAVVTAAAVLHLLAGPEFSLSLLMVPLTVYNLAANAPRSVSVAGL
+LLGLVGGVANGVKVWLFPAQFVTPDGLTVRSPAEPLAMVIMAIGCGLMVLTAWAFGDVVR
+NRRLTVRALEDRAHRLEVQSRQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYA
+AAAKPALAVTALETIGQTGRSALADMRQLLGVLRETGETVAGVPGVTDDDARRPAADVVA
+SPDGRGTRLPPGRRPQPRLADLPALVETMRLSGLEVSLLETGTPRRTLPAGGELAAYRIV
+QEALTNTLRHGGPDADAFVTLAWTAHGLDLQIDDDGCGAAADPATRGSGQGLRGAAERTA
+LFGGTLETGPRVGAGYRVSAHLPYSAV
+>NAFOICDF_00521
+MNPLRRLDVLLRRHPVRTDVTAAVLLTLVLVLAPLVMLGGGVGSPAAWQTAGTVVAGLLM
+TGAWGLRRVRPVAAAGVTVAGALLHLAVGPEFTIALAMVPATVYNLAAIGPRWASLAGLA
+TGLAGGLANGLKVWLFPPRFTTPDGVQVQSPAEPVAMVVMAVLCGMAVLTAWAFGDVVRN
+RRLAVQALEDRARRLETQALQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYAA
+AAKPELAVETLETIGQTGRSALADMRQLLGVLRGPAEPTGGPDRARRDPAAPDGHRAPPG
+LADLPALFQTLRLSGLEISLLEQGSPRRDLPAGGELTAYRTVQEALTNTLRHGGEGAHAF
+LTLRWTARGLEIQADDDGRSQADAETTGSGQGLRGIAERVALFGGTMEAGPRVGAGWRVW
+AELPYADV
+>MHAAABBN_01872
+MNPLRRLDQWTRLHPVRTDVMAAAALFTVLVALPWIALGPMVAPDPQGRQTAVSLLAGAG
+MVLPWAVRRVRPVASAAVVTAAAVLHLLAGPEFSMSLLMVPLTVYNLAANAPRSISVAGL
+LLGLVGGVANGVKVWLFPAQFVTPDGLTVRSPAEPLAMVIMAIGCGLMVLTAWAFGDVVR
+NRRLTVRALEDRAHRLEVQSRQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYA
+AAAKPALAVTALETIGQTGRSALADMRQLLGVLRETGETVAGVPGVTDDDARRPAADVVA
+SPDGRGTRLPPGRRPQPRLADLPALVETMRLSGLEVSLLETGTPRRTLPAGGELAAYRIV
+QEALTNTLRHGGPDADAFVTLAWTAHGLDLQIDDDGCGAAADPATRGSGQGLRGAAERTA
+LFGGTLETGPRVGAGYRVSAHLPYSAV
+>LFPAFLNI_02103
+MNPLRRLDQWTRLHPVRTDVMAAAALFTVLVALPWIALGPMVAPDPQGRQTAVSLLAGAG
+MVLPWAVRRVRPVASAAVVTAAAVLHLLAGPEFSLSLLMVPLTVCNLAANAPRSVSVAGL
+LLGLVGGVANGVKVWLFPAQFVTPDGLTVRSPAEPLAMVIMAIGCGLVVLTAWAFGDVVR
+NRRLTVRALEDRAHRLEVQSRQERELAAADERSHIAREMHDIVAHSLQVIISQADGARYA
+AAAKPALAVTALETIGQTGRSALADMRQLPGVLRETGETVAGVPGVTDDDTRRPADPAPD
+RADPTGTRPDVVAAPDGRGARLPPGRRPQPRLADLPALVETMRLSGLEVSLLETDTPRRA
+LPAGGELAAYRIVQEALTNTLRHGGPDADAFVTLAWTARGLDLQIDDDGRGAAADPATRG
+SGQGLRGAAERTALFGGTLETGPRVGTGYRVSAHLPYSAV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000473.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000473.fa
new file mode 100644
index 0000000000000000000000000000000000000000..64bfc6c0905964e603c86f5bbd455086d5b5690d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000473.fa
@@ -0,0 +1,100 @@
+>ACLBLIBL_00609
+MDGVVTDTAGVHAQAWKELFDEALPAVGALPANAAAVAADPEALRPFDAAADYLHHVDGR
+PREDGVRTFFHSRGLRVPEADSPEAATTPQLTVLALAERKQGYFEQVLARDGVRVFPEAQ
+DLLEKLRAKGVPVALVTSSKNSRAVLGAGGVLDFFPVIVDGHTAIERGLPGKPDPAMFWE
+AARELGVDVADAMVLEDAVSGVKAAADGRFGLVIGVDREPDLGKGRLKGAGAHLVVQDYG
+TLCLEQRTTTPFDPAWVLRWDEFDPASEGTREVLCTLANGYWGTRGAVPGTRISDVHYPG
+TYMAGVFNRLTSMVQGRAVDTEHMVNIQDWTPLVVTPRGGRPLLPGEETLVDFSQEMDLR
+RGVLSRTMAFEDEQGRRTSLHTRQFTSLANRHLAAIELTVVAENWTGELTVRSTIEGRVA
+NLNVSDDRTLANQHLEPSQAREIDGETVLLETTTSQSRIDIAVATRTRQMAPVGHHEPIR
+RPVDGSDLRVGQDIRLHVEEGVPLVIEKIAAVATSHDHAQASVWESAVKDVQRANNFRNL
+LTLHEQRWGTNWDRFSVRIDIAEPYRHQRRSAAAAEGAEYAPPVVDAGRSASVGSAVPMG
+KDGASLRQQLALNLHTFHVLQTAYGRRRDLDASVGARGLHGEGYRGHIFWDEIYVYPMLT
+LRRPEITRGILMYRYRRLNEARANAQAEGWAGAMYPWQSGADGSEETPTELWNPRSRMWM
+PDNSHNQRHVSLDIAYSVLRYIEITKDTSFISDYGAEMLVEVSRFFMSMALHNADTDRYE
+IHGVMGPDEFHDGYPETPGSGLRNNAYTNVLTSWVLSETARLVRWLDTLDDGLPEIMEIT
+EEEIERWEDVSARLTVPFFEDGEEAGILAQFEGYQDLKEFDWEAYRAKYGNIGRMDLILQ
+AEGDATNRYKLSKQADTLMLGYLFSAEELDGILRRMGYELPQEAFERMVTYYEARSTHGS
+TLSRLVHAWVAARTDPDRSWDLFTEALESDLSDTQGGTTREGIHLGLMAGTVDTVIRCYA
+GLETREDVVRVDPRMPSQLPGASFTIRFRQQPVQIHMRRSEVTVRAGSGMWHDVPMIIAG
+QEHTLSPGAEITVPLG
+>MOLHKGIG_02154
+MSQTLTPAAPQDLNARRHRLRRYRAVIFDMDGVITDTAGVHAQAWKELFDGALPAVGALP
+ANAAVVAADPDVLRPFDAAADYLHHVDGRPREDGVRTFFASRGLRVPEADAPEADAAPEL
+TVLALAERKQGYFEQVLERDGVRVFPEAQDLLERLRAKGVPVALVTSSKNSRAVLTAGGV
+LDFFPVIVDGNTAVERGLPGKPDPAMFWEAARELGVDVADAMVLEDAVSGVKAAADGRFG
+LVIGVDREPELGKGRLKAAGAHLVVQDYGTLHLEDRTTTPFDPAWVLRWDHFDPASEGTR
+EVLSTLANGYWGTRGAVPGTRISSVHYPGTYMAGVFNRLTSMVQGRVVETEHMVNIQDWT
+PLVVTPRHGRPLLPGEENLVEYGQEMDLRRGVLSRTMTFEDEQGRRTTVHTRQFTSLANR
+HLAAIELTVVAENWSGDLTVRSKIEGRVANLNVSDDRTLANQHLEPVQAREIDGETVLLE
+TATNQSGIHVAVATRTRQVAPVGHHEPIRRPVDGSDLVVGQDILLHVDEGVPLVLEKVAA
+VATSHDHASASVWESAVKDAQRAQNFRNLLTLHEQRWGTNWDRFSVRIDLAEPYRHHRRS
+TAAETGGEYAPPVVAAGHSAPVGSAVPMGKDGASLRQQLALNLHTFHVLQTAYGRRRDLD
+ASVGARGLHGEGYRGHIFWDEIYVYPMLTLRRPEITRGLLMYRYRRLNEARANAQAAGWA
+GAMYPWQSGADGSEETPTELWNPRSRMWMPDNSHNQRHVSLDIAYSVLRYIEITKDTSFI
+SDYGAEMLVEISRFFMSMTLHNAVTDRYEIHGVMGPDEFHDGYPETPGSGLRNNAYTNVL
+TSWVLAETARLVRWLDTIDDGLPELMEISEEEIERWEEVSTRLTVPFFEEGEEAGILAQF
+EGYQDLLEFDWEAYRAKYGNIGRMDLILQAEGDATNRYKLSKQADTLMLGYLFSSEELDR
+ILRRMGYELPQEAFERMVTYYEARSTHGSTLSRLVHAWVAARTDPDRSWDLFTEALESDL
+SDTQGGTTKEGIHLGLMAGTVDTVIRCYAGLETRDDVVRLHPRMPAQLPGARFTIRFRQQ
+PVVIHMTQREVTVAAGEGMWHDVPMIIAGREHTLSPGEKLTVPLD
+>NAFOICDF_00533
+MTQTLTPVDQQDRNARRHRLRRYRAVIFDMDGVITDTAGVHAAAWKELFDQALPAVGALD
+ANRAAVAADPGVLRPFDPEADYLHHVDGRPREDGVRAFFASRGLTVPEVDDADAPVDLTV
+LALAERKQGFFEKVLERDGVRVFPEATDLLEKLRDKGVPVALVTSSKNSRAVLTAGGVLD
+YFPVIVDGHTAIERGLPGKPDPAMFWEAARELGVDVADAMVLEDAVSGVKAAADGRFGLV
+IGVDREHGEGGKPRLKDAGAHIVVKDYGTLRLADRTTAPFDAAWVLRWDHFDPATEGTRE
+VLCTLANGYWGTRGSIPGTRISDVHYPGTYLAGVFNRLTSMVQGRQVETEHMVNMQDWTP
+LQVIPAGGRPLIPGEETLLDYHQEMDLRRGVLSRSMRFEDAQGRITTLHTRQFQSLADRH
+LGAIELTVEAENWSGDLVVRTLVDGRVANLNVSDDRTLANQHLEPVAAREVDGETLLLET
+VTSQSRVHVAVAARTRQMAPKGHHQPIRRPVEGSDLMVGQDIHLHVEQDVPLVLEKVAAV
+ANTHDHALASVDASAIKKVQRAQNFRNLLTLHEQRWGMNWDRFSVRIDLAEEHRNQRRST
+AVLAEGEEFEAPVFEAGRSASVGSAATMGKDGASLRQQLALNLHTYHVLQTAFGKRRDLD
+ASVGARGLHGEGYRGHIFWDEIFVYPMLTLRRPEITRGILMYRYRRLNEARANAQAEGWA
+GAMYPWQSGSDGREETPAELWNPRSHMWMPDNSHNQRHVSLDIAYSVLRYIEITKDASFI
+SDYAAEMLVEISRFFTSMTLHNAETGRYEIHGVMGPDEFHDGYPETPGSGLRNNAYTNVL
+TSWVLSETARLLRWLDTLDDGLPEVMEVTEEEIARWEEIAAKLTVPFFTEGPEAGILAQF
+EGYQDLLEFDWEGYRAKYGNIGRMDLILQSEGDATNRYKLSKQADTLMLPYLFSGAELEQ
+ILGRMGYELHQEALERTVEYYEARSTHGSTLSRLVHAWVAARTDPDRSWDLFTEALESDL
+SDTQGGTTREGIHLGLMAGTVDTVIRCYSGLETRDDVVRLDPRLPRQLPGARFTIRYHQQ
+PVVIHMTQRDVTVTAGEGMWHEVPMVIAGREHTLEPGGEVTVALG
+>MHAAABBN_01867
+MSQTLTPAAPQDLNARRHRLRRYRAVIFDMDGVITDTAGVHAQAWKELFDGALPAVGALP
+ANAAVVAADPDVLRPFDAAADYLHHVDGRPREDGVRTFFASRGLRVPEADAPEADAAPEL
+TVLALAERKQGYFEQVLERDGVRVFPEAQDLLERLRAKGVPVALVTSSKNSRAVLTAGGV
+LDFFPVIVDGNTAVERGLPGKPDPAMFWEAARELGVDVADAMVLEDAVSGVKAASDGRFG
+LVIGVDREPELGKGRLKAAGAHLVVQDYGTLHLEDRTTTPFDPAWVLRWDRFDPASEGTR
+EVLCTLANGYWGTRGAVPGTHISSVHYPGTYMAGVFNRLTSMVQGRVVETEHMVNIQDWT
+PLVVTPRHGRPLLPGEENLVEYGQEMDLRRGVLSRTMTFEDEQGRRTTVHTRQFTSLANR
+HLAAIELTVVAENWSGDLTVRSKIEGRVANLNVSDDRTLANQHLEPVQAREIDGETVLLE
+TATNQSGIHVAVATRTRQVAPVGHHEPIRRPVDGSDLVVGQDILLHVDEGVPLVLEKIAA
+VATSHDHANASVWESAVKDVQRAQNFRNLLTLHEQRWGTNWDRFSVRIDLAEPYRHQRRS
+TAAEAGGEYAPPVVDAGHSAPVGSAVPMGKDGASLRQQLALNLHTFHVLQTAYGRRRDLD
+ASVGARGLHGEGYRGHIFWDEIYVYPMLTLRRPEITRGLLMYRYRRLNEARANAQAEGWA
+GAMYPWQSGADGSEETPTELWNPRSRMWMPDNSHNQRHVSLDIAYSVLRYIEITKDTSFI
+SDYGAEMLVEISRFFMSMTLHNAVTDRYEIHGVMGPDEFHDGYPETPGSGLRNNAYTNVL
+TSWVLAETARLVRWLDTIDDGLPELMEISEEEIERWEEVSTRLTVPFFEEGEEAGILAQF
+EGYQDLLEFDWEAYRAKYGNIGRMDLILQAEGDATNRYKLSKQADTLMLGYLFSAEELDR
+ILRRMGYELPEEAFERMVTYYEARSTHGSTLSRLVHAWVSARTDPDRSWDLFTEALESDL
+SDTQGGTTKEGIHLGLMAGTVDTVIRCYAGLETRDDVVRLHPRMPAQLPGARFTIRFRQQ
+PVVIQMTQREVTVAAGEGMWHDVPMIIAGREHTLSPGEKLTVPLG
+>LFPAFLNI_02097
+MSQTLTPAAPQDLNARRHRLRRYRAVIFDMDGVITDTAGVHAQAWKELFDGALPAVGALP
+ANAAVVAADPDVLRPFDAAADYLHHVDGRPREDGVRTFFASRGLRVPEADAPEADAAPEL
+TVLALAERKQGYFEQVLERDGVRVFPEAQDLLERLRAKGVPVALVTSSKNSRAVLTAGGV
+LDFFPVIVDGNTALERGLPGKPDPAMFWEAARELGVDVADAMVLEDAVSGVKAAADGRFG
+LVIGVDREPELGKGRLKAAGAHLVVQDYGTLHLEDRTTTPFDPAWVLRWDRFDPASEGTR
+EVLCTLANGYWGTRGAVPGTHISSVHYPGTYMAGVFNRLTSMVQGRVVETEHMVNIQDWT
+PLVVTPRHGRPLLPGEENLVEYGQEMDLRRGVLSRTMTFEDEQGRRTTVHTRQFTSLANR
+HLAAIELTVVAENWSGDLTVRSKIEGRVANLNVSDDRTLANQHLEPVQAREIDGETVLLE
+TATNQSGIHVAMATRTRQVAPVGHHEPIRRPVDGSDLVVGQDILLHVDEGVPLVLEKIAA
+VATSHDHANASVWESAVKDVQRAQNFRNLLTLHEQRWGTNWDRFSVRIDLAEPYRHQRRS
+TAAEAGGEYAPPVVDAGHSAPVGSAVPMGKDGASLRQQLALNLHTFHVLQTAYGRRRDLD
+ASVGARGLHGEGYRGHIFWDEIYVYPMLTLRRPEITRGLLMYRYRRLNEARANAQAAGWA
+GAMYPWQSGADGSEETPTELWNPRSRMWMPDNSHNQRHVSLDIAYSVLRYIEITKDTSFI
+SDYGAEMLVEISRFFMSMTLHNAVTDRYEIHGVMGPDEFHDGYPETPGSGLRNNAYTNVL
+TSWVLAETARLVRWLDTIDDGLPELMEISEEEIERWEEVSTRLTVPFFEEGEEAGILAQF
+EGYQDLLEFDWEAYRAKYGNIGRMDLILQAEGDATNRYKLSKQADTLMLGYLFSAEELDR
+ILRRMGYELPQEAFERMVTYYEARSTHGSTLSRLVHAWVAARTDPDRSWDLFTEALESDL
+SDTQGGTTKEGIHLGLMAGTVDTVIRCYAGLETRDDVVRLHPRMPAQLPGARFTIRFRQQ
+PVVIHMTQREVTVAAGEGMWHDVPMIIAGREHTLSPGDKLTVPLD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000474.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000474.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26d3c23ecbb5ce92896cb0b877419e9fdfbffca3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000474.fa
@@ -0,0 +1,41 @@
+>ACLBLIBL_00610
+MQCHHYDAGRCRSCALMGVPYGVQLTDKDAAVCARLDAAVPAEAWLPPQASAESGFRNKA
+KLVATGTAAAPRLGILDPEQHPRHHDGTGHDLRDCGLYEDGMEAAFHAIAETIPAAGLEP
+YDVAARTGELKSVIVTLSPDRELMVRFVLRSAARLDALRAAVPGLRSALAGLGTPAAVVT
+ANLHPEHVALPEGPDEVHLAGDPTLRMELNGIGLRLRPQGFFQTNTDVTRRLYATAAAWL
+AEAAAADGTPVHSAWDLYCGVGGFAFHLARPVAEGGAGVAEVWGLETSEDAVAAARDTAA
+ELGLAGAVRFTAGDATRALSPGRREPSEALSSGKREAWDALSSGSREPSDAGAHPDDDAA
+PAAMPDAVVVNPPRRGIGPELAARLQDSGVPHVLYSSCNAASLAKDLAAMPAYRARRAQV
+FDMFPQTGHAETLVLLSRA
+>MOLHKGIG_02152
+MQCPHFDVGECRSCPLMGVPYARQLADKQAAVLAALADALDADTVVAEPFASAEAGFRNK
+AKLVVTGSAAAPRLGILDPRQHPRHHDGAGVDLRDCGLYEAGMEGVFEACAAAVTAAGLE
+PYDVAARTGELKNVIVTLSPDREAMVRFVLRSADRLDALRAAVPGLLDDLAARGTPAAVV
+SANLLPEHVALPEGDEEIVLAGGPTLRMELNGIGLRLRPQGFFQTNTAVTEGLYATAAAW
+VAEGGVPASAWDLYCGVGGFAFHLARAGVRDVWGMESSAEAVAAARETAAELGLADRARF
+SAGDATSALSFEKRRAPEALSFEKRRSRPDAVVVNPPRRGIGAELADALEDSGAPTVLYS
+SCNPTTLAQDLARMPSYRVARVQLFDMFPQTLHAEVLTLLTRR
+>NAFOICDF_00534
+MQCPHFDAGECRSCALMGVPYGAQLADKDAAVRARLAEATDARTRWEAPAASAESGFRNK
+AKLVVTGTAAAPRLGILDPRQHPRHHDGTGVDLRDCGLYEDGMEAAFHAIAGAVTAAGLE
+PYDVAARTGELKNVIVTRSPDRELMVRFVLRSADRLEALRPEVPALREALAALGTPAAVV
+TANLHPEHVALPEGPEEVHLAGDATLRMELNGIGLRLRPQGFFQTNTDITQRLYATAAAW
+LAEAAAEGGTPVERAWDLYCGVGGFAFHLARPVAEGGAGVAEAWGLEVSAEAIEAAREAA
+AELGVAERVRFTAGDATTALAAPGGTRPDAVVVNPPRRGIGAELAGRFEESGVPFVLYSS
+CNAATLATDLTAMPSYRVARAQVFDMFPQTGHAETLVLLARR
+>MHAAABBN_01865
+MQCPHFDVGECRSCPLMGVPYARQLADKQAAVLAALADAVDADTVVAEPFASAEAGFRNK
+AKLVVTGSAAAPRLGILDPRQHPRHHDGAGVDLRDCGLYEAGMEGVFDACAAAVTAAGLE
+PYDVAARTGELKNVIVTLSPDREAMVRFVLRSADRLDALRAAVPGLLDDLAARGTPAAVV
+SANLLPEHVALPEGDEEIVLAGGPTLRMELNGIGLRLRPQGFFQTNTAVTEGLYATAAAW
+VAEGGVPASAWDLYCGVGGFAFHLARAGVRDVWGMESSAEAVAAARETAAELGLADRARF
+SDGDATSALSFEKRRAPEALSSKKRRPRPDAVVVNPPRRGIGAELADALEDSGVPTVLYS
+SCNPATLAQDLARMPSYRVARVQVFDMFPQTRHAEVLTLLTRR
+>LFPAFLNI_02095
+MQCPHFDVGECRSCPLMGVPYARQLADKQAAVLAALADAVDADTVVAEPFASAEAGFRNK
+AKLVVTGSAAAPRLGILDPRQHPRHHDGAGVDLRDCGLYEAGMEGVFDACAAAVTAAGLE
+PYDVAARTGELKNVIVTLSPDREAMVRFVLRSADRLDALRAAVPGLLDDLAARGTPAAVV
+SANLLPEHVALPEGDEEIVLAGGPTLTMRLNGVGLRLRPQGFFQTNTAVTEGLYATAAAW
+VAEAGLPAAAWDLYCGVGGFAFHLARAGVRDVWGMESSAEAVAAARETAAELGLADRARF
+SAGDATSALSFEKRRAPEALSSKKRRPRPDAVVVNPPRRGIGAELADALEDSGVPTVLYS
+SCNPATLAQDLARMPSYRVARVQVFDMFPQTRHAEVLTLLTRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000476.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000476.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5d7ef9f6fb5c7625c7820788bd0d7d1edc03779e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000476.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00612
+MKPAGALALEFRADSFDHPGGLVDAGTVISWIEKAGYAVAASWAGTFVRARYMGHTQFRH
+SVPVDHRAVVQARVVHTDGADVHVQTRLLLPEVKDESGDPVVATSSLVVYSAEEDGARVT
+VPAWVPSTPGQIERDEQASRSTVARRAVERGMARLPFPSPGQAPEEMSTLAFLAPASEAT
+VGGTMNAGAILRWLDEAAAVCAARWTGHESVVAVFGGGVRFVRNILVGDLVRVDALLVNT
+TERSMQVALRVYAGRPTGVQPRLVAHSIAVMVDVSAEDKAQPVRQYVPESEGARSLQEAA
+VQLVRLRSEVGAAWTETRRSPESR
+>MOLHKGIG_02150
+MRPPGALALEFRADSFDHPTGLVDAGTVISWIEKAGYAVAASWAGTFVRARYMGHTQFRH
+PVPVDRRAVVQARVVHTDGAEVHVQTRLLLPEIRDDDGDPVVATSSLVVYAAEEGGVPVT
+VPVWEPSTPGQIERDEQARRSTVARRAVERGMARLPFPAPGEAPEEMSTLAFLAPNAEAT
+VGGTINAGAILRWVDEAAAVCAARWTGHESVVAVFGGGVRFVRNIHVGDLVRVEALLVNT
+TERSMHVALRVYASRRTGAESRLVAHSIAVMVDVSAEDQAQRVRQYIPESESARRLQETA
+IELVRMRSEVSAAWTEMRRSTDPR
+>NAFOICDF_00536
+MMRSGALSLDFRADSFDHPSGLVDAGTAIGWIDKVGYAVAASWSGTYVRARYMGTMQFRH
+PVPVDMRVTVQGRVVRTHGAAVHVQLRLLLPEVLDDDGRPVVSTSTLSVYYAEEDGQMLQ
+VPEWTPSTPDQIERDERARVSSVERRGIEQVMARLPFPEPGQEHEEMTTLAFIAPMAEAS
+VGGTVAAGAVMRWLDEAAGVCAARWTGHENVVAVFAGGVRFVRPVKVGDLVRVDALLVHT
+SERSMHVALRVHAGPRHQRDHRLVAHSIAVMVDVTREGRAESVRPYAPGSPAAHRLEESA
+VELVRLRSEAGAVWSDPS
+>MHAAABBN_01863
+MRPPGALALEFRADSFDHPTGLVDAGTVISWIEKAGYAVAASWAGTFVRARYMGHTQFRH
+PVPVDRRAVVQARVVHTDGAEVHVQTRLLLPEIRDDDGDPVVATSSLVVYAAEEGGVPVT
+VPVWEPSTPGQIERDEQARRSTVARRAVERGMARLPFPAPGEAPEEMSTLAFLAPNAEAT
+VGGTINAGAILRWVDEAAAVCAARWTGHESVVAVFGGGVRFVRNIHVGDLVRVEALLVNT
+TERSMHVALRVYASRRTGAESRLVAHSIAVMVDVSAEDQAQRVRQYIPESESARRLQETA
+IELVRMRSEVSAAWTEMRRSTDPR
+>LFPAFLNI_02093
+MRPPGALALEFRADSFDHPTGLVDAGTVVSWIEKAGYAVAASWAGTFVRARYMGHTQFRH
+PVPVDRRAVVQARVVHTDGAEVHVQTRLLLPEIRDDDGDPVVATSSLVVYAAEEDGVPVT
+VPAWEPSTPGQIERDEQARRSTVARRAVERGMARLPFPAPGEAPEEMSTLAFLAPNAEAT
+VGGTINAGAILRWVDEAAAVCAARWTGHESVVAVFGGGVRFVRNIHVGDLVRVEALLVNT
+TERSMHVALRVYASRRTGAESRLVAHSIAVMVDVSAEGQAQPVRQYVPESESARRLQETA
+IELVRMRSEVSAAWTETRRSTDPR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000478.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000478.fa
new file mode 100644
index 0000000000000000000000000000000000000000..295586eb7d73daea2fe9f7a25555749859661f96
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000478.fa
@@ -0,0 +1,47 @@
+>ACLBLIBL_00614
+MLLERIYDEDLAQASYFIGCQAKNEAIVVDPRRDVQEYLDLAAHHGMTITHVTETHIHAD
+FLSGTRELAARTGAQIHVSGEGGEDWTYGFEGNLLHDGDVITLGNITVTAQHTPGHTPEH
+LSYLITDGAFAQAPGYYLTGDFVFSGDLGRPDLLDEAAGFQDTRFAGAKQLFRSLKEKFV
+GLPDHVQVFPGHGSGSACGKALGALPSTTVGYERTYAWWAEYVANDDEQGFVDELLDGQP
+DAHAYFARMKKQNKLGPAVLGELTPLAELTGEQAVARVAAGDVLADTRSVDEIHAGTVPG
+ALALPAKDKAATHIGWAYDPEQDDAAIILLADDQGDAEAIRSHMIRVGVDAADAFVTSLD
+GFELQPAAVISPEELQRRIDAGDVVPATADAAPGEGGLALLDVRNRTEHAEGTVPASGGA
+EAAQLNSGKVLFHQGELPKDATLVTFCQSGLRNVVAAQSLRRAGFDVVELEGSYLGWLGR
+TRA
+>ACLBLIBL_02660
+MLLERIYDEDLAQAGYFIGCQAKGEAVVIDARRDIADYLALAAKHGMRIVAVTETHIHAD
+YLSGTRELAAAVGAEVYVSGEGGADWQYGFDARRLYDRDTITIGNITIQARHTPGHTPEH
+LVFLVTDGAFASEPGYLISGDFVFAGDLGRPDLLDEAAGGVDTRFEGARQLFTSLREVFL
+TLPDHVQVHPGHGSGSACGKALGALPSTTVGYERANAWWSRHLAADDEQGFIEELLDGQP
+DAHAYFARMKKQNREGPAVLGERGPVPELAVAEVARRLEADETTFVDTRPPAQAHQGTVA
+GSLNIPDGSKTATYAAWAYDPEADSRPLVLLAEDQTAAQAIADRLLRVGIDQTAGYVTTI
+DGLPRFVPPLIEPAELAGFDAALLLDVRQRGEYAAGHIPGATQLSAARVLWHKDELPRSG
+TIVTYCQSGMRNTVAASALRRAGHAVVELDGSYNAWRAWQETTSETALA
+>NAFOICDF_00538
+MLLERIYDEDLSQASYFIGCQAKNEAIVVDPRRDVQEYLDLAAHHGMTITHVTETHIHAD
+FLSGTRELAARTGAQIHLSGEGGEDWTYGFEGHLLHDGDTIQLGNITVQAMHTPGHTPEH
+LSYLVTDGAFAAAPGYYLTGDFVFSGDLGRPDLLDEAAGLQDTRFAGATQLFQSLKEKFV
+NLPGHVQVFPGHGSGSACGKALGALPSTTVGYESTYAWWAEYVENDDEQGFVGELLDGQP
+DAHAYFARMKRQNKQGPAVLGELTPLAELTGEQAVARVSAGDVLADTRPVDQIHAGTVPG
+ALALPAKDKTATHIGWAYDPESDDAAIILLADAQDDAEQIRAHLIRVGVDAADAFVTSLD
+AFDLRPTAVISPEELERRIQDGGVVPATADAAPAEDGLALLDVRNRTEHADGTVPASDDA
+EAAQLSAGKVLFHQDQLPKEATIVTFCQSGLRNVVAAQALRRAGFDVVELDGSHLGWLGR
+SQA
+>MHAAABBN_01860
+MLLERIYDEDLAQASYVIGCQAKNEAMVVDPRRDIQVYLDLAAKNGMTITHVTETHIHAD
+YLSGTRELAHATGAQIHLSGEGGEDWAYGFEGNLLKDGDTVTLGNITVEAVHTPGHTPEH
+LSFLVTDGAFADAPGYMLTGDFVFSGDLGRPDLLDEAAGGVDTRFEGAQQLFASLKAKFL
+TLPDHVQVFPAHGAGSACGKALGALPSTTVGYERKYAWWSDYLKNDDEQGFIDELLDGQP
+DAHAYFARMKRQNKQGPAILGELPELEELDAGGVQATLAEGAVFADTRGVDEILAGTVPG
+ALAFPSRGKVATHAGWAYDPESDDAALVLLAEDREDAHTMRDHMIRVGVDAAAAFTTSVD
+GLTLEPVPTVQADELRSRIEAGEVGAEQDTVLVDVRNKTEFSHGTVADARQLNAGKVLFH
+QEELPKDKTLVTFCQSGLRNIVAAQALRRAGFDVIELEGSYAAWQQS
+>LFPAFLNI_02090
+MLLERIYDEDLAQASYVIGCQAKNEAMVVDPRRDIQVYLDLAAKNGMTITHVTETHIHAD
+YLSGTRELAHATGAQIHLSGEGGEDWAYGFEGNLLKDGDTVTLGNITVEAVHTPGHTPEH
+LSFLVTDGAFADAPGYMLTGDFVFSGDLGRPDLLDEAAGGVDTRFEGAQQLFASLKAKFL
+TLPDHVQVFPAHGAGSACGKALGALPSTTVGYERKYAWWSDYLKNDDEQGFIDELLDGQP
+DAHAYFARMKRQNKQGPAILGELPELEELDAGGVQATLAEGAVFADTRGVDEILAGTVPG
+ALAFPSRGKVATHAGWAYDPESDDAALVLLAEDREDAHTMRDHMIRVGVDAAAAFTTSVD
+GLTLEPVPTVQADELRSRIEAGEVGAEQDTVLVDVRNKTEFSHGTVADARQLNAGKVLFH
+QEELPKDKTLVTFCQSGLRNIVAAQALRRAGFDVIELEGSYAAWQQS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000480.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000480.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a31ae97ea71a48359e3dc6e861eb8b898ecc60c9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000480.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_00621
+MLWTLLRRPRRPDLGAVTAVVVLQLISTLAMLYLPSLNARIIDEGVARGDTDRIWDLGLV
+MLGVALVQVVAAIVAVWFGAKVAMGIGRDLRRAVYTRVDGFSAEELGRFGAPTLITRGTN
+DVNQVQMVTLMGLNFMVAVPIMAIGGIIMAVREDPGLSWLVWVSVPVLLVIVAWIVAKLM
+PLFQRMQDDIDRVNGVMREQVMGIRVVRAFVREPHESARFSGANAALTRTSVLIGRLFVL
+LGPVITMILHLATAAVLWFGGHRVADGLVEVGALTAFMQYLLQILMAVMMGTFMMMMLPR
+AVVSAGRIGEVLDTVPTLAEPVNPVTPADPRGAVELRDVTFAYPGAEAPVLDGVSFTVAP
+GSTTAIIGATGSGKSTLVNLIPRLYDATSGQVLIDGVPVTELARAELTRAVALVPQKPYL
+FSGTVAENMRFGAPEATEEEIWAALETAQAAGFVRERTTGEGETAAGGLDSRLSQGGTDV
+SGGQRQRLSIARALVARPRILLFDDSFSALDVATDARLRGALDATAAGTTRIVVAQRVAT
+ITEADQIIVLDEGRVVGRGTHAELLAGNETYKAIVDSQVREEELA
+>MOLHKGIG_02148
+MLWTLLRRHGRRYRGDVAAVVVLQLISTLAMLYLPSLNARIIDEGVARGDTARIWDIGLV
+MLGVALVQVVAAIAAVWFGAKASMGVGRDLRRAVYTRVDAFSAEELGRFGAATLITRGTN
+DVNQVQMLTLMALNFMVAVPIMAVGGIVMAIREDPGLSWLVWVSVPVLLVIVAWIVARLM
+PLFQQMQDNIDDVNGVLREQIQGIRVVRAFVRERHETRRFTDANAALTETSVRIGRLFVL
+LGPVITMILHLATAAVLWFGGQRVDAGLVQVGALTAFMQYLLQILMAVMMGTFMMMMLPR
+AVISARRIGEVLDTVPTLGEPVRPVTPERRDGAVELRHVTFQYPGAEAPVLDDVSFAVAP
+GTTTAIIGSTGSGKSTLISLLPRLYDATSGEVLVDGVPVTDLARAELTEAVALVPQKPYL
+FSGTVRENMQFGAPDASDERIWAALETAQAADFVRARTTGKGEAAASGLDSRLSQGGTDV
+SGGQRQRLSIARALVAEPRILVFDDSFSALDVTTDARLRAALDRAAAGVTRIVVAQRVAT
+ITDADQIIVLDEGRVVGRGTHAELLADNQTYREIVDSQLTAEDVA
+>NAFOICDF_00546
+MLWTLLRRHLNPYAGAVTAVIVLQLVSTLAMLYLPSLNARIIDEGVARGDTARIWDLGLV
+MLGVAAVQVVAAISAVWFGAKASMGVGRDLRRAVYTRVDGFSAEELGRFGAATLITRGTN
+DVNQVQMLTLMALNFMVAVPIMAVGGIVMAVREDAGLSWLVWVSVPLLLVIVGFIVSRLM
+PLFQRMQDDIDAVNGVMREQVMGIRVVRAFVRQDHEAARFTDANQALTDTSVRIGRLFVL
+LGPVITMVLHLATAAVLWFGGHRVDQGLVQIGSLTAFMQYLLQILMAVMMGTFMMMMLPR
+AVISARRIGEVLDTAPTLGEPVHPVTPERREGRVELRDVTFAYPGAEAPVLDGVSFTAEP
+GTTTAIIGATGSGKSTLVNLIPRLYDATSGQVLVDGVPVTDLARAELTDAVAIVPQKPYL
+FSGTVRDNMRFGAPEATDEQIWAALETAQAADFVRERTTGEGETAASGLDSSLSQGGTDV
+SGGQRQRLSIARALVADPRILLFDDSFSALDVTTDATLRAALDASAAQTTRVVVAQRVAT
+ITDADQIVVLEAGRVVGRGTHAELLAGNETYRQIVDSQVREEELA
+>MHAAABBN_01856
+MLWTLLRRHGRRYRGAVAAVVVLQLISTLAMLYLPSLNARIIDEGVARGDTARIWDIGLV
+MLGVALVQVVAAIAAVWFGAKASMGVGRDLRRAVYTRVDAFSAEELGRFGAATLITRGTN
+DVNQVQMLTLMALNFMVAVPIMAVGGIIMAIREDPGLSWLVWVSVPVLLVIVAWIVARLM
+PLFQRMQDNIDDVNGVMREQIQGIRVVRAFVRERHETRRFTDANAALTETSVRIGRLFVL
+LGPVITMILHLATAAVLWFGGERVDAGLVQVGALTAFMQYLLQILMAVMMGTFMMMMLPR
+AVISARRIGEVLDTVPTLAEPVRPVTPARRDGAVELRHVTFQYPGAEAPVLDDVSFAVAP
+GTTTAIIGSTGSGKSTLISLLPRLYDATSGEVLVDGVPVTDLARAELTEAVALVPQKPYL
+FSGTVRENMQFGAPDASDERIWAALETAQAADFVRARTTGKAETAASGLDSRLSQGGTDV
+SGGQRQRLSIARALVAEPRILVFDDSFSALDVTTDARLRAALDRAAAGVTRIVVAQRVAT
+ITDADQIIVLDEGRVVGRGTHAELLADNQTYREIVDSQLTAEDVA
+>LFPAFLNI_02086
+MLWTLLRRHGRRYRGAVAAVVVLQLISTLAMLYLPSLNARIIDEGVARGDTARIWDIGLV
+MLGVALVQVVAAIAAVWFGAKASMGVGRDLRRAVYTRVDAFSAEELGRFGAATLITRGTN
+DVNQVQMLTLMALNFMVAVPIMAVGGIIMAIREDPGLSWLVWVSVPVLLVIVAWIVAGLM
+PLFQRMQDNIDDVNGVMREQIQGIRVVRAFVRERHEARRFTDANAALTETSVRIGRLFVL
+LGPVITMILHLATAAVLWFGGQRVDAGLVQVGALTAFMQYLLQILMAVMMGTFMMMMLPR
+AVISARRIGEVLDTVPTLGEPARPVSPARRDGAVELRHVTFQYPGAEAPVLDDVSFAVAP
+GTTTAIIGSTGSGKSTLISLLPRLYDATSGEVLVDGVPVTDLARAELTEAVALVPQKPYL
+FSGTVRENMQFGAPDASDERIWAALETAQAADFVRARTTGKGEAAASGLDSRLSQGGTDV
+SGGQRQRLSIARALVAEPRVLVFDDSFSALDVTTDARLRAALDRAAAGVTRIVVAQRVAT
+ITDADQIIVLDEGRVVGRGTHAELLADNQTYREIVDSQLTAEDVA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000481.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000481.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb8cc6f4edffff0425def27322a3fa8ca25544f7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000481.fa
@@ -0,0 +1,65 @@
+>ACLBLIBL_00622
+MSGTEKHGSTAAPQGEVGELTDAEIAAFQEAGVTDEWGEGPPRKAKAFWPSAMRLLGLFA
+PERTGLILVSLMVLVAVVLNVWAPHVLGQAMDVIFGGLISRDMPAGLTREQVIEGLRGQG
+QGQAADMLSGMAFVPGQGIDFAELARLILIVLGMYVVAQLFMWLQGRVLNDLVMRIVFRL
+REDIEAKLNRLPLSYFDTRQRGDLLSRTTNDVDNVQQAMQQAFATLVYSVLTIIGIVGMM
+FWLSWQLALIALIALPVAGVMVGVIGSKSQKLFTAQWRETGRLNGHIEESFTGHELVTVF
+GRQADMAERFDERNEAMYEASFKAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMT
+LGAVTAFIQYSREFNQPLGQVAGMSNMLISGVASAERIFELLDEDEQDSDAEVARRASDD
+DVAEPADASVRETGASADDDVAHLPQPVAGRVEFEHVRFSYTEAKPLITDLNLVAEPGQT
+IAIVGPTGAGKTTLVNLIMRFYEVDGGRILVDGVDTRTVSREELRSHTGMVLQDAVLFGG
+TIRENIRYGRQDATDEEVVAAAKATFVDRFVHTLPEGYDTVIEQDASNVSAGERQLITIA
+RAFLAQPSLLILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVME
+HGDIVEQGNHAELLAARGAYHRLYMSQFKGGEDDGGGAASGEDAR
+>MOLHKGIG_02147
+MSEHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLVVVALMVLV
+AVVLNVWAPHVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTP
+GEGIDFTELGRLILIVLGMYLVAQTFMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSY
+FDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMMFWLSWQLALIALIAL
+PVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNE
+ELYEAAFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN
+QPLGQIAGMSNMLISGVASAERIFELLDEPEETPDGTPARTPARTFVRETAPSEGTFVRE
+TAPSAASGPDVVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNLVAEPGQTVAIVGPTGA
+GKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRSELRAATGMVLQDAVLFGGTIRENIRYG
+RLDATDEEVVAAAKATYVDRFVHTLPEGYDTVIEHDASNVSAGERQLITIARAFLAQPSL
+LILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVMEHGDIVEQGS
+HAELLAAKGAYHRLYMSQFKGGEDDDGAASRDDAR
+>NAFOICDF_00547
+MSEQLTDQEIVELQESGATDEWGGGPGRKAKAFWPSAKRLLGLFRTEKAGLALVAAMVLV
+AVVFNVWAPHVLGRAMDVLFGGVISKGMPAGVSREQVIEGLRGQGQGQAADMLSGMDFTP
+GQGIDFDALARLILTVLGMYVVAQGFMWLQGRVLNDVVMRIVFRLREQIEAKLNRLPLSH
+FDTRQRGDLLSRATNDVDNVQQAMQQAFATLVYSVLTIFGIVGMMFWLSWELALIALIAL
+PVAGVVVGVVGKKSQALFTAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAERFDERND
+AMYEASFKAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN
+QPLGQVAGMSNMLISGVASAERIFELLDEPEEEPDDVVAARADDDVAHLPQPVAGRVEFE
+HVRFSYTEAKPLITDLNLVAEPGQTIAIVGPTGAGKTTLVNLIMRFYEVDGGRILLDGVD
+TRRVPRQELRAATGMVLQDAVLFGGTIRENIRYGRLEATDEEVLAAAKATYVDRFVHTLP
+DGYDTVIEQDASNISAGERQLITIARAFLAQPSLLILDEATSSVDTRTEVLVQQAMAALR
+NDRTSFVIAHRLSTIRDADVILVMEHGDIVEQGSHEELLAARGAYHRLYTSQFRGGEDEH
+HDDGAPASR
+>MHAAABBN_01855
+MSEHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLVVVALMVLV
+AVVLNVWAPHVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTP
+GEGIDFTELGRLILIVLGMYLVAQTFMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSY
+FDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMMFWLSWQLALIALVAL
+PVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNE
+ELYEAAFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN
+QPLGQIAGMSNMLISGVASAERIFELLDEPEETPDGTPARTPDGTFVWETAPSESAFVRE
+TAPSAIPGPDGVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNFVAEPGQTVAIVGPTGA
+GKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRGELRAATGMVLQDAVLFGGTIRENIRYG
+RLDATDEEVVAAAKATYVDRFVHTLPDGYDTVIEQDAANVSAGERQLITIARAFLAQPSL
+LILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVMEDGDIVEQGS
+HDQLLAARGAYFRLYRSQFQGGEQAEEQDDDGAPAAREDAR
+>LFPAFLNI_02085
+MSEHLTDEEILEIQEQGATDDWGGGPARKAKAFWPSAKRLMSLFRTEKLGLAVVAVMVLV
+AVVFNVWAPRVLGRAMDVIFGGVVSAQMPGGLSREQVIDGLRAQGEDQAAEMLSGMAFTP
+GEGIDFTELGRLILIVLGMYLVAQTFMWLQGRVLNDIVMRIVFRLREEIEAKINRLPLSY
+FDRGQRGDLLSRATNDVDNVQQALQQAFASLVYSVLTVIGIVGMMFWLSWQLALIALVAL
+PVAGVVVGVIGKKSQALFSAQWRETGRLNGHIEESFTGHELVTVFGRQRDMAARFDERNE
+ELYEAAFTAQFYSGMIMPIMQWVNWLGYVGIAVVGGLRVANGQMTLGAVTAFIQYSREFN
+QPLGQIAGMSNMLISGVASAERIFELLDEPEETPDGTPARTPDGTFVWETAPSESAFVRE
+TAPSAIPGPDGVAHLPRPLRGRVEFEHVRFSYTPEKPLITDLNFVAEPGQTVAIVGPTGA
+GKTTLVNLIMRFYEVDGGRILLDGVDTRTVSRGELRAATGMVLQDAVLFGGTIRENIRYG
+RLDATDEEVVAAAKATYVDRFVHTLPDGYDTVIEQDAANVSAGERQLITIARAFLAQPSL
+LILDEATSSVDTRTEVLVQGAMAALRSDRTSFVIAHRLSTIRDADVILVMEDGDIVEQGS
+HDQLLAARGAYFRLYRSQFQGGEQAEEQDDDGAPAAREDAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000483.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000483.fa
new file mode 100644
index 0000000000000000000000000000000000000000..258b86dd5e1cda7a3e93fd61b0eba4d4deb1fd83
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000483.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00627
+MSKVTRWAALVLTLVLVAALAFWAGRATLTPPAQADQRPSEDAVVTVAEQELGRVITLGV
+SVAREQAPAAVNALSGVVTRAGESGEVAAGDVLYAVAQQPVIAVQGELPQWRALDEGATG
+SDVAAFQRMLAATGAKVEVTGTWDEATAVAWNGWLTERDYPAAGTVELGQLVVLESLPAA
+LSVDAKATAVGGALAGGETIVARPGDEPTFAIEVNQDQAAMIPAGTAVTVPHGEHEWEAV
+AGESTADDQGLIRIPLTAPDGGAVCGADCDSLPAEASTSLLSKVNVVPPVTGPVVPVSAL
+RTQPGGAVVVTVVQDGVEEERTVTVRGSADGLAVVDGVDAGETVRVLNGAP
+>MOLHKGIG_02145
+MTRPLRWATLAGVLLIVAVLAFWAGRATLTPPAQAEQRPSEDALVTVAEQELGRVITLGV
+SVTREQAPAAVNALSGVVTRAGESGEVAAGDVLYAVAQQPVITVQGELPQWRALGEGATG
+SDVAAFQRMLAATGAKVEVTGTWDEATAVAWNGWLTERDYPAADTVELGQLVVLESLPAA
+LSVDAKATAVGGALAGGETIVARPGDEPTFAIEVNQDQAAIIPAGTAVTVPHGEHEWEAV
+AGESTADDQGLIRIPLTAPDGGAVCGADCDSLPAEASTSLLSKVNVVPPVTGPVVPVSAL
+RTQPDGAARVTVVRDGVQEERTVIVRGSADGLAVVDGVDAGETVRVLNGAP
+>NAFOICDF_00551
+MTRPARWAALVLAVVLVAALAFWAGRVTLTPPAQAEQRPSEDAVVTVAEQELGRVITLGV
+SVTREQAPAAVNALSGVVTRAGQSGEVAAGDVLYAVAQKPVIAVQGELPQWRALGEGATG
+SDVTAFQRMLTATGTKVKATGTWDEATATAWNAWLTTRGYPAADTVELGQLVVLESLPTA
+LSVDAKATAVGGTLAGGETIVARPGDEPTFAIEVNQDQAAMIPAGTAVTVPHGEHEWKAV
+AGESISDEQGLIRITLTAPDGGVVCGEDCDTLPADPTTSLLSQVSVVPPVSGPVVPVSAL
+RTQPDGAATVTVVRDGAAEDRTVTVLGSADGLAVVDGVDAGEQVRVLNGTR
+>MHAAABBN_01852
+MNRPARWAALVLALVAVAALAFWAGRVTLTPPAQAEQRPAASALVTVAEQELGRVITLGV
+SVSREQTPAAVNALTGVVTRAGESGEVAAGEVLYAVAQKPVLVLQGELPQWRPLGEGTSG
+DDVAAFQRMLAATGAKVEATGTWDEATADAWDDWLTERGYPAADTVELGQLVVLDALPAP
+LSVDAKTTAVGTTLAGGENVVARPGDQPDFALEVNQEQAALIPAGTQVTVPHGEHEWKAV
+AGESTSDEQGLIRITLTAPDGGVVCGEDCDTLPADATTSLLSQVSVVPPVSGPVVPVSAL
+RTQPDGAATVTVVRDGAAEDRAVTVLGSADGLAVVDGVDAGEQVRVLNGTR
+>LFPAFLNI_02082
+MNRPARWAALVLALVAVAALAFWAGRVTLTPPAQAEQRPAASALVTVAEQELGRVITLGV
+SVSREQTPAAVNALTGVVTRAGESGEVAAGEVLYAVAQKPVLVLQGELPQWRPLGEGTSG
+DDVAAFQRMLAATGAKVEATGTWDEATADAWDDWLTERGYPAADTVELGQLVVLDALPAP
+LSVDAKTTAVGTTLAGGEKVVARPGDQPDFALEVNQEQAALIPAGTQVTVPHGEHEWKAV
+AGESTSDEQGLIRITLTAPDGGVVCGEDCDTLPADATTSLLSQVSVVPPVSGPVVPVSAL
+RTQPDGAATVTVVRDGAAEDRTVTVLGSADGLAVVDGVDAGEQVRVLNGTR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000486.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000486.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5d3030206e2fa62d7ebbb4e329d066e3edfb766e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000486.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00632
+MALFSQPVFINLPTTDTERIREFWTSLGAQAIEDFSDENSVCIELTESTFAMYLSPGYYT
+DFIGDREIADCMTTNSALMALTVGDAAAVDALADRAIEAGAAEVPLPVDLREEMVDSGMH
+SREIVDPDGHQWEFVTA
+>MOLHKGIG_02140
+MALFSQPVFINLPTTDTERIREFWTTLGATAMDDYSDEHSVCIELTESTYAMYLSPGYYT
+DFIGNREIADCLTTNSALMALTVGDAAAVDALADRAIELGAAEVPLPEDLREEMADSGMH
+SREIVDPDGHQWEFVTA
+>NAFOICDF_00556
+MRTRWSTVLVMALFSQPVYINLPSTDTERIREFWTSMGADIDEDFSDENSVCVQLTESTF
+AMYLSPGFYTDFIGDREIADCLTTNSVLLQLTAPDRGAVDALVRAAVEAGGSEVPLPDEL
+QEDMTATGVHSRQVVDPDGHQWEFMAA
+>MHAAABBN_01848
+MALFSQPVFINLPTTDTERIREFWTTLGATAMDDYSDEHSVCIELTESTYAMYLSPGYYT
+DFIGNREIADCLTTNSALMALTVGDAAAVDALADRAIELGAAEVPLPEDLREEMADSGMH
+SREIVDPDGHQWEFVTA
+>LFPAFLNI_02078
+MALFSQPVFINLPTTDTERIREFWTTLGATAMDDYSDEHSVCIELTESTYAMYLSPGYYT
+DFIGNREIADCLTTNSALMALTVGDAAAVDALADRAIELGAAEVPLPEDLREEMADSGMH
+SREIVDPDGHQWEFITA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000489.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000489.fa
new file mode 100644
index 0000000000000000000000000000000000000000..779ffec033e1870b931b7df707a7328ee2ec5ed3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000489.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00635
+MQTPLEISSVVFKPILIRAVVALAFGLTTVFVAAPGLTWMKVSLALYLAFSGSAMWEYLR
+REPVPVAMRSPLSMAAAASMLGVIVLLFLGTPAGVGLAAAAALVLGGAAELVAWARHRRE
+FIPARDQLWTGLVGLLSGLGVAFGALQGFGPHALLGIAGGGAIIIGVLLLVSGLGFHHEV
+RRDRGTAKGL
+>MOLHKGIG_02137
+MQTPLEISSVVFKPILIRAVVALAFGLTTVFVAEPGLTWMKVMFALYLAFSGSAMWEYLR
+RDPVPVAMRSPLSLAAAAWMLGVIVLLFLGSPAAVGVAAGAALVLGGVAELVAWARHRRE
+FIPARDQLWTGLVGLLSGGGVVVAALQGFGPHALLGIAGGGAILIGVLLMVSGLGFHHEV
+RRDRGTARGL
+>NAFOICDF_00559
+MTSPQTPLEISSEVFKPVLIRAGVALIFGLTTVFVQNPGLTWMKVAFALYLVFSGSALWE
+YLRRDPVPVGMRSPLSLAAAAWMLGTVVLVIMGSPAAVGIVVGLALLAGGAAELTAWARF
+RREFIPARDQLWTGLVGALSGLGVLVGAVQGFGPHALLGIAGGGAIIVGVLMLISGLGFH
+HEVRRDRGTAKGL
+>MHAAABBN_01845
+MQTPLEISSVVFKPILIRAVVALAFGLTTVFVAEPGLTWMKVMFALYLAFSGSAMWEYLR
+RDPVPVAMRSPLSLAAAAWMLGVIVLLFLGSPAAVGVAAGAALVLGGVAELVAWARHRRE
+FIPARDQLWTGLVGLLSGGGVVVAALQGFGPHALLGIAGGGAILIGVLLMVSGLGFHHEV
+RRDRGTARGL
+>LFPAFLNI_02075
+MQTPLEISSVVFKPILIRAVVALAFGLTTVFVAEPGLTWMKVMFALYLAFSGSAMWEYLR
+RDPVPVAMRSPLSLAAAAWMLGVIVLLFLGSPAAVGVAAGAALVLGGVAELVAWARHRRE
+FIPARDQLWTGLVGLLSGGGVVVAALQGFGPHALLGIAGGGAILIGVLLMVSGLGFHHEV
+RRDRGTARGL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000490.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000490.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c05e59e8ac72a45e5b5f94329f312650532dfd93
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000490.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00636
+MSAPSPRPSADRAGTGRPARGGLRTTVKGPLVFSAVLGVIGGVIAGITASGGTQNPLRID
+IALIAFGVFFMTSLVVVAMLQLAARENPDHLSAGSGINRSSEETFQKAAAERRAQVARER
+REQDGTGGDAPRA
+>MOLHKGIG_02136
+MSAPSPRPSADRAGSGRPARGGLRTTVKGPLVFSAVLGLIGGVIAGITASGGTQNPLRID
+IALIAFGVFFMTSLVVVAMLQLAARENPDHLSQGSGVNRSSEEMFRKAAADRRAQAARER
+REQGGTGGDAPRA
+>NAFOICDF_00560
+MSAQSPRPSDDRTRPGAGRPARGGLRTTVKGPLVFSAVLGLVGGVVAALTASGGTANPLR
+IDIGLIAFGVFFMTSLVVVAMLQLASRENPDHLSRGSGVNRSSEETFQRRAAERRAKAAA
+ERRAAQGDAGR
+>MHAAABBN_01844
+MSAPSPRPSADRAGSGRPARGGLRTTVKGPLVFSAVLGLIGGVIAGITASGGTQNPLRVD
+IALIAFGVFFMTSLVVVAMLQLAARENPDHLSQGSGVNRSSEEMFRKAAADRRAQAAAER
+REQGGTGGDAPRA
+>LFPAFLNI_02074
+MSAPSPRPSADRAGSGRPARGGLRTTVKGPLVFSAVLGLIGGVIAGITASGGTQNPLRVD
+IALIAFGVFFMTSLVVVAMLQLAARENPDHLSQGSGVNRSSEEMFRKAAADRRAQAAAER
+REQGGTGGDAPRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000491.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000491.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e47e2987b7e849afd8b93b0264b4f82bcd935d8d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000491.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00638
+MLSPRTLARLSSVAAFLNTAPGPRGGQEAPERFTAATQLPALVPELQEGEVRLRLAAAAA
+VRARELRERLTRVWALAATDESAAVERVNELLAEAGPLRLTAGGDVVGLAPAQVPADAVE
+RLAAMATLALAETAMDGELARLRVCEGEDCENALVDGSRNRSKRFCDEANCANRTHVRSY
+RARLAEAAEAAPATDPAGPEEAEGTEAVVDEAAPADEPLQETEKEKKERRKAQKKARKKA
+EKKAGKKKSDKKKSDKKKD
+>MOLHKGIG_02134
+MLSAPTLTRLASLAAFLNTAPGLRGGQPADERFTAATQLPSLVPELQEDEVRLRLAAAAA
+VRGRELRGRLAEVWALAAVDEAAAVERVNALLAAAGPLRLTAGGDVVGLAPAQVPADAVE
+RLAAMAALALAETAMDGELVRLRVCEGEDCENALVDASRNRSKRFCDEANCANRTHVRSY
+RARLAEAAEAAPATDPAGPEEAEAPEAVADEAAPADKPRQETEKEKKERKKAEKKAEKKA
+RKKAEKKARKKKSDKKKD
+>NAFOICDF_00561
+MLSPHTLARLASISAFLNTAPGVRGGQEAEERLTAGTQLPALVPELQEGESRLRVAAAAR
+TRAHELRARLTELWAAADAEDVPAAVAAVNELLAETGPLRLEVSDGSADLAPAQVPADAV
+ERLTAMAALALTEAALEGELTRLRVCAGEDCENTLVDASRNRSKRFCDAANCANRTHVRS
+YRARLAEAEDTQADVEAADAAPLPEVAPEADPQDATDLEAIEAAEGVESAVQEPVKKDST
+KDKKSKSEKKARRAAKKKAEKESEAAAEGKKGKREKSKKSEKHKKKAAKD
+>MHAAABBN_01842
+MLSAPTLSRLASLAAFLNTAPGLRGGQPADERFTAATQLPSLVPELQEDEVRLRLAAAAA
+VRGRELRGRLAEVWALAAGDEAAAVERVNALLAAAGPLRLTAGGDVVGLAPAQVPADAVE
+RLAAMAALALAETAMDGELTRLRVCEGEDCENALVDASRNRSKRFCDEANCANRTHVRSY
+RARLAEAAESAPAADPAGPEEAEAPEAVVDSEAAADEPRRETKKEKKERRKAEKKARKKA
+EKKAGKKKSDKKKD
+>LFPAFLNI_02072
+MLSAPTLSRLASLAAFLNTAPGLRGGQPADERFTAATQLPSLVPELQEDEVRLRLAAAAA
+GRGRELRGRLAEVWALAAVDEAAAVERVNALLAAAGPLRLTAGGDVVGLAPAQVPADAVE
+RLAAMAALALAETAMDGELTRLRVCEGEDCENALVDASRNRSKRFCDEANCANRTHVRSY
+RARLAEAAESAPAADPAGPEEAEAPEAVVDSEAAADEPRRETKKEKKERRKAEKKARKKA
+EKKAGKKKSDKKKD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000500.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000500.fa
new file mode 100644
index 0000000000000000000000000000000000000000..63ae6e440ba7ba875e047d98994c46502a41974f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000500.fa
@@ -0,0 +1,14 @@
+>ACLBLIBL_00655
+MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAAELFRGARATSFALTRQVEDPARY
+RLLIGWRTLEDHTVGFRESEAFGQWRALVTPHLAQPPAATHWESVAAAF
+>MOLHKGIG_02125
+MSAGQGATTAGPVIESVELHVAAGAEAAFEAAVAEAEPLFRDGGATSFALSRQVEDPARY
+RLLIGWRTLEDHTVAFRESDSFLAWRALVTPHLAQLPAATHWSAV
+>NAFOICDF_00572
+MEDPARYRLLIGWRTLEDHTVGFRESDAFLAWRALVTPHLAQPPAATHWSAV
+>MHAAABBN_01833
+MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAEPLFRDKGATSFALSRQVEDPARY
+RLLIGWRTLEDHTVAFRESDAFLAWRALVTPHLAQPPAATHWSAV
+>LFPAFLNI_02063
+MSAGQDATTAGPVVESVELHVAAGAEAAFEAAVAEAEPLFRDGGATSFALSRQVEDPAHY
+RLLIGWRTLEDHTVAFRESDAFLAWRALVTPHLAQPPAATHWSAV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000502.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000502.fa
new file mode 100644
index 0000000000000000000000000000000000000000..be3c7d4e99223965072fcf306b50c2f77209e9a3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000502.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_00659
+MTTTDLKITGMTCGHCVASVQEELGEIAGVTAVDVDLTAGGVSTATVTSESPLDPAAARA
+AVEEAGYRLVEG
+>MOLHKGIG_02121
+MTTTDLKITGMTCGHCVASVQEELGEIAGVSAVDVDLNSGGVSTATVTSEAPLDPAAARA
+AVEEAGYTLVEA
+>NAFOICDF_00576
+MTTTDLKITGMTCGHCVASVREELGEIAGVSAVDVDLNAGGVSTATVTSEGPLGPAAARA
+AVEEAGYTLVEG
+>MHAAABBN_01829
+MTTTDLKITGMTCGHCAASVREELGEIAGVSAVDVDLNAGGVSTATVTSEGPLDPAAARA
+AVEEAGYTLVEA
+>LFPAFLNI_02059
+MTTTDLKITGMTCGHCAASVREELGEIAGVSAVDVDLNAGGVSTATVTSEGPLDPAAARA
+AVEEAGYTLVEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000503.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000503.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ccc9b9e4a88aa8a2899d113355a26d265bf023d6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000503.fa
@@ -0,0 +1,18 @@
+>ACLBLIBL_00660
+MSTLPTTTDAHDGADPCAGAHPPHAAHRDKDAHLTRLRRIEGQVRGIHRMVDEDVYCIDI
+LTQVAAVTKALQAMSLNLTSEHLRHCVAEAAVEAEASGRTELIDEKVAEATAAIGRLLR
+>MOLHKGIG_02120
+MSTDSTTTAPAAASPLPSAAADACDGHRPPHEVHRDKAKHLARLRRIEGQVRGLHRMVDE
+DVYCIDVLTQVAAVTKALQSLSLNLTSEHLRHCVAEAAVQAEAEGRTELIDEKVAEATAA
+LGRLLR
+>NAFOICDF_00577
+MEHDRHAGPGYSPQREAYLKRLKRIEGQVRGIHRMVEEDVYCIDVLTQVAAATKALHAVS
+LGLVEDHLRHCVAEAAVQAEAEGRTELIDEKVAEATAALGRLLR
+>MHAAABBN_01828
+MSTDSTTTAPAAASPLPSAAADACDGHRPPHEVHRDKAKHLARLRRIEGQVRGLHRMVDE
+DVYCIDVLTQVAAVTKALQSLSLNLTSEHLRHCVAEAAVQAEAEGRTELIDEKVAEATAA
+LGRLLR
+>LFPAFLNI_02058
+MSTDSTTTAPAAASPLPSAAADACDGHRPPHEVHRDKAKHLARLRRIEGQVRGLHRMVDE
+DVYCIDVLTQVAAVTKALQSLSLNLTSEHLRHCVAEAAVQAEAEGRTELIDEKVAEATAA
+LGRLLR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000507.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000507.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9f66fcb3a68bc913ed88574bbace8c00065253d6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000507.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_00665
+MSDYQPRRPGSNPAPARRTDRAGKPALGRPKRGLIDESEARQLAEDRERMRRAGVGHQLS
+APKRREAATAERPQVMPQTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLAERQAKA
+KEIGLPAFRAKQLSVHYFERYTTDPEQMTDLPKDKREVIAEAFFPPLLTEVRRMETDRGD
+TVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTAEIVE
+QIVRANQVIAEGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPAPEG
+LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID
+AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW
+TASEKDVTREFVERLNAAGIPTTLRDTRGKEIDGACGQLAAGDEDA
+>MOLHKGIG_02115
+MSDYQPRRPGSKPTPNRQRDRAGKPALGRPERGLIDESEARQLAEDRERMRRAGVGHQLS
+APKRREAATAERPQVMPKTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLKERQEKA
+KEIGLPAFRAKQLSVHYFEHYTTDPEQMTDLPKDKREAIAEAFFPPLLTEVRRMETDRGD
+TIKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTAEIVE
+QIVLANQVIAQGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPSPEG
+LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID
+AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW
+TASEKDVTREFVDRLNAAGIPTTLRDTRGKEIDGACGQLAAEDVD
+>NAFOICDF_00581
+MEGMSDYTPRRPGSKPTPARQKDRAGKPALGRPRRGMIDEPEARQLAEDRERMHRAGVGH
+QLSAPPRRAAEVDADRPQVMPKTEGWQQPMGPDGRPQLQFKQPRVSQPPQHLADMTLAER
+QAKAKEIGLPAFRAKQLSVHYFEHFTTDPEQMTDLPKGKREEIAEAFFPPLLTEVRRLTT
+DRGDTVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTA
+EIVEQIVRANQVIAEGGLGGTRRDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDP
+APEGLGMSARHVTLSTVGLVPAIKKLAQEGVPLTFALSLHAPDDELRDELIPVNARWKAD
+EAIDAAYEYFLATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTP
+GSIWTASEKDVTREFVDRLNAAGIPATLRDTRGKEIDGACGQLAADDEDVAARA
+>MHAAABBN_01823
+MSDYQPRRPGSKSTPNRQRDRAGKPALGRPERGLIDESEARQLAEDRERMRRAGVGHQLS
+APKRREAATAERPQVMPKTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLKERQEKA
+KEIGLPAFRAKQLSVHYFEHYTTDPEQMTDLPKDKREAIAEAFFPPLLTEVRRMETDRGD
+TVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSTAEIVE
+QIVLANQVIAQGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPSPEG
+LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID
+AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW
+TASEKDVTREFVDRLNAAGIPTTLRDTRGKEIDGACGQLAAEDVD
+>LFPAFLNI_02053
+MSDYQPRRTGSKPTPNRQRDRAGKPALGRPERGLIDESEARQLAEDRERMRRAGVGHQLS
+APKRREAATAERPQVMPKTEGWTQPMGPDGRPQLQFKQPRVSQPPTHLADLTLKERQEKA
+KEIGLPAFRAKQLSVHYFEHYTTDPEQMTDLPKDKREAIAEAFFPPLLTEVRRMETDRGD
+TVKFLWRLFDGALVESVLMRYPGRVTLCVSSQAGCGMNCPFCATGQAGLTRNMSPAEIVE
+QIVLANQVIAQGGLGGKRKDGGHDADRVTNVVFMGMGEPLANYKRVMAAVHRMVDPSPEG
+LGMSARNITLSTVGLVPAIRKLAEEGVPLTFALSLHAPDDELRDELIPVNSRWKADEAID
+AAYDYFVATGRRVSIEYALIKDMNDHAWRADLLAKKLNARGKGWVHVNPIPLNPTPGSIW
+TASEKDVTREFVDRLNAAGIPTTLRDTRGKEIDGACGQLAAEDVD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000508.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000508.fa
new file mode 100644
index 0000000000000000000000000000000000000000..87e0544540c6ec1dbc6c2144ab414c8ffb4279e4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000508.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00666
+MGHKDPRTHLLEKLEKSNVCMLTTSETDGTLTTRPMGLQKAEETGTLWFMTRAASDVASD
+ASQRPVNVSVQDKDFWASVAGHGQVVRDDARKKEFWNPATEAFFGEGAKPEDPQIVLVRV
+DVESAQYWESPGAVGTVVELIKAKVTGGEAHPGESTTVQF
+>MOLHKGIG_02114
+MGTQDPRARLLEKLAKVNVCMLTTAEPDGTLVTRPMGLQQAEDGGTLWFLTRATSDVAAD
+APQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNPATEAFFGEGSSPEDPQIVLVRV
+DVQTAQFWESPGAVATAVELVKAKVTGGEAHPGDSETVRF
+>NAFOICDF_00582
+MTEQDPRTALLEKIEKAGVVMLTTAEEDGTLASRPMAVQEVEQEPGVLWFITRATGDAAQ
+DSAGRPVNVAVQEKGFWASVAGHGEIVRDEARKTEYWNSATEAFFGEGARPEDPQIVLVR
+VQADSAEYWDGGGAASVVEIVKAKVTGGEARPGDHDTVEF
+>MHAAABBN_01822
+MGTQDPRTHLLEKLAKVHVCMLTTAEADGTLVTRPMGLQQAEDGGTLWFMTRSTSDVAAD
+APQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNSATEAFFGEGSSPEDPQIVLVRV
+DVNTAQFWESPGAVATAVEMVKAKVTGGTAEPGDSETVRF
+>LFPAFLNI_02052
+MGTQDPRARLLEKLAKVNVCMLTTAEQDGTLVTRPMGLQQAEDGGTLWFLTRATSDVAAD
+APQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNPATEAFFGEGSSPEDPQIVLVRV
+DVDTAQFWESPGAVATAVELVKAKVTGGTAEPGDSETVRF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000510.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000510.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b0b2cc19d149d9a1154b575830eaedf74b33e08
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000510.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00668
+MATKDLTLEEFGTTVSENDTVLVDFWADWCGPCKQFAPVFDAASEKHEDIVFAKVDTEDQ
+QQLAAMAGITSIPTLMAFRGGVLVFSQAGALPAPALDQLLEQVKGLDIAEVRAMAEQQAG
+EAEAEPSQDEAVQSTASHLDEVNGR
+>MOLHKGIG_02110
+MATKDLTLEEFGSTVAENDTVLVDFWAGWCGPCRQFAPVFEAASEKHEDVVFAKVDTEDQ
+QQLAAMAGITSIPTLMAFRGGVLVFSQAGALPGTALEQLLDQVKGLDIAEVRRLAEEQQG
+QQGDAEPGQDEAVQSTAAHLDDVNGR
+>NAFOICDF_00585
+MATTDLTLEAFGTTVSENDTVLVDFWAEWCGPCKMFGPVFETASEKHQNVVFAKVDTEDQ
+QQLAAMAGITSIPTLMAFRGGVLVFSQAGALPGQALDQLIDQVTALDIAEVRAMAEQQGA
+QDAEPSEEEAVQSAAAQLDDVNGR
+>MHAAABBN_01817
+MATKDLTLEEFGSTVAENDTVLVDFWAGWCGPCRQFAPVFEAASEKHEDVVFAKVDTEDQ
+QQLAAMAGITSIPTLMAFRGGVLVFSQAGALPGAALEQLLDQVKGLDIAEVRRLAEEQQG
+QQGDAEPGQDDAVQSTAAHLDDVNGR
+>LFPAFLNI_02050
+MATKDLTLEEFGSTVAENDTVLVDFWAGWCGPCRQFAPVFEAASEKHDDVVFAKVDTEDQ
+QQLAAMAGITSIPTLMAFRGGVLVFSQAGALPGTALEQLLDQVKGLDVAEVRRLAEEQQG
+QQDDAEPGQDDAEPGQDEALQSTAAHLDDVNGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000513.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000513.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00f9dfcabed30a8fd7574c5742a79276381c4c9e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000513.fa
@@ -0,0 +1,32 @@
+>ACLBLIBL_00673
+MPADAPLYTRTARAAAGRVIRRYSTSFSWACRTLPREARRDVEAIYAMVRVADEAVDGVA
+QAAGLDSQRVRAALDDYERACEAAMASGFSTDLVLHAFGDVARRHGITPELTRPFFASMR
+ADLGVSEHGAESLAAYIHGSAEVVGLMCLQVFLSLPGTRARTPAEREAIRAQAARLGAAF
+QKVNFLRDLAADHDGLGRTYLTGAAPDELTEARKAELVAEVRADLAAALPGIRALDPRAG
+RAVALAHGLFAALADRIETTPAAELARRRVRVPDAQKARIAARVLAEQAGLAVARRRRGG
+RR
+>MOLHKGIG_02106
+MAAPTPSPAALYTRTAHTAAAQVIRRYSTSFSWACRTLPRQARQDVATIYAMVRVADEVV
+DGVAVAAGLDEAGVRAALDDYERACEAAMASGFATDPVLHAFADVARRHGITPELTRPFF
+ASMRADLGIREHGAESLDAYIHGSAEVVGLMCLQVFLSLPGTRARTPGQRQELRAQASRL
+GAAFQKVNFLRDLAADHHELGRTYLPGAAPGVLTEARKAELVAEVRADLDAALPGIRVLD
+PGAGRAVALAHGLFAALVDRIEATPAAELAHRRVRVPDHQKARIAARVLARGRRGGRR
+>NAFOICDF_00589
+MTGTTTPPAPAGPECGTVRARTGETDLELYTATALRVAGEVIGRYSTSFSWACRVLPPDA
+RRDIAAIYAMVRVADEVVDGAAEEAGLPVARVAAGLDAYERACEDAMDTGFSTDLVLHAF
+ADVSRRHGITAELTRPFFVSMRADLTVAEHGEDSLAAYIHGSAEVVGLMCLQVFLSMDGT
+RADGPADRAALRAAASRLGAAFQKVNFLRDLAADHDALGRTYFSGAAPEALTEERKAELL
+ADLDADLDASLPGILALDPRAARAVLLAHGLFAELSRRLAATPAAELARRRVRVPDPVKA
+RIAVRVLAASPVGIGRRGRPLPAGCAEDLAAHQDGDRRP
+>MHAAABBN_01813
+MAAPTPSPAALYTRTAHAAAAQVIRRYSTSFSWACRTLPRQARQDVATIYAMVRVADEVV
+DGVAVAAGLDEAGVRAALDDYERACEAAMASGFATDPVLHAFADVARRHGITPELTRPFF
+ASMRADLGIREHGAESLDAYIHGSAEVVGLMCLQVFLSLPGTRARTPGQRQELRAQASRL
+GAAFQKVNFLRDLAADHHELGRTYLPGAAPGVLTEARKAELVAEVRADLDAALPGIRVLD
+PGAGRAVALAHGLFAALVDRIEATPAAELAHRRVRVPDHQKARIAARVLARGRRGGRR
+>LFPAFLNI_02046
+MAAPAPIPAALYTRTAHAAAAQVIRRYSTSFSWACRTLPRQARQDVATIYAMVRVADEVV
+DGVAVAAGLDEAGVRAALDDYERACEAAMASGFATDPVLHAFADVARRHGITPELTRPFF
+ASMRADLGIREHGAESLDAYIHGSAEVVGLMCLQVFLSLPGTRARTPGQRQELRAQASRL
+GAAFQKVNFLRDLAADHHELGRTYLPGAAPGVLTEARKAELVAEVRADLDAALPGIRVLD
+PGAGRAVALAHGLFAALVDRIEATPAAELAHRRVRVPDHQKARIAARVLARGRRGGRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000514.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000514.fa
new file mode 100644
index 0000000000000000000000000000000000000000..019ce8a8592dbe0f00eaec67a7f0a35aab7c7d9f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000514.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_00674
+MSAAPNVASGAAAHDDGPRAVVIGGGFAGLATAGLLARDGHRVTLLERNDGLGGRSGRWS
+AEGFAFDTGPSWYLMPEVIDRWFRLMGASAAERLDLRRLDPGYRVYFEDHLDAPPVDVRT
+GHAEELVESLEPGAGERLRAYLDSAGRVYELAKEHFLYTDFRRPADLARPAVLRALPSLG
+PQLLGGLRAHVAARFRDPRIRQILGYPAVFLGTSPDRAPAMYHLMSHLDLRDGVQYPIGG
+FAALVDAMADLVREAGVEVVTGAEATRIEVEDAERRRRRRGRVTGVVVRQDGTERRLSAD
+VVVAAADLHHVQTALLPPAQRVAESAWDRRDPGPSGVLVCVGVRGALPQLAHHTLLFTAD
+WEDNFGRIERGEDLAADTSLYVSRTSATDPGVAPDGDESLFVLVPAPAEPGWGRGGIRVR
+EGDGWRVEREGDAQVEAVADRALDQLARWAGIEDLHERIVVRRTIGPGDFAADVHAWRGS
+MLGPGHTLAQSAMFRPSVRDADVAGLLYAGSSVRPGIGVPMCLISAEVVREELRHAARRD
+ALRAQRRGRSQDDDDGARRGRVAAS
+>MOLHKGIG_02105
+MSARDTALGPRTVVVGGGFAGLATAGLLARDGHRVTLLERGAVLGGRAGRWSEAGFTFDT
+GPSWYLMPEVIDRWFRLMGTSAAERLDLRRLDPGYRVYFEGHLHEPPVDVRTGHAETLFE
+SLEPGAGRRLRAYLDSASRIYGLAKEHFLYTDFRRPAALAHPDVLRALPALGPQLLGGLR
+SHVAARFQDPRLRQILGYPAVFLGTSPDRAPAMYHLMSHLDLADGVQYPLGGFAALVDAM
+AEVVREAGVEIRTGVEATAVEVVDRPAPAGRLGRLAARLPRPGAARGDEGRRRRPGRVTG
+VAWRSDDGAAGRLDADVVVAAADLHHVQTRLLPPGRRVAESTWDRRDPGPSGVLVCVGVR
+GSLPQLAHHTLLFTADWEDNFGRIERGEDLAADTSIYVSRTSATDPGVAPEGDENLFILV
+PAPAEPGWGRGGIRVRDGQGWRVDRAGDAQVEAVADRALDQLARWAGIPDLAERIVVRRT
+YGPGDFAADVHAWRGSLLGPGHTLAQSAMFRPSVRDADVAGLMYAGSSVRPGIGVPMCLI
+SAEVVRDELRHDARRVRPAGPGGSGT
+>NAFOICDF_00590
+MTPTTPAARPAAAPSGSRRVVVIGGGFAGLATAGLLAQDGHRVTLLEKNPVLGGRSGRWS
+AEGFTFDTGPSWYLMPEVIDRWFRLMGTSADEALDLRALSPAYRVYFQEHAADDAAAPGD
+GSTPGARAPLDVVSGREESLALAEELEPGAGGRLAAYLDSAERIYALAKRRFLYTDFQDL
+TELLRPDVLRALPALAPQLLGDLRGFVARRFEDGRLRRVLGYPAVFLGTSPGKAPAMYHL
+MSHLDLADGVQYPIGGFAALVDAMAELVRAAGVEIVTAAEVTAVDVVSDPRPRGRLPRLL
+DGAPRPWEPRTPAGGRRRSGHVRGVSWRDAEGGSHRLDADAVVAAADLHHVQTALLPGDQ
+RVAERTWDRRDPGPSAVLVCVGVRGRLPELLHHTLLFTEDWDENFRRIDEGEDLQEETSL
+YVSMTSATDPGVAPEGDESLFLLVPAPAVPEWGRGGVRTPEEDRAGDAQVETVADRALAQ
+LARWAGVPDLGERIVVRRTWGPADFTADVHAWRGSLLGPGHVLRQSALFRPPVRDPRVAG
+LVYAGSSVRPGIGVPMCLISAELARDAVSGVRPGGAAPGAPAMAGR
+>MHAAABBN_01812
+MSARDTALGPRTVVVGGGFAGLATAGLLARDGHRVTLLERGAVLGGRAGRWSEAGFTFDT
+GPSWYLMPEVIDRWFRLMGTSAAERLDLRRLDPGYRVYFEGHLHEPPVDVRTGHAETLFE
+SLEPGAGRRLRAYLDSASRIYGLAKEHFLYTDFRRPAALAHPDVLRALPALGPQLLGGLR
+SHVAARFQDPRLRQILGYPAVFLGTSPDRAPAMYHLMSHLDLADGVQYPLGGFAALVDAM
+AEVVREAGVEIRTGVEATAVEVVDRPAPAGRLGRLAARLPRPGAARGDEGRRRRPGRVTG
+VAWRSDDGAAGRLDADVVVAAADLHHVQTRLLPPGRRVAESTWDRRDPGPSGVLVCVGVR
+GSLPQLAHHTLLFTADWEDNFGRIERGEDLAADTSIYVSRTSATDPGVAPEGDENLFILV
+PAPAEPGWGRGGIRVRDGQGWRVDRAGDAQVEAVADRALDQLARWAGIPDLAERIVVRRT
+YGPGDFAADVHAWRGSLLGPGHTLAQSAMFRPSVRDADVAGLMYAGSSVRPGIGVPMCLI
+SAEVVRDELRHDARRVRPAGPGGSGT
+>LFPAFLNI_02045
+MSARDTALGPRTVVVGGGFAGLATAGLLARDGHRVTLLERGAVLGGRAGRWSEAGFTFDT
+GPSWYLMPEVIDRWFRLMGTSAAERLDLRRLDPGYRVYFEGHLHEPPVDVRTGHAETLFE
+SLEPGAGRRLRAYLDSASRIYGLAKEHFLYTDFRRPAALAHPDVLRALPALGPQLLGGLR
+SHVAARFQDPRLRQILGYPAVFLGTSPDRAPAMYHLMSHLDLADGVQYPLGGFAALVDAM
+AEVVREAGVEIRTGVEATAVEVVDRPAPAGRLGRLAARLPRPGAARGDEGRRRRPGRVTG
+VAWRSDDGAAGRLDADVVVAAADLHHVQTRLLPPGRRVAESTWDRRDPGPSGVLVCVGVR
+GSLPQLAHHTLLFTADWEDNFGRIERGEDLAADTSIYVSRTSATDPGVAPEGDENLFILV
+PAPAEPGWGRGGIRVRDGQGWRVDRAGDAQVEAVADRALDQLARWAGIPDLAERIVVRRT
+YGPGDFAADVHAWRGSLLGPGHTLAQSAMFRPSVRDADVAGLMYAGSSVRPGIGVPMCLI
+SAEVVRDELRHDARRARPAGPGGSGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000518.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000518.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5432d9935a2dfb60409cba97ab2acaf1c7c32a04
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000518.fa
@@ -0,0 +1,54 @@
+>ACLBLIBL_00680
+MGGRLIPELLAAGFDVRAGARNPSDLADRPWSEGVEAVELDLTEADLVEAAMQDVHTVLY
+LVHSMGGGGDFVTQEQRIADIVGTAADTAGVAQLVYLSGLHPDTIPVAELSDHMRSRALV
+AERLEQAATPALTFEAGVIIGSGSTSFEMIRHLAERLPVMPGPSWLKNRVEPLAIRDVLY
+YLLQACALPEPVQLRAQIGNGHPQSFASVLVDYAKAAGLSRRIVIPTPFPLQTLAGFWIG
+TVTPIPVAVALPLAASLAEEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDV
+TFDADVHAAADPADPLPSDPAWSGTTVYTDERERESDLPPQDVWPVIESVGGANGWYSTP
+MLWKVRGLADKLVGGPGLIRGRRDQDRLRRGDAVDWWRVEDVEHGRRLTLRAEMKAGGRA
+WLQMSTEPRDGGGSVYRQRAIFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEAQRRTT
+GGERRRPRSLARALVDRLPLRRNPLDRGASA
+>MOLHKGIG_02099
+MASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRA
+GARNPSDLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRI
+ADIVGTAADTAGVAQLVYLSGLHPDTVPVAELSDHMRSRALVAERLERAATPALTFEAGV
+IIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQACALPEPVQLRAQI
+GNGHPQSFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLA
+EEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPS
+DPEWAGTTVYTDERERESDLPAQEVWPVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGL
+TRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQLSTEPREGGGSVYRQ
+RAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRL
+PLRRNPLDRRARGAGGAQSRD
+>NAFOICDF_00594
+MSTPSTSRGSGLTSAAASGDTPAGTGATTASLSPLGLALPDGHDRRVLVTGATGYVGGRL
+IPELLAAGFRVRAGARTPRDLEDRPWSDRVEVVELDLEKPDLVKAAMQDVHTALYLVHSM
+GAGGDFVEQEQKIADIVATAADEAGITQLVYLSGLHPAGKPVEELSDHMRSRALVAERLE
+AAATPALTFEAGVVIGSGSASFEMIRHLSERLPIMPGPSLLKNRVEPIAVRDVLHYLVQA
+CALEEPVQLHAQIGNGRPQSFASVLVDYAEVAGLSKRIVIPTPLPLSRLAGLWVGVVTPI
+PVKVALPLAASLAEDAVVEDHAIRDVIPAPEGGLTSYKEAVRRALAAEKNGPLDVTFEAD
+VYDSSDPAAPLPSDPEWAGHTVYTDDRERESDLAPEDVWPVIESIGGRNGWYSTPLLWKV
+RGYMDKVVGGPGLMRGRRDQDHLRRGDAVDWWRVEEVDPGHRLTLRAEMKAGGRAWLQLT
+TEPREQGGSVYRQRAIFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEAERRRTGGARR
+RTRGLVRALADRLPLRRSPLDRRAG
+>MHAAABBN_01806
+MASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRA
+GARNPSDLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRI
+ADIVGTAADTAGVAQLVYLSGLHPDTVPVAELSDHMRSRALVAERLERAATPALTFEAGV
+IIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQACALPEPVQLRAQI
+GNGHPQSFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLA
+EEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPS
+DPEWAGTTVYTDERERESDLPAQEVWPVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGL
+TRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQLSTEPREGGGSVYRQ
+RAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRL
+PLRRNPLDRRARGAGGAQSRD
+>LFPAFLNI_02039
+MASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRA
+GARNPSDLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRI
+ADIVGTAADTAGVAQLVYLSGLHPDTVPVAELSDHMRSRALVAERLERAATPALTFEAGV
+IIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQACALPEPVQLRAQI
+GNGHPQPFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLA
+EEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPS
+DPEWAGTTVYTDERERESDLPAQEVWPVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGL
+TRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQLSTEPREGGGSVYRQ
+RAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRL
+PLRRNPLDRRARGAGGAQSRD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000522.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000522.fa
new file mode 100644
index 0000000000000000000000000000000000000000..65891a0b6ed2f95739465b31afc9c1029cfbe10b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000522.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_00697
+MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE
+YSRGSNPTRNGFETQLAALEHGERAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH
+RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH
+DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA
+EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG
+LPDHPGHDLAARQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE
+MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAVGRGTPSSSAVPRPA
+PAHHRTTRVRTPERTR
+>MOLHKGIG_02086
+MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE
+YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH
+RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH
+DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA
+EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG
+LPDHPGHALAARQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE
+MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGAPPSSAVPRPA
+PAHHRTTRARTPERTR
+>NAFOICDF_00607
+MTAVHHPTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE
+YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH
+RLITTVLEPWGVSNTPVDITDTTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH
+DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA
+EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG
+LPDHPGHDLATRQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE
+MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGTPSSSAVPRPA
+PAHHRTTRVRTPERTR
+>MHAAABBN_01791
+MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE
+YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH
+RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH
+DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA
+EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG
+LPDHPGHALAARQMDGFGGIVSVRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE
+MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGAPPSSAVPRPA
+PAHHRTTRARTPERTR
+>LFPAFLNI_02025
+MTAVHHTTRSVSRPAVRGFTTTAVHAGQEPDPLTGAVVPPIYQTSTFVQDGINVLRAGHE
+YSRGSNPTRNGFETQLAALEHGDRAFAFASGLAAEDALLRAVLRPGDHIVLGGDGYGGTH
+RLITTVLEPWGVSNTPVDITDPTAVAAAVRPGRTALLWVETPSNPLLGIADLAAWAQIAH
+DAGALLVVDNTFASPYLQRPLDLGADVVVHSTTKYIGGHSDVLGGAVVVADREFRGRALA
+EAVAYQQFAAGAVAGPQDSYLAARGLKTLGLRMDRHGANAAALAGWLQGRPEVAQVFYPG
+LPDHPGHALAARQMDGFGGIVSIRLAGGEAAARAFAEATELFALSVSLGGVESLLCYSSE
+MTHASVRGTPLAVPTDLVRLSVGIEDVADLQADLEAGLECAARVAAGRGAPSSSAVPRPA
+PAHHRTTHARTPERTR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000525.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000525.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3e5dd13323c13aaf653309590c01f94647df99aa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000525.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00700
+MDPDASPRARLTADDPRPGGRPATSTEGPHRQLDQQSSPELWGRLIAAVFALDGVEEGHS
+TVSPATSRAVHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG
+>MOLHKGIG_02083
+MDPDASPRVRLTADDPRPGSRPATSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS
+TVSPATSRALHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG
+>NAFOICDF_00610
+MDPDASPRARLTADDPRPGGRPATSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS
+TVSPATSRAVHLTGRPKERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLPPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG
+>MHAAABBN_01788
+MDPDASPRVRLTADDPRPGSRPATSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS
+TVSPATSRALHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG
+>LFPAFLNI_02022
+MDPDASPRVRLTADDPRPGSRPVTSTEGPHRQLDQRSSPELWGRLVAAVFALDGVEEGHS
+TVSPATSRALHLTGRPEERTPEVNLSPGRRWEPVHLHGVDDTSVHLVLAPERGVRLAELG
+WLEPHGYADFGTEWMLYGPRDEAELAVVVGIIEESLAYARG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000528.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000528.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e46507a0e0170818660c87f8ae6eb73c6f6d4efa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000528.fa
@@ -0,0 +1,29 @@
+>ACLBLIBL_00704
+MNLDQLQVLLRRGTPCEPTEAGVGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPAD
+VLGTWFGPVLAEAADWDDLVLDLHVEDQDHSAQLLRRGEVLAAVTTEPQPVQGCAAEPLG
+SMRYVPLVAPALLARHAAGDVVDLGAMPMMRYNVKDDLQRLALSDAGLDVAPPTLPVTRL
+VRLTRAVREAAQRTLEPG
+>MOLHKGIG_02080
+MNLDQLQALRAIADEGSFEAAAYELDVSASAVSQRIRALEREVGQVLLRRGTPCEPTEAG
+IGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPADVLGTWFGPVLAEAADWEDTVLD
+LHVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAGPLGSMRYVPLASPALLARHAADDVV
+DLGAMPMMRYNAKDDLQRLALSGAGLDIAPPTHLAPSFDGFHRSVRAGLGWGMLVDAQAV
+EDVRAGRLVRVPGLDDVLVPLYWQAATLPVTRLVRLTRAVREAAQRTLERG
+>NAFOICDF_00614
+MNLDQLQALRAIADEGSFEAAAYELGVSASAVSQRIRALEREVGQVLLRRGTPCEPTEAG
+VGLVRVARHMRVLEQEAWAGLGRMAAGRSVTSLAVPADVLGTWFGPVLAEAADWDDTVLD
+LRVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAEPLGSMRYVPLASPALLARHAAGDVV
+DLGAMPMMRYNAKDDLQRLALSGAGLDVAPPTHLAPSFDGFHRSVRAGLGWGMLVDAQAV
+EDVRAGRLVRVPGLDDVLVPLYWQATTLPVTRLARLTQAVREAAQRTLERG
+>MHAAABBN_01784
+MPKLCFMNLDQLQALRAIADEGSFEAAAYELGVSASAVSQRIRALEREVGQVLLRRGTPC
+EPTEAGVGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPADVLGTWFGPVLAEAADW
+DDTVLDLHVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAEPLGSMRYVPLASPALRARH
+AAGDVVDLGAMPMMRYNAKDDLQRLALSGAGLDVAPPTHLAPSFDGFHRSVRAGLGWGML
+VDAQAVEDVRAGRLVRVPGLDDVLVPLYWQAATLPVTRLVRLTRAVREAAQRTLERG
+>LFPAFLNI_02018
+MPKLCFMNLDQLQALRAIADEGSFEAAAYDLGVSASAVSQRIRALEREVGQVLLRRGTPC
+EPTEAGVGLVRVARHMRVLEQEAWAGLGRTAAGRSVTSLAVPADVLGTWFGPVLAEAADW
+DDTVLDLHVEDQDHSARLLRRGEVLAAVTTEPQPVQGCAAEPLGSMRYVPLASPALLARH
+AAGDVVDLGAMPMMRYNAKDDLQRLALSGAGLDVAPPTHLAPSFDGFHRSVRAGLGWGML
+VGAQAVEDVRAGRLVRVPGLDDVLVPLYWQAATLPVTRLVRLTRAVREAAQRTLERG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000529.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000529.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d56fc5fdf5e1cfce5fb6180d8cc4397dca4ac93a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000529.fa
@@ -0,0 +1,21 @@
+>ACLBLIBL_00711
+MDTSTAPGADHGRAADDISYRTRKWVKPEDLNANGTLFGGSLLRWIDEEAAIYAIIQLGN
+PRSVTKLISEINFRSSARQGDMIEMGLRAVEFGRTSLTMRAKVRNIISGEVILTIEKIVF
+VSLDEDGNPVPHGYTDITFDRDRLPQDTAR
+>MOLHKGIG_02055
+MDSTLFTRSADRAAHNDVNFRTRKWVKPEDLNANNTLFGGSLLRWVDEEAAIYATLQLGN
+PRCVTKLISEINFLASAKQGDMIEMGLRATEFGRTSLTMRAKVRNIVTGEMILTIDKIVF
+VSLGEDGKPVPHGFTEITYDRDRLPLDNPL
+>NAFOICDF_00726
+MATHHAPNLTAHEDDDVSYRTRKWVKPEDLNANGTLFGGSLLRWIDEEAAIYSIIQLGNP
+RSVTKLISEIEFSASARQGDMIEMGLRAVKFGRTSLTMRAKVRNIVTGEVILTIDKIVFV
+SLDEEGRPQPHGYTDITYDRDRLPLDTSR
+>MHAAABBN_01761
+MDSTLFTRSADRAAHDDVNFRTRKWVKPEDLNANNTLFGGSLLRWVDEEAAIYATLQLGN
+PRCVTKLISEINFLASAKQGDMIEMGLRATEFGRTSLTMRAKVRNIVTGEMILTIDKIVF
+VSLGEDGKPVPHGFTEITYDRDRLPLDNPL
+>LFPAFLNI_01989
+MPAATVKPSTGTSRQVASGVAGSGWGRMVIGRVPPVWSVADPSGDPTARSSTSPHRAPSL
+VPASASLYRGAMDSTLFTRSADRAAHDDVNFRTRKWVKPEDLNANNTLFGGSLLRWVDEE
+AAIYATLQLGNPRCVTKLISEINFLASAKQGDMIEMGLRATEFGRTSLTMRAKVRNIVTG
+EMILTIDKIVFVSLGEDGKPVPHGFTEITYDRDRLPLDNPL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000530.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000530.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c5e204371baed08e2837a7bdddf91b870299b59a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000530.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_00715
+MTLTPPHAPALPAGASAHIRAECITLTLGDRTVLDQADVTVSAGSRLAIVGENGRGKTTL
+LHVLAGTLAPDAGTVTRAGTLALVEQDLDADDDRTVGDLIHDAVGESLAVLDRLEAATRA
+LAEGRPGADDDYARALETATALEAWDAERRIDVALEGLSACTDRTRPLNSLSVGQRYRVR
+LAVVLGSAVDLLLLDEPTNHLDAGALEHLTRALREHPGGVAVVTHDRALLKDVAETFLDL
+DPTSDGRPRQYAGGYAGWEKGRSAERAAWEQAHEQQVAEHAALAEAAEAARGRLQDRWRP
+DKGTGKHQRATRAAGVVQAFNRRVRDLEAHEVTVPEPPRALAWPASSTRAARPLLNAEGV
+DVAGRLRGPVSADLTGGDRLLLTGPNGAGKSTLLHVLAGRLDPTAGRVLRHTGARIALLT
+QEAPAWNPRHTARQAFEVHLHRRGLLADDDGGAPPLASLGLLEPRSMDAPVGRLSQGQQR
+RLHLALCLAERPDLLMLDEPSNHLSATLVDELTEALRATRSAVVVATHDRQMLRDLSDWP
+RLELTAEAVAR
+>MOLHKGIG_02241
+MTSGPPSPALPAGPAAHLRGEHLTVSLGGHRVLTDATVRINAGSRLGIVGENGRGKTTLL
+HVLTGRITPDVGRVTRAGTLAFVPQALRARADGRSRTVGDLVRDALTGPHAALEALDAAA
+AALAEAPDDAGAGHRYSTALERAHLYDAWDAGRRVDMDLEGLHACTDREHPLTSLSVGQR
+HRVRLAVTLGSRPDLLLLDEPTNHLDDVALDFLTRRLVEHPGGVAVVSHDRALLRAVCTD
+IVDLDPSQDGRPRRYSGGYAGWAKGRRRARAAWEQEYAEQNAERERLELAVEDAREQMQG
+SWRPPKGTGKHQRSSRSAGIVQMFNRRFDELEAHRITVPEPPLRLDWPFADMPDGDPRDG
+ADAAAGTAGGPGTAGDDVLLTADAVRVAGRLEQPMGAALVPGGRVLVTGPNGAGKSTLLR
+VLAGDLEPTSGLVTVGADVRVRLVAQETPAWDEERTAAAVFEEHVRRVGADEAGVDDLGR
+PLPAPTLPSLGLLTAEAADTPVGRLSQGQQARLHLAMVLIERPHVLLLDEPTNHLSPALV
+DEMTEALQVTEQAVVVVTHDRQMLADLADWPRVELRTDAAAV
+>MHAAABBN_01943
+MTSGPPSPALPAGPAAHLRGEHLTVSLGGHRVLTDATVRINAGSRLGIVGENGRGKTTLL
+HVLTGRITPDVGRVTRAGTLAFVPQALRARADGRSRTVGDLVRDALTGPHAALEALDAAA
+AALAEAPDDAGAGHRYSTALERAHLYDAWDAGRRVDMDLEGLHACTDRERPLTSLSVGQR
+HRVRLAVTLGSRPDLLLLDEPTNHLDDVALDFLTRRLVEHPGGVAVVSHDRALLRAVCTD
+IVDLDPSQDGRPRRYSGGYAGWAKGRRRAQAAWEQEYAEQNAERERLELAVEDAREQMQG
+SWRPPKGTGKHQRSSRSAGIVQMFNRRFDELEAHRITVPEPPLRLDWPFADMPDGDPRDG
+ADAAAGTAGGPGTAGDDVLLTADAVRVAGRLEQPMGAALVPGGRVLVTGPNGAGKSTLLR
+VLAGDLEPTSGLVTVGADVRVRLVAQETPAWDEERTAAAVFEEHVRRVGADEAGVDDLGR
+PLPAPTLPSLGLLTAEAADTPVGRLSQGQQARLHLAMVLIERPHVLLLDEPTNHLSPALV
+DEMTEALQVTEQAVVVVTHDRQMLADLADWPRVELRTDAAAV
+>LFPAFLNI_02173
+MTSGPPSPALPAGPAAHLRGEHLTVSLGGHRVLTDATVRINAGSRLGIVGENGRGKTTLL
+HVLTGRITPDVGRVTRAGTLAFVPQALRARADGRSRTVGDLVRDALTGPHAALEALDAAA
+AALAEAPDDAGAGHRYSTALERAHLYDAWDAGRRVDMDLEGLHACTDRERPLTSLSVGQR
+HRVRLAVTLGSRPDLLLDEPTNHLDDVALDFLTRRLVEHPGGVAVVSHDRALLRAVCTDI
+VDLDPSQDGRPRRYSGGYAGWAKGRRRARAAWEQEYAEQNAERERLELAVEDAREQMQGS
+WRPPKGTGKHQRSSRSAGIVQMFNRRFDELEAHRITVPEPPLRLDWPFADRPDGDPRDGA
+DAAAGTAGGPGTAGDDVLLTADAVRVAGRLEQPMGAALVPGGRVLVTGPNGAGKSTLLRV
+LAGDLEPTSGLVTVGADVRVRLVAQETPAWDEERTAAAVFEEHVRRVGADEAGVDDLGRP
+LPAPTLPSLGLLTAEAADTPVGRLSQGQQARLHLAMVLIERPHVLLLDEPTNHLSPALVD
+EMTEALQVTEQAVVVVTHDRQMLADLADWPRVELRTDAAAV
+>LFPAFLNI_02213
+MPTSRSLRSCVWNGTPQGHAAHIRAESIHITLGDRHVLNGVDVTVSVGSRLAIVGDNGRG
+KTTLLHLLAGILQPDSGVVTQAGSLVLVKQDMATEGDRTVGDLIAEATGPSKSALEALDA
+TSAALAEGDDAADAYSAALERATLLDAWDAERRVDIALEGLNACSDRDRVLSTLSVGQRY
+RVRLAVALGSTPDLLLLDEPTNHLDAAGLSFLTERLRDHAGGLALVSHDRALLRDVATTF
+LDLDPTRDGRPRTYAGGYQGWVEGRQRERVSWEQDHAAQVARHAQLTRAAAEARSRLSQG
+GWRPDKGTGKHQRATRAAGVVQAFNRRVEDLERHEIDVPEPPLRLAWPKSSARRGMSIVN
+ASMLTVERRLDTPVSIGVNGGDRLVVTGPNGAGKSTLLAVLGQRLVPTTGYVQVNPSARI
+ALLSQEVPDWDRTSPAHVAYETYLGKLGCRSQAPSLGSLGLLEASATSTPVGRLSQGQQR
+RLHLALCLAQDPDLLLLDEPTNHLSSSLVDDITTELLQTPCAVIVATHDRQMLDDLADWP
+HLDLDPKDMP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000532.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000532.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1127b9e3f09a19095c6511bea609e4aa210e691f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000532.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_00728
+MRATTHTPVEELETDDEHETPWWADRAVLIPIASGVAFVAGLACEWSGAQSAALVLFWVG
+LLLGASTFVPGALRKLATGKLGIALLMTMSATGAVILGHVEEAAALAFLYSIAEALEDRA
+MDRARAGLRALLKLVPQSATVLTDGHSASVPARDLAAGQVMLIRPGERIATDGIVRSGHS
+SVDTSAITGESIPVEVGPGDEVSAGAINAAGALQVEATAPGTDNSLTTIVSLVERAQAEK
+GQRARLADRIARPLVPGVLVLAVLVALIGSLAGDPQTWITRALVVLVAASPCALAIAVPI
+TVVSAVGSASKFGVIIKSGAIFERFGDIGHVAFDKTGTLTRNQPTVTAVVPAADVTEQQV
+LAWAAALEQHSTHPLATAITHAAPHNPRRPGHHRGSRPRNPRHRRRRRSAGRQPPLGRPR
+RPHLPGP
+>ACLBLIBL_00729
+MLVGSPRWVDPGDLTYRVRDLEAQGMTVVVVHRDGAVAGAIGVRDELRPEVPEVITTLAG
+QGIDVTMLTGDNERTARALAAQAGISDVRAELRPEGKSAAVGELSVRRPTAMIGDGINDA
+PALAAADVGIAMGATGSDAAIESADIAFTGQDLRLLPQAIAHARRGRRIVNQNIVLSLLI
+IAALPPLAITGVLGLAAVVLIHEVAEVLVILNGLRAARTHQPTRGH
+>ACLBLIBL_02365
+MVPVFSGVAFLTGLVLEWAGLEVPALVLFWIGLLLGASTFTPGAIRKLFKGKLGIGLLMT
+ISAVGAVILGYVEEAAALAFLYSIAEALEDKAMDRARGGLRALLKLVPETATIRRDGASV
+EVPAKDLAVGQLMLVRPGERIATDGIVRTGRSSLDTSAITGESIPVEVEPGDTVSAGAIN
+TAGALEVETTAAGTDNSLTTIVDLVEKAQADKGDRARLADRIARPLVPGVLILAALVAII
+GSLLGDPELWITRALVVLVAASPCALAISVPLTVVAAIGSASKFGVIIKSGAVFERFGVI
+RHVAVDKTGTLTRNEPAVTAVLTAEGVTEKQALAWAAALEQHSTHPLAAAITAAAPGAPA
+ADGVTEQAGHGIEGTLDGARITVGSPRWLDAGTLGEQVAGLEEQGMTVVIVHRDGTPVAA
+IGVRDELRPEVPEVVRTLAAQGIGVTMLTGDNARTARALAAQAGIGDVRAELRPEDKAAA
+IAELGEKGAVAMIGDGINDAPALAAADIGIAMGATGSDAAIESADVAFTGHDLRLLPRAF
+DHARRGRHIINQNLILSLLIITALLPLALFGVLGLAAVVLVHEIAEVVVILNGLRAARTR
+KSAA
+>MOLHKGIG_00608
+MSSACGCEAPTPGAPEEPEEHRPWWRDAAILLPVLSGVAFIAGLVLEWSGAGLVATVVFW
+VGLVLGAWTFVPGALRGLFTRGRLGIGLLMTISAIGAVILGYIEEAAALAFLYSIAEALE
+DKAMDRARAGLRALLKLVPETATIRQGGATVQVEAKDLHPGQVLVVRPGERIATDGIVRT
+GRSSLDTSAITGESIPVEVGPGDTVSAGSINTSGALEIDATAAGTDNSLTTIVHLVEQAQ
+TEKGARARLADRIAKPLVPGVLVLAVLVAALGSLFGDPELWITRALVVLVAASPCALAIA
+VPVTVVSAIGAASRFGVVIKSGAAFERLGGIRHLAVDKTGTLTRNQPTVTAVLTTPGLTE
+DQVLGWAAALEQHSTHPLAAAIIAAAPDAPGAKAVTETAGHGITGRIDGATITVGSPRWL
+DPGPLAAQVQQLEDQGMTVVIIHRDGTVAGAIGVRDELRPEVPAVVTTLTGQGIGLTMLT
+GDNARTARAIAAQAGIGDVRAELRPEDKAAAVGQLTGTRPTAMIGDGINDAPALAAAEVG
+IAMGATGSDAAIESADVAFTGHDLRLIPQALAHARRGRAIMNQNIVLSLLIIGVLLPLAI
+TGMLGLAAVVLVHEVAEVIVIGNGLRAATTRRTALASLTDRQAQRSTVG
+>MHAAABBN_01768
+MSAACGCEAPTPTPGAPEEHEEHRPWWRDAAILLPALSGLAFLTGLVLEWSGAGLVATVV
+FWVGLVLGAWTFVPGALRGLFTRGRLGIGLLMTISAIGAVILGYIEEAAALAFLYSIAEA
+LEDKAMDRARAGLRALLKLVPETATIRAGGATVEVEAKDLRPGQVLVVRPGERVATDGIV
+RTGRSSLDTSAITGESIPVEVGPGDTVSAGSINTAGALEIDATAAGTDNSLTTIVHLVEQ
+AQAEKGDRARLADRIAKPLVPGVLILAVLVAALGSLLGDPELWITRALVVLVAASPCALA
+IAVPVTVVSAIGAASRFGVVIKSGAAFERLGGIRHLAVDKTGTLTRNQPTVTAVLAAPGI
+TEDQVLGWAAALEQHSTHPLAAAITAATPDTPAAEGVTETAGHGITGRLDGATVTVGSPR
+WLAPGPLAAQVQGLEDQGMTVVIIHRDGAVAGAIGVRDELRPEVPTVVTTLTGQGIDLTM
+LTGDNARTARAIADQAGIDDVRAELRPEDKATAVHQLTGTRPTAMIGDGINDSPALAAAE
+VGIAMGATGSDAAIESADVAFTGHDLRLIPQALAHARRGRAIINQNIILSLLIIAVLLPL
+AITGVLGLAAVVLVHEVAEVIVIGNGLRAATTRRTALEPLTDRQAQPATTG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000533.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000533.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24b0647321993d3373fe4f89946a3102b0a0cf92
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000533.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00760
+MPTSDTLASGRPAHSTDDRRPRRSSAGSGLARVAVFAALMAVLGLVPPVPVAGIPAPIVL
+QNLAVTLAGVILGPWRGAAAILLFNVLVALGLPLLTGGRGGLGVFVGPSSGFILGYVVAA
+AAVGLVFWALTGRARPGLRPGRVLAAALVAGLVGMVVLYAAGAVGFIVAAHMEPGAAVLA
+MGAFVPGDTVKVVLAALLVTGLWKAYPRAFR
+>MOLHKGIG_02058
+MSTSVPSSHDGHVRPAATTTADRPTDAGRPRRGSAGGSLARIAVMTALMAVLGLVPPIAV
+AGVPAPIVLQNIAVILAGVILGPWRGAASMALFAGLVALGLPLLSGGRGGLGVFAGPTAG
+FILGWIPSALIVGLIFWALTSRARPGLDAGRVALGAAVAGLIGGVVMVYFFGVLGFVGIA
+GMEFGAAVLSMAPFVPGDLIKLVVSVILIVGLWKAYPRAFR
+>NAFOICDF_00723
+MTSPSAPQTAVVDAPATHRPRRSPGADLARIAVMAALIAVLGAMPGIPVPGIPTPITLQT
+LGVMLAGLVLGAWRGAASVALFHLLVALGLPLLAGGRGGAAVFVGPSAGFLWGWIPGAFV
+VGLLFHLYLRGRRDGRNTGGLVAAALTACVVGGIAVIYLFGIPGMNLFGGVPLDKAAIGS
+LAFIPGDLLKAVVAALLAAGLWKAYPRAFA
+>MHAAABBN_01764
+MSTSVPSSHDGHVRPAATTTADRPTDAGRPRRGSAGGSLARIAVMTALMAVLGLVPPIAV
+AGVPAPIVLQNIAVILAGVILGPWRGAASMALFAGLVALGLPLLSGGRGGLGVFAGPTAG
+FILGWIPSALIVGLIFWALTSRARPGLGAGRVALGAAVAGLIGGVVMVYFFGVLGFVGIA
+GMEFGAAVLSMAPFVPGDLLKLVVSVILVVGLWKAYPRAFR
+>LFPAFLNI_01994
+MSTSVPSSHDGHVRPAATTTADRPADAGRPRHGSAGGSLARIAVMTALMAVLGLVPPIAV
+AGVPAPIVLQNIAVILAGVILGPWRGAASMALFNALVALGLPLLTGGRGGLGVFVGPSVG
+FILGWIPSAMIVGLIFWALTSRSRPGLSAGRIALAAAVAGLIGGVIMVYVFGAFGFVGVQ
+GMEFGAAMLSMAVFVPGDLTKLVIAVLLCAGLWKAYPRAFR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000539.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000539.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f25555c5923c95e14378956d2601b31ff77d293
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000539.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_00780
+MDVQQFFADLSDVPWLLTTLDLIGIFFFATSGALLASRKEFDLVGSMALALLAGLGGGFT
+RDILLDRGLPASLENPIYLAPPVLVSLLVYVKALHPNRLNLTITLFDAGGLALFTVSGVL
+IAHSMDVHPVSTVVVAMVAALGGGVLRDIVANEVPSIFDPRGVYVMPTFVGATVATIAAM
+NGVLNAFTGFLIAFLIFAVRMLAYRYQWRLFGADISQDKESLDRLRRLATQAQDAAARRV
+ERARERRLRSASGPGGMDVGEAEAIADRAVHHPPAPAGYHYDAVEDAYTRDHAFDDDGEP
+GSASYGPRQEYEDQVRVDEYDPETQTITVIDPASRQQVRLDPATGVMDVTDLRTGRTRSY
+DDPEHDWIADDAEDDARG
+>MOLHKGIG_02036
+MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT
+RDILLDRGLPASLENPVYLAPPLLVSLLVYVKVIHPNRLNLTITLFDAAGLALFTVSGVL
+LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM
+NGALNAFTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLARLRRLATQAQEAAARRV
+ERTLERRLRSPGAPAFPDDDADGSYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRL
+DRGTGVMDVTDLRTGRTRSFDDPEHDWIADDPEDEKG
+>NAFOICDF_00747
+MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT
+RDILLDRGLPASLENPVYLAPPVLVSLLVYVKLIHPNRLNLTITLFDAAGLALFTVSGVL
+LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM
+NGALNAFTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLERLRRLATQAQEAAARRV
+ERTLERRLRAPGAPAFPDDDTHGSYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRL
+DRGTGVMDVTDLRTGRTRSFDDPEHDWIADDPEDSRD
+>MHAAABBN_01743
+MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT
+RDILLDRGLPASLENPVYLAPPLLVSLLVYVKVIHPNRLNLTITLFDAAGLALFTVSGVL
+LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM
+NGALNGYTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLERLRRLATQAQEAAARRV
+ERTLERRLRSPGAPAFPDDDTHGSYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRL
+DRGTGVMDVTDLRTGRTRSFDDPEHDWIADDPADPRD
+>LFPAFLNI_01971
+MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT
+RDILLDRGLPASLENPVYLAPPLLVSLLVYVKVIHPNRLNLTITLFDAAGLALFTVSGVL
+LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM
+NGALNGYTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLERLRRLATQAQEAAARRV
+ERTLERRLRSPGAPAFPDDDTHGSYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRL
+DRGTGVMDVTDLRTGRTRSFDDPEHDWIADDPADPRD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000543.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000543.fa
new file mode 100644
index 0000000000000000000000000000000000000000..910f0c375231aae2326df3486d026c24c6704797
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000543.fa
@@ -0,0 +1,27 @@
+>ACLBLIBL_00787
+MTELDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKWWDAPYFHAA
+DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGSGWWELGILLFDP
+TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW
+EGRRWDSVRLALLRRDWDSARASV
+>MOLHKGIG_02033
+MTDLDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKSWDAPYFHAA
+DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGAGWWELGILLFDP
+TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW
+EGRRWDSVQLAVLRRDWWPASTDG
+>NAFOICDF_01226
+MDTHRSTPVVALRPVEAGDEEFLWTWIHGTPDAEWKRWDAPYFHAAEQAAPMGRAAFARS
+FAPWPDDADRRIITADGAAIGLVTRHEEAPAGGGWWELGILLFDPSRWGGGIGTRALAAW
+TEATLTETDAHVLTLTTWSGNARMAGAAERAGFRMCARVPESRAWDGRRWDSLRFALLRG
+DHEGEQASAPEPPARRPELADLTVVTGRIPDAAALRALYDAVGWTAYTRNPDALAAGVAG
+SACVATAWAGQELVGLARVVSDGHTIAYLQDVLVHPERRRQGVAGKLLDAVFAPFAHVRQ
+QVLITDEEPGQRAFYEACGFRQFGGGGPVPGRTFVRFAG
+>MHAAABBN_01740
+MTDLDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKSWDAPYFHAA
+DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGAGWWELGILLFDP
+TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW
+EGRRWDSVQLAVLRRDWWPASTDG
+>LFPAFLNI_01968
+MTDLDPATPRPSGTRADAPPRTDVALRPVAADDADFLWTWIHGAEDPEWKSWDAPYFHAA
+DTAAPPSRADFDADHARRRVGDPDVRVVTVDGTPVGLVTRTEQHPAGAGWWELGILLFDP
+TTWGRGVGRAALTLWSDASFAETDAHLLSLVTWSGNARMIASAVRVGYTEVARIPEARSW
+EGRRWDSVQLAVLRRDWWPASTDG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000545.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000545.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3472c737f66c026ea7506ef23e9d3564c80a6fde
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000545.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_00792
+MLEASIPNPYTPAPLPAPADRGAQDPEETMSRDQIEALQFERLRWSLHHAYENVPAYTEH
+FDAHGVHPSDFKALEDLAKFPYTDKEFLRKNYPFGAFAAQGPELRRIHASSGTTGQPTVV
+GYTDDDLATWATLVARCFRAGGIRPGDRVHNAYGYGLFTGGLGAHYGAERIGAAVIPMSG
+GQTEKQVQLITDFQPRAILSTPTYLLTIADGFKKLGLDPRESSLEVAILGAEPWTDEMRR
+EIEQTFDLDALDIYGLSEVMGPGVAGESAATKDGSHIWEDHFRPEIIDPLTDEVLETGRH
+GELVFTSLTKQALPIIRYRTHDLTRLLPGTTHPGHRRMGRITGRSDDMIILRGVNLFPSQ
+IEELALKEPALSPHFTLEITRPDRMDQMAVNIERRDHATLEEAQACAAHLRMEIKTKIGS
+SCVINVVEPETLARSSGKLKRIYDLRDKG
+>MOLHKGIG_02027
+MLEASIPNPYTPAPLPAPADRGAPDPEETMSRDQIEALQFERLRWTLHHAYENVPAYREH
+FDAHGVHPSDFTELGDLAKFPYTDKEFLRKSYPFGAFAATGPELRRIHASSGTTGQPTVV
+GYTDDDLATWATLVARCFRAGGIRPGDRVHNAYGYGLFTGGLGAHYGAERIGAAVIPMSG
+GQTEKQVQLITDFQPRAILSTPTYLLTIADGFKKLGLDPRESSLEVAILGAEPWTEEMRR
+EIEQTFDLDALDIYGLSEVMGPGVAGESAATKDGSHIWEDHFRPEIIDPLTDEVLETGRH
+GELVFTSLTKQALPIIRYRTHDLTRLLPGTTHPGHRRMGRITGRSDDMIILRGVNLFPSQ
+IEELALKEPALSPHFTLEITRPDRMDQMAVNIERRDHATLEEAQACAAHLRMEIKTKIGS
+SCVINVVEPETLARSSGKLKRIYDLRDQA
+>NAFOICDF_00753
+MLEASIPNPYSPAPVPAPADRGAPDPEETMSRDQIEALQFERLRWTLHHAYENVPAYKEH
+FDNHGVHPSDFTALEDLELFPYTDKEFLRKSYPFGAFAATGPELRRIHASSGTTGQPTVV
+GYTDDDLATWATLVARCFRAGGIRPGDRVHNAYGYGLFTGGLGAHYGAERIGAAVIPMSG
+GQTEKQVQLITDFQPRAILSTPTYLLTIADGFRKLGLDPRESSLEVAILGAEPWTEAMRR
+EIEQTFDLDALDIYGLSEVMGPGVAGESAATKDGSHIWEDHFRPEIIDPLTDEVLETGRP
+GELVFTSLTKQALPIIRYRTHDLTRLLPGTTHPGHRRMGRITGRSDDMIILRGVNLFPSQ
+IEELALKEPALSPHFTLEITRPDRMDQMAVNIERREHATLEEAQACAAHLRMEIKTKIGS
+SCVINVVEPETLARSSGKLKRIYDLRDQA
+>MHAAABBN_01736
+MLEASIPNPYTPAPLPAPADRGAPDPEETMSRDQIEALQFERLRWTLHHAYENVPAYREH
+FDAHGVHPSDFTELGDLAKFPYTDKEFLRKSYPFGAFAATGPELRRIHASSGTTGQPTVV
+GYTDDDLATWATLVARCFRAGGIRPGDRVHNAYGYGLFTGGLGAHYGAERIGAAVIPMSG
+GQTEKQVQLITDFQPRAILSTPTYLLTIADGFKKLGLDPRESSLEVAILGAEPWTEEMRR
+EIEQTFDLDALDIYGLSEVMGPGVAGESAATKDGSHIWEDHFRPEIIDPLTDEVLETGRH
+GELVFTSLTKQALPIIRYRTHDLTRLLPGTTHPGHRRMGRITGRSDDMIILRGVNLFPSQ
+IEELALKEPALSPHFTLEITRPDRMDQMAVNIERRDHASLEEAQACAAHLRMEIKTKIGS
+SCVINVVEPESLARSSGKLKRIYDLRDQA
+>LFPAFLNI_01964
+MLEASIPNPYTPAPLPAPADRGAPDPEETMSRDQIEALQFERLRWTLHHAYENVPAYREH
+FDAHGVHPSDFTELGDLAKFPYTDKEFLRKSYPFGAFAATGPELRRIHASSGTTGQPTVV
+GYTDDDLATWATLVARCFRAGGIRPGDRVHNAYGYGLFTGGLGAHYGAERIGAAVIPMSG
+GQTEKQVQLITDFQPRAILSTPTYLLTIADGFKKLGLDPRESSLEVAILGAEPWTEEMRR
+EIEQTFDLDALDIYGLSEVMGPGVAGESAATKDGSHIWEDHFRPEIIDPLTDEVLETGRP
+GELVFTSLTKQALPIIRYRTHDLTRLLPGTTHPGHRRMGRITGRSDDMIILRGVNLFPSQ
+IEELALKEPALSPHFTLEITRPDRMDQMAVNIERRDHATLEEAQACAAHLRMEIKTKIGS
+SCVINVVEPESLARSSGKLKRIYDLRDQA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000547.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000547.fa
new file mode 100644
index 0000000000000000000000000000000000000000..524eb8de43fde2740aeea55dad8fd819a7d85acf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000547.fa
@@ -0,0 +1,33 @@
+>ACLBLIBL_00794
+MTPSRLPLLGVLAVGALALAGCAGGGAEPSSPAPSPASSSASPTTTAASSASTSPAASAS
+ASSTPTATALSLDLPEELSGESATRLRAVVQDAAGPAAELGQTFSSPLERRAALEEDAAI
+VDALEEDAGDDAGRRACVDATRAAREADQASGAAQAAWYAQPQTASTTGGSTDGTAASGR
+PGLQVEPLGVQVAVYPDEATARSVAEAARDAAEACEGQEMSSMGVSSVEPLTGAPGETAF
+TVVPVSGSIIYAVSTVVQVGDRVYAVSQGEDGAGVPEGAEERAVALVEDLEAALEG
+>MOLHKGIG_02025
+MTTSRLPLLGALAVGALALAGCAGGGAEPSSPAPSSASSTTTAASSASPAASSSTAPTSP
+AASASTASMGGASASGSLSLEMPPALDGQRTLAVQAAVQRAAGPGSEVGLSAASPLERQT
+ELRQRAAGLEQTVDAGASPASTRSAEQQACLDATRSDLERDAEAGAADLGLTAQPETAAT
+TGGGPTSTPVPSFTASPDAEVTPLGVRVTVYPTEEAARAALEDARAAAQACTGVDLAGLG
+VESVTRTEHEGGTAYTALPAPGGSVYSHLTAVQDGARTVAVAQADADGGVPADAEDRAAS
+IVADVLAALDGEG
+>NAFOICDF_00756
+MTHMTAVPSRRLRAGFALGAAALVLTGCAGGGGSASSSTAAGSPTAGGAGSSVTSPAASS
+SAASSSALSLSMPDRFGNEARTGLTEAVTAAAPEGFEVTTRSVSPLERKTDLEDQATILT
+DGPLEPAAEGSSASPTYTEAQQRCADAAAERFRTEAAAGGAQLRSDAMPTVAGGGYTSVR
+ADVVAYPDVSAAVAALADGSAPIELCTDVQVPGAEQPTDIAPVTGIGDEAVGGELAGGRW
+LAVRRGTDVVSVMVAGPGETAPAGAADQARALAEQVLEAVPAG
+>MHAAABBN_01734
+MTTSRLPLLGALAVGALALAGCAGGGGAEPSSPAPSSASSTTTAASSAPTSPAASSSTES
+TGAAESTAGASASGSLSLEMPPALDGQRTLAVQAAVQRAAGPGSEVGLSAASPLERQTEL
+RQRAAGLEQAVDAGASPASTRSAEQQACLDATRSDLERDAEAGAADLGLTAQPETAATTG
+GGPTTTPAPSFTASPDAEVTPLGVRVTVYPTEEAARAALEDARAAAQACTGVDLAGLDVE
+SVTRTEHEGGTAYTALPAPGGSVYSHLTAVQDGARTVAVAQADADGGVPADAEDRAASIV
+ADVLAALDGEG
+>LFPAFLNI_01962
+MTTPRLPLLGALAVGALALAGCAGGGGAEPSSPAPSSASSTTTAASSASTSPAASSSTAP
+TSPAASASTESTAGASASSSLSLEMPPALDGQRTLAVQTAVQRAAGPGSEVGLSAASPLE
+RQTELRQRAAGLEQAVDAGASPAPTRSAEQQACLDATRSALERDAEAGAADLGLTAQPET
+AATTGVGPTTTPAPSFTASPDAEVTPLGVRVTVYPTEEAARAALEDARAAAQACTGVDLA
+GLGVESVTRTEHEGGAAYTALPAPGGSVYSHLTAVQDGARTVAVAQADADGGVPADAEDR
+AASIVTDVLAALDGEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000548.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000548.fa
new file mode 100644
index 0000000000000000000000000000000000000000..771adbc9ee0ab12a098c0d28340a9df900884a2f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000548.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00795
+MSEFTRFEQVAVLGTGVLGSQIIMQAAYHGKKVMAYDAVPAALEGIERRWAWIRQGYEAD
+LGEGYDPQRFDEAIARITPTSDLGEALADADIVIEAVPENLELKRKVWAQVGELAPATTL
+FATNTSSLLPSDFADASGHPERFLALHYANRIWAQNTAEVMGTAATSPEAVAGALQFAEE
+TGMVPVHVRKEIPGYFLNSLLIPWLQAGSKLYMHGVGNPADIDRTWRVATGNERGPFQTY
+DVVGFHVAANVSRNTGVDWQRGFAELLEKSIAEGHSGVADGQGFYRYGPDGENLGPVEDW
+NLGDKDTPLG
+>MOLHKGIG_02024
+MSEFTRFDQVTVLGTGVLGSQIIMQAAYHGKRVMAYDAVPAALEGIERRWAWIRQGYEAD
+LGEGYDPQRFDEAIARITPTSDLGEALADADIVVEAVPENLELKRKVWAQVGELAPATTL
+FATNTSSLLPSDFADASGHPERFLALHYANRIWAQNTAEVMGTAATSPEAVAGALQFAEE
+TGMVPVHVRKEIPGYFLNSLLIPWLQAGSKLYMHGVGNPADIDRTWRVATGNERGPFQTY
+DIVGFHVAANVSRNAGADWQRGFAELLEKSIAEGHSGVADGQGFYRYGPDGENLGPVEDW
+NLGDKDTPLG
+>NAFOICDF_02090
+MTTIQKVTVFGTGVLGSQIIMQAAYHGKDVTAYDVDDKALAQLPARWEWMRGYYQRDLPD
+FDAERFDKAVSSIRTTTDVADAVTDADVVIESIPENLELKKSVWAKIGEAVPERTVLLTN
+TSSLLPSSFADSTGHPERFLALHFANLVWKNNTGEVMATAKTAPEHFDAVLAFAGEIGLV
+PVPVRKEVPGYVLNSLLIPWLDAGAKLYQGGVSDPEDIDNVWKIATGAPKGPFEVYDVVG
+FNVAYNISRVSADPLKKAFAEETLKKGIDAGTTGLGVGEGFYRYDKDGNNLGAVESWKQE
+NRG
+>MHAAABBN_01733
+MSEFTRFDQVTVLGTGVLGSQIIMQAAYHGKKVMAYDAVPAALEGIERRWAWIRQGYEAD
+LGEGYDPQRFDEAIARITPTSDLGEALADADIVIEAVPENLELKRKVWAQVGELAPATTL
+FATNTSSLLPSDFADASGHPERFLALHYANRIWAQNTAEVMGTAATSPEAVAGALQFAEE
+TGMVPVHVRKEIPGYFLNSLLIPWLQAGSKLYMHGVGNPADIDRTWRVATGNERGPFQTY
+DIVGFHVAANVSRNTGVDWQLGFAELLEKSIAEGHSGVADGQGFYRYGPDGENLGPVEDW
+NLGDKDTPLG
+>LFPAFLNI_01961
+MSEFTRFEQVAVLGTGVLGSQIIMQAAYHGKKVMAYDAVPAALEGIERRWAWIRQGYEAD
+LGEGYDPQRFDEAIARITPTSDLGEALADADIVIEAVPENLELKRKVWAQVGELAPATTL
+FATNTSSLLPSDFADASGHPERFLALHYANRIWAQNTAEVMGTAATSPEAVAGALQFAEE
+TGMVPVHVRKEIPGYFLNSLLIPWLQAGSKLYMHGVGNPADIDRTWRVATGNERGPFQTY
+DIVGFHVAANVSRNTGVDWQLGFAELLEKSIAEGHSGVADGQGFYRYGPDGENLGPVEDW
+NLGDKDTPLG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000549.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000549.fa
new file mode 100644
index 0000000000000000000000000000000000000000..96e6ace79351565a2804713ce408cfe075c55aa2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000549.fa
@@ -0,0 +1,65 @@
+>ACLBLIBL_00796
+MTVTLPSLPEILPSYVNGAWWTPQSPSKVTDVTDANTGERLTGVSTDGLDTAAAIEHART
+VGRKSLGELTIHERALKLKELALYLNSRIQELYDVSFATGATQRDHAFDVDGGIGTLFTF
+SGKGRRELPNSNVITDGPVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP
+SFVAGVPTVVKPATPTGYVTQKCVELMLESGVLPEGSLQLISGSARDLLDHLDYRDHVSF
+TGSAATAQTLRKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVK
+AGQKCTAIRRVIVPQDRVDAVVEALSARLGKVVLGDPRVEGTTMGALASKEQQGEVRGAV
+QRLVDAGGQVRLGGPDASTGDADAESGAFFAPTVLSFEDARTPEVHAVEAFGPVTSVVGY
+TDVEDAVALAALGSGSLVATVATDDGETARAFAAGIGAHHGRVHFLNRQTATTTTGHGAP
+VPVLVHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTRED
+VEAGTAVHPFYKSLAELTVGDQFASGLRTVTLQDITDFAEETGDKFYAHTDEEAAMANPF
+FPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFITPVTYDDAIRVTLTAKRITPR
+VSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG
+>MOLHKGIG_02023
+MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGARLTGVSTDGLDTAAAIEHART
+VGQQALGALTIHERALKLKELALYLNSRVQELYDVSFATGATQRDHAFDVDGGIGTLFTF
+SGKGRRELPNSNVIIDGDVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP
+AFVAGVPTVVKPATPTGYVAQKCVELMLESGVLPEGSIQLISGSARDLLDHLDYRDHVAF
+TGSAATAATLKKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVK
+AGQKCTAIRRVIVPQDRVEAVTAALTERLAAKVVLGDPRVEGTTMGALASKEQQGEVRGA
+VQRLVDAGGQVRLGGPEGSTGDADAESGAFFAPTVLTFEDARTPEVHSVEAFGPVTSVIG
+YTDVADAVALAALGSGSLVATVATNDGETARAFAAGIGAHHGRVHVLNRQTATTTTGHGA
+PVPVLIHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTRE
+DVEAGTAVHPFYKSLAELTVGDQFASGLRTVTLEDITAFAEETGDRFYAHTDEEAAMANP
+FFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFITPVTYDDAIRVTLTAKRITP
+RVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG
+>NAFOICDF_00757
+MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGELMARVSTDGIDTAGAIEHART
+VGQRNLGELTIHERALKLKELALYLNSRIQELYDLSFATGSTQRDHAFDVDGGIGTLFTF
+SGKGRRELPNSNVIIDGDVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP
+AFVAGVPTVVKPATPTGYVTEACVRMMVESGVLPEGSIQLISGSARDLLDHLDYRDHVAF
+TGSAGTAQTLRQHENVLNGGVRFTAETDSLNAAILGPDAGVDTPEFEAFVKVVFQEMTVK
+AGQKCTAIRRVIVPEAMVEDVTAALTERLSSTVVLGDPRAEGTTMGALASKEQQSEVRKA
+VQTLVDAGGQVRLGGPEGSTGDADAEAGAFFAPTVLTFADADTPQVHSVEAFGPVTSVIG
+YTDVADAVRLAALGSGSLVATLATNDGATASEFIAGIGAHHGRVHVLNRQTAKTTTGHGA
+PVPVLIHGGPGRAGGGEELGGVRAVKHYMQRTAVQGSPDMLTAITGVWHQGAAAQTATRE
+DVEAGKAKHPFYKALDELQIGDQFASGLRTVTIEDITAFAESTGDKFYAHTDEEAAMANP
+FFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLDDLRFITPVTYDDAIRVTLTAKRITP
+RVTDEYGEVAWDCRLHNQKDELVAQYDVLTLVAKTWPMPEAEPKA
+>MHAAABBN_01732
+MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGARLTGVSTDGLDTAAAIEHART
+VGQQALGELTIHERALKLKELALFLNSRVQELYDVSFATGATQRDHAFDVDGGIGTLFTF
+SGKGRRELPNSTVIIDGDVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP
+AFVAGVPTVVKPATPTGYVTQKCVELMLESGVLPEGSIQLISGSARDLLDHLDYRDHVAF
+TGSAATAATLKKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVK
+AGQKCTAIRRVIVPQDRVEAVTAALTERLAAKVVLGDPRVEGTTMGALASKDQQGEVRGA
+VQRLVDAGGQVRLGGPEGSTGDADAESGAFFAPTVLTFEDARTPEVHSVEAFGPVTSVIG
+YTDVADAVALAALGSGSLVATVATNDGETARAFAAGIGAHHGRVHVLNRQTAATTTGHGA
+PVPVLIHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTRE
+DVEAGTAVHPFYKSLAELTVGDQFASGLRTITLEDITAFAEETGDRFYAHTDEEAAMANP
+FFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFITPVTYDDAIRVTLTAKRITP
+RVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG
+>LFPAFLNI_01960
+MTVTAPSLPEILPSYVAGSWWTPSHPSKVTDVTDANTGARLTGVSTDGLDTAAAIEHART
+VGQQALGALTIHERALKLKELALYLNSRVQELYDVSFATGATQRDHAFDVDGGIGTLFTF
+SGKGRRELPNSTVIIDGDVEPLSRDGSFIGEHIYQRIPGVAVQINAFNFPVWGMLEKFAP
+AFVAGVPTVVKPATPTGYVTQKCVELMLESGVLPEGSIQLISGSARDLLDHLDYRDHVAF
+TGSAATAATLKKHPNVQEGGVRFTAETDSLNAAILGPDADPESPEFEAFVKVVFQEMTVK
+AGQKCTAIRRVIVPQDRVEAVTAALTERLAAKVVLGDPRVEGTTMGALASKEQQSEVRGA
+VQRLVDAGGQVRLGGPEGSTGDADAESGAFFAPTVLTFEDARTPEVHSVEAFGPVTSVIG
+YTDVADAVALAALGSGSLVATVATNDGETARAFTAGIGAHHGRVHVLNRQTATTTTGHGA
+PVPVLVHGGPGRAGGGEELGGVRAVKHYMQRTAIQGSPDMLTAITGVWHQGAAAHTVTRE
+DVEAGTAVHPFYKSLAELTVGDQFASGLRTVTLEDITAFAEETGDRFYAHTDEEAAMANP
+FFPRRVAHGYLLVSWAAGLFVAPDPGPVLANYGLENLRFITPVTYDDAIRVTLTAKRITP
+RVSDEYGEVAWDCRIHNQKDELCAQYDVLTLVAKTWPMAPSETSQG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000552.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000552.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5b5d2c047924e4e393777caa22fbdbc8a57bd194
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000552.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00802
+MPASARRPFRFTHRWAVPRPAAEVAALLADPLGYPTWWPSVPRARRIDGAGHDGDPRVAV
+LLRGLVPVRLVMARELDDRERGRLVARLDGDLRGTVRVTVHDDDGPAGGTGGCTVAWEQE
+VVLGAGRLRAAARLPGARAAMRLSHAWAMRSARRALGARALPAGR
+>MOLHKGIG_02020
+MSVDRPFRFTHRWAVPADARSVLALLADPAGYPRWWPAVPRVRRLGPDRAAVRLRGFVPV
+RLTMERLIDDRARGLLVARLSGGLTGTVRATVHDDGAPAGHAPRCIVVWEQEVVLTSPWM
+RAVARVPGARTAMGLSHAAAMRSARRALGAKAVPTADPA
+>NAFOICDF_00760
+MSVDRPFRFTHRWSVPADARSVLALLADPAGYPRWWPAVPRVRHLGPDRAAVRLRGFVPV
+RLTMERLIDDRARGLLVAHLSGDLTGTVRVTVHDDGAPAGHAPRCIVVWEQEVVLTAPWM
+RAVDRVPGARTAMGLSHAAAMRSARRALGAKAMPTADPAPTTRP
+>MHAAABBN_01729
+MSADRPFRFTHRWAVPADARSVLALLADPAGYPRWWPAVPRVRRLGPDRAAVRLRGFVPV
+RLTMERLIDDRARGLLVARLSGGLTGTVRVTVHDDGAPAGHAPRCIVAWEQEVVLTSPWM
+RAVAHVPGARTAMGLSHAAAMRSARRALGAKAVPTADPARTSRP
+>LFPAFLNI_01957
+MSVDRPFRFTHRWAVPADARSVLALLADPAGYPRWWPAVPRAHRLGPDRAAVRLRGLVPV
+RLTMERLIDDRARGLLVAHLSGDLTGTVRVTVHDDGAPAGHAPHCVVTWEQEVVLTSPWM
+RAVARVPGARTAMGLSHAAAMRSARRALGAKAVPTADPARTTRP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000553.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000553.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5bd4758cb6cd6d8bdb7e45768ed96a8f66b6bcca
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000553.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00804
+MTDFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ
+VESKREPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG
+GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA
+QEALELKLVTELHEPEALEVAAHALADRIAKQDPLAVRISKRVFHLPREAHPHVDEIAQA
+ILFESEAKFDRMQAFLDRKKK
+>MOLHKGIG_02017
+MTDFSHFSALHVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ
+VESTREPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG
+GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA
+QEALELKLVTELHEPDALLDAADALADRIAQQDPLAVRLSKRVFHLPRGAHPHVDEIAQA
+ILFESDAKFERMQAFLDRKKK
+>NAFOICDF_00763
+MADFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ
+VESKREPGRFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG
+GGAELAYAADFRIATPALKMGQPETGLGITAAAGAQWRLKELVGEPVALELLLAGRILDA
+QEALELKLVTELHEPDALLDAADALADRIAQQDPLAVRISKRVFHLPREAHPHVDEIAQA
+ILFESQAKFERMQAFLDRKKK
+>MHAAABBN_01726
+MDDFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ
+VESKCEPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG
+GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA
+QEALELKLVTELHEPEALLDAADALADRIAQQDPLAVRLSKRVFHLPREAHPHVDEIAQA
+ILFESEAKFERMQAFLDRKKK
+>LFPAFLNI_01954
+MTDFSHFTALRVEEREDRVHARMDRPGVRNAIDQTMVDEFHELCAHLEREPKILIISGTQ
+VESTREPGTFSGIFASGADIGQLRERRRDDALRGVNSQVFDRIHRLPMPVIAAIDGFALG
+GGAELAYAADFRIATPALKMGQPETSLGITAAAGAQWRLKELVGEPVALELLLAGRILDA
+QEALELKLVTELHEPDALLDAADALADRIAQQDPLAVRLSKRVFHLPREAHPHVDEIAQA
+ILFESEAKFERMQAFLDRKKK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000556.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000556.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d751fe618a4c39750777ff9396ec6dab7836a648
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000556.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00830
+MTETTVTPATGKRRATFNTLEVSELRRLTDDSVEVTFAVPEELADDYDYVPGQYVALRKE
+LDGQEVRRSYSICAIPKRGEIRVAVKKDIGGKFSTWANEVLEVGEKIDVMNPQGAFTSRS
+HVTSLNDAEKVAAEKVAQNKNTHLVAFAAGSGITPIMAIAKAVLAASETSRFDLVYANRS
+AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDAEKLTTLLDRVIDVDGTD
+EWFLCGPFELVQLARETLSARGVDEDDVRFELFTTGRPENPQGHSGRVVEADPSGDNVTI
+EFNLDGLSGKVESPKSAHETILNAALRVRSDVPFACAGGVCGTCRAKVTDGEYEMDENYA
+LEKDEVEAGYVLTCQTRATSDSITVDYDA
+>MOLHKGIG_02012
+MTETTDAPTTGKRRATFNTLEVSELRRLTEDSVEVTFAVPEELADDYDYVPGQYVALRKE
+LDGAEVRRSYSICAVPKRGEIRVAVKKDIGGTFSTWANESLEVGEKIDVMNPQGAFTSRT
+HVTSLNDAQKVAAEKVAEKKDTHLVAFAAGSGITPIMAIAKAVLAASETSRFDLVYANRS
+AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDEDKLTTLLDRVIDVEGTD
+EWFLCGPFELVQLTRETLAARGVPEDDVRFELFTTGRPENPQGHSGRVVEVDPKGDNVTI
+EFNLDGLTAKVESPKSAHETVLNAALRVRSDVPFACAGGVCGTCRAKVVDGAYEMDENYA
+LEKDEVEKGYVLTCQTRPTSDSITLDFDA
+>NAFOICDF_00767
+MTETTDAPITGKRRATFNTLEVSGLRKLTDDSVEVTFAVPEELADDYDYVPGQYVALRKE
+LDGAELRRSYSICAVPQRGEIRVAVKKDLGGTFSTWANEVLEVGEKIDVMNPQGAFTSRT
+NVTSMNDPEAVAAEAVKQDQTHLVALAAGSGITPIMAIAKSVLAASDSARFDLIYANRSA
+MDVMFAEEIGDLKDKYPARFTVNHVLSREQRVAPLLSGRIDDEKLNTLLDRVIDVENTDE
+WFLCGPFELVQLARDTLSERGVAEDDVRFELFTTGKPEAPQGQSGRGVEADPSGDNVTIE
+FNLDGLSAKVESPKSAHETILNAALRVRSDVPFACAGGVCGTCRAKVTEGEFTMEENYAL
+EKDEVEQGYVLTCQTRPTTDSIKVDFDA
+>MHAAABBN_01722
+MTETTDVPTTGKRRATFNTLEVSELRRLTDDSVEITFAVPEELADDYDYVPGQYVALRKE
+LDGAEVRRSYSICAVPKRGEIRVAVKKDIGGKFSTWANESLEVGEKIDVMNPQGAFTSRT
+HVTSLNDAQKVAAEKVAEKKDTHLVAFAAGSGITPIMAIAKAVLAASETSRFDLVYANRS
+AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDEDKLTTLLDRVIDVEGTD
+EWFLCGPFELVQLTRETLAARGVSEDDVRFELFTTGRPENPQGHSGRVVEVDPKGDNVTI
+EFNLDGLTAKVESPKSAHETVLNAALRVRSDVPFACAGGVCGTCRAKVVDGAYEMDENYA
+LEKDEVEKGYVLTCQTRPTSDSITLDFDA
+>LFPAFLNI_01950
+MTETTAAPTTGKRRATFNTLEVSELRRLTDDSVEVTFAVPEELADDYDYVPGQYVALRKE
+LDGAEVRRSYSICAVPKRGEIRVAVKKDIGGKFSTWANESLEVGEKIDVMNPQGAFTSRT
+HVTSLNDAQKVAAEKVAENKDTHLVAFAAGSGITPIMAIAKAVLAASESSRFDLVYANRS
+AMDVMFAEEIGDLKDKYPARFTVHHVLSREQRVSPLLSGRIDEDKLTTLLDRVIDVEGTD
+EWFLCGPFELVQLTRETLAARGVSEDDVRFELFTTGRPENPQGHSGRVVEVDPKGDNVTI
+EFNLDGLTAKVESPKSAHETVLNAALRVRSDVPFACAGGVCGTCRAKVVDGAYEMDENYA
+LEKDEVEKGYVLTCQTRPTSDSITLDFDA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000557.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000557.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec137df44fac024377f629a0e1cfee564cec30e5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000557.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00831
+MTTASELRPADPADARVWDAASTVHDPEIPVLSIADLGILREARAEGEKAVVVITPTYSG
+CPAMDTITTDVSRALERSGFEESEVRLVLQPAWTTDWMTDEGKAKLAEYGIAPPSARTTD
+GPVMIGMAVKCPRCHSLNTREITRFGSTSCKALYTCRECLEPFDYFKVH
+>MOLHKGIG_02011
+MTTASELRPADPAGARVWDAASTVHDPEIPVLSIADLGILREARVEGERAVVVITPTYSG
+CPAMDTITTDVARALGRAGFPDAEVRLVLQPAWTTDWMTDEGKAKLNEYGIAPPVARTTD
+GPVRIGMAVKCPRCHSLNTREITRFGSTSCKALYTCRECLEPFDYFKVH
+>NAFOICDF_00768
+MTTAAELRPSDPAAAQVWDAAATVHDPEIPVLSIADLGILRDVQVEDGRAVVVITPTYSG
+CPAMGTITADVTTALGRAGYPDAEVRTVLQPAWTTDWMTDEGKAKLAEYGIAPPSARTDE
+GPVRVGLAVKCPRCHSLNTREITRFGSTSCKALYTCQECLEPFDYFKVH
+>MHAAABBN_01721
+MTTASELRPADPADARVWDAASTVHDPEIPVLSIADLGILREARAEGERAVVVITPTYSG
+CPAMDTITTDVTRALERAGFPDAEVRLALQPAWTTDWMTDEGKAKLNEYGIAPPVARTTD
+GPVMIGMAVKCPRCHSLNTREITRFGSTSCKALYTCRECLEPFDYFKVH
+>LFPAFLNI_01949
+MTTASELRPADPADARVWDAASTVHDPEIPVLSIADLGILREARVEGERAVVVITPTYSG
+CPAMDTITTDVTRALERAGFPDAEVRLVLQPAWTTDWMTDEGKAKLNEYGIAPPVARATD
+GPIRIGMAVKCPRCHSLNTREITRFGSTSCKALYTCRECLEPFDYFKVH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000558.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000558.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ab3994c11788bd0adab482ef495544e7aa2ae98
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000558.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00832
+MSFATNDSATKHSAGVAITAEEIASGEQKASEETARYALYLGDDALMLGQRLSWWISRTP
+ELEEDIALGNIALDLVGHARFLLSYAGTAWGQSEDELAYFRDEEEFRSVRLVEAENGDFA
+KTIARQLYYSFYAFELYTRLKESTDATLAAIADKALKEVLYHQDHAALWLNRLGLGTDES
+KFRMQRGLDELWPYLPELFHDDETTRPLAEQGIAVLPSSLEEPTMTRIREAIEAAGLEVP
+TTGTARGGDRSGAMSEYRGYILAEMQSLARRHPGASW
+>MOLHKGIG_02010
+MSFATNDSATRHSAGVAITAEEIAAGEQKANDDVARYALALGDDALMLGQRLSWWISRAP
+EIEEDIALGNIALDLVGHARFLLSYAGTAWGKTEDELAYFRDEEEFRSVRLVEAENGDFA
+KTIARQLYYSFYSYELYTRLRESTDPTLAAIADKALKEVLYHQDHAALWLQRLGLGTEES
+KRRMQRGLDELWPYVAELFHDDDVVRALAEQGVAVLPSSLEEPTMTRIRAAIEEACLTVP
+TTGTARGGDRSGAMSEYRGYILAEMQSLARRHPGATW
+>NAFOICDF_00769
+MSFATNDSATRHSAGVANTAEEIASGGQKASDEVARYAVYLGDDALMLGQRLSWWISRAP
+ELEEDIALGNIALDLVGHARFLLSYAGTAWDKSEDDLAYFRDEEEFRSTRLVEAENGDFG
+KTIARQLYYSVYAHGLYTRLKDSKDATLAAIADKALKEVEYHLDHAEQWVNRLGLGTEES
+NARLQRGLDELWPYLPELFHDDELTRSLAEQGIAVLPSSLEESTMARIRAAIEGADLKVP
+ETGAARGGDRSGQMSEYRGYILAEMQSLARRHPGASW
+>MHAAABBN_01720
+MSFATNDSATRHSAGVAITAEEIAAGEQKASDDVARYALALGDDALMLGQRLSWWISRAP
+ELEEDIALGNIALDLVGHARFLLSYAGTAWGKTEDELAYFRDEEEFRSVRLVEAENGDFA
+KTIARQLYYSFYSYELYTRLRESTDSTLAAIADKALKEVLYHQDHAALWLQRLGLGTEES
+KRRMQRGLDELWPYVAELFHDDDVVRALAEQGVAVLPSSLEEPTMTRIRAAIEEAGLTVP
+TTGTARGGDRSGAMSEYRGYILAEMQSLARRHPGATW
+>LFPAFLNI_01948
+MSFATNDSATRHSAGVAITAEEIAAGEQKASDDVARYALALGDDALMLGQRLSWWISRAP
+ELEEDIALGNIALDLVGHARFLLSYAGTAWGKTEDELAYFRDEEEFRSVRLVEAENGDFA
+KTIARQLYYSFYSYELYTRLRESADPTLAAIADKALKEVLYHQDHAALWLQRLGLGTEES
+KRRMQRGLDELWPYVAELFHDDDVVRALAEQGVAVLPSSLEEPTMTRIRAAIEEAGLTVP
+TTGTARGGDRSGAMSEYRGYILAEMQSLARRHPGATW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000559.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000559.fa
new file mode 100644
index 0000000000000000000000000000000000000000..79572d51ff402356e76acbe4f58c28b8da77cd39
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000559.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_00833
+MGENTAASNAWPLWEVFVRANRGLSHVHAGSLHAPDASLALRNARDLYTRRNEGTSVWVV
+PAEAIAASDPDSKGGFFESPQGKSYRHATYYQQSEGVPHL
+>MOLHKGIG_02009
+MSETTAASHAWPLWEVFVRANRGLSHVHAGSLHAPDATLALRNARDLYTRRNEGTSVWVV
+PAEAIAASDPDSKGGFFESAQGKSYRHATYYQQSEGVPHL
+>NAFOICDF_00770
+MTENTAPSNEWPLWEVFVRANRGLSHVHAGSLHAPDATMALRNARDLYTRRNEGTSVWVV
+PADAVAASDPDSKGGFFESPQGKSYRHATYYQKSEGVPHL
+>MHAAABBN_01719
+MSETTAASHAWPLWEVFVRANRGLSHVHAGSLHAPDATLALRNARDLYTRRNEGTSVWVV
+PAEAIAASDPDSKGGFFESAQGKSYRHATYYQQSEGVPHL
+>LFPAFLNI_01947
+MSETTAASHAWPLWEVFVRANRGLSHVHAGSLHAPDATLALRNARDLYTRRNEGTSVWVV
+PAEAIAASDPDSKGGFFESAQGKSYRHATYYQQSEGVPHL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000560.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000560.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d1585f2a25795cc667b975eafb16e6655a2f4f5a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000560.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00834
+MTQTSSTTRLASVPSPEDAAGQENFDRLIAEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE
+IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDVLNDQLLEGKA
+KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRSSYGPYGRAMVRICKEESFHQRQG
+WEILYELSHGTPEQKQMAQDAVDRFYGPALQMFGPPDEDSPNSKQSMAWKVKRFSNDELR
+QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDELMSVIKGNGPMNTQRLARR
+IQAHEDGAWVRDAAAAYARRQAEQHAPAETHLIGA
+>MOLHKGIG_02008
+MTQTSSPQHLASVPSPEDAAGQENFDRLIAEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE
+IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDELNEQLLSGRA
+KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRASYGPYGRAMVRICKEESFHQRQG
+WEILYELSHGTPEQKQMAQDAVNRFYGPALQMFGPTDEDSPNSRQSMAWKVKRFSNDDLR
+QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDEFMSVIKGDGPMNTQRMARR
+IQAHEDGAWVREAAAAYARRQAEQNAPAETHLIGA
+>NAFOICDF_00771
+MTQTSSSPHLASVPSPDDAAGQENFDRLIQEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE
+IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDELNEQLLSGRA
+KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRASYGPYGRAMVRICKEESFHQRQG
+WEILYELSHGTPEQKQMAQDAVNRFYGPALQMFGPPDEDSPNSQQSMAWKVKRFSNDELR
+QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDEFMSVIKGNGPMNTQRLARR
+VQAHEDGAWVREAAAAYARRQAEQHVPADTQLIGA
+>MHAAABBN_01718
+MTQTSSPQHLASVPSPEDAAGQENFDRLIAEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE
+IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDELNEQLLSGRA
+KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRASYGPYGRAMVRICKEESFHQRQG
+WEILYELSHGTPEQKQMAQDAVNRFYGPALQMFGPPDEDSPNSRQSMAWKVKRFSNDDLR
+QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDEFMSVIKGDGPMNTQRMARR
+IQAHEDGAWVREAAAAYARRQAEQNAPAETHLIGA
+>LFPAFLNI_01946
+MTQTSSPQHLASVPSPEDAAGQENFDRLIAEDSRIEPRDWMPEAYRKSLTRQVSQHAHSE
+IIGMQPEANWITRAPSLKRKAILMAKVQDEAGHGLYLYSAAETLGTPRDELNAQLLSGRA
+KYSSIFNYPARTWADMGAIGWLVDGAAICNQVPLCRASYGPYGRAMVRICKEESFHQRQG
+WEILYELSHGTPEQKQMAQDAVDRFYGPALQMFGPPDEDSPNSRQSMAWKVKRFSNDDLR
+QRFVDMIVPQAEALGLTLPDPDLKWNEERGHYDFGELDWDEFMSVIKGDGPMNTQRMARR
+IQAHEEGAWVREAAAAYARRQAEQNAPAETHLIGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000564.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000564.fa
new file mode 100644
index 0000000000000000000000000000000000000000..81da425cb0805d8a012d23b537218c55b72146a4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000564.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00839
+MTDDAQLTPAAVAPHKKVGMLPPYAAGKPPVAVPGLRPYKLSSNENPHAPVAGVIERVRG
+VVTGPEGAPSTLCRYPDTLSTGLREALAAHLDVPADDVVTGAGSLGALSQVITAFAGHGE
+AGRGDEVIFAWRSFEAYPIVVRTAGAVDVQVPLTADHRHDLPAMLAAITDRTRVILLCTP
+NNPTGPVLTTAEVEGFLAEVPEHVLVVIDEAYVEFVRDEDAVRGLDMYRKHANVVVLRTF
+SKAHGLANLRVGYSVSRPEITKALRTVATPFAVSTVAEEAAIASLEHLDEVLEGVQLVVD
+ERERVAAALAEAGWDVPASQANFVWLPLGERTADFAAAAQAKALSVRAFAGEGVRVSIGE
+QEANDRFLEVARDFLK
+>MOLHKGIG_02003
+MGRITASAARITLVAMTDDAQQTPAVVAPHKKVGMLPPYAAGKPPVAVPGLHPYKLSSNE
+NPYAPVSGVIDRVRQVVTGPEGAPSTLCRYPDTLSTGLRQALAAHLDVPADDVVTGAGSL
+GALAQVITAFAGHGEAGEGDEVIFAWRSFEAYPIVVRTAGAVDVQVPLTADHRHDLPAML
+EAITERTRVILLCTPNNPTGPVLTTAEVEDFLARVPAHILVVIDEAYVEFVRDEDAVKGL
+EMYRKHANVVVLRTFSKAHGLANLRVGYSVSQPEITKALRTVATPFAVSTVAEEAAIASL
+EHLDEVLERVQIVVDERERVAAALAEAGWDLPASQANFVWLPLGERTQAFAEAAQARALS
+VRAFAGEGVRVSIGEKEANDRFLEVARDFLA
+>NAFOICDF_00776
+MTDVTSGSSGVAAHRKVSLLPPYAAGKPPVAVPGLRPYKLSSNENPFAPVPAVVERIHEV
+VAGAEGEPSPVCRYPDPLSTALRERLAAHLDVPADDIVTGGGSLGALTQVITAFAGDGGE
+DGAPDEVVFAWRSFEAYPIVVRTAGAKDVQVPLTADGRHDLPAMLAAITERTKVMLLCTP
+NNPTGPVLTTAEVEDFLAQVPPHVLVVIDEAYVEFVRHPDAVDGPAMYRRHPNVVVLRTF
+SKAHGLANLRVGYSVSRPEVTASLRTVAVPFAVSTVAEQAAIASLDHLDEVLERVQTVVD
+ERERVVAALAEAGWDVPETHANFVWLPLGERGADFAAAAGERALSVRAFPEGVRVSISER
+EANDRFLEVARAFQR
+>MHAAABBN_01713
+MVPLTASAARITLVAMTDDAQQTPAVVAPHKKVGMLPPYAAGKPPVAVPGLHPYKLSSNE
+NPYAPVPGVIDRVRQVVTGPEGAPSTLCRYPDTLSTGLRQALAAHLDVPADDVVTGAGSL
+GALAQVITAFAGHGEAGEGDEVIFAWRSFEAYPIVVRTAGAVDVQVPLTADHRHDLPAML
+EAITERTRVILLCTPNNPTGPVLTTAEVEDFLARVPAHILVVIDEAYVEFVRDEDAVKGL
+EMYRKHANVVVLRTFSKAHGLANLRVGYSVSQPEITKALRTVATPFAVSTVAEEAAIASL
+EHLDEVLERVQVVVDERERVAAALAEAGWDLPSSQANFVWLPLGERTQAFAEAAQARALS
+VRAFADEGVRVSIGEKEANDRFLEVARDFLT
+>LFPAFLNI_01941
+MGRITASAARITLVAMTDDAPQTPAVVAPHKKVGMLPPYAAGKPPVAVPGLHPYKLSSNE
+NPYAPVSGVIDRVRQVVTGPEGAPSTLCRYPDTLSTGLRQALAAHLDVPADDVVTGAGSL
+GALAQVITAFAGHGEAGEGDEVIFAWHSFEAYPIVVRTAGAVDVQVPLTADHRHDLPAML
+EAITERTRVILLCTPNNPTGPVLTTAEVEDFLARVPAHILVVIDEAYVEFVRDEDAVKGL
+EMYRKHANVVVLRTFSKAHGLANLRVGYSVSQPEITKALRTVATPFAVSTVAEEAAIASL
+EHLDEVLERVQVVVDERERVAAALAGAGWDLPSSQANFVWLPLGERTQAFAEAAQAQALS
+VRAFAGEGVRVSIGEQEANDRFLEVARDFLT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000565.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000565.fa
new file mode 100644
index 0000000000000000000000000000000000000000..edee8e53ce88cee112fb797df4d7ab7d81ebb259
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000565.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_00857
+MAEPIHIGAAADIPEGEAVVVPAATAGTSDDVAVFHAEDGAFYAIDDTCTHEDASLAEGW
+LEGTQVECPLHSAQFCLKSGEALCLPATRPVGTHPVQERDGQLYLTPGA
+>MOLHKGIG_02000
+MAEPIHIGAAADVPEGEAIVVPAATAGTRDDVAVFHTDAGEFHAIDDTCTHEDASLAEGW
+LEDDRVECPLHAAQFCLRTGEALCLPATKGVGVHRVEEREGQLYLVPGA
+>NAFOICDF_00793
+MSREINVGPASAVPEGESLLVPNDTTGTKDHIGVFHAEDGAFYAIDNTCTHQDYALSEGF
+VEDCRVECPLHGASFDLRTGEALSLPATKPVGTHRVEERDGDLWLTVEDGE
+>MHAAABBN_01694
+MAEPIHIGAAADVPEGEAIVVPAATAGTRDDVAVFHTDAGEFHAIDDTCTHEDASLAEGW
+LEDDRVECPLHAAQFCLRTGEALCLPATKGVGVHRVEEREGQLYLVPGA
+>LFPAFLNI_01926
+MAEPIHIGAAADVPEGEAIVVPAATAGTRDDVAVFHTDAGEFHAIDDTCTHEDASLAEGW
+LEDDRVECPLHAAQFCLRTGEALCLPATKGVGVHRVEEREGQLYLVPGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000574.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000574.fa
new file mode 100644
index 0000000000000000000000000000000000000000..474f719471cc28485dad0552eb4945135f813f39
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000574.fa
@@ -0,0 +1,32 @@
+>ACLBLIBL_00868
+MRQRPASRAVLLVGAAAAVGLLGGCAAEPGAPAADGSAQGDALPRPEVDGYAPLTVWLTV
+PAAEAVPGSTGRAYGCDDLLVPVQTVPADAPDDADAALDFLFSDERGWHGDPSLWNAVFE
+TRESLTPTGHRLEGDVDVFTFTGTVTAEGECEAERIRAQLQETAAAHTSAGQVRLEVDGR
+PLDDVLGLAPLALGDEVDVPESGADPSESPTEPADEPWEEPAEDPWAEPTEDTWSEPTED
+PWAESEESAEPSPTAWEEPAEETWEPQDETAPTEEDAPTEWDGTVDDGSASEDVPAEVEE
+PPAQDEGADAADESAPAEDAGADGAGNLGIGDPDATEPSAP
+>MOLHKGIG_01989
+MRPPSPPRALRLMGAVAAACLLAGCAVDPGLAEDSASDDGVPLPATEGYQPLTVYLAVAE
+TEAVPGTSGRPFGCGDLLVPVQTVPTDTEDEADAALDFLFADEQGWHGDPSLWNAVFDAR
+ETLTPTGHRREGDVEIFTFTGTVTPEDDCTAERIRAQLQATAAAFTSAGQVRLEVDGRDL
+DDVLGLEPLRLGESVDVPQGDPTPSGEPSDESGEQTWAPEGESPEDTWAPAEPSDETWAP
+AEESSWGPAEPTQGTWSPGPEPSAP
+>NAFOICDF_00805
+MRIRPTPRVRLAAVLATSAALTSGCGALTGQGLDEPKELTVHLTVPRADAASSFEGRPYG
+CDDLLVPVTTAPSSGVDHGDAALDFLFSDLQGEHGDPALQNAVKATADTLHPTGHHRDGS
+TEVFTFDGTVTAEDECAAQRIRAQLQETARAQSPVPDVRLEVGGRPLDEVLGLPALSLGD
+PVKGGAASTPRATPTPESTPSPTATPTPTPTTVPGSSASPAPTSASPTATPAPSTSAAPS
+TTGPSSASPTAETSSAAPASPDPASADPATAAPTSASATAGGASPSVEPTDGTSLRSPGA
+GDATATTAPLDGLDGGAAGGTGTGGADATAPGGAPSAGAAAGAGAGSSATG
+>MHAAABBN_01683
+MRPTPPSRALRLTGAVAAACLLAGCAVAPDLAEDSASDDGVPLPATEGYQPLTVYLAVAE
+PEAVPGTSGRPFGCGDLLVPVQTVPTDTEDEADAALDFLFADERGWHGDPSLWNAVFDAR
+ETLTPTGHRRAGDVEIFTFTGTVTPEDDCTAERIRAQLQATAAAFTSAGQVRLEVDGRDL
+DDVLGLEPLRLGESVDVPQGDPTPSGEPSDGSGEQTWAPEGESSEDTWAPAEPSTWAPTE
+ESSWGPAEPTQGTWSPGQEPSAP
+>LFPAFLNI_01915
+MRPPSPSRALRITGAVAAACLLAGCAVDPGLAEDSASDDGVPLPATEGYQPLTVYLAVAE
+AEAVPGTSGRPFGCGDLLVPVQTVPTDTEDEADTALDFLFADERGWHGDPSLWNAVFDAR
+ETLTPTGHRRAGDVEIFTFTGTVTPEDDCTAERIRAQLQATAAAFTSAGQVRLEVDGRDL
+DDVLGLEPLRLGEPVDVPRGVPAPSGEPSDGSGEQTWAPEGESSWGPAEPTQGTWSPAQE
+PSTP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000576.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000576.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af70db45a35c5e6f0c6c43e9df046cc52dc571d8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000576.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00871
+MSDERARSFSASTASAADDGARGTGTTRVKRGLADMMKGGVIMDVVNAEQARIAEDAGAV
+AVMALERVPADIRAQGGVARMSDPDLIDGIVEAVSIPVMAKARIGHFVEAQVLQALKVDF
+IDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITEGAAMIRSKGEAGTGDVSEA
+VKHIRTIRKEIAQLQGLAQDELYVAAKELQAPYELVREVAETGALPVVMFTAGGVATPAD
+AALMMQMGADGVFVGSGIFKSGNPAERARAIVKATAQFDDPMAVAEASRGLGEAMVGINV
+GDLPAPHRLAERGW
+>MOLHKGIG_01986
+MSDERARSFSASTASAADDGARGTGTTRVKRGLADMMKGGVIMDVVNAEQARIAEDAGAV
+AVMALERVPADIRAQGGVARMSDPDLIDGIVEAVSIPVMAKARIGHFVEAQVLQALKVDF
+IDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITEGAAMIRSKGEAGTGDVSEA
+VKHIRTIRKEIAQLQGLAQDELYVAAKELQAPYELVREVAETGALPVVMFTAGGVATPAD
+AALMMQMGADGVFVGSGIFKSGNPAERARAIVKATAQFDDPMAVAEASRGLGEAMVGINV
+GDLPAPHRLAERGW
+>NAFOICDF_00807
+MSDDRAQSFSASTGAAADDGARGTGTTRVKRGLADMLKGGVIMDVVTPEQARIAEDAGAV
+AVMALERVPADIRAQGGVARMSDPDLIDGIVEAVSIPVMAKARIGHFVEAQVLQALKVDF
+IDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITEGAAMIRSKGEAGTGDVSEA
+VKHIRTIRKEIAQLQGLAQDELYVAAKELQAPYELVCEVAETGALPVVMFTAGGVATPAD
+AALMMQMGADGVFVGSGIFKSGNPAERARAIVKATAQFDDPMAVAEASRGLGEAMVGINV
+GDLPAPHRLAERGW
+>MHAAABBN_01680
+MSDERARNFSASTASAADDGARGTGTTRVKRGLADMMKGGVIMDVVNAEQARIAEDAGAV
+AVMALERVPADIRAQGGVARMSDPDLIDGIVEAVSIPVMAKARIGHFVEAQVLQALKVDF
+IDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITEGAAMIRSKGEAGTGDVSEA
+VKHIRTIRKEIAQLQGLAQDELYVAAKELQAPYELVREVAETGTLPVVMFTAGGVATPAD
+AALMMQMGADGVFVGSGIFKSGNPAERARAIVKATAQFDDPMAVAEASRGLGEAMVGINV
+GDLPAPHRLAERGW
+>LFPAFLNI_01912
+MSDERARSFSASTASAADDGARGTGTTRVKRGLADMMKGGVIMDVVNAEQARIAEDAGAV
+AVMALERVPADIRAQGGVARMSDPDLIDGIVEAVSIPVMAKARIGHFVEAQVLQALKVDF
+IDESEVLSPADYVNHIDKWDFDVPFVCGATNLGEALRRITEGAAMIRSKGEAGTGDVSEA
+VKHIRTIRKEIAQLQGLAQDELYVAAKELRAPYELVREVAETGTLPVVMFTAGGVATPAD
+AALMMQMGADGVFVGSGIFKSGNPAERARAIVKATAQFDDPMAVAEASRGLGEAMVGINV
+GDLPAPHRLAERGW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000579.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000579.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fca0dbd3af5f4838aacd20b3b148e1e091a39fb0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000579.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_00877
+MDPLIQASAPVGTFTATTDAVAGSLGLSAALGTIPLLTFFVMLLLVKAKAWQAGLVSLTA
+AVLVAILAFGMPADLTLLSASQGAVFGFFPIVWIVVMALWFYQVTVLSGRFEDMRAIFDT
+VGGGDIRIQAVLIAFCFGGMLEALAGFGAPVAITATMLLALGLPPLKTAVVVLLANTAPV
+AFGAVGIPITTAGQLTDIPAAEIGAIVGHQAPFVAVLVPFFLVWIIDGFRGIRETWPALL
+TIGGTFALGIWWASTQFSYELTDVVASLLAMASAVVLLRFWRPKGAAEADARLGITPTRP
+AGDLTPGRIWMAVLPYLLVITVFGIAKLWTLGFDLPGWLASTNVRIPWPGLDGRLVTAAG
+EPITGTVYSFQWLSSPGTLLLITGLLVALIYSVFTGGGRFPLRFGDALAEIGRCFWKMRW
+SGLTIVLVLSLAYVMNFSGQTLAMGTAVAGVGAAFAFLSPVLGWLGTAVTGSDTSANALF
+ATLQQTAAEEAGLDPSLMVAANTSGGVVGKMISPQSLAIAATAVSMEGQESKILRTVLPW
+SVALLLMVCTIVFLQSNVLSWMLP
+>MOLHKGIG_01981
+MHTFTPTPDAAGSVALSAALGVLPLLTFFATLLGLRLKAWQSGLAALVVALLVAVLGFHM
+PAHLAALAAAQGATFGLFPIVWIVVMALWFYQVTVLSGRFDDMRAIFDSLGGGDIRIQAV
+LIAFCFGGLLEALAGFGAPVAITATMVLGLGVPPLRAATAVLLANTAPVAFGAVGTPITT
+AGTLTGIPATHIGAIVGHQAPFVAVFVPFLLVFIIDGLRGVRQTWPALIVIGASFAVAIW
+LASTHFSYELTDVVASLVSLAAAVLLLRFWRPRGAEEARQRLDAPARAAAQDLTPGRIFM
+AVLPYIVVVAVFALAKLVPSITAALNSATAKIPWPGLDGHLVDASGAPLASTVYKFEWLA
+SPGTLLLIAGLIMAVVYSRFDHDGRFPLSVGNALAEIGRCFARMRWSALTIVIVLSLAYV
+MNFSGQTVAMGTWVAGLGAAFVFLSPVLGWLGTAVTGSDTSANALFSTLQQTAATNIGAD
+PALLVAANTSGGVVGKMISPQSLAIAATAVGMEGRESEILRRVVVWSLVLLLAVCTLVYL
+QSNVLAWMLPAAG
+>NAFOICDF_00812
+MHTFTPTPDAAGSVALSAALGVLPLLTFFATLLGLRLKAWQSGLAALVVALLVAVLGFHM
+PAHLAALAAAQGATFGLFPIVWIVVMALWFYQVTVLSGRFDDMRAIFDSLGGGDIRIQAV
+LIAFCFGGLLEALAGFGAPVAITATMVLGLGVPPLRAATAVLLANTAPVAFGAVGTPITT
+AGTLTGIPASHIGAIVGHQAPFVAVFVPFLLVFIIDGLRGVRQTWPALIVIGASFAVAIW
+LASTHFSYELTDVVASLVSLAAAVLLLRFWRPRGAEEARQRLDAPARAAAQDLTPGRIFM
+AVLPYIVVVAVFALAKLVPPITAALNSVTAKIPWPGLDGHLVNASGAPLASTVYKFEWLA
+SPGTLLLIAGLIMAVVYSRFDHDGRFPLSVGNALAEIGRCFARMRWSALTIVIVLSLAYV
+MNFSGQTVAMGTWVAGLGAAFVFLSPVLGWLGTAVTGSDTSANALFSTLQQTAATNIGAD
+PALLVAANTSGGVVGKMISPQSLAIAATAVGMEGRESEILRRVVVWSLVLLLAVCTLVYL
+QSNVLAWLLPAAG
+>MHAAABBN_01675
+MHTFTPTPDAAGSVALSAALGVLPLLTFFATLLGLRLKAWQSGLAALVVALLVAVLGFHM
+PAHLAALAAAQGATFGLFPIVWIVVMALWFYQVTVLSGRFDDMRAIFDSLGGGDIRIQAV
+LIAFCFGGLLEALAGFGAPVAITATMVLGLGVPPLRAATAVLLANTAPVAFGAVGTPITT
+AGTLTGIPASHIGAIVGHQAPFVAVFVPFLLVFIIDGLRGVRQTWPALIVIGASFAVAIW
+LASTYFSYELTDVVASLVSLAAAVLLLRFWRPRGAEEARQRLDAPARAAAQDLTPGRIFM
+AVLPYIVVVAVFALAKLVPSITAALNAATAKIPWPGLDGHLVDASGAPLASTVYKFEWLA
+SPGTLLLIAGLIMAVVYSRFDHDGRFPLSVGNALAEIGRCFARMRWSALTIVIVLSLAYV
+MNFSGQTVAMGTWVAGLGAAFVFLSPVLGWLGTAVTGSDTSANALFSTLQQTAATNIGAD
+PALLVAANTSGGVVGKMISPQSLAIAATAVGMEGRESEILRRVVVWSLVLLLAVCTLVYL
+QSNVLAWMLPAAG
+>LFPAFLNI_01907
+MHTFTPTPDAAGSVALSAALGVLPLLTFFATLLGLRLKAWQSGLAALVVALLVAVLGFHM
+PAHLAALAAAQGATFGLFPIVWIVVMALWFYQVTVLSGRFDDMRAIFDSLGGGDIRIQAV
+LIAFCFGGLLEALAGFGAPVAITATMVLGLGVPPLRAATAVLLANTAPVAFGAVGTPITT
+AGTLTGIPASHIGAIVGHQAPFVAVFVPFLLVFIIDGLRGVRQTWPALIVIGASFAVAIW
+LASTYFSYELTDVVASLVSLAAAVLLLRFWRPRGAEEARQRLDAPARAAAQDLTPGRIFM
+AVLPYIVVVAVFALAKLVPSITAALNSATAKIPWPGLDGHLVDASGAPLASTVYKFEWLA
+SPGTLLLIAGLIMAVVYSRFDHDGRFPLSVGNALAEIGRCFARMRWSALTIVIVLSLAYV
+MNFSGQTVAMGTWVAGLGAAFVFLSPVLGWLGTAVTGSDTSANALFSTLQQTAATNIGAD
+PALLVAANTSGGVVGKMISPQSLAIAATAVGMEGRESEILRRVVVWSLVLLLAVCTLVYL
+QSNVLAWMLPAAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000585.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000585.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2a07fcf87d38795d1778b1de86d44c7177bb779
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000585.fa
@@ -0,0 +1,39 @@
+>ACLBLIBL_00888
+MSDGAAAVSRPGASARPSRRRRVLYYAHQHGSGHVRHAANLAATGAFDVTVVSAHPDAAR
+MLLAGTPVLPLPSDVVPGHVQPERSPLHWTPVGPQIRDRFAALHDAARDVRPDVCVVDVS
+VEAALFLRLAGWPVLHRRMHGERTDPAHALVYAEADGLFAHYAEELEDPAWREAHAGRTA
+FLGVPDVTGRLGARATTTTATTTAAGGSAPRVAVIAGTGGGGVRAADLARAAAAVPEATW
+EVYGPVAGADELQAPGGAAGSRSSDADATTGTAPTAGVALPANVTLHGWVEAPASRAAEA
+DVVVVSAGHNAAVDAARSGRPVVLAPEPRPFDEQHVFAREARRAAGVPWCAWEDPDADWA
+GAVRGALADPSAADRLAALLLVEPGEYRRRWEAAVEAALEATQG
+>MOLHKGIG_01971
+MAPARRRVLYYAHQHGAGHLRHAAGLASTGAFDVTVVTAHPRAAELLPADVPVIPLPSDL
+VPGHEQPARSPLHWSPVGPEIRARFDALHAAAQRVGPDVCVVDVSVEAALFLRLAGWPVL
+HRRMHGERTDPAHALVYAEADGLFAHYAAELEVPAWRAAHADRVTYLGVADVTGRLGTRT
+TTTSTARAAPRVAVIAGTGGGGVRAADLARAASAVPEATWEVYGPIAGVGEPEAPGGLAA
+EAMPATVTLHGWVQAPARRAADADVVVVSAGHNAVVDAARSGRPVVLAPEPRPFDEQRVF
+VREIHRAAGVPWCAWEDPDADWAGAVRGALADPTAADRLAGLLLVAPDEYRRRWEAAIEG
+ALG
+>NAFOICDF_00829
+MSGRRLRVLHYAHQHGSGHVRHAATLIRADVADVTVATAHPDAARLLPTGTRIVPLPTDI
+VPGHGQPEGSPLHHTPVGPAIQARFDALHDAARAVRPDVCVVDVSAEAALFLRLAGYPVV
+HRRMHGDRTDPAHRLVYAEADALFAHYGEVLEDPAWQAEFGARTAHLGVPDADGRLGRTA
+APARAGEAPRVVAVTGTGGGGVAARDIARAARSTPGARWHVIGPVRDAGGADLPENLELQ
+GWVEDVPAALAAADVVVVSAGHNAAVDAAHSGRPVVLAPEERPFAEQRRFAEAVERAAGV
+PWRAWEDPEADWAGAVARALGDPAAADRLAAALLRPPAEHAAGWGALLERAAASAQ
+>MHAAABBN_01665
+MAPARRRVLYYAHQHGAGHLRHAAGLASTGAFDVTVVTAHPRAAELLPADVPVIPLPSDL
+VPGHQQPARSPLHWSPVGTEIRARFDALHAAAQRVDPDVCVVDVSVEAALFLRLAGWPVL
+HRRMHGERTDPAHALVYAEADGLFAHYAAELEVPAWRAAHADRVTYLGVADVTGRLGTRA
+TTTSSAGAAPRVAVIAGTGGGGVRAADLARAASAVPEATWEVYGPIAGVGEPEAPGGLAA
+EAMPATVTLHGWVQAPARRAADADVVVVSAGHNAVVDAARSGRPVVLAPEPRPFDEQRVF
+VREIHRAAGVPWCAWEDPDADWAGAVRGALADPAAADRLAGLLLVAPGEYRRRWEAAIEG
+ALG
+>LFPAFLNI_01897
+MAPARRRVLYYAHQHGAGHLRHAAGLASTGAFDVTVVTAHPRAAALLPADVPVIPLPSDL
+VPGHQQPARSPLHWSPVGTEIRARFDALHAAAQRVDPDVCVADVSVEAALFLRLAGWPVL
+HRRMHGERTDPAHALVYAEADGLFAHYAAELEVPAWRAAHADRVTYLGVADVTGRLGTRA
+TTTSSAGAAPRVAVIAGTGGGGVRAADLARAASAVPEATWEVYGPIAGVGEPEAPGGLAA
+EAMPATVTLHGWVQAPARRAADADVVVVSAGHNAVVDAARSGRPVVLAPEPRPFDEQRVF
+VREIHRAAGVPWCAWEDPDADWAGAVRGALADPAAADRLAGLLLVAPDEYRRRWEAAIEG
+ALG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000588.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000588.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5a50ae6c22b7983383348ea4f5a6c74f48255467
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000588.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_00891
+MSAAVSVVVPYYRAQADLDRLTAALAAQRGVTGGLQLVVADDGSPVPPMVGPDLPFDVVT
+VRQQDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLAAAVAAVAEAPRDAAVVGRR
+RHLAEAWLERAWADGWRPGHEVPADARLADPAWLREGYRTTDELRRADSTGYRYVISAVL
+TVAREVYEDAGGFDPAFVGYGGEDWELAHRLWRVGAALRHAPDAVAWQAGADFGGRGDAA
+EAARVKAREALALASRIPATTARGHGLSLAGPLRVEARVRVPERADGAAAAVVAVDAVLR
+AAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAASQDLPPTPARGDLDAVRSVPDW
+SVDVRVPLRPAAAGARPDADAVAAWLLRLERAGVERVEVLGEPGERAERAVLAVLTCARA
+RWRRRRGGTSRVWRVPASRLGWAPVAAVPDLEAWWGGWG
+>MOLHKGIG_01968
+MSAAVSVVVPYYRAQADLDRLTAALAAQRGVTGGLQLVVADDGSPVPPRVDPGLPFDVVT
+VRQQDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLAAALAAVAEAPRDAAVVGRR
+RHLAEAWLERAWADGWRPGHEVPADALLAEPAWLRDGYRATDDLRRADSTGYRYVISAVL
+TVAREVYEDAGGFDPAFVGYGGEDWELAHRLWRVGAALRHAPDAVAWQAGADFGGRGDAA
+EAARVKAREALVLVSRIPATTSRGHGLSLAGPLRAEARVRVPEGADGAAAAVVAVDAVLR
+AAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAAPEDLPPTPARGDLDAVRSVPDW
+SVDVQVPLRPAAAGARPDTDAVAAWLLRLERAGVERVEVLGEPGERAERDVLAVLTCARA
+RWRPRRGGTARVWRVPASRLGWAPVAAVPDLEAWWGGWG
+>NAFOICDF_00832
+MTAPVAGREAAAETAGPEASVPEVSVVVPHYRAPADLERVVAALAAQDHPASRLQLVVAD
+DGSPEPPVLPAGLPFEAVVVAQEDHGFRASAARALGASAAEGRILAFLDGDMLPEPGYLT
+AACAAPAASVDAVVVGRRRHLDPALLESGWRPGEPVPEAARLPEPAWLAEAYQRSGDLAA
+ADSTSYRYVISAVLTVAREVYADAGGFDPAFVGYGGEDWELAHRLWRVGGAFRHQPAAVA
+WQAGEDFGGRGDAAERTAVKQREALRLAARITATTARGHGLSLPGPLRVGARVRAEASGD
+AAAVVGVDALLAAAPGARVGVTGLGSGAARAALADPRVWIMDGGGEAARADLPPAPARGD
+LGAVRGIPDWSCDVRTPLRPAAPGARPDAARAADWLLRLERAGVERVEVLGEPQAAEEPG
+EAGRGERPVLAVLTCSRALWRSRRGGDSRVWRVPAARLGWAPVARDVDLEAWWGGWG
+>MHAAABBN_01662
+MSAAVSVVVPYYRAQADLDRLTAALAAQRGLTGGLQLVVADDGSPVPPRVGPGLPFDVVT
+VRQQDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLAAALAAVAEAPRDAAVVGRR
+RHLAEAWLERAWVDGWRPGDEVPADARLAEPAWLREGYRATDDLRRADSTGYRYVISAVL
+TVAREVYADAGGFDPAFVGYGGEDWELAHRLWRVGAALRHAPDAVAWQAGADFGGRGDAA
+EAARVKAREALVLASRIPATTARGHGLSLAGPLRVEARVRVPEGADGAAAAVVAVDAVLC
+AAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAASQDLPPTPARGDLDAVRSVPDW
+SVDVHVPLRPAAAGARPDADAVAAWLLRLERAGVERVEVLGEPGERAERAVLAVLTCARA
+RWRRRRGGTARVWRVPASRLGWAPVATVPDLEAWWGGWG
+>LFPAFLNI_01894
+MSAAVSVVVPYYRAQADLDRLTAALAAQRGLTGGLQLVVADDGSPVPPRVDPGLPFDVVT
+VRQPDRGFRASAARALGAEAADGDVLAFLDGDMLPEPGYLAAALAAVAEAPRDAAVVGRR
+RHLAEAWLERAWAHGWQPGHEVPADARLAEPAWLREGYRATDDLRRADSTGYRYVISAVF
+TVAREVYEDAGGFDPAFVGYGGEDWELAHRLWRVGAALRHAPDAVAWQAGADFGGRGDAA
+EAARVKAREALVLASRIPATTARGHGLSLAGPLRVEARVRVPEGADGAAAAVVAVDAVLC
+AAPGARVGVVGGLDEAAARALGDPRVRLLGEPDGGAAADEDLPPTPARGDLDAVRSVPDW
+SVDVHVPLRPAAAGARPDADAVAAWLLRLERAGVERVEVLGEPAEPGERAVLAVLTCARA
+RWRHRRGGTARVWRVPASRLGWAPVATVPDLEAWWGGWG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000589.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000589.fa
new file mode 100644
index 0000000000000000000000000000000000000000..413c686b2dac5283744a9dc198bc6751b1162c14
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000589.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_00893
+MHEDEGRRRHYGHFYGLEDLPEGDLLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVP
+PAFEVQPDEVEHLERLLPRVKALVTQPIPHDYRGMPIGTDQLVARLPEDAAVVRIPVVYD
+VSRFPWQVTLRNWKFAPGAAERPGEDPPVVPYHDLRVLAEAATGRRREVAPAAIREAAAA
+SVQALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTVLTRVAERVAEHLPGDVAAQPV
+PAARVLLGGVRAPLEAVVVEALDLDAEPTEDWTVGGETIPAEQLRQTHLDWYAQNPQAVE
+VGMRKYADQLRLLGLAA
+>MOLHKGIG_01966
+MHEDEGRRRHYGHFYGLEDLPEDDLLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVP
+PAFEAQPDEVAHLERLLPRVKALVTQPIPHDYRGMPIGTDQLVARLPEDAAVVRIPVVYD
+VSRFPWQVTLRNWKFAPGAAERPGEDPPVVPYHDLRVLAEAATGRRREVAPAAIREAAAA
+SVQALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTLLTRVAERVAERLPGDVAVQPV
+PASRVLLGGVRAPLEAPVVEALDLDAAPTEDWTVAGQTVPAEQLRQTHLDWYAQNPQAVE
+VGMRKYADQLRLLGLTG
+>NAFOICDF_00833
+MSEETPMDDQTRTAGAEPGDEGVQVRGAAERAPSSDLPADEGRRRHYAHFYGLEPLPEGE
+LLTVMGGCQAEATRLLLCGEPGRAEGGTPASVRVPPMFELGPDDLPHLLALLKRTTVLVV
+KPVRDDYQGLPLGLGQLESLLPAGARSIRVPALYDSSRFPWLVTLRHPTRPWEDPPVVPY
+HDLRTVAEAAAEAGLIPWPAALGGPGEAGAYDAGPRLPLSAEALRGLAAESVARLRAREE
+HFGTVRVSDAVADERGVGFHTVNHPDNPLLEALARTVLAELGVDKEVHAPDRLLLGHVLA
+PIEEQVVDALGLQTAPRAAWRVGGAEVSDAEVRRAHLGWFRANPEALAPGLERHGALMRE
+LGLLA
+>MHAAABBN_01660
+MNEDEGRRRHYGHFYGLEDLPEGDLLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVP
+PAFEAQPDEVEHLERLLPRVKALVTQPIPHDYRGMPIGTDQLVARLPKDAAVVRIPVVYD
+VSRFPWQVTLRNWKVAPGAAERPGEDPPVLPYHDLRVLAEAATGRRRQVAPAAIREAAAA
+SVQALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTLLTRVAERVAGHLPGDVAVQPV
+PASRVLLGGVRAPLEAVVVEALDLDAEPTEDWTVAGQTIPAEQLRQTHLDWYAQNPQAVE
+VGMRKYADQLRLLGLAA
+>LFPAFLNI_01892
+MNEDEGRRRHYGHFYGLEDLPEGDLLLVWGNCQGESYRRLLGGEPGTPLHGADLVSVRVP
+PAFEVQPDEVAHLERLLPRVKALVTQPIPHDYRGMPIGTDQLVARLPEDAAVVRIPVVYD
+VSRFPWQVTLRNWKFAPGAAERPGEDPPVVPYHDLRVLAEAATGRRREVAPAAIREAAAA
+SVQALRAREEAKGTLSMADLVAAERGVGFYTVNHPTNTLLTRVAERVAERLPGDVAVQPV
+PASRVLLGGVRAPLEAVVVEALDLDAEPTEDWTVAGQTVPAEQLRQTHLDWYAQNPQAVE
+VGLRKYADQLRLLGLTG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000592.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000592.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1356ea49c4b9684ce59d3405651c06763203be20
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000592.fa
@@ -0,0 +1,68 @@
+>ACLBLIBL_00906
+MVAAREVTLQELLGGSYQYTVPLYQRTYSWGRPQWQRLWEDVVDVADHRRDNPSATHFIG
+SLVLAGFRDNGPGGVQRWLVVDGQQRLTTLTLLLAAVRDHRAEHEGPMHADRVNEKYLVN
+KWEDGDLRYKVLPTQADRAAYRGRIEHAPDAAEGSRISEAHQFFLTKLFGLSQPSADGEE
+EQLTLAEVESAVVAGLSIVSVTTGENDNAHRIFESLNNTGLKLTQGDLLRNYLFMQLPTR
+ADEVYTTLWLPLQNLLSNEELETLFWLDLVQQDPKVRQTEIYAGQQRRMRGLQDESQVRA
+EVERFLALGRLYDVMLRPEKEKDAAVRFRLARLRAWRTTTTFPITLHLMERRSLGDIDSD
+ELARALLYLESYLVRRLVFGRYSDGLNTTLLAATADIQGQDDPADALQRFLSSGRKHFAS
+DDQIRQAVITAPFYTTGRAAHRKLILRWIEESYGSKEPVDLDSATIEHVMPQTLTEEWER
+ALAGQLEAHQDLREVHTELLHTLGNLTLTGYNSELSNGPFAVKRAELAKSGIRMNQEIST
+VPVWGPAQIRARAERLADRIVGIWPGPSAEAASGVAHTAWQTLTDAVEAIPAGSWTSYGE
+LARLIGSHPVPVGTYLARTALPHAHRVLQAGGTVSPSFRWTDVHRKDDPHDVLAAEGVRF
+SEDGRAYGGQRLVAEQLAELIDVDVDLTDPRSLAAPGNDPALRDRWVDRLHDHNDPESAR
+ALIEVQRGWVERGGRAEFADNAAGGCFLVVPRASARAIWPVILYPTYGVEVVFYHLAKWP
+PFTDEALLDDFRGRLNLIPGVEFGPEALRRRPSIRPQILQPAAAQEAFLDALEWFLHTIQ
+EDDRSA
+>MOLHKGIG_01951
+MINSAEPRHVHELFSSQTKAHYVVPPYQREYSWHRAQWEALFADLVESEDEHFLGTIITL
+SRTKDSLSGPVLEVIDGQQRLTTLTILLAAVHSHLQDAEDLDEDARFERMTLRRELVRDE
+AKAPRLTPQVQGANRADYQAMLADAGLPVKSEKKAYYPSRKVAKAFWFFRAAITELAEER
+GESLSTTALSVLAAARRALIVNIEVASAADAFVLFESLNNRGVPLTPVDLIKNSFLARAE
+HRAGMEVEEAFELWSDTLAHLGDSYATHERFLRHFYNAFRGDLPPVKLAPVATRKNLIRI
+YETLLDQDLEGTVRSLERAAQVYGRIAGGGDVDEPTSLDQELTALRRAQAAPSYVLVMWL
+LVRQEKAGWSEEDLAAVARLLVSFFVRRNLTGFPATYALPRLFMDVIDQVAAGEPDRLLT
+IVRGSLVAASASDATFRERLEGPVYEENRDVTRFLLATLAEDAMTKETRVDLWAQSGKTF
+VWTIEHILPQGENLPQEWVDALGGPEAAAETQNRFVHTLGNLTITGFNSTLGNQTFLRKR
+DRIDHQGRAIGYRNGLALNAELAEKEAWSSADIEARTVRLVERALERFAL
+>NAFOICDF_00292
+MSHERVYRIGSPGAEPLVPVSFAEAGLRERQDLQEWVIAHPEILGEDIRIVAFEFDRWED
+ADGGRQRDRLDVLGLDQSGCLVLAELKRDAAPDTVEMQAIKYAAMASRFTEEKLVAWHAA
+MLGRLENRPVSEEEAREALTDHAGELDVEQLRRPRIVLVAGAFTRSTTAAVVWLTEMGLD
+ITLQRVQAYRMGGDDVVITVSQLFPVPDVEEFTVSPMRMESTARRTSSTRSPSTVRRLVK
+AGTLPDGTVLTLVPTTEVNAETREAIADWISDDPRRGRATWWNDPTKPMEWELDGNRYRP
+SRIVQQALREATGITRSPRGPAWWVTESGMSLTELAGDVENGAFDWTQLHRLLCELPAGR
+WTTYGEVARLIGTAPQPLGGHFRTCTLCRNAYRVLDANGAVSSGFTWGDPQETRTQQEVL
+EAEGISFDGGRAAPSQRLQPSELESVWKVAQAALGE
+>NAFOICDF_00845
+MVAAREVTLQELLGGSYQYTVPLYQRTYSWGRPQWQRLWEDVVDVADHRRDNPSATHFIG
+SLVLAGFRDNGPGGVQRWLVVDGQQRLTTLTLLLAAVRDHRAEHEGPMHADRVNEKYLVN
+KWEDGDLRYKVLPTQADRAAYRGRIEHAPDAAEGSRISEAHQFFLTKLLGLSQPSAAGEE
+EPLTLAEVESAVVAGLSIVSVTTGENDNAHRIFESLNNTGLKLTQGDLLRNYLFMQLPTR
+ADEVYTTLWLPLQNLLSNEELETLFWLDLVQQDPKVRQTEIYAGQQRRMRDLQDESQVRA
+EVGRFLALGRLYDVMLRPEKEKDAAVRFRLARLRAWRTTTTFPITLHLMERRSLGDIDSD
+ELARAFLYLESYLVRRLVFGRYSDGLNTTLLAATADVQGQDDPADALQRFLSTGRKHFAS
+DDQIRQAVMTAPFYTTGRAAHRKLILRWIEESYGSKEPVDLDSATIEHVMPQTLTEEWER
+ALAGQLEAHQDLREVHTELLHTLGNLTLTGYNSELSNGPFAVKRAELAKSGIRMNQEISA
+EPVWGPAQIRARAERLADRIVDIWPGPSAEAASGVAHTAWQTLTDAVEAIPAGSWTSYGE
+LARLIGSHPVPVGTYLARTALPHAHRVLQAGGTVSPSFRWTDVHRTDDPHDVLAAEGVRF
+SEDGRADGGQRLVAEQLAELIDVDVDLIDPRSLAAPGNDPALRDRWVDRLHDHNDPESAR
+ALIEVQRGWVERGGRAEFADNAAGGCFLVVPRTSARAIWPVILYPTYGVEVVFYHLAKWP
+PFTDEALLDDFRGRLNLIPGLEFGPEALRRRPSIRPQTLQPAAAQEAFLDALEWFLHTVQ
+EDDRSA
+>LFPAFLNI_01872
+MVAAREVTLQELLGGSYQYTVPLYQRTYSWGRPQWQRLWEDVVDVADHRRDNPSATHFIG
+SLVLAGFRDNGPGGVQRWLVVDGQQRLTTLTLLLAAVRDHRAEHEGPMHADRVNEKYLVN
+KWEDGDLRYKVLPTQADRGAYRGRIEHAPDAAEGSRISEAHQFFLTKLLGLSQPSADGEE
+EPLTLAEVESAVVAGLSIVSVTTGENDNAHRIFESLNNTGLKLTQGDLLRNYLFMQLPTR
+ADEVYTTLWLPLQNLLSNEELETLFWLDLVQQDPKIRQTEIYAGQQRRMRGLQDESQVRA
+EVERFLALGRLYDVMLRPEKEKDAAVRFRLARLRAWRTTTTFPITLHLMERRSLGDIDSD
+ELARALLYLESYLVRRLVFGRYSDGLNTTLLAATADIQGQDDPADALQRFLSSGRKHFAS
+DDQIRQAVMTAPFYTTGRAAHRKLILRWIEESYGSKEPVDLDSATIEHVLPQTLTEEWER
+ALAGQLEAHQDLREVHTELLHTLGNLTLTGYNSELSNGPFAVKRAELAKSGIRMNQEISA
+EPVWGPAQIRARAERLADRIVGIWPGPSAEAASGVAHTAWQTLTDAVEAIPDGSWTSYGE
+LARLIGSHPVPVGTYLARTALPHAHRVLQAGGTVSPSFRWSDVHRTDDPHDVLAAEGVRF
+SEDGRADGGQRLLAEQLAELIDVDVDLTDPRSLAAPGNDPALRDRWVDRLHDHNDPETAR
+ALIEVQRGWVERGGRAEFADNAAGGCFLVVPRTSARAIWPVILYPTYGVEVVFYHLAKWA
+PFTDETLLDEFRGRLNLIPEVEFGPESLRRRPSIKPQTLQPAAAQEAFLDALEWFLRTVQ
+EDDRTS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000596.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000596.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6d4acc872fbc747e637ea6d32ee6230886b85c1d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000596.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_00913
+MTEQTSPAAPTADSPSPEDTIGRLFTRAAARHPETVALRFEDRDWTYAQLLDGVHRVARR
+LLATGLPRGTRVAAYGANSDAYAVLFLACVTAGYVHVPVNFALKGGELAHALEDSGAEVL
+VADAGMLERVEQVRADGGGAGLRHVWTMLPAGHAEPSLLETARDEAADATAPDVPVTATD
+LAQLLYTSGTTSTPKGAMMSHRALITEYLSSIIALDFTAEDRPLVAMPLYHSAAMHVFLL
+PYLSLGATVRLLATPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLRKAQ
+YGASIMPVTVLQRLRQSQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHVEA
+RVMTADGAPAAPGEPGEIQYRSPQLLSGYWNRPDATADAFTDDGWFRSGDQVTQDAAGYI
+QVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVIGLPDERWIEAVTAVVVLKEGAE
+LTAETVRTHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR
+>MOLHKGIG_01943
+MPDQITHPTDAAAHPSPAPEDTIGRVFARAVARSPQAVALRFEDRDWTYTQLRDGAHRVA
+RRLQDTGLPAGTRVAAYATNSDAYALLFLACVTAGYVHVPVNFALKGGELAHALEDSGAE
+LLVADAGMLERVDQVRAEGRASALRHVWTMLPAGHAEPSVLETARDETLDAAAPEAEVSA
+TDLAQLLYTSGTTSTPKGAMMSHRALVAEYLSSMIALDFTAEDRPLVAMPLYHSAAMHVF
+LLPYLSLGATVRLLAAPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLRK
+AQYGASIMPVTVLQRLRQSQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHV
+EARVMTADGAPAAPGEPGEIQYRSPQLLSGYWNRPDATADAFTDDGWFRSGDQVTQDAAG
+YIQVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVVGLPDERWIEAVTAVVVLKEG
+AELTAETVRAHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR
+>NAFOICDF_00851
+MPDQITHPTDAAAHLSPAPEDTIGRVFARAVARSPQAVALRFEDRDWTYAQLRDGAHRVA
+RRLQGTGLPAGTRVAAYATNSDAYALLFLACVTAGYVHVPVNFALKGGELAHALEDSGTE
+LLVADAGMLERVDQVRAEGRASALRHVWTMLPAGHAEPSVLETAQDEALDAAAPEAEVSA
+TDLAQLLYTSGTTSTPKGAMMSHRALVAEYLSSIIALDFTAEDRPLVAMPLYHSAAMHVF
+LLPYLSLGATVRLLAAPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLRK
+AQYGASIMPVTVLQRLRQSQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHV
+EARVMTADGVPAAPGMPGEIQYRSPQLLSGYWNRPDATADAFTDDGWFRSGDQVTQDAAG
+YIQVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVIGLPDERWIEAVTAVVVLKEG
+AELTAETVRTHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR
+>MHAAABBN_01639
+MPDQITHPTDAGHLSPAPEDTIGRVFARAVARSPQAVALRFEDRDWTYAQLRDGAHRVAR
+RLQDTGLPAGTRVAAYATNSDAYALLFLACVTAGYVHVPVNFALKGGELAHALEDSGAEL
+LVADAGMLERVDQVRAEGRASALRHVWTMLPAGHAEPSVLETAQDETLDAAAPEAEVSAT
+DLAQLLYTSGTTSTPKGAMMSHRALVAEYLSSIIALDFTAEDRPLVAMPLYHSAAMHVFL
+LPYLSLGATVRLLAAPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLHKA
+QYGASIMPVTVLQRLRQSQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHVE
+ARVMTADGAPAAPGEPGEIQYRSPQLLSGYWNRPDATADAFTDDGWFRSGDQVTQDAAGY
+IQVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVIGLPDERWIEAVTAVVVLKEGA
+ELTAETVRTHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR
+>LFPAFLNI_01862
+MPDQITHPTDAGHLSPAPEDTIGRVFARAVARSPQAVALRFEDRDWTYAQLRDGAHRVAR
+RLQDTGLPAGTRVAAYATNSDAYALLFLACVTAGYVHVPVNFALKGGELAHALEDSGAEL
+LVADAGMLERVDQVRAEGRASALRHVWTMLPAGHAEPSVLQTAQDETLDAAAPEAEVSAT
+DLAQLLYTSGTTSTPKGAMMSHRALVAEYLSSIIALDFTAEDRPLVAMPLYHSAAMHVFL
+LPYLSLGATVRLLAAPDIPRMLELVETEHIGSLFLAPTVWVPLANHPDLATRDLSSLHKA
+QYGASIMPVTVLQRLRQSQPGIGFYNCFGQSELGPLCTVLRPEEHDARPASCGRPVFHVE
+ARVMTADGAPAAPGEPGEIQYRSPQLLSGYWNRPDATADAFTDDGWFRSGDQVTQDAAGY
+IQVVDRIKDVINTGGVLVAPREVEDAIYELDEVAEVAVIGLPDERWIEAVTAVVVLKEGA
+ELTAETVRAHVKERLAGFKVPKRVDFVAELPRNQSGKLLKRALRAERTQEAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000597.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000597.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1bf80102f985c4912274b5698a83f97025d6ecc8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000597.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00914
+MPEAYIIDAVRTPVGRRGKGLAQVHPLDLAAAPLREIVGRQDIDSAEYDEVILGCIDQLG
+PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAVMSGTADLVVAGGVQSMS
+AIPLSHSNRAAAEFGFADPFTGSESWAARYGNEEISQFRGAEMMARHWNLDRDVLEEFAV
+RSHERALAAQADGRFDREILPLAGLTADEGPRTPDAAKIASLDPIVPGGLHTAATASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERSGG
+RYGLQTMCEGGGQANVTVIERL
+>MOLHKGIG_01942
+MPEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPLRELVARQDIDSAEYDEVILGCIDQLG
+PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAIMSGTADLVVAGGVQSMS
+AIPLSLSNTAARELGFPDPFTGSESWAARYGDEEISQFRGAEMMARHWNLDRDALEEFAV
+RSHERALAAQADSRFDREILPLAGLTADEGPRTPDAAKIASLDPIVPGGLHTAATASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERSGG
+RYGLQTMCEGGGQANVTVIERL
+>NAFOICDF_00852
+MGEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPIRELVGRQDVDSAEYDEVILGCIDQLG
+PQAMDVARSAWLAAGLSEDVPGSTIERQCGSGQQAIHYAAQAVMSGTADLVVAGGVQSMS
+AIPLSRSNTAARELGFPDPFTGSESWAARYGDEEISQFRGAEMMARHWNLDRDALEEFAV
+RSHERALAAQADGRFDREILPLAGLTADEGPRTPDAAKIASLDPIVPGGLHTAASASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAFALRRMGLGIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERTGG
+RYGLQTMCEGGGQANVTVIERL
+>MHAAABBN_01638
+MPEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPLRELVGRQDIDSAEYDEVILGCIDQLG
+PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAVMSGTADLVVAGGVQSMS
+AIPLSRSNTAARDLGFPDPFTGSESWAARYGSEEISQFRGAEMMARHWNLDRDALEEFAV
+RSHERALAAQADGRFDREILPLAGLTADEGPRTPDATKIASLDPIVPGGLHTAATASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERTGG
+RYGLQTMCEGGGQANVTVIERL
+>LFPAFLNI_01861
+MPEAYIIDAVRTPVGRRGKGLAGVHPLDLAAAPLRELVGRQDIDSAEYDEVILGCIDQLG
+PQAMDVARNAWLAAGLSEDVPGTTVERQCGSGQQAVHYAAQAVMSGTADLVVAGGVQSMS
+AIPLSRSNTAARDLGFPDPFTGSESWAARYGSEEISQFRGAEMMARHWNLDRDALEEFAV
+RSHERALAAQADGRFDREILPLAGLTADEGPRTPDATKIASLDPIVPGGLHTAATASQMS
+DGAAALLLASEEAVRRHGLTPRARIHHLSARGADPVMMLSAPIPATAYALDRMGLTIDDM
+DLVEINEAFAAVVLAWLTETGADPAKVNVNGGAIALGHPIGATGARLMTSLLHELERTGG
+RYGLQTMCEGGGQANVTVIERL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000599.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000599.fa
new file mode 100644
index 0000000000000000000000000000000000000000..35cdd946ffada5f20fb8f701710118ba214a3e83
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000599.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_00921
+MRVVAAPLAMLPGVDHGPALRMDLHPVPGGIVYVARDLVLRELGDDVRGHVHAGMVGTAQ
+LHAFWSTVTVDLPPDRPVIVRLRSDRDAELLSLLEVLAPVEMRVVSYRLDESPVGTQRSS
+YLLPDVDPEIVARAESPRVPLEAIEATQEEEDALRRSSGVFLSRRRTDRFLRRTLPTVTH
+SLSFSDEADVADVYVDGSVLRSSRIGGAAAVGGPSMWAVQAVNGATTPLEVELEALVLGH
+VVSAWAGVPGERVTIHSDSRAALALLNAARRERLTLGGARGERVRRTLRRLLAAVDLAQA
+ADVRVETTWVKGHVGVQGNELADDLARAAARHAGVGTSEEDLRRRLDRLIDLHEEAEAEA
+GQTPARAVAAEGHRPMPPGRRPGPRL
+>MOLHKGIG_01938
+MGARINHPRTVVDRTLHHDVEPAHPAALVDVGWDFRGPGAKAEEQHRPLRVVRARRPRGT
+PRDRNGVDLTRTGPVVPRPSPPRTRIRRDGVRVVASPLAMLPGVDHGPALRLDLHPTTGG
+IVYVARELELRELGDDVRGHVYTGMVGTAHLSVFWSTVTVDLPPERPVIVRLRSDRDAEL
+LSLLEVLAPVDTRVVSYRLDESPVGTQRSSYLLPDVDPETVAQTGAARIPLEAIEAAQEE
+EDALRRSSGVFLSRRRTDRFLRRNLPGVTHSLTFADEADVTDVYVDGSVLRGSRIGGAAA
+VAGPSMWAVQAVAGATMPLEVELEALVLGHVICAWAGTPGGRVTIHSDSRAALALLNAAR
+RERLTLGGARGERIRRTLRRLLAAVDLAQAADVQVDTTWVKGHVGVHGNELADDLARAAA
+RHASVGTPEGDLPERMGQLIQLRVEDDAAG
+>NAFOICDF_00855
+MDNSSTHPREGQVRSLHFDTDASSPDALLDPMWAFTGPRASRAGAPAPDGADVLARRARP
+AHPGAALVRAATSLFTLPGPPGMPHRSRSAALEAARAPAGYLSPVPHRLALPRPARPRPA
+PPRMRVRQDGVRVVARPLAMLPGVDHGRALRLDLHPVRDGIVFVSRHLELRELGDDVKGL
+VLTGVVPAARLGYFWDTVAGDLPEGRPVIVRLRSNDDAELLTLLRAIAPPWLRVVSYRLD
+ESPVGSQRSSYLLPDVDGEAVAASGAERVPLETLREAHQASAEVERASRVFLARRRVDRF
+VRRSVPDLMHSLSYTDPAEVRHVYVDGSVLRGTRTGGAAAVTRSGPWAAHALPGATIPLE
+AELEALTLGHLMAAWSGTPDERVLIHSDSRAALALLREAHRERLTLGDARGERIRRALRR
+LLAAVDLAGSAGVEVSTLWVKGHAGTHGNELADDLARSAARNTAAGVSADEMRRRMRHVV
+QLWDATTHPQA
+>MHAAABBN_01634
+MGARINHPRTVVDRTLHHDVEPAHPAALVDVGWEFRGPGAKAEEQHRPLRVVRARRPRGT
+PRDRNGVDLTRTGPVVPRPSPPRTRIRRDGVRVVASPLAMLPGVDHGPALRLDLHPTTGG
+IVYVARELELRELGDDVRGHVYTGMVGTAHLSAFWSTVTVDLPPERPVIVRLGSDRDAEL
+LSLLEVLAPVDTRVVSYRLDESPVGTQRSSYLLPDVDPETVAQTGAARIPLEAIEAAQEE
+EDALRRSSGVFLSRRRTDRFLRRNLPGVTHSLTFADEADVTDVYVDGSVLRGSRIGGAAA
+VAGPSMWAVQAVAGATMPLEVELEALVLGHVICAWAGTPGGRVTIHSDSRAALALLNAAR
+RERLTLGGARGERIRRTLRRLLAAVDLAQAADVQVDTTWVKGHVGVHGNELADDLARAAA
+RHASVGTPEGDLPERMGQLIRLRVEDDAAAG
+>LFPAFLNI_01857
+MGARINHPRTVVDRTLHHDVEPAHPAALVDVGWDFRGPGAKAEEQHRPLRVVRARRPRGT
+PRDRNGVDLTRTGPVVPRPSPPRTRIRRDGVRVVASPLAMLPGVDHGPALRLDLHPTTGG
+IVYVARELELRELGDDVRGHVYTGMVGTAHLSVFWSTVTVDLPPERPVIVRLRSDRDAEL
+LSLLEVLAPVDTRVVSYRLDESPVGTQRSSYLLPDVDPETVAQTGAARIPLEAIEAAQEE
+EDALRRSSGVFLSRRRTDRFLRRNLPGVTHSLTFADEADVTDVYVDGSVLRGSRIGGAAA
+VAGPSMWAVQAVAGATMPLEVELEALVLGHVICAWAGTPGGRVTIHSDSRAALALLNAAR
+RERLTLGGARGERIRRTLRRLLAAVDLAQAADVQVDTTWVKGHVGVHGNELADDLARAAA
+RHASVGTPEGDLPERMGQLIQLRVEDDAAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000600.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000600.fa
new file mode 100644
index 0000000000000000000000000000000000000000..334eadc83bf7247ebeb0b063132bd75641ec9f73
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000600.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00922
+MSSPPRAGSSRGRLSATDVVDAAVGILQDFGMGDLSMRRVASVLGVQASALYWHVPDKQT
+LLARVADRIVAEAEEAVRHRGIADLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLH
+ALLTEAAPTPEEGERALALLLGGVSLRQQRAQAEALGVRVGPDVQRHRTDPL
+>MOLHKGIG_01937
+MTPPAPRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAGVLGVQASALYWHVPDKQSLLAR
+VADRIVAEAEETVRARRVTDLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLHRLLT
+EAADTPEDGERALALLLGTVSLRQQRAQAQALGVATGPDVQRHRTDPL
+>NAFOICDF_00856
+MSTSSARGRLSAEDVVDAAVGILQDFGMGDLSMRRVASMLGVQASALYWHVPDKQTLLAR
+VADRIVADVERACAARRVEDLAGRAEEAEAVLLRHRDGADVVLSALALGLGGLGLHRLLV
+DAAHTPEEGERALAALLGTAALRQQRNQAAALGLRLGPDVQARRTGAL
+>MHAAABBN_01633
+MTPPAPRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAAVLGVQASALYWHVPDKQSLLAR
+VADRIVAEAEETVRARRITDLAGRAEAAEAALLRHRDGADLVLSALALGLGGLGLHRLLT
+EAADTPEDGERALALLLGTVSLRQQRAQAQALGVPTGPDVQRHRTDPL
+>LFPAFLNI_01856
+MTPPAPRPRLTAQDVVDAAVGILQDFGMGDLSMRRVAGVLGVQASALYWHVPDKQSLLAR
+VADRIVAEAEETVRARRVTDLAGRAEAAEAALLRHRDGADVVLSALALGLGGLGLHRLLT
+EAADTPEDGERALALLLGTVSLRQQRAQAQALGVATGPDVQRHRTDPL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000602.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000602.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ae37c5cad04719e154e150e485a68277ba5bc6b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000602.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_00924
+MDGPARGGGLLTVGLTSVPAPVGGPGAPPGAPGPAASGGRRRRRTAGGDGIGAWWLLAAV
+VPVAFLLVFFAWPVGAMLWRGVSAEGVLDLGAFAEVLGRERTWRIVGQTLGMAAAGTVLA
+VALGLPAAFVLHRRAFPGRAALRAVITVPFVLPTVVVGVAFRALLAPGGPFGWTGLDQST
+AAVVLAMVFFNVSVVVRQVGALWASLDPRQAEAARTLGSSGWRAFRTVTLPQLAPALASS
+AALVFLFCASAFGIVQTLGRPGVGTLESEIWVQTVVYFDLGTAAVFSTLQFLVVLAAVLV
+SGATARRTRRALRLRDAPVRRLTRADAAPVAVTLATALLVLAPLATLLVRSFHSSEGWGL
+RNYRLLASSPGAGFSGGVTPAQALEHSLRIALDATLLTLLIGVPLALLLTRPVRSAAGRR
+AQRGLDGALLLPLGVSAVTVGFGFVVSLRAEAPALAASGALVPIAQAVVALPLVVRSLVP
+VLGAVDPRLREAARTLGAGPLRVLATVDGPFLLRGLGVAAGFAFAVSLGEFGATSFLSSP
+DYQTLPLLIVKLLGRPGADNYGMALAAATVLAVLSAGTMMACERLGPRAAASRGGI
+>MOLHKGIG_01935
+MSALTEVAAPGTDLPRRRARGRGDGLGPWWLVAAVLPVAFLLVFFAWPVAAMLWRGIGGD
+ADAFTGAVDLTAFGETLARERTWRILGQTLGMAAAGTVVSVALGLPTAFVLHRRRVPGRA
+VLRALVLVPFVLPTVVVGVAFRALLAPGGPLGFTGLDQTTTAVVLAMVFFNVSVVVRQVG
+ALWNALDPRQTEAARTLGASPWRAFRTVTLPQLAPAIAASAALVFLFCASAFGIVQTLGR
+PGYGTLESEIWVQTSVYLDLRTAAVFSVLQFAVVLVAVVVSGVTAARTQRALRLRETPPA
+RLTRADAVPVAVMLAVVALVVAPILTLVVRSFHTRHGWGLGNYRLLSTSAGSGFVGGSTP
+ARALEQSLRVAVDATLVTLVVAVPLALLLTRPFRSRAALAAQRALDGALLLPLGVSAVTV
+GFGFVVSLRAAFPELAASGVLVPLAQAVVALPLAVRALVPVLAAVDPRLREAARTLGAGP
+WRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLASPSAPTLPVLIARLLGRPGADN
+YGMALAAATVLAVLSAGIMLVCERLRPRGPAGAGGL
+>NAFOICDF_00858
+MPTPAPARGRRRATLRPPRGRRAAGDGLAPLWLLSAAVPVAFLLVLFAWPVAAMLWRGVA
+SVDAAGDPTGGLDLSAFAQTLGAPRTWRILGNTLGLAAAGTAASVALGVPTAFALHRRAF
+PGRGLARAVVTVPFVLPTVVVGAAFRALLAADGPLGWTGLDQTSTAVVMAMVFFNVSVVV
+RQVGGLWAALDPRQAEAARTLGASPWRAFRTVTLPQLAPAVAGAAALVFLFCASAFGIVQ
+TLGRPGPGTLETEIWAQTTVYLDLRTAAVLSTVQLAVVLAAILASGAAAARARRALRLGE
+APARPLTRADAVPAAVTLAVLALVVAPILALLAGSLHSAEGWGLRNYRLLATSPGTGFAG
+GVTPAQALEQSLRTAVDATVVTLVVAVPLALVLTRPVRSRAGRAAQRALDGALLLPLGVS
+AVTVGFGFIVSLRATAPDLAASGALVPLAQSVIAVPLAVRALVPVLGAVDPRLREAARTL
+GAGPWRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLAAADRPTLPVLIARLIGRP
+GADNHGMALAAAVVLAVLSAGALLACERLRPRGAAPSGGL
+>MHAAABBN_01631
+MSALTEVAAPGTDLPRRRARGRGDGLGPWWLVAAVLPVAFLLVFFAWPVAAMLWRGIGGD
+ADAFTGAVDLTAFGQTLARERTWRILGQTLGMAAAGTVVSVALGLPTAFVLHRRRVPGRA
+VLRALVLVPFVLPTVVVGVAFRALLAPGGPLGFTGLDQTTTAVVLAMVFFNVSVVVRQVG
+ALWNALDPRQTEAARTLGASPWRAFRTVTLPQLAPAIAASAALVFLFCASAFGIVQTLGR
+PGYGTLESEIWVQTSVYLDLRTAAVFSVLQFAVVLAAVVVSGVTAARTQRALRLRETPPA
+RLTRADAVPVAVMLAVVALVVAPILTLVVRSFHTRHGWGLGNYRLLSTSAGSGFVGGSTP
+AQALEQSLRVAVDATLVTLVVAVPLALLLTRPFRSRAALAAQRALDGALLLPLGVSAVTV
+GFGFVVSLRAAFPELAASGVLVPLAQAVVALPLAVRALVPVLAAVDPRLREAARTLGAGP
+WRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLASPSAPTLPVLIARLLGRPGADN
+YGMALAAATVLAVLSAGIMLVCERLRPRGPAGAGGL
+>LFPAFLNI_01854
+MSALTEVAAPGTDLPRRRARGRGDGLGPWWLVAAVLPVAFLLVFFAWPVAAMLWRGIGGD
+ADAFTGAVDLTAFRETLARERTWRILGQTLGMAAAGTVVSVALGLPTAFVLHRRRVPGRA
+VLRALVLVPFVLPTVVVGVAFRALLAPGGPLGFTGLDQTTTAVVLAMVFFNVSVVVRQVG
+ALWNALDPRQTEAARTLGASPWRAFRTVTLPQLAPAIAASAALVFLFCASAFGIVQTLGR
+PGYGTLESEIWVQTSVYLDLRTAAVFSVLQFAVVLAAVVVSGVTAARTQRALRLRETPPA
+RLTRADAVPVAVMLAVVALVVAPILTLVVRSFHTRHGWGLGNYRLLSTSAGSGFVGGSTP
+AQALEQSLRVAVDATLVTLVVAVPLALLLTRPFRSRAALVAQRALDGALLLPLGVSAVTV
+GFGFVVSLRAAFPELAASGVLVPLAQAVVALPLAVRALVPVLAAVDPRLREAARTLGAGP
+WRVLATVDGPFLARGVGVAAGFAFAVSLGEFGATSFLASPSAPTLPVLIARLLGRPGADN
+YGMALAAATVLAVLSAGIMLVCERLRPRGPAGAGGL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000603.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000603.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37219b3d54fecc367669153f90cdd9715029800a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000603.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_00925
+MTTAPHRVRTRPRRHGALAALSVAALALTGCSVADRGGSGDQGSSSAEARTVTIMTHDSF
+SLPDELIARFEQESGHTLVTTAPGDAGSVVNQLLLAKDAPTVDGVYGIEDHSAHRLVSEG
+VIAEHVPADLPDSARDLVVDGRMTPVDQGQVCLNVDTPWFQEQGLAAPTTLEQVAAPEYA
+ELTVVTSPVSSSPGLALLAATVAEFGEDGWQDWWRTALQGGMQVDASWSDAYNTSFSGGE
+GTGTRPIVLSYSSSPAFAPDTDVVAASCTPQVEYAGVVEGAENPEGARAFVDFLLTEDVQ
+AAIPDAMYMYPVDSSVPLPEAWAEHAPLVEDPIVPDAGLLDSRREDLLKEWTALHEEAAS
+>MOLHKGIG_01934
+MSRTPHRALAALSVAALALTGCSVSGSSGDGASSSAAGAGGEPTTVTIMTHDSFNLPQEL
+VQKFEQESGYTLKTTAPGDAGSVVNQLLLAKDEPTVDGVYGVEDHSAHRLVREGVVAEYT
+PQDLPASAQDRMVEDRMTPVDQGQVCFNTDPAWFEAHDVEAPTSIDQLDDPEYAKLTVAT
+SPVASSPGLALLAATTEKYGDDGWQDWWRGLKENGGKVADSWSDAYNSDFSGGEGKGRFP
+VVLSYSSSPAFAPETEVIEDSCTPQVEYAGVLEGAKNPEGAQAFVDFMLTEEVQSALPES
+MYMYPIDESVQLPEEWAQNAPLVEDAITPDPARIDERREDLLKEWTALAEASRR
+>NAFOICDF_00859
+MSVHRTATTRRGVLAAACLSALALTGCSVSAPSTGSSSSAASSSAAPSSASGSSSTSASG
+TAAAGSKGTVTIMTHDSFALPKELIAQFEAESGYRLVTTAPGDAGAVVSQVLLSKDAPVA
+DGVYGVENHSAHRLVDQGAVQDVAPADLPASAEDLVVDGKMIPVDQGQVCFNTDPAWFTE
+HGVAEPTSIDQLRDPEYAKLTAVTSPVTSSPGLALLAATTEKYGDDGWQGWWEDLLKGGA
+KVDSTWSDAYSTDFSGGEGKGEFPVVLSYSSSPAFAPQTAVIEDSCTPQVEYAGVLTGAE
+NPEGAKAFVEFLLSKDVQAAIPENMYMYPVDDTVELPAEWAANGPLVEDPITPDPAEIDT
+EREGLLKEWTALSESAGSR
+>MHAAABBN_01630
+MSRTPHRALAALSVAALALTGCSVSGSSGDGASSSASGAGGGEPTTVTIMTHDSFNLPQE
+LVQKFEQESGYTLKTTAPGDAGSVVNQLLLAKDEPTVDGVYGVEDHSAHRLVREGVVAEY
+TPQDLPASAQDRMVEDRMTPVDQGQVCFNTDPAWFEAHDVEAPTSIDQLDDPEYAKLTVA
+TSPVASSPGLALLAATTEKYGDDGWQDWWRGLMENGGKVADSWSDAYNSDFSGGEGKGRF
+PVVLSYSSSPAFAPETEVIEDSCTPQVEYAGVLEGAKNPEGAQAFVDFMLTEEVQSALPE
+SMYMYPIDESVQLPEEWAQNAPLVEDAITPDPARIDERREDLLKEWTALAEASRR
+>LFPAFLNI_01853
+MSRTPHRALAALSVAALALTGCSVSGSSGDGASSSAAGAGGEPTTVTIMTHDSFNLPQEL
+VQKFEQESGYTLKTTAPGDAGSVVNQLLLAKDEPTVDGVYGVEDHSAHRLVREGVVAEYT
+PQDLPASAQDRMVEDRMTPVDQGQVCFNTDPAWFEAHDVEAPTSIDQLDDPEYAKLTVAT
+SPVASSPGLALLAATTEKYGDDGWQDWWQGLMENGGKIADSWSDAYNSDFSGGEGKGQFP
+VVLSYSSSPAFAPETEVIEDSCTPQVEYAGVLEGAKNPEGAQAFVDFLLTEEVQSALPES
+MYMYPIDESVQLPEEWAQNAPLVEDAITPDPARIDERREDLLKEWTALAEASRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000605.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000605.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c63bddd0af70e1faaa694c22f2c1e65acfecc49
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000605.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_00927
+MPAAETVPADAAGRPDARPRVPGPREQPERAWLALPRRHPVPALLDEARDAVAGLAETLA
+EVLPVTVLTDPADHAVRSLIPPEVDLLAAPVDSPLLGRTGPGFVRRPEGLAAIAWRPAAG
+AGGPGPRDAGVAAAVAAAAGLPLLTPMLRAPRDAWVADGEGTAVVAADPVLDGRTNPAWT
+PEQVEAEFAALLGITRVAWLPPVPRIPTGPWGGAGHLGAWVRLLGGGEAAVHWRADRFHP
+EHLHGAAALRILQDAPDAAGRPLRVRTVPGGALPPEHDPAEIGPRSLVDTVPLGSAVLRP
+AFEDAATEEAAAAACAALHPGLRPVPFPGPPLLRLAGSLSDLVLVQPHP
+>MOLHKGIG_01932
+MAAVDPAPTDARERRDLVVPVPGPEDPPERAWLVLPHRHPVPTLLEETRDAVVGLAETLA
+AVLPVTVLAHPRDAGAARLVPPEVDLLRAPVGSPLLGRTGPSFVRRPEGLAAVAWRSAAG
+LTGTGPLDGAAATAVAEAAGLPLLTPLLCAPRGAWVSDGEGTAVVAADPVLDGRINGAWT
+PGQVAAEFAALLGITRVLWVPPAPRPDTGPWGGPGHLASWVRLQGDGEAAVHWRGDRFNP
+EHPYAAAALRFLQGADDAAGRPLRVRTVTGAAQPAEYDPAERGPRSLLDTLPLGAAVLRP
+AFEDAAGEEAAAAACAALHPGRPQLSFPAPPLLRLAGALNDLVLLQPRP
+>NAFOICDF_00861
+MSTPAVPEPPRAPAPWEVPERLWLALPAVHPVPGLLAEARDAVAGLAETLGAHAPVAVLT
+DPDDADAARLLPGVVERVPVRGASPLPGREGPTFVHAAGTRGSVEAVHWRLPSDAAGTAG
+RAAATADAVARSAGLPLRTPLFSAPAGTWAADGDGTAVVSAALLDPAVNEGWTRAQAEDA
+LAGLLGAERVLWLPPVAGHAAGPWDGGGAAQPHPHPWLRFVAPGEVAVHWQPGRLHPDHA
+ASAAALHALTGARDARGRALSVRTVRALPPGPDADLEARGPLSALDLLPLAPGVVLRPAH
+ADPEADAATAEAAAALFPGAEQVPFPGPPLLRLLGTLSDLVLPQPPGARTRRPSPAPAHP
+EGPRAAP
+>MHAAABBN_01628
+MAAVDPAPTDARERRDVVVPVPGPEDPPERAWLVLPHRHPVPTLLDETRDAVVGLAETLA
+AVLPVTVLAHPRDAGAARLVPPEVDLLRAPVGSPLLGRTGPSFIRRPEGLAAVAWRSAAG
+LTGTGPLDGAAATAVAEAAGLPLLTPLLCAPRGAWVSDGEGTAVVAADPVLDGRINGAWT
+PGQVAAEFAALLGITRVLWVPPAPRPGTGPWGGPGHLASWVRLRGDGEAAVHWRGDRFHP
+EHPYAAAALRFLQGADDAAGRPLRVRTVTGAAQPAAYDPAERGPRSLLDTLPLGAAVLRP
+AFEDAAGEEAAAAACAALHPGLPQLSFPAPPLLRLAGALNDLVLLQPRP
+>LFPAFLNI_01851
+MAAADPVPTDARERRDVVVPVPGPEDPPERAWLVLPHRHPVPTLLDETRDAVVGLAETLA
+AVLPVTVLAHPRDAGAARLVPPEVDLLRAPVGSPLLGRTGPSFIRRPEGLAAVAWRSAAG
+LTGTGPLDGAAATAVAEAAGLPLLTPLLCAPRGAWVTDGEGTAVVAADPVLDGRINGAWT
+PGQVAAEFAALLGITRVLWVPPAPRPGTGPWGGPGHLASWVRLRGDGEAAVHWRGDRFHP
+EHPYAAAALRFLQGADDAAGRPLRVRTVTGAVQPAEYDPAERGPRSLLDTLPLGAAVLRP
+AFEDAAGEEAAAAACAALHPGLAQLSFPAPPLLRLAGALNDLVLLQPRP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000607.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000607.fa
new file mode 100644
index 0000000000000000000000000000000000000000..11bb142c290c928ea9296b08f14eb28cd4e16873
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000607.fa
@@ -0,0 +1,62 @@
+>ACLBLIBL_00930
+MNNRLLIVATLSLGALVVVLVAAIGNGAWWVLAAIVVGLLILAVRDMTQKRHAILRNFPV
+LGHMRYLLESIRPEIQQYFIERNFDGKPFDRDTRSLVYARSKGLDSHKAFGTERDTSEIG
+YEFLLHSSAPVNAPAEAPTVRIGGPDCRQPVDISLMNISSMSFGSLSANAVQAMNKGAGL
+GGFIHETGEGGLTKYHRGNGADLFWEIGSGYFGCRNGDGTFSAEKFAAKAALPEVKGITI
+KMSQGAKPGLGGMLPKEKITAEIAEAREIPMDQDCLSPASHSAFRTPREMVRFIGHLREL
+SDGKPVGIKFCVGSRVDVLAMCKAIWEERIAPDFIIVDGSEGGTGAAPLEYSDRVGTPLT
+EGLMLVHNALVGTGLRHMIKLGAAGKVATGSDIVKRLIQGADFTMSARAMMMATGCIQAQ
+KCHTNECPVGVATQDPRLMRALDVTDKSNRVFNYHRLTVREAVQIMASMGVTHPSQLNTR
+MLRRRVDHLATRSYASIYHWLRTDELLNDPPAGWAMDWDEADGDHFGEHARVDYLTERDP
+EWRSELLIPGRQEQGAPVQGSPASGAGSRVAVGDSRDTAPVTTSPLPRVSTLAEGETLYS
+RSTRSHDPAREQAGVTQRVDTDGNDGLSPHAGEDPERQDGEEVTQRGTTGRVDAEPRGEG
+RVG
+>MOLHKGIG_01929
+MNNRLLIVATLSLAALVVVLVAAIGGGAWWVLAVLLVALLVLAVWDMTQKRHAILRNYPV
+LGHMRYLLESIRPEIQQYFIERNFDGKPFDRDTRSIVYARAKGLDSHKAFGTERDTSEIG
+YEFLLHSTAPVNPPEEPPTVRIGGPDCRRPVDISLMNISSMSFGSLSANAVIAMNKGAGL
+GGFIHETGEGGLTKYHRGNGADLFWEIGSGYFGCRNEDGTFSPEKFAEKAVLPEVKGITI
+KISQGAKPGLGGMLPKEKISPEIAEAREIPMDKDCLSPASHSAFRTPREMVKFIEQLREL
+SDGKPIGIKFCVGSRVDVLAMTKAIWEERIAPDFIIVDGSEGGTGAAPLEYSDRVGTPLT
+EGLMLVHNALVGTGLRHMIKLGAAGKVATGSDIVKRLIQGADFTMSARAMMMATGCIQAQ
+KCHTNECPVGVATQDPRLMRALDVEDKGNRVFNYHRLTVREAVQIMASMGLTHPSQLNTR
+MLRRRVDHLSTRSYASIYHWLRTDELLNDPPAGWAMDWEEADADHFGEHARVDYLTERDP
+QWRSELLIPGREAAGAPVQGSPISGTGSTLVDARRTESVPLTTSPMPRVSSLGEGESLCT
+PGGRRRAPQDPAPAATAGETPTDENEGLPAEAGERPERQDGEEVTRRGTTGRVEGEHRGE
+GRVG
+>NAFOICDF_01592
+MNSKTLAAAAAALGVAGVAVRDLTQKQHALRHNFPVLARARWALETIGPELRQYIVAANN
+EERPFSRDQRRWVYTSSKGKNNYYGFGTDNDVEHTSYAVVKHRTFSDVAPMSALALDPGK
+ALPSAKVLGGPRGRRHAFRPNSVVNVSAMSFGSLSPQAITALNKGAALGGFMHNTGEGGL
+SDHHRQGGDLMLQIGTGYFGCRDAHGNFDMEKLAAVVESAPVRALEIKLSQGAKPGLGGH
+LPGAKVNAEIARIRGVEEGKDVASPSRHSEFSTVDEMLDFVERVAERTGLPVGIKSAVGD
+LGFWHELADAMADGTRGVDFITIDGGEGGTGAAPLIFSDSVAFPFRVAFTEVYRIFAARG
+LTDRVTWIGSGKLGLPDNALVAFALGVDMVNVAREAMLAIGCIQAQKCHLDTCPAGVATQ
+NPWLAAGLDPQEKSQRLVGYVQTLRRDLIKVSEAAGVPHPALLSPDDVALVEQTRSQTPL
+REIYGYERGWGVPGEEIRAEITRIMVDEDSSRADEDHLVQHEPLPQDDVDTTH
+>MHAAABBN_01625
+MNNRLLIVATLSLAALVVVLVAAIGGGAWWVLAVLLVALLVLAVWDMTQKRHAILRNYPV
+LGHMRYLLESIRPEIQQYFIERNFDGKPFDRDTRSIVYARAKGLDSHKAFGTERDTSEIG
+YEFLLHSTAPVNPPEEPPTVRIGGPDCRQPVDISLMNISSMSFGSLSANAVVAMNKGAGL
+GGFIHETGEGGLTKYHRGNGADLFWEIGSGYFGCRNEDGTFSPEKFAEKAVLPEVKGITI
+KISQGAKPGLGGMLPKEKISPEIAEAREIPMDKDCLSPASHSAFRTPREMVKFIEQLREL
+SDGKPIGIKFCVGSRVDVLAMTKAIWEERIAPDFIIVDGSEGGTGAAPLEYSDRVGTPLT
+EGLMLVHNALVGTGLRHMIKLGAAGKVATGSDIVRRLIQGADFTMSARAMMMATGCIQAQ
+KCHTNECPVGVATQDPRLMRALDVEDKGNRVFNYHRLTVREAVQIMASMGLTHPSQLNTR
+MLRRRVDHLSTRSYASIYHWLRTDELLNDPPAGWAMDWEEADADHFGEHARVDYLTERDP
+EWRSELLIPGREAGGAPVQGSPISGTGSTLVDARQTESVPLTTSPMPRVSSLGEGESLSP
+HGGRRRAPQDPAPAATAGETPTDENEGLPAEAGERPERQDGEEVTQRGTTGRVEGEHRGE
+GRVG
+>LFPAFLNI_01848
+MNNRLLIVATLSLAALVVVLVAAIGGGAWWVLAVLLVALLVLAVWDMTQKRHAILRNYPV
+LGHMRYLLESIRPEIQQYFIERNFDGKPFDRDTRSIVYARAKGLDSHKAFGTERDTSEIG
+YEFLLHSTAPVNPPEEPPTVRIGGPDCRRPVDISLMNISSMSFGSLSANAVIAMNKGAGL
+GGFIHETGEGGLTKYHRGNGADLFWEIGSGYFGCRNEDGTFSPEKFAEKALLPEVKGITI
+KISQGAKPGLGGMLPKEKISPEIAEAREIPMDKDCLSPASHSAFRTPREMVKFIEQLREL
+SDGKPIGIKFCVGSRVDVLAMTKAIWEERIAPDFIIVDGSEGGTGAAPLEYSDRVGTPLT
+EGLMLVHNALVGTGLRHMIKLGAAGKVATGSDIVKRLIQGADFTMSARAMMMATGCIQAQ
+KCHTNECPVGVATQDPRLMRALDVEDKGNRVFNYHRLTVREAVQIMASMGLTHPSQLNTR
+MLRRRVDHLSTRSYASIYHWLRTDELLNDPPAGWAMDWEEADADHFGEHARVDYLTERDP
+QWRSELLIPGRAAAGAPVQGSPISGTGSTLVDARQTESVPLTTSPMPRVSSLGEGESLSP
+HGGRRRAPQDPAPAATAGETPTDENEGLPAEAGERPERQDGEEVTQRGTTGRVEGEHRGE
+GRVG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000608.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000608.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34aca4425b4b02f17437f11e5f60db35030e7432
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000608.fa
@@ -0,0 +1,42 @@
+>ACLBLIBL_00931
+MTPPSSAPAAARSGPSTALLWVLLAAMGAGPLFNYGISASSTVIIERLGVTSGQLGTVMT
+AVFAAAAVTSLGLGRAADRLSSRAQMSIIFGGTAVALVMGAFAPSLPVLYAAAAVAGVTQ
+AISNPTTNRIIRTVVPPERRIGWIGVKQSGVQAAQLFGGLFFPAASLALGWTGAALVVAV
+LACVLWGFALWAAPPLPGTAPTADPDAGRASAPDVDRASAPDAGPAAARARRRDGRRRRG
+TTALPASVWFFAAIAFLTGLGMQATNMYLPLFAVESLDLTLVAGGAAAAVSGVIGVFSRI
+WWSRRMAVGARPTTLLAAICLGALAGVVVLLAADLAHLPALLWVGAAVHGLTVLGANVVT
+NAGLMSEVPAESLGRASGANAMGMYAGFALGPLVMGVLRDLTGDYRAGFAAVGLGYILAF
+LVVLLLRRHVGRRAADPRAEAA
+>MOLHKGIG_01928
+MTLPAPAARRPSAALLWVLLAAMGAGPLFTYGVSASSTVVMERLDVTSGQLGTVMTVVFA
+AAAVTSLGLGRAADRLSARAQLSIIFGGTAAALVLGAVAPSLPVLYAAAAVAGVTQAISN
+PTTNRIIRTVVPPERRIGWVGVKQSGVQAAQLVGGLFFPAASLALGWTGAALGAAVLIGA
+LWVLALVAAPPLPGAPPSATGPAGGRRRRDTSPLPATVWFSAAIAFLTGLGMQATNTYLP
+LFAVETLGMTLVAGGAAAAVSGVVGVLSRIGWSRRMSSGDRPTTLLTVICLGAVAGVVVF
+LAADLLDLPALLWVGAAVHGLTVLGANVVVNAGLLSEVPAERLGRATGANSMGMYAGFAL
+GPLLMGVLRDVTGDYRAGFAVVALGYLLALGVVLLLRRHVGRRGAA
+>NAFOICDF_00863
+MGDAGAGRRLTGSSGGPAAPGGPTLGAVTASPPSRPADRAPGTLLLWTLLAAMGAGPVFN
+YAVSTSSTVIIERLGVTSGQLGTVMTVVFAAAAVTSVGLGRAADRLSSRTQMAIIFFGSA
+LALAVGGFAGSLWALYGAAVLAGVTQTISNPTTNRIIRTSVPAERRIGWIGVKQSGVQAS
+QLFAGLFFPVAALGLGWTGASLVAAALVGLLGVVALRAAPPLPGAPAAPPTTTPDAGRPR
+AGRARAPLPATVWFFAGIAFLTGFGMQATNMYLPLFAVESLDQTLVIGGAAAATSGVIGV
+FSRIWWSRRMAAGHRPTTLLAGIALGAVVGVVVFLGADLLHAPALLWVGAAVHGLTVLGT
+NVVTNAGLMDAVPAHHLGRASGVNAMGMYAGFACGPLVMGLMRDLTGDFRAGFLAVGVFY
+LLALAVVGLLRRHTDRQGAPRAA
+>MHAAABBN_01624
+MTLPAPAARRPSAALLWVLLAAMGAGPLFNYGVSASSTVVMERLDVTSGQLGTVMTVVFA
+AAAVTSLGLGRAADRLSARAQLSIIFGGTAAALVLGAVAPSLPVLYAAAAVAGVTQAISN
+PTTNRIIRTVVPPERRIGWVGVKQSGVQAAQLVGGLFFPAASLALGWTGAALGAAVLIGA
+LWVLALVAAPPLPGAPPPATGPVGGRRRRDTSPLPATVWFFAAIAFLTGLGMQATNTYLP
+LFAVETLGMTLVAGGAAAAVSGVVGVLSRIGWSRRMSSGDRPTTLLAVICLGAVAGVAVF
+LAADLLDLPALLWVGAAVHGLTVLGANVVINAGLLSEVPAERLGRATGANSMGMYAGFAL
+GPLLMGVLRDVTGDYRAGFAVVALGYLLALGVVLLLRRHVGRRGAA
+>LFPAFLNI_01847
+MTPPAPAARRPSAALLWVLLAAMGAGPLFNYGVSASSTVVMERLDVTSGQLGTVMTVVFA
+AAAVTSLGLGRAADRLSARAQLSIIFGGTAAALVLGAAAPSLPVLYAAAAVAGVTQAISN
+PTTNRIIRTVVPPERRIGWVGVKQSGVQAAQLVGGLFFPAASLALGWTGAALGAAVLIGA
+LWVLALVAAPPLPGAPPPATGPVGGRRRRDTSPLPATVWFFAAIAFLTGLGMQATNTYLP
+LFAVETLGMTLVAGGAAAAVSGVVGVLSRIGWSRRMSSGDRPTTLLTVICLGAVAGVVVF
+LAADLLDLPVLLWVGAAVHGLTVLGANVVINAGLLSEVPAERLGRATGANSMGMYAGFAL
+GPLLMGVLRDVTGDYRAGFAVVAAGYLLALGVVLLLRRHVGRRGAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000611.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000611.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dba57fc3c124b296ae857e844e51aad1672b7834
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000611.fa
@@ -0,0 +1,17 @@
+>ACLBLIBL_00936
+MPHRRRRPCVPVALSVAAALGLSLSACASTTTAGVGSQSPAPSSAAGAASSAAGTSSAAP
+TTSAALTTSGTAAEIAGDEAAAQAQDDAATRTALNRAVAEDGIPYAELDPSLTPVPDGAS
+ILWEGLAVGAQSLRVDARAGEEYTVVLLCAEQDGSRRSLVMATVPGEDFSDVMAESPGCG
+HWSAGLPAREADGPLTLTGVVPDGGPFRMVVYRSEG
+>MOLHKGIG_01924
+MTLVEYTRRHPDADHLDPEKESVLEEAVGTGTQQITVDAQQGAVLRVIVLCPSDATGETE
+ILTSRGGGGTKTWMAGSEALCGGWSAATPPVDEAGPMTFTVTVDNDKPFRMVLTAPSA
+>NAFOICDF_00868
+MTLEEYTRQNPDSDYLHPETESVLQEKVGTGTQQITVDAQEGAVLRVILLCPSDATGKTD
+IHTSRGAEGEKTWMAGSEALCGGWSAATPPVEKAGPMTFSATVDNDKPFRMVLTAPAA
+>MHAAABBN_01620
+MTLVEYTRQHPDADYLDPEKESVLEEAVGTGTQQITVDAQQGAVLRVIVMCPSDATGETE
+ILTSRGGGGTKTWMAGSEALCGGWSAATPPVDEAGPMTFTVTVDNDKPFRMVLTAPSA
+>LFPAFLNI_01844
+MTLVEYTRRHPDADHLDPEKESVLEEAVGTGTQQITVDAQQGAVLRVIVLCPSDATGETE
+ILTSRSGGGTKTWMAGSEALCGGWSAATPPPVDEAGPMTFTATVDNDKPFRMVLTAPSA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000612.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000612.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3901ccfb2448faddcc3a24a145d55b8fff396549
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000612.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00937
+MSGSVRVSGAVRVDAWLWAVRVYKTRSAATAAVRGGHVRVNDEPVKAAHTLAVGDRVRVR
+KDQRERILEVTGLIGTRVGAPVAVTNYIDHSPPPIPRELLAVPHRERGAGRPTKRDRRKL
+DELRGRASDERS
+>MOLHKGIG_01923
+MSGVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI
+LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRD
+RR
+>NAFOICDF_00872
+MGAVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI
+LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRA
+STGRG
+>MHAAABBN_01619
+MSGVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI
+LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRD
+RR
+>LFPAFLNI_01843
+MSGVRIDAWLWAVRLYKTRSAATAAVRAGHVRIDGEPVKAATPVVVGNRVRVRQDGRERI
+LEVTGLIAKRVGAPVARQQYVDHSPPPVPRELLAVPYRERGAGRPTKRDRRQLDALRGRD
+RR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000613.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000613.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c33e22168feccac4809a33cf838632f993ec003
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000613.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_00938
+MEADRPRGPGPAAAVVVPRRCTPTPAPPTSLEDPVLSVTDLRQIDTAAADLSRIIPRADV
+DVASTVPVVAPILEQVRTGGEAALLELAERFDGVRPPALRVPAEALAAALEGLDADVRAA
+LEESIRRARLVHAAQLPQDSTVELGEGASVQNHWIPVDRVGLYVPGGRAVYPSSVVMNVV
+PAQAAGVGSLAVTSPPQADHGGLPHPTVLAACALLGVDEVYAAGGAQAVAMLAHGVRDER
+GGWLCAPVDMVTGPGNVYVAAAKRALQGIIGVDAEAGPSEIAVIADGTARADWVAADLIS
+QSEHDPLAASVLITDSEDLVRDVLAAIEAQVPGSFHEEQIRVALTGPQSGVLLVRDLDQA
+VEVSDRYATEHLEIQTRDPEAVAARIRNAGAVFVGPHAPVPLGDYSAGSNHVLPTSGTAR
+HSSGLSTVTFLRLQQRIRYTETGLKELAEGISVLAEDERLPAHGVAVRARFA
+>MOLHKGIG_01922
+MLSVTDLRPLDTATADLSRIIPRANVDVSSVVPVIAPIIEQVRHGGEQTLLDLAERFDGV
+RPPALRVPGEALEAALAGLDPRVRAALEESIRRARLVHAAQHPQDSTVELGEGAVVENHW
+IPVGRVGLYVPGGRAVYPSSVVMNVVPAQAAGVGSLAVTSPPQRDHGGLPHPTVLAACAL
+LGVDEVYAAGGAQAVAMLAHGVQDDDGGWLCAPVDLVTGPGNVYVAAAKRALQGVIGVDA
+EAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSEDLLRDVQAAIEAQVPGA
+FHEDQIREALTGPQSGVLLVRDMDQAVEVSDRYATEHLEIQTRDPEALVGRIRNAGAVFV
+GPYAPVPLGDYSAGSNHVLPTSGTARHSSGLNTVTFLRLQQRIRYTETGLEEVADGIGVL
+AEDERLPAHGAAIRARFA
+>NAFOICDF_00873
+MEADRTALDPQEEPVLSVTDLRELDTAAADLSAIVPRAEVDVAYTVPVVAPIIEQVRTGS
+EQTLLDLAERFDGVRPPALRVPAEALTAALEGLDPAVRAALEESIARARKVHAAQVPSGS
+TVELGEGAVVENRWVPVERVGLYVPGGRAVYPSSVVMNVVPAQAAGVESLVVTSPPQRDH
+GGLPHPTVLAACALLGVDEVYAAGGAQAVAMLALGVRADDGDGWLCAPVRMVTGPGNVYV
+AAAKRALQGVIGTDAEAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSADL
+LRDVLASVEAQVPGSFHEEQIRVALTGPQSGVLLVRDMEQALEVSDLYATEHLEIHTRDA
+DALAARVRNAGAVFVGPYSPVPLGDYSAGSNHVLPTSGTARFSSGLNTVTFLRSQQLIRY
+GEAGLKALADGISALAEDERLPAHGVAVRARFA
+>MHAAABBN_01618
+MLSVTDLRPLDTATADLSRIIPRANVDVSSVVPVVAPIIEQVRHGGEQTLLDLAERFDGV
+RPPALRVPGEALEAALAGLDPRVRAALEESIRRARLVHAAQHPQDSTVELGEGAVVENHW
+IPVGRVGLYVPGGRAVYPSSVVMNVVPAQAAGVGSLAVTSPPQRDHGGLPHPTVLAACAL
+LGVDEVYAAGGAQAVAMLAHGVQDDDGGWLCAPVDLVTGPGNVYVAAAKRALQGVIGVDA
+EAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSEDLLRDVQAAIEAQVPGA
+FHEDQIREALTGPQSGVLLVRDMDQAVEVSDRYATEHLEIQTRDPEDLVGRIRNAGAVFV
+GPHAPVPLGDYSAGSNHVLPTSGTARHSSGLNTVTFLRLQQRIRYTETGLEEVADGIGVL
+AEDERLPAHGAAIRARFA
+>LFPAFLNI_01842
+MLSVTDLRPLDTATADLSRIIPRANVDVSSVVPVIAPIIEQVRHGGEQTLLDLAERFDGV
+RPPALRVPGEALEAALAGLDPRVRAALEESIRRARLVHAAQHPQDSTVELGEGAVVENHW
+IPVGRVGLYVPGGRAVYPSSVVMNVVPAQAAGVGSLAVTSPPQRDHGGLPHPTVLAACAL
+LGVDEVYAAGGAQAVAMLAHGVQDDDGGWLCAPVDLVTGPGNVYVAAAKRALQGVIGVDA
+EAGPSEIAVIADGTARADWVAADLISQSEHDPLAASVLITDSEDLLRDVQAAIEAQVPGA
+FHEDQIREALTGPQSGVLLVRDMDQAVEVSDRYATEHLEIQTRDPEALVGRIRNAGAVFV
+GPYAPVPLGDYSAGSNHVLPTSGTARHSSGLNTVTFLRLQQRIRYTETGLEEVADGIGVL
+AEDERLPAHGAAIRARFA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000619.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000619.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a7ba484335fb530b2b7ee7fb0820ca392cb6d1a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000619.fa
@@ -0,0 +1,10 @@
+>ACLBLIBL_00949
+MAKDKDVRPIIKLKSTAGTGYTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER
+>MOLHKGIG_01909
+MAKDKDVRPIIKLKSTAGTGFTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER
+>NAFOICDF_00889
+MAKDKDVRPIIKLKSTAGTGYTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER
+>MHAAABBN_01605
+MAKDKDVRPIIKLKSTAGTGFTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER
+>LFPAFLNI_01829
+MAKDKDVRPIIKLKSTAGTGFTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000620.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000620.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cdd679f441f5c50d53238a08ea792a742c6b29d1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000620.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_00950
+MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV
+RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW
+>MOLHKGIG_01908
+MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV
+RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW
+>NAFOICDF_00890
+MAKKSKIAKNEQRKVMVARNAEKRLELKKTLIDPNASDEAREAARVGLQKLPRDASPVRV
+RNRDAIDGRPRGTFQRFGISRVRFREMAHRGELPGVTKSSW
+>MHAAABBN_01604
+MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV
+RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW
+>LFPAFLNI_01828
+MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV
+RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000621.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000621.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5bf3d9e78ed5c0e00fdde3f5f5da5607bf4c827
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000621.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_00951
+MAMNRKELVAAVAERSGNTQAAVSDVLDALFEVFTAQVKKGEKVSIPGWMAVERTERKER
+TGRNPRTGEEITIPAGYSVKVTAGSKLKAAASE
+>MOLHKGIG_01907
+MAMNRKELVAAVAERSGNTQAAVSDVLDALFEVFTAQVKKGEKVSIPGWLAVERTERKER
+TGRNPRTGEEITIPAGHSVKVTAGSKLKAAASE
+>NAFOICDF_00891
+MAMNRKELVAAVAERSGNTQAAVSDVLDALFEAFTAQVKKGEKVSIPGWLAVERTERKER
+TGRNPRTGEEITIPAGYSVKVTAGSKLKAAASE
+>MHAAABBN_01603
+MAMNRKELVAAVAERSGNTQAAVSDVLDALFEVFTAQVKKGEKVSIPGWLAVERTERKER
+TGRNPRTGEEITIPAGHSVKVTAGSKLKAAASE
+>LFPAFLNI_01827
+MNRKELVAAVAERSGNTQAAVSDVLDALFEVFTAQVKKGEKVSIPGWLAVERTERKERTG
+RNPRTGEEITIPAGHSVKVTAGSKLKAAASE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000625.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000625.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a9ef9d083fd7ab157494804d47970407c95a1dd3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000625.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_00955
+MGGGLLGTALGYGAGHASAAPAAPAASGAAGAGASPSEVMGDTGIEGEVGRAGWAEPGGQ
+SARVAVSSPVGTDTVPFHGPRQAGVDTPAQAHAVFLAFDLLPDTDRLGIERMLRLLTDDA
+ARLTQGRATIADTEPELAAAPARLTVTFGFGPELLARVAPDRAPAWLRPLPAFPQIDRLD
+PAFGDGDLLLQICGDDRMSVAHARRMLIKAARPFAAERWAQEGFRASRGAHPTGTTMRNL
+FGQVDGTANPAAQTPHLDRVVWGVGAEQVGITPWIQDGTSLVVRRIEMLLDTWDELDRPG
+KERVIGRTLGTGAPLTGEQEHDEPDFVALGPAGFPVIPDISHLRRARMDVPEYGMLRRGY
+NYDDPRGAIESGAGLIFAAYQADVDRQFVPVQERLAESDHLNLWTVPVGSAVFAIPPGCA
+EGGFVGDVLFA
+>MOLHKGIG_01903
+MPTTDPAVRPDDHHGSGGREGARPAPGGPSRRGLLLGAGAVGGGLLGTALGYGAGHASAS
+TAPGASAAPGAGASPSEVMGDTGIEGDVGRAGWAEPGGQAARVAVSSPVGTDTVPFHGPR
+QAGVDTPAQAHAVFLALDLREDADRVRIERMLRLLTDDAARLTQGRATIADTEPELAAAP
+ARLTVTFGFGPELVRRVAPDRAPAWLRPLPAFEQIDRLDPAFSDGDLLLQICGDDRMSVA
+HTRRMLLKAARPFATERWVQEGFRSARGAHPTGTTMRNLFGQVDGTGNPAADTPHLDRVV
+WGVGAEQVGVTPWIPDGTSVVIRRIEMLMDTWDELDRPAKEKVIGRRLGTGAPLTGEQEH
+DEPDFDAVGPTGFPVISDIAHLRRARGEEPEYGMLRRGYNYDDPRGALEAGSGLIFAAYQ
+ADVDRQFVPVQARLAESDHLNLWTVPVGSAVFAIPPGCAEGGFVGDALFA
+>NAFOICDF_00895
+MPTTDPSRRGVLFGLGAVGGGLLGGAVGYGAGAAQATPAPGGAPSGVDASPSGVMEDTGL
+EGEVGRAGWAEPGGEASRVAVSSPVGTDTVPFHGPRQAGVDTPAQTHAMLVALDLLPETD
+RAGVRALLRLLSDDAARLTQGRATLADTEPELAAAPARLTVTFGFGPELLARVAPERAPA
+WLKPLPAFPTIDALEDRWSGGDLLLQICGDDRISVAHARRMLGKVARPFAEVRWVQEGFR
+AARGTHPTGTTMRNLFGQVDGTANPQGGSPALERIVWGAGQEAADLGIAPWIPDGTSLVV
+RRIDMLMDTWDELDRPAKEKVIGRTLGTGAPLTGELETDAPDLEAIGPTGFPVIPDTAHL
+RRARGPEPEYGMLRRGYNYDDGAGASGTGAGLIFAAFQADVDRQYIPVQERLAASDHLNL
+WTRPVGSAVFAIPPGCAEGGFVGDVLFA
+>MHAAABBN_01599
+MPTTDPVVRSDDHHGPDDHHGPDGREGARPTPGGPSRRGLLLGAGAVGGGLLGTALGYGA
+GHASASTAPGASAASGTGASPSEVMGDTGIEGDVGRAGWAEPGGQAARVAVSSPVGTDTV
+PFHGPRQAGVDTPAQAHAVFLAFDLHEDTDRVRIERMLRLLTDDAARLTQGRATIADTEP
+ELAAAPARLTVTFGFGPELVRRVAPDRAPAWLRPLPAFEQIDRLDPAFSDGDLLLQICGD
+DRMSVAHARRMLLKAARPFATERWVQEGFRSARGAHPTGTTMRNLFGQVDGTGNPAADTP
+HLDRVVWGVGAEQVGVTPWIADGTSVVIRRIEMLMDTWDELDRPAKEKVIGRRLGTGAPL
+TGEQEHDEPDFDAVGPAGFPVISDIAHLRRARGEEPEYGMLRRGYNYDDPRGALEAGSGL
+IFAAYQADVDRQFVPVQARLAESDHLNLWTVPVGSAVFAIPPGCAEGGFVGDALFA
+>LFPAFLNI_01823
+MPTTDPAVRPDDHHGPDGREGARPAPGGPSRRGLLLGAGAVGGGLLGTALGYGAGHASAS
+TAPGASAAPGAGASPSEVMGDTGIEGDVGRAGWAEPGGQAARVAVSSPVGTDTVPFHGPR
+QAGVDTPAQAHAVFLAFDLHEDTGRVRIERMLRLLTDDAARLTQGRATIADTEPELAAAP
+ARLTVTFGFGPELVRRVAPDRAPAWLRPLPAFEQIDRLDPAFSDGDLLLQICGDDRMSVA
+HARRMLLKAARPFATERWVQEGFRSARGAHPTGTTMRNLFGQVDGTGNPAADTPHLDRVV
+WGVGAEQVGVTPWITDGTSVVIRRIEMLMDTWDELDRPAKEKVIGRRLGTGAPLTGEQEH
+DEPDFDAVGPTGFPVISDIAHLRRARGEEPEYGMLRRGYNYDDPRGALEAGSGLIFAAYQ
+ADVDRQFVPVQARLAESDHLNLWTVPVGSAVFAIPPGCTEGGFVGDALFA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000626.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000626.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f68deb82bc7ee1119015dd5909fac1c21d9893e3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000626.fa
@@ -0,0 +1,70 @@
+>ACLBLIBL_00956
+MLVAAAGAGALAVAAWLTGITAVRELSDPGWITRWGVPAGELVSNLAMTMAIAAIIFAAG
+ILPPHAAGTERWHRSAAQRRADAQEGPLPEHPAFTRTLRVAAVSAGVWTVAALAVGILSY
+SDLAGIPVTAGEGFTAGLVAYVAGISVGQAWFWVTVIAAVVTTLVIAVRSHNGLFWTGIL
+AMIGIVPLALIGHAAGGDDHYGAVNSIGLHLLGVVVWVGGLLVLVAISDTLVGPDGAQGR
+ARAPREQGPTPLLHTALSRYSVLAGLGLVTVALSGVVNASIRMDDPAQLTSPYGMLVVIK
+FLATLGLGLVGLMHRRWVIPRLDAGPDRPSPAPARRLLWQLIAVEAVVMAAVMGLSAVLS
+RTAPPVPEELAPDATPARILTGYELPPELTGARWITEWRLDWLWVAIIAFLALWYLRSVW
+RLHRRGDRWPVLRTLSWMVGLAVLLWATSGSPAVYGRVLFSSHMMGHMTLTMISPLFLVL
+GAPITLALRALPSRTDGSRGPREWILWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFF
+RFSLETHVGHEFMNVHFLLTGFLFALVMVGSDPLPSRPAYPLRLVLLLATMVFHAFIGVA
+MTGSAGLIQASWFGNMGRDWGPSALEDQHIGGAVMWGIGEFPTVVMAVMVAVLWYRNDRR
+NAERLDRRADRDGDAELHRWNEMYARMHGTPAAPAEPAPAAASPADPTPAASAPRPRRPG
+DPRWPLSTAHPPEDPAGPEDRAAPARWPRPPSSGCWR
+>MOLHKGIG_01902
+MSAATAPARGSHPAENDDAARPGPSGPVGVPRWIWVLVAAAGAAGLAAAGWLTGVTAARQ
+LSDPGWITRWGVPVGELVSNVAMSLTIAALIFAAGVLPPHAAGTERWHRSARQRREDADA
+APLPEHPAFTRVMRIAAVSAGVWTVAALAVGVLSYSDLAGIPVTAGQGFTDGLAAYVVGI
+SVGQAWFWVTVIAAVVTTLAIAVRSHNGLFWTGILAMLALVPLALIGHAAGGDDHTGAVN
+SIGLHLLGVVVWVGGLLVLVAISDTLVGPNGAQGRGRSLRRQGPAPLLHTVLTRYSVLAG
+LGLVTVALSGVVNASIRMDDPAQLLSPYGILVSAKFLAALGLGLIGLLHRRWVIPRLDAG
+PDRPSPAPARRLLWQLIAVEAVIMGAVMGVSSVLSRTAPPVPEELAPDASPARILTGYEL
+PPALEGARWITMWRFDWLWVAIIAFLTLWYLRSVWQLRRRGDRWPVLRTVAWLAGLAVLL
+WATSGSPAVYGRVLFSAHMVGHMTLTMLSPVFLVLGAPITLALRALPSRTDGTRGPREWI
+LWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFFRFSLETHVGHEFMNVHFLLTGFLFA
+LVMIGSDPLPRRPPYALRLVLLMATMVFHAFIGVAMTTSTGLLQASWFGNMGRDWGPTAL
+EDQRIGGAVMWGIGEFPTVMMAVMVAVLWYRSDRKNAVRLDRQADRDGDAELRRWNEMYA
+RMHGTPATDAPSGAEPAARDSSTGPEEARDVR
+>NAFOICDF_00896
+MPTSTAVPPATAQHPLGVPRPVLLGAAVVGVLALVLAAWFAGVTAPRELSDPGALTRWGV
+PVGKAVNNAAMAVTIGALIFAAGILPPHAAGTERWHRSPRQRAQDAEEGPRPEHPAFGRV
+MAVAAAAAGVWTVAALAVGVLSYSDLAGIPVSAGGSFTDGLLAYTLDISVGRAWFWVTVI
+AAVVTTLAIGVRSHTGLFWTGVLAMLGIVPLALIGHAAGGDDHYGAVNSIGLHLLGVVVW
+VGGLLVLALISDTLVGPNGAQGRGASLRRQGPAPLLHTVVSRYSVLAGLGLVTVALSGVV
+NASIRMDDPAQLLSPYGTMVLTKAGAVLLLGGIGLLHRRWIIPRLDDDGAAESPPAARRL
+LWQLIAVEAVVMAAVVGVSAVLARTAPPVPEELAPDATPARILTGYELPPELTGDRWFTM
+WRWDWLWVAIIAFLAVWYVRAAWQLRRRGDRWPVLRTLSWLIGLAVLAWATSGAPAVYGM
+VLFSAHMVGHMVLTMIVPLFLVLGAPITLALRALPARTDGTRGPREWILWIVHSPWGAFI
+TNPIVAGVNFAGSILVFYYTDFFRFSLETHVGHEFMNVHFLLTGFIFATVMVGADPLPSR
+PPYPLRLVLLLATMVFHAFIGVAMTTSTGLLQASWFGSIGRDWGPDALTDQHIGGGIMWG
+IGEFPTVLMAVTVAVLWARSDTKTAARLDRRADQDGDAELARWNQMYAAMNHPGADQDPA
+RGDRP
+>MHAAABBN_01598
+MSAATAPARGSHPTENDDAARPGPSGPVGVPRWIWVLVAAAGAAGLAAAGWLTGVTAARQ
+LSDPGWITRWGVPVGELVSNLAMSLTIAALIFAAGVLPPHAAGTERWHRSARQRREDADA
+APLPEHPAFTRVMRIAAVGAGVWTVAALAVGVLSYSDLAGIPVTAGQGFTDGLAAYVVGI
+SVGQAWFWVTVIAAVVTTLAIAVRSHNGLFWTGILAMLALVPLALIGHAAGGDDHNGAVN
+SIGLHLLGVVVWVGGLLVLVAISDTLVGPNGAQGRGRSLRRQGPAPLLHTVLTRYSVLAG
+LGLVTVALSGVVNASIRMDDPAQLLSPYGILVSAKFLAALGLGLIGLLHRRWVIPRLDAG
+PDRPSPAPARRLLWQLIAVEAVIMGAVMGVSSVLSRTAPPVPEELAPDASPARILTGYEL
+PPALEGARWITMWRFDWLWVAIIAFLSLWYLRSVWQLRRRGDRWPVLRTVAWLAGLAVLL
+WATSGSPAVYGRVLFSAHMVGHMTLTMLSPVFLVLGAPITLALRALPSRTDGTRGPREWI
+LWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFFRFSLQTHVGHEFMNVHFLLTGFLFA
+LVMIGSDPLPRRPPYALRLVLLMATMIFHAFIGVAMTTSTGLMQASWFGNMGRDWGPTAL
+EDQRIGGAVMWGIGEFPTVMMAVMVAVLWYRSDRKNAVRLDRQADRDGDAELRRWNEMYA
+RMHGTPVTDAPSGAEPVARDSSTGPEEARDVR
+>LFPAFLNI_01822
+MSAATAPARGSHPAENDDAARPGPSGPVGVPRWIWMLVAAAGAAGLAAAGWLTGVTAARQ
+LSDPGWITRWGVPVGELVSNLAMSLTIAALIFAAGVLPPHAAGTERWHRSARQRREDADA
+APLPEHPAFTRVMRIAAVSAGVWTVAALAVGVLSYSDLAGIPVTAGQGFTDGLAAYVVGI
+SVGQAWFWVTVIAAVVTTLAIAVRSHNGLFWTGILAMLALVPLALIGHAAGGDDHTGAVN
+SIGLHLLGVVVWVGGLLVLVAISDTLVGPNGAQGRGRSLRRQGPAPLLHTVLTRYSVLAG
+LGLVTVALSGVVNASIRMDDPAQLLSPYGILVSAKFLAALGLGLIGLLHRRWVIPRLDAG
+PDRPSPAPARRLLWQLIAVEAVIMGAVMGVSSVLSRTAPPVPEELAPDASPARILTGYEL
+PPALEGARWITMWRFDWLWVAIIAFLTLWYLRSVWQLRRRGDRWPVLRTVAWLAGLAVLL
+WATSGSPAVYGRVLFSAHMVGHMTLTMLSPVFLVLGAPITLALRALPSRTDGTRGPREWI
+LWIVHSPWGRFITNPIVAGVNFAGSILVFYYTDFFRFSLETHVGHEFMNVHFLLTGFLFA
+LVMIGSDPLPRRPPYALRLVLLMATMVFHAFIGVAMTTSTGLLQASWFGNMGRDWGPTAL
+EDQRIGGAVMWGIGEFPTVMMAVMVAVLWYRSDRKNAVRLDRQADRDGDAELRRWNEMYA
+RMHGTPATDAPSGAEPAARDSSTGPEEARDVR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000630.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000630.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71ade8649d67942b8cbda3a55234fa67750dfdf0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000630.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00962
+MTQVLSGFVVVWVIIAVGFLVGRSGVLGEDARTVLSRTAFYIGSPALLFVTLSGADVAAV
+LGPQLWVATLSALAAAALFLAISIPVFKQRPASERIMAALSASMVNSANLGIPIAAYVLG
+DAALAAPVLIFQLAIYTPLYVAAMDVATTSEARARAAGGRPAVRRSRGQALAAQLRQTGT
+NPMILGSAAGLLFSLNDWTLPGPLMQSVELIGGLSIPAMLLAFGMSLVGSRPLERAGGRR
+ADVLLASGVKLLVHPLIAWVLAQFVLGLDAREVFVAVVLASLPTAQNVFVSAVRYDAGLR
+VAKDTILITTIVAIPAMIAVALLLA
+>MOLHKGIG_01896
+MTQVLSGFAVVWVIILVGVLVGRTGVLGEHGRTVLSRAAFFIGNPALLFVTLSRADVGAV
+LGPQLWVATLSAFTAAALYLAVTVPLLKGRSASERIMSALSASLVNSANLGIPIAAYVLG
+DAALAAPALIFQLAIYTPLYVAAMDAATAREARRRTTAGRRRAVRRSPGRAVADQVRHTV
+TNPLILGSVAGLVFSLTGWSLQGPLMESVELIGGLSIPAMLLAFGMSLVGSRPLERAGGR
+RADVLLASAVKLVVHPLLAWLLAQFVFGLDARHVFVAVVLASLPTAQNVFVTAVRYDTGL
+RVSKDTILVTTIVAIPAMIAVALLLA
+>NAFOICDF_00901
+MIEVLSGFSVVWVIILVGLLLGRTGVLGDEAREVLSRTAFFVGNPALLFVTLSRADVGAV
+LGPQLWVACLSAFAAAVVFLGLSIPLLKGRPASERVMSGLSASLVNSANLGIPIATYVLG
+DAALAAPALIFQLAIYTPVYVAVMDWATTHEAAARASSAGAAHDAGAPAPRTVRPRNPVL
+AQLRQTATNPMILGAFGGLLLSFTGWTLPGPLMTSVELIGGLSIPAMLIAFGMSLAGSRP
+LARDSGRRADVLLASAVKLVVHPLVAWMIAQFVFGLDARRVFVAVVLASLPTAQNVYVSA
+VRYRAGETVSKDTILVTTIVAIPAMIAVALLLA
+>MHAAABBN_01592
+MTQVLSGFAVVWVIILVGVLVGRTGVLGEHGRTVLSRAAFFIGNPALLFVTLSRADVGAV
+LGPQLWVATLSAFTAAALYLAVTVPLLKGRSASERIMSALSASLVNSANLGIPIAAYVLG
+DAALAAPALIFQLAIYTPLYVAAMDAATAREVRRRTTAGRRRAVRRSPGRAVADQVRHTV
+TNPLILGSVAGLVFSLTGWSLPGPLMESVELIGGLSIPAMLLAFGMSLVGSRPLERAGGR
+RADVLLASAVKLVVHPLLAWLLAQFVFGLDARHVFVAVVLASLPTAQNVFVTAVRYDTGL
+RVSKDTILVTTIVAIPAMIAVALLLA
+>LFPAFLNI_01816
+MTQVLSGFAVVWVIILVGVLVGRTGVLGEHGRTVLSRAAFFIGNPALLFVTLSRADVGAV
+LGPQLWVATLSAFTAAALYLAVTVPLLKGRSASERIMSALSASLVNSANLGIPIAAYVLG
+DAALAAPALIFQLAIYTPLYVAAMDAATAREARRRTTAGRRRAVRRSPGRAVADQVRHTV
+TNPLILGSVAGLVFSLTGWSLQGPLMESVELIGGLSIPAMLLAFGMSLVGSRPLERAGGR
+RADVLLASAVKLVVHPLLAWLLAQFVFGLDARHVFVAVVLASLPTAQNVFVTAVRYDTGL
+RVSKDTILVTTIVAIPAMIAVALLLA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000633.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000633.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b7ccb4fe7ec537f3bb64026d2c205c5ab5762e7e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000633.fa
@@ -0,0 +1,95 @@
+>ACLBLIBL_00969
+MLVTLSALFVVALAAPAVFRWTGRQGFYLLAAVPAAGFVWLLTQLPHVFALQEALDAGRP
+IPASAAHLDRSVPWVPYLDIELAFRMDVLAAFMSLIVLGVGALVLAYCARYFREHEPRNA
+VFGGQLLAFAGAMFGLVTTDDLMVLYTFWEITSVLSFLLIGYSGHRIFARRSAITALIVT
+TFGGLAMLAGLIMLAHVSGSWRISGVLEAAPALMADPGMRGLLEVAVALVLIGALTKSAQ
+APFHFWLPAAMAAPTPVSAYLHAAAMVKAGVFLVARLAPEFHDLTSWQVLVLGVGLWTLV
+LGGWRALRQTDVKLVLAYGTVSQLGFLMVANGLGTRDAAMAGLAMLLAHAVFKAPLFMIV
+GIIDHEAGTRDLRQLSGIGRRHPVLAAVAVAAGLSMAGLPPLFGFVAKESVLASLAAHGA
+AHGGVWAWTPLVVMALGSVLTFAYTWRFLWGSFAVKRDEEGAPVPATRFRTRVTTLELAP
+AALLALAGLVLAFLPGPVEGIITAHTGSLPPLDPAEKPAYLALWHGWTPILALSAGIWVL
+GALLALARRPFEALQERTESPLDAARGYRRLTGYVDETAVWVTGRTQTGSLRRYLGIILA
+TAFLLPAAFLLFPVGRAERPLATSFLAADLIWFETPAQLLIVAIIAVATVFAVRARRRFK
+AIMLVSVTGYGAAALFALRGAPDLAITQVLVETIILVTLILGLRVLPPDWHDRRTGSRRL
+GRLAVAVGFALTMMWIAATALAARTAERISLPMPELAYTDGYGANAVNVTLVDIRAWDTW
+GEITVLAAAATGVASLIFLQHRDGRTRSIDDVAPGSVGAFGADSALGSRELSVVRSFAVD
+DREGQWLVAGHTMAPERRSIILEVVTRFMFPIMMLLSVYLLLAGHNTPGGGFAGGLLAGL
+ALTLRFLAGGRYELQEASVIPAGPMIGLGLAIATLTGIAPLFFGGQILQSYVVEFTDLPL
+FGDALKLVSATAFDIGVYLVVVGLVIDVLRSLGGEVDRRGEEARRARLRAAGRRRHPRMP
+TPSTPDAPEAAR
+>MOLHKGIG_01889
+MLVILTALFVVALAAPVLFRWTGRQGFYLLAAAPAAGFVWLLTQLPHVFALQEALDAGRP
+VPASAARLDRAVPWVPYLETELAFRMDVLAAFMSLIVLGVGALVLAYCARYFREHEPRNA
+VFGGQLLAFAGAMFGLVTTDDLMVLYTFWEITSVLSFLLIGYSGHRIFARRSAITALIVT
+TFGGLAMLAGLIMLAHFAGSWRISGVLEAAPALMADAGLRGLLEVAVALVLIGALTKSAQ
+APFHFWLPGAMAAPTPVSAYLHAAAMVKAGVFLVARLAPEFHGLAMWQVLVIGVGLWTLL
+LGGWRALRQTDIKLVLAYGTVSQLGFLMVANGLGTRDAAMAGLAMLLAHAVFKAPLFMVV
+GIIDHEAGTRDLRQLSGIGRRHPALAAVAVVAGLSMAGLPPLFGFVAKESVLEGLAAHGV
+AHADVWGWTPLVLMTVGSVLTFAYTWRFLWGSFAAKRDEEGAAVPVTRFHTRVTTLELAP
+AALLALAGLVLAFLPGPVEGIITAHTGSLPPLDPEEAPAYLALWHGWTPILALSAGVWVL
+GALLALGRPGVEAFQRRVEFPVDALRTYRKITGALDEVAIWVTGRTQTGSLRRYLGIILA
+TAFLLPAAFLLFPVGRSERTLATSFLSADVAWFQTPAQLVVVLMIAVATVFAVRARRRFK
+AIMLVSVTGYGAAALFAMRGAPDLAITQVLVETIILVTLILGLRVLPPDWYDRRTGSRRL
+GRLAVAVGFALTMMWIAATALAARTAERISLPMPELAYTDGYGTNAVNVTLVDIRAWDTW
+GEITVLAAAATGVASLIFLQHRDGRTRSIDDVAPGSVGDFGADSSLGARELSVVRSFAVD
+DRKGQWLVAGHTMAPERRSIILEVVTRFMFPIMMLLSVYLLLAGHNTPGGGFAGGLLAGL
+ALTLRFLAGGRYELQEASVIPAGPMIGLGLAIATLTGIAPLFFGGQILQSYVVEFTDLPL
+FGDALKLVSATAFDIGVYLVVVGLVIDVLRSLGGEVDRRGEEARRARLRAAARRRHPRMP
+TPSTPSTQEAAR
+>NAFOICDF_00907
+MTVLLTALFAVALLAPVLFRRTGRRGFHLLAAAPAAGFVWVLAQLPQVFVLQDALDRGAP
+VPASAAHLDTTVEWIPYLDIALSFRLDALSAFMSLIVLGVGALVLSYCASYFREHEPRHA
+VFGAELLAFAGAMFGLVTTDDVMVLYTFWEITSVLSFLLIGYSGQRIFARRSAIQALIVT
+TFGGLAMLAGLVMLAVQAGSWRVSGILAAAPELMERAPRGLLEAAVALVLVGALSKSAQV
+PFHFWLPAAMAAPTPVSAYLHAAAMVKAGVFLVARLAPGFASLASWQVLVLGVGLWTLIL
+GGWRALRQTDVKLVIAYGTVSQLGFLMVANGLGTRDAALAGLAMLLAHAVFKAPLFMVVG
+IIDHEAGTRDLRRLSGIGRREPALAAVAIVAAASMAGLPPLFGFVAKESVLESLAGHGEH
+AGTVWGWTPLVGMALGSVLTFAYTWRFLWGAFATKDGRDSPDGEPVPETRFHSRLTAEDL
+LPPGLLALACLVLGLAPGLPEALISAHTAGLAPLDAAEEPAHLALWHGITPILGVSVAIW
+VLGAALAVARRPLQRLQARVAFPVEAAAVYQRITGAVDAAAVWVTGRTQTGSLRRYLFII
+LATATALPALTMLVPAGEEDRVLATAFLEADLVPFTTPAQLGIAALVCVAAVLAVRARRR
+FMAIMLVSVTGYGSAALFALRGAPDLAVTQVLVESIVLITVILGLRVLPPDWHSKTTGRR
+RVPRLLLGVGFALVMMWVAATALGARTAERISLDMPRLAYEHGYGANAVNVTLVDLRAWD
+TWGEITVLAVAATGVASLVFLEHRDKRRRDLDTVVPGSVGNYGAESALGTRELSVVRSFA
+VDDRNDQWLIAGHTMAPERRSIILEVVTRFLFPAMMLLSVYLLLAGHNTPGGGFAGGLLA
+GLALALRYLAGGRYELQEASRIPAGTLLGLGLGIATLTGLAPLLFGGQVLQSYKVEFHDL
+WLFGDSLKIVSATAFDVGVYLVVVGLSIDVLRSLGAEIDRRGDEWQDARRRAARRRASPR
+PARPRPRPVPEGRAPAARAIPAHAARHRSEEDPR
+>MHAAABBN_01585
+MLVILTALFVVALAAPVIFRWTGRQGFYLLAAAPAAGFVWLLTQLPHVFALQEALDAGRP
+VPASAAHLDRAVPWVPYLEIELAFRMDVLAAFMSLIVLGVGALVLAYCARYFREHEPRNA
+VFGGQLLAFAGAMFGLVTTDDLMVLYTFWEITSVLSFLLIGYSGHRIFARRSAITALIVT
+TFGGLAMLAGLIMLAHFAGSWRISGVLAAAPGLLADDGGRVLLEVAVGLVLIGALTKSAQ
+APFHFWLPGAMAAPTPVSAYLHAAAMVKAGVFLVARLAPAFHELATWQVLVLGLGLWTLL
+LGGWRALRQTDVKLVLAYGTVSQLGFLMVANGLGVRDAALAGLAMLLAHALFKAPLFMVV
+GIIDHEAGTRDLRELSGIGRRHPALAAVAVAAGLSMAGLPPLFGFVAKESVLEGLAAHGV
+AHADVWGWTPLVLMTVGSVLTFAYTWRFLWGSFAAKRDEEGAAVPVTRFHTRVTTLELAP
+AALLALAGLVLAFLPGPVEGIITAHTGSLPPLDPAEKPAYLALWHGWTPILALSAGIWVL
+GALLALGRPGVEAFQRRVEFPVDALRTYRKITGALDEVAIWVTGRTQTGSLRRYLGIILA
+TAFLLPAAFLLFPVGRSERTLATSFLSADVAWFQTPAQLVVVLMIAVATVFAVRARRRFK
+AIMLVSVTGYGAAALFAMRGAPDLAITQVLVETIILVTLILGLRVLPPDWYDRRTGSRRI
+ARMAVAGGFALTMMWIAATALAARTAERISLPMPELAYTDGYGTNAVNVTLVDIRAWDTW
+GEITVLAAAATGVASLIFLQHRDGRTRSIDDVAPGSVGDFGADSSLGARELSVVRSFAVD
+DRKGQWLVAGHTMAPERRSIILEVVTRFMFPIMMLLSVYLLLAGHNTPGGGFAGGLLAGL
+ALTLRFLAGGRYELQEASVIPAGPMIGLGLAIATLTGIAPLFFGGQILQSYVVEFTDLPL
+FGDALKLVSATAFDIGVYLVVVGLVIDVLRSLGGEVDRRGEEARRARLRAAARRRHPRMP
+TPSTPDAPEAAR
+>LFPAFLNI_01809
+MLVILTALFVVALAAPVLFRWTGRQGFYLLAAAPAAGFVWLLTQLPHVFALQEALDAGRP
+VPASAARLDRAVPWVPYLEIELAFRMDMLAAFMSLIVLGVGALVLAYCARYFREHEPRNA
+VFGGQLLAFAGAMFGLVTTDDLMVLYTFWEITSVLSFLLIGYSGHRIFARRSAITALIVT
+TFGGLAMLAGLIMLAHVSGSWRISGVLEAAPALMADPGMRGLLEVAVALVLIGALTKSAQ
+APFHFWLPAAMAAPTPVSAYLHAAAMVKAGVFLVARLAPEFHDLTSWQVLVLGVGLWTLV
+LGGWRALRQTDVKLVLAYGTVSQLGFLMVANGLGTRDAAMAGLAMLLAHAVFKAPLFMIV
+GIIDHETGTRDLRQLSGIGRRHPVLAAVAVAAGLSMAGLPPLFGFVAKESVLESLAAHGA
+AHGGVWGWTPLVLMTVGSVLTFAYTWRFLWGSFAAKRDEEGAAVPVTRFHTRVTTLELAP
+AALLALAGLVLAFLPGPVEGIITAHTGSLPPLDPEEAPAYLALWHGWTPILALSAGVWVL
+GALLALGRPGVEAFQRRVEFPVDALRTYRKITGALDEVAIWVTGRTQTGSLRRYLGIILA
+TAFLLPAAFLLFPVGRSERTLATSFLSADVAWFQTPAQLVVVLMIAVATVFAVRARRRFK
+AIMLVSVTGYGAAALFAMRGAPDLAITQVLVETIILVTLILGLRVLPPDWYDRRTGSRRL
+GRLAVAVGFALTMMWIAATALAARTAERISLPMPELAYTDGYGTNAVNVTLVDIRAWDTW
+GEITVLAAAATGVASLIFLQHRDGRTRSIDDVAPGSVGDFGADSSLGARELSVVRSFAVD
+DRKGQWLVAGHTMAPERRSIILEVVTRFMFPIMMLLSVYLLLAGHNTPGGGFAGGLLAGL
+ALTLRFLAGGRYELQEASVIPAGPMIGLGLAIATLTGIAPLFFGGQILQSYVVEFTDLPL
+FGDALKLVSATAFDIGVYLVVVGLVIDVLRSLGGEVDRRGEEARRARLRAAARRRHPRMP
+TPSTPDAPEAAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000635.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000635.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b73ad5bf9d201c86fb946d836391e97568e0b997
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000635.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_00971
+MSIGSVPMTDLAPLAVMMPVLGAAVTFMLVRRPRAQVVVTVAALVLTLLLNCLLLAAVWE
+GGVASVHVGGWPAPLGITLVVDRLSALMLVVSALITLAVLLYASAQGMVNRDEGGPVSIF
+HPTFLILVAGVFNAFLAGDLFNLYVGFEILLTASYVLLTMGGTAQRIRAGITYVVVSVIS
+SVVFLIAIAMVYAATGTVNMADLAVKLGELPSDVQMVLHVLLLVGFGIKAAVFPLSFWLP
+DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA
+QTDIKRILSFILVSHIGYMIFGLGLATQMGLAATVFYVGHHITVQTALFLVTGLIENRAG
+TANIDRLGSLAKVSPFISVLFLIPALNLGGIPPFSGFLGKVGLLRGGVEQGTGLSYTLVG
+VSLLASLLTLLVVVRVWTRAFWRKVEDVEHPPAQLVAAYERTIDRGLRPRRLEPGLVLPT
+AALVVMTLAFTVLAGPLFDLADAAATDMLDRTPYIASVLDEAAAERAAETLSHDPTEVHD
+ARH
+>MOLHKGIG_01887
+MSIGTLPLTDLAPLAVMLPVLGAAVTFMLVRRPRAQITVTVSALVLTLVLDALLLAAVWD
+TGVAAVHLGGWPAPLGISLVVDRLSALMLVVSALITLAVLLYASAQGLINRDEGGPVSIF
+HPTFLILVAGVSNAFLAGDLFNLYVGFEILLTSSYVLLTMGGTAQRIRAGVTYVVVSVLS
+SVVFLIAIAMIYAATGTVNMADLAVKLGELPTDVQMVLHVLLLVGFGIKAAVFPLSFWLP
+DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA
+QTDIKRILSFILVSHIGYMIFGLGLATEAGLAATVYYVAHHITVQTALFLVTGLIENRAG
+TANIDRLGSLAKVSPFVSVLFLVPALNLGGIPPFSGFLGKVGLLRGGVEQATPLAYTLVG
+VSLLVSLLTLLVVVRVWTRAFWRRVEDVEHPPAQLVAAYERAVARGERPRPLEPGLVLPT
+TALVGLTLVFTVAAGPLFALADEAATDMLDRSPYIAAVLDDAAAERAAATLSVDPTEVHD
+ARK
+>NAFOICDF_00909
+MLGSTPLTDLAPLAVMLPVLGAAITFALVGRARAQVVVTVSALTLTLVLDCLLLADVWTG
+GVAVVELAAWPAPVGITMVVDRLSALLLVVSSLITLAVLLYASAQGLINKDEGGPVSIFH
+PTFLVLVAGVSNAFLAGDLFNLYVGFEILLTASYVLLTLGGTEARIRAGITYVVVSVISS
+VLFLIAIAMIYAATGTVNMADLAVKLGELPHDLQLVLHVMLLAGFGIKAAVFPLSFWLPD
+SYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPAEHVNGLLMGVAALTMLVGILGALAQ
+SGLKRILSFILVSHIGYMVFGLALATQVGLAATVYYVGHHITVQTALFLVTGLIEQRAGT
+ASIDRLGSLAKVSPLLGVLFLVPALNLGGIPPFSGFLGKVGLIRGGVEDGGVLAWVLVGV
+SLLVSLLTLLVLVRAYTRAFWRKVEDVEHPTPQLVAAYERVTRRGLRPKPLSRGLVLPTA
+GLVAMTLAFTVFAGPLYDLADRAAVDMLERSPYISAVLGPEAADRAAVTLSHDPSEVHDA
+GR
+>MHAAABBN_01583
+MSIGSVPLTDLAPLAVMLPVLGAAVTFMLVRRPRAQITVTVSALVLTLVLDALLLAAVWD
+TGVAAVHLGGWPAPLGISLVVDRLSALMLVVSALITLAVLLYASAQGLINRDEGGPVSIF
+HPTFLILVAGVSNAFLAGDLFNLYVGFEILLTSSYVLLTMGGTAQRIRAGITYVVVSVLS
+SVVFLIAIAMIYAATGTVNMADLAVKLGELPTDVQMVLHVLLLVGFGIKAAVFPLSFWLP
+DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA
+QTDIKRILSFILVSHIGYMIFGLGLATEAGLAATVYYVAHHITVQTTLFLVTGLIENRAG
+TANIDRLGSLAKVSPFVSVLFLVPALNLGGIPPFSGFLGKVGLLRGGVEQATPLAYTLVG
+VSLLVSLLTLLVVVRVWTRAFWRRVEDLEHPPAQLVAAYERAVARGERPRPLEPGLVLPT
+TALVGLTLVFTVAAGPLFALADEAATDMLDRSPYIAAVLDDAAAERAAATLSVDPTEVHD
+ARK
+>LFPAFLNI_01807
+MSIGTLPLTDLAPLAVMLPVLGAAVTFMLVRRPRAQITVTVSALVLTLVLDALLLAAVWD
+TGVAAVHLGGWPAPLGISLVVDRLSALMLVVSALITLAVLLYASAQGLINRDEGGPVSIF
+HPTFLILVAGVSNAFLAGDLFNLYVGFEILLTSSYVLLTMGGTAQRIRAGVTYVVVSVLS
+SVVFLIAIAMIYAATGTVNMADLAVKLGELPTDVQMVLHVLLLVGFGIKAAVFPLSFWLP
+DSYPTAPAPVTAVFAGLLTKVGVYAMIRTETLLFPGEHVNALLLVVAALTMVVGILGALA
+QTDIKRILSFILVSHIGYMIFGLGLATEAGLAATVYYVAHHITVQTALFLVTGLIENRAG
+TANIDRLGSLAKVSPFVSVLFLVPALNLGGIPPFSGFLGKVGLLRGGVEQATPLAYTLVG
+VSLLVSLLTLLVVVRVWTRAFWRRVEDVEHPPAQLVAAYERAVARGERPRPLEPGLVLPT
+TALVGLTLVFTVAAGPLFALADEAATDMLDRSPYIAAVLDDAAAERAAATLSVDPTEVHD
+ARK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000643.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000643.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5a9880efba93fd9a7bb6b7c82129427906cd367
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000643.fa
@@ -0,0 +1,60 @@
+>ACLBLIBL_00983
+MSRAVGIDLGTTNSVVAALEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN
+NPERTYASVKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA
+YFNDAERQATKEAGEIAGLNVTRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL
+LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE
+AAEQAKKELSSATSTSISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFEDVI
+KEAGVKVSDIDHVVLVGGSTRMPAVSDLVKELTGGKEPNKSVNPDEVVAIGAAVQAGVLA
+GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG
+EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG
+GSSLSKEDIDRMVKDAEAHADEDKKRREAADRRNQAEQSAYSVDKLLQDNADKLPEDVKT
+EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG
+DDEDIVDAEVVDEDDEKKA
+>MOLHKGIG_01876
+MSRAVGIDLGTTNSVVAALEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN
+NPERTFASVKRHMGTDWTAEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA
+YFNDAERQATKEAGEIAGLNVTRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL
+LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE
+AAEQAKKELSSATSTNISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFEDVI
+KEAGVKVSDIDHVILVGGSTRMPAVSDLVKELTGGKEPNKGVNPDEVVAIGAAVQAGVLA
+GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG
+EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG
+GSSLSKEDIDRMVKDAEAHADEDRKRREAADRRNQAEQSAYSVERLLQDNADKLPEDVKT
+EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG
+DDEDIVDAEVVDEDDEKKA
+>NAFOICDF_00921
+MSRAVGIDLGTTNSVVAVLEGGDPVVIANAEGARTTPSVVAFSKGGEVLVGEVAKRQAVN
+NPDRTYASVKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA
+YFNDAERQATKEAGEIAGLNVKRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL
+LEVAKDEDDFATIQVRATSGDNRLGGDDWDQRIVDWLLQQAKSKGADLSNDKIALQRLKE
+AAEQAKKELSSATSTNISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFNDVI
+KEAGVKVSDIDHVVLVGGSTRMPAVSELVKELTGGKEPNKGVNPDEVVAIGASVQAGVLA
+GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG
+EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG
+GSSLSKEDIDRMVKDAESHAEEDKARREAAERRNQAEQSAYSVDKLLADNADKLPEDVTT
+EVQADVDALKAALEKQDNDDEVKAAFEKLQASQVKIGEALYAQQSAEGAQPDAESGSAQA
+DEDIVDAEVVEDEDEKKN
+>MHAAABBN_01572
+MSRAVGIDLGTTNSVVAVLEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN
+NPERTYASVKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA
+YFNDAERQATKEAGEIAGLNVKRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL
+LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE
+AAEQAKKELSSATSTSISLQYLSVTPEGPVHLDEHLSRAKFEDLTKDLLERTRKPFEDVI
+KEAGVKVSDIDHVILVGGSTRMPAVSDLVKELTGGKEPNKSVNPDEVVAIGAAVQAGVLA
+GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG
+EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG
+GSSLSQEDIDRMVKDAEAHADEDKKRREAADRRNQAEQSAYSVERLLQDNGDKLPEDVKT
+EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG
+DDEDIVDAEVVDEDDEKKA
+>LFPAFLNI_01796
+MSRAVGIDLGTTNSVVAVLEGGDPVVIANAEGARTTPSVVAFSKGGDVLVGEVAKRQAVN
+NPERTFASIKRHMGTDWTTEVDGKKYTPQEISARTLMKLKHDAEEYLGEKVTDAVITVPA
+YFNDAERQATKEAGEIAGLNVKRIINEPTAAALAYGLEKGKEDELILVFDLGGGTFDVSL
+LEVAKDEDDFATIQVRATAGDNRLGGDDWDQRIVDWLLQQAKSKGADLSKDKIALQRLKE
+AAEQAKKELSSATSTNISLQYLSVTPEGPVHLDEHLSRAKFQDLTKDLLERTRKPFEDVI
+KEAGVKVSDIDHVILVGGSTRMPAVSELVKELTGGKEPNKSVNPDEVVAIGAAVQAGVLA
+GERKDVLLIDVTPLSLGIETKGGVMAKLIERNTAIPTKRSETFTTAEDNQPSVSIQVFQG
+EREFTRDNKALGTFELTGIAPAPRGMPQIEVTFDIDANGIVHVSAKDKGTGTEQSMTITG
+GSSLSQEDIDRMVKDAEAHADEDKKRREAADRRNQAEQSAYSVEKLLQDNGDKLPEDVKT
+EVQADVDALKAALEKQDNDDEVAAAFEKLQASQVKIGEALYAQQGAESADAGAESAAPQG
+DDEDIVDAEVVDEDDEKKA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000645.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000645.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e67ae108b93400041ff88c81c74bcfaee5047cc1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000645.fa
@@ -0,0 +1,32 @@
+>ACLBLIBL_00986
+MSLRAADGETIEVKIPKGIRDGQKVRARGKGAPGAAGRGDLLVTVHVREHEFFRRDGDDL
+RITVPVTFPEAALGATIEVPTLERPVKMKVPAGSQSGRVLRLKGRGVERGTTKGDLLVEL
+HVTVPTELNDDARAAVEALQSALAGDDPRRELARKAAW
+>MOLHKGIG_01874
+MASQDWMDKDFYATLGVSKDASDADVKKAYRKLARMYHPDQNPGDEAAEKKFKEISEAYA
+VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRATQSEPDLSDL
+FSGMFSGAAGQPGGFGPGGFGDAGYARPRPTKGADRTATTTISFRGSIQGTTVSLRGPDG
+ETIEVKIPKGIRDGQKVRARGKGSPGPAGRGDLLVTVHVREHEFFRRDGDDLRITVPITF
+PEAALGATIEVPTLERPVKVKVPAGSQCGRVLRLKGRGVERGKTTGDLLVELRVTVPTTL
+NDDARAAVEALQSATAGDDPRRELARKAAW
+>NAFOICDF_00923
+MASQDWLEKDFYQVLGVSKDASESDIKKAYRTLARKHHPDQNPGDAAAEQRFKEISEAYD
+VLSDPKDRQEYDAIRSMGGGARFGAPGGFGGAGGGAGAGGFEDVFGGMFGGGGGSRTFRT
+GGAQGGPDLSDLLGAFTGGGAGGFGGGQGFGGGGFGQPAPTKGADRTATTTISFRGAVEG
+TTVSLRAADGETVDVRIPKGVKDGQKVRARGKGSPGTAGRGDLIVTVQVREHPFFQRDGD
+DLRITVPVTFAEAALGATVEVPTLDRPVKVKVPAGSQSGRVLRLKGRGVAGAKHTGDLLV
+ELQVAVPAELSAEARGAVEAYAAATAGDDVREGLAGKAQW
+>MHAAABBN_01570
+MASQDWMDKDFYATLGVSKDASDADVKKAYRKLARTHHPDQNPGDEAAEKKFKEISEAYA
+VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRTTQSEPDLSDL
+FSGMFSGAAGQPGGFGPGGFGDAGYARPRPTKGADRTATTTISFRGSIQGTTVSLRGPDG
+ETIEVKIPKGIRDGQKVRARGKGSPGPAGRGDLLVTVHVREHEFFRRDGDDLRITVPITF
+PEAALGATIEVPTLDRSVKVKVPAGSQCGRVLRLKGRGVERGTTTGDLLVELRVTVPTTL
+NDDARAAVEALQSATAGDYPRRELARKAAW
+>LFPAFLNI_01794
+MASQDWMDKDFYATLGVSKDASESDVKKAYRKLARTHHPDQNPGDEAAEKKFKEISEAYA
+VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRTTQSGPDLSDL
+FSGMFGGAAGQTGGFGDAGYPRPRPTKGADRTATTTISFRGSIQGTTVSLRAPDGETIEV
+KIPKGIRDGQKVRARGKGSPGAAGRGDLLVTVHVREHEFFHRDGDDLRITVPVTFPEAAL
+GATIEVPTLERPVKVKVPAGSQSGRVLRLKGRGVERGTTTGDLLVELHVTVPTELDDDAR
+AAIEALQSALAGDDPRRELARKAAW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000646.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000646.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c6e1db05567e01ea929d90f28aeae4179cd9e57
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000646.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_00987
+MSARDGAARADRGRERGLDRNAPVFVVSVAAEMADMHPQTLRQYDRLGLVVPARQGGRHR
+RYSLADVERLQTVQALSREGISLEGIRRVIALQREVEQLQDTVVELAAQVDRLHHASRLA
+RVFTVGSGGDVSARYADRMAARRQAAARTEADAAGQASPGVLRMLPSGGARPRRVLTWQP
+EQD
+>MOLHKGIG_01873
+MSARDGAARADRGREGGPDRHAPVFVISVAAEMADMHPQTLRQYDRLGLVVPARQDGRHR
+RYSLADVERLQTVQTLSREGISLEGIRRVIALQREVEQLQDTVVELAAQVDRLHHASRLA
+RVFTVGSGGDVSARYADRMAVRRHAAARAGADTAGEACPSGLRRLPSGVAGLRRVPTWQS
+EQD
+>NAFOICDF_00924
+MVSGVAGEHPTGAGRLRGTAGRPGRHDPVFVISVAAEMAGMHPQTLRQYDRLGLVVPQRQ
+GGRHRRYSAADVEHLRAVQRLSREGVSLEGIRRILDLQREVERLQDTVVELASQVDRLHS
+ASALARVFSVGLAGDVSARYAAPAAHRAAEAVQGQRRPGEGATRSAARGGLLRALPAGRA
+AAPRGLTRLPAPRD
+>MHAAABBN_01569
+MSARDGAARADRGREGGPDRHAPVFVISVAAEMADMHPQTLRQYDRLGLVVPARQDGRHR
+RYSLADVERLQTVQTLSREGISLEGIRRVIALQREVEQLQDTVVELAAQVDRLHHASRLA
+RVFTVGSGGDVSARYADRMAVRRHAAARAGADTAGEACPSGLRRLPSGVAGLRRVPTWQS
+EQD
+>LFPAFLNI_01793
+MSARDGAARADRGREPGLDRNAPVFVISVAAEMADMHPQTLRQYDRLGLVVPARQGGRQR
+RYSLADVERLQTVQALSREGISLEGIRRVIALQREVEQLQDTVVELAAQVDRLHHASRLA
+RVFTVGSGGDVSARYADRMAARRQAAARTEADAAGQASPGVLRMLPSGGARPRRVLTWQP
+EQD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000652.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000652.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec40db6710bd048911a81dcfa3f0debce3d24e48
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000652.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00993
+MAQQTPQPAASAVDAAGVHVADLNKSYGSNHVLRGIDLDVAPGEVVCLIGPSGSGKSTLL
+RCVNLLEKPDSGRITVGEFDVTDEDVDLDALRRHVGMVFQQFNLFPHLSVLENCTVAQVK
+VLKRSKAEAAEVARRQLARVGLAELEDRFPDQLSGGQQQRVAIARALAMDPQLMLFDEPT
+SALDPETVGEVLAIMRQLARDGMTMLVVTHEMGFAREVADRVVSMDAGVVVETGPAAALI
+ADPQQPRTQDFLRRVLHPTEIDL
+>MOLHKGIG_01867
+MAQQNPITGSFGAVAAADAAGVHVAGLNKSFGANHVLRGIDLDVAPGEVVCLIGPSGSGK
+STLLRCVNLLEKPDSGVVTVGEFTVTDEDVDLDVLRRHVGMVFQQFNLFPHLSVLENCTV
+AQLKVLKRGKAEAVDIARRQLARVGLAELEDRYPDQLSGGQQQRVAIARALAMDPQLMLF
+DEPTSALDPETVGDVLAIMRQLARDGMTMLVVTHEMGFAREVADRVVFMDGGVVVEAGPA
+AAVISDPQQPRTQDFLRRVLHPTEIDL
+>NAFOICDF_00931
+MTEQTASPRPSDAGTAAGVHIAGLHKSYGSNHVLRGIDLDVAPGEVVCLIGPSGSGKSTL
+LRCVNLLEVPDSGGVQVGEFTVTDPDVDLDRLRQHVGMVFQQFNLFPHLTVLENCTVAQV
+KVLKRSAAEAADTARRQLARVGLGELEGRYPDQLSGGQQQRVAIARALSMDPRLMLFDEP
+TSALDPETVGDVLAIMRKLAREGMTMLVVTHEMGFAREVADRVVFMDGGVVVEQGPASAV
+ITDPQEPRTQDFLRRVLNPAGVDI
+>MHAAABBN_01563
+MAQQNPITGSFGAVAAADAAGVHVAGLNKSFGANHVLRGIDLDVAPGEVVCLIGPSGSGK
+STLLRCVNLLEKPDSGVVTVGEFTVTDEDVDLDVLRRHVGMVFQQFNLFPHLSVLENCTV
+AQLKVLKRGKAEAVDVARRQLARVGLAELEDRYPDQLSGGQQQRVAIARALAMDPQLMLF
+DEPTSALDPETVGDVLAIMRQLARDGMTMLVVTHEMGFAREVADRVVFMDGGVVVEAGPA
+AAVISDPQQPRTQDFLRRVLHPTEIDL
+>LFPAFLNI_01787
+MAQQNPITGSFGAVAAADAAGVHVAGLNKSFGANHVLRGIDLDVAPGEVVCLIGPSGSGK
+STLLRCVNLLEKPDSGVVTVGEFTVTDEDVDLDVLRRHVGMVFQQFNLFPHLSVLENCTV
+AQLKVLKRGKAEAVDVARRQLARVGLAELEDRYPDQLSGGQQQRVAIARALAMDPQLMLF
+DEPTSALDPETVGDVLGIMRQLARDGMTMLVVTHEMGFAREVADRVVFMDGGVVVEAGPA
+AAVISDPQQPRTQDFLRRVLHPTEIDL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000654.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000654.fa
new file mode 100644
index 0000000000000000000000000000000000000000..10cf92a021a48213b863e057399ddb46433191e0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000654.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00995
+MGLTASAALLTGCAVLGGDSGVAGVVSDDDLSTTYNLVQPGVLTVCSDIPYPPFEFELDG
+ELTGYDIQLVHAIAEELELGVNVIDSSFEAIESGASLTGCDLNASSISITEQRQRAMAFT
+LPYLDDDLVLVAATDSGITDVESAKGRRVGVQAATTGDAYAKENGLNPIEFEDGGMQVQA
+LQAGTVDALLGNQSVILYSLKDDERFEVVENLPTGEQLGMAVAPQNAQLGSAVNRALQQL
+RNDGTVAELQERWFGLAQEDYR
+>MOLHKGIG_01865
+MTRIHSRLLGAVGLTASAALLTGCAVLGGDAGSAGIVSDDDLSTSYGLVQPGVLTVCSDV
+PYPPFEFEENGELTGYDIQLVEAVAEKLGLGVNVIDSSFEAIESGASLTGCDVNASSISI
+TEARQRVMAFTLPYLDDDLVLVAKKGSGITDVDSAKGRRIGVQAATTGDEYAQQNGLSPV
+QFEDGGMQVQALQAGTVDAALGNQSVLLYSLKDDDRFEVVESLPTGEQLGMAVGPQKAQL
+GSAVNRALQELRNDGTVAELQERWFGQAQEDYR
+>NAFOICDF_00933
+MPRTPSRALGAVGAGLSAALLSGCAVIGGDAGTTGPLAEDDLRATYRLHEPGVLTVCADV
+PYPPFEFEQDGQLTGYDIDLTRKLAETMDLQLKVVDTSFEAIESGASLTGCDLNASAISI
+TEPRQHVMAFTLPYLDDDLVLVARKDSGITDVASAQGKRVGVQTATTGEEYAQSQGLDTV
+QFEDGGMQVQALQAGTVDALLGNQSVLLYSLKDDPRFGVVESLPTGEQLGMGVAPDNALL
+GSAVNRALQTLRNDGTVAELQQKWFGTAQKDYQ
+>MHAAABBN_01561
+MTRIHSRLLGAVGLTASAALLTGCAVLGGDAGSAGIVSDDDLSTSYGLVQPGVLTVCSDI
+PYPPFEFEEKGELTGYDIQLVEAVAEKLGLGVNVIDSSFEAIESGASLTGCDVNASSISI
+TEARQRVMAFTLPYLDDDLVLVAKKGSGITDVDSAKGRRIGVQAATTGDEYAQQNGLSPV
+QFEDGGMQVQALQAGTVDAALGNQSVLLYSLKDDDRFEVVESLPTGEQLGMAVGPQKAQL
+GSAVNRALQELRNDGTVAELQERWFGQAQEDYR
+>LFPAFLNI_01785
+MTRIHSRLLGTVGLTASAALLTGCAVLGGDAGSAGIVSDDDLSTSYGLVQPGVLTVCSDV
+PYPPFEFEENGELTGYDIQLVEAVAEKLGLGVNVIDSSFEAIESGASLTGCDVNASSISI
+TEARQRVMAFTLPYLDDDLVLVAKKGSGITDVDSAKGRRIGVQAATTGDEYAQQNGLSPV
+QFEDGGMQVQALQAGTVDAALGNQSVLLYSLKDDDRFEVVELLPTGEQLGMAVGPQKAQL
+GSAVNRALQELRNDGTVAELQERWFGQAQEDYR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000656.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000656.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c3418978484f3648951291673920179bc8838a37
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000656.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_00997
+MSGSTAAPRRLRTYARPRVSLLYVLRRTTHRLLELQVWDVAAAMTFFAALSLLPTVVALV
+SLVSLLGVQEETVDAAAQLATEIWPSLTPDTVREWILTLGSAGTGTAAVVLGILGAVVSA
+SGAVGAFHRAMHRIHDTREGRPFLQFRLVLLVETLALMVGIVLVVILVVLGGDLSLRIGQ
+AVGLPEETVLTWNVVKWPVILVVIALTVTLAYRLGPNVVPPRYRPLSAGAVSVVVLLFAA
+TLALGWITDRFGQFAVVGRINSAIGVLVLAWIACIVLLAGAALDAEMLRGRQLAVGVDAA
+SEIQLATRHTVVLEAAERHEDRSRRLARLVAEAVREDEDLSIDATPLLSQEGRMFAIGSA
+RRTAAEVSSGRPFHAAPVLDDGARLEPTSRPDD
+>MOLHKGIG_01863
+MAGSTAAPRRLRTYTRPRVSLLYVLRRTLHRLFELQVWDVAAAMTFFGALSLLPTVIALL
+SVVSLLGVEEETVDAAAHLAAEIWPSLTPDVVREWILTLGSAGPGTGAVVLGAVGTVVSA
+SGAVGAFHRAMHRIHDTREGRPFLHFRLVVFVETLALMLGAVLITILVVVGGDLSLRLGQ
+AVGLPEETVQTWNVVKWPVILVVIALIVTLAYRLGPNVRQPRYRPLSLGAVAVVVLLFGA
+TVALGWITDRFGQFAVVGRINSAIGVLALAWVACIVLLAGAAFDAEVLRARQLAVGIDAS
+VEIQLATRHTAVLEASERYEARNRRLARLVADAVRAGEDLTIEATPLLSEEGRLLAVESG
+RRDPEDVSSGSPFHADPVSHDGARLEPTPRPDD
+>NAFOICDF_00936
+MPSSPVPDASTGGRAPRTYARPRASLLYVLERTWTRLVGMQVWDVAAAMTFFAVLSLLPT
+LVALVSLVSLLGVEARTVETAARLATEVWPSLDAAEVSAWILNAGRTATGTPGLVLGAAG
+AVVSASGAVGAFHRAMHRIYDTREGRPFLVYRLVVLLETLALIVGAALVMSLMVLGGDLS
+ERLGRLLGVGRGAVAVWNASTWPMILVLLALIVSVAYRRGPNVRPPCHRPFSLGAVGAVA
+LLFAAALALGWIVARFGGLALVGRLNSALGVLGLAWAACIVLVAGAAFDAEMLRARQLAV
+GVESADELQLATRDTWVLRQVERQEARHLRVGRLVAEAVRTEEPVTTPATRLLAEAGSLF
+AVDAAGRSASDLTSGRPFHAVPPADRAGV
+>MHAAABBN_01559
+MAGSTAAPRRLRTYTRPRVSLLYVLRRTLHRLFELQVWDVAAAMTFFGALSLLPTVVALL
+SVVSLLGVEEETVDAAAHLAAEIWPSLTPDVVREWILTLGSAGPGTGAVVLGAVGTVVSA
+SGAVGAFHRAMHRIHDTREGRPFLHFRLVVFVETLALMLGAVLITILVVVGGDLSQRLGQ
+AVGLPEETVQTWNVVKWPVILVVIALIVTLAYRLGPNVRQPRYRPLSLGAVAVVVLLFGA
+TVALGWITDRFGQFAVVGRINSAIGVLALAWVACIVLLAGAAFDAEVLRARQLAVGIDAS
+VEIQLATRHTAVLEDFERYEARIRRLARLVAEAVRAGESLTIEATPLLSEEGRLLAVESG
+GRGPEDVSSGSPFHADPVSDDGARLEPTPRPDD
+>LFPAFLNI_01783
+MAGSTAAPRRLRTYTRPRVSLLYVLRRTLHRLFELQVWDVAAAMTFFGALSLLPTVIALL
+SVVSLLGVEEETVDAAAHLAAEIWPSLTPDVVREWILTLGSAGPGTGAVVLGAVGTVVSA
+SGAVGAFHRAMHRIHDTREGRPFLHFRLVVFVETLALMLGAVLITILVVVGGDLSLRLGQ
+AVGLPEETVQTWNVVKWPVILVVIALIVTLAYRLGPNVRQPRYRPLSLGAVAVVVLLFGA
+TVALGWITDRFGQFAVVGRINSAIGVLALAWVACIVLLAGAAFDAEVLRARQLAVGIDAS
+VEIQLATRHTAVLEASERYEARNRRLARLVADAVRAGEDLTIEATPLLSEEGRLLAVESG
+RRDPEDVSSGSPFHADPVSDDGARLEPTSRPDD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000658.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000658.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54e28fb137145e5c591235ccb020b74913fef9d4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000658.fa
@@ -0,0 +1,46 @@
+>ACLBLIBL_00999
+MSMRRRPALLAASVLAASLAVAPAAAAIPGHAAGGPAPAASAADRAGGNPNSPEKLVAAI
+SAANLERDIRAFADIAEEHGNRAAGTPGYDASVDYAVAELEKAGYDVELEEFEITYTETL
+RNEFTQEGPVQRELPHEVLTYSPSATAESAQLAVPTGALGCTTADWGGADLTGRIALVSR
+GECPFAQKSTTAAELGAEAVVIYNNADGPLNGTLGAPSDDYVGTVGITRDLGQELVAQAA
+AGPVTVSLDLEQLVEQRPTVNILAETRTGRDDNVVMVGAHLDGVPAGPGIHDNASGSAVT
+LEVARQMAKVNKTGNTVRFALWGAEEIGLLGAAHHVAELSQSERDAIAMYVNLDMVAPLD
+HQNTLGVLTGDFSLGAESFLQEQLERDGHEHGPAGNGGNSDYAPFVAAGIPATGLLSYRD
+DNYHTAQDDIENVSITSLTHSARAVANLVGTFMHDTSSVNDKCNAGKSGKPKQC
+>ACLBLIBL_01510
+MSTSSLSRRSFLALAGAAGAAGAFAMPAWGLDDVRPGAARAPRLTGQDRQIINQIRPARA
+VDHLTLLTEEIGQRYTGTPAEHRAADYIAAQLEGYGYDVELEWFDVPDRRVGLLEAPELD
+GRWSWGVGSAAAAAQDVTVAGRVVLAPSGSVADLTGMVLMRVVTASEDITPLAVAAQARG
+AVAVIATRRDSNPPGQASAFAPALTTARLDIPVVGVSQVQKHALLGVLAAGPLRLTVSTV
+EHRGTRSANVVGTRAGRKGPGKGGRERVMLGAHYDSVIGSRGANDNASGTAACLELARVM
+RNAPTAADLSFGFWGSEEVGLVGSRIHAQAMPADERSRLRGVFNNDMIATSWDPAEKYWL
+LDLRGEANDVNRAVYAAGERLGYRTSMSDLFTMGRSDHQSFSEIGVPSGNFGWLHRDGFI
+LEPEYHSSDDTVKENISVERLMAAMEIQGCAAYALASR
+>MOLHKGIG_01861
+MRRTPTLLAAATLAATLTAAPVSLAAPAAPAAPAKAPMGTTQTADRGLGPGQNRAGGNPN
+SPKKLVRSISSDHLRQDITAFAAIADEHGNRAAGTPGFQASLDYAVGELEEAGYDVELQE
+FEITYTETLRDRLQQTGPVQRDLEHTVFTSSPSAQVTDAPLAAPAGAATGCADADWAGAD
+LTGSVALVSRGDCTFAQKSQVAAASGAEAVIIYNNAEGALNGTLGAAPGDVVGTVGVTRE
+LGADLLAQTRAGGATVTLDLEQLVEQRPTWNVLAETRTGSDDDVVMLGAHLDGVPEGPGI
+HDNASGVAATLEVARQAAKANKAESKVRFALWGAEEIGLLGSHHYVDTLTAAEREDIILY
+TNLDMVAPLDHQNTLGVLTADWSIGAESLLGAQLDRDGHGHQPEGSNGRSDYAPFVDAGI
+ASTGLLSIRDDNYHTPQDDIDNVSITTLTHTARAVANLIGTLQQDADALGTR
+>MHAAABBN_01557
+MGYVAYVTSTPTMRMPMRRTPTLLAAATLAATLTAAPVSLAAPAAPAKAPVATTQTADRG
+LGPGQNRAGGSTNSPKKLVRSISSDHLRQDIEAFAAIADEHGNRAAGTPGFQASLDYAVG
+ELEEAGYDVELQEFEITYTETLRDRLQQTGPVQRDLEHTVFTSSPSAQVTDAPLTAPAGA
+ATGCADADWAGADLTGSVALVSRGDCTFGQKSQVAAASGAEAVIIYNNAEGALNGTLGTE
+PGDVVGTVGVTRELGADLLAQTRAGGATVTLDLEQLVEQRPTWNVLAETRTGSDDDVVML
+GAHLDGVPAGPGIHDNASGVAATLEVARQAAKANKAESKVRFALWGAEEIGLLGSHHYVD
+TLTAAEREDIILYTNLDMVAPLDHQNTLGVLTADWSIGAESLLGAQLDRDGHAHQPEGSN
+GRSDYAPFVDAGIASTGLLSIRDDNYHTPQDDIDNVSITTLTHTARAVANLIGTLQQDAD
+ALGTR
+>LFPAFLNI_01781
+MRRTPTLLAAATLAATLTAAPVSLAAPAAPAAPAKASAATAQTADRGLGPGQNRAGGNPN
+SPEKLVRSISSDHLRQDIEAFAAIADEHGNRAAGTPGFQASLDYAVGELEEAGYDVELQE
+FEITYTETLRDRLQQTGPVQRDLEHTVFTSSPSAQVTDAPLAAPAGAATGCADADWAGAD
+LTGSVALVSRGDCTFAQKSQVAAASGAEAVIIYNNAEGALNGTLGAAPGDVVGTVGVTRE
+LGADLLAQTRAGGATVTLDLEQLVEQRPTWNVLAETRTGSDDDVVMLGAHLDGVPEGPGI
+HDNASGVAATLEVARQAAKANKAESKVRFALWGAEEIGLLGSHHYVDTLTAAEREDIILY
+TNLDMVAPLDHQNTLGVLTADWSIGAESLLGAQLDRDGHTHQPEGSNGRSDYAPFVDAGI
+ASTGLLSIRDDNYHTPQDDIDNVSITTLTHTARAVANLIGTLQQDADALGTR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000659.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000659.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d88dd6e59f08b0b219066b7aefb49fb0a65f5d6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000659.fa
@@ -0,0 +1,41 @@
+>ACLBLIBL_01001
+MTPPSPLAPEPVPDRAPAQDPGSGHAPSPASAALPPGHRPTGALPVAPGFDRDLHRLWWY
+TAAGLLSAVVVVAGFLVFVMARRLAVAEGPDASPLAVTVLVAGIAAAVAAAVGQTLATLR
+LRRAWEEEREPLRRTAVAALLPALLVALTPLAVPSLSAWPVLSLWLSVCLIAPQAAAHVR
+TAVLTSGAAATLGLTALALVRTPAGPADSAVGVLLWWAMVLLVVLPTVWVWRVAVRLEEA
+RAQAGELAVARERLRFAADLHDVQGHHLQVIALQAELAGRLLEKGRTDQAGAALRDVREQ
+AAEALGETRALVRGLRQVSVASEIENAREVLAATGAVVEVDVDPAAARLAREAARLVGLA
+VREATTNALRHAEPRRVRLALGPADGAAGGVRLTVTNDGARPPAAPPGTGLAGLAARAAE
+VSGRLSAGPDDDGGFRLELTVPSSSGATTRTDPTTTTGEDA
+>ACLBLIBL_02588
+MTSEPTSETRRLRSRTSFVLLAVFGVAAIVALLTSAVEPWPPLVLAPGLIAGLWLLSQWH
+REVAAPTRWAVLALGTLTWALSALWELTPLGALAFALAGALEVMWSRHARAVVTLLVLTV
+GAAAGALVFVTDPPALWVYVGMGALLTGVACVTIPVSRTSFDLMRLQDQRAEQERAASLD
+AERLRFSQDLHDIQGHALHVVKLKIAVAQRMLSTDTDAARRELDEAQQTLRQTMAETKAL
+AQDGHTLTLRGELANSVALLEAAGITVTTDDDGDPRREEFEHVAGVVIREGTTNILRHSD
+ARRVEISLAPGHVVISNDGVAGAPAEDHTGGLDNLRSRLAGVGGRLDVSCGDGRFTLEAR
+WEADEEETV
+>MOLHKGIG_00374
+MTSEHTSETRRLRSRTSFVLLAVFGVAAIVALLTSAVEPWPPLVLAPGLIAGLWLLSQWH
+REVAAPTRWAVLALGTLTWALSALWDLTPLGALAFALAGALEVMWSRHARAVVTLLVLTV
+GSAAGALVFVTDPQALWVYVGMGALLTGVACVTIPVSRISFDLMRLQDQRAEQERAASLD
+AERLRFSQDLHDIQGHALHVVKLKIAVAQRMLSTDTDAAQRELDEAQQTLRQTMAETKAL
+AQDGHTLTLRGELANSVALLEATGITVTTDDDGGPRGEEFEHVAGVVIREGTTNILRHSD
+ARRVEISLAPGHVVISNDGAAGVSAEDHTGGLDNLRSRLAGVGGRLDVSCVDGRFTLGAR
+WEADEEESV
+>NAFOICDF_01178
+MSPAGGPPAPARPTVGTAEHDPAVLPLHLWPSTMGFAGVWLISFGFVLVELLRRAFTPGD
+GRGEAILGVAAIAVFILVYLAAFVVPRPVRAWPAWANTVLTWFVLAGCVAVLTRILGVHA
+LLYSPFLVATWIFPHRLRVGLTGAGATMAAALATGLLFFPGDPALPVVLGNLAVLLVVLV
+GMRLAIARDDRVVEMTHELDLAGQRERLGRDLHDILGHSLTTINVKTQLVHRLIDTDPAR
+AKEEAAEVIALSRTALAEARAAVAELAAPELGGQLSLSVGALRDAGMAVEAPPPGAVTEV
+PQRRRALAAWIVREAVTNVLRHAGARRVRISLDAHHVAVLDDGAGLPAAVVAGVGPRTLA
+ERAAAEGARLEVGPGLGGAGTGVAVHWGGTTPEAARGVLPATEGRMDA
+>LFPAFLNI_00381
+MTSEHTSETRRLRSRTSFVLLAVFGVAAIVALLTSAVEPWPPLVLAPGLIAGLWLLSQWH
+REVAAPTRWAVLALGTLTWALSALWDLTPLGALAFALAGALEVMWSRHARAVVTLLVLTV
+GSAAGALVFVTDPQALWVYVGMGALLTGVACVTIPVSRISFDLMRLQDQRAEQERAASLD
+AERLRFSQDLHDIQGHALHVVKLKIAVAQRMLSTDTDAAQRELDEAQQTLRQTMAETKAL
+AQDGHTLTLRGELANSVALLEATGITVTTDDDGGPRGEEFEHVAGVVIREGTTNILRHSD
+ARRVEISLAPGHVVISNDGAAGVSAEDHTGGLDNLRSRLAGVGGRLDVSCVDGRFTLGAR
+WEADEEESV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000663.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000663.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b41c1d83ed6e0d64d495cf9268c0bcf8820d700b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000663.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01006
+MSMSTSTSTSLPCPQDRRPPVPARPLDVVAAGGPLFTRADLSAAGLPADRLRAADVRRVT
+HGVHRRADDVPGDWGALGYAEPPVAFAPEETAAIVTASRGVASHLSALLLHGIPVPPFLV
+DDGRVHVSRPHSRGASERPEVRSHARSVPEADAVVLHGIRVTSVERTWADLAALVRPGHL
+DPVVAAGDAVVTGIWTPQGRLPPRATILRLRAGLARSGRFKGARTARAALELIRAGADSP
+PETALRLALLHAGLPEPELQLVLHRGRRRSPDADLGWRAWRLVVHYDGDPHLDPAQQAVD
+AWRNGGWARAGWSQIVATVDDARDDFRRVVAEVLAHRARLGGRAYVA
+>MOLHKGIG_01858
+MATSSLPLSDIVETGRPFTRGDLRAAGVSERLVRGGDVRRVTHGVHRLRSDHLGSWADLG
+YVEAPAPFAPEETAAIVEASGGVASHLTALLLHRVPLPPFLAEDGTVHVSRPHPRGASVR
+PEITSHARLVPAADVTALHGIRLTSLERSWADLAALLRPGMLEPVVAAGDALIHRPWSPE
+GRRSPRTTTAALRSALLRAGRFKGVRTARAALELVRVGADSPQETALRLALLHAGLPEPE
+LQLVLHPGRARSPDADLGWRQWRLVVHYDGGHHLDPAQLAVDSWRDEGWARAGWTQIWAT
+VDDARDDFRRVVAEVQTHRARLGGRVFAS
+>NAFOICDF_00950
+MALESLADVLGSAPLPIRAEGPPPLGLFTRSDLRAAGLGGHRVHGRDVRRVTHGVHRLAT
+DPAGDWAVLGHRCPPAPFAPEETAAIVEAAGGVASHLTALLLHGVPLPPFLAEDGTVHVS
+RPHARGASGRLEVTSHARSVPAADVTSLHGIRVTSLERTWADLASLVPPGLVDPVVAAGD
+AVVRHPWTPQGRSAPRTTPARLAAALDRAGRFKGVRTARRALEAVRVGSDSPQETALRLA
+LVHAGIPEPELQLVLHPGRERSPDADLGWRMWRLVVHYDGASHLEPAQRAVDARRHEGWE
+RAGWAQIVATVDDARDDFRRVVAEVQAHRRRLGGRVYVC
+>MHAAABBN_01554
+MVTSSLPLSDIAEAGRPFTRGDLRAAGVSERLVRGADVRRVTHGVHRLRSDHLGSWADLG
+YVEAPAPFAPEETAAIVEASGGVASHLTALLLHRVPLPPFLAEDGTVHVSRPHPRGASVR
+PEITSHARLVPAADVTALHGIRLTSLERSWADLAALLRPGMLEPVVAAGDALIHRPWSPE
+GRRSPRTTTAALRSALLRAGRFKGVRTARAALELVRVGADSPQETALRLALLHAGLPEPE
+LQLVLHPGRARSPDADLGWRQWRLVVHYDGGHHLDPAQLAVDSWRDEGWARAGWTQIWAT
+VDDARDDFRRVVAEVQTHRARLGGRIFAS
+>LFPAFLNI_01778
+MATSSLPLPDIVETGRPFTRGDLRAAGVSERLVRGGDVRRVTHGVHRLRTDHLGSWADLG
+YAEAPAPFAPEETAAVVEASGGVASHLTALLLHRVPLPPFLAEDGTVHVSRPHPRGASVR
+PEITSHARLVPAADVTALHGIRLTSLERSWADLAALLRPGMLEPVVAAGDALIHRPWSPE
+GRRSPRTTTAALRSALLRAGRFKGVRTARAALELVRVGADSPQETALRLALLHAGLPEPE
+LQLVLHPGRARSPDADLGWRQWRLVVHYDGGHHLDPAQLAVDSWRDEGWARAGWTQIWAT
+VDDARDDFRRVVAEVQTHRARLGGRIFAS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000665.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000665.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c36170c6f023b240061c39c826c220020d797c1b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000665.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_01008
+MIASRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAG
+IAASDGKRIGVYKDIGLVSQVFDESTLATFTGHIAVGHCRYSTTGANKWANAQPTLGATA
+GGDTVALAHNGNLVNSGELLRMVQARDGLQLRGEMKQGNTTDTALVTALLHGEEGRKLEE
+TALELLPKVRGAYCFVFMDEHTLYAARDPHGVRPLVLGRLERGWVVASEQSALATVGASF
+IREVEPGEMIAIDEEGIRSTRFAEATPAGCVFEYVYLARPDASIAGRSVYESRVDMGRRL
+ALEGPVDADVVIPVPESGTPAAVGYAEASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIR
+LKLNVQPSVVAGKRVVVVDDSIVRGNTQRAIVRMLKEAGAAEVHVKISSPPVKWPCFYGI
+DFASRAELIANGAGVAEIASSIGADSLGYISEEAMIAATGQPRERLCTACFTGTYPIELA
+DESERGKSVLETDAGSAAVTVMAPDGDATTVASTGCEPGPDADDEKLLTETDRTPL
+>MOLHKGIG_01856
+MIAPRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAG
+IAVSDGGRIAVYKDIGLVSQVFDEATLTALSGHIAVGHCRYSTTGVNKWANAQPTLGATA
+DDGTVALAHNGNLVNSAELLRMVHAADGRHTHGEMKQGNTTDTALVTALLHGAPGDRLEE
+TALELLPKIRGAYCFVFMDEHTLYAARDPQGVRPLVLGRLERGWVVASEQSALATVGASF
+IREVEPGEMIAIDEEGIRSTRFAESKPAGCVFEYVYLARPDATIAGRSVYESRVEMGRRL
+ALEQPVEADVVIPVPESGTPAAVGYADASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIR
+LKLNVESTVVAGKRVVVVDDSIVRGNTQRAVVRMLKEAGAAEVHVKISSPPVKWPCFYGI
+DFATRAELIANGAAVDQIAASIGADSLAYISEEGMIEATGQPRERLCTACFTGDYPIPLA
+DEGERGKGLLEPVAVSPASTVVLDEDGETTTVTATGCEPGPDADDEKLLTETDRTPL
+>NAFOICDF_00952
+MISARTRRGDGRLTAALDPQEAGPQDECGVFGVWAPGEEVAKLTYYGLYALQHRGQESAG
+IAASDGKRIAVYKDMGLVSQVFDEPTLAALTGHVAVGHCRYSTTGVNKWANAQPTLGATA
+DDGTVALAHNGNLVNSAELLRMVESKEGAHTLGEIKQGNTTDTALVTALLHGEKGVSVEE
+TALELLPKVRGAYCFVFMTERTLYAARDPHGVRPLVLGRLERGWVVASEQSALATVGASF
+IREVEPGEMIAIDEEGIRSTRFAEATPAGCVFEYVYLARPDAAINGRSVYESRVEMGRRL
+AQEHPVDADVVIPVPESGTPAAVGYADASGIPFRQGFVKNAYVGRTFIQPSQTLRQLGIR
+LKLNVQPSVVAGKRVVVVDDSIVRGNTQRAIVRMLKEAGAAEVHVKISSPPVKWPCFYGI
+DFATRAELIANGAGVQEIASSIGADSLAYISEEGMIAATEQPRERLCTACFTGTYPIELA
+DEKERGKAVLENGTPTAEATDVVSEDGTVTTVASTGCEPGPDSEDEKLLTQTDRTPL
+>MHAAABBN_01552
+MIAPRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAG
+IAVSDGGRIAVYKDIGLVSQVFDEATLTALSGHIAVGHCRYSTTGVNKWANAQPTLGATA
+DDGTVALAHNGNLVNSAELLRMVHAADGRHTHGEMKQGNTTDTALVTALLHGAPGDRLEE
+TALELLPKIRGAYCFVFMDERTLYAARDPQGVRPLVLGRLERGWVVASEQSALATVGASF
+IREVEPGEMIAIDEEGIRSTRFAESKPAGCVFEYVYLARPDAAIAGRSVYESRVEMGRRL
+ALEQPVDADVVIPVPESGTPAAVGYADASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIR
+LKLNVQSTVVAGKRVVVVDDSIVRGNTQRAVVRMLKEAGAAEVHVKISSPPVKWPCFYGI
+DFATRAELIANGAAVDQIAASIGADSLAYISEKGMIEATGQPRERLCTACFTGDYPIPLA
+DEGERGKGLLEPVAVSPASTVVLDEDGETTTVTATGCEPGPDADDEKLLTETDRIPL
+>LFPAFLNI_01776
+MIAPRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAG
+IAVSDGGRIAVYKDIGLVSQVFDEATLTALSGHIAVGHCRYSTTGVNKWANAQPTLGATA
+DDGTVALAHNGNLVNSAELLRMVHAADGRHTHGEMKQGNTTDTALVTALLHGAPGDRLEE
+TALELLPKIRGAYCFVFMDEHTLYAARDPQGVRPLVLGRLERGWVVASEQSALATVGASF
+IREVEPGEMIAIDEEGIRSTRFAESKPAGCVFEYVYLARPDATIAGRSVYESRVEMGRRL
+ALEQPVDADVVIPVPESGTPAAVGYADASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIR
+LKLNVQSTVVAGKRVVVVDDSIVRGNTQRAVVRMLKEAGAAEVHVKISSPPVKWPCFYGI
+DFATRAELIANGAAVDQIAASIGADSLAYISEEGMIEATGQPRERLCTACFTGDYPIPLA
+DEGERGKGLLEPVAVSPASTVVLDVDGETTTVTATGCEPGPDADDEKLLTETDRTPL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000666.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000666.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7998e6e82d5d35140892864c890223aa6adbfc58
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000666.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01009
+MTTGPERSQHQHAYTVRRAPRLAAVLAVALALGLVIALVITTAVHGSPTPPADPYSGIPL
+SFSETFGFAALLSMLGTGVLGLVVWLLLDRRSRATTRTVVLERTDDPAAADIRLDRSAAD
+ALRSRTAPTERTPEQ
+>MOLHKGIG_01855
+MTSAPEPTPDQRAYTVRRAPRLTAVLAVALALGLLIALVITTAVHASPTPPADPYSGIPL
+SFSETFGFASLLSMLGTSVLGLLVWLLLDRRSRSTARTVVLERTDDPAVADVRLDRVDAG
+APPARTTPTERTPEQ
+>NAFOICDF_00953
+MTSGPERSTPSAPQQQEYVLRRAPRLSAAVIVSALVGVVLALLGTAAVHAGPQPPADPYS
+GMPLSFASTFGYMVVAAVLACLVLGLLVWLLLDRRSRRTQRTVLLERTDDPAAADVALPR
+PEAVAPAARPAADPSDGRTPEQ
+>MHAAABBN_01551
+MTSAPEPTPDQRAYTVRRAPRLTAVLAVALALGLLIALVITTAVHASPTPPADPYSGIPL
+SFSETFGFAALLSMLGTGVLGLIVWLLLDRRSRSTARTVVLERTDDPAVADVRLDRVDAG
+TPPARTTSTERTPEQ
+>LFPAFLNI_01775
+MTSAPEPTPDQRAYTVRRAPRLTAVLAVALALGLLIALVITTAVHASPTPPADPYSGIPL
+SFSETFGFASLLSMLGTSVLGLLVWLLLDRRSRSTARTVVLERTDDPAVADVRLDRVDAG
+APPARTTPTERTPEQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000667.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000667.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0db87c2dbd4cfb41e1537c359ab664cdd64edda9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000667.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01014
+MTTGSVPRRRIPVPEGHAALTSWARTHAQDPAAAAALPRSTRATAVRFALEELATRVPGN
+AVEVRVPPFGVAQAIPGPRHTRGTPPNVVEMDAVTWLSLATGLLGWADAVGTGAVRASGT
+RADLGAHLPLIRP
+>MOLHKGIG_01854
+MTTGSVPRRRVPVVEGHAALLAWARAHEEDPAAAAALPRPTRATAVRFALEELATRVPGN
+SVEVRVPPFGVAQCLPGPRHTRGTPPNVVEMDAVTWLSLATGLTTWEDATAAGGVRASGV
+RADLGAHLPLVRP
+>NAFOICDF_00956
+MTTGSVPKRRVPVVEGHAALTAWARAHAEDPAAAAALPRSTRATAVRFALEELATRAPGN
+SVEVRVPPFGVAQCIPGPRHTRGTPPNVVETDPVTWLSLATGLTRWNDAVASGAVRASGV
+RADLAGHLPLVRP
+>MHAAABBN_01550
+MTTGSVPRRRVPVVEGHAALLAWARAHEEDPAAAAALPRPTRAMAVRFALEELATRVPGN
+SVEVRVPPFGVAQCLPGPRHTRGTPPNVVEMDAVTWLSLATGLTSWDEATAAGGVRASGV
+RADLGAHLPLVRP
+>LFPAFLNI_01774
+MTTGSVPRRRVPVVEGHAALLAWARAHEEDPAAAAALPRPTRAMAVRFALEELATRVPGN
+SVEVRVPPFGVAQCLPGPRHTRGTPPNVVEMDAVTWLSLATGLTTWEDATAAGGVRASGV
+RADLGAHLPLVRP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000670.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000670.fa
new file mode 100644
index 0000000000000000000000000000000000000000..050f11f3599649ac2b57528a2af9f1c9f81f6229
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000670.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_01018
+MPTTRPSADTAGAPAETGAAAVLAGLRVALHVAFAVLLAVGLGRALADLSRTGAPAPAVL
+ALTGCTALLAGVYLAGTLVERRRWGRGEDVGRGPALLWLALVLALWGLLVAQHRDFAWVA
+FPLFFVALHVVARTARTAMARRIAGPVLVAAMAAVVVAGMAAGVDEGVRPAAVIGPLVGA
+AVAVVLSGAYRALHQESERQRDVAEQLRAAQAELARTQHRAGVGEERERLAREIHDTLTQ
+GLASIVLVSRAAQDALDAQDPALARTRMETVRTTAAENLDESRRFVRDLRATGGASLVAA
+VERAVAGFAERQAAAGTPVAADVEVVGTPVPLAEAVEAALLRAVQASLANVAAHARATRA
+RVTLAWMPGELAVDVADDGVGFRPEAVVTGDAGTQGTGAGTQGARAGRASRPGAGTGVGL
+ASVRERLAGVGGHASVESAPGEGTVVALRVPLPAAAGRAEEDEGRERG
+>MOLHKGIG_01850
+MSVAPRAAVPPAPTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPEASSGPFPAT
+TLVLLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVAHHGDFAWVA
+FPLFFVVLHVVDRVARQAWVRHVVGPALVVAMAVVVVAGMAAGAGGVRVPAVIGPLVGAA
+VAVVLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLTQG
+LASIVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGTGAPSLIEAL
+ERAVAGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLANVGAHAGARRAR
+VTLGYLGDELTVDVADDGAGFDPAVVAARPRAGAAGADPGAGTGVGLASVRERLAAVGGE
+ATVESAPGEGTVVALRVPLVAAGAGRSADPEQTESEETA
+>NAFOICDF_00960
+MRTSDPADGPRGANGTAALLSGLRVAVHVGFAVLLALALVRALAGPDAGARLTGRPALAL
+VGLTVVLAGVYLTGTVAERRLHAAGRAPGRTAAGTWLAVLLGVWALAVLRHPDMMWVAFP
+LFFVALHAVHVILGRPRLALACVAAMTVVVVVASLERGTAPGAVLGPAVGAAVAVVVFHA
+CRLLVVESERQRSVAEQLRATRAELAASERHAGVLAERERLAREIHDTLTQGLASIVLVS
+RAAQDAVRAGDAALADERLETVRTTAAENLAESRAFVRGLRAPVDGVQGGADRAGSALEA
+ALGAAVRGFRARRQALGRPVEAELAVVGEPVAVGEAVETVLVRAAQSSLANVDQHARTDR
+CRVTLTWMDGEVALDVADDGVGFDPEAARARASRAAVSDPAAPRPAEEGTGVGLAGLAER
+VAGVGGRVDVESAPGQGCVVAVRIPVPRQHERRGA
+>MHAAABBN_01546
+MSVAPRAAVPPAPTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPDASGPFPATT
+LVLLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVGHHGDFAWVAF
+PLFFVVLHVVDRVARQAWVRHVVGPALVVAMAAVVVAGMAAGAGGVRVPAVIGPLVGAAV
+AVVLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLTQGL
+ASIVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGTGAPSLVEALE
+RAVTGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLANVGAHAGARRARV
+TLGYLGDELTVDVADDGAGFDPAVVVARARAGAAGADPGAGTGVGLASVRERLAAVGGEA
+TVESAPGEGTVVALRVPLAAAGAGRSADPEQTESEETA
+>LFPAFLNI_01770
+MSVAPRAAAPTETGTTAVLAGLRVALHVTFAALLTVGLARALADRSPEASSGPFPVTTLV
+LLTAALAGVYLAGTVLERRRWARGDDVGRGPAVAWLALVLLLWGLLVAHHGDFAWVAFPL
+FFVVLHVVDRVARQAWVRHVVGPALVVAMAVVVVAGMAAGAGGVRVPAVIGPLVGAAVAV
+VLSGAYRALHAESERQRAVAEQLRAAQAELARTEHRAGVSAERERLAREIHDTLTQGLAS
+IVLVSRAAQDALDAADPALARQRMETVRATAAENLAESRRFVRDLRGTGAPSLIEALERA
+VTGFADRQAAAGTPVAADVEVVGEPVAVAEAVETAVLRAVQASLANVGAHAGAHRARVTL
+GYLGDELTVDVADDGAGFDPAVVAARPRAGAAGADPGAGTGVGLASVRERLAAVGGEATV
+ESAPGEGTVVALRVPLVAAGAGRSADPEQTESEETA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000679.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000679.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f208a0be7ef6db09211dfa70e175164f8debdcd6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000679.fa
@@ -0,0 +1,31 @@
+>ACLBLIBL_01030
+MVLVRDGEDGPEVFLRHRPGRTPLGRVGLPGGALSEADADACAWFGPDPAHWARVLGTTD
+RRCARQQVVAAVRELHDEAGVLLAGRTDADVVLDARGETWGGGGSSLEEGAESLPRMLAA
+RGLGLRTDLLRPVARWHSAPHAHRRFDTAVFAAAVPPLQRPLERPETAPALQAWVSARRA
+VAGPVPLPGPAGEEGVAPLDQVATPLTQVLVRRVAAHRTAAAFLLSLTQGAGHGPVPEYR
+LVTEAGDDGAPRMRVERVTRD
+>MOLHKGIG_01838
+MSADPAGLLLPVPGQEEDLTRQWLDRRFRQVRPARPGSSVVLVRDGDDGPEVFLRHRAGR
+TPLGRVGLPGGALIESDADSCPWYGPEPSQWARTFGTTDRRRARQHVVAAVRELHDEAGV
+LLAGRSDTDVVSTARIETWGGGRSSLEEGSESLPHLLAARGLGVRADLLRPVMRWRSAPH
+VHRRFDTAVFATMTPPLQSAPASEEPGPELQAWVSARRALAGPLRLPGPAGAEGTAPFDQ
+VATPLTQVIVRRVAAHRTAAAFLLSVTPCARRGPVPEYHLVTEAGDDGTPRMRVKRATRD
+>NAFOICDF_00971
+MSAEPDAPRVRVPGHEEELTRQWLAQRHRQVRPARPASAVVLVRDGADGVEVLLRHRSGR
+TPLGRIGLPGGSLVDSDADPCTWYGPAPDEWARALGLADRRRVRQHVVAAVRELFEESGV
+LLAGPADMDLVQDARGETWGASRSSLEEGDESLPRLLGDRGLGLRTDLLRGVGRWLSAPH
+SPRRFDTVVFAAALPPQQELVHRPEGPVLQGWFSARRLLSEPAALPGPDGWLGESGVVAL
+EEVSTPMTQLVLRRVAEHRTAAGFLLSPAGCRGPVPVVKLRTEAEHDDLATGTLYTVAER
+VDPVG
+>MHAAABBN_01535
+MSADPAGLLLPVPEQEEDLTRQWLDRRFRQVRPARPGSAVVLVRDGDDGPEVFLRHRAGR
+TPLGRVGLPGGALIESDADLCPWYGPEPSQWAHTFGTTDRRRARQHVVAAVRQLHDEAGV
+LLAGRSDTDVVSTARVETWGGGRSSLEEGSESLPHLLASRGLGLRADLLRPVMRWHSAPH
+VHRRFDTAVFATTTPPVQSAPASEEPGPELQAWVPACRALAGPLRLPGPAGAEGTAPFDQ
+VATPLTQVIVRRVAAHRTAAAFLLSVTPCARRGPVPEYHLVTEAGDDGTPRMRVERATRD
+>LFPAFLNI_01759
+MSADPAGLLLPVPEQEEDLTRQWLDRRFRQVRPARPGSAVVLVRDGDDGPEVFLRHRAGR
+TPLGRVGLPGGALIESDADLCPWYGPEPSQWAHTFGTTDRRRARQHVVAAVRQLHDEAGV
+LLAGRSDTDVVSTARVETWGGGRSSLEEGSESLPHLLASRGLGLRADLLRPVMRWHSAPH
+VHRRFDTAVFATTTPPVQSAPASEEPGPELQAWVPACRALAGPLRLPGPAGAEGTAPFDQ
+VATPLTQVIVRRVAAHRTAAAFLLSVTPCARRGPVPEYHLVTEAGDDGTPRMRVERATRD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000680.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000680.fa
new file mode 100644
index 0000000000000000000000000000000000000000..967aab0842ee73956719df8d54dbb2926c1de6b8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000680.fa
@@ -0,0 +1,26 @@
+>ACLBLIBL_01031
+MDLEVLRKAPLFTNLDDEVFAILTSELTEVELSRGASAFHEGDQGDQLYVIMSGKIKLGR
+TASDGRENLVAVLGPGEIFGEMALFNPAPRSATATAVSATRLAGLRHENLRRAIGSSPDV
+SVQLLQALAQRLSKTNESLADLVFSDVPGRVAKALLDLADRFGRPAADGLLVAHDLTQEE
+LAQLVGASRETVNKALAEFVQRGWIRLENRAVVILDLQRLRQRSR
+>MOLHKGIG_01837
+MDLEVLRKAPLFTNLDDEVFAILTSELTEVELSRGASAFHEGDQGDQLYVIMSGKIKLGR
+TASDGRENLVAVLGPGEIFGEMALFNPAPRNATATAVSATRLAGLRHENLRRAIASSPDV
+SVQLLQALAQRLSKTNESLADLVFSDVPGRVAKALLDLADRFGRPAADGLLVAHDLTQEE
+LAQLVGASRETVNKALAEFVQRGWIRLENRAVVILDLQRLRQRSR
+>NAFOICDF_00972
+MGHNGTDIPGAPRPRLAVSQKGRARMDLEVLRKAPLFTNLDDEVFSILTSELTEVELSRG
+ASAFHEGDQGDQLYVIMSGKIKLGRTASDGRENLVAVLGPGEIFGEMALFNPAPRSATAT
+AVSAARLAGLRHENLRRAIASSPDVSLQLLQALAQRLSKTNESLADLVFSDVPGRVAKAL
+LDLADRFGRPAADGLLVAHDLTQEELAQLVGASRETVNKALAEFVQRGWIRLENRAVVIL
+DLQRLRQRSR
+>MHAAABBN_01534
+MDLEVLRKAPLFTNLDDEVFAILTSELTEVELSRGASAFHEGDQGDQLYVIMSGKIKLGR
+TASDGRENLVAVLGPGEIFGEMALFNPAPRNATATAVSATRLAGLRHENLRRAIASSPDV
+SVQLLQALAQRLSKTNESLADLVFSDVPGRVAKALLDLADRFGRPAADGLLVAHDLTQEE
+LAQLVGASRETVNKALAEFVQRGWIRLENRAVVILDLQRLRQRSR
+>LFPAFLNI_01758
+MDLEVLRKAPLFTNLDDEVFAILTSELTEVELSRGASAFHEGDQGDQLYVIMSGKIKLGR
+TASDGRENLVAVLGPGEIFGEMALFNPAPRNATATAVSATRLAGLRHENLRRAIASSPDV
+SVQLLQALAQRLSKTNESLADLVFSDVPGRVAKALLDLADRFGRPAADGLLVAHDLTQEE
+LAQLVGASRETVNKALAEFVQRGWIRLENRAVVILDLQRLRQRSR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000681.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000681.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c43ab6552f7a99de71c91cabba4bc978b23040dd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000681.fa
@@ -0,0 +1,54 @@
+>ACLBLIBL_01033
+MSSTVSAPAAAPTRTREEFAGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI
+ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTESVGWWQVLICVVIAVYYAAIIGWA
+IMYTWFSVDQRWGADPETFMMGEFLQVSETPNPTFDVVSGVFWPMLAVWVITLLIMGFGV
+RRGVAMASMIGIPLLVVMFLVLVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI
+FFSLSVGFGIMITYASYLKKRTNLTSSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS
+VADVAGSGIGLAFIAFPTLISQAPVGALIGVLFFGSLVLAGFTSLISILEVVISAVKDKL
+GWGRWTATIIVVGLAGVVSMALFSTTSGLHMLDTMDAFANNFGIVGAALVSVLLVTGVLG
+SARRVTAHLNAVSSFKLGRGYVLLIGVLMPIVLAYIWLSWIMKVISEGYGGYPGDFLGVY
+GWGVAIGSVVLAVVLSLIPWSRKSNLYAEEMETEIHGDLIPHNAVPEGTTPTGAIPLVPA
+DHTRKEL
+>MOLHKGIG_01835
+MSSTVSAPATAPKRTREEFAGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI
+ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTETVGWWQVLICVVIGIYYAAIIGWA
+IMYTWFSVDQRWGDDPETFLMGDYLQVADDPSPSFDVVSGVFWPMLAVWVITLLIMGFGV
+RRGVALASMVGIPLLIVMFLVLVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI
+FFSLSVGFGIMITYASYLNRRTNLTGSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS
+VSEVAGSGIGLAFIAFPTLISQAPLGALIGVLFFGSLVVAGFTSLISILEVVISAVKDKL
+GWGRWTATIVVIGLSGVVSLALFSTTTGLQMLDTMDAFANNFGIVGAALLSVLLVTGALG
+SARRITAHLNAVSSFKVGRGYVLLIGVLMPIVLAYIWLSWIMKVIAEGYEGYPGDFLGVF
+GWGIALGSVALAVLLSLIPWSRKSNLYAEDLDSEIHGDLIPHNAVPEGTVPTGALPVVPV
+ATTRKEL
+>NAFOICDF_00974
+MSTSTGATAAPSRTREEFTGRWAFILAAIGSAVGLGNIWRFPYVAYEHGGGAFVIPYLVA
+LLTAGIPLLFLDYAIGHRFRGSAPMAFRRMSRWTEAIGWWQVLICAVIGVYYAAIIAWSI
+MYTWFSLDQRWGDDPEGFLFSTYLQQVKDPNPSFDIVPGVFWPMVAVWGVLLLIMGLGIR
+RGVALASMIGIPLLVVMFVVLVIISLTLPGAMQGLDALFTPNWAALKEPGVWIAAYGQIF
+FSLSVGFGIMITYASYLKKRTNLTASGLVVGFSNSGFEILAGIGVFSALGFMAQASGVQV
+SEVAGSGIGLAFIAFPTLITQAPAGALIGVLFFASLVIAGFTSLISILEVVVSAVKDKLG
+WGRWTAVLVVVGISAVISISLFSTTTGVAMLDTMDAFANNFGIVGAALVAVIAVMWIARR
+GGELVAHLNSVSSFRVGRVYRILVGVVMPVLLGWMWIEWIRENAATPYGGYPTDFLAVYG
+WGLAIGSVVLAVLLSLIPWSHKSSLHAEESVNEIDHTAPVASKES
+>MHAAABBN_01532
+MSSTVSAPATAPKRTREEFTGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI
+ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTETVGWWQVLICVVIGIYYAAIIGWA
+IMYTWFSVDQRWGEDPETFLMGDYLRVADDPSPSFDFVSGVFWPMLAVWVITLLIMGFGV
+RRGVALASMVGIPLLIVMFLILVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI
+FFSLSVGFGIMITYASYLNRRTNLTGSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS
+VSEVAGSGIGLAFIAFPTLISQAPLGALIGVLFFGSLVVAGFTSLISILEVVISAVKDKL
+GWGRWTATIVVIGLSGVVSLALFSTTTGLQMLDTMDAFANNFGIVGAALLSVLLVTGALG
+SARRITAHLNAVSSFKVGRGYVLLIGVLMPIVLAYIWLSWIMKVIAEGYEGYPGDFLGVF
+GWGIALGSVALAVLLSLIPWSRKSNLYAEDLDSEIHGDLIPHNAVPEGTVPTGALPVVPT
+AATRKEL
+>LFPAFLNI_01756
+MSSTVSAPATAPKRTREEFTGRWAFILAAIGSAVGLGNIWRFPYVAYENGGGAFVIPYLI
+ALLTAGIPLLFFDYAIGHRFRGSAPLAFRRLSRWTETVGWWQVLICVVIGIYYAAIIGWA
+IMYTWFSVDQRWGEDPETFLMGDYLRVADDPSPSFDFVSGVFWPMLAVWVITLLIMGFGV
+RRGVALASMVGIPLLIVMFLILVGIALTLPGAAQGLDALFTPNWAALADPGVWIAAYGQI
+FFSLSVGFGIMITYASYLNRRTNLTGSGLVVGFSNSGFEILAGIGVFSALGFMAQASGVS
+VSEVAGSGIGLAFIAFPTLISQAPLGALIGVLFFGSLVVAGFTSLISILEVVISAVKDKL
+GWGRWTATIVVIGLSGVVSLALFSTTTGLQMLDTMDAFANNFGIVGAALLSVLLVTGALG
+SARRITAHLNAVSSFKVGRGYVLLIGVLMPIVLAYIWLSWIMKVIAEGYEGYPGDFLGVF
+GWGIALGSVALAVLLSLIPWSRKSNLYAEDLDSEIHGDLIPHNAVPEGTVPTGALPVVPA
+ATTRKEL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000685.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000685.fa
new file mode 100644
index 0000000000000000000000000000000000000000..635d401f91080dbe8ea601eb5f15d36b4561c1ee
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000685.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01037
+MDAEQADTPTGESRLALVRRARRIDRELAATYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAATPALFARFPDAAAMAGASEAELQGLVRSTGFYRNKASAILRLSQELVERHGGEVP
+GRLEDLVALPGVGRKTAFVVLGNAFGRPGITVDTHFGRLARRLGFTQDTDPVKVEHAVAE
+LFPRRDWTMLSHRLIFHGRRICHARRPACGACPIARWCPSYGEGETDPEKARALLSYELK
+PGREELLALMRAGLSRRELRARGHGLDA
+>MOLHKGIG_01831
+METEPTDTPTGETRLALVRRARRIDRILAETYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAATPALFARFPDAHAMAAATEPELQELVRSTGFYRNKASAILRLSQELVARHDGEVP
+ARLEDLVALPGVGRKTEFVVLGNAFGQPGITVDTHVGRLARRLGFTDETDPVKVEHAVGA
+LFPRRDWTMLSHRLIFHGRRVCHARRPACGACPIARWCPSYGEGETDPERARALLAYELK
+PGREELLELLRAGRTRRELRALGHGLEA
+>NAFOICDF_00977
+MAPADTTTPTGETPLALTRRARRIDRALAEAYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAVTPALFARFPDAVAMAGADEVELQELVRPTGFYKNKASAVLRLSRELVERFDGEVP
+DRLEDLVTLPGVGRKTAFVVLGNAFGRPGITVDTHFGRLARRLGFTEETDPVKVEHAVAA
+LFPPRDWTMLSHHLVFHGRRVCHARKPACGACPIARWCPSYGAGETEPEAARALLSYELK
+PGREELLARMRAGATRRQLRDEGWTLEA
+>MHAAABBN_01528
+MEPEPTDTPTGETRLALVRRARRIDRILAETYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAATPALFARFPDAHAMAAATEPELQELVRSTGFYRNKASAILRLSQELVARHDGEVP
+ARLEDLVALPGVGRKTAFVVLGNAFGQPGITVDTHVGRLARRLGFTDETDPVKVEHAVGA
+LFPRRDWTMLSHRLIFHGRRVCHARRPACGACPIARWCPSYGEGETDPERARALLAYELK
+PGREELLELLRAGRTRRELRALGHGLEA
+>LFPAFLNI_01752
+METESTGTPTGETRPALVRRARRINRILAETYPYAVAELDFETPFELLVATVLSAQTTDV
+RVNAATPALFARFPDAHAMAAATEPELQELVRSTGFYRNKASAILRLSQELVARHDGEVP
+ARLEDLVALPGVGRKTAFVVLGNAFGQPGITVDTHVGRLARRLGFTDETDPVKVEHAVGA
+LFPRRDWTMLSHRLIFHGRRVCHARRPACGACPIARWCPSYGAGETDPERARALLAYELK
+PGREELLELLRAGRTRRELRALGHGLEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000686.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000686.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0d63b739a274132c789e62aaa8cd0e33f5ee3fb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000686.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01040
+MAAVRDRLAALVERHGVPADQAPRDALTEIPASAVSTWGFDWPRAQRARPSAVLILFGSL
+DDVPAHHADDRVHPDVDVLLTQRAATLRTHAGQIAFPGGRVDPEDADVVATALREAEEET
+DLDPDGVEVLGVLPPVPVVVSGHVVHPVIGWWRDPSRVAVVDQAEAAAVFRMPVGDLVDP
+ANRCRVARPGGRRGETPGFLVGERLVWGFTAALLDRILTLLDWDTPWDSGRVIDAHTHAP
+LRG
+>MOLHKGIG_01829
+MPETPASPRPTSRDAVGTSDASLAGARDQLADLVARWGAAPADAPGHHDPVSLTTVPPEA
+VPMWGFDWPRSGDPRPSAVLILFGALDDVPARHDAERVHPHVDVLLTQRAATLRQHAGQI
+AFPGGRVDPEDGDVVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGHVVHPVLGWWRD
+PSRVAVVDQAEAAAVFRMPVADLVDPANRCRVARPGGRRGETPGFLVGERLVWGFTAALL
+DRVLGLLGWDVPWDDSRVRDARTHEILRD
+>NAFOICDF_00979
+MSIPPLPPSSPSSARADLQRIVAEHGVAPVAGDDEAGLTTIPASSVRVWGFDWPQAARPR
+ASAVLILVGELDDVPAAHDGRACGVSPAVDVLLTQRAAGLRTHAGQVAFPGGGVEAQDAD
+VVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGYVVHPVIGWWRDPSRVAVVDHNEAT
+AVFRVPVADLAAPANRVRVRRPGGRRGETPGFLAGDRLVWGFTAALLSRVLELAGWDEPW
+AGAPLIDAGSRAVLEG
+>MHAAABBN_01526
+MPETPASPHPTSRDAAGTSDASLAGAREQLADLVARWGAPPAEAPGHHDPASLTTVPPEA
+VPMWGFDWPRSGDPRPSAVLILFGALDDVPARHDAGRVHPHVDVLLTQRAATLRQHAGQI
+AFPGGRVDPEDGDVVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGHVVHPVLGWWRD
+PSRVAVVDQAEAAAVFRMPVADLVDPANRCRVARPGGRRGETPGFLVGERLVWGFTAALL
+DRVLALLGWDVPWDDSRVRDARTHRILRD
+>LFPAFLNI_01750
+MPETPASPRPTSRDAAGTSEASLTGARDQLADLVARWGTAPADAPGHHDPASLTTIPPEA
+VPMWGFEWPRSGDPRPSAVLILFGALDDVPARHDAERVHPHVDVLLTQRAATLRQHAGQI
+AFPGGRVDPEDADVVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGHVVHPVLGWWRD
+PSRVAVVDQAEAAAVFRMPVADLVDPANRCRVARPGGRRGETPGFLVGERLVWGFTAALL
+DRVLALLGWDVPWDDSRVRDARTHEILRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000700.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000700.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b7f8e612b9c525c2f3f9e582e7fa9191dd1ff15e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000700.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01059
+MADPQRTDPNAPVLVVGLGRFGAATAEELVAQGREVLAIERDPVLVQRFAPSLTHVVEAD
+ATDPEALRQLGAQDFSTAVVGVGTSIEASVLITANLVDLEIQHIWVKAISEAHGTILKRI
+GANHVIFPEHDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPAECVGFTLGESNVRSKYG
+VTVVGVKTPGEDFTYAQPDTRVGARDTLIVSGHTDLIDRFAARP
+>MOLHKGIG_01815
+MADTPQRTDPNAPVLVVGLGRFGAATAEELVAQGREVLAVERDPVLVQRYAPSLTHVVEA
+DATDSEALRQLGAQDFSTAVVGVGTSIEASVLITVNLVDLEIPHIWVKAISEAHGTILKR
+IGANHVIFPEHDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPAECVGFTLAESHVRSKY
+GVTVVGVKTPGEDFTYAQPDTRVGPRDTLIVSGHTDLIDRFAARP
+>NAFOICDF_00994
+MADQPRTDPNAPVLVIGLGRFGAATAEELVTQGREVLAIERDPVLAQRFAPTLTHVVEAD
+ATDAEALRQLGAQDFDVAVVGVGTSIEASVLITANLVDLEIPHIWVKAISDAHGTILKRI
+GAQHIIFPEKDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPTETVGFTLEESNVRQKYG
+VTIVGVKTPGEDFTYAQPHTRVGPRDTLIVSGHTDLIDRFAARP
+>MHAAABBN_01512
+MADTPQRTDPNAPVLLVGLGRFGAATAEELVAQGREVLAVERDPVLVQRYAPSLTHVVEA
+DATDSEALRQLGAQDFSTAVVGVGTSIEASVLITVNLVDLEIPHIWVKAISEAHGTILKR
+IGANHVIFPEHDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPAECVGFTLAESKVRSKY
+GVTVVGVKTPGEDFTYAQPDTRVGPRDTLIVSGHTDLIDRFAARP
+>LFPAFLNI_01736
+MADTPQRTDPNAPVLVVGLGRFGAATAEELVAQGREVLAVERDPVLVQRYAPSLTHVVEA
+DATDPEALRQLGAQDFSTAVVGVGTSIEASVLITVNLVDLEIPHIWVKAISEAHGTILKR
+IGANHVIFPEHDAGVRAAHLVNGRMLDFIEFDDDFAIVKMYPPAECVGFTLAESHVRSKY
+GVTVVGVKTPGEDFTYAQPDTRVGPRDTLIVSGHTDLIDRFAARP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000703.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000703.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d9b77ff9ab5073ea8c3eb8f2fdef2419c739c269
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000703.fa
@@ -0,0 +1,10 @@
+>ACLBLIBL_01062
+MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK
+>MOLHKGIG_01812
+MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK
+>NAFOICDF_00997
+MGSVIKKRRKRMAKKKHRKLLRKTRHQRRNKK
+>MHAAABBN_01509
+MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK
+>LFPAFLNI_01733
+MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000705.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000705.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7dde9ead1b6cde3fd3f02571fdd324a246e76618
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000705.fa
@@ -0,0 +1,29 @@
+>ACLBLIBL_01064
+MSGTSPTDPQRGQNPYGQEAPGPSPYGENPYGAHPYGQAPYGQGGPAQGQPGQGHPNPGH
+PAPSYADQGYPAQGGWPGQQAPGPLTAPRRPGAITASFWLILAGGLVLLASTLLAAFAMT
+LPESRAMLEQQMRETYEQMGLPADQLAQMEQMTDQLLPVMSVVAAAFGVVAFLVYLLIAL
+KIRKGSRAARTVGTVLAALSVLMIVTNLMMGAFNPFDLLWVGLGVAGIVMAFRPEASEYM
+RLKAWERAGTR
+>MOLHKGIG_01810
+MSGTSPTDPHGSQNPYGTDPYGAAPQGPTPGSPDPAGASPYGQNPYGAPPAAPYGAPGQA
+GMPQAPSPHGPAGWQSPGPVELPPRPRSLTAAFWLIVSGGLLLLATTLLAAFAITQPEGQ
+VAIQQELDRSVEQMNLPADQAEQMRTMMDGMLPALATTAAVFGVLAFLVYLWVAFAIRGG
+SRAARIVGTVLASLSVLVLVSNAVMGAFSPLDLVWVGLGVAGIVLAYRPDATEYMRLKTW
+QRFARR
+>NAFOICDF_00999
+MSGTENSNPYGRPAGQSGPQWPDAAAQAPYGQAPDASAQAPYGAPPQGWGAPQQWGGQPG
+WPAAAPVPARRPGPINAAFWLIVSAGVVFLASTVLSALVATSDAGRRELEAAMTKVWGDY
+GMTPEQIREYQDMLPPMMPVMAGVMVAVGVLALLVYLLIASKIRGGSRAARTVGTVLAVL
+SVLMVLAPLASGQFSPLDLLWCLLGVAGIATAYRKEATEFMRLRAWERAARR
+>MHAAABBN_01507
+MSGTSPTDPHGSQNPYGTDPYGAAPQGPTPGSPGPAGASPYGQNPYGAPPAAPYGAPGQA
+GMPQAPSPHGPAGWQSPGPVELPPRPRSLTAAFWLIVSGGLLLLATTLLAAFALTQPEGQ
+AAIQQELDRSVEQMDLPADQAEQMRAMMDGMLPALATTAAVFGVVAFLVYLWVAFAIRGG
+SRAARIVGTVLAALSVLVLVSNAVMGAFSPLDLVWVGLGVAGIVLAYRPDATEYMRLKAW
+QRFARR
+>LFPAFLNI_01731
+MSGTSPTDPHGSQNPYGADPYGAVPQGSTPGSPDPAGASPYGQNPYGAPPATPYGAPGQA
+GMPQAPSPHGPAGWQSPGPVELPPRPRSLTAAFWLIVSGGLLLLATTLLAAFALTQPEGQ
+AAIQQELDRSVEQMDLPADQAEQMRAMMDGMLPALATTAAVFGVLAFLVYLWVAFAIRGG
+SRAARIVGTVLAALSVLVLVSNAVMGAFSPLDLVWVGLGVAGIVLAYRPDATEYMRLKAW
+QRFARR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000706.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000706.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4034c8f59ea878bd9f1cce2274fd72686915bcff
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000706.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01067
+MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG
+RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL
+QQERRVHFKPAAGLAGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY
+CLGLGLPFVLMALGMERGMRALGFFRRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ
+LWFANEWEMPL
+>MOLHKGIG_01807
+MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG
+RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL
+QQERRVHFKPAAGLVGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY
+CLGLGLPFVLMALGMERGMRAVGFFTRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ
+LWFANEWEMPL
+>NAFOICDF_01002
+MQDNRFAEIALDGSLLAAAPVAFLAGLISFLSPCVLPLVPGYLGYVSGLGGAALDGARRG
+RVALGAALFVLGFTVVFMVMNILFAQVAFRILRDLSWVMQLLGVLVILMGVVFMGGLRWF
+QTERKVHVKPAAGLTGAPLLGMTFGLGWAPCIGPTLAAVFALSYTQDSSSVARAALLAFV
+YCLGLGLPFVLISFGVERGMRALGFFRRHRRGVMVFGGAVLILLGAVMVTGLWTQWMVQL
+QTWFQNEWVMPL
+>MHAAABBN_01504
+MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG
+RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL
+QQERRVHFKPAAGLVGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY
+CLGLGLPFVLMALGMERGMRALGFFLRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ
+LWFANEWEMPL
+>LFPAFLNI_01728
+MQSNPFAEIALDGSLLLAAPIAVLAGLISFLSPCVLPLVPGYLGYVTGLGGDVLTSRRRG
+RLVLGSVLFVLGFAVVFVGITVVFTQAMVWLRRDGAWVTPVLGVLVMLMGLVFLGGGGRL
+QQERRVHFKPAAGLVGAPLLGMTFGLGWAPCIGPTMAAVLAMSTASSGSVGRGALLAFLY
+CLGLGLPFVLMALGMERGMRALGFFRRHRVLIMRLGGALLIALGLLMVTGVWTAWTTQLQ
+LWFANEWEMPL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000709.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000709.fa
new file mode 100644
index 0000000000000000000000000000000000000000..510d4730a376ce27714242c430178509af32fa63
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000709.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01071
+MAATLSQWVAAARLRTLPMAIAPVIVGSAAAAELGSFHLGAALLALVVSLALQIGVNYAN
+DYSDGIRGTDDERVGPFRLTVSGLVPAAQVKQAAFAFFGLAGLAGLGLILLSGHWWFLLV
+GVACVLAAWFYTGGKRPYGYLGLGEVFVFVFFGLVAVLGTTYTQADAVSRLAWAGAIGCG
+LISTALLMANNIRDIPTDREVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPGL
+LLVPIGGLLAIRPIRTVLRADDRRTLIPVLRATGVIGIVYALTFTLGVLL
+>MOLHKGIG_01802
+MAATLSQWVAAARPRTLPMAIAPVIVGSAAAAELGSFHLGAALLALVVSLALQIGVNYAN
+DYSDGIRGTDDERVGPFRLTVSGLVPAARVKQAAFAFFGLAGLAGLGLILLSGHWWFLLV
+GVACVLAAWFYTGGKRPYGYLGLGEVFVFVFFGLVAVLGTTYTQADAVSGLAWAGAIGCG
+LISTALLMANNIRDIPTDREVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPGL
+LLVPIGGLLAIRPIRTVLRADDRRALIPVLRATGVIGIVYAITFTLGALL
+>NAFOICDF_01007
+MAATLSQWVAAARLRTLPMAVAPVIVGSAAAHALDQFRPGRALLALVVSLALQIGVNYAN
+DYSDGIRGTDDARVGPFRLTVSGLVPAKTVKHAAFACFGVAAVAGLALVALSGTWWLLIV
+GVASIVAAWYYTGGKKPYGYMGLGEVFVFVFFGLVAVLGTTYTQALAVNGLAWAGAVGCG
+LISTALLMANNIRDIPTDREVGKMTLAARIGDGPARASYVAMLAVAVVLPLLFTGAHPWL
+WLVLAAGAVAVKPCLTVLHAHERAALIPVLKATGIVGVVYAAAFALGVAL
+>MHAAABBN_01499
+MAATLSQWVAAARLRTLPMAIAPVIVGSAAAAELGRFHLGAALLALVVSLALQVGVNYAN
+DYSDGIRGTDDERVGPFRLTVSGLVPAAQVKQAAFASFGLAGLAGLGLILLSGHWWFLLV
+GVACVVAAWYYTGGKKPYGYLGLGEVFVFVFFGLVAVLGTTYTQAGQVSGLAWAGAIGCG
+LISTALLMANNIRDIPTDRAVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPWL
+LLVPLGGLLAIRPVRTVLRAQDRRALIPVLRATGVIGIVYALTFTLGVLL
+>LFPAFLNI_01723
+MAATLSQWVAAARPRTLPMAIAPVIVGSAAAAELGSFHLGAALLALVVSLALQIGVNYAN
+DYSDGIRGTDDERVGPFRLTVSGLVPAAQVKQAAFAFFGLAGLAGLGLILLSGHWWFLLV
+GVACVLAAWFYTGGKRPYGYLGLGEVFVFVFFGLVAVLGTTYTQADAVSGLAWAGAIGCG
+LISTALLMVNNIRDIPTDREVGKMTLAARLGDGPARASYGVMLAVALLLPLFWVAVHPGL
+LLVPIGGLLAIRPIRTVLRADDRRALIPVLRATGVIGLVYAITFTLGVLL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000713.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000713.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b63ec016910adadbecda5e98cd90d0a696baef9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000713.fa
@@ -0,0 +1,70 @@
+>ACLBLIBL_01078
+MPQTTSHAPVPPSVSAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD
+QAPLRAAIFGEIKARTVETDRSVPSRRDGWWYFARTKEGAEYPVHCRVPAADTGDLEADW
+TPPVVTPDAPLEGEQVILDGNAEAEGHPFFALGGLHISPDSTRVAYAVDHTGDERFTLRV
+REIATGEDLPDVVENIAHGVRFDRSGARVLYTVWDDSWRPYQVKAHVLGTDPAQDQLLYE
+ESDPGMWTGFTGTADRTQLLIGVGNSEVSETHVVDLPESPDAPLPAPRLLIPRAWGMLAD
+VEPVTGADGVRRLLVVHDRTVARQDAADAGADAPAPNGMLSLVAEADVADRGAWRTVVPH
+REDVKVDGVMVTLTHAALAVRRETTPRVVVAPLDSVLAGEAADWREPAFEEELYACHLAS
+TAAESPFLRLAYTSWISPARVLDVSAATGEVHLRRETEVPGYDPSLYVAERVWAPASEPS
+SVTGEPVRIPVTVIRRKDVAADGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVYAVA
+HVRGGGELGRRWYEDGKKLAKRHSFTDFVDATRHLVDLGWADPARVACTGGSAGGLLMGA
+VLNLAPELYRACLAVVPFVDALTSILDPELPLSALEWEEWGNPIEDPEVYAAMRDYTPYE
+NVRAVDYPTIAAVTSLHDTRVLYVEPAKWVARLRRTVTSDQATPLAEGGAPVLLRTEMDG
+GHGGASGRYQGWEDTAWEYAFLLTALGATQRVD
+>MOLHKGIG_01798
+MPQTTSHAPVPPSASAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD
+QAPLREAIVGEIKARTVETDRSVPARRDGWWYFVRTREGAEYPIHCRVPARDTGDLEADW
+TPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPDATRVAYAVDHTGDERFTLRV
+REIATGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVRAHVLGTDPAEDVLLHE
+EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLAD
+VEPVTDADGVRRLLVVHDRALDDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVK
+VDGVMVTLTHAALAVRRETTPRVVVAELDAVLAGQAAHWREPAFDEELYACHLSATAAES
+PFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPSSVTGE
+DVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGG
+GELGRRWYEDGKKLAKRHSFTDFVDATRHLVGLGWADPARVACMGGSAGGLLMGAVLNLA
+PELYRACLAVVPFVDALTTILDPELPLSALEWEEWGNPIEDAAVYAAMRAYTPYENVRAV
+DYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQATPLAEGGAPILLRTEMDGGHGGA
+SGRYQGWEDTAWEYAFLLTALGATARIV
+>NAFOICDF_01013
+MYETSLPTPPRAAARPTARTVHGETFTDDFEWMRAKTEQEVLDHLQAENAYTEAATADQA
+DLRAAIYGEIKAHTVETDQSVPARRDGWWYFVRTVEGKDYAVHCRVPAQDTGDALADWTP
+PVVPADAALPGEQVILDGNAEAAGHPFFSLGGMHISPDGALAAYAVDLAGDERYTLRVRE
+IATGTDLPDVVRNIAPGVRFDRSGTRLIYTVWDETWRPYQVRVHTLGTDAAEDAVLYEES
+DPGMWTGFDASADRTQLLIGVGNSEVSETWAVDLPVDASPLPAPRVLVPRTARMLADVEP
+FDMDGRRRLLIVHDRLADGTTAPNGMLSIVDEADVADRDAWRPVVPHADDVRVDGVLVTR
+THVGLAVRRDTTPRVLIAPLEGLREGSAPAWTEPSFDEELYMCRLAGVNLDSPFLRLSYA
+SWTTPARVLDVVAATGEVRLRREVEVPGFDREDYVAERWWAPASEPSSLTGEQVRIPLTV
+IRRRDVAQDGTAPAVVYGYGSYEMSMDPVFGVARLSLLDRGVVYVVAHVRGGGELGRAWY
+EDGKKAAKRHSFTDFVDATRFVADSGWVDPARIACTGGSAGGLLMGAVLNLAPELYRACL
+AVVPFVDALTSILDPDLPLSALEWEEWGNPIEDPEVYATMKAYTPYENVRAVDYPAIAAV
+TSLNDTRVLYVEPAKWVAQLRRTVTSDQTTPIAAGGSPILLRTEMDGGHGGASGRYQGWE
+DTAWEYAFLLTALGATARVD
+>MHAAABBN_01495
+MPQTTSHAPVPPSASAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD
+QAPLREAIVGEIKARTVETDRSVPARRDGWWYFVRTREGAEYPIHCRVPARDTGDLEADW
+TPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPDATRVAYAVDHTGDERFTLRV
+REISTGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVKAHVLGTDPAEDVLLHE
+EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLAD
+VEPVTDADGVRRLLVVHDRALDDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVK
+VDGVMVTLTHAALAVRRETTPRVVVAELDAVLAGQAAHWREPAFEEELYACHLSATAAQS
+PFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPSSVTGE
+DVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGG
+GELGRRWYEDGKKLAKRHSFTDFVDATRHLVDLGWADPARVACMGGSAGGLLMGAVLNLA
+PELYRACLAVVPFVDALTTILDPELPLSALEWEEWGNPIEDAAVYEAMRAYTPYENVRAV
+DYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQATPLAEGGAPILLRTEMDGGHGGA
+SGRYQGWEDTAWEYAFLLTALGATARID
+>LFPAFLNI_01717
+MPQTTTHAPVPPSVAAEPVTRRHHGHTFQDDFEWLRGKAEPRVLEHLAAENAYTEAVTAD
+QAPLREAIVGEIKARTVETDRSVPARRDGWWYFVRTREGAEYPIHCRVPARETGDLEADW
+TPPVITPDAALPGEQVILDGNAEAEGHPFFALGGLHISPDATRVAYAVDHTGDERFTLRV
+REIATGEDLPDAVENVAHGVRFDRSGTRVFYTVWDDSWRPYQVKAHVLGTDPAEDVLLHE
+EADPGMWTGFEGVADRTQLLIGVGNSEVSETLVVDLPEDPAAPLPAPRVLIPRAWRMLAD
+VEPVTDADGVRRLLVVHDRALDDDGAPVAAPNGMLSVVAEADVADRGAWRTVVPHREDVK
+VDGVMVTLTHAALAVRRETTPRVVVTELDAVLAGQAAHWREPAFDEELYACHLSATAAES
+PFLRLAYTSWITPARVLDVSAATGEVHLRRETEVPGYDPADYVAERVWAPASEPSSVTGE
+DVRIPVTVIRRRDVKPDGTAPCVVYGYGSYEMSMDPVLGVARLSLLDRGVVFAVAHVRGG
+GELGRRWYEDGKKLAKRHSFTDFVDATRHLVDLGWADPARVACMGGSAGGLLMGAVLNLA
+PELYRACLAVVPFVDALTTILDPELPLSALEWEEWGNPIEDAAVYAAMRAYTPYENVRAV
+DYPAIAAVTSLNDTRVHYVEPAKWVAQLRRTVTSDQARPLADGGAPVLLRTEMDGGHGGA
+SGRYQGWEDTAWEYAFLLTALGATRRVV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000715.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000715.fa
new file mode 100644
index 0000000000000000000000000000000000000000..31c60c5b3f8cbff8d4bdd3c0e00ae2bb51ec52d4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000715.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01093
+MPTEALDRVDRAIVRALTQDGRMSVAALAERVHISRAHCYSRLNRLQDAGVITGFTVRVD
+PVKVGFGASAHVTLKLRQHNWRELRATLLAIPEVWHVSLVGGNVDVILLVRARDTADLRR
+VIFDELQTLPGVVDTQTYMVFDDHASGQTLPPEDPAA
+>MOLHKGIG_01785
+MAAEPLDRVDRAIVRELTQDGRMSVAALAERVHISRAHCYSRLNRLQDAGVITGFTVRVD
+PVKVGFGASAHVTMKLRQHDWRELRATLLAIPEVSHVSLVGGNMDVILLVRARDTADLRR
+VIFDELQTLPSVVDTQTYMVFDDQASGQTIPPDETAD
+>NAFOICDF_01016
+MSTSSPLDRVDRAIVRELSQDGRLSVAALAERVHVSRAHCYSRLNRLQNSGVITGFSARV
+DPVKTGFTASAHVMLKLRQHDWRELRAALLAIPEVWHVSLVGGNMDVVLLVRARDTADLR
+HVIFEKLQSLPAVVDTQTYMIFDDHASGQTMPPEEGADAPRTPTAFG
+>MHAAABBN_01492
+MAAEPLDRVDRAIVRELTQDGRMSVAALAERVHISRAHCYSRLNRLQDAGVITGFTVRVD
+PVKVGFGASAHVTMKLRQHDWRELRATLLAIPEVSHVSLVGGNMDVILLVRARDTADLRR
+VIFDELQTLPSVVDTQTYMVFDDQASGQTIPPDETAD
+>LFPAFLNI_01714
+MAAEPLDRVDRAIVRELTQDGRMSVAALAERVHISRAHCYSRLNRLQDAGVITGFTVRVD
+PVKVGFGASAHVTMKLRQHDWRELRATLLAIPEVSHVSLVGGNMDVILLVRARDPADLRR
+VIFDELQTLPSVVDTQTYMVFDDQASGQTIPPDETAD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000716.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000716.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a14638162346255f57fd808aab9ab448811f4ee
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000716.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01094
+MSDPTPAVSGSARTDQAEARPNAGAAFGISLEEYLLPATRRIQLIGEDGTLLSPEEQGAE
+PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLG
+KQDWLFPTYRDTVAVIARGVPPLEVMVSYQGTWHQGYDPNEHHVSVQSTPLTTQLLHAVG
+MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ
+SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVDLCRQGQGPFLVEADTYRMQAHTN
+TDDPTRYREDAEVQEWEARDPLRRMTAYLESTGALTEEVSAEIAQAAEDVAKDLRDAMNA
+EAELDPLELFDHVYSVQTPQLAAQRAQLTEELSRSENQEA
+>MOLHKGIG_01784
+MSDPTPAVPGAARTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQGTE
+PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLG
+EDDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHAVG
+MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ
+SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAHTN
+TDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQIARDAEDVAQQLRDAMNA
+ETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA
+>NAFOICDF_01017
+MTSTRPGPATPDTRTEAAAAFGITLEEYLLPAARRIQLISPEGELLPAEEQGTAPGHEYP
+LPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLGQDDWLF
+PTYRDTVAVIARGVAPLDVMVSFQGTWHQGYDPKEHRVSVQSTPLTTQLLHAVGMAKAAR
+LRGEDVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFLVQNNKFAISVPFAKQSAAPSL
+AHKAVGYGLAGERVDGNDLAALLAVLGRAVDLCREGKGPFLVEADTYRMQAHTNTDDPTR
+YREDSEVKEWEVRDPLRRMTAYLESTGALTAEVSTSIAKDAEDVAQQLRDAMNADVELDP
+LELFDHVYSVQTPQLAAQRAQLAEELSRSENKEA
+>MHAAABBN_01491
+MSDPTPAVPGAVRTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQGTE
+PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLG
+EHDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHAVG
+MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ
+SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAHTN
+TDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQITRDAEDVAQQLRDAMNA
+ETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA
+>LFPAFLNI_01713
+MSDPTPAVPGAVRTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQGTE
+PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVSLG
+EDDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHAVG
+MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ
+SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAHTN
+TDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQIARDAEDVAQQLRDAMNA
+ETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000723.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000723.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7cd6c2c53545e6e6e094778652b9d22712129ca8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000723.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01103
+MSGPRLRSHAPEGYVCPFCGLVAGDVSDPGNRCELADTVYQDEDLLVLIAVDGFGDHEGH
+AMVCPAGHYENLYELPPRVLQRIALMAREVALAMKRAWSPDGVSTRQHNEPAGNQHVWHY
+HLHVFPRFEGDLLYRQLRHPVSPEVRALKARELAAELDPAPTFLD
+>MOLHKGIG_01774
+MTAPAPVSHAPDDYVCPFCGLVASDVSDPGNRCELGDTVYQDEDLLVLIAVDGFGDHEGH
+AMVCPAEHYENLYDLPPRVLQRIALMAQQVALAMKRAWAPDGVSTRQHNEPAGNQHVWHY
+HLHVFPRFEGDMLYRQLRHPVAPEVRAGKARELAAALDPAPTRLD
+>NAFOICDF_01028
+MSAQPLSHAPEGYVCPFCGLVAGDVSDPGNRCELEDTVYQDEDVLVLIAVDGFGEHDGHA
+MVCPSGHYENLYDLPPRVLQRIALMAQQVALAMKRAWGPDGVSTRQHNEPAGNQHVWHYH
+LHVFPRYEDDLLYRQLRHPVAPEVRAARARELAAALDPAPTLLD
+>MHAAABBN_01481
+MTAPAPVSHAPDGYVCPFCGLVAGDVSDPGNRCELGDTVYQDEDLIVLIAVDGFGDHEGH
+AMVCPAEHYENLYDLPPRVLQRIALMAQQVALAMKRAWAPDGVSTRQHNEPAGNQHVWHY
+HLHVFPRFEGDMLYRQLRHPVAPEVRAGKARELAAALDPAPTRLD
+>LFPAFLNI_01703
+MTAPAPVSHAPDGYVCPFCGLVAGDVSDPGNRCELGDTVYQDEDLLVLIAVDGFGDHEGH
+AMVCPAEHYENLYDLPPRVLQRIALMAQQVALAMKRAWAPEGVSTRQHNEPAGNQHVWHY
+HLHVFPRFEGDMLYRQLRHPVAPEVRALKARELAAALDPVPTRLD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000726.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000726.fa
new file mode 100644
index 0000000000000000000000000000000000000000..db50ea4405532495d932ef7c93163f0a1dbd0a95
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000726.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_01107
+MARLLVDLTPLKVSPAYRRLWVGNTLSFVGTQLTLVAVSLEVFALTGSSFAVGLLGLAAL
+VPLVVAGLYGGAVADRHDRRTVALASSAVMWLTTVGIAAHAWAGIESVPLLYALVALHSG
+ASGINQPTRGAIIPALVGMKLVPAANALNMMTFSVAMMAGPVLGGVLVASVGYAWTYSID
+VVTFLAALYAVWRLPSLPPQRAEGEAAPTGRVGVRSVVEGLRFLGSRPNLRMTFLADIVA
+MATAFPRALLPAVGGVVLGGGEAAVGVLLAAMAAGAFLAGLFSGPFTRLHAQGWGVYVSI
+LVWGASVAAFGGVVWWAQGLPDGDPRLTGAFVAAALCLAVGGAADSISGVFRTTILQSAT
+PDHLRGRLQGVFVVVVAGGPRVGELLTGGASVAVGEGLTLLLGGLACVLGVSLLMRRQPE
+FLKYDARSPTP
+>MOLHKGIG_01770
+MARLLVDITPLRVSPAYRRLWLGNTLAYVGTQLTLVAVSLEVFALTGSSFAVGLLGLAAL
+VPLVVAGLYGGAIADRHDRRRVALTSSAVMWLTTVGIAAQAWAGFESVPVLYALVALHSG
+ASGINQPTRGAIIPALVGLPLVPAANALNMMTFSVALMVGPVLGGVLVAAVGYAWTYSID
+VVTFLAALYAVWRLPSLPPQQAEAAAASGTRGGLASVVEGLRFLGSRPNLRMTFLADIVA
+MTTAFPRALLPAIGAVVLGGGEAAVGVLLAAMAAGAFLAGLFSAPFTRLHAQGWGVYVSI
+LVWGGAVAAFGGVVWWAQSLPDGDPRLTLAFALAALCMAVGGAADSLSGVFRGSILQSAT
+PDHLRGRLQGVFVVVVAGGPRLGELITGGASVVLGEGPTLLAGGVLCMLGVSALMRWQPG
+FLRYDARNPTP
+>NAFOICDF_01033
+MPRLLVDLAPLEASPAYRRLWLGNALAFVGTQLTLVAVSLEVFALTGSSFAVGMLGLAAL
+IPLVVAGLYGGAVADRHDRRTVALASGAVMWAATALIAAHAWAGVESVGVLYGLVALHSA
+ASGINQPTRGAIIPALVGPALLPAANALNMLTFSTAMMAGPLLGGVLVASVGYAWTYTVD
+VVTFLAALWAVWRLPSLPPDRSAAPDDAGRGGLSSVLDGFRFLGTRRNVRMTFVADIVAM
+ATAFPRALLPAVGGTILGGGEAAVGVLLASMAAGTFLAGLFSGTFTRVHRQGRGVAVAIA
+AWGLSVAAFGAVVLWAAPLPDGDPRLGPALAACAACLVVAGAADSVSAVFRTTILQSATP
+DHLRGRLQGVFVVVVAGGPRVGEMIQGTASAALGEGATLVLGGVLCVAGIALLMRVQPGF
+LHYDARRPTP
+>MHAAABBN_01477
+MARLLVDITPLRVSPAYRRLWLGNTLAYVGTQLTLVAVSLEVFALTGSSFAVGLLGLAAL
+VPLVVAGLYGGAIADRHDRRRVALTSSAVMWLTTVGIAAQAWAGLESVPVLYALVALHSG
+ASGINQPTRGAIIPALVGLPLVPAANALNMMTFSVALMVGPVLGGVLVAAVGYAWTYSID
+VVTFLAALYAVWRLPSLPPQRAETATASGTRWGLASVVEGLRFLGSRPNLRMTFLADIVA
+MTTAFPRALLPAIGAVVLGGGEAAVGVLLAAMAAGAFLAGLFSAPFTRLHAQGWGVYVSI
+LVWGAAVAAFGGVVWWAQSLPDGDPRLTLAFALAALCMAVGGAADSLSGVFRGSILQSAT
+PDHLRGRLQGVFVVVVAGGPRLGELLTGGASVGLGEGPTLLAGGVLCMLGVTALMRWQPG
+FLRYDARNPTP
+>LFPAFLNI_01699
+MARLLVDITPLRVSPAYRRLWLGNTLAYVGTQLTLVAVSLEVFALTGSSFAVGLLGLAAL
+VPLVVAGLYGGAIADRHDRRRVALTSSAVMWLTTVGIAAQAWAGLESVPVLYALVALHSG
+ASGINQPTRGAIIPALVGLPLVPAANALNMMTFSVALMVGPVLGGVLVAAVGYAWTYSID
+VVTFLAALYAVWRLPSLPPQRGEAAAASGTRGGLASVVEGLRFLGSRPNLRMTFLADIVA
+MTTAFPRALLPAIGAVVLGGGEAAVGVLLAAMAAGAFLAGLFSAPFTRLHAQGWGVYVSI
+LVWGAAVAAFGGVVWWAQSLPDGDPRLTLAFALAALCMAVGGAADSLSGVFRGSILQSAT
+PDHLRGRLQGVFVVVVAGGPRLGELLTGGASVGLGEGPTLLAGGVLCMLGVSALMRWQPG
+FLRYDARNPTP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000729.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000729.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a0c7d7239cae4d99e85a007359ee351719b7b71
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000729.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01112
+MTTAFEPRPHTGLAPREPEPHGPGTPGPLRPGVRGSVLIVSEHADPDTAMRHAMAWITAF
+EDDCGLVLDADGTELYAVGLAGELGASLRRSPGVAEDGTPTDTSEFVDAILTGGVWRLRE
+PDARAWSTAYRAAILGAAPHAVCTVWDVLPLPAA
+>MOLHKGIG_01765
+MTTAFEPRPHTAAAPREPDPHGPGTPGSLRPGERGSVLIVTRHPDPDEAMRHAMAWITAF
+EEDCGLVLDTDETALYAVGRAGDLGEALRRGPLVHEDGSPADTSAFVDAVLADGTWRLRD
+ADPRAWSTTYRATILGAAPEAVCTIWDVFPLPAA
+>NAFOICDF_01037
+MTAQHAEPTRTDRAEPHGPGTPATLRPGERGSVLVLSPAGPPEAAMGHAVAWITAFEDDC
+GLVLDRDATSLYAVSPADGLRREGDVPSDGGIAEHLDFVLAGDVWHHRGTCPPAPAGSDV
+DGWALLVHRLQREAPRGALGTVWDVFPLPAAG
+>MHAAABBN_01472
+MTTAFEPRPHAAAAPREPDPHGPGTAGSLRPGARGSVLIVTRHPDPDEAMRHAMAWITAF
+EEDCGLVLDTDETALYAVGRAGDLGEALRRGPLVHEDGSPADTSAFVDAVLTDGTWRLRD
+ADPRAWSTTYRATILGAAPEAVCTIWDVFPLPAA
+>LFPAFLNI_01694
+MTTAFEPRPHTAAAPREPDPHGPGTPGSLRPGERGSVLIVTRHPDPDEAMRHAMAWITAF
+EEDCGLVLDTDETALYAVGRAGDLGEALRRGPLVHEDGSPADTSAFVDAVLTDGTWRLRD
+ADPREWSTTYRAAILGAAPEAVCTIWDVFPLPAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000730.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000730.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a326e0c72a74aaa09a5426f6a259e83bb52e3119
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000730.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01113
+MSAPDAVRRVRVPVPVDVPLTLRPLQRGAADPTVRAVPEGVWLTLRVPDQGAPAGSPGRP
+TSLLVSGAREAAGPGTVVTARAWGPGARAAVASVERLLGVDDAGWDAFDALLHRDSSAPA
+LPRHVREARRTRAGLRLPAAGALSGQLITVVLEQKVTHDQARHGWRTLVRLAARIDDDGP
+APGPVPSGMLPPPSPAAVLRIPSWDWHARAWVQPAQSHTVLEVARRAASIDRLGAAVAPG
+DTAGIAALARRLESLPGIGPWTTAEALQRSHGAADLVAVGDYHLAQFVGQVLTGRRTDDA
+GMLRLLEPWAGHRQRVVRMIGISGARKQAFGPKLAPADHRAY
+>MOLHKGIG_01764
+MIAPDAERCVRVPVPVDVALTLRPLQRGAADPTVRATPQGVWLTLRSPAPDAASGGPGRP
+TSLLVSGVRETAGGGTAVTARAWGAGARTAVADVERLLGLHDDGWAAFDALLRPDSGAPA
+LPRHVREARRTRAGLRLPAAGALSRQLLTAVLEQKITHDQARHGWRTLVRLAARIDGDGP
+APGPVPPGMLPPPTPAAVLRIPSWDWHARAWVQPSQSRTVLEVARRAASIDRLGDAVAPG
+DTAGVAALARRLESVPGIGPWTTAEALQRSHGAADLVSVGDYHLAQYVGQVLTGRRTDDA
+GMLRLLAPWAGHRQRVVRMIGLSGERKQAFGPKLAPADHRAH
+>NAFOICDF_01038
+MVPPLSVPPDAVVRLAPGVPVDVAATLRPLQRGAADPTVRAAPTGVWLTRRERVDGATLP
+ATLLVSPQVRGEVTARAWGPGAAAALAGLPALLGLHDTGWDAFDALLAPDPRRPSLPHAL
+REARRTREGLRLPAAGHLSTQLMTVVLEQKVTHDQARHGWRTLVRLAHGIDDATPPGPAP
+AGMLLPPTPRAVLAIPSWDWHARAWVQPAQSRTVLEVARRASAVDRLGAAVAPGDVAGTA
+ALAARLQAIPGVGPWSAAEALQRSHGSADLVSVGDFHLAHLVGQVLAGRRTDDAGMLRLL
+QPWEGHRQRVVRMIGASGASKERFGPRLAPADHRAY
+>MHAAABBN_01471
+MTAPDAERRVRVPVPVDVALTLRPLQRGAADPTVRATPQGVWLTLRSPAPDVASGGPGRP
+TSLLVSGVREAAGGGTAVTARAWGAGASAAVAGVERLLGLHDDGWDAFDALLRPDSGAPA
+LPPHVREARRMRAGLRLPAAGALSRQLLTAVLEQKVTHDQARHGWRTLVRLAARIDDDGP
+APGPVPPGMLPPPTPAAVLRIPSWDWHARAWVQPSQSRTMLEVARRAASIDRLGDAVTPG
+DTAGVAALARRLESVPGIGPWTTAEALQRSHGAADLVSVGDYHLAQYVGQVLTGRRTDDA
+GMLRLLAPWAGHRQRVVRMIGLSGERKQGFGPKLAPADHRAH
+>LFPAFLNI_01693
+MTAPDAERRVRVPVPVDVALTLRPLQRGAADPTVRATPQGVWLTLRSPAPDAASGGPGRP
+TSLLVSGVREAAGGGTAVTARAWGAGASAAVAGVERLLGLHDDGWGAFDALLRADSGAPA
+LPRHVREARRTRTGLRLPAAGALSRQLLTVVLEQKVTHDQARHGWRTLVRLAARIDDDGP
+APGPVPPGMLPPPTPAAVLRIPSWDWHARAWVQPSQSRTMLEVARRAASIDRLGDAVAPG
+DTAGVAALARRLESVPGIGPWTTAEALQRSHGAADLVSVGDYHLAQYVGQVLTGRRTDDA
+GMLRLLAPWAGHRQRVVRMIGLSGERKQAFGPKLAPADHRAH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000734.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000734.fa
new file mode 100644
index 0000000000000000000000000000000000000000..173dbeb91c6d61e86d1a2d49baa4f345ccf22898
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000734.fa
@@ -0,0 +1,26 @@
+>ACLBLIBL_01117
+MPQNSEDRPLARGLGRAAGRAARSFQESQRADDARLRAERARLAAEDEERLSRRREDRER
+GLAERDAAESDAGLVHPLLRIARMYWLALTVVLAVVAGAFVWNGMRARESGEPVVDPLTG
+IESVGVLGGATGQFTMGVTVALFAAAALWGWIGLLRRRRSAIGTLTFIALLLAAPAFLRA
+NGLLIVLAVIMLVGAALLWLPPVRSRLRR
+>MOLHKGIG_01760
+MPQNSEDRPLARGLGRAAGRAAQSFRENQRADDARLRAERARLTAEDEERLERRRADRER
+DLVARDAAESDAGLVHPLLKVARLYWLAVTVVLIGIAGAFLWNGARAQDSGEPVIDPLTG
+MESVGVLGGATGQFTMGTAVALLAAASLWGWIGLLRRRRSAIGTLTFIAVLLAAPAFLRA
+NGLLIILAVVMLLGAALVWLPPVRSRVRR
+>NAFOICDF_01042
+MADNSAENSSDRIARAAGRAARAFREGQDAERIRREQARAEAPRTADADGSRATGLRERA
+VRAAAQAAERAEPLKERVGHAAGEAGRSFKENQAQDAARLRGVREQVRADDDAARAERQA
+ERERALDARDETEAGRVHPLLRLTRLWWLAVSLLLLGLATAFVYNGVRADRDGGEVIDPV
+TGLQSIGPLGGATGQYTVGGVLAALALVTLWGWVGLLRRRRASLGTLTTVAVLLAIPAVL
+RPNPLFIVLGAAMAIGAVLLWLPPVRSRVRR
+>MHAAABBN_01467
+MPQNSEDRPLARGLGRAAGRAAQSFRENQRADDARLRAERARLTAEDEERLERRRADRER
+DLVARDAAESDAGLVHPLLKVARLYWLAVTVVLIGIAGAFLWNGARAQDSGEPVIDPLTG
+MESVGVLGGATGQFTMGTAVALLAAASLWGWIGLLRRRRSAIGTLTFIAVLLAAPAFLRA
+NGLLIILAVVMLLGAALVWLPPVRSRVRR
+>LFPAFLNI_01689
+MPQNSEDRPLARGLGRAAGRATQSFRENQRADDARLRAERARLTAEDEERLERRRADRER
+DLAARDAAESDAGLVHPLLKVARLYWLAVTVVLVGIAGAFIWNGARAQDSGEPVIDPLTG
+MESVGVLGGATGQFTMGTAVALLAAASLWGWIGLLRRRRSAIGTLTFIAVLLAAPAFLRA
+NGLLIILAVVMLLGAALVWLPPVRSRVRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000740.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000740.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6def85b862cd374040c9b5583469fcf70f9c8603
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000740.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01125
+MTSAAPPPSPPPDAAAVPTVGLIGWRGMVGSVLMQRMAEEGDFARIRPVFFSTSNAGGPA
+PTFEGLPGDAGPLQDAYDLNVLASLPVIVTAQGGDYTKDVYPRLRAAGWDGIWIDAASTL
+RMEDTSVIALDPVNRSVIDAALASGVKDFIGGNCTVSCMLMGLGGLFKAGLVEWGTAMTY
+QAASGGGARHMRELLTQYADLGGVVRDELADPASAILEIDRKVLELQRDGLDATQFGVPL
+GGSLIPWIDSDLGNGVSREEQKAFDETNKVLGLRGEDRIAFDSLCVRIGAMRSHSQALTL
+KLTRDVPLDEVEQIIAEDNEWVRLVANTKEASVAELTPIAATGTLQIPVGRLRKLNMGPE
+YLSAFTVGDQLLWGAAEPVRRMLMIATGNL
+>MOLHKGIG_01752
+MRSRAASLEGMTSAAPASVNAPDAAAVPTVGLVGWRGMVGSVLLQRMAEEGDFARVHPVF
+FSTSNAGGPAPVLEGMAGDPGVLQDAYDVDALKALPVILTAQGGDYTQAVYPKLRAAGWD
+GIWIDAASTLRMADTSVIALDPVNRGVIDAALANGTKDFIGGNCTVSCMLMGLGGLFKAG
+LVEWGTAMTYQAASGGGARHMRELLTQYAELGGAVRAELADPASAILEIDRKVIELQRGG
+LDSTQFGVPLGGSLIPWIDSDLGDGVSREERKAYDETNKVLGLTGADRIPFDSLCVRIGA
+MRSHSQALTLKLTQDVPLDEVEQIIAADNEWVQVVPNTKEVTVTDLTPIAATGTLQIPVG
+RLRKLNMGPEYLSAFTVGDQLLWGAAEPVRRMLMIATGNL
+>NAFOICDF_01050
+MTSAAPAPVSPAAPAAVPTVGIVGWRGMVGSVLMQRMAEEGDFARIHPVFFSTSNAGRPA
+PVFEGMDGDAGTLQDAHDVEALKALPIIVTAQGGDYTKAVYPALRAAGWDGIWIDAASTL
+RMEDSSVIVLDPVNRSVIDAALASGTKDFIGGNCTVSCMLMGLGGLFREGLVEWGTAMTY
+QAASGGGARHMRELLTQYAALGGVVAEELADPSSAILEIDRKVLELQRGGLDASQFGVPL
+GGSLIPWIDSDLGNGVSREEQKAYDETNKVLGLTGDDRIPFDSLCVRIGAMRSHSQALTL
+KLTRDVPLDEITEIVADGTEWAQVVPNEKEASLRDLTPIAASGTLQIPVGRLRKLNMGPE
+YLSAFTVGDQLLWGAAEPIRRMLMIATGNL
+>MHAAABBN_01459
+MRSRAASLEGMTSAAPASVNAPDAAAVPTVGLVGWRGMVGSVLLQRMAEEGDFARVHPVF
+FSTSNAGGPAPVLEGMAGDPGVLQDAYDVDALKALPVILTAQGGDYTQAVYPKLRAAGWD
+GIWIDAASTLRMADTSVIALDPVNRGVIDAALANGTKDFIGGNCTVSCMLMGLGGLFKAG
+LVEWGTAMTYQAASGGGARHMRELLTQYAELGGAVRAELADPASAILEIDRKVIELQRGG
+LDSTQFGVPLGGSLIPWIDSDLGDGVSREERKAYDETNKVLGLTGADRIPFDSLCVRIGA
+MRSHSQALTLKLTQDVPLDEVEQIIAADNEWVQVVPNTKEVTVTDLTPIAATGTLQIPVG
+RLRKLNMGPEYLSAFTVGDQLLWGAAEPVRRMLMIATGNL
+>LFPAFLNI_01681
+MTSAAPASVNAPDAAAVPTVGLVGWRGMVGSVLLQRMAEEGDFARIHPVFFSTSNAGGPA
+PVLEGMAGDPGVLQDAYDVDALKALPVILTAQGGDYTQAVYPKLRAAGWDGIWIDAASTL
+RMADTSVIALDPVNRGVIDAALANGTKDFIGGNCTVSCMLMGLGGLFKAGLVEWGTAMTY
+QAASGGGARHMRELLIQYAELGGAVRAELADPASAILEIDRKVIELQRDGLDSTQFGVPL
+GGSLIPWIDSDLGDGVSREERKAYDETNKVLGLTGADRIPFDSLCVRIGAMRSHSQALTL
+KLTRDVPLDEVEQIIAADNEWVQVVPNTKEATVTDLTPIAATGTLQIPVGRLRKLNMGPE
+YLSAFTVGDQLLWGAAEPVRRMLMIATGNL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000741.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000741.fa
new file mode 100644
index 0000000000000000000000000000000000000000..04fa3c72dab8bd38c29ddfddf55e512e5d1caa29
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000741.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01126
+MAPTDPQDRLFTPQAVTFLALVACPVLAFVCAVMGLILVLQGKTIAGLVFLIVLTQVFAV
+GGLIAWNKRKRAQQGR
+>MOLHKGIG_01751
+MAPTDSDQRLLSPQAVSFLALVALPVLAFVCAVFGLILVLQGKTIAGLVFLLVLTQVFAV
+GGLIAWNRRKRAQQGR
+>NAFOICDF_01051
+MADLPSDEKAPLLDAQAVTFLTLIAFPVLAFVCAVMGLILVLQGKVVAGVVFLVVLTQVF
+AAGGLITWNRRRRDRSGR
+>MHAAABBN_01458
+MAPTDSDQRLLSPQAVSFLALVALPVLAFVCAVFGLILVLQGKTIAGLVFLLVLTQVFAV
+GGLIAWNRRKRAQQGR
+>LFPAFLNI_01680
+MAPTDSDQRLLSPQAVSFLALVVLPVLAFVCAVFGLILVLQGKTIAGLVFLLVLTQVFAV
+GGFIAWNKRKRAQQGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000742.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000742.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a5d22fa5bd4cb365504d1d3225563e2f494c0cda
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000742.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01127
+MRSDPMSRATRPTEPAIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR
+TWESFPARFRPLPGRTNIVVSRTLTASEEAGAELRAAGAVVVPDFGAALAAAAEADGCDT
+VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPVLDPRWRRTAVDPAPDAWLDSASG
+PRHRFERWERD
+>MOLHKGIG_01750
+MRSDPMSRATRPTEPVIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR
+TWESFPARFRPLPGRTNIVVSRTLTATEEAGAELRAAGAVVVPNFGAALAAAAEADGCDT
+VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPPLDARWRRTAVDPAPDAWLDSASG
+PRHRFERWERD
+>NAFOICDF_01052
+MARHHDDGARPRQTIAMIWAQTPDGVIGADGTMPWHLPEDLARFKALTLGHPVIMGRRTW
+DSFPARVRPLPGRTNIVVSRTLTATPEAGEAVRAAGAVVVPDFGAALTAADEADGLDLVW
+VIGGATLYEQALDVATRAEITVVDVDAPGDTHAPALDSRWRLVAADPSPDGWLDSAAGPR
+RRDERWERD
+>MHAAABBN_01457
+MRSDPMSRATRPTEPVIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR
+TWESFPARFRPLPGRTNIVVSRTLTATEEAGAELRAAGAVVVPNFGAALAAAAEADGCDT
+VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPPLDARWRRTAVDPAPDAWLDSASG
+PRHRFERWERD
+>LFPAFLNI_01679
+MRSDPMSRATRPTEPVIAMIWAQTPERVIGRDGTMPWHVPEDLAHFRAHTHGHPVIMGRR
+TWESFPARFRPLPGRTNIVVSRTLTATEEAGAELRAAGAVVVPDFGAALAAAAEADGCDT
+VWVIGGATLYEQALDVASRAEVTVIDADVDGDTHAPLLDARWRRTAVEPAPDAWLDSASG
+PRHRFERWERD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000743.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000743.fa
new file mode 100644
index 0000000000000000000000000000000000000000..861ea171abf28a2f5cea755511475a065c09494c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000743.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01128
+MSIPTPYEDLLADVMANGAVKSDRTGTGTRSVFGRQMRFDLSRSFPLITTKRVHFKSVAL
+ELLWFLRGDSNVRWLQERGVRIWNEWADEDGELGPVYGVQWRSWPTPDGGHIDQIAKVVE
+QIRTNPDSRRHIVTAWNPAEVDEMALPPCHALFQFYVSPGQDGAPGRLSCQLYQRSADLF
+LGVPFNIASYALLTVIVAQQTGLAPGEFVWTGGDVHIYANHEEQVREQLSREPYPYPRLW
+LRRTPASIFDYDYEDFEVLDYRHHPTITAPIAV
+>MOLHKGIG_01749
+MGRVSIPTPYEDLLADVMAHGAVKTDRTGTGTRSVFGRQLRFDLAESFPLITTKRVHFKS
+VALELLWFLRGDSNVRWLQERGVRIWNEWADEDGELGPVYGVQWRSWPTPDGGHIDQIAK
+VVEQIRTNPDSRRHIVTAWNPAEVDEMALPPCHALFQFYVSPGQDGAPGRLSCQLYQRSA
+DLFLGVPFNIASYALLTVMVAQQTGLTPGEFVWTGGDVHIYANHEEQVREQLSREPYPYP
+RLRLRRTPASIFDYDYEDFEVLDYRHHPTITAPIAV
+>NAFOICDF_01053
+MSIPTPYEDLLADVLAHGAVKADRTGTGTRSVFGRQLRFDLAESFPLITTKRVHFKSVAL
+ELLWFLRGDSNVRWLQERGVTIWDEWADEGGELGPVYGVQWRSWPTPDGGSIDQIAKVVE
+QIRTSPDSRRHLVTAWNPAEVDEMALPPCHAMFQFYVAPDVDGAPGVLSCQLYQRSADLF
+LGVPFNIASYALLTLMVAQQTGLTPGEFVWTGGDCHIYANHEEQVREQLSREPYPYPTLR
+IRRTPESIFDYEYDDFELVDYRHHPAIKAPVAV
+>MHAAABBN_01456
+MGRVSIPTPYEDLLADVMAHGAVKTDRTGTGTRSVFGRQLRFDLAESFPLITTKRVHFKS
+VALELLWFLRGDSNVRWLQERGVRIWNEWADEDGELGPVYGVQWRSWPTPDGGHIDQIAK
+VVEQIRTNPDSRRHIVTAWNPAEVDEMALPPCHALFQFYVSPGQDGAPGRLSCQLYQRSA
+DLFLGVPFNIASYALLTVMVAQQTGLTPGEFVWTGGDVHIYANHEEQVREQLSREPYPYP
+RLRLRRTPASIFDYDYEDFEVLDYRHHPTITAPIAV
+>LFPAFLNI_01678
+MGRVSIPTPYEDLLADVMAHGAVKTDRTGTGTRSVFGRQLRFDLAESFPLITTKRVHFKS
+VALELLWFLRGDSNVRWLQERGVRIWNEWADEDGELGPVYGVQWRSWPTPDGGHIDQIAK
+VVEQIRTNPDSRRHIVTAWNPAEVDEMALPPCHALFQFYVSPGQDGAPGRLSCQLYQRSA
+DLFLGVPFNIASYALLTVMVAQQTGLTPGEFVWTGGDVHIYANHEEQVREQLSREPYPYP
+RLRLRRTPASIFDYDYEDFEVLDYRHHPTITAPIAV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000752.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000752.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1faba259624fbd2d6f1cd775640fe15170f1d33c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000752.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01137
+MRVGMLTSGGDCPGLNAVIRSAVLHGIKTYDMEMVGIRNGWSGLIEKDVEELPRTRVRGL
+ARNGGTILGTSRTHPYDTEGGGPENMRRNMRELGLDAVIAIGGEGTLAGANRLAADGLPI
+VGVPKTIDNDLRGTDYTFGFDTAVQIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH
+SGMAAGAHAILIPEVRTPMEQVAEWVKQVHDRGRSPLVVVAEGFIPEGHDDPLSEAGVED
+SGRPRLGGIGEWVTREIEAMTGVETRNTVLGHIQRGGAPTATDRVLSTRFGMGAVDLAAQ
+KRWGQMVAANGTDIISIPMSAALKGLKEVPVERYEEAKVLFGR
+>MOLHKGIG_01740
+MRVGMLTSGGDCPGLNAVIRSAVLHGIKSYDMEMVGIRNGWSGLIEKDVEDLPRSRVRGL
+ARTGGTILGTSRTHPYNAEGGGPENMLRNLRELDIDAVIAIGGEGTLAGANRLAADGLPI
+VGVPKTIDNDLQGTDYTFGFDTAVQIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH
+SGMAAGAHAILIPEVRTPMSQVAEWVQQVHDRGRSPLVVVAEGFIPEGHDDPLAEAGVEA
+SGRPRLGGIGEWVTREIEEMTGIETRSTILGHIQRGGAPTATDRVLSTRFGMGAVDLVAQ
+RRWGQMVAANGTEIISIPMSAALKGLKKVPVSRYDEAKILFGR
+>NAFOICDF_01066
+MRVGLLTSGGDCPGLNAVIRAAVLHGIKTYDMEMVGIRNGWAGIIEQDVEDLPRTRVRGL
+ARTGGTILGTSRTHPYDADGGGPENMARNLRELGIDAVVAIGGEGTLAGANRLAQDGLPV
+VGVPKTIDNDLQGTDYTFGFDTAVEIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH
+SGMAAGAHAILIPEVRTPMSQVAEWVTQVHEKGRSPLVVVAEGFIPEGHDDPLADAGMEA
+SGRPRLGGIGEWVTREIEEMTGIETRNTVLGHIQRGGAPTARDRVLSTRFGMGAIDLAAQ
+HRWGSMVAARGTDIITIPMSAALKGLKEVPRERYDEAKVLFGR
+>MHAAABBN_01447
+MRVGMLTSGGDCPGLNAVIRSAVLHGIKSYDMEMVGIRNGWSGLIEKDVEDLPRSRVRGL
+ARTGGTILGTSRTHPYDAEGGGPENMLRNLRELDIDAVIAIGGEGTLAGANRLAADGLPI
+VGVPKTIDNDLQGTDYTFGFDTAVQIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH
+SGMAAGAHAILIPEVRTPMSQVAEWVQQVHDRGRSPLVVVAEGFVPEGHDDPLAEAGVEA
+SGRPRLGGIGEWVTREIEEMTGIETRSTILGHIQRGGAPTATDRVLSTRFGMGAVDLVAQ
+RRWGQMVAANGTEIISIPMSAALKGLKKVPVSRYDEAKILFGR
+>LFPAFLNI_01669
+MRVGMLTSGGDCPGLNAVIRSAVLHGIKSYDMEMVGIRNGWSGLIEKDVEDLPRSRVRGL
+ARTGGTILGTSRTHPYNAEGGGPKNMLRNLRELDIDAVIAIGGEGTLAGANRLAADGLPI
+VGVPKTIDNDLQGTDYTFGFDTAVQIATDAMDRLRTTGESHHRCMVAEVMGRHVGWIALH
+SGMAAGAHAILIPEVRTPMSQVAEWVQQVHDRGRSPLVVVAEGFVPEGHDDPLAEAGVEA
+SGRPRLGGIGEWVTREIEEMTGIETRSTILGHIQRGGAPTATDRVLSTRFGMGAVDLVAQ
+RRWGQMVAANGTEIISIPMSAALKGLKKVPVSRYDEAKILFGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000753.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000753.fa
new file mode 100644
index 0000000000000000000000000000000000000000..50a042719546a0825a54ca63222464413b8c5bc4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000753.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_01139
+MRRSDSSWVGGVLAGVAERYRVDPLLARGVFVALCVVSAGFGLLAYAVAWALLPDGDGTV
+HYGRLRRGEWQDATVAIAVIGGIGVLNVVLGAGFTLLAPVVGGPGSLLGLAAVAVLVWWL
+VTRWDGSTQSRVGPAPASEPEASGRAAARPAWYLRRDDARAAASRQDAHGFRADWLDPET
+GTWRSPVHSRELRAAARLAEEEQAAPAGPSGRGSAVVAAPRRLSPAVQAVTYAVAALAAA
+AAVGASLLVGVGSLTLLAVPAIVAALAVIAPVMLAALLTGRRPGSLAPASGILVGAAALQ
+VAVAVAVL
+>MOLHKGIG_01739
+MTSTHDPFTGPGPHVAPDGAAAGETGPDGLDALPGWLRRAVLSWGVRRSPASWVGGVLGG
+VAERYRIDPLLARGVFVAVCMVSAGLGLLAYAAAWAVLPDPDGRVQFGRLRRGEWQDATV
+AIGVIGAIGALNLLLGAGFTLIAPAVGGPGSLVGLGALAVLVWWLVTRWDGRAQARVAPG
+RVPDADQPAHAVPRPAWYVGGGPRERAAEVTDPHGFRPEWIDPATGTWRDHVHSRERRAA
+TRLAEEAPRAATAPTGSGSAATAAKPRLGPIAQAATYAGAVLAALAALGISLLLGVGPTP
+TLLAVPMLVAALAVIAPVLLGALLSGRRPGTLGPASGILVGATALQVAVLVALG
+>NAFOICDF_01068
+MDTAHDPFPAPRSSPATRPLPPGPASDARSRSAGTDGPAPDGLEVLPVWLRRPVEGWGVR
+RSRSSWVGGVLAGVAERYRIDPLLSRGVFVALCVVSAGIGLLGYALAWAVLPDADGRVHY
+GRLRRGEWSDAPVAIAAIAAIGALNVVLGAGFTLIAPVLGGPGSLIGLTALAVLVWWLVT
+RWDGEGERRMAPAQPARDAAARPAAEPSWYLRRHRPESATVDAHGFRSDWIDPETGSWRE
+QPHSREHRAAARLAEAQVRAAGQAAGRRPAGTGRGSHSAVKPLLGRGTRIATCVVAAGVA
+LAVSLAMVLGNVSTSATLFPVWPALAALGVMAAVMTAGLLRGRRPGLLAPLSGILVGVVA
+LQVCAHLLFTPLP
+>MHAAABBN_01446
+MTSTHDPFTGPGPHVAPDGAASGETGPDGLDALPGWLRRAVLSWGVRRSPASWVGGVLGG
+VAERYRIDPLLARGVFVAVCMVSAGLGLLAYAAAWAVLPDADGRVQFGRLRRREWQDATV
+AIGVIGAIGALNLLLGAGFTLIAPAVGGPGSLLGLGALAVLVWWLVTRWDGRAQARVAPG
+RAPDADQPSHAVPRPAWYVGGGPRERAAEVTDPHGFHPEWIDPATGTWRDHVHSRERRAA
+ARLAEEAPRAATAPTGSGSAATAAKPRLGPIAQAATYAGAVLAALAALGISLLLGVGPTP
+TLLAVPMLVAALAVIAPVLLGALLSGRRPGTLGPASGILVGATALQVAVLVALG
+>LFPAFLNI_01668
+MTSTHDPFTGPGPHVAPDGAAAGETGPDGLDALPGWLRRAVLSWGVRRSPASWVGGVLGG
+VAERYRIDPLLARGVFVAVCMISAGLGLLAYAAAWAVLPDADGRVQFGRLRRGEWQDATV
+AIGVIGAIGALNLLLGAGFTLIAPAVGGPGSLVGLGALAVLVWWLVTRWDGRAQARVAPG
+RVPDADQPAHAVPRPAWYVGGGPRERAAEVTDPHGFRPEWIDPATGTWRDHVHSRERRAA
+ARLAEEAPRAATAPTGSGSAATAAKPRLGPIAQAATYAGAVLAALAALGISLLLGVGPTP
+TLLAVPMLVAALAVIAPVLLGALLSGRRPGTLGPASGILVGATALQVAVLVALG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000757.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000757.fa
new file mode 100644
index 0000000000000000000000000000000000000000..42f15dc5ad1ccc03520067233ef70cd9c31cbd80
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000757.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01144
+MTDIAANGGGSTPAPDRQRRGLFARIALFLRQVVDELRKVVTPTSEELLRTTGVVLAFVA
+FMILLVMGLDWVFGTVAGLLFGGGGGL
+>MOLHKGIG_01734
+MAANGGGPAPTPSRQRRGLFARIALFLRQVVDELRKVVTPTSEELLRTTGVVLAFVAFMI
+LLVMGLDWVFGTVAGLLFGAGGL
+>NAFOICDF_01073
+MTANHGSSASGPESRRRGPFGRIALFLRQVLDELRKVVTPTGDELLKMTGVVLAFVAVMI
+LLVMGLDWVFGTLAGLLFGAGPA
+>MHAAABBN_01441
+MAANGGGPTPTPSRQRRGLFARIALFLRQVVDELRKVVTPTSEELLRTTGVVLAFVAFMI
+LLVMGLDWVFGTVAGLLFGAGGL
+>LFPAFLNI_01663
+MAANGGGPAPTPSRQRRGLFARIALFLRQVVDELRKVVTPTSEELLRTTGVVLAFVAFMI
+LLVMGLDWVFGTVAGLLFGAGGL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000759.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000759.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6dd8f20f2d4577404c265a10de1776fd5f26901d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000759.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01146
+MAPKKKVSGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI
+TVYEDRSFTFITKTPPAAELIKKAAGVAKGSATPHTAKVGKLTQAQCEEIAQTKMEDLNA
+NDVKAAAKIIAGTARSMGITVEG
+>MOLHKGIG_01732
+MAPKKKVTGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI
+TVYEDRSFTFVTKTPPAAELIKKAAGVAKGSATPHTAKVGTLTQAQCEEIAQTKMEDLNA
+NDVQAAAKIIAGTARSMGITVEG
+>NAFOICDF_01075
+MAPKKKVAGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATEAQRGNVIPVEI
+TVYEDRSFTFITKTPPAVELIKKAAGVQKGSSTPHTAKVGTLTQAQCEEIAQSKMEDLNA
+NDVKAAAKIIAGTARSMGITVEG
+>MHAAABBN_01439
+MAPKKKVTGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI
+TVYEDRSFTFVTKTPPAAELIKKAAGVAKGSATPHTAKVGTLTQAQCEEIAQTKMEDLNA
+NDVQAAAKIIAGTARSMGITVEG
+>LFPAFLNI_01661
+MAPKKKVTGLIKLQIQAGAANPAPPIGPALGQHGVNIMEFCKAYNAATESQRGNVVPVEI
+TVYEDRSFTFVTKTPPAAELIKKAAGVAKGSATPHTAKVGTLTQAQCEEIAQTKMEDLNA
+NDVQAAAKIIAGTARSMGITVEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000761.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000761.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c17ffa4fc262781c310726c2730d88abdeaf322
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000761.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01148
+MATSAKESAVAELTDLFRESNAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA
+AKEAGVEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI
+KKIADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAQQGEAA
+>MOLHKGIG_01730
+MATSAKESAVAELTDLFRESSAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA
+AKDAGLEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI
+KQLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAAQGEAA
+>NAFOICDF_01077
+MATSAKESAVAELTDLFRSSSAAVLTEYRGLTVSELKQLRDSIRQDATYSVAKNTLTEIA
+AKEAGVEGLDAHLAGPTAIAFVTGDPVTVAKALRDFAKDHDKLVLKGGYMDGQPLDEAGI
+EKLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTARTVEALRAQQDQAA
+>MHAAABBN_01437
+MATSAKESAVAELTDLFRESSAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA
+AKDAGLEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI
+KKLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAAQGEAA
+>LFPAFLNI_01659
+MATSAKESAVAELTDLFRESSAAVLTEYRGLTVTELKQLRDSIRQDATYAVAKNTLAEIA
+AKDAGLEGLEAHLSGPTAIAFVTGDPVNVAKALRDFAKDHEKLVLKGGYMDGQPLDEAGI
+KKLADLESREVLLAKFAGAMKGSMSKAAALFQAPLSKTVRTVEALRAAQGEAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000762.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000762.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b95b3524cb371d268b1d689334f71545dfa6ea3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000762.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01149
+MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAAGAAGGDAAAAEEKD
+EFDVVLESAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLEG
+AGATVTLK
+>MOLHKGIG_01729
+MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAGGAAGGAEAAAAEEK
+DEFDVVLEAAGDKKIGVIKEVRAITSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE
+GAGATVTLK
+>NAFOICDF_01078
+MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAMAAAGAPAGGDAAAAEEKD
+EFDVILEAAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLEG
+AGATVTLK
+>MHAAABBN_01436
+MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAGGAAGGAEAAAAEEK
+DEFDVVLEAAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE
+GAGATVTLK
+>LFPAFLNI_01658
+MAKLTTEELLAAFEELTLIELSEFIKAFEEKFDVTAAAPVAVAAAGGAAGGAEAAAAEEK
+DEFDVVLEAAGDKKIGVIKEVRALTSLGLKEAKDLVDGAPKPILEGVNKETAEKAKEQLE
+GAGATVTLK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000765.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000765.fa
new file mode 100644
index 0000000000000000000000000000000000000000..36db97e44fc1bf036e44fb4758f2b9d4a09b1e2b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000765.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01152
+MPTIQQLVRKGRSPKVVKTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG
+IEVTAYIPGEGHNLQEHSIVLVRGGRVRDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK
+KEKK
+>MOLHKGIG_01726
+MPTIQQLVRKGRSPKVVNTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG
+IEVTAYIPGEGHNLQEHSIVLVRGGRVRDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK
+KEKK
+>NAFOICDF_01082
+MPTIQQLVRKGRSPKVVKTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG
+VEVTAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK
+KEKK
+>MHAAABBN_01433
+MPTIQQLVRKGRSPKVVNTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG
+IEVTAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK
+KEKK
+>LFPAFLNI_01655
+MPTIQQLVRKGRSPKVVNTKAPALQGNPMRRGVCTRVYTTTPKKPNSALRKVARVRLNGG
+IEVTAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYKIVRGALDTQGVKNRGQARSRYGAK
+KEKK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000767.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000767.fa
new file mode 100644
index 0000000000000000000000000000000000000000..091b9510a7688b09a994e1fa0a8168909077be35
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000767.fa
@@ -0,0 +1,65 @@
+>ACLBLIBL_01154
+MAQDVLTDLNKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGASTTDWMEQEKE
+RGITITSAAVTCFWNDNQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET
+VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVNRLGARPLVMQLPIGAENDFVGVVDL
+LSMKAFVWPGDAKGDVTMGAEYETREIPAELQEKAEEYRAQLVEAVADTSEELMEKYLEG
+EELTTEEIQAGVRHLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGAVKGHDV
+KDEEVELEREASKDAPFSALAFKIASHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI
+GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDAAHPIILESMTFPEPVISVAI
+EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE
+ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTADGEIYEFENAVT
+GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF
+KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVKALVPLS
+EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE
+>MOLHKGIG_01724
+MAQDVLTDLHKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGGATTDWMEQEKE
+RGITITSAAVTCFWNDHQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET
+VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGARPLVMQLPIGAENDFVGVVDL
+LSMKAFVWPGDAKGDVTMGASYETREIPAELQEKAEEYRNELVEAVAETSEELMEKYLEG
+EELTVEEIQAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGSVKGHAV
+NDEEEVLEREASKEAPFSALAFKIATHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI
+GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPANPIILESMTFPEPVISVAI
+EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE
+ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT
+GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF
+KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVNALVPLS
+EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE
+>NAFOICDF_01084
+MAQDVLTDLNKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGASTTDWMEQEKE
+RGITITSAAVTCFWKNNQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET
+VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGAKPLVMQLPIGSESDFIGVVDL
+LTMKAFVWPGDAKGDVTMGAEYETQEIPADLQEKAEEYRTQLLEAVADTSEELMEKYLEG
+EEISEEEIVAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGAVKGHAV
+GDEEQVLEREPSKEAPFSALAFKIASHPFFGTLTFIRVYSGRLEGGAQILNATKGKKERI
+GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPQNPIILESMTFPEPVISVAI
+EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNDETGQTEIGGMGELHLDVFVDRMRREFKVE
+ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT
+GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF
+KEGVRKANPVLLEPLMAVEVRTPEEFMGDVVGDLNSRRGQIQSMEDATGVKVVNALVPLS
+EMFGYIGDLRSRTQGRAVYSMTFHSYSEVPKNVADEIIQKSQGE
+>MHAAABBN_01431
+MAQDVLTDLHKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGGATTDWMEQEKE
+RGITITSAAVTCFWNDHQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET
+VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGARPLVMQLPIGAENDFVGVVDL
+LSMKAFVWPGDAKGDVTMGASYETREIPAELQEKAEEYRNELVEAVAETSEELMEKYLEG
+EELTVEEIQAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGSVKGHAV
+NDEEEVLEREASKEAPFSALAFKIATHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI
+GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPANPIILESITFPEPVISVAI
+EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE
+ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT
+GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF
+KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVNALVPLS
+EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE
+>LFPAFLNI_01653
+MAQDVLTDLHKVRNIGIMAHIDAGKTTTTERILFYTGVNHKLGETHDGGATTDWMEQEKE
+RGITITSAAVTCFWNDHQINIIDTPGHVDFTVEVERSLRVLDGAVAVFDGKEGVEPQSET
+VWRQADKYNVPRICFVNKMDKLGADFYFTVDTIVKRLGARPLVMQLPIGAENDFVGVVDL
+LSMKAFVWPGDAKGDVTMGASYETREIPAELQEKAEEYRNELVEAVAETSEELMEKYLEG
+EELTVEEIQAGVRQLTVNAEAYPVFCGSAFKNRGVQPMLDAVVAYLPNPLDAGSVKGHAV
+NDEEEVLEREASKEAPFSALAFKIATHPFFGTLTFIRVYSGRLESGAQILNATKGKKERI
+GKLFQMHANKENPVDEVVAGHIYAVIGLKDTTTGDTLCDPANPIILESMTFPEPVISVAI
+EPKTKGDQEKLSTAIQKLVAEDPTFRVNLNEETGQTEIGGMGELHLDVFVDRMKREFKVE
+ANVGKPQVAYRETIKRKVDKVDYTHKKQTGGSGQFAKVQLSFEPLDTAEGEVYEFENAVT
+GGRVPREYIPSVDAGIQDAMQFGVLAGYPMVGVKATLLDGAYHDVDSSEMAFKIAGSQAF
+KEGVRKANPIILEPLMAVEVRTPEEFMGDVIGDLNSRRGQIQSMEDATGVKVVNALVPLS
+EMFGYIGDLRSKTQGRAVYSMTFHSYAEVPKAVADEIIQKSQGE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000771.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000771.fa
new file mode 100644
index 0000000000000000000000000000000000000000..550aaccbd2ec181bae721251977e10860861d652
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000771.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01158
+MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD
+SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL
+>MOLHKGIG_01720
+MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD
+SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL
+>NAFOICDF_01088
+MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD
+SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL
+>MHAAABBN_01427
+MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD
+SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL
+>LFPAFLNI_01649
+MAGQKIRIRLKSYDHEVIDVSARKIVDTVTRAGATVVGPVPLPTEKNVYCVIRSPHKYKD
+SREHFEMRTHKRLIDIIDPTPKAVDSLMRLDLPADVNIEIKL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000775.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000775.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6ace828ca3cf6d9140a4cb9b86c6435c81e0ac8f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000775.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01162
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG
+PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG
+EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR
+>MOLHKGIG_01716
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG
+PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG
+EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR
+>NAFOICDF_01092
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLIDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLQQGDVVEAG
+PNADIKPGNNLPLRNIPVGTTIHAVELRPGGGAKMARSAGASIQLVAREGKYAQLRLPSG
+EIRNVDVRCRATVGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNPNGKPEGRTRRPNKESDKLIVRRRRTGKNKR
+>MHAAABBN_01423
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG
+PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG
+EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR
+>LFPAFLNI_01645
+MAIRKYKPTTPGLRGSSVADFAEITRSTPEKSLLRPLHKTGGRNNTGRITTRHKGGGHKR
+QYRLVDFRRHDKDGVPATVAHIEYDPNRTARIALLHYADGAKRYILAPAKLKQGDVVEAG
+PNADIKPGNNLPMRNIPVGTTIHAVELRPGGGAKMARSAGASVQLVAREGKYAQLRLPSG
+EIRNVDVRCRATIGEVGNAEQSNINWGKAGRMRWKGVRPTVRGVVMNPVDHPHGGGEGKT
+SGGRHPVNRNGKPEGRTRRPNKESDKLIVRRRRTGKNKR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000777.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000777.fa
new file mode 100644
index 0000000000000000000000000000000000000000..398dce7c5aa93b4649edf30443dd0ca9754f2ce9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000777.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01164
+MEAKAIARHLRVTPMKARRVVDLVRGKQATEALAILKFAQQGASEPVYKLVASAVANARV
+KADREGQAFDEDALYITEAFVDEGPTMKRFQPRAQGRAYRINKRTSHVTVVVASKDEKGG
+N
+>MOLHKGIG_01714
+MEAKAIARHLRVTPMKARRVVDLVRGKQATEALAILKFAQQGASEPVYKLVASAVANARV
+KADREGQAFDEDALYITEAFVDEGPTMKRFQPRAQGRAYRINKRTSHVTVVVASKDEKGG
+N
+>NAFOICDF_01094
+MEAKAIARHLRVTPMKARRVVDLVRGKQATEALAILKFAQQGASEPVYKLVASAVANARV
+KADREGVAFNEDALYITEAFVDEGPTMKRFQPRAQGRAYRINKRTSHVTVVVASQDEKGG
+N
+>MHAAABBN_01421
+MEAKAIARHLRVTPMKARRVVDLVRGKQATEALAILKFAQQGASEPVYKLVASAVANARV
+KADREGQAFDEDALYITEAFVDEGPTMKRFQPRAQGRAYRINKRTSHVTVVVASKDEKGG
+N
+>LFPAFLNI_01643
+MEAKAIARHLRVTPMKARRVVDLVRGKQATEALAILKFAQQGASEPVYKLVASAVANARV
+KADREGQAFDEDALYITEAFVDEGPTMKRFQPRAQGRAYRINKRTSHVTVVVASKDEKGG
+N
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000779.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000779.fa
new file mode 100644
index 0000000000000000000000000000000000000000..63528e06de4bb8df03957c41e02f041c4889870f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000779.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01166
+MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR
+GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVSEEVAREALRL
+AIHKLPLKARVIRREGGE
+>MOLHKGIG_01712
+MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR
+GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVTEDVAREALRL
+AIHKLPLKARIIRREGGE
+>NAFOICDF_01096
+MLIPRRVKHRKQHHPKRSGMAKGGTTVTFGEWGIQALSPAYVTNRQIEAARIAMTRYIKR
+GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVSEEVAREALRL
+AIHKLPLKARIIRREGGE
+>MHAAABBN_01419
+MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR
+GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVTEDVAREALRL
+AIHKLPLKARIIRREGGE
+>LFPAFLNI_01641
+MLIPRRVKHRKQHHPKRSGAAKGGTTVTFGEWGIQALTPAYVTNRQIEAARIAMTRYIKR
+GGKVWINIYPDRPLTKKPAETRMGSGKGSPEWWVANVKPGRVLFELSGVTEDVAREALRL
+AIHKLPLKARIIRREGGE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000781.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000781.fa
new file mode 100644
index 0000000000000000000000000000000000000000..631a9c66a0d0c928f3e18b0b807efb66e8f737fc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000781.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01168
+MTEQTPAVSEERGYRKALRGVVVSDKMDKTIVVEVEDRKKHSLYGKVMKTSKRVKAHDED
+NTAGIGDRVRIAETRPLSASKRWRLVEIVERAK
+>MOLHKGIG_01710
+MTEQTPAVSEERGYRKALRGIVVSDKMDKTIVVEVEDRKKHSLYGKVLKTSKRVKAHDED
+NTAGVGDRVRLAETRPLSASKRWRLVEIVERAK
+>NAFOICDF_01098
+MTEQTAAPVEERNYRKSLRGVVVSDKMDKTIVVEVEDRKKHALYGKVMKTSKRVKAHDED
+NTAGVGDRVLIVETRPLSADKHFRLVEIVERAK
+>MHAAABBN_01417
+MTEQTPAVSEERGYRKALRGIVVSDKMDKTIVVEVEDRKKHSLYGKVLKTSKRVKAHDED
+NTAGVGDRVRLAETRPLSASKRWRLVEIVERAK
+>LFPAFLNI_01639
+MTEQTPAVSEERGYRKALRGIVVSDKMDKTIVVEVEDRKKHSLYGKVLKTSKRVKAHDED
+NTAGVGDRVRLAETRPLSASKRWRLVEIVERAK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000785.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000785.fa
new file mode 100644
index 0000000000000000000000000000000000000000..23a2f0d8dcc84236c961e82385af191d2d6567c7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000785.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01172
+MTMTDPVADMLTRLRNANSAYHDTVSMPSSKLKTRVAEILKSEGYIQDWREEEAEVGKKL
+TIDLKFGPQRERAIAGLRRISKPGLRVYAKSTNLPHVLGGLGIAILSTSSGLLTNQQAAK
+KGVGGEVLAYVW
+>MOLHKGIG_01706
+MTMTDPVADMLTRLRNANSAYHDTVSMPSSKLKTRVAEILKAEGYIQDWREEEAEVGKKL
+TIDLKFGPQRERAIAGLRRISKPGLRVYAKSTNLPHVLGGLGIAILSTSSGLLTNQQAAK
+KGVGGEVLAYVW
+>NAFOICDF_01102
+MTMTDPVADMLTRLRNANSAYHDTVSMPSSKLKVRVAEILKAEGYIQDWREEEAEVGKKL
+TIDLKFGPQRERAIAGLRRISKPGLRVYAKSTNLPHVLGGLGIAILSTSSGLLTDRQASQ
+KGVGGEVLAYVW
+>MHAAABBN_01413
+MTMTDPVADMLTRLRNANSAYHDTVSMPSSKLKTRVAEILKAEGYIQDWREEEAEVGKKL
+TIDLKFGPQRERAIAGLRRISKPGLRVYAKSTNLPHVLGGLGIAILSTSSGLLTNQQAAK
+KGVGGEVLAYVW
+>LFPAFLNI_01635
+MTMTDPVADMLTRLRNANSAYHDTVSMPSSKLKTRVAEILKAEGYIQDWREEEAEVGKKL
+TIDLKFGPQRERAIAGLRRISKPGLRVYAKSTNLPHVLGGLGIAILSTSSGLLTNQQAAK
+KGVGGEVLAYVW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000786.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000786.fa
new file mode 100644
index 0000000000000000000000000000000000000000..53668ccd2d43a8f99ec87052a5e8d73138c38bfd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000786.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01173
+MSRIGRLPITIPSGVDVTIDGDRVSVKGPKGQLEHSLPTPITATLEEGQVTVARPDDERE
+SRSLHGLTRTLISNMVEGVTTGFSKQLEVVGTGYRVQAKGQDLEFALGYSHPVPVKAPQG
+ITFTVEGNKVTVAGIDKQQVGETAANIRKLRRPDPYKGKGVRYAGEQIRRKAGKAGK
+>MOLHKGIG_01705
+MSRIGRLPITIPAGVDVTIDGDRVSVKGPKGQLEHSLPTPITATLEEGQVTVARPDDERE
+SRSLHGLTRTLISNMVEGVTNGFSKQLEVVGTGYRVQAKGQDLEFALGYSHPVPVKAPQG
+ITFTVEGNKVTVAGIDKQQVGETAANIRKLRRPDPYKGKGVRYAGEQIRRKAGKAGK
+>NAFOICDF_01103
+MSRIGRLPITVPSGVDVTIDGARISVKGPKGQLEHTLPSPITATLEEGQVIVARPDDERE
+SRSLHGLSRTLINNMVLGVTEGFTKALEVVGTGYRVQAKGQDLEFALGYSHPVPVKCPEG
+ISFTVEGNKVTVAGIDKQKVGETAANIRKLRKPDPYKGKGVRYAGEQIRRKAGKAGK
+>MHAAABBN_01412
+MSRIGRLPITIPAGVDVTIDGDRVSVKGPKGQLEHSLPTPITVTLEEGQVTVARPDDERE
+SRSLHGLTRTLISNMVEGVTNGFSKQLEVVGTGYRVQAKGQDLEFALGYSHPVPVKAPQG
+ITFTVEGNKVTVAGIDKQQVGETAANIRKLRRPDPYKGKGVRYAGEQIRRKAGKAGK
+>LFPAFLNI_01634
+MSRIGRLPITIPAGVDVTIDGDRVSVKGPKGQLEHSLPTPITVTLEEGQVTVARPDDERE
+SRSLHGLTRTLISNMVEGVTNGFSKQLEVVGTGYRVQAKGQDLEFALGYSHPVPVKAPQG
+ITFTVEGNKVTVAGIDKQQVGETAANIRKLRRPDPYKGKGVRYAGEQIRRKAGKAGK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000797.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000797.fa
new file mode 100644
index 0000000000000000000000000000000000000000..83586b0888f108314412f45b8ce04496a3700009
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000797.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01184
+MPPKTRASAARKPRRKDKKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS
+RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP
+MAHNGARPAKRRRV
+>MOLHKGIG_01694
+MPPKTRASAARKPRRKANKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS
+RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP
+MAHNGARPAKRRRV
+>NAFOICDF_01114
+MPPKTRSAVRKPRRKDKKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGSR
+KSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTPQ
+AHNGARPAKRRRV
+>MHAAABBN_01401
+MPPKTRASAARKPRRKANKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS
+RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP
+MAHNGARPAKRRRV
+>LFPAFLNI_01623
+MPPKTRASAARKPRRKANKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS
+RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP
+MAHNGARPAKRRRV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000800.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000800.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b48df7f113692259c580f98101a51f91c0c404ec
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000800.fa
@@ -0,0 +1,31 @@
+>ACLBLIBL_01187
+MTEQPAPSAPRPSAAGEEPVRVRLDLAYDGGAFRGWARQPGLDSVQGALEDGLERILRRP
+VRTVVAGRTDAGVHARGQVVHLDLAEGEWAGLTRGRPDLEPGASLARRLGGVLSGWDGAV
+VVHGARRAPAGFDARFSALWREYEYRIDDAPDRRDPRTRAFTHWHGAALDERLMALEADA
+VLGLHDFLSFCRPREGATTIREVQDLRVARDEDGSVRVRIRADAFCHNMVRAVVGALLQV
+GEGSREPGWLGLRVATPARDSQVRLAPPRGLTLLAVGYPEDGEGLRRRAEGTRARRTL
+>MOLHKGIG_01691
+MSEQHRPDAPTAPGEPPSVRVRLGLAYDGGTFHGWARQPGLDSVQGALEDGLERILRRPV
+RTVVAGRTDAGVHARGQVVHLDLTETEWAGLTRGRPGLEPATSLIRRLGGVLSGWGGAVV
+VHGARRAPAGFDARFSALWREYEYRIDDAPAARDPRTRGFTHWHGAALDDRLMALEADAV
+LGLHDFLSFCRPRAGATTIREVQHLEVRRDEDGVVRVRIRADAFCHNMVRAIVGALLQVG
+EGAREPGWLAHRVARPARDSEVRLAPPGGLTLLAVGYPDEAEELHRRAEGTRAKRTL
+>NAFOICDF_01117
+MVGMPDDALPAAPVEPRPEPTTGLPREGEVRLRLDLAYDGSDFRGWAAQPGLATVQGALE
+GALETIVRRPVRTVVAGRTDAGVHARGQVVHCDLTEAEWSALARGRADVDPADALVRRLQ
+GVLRPWQGAVVVRGARRAPDGFDARFSALWRAYEYRISDRPETRDPLARHGVLWHGARVD
+ERLMAVEAGALLGLHDFLSFCRPREGATTVREVQDAEVVRTPDGLVRVRLRADAFCHSMV
+RTIVGALLEVGEGRRTPGWTAARVAGPVRDSAARLAPAHGLTLLEVGYPETGEELRARAE
+GTRARRAPLADLG
+>MHAAABBN_01398
+MSEQHRPDAPSAPGEPASVRVRLDLAYDGGTFHGWARQPGLDSVQGALEDGLERILRRPV
+RTVVAGRTDAGVHARGQVVHLDLTETEWAGLTRGRPGLEPATSLTRRLGGVLSGWGGAVV
+VHGARRAPAGFDARFSALWREYEYRIDDAPAARDPRTRGFTHWHGAALDDRLMALEADAV
+LGLHDFLSFCRPRAGATTIREVTHLEVRRDEDGVVRVRIRADAFCHNMVRAIVGALLQVG
+ERAREPGWLAHRVARPARDSEVRLAPPGGLTLLAVGYPDEAEELHRRAEGTRAKRTL
+>LFPAFLNI_01620
+MSEQHRPDAPSAPGEPASVRVRLDLAYDGGTFHGWARQPGLDSVQGALEDGLERILRRPV
+RTVVAGRTDAGVHARGQVVHLDLTETEWAGLTRGRPGLEPATSLIRRLGGVLSGWGGAVV
+VHGARRAPAGFDARFSALWREYEYRIDDAPAARDPRTRGFTHWHGAALDDRLMALEADAV
+LGLHDFLSFCRPRAGATTIREVKHLEVRRDEDGVVRIRIRADAFCHNMVRAIVGALLQVG
+EGAREPGWLAHRVARPARDSEVRLAPPGGLTLLAVGYPDEAEELRRRAEGTRAKRTL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000805.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000805.fa
new file mode 100644
index 0000000000000000000000000000000000000000..314afdc20e4fbaf28d35d01b5aed06a1b15e1907
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000805.fa
@@ -0,0 +1,14 @@
+>ACLBLIBL_01193
+MSSEAVPRPPRWSPFGALLAGLAVLWGAAFLAVDAPVCERHGAPVEWLPCLDRDRGDPDV
+APQR
+>MOLHKGIG_01685
+MTSDAAPRPRRWTLFAGLLAGLAVLWSAAFLAVDAPVCARQSAPVEWLPCLDPDRQDSEV
+APDAGSSADRTTSRP
+>NAFOICDF_01123
+MSPRRDPGRLRPLAGPAALLAALWVAAWLAVSVPVCDRGGPADWLPCVDPGRSVPAPGAP
+>MHAAABBN_01389
+MTSDAAPRPRRWTLFAGLLAGLAVLWSAAFLAVDAPVCARQSAPVEWLPCLDPDRQDSEV
+APDAGSSADRTTSRP
+>LFPAFLNI_01614
+MTSDAAPRPRRWTLFAGLLAGLAVLWSAAFLAVDAPVCARQSAPVEWLPCLDPDRQDSEV
+APDAGSSADRTTSRP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000806.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000806.fa
new file mode 100644
index 0000000000000000000000000000000000000000..95bcdafd6a074a1466c18ec89246fc903b934123
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000806.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01194
+MKGNVIDLAVAVVIGAAFGAVINAVVDSVLMPLIAALFAAPSFDDWLVLDINGVLVKFGV
+VLTAVVNFLLIAAAIYFAIVLPMNKMIERRNRRLGIDPAEEEVPEDVALLTEIRDLLSAQ
+RGGAAGTTHTTL
+>MOLHKGIG_01684
+MLQGFKDFIMKGNVLDLAVAVIIGAAFGKIVNALVEAVLMPLIAAAVGSPNFDSFAVLTV
+NGNDVKFGVLLTAIVNFLLIAAAVYFAIVMPMNKMIEARNRRLGIDPAEEEVPADVAVLT
+EIRDLLAERRGGPTSGTTTL
+>NAFOICDF_01124
+MKGNVVDLAVAVVIGAAFGKVVTALVDSVLMPLIAALFKAPSFDSWLVLNLNGVDVKFGV
+VLTAIVNFLLIAAAVYFCIVLPMNTMIERRNRRLGITPAEDEVAPDVAVLTEIRDLLARQ
+NGAPRV
+>MHAAABBN_01388
+MLQGFKDFIMKGNVLDLAVAVIIGAAFGKIVNALVEAVLMPLIAAAVGSPNFDSFAVLTV
+NGNDVKFGVLLTAIVNFLLIAAAVYFAIVMPMNKMIEARNRRLGIDPAEEEVAADVAVLT
+EIRDLLAERRGGPTSGTTTL
+>LFPAFLNI_01613
+MLQGFKDFIMKGNVLDLAVAVIIGAAFGKIVNALVEAVLMPLIAAAVGSPNFDSFAVLTV
+NGNDVKFGVLLTAIVNFLLIAAAVYFAIVMPMNKMVEARNRRLGIDPAEEEVPADVAVLT
+EIRDLLAERRGGPTSGTTTL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000807.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000807.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3322222fa541df08aafe755091d374c556a579c8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000807.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_01196
+MKDSTQPAPSVPEDLEDDLVSDHHRSPFVELERQTWARLATEMAQPFDQGDVERLRGLGE
+HLSLREVAEVYLPLSRLLSINVEASGALRSATNAFLGERTGRTPYVIGVAGSVAVGKSTT
+ARVLQEMLRRWPTTPRVELITTDGFLHPNAVLQERGIMARKGFPESYDRRALLRFMVDVK
+SGAQEVRAPVYSHITYDIVPGEEQVVRRPDVLIVEGLNVLAPPVTRADGTAGLSVSDFFD
+FSVYVDARADWIRSWYIERFMGLRSGAFADPRSYFHRYATLSDAEAQGTAESIWDSINGP
+NLQQNVQPTRGRARLVLTKNAQHEVTRVLLRKV
+>MOLHKGIG_01682
+MDRVTYTPPTSELPLVGPEEPADAVPDGHQRSPFVELDRQTWARLASEMAQPFDQADVER
+LRGLGEHLSLREVAEVYLPLSRLLSINVEASAALRSATNAFLGERTGRTPYVIGVAGSVA
+VGKSTTARVLQEMLRRWPTTPRVELVTTDGFLHPNAVLHERGIMSRKGFPESYDRRALLR
+FMADVKSGAQEVRAPVYSHITYDIVPGEEQVVHRPDVLIVEGLNVLAPPRTRADGTAGLS
+VSDFFDFSVYVDARASWIRSWYIDRFMGLRSGAFADPRSYFHRYSSLSDAEAQATAESIW
+DSINGPNLEQNVRPTRGRARLVLTKNAQHEVTRVLLRKV
+>NAFOICDF_01125
+MRADAPPPPPPPCAVVLAGRRDAVAGRRPRACHDGPVKDTRDGGGGAPTAPADAPGPASA
+GDPHLSPFVELERQTWARLADQLDQPFDQDDVERLRGLGETLSLREVAEVYLPLSRLLGI
+HVEAAGALRRATNEFLGERTGRTPYVIGVAGSVAVGKSTTARVLQEMLRRWPSTPRVELI
+TTDGFLHPNAVLQERGIMDRKGFPESYDRRALLRFMADVKSGAAEVSAPVYSHVTYDIVP
+ERRQVVHRPDVLIVEGLNVLAPPLLRADGTPGLSVSDFFDFSVYVDARADWIRDWYVERF
+MGLRSSAFRDPDAFFHRYASLSDEEARETARSIWDRINGPNLAQNVQPTRGRARLVLTKN
+RQHEVTRVLMRKV
+>MHAAABBN_01386
+MDRVTYTPPTSELPLVGPEEPADAVPDGHQRSPFVELDRQTWARLASEMAQPFDQADVER
+LRGLGEHLSLREVAEVYLPLSRLLSINVEASAALRSATNAFLGERTGRTPYVIGVAGSVA
+VGKSTTARVLQEMLRRWPTTPRVELVTTDGFLHPNAVLHERGIMSRKGFPESYDRRALLR
+FMADVKSGAQEVRAPVYSHITYDIVPGEEQVVHRPDVLIVEGLNVLAPPRTRADGTAGLS
+VSDFFDFSVYVDARASWIRSWYIDRFMGLRSGAFADPRSYFHRYSSLSDAEAQATAESIW
+DSINGPNLEQNVRPTRGRARLVLTKNAHHEVTRVLLRKV
+>LFPAFLNI_01611
+MDRVTYTPPTSELPLVGPEEPADAVPDGHQRSPFVELDRQTWARLASEMAQPFDQADVER
+LRGLGEHLSLREVAEVYLPLSRLLSINVEASAALRSATNAFLGERTGRTPYVIGVAGSVA
+VGKSTTARVLQEMLRRWPTTPRVELVTTDGFLHPNAVLHERGIMSRKGFPESYDRRALLR
+FMADVKSGAQEVRAPVYSHITYDIVPGEEQVVHRPDVLIVEGLNVLAPPRTRADGTAGLS
+VSDFFDFSVYVDARASWIRSWYIDRFMGLRSGAFADPRSYFHRYSSLSDAEAQATAESIW
+DSINGPNLEQNVRPTRGRARLVLTKNAQHEVTRVLLRKV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000808.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000808.fa
new file mode 100644
index 0000000000000000000000000000000000000000..576a8c4ac119bc8bd30daf06b64b6b9b3123850b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000808.fa
@@ -0,0 +1,60 @@
+>ACLBLIBL_01198
+MCGIVGYIGQPSSTREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGELYHRKKAGKLANL
+AQELEEHPVPTGLVGIGHTRWATHGGPTDVNAHPHVADEGRLAMIHNGIIENYAELREEL
+LAKGAEFLSETDTEVAAHLLTDVYRNAGGQDLTRSLQLASQRLEGAFTLLAVHVDHPDRV
+VASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITAEGVEITDFAGSPA
+EGKRFTVDWDASAAEKGGYETFMEKEIHDQPQAVQDTLLGRMDAAGTLVLDELRIDPEEL
+KAVNKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDPNTLVVSISQS
+GETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQIT
+AAYLLGLYLAQLNKKLFSGQIKDILADLHAIPGKIQEILDDKEQVKELARSMADTSSVLF
+LGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQAVFVVMPSPMDRHSL
+HAKVVSNIQEVRARGARTFVVAERGDQAVRSHAEVVIEVPETQPMLMPLLTTVPLQIFAL
+ELASAKGYDVDQPRNLAKSVTVE
+>MOLHKGIG_01680
+MRRSRARSGILVRMCGIVGYIGQPQSDREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGQ
+LYHRKKAGKLANLAEELAEHPVPTGLVGIGHTRWATHGGPTDRNAHPHVADEGRLAFIHN
+GIIENYAELREELLAKGVEFLSETDTEVAAHLLADVYRNAAGQDLTRAMQLASQRLEGAF
+TLLAVHVDHPDRVVASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITA
+DAVEISDFRGGPAEGKRFTVDWDASAAEKGGFETFMEKEIHDQPQAVQDTLLGRTDAAGA
+LMLDELRIDPEELKAVDKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPI
+IDPHTLVVSISQSGETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEI
+AVASTKAFLAQITAAYLLGLYLAQLNKKLFSGQIKDILADLGAIPGKIEEILAGKDQVKE
+LARSMADATSVLFLGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQPV
+FVVMPSPLDRHSLHAKVVSNIQEVRARGARTFAVAERGDAAVRAQAEVVFEVPETQPMLM
+PLLTTVPLQIFALELATAKGYDVDQPRNLAKSVTVE
+>NAFOICDF_01127
+MRMCGIVGYIGQPSSTREHDALEVLMEGLRRLEYRGYDSAGVAVVADGELYHRKKAGKLA
+NLAAELEAEPVPSAQVGIGHTRWATHGGPTDVNAHPHVADEGRLALIHNGIIENYAELRA
+ELLEKGVTFLSETDTEVAAHLLADVYRGAGEGDLTRTMQLASQRLEGAFTLLAVHVDHPD
+RVVASRRNSPLVVGVGEGENFLGSDVSGFIDFTKEAIELEQDQVVTITADAVEITDFQGA
+PAQGKAFTVDWDASAAEKGGFDTFMEKEIHDQPQAVQDTLLGRTDATGALVLDELRIDPE
+ELKAVRKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDDHTLVVSIS
+QSGETMDTLMAVRYAKEQGARTLSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQ
+ITAAYLLGLYLAQLNKKLFTGQIKDILADLAEIPGKIQEILDSSTPVRELARSMADTSSV
+LFLGRNVGFPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDEGQAVFVVMPSPLDRH
+SLHAKVVSNIQEVRARGARTFVVAERGDEAVRDHAEVVFEVPETQPVLMPLLTTVPLQIF
+ALELASAKGYDVDQPRNLAKSVTVE
+>MHAAABBN_01384
+MCGIVGYIGQPQSDREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGQLYHRKKAGKLANL
+AEELAEHPIPTGLVGIGHTRWATHGGPTDRNAHPHVADEGRLALIHNGIIENYAELREEL
+LAKGVEFLSETDTEVAAHLLADVYRHAAGQDLTRAMQLASQRLEGAFTLLAVHVDHPDRV
+VASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITADAVEISDFRGGPA
+DGKRFTVDWDASAAEKGGFETFMEKEIHDQPQAVQDTLLGRTDAAGALMLDELRIDPEEL
+KAVDKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDPHTLVVSISQS
+GETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQIT
+AAYLLGLYLAQLNKKLFSGQIKDILADLGAIPGKIEEILAAKDQVKELARSMADATSVLF
+LGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQPVFVVMPSPLDRHSL
+HAKVVSNIQEVRARGARTFAVAERGDAAVRGQAEVVFEVPETQPMLMPLLTTVPLQIFAL
+ELATAKGYDVDQPRNLAKSVTVE
+>LFPAFLNI_01609
+MCGIVGYIGQPQSDREHGALDVLMEGLRRLEYRGYDSAGVAVVDGGQLYHRKKAGKLANL
+AEELAEHPIPTGLVGIGHTRWATHGGPTDRNAHPHVADEGRLALIHNGIIENYAELREEL
+LAKGVEFLSETDTEVAAHLLADVYRNAAGQDLTRAMQLASQRLEGAFTLLAVHVDHPDRV
+VASRRNSPLVVGLGEGENFLGSDVSGFIDFTREAIELEQDQVVTITADAVEISDFRGGPA
+EGKRFTVDWDASAAEKGGFETFMEKEIHDQPQAVQDTLLGRTDAAGALMLDELRIDPEEL
+KAVDKIIVLACGTSAYAGTVAKYAIEHWCRIPVEVELSHEFRYRDPIIDPHTLVVSISQS
+GETMDTLMAVRYAKEQGARTVSICNTNGSTIPRESDAVLYTHAGPEIAVASTKAFLAQIT
+AAYLLGLYLAQLNKKLFSGQIKDILADLGAIPGKIEEILAAKDQVKELARSMADATSVLF
+LGRNVGYPVAMEGALKLKELAYIHAEGFAAGELKHGPIALIDDGQPVFVVMPSPMDRHSL
+HAKVVSNIQEVRARGARTFAVAERGDAAVRGQAEVVFEVPETQPMLMPLLTTVPLQIFAL
+ELATAKGYDVDQPRNLAKSVTVE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000809.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000809.fa
new file mode 100644
index 0000000000000000000000000000000000000000..efcf05c60b6a05bf92d3c42843e838e81248708f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000809.fa
@@ -0,0 +1,65 @@
+>ACLBLIBL_01200
+MHTVDIGQPYPLGATVDETGTNFAVALAREAESVELCLVDEDGVETRLPVVERHGTTWHV
+HVAGVGHGQRYGYRVTGPWDPSRGLWHNPAKILVDPYARAFAGEHEWGQQHHSYDFDEPD
+RMDTSDNLGTTMLGVVTDDDFDWGEDAPPNIEMTDTVVYETHVKGMTMRHPAVPEELRGT
+YAGMAHPEVVRHLTDLGVTAVELMPVHQFVDDATLQEKGLSNYWGYNTLGFFAPHAAYAA
+SQEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSMRGLDNAGYYHLVEA
+DERHYMDYTGTGNSVDLSSPKALQLVMDSLRHWVTEMHVDGFRFDLATTLTRVEGEQGPD
+MFSAFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGIWSEWNGMYRDTVRDFWRGEP
+GTLGEFATRLTGSADLYEGDGRSPGASVNFVTAHDGFTLRDLVSYNEKHNAANGEDNNDG
+ESHNRSWNCGVEGETDDPEVLTLRARQQRNFLATLLISQGVPMISHGDELGRTQGGNNNV
+YCQDNEISWIDWSAVDDSLVAFTRDLIALRHDHAVFRRRHHFDGRPAARDVEAPLPDIVW
+LEPDATAKTEDDWGAEARSIGFYLNGHTLTRGDEDEEGPYRDFYVLMNAWWEPVPYTLPG
+PLFPETWEVVVDTSSHVAPSGSRPRVRAGEVLEVPARSTVILRQVPEGA
+>MOLHKGIG_01678
+MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHA
+HVAGIGHGQRYGYRVHGPWDPARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPD
+RIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYETHVKGMTKLHPAVPEELRGT
+YAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS
+SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEG
+DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD
+MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGLWSEWNGMYRDAVRDFWRGEP
+GTLGEFATRLTGSADLYEGDGRGPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG
+EAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNV
+YCQDNEISWIDWSAMDDSLVAFTRDLIALRRDHAVFRRRHHFDGRPAARDVEAPLPDIVW
+LEPDATAKTEDDWGAEARSIGFYLNGHMLTRGDEEGEEPYRDFYVLMNAWWEPVPYTLPG
+PTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQVPEGA
+>NAFOICDF_01128
+MHTVDIGQPYPLGATVDEAGTNFAVAVGREVEAVELCLIAEDGSEERIPVTERHDTTWHV
+HVAGIGGGQRYGWRVHGPWDPARGLWHNPHKLLADPYARAFTGDYAWGQQHFSYAFDEPD
+RMDTADSRGTSMVGVVVDDDFDWGDDAPPQRLLTDTVVYETHVKGLTALHPDVPEELRGT
+YAGVAHPSVLEHLTSLGVTAVELMPVHQFVNDSILQEKGLSNYWGYNSLGYLAPHAAYSS
+ADTVGGQVHEFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPLLSFRGFDNAGYYHLVEG
+DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD
+MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGIWSEWNGMYRDTVRDFWRGEP
+GTLGEFATRLTGSADLYEGDGRNPGASVNFVTAHDGFTLRDLVSYNEKHNHANGEDNNDG
+DSHNRSWNCGVEGETDDPEVLTLRARQQRNFLTTLMVSEGVPMLSHGDELGRTQKGNNNV
+YCQDNELSWIDWSTRDDALIAFTRDVIALRRDHAVFRRRQHFDGRPAERDVEAPLPDIVW
+LEPDATAKTEADWGAEARSIAFYLNGHDLQRREGEPDEAFRDFYVLMNAWWEPVPYTLPG
+PLFPGEWEIVVDTSSHVAPAGTRPHVVAGEVIEVPGRSTMILREVVRQEQG
+>MHAAABBN_01383
+MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHA
+HVAGIGHGQRYGYRVHGPWDPARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPD
+RIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYETHVKGMTKLHPAVPEELRGT
+YAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS
+SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEG
+DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD
+MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGLWSEWNGMYRDAVRDFWRGEP
+GTLGEFATRLTGSADLYEGDGRGPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG
+EAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNV
+YCQDNEISWIDWSAMDDSLVAFTRDLIALRRDHAVFRRRHHFDGRPAARDVEAPLPDIVW
+LEPDATAKTEDDWGAEARSIGFYLNGHMLTRGDEEGEEPYRDFYVLMNAWWEPVPYTLPG
+PTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQVPEGA
+>LFPAFLNI_01608
+MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHA
+HVAGIGHGQRYGYRVHGPWDPARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPD
+RIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYETHVKGMTKLHPAVPEELRGT
+YAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS
+SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEG
+DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD
+MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGLWSEWNGMYRDTVRDFWRGEP
+GTLGEFATRLTGSADLYEGDGRSPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG
+DAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNV
+YCQDNEISWIDWSAMDDSLVAFTRDLIALRRDHAVFRRRHHFDGRPAARDIEAPLPDIVW
+LEPDATAKTEDDWGAEARSLGFYLNGHTLPRGDEEGEEPYRDFYVLMNAWWEPVPYTLPG
+PTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQVPEGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000810.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000810.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa085815dc25135d48e803965d805f4e7be02928
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000810.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01201
+MSEGSDRARARRGARGVPRGVRALLSAAAGTATLALAFGVGWAAHAVTSPRPDDPERVDA
+LLVLYSQPRVYDAAIELAADGVADRLFVSAHLGPDGHERLCGPEERRDPRLAGVSVECFA
+PDPLTTQGEAMHAAARMRELGLEHLGVLTFHQHLERSRLLVERCWTPQEGRVSMFAFDAG
+LDRWGRVRHGAYGVLAYGKAMATPGCDQELPGVLQWPLDLAKRLRGQPVGAEAGAAGPAG
+AVSAAPAAATPAAPARGEGPA
+>MOLHKGIG_01677
+MNERVDRGRVRRGLPRWARALCATVATLAALALAFGAGWATHAVTDPHPDDAPRVDALLV
+LYSQPRVYDAAIELAASGLTDRLFVSAYLGPDGHEKLCGGPEERDPRLAGVTVECFAPDP
+VTTQGEVIHAGERMRELGLHHLGVLTFHQHVERARLLAERCFTPEEGRVSLYAFDAGFDR
+LGRLQHGVYGVLAYGKAMLTPGCDQQLPGVLQWPLDLAKRLRGQPVGDEAGAVVVGARRA
+GAA
+>NAFOICDF_01129
+MSRPAGSAPAVDGDAQAAPRGPQAGRRVQADRGRGRRRRRILGAVLAAAALVLAAAFGPG
+LMRAADMTLHPRPDDPPRVDALLVLYSQPAVYDAALELLDRGVADRVFVSAHLGPDGFEK
+FCGTPAQRDPRTRGVEVECFSPDPVTTQGEVMFAADRMRALGLRRLGVLTFDQHLERARL
+LAERCLPAADGSVSMYRFDGGYTGAEKVRQDVYGTAAFAKVALTTDCSGELPDVLQWPLD
+LVKRTAGMPVGAVAESAAGVGRAGAGVRP
+>MHAAABBN_01382
+MNERVDRGRVRRGLPRWARALCATVATLAALALAFGAGWATHAVTDPHPDDAPRVDALLV
+LYSQPRVYDAAIELAASGLTDRLFVSAYLGPDGHEKLCGGPEERDPRLAGVTVECFAPDP
+VTTQGEVIHAGDRMRELGLHHLGVLTFHQHVERARLLAERCFTPEEGRVSLYAFDAGFDR
+LGRLQHGVYGVLAYGKAMLTPGCDQQLPGVLQWPLDLAKRLRGQPVGDEAGAVVVGARRA
+GAT
+>LFPAFLNI_01607
+MSAQADRGRVRRGLPRWARALCATVATLAALGLAFGAGWATHAVTEPHPDDAPRVDALLV
+LYSQPRVYDAAIELAASGVTDRLFVSAYLGPDGHEKLCGGPGERDPRLAGVSVECFAPDP
+VTTQGEVIHAADRMRELGLHHLGVLTFHQHVERARLLAERCFTPEEGRVSLYAFDAGFDR
+LGRLQHGVYGVLAYGKAMLTPGCDQQLPGVLQWPLDLAKRLRGQPVGDEAGAVVVGARRA
+GAV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000811.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000811.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d7bda59c8e55b5387c069f79944c16806cee7f4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000811.fa
@@ -0,0 +1,19 @@
+>ACLBLIBL_01202
+MIVGVGMDVVDVPRFRAQLERTPALRERLFTEDERDLPLRSLAARFAAKEAIAKAMGAPP
+GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEAQGITHWHLSLSHDGDVAAAYVVAERRA
+GEDGA
+>MOLHKGIG_01676
+MIVGVGVDVVDVPRFRAQLERTPALRARLFTEDERDLPLRSLAARFAAKEAIAKAMGAPP
+GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEALGITHWHLSLSHDGDVATAYVVAERRA
+AEEESA
+>NAFOICDF_01130
+MIVGIGVDVVDVPRFERQLARTPALRERLFTEEERDLSLRSLAARFAAKEAIAKALGAPP
+GMMWHHCSIPRPAHGDGRPEVRLTDSVRDRADELGVTHWHLSLSHDGDVAVAYVVAERHD
+>MHAAABBN_01381
+MIVGVGVDVVDVPRFRAQLERTPALRARLFTEDERDLPLRSLAARFAAKEAIAKAMGAPP
+GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEALGITHWHLSLSHDGDVATAYVVAERRA
+AEEESA
+>LFPAFLNI_01606
+MIVGVGVDVVDVPRFRAQLERTPALRARLFTEDERDLPLRSLAARFAAKEAVAKAMGAPP
+GMMWHHCWIPRPDHGDGRPTVHLTGTVQAQAEALGITHWHLSLSHDGDVATAYVVAERRA
+AEEESA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000814.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000814.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dec6b44b3b01252ba195159eb229c6f0c643015d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000814.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01205
+MSRHEPPAPDPALPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF
+TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAT
+VDRSVTVVEWGRGLAESLAGFPEDPDASWLDVEIVRARGGEDPAPAGPGADDGGIVTDFS
+DEDGEQAEELRSAVVTGYGPRWAGVRLP
+>MOLHKGIG_01673
+MSDHAIPAPGATLPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF
+TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAS
+VDRSVTVVEWGRGMAESLAGFPEDPDASWLDIEIVRARGGEDAPAASAGEGEDGIVTDFS
+DEDGGQAEELRSAVVTGRGPRWAGVVLP
+>NAFOICDF_01133
+MIAGRRAEQPLPAPVWERRVPLDGAAGTREFGAALAGVLRAGDVLILTGELGAGKTTLTQ
+GLGAGLGVREGVISPTFVLSRIHPSLADGPDLVHVDAYRLRSAGELTDLDLEATADRSVT
+VVEWGRGMAESLAGFPEDPEASWLDVEVLRARGGADLPDGPAGGDAAPDAPVIVTDFSDE
+EGEAAEEVRTAVVRAHGPRWAAVALP
+>MHAAABBN_01378
+MSDHAIPAPGATLPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF
+TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAS
+VDRSVTVVEWGRGMAESLAGFPEDPDASWLDIEIVRARGGEDAPAAPAGEGEDGIVTDFS
+DEDGGQAEELRSAVVTGRGPRWVGVVLP
+>LFPAFLNI_01603
+MSDHEFPAPGPTLPEPVLTATVPLEGADGTRAFGRALAGVLRAGDVLILTGDLGAGKTTF
+TQGLASGFGVASGVVSPTFVLSRVHPAPADAPAGTPDLVHVDAYRLRSAGELTDLDLDAS
+VDRSVTVVEWGRGMAESLAGFPEDPDASWLDIEIVRARGGEDGPAASAGEEDGIVTDFSD
+EDGGQAEELRTAVVTGRGPRWAGVVLP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000816.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000816.fa
new file mode 100644
index 0000000000000000000000000000000000000000..01d6f18cc426ed7ec00ed58f194c1268a3ba02ba
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000816.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01207
+MSPVEPAPGGDERPAEDEHGLPPGYLLRPMTVWDIPEVLAQEATLFPLDAWPARFYEEEL
+AQTGPAGGRDAHGRPPTRDYRVVVRDVPAPVAPDEDGPAPGEIVGYGGIMVVGDVADVQT
+VGTVAAAQGRGIGAAQLRWMAAEAAARGASALMLEVRASNAAARRLYARHGFEELHVRRR
+YYPGGEDAVIMRKAL
+>MOLHKGIG_01671
+MSPAEPDPAGDGRPAEDAHGLPPGYLLRPMTVWDIPEVLAHEATLFPLDAWPAHFYEEEL
+AQTGPAGGRDAHGRPPTRDYRVVVRDVAAPGSADDDGPAPGEIVGYGGIMVVGDVADVQT
+VGTVAAAQGRGIGAAQLRWMAAEAAARGASSLMLEVRASNAAARRLYARHGFEELHVRRR
+YYPGGEDAVIMRKVL
+>NAFOICDF_01135
+MSLPDATDPGDDAAPAHGLPAGFLLRPMTVWDVPEVLEHEETLFPLDAWPGHFYAEELAQ
+AGPAGALDAHGRPTTRDYRVVVRQDTGEIVGYGGIMAVGDTADVQTIGTAAAVQGRGIGA
+AQLRWMVAAARERGAESLLLEVRESNAAARRLYARHGFEPIAVRRGYYPGGEDAVVMRRA
+L
+>MHAAABBN_01376
+MSPAEPAPTDDGRPAEDEHGLPPGYLLRPMTVWDIPEVLAHEATLFPLDAWPAHFYEEEL
+AQTGPAGGRDAHDRPPTRDYRVVVRDVPAPGSADDDGPAPGEIVGYGGIMVVGDVADVQT
+VGTVAAAQGRGIGAAQLRWMAAEAAARGASSLMLEVRASNAAARRLYARHGFEELHVRRR
+YYPGGEDAVIMRKAL
+>LFPAFLNI_01601
+MSPAEPAPAGDGRPAEDGHGLPPGYLLRPMTVWDVPEVLAHEATLFPLDAWPAHFYEEEL
+AQTGPAGGRDAHGRPPTRDYRVVVRDAAAPSSADDDGPAPGEIVGYGGIMVVGDVADVQT
+VGTVAAAQGRGIGAAQLRWMAAEAAARGAGFLMLEVRASNAVARRLYARHGFEELHVRRR
+YYPGGEDAVIMRKTL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000820.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000820.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3814724fbd275ba87aaf2716402ff957a560a667
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000820.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01227
+MTITRRAALTGLLGGAVLGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDASGA
+EPVGPEPDLIRGFAAAHDAEIAWTVSGEEALLTALEKGDVDLVAGGLTSDSPWTTHASLT
+RDYAEAAGPDGEPVKLVMAVPPGENQMLAALEAHLDAQAREAGR
+>MOLHKGIG_01667
+MRTRTLTRRAALTGLLGSAALGFTACTSSGYPADPDGTLDRVTGGVLRVGVVHHPPHVDV
+SGAEPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHA
+SITRDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR
+>NAFOICDF_01138
+MQTPRRTLLTGALAAAGVVLTGCTSSGYPADPDGTLDRITGGTLRVGASHHPPHVDAAGA
+EPQGPEPDLVRAFAAERDARVEWTVSGEEALMTALKQGDLDLVVGGLTKKSPWTTDAGLT
+RPYAETTGPDGEKAELVMAVPLGENQFQSALERFLDAHGEEAGA
+>MHAAABBN_01372
+MTITRRAALAGLLGGAALGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDASGA
+EPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHASIT
+RDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR
+>LFPAFLNI_01597
+MTITRRAALAGLLGGAALGFTACTSSGYPADPDGTLDRVTGGVLRAGVVHHPPHVDASGA
+EPVGPEPDLIRGFAAAHDARVEWTVAGEEALMTALEKGDMDLVAGGLTSASPWTSHASIT
+RDYAEAEGPDGEPVKLVMAVPLGENQMLTALEAYFDQRAAEEAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000823.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000823.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f9d2c31e66b70224d10314586a1a5ee7216e8e9d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000823.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01230
+MNLPFADSTQSTLGIEWEVALVDAATGDLRSEAPAILHELHKEAGLAEGEDHPHVTGELL
+QNTVELVTGVHEAVPTAVAELGTIAARVARAAADRGLALYCQGTHPFGEAMTQPITPKER
+YGRMVDLTQYWGRQMLIFGVHVHVGLDDPAKAMPAVNRLISRFPHLLALSASSPFWVGAD
+TGYQSQRTQLFQQLPTAGLPFQFETWAEFEACVQQMTDVGMVEDVTECRWDVRAVPRLGT
+VEMRACDGMATLEEIAAVAAYTQCLVHELSADVERGRHMEILPPWYTQENKWRASRYGMD
+ATVIVDAAGTQVPLAEHLGADLERLAPIAEELGCAAELAHARVLMEHSPADRQRAVEAEA
+LAGPPAEGESAHDAAAPLRAVVLDAAARTRESLERVGG
+>MOLHKGIG_01664
+MTLPFADSAQSTLGIEWELALVDAVSGELRSEAPDLLRALHVTEGLAEDDVNPHMTSELL
+QNTVELVTGVHERVDAATADLGRIAARVADAAAERGISLFCQGTHPFADAIAQPSTPSER
+YDRMLDLTQYWGRQLLIFGVHVHVGLDDVSKAMPVVNGLVNRVPHLLALSASSPFWAGTD
+TGYQSQRTLLFQQLPTAGLPFQFQEWEGFERCVAQMEQVGMIADVTECRWDVRAVPRLGT
+VEMRACDGLATLEEIAAVTAYTQCLVDDLSASLERGETVEVLPPWHVQENKWRAARYGMD
+ATVIVDARGTQVPLAEHLPAEIERLTPVAERLGCAAELAGVQAMIDDGGAARQRRVEAQA
+LAGPPAAGEDADDAVAPLRAVVLDAAARTRASLDGRAG
+>NAFOICDF_01141
+MSLPFADSAQSTLGIEWELALVDPLTGDLRSEAPGILEELRAEAGLDADADHPHVTGELL
+QNTVELVTGVHGSVPDAVADLGGIAARVQRAAADRGLALFCQGTHPFGEAMTQPITPKAR
+YGRMVDLTQYWGRQMLIFGVHVHIGLDDRAKAMPAVNRLISRLPHLLALSASSPFWVGAD
+TGYQSQRTQLFQQLPTAGLPFQFETWEGFEHCVEQMTGVGMVEDVTECRWDVRAVPRLGT
+VEMRVCDGMATLEEIGAVAAYAQCLVHELSAQVEDDEPVAILPPWYTQENKWRAARYGLE
+ATVITDDAGTQVPLAEHLAADLERLAPVAEELGCAAELAHARVLMEHSPADRQRRVAAEA
+AAGPPRTGEDPADPVAPLRAVVRDAADRTRESLRAFQG
+>MHAAABBN_01369
+MTLPFADSAQSTLGIEWELALVDAVSGELRSEAPDLLRTLHATEGLAEDDVNPHMTSELL
+QNTVELVTGVHERVDAATADLGRIAARVADAAAARGISLFCQGTHPFADAIAQPSTPSER
+YDRMLDLTQYWGRQLLIFGVHVHVGLDDVSKAMPVVNGLVNRVPHLLALSASSPFWAGTD
+TGYQSQRTLLFQQLPTAGLPFQFQEWEGFERCVAQMEQVGMIADVTECRWDVRAVPRLGT
+VEMRACDGLATLEEIAAVTAYTQCLVDDLSASLERGETVEVLPPWHVQENKWRAARYGMD
+ATVIVDARGTQVPLAEHLPAEIERLTPVAERLGCAAELAGVQAMIDDGGAARQRRVEAQA
+LAGPPAAGEDTDDAVAPLRAVVLDAAARTRASLDGRTG
+>LFPAFLNI_01594
+MTLPFADSAQSTLGIEWELALVDAVSGELRSEAPDLLRALHVTEGLAEDDVNPHMTSELL
+QNTVELVTGVHERVDAATADLGRIAARVADAAAERGISLFCQGTHPFAEAIAQPSTPSER
+YDRMLDLTQYWGRQLLIFGVHVHVGLDDVSKAMPVVNGLVNRVPHLLALSASSPFWAGTD
+TGYQSQRTLLFQQLPTAGLPFQFQEWEDFERCVAQMEQVGMIADVTECRWDVRAVPRLGT
+VEMRACDGLATLEEIAAVTAYTQCLVDDLSASLERGETVEVLPPWHVQENKWRAARYGMD
+ATVIVDARGTQVPLAEHLPAEIERLTPVAERLGCAAELAGVQAMIDDGGAARQRRVEAQA
+LAGPPAAGEDADDAVAPLRAVVLDAAARTRTSLDGRTG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000826.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000826.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0f5e95fdc9512f8a5a8f3c2298ab60dcc385b33
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000826.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01233
+MTDLHPGVADARTRLPEPGPGERVCWVPPTVLRPQRSRWQRTWPLLAGVAVTVLLAVVSL
+FVGVYDVGAEGGREMFAITRVPRTVALVLAGAAMAMCGLIMQLMTQNRFVEPSTTGTTEW
+AGLGLLVTMILIPGASIVTRMTGAVLFAFVGTMVFFLFLRRVRLQSSLIVPIVGIMLGAV
+VGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLVVCVAVFVIADRFTVAGLG
+KDVATNVGLNYNAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNIVSMVRGDNLRTNLP
+WVVMVGIWVVIVCDLIGRTVIAPFEVPISLILGLVGAVVFLGLLIRQAKHG
+>MOLHKGIG_01661
+MTLDVRHHVADAPPRLEEPGRGDRVCWVPPAVLRPERTRWQRTWPLLVGVVVTAALIVVS
+LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE
+WAGLGLLVTMVLVPGAGLVTRMAGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA
+VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFVIADRFTVAGL
+GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRMNL
+PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG
+>NAFOICDF_01144
+MTLDVRHHVADAPPRLEEPGRGDRVCWVPPAVLRPERTRWQRTWPLLVGVLVTAALIVVS
+LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE
+WAGLGLLVTMVLVPGSGLVTRMVGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA
+VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFVIADRFTVAGL
+GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRTNL
+PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG
+>MHAAABBN_01366
+MILDVRHHVADAPPRLEEPGRGDRVCWVPPAVLRPERTRWQRTWPLLAGIVVTAVLVVVS
+LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE
+WAGLGLLVTMVLVPGAGLVTRMAGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA
+VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFVIADRFTVAGL
+GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRTNL
+PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG
+>LFPAFLNI_01591
+MILDVRHHVADAPPRLEELGRGDRVCWVPPAVLRPERTRWQRTWPLLVGVVVTAALIVVS
+LFVGVYDVGAEGGREMFAITRVPRTVALVLAGASMAMCGLIMQLMTQNRFVEPSTTGTTE
+WAGLGLLVTMVLVPGAGLVTRMVGAILFAFVGTLVFFLFLRRVRLQSSLIVPIVGIMLGA
+VVGAASTFLALQTDMLQQVGAWFAGSFTSVVRGRYELLFLVLIVCVAVFLIADRFTVAGL
+GKDVATNVGLNYDAVILTGVAMVAVATGVVTVVIGALPFLGLVVPNLVSMVRGDNLRTNL
+PWVVMVGVWIVIVCDLIGRTVIAPFEVPISLILGLVGAIVFLALLLRQAKHG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000828.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000828.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec3ec9a53b0b1440d47abd7004f4d92784bde028
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000828.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01235
+MIELRGVVKRHSDEVCIGPVDLDIEAGGITALVGPNGAGKSTVLTMIGRLQDVDAGTIAV
+GGQDITSTPSRRIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTRGRLTLEDERYVSEAI
+DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR
+AADMLGRTVVIVLHDINFAARYADHIVAMGDGQVVETGTPGEILRPEVLERIFRTPCSVV
+DGPHGPLAVYY
+>MOLHKGIG_01659
+MIELRGVVKRHSDEVCIGPVDLDIQAGGVTALVGPNGAGKSTLLTMIGRLQDADAGTIAV
+GGHDITTTPSRRIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTRGRLTLEDERHVSDAI
+DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR
+AADELGRTVVIVLHDINFAAHYADRIVAMGDGQVVETGTPAEILRPEVLERIFKTPCSVV
+DGPHGPLAVYY
+>NAFOICDF_01146
+MIELRGVVKRHSDEVCIGPVDLDIQAGGVTALVGPNGAGKSTLLTMIGRLQDADAGTIAV
+GGHDITTTPSRKIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTRGRLTLEDERHVSDAI
+DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR
+AADELGRTVVIVLHDINFAAHYADRIVAMGDGQVVETGTPAEILRPEVLERIFKTPCSVV
+DGPHGPLAVYW
+>MHAAABBN_01364
+MIELRGVVKRHSDEVCIGPVDLDIQAGGVTALVGPNGAGKSTLLTMIGRLQDADAGTIAV
+GGHDITTTPSRKIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTRGRLTLEDERHVSDAI
+DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR
+AADELGRTVVIVLHDINFAAHYADRIVAMGDGQVVETGTPAEILCPEVLERIFKTPCSVV
+DGPHGPLAVYY
+>LFPAFLNI_01589
+MIELRGVVKRHSDEVCIGPVDLDIQAGGVTALVGPNGAGKSTLLTMIGRLQDADAGTIAV
+GGHDITTTPSRKIAQTLSILRQENHFVTRLTVRQLVGFGRYPYTCGRLTLEDERHVSDAI
+DFLNLGPFENRYLDQLSGGQRQRAYVAMVLAQNTEYVLLDEPLNNLDMQHSVQMMQQLRR
+AADELGRTVVIVLHDINFAAHYADRIVAMGDGQVVETGTPAEILRPEVLERIFKTPCSVV
+DGPHGPLAVYY
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000829.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000829.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1854dfd994ebda8fc2be022d57e15f14d03cc379
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000829.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01237
+MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGNRVPVD
+VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVTK
+>MOLHKGIG_01657
+MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGNRVPVD
+VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVAK
+>NAFOICDF_01148
+MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGTRVPVD
+VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVTK
+>MHAAABBN_01362
+MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGNRVPVD
+VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVTK
+>LFPAFLNI_01587
+MSVSIKPLEDRIVVRPLEAEQTTASGLVIPDTAKEKPQEGQVVAVGPGRVAENGNRVPVD
+VAEGDVVLYSKYGGTEVKVGGEEYLVLSARDVLAVVTK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000843.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000843.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1dafbfb146a2062e394fb0cf802cb9f051e62665
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000843.fa
@@ -0,0 +1,60 @@
+>ACLBLIBL_01254
+MDAPQQTPAPADVGPTAVLARVRTLLAEARTSGAPEDAVDAAPVDHDARQWWELSLEAAL
+RDEPRESARCAESGLAALGPGEDGVRLSLLRALAVAADRLGDETGLTRWVEARAALLRTL
+GRPRQAALETQLGASLVREPDGFEAAVLAGVVEEEPGVPGEDPGDTVLPEAALALAVHRV
+HASDLDGALAAARRAVESLRGLRAAGAVLPVGSWSSAHLLLSRLHLWRGEHAEADEAAAV
+VTSLPAARAVLASATTVRAIAAHEQDRPTAALALALDAADRMARVGLRRGAASAAALAGR
+VAGDLEGHEEAAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRPDEAEPLLARLVR
+REAAQGHDVEQARALVDLGHAHHDQDRSENALPLWREAAGLFEAHGRWEDAARTLLAAGA
+LVNRERDELTRPSALDLFERAVAAARRAVDEDPAVLPAALHAHGYLLCESGRPEGLELLD
+EAVALVREAEAPWQVADYTDTRARALWSLEQGAEAVSTALHAADLFTAAQDPEGAAQAEL
+FAASVVAEDGSPEQAATLFRLVSESTQSTLVRLGALTGLHQCLSAVGDHDGAARVRDDLD
+AVREQLGAD
+>MOLHKGIG_01641
+MDTPQDPPHRDDPSGGPVEPAVDAALDRVRALLRQARGTAAPDAPTALDARGWWELSLEA
+ALRDEPRESARLADSGLAALGPGQDDVRLALLRALAVAAGQVGDEAALTRWVEARAALLR
+HLGRPRQAELESQLGAALVRDPDTVEAAVLAGVVEDEPGAPGEDPGDTVLPEAALALAVH
+RVHTGDLDAALELARRVIAVLGGLRAAGALLPTGSWSSAHLLLARLHLWRGEHAEADAAA
+AVVTALPAARAVLASATTVRAIAAHELDRPTAALDLALEAAERMASVGLRRGAASAAALA
+GRVAGDLDGYEEVAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRADEAEPLLARL
+VRREATHGRDVEQARALVDLGHAHHDQDRAENALPLWREAAGLFEAHGQWEDAARTLLAA
+GALVNRERDERTRPSALDLFERAVAAARQAVDEDPAVLPAALHAHGYLLCESGQAEGLDL
+LEEALALVRDAGADWQVADYTDTRARALWSLERGPEAIATALQAADLFTAAGDREGAAQA
+ELFAAYVVAEDGSPEQAATLFRLVCDSTDSTLVRLGALTGLHQCLSALGDHDGAARVRDE
+LDALREGLGAD
+>NAFOICDF_01163
+MAEDAPALLAGRDPLAAVEALLAAARDDAALPLPAGSDAPSLRERALEALLREDPASAAR
+AAEDGLDAPGGQDPALRLALLRLRATAAAHAGDEPALEEWTARRADLLRRLGRPRQADLE
+VQLGASLLREPDAFEATVLAGVAEDERGRITADPAALEDTVLPDALLALCAQRVQAHDLD
+AALEAAEEALAVIRAQETAGVVLGEAAEPHALLMLARLHLWREEHRASDDAARAVLARPC
+AAVVRASATLVRALAAHGQDRPEAALDFALRAAEAMSRAGLRRGAASAAALVGRVAGARA
+DRQDLAVAAWELSCVHAEKAEAPEAPSLAYWWAHQLLIAGRAEEAEPVLTALVRREAAAG
+DEAAQARALVDLGHACHELDRPSEALPLWREAAELFTRRGHHADAAHTLLAAGALCHRDP
+HDAAHAGALDLFEQAVDAARRSEGDSAVLASALHALGYLRCETGRGDGLELIDEAIALAE
+GSGAAWQKADYLDTRARSLWALHRGDDAVSAALTSADLFTDAGDPSGAAQAELFAAHVVA
+EDGRPEQAATLFRLVSESTHSDLVRLGALTGLQQCLAALGEHAEADRVRADADAVRRALG
+GRD
+>MHAAABBN_01346
+MDTPQDPPRRDDPSGGPVEPAVDAALDRVHALLRQARVIAAPDAPTALDARGWWELSLEA
+ALRDEPRESARLADSGLAALVPGQDDVRLALLRALAVAAGQVGDEAALTRWVEARAALLR
+HLGRPRQAGLESQLGAALVRDPDTVEAAVLAGVVEDEPGAPGEDPGDTVLPEAALALAVH
+RVHTGDLDTALELTRRVIAVLGGLRAAGALLPIGSWSSAHLLLARLHLWRGEHAEADAAA
+AVVTVLPAARAVLASATTVRAIAAHELDRPTAALDLAFEAAERMASVGLRRGAASAAALA
+GRVAGDLDGYEEVAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRADEAEPLLARL
+VRREATHGRDVEQARALVDLGHAHHDQDRAENALPLWREAAGLFEAHGQWEDAARTLLAA
+GALVNRERDERTRPSALDLFERAVAAARQAVDEDPAVLPAALHAHGYLLCESGQAEGLDL
+LEEALALVRDAGADWQVADYTDTRARALWSLERGPEAIATALQAADLFTAAGDREGAAQA
+ELFAAYVVAEDGSPEQAATLFRLVCDSTDSTLVRLGALTGLHQCLSALGDHDGAARVRDE
+LDALREGLGAD
+>LFPAFLNI_01571
+MDTPQDPPHRDDPSGGPVEPAVDAALDRVRALLRQARGTAAPDAPTALDARGWWELSLEA
+ALRDEPRESARLADSGLAALGPGQDDVRLALLRALAVAAGQVGDEAALTRWVEARAALLR
+HLGRPRQAGLESQLGGALVRDPDTVEAAVLAGVVEDEPGAPGEDPGDTVLPEAALALAVH
+RVHTGDLDAALELARRVIAVLGGLRAAGALLPTGSWSSAHLLLARLHLWRGEHAEADAAA
+AVVTALPAARAVLASATTVRAIAAHELDRPTAALDLALEAAERMASVGLRRGAASAAALA
+GRVAGDLDGYEEVAVAAWELASVHAEKAEAPEASSLSYWWAHQLVLAGRADEAEPLLARL
+VRREATHGRDVEQARALVDLGHAHHDQDRAENALPLWREAAGLFEAHGQWEDAARTLLAA
+GALVNRERDERTRPSALDLFERAVAAARQAVDEDPAVLPAALHAHGYLLCESGQAEGLDL
+LEEALALVRYAGADWQVANYTDTRARALWSLERGPEAIATALQAADLFTAAGDREGAAQA
+ELFAAYVVAEDGSPEQAATLFRLVCDSTDSTLVRLGALTGLHQCLSALGDHDGAARVRDE
+LDALREGLGAD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000844.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000844.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7bd70a9393826e7d838e819d503c796859f31ea7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000844.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01255
+MSPTPVPDAEPARADAPAGPFQTRAGAYALIVDGGRVLLSSWQGPEHLVWTLPGGGIELG
+ESPEEACRREVWEETGHTAELTGLLGVTTGVIPAERRLRGEALPLLTVQVLYTARITGGV
+LRPEVGGSSTDARWFDLAGLDAVRTAPWVREALARAGAAA
+>MOLHKGIG_01640
+MSTTPAAPDAAGAHPAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIELGES
+PEEACLREVWEETGHTAELTGLLGVTTGTIPVEKRLRGEPLPLLTVQVLYTARITGGVLR
+PEVGGSSTDARWFDLAELSELRTASWVTEALARAGVDT
+>NAFOICDF_01164
+MSAASPTAASTAPGPFETRAGAYALIVEDGRVLMSAWAGPTGIVWTLPGGGIELGESPEE
+ACVREVEEETGHTAELTGLLGVTTGTIPVERRLRGEPLPLLTVQVLYTARLTGGVLRPEA
+DGSSVDAAWFALDGLADVRTSAWVDRALALAGLAADDAAGTAR
+>MHAAABBN_01345
+MSTTPAAPDAAGAHPAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIELGES
+PEEACLREVWEETGHTAELTGLLGVTTGTIPVERRLRGEPLPLLTVQVLYTARITGGVLR
+PEVGGSSTDARWFDLAELSGLRTASWVTEALARAGVAT
+>LFPAFLNI_01569
+MSTTPAAPDAAGAHPAGPFQTRAGAYALIVDGGRVLLSSWQGPEFLQWTLPGGGIELGES
+PEEACLREVWEETGHTAELTGLLGVTTGTIPVEKRLRGEPLPLLTVQVVYTARITGGVLR
+PEVGGSSTDARWFDLAELSELRTASWVTEALARAGVDT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000846.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000846.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71edbd941d22d6141e70cf475890958cf266b0fa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000846.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01257
+MPTPRPRQIRQSAKLLNVRYDVRGPILEEAQRMEAAGHRIMKLNIGNPAPFGFEAPDAIL
+QAMYRHLPHAQGYSDSQGIYSARTAVSQYYESRGIRDIGVEDVFIGNGVSEMISMVLQAL
+VDDGDEILVPSPDYPLWTGATTLAGGRAVHYRCVEEEGWAPDLEHIESLVTERTKGIVLI
+NPNNPTGAVYSRQILQGIIDVARRHGLVLMADEIYEKITYDGARHINAAGLSDDVLTLTF
+SGLSKAYRVAGFRSGWVAVSGPKHRARDFLEGLTLLANMRMCANVPAQHAIQVALGGYQS
+IDDLVLPGGRLLEQRNLAQKRLNDIPGVSVQPAQGALYLFPRLDPEVYAIEDDQEFVIDL
+LRAKKILVSHGGAFNYPHTDHFRLVTLPSVEDLDVALDRLEDFLEDWRERRG
+>MOLHKGIG_01638
+MPTPHPRQIRQSAKLLNVRYDVRGPILEEAQRMEAAGHRIMKLNIGNPAPFGFEAPDAVL
+AAMHQHLPHAQGYSDSKGIYSARTAVSQYYESRGIRDIGVDDVFIGNGVSEMITMVLQAL
+VDDGDEILVPSPDYPLWTGATTLAGGRAVHYRCVEEEGWEPDLEHIESLVTERTKGIVLI
+NPNNPTGAVYSRAVLQGIVDVARRHNLVLMADEIYEKITYDGARHINAAGLSDDVLTLTF
+SGLSKAYRVAGYRSGWVAVSGPKHRAADFLEGLTLLANMRMCANVPAQHAIQVALGGYQS
+INDLVLPGGRLLEQRNLAQDRLNAIPGVSVQPAHGALYLFPRLDPEVYAIDDDEAFVIEL
+LRAKKILVSHGGAFNYPHSDHFRLVTLPSVKDLDVALDRLEDFLEDWRERHG
+>NAFOICDF_01166
+MAPSTPREFRQSSKLLNVRYDVRGPILEEAQRMEAAGHRIMKLNIGNPAPFGFEAPDAIL
+QAMYQHLPHAQGYSDSKGIYSARTAVSQYYESRGIRDISVDDVFIGNGVSEMITMVLQAL
+VDDGDEILVPSPDYPLWTGATTLSGGRAVHYRCVEEEGWAPDLEHLESLITERTKGLVII
+NPNNPTGAVYSREVLNGVVDIARRHNLVLLADEIYEKITYDGARHINAAGLSDDVLTLTF
+SGLSKAYRVAGYRSGWVAVSGPKHRAKDFLEGLTLLSNMRMCANVPAQHAIQVALGGYQS
+IEDLILPGGRLLEQRNLAQKRLNDIPGVSVQPAHGALYLFPRLDPEVYAIDDDEKFVIEL
+LQAKKILVSHGGAFNYPQPDHFRLVTLPSVKDLDIALDRLEDFLEDWRERRG
+>MHAAABBN_01343
+MPTPHPRQIRQSAKLLNVRYDVRGPILEEAQRMEAAGHRIMKLNIGNPAPFGFEAPDAVL
+AAMHQHLPHAQGYSDSKGIYSARTAVSQYYESRGIRDIGVDDVFIGNGVSEMITMVLQAL
+VDDGDEILVPSPDYPLWTGATTLAGGRAVHYRCVEEEGWEPDLEHIESLVTERTKGIVLI
+NPNNPTGAVYSRAVLQGIVDVARRHNLVLMADEIYEKITYDGARHINAAGLSDDVLTLTF
+SGLSKAYRVAGYRSGWVAVSGPKHRAADFLEGLTLLANMRMCANVPAQHAIQVALGGYQS
+INDLVLPGGRLLEQRNLAQDRLNAIPGVSVQPAHGALYLFPRLDPEVYAIDDDEAFVIEL
+LRAKKILVSHGGAFNYPHSDHFRLVTLPSVKDLDVALDRLEDFLEDWRERHG
+>LFPAFLNI_01567
+MGGMPTPHPRQIRQSAKLLNVRYDVRGPILEEAQRMEAAGHRIMKLNIGNPAPFGFEAPD
+AVLAAMHQHLPHAQGYSDSKGIYSARTAVSQYYESRGIRDIGVDDVFIGNGVSEMITMVL
+QALVDDGDEILVPSPDYPLWTGATTLAGGRAVHYRCVEEEGWEPDLEHIESLVTERTKGI
+VLINPNNPTGAVYSRAVLQGIVDVARRHNLVLMADEIYEKITYDGARHINAAGLSDDVLT
+LTFSGLSKAYRVAGYRSGWVAVSGPKHRAADFLEGLTLLANMRMCANVPAQHAIQVALGG
+YQSINDLVLPGGRLLEQRNLAQDRLNAIPGVSVQPAHGALYLFPRLDPEVYAIDDDEAFV
+IELLRAKKILVSHGGAFNYPHSDHFRLVTLPSVKDLDVALDRLEDFLEDWRERHG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000851.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000851.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28114d34a88dad47939836539c2af43ef022d4e7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000851.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01263
+MGGMSAPSVSARPSAVGLGMPQVPRVRRTREDVEAAAPVSGDKRVLLAAPRGYCAGVDRA
+VVAVEKALEHHGAPVYVRKEIVHNRHVVDTLTERGVVFVEELDEIPEGALTVFSAHGVSP
+AVVQDAERRSLRTIDATCPLVTKVHREAVRFAKQDKQILLIGHEGHEEVEGTYGEAPEHT
+TVINDVAEARAVQVADPDNLIWLSQTTLSVDETLEIVAVLRERFPNLQDPPSDDICYATS
+NRQAAIKSISPECDLVIIVGSANSSNSVRLKEVAAEYGASRAERVDFASQVDESWFEGVS
+TVGLSSGASVPEVLIQDVLALLAEYGYGQVDEVVTAEEDIMFSLPKELRAELKRVGDDSR
+GLGGRRQTEG
+>MOLHKGIG_01632
+MEGMSAPSVSARPSAVGLGMPQVPRVRRSREEVEAAAPVSGEKRVLLAAPRGYCAGVDRA
+VVAVEKALEHHGAPVYVRKEIVHNRHVVDTLTERGVVFVDELDEVPEGALTVFSAHGVSP
+AVVEEAAQRNLRTIDATCPLVTKVHREAVRFAKQDKRILLIGHDGHEEVEGTFGEAPEHT
+TVINDVAEARTVQVEDPDNLIWLSQTTLSVDETLEIVSVLRERFPNLQDPPSDDICYATS
+NRQAAIKSISPECDLVIIVGSANSSNSVRLKEVAAEYGASRAERVDFANQVDESWFEGVA
+TVGLSSGASVPEVLVQEVLALLAEYGYGQVDEVVTAEEDIIFSLPKELRAEMKRVGDDGR
+ALGGRRRAAEA
+>NAFOICDF_01172
+MDGMSVPTASAPSTVGLGMPQVPRTRRSREEVEAAAPVAGDKRVLLAAPRGYCAGVDRAV
+VAVEKALEHHGAPVYVRKEIVHNRHVVDTLTERGAVFVQELDEVPAGALTVFSAHGVSPA
+VVAEAAERDLQTIDATCPLVTKVHREAVRFARQDKRILLIGHTGHEEVEGTYGEAPEHTT
+VINDVEEARTVQVDDPDNLIWLSQTTLSVDETLEIVAVLRERFPNLQDPPSDDICYATSN
+RQAAIKRISPQCDLVIIVGSANSSNSVRLKEVALEYGAARAERVDFASQVDESWFEGVAT
+VGLSSGASVPEVLVQDVLALLADYGYGQVEEVVTAEEDIIFSLPKELRAQLKQAGDEERS
+LGGRRRPAE
+>MHAAABBN_01337
+MEGMSAPSVSARPSAVGLGMPQVPRVRRSREEVEAAAPVSGEKRVLLAAPRGYCAGVDRA
+VVAVEKALEHHGAPVYVRKEIVHNRHVVDTLTERGVVFVDELDEVPEGALTVFSAHGVSP
+AVVEEAAQRNLRTIDATCPLVTKVHREAVRFAKQDKQILLIGHEGHEEVEGTFGEAPEHT
+TVINDVAEAQTIQVEDPDNLIWLSQTTLSVDETLEIVSVLRERFPNLQDPPSDDICYATS
+NRQAAIKSISPECDLVIIVGSANSSNSVRLKEVAAEYGASRAERVDFTNQVDESWFEGVA
+TVGLSSGASVPEVLVQEVLALLAEYGYGQVDEVVTAEEDIIFSLPKELRAELKRVGDESR
+SLGGRRRDAEA
+>LFPAFLNI_01561
+MSAPSVSARPSAVGLGMPQVPRVRRSREEVEAAAPVSGEKRVLLAAPRGYCAGVDRAVVA
+VEKALEHHGAPVYVRKEIVHNRHVVDTLTERGVVFVDELDEVPEGALTVFSAHGVSPAVV
+EEAAQRNLRTIDATCPLVTKVHREAVRFAKQDKQILLIGHEGHEEVEGTFGEAPEHTTVI
+NDVAEAQTIQVEDPDNLIWLSQTTLSVDETLEIVSVLRERFPNLQDPPSDDICYATSNRQ
+AAIKSISPECDLVIIVGSANSSNSVRLKEVAAEYGASRAERVDFANQVDESWFEGVATVG
+LSSGASVPEVLVQEVLALLAEYGYGQVDEVVTAEEDIIFSLPKELRAEMKRVGDDGRALG
+GRRRDAEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000855.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000855.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ac486175a15ccb8e9a970453fa2f738e1bb0e4e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000855.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01271
+MARPIDPFREMERPFREMERLVNGLTRTSGTASMPMNLFREGDRFVAEVELPGVDPASID
+VDVEERTLTVRAERKESPAGEDRRWLTRERSAGTFARQLTLGEGLALDRIEADYEDGVLT
+LTIPVAEQAKPRKISVKHSGAGAGAGQTVPGETAEVEERSAEQEAAQNGGAPQA
+>MOLHKGIG_01626
+MARPIDPFREMERLVNGLTPRATGTVSMPMNLYREGDVFVAEVELPGVDPASIDVDVEER
+TLTVRAERKEDPAREDRRWLTRERSAGTFARQLTLGEGLALDRIQADYSDGVLTLTIPVA
+EQAKPRKISVTHGGAAPVAGQTVEGETAETTGE
+>NAFOICDF_01181
+MARPIDPFREMERPFREMERLVNGLTTRATGTASMPMNLYREGDAFVAEVELPGVDPASI
+DVDVEERTLTIRAERKEAAASEGRQWLTRERSSGTFARQLTLGQGLALDRIEADYRDGVL
+VLSIPVAEQAKPRKIQVKHSAADQVEGQEVAGQESVQDSAAVEAPQQPSGE
+>MHAAABBN_01332
+MARPIDPFREMERLMTGFARTSGAASMPMNLYREGDVFVAEVELPGVDPSSIDVDVEERT
+LTVRAERKEAPAGEDRRWLTKERPAGTFARQLNLGQGLALDKIEADYSDGVLLLTIPVAE
+QAKPRKIQVKHTGSAAQVEGEAVEGEAVEGSAAEASGE
+>LFPAFLNI_01555
+MARPIDPFREMERLVNGLTPRATGTVSMPMNLYREGDVFVAEVELPGVDPASIDVDVEER
+TLTVRAERKEDPAREDRRWLTRERSAGTFARQLTLGEGLALDRIQADYSDGVLTLTIPVA
+EQAKPRKISVTHGGTAPVAGQTVEGETAETTGE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000856.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000856.fa
new file mode 100644
index 0000000000000000000000000000000000000000..72d1ce5f463e294aa29e26367621bf9dabe1232b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000856.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01286
+MSAADVPAGELVAGELTLTGRITTASNATFLGAIGDTSVVYKPVAGEAPLWDFPAGTLAR
+REVAAYLVSEALGWDIVPRTWLREGPFGEGMVQLWQEQDPEQDAVDLFPADEVPASGWLT
+ILEGEDEGGNRLALAHEDSAALRRMAVFDVLVNNADRKGAHILAMPGGHRYGVDHGLTFH
+VADKLRTVLWGWLGEALSEEERDGVARVLDGLDGELGRGLVQLLSAEEVEALAERCAQLL
+DDGVFPAPSGLTPAVPWPLF
+>MOLHKGIG_01612
+MSAADVPAGELMSGELTLTGRITTASNATFLGAIGDTPVVYKPVAGEAPLWDFPAATLAR
+REVAASLVSEALGWDIVPRTWLRDGPFGKGMVQLWQEQDPEQDAVDLFPADEVPASGWLT
+VLEGEDEGGNRLVLAHEDSAALRRMAVFDVLVNNADRKGAHILAMPGGHRHGVDHGLTFH
+VQDKLRTVLWGWLGEALSEEERDGVARVLDGLDGELGQGLAELLGAEEVEALAARCAQLL
+DDGIFPAPSGLTPAVPWPLF
+>NAFOICDF_01191
+MSAADVPAGELVDGELTLTGRITTASNATFLGAIGDTPVVYKPVAGEAPLWDFPAGTLAR
+REVAAHLVSEALGWEIVPRTWLRDGPFGEGMVQLWQEQDPEQDAVDLFPADEVPAAGWLT
+ILEGEDEEGRRLALAHENSAALRRMAVFDVIVNNADRKGAHILAMPGGHRYGVDHGLTFH
+VAGKLRTVLWGWLGEALSEEERDGVGRVLDGLDGELGRGLAELLSAEEVEALAERGARLL
+DDGIFPAPSGRTPAVPWPLF
+>MHAAABBN_01323
+MSAADVPAGELVAGELTLTGRITTASNATFLGAIGDTPVVYKPVAGEAPLWDFPAGTLAR
+REVAASLVSEALGWDIVPRTWLRDGPFGEGMVQLWQEQDPEQDAVDLFPAGQVPASGWLT
+ILEGEDADGNRLVLAHEDSAALRRMAVFDVIVNNADRKGAHILAMPGGHRHGVDHGLTFH
+VADKLRTVLWGWLGEELSEEERDGVGRVLDGLDGELGRGLAELLSAEEVQALAERSAGLL
+DDGRFPAPSGLTPAVPWPLF
+>LFPAFLNI_01538
+MSAADVPAGELVSGELTLTGRITTASNATFLGAVGDTPVVYKPVAGEAPLWDFPAGTLAR
+REVAAHLVSEALGWDVVPRTWLRDGPFGEGMVQLWQEQDPEQDAVDLFPADEVPASGWLT
+ILEGEDEDGNRLALAHEDSAALRRMAVFDVLVNNADRKGAHILAMPGGHRHGVDHGLTFH
+VEDKLRTVLWGWLGEALSDEERDGVARVLDGLDGELGRGLAELLSAVEIGALAERSAGLL
+DDGTFPAPSGLTPAVPWPLF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000857.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000857.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fe8e2e8901caea425d5f3111410be8040b0c0203
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000857.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01287
+MTESPAHVHEFDWPDRVVIGTIGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMLDEI
+LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLIDAHPLSD
+DDADPALEVDAEAVRVRMPVGAARAFARRTREVVDAGRPICSDCGQPIDPDGHDCTLPDS
+>MOLHKGIG_01611
+MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI
+LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLVDAHPLTD
+DDADPALEADAEAVRVRMPVGAARAFARRTREVVDAGRPVCSDCGQPIDPDGHDCTFPDS
+>NAFOICDF_01192
+MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI
+LDDLMALDGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLIDAHPLTD
+DDADPVLETDAEAVRVRMPVGAARAFARRTREVVDAGRPICSDCGQPIDPDGHDCTLPDS
+>MHAAABBN_01322
+MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI
+LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGGIGLGWDPTTAQVLIDAHPLSD
+DDADPALEADAEAVRVRMPVGAARAFARRTREVVDAGRPFCSDCGQPIDPDGHDCTLPDS
+>LFPAFLNI_01537
+MTDAPAPAHEFDWPDRVVIGTLGRPGARTFYLQVRTGPRLVSLALEKQQSALMAEMIDEI
+LDDLMALEGNPHSVPASTPVELVDNDPLDPVQEWFRVGAIGLGWDPTTAQVLIDAHPLSD
+DDADPALEADAEAVRVRMPVGAARAFARRTREVVDAGRPICSDCGQPIDPDGHDCTLPDS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000858.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000858.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6699fd4a26258ed2eadcf5bd4776ef12cf7fd8fa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000858.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01288
+MATVLLVRHGRTTANASGLLAGRTPGVSLDEHGREQAARTADRIAAVPVTAVVASPLERC
+AQTARALLDRQPGTVPSLVDDDLTECDYGQWQGRALSDLATEPLWATVQSRPSAVVFPGG
+ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGMHLDMFQRLDV
+GPASVSIVSYGSSRPRVLTVNTDAGDLSWLATKGPSGDAPVGGGAGTDPVADSANGRTPR
+IDA
+>MOLHKGIG_01610
+MATVLLVRHGRTTANATGLLAGRTPGVSLDDHGREQAARTGGRIAAVPVAAVVASPLERC
+AQTARALLDRQPGTVPSLVDDDLTECDYGQWQGRALSDLATEPLWATVQTQPSAVVFPGG
+ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGTHLDLFQRIEV
+GPASVSIVSYGPARPRVWAMNTDAGDLSWLATLGPSDDAPVGGGAGTGAGAVDERTPRIV
+A
+>NAFOICDF_01193
+MATVLLVRHGRTTANATGLLAGRTPGVSLDDHGREQAARTADRVAAVPVAAVVASPLERC
+AQTARALLDRQSGAVPSLVDDDLTECDYGQWQGRALSDLATEPLWATVQTQPSAVVFPGG
+ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGTHLDLFQRIEV
+GPASVSIVSYGPSRPRVWATNTDAGDLSWLSSLGPSDDAPVGGGAGTGPGAVDEQTPRIV
+T
+>MHAAABBN_01321
+MATVLLVRHGRTTANATGLLAGRTPGVSLDDHGREQAARTADRIAAVPVAAVVASPLERC
+AQTARALLDRQPGTVPSLVDDDLTECDYGQWQGRALSDLATESLWATVQTQPSAVVFPGG
+ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGTHLDLFQRIEV
+GPASVSIVSYGPARPRVWAMNTDAGDLSWLATLGPSDDAPVGGGAGTGTGAVDERTPRIV
+A
+>LFPAFLNI_01536
+MATVLLVRHGRTTANASGLLAGRTPGVSLDDHGREQAARTADRIATLPVAAVVASPLERC
+AQTARALLDRQPGTVPSLVDDDLTECDYGQWQGRALSDLATESLWATVQTQPSAVVFPGG
+ESMAGMQARAVAAIRRHDAAVEAEHGPGAVWVAVSHGDVIKSILADALGTHLDLFQRIEV
+GPASVSIVSYGPARPRVWAMNTDAGDLSWLATLGPSDDAPVGGGAGTGTGAVDEQTPRIV
+T
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000868.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000868.fa
new file mode 100644
index 0000000000000000000000000000000000000000..123e65d23e72568a9e9fe54e5810cf5fe7cd506d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000868.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_01333
+MRDMFVVLGPAPASVGSPGAWWAVDGDDATPLGSCPAGSVAGLVAGLPARLGVDPSTVRW
+VLADVGTEYAAWLAAGVRVDRCWDVALVQRILRHAATAPGSGVRYTPVAQLEVADPTEPE
+RPARVPAGQESFFDLPDGTGSAPDVTVLAAELAAQRAAVEGSAHPHRLRLLAAAESQGAL
+VAAEIRAAGLPWDRGVHEALLTEQLGPRPAQGERPARLQALAERIADVLGSPGLSPDSQP
+SLLRALQTAGVAVESTRQWDLKHWIDAGGAEREARAALLAPLLEYKALARLWTANGWHWL
+DQWIGDDGRFHAAYLVGGVVTGRWAAHGGGAMQIPAGVRDAVRADPGWALTVADASQVEP
+RILAAMAADEALARAGTTPDLYREVAEQGRAAGTALADRGRAKVALLGAMYGSTTGDSAA
+LMPHLRRLYPRAIGLLERAASVGEAGGQVATWLGRWSPAPEQAWLDSVADVGTQAAESAA
+RRRRRSQGRFTRNFVVQGTAAEWALCWMGEIRRRLRAAGLGTELVFFVHDEVVLHGPAPE
+AEAVRGVVAEAASAAGRLLFGAAPVDFPLTVASLDSYADAK
+>MOLHKGIG_01589
+MFVVLGPAPASVGSPGAWWALDGEGDGASPLGSCAAGSVAGLVAGLPARLGVDPSTVRWV
+LADVGTEYAAWLVAGVRVDRCWDLALVQRILRHAATAPGSGVRYTPVAQLEVADPTEPVR
+PARVPAGQESFFDLPDEAGPAPDVTVLAAELAAQRAAVEGSAHPHRLRLLAAAESQGALV
+AAEIRAAGLPWDRGVHEALLAEQLGPRPAPGERPARLQTLAERIADVLGSPGLSPDSQPS
+LLRALQTAGVAVESTRQWDLKHWIDAGGAEREARAALLAPLLEYKALARLWTANGWHWLD
+QWIGDDGRFHAAYLVGGVVTGRWAAHGGGAMQVPAGVRDAVRADPGWTLTVADASQVEPR
+ILAAMAADEALARAGTTPDLYREVAEQGRAAGTALADRGRAKIALLGAMYGSTTGDSAAL
+MPHLRRLYPRAIGLLERAASVGEGGGQVSTWLGRWSPAPGRKWQESVSDVGTQAAESAAR
+RRRRSQGRFTRNFVVQGTAAEWALCWMGEIRRRLRSAGMRTELVFFVHDEVVLHGPATEV
+EAVRTVVAESASAAGRLLFGPAPVDFPLTVSSVGSYADAK
+>NAFOICDF_01231
+MVIVLGPDPAPGTPPGRWCALVLPDDAAPSPADASPGQGDGGPVARFARDELADVVRALP
+GRLGVDPAVVRWTVADAAEVYPALLAAGVRWDRCRDLSLGQRILRGAAAAGLAYAPTVDL
+PVHEPEAEDPATARRAPGQGAMFELAGPEPAPDAAALARELAAQQAAVAASAHPHRLRLL
+LAAESQGALVAAEMHHAGLPWRADVHEALLAEQLGPRPPEGARPARLQALGERVAAALGS
+PGLNPDSPPALLRALQTAGVTVDSTRKWELTAWADQGGAQRQAREALIAPLLEYKALYRL
+WTAHGWHWLDTWARDGRFRPTYLVGGVVTGRWAAHGGGAMQVPSGVRDAVRADPGHVLTV
+ADASQVEPRILAAMSRDAALAAAGATPDLYREVAEQGRSAGTALDDRSRAKVALLGAMYG
+ATTGDSAALLPHLRRLYPAALAMLEAAAADGEAGRPVHTWLGRTSPAPAERWLERVADRS
+TREAEARARSLRRSAGRFTRNFVVQGTAAEWALCWMGQIRGGLHRAGLSTALVFFVHDEV
+VLHGPAEEAGAVARIVTEAASQAGRLLFGAAPVDFPLTVAQVESYAQAK
+>MHAAABBN_01300
+MRAMFVVLGPAPASVGSPGTWWALDGEGDDAVPLGSCAAGSVAGLVAGLPARLGVDPSTV
+RWVLADVGTEYAAWLAAGVRVDRCWDLALVQRILRHAATAPGSGVRYTPVAQLEVADPTE
+PERPARVPAGQESFFDLPDEADPAPDVTVLAAELAAQRAAVEGSAHPQRLRLLAAAESQG
+ALVAAEIRAAGLPWDRGVHEALLAEQLGPRPAPGERPARLQALAERIADVLGSPGLSPDS
+QPSLLRALQTAGVAVESTRQWDLKHWIDAGGAEREARAALLAPLLEYKALARLWTANGWH
+WLDQWIGDDGRFHAAYLVGGVVTGRWAAHGGGAMQIPAGVRDAVRADSGWTLTVADASQV
+EPRILAAMAADQALARAGTTPDLYREVAEQGRAAGTALADRGRAKIALLGAMYGSTTGDS
+AALMPHLRRLYPRAIGLLERAASVGEGGGQVSTWLGRWSPAPGPTWQESVSDVGTQAAES
+AARRRRRSQGRFTRNFVVQGTAAEWALCWMGEIRRRMRSAGMRTELVFFVHDEVVLHGPA
+TEAEAVRTVVAESASAAGRLLFGPAPVDFPLTVSSVGSYADAK
+>LFPAFLNI_01516
+MFVVLGPAPASVGSPGAWWALDGEGDGASPLGSCAAGSVAGLVAGLPARLGVDPSTVRWV
+LADVGTEYAAWLVAGVRVDRCWDLALVQRILRHAATAPGSGVRYTPVAQLEVADPTEPVR
+PARVPAGQESFFDLPDEAGPAPDVTVLAAELAAQRAAVEGSAHPHRLRLLAAAESQGALV
+AAEIRAAGLPWDRGVHEALLAEQLGPRPAPGERPARLQTLAERIADVLGSPGLSPDSQPS
+LLRALQTTGVAVESTRQWDLKHWIDAGGAEREARAALLAPLLEYKALARLWTANGWHWLD
+QWIGDDGRFHAAYLVGGVVTGRWAAHGGGAMQVPAGVRDAVRADPGWTLTVADASQVEPR
+ILAAMAADEALARAGTTPDLYREVAEQGRAAGTALADRGRAKIALLGAMYGSTTGDSAAL
+MPHLRRLYPRAIGLLERAASVGEGGGQVSTWLGRWSPAPGRKWQESVSDVGTQAAESAAR
+RRRRSQGRFTRNFVVQGTAAEWALCWMGEIRRRLRSAGMRTELVFFVHDEVVLHGPATEA
+EAVRTVVAESASAAGRLLFGPAPVDFPLTVSSVGSYADAK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000872.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000872.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b2a1aa59babe75bbbc7541db655999d76896d6eb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000872.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01345
+MPAPEARVTVAVSTAVFGVRPDPSGAPRLHVALVPRMREPFLDRWALPGTWLAADEELAD
+AAARVAAETVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPALDDDGAAPSHGGGLD
+VAGLPAGVHVRWQRADAPPAMAFDHAEILTAAVARLRADLPRAGVAHALLGPSFTLAELR
+AVHEAVLGRTLDAANFRRATLATGVLEETGEVRAGTRHRPPKLYRYRPADGAPPPAAPDD
+PGDLS
+>MOLHKGIG_01578
+MPVAEARVSVAVSTAVFGVRPDPHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD
+VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPVLDDDGAAPASRPDPD
+VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR
+AVHEAVLGRGLDAANFRRATLAAGTLEETGEVRGGTPHRPPKLYRYRPAGPGTDPDPAGP
+DARR
+>NAFOICDF_01238
+MPVAEARVSVAVSTAVFGVRPDAHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD
+VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPTLDDDGAAPASRPDPD
+VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR
+AVHEAVLGRGLDAANFRRATLAAGTLEETGEVRDGTPHRPPKLYRYRPAGPGTDPNPAGP
+DASR
+>MHAAABBN_01288
+MPVAEARVSVAVSTAVFGVRPDPHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD
+VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPALDDDGAAPASSPDPD
+VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR
+AVHEAVLGRGLDAANFRRATLAAGALEETGEVRGGTPHRPPKLYRYRPAGPGTDPDPAGP
+DARR
+>LFPAFLNI_01505
+MPVAEARVSVAVSTAVFGVRPDPHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD
+VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPALDDDGAAPASSPDPD
+VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR
+AVHEAVLGRGLDAANFRRATLAAGTLEETGEVRGGTPHRPPKLYRYRPAGPGTDPDPAGP
+DARR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000874.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000874.fa
new file mode 100644
index 0000000000000000000000000000000000000000..321d111d3628e6860e042989b29469f18e5c4069
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000874.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01348
+MSGLVALLDDVAALARLAAASVDDVAAGAAKASAKAAGVVVDDAAVTPQYMAGAAANREL
+PMIWRITKGSLRNKLLIILPALLLLDWLAPWVLPWLLLAGGTYLAYEGAHKVWGKLTGHS
+PERDEPAVEKGPEAEDKVVRGAITTDFILSAEIMVISMNEVADVDFWLKAVILVVVAILI
+TAVVYGAVALIVKMDDVGLHMTQNGRTAGGRRFGAGLVKAMPHVLTAITVIGTVAMLWVG
+GHIVLVELAALGVPWPYDVQHGIVHAVEAAGGFVAWLVETLTSALWGLIWGSLALGVVLV
+VNRLRGKKDTLAH
+>MOLHKGIG_01576
+MVGLVALLDDVAALARLAAASVDDVAAGAGRAAAKAAGVVVDDAAVTPQYMAGAAAAREL
+PMIWRITKGSLRNKLVFILPALLLLDWLAPWILPWLLLAGGTYLSYEGAHKVWGKLTGHG
+HADDEEPAVERGPEAEDTVVRGAITTDFILSLEIMVISMNEVADLGFWMQAAVLAVVAVL
+ITVGVYGAVGLIVKMDDVGLHLHQNASTSGGRSFGAGLVKAMPHVLRVVTVIGTVAMLWV
+GGHIALVELDALGVPWPYAVQHGIVEPVTHAAGAFLGWLTETATSAVWGLLWGSVALGVV
+LLVGRLRGNKAAPAH
+>NAFOICDF_01241
+MSGLVALLDDVAALARLAAASVDDVAAGAAKASAKAAGVVVDDAAVTPQYMEGAAAQREL
+PMILRIVRGSLRNKLVFILPGLLLLDWLAPWALPWLLLAGGTYLSFEGAEKVWHKLTGHH
+EPQEDTPAVEQGPEAEDKVVRGAITTDFILSLEIMVISMNEVSDQGFWMKAAILAIVAVV
+ITVAVYGAVALIVKMDDVGLHMHENAHTSGARRFGLGLVKAMPVVMGVISVIGTVAMLWV
+GGHIVLMELATLGLPWLYELQHTIVHAVEGAGSVIAWLVETLTSAIWGLVWGSLVVAVVG
+LVRRLRT
+>MHAAABBN_01286
+MVGLVALLDDVAALARLAAASVDDVAAGAGRAAAKAAGVVVDDAAVTPQYMAGAAAAREL
+PMIWRITKGSLRNKLVFILPALLLLDWLAPWILPWLLLAGGTYLSYEGAHKVWGKLTGHG
+HADDEEPAVERGPEAEETVVRGAITTDFILSLEIMVISMNEVADLGFWMQAAVLAVVAVL
+ITVGVYGAVGLIVKMDDVGLHLHQNASTSGGRSFGAGLVKAMPHVLRVVTVIGTVAMLWV
+GGHIALVELDALGVPWPYAVQHGIVEPVTHAAGAFLGWLTDTATSAVWGLLWGSVALGVV
+LLVGRLRGKKAAPAH
+>LFPAFLNI_01503
+MVGLVALLDDVAALARLAAASVDDVAAGAGRAAAKAAGVVVDDAAVTPQYMAGAAAAREL
+PMIWRITKGSLRNKLVFILPALLLLDWLAPWILPWLLLAGGTYLSYEGAHKVWGKLTGHG
+HADDEEPAVERGPEAEDTVVRGAITTDFILSLEIMVISMNEVADLGFWMQAAVLAVVAVL
+ITVGVYGAVGLIVKMDDVGLHLHQNASTSGGRSFGAGLVKAMPHVLRVVTVIGTVAMLWV
+GGHIALVELDALGVPWPYAVQHGIVEPVTHAAGAFLGWLTDTATSAVWGLLWGSVALGVV
+LLVGRLRGKKAAPAH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000877.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000877.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fecc58f93d8729caa958f9ed52253d6f40c3ce2b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000877.fa
@@ -0,0 +1,31 @@
+>ACLBLIBL_01351
+MRTPMTSNVTDTALLFEGGGMRASLTSAVVAELLRERIHVDFVAGISAGSSNSVNYLARD
+PERARRSFVDFADDPRFGNWLSFVRGKGLFNAEYIYEHAGLPEADLPYDFATFQANPARL
+VLVGFDAVTGQTRWWDRSDMGTLADLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG
+IPVTAAEEAGFEKLFVVMTRERSYVKRPERFPAFYQRTFRRYPAVAEALISRWRRYNETR
+ERLFEMERQGRAYLFVPESMPVSNGERSVAKLAAAHELGLAQVRREMPAIREFLGL
+>MOLHKGIG_01573
+MTEPMTSNVTDTALLFEGGGMRAALTSAVVAELLRERIHVDFVAGISAGSSNAVNYLSRD
+PARARRSFVDFADDPRFGNWLSFVRGKGLFNAEYIYEHAGLPEADLPYDFATFRANPARL
+VLGGFDAASGETRWWDRSDMTTLTDLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG
+IPLTAAEDAGFEKVLVVLTRERGYVKRPERFPSFYQRTFRRYPAVADALLTRWRRYNATR
+ERLFEMERQGRAYLFAPETMPIANGERSVAKLAAAHELGLDQVRREMPAIRAFLGLPASR
+>NAFOICDF_01244
+MAEQQDHTAEALTSNVTDTALLFEGGGMRASHTSAVVAELLRAGVHVDFVAGISAGSSNA
+VNYLARDPLRARQAFVDFADDPRFGNWRTFLRGKGMFNAEYIYEHAGLPEADLPYDFAAY
+RANPARLALAGFDAVTGETRWWGREDMTTLQDLMVRVRASSTMPILMPPVHLEDTVYVDG
+ALGVDGGIPVTAAEEAGLAKLLVVMTRERSYVKRPERFPAFYQRAFRRYPAVAEALVTRW
+QRYNATRERLFEMEREGTAYLFVPEVMPVSNGERSVAKLAAAHELGLAQARREMPAIKEF
+LGL
+>MHAAABBN_01283
+MTEPMTSNVTDTALLFEGGGMRAALTSAVVAELLRERIHVDFVAGISAGSSNAVNYLSRD
+PARARRSFVDFADDPRFGNWLSFVRGKGLFNAEYIYEHAGLPEADLPYDFATFRANPARL
+VLGGFDAASGETRWWDRSDMTTLTDLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG
+IPLTAAEDAGFEKVLVVLTRERGYVKRPERFPSFYQRTFRRYPAVADALLTRWRRYNATR
+ERLFEMERQGRAYLFVPATMPISNGERSVAKLAAAHELGLDQVRREMPAIRAFLGLPASR
+>LFPAFLNI_01500
+MTEPMTSNVTDTALLFEGGGMRAALTSAVVAELLRERIHVDFVAGISAGSSNAVNYLSRD
+PARARRSFVDFADDPRFGNWLSFLRGKGLFNAEYIYEHAGLPEADLPYDFAAFRANPARL
+VLGGFDAASGETRWWDRSDMTTLTDLMVRVRASSTMPVLMPPVHAEGTVFVDGALGVDGG
+IPLTAAEDAGFKKVLVVLTRERGYVKRPERFPSFYQRTFRRYPAVADALLTRWRRYNATR
+ERLFEMERQGRAYLFAPETMPIANGERSVAKLAAAHELGLDQVRREMPAIRAFLGLPASR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000880.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000880.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0568ef0c646da7e2c0957c12d8dccb8fcd866b31
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000880.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01354
+MDPLWIALALTAFAGLATVLGGVLAVVGKEPSGRGLGAALGLAAGVMIAVSFLEMLPVAV
+EGLAGAVGGAATALAVGALAVGTAGYVLLERAVPVPAAGVPDDVDGPDGLSRLRLMRLGM
+VTALAIGLHNVPEGFVTFAGALQDPSVGVALAVAMAVHNVPEGIAVAVPVRRATGSRRKA
+FAWTAFTGLAEPVGALVGWLLLAPFLTPALVAVVFAAVTGVMITVSLDALLPAARAAGGR
+AATLAGVLLGVAAMAISLDLLG
+>MOLHKGIG_01570
+MDPFWTALALTTFAGLATVLGGVLAIVGREPSGRGLGAALGLAAGVMLAVSFLEMLPAAV
+EGLGGAVGPAATAVAVAALILGAGSYVLLERAVPDPVSEMPGDVDDPAGLDRRRMLRLGT
+VTALAIGLHNLPEGFVTFAGTLQDPSVGLALAVAMAVHNVPEGVAVAVPVRQATGSRRKA
+FAWAAFTGIAEPLGALIGWLLLAPFLTPALLAAVFAAVAGVMVTVSLDALLPAARAAGGR
+AAALGGVLLGVAAMALSLDLLS
+>NAFOICDF_01247
+MEPFWTAVALTSLAGAATIVGGALGALGRPVSDRALAAALGLAAGVMLTVGAVEMGPAAA
+RGLATAVGDGPGVLAAGAAVGGGALAYLLIDRLLPEAATPSGSSASAAREARVGRLGVAT
+ALAIGAHNLPEGFVTFAGALEDSAVGLALAVAMAVHNVPEGIAVSVPVRRATGSARTGFL
+WAATAGILEPAGALLGYWLLRPLLTDAVLGGVYGAVTGVMAALSLAALLPGAVRCGGVPT
+ALAGAAAGAAAMLGSLSLLA
+>MHAAABBN_01280
+MDPFWTALALTTFAGLATVLGGVLAIVGREPSGRGLGAALGLSAGVMLAVSFLEMLPAAV
+EGLGGAVGPAATAVAVAALALGAGAYVLLERAVPDPVSEMPGDVDDPAGLDRRRMLRLGT
+VTALAIGLHNLPEGFVTFAGTLQDPSVGLALAVAMAVHNVPEGVAVAVPVRQATGSRCKA
+FAWAAFTGIAEPLGALIGWLLLAPFLTPALVAAVFAAVAGVMVTVSLDALLPAARAAGGR
+GAALGGVLLGVAAMALSLDLLA
+>LFPAFLNI_01497
+MDPFWTALALTTFAGLATVLGGVLAIVGREPSGRGLGAALGLAAGVMLAVSFLEMLPASV
+EGLGGAVGPAATAVAVAALTLGAGSYVLLERAVPDPVSEMPGDVDDPAGLDRRRMLRLGT
+VTALAIGLHNLPEGFVTFAGTLQDPSVGLALAVAMAVHNVPEGVAVAVPVRQATGSRRKA
+FAWAAFTGIAEPLGALIGWLLLAPFLTPALLAAVFAAVAGVMVTVSLDALLPAARAAGGR
+AAALGGVLLGVAAMALSLDLLS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000882.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000882.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c1a1ebd378fe8409305e08abfe50a77a29b4474
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000882.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_01359
+MLKFILKRLGSSLLVLFGASILLFFLVAHSGDPLQDLRESQNPNRETLIAARTEFMGLDQ
+PWYARYWDWLQGIGGCVTGQCDLGLSRNGQSVGDLLSSAAASTLRLVVLATVLAIIIGIA
+IGIVTAIRQYSGLDYVVTFLIFLFFSLPVFWAAVLLKEYMGIRFNDWIRSPELNWPLLIG
+VAVLAGLVLQAVMAGDLRRRAFTFGATAAFILLAGWVLFAVDFWRHPQMGPVVQLVIGLA
+AAVGATAVISGLRNRSVLKAALVTVAIGLVAYYATYGLLWRTPSALLLAGLGVILVLVAI
+LVGRLLGGFSKGSAVSASLVTALIMGVAIVAEHLMNYWPTFLKVKPRPISTIGSGTPNLD
+AHFWVVFLDRGAQLLLPTILLTIISVATYSRYTRSSMLEVSRQDYIRTARAKGLSERQVI
+LKHAFRNSLIPITTIMAFDFAGLIGGAVITEQVFGWKGMGELFATGLRDVDPMPVMAFFL
+VTGTAAVLMNLVADVLYAVLDPRIRV
+>MOLHKGIG_01567
+MLKFILKRLGSSLLVLFGASILLFFLVAHSGDPLQDLRESQNPNRETLIAARTAFMGLDQ
+PWYARYWDWLQGIGGCVTGQCDLGLSRNGQSVADLLSNAAASTLRLVVLATVLAIIIGIA
+IGIVTAIRQYSGLDYVVTFLIFLFFSLPVFWAAVLLKEYMGIRFNDWIRSPELNWPLLIG
+VAVLAGLVLQAVMAGDLRRRAFTFGATAAFILLAGWVLFAVDFWRHPQMGPVVQLVIGLA
+AAVGATAVISGLRNRSVLKAALVTVAIGLVAYYATYGLLWRTPSALLLAGLGVILVLVAI
+LVGRLLGGFSKGSAVSASLVTALIMGVAIVAEHLMNYWPTFLKVKPRPISTIGSGTPNLD
+AHFWVVFLDRGAQLLLPTILLTIISVATYSRYTRSSMLEVSRQDYIRTARAKGLPERQVI
+LKHAFRNSLIPITTIMAFDFAGLIGGAVITEQVFGWKGMGELFATGLRDVDPMPVMAFFL
+VTGTAAVLMNLVADVLYAVLDPRIRV
+>NAFOICDF_01250
+MLKFILRRLGSSALVLFGASILLYVLTVNSGDPLKDLRESQASNREQLMQARIDYMGLDD
+PWYERYWNWLTGVVKYLIGAGTLGTDRSGVQVESLLGNAAASTLRLVVLATVLAIVIGVA
+IGIITAIRQYSGLDYAVTFLIFLFFSLPVFWAAVLLKEYLAIGFNNWIARPTMDWPLVIG
+LAVVLGLALQAAMGGRLVRRLLTFAATVAVIVLGGYLLFALDMWRNPRMGPLVQLLIGLA
+VAVGGTALVAGLKNRSVLKAALATVAVGVVAYYATYGVLMQSPSGWLIAGLGVIAVLVGV
+LAGRLLGGFSKGSAVSVSVVTALVMGLSILAEHMMNYWPQLLKAKPRPIATIGAETPNLT
+GHFWVLFLDKGTQLLLPTVLLTIISVATYSRYTRSSMLEVSRQDYIRTARAKGLGERQVI
+LKHAFRNSLIPITTIMAFDFAGLIGGAVITESVFGWKGMGELFRTGLDQVDPAPVMAFFL
+VTGTAAVLMNLVADILYAVLDPRIRV
+>MHAAABBN_01277
+MLKFILKRLGSSLLVLFGASILLFFLVAHSGDPLQDLRESQNPNRETLIAARTAFMGLDQ
+PWYARYWDWLQGIGGCVTGQCDLGLSRNGQSVADLLSNAAASTLRLVVLATVLAIIIGIA
+IGIVTAIRQYSGLDYVVTFLIFLFFSLPVFWAAVLLKEYMGIRFNDWIRSPELNWPLLIG
+VAVLAGLVLQAVMAGDLRRRAFTFGATAAFILLAGWVLFAVDFWRHPQMGPVVQLVIGLA
+AAVGATAVISGLRNRSVLKAALVTVAIGLVAYYATYGLLWRTPSALLLAGLGVILVLVAI
+LVGRLLGGFSKGSAVSASLVTALIMGVAIVAEHLMNYWPTFLKVKPRPISTIGSGTPNLD
+AHFWVVFLDRGAQLLLPTILLTIISVATYSRYTRSSMLEVSRQDYIRTARAKGLPERQVI
+LKHAFRNSLIPITTIMAFDFAGLIGGAVITEQVFGWKGMGELFATGLRDVDPMPVMAFFL
+VTGTAAVLMNLVADVLYAVLDPRIRV
+>LFPAFLNI_01494
+MLKFILKRLGSSLLVLFGASILLFFLVAHSGDPLQDLRESQNPNRETLIAARTEFMGLDQ
+PWYARYWDWLQGIGGCVTGQCDLGLSRNGQSVGDLLSNAAASTLRLVVLATVLAIIIGIA
+IGIITAIRQYSGLDYVVTFLIFLFFSLPVFWAAVLLKEYMGIRFNDWIRSPELNWPLLIG
+VAVLAGLVLQAVMAGDLRRRAFTFGATAAFILLAGWVLFAVDFWRHPQMGPVVQLVIGLA
+AAVGATAVISGLRNRSVLKAALVTAAIGLVAYYATYGLLWRTPSALLLAGLGVILVLVAI
+LVGRLLGGFSKGSAVSASLVTALIMGVAIVAEHLMNYWPTFLKVKPRPISTIGSGTPNLD
+AHFWVVFLDRGAQLLLPTILLTIISVATYSRYTRSSMLEVSRQDYIRTARAKGLPERQVI
+LKHAFRNSLIPITTIMAFDFAGLIGGAVITEQVFGWKGMGELFATGLRDVDPMPVMAFFL
+VTGTAAVLMNLVADVLYAVLDPRIRV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000883.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000883.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a376e8a49d3e8e3465d910f670029c7054633f6b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000883.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01360
+MTTNNSSTTGAQLDEKQIFDLAEAEDAKLRVKAGKSYSQGALVRKRFFRHKAAMISLIVL
+VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD
+TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSVLMRLTDLIIVI
+PLLVLAAVLGQMASGANMGILPLALVLGLVTWTSLARLVRGEVLSLREKEFVAAAVAMGA
+KPGRVIGKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISLYQNS
+FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGAAAGRKRGLFSRRAAKTDAGAT
+TAGGLGTAPTARDGEADDLIADPDAPEHRRGGAGGPAGGVGQ
+>MOLHKGIG_01566
+MTTNNSSMTGAQLDEKQIFDLAEAEDAKLRAKAGKSYSQGALVRKRFFRHRAAMISLIVL
+VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD
+TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSLLMRLTDLIIVI
+PLLVLAAVLGQMASGMKMGILPLAVVLGLVSWTSLARLVRGEVLSLREKEFVAAAVAMGA
+KPGRLIFKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISDYQNA
+FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGGGAHRRLRFFGRRAAATEAGAT
+TAGGLAAAPTAGRIEAPVEEAGGSARISDADEDGQR
+>NAFOICDF_01251
+MTMSHSAQQNPRSTSPAVVDLAEAEDLKLQQKTGKSYSQGALIRMRFFRHKAAMVSLVVL
+AFIALMAFTSIGFAGIPGWWDESYSAASTVVDGGRPTLSVVPQFLGGEGLRWGAHPFGQT
+STGTDFFALVMRGTQQSLIIAFIVGLISTAIGALVGAASAYFGGWVDSVLMRLTDLIIVI
+PLLVLAAVLGKMAGGLQLGILPLAFVLGIVSWTSLARLVRGEILSLREKEFVAAAVAMGA
+KPGRIIGKHLLPNTIGVIVVNATFAIAGAVLLETSLSYLGFGVKSPDSSLGLLISDYQTA
+FTTRPWLFWWPGMTILAIALSVNFLGDGLRDAFDPRQSGSGRRKRGLFSRRAAVTEATPT
+TAGGLQASPASAPAGHADVVTDSRGLDAPAAWTVTDADGTSRPAGDDVDTTEGDAR
+>MHAAABBN_01276
+MTTNNSSMTGAQLDEKQIFDLAEAEDAKLRAKAGKSYSQGALVRKRFFRHRAAMISLIVL
+VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD
+TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSVLMRLTDLIIVI
+PLLVLAAVLGQMASGMKMGILPLAVVLGLVSWTSLARLVRGEVLSLREKEFVAAAVAMGA
+KPGRLIFKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISDYQNA
+FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGAGAHRRPRFFGRRAAATEAGAT
+TAGGLAAAPTAGRIEAPVEAAGGSARISDADEDGQR
+>LFPAFLNI_01493
+MTTNNSSTTGAQLDEKQIFDLAEAEDAKLRAKAGKSYSQGALVRKRFFRHKAAMISLIVL
+VFITLMAFSSIGFAGIPGWWDKSYTAAASVVNGGRPTLSVVPQAFGGEGLRWGEHPFGQD
+TTGKDYFALVMRGTQQSMIIAAIVGLLSTVIGAIVGAVSGYFGGWVDSVLMRLTDLIIVI
+PLLVLAAVLGQMASGMKMGILPLAVVLGLVSWTSLARLVRGEVLSLREKEFVAAAVAMGA
+KPGRLIFKHLLPNTIGVIVVNATFAIAGAVLLETSLSFLGFGVKAPDSSLGLLISDYQNA
+FTTRPWLFWWPGMIILAIALSVNFLGDGLRDAFDPRQGAGAHRRPRFFGRRAAATEAGAT
+TAGGLAAAPTAGRIEAPVEEAGGSARISDADEDGQR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000885.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000885.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1025962a1c6120b28585b6f146d0d719dc9755ee
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000885.fa
@@ -0,0 +1,60 @@
+>ACLBLIBL_01362
+MTSTDTRRSDLRNVAIVAHVDHGKTTLVDAMLRQGGAFAAHGEVAERVMDSGDLEREKGI
+TILAKNTTVFYSGPSAPEGQTVTFNVIDTPGHADFGGEVERGLSMVDGVVLLVDSSEGPL
+PQTRFVLRKALAAKLPVILVVNKTDRPDARIDGVVSDSMDLLLGLASDLADEVEDLDLDS
+VLNLPVVFASGKAGRASLNQPEDGSLPDSEDLEPLFATMMEHIPAPAYTKGEVLQAHVTN
+LDASPFLGRLALLRIFNGTLKKGQQVAWARQDGTLKTVKITELLGTKGLSREPIEEAGPG
+EIVAVAGIEDIMIGETLTDVENPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ
+VKDRLDAELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTK
+TVDGKVHEPMELMTIDTPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFSVPARGLIG
+FRTQFLTDTRGAGIASSIANGYEPWAGTIEYRNNGSLVADRAGTATPFAMINLQERGSFF
+IQPGSEVYEGMIVGENSRADDMDVNITKEKKLTNMRAASSDSFEGLTPPRQLTLEESLEF
+AREDECVEITPEDIRIRKVVLDANERLKAARARARA
+>MOLHKGIG_01564
+MTSTETRRSDLRNVAIVAHVDHGKTTLVDAMLRQTGAFNTHGDVAERVMDSGDLEKEKGI
+TILAKNTTVFYSGPSAPEGETVTINVIDTPGHADFGGEVERGLSMVDGVVLLVDSSEGPL
+PQTRFVLRKALAAKLPVILVVNKTDRPDARIDGVVSDSMDLLLGLASDLAEEDPDLDLDS
+VLDVPVVYASGKAGRASLTQPADGALPEAEDLEALFNVIMEHIPAPSYTEGEVLQAHVTN
+LDASPFLGRLALLRIFNGTLRKGQQVAWARQDGALKTVKITELLATKGLERVPAEEAGPG
+EIVAVAGIEDIMIGETLTDAENPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ
+VKDRLDKELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTR
+TVDGKVHEPMERMTIDIPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFLVPARGLIG
+FRTRFLTETRGAGIASSYAAGYEPWTGEIEYRTNGSLVADRAGSATPFAMINLQERGTFF
+VQPGAEVYEGMIVGENSRADDMDVNITKEKKLTNMRAASSESFEGLTPPRRLTLEESLEF
+AREDECVEITPEDIRIRKVVLDANERLKAARARARA
+>NAFOICDF_01253
+MTSTDTRRSDLRNVAIVAHVDHGKTTLVDAMLRQTGAFNTHGDVAERVMDSGDLEKEKGI
+TILAKNTTVFYSGPSAPEGETVTINVIDTPGHADFGGEVERGLSMVDGVVLLVDASEGPL
+PQTRFVLRKALAAKLPVVLVVNKTDRPDARIDGVVSDSMDLLLGLASDLAEEDPELDLDS
+VLDVPVVYASGKAGRASREQPGDGALPDSEDLEPLFNVIMEHIPAPVYDESEVLQAHVTN
+LDASPFLGRLALVRIVNGTLKKGQTVAWARQDGQLKSVKITELLATKGLERVPADEAGAG
+EIVAVAGIEDIMIGETLTDLEDPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ
+VKDRLDKELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTK
+QIDGKLHEPMERMTIDIPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFLVPARGLIG
+FRTRFLTDTRGAGIASSEAAGYEPWTGDIEYRTNGSLVADRAGTATPFAMINLQERGTFF
+IQPGAEVYEGMIVGENARADDMDVNITKEKKLTNMRAASSESFEGLTPPRTLTLEESLEF
+AREDECVEITPEDIRIRKVVLDANERLKAARARARA
+>MHAAABBN_01274
+MTSTETRRSDLRNVAIVAHVDHGKTTMVDAMLRQTGAFNTHGDVAERVMDSGDLEKEKGI
+TILAKNTTVFYSGPSAPEGETVTINVIDTPGHADFGGEVERGLSMVDGVVLLVDSSEGPL
+PQTRFVLRKALAAKLPVILVVNKTDRPDARIDGVVSDSMDLLLGLASDLAEEDPDLDLDS
+VLDVPVVYASGKAGRASLTQPADGALPEAEDLEALFNVIMEHIPAPSYTEGEVLQAHVTN
+LDASPFLGRLALLRIFNGTLRKGQQVAWARQDGALKTVKITELLATKGLGRVPAEEAGPG
+EIVAVAGIEDIMIGETLTDAENPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ
+VKDRLDKELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTR
+TVDGKVHEPMERMTIDIPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFLVPARGLIG
+FRTRFLTETRGAGIASSYAAGYEPWTGEIEYRTNGSLVADRAGSATPFAMINLQERGTFF
+VQPGAEVYEGMIVGENSRADDMDVNITKEKKLTNMRAASSESFEGLTPPRRLTLEESLEF
+AREDECVEITPEDIRIRKVVLDANERLKAARARARA
+>LFPAFLNI_01491
+MTSTETRRSDLRNVAIVAHVDHGKTTMVDAMLRQTGAFNTHGDVAERVMDSGDLEKEKGI
+TILAKNTTVFYSGPSAPEGETVTINVIDTPGHADFGGEVERGLSMVDGVVLLVDSSEGPL
+PQTRFVLRKALAAKLPVILVVNKTDRPDARIDGVVSDSMDLLLGLASDLAEEDPDLDLDS
+VLDVPVVYASGKAGRASLTQPADGALPEAEDLEALFNVIMEHIPAPSYTEGEVLQAHVTN
+LDASPFLGRLALLRIFNGTLRKGQQVAWARQDGALKTVKITELLATKGLERVPAEEAGPG
+EIVAVAGIEDIMIGETLTDAENPKPLPLITVDDPAISMTVGINTSPLAGRVKGAKVTARQ
+VKDRLDKELIGNVSLKVLPTERPDAWEVQGRGELALAILVEQMRREGFELTVGKPQVVTR
+TVDGKVHEPMERMTIDIPEEFMGAVTQLMAARKGRMQEMSNHGTGWIRMEFLVPARGLIG
+FRTRFLTETRGAGIASSYAAGYEPWTGEIEYRTNGSLVADRAGTATPFAMINLQERGTFF
+VQPGAEVYEGMIVGENSRADDMDVNITKEKKLTNMRAASSESFEGLTPPRRLTLEESLEF
+AREDECVEITPEDIRIRKVVLDANERLKAARARARA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000888.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000888.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ddf27785cbffe89901bf17f603fb857c28e8ed9f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000888.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_01366
+MTQNESVRLTVGEQSLDLGVERATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTF
+IDGDEGILRYRGYAIEDLAANSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL
+KLFFNGFPRDAHPMPVLSSSVSGLSTFYPDSLDPHDPEQVHISTVRLLGKLPVLASYAFK
+KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYEIDPDVVKALDLLLMLHADHEQNASTST
+VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRTIQSDGIKPEDFMEKVKNKED
+GVRLMGFGHRVYKNYDPRAKIIKKTAEDILSKMGGNDELLEIAQRLEEKALADDYFVERK
+LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPATKIGRPRQIYVGE
+PLRQYPQR
+>MOLHKGIG_01560
+MTHHESVRLTVGEQSLDLGVEHATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTF
+IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL
+KLFFNGFPRDAHPMPVLSSSVSALSTFYPDSLDPHDQEQVHISTVRLLGKLPVLASYAFK
+KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYDIDPDVVKALDLLLMLHADHEQNASTST
+VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRKIKSEGITPEDFMEKVKNKED
+GVRLMGFGHRVYKNYDPRAKIIKKTAEDILGKMGGNDELLEIAQRLEEKALADDYFVERK
+LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPAAKIGRPRQIYVGE
+QLRQYPQR
+>NAFOICDF_01257
+MSEIESARLTVGEKTLDLGVEKAAEGNDGIVVAPLLKETGKVTYDPGFMNTANAKSAITY
+IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKEALEAWETNILRHNMVHEDL
+KMFFNGFPRDAHPMPVLSSSVSALSTFYADSLDPKDPEQVHISTVRLLGKLPVLASYAFK
+KSLGQPFMYPHNNLNYVENFLRLCFGVPAEEYEIDPDMVKALDLLLMLHADHEQNASTST
+VRLVGSTDANLFASVSAGINALYGPLHGGANEAVLNMLRRIQAEGIKPEDFMEKVKHKED
+GVRLMGFGHRVYKNYDPRAKIVKKTAEDILAKLGGNDELLEIAMRLEEKALADDYFVERR
+LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELTEDPATKIGRPRQIYVGE
+QLRQYPQR
+>MHAAABBN_01270
+MTHHESVRLTVGEQSLDLGVEHATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTY
+IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL
+KLFFNGFPRDAHPMPVLSSSVSALSTFYPDSLDPHDPEQVHISTVRLLGKLPVLASYAFK
+KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYDIDPDVVKALDLLLMLHADHEQNASTST
+VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRKIKSEGITPEDFMEKVKNKED
+GVRLMGFGHRVYKNYDPRAKIIKKTAEDILGKMGGNDELLEIAQRLEEKALADDYFVERK
+LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPATKIGRPRQIYVGE
+QLRQYPQR
+>LFPAFLNI_01487
+MTHHESVRLTVGEQSLDLGVEHATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTF
+IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL
+KLFFNGFPRDAHPMPVLSSSVSGLSTFYPDSLDPHDPEQVHISTVRLLGKLPVLASYAFK
+KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYDIDPDVVKALDLLLMLHADHEQNASTST
+VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRKIKSEGITPEDFMEKVKNKED
+GVRLMGFGHRVYKNYDPRAKIIKKTAEDILGKMGGNDELLEIAQRLEEKALADDYFVERK
+LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPATKIGRPRQIYVGE
+QLRQYPQR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000889.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000889.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d7f64b06bbf8a894f5181ad36df311afbc27bcf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000889.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01367
+MTETAAQHPSARLVSGHGLATTAADGTVLDVWFPAPVAGPLADADATLAETLRSLAADDA
+DRGTTQSVVELEADLDAAPATAEDAWLRLHALSHRLVRPNELNLDGVFGLLANVVWTNFG
+PCAVEGFELTRARLRARGAVNVYGVDKFPRMTDYVVPTGVRIGDADRVRLGAHLAEGTTV
+MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDLGGGVSIMGTLSGGGTQKVVIGEHVLL
+GANSGVGISIGDDCVVEAGLYVTAGALVTVVRPGEEPRTVKAVELSGVPNLLFRRNSATG
+VVEVLPRAGRTVELNAALHAN
+>MOLHKGIG_01558
+MTQTAAQQPSSRLVSGHGLATTAADGAVLDVWFPAPVAGPLSAADASLRDTLRALAADDA
+DRGTTQAVVELEVDLDAAPASTADAWLRLHALSHRLTRPNELNLDGVFGLLTNVVWTNHG
+PCAVADFELTRARLRARGAVQVYGVDKFPRMTDYVVPSGVRIGDADRVRLGAHLAEGTTV
+MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTQRIVIGEHVLL
+GANSGVGISVGDDCVVEAGLYVTAGTRVSVLQDGEAAHTVKAVDLSGVPNLLFRRNSTTG
+GVEALPRAGRTVELNAALHAN
+>NAFOICDF_01258
+MTDTSQTSSARLVSGHGLATRAADGAVLDVWFPAPVTGPLASADASLAGTLEGLAAADAD
+RGTTQDIVALEADLDVAPASAEDAWLRLHALSHRLVRPNELNLDGVFGLLTNVVWTNFGP
+CAVEGFEATRAKLRARGAVNVYGVDKFPRMTDYVVPTGVRIGDADRVRLGAHLAEGTTVM
+HEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDLGGGVSIMGTLSGGGTQKVVIGEHVLLG
+ANSGVGISIGDDSVVEAGLYVTAGTVVTVVEPGRKPRTVKAVELSGVTNLLFRRNSVTGG
+VEVLPRDGRTVALNAELHAN
+>MHAAABBN_01268
+MTQTAAQQPSPRLVSGHGLATTAADGAVLDVWFPTPVAGPLSAADASLRDTLRALAADDA
+DRGTTQAVVELEVDLDAAPASTADAWLRLHALSHRLARPNELNLDGVFGLLTNVVWTNHG
+PCAVADFELTRARLRARGAVQVYGVDKFPRMTDYVVPSGVRIGDADRVRLGAHLAEGTTV
+MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTQRIVIGEHVLL
+GANSGVGISVGDDCVVEAGLYVTAGTRVSVLQDGEAARTVKAVDLSGVPNLLFRRNSTTG
+GVEALPRAGRTVELNAALHAN
+>LFPAFLNI_01485
+MTQTAAQQPSSRLVSGHGLATTAADGAVLDVWFPAPVAGPLSAADASLRDTLRALAADDA
+DRGTTQAVVELEVDLDAAPASTADAWLRLHALSHRLTRPNELNLDGVFGLLTNVVWTNHG
+PCAVADFELTRARLRARGAVQVYGVDKFPRMTDYVVPSGVRIGDADRVRLGAHLAEGTTV
+MHEGFVNFNAGTLGHSMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTQRIVIGEHVLL
+GANSGVGISVGDDCVVEAGLYVTAGTRVSVLQDGEAARTVKAVDLSGVPNLLFRRNSTTG
+GVEALPRAGRTVELNAALHAN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000896.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000896.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a104efdd807049468e5693e038b639dd3c093f44
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000896.fa
@@ -0,0 +1,18 @@
+>ACLBLIBL_01374
+MSTPLWIAVIAALVVVVAALAAAAAGRLTLRAGEPAGQAPVHPVALPERPRADDVAFVRL
+AVAVPGYQRDQVDAVLLRLRDALADHEDEVAALRARLAELEADAARDAERTGPR
+>MOLHKGIG_01551
+MRAPLGGEGRRVSGPQWIVLVAVLVVVLAALAAALAGRLTLRADDPAGRTPGHPVLLPER
+PRAADVDLLRLAVAVPGYQRDQVDAVLLRLRDALAQCEDEVTALRARVAELEAADPSRSD
+PAGRA
+>NAFOICDF_01265
+MTQPIWIAVLVVAVVAVAALAAAALGRALPRPADPAGQAPPHPVLLPEHPRAADVDRLRL
+ATAVPGYQRDQVDEVLARLRAALAADEERIAALEARLGEGDGVGR
+>MHAAABBN_01261
+MRAPLGGEGRRVSGPQGIVLVAVLVVVLAALAAALAGRLTLRADDPAGRTPGHPVLLPER
+PRAADVDLLRLAVAVPGYQRDQVDAVLLRLRDALAQREDEVTALRARVAELEAADPSRSD
+PAGRA
+>LFPAFLNI_01478
+MRAPLGGEGRRVSGPQGIVLVAVLVVVLGALAASLAGRLTLRADDPAGRTPGHPVLLPER
+PRAADVDLLRLAVAVPGYQRDQVDAVLLRLRDALAQREDEAAALRARLAELEAADPSRSD
+PAARA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000898.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000898.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a3b2221e44570630df272700089b07b37ace354
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000898.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01377
+MGRGHTLRHLDAYLEDALPSASRRRIARHLDGCPDCRAAVRARARVLDAARTVHQRPAGV
+VASPVLRSRGISGRVVVGLLAFVVLVGGLLAAVWMAGAPRAGVARLAPSPTDAVGLVSGG
+SADGRAAVAQLRGHGWTVPSLLGAGLEPLTVDAAQTPRDVEVVVGWGLQEPTVTVRECRP
+RIAGAAPEGCASAAPLPEDAQERTLTGGDVYRIQPAEADGAWTAELTTAQAAYRVEARLP
+DERADAVLTHLLVSERSRVRELGGPDAVEERLERGIERIVESVPRVRD
+>MOLHKGIG_01548
+MGRRHTQRHMDAYLEGSLPAASRARIARHLDRCPECRATVQARARVLDAARTVHQRPAGA
+VVAPVLRARGVSGRLVVGLLTFVVLLGGLFTAVWVAGAPRTAAVRTAPTPTDTVALPAAG
+TASTDRRGTVAELRGQGWTVPSLVGAGLEPLTVDTAQTAEDVEVVVGWGRDEPTVTVREC
+RPRIVGATPKGCASTAPLSTGVQERRLAGGGVYRIVPAGEQDGWTAELTTPQAAYRVEAS
+LPDERADAVLTHLLVSERARVLELGGGDAVEERLERGLERIADAVPRPRG
+>NAFOICDF_01268
+MGVLARGHCLPVLDSYLEGVLAPRASRRVEAHLSRCPDCRAVAGQRARVLDAARSVDARP
+AAGAVMRPRGVSGRAVVCGLLVLVVLAGLVAAVWMLGGPASTAAPADVDPVRAVSAPVSA
+SADEDDVATRVDELRGQGWALPSLSASGMRPLSVHADRVGEAAEVSVAWGRTSPVVTVRE
+CRGADADERTRCARQGGVGVSGASEARLPVGMDYRIADHADGGWEAWLSTSDAVYRVDAS
+VPRSQAEALLSQLVVVERSGLAPPRRDEDPRDRLERGLDRLLDGRVGGAAVRNPAAGAR
+>MHAAABBN_01258
+MGRRHTQRHMDAYLEGSLPAASRARIARHLDRCPECRATVQARARVLDAARTVHQRPAGA
+VVAPVLRARGVSGRLVVGLLTFVVLLGGLFTAVWVAGAPRTAAVRTAPTPTDTVALPAAG
+TASTDRRGTVAELRGQGWTVPSLVGAGLEPLTVDTAQTAEDVEVVVGWGRDEPTVTVREC
+RPRIVGATPKGCASTAPLSTGVQERRLAGGGVYRIVPAGEQDGWTAELTTPQASYRVEAS
+LPDERADAVLTHLLVSERARVLELGGGDAVEERLERGLERIADAVPRPRG
+>LFPAFLNI_01475
+MGRRHTQRHMDAYLEGSLPAASRARIARHLDRCPECRATVQARARVLDAARTVHQRPAGA
+VVAPVLRARGVSGRLVVGLLTFVVLLGGLFTAVWVAGAPRTAALRTAPTPTDTVALPAAG
+TASTDRRGTVAELRGQGWTVPSLVGAGLEPLTVDTAQTAEDVEVVVGWGRDEPTVTVREC
+RPRIVGAAPEGCASTAPLSTGAQERRLAGGGVYRIVPAGEQDGWTAELTTPQAAYRVEAS
+LPDERADAVLTHLLVSERARVLELGGGDAVEERLERGLERIADAVPRPRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000901.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000901.fa
new file mode 100644
index 0000000000000000000000000000000000000000..183ae3a633c40aa807c8f993d35622e674162f78
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000901.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01380
+MSQTSRDARPSRGTGLDTPLSASGRRVPRLAPNPDAFGEATEGIARFMGTPQFLVWMTLF
+CAAWLGWNTFGPEDLRFDSAALGFTALTLMLSLQASYAAPLLLLAQNRQDDRDKVALRED
+RDRAERNLADTEFLTREISGLRLAVQEVATRDFVRGELRGVQEDLRDELREALRAELREE
+IRAELRAELAEGRRERTDPGAEPRPRKQKKHKGRDRGRDERRAGDDGVDPSTTTLAVIAA
+REAAQAAQSAQAGQDAGPEAGRAVDGRDDADGAAR
+>MOLHKGIG_01545
+MTQTARDLRPGRGTGLDTPLSASGRRVPRLAPNPDAFGEATEGIARFMGTPQFLVWMTLF
+CAAWLGWNTFGPMEWRFDSAELGFTALTLMLSLQASYAAPLLLLAQNRQDDRDRVALRED
+RDRAERNLADTEFLTREIAGLRLAVQEVATRDFVRGELRGVQDDLRDDLREALRAELREE
+IREEIREELRAGLPGAEAQPRKNKKTKGRGRDARRGDAGAEPTTTTLATLAAQEAREAGG
+SGPAAGPADGAGPVDGGGR
+>NAFOICDF_01271
+MPQSPRDPRDTRATGLDTPMRARERVMPRLTPNPDAFGEWTEGIARFMGTPQFLLWMTLF
+CLVWVGWNSYAPEPWRFDSAALGFTALTLMLSLQASYAAPLLLLAQNRQDDRDKVALRED
+RDRAERNLADTEFLTREISGLRIALQDMATRDYVRGELRAMNEDLVAALREVVREEVREE
+LRAEEAGPAVAPKPKEKSKKKSSRREPGRPDGTEAHTTTLAIIAAQEAADQGGAAPDAAH
+AADDAGQDAP
+>MHAAABBN_01255
+MTQTARDLRPGRGTGLDTPLSASGRRVPRLAPNPDAFGEATEGIARFMGTPQFLVWMTLF
+CAAWLGWNTFGPMEWRFDSAELGFTALTLMLSLQASYAAPLLLLAQNRQDDRDRVALRED
+RDRAERNLADTEFLTREIAGLRLAVQEVATRDFVRGELRGVQDDLRDDLREALRAELREE
+IREEIREELRAGLPGAEAQPRKNKKTKGRGRDARRGDAGAEPTTTTLATLAAQEAREAGG
+SGPAAGPADGAGPVDGGGR
+>LFPAFLNI_01472
+MTQTARYLRPGRGTGLDTPLSASGRRVPRLAPNPDAFGEATEGIARFMGTPQFLVWMTLF
+CAAWLGWNTFGPMAWRFDSAELGFTALTLMLSLQASYAAPLLLLAQNRQDDRDKVALRED
+RDRAERNLADTEFLTREIAGLRLAVQEVATRDFVRGELRGVQDDLRDDLREALRAELREE
+IREEIREELRAGLPGAEAQPRKNKKTKGRGRDARRGDAGAEPTTTTLATLAAQEAQEARE
+AGGSGPVTGPAGGAGPVDGGGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000904.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000904.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9a627f5bae471274f3fe5f9472be567b2d8064ba
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000904.fa
@@ -0,0 +1,59 @@
+>ACLBLIBL_01383
+MDIDLTTELTALRDRLLSAEAEHADLISRVRDRHRASARNLVHYVALRGTDLRPLQDALS
+DVGLSSLGRMEAGVLGHVDAVLAAARALDGEDAPSPDDDALTPARGREILARDADRLLGP
+ARPDRAARIMVTLPSEAAQDPDLVARMAEAGMDLARVNCAHDDEAAWAAMIEAVRACATP
+ERPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPARTPAGLVTEPSRVWLAAAGAADAPAGA
+VVVPVTEAGAEVLAGLAAGDEVELTDARGSHHVLTVEQAGAAGALVRADKTVYWGTGLAV
+DTPRGTLTVGELAPLEQSMRVRRRDQVVLTRSLDPVPAASAPPYRIGLTLAQAFEDVAVG
+DRVSIDDGKIDAVVRAANADEITLEVTEAGPNGTKLKAEKGVNFPDTALSIPALTDEDLA
+HIPFVARHADMVNLSFVRSAEDVAQLIDALAAEDATDVDITLKIETVGAFEQLPRMLLEA
+MRWRDVGVMIARGDLAVEAGFERMAELQEEILWLCEAAHVPAIWATQILESLAKTGLPSR
+AEITDAAMAQRAEAAMLNKGPYIEEAITALGDILGRMGGHARKKRDMLRRLESWSL
+>MOLHKGIG_01542
+MGIDLTTELTALRDRLLSAEAEHADLISRVRDRHRASARNLVHYVALRGTDLRPLQEALS
+DAGLSSLGRMEAGVLGHVDAVLAAARALDGDLATAPEDDALTSAEGRAILARNAASLLGP
+ARGDRDARIMVTMPSEAATDPELVARIAEAGMDLARVNCAHDDEQAWAAMIAAVRRCAGA
+GRPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPARDPSGIVTEPSRVWLAAGPHDAVAVAD
+RPDGAVVVPLAAPDGKTLAGLQRGDEIELTDARGAHRRLEVERVSGEGVLVRADKTVYWA
+TGTALTTPHGPLEVGPLPPLEQSMRVHEGEQIVLTRSLEPVPAVDTPPYRIGLTLAQAFA
+DATVGDRVSLDDGRIGTRITGVSDDEITLEVTQAGPRGAKLKAEKGVNFPDTHLDIPALT
+DEDLAHIPFAARHADMVNMSFVRSAEDVAQLIDALEAEDAPDVDITLKIETVEAFRQLPR
+MLLEAMRWRDVGVMIARGDLAVEAGFARMAELQEEILWLCEAAHVPAIWATQVLESLAKT
+GLPSRAEITDAAMAQRAEAAMLNKGPYIDRAVTVLGDILGRMHGHASKKRDMLRRLESWS
+L
+>NAFOICDF_01274
+MSTLPENAPDSRPTAESPVVAPGAAVTELIEAIDALRARIVAAEQAHAERLDRVADRHRA
+SARNLVHYVTLRGEDLRPLQDALSAVGLSSLGRMEAGVLGHLDAVRTALHPLGGRPAPDP
+ADDDPLSPAEGRALLAANAESLLGPSRPGRETRIMVTMPSEAATNAALVQGMADAGMDLA
+RVNAAHDGEAAWAAMVANIRGVARDGGRPAPRICMDLAGPKLRTGPLEPGPGVVKVKPRR
+DVDGTVLERSRVWLGEADAPEAADAVVLPLDPAGSGHSPVLSALRPGDHAMLTDARDSDR
+TLHVLAATEAGVLLACRKTVYWHTGLEVDTPRGTLVVGALPSVPQAMRVHAGDEIVLTRS
+MDPRPAVSEGPFTIGCSLPQAFQDVRPGERVLIDDGKITGEVVSNDGEAITLTVTEAGPT
+GAKLRAEKGVNFPDTDLRLPALTDEDRSHLPFAAAHADVVNMSFVRSPADVAALIDALDA
+EDARGVGVSLKIETVGAFERLPAMLLEAMRWNDVGVMIARGDLAVEAGFERMAELQEEIL
+WLCEAAHVPAVWATQILETLAKQGLPSRAEITDAAMAQRAEAAMLNKGPYIDEAIGALSD
+ILTRMGGHADKKRDMLRRLRSWSL
+>MHAAABBN_01252
+MGIDLTTELTALRDRLLSAEAEHADLISRVRERHRASARNLVHYVALRGTDLRPLQEALS
+DAGLSSLGRMEAGVLGHVDAVLAAARALDGDPAPAPEDDALTSAEGRAILARNAASLLGP
+ARGDRDARIMVTMPSEAATDPELVARIAEAGMDLARVNCAHDDEQAWAAMIAAVRRCAGA
+GLPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPARDPSGIVTEPSRVWLAAGPHDAVATAD
+RPDGAVVVPLADPEGTTLAVLQRGDEIELTDARGAHRRLEVEQVDGEGVLVRAEKTVYWA
+TGTALTTPHGPLEVGPLPPLEQSMRVHEGEEIVLARSLEPVPAVDTPPYRIGLTLAQAFA
+DAAVGDRVSLDDGRIGARITAVSADEITLEVTQAGPRGAKLKAEKGVNFPDTHLAIPALT
+DEDLAHIPFAARHADMVNMSFVRSAEDVAQLIDALEAEDAPDVDITLKIETVEAFRQLPR
+MLLEAMRWRDVGVMIARGDLAVEAGFARMAELQEEILWLCEAAHVPAIWATQVLESLAKT
+GLPSRAEITDAAMAQRAEAAMLNKGPYIDRAVTVLGDILGRMHGHASKKRDMLRRLESWS
+L
+>LFPAFLNI_01469
+MGIDLTTELTALRDRLLSAEAEHADLISRVRERHRASARNLVHYVALRGTDLRPLQEALS
+DAGLSSLGRMEAGVLGHVDAVLAAARALDGDPAPAPEDDALTSAEGRAILARNAASLLGP
+ARGDRDARIMVTMPSEAATDPELVARIAEAGMDLARVNCAHDDEQAWAAMIAAVRRCAGA
+GRPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPTRDPSGTVTEPSRVWLAAGPHDAVAAAD
+RPDGAVVVPLADPEGTTLAVLQRGDEIELTDARGAHRRLEVEQVDGEGVLVRAEKTVYWA
+TGTALTTPHGPLEVGPLPPLEQSMRVHEGEQIVLTRSLEPVPAVDTPPYRIGLTLAQAFA
+DATVGDRVSLDDGRIGTRITGVSDDEITLEVTQAGPRGAKLKAEKGVNFPDTHLDIPALT
+DEDLAHIPFAARHADMVNMSFVRSAEDVAQLIDALEAEDAPDVDITLKIETVEAFRQLPR
+MLLEAMRWRDVGVMIARGDLAVEAGFARMAELQEEILWLCEAAHVPAIWATQVLESLAKT
+GLPSRAEITDAAMAQRAEAAMLNKGPYIDRAVTVLGDILGRMHGHASKKRDMLRRLESWS
+L
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000907.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000907.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08001515b463e63809b5453eb7f212847037f666
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000907.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_01387
+MPHRAVALRGRPDPALIERLAALRTELELPAGFPPEVLEEADAAARDVLAALASDPAYAD
+RTDVPFVTVDPAGSTDLDQALYLEAADGDAITVRYAIADVPAFVAPGGAVDVEARRRGQT
+VYLPDGRVPLHPEALSEDAASLLPDRERPAFVWTFVLDAAGAVVDTSLERARIRSRAQLT
+YAQVQAFLDALPDAKAPAAPRPGLDEADHAAHRGWDAPLRDSLALLPEVGRRRAAQEAAR
+GGASLNLPDQEVHVAEDGRHCLVQRAPLPAEDHNAQLSLMTGMAAARLMLEAGVGILRTM
+PAPDAEAVAAFRSRTRALGAPWEEGQDYGAYLRTLDPADPGHLAVLHEATSLFRGAGYTA
+FDAHAEDPELRTPPSEPEQAALAAPYAHATAPLRRLVDRFVLALCHAHATGAPAPEWARA
+ALPEVPALMTESSRRTSAADRAATDLVEAAALQDHVCAELEGIAVRRVKGGAEVWLLDPA
+VTLRVPGEAEPGTRVRVRIEGVDRASGEVTASGVDWPHSSR
+>MOLHKGIG_01538
+MTPHALGLRGPADPTLLERLAALRTELELPPAFPAPVLAEAEAAAREVHAGLTGSPDHAD
+RTALPFVTVDPAGSTDLDQALLLTPADDDGILVRYAIADVPAFVTPGGAVDGEARRRGQT
+VYLPDGRVPLHPEVLSEDAASLLPDREHPAFVWTFLLDAAGAVVETGLERARIRSRAQLT
+YGQVQAFLDAQPGAQAPTTPRPGVTDADRAAAEGWPAEVRDSLALLPEVGRRRAAQEAAR
+GGASLNLPDQEVRVTEDGAHELVHRAPLPAEEHNAQLSLLTGMAAAELMLAAGVGILRTM
+PAPDTDAVAAFRERTRALGAPWDEGQDYGAYLRSLDPADARHLAVLHAATGLFRGAGYTA
+FDAQAEDPALRTPPDEPAQAALAAPYAHATAPLRRLVDRFVLALCHAHAIGAPAPAWVRS
+ALPALPALMADSSRRASAASRTAADLVEAAALESRVGAELEGIAVREAKDGTEVWLLDPA
+VSLRVPGSVPAGTRVRVRIEGVDRASGAITAAGVDWPHSSR
+>NAFOICDF_01278
+MPHHALEVRGGPDAALAARLRALRAELDVPGEFPADVLTEAERAAAEVPGRVAADPDRAD
+LTAVPFVTVDPAGSTDLDQALHLQAGPGRDELTVRYAIADVPGFVAPEGAVDAEARRRGQ
+TVYLPDGRVPLHPEVLSEDAASLLPEVERPTFVWTFVLDAEGAVASTDLVRARIRSRAQL
+AYPQVQALLDDDAAPEAADWPAEVRASLALLPEVGARRTAQEAARGGASLSMPDQEISVV
+DGAYTLVQRVPLAAEDHNAQLSLMTGMAAARIMLEAGVGILRTMPAPDPDAVDAFRARTR
+ALGLPWGEELDYGAYLRTVDPTDPRGLAVMHAATTLFRGAGYTAFDRGSVDPALRALPED
+PEQAALAAPYAHTTAPLRRLVDRFVLVLCHAHVAGEPVPDWVRRALPDLPALMAESGRRA
+SAADRAATDLVEAALLAARVGSVLEGTAVRTSEKGTDVQLTDPAVSLRVPGRAEPGTVVR
+VRVDAVDVAAGKVTASGVDWPHSAR
+>MHAAABBN_01248
+MSSHALGLRGPADPALLERLAALRTELELPSAFPTPVLAEAEAAAHGVHVGLAGSPDHAD
+RTALPFVTVDPAGATDLDQALLLTPSDDDGILVRYAIADVPAFVAPGGAVDAEARRRGQT
+VYLPDGRVPLHPEVLSEDAASLLPDRERPAFVWTFLLDAAGAVVETGLERARVRSRAQLT
+YGQVQAFLDARPGAQAPATPRPGVTDADRAAAEGWPAEVRDSLALLPEVGRRRAAQEAAR
+GGASLNLPDQEVLVTEDGAHELVHRAPLPAEEHNAQLSLLTGMAAAELMLAAGVGILRTM
+PAPDADAVAAFRERTRALGVPWDEGQDYGAYLRSLDPADARHLAVLHAATGLFRGAGYTA
+FDAQAEDPALRTPPAEPAQAALAAPYAHATAPLRRLVDRFVLALCHAHASGAPAPAWVRS
+ALPELPALMADSSRRASAASRTAADLVEAAALESRVGAELEGIAVREAKDGTEVWLLDPA
+VSLRVPGSVPAGTRVRVRIEGVDRASGAITAAGVDWSHSSR
+>LFPAFLNI_01465
+MSSHALGLRGPADPALLERLAALRTELELPSAFPTPVLAEAEAAAHGVHVGLAGSPDHAD
+RTALPFVTVDPAGATDLDQALLLTPSDDDGILVRYAIADVPAFVAPGGAVDAEARRRGQT
+VYLPDGRVPLHPEVLSEDAASLLPDRERPAFVWTFLLDAAGAVVETGLERARIRSRAQLT
+YGQVQAFLDAQPGAQAPTTPRPGVTDADRAAAEGWPAEVRDSLALLPEVGRRRAAQEAAR
+GGASLNLPDQEVRVTEDGAHELVHRAPLPAEEHNAQLSLLTGMAAAELMLAAGVGILRTM
+PAPDTDAVAAFRERTRALGAPWDEGQDYGAYLRSLDPADARHLAVLHAATGLFRGAGYTA
+FDAQAEDPALRTPPDEPAQAALAAPYAHATAPLRRLVDRFVLALCHAHAIGAPAPAWVRS
+ALPALPALMADSSRRASAASRTAADLVEAAALESRVGAELEGIAVREAKDGTEVWLLDPA
+VSLRVPGSVPAGTRVRVRIEGVDRASGAITAAGVDWPHSSR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000910.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000910.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b6c8979dad6113189c146afb1981b4153ac09b75
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000910.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_01390
+MADVVTVFSLVASHQHLDLDTVARLSAGATGVGPALPGSGAAGAVVLATCNRVEIYAEAD
+ESGVEAAREGLVAAVAAHSSLPDEAVRSAFRVLDSEATARHLFEVGAGLDSAVVGEREIA
+GQVRRALSMARESGTASGSLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLTEELRG
+LADDDAKAAFWADASVLLIGTGAYAGTTLAQLAERGATAVAVHSASGRAEQFVEDRGGWA
+LALGGGAVAGAVAEADVIIGSSGGERQISPERLQELREDVDRPLTVVDLALSRDFDPAVG
+DLPDVDLITLESVRLAAPEQARAAVAEARVLVDGAVAEYRAAQRGRSADASIKALRRHTL
+AALDREMERVRARHGCTAAAEEVEFALRRMVNQLLHEPIVRAKRLAAEGRLDRYEDGLEA
+VFGIEPPGSTSSPAERPDAGCPAHEDEAGTARIA
+>MOLHKGIG_01535
+MTVFSLVASHHDLDLDTVARLSAGATGVGPALPGSGAAGAVVLATCNRVEIYAEADAAGV
+EAARAGLLSAVAASTSLPDEDVHAAFRTLDADATARHLFEVGAGLDSAVVGEREIAGQVR
+RALTAAQEAGTASGPLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLAEELRGLTDA
+AAQRDFWAGATILLIGTGAYAGTTLAQLADRGATTVGVHSASGRAEQFVADRGGWALALG
+GEAVAGAVAEADVIIGSSGGERQISPERLQELRKGGRRPLTVVDLALSRDFDPAVADLPD
+VDLITLESVRLAAPEQAQVAVAEARALVDDAVEEYRAAQRGRSADAAIKALRRHTLGVLD
+RELERVRARHGCTAAAEEVEFALRRMVNQLLHEPSVRAKRLAAEGRLDRYEDALEAVFGI
+EAPGRPAPAVGTVEAVCPAHEDEGGAARIA
+>NAFOICDF_01281
+MDVAVTVFSLVASHKDLSLDTVARLSAGSAGVGSALASSTDDGAVVLATCNRVEVYADAR
+DADAARERIVAAIAEQSGLPEDAVRSAFRVLDDDASARHLFEVGAGLDSAVVGEREIAGQ
+VRRALVDARDAGTATGSLTRLFESATRTAKDVGSHTALGATGRSVVSVALDLAEELRGLT
+DAMARRTFWQEANVLLIGTGAYAGTTLAQLADRGAQAVGVHSASGRAAQFVADRGGWALA
+LGGADVAGAVAEADVIIGSSGGDRQISPERMAGLRRGAERPVTVVDLALSRDFDPAVGEL
+EGVDLITLESVRLAAPEQAQAAVAEARGLVETALEEYTSARRGRTADAAIKALRGHTMAA
+LDREMERVRARHGCTAAADEVQFALRRMVNQLLHTPSVRARELAAQGRLDEFEHALEVLF
+DIPVPGTRPADAPGDACPATEADDARRTA
+>MHAAABBN_01245
+MTVFSLVASHHDLDLDTVARLSAGATGVGPALPGSGAAGAVVLATCNRVEIYAEADAAGV
+EAARAGLLSAVAASTSLPDEDVHTAFRTLDADATARHLFEVGAGLDSAVVGEREIAGQVR
+RALTAAQEAGTASGPLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLAEELRGLTDA
+AAQRDFWAGATILLIGTGAYAGTTLAQLADRGATTVGVHSASGRAEQFVADRGGWALALG
+GEAVAGAVAEADVIIGSSGGERQISPERLQELRKGGRRPLTVVDLALSRDFDPAVADLPD
+VDLITLESVRLAAPEQAQVAVAEARALVDDAVEEYRAAQRGRSADAAIKALRRHTLGVLD
+RELERVRARHGCTAAAEEVEFALRRMVNQLLHEPSVRAKRLAAEGRLDRYEDALEAVFGI
+EAPGRPAPAVGTVEAACPAHEDDGGAARIA
+>LFPAFLNI_01462
+MTVFSLVASHHDLDLDTVARLSAGATGVGPALPGSGAAGAIVLATCNRVEIYAEADGAGV
+EAARTGLLSAVAASTSLPDEDVHTAFRTLDADATARHLFEVGAGLDSAVVGEREIAGQVR
+RALTAAQEAGTASGPLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLAEELRGLTDA
+AAQRDFWAGATILLIGTGAYAGTTLAQLADRGATTVGVHSASGRAEQFVADRGGWALALG
+GEAVAGAVAEADVIIGSSGGERQISPERLQELREGGRRPLTVVDLALSRDFDPAVADLPD
+VDLITLESVRLAAPEQAQVAVAEARALVDDAVEEYRAAQRGRSADAAIKALRRHTLGVLD
+RELERVRARHGCTAAAEEVEFALRRMVNQLLHEPSVRAKRLAAEGRLDRYEDALEAVFGI
+EAPGRPAPAVGTVEAACPAHEDDGGAARIA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000912.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000912.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a92d7948bfb6646f2f4a55d21d2754a7557eddb5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000912.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_01392
+MTGTALVVGGGIAGLVAAHRLCAAGWEVTLAEATSVLGGAVSARFLDVPSHGETGAPESQ
+TLELDAGAESFAVRGTAVRALLEELGLGGKVVAPEPLGSWLHGPAGPVPAPRLGLVSIPG
+DLEAEDLAAALSGPGLARAREDAVAPMDRWADALAAGEPVTVAAIVADRLGEEVLKRLVA
+PVVAGVHSADPAVVELERVAPGLLASAVEHGGLAAGVAALRGSSTPGSLVAGVDGGMSRV
+TGRLVDALREAGATVLRGVRVAALSRVPAMGGWWAQISDRDDEVVRGLDVDRVVLAVDGA
+TAWDLLAPLSGGDLDPDAGPALGDGVALTTLVVEAPGLDAAPRGTGMLVGAGTDVAAKAL
+THATAKWAWLREVVARPDHDGVARHPHRHVVRLSYGRSGAEPGGLGHRSTDEELLARAVV
+DAAALTGVPLSEQDVVARAVVRWRPSIPPQAGPDREAADALIAWSRGQAGLDLVGSWVHG
+TGLAAVVASVDRAFDAPPPAG
+>MOLHKGIG_01533
+MSGTALVVGGGIAGLVAAHRLSAAGWDVTLAEATSVLGGAVSPRFLDVPSHGETGAPETQ
+TLELDGGAESFAVRGAAVRALVEELGLGEKIVAPEPLGSWLHGPAGPVRAPRLGIVGIPG
+DLDAEDLAAALTPAGLERARQDAEAPMDRWAAALAAGEPVTVAQVVADRLGDEVLDRLVA
+PVVAGVHSADPAVVELERVAPGLLAAAVEHGGLAAGVAALRSTGTPGSLVAGLDGGMVRL
+TGRLVEALREDGATVLRGVRVAALSRVPATGGWWAQISDRDDEVVRGLDVDRVVLAVDGV
+TAWDLLAPLSAEALDPDAGPALGEGIALATLVVEAAGLDDAPRGTGVLVGAGTDVAAKAL
+THVTAKWAWLREVVARPQEDGVARHPHRHVLRLSYGRQGGGPEALGHRSADEELLAQALV
+DTATLTGVPLAEEDVVARTVTRWRRSIPPQAGPDRAKADTLIDWARDVPGLDLVGSWVHG
+TGLAAVVAGVDRTLGADAPPAG
+>NAFOICDF_01283
+MSGSALVVGGGIAGLLAARRLNQQGWEVTLAEATSVLGGTLSARFLDVPSVSDSGAVERQ
+TLELDGGAESFAVRGAAVRALVDELGLGDDVVSPEPLGSWLHGPAGAVPAPRVGLVGIPG
+DLDAPDVAAALSPAGLERARRDLTEPMDRWAAARAAGEPVTVAALVADRLGDDVLERLVV
+PVVGGVHSADPAVVDVERVAPGLLAAAVEQGSLARGVAALRGGQTPGAAVAGVDGGMAKV
+TGRLVQTLREDGVTVLRGVRVAALSRLGADGRWWAQISDRDEEVVRGLEADRVVLAVDGV
+AAWELLAPVSGDAVDPDAGPALGEGVALATLVVEAPGMDAAPRGTGLLVAPGTDVRAKAL
+THSTAKWAWLRSVVDRPDESGAPRHPHRHVLRLSYGRHGGAAGDLGFRSADEDLLAAAVA
+DAEALTGVELSADDVLASTVTRWRRPIPPQHGPDREAMDRLIAWAQDVPGLDLVGSWVHG
+TGLAAVVAGVERTVAPAAA
+>MHAAABBN_01243
+MSGTALVVGGGIAGLVAAHRLSAAGWDVTLAEATSVLGGAVSPRFLDVPSHGETGAPETQ
+TLELDGGAESFAVRGAAVRALVEELGLGEKIVAPEPLGSWLHGPAGPVRAPRLGIVGIPG
+DLDAEDLAAALTPAGLERARQDAEAPMDRWAAALAAGEPVTVAQVVADRLGDEVLDRLVA
+PVVAGVHSADPAVVELERVAPGLLAAAVEHGGLAAGVAALRSTGTPGSLVAGLDGGMVRL
+TGRLVEALREDGATVLRGVRVAALSRVPATGGWWAQISDRDDEVVRGLDVDRVVLAVDGV
+TAWDLLAPLSAEALDPDAGPALGEGIALATLVVEAAGLDDAPRGTGVLVGAGTDVAAKAL
+THATAKWAWLREVVARPQEDGVARHPHRHVLRLSYGRQGGGPEALGHRSADEELLAQALV
+DTATLTGVPLAEEDVVARTVTRWRRSIPPQAGPDRAKADTLIDWARDVPGLDLVGSWVHG
+TGLAAVVAGVDRTLGADAPPAG
+>LFPAFLNI_01460
+MSGTALVVGGGIAGLVAAHRLSAAGWDVTLAEATSVLGGAVSPRFLDVPSHGETGAPETQ
+TLELDGGAESFAVRGAAVRALVEELGLGEKIVAPEPLGSWLHGPAGPVRAPRLGIVGIPG
+DLDAEDLAAALTPAGLERARQDAEAPMDRWAAALAAGEPVTVAQVVADRLGDEVLDRLVA
+PVVAGVHSADPAVVELERVAPGLLAAAVEHGGLAAGVAALRSTGTPGSLVAGLDGGMVRL
+TGRLVEALREDGATVLRGVRVAALSRVPATGGWWAQISDRDDEVVRGLDVDRVVLAVDGV
+TAWDLLAPLSAEALDPDAGPALGEGIALATLVVEAAGLDDAPRGTGVLVGAGTDVAAKAL
+THATAKWAWLREVVARPQEDGVARHPHRHVLRLSYGRQGGGPEALGHRSADEELLAQALV
+DTATLTGVPLAEEDVVARTVTRWRRSIPPQAGPDRAKADTLIDWARDVPGLDLVGSWVHG
+TGLAAVVAGVDRTLGADAPPAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000913.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000913.fa
new file mode 100644
index 0000000000000000000000000000000000000000..53d975a89f8968b3db1dcd322e04b4ffc3e8aef0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000913.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01393
+MTKDTATTPAEAGKDWFTTYTVFARPQGQPGWLGLEGRDAKKAVQEFDALVADLAKAGVT
+VRGVYDVSGMREAGDVMVWMYGQVPEDLQAAIRRLRRTRLLERTTMVLSAMGADRLAEFN
+KDHIPAFAMGRKALPWLCFYPFVRSYDWYLMEPKERARMLREHGQLGQEFPQVWANTTSA
+FGLNDWEWLLGLEAPELKDLVDMMRHLRNNETRLYVRAEVPFYTGRRVETADLLEVLA
+>MOLHKGIG_01532
+MTKDSTTTPAEAGKDWFTTYTVFARPQGEPGWLGLEGRDAKKAAKEFDEAVARVAQTGVT
+VRGVYDVSGMREAGDVMVWMYGQVPEDLQAAIRELRRTRLLEGTTMVLSAMGADRMAEFN
+KDHVPAFAMGRKALKWLCFYPFVRSYDWYLLDPKERARMLREHGQLGQDFPQVWANTTSA
+FGLNDWEWLLGLEADELTDLVDMMRHLRNNETRLHVRSEVPFYTGRRLETAEIAEVLA
+>NAFOICDF_01284
+MSNTAAQPGQDWFTTYTVFARPQGEPGWLGLDGREAKKAVKEFDGVVKSLATRGVTVRGV
+YDVSGMRAEGDVMVWMYAHAPEDLQAAIRDLRRTRLLDGTNMVLSAMGADRMAEFNKDHI
+PAFAMGRKPLDWLCFYPFVRSYDWYTLDPKERARMLREHGKLGQDFPQVWANTTSAFALN
+DWEWLLGLEAPKLNDLVDMMRHLRDNETRHYVREEVPFYTGRRLETSELPEVLA
+>MHAAABBN_01242
+MTKDSTTTPAEAGKDWFTTYTVFARPQGEPGWLGLEGRDAKKAAKEFDEAVARVAQTGVT
+VRGVYDVSGMREAGDVMVWMYGQVPEDLQAAIRELRRTRLLEGTTMVLSAMGADRMAEFN
+KDHVPAFAMGRKALKWLCFYPFVRSYDWYLLDPKERARMLREHGQLGQDFPQVWANTTSA
+FGLNDWEWLLGLEADELTDLVDMMRHLRNNETRLHVRSEVPFYTGRRLETAEIAEVLA
+>LFPAFLNI_01459
+MTKDSTTTPAEAGKDWFTTYTVFARPQGEPGWLGLEGRDAKKAAKEFDEAVARVAQTGVT
+VRGVYDVSGMREAGDVMVWMYGQVPEDLQAAIRELRRTRLLEGTTMVLSAMGADRMAEFN
+KDHVPAFAMGRKALKWLCFYPFVRSYDWYLLDPKERARMLREHGQLGQDFPQVWANTTSA
+FGLNDWEWLLGLEADELTDLVDMMRHLRNNETRLHVRSEVPFYTGRRLETAEIAEVLA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000919.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000919.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4863af749c62e81a8be190e87c1b12e6888cc973
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000919.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_01399
+MPPHLRPGQTLLLASLVFGLFFGAGNLIFPASLGRDAGAAVTPATLGFLVTAVGLPVLGI
+VASAVTGARSVREMTAPVSRRFAVAFTCLLYLTIGPLFAIPRTATVSYEIGVAPLAGDGS
+LRLLGFTAAFFAVAAVAAFRPGRLMEWVGRYLTPAFLVLLGALVAAAVVTPMSTGALPSP
+APAYADGALVRGLLDGYTTMDALASLAFAVVIVDAARRLGVTGPRRMAVELGKAGLLGGA
+AMAVVYASLAYIGATSHGAFAQAANGGDVLARTASHFFGTAGAYLIAAIVFVACLKTCIG
+LIVACAEMFAEMFPGSYRLWAGLFLVVSFALANLGLEAIIAWSVPVLMLLYPIAVVVILL
+GLAWAWVRDRPAVARWVVACTGLAAVFDLLGALPEALGTTALVTALTGLAGRVLPGYAVG
+FGWVVPALVGLVVGAVAAASRPRPRRGEREATPIAAGHGRTAAD
+>MOLHKGIG_01526
+MPPRLRPGQTLLLASLVFGLFFGAGNLIFPAGLGRDAGAAVTPATLGFLVTAVGLPVLGI
+VASAVTGARSVREMTAPVSRRFAVAFTCLLYLTIGPLFAIPRTATVSYEIGVAPLAGDGG
+LRLLGFTAAFFAVAAVAAFRPGRLMEWVGRYLTPAFLVLLGALMAAAVVAPMSTGALPSP
+TPAYADGALVRGLLDGYNTMDALASLAFAVVIVDAARRLGVTGPRRMAVELGKAGLLGGA
+AMAVVYASLAYVGATSHGAFAQAANGGDVLARSASHFFGAAGVYLIAAIVVVACLKTCIG
+LIVACTEMFAEMFPGSYRLWASLFLVVSFALANLGLEAIIAWSVPVLMFLYPIAVVVILL
+GLAWAWVRDHPAVARWVVACTGLAAFFDLLGALPEALATTPPVTALTGLAGRVLPGYAVG
+FGWVVPALVGLVVGTVAAASRPRPRRGEREAIPVTAGHGRTAAD
+>NAFOICDF_00047
+MSARLRPGQTLLLASLVFGLFFGAGNLIFPAGLGRDAGSAVVPATLGFLLTAVGLPVLGI
+IASALTRSRSVREMTAPISPWFATAFTCLLYLAIGPLFAIPRTATVSYEIGVAPLAGDGP
+WLPVFTLVFFGVAAVAAFRPGRLLDWVGRFLTPVFLLLLGALAVAAVVAPMSSGDLPAPA
+GPYADGALTAGILDGYNTMDALASLAFAVLIVEAAGRLGVDSPRRLAVELGKAGIVGGLG
+MAVVYGALAYIGATSHGALPGAASGGAVLAGTASHYFGPAGTWLIAAIVLAACLKTSIGL
+IVACGEMFAEMFPGSYRVWASVFLLVSLVIANLGLEAIIAWSIPVLMFLYPLAIVIIALG
+LGWGWVRHHLTVARAVVAFTAVAAVFDLLAALPETLAATGPVTALTDLAGRILPWYENGF
+GWVVPALVGLVVGLVLEAARGRGRSAAVADA
+>MHAAABBN_01235
+MPPRLRPGQTLLLASLVFGLFFGAGNLIFPAGLGRDAGAAVTPATLGFLVTAVGLPVLGI
+VASAVTGARSVREMTAPVSRRFAVAFTCLLYLTIGPLFAIPRTATVSYEIGVAPLAGDGG
+LRLLGFTAAFFAVAAVAAFRPGRLMEWVGRYLTPAFLVLLGALVAAAVVAPMSTGALPSP
+TPAYADGALVRGLLDGYATMDALASLAFAVVIVDAARRLGVTGPRRMAVELGKAGLLGGA
+AMTVVYASLAYVGATSHGAFAQATNGGDVLARSASHFFGTAGAYLIAAIVFVACLKTCIG
+LIVACAEMFAEMFPGSYRLWAGLFLVVSFALANLGLEAIIAWSVPVLMFLYPIAVVVILL
+GLAWAWVRDRPAVARWVVACTGLAAFFDLLGALPEALVTTPPVTALTGLAGRVLPGYAVG
+FGWVVPALVGLVVGTLAAASRPRSRRGEREAIPVTAGHGRTAAD
+>LFPAFLNI_01453
+MPPRLRPGQTLLLASLVFGLFFGAGNLIFPAGLGRDAGAAVTPATLGFLVTAVGLPVLGI
+VASAVTGARSVREMTAPVSRRFAVAFTCLLYLTIGPLFAIPRTATVSYEIGVAPLAGDGG
+LRLLGFTAAFFAVAAVAAFRPGRLMEWVGRYLTPAFLVLLGALVAAAVVAPMSTGALPSP
+TPAYADGALVRGLLDGYATMDALASLAFAVVIVDAARRLGVTGPRRMAVELGKAGLLGGA
+AMAVVYASLAYVGATSHGAFAQAANGGDVLARTASHFFGTAGAYLIAAIVFVACLKTCIG
+LIVACAEMFAEMFPGSYRLWASLFLVVSFALANLGLEAIIAWSVPVLMFLYPIAVVVILL
+GLAWAWVRGRPAVARWVVACTGLAASFDLLGALPEALATTPPVTALTGLAGRVLPGYAVG
+FGWVVPALVGLVVGTVAAASRPRPRRGEREAIPVTAGHGRTAAD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000923.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000923.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1b7fff7fc1f4549760a37f08c3967832e7ecc3f9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000923.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01403
+MTTPPADPRPVPDGPLTLGEGLEAVARLVPAGRAVSYGDLAGLLGVGGPRQAGRAMAKSA
+PGTPWWRVVSADGSLPGELARRAAVEHAREGTPVRPGGRVDLPRARWEPDEAALGAVAAI
+AARIVSGPGARMQA
+>MOLHKGIG_01522
+MTDHPVLPGARHRDDGPLTLGEGLEALARLVPPGRAVSYGGLAGLLGVGGPRQAGRAMAE
+SSPGTPWWRVVRADGSLPPELAARAAVEHEREAMPRTPAGRVDLPRARWEPDDGAARAIR
+AIADRIVSGPGARMRP
+>NAFOICDF_01302
+MSPVPSTPPDPDPHLPTDGPVTLGEALAAAARLIPSGRAASYGALAGLLGRGGPRQAGRA
+MAESEPGTPWWRVVRADGSLPEPLRRQARERWAAEGTPVRGSGTVRDQRVDLAQAGWEPD
+AAARAALADLAARVG
+>MHAAABBN_01231
+MTDHPVLPGARHRDDGPLTLGEGLEALARLVPPGHAVSYGGLAGLLGVGGPRQAGRAMAE
+SSPGTPWWRVVRADGSLPPELAARAAVEHEREATPRTPAGRVDLPRARWEPDDGAARAIR
+AIADRIVSGPGARMRP
+>LFPAFLNI_01449
+MTDHPVLPGARHRDDGPLTLGEGLEALARLVPPGRAVSYGGLAGLLGVGGPRQAGRAMAE
+SSPGTPWWRVVRADGSLPPELAARAAVEHEREGTPRTPAGRVDLRRARWEPDDGAARAIR
+AIADRIVSGPGARMGP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000930.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000930.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ed7e269cba328d837f510b8cfedaee1b12629a5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000930.fa
@@ -0,0 +1,26 @@
+>ACLBLIBL_01410
+MADNGRMPPADAAVPVPAEHERGEPVPAAAAVSALARRPVRRGAVRQSTDLDWEGTPVRL
+VRSTARTRTVSAAWREGRLQVNVPARLTPAHEREWIARMVEQVARRAGAGASPGRPGAGS
+QPGSGPGAGSGGDEALMAWAQRLSAAHLGGRARPASVAWSARQRRRWGSCTPSRGTIRLS
+DRLRGMPDWVVAAVLVHELAHLLESGHGPAFRRLVAAYPRYAEAMAFLDGVAFAESRGRT
+AQDTWVDDEDAMDADAPDDGPTEDERA
+>MOLHKGIG_01515
+MRLVRSTARTRTVSAAWRDGRLQVNVPARLSAAQEREWIGRMVAKVGARGGTGQPAADPD
+GRPADARSDDALLAWAGRLSAAHLGGRARPVAVTWSARQRRRWGSCTPARGTIRLSTQLR
+GMPDWVVAAVLVHELAHLLESGHGPAFRRLVDRYPRYAEAMAFLEGVTFAEGRGRTAPDR
+WAEDEDAG
+>NAFOICDF_01309
+MSPSRTVTDLDWHGTPVRLVRSARRTRTVAAVWREGRLQVSVPARLSRAEERRWIERMVD
+RAGPAPAAHPAPSASAPSTGLGSAPDPRGDADLLARADALASAHLDGAAPGGRAPRPASV
+TWSSRQRQRWGSCTPARGTIRLSAQLRGMPDWVVDAVLVHELAHLSERGHGPRFQALVGR
+LPRYTEAMAFLAGVTYATSRGLPGAYPADADVADHARGWPGGDDDVVEG
+>MHAAABBN_01224
+MRLVRSTARTRTVSAAWRDGRLQVNVPARLSAAQEREWIGRMVAKVGARGGTGQPAADPD
+GRPADARSDDALLAWAGRLSAAHLGGRARPVAVTWSARQRRRWGSCTPARGTIRLSTQLR
+GMPDWVVAAVLVHELAHLLESGHGPAFRRLVDRYPRYAEAMAFLEGVTFAEGRGRTAPDR
+WAEDEDAG
+>LFPAFLNI_01442
+MPDNGRMRPVPPAPGRPPRAVPAAHRGPARESTDLDWEGTPVRLVRSTARTRTVSAAWRD
+GRLQVNVPARLSAAQEREWIGRMVAKVGARGGTGQPAADPDGRPADARSDDALLAWAGRL
+SAAHLGGRARPVSVTWSARQRRRWGSCTPGRGTIRLSTQLRGMPDWVVAAVLVHELAHLL
+ESGHGPAFRRLVDRYPRYAEAMAFLDGVTFAEGRGRTAPDRWAEDEDAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000931.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000931.fa
new file mode 100644
index 0000000000000000000000000000000000000000..21830b41d8990e7f6350d77cf01959fee79fe388
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000931.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01412
+MRAVPPRTTRAYRLPASGWLALGSAGLALLLPTPYILESPGPAVDLLGERDGAEVLRVEG
+GTPDEGEGTLDMTTVMVGGPPISTTSVIDLARSLVDPAVDVVPRELMYPTGMSSEEVGAA
+NTAAMSDSQDTAAAAALHALGRPVPSTLVVHELVPGGPSEGVLRPGDEVIAAAGEPAEDL
+EDLRAAVGAAGPDPVTLTVRRDGAVTELRVPVAAAPEGAPQPWQMGALIETVVDVPLDVE
+LTVPDIGGPSAGLMFALTVLERLTPGAMTGGAPIAGTGTITPDGVVGPIGGIPQKVRGAA
+QAGATTFLAPTANCGELDGRVPEGLQVYAVDTLAQAREIVEAVGRGEPPESARTCG
+>MOLHKGIG_01513
+MRAVPSRTTRAARVPFSGWLALGSAGLALLAPTPYILEGPGPAVDLLGEREGRPVLRVEG
+GEADPGEGTLHMTTVMVGGPPIGTTSLLDLGRGLTDPAVDVAPRELMYPTGVTSDEVGEA
+NSAAMSDSQQTATAAALHELGREVPQRLVVQQLVPGGPAEGVLRAGDEVIAAEGRPVADL
+EAVRAAVGAAGPDPVTLTVRRDGVEQDLEVPVAAAPEGAPQPWQMGALIETAYDVPVDVE
+LTVPDIGGPSAGLMFALTVIERLTPGAMTGGASIAGTGTITGDGVVGPIGGIPQKVRGAA
+EAGATTFLAPTANCEELAGRVPEGLTVYPVDTLGQARDIVEAVARGESPAAARTCG
+>NAFOICDF_01311
+MPYILEGPGPAIDVLGEQDGTPVLTVEGGTADPGEGRLDMTTVLVSGPPGGTTGLGDLVT
+ALADGTVDAQPRELVHPSGVSADTVAQSNAAAMTDSQDVATAAALRALGRDVPAHLAVHA
+TVPGAPAEGILREGDVILAAAGRSVTDMAGIRAAVDAAGPGDLALTLRRDGTERQVSVPV
+TAADPATGRSWQLGVLLEQRFDLPVQVEFALEDIGGPSAGMMFALAVIERLTPGDMTGGA
+RIAGTGTITADGVVGPIGGIPQKMQGAARDGADVFLAPRENCADLAGRVPAGMTVYAVDT
+LATARAVVEAVGRGERPDDVPTCS
+>MHAAABBN_01222
+MRAVPSRTTRAARVPFSGWLALGSAGLALLAPTPYILEGPGPAVDLLGEREGRPVLRVEG
+GEADPGEGTLHMTTVMVGGPPIGTTSLLDLGRGLTDPAVDVAPRELMYPTGVTSDEVGEA
+NSAAMSDSQQTATAAALHELGREVPQRLVVQQLVPGGPAEGVLRAGDEVIAAEGRPVADL
+EAVRAAVGAAGPDPVTLTVRRDGVEQDLEVPVAAAPEGAPQPWQMGALIETAYDVPVDVE
+LTVPDIGGPSAGLMFALTVIERLTPGAMTGGAPIAGTGTITGDGVVGPIGGIPQKVRGAA
+EAGATTFLAPTANCEELAGRVPEGLTVYPVDTLGQARDIVEAVARGETPAAARTCG
+>LFPAFLNI_01440
+MRAVPSRTTRAARVPFSGWLALGSAGLALLAPTPYILEGPGPAVDLLGEREGRPVLRVEG
+GEADPGEGTLHMTTVMVGGPPIGTTSLLDLGRGLTDPAVDVAPRELMYPTGVTSDEVGEA
+NSAAMSDSQQTATAAALHELGREVPQRLVVQQLVPGGPAEGVLRAGDEVIAAEGRPVADL
+EAVRAAVGAAGPDPVTLTVRRDGVEQDLEVPVAAAPEGAPQPWQMGALIESAYDVPVDVE
+LTVPDIGGPSAGLMFALTVIERLTPGAMTGGAPIAGTGTISGDGVVGPIGGIPQKVRGAA
+EAGATTFLAPTANCEELAGRVPEGLTVYPVDTLGQARDIVEAVARGESPAAARTCG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000933.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000933.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88b5b15366b252744b71caaf236d0562c147f002
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000933.fa
@@ -0,0 +1,41 @@
+>ACLBLIBL_01415
+MQEQFTAWSVLVDAGLIGALLAVGTLARAVIKPLQTLMIPASVIAGILGLVLGPNVLGWL
+PFSTQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGSFASYGVLIYASQVAIGALVALL
+VLQPLFSTPDSFAALLFAGWAGGFGSAAAVGQAYAANGDMTVTSLAYTSATVGMIVGVVG
+GIIQAKIGARRGHAKEFAGLTSIPDELRTGVLDQVQERPVIGRHTFSAASVESLAFQVGV
+VAMIAAAAHGVVTWITAVWPNIVGEDGPKLIIPAFAVAFILGLIGRVVFQATKTAKFLDP
+GSLNSVSGTATDILIVCGIASIAPTVVVDYWQPLLVLFVIGLALALFLGLVVAPRVMTDA
+WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL
+IAGLSWAVVGIWGAIAIAAILAAIWLRRTDPGVRSPAQQAVRAASR
+>MOLHKGIG_01487
+MQEQFTAWSVLVDAGLIGALLAVGTLARAVITPLQTLMIPASVIAGILGLVLGPNGLGWL
+PFSSQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGAFASYGVLIYASQVAIGALVTLV
+LLQPLFDAPDSFAALLFAGWAGGFGSAAAVGQAYAANGDATVTSLAYTSATVGMIVGVVG
+GIIQAKIGAQRGHAREFAGLTSIPEELRTGVLNQVEERPVIGRHTFSAASVESLAFQVGV
+VAMIAAAAHGVVSWITSVWPSVVGEDGPQLIIPAFAIAFLLGLIARVLFQATKTAKFLDP
+GSLNSVSGTATDILIVCGIAAIAPTVVVDYWQPLLLLFVIGLALALFLGIVVAPRVMTDA
+WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL
+LAGLSWAVVGIWGAIAVIAIIAAVWLRRTDPGRRTPAQQAVRASSR
+>NAFOICDF_01314
+MTWFQGVWPSIVGPEGPKLMIPAFAVAFVLGIIGRLLLQVTKTATFLDSASLNSVSGTAT
+DILIVCGIASIAPKVVLDYWQPLLILFVVGLALAVLLGLVVAPHVMTESWFEKQLFTWGW
+ATGAVATGVAMLRIVDPKLKSGTMEQFGVAYITVVPVEIAAVSFVPLLIIAGLSWAVVGI
+WDAIAEAAIIAAVFLVRSDPARKSAVPA
+>MHAAABBN_01219
+MQEQFTAWSVLVDAGLIGALLAVGTLARAVITPLQTLMIPASVIAGILGLALGPNGLGWL
+PFSSQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGAFASYGVLIYSSQVAIGALVTLV
+LLQPLFDAPDSFAALLFAGWAGGFGSAAAVGQAYAANGDATVTSLAYTSATVGMIVGVVG
+GIIQAKIGAQRGHAREFAGLTSIPEELRTGVLNQVEERPVIGRHTFSAASVESLAFQVGV
+VAMIAAAAHGVVSWITAVWPSVVGEDGPQLIIPAFAIAFLLGLIARVLFQATKTAKFLDP
+GSLNSVSGTATDILIVCGIAAIAPTVVVDYWQPLLLLFVIGLALALFLGIVVAPRVMTDA
+WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL
+LAGLSWAVVGIWGAIAVIAIIAAVWLRRTDPGRRTPAQQAVRASSR
+>LFPAFLNI_01437
+MQEQFTAWSVLVDAGLIGALLAVGTLARAVITPLQTLMIPASVIAGILGLALGPNGLGWL
+PFSSQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGAFASYGVLIYSSQVAIGALVTLV
+LLQPLFDAPDSFAALLFAGWAGGFGSAAAVGQAYAANGDATVTSLAYTSATVGMIVGVVG
+GIIQAKIGAQRGHAREFAGLTSIPEELRTGVLNQVEERPVIGRHTFSAASVESLAFQVGV
+VAMIAAAAHGVVSWITAVWPSVVGEDGPQLIIPAFAIAFLLGLIARVLFQATKTAKFLDP
+GSLNSVSGTATDILIVCGIAAIAPTVVVDYWQPLLLLFVIGLALALFLGIVVAPRVMTDA
+WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL
+IAGLSWAVVGIWGAIAIIAIIAAVWLRRTDPGRRTPAQQAVRASSR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000934.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000934.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b7c93959d0048619e5322962d198901c9773ded2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000934.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01416
+MVKQSIFGRISTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMI
+EDDYREDQDAARSWGQKALAASQKADDFRTKGDAASAEKFDNLAKVAIERQMDSERQAKS
+AEPTITSQREIVERLKTGLDQMKVKRQQLVSKRDELTARAKSAHAQSAVADAVKSIDLLD
+PTSEVSRFEEKVRREEARVRGQQELAASSLDAQFESLEDLGEKTEVEARLAALKSGGAGQ
+SALTAGGSEGSDLALDYGAETTAEQGAEQTRVERG
+>MOLHKGIG_01486
+MVKQSIFGRISTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMI
+EDDYREDQDASRSWGQKALAASQKADDFRAKGDTASADKFDNLAKVAIERQMDFERQAKS
+AEPTIASQREIVERLKTGLDQMKVKRQQLVAKRDELTARAKSAHAQSAVADAVKSIDLLD
+PTSEVSRFEEKVRREEARVRGQQEIAASSLDAQFESLEDLGEKTEVEARLAALKAGGAGQ
+AALTSGDVDADETLTLDYAAEGTAEETGTARG
+>NAFOICDF_01316
+MVKQSILGRITTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMM
+EDDYREDQEAARSWGQKALAASQKADEFRTKGEAANADKFDNLAKVAIERQMDAERQAKT
+AEPTITSQREIVDRLKTGLDQMKVKRQQLVSKRDELTARSRTAEAQTKVNEAVKSIDIMD
+PTSEISRYEEKVRREEARVRGQQELAASSLDAQFESLEDLGEQTEVEARLAALKSGSAPS
+ALTAGSEELTLDYSGAETGTQTGTAERA
+>MHAAABBN_01218
+MVKQSIFGRISTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMI
+EDDYREDQDASRSWGQKALAASQKADDFRTKGDTASADKFDNLAKVAIERQMDFERQAKS
+AEPTIASQREIVERLKTGLDQMKVKRQQLVAKRDELTARAKSAHAQSAVADAVKSIDLLD
+PTSEVSRFEEKVRREEARVRGQQEIAASSLDAQFESLEDLGEKTEVEARLAALKAGGAGQ
+AALTSGDVDADETLTLDYAAEGTAEETGTARG
+>LFPAFLNI_01436
+MVKQSIFGRISTLAKANINAMLDKAEDPQKMLDQMVRDYTNNIAEAEAAVAQTIGNLRMI
+EDDYREDQDASRSWGQKALAASQKADDFRTKGDTASADKFDNLAKVAIERQMDFERQAKS
+AEPTIASQREIVERLKTGLDQMKVKRQQLVAKRDELTARAKSAHAQSAVADAVKSIDLLD
+PTSEVSRFEEKVRREEARVRGQQEIAASSLDAQFESLEDLGEKTEVEARLAALKAGGAGQ
+AALTSGDVDADETLTLDYAAEGTAEETGTARG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000937.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000937.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1778e3d9f3ef8cde31d43e595996549e1afc2ee1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000937.fa
@@ -0,0 +1,29 @@
+>ACLBLIBL_01419
+MTTPITPAALAAEHGWRTVLAVGAHPDDLDFGAAATLAGLSAAGLRVELCVVTDGDAGGF
+DSEGPEAMTARRHAEQRAAAAVVGAHEVHFLGERDGHLEPDHGVRRKLVALMRRVRPDVV
+LSTHPERDWELMQAAHPDHLACGEAVVRAAYPAVENPYAYPELAAEGLEAFKIRHLLLYS
+APAARRNTVVDVTGLEDVKLRALDAHISQHPDVAAMRRHVLAQMTEHHRRAAGPAAAPGL
+AEAFHLVTVNGPGTISGF
+>MOLHKGIG_01483
+MAVGAHPDDLDFGAAATLAGFSAAGLHIELCIVTDGDAGGFDSEGAEAMTARRHAEQRAA
+AAVVGAAEVHFLGERDGHLEPDHGVRRKLVALMRRVRPDVVLSTHPERDWERMQAAHPDH
+LACGEAVVRAAYPAVENPYAYPELAAEGLEAFKIRNLLLYAAPAARRNTVVDVTGLAEQK
+LRALDAHLSQHPDVDAMRRHVLAQMAEHHRHAAGPAAGPGHAEAFHLVTVNGPGTIAGF
+>NAFOICDF_01319
+MSAVPESLPTPADLAVRHGWRTVLAFGAHPDDLDFDASATLAGLAAAGVRVELCVVTDGD
+AGGFDSDGPEAMTARRHAEQRAAAAVIGAADVHFLGERDGHLEPTHEVRRRIVELMRRVR
+PDVVLCPHPERDWESMQASHPDHLACGEAVVRAAYPAVENPYAYPELADAGLDAFRIRHL
+MLYTAPAARRNLTVDVTGLEDVKLRALDAHVSQHPDAPAMREAVRAKLTRRHREAAGPDA
+PAGSGEAYHLVTVNGDGVIAGF
+>MHAAABBN_01215
+MTTTLTTPAALAAHHGWRRVLAVGAHPDDLDFGAAATLAGFSAAGLHIELCIVTDGDAGG
+FDSEGPEAMTARRHAEQRAAAAVVGAAEVHFLGERDGHLEPDHGVRRKLVALMRRVRPDV
+VLSTHPERDWERMQAAHPDHLACGEAVVRAAYPAVENPYAYPELAAEGLEAFKVRNLLLY
+AAPAARRNTVVDVTGLAEQKLRALDAHLSQHPDVDAMRRHVLAQMAEHHRRAAGPAAAPG
+HAEAFHLVTVNGPGTIAGF
+>LFPAFLNI_01433
+MTTTLTTPAALAAHHGWRRVLAVGAHPDDLDFGAAATLAGFRAAGLHIELCIVTDGDAGG
+FDSEGPEAMTARRHAEQRAAAAVVGAAEVHFLGERDGHLEPDHGVRRKLVALMRRVRPDV
+VLSTHPERDWERMQAAHPDHLACGEAVVRAAYPAAENPYAYPELAAEGLEAFKVRNLLLY
+AAPAARRNTVVDVTGLAEQKLRALDAHLSQHPDVDAMRRHVLAQMAEHHRRAAGPAAAPG
+HAEAFHLVTVNGPSTIAGF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000940.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000940.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f8a48f0bdc5a546a3cf5b61f2b03abfed7ece670
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000940.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01422
+MSAADEHCTAYEVLGVDRDADDAAVRRAYRAAARRTHPDAGGDPAEFRAVSRAWQVLGDA
+DARRRYDLSLPAPGAGRAPASGGAARPGRAAASRPARGAAGRPARTVRYEPPPGEGESDA
+AVLDLPRSSQRVHGAPRPRGILPDEHRVLRQARTLDVLLRHVADALPAARVLTGLRLAGR
+WGRPLDVDHAVLCGHRLALVGSVMVPEGAYTWDGSDLRSRGRPVAPPLLGPAMMAWQQVL
+PQVTVGGFVHVMTDRDALHGPVVRHARGADDPGARADLLTVPPAPGREFVRDLLLFLGTG
+EDPDLVDRRVLGTLVERLH
+>MOLHKGIG_01480
+MSAAEEHRTAYEVLGVPRDATAEEVRRAYRRAARAAHPDVGGDPAAFRAVTRAWDLLGDA
+EARRRYDLSLPGPDVGPRGPRATAGSGRARPSGRSGPGGRAARPVRYEPPPGEAEADPTV
+LDLPRSSQRVHGAPRPRGILPDEHRVLRQARTLDVLLRHVADALPAARVLTGLRLGGRWG
+RHLDVDHAVLCGHRLALIGSVMVPEGTYTWDGADLRSRGRPVAPPLLGPAMMAWQQALPQ
+VTVGGFVHVMTDRDARHAPVIRHTRGADAPEAQADLLTAPPAPGIAFAREVALFLGTGTD
+PDLVDRRALGALVGRLH
+>NAFOICDF_01322
+MSGTGDRRTAYEVLGVPRDADAERIRRAWRAAARRTHPDAGGDARDFRAVTRAWEQLGDP
+EARRRYDLSLPPEPAGTTGRTASAGRSAAQAWPPAGVRERDRPAPGSVVYDPPPGQGEHD
+SSVLDLVRSSQRLHGAPRPRGILPDEHRVVRQARTLDLLARTLPPVLPAVRILTGLHLGG
+RFGRGLDVDHAVLCGRRLALVGSVQVPDGTYTWDGADLRAGARGRPVAPPLLGPAMQAWQ
+HALPQVTVGGFVLVMTDRDAVHSPVIRQARGADRPEAQADLLTAAPAAGRDLLRELQLFL
+GSGPDPDVVDRRALAVLVRHLH
+>MHAAABBN_01212
+MSAAEEHRTAYEVLGVPRDATAEEVRRAYRRAARAAHPDVGGDPAAFRAVTRAWDLLGDA
+EARRRYDLSLPGPDVGPRGPRATAGSGRARPSGRSGPGGRAARPVRYEPPPGEAEADPTV
+LDLPRSSQRVHGAPRPRGILPDERRVLRQARTLDVLLRHVADALPAARVLTGLRLGGRWG
+RHLDVDHAVLCGHRLALIGSVMVPEGTYTWDGADLRSRGRPVAPPLLGPAMMAWQQALPQ
+VTVGGFVHVMTDRDARHAPVIRHTRGADAPEAQADLLTAPPAPGIAFAREVALFLGTGTD
+PDLVDRRALGALVDRLH
+>LFPAFLNI_01430
+MSAAEEHRTAYEVLGVPRDATAEEVRRAYRRAARAAHPDVGGDPAAFRAVTRAWDLLGDA
+EARRRYDLSLPGPDVGPRGPRATAGSGRARPSGRSGPGGRAARPVRYEPPPGEAEADPTV
+LDLPRSSQRVHGAPRPRGILPDEHRVLRQARTLDVLLRHVADALPAARVLTGLRLGGRWG
+RHLDVDHAVLCGHRLALIGSVMVPEGTYTWDGADLRSRSRPVAPPLLGPAMMAWQQALPQ
+VTVGGFVHVMTDRDARHAPVIRHTRGADAPEAQADLLTAPPAPGIAFAREVALFLGTGTD
+PDLVDRRALGALVDRLH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000946.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000946.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1321bc1b4335a52b27e6ed9f94cfeda18c627859
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000946.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01428
+MPEAHDDGARPVALGGSPWAGTDAAEAQRVTLGELGAEHWPVLPELPSRGPGADATGRSA
+ALLSELAVDLQPHGWRVSPPGAAGSGMDRRRAASFWREDAHRWADTAGAEGAVVERLAVR
+VRGPLSLLGGLWLPGGERVLADHGARRDVAASYLEGLLEAVPRLRAATGAAGLGLLVDEP
+WAAAVLAGALPTASGYRTVRSLPRDEARGLWRELLAGLTALPGVASVWLAPGRRTASAAD
+VPATAELAALAGECLPAAGGEDDDAGAPVRLVVPVGDLDDGPDGTAGTRAAWESAAGWAD
+AGRGLTLSPAAHLRPADVVTTWERLGADPAHLRGTGLTAPGRHDATVLRRLRTDAAELAA
+RLDDALG
+>MOLHKGIG_01472
+MTEAAHDDGATGPVALGGTPWRGTDVAEAQRVTLGELGADHWPVLPELPDRGPGADATGR
+SAALLQQLAVDLQPHGWRVSPPGAAGSGRDRRRAVSLWREDAHRWADTAGAEGAVVERLA
+VRVRGPLSLLACLWLPGGERVLGDHGARRDVAESYLEGLQDALPRLRRATGAGRLGVVVD
+EPWAAAVLAGTLPTASGYRTVRSLPREEARGLWRAALDGLTALPDVARVWLAPGRRAASP
+GAELPGPAALSTLTGESLPRPDAAADAPAPAPVSLVVGVGALDDGADGTPGTREAWEAAA
+GWADIGRGLTLAPEPGVRPVEVVRTWERLGVDPGRVGDVGLTAAGLHDPVVLHTLRRDAE
+ELTARLAELRG
+>NAFOICDF_01330
+MPEASDDVGAVRVAALGGAPWRGTDAAEAQLATLGELGAEHWPVLPELPDRGPGADATGR
+SAALLHELAVDLQPHGWRVSPPGVVGSGMDRRRAASFWREDAHRWADTAGAEGAVVERLG
+VRLRGPLSLLGSLWLPGGERVLVDHGARRDVAASYVEGLRDAVPRLAAATGARTLGVVLD
+EPWAAAVLAGALPTASGYRTVRSVPRDEVRALWRDALAALADLPGVGRVWLAPGRRSAGV
+DVPLPDVSALAALAGESLPAAAPSADDDAPAPTRVDLVVPVGALDPGPDGTGGTRAGWET
+AAGWTDAGRGLTLSTATGVRPADVARTWERLGADPGHLAGVGLTVPGPHDAAVLGRLRAD
+AEELAARVGELLG
+>MHAAABBN_01204
+MTEAAHDDGATGPVALGGTPWRGTDVAEAQRVTLGELGADHWPVLPELPDRGPGADATGR
+SAALLQELAVDLQPHGWRVSPPGAAGSGRDRRRAVSLWHEDAHRWADTAGAEGAVVERLA
+VRVRGPLSLLAGLWLPGGERVLGDHGARRDVAESYLEGLQDALPRLRRATGAGRLGVVVD
+EPWAAAVLAGTLPTASGYRTVRSLPREEARGLWRAALDGLTALPDVARVWLAPGRRAASP
+GAELPGPAALATLTGESLPRPDAAADAPVPAPVSLVVGVGALDDGADGTPGTREAWEAAA
+GWADIGRGLTLAPEPGVRPVDVVRTWERLGVDPGRVGDVGLTAAGSHDPAVLRTLRRDAE
+ELTARLAELRG
+>LFPAFLNI_01422
+MTEAAHDDGATGPVALGGTPWRGTDVAEAQRVTLGELGADHWPVLPELPERGPGADATGR
+SAALLQELAVDLQPHGWRVSPPGAAGSGRDRRRAVSLWREDAHRWADTAGAEGAVVERLA
+VRVRGPLSLLAGLWLPGGERVLGDHGARRDVAESYLEGLQDALPRLRRATGAARLGVVVD
+EPWAGAVLAGTLPTASGYRTVRSLPREEARGLWRAALARLTALPDVARVWLAPGRRAASP
+GAELPGPAALATLTGESLPRPDAAADAPARAPVSLVVGVGPLDDGADGSPGTREAWEAAA
+GWADVGRGLTLAPEPGVRPVDVVRTWERLGVDPGRVGDVGLTAAGPHDPAVLRTLRRDAE
+ELAARLAELRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000947.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000947.fa
new file mode 100644
index 0000000000000000000000000000000000000000..551887e16f21bbc12dd66e2fa6c3533a76c4e752
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000947.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01429
+MSRAKILVVDDDEALAEMIGIVLRNDGFEAAFAADGTAALPAFHRERPDLVLLDLMLPGM
+DGIEVCKLLRSESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEAKPAEVLQIGDLEIDVAGHQVTRDGAAISLTPLEFDLLVALARRPRQVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG
+>MOLHKGIG_01471
+MGKAKILVVDDDEALAEMIGIVLRNDGFEPAFAADGTSALPAFHRERPDLVLLDLMLPGI
+DGIEVCRLIRDESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEAKPAEVLHIGDLEIDVAGHEVTRGGVGIALTPLEFDLLVALARRPRHVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG
+>NAFOICDF_01331
+MSKARILVVDDDEALAEMIGIVLRNDDFEPSFAVDGTSALPAFRSARPDLVLLDLMLPGI
+DGIEVCKQIRAESDVPIIMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEQRPAEALAIGDVRIDVAGHQVSRGGAPISLTPLEFDLLVALARKPRQVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRAKVEPDPENPTVVLTVRGVGYKAGQV
+>MHAAABBN_01203
+MGKAKILVVDDDEALAEMIGIVLRNDGFEPTFAADGTSALPAFHRERPDLVLLDLMLPGI
+DGIEVCKLIRAESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEAKPAEVLHIGDLEIDVAGHQVTRAGVGIALTPLEFDLLVALARRPRHVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG
+>LFPAFLNI_01421
+MGKAKILVVDDDEALAEMIGIVLRNDGFEPAFAADGTSALPAFHRERPDLVLLDLMLPGI
+DGIEVCRLIRDESDVPIVMLTAKSDTADVVRGLESGADDYVPKPFKPAELVARVRARLRE
+GEAKPAEVLHIGDLEIDVAGHEVTRGGVGIALTPLEFDLLVALARRPRHVFTREMLLEEV
+WGYRHQADTRLVNVHVQRLRSKVEPDPENPCVVLTVRGVGYKAGQG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000951.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000951.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f920c86fc9cb7bf7d2e1f3b93827aab14dd3a8b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000951.fa
@@ -0,0 +1,85 @@
+>ACLBLIBL_01434
+MPSIIDRVLKISDNRVLRRMQGTVDAVNLLEEDFRALSDAELRAETDTLKARHADGESLD
+LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL
+TGRGVHVITVNDFLASYQAELMGRVFRFLGMETGVVVAGQLPAVRREQYAADITYGTNNE
+FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA
+RLVRRLEEGSDYEVDHKKRTVGVLGPGIEKVEDHLGIANLYETQNTTLIQFLNNAVKAKE
+LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ
+NYFRGYDKLAGMTGTAETEAAEFTSTYGLGVVVIPPNRERQRVDRNDVVYKNEKVKFDAV
+VEDIAERHERRQPVLVGTTSVEKSEYLSTLLAKRGIRHEVLNAKNHAREAAIVAQAGRPG
+AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPQVLAEAEAAVED
+ANREVLEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA
+QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLKYDDVMNRQREAIYADR
+RSILEGEDLKDRVRRFVEDAVGNIVDATTEEGHAADWDLDQLWRDLSELYPVGITQEDVL
+EEVGGRGRLKAEDLRRELVSDALLAYEDREAQVGSEALREAERRVVLSAIGRRWQEHLYE
+MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAGIREDSVSTLFKAQITAAPAPTSLP
+GIKDARGLTMTPQISVEGVEAPQRPSQLRFTGPSEDGQGAVTRAGTETGATVEAGTNRRS
+RREAERRERRS
+>MOLHKGIG_01466
+MPSIIDRVLKISDNRVLKRMQATVDAVNLLEDDFRALSDAELRAETDTLRARHADGESLD
+LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL
+SGRGVHVVTVNDFLASYQADLMGRVFRFLGMQTGVIVAGQTPAVRREQYAADITYGTNNE
+FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA
+RLVRRLEADTDYEVDHKKRTVGILGPGIEKVEDHLGITNLYETQNTTLIQFLNNAVKAKE
+LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ
+NYFRGYEKLAGMTGTAETEAAEFTSTYGLGVVVIPPNRERQRVDRNDVVYKNEKVKFDAV
+VDDIAERHAKGQPVLVGTTSVEKSEYLSTLLAKRGVRHEVLNAKNHAREAAIVAQAGRPG
+AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLAQAEAAVED
+AHRAVIEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA
+QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLKYDDVMNRQREAIYTDR
+RSILEGEDLQDRVRRFVEDAVGNIVDAATEEGHATDWDLDQLWRDLAELYPVGISQEDVL
+DEVGGRGRLKAEVLKRELVSDALLAYEDREAQVGSEALREAERRVVLATIGRRWQEHLYE
+MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAAIREDAVRTLFQAQISAAPASTSLP
+GVQDARAVTMAPQISVEGIDAPQQPAQLRFTGPSEDGQSAVTRSGTDSGATVAAGTNRRS
+RRQAERRGRRG
+>NAFOICDF_01337
+MPSIIDRVLKISDNRVLKRMRGTVDAVNLLEDDFRALSDAELRAETDSFKKRLADGETLD
+LLLPEAFAAVREAAGRTLGQRHYDVQLLGGLALHQGNIAEMKTGEGKTLVATAPAYLNAL
+TGKGVHVVTVNDFLASYQADLMGRVYRFLGMETGVIVSGQDPATRRAQYAADITYGTNNE
+FGFDFLRDNMAWSKEELVQRGHHFAIVDEVDSILIDEARTPLIISGPAQGDISRWYGEFA
+RLVRSLERGTDYEVDEKKRTVGVLEPGIEKVEDHLGIANLYESQNTTLVQFLNNAVKAKE
+LFKRDKDYVVLDGEVQIVDEHTGRVLAGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ
+NYFRGYEKLSGMTGTAETEAAEFTSTYGLGVVVIPPNREKQRVDRNDLVYKNEKVKFDAV
+VKDIAERHATGQPVLVGTTSVEKSEYLSTLLTKAGVRHEVLNAKNHAREAAIVAQAGRPG
+AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLEQAEAAVQD
+AREKVREAGGLYVLGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDDLMRNFNPGAA
+QRIMNSASIPDDMALEFKMVSSAIQNAQSQVEGRNAEQRKNVLKYDDVMNRQREAIYADR
+RAILEGDSLGERVRGFVEDAVGAVVDAATEEGAPVDWDLEKLWETLREVYPVGISPEDVL
+EQVGGRGRLKAADLKRELVSDALLAYDDREAQVGSEALREAERRVVLAMIGRHWQEHLYE
+MDYLKEGIGLRAMAQREPLVEYQREGFTMFQAMLAAIKEDSARTLFHAQIAAAPAPTQLP
+GVKDARAMTMVPQISVEGVETPRQPARLHLSGPSEDGEGVEEKDLAADGAQTPAGANRAS
+RRAEARRRRRGED
+>MHAAABBN_01198
+MPSIIDRVLKISDNRVLKRMQATVDAVNLLEDDFRALSDAELRAETDTLRARHADGESLD
+LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL
+SGRGVHVVTVNDFLASYQADLMGRVFRFLGMQTGVIVAGQTPAVRREQYAADITYGTNNE
+FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA
+RLVRRLEANTDYEVDHKKRTVGILGPGIEKVEDHLGITNLYETQNTTLIQFLNNAVKAKE
+LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ
+NYFRGYEKLAGMTGTAETEAAEFTSTYGLGVVVIPPNREPQRVDRNDVVYKNEKVKFDAV
+VDDIAERHAKGQPVLVGTTSVEKSEYLSTLLAKRGIRHEVLNAKNHAREAAIVAQAGRPG
+AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLAEAEAAVED
+AHRAVIEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA
+QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLKYDDVLNRQREAIYTDR
+RSILEGEDLQDRVRRFVEDAVGNIVDAATEEGQATDWDLDQLWRDLAEIYPVGVSQEDVL
+DEVGGRGRLTAEVLKRELVSDALLAYEDREAQVGSEALREAERRVVLATIGRHWQEHLYE
+MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAAIREDAVRTLFQAQISAAPAPTSLP
+GVKDARAVTMAPQISVEGIDAPQQPAQLRFTGPSEDGQSAVTRSGTDSGATVAAGTNRRS
+RRQAERRGRRG
+>LFPAFLNI_01416
+MPSIIDRVLKISDHRVLKRMQATVDAVNLLEDDFRALSDAELRAETDALRARHADGESLD
+LLLPEAFAAVREAAGRTLGQRHYDVQLLGGIALHQGNIAEMKTGEGKTLVATAPAYLNAL
+SGRGVHVVTVNDFLASYQADLMGRVFRFLGMQTGVIVAGQTPAVRREQYAADITYGTNNE
+FGFDFLRDNMAWSLDELVQREHHYAIVDEVDSILIDEARTPLIISGPAQGEANRWYGEFA
+RLVRRLEADTDYEVDHKKRTVGILGPGIEKVEDHLGITNLYETQNTTLIQFLNNAVKAKE
+LFKRDKDYVVLDGEVQIVDEHTGRVLKGRRYNEGLHQAIEAKEGVEVKPENQTLATVTLQ
+NYFRGYEKLAGMTGTAETEAAEFTSTYGLGVVVIPPNRERQRVDRNDVVYKNEKVKFDAV
+VDDIAERHAKGQPVLVGTTSVEKSEYLSTLLAKRGVRHEVLNAKNHAREAAIVAQAGRPG
+AVTVATNMAGRGTDIMLGGNAEFTAVARMQELGLDAAEDPEAYEARWPEVLAEAEAAVED
+AHRAVIEAGGLYVVGTERHDSRRIDNQLRGRSGRQGDPGESRFYLSLTDELMRNFNPGVA
+QRIMNSPSIPDDMALEFGFVSKAIQNAQAQVEGRNAEQRKNVLQYDDVMNRQREAIYTDR
+RSILEGEDLQDRVRRFVEDAVGNIVDAATEEGHATDWDLDQLWRDLAELYPVGISQEDVL
+DEVGGRGRLKAEVLKRELVSDALLAYEDREAQVGSEALREAERRVVLATIGRRWQEHLYE
+MDYLKEGIGLRAMAQREPLVEYQREGYTMFQNMLAAIREDAVRTLFQAQISAAPAPTSLP
+GVKDARAVTMAPQISVEGIDAPQQPAQLRFTGPSEDGQSAVTRSGTDSGATVAAGTNRRS
+RRQAERRGRRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000952.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000952.fa
new file mode 100644
index 0000000000000000000000000000000000000000..657c586c9af44e7d55fac0f34fb6d7be055806da
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000952.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01435
+MIAVACVEVETGRRALRDLSAWLSPEVLDKMTRRMDLLGLAEQDRPRARSAAAGVSRAPA
+AAPRPVGARVCEVAPGRVEASATVLCDGRARAFALRLERRISRWKVTSVEIG
+>MOLHKGIG_01465
+MTTLATRPRAASDRRTADTLLHGPAHSPAVLPRGEEIARRARTEQGREELRRVRSLAAVI
+AVACVEVETGRRALRDLSAWLSPEVLDKLTRRMELLGAVAPTGPGRRPSAAVPPRTPKSA
+PRPVGARVCEVAPGRVEASATVLWEGRARAFALRLERRLSRWKVTSVEIG
+>NAFOICDF_01338
+MTHSVRADRTMIRTSADRPAHRPAQEDPMTTLAPALAHGPTRPRPVSRTAPSRRDTESAL
+LRGPARRMSAVPTGEDLVRRAEQEDDREELRRLRSLAAVVAVACVETEAGRRPVRDLAGW
+LAPETYEKMCRRVDLLERTGTRPPSGSAPRPVGARVCAVRPGAVEASATVLVAGRARAVA
+LRIERRLSRWKVTHLEIG
+>MHAAABBN_01197
+MTALATRPRTASARRTADTLLHGPAHSPAVLPRGEEIARRARTEQGREELRRVRSLAAVI
+AVACVEVETGRRALRDLSAWLSPEVLDKLTRRMELLGAVAPTGPGRRPSAAVPPRTPASA
+PRPVGARVCEVAPGRVEASATVLWEGRARAFALRLERRLSRWKVTSVEIG
+>LFPAFLNI_01415
+MTTLATRPRAASDRRTADTLLHGPAHSPAVLPRGEEIARRARTEQGREELRRVRSLAAVI
+AVACVEVETGRRALRDLSAWLSPEVLDKLTRRMELLGAVAPTGPGRRPSAAVPPRTPASA
+PRPVGARVCEVAPGRVEASATVLWEGRARAFALRLERRLSRWKVTSVEIG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000955.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000955.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c0c2943a613b8f758e29f630f1dd9e13881b35c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000955.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01438
+MQRFLTLTDVAETLNISGQAARALIRSGELQAIQVGGRGQWRIEESWLQEYVDRQREATR
+ARVQEWAEADAKSR
+>MOLHKGIG_01462
+MQRFLTLTDVAETLNISGQAARALVRSGELQAIQVGGRGQWRIEVSWLEDYVERQKEVTR
+ARVREWTEADAKAR
+>NAFOICDF_01341
+MPQFLTLTDVAEVLNVSVGQARTLVRTGQLQAIQVGGRGQWRIEAGWLDEYVERQRELTR
+SRVAERTREDAGHGA
+>MHAAABBN_01194
+MQRFLTLTDVAETLNISGQAARALVRSGELQAIQVGGRGQWRIEVSWLEDYVERQKEVTR
+ARVREWTETDAQAR
+>LFPAFLNI_01412
+MQRFLTLTDVAETLNISGQAARALVRSGELQAIQVGGRGQWRIEVSWLEDYVERQKEVTR
+ARVREWTETDAKAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000958.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000958.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c6fce9562784eb1462f2445cbfa00fdc39fce06
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000958.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_01441
+MVSSLAQDPLTSHPDLADEDRSWLQLLVGDWQLVADLALADLVLWCPAPRPDPAEGFVAV
+AQVRPFTAPTLFHRDIVGSRARADLRAVVASTWSGGERPEGAGPVETPDGTLQVRLWPVV
+RRGRVVAVLSAHGDPNGRPSRSVIEENYIRTADSLLDMMQHGRWPAPEESAGLWAGGTPR
+VGDGLVVLGPDSVARFTSPNAVSALRRLGIGATLEGHRLTDVLAGTDAARQPSEEGTWAV
+LTGLRAGRREVQSRGASLTVRSVPLLGPDGWHGALLLLRDVTELRRQEQRLVSKDATIRE
+IHHRVKNNLQTVGSLLRMQARRTSSPEADRALRQAMRRVDTIALVHQTLSEEIDGQVPVD
+DLLKRQFRLAVEVSGDGRPLEAAASGEFGELPSHVTTPLALVLNELAANAVEHGTAPAGG
+RVELHAERELTPAGSVLVVSVTDGGSGVQDGWSPGEFQPAADGAGLGLRIVQTMVEGDLR
+GTLRWERLPDGGTRVVLRIPTA
+>MOLHKGIG_01459
+MVSSLAQDPLTSHPDIGDEDRAWLQRLVGDWQLVADLALADLVLWCPVPRRDEAGGFVAL
+AQVRPFTAPTLFHRDIVGSRARADLRAVVGQTWHGGERAEGAGPVEAPGGTLQVRLWPVV
+RAGRVIAVVSAHADPNGRPARSVIEENYSRTASTLLDMMQHGRWPAPEEPSGLWAGGTPR
+VGDGLVVLGPDSVAEFTSPNAVSALRRLGIASTLEGHRLTDVLASTEAARVPTDEGTWAV
+LTGLRAGRREVQSGGASLTVRSVPLLGPDGWQGALLLLRDVTELRRQEQRLLTKDATIRE
+IHHRVKNNLQTVGSLLRMQARRTSSPEAERALRQAMQRVDTIALVHQTLSEEIEDQVPVD
+GLLQRQFRLAVEVAGDGRPLQVAVTGEFGELPSHVTTPLALVLNELAANAVEHGTAPGGG
+CVGLHADRESTPAGTVLVVSVTDGGPAAPDGWVPGESPRAGEGSGLGLRIVHSLVEGDLR
+GTLRWERSDDGGTRVVLRLPLT
+>NAFOICDF_01344
+MVSTIASDPLNTHPDLGAEDRAWLQQLVGDWQLIADLALADLVLWCPLPVEVDGTGHLAM
+AQVRPFTAPTLFHRDIVGSRARADLRALVDRVWAAGAPADGTGPLVEPGATLKVRLWPVV
+RAGRVVGVVSAHEDPRTRPARSAVEDNYRTSADTLLDMVQHGRWPNPEDPPAYWIGGTPR
+VGDGLVVLGDDSRATFTSPNAVSALRRLGLPTTLAGHSLTELLGGTEAARRPVEEGSWAM
+LNGQRAGRTEVQANGATLTVRSVPLRNRDGWCGALIMLRDVTELRRQEQRLISKDATIRE
+IHHRVKNNLQTVGSLLRMQARRSDSPETGRALRQAMQRVDTIALVHQTLSEQIDAQLSVD
+ALMARQFRLAVEVAGDGRPLGTRVEGTFGELASHVVTSVALVLNELATNAVEHGTGEEGG
+VVSLQAHREDTPAGDVLVFSVTDGASVEDGPGEGFVPQPAPNGLGLRIVHSLVEGDLRGS
+IQWRRMPDGGTRVTVRLPVE
+>MHAAABBN_01191
+MVSSLAQDPLTSHPDIGDEDRAWLQRLVGDWQLVADLALADLVLWCPVPRRDEAGGFVAL
+AQVRPFTAPTLFHRDIVGSRARADLRAVVGQTWHGGERAEGAGPVEAPGGTLQVRLWPVV
+RAGRVIAVVSAHADPNGRPARSVIEENYSRTASTLLDMMQHGRWPAPEEPSGLWAGGTPR
+VGDGLVVLGPDSVAEFTSPNAVSALRRLGIASTLEGHRLTDVLASTEAARVPTDEGTWAV
+LTGLRAGRREVQSGGASLTVRSVPLLGPDGWQGALLLLRDVTELRRQEQRLLTKDATIRE
+IHHRVKNNLQTVGSLLRMQARRTSSPEAERALRQAMQRVDTIALVHQTLSEEIEDQVPVD
+GLLQRQFRLAVEVAGDGRPLQVAVTGEFGELPSHVTTPLALVLNELAANAVEHGTAPGGG
+CVGLHADRESTPAGTVLVVSVTDGGPAAPDGWVPGESPRAGEGSGLGLRIVHSLVEGDLR
+GTLRWERSDDGGTRVVLRLPLT
+>LFPAFLNI_01409
+MVSSLAQDPLTSHPDIGDEDRAWLQRLVGDWQLVADLALADLVLWCPVPRRDEAGGFVAL
+AQVRPFTAPTLFHRDIVGSRARADLRAVVGQTWHGGERAEGAGPVEAPGGTLQVRLWPVV
+RAGRVIAVVSAHADPNGRPARSVIEENYSRTASTLLDMMQHGRWPAPEEPSGLWAGGTPR
+VGDGLVVLGPDSVAEFTSPNAVSALRRLGIASTLEGHRLTDVLASTEAARVPTDEGTWAV
+LTGLRAGRREVQSGGASLTVRSVPLLGPDGWQGALLLLRDVTELRRQEQRLLTKDATIRE
+IHHRVKNNLQTVGSLLRMQARRTSSPEAERALRQAMQRVDTIALVHQTLSEEIEDQVPVD
+GLLQRQFRLAVEVAGDGRPLQVAVTGEFGELPSHVTTPLALVLNELAANAVEHGTAPGGG
+CVGLHADRESTPAGTVLVVSVTDGGPAAPDGWVPGESPRAGEGSGLGLRIVHSLVEGDLR
+GTLRWERSDDGGTRVVLRLPLT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000959.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000959.fa
new file mode 100644
index 0000000000000000000000000000000000000000..517238e395d7bb5f65b75bc0def559ba57cc1f71
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000959.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01442
+MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW
+GGMSEDERRAMKRRAARARRAS
+>MOLHKGIG_01458
+MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW
+GGMSEDERRAMKRRAARARRAS
+>NAFOICDF_01345
+MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRTCEVIDTCLKWAMESGQDSGVW
+GGMSEDERRAMKRRAARARRAS
+>MHAAABBN_01190
+MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW
+GGMSEDERRAMKRRAARARRAS
+>LFPAFLNI_01408
+MDWRSKAACLDKDPELFFPVGNTGPALLQIEEAKAVCRSCEVVDTCLKWAMESGQDSGVW
+GGMSEDERRAMKRRAARARRAS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000960.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000960.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df91c8953a42f7ca399b2173f10f4b768c55df80
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000960.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01443
+MAQSRRPDPVDPREAPAAPAPEGPRTGGRAPVAALVVAAALALQAAALLWLAGDAIAHLG
+DGVLPAGARVMLIVIYVLLGLWILVTSVALLRGRAWSRGAATAVQLFGVLLSSRLLSVGE
+PVVGGVLLAVSGIALVTLFSRPVTAHLSQAAREPSAE
+>MOLHKGIG_01457
+MAQSRRPDPVAPSESSGADATTVPPRPGRGLPVAVLVVAAALVLEAGALLWLAVDAVVHA
+ADGVLPAGARVMLVVIYALLTLWILATAVALLRGRAWSRGAAVAIQLFGVLLSSWLFSVD
+AAALGGPLLAVSGVALLTLFTTPVTRHLTPAPEASTDA
+>NAFOICDF_01346
+MSSSIPASPSGRRRMPAQAVVVAGVLGLEALTLVWLAVDGVAHLGAGALPTAAGVFLVVV
+YVLLAAWVGAVCGGMVRGRRFSRGAAVAIQLFAVILSTWLMSIGAPIAGGLLLVGSGAAL
+LCLFSGAVQAHLAGPDAGRPDAGRPDVG
+>MHAAABBN_01189
+MAQSRRPDPVAPSESSGADATTVPPRPGRGLPVAVLVVAAALVLEAGALLWLAVDAVVHA
+ADGVLPAGARVMLVVIYALLTLWILATAVALLRGRAWSRGAVVAIQLFGVLLSSWLFSVD
+AAALGGPLLAVSGVALLTLFTTPVTRHLTPAPEASTDA
+>LFPAFLNI_01407
+MAQSRRPDPVAPSESSGADATTVPPRPGRGLPVAVLVVAAALVLEAGALLWLAVDAVVHA
+ADGVLPAGARVMLVVIYALLTLWILATAVALLRGRAWSRGAVVAIQLFGVLLSSWLFSVD
+AAALGGPLLAVSGVALLTLFTTPVTRHLTPAPEASTDA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000962.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000962.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2b6c5a0316b5366877c82889a14facef1170590c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000962.fa
@@ -0,0 +1,39 @@
+>ACLBLIBL_01445
+MNPSSQHRSSTISDPRINERIRVPEVRLVGPNGEQVGIVRVEDALRLAAEADLDLVEVAP
+TAKPPVCKLMDFGKYKYEAAVKARESRKNQVNTVLKEVRFRLKIDKHDYETKTGHAKKFL
+SQGDKVKAIIQFRGREQQRPELGIKLLQQFAEDVAELGTVESQPRQDGRNMVMVIGPLRT
+KADARADQRKNSEDSHRERQGGGSRRDQAAREAKARAAEKAAANAAPVKNSVGDAFPEQL
+KAMAARTQESAPAAPAASAEPKQAPKAPAKPAAQAAPKQAPKAPAKPAAAAKPAAKPAAA
+PKPAAASKPASSGKPAAPASAPKPAAKPMPAPPKPAAPRGGAAKPGPRA
+>MOLHKGIG_01455
+MHGPGAAKWRPLSHPRQQDVRFAPGRVAGSPVGTAASWRAARTEGPVRRDRVEASVCVRA
+GEAFLVSEGPSGGRGVTRRLTQRSTTISDPRINERIRVPEVRLVGPNGEQVGIVRVEDAL
+RLAAEADLDLVEVAPTAKPPVCKLMDFGKYKYEAAVKARESRKNQVNTVLKEVRFRLKID
+KHDYETKTGHAKKFLSQGDKVKAIIQFRGREQQRPELGIKLLQQFAEDVAELGTVESQPR
+QDGRNMVMVVGPLRTKADARADQRKNSAESHRERQGGGSRRDQAAREAKERAAQKAASDS
+APVRNSVGDAFPEQLKAMAARTQENASAAPAETTQAPKTPAPAAPRPAAAAPAAKPASSA
+TPASAPKPAATPKPQSSAAPAATPKPRSAAKPAAPSSAPKPAAKPMPAPPKPAAPRGGAP
+KPGPRA
+>NAFOICDF_01348
+MESSSHPRQQDVRHGRAELPGHRVSAAVAPGSDDPWRPGGTAKGPIRGRFEASRLHPQGR
+PSAWRAPGVRSHQRPANRSGTISDPRINERIRVPEVRLVGPNGEQVGIVRVEDALRLAAE
+ADLDLVEVAPTAKPPVCKLMDFGKYKYEAAVKARESRKKQVNTVLKEVRFRLKIDQHDYE
+TKTGHAKKFLSQGDKVKAIIQFRGREQQRPELGIRLLQKFAEDVAELGTVESQPRQDGRN
+MVMVIGPLKAKAEAREEQRKSTEGTQRERKGGGSRRDQAAREAKAAAAEKAAANSAPVRN
+SIGDAFPEQLRSFAAQQTEAPAEQAPVPAPKAAPAKATPAKAPAPKPAATPAPKPPASAP
+KPPAAPKPAAAPKPAAKPMPAPPKPAAPKGAPKPGPRG
+>MHAAABBN_01187
+MEVAPTAKPPVCKLMDFGKYKYEAAVKARESRKNQVNTVLKEVRFRLKIDKHDYETKTGH
+AKKFLSQGDKVKAIIQFRGREQQRPELGIKLLQQFAEDVAELGTVESQPRQDGRNMVMVV
+GPLRTKADARADQRKNSAESHRERQGGGSRRDQAAREAKERAAQKAASDSAPVRNSVGDA
+FPEQLKAMAARTQENASAAPAETTQAPKTPAPAAPRPAAAAPAAKPASSATPASAPKPAA
+TPKPQSSAAPAATPKPRSAAKPAAPSSAPKPAAKPMPAPPKPAAPRGGAPKSGPRA
+>LFPAFLNI_01405
+MHGPGAAKWRPLSHPRQQDVRFAPGRVAGSPVGTAASWRAARTEGPVRRDRVEASVCVRA
+GEAFLVSEGPSGGRGVTRRLTQRSTTISDPRINERIRVPEVRLVGPNGEQVGIVRVEDAL
+RLAAEADLDLVEVAPTAKPPVCKLMDFGKYKYEAAVKARESRKNQVNTVLKEVRFRLKID
+KHDYETKTGHAKKFLSQGDKVKAIIQFRGREQQRPELGIKLLQQFAEDVAELGTVESQPR
+QDGRNMVMVVGPLRTKADARADQRKNSAESHRERQGGGSRRDQAAREAKERAAQKAASDS
+APVRNSVGDAFPEQLKAMAARTQENASAAPAETKQAPKTPAPAAPRPATKPASSATPASS
+PKPAATPKPQSSAAPAATPKPRSAAKPAAPSSAPKPAAKPMPAPPKPAAPRGGAPKPGPR
+A
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000967.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000967.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1ff61718601f1c77493d899fa857aae4478f3bdf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000967.fa
@@ -0,0 +1,37 @@
+>ACLBLIBL_01451
+MRWEAQTLRSESGAQRAAAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNAV
+PAASAMPFRWTVNPYRGCTHACRYCYARSTHAFLDLDAGEDFDRQIVVKVNVAQVLRAEL
+ARPTWGREAVALGTNTDPYQRAEGRYSLMPGIIEALADSGTPFSVLTKGTLLARDVPLLQ
+AASRSVPVQVSLSLAMLDPAVAAAVEPGTPSPAARLRLIERLAAAGADVTVMAMPLLPWL
+TDGDRDLDALMRALAAAGAARVMPGALHLRPGAKEWYLRWIRQEHPDLLAGYEQMYARSA
+YAPESYRRTLARAAGEAAARHGLTRGGAHGIRREDGPVARPVPRSTPVAVPAPAAPAQPA
+LF
+>MOLHKGIG_01448
+MRWEAQTLRSEGGAQRATAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNSV
+PSASAMPFRWTVNPYRGCTHACRYCYARSTHTFLELDAGADFDRQIVVKVNVAEVLRAEL
+ARPTWGREAVALGTNTDPYQRAEGRYALMPGIIRALADSGTPFSVLTKGTLLARDVPLLQ
+AASRQVPVQVSLSLAMLDPAIAAAVEPGTPSPTARLRLIERLAAAGADVTVMAMPLLPWL
+TDGDREIDALMRALADAGAARVMPGALHLRPGAKEWYLDWIRREHPDLLAGYEQMYARSA
+YAPESYRRMLTRMAGEAAARHGLARGGAHGIRREDGPPARRRPASRPSAPAAQPALF
+>NAFOICDF_01355
+MRWEAQTLRTGGGAQRPGAGTPAGSPATLPLPGLQRIVSPPEFAGVTFHEVLARSALNKV
+PASSAMPFRWTVNPYRGCTHACVYCYARGTHRYLDLGPGEDFDRQIVVKTNAPEVLRAEL
+SRPGWTREPVALGTNTDPYQRAEGRYRLMPGIITALADTGTPFSILTKGTLLGRDAPALQ
+AAAAQTSVQVGLSLALLDPSLAAAVEPGTPSPAARLRLISRLAEAGVEVSVMAMPLLPWL
+TDSDRQLDRLMAALADAGAHSVLAGTLHLRPGAREWFLGWIDREHPHLAADYRRMYARSA
+YAPQAYRRVVSQAAREAAARHGLRHGGAHTITREDGPGPRGGASAPLSAPAGTTGAEQAD
+TAADAVRPVIAQPTLF
+>MHAAABBN_01180
+MRWEAQTLRSEGGAQRATAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNSV
+PSASAMPFRWTVNPYRGCTHACRYCYARSTHTFLELDAGADFDRQIVVKVNVAEVLRAEL
+ARPTWGREAVALGTNTDPYQRAEGRYALMPGIIRALADSGTPFSVLTKGTLLARDVPLLQ
+AASRQVPVQVSLSLAMLDPAIAAAVEPGTPSPTARLRLIERLAAAGADVTVMAMPLLPWL
+TDGDREIDALMRALADAGAARVMPGALHLRPGAKEWYLDWIRREHPDLLAGYEQMYARSA
+YAPESYRRMLTRMAGEAAARHGLARGGAHGIRREDGPPARRRPASRPSAPAAQPALF
+>LFPAFLNI_01398
+MRWEAQTLRSEGGAQRATAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNSV
+PSASAMPFRWTVNPYRGCTHACRYCYARSTHTFLELDAGADFDRQIVVKVNVAEVLRAEL
+ARPTWGREAVALGTNTDPYQRAEGRYALMPGIIRALADSGTPFSVLTKGTLLARDVPLLQ
+AASRQVPVQVSLSLAMLDPAIAAAVEPGTPSPTARLRLIERLAAAGADVTVMAMPLLPWL
+TDGDREIDALMRALADAGAARVMPGALHLRPGAKEWYLDWIRREHPDLLAGYEQMYARSA
+YAPESYRRMLTRMAGEAAARHGLARGGAHGIRREDGPPARRRPASRPSAPAAQPALF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000970.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000970.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f9d7514aad687e5133cb070d03244d891854949
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000970.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01454
+MTPSPETGAEPTAPAAEISPVDAAAVDAAVQAALAAFDAATDLDELKAARLAHTGDRAPL
+TLANKGIGALPKERKAEAGKLMGDARGRLNKALAARTEVLEAEQAERILREETVDVTAAV
+RRRRVGARHPLSLTMDRVSEIFVGMGWEIAEGPELESEWFNFDSLNFAPDHPAREMQDTF
+FVEPSEAHLLLRTHTSPVQMRSLLERGAPTYVLCPGRTFRTDELDATHTPVFHQFEGLAV
+DRGLTMAHLRGTLEYFARQMFGEEAAIRLRPNFFPFTEPSAELDIWHPGAKGGPRWIEWG
+GCGMVHPNVLRAAGLDPEEFSGFAFGMGVERTLMFRNEVPDMRDMIEGDVRFSQHFGMEV
+>MOLHKGIG_01444
+MTPSPETGAEPTAPVAEISPVDAEAVEAAVQAALAAYEAAADLDELKAARLAHTGDRAPL
+TLANKAIGALPKERKAEAGKLMGAARGRLGKALAARTEVLEAEQAARILREETVDVTTAV
+RRRRVGARHPLSLTMDRVSEIFVGMGWEIAEGPELESEWFNFDSLNFAPDHPAREMQDTF
+FVDPAEAHLLLRTHTSPVQMRSLLERGAPTYVLCPGRTFRTDELDATHTPVFHQFEGLAV
+DKGLTMAHLRGTLEYFARQMFGAEAAIRLRPNFFPFTEPSAELDIWHPGAKGGPRWIEWG
+GCGMVHPNVLRAAGLDPEEYSGFAFGMGVERTLMFRNEVPDMHDMIEGDVRFSQHFGMEV
+>NAFOICDF_01362
+MTSSPETGASEDAPQLSPVDGPAVDAAVAEALAAFEAAADLEELKAARLAHQGDRAPLTL
+ANKAIGTLPKEQKAEAGKTMGAARSRIGKALAARTEVLEAEHAARMLAEETVDVTAAAAR
+RLPGARHPLSLLQERVSDIFVGMGWEIAEGPELEHDWFNFNALNFPPDHPAREMQDTFFV
+EPLESNLLLRTHTSPVQVRSMLERGAPVYVLCPGRTFRTDELDATHTPVFHQFEGLAVDR
+GLTMADLRGTLEYFARQMFGPEAEIRLRPNFFPFTEPSAEMDIWHPQAKGGPRWIEWGGC
+GMVHPNVLRSAGIDPEEFSGFAFGMGIERTLMFRNEVPDMRDMIEGDVRFSQHFGMEL
+>MHAAABBN_01176
+MTPSPETGAEPTAPVAEISPVDAEAVEAAVQAALAAYEAAADLDELKAARLAHTGDRAPL
+TLANKAIGALPKERKAEAGKLMGAARGRLGKALAARTEVLEAEQAARILREETVDVTTAV
+RRRRVGARHPLSLTMDRVSEIFVGMGWEIAEGPELESEWFNFDSLNFAPDHPAREMQDTF
+FVAPAEAHLLLRTHTSPVQMRSLLERGAPTYVLCPGRTFRTDELDATHTPVFHQFEGLAV
+DKGLTMAHLRGTLEYFARQMFGAEAAIRLRPNFFPFTEPSAELDIWHPGAKGGPRWIEWG
+GCGMVHPNVLRAAGLDPEEYSGFAFGMGVERTLMFRNEVPDMHDMIEGDVRFSQHFGMEV
+>LFPAFLNI_01394
+MTPSPETGAEPTAPVAEISPVDAEAVEAAVQAALAAYEAAADLDELKAARLAHTGDRAPL
+TLANKAIGALPKERKAEAGKLMGAARGRLGKALAARTEVLEAERAARILREETVDVTTAV
+RRRRVGARHPLSLTMDRVSEIFVGMGWEIAEGPELESEWFNFDSLNFAPDHPAREMQDTF
+FVAPAEAHLLLRTHTSPVQMRSLLERGAPTYVLCPGRTFRTDELDATHTPVFHQFEGLAV
+DKGLTMAHLRGTLEYFARQMFGAEAAIRLRPNFFPFTEPSAELDIWHPGAKGGPRWIEWG
+GCGMVHPNVLRAAGLDPEEYSGFAFGMGVERTLMFRNEVPDMHDMIEGDVRFSQHFGMEV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000971.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000971.fa
new file mode 100644
index 0000000000000000000000000000000000000000..243bf1045eae069de54ef24a2bc839f8b4ccfcd7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000971.fa
@@ -0,0 +1,80 @@
+>ACLBLIBL_01455
+MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPSDELRGPIVVGQVLSKEPEP
+QKNGKTINWCTVRVVPEGAEQTLTGEGIDPSGVQGVVCGAHNFEVGDKVVVTLPGAVLPG
+DFRISPRKTYGHVSAGMIASVRELGIGDDHDGILVLSTLGLDPEPGTDALEVLDLQGEAA
+EINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAALTPPAADDAGHPVRIADDAPIYGAP
+GATRFVARTVSGVDASRPTPPWMAARLRLAGIRSISLPVDISNYVMWELGQPLHFYDAQK
+LAGEIVVRRARAGETLRTLDDKERTLDPEDLLITDDSGPIGLAGVMGGLATEVTDATTTI
+VIESANFDPISIARTRRRHRLPSEASKRNERGVDWEIADEAAERAVQLLVELAGGTAEPG
+VTDVGTRPELAVVEMAADFPTALVGVEYTADEVAETLRALGAQVEAAEAADGAAPRLRVT
+APSWRTDLRIPEDLVEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGHT
+EVLAYPFVSAEQNRRFGVDSEEQGEALEMVALANPISSQYRYMRLSLLPGLVEIARRNLG
+RGFRDLALYEAGLVFLPGTQLGSASIPPRAAHPAPEVLADLEAGIPAQPWRVAGLYAGHD
+SAPGPDHAPRPVDWQDAVSGALAVADVLGVELAVRQGRHHAFHPGRVAELVVLGERGDQV
+VGVAGELHPQWLEAEDLPARTSVWELDLDALCAAAPPAVVAVPLSTYPMSTQDVALVVEE
+AVVAGDVRASLAEGAGELLESVELFDVYRGPGVPEGSKSLAFSLRFRAPDRTLTAEEASE
+ARAAATALAAQRHGAVQR
+>MOLHKGIG_01443
+MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPAAELQGPIVVGQVLSKEPEP
+QKNGKTINWCSVRVVPEGAAQPLTGEGIEPSGVQGIVCGAHNFEVGDKVVVALPGAVLPG
+DFRISPRKTYGHVSAGMIASSTELGMGDDGTDGIIVLGDLGLDPEPGTDARDVLDLHGEA
+AEINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAAVHPPAADDAGPAVRIDDDAPIHGE
+PGATRFVARTVSGVDATRPTPPWLAARLRLAGIRTISLPVDISNYVMWELGQPLHFYDAD
+TLSGEIVVRRARAGETLTTLDGKERELDPEDLLITDDSGPIGLAGVMGGAATEVTDATTT
+IVVESANFDPVSIARTRRRHRLPSEASKRNERGVDWEIADEAAERAVQLLVELAGGTAEP
+GVTDVGTRPQPAVVEMAADFPSALVGVAYTTDEVVETLRALGAEVAVAEAAADVAPRLTV
+TAPSWRTDLRIPEDLAEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGL
+TEVLAYPFVSEEQNRRFGADSDAQGQALAMVALANPIASQYRYLRLSLLPGLVETARRNL
+GRGFRDLALYEMGLVFLPGAQLGSATIPPRAVHPSAEVLADLEAGIPAQPWHVAGLYAGH
+DSAPGPDHDPRPVDWQDAIAGALDVADVLGVELTVRQGRHHAFHPGRVAELVVVTEHGDR
+VVGVAGELHPQWLEAEDLPARTSVWELDLDALCAAAPEIVVAAPLSTFPVSTQDVALVVD
+EAVVAGDVRATLAEGAGELLEAVELFDVYRGAGVPEGRKSLAFSLRFRAPDRTLTAEEVS
+EARAAATALAAQRHGAVQR
+>NAFOICDF_01363
+MRIPLDWLREFAQVPADATAEDVLADLVTVGLEEEDVHRPSDELTGPLVVGQVLTREPEP
+QKNGKTINWCSVRVVPEGAEQTLTGEGIDPSGVQGIVCGAHNFEVGDKVVVCLPGAVLPG
+DFRISPRSTYGHVSAGMMASARELGLGDDHDGIIVLGDMGLDPEVGTDVVDLFHLREEAA
+EVNVTPDRSYAFSIRGIAREYAHATGTAFTDPAAAVTAPEANDAGPAVTLADGAGIYGVP
+GCDRFVARVVEGIDPAAATPPWMAARLRLAGIRPHSLAVDVSNYVMWELGQPLHFYDADR
+LTGGITVRRAAAGETLRTLDDKERTLDPEDLVIADESGAIGLAGVMGGAATEVSEGTTRV
+LIESAHFDAVSIARTRRRHRLPSEASKRNERGVDWEIADEAAERAVQLLVELAGGTPAQG
+VTDVGTRPEPVVVELDPEYPARRIGVDYPRERVVELLTGLGASVEDAGDLLQVTAPTWRH
+DLRIPEDLVEEVARLDGYANIPSTLPVAPPGRGLTRAQVHRRRVADTLAAAGLTEVLDYP
+FVSEGQNRLFGSATPEEGAAQRMVRLANPISSEFGWMRTTLLPNLLETVRRNVSRGFKDV
+ALFEVGAVFLPGDGALGSPSNEPIGVKPSAETLAELDAGIPAQPRHVAGAFAGHEAAPGA
+GFAPRAFDWQDPIAAALAVGRAVGVELTVVQGTHQAFHPGRTATLSLPDGTAVGVAGELL
+PAWLEDADMPARTGAFELDLDAVLAAAADRVVARPLSTYPASQQDVALVVADDVVAGDVR
+ATLAEGAGELLEEVALFDVYAGKGVPEGHKSLAFSLRFRAPDRTLTADEASEAREAATAL
+AAERHGAVQR
+>MHAAABBN_01175
+MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPAAELQGPIVVGQVLSKEPEP
+QKNGKTINWCSVRVVPEGAAQPLTGEGIEPSGVQGIVCGAHNFEVGDKVVVTLPGAVLPG
+DFRISPRKTYGHVSAGMIASSTELGVGDDGTDGIIVLGDLGLDPEPGTDARDVLDLHGEA
+AEINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAAVHPPAADDAGPAVRIDDDAPIHGE
+PGATRFVARTVSGVDATRPTPPWLAARLRLAGIRTISLPVDISNYVMWELGQPLHFYDAD
+TLSGEIVVRRARAGETLTTLDGKERELDPEDLLITDDSGPIGLAGVMGGAATEVTDATTT
+IVVESANFDPVSIARTRRRHRLPSEASKRNERGVDWEIADEAAERAVQLLVELAGGTAEP
+GVTDVGTRPQPAVVEMAADFPSALVGVAYTTDEVVETLRALGAEVAVAEAAADVAPRLTV
+TAPSWRTDLRIPEDLAEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGL
+TEVLAYPFVSEEQNRRFGADSDAQGQALAMVALANPIASQYRYLRLSLLPGLVETARRNL
+GRGFRDLALYEMGLVFLPGAQLGSATIPPRAVHPSAEVLADLEAGIPAQPWHVAGLYAGH
+DSAPGPDHDPRPVDWQDAIAGALDVADVLGVELTVRQGRHHAFHPGRVAELVVVTEHGDR
+VVGVAGELHPQWLEAEDLPARTSVWELDLDALCAAAPEIVVAAPLSTFPVSTQDVALVVD
+EAVVAGDVRATLAEGAGELLEAVELFDVYRGAGVPEGRKSLAFSLRFRAPDRTLTAEEVS
+EARAAATALAAQRHGAVQR
+>LFPAFLNI_01393
+MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPAAELQGPIVVGQVLSKEPEP
+QKNGKTINWCSVRVVPEGAAQPLTGEGIEPSGVQGIVCGAHNFEVGDKVVVTLPGAVLPG
+DFRISPRKTYGHVSAGMIASSTELGMGDDGTDGIIVLGDLGLDPEPGTDARDVLDLHGEA
+AEINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAAVHPPAADDAGPAVRIDDDAPIHGE
+PGATRFVARTVSGVDATRPTPPWLAARLRLAGIRTISLPVDISNYVMWELGQPLHFYDAD
+TLSGEIVVRRARAGETLTTLDGKERELDPEDLLITDDSGPIGLAGVMGGAATEVTDATTT
+IVVESANFDPVSIARTRRRHRLPSEASKRNERGVDWEVADEAAERAVQMLVELAGGTAEP
+GVTDVGTRPQPAVVEMAADFPSALVGVAYTTDEVVETLRALGAEVAVTEAADGAAPRLTV
+TAPSWRTDLRIPEDLAEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGL
+TEVLAYPFVSEEQNRRFGADSDAQGQVPAMVALANPIASQYRHLRLSLLPGLVETARRNL
+GRGFRDLALYEMGLVFLPGAQLGSATIPPRAVHPSPEVLADLEAGIPAQPWHVAGLYAGH
+DSAPGPDHAPRPVDWQDAVAGALDVADVLGVELTVRQGRHHAFHPGRVAELVVVTEHGDR
+VVGVAGELHPQWLEAEDLPARMSVWELDLDALCAAAPETVVAAPLSTFPVSTQDVALVVD
+EAVVAGDVRATLAEGAGELLEAVELFDVYRGAGVPEGRKSLAFSLRFRAPDRTLTAEEAS
+EARAAATALAAQRHGAVQR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000972.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000972.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f11fdeb18831bf7672963f39675b360ffe9ace94
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000972.fa
@@ -0,0 +1,24 @@
+>ACLBLIBL_01456
+MPGGDGDGAEDAAGPDDGPAAAPGLGLDVERVDAPAFADRDALGEVGFSTAERAWVAALP
+RSERPAARARLWTRKEALVKAAGTGFTGDPADVAALHPPPGVVLLDVAAGLPDGIVGSVA
+LRRA
+>MOLHKGIG_01442
+MSVATGPWGLTSAVPASAGAADAVSALLGQVRTALTAAWGVPVGPLGLRHACPRCGSAAH
+GVPALTGLPPGRVALVSFTRVRMPGTEDRARIGAWWAPARPADGLGLGVDVERADAAAFA
+DEDGLGGVGFSTAERARVRELPAPERPAARARLWTRKEALVKAAGTGFTGDPAAVDALTV
+PADVVLVDLTDRLPGGLLGALALRGR
+>NAFOICDF_01364
+MTTAPTSPTRGIEVGAVGVSRTEGTAQVLAALGTRLGLGPRALALAHSCPGCGATDHGAP
+ALRRAGDGTTPGGAPGDDGGPVLPAVSLTHVDGPRPVTVLAWCTPSVAGTAWGIGVDAED
+PTAPQTLRAFAAGADGAAEIDAVAFAAEERAALAGLSPEGALAERVRLWTVKEALVKARG
+TGLDRDPAEVRPQLGEAVVPLADPRLPPGVVGTVAWRPAS
+>MHAAABBN_01174
+MSVATGPWGLTSAVPASAGAADAVSALLGQVRTALTAAWGVPVGPLGLRHACPRCGSAAH
+GVPALTGLPPGRVALVSFTRVRMPGTEDRARIGAWWAPARPADGLGLGVDVERADAAAFA
+DEDGLGGVGFSTAERARVRELPAPERPAARARLWTRKEALVKAAGTGFTGDPAAVDALTV
+PADVVLVDLTDRLPGGLLGALALRGR
+>LFPAFLNI_01392
+MSAATGPWGLTSAVPASAGAADAVSALLGQVRTALTAAWGVPVGPLGLRHACAGCGSAAH
+GVPALTGLPPGRVALVSFTHVRMPGAEDRARIGAWWAPARPADGLGLGVDVERADAAAFA
+DEDGLGGVGFSTAERARVRELPAPERPAARARLWTRKEALVKAAGTGFTGDPAAVDALTV
+PADVVLVDLTDRLPGGLLGALALRGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000975.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000975.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c9e69508cf8f67ca294e28756cb50eee6d9a2fe7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000975.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01460
+MTHTVAVSGASGYAGGEALRLLAGHPDVAVGAITAHSNAGERLGALQPHLHSLADRVLEE
+TTADVLAGHDVVILALPHGASGALAAQIAERSPETLVIDAGADHRLESAADWEAFYGSEH
+AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT
+SGAGKAAKPHLLGSEVMGGMSPYGVGGGHRHTPEIEQGLSQAAGERVQISFTPTLAPMAR
+GILATATARLRPGADPAAVRGAWERAYADERFVHLLPEGLWPATKSVLGSNHVQMQLAVD
+ERAGRVIVTAALDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP
+>MOLHKGIG_01438
+MTHTVAVSGASGYAGGEALRLLAGHPSVTVGAITAHSNAGERLGALQPHLHALADRVLAE
+TTAEVLAGHDVVILALPHGASGALAAEIAERSPDTLVIDAGADHRLESAADWEAFYGTAH
+AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT
+SGAGKALKPHLLGAEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVRVSFTPTLAPMPR
+GILATATARLRPGVAAADVRAAWAAAYGGERFVHLLPEGQWPTTKAVLGSNHVQLQLAVD
+ERAGRVIVCAVLDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP
+>NAFOICDF_01368
+MTFTVAVSGASGYAGGEVLRLLAGHPEVQIGAISAHSNAGERLGSLQPHLHALADRVLDD
+TTADVLAGHDVVVLALPHGASAAVAAELAERSPRTLVIDAGADHRLESAADWERFYGTDH
+AGTWPYGLPELPGQRERLAGATRIAVPGCYPTTSILALAPGFAAGLLETRDVVIVAASGT
+SGAGRAAKPHLLGSEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVQISFTPTLAPMPR
+GILATATARLKEGVTADRVRAAWEDAYGPERFVHLLPEGQWPTTKAVVGSNHVVMQLAVD
+PHAGRVIVTAALDNLTKGTAGGALQSMNIALGLPEQLGLEIQGVAP
+>MHAAABBN_01170
+MTHTVAVSGASGYAGGEALRLLAGHPSVTVGAITAHSNAGERLGALQPHLHALADRVLAE
+TTADVLAGHDVVILALPHEASGALAAEIAERSPDTLVIDAGADHRLESAADWEAFYGTAH
+AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT
+SGAGKALKPHLLGAEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVRVSFTPTLAPMSR
+GILATATARLRPGVAAADVRAAWAAAYGGERFVHLLPEGQWPTTKAVLGSNHVQLQLAVD
+ERAGRVIVCAALDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP
+>LFPAFLNI_01388
+MTHTVAVSGASGYAGGEALRLLAGHPSVTVGAITAHSNAGERLGALQPHLHALADRVLAE
+TTAEVLAGHDVVILALPHGASGALAAEIAERSPDTLVIDAGADHRLESAADWEAFYGTAH
+AGTWPYGLPELPGQRERLAGTRRIAVPGCYPTTSILALAPGFAAGLLEPQDVVIVAASGT
+SGAGKALKPHLLGAEVMGGMSPYGVGGGHRHTPEIEQGLAQAAGEPVRVSFTPTLAPMSR
+GILATATARLRPGVAAADVRDAWAEAYGGERFVHLLPEGQWPTTKAVLGSNHVQLQLAVD
+ERAGRVIVCAALDNLTKGTAGGAVQSMNIALGLPEQAGLEQQGVAP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000976.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000976.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1dc1e8b34d65c31698708bab5e1c9fa79673c191
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000976.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01461
+MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNDGPRRAAAAVFTANRVAAAPVLWSRQAVS
+DGRADAVVLNSGGANAATGAPGFQDAHATAEHAAEALGVSSGDVLVCSTGLIGERLDRER
+LFAGVAAAAGALSADGGEDAAVAIKTTDTVAKTAQARGEGFIVGGMAKGAGMLAPGMATM
+LCVITTDADVPAAVLDAALKDAVRTTFNRVDSDGCMSTNDTVILLASGAAGVAPDPEAFA
+ATLHEVCADLSRQLVADAEGAAHDVAVRVHGAQTEDAAEAVARAVTRSNLFKAAIFGQDP
+NWGRVIAAVGTVPEEVAAFDPYALDVSFNGVQVCRGSGVGEDRALVDLSAREVLVEVDLH
+AGDAEATVWTNDLTHDYVHENSAYST
+>MOLHKGIG_01437
+MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNQGPRDAAAAVLTENRVAAAPVVWTRRAVR
+DGRATAVVLNSGGANAATGAEGLEDARRTAEHAAAALGTAADDVLVCSTGLIGERLPMDT
+LTAGVAEAVAALSPDGGEDAAVAIKTTDTVAKTAVARGAGFTVGGMAKGAGMLAPGMATM
+LSVITTDADVPAPALDAALREAVRATFNRVDSDGCMSTNDTVILLASGASGTAPEPAAFA
+AALHEVCADLSRQLVADAEGARHDIAVRVVHAETEEAAEAVARAVGRSNLFKTAIFGQDP
+NWGRVIAAVGTVPESVAAFDPYALDVRFNGVQVCRASGVGEDRSRVDLTAREVLVEVDLH
+AGDAEATVWTNDLTHDYVHENSAYST
+>NAFOICDF_01369
+MSVTAAQGFRAAGVTAGLKPSGKPDVAVVVNDGPSHTAAGVFTTNRVAAAPVRWSRQVLT
+DGRADAVVLNSGGANAATGHAGFQDAHRTAEHAAEALGVSAGDVVVCSTGLIGERLPLDT
+LLAGVDAAAAGLAEDGGADAALAIMTTDTVPKEAQASGEGWTVGGMAKGAGMLAPGMATM
+LCVVTTDADLPAAALRAALEEAVRTTFNRVDSDGCMSTNDTVVLLASGASGVAPEPTQFG
+AALHAVCADLARQLVGDAEGAGHDVLIRVVNASDEDAGEAVARAVSRSNLLKTAIFGQDP
+NWGRVISAVGTVPEEVAPFDADALDVSFNGVQVCRAAGVGDSRAGVDLSGREVVIEIDLH
+AGDAVVELWTNDLTHDYVHENSAYST
+>MHAAABBN_01169
+MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNEGPRDAAAAVLTENRVAAAPVVWTRRAVR
+DGRATAVVLNSGGANAATGAEGLEDARRPAEHAAAALGTSADDVLVCSTGLIGERLPMDT
+LTAGVAEAVAALSPDGGEDAAVAIKTTDTVAKTAVARGAGFTVGGMAKGAGMLAPGMATM
+LSVITTDADVPAPALDAALREAVRATFNRVDSDGCMSTNDTVILLASGASGTAPEPEAFA
+AALHEVCADLSRQLVADAEGARHDIAVRVVHAETEEAAEAVARAVGRSNLFKTAIFGQDP
+NWGRVIAAVGTVPESVAAFDPYALDVRFNGVQVCRASGVGEDRSRVDLSAREVLVEVDLH
+AGDAEATVWTNDLTHDYVHENSAYST
+>LFPAFLNI_01387
+MSVTAAQGFRAAGVTAGLKASGTPDVAVVVNEGPRRAAAAVLTENRVAAAPVVWTRRAVR
+DGRATAVVLNSGGANAATGAEGLADARRTAEHAAAALATAADDVLVCSTGLIGERLPMDT
+LTAGVSEAVAALSPDGGEDAAVAIKTTDTVAKTAVARGAGFTVGGMAKGAGMLAPGMATM
+LSVITTDADVPAPALDAALREAVRATFNRVDSDGCMSTNDTVILLASGASGTAPEPEAFA
+AALHEVCADLSRQLVADAEGARHDIAVRVVHAETEEAAEAVARAVGRSNLFKTAIFGQDP
+NWGRVIAAVGTVPESVAAFDPYALDVRFNGVQVCRASGVGEDRSRVDLTAREVLVEVDLH
+AGDAEATVWTNDLTHDYVHENSAYST
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000978.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000978.fa
new file mode 100644
index 0000000000000000000000000000000000000000..63e521a89229198022ca67721aba8ad96e9bb692
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000978.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_01463
+MSTTQDALLARYADSLTGVFGRPARVLVRGEGVHVWDADGRRYTDLLAGIAVNSLGHAHP
+AVVRAVREQIAGLGHVSNLFTSEPQIRLAEELLAVADAPAGSTVFFANSGTEANEAAFKL
+ARRHGGQDPSGSRTRVIALERAFHGRTMGALALTHKEAYRAPFEPLPGGVEHVPGGDVDA
+LRAALAPGASGATVAAVVLEPVQGEAGVHGWPVGYLAQVRALTREAGALMILDEVQSGMG
+RTGTWFGFQNPSVTGSDDPVLPDAFTLAKGLGGGVPIGALVCVGPEVSGLLSAGQHGTTF
+GGNPLATAAGLAVLETIRSEGLLEHVRAAGERAAKLLADLPEVAAVRAHGLWIGVDLAAP
+RGPVPDGGLAPAVVAAGLEAGWILNATGPDTLRLAPPLVIAAEDLERFVELLPALVAAAT
+TEGDPS
+>MOLHKGIG_01435
+MSTDQSALLERYHAALTGVFGRPTRVLVRGEGVHVWDADGRRYTDLLAGIAVNALGHGHP
+ALVRAVSEQVATLGHVSNLFTSEPQIRLAERLLELAGAPAGSTVFFANSGTEANEAAFKL
+ARRHGADDPSGRRTRVIALERAFHGRTMGALALTHKEAYRAPFEPLPGGVKHVPGGDAAA
+LRAALAPDDDGATVAAVILEPVQGEAGVHGWPAGYLAEVRAATREAGALMILDEVQSGVG
+RTGTWFGFQNPAVTGAAEPVVPDAFTLAKGLGGGVPIGALVCVGPAVSGLLTAGQHGTTF
+GGNPLATAAGLAVLQTVEDEGLLGHVRAAGEAVAALLEDLPEVAAVRGHGLWIGVDLADP
+AGPAPAGGLAPAVVAAGLEAGWILNATGPSTLRLAPPLTVPVAELERFAAALPGLVAAAL
+TPAEGDRP
+>NAFOICDF_01371
+MSTAPGTDPAAPQEELLARYAHALTGVFGAPARALVRGSGTSVWDADGREYTDLVAGIAV
+NSLGHAHPAVVEAVSRQVATLGHVSNLFTSEPQVRLAEALLDRAGLPEGSSVFFCNSGTE
+ANEAALKLARRHGTQDPTGRRTRVLALERAFHGRTMGALALTHKEAYRAPFEPLPGGVEF
+IAGGDAGALAAALAPDAEGRTVAAVVLEPVQGEAGVHGWPAAYLARVRDLTREAGALMIL
+DEVQSGVGRTGTWFAFQNPQVTGSGAPVVPDAFTLAKGLGGGVPIGALVSVGPQVSRLLA
+PGQHGTTFGGNPLATAAGLAVVETLEAEGLLDHVRTVGARVSERLETLAEVTAVRAYGLW
+IGVDLADDAAASPTGGLAPAVVRAGLDAGWILNATGPRTLRLAPPLNVEAADLDRFADAL
+PALVRAARAAAPTPHAPKEETA
+>MHAAABBN_01167
+MSTDQSALLKRYHAALTGVFGRPTRVLVRGEGVHVWDADGRRYTDLLAGIAVNALGHGHP
+ALVRAVSEQVATLGHVSNLFTSEPQIRLAERLLELAGAPAGSTVFFANSGTEANEAAFKL
+ARRHGADDPSGRRTRVIALERAFHGRTMGALALTHKEAYRAPFEPLPGGVEHVPGGDAAA
+LRAALAPDDDGATVAAVILEPVQGEAGVHGWPAGYLAEVRAATREAGALMILDEVQSGVG
+RTGTWFGFQNPAVTGAAEPVVPDAFTLAKGLGGGVPIGALVCVGPAVSGLLTAGQHGTTF
+GGNPLATAAGLAVLQTVEDEGLLGHVRAAGEAVAALLEDLPEVAAVRGHGLWIGVDLADP
+AGPAPAGGLAPAVVAAGLEAGWILNATGPSTLRLAPPLTVPVAELERFAAALPGLVAAAL
+TPAEGDRP
+>LFPAFLNI_01385
+MSTDQSALLERYHAALTGVFGRPTRVLVRGEGVHVWDADGRRYTDLLAGIAVNALGHGHP
+ALVRAVSEQIATLGHVSNLFTSEPQIRLAERLLELAGVPAGSTVFFANSGTEANEAAFKL
+ARRHGADDPSGRRTRVIALERAFHGRTMGALALTHKEAYRAPFEPLPGGVEHVPGGDAAA
+LRAALAPDDDGATVAAVILEPVQGEAGVHGWPAGYLAEVRAATREAGALMILDEVQSGVG
+RTGTWFGFQNPAVTGAAEPVVPDAFTLAKGLGGGVPIGALVCVGPAVSRLLTAGQHGTTF
+GGNPLATAAGLAVLQTVEDEGLLGHVRAAGEAVAALLEDLPEVAAVRGHGLWIGVDLADP
+AGPVPAGGLAPAVVAAGLEAGWILNATGPSTLRLAPPLTVPVAELERFAAALPGLVAAAL
+TPAEGDRP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000979.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000979.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ffa006d492726b3a39e1368674c42b20f9c6661
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000979.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01464
+MTPAPTPAPAAVRHFLVDTDLTPGEQAEVLDLAAQMKTDRFAHRPLAGPRTGVVFFDKTS
+TRTRVSFAAGIAELGGSPLIVNPGESQLGHKESVADTARVLERMVGIIVWRTFAQSGLEE
+MAAHSRVPVVNALSDDYHPCQILADLLTVREHLGGTQGRVLAYLGDAANNMAHSYLLGCA
+TAGMHVRIAGPAGHLPAEHVVAAARERAAETGGSVLVTTDAAEALDGADVVVTDTWVSMG
+QEDEKEARLALFRDYQVDAAAMARAGSDAIFLHCLPAYRGYEVSAEVIDGPQSVVFDEAE
+NRLHAQKALMAWLLYRSGLAEDPR
+>MOLHKGIG_01434
+MTPAAAVRHFLVDTDLTPAEQAEVLDLAAQMKADRFRHRPLAGPRTGIVFFDKTSTRTRV
+SFAAGIAELGGTPLIVNPGESQLGHKESVADTARVLERMVGVIVWRTFAQAGLEEMAAHS
+SVPVVNALSDDYHPCQILADLLTVREHLGGTAGRTLTYLGDAANNMAHSYLLGCATAGMH
+VRVAGPEGHLPAEDVVAAARQRAAETGGSVLVTTDAAEALAGADVVVTDTWVSMGQEEEK
+EARLALFRDYQVDAAAMARAADDAIFLHCLPAYRGYEVTAEVIDGPRSVVFDEAENRLHA
+QKALIAWLLYRSGLAEEPR
+>NAFOICDF_01372
+MTAAPGTDVPVRHFLVDTDLSPAEQAEVLDLALEMKADRFRHRPLAGPQTGIVFFDKTST
+RTRVSFAAGIADLGGTPLIVNPGESQLGHKESIADTARVLERMVGVIVWRTYAQSGLEEM
+AAHSRVPVVNALSDDYHPCQLLADLLTVREHKGRTRGLTMAYLGDAANNMANSYLLGGVT
+AGMHVRVAGPEGFLPDPAVVRAAEERAGETGGSVLVTTDAAAALDGADVVVTDTWVSMGQ
+EDEKEERLRLFADYRVDAAAMARAASDAVFLHCLPAYRGYEVTEDVIDGPQSVVFDEAEN
+RLHAQKALMAWLLYRSGLAQDPR
+>MHAAABBN_01166
+MTPAAAVRHFLVDTDLTPAEQAEVLDLAAQMKADRFRHRPLAGPRTGIVFFDKTSTRTRV
+SFAAGIAELGGTPLIVNPGESQLGHKESVADTARVLERMVGVIVWRTFAQAGLEEMAAHS
+SVPVVNALSDDYHPCQILADLLTVREHLGGTAGRNLTYLGDAANNMAHSYLLGCATAGMH
+VRVAGPEGHLPAEDVVAAARQRAAETGGSVLVTTDAVEALAGADVVVTDTWVSMGQEEEK
+EARLALFRDYQVDAAAMARAADDAIFLHCLPAYRGYEVTAEVIDGPRSVVFDEAENRLHA
+QKALIAWLLYRSGLAEEPR
+>LFPAFLNI_01384
+MTPAAAVRHFLVDTDLTPAEQAEVLDLAAQMKADRFRHRPLAGPRTGIVFFDKTSTRTRV
+SFAAGIAELGGTPLIVNPGESQLGHKESVADTARVLERMVGVIVWRTFAQAGLEEMAAHS
+SVPVVNALSDDYHPCQILADLLTVREHLGGTAGRNLTYLGDAANNMAHSYLLGCATAGMH
+VRVAGPEGHLPAEDVVAAARQRAAETGGSVLVTTDAVEALAGADVVVTDTWVSMGQEEEK
+EARLALFRDYQVDAAAMARAADDAIFLHCLPAYRGYEVTAEVIDGPRSVVFDEAENRLHA
+QKALIAWLLYRSGLAEEPR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000980.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000980.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6bd84a6075f8ff219ec17710e3b292487cff8f3c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000980.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01465
+MAVPTTKTARQAAIREILATRGIRSQAELSDALGDRGLSVTQGTLSRDLVDLGAVRTRGP
+GGMVYALPAEGDDGALPGRGSDAQLSRLSSMARELLISAEPTENLVVLHTPPGAAQFLAS
+VIDQARVENVMGTIAGDDTILLITTGVSAAPVVAAHLLGLAG
+>MOLHKGIG_01433
+MAAPTTKIARQAAIREILATRGIRSQAELSDALGDRGLSVTQGTLSRDLVDLGAVRTRGP
+AGMVYALPAEGDDGAVPGRGSDAQLNRLASMARELLVSAEPTANLVVLRTPPGAAQFLAS
+VIDQARVEHVMGTIAGDDTILLITTGTTSAPAVAAHLLGLAG
+>NAFOICDF_01373
+MATPATKTARQAAIRDVLQTRAIRSQAELSDALAERGLSVTQGTLSRDLVDLGAVRLRGA
+EGMVYAVPADGEEAVAGRSAESQTGRLASMARELLLSAEPTENLVVLRTPPGAAQFLASV
+VDQARVEGIVGTIAGDDTVLLITAGTREAPAVAARLLGMAG
+>MHAAABBN_01165
+MAAPTTKIARQAAIREILATRGIRSQAELSDALGDRGLSVTQGTLSRDLVDLGAVRTRGP
+AGMVYALPAEGDDGAVPGRGSDAQLNRLASMARELLVSAEPTANLVVLRTPPGAAQFLAS
+VIDQARVEHVMGTIAGDDTILLITTGTTSAPAVAAHLLGLAG
+>LFPAFLNI_01383
+MAAPTTKIARQAAIREILATRGIRSQAELSDALGDRGLSVTQGTLSRDLVDLGAVRTRGP
+AGMVYALPAEGDDGAVPGRGSDAQLNRLASMARELLVSAEPTANLVVLRTPPGAAQFLAS
+VIDQARVEHVMGTIAGDDTILLITTGTTSAPAVAAHLLGLAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000981.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000981.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5463cd97f96508c27efc169af4cae18b5182dc8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000981.fa
@@ -0,0 +1,33 @@
+>ACLBLIBL_01467
+MDTMTLFTSTRTRRTTASVAAGMTLMGAAAVGFSAPAQAATEETWDAIAFCESTNRWDIN
+TGNGFYGGLQFTLSSWQGVGGQGYPHQASKAEQIKRAEMLQDLQGWGAWPKCAAGLTQAD
+ADATDAAPVAVERTSSVQRQAAAEQAAAEEAAAEQAAAEEAAAEQAAAEQWAAEQAAAEQ
+AAAERAEAKRAAAAEKAAAKKAAAAERAAAHQAAAEQAVVAEAETIVVKAGDSLWKLAAE
+HEVEGGWTALYEANKDTVSDAAMIYVGQELVLPQA
+>MOLHKGIG_01432
+MDTMTLFTTSATRSRRATASIVAGMTLAGAAAVGFSAPAQAATVDTWDRLAECESSGTWD
+INTGNGFYGGVQFTLSSWQAVGGEGYPHQASKAEQIKRAEILQDLQGWGAWPLCSQKLGL
+TQADADAGDVDAAPVAVERTATVQRQSAADETAADQAAAEQAAADQAAAEQAAADQAAAE
+RWAAKQAAADQAAAERWAAKQAAAEQAAADKAAAQRAAAAEKAAAQKAAAAEKAAAQKAA
+AAEKAAAQKAAAAEQAAAAEQAVVAEAETIVVKSGDSLWKLANEYEVEGGWTALYEANKG
+AVSDAAVIYVGQELVLPQA
+>NAFOICDF_01374
+MTFFTTSSRRATATALTGMTLVGAAAAFAAPAQAASVETWDKIAACESNGNWAINTGNGY
+YGGLQFSLTSWRGVGGTGYPHEASKAEQIKRAEILQDMQGWRAWPVCSVKAGLSGADTAP
+DAYSTTPVQRQSTQASASAAQDWAAEQSAAEQRAAEKAAAQRAAAAAHTPKSVLKAAEKA
+NTENATELAAAEDTVFVKPGDSLWKIAKTHKVAGGWKALHEANKDIIEDASVIYVGQELV
+LPTA
+>MHAAABBN_01164
+MDTMTLFTTSATRSRRATASIVAGMTLAGAAAVGFSAPAQAATVDTWDRLAECESNGTWD
+INTGNGFYGGVQFTLSSWQAVGGEGYPHQASKAEQIKRAEILQDLQGWGAWPLCSQKLGL
+TQADADAGDVDATEAAPVAVERTATVQRQSAADEAAAEQAAAEQAAADQAAAERWAAEQA
+AADQAAAERWAAEQAAAEQAAAERWAAKQAAAEQAAADKAAAQRAAAAEKAAAQKAAAAE
+KPAAQKAAAAEKAAAQKAAAAEQAAAAEQAVVAEAETIVVKSGDSLWKLANEYEVEGGWT
+ALYEANKGAVSDAAVIYVGQELVLPQA
+>LFPAFLNI_01382
+MDTMTLFTTSATRSRRATASIVAGMTLAGAAAVGFSALAQAATVDTWDRLAECESNGTWD
+INTGNGFYGGVQFTLSSWQAVGGEGYPHQASKAEQIKRAEILQDLQGWGAWPLCSQKLGL
+TQADADAGDVDATEAAPVAVERTATVQRQSAADEAAAEQAAAEQAAADQAAAERWAAEQA
+AADQAAAERWAAEQAAADQAAAERWAAEQAAAEQAAADKAAAQRAAAAEKAAAQKAAAAE
+KAAAQKAAAAEQAAAAEQAVVAEAETIVVKSGDSLWKLANEYEVEGGWTALYEANKGAVS
+DAAVIYVGQELVLPQA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000983.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000983.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ae3a4ae0c58628d2196927c297137a3599011b46
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000983.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_01469
+MTENPEARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHAA
+GLLGAEDLEGMIAALDRLETDVRSGAYAPADSDEDVHGSLERGLIERAGPELGGRLRAGR
+SRNDQVATLGRMFLRDHARIIARGLVATVDALLSQVQAHPYAPMPGRTHLQHAQPVLLSH
+HLLAHAWAFARDLQRLVDWDARTAVSPYGSGALAGSSLGLDPEAVAAELGFDSAVWNSID
+GTASRDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVKLHDAYSTGSSIMPQKKNPD
+VAELARGKSGRLIGDLAGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA
+TLEFETERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVKAAEARGVELWDLTD
+EEYAAISPALTPQVREVLSTEGSLNSRDAQGGTAPAAVAAQVEALERTLEPLRRWAQTPG
+SVVDAR
+>MOLHKGIG_01430
+MTENTDARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA
+GLLSADDLDGMIAALDRLEADVRSGAYTPAASDEDVHGSLERGLIERAGPELGGRLRAGR
+SRNDQVATLGRMFLRDHARIIARGVIATVDALLDQARAHPHAPMPGRTHLQHAQPVLLSH
+HLLAHAWAFARDLQRLVDWDARAAVSPYGSGALAGSSLGLDPNAVATELGFESAVWNSID
+GTAARDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVTLHDAYSTGSSIMPQKKNPD
+VAELARGKSGRLIGDLTGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA
+TLEFQTERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVKAAEARGVELWDLTD
+DEYAAISPALTPQVREVLSTEGSLASRDAQGGTAPTAVAAQIGALEDALEPLRRWADTPG
+SVVDAR
+>NAFOICDF_01376
+MSENSTPRHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA
+GLLTADELAGMIDALDRLEADVRSGAYAPAESDEDVHGSLERGLIERAGAELGGKLRAGR
+SRNDQVATLGRMFLRDHARVVARGVLATVDALVEQAEAHPFAPMPGRTHLQHAQPVLLSH
+HLLAHAWAFTRDLQRLVDWDARAAVSPYGSGALAGSTLGLDPNAVAAELGFDSAVWNSID
+GTAARDVYAEFAWVAGMIGVDLSRISEEVIFWATKEAGFVRLHDSYSTGSSIMPQKKNPD
+VAELARGKAGRLIGDLAGLMATLKGLPLAYNRDLQEDKEPVFDAVDTLELLLPAVSGMIA
+TLSFNTERMAALAPQGFALATDIAEWLVRQGVPFRVAHELSGEAVQVAESRGVELWDLTD
+EEYAGISAHLTPAVREVLSTEGSLNARRGQGGTAPEAVAEQLAALKAALEPLRAFAASAG
+SVVDAR
+>MHAAABBN_01162
+MTENTDARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA
+GLLSADDLDGMIAALDRLEADVRSGAYTPAASDEDVHGSLERGLIERAGPELGGRLRAGR
+SRNDQVATLGRMFLRDHARIIARGVIATVDALLDQARAHPYAPMPGRTHLQHAQPVLLSH
+HLLAHAWAFARDLQRLVDWDARAAVSPYGSGALAGSSLGLDPNAVAAELGFESAVWNSID
+GTAARDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVRLHDAYSTGSSIMPQKKNPD
+VAELARGKSGRLIGDLTGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA
+TLEFQTERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVMAAEARGVELWDLTD
+DEYAAISPALTPQVREVLSTEGSLASRDAQGGTAPTAVAAQIGALEDALAPLRRWADTPG
+SVVDAR
+>LFPAFLNI_01380
+MTENTDARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA
+GLLSADDLDGMIAALDRLEADVRSGAYTPAASDEDVHGSLERGLIERAGPELGGRLRAGR
+SRNDQVATLGRMFLRDHARIIARGVIATVDALLDQARAHPYAPMPGRTHLQHAQPVLLSH
+HLLAHAWAFARDLQRLVDWDARAAVSPYGSGALAGSSLGLDPNAVATELGFESAVWNSID
+GTAARDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVTLHDAYSTGSSIMPQKKNPD
+VAELARGKSGRLIGDLTGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA
+TLEFQTERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVKAAEARGVELWDLTD
+DEYAAISPALTPQVREVLSTEGSLASRDAQGGTAPTAVAAQIGALEDALAPLRRWADTPG
+SVVDAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000984.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000984.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07b57d31551633959e90be3e27c644c447e093dd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000984.fa
@@ -0,0 +1,70 @@
+>ACLBLIBL_01470
+MTDAVSVRQSELELERARVAERYARLDALREEKERQLAAVRRTGLEGSLQNHSERDAFAS
+LYEDRLAQLLAVDDRLVFGRLDLDPERAGDPDEERYIGRIGLTTEEHERLLVDWRAAEAG
+AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDVLDPDLLGQEGVRADAQGALLAAVTARR
+TGRMGDIVATIQAEQDEVIRAPLAGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG
+VLIVGPSTAFMRYIERVLPSLGETGVVMASLGTLMPGVQAGPERDLDAAAVKGRLEMAQV
+IAHAVAQRQRLLAQPRRLMIEGTAVKLKPAAVRRARDRARATGKPHNEARVTFVKILVRE
+LAEKLSKKLEKSSGAPVQRDLLLEDVRTSRDVRVALNLCWMPLTPQKLVGDLLTREHLLR
+AAAPWLSDGEVGALLRPADAPWTEADVPLLDEAAELLGRLEAPAKGGESAAQHERNLENA
+RASLENMHQTLADMGVDGVVDAEQLAAANEARAVRRTTAETAAHDRTWTYGHVVVDEAQE
+LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLEPEFGDRWRLEELTVNYRSP
+ARVMRWASQVAQAAGLEVSRPRAVREGEHAPRLTVRPGADLVALTLDAVAGERDRVPEGL
+VAVITAAAHAPELLAALRERWGRARVDTAPLPGVEIVVATPWETKGLEFDAVVLAAPERL
+VDDARGVVGDLYVAMTRATQSLSVVSTAAVAALPAGLADPPA
+>MOLHKGIG_01429
+MTDTVSVRQSELDLERGRVAERYARLDALREEKERQLAAVRRTGPQGSLQNHSERDAFAS
+LYEDRLAQLYAVDDRLVFGRLDLDAEREGGADEQRYIGRIGLTTEDHERLLVDWRAAEAG
+AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDILDPTLLGEDGVRADAQGALLAAVTARR
+TGRMGDIVATIQAEQDEVIRAPLPGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG
+VLIVGPSTAFMRYIERVLPSLGETGVVMSSLGTLMPGVRAVPERDLDAAAVKGRLDMVDA
+VAHAVAQRQRLLVEPRRLMIDGTAVKLKPAMVRRARDKARATRKPHNEARVTFVKILVRE
+LAEKLRKKLEKSSGTPVQRDLLLEDVRTSRDVRIALNLCWMPLTPEKLIGDLLTREDLLR
+AAAPWLSDAEVGALLRPADAPWTEADVPLLDEAAELLGRLDTPGRGGESAAQHERNLENA
+RASLENMHQTLADLGVDGVVDAEQLAAANEARGVRRTTAETAAHDRTWTYGHVVVDEAQE
+LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLAPEFGDRWRLEELTVNYRSP
+ARVMRWAAQVARAAGLEVSHPRAVREGDHRPRLVTEPGGDVAALALDAVEAERDRVPEAL
+TAVIAPAERTGELLTALRERWGEAAVDTAPLPGVEIVVATPWETKGLEFDTVVLVLPERI
+VADARGVVGDLYVAMTRATQSLSVVAGTDAAALPAGLADVPE
+>NAFOICDF_01377
+MTDTVSSRQAELELERERVAVRYARLDALRAEKEEQLARVRRSGLQGSVQNHSERDAFAS
+LYEDRLAQLYAVDERLVFGRLDLDADDAGDVEQRYIGRIGLTDEGQERLLVDWRAQEAGA
+FYQATAARRLGVGRRRHLLLRGREVRDFEDDVLDPSLIAEGAAGAQSQGALLAAVTARRT
+GRMGDIVATIQAEQDEVIRADTSGALVVQGGPGTGKTAVALHRAAYLLYTHRDRLAKSGV
+LVVGPSNAFMRYIERVLPSLGETGVVMASLGTLMPGVQAGPDRSARAAELKGRLEMADVV
+AAAVAQRQRLIPETRRLEIEGTVVKLKPAMVRRARDRARATGKPHNEARTTFVKILVREL
+AEKLRKKLEKSSGVPVQRDLLLEDVRTARDVRVALNLCWMPLTPQKLVGDLLTKEHLLRA
+AAPGLSDGDVAALLRTDPDAWVESDVPLLDEAAELLGELEEPHRPGESEAQHRRNVENAQ
+ASLENMHQTLAELGVDGVVDAEQLAAANEVRAVRRTTAEQAAHDRTWTFGHVVVDEAQEL
+SPMQWRLLARRCPLKSFTVVGDIAQASRRGGARSWKDVLGPEFGDRMRLEELTVNYRSPA
+RITRWAAQVAQAAGLEISSPEAVREGEHEPLLTVEPGADPTRLAQRVVEAERGRVGDGLV
+AVIVPADDAAEHLTHLQDRWGSLVDRAPAPGVEVVVVTARETKGLEFDAVVLVSPERIVA
+DADGVVGDLYVAMTRCTQSISVVSGAAEEELPAGLMPVPA
+>MHAAABBN_01161
+MTDTVSVRQSELDLERGRVAERYARLDALREEKERQLAAVRRTGPQGSLQNHSERDAFAS
+LYEDRLAQLYAVDDRLVFGRLDLDAEREGGADEQRYIGRIGLTTEDHERLLVDWRAAEAG
+AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDILDPTLLGEDGVRADAQGALLAAVTARR
+TGRMGDIVATIQAEQDEVIRAPLPGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG
+VLIVGPSTAFMRYIERVLPSLGETGVVMSSLGTLMPGVRAVPERDLDAAAVKGRLDMVDA
+VAHAVAQRQRLLVEPRRLMIDGTAVKLKPAMVRRARDKARATRKPHNEARVTFVKILVRE
+LAEKLRKKLEKSSGTPVQRDLLLEDVRTSRDVRIALNLCWMPLTPEKLIGDLLTREDLLR
+AAAPWLSDVEVGALLRPADAPWTEADVPLLDEAAELLGRLETPGRGGESAAQHERNLENA
+RASLENMHQTLADLGVDGVVDAEQLAAANETRGVRRTTAETAAHDRTWTYGHVVVDEAQE
+LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLAPEFGDRWRLEELTVNYRSP
+ARVMRWAAQVARAAGLEVSHPRAVREGDHRPRLVTEPGGDVAALALEAVEVERDRVPEAL
+TAVIAPAGRTGELLTVLRERWGEAAVDTAPLPGVEIVVATPWETKGLEFDTVVLVSPERI
+VADARGVVGDLYVAMTRATQSLSVVAGTDAAALPAGLADVPE
+>LFPAFLNI_01379
+MTDTVSVRQSELDLERGRVAERYARLDALREEKERQLAAVRRTGPQGSLQNHSERDAFAS
+LYEDRLAQLYAVDDRLVFGRLDLDAEREGGADEQRYIGRIGLTTEDHERLLVDWRAAEAG
+AFYQATAAHRGRVRRRRHLMLRGREVRDLEDDILDPTLLGEDGVRADAQGALLAAVTARR
+TGRMGDIVATIQAEQDEVIRAPLPGAVVVQGGPGTGKTAVALHRAAYLLYTHRERLARSG
+VLIVGPSTAFMRYIERVLPSLGETGVVMSSLGTLMPGVRAVPERDLDAAAVKGRLDMVDA
+VAHAVAQRQRLLVEPRRLMIDGTAVKLKPAMVRRARDKARATRKPHNEARVTFVKILVRE
+LAEKLRKKLEKSSGTPVQRDLLLEDVRTSRDVRIALNLCWMPLTPEKLIGDLLTREDLLR
+AAAPWLSDAEVGTLLRPADAPWTEADVPLLDEAAELLGRLETPGRGGEFAAQHERNLENA
+RASLENMHQTLADLGVDGVVDAEQLAAANEARGVRRTTAETAAHDRTWTYGHVVVDEAQE
+LSPMQWRLLARRCPMKSFTIVGDIAQSSRRDAAGSWASVLAPEFGDRWRLEELTVNYRSP
+ARVMRWAAQVARAAGLEVSHPRAVREGDHRPRLVTEPGGDVAALALDAVEVERDRVPEAL
+TAVIAPAGRTGELLTVLRERWGEAAVDTAPLPGVEIVVATPWETKGLEFDTVVLVSPERI
+VADARGVVGDLYVAMTRATQSLSVVAGTDAAALPAGLADVPE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000987.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000987.fa
new file mode 100644
index 0000000000000000000000000000000000000000..72060d6ad193c0ea6b4687fa3f04e75cdd4b102b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000987.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01476
+MSPTLPRGHDGLLCDLDGVVYAGGGAVPGAVETLTALAERGVPVGFVTNNASRAPESVAE
+HLRSLGVPARPEQVFGSAPAGVDLLEETLGARTGRVLVVGSDYLRQVVRDRGFEVVAASQ
+DRPDAVIQGFDPGVGWAELAQAAYAVNAGAAWVATNLDASIPRAEGIAPGNGALVGAVGQ
+ATGTAPAAAGKPEPLLFRTAARALGLTRPLVVGDRLDTDIRGGNAAGFDTVLVLTGIDTR
+ENAGSAPEADRPTWIVEDLPALLSEPDGQAGTADGRRG
+>MOLHKGIG_01423
+MSTTFFDGHDGLLCDLDGVVYAGDGAIAGAVETLSTLQERGVPVGFVTNNASRAPESVAE
+HLRTLGVPAEAGQVFGSAPAGVDLLEETLGRRTGRVLVVGSAYLRAVVEERGYEVVASAA
+QCPDAVIQGFDPGLGWADLAEAAYAVRAGATWVATNLDTSIPRAEGIAPGNGALVEAVGR
+ATGTAPVAAGKPEPRLFRTAADALGLARPLVVGDRLDTDIRGGNAAGFDTVLVLTGIDTR
+ETAAAAPGPDRPTWVRAHLPALLAGGAEASADPRRG
+>NAFOICDF_01384
+MTDPAASTFFGGHDGLLCDLDGVVYAGGEAIPGAVETVSALAERGVPVGFVTNNASRPPE
+AVAEQLRRFGLEVSPSHVFGSAPVGVDLLEERLTAAGHEGPARVLVVGSVHLADLVAARG
+HHVVETAAERPDAVLQGFDPRVDWSRLAEAAYAVNAGAAWVATNLDLSIPRAEGVAPGNG
+ALALAVTQATGVIPVAAGKPEPRLFHTAAAALGLQAPLMVGDRLDTDIRGGNAAGMETVL
+VLTGVGSRHAAGEAPEEDRPTWIVDDMTALLGEPAEAARG
+>MHAAABBN_01154
+MSATFFAGHDGLLCDLDGVVYAGGGAIAGAVETLSTLQERGVPVGFVTNNASRAPESVAE
+HLRTLGVPAQAGQVFGSAPAGVDLLEETLGRRTGRVLVVGSAYLRAVVEERGYEVVASAA
+QRPDAVIQGFDPGLGWADLAEAAYAVRAGATWVATNLDTSIPRAEGIAPGNGALVEAVGR
+ATGTAPVAAGKPEPRLFRTAAEALGLARPLVVGDRLDTDIRGGNAAGFDTVLVLTGIDTR
+ETAAAAPGPDRPTWVRAHLPALLAGGAEAFADPRRG
+>LFPAFLNI_01373
+MSATFFAGHDGLLCDLDGVVYAGGGAIAGAVETLSTLQERGVPVGFVTNNASRAPESVAE
+HLRTLGVPAQAGQVFGSAPAGVDLLEETLGRRTGRVLVVGSAYLRAVVEERGYEVVASAA
+QRPDAVIQGFDPGLGWADLAEAAYAVRAGATWVATNLDTSIPRAEGIAPGNGALVEAVGR
+ATGTAPVAAGKPEPRLFRTAAEALGLARPLVVGDRLDTDIRGGNAAGFDTVLVLTGIDTR
+ETAAAAPGPDRPTWVRAHLPALLAGGAEAFADPRRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000988.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000988.fa
new file mode 100644
index 0000000000000000000000000000000000000000..257faa84fb080d4df508926e3d5e3e79000febcc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000988.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01477
+MAEAVRADVALAARGLARSRTEASALIRAGQVLVDGRPVRRASERVAPTASLTLADDGPR
+WVSRAAHKLVSALEAFPDVAVRGRRALDAGASTGGFTQVLLEGGAARVAAVDVGHGQLVD
+LVRTDPRVLVREGLNVRDLTVQDVEGEVDLVVSDLSFISLRLVMDALAGVCRPGADLLLM
+VKPQFEVGRAALPRTGVVTDPAARRDVVAAVAAAALDSGLELRGLARSGLPGQDGNVEFF
+LRLRRPAADAAGAPGTGLDDDAPAAEAVAAAWTAAAEVDWA
+>MOLHKGIG_01422
+MAETARADVALAARGLARSRTEGAALIRAGQVLLDGRPVRRPADRVAADATLRLRDPGPR
+YVSRAAHKLVSALEAFPDVGVAGRRALDAGASTGGFTQVLLERGAERVAAVDVGHNQLAP
+PVRADPRVLVREGLNIRDLTAEDIDGPVDLVVSDLSFISLRLVLAPLASVCRPGAELLLM
+VKPQFEVGRRALPRSGVVTDPDARRHAVVGVTAAALGAGLAPRGLARSGLAGQDGNAEFF
+LRLRRPDATAADNPAGGTSPAPPAGERAAGWVRGAHIDWS
+>NAFOICDF_01385
+MGEARRADVALAADGLARSRTEAAALVKEGVVLVDGTPVRRPSQPVASGAVLSLLDQGPR
+WVSRAAHKLVSALEAFPVPVAGRRALDAGASTGGFTQVLLERGAARVAAVDVGHGQLVQE
+LRADPRVLVREGLNVRDLTATDVEGSVDLVVSDLSFISLRLVLDALAGVCRPDADLLLMV
+KPQFEVGRAALPRTGVVTDPRARRSAVEGVVAAALGTGLAARGVARSGLPGQDGNVEFFL
+HLRAPAAPRDGGAVAGDADEDERRRRAAALVAAADVDWS
+>MHAAABBN_01153
+MAETARADVALAARGLARSRTEGAALIRAGQVLLDGRPVRRPSDRVAADATLRLRDPGPR
+YVSRAAHKLVSALEAFPDVAVAGRRALDAGASTGGFTQVLLERGAERVAAVDVGHDQLAP
+PVQADPRVLVREGLNVRDLRAEDIDGPVDLVVSDLSFISLRLVLAPLAGVCRPGAELLLM
+VKPQFEVGRRALPRSGVVTDPDARRDAVAGVAAAALGAGLAPRGLTRSGLAGQDGNAEFF
+LRLHRPDATAADDPAGRTSPATPADERAAGWVRGAHIDWS
+>LFPAFLNI_01372
+MAETARADVALAARGLARSRTEGAALIRAGQVLLDGRPVRRPSDRVAADATLRLRDPGPR
+YVSRAAHKLVSALEAFPDVAVAGRQALDAGASTGGFTQVLLERGAERVAAVDVGHDQLAP
+PVRADPRVLVREGLNVRDLRAEDIDGPVDLVVSDLSFISLRLVLAPLAGVCRPGAELLLM
+VKPQFEVGRRALPRSGVVTDPDARRDAVAGVAAAALGAGLAPRGLTRSDLAGQDGNAEFF
+LRLHRPDATAADDPAGRTSPATPADERAAGWVRGAHIDWS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000990.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000990.fa
new file mode 100644
index 0000000000000000000000000000000000000000..05fc6b2b19859731b2e7ef41f64ccc556b0d526b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000990.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_01479
+MIEHLRISGLGVIGEATVDLDPGLTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGAA
+RAVVDAGVRLPEAHAALALAEDAGAVLDEADDGVRELVLSRSVTASGEGTRSRAAAGGRT
+VPVGLLAEIGATLVAVHGQNDQVRLQGAEAQRRALDAFGGAELAASLRAYRADHAAVSAA
+RRERDELTAHRQERAREAEALQRSLEEIDLAEPLAGEDAELRELIRRLEDVEELRAASGE
+AHARLAGAEMDALEETPGAVSLVEGARQAVLAAPGDDPALAAAAERLAEAAVVLTDIAAD
+LARYTADLDTDAASDLDAAQSRLAELTRLQRLYGPELEDVIGWAETQRPRLDELQGDSGR
+LEELEGELERLESALRERAAALTALRTAAAGRLEEAVTQELHALFMPDASFHVDLAPVGG
+DGLGPHGAEDVALALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV
+DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV
+TLSAEERVEELARMLAGHGDSAAAREHARELLEASARERG
+>MOLHKGIG_01420
+MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSS
+RAVVDAGVRVTADHAALRLAQEAGAVVDEGDNGTHDLVLSRSVTASGDGTRSRATAGGRS
+VPVGLLSEIGATLVAVHGQNDQVRLQGADAQRHALDAFGGAELAAALRAYRADHAAWTAA
+RREREELTAHRQERAREAEALQRSLEEIDLAEPREGEDEELRALIRRLEDVEELRAASGE
+AHARLAGPDVDAMDETPGAVSLVEAARQAVLAAPGDDPDLAAAAARLAEAAVVLTDIAGD
+LARYTADLDADAASDLDAAQSRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGR
+LEELEAEVDRLDAALRERAATLTALRTAAAERLETAVTEELHALFMPDASFHVGLTPVAG
+DGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV
+DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV
+TLTADERVEELARMLAGHGDSAAAREHARELLESSARERG
+>NAFOICDF_01387
+MIDWMQITGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGRRADAGAVRRGSR
+RAAVDAGVRLPADHPALSLAVEAGAVLDDAGDGSADLVLSRSVTASGDGTRSRAGLGGRA
+VPVGVLAEVGSALVAVHGQNDQVRLQSAAAQRHALDAFGGPQLVAAAAAYRADHTAYVAA
+RRERDLLVERQQERAREAEALQRGLEEIDRAEPEAGEDETLRALIRRLEDVEELRAAADG
+GHAHLAGPDIESGDDLPGAITLVESARAAVQAAPGDDPELAAAAGRLAEASVILGDIAAD
+LARFSADLDGDAVSDLDAAQTRLAELSRLQRLYGPELTDVLAWAEAQRPRLEELQGDSGR
+IDELEADLARLDASRRERAAELTTLRTAAAGRLEQAVTAELHALFMPDASFHVSLVPLDD
+GDPGPHGAEDVALALRPHAGAEPRPLGRGASGGELSRVMLALEVVLAETDPVPTFVFDEV
+DAGVGGEAAVSIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPEAGVTTSDVV
+TLGQQERVDELARMLAGHGDSAAARAHARELLEASAAERA
+>MHAAABBN_01151
+MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSS
+RAVVDAGVRLPEAHAALALAEDAGAVLDEADEGVRELVLSRSVTASGEGTRSRAAAGGRT
+VPVGLLAEIGATLVAVHGQNDQVRLQGADAQRHALDAFGGAELAAALRAYRADHAAWTAA
+RREREELTAHRQERAREAEALQRSLEEIDLAEPQEGEDEELRALIRRLEDVEELRAASGE
+AHARLAGPDVDTMDETPGAVSLVEAAQQAVLAAPGDDPELAAAAARLAEAAVVLTDIAGD
+LARYTADLDADAASDLDAAQSRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGR
+LEELEAEVDRLDAALRERAATLTALRTAAAERLETAVTEELHALFMPDASFHVGLTPVAG
+DGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV
+DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV
+TLTADERVEELARMLAGHGDSAAAREHARELLESSARERG
+>LFPAFLNI_01370
+MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSS
+RAVVDAGVRLPEAHAALALAEDAGAVLDEADEGVRELVLSRSVTASGEGTRSRAAAGGRT
+VPVGLLAEIGATLVAVHGQNDQVRLQGADAQRHALDAFGGAELAAALRAYRADHAAWTAA
+RREREELTAHRQERAREAEALQRSLEEIDLAEPQEGEDEELRALIRRLEDVEELRAASGE
+AHARLAGPDVDAMDETPGAVSLVEAARQAVLAAPGDDPELAAAAARLAEAAVVLSDIAGD
+LARYTADLDADAASDLDAAQSRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGR
+LEELEAEVDRLDAALRERAATLTALRTEAAERLETAVTEELHALFMPDASFHVGLTPVAG
+DGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV
+DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV
+TLTADERVEELARMLAGHGDSAAAREHARELLESSARERG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000994.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000994.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5ebd5cb21f2018d43c298ebf11d49691e50ae49a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000994.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01484
+MLYSTKTAEQKRVDLRAALAEGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL
+PDVGLTTLTEVALRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ
+FNPKRCGHLDGKNMVDLDTAVKRIAAAVDARRDPNFLIMARTDLRAVEGLDAAIARMKAL
+VEAGADAIFPEALKDIGEFETVCRELAPLGVPVLANMTEFGKSELFTRQQLADAGVAMVI
+YPVTLLRSAMGAAERVLDAIKDEGTQASQVDQMLTRARLYELVDYEGYNAFDTGIFNFDV
+PTLDIDENNANL
+>MOLHKGIG_01415
+MLYSTKTAEQKRIDLRETLKQGGAQQFPGAFTPLSAKLIQEKGFPGVYISGGVLANELGL
+PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ
+FNPKRCGHLDGKNMVELDTAVKRIAAAVHARRDPNFLIMARTDLRAVEGLDAAIARMKAL
+VEAGADAIFPEALKDIGEFETVCRELEPLGVPVLANMTEFGKSELFTRRQLADAGVAMVI
+YPVTLLRSAMGAAERVLNAIKEEGTQQSQVEQMLTRARLYELVDYEGYNAFDTGIFNFDV
+PTLDIGANHADL
+>NAFOICDF_01391
+MLYSKKTAAQKRIDLRETLKQGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL
+PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFEDAGLAGCHIEDQ
+FNPKRCGHLDGKNMVDLDTAVKRIAAAVDARRDPNFLIMARTDLRAVEGLDAAIARMKAL
+VEAGADAIFPEALKDIGEFETVCRELAPLGVPVLANMTEFGKSELFTRQQLADAGVAMVI
+YPVTLLRSAMGAAERVLDAIREEGTQQSQVDQMLTRARLYELVDYEGYNAFDTGIFNFDV
+PTLDIDSNNANL
+>MHAAABBN_01146
+MLYSTKTAEQKRIDLRQTLKQGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL
+PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ
+FNPKRCGHLDGKNMVELDTAVKRIAAAVHARRDPNFLIMARTDLRAVEGLDAAIARMKAL
+VEAGADAIFPEALKDIGEFETVCRELEPLGVPVLANMTEFGKSELFTRRQLADAGVAMVI
+YPVTLLRSAMGAAERVLHAIKEEGTQQSQVEQMLTRARLYELVDYEGYNAFDTGIFNFDV
+PTLDIGANHADL
+>LFPAFLNI_01365
+MLYSTKTAEQKRIDLRQTLKQGGAQQFPGAFTPLTAKLIQEKGFPGVYISGGVLANELGL
+PDVGLTTLTEVAVRGGQIARLTDLPCLIDADTGFGEPMNVARTVQEFENAGLAGCHIEDQ
+FNPKRCGHLDGKNMVDLDTAVKRIAAAVDARRDPNFLIMARTDLRAVEGLDAAIARMKAL
+VEAGADAIFPEALKDIGEFETVCRELEPLGVPVLANMTEFGKSELFTRQQLADAGVAMVI
+YPVTLLRSAMGAAERVLDAIKEEGTQQSQVEQMLTRARLYELVDYEGYNAFDTGIFNFDV
+PTLDIGANHADL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000995.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000995.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3f34ae158295361e25d944c51f41262f3e49e00
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000995.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_01485
+MKNHHVRVHRSEENLERKDQLAWKLAEVAVDDVEVLPEVEEMIVNRIIDNASVAVASLQR
+GPIVAARAQALSHPVSTGGAGATVFGVEQKVSPEWAAWANGVAVRELDYHDTFLAAEYSH
+PGDNIPPILAVAQHAGRSGKDLIRGIATGYEVQVDLVKSICLHKHKIDHVAHIGPSASAG
+IGTLLGLDTETVFQAVGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAADRAMRGQ
+TSPVPIYEGEDGVIAWMLDGPDASYEVPLPEAGEPKRGILDTYTKEHSAEYQAQAWIDLA
+RKLNKEHPEATDPANVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSIPYIFTV
+ALQDGAWHHVDSYAPERAAREDTVALWHKVTTVEDPEWTRRYHSNDLTEKAFGGAVEITL
+TDGTVITDEIAVADAHPLGARPFAREQYIQKFRTLAEGIVTQEEQDRFLDAVQRVSELGP
+GELDQLNVTADPAFLSQADLDNAPKGLF
+>MOLHKGIG_01414
+MKNHHVRVHRSEENLERKDQLAWKLAEVAVDDVEVLPEVEEMIINRIIDNASVAVASLRR
+GPIVAARAQALSHPVSTGGEGASVFGVEQKVSPEWAAWANGVAVRELDYHDTFLAAEYSH
+PGDNIPPILAVAQHAGRSGKDLIRGIATGYEIQVDLVKSINLYGHKIDHVAHIGPSASAG
+IGTLLGLDTETIFQAIGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAVDRAMRGQ
+TSPVPIYEGEDGVIAWLLDGPDASYEVPLPEQGEPKRGILDTYTKEHSAEYQAQAWIDLA
+RKLHREHPEATDPANVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSIPYIFTV
+ALQDGSWHHVDSYAPERAQREDTVALWHKVTTVEDPEWTRRYHSLDLAEKAFGGAVEITL
+KDGTVITDEIAVADAHPLGARPFAREQYIQKFRTLAEGIVSKEEQDRFLAAAERVAELQP
+GELDQLNILADPAFLSEADLAAAPKGLF
+>NAFOICDF_01392
+MKKHDVRVHPSADNLAREDQLAHKLAEVAVDPVEVLPEVEEMIINRIIDNASVAVASLKR
+GPIVAARAQALSHPVSTGGAGATVFGVDQKVSPEWAAWANGVAVRELDYHDTFLAEEYSH
+PGDNIPPILAVAQHAGRSGADLIRGIATGYEVQVDLVKSICLHKHKIDHVAHIGPSASAG
+IGTLLGLDAETVFQAIGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAADRAMRGQ
+TSPVPIYEGEDGVIAWMLDGKDAHYEVPLPEQGEPKRGILDTYTKEHSAEYQAQAWIDLA
+RKLHSEHPEAMDPENVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSVPYIFTV
+ALQDGAWHHVDSYAPERAARPDTVALWHKVTTVEDPEWTRRYHSNDLSEKAFGGAVEITL
+TDGTVITDQIAVADAHPLGARPFAREQYIQKFRTLAEGVVTPEEQDRFLDAVQRLSELQA
+GELDQLNVLANPAFLSEADLAAAPKGLF
+>MHAAABBN_01145
+MKNHHVRVHRSEENLERKDQLAWKLAEVAVDDVEVLPEVEEMIINRIIDNASVAVASLKR
+GPIVAARAQALSHPVSTGGAGASVFGVEQKVSPEWAAWANGVAVRELDYHDTFLAAEYSH
+PGDNIPPILAVAQHTGRSGKDLIRGIATGYEIQVDLVKSINLYGHKIDHVAHIGPSASAG
+IGTLLGLDTETIFQAIGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAVDRAMRGQ
+TSPVPIYEGEDGVIAWLLDGPDASYEVPLPEQGEPKRGILDTYTKEHSAEYQAQAWIDLA
+RKLHREHPEATDPANVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSIPYIFTV
+ALQDGSWHHVDSYAPERAQREDTVALWHRVTTVEDPEWTRRYHSLDLAEKAFGGAVEITL
+KDGTVITDEIAVADAHPLGARPFAREQYIQKFRTLAEGIVSKEEQDRFLAAAERVAELQP
+GELDQLNILADPAFLSEADLAAAPKGLF
+>LFPAFLNI_01364
+MKNHHVRVHRSEENLERKDQLAWKLAEVAVDDVEVLPEVEEMIINRIIDNASVAVASLKR
+GPIVAARAQALSHPVSTGGEGASVFGVAQKVSPEWAAWANGVAVRELDYHDTFLAAEYSH
+PGDNIPPILAVAQHAGRSGKDLIRGIATGYEIQVDLVKSINLYGHKIDHVAHIGPSASAG
+IGTLLGLDTETIFQAIGQGLHTTTATRQSRKGEISTWKAHAPAFAGKMAVEAVDRAMRGQ
+TSPVPIYEGEDGVIAWLLDGPDASYEVPLPEQGEPKRGILDTYTKEHSAEYQAQAWIDLA
+RKLHREHPEATDPANVESVLIKTSHHTHYVIGSGANDPQKYDPTASRETLDHSIPYIFTV
+ALQDGSWHHVDSYAPERAQREDTVALWHKVTTVEDPEWTRRYHSLDLAEKAFGGAVEITL
+KDGAVITDEIAVADAHPLGARPFAREQYIQKFRTLAEGIVSKEEQDRFLAAAERVAELQP
+GELDQLNILADPAFLSEADLAAAPKGLF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001000.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001000.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ae404b4f5b658430a8aa2ba3b2845d8a28400a5c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001000.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_01491
+MTEHTRDDVATTPLVVAVDGPSGSGKSSVSKAVARRLGAAYLDTGAMYRAVAWHCLNEGV
+DLADADAVAAAAVAMELEQSTDPDVEAVRVGGTDVTEAIRGAEVTDTVSTVAVVIPVREE
+LRRRQRETIAAAGRMVAEGRDITTVVAPDAHARVLLTASEAVRTARRSGQLAAAGEPGVD
+AGTLHRQGGRAGRPRRHRVHVRPPRRGRGARGLHRARLRADRGGRPGRRRGPGRHPGREG
+RPTMTDNPQHRSGDDEFVPAGEDQVAERLAAMTEEEAEARAASLRAGLADYELEDDDAAL
+LDAWQLGPDEDLDAPVPPVLAIVGRPNVGKSTLVNRIIGRREAVVEDVPGVTRDRVSYDA
+EWNGREFTVVDTGGWEHDAKGIHRRVAEQAELAVDVADAVVFVVDATVGMTATDEAVVSM
+LRRKDRPVIVAANKVDDMVQEADAASLWSLGFGYPYPVSAVHGRGVADLLDAALEAMPEE
+SAHGGLVPRGGPRRIALVGRPNVGKSSLLNRLAGSDRVVVDDLAGTTRDPVDELVELGGR
+LWRFVDTAGIRRRQHMAHGADYYAALRTASALDRAEVAVVLLEAPSVISEQDVRILQMVL
+DSGRALVIAFNKWDQVDEDRRHQLEKEIERDLAHVAWAPRVNISAKTGWHKDRLVPALDT
+ALDSWDTRIPTGKLNAFLGELVAAHPHPLRGGKQPRILFATQVSSRPPKFVLFTTGFLDP
+GYRRFIVRRLRETFGFEGTPLEIGMRVREKRGLAPLSAAAADDDGVPRARRGSTDPAPAG
+GRRRPTPSRGSSHGFLMFRA
+>MOLHKGIG_01404
+MTENPQHRSGEDEFVPAGDDQVAERLAAMTEEEAEARAASLRAGLADYELEEDDAALLDA
+WQLGPDEDVDAPVPPVLAIVGRPNVGKSTLVNRIIGRREAVVEDVPGVTRDRVSYDAEWN
+GREFTVVDTGGWEHDAKGIHRRVAEQAELAVDVADAVVFVVDATVGMTATDEAVVSMLRR
+KDRPVIVAANKVDDMVQEADAATLWSLGFGYPYPVSAVHGRGVADLLDAALEALPEESAH
+GGLVPRGGPRRIALVGRPNVGKSSLLNKLAGSDRVVVDDLAGTTRDPVDELVELGGRLWR
+FVDTAGIRRRQHMAHGADYYASLRTASALDRAEVAVVLLEAPQVISEQDVRILQMVLDSG
+RALVIAFNKWDQVGEDRRLQLAKEIERDLAHVAWAPRVNISAKTGWHKDRLVPALDLALD
+SWDTRIPTGKLNAFLGELVAAHPHPLRGGKQPRILFATQVSSRPPKFVLFTTGFLDPGYR
+RFIVRRLRETFGFEGTPLEIGMRVREKRGRRR
+>NAFOICDF_01403
+MTENTPLTEGEEYQPAGEDHLAERLAAISDEEADARAASLRAGLGDYELEEDDAALLADW
+DGDDEFDLDLPVPPVLAIVGRPNVGKSTLVNRIIGRREAVVEDVPGVTRDRVSYEAEWNG
+RVFTVVDTGGWEHDAKGIHKRVADQAELAVDVADAVVFVVDATVGMTATDEAVVTMLRRK
+DRPVIVAANKVDDMVQEADAASLWSLGFGYPWPVSAVHGRGVADLLDAALEELPEESAHG
+GLVPRGGPRRIALVGRPNVGKSSLLNKLAGADRVVVDDYAGTTRDPVDELVELGGRLWRF
+VDTAGIRRRQHMAHGADYYASLRTASALDRAEVAVVLLEAPSVISEQDVRIVQMALESGR
+ALVLAFNKWDQMDEDRRPQLEKEIERDLAHVAWAPRVNISALTGWHKDRLVPALDTALES
+WDRRIPTGKLNAFLGELVAAHPHPLRGGKQPRILFATQASTRPPTFVLFTTGFLDPGYRR
+FIVRRLRETFGFEGTPIEIGMRIRERRGRKR
+>MHAAABBN_01134
+MTENPQHRSGEDEFVPAGDDQVAERLAAMTEEEAEARAASLRAGLEDYELEEDDAALLDA
+WQLGPDEDVDAPVPPVLAIVGRPNVGKSTLVNRIIGRREAVVEDVPGVTRDRVSYDAEWN
+GREFTVVDTGGWEHDAKGIHRRVAEQAELAVDVADAVVFVVDATVGMTATDEAVVSMLRR
+KDRPVIVAANKVDDMVQEADAATLWSLGFGYPYPVSAVHGRGVADLLDAALEALPEESAH
+GGLVPRGGPRRIALVGRPNVGKSSLLNKLAGSDRVVVDDLAGTTRDPVDELVELGGRLWR
+FVDTAGIRRRQHMAHGADYYASLRTASALDRAEVAVVLLEAPQVISEQDVRILQMVLDSG
+RALVIAFNKWDQVDEDRRLQLAKEIERDLAHVAWAPRVNISAKTGWHKDRLVPALDLALD
+SWDTRIPTGKLNAFLGELVAAHPHPLRGGKQPRILFATQVSSRPPKFVLFTTGFLDPGYR
+RFIVRRLRETFGFEGTPLEIGMRVREKRGSRR
+>LFPAFLNI_01354
+MTENPQHRSGEDEFVPAGDDQVAERLAAMTEEEAEARAASLRAGLEDYELEEDDAALLDA
+WQLGPDEDVDAPVPPVLAIVGRPNVGKSTLVNRIIGRREAVVEDVPGVTRDRVSYDAEWN
+GREFTVVDTGGWEHDAKGIHRRVAEQAELAVDVADAVVFVVDATVGMTATDEAVVSMLRR
+KDRPVIVAANKVDDMVQEADAATLWSLGFGYPYPVSAVHGRGVADLLDAALEALPEESAH
+GGLVPRGGPRRIALVGRPNVGKSSLLNKLAGSDRVVVDDLAGTTRDPVDELVELGGRLWR
+FVDTAGIRRRQHMAHGADYYASLRTASALDRAEVAVVLLEAPQVISEQDVRILQMVLDSG
+RALVIAFNKWDQVDEDRRLQLAKEIERDLAHVAWAPRVNISAKTGWHKDRLVPALDLALD
+SWDTRIPTGKLNAFLGELVAAHPHPLRGGKQPRILFATQVSSRPPKFVLFTTGFLDPGYR
+RFIVRRLRETFGFEGTPLEIGMRVREKRGRRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001005.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001005.fa
new file mode 100644
index 0000000000000000000000000000000000000000..04df89cf83bbef8b40f779a2f2ef4c22f5173df2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001005.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01514
+MTEPQHADAGPRTRPAGRLGIGEVVAALKSDFPGVSASKVRFLEDRGLVLPERTPAGYRR
+YRPEDVDRLRFVLTVQRDHFLPLKVIAAQLAALDRGEVPADLPGGVVAPGASDASRLGRE
+VAAGRRGWTRSELAEESGAGEELLAELDQYSLLPADEDGAYSSHAMEVARAAVVLAGHGL
+EPRHLRPFRAAADRELGLVERAVAPLQARRDANMRPRVARSAQEIAQASLRLHSALVAEG
+LEQWDDGAVG
+>MOLHKGIG_01378
+MIDPRPLPDAVPTARPAGRLGIGEVVAALEAEFPGVTASKVRFLEDRGLVLPERTPAGYR
+RFRPEDVDRLRFVLALQRDHFLPLKVIADHLAALDRGERPTGLPGTAAVPASSDAARLGR
+EVAGGRRSWTRAELAAESGAGEELLAELDQYSLLPVDPDGGYPSHAMDVARAAVVLAGHG
+LEPRHLRPLRAAADRELGLVERAVAPLQARRDAGTRPRVARSAREIAQASLRLHAALVAV
+GLEQWDD
+>NAFOICDF_01409
+MSAPHEPSAAPPPAGAALGIGDLVAALEPSFPGVSASKVRFLEDRGLVRPERTAAGYRRY
+RPADVDRIRLVLTLQRDRFLPLKVIREHLDALDRGERPEDLGEAPAAAQEAVRLGHGIAD
+PDRRWTRAELAREAEVPAPLVDELDQYALLPRAEDGLHPPAALGVVRAAGRLAAHGIEPR
+HLRPFRAAADRELGLVQSAVAPLATRRDAGTRERAARTAEEIATACLALHAALVRAGLES
+LDG
+>MHAAABBN_01098
+MTDPRPRPDAVPTARPAGRLGIGEVVASLEVEFPGVTASKVRFLEDRGLVLPERTSAGYR
+RFRPEDVDRLRFVLALQRDHFLPLKVIADHLAALDRGERPTGLPGTAAAPASSDAERLGR
+EVAGGRRSWTRAELAAESGAGEELLAELDQYSLLPVDPDGGYPSHAMDVARAAVVLAGHG
+LEPRHLRPLRAAADRELGLVERAVAPLQARRDAGTRPRVARSAREIAQASLRLHAALVAV
+GLEQWDD
+>LFPAFLNI_01333
+MTDPRPRPDAVPTARPAGRLGIGEVVASLEVEFPGVTASKVRFLEERGLVLPERTSAGYR
+RFRPEDVDRLRFVLALQRDHFLPLKVIAEHLAALDRGERPTGLPGTAAAPASSDAERLGR
+EVAGGRRSWTRAELAAESGAGEELLAELDQYSLLPVDPDGGYPSHAMDVARAAVVLAGHG
+LEPRHLRPLRAAADRELGLVERAVAPLQARRDAGTRPRVARSAREIAQASLRLHAALVAV
+GLEQWDD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001010.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001010.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5c89e624f6f9e40b5c02044078e27c696da47b0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001010.fa
@@ -0,0 +1,60 @@
+>ACLBLIBL_01519
+MREISEPYHPRLSPESNITDFLERQAEERPDHGLFAVADEQDQWTDVSARDARERVRALA
+KGLIAAGVGAGDRVGLIAATRLEWTLVDFAIWYAGAVTVPIYETSSATQVAWIVEDADVC
+AVVAGDESLVKTVRDAVHREHLPELRGVWVMDVAGGEPGSGLDELAALGADVSDEDLEAR
+RSAANLEDLATIIYTSGTTGRPKGCELTHENFAELVNQTLSSSLGEVVRPDTSTVLFIPL
+AHVFARFVSVLTVAAGARCGHVTDLKRLSNSLQTFQPSFVLAVPRVFEKIYNAALLNAQS
+GGKDKIFRRGADVAVRWSRALDSGKMTAPLRLQRAFYSALIYRRIRAAMGGRLEYAVSGG
+GPLSPDLAHFFRGVGLTILEGYGLTETTAPITVGRPGRLKIGTVGLPLGGNAVRIAEDGE
+ILTRGTSLMRGYHDRPEANEEAFEDGWFRTGDLGSLDEDGFLTITGRKKELIVTAGGKNV
+APAMLEDAIRSDALISQVMVVGDAKPFIAAIVTLDADTLPSWLAAHGLPKDLDVAAAAKE
+ERVRRHVQEIVDKASSAVSRAEGIREFRILDRDFSMEEGHMTPSLKMKRAVIMQDFAAEI
+ADIYGEAPAQG
+>MOLHKGIG_01373
+MHEISEPYHHPRLSPEANITDFLERQATERPDHGLFAVPDAQDQWTDVSARDARERVRAL
+AKGLIAAGIQPGETVGLLASTRLEWTLVDFAIWYAGAVTVPVYETSSVSQVSWIIEDSDV
+RAVVTGNEDLAKTVRDAVQREGLPELIGLWTMDPADGAPGSGLEALVALGADVTDEELET
+RRSSAGLADLATIIYTSGTTGRPKGCELTHENFAELVNQTLSSSLGDVVREDTSTVLFIP
+LAHVFARFVSVLTVAAGARCGHVSDIKRLSVSLQTFQPSFVLAVPRVFEKIYNAALLNAQ
+SGGKEKIFRRGADVAIRWSRALDSGQMTAPLRLQRAFYSALVYRRIRTAMGGRLAYAVSG
+GGPLSTDLAHFFRGVGVTILEGYGLTETTAPITVGRPDRLKIGTVGHPLGGNQVRIAEDG
+EILTRGTSLMRGYHNRPEANEEAFEDGWFRTGDLGALDDDGFLTITGRKKELLVTAGGKN
+VAPAMLEDAIRSDALVSQVMVVGDGKPFIAAIVTLDTDTLPAWLAANGLPKDLDVAAAAR
+EDAVRRHIQEAVDKANSLVSRAEGIREFRILDRDFSLEEGHVTPSLKMRRSAIMKDFAAQ
+IADIYGEPAPQN
+>NAFOICDF_01414
+MRQISEPYLPRLSPDAAITDFLRDQAVQHPERALFAVPREDGSWDDVTAAEAWDRVRALA
+RGLVAAGVGPGDRVAIVSATRLEWTLADFAIWTAGAVTVPVYETSSASQIAWIFEDAGVG
+AAIADTPARAKSVSDAVHREGLPELKGLWVMDEDGGAPGAGLDRLTDAGADVPADELDAR
+REGVTLESLATIIYTSGTTGRPKGCELTHGNFAELVNQTLRSSLGEVVDEGASTLLFIPL
+AHVFARFVSVLTVAAGARCGHVPDLSRLATSMDTYHPTFLLAVPRVFEKIYNASLLKAQA
+GGKEKIFRRGADVAVRWSRALEEGRMTAPLRLQRAFYSALLYRRIREAMGGHLKYAVSGG
+GPLSPDLAHFFRGVGVTILEGYGLTETTAPITVGRPGKLKIGRVGQPLGGNEVRIDDDGE
+ILTRGTSLFRGYRNRPEANAEAFTEDGWFRTGDLGELDDDGFLKITGRKKEIIVTAGGKN
+VAPAQLEDAIRSDALVSQVMVVGEAKPFVAAIVTLDADTLPSWASAHGLDPQISMAEAAR
+EPQVIAHVQKAVDRANDTVSRAEGIREFRILDRDFSADEGHMTPSLKMRRTAILKDFQPV
+LDEIYGAGPARG
+>MHAAABBN_01093
+MHEISEPYHPRLSPEANITDFLERQATERPDHGLFAVPDAQDQWTDVSARDARERVRALA
+KGLIAAGIQPGETVGLLASTRLEWTLVDFAIWYAGAVTVPVYETSSVSQVSWIIEDSHVR
+AVVTGNENLAKTVRDAVQREGLPELIGLWTMDPADGAPGSGLEALVALGTDVTDEELETR
+RSSAGLADLATIIYTSGTTGRPKGCELTHENFAELVNQTLSSSLGDVVRQDTSTVLFIPL
+AHVFARFVSVLTVAAGARCGHVSDIKRLSVSLQTFQPSFVLAVPRVFEKIYNAALLNAQS
+GGKEKIFRRGADVAIRWSRALDSGQMTAPLRLQRAFYSALVYRRIRTAMGGRLAYAVSGG
+GPLSTDLAHFFRGVGVTILEGYGLTETTAPITVGRPDRLKIGTVGHPLGGNQVRIAEDGE
+ILTRGTSLMRGYHNRPEANEEAFEDGWFRTGDLGALDDDGFLTITGRKKELLVTAGGKNV
+APAMLEDAIRSDALVSQVMVVGDGKPFIAAIVTLDTDTLPAWLAANGLPKDLDVAAAARE
+DAVRRHIQEAVDKANSLVSRAEGIREFRILDRDFSLEEGHVTPSLKMRRSAIMKDFAAQI
+ADIYGEPAPHN
+>LFPAFLNI_01328
+MHEISEPYHHPRLSPEANITDFLERQATERPDHGLFAVPDAQDQWTDVSARDARERVRAL
+AKGLIAAGIQPGETVGLLASTRLEWTLVDFAIWYAGAVTVPVYETSSVSQVSWIIEDSHV
+RAVVTGNENLAKTVRDAVQREGLPELIGLWTMDPADGAPGSGLEALVALGTDVTDEELET
+RRSSAGLADLATIIYTSGTTGRPKGCELTHENFAELVNQTLSSSLGDVVRQDTSTVLFIP
+LAHVFARFVSVLTVAAGARCGHVSDIKRLSVSLQTFQPSFVLAVPRVFEKIYNAALLNAQ
+SGGKEKIFRRGADVAIRWSRALDSGQMTAPLRLQRAFYSALIYRRIRTAMGGRLAYAVSG
+GGPLSTDLAHFFRGVGVTILEGYGLTETTAPITVGRPDRLKIGTVGHPLGGNQVRIAEDG
+EILTRGTSLMRGYHNRPEANEEAFEDGWFRTGDLGALDDDGFLTITGRKKELLVTAGGKN
+VAPAMLEDAIRSDALVSQVMVVGDGKPFIAAIVTLDTDTLPAWLAANGLPKDLDVAAAAR
+EDAVRRHIQEAVDKANSLVSRAEGIREFRILDRDFSLEEGHVTPSLKMRRSAIMKDFAAQ
+IADIYGEPAPHN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001011.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001011.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4dd547005d0b75db6ab4f9f2fd85b090ccc27474
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001011.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01520
+MDRPVPPVEPAPPAVPAPAVDPVHLPLRLAPGSGAGADRCVVVLHGFTSGPDSVRAWAEG
+IAAGGSHVSVPLLPGHGTRWQDLAATGADEIRGAVRETVDRELSRHRHVVVAGISMGGAL
+ALDAAAHRPVSAAIVVNPALRFASPLAPLAPALAPFVPSVAPIANDIADPDARELAYPRT
+PVAGVAAVGRIQRAARRALPRITAPVTVFRSARDAVVPAASHRTLLRGLRRAPVDVVPLP
+RSRHVATLDYDLPLLIERSRAAVEAATRA
+>MOLHKGIG_01372
+MPRPVAVAPEDLPLRLMPAAPARRDHCVVLLHGFTSTPASVRAWAEGLAAGGSPVSVPLL
+PGHGTRWEDLAATGADEIRAAVRAVVDLELARHGRVVMAGISMGGALALDAAAHRPVAGV
+LVVNPALRFASPLAPFAPLLAPFVPTVAPIADDIADPTARERAYPRTPVAGVAALGRIQR
+AARRALPRITAPVTVYRSARDAVVPASSHRTLVRGLRQAPVEVVGLPRSRHVATLDYDLP
+LLIDHGRSAVAAMTTH
+>NAFOICDF_01416
+MTRLRPAAPDRRPAPGVDPAQRPFRLPATSLPGVAVVMLHGFTSGPDSVRAWAEGVAAGG
+AAVHVPLLPGHGTRWEDLGTTDADELRAAVRDAVDAALATHRRVVVAGISMGGALALDAA
+AHRDVAGVLVVNPALRFGSPLAVAAPLLRHVVPSVPSIAGDIADPDARELAYERAPVAGV
+AQVGRIQTAARRGLGRITAPVTVFRSAEDAVVPERSHHTLLRGLTAAPVEVVRLLHSRHV
+ATLDRDLPLLVARSRDAVAAAAR
+>MHAAABBN_01092
+MPRPVAVAPEDLPLRLMPAAPARRDHCVVLLHGFTSTPASVRAWAEGLAAGGSPVSVPLL
+PGHGTRWEDLAATGADEIRAAVRAVVDLELARHGRVVMAGISMGGALALDAAAHRPVAGV
+LVVNPALRFASPLAPFAPLLAPFVPTVAPIADDIADPTARERAYPRTPVAGVAAVGRIQR
+AARRALPRITAPVTVYRSARDAVVPASSHRTLVRGLRQAPVEVVGLPRSRHVATLDHDLP
+LLIDHGRSAVAAMTTH
+>LFPAFLNI_01327
+MPRPVAVAPEDLPLRLMPAAPARRDHCVVLLHGFTSTPASVRAWAEGLAAGGSPVSVPLL
+PGHGTRWEDLAATGADEIRAAVRAVVDLELARHGRVVMAGISMGGALALDAAAHRPVAGV
+LVVNPALRFASPLAPFAPLLAPFVPTVAPIADDIADPTARERAYPRTPVAGVAALGRIQR
+AARRALPRITAPVTVYRSARDAVVPASSHRTLVRGLRQAPVEVVGLPRSRHVATLDYDLP
+LLIDHGRSAVAAMTTH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001015.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001015.fa
new file mode 100644
index 0000000000000000000000000000000000000000..719f523ad2c777d3c830b8321ad19fe2ada46813
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001015.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01526
+MGRESAAPTRRSLAHVSTSSSDTPVPADAIPAELDALVGDWLTMPDVAERLDQRVTRVHN
+LVKDHRLLAVRRPDPAVRAVPALFLTETGLLEPLQGTLVLLADAGYSDEESLRWLFTEDP
+SLPGRPIDALRDGRKTEVRRRAQALAW
+>MOLHKGIG_01367
+MSTTSSDTPVPADAIPAELDALVGEWLSVPDVAEHLDQRVTRVHNLVHDRRLLAVRRPEP
+AVRSVPALFLTETGVLDSLQGTLVLLADAGFSDEEALRWLFTEDESLPGRPIDALRDGRK
+TEIRRRAQALAW
+>NAFOICDF_01421
+MTTEHPVDRVPSDAVSPELDALVGDWLTLPDVAERLDLRVTRVHNLINDRRLLAVRRPEP
+SVRAVPAAFLTERGLLEPLHGTLVLLQDAGFDDEEALRWLFTPDESLPGRPIDALRDGHK
+TEVRRRAQALGW
+>MHAAABBN_01087
+MSTTSSDTPVPADAIPAELDALVGEWLSVPDVAEHLDQRVTRVHNLVHDRRLLAVRRPEP
+AVRSVPALFLTETGVLDSLQGTLVLLADAGFSDEEALRWLFTEDESLPGRPIDALRDGRK
+TEIRRRAQALAW
+>LFPAFLNI_01322
+MSTTSSDTPVPADAIPAELDALVGEWLSVPDVAERLDQRVTRVHNLVHDRRLLAVRRPEP
+AVRSVPALFLTETGVLDSLQGTLVLLADAGFSDEEALRWLFTEDESLPGRPIDALRDGRK
+TEIRRRAQALAW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001016.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001016.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b94818af808db64491b97759f65fb6af710e6fae
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001016.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01527
+MPVDAAVTRPRPADQDRFRAAVAEELTRTLDEHRERARAVHPLTVPLVDAVGDLAAGGKR
+LRAVLGWLGWRAAGGDPENPRIARTGAALELFQAAALIHDDILDRSDTRRGMPSVHRRFE
+AEHRASGWRHDAGHFGVSAAILAGDVALGMSETAFAAALEGAGRPARARDEFERMRFGVM
+VGQYLDVAAEMAPPATDPAEAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDALVAAFA
+EVSLPFGLAFQYQDDLLGVFGDPAATGKPAGDDLREGKRTVLIARAVALLSPADAAALDA
+DLGDPGLSAERIAHWQRALEECGARQAVTDRVAALSARAAEAVGALEAHGVPADVRAELT
+ALIEAATTRRH
+>MOLHKGIG_01366
+MPADVAVPRPRPADQDRFRAAVADALDRLLAEHRDLARDVHPLTAPLVDAIADLTAGGKR
+LRAVLAWLGWRAAGGEAEDPRIAEAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRRFE
+SLHREAGWRHAAEHFGVSAAILAGDVALGMSETAFARVLAGTPREDRARAELERMRFGVM
+AGQYLDVVAEMAPAARDAREAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDGLVTAFA
+RVSLPFGMAFQYRDDLLGVFGDPATTGKPAGDDLREGKQTVLIARAVELLAPDEAAALDA
+DLGDPDLGADRVAHWQGVLEACGARRAVEERVAALSHEAAGAVAGLLAHGVPEDVSAELT
+QLIDAYTSRRH
+>NAFOICDF_01422
+MPTPETASVSDFRAAVAERLTAVLDGHARGAARIHPDADPVVEAVSVLTSGGKRLRAVLC
+WLGWRAAGGSPTDPRAAVAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRRFEARHREH
+GWRHEAEHFGVSAAILAGDVALALSDSMFSRAIEGTPRAERARREMERMRFEVMVGQYLD
+VAAEMAPPAADPAAAERAARAVVEHKSARYSAVHPLALGALLAGADDDLVAAFEAVSLPF
+GMAFQLQDDLLGVFGDPAHTGKPAGDDLREGKRTVLVARAEALLPRGEAAALDAELGDPA
+LSAERVAHWQRRLEEVGARTAVADEVDRLSAEARRGLERLAALGVGTDVRGELAELIDAY
+TVRTA
+>MHAAABBN_01086
+MPADVAVPRPRPRPADQDRFRAAVADALDRLLAEHRELARDIHPLTAPLVDAIADLTAGG
+KRLRAVLAWLGWRAAGGEAEDPRIAEAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRR
+FESLHREAGWRHAAEHFGVSAAILAGDVALGMSETAFARVLAGTPREDRARAELERMRFG
+VMAGQYLDVVAEMAPAARDAREAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDGLVTA
+FARVSLPFGMAFQYRDDLLGVFGDPATTGKPAGDDLREGKQTVLIARAVELLAPDEAAAL
+DADLGDPDLGADRVAHWQAVLEACGARRAVEERVAALSHEAAGAVAGLLAHGVPEDVSTE
+LTRLIDAYTPRRH
+>LFPAFLNI_01321
+MPADVAVPRPRPADQDRFRAAVADALDRLLAEHRERARDVHPLTAPLVDAIADLTAGGKR
+LRAVLAWLGWRAAGGEAEDPRIAEAGAAFELFQAAALIHDDILDRSDTRRGMPSVHRRFE
+SLHREAGWRHAAEHFGVSAAILAGDVALGMSETAFARVLAGTPREDRARAELERMRFGVM
+AGQYLDVVAEMAPAARDAREAEAAAEAVVEHKSARYSAVHPLALGGLLAGADDGLVTAFA
+RVSLPFGMAFQYRDDLLGVFGDPATTGKPAGDDLREGKQTVLIARAVELLAPDEVAALDA
+DLGDPDLGADRVAHWQAVLEACGARQAVEERVAVLSHEAAGAVAGLLAHGVPEDVSAELT
+RLIDAYTSRRH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001020.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001020.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f26a8abf7c134967da2841f82f40d8f0faaa0d71
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001020.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01531
+MDADQLRPEDRHVPVMRDRVVDLLAPAVQAALDAGRAPVAVDGTLGMGGHTEAMLTRFPE
+LTVIGIDRDAHAQALAAERLGPLAERLVPFHGTYDLVPEAMAAAGVEKVDAALYDLGVSS
+YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEHELRRIIRRDGEERFAGPIAR
+AIVRARAEAPIETTGRLVEVIRTAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP
+AILDALHVGGRLVVMSYHSLEDRIAKRHLSAWAASTAPPGFPVVLEEHEPVVRTLTRGTE
+KPTEEEILENRRASSAKVRAVEKIRTSRTPA
+>MOLHKGIG_01362
+MDAGQPRPEDRHLPVMRDRVVDLLAPAVQAALEAGRTPVAVDGTLGMGGHTEALLTRFPH
+LRVIGIDRDVHAQAMAVERLGPLAERLIPFHGTYDRVPEAMAAAGVTKVDAALYDLGVSS
+YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEQELRRIIRRDGEERFAGPIAR
+AIVRARDEAPIETTGRLVEVIRSAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP
+AILDALHVGGRLVVMSYHSLEDRITKRHLSAWATSTAPPGFPVVLEEHEPVVRVLTRGTE
+KPTEEEISENRRASSARVRAVEKIRTSRTTA
+>NAFOICDF_01426
+MDPTQPLPRDRHVPVMRDRVVDLLAPAVEAAAAAGRTPVAVDGTLGMGGHTEVLLRRFPT
+LRVVGIDRDPNALAMAQERLGPLAERLVPFHGTYDQVPEALAAAGAERMDAALYDLGVSS
+YQLDARERGFAYSYDAPLDMRMDTTAPVTAADLVAELDEQSLRRIIRRDGEDRFAGPIAR
+AIVRAREEEPILTTGRLVDVIRAVVPVSAGNKGGHPAKRTFQALRIAVNEELDILDAAVP
+AVLDALEVGGRLVVMSYHSLEDRIAKRHLQEWAASTAPPGFPVELPEHRPLVKVLTRGTE
+KPTEEEIEENRRASSAKVRAVEKIRTSRTTA
+>MHAAABBN_01082
+MDAGQPRPEDRHLPVMRDRVVDLLAPAVQAALEAGRTPVAVDGTLGMGGHTEALLTRFPH
+LRVIGIDRDVHAQAMAAERLGPLADRLIPFHGTYDRVPEAMAAAGVTKVDAALYDLGVSS
+YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEQELRRIIRRDGEERFAGPIAR
+AIVRARAEAPIETTGRLVEVIRSAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP
+AILDALHVGGRLVVMSYHSLEDRITKRHLSAWATSTAPPGFPVVLEEHEPVVRVLTRGTE
+KPTEEEISENRRASSAKVRAVEKIRTSRTTA
+>LFPAFLNI_01317
+MDAGQPRPEDRHLPVMRDRVVDLLAPAVQAALEAGRTPVAVDGTLGMGGHTEALLTRFPH
+LRVIGIDRDVHAQAMAVERLGPLAERLIPFHGTYDRVPEAMAAAGVTKVDAALYDLGVSS
+YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEQELRRIIRRDGEERFAGPIAR
+AIVRARDEAPIETTGRLVEVIRSAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP
+AILDALHVGGRLVVMSYHSLEDRITKRHLSAWATSTAPPGFPVVLEEHEPVVRVLTRGTE
+KPTEEEISENRRASSARVRAVEKIRTSRTTA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001021.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001021.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f14bc9b42803b355c6aa18133172312232ec335a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001021.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01532
+MTLHEEMSMAAHARIAEPLRHTGAPARPAPQERTPLSVVPAPLPRSRSGMTVLCVVVLLA
+ALAAVLVMNITMSNRQYALLDLRQEQQAVTEVNERLAEQVGYLEAPQNVAARADALGMVA
+PAGTASVDAATGEFRGEAQPAREGEISATFVAPPVNADAVRQGSAGSADADRGDIEGPRT
+LGAPAAAPGAAASDDRDASDR
+>MOLHKGIG_01361
+MTLHEEMSMAAHARIAESLRPGSTPVAPARPTPQERTPLSVVPAPLPRSRSGVTVLCVLV
+VLAALAAVLVMNITMSNRQYALLDLRQEQQAVTETNERLAEQVGHLEAPQNLAARADALG
+MVAPAGTASVDAGTGQFSGEAQAAQDGDISATYVAPPADADAVRQGTAGDGQDEIEGPRT
+LGGEDASAAPDQDAADR
+>NAFOICDF_01427
+MTAYEETGMSAQAWRDEARTAWPRTGATPEREHRQRTPLSVVPTPLPRSGSGVAVLCGLV
+LLVALGLVLVMNITMSNRQFTLLDLRAQQTTLTETNERLAEQAGYLDAPQNLAARAGAMG
+MVSPGATSTVDVASGAVAGPSTGAGSTTLPEGRIAPPADADLARQGEAQGQIPGPRTVDP
+AAPTAAPSGETAPTPAPTDAPAGR
+>MHAAABBN_01081
+MTLHEEMSMAAHARIAESLRPGSTPVAPARPAPQERTPLSVVPAPLPRSRSGVTVLCVLV
+VLAALAAVLVMNITMSNRQYALLDLRQEQQAVIETNERLAEQVGNLEAPQNLAARADALG
+MVAPAGTASVDAGTGEFGGEAQAAQDGDVSATYVAPPADADVVRQGASAEGQDEIEGPRT
+LGGEDASAAADQDAADR
+>LFPAFLNI_01316
+MTLHEEMSMAAHARIAESLRPGSTPVAPARPTPQERTPLSVVPAPLPRSRSGVTVLCVLV
+VLAALAAVLVMNITMSNRQYALLDLRQEQQAVTETNERLAERVGHLEAPQNLAARADALG
+MVAPAGTASVDAGTGQFSGEAQAAQDGDISATYVAPPADADAVRQGTAGDGQDEIEGPRT
+LGGEDASAAPDQDAADR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001024.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001024.fa
new file mode 100644
index 0000000000000000000000000000000000000000..983564f5566e8c2b6ae9888fc53ddd9cffca74c4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001024.fa
@@ -0,0 +1,56 @@
+>ACLBLIBL_01535
+MIALTAAQIAEAVSGTLSPALDPQTVLVHVTPDSREVAAEGTLYVAKPGERADGHDFIDA
+ALAAGAVAVLAERPTQAPDGAEHPSIVVEDAVLAMGALAREVVSRIREHSPTTVIGITGS
+AGKTTTKDLLAALLATQGPTVAPVGSYNGEVGVPLTVFRAELETRYLVVEMGADHVGNIA
+YLCDIVRPDVGVVLMVGTAHAGSFGGVANIAATKGELAEAVGPEGAVILNLDDDRVAAMA
+SRAQAPVTWFTADEAGAARAAQDVAAGRAAGLVAARALHADDHERAAFDLQIGADADAPR
+HPLTSGLTGLHHAHNVLAAAAAAHAAGMAPADVARVLDGLGPTSRFRMERTDRPDGVTII
+NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARVREHTLVGESVVRLNIA
+QLLVVGAGARPLYIGALNEGSWGDEAHFVEDVAQAEEFLAEHLAPGDLVLVKSSNGVGLA
+ALGERLATAGASDPAPRPVRLPEGVPTVIGLLIGGVLGLVLSAAGTPLFIRFLVKRGYGQ
+FVRDDGPTTHKTKRGTPTMGGAVIIGAFVLAYLLTHGILALLGVGFGGPTASGLILLFLT
+VGMAFVGFVDDFTKITKQQSLGLTPRGKIILQGLIGTAFAVLALNFPDDRGLTPASTAIS
+FARDVPWLDLAFAGPVVGLILFVIWSNLITTATTNAVNLTDGLDGLATGATAMITGAYVL
+MSIFQSSQACSLVDEPGCYEVRDPMDLALLGAILTGSLLGFLWWNTSPAKIFMGDTGSLG
+LGGALAGFAILSRTELLVVLLAGLMVAITVSVIVQVGWFRISGGKRVFLMAPLQHHFELK
+GWAEVTVVVRFWLVSLMCVTAGLAVFYGEWIVRQGGLAGVTP
+>MOLHKGIG_01358
+MIALTAAQIAEAVSGTLSATLDPATVLVHVTPDSREVTAEGTLYVAKPGERADGHDFIDA
+ALGAGAAAVLAERATHAPDGAAHPAIIVEDAVLAMGALAREVVRRVRGHSPTTVIGITGS
+AGKTTTKDLLAALLATQGPTVAPVGSYNGEVGVPLTVFRAELDTRFLVVEMGADHVGNIA
+YLCDIVRPDIGVVLMVGTAHAGSFGGVANIARTKGELVEALGPEGVAVLNLDDERVAGMA
+ARTAAPITWFTADERGVARAAEDVAAGRASGLVAARDVRADDQERPVFDLQVGTEEAAVR
+HPVASGLTGLHHVHNVLAAAAAAHAAGMDPAEIARGLDGLGPASRFRMERTDRADGVTII
+NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARVREHTLVGESVVRLNIA
+QLLVVGAGARPLYIGALNEGSWGEEAHFVDDAAQAEAFLAEHLRPGDLVLVKSSNGVGLA
+ALGERLATADAVAAPSASPKESRP
+>NAFOICDF_01430
+MIALTAAQIAEAVSGTLSSTLDPETVLVHVTPDSREVVGEGTLYVAKPGEHADGHDYIDA
+ALAAGASAVLAERPTQDADGAAHPAILVADAVLAMGALAREVVRRIREHSPTTVIGITGS
+AGKTTTKDLLAALLSTQGPTVAPVGSFNGEVGVPLTVFRAALDTRYLVVEMGADHVGNIA
+YLCDVVTPDIGVVLMVGTAHAGSFGGVENIAKTKGELVEALGPDGVAVLNRDDGRVAAMA
+SRTQAPVVWFSTEESGAAAAAEDVAAGRASGLSVARALTADAEERPVFDLQLGADLDAPR
+HAVRAGLTGLHHAHNMLAAAAAAQAAGMDPADIARGLDGLGPTSRHRMERSERADGVSII
+NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARIREHTLVGESVVRLNIS
+QLLVVGAGARPLYIGAMNEGSWGDEAHFVDDVEQAEAFLAEALQPGDIVLVKSSNGVGLA
+ALGDRLAAADVTPSTASPSDTTKETRP
+>MHAAABBN_01078
+MIALTAAQIAEAVSGTLSATLDPATVLVHVTPDSREVTAEGTLYVAKPGERADGHDFIDA
+ALGAGAAAVLAERATHAPDGAAHPAIIVEDAVLAMGALAREVVRRVREHSPTTVIGITGS
+AGKTTTKDLLAALLATQGPTVAPVGSYNGEVGVPLTVFRAELDTRFLVVEMGADHVGNIA
+YLCDIVRPDIGVVLMVGTAHAGSFGGVANIARTKGELVEALGPDGVAVLNLDDERVAGMA
+ARTAAPITWFTADERGVARAAEDVAASRASGLVAARDVRSDDQERPVFDLQVGTDEAAVR
+HPVASGLTGLHHVHNVLAAAAAAHAAGMDPAEIARGLDGLGPASRFRMERTDRADGVTII
+NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARVREHTLVGESVVRLNIA
+QLLVVGAGARPLYIGALNEGSWGEEAHFVDDAAQAEAFLAEHLRPGDLVLVKSSNGVGLA
+ALGERLATADAVAAPSASPKESRP
+>LFPAFLNI_01313
+MIALTAAQIAEAVSGTLSATLDPATVLVHVTPDSREVTAEGTLYVAKPGERADGHDFIDA
+ALGAGAAAVLAERATHAPDGAAHPAIIVEDAVLAMGALAREVVRRIRGHSPTTVIGITGS
+AGKTTTKDLLAALLATQGPTVAPVGSYNGEVGVPLTVFRAELDTRFLVVEMGADHVGNIA
+YLCDIVRPDIGVVLMVGTAHAGSFGGVANIARTKGELVEALGPDGVAVLNLDDERVAGMA
+ARTAAPITWFTADERGVARAAEDVAAGRASGLVAARDVRADDQERPVFDLQVGTDEAAVR
+HPVASGLTGLHHVHNVLAAAAAAHAAGMDPAEIARGLDGLGPASRFRMERTDRADGVTII
+NDAYNANPESMRAALRTLATLGRSSGRRTWAVLGEMLELGDARVREHTLVGESVVRLNIA
+QLLVVGAGARPLYIGALNEGSWGEEAHFVDDAAQAEAFLAEHLRPGDLVLVKSSNGVGLA
+ALGERLATADAVAAPSASPKESRP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001026.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001026.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ed986116cd874fde9ea29395aff2fd1e26b4de2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001026.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_01537
+MSPTELHPVRTPADEEETEARSRPLQRLWRLVEGRRALDLSVLLIGGSTFLLTALGLVMV
+LSSSSVEAIGTGGGSYGLFLRQTMWAVAGLAALLLFSRLPIGWIKALAWPAFGLAVVLLS
+LVAFTPLGVTVGGNTNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALVPV
+LPGGLLLIGLVMAGSDLGTAIILALVLAAVLFVAGTHHGVFIAFSAVTVVGAIALTLLAP
+HRMVRVQAWLGDCSDASDPCFQPDHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT
+ILGEELGLVGTLGVLLAYLALAVGMYRVAAGTTSPFIRLATWGIMAWLVGQAFVNIAMVS
+GVIPVVGVPLPFISYGGSALTLSLTAVGIVLAFARHERRRAEEPDARPDADDPDTDPLPV
+IPAPASQES
+>MOLHKGIG_01355
+MSPIELRPVRPRAADDAPEHRERILRRMWRVLEGRRALDLSVLLISGCTALLTVLGLVMV
+LSSSSVEAIGTGGGSYALFLRQSAWAVAGVAALLVFSRLPVRVLKALAWPAFGVAVILLA
+LVAFSPLGVTVGGNRNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALIPV
+LPGGLLLLVLVMAGSDLGTAIILAIVLATVLYVAGTHWGVFLTFLALSVLGILALTLLAP
+HRMVRVQAWMGDCSDATDPCFQPAHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT
+ILGEELGLVGTLVVLLAYLGLAIGIYRVAAGTTSTFIRLSTWGILAWLVGQAAVNIAMVS
+GVIPVVGVPLPFISYGGSALTLSLSAVGIVLAFARHERRRAAQPDARPQADEPDTDPLPV
+IPTPALQEPR
+>NAFOICDF_01433
+MPSTATRPEASSRASARTAVRPRLAGFWGALEGRRALDWAALLIGLCTAVLTVLGLVMVL
+SASSVEAISSSGGSYGLFLRQGGWALGGAVLLAVLRRLPVDLYRRLAWAAYLFAFLLLAL
+VAFTPLGKEVNGNTNWLQLGPVTFQPSEAAKLAMALWAAAVLQRKERLVHLVSHALVPVL
+PFGVALILLVLKGRDLGTALILAFILAVILFVAGTPGRVFAVLAGIGVVAALGMTVFAAN
+RMERVQAWLFGCEGLQGDPCMQPDHGIYALASGGWWGVGLGQSRQKWNYIPEAENDFIFT
+ILGEELGLVGTLLVLACFVGLAVGMYRVAAGASSTFVRLATWGILAWIVGQAAMNIAMVT
+GLLPVVGVPLPFISYGGSALTLSLAAVGVVLSFARHERDLLPAAEASAADPASSASPQES
+R
+>MHAAABBN_01075
+MSPIELRPVRPRADDDAPEHRERLLHRMWRVLEGRRALDLSVLLISGCTALLTVLGLVMV
+LSSSSVEAIGTGGGSYALFLRQSAWAVAGVAALLVFSRLPVRVFKALAWPAFGVAVILLA
+LVAFSPLGVTVGGNRNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALIPV
+LPGGLLLLGLVMAGSDLGTAIILAIVLATVLYVAGTHWGVFLTFLALSVLGILALTLLAP
+HRMVRVQAWMGDCSDATDPCFQPAHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT
+ILGEELGLVGTLVVLLAYLGLAIGIYRVAAGTTSTFIRLSTWGILAWLVGQASVNIAMVS
+GVIPVVGVPLPFISYGGSALTLSLSAVGIVLAFARHERRRAAQPDARPQADEPDTDPLPV
+IPTPALQEPR
+>LFPAFLNI_01310
+MSPIELRPVRPRADDDAPEHRERLLPRMWRVLEGRRALDLSVLLISGCTALLTVLGLVMV
+LSSSSVEAIGTGGGSYALFLRQSAWAVAGVAALLVFSRLPVRVFKALAWPAFGVAVILLA
+LVAFSPLGVTVGGNRNWLGIGGFRMQPSEAAKLALALWAAAVLERKHRLVTQVRHALIPV
+LPGGLLLLILVMAGSDLGTAIILAIVLATVLYVAGTHWGVFLTFLALSMLGILALTLLAP
+HRMVRVQAWMGDCSDATDPCFQPAHGMYALASGGWWGAGLGQSRQKWSYIPEAENDFIFT
+ILGEELGLVGTLVVLLAYLGLAIGIYRVAAGTTSTFIRLSTWGILAWLVGQAAVNIAMVS
+GVIPVVGVPLPFISYGGSALTLSLSAVGIVLAFARHERRRAAQPDARPQADEPDTDPLPV
+IPTPALQEPR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001027.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001027.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da4d2ae42bf033a742c66471e496882666e784a1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001027.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01538
+MPQTPDPARELRVVLAGGGTAGHISPMLAIARALESDDAGPVRCTMVGTASGMETRLVPE
+AGYELDLIERVPMPRRPSMDVVHFPARMRAAVAAAGRILAERRADVVVGVGGYVATPVYL
+AAFRAGVPVVVHEANARPGLANRIGALRAAHVGTALPDTRLRGARWVGMPMRPEISGLDR
+AAQRRAARAALGLDPERTTVVVTGGSSGALAVNRTVRDSLDDLLGAGLQVFHLTGRDKAL
+TEADGTPLRREGYVQREYLDGMEQAYAAADLLVARSGAGTVCEVSAVGLPAVYVPLPIGN
+GEQALNARPVVEAEGALTVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV
+TMAGLVRSAAEEGARR
+>MOLHKGIG_01354
+MTQTSHPSGPLRVVLAGGGTAGHISPMLAIARALEGDGGGPVECTMVGTASGMETRLVPE
+AGYELDLIDRVPMPRRPSMDVVRFPARMRAAVATAARILRDRRADVVVGVGGYVATPVYL
+AAFRAGVPVVVHEANARPGLANRIGALRATHVGTALPDTRLRGARWVGMPMRPEISGLDR
+AAARRAAREALGLDPDRTTVVVTGGSSGALAVNRTVRAALGDLLDAGLQVFHLTGRDKAL
+TEDDGSLLVRDGYVQREYLAGMEQAYAAADLIVARSGAGTVCEVSAVGLPAVYVPLPIGN
+GEQALNARPVVEAEGALLVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV
+TMAGLVRSAAQEGARR
+>NAFOICDF_01434
+MTTPNDASRPLRVVLAGGGTAGHISPMLAIARALGRQDPSTVCTMVGTDSGMETRLVPQA
+GYELDFVERVPMPRRPSMDVVRFPGRFQASVRQAGEILRRRGADVLVGVGGYVSTPMYLA
+ASRAGVPVVVHEANARPGLANRVGALRAARVGTALPDTRLPKAQWVGMPMRPEISGLDRA
+AARDAARAELGLDPERTTVVVTGGSSGALNVNRTVRESLDDLLGAGLQVFHLTGRGKELT
+DEAGQRVTRPGYVQREYLDGMEKAYAAADLIVARSGAGTVCEIAAVGLPAVFVPLPVGNG
+EQALNARPVVDAGGALLVRDETFRADWVRRELIPLATDPQRLAAMGEAAARLGVRDADVR
+TADLVREAAREGARR
+>MHAAABBN_01074
+MTQTSHPSGPLRVVLAGGGTAGHISPMLAIARALEGDGGGPVECTMVGTASGMETRLVPE
+AGYELDLIDRVPMPRRPSMDVVRFPARMRAAVATAARILRDRRADVVVGVGGYVATPVYL
+AAFRAGVPVVVHEANARPGLANRIGALRAAHVGTALPDTRLRGARWVGMPMRPEISGLDR
+AAARRAAREALGLDPDRTTVVVTGGSSGALAVNRTVRAALGDLLDAGLQVFHLTGRDKAL
+TEDDGSLLVRDGYVQREYLAGMEQAYAAADLIVARSGAGTVCEVSAVGLPAVYVPLPIGN
+GEQALNARPVVEAEGALLVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV
+TMAGLVRSAAQEGARR
+>LFPAFLNI_01309
+MTQTSHPSGPLRVVLAGGGTAGHISPMLAIARALEDDGGGPVECTMVGTASGMETRLVPE
+AGYELDLIDRVPMPRRPSMDVVRFPARMRAAVATAARILRDRRADVVVGVGGYVATPVYL
+AAFRAGVPVVVHEANARPGLANRIGALRATHVGTALPDTRLRGARWVGMPMRPEISGLDR
+AAAGRAAREALGLDPDRTTVVVTGGSSGALAVNRTVRAALGDLLDAGLQVFHLTGRDKAL
+TEDDGSLLVRDGYVQREYLAGMEQAYAAADLIVARSGAGTVCEVSAVGLPAVYVPLPIGN
+GEQALNARPVVEAEGALLVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV
+TMAGLVRSAAQEGARR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001033.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001033.fa
new file mode 100644
index 0000000000000000000000000000000000000000..47b6260290920445030f08847e6aafe44b4d55cc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001033.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01544
+MAGALKKTMIYLGLADGEEYDEQQRAAERDAAERRDVVEARRAAEPDTDPSMEPVRSATV
+VRPESIERAESPAPSGSTAAAPAEPAELRRSSRPEPVDPGYRAPVTPIKRAAASSAEGAP
+VSTLSTVHPRSYNDAKAIGEAFRSGMPVIMNVTELGENEAKRLVDFAAGLVFGLHGSISR
+ITSKVFLLTPANVDVVGAEQGDAEESGDPYDGD
+>MOLHKGIG_01348
+MAGALKKTMIYLGLADGDEYDEQPRAAERETAPRHEVVEARRPAEPDTDPHMEAVRPAAV
+RDPEPAERPEPVTPSGSTAADPVEPRRPARPEPVDPGYRAPVTPIKRAAASSAEGASVHT
+LSTVHPRSYNDAKAIGEAFRSGVPVIMNVTDLGENEAKRLVDFAAGLVFGLHGSISRITS
+KVFLLTPATVDVVGAEQGESGAADSPFDGD
+>NAFOICDF_01440
+MAGGLKKTMIYLGLADGDEYDDDPRHEAVDAAPRREPVEARRVAEPAPRLEPEDEEFDEP
+STPSHAGSTAAAAAEPAPRRAASRPETADPGHRAPVTPIKRAAAPSAEGDAVRTLSTVHP
+RSYNDAKRIGEAFRTGTPVIMNVTDLGENEAKRLVDFAAGLVFGLHGSISRITSKVFLLT
+PSSVEVVGEEPPAGRDGDAPYDND
+>MHAAABBN_01068
+MAGALKKTMIYLGLADGDEYDEQPRAAEREAAPRHEVVEARRPAEPDTDPHMEAVRPAAV
+RDPEPAERPEPVTPSGSTAAEPVEPRRPARPEPVDPGYRAPVTPIKRAAASSAEGASVHT
+LSTVHPRSYNDAKAIGESFRSGVPVIMNVTDLGENEAKRLVDFAAGLVFGLHGSISRITS
+KVFLLTPATVDVVGAEQGESGVADSPFDGD
+>LFPAFLNI_01303
+MAGALKKTMIYLGLADGDEYDEQPRATEREAAPRHEVVEARRPAEPDTDPHMEAVRPAAV
+RDPEPAERPEPVTPSGSTAADPVEPRRPARPEPVDPGYRAPVTPIKRAAASSAEGASVHT
+LSTVHPRSYNDAKAIGEAFRSGVPVIMNVTDLGENEAKRLVDFAAGLVFGLHGSISRITS
+KVFLLTPATVDVVGAEQGESGAADSPFDGD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001035.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001035.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7ec10f1af2fec1e6e3eee25930f5f6a18cbdf40
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001035.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01546
+MALSWEDVVNKQFQPTKFREGYDQGEVDDFLDEIVGELKRLQGLNEQLTAENEALRAGGA
+VPDADAAVDAPVADADAAAVVDAGQSPAPAALADAEPGLEVEPTPSSADPASASAAGVLA
+MAQRVHDEHVAAGEQRRDELISEAEARAEALVAEAEETRTRTLEELAADKAGLEAEVEQL
+RGFETDYRSRLTAYIEGQLREIRSQERVEPAQRPA
+>MOLHKGIG_01346
+MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA
+APAAGPAADTPEAAATPASAEESAPAAAPESADAAATSAAGVLAMAQRLHDEHVAAGEQR
+STELVAEAEATAARLVSDAEEQKARTLEALAEEKAGLEGEVEQLRSFETDYRSRLTSYIE
+GQLREIRAQKRVEPPTPTA
+>NAFOICDF_01442
+MVLSWEDVVNKEFQLTKFREGYDREEVEDFLDEVVEELKRLTEENDRLRSDLDACREGAP
+AQAEASAPAAGEAAPALQAPAPVAPVEPSAPGEPVAPTDSATSAAGVLAMAQRLHDEYVA
+EGEQRRDRIIADAEAEATTVVRQAEETRTRTLSDLESRRKGLEADVERLRAFETDYRSRL
+TAYIEGQLREITAQERLEPAKGTV
+>MHAAABBN_01066
+MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA
+APVADTPEAAETPSPVEEPAPAAAPEAADAAATSAAGVLAMAQRLHDEHVAAGEQRSTEL
+VAEAEATAARLVSDAEEQKARTLEALAEERAGLEGEVEQLRSFETDYRSRLTSYIEGQLR
+EIRAQKRVEPPTPTA
+>LFPAFLNI_01301
+MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA
+APAAAPAADTPEAAATPASVEEAAPAAAPESADAAATSAAGVLAMAQRLHDEHVAAGEQR
+STELVAEAEATAARLVSDAEEQKARTLEALAEEKAGLEGEVEQLRSFETDYRSRLTSYIE
+GQLREIRAQKRVEPPTPTA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001037.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001037.fa
new file mode 100644
index 0000000000000000000000000000000000000000..46d32953dd49d04dff5569c14730610150cd12d6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001037.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01548
+MEPIPGATARIEVTPDRAGRRADAVLAEVLGLSRSALADWFSRGLVRAESRTGRRDRVLA
+KSAKAVAGEVLAVDVPDDPDPLEVRAERVDALRILHEDEHLIAVDKPTGVAAHPSPGWAG
+PTVVGALAALGHDISTSGAPERQGIVHRLDVGTTGVMVVAKTEQAYAALKDQFRRRVPEK
+VYHALVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDGGRPSVTHYETLEVFGRATLLEVHL
+ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLSFPHPVTGEPVSV
+TSEHPDDLAHALARLRRDGS
+>MOLHKGIG_01344
+MGMRPGLTERLEVTEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA
+KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG
+PTVVGALAALGYDITTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK
+VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLEDGRPSVTHYETLEVFGRATLLEVHL
+ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLAFPHPVTGEPVTI
+TSPYPDDLAHALAALRGDED
+>NAFOICDF_01444
+MGLRPGLTERLAVTEDDAGRRADAVLADAFGVSRASLADLFSRGLVRAESRTGRRDRVLA
+KSAKAVAGETLAVDVPVDPDPLEVRAERVDAMTVLYEDDDLLAVDKPTGVAAHPSPGWFG
+PTVVGGLAGLGRRISTSGAPERQGIVHRLDVGTTGVMVVAKSERAYTALKDQFRERVPEK
+VYHAVVQGMPDPLEGTIDAPIGRDPNHHWRFAVLEGGRPSVTHYETVEAFGRATLLEIHL
+ETGRTHQIRVHTSALRHPCAGDLTYGADPRLAAELGLTRQWLHAHRLALPHPATGERLEI
+VSPYPDDLAHALRVLRGEDRGAAPDA
+>MHAAABBN_01064
+MGMRPGLTERLQVAEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA
+KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG
+PTVVGALAALGYDITTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK
+VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDDGRPSVTHYATLEVFGRATLLEVHL
+ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLAFPHPVTGEPVTI
+TSPYPDDLAHALAALRGDED
+>LFPAFLNI_01299
+MGMRPGLTERLEVTEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA
+KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG
+PTVVGALAALGRDISTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK
+VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDDGRPSVTHYETLEVFGRATLLEVHL
+ETGRTHQIRVHTSALRHPCVGDLTYGADPRMAAELGLTRQWLHAHRLAFPHPVTGEPVTI
+TSPYPDDLAHALAALRGDAD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001042.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001042.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b78b063d529ba0d6cca67019c69432836d1d5b45
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001042.fa
@@ -0,0 +1,31 @@
+>ACLBLIBL_01554
+MLTAYDAMTAALFDEAGIEVLLVGDSVGNTVLGHSSTLPVTLDQMILFSQAVVRGAQRAL
+VVADLPFGSYEASPQQAVESAVRLVKESGAHAVKVEGDERFAEHVAAMTAAGVAVIAHIG
+FTPQSEHVIGGYRVQGRGEGAVEAMTASARALEAAGAFAVLMEMVPSDVAAAVDAALRVP
+TVGIGAGPGTTGQVLVWQDMLGLREGRTPRFVRQYARLHEVIGAGVRAYRRDVLDGAFPA
+PEHGFEA
+>MOLHKGIG_01338
+MSAPQSPRQPDDTAPYGPPAPSRYRTVHLQRAKDEGRRFAMLTTYDAMTAALFDEAGVEV
+LLVGDSVGNTVLGHPTTLPVTLDQMILFTQAVVRGAERALVVADLPFGSYEASPRQAVES
+AVRLVKESGAHAVKVEGDERFAEHVAAMTAAGVAVMAHIGFTPQSEHVLGGYRVQGRGAG
+AVERMTASARALEAAGAFAVLMEMVPSDVAAAVDAALRVPTVGIGAGPGTTGQVLVWQDM
+LGLREGRVPRFVRQYARLHEVVGDAVRAYRADVLDGAFPAPEHGFQG
+>NAFOICDF_01450
+MDSRTVTPPASSPAASEAAAPYGGAATAAAAAPVEAPARYRTVHLQRAKDEGRRFAMLTT
+YDAMTAALFDEAGVEVLLVGDSLGNTVLGHGSTLPVTLEDMIVFSAAVARGARRAFVLAD
+LPFGSYEASPEQAVRAGVRLMKEAGVHGVKVEGDERFAPHIAAMVAAGVPVMGHIGFTPQ
+SEHVLGGYRVQGRGEGAAERLIASARALEDAGAFAVLMEMVPSDVAAAVDAALRVPTVGI
+GAGPKTTGQVLVWQDMLGLGAGRTPRFVKRYADLRAVMGDAVRAYRADVLSGAFPDPAHA
+FES
+>MHAAABBN_01058
+MSAPQSPRQPDDTAPYGPPAPSRYRTVHLQRAKDEGRRFAMLTTYDAMTAALFDEAGVEV
+LLVGDSVGNTVLGHPTTLPVTLDQMILFTQAVVRGAERALVVADLPFGSYEASPRQAVES
+AVRLVKESGAHAVKVEGDERFAEHVAAMTAAGVAVMAHIGFTPQSEHVLGGYRVQGRGAG
+AAERMTASARALEAAGAFAVLMEMVPSDVAAAVDAALRVPTVGIGAGPGTTGQVLVWQDM
+LGLREGRVPRFVRQYARLHEVVGEAVRAYRADVLDGAFPAPEHGFEG
+>LFPAFLNI_01293
+MSAPQSPRQPDDTAPYGPPAPSRYRTVHLQRAKDEGRRFAMLTTYDAMTAALFDEAGVEV
+LLVGDSVGNTVLGHPTTLPVTLDQMILFTQAVVRGAERALVVADLPFGSYEASPRQAVES
+AVRLVKESGAHAVKVEGDERFAEHVAAMTAAGVAVMAHIGFTPQSEHVLGGYRVQGRGAG
+AAERMTVSARALEAAGAFAVLMEMVPSDVAAAVDAALRVPTVGIGAGPGTTGQVLVWQDM
+LGLREGRVPRFVRQYARLHEVVGEAVRAYRADVLDGAFPAPEHGFEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001044.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001044.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a57b57ed96893bdc098140ca30a4a20cd0e2890
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001044.fa
@@ -0,0 +1,95 @@
+>ACLBLIBL_01556
+MSALPDAATADAPDRRALAQAGVADARRVQSLLASPEFEGADVAPLVKRLGHAADPDRAL
+LLWVRLAEREPRVHRALRDPETTARLLRLLGASEALGEFLIRRPEHLDLVLEPESAAATA
+PALAQPDPADGEEWADEPAALRRLLLEAVEADPDADRPRAGLTGADAAVALRRAYRRQLA
+AIALRDLDSADPAAVMPSVGRWLADLAGAAVDAALAVSRATLAEREGPAVDRVDLAVIGM
+GKCGARELNYISDVDVVFVHELLDPGPDAAGEAGADGADGEASDAVDGTRAAVLAAELAA
+GIGRVIQAAAPEPGLWEVDANLRPEGKDGALSRTLDSHAEYYRRWAHGWEFQALLKARPI
+AGSADLGARYLERIWPRVWESSAREGFVDSVRAMRSRVLETIAPAEREREIKLGSGGLRD
+VEFTAQLLQLVHGRADESIRVRGTLDAVRALHEASYISTRDAAAFDEHYRWLRTLEHRIQ
+LVHLRRTHLMPVKDEALRIVARSLRGAQETGPATGEDLQAAFTRVRRAVRGLHETVFYRP
+LLSTTAALSDDEVRLSAEAVRERLAALGYRDPKGALRHIEALTQGVSRRAAIQRQLLPAM
+LGWFAEGADPDGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLAASRFVGDLLEH
+SPEAVAWVGDDRELEPRGTVQLWRQADARLDRRIEAQETPAAVRHVRQVRRSETLRVALA
+DISGLLDLEAVTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYG
+SDLDALFVHRPRPGVDEGRAREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGR
+QGPLVRTLDSYREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAGDLTTAD
+AREIRRIKARVEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGTL
+PALRAIARHGLLPEAEVAVLEEAWLLASRIRAAVLLWTGKVGDVLPTNMRDLEAIARLSG
+VGTAGGELEERYLRVTRLARQVFEARFYGL
+>MOLHKGIG_01335
+MSSLSTTGALPAVPDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRA
+LLLWVRLAEREPRVHHALRDPETTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAAT
+APALAQPDPADGEPWGDASATLRRLLLDSVGADPDTDRPVAAVTGKDAAVALRRAYRRQL
+AAIALRDLDSAEPTAAMPSVGRWLADLAGATVDAALAVSRAVLTEREGPVVDRVDLAVIG
+MGKCGAGELNYVSDVDVVFAHAVREAADGADPDAEVPDGPRAAALAAELAAGIGRVIQGA
+APEPGLWEVDANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGER
+YIAEIWPRVWESSSRDGFVESVRAMRARVLDTLAPAEREREIKLGPGGLRDVEFTAQLLQ
+LVHGRADESLRVRGTLDAVRALHAASYITTRDARAFDEHYRWLRTLEHRIQLVHLRRTHL
+MPVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALS
+AEDVRLSAEAVRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGAD
+PDGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLSGSRFVGDLLEHSPEAVAWVG
+DDRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVALADISGLLDLE
+AVTGALSDIDQVTVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVH
+RPRPGVDEGRAREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGRQGPLVRTLD
+SYREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAGDLTTADAREIRRIKA
+RVEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGTLPALRAIARH
+GLLPEAEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTAGGELE
+ERYLRVTRLARQVFETRFYGL
+>NAFOICDF_01452
+MAPTPDSHVPGPRRALVHAGVADLTRAERLLSSPELAEQDADAALAALAHAADPDSALLL
+YIRLAERDPQVHRVLAEADRARDLLRLLGASEALGEFLIRRPEHLDLVLDPARAAATAPA
+LAQQDPTDGGDWHDEPAALRALLLEAVGADPAADQPVAGLTGADASVALRRAYRRQLTAI
+ALADLASREPTLVMPAVGRWLADLAGAALEAALAVSRAELRAREGAAVDCVELAVIGMGK
+CGARELNYVSDVDVVFVHDVLEPGAPDAPSAQEAARLAAELAAGISRVLSGPAPEPGLWE
+VDANLRPEGRDGALSRTLDSHVEYYRRWAHGWEFQALLKARPVAGSPALGERYVAAVWPR
+VWESSAREGFVENVRAMRTRVLDTIARDERDREIKLGAGGLRDVEFTAQLVQLVHGRADE
+SVRVRGTLDALRVLHAASYISSRDMRAFDAAYRWLRLLEHRIQLVHLRRTHLMPVKEGPR
+RVVARSMRGAGDVHPVAGDDLQDRFSRVRREVRALHETVFYRPLLSTTAALSDEDVRLSA
+DAVQARLSALGYRDPRRALAHIEALTRGVSRRAAVQRQLLPAMLGWFADGADPDAGLLAF
+RRLSESLGSSPWFLRMLRDSTDAARRLCLVLAGSRRVGDLLEHAPESVAWIGETRELAPR
+GLSALTSEVTARLDRRSPEESAAQVIRHVRQIRQREILRTALADITGVVGLEEVGHALAD
+VDQAAVQGALRVAGQAVLDGADPLTEVVVVAMGRQGGREIAYGSDLDAMFVHRPLAGADE
+TAAAAQAEAVARQLMALLQQPAAPPLPSEQPLDVDADLRPEGRQGPLVRTLDSYREYYAR
+WAEVWERQALLRARVVAGPAGLAEEFTAWADGVRYGDELSAGDAREIRRIKARVEAERLP
+RGADPARHVKLGRGGLSDVEWLVQSLQLRHAHDEPELRVTGTLPALRALARLDLLPPSEA
+ALLEEAWLLATRVRSALVLWTGKGSDVLPTNARDLGALARLAGDACGGGVAFEERYLRVT
+RQARQVFEQRFYGL
+>MHAAABBN_01056
+MSALPDAATADAPDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRAL
+LLWVRLAEREPRVHHALRDPGTTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAATA
+PALAQPDPTAGEPWGDASAALRRLLLDSVGADPDADRPLAAVTGKDAAVALRRAYRRQLA
+AIALRDLDSAEPTAAMPSVGRWLADLAGATVDAALAVSRAVLTEREGPVVDRVDLAVIGM
+GKCGAGELNYVSDVDVVFAHAVREAADGADPDAQVPDGPRAAALAAELAAGIGRVIQGAA
+PEPGLWEVDANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGERY
+IAEIWPRVWESSARDGFVESVRAMRARVLDTLAPAEREREIKLGPGGLRDVEFTAQLLQL
+VHGRADESLRVRGTLDAVRALHAASYVTTRDARAFDEHYRWLRTLEHRIQLVHLRRTHLM
+PVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALSA
+EDVRLSAEAVRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGADP
+DGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLSGSRFVGDLLEHSPEAVAWVGD
+DRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVALADISGLLDLEA
+VTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVHR
+PRPGVDEGRAREQAEEVVRTLMALLQKPVAPPLPGERRLEVDADLRPEGRQGPLVRTLDS
+YREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAQDLSAADAREIRRIKAR
+VEAERLPRGADPARHVKLGRGGLSDVEWLVQSMQLKHAGQIEDLRVTGTLPALRAIARHD
+LLPESEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTTGGELEE
+RYLRVTRLARQVFETRFYGL
+>LFPAFLNI_01291
+MSALPDAATADAPDRRTLAHAGVADAGRVQTLLTSPEFEGVDVRPLVELLGHAADPDRAL
+LLWVRLAEREPRVHHALRDPGTTARLLRLLGASEALGEFLIRRPEHLDLVLDPDAAAATA
+PALAQPDPTAGEPWGDASAALRRLLLDSVGADPDADRPLAAVTGKDAAVALRRAYRRQLA
+AIALRDLDSAEPTAAMPSVGRWLADLAGAAVDAALAVSRAVLTEREGPVVDRVDLAVIGM
+GKCGAGELNYVSDVDVVFAHAVREAADGADPDAQVPDGPRAAALAAELAAGIGRVIQGAA
+PEPGLWEVDANLRPEGKDGALSRTVESHAEYYRRWAHGWEFQALLKARPIAGSPQLGERY
+IAEIWPRVWESSARDGFVESVRAMRARVLDTLAPAEREREIKLGPGGLRDVEFTAQLLQL
+VHGRADESLRVRGTLDAVRALHAASYVTTRDARAFDEHYRWLRTLEHRIQLVHLRRTHLM
+PVKEEARRVVARSMRGAADRGPATGEDLQAEFTRVRRAVRGLHETVFYRPLLSTTAALSA
+EDVRLSAEAVRDRLAALGYRDPQGALRHIEALTQGVSRRAAVQRQLLPAMLGWFARGADP
+DGGLLAFRRLSESLGGTAWYLRMLRDSSDAARRLCLVLSGSRFVGDLLEHSPEAVAWVGD
+DRELDPRGAIQLWRQVDARLDRRVAAQEAPAAVRHVRQVRRSETLRVALADISGLLDLEA
+VTGALSDIDQITVVGALRVASRAVVGDADPLTDVLVVAMGRQGGREITYGSDLDALFVHR
+PRPGVDEGRAREQAEEVVRTLMSLLHRPATPPLPGERPLEVDADLRPEGRQGPLVRTLDS
+YREYYGRWAEVWERQALLRARPLAGDDDLATDFRRWADGVRYAGDLTTADAREIRRIKAR
+VEAERLPRGADPSRHVKLGRGGLSDVEWLVQSLQLRHAGEVEDLRVTGTLPALRAIARHG
+LLPEAEVAVLEEAWLLATRIRAALLLWTGKVSDVLPTNMRDLEAVARLSGVGTAGGELEE
+RYLRVTRLARQVFETRFYGL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001051.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001051.fa
new file mode 100644
index 0000000000000000000000000000000000000000..31cf19c5d1d9b0a1d089cbe0f79135ae7ac0c799
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001051.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01564
+MDILHSILVAVHIVSAAAIVGGWFAHFRNPTVTTSQWWGSVGMIVSGVVLFGLAMSGEPN
+HMKLGVKFLIGVIVFVAALIGRRKSNRGEVVPTGLAHAVGGLGLVNILVAVLWQ
+>MOLHKGIG_01327
+MDILHSILVAVHIVSAAAIVGGWFAHFRNPTVTTSQWWGSVGMIVSGVVLFGLAMSGEPN
+HMKLGVKFLIGVIVFVAALIGRRKSNRGEVVPTGLAHAVGGLGLVNILVAVLWQ
+>NAFOICDF_01460
+MEILHNVVVAIHIVSAAAIVGGWFAHFKNPTVTVSQWWGALGMILSGVVLFGWAMTGEPN
+HMKLGIKFLIGVIVFIAALLGRRKANRGEVVPKGLAHAVGGMGLVNILVAVLWS
+>MHAAABBN_01048
+MDILHSILVAVHIVSAAAIVGGWFAHFRNPTVTTSQWWGSVGMIVSGVVLFGLAMSGEPN
+HMKLGVKFLIGVIVFVAALTGRRKSNRGEVVPTGLAHAVGGLGLVNILVAVLWQ
+>LFPAFLNI_01283
+MDILHSILVAVHIVSAAAIVGGWFAHFRNPTVTTSQWWGSVGMIVSGVVLFGLAMSGEPN
+HMKLGVKFLIGVIVFVAALIGRRKSNRGEVVPTGMAHAVGGLGLVNILVAVLWQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001055.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001055.fa
new file mode 100644
index 0000000000000000000000000000000000000000..02336ddcc05bbc9bfe0b72dcd562078352f617b2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001055.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01568
+MQDAAPIYTRHDAEAVPPGLALLVTLTGHMDAGRVSRQVRTALREHLEHRTVASFDVDSM
+FDYRARRPRMRFDRDRYRDLRLPTLEVQLVEDLIGHPFLLLAGPEPDFRWQAVVEAVLGL
+AEEWQVDSLTFLDAAPLPVPHTRRIGVTTHGTRAEAVEGLSTWSPEAEIVSGLLQMLELR
+ADEAGIPTAGYTVHVPHYVAEASFPQAAVAALEYAGAAMGLMLPSDDLRDASREIEAELE
+RQVSGSEEVQQMIAGLERNFDQNAEDQERSLLETEEGLPDGDELASAVEAYLAGRAGPDG
+SAPAQEDGPPRPSTDDER
+>MOLHKGIG_01323
+MQDAAPLYTRHEGAPVPPGLGMLVALTGHMDAGRVARQVRAALHEHLTHRTVVSFDVDSM
+FDYRARRPRLRFDRDRYRDLRLPALEVQLVEDLLGHPFLLLSGPEPDFRWQAVTEAVLGL
+AQEWEVDSLTFLDAAPLPVPHTRRLGVTTHGSRADAVEGLSTWSPQADIVAGLLQMLELR
+AEEADLPTAGYTVHVPHYVAEASFPQAAVAALEYAGAAMGLMLPSDDLRDASRDIEAELE
+RQVSGSGEIQQMIAGLERNYDQNAEDQERSLLETEQGLPDGDELASAVEAYLAARDAGGG
+SAPAQEDGPGRPSTGDGD
+>NAFOICDF_01464
+MQDPTQLYTRHDAAPGDAVPDGLGVLVTLTGHLDAGHVGRQVGAGLRERLAHRTVARFDV
+DQLHDYRARRPRIRFDRERYTDLRMPALDVELMEDLLGHPFLLVAGPEPDMQWGRFTAAL
+LGLLQEWEASSATFLDAAPLPVPHTRRIGVTTHGSRADALEGLSTWSPEADVVAGLVQVL
+ELRAEEAGLPTAGYTVHVPHYVAEAGYPQAAVAALEYAGASLDLMLPTDELRDAAREVDA
+ELERQVAGSPEVQTMITGLEKNYDQNSEGQERSLLESHGELPDGDELASAVEAYLAERDE
+SVQPRPTTPAQDDEGPAPSPDPQV
+>MHAAABBN_01044
+MQDAAPLYTRHEGAPVPPGLGMLVALTGHMDAGRVARQVRAALHEHLTHRTVVSFDVDSM
+FDYRARRPRLRFDRDRYRDLRLPALEVQLVEDLLGHPFLLLSGPEPDFRWQAVTEAVLGL
+AQEWEVDSLTFLDAAPLPVPHTRRLGVTTHGSRADAVEGLSTWSPEADIVAGLLQMLELR
+AEEADLPTAGYTVHVPHYVAEASFPQAAVAALEYAGAAMGLMLPSDDLRDASRDIEAELE
+RQVSGSGEIQQMIAGLERNYDQNAEDQERSLLETEQGLPDGDELASAVEAYLAARDAGGG
+SAPAQEDGPGRPSTDDGD
+>LFPAFLNI_01279
+MQDAAPLYTRHEGAPVPPGLGMLVALTGHMDAGRVARQVRAALHEHLTHRTVVSFDVDSM
+FDYRARRPRLRFDRDRYRDLRLPALEVQLVEDLLGHPFLLLSGPEPDFRWQAVTEAVLGL
+AQEWEVDSLTFLDAAPLPVPHTRRLGVTTHGSRADAVEGLSTWSPQADIVAGLLQMLELR
+AEEADLPTAGYTVHVPHYVAEASFPQAAVAALEYAGAAMGLMLPSDDLRDASRDIEAELE
+RQVSGSGEIQQMIAGLERNYDQNAEDQERSLLETEQGLPDGDELASAVEAYLAARDAGGG
+SAPAQEDGPGRPSTGDGD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001059.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001059.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5100245adb45efea70a28209b2a868b16aaabb1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001059.fa
@@ -0,0 +1,66 @@
+>ACLBLIBL_01572
+MPANSEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGYGQSI
+EITLHPDGSVEVEDSGRGIPVDVEPRTGLSGVEVVFTKLHAGGKFGGGSYAASGGLHGVG
+ASVVNALSSRLDVQVLRGGKVHQMSFRRGEPGRFQDGSRPSPDAPFEPSTDASPLDVVGK
+AKRGQTGTRVRYWADEQIFIKDAAFSADDLHARARQTAYLIPGLRITVKDLRRRPGTPGA
+EGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGSFKERVPVLGEDGRTAMQDVQRT
+CEVDLALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAALLKAFRTQVESNARRLKAGSD
+KVEKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTSAVRRIVAQVVEKELTARLTATARAQ
+KQQVHVLLEKVVAEMKSRISARTHKENQRRKNALETSTMPAKLADCRSNDVASSELFIVE
+GDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILANAECAALIQVVGGGAGRSFDL
+DAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVFAAVPPLHRIEAVTKGVK
+EREVIYTYSEQELYATLARLEKEGRSYKEPIQRYKGLGEMDADQLAETTMDPRHRTLRRV
+NIAEVEAAERVFDLLMGSSVAPRKDFIVSHADELDRERIDA
+>MOLHKGIG_01319
+MSGPRSRLDRPLSSTERPAPVPANTEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHC
+LWEIIDNSVDEALAGFGQSIEITLHPDGSVEVEDNGRGIPVDVEPRTGLSGVEVVFTKLH
+AGGKFGGGSYAASGGLHGVGASVVNALSSRLDVQVLRGGKVHQMSFRRGEPGRFQDGSRP
+SPDAPFEPSTDASPLDVVGKAKRGQTGTRVRYWADEQIFVKDATFSAEELQARARQTAYL
+IPGLRITVKDLRRRPGTPGADGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGTFK
+ERVPVLGEDGRTSMQDVQRTCEVDVALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAAL
+LKVFRAQVEANARRLKAGSDKVEKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTSAVRRI
+VSQVVEKQLTARLTSTARAQKQQVHTLLEKVVAEMKSRISARTHKENQRRKNALETSTMP
+AKLADCRSNDVASSELFIVEGDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILAN
+AECAALIQVVGGGAGRSFDLDAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAG
+RVYAAVPPLHRIEAVTRGVKEREVIYTYSEQELHATLARLEREGRSYREPIQRYKGLGEM
+DADQLAETTMDPRHRMLRRVNIAEVEAAERVFDLLMGSAVAPRKDFIVSHADELDRARID
+A
+>NAFOICDF_01468
+MPANTEYSARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGFGQSI
+DVTLHPDGSVEVADNGRGIPVDVEPRTGLTGVEVVFTKLHAGGKFGGGSYAASGGLHGVG
+ASVVNALSSRLDVQVVRGGKVHQLSFRRGEPGRFQDGSRPTPDAPFEPAADAAPLDVVGK
+AKRGQTGTRVRYWADEQIFTPDATFSMEDLQARARQTAYLIPGLRIAVTDLRRLTGTAGE
+AGPVQEVYQYDGGIAEFVDHLTPAKPVTDVWRIQGSGTFTERVPVLGEDGRTQMQDVQRT
+CEVDVALRWDVGYETVFRSFVNIIATPKGGTHQSGFESALLKVFRAQVEAGARRLKAGSD
+RPDKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTPAVRRIVARVVEKELTALLTSTARGQ
+KQQVGALLEKVVAEMKSRISARTHKENQRRKNALETSTMPAKLADCRSNDVAASELFIVE
+GDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILSNAECAALIQVVGGGAGRGFDL
+DAARYGKVILMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVYAAVPPLHRIEAVTRGKK
+EREVIYTYSEAELHEVLARLEAEGRTYREPIQRYKGLGEMDADQLAETTMDPRHRMLRRV
+TISEVEAAERVFELLMGSSVAPRKAFIVSNADELDRERIDA
+>MHAAABBN_01040
+MPANTEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGFGQSI
+EITLHPDGSVEVEDNGRGIPVDVEPRTGLSGVEVVFTKLHAGGKFGGGSYAASGGLHGVG
+ASVVNALSSRLDVQVLRGGKVHQMSFRRGEPGRFQDGSRPSPAAPFEPSTDASPLDVVGK
+AKRGQTGTRVRYWADEQIFVKDATFSAEELQARARQTAYLIPGLRITVKDLRRRPGTPGA
+DGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGTFKERVPVLGEDGRTSMQDVQRT
+CEVDVALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAALLKVFRAQVEANARRLKAGSD
+KVEKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTSAVRRIVSQVVEKQLTARLTSTARAQ
+KQQVHTLLEKVVAEMKSRISARTHKENQRRKNALETSTMPAKLADCRSNDVASSELFIVE
+GDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILANAECAALIQVVGGGAGRSFDL
+DAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVYAAVPPLHRIEAVTRGVK
+EREVIYTYSEQELHATLARLEREGRSYREPIQRYKGLGEMDADQLAETTMDPRHRMLRRV
+NIAEVEAAERVFDLLMGSAVAPRKDFIVSHADELDRERIDA
+>LFPAFLNI_01275
+MPANTEYNARHLSVLEGLEAVRKRPGMYIGSTDSRGLMHCLWEIIDNSVDEALAGFGQSI
+EITLHPDGSVEVEDNGRGIPVDVEPRTGLSGVEVVFTKLHAGGKFGGGSYAASGGLHGVG
+ASVVNALSSRLDVQVLRGGKVHQMSFRRGEPGRFQDGSRPSPDAPFEPSTDASPLDVVGK
+AKRGQTGTRVRYWADEQIFVKDATFSAEELQARARQTAYLIPGLRITVKDLRRRPGTPGA
+DGPVEEVFQYDGGISEFVEHLTPATPVTDVWRIQGSGTFKERVPVLGEDGRTSMQDVQRT
+CEVDVALRWDVGYDTVFRSFVNIIATPKGGTHQSGFEAALLKAFRAQVEANARRLKAGSD
+KVEKDDVLAGMTAVLTVRLAEPQFEGQTKEILGTSAVRRIVSQVVEKQLTARFTSTARAQ
+KQQVHTLLEKVVAEMKSRISARTHKENQRRKNALETSTMPAKLADCRSNDVASSELFIVE
+GDSALGTAKLARSSDFQALLPIRGKILNVQKASVSDILANAECAALIQVVGGGAGRSFDL
+DAARYGKVVLMTDADVDGAHIRTLLLTLFFRYMRPMVEAGRVYAAVPPLHRIEAVTRGVK
+EREVIYTYSEQELHATLARLEREGRSYREPIQRYKGLGEMDADQLAETTMDPRHRMLRRV
+NIAEVEAAERVFDLLMGSAVAPRKDFIVSHADELDRERIDA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001063.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001063.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4fc0dc89f5f3d8413400995fd1840d03e4dfbf12
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001063.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_01579
+MDPLDLARWQFGITTVYHFLMVPLTIGLGLVVAVMQTLWVRTGREQYLRMTKFWGKLFLI
+NFIMGVATGIVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGVWIFGWGRV
+PRRLHLAAIWCAVIGAHLSAYFILTANAFMQHPVGYEVVDGRPVLNDIGAVLANPIVLTH
+FPHTIAGSWAVAGGFLLGISWYHLWKRRRDGIDTVDEHGRVVVGTTDSKARDRLDHRVWI
+TSLRAGAAVAIVGFLGTAFTGHAQAQQMIEFQPTKMASAEAACHDGTAFSVLTLGDLGAG
+DRTTCTDVTTVIELPGLLSYLAYEDFTTPVPGLNSLLPDFEERYGTHLPDDPLYGERAGA
+PIDYQPLMEVTYWGFRLMITFGGLGALAGALTLWMTRRGTVPDSRGWTATAVASIGAPFA
+ANVAGWVFTEMGRQPFVVYPNPAMGVDEVYMFTAAAVSPGVSAQEVLASLIVLVGIYAVL
+LVVEVVLMVRYVRGGVPAGMPELTADEHRDPDEDRHDRDDVLAFAY
+>MOLHKGIG_01313
+MDPLDLARWQFGITTVYHFLMVPLTIGLGLVVAVMQTLWVRTGREQYLRMTKFWGKLFLI
+NFIMGVATGIVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGVWIFGWGRV
+PRRLHLAAIWCAVIGAHLSAYFIMTANAFMQHPVGYEVVDGRPVLNDIGAVLANPIVLTH
+FPHTIAGSWAVAGGFLLGISWYHLWKRRRDGIDTVDEHGRVVVGTTGSKARDRLDHRVWI
+TSLRAGAAVAIVGFLGTAFTGHAQAQQMIEFQPTKMASAEAACHDGTAFSVLTLGDLGAG
+DRTTCTDVTTVIELPGLLSYLAYEDFTTPVPGLNSLLPDFEERYGTHLPDDPLYGERAGA
+PIDYQPLMEVTYWGFRLMITFGGLGALAGALTLWMTRRGTVPDSRGWTATAVASIGAPFA
+ANVAGWVFTEMGRQPFVVYPNPAMGVDEVYMFTAAAVSPGVSAQEVLASLIVLVGIYAVL
+LVVEVVLMVRYVRGGVPAGMPELTADEHRDPDEDRHDRDDVLAFAY
+>NAFOICDF_01475
+MDPLELARWQFGITTVYHFLMVPLTIGLGLVVAVLQTLWVRTGREHYLRMTKFWGKLFLI
+NFIMGVATGLVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGMWIFGWDRL
+PRRLHLAAIWCAVIGAHLSAYFIMAANAFMQHPVGYEVVDGRPVLNDIVAVLTNPIVLTH
+FPHTIAGSWAVAGGFLLGISWYHLWKRRRDGIDTVDAEGRVVVGTTGSKARDALDHRVWI
+TSLRAGAAVVIVGFLGTAFTGHAQAQQMIHYQPTKMASAEAACHDGTAFSVLTLGDVNTP
+GATTCDDVTGVIEIPGLLSFLAYSDFTTPVPGITTLLPQFEARYGTQLPDDPMYGERAGQ
+EISYLPLMEVTYWGFRLMITFGGLAALAGALTLWMTRKGTVPDSKPWMITAVASIGASFA
+ANVAGWVFTEMGRQPFVVYPNPAMGVDEVYMFTAAAVSPGVSGEEVLTSLIVFVVLYAVL
+LVVEVALLARYVRGGVPAGMPELTADEHRDPDDDRHDRDDVLAFAY
+>MHAAABBN_01036
+MDPLELARWQFGITTVYHFLMVPLTIGLGLVVAVLQTLWVATGKDHYLRMTKFWGKLFLI
+NFIMGVATGLVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGIWIFGWDRI
+PRRLHLAALWCAVLGINLSAYFIMVANGFMQHPVGYEVVDGRPVLNDLGAVLTNPIVLTH
+YPHTIFGSWAVAGGFLVGIAWYHLWKRRRDGIDVVDEAGRVVVGDAGTAARDRTDHRVWL
+TSLRAGAAVALIGFVGTAFSGHAQAQQMIHFQPTKMAAAEAACHDGTAFSVLTLGDVRSG
+GATTCEDVQGVIEVPGLLSYLAYEDFTTPVRGINTLLPEFEQKYGTHLPDSELYGDRAGS
+EISYLPLMEVTYWGFRLMILFGGLGALAALGALWFSRRGTVPASRGWMRLAVASIGAPFA
+ANMTGWVFTEMGRQPFVVYPNPAMGVDQVYMFTAAAVSPGVTGEEVLVSLIVLVGIYAVL
+LGVEVFLLTRFVRGGVPAAMPELTAAEHSDEQKRDRDDVLAFAY
+>LFPAFLNI_01271
+MDPLELARWQFGITTVYHFLMVPLTIGLGLVVAVLQTLWVATGKDHYLRMTKFWGKLFLI
+NFIMGVATGLVQEFQFGMAWSEYSRFVGDVFGAPLALEALIAFFLESVFLGIWIFGWDRI
+PRRLHLAALWCAVLGINLSAYFIMVANGFMQHPVGYEVVDGRPVLNDLGAVLTNPIVLTH
+YPHTIFGSWAVAGGFLVGIAWYHLWKRRRDGIDVVDEAGRVVVGDAGTAARDRTDHRVWL
+TSLRAGAAVALIGFVGTAFSGHAQAQQMIHFQPTKMAAAEAACHDGTAFSVLTLGDVRSG
+GATTCEDVQGVIEVPGLLSYLAYEDFTTPVRGINTLLPEFEQKYGTHLPDSELYGDRAGS
+EISYLPLMEVTYWGFRLMILFGGLGALAALGALWFSRRGTVPASRGWMRLAVASIGAPFA
+ANMTGWVFTEMGRQPFVVYPNPAMGVDQVYMFTAAAVSPGVTGEEVLVSLIVLVGIYAVL
+LGVEVFLLTRFVRGGVPAAMPELTAAEHSDEQKRDRDDVLAFAY
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001065.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001065.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51848751bf10a41e956cfc1cc88e3fcd68d4338e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001065.fa
@@ -0,0 +1,107 @@
+>ACLBLIBL_01581
+MTDDGAPRGPGREHDDGPRRRRGPDLSPAARRAVAAMLGLAALRAAGWILLAESLARLLT
+RMADTLDPEGTAQLFEMLFLPPAPVGPVGAASSFAGALALGAAGVGLRALADAGQRVWGR
+RAALGVQVGVRRDLVAHRLASADGSRPRSGADAVLVTHGLQGLDDYYTEVLPALASAAVV
+PPVLGAWILTRDPLSALVVLLTVPLVPFFMVLIGRHTQERIDAAQDGLDRLSGHLVELAR
+GLPVLVGLRRAGVQRRALERASQRYHAATLGTLRTAFVSGMALELIASLSVAVMAVFIGL
+RLVYGQMDLGAGLVVLVLAAEVYLPLRDVGSAYHASEDGREAEGRARAAARAPVPEAARD
+ALADPTAAPARAADPAAAPRRAVVLEDVGVAFGDRRVLQGVDLRAAPGTLTVLGSASGTG
+KSTLLHLLAGLLRTTDARVQGSVSGVDPERTVWVGQHPRLLEPTVGEELDAAAGRALADS
+ERAAVLAAVALDGAAHRRPVELSPGELRRVALARALARLSTAGADRRPWLVLLDEPTAHL
+DDAAAAAVRAGVVALARAGVPGLALPPCIVVAASHDPALQRAADALVDAQGTPLAPGAAD
+GAADPEAAAPAGPEPASPAAVASPVEAEPVPASATSTAPSPAAARRARTRAALRILPWRS
+GRLWAGVAWATGTHLSAALLAGLSGWLIVTAAGRPPVLYLLSVIVLVRAFGLSRAVFRYL
+DRLATHDAVLGWASRLRLRLWDALGRRPALWGRLSRADGALSVLVADVDALRDAAPRVMV
+PVPAAVLAWLVSAGAVALLAPELAAAALVPGALGLVAIPVVVAALDRRQTQAAVRHRAGL
+LDRVAAVLAAAPDLHGLGRARAAADRLAEADAALQAPQRRAAWAAGAGRALAVLVSGGTA
+LAVALTATQTGTAAAVAAFAVLLVLSWAEPYGALAQSAQELGTLASQARAAADLLGEDEP
+GTAVPDAADPGRASATPDPTSAPMSADPEPAAPVRVTGLALRGAAVRFEGADAPLWSGVD
+LRVEPGQTAVVTGPSGAGKSTLLAVLLGFQPLAEGAYLLRTEADGRRVEAPADAAALARV
+AWTPQDALLFDSSLRGNLALARDPEDAPDDAELTAVLERVGLGPWLAAAPEGLDTPVGAG
+GRVLSGGQRQRLAVARALVARADVVLLDEPTAHVGQDEALALMADLRAALAGRIAVVVTH
+DERLAAEADVRLRLGVSPPRPSRGRPRPAAR
+>MOLHKGIG_01311
+MTDDGAPRGPGRGHDDGPRRRRGPDLSPAARRAVAAMLGLAALRAAGWILLAESLARLLT
+RMAGTLDPEGTAQLFEMLFLPPAPVGPVGAASSFAGALALGAAGVGLRALADAGQRVWGR
+RAALGVQVGVRRDLVAHRLASADGSRPRSGADAVLVTHGLQGLDDYYTEVLPALASAAVV
+PPVLGAWILTRDPLSALVVLLTVPLVPFFMVLIGRHTQERIDAAQDGLDRLSGHLVELAR
+GLPVLVGLRRAGVQRRALERASQRYHAATLGTLRTAFVSGMALELIASLSVAVMAVFIGL
+RLVYGQMDLGAGLVVLVLAAEVYLPLRDVGSAYHASEDGREAEGRARAAARAPVPEAARD
+ALADPTAAPARAAGPAAAPPGAVHLEDVGVAFGDRRVLQGVDLRAAPGTLTVLGSASGTG
+KSTLLHLLAGLLRTTDARVQGSVSGVDPDRTVWVGQHPRLLEPTVGEELDAAAGRALADS
+ERAAVLAAVALDGAAHRRPVELSPGELRRVALARALARLSTAGADRRPWLVLLDEPTAHL
+DDAAAAAVRAGVVALARAGVPGLALPPCIVVAASHDPALQRAADALVDAQGTPLAPGAAD
+GPADPEAAAPAGPEPASPAAVASPVEAEPVPASATSTAPSPAAARRARTRAALRILPWRS
+GRLWAGVAWATGTHLSAALLAGLSGWLIVTAAGRPPVLYLLSVIVLVRAFGLSRAVFRYL
+DRLATHDAVLGWASRLRLRLWDALGRRPALWGRLSRADGALSVLVADVDALRDAAPRVMV
+PVPAAVLAWLVSAGAVALLAPELAAAALVPGALGLVAIPVVVAALDRRQTQAAVRHRAGL
+LDRVAAVLAAAPDLHGLGRARAAADRLAEADAALQAPQRRAAWAAGAGRALAVLVSGGTA
+LAVALTATQTGTAAAVAAFAVLLVLSWAEPYGALAQSAQELGTLASQARAAADLMGEDEP
+GTAVPDAADPGRASATPDPTSAPMSADPEPAAPVRVTGLALRGAAVRFEGADAPLWSGVD
+LCVEPGQTAVVTGPSGAGKSTLLAVLLGFQPLAEGAYLLRTEADGRRVEAPADAAALARV
+AWTPQDALLFDSSLRGNLALARDPEDAPDDAELTAVLGRVGLGPWLAAAPEGLDTPVGAG
+GRVLSGGQRQRLAVARALVARADVVLLDEPTAHVGQDEALALMADLRAALAGRIAVVVTH
+DERLAAEADVRLRLGVSPPRPSRGRPRPAAR
+>NAFOICDF_01477
+MTDRPPRRRGRVRAGRGPGPGLDRRARRAVGVMALLAGVRALGWILLAESLARLLTSLAM
+TLDPEASAQLFQLLFMPPAPVGPVGPVADVAGVVVLGAAGVVLRALADQGQHVAGRRAAL
+GAQVGIRRELVAHRLAATDGTRPRSGADAVLVTHGLAGLDDYYTEVLPALASAAVVPPML
+GVWILTRDGVSAAVVLLTVPLIPFFMVLIGRHTQERIAAAQDGLDRISGQLLELARGLPV
+LVGLRRAGVQRRALEKASERYHAATLGTLRTAFVSGLALELIASLSVAIMAVFIGVRLVY
+GQMDLYSGLVVLVLAAEVYLPLREVGSAYHSSEDGRAAAERAAAAVAEPVPTPALASLAW
+PGPETGQDHGTDGGMDDGMDDRTPAAGTVLLRDVSVSRGPRPVVRGADLTLRPGGLTVLG
+SASGAGKSTLLHLLAGVLRTPDVAVSGTVAGVDSDRTLWVGQHPRFLEATVDAELDAAAG
+GALAAPVRREVLRAAALADFGARAPHELSPGEQRRVALARAMSRLAADRTAVETRPWLVL
+LDEPTAHLDDASAAVVRATVGALARGAVPGLPTPPAAVLAASHDPVLQRAADALVDVEGR
+PLAPGADAAPYADPDAAGPPLAAGAPDDAGPGDAPDAPRGEGSEGRPSLRAVLAVLPWGA
+PRLWAGVGWATLTHLAAALLAGLSGWLIVTAAGRPPILYLLSVIVLVRGFGLFRAVFRYA
+DRLATHDAVLRWASELRLRLWDAMGRRPALWSRLSRADGALSVLLSDVDALRDAAPRVLV
+PVPAAVLAWAVTALLIGGLAPELAVTALVPGAVGLLVIPVVVAALDRRDTLLTARRRAAL
+LDRVSAVLGAAPDLHGLGRTREAAAALTAWDEDLQRPQRRAAWVAGLGRALAVLASGGAA
+LAAALTATQTGTSTPVAAFVVFLALSWAEPLGALAQAAQQTGTLVDQARQAAGLLGVEDE
+AASGATSAAPDEAAASAAGSSAPAGRITGVRLEDAAYAYPGSTRVLWSGLDVALESGQTA
+AVTGPSGAGKSTLLAVLLGFLTPTAGRHLLTVERDGVSREAPADPAALARVAWTPQDALV
+FDSTVRGNLALARDADDAPTDAELADTLRLVGLGRWLDAAPDGLDTPVGPGGDRLSGGER
+QRLAVARALVARADVVLLDEPTAHVGQDEALALMADLRRALAGRIAVVATHDPRVAAAAD
+VRVRLGGDAAGHP
+>MHAAABBN_01034
+MTPAALRALPALLALAVLRALGWILLAESLARLITGLAMTLDPEDSARLLDLLFHPPAPV
+GPVPAAQTLSGPVLLGAAGVALRALAEAGQRVVGRRAALGAQQQVRAAVVAQRLAAADGG
+RPRSGADAVVVTHGLKSLDDHYTEALPALAATAVVPAALGVWILTHDLVSAVVAAITLPL
+VPLFMILVGRHTQERIDAAQDGLDRLAGHLLELARGLPVLVGLHRAGVQRRALQEVSQRH
+HAATMVTLRTAFLSGLALELIASLSVAVMAVFIGLRLVNGQMALLDGLVVLILAAELYLP
+LREVGAAFHASEDGREAESRARAAADAPVPAPVLDTLGPASGPDRDGGVLVQDLSVRMAG
+RQVLEGLDLTAPPGHLTALAGPSGTGKSTVLRLLAGLLRQDAAEATGRVAGVDTERTLWI
+GQHPVLTERTVAGELDLAAGGALPGPVRSAVLAAVALEGLQERDPADLSPGECRRVAVAR
+LLARLHAADGTGPWLVLLDEPTAHLDGAVAAVVVETLAALPSGAVPGLSTPQCTVLAASH
+DPTLLTAADAIVRLAPGAGPTAGSPATAMPVAAAQGRARPEPVTPRQVSLRAGLRLLPWR
+QPKLWAGIGWAAGTHVSAALLAALSGWLIVTASTRPPVLYLLAVIVLVRGFGLSRAVFRY
+LDRLTTHDAVFGWATELRLRLWDALGRQPRLWGRVGRTDGALSLLVSDVDAFRDAVPRVL
+VPAPAALLAWLATAALTWALAPELAVVALVPGAVALVVIPALVAVLDRRQTAAQVRGQGA
+LVDRVAAVLNAAGDLRGLGLTEPALRGLAVLDDRLQRPRRRAAWAAGGGRALAVAASGGI
+AVAAAAAAAHTGTSAPVAALVVLLALSWAEPYGALAAAAQHWGTLADRARATGELLGPEE
+GGAAAAPPEPAEAAEPEARVCRLRLVEAAFAHPGAPPLWTDLELDLAPGDVAVVTGPSGS
+GKSTLLAVLLGFLPLTAGRYTLETVPPTPQPDPVRPDATALARVAWTPQDALIFDSTARG
+NLALARGVADAPSDAELTAALELVGLGPWLAAAPQGLDTRVGPGGQRLSGGQRQRLAVAR
+ALVARADVVLLDEPTAHVDADEARALITDLRRALADRIVVIVTHDGRLLEDGDVPVRVGC
+>LFPAFLNI_01269
+MSPSRPAAPAVERSASAAGPHPGRTRRARPPMTPAARRALPALLALAVLRALGWILLAES
+LARLITGLAMTLDPEDSARLLELLFHPPAPVGPVPAAQTLSGPVLLGAAGVALRALAEAG
+QRVVGRRAALGAQQQVRAAVVAQRLAAADGGRPRSGADAVLVTHGLKSLDDHYTEALPAL
+AATAVVPAALGVWILTHDLVSAVVAAITLPLVPLFMILVGRHTQERIDAAQDGLDRLAGH
+LLELARGLPVLVGLHRAGVQRRALQEVSQRHHAATMVTLRTAFLSGLALELIASLSVAVM
+AVFIGLRLVNGQMTLLDGLVVLILAAEVYLPLREVGAAYHASEDGREAESRARAAADAPV
+PAPVLETLAPASGPDRDGGVVIRDLSVRLAGRQVLGGLDLSALPGRLTALAGPSGTGKST
+VLRLLAGLLRQDAAEATGRVAGVDTERTLWIGQHPVLTERTVAGELDLAAGGALPGPVRS
+AVLAAVALEGLQERDPADLSPGECRRVAVARLLARLHAADGTGPWLVLLDEPTAHLDGAV
+AAVVVETLAALPSGAVPGLSTPQCTVLAASHDPTLLTAADAIVRLAPGAGPTAGSPATAM
+PVAAAQGRARPEPVTPRQVSLRAGLRLLPWRQPKLWAGIGWAAGTHVSAALLAALSGWLI
+VTASTRPPVLYLLAVIVLVRGFGLSRAVFRYLDRLTTHDAVFGWATELRLRLWDALGRQP
+RLWGRVGRTDGALSLLVSDVDAFRDAVPRVLVPAPAALLAWLATAALTWALAPELAVVAL
+VPGAVALVVIPALVAVLDRRQTAAQVRGQGALVDRVAAVLNAAGDLRGLGLTEPALRGLA
+VLDDRLQRPRRRAAWAAGGGRALAVAASGGIAVAAAAAAAHTGTSAPVAALVVLLALSWA
+EPYGALAAAAQHWGTLADRARATGELLGPEEGGAAAAPPEPAEAAEPEARVCRLRLVEAA
+FAHPGAPPLWTDLELDLAPGDVAVVTGPSGSGKSTLLAVLLGFLPLTAGRYTLETVPPTP
+QPDPVRPDATALARVAWTPQDALIFDSTARGNLALARGVADAPSDAELTAALELVGLGPW
+LAAAPQGLDTRVGPGGQGLSGGQRQRLAVARALVARADVVLLDEPTAHVDADEARALITD
+LRRALADRIVVIVTHDGRLLEDGDVPVRVGC
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001068.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001068.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51578fdbd77e5173a1bcc2ce3b4183fc721b3cda
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001068.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01584
+MEPMSPFRRSHESGRPEHRPGAPASGEHRHEARTLEGAGGLGASLARAGFYPELVAHAIA
+VELGERTPDAHLVHVDTHFDYEEIHRHITVLVLAQDALLAVHLDDHAADAAGQAVLAQVS
+TEMVPVRALGSVVLTTGHADPARFSPADPVAEMTLALIWAGGQRLDLQPAGCADPQCDLD
+HGYTGTATREDLVIRVAADADGQGAVDGALAFARALRRAHLAATA
+>MOLHKGIG_01308
+MGDMSPFRRSHEPGRPDHRSGTPEAEGRQREARTLDGSGGLDASLVRAGFYPDLVAHAIA
+VELEGRTPDAHLVHVDTHFDYEEIHRHITALVLAGDTLLAVHLDDHAADPAGQAVLAQVS
+TEMVPVRALGSVVLTTGHADPARFRPSDPVAEMTLGLMWAGGQRLDLQPAGCADPQCDLD
+HGYTGTATREDLVIRVAADADGQGAVDGALAFARALRRAHLAATT
+>NAFOICDF_01480
+MEGMTPLRWNNHDDSASDGRRPAGEVRRTRQTVDATGTLEQALARAGYYPELVSHAVALE
+LEGRTVHAHLVHVDTHFDYEEIHRHITVLVVADDVMLAVHLDDHAADPAGHSVLAQVATE
+MVPLRAIESVLITTGHATPERYRPTDPVAEVTLGVQWAGGQRLDLQPAGCADPQCDADHG
+YTGTSVREDLVIRVAADAEGQGAVDAALAFARTLRRVHLAAVA
+>MHAAABBN_01031
+MGDMSPFRRSHEPGRPDHRPDAPEAEGRQREARTLDGSGGLDASLVRAGFYPDLVAHAIA
+VELEGRTPDAHLVHVDTHFDYEEIHRHITALVLAGDTLLAVHLDDHAADPAGQAVLAQVS
+TEMVPVRALGSVVLTTGHADPARFRPSDPVAEMTLGLMWAGGQRLDLQPAGCADPQCDLD
+HGYTGTATREDLVIRVAADADGQGAVDGALAFARALRRAHLAATT
+>LFPAFLNI_01266
+MGDMSPFRRSHEPGRPDHRPDAPEAEGRQREARTLDGSGGLDASLVRAGFYPDLVAHAIA
+VELEGRTPDAHLVHVDTHFDYEEIHRHITALVLAGDTLLAVHLDDHAADPAGQAVLAQVS
+TEMVPVRALGSVVLTTGHADPARFRPSDPVAEMTLGLMWAGGQRLDLQPAGCADPQCDLD
+HGYTGTATREDLVIRVAADADGQGAVDGALAFARALRRAHLAATT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001071.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001071.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f07a3dc92f52b29f55d6dd62d5f2f479d0ef4b0b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001071.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01588
+MREPQQHPVSDAPVDRPQDPAQGSDRVLFEERLTPSAGVWVVALMLASLTILVFAPIDLW
+FGVAAAVVFFGLEALLLLTTTPRIVVRERTLQVGRASIERRHVGEVTGHRGEDARRQRGP
+LLHGLAYVVVRGWISPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMVQEDPADEDR
+>MOLHKGIG_01304
+MRDPQQHPVADASRRAPGGAAAGPDPVLFEERLTPSPGVWAVALMLAALTILVFAPIDLG
+VGIAAAVAFFAVEVLILVATTPRIVVRERTLQVGRASIERHHVGQVTGYRGEDARAQRGP
+LLHGLAFVNVRGWIAPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMARQEGTAEGR
+>NAFOICDF_01484
+MQDASATPDHHAPRTVAASADPVQYEERLSPSVGVWLVALLLAGLCIFVLAPVALWAGFL
+AAAVFFVVEAVVLLASTPRIVVRERTLQVGRAQIERRHLGAVTGHRGEAARAQRGPLLHG
+LAYVCVRGWISPVVRIQIEDERDATPYWLASTRHPEDLVAALGGRMAGEG
+>MHAAABBN_01027
+MRDPQQHPVADASRRAPGGAAAGPDPVLFEERLTPSPGVWAVALMLAALTILVFAPIDLG
+VGIAAAVAFFAVEVLILVATTPRIVVRERTLQVGRASIERHHVGQVTGYRGEDARAQRGP
+LLHGLAFVNVRGWIAPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMARQEGTAEGR
+>LFPAFLNI_01262
+MRDPQQHPVADASRRAPGGAAAGPDPVLFEERLTPSPGVWAVALMLAALTILVFAPIDLG
+VGIAAAVAFFAVEVLILVATTPRIVVRERTLQVGRASIERHHVGQVTGYRGEDARAQRGP
+LLHGLAFVNVRGWIAPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMARQEGTAEGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001080.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001080.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b7b1970b6ef5f8db1cc2f4a7fd533e8913dc9ab3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001080.fa
@@ -0,0 +1,80 @@
+>ACLBLIBL_01597
+MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAEKLPYSLKVLLENLLRTEDGANVTAEQIK
+ALASWNPDAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE
+LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN
+IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM
+LIPRVVGFKLTGSIPAGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG
+NMSPEFGSTAAMFPIDEVTLDYLRLTGRTAEQVDLVEAYTKEQGMWHDPSSEVKYSEYLE
+LDLSTVVPSISGPKRPQDRIELSDSKDQFRKDLHNYATQDEAGEGRPSKLVDVSMEDGRQ
+FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY
+YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR
+INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDSEGNDVFLKDIWPDPTEVQKIID
+ESIDTEMFTSQYGTIFDGDERWQSLETPSGSTFEWDEQSTYVRKPPYFEGMTMQPDAVSD
+ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGKYLLENGVERKDFNSYGSRRGNHEVMIR
+GTFANIRIKNQLLDGVEGGFTRDFTQDGAPQAYVYDAAQNYAAAGTPLVVLGGKEYGSGS
+SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS
+GITALNEGTTPKTVKVTATGGDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA
+>MOLHKGIG_01295
+MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAQKLPYSLKVLLENLLRTEDGANVTADQIK
+ALAAWDPNAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE
+LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN
+IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM
+LIPRVVGFKLTGSIPSGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG
+NMSPEFGSTAAIFPIDEVTLDYLRLTGRSEEQVALVEAYTKEQGMWHDPSSEVAYSEYLE
+LDLSTVVPSISGPKRPQDRIELTDSKDQFRKDLHNYATQDEAGEGRPSKLVDVAMPDGRQ
+FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY
+YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR
+INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDTEGNDVFLKDIWPDPTEVQQIID
+ASIDTEMFTSQYATIFDGDERWQSLETPSGSTFEWDEKSTYVRKPPYFEGMTMQPDPVSD
+ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGRYLLENGVQRKDFNSYGSRRGNHEVMIR
+GTFANIRIKNQLLDGVEGGFTRDFTQEGAPQAYVYDAAQNYAEQGTPLVVLGGKEYGSGS
+SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS
+GITALNEGTTPKTVKVTATGEDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA
+>NAFOICDF_01493
+MTTVDSFGSKGVLDVNGSEYEIFRLNAVEGAQKLPYALKVLLENLLRTEDGANVTAEQIK
+ALASWDPTAEPDTEIQFTPARVIMQDFTGVPCIVDLATMREAIADLGGDPSRVNPLSPAE
+LVIDHSVQIDSFGNDAAVERNMDIEYQRNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN
+IENLARAVMVRDVDGVKRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM
+LIPRVVGFKLTGQIPAGATATDVVLTITEQLREHGVVGKFVEFYGEGVGAVPLANRATIG
+NMSPEFGSTAAMFPIDDVTLDYLRLTGRSEEQVALVEAYTKEQGLWHDPSAEVQYSEYLE
+LDLSTVVPSISGPKRPQDRIVLSDSKDQFRKDLHNYATQDEAGEGRPSKLVDVHMEDGRE
+FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLTAKPWVKTSVAPGSRVVTDY
+YEKSGLNASLDALGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR
+INPDVKMNYLASPPLVVAYALAGTMDCDFENEALGTDQDGNDVFLKDIWPDPAEVQRIID
+ESIDTEMFTSQYGTIFDGDERWQSLETPTGKTFEWDEASTYVRKPPYFEGMPAQPEPVQD
+IAGARVLLKLGDSVTTDHISPAGSFKSDTPAGQYLLANGVERKDFNSYGSRRGNHEVMIR
+GTFANIRIKNQLLDGVEGGFTRDFTQDGAPQAYVYDAAQNYAAAGTPLVVLGGKEYGTGS
+SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPAGESADSLGLTGTETFAIS
+GIAELNEGRTPKTVKVTATAEDGKVTEFDAVVRIDTPGEADYYRNGGILQYVLRQIAAKA
+>MHAAABBN_01018
+MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAQKLPYSLKVLLENLLRTEDGANVTADQIK
+ALAAWDPNAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE
+LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN
+IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM
+LIPRVVGFKLTGSIPSGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG
+NMSPEFGSTAAIFPIDEVTLDYLRLTGRSEEQVALVEAYTKEQGMWHDPSSEVAYSEYLE
+LDLSTVVPSISGPKRPQDRIELTDSKDQFRKDLHNYATQDEAGEGRPSKLVDVAMPDGRQ
+FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY
+YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR
+INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDTEGNDVFLKDIWPDPTEVQQIID
+ASIDTEMFTSQYATIFDGDERWQSLETPSGSTFEWDEKSTYVRKPPYFEGMTMQPDPVSD
+ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGRYLLENGVQRKDFNSYGSRRGNHEVMIR
+GTFANIRIKNQLLDGVEGGFTRDFTQEGAPQAYVYDAAQNYAEQGTPLVVLGGKEYGSGS
+SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS
+GITALNEGTTPKTVKVTATGEDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA
+>LFPAFLNI_01253
+MTTVDSFGSKGVLDVKGAEYEIFRLNKVEGAQKLPYSLKVLLENLLRTEDGANVTADQIK
+ALAAWDPNAQPDTEIQFTPARVIMQDFTGVPCVVDLATMREAIQDLGGDPERVNPLSPAE
+LVIDHSVQIDSFGNDAAIERNMEIEYERNGERYKFLRWGQTAFDDFKVVPPGMGIVHQVN
+IENLARTVMTREVDGVLRAYPDSCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM
+LIPRVVGFKLTGSIPSGATATDVVLTITEMLRQHGVVGKFVEFYGEGVGSVPLANRATIG
+NMSPEFGSTAAIFPIDEVTLDYLRLTGRSEEQVALVEAYTKEQGMWHDPSSEVAYSEYLE
+LDLSTVVPSISGPKRPQDRIELTDSKDQFRKDLHNYATQDEAGEGRPSKLVDVAMADGRQ
+FQLDHGAVSIASITSCTNTSNPSVMMAAGVLARNAVAKGLKSKPWVKTSVAPGSRVVTDY
+YEKSGLRESLNDLGFNVVGYGCTTCIGNSGPLESEISEAIQENDLSVTAVLSGNRNFEGR
+INPDVKMNYLASPPLVVAYALAGTMDFDFENEALGQDTEGNDVFLKDIWPDPTEVQQIID
+ASIDTEMFTSQYATIFDGDERWQSLETPSGSTFEWDEKSTYVRKPPYFEGMTMQPDPVSD
+ISGARVLLKLGDSVTTDHISPAGSFKSDTPAGRYLLENGVQRKDFNSYGSRRGNHEVMIR
+GTFANIRIKNQLLDGVEGGFTRDFTQEGAPQAYVYDAAQNYAEQGTPLVVLGGKEYGSGS
+SRDWAAKGTALLGVKAVITESFERIHRSNLIGMGVLPLQFPEGENADSLGLTGTETFDIS
+GITALNEGTTPKTVKVTATGEDGKVTEFDAVVRIDTPGEAEYYRNGGILQYVLRQIASKA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001082.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001082.fa
new file mode 100644
index 0000000000000000000000000000000000000000..10e4d3b7e8ccde22dbf4d648b4544e83cab99802
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001082.fa
@@ -0,0 +1,21 @@
+>ACLBLIBL_01599
+MSIVRLYRETTNEDGSRLFEYREAWADVEGGEFVVHHGRVGHPGTVGEQPLADEAEGEEL
+LAAFLAQGAEEGFAEADPAGFALLPVAFRLRGREASDIERRNVEHLRVEVTHQLAWRGLG
+EVEDVTEEPGALVLAVRTPHARKAAAEIPVAARRADGVQPNKVEVRSAVQED
+>MOLHKGIG_01286
+MSIVRLYRESVGDDGARLFEYREAWADAEAGEFVVHHGRVGQPGTVGEQPLADQAEGDQL
+LAAFVAQGAEEGFAEADPATFAVLPVAYRLRGREATAIERRTVERLRVEMTHQLAWRGLG
+EVEDVVEEVGALVLRVRTPHARKAAAEIPAAAKRADGVQPNKVDVRTAEQEG
+>NAFOICDF_01495
+MSISRLYRDRTEEDGRRSFEYREAWIDPSGELFTVHHGRVGHPGTVGDQPLTSEAEGAEL
+MDAFLAQGEADGFAPADEDAFDVLEVAYRLRGRAITEIERRHGRTLREEVTHQLAWRGLG
+EVTDVVDGDGELVLVVRTPHAPKAAAEVPAAAKRAHGIQPNKVEVRRVDAPRTPAGAAPD
+ADGEG
+>MHAAABBN_01005
+MSIVRLYRETVGDDGTRLFEYREAWADAEAGEFVVHHGRVGQPGTVGEQPLADQVEGDQL
+LAAFVAQGAEEGFAEADPATFAVLPVAYRLRGREATVIERRTVERLRVEVTHQLAWRGLG
+EVEDVVEEAGALVLRVRTPHARKAAAEIPAAAKRADGVQPNKVDVRTAEQEG
+>LFPAFLNI_01244
+MSIVRLYRETVGDDGTRLFEYREAWADAEAGEFVVHHGRVGQPGTVGEQPLADQVEGDQL
+LAAFVAQGAEEGFAEADPATFAVLPVAYRLRGREATVIERRTVERLRVEVTHQLAWRGLG
+EVEDVVEEAGALVLRVRTPHARKAAAEIPAAAKRADGVQPNKVDVRTAEQEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001089.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001089.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e90e76a90e4967dea10ffdffb4c9691796ea7a0c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001089.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01607
+MTVIGPRRLAPVTGPRGAVAPAPAPLPAAFRRALADLRTARPRPEVRLREIAAPAGQAPH
+AVALAAEVCGSPGADDVLATGRFVLLHDPSPAARWPGGFRAVTWIRASLEPDVALDQLAG
+AVAWTWLVEALERRHAEHTQAGGTATRSIAEGFGTLGTAPDATDIELRASWTPAPRDLGA
+HLEAWSDMIGAFAGLPPR
+>MOLHKGIG_01279
+MSVIGPRRLSAAPGAVEAPVPPGVFRRALADLRDARPRTEVRLREIPAPEGQAPFAVALA
+ADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLAGAVAW
+TWLVEALERHHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLGSHLEA
+WSDMICAFAGLPPEHAADVHTAGP
+>NAFOICDF_01502
+MTESGPRAPAPAAGGASGAFADALADLRAAHPRPEVRLRPIPDPPGLAPFAVTLAADVLD
+PHGAEADPLATGRFVLLHDPAGSPVWRGDFRVVTYIRASLEPDVATDHLAGAVAWDWLAE
+ALERRHAAHTEAGGTATRQLAEHFGTLALEPGWTDIELRASWTPGPRDLGAHLEAWSDMI
+CAFAGLPPLADDDVPAAVPLRP
+>MHAAABBN_00998
+MSVIGPRRLSAAPGAVEAPVPPGVFRRALADLRDARPRTEVRLREIPAPEGQAPFAVALA
+ADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLAGAVAW
+TWLVEALERRHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLGSHLEA
+WSDMICAFAGLPPEHAADVHTAGP
+>LFPAFLNI_01237
+MSVIGPRRLSAAPGAVEAPVPPGVFRRALADLRDARPRTEVRLREIPAPEGQAPFAVALA
+ADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLAGAVAW
+TWLVEALERRHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLGSHLEA
+WSDMICAFAGLPPEHAADVHTAGP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001091.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001091.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f77fdbf591cf2009f377ac5bb1242d78a0ff7f17
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001091.fa
@@ -0,0 +1,44 @@
+>ACLBLIBL_01610
+MRTGVKAASPLARWTPPVLSVLASSAFVLAGASSALAGVFARTVVTPVRRHTETTAVLAV
+VDTPTGPEVILKADEYTTVPGVYSLTFDGGAGCARIGRISSFDPRDGTVQRVVEEVYFGD
+LAAATRGRLTGFVYPTPADAGLDAEEVLVPVPGGHAPAWLVGPDPDDDGAARPAAGIWAI
+MVHGRGARRNEGIRTVPTAQRLGMTSLLISYRNDGDAPDAADSRYGLGTTEWEDVEAAIR
+YALDNGASDVVLFGWSMGGAVVLQAVDRSDLAPQVRGVVLTGPVVDWVDVLQHQARLNRI
+PEAVGVLGQWLLSNRAGRFITGLAAPVDLKSLDWVTRAEHVRVPTLIIHSEDDEYVPVGP
+SQDLAERNPGLVRFVRFHQARHTREQNVDPKRWDTTVRGWLRAVLNADRPGAAER
+>MOLHKGIG_01277
+MAARPRRPRPHPADLPPALAAAVTVAARRAGSRESRVRRAGRLVRRGVTGSVRGGVAVAS
+PVARWAPPVLSVAAAYAFVLAGASSALAGVFARTVVTPVRRHAESTPILAVVDTPAGQDV
+ILQADEYTTVPGQYSLTFDDGAGCARIGEITSFDPRDGTVQRAVEEVFSGDLTTATRGRF
+TGFVYPTPADAGLDAEDVQVPVPGGHARAWRIAPYPSEDGEPRPAEGLWAVMVHGRGARR
+NEGIRAVPTARRLGMTSLLISYRNDGDAPDAADARYGLGTTEWEDVEAAIRYALDHGARD
+VVLFGWSMGGAVVLQTVDRSALAPHVRGVVLTGPVIDWVDVLRHQARLNRIPEAVGLLGQ
+WLLANRAGRFITGLAAPVDLKALDWVTRADHVRVPTLILHSEDDEYVPVGPSQDLAERNP
+DLVRFVRFHQARHTREQNVDPRKWDTAVRGWLRAVLSAPRPGGRGR
+>NAFOICDF_01505
+MACPRRHSPRLRARPDLRDALLGSLRGSAAVARPAARLAPAAASVAASAAFVLAGASAGL
+AGVFARTVVTPVRSRPEHTAVLAVLDTGDGMDVILPADEHTTVPGTYSLTFHGGEGCARI
+GAIRSYDPRDGTVQRVVEEVYSGDLRSAVRGRFTAFIWPGPAEAGLEAADVEVPVPGGAA
+PAWRIDPPPAEDGEERAGEGMWAVMVHGRGAVRNEGLRAVPTAARLGMTSLLVSYRNDGD
+APDAEDARYGLGTTEWEDVEAAVRYALDHGARDVVLFGWSMGGAVVLQTADRSDLTSRVR
+GIVLTGPVVDWMDVLRHQARLNRIPEGIGLLGQWLLSNRAGRLVTGLAAPVDLKALDWVT
+RADHVRVPTLILHSEDDEYVPVGPSQDLAERNPALVRFVRFHQARHTREQNVDPVKWDRS
+VRGFLRAVLTAPRPGAVSPPGAPQAPSGSSPRRRSSGSSSASRPRNAR
+>MHAAABBN_00996
+MAARPRRPRPHPADLPPALAAAVTVAARRAGGRDSRVRRAGRLVRRGVTGSVRGGVAVAS
+PVARWAPPVLSVAAASAFVLAGASSALAGVFARTVVTPVRRHAESTPILAVVDTPAGQDV
+ILQADEYTTVPGQYSLTFDDGAGCARIGEITSFDPRDGTVQRAVEEVFSGDLTTATRGRF
+TGFVYPTPADAGLDAEDVQVPVPGGHARAWRIEPDPSEDGEPRPAEGLWAVMVHGRGARR
+NEGIRAVPTARRLGMTSLLISYRNDGDAPDAADARYGLGTTEWEDVEAAIRYALDHGARD
+VVLFGWSMGGAVVLQTVDRSPLAPHVRGVVLTGPVIDWVDVLRHQARLNRIPEAVGLLGQ
+WLLANRAGRFITGLAAPVDLKALDWVTRADHVRVPTLILHSEDDEYVPVGPSQDLAERNP
+DLVRFVRFHQARHTREQNVDPRKWDTTVRGWLRAVLSAPRPGGRGR
+>LFPAFLNI_01235
+MAARPRRPRPHPADLPPALAAAVTVAARRAGGRDSRVRRAGRLVRRGVTGSVRGGVAVAS
+PVARWAPPVLSVAAASAFVLAGASSALAGVFARTVVTPVRRHAESTPILAVVDTPAGQDV
+ILQADEYTTVPGQYSLTFDDGAGCARIGEITSFDPRDGTVQRAVEEVFSGDLTTATRGRF
+TGFVYPTPADAGLDAEDVQVPVPGGHARAWRIEPDPSEDGEPRPAEGLWAVMVHGRGARR
+NEGIRAVPTARRLGMTSLLISYRNDGDAPDAADARYGLGTTEWEDVEAAIRYALDHGARD
+VVLFGWSMGGAVVLQTVDRSPLAPHVRGVVLTGPVIDWVDVLRHQARLNRIPEAVGLLGQ
+WLLANRAGRFITGLAAPVDLKALDWVTRADHVRVPTLILHSEDDEYVPVGPSQDLAERNP
+DLVRFVRFHQARHTREQNVDPRKWDTTVRGWLRAVLSAPRPGGRGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001093.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001093.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2fce2f6caebd594a95cad0db25b4a69be62805d8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001093.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01612
+MAGHSKWATTKHKKAVIDARRAKAFAKYIKNIEVAARAGGADLAGNPALDLAVSKAKKAS
+VPNDNIDRAVKRGAGLTGEVVDYAEIMYEVRGPQGSAVLVECLTDNKNRAAAEVRTAVTR
+NGGTMADSGSVSFLFTRQGVVRLPAEGRTEDELLEAVIEAGAEEVVLSGDEFEILSDPSD
+LRAVAEALDAAGIDYESDETEFVPTMKVELEDAKGAGTFLKLADALEELDDVQNVYSNVD
+ISPEVLAELDQD
+>MOLHKGIG_01275
+MAGHSKWATTKHKKAVIDARRAKAFAKYIKNIEVAARAGGPDVAGNPALDLAVSKAKKAS
+VPNDNIDRAVKRGAGLTGEVIDYAEIMYEVRGPQGSALLVECLTDNKNRAAADVRAAVTR
+NGGTMADSGSVSFLFERKGLVRLPAEGNTEDGLLEAVLEGGADAEEVVVSGDSFEILSDP
+SDLQSVAKALDEAGVEYESDELEFVPTMKVDLDASGARTFLKLADALEDLDDVQNVFSNV
+DIAPEVLAELDED
+>NAFOICDF_01507
+MSGHSKWATTKHKKAVIDQRRAKAFAKYIKGIEVAARAGGADLSGNPALDLAVSKAKKNS
+VPNDNIDRAIKRGAGLTGEVIDYTEIMYEVRGPQGSALLVECLTDNKNRAAADVRAAVTR
+NGGTMADSGSVSFLFHRKGVVRLPAAGNTEDSLLEAVLEGGADAEEVVLSGDDFEIVSEP
+GDLRAVAEALDAAGIDYETDEMEHLPTMKVELDAKGARTFLKLADALEDLDDVQNVFSNV
+DIAPEVMDELEQD
+>MHAAABBN_00994
+MAGHSKWATTKHKKAVIDARRAKAFAKYIKNIEVAARAGGPDVAGNPALDLAVSKAKKAS
+VPNDNIDRAVKRGAGLTGEVIDYAEIMYEVRGPQGSALLVECLTDNKNRAAADVRAAVTR
+NGGTMADSGSVSFLFERKGLVRLPAEGNTEDGLLEAVLEGGADAEEVVVSGDSFEILSDP
+SDLQSVAKALDEAGVEYESDELEFVPTMKVDLDASGARTFLKLADALEDLDDVQNVFSNV
+DIAPEVLAELDED
+>LFPAFLNI_01233
+MAGHSKWATTKHKKAVIDARRAKAFAKYIKNIEVAARAGGPDVAGNPALDLAVSKAKKAS
+VPNDNIDRAVKRGAGLTGEVIDYAEIMYEVRGPQGSALLVECLTDNKNRAAADVRAAVTR
+NGGTMADSGSVSFLFERKGLVRLPAEGNTEDGLLEAVLEGGADAEEVVVSGDSFEILSDP
+SDLQSVAKALDEAGVEYESDELEFVPTMKVDLDASGARTFLKLADALEDLDDVQNVFSNV
+DIAPEVLAELDED
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001095.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001095.fa
new file mode 100644
index 0000000000000000000000000000000000000000..863f13bd68669dbfb1a6f89cf04c51f4688b4cf4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001095.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01614
+MIASLSGTVEHVALDRAVIAVGGFGVQFSATPQTLATLHEGRTGSVQTHLVVKEDALTLF
+GFADRHEREVFEVLITANGVGPRLALAVLSVHHPEAVRRAVTEEDENALTRVPGVGPKLA
+RKIIVELSGRLTPTGEQVPAPEEPAAPETPEAAWHADVVQAMTGLGWSEKEALKAVEATV
+AARPELDEARDVAALLRATLRDVGTAGTVRGGR
+>MOLHKGIG_01273
+MIASLSGTVEHVALDRAVIAVGGLGVQFSATPQTLSTLHEGRPGAVQTHLVVKEDALTLY
+GFADRDEREVFEVLITANGVGPRLALAILSVHHPETVRRAVTEEDEKTLTRVPGIGPKMA
+RKIIVELSGRLAPTGEPVPEAEAEASAEPTVEALWHADVVQAMAGLGWSEKEALKAVEAT
+VAARPELDEGRDVAALLRATLRDVGMAGSVRGGR
+>NAFOICDF_01509
+MIASLSGTVEHVGLDHAVIAVGGVGLSFSATPQTLSHLHEGRDGAVQTHLVVKEDSLTLF
+GFADRAEREVFEVLLGANGVGPRLALAILAVHRPEAVRRAVTDEDEKALTLVPGIGPKMA
+RKIIVDLAGRLAPTGEVEPEAAVVEPEAAADAWHADVVQAMTGLGWSEKEAAKAVAATVA
+THPDVDASGDVAALLRATLRDVGAAAAVRGGRRA
+>MHAAABBN_00992
+MIASLSGTVEHVALDRAVIAVGGLGVQFSATPQTLATLHEGRPGAVQTHLVVKEDALTLY
+GFADRDEREVFEVLITANGVGPRLALAILSVHHPETVRRAVTEEDEKTLTRVPGIGPKMA
+RKIIVELSGRLAPTGEPVPEAEAEASAEPTVEALWHADVVQAMAGLGWSEKEALKAVEAT
+VAARPELDEGRDVAALLRATLRDVGMAGSVRGGR
+>LFPAFLNI_01231
+MIASLSGTVEHVALDRAVIAVGGLGVQFSATPQTLATLHEGRPGAVQTHLVVKEDALTLY
+GFADRDEREVFEVLITANGVGPRLALAILSVHHPETVRRAVTEEDEKTLTRVPGIGPKMA
+RKIIVELSGRLAPTGEPVPEAEAEASAEPTVEALWHADVVQAMAGLGWSEKEALKAVEAT
+VAARPELDEGRDVAALLRATLRDVGMAGSVRGGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001098.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001098.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5579d0045d2f3733953ecc9558d537a004bc88e9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001098.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01618
+MNRFADWGNALYSGRVSYPFVQRWRLWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF
+TVSQTAATDIAAGERAVTDVLAGGHATVTNIAPGTVRVQTEQLDDAQTRQVAANLQDAYG
+VGQDQVTSTFVGPTWGAAVSQQALLGLVIFVVLVTLFMAFYFRTWKMSLAAVIGMLYVVA
+LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGQEEDPERTFEQNVNL
+AVNQTLVRSITTSIVGILPVGSILFIGAGLLGAGTLRDIALAIFVGIIVGTLSTLFIQAP
+LYALLRRGDEDVRDHDARAAARAARENRGDTVTDPDVAPWEDGARL
+>MOLHKGIG_01269
+MNRFADWGNALYSGRISYPFIQRWRRWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF
+TVSQTASTDVAAGERAVTDVLADGHATVTNVAPGTVRVQTEQLDDAQTRAVAANLQEAYG
+VGQDQVTSTFVGPTWGAAVSQQALIGLVIFVVLVTLFMAVYFRTWKMSLAAVLGMLYVVA
+LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGAEEDPERSFVENVNL
+AVNQTLVRSITTSVVGILPVGSILFIGAGLLGAGTLRDIALALFVGIIVGTLSTLFLQAP
+LYALLRRNDPDVRDHDARAAARAARERASEAVTDPDVAPWDDGARL
+>NAFOICDF_01513
+MNRFADWGNALYSGRISYPFVRKWKTWFLIAAALLAVAFGLTALRGGFNLGIDFRGGSEF
+TVSDAASSELDPGRAAVTDVVAGAEPTVTQVAPGTMRVQTEQLDDAQTRQVAQNLQQAYG
+VTGDHVTSTFVGPTWGQAVSQQAVIGLVIFVVLVTLFMALYFRTWKMSLAAVVGMLYVVA
+LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTRGVEEDPDRTFDGSVNL
+AVNQTLVRSITTSIVGLLPVGSILFIGAGLLGAGTLRDISLAIFVGIIVGTLSTLFIQAP
+LYALLRRGDADVVAHDARVGADHDEREQEEDLADARGAVL
+>MHAAABBN_00988
+MNRFADWGNALYSGRISYPFIQRWRRWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF
+TVSQTASTDVAAGERAVTDVLADGHATVTNVAPGTVRVQTEQLDDAQTRAVAANLQEAYG
+VGQDQVTSTFVGPTWGAAVSQQALIGLVIFVVLVTLFMAVYFRTWKMSLAAVLGMLYVVA
+LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGAEEDPERSFVENVNL
+AVNQTLVRSITTSVVGILPVGSILFIGAGLLGAGTLRDIALALFVGIIVGTLSTLFLQAP
+LYALLRRNDPDVRDHDARAAARAARERASEAVTDPDVAPWDDGARL
+>LFPAFLNI_01227
+MNRFADWGNALYSGRISYPFIQRWRRWFALAALLLVLAGGLTALRGGFNLGIEFRGGSEF
+TVSQTASTDVAAGERAVTDVLADGHATVTNVAPGTVRVQTEQLDDAQTRAVAANLQEAYG
+VGQDQVTSTFVGPTWGAAVSQQALIGLVIFVVLVTLFMAVYFRTWKMSLAAVLGMLYVVA
+LTAGIYGATGFEITPSAIIGFLTILSYALYDTVVVFDKIRENTIGAEEDPERSFVENVNL
+AVNQTLVRSITTSVVGILPVGSILFIGAGLLGAGTLRDIALALFVGIIVGTLSTLFLQAP
+LYALLRRNDPDVRDHDARAAARAARERASEAVTDPDVAPWDDGARL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001099.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001099.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40c19f976dd5da79ddb66bc5a24c0918852ac07d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001099.fa
@@ -0,0 +1,70 @@
+>ACLBLIBL_01619
+MSEHDPTHAPARVAAVRPRGRIARLTGRHATEYSPLLEPLMRTVRQRATKAELADLIRAF
+EVARAAHEGQMRRSGDPYITHPVAVATILAEIGVSGPTLLAALLHDTVEDTDYSLERLRA
+DFGPEVALLVDGVTKLDKVTYGAAAQAETVRKMVIAMAQDVNVLLIKLADRLHNARTWRY
+VSPESSARKAQETLDIYAPLAHRLGMNTVKWELEDLSFAALKPKMYAEIVRLVGERNPER
+EKHIAALRTVIEDHLREHRIRAEVTGRPKHYYSIYQKMVMRGKDFDEIHDLTGIRVLVDS
+VRDCYAVLGVIHARWNPVPGRFKDYIAVPKLNMYRSLHTTVMGPGGRPVEIQIRTHEMHR
+QAEYGVAAHWRYKAQAAAESSSSSSGTPAWLRSVMDWQKDTRDPDEFLDSLRTQIGADEV
+YVFTPSGEIRSLPAGSTPVDFAYAIHTDVGHRTIGAKVNGKLVPLSTPLNHGDTVEAFTS
+RAEDAGPSRDWLGFVVSPRARSKIRHHFATQRRDEQAERGRESLTRQLRRAGLAVQSVLG
+GEELAQVASDMGYADLDGLLVALGDGHVSAQAVQERVSERLAPPPPARTEPQGELTVGEV
+DLAELVPAQARRTPARATNDAGVLVDGDGGVMAKLARCCNPLPPDAIDGFVTRGSGVSVH
+RLDCPNLATLLEQEPERRTPVGWAPSRHTVYLVEIQVEALDRKSLLSDVTRVLSENHVNI
+LSASVNTTRDRVAMSRFVFEMGDPRFLGHVIAAVRRIDGVFDVHRT
+>MOLHKGIG_01268
+MSEQDPTPVPVRPRGRIARLTGRHATEYSPLLEPLMRTVRQRATKTELADIVRAFEVARA
+AHEGQMRRSGDPYITHPVAVATILAEIGVTGPTLLAALLHDTVEDTDYSLERLRADFGSD
+VALLVDGVTKLDKVTYGAAAQAETVRKMVIAMAQDVNVLLIKLADRLHNARTWRYVSPES
+SARKAQETLDIYAPLAHRLGMNTVKWELEDLSFAALKPKMYAEIVRLVGERNPEREKHIA
+ALRTVIEDHLREHRIRATVTGRPKHYYSIYQKMVTRGKDFDDIHDLTGIRVLVDSVRDCY
+AVLGAIHARWNPVPGRFKDYIAVPKLNMYRSLHTTVMVPGGKPVEIQIRTQEMHRQAEYG
+VAAHWRYKAQAAGQAPVQATPAWLRSVMDWQADTRDPDEFLASLRTQIGADEVYVFTPKG
+EIRTLPAGSTPVDFAYAIHTDVGHRTIGARVNGKLVPLSTPLSHGDTVEVFTSRAEDAGP
+SRDWLGFVVSPRARSKIRHHFATQRRGEQADRGRESLTRQLRKAGMTVQHVLGGEELVQL
+ATDLGYADLDGLFVALGDGHVSAQSVQERVAERLAPPTPTQAEPEGELTVGEVDLQELVP
+AQARRAPARATNDAGVLVDGDGGVMAKLARCCNPVPPDAIDGFVTRGSGVSVHRVDCPNL
+ATLLAQEPERHTPVSWAPSRDTVYLVEIQIEALDRKSLLSDVTRVLSENHVNILSASVNT
+TRDRVAMSRFVFEMGDPRFLGHVIDAVRRIDGVFDVHRT
+>NAFOICDF_01514
+MTEQDRRPAAPPRRGRIARLTGRRATEYSPLLEPLMRTVRQSATHAEQEDIVRAFEVAER
+AHRGQMRRSGDPYITHPVAVATILAELGVTGPTLLAALLHDTVEDTDYSLEQLTADFGPQ
+VALLVDGVTKLDKVTYGAAAQAETVRKMVIAMAQDVNVLLIKLADRLHNARTWRYVSPES
+SAKKARETLDIYAPLAHRLGMNTVKWELEDLSFAALQPKVYAEIVRLVGERNPEREKQLA
+ALRGVLEEQLREQRVRATVTGRPKHYYSVYQKMVTQKKDFAQIYDLTGIRVLVDSVQDCY
+AVLGVVHARWNPVPGRFKDYIAVPKLNMYRSLHTTVMGPEGKPVEIQIRTWEMHRQAEYG
+VAAHWRYKAGARGELEAGRSQQTPGWLRSVMDWQEDTRDPDEFLAALRTQIGADEVYVFT
+PKGEIRSLPADSTPVDFAYAIHTDVGHRTVGARVNGRLVPLSTVLRHGDTVEVFTSKAED
+AGPSRDWLNFVVSPRAKSKIRHHFATRRRDEQIERGREAFTRQLRKAGLSVQRVLGGEDL
+GVVAGELGYHDPDTLFAAMADGHVSPQAVTERLEARLAPPPAPTAPDAELRVGEVDLAGL
+VPEKARRAPTRSTNEAGVLVNGDGGVLAKLARCCNPVPPDEVVGFVTRGSGVSVHRGDCR
+NLATMLENEPERRVDVAWAPSRDAVYLVEIQVQALDRTSLLSDVTRVLSENHVNILSASV
+NTTRDRVAMSRFVFEMGDPKFLEHVVNAVRRIDGVFDVRRT
+>MHAAABBN_00987
+MSEQDPTPAPARPAPARPAPVRPRSRIARLTGRHATEYSPLLEPLMRTVRQRATKTELAE
+IVRAFEVARAAHEGQMRRSGDPYITHPVAVATILAEIGVTGPTLLAALLHDTVEDTDYSL
+ERLRADFGSEVALLVDGVTKLDKVTYGAAAQAETVRKMVIAMAQDVNVLLIKLADRLHNA
+RTWRYVSPESSARKAQETLDIYAPLAHRLGMNTVKWELEDLSFAALKPKMYAEIVRLVGE
+RNPEREKHIAALRTVIEEHLREHRIRATVTGRPKHYYSIYQKMVTRGKDFDDIHDLTGIR
+VLVDSVRDCYAVLGVIHARWNPVPGRFKDYIAVPKLNMYRSLHTTVMVPGGKPVEIQIRT
+QEMHRQAEYGVAAHWRYKAQVAGQAPVQATPAWLRSVMDWQADTRDPDEFLASLRTQIGA
+DEVYVFTPKGEIRTLPAGSTPVDFAYAIHTDVGHRTIGARVNDKLVPLSTPLSHGDTVEV
+FTSRAEDAGPSRDWLGFVVSPRARSKIRHHFATQRRDEQADRGRESLTRQLRKAGMAVQQ
+VLGGEELVQVATDLGYADLDGLFVALGDGHVSAQSVQERVAERLAPPTSTQAEPEGELTV
+GEVDLQELVPAQSRRAPARATNDAGVLVDGDGGVMAKLARCCNPVPPDAIDGFVTRGSGV
+SVHRVDCPNLATLLAQEPERRTPVSWAPSRDTVYLVEIQIEALDRKSLLSDVTRVLSENH
+VNILSASVNTTRDRVAMSRFVFEMGDPRFLGHVIDAVRRIDGVFDVHRT
+>LFPAFLNI_01226
+MSEQDPTPAPARPAPARPAPVRPRSRIARLTGRHATEYSPLLEPLMRTVRQRATKTELAE
+IVRAFEVARAAHEGQMRRSGDPYITHPVAVATILAEIGVTGPTLLAALLHDTVEDTDYSL
+ERLRADFGSEVALLVDGVTKLDKVTYGAAAQAETVRKMVIAMAQDVNVLLIKLADRLHNA
+RTWRYVSPESSARKAQETLDIYAPLAHRLGMNTVKWELEDLSFAALKPKMYAEIVRLVGE
+RNPEREKHIAALRTVIEEHLREHRIRATVTGRPKHYYSIYQKMVTRGKDFDDIHDLTGIR
+VLVDSVRDCYAVLGVIHARWNPVPGRFKDYIAVPKLNMYRSLHTTVMVPGGKPVEIQIRT
+QEMHRQAEYGVAAHWRYKAQVAGQAPVQATPAWLRSVMDWQADTRDPDEFLASLRTQIGA
+DEVYVFTPKGEIRTLPAGSTPVDFAYAIHTDVGHRTIGARVNDKLVPLSTPLSHGDTVEV
+FTSRAEDAGPSRDWLGFVVSPRARSKIRHHFATQRRDEQADRGRESLTRQLRKAGMAVQQ
+VLGGEELVQVATDLGYADLDGLFVALGDGHVSAQSVQERVAERLAPPTSTQAEPEGELTV
+GEVDLQELVPAQSRRAPARATNDAGVLVDGDGGVMAKLARCCNPVPPDAIDGFVTRGSGV
+SVHRVDCPNLATLLAQEPERRTPVSWAPSRDTVYLVEIQIEALDRKSLLSDVTRVLSENH
+VNILSASVNTTRDRVAMSRFVFEMGDPRFLGHVIDAVRRIDGVFDVHRT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001101.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001101.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b896bf66cef654e3b2aa25d7083892d81af1d972
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001101.fa
@@ -0,0 +1,49 @@
+>ACLBLIBL_01621
+MPDASSEDALAYFVRKYDDVRAQMALFEQRIAAGAPSSELGKALGQMTSAVNERHMVGDM
+DALRTRLAALETLLGDYRGAEQEARQAAQAQQLATREAIVAEAEEFAATPAERMPWKTAS
+TRMTALFEEWKAAQKAGPRLSKSVEDGLWKRFRGARTAFDKTRRAHFSQLDAKSAEAKQV
+KERLIARAEELSSSTDWGVTAGKYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFDAR
+KAVNQEIDREYGANLKVKEQILADGKKLLPFKDVKAGRRALNELRGRWEDAGRVPRGDVR
+RMEEGFRSLEDALKQAENEHWRRTDPETKARTSSALTQLEETIAGLEADLAKAQASGDER
+AVKKAQEALDARLQWKQALEASASELS
+>MOLHKGIG_01266
+MQPDDQQSPATEATPASAEAAETTVPAEARPVPEIVPDAPAHGDSAQPAEAPAVPSPAAM
+KKASPAAVRPATPAAASAVPAPVVAPTVPPTPVEEAARFARVSEDGHVTLLDGQEEHAVG
+QVPDASTEDALAYFVRKYDDVRAQMALFEQRIAAGAPSSELGRALGQMTTAVNERHMVGD
+MDALRTRLAALETLLADYRAAEQEARQAAQAEQLATREAIVAEAETFAQTPAERMPWKTA
+SKRMTELFEEWKAAQKAGPRLAKSVEDDLWKRFRGARTTFDKTRRAHFSRLDAASAEAKQ
+VKERLIARAEELSTSTDWGVTAGKYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFAA
+RKAANQEIDREYGANLKVKEQILADGQKLLPFTDVKAGRRALNELRGRWEDAGRVPRGDV
+RRMEEGFRRLEDALKQAENEHWRRTDPETKARTNSALTQLEETIAGLEADLARAQAQGDQ
+RAVKKAQEALDARLKWKQALEASASELR
+>NAFOICDF_01516
+MTHQPQSDDQQTPDAEQATPAAAPQQTSPAQDAPEQVVQDQTPAAQADLADALGSIESVE
+APAPAQGEEPADAAETDAEKTPEAAPSPAVPAAPSPAALKRSAAPRSAAPRPATAAVPVA
+PAPSVEPTPLGEAAAFARVSEDGHVTLLDGADEVAVGQVPDATEQDALAYFVRKYDDVRA
+QMALFEQRIAAGAPSSELGKALGQMTAAVTERHMVGDMPALRTRLAALETLLGDYRAAEA
+ERRQAAQAEQLATREAIVTEAEKFAATPAERMPWKQASARMTELFDEWKTAQKAGPRLSK
+SVEDGLWKRFRGARTQFDKTRRAHFSQLDARSAEAKQVKERLIARAEELSSSTDWGVTAG
+KYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFAARKAENAAVDREFGENLKVKEQIL
+ADGQKLLPFTDLKAGRKALNELRGRWEDAGKVPRGDIRRMEDGFRKLEDALKQAENEHWR
+RTDPETKARTNSALTQLEETIAGLEADLAEAQAAGDQKRIATAQEALDARLQWKQALEAS
+ASELR
+>MHAAABBN_00985
+MQPDDQQSPATESTPASAEAADTTVPAEARPVPEIVPDAPAHGDSSQPAETPAVPSPAAM
+KKASPAAVRPATPAAASVAPAPVVAPTVPPTPVEEAARFARVSEDGHVTLLDGQEEHAVG
+QVPDASTEDALAYFVRKYDDVRAQMALFEQRIAAGAPSGELGRALGQMTTAVNERHMVGD
+MDALRTRLAALETLLGDYRAAEQEARQAAQAEQLATREAIVAEAETFAQTPAERMPWKTA
+SKRMTELFEEWKAAQKAGPRLAKSVEDDLWKRFRGARTAFDKTRRAHFSRLDAASAEAKQ
+VKERLIARAEELSTSTDWGVTAGKYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFAA
+RKAANQEIDREYGANLKVKEQILADGQKLLPFTDVKAGRRALNELRGRWEDAGRVPRGDV
+RRMEEGFRKLEDALKQAENEHWRRTDPETKARTNSALTQLEETIAGLEADLARAQARGDQ
+RAVKKAQEALDARLQWKQALEASASELR
+>LFPAFLNI_01224
+MQPDDQQSPATESTPASAEAADTTVPAEARPVPEIVPDAPAHGDSSQPAETPAVPSPAAM
+KKASPAAVRPATPAAASVAPAPVVAPTVPPTPVEEAARFARVSEDGHVTLLDGQEEHAVG
+QVPDASTEDALAYFVRKYDDVRAQMALFEQRIAAGAPSGELGRALGQMTTAVNERHMVGD
+MDALRTRLAALETLLGDYRAAEQEARQAAQAEQLATREAIVAEAETFAQTPAERMPWKTA
+SKRMTELFEEWKAAQKAGPRLAKSVEDDLWKRFRGARTAFDKTRRAHFSRLDAASAEAKQ
+VKERLIARAEELSTSTDWGVTAGKYRDLMDEWKRAPRASRKEDDALWARFRAAQDVFFAA
+RKAANQEIDREYGANLKVKEQILADGQKLLPFTDVKAGRRALNELRGRWEDAGRVPRGDV
+RRMEEGFRKLEDALKQAENEHWRRTDPETKARTNSALTQLEETIAGLEADLARAQARGDQ
+RAVKKAQEALDARLQWKQALEASASELR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001102.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001102.fa
new file mode 100644
index 0000000000000000000000000000000000000000..62b7b4e7e18319c19560460cd444a4f362b46ca9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001102.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_01622
+MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE
+VYAVSRLAEDEEVAAGRREAKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ
+KVWRGERPQEGRAREFTQADIDVVGDGELSPRHDADVALVMAEALGALPIGDFLIRVNNR
+KLAEGFYRGIGLTDAAGVLRSIDKLEKIGADEVARLLQEEVGASPEQARQALALAAIRTE
+DVSFVEQVRALGVSDPLLEEGLAELADVVETLHRRAPGRAVADLSIARGLDYYTGTVYET
+VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQEMAQASRSVPTAV
+YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFLGRDDAG
+ARVHEVKDIRSGDQHPADPADWTPPSEDLLPQVTRTESTEG
+>MOLHKGIG_01265
+MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE
+VYAVSRLAEDEEVAAGRREPKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ
+KVWRGERPQEGRAREFTQADIDVVGDGALSPRYDADVALVMAEALGALPIGDFLIRVNNR
+KLAEGFYRGIGLEDTAGVLRSIDKLEKVGPEEVARLLQEEVGASPEQAAQALALADIRTS
+DTSFVERVRALGVTHELLEEGLTELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET
+VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQQMAVASRSVPTAV
+YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFMGRDDAG
+ARVHEVKDIRSGEQHAVDPADWTPPTEDLLPQITRTQD
+>NAFOICDF_01517
+MSRKQSLSGFHEWLPAERIVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE
+VYAVSRLAEDQEVAEGVREAKDPSDPKRLALHFDLTVPFARYVTENAGHLAFPFRRHQIQ
+KVWRGERPQEGRAREFTQADIDVVGDGELSPRYDADVALVMAEALGALPIGDFRIRVNNR
+KLAEGFYRGIGLEDAAGVLRSIDKLEKVGAEEVARLLQEEVGATAEQAAQALKLAEIRTP
+DTAFVEQVRALGVEDPLLEEGLAELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET
+VLVGHEQLGSICSGGRYDALATKGNRAFPGVGLSIGVTRLVMRMLSQEMAVASRAVPTVV
+YVALTHDDDWSRAQDVAAGLRGRGIAAEVAVSAEKFGKQIKYADRRGIPFVWFLGAEGAS
+DEVKDIRSGEQVPADAATWAPPAEDLVPQVTESPRAED
+>MHAAABBN_00984
+MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE
+VYAVSRLAEDEEVAAGLRDPKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ
+KVWRGERPQEGRAREFTQADIDVVGDGALSPRYDADVALVMAEALGALPIGDFLIRVNNR
+KLAEGFYRGIGLEDTAGVLRSIDKLEKVGPEEVARLLQEEVGASPEQAAQALALADIRTS
+DTSFVERVRALGVTHELLEEGLTELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET
+VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQQMAVASRSVPTAV
+YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFMGRDDAG
+ARVHEVKDIRSGEQHAADPADWTPPAEDLLPQVARAQD
+>LFPAFLNI_01223
+MSRKASLSGFHEWLPAERLVEQHVLDTLRRTFELHGFAGIETRAVETLGQLLRKGEVDKE
+VYAVSRLAEDEEVAAGLRDPKDPADPKRLALHFDLTVPFARYVVENAGHLAFPFRRYQMQ
+KVWRGERPQEGRAREFTQADIDVVGDGALSPRYDADVALVMAEALGALPIGDFLIRVNNR
+KLAEGFYRGIGLEDTAGVLRSIDKLEKVGPEEVARLLQEEVGASPEQAAQALALADIRTS
+DTSFVERVRALGVTHELLEEGLTELADVVATLHRRAPGRAVADLSIARGLDYYTGTVYET
+VLVGHEQLGSICSGGRYDALASKGNRVFPGVGLSIGVTRLVMRMLSQQMAVASRSVPTAV
+YVALTADEDWSEAQDVAALLRERGIPAEVAVSAEKFGKQIKYADRRGIPFVWFMGRDDAG
+ARVHEVKDIRSGEQHAADPADWTPPAEDLLPQVARAQD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001106.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001106.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ad0e25ff2644f54aba8d5419c648e8cc10cf916
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001106.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_01627
+MRTLSRLAAATSMVALSAAVVAPLTVAAPAANPSGRSIELTAAGTHATGVFDASAAEIPA
+FDKTTGRLFVVNAQKGAIDVLTVGEDAEPAAESVLSVAGLPAADGSVTGAGAVVNSVAVA
+GAVMAATVEAEDKTGHGWLVFFDTRTLGFLGGVRVGALPDSVALAPNGAYAVVANEGEPA
+DDFSSDPEGTISVVSVPKNARQFARLGQDAVRTVDFRAYDEGAALPEGVRVFGPDVAVPS
+GHEEAGRIARNLEPEYASIDPTGRTAYVSVQEANAVVAVDLASASLADFWALHLTDWSTE
+GVLDVSDKDGAISPAYQPVLGVPMPDGLATYKHRGQTLVVTANQGDSREWGDFVDAERVK
+DLELCGDVFPHAKALQKNEALGRLNVLTDLGYDAERGCHTELHALGGRGFSIYTADGQRL
+FDSSGMLEEQIARLIAAGELPAHAFNANNDETPSFDSRSDDKGVEPESVVVGEVQGRQYA
+FVGLERIGGVMVFDITDPTDARYVDYINERAWDAVGEDGDAGLGDMGAEGLAFVPASDSP
+SGTALLIVATEVSGSTTVYEVDPVKGGKRT
+>MOLHKGIG_01261
+MPRLARLATAVTAAALSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHET
+GVFGESAAEIPAFDAVSGRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVT
+DKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTTTLRYLGGVRVGALPDSLAFSPNG
+AYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTALPAG
+VRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLED
+LWALTPTDWSTEGVLDASDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGR
+EWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLKVLTDLGYDSERECHSSLTTLGGR
+SFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPEPES
+VVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGA
+EGLTFVPADESPSGTALLIVANEVSGSTTVYEVNPTRRQ
+>NAFOICDF_01524
+MSRIVRLTRLGAAAGALALSAAVVAPSAVSAPVTATAAAANPSGKTVELSLAGTHETGVF
+GESAAEIPAFDAATGRLFVVNAEKGAVDVLRVGADGAPAAETVLSAEGLRTADGSVTDGG
+ATVNSVAVSGGVLAVAVEAADKTGLGWVAFFDTTTLSYLGGVRVGALPDSIAFSPDGAYA
+VVANEGEPADDFSADPEGTISVISVPKNVRQFARLTQAAVRTVDFRAYDAGTALPEGVRV
+FGPDVQVPEGQEPAGRIARNLEPEYVTIDDTGRTAYVSVQEANAVVAVDLKSATLKDFWA
+LQLTDWSKEGVLDASNEDKAITLRNQPVLGVPMPDGVDTYRYRGQDLVVTANEGDSREWG
+DFVDAARVKDLELCTAEYPDAKALQKKPALGRLNVVTDLGYDADRDCFSQLHAFGGRSFS
+IYTADGTRLFDSAGMIEEQIAQLIADGELPESAFNANNDETPSFDSRSDDKGPEPEAVVV
+GRVQGRTYAFVGLERIGGVMVFDITDPTKATYVDYVNERNWDAEGDDAAAGLGDMGAEGL
+TFVPANESPSGTALLVVANEVSGSTTVYEVNPVRR
+>MHAAABBN_00980
+MPRLARLATAVTAATLSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHET
+GVFGESAAEIPAFDAVSGRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVT
+DKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTTTLRYLGGVRVGALPDSLAFSPNG
+AYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTALPAG
+VRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLED
+LWALTPTDWSTEGVLDASDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGR
+EWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLKVLTDLGYDSERECHSSLTTLGGR
+SFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPEPES
+VVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGA
+EGLTFVPADESPSGTALLIVANEVSGSTTVYEVNPTRRQ
+>LFPAFLNI_01219
+MPRLARLATAVTAATLSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHET
+GVFGESAAEIPAFDAVSGRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVT
+DKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTTTLRYLGGVRVGALPDSLAFSPNG
+AYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTALPAG
+VRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLED
+LWALTPTDWSTEGVLDASDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGR
+EWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLKVLTDLGYDSERECHSSLTTLGGR
+SFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPEPES
+VVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGA
+EGLTFVPADESPSGTALLIVANEVSGSTTVYEVNPTRRQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001108.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001108.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a37175293d886610113d5c656c31d9df6066e8b4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001108.fa
@@ -0,0 +1,23 @@
+>ACLBLIBL_01629
+MSQHQPYAQDPRSTVPATTADAAYAGGPLGAADHRVLESVPDYARAQAIVDQLSDAGFPV
+EHVRIVGTGLRTVEQVLGRMTTGKAAGRGAVQGLWFGLLLGLLFSIFSPGFGFLWILLIS
+LGLGALWGAVFGAIGHAATRGRRDFSSLQTMDAASYEVQVEAAHLDRARQTLGAGPAAPR
+A
+>MOLHKGIG_01258
+MTQSTPQQSTPQHTAAQQPAPYGRPGAGGPALPQADYRILRSVPAYAEAQALVDQLSDAG
+FPVERVRIVGTGLRSVEQVLGRMTTGKAAVRGGLQGLWFGLLLGLLFSIFAPGFGFLWIL
+LISLGLGALWGAVFGAIGHAATGGRRDFTSLQTMEAESYDVLVEASHLDQAGQLLGADPG
+TAATPRA
+>NAFOICDF_01527
+MSASAAHYAVLSTVPDYAHAQSTVDRLSDSGFPVEHVRVAGTGLRSVEQVTGRLTTGAVG
+VC
+>MHAAABBN_00977
+MTQSTPQQSTPQHTAAQQPAPYGRPGAGGPALPQADYRILRSVPAYAEAQALVDQLSDAG
+FPVERVRIVGTGLRSVEQVLGRMTTGKAAVRGGLQGLWFGLLLGLLFSIFAPGFGFLWIL
+LISLGLGALWGAVFGAIGHAATGGRRDFTSLQTMEAESYDVLVEASHLDQAGQLLGADPG
+TAATPRA
+>LFPAFLNI_01216
+MTQSTPQQSTPQHTAAQQPAPYGRPGAGGPALPQADYRILRSVPAYAEAQALVDQLSDAG
+FPVERVRIVGTGLRSVEQVLGRMTTGKAAVRGGLQGLWFGLLLGLLFSIFAPGFGFLWIL
+LISLGLGALWGAVFGAIGHAATGGRRDFTSLQTMEAESYDVLVEASHLDQAGQLLGADPG
+TAATPRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001112.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001112.fa
new file mode 100644
index 0000000000000000000000000000000000000000..04c29360e530b2b743b0aa4d56a74014bb7dd488
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001112.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01634
+MSAGQDGAATATDAVRRGRTLGVDVGRARVGLATADPDGLIATPVATLARDARRGRDVGE
+LVAHALELDVVAVYVGLPVNLRGEHTPSTQDALDYARSVARAPAAAGHAVPVRLVDERLS
+TVSAQAGLRAAGRTVKDSRGVIDQAAAVAILQAAVDEQRRTGRWAGQDPEEIA
+>MOLHKGIG_01254
+MSAGQDGANAATDAVRRGRTLGVDVGRARVGVASADPDGLIATPVATLRRDARRRRDVDE
+LVAHARELDVVAVYVGLPVNLRGEHTPSTQDALDYADAVAAALAEAGHPVPVRLVDERLS
+TVSAQAGLRAAGRSVKDSRGVIDQAAAVAILQAAVDEQRRTGRWAGQDREPIR
+>NAFOICDF_01531
+MSAQAAVRGRVLGVDVGRARVGLAASDPDGLIATPVETLRRDARQRRDHAELLDRARELD
+AVAVYVGLPRNLRGEHTPSTQDAVEYAAAIEALVAEAGTPIPVRLVDERLSTVSAQAALH
+RAGRTVKDSRGVIDQAAAVELLQDALEVQRRRGAWAGITVAEARA
+>MHAAABBN_00973
+MASDAVRRGRTLGVDVGRARVGVASADPDGLIATPVATLRRDARRRRDVDELVAHARELD
+VVAVYVGLPVNLRGEHTPSTQDALDYADAVAAALVEAGHPVPVRLVDERLSTVSAQAGLR
+AAGRSVKYSRGVIDQAAAVAILQAAVDEQRRTGRWAGQDREQIR
+>LFPAFLNI_01212
+MASDAVRRGRTLGVDVGRARVGVASADPDGLIATPVATLRRDARRRRDVDELVAHARELD
+VVAVYVGLPVNLRGEHTPSTQDALDYADAVAAALVEAGHPVPVRLVDERLSTVSAQAGLR
+AAGRSVKDSRGVIDQAAAVAILQAAVDEQRRTGRWAGQDREQIR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001122.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001122.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9af4602d3150b90db3a82d6020f7d0aef807c3a0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001122.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01646
+MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT
+SPHIGNTGVNDTDRESRAIFAAGYVVRDAARRPSNWRAERTLDEELEAFGVVGIREVDTR
+AITRRLRTEGSMRAGVYSGEHAGRPEAELLAEVREQPSMAGARLAETVTTEQPYVIEPAA
+HGWEGEPLAEIAALDLGIKAATPRHLASRGIRVHVLPATAGLEEIRAVSPDGVFLSNGPG
+DPATADAQVALLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVMDNATG
+RVAITSQNHGFAVDAPLGEPVEAPETRYGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP
+ESAAGPNDTLDLFDRFVRMLTEHRDAAAPAATEGA
+>MOLHKGIG_01242
+MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT
+SPHIGNTGVNDADRESRAIFAAGYVVRDAARRPSNWRAERTLDEELEAFGVVGIREVDTR
+AITRRLRTEGSMRAGVFSGEHAARPEAELLAEVRAQPSMAGARLAESVTTEQPYVIEPAE
+HGWEGEPIAEIAALDLGIKAATPRHLASRGIRVHVLPAATDLAGIRAVDPDGVFLSNGPG
+DPATADAQVELLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVLDKATG
+RVAITSQNHGFAVAAPLGEPIEAPESRFGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP
+ESAAGPNDTLDLFDRFVQLLTEHRAATTPATEGA
+>NAFOICDF_01543
+MSTPTPETALLVLEDGTVHRGRAYGARGSTLGEAVFTTGMTGYQETLTDPSYARQIVVQT
+APHIGNTGVNDEDAESRAIWVAGYVVRDAARRPSNWRSQRTLDEELAAHGVVGIQDVDTR
+AITRALRTEGSMKAGIFSGEAAQRPEAELLAEVREQPSMAGARLAETVSAPSAYVVEPSD
+HGWDGEPIADVAALDLGIKAATPHHLAARGIRVHVLPADSDFAAIQAVRPDGVFMSNGPG
+DPATADAQVAVLREVLDAGLPYFGICFGNQIFGRALGFGTYKLPFGHRGPNQPVMDKATG
+RVEITSQNHGFAVDAPIGEVVEAPEARYGRVEVSHWSLNDDVVEGLRLLDRPAFSVQFHP
+EAAAGPHDSLGLFDRFAHTLTERRAAAPSATPEGA
+>MHAAABBN_00961
+MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT
+SPHIGNTGVNDADRESRAIFAAGYVVRDAARRPSNWRAERTLDEELETFGVVGIREVDTR
+AITRRLRTEGSMRAGVFSGEHAARPEAELLAEVRAQPSMAGARLAESVTTEQPYVIEPAE
+HGWEGEPIAEIAALDLGIKAATPRHLASRGIRVHVLPAATDLAGIRAVDPDGVFLSNGPG
+DPATADAQVELLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVLDKATG
+RVAITSQNHGFAVDAPLGEPIEAPESRFGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP
+ESAAGPNDTLDLFDRFVQLLTEHRAATTPATEGA
+>LFPAFLNI_01200
+MSTPTDDLALLVLEDGTVHRGRAYGARGRTLGEAVFTTGMTGYQETLTDPSYAGQIIVQT
+SPHIGNTGVNDADRESRAIFAAGYVVRDAARRPSNWRAERTLDEELEAFGVVGIREVDTR
+AITRRLRTEGSMRAGVFSGEHAARPEAELLAEVRAQPSMAGARLAESVTTEQPYVIEPAE
+HGWEGEPIAEIAALDLGIKAATPRHLASRGIRVHVLPAATDLAGIRAVDPDGVFLSNGPG
+DPATADAQVELLREVLDAGLPFFGICFGNQIFGRALGFDTYKLKFGHRGPNQPVLDKATG
+RVAITSQNHGFAVAAPLGEPIEAPESRFGRVEVSHWSLNDQVVEGLRLLDRPAFSVQFHP
+ESAAGPNDTLDLFDRFVQLLTEHRAATTPATEGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001125.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001125.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa5d6a6ec0e3d2220ba1efa86f44042265b65c32
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001125.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01649
+MALRQLSVEERAEARSKALAARQERAALKADFAAGQVSLAEVFSRADAEDAIGRLRTVDL
+LQALPGVGEVRAREAMAGCGISPRRRLRGLGRRQREALIAYIGR
+>MOLHKGIG_01239
+MALRQLSVQERAEARRKALQARQARAELKAAFAAGEVGLADIFARADADDAVARLRTVDL
+LLALPGVGEVRAREAMAGCGISPRRRLGGLGRRQREALIAYIGR
+>NAFOICDF_01546
+MALRQLSVEERAEARAKALRARQERATLKTSFANRDLSLQEVFARADVDPAIGRLRTVDL
+LQAMPGVGEVRASAVMEACEISPARRLKGLGRRQREALIAYIGR
+>MHAAABBN_00958
+MALRQLSVQERAEARRKALQARQARAELKAAFAAGAVGLADVFARADTEDAVARLRTVDL
+LLALPGVGEVRARETMAGCGISPRRRLGGLGRRQREALIAYIGR
+>LFPAFLNI_01197
+MALRQLSVQERAEARRKALQARQARAELKAAFAAGEVGLADIFARADADDAVARLRTVDL
+LLALPGVGEVRAREAMAGCGISPRRRLGGLGRRQREALIAYIGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001127.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001127.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f8a285035005dda72cd55c57e1ed46b8edcd3ae7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001127.fa
@@ -0,0 +1,21 @@
+>ACLBLIBL_01651
+MTEQYDGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL
+NEKPLSIALREIETDLLESHEAVEATPEADLAAEDFGDFSLPGEDDPFATLEPSDAGQPV
+GDPEAIEEAAEAVRAEEGTSEDAPEA
+>MOLHKGIG_01237
+MTEQYEGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL
+NEKPLSIALREIEAGLLESHEAVEATPEAELAAEDFGDFSLPGEDDPFATLESSDAHQPT
+GDPAAIEEAAETVRAEEGISEDAPEA
+>NAFOICDF_01548
+MTPPPPPDGPPPAAPCVPTHGQKTTREQTLETYVTDQYEGIVNPPIDSLLERVDSKYALV
+LFAAKRARQINAYYSQLHEGLFEYVGPLVDTQLNEKPLSIAMREIESDMLVMAETAAVEP
+AIELAEEEFGDFALPGDDDPFVAEPTAEGVSPEEYGAPVTTGDDDAVEDILSGADVADED
+A
+>MHAAABBN_00956
+MTEQYEGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL
+NEKPLSIALREIEADLLESHEAVEATPEADLAAEDFGDFSLPGEDDPFATLESSDAHQPM
+GDPAAIEEAAETVRAEEGTSEDATEA
+>LFPAFLNI_01195
+MTEQYEGIVNPPIDSLLERVDSKYALVLFAAKRARQINAYYSQLHEGLFEYVGPLVDTQL
+NEKPLSIALREIEADLLESHEAVEATPEADLAAEDFGDFSLPGEDDPFATLESSDAHQPM
+GDPAAIEEAAETVRAEEGTSEDATEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001129.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001129.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3a13f89df88bd84e50864bdc83db7ca114d298a5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001129.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01653
+MTDAAQPSPARHADPYTGVGGGELRLFTSESVTEGHPDKICDQISDAILDAILAADPAAK
+VAVETLTTTGLVQVAGEVNTSAYVEIPRIVRETILDIGYDSSANGFDGAQCGVNISIGQQ
+SSDIFAGVTRSLEAREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL
+TAVRRQENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHDWVGQEQLRKDVEEH
+VIRPVIERSGLDTSGMRVIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG
+KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTAVVPEER
+IIQAVNEVFDLRPAAIVKELNLLRPIYRKTAANGHFGRDDADFTWERTDRVERLRAAAGL
+>MOLHKGIG_01235
+MTDAASLSPARHADPYSGVGGGELRLFTSESVTAGHPDKICDQISDAILDAILAADPSAK
+VAVETLTTTGLVQVAGEVNTSAYVEIPKIVRETILDIGYDSSANGFDGAQCGVNISIGQQ
+SSDIFAGVSRSLETREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL
+TAVRRAENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHEWVTQEQLRADVEEH
+VIRPVIERSGLDTSGMRIIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG
+KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTATVPEEK
+IIEAVNAVFDLRPAAIVKELNLLRPIYRRTAANGHFGRDDADFTWERTDRVEQLRAAAGL
+>NAFOICDF_01550
+MSDTPTPTPSAAAQPYRGVGGGDLRLFTSESVTSGHPDKMCDQISDAILDAILAADPSAK
+VAVETLSTTGLVQVAGEVNTSAYVEIPHIVRETILDIGYDSSANGFDGAQCGVNVSIGQQ
+SSDIFAGVSRSLEAREQGSADEVDEQGAGDQGIMFGYATNETPSYMPTPIYLAHRLSERL
+TAVRRQENTPMPYLLPDGKTQVTVGYDADHRPRTVETVVVSTQHHDVVTQEQLRADVAEH
+VIRPVIERSGLDVSNARFIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG
+KDPSKVDRSAAYALRWVAKNVVAAGLAGRAEFQVAYAIGSARPVGLYVDTFGTNAVPEET
+IIAAVNEVFDLRPAAIVKSLNLLRPIYRKTAAHGHFGRDDADFTWERTDKVEELRRAAGV
+>MHAAABBN_00954
+MTDAASLSPARHADPYSGVGGGELRLFTSESVTAGHPDKICDQISDAILDAILAADPSAK
+VAVETLTTTGLVQVAGEVNTSAYVEIPRIVRETILDIGYDSSANGFDGAQCGVNISIGQQ
+SSDIFAGVSRSLEAREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL
+TAVRRAENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHEWVTQEQLRADVEEH
+VIRPVIERSGLDTSGMRIIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG
+KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTATVPEEK
+IIEAVNAVFDLRPAAIVKELNLLRPIYRRTAANGHFGRDDADFTWERTDRVEQLRAAAGL
+>LFPAFLNI_01193
+MTDAASLSPARHADPYSGVGGGELRLFTSESVTAGHPDKICDQISDAILDAILAADPSAK
+VAVETLTTTGLVQVAGEVNTSAYVEIPRIVRETILDIGYDSSANGFDGAQCGVNISIGQQ
+SSDIFAGVSRSLEAREYGSADEVDEQGAGDQGIMFGYATDETPAYMPMPIYLAHRLSERL
+TAVRRAENTPMPYLLPDGKTQVTIGYAPGHVPTTVEAVVVSTQHHEWVTQEQLRADVEKH
+VIRPVIERSGLDTSGMRIIINPGGKFVIGGPVGDAGLTGRKIIVDTYGGMARHGGGAFSG
+KDPSKVDRSAAYMLRWVAKNVVAAGLASRAEFQVAYAIGSARPVGLYVDTFGTATVPEEK
+IIEAVNAVFDLRPAAIVKELNLLRPIYRRTAANGHFGRDDADFTWERTDRVEQLRAAAGL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001130.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001130.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0da452c60c6c44d921370254b8bc9c05d4cf9cef
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001130.fa
@@ -0,0 +1,65 @@
+>ACLBLIBL_01654
+MARVLLDSPVPHLDREFDYLIPVTLDERARPGSRVAVRFGGRPMTGWLVSREDEPATGAQ
+LTELTAVLTSVPPLTEEVLASARAVARRQAGVVTDVLRAAVPPRVAQVEKAALAEDAGAA
+ADHPVALAVEEAPEGEPVGAGDGIAPTVWESLEGGRAFVAAVLAGDGPRAAAVVPSRLLE
+WDEAAAMAHLARAVAAGGGGVLLLVPDHRDLDRLCAALDDAVGEEAYARIGSEDGNTPRY
+RAHLAALRGTRRIVAGTRAAAWAPVRDLRLTVLWDDGDDAWAEPRAPYFHAREVVLERTR
+RTGSALLFAGPSRSVPVQRLVESGWLLHLGPSRAAQREIGPRIVSTADAWETARDPFAQR
+ARLPQAAWGAARAALLGERPGPVLVQVARAGFIPALVCDRCRTPARCRRCAGPLGFRDAR
+AARLGEVACRWCGTRERGFRCTECGAGALRAGARGVDRTAEELGRAFPRIPVHSSSAQHR
+LGTIPPGPSLVVATVGAEPVAEDGYAAALLLDGDAQLQREGLDVPGRVLARWLAAACLVR
+PAADGGVVVVTADAGEAVNALVRRDPDGFAAHQVAERRELHLPPAGRLAEVTGEASAVRE
+YLDLVEAARRERPEEDVHEDPHSAPLDGGPARLPWIGPVPDAADETRSRALLLFPYAAAD
+ATVAALRAARSAASARRETSPVRVRLDPAGVL
+>MOLHKGIG_01234
+MPHLDREFDYLVPVALDARAVPGSRVSVRFGGRAMTGWLVSREQEPATGAQLTELTGVLT
+VIPPLTEEVLATARAVARRQAGVVTDVLRAAVPPRVAQVEKAALAEDAEAAADHPVTLTG
+TDAERPEPPAAEEGLVPTVWESLEGGTAFVSAVLAGDAARAAAVVPSRLFEWDEAGALAA
+LARTVAASDGGVLLLVPDHRDLDRLCAALDEHVGEDAYARIGSEDGNTPRYRAHLAALRG
+TRRIVAGTRAAVWSPVRDLRLVVLWDDGDDAWAEPRAPYFHAREVVLERARATGAALLFA
+GPSRSVPVQRLVESGWLLHLGPSRAAQRELGPRVVSTADAWETARDPFAQRARLPQAAWA
+AARAALLGPRPGPVLVQVARAGFIPALVCERCRTPARCRVCAGPLGFRDARAARHGEVAC
+RWCGTRERGFRCTECGGTTLRAGARGVDRTAEELGRAFPRVPVHASSAQHMLGSVPPGPS
+LVVATVGAEPVTPDGYAAALLLDGDSQLQREGLDVPGRVLARWLAAACLVRPASDGGVVV
+VTADASEAVNALVRRDPDGFAARQVAERRELHLPPAGRLAEVSGDAAAVAEYLELVEAAR
+RERPDEDIHEDPHSAPLDGGPARLPWIGPVPDPADETRSRALLIFPYAAAEATVGALRAA
+RSAASARRETAPVRVRLDPAGVL
+>NAFOICDF_01551
+MARVLLDSPVPHLDREFDYLVPPALDERAVPGSRVSVRFGGRETTGWLVERVAAPATHAR
+LTELAGVLTAVPPLTEHVLAVARAVAARQAGVVSDVLRSAVPPRVVSVEKEVLAELASGP
+EVDHPVQGVVADPHARLVWEELTGGTAFVASAVAGDPVRAAAVVPSRVGDWDESSALAAL
+ATAVSRAGGGVLLLVPDHRDLDRLSAALAREVGEDGFVRVGSEDGNTPRYRAHLRALTGL
+ARVVAGTRAAAWAPVQDLRLVVVWDDGDDAHAEPRAPYFHVREVALERARQSGSALLFAG
+PSRSVPVQRLVEHGWLLEVSADRASQRAASPRIVASADSWESARDPFARRARLPHAAWAA
+AGEALSGPTPGPVLVQVARAGFIPAVVCGRCRTPARCRVCAGPLAFRDRRSAERGELACR
+WCGTRERDFHCAECGFTGLRAGVRGVDRTAEELGRAFPQVPVHSSSADHRLGEVGEGPAL
+VVATVGAEPHARGGYAAALLLDGDAQLQREGLDVPVRVLTRWLAAASLVRPAAEGGTVVV
+TAEHDAAVGALVRRDPQGFAGHLLAERRELHLPPAGRLAEVTGEAGAVAEYLALVEAARR
+ERRRVGPDADPSLDLDVEARPGDATPLPWIGPVPDVADESRSRALLLFPWAASAATVDAL
+RVARSAASARRERSAVRVRLDPPGVL
+>MHAAABBN_00953
+MPHLDREFDYLVPVALDDRAVPGSRVSVRFGGRAMTGWLVSREQEPATGAQLTELTGVLT
+VIPPLTEEVLATARAVARRQAGVVTDVLRAAVPPRVAQVEKAALAEDAETAADHPVTLTG
+TDAERPEPPAAEEGLVPTVWESLEGGTAFVSAVLAGDAARAAAVVPSRLFEWDEAGALAA
+LARTVAASDGGVLLLVPDHRDLDRLCAALDEHVGEDAYARIGSEDGNTPRYRAHLAALRG
+TRRIVAGTRAAVWSPVRDLRLVVLWDDGDDAWAEPRAPYFHAREVVLERARATGAALLFA
+GPSRSVPVQRLVESGWLLHLGPSRATQRELGPRVVSTADAWETARDPFAQRARLPQAAWA
+AARAALLGPRPGPVLVQVARAGFIPALVCERCRTPARCRVCAGPLGFRDARAARHGEVAC
+RWCGTRERGFRCTECGGTTLRAGARGVDRTAEELGRAFPRVPVHASSAQHMLGSVPPGPS
+LVVATVGAEPVTPDGYAAALLLDGDSQLQREGLDVPGRVLARWLAAACLVRPASDGGVVV
+VTADAGEAVNALVRRDPDGFAARQVAERRELHLPPAGRLAEVTGEAAAVAEYLELVEAAR
+RERPDEDVHEDPHSAPLDGGPARLPWIGPVPDPADEIRSRALLIFPYAAAEATVGALRAA
+RSAASARRETAPVRVRLDPAGVL
+>LFPAFLNI_01192
+MPERAEGWPERPIARVLLDSPVPHLDREFDYLVPVALDARAVPGSRVSVRFGGRAMTGWL
+VSREQEPATGAQLTELTGVLTAIPPLTEEVLATARAVARRQAGVVTDVLRAAVPPRVAQV
+EKAALAEDAEAAADHPVTLTGTDAERPEPPAAEEGLVPTVWESLEGGTAFVSAVLAGDAA
+RAAALVPSRLFEWDEAGALAALARTVAASGGGVLLLVPDHRDLDRLCAALDEHVGEDAYA
+RIGSEDGNTPRYRVHLAALRGTRRIVAGTRAAVWSPVRDLRLVVLWDDGDDAWAEPRAPY
+FHAREVVLERARATGAALLFAGPSRSVPVQRLVESGWLLHLGPSRAAQRELGPRVVSTAD
+AWETARDPFARRARLPQAAWAAARAALLGPRPGPVLVQVARAGFIPALVCERCRTPARCR
+VCAGPLGFRDARAARHGEVACRWCGTRERGFRCTECGGTTLRAGARGVDRTAEELGRAFP
+RVPVHASSAQHMLGSVPPGPSLVVATVGAEPVTPDGYAAALLLDGDSQLQREGLDVPGRV
+LARWLAAACLVRPASDGGVVVVTADAGEAVNALVRRDPDGFAARQVAERRELHLPPAGRL
+AEVTGEAPAVAEYLELVEAARRERPDEDVHEDPHSAPLDGGPARLPWIGPVPDPADETRS
+RALLIFPYAAAEATVGALRAARSAASARRETAPVRVRLDPAGVL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001134.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001134.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9deb5294b2824367c7b55f10e4a9cc61c647d882
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001134.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01658
+MATIEQWRDDALVRLRSRRSQLVGRARYGLKPPRRDRTAVVTDSAAALPAAALGHSLAAG
+IRQVPLPVMVGDQIHAEGTDDLALELPLALAAGTAVRTSRPSPGAFRSVYAQLAREGYAR
+ILSVHLSGELSGTAEAARLAAVDAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMTVARI
+RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLIGTLLHVRPVLAVDDGAISLVDRPR
+SAARAVDRLVELATERAGDVPVRIAVHEYGDPETAAALAERLTPVSTTPVPVVELPAVLA
+AHLGLGALGVVVCPLESPTGGSGD
+>MOLHKGIG_01230
+MASIEQWRDDALVRLRSRRSQLAGRARYGLRPPRRDRTAVVTDSAAALPGAVLGHGLAAG
+IRQVALPVMVGEQIHTEGTDELALELPLALAAGTPVRTSRPSPGAFRTVYAELARAGYAR
+ILSVHLSGELSGTVEAARLAAADAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMPVARI
+RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLLGTLLQVRPVMAVDDGAIGLVDRPR
+SAARAVDRLVELAVERAGEDPVRIAVHEYGDPETAMQLAERLQPISTTPVPVVELPAVLA
+AHLGLGALGVVICPLESPTGGSGD
+>NAFOICDF_01555
+MASTSQWLEDAVERLRARRGQLVGRARYGLKPARRDRTGIVTDSAAALPVEVFAHPFAAG
+IRQVALPVMVGEQIHVEGDADLDLELQLALAAGTPVRTSRPAPGAFRAAYADLAQAGCAR
+ILSVHLSGELSGTVEAARLAAADAPVPVVVLDSRTAGLALGHAVLDAAVEAGFGRPLDQV
+AAIAQACADQSSVLFTVPHLEQLRRGGRIGAVPSLLGALLQVRPVLGLQDGSVHLVDRAR
+TSPRALERMVDLARERAAGGPARIAVHEYGDPAGATALAERLQSASATPVPVVPLPAVLA
+AHLGLGTLAVVLSPLEPVPSTSSSPAQAN
+>MHAAABBN_00949
+MASIEQWRDDALVRLRSRRSQLAGRARYGLRPPRRDRTAVVTDSAAALPGAVLGHGLAAG
+IRQVALPVMVGEQIHTEGTDELALELPLALAAGTPVRTSRPSPGAFRTAYAELARAGYAR
+ILSVHLSGELSGTVEAARLAAAEAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMPVARI
+RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLLGTLLQVRPVMAVDDGAIGLVDRPR
+SAARAVDRLVELATERAGEDPVRIAVHEYGDPETAVQLAERLQPVSTTPVPVVELPAVLA
+AHLGLGALGVVICPLESPTGGSGD
+>LFPAFLNI_01188
+MASIEQWRDDALVRLRSRRSQLAGRARYGLRPPRRDRTAVVTDSAAALPGAVLGHGLAAG
+IRQVALPVMVGEQIHTEGTDELALELPLALAAGTPVRTSRPSPGAFRTAYAELARAGYAR
+ILSVHLSGELSGTVEAARLAAAEAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMPVARI
+RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLLGTLLQVRPVMAVDDGAIGLVDRPR
+SAARAVDRLVELATERAGEDPVRIAVHEYGDPETAVQLAERLQPVSTTPVPVVELPAVLA
+AHLGLGALGVVICPLESPTGGSGD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001135.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001135.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5677bce890435be3e6bc524e840cd8261400114a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001135.fa
@@ -0,0 +1,31 @@
+>ACLBLIBL_01659
+MSHPHRLAPDAALSDDPRRGRPASDLVPVPPALAARGPSAWERVPPRGRVLRWRPALLAV
+TVLLVAAAAWWAVAWLTSPAPPSPAPAASAVEARVEPETEDGPDAADAAPPSDGAGPAAE
+PSGGSGPVATLLRVHVVGEVERPGVVSLAPGARVADAVRAAGGATREARTERINLAAPLA
+DGRQVLVPSARTPEEDLARVAGGQDGPGGPEGGAAGTAPDAAASAPAGPARAGGSGGAGA
+GPVDLNAADAVALQTLPGVGPATAEKIIAHRETVGPFTGLQDLDAVPGVGPAALERLRDR
+VTW
+>MOLHKGIG_01229
+MSPSHRLCDDPPAFAPDPAAVPDVDTAGPHAASRWERTPPRGPVLRWRPALLAVTVLLVA
+AAAWWAVAWLTTPAPPAAVPAAAAGAGIPQTGAPSAASTAAGTDARTPEAGPSGEASGSA
+GSTPLRVHVVGEVARPGVVSLAPGSRVADAVRAAGGPTRHARAERINLAAPLDDGQQVLV
+PSAHTPQDALDRVAGAAQAQPTPTTGGAGATGEPGGAEPRGTVDLNTADAAGLQTLPGVG
+PATAEKIIAHRETVGPFTGLQDLDAVPGIGPATLDRLRDLVSW
+>NAFOICDF_01556
+MDTKTLTPAVDEPDWEDPPPRGPLLRWRTAGAGLTLVAILGLTWWLVAWLTAPAPPDAVP
+AGAVGSASAAGSAAHEASAAPLRATAATPEGQDGGGRSAAAANPSGRVRVHVVGQVRRPG
+VVELPAGARVADAVAAAGGARELARTDRINLAAPVVDGQQVVVPDAQTAVEPAAVAGEAP
+DGGPTPRTGSGASAADGSGGGPATVDLNTADLAALQTLPGVGPATAEKIIAQRESVGPFS
+GLQDLDAVPGIGPATLDRLKDHVTW
+>MHAAABBN_00948
+MRDAPDSATGPQTARMSPSHRLCDDPPAFAPDPAPAAAPDVDTAGPHAASRWERTPPRGP
+VLRWRPALLAVTVLLVAATAWWAVAWLTTPAPPAAIPAAAAGAGIPQTDAPSTAPSAAGT
+DARTSEAGPSGEASGPAGSGPLRVHVVGEVARPGVVSLAPGSRVADAVGAAGGPTRHARA
+ERINLAAPLDDGQQVLVPSARTPQDALDRVAGAAQAQPTPTTGRAGGGGEPGGAESGDTV
+DLNTADATELQTLPGVGPATAEKIIAHRETVGPFTGLQDLDAVPGIGPATLDRLRDHVSW
+>LFPAFLNI_01187
+MSPSHRLCDDPPAFAPDPAPAAAPDVDTAGPHAASRWERTPPRGPVLRWRPALLAVTVLL
+VAATAWWAVAWLTTPAPPAAIPAAAAGAGIPQTDAPSTAPSAAGTDARTSEAGPSGEASG
+PAGSGPLRVHVVGEVARPGVVSLAPGSRVADAVGAAGGPTRHARAERINLAAPLDDGQQV
+LVPSARTPQDALDRVAGAAQAQPTPTTGRAGGGGEPGGAESGDTVDLNTADATELQTLPG
+VGPATAEKIIAHRETVGPFTGLQDLDAVPGIGPATLDRLRDHVSW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001138.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001138.fa
new file mode 100644
index 0000000000000000000000000000000000000000..16a9a7f6c6b1db30535a0eb856fed55c596357a2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001138.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01662
+MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG
+>MOLHKGIG_01226
+MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEPEAAAAALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG
+>NAFOICDF_01559
+MANIKSQKKRILTNEKARQRNIAVKSELKTAIRAVDKAVAAGEQDAAVEALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG
+>MHAAABBN_00945
+MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG
+>LFPAFLNI_01184
+MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001139.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001139.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71c3e020c03c0d16142460f98fa824fbb0761dd7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001139.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01663
+MAFDLNRALALGRRAIRLIGSLRDDDARRSWTGDAAGRGSGAAPFPGPPGPAGRAWDPKE
+PTDSWPFPDRGHDGRPRGGQDRTRPASGATDPQGRALLADFTGMGRVEYAPVPGPAAGPG
+EVVWTWVPYEEMDGRGKDRPVLLVGRDGDLLLGLMLTSRDRNNARVRDEDYVDVGSGPWD
+RAGRPSEAKLDRVLRVDPAAVRREGGVLDPAAFERVGDALARAQGWRR
+>MOLHKGIG_01225
+MAFDLHRALSLGRRTARLIGALRDDARPRRAASEAGRRAGDRSGPSPFPGPPGPPGPAWD
+PTEPTDSWPMPGPGQERRPRRQDAGRHVSLPDFTGTVRVEYAPVPGPTAGPGEVVWTWVP
+YEEMDGRGKDRPVLLIGRDGAHLLGLMLTSRDRNNALARDEDYVDVGAGAWDRSGRASEV
+KLDRVVRVDPAAVRREGGVLDRAAFDRVTAALARARRRGR
+>NAFOICDF_01560
+MAFDFQRALTLGRTALRLVEQVRSMSGAGTTRGAAPSSPASRAGRRRRADAEETRGARSG
+GAGSDHALLPDFTGRARVEYAPVPGATPDPGEVVWTWVPFEEMDGRGKDRPVLLVGRDGD
+LLLALMLTSKDHTNAARRDADYVDVGTGPWDRGGRASEAKLDRILRVDPAAVRREGGVLE
+RSRFDAVAEALARAQGWDR
+>MHAAABBN_00944
+MAFDLHRALSLGRRTARLIGALRDDARPRRAASEAGRRAGERSGPSPFPGPPGPPGPAWD
+PTEPTDSWPMPGPGQERRPRRQDTDRHVSLPDFTGTVRVEYAPAPGPTAGPGEVVWTWVP
+YEEMDGRGKDRPVLLIGRDGALLLGLMLTSRDRNNALTRDEDYVDVGAGAWDRSGRASEV
+KLDRVVRVDPAAVRREGGVLDRAAFDRVTAALARARRRVR
+>LFPAFLNI_01183
+MAFDLHRALSLGRRTARLIGALRDDARPRRAASEAGRRAGDRSGPSPFPGPPGPPGPAWD
+PTEPTDSWPMPGPGQERRPRRQDTGRHASLPDFTGTVRVEYAPVPGPTAGPGEVVWTWVP
+YEEMDGRGKDRPVLLIGRDGAHLLGLMLTSRDRNNARARDEDYVDVGAGAWDRSGRASEA
+KLDRVVRVDPAAVRREGGVLDRAAFDRVTAALARARRRGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001144.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001144.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6d972cb1d24f4b75a2e68e6a2b38fe73e1cd34bf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001144.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01669
+MTDHYATLGVSRDASTEEIRRAYRKLARTHHPDVNPDPESAEQFKRISHAYEVLSDEGRR
+RAYDTTGNENGQSGFPGGFGGGGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT
+APIDLEDAVFGGEQTITLDTAVRCKRCEGSCCEPGTEPETCQTCQGHGMIQRPMRSLLGT
+VMATEACPACQGFGTVIPDPCHECAGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP
+GGGPNGDLYVEIAVRPHETFRREGDHLATTVTVPMAAAALGTTVTLATLDGEQTVRLEPG
+VQSGHVETLAGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRELLERLAELRGEEVVHGT
+PPARGMFARLRENLRNL
+>MOLHKGIG_01219
+MTDHYETLGVSRDASTEEIRRAYRKLARTHHPDVNPDPEAAEQFKRISHAYEVLSDEGRR
+RAYDTTGNENGQAGFPGGFGGAGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT
+ARIDLRDAVFGGEQTIELDTAVRCDRCEGSCCEPGTQPETCQTCHGHGMIQRPVRSLLGT
+VMATEACPACQGFGTVIPTPCHECDGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP
+GGGPNGDLYVEIAVRPDETFRREGDHLATTVTVPMAAAALGTTVTLDTLDGKQSLSLDPG
+VQSGHVEVLHGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRQLLERLAEVRGEEVVHGA
+PQAKGMFARLRENLRNL
+>NAFOICDF_01566
+MADHYATLGVSRDASAEEIKRAYRKLARQHHPDVNPSEEAAEEFKRISHAYEVLSDEDKR
+RVYDQTGNENGTAGGFGGGGFGGAGFGGFADIFETFMNAAGTPGGGRGPMPRARRGQDAL
+VTARIELRDAVFGGEATLQLDTAVTCERCSGTCCEPGTHPETCSTCQGQGMTQRPVRSML
+GTIMAAETCPVCRGFGTVIPHPCTECSGQGRVRVQQPLTIRIPAGVDDGTRIHLAGRGEA
+GPGGGPNGDLYVEVQVRPDEVFRREGDHLATTVTVPMAAAALGTSVTLETLDGPQEVDIE
+PGTQSGHVETLRGLGVGRLRGAGRGDLKVDVVVTTPTDVTDEQRALLEQLAGLRGEEVVH
+GAPPQSKGMFARLRENLKNL
+>MHAAABBN_00938
+MTDHYETLGVSRDASTEEIRRAYRKLARTHHPDVNPDPEAAEQFKRISHAYEVLSDEGRR
+RAYDTTGNENGQAGFPGGFGGAGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT
+ARIDLRDAVFGGEQTIELDTAVRCDRCEGSCCEPGTQPETCQTCHGHGMIQRPVRSLLGT
+VMATEACPACQGFGTVIPTPCHECDGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP
+GGGPNGDLYVEIAVRPDETFRREGDHLATTVTVPMAAAALGTTVTLDTLDGKQSLSLDPG
+VQSGHVEVLHGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRQLLERLAEVRGEEVVHGA
+PQAKGMFARLRENLRNL
+>LFPAFLNI_01177
+MTDHYETLGVSRDASTEEIRRAYRKLARTHHPDVNPGPEAAEQFKRISHAYEVLSDEGRR
+RAYDTTGNENGQAGFPGGFGGAGGFGGFADIFETFMNAAGQGGRGGPASRARRGQDALVT
+ARIDLRDAVFGGEQTIELDTAVRCDRCEGSCCEPGTQPETCQTCHGHGMIQRPVRSLLGT
+VMATEACPACQGFGTVIPTPCHECDGQGRVRTRTPLTLRIPAGVDDGTRIHLAGRGEAGP
+GGGPNGDLYVEIAVRPDETFRREGDHLATTVTVPMAAAALGTTVTLDTLDGKQSLSLDPG
+VQSGHVEVLHGLGVGRLRGQGRGDLKVDVVVTTPTDLDDEQRQLLERLAEVRGEEVVHGA
+PQAKGMFARLRENLRNL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001148.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001148.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb6e494f302361ac9b288e84ff47714c8426ad19
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001148.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_01673
+MLTPAVLFALFLVFLALVWTLSLAESAFTYLSRRDAEDIVRRRPGSRVLDVTAERDSHLG
+ALRVWRFVAEALSAVCLTAAADAVVDNTWFAVLIAAAVLVGVAALLGVWSPRPFGSRNEA
+AVARRLGGLVWGLRRALGPLADRLGRDRRRREDELEEEDDFQERHLREVVARAHDADVLA
+DSEAELIQSVFSMNDTIVRSVMVPRTDVVTIDADHTLGQAMALFLRSGNSRIPVIGEDAD
+DIRGMLHLKDVTRALHQDGAAQSGPVTAAMRDVRFVPESKSVAALLQELQRESTHVAVVV
+DEYGGTAGLVTLEDLIEEIVGEIYDEDDLPDRAEVEMIEPGVYSVDARMGLHHFREEFEL
+PEEEDEDDDVDTVGGLLAKELGRVPIQGSRVVVQGLELLADTLEPRRNRVARLRVSETPD
+RPARLRRRDEEPHGSSAAETAA
+>MOLHKGIG_01215
+MLTPAVLFALFLVFLGLTWTLSLAESAFSYLSRRDAEDIVRERPGSKVLEIARERESHLG
+ALRVWRFVAEALSAVCLTAAADAVVDDTWLAVAIAAVVLVGVAALLGVWSPRPIGSRNEA
+AVARRLGGLVWVLRRALGPLAARLDRDRRRREVEPEDEDDFQERHLREFVARAHDADVLA
+DSEAELIQSVFSMNDTIVRSVMVPRTDVVTIDADHTLGQAMALFLRSGNSRIPVIGEDAD
+DIRGMLHLKDVTRALHHDGAATDTPVTEVMRDVRFVPESKSVATLLQELQRESTHVAVVV
+DEYGGTAGLVTLEDLIEEIVGEIYDEDDQPDRPEVEFVAPGVYSVDARMGIHDFREEFEL
+PEEDEDDDVDTVGGLLAKELGRVPIQGSRVVVQGIELVADTLEPRRNRVARLRVSETPDR
+PVRLRRREEQAHGAAPADPVA
+>NAFOICDF_01570
+MATAVSLVLLFLACLACTWVLALAESAFTYLPRKDAEDVARTRPGSRILDVTADLDGHLG
+ALRVWRFLSEAFAAMFLTAGLHALTDSVWAALAVTAVLLVGTAAVLGVWSPRPIGSRNEA
+AVAARTAGLVHGLKQALGPVGDRLGRDRRRTEAEAADEDDFHERHLREVVARAHDAEVLE
+DSEAELIASVFSMGDTLVRSVMVPRTDVVTIDADHTLGQALDLFLRSGCSRVPVIGEDSD
+DVRGMLYLKDAVRALHHEGHASQDAVTAVMREVRFVPESKPVSVLLEELQRESTHVAIVV
+DEYGGTAGLVTLEDLIEEIVGEIWDEDDRPDRPEIEELAPGVYSVDARMGIGDFREEFEL
+PEDEDEDDDVDTVGGLLAKELGRVPIRGSRVVVHGLELTADTLEPRRNRVARLKVVETED
+RPARLRRQHDPTDPD
+>MHAAABBN_00934
+MLTPAVLFALFLVFLGLTWTLSLAESAFSYLSRRDAEDIVREQPGSKVLEIARERESHLG
+ALRVWRFVAEALSAVCLTAAADAVVDDTWLAVAIAAVVLVGVAALLGVWSPRPIGSRNEA
+AVARRLGGLVWVLRRALGPLAARLDRDRRRREVEPEDEDDFQERHLREFVARAHDADVLA
+DSEAELIQSVFSMNDTIVRSVMVPRTDVVTIDADHTLGQAMALFLRSGNSRIPVIGDDAD
+DIRGMLHLKDVTRALHHDGAATDTPVTEVMRDVRFVPESKSVATLLQELQRESTHVAVVV
+DEYGGTAGLVTLEDLIEEIVGEIYDEDDRPDRPEVEFVAPGVYSVDARMGIHDFREEFEL
+PEEDEDDDVDTVGGLLAKELGRVPIQGSRVVVQGIELVADTLEPRRNRVARLRVSETPDR
+PVRLRRREEQAHGAEPADPVA
+>LFPAFLNI_01172
+MLTPAVLFALFLVFLGLTWTLSLAESAFSYLSRRDAEDIVRERPGSKVLEIARERESHLG
+ALRVWRFVAEALSAVCLTAAADAVVDDTWLAVAIAAVVLVGVAALLGVWSPRPIGSRNEA
+AVARRLGGLVWVLRRALGPLAARLDRDRRRREVEPEDEDDFQERHLREFVARAHDADVLA
+DSEAELIQSVFSMNDTIVRSVMVPRTDVVTIDADHTLGQAMALFLRSGNSRIPVIGEDAD
+DIRGMLHLKDVTRALHHDGAATDTPVTEVMRDVRFVPESKSVATLLQELQRESTHVAVVV
+DEYGGTAGLVTLEDLIEEIVGEIYDEDDQPDRPEVEFVAPGVYSVDARMGIHDFREEFEL
+PEEDEDDDVDTVGGLLAKELGRVPIQGSRVVVQGIELVADTLEPRRNRVARLRVSETPDR
+PVRLRRREEQAHGAAPADPVA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001153.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001153.fa
new file mode 100644
index 0000000000000000000000000000000000000000..114c59077e820d598b1831ef461f04a1730274c7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001153.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01678
+MQLPDPKAAVDGVLTSRAPRLYPPFFRAVFGGMDAEQAHHRGFDAIRLAERTGASAALRA
+AFRPDPLLARTVMGLRFPTPFGLAAGFDKEGRGTAALADLGFGHIEVGTITAQAQPGNPQ
+PRLFRLVEDRALVNRMGFNNDGAAAVAPRLARTRAVLERRFGAVRPVLGVNIGKTKVVAL
+EDAAEDYRASTRLLTPHADYLTVNVSSPNTPGLRQLQEIDALEPILTAVREEADRVVTGR
+RVPLTVKIAPDLTDEDVRAVAALAERLGLDGVIATNTTISREGLATPRADVDALGAGGLS
+GAPLKERSTEVLRVLRAALPVGTAVISVGGVTDADDVQARLDAGADLVQGYTAFLYEGPF
+WAGRISAGLACALRG
+>MOLHKGIG_01209
+MQLPDPKSAVDGLLTSRAPRLYPPFFRAVFGGMDAEQAHHRGFDAIRLVERTGASAALRA
+AFRPDPLLARTVMGLRFPTPFGLAAGFDKDGRGTAALADLGFGHIEVGTITAQPQPGNPQ
+PRLFRLVDDRALVNRMGFNNDGAAAVAPRLARTRQTLERRFGPTRPVLGVNIGKTKVVPL
+EDAADDYRASTRLLAPHADYLTVNVSSPNTPGLRQLQEIDALEPILTAVREEADRAVPGR
+RVPLTVKIAPDLADDDVRAVGALAERLGLDGVIATNTTVSREGLRTPRADVDALGAGGLS
+GAPLQERSMRVLQVLRAALPTGTAVVSVGGVTDADDVQARLDAGADLAQGYTAFLYEGPF
+WAGRITAGLARSLRG
+>NAFOICDF_01576
+MQLPDPRFRVQSVLRSSAPRIYPPFFRAVFAGMDPERAHHVGFAGIRAAEASGASRALRS
+TMAPDLGLARTVMGLRFPSPFGLAAGFDKTGVGTTALAELGFGHIEVGTITAQAQPGNPA
+PRLFRLPEDRALINRMGFNNDGAAAVAPRLAATRRTLEERFGAVRPVLGVNIGKTKVVPL
+DGAVEDYRASARLLAPHADYLTVNVSSPNTPGLRQLQEISSLEPILAAVREEADRAVPDR
+RVPLTVKIAPDLADEDVRAVAELAGRIGLDGVIATNTTIGRGGLSTPASEVEAMGAGGLS
+GAPLAARSLEVLRTLRAALPAGVALIAVGGVTDGDDVLQRLDAGADLVQGYTAFLYEGPF
+WAGRINAGLDAAQRAR
+>MHAAABBN_00928
+MQLPDPKSAVDGILTSRAPRLYPPFFRAVFGGMDAERAHHRGFDAIRLAERTGASAALRA
+AFRPDPMLARTVMGLRFPTPFGLAAGFDKDGRGTAALADLGFGHIEVGTITAQPQPGNPQ
+PRLFRLVDDRALVNRMGFNNDGAAAVAPRLARTRQTLERRFGPARPVLGVNIGKTKVVPL
+EDAADDYRASTRLLAPHADYLTVNVSSPNTPGLRQLQEIDALEPILTAVREEADRAVPGR
+RVPLTVKIAPDLADADVRAVGALAERLGLDGVIATNTTVSREGLRTPRADVDALGAGGLS
+GAPLQERSMRVLQVLRAALPTGTAVVSVGGVTDADDVQARLDAGADLVQGYTAFLYEGPF
+WAGRTTAGLARSLRG
+>LFPAFLNI_01166
+MQLPDPKSAVDGLLTSRAPRLYPPFFRAVFGGMDAEQAHHRGFDAIWLVERTGASAALRA
+AFRPDPLLARTVMGLRFPTPFGLAAGFDKDGRGTAALADLGFGHIEVGTITAQPQPGNPQ
+PRLFRLVDDRALVNRMGFNNDGAAAVAPRLARTRQTLERRFGPARPVLGVNIGKTKVVPL
+EDAADDYRASTRLLAPHADYLTVNVSSPNTPGLRQLQEIDALEPILTAVREEADRAVPDR
+RVPLTVKIAPDLADDDVRAVGALAERLGLDGVIATNTTVSREGLRTPRADVDALGAGGLS
+GAPLQERSMRVLEVLRAALPTGTAVVSVGGVTDADDVQARLDAGADLVQGYTAFLYEGPF
+WAGRITAGLARSLRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001155.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001155.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c44b13acc39c7f830e262c463bf242d478a3079
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001155.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_01680
+MTETTPPVRDDAALVAAVRDAVDARFPQTLQTLTDLVAIPGIAWDSADRAQLERSSEAVA
+ALLRQAGLQGVEIVTETREDGRPGGPAVIGEKPGASDKPTVLLYAHHDVQPIGDEALWDT
+EPLVATEKGGRLYGRGAADDKAGIMVHLAALAALKDVLPDAGVGVRVFIEGEEEAGSPTF
+RTFLENHRARLEADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP
+VLDAVVLLSRLIATLHDADGAVAVPGLEPRRSASLDYPEDVFRADAGVLDSVTLAGRGPV
+ADRLWNAPALSVIGIDVPSVAESSNTIQPQARAKFSLRLGPGMDPAEAFEALKAHLEAQS
+AAVLGAEITVEAGEFGQPFDTDTSDPLAAAMMGALGDAWGVAPKEAGMGGSIPFTADLAE
+VFPDATILITGVEDPDSRAHSANESLHIEDFRRAVVAEALWFARLAG
+>MOLHKGIG_01207
+MTDITSRAPQDAALVSAVREAVEARFPTTLQTLTDLVAIPGIAWDSADRAQLERSAEAVA
+GLLREAGLQDVEIVSEIRDDGRPGGPAVIGEKPGTSDKPTVLFYAHHDVQPIGDEDLWDT
+PPLVATERGGRLYGRGAADDKAGIMVHLAALAALRDVLPDAGVGVRVFIEGEEEAGSPTF
+RTFLEKHRARLDADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP
+VLDAVVLLSRLIATLHDADGAVAVPGLEPRQTAGLDYPEDVFRADAGVLDGVTLAGRGPV
+ADRLWNAPALSIIGIDAPSVAESSNTIQPAARAKFSMRLGPGMEPAEAFEALRTHLEAQS
+AAVLGAEITVTAGEFGQPFTTDTSAPAAAAMMAALEDAWGVEPRAIGMGGSIPFTADLAE
+VFPEATLLITGVEDPDTRAHSANESLHIDDFQRAVVAEALWLARLSA
+>NAFOICDF_01578
+MTQSTQNTPVGAAPDPELVSAIRAAVDRRFPETLQSLKDLVSIPGIAWDSMDREPLERSA
+AAVADLLRTAGLEGVETAVEERADGRPGGPAVIGGRPAVGDKPTVLLYAHHDVQPLGEEG
+LWDTPPLVATERDGRLYGRGAADDKAGIMVHLAALAALDEVCPDAGVGVRVFIEGEEEAG
+SPTFRPFLERHRDRLAADAIVVADSSNWAVGEPALTTSLRGVVSATVTVRALDHAVHSGM
+FGGPVLDAVVLMSRLIATLHDADGAVAVPGLEPRHHADVDYPEDAFRADSGILPGTRLAG
+RGALADRLWNGPALSVIGLDAPSVDTSSNTIQPAARAKISLRLGPGMDPAASLDALRAHL
+EAQSDAVLGAEITVEPGELGQPFSTDTSAPAAAAMMGALGAAFATPARETGLGGSIPFTA
+DLKELFPEATILITGVEDPDSRAHSANESLHLEDFRRAIVAEALWLAAMGA
+>MHAAABBN_00926
+MTDITSRAPQDAALVSAVREAVEARFPTTLQTLTDLVAIPGIAWDSADRTQLERSAEAVA
+GLLRAAGLQHVEIVTETRDDGRPGGPAVIGEKPGASDKPTVLLYAHHDVQPIGDEDLWDT
+PPLVATERGGRLYGRGAADDKAGIMVHLAALAALRDVLPDAGVGVRVFIEGEEEAGSPTF
+RTFLEKHRARLDADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP
+VLDAVVLLSRLIATLHDADGAVAVPGLEPRQTAGLDYPEDVFRADAGVLDGVTLAGRGPV
+ADRLWNAPALSIIGIDAPSVAESSNTIQPAARAKFSLRLGPGMDPAEAFEALRTHLEAQS
+AAVLGAEITVTAGEFGQPFTTDTSATAAAAMMAALEDAWDVEPRAIGMGGSIPFTADLAQ
+VFPEATLLITGVEDPDTRAHSANESLHIDDFQRAVVAEALWLARLSA
+>LFPAFLNI_01164
+MTDITSRAPQDAALVSAVREAVEARFPTTLQTLTDLVAIPGIAWDSADRTQLERSAEAVA
+GLLREAGLQEVEIVTETRDDDRPGGPAVIGEKPGASDKPTVLLYAHHDVQPIGDEDLWDT
+PPLEATERGGRLYGRGAADDKAGIMVHLAALAALRDVLPDAGVGVRVFIEGEEEAGSPTF
+RTFLEKHRARLDADAIVVADSSNWAVGEPALTTSLRGLVDGTVTVRVLDHAVHSGMFGGP
+VLDAVVLLSRLIATLHDADGAVAVPGLEPRQTAGLDYPEDVFRADAGVLDGVTLAGRGPV
+ADRLWNAPALSIIGIDAPSVAESSNTIQPAARAKFSLRLGPGMEPAEAFEALRTHLEAQS
+AAVLGAEITVTAGEFGQPFTTDTSAPAAAGMMAALEDAWGVEPRAIGMGGSIPFTADLAE
+VFPEATLLITGVEDPDTRAHSANESLHIDDFQRAVVAEALWLARLSA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001156.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001156.fa
new file mode 100644
index 0000000000000000000000000000000000000000..44bb65cc3e05ff11fb03d0f08bed33eefcac2c61
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001156.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01681
+MALSADETGVEIGATQDSEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVQVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAV
+GSCACGDSFH
+>MOLHKGIG_01206
+MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAG
+GSCACGDSFH
+>NAFOICDF_01579
+MALSAEETGVEIGATEDATGLPPHEVELTDVAAAKVRALLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAV
+GSCACGDSFH
+>MHAAABBN_00925
+MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAG
+GSCACGDSFH
+>LFPAFLNI_01163
+MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYIMGATIDFEDTISKQGFTIDNPNAG
+GSCACGDSFH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001157.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001157.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b8ff68e6e3d090299adf33107b84637afc623e66
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001157.fa
@@ -0,0 +1,31 @@
+>ACLBLIBL_01682
+MGTTALLVLTGCSAEVQRGWYPGTRDTTNHNAQLTDLWVNSWIAAMVVGLLAWGAMIWCM
+VAYRRRKNDQGFPKQTAYNVPLETMFTIIPILMVFTLWGFTNRVQTEVDRPVDDSPLTVT
+VYGKQWSWDFNYSYEQENGEVVEANYSGIQAQLDGTEGVRDTLPVLYLPKDVPVHFELKS
+RDVAHSFWIPQFLQKRDLIPGKTNHLYLTPQELGSYDGKCAELCGEFHSEMLFNVEVVDE
+AEFVDRLAEMEPGLVGDEYSRNPNNNPDGAREMERDLQTPRGGGSH
+>MOLHKGIG_01205
+MGTTALLVLTGCSAEVQRGWYPGTRDTTNHNAQLTDLWVNSWIAAMVVGLLVWGAMIWCM
+VAYRRRKNDQGFPKQTAYNVPLETMFTAIPILTVFTLWGFTDRVQTEVDRPVDDSPLTVT
+VYGKQWSWDFNYSYEQEDGEVIEAHYSGIQAQLDGTEGVRDTLPVLYLPNDVPVHFELKS
+RDVVHSFWIPQFLQKRDMVPGKTNHLYLTPQELGSYDGKCAELCGEFHSEMLFNVEVVDE
+AEFVQRLEEMESGQVGEEYSRNPNNNPDGAGTMERDLQTPRGGGSH
+>NAFOICDF_01580
+MRAQNDAGRRTRRRLTAGALGATALVALTGCSAEAQRGWLPGTDNTTNHNAQLTDLWVNS
+WIAALAVGLIAWGAMIWCMIAYRRRKNDQGFPRQTAYHMPIETMFTVIPILMVFTLWGFT
+DRVQAEVDTPIDDSPLTVTVYGKQWSWDFNYSYEKDGQTREAHFQGVQAQLDGSDGKRET
+LPTLYLPKDVPVHFELKSRDVAHSFWIPQFLQKRDMLPGKTNNLYLTPQEIGRFDGKCAE
+LCGEFHSEMLFNVEVVDEATFVQKMNEMEPGLVGDELNRNPNQNPDGARNMEVDLQTPRG
+GGNH
+>MHAAABBN_00924
+MGTTSLLVLTGCSAEVQRGWYPGTRDTTNHNAQLTDLWVNSWIAAMVVGLLAWGAMIWCM
+VAYRRRKNDQGFPKQTAYNVPLETMFTAIPILMVFTLWGFTNRVQTEVDRPVDDSPLTVT
+VYGKQWSWDFNYSYEQENGEVIEAHYSGIQAQLDGTEGVRDTLPVLYLPNDVPVHFELKS
+RDVAHSFWIPQFLQKRDMVPGKTNHLYLTPQELGSYDGKCAELCGESHSEMLFNVEVVDE
+AEFVQRLEEMEPGQVGDEYSRNPNNNPDGAGTMERDLQTPRGGGSH
+>LFPAFLNI_01162
+MGTTALLVLTGCSAEVQRGWYPGTRETTNHNAQLTDLWVNSWIAAMAVGLLAWGAMIWCM
+VAYRRRKNDQGFPKQTAYNVPLETMFTAIPILMVFTLWGFTDRVQTEVDRPVDDSPLTVT
+VYGKQWSWDFNYSYEQENGEVIEAHYSGIQAQLDGTEGVRDTLPVLYLPNDVPVHFELKS
+RDVAHSFWIPQFLQKRDMVPGKTNHLYLTPQELGSYDGKCAELCGEFHSEMLFNVEVVDE
+AEFVQRLEEMEPGQVGDEYSRNPNNNPDGAGTMERDLQTPRGGGSH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001161.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001161.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4282fe4fee1ad5545d8864419210ef7641e17617
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001161.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01687
+MGEKGFEGTEHGSGSLEHAGEDAPRYAIDNPGLPPHRPRLADEDPKAAKRAERQVSVMFL
+ISIVGTLLFFVGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD
+HETVEDRHEIRSEADRVAATGMISEILDESQIKRRPLLRNTLIGAAVLAPLPFIAVFRDL
+DDSDNFSDEETHNFGPERLRHTMWSEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL
+GPDKLNQKAKAVVLLMRLDPAKVKITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGFLVAQSDFHEPVGPVYWERG
+>MOLHKGIG_01200
+MGEKGLEGTERRSGSLEHAGEDAPRYAIDDPGLPPHRPRLADEDPKAAKRAERQVSVMFL
+ISIVGTVLFFIGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD
+HETVEDRHEIRSEDDRVAATGMISEILDESQIKRRPLLRNTLIGAALLAPLPFIAVFRDL
+DDSDNFSDQEAHNFGPERLRHTMWAEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL
+GPDKLNQKAKAVVLLMRLDPAKVRITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGFLVAQSDFHEPVGPVYWERG
+>NAFOICDF_01584
+MGEKGYEGAERHSDALEHAGEESPRYAIDNPGLPPHRPRLADEDPRAAKRAERQVSVFFL
+ISVIGTVLFFIGYFGVGQVGNGESTSVLYLQNLLLGLGVALAMFGIGIGVVHWAKTLMPD
+HEVVEERHEIRTEADRAAAQGMIADILDESQIKRRPLLRNTLIGAAVLAPLPFIAAFRDL
+DNTDNFSDEAAKNFGPERLRHTMWHEGVRLVRDPTGSPIKASDVTLGSALHVIPDGLNDL
+EHGKLNEKAKAVVLVMRLDPSKVKISPGRENWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLAQECKVIFGPASHALPQLPITVDDEGYLVAQSDFHEPVGPVYWERG
+>MHAAABBN_00920
+MGEKGFEGTEHRSGSLEHAGEDAPRYAIDNPGLPPHRPRLADEDPKAAKRAERQVSVMFL
+ISIVGTVLFFIGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD
+HETVEDRHEIRSEDDRVAATGMISEILDESQIKRRPLLRNTLIGAALLAPLPFIAVFRDL
+DDSDNFSDQEAHNFGPERLRHTMWAEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL
+GPDKLNQKAKAVVLLMRLDPAKVKITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGYLVAQSDFHEPVGPVYWERG
+>LFPAFLNI_01154
+MGEKGFEGTEHRSDSLEHAGEDAPRYAIDNPGLPPHRPRLADEDPKAAKRAERQVSVMFL
+ISIVGTVLFFIGYFGVGQIGNGEAFSKIYLQNLLLGLGTALAMFGIGIGVVHWAKTLMPD
+HETVEDRHEIRSEDDRVAATGMISEILDESQIKRRPLLRNTLIGAALLAPLPFIAVFRDL
+DDSDNFSDEEIHNFGPERLRHTMWAEGVRLVRDPTGSPIKASDVTLGSAVHVIPDGLNDL
+GPDKLNQKAKAVVLLMRLDPAKVKITPGREDWNVDGIFAYSKVCTHVGCPIALYEQHTHH
+LLCPCHQSTFDLTQECKVIFGPASHALPQLPITVDDEGYLVAQSDFHEPVGPVYWERG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001162.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001162.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e374325db17d4e941671180db01e38898974a7f4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001162.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01688
+MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDITEGEKLF
+NANCATCHGMGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAPAKPNQFNEEQTA
+QLAAYVASLGAGPAIPEDEYLDINNEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKFA
+PSLQGVEEKYIYEAMETGPQNMPVFSDANIKPEDKRDIIAYLKTIENQGSPGGLSLGSLG
+PVSEGLFIWTAGLALIIGFMVWLTSRSS
+>MOLHKGIG_01199
+MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDISEGEKLF
+NANCASCHGTGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAQVKPNQFNDEQTA
+QLAAYVASLGAGPAVPEDEYLDVNHEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKYA
+PSLQGVEEKHIYEAMETGPQNMPVFSDSNIKPEDKRDIIAYLKTIENQGSPGGLALGSLG
+PVSEGLFIWTAGLALIIGFMVWLTSRSS
+>NAFOICDF_01585
+MKALSQNRRHPLVGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAAAADDITAGEKLF
+NANCASCHNMGATGTADGPSLVGVGAAAVDFQVGTGRMPMQMNGPQAQRKPNQFSEEQTA
+QLAAYVASLGAGPAVPADEDLDPNAEGVNIAKGGDLFRINCAMCHNAAAAGGALTRGKFA
+PSLEGVSEKHIYEAMETGPQNMPVFSDANLKPEDKRDIIAYLKTIEANGSPGGLQLGSLG
+PVAEGLFIWTAGLALIVGFMVWLTSRSS
+>MHAAABBN_00919
+MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDITEGEKLF
+NANCASCHGMGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAPAKPNQFNEEQTA
+QLAAYVASLGAGPAIPEDEYLDVNHEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKYA
+PSLQGVDEKHIYEAMETGPQNMPVFSDSNIKPEDKRDIIAYLKTIENQGSPGGLTLGSLG
+PVSEGLFIWTAGLALIIGFMVWLTSRSS
+>LFPAFLNI_01153
+MKALSQNRRHPLMGLALLLLGLLVTGGLYSVASTVNQAQAATQVTAAASADDISEGEKLF
+NANCASCHGTGAAGGPSGPSLIGVGAASVDFQVGTGRMPMQMNGPQAQVKPNQFNDEQTA
+QLAAYVASLGAGPAVPEDEYLDVNHEDVDITRGGDLFRINCAMCHNAAAAGGALTRGKYA
+PSLQGVEEKHIYEAMETGPQNMPVFSDSNIKPEDKRDIIAYLKTIENQGSPGGLALGSLG
+PVSEGLFIWTAGLALIIGFMVWLTSRSS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001163.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001163.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e2c8b42885cc402dbe01304b4061493c1e27900c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001163.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01689
+MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAENTAILNVPLAAANTLILVLSSVT
+AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTIA
+ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV
+WIALFFIVYFLK
+>MOLHKGIG_01198
+MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTTILVLSSVT
+AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTVA
+ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV
+WIALFFIVYFLK
+>NAFOICDF_01586
+MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTVILVLSSFT
+AQFGVLAAERLQPRRTGGLFSVKSWGMVEWFILTFIMGSIFVAVQAFEYATLVSEGVTIA
+ANAYGSAFYITTGFHALHVTGGLIAFLFIIGRAFLARRFGHHEATSAIVVSYYWHFVDVV
+WIALFFIVYFLK
+>MHAAABBN_00918
+MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTTILVLSSVT
+AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTVA
+ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV
+WIALFFIVYFLK
+>LFPAFLNI_01152
+MVQVGTMVWLASELMFFGGLFAMYFTLRSTSPELWAEHTAILNVPLAAVNTTILVLSSVT
+AQFGVLAAERLQPRRTGGFLQFGKWGMVEWFILTFIMGSIFVAVQSYEYAVLVSEGVTVA
+ANAYGSAFYITTGFHAIHVTGGLIAFLFIIGRAYMARRFGHHEATSAIVVSYYWHFVDVV
+WIALFFIVYFLK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001166.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001166.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d18710ae06e347f4ac95b7c2714e8d4fd84ddc50
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001166.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01692
+MADTLSENRSETMAQTGGMTDSPTRRHSPASPPSPLWAATALAVDAVLVVVFVALGQDQH
+TTDRGLGGLLATALPFLLGLVAATVLTAGHRTWHRVWPHGVAVWLGTVAVGMALRVLWDQ
+GGAPLSFVLVALGVLGVFLLGRRAVTAWVIRRRARV
+>MOLHKGIG_01195
+MTSSPTARRAAPAEHRDPRGALPALAVDLLLTLLFVALGQGQHSTERGPLGLLVTAAPFL
+AGLLLMTGVTAGHRTWARAWPHGVIVWLGTVAVGMLLRVAFGLGGAPVSFVLVALGVLGV
+LLLGRRAVTAWLVRRTRR
+>NAFOICDF_01590
+MSTTPLPQDSSPAAHPSDRRRGSAPWVAFALDAALVVLFVALGQREHATDRGGLALVTAA
+APFLLAWVAGTALAGGPRTWARVWPQGVVVWAVTVAAGMGLRVLWGLGGAPVPFVLVASA
+VLAVFLLGRRWASTLLAHRATDRASRAS
+>MHAAABBN_00915
+MTSSPTARRAVPAEHRDPRGAQPALAVDLLLTLLFVALGQGQHATERGPLGLLVTAAPFL
+AGLLVMTGLTAGHRTWARVWPHGVIVWLGTVAVGMVLRVAFGLGGAPVSFVLVALGVLGV
+LLLGRRAVTAWLVRRTRR
+>LFPAFLNI_01149
+MTSSPTARRVVPAEHRAPRGALPALAVDLLLTVLFVALGQGQHSTERGPVGLLVTAAPFL
+AGLLLMTGLTSGHRTWARVWPHGVIVWLGTVAVGMVLRVAFGLGGAPVSFVLVALGVLGV
+LLLGRRAVTAWLVRRTRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001167.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001167.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7bc687be4c8756bb7508154064f4c780b078c7de
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001167.fa
@@ -0,0 +1,24 @@
+>ACLBLIBL_01693
+MIVLHLLPLTAPDAADAAWTRVGDELNRPGAVSSLVMPFDRQGEGSEARLVGGMDSGVEA
+VGILLSLVRSGAWAVVVEVAEGRAAGESLLQREAERARRANGHCAVLGPSGPSAAWIEPA
+LQLLGALERRRSEPQQDAGRRVEAGASQREVAAELQVSQQAVHARLRGGLWNETRALAGA
+TADALDVLARRGDRVSDGGASPSTSERG
+>MOLHKGIG_01194
+MVSVHLVPIRPTAATADDAQRLSAALLDDPRPGAAVISAAWHIDETDAAPGDGELAVTLD
+GMAAGVGLALWAVRSGSWAVLLDTEGNYDKQSALSHITAGERRRARRAPGRLVLPHGRRP
+GRASETGREADLRCAEATLQLVATVERRRSDDQHAAGRLVEAGASQREAAAELGISQQAV
+HSRLRHGLWHESRTAVAAVLPLLERLSADPGE
+>NAFOICDF_01591
+MVPVAVRCGSAGAAGRWAASIPGARRLGREGGRDLIVHADDAAAAVALMLAVRRAGAGAV
+GAGVAIEQVEGALRRARRRPGGIAVSRVPGSTGTEEERGLLEAGLGVLLTLESRRSAPQQ
+AAGVLIEAGRSQREAAADLGVSQQAVQQRLRAGLWEETRTLLDALLPMARRVLEA
+>MHAAABBN_00914
+MVFVHLVPIRPTAATADDARRLAAVLLDDPHPDASVAAAVWRGDEGNPDADAAPGDGELA
+VVVESMAAAVGLALWAVRTGSWAVLLDPEDALDKDSLLSYLTPAERRRARRAPGRLVLPH
+GRRPGRASETGREADLRCAEATLQLVATVERRRSDDQHAAGRLVEAGASQREAAAELGIS
+QQAVHSRLRHGLWHESRTAVAAVLPLLERLSADPGE
+>LFPAFLNI_01148
+MVSVHLVLIRPTTATAEDARRLATALRDDPRPDAAVTAAMWLGDESDPVDDDAAPHDGEL
+AVVLDDAAAAVGLALWAVRTGSWAVMLDPEGGSDKDSALSYLTPAELRRARRAPGRLVLP
+AGGRPGRASESGREADLRCAEATLQLVAAVERRRSADQHAAGRLVEAGASQREAAAELGI
+SQQAVHSRLRHGLWHVSRTAVAAVLPLLERLSTDPGE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001168.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001168.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c213ae0fa37f1a8a509f45cfcb1ae99e01d28397
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001168.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01695
+MALIYTAQLDPDKPEWIRRRLVAHGLPEDVDAEKVGSYRFDDPAGEVGVESMIVRVGDRL
+YQTAFAYRGEAPTEGDIVAEADHSVLGRRWVMDAATDPDARRILTAGLRGEIPQAVMDFH
+DESGAYLETRQPDVTLRLVGEGDGGELELPVELADAAEESGDGPRRLVAEGEGFTAVVAR
+LA
+>MOLHKGIG_01193
+MALIYTARLDPDKPEWIRRRLVAHGLPEDVTAEKVGSYRFDDPTGEIGVESMLVRVGDRL
+YQTAFAYRGDAPAEGDVVAEVEHSVLGHRWVVDAATDPDARRILAAAVRGEIPQARLEMH
+DESGTYLETRAPDLTLRVIGADATGELEVPVELSETGEADVDGPRCLIAEGDGVRAVVAR
+LT
+>NAFOICDF_01594
+MSFIYSAQLDPDKNEWIRRALVAHGEDPDVPFTRAGSYRFDDPAGELGLEVMLVRVGGAD
+DGRLVQTPLSYRSAARDGATVLLTAEHSVLGTRWIHDALTDPEAREVLRRGVAGELAQEV
+LEVHDEHGVRTGTRQPDMTVTAVGTGPAAGELDMPYELDPADTADGGRALVAEGDGFSGL
+VVARLV
+>MHAAABBN_00912
+MALIYTARLDPDKPEWIRRRLVAHGLPEDVTAEKVGSYRLDDPAGEIGVESMVVRVGDRL
+YQTPFAYRGDAPAEGDVVAEVEHSVLGHRWVVDAATDPDARRILAAAVRGEIPQARLEMH
+DESGTYLETRAPDLTLRVIGADATGELEVPVELSETDEADVDGPRCLVAEGDGVRAVVAR
+LS
+>LFPAFLNI_01143
+MALIYTARLDPDKPEWIRRRLVAHGLPEDVTAEKVGSYRFDDPTGEIGVESMLVRVGDRL
+YQTAFAYRGDAPAEGDVVAEVEHSVLGHRWVVDAATDPDARRILAAAVRGEIPQARLEMH
+DESGTYLETRAPDLTLRVIGADATGELEVPVELSETDEADVDGPRCLVAEGDGVRAVVAR
+LS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001172.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001172.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed336d10f9540250310cb1c5e926fad3a180e8d3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001172.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01699
+MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK
+EAFLVSGEKPAEAEGKPVRTHWDMLRERRSLEELQETYALQLNKLRASRGEDVDA
+>MOLHKGIG_01189
+MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK
+EAFLVSGEKPAETEGKPVRTHWDMLRERRSLEELEETYKIQLNKLRASRGEEVDA
+>NAFOICDF_01598
+MSDRSLRGMRLGAQSLESEAGVEPAPRQRVEYRTEDGEQVFVTFAQEAEVPTTWTSKTGK
+EALRVDGEKPEENPGKPVRTHWDMLLERRSMEELEETFQIQLKKLHASRGEAV
+>MHAAABBN_00908
+MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK
+EAFLVSGEKPAETEGKPVRTHWDMLRERRSLEELEETYKIQLNKLRASRGEDVDA
+>LFPAFLNI_01139
+MSDRSLRGMRLGAQSLESEAGVEPAARQRVEYRTEDGEQVFVTFSVEADVPATWTSKTGK
+EAFLVSGEKPAETEGKPVRTHWDMLRERRSLEELEETYKIQLNKLRASRGEEVDA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001183.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001183.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b04b07d705fcd7851bf6878f4e4f86e568f4113e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001183.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01712
+MIRDESIEAYLGRLASGEPTPGGGATGALAVAEGAGLLAMAARFSAAEEDARASEVLIAA
+CLGLADGDERGFGAVAEAFGLPRDTPVARSRRSAAIQAALAEAVRPPRGIVDAAARALDL
+AERVLDAANPNVLSDVGAALGCIRGGLTAATVTLETNLGPLRDEGVEGILRTDVDRADRL
+VARADALLGRVRAAITG
+>MOLHKGIG_01177
+MIRDESIESYLGRLASGEPTPGGGATGALAVAEGAGLLAMAARFSAAEEDARASEGLIAA
+CLGLADGDERGFGAVAEAFGLPRDTLEDRARRSAAIQAALAEAVQPPRGIVDVAERALDL
+AERVLDAANPNVLSDVGAALGCVRGGLTAAAVTLETNLGPLRDEGLEGIVRTDVDRADRL
+VARADALLGRVRAAVTG
+>NAFOICDF_01610
+MIRHETVEDHLTRLASGEPTPGGGATGALVVAQGAGLVAMAARFSGREEVAVECERVIRD
+SLAISDEDEEGFAAVADAYTLPKDGDAARARRSAAVQAALDQAVRPPRAIVDAVDRTVGL
+AERVLDDANPHVLSDVGAALGCARAGAGAAVVTLLTNLSPLHDEQLGAELRAEIARADEL
+TSRIDALAARVRERIAR
+>MHAAABBN_00896
+MIRDESIESYLGRLASGEPTPGGGATGALAVAEGAGLLAMAARFSAAEEDARASEGLIAA
+CLGLADGDERGFGAVAEAFGLPRDTPEDRARRSAAIQAALAEAVQPPRGIVDVAERALDL
+AERVLDAANPNVLSDVGAALGCVRGGLTAAAVTLETNLGPLRDEGLEGVLRTDVDRADRL
+VARADALLGRVRAAVAG
+>LFPAFLNI_01127
+MIRDESIESYLGRLASGEPTPGGGATGALAVAEGAGLLAMAARFSAAEEDARASEGLIAA
+CLGLADGDERGFGAVAEAFGLPRDTPEDRARRSAAIQAALAEAVRPPRGIVDAAARALDL
+AERVLDAANPNVLSDVGAALGCVRGGLTAAAVTLETNLGPLRDEGLEGVLRTDVDRADRL
+VARADALLGRVRAAVTG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001185.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001185.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0067a35cf2c0ca8d6b198be05a7746a7c0458f31
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001185.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_01714
+MDQDAQGGPEQLERRLGEARELLRQSQAEAERLRHQLDSAQRHAARLSERRREAEAQTQT
+AARNNRRMVELLETTRAEITTLKENLDAVTHPPFTFATLEAVHAPREPEEGVETGAVVRG
+GADVVQNGRRLRVTVSPLLDAARLVPGAQVLLDESSAIVGVAPGTGSGQLLRVKEALPDG
+GLVLAGTADEERVVRRAPALEGVELRHGDAVTVDSRVEWALRRVELSEVDEVLLEEVPDV
+TFEDIGGLGPQIDRIREAVEIPFLHPEVYREHGLRAPKGIMLYGPPGTGKTMLAKAVANA
+LSARSADGERSFFLNVKGPELLNKYVGETERQIRVIFDRAREKADAGFPVVIFFDEMESL
+FRTRGSGVSSDVETTIVPQLLTEIDGVEALENVIVIGASNREDMIDPAVLRPGRLDVKIR
+VDRPDAAGAAEIMAKHLTADVPLHADDVATAGSADAARATLIARTVAALYDRGTGTALAE
+LTDVSGTTRALHLADLVSGAVVADVVDRAKRHAVRDYLAAGQAPAALGVREGHLREAVVA
+VLEDQTDLLATVAPAEWARTSGWRGPRLRSLRMVRGVEA
+>MOLHKGIG_01175
+MDHHAQSGTEHAEQRLAEARELLRQSQAEAERLRHQLQSAQRHAAGLSERRRAAEAQTQT
+AARNNRRMVELLEATRAEITTLKENLDAVTHPPFTFATLEAVHAPREPEEGVETGAVVRG
+GADVVQNGRRLRVTVSPLLDAARLTPGAQVLLDESSSIVGVAPGTGSGQLLRVKEALPDG
+GLVLAGTADEERVVRRAPALEGVDLRHGDAVTVDARVEWALRRVELSEVDEVLLEEVPDV
+TFEDIGGLGPQIDRIREAVEIPFLHPEVYREHGLRAPKGIMLYGPPGTGKTMLAKAVANA
+LSARSADGERSFFLNVKGPELLNKYVGETERQIRVIFDRAREKADAGFPVVIFFDEMESL
+FRTRGSGVSSDVETTIVPQLLTEIDGVEALENVIVIGASNREDMIDPAVLRPGRLDVKIR
+VDRPDAAGAAEIMAKHLTADVPLHADDVAAAGSADAARATLIARTVAALYDRGADTALAE
+LTDVSGTTHALHLADLVSGAVVADVVDRAKRHAVRDYLAAGQAPAALGVREGHLREAVAA
+VLEDQTDLLATVAPAEWARTSGWRGPRLRSLRMVRGVEA
+>NAFOICDF_01612
+MTEDDTQDRAGVLPAGDDARRLAEARELLRQSQAEAERLRHQLASAQRHGAQLSERRRAA
+QAQLDVAARNNRRMVELLEATRTEMTSLKEALDDTTKAPFTFARLEAVHAARAPREGVET
+GAVVRAGADVVQNGRRLRVAVSPLLDAAALTAGAEVLLDESSTIVGEVEHSVSGQLLRVK
+ESLPDGSLVLAGAADEERVVRRAPALAGEVLRHGDAVTVDPRLEWALARVELSEVDDVLL
+EEVPDVTFDDIGGLGPQIERIREAVEVPFLHPDLYREHGLRAPKGIMLYGPPGTGKTMLA
+KAVANALSARSAEGGRSFFLNIKGPELLNKYVGETERQIRIIFQRAREHAAAGSPVVVFF
+DEMESLFRTRGSGVSSDVETTIVPQLLAEIDGVESLDNVIVIGASNREDMIDPAVLRAGR
+LDVKIRVDRPDARGAVDIMARHLDEEVPLHVDEVRDAGSAEQAREELIGAAVTALYERSP
+RTALAELTDITGATSTLHLADLVSGAVVADVVDRAKRAAVRDLLAADLDPAARGLRTRHL
+LDAVDAVLADQADLLGTVAPGEWARTSGWRGPRLAELRMLPGAGGRP
+>MHAAABBN_00894
+MDHHAQSGTEHAEQRLAEARELLRQSQAEAERLRHQLQSAQRHAAGLSERRRAAEAQTQT
+TARNNRRMVELLEATRAEITTLKENLDAVTHPPFTFATLEAVHAPRDPEEGVETGAVVRG
+GADVVQNGRRLRVTVSPLLDAARLTPGAQVLLDESSSIVGVAPGTGSGQLLRVKEALPDG
+GLVLAGTADEERVVRRAPALEGVDLRHGDAVTVDARVEWALRRVELSEVDEVLLEEVPDV
+TFEDIGGLGPQIDRIREAVEIPFLHPEVYREHGLRAPKGIMLYGPPGTGKTMLAKAVANA
+LSARSADGERSFFLNVKGPELLNKYVGETERQIRVIFDRAREKADAGFPVVIFFDEMESL
+FRTRGSGVSSDVETTIVPQLLTEIDGVEALENVIVIGASNREDMIDPAVLRPGRLDVKIR
+VDRPDAAGAAEIMAKHLTADVPLHADDVAAAGSADAARATLIARTVAALYDRGGDTALAE
+LTDVSGTTHALHLADLVSGAVVADVVDRAKRHAVRDYLAAGQAPAALGVREGHLREAVAA
+VMEDQTDLLATVAPAEWARTSGWRGPRLRSLRMVRGVEA
+>LFPAFLNI_01125
+MDHHAQSGTEHAEQRLAEARELLRQSQAEAERLRHQLQSAQRHAAGLSERRRAAEAQTQT
+AARNNRRMVELLEATRAEIATLKENLDAVTHPPFTFATLEAVHAPREPEEGVETGAVVRG
+GADVVQNGRRLRVTVSPLLDAARLTPGAQVLLDESSSIVGVAPGTGSGQLLRVKEALPDG
+GLVLAGTADEERVVRRAPALEGVDLRHGDAVTVDARVEWALRRVELSEVDEVLLEEVPDV
+TFEDIGGLGPQIDRIREAVEIPFLHPEVYREHGLRAPKGIMLYGPPGTGKTMLAKAVANA
+LSVRSADGERSFFLNVKGPELLNKYVGETERQIRVIFDRAREKADAGFPVVIFFDEMESL
+FRTRGSGVSSDVETTIVPQLLTEIDGVEALENVIVIGASNREDMIDPAVLRPGRLDVKIR
+VDRPDAAGAAEIMAKHLTADVPLHADDVVAAGSADAARATLIARTVAALYDRGADTALAE
+LTDVSGTTHALHLADLVSGAVVADVVDRAKRHAVRDYLAAGQAPAALGVREGHLREAVAA
+VLEDQTDLLATVAPAEWARTSGWRGPRLRSLRMVRGVEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001191.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001191.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5796eef25af9471bb57bbb1493132a52378e9aad
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001191.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01720
+MTWIEAIILGLVQGLTEFLPISSSAHIRIVGEFLPSASDPGAAFTAITQIGTELAVLIYF
+WRDITRIIGRWFQALAGRLPHSDPDVRMGWLIILGSLPIAVLGLLLQDWIDTEFRSLWIT
+ATMLIVFGVLLALADRLGRQAKPLERLTVRDGVLYGFAQALALIPGVSRSGGTITAGLAM
+GYTRSAAARYAFLLAVPAVFASGFYKLFQSLAEPGTQGPYGMGETFLATVIAFVVGYAVI
+AWLMKFITTNSYMPFVWYRIALGLGLFALLGTGVISA
+>MOLHKGIG_01169
+MTWIEAIILGLVQGLTEFLPISSSAHIRIVGEFLPSATDPGAAFTAITQLGTELAVLIYF
+WRDITRIIGRWCAAVTGRIPHSDPDARMGWLIIVGSIPIAVLGLLLEDWIDTEFRSLWIT
+ATMLIVFGVLLALADRLGRQTKPLEKLTVRDGVLYGLAQALALIPGVSRSGGTIAAGLAM
+GYTRPAATRYAFLLAVPAVFASGLYKLYTSLTDPGTQGPYGMGETLVATAIAFVVAYAVI
+AWLMRFISTNSYLPFVWYRILLGGVLFALLGAGVISA
+>NAFOICDF_01618
+MTWIEAIILGLVQGLTEFLPISSSAHIRIVGEFLPSAADPGAAFTAITQLGTETAVLIYF
+WKDISRIISRWFQALAGKVPHSDPDVRMGWLIIIGSIPIGVLGLLLQDWIDTEFRSLWIT
+ATMLIVFGVLLALADRKGRQTKPLEKLTLKDGIVYGFAQALALIPGVSRSGGTITAGLAM
+GYTREAAARYAFLLAVPAVFASGLYKVAKVVTEPGQAGPYGMGETILATAIAFVVGYAVI
+AWLMKFITTNSYMPFVWYRIALGLVLFVLLGTGLIAA
+>MHAAABBN_00888
+MTWIEAIILGLVQGLTEFLPISSSAHIRIVGEFLPSATDPGAAFTAITQLGTELAVLIYF
+WRDITRIIGRWCAAVTGRIPHSDPDARMGWLIIVGSIPIAVLGLLLEDWIDTEFRSLWIT
+ATMLIVFGVLLALADRLGRQTKPLEKLTVRDGVLYGLAQALALIPGVSRSGGTIAAGLAM
+GYTRPAATRYAFLLAVPAVFASGLYKLYTSLTDPGTQGPYGMGETLVATAIAFVVAYAVI
+AWLMRFISTNSYLPFVWYRILLGGVLFALLGAGVISA
+>LFPAFLNI_01119
+MTWIEAIILGLVQGLTEFLPISSSAHIRIVGEFLPSATDPGAAFTAITQLGTELAVLIYF
+WRDITRIIGRWCAAVTGRIPHSDPDARMGWLIIVGSIPIAVLGLLLEDWIDTEFRSLWIT
+ATMLIVFGVLLALADRLGRQTKPLEKLTVRDGVLYGLAQALALIPGVSRSGGTIAAGLAM
+GYTRPAATRYAFLLAVPAVFASGLYKLYTSLTDPGTQGPYGMGETLVATAIAFVVAYAVI
+AWLMRFISTNSYLPFVWYRILLGGVLFALLGAGVISA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001193.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001193.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9705c3721d7baa2883219ba568cc71b91b104c62
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001193.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01722
+MREQLMSSTLDSIARGQKWEYLVITVSPDESLGDARRRLVEHAEYGRWELQRSVHFRGGA
+RRYWLRRRVVRVASTLASA
+>MOLHKGIG_01167
+MREQLMSSTLDAISRGQKWEYLVMTVAAHESLADARRRLVEHAEYGQWELQRSVHYRDGA
+RRYWMRRRVMRVASTLQTL
+>NAFOICDF_01620
+MDGMREQLMSSTLDSIARGEKWEYLVITVAPHESLADARRRLVDHAEYGQWELQRSVHYR
+GGTRRHWMRRRVIRVRSTLQS
+>MHAAABBN_00886
+MREQLMSSTLDAISRGQKWEYLVMTVAAHESLADARRRLVEHAEYGQWELQRSVHYRDGA
+RRYWMRRRVMRVASTLQTL
+>LFPAFLNI_01117
+MREQLMSSTLDAISRGQKWEYLVMTVAAHESLADARRRLVEHAEYGQWELQRSVHYRDGA
+RRYWMRRRVMRVASTLQTV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001194.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001194.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0e64a0002a34fbaab8e41c5fbd2bad5eca232f6a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001194.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_01723
+MIQNAHDTPVSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAALCARLMEEAGMRPRL
+FESSPGRVSVVGHLPGWDEDAPGLVVHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV
+DMKGMDAMVLSVLLHLTRTGRRPRRPLTVAFFADEEAGGVYGARWLVEHHPELFDGCTEA
+ISEVGGFSTEVHGSRAYLVQTAEKGIAWLNLRAEGAPGHGSAPHPDNAVTRLAGAMTRIG
+GHEWPLVYTKTTRALLEQVAEIMGVDFDEQDPTPQLDALGQARSWVAGTLRTSSNPTGMT
+SGYKHNVIPSTATGTVDARLLPGEEEAALATLQELAGPGVSIEPEHRDVALETPFSGDLV
+ELMVASLQAEDPGAEVLPFMLGGGTDNKSLARLGITGYGFAPMRLPADLAFTSLFHGIDE
+RVPVDALEFGCRVLERMLEPR
+>MOLHKGIG_01166
+MVENIVNPARSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAEYCARLMAEAGMTPRF
+FESAPGRVSVVGHLPGWDPEAPGLVIHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV
+DMKGMDAMVLAVLLHLARTGRRPRRPLTVAFFADEEAGGVYGARWVVDHHPEVFDGCTEA
+ISEVGGFSTEVHGSRAYLVQTAEKGLAWLNLTAEGAPGHGSAPHPDNAVTRLAGAMTRIG
+GHEWPLVYTKTTRALLEQVAEIMGVDFDEADPTPQLDALGQARSWVAGTLRTSSNPTGLT
+AGYKHNVIPSSATGTVDVRLIPGEEESALATIAELAGPEVTIAPEHRDVALETPFSGDLV
+ELMIASLQAEDPEAQVLPFMLGGGTDNKSLSRLGITGYGFAPMRLPADLAFTSLFHAIDE
+RVPVDALEFGCRVLERMLEPR
+>NAFOICDF_01621
+MDASTPSTAPSTADADVVEICRDLIRIDTTNHGGGRSVGEPEAAELCAAWMRKAGMEPEL
+IESAPGRVSVVGRLEGWDPEAPGLVLHGHTDVVPAEPDEWTVDPFGAEFRDGMIWGRGAV
+DMKGMDAMILSVLVHLARTGRRPRRPVVVAFFSDEEAGGVFGAQWLVAHRPELFAGCTEA
+ISEVGGFSTDVAGTRAYLVQTGEKGLAWLNLRAQGAPGHGSAPHTDNAVTRLAGAMERIG
+RHPWPLTYTKTTRQLLEEVAEITGTPFDERDPTPQLQALGHARDWVAGTLRTSSNPTGLT
+AGYKHNVIPSTATGTVDVRLIPGEEEQTLAELADLAGDGIEISPEHQDTGLEVPFSGDLV
+ERMASALDAEDPGAHVLPFMLGAGTDNKSLHRLGIAGYGFSPLQLPSGLEFTRLFHGIDE
+RVPVESLRFGCRVLEHVLEPRA
+>MHAAABBN_00885
+MVENIVNPARSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAEYCARLMAEAGMTPRF
+FESAPGRVSVVGHLPGWDPEAPGLVIHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV
+DMKGMDAMVLAVLLHLARTGRRPRRPLTVAFFADEEAGGVYGARWVVDHHPEVFDGCTEA
+ISEVGGFSTEVHGSRAYLVQTAEKGLAWLNLTAEGAPGHGSAPHPDNAVTRLAGAMTRIG
+GHEWPLVYTKTTRALLEQVAEIMGVDFDETDPTPQLDALGQARSWVAGTLRTSSNPTGLT
+AGYKHNVIPSSATGTVDVRLIPGEEESALATIAELAGPDVTIAPEHRDVALETPFSGDLV
+ELMIASLQAEDSEAQVLPFMLGGGTDNKSLSRLGITGYGFAPMRLPADLAFTSLFHAIDE
+RVPVDALEFGCRVLERMLEPR
+>LFPAFLNI_01116
+MVENIENPARSRPEDRVVEICRDLIRIDTTNRGGNVSVGEPEAAEYCARLMTEAGMTPRF
+FESAPGRVSVVGHLPGWDPEAPGLVIHGHTDVVPAEADEWSVDPFGAELKDGMIWGRGAV
+DMKGMDAMVLAVLLHLARTGRRPRRPLTVAFFADEEAGGVYGARWVVDHHPEVFDGCTEA
+ISEVGGFSTEVHGSRAYLVQTAEKGLAWLNLTAEGAPGHGSAPHPDNAVTRLAGAMTRIG
+GHEWPLVYTKTTRALLEQVAEIMGVDFDETDPTPQLDALGQARSWVAGTLRTSSNPTGLT
+AGYKHNVIPSSATGTVDVRLIPGEEESALATIAELAGPDVTIAPEHRDVALETPFSGDLV
+ELMIASLQAEDPEAQVLPFMLGGGTDNKSLSRLGITGYGFAPMRLPADLAFTSLFHGIDE
+RVPVDALEFGCRVLERMLEPR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001197.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001197.fa
new file mode 100644
index 0000000000000000000000000000000000000000..efcd48caa45b27645b71bb7b24ee5c772976ff60
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001197.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_01728
+MTDRYGAFAASALGRRLTGALGLPQPVELRRHAPGEPVLHGSVLVLGAGPAAADARTLLA
+SWGLEVADAPREGARLAGVVACFDDAAAPGDLGETVLQIGGALRSLGASSRVVTVSVDPE
+AAAEPAVRAARQGVQGLTRSLAQEMRRGGTANGIVLGEGVPLTAPGAAGALAFLLSGRSA
+YVSGQFLPVTTRDGATPADAARPLADKVAVVTGAARGIGAAIVRTLARDGATVVGVDVPV
+AGESLAAVVNEVGGTALALDITAPEAGARILEHCRARHGRMDVVVHNAGITRDRMLANMD
+AARWDSVIAVNTASQLAMNEAFLADDAREVTGEGLRIIGLASISGIAGNRGQTNYAASKA
+GVIGLTAASAPALAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNSLQQGGLPQDVA
+EAVAWFASDAAGGTNGATLRVCGQSKLGA
+>MOLHKGIG_01162
+MTDRYGTFVASPLGRRLTGALGLPQPVELRRHTPGDPVLPGSVLVLGATPAAADARTLLA
+SWGLEVADAPREGARHAAIVACFDGVATPADLGAVALEIGGALRSLGSSSRVVTVFEDPE
+AATDPTLRAARQGVTGLTRSIAHEMRRGGTANGLVLGEGVPLTAPGAAGALAFLLSGRAA
+YVSGQFVPVATADGAVPADAARPLAGKVAVVTGAARGIGAAIVRTLARDGAVVVGVDVPA
+AGEALAEVVNEVGGTALALDITAPDAGARILEHCRTRHGRMDAVVHNAGITRDRMLANMD
+AARWDSVLAVNTTAQLAMNEAFLAEDARDVAGQGLRIVGLASISGIAGNRGQTNYAASKA
+GVIGLTAASAPVLAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNALQQGGLPQDVA
+ETVAWLASDAAGGTNGATLRVCGQSKLGA
+>NAFOICDF_01625
+MPANDPYGDLVRTRLGRRLTGALGLPQPAELRRHTAGDPAVRGTVLVLGATSAADAARAL
+VTAEGARAVAHPAEGERLAAVIACFDGVAAPGDLSDTALALGGALRSLEPSAHVVTVVED
+PEEAEVPAVRAARAGVMGLTRSLAHEMRRGGVANGLLLRGGARLGDAGPAGALRFLLSGR
+AAFVSGQFLPAAAGAGSAPASADARPLEGRVAVVTGAARGIGAAILRTLARDGATVVGVD
+LPAAGEDLVRIVNELGGTALPLDITAPDAGARIVEHARARHGRLDVVVHNAGITKDKLLA
+NMDAARWDAVLAVNTASQLAINEVLLSAEAADVVSPDIRIVGLASISGIAGNRGQTNYAA
+SKAGVIGLTAATAPDLAARGGGITAVAPGFIETEMTAKIPLVTRELGRRVNSLQQGGRPE
+DVAEAVAFLSSPAASGINGTTLRVCGQSMLGA
+>MHAAABBN_00881
+MTDRYGTFVASPLGRRLTGALGLPQPVELRRHTPGDPVLPGSVLVLGATPAAADARTLLA
+SWGLEVADAPREGARHAAIVACFDGVATPADLGAVALEIGGALRSLGSSSRVVTVFEDPE
+AATDPALRAARQGVTGLTRSIAHEMRRGGTANGLVLGEGVPLTAPGAAGALAFLLSGRAA
+YVSGQFVPVSTADGAVPADAARPLAGKVAVVTGAARGIGAAIVRTLARDGAVVVGVDVPA
+AGETLAKVVNEVGGTALALDITAPDAGARILEHCRTRHGRMDVVVHNAGITRDRMLANMD
+AARWDSVLAVNTTAQLAMNEAFLAEDARDVAGHGLRIVGLASISGIAGNRGQTNYAASKA
+GVIGLTAASAPVLAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNALQQGGLPQDVA
+ETVAWLASDAAGGTNGATLRVCGQSKLGA
+>LFPAFLNI_01112
+MTDRYGTFVASPLGRRLTGALGLPQPVELRRHTPGDPVLPGSVLVLGATPAAADARTLLA
+SWGLEVADAPREGARHAAIVACFDGVATPADLGAVALEIGGALRSLGSSSRVVTVFEDPE
+SATDPTLRAARQGVTGLTRSIAHEMRRGGTANGLVLGEGVPLTAPGAAGALAFLLSGRAA
+YVSGQFVPVATADGAVPADAARPLAGKVAVVTGAARGIGAAIVRTLARDGAVVVGVDVPA
+AGEALAEVVNEVGGTALALDITAPDAGARILEHCRTRHGRMDVVVHNAGITRDRMLANMD
+AARWDSVLAVNTTAQLAMNEAFLAEDARDVAGQGLRIVGLASISGIAGNRGQTNYAASKA
+GVIGLTAASAPVLAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNALQQGGLPQDVA
+ETVAWLASDAAGGTNGATLRVCGQSKLGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001198.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001198.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bee6b2c6603605d05b743a89f3087a85377ec0ae
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001198.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_01729
+MTQPETTARPAVAGGALRPAVVVGGNRIPFARANTAYAEVGNQEMLTAALEGLVARFGLQ
+GERVGQVSAGAVLKHPRNFNLTREAVLGSALASDTPAADLQVACATGMEAIGTLADKIRL
+GRIDSAIGGGVDSISDAPVSLSDGARRALLRLNAAKTMKDRLAALKDLRPGHLAPEPAGA
+GEPRTGMSMGDHQALTTHRWGITRQAQDELAAASHRNLGAAYAAGYMDDLVTPFRGLDRD
+NNLRPDSTPEKLAGLKPAFGRHLGEEATMTAGNSTPLTDGASAVLLSSEDWAAERGLPVL
+AEFVDVENAAVDFVDGDEGLLMSPAYAVPRLLARHGLTLQDLDFVEIHEAFAGTVLSTLA
+AWEDEEYCRERLGLPGALGSVDRAKLNVHGSSLAAGHPFAATGGRIVALLSKMLHEKGEG
+SLGLVSVCAAGGQGIVALLRGR
+>MOLHKGIG_01161
+MTHHETPASETASRPAVAGGALRPAVILGGNRIPFARANTAYAEVGNQEMLTATLDGLVA
+RFGLQGERLGQVTAGAVLKHPRNFNLTREAVLGSALSAATPAADVQVACATGMEALGTLA
+NKIRLGQLDSAIGGGVDSISDAPVSLSDGARRVLLQLNTAKTMKDRLRALAQLRPGQLVP
+EPAGAGEPRTGMSMGEHQALTTHKWGITRQTQDELAAASHRNLGAAYAAGYMDDLVTPFH
+GLARDNNLRPDSTPEKLAGLKPAFGRQLGDEATMTAANSTPLTDGASAVLLSSEEWAAER
+GLPVLAEFVDMENAAVDFVDGHEGLLMAPAYAVPRLLARHGLTLDDLDFVEIHEAFAGTV
+LSTLAAWEDEEYCRERLGLPGALGSVDRARLNVHGSSLAAGHPFAATGGRIVALLAKMLH
+EKGEGSLGLISVCAAGGQGIVALLRGR
+>NAFOICDF_01626
+MSTESPRVPAETARPAIAGGELRPAVVVGSNRIPFARAFTAYAEVGEQEMLTAAIDGLVA
+RLGLQGERLGQVSAGAVMKHPKDFNLTREAVMGSALSSETPAADIQVACATGMEAIGTLA
+DKIRLGRIDSAIGGGVDSISASPMTVSESARRVLLQLNSAKTVKDRLKALSSLRPGQLVP
+EPAAAGEPRTGMSMGEHQALTTHQWGITRQAQDELAAASHRNLGASYASGYQDDLVTPFR
+GLAKDNNLRPDSTVEKLAGLKPAFGRHLGDEATMTAGNSTPLTDGASAVLLSSEDWAVQR
+NLPVLAEIVDMENAAVDFVDGEDGLLMSPVYAVPRLLARHGLTLDDLDFVEIHEAFAGTV
+LATLAAWEDEEFGRTRLGLPGAYGSVDRAKLNVNGSSLAAGHPFAATGGRIVGLLSKMLH
+EKGEGSLGLVSVCAAGGQGIVALLRGR
+>MHAAABBN_00880
+MTHHETPASETASRPAVAGGALRPAVILGGNRIPFARANTAYAEVGNQEMLTATLDGLVA
+RFGLQGERLGQVTAGAVLKHPRNFNLTREAVLGSALSAATPAADVQVACATGMEAVGTLA
+NKIRLGQLDSAIGGGVDSISDAPVSLSDGARRVLLQLTTAKTMKDRLRALAQLRPGQLVP
+EPAGAGEPRTGMSMGEHQALTTHKWGITRQAQDELAAASHRNLGAAYAAGYMDDLVTPFH
+GLARDNNLRPDSTPEKLAGLKPVFGRQLGDEATMTAGNSTPLTDGASAVLLSSEEWAAER
+GLPVLAEFVDMENAAVDFVDGHEGLLMAPAYAVPRLLARHGLTLDDLDFVEIHEAFAGTV
+LSTLAAWEDEEYCRERLGLPGALGSVDRARLNVHGSSLAAGHPFAATGGRIVALLAKMLH
+EKGEGSLGLISVCAAGGQGIVALLRGR
+>LFPAFLNI_01111
+MTHHETPASETASRPAVAGGALRPAVILGGNRIPFARANTAYAEVGNQEMLTATLDGLIA
+RFGLQGERLGQVTAGAVLKHPRNFNLTREAVLGSALSAATPAADVQVACATGMEALGTLA
+NKIRLGQLDSAIGGGVDSISDAPVSLSDGARRVLLQLNTAKTTKDRLRALAQLRPGQLVP
+EPAGAGEPRTGMSMGEHQALTTHKWGITRQAQDELAAASHRNLGAAYAAGYMDDLVTPFH
+GLARDNNLRPDSTPEKLAGLKPAFGRQLGDEATMTAANSTPLTDGASAVLLSSEEWAAER
+GLPVLAEFVDMENAAVDFVDGHEGLLMAPAYAVPRLLARHGLTLDDLDFVEIHEAFAGTV
+LSTLAAWEDEEYCRERLGLPGALGSVDRARLNVHGSSLAAGHPFAATGGRIVALLAKMLH
+EKGEGSLGLISVCAAGGQGIVALLRGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001200.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001200.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5ee4ca7657aa0a74f69d6f11ef0a94bf65065476
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001200.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01731
+MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGEPRDPDYHGARVLTYPNPP
+GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANMAGHLGKLMHGVPHVLSAHSLEPL
+RPWKAEQLGGGYALSSWAEKTAYLGADAVIAVSDGMRRDILACYPEVDPEKVHTVHNGID
+TEAWTPQTETDALEKYGIDPTRPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP
+DTPELAHEVNGLIAELRRTREGVVVIEGMIPRREVTQILSAATVFACPSVYEPLGIVNLE
+AMACGTAVVASAVGGIPEVVQDGETGLLVPIEQVADGTGAPADEDAFAADFAAALTRVLE
+DPERATAMGEAGRARAIEHFSWEAIAERTIEVYEAVLR
+>MOLHKGIG_01158
+MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGAPRDPDYHGARVLTYPNPP
+GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANLAGHLGKLLHQTPHVLSAHSLEPL
+RPWKAEQLGGGYALSSWAERTAYLGADAVIAVSDGMRRDILACYPDVDPAKVHTVHNGID
+TQVWTPQTGTAALEKYGIDPDKPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP
+DTAELAHEVNELISELRRTRQGVVVIEGMIPRHEVMEILTAATVFACPSVYEPLGIVNLE
+AMACGTAVVASAVGGIPEVVQDGETGLLVPFEQVDDGTGAPVDEERFAADFAAALTRVVE
+DPERARAMGEAGRARAIEHFSWETIAERTIEVYEAVLR
+>NAFOICDF_01629
+MRIDIVTKEFPPTIYGGAGVHVAELTRVLSSRADVHVHAFGGAREPDYHGATVTSYAQPA
+GFESANGAVQTLVTDLDIVGDLDGADVIHSHTWYANMAGHLGGLMHGVPHVLSAHSLEPL
+RPWKAEQLGGGYALSSWAESTAYHGAAAVIAVSEGMRRDILRCYPDVDPAKVHTVHNGID
+TQLWTPQTGTDALTKYGIDPDRPSVAFVGRITRQKGVPHLLRAALQLPEDVQLVLCVGAA
+DTPELAREVEGLIGRLRAEREGVVVVEGMIPRGEVTQILSAATVFACPSIYEPLGIVNLE
+AMACGTAVVASAVGGIPEVVDDGVTGLLVPVEQADDGTGTPVDEEKFAADLAKALSTVLA
+DPERATAMGEAGRARAIEHFSWETIADRTMEVYAAVAR
+>MHAAABBN_00877
+MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGAPRDPDYHGARVLTYPNPP
+GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANLAGHLGKLLHQTPHVLSAHSLEPL
+RPWKAEQLGGGYALSSWAERTAYLGADAVIAVSDGMRRDILACYPDVDPAKVHTVHNGID
+TQVWTPQTGTAALEKYGIDPDKPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP
+DTAELAHEVNELIAELRRTRQGVVVIEGMIPRHEVMEILTAATVFACPSVYEPLGIVNLE
+AMACGTAVVASAVGGIPEVVQDGETGLLVPFEQVDDGTGAPVDEERFAADFAAALTRVVE
+DPERARAMGEAGRARAIEHFSWETIAERTIEVYEAVLR
+>LFPAFLNI_01108
+MRIDIVSKEFPPSIYGGAGVHVAELTRVLASRADVRVHAFGAPRDPDYHGARVLTYPNPP
+GFDAANGAVQTLATDLTILGDLEGADVIHSHTWYANLAGHLGKLLHQTPHVLSAHSLEPL
+RPWKAEQLGGGYALSSWAERTAYLGADAVIAVSDGMRRDILACYPDVDPAKVHTVHNGID
+TQVWTPQTGTAALEKYGIDPDKPSVAFVGRITRQKGVPHLLRAALRLPEDVQLVLCVGAP
+DTAELAHEVNELISELRRTRQGVVVIEGMIPRHEVMEILTAATVFACPSVYEPLGIVNLE
+AMACGTAVVASAVGGIPEVVQDGETGLLVPFEQVDDGTGAPVDEERFAADFAAALTRVVE
+DPERARAMGEAGRARAIEHFSWETIAERTIEVYEAVLR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001201.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001201.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d401b7a3f14b534dc2cbd22bb003b5cb71846f39
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001201.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01732
+MVQKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGTYRLIDFALSNLVNSRYREIVVLTQ
+YKSHSLDRHISETWRMSTLLNNYVASVPAQQRRGKDWFTGSANAIYQSMNLIHDARPDIV
+VVIGADHVYHMDFQQMVDQHIASGAKATVAAVRQPLELASSFGVIETDPQDRTRISAFVE
+KPQTTPGLPDDPTLFLASMGNYVFDTDALVAALNQDEENPESNNDMGGDIIPLFVERGEA
+GVYDFTANEVPGGTAGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNRDWPLYTRQSVSP
+PAKLVRSSTRRPGSANDSILSQGVVISGGTVAQSVLSTDVRVANEAWVEQSVLLDSVVIG
+EGAHVRNAILDKNVVVPPGARIGFDRAEDEANGYTVTDSGLTVLAKDQSVPKPH
+>MOLHKGIG_01157
+MVQKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGTYRLIDFALSNLVNSRYREIVVLTQ
+YKSHSLDRHISETWRMSTLLNNYVASVPAQQRRGKDWFTGSANAIYQSMNLIHDARPDIV
+VVIGADHVYHMDFQQMVDQHIASGAKATVAAVRQPLELASSFGVIETDPQDRTRISAFVE
+KPETTPGLPDDPTQFLASMGNYVFDTDALVAALNQDEENPESNNDMGGDIIPLFVERGEA
+GVYDFTANEVPGGTAGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNREWPLYTRQSVSP
+PAKLVRSSTRRPGSANDSILSQGVVISGGTVAQSVLSTDVRVHNEAWVEQSVLLDSVVIG
+EGAHVRNAILDKNVVVPPGARIGFDRAEDEANGYTVTESGLTVLSKGQPVPTPH
+>NAFOICDF_01630
+MVEKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGEYRLIDFALSNLVNSRFREIVVLTQ
+YKSHSLDRHISETWRMSTMLNNYVATVPAQQRRGKDWFTGSANAIYQSMNLISDARPDIV
+VVIGADHVYHMDFQQMVDHHVASGAKATVAAVRQPLELADQFGVIETDATDPGRITAFVE
+KPATTPGLADDPAQFLASMGNYVFDTDALVEALNADDANPESNNDMGGDIVPYFVGRGEA
+GVYDFTTNEVPGGTPGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNRAWPLYTRQSVSP
+PAKLVRSASRRPGTAGDSILAQGVVISGGTVAQSVLSTDVRVGNEAWVEQSVLLDSVTVG
+EGAHVRNAIIDKNVVIPAGARIGFDRAEDEANGYTVTDSGLTVLSKNQRVPDPR
+>MHAAABBN_00876
+MVQKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGTYRLIDFALSNLVNSRYREIVVLTQ
+YKSHSLDRHISETWRMSTLLNNYVASVPAQQRRGKDWFTGSANAIYQSMNLIHDARPDIV
+VVIGADHVYHMDFQQMVDQHIASGAKATVAAVRQPLELASSFGVIETDPQDRTRISAFVE
+KPETTPGLPDDPTQFLASMGNYVFDTDALVAALNQDEENPESNNDMGGDIIPLFVERGEA
+GVYDFTANEVPGGTAGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNREWPLYTRQSVSP
+PAKLVRSSTRRPGSANDSILSQGVVISGGTVAQSVLSTDVRVHNEAWVEQSVLLDSVVIG
+EGAHVRNAILDKNVVVPPGARIGFDRAEDEANGYTVTESGLTVLSKGQPVPTPH
+>LFPAFLNI_01107
+MVQKKVLSVVLAGGEGKRLMPLTADRAKPAVPFGGTYRLIDFALSNLVNSRYREIVVLTQ
+YKSHSLDRHISETWRMSTLLNNYVASVPAQQRRGKDWFTGSANAIYQSMNLIHDARPDIV
+VVIGADHVYHMDFQQMVDQHIASGAKATVAAVRQPLELASSFGVIETDPQDRTRISAFVE
+KPETTPGLPDDPTQFLASMGNYVFDTDALVAALNQDEENPESNNDMGGDIIPLFVERGEA
+GVYDFTANEVPGGTAGKHYWRDVGTLDSYYDAHMDLVQPWPEFNLYNREWPLYTRQSVSP
+PAKLVRSSTRRPGSANDSILSQGVVISGGTVAQSVLSTDVRVHNEAWVEQSVLLDSVVIG
+EGAHVRNAILDKNVVVPPGARIGFDRAEDEANGYTVTESGLTVLSKGQPVPTPH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001207.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001207.fa
new file mode 100644
index 0000000000000000000000000000000000000000..303f9e5cb9f5aaa314c8081a7d58b7565187fff2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001207.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01743
+MSTLRRLVVTADPALLADRTPPAGVPDDAERLLEDGLLGWRFAADEWAAAPEPGPGWAVH
+TLPAAVAEAPVPLVVTDVDSTLIRQEVIELLAAHAGREAEVAAVTERAMRGELDFAASLH
+ARVEALAGLPVGVVDDVVRAIRPTAGALALIEAVTAAGGRVCAVSGGFSQVLAPLAQAWG
+VHAYCANELEVHDGHLTGRVAGDVVDRAAKAAMLRAWAEDAGLSPEQAVGVGDGANDIDL
+LDAAGAGVALCAKPVLREHADVVVDVPSFTPLRWLLGL
+>MOLHKGIG_01149
+MSTLRRLVVTADPALLVTDAPPAGVPDDAERLTDDGLLGWRFAADEWAAAPEPGSGWDVL
+TVPATVAAAPAPLVVTDVDSTLIRQEVIELLAAHAGREAEVAEVTERAMRGELDFAASLH
+ARVEALAGLPVGVVADVVRAIRPTDGALALIEAVTAAGGRVCAVSGGFTQVLAPLAEAWG
+VHAYCANELEVQDGHLTGKVLGDVVDRAAKAAMLRAWAEDAGLTPEQAVGVGDGANDIDL
+LEAAGCGVALCAKPILREHADVVVDVPSFTPLRWLLGL
+>NAFOICDF_01637
+MTQARHLLYRAVPAGTDSPVAPAWAPLPADAEHLAADGLAGLRWEGSVPSAEEATALPED
+WALASLPQSVAAAPTPLVVTDVDSTLIQQEVIELLAAHTGREAEVAAVTERAMRGELDFA
+QSLHARVEALAGLPASVVDDVVARVRPTDGAVELIAAVNAAGGRVCAVSGGFTQVLAPLA
+EAWGVHAYCANELEVRDGHLSGKVLGDVVDRAAKAAMLRAWAEDAGLSPEQAVGVGDGAN
+DIDLLEVAGCGVALCAKPILREHADVVIDVPSFTPLRWLLGL
+>MHAAABBN_00868
+MSTLRRLVVTADPALLVTDAPPAGVPDDAERLTDDGLLGWRFAADEWAAAPEPGSGWDVL
+TVPATVAAAPAPLVVTDVDSTLIRQEVVELLAAHAGREAEVAEVTERAMRGELDFAASLH
+ARVEALAGLPVGVVADVVRAIRPTDGALALIEAVTAAGGRVCAVSGGFTQVLAPLAEAWG
+VHAYCANELEVRDGHLTGKVLGDVVDRAAKAAMLRAWAEDAGLTPEQAVGVGDGANDIDL
+LEAAGCGVALCAKPILREHADVVVDVPSFTPLRWLLGL
+>LFPAFLNI_01099
+MSTLRRLVVTADPALLVTDAPPAGVPDDAERLTDDGLLGWRFAADEWAAAPEPGSGWDVL
+TVPATVAAAPAPLVVTDVDSTLIRQEVVELLAAHAGREAEVAEVTERAMRGELDFAASLH
+ARVEALAGLPVGVVADVVRAIRPTDGALALIEAVTAAGGRVCAVSGGFTQVLAPLAEAWG
+VHAYCANELEVRDGHLTGKVLGDVVDRAAKAAMLRAWAEDAGLTPEQAVGVGDGANDIDL
+LEAAGCGVALCAKPILREHADVVVDVPSFTPLRWLLGL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001208.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001208.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85af4b38ddca86a895ba817c09614e365fc5d4d7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001208.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01744
+MTEKDLTGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQKIEEAGGRA
+VAVGGDVTSAEDRAALLDAAVESFGSLDVLVLNASGGMESQFGEDYAMKLNRDAQAALAD
+AALERMSAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFEAKGVGF
+AVVSGDMIEGTITATLLDRAEPGAIDARREAAGRLYSVEEFAAEVAALVGRDDLEVGHTE
+LVGGARDFLARGEG
+>MOLHKGIG_01148
+MTEQDLAGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQRIEDAGGRA
+VAVGGDVTVAEDRAALLDAAVEHFGSLDVLVLNASGGMESQFGEDYALKLNRDAQAALAD
+AALERMGAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFTEKGVGF
+VVVSGDMIEGTITATLLDRAEPGAIEARREAAGKLYSVEEFAAEIASLVGREGLEVGHTE
+LVGGAEDFLGQD
+>NAFOICDF_01638
+MTTQDLAGKGVVVTGSSRGIGAETAQLLAARGAGVVVNYRQKAPRANKVVQAIEAARGRA
+VAVGGDVTVAEDRAALLDAAIDNFGSLDVLVLNASGGMESQFGEDYAMTLNRDAQAALAD
+AALERMSAGGQIVFVTSHQAHFIDEVATMDAYEPVARSKRAGEDALRERIPAFEAKGVGF
+VVVSGDMIEGTITATLLNRAEPGAIEARREAAGKLYSVEEFAAEVAALVGRTDLEVGHTE
+LVGGAQDFLGQD
+>MHAAABBN_00867
+MTEQDLAGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQRIEDAGGRA
+VAVGGDVTVAEDRAALLDAAVEHFGSLDVLVLNASGGMESQFGEDYALKLNRDAQAALAD
+AALERMGAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFAEKGVGF
+VVVSGDMIEGTITATLLDRAEPGAIEARREAAGKLYSVEEFAAEIASLVGREDLEVGHTE
+LVGGAEDFLQQN
+>LFPAFLNI_01098
+MTEQDLAGRGVVVTGSSRGIGAATAELLAARGAGVVVNYRQKAPRANKVVQRIEDAGGRA
+VAVGGDVTVAEDRAALLDAAVEHFGSLDVLVLNASGGMESQFGEDYALKLNRDAQAALAD
+AALERMGAGGQIVFVTSHQAHFIDEVATMDSYEPVARSKRAGEDALRERIPAFAEKGVGF
+VVVSGDMIEGTITATLLDRAEPGAIEARREAAGKLYSVEEFAAEIASLVGREDLEVGHTE
+LVGGAEDFLQQN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001209.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001209.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2c48f5431ec57e468602bbf9323c02cb8a9d6c7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001209.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01746
+MTSSAAGSRAGRPARAGRSTGPQVQGVTTASAARSEDREARMKVYLVQMLIRTVCFGAAL
+FTTGWWQLLFILGAVALPYVAVVQVNNAGPRQAGSLRAVPAEGPELTARPADAPGPASPV
+VLTGDVVDDPREVGPRALPPGSPSEGARRLPGRGAA
+>MOLHKGIG_01146
+MTSSAAGSRAGRPARAGRGTTPEVQGVTTAAAGRSADREARMRVYLVQMLVRTACFVAAL
+FTHGWWQLGFILGAVVLPYVAVVRVNNTGPQQAGTLRAVPAQGPALAPRPDDTAAPEPVV
+LTGDLVDDPRDRAPRALGRGSSSAGSPGLPGRGGA
+>NAFOICDF_01640
+MAAIVREPDAVQGVTTAAAPRSADRDARTRVYVVQMAVRTACFIAALFTHGWWQILFILG
+AVVLPYVAVVRVNNTGPREAGRRRDVARTAPAVPALPAEPSPVPTGPVVLVGEVVEDDDP
+AARRALPAGSPGETGRGRP
+>MHAAABBN_00865
+MTSSAAGSRAGRPARAGRGTTPEVQGVTTAAAGRSADREARMKVYLVQMLLRTACFVAAL
+FTHGWWQLGFILGAVVLPYVAVVRVNNTGPQQAGTLRAVPAQGPALAPRPDDTAAPKPVV
+LTGDLVDDPRDRAPRALGRGSSSAGGPGLPGRGAA
+>LFPAFLNI_01096
+MTSSAAGSRAGRPARAGRGTTPEVQGVTTAAAGRSADREARMKVYLVQMLLRTACFVAAL
+FTHGWWQLGFILGAVVLPYVAVVRVNNTGPQQAGTLHAVPAQGPALAPRPDDTAAPKPVV
+LTGDLVDDPRDRAPRALGRGSSSAGGPGLPGRGAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001214.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001214.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ecc0c632475a75331a5fb6a0ebaf5328ffddafe4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001214.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01752
+MATLQITDLHVQIETENGPKEILKGLSLTIETGQTHAIMGPNGSGKSTLASTIAGHPRYE
+VTSGSITLDGEDVLEMGVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTALDGEAPSLR
+TWTKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV
+DALRIVSEGVNRAAEQNEMGTLLITHYTRILNYIKPDHVHVLVDGRVAESGGPELAAQLE
+AEGYARFEKAAAGV
+>MOLHKGIG_01140
+MATLQITDLHVQIATENGPKEILKGLSLTIETGETHAIMGPNGSGKSTLASTIAGHPRYE
+VTSGSITLDGEDVLEMGVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTALDGEAPSLR
+TWTKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV
+DALRIVSEGVNRAQAQNEMGTLLITHYTRILNYIKPDHVHVLVDGRVAESGGPELAEQLE
+AEGYARFEKAAAGA
+>NAFOICDF_01646
+MATLQITDLHVQIETENGPKEILKGLSLTINTGETHAIMGPNGSGKSTLASTIAGHPRYE
+VTSGSITLDGEDVLEMSVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTAIDGEAPSLR
+TWSKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV
+DALRIVSEGVNRAAEANEMGTLLITHYTRILNYIKPQHVHVLVDGRVAESGGPELAARLE
+SEGYARFEKAAAEA
+>MHAAABBN_00859
+MATLQITDLHVQIETENGPKEILKGLSLTIETGETHAIMGPNGSGKSTLASTIAGHPRYE
+VTSGSITLDGEDVLEMSVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTALDGQAPSLR
+TWTKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV
+DALRIVSEGVNRAQAQNEMGTLLITHYTRILNYIKPDHVHVLVDGRVAESGGPELAEQLE
+AEGYARFEKAAAGA
+>LFPAFLNI_01090
+MATLQITDLHVQIATENGPKEILKGLSLTIETGETHAIMGPNGSGKSTLASTIAGHPRYE
+VTSGSITLDGEDVLEMGVDERAQAGLFLAMQYPVEIPGVTMTNFLRTAKTALDGQAPSLR
+TWTKDVKGAFEALQIDPAFMNRNVNEGFSGGEKKRAEILQLELFKPKFAILDETDSGLDV
+DALRIVSEGVNRAQAQNEMGTLLITHYTRILNYIKPDHVHVLVDGRVAESGGPELAEQLE
+AEGYARFEKAAAGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001219.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001219.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aac0a55e532790a5ca3ffcaf3f534bc2251d687e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001219.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01757
+MSAPIAPGSAEPRTAGQVPEPGTAPHAGAAPLATRVLRQAAYETGTALRNGEQLLVTVVL
+PLLALVGVHVTGLLDEPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALAT
+TPLGTLGLVAGKALSVVALLLVQVAVIGGVGLALGWRPEAAGILPAVVALALGAAAFTAL
+GLLLAGTARPEATLAAANLLWVLFGAVGGTVFPSRVPGVDLLPSGALGSALRAALVDGAG
+APIPLLVLALWCAVAVAAALRWFRWRP
+>MOLHKGIG_01135
+MSTPVVDHRAPAGTGAHAGAAPLAARVLRQAGYETGTALRNGEQLLVTVVLPLLALVGVH
+VTGLLDAPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALATTPLGTLGLV
+AGKALAVVALLLVQVSVIGGVGLALGWRPDPEGILPALVALALGAAAFTALGLLLAGTAR
+PEATLAVANLLWVLFGAVGGTVFPARVPGVDLLPSGALGTALRAALLDGAWSPVPLLVLT
+LWGAVAVAAALRWFRWRP
+>NAFOICDF_01651
+MSAPAAPIPASHAGAAPLGARILAQARYETVTALRNGEQLLVTLVLPLLALVGVHVTGLL
+DAPGRNGLDLAVPGVLALAVISAAFTATAISTGFERRYDVLAALATTPLGTGGLVAGKAA
+AVAAVLLLQTIVIGGVGLALGWSPDPAGIPPAVVALLLGAAAFTALGLLLAGTARPEATL
+AVANLVWVLLGALGGTVFPSRWAWMDLLPSGALGTALRSALQDGAWAPSALAVLAAWTVM
+AVAAALRWFRWRP
+>MHAAABBN_00854
+MSTPVVDHRAPAGTGAHAGAAPLAARVLRQAGYETGTALRNGEQLLVTVVLPLLALVGVH
+VTGLLDAPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALATTPLGTLGLV
+AGKALAVVALLLVQVSVIGGVGLALGWRPDPEGILPALVALALGAAAFTALGLLLAGTAR
+PEATLAVANLLWVLFGAVGGTVFPARVPGVDLLPSGALGTALRAALLDGAWSPVPLLVLT
+LWGAVAVAAALRWFRWRP
+>LFPAFLNI_01085
+MSTPVVDHRAPAGTGAHAGAAPLAARVLRQAGYETGTALRNGEQLLVTVVLPLLALVGVH
+VTGLLDAPGRSGLDVAVPGVLALAVISSAFTATAIATGFERRYDVLAALATTPLGTLGLV
+AGKALAVVALLLVQVSVIGGVGLALGWRPDPEGILPALVALALGAAAFTALGLLLAGTAR
+PEATLAVANLLWVLFGAVGGTVFPARVPGVGLLPSGALGTALRAALLDGAWSPVPLLVLT
+LWGAVAVAAALRWFRWRP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001223.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001223.fa
new file mode 100644
index 0000000000000000000000000000000000000000..045341f3cdfe01532ccac22199b98e590767d735
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001223.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01761
+MSTQQNPNTAALAEAGVSIWLDDLSRKRLDEGTLEELMATRSVTGVTTNPSIFAVALADA
+GSYEGQLRELAAAGADVDEAVTALTTQDVRRAADVLAPVHERTGGADGFVSLEVDPRLAR
+DAEGTARQAQELAAAVDRPNLMVKIPATVEGLAAITDVLAEGISVNVTLIFSLPRYRQVL
+NAWLAGLEKARENGHDLSRIHSVASFFVSRVDTEVDARLRALGTPEAEALTGQAALANAR
+LAYRAFEQALDSERWRLLEAAGAPVQRPLWASTGVKDPALPDTLYVTGLVAPRTVTTLPE
+QTLEAVADHGEVAGDTVTGGYAEADALLDAVGAAGVSYQDVVDVLETEGLQKFESAWEEL
+LGSVRDGLAAHR
+>MOLHKGIG_01131
+MSTPQNPNTAALAQAGVSIWLDDLSRTRLDEGTLEELIATRSVTGVTTNPSIFAVALADA
+GAYQGQLRDLAAAGASVDEAVVALTTEDVRRAADVLAPVHERTGGADGFVSLEVDPRLAR
+DAAGTVAQARELAAAVDRPNLMVKIPATVEGLSAIADVLGAGISVNVTLIFSLPRYRRVL
+NAWLTGLEKARANGHDVRRLHSVASFFVSRVDTEVDARLRAIGTPEAEALTGRAAVANAR
+LAYRAFEQALDSERWRLLEAAGAPVQRPLWASTGVKDPALPDTLYVTELVAPHTVTTLPE
+KTLEAVADHGVIAADTVTGAYAEADALLDAVGAAGVSYQDVVDVLETEGLEKFEAAWDEL
+LGSVRSGLDAHR
+>NAFOICDF_01655
+MTTETTPATAALAAAGVSLWLDDLSRTRLNEGSLERLIATRNVTGVTTNPSIFAAALKDA
+GAYEAQLAELAAAGADVDAAVTALTTTDVRRACDLLAPVHQETGGRDGYVSIEVDPRLAR
+DTAGTVAQARELVALVDRPNLMVKIPATVEGLPAITEVLGAGISVNVTLIFSLPRYREVL
+NAWLSGLELARANGHDVSRIHSVASFFVSRVDTDVDAQLRALAEQGRPEAGELTGRAGLA
+NARLAYRAFEQMKDTERWSLLEAAGAPVQRPLWASTGVKDPALADTLYVTALVAPDTVNT
+MPEKTLEAYADHGELTAEPVVGGYAQADADLDAIGELGISYTELVDRLETEGLQKFEAAW
+DELLASVRAGLAAHR
+>MHAAABBN_00850
+MSTPQNPNTAALAQAGVSIWLDDLSRTRLDEGTLEELIATRSVTGVTTNPSIFAVALADA
+GAYQGQLRDLAAAGASVDEAVVALTTEDVRRAADVLAPVHERTGGADGFVSLEVDPRLAR
+DAAGTVAQARELAAAVDRPNLMVKIPATVEGLSAIADVLGAGISVNVTLIFSLPRYRRVL
+NAWLTGLEKARANGHDVRRLHSVASFFVSRVDTEVDARLRAIGTPEAEALTGRAAVANAR
+LAYRAFEQALDSERWRLLEAAGAPVQRPLWASTGVKDPALPDTLYVTELVAPHTVTTLPE
+KTLEAVADHGVIAADTVTGAYAEADALLDAVGAAGVSYQDVVDVLETEGLEKFEAAWDEL
+LGSVRSGLDAHR
+>LFPAFLNI_01081
+MSTPQNPNTAALAQAGVSIWLDDLSRTRLDEGTLEELIATRSVTGVTTNPSIFAVALADA
+GAYQGQLRELAAAGASVDEAVVALTTEDVRRAADVLAPVHERTGGADGFVSLEVDPRLAR
+DAAGTVAQARELAAAVDRPNLMVKIPATVEGLSAIADVLGAGISVNVTLIFSLPRYRRVL
+NAWLTGLEKARANGHDVRRLHSVASFFVSRVDTEVDARLRAIGTPEAEALTGRAAVANAR
+LAYRAFEQALDSERWRLLEAAGAPVQRPLWASTGVKDPALPDTLYVTELVAPHTVTTLPE
+KTLEAVADHGVIAADTVTGAYAEADALLDAVGAAGVSYQDVVDVLETEGLEKFEAAWDEL
+LGSVRSGLDAHR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001224.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001224.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fcc4003dca9195c07bd6b8a7f84ae171d3210521
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001224.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_01762
+MSTLGLSATGSALEAIDRHLPTLLEDRVASRLGAQDAGLWGEAAREESARRLGWIDLFED
+SRALVRHIDALSRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA
+LERDLERTVLVVSSKSGSTVETDSQRRVMEAAFREAGIDPRSRLVAVTDPGSPLHAECES
+AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLTADDADNPGLQ
+LGAALGGTAPLRDKLVFTDHGSGIDGLPAWAEQLIAESTGKDGTGLLPVVVADGDPETGW
+DAPDMLQVQLVGEDAPAAPAHGVQVSGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA
+KTAARSLLDAPARERTADRTVDGVELSGPEAVVSAADLAGVLRATADLVPENGYLAVHAY
+LSRHDDAELEEVRADLARLAGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQVTGDADLDV
+EVPGRPFSLGRLIAAQAAGDARVLVEHGRPVVTLHLPHRAAGIDAIRTAARAR
+>MOLHKGIG_01130
+MSTLGLTATGAALEAIDRHLPALLQDRVASRLGAQDADLWGAPARDEAAKRLGWIDLFED
+SRALVPDIAQLTRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA
+LERDLERTVLVVSSKSGSTVETDSQRRVVEAAFRDAGIDPRTRLVAVTDPGSPLHAACES
+AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLIADDEDNPGLQ
+LGAALGGTRPLRDKLVFADHGSGIAGLPAWIEQLIAESTGKDGTGLLPVVVAPGDPETVW
+DAPDLLQVQLVGEDDVAAPGHGVQVAGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA
+KAAARTLLDGPAAERPADGEVEGVEVSGPASVTSAPDLAGVLRATAALVPEGGYLAVHAY
+LSRHDDAELEELRADLADLVGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQITGDAGLDL
+EVPGRPFSLGRLIAAQAAGDARVLGDLGRPVVTLHLRRRDAGIEALRSAVRGR
+>NAFOICDF_01656
+MSTFGLTATGAALDAVDRHVPALVAERFASRLAAEDADLWGPDARDEAAKRLGWISLFEE
+SRTVAAEAAALAEELRGQGLTRVVLAGMGGSSLAPEVIAATAGAELEVLDSTDPQQVAAV
+LDHDLERTVLVVSSKSGSTVETDSQRRIVEAALAAEDIDPASRIVVVTDPGSPLEEASVE
+AGYRAVFTADPTVGGRYSALTAFGLVPAALAGVDVESLLDEAEDVLDLVTADDADNPALQ
+LGAAIGGTEPLRDKLVIQDLGSGIDGFGDWVEQLIAESTGKDGTGLLPVVVRPGDPETAW
+EAPDLLKVTLVSESEESPAGGDGVRLHGSLGALLLTWEAATAVAGRLLGINPFDQPDVEA
+AKAAARELLDSPAEEAEPGTVIHGVEVSGPESVTSADDLRGVLAAVRELVPEDGYLAVHA
+YLDRHADVDLAGIRADLASALGRPVTFGWGPRFLHSTGQYHKGGPRNGVYLQVTGDAALD
+VEVPGRPFTLGRLIAAQAAGDADVLRRLGRPVVTLRLRDRSAGIAALRTAAREA
+>MHAAABBN_00849
+MSTLGLTATGAALEAIDRHLPALLQDRVASRLGAQDADLWGAPARDEAAKRLGWIDLFED
+SRALVPDIAQLTRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA
+LERDLERTVLVVSSKSGSTVETDSQRRVVEAAFRDAGIDPRTRLVAVTDPGSPLHAACES
+AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLIADDEDNPGLQ
+LGAALGGTRPLRDKLVFADHGSGIAGLPAWIEQLIAESTGKDGTGLLPVVVAPGDPETVW
+DAPDLLQVQLVGEDDVAAPGHGVQVAGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA
+KAAARTLLDGPAAERPADGEVEGVEVSGPASVTSAPDLAGVLRATAALVPEGGYLAVHAY
+LSRHDDAELEELRADLADLVGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQITGDAGLDL
+EVPGRPFSLGRLIAAQAAGDARVLGDLGRPVVTLHLRRRDAGIEALRSAVRGR
+>LFPAFLNI_01080
+MSTLGLTATGAALEAIDRHLPALLQDRVASRLGAQDADLWGAPARDEAAKRLGWIDLFED
+SRALVPHIAQLTRELRAEGVDRVVLAGMGGSSLAPEVIAATAGVELEVLDSTDPLQVSRA
+LERDLERTVLVVSSKSGSTVETDSQRRVVEAAFRDAGIDPRTRLVAVTDPGSPLHAACES
+AGWRAVFTADPTVGGRFSALTAFGLVPTGLAGVDVAALLDDAEAVLDLLIADDEDNPGLQ
+LGAALGGTRPLRDKLVFADHGSGIAGLPAWIEQLIAESTGKDGTGLLPVVVAPGDPETVW
+DAPDLLQVQLVGEDDVAAPGHGVQVAGSLGAQLLLWEVATAVAGRLLGINPFDQPDVEAA
+KAAARTLLDGPAAERPADGEVEGVEVSGPASVTSAPDLAGVLRATAALVPEGGYLAVHAY
+LSRHDDAELEELRADLADLVGRPVTFGWGPRFLHSTGQFHKGGPAVGVFLQITGDAGLDL
+EVPGRPFSLGRLIAAQAAGDARVLGDLGRPVVTLHLRRRDAGIEALRSAVRGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001227.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001227.fa
new file mode 100644
index 0000000000000000000000000000000000000000..259d36cbd785e04f0104b743e620a1ae55875fe6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001227.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01765
+MDMLTLILQILVVVLSVVIVLLVLLHKGRGGGVSDMFGGGVTTSMSSSGSAQRLLTRLTV
+GTVAAWALLIVTLGVLPRLAMES
+>MOLHKGIG_01127
+MDVLTLALQILVVVLSVVIVLLILLHKGRGGGVSDMFGGGVTSSMSSSGSAQRLLTRLTV
+GSVVAWGVVIALLGVLPRLTMES
+>NAFOICDF_01659
+MDILTLLLQIAVVALSVVIIMLVLLHKGRGGGVSDMFGGGVTTSMSSSGSAQRLLTRVTV
+SATVLWGLAIVALALIARFSVES
+>MHAAABBN_00846
+MDVLTLALQILVVVLSVVIVLLILLHKGRGGGVSDMFGGGVTSSMSSSGSAQRLLTRLTV
+GSVVAWGVVIALLGVLPRLTMES
+>LFPAFLNI_01077
+MDVLTLALQILVVVLSVVIVLLILLHKGRGGGVSDMFGGGVTSSMSSSGSAQRLLTRLTV
+GSVVAWGVVIALLGVLPRLTLES
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001228.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001228.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b238692a427c6f25a8a5a5363b6def8c8e27df0b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001228.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01766
+MAETAARVPLIAGNWKMNLDHREAVTLVQRLAWLLTDADHDHEDVEVAVFPPFTDLRAVQ
+VLVTGDRLDVAYGAQDLSPEDSGAYTGDVSGAFLAALGCRYAIVGHSERRTIHGEDDALV
+ARKAAAALRHGLSPVVCVGEGLDVRQAGRHVAHTVAQLEGSLVGLSAEDVARTVVAYEPV
+WAIGTGEVAGAGDAQEMCAALRARVGELHGDDVAAGLRILYGGSVKSTSAPELLAQPDVD
+GALVGGASLDAEEFARIVRFDQA
+>MOLHKGIG_01126
+MAEQTTRVPLIAGNWKMNLDHLEAVTLVQRLTWLLSDADHDQEAVEVAVFPPFTGLRSVQ
+TLVTGDRLDLVYGAQDLSPEDAGAYTGDVSGAFLAALGCRYAIVGHSERRTLHGEDDALV
+ARKAAAALRHGLTPVICVGEGLEVRQAGRHVEHTLAQLEGSIAGLSAQDVAGVVVAYEPV
+WAIGTGEVAGPEDAQQMCAALRARVAALHGDDVAAGLRILYGGSVKSSSAPALLAQPDVD
+GALVGGASLDADEFAKIVRFDQA
+>NAFOICDF_01660
+MSVVQPVRVPLIAGNWKMNLDHQEAVTLVQRLGWLLGDADHEQGNVEAAVFPPFTDLRSV
+QTLVAADRIGVAYGAQDVSAEDSGAFTGEVSGAFLAKLGCAYAIVGHSERRTLHHEDDAL
+VARKAAAALRHGLVPVVCVGEGLDVRQAGRHVEHTVAQLRGSLDGLSSEDVARVVVAYEP
+VWAIGTGEVASAADAQEMCAALRADLAERHGAEVAERVRVLYGGSVKSSSAPELLAQPDV
+DGALVGGASLDADEFARIVRSDAAH
+>MHAAABBN_00845
+MAEQTTRVPLIAGNWKMNLDHLEAVTLVQRLTWLLTDADHDQEAVEVAVFPPFTGLRSVQ
+TLVTGDRLDLVYGAQDLSPEDAGAYTGDVSGAFLAALGCRYAIVGHSERRTLHGEDDALV
+ARKAAAALRHGLTPVICVGEGLEVRQAGRHVEHTLAQLEGSIAGLSAQDVAGVVVAYEPV
+WAIGTGEVAGPEDAQQMCAALRARVAALHGDDVAAGLRILYGGSVKSSSAPALLAQPDVD
+GALVGGASLDADEFAKIVRFDQA
+>LFPAFLNI_01076
+MAEQTTRVPLIAGNWKMNLDHLEAVTLVQRLTWLLTDADHDQEAVEVAVFPPFTGLRAVQ
+TLVTGDRLDLAYGAQDLSPEDAGAYTGDVSGAFLAALGCRYAIVGHSERRTLHGEDDALV
+ARKAAAALRHGLTPVICVGEGLEVRQAGRHVEHTLAQLEGSIAGLSAQDVAGVVVAYEPV
+WAIGTGEVAGPEDAQQMCAALRARVAALHGDDVAAGLRILYGGSVKSSSAPALLAQPDVD
+GALVGGASLDADEFAKIVRFDQA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001231.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001231.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3cdaa843ea941b06a58b4c2949882fef4733c6ee
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001231.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01770
+MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAARDADDFAAVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEHFGSFDKFRAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQARFEAARQGASGLILPA
+>MOLHKGIG_01123
+MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAAREAGDFGSVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEYFGSFDQFQAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQARFEAARAGASGLILPA
+>NAFOICDF_01663
+MTEFVLPELDYDYAALEPHISAKIMELHHSKHHATYVKGANTALEKLAAAREAEDFASVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEFFGSFDKFQAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQQRFEAARNGASGLILPA
+>MHAAABBN_00842
+MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAAREAGDFGSVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEYFGSFDQFQAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQARFEAARAGASGLILPA
+>LFPAFLNI_01073
+MTEYTLPELDYDYAALEPHISARIMELHHSKHHATYVKGANTALEKLAAAREAGDFGSVN
+QLSKDLAFNLGGHTNHSIFWKNLSPEGGDKPTGELAAAIDEYFGSFDQFQAHFTAAALGI
+QGSGWAVLAYEPIGGNLVIEQFYDQQNGVPVATIPLFQLDMWEHAFYLDYQNVKADYVKA
+IWNIVNWADVQARFEAARAGASGLILPA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001232.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001232.fa
new file mode 100644
index 0000000000000000000000000000000000000000..16d0b1ed7ef2796aa1ab7de596ec466577ed9ae1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001232.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01771
+MALTMTLKEELARVPVAATPERRAETAAMLRFAGGLHLVSGRVVVEAELDHGASARRLRA
+SITELYGLATEIVVVSGGNLRRGQRYVIRVVRGGEDLARRTGLIDQRGRPVRGLASALVT
+GTTADTAAVWRGALLAHGSLTEPGRSAALEVTTPGPEAALALVGAARRLDVAAKAREVRQ
+ADRVVVRDGEAIATLLTAVGAEQTAALWRERRERKEVRATANRLANFDDANLRRSAQAAV
+AAGAKVERALEILGDEVPEHLRYAGRLRLEHKQASLDELGRLADPPMTKDAVAGRIRRLL
+AMADKRAAERGVPGTDTPAED
+>MOLHKGIG_01122
+MALTMTLKEELARVPVAATPERRAETAAMLRFAGGLHLVAGRVVVEVELDHGASARRLRA
+AITELYGLAPEIVVVSGGNLRRGQRYVLRVVRGGEDLARQTGLIDQRGRPVRGLAPVLVS
+GTTAATAAVWRGALLAHGSLTEPGRSAALEVTTPGPEAALALVGAARRLRVAAKAREVRQ
+SDRVVVRDGEAIATLLAAVGAEQTATLWRERRERKEVRATANRLANFDDANLRRSAQAAV
+TAGAKVERALEILGDEVPDHLRYAGRLRLEHKQASLDELGRLADPPMTKDAVAGRIRRLL
+AMADKRAAERGIPGTDAASEG
+>NAFOICDF_01664
+MALTMTLKEELARVPVGAVPERRAETATMLRFAGGLHLVSGRVVIEAELDHGASARRLRA
+AITELYGHATEIVVISGGNLRRGQRYVIRVVRGGEDLARQTGLLDLRGRPVRGLPPALVQ
+GSAADTAAVWRGALLAHGSLTEPGRSSCLEVTTPGPEAALALVGAARRLGVAAKAREVRQ
+ADRVVVRDGEAIAALLTAVGADQTAALWQERRERKEVRATANRLANFDDANLRRSAQAAV
+AAGARVERALEILGDDVPDHLGYAGRLRLEHKQASLDELGRLADPPMTKDAVAGRIRRLL
+SMADKRAAAEGIPGTAVDGA
+>MHAAABBN_00841
+MALTMTLKEELARVPVAATPERRAETAAMLRFAGGLHLVAGRVVVEAELDHGASVRRLRA
+AITELYGLAPEIVVVSGGNLRRGQRYVLRVVRGGEDLARQTGLIDQRGRPVRGLAPVLVS
+GTTAATAAVWRGALLAHGSLTEPGRSAALEVTTPGPEAALALVGAARRLRVAAKAREVRQ
+SDRVVVRDGEAIATLLAAVGAEQTATLWRERRERKEVRATANRLANFDDANLRRSAQAAV
+TAGAKVERALEILGDEVPDHLRYAGRLRLEHKQASLDELGRLADPPMTKDAVAGRIRRLL
+AMADKRAAERGIPGTDAASEG
+>LFPAFLNI_01072
+MALTMTLKEELARVPVAATPERRAETAAMLRFAGGLHLVAGRVVVEVELDHGASARRLRA
+AITELYGLAPEIVVVSGGNLRRGQRYVLRVVRGGEDLARQTGLIDQRGRPVRGLAPVLVS
+GTTAATAAVWRGALLAHGSLTEPGRSAALEVTTPGPEAALALVGAARRLRVAAKAREVRQ
+SDRVVVRDGEAIATLLAAVGAEQTATLWRERRERKEVRATANRLANFDDANLRRSAQAAV
+TAGAKVERALEILGDEVPDHLRYAGRLRLEHKQASLDELGRLADPPMTKDAVAGRIRRLL
+AMADKRAAERGIPGTDAASEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001233.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001233.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98b1ca99981851439d1606a05831859c7796989c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001233.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01772
+MTSPLTGQLPLPPGVGTAVRGPAGGMARPAIRVTALGGGHGLSASLTALRHVAGHLTAIV
+TVADDGGSSGTIRREMAVLPPGDLRMALAALCDDTDWGRTWAQVMQHRFRSTEVDAEEAT
+LDNHALGNLLIVALWELLGDPVDGLRWAGALLRAHGEVLPVSRVPLTIGGDVLSAGPDGG
+LRTRRVEGQVALAVAAFEGRVTDVRLSPSDAPATPEALAAIELADWVVLGPGSLYTSVLP
+HLLMPEVCQALDATAARRLMVLNLRTGDQETTGLTHADHLRVLHSHAPDLRLDVVIADVD
+AVTDRAAVEAEAARMGARVAFSRVSSAQDPQVHDPLRLAVAIDEAMTD
+>MOLHKGIG_01121
+MTSPLTGQLPLPPGMGSEGRGVGAGMSRPTARVTALGGGHGLSASLAALRHVAGHLTAIV
+TVADDGGSSGTIRREMAVLPPGDLRMALAALCDDTDWGRTWAHVMQHRFHSTEVPADQAT
+LDNHALGNLLIVALWELLGDPVDGLRWAGALLRAHGEVLPVSRVPLTIGGDVLSAGPDGR
+LRTRCVEGQVALAVAAFEGRVTDVRLSPSDAPATPEALSAIEMADWVVLGPGSLYTSVLP
+HLLMPDVRAALAATTARRLMVLNLRTGDQETTGLTHADHLKVLRSYAPDLRLDVVIADVD
+AVTDRAAVEAEAARMGARVAFSRVSSAQDPQVHDPLRLAVSIGEAMTH
+>NAFOICDF_01665
+MTGPVTGPSTSSLPLPPAAARGAWATTSGTVRPQVRVTALGGGHGLSASLAALRLVAGHL
+TAVVTVADDGGSSGTIRREMAVLPPGDLRMALAALCDDTDWGRTWAQVMQHRFRSTEVPE
+AEATLDGHALGNLLIVALWELIGDPVDGLRWAGALLRAHGEVLPVSRVPLTIGGDLLAED
+DAGRLVRRHVEGQVALAQAAHDGRVVDVRLSPADAPATPEALAAIELADWVVIGPGSLYT
+SVLPHLLMPEVRGALEVTTARRIFVLNIDTGTQETTGMTHADHLKVLREHAPGLQLDVVI
+ADADAVADRAAVVQEARRLGARVAFSRVAHAANRLAHDPLRLAVAIDEAMSS
+>MHAAABBN_00840
+MTSPLTGQLPLPPGMGSEGRGVGAGMSRPTARVTALGGGHGLSASLAALRHVAGHLTAVV
+TVADDGGSSGTIRREMAVLPPGDLRMALAALCDDTDWGRTWAHVMQHRFRSTEVPADQAT
+LDNHALGNLLIVALWELLGDPVDGLRWAGALLRAHGEVLPVSRVPLTIGGDVLSAGPDGR
+LRTRCVEGQVALAVAAFEGRVTDVRLSPSDAPATPEALSAIELADWVVLGPGSLYTSVLP
+HLLMPEVRSALAATAARRLMVLNLRTGDQETTGLAHADHLKVLRSYAPDLRLDVVIADVD
+AVTDRAAVEAEAARMGARVAFSRVSSAQDPQVHDPLRLAVAIDEAMTH
+>LFPAFLNI_01071
+MTSPLTGQLPLPPGMGSEGRGVGAGMSRPTARVTALGGGHGLSASLAALRHVAGHLTAIV
+TVADDGGSSGTIRREMAVLPPGDLRMALAALCDDTDWGRTWAHVMQHRFRSTEVPADQAT
+LDNHALGNLLIVALWELLGDPVDGLRWAGALLRAHGEVLPVSRVPLTIGGDVLSAGPDGR
+LRTRCVEGQVALAVAAFEGRVTDVRLSPSDAPATPEALSAIELADWVVLGPGSLYTSVLP
+HLLMPDVRAALAATTARRLMVLNLRTGDQETTGLTHADHLKVLRSYAPDLRLDVVIADVD
+AVTDRAAVEAEAARMGARVAFSRVSSAQDPQVHDPLRLAVAIDEAMTH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001235.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001235.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b1dfe38199a1b981d9b681ab82e85b04d6e5701f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001235.fa
@@ -0,0 +1,60 @@
+>ACLBLIBL_01774
+MADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLGSYFQDPARLTTKTRTM
+VFTAAAVEWTVVGSELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQVM
+RGDRRPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRARAQDRPCLLGYIGKCS
+APCVGRISPAEHRELAQDFCDFMAGDAQRFIRELERAMQGAVEELRYEDAARLRDDIAAL
+RRVFERNAVVLPESTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVSEPEM
+VTHLLQQVYGDLAGEDRIPHEILVPAEPDDAAQLVEWLSGLRGARVNVRVPRRGTKADLM
+ETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEIAEPLLRIECYDISHSQGTNVVG
+SMVVMEDGLPKKKDYRRFNVTGEAARDDTASMKDVLSRRFARLAEERAEGAPLSGQLEGE
+EEGRDRRFAYPPSLVVVDGGPPQVAAAAAVLEELGLDDLPVVGLAKRLEEVWLPGDEFPV
+VLPRTSEALYLLQRIRDESHRFAIAGHRGRRAKAMTASALDGISGLGPAKRTALLNHFGS
+VAQIRAAGVERLTEVAGIGPTLAQTVHAALAPAEPTDTVEP
+>MOLHKGIG_01119
+MPVADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLSSYFQDPARLATKTR
+TMVFTAAAVEWTVVGSELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQ
+VMRGDRKPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRARAQDRPCLLGYIGK
+CSAPCVGRISPADHRALAQDFCDFMAGDANRFIRELEKAMARAVEELRYEDAARLRDDIA
+ALRRVFERNAVVLPENTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVAEP
+EMVAHLLQQVYGDLEGPERIPHEILVPVEPDDAAQLTEWLSGLRGSRVAVRVPRRGSKAD
+LMETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEITEPLLRIECYDISHSQGTNV
+VGSMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARLAKERAEGAPLSGQVE
+ADDQEAGRRFAYPPSLVVVDGGPPQVAAAAAVLEELGLDDLPVVGLAKRLEEVWLPGDEF
+PVVLPRTSEGLYLLQRIRDESHRFAIAGHRSRRSKAMTVSALDGIPGLGPAKRTALLNHF
+GSVAEIRAAGVDRLTEVAGIGPRLAEAVHTALTADTPADTVES
+>NAFOICDF_01667
+MADPRTYRPAPGEISTSPGVYRFRDPDGRVIYVGKAKNLRARLSSYFQDPARLATKTRTM
+VFTASAVEWTVVASELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNERFPRVQVM
+RGDKRPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRAQAQDRPCLLGYIGKCS
+APCVGRISPDEHRALAQDFCDFMAGDADRFVRELEKAMAGAVEELRFEDAARLRDDIAAL
+RRVFERNAVVLAESTEADVFALHSDELETAVQVFHVRQGRIRGQRGWIMERVEDVGEDEA
+VAELLTQVYGDVPDTERIPHEVLVPVLPAGAEQVTEWLSGLRGARVQVRVPQRGPKADLM
+GTVRENAEMALKLHKTRRSGDLTTRSAALRELQDALEIDEPLLRIECYDISHSQGTNVVG
+SMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARMAEDRREGGVLTGQIDAE
+EAEGERRRFAYPPSLVVVDGGPPQVAAAAEVLAELGLDDLPVVGLAKRLEEVWLPGDEFP
+VVLPRTSEGLFLLQRIRDESHRFAIAGHRSRRTKAMTASALDDVPGLGPTRRRALLTHFG
+SVERMRQAGPAGLTEVAGIGPALAEAVHAALTASDGGDTVAP
+>MHAAABBN_00838
+MADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLSSYFQDPARLATKTRAM
+VFTAAAVEWTVVGSELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQVM
+RGDRKPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRARAQDRPCLLGYIGKCS
+APCVGRISPADHRALAQDFCDFMAGDANRFIRELEKAMARAVEELRYEDAARLRDDIAAL
+RRVFERNAVVLPENTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVAEPEM
+VAHLLQQVYGDLEGPERIPHEILVPVEPDDAAQLTEWLSGLRGSRVAVRVPRRGSKADLM
+ETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEVTEPLLRIECYDISHSQGTNVVG
+SMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARLAKERAEGAPLSGQVEGD
+DQEAGRRFAYPPSLVVVDGGPPQVAAAAAVLAELGLDDLPVVGLAKRLEEVWLPGDEFPV
+VLPRTSEGLYLLQRIRDESHRFAIAGHRSRRSKAMTVSALDGIPGLGPAKRTALLNHFGS
+VAEIRAAGVDRLTEVAGIGPRLAEAVHTALTADTPADTVES
+>LFPAFLNI_01069
+MPVADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLSSYFQDPARLATKTR
+TMVFTAAAVEWTVVGSELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQ
+VMRGDRKPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRARAQDRPCLLGYIGK
+CSAPCVGRISPADHRALAQDFCDFMAGDANRFIRELEKAMARAVEELRYEDAARLRDDIA
+ALRRVFERNAVVLPENTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVAEP
+EMVAHLLQQVYGDLEGPERIPHEILVPVEPDDAAQLTEWLSGLRGSRVAVRVPRRGSKAD
+LMETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEITEPLLRIECYDISHSQGTNV
+VGSMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARLAKERAEGAPLSGQVE
+GDDQEAGRRFAYPPSLVVVDGGPPQVAAAAAVLEELGLDDLPVVGLAKRLEEVWLPGDEF
+PVVLPRTSEGLYLLQRIRDESHRFAIAGHRSRRSKAMTVSALDGIPGLGPAKRTALLNHF
+GSVAEIRAAGVDRLTEVAGIGPRLAEAVHTALTADTPADTVES
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001238.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001238.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff1930468ba6ac139ac385265749472fd35cab87
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001238.fa
@@ -0,0 +1,80 @@
+>ACLBLIBL_01779
+MTSPATNPPSLTDRIDALPPTPDADDVFGAFAAWTEVRGISLYPAQEEAALELVQGRHVI
+LATPTGSGKSLVALAAHADALAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS
+TVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQVPLLELPQAR
+FLLMSATLGDTTRLEADLIERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEELVSTHQA
+PVYIVHFSQLDAVETAQGLSSISVTSKEEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGV
+HHAGMLPKYRRLVEKLAQDGLLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQA
+REFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAAAKFANVKDEAERAKRMKQSV
+KSGKRKSPPAGFVSWGPATFERLVAAEPEPLVSRMQITHSMLLNILDRPGDPVVAVRRLL
+RGTHETPARQAILMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLS
+PFALAALELLDPAEPDHALDVVSVIEATLDPPRQVLSAQVKKAKGEAVAAMKAEGMDYND
+RMRALDEVTHPQPLADLLEQQFEVYRASAPWLAEFELTPKSVVRDMFERAMGFGDYVRFY
+GIARSEGVLLRYLTDAVKALRQTVPEASRTEELQVLLDWLDEMVKQTDSSLLEEWEDLVA
+GDIEELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEELARLSGDLSA
+DDWADALDAYFGDHEDIDDGPAARGTELFRVAESPDVAPPVELAGSRWWAVRQVLKDPDG
+VHDHGVNAVVDLDASDEAGHPVIRVVSVGAPESGWGL
+>MOLHKGIG_01114
+MTSAATNPPSLTDRIDALPPAPDADDVFGAFAAWTEDRGISLYPAQEEAALELVQGRHVI
+LATPTGSGKSLVALAAHADALAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS
+TVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQVPLLELPQAR
+FLLMSATLGDTTRLEADLTERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEEFVSTHQA
+PVYIVHFSQLDAVETAQGLSSISVTSREEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGV
+HHAGMLPKYRRLVEKLAQDGLLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQA
+REFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAAAKFANVKDEAERAKRMKQSV
+KSGKRKTPPAGFVSWGPATFERLVSAEPEPLVSRMRITHSMLLNILDRPGDPVIAVRRLL
+RGTHETPARQAVLMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLS
+PFALAALDLLDPADPDHALDVVSVIEATLDPPRQVLSAQVKHAKGEAVAAMKAEGMDYND
+RMRALDEITHPRPLAELLEQQFELYRQDAPWLAEFELTPKSVVRDMFERAMGFGDYVRFY
+GIARSEGVLLRYLTDAVKALRHTVPEAARTEELQVLLDWLDEMVKQTDSSLLEEWEDLVA
+GDIDELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEALARLSGELSA
+DDWADALDAYFDDHEDIDDGPAARGPELFRVAAAPDVAAPLELAGPRWWAVRQVLKDPDG
+DLDHGINAVVDLDASDEAGHPVIRVVSVGAPESGWGL
+>NAFOICDF_01672
+MTPSATNPPSLTDRLDALPASPDADDVFGAFAAWTEDRGISLYPAQEEAVLELVQGRHVI
+LATPTGSGKSLVALGAHADALAHGKVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS
+SVNADAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQLPLLELPQAR
+FLLMSATLGDTSMLERDLAERTGREVAVVAHAERPIPLSFEWSEVPLQEKVEELVSTHQA
+PVYIVHFSQLDAVETAVGLASISVTTKEEKEAIAERIAGFRFSAGFGKTLNRLVRAGIGV
+HHAGMLPKYRRLVEKLAQEGRLKVISGTDTLGVGINVPIRTVLLTALSKFDGEKTRILQS
+REFHQIAGRAGRAGFDTQGYVVVQAPEHVIENKAAERKAAAKFAGIKDEAERAKRMKQSV
+KGSKRKTPPQGFVSWGPATFDKLVASEPEPLVSRMRITHSMLLNILDRPGDPVLAVRRLL
+RATHETPARQAQLMRRALGIFRELLATGVVEVLPEPDAEGRTVDLTVDLQPDFALNQPLS
+PFALAALDLLDPAAPDHHLDVVSVIEATLDAPRQVLSAQVKKAKGEAVAAMKAEGMDYSD
+RMRALDEVTHPQPLAELLEQAFERYRQDAPWLAEFELSPKSVVRDMFERAMGFGDYVRFY
+GLARSEGVLLRYLTDAVKALRQTVPQEDRTEDLQVLLDWLDEMVKQTDSSLLEEWEDLMS
+GDIAELRRDLESLEPTPPPRLTDNAAVFRVMVRNAMFHRVRLFGDEQDARLAELSGDLSA
+NDWADALDAYFDEHEDIDDGPDARGQEFFRVATAPGARCPVELEGSRWWAVRQVLKDHDG
+DHDHGINAVVDLEASDEAGHPAIRVVSVGAPVPGWDL
+>MHAAABBN_00833
+MTSAATNPPSLTDRIDALPPTPDADDVFGAFAAWTEDRGISLYPAQEEAVLELVQGKHVI
+LATPTGSGKSLVALAAHADALAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS
+TVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQVPLLELPQAR
+FLLMSATLGDTTRLEADLTERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEELVSTHQA
+PVYIVHFSQLDAVETAQGLSSISVTSREEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGV
+HHAGMLPKYRRLVEKLAQDGLLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQA
+REFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAAAKFANVKDEAERAKRMKQSV
+KSGKRKTPPAGFVSWGPATFERLVSAEPEPLVSRMRITHSMLLNILDRPGDPVIAVRRLL
+RGTHETPARQAVLMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLS
+PFALAALDLLDPADPDHALDVVSVIEATLDPPRQVLSAQVKHAKGEAVAAMKAEGMDYND
+RMRALDEITHPRPLAELLEQQFELYRQDAPWLAEFELTPKSVVRDMFERAMGFGDYVRFY
+GIARSEGVLLRYLTDAVKALRHTVPEAARTEDLQVLLDWLDEMVKQTDSSLLEEWEDLVA
+GDIDELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEALARLSGELSA
+DDWADALDAYFDDHEDIDDGPAARGPELFRVAAAPDVAAPLELAGPRWWAVRQVLKDPDG
+DLDHGINAVVDLDASDEAGHPVIRVVSVGAPESGWGL
+>LFPAFLNI_01064
+MTSAATNPPSLTDRIDALPPTPDADDVFGAFAAWTEDRGISLYPAQEEAVLELVQGKHVI
+LATPTGSGKSLVALAAHADALAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS
+TVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQVPLLELPQAR
+FLLMSATLGDTTRLEADLTERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEELVSTHQA
+PVYIVHFSQLDAVETAQGLSSISVTSKEEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGV
+HHAGMLPKYRRLVEKLAQDGLLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQA
+REFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAAAKFANVKDEAERAKRMKQSV
+KSGKRKTPPAGFVSWGPATFERLVSAEPEPLVSRMRITHSMLLNILDRPGDPVIAVRRLL
+RGTHETPARQAVLMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLS
+PFALAALDLLDPADPDHALDVVSVIEATLDPPRQVLSAQVKHAKGEAVAAMKAEGMDYND
+RMRALDEITHPRPLAELLEQQFELYRQDAPWLAEFELTPKSVVRDMFERAMGFGDYVRFY
+GIARSEGVLLRYLTDAVKALRHTVPEAARTEDLQVLLDWLDEMVKQTDSSLLEEWEDLVA
+GDIDELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEALARLSGELSA
+DDWADALDAYFDDHEDIDDGPAARGPELFRVTAAPDVAAPLELAGPRWWAVRQVLKDPDG
+DLDHGINAVVDLDASDEAGHPVIRVVSVGAPESGWGL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001242.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001242.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f698fce335c4835a3736a55f580a39be606f569
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001242.fa
@@ -0,0 +1,65 @@
+>ACLBLIBL_01785
+MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW
+LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK
+DSSVNEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGEEMDRDV
+LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG
+QVVREETEMYIFPASHYVAGDERMGRAVTAIEDELRERLQELESQDRLLEAQRLRMRTTY
+DLEMMQQMGYCNGIENYSRHIDGRPDGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE
+GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII
+RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLDAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT
+SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIEETERRRAVQIAYNEEHGIDPQPLRKRI
+ADITDQLAREDADTADFLKGMGGVKSGFDYGMGHRGLSSLDREEGQERAGGGPAVDAASL
+PAKDLADLIEQMSLQMHQAAADLQFELAARLRDEVGELKKELRQMRREQ
+>MOLHKGIG_01108
+MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW
+LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK
+DSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGAEMDRDV
+LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG
+QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDRLLEAQRLRMRTTY
+DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE
+GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII
+RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT
+SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRI
+ADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSLDRAPATGEGAEAPAVDPASL
+PAKDLADLIEQMSQQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ
+>NAFOICDF_01677
+MSLAKQINRVVAPFEVVSPYQPSGDQPTAIAEIAERVQAGEKDVVLMGATGTGKSATTAW
+VIEQLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK
+DSSINEEVERLRHSATNALLTRRDVVVVATVSCIYGLGTPEEYIAQMVTLRRGQEMDRDA
+LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEVESIQTLHPLTG
+QVVREEEEMYIFPASHYVAGDERMGRAIATIEDELRERLQELESQDKLLEAQRLRMRTTY
+DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE
+GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGQYELSQADGVVEQII
+RPTGLVDPTVVVKPTQGQIDDLLEQIRTRTEKDERVLVTTLTKRMAEDLTEYLLEAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVSILDADKEGFLRSTT
+SLIQTIGRAARNVSGEVHMYADRVTDSMRRAIEETERRREVQIRYNAEHGIDPQPLRKKI
+ADITDALAREDADSADFLKGMGGVKAGFDYGMGHRGLGSLDHEPPAGEVPSGSPAVDPAA
+LPAKDLAQLIEQMSAQMHQAAADLQFELAARLRDEIGDLKKELRQMKREQ
+>MHAAABBN_00827
+MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW
+LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK
+DSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGAEMDRDV
+LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG
+QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDKLLEAQRLRMRTTY
+DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE
+GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII
+RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT
+SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRI
+ADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSLDRDATTGEGTEAPAVDPASL
+PAKDLADLIEQMSKQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ
+>LFPAFLNI_01057
+MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW
+LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK
+DSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGAEMDRDV
+LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG
+QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDKLLEAQRLRMRTTY
+DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE
+GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII
+RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT
+SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRI
+ADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSLDRDATTGEGTEAPAVDPASL
+PAKDLADLIEQMSKQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001244.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001244.fa
new file mode 100644
index 0000000000000000000000000000000000000000..717771e97114e062b4ce55a53d2fd1eb3dc8e542
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001244.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01789
+MSAPPARCTVLPRLAAGEDGWIVHELEVRRSRFLTVLGRVADEAQARAMIAALRRRHHDA
+RHVCSAFVLGPERSVARSSDDGEPAGTAGTPMLEALTARETAPGRTDLTDVCAVVVRWFG
+GVKLGAGGLVRAYSESVSAALDTTPLVTRSRRAILAVDAPHAQAGRWENELRAAGVAVLD
+AGYGAAGVRLRVGVPDSDAQRADFAARLADITAGAGRAEPIGTEWIDHD
+>MOLHKGIG_01105
+MPDPAPAPTARCTVLPASARDPDGWLEREVEIRRSRFLTYLGRLEDEAQAREMVAVLRRR
+HHDARHVCSAFVLGPARDRMRSSDDGEPAGTAGVPMLEAVLQRETAPGRTDLTDVCAVVV
+RWFGGIKLGAGGLVRAYSDSVSGALDAAPLRTRSRLALLAVEAPHTDAGRWENELRAAGV
+SVLEASYGAAGVRLTVGVPDTEEARAAFAARLADVTAGAGRAERIGEDWVDHE
+>NAFOICDF_01680
+MDSPAPPAGGPVACTVLAAGALAEDGWVVHEEEVRRSRFLAVLARTPDEEAARAVVATLR
+RRHHDARHVCSAWILGPGRRRMRSNDDGEPAGTAGVPMLEALSLRDTGGGATDLTDVTAV
+VVRWFGGVKLGAGGLVRAYSDAVSRALDAAPLVRRTRRARYELAAPHGEAGRWAHELELT
+GASLEGVRWDGPQAVIDLAVPDVPDGHSALASAVARITSGSAVAAPAGHVWVDGALA
+>MHAAABBN_00824
+MPDPAPAPTARCTVLPASARDPDGWLEREVEIRRSRFLTYLGRVEDEAQAREMVAVLRRR
+HHDARHVCSAFVLGPARDRMRSSDDGEPAGTAGVPMLEAVLQRETAPGRTDLTDVCAVVV
+RWFGGIKLGAGGLVRAYSDSVSGALDAAPLRTRSRLALLAVEAPHTDAGRWENELRAAGV
+SVLEASYGAAAVRLTVGVPDTEEARAAFAARLADVTAGAGRAERIGEDWVDHE
+>LFPAFLNI_01054
+MPDPAPAPTARCTVLPASARDPDGWLEREVEIRRSRFLTYLGRVEDEAQAREMVAVLRRR
+HHDARHVCSAFVLGPARDRMRSSDDGEPAGTAGVPMLEAVLQRETAPGRTDLTDVCAVVV
+RWFGGIKLGAGGLVRAYSDSVSGALDAAPLRTRSRLALLAVEAPHTDAGRWENELRAAGV
+SVLEASYGAAAVRLTVGVPDTEEARAAFAARLADVTAGAGRAERIGEDWVDHE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001245.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001245.fa
new file mode 100644
index 0000000000000000000000000000000000000000..819378fae14b1492688c7fbd5b218985c303d904
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001245.fa
@@ -0,0 +1,37 @@
+>ACLBLIBL_01790
+MDLGCGNGLLGVGAARLWPHVRVLATDQSAVAVASTLATARANGVADRLEAVRDDALAGR
+PDASEECILLNPPFHDGNAVDPAVAHRLVAEAARVLAPGGRLWCVWNSHLRHRPVLEAEV
+GPTRQVARDRTFTVTVSTRR
+>MOLHKGIG_01104
+MSEPLPRGVTPDVAHGGLPDDLTAGVDFAALDRWPLPPEPDRQAHDAADLLLLDTLAGWI
+ASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDANLAAWRAAGRLGGEA
+GELERTATPEDAARGARTVLLPLPRSLDELDRLSRIVAAAADPGVVLLAGGRDKHMSPRM
+NAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTPRPPEEADRDVPGVGSLHLVAHAGAFG
+GAAADPGSRLLLASLADDPRPPGRLVDLGCGNGLLSVGAARLWPHVTVLATDQSAVAVAS
+TLATARANRVADRVRAVRDDALATWPDGTEECVLLNPPFHDGNAVDPSVAHRLVAAAARV
+LEPGGRLWCVWNSHLRYRPVLEDLVGPTRQTARDRTFTVTVSERR
+>NAFOICDF_01681
+MDAIAQTPPRDPGPARLTATELVTPDAAGRGLPRDWTAEFPFERLGRWPLPESRERQAHD
+AADLLLVDTLAGWTADGRVPGPVAVLHDQHGAVSLPLLARGLNVRLGLDEASAARSVERN
+LDLFRDADGALPAGWGRLTVGGVDAATLADARTVLLLLPRALDALHLTAARIAVHAAPDV
+LVLGAGRDKHMTPSMNDVLARSFAAVVPGRGRSKSRVITAARPVDDATEPAPRRAQHRLG
+RLGAVTLVGGWATFGGAAADPGSLLLAGTLADRAPALPVPAPHRMRTDSGLGVDIPWATR
+AGAPDVVDAGSGNGMLSVVAARVWPEAAVLASDQSADAVASSAATAEANGLAERITAVQD
+DALGALPDASVRAVLLNPPFHDGTAVDPTVAHRMIEAAGRILAPGGELWCVWNSHLRHRP
+VLETAVGPTRQVARNRTFTVTVSTRR
+>MHAAABBN_00823
+MSEPLPRGVTPDVARGGLPDDLTAGVDFAALDRWPLPTEPDRQAHDTADLLLLDTLAGWI
+ASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDANLAAWRAAGRLGGET
+GELERTATPEEAARGARTVLLPLPRSLDELDRLSRIVSAAADPGVVLLAGGRDKHMSPRM
+NAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTARPPEEADRDVPGVGRLHLVAHAGTFG
+GAAADPGSRLLLASLADDPRPPGRVVDLGCGNGLLSVGAARLWPHVTVVATDQSAVAVAS
+TLATARANRVADRVRAVRDDALATWPDGEEECVLLNPPFHDGNAVDPSVAHRLVAAAARV
+LEPGGRLWCVWNSHLRYRSVLEDLVGPTRQTARDRTFTVTVSERR
+>LFPAFLNI_01053
+MSEPLPRGVTPDVARGGLPDDLTAGVDFAALDRWPLPTEPDRQAHDAADLLLLDTLAGWI
+ASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDANLAAWRAAGRLGGET
+GELERTATPEEAARGARTVLLPLPRSLDELDRLSRIVSAAADPGVVLLAGGRDKHMSPRM
+NAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTARPPEEADRDVPGVGRLHLVAHAGTFG
+GAAADPGSRLLLASLADDPRPPGRVVDLGCGNGLLSVGAARLWPHVTVVATDQSAVAVAS
+TLATARANRVADRVRAVRDDALATWPDGEEECVLLNPPFHDGNAVDPSVAHRLVAAAARV
+LEPGGRLWCVWNSHLRYRSVLEDLVGPTRQTARDRTFTVTVSERR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001246.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001246.fa
new file mode 100644
index 0000000000000000000000000000000000000000..db214b414f7c3db41fd86edd6c06cfa8a8f49d92
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001246.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_01791
+MTTTSNAPQVAINDIGTAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG
+VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE
+EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN
+NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS
+WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV
+TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS
+LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVESNEWMEGFESERAAWEQQY
+ADAQSRWEQHKEQVRRSFEEEANAGADTGAGMGGSSYSSEAPASDGGTLASDEALAALRE
+KLTGN
+>MOLHKGIG_01103
+MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG
+VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE
+EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN
+NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS
+WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV
+TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS
+LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVETNEWMEGFETERAAWEQQY
+ADAQARWEAHKEQVRRSLQEEATAGADAGAGLGGSSYSSEAPSSDGGTLASDEALAALRE
+KLTGN
+>NAFOICDF_01682
+MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG
+VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKVKE
+EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN
+NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRQGTVSSIVNFGAFVDLGGVDGLVHVSELS
+WKHIDHPSEVVEVGQDVTVEVLDVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV
+TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDQLFVKVIDIDLERRRISLS
+LKQANEGVDPEGTEFDPALYGMAAEYDDEGNYKYPEGFDVETNEWMEGFESERASWEQQY
+ADAQTRWEAHKEQVRRSLEEEAQAPAGNASTASSYSSEAPASDGGTLASDEALAALREKL
+TGN
+>MHAAABBN_00822
+MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG
+VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE
+EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN
+NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS
+WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV
+TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS
+LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVETNEWMEGFETERAAWEQQY
+ADAQARWEAHKEQVRRSLQEEATAGADAGAGLGGSSYSSEAPSSDGGTLASDEALAALRE
+KLTGN
+>LFPAFLNI_01052
+MTTTSNAPQVAINDIGSAEDLLAAIDATIKYFNDGDLVEGTVVKVDRDEVLLDIGYKTEG
+VIPSRELSIKHDVDPDEVVAVGDTVEALVLTKEDKEGRLILSKKRAQYERAWGDIEKIKE
+EDGVVEGTVIEVVKGGLILDIGLRGFLPASLVEMRRVRDLAPYIGQKLEAKIIELDKNRN
+NVVLSRRAWLEQTQSEVRSNFLHKLEKGQVRNGTVSSIVNFGAFVDLGGVDGLVHVSELS
+WKHIDHPSEVVEVGQEVTVEVLEVDMDRERVSLSLKATQEDPWQLFARTHALGQVVPGKV
+TKLVPFGAFVRVEDGIEGLVHISELASRHIDTAEQVVSVNDELFVKVIDIDLERRRISLS
+LKQANEGVDPEGTEFDPALYGMAAEYDEEGNYKYPEGFDVETNEWMEGFETERAAWEQQY
+ADAQARWEAHKEQVRRSLQEEATAGADAGAGLGGSSYSSEAPSSDGGTLASDEALAALRE
+KLTGN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001247.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001247.fa
new file mode 100644
index 0000000000000000000000000000000000000000..99e5ab8f0614a7239c9c91f9488485991eb8e311
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001247.fa
@@ -0,0 +1,85 @@
+>ACLBLIBL_01794
+MAADPTPEDPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR
+PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTITLEGYEA
+DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVMAKYG
+VSPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLTQYGDLDGVLAHADEIKGKKGEALR
+AHLDDVRRNRRLNALVRDLDLPIGLEAMALEMPEREPVEELFDALQFNRIRERVFEVFSE
+RIGETAPAAQVEEAPEFTEAATAQDVADFLAAEAGNLLGVHVDVEGPALLPKRKVPVPGT
+FGTAVGVALVGEHAGLHVSLDADAPDPALLAALREALGEGGLSKAVHDLKRVLKAIAEPA
+EATALEAGTPLDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLAAPREPAEADAQGA
+FDLDGGAAAAERAARAADAVRAAWVVRRLSVLFTPQVLERGAQRLLQELEIPLARLLARI
+ELTGIAVDAQALETLRADFSEAAAAAQESAWASVAEETGGMKVNLGSPKQLQEVLFEHLD
+MPRTRKTKTGWSTDVDSLQDLLEQTRHPFLENLMRHRDATKLRQTVEGLLETVAPDGRIH
+TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIREVFVADRVAGEDAVLLSADYSQIEMR
+IMAHLSEDAGLIQAFREGEDLHSFVGSQVFGVAPDEVSSEQRAKVKAMSYGLAYGLSSFG
+LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARRDGYTSTIEGRRRYLPDLSSDN
+RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLAEHGMASRLLLQVHDELILEVPAAE
+LEQATALLQERMGRAAELAVPLDVHVGQGRSWHDAAH
+>MOLHKGIG_01101
+MAADPTPEAPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR
+PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTLEGYEA
+DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVKAKYG
+VAPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLKQYGDLDGVLAHAHEITGKKGEALR
+EHLEDVRRNRRLNALVRDLDLPIGLETMRLEMPEREPVEELFDALQFHRIRERVFEVFGE
+RVGEDAPPPEVEAAPEFTEATTAEDVRAFLAAEAGNLLGVHVDVEGPALLPRRKVPVPGT
+FGTPVGVALVGEHAGLHVTLDGDAPDPALVAAVREALGEGGLAKAVHDLKRTLKALAAPT
+EGDGLGPDAALDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLTAPRESAQQRAQGS
+FDLDGGQAAAERADRAADAVRAAWVVRRLSTQFTPQVLDRGAQRLLQELEIPLSRLLARM
+ELTGIAVDVDALTGLREDFTDAADAAKESAWASVAEETGGMQVNLGSPKQLQEVLFERLN
+MPRTRKTKTGYSTDVDSLQDLLEQTRHPFLENLMAHRDATKLRQTVEGLLETVAPDGRIH
+TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIREVFVADEVAGEQAVLLSADYSQIEMR
+IMAHLSEDEGLIQAFREGEDLHSFVGSQVFGVDPDDVTAEQRAKVKAMSYGLAYGLSSFG
+LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARQDGYTSTIEGRRRYLPDLSSDN
+RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLEEHGLASRLLLQVHDELILEVPAAE
+LEKATALLKERMGRAAELSVPLDVHVGQGRSWHDAAH
+>NAFOICDF_01684
+MGENSTEARPRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTSMLLTMIRQQAP
+THVAVAFDLSGPTFRSAEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTKEDFEAD
+DIVATLSAQAEAQGWDVCVVSGDRDAFQLISERTQVLYPKKGVSDIPPMTAADVEAKYGV
+RPEQYPELAALVGESADNLPGVPGVGPGFAAKWLQKYGDLDGVLAHADEITGKKGEALRA
+HLDDVRRNRRLNALVRDLDLDVSLDAMELTMPEREVVEELFDALQFQRIRERVFEVFAER
+LGSAAPAAPVAEAPAAVLAATADDVHAFVSAHAGTLLGLHVEIDGPDLLPKRKVPVPGTF
+GTPVGLALAAEDAALYVDLTDADADPGLVAALGDLLAEDGAAKAVHDLKRTLKAIAVPTG
+PTALPADTSLHGVVDDVALSAYLIQPDRRDTDLATLSQAHLQEPLEAPESAAAGAQGAFD
+LDGAQEEAERTARAARAARSAWVVRRLSQAFTPQVLERGAQRLLQEMEIPLARLLARMEL
+AGIAVDGDALSALLADFTDRAEAAKESAWASVAEETGGMKVNLGSPKQLQEVLFEHLDMP
+KTRKTKTGWSTDVDSLQDLLEQTQHPFLENLMAHRDATKLRQTVEGLRETVAPDGRIHTT
+YSQTVAATGRLSSLHPNLQNIPVRTEAGRRIREAFVAAPVDGEPAELLSADYSQIEMRIM
+AHLSEDAGLIEAFNSGEDLHSFVGSQVFGVDPDDVTSEQRSKVKAMSYGLAYGLSSFGLS
+KQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARRDGFTSTIEGRRRYLPDLTSDNRQ
+LRDMAERAALNAPIQGSAADIIKRAMLDVQAGLVEQGLRSRLLLQVHDELILEVPASELD
+AATALLQERMGRAADLSVPLDVHVGHGGTWHAAAH
+>MHAAABBN_00820
+MAADPTPEAPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR
+PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTLEGYEA
+DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVMAKYG
+VAPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLKQYGDLDGVLAHAHEITGKKGEALR
+EHLEDVRRNRRLNALVRDLDLPIGLEAMRLEMPEREPVEELFDALQFNRIRERVFEVFGE
+RVGEDAPPPEAEAAPEFTEATTAEDVRSFLAAEAGNLLGVHVDVEGPALLPRRKVPVPGT
+FGTPVGVALVGEHAGLHVTLDGDAPDPALVAAVREALGEGGLAKAVHDLKRTLKALAAPT
+EGDGLGRDAALDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLTAPREPAQQRAQGT
+FDLDGGQAAAERADRAADAVRAAWVVRRLSTQFTPQVLDRGAQRLLQELEIPLSRLLARM
+ELTGIAVDVDALTGLREDFTDAADAAKESAWASVAEETGGMQVNLGSPKQLQEVLFERLN
+MPRTRKTKTGYSTDVDSLQDLLEQTRHPFLENLMAHRDATKLRQTVEGLLETVAPDGRIH
+TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIREVFVADEVAGEQAVLLSADYSQIEMR
+IMAHLSEDEGLIQAFREGEDLHSFVGSQVFGVDPDDVTAEQRAKVKAMSYGLAYGLSSFG
+LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARQDGYTSTIEGRRRYLPDLSSDN
+RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLEEHGLASRLLLQVHDELILEVPAAE
+LEQATALLKERMGRAAELSVPLDVHVGRGRSWHDAAH
+>LFPAFLNI_01050
+MAADPTPEAPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR
+PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTLEGYEA
+DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVKAKYG
+VAPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLKQYGDLDGVLAHAHEITGKKGEALR
+EHLEDVRRNRRLNALVRDLDLPIGLEAMRLEMPEREPVEELFDALQFNRIRERVFEVFGE
+RVGEDAPPPEVEAAPEFTEATTAEDVRAFLAAEAGTLLGVHVDVEGPALLPRRKVPVPGT
+FGTPVGVALVGEHAGLHVSLDGDAPDPALVGAVREALGEGGLAKAVHDLKRTLKALAAPT
+EGDGLGRDAALDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLTAPREPAQQRAQGT
+FDLDGGQAAAERADRAADAVRAAWVVRRLSTQFTPQVLDRGAQRLLQELEIPLSRLLARM
+ELTGIAVDVDALTGLREDFTVAADAAKESAWASVAEETGGMQVNLGSPKQLQDVLFERLN
+MPRTRKTKTGYSTDVDSLQDLLEQTRHPFLENLMAHRDATKLRQTVEGLLETVAPDGRIH
+TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIRGVFVADEVAGEQAVLLSADYSQIEMR
+IMAHLSEDEGLIQAFREGEDLHSFVGSQVFGVDPDDVTAEQRAKVKAMSYGLAYGLSSFG
+LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARQDGYTSTIEGRRRYLPDLSSDN
+RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLEEHGLASRLLLQVHDELILEVPAAE
+LEQATALLKERMGRAAELSVPLDVHVGRGRSWHDAAH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001248.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001248.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff4ff868b419d1c2d7f36c225bbbd8c126344cb3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001248.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01795
+MTDHAERADAAPAPTSDLVYRPGVTPELTDAQREAACAAAGLTPELVAALGGATVSPLAQ
+KMGIRFLELTPERAVATMPVAGNEQPAGLLHGGAHLVLAESLGSMAAKLHAGPERGVVGI
+EIGATHHRAARSGLVTGTATAIHLGGTLTTHEVVMTDEQGRRLSTARITNMVLRGRG
+>MOLHKGIG_01100
+MSEHTETTPAASERVYRPGVTPELSPAELEAACAEAGLTPELVTALGGAVISPLAQKMGL
+RFLELTAERAVATLPVAGNEQPVGLLHGGAHLVLAESLGSMAAKIHAGPDRNVVGVEISA
+THHRAVRSGLVTGTATAVHLGGTLVTHEVVMTDEQGRRLSTARITNLVLAPRP
+>NAFOICDF_01685
+MTDTTTAPERAQALLAGLTFHAGIRPELTDEERAALATAAGMTPAVQEALGGPAVSHLAL
+KMGIRFLELSAERSVATMPVAGNEQPVGLLHGGAHLVLAESLGSLSAKVHAGPHRGAVGT
+EIGATHHRSVRSGLVTGTATAIHLGRTLTTHEIVMTDEEGRRLSTVRMTNMLLDPR
+>MHAAABBN_00819
+MSEHTATTPAASDRVYRPGVTPELSPAELAAACAEAGLTPELVAALGGAAISPLAQKMGL
+RFLELTAERAVATLPVAGNEQPVGLLHGGAHLVLAESLGSMAAKIHAGPDRNVVGVEISA
+THHRAVRSGLVTGTATAVHLGGTLVTHEVVMTDEQGRRLSTARITNLVLAPRP
+>LFPAFLNI_01049
+MSEHTETTPAASERVYRPGVTPELSPAELEAACAEAGLTPELVTALGGAAISPLAQKMGL
+RFLELTAERAVATLPVAGNEQPVGLLHGGAHLVLAESLGSMAAKIHAGPDHNVVGVEISA
+THHRAVRSGLVTGTATAVHLGGTLVTHEVVMTDEQGRRLSTARITNLVLDAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001251.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001251.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89b73b73de62735f163264b1f4a5a5b4eed317f8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001251.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01798
+MHADPSSDRPVPADGTVVLAPGRASALSWPWRWLVFWCWYAWALVTSSEAVLKDLVTPGD
+QARSGIARIRSNCRTDAEVTLLSALITLTPGTLTLGTRRAGARGEEPGDPGATRLLYVHG
+LYADDADALRGEIHDMERRLLHAMRKQGVA
+>MOLHKGIG_01097
+MHTVAPADGTVDLAPGTASAVSWPWRWLVFWCWYAWALVTSSKAVIKDLVTPGVQARSGI
+ARVRSNCRTDAEVTLLSALITLTPGTLTLGTRRAGAVGDEDGDPDARRLLYVHGLYADDA
+DALRAEIHDMEARMLHAMRKTGVA
+>NAFOICDF_01688
+MTVHHPDGGVDLTPGTASAASWPLRWLLFWCWYAWALVTSSGAVLHDLLTPGDQARSGIA
+RVRSNCRTDAEVTLFSALITLTPGTLTLGTRREGAQGQEPGDPEARRLLYVHGLYADDAD
+ALRAEIHDMEARMLHAMRRTGVAR
+>MHAAABBN_00816
+MHTVAPADGTVDLAPGTASAVSWPWRWLVFWCWYAWALVTSSKAVIKDLVTPGVQARSGI
+ARVRSNCRTDAEVTLLSALITLTPGTLTLGTRRAGAVGDEDGDPDARRLLYVHGLYADDA
+DALRAEIHDMEARMLHAMRKTGVA
+>LFPAFLNI_01046
+MHTVAPADGTVDLAPGTASAVSWPWRWLVFWCWYAWALVTSSKAVIKDLVTPGVQARSGI
+ARVRSNCRTDAEVTLLSALITLTPGTLTLGTRRAGAVGDEDGDPDARRLLYVHGLYADDA
+DALRAEIHDMEARMLHAMRKTGVA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001262.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001262.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e5d36d10a2e52b84f2a7502c93c0f949b921773
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001262.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01812
+MSVLQEIIDGVREDLAPRRRDVPEARLAELVAAAPAPRDAHAALLGGRTDPAGIRVISEV
+KRSSPSKGALAEIPEPAALARAYERGGASAVSVLTEARRFGGSLADLDAVRGAVDLPVLR
+KDFTVTEYQIHEARAPGADLVLLIVAALDDAELTGFLQLTESLGMHALVEAHTPEEIERG
+VTAGARILGVNVRNLKTLDVDPARYAALADGLPEDVVRVAESGVESDEQIKAYAAAGADA
+VLVGEALVRHGAPEEALRAFRAASLTVR
+>MOLHKGIG_01085
+MSVLQEIIDGVREDLEPRRRALPEARLSELVAATPAPRDAHAALHGGRTDPAGIRVISEV
+KRASPSKGALAEIPEPATLARAYERGGASAVSVLTEARRFGGSLADLDAVRAAVDLPVLR
+KDFTVTEYQIHEARAHGADLVLLIVAALDDAELAGFLQLTESLGMHALVEAHTPEEIERG
+VAAGARILGVNVRNLKTLDVDPARYAALADGLPEDVVRVAESGVESEEQIKAYAAAGADV
+VLVGEALVRHGAPEEALRAFRAASLTVR
+>NAFOICDF_01700
+MPETVLDSIVAGVLEDLAPRREAVPEARLQELIAQAPAPRDAYAALRDGRSDPAGIHVIA
+EVKRRSPSKGALAEITEPAALAASYADGGAGAISVLTEQRRFGGSLADLDAVRAAVARPV
+LRKDFTVTEYQILEARAHGADLVLLIVASLDDARLRGFRELAESLGMHALVEAHTSEEIA
+RGVDSGARILGVNVRNLKTLDVDPDRYAALAGDLPEDVVRVAESGVESEAQVRQYAAAGA
+DAILVGEALVRHGAPADALRAFRAASLTVR
+>MHAAABBN_00804
+MSVLQEIIDGVREDLEPRRRALPEARLAELVAAAPAPRDAHAALHGGRTDPAGIRVISEV
+KRASPSKGALAEIPEPATLARAYERGGASAVSVLTEARRFGGSLADLDAVRAAVDLPVLR
+KDFTVTEYQIHEARAHGADLVLLIVAALDDAELAGFLQLTESLGMHALVEAHTPEEIERG
+VAAGARILGVNVRNLKTLDVDPARYAALADGLPEDVVRVAESGVESEEQIKAYAAAGADV
+VLVGEALVRHGAPEEALRAFRAASLTVR
+>LFPAFLNI_01034
+MSVLQEIIDGVREDLEPRRRALPEARLAELVAAAPAPRDAHAALHGGRTDPAGIRVISEV
+KRASPSKGALAEIPEPATLARAYERGGASAVSVLTEARRFGGSLADLDAVRAAVDLPVLR
+KDFTVTEYQIHEARAHGADLVLLIVAALDDAELAGFLQLTESLGMHALVEAHTPEEIERG
+VAAGARILGVNVRNLKTLDVDPARYAALADGLPEDVVRVAESGVESEEQIKAYAAAGADV
+VLVGEALVRHGAPEEALRAFRAASLTVR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001265.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001265.fa
new file mode 100644
index 0000000000000000000000000000000000000000..18210cca63280a8e55e0eec09a6d08a26de94821
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001265.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_01815
+MSAATTPSREEFLRLADTARVIPVVRTVLADGLTPLAIHRRLAGSRPGTFLMESAAPGAV
+WSRYSFVGAGSAVTLTSRDGQAHWQGVPPEGLPTEGRALDVLAACLRLLRTDARTHLDGA
+LPHLVSGMAGFLGWNTVRAWERLPNPPQDDLGLPDLAMNLVTDLAVHDALDGTVTLIANA
+VNGNGLATGAEGAYEDALARLDAMVDQLAAPAAEPVSTVPRRWLDADADEVAAQAEDRWG
+AAGFREAVGKAQEAIRDGEVFQAVVSRRLSVTTGATGADVYRVLRMVNPSPYMYLFSFET
+PDGEPYEIVGSSPEALVTVQDRRVVTHPIAGSRRRGATLEDDRLLGKDLMEDEKERAEHL
+MLVDLSRNDLSRVCRPGTVEVTQFMELEAFSHILHLVSHVEGRMREDVDALDVLRAAFPA
+GTLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSATLHRGQAHVQAG
+AGVVADSDPDAETAETVTKATAPLRSVLTAGEMGRA
+>MOLHKGIG_01082
+MTAATTPSRAEFLRLADTARVIPVVRTVLADGLTPLAIHRRLAGSRPGTFLMESATPGAA
+WSRYSFIGAGSSVTLTSRNGEAHWQGTPPEGLPTQGRALDVLAACLRLLRTDVRAEVGGV
+LPHLVSGMAGFLGWNTVRAWERLPHPPEDHLGLPDLAMNLVTDLAVHDALDGTVTLIANA
+VNGNGLATGADRAYDDALARLDAMVERLAAPAADPVSDVPRRWLEADADEVAAQAEDRWG
+AEGFREAVAKAQRAIRDGDVFQAVVSRRLSVTTDATGLDVYRVLRTVNPSPYMYLFSFET
+PDGEPYEIVGSSPEALVTVRDRRVVTHPIAGSRRRGATEKDDRLLGKDLLEDEKERAEHL
+MLVDLSRNDLSRVCRPGTVEVTQFMELEAFSHILHLVSHVEGRMRDDVDALDVLRAAFPA
+GTLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSATLHRGQAHVQAG
+AGIVADSDPDAETAETVTKATAPLRSVLTAGELGQA
+>NAFOICDF_01703
+MSGVVPSREEFLAVAPTSRVIPVVRRVLADGLTPLAIHRRLADSRPGTFLLESATPGAAW
+SRYSFIGAGSAATLTARGEDAVWLGEPPEGLPTEGRALDVLAESLRLLSTDARTRVDAAL
+PHLVSGMAGFLGWPAVRAWERLPHPPEDHLGLPLLAMNLISDLAVHDAQDGTVTLIALAI
+NGDGLATGAERAYDDAVARLEDMVARLRAGAEDPVDEVPRRWLDATAEEVAAEAEDRWGA
+AGFRDAVGRAQQAITDGEVFQIVVSRRFSVDTAASGVDVYRVLRMVNPSPYMYLFSFQTP
+DGEPYEIVGSSPEALVTVQDRRVVTHPIAGSRRRGATPEDDRLLGKELAEDEKERAEHLM
+LVDLSRNDLSRVCEAGTVEVTQFMELEAFSHILHLVSHVEGRLRDDVTSLDALRSAFPAG
+TLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSVTLAGRQAHVQAGA
+GIVADSDADAETAETVTKATAPLRAVLTAAELRGA
+>MHAAABBN_00801
+MTAATTPSRAEFLRLADTARVIPVVRTVLADGLTPLAIHRRLAGSRPGTFLMESATPGAA
+WSRYSFIGAGSAVTLTSRDGEAHWQGTPPEGLPTQGRALDVLAACLRLLSTDVRAEVGGV
+LPHLVSGMAGFLGWNTVRAWERLPHPPEDHLGLPDLAMNLVTDLAVHDALDGTVTLIANA
+VNGNGLATGADRAYDDALARLDAMVERLTAPAADPVSDVPRRWLEADADEVAAQAEDRWG
+AEGFREAVGKAQRAIRDGEVFQAVVSRRLSVTTDATGLDVYRVLRMVNPSPYMYLFSFET
+PDGEPYEIVGSSPEALVTVRDRRVVTHPIAGSRRRGATAEDDRLLGKDLLEDEKERAEHL
+MLVDLSRNDLSRVCRPGTVEVTQFMELEAFSHILHLVSHVEGRMRDDVDALDVLRAAFPA
+GTLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSATLHRGQAHVQAG
+AGIVADSDPDAETAETVTKATAPLRSVLTAGELGQA
+>LFPAFLNI_01031
+MTAATTPSRAEFLRLADTARVIPVVRTVLADGLTPLAIHRRLAGSRPGTFLMESATPGAA
+WSRYSFIGAGSAVTLTSRDGEAHWQGTPPEGLPTQGRALDVLAACLRLLSTDVRAEVGGV
+LPHLVSGMAGFLGWNTVRAWERLPHPPEDHLGLPDLAMNLVTDLAVHDALDGTVTLIANA
+VNGNGLATGADRAYDDALARLDAMVERLTAPAADPVSDVPRRWLEADADEVAAQAEDRWG
+AEGFREAVGKAQRAIRDGEVFQAVVSRRLSVTTDATGLDVYRVLRMVNPSPYMYLFSFET
+PDGEPYEIVGSSPEALVTVRDRRVVTHPIAGSRRRGATAEDDRLLGKDLLEDEKERAEHL
+MLVDLSRNDLSRVCRPGTVEVTQFMELEAFSHILHLVSHVEGRMRDDVDALDVLRAAFPA
+GTLSGAPKPRALQLLDEWEPTERGPYGGVVGYFDLAGNMDMAINIRSATLHRGQAHVQAG
+AGIVADSDPDAETAETVTKATAPLRSVLTAGELGQA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001278.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001278.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9d7e2ea1a3b08fa2d3df7c25c3ed890a1e81d22d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001278.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01834
+MAQIVHLADRSPQVTPDQLLAGFHPSYRFGEVSFDTYIPDPAHPSQAQAVERLRRFAAAL
+GRGSGSGGGFLSGLFGGGRKRAAGPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTFVE
+YTNLVGALSFRKAVDVLKEYTLVCIDEFELDDPGDTVLMSRLMRELADAGVHLVATSNTL
+PGSLGEGRFAAQDFQREIQVLAEQFEVIRVDGEDYRHRGLSAAPDPLPDDQVVSTAEANF
+PDSGVLAVDDFDALTAMLSRVHPSRYRELVKDVDVIALHDVKTITEQATALRFVVFADRL
+YDKDVPVVASGVPFDDLFTQEMMHGGYMKKYFRTVSRMTALVREGQLGIAEEK
+>MOLHKGIG_01052
+MAQIVHLADRSPQVTPDQLLAGFHPSYRFGTVSFDTYIPDPAHPTQAQAVERLRRFAADL
+GRGGSGGGFLGGLFGGKKRAAGPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTFVEYT
+NLVGALSFRKAVDELKEYTLVCIDEFELDDPGDTVLMSRLMRELADAGVRLVATSNTLPG
+SLGEGRFAAQDFKREIQVLADQFEVIRVDGEDYRHRGLSAAPSPLDDAAVEATAQENFPD
+AGVLAVDDFADLTAMLSRVHPSRYRELVKDVDVLALHDVHTITEQATALRFVVFADRLYD
+KDVPVLASGVPFDALFTQEMMHGGYMKKYFRTVSRMTALVREGQTGVAEHK
+>NAFOICDF_01724
+MPQTVHLADRSPQVSADQLLAGLHPSYRFGEVSFDSYIPDPAHPSQAQAVERLRRFAASL
+GGPRGGSGGGGFLGGLFGGGRKRGPEPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTF
+VEYTNLVGALSFRQAVDVLKGYTLVCIDEFELDDPGDTVLMSRLMRELADAGVRLVATSN
+TLPGSLGEGRFAAQDFKREIQVLADQFEVIRVDGEDYRHRGLSAAPEPLADDAVESTAQA
+NFPHADVVSVDDFAALTAMLSRVHPSRYRELVKDVDVAAFHDVQTITEQATALRFVVFAD
+RLYDKDVPVVASGVPFDQLFTSEMMHGGYMKKYFRTVSRMTALVREGQTGETVEK
+>MHAAABBN_00765
+MAQIVHLADRSPQVTPDQLLAGFHPSYRFGTVSFDTYIPDPAHPSQAQAVERLRRFAADL
+GRGGSGGGFLGGLFGGKKRAAGPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTFVEYT
+NLVGALSFRKAVDELKEYTLVCIDEFELDDPGDTVLMSRLMRELADAGVRLVATSNTLPG
+SLGEGRFAAQDFKREIQVLADQFEVIRVDGEDYRHRGLSAAPSPLDDAVVEATAQENFPD
+AGVLAVDDFADLTAMLSRVHPSRYRELVKDVDVLALHDVHTITEQATALRFVVFADRLYD
+KDVPVLASGVPFDALFTQEMMHGGYMKKYFRTVSRMTALVREGQTGVAEHK
+>LFPAFLNI_00993
+MAQIVHLADRSPQVTPDQLLSGFHPSYRFGTVSFDTYIPDPAHPSQAQAVERLRRFAADL
+GRGGSGGGFLGGLFGGKKRAAGPAGIYLDGGFGVGKTHLLASTWHAAPGPKAFGTFVEYT
+NLVGALSFRKAVDELKEYTLVCIDEFELDDPGDTVLMSRLMRELADAGVRLVATSNTLPG
+SLGEGRFAAQDFKREIQVLADQFEVIRVDGEDYRHRGLSAAPSPLDDAAVEATAQENFPD
+AGVLAVDDFADLTAMLSRVHPSRYRELVKDVDVLALHDVHTITEQATALRFVVFADRLYD
+KDVPVLASGVPFDALFTQEMMHGGYMKKYFRTVSRMTALVREGQTGVAEHK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001279.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001279.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f88721e8c1297f16e0d22ba5272cbb05f37774d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001279.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01835
+MTETATEFSQYAHPEKLVSTQWVADHVGEEGVVVLESNEDALLYATGHIPGAQRIDWHTE
+LNDPVTRDFIGPEAFAEMAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDVRLMN
+GGRDKWIAEGRETTREVPTVARGEYPVVPRDDTTERAAREDVLQAVGTTPLIDVRSRPEY
+TGETTHMDGYPQEGTLRGGHIPTAASVPWAQAANEDGTFKSREELEAVYRDGAGLKDGDD
+VIAYCRIGERSSHTWFVLKHLLGHENVRNYDGSWTEWGNSVRLPIVVGEEPGAAPAR
+>MOLHKGIG_01051
+MTDTAAKFSEYAHPEKLVSTQWVADHVGDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE
+LNDPVTRDFVGPEAFAEFAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD
+GGRDKWIAEGRETTREVPTVARAEYPVIERDDHTERAAREDVLQAIGTTPLIDVRSRPEY
+TGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRAGAGLQEGDD
+VIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR
+>NAFOICDF_01725
+MTETPAEFAEYAHPEKLVSTQWVADHIDDEGVVVLESNEDTLLYSTGHIPGAVKIDWHTE
+LNDPVSRDFVGPEAFAELVASKGIGPDTTVVFYGDKSNWWAAYALWVFTLYGHRDVRLMN
+GGRDKWIAEGRPTTREVPEVTPAPSYPVSQRDDATDRAAREDVLAAIGSTPLVDVRSPKE
+YTGETTHMDGYPQEGTLRGGHIPTAASVPWAKAANEDGTFKSRAELEEIYKEGAGLGESD
+SVIAYCRIGERSSHTWFVLKQLLGYENVRNYDGSWTEWGNGVRLPIALGDEPGEAPAR
+>MHAAABBN_00764
+MTDTAAKFSEYAHPEKLVSTQWVADHVDDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE
+LNDPVTRDFVGPEAFAEVAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD
+GGRDKWIAEGRETTREVPTVARAEYPVIERDDHTERAAREDVLQAIGTTPLIDVRSRPEY
+TGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRTDAGLREGDD
+VIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR
+>LFPAFLNI_00992
+MTDTAAKFSEYAHPEKLVSTQWVADHVGDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE
+LNDPVTRDFVGPEAFAEFAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD
+GGRDKWIAEGRETTREVPTVARAEYPVIERDDHTDRAAREDVLQAIGTTPLIDVRSRPEY
+TGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRAGAGLQEGDD
+VIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001281.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001281.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c5f4fbbec46c75d1a7067c7e5debf3da4e8777b8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001281.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01837
+MAKTGRGRGRAHGAATPAVAALETAGVPYTLHTFEVDLDAGGERFGVQVARAMGVPPERM
+FKTLMVAAPDGGLAACVVPVSGQLDLRAAAAVLGVKRLALADLALVERRTGYVRGGVSPL
+GQRHRHPVLLDSSALDAPVMYVSGGQRGLDLELAPADLAAATDAVVAPIAAR
+>MOLHKGIG_01049
+MGQRKKDRGARHGAATPAVAALEAAGVPYRLHTFDVALDAGGERFGVQVARALSVPADRL
+FKTLMVADPDGALAACVVPVSGQLDLRAAAAVLGVKRLALADLAVVERRTGYVRGGVSPL
+GQRRPHPVVLDSSALDAELMYVSGGQRGLDVEIAPADLVRVTGAVVAEIAAG
+>NAFOICDF_01727
+MGRRKAADAAHGAATPAIRALVDAGVPHRVLSFDVHLDAVGERFGVQAAKALGVPPERTF
+KTLMVALPDGSLAACCVPVSGQLDLRAAATALGVKKVAMADLAVAERRTGYVRGGISPLG
+QRQRHPVVVDSSALDGDVLYVSAGQRGRDLELAPADLVAVTDAVVAPIAAR
+>MHAAABBN_00762
+MGQRKKDRGARHGAATPAVAALEAAGVPYRLHTFDVALDAGGERFGVQVARALSVPADRL
+FKTLMVADPDGALAACVVPVSGQLDLRAAAAVLGVKRLALADLAVVERRTGYVRGGVSPL
+GQRRPHPVVLDSSALDAELMYVSGGQRGLDVEIAPADLVQVTGAVVAEIAAD
+>LFPAFLNI_00990
+MGQRKKDRSARHGAATPAVAALEAAGVPYRLHTFDVALDAGGERFGVQVARALSVPADRL
+FKTLMVADPDGALAACVVPVSGQLDLRAAAAVLGVKRLALADLAVVERRTGYVRGGVSPL
+GQRRPHPVVLDSSALDAELMYVSGGQRGLDVEIAPADLVQVTGAVVAEIAAD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001283.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001283.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb3971598660295264e65a647eedfedb32fd6987
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001283.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01841
+MTRPEASDADARDLARASADASATDGFALPGAPDAFERFWNAHRMAYVTQGSDQVKDEHT
+CPFCAAPQRSDEASLIVHRGRAAYVVLNLYPYNPGHLLVCPYRHVPLYTDTTAEEAAEMA
+ELTQTAMLALGHATRAAGYNLGMNQGSVAGAGIAAHLHQHVVPRWTGDGNFLPIIARTKN
+MSQTLGETREILAGVWDEAAADHARLQEANARAAAERAGRRDEDRP
+>MOLHKGIG_01047
+MTSPGTGGSDARAQARASADAAATDGFELPGAPDAFERFWNAHRMAYVSKGTGQVKDEHT
+CPFCAAPQRDDEDSLIVHRGRTAYVVLNLYPYNPGHLLVCPYRHVPLYTDTTTEEAAEMA
+ELTQTAMLALGQAAGASGYNLGMNQGAVAGAGIAAHLHQHVVPRWTGDGNFLPIIARTKN
+MSQTLGETRQILADVWDRAAQDHAARQAANARAAGEHPRPGAGGPA
+>NAFOICDF_01729
+MTTTPHDDAAEVSADGAPAGERPYGDPAADAAALDGFELPGTPDAFDRLWNPHRLAYIQK
+GPEQVKDEDTCPFCAAPGRDDASALIVHRGATCFVILNLFPYNPGHLLICPYRHIPMYTD
+ATAEETAELADLAQTAMIAFELATRPKGYNLGMNQGVAGGAGIAAHLHQHVVPRWTGDGN
+FLPIIAQTKNMSQTLGQTREILADVWPQALAEHAERRARNAAAAAQAPRADA
+>MHAAABBN_00760
+MTSPGTGGSDARAQARASADAAATDGFELPGAPDAFERFWNAHRMAYVSKGTGQVKDEHT
+CPFCAAPQRDDEDSLIVHRGRTAYVVLNLYPYNPGHLLVCPYRHVPLYTDTTTEEAAEMA
+ELTQTAMLALGQAAGASGYNLGMNQGAVAGAGIAAHLHQHVVPRWTGDGNFLPIIARTKN
+MSQTLGETRQILADVWDRAARDHAARQAANARAAGEHPRPGAGGPA
+>LFPAFLNI_00988
+MTSPGTGGSDARAQARASADAAATDGFELPGAPDAFERFWNAHRMAYVSKGTGQVKDEHT
+CPFCAAPQRDDEDSLIVHRGRTAYVVLNLYPYNPGHLLVCPYRHVPLYTDTTTEEAAEMA
+ELTQTAMLALGQAAGASGYNLGMNQGAVAGAGIAAHLHQHVVPRWTGDGNFLPIIARTKN
+MSQTLGETRQILAGVWDRAARDHAARRAANARAAAEHPRPGAGDPA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001287.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001287.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e4f9aaf0c88692bb092d77692c16cd79cc869cb6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001287.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01846
+MCGRYVMARAAGDLVALGGGELPDERLELRRSWNVAPTSDVPILLEREADGAVRRELHVA
+RWGLVPSWAKELAVGSRAFNARSETVASKPTFRAAVRARRCAVPVEGYYEWKAPAPGAKG
+PDGKAAKKQPYYVHPAGAGDGEGPVIWFAGLYEWWQDPEAEAAGRDPWVLSTTILTMAAP
+DADDEDEVLGSLGDLHDRLPVPLDAETMDAWLTPGRLGSAEEADALVGQVCAGAYDVAAG
+WVLRPVGTAVGNVRNDGPELIQAEEPAQGTLL
+>MOLHKGIG_01039
+MCGRYVMARATSDLVALGDAEANEDLVLRQSWNVAPTAEVPILVAHADDVGAGGTRGGDG
+GAGVTRRIHVARWGLVPPWAKELSVGSRAFNARSETVASKPTFRAAVRARRCAVPVEGYY
+EWKTPEPGAKGPDGRIAKKQPYYVHPAGAGDGEGPVIWFAGLYEWWQDPEAKAAGEDAWV
+LSTTILTMAAPDADDDDPVLAALGQLHDRLPVPMDAETMDRWLAPDTLGSAEEADALVGQ
+VCAGAYDVAAGWSLRPVGSAVGNVRNNGPELIQEMREQQGTLL
+>NAFOICDF_01736
+MARAAGDLVALGGGLLPEEGLELRPNWNVAPTADVPILLEREDAGVVRRELHVARWGLVP
+TWAKELSVGSRAFNARSETVTSKPTFRSAVRARRCAVPVEGYYEWKAPEPGSTGPDGKAA
+VKQPFYVHPAGGGDGEGPVIWFAGLYEWWKDAGAEARGDDPWVLSTTILTMPSPADDEPG
+VLGELADLHDRLPMPMGPAAMDSWLSPDKLGSADEAAALVDEMTAQAYDVARGWELRPVG
+RAVGNVRNNGPELIAPPAEVQDALL
+>MHAAABBN_00752
+MCGRYVMARATSDLVALGDAEANEDLVLRQSWNVAPTAEVPILVAHADDVGAGGARGGDG
+GAGVTRRIHVARWGLVPPWAKELSVGSRAFNARSETVASKPTFRAAVRARRCAVPVEGYY
+EWKAPEPGAKGPDGRAAKKQSYYVHPAGAGDGEGPVIWFAGLYEWWQDPEAKAAGEDAWV
+LSTTILTMAAPDADDDDPVLAALGQLHDRLPVPMDAETMDRWLAPDTLGSAEEADALVGQ
+VCAGAYDVAAGWSLRPVGSAVGNVRNNGPELIQEMREQQGTLL
+>LFPAFLNI_00981
+MCGRYVMARATSDLVALGDAETNEELVLRQSWNVAPTAEVPILVAHADDVGAGVTRRIHV
+ARWGLVPPWAKELSVGSRAFNARSETVASKPTFRAAVRARRCAVPVEGYYEWKTPEPGAK
+GPDGRAAKKQPYYVHPAGAGDGEGPVIWFAGLYEWWQDPEAKAAGEDAWVLSTTILTMAA
+PDADDDDPVLAALGQLHDRLPVPMDAETMDRWLAPDTLGSAEEADALVGQVCAGAYDVAA
+GWSLRPVGSAVGNVRNNGPELIQEMREQQGTLL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001295.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001295.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fdd9cadce29e47e598168001a6c6a9406ca9fc74
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001295.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01860
+MTVAADPGHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVQKLELPEDRVARLPLITREPT
+LGATAPYVLLTPTYGGGDGPGAVPKQVIKFLNVPGNRTWIRGVIASGNTNFHEAYCLAGY
+IIARKCQVPLMYKFELMGTPEDVDSVRGGLEGLWT
+>MOLHKGIG_01025
+MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREPT
+LGATAPYVLMTPTYGGGSGPGAVPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLAGY
+IISRKCQVPLMYKFELMGTPDDVERVRGGLEGMWT
+>NAFOICDF_01750
+MTTATAGPNHMRDAEAQGLVPTDARLIYFSSASGYTHRFVEKLGLPLGQAARLPLLTREP
+TLGATAPYVLLTPTYGGGGDTGGEVPKQVIKFLNVPGNRALIRGVIASGNTNFSGAYAAA
+GYIISRKCQVPLMYKFELMGTPEDVVAVREGLERLEEGQHA
+>MHAAABBN_00740
+MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREPT
+LGATAPYVLMTPTYGGGSGPGAVPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLAGY
+IISRKCQVPLMYKFELMGTPDDVERVRGGLEGLWT
+>LFPAFLNI_00969
+MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREPT
+LGATAPYVLMTPTYGGGSGPGAVPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLAGY
+IISRKCQVPLMYKFELMGTPDDVERVRGGLEGLWT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001297.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001297.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b4e3da2a0063c284703f0815fef78d750d0e12b9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001297.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_01865
+MTARDAAGGPAVTRNDAESRYELHDGGTLLAVLDYRDNGTAVALTRAFTIPVHRGHGHAA
+TLTAGAVEDIEARGGAAGGRQIVPLCWYVAQWLEEHPEKAHLVAPR
+>MOLHKGIG_01023
+MSTSPTVTRNDAESRYELHDGGTLLAVLDFRDNGAAVSLNRAFTIPVHRGRGHAAALTAG
+AVEDIATNGGPAGGRRIVPMCWYVAQWFDEHPEKSALLAPR
+>NAFOICDF_01758
+MDASDSPTTFTRNDAASRYELHDASGELLAALDYRDNGTAVSLTRAFTVPVHRRQGHAAT
+LTAGAVADIEARGGAAGGTTVVPMCWYVARWFEEHPEKAGLLDAR
+>MHAAABBN_00738
+MSTSPTVTRNDAESRYELHDGGTLLAVLDFRDNGAAVSLNRAFTIPVHRGRGHAAALTAG
+AVEDIETNGGPAGGRRIVPMCWYVAQWFDEHPEKSALLAPR
+>LFPAFLNI_00967
+MTTGGCPGMSTSPTVTRNDAESRYELHDGGTLLAVLDFRDNGAAVSLNRAFTIPVHRGRG
+HAAALTAGAVEDIATNGGPAGGRRIVPMCWYVAQWFDEHPEKSALLAPH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001299.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001299.fa
new file mode 100644
index 0000000000000000000000000000000000000000..90cd62e3209ffc06039f09c53e7dc231b3d420b9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001299.fa
@@ -0,0 +1,31 @@
+>ACLBLIBL_01867
+MTGPAAPWESIDAAPVHVEVHQDGERIVGASVEHTQMNEAGELDPDPQTVGWYGAPQWGT
+DPGERSPYAGILAGHVVYYGVKDVFWNLDAVRAGDVVVLTYDDGSQAVFEADADAVSVEK
+EALTQDPANRWAWEPGGDDARLTLITCDLVPGTGMAGNAFNNWVVQATRVA
+>MOLHKGIG_01020
+MNTTVRRALWVVLVLLCLGLVFLALRGVLAVGAVPISAAPTLSATASATPSPSPSPSSAR
+FTPSPATTATPTPTPSPSSASPTREAAVPVETQELAGTPTPSEEPTPTEEPAPSEEPAPS
+EEPTPAAAAHLSGPAAPWDEVTATPVHVDVHQDGEQIVGAGIDLTQLDEGGDLDPEPQTV
+GWYGPPQWGTTPGERSRYAGVLAGHVVYHGVRDVFWNLGDVRAGAVVVVTYDDGTQAAFE
+ADSDAVSVEKEALTQDPANRWAWEPGGDDAKVTLITCDLVPGTGMAGNAFNNWVVQATRV
+A
+>NAFOICDF_01763
+MSTTVKRAVWALLLLICLGVGAFALRGMFAFGDVPISAAPTVSARASTASSTPSAATGSP
+SSTSASASAGPSVPAATSASSAAASTTTPASPTSSTTTPASPTSSTTPASTEAAAPAVGA
+ASSTATASSSATPTGTDSRMTKPAASWERITAAPVHIDVYADGEQVVGAPVELVQTRDDG
+ELNPDPQMAGWYGPPQWTTTPGERSAHPGVIAGHVIHSGLKDVFWNLQTLKAGSIVVITY
+DDGTQAEFRTDFDVRSMDKDDLTQSPDYAWAWELPEAGNKVTLITCDLVDGSGMTGWSTN
+NWVTQATRIG
+>MHAAABBN_00734
+MNTTVRRALWVVLVLLCLGLVFLALRGVLAVGAVPISAAPTLSATASATPSPSPSPSSAR
+FTPSPAPTATPIPTPSPSSASPTREAAVPVETQELAGTPTPSEEPTPTEEPAPSEEPAPS
+EEPTPAAAAHLSGPAAPWDEVTATPVHVDVHQDGEQIVGAGIDLTQLDEGGDLDPEPQTV
+GWYGPPQWGTTPGERSRYAGVLAGHVVYYGVRDVFWNLGDVRAGAVVVVTYDDGTQAAFE
+ADADAVSVEKEALTQDPAHRWAWEPGGDDAKVTLITCDLVPGTGMAGNAFNNWVVQATRV
+A
+>LFPAFLNI_00964
+MNTTVRRALWVVLLLLCLSLVFLALRGVLAVGAVPISAAPTLSATASVSPSSAATTREAA
+VPVETQELAGTPTPSEEPTPTEEPAPSEEPTPAAAAHLSGPAAPWDEVTATPVHVDVHQD
+GEQIVGAGIDLTQLDEGGDLDPEPQTVGWYGPPQWGTTPGERSRYAGVLAGHVVYHGVRD
+VFWNLGDVRAGAVVVVTYDDGTQAAFEADADAVSVEKEALTQDPSHRWAWEPGGDDAKVT
+LITCDLVPGTGMAGNAFNNWVVQATRVA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001300.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001300.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f4c06f9e0157ea558e76b2722a8956c17777f4d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001300.fa
@@ -0,0 +1,33 @@
+>ACLBLIBL_01868
+MEERLLRAFVTVAEAGTVSAAAQRLDLVQSALSRQLQRLQRELRLPLFARVGSRLELTTA
+GEAFLPVARRVLAAHRQAEQAARTLASGSLAEVAIAAPGTTLIDVVLPFVATLDEDDPRP
+RVAETQLDDSLQDAVARHDLVVMPMAPGPTVQALHLIDLPVWAYVAPGHPWADRADVALE
+ELVDVRVVAPSRSFMARRVLDGAVAVAGLTAPELSEANSGRVAQALVATGAGVAVVTEDP
+AFGLVPLRVLLDGRALSVGLHAAWRADHFAAATLARIAASLQDFVRTRYPQPGPADDIPV
+TTRASPLSAAPSQ
+>MOLHKGIG_01019
+MEEKLLRAFVTVAEVGTVSGAAIRLDLVQSALSRQLQRLQRELRLPLFARVAGRLELTTA
+GEAFLPVAREVLVAHRRAEQAARALASGRLTDVAVAAPGTTLIDVVLPFVATFGEEDPRP
+RVAETQLDDSLLDAVARHDLVVMPTVPPPSVASLPLMDLPVWAYVAPGHPWAGRTRVSLD
+DLVAQPVVAPARTFMARRVLDGAVAVAGLTPPALTEANSGRVAQALVAAGAGVAVVTEDP
+AFGLTPVRVIAQGRTLTVRLHAAWRGDHFAAETLEAIARRLQAFVRDRYAEPGDDAPGRG
+RSA
+>NAFOICDF_01760
+MDSIAAGGRALDLDHLLDPALLRTFVAVVDEGTVTAAARELGLGQSALTRHLQRLQRDLG
+LALFAPEGARLRITPAGQAWLPVARSLLAAHAHARQAARILAAGRLTELSLGAPGTTLID
+VVIPFLTVLGEGDPAVRVTETQLDDSLQDSVARLDLVVLPSTPPDDVAALPLQSMPVWAC
+VAPGHPWADRDELDAAELAGARLVLPSRSFKARRVFDAALEVAGAAPRQVVEANSGRVAQ
+ALAANGTAVAVVTEDPAFGLRPLPIRAGGRRLEVHLHAVWRRDHFAAEEIAGVAAQLRVF
+VRRRYDVAEAQDDADGSLSRAVSVD
+>MHAAABBN_00733
+MDEKLLRAFVTVAEVGTVSGAAIRLDLVQSALSRQLQRLQRELRLPLFARVAGRFELTTA
+GEAFLPVAREVLVAHRRAEQAARALASGRLTDVAVAAPGTTLIDVVLPFVATFGEEDPRP
+RVAETQLDDSLLDAVARHDLVVMPTVPPPSVASLPLMDLPVWAYVAPGHPWAGRTRVSLD
+DLVAQPVVAPARTFMARRVLDGAVAVAGLTPPALVEANSGRVAQALVATGAGVAVVTEDP
+AFGLTPVRVIAQGRTLAVRLHAAWREDHFAAETLQALARRLQAFVRDRYAEPGDDAPR
+>LFPAFLNI_00963
+MEEKLLRAFVTVAEVGTVSGAAIRLDLVQSALSRQLQRLQRELRLPLFARVGGRLELTTA
+GEAFLPVAREVLVAHRRAEQAARTLASGRLTDVAVAAPGTTLIDVVLPFVATFGEEDPRP
+RVAETQLDDSLLDAVARHDLVVMPTVPPPSVASLPLMDLPVWAYVAPGHPWAGRTRVSLD
+DLVAQPVVAPARTFMARRVLDGAVAVAGLTPPALVEANSGRVAQALVATGAGVAVVTEDP
+AFGLTPVRVIAQGRALAVRLHAAWREDHFATATLEKIARRLQAFVRDRYAEPGDDAPR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001301.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001301.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ee56d3baa52064ffe477ab500c236c8c6d9a3e3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001301.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_01869
+MSSTPDLEQSRHLATALPGPRSQALAERQKAAVPAGVATTMPVYAARAAGGILEDVDGNR
+LIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTAPISGQ
+TRTALFNSGAEAVENAVKVARSYTGKQAVAAFDHAYHGRTTLTMALTAKNMPYKHHFGPF
+APEVYRVPGSYPLRDGLSGAEAARRAIGALETQIGAENLAAVIMEPIQGEGGFIVPAEGF
+LPAVVEWCRANDVLFIADEVQSGVARTGSWFACEAEGVEPDLMTTAKGIAGGMPLSGVTG
+RAEVMDSVHPGGLGGTYGGNPVAAAAALAVFEAIEDEDLLAKATRIEEVIREHFAAHADD
+RIAEVRGRGAMMAIELVEPGTGEPDAALTAAVAAAVRATGVILLTCGTYGNVIRFLPPLT
+IGEDLLKEGLSEVTKALQSA
+>MOLHKGIG_01018
+MTATPDLEQTRHLATELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGNR
+LIDLASGIAVTSVGASHPRVVAAVQDQVAQFTHTSFMITPYEGYVAVAEQLDRTSPIPGE
+TRTALFNSGAEAVENAVKVARAYTGKQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGPF
+APEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEGF
+LPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVTG
+RAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIREHFEQNADD
+RIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRATGVILLTCGTYGNVVRFLPPLT
+IGEDLLKEGLSEVTKALQSA
+>NAFOICDF_01761
+MTSPVTAPEQSRHIATELPGPKSRELAARQAGAVPAGVATTMPVFASRAGGGIIEDVDGN
+RLIDLGSGIAVTSVGASHPKVVEAVQEQVADFTHTCFMITPYEGYVAVAEKLGEKAPISG
+ETRTALFNSGSEAVENAVKVARAYTRKQAVVAFDHAYHGRTTLTMSLTAKSMPYKHSFGP
+FAPEVYRVAGSYPLRDGLNGAAAAKKAISAMEKQIGADNLAAVIMEPLQGEGGFIVPAEG
+FLQAIVEWCTANDVLFIADEVQSGFARTGAWSASELEGIEPDLMCTAKGIAGGMPLSAVT
+GRAEVMDAVHPGGLGGTYGGNPVATAASLAVFEAIEEDGLLQEAQMIERVIREHFEQNAD
+ERIAEVRGRGGMMAIEFVDPASGEPDAALTGKLAAAVRAAGVVLLTCGTYGNVVRFLPPL
+TIGEELLREGLAEVTTALQSA
+>MHAAABBN_00732
+MTATPDLEQTRHLATELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGNR
+LIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTSPIPGE
+TRTALFNSGAEAVENAVKVARAYTGKQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGPF
+APEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEGF
+LPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVTG
+RAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIREHFAQNADD
+RIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRAAGVILLTCGTYGNVVRFLPPLT
+IGEDLLKEGLSEVTNALQSA
+>LFPAFLNI_00962
+MTATPDLEQTRHLVTELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGNR
+LIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTCPIPGE
+TRTALFNSGAEAVENAVKVARAYTGRQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGPF
+APEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEGF
+LPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVTG
+RAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIRDHFEQNADD
+RIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRATGVILLTCGTYGNVVRFLPPLT
+IGEDLLKEGLSEVTKALQSA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001304.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001304.fa
new file mode 100644
index 0000000000000000000000000000000000000000..57ea6e8cf0195bdafa1b1fec3a8702a52eaf7bc9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001304.fa
@@ -0,0 +1,24 @@
+>ACLBLIBL_01882
+MRLILLRHGETDWNAGDRYQGRTDVELNAVGERQARRAAVGPVGDLLEEAAELVAVASPL
+ARARRTAEILLEARVGAADLALDEQLMELHGGDWEGLGLTAIAQRWPEEHRSWRAVPALD
+AGPVGGETLRAAGERALGALRGRVPQHWAVYAAAL
+>MOLHKGIG_01008
+MRLILLRHGETDWNVLDRYQGHTDIELNAEGERQARRAAGGPVGDLVEDAEELVAVCSPL
+ARARRTAEIVLEARVGAASVAVDPELMELAGGEWEGLELSAIAERWPDEHRLWRAEPALD
+AGPVGGETLRGGGERALRALRGHVPPHWADTPRDGGAHTLLVVAHGALIRAATGLLLRHE
+GEAFAAMERIGNARAAVLQGAFTADTGAEGWGDWTLEGYGI
+>NAFOICDF_01809
+MRLVLLRHGETDWNALDRYQGRTDVPLNALGERQAAAAAAGPVGELLRSAEDLVAVSSPL
+IRARRTAEIVLEDAVGAVELAVDSRLVELGGGEWEGLDFTEIGARWPHEHHAWRTVPDLD
+GGPVGGEVLRAGGERVLAAAAAHVPEDWSTPRPARVPDARTLLIVAHGAVIRAAAGLALA
+LEGADFAHLARVSNARAVILDGTFAGEGPGAWSLLGYDV
+>MHAAABBN_00722
+MRLILLRHGETDWNVLDRYQGHTDIELNAEGERQARRAAGGPVGDLVEDAEELVAVCSPL
+ARARRTAEIVLEARVGAASVAVDPELMELAGGEWEGLELSAIAERWPDEHRLWRAEPALD
+AGPVGGETLRGGGERALRALRGHVPPHWADTPRDGGAHTLLVVAHGALIRAATGLLLRHE
+GEAFAAMERIGNARAAVLQGAFTADTGAEGWGDWTLEGYGI
+>LFPAFLNI_00951
+MRLILLRHGETDWNALDRYQGHTDIELNAEGERQARRAAGGPVGDLLEDAEELVAVCSPL
+ARARRTAEIVLQARVGAASVAVDPELMELAGGEWEGLELSAIAERWPDEHRLWRAVPALD
+AGPVGGETLRGGGERALRALRGHVPPHWADTPRDGGAHTLLAVAHGALIRAATGLLLRHE
+GEAFAAMERIGNARAAVLQGAFAPATEGWGDWTLEGYGI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001305.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001305.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2823a1a519e54bcb979f107ea28b675cea1d35b9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001305.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01883
+MTVPQTTLDALTVAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE
+EALLKEEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLA
+EEHTRPDAAGEGAADDAAPHAS
+>MOLHKGIG_01007
+MTVPQTTLDALTTAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE
+EALLKDEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLP
+EESTRPDAATQDDGASASHAS
+>NAFOICDF_01810
+MTVPQTTLDALQVAAAAAAEKVATHIVAVDVAERLGLTDAFLIASGASERQVNAIVDGIE
+EDLLVKEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDSPAIDLGLP
+EEATRPDDALDAAAQD
+>MHAAABBN_00721
+MTVPQTTLDALTTAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE
+EALLKDEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLP
+EESTRPDAATQDDGASASHAS
+>LFPAFLNI_00950
+MTVPQTTLDALTTAAAAAADKLGTHIVAFDVAERLGLTDAFLIASGASERQVNAIVDGVE
+EALLKDEQLKPLRREGRSDGHWVLLDYGHFVVHVQHREDREFYALDRLWKDTPAIDLGLP
+EESTRPDAAAQDDDASASHAS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001314.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001314.fa
new file mode 100644
index 0000000000000000000000000000000000000000..153f37a9b8e61a8fd8fdb682c89073e5b507e6cd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001314.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01892
+MPSTPTADRVRPAQPAETPASDGTLSWYARPAGMAWTLLVTSLVALTATIVIIVERSILA
+ADPGHRTSCDLNPWVSCGRVMQSWQAMTFGFPNTYIGIVAFSVLITVAVSLFAGARFARW
+YWLLMNVGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNIQTGTLPA
+SPGAARLARELAWPVILILYVLVFATILLELGFGVIGLD
+>MOLHKGIG_00998
+MPATPLTDDIRLSPADDIPAEEARLTWYARPAGTAALLLITSLVALTATIIIIVERTLLT
+ADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLLAGARFARW
+YWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNLQTGTLPA
+PAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID
+>NAFOICDF_01838
+MDVTETAENPPAPRAHHAAHALPEDRSLSWYARPLGTAWMLLITSIVAVTATIIIIVERS
+ILAENPNYRTSCDINPWLSCGTVMQSWQAHTFGFPNTFVGIVAFPVLITVAVSLFAGARF
+ARWYWVLMNVGILAGFAFAAWLWYSAVYSIGTLCLYCMIVWAMVILQLVLVTSRNLQTGA
+LPSSPGLARLAQDFAWPVIVLLYALVFASILLQLGLGVIGIR
+>MHAAABBN_00712
+MPATPLTDDIRLSPADDIPAEEARLTWYARPAGTAALLLITSLVALTATIIIIVERTLLT
+ADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLLAGARFARW
+YWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNLQTGTLPA
+PAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID
+>LFPAFLNI_00941
+MSMPTTPPTDDVRLSPADDVPAEEARLTWYARPAGTAALLLITSLVALTATIVIIVERAL
+LTADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLLAGARFA
+RWYWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNLQTGTL
+PAPAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001315.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001315.fa
new file mode 100644
index 0000000000000000000000000000000000000000..834ab94c5ea8152972980c56fe7f314900461274
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001315.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_01893
+MAQHIEETLVLVKPDGVERNLVGEILARIERKGYVIADLKMLTPTRSMLERHYEEHQGKP
+FFDPLVDFMASGPVVAVRVTGNSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGESVQKN
+LVHGSDSSLSAERELGIWFG
+>MOLHKGIG_00997
+MTHHTEETLVLIKPDGVARNLVGEILARIERKGYVIADLKMLTPTRAMLERHYEEHQGKP
+FFEPLVAFMASGPVVAARVTGDSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGEAVQKN
+LVHGSDSTLSAERELAIWFG
+>NAFOICDF_01839
+MTHHPEETLVLVKPDGVERRLTGEIIARIERKGYEVVDLKMLVPTREMLAAHYEEHEGKP
+FYEPLLEFMGSGPVVALRLAGDRVIEGFRSLAGATDPTVAAPGTIRGDYARDWGAGVQKN
+LVHGSDSTLSAERELAIWFA
+>MHAAABBN_00711
+MTHHTEETLVLIKPDGVARNLVGEILARIERKGYVIADLKMLTPTRAMLERHYEEHQGKP
+FFEPLVAFMASGPVVAARVTGDSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGEAVQKN
+LVHGSDSTLSAERELAIWFG
+>LFPAFLNI_00940
+MTHHTEETLVLIKPDGVARNLVGEILARIERKGYVIADLKMLTPTRAMLERHYEEHQGKP
+FFEPLVAFMASGPVVAARVTGDSVIEGFRSLAGKTDPTVAAPGTIRGDLGRDWGEAVQKN
+LVHGSDSTLSAERELAIWFG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001317.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001317.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4f801c21d1c7ffb47c006eff8ee1713969f74feb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001317.fa
@@ -0,0 +1,100 @@
+>ACLBLIBL_01895
+MYPLASSAPDGRTPASPRFPEIERRILAYWDEDGTFQASIDQRPALNEDGSQNEFVFYDG
+PPFANGLPHYGHLLTGYVKDLVARYQTQQGRRVERRFGWDTHGLPAELEAMKQLGMTDKS
+EIEAMGIDTFNDACRSSVLKYTDQWQDYVTRQARWVDFENDYKTLTPDFMESVIWAFSEL
+HRKGLTYRGFRVLPYCWNDETPLSNHELRMDDDVYKMRQDPSVTVTFPITGLPADPALVP
+DGGADAALAAHLAGVHVLAWTTTPWTLPTNAALAVGPQIQYAVVPAGPEGATADGDRFLL
+AVDLVGAHATELGYADADAARAAVTETIPGARLGGLAYEPLFTDVFDAHADETFTVNGRD
+LGVEGAHRILVDDYVSTEDGTGVVHQAPAYGEDDQRVCEANGIPVLLSVDSGARFLPLFA
+REDVGRGDLREIAGVQVFEANRTIVRALRGLGRVAREASYEHSYPHCWRCRTPLIYRAVT
+SWYVKVTQVKERMLELNEEITWIPGNVKHGQFGTWVANARDWSISRNRYWGSPIPVWESD
+HPDYPLQEVYGSLAEIEEAFGRLPRNAEGEVDLHRPWVDDLTRPHPDPEAAAAGAVMRRV
+EDVLDVWFDSGSMPYAQVHYPFERADWFPTHNPADFIVEYIGQTRGWFYTMHILATALFD
+RPAFSNVISHGIVLGSDGQKMSKSLRNYPDVTEVLDRDGADAMRWFLMASPILRGGNLVV
+TEEGIREGVRQVLLPAWNAYHFFTLYANTAHDGGARPDGYRAQERHTAEDPLDQYILAAT
+GRMLREVKTGLDAYEVSDATDALRGFMDTLTNWYIRRSRQRFFDEDTAAMDVLYTALEAF
+ARAAAPLMPLVAEEIWRGLTGGRSVHLTDYPDADLFPHGPEADSLVARMDAVRRISSAGS
+ALRKGAGRRVRLPLPRLSVVVPDAEGLEGTYARIVADELNLKDVSLTELSDEAIARYGIG
+TELKLNFRELGKVYGKQVPLVKKAVDAGSYEETADGLAVTLADGATVTLDPALYELRTVS
+TGAPEGTAVGVLPGAAGFLVLDTEVSAELAAEGTARDVVRAVQAARKDAGLDVSDRVRTR
+IDGPAAVVAALEAHRDLVAEETLTVELELVDSGEADPRKDPADDAMKTVAVTVAKADA
+>MOLHKGIG_00994
+MYPLASSAPDGRTPASPRFPEIERRILAYWDEDGTFQASIDQRPTRNEDGSQNEFVFYDG
+PPFANGLPHYGHLLTGYVKDLVARYQTQQGRRVERRFGWDTHGLPAELEAMKQLGMTDKS
+EIEAMGIDTFNDACRSSVLKYTDQWQDYVTRQARWVDFENDYKTLTPDFMESVIWAFSEL
+HRKGLTYRGFRVLPYCWNDETPLSNHELRMDDDVYKMRQDPSVTVTFPITGLPADPALVP
+DGGADAALAAHLAGVHVLAWTTTPWTLPTNAALAVGPQIQYAVVPAGPEGATADGDRFLL
+AVDLVGAHARELGYADADAARAAVTETIPGARLGGLAYAPLFTDVFDAHRGETFTVNGRD
+LGVEGAHRILVDDYVSTEDGTGVVHQAPAYGEDDQRVCEANGIPVMLSVDSGARFLPLFA
+REDVGRGDLREIAGVQVFEANRTIIRALRALGRVAREASYEHSYPHCWRCRTPLIYRAVT
+SWYVKVTQIKERMLELNEEITWIPGNVKHGQFGTWVANARDWSISRNRYWGSPIPVWESD
+HPDFPRQEVYGSLAEIEEAFGRLPRNAEGEVDLHRPWVDDLTRPHPDPEAAAAGAVMRRV
+EDVLDVWFDSGSMPYAQVHYPFERADWFPTHNPADFIVEYIGQTRGWFYTMHILATALFD
+RPAFSHVISHGIVLGSDGQKMSKSLRNYPDVTEVLDRDGADAMRWFLMASPILRGGNLIV
+TEEGIREGVRQVLLPAWNAYHFFTLYANTAHDGGARPEGYRAQERHTAEDPLDQYILAAA
+GRMLREVKAGLDAYEVSDATDALRGFMDTLTNWYIRRSRERFFDEDTVAFDVLYTVLEAF
+TRAAAPLMPLIAEEIWRGLTGGRSVHLTDYPDADLFPHGPEADSLVARMDAVRRISSAGS
+ALRKGAGRRVRLPLPRLSVVVPDAAGLEGTYARIVADELNLKDVELTELSEEAIARYGIG
+TELKLNFRELGKAFGRQVPLVKQAVDAGAYEETAEGLAVTLADGETVTLAPALYELRTVS
+TGAPEGTAVGVLPGTAGFLVLDTEVSAELAAEGTARDVVRAVQAARKDAGLDVSDRVRTR
+IEGPTAVVAALEAHRGLVAEETLTVDLELVDSGAADPRKDPADDAMKTVAVSVAKADA
+>NAFOICDF_01842
+MYPLASTDPAGATPASPLLPEIEQRILRYWDEDGTFQASIDARPAVNEDGSQNEFVFYDG
+PPFANGLPHYGHLLTGYVKDLVARYQTQQGRRVERRFGWDTHGLPAELEAMKQLGMTDKS
+EIEAMGIDRFNDACRSSVLKYTEEWRRYVTRQARWVDFDNDYKTLTPDFMESVIWAFSEL
+HRKGLTYRGFRVLPYCWHDETPLSNHELRMDDDVYKMRQDPSVTVSFPILGLPDDAALVP
+AGGADAALADELAGVHVLAWTTTPWTLPTNAALAVGPEIEYAVVPAGPEGATVAAAERFL
+LAVDLVGAHAKELGYADADAARAAVERTVLGARLGGLRYEPLFTDVFEAHAGETFPVGAR
+TLTLDGVHRILVDDYVSTDDGTGVVHQAPAYGEDDQRVCEANGIPVLLSVDEGARFLPLF
+AREGQGRGDLKDIAGVQVFEANRTIIRALRALGRIAREASYEHSYPHCWRCRTPLIYRAI
+TSWYVSVTKVKDRMLELNEDITWIPGNVKHGQFGTWVANARDWSISRNRYWGSPIPVWES
+DHPDYPLQEVYGSLAELEEAFGRLPRNADGEVDLHRPWIDDLTRPHPDPEAAAAGATMRR
+VEDVLDVWFDSGSMPYAQVHYPFERADWFPTHNPADFIVEYIGQTRGWFYTMHILATALF
+DRPAFSHVISHGIVLGSDGQKMSKSLRNYPDVTEVLDRDGSDAMRWFLMASPILRGGNLI
+VTEEGIREATRQVILPLWNAWHFFTLYANTAHDGGARPEGYRASERHTAEDPLDQYVLAA
+CGTMLRQVKAALDAYEVSDAADALRAFMDTLTNWYIRRSRERFFAEDTAAMDVLSTVLEA
+FTRAAAPLLPLVAEEIWRGLTGGRSVHLTDYPDADLFPHGPEADALVARMDLVRSITSAG
+SALRKGAKRRVRLPLAAMSVVVPDAAALEGTFTRIVADELNLKEVRLTELSEEAISRYGI
+GTELKLNFRELGKHFGRQVPLIKKAVDAGAYAEGEQGLDVTLADGAVVTLAPELYELRTV
+STGAPEGTAVGVLPGGGFLVLETAVSAELAAEGVARDVIRAVQAARKDAGLDVADRVRTR
+IEGPAPVVAALESHRDLVAQETLTVELDLVDSGAADPRRDPADDAMKTVAVAVAKAQA
+>MHAAABBN_00708
+MYPLASSAPDGRTPASPRFPEIERRILAYWDEDGTFQASIDQRPAFNEDGSQNEFVFYDG
+PPFANGLPHYGHLLTGYVKDLVARYQTQQGRRVERRFGWDTHGLPAELEAMKQLGMTDKS
+EIEAMGIDKFNDACRSSVLKYTDQWQDYVTRQARWVDFENDYKTLTPDFMESVIWAFSEL
+HRKGLTYRGFRVLPYCWNDETPLSNHELRMDDDVYKMRQDPSVTVTFPITGLPADPALVP
+DGGADAALAAHLAGVHVLAWTTTPWTLPTNAALAVGPQIQYAVVPAGPEGATADGDRFLL
+AVDLVGAHARELGYADADAARAAVTETIPGARLGGLAYAPLFTDVFDAHRGETFTVNGRD
+LGVEGAHRILVDDYVSTEDGTGVVHQAPAYGEDDQRVCEANGIPVLLSVDSGARFLPLFA
+REDVGRGDLREIAGVQVFEANRTIIRALRALGRVAREASYEHSYPHCWRCRTPLIYRAVT
+SWYVKVTQIKERMLELNEEITWIPGNVKHGQFGTWVANARDWSISRNRYWGSPIPVWESD
+HPDFPRQEVYGSLAEIEEAFGRLPRNAQGEVDLHRPWVDDLTRPHPDPEAAAAGAVMRRV
+EDVLDVWFDSGSMPYAQVHYPFERADWFPTHNPADFIVEYIGQTRGWFYTMHILATALFD
+RPAFSHVISHGIVLGSDGQKMSKSLRNYPDVTEVLDRDGADAMRWFLMASPILRGGNLIV
+TEEGIREGVRQVLLPAWNAYHFFTLYANTAHDGGARPEGYRAQERHTAEDPLDQYILAAT
+GRMLREVKTGLDAYEVSDATDALRGFMDTLTNWYIRRSRERFFDEDTVAFDVLYTVLEAF
+TRAAAPLMPLIAEEIWRGLTGGRSVHLTDYPDADLFPHGPEADSLVARMDAVRRISSAGS
+ALRKGAGRRVRLPLPRLSVVVPDAAGLEGTYARIVADELNLKDVELTELSEEAIARYGIG
+TELKLNFRELGKAFGRQVPLVKQAVDAGAYEETAEGLAVTLADGETVTLAPALYELRTVS
+TGAPEGTTVGVLPGTAGFLVLDTEVSAELAAEGTARDVVRAVQAARKDAGLDVSDRVRTR
+IEGPTAVVAALEAHRGLVAEETLTVDLELVDSGAADPRKDPADDAMKTVAVTVAKADA
+>LFPAFLNI_00937
+MYPLASSAPDGRTPASPRFPEIERRILAYWDEDGTFQASIDQRPTRNEDGSQNEFVFYDG
+PPFANGLPHYGHLLTGYVKDLVARYQTQQGRRVERRFGWDTHGLPAELEAMKQLGMTDKS
+EIEAMGIDTFNDACRSSVLKYTDQWQDYVTRQARWVDFENDYKTLTPDFMESVIWAFSEL
+HRKGLTYRGFRVLPYCWNDETPLSNHELRMDDDVYKMRQDPSVTVTFPITGLPADPALVP
+DGGADAALAAHLAGVHVLAWTTTPWTLPTNAALAVGPQIQYAVVPAGPEGATADGDRFLL
+AVDLVGAHARELGYADADAARAAVTETIPGARLGGLAYAPLFTDVFDAHRGETFTVNGRD
+LGVEGAHRILVDDYVSTEDGTGVVHQAPAYGEDDQRVCEANGIPVLLSVDSGARFLPLFA
+REDVGRGDLREIAGVQVFEANRTIIRALRALGRVAREASYEHSYPHCWRCRTPLIYRAVT
+SWYVKVTQIKERMLELNEEITWIPGNVKHGQFGTWVANARDWSISRNRYWGSPIPVWESD
+HPDFPRQEVYGSLAEIEEAFGRLPRNAQGEVDLHRPWVDDLTRPHPDPEAAAAGAVMRRV
+EDVLDVWFDSGSMPYAQVHYPFERADWFPTHNPADFIVEYIGQTRGWFYTMHILATALFD
+RPAFSHVISHGIVLGSDGQKMSKSLRNYPDVTEVLDRDGADAMRWFLMASPILRGGNLIV
+TEEGIREGVRQVLLPAWNAYHFFTLYANTAHDGGARPDGYRAQERHTAEDPLDQYILAAT
+GRMLREVKTGLDAYEVSDATDALRGFMDTLTNWYIRRSRERFFDEDTVAFDVLYTVLEAF
+TRAAAPLMPLIAEEIWRGLTGGRSVHLTDYPDADLFPHGPEADSLVARMDAVRRISSAGS
+ALRKGAGRRVRLPLPGLSVVVPDAAGLEGTYARIVADELNLKDVELTELSEEAIARYGIG
+TELKLNFRELGKAFGRQVPLVKQAVDAGAYEETAEGLAVTLADGETVTLAPALYELRTVS
+TGAPEGTTVGVLPGTAGFLVLDTQVTAELAAEGTARDVVRAVQAARKDAGLDVSDRVRTR
+IEGPTAVVAALEAHRGLVAEETLTVDLELVDSGAADPRKDPADDAMKTVAVTVAKADA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001318.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001318.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b1cb9330410e9612583f93f853744f6cfbffbce
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001318.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_01898
+MTASDLYPTSLRLLGRPVLMVGGGRVAGRRVGALLDAGALVTVVAPEPGEEVERLAAAGL
+LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVV
+RAGDVTVAVNAGGDPRRARALKDAITLALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL
+ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA
+RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSAVSVPAAAGIPVTHRGVA
+TGFTLVTGHEELSEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD
+QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGARAAGVPAPILTLNPTSEGA
+RA
+>MOLHKGIG_00991
+MTASDLYPTSLRLLGRPVLIVGGGRVAGRRVGALLDAGALVSVVAPEPGEEVERLAAAGL
+LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVV
+RAGDVTVAVNAGGDPRRARALKDAIALALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL
+ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA
+RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSAVSVPAAAGIPVTHRGVA
+TGFTLVTGHEELAEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD
+QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGAPAAGIPAPISTLNPTSEGA
+RA
+>NAFOICDF_01845
+MTASDLYPTSLCLLGRPVLIVGGGRVAGRRVGALLDAGALVTVVAPEPGEEVERLAAAGL
+LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVA
+RAGDVTVAVNAGGDPRRARALKDAITLALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL
+ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA
+RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSAVSVPAAAGIPVTHRGVA
+TGFTLVTGHEELAEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD
+QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGAPAAGVPAPISTLNPTSEGA
+RA
+>MHAAABBN_00705
+MTASDLYPTSLRLLGRPVLMVGGGRVAGRRMGALLDAGALVTVVAPEPGEEVERLAAAGL
+LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVV
+RAGDVTVAVNAGGDPRRARALKDAITLALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL
+ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA
+RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSAVSVPAAAGIPVTHRGVA
+TGFTLVTGHEELSEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD
+QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGAPAAGVPAPISTLNSTSEGA
+RA
+>LFPAFLNI_00934
+MTTSDLYPTSLRLLGRPVLVVGGGRVAGRRMGALLDAGALVTVVAPKPGEEVERLAAAGL
+LTLHRRPYRPSDLDGVWFAQTATGDRAVDGAVASDAEARRVWCVDASDAESSAAWTPAVV
+RAGDVTVAVNAGGDPRRARALKDAITLALSTGRLPLRRRRASSEPGRVALVGGGPGDSGL
+ITVRGRQLLAEADVVVADRLGPRALLAELDPAVPVIEVGKAPGNHLATQDEINAVLVREA
+RAGRLVVRLKGGDPYVLGRGGEEAAHCRAHGVDVEVVPGVTSVVSVPAAAGIPVTHRGVA
+TGFTLVTGHEELSEVPTRADHTLVLLMGVRRLADTARRLTERGLDGATPVAIIERGWMPD
+QRVTVGTVETIAAQAAAVGVENPAVIVVGDVVRLSPYATGAPAAGIPAPILTLNPTSEGA
+RA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001319.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001319.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20222ff42de70419218e7f1bf28affec4eeb5099
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001319.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_01899
+MRTDTPTLDAPGRAPGAAADDELRELDSGLDALQAVDSARRTGLAGWDWSRVLLPVAAVV
+LLVAIWQVAAWLAGARGEPITGPGDVLGAFGALWAQGLVQQAVATSVGRAVVGFALAVVA
+GVGLGLLLAQVGVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVILTGAVPAV
+VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA
+EIIAVGAPMGVGLGTLLHQGRTESDLAVVLCAVLAILAVGVLVELTAFGPVERRMLRRQG
+LLEGSTR
+>MOLHKGIG_00990
+MRTDTPTLDAPGRAPGAATDDELRELDSGLDALQAVDSTRRTGLAGWDWSRVLLPVAAVV
+LLVAIWQAFAWLAGARGEPITGPGDVVGAFGTLWAQGLVQQAVATSVGRAVVGFALAVVV
+GVGLGLLLGQVSVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVMLTGAVPAV
+VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA
+EIIAVGGPMGVGLGTLLHEGRAESDLAVVLCAVLAILAVGVLVELTAFGPAERRMLRRRG
+LLEGSTR
+>NAFOICDF_01846
+MRTDTPTLDAPGRAPGAAADDELRELDSGLDALQAVDSTRRTGLAGWDWSRVLLPVAAVV
+LLVAIWQVAAWLAAARGEPITGPGDVLRAFGTLWAQGLVQQAVATSVGRAVVGFALAVVV
+GVGLGLLLGQVSVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVMLTGAVPAV
+VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA
+EIIAVGGPMGVGLGTLLHQGRAESDLAVVLCAVLAILAVGVLVELTAFGPVERRMLRRQG
+LLEGSTR
+>MHAAABBN_00704
+MRTDTPTLDAPGRAPGAATDDELRELDSGLDALQAVDSTRRTGLAGWDWSRVLLPVAAVV
+LLVAIWQAFAWLAGARGEPITGPGDVVGAFGTLWAQGLVQQAVATSVGRAVVGFALAVVV
+GVGLGLVLGQVGVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVMLTGAVPAV
+VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA
+EIIAVGGPMGVGLGTLLHEGRAASDLAVVLCAVLTILAVGVLVELAAFGPVERRMLRRRG
+LLEGSTR
+>LFPAFLNI_00933
+MRTDTPTLDAPGRAPGAATDDELRELDSGLDALQAVDSTRRTGLAGWDWSRVLLPVAAVV
+LLVAIWQAFAWLAGARGEPITGPGDVLGAFGTLWAQGLVQQAVATSVGRAVVGFALAVVV
+GVGLGLVLGQVSVLRRAFGPLLTALMVLPNVAWVPLAVLWFGLSDATAYFVMLTGAVPAV
+VAGLTTGTDQVPPQLRRAARVLGASRLETALLVVLPAALPAFVSGLRQGWAFAWRGLMAA
+EIIAVGGPMGVGLGTLLHEGRAASDLAVVLCAVLTILAVGVLVELAAFGPVERRMLRRRG
+LLEGSTR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001323.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001323.fa
new file mode 100644
index 0000000000000000000000000000000000000000..466ae638421b23cff67acf83325db9913c025ca1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001323.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01903
+MSTVPPTRPTEELERLQALAESGAAELGWDAPAAAVVDWAARHVDLRRAAVACSMADAVL
+PHLVAQRMPGVDVLFLETGYHFTETLATRDEVARRLDVTVVDVLPELTVAEQDERHGKDL
+FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA
+PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWTGTAKTECGIH
+V
+>MOLHKGIG_00986
+MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL
+PHLVAQRMPGVDVLFLDTGYHFTETLATRDEVARRLAVTVVDVLPELTVAEQDERHGKDL
+FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA
+PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH
+V
+>NAFOICDF_01850
+MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL
+PHLVAQRMPGVDVLFLETGYHFTETLATRDEVARRLDVTVVDVLPELTVAEQDERHGKDL
+FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA
+PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH
+V
+>MHAAABBN_00700
+MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL
+PHLVAQRMPGVDVLFLETGYHFTETLATRDEVARRLDVTVVDVLPELTVAEQDERHGKDL
+FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHGMVKVNPVA
+PWSLDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH
+V
+>LFPAFLNI_00929
+MSTVPPTRPTEDLERLQALAESGAAELGWDAPAEAVVDWAARHVDLRRAAVACSMADAVL
+PHLVAQRMPGVDVLFLDTGYHFTETLATRDEVARRLAVTVVDVLPELTVAEQDERHGKDL
+FARDPGLCCAMRKVEPLNRALAGYDLWFTGVRRDEAPTRTNTPLVGWDEAHSMVKVNPVA
+PWSFDDLVGYATDHDVPVNLLLQNGYPSIGCRPCTRPVAPGEDPRAGRWAGTAKTECGIH
+V
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001326.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001326.fa
new file mode 100644
index 0000000000000000000000000000000000000000..342c454f45cf71e345167831ee5a82497b852b08
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001326.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_01906
+MDVSHTTENQSPRAAVVTGATTGIGRATALELARRGWRVYAVGRRAERLDALAAQAREEA
+VPGEVVPAPLDVTDEAAVAGLVARVDTDGGIDTLVNIAGGARGTDFVGAGNREDWEWMYR
+ANVLGTLAMCQAFLPGLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTAALRLE
+EAEHNVRVIEVLPGMVHTEEFSLMRLGGDAAAAEKVYAGVEKPLTAEDVAEVCVHAVELP
+HHVNLDQIVIRPVAQAAQHKVIRR
+>MOLHKGIG_00983
+MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG
+VSGDVVPAALDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGDGDRADWEWMYR
+VNVLGTLTMCQAFLPMLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE
+EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP
+HHVNLDQIVMRPVAQAAQHKVIRR
+>NAFOICDF_01853
+MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG
+VSGDVVPAPLDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGDGDRADWEWMYR
+VNVLGTLTMCQAFLPMLRTHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE
+EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP
+HHVNLDQIVMRPVAQAAQHKVIRR
+>MHAAABBN_00697
+MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG
+VSGDVVPAALDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGVGDRADWEWMYR
+VNVLGTLTMCQAFLPMLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE
+EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP
+HHVNLDQIVMRPVAQAAQHKVIRR
+>LFPAFLNI_00926
+MSHTHEPAKNPARAAVVTGATSGIGRATALELARRGWRVYAVGRRAERLETLAADARAEG
+VSGDVVPAALDVTDEAAVAALASRVEADGGADTLVNIAGGALGTDAVGDGDRADWEWMYR
+VNVLGTLTMCQAFLPMLRAHGEGTVLNLTSTAAVTAYEGGAGYNAAKMGQHGLTGALRLE
+EAEHNVRVIEVLPGMVHTEEFSRNRLGGDQSAADAVYAGVEKPLTAEDVAEVCVHAVELP
+HHVNLDQIVMRPVAQAAQHKVIRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001333.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001333.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28d5a747d64f8771e82c22016865fb256eba0c5e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001333.fa
@@ -0,0 +1,47 @@
+>ACLBLIBL_01914
+MVKSTAENLSPTRVKLNVEVPFEEVKPSLDKAYKDIANQVQIPGFRKGKIPARLIEQRFG
+REAVVDQAVNEGLNTWFSAAISEAELTPISRPEVDVTATPDSENAEGPVVFTAEFDVRPT
+IELPDYKGLKVTVEPAKATEEDEQKALDALRSRFGSLKDVDRPAAQDDFVTMNLTASVDG
+EQVDQAEGLSYQVGAGTMLEGIDEALDGLSAGEDATFESTLNGGEHDGKTAVVKLELTAV
+KERELPEADDEFAQLASEFDTIDELKEDLKKQAAEDAVNRQGVEARDKVLAELAKLVEVP
+VPDGVITEQVEQHFSAGGHAAGDDHDTPEHRAELEANTREAFANEVILDEVAEAEEVTVD
+QGELIEYIIATSSEYGMDPNQFAMMLDQGGQIPMIMGEVRRRKALAKVLEFAEVTDTDGK
+AVDLKAFVTPGGQEALDAEAEGADPAEAEEKPAKKAAAKKPAAKKAPAKKKAEEKADDAE
+ASEQA
+>MOLHKGIG_00976
+MVKSTAENLSPTRVKLTVEVPFEEVKPALDKAFKDIANQVQIPGFRQGKIPARLIEQRFG
+REIVVDQAVNEGLNTWFSAAIAEAEVTPISRPEVDVTATPDAENAEGPVAFTAEFDVRPT
+IELPDYKGLKVTVEPAQATEEDEQKALDALRSRFGSLKDVDRPAAQDDFVTMNLTATVDG
+EQVDQAEGLSYQVGAGTMLEGIDEALDGLSAGEDATFETTLNGGEHDGETAVVKLELTAV
+KERELPEADDEFAQLASEFDTIAELKEDLKKQAAEEAVNRQGVEARDKVLEELAKLVEVP
+VPDGVIAEQVEQHFSAGGHTAGDDHDTAEHRAELEQNTREAFANEVILDEVAEAEEVTVD
+QGELIEYIIATSSEYGMDPNQFAMMLDQGGQIPMIMGEVRRRKALAKVLEYAEVTDTDGK
+AVDLTAFVTPGGQEALDAEAEGAEAEGADEAEEKPAEKAPAKKKSTAKKAPAEQADDAEA
+AEQA
+>NAFOICDF_01861
+MVKSTAENLSPTRVKLTVEVPFEEVKPVLDKAYKDIAMQVQVPGFRQGKVPARLIEQRFG
+REAVVDQAVNDGLNTWFGQALAEAEVTPISTPEVDVTATPAAAEGPVEFTAEFDVRPTIE
+LPDYKGIEVTVEPAQATDEDEQAQLDALRSRFGTLKDVDRPAAKDDFVTMDLTATVGEEQ
+VDQAQGLSYQVGAGTMLDGIDEALEGLSAGEDATFETTLNGGEHDGETATVKLVLQAVKE
+RELPEADDDFAQLASEFDTIAELKEDLKKKAAEAAETRQGVEARDKVLAELGKLVEVPVP
+ENVIAEQLEQHFSQGGHSAGDEHDTPEHREELEKNTREAFANEVILDEVAEAESVTVDQG
+ELIEYIFATSAEYGMDPNQFAMMLDQAGQIPMIMGEVRRRKALAKVLEHAVVTDTDGNAV
+DLTAFVTPAAAEEEKAEEKPAKKAPAKKAAAKKAAAKKPAAKKAEAEESEEA
+>MHAAABBN_00690
+MVKSTAENLSPTRVKLTVEVPFEEVKPALDKAFKDIANQVQIPGFRQGKIPARLIEQRFG
+REVVVDQAVNEGLNTWFSAAIAEAELTPISRPEVDVTATPDAENAEGPVVFTAEFDVRPT
+IELPDYKGLKVTVEPAQATEEDEQKALDALRSRFGSLKDVDRPAAQDDFVTMNLTATVDG
+EQVDQAEGLSYQVGAGTMLEGIDEALDGLSAGEDATFETTLNGGEHDGETAVVKLELTAV
+KERELPEADDEFAQLASEFDTIAELKEDLKKQAAEEAVNRQGVEARDKVLEELAKLVEVP
+VPDGVIAEQVEQHFSAGGHTAGDDHDTAEHRAELEQNTREAFANEVILDEVAEAEEVTVD
+QGELIEYIIATSSEYGMDPNQFAMMLDQGGQIPMIMGEVRRRKALAKVLEYAEVTDTDGK
+AVDLTAFVTPGGQEALDAEAEGADEAAEQA
+>LFPAFLNI_00919
+MVKSTAENLSPTRVKLTVEVPFEEVKPALDKAFKDIANQVQIPGFRKGKIPARLIEQRFG
+REIVVDQAVNEGLNTWFSAAIAEAELTPISRPEVDVTATPDAENAEGPVAFTAEFDVRPT
+IELPDYKGLKVTVEPAQATEEDEQKALDALRSRFGSLKDVDRPAAQDDFVTMNLTATVDG
+EQVDQAEGLSYQVGAGTMLEGIDEALDGLSAGEDATFETTLNGGEHDGETAVVKLELTAV
+KERELPEADDEFAQLASEFDTIAELKEDLKKQAAEEAVNRQGVEARDKVLEELAKLVEVP
+VPDGVIAEQVEQHFSAGGHTAGDDHDTAEHRAELEQNTREAFANEVILDEVAEAEEVTVD
+QGELIEYIIATSSEYGMDPNQFAMMLDQGGQIPMIMGEVRRRKALAKVLEYAEVTDTDGK
+AVDLTAFVTPGGQEALDAEAEGAEAEGADEAAEQA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001335.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001335.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d15863cc2d9519a233af353422ddd075712961e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001335.fa
@@ -0,0 +1,34 @@
+>ACLBLIBL_01918
+MPEGHSIHRLARQFTDVFGGWPIRASSPQGRFAEGAARMDGQVLEAARAHGKHFFADLAD
+GHVLNVHLGMYGAWSFGGDERFDAASSIGAPRRIGEREVHADGAAAAEPDRDDDGWVLPP
+PPVPTVRLRVRAEHGWADLIGASTCRLLTPAEAGDVVAKLGPDPLNDDDPAPFLDLAGRT
+RRPIGAVLMDQAAVGGIGNIFRAEALFRAGLDPWRPSNAVPREVLRRLWSDNAELMREGV
+RLGRIVTTRPEHRPGVPAEQAWPEHANYVYQRQGSPCLVCGQDAIVVEGMAARKLYRCTV
+CQR
+>MOLHKGIG_00972
+MPEGHSVHRLARQFTDVFGGRRIRATSPQGRFAEGAALLDGQVLKRARAHGKHFFADVSG
+GHVLHVHLGMYGAWTFGGDQDFAAASSIGAPRRIGEREVHDDGAPAAEPARDADGWVQPP
+PPAATVRLRLRAEHGWADLIGASRCRALTPAEAADVVAGLGPDPLSDDDPAPFYDLARRT
+RRPIGVVLMDQAAVSGIGNIFRAEALFRVGIDPWRPARDVSASELESLWADNAALMREGV
+RLGRIVTTRPEHRPGIPAEAAWPEHASYVYQRQGLACLVCGRETIVVEEMAARKLYRCLT
+CQS
+>NAFOICDF_01866
+MPEGHSIHRLARQVQDVFGGQALAASSPQGRFADGAALLDGRVLERAWAHGKHFFADIEG
+GLTLNVHLGMYGAMTFGGDEAFAAASSIGAPRRIGETEDHGALAAAEPPPARPTVRLRLR
+SAHGWADLIGAGTCRVLTPQELAEVTSKLGPDPLNDDDPAAFVARAARTGRPVGVVLMDQ
+SMVGGIGNIYRAEVLFRAGLDPWTPARDVGADVLAALYADAQALMRDGVRLGRIVTTAPE
+HRPGVAAEDAWPEHANYVYRRQGMPCRVCGQDAIVREEMAARNLFRCTDCQR
+>MHAAABBN_00685
+MPEGHSVHRLARQFTDVFGGRRIRATSPQGRFAEGAALLDGQVLKRARAHGKHFFADVSG
+GHVLHVHLGMYGAWTFGGDQDFAAASSIGAPRRIGEREVHDDGAPAAEPARDADGWVQPP
+PPASTVRLRLRAEHGWADLIGANRCRALTRAEAADVVAGLGPDPLNDDDPAPFYDLARRT
+RRPIGVVLMDQGAVSGIGNIFRAEALFRAGIDPWRPAREVSAPDLAFLWADNAALMREGV
+RLGRIVTTRPEHRPGIPAEAAWPEHANYVYQRQGLACLVCGRETIVVEEMAARKLYRCLT
+CQS
+>LFPAFLNI_00915
+MPEGHSVHRLARQFTDVFGGRRIRATSPQGRFAEGAALLDGQVLKRARAHGKHFFADVSG
+GHVLHVHLGMYGAWTFGGDQDFAAASSIGAPRRIGEREVHDDGAPAAEPARDADGWVQPP
+PPAATVRLRLRAEHGWADLIGASRCRALTPAEAADVVAGLGPDPLSDDDPAPFYDLARRT
+RRPIGVVLMDQAAVSGIGNIFRAEALFRAGIDPWRPAREVSASDLAFLWADNAALMREGV
+RLGRIVTTRPEHRPGIPAESAWPEHANYVYQRQGLACLVCGRETIVVEEMAARKLYRCLT
+CQS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001336.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001336.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba91bf50fef10a3a0c18c137749ed6f65719b879
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001336.fa
@@ -0,0 +1,80 @@
+>ACLBLIBL_01920
+MSSSARLNITREEAAQRAAALTVDAYEVSLDLTRGPERFRTASTVTFAASEDAVGTHTWI
+DFVASQAPEVTLNGERVAVEDYDGARLPIGPLAAQNTLVVEGLGDYSNTGEGLHRFVDPV
+DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEASRRTLGVVEN
+EDQLSGVDAAVWEFVPTPRISSYITALVAGPYAAVHSELTSADGRTIPLGVYCRASLVEH
+LDADNVFELTRQGFEFFEAQYGHPYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VPEAMVERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTRYTGSWT
+TFSSMEKNWAYRQDQLSSTHPIKAQIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MAGVRAYIAKHAWSNTELPDLMSELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGV
+ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLTRTERFELDVAGEVTEVA
+EAAGRRRPALILPNDDDLAYAKLRLDHASWEAASTRLKDVDSSLARTLLWGAAWDAVRDG
+EASAAWFADLILANIGHEQDSSVVQTLLRQLATSLGQYLPEEQSTAARAAVADRLWGLVA
+GAEDGSDSQLQFVKAFALHARTAAQLDRLAGVVDGTHTVPGLDLTTDLRWELLTALVAAG
+RAGEAEIAAAEREDATATGALAAIQARAAVPTAEAKQAAWDRVMAGELSNTEQRQALIGF
+ARAHEAALLAPFADAYFEGVEAMWDSRSHEMAETAAVLGYPAAQVSDETAQRATALSEKT
+AGTRAGLSRVLAEGRDETVRALAAREHAAAHVHEVSASA
+>MOLHKGIG_00967
+MTTAAAMNITREEAAARAAALTVDAYEVSLDLTRGAEHFHTATTVTFAATQDAVGTHTWI
+DFVAEQAPTVTLNGEALDVADFDGARLRIGPLAAQNTLVVDGLGDYSNTGEGLHRFVDPV
+DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEASRRTLGVVAN
+EENPQGVDAAVWEFKPTPRIPSYITALVAGPYASVHSELTSADGRTIPLGVYCRASLVEH
+LDAENVFELTRQGFEFFEAQYGHAYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VPEALIERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTQYTGAWT
+TFSSMEKNWAYRQDQLSSTHPIKARIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MVGVRAYIAKHAWQNTELPDLMTELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGT
+ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLIRTERFELDVAGEVTEVV
+EAAARRRPAVILPNDDDLAYAKLRLDDASWEAASTRLKDVDGSLARTLLWGAAWDTVRDG
+EASAAWFVDLVLANVGHERDSSVVQTLLRQLATAIGLYLPEDQAEAVRVAAADRLWGLVA
+EAEDGSDNQLQFVKAFALHARTTAQLDRLSALVDGTRTVPGLDLTTDLRWELLTALVAAG
+RAGEAEIAEAERADATATGALAAIQARAAVPTAEAKRAVWDRVMAGELSNTEQRQALIGF
+ARVHDAALIAPFADAYFEGVEAMWDSRSHEMAETAATLGYPTAQVTPEIADRATALSERL
+ADTRAGLSRVLAEGRDETIRALAAREHATAHVHQVHAGA
+>NAFOICDF_01868
+MTTAAAMNITREEAAARAAALTVESYQVALDLTRGAERFGSTTTVTFSAADEAVGTQTWI
+DFMATQAPEVTLNGQAVDVADFDGARLPIGPLAAENTLVVDGLADYTTTGEGLHRFVDPV
+DDEVYLYSQFEVPDSRRMFAVFEQPDLKATFAFTVTAPAHWAVVSNQPEAAHRTLGVVET
+PEAPEGVDAAVWEFTPTPRISSYITALVAGPYKSVHSELTSADGRTVPLGVYCRGSLFEH
+LDADEVFDLTRRGFEFFEAQYGHPYPFDKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VTDAVRERRAITILHELAHMWFGDLVTMKWWNDLWLNESFAEFMSTLAAAENTRYEGAWT
+TFSSMEKNWAYRQDQLSSTHPITAEIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MAGVRAYIEKNAWSNTELPDLMTELEAASGRDLSEWTRLWLETSGVNTLAVQVDADYAGT
+ITSLRLHQSAPDGSPAAPGDDVLRPHRIAVGFYDLDEATGRLTRTERFELDAAGEVTEVA
+EAAGRRRPALILPNDDDLAYAKIRLDDASWETAGARLADVDSSLARTLLWGAAWDTVRDG
+EASAAWFVDLILTNIGREQDSTVIQTLLRQLATAISQYLPEERSAQVRADAANRLWMLVE
+QAEPGSDAQLQFVKAFALHAREEGQLTALADVWDRSSELPGLDLTTDLRWELLTALVAAG
+RAGETEIAAAETEDPTATGALAAALARAAVPTAEAKQTAWDQVVAGTLSNTTQRQVLLGF
+QRAHDPALLAPFTDAFFGSIQDVWGSRSHEMAETVAVLGFPSSQVCQEVVDRATALSDEV
+RGTNAGLARTLAESRDEMARALKARAAA
+>MHAAABBN_00680
+MTTAAAMNITREEAAARAAALTVDAYEVSLDLTRGAEHFHTATTVTFAATQDAVGTHTWI
+DFVAGQAPTVTLNGEALDVADFDGARLRIGPLAAQNTLVVDGLGDYSNTGEGLHRFVDPV
+DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEDSRRTLGVVAN
+EENLQGVDAAVWEFTPTPRISSYITALVAGPYASVHSELTSADGRTIPLGVYCRASLVEH
+LDAENVFELTRQGFEFFEAQYGHAYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VPEALIERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTQYTSAWT
+TFSSMEKNWAYRQDQLSSTHPIKARIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MAGVRAYIAQHAWGNTELPDLMSELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGT
+ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLTRTERFELDVAGEVTEVA
+EAVGRRRPAVILPNDDDLAYAKLRLDDASWEAASTRLKDVDGSLARTLLWGAAWDTVRDG
+EASAAWFVDLVLANVGHERDSSVVQTLLRQLATAIGLYLPEDQAEAVRVAAADRLWGLVA
+EAEDGSDNQLQFVKAFALHARTTAQLDRLAALVDGTRTVPGLDLTTDLRWELLTALVAAG
+RAGEAEIAEAERADATATGALAAIQARAAVPTAEAKRAAWDRVMAGELSNTEQRQALIGF
+ARVHDAALIAPFADSYFEGVEAMWDSRSHEMAETAATLGYPTSQVSRETADRATALSERL
+ADTRAGLSRVLAEGRDETVRALAAREHATAHVHQVHAGA
+>LFPAFLNI_00913
+MTTVAAMNITREEAAARAAALTVDAYEVSLDLTRGAEHFHTATTVTFAATQDAVGTHTWI
+DFVAEQAPTVTLNGEALDVADFDGARLRIGPLAAQNTLVVDGLGDYSNTGEGLHRFVDPV
+DQEVYLYTQFEVPDSRRMFAVFEQPDLKAAFRFTVTAPAHWAVVSNQPEASRRTLGVVAN
+EENPQGVDAAVWEFKPTPRIPSYITALVAGPYASVHSELTSADGRTIPLGVYCRASLVEH
+LDAENVFELTRQGFEFFEAQYGHAYPFEKYDQLFVPEFNAGAMENAGCVTFLESYVFRGT
+VPEALIERRAITILHELAHMWFGDLVTMRWWNDLWLNESFAEFMSTLAAAENTQYTSAWT
+TFSSMEKNWAYRQDQLSSTHPIKARIRDLDDVLVNFDGITYAKGASVLRQLVAWVGQENF
+MAGVRAYIAQHAWGNTELPDLMSELEAASGRDLSEWTRVWLETSGVNTLRTEVETDEAGT
+ITALRLRQSAPDGSPSAPGDDVLRPHRLAVGFYDVDEATGRLTRTERFELDVAGEVTEVA
+EAVGRRRPAVILPNDDDLAYAKLRLDDASWEAASTRLKDVDGSLARTLLWGAAWDTVRDG
+EASAAWFVDLVLANVGHERDSSVVQTLLRQLATAIGLYLPEDQAEAVRVAAADRLWGLVA
+EAEDGSDNQLQFVKAFALHARTTAQLDRLAALVDGTRTVPGLDLTTDLRWELLTALVAAS
+RAGEAEIAEAERADATATGALAAIQARAAVPTAEAKRAAWDRVMAGELSNTEQRQALIGF
+ARVHDAALIAPFADSYFEGVEAMWDSRSHEMAETAATLGYPTAQVTREIADRATALSERL
+AGTRAGLSRVLAEGRDETVRALAAREHATAHVHQVHAGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001337.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001337.fa
new file mode 100644
index 0000000000000000000000000000000000000000..810d1cacae60914cd739c8705b7c645f1d0c6870
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001337.fa
@@ -0,0 +1,37 @@
+>ACLBLIBL_01921
+MKHTFALRTEWTGNRGTGTSGVRDYDRSVVIQDAAVGEIHASAARPFRGDDSKWNPETLL
+LGALAECHVLSYLHVAATSGLVVTGMACAAEGVLEVDGDGAGRFAAVTLRPEVALQDEAD
+RERADALHAEAHRLCFIANSLSAPVSVEPAVAGSGAAASGGPALPDHSSRLGAPLAVLRP
+RVAKRPSQVTGLAERPTEVEPVMKAGAPAPVDQMQARDAAAGRAASPATPAPAAETAAPG
+QAASFYEAVGGRETFDRLTAEFYARVREDELLSPMYPQDDFEGAQRRLLMFLEQYWGGPR
+TYSEERGHPRLRMRHAPYRIDPAARDAWLTHMRAAVDTLGLSPLHEAELWDYLERAAHSL
+QNSA
+>MOLHKGIG_00966
+MKHTFSLRTEWTGDRGSGTSGVRDYDRSVVIQDAAVGEIQASAARPFRGDDSKWNPETLL
+LGALAECHVLSYLHVAATSGVVVTGMTCGVEGELEVDGDGAGRFTAITLRPEVTLQDEAD
+RERAEALHAEAHRLCFIANSLSAPVAVEPVRPEALPTGAPTLPDHSARLGAPLAVLRPRV
+AKGPSRVTGLAERPTEVEPVMQEGTPAPVEQVRARDAAAGPAGATPGTPAAPGQAASFYD
+AVGGRPTFDRLTAEFYARVREDEILAPMYPQDDFEGAQRRLLMFLEQYWGGPRTYSEERG
+HPRLRMRHAPYRIDPAARNAWLRHMRAAVDTLELSPLHEAELWDYLERAAHSLQNSA
+>NAFOICDF_01869
+MKHTFSLRAEWTGDRGTGTTGVRDFDRSVVIQESEVGEIHASAARPFRGDAAKWNPETLL
+LGALAECHVLSYLHAAATGGLVVTGMTCAAEGTLEVDSDGAGRFASITLRPEVALRDEAD
+RARADELHAEAHRMCFIANSISAPITVEAGPGSSPTRGDGAALPDHSARLGAPLAVLRPR
+VANRPTRVTGLADRPTEAEPVVRADAPSGAEQARARDEATARGERPPSATPIATPAPGAT
+PAASPATAAPGQATSFYEAVGGHPTFEKLVHVFYQGVREDPLLAPMYPHQDWDGAEERLR
+MFLEQYWGGPRTYSERRGHPRLRMRHMPFTVDPAARDAWLRHMRAAVDAVELSPLHEAEL
+WDYLERAAHSLQNSA
+>MHAAABBN_00679
+MKHTFSLRTEWTGDRGSGTSGVRDYDRSVVIQDAAVGEIQASAARPFRGDDSKWNPETLL
+LGALAECHVLSYLHVAATSGVVVTGMTCGVEGELEVDGDGAGRFTAITLRPEVTLQDEAD
+RERAEALHAEAHRLCFIANSLSAPVAVEPVRPEALPTGTSTLPDHSARLGAPLAVLRPRV
+AKGPSRVTGLAERPTEVEPVMQEGTPAPVEQVRARDAAAGPTGATPGTPAVPGQATSFYD
+AVGGRPTFDRLTAEFYARVREDEILAPMYPQDDFEGAQRRLLMFLEQYWGGPRTYSEERG
+HPRLRMRHAPYRIDPAARDAWLRHMRAAVDTLELSPLHEAELWDYLERAAHSLQNSA
+>LFPAFLNI_00912
+MKHTFSLRTEWTGDRGSGTSGVRDYDRSVVIQDAAVGEIQASAARPFRGDDSKWNPETLL
+LGALAECHVLSYLHVAATSGVVVTGMTCGVEGELEVDGDGAGRFIAITLRPEVTLQDEAD
+RERAEALHAEAHRLCFIANSLSAPVTVEPVRPEALPTGTPTLPDHSARLGAPLAVLRPRV
+AKGPSRVTGLAERPTEVEPVMQEGTPAPVEQVRARDAAAGPAGATPGTPAAPGQATSFYD
+AVGGRPTFDRLTAEFYARVREDEILAPMYPQDDFEGAQRRLLMFLEQYWGGPRTYSEERG
+HPRLRMRHASYRIDPAARDAWLRHMRAAVDTLELSPLHEAELWDYLERAAHSLQNSA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001344.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001344.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9af1377af74623b68e4d651f795e52e353cdd826
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001344.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_01931
+MSETSTPAPENAPLVWIDCEMTGLHPHVDELVEVAVLITDAELNILDEGIDLVIRPSEAA
+LAQMDPFVRDMHTTSGLLPELEHGLTLENATARVMEYLTARVPAGKALLAGNTVGQDKLF
+LSAYMPAVVEHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIRDSITELRYY
+RAAVMAPSPGPTSEEAQAIARVVAEAQA
+>MOLHKGIG_00956
+MSETSTPTPESAPLVWIDCEMTGLHPQVDELVEVAVLITDAELNILDEGIDLVIRPSAAA
+LEQMDPFVRDMHTTSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNTVGQDKLF
+LARYMPAVVDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIKDSITELRYY
+RAAVMAPAPGPTTEEARAIAEVVSGAQA
+>NAFOICDF_01883
+MSETSTPAPESAPLVWIDCEMTGLDPDVDVLVEVAVLITDSELNVLDEGLDLVIRPTPEA
+LAQMDPFVRDMHTSSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNSVGQDKLF
+LARYMPAVIDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIRDSITELRYY
+REAVMVPAPGPTSEEARAIAEVVSGAQA
+>MHAAABBN_00669
+MSETSTPAPESAPLVWIDCEMTGLHPQVDELVEVAVLITDAELNTLDEGIDLVIRPSAAA
+LEQMDPFVRDMHTTSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNTVGQDKLF
+LARYMPAVVDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIKDSITELRYY
+RAAVMAPAPGPTTEEARAIAEVVSGAQA
+>LFPAFLNI_00902
+MSETSTPTPESAPLVWIDCEMTGLHPQVDELVEVAVLITDAELNILDEGIDLVIRPSEAA
+LEQMDPFVRDMHTTSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNTVGQDKLF
+LARYMPAVVDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIKDSITELRYY
+RAAVMAPAPGPTTEEARAIAQVVSGAQA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001348.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001348.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38beff8559418ed7912c6cd68d6d7140d0dcdf95
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001348.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_01996
+MADTASTQTPEWNTQQELAERMVPLLGSLYRENNVVTSIYGRSLVNRGVIDIIKAHRYAR
+RVQDAPLSVAATYPLVEAMAAMDLGAANVDLAELAARHKESGQEVQAFLDAELAEVKGKG
+GEGLGEPQDVVLYGFGRIGRLLARILLDHAGGGSKLRLRAVVVRKNSEDDLVKRASLLRR
+DSIHGPFDGTIVVDEDRNVITANGTEIQVIYSNDPTTVDYTAHGIKDALVIDNTGRWRDD
+EGLSQHLQAKGVKKVLLTAPGKGEMKNIVFGVNSDDITPEDTIVSAASCTTNGITPVLKV
+IQDDYGIDHGHVETVHAYTNDQNLTDNFHKGSRRGRSAGLNMVLTETGAAKAVAKALPEL
+KGKLSGNAIRVPTPDVSMAILNLELNKATSVEELNARLKQESLTGVLRGQVGYVDSPEVV
+STDFVGSDRAGVVDGLATLVNNEGKNAILYVWYDNEYGYSHQVVRVVSGPRPGRDQAPSA
+RPWSASGPCCSIASASSSSSCPKGSSSVPGSQVTPGTFMRSARCARFQRRCHLPSRRLT
+>MOLHKGIG_00942
+MADTASTQTPEWNTQQKLAEKMVPLLGTLYREHNVVTSIYGRSLVNRGVIDIIKAHRYAR
+RVQEAPLSVESTYPLVEAMAAMDLGAATIDLAELAAKHKASGQDVQAFLDAELAEVKGKA
+GEGLGETQDVVLYGFGRIGRLLARILLDHAGGGSKLRLRAVVVRKNSEDDLIKRASLLRR
+DSIHGPFDGTIVVDEDRDVITANGTEIQVIYSNDPTTVDYTSYGIKDALVVDNTGRWRDD
+EGLSQHLQAKGAAKVLLTAPGKGEMKNIVFGVNSDDITPQDTIVSAASCTTNGITPVLKV
+IQDDYGIDHGHVETVHAYTNDQNLVDNFHKGARRGRAAGMNMVLTETGAAKAVAKALPEL
+KGKLSGNAIRVPTPDVSMAILNLELTTPTSVEELNARLKQESLTGPLRGQVGYVDSPEVV
+STDFVGSDRAGVVDGLATLVNNDGKNAILYVWYDNEYGYSHQVIRVVEKMAGQQVPAFPQ
+A
+>NAFOICDF_01894
+MADTASTQTPEWNTQQKLAEKMVPLLGTLYREHNVVTSIYGRSLVNRGVIDIIKAHRYAR
+RVQEAPLSVEATFPLVEAMAGMDLGAANIDLAELAAKQQASGQDVQAFLDAELADVTGKS
+GEGLGETQDVVLYGFGRIGRLLARILLDHAGGGSKLRLRAVVVRKNSEDDLIKRASLLRR
+DSIHGPFDGTIVVDEDRNVITANGTEIQVIYSNDPTTVDYTSYGIKDALVVDNTGRWRDV
+EGLSQHLQAKGATKVLLTAPGKGDMKNIVFGVNSDDILDEDTIVSAASCTTNGITPVLKV
+IQDEYGVQHGHVETVHAYTNDQNLVDNFHKGARRGRAAGMNMVITETGAAKAVAKALPEL
+KGKLSGNAIRVPTPDVSMAIINIALEKPTSVEEINARLKQESLTGDLRGQIGYVDSPEVV
+STDFVGSDRAGVVDGLATIVNNEGKNAILYVWYDNEYGYSHQVVRVVEKMAGQQVPSFPK
+A
+>MHAAABBN_00661
+MADTASTQTPEWNTQQKLAEKMVPLLGTLYREHNVVTSIYGRSLVNRGVIDIIKAHRYAR
+RVQQAPLSVESTYPLVEAMAAMDLGAATIDLAELAAKQKASGQDVQAFLDAELAEVKGKA
+GEGLGETQDVVLYGFGRIGRLLARILLDHAGGGSKLRLRAVVVRKNSEDDLIKRASLLRR
+DSIHGPFDGTIVVDEDRDVITANGTEIQVIYSNDPTTVDYTSYGIKDALVVDNTGRWRDD
+EGLSQHLQAKGAAKVLLTAPGKGEMKNIVYGVNSDDITPQDTIISAASCTTNGITPVLKV
+IQDDYGIDHGHVETVHAYTNDQNLVDNFHKGARRGRAAGMNMVLTETGAAKAVAKALPEL
+KGKLSGNAIRVPTPDVSMAILNLELTKPTSVGELNARLKQESLTGPLRGQVGYVDSPEVV
+STDFVGSDRAGVVDGLATLVNNDGKNAILYVWYDNEYGYSHQVIRVVEKMAGQQVPAFPQ
+A
+>LFPAFLNI_00891
+MADTASTQTPEWNTQQNLAEKMVPLLGTLYREHNVVTSIYGRSLVNRGVIDIIKAHRYAR
+RVQEAPLSVESTYPLVEAMAAMDLGAATVDLAELAAKQKASGQDVQAFLDAELAEVKGKA
+GEGLGETQDVVLYGFGRIGRLLARILLDHAGGGSKLRLRAVVVRKNSEDDLIKRASLLRR
+DSIHGPFDGTIVVDEDRDVIIANGTEIQVIYSNDPTTVDYTSYGIKDALVVDNTGRWRDD
+EGLSQHLQAKGAAKVLLTAPGKGEMKNIVFGVNSDDITPEDTIVSAASCTTNGITPVLKV
+IQDDYGIDHGHVETVHAYTNDQNLVDNFHKGARRGRAAGMNMVLTETGAAKAVAKALPEL
+KGKLSGNAIRVPTPDVSMAILNLELNTPTSVEELNARLKQESLTGPLRGQVGYVDSPEVV
+STDFVGSDRAGVVDGLATLVNNDGKNAILYVWYDNEYGYSHQVIRVVEKMAGQQVPAFPQ
+A
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001354.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001354.fa
new file mode 100644
index 0000000000000000000000000000000000000000..67baf8ae02af2f878382c9981499b4acb41f9508
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001354.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02003
+MTDSPRTEPLGASSAPADVRELTLAGGCFWCLDAVYRRVRGVLAVESGYTGGDDPAPSYE
+SVCTGTTGHAEAVRVRFDAAVVPPEVIMDLFFTGHDPTSLNRQGADVGTQYRSAVFAHDE
+AEARFFADEIARAQANYDSPIVTRVEPASAWHPAEDIHQDFYARRRSDGYCRVVIDPKLA
+KVRRNYSAWLVDA
+>MOLHKGIG_00936
+MTDFPRTEPLGASGAPADVRELTLAGGCFWCLDAVYRRVRGVLAVESGYTGGDDPAPSYE
+SVCTGTTGHAEAVRVRFDAAVVPPEVIMDLFFTGHDPTSLNRQGADVGTQYRSAVFAHDE
+AEARFFADEIARAQENYDSPIVTRVEPASAWHPAEDIHQDFYARRRSNGYCRVVIDPKLA
+KVRRNYSAWLVDA
+>NAFOICDF_01900
+MSETPETPSTPAAHAPRVRELTLAGGCFWCLDAVYRRVRGVLAVESGYTGGHTPDPDYEA
+VCTGQTGHAEAVRVRFDEAQVPAEVIMDLFFTGHDPTSLNRQGADVGTQYRSAVFAHDEA
+EADFFRSQLARAQELYEAPIVTTIEPAAAWHPAEWYHQDFYASRPGNGYCRVVIDPKLAA
+VRRRHAAWLTDGA
+>MHAAABBN_00655
+MTDSPRTEPLGASDAPADVRELTLAGGCFWCLDAVYRRVRGVLAVESGYTGGDDPAPSYE
+SVCTGTTGHAEAVRVRFDAAVVPPEVIMDLFFTSHDPTSLNRQGADVGTQYRSAVFAHDE
+AETRFFADEIARAQANYDSPIVTRVEPASAWHPAEDIHQDFYARRRSNGYCRVVIDPKLA
+KVRRNYSAWLVDA
+>LFPAFLNI_00885
+MTDSPRTEPLGASGAPADVRELTLAGGCFWCLDAVYRRVRGVLAVESGYTGGDDPAPSYE
+SVCTGTTGHAEAVRVRFDAAVVPPEVIMDLFFTGHDPTSLNRQGADVGTQYRSAVFAHDE
+AEARFFADEIARAQANYDSPIVTRVEPASAWHPAEDIHQDFYARRRSNGYCRVVIDPKLA
+KVRRNYSAWLVDA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001356.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001356.fa
new file mode 100644
index 0000000000000000000000000000000000000000..659a8c88ee20daddecaf0d7668b61c345a4fb678
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001356.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02005
+MGLLARIKEDLDNVRSHDPAARGDLEVALVYSGLHAVWAHRIAHRMWRHERLRMPARILS
+QATRAATGIEIHPGATIGRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLAKVKRH
+PTLRDGVVVGAGAKILGPVEIGAGSAVGANAVVVKDTPADAIATGIPATYRLRRSPAEGK
+PLVDPAEYVDPAMWI
+>MOLHKGIG_00934
+MGLFSRIKEDIATVRSHDPAARGDLEVALVYSGLHAVWAHRVAHRMWRHDRLKMPARVLS
+QVTRAATGIEIHPGASIGRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLAKVKRH
+PTLRDGVVVGAGAKILGPVEIGEGTAVGANAVVVKDTPADAIATGVPATVRPRKGPSEGK
+PLVDPAEYVDPALWI
+>NAFOICDF_01902
+MGIRSRIKEDIATVRSHDPAARGDLEVVLAYSGLHAVWSHRVAHRMWQVGRLKTPARLLS
+QAARALTGIEIHPGATIGRRLFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLEKVKRH
+PTLRDGVVVGAGAKILGPVEIGEGTSVGANAVVVKDTPPDSIATGIPASVRLRTSPAEKK
+PLVDPAEYVDPAMWI
+>MHAAABBN_00653
+MGLFSRIKEDIATVRSHDPAARGDLEVALVYSGLHAVWAHRVAHRMWRHDRLKMPARVLS
+QVTRAATGIEIHPGASIGRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLAKVKRH
+PTLRDGVVVGAGAKILGPVEIGEGTAVGANAVVVKDTPADAIATGVPATVRPRKGPAEGK
+PLVDPAEYVDPALWI
+>LFPAFLNI_00883
+MGLFSRIKEDIATVRSHDPAARGDLEVALVYSGLHAVWAHRVAHRMWRHDRLKMPARVLS
+QVTRAATGIEIHPGASIGRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGRSLAKVKRH
+PTLRDGVVVGAGAKILGPVEIGEGTAVGANAVVVKDTPADAIATGVPATVRPRKGPAEGK
+PLVDPAEYVDPALWI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001357.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001357.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37adbcf9aed5e2d0052791a5c24ea191fe614d7f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001357.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_02007
+MTEQTTTVPVGAADIGVTGLAVMGANLARNFARHGYTVALHNRSHGRTDQFVAEHGDEGA
+FVATETLAELVQSLAVPRRVLIMVKAGAPVDAVIDQLVPLLDEGDIVIDAGNSHYEDTRR
+REAALAEKGLHFVGVGVSGGEEGALHGPAIMPGGPEKSYEALGPMLEKISAQFEGEPCCA
+WVGTDGAGHYVKMVHNGIEYADMQVIGEAYDLLRRVGGLEPAEQAEVFTAWNQTDLASYL
+IEITAEVLAQVDAATGRPLVDVIVDEAGQKGTGRWTAISGLDVGSPVAAIAESVFARSLS
+SQREVRAAAREVLQAGVDEAAVPAVTDTDAFVEDVRQALFASKLVAYAQGMDMLAAAAEE
+YGWSLDLGTIASLWRDGCIIRADLLDVIMKAFGGRDTARHPEPGTRAEGQPLNLLFAPEF
+AQAIAEALPAWRRVVGTAVAAGVPVPVFSSALAYYDGLRADRLPAALVQGQRDYFGAHTY
+LRVDREGSFHTLWSGDRTEVDGEGVPVVMPQPAEGDPTQD
+>MOLHKGIG_00933
+MTEQTTTVPVGAADIGVTGLAVMGANLARNFARHGYTVALHNRSRARTDQLVAEHGDEGA
+FVATETLAELVQSLAVPRRVLIMVKAGAPVDAVIDQLVPLLDEGDIVIDAGNSHFEDTRR
+REAALAEKGLHFVGVGVSGGEEGALHGPAIMPGGPEKSYEALGPMLEKIAAQFEGEPCCA
+WVGTDGAGHYVKMVHNGIEYADMQVIGEAYDLLRRVGGLEPAEQAEVFTAWNQTDLASYL
+IEITAEVLAQVDAATGRPLVDVIVDEAGQKGTGRWTAISGLDVGSPVAAIAESVFARSLS
+SQRAVREVARETLAAGVDEEAQRAPQDTDAFVEDVRQALFASKLVAYAQGMDMLAAAAEE
+YGWSLDLGTIASLWRDGCIIRADLLDVIMQAFGGRDTSRHPAPGTRAPGQPLNLLFAPEF
+AQAIAEALPAWRRVVGTAVAAGVPVPVFSSALAYYDGLRADRLPAALVQGQRDYFGAHTY
+LRVDREGSFHTLWSGDRTEVDGEGVPVVMPQPTEGDPTQD
+>NAFOICDF_01903
+MTETSTVRGTADIGVTGLAVMGANLARNFARHGYTVALHNRSRAKTDALVAEHGHEGSFV
+ATETLEELVGSLASPRRVLIMVKAGAPVDAVIDQLVPLLDEGDIVIDAGNSHYEDTRRRE
+AALAEKGLHFVGVGVSGGEEGALNGPAIMPGGPEESYAALGPLLEDIAASYDGEPCCAWI
+GTDGAGHYVKMVHNGIEYADMEVIGEAFDLLRRVAGIEPAEQAQVFDAWNQTELASYLIE
+ITAEVLQQVDAATGAPLVDVIVDEAGQKGTGRWTAISGLDVGSPVAAIAESVFARSLSAQ
+TEVRATAREVLAAGVESAPAVSPQDRDAFVEDVRQALFASKLVAYAQGLDMLSAAAIEYG
+WALDLGTIASLWRDGCIIRADLLDVIMKAFGGRDTSRHPEPGTRAEGQPLNLLFAPEFAQ
+AMAEALPAWRRVVGAAVAAGVPVPVFSSALAYYDGLRADRLPAALIQGQRDFFGAHTYRR
+TDRDGSFHTLWSGDRTEVDGDGAPVVMPQPAEGDPTDETAR
+>MHAAABBN_00652
+MTEQTTTVPVGAADIGVTGLAVMGANLARNFARHGYTVALHNRSRARTDQLVAEHGDEGA
+FVATETLAELVQSLAVPRRVLIMVKAGAPVDAVIDQLVPLLDEGDIVIDAGNSHFEDTRR
+REAALAEKGLHFVGVGVSGGEEGALHGPAIMPGGPEKSYEALGPMLEKISAQFEGEPCCA
+WVGTDGAGHYVKMVHNGIEYADMQVIGEAYDLLRRVGGLEPAEQAEVFTAWNQTDLASYL
+IEITAEVLAQVDAATGRPLVDVIVDEAGQKGTGRWTAISGLDVGSPVAAIAESVFARSLS
+SQRAVRQVARETLAAGVDEEAQRAPQDTDTFVEDVRQALFASKLVAYAQGMDMLAAAAEE
+YGWSLDLGTIASLWRDGCIIRADLLDVIMQAFGGRDTSRHPAPGTRAPGQPLNLLFAPEF
+AQAIAEALPAWRRVVGTAVAAGVPVPVFSSALAYYDGLRADRLPAALVQGQRDFFGAHTY
+LRVDREGSFHTLWSGDRTEVDGEGVPVVMPQPTEGDPTQD
+>LFPAFLNI_00882
+MTEQTTTVPVGAADIGVTGLAVMGANLARNFARHGYTVALHNRSRARTDQLVAEHGDEGA
+FVATETLAELVQSLAVPRRVLIMVKAGAPVDAVIDQLVPLLEEGDIVIDAGNSHYEDTRR
+REAALAEKGLHFVGVGVSGGEEGALHGPAIMPGGPEKSYEALGPMLEKISAQFEGEPCCA
+WVGTDGAGHYVKMVHNGIEYADMQVIGEAYDLLRRVGGLEPAEQAEVFTAWNQTDLASYL
+IEITAEVLAQVDAATGRPLVDVIVDEAGQKGTGRWTAISGLDVGSPVAAIAESVFARSLS
+SQRAVREVARETLAAGIDEDAQRVPQDTDAFVEDVRQALFASKLVAYAQGMDMLAAAAEE
+YGWSLDLGTIASLWRDGCIIRADLLDVIMQAFGGRDTSRHPAPGTRAPGQPLNLLFAPEF
+AQAIAEALPAWRRVVGTAVASGVPVPVFSSALAYYDGLRADRLPAALVQGQRDYFGAHTY
+LRVDREGSFHTLWSGDRTEVDGEGVPVVMPQPTEGDPTQD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001362.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001362.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3849df533600c46c0f2c336808748cc04f1e136e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001362.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_02012
+MNAPSLQPSPYPAPPPSRGAEVRAGVRLSLAAGLGLFPLGVAFGMLVVQAGLPAWVAPLF
+SVVVFAGSVELLLVSLAVAATPLLTIAVTVFLVNFRHVFYAFSFPLRVVRHPLARLYSMG
+ALIDEAYAIAAAHPRGWTAPRLIALQVALHAYWVLGGLAGVAVAWLLPGPVEGLEFALVA
+LFIVLALDAARTRAQAPLVLAAALAVGVGLLVAPGQLLVAAFAVYAAVLIALHVLARRGV
+DLPLPAPTPATGPVPVVAGPAPGEEPR
+>MOLHKGIG_00928
+MLTIMSSSTESLRAPVTPSRWAEVRSGVAVTLGAGLGLFPLGMAFGMLVVQAGLPAWVAP
+LFSVVVFAGSVELLLVSLVVAGTPLLTIAVTVFLVNFRHVFYAFSFPLRVVRGRFARIYS
+MGALIDEAYAIAAARPRGWTGPRLVAMQVALHAYWVLGGLAGVAVAWLLPGPVEGLEFAL
+VALFIVLAMDAARTRAQLPLVLAAAVAVGVALLLAPAQVLVVAFALYAAVLIAFHVLAAR
+GTALPLPEPVPVTGPVPVVAATGERAGTDAEPGAGEDPR
+>NAFOICDF_01911
+MTEITPPSPAASGVPDALPTRRAEVAEGVRLSGPAGLGLFPLGVAFGMLVVQAGLPGWAA
+PLLSVVVFAGSVELLLVSLLAAGTSLAGIAVTVFLLNFRHVFYAFGFPLRVVRNPLARLY
+SMGGLIDEAYAITAAHPRGWTAPRLLATQVSLHLYWVVGGLVGVVAAGLLPAPVEGLEFA
+LTALFIVLALDAARTRRHVLLVLAAAAAVGVGLVVAPSALLVASFLGFVAALMAAHVAAE
+RGARLPLPAVKELGATSPGAAEAAELTTVDAEAGR
+>MHAAABBN_00647
+MLTIMGSSSASSRASAPPSRWAEVRSGVAVTLGAGLGLFPLGVAFGMLVVQAGLPAWVAP
+LFSVVVFAGSVELLLVSLVVAGTPLLTIAVTVFLVNFRHVFYAFSFPLRVVRGRLARIYS
+MGALIDEAYAIAAAQPRGWTAPRLLAMQIALHAYWVLGGLAGVAVAWLLPVPVEGLEFAL
+VALFIVLAMDAARTRAQLPLVLAAAVAVGVALLLAPAQVLVVAFALYAAVLIAFHVLAAR
+GTALPLPEPVPVTGPVPVVAAAGERAVTDAEPGVEEDPR
+>LFPAFLNI_00876
+MLTIMGSSSASSRASAPPSRWAEVRSGVAVTLGAGLGLFPLGMAFGMLVVQAGLPAWVAP
+LFSVVVFAGSVELLLVPLVVAGTPLLTIAVTVFLVNFRHVFYAFSFPLRVVRGRLARIYS
+MGALIDEAYAIAAARPRGWTGPRLVAMQVALQAYWVLGGLAGVAVAWLLPGPVEGLEFAL
+VALFIVLAMDAARTRAQLPLVLAAAVAVGVALLLAPAQVLVVAFALYAAVLIAFHVLAAR
+GTALPLPEPVPVTGPVPVVAATGERAGTDAEPGAGEDPR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001363.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001363.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5e2bc9cfb4c6dd3b0006e52b8987757d050f43b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001363.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02015
+MAEEPGAVPALRDDRGQDWPWPPTRGPEDAAAPRATWLVLLPGAFTPVCTGELGWLGELA
+TDLAADDVAVRVIACDAAPVLRRVREELGLPEDLVLLSDFWPHGAACAALDAFDAASGRA
+RRVSVLLDADGVEVSRVTAAPGRPRSRTEHEAATRALLGDR
+>MOLHKGIG_00926
+MAEPPSGGTRGADVVPALRDDHGQTWPWPPTRGPQDAAGPRGTWLVFLPGAFTPVCTDEL
+GWIGALAEDVAVDDVAVRVVSCDAAPVLRRVREELALPEPLTLLSDFWPHGAACRALDVF
+DVETGRPRRVSVLLDADGVEAARVVAAPGQARTRSEHEAATRDLLADR
+>NAFOICDF_01914
+MAEPALRDIHGTPWPWPPVVSGERAAWLVFLPGAFTPVCAGELAWLGPLAVELAAEDVGL
+RVVSCDAAPVLREVADRTGLPAECVLLSDFWPHGAAAARFGLLDETTGRPRRVSVLVDES
+GTELVRVRPGEPGGPRTAQAHRRAAEGALGRRR
+>MHAAABBN_00645
+MAEPPSGGTRGADVVPALRDDHGQTWPWPPTRGPQDAAGPRGTWLVFLPGAFTPVCTDEL
+GWIGALAEDVAVDEVAVRVVSCDAAPVLRRVREELALPEPLTLLSDFWPHGAACRALDVF
+DAETGRPRRVSVLLDADGVEAARVVAAPGQARTRGEHEAATRDLLVDR
+>LFPAFLNI_00874
+MAEPPSGGTRGADVVPALRDDHGQTWPWPPTRGPQDAAGPRGTWLVFLPGAFTPVCTDEL
+GWIGALAEDVAVDDVAVRVVSCDAAPVLRRVREELALPEPLTLLSDFWPHGAACRALDVF
+DVETGRPRRVSVLLDADGVEAARVVAAPGQARTRSEHEAATRDLLADR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001366.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001366.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bff602bfe48224cdd99b9c74d9cb998f395e5151
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001366.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02018
+MPEPRSAASRPVSTEGRARLRSHLGALNTAVLQRLDATLPWYRGLTPDERSALGLVAQRA
+LQGFISWFDRPKTTGHVLQDVFGPAPTDLTRAISLQRALQLIRTMVDVVETRVPELLAER
+DQAPIREHVLHYSREVAFALADVYARAAEMRGAMDSRLEAVLLDAVLRGQDPDEIRHRAT
+ALGWRGDHRVMVMAGLAPGQDQPAFIPGLRRAAAKLDCDLLVGVQAERLVLVIGSVTDAQ
+VVGEALTPWFAPGPVILGPVVDSLVEAHVSARHTLAGLGAAPAHPRAIRPTPAEDLLPER
+ALLGDPTACEALVEGVYAPLADAGTALLDTVDAYGALGHSLEGTARELFVHANTVRYRLK
+RVAEVTGWDPLVPRDAYVLQTAVTLGRLAGSRPGVAEASA
+>MOLHKGIG_00923
+MPEPRPAAPRPVSTDGLARLRSHLGALNTAVLQRLDATLPWYRRLTPDERSALGLVAQRA
+LQGFLTWFERPTSTGHVLQDVFGPAPTDLTRAISLQRALQLIRTMVDVVETRVPELLAER
+DQAPVREHILHYSREVAFALADVYARAAEMRGAMDSRLESVLLDAVLRGQDPDEIRHRAT
+ALGWRGDHDVMVMAGLAPGQDKPAFIPDLRRAAARLDCDLLVGVQSERLVLVVGSVRDAR
+AVGEALAPWFAPGPVIVGPVVDSLVSAHVSARHTLAGLSAAAAHPRASRPTPAEDLLPER
+ALLGDPTAREALVDGVFTPLADAGTSLLETVDAYGALGHSLEGTARELFVHANTVRYRLK
+RVAEVTGWDPLVPRDAYVLQTAITLGRLAGARPTTGTGSD
+>NAFOICDF_01917
+MPAPRPSAPRRVSADGLARLRAHLGTFNTATLRRLDETLPWYRELTPDERSALGLIAQRA
+LQGFITSFERPQTTTVDVLRDVFGQSPTELTRAISLHRALQLIRTIVDVVETGVPDAVSE
+ADQPVVAEHVLHYSREIAFAIADVYARAAELRGAMDSRLEAVLLDAVLRGQEPDEIQHRA
+TAFGWRGGDGVMVMAGSARDGATAAFLPGLRRDAARLQCELLVGVQSRRLVLVVGSVSDP
+DAVAEALLPWFADGPVIVGPVVDSLLEAHVSAHHALAGLGAAAAHPRAGRPARSDDLLPE
+RALAGDATACAALVDGVYAALADAGPSLLETVDVYTACGHSLEGTARELYVHANTVRYRL
+RRAAEVTGWDPQRPRDAYVLQTAVALGRLSEGAPRL
+>MHAAABBN_00642
+MPEPRPAAPRPVSTDGLARLRSHLGALNTAVLQRLDATLPWYRRLTPDERSALGLVAQRA
+LQGFLTWFERPTSTGHVLQDVFGPAPTDLTRAISLQRALQLIRTMVDVVETRVPELLAER
+DQAPVREHILHYSREVAFALADVYARAAEMRGAMDSRLESVLLDAVLRGQDPDEIRHRAT
+ALGWRGDHDVMVMAGLAPGQDKPAFIPDLRRAAARLDCDLLVGVQSERLVLVVGSVRDAR
+AVGEALAPWFAPGPVIVGPVVDSLVSVHVSARHTLAGLSAAAAHPRASRPTPAEDLLPER
+ALLGDPTAREALVDGVFTPLADAGTSLLETVDAYGALGHSLEGTARELFVHANTVRYRLK
+RVAEVTGWDPLVPRDAYVLQTAITLGRLAGARPTTGAGSD
+>LFPAFLNI_00871
+MPEPRPAAPRPVSTDGLARLRSHLGALNTAVLQRLDATLPWYRRLTPDERSALGLVAQRA
+LQGFLTWFERPTSTGHVLQDVFGPAPTDLTRAISLHRALQLIRTMVDVVETRVPELLAER
+DQAPVREHILHYSREVAFALADVYARAAEMRGAMDSRLESVLLDAVLRGQDPDEIRHRAT
+ALGWRGDHDVMVMAGLAPGQDKPAFIPDLRRAAARLDCDLLVGVQSERLVLVVGSVRDAR
+AVGEALARWFAPGPVIVGPVVDSLISAHVSARHTLAGLSAAAAHPRACRPTPAEDLLPER
+ALLGDPTAREALVDGVFTPLADAGTSLLETVDAYGALGHSLEGTARELFVHANTVRYRLK
+RVAEVTGWDPLVPRDAYVLQTAITLGRLAGARPTTGTGSD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001374.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001374.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7602f7d41dc13b3167c46e60cdf2302a2553f49b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001374.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_02027
+MSGIGRTRSISLSGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGAGHDLAIVLAAYAADGRVRGVEGPVFLAELGLDGALHRSPE
+TVAMVMASVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVILAFGGEPEGEAPQRRP
+VRPADDDGAPGLGPGAPDLSEVAGQAEARFALEVAAAGAHHLLLRGAPGAGKTMLAERLP
+GILPPLDRRTALECAALRSLRGADALARRGVGQGSAGTRAAGDLDRTPPFEAPHHSASMA
+ALVGGGANLARPGAVSLAHGGVLFLDEAPEFERRALESLRQPLESGEVLLHRARGTVAYP
+ARFQLVLAANPCPCGKGGGNGVECRCSVTERRRYGQRLSGPLLDRVDLQVTVRPVQARQL
+AGAPAAETSAQVAARVAEAARRQAERWARAAEEGLVAPGLRRNAHAPAGVLRHGPYAVPR
+AARRAADEAVDHGLLSARGHARVLRLAWTLADLRGAETPAPEDTDVALTLRHQEEDET
+>MOLHKGIG_00915
+MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGACHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPE
+TVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVIRAFGGEPDGEPPHRPA
+RRQVTAPEPEPTRAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTMLAERLPG
+ILPPLDRRTALECAALRSLRGGDARVRRRGGTSQGFDGEIDRTPPFEAPHHSASRSALVG
+GGSGLARPGAASLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQ
+LVLAANPCPCGKGGGTGVECRCSVPERRRYAQRLSGPLLDRVDLQVTVRPVEARQLTGAP
+ASETTSQVAVRVAAAADRQARRWATAAERGVVPPGLRRNAHVPAGVLRHGPYAVPRAARR
+PADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA
+>NAFOICDF_01925
+MSGIGRTRSISLTGLRGTVVDVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGAAHDLAIVLAAYAADGRVQGVDGPVFLAELGLDGTLHRAPE
+TVAMVMAAVDAGHDRVVVAADAVAEAELVPGARVRGFAHLHEAILAFGGRPDASVARPSG
+PSGTAGRGPAAGQEGPSGPVPDLAEVAGQAEARFALEVAAAGGHHLLLSGPPGAGKTMLA
+ERLPGILPPLDDRTALETAALRSLRGLEPSARGLRRTPPFEAPHHSASMAALVGGGTGLG
+RPGAVSLAHGGVLFLDEAPEFERRALDALRQPLESGEMIVHRAHGSVAYPARFQLVLAAN
+PCPCGFGSGTGAHCRCTSLQRRKYAARLSGPLLDRVDVQVSVRPVRADQLAAAPEAEPSR
+AVAARVAAAVAAQDARWAAAAREGSLPPGVCRNAHVPAALLRSGRFAVPPEARATADRAV
+DRGELSARGHGRVLRLAWTLADLRGASCPEAQDVEIALQLRIRSEEDR
+>MHAAABBN_00634
+MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGACHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPE
+TVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVIRAFGGEPDGEPPHRPA
+RRQVTAPEPEPARAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTMLAERLPG
+ILPPLDRRTALECAALRSLRGGDARVRRRGGTAQGFDGDIDRTPPFEAPHHSASRSALVG
+GGSGLARPGAASLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQ
+LVLAANPCPCGKGGGTGVECRCSVPERRRYAQRLSGPLLDRVDLQVTVRPVEARQLTGAP
+ASETTSQVAARVAAAADRQARRWATAAERGLAPSGLRRNAHVPAGVLRHGPYAVPRAARR
+PADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA
+>LFPAFLNI_00863
+MSGIGRTRSITLAGLRGEVVHVEADIAQSLPGFTLLGLPDQALQESRDRIRSAARNAGLP
+LTRRHLTVNLLPAGVHKRGACHDLAIVLAAYAADGRVRNVEGPVFLAELGLDGALHRSPE
+TVAMVMAAVDAGCSEVVVAEDAEAEARLVPGAEVRGFAHLHDVIRAFGGEPDGEPPHRPA
+RRQVTAPEPEPTRAVPDLAEVAGQAEARFALEVAAAGAHHLLLMGAPGAGKTMLAERLPG
+ILPPLDRRTALECAALRSLRGGDARVRRRGGTSQGFDGEIDRTPPFEAPHHSASRSALVG
+GGSGLARPGAASLAHGGVLFLDEAPEFERRTLEALRQPLESGEVLLHRALGAVVYPARFQ
+LVLAANPCPCGKGGGTGVECRCSVPERRRYAQRLSGPLLDRVDLQVTVRPVEARQLTGAP
+ASETTSQVAVRVAAAADRQARRWATAAERGVVPPGLRRNAHVPAGVLRHGPYAVPRAARR
+PADDAVDQGLLSARGHARVLRLAWTLADLRGAERPAPEDTDVALTLRHQNEEDA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001375.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001375.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e4432420d818fa67d37d11d98a41db0b52fd818e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001375.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02028
+MTGTAEKVGADSPGGGRGSRAHTALGRFGEDAAARWLADRGYVIADRNWRGEAGELDLVA
+HHAGWWVGVEVKTRSGLAFGDPLESIDRRKLLRLHRLTAAWVRAHGEGRRAERWRVDAVA
+VLVPRTGGIRFDLLQDVRP
+>MOLHKGIG_00914
+MTGTAEQVGAQPPGERRASRAHTALGRFGEDAAARWLAERGYVIADRNWRGEAGELDIVA
+HHAGWWVGVEVKTRSGLAFGDPFESIDRRKLTRLHRLTAAWVRAHAADRRGTPWRVDAVA
+VLVPRTGGIRFDLLQDVRP
+>NAFOICDF_01926
+MVPLDTTTTTPAARRGSTAHTALGRYGEDAAARWLAERGYQIVARNWRGEDGELDLVARH
+GPWWVGVEVKTRSGLAYGDPLEAIGRRKLLRLHRLTAAWVREAAAREGRPLRSQQWRVDA
+VAVLVPRTGGVHFDLVQDVRP
+>MHAAABBN_00633
+MTGTAERIGAQPPGDRRASRAHTALGRFGEDAAARWLAERGYVIADRNWRGEAGELDIVA
+HHAGWWVGVEVKTRSGLAFGDPFESIDRRKLTRLHRLTAAWVRAHAADRRGTPWRVDAVA
+VLVPRTGGIRFDLLQDVRP
+>LFPAFLNI_00862
+MTGTAEQVGAQPPGERRASRAHTALGRFGEDAAARWLAERGYVIADRNWRGEAGELDIVA
+HHAGWWVGVEVKTRSGLAFGDPFESIDRRKLTRLHRLTAAWVRAHAADRRGTPWRVDAVA
+VLVPRTGGIRFDLLQDVRP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001376.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001376.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c956d8b8f6d2a74087698c33f112178b85f625c3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001376.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_02029
+MSTDDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANDVRLTPRQSDGDVFFEIL
+LEDAWVWDVYRTQRFIKRVKVLTFKDVNIEELPRDELQVPPDGQLPD
+>MOLHKGIG_00913
+MSADDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANDVRLTPRQADGDVFFEIL
+LEDAWVWDVYRTQRFIKRVKVLTFKDVNIEELPTEDLTVPPDGQLPS
+>NAFOICDF_01927
+MSTDDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANAVTLTPHQTDGEVFFELT
+LEDAWVWDVYRTARFIRRVRVLTFKDVNIEELPRDELQVPEDGGLRGDLGR
+>MHAAABBN_00632
+MSADDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANDVRLTPRQADGDVFFEIL
+LEDAWVWDVYRTQRFIKRVKVLTFKDVNIEELPTEDLTVPPDGQLPS
+>LFPAFLNI_00861
+MSADDVEDFEAEAELLLYREYRDVVGLFRYVVETERRFYLANDVRLTPRQADGDVFFEIL
+LEDAWVWDVYRTQRFIKRVKVLTFKDVNIEELPTEDLTVPPDGQLPS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001378.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001378.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1507ea686a5e87624d9858f95e84b43fefbee90f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001378.fa
@@ -0,0 +1,26 @@
+>ACLBLIBL_02031
+MSRPDHRLVPPAAGHAHDSGAAPADDAARPAGPTGALLGHAVPSGAGSQALPAEPGRGPL
+RAVLAVVVLTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPEPYPVRRGDVV
+VFDDTKGWLADGGHVIKRVVGLPGDTVSFTPGEAALRVNGVPVAEPYLAPGDAPAQDAFE
+ATVPAGRLWVLGDHRSASADSRAHRDGPGGGFVSLDDVVGRARFVVWPLDRIGGAGAAPE
+AFEAVPDARGAGS
+>MOLHKGIG_00911
+MTGRRTALIAAAVTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPDPFPVRR
+GDVVVFEDTKGWLPGGGHVIKRAVGLPGDIVSWTPGEETLRVNGVPVEEPYLAPGETPAQ
+EAFEVTVPAGRLWVLGDHRSASADSRAHRAGPGGGFVALDDVVGRARFVVWPLDRIGGAG
+TDPDAFATVPDAPAPEART
+>NAFOICDF_01929
+MAEAPVTPAAAGTADPAAAPAAEHPGHPLRAAAVTVAVTLALLLAVQLLLVRMFAIPSAS
+MEPTLRPGDRVAVDLLVPGPLELRRGDVVVFRDARGWLAGAEAVHADPLHAAVAALGLGT
+QEGHLVKRVVGLPGDRVRWSPEDARLEVNGVPVDEPYVAGPAAQEAFDVVVPDGGLWVLG
+DHRSASQDSRQHQHGPGGGMVSVDDVVGRVEGVVWPLDRAGAVGPGPLAKLP
+>MHAAABBN_00630
+MTGRRTALIAAAVTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPDPFPVRR
+GDVVVFEDTKGWLPGGGHVIKRAVGLPGDIVSWTPGEETLRVNGVPVEEPYLAPGETPAQ
+EAFEVTVPAGRLWVLGDHRSASADSRAHRAGPGGGFVALDDVVGRARFVVWPLDRIGGAG
+TDPDAFATVPDAPAPEART
+>LFPAFLNI_00859
+MTGRRTALIAAAVTVLACVLAWAFLARMYAIPSSSMEPGLRAGDRVVATLLTPDPFPVRR
+GDVVVFEDTKGWLPGGGHVIKRAVGLPGDIVSWTPGEETLRVNGVPVEEPYLAPGETPAQ
+EAFEVTVPAGRLWVLGDHRSASADSRAHRAGPGGGFVALDDVVGRARFVVWPLDRIGGAG
+TDPDAFATVPDAPAPEART
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001379.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001379.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45da7307753a6ae9336e438ca56e044fa63350b4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001379.fa
@@ -0,0 +1,29 @@
+>ACLBLIBL_02032
+MSHPEPRDPRRSRGSAVSRSVAPGSGRGTTPARGSGGTAWWAWIGLTVAAAVGAAAVLRA
+LTGPVYLIPSGSMEPTLHPGDRVRVDASAAGGEGVRRGDVVVFDGAGSLAPYRSVGSLER
+GLEDVARSWGLGASGDAFVKRVLALPGDRLECCAPDGRLLRDGAPVDEPYLGRPVTAQDP
+AADGSWTFEVPEGRMVVLGDNRSASRDSRALLGGAGGGLIPLKRVEGRAAEVVWPLDRRG
+PVDASAPEAAPGAAP
+>MOLHKGIG_00910
+MRTSEPRDPRRSRGSVASGAGSSPGTTAAPASGASRWWAWLGLTVVAAVVVAAVLRALTG
+PVYLIPSGSMEPTLQPGDRVRVDAAAAGGQGLHHGDVVVFDGAGSLAPYRSAGSLERGLE
+DVARWWGVGAAEDVFVKRVLALPGDRLECCAPDGRLLREGEPLDEPYLGRPVTADEPAAA
+GTWSFEVPDGRMVVLGDHRAASRDSRALLGAPGGGLIPLERVEGRAAEIVWPLSRRGTVD
+APSGDTP
+>NAFOICDF_01930
+MRAQEPRDRNRSRGSRASGEAGRPWWALVLLTLAGAVVAAALLRAFTGPVYLVPSGSMEP
+TLLPGDRVHVDTAAADGAGLEHGDVVVFDGAGSLAPYRSRTALDRGLEDVAAFWGVGAAQ
+DVYVKRVLALPGDTLSCCTADGRLERNGAPLDESYLGRTVDAAAPASRSTWAFEVPEGRM
+VVLGDNRDVSRDSRALLGAPGGGLIPVEKVIGRVDSVAWPLDRRGDVPAGAQDGSRG
+>MHAAABBN_00629
+MRTSEPRDPRRSRGSVASGAGSSSGPTAAPASGTSRWWAWLGLTVVAAVVVAAVLRALTG
+PVYLIPSGSMEPTLQPGDRVRVDAAAAGGQGLHHGDVVVFDGAGSLAPYRSAGSLERGLE
+DVARWWGVGAAEDVFVKRVLALPGDRLECCAPDGRLLRNGEPLDEPYLGRPVTADEPAAA
+GTWSFEVPDGRMVVLGDHRAASRDSRALLGAPGGGLIPLERVEGRAAEIVWPLSRRGTMD
+APSGDTP
+>LFPAFLNI_00858
+MRTSEPRDPRRSRGSVASGAGSSSGPTAAPASGTSRWWAWLGLTVVAAVVVAAVLRALTG
+PVYLIPSGSMEPTLQPGDRVRVDAAAAGGQGLQRGDVVVFDGAGSLAPYRSAGSLERGLE
+DVARWWGVGAAEDVFVKRVLALPGDRLECCAPDGRLLREGEPLDEPYLGRPVTADEPAAA
+GTWSFEVPDGRMVVLGDHRAASRDSRALLGAPGGGLIPLERVEGRAAEIVWPLSRRGTVD
+APSGDTP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001384.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001384.fa
new file mode 100644
index 0000000000000000000000000000000000000000..76334ebcd43d092b5b78e7016f51bb22be20b926
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001384.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02037
+MAVKIRLKRFGKIRAPYYRIVVADSRTRRDGRAIEEIGKYHPTEEPSYIEVDSERAQYWL
+SVGAQPTEQVAALLKITGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKAEE
+PKAKESAEAETPAEEAPEAPAEDAEKSE
+>MOLHKGIG_00905
+MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL
+SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE
+APAESEQAAEAPAAEAPAEDAEKSE
+>NAFOICDF_01935
+MAVKIRLKRFGKIRAPYYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL
+SVGAQPTEQVAALLKITGDWQKFKGEAGAEGTLKTKGEKEAFVAPAKESVILPEEPKQEE
+APAESAEAEAPVEEAADAEAPAEDAEKAE
+>MHAAABBN_00624
+MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL
+SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE
+APAESEQAAEAPAEEAAEAPAEDAEKSE
+>LFPAFLNI_00853
+MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL
+SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE
+APAESEQAAEAPAEEAAEAPAEDAEKSE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001386.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001386.fa
new file mode 100644
index 0000000000000000000000000000000000000000..466cd762d49455a02ba155b69774152fc698e972
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001386.fa
@@ -0,0 +1,43 @@
+>ACLBLIBL_02039
+MNEMTLDAGTVWMVVSAGLVLLMTPGLALFYGGMTRSKSALNMMMMSFVSMGLVGVVWIL
+WVSGMTGGEGWLGLVGSPLADPGLTTAMEEGGLIAAGFGATFAIITVALISGAVADRARF
+LTWCVFVPVWVTLVYAPLAYMVWGGGLLAEEGAIGSRLGEALDFAGGLVVHISAGVAALV
+LALMMGKRKGFGVDPGHKPHNVPFTMLGAALLWFGWFGFNGGAAGDTGQLGLIWINTLAA
+AAAGMLGWVVVEWVRRGRPTSIGTASGIVAGLVGITPACAFVSPLGALVIGVASGAASAL
+AVNLKYRLGFDDSLDVVGVHLTAGILGTVLIGFFALPSEGPAGLFYGGDGRLLLAQTVAV
+VVAVVFTAVLTFLIALVLKATLGLRVSEEDEERGVDLTLHDESAYHYDVGFGGVPVPADA
+QAHRGGAAG
+>MOLHKGIG_00903
+MNEMTLDAGTVWMVVSAGLVLLMTPGLALFYGGMTRSKSALNMMMMSFVSMGLVGVVWIL
+WVSGMTGGEGWLGLVGSPLADPGLTTAMEEGGLIAAGFGATFAIITVALISGAVADRARF
+LTWCVFVPVWVTLVYAPLAYMVWGGGLLAEEGAIGSRLGEALDFAGGLVVHISAGVAALV
+LALMMGKRKGFGVDPGHKPHNVPFTMLGAALLWFGWFGFNGGAAGDTGQLGLIWINTLAA
+AAAGMLGWVVVEWVRRGRPTSIGTASGIVAGLVGITPACAFVSPLGALVIGVASGAASAL
+AVNLKYRLGFDDSLDVVGVHLTAGILGTVLIGFFALPSEGPAGLFYGGDGRLLLAQTVAV
+VVAVVFTAVLTFLIALVLKATLGLRVSEEDEERGVDLTLHDESAYHYDVGFGGVPVPADA
+QAHRGGAAG
+>NAFOICDF_01937
+MTETTPLDAGAVWTVTAAALVLLMTPGLALFYGGMTRAKSALNMMMMSFVSMGLIGVAWI
+LWAYGMTSGDGLAGIVGSPLNDLGAVQSMADGDLISVGFSATFAIIAVALISGAVADRAK
+FSTWCVFVPVWVTLVYAPLAYMVWGGGLLSADGAIGARLGEALDFAGGLVVHISAGVAAL
+VLAMMMGKRQGFGVDAAHRPHNVPFTMLGAALLWFGWFGFNSGAASDVEQLGLTWVTTLV
+AAAAGMLGWVLVEWLRRGRPTSIGTASGIVSGLVAITPACAFVSPLGAVVIGLVAGAACA
+LAVNLKYRWGFDDSLDVVGVHLTAGILGTLLIGLFALPETGHAGLFHGGDGSLLLAQTVA
+VVVAVVFTAVVTAVIAFVLRATLGLRVSVEEEERGVDLTLHDETAYDVGFGGVPVPTDAQ
+ARSTAAAE
+>MHAAABBN_00622
+MEESNVLDAGTVWMVTSAAMVLLMTPGLAIFYGGMTRAKSSLNMIMMSFVSMGLVGVVWV
+LWVHGMTGGDGWAGVVGNPAGDLGLTGTMAEGGLVAAAYGATFAIIAVALISGAVADRFK
+FVTWCVFVPVWTTVVYAPLAYMVWGGGLLSEDGAIGARLGEALDFAGGLVVHISAGVAAL
+VLALLLGKRHGFGVDPGHRPHNVPFTMLGAALLWFGWFGFNGGAAGGVDELGLIWVDTLA
+AGAAGMLGWVFVEWLRRGRPTSIGTASGIVSGLVAITPACAYVSPLGAVVIGLVSGAASA
+LAVNLKYRLGFDDSLDVVGVHLTSGILGTVLIGFFALPGEGRAGLFYGGDAGLLVAQTVA
+VLVAVVFTAVVTTAIALVLRGTMGLRVSKEDEERGVDLTLHDESAYDVGFGGVPVPAEAR
+>LFPAFLNI_00851
+MEESNVLDAGTVWMVTSAAMVLLMTPGLAIFYGGMTRAKSSLNMIMMSFVSMGLVGVVWV
+LWVHGMTGGDGWAGVVGNPAGDLGLTGTMAEGGLVAAAYGATFAIIAVALISGAVADRFK
+FVTWCVFVPVWTTVVYAPLAYMVWGGGLLSADGAIGARLGEALDFAGGLVVHISAGVAAL
+VLALLLGKRHGFGVDPGHRPHNVPFTMLGAALLWFGWFGFNGGAAGSVDELGLIWVATLA
+AGAAGMLGWVFVEWLRRGRPTSIGTASGIVSGLVAITPACAYVSPLGAVVIGLVSGAASA
+LAVNLKYRLGFDDSLDVVGVHLTAGILGTVLIGFFALPDEGRAGLFYGGDAGLLVAQTVA
+VLVAVVFTAVVTTAIALVLRGTMGLRVSKEDEERGVDLTLHDESAYDVGFGGVPVPAEAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001387.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001387.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3eb611de71c1843a3e7b06bee1a417caad8dc6b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001387.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02040
+MCQTGHVEIVLIISVVLALLVGGLIVGLLDRRPAPPKGSYQGVRDADDPRPAPRHAAPGG
+STAVLERPEAEEAPVDLVEPEVVEEVEAEPAAPELERPEAAGSRLARLRARLLKSNNVFG
+KGLLALLSRDRIDEDTWDEIEETLLMADLGTEPTMVLVDRLKSRVTVEGTREPEQVRELL
+REELVAMVDPSMDRRLAASRRDGRPAVTLVVGVNGVGKTTTVGKLARVLVAEDRDVVLGA
+ADTFRAAAAEQLATWGARVGVPTVRSEKEGADPASVAYEAVAEGIRLEADVVLVDTAGRL
+QNKSNLMDELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLD
+GTAKGGIVVAIQRQLGVPVKLIGLGEGADDLAPFTAEGFVDALLAD
+>MOLHKGIG_00902
+MCETGHVEIVLIISVVLALLVGGLIVGLLDRRPAPPKGSYQGVRDADDPRPGPRHAAPGG
+STAVLERPDAEEATVDVAEPEVVEEVETAPAAPELERPEAAGSRLSRLRARLLKSNNVFG
+KGLLALLSQDRIDEDVWDEIEETLLMADLGTEPTMELVDRLKARVTVEGTRDPEQVRALL
+REELVAMVDPSMDRRLAATRRDGRPAVTLVVGVNGVGKTTTVGKLARVLVAEDRDVVLGA
+ADTFRAAAAEQLATWGARVGVPTVRSEKEGADPASVAFEAVAEGIRAEADVVLVDTAGRL
+QNKSNLMDELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLD
+GTAKGGIVVAIQRQLGVPVKLIGLGEGADDLAPFTAEGFVDALLAD
+>NAFOICDF_01938
+MITVIVISVVLALLLGVVLVGLLDRPVAPPKGTYTELRDSDDPAPAGLVADPSSAPAPEE
+ALEETGRAGSHAAAPVAEPVEAAEAPERQLERPEAAGTRLQRLRARLLKSNNVFGKGLLA
+LLSRDHIDEDVWDEIEETLLMADLGTEPTMELVDRLKARVTVDGTRDPESVRALLREELV
+AMVDPSMDRRLAATPHDGHPAVTMVVGVNGVGKTTTVGKLARVLVAEDRTVVLGAADTFR
+AAAAEQLATWGARVGVETVRSDVEGADPASVAFEAVKTGIEREADVVLVDTAGRLQNKAN
+LMDELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLDGTAKG
+GIVVAIQRQLGVPVKLIGLGEGADDLAPFSAEGFVDALLAA
+>MHAAABBN_00621
+MLIVSVVAALLLGGVLVGLLDRRPAPPKGSYQGVRDADDPRPSPRHAAPSGSTAVLERPE
+VDEAPAVVAEPEPAVVEEVEPAPAKPEYERPEAAGSRLARLRARLLKSNNVFGKGLLALL
+SQDRIDDDVWDEIEETLLMADLGTEPTLELVDRLKARVTVEGTRDPEQVRTLLREELVAM
+VDPSMDRRLAATRKGDRPAVTMVVGVNGVGKTTTVGKLARVLVAEDRTVVLGAADTFRAA
+AAEQLATWGARVGVETVRSEKEGADPASVAFEAVELGIAEGVDVVLVDTAGRLQNKANLM
+DELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLDGTAKGGI
+VIAIQRQLGVPVKLIGLGEGPDDLAPFTAEGFVDALLTD
+>LFPAFLNI_00850
+MLIVSVVAALLLGGVLVGLLDRRPAPPKGSYQGVRDADDPRPSPRHAAPSGSTAVLKRPE
+VDEAPAVVAEPEPAVVEEVEPAPAKPEYERPEAAGSRLARLRARLLKSNNVFGKGLLALL
+SQDRIDDDVWDEIEETLLMADLGTEPTLELVDRLKARVTVEGTRDPEQVRTLLREELVAM
+VDPSMDRRLAATRKGDRPAVTMVVGVNGVGKTTTVGKLARVLVAEDRTVVLGAADTFRAA
+AAEQLATWGARVGVETVRSEKEGADPASVAFEAVEHGIAEGVDVVLVDTAGRLQNKANLM
+DELGKIKRVIEKQAEVDEVLLVLDATTGQNGLTQAKVFAEVVDVTGIVLTKLDGTAKGGI
+VIAIQRQLGVPVKLIGLGEGPDDLAPFTAEGFVDALLAD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001394.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001394.fa
new file mode 100644
index 0000000000000000000000000000000000000000..829172590f5fc30c62388d5d321ccdd0a0573063
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001394.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02054
+MSQPPAASWTPEPLPRPARSPEPPRPARRRRWPWVLGVLAAVLVVLLALGAWYAVSLART
+FDDHRQTVDAGALEQAGGGEPVNVLVLGSDSRGGEGEEDMGERSDAMMLVHLPADRSQVF
+VMSVLRDSWVEIPGHGEAKVNAAFDLGGYPLAVDTVEQLLGVPVHHVVEMDFQGFRGVTN
+ALGGVEVCNPVAFSSGQTSPSYYPRGPVLLQDTAALRYVRERHAFDDGDVSRVQNQQRYL
+AGAVERFLSPQILGNPARTTEVVATFSDHLGVDAGLTSGVVASLAWQLRGVRAGDVEMFT
+VPRAGFGYSPDGDSIVELDEAKLADLRSALKDDDVQRYVAEHESEDGQDASAAGADPAPV
+LALLAQPAPTPAVGEDPCAD
+>MOLHKGIG_00881
+MSHPPAASWTPEPLPRPEPPRDDAPPVARRRRRWPWVVGLLAVLLAALLGLGAWYTSSLG
+RTFDDHRQTVDVGALEQAAGNGPLNVLVLGSDSREGEGEQDMGQRSDTMMLVHIPADRRQ
+VYVMSVLRDSWVTVPGHGEAKINSAFDTGGYTLAVDTVELLLGVSIHHVLEVDFQGFRGV
+TNALGGVEVCNPRAFSSGQANPSYYPRGHILLQDTAALRYVRERHAFDDGDVTRVENQQR
+YLAGAMDRFLSPQILGNPARTTEVVATFSDHLGVDEGLTSGVIASLAWQLRDVRGEDVEM
+FTVPRKGFAEGPNGDAIVELDEDKLADLRSALADDDVQRYVDEHEPTKEKKAQAAGGPAP
+VLTLLTGTTPAPVLGEDPCDD
+>NAFOICDF_01948
+MTQPPQQPWIPPERPGGAADPLEGLRGPAPAAPPTSTPPATRRSGGGRARRRRPLRRFLA
+VLGVLALLLVVALGAYGLLLARTFDGHRQTVSAAAFADPGNDGPVNFLVLGSDSRAAEDS
+AETSQRSDTMMLVHVPADRRHVYVISVLRDSLVEIPGRGQRKANAAYELGGPELTAAMLD
+KLLGVPVHHLAELDFQGFRGMTTALGGVEVCNPHAFSSGQKNPSFYPRGRIELKDTAALR
+YVRERHAFPEGDVMRVQNQQRFVRGAVAAFLDPAVVLNPPRAVDVVAGLSDHLTVDEGLD
+SATLASLAWQLRGVDRSALTMFTVPRAGYGTSPDGQDVVLLDADRMAALRDALQRDDVES
+YLRAHDPEALAAGEDVQPALAAAPGATPLLTELAAAPPAGEGTLLGEDPCGG
+>MHAAABBN_00603
+MSHPPAASWTPEPLPRPEPPRDDAPPVARRRRRWPWVVGLLAVLLAALLGLGAWYAGSLG
+RTFDDHRQTVDVGALEQAAGDGPLNVLVLGSDSREGEGEQDMGQRSDTMMLVHIPADRRQ
+VYVMSVLRDSWVTVPGHGEAKINSAFDTGGYALAVDTVELLLGVPIHHVLEVDFQGFRGV
+TNALGGVEVCNPQAFSSGQANPSYYPRGHILLQDTAALRYVRERHAFDDGDVTRVKNQQR
+YLAGAMDRFLSPQILGNPARTTEVVATFSDHLGVDEGLTSGVIASLAWQLRDVRGEDVEM
+FTVPRKGFAEGPNGDAIVELDEDKLADLRSALADDDVQRYVDEHEPEKEKKAQAAGGPAP
+VLTLLTGTTPAPALGENPCDD
+>LFPAFLNI_00840
+MSHPPAASWTPEPLPRPESPRDDASSVARRRRRWPWVVGVLAVLLAALLGLGAWYAGSLG
+RTFDDHRQTVDVGALEQAAGNGPLNVLVLGSDSREGEGEQDMGQRSDTMMLVHIPADRRQ
+VYVMSVLRDSWVTVPGHGEAKINSAFDTGGYALAVDTVELLLGVPIHHVLEVDFQGFRGV
+TNALGGVEVCNPQAFSSGQANPSYYPRGHILLQDTAALRYVRERHAFDDGDVTRVKNQQR
+YLAGAMDRFLSPEILGNPARTTEVVATFSDHLGVDEGLTSGVIASLAWQLRDVRGEDVEM
+FTVPRKGFAEGPNGDAIVELDEDKLADLRSALADDDVQRYVDEHEPTKEKKAQAAGGPAP
+VLTLLTGTTPAPALGEDPCDD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001398.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001398.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7ebcba8892a6d751eff8e21bde0e481db8c2e47
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001398.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02058
+MDTTQRQDADSSWVIPVRDLTRGAGVQRELTAQWPAPAGVTTPLLGIPEGDPVELDLRLE
+SVHEGVLVTGTADATLKGECSRCLLPLHEGITVDLQELYLTGASEDEAGEQPLVVRETVD
+LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS
+ETSITETEER
+>MOLHKGIG_00877
+MDSIQHHGADSPWVIPVRDLTRGAGVQRELTAEWPAPAGVSTPLLGIPEGDPVELDLRLE
+SVHEGVLVTGTADATLKGECGRCLRPLHEGITVDLQELYLTGTSEDDAGEQPLVVRETVD
+LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS
+ETSITETEER
+>NAFOICDF_01952
+MATTVPSGAPSPWVLSVRDLARGAGVQRELTTRLPAPAAVSMPMLGIPEGDPVDLELRLE
+AVHEGVLVTGTAHADLTGECSRCLLPLHEGITVDLQELFLADPPAEGDDEQPLVEHETVD
+LEPVFRDAVVTALPFQPLCRPDCEGLCADCGIRLEDAPAGHAHERVDPRWAALAALADTT
+EETSITETEKR
+>MHAAABBN_00599
+MDSIQHHGADSPWVIPVRDLTRGAGVQRELTAEWPAPAGVSTPLLGIPEGDPVELDLRLE
+SVHEGVLVTGTADATLKGECGRCLRPLHEGITVDLQELYLTGTSEDDAGEQPLVVRETVD
+LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS
+ETSITETEER
+>LFPAFLNI_00836
+MDSIQHHGADSPWVIPVRDLTRGAGVQRELTAEWRAPAGVSTPLLGIPEGDPVELDLRLE
+SVHEGVLVTGTADATLKGECGRCLRPLHEGITVDLQELYLTGTSEDDAGEQPLVVRETVD
+LEPVFRDAVVIALPFQPLCRPDCEGLCADCGIRLEDAPEGHAHERVDPRWAALAHLAGTS
+ETSITETEER
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001399.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001399.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9701f18ba3486e9d119420140360e3fce829c05b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001399.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02059
+MTVPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVAEARRAGLQDVLM
+ITGRNKRALEDHFDRHPALEATLERKGDATRLAQIRESDLVGDIHYVRQGEALGLGHAVN
+CARRHVGDEPFAVLLGDDIIGDGEALLARMIDVQQRLGGSVVALMEVPEEAVSAYGVAAV
+EAVPGEGEDVVRVTGLVEKPAREDAPSTLAVIGRYVLASQVFDVLDRTPPGRGGEIQLTD
+ALQTLADDDGEGGGVHAVVFDGRRYDTGDKLGYLQAVVEFGTRHEELGGDLRAWLKAFAA
+GL
+>MOLHKGIG_00876
+MTVPPPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVTEARRAGLADV
+LMITGRNKRALEDHFDRHPALEAALEHKGDTKRLAQIHESDLVGDIHYVRQGEALGLGHA
+VNCARRHVGEEPFAVLLGDDIIGDGEALLERMIDVQQRLGGSVIALMEVPEEAVSAYGVA
+AVQAVPGEGDDVVRVTDLVEKPAREDAPSTLAIIGRYVLAPQVFDVLDETPPGRGGEIQL
+TDALQRLATEDGEGRGVHAVVFDGRRYDTGDKLGYLQAVIEFGTRHEDLGADLRAWLREF
+TAGL
+>NAFOICDF_01953
+MTEQSTAASPTRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVAEAVSAG
+LGDVLMITGRNKRALEDHFDRHPALEQVLEAKGDTKRIDLIRASDLVGDIHYVRQGEALG
+LGHAVGCARRHVGDEPFAVLLGDDLIGEDEGLLARMIDVQHRLGGSVIALMEVPEDAVSA
+YGVAAVAPVDGEDDDVVAVTSLVEKPARGDAPSNLAIIGRYVLAPQVFEVLERTAPGRGG
+EIQLTDALQTLAAGEGEGFGVHAVVFRGRRYDTGDKLGYLQAVVELGVRHPELGGDLREW
+LKGFAAGL
+>MHAAABBN_00598
+MTVPPPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVTEARRAGLADV
+LMITGRNKRALEDHFDRHPALEAALEHKGDAKRLAQIHESDLVGDIHYVRQGEALGLGHA
+VNCARRHVGEEPFAVLLGDDIIGDGEALLERMIDVQQRLGGSVIALMEVPEEAVSAYGVA
+AVEAVPGEGDDVVRVTDLVEKPAREDAPSTLAIIGRYVLAPQVFDVLDETPPGRGGEIQL
+TDALQRLATEDGEGRGVHAVVFDGRRYDTGDKLGYLQAVIEFGARHEDLGADLRAWLREF
+TAGL
+>LFPAFLNI_00835
+MTVPPPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVTEARRAGLADV
+LMITGRNKRALEDHFDRHPALEAALEHKGDATRLAQIHESDLVGDIHYVRQGEALGLGHA
+VNCARRHVGEEPFAVLLGDDIIGDGEALLERMIDVQQRLGGSVIALMEVPEEAVSAYGVA
+AVQAVPGEGDDVVRVTDLVEKPAREDAPSTLAIIGRYVLAPQVFDVLDETPPGRGGEIQL
+TDALQRLATEDGEGRGVHAVVFDGRRYDTGDKLGYLQAVIEFGTRHEDLGADLRAWLREF
+TAGL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001401.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001401.fa
new file mode 100644
index 0000000000000000000000000000000000000000..57ee49568ab9749fd0415a0f2581054ba1d4f358
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001401.fa
@@ -0,0 +1,41 @@
+>ACLBLIBL_02061
+MNADASDRTRPPRTGPAPAPATGPAPADVAGTAFVAGPWRRTAAAAGLLDDGAPVPTVFE
+TMTGLAVEHGAVNLGQGFPDADGPDALLRLAAEAVLAGPNQYAPGTGDPVLRQAVAEHRR
+RHWGVTEDPATQVMITTGATEGIAATVLAFVRPGDEVITVEPFYDSHAATIALAGGRHVS
+VPVEAPDFLPDPARVADAITDRTRLLIVNTPHNPTGAVYPRELLEELVTLCRSRGVLILS
+DEVYDHLVYEGEHVSLRSVAGAEDIALTVSSAGKAFAVTGWKVGWLTGPAELVGAARAVK
+QFLTYSSGPAFQRALGAYLPTEDAKRHLAGQRERYRDARDRLVAGLRAADLDPVVPAAGY
+FVVVDLAPWGVTDAAEAAVRWTREAGVTGIPVGALCRPDGGHLRSWLRLAFCKSPDAIDE
+AMRRLAAAAPALDGRRPRP
+>MOLHKGIG_00874
+MDGTQPTPGAAPHDVDVDAPWRRTAAAAGLLGDAGPVPTVFETMTGLAVEHGAVNLGQGF
+PDADGPDALLRLAADAVLAGPNQYAPGTGDPALRQAVAEHRRRHWGVTEDPATQVMITTG
+ATEGIAATVLAFVRPGDEVVTVEPFYDSHAATIALAGARHVSVPVEAPDFLPDPARVAAA
+MTDRTRLLIVNTPHNPTGAVYPRELLEELVALCRSRGVLILSDEVYDHLVYEGEHVSLRS
+VAGAEDIALTVSSAGKAFAVTGWKVGWLTGPAELVGAARAVKQFLTYSSGPAFQRALGAY
+LPTDGAERHLAGQRERYRDARDRLVAGLREAGLDPVVPAAGYFVVVDLAPWGVTDAAEAA
+VRWTREAGVTGIPVGALCRPDGGHLRSWLRLAFCKSPDAIDEAMRRLAEAAPRLRAA
+>NAFOICDF_01955
+MSHDSPSPTDAAAAPSDVRLAGPWRAASAAAGVLRDGAPVPTVFETMTALAVEHGAVNLG
+QGFPDADGPPELLALAAEAVTTGPNQYAPGTGRADLRAAVAAHRARHWGVAEDPDTQVLA
+TTGATEAIAATVLALVRPGDEVITVEPFYDSHAAVVALAGGRHVTVPVHAPDFLPDPARI
+AAAITPRTRLLIVNTPHNPTGAVYPRALLEELVALCRARDVLMLSDEVYDHLVHEGRHVT
+LRAIPGAERIALTASSAGKSLAVTGWKVGWLTGPADLVAAVRGVKQFLSYSSGPAFQQAV
+AAFLPRADDFLAGQLARHRRSRDLLVSGLRDIGLDPVVPAAGYFTVVDLAPWGVRDAAAA
+ARTWTERAGVAGIPVSALCRPDGDHLRSWLRLTFCKSEDTVAEAVARLTRHAADLRAG
+>MHAAABBN_00596
+MDGTQPTPGSARHDVDVDAPWRRTAAAAGLLGDTGPVPTVFETMTGLAVEHGAVNLGQGF
+PDADGPDALLRLAADAVLAGPNQYAPGTGDPVLRQAVAEHRRRHWGVTEDPATQAMITTG
+ATEGIASTVLAFVRPGDEVITVEPFYDSHAATIALAGGRHVSVPVEAPDFLPDPARVADA
+ITDRTRLLIVNTPHNPTGAVYPRELLEELVALCRSRGVLMLSDEVYDHLVYEGEHVSLRS
+VAGAEDIALTVSSAGKAFAVTGWKVGWLTGPAELVGAARAVKQFLTYSSGPAFQRALGAY
+LPTDDAERHLAGQRERYRDARDRLVAGLREAGLDPVVPAAGYFVVVDLAPWGVTDAAEAA
+VQWTREAGVTGIPVGALCRPDGGHLRSWLRLAFCKSPDAIDEAMRRLAEAAPRLRAP
+>LFPAFLNI_00833
+MDGTQPTPRSAPHDVDVDAPWRRTAAAAGLLGDAGPVPTVFETMTGLAVEHGAVNLGQGF
+PDADGPDALLRLAADAVLAGPNQYAPGTGDPALRRAVAEHRRRHWGVTEDPATQVMITTG
+ATEGIAATVLAFVRPGDEVVTVEPFYDSHAATIALAGGRHVSVPVEAPDFLPDPARVAAA
+MTDRTRLLIVNTPHNPTGAVYPRELLEELVALCRSRGVLILADEVYDHLVYEGEHVGLRS
+VAGAEDIALTVSSAGKAFAVTGWKVGWLTGPAELVGAARAVKQFLTYSSGPAFQRALGAY
+LPTDDAERHLAGQRERYRDARDRLVAGLREAGLDPVVPAAGYFVVVDLAPWGVTDAAEAA
+VQWTREAGVTGIPVGALCRPDGGHLRSWLRLAFCKSPDAIDEAMRRLAEAAPRLRAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001407.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001407.fa
new file mode 100644
index 0000000000000000000000000000000000000000..79272e1211ae298f6b96e00812efe9e60f469e03
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001407.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02067
+MLLLFGGRSSEHPISCVTAAGVLHAADPQRWDVVPVGVARSGLWSHDELDVAAFRLDGET
+LPEVPEPEAPVSLRTLPDGTVELTAEDGSSLGRVDVVFPLLHGPWGEDGTLQGMFESLGL
+PYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITDRDWARDPEAALARAGALAFPLF
+VKPARGGSSFGITRVSDPADLRAAVEEARRFDPKVVVEAGIVGREIECAVLDGHGSDAPR
+ASLPGEIVVKHDEGDLQFYDFQAKYQDDDAAQLSCPAELPEEQTRRLRELAVRAFEAVDG
+SGLGRCDFFHTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSYDALISELLDLALERGV
+GLH
+>MOLHKGIG_00868
+MTATPAPEAAADARPRVLLLFGGRSSEHPISCVTAAGVLHAADRQRWDVVPVGVARSGLW
+SHDELDVASFRLDGDALPEVPEPEAPVSLRALPDGTVELTAADGSSLGPVDVVFPLLHGP
+WGEDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITARDWARD
+PEAALARAGALAYPLFVKPARAGSSFGITRVTEPAGLRAAVEEARRFDPKVVVEAGIVGR
+EIECAVLDGHGSAAPRASLPGEIVVAHDEGETQFYDFESKYQDTGTTQLSCPAELPEEEI
+ERLRALAIRAFEAVDGSGLGRCDFFFTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSY
+DDLISELLDLALERGVGLH
+>NAFOICDF_01961
+MTQPPETAPGRRPRVLLLFGGRSSEHPISCVTAAGVLHAADRERWDVVPVGVAHSGLWSH
+GEVDAAAYALGDGELPSVPEPERPVSLRARADDAVELVGADGEDLGVVDVVFPLLHGPWG
+EDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAGGLEVGPWETITDRQWRNDPE
+AALERAGALDYPLFVKPARGGSSFGITKVDAPEDLRAAVEEARRFDPKVVVEAGILGREI
+ECAVLDGHGAESPRASLPGEIVVKGAESGHQFYDFEAKYQDASAAQLSCPAELPEEAIER
+LREQAVRAFEAVDGAGLGRCDFFYTPDGRWVVNEINTMPGFTSISMYPAMWERTGLPYGE
+LISELLDLALERGVGLH
+>MHAAABBN_00590
+MTATPAPEAAADARPRVLLLFGGRSSEHPISCVTAAGVLHAADRQRWDVVPVGVARSGLW
+SHDELDVASFRLDGDALPEVPEPEAPVSLRALPDGTVELTAADGSSLGPVDVVFPLLHGP
+WGEDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITARDWARD
+PEAALARAGALAYPLFVKPARAGSSFGITRVTEPAGLRAAVEEARRFDPKVVVEAGIVGR
+EIECAVLDGHGAAAPRASLPGEIVVAHDEGETQFYDFESKYQDTGSTQLSCPAELPEEEI
+ERLRALAIRAFEAVDGSGLGRCDFFFTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSY
+DDLISELLDLALERGVGLH
+>LFPAFLNI_00827
+MTAIPAPEAAAGARPRVLLLFGGRSSEHPISCVTAAGVLHAADRQRWDVVPVGVARSGLW
+SHDELDVASFRLDGGALPEVPEPEAPVSLRALPDGTVELTAADGSSLGPVDVVFPLLHGP
+WGEDGTLQGMFESLGLPYVGCGVLASAVGMDKHFMKVAFQAAGLEVGPWETITARDWARD
+PEAALARAGALAYPLFVKPARAGSSFGITRVTEPAGLRAAVEEARRFDPKVVVEAGIVGR
+EIECAVLDGHGSAAPRASLPGEIVVAHDEGETQFYDFESKYQDTGTTQLSCPAELPEEEI
+ERLRALAIRAFEAVDGSGLGRCDFFFTPDGRWVVNEINTMPGFTPISMYPAMWERTGLSY
+DDLISELLYLALERGVGLH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001408.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001408.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a3652f093545406e3ddf6258d723bad233824dbc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001408.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_02068
+MSDPQTVAVLGAGSWGSAFARVLGTSTSPEGARARDVVIWSRRPEVAEVVNRDHANPEYL
+PGIELPACVRAVTDAFEAVRGAGVVVVAVPAQHVRETLRTLREDLAPDAVVVSLVKGLER
+GTDARMSQVCTEELGLTPDRFAVVSGPNLALEIARGEPTATVVASGSSATAERIAALTAG
+PTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG
+GDPATMAGLAGLGDLVATCASPLSRNRTAGRHIGTGMSAEEAVAAMSQTAEGIKSVSAVV
+HVARAHGVEMPISELMDRVVAGDVAVHRLAELLLARDLKSEGRTA
+>MOLHKGIG_00867
+MSDPRTVAVLGAGSWGSAFARVLGLSTSPESARASEIVMWSRRAEVAEAITERHENPEYL
+PGITLPTCVRAVTDAAEAVRGAGVVVVAVPAQHVRETLRTVRADLAPDAVVVSLVKGLER
+GTDARMSQVCAEELGLSPDRFAVVSGPNLALEIARGEPTATVVASASRATAERIAALTAG
+RTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG
+GDTDTMAGLAGLGDLVATCASPLSRNRTAGRHIGTGLSAEEAVAAMSQTAEGIKSVSAIV
+HAARAHGVEMPISELMDRVVAGDVAVDRLAELLLARDLKSEGRTA
+>NAFOICDF_01962
+MSPAPSAGPEPAFASASAGDRAGDPTRVAVLGAGSWGTAFACVLGSSTSPAGRRAREVVV
+WSRRAEVARAITEDHANPEYLPDVALPECVRAVTDAREAVAEAGVVVVAVPAQQARTVLE
+GLADALAPDAIAVSLMKGLERGTDARPSQVCQEALGIGPERFAVLSGPNLALEIARGEPT
+ATVVASASRATADRVAALTAGPTFRPYTNGDVVGVEIGGIVKNVIALAVGICDGQGLGDN
+SKASVITRGLAETTRLAVALGGEASTLAGLAGLGDLVATCASPLSRNRSAGRLMGTGLSA
+DEAVAAMKQTAEGIKSVSAVVHVARAHGVEMPISEAMDRVVAGTLDVDRLAGLLLARDLK
+SEGRHA
+>MHAAABBN_00589
+MSDPRTVAVLGAGSWGSAFARVLGLSTSPESARASEIVMWSRRAEVAEAITERHENPEYL
+PGITLPTCVRAVTDAAEAVRGAGVVVVAVPAQHVRETLHAVRADLAPDAVVVSLVKGLER
+GTDARMSQVCAEELGLSPDRFAVVSGPNLALEIARGEPTATVVASASRATAERIAALTAG
+RTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG
+GDPATMAGLAGLGDLVATCASPLSRNRTAGRHIGTGLSAEEAVAAMSQTAEGIKSVSAIV
+HAARAHGVEMPISELMDRVVAGDVAVDRLAELLLARDLKSEGRTA
+>LFPAFLNI_00826
+MSDPRTVAVLGAGSWGSAFARVLGLSTSPEPARASEIVMWSRRAEVAEAITERHENPEYL
+PGITLPTCVRAVTDAAEAVRGAGVVVVAVPAQHVRETLRTVRADLAPDAVVVSLVKGLER
+GTDARMSQVCAEELGLSPDRFAVVSGPNLALEIARGEPTATVVASASRATAERIAALTAG
+RTFRPYTNTDVVGVEIGGVVKNVIALAVGICDGQGLGDNSKASVITRGLAETTRLAVALG
+GDPATMAGLAGLGDLVATCASPLSRNRTAGRHIGTGLSAEEAVAAMSQTAEGIKSVSAIV
+HAARAHGVEMPISELMDRVVAGDVAVDRLAELLLARDLKSEGRTA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001412.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001412.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a21433632649b7222291fdb91009702080fc7601
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001412.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_02072
+MTSETTRPRTLAEKVWDEHVVVRGEGEGSSRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR
+PVRRPDLTIATEDHNTPTLEIDKPIADPTSRTQIETLRANAAEFGVRLHPLGDAEQGIVH
+VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAIT
+VDGTLRPGVTAKDVILAVIAKIGTGGGQGFVLEYRGEAIRSLSMEGRMTICNMSIEAGAR
+AGMVAPDETTFAYLKGRPHAPEGADWDAAVEHWRTLATDEGAEFDAEVVIDADELEPFVT
+WGTNPGQGVSLNGAVPAPEDFDDPVAQESARKALGYMDLTPGTPMKEVAVDTVFMGSCTN
+SRIEDLRAFAEVVKGRKKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM
+CLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT
+PQEA
+>MOLHKGIG_00863
+MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR
+PVRRPDLTIATEDHNTPTLDIDQPIADATSRTQIETLRANCAEFGVRLHPLGDAEQGIVH
+VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAVT
+VDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAGAR
+AGMVAPDETTFAYLKGRPHAPEGDDWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPFVT
+WGTNPGQGVSLNDTVPAPEDFADPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSCTN
+SRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM
+CLGMNPDQLSPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT
+PQEA
+>NAFOICDF_01966
+MSTQTQTPRPRTLAEKVWDEHVVVRGEGEGARRTPDLLYIDLHLVHEVTSPQAFDGLRLA
+DRPVARPELTIATEDHNTPTLEIDRPIADETSRVQIETLRANAEEFGVRLHSLGDREQGI
+VHVVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLRLKPFRTMA
+ITVDGTLRPGVTAKDVILAVIAKIGTGGGQGYVLEYRGEAIRSLSMEGRMTLCNMSIEAG
+ARAGMVAPDDTTFEYLKGRPHAPQGADWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPF
+VTWGTNPGQGVSLNDAVPAPEDFSDPAAQEAARKALSYMDLTPGTPMKDVAVDTVFMGSC
+TNSRIEDLRAFAEVVKGRTKADGLRVMVVPGSARVRLQAMDEGLDKVFEDFGAEWRFAGC
+SMCLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPLVAAATAVLGRLASPSDLPA
+LENQEA
+>MHAAABBN_00585
+MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR
+PVRRPDLTIATEDHNTPTLDIDQPIADPTSRTQIETLRANCAEFGVRLHPLGDAEQGIVH
+VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAVT
+VDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAGAR
+AGMVAPDETTFAYLKGRPHAPEGADWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPFVT
+WGTNPGQGVSLNDTVPAPEDFTDPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSCTN
+SRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM
+CLGMNPDQLAPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT
+LQEA
+>LFPAFLNI_00822
+MTTATTRPRTLAEKVWDEHVVVRGEGEGASRTPDLLYIDLHLVHEVTSPQAFEGLRLAGR
+PVRRPDLTIATEDHNTPTLDIDQPIADATSRTQIETLRANCAEFGVRLHPLGDAEQGIVH
+VVGPQLGLTQPGLTVVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLPLKPFKTMAVT
+VDGTLRPGVTAKDIILAVIAKIGTGGGQGFVLEYRGEAIRNLSMEGRMTICNMSIEAGAR
+AGMVAPDETTFAYLKGRPHAPEGDDWDAAVEHWRTLATDEGAEFDAEVVIDADTLEPFVT
+WGTNPGQGVSLNDTVPAPEDFADPVAQEAARKALSYMDLAPGTPMKQVEVDTVFMGSCTN
+SRIEDLRAFAEVVRGRRKAEGLRVMVVPGSARVRLQAMDEGLDRVFEDFGAEWRFAGCSM
+CLGMNPDQLSPGERCASTSNRNFEGRQGKGGRTHLVSPVVAAATAVLGRLASPSDLPALT
+PQEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001413.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001413.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc997213414fd0c83e779037e6884d0d557dcbac
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001413.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_02073
+MTAEPARAQADDDVLGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVTATGIARPTL
+HRLAAALTHHRLVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV
+FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT
+PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRNHAD
+AVVAAATRLTELIRAGEA
+>MOLHKGIG_00862
+MTTEPVRPPTEDDLIGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVIATGIARPTL
+HRLAAALTHHRMVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV
+FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT
+PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRLHAD
+AVVSAATRLTELIRAGEA
+>NAFOICDF_01967
+MTTTPLPDAGADIGPALHVHPSGVGVVDKSVAILDALESGPATLAQLVTATGIARPTLHR
+LAAALTHHRLVAKDLQGRYVLGSRLAELASAAGEDRLTSAAGPVLQWLRDACGESAQVFR
+RQADSRVCVASAERPWGLRDTIPVGTRMSMKAGSAAQVLLAWEDNERLVDGLVGAVFTPT
+VLAAVRRRGWAQSLAEREPGVASVSAPVRGPNGKVIAALSISGPLERLSRQPGRLHAGSV
+VAAADRLTELIRAGEA
+>MHAAABBN_00584
+MTTEPVRPPTEDDLIGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVIATGIARPTL
+HRLAAALTHHRMVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV
+FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT
+PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRLHAD
+AVVSAATRLTELIRAGEA
+>LFPAFLNI_00821
+MTTEPVRPPTEDDLIGPSLHRHPSGVGVVDKSVAILDALESGPATLAQLVTATGIARPTL
+HRLAAALTHHRMVGKDLQGRYVLGTRLAELASAAGEDRLTTASGPVLLWLRDATGESAQV
+FRRQADSRVCVASAERPWGLRDTIPVGARMSMKAGSAAQVLLAWEDHERLVEGLAGAVFT
+PTVLAAVRRRGWAQSLAEREPGVASVSAPVRGPSGRVIAAVSISGPLERLSRQPGRLHAD
+AVVSAATRLTELIRAGEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001420.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001420.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb0f5c1a1618c030316db1811de7b07e717da062
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001420.fa
@@ -0,0 +1,70 @@
+>ACLBLIBL_02085
+MSSHRSAAPAEGMAPRDPARDGGPDGLPPVEAAQRPRWTPLKIAVWVVVALVGGVAWTML
+ALHRGESINAIWFVFAAVATFAIGYRFYSKYVERMIVRPDDTRATPAEYRADGRDYVATD
+RRVLYGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGG
+RSLGQMARDELGRIGGTAAIVATLLIMVIITAILALVVVNALGESPWGVFSVALTIPIAI
+FMGLYLRYLRPGRITEVSIIGFVLLMAAIIGGGWVAETDWGVALFTLDRVTIAWGIIIYG
+FVAAVLPVWLLLAPRDYLSTFMKIGVIAGLAVAIVIVQPQITAPAISEFASGQTGPVWPG
+SLFPFLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAVMALVAAV
+SIDRGIYFAMNAPAALTGGTPETAAAWVMSLGLAGVDVTPEQLTALANLVGEDTVVSRTG
+GAPTLAVGLSIIMGQLIGGEALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDSLGNV
+APRFKDTGWRVGAWVCTGIMVAAWGAVLIMGVTDPLGGINTLFPLFGIANQLLAAIALAV
+VLAIVAGRRHFRGLWIVALPLGFITVVTTVASFQKIFSSVPAVGYWAQHNAFKDALASGA
+TSFGAAKSVPAMEAVVRNTFIQGTLSIVFLVLALVVITTSVLATIRAFRSTEVVDHADPY
+VPSRRFAPAGLIATAEEKELQRQWDALPADQRPERGH
+>MOLHKGIG_00850
+MSSHRSSAAAEGAPLPATTPEDLPPTEAAGRPRWTPAKIAVWVAVALLGGVAWTMLALHR
+GETINAIWFVFAAVATFAIGYRFYSKYVERMIVHPDDTRATPAEYRADGRDYVATDRRVL
+YGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGGRSLG
+QMARDELGRVGGTAAIVATLLIMVIITAILALVVVNALGESPWGVFSVAMTIPIALFMGV
+YLRWIRPGRITEISVIGFVLLLAAIIGGGWVAGTEWGAALFTLDRTTIAWAVIIYGFVAA
+VLPVWLLLAPRDYLSTFMKIGVIAGLALAIVVVQPRIGTPAFSEFASGQTGPVWPGSLFP
+FLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAVMALVAAVSIDR
+GIYFAMNAPAALTGGTPETAAAWVMSLGLAGVDVTPEQLTALANLVGEDTVVSRTGGAPT
+LAVGLSIIMGQLIGGEALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDSLGNVVPRF
+KDTGWRVGAWVCTGIMVAAWGAVLIMGVTDPLGGINTLFPLFGIANQLLAAIALAVVLAI
+VAGRRHFRGLWIVALPLGFITVVTTVASFQKIFSSVPAVGYWAQHNAFKDALASGATSFG
+AAKSVPAMEAVVRNTFIQGTLSIVFLVLALVVITTSVLATVRAFRGTEVIDHQDPYVPSQ
+RFAPAGLFATAEEKELQAQWDALPAEKQPVRGH
+>NAFOICDF_01985
+MSSTRSVIPTGGSAPHDARPDGLPPVEAPHEQRWTPARVAVWAVIALLGAVAWTMLALHR
+GESINAIWFVFAAVSTFLIGYRFYSKYVERAIVRPDDTRATPAEYNADGRDFVATDRRVL
+FGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGGRSLG
+QMARDELGRIGGTAAIIATLLIMVIITAILALIVVNALGDSPWGVFSVGMTIPIALFMGL
+YLRYLRPGAITEVSIIGFVLLLAAIIGGGFIAETPWGAALFTLDRVTLAWAVIVYGFVAA
+VLPVWLLLAPRDYLSTFMKIGVIAGLAIAIVIVQPRVQAPAFSEFAGGQAGPVWAGSLFP
+FLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAIMALVAAVTIDR
+GVYFAMNAPTALTGGAVDSAVAWVNGLGLANADLTPDQLTTLANQVGEETVVSRTGGAPT
+LAVGLAQIMGQLIGGDALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDTLGNVFPKF
+KDHNWTPGAWLATAVMVAAWGAVLVMGVTDPLGGINTLFPLFGIANQLLASIALAVVMAI
+VAKRRTFKGLWIVALPLAFITVVTTVASLHKIFSPVPAVGYWAQHRAFQDALAAGKTSFG
+AATTVPAMEAVVRNTFVQGTLSVLFLALALIVITSSIVATVRAFRSTEVVDHQDPYVPSR
+RFAPAGLTATPAEKEIQAQWDALPADRQPVRGH
+>MHAAABBN_00572
+MSSHRSSAPAEGAPRPATTPEDLPPTEAADRPRWTPVKIAVWVAVALLGGVAWTMLALHR
+GETINAIWFVFAAVATFAIGYRFYSKYVERMIVHPDDTRATPAEYRADGRDYVATDRRVL
+YGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGGRSLG
+QMARDELGRVGGTAAIVATLLIMVIITAILALVVVNALGESPWGVFSVAMTIPIALFMGV
+YLRWIRPGRITEISVIGFVLLLAAIIGGGWVAGTEWGAALFTLDRTTIAWAVIIYGFVAA
+VLPVWLLLAPRDYLSTFMKIGVIAGLALAIVVVQPRIGTPAFSEFASGQTGPVWPGSLFP
+FLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAVMALVAAVSIDR
+GIYFAMNAPAALTGGTPETAADFVMGLGLAGVNLAPGDLTHLADLVGEETVVSRTGGAPT
+LAVGLAHIMGQLVGGDALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDSLGNVVPRF
+KDTSWRVGAWVCTAIMVAAWGAVLIMGVTDPLGGINTLFPLFGIANQLLAAIALAVVLTI
+VARRRDFRGLWIVALPLAFITVVTTVASFQKIFSSIPAVGYWAQHRAFQDALAAGKTSFG
+AAKSVPAMEAVVRNTFIQGTLSVVFLVLALIVITTSVLATVRAFRGTEVIDHQDPYVPSQ
+RFAPAGLFATAEEKELQRKWDALPADRQPVRGH
+>LFPAFLNI_00809
+MSSHRSSAPAEGAPRPATTPEDLPPTEAADRPRWTPVKIAVWVAVALLGGVAWTMLALHR
+GETINAIWFVFAAVATFAIGYRFYSKYVERMIVHPDDTRATPAEYRADGRDYVATDRRVL
+YGHHFAAIAGAGPLVGPVLAAQMGYLPGTIWIIVGVILAGAVQDYLVLFFSMRRGGRSLG
+QMARDELGRVGGTAAIVATLLIMVIITAILALVVVNALGESPWGVFSVAMTIPIALFMGV
+YLRWIRPGRITEISVIGFVLLLAAIIGGGWVAGTEWGAALFTLDRTTIAWAVIIYGFVAA
+VLPVWLLLAPRDYLSTFMKIGVIAGLALAIVVVQPRIGTPAFSEFASGQTGPVWPGSLFP
+FLFVTIACGALSGFHALIASGTTPKMVEKERQTRFIGYGGMLMEAFVAVMALVAAVSIDR
+GIYFAMNAPAALTGGTPETAADFVMGLGLAGVNLAPGDLTHLADLVGEETVVSRTGGAPT
+LAVGLAHIMGQLVGGDALMGFWYHFAIMFEALFILTAVDAGTRVARFMLQDSLGNVVPRF
+KDTSWRVGAWVCTAIMVAAWGAVLIMGVTDPLGGINTLFPLFGIANQLLAAIALAVVLTI
+VARRRDFRGLWIVALPLAFITVVTTVASFQKIFSSIPAVGYWAQHRAFQDALAAGKTSFG
+AAKSVPAMEAVVRNTFIQGTLSVVFLVLALIVITTSVLATVRAFRGTEVIDHQDPYVPSQ
+RFAPAGLFATAEEKELQRKWDALPADRQPVRGH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001421.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001421.fa
new file mode 100644
index 0000000000000000000000000000000000000000..56ace4c5ae55cd345194a124dc703053ed199ee5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001421.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02086
+MSETVFTRQPHLSPLSEEERVEILQDPGFGKVFTDHMVSIDWTWSEDGGAWHDARVEPYG
+PLSLDPSASVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEEMF
+LGSLKAQLEADRDWVPTGEGQSLYLRPFMFATEAFLGVRPAKEVRYMVIASPAGNYFGGE
+LKPVTIWVSREYARAGRGGMGAAKTGGNYAASLLPQLEAASKGADQVVFLDQYHDDSIEE
+LGGMNVFFVFDDGRLVTPELTGTILEGVTRSSILQLGRDMGLTVEERRITLAEWAEGVRS
+GAIREVFACGTAAVVTPIGRLLDGDDVIESAGGTEVTLKIRAELEGIQTGRVEDRHGWLH
+RLV
+>MOLHKGIG_00849
+MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG
+PLSLDPAAAVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEELF
+LGSLRAQLEADRAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE
+LKPVTIWVSRDYARAGKGGTGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE
+LGGMNVFFVHADGRLVTPALTGTILEGVTRSSILQLGRDMGLTVEERRVTLAEWAEGVRS
+GEITEVFACGTAAVVTPIGRLLDGDDVIESAGGADVALKIRTELEGIQTGRVEDRHGWLH
+RLV
+>NAFOICDF_01986
+MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG
+PLSLDPSAAVLHYGQEIFEGLKAYGHEDGSVWTFRPEANAARLNRSARRLALPELPEELF
+LGSLRAQLEADQAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE
+LTPVTIWVSRDYARAGKGGMGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE
+LGGMNVFFVHADGRLVTPELTGTILEGVTRSSILQLGRDMGMSVEERRVTLAEWAEGVRT
+GAITEVFACGTAAVVTPIGRLLDGDDVIESTGGTEVAMKIRAELEGIQTGTVEDRYGWMH
+RLV
+>MHAAABBN_00571
+MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG
+PLSLDPAAAVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEELF
+LGSLRAQLEADRAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE
+LKPVTIWVSRDYARAGKGGTGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE
+LGGMNVFFVHADGRLVTPALTGTILEGVTRSSILQLGRDMGLTVEERRVTLAEWAEGVRS
+GEITEVFACGTAAVVTPIGRLLDGDDVIESAGGTDVTLRIRAELEGIQTGRVEDRHGWLH
+RLV
+>LFPAFLNI_00808
+MSETVFTRQPHLSPMSDQQRVEILQDPGFGNVFTDHMVSIDWTWDEDGGAWHDARVEPYG
+PLSLDPAAAVLHYGQEIFEGLKAYRHEDGSVWTFRPEANAARLNRSARRLALPELPEELF
+LGSLRAQLEADRAWVPTGPGQSLYLRPFMFASEAFLGVRPARQVRYMVIASPAGNYFGGE
+LKPVTIWVSRDYARAGKGGTGAAKTGGNYAASLLPQLQAAAKGADQVVFLDQYHDDAIEE
+LGGMNVFFVHADGRLVTPALTGTILEGVTRSSILQLGRDMGLTVEERRVTLAEWAEGVRS
+GEITEVFACGTAAVVTPIGRLLDGDDVIESAGGTDVTLRIRAELEGIQTGRVEDRHGWLH
+RLV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001428.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001428.fa
new file mode 100644
index 0000000000000000000000000000000000000000..032f08e94bd93a8b354e2caeccf44d1ba0219dbe
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001428.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_02094
+MDTAASTPRTPSAAPDMKPRSRDVTDGMERAASRGMLRAVGLGDADFAKPQIGIASSWNE
+ITPCNLSLDRLAQAAKEGVHADGGFPLEFGTVSVSDGISMGHEGMHFSLVSREVIADSVE
+TVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSTMPGHARLSDGTEKQVTI
+IDAFEAVGACARGLMSEEDLLRIEKAIVPTEGACGGMYTANTMASVGEALGMSLPGSATP
+PSPDRRRDDFARRSGAAVVNLLRQGITARDIMTKEAFENAIAVTMAFGGSTNAVLHLLAI
+AREAGVDLSLEDFNRVGDRTPHIADLKPFGRYVMTDVDRVGGVPVVMKALLDEGLLHGDA
+LTVTGRTVAENLAELAPDPVDGDVIRTMDRPMHPNGGIAILHGSLAPEGAVVKSAGFDAD
+VFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPRGGPGMREMLAITGAIKGAGLGK
+DVLLLTDGRFSGGTTGLCIGHIAPEAADGGPIGLVRDGDRIRVDIAGRTLDVQVAEEELE
+ARRREWTPVPPKFTTGVLGKYAKLVHSAAEGAYLG
+>MOLHKGIG_00828
+MLTRLRGMDSAASTPSTPSAAPDIKPRSRDVTDGMERTAARGMLRAVGMGDEDFGKPQIG
+IASSWNEITPCNLSLDRLAQASKDGVHAAGGYPLEFGTVSVSDGISMGHEGMHFSLVSRE
+VIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSIMPGVARLTDG
+TERQVTIIDAFEAVGACARGLMSEEDLLRIEKSIAPGEGACGGMYTANTMASIGEALGMS
+LPGSAAAPSADRRRDAFARRSGKAVVNMLRQGITARDIMTKPAFENAIAVTMAFGGSTNA
+VLHLLAIAREAGVDLQLSDFNRIADRTPHIADLKPFGQYVMTDVDRIGGVPVVMKALLDE
+GLLHGDTLTVTGKTLAENLAALDPDPVDGKVIRTMDDAMHPNGGIAILHGSLAPEGAVVK
+SAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPKGGPGMREMLAITGAI
+KGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAAEGGPIGLVQDGDRIRVDIAGRTMDLL
+VDEAELAARRESWEPVEPKFTTGVLGKYAKLVHSAAEGAYLG
+>NAFOICDF_01993
+MDTSAADRTPQDVVTAPDMKPRSRDVTDGMERTAARGMLRAVGLGDEDFAKPQIGIASSW
+NEITPCNLSLDRLAQASKDGVHAAGGFPLEFGTVSVSDGISMGHEGMHFSLVSREVIADS
+VETVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSIMPGVARLTDGTEKQV
+TIIDAFEAVGACARGLMSEEDLLRIEKAIAPGEGACGGMYTANTMASIGEALGMSLPGSA
+AAPSADRRRDAFARRSGEAVVNMLRLGITARDVMTKPAFENAIAVTMAFGGSTNAVLHLL
+AIAREAGVDLQLSDFNRIADRTPHIADLKPFGQYVMTDVDRVGGVPVVMKALLDEGLLHG
+DTLTVTGKTLAENLAALDPDPVDGTVIRTMENALHPNGGIAILHGSLAPEGAVVKSAGFD
+ADVFEGTARVFDRERAAMDALEEGVIQAGDVVVIRYEGPKGGPGMREMLAITGAIKGAGL
+GKDVLLITDGRFSGGTTGLCIGHIAPEAADGGPIGLVRDGDRIRVDIASRTLDLLVEEAE
+LEARRTSWQPVPPKFTTGVLGKYAKLVHSAAEGAYLG
+>MHAAABBN_00560
+MLTRLRGMDSAASTPSTPSAAPDIKPRSRDVTDGMERTAARGMLRAVGMGDEDFGKPQIG
+IASSWNEITPCNLSLDRLAQASKDGVHAAGGYPLEFGTVSVSDGISMGHEGMHFSLVSRE
+VIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSIMPGVARLTDG
+TERQVTIIDAFEAVGACARGLMSEEDLLRIEKSIAPGEGACGGMYTANTMASIGEALGMS
+LPGSAAAPSADRRRDAFARRSGKAVVNMLRQGITARDIMTKPAFENAIAVTMAFGGSTNA
+VLHLLAIAREAGVDLQLSDFNRIADRTPHIADLKPFGQYVMTDVDRIGGVPVVMKALLDE
+GLLHGDTLTVTGKTLAENLAALDPDPVDGKVIRTMDDAMHPNGGIAILHGSLAPEGAVVK
+SAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPKGGPGMREMLAITGAI
+KGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAAEGGPIGLVQDGDRIRVDIAGRTMDLL
+VDEAELAARRESWEPVEPKFTTGVLGKYAKLVHSAAEGAYLG
+>LFPAFLNI_00797
+MLTRLRGMDSAASTPSTPSAAPDIKPRSRDVTDGMERTAARGMLRAVGMGDEDFGKPQIG
+IASSWNEITPCNLSLDRLAQASKDGVHAAGGYPLEFGTVSVSDGISMGHEGMHFSLVSRE
+VIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSIMPGVARLTDG
+TERQVTIIDAFEAVGACARGLMSEEDLLRIEKSIAPGEGACGGMYTANTMASIGEALGMS
+LPGSAAAPSADRRRDAFARRSGEAVVKMIRQGITARDIMTKPAFENAIAVTMAFGGSTNA
+VLHLLAIAREAGVDLQLSDFNRIADRTPHIADLKPFGQYVMTDVDRIGGVPVVMKALLDE
+GLLHGDTLTVTGKTLAENLAALDPDPVDGKVIRTMDDAMHPNGGIAILHGSLAPEGAVVK
+SAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPKGGPGMREMLAITGAI
+KGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAAEGGPIGLVQDGDRIRVDIAGRTMDLL
+VDEAELAARRESWKPVEPKFTTGVLGKYAKLVHSAAEGAYLG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001431.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001431.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1c2825857a99438bf58dca1074c45474a1b80206
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001431.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_02107
+MQPSRRALLGAGLGALGLGLGGCAGTPTPAPSASGTAPATPSGPSRLLVVGAPGRPFTRD
+SARAWDSESFRIIRQVLETLLGVDPDTGAPTPRLAERHEVSADGRVHAFHLVPGLVFDDG
+EPCDADAVVANIRRWAQAPAPVEGSVPMPSSFVSAFGGHEGEEGSVYAGVEARGAHEVRL
+RLTSPLRHLAAALSSPAFAISSPASWERTVPVDGVETVTPAGTGPYRWATEAEVAELSRD
+QPDGADVAYLVPSASHRGEEPAVRPVVVHPWGRATTRLRELRRGTADVIDVVAPGQLRPL
+VEAGTQVLPRDPLAVLYVGMNLDHPRIRSQYLRQAIAYAVDRPRIAASDVFLEGTRLAHD
+LVPPALGVGDEEARRYDVNPAQARRLVELSGYDGEELEFLYPAGTSSPSLPEPERVYAMV
+AQDLGAIGLHITPVPVPADHDYLRAVVSRPTRALHLMGRNGAYRDPHAFLEPFARSWRAE
+TGYRNPRVIQDVDAAASEQDDEARRGLFRRVVRAMALDLPALPLVYPISALATGPRVASY
+PTSPQLDEPFARVRLTEG
+>MOLHKGIG_00823
+MQPTRRAFLGGGLGLLGLGVAGCTTSPAAPSSAAPSSSGPGRLLVVGAPARALTRDPARA
+LDVESFRLIRQVFETLLGVDADTGAPTPRLAERHEESDGGRLHTFHLVSGVVFDDGEPCD
+AAAVVANIERWAAAPAPVDGTVSPPSSFVSAFGGYAGDADSAFAGVEAHGELEVRLRLHS
+PRRHLAAALASPAFAISSPASWDRTVDVDGSEVTTPAGTGPYRWADAAETAELTRAHPGA
+SGATFLVPSARHRGSDPAAHPVAVQAWGRASVRLRELRRGTADVIDVVAPGQLRPLVEAG
+TQVLPRDPLGVLYVGMNLDHPLVHAQYLRQAIAYAVDRPRIAGSDVFLEGTRLAHDLVPP
+SLGVGDEEARRYDVNPGRAREFLGLAGYDGEPLEFLYPAGTARPSLPEPERVYAMVARDL
+GAVGMHIVPVPVPEDQDYLHAVVSRPTRALHLMGRTGDYRDPHAFLEPFARSGRAETGYR
+NPRVVEDVDAAAAETDDDTRRALFRRVVRAMALDLPALPLVYPISALATGPRVASYPTSP
+QLDEPFSRVRLTEG
+>NAFOICDF_01998
+MDASRRSVLSLGLAGLGLGLSACGAGRATPASSSSSAASAPAVRPLVLGAPGRPLTRTPA
+LAWDTESLRLIAQVLEPLLGVDQDTGAPTPLLAEHRESEDGLTHTFVLTPDLRFSDGVAC
+DADAVVANLRRWSEGEPAEAVAMPSPFVAAFGGLAGEDSTAFRDATAADARTVRLRLRRR
+LRHLPAALASPRFAISSPASWKRTQDVDGAPVATPAGTGPHRWADPTESVEVLEPLGGTG
+PATVLVPNEHARAGLPTPPTAVVHSWGRASTRLRELRRGNADVIDVVAPGQLRPLVEAGT
+QVLPRDPFSVLYLGMNLDHPLLHSLYLRQAVAYAVDRPRLASSDVFLQGTALAHDLVPPA
+LGVAVEDGPRYDVDPARARRLLELAGYRGEPLEFLYPSGHAWPSLPEPERVFAMVSSDLG
+VVGLRVVPVPVPADQDYRRAVLGRRGRALHLMGRDGHYRDPHAFLEPFARSARTETGYVN
+AALTADVDAAASETDDERRRELHRRAGRTLLLDLPALPLVHPISALATGPRVASYPTSPQ
+LDEPLAQVRLADS
+>MHAAABBN_00555
+MQPTRRAFLGGGLGLLGLGVAGCTTSPAAPSSAAPSSSGPGRLLVVGAPARALTRDPARA
+LDVESFRLIRQVFETLLGVDADTGAPTPRLAERHEESDGGRLHTFHLVSGVVFDDGEPCD
+AAAVVANIERWAAAPAPVDGTVSPPSSFVSAFGGYAGDADSAFAGVEAHGELEVRLRLHS
+PRRHLAAALASPAFAISSPASWDRTVDVDGSEVTTPAGTGPYRWADAAETAELTRAHPGA
+SGATFLVPSARHRGSDPAAHPVAVQAWGRASVRLRELRRGTADVIDVVAPGQLRPLVEAG
+TQVLPRDPLGVLYVGMNLDHPLVHAQYLRQAIAYAVDRPRIAGSDVFLEGTRLAHDLVPP
+SLGVGDEEARRYDVNPGRAREFLGLAGYDGEPLEFLYPAGTARPSLPEPERVYAMVARDL
+GAVGMHIVPVPVPEDQDYLHAVVSRPTRALHLMGRTGDYRDPHAFLEPFARSGRAETGYR
+NPRVVEDVDAAAAETDDDTRRALFRRVVRAMALDLPALPLVYPISALATGPRVASYPTSP
+QLDEPFSRVRLTEG
+>LFPAFLNI_00792
+MQPTRRAFLGGGLGLLGLGVAGCTTSPAVPSSAAPSSSGPGRLLVVGAPARALTRDPARA
+LDVESFRLIRQVFETLLGVDADTGAPTPRLAERHEESDGGRLHTFHLVSGVVFDDGEPCD
+AAAVVANIERWASAPAPVDGTVAPPSSFVSAFGGYAGDADSAFAGVEARGELEVRLRLHS
+PRRHLAAALASPAFAISSPASWDRTVDVDGSEVTTPAGTGPYRWADAAETAELTRAHPGA
+SGATILVPSARHRGSDPAAYPVAVQAWGRASVRLRELRRGSADVIDVVAPGQLRPLVEAG
+TQVLPRDPLGVLYVGMNLDHPRVRSQYLRQAIAYAVDRPRIAGSDVFLEGTRLAHDLVPP
+SLGVGDEEARRYDVNPGRAREFLHLAGYDGEPLEFLYPAGTARPSLPEPERVYAMVARDL
+GAVGMHIVPVPVPEDQDYLHAVVSRPTRALHLMGRTGDYRDPHAFLEPFARSGRAETGYR
+NPRVVEDVDAAAAETDDDARRALFRRVVRAMALDLPALPLVYPISALATGPRVASYPTSP
+QLDEPFSRVRLTEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001434.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001434.fa
new file mode 100644
index 0000000000000000000000000000000000000000..31c19055759d609787a2ddc3627a052ada8c9b88
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001434.fa
@@ -0,0 +1,91 @@
+>ACLBLIBL_02110
+MRIHRMRLQGIGPYAEAQDVDMDRLNDAGLFLLDGPTGAGKSTVLAALCYALYGSVPGGR
+SPESLVTTLRPPGAVVPEVLVEFTVQGRRFEVVRSPRHERLKKRRSASGKDTTPTPAAVS
+LREHVDGAWQEPLTRNDEVGVQVADVMHLDAAQFMQVVMLPQGRFAEFLTARSDERQRLL
+RRLFGTQRFDGVEEHLKAEAERLGSRAAADAKVAASAREQLREAVAAELGEDWHAPEPFP
+ATDEELVERTAERTREAVDAARAGRDAAAAEEAAARGTQAELRATGEALAAAAAWTERER
+AHREGAEAAAGDRTAVAAHERAGRVLGAADRSESARAAEDRAREADGTAQAAAAEDPLSA
+GWLEQARRDAAETPADDAAETSADAAALPRDAVALAERAVEEVVRAVRDRAAAERLEETE
+RTEAARRTQIVAEREAAEAERSGREEGLAAVREAVEAASARLGAQADVDRRVAEAEQGLA
+AAREAERHALAADAADRAREAARTGRDAAAQHRLGLLRSRYEQAAADLAADLEDGTPCAV
+CGSPEHPDPAPRVGTAVTEADVAAAEEGLAAAEAVLADAETARTAAHERVRASSAAAGGR
+TPAQAEEALAAARTEHAELAAVRKALAADRRRLRALETERDEAAAAETARTAEDARLQEA
+ARQRHERLLELRAGIERARGDAPDLDARGALVRAARGRLEALAGAVEVRERAVAVAADAD
+RALAAALREQEFEDVGAARAARLPAEDAAARTARVRAWDDEQARLAELAQSDAVRRGREL
+QDQQATAPTPEDLEAAAARLLEAERSRREQDEALGRRTAVAAAVERQAALLRGVLDRSAA
+LLAEHERVTGLLALVRGGGENRLKMPLASYVLAGRLEEVAAAATERLLAMTDGRYSIEYS
+DDSAGRGNKGLELVVRDHYVDETRHPSTLSGGETFMASLALALGLADTVQAEAGGVELDT
+LFVDEGFGSLDSDTLDDVLDVVDGLRSGGRTVGLVSHVERMKQEIPVRLAVTKEREGSSL
+AVHVDA
+>MOLHKGIG_00820
+MRIHRMRLEGLGPYAQAQDVDFDRLNAGGLFLLDGPTGAGKSTVLAALCFALYGTVPGGR
+SAESLVTTLREPGAVIPEVQVEFTVQGRRFEVVRSPKHERPRRRRSAAGGATVTTQATVS
+LRERVAGEWTAPLTRADEVGQQIAAVLHLDAEQFMQVVLLPQGQFAQFLTAKSDERRALL
+RRLFGTQRFDGVEEHLRVETARLDTAVAVDADVARTARAQLAEALHEALGPDWHAPEPSP
+DTDDRLLALAAERAGRAHEDARADLATARAAEQRARVTARELETRGRDLAAAEAWASRRR
+DHDAEAETAAARRRAVDAHERAGRVLAAAQRATAAADAAGTASETVTEALAHVEDEPTAA
+AWLAAARADGAADAPASRQALGEAERAAEAVARAVQDRARMGELEQEAAAAAERRAEIGR
+DRAALVESRPEREAAVAAHRAAVERGTERLGAREAVDRAVSEAAARRTAAEAAAARAVEA
+ETAARAHREAQERRREAAERHVGLLRARYEQAASELAERLVPGEPCAVCGSPEHPAPAAT
+ADTAVTEADVRDAEQARTAADRAATDAETALRAAEQTLRTAREAAAGLAPEAAREALERA
+EAERAALDQAAKDLAADRRRLTAAEKTLAGADETAAALAAEDGRLAEAAAHRAARLTELR
+DAVEAARGDAETLDARRDQVTAARRVLAALAAAQDEDARARAVADETDQALTAALAEQHF
+DDVDAARAARLEETEAAARTAAVQEWHAERARLAELEASEPVRRGRALAEAGVEPPTEEQ
+TRAAAEALAAAEAASSSRATAVGRLDSLVATVRRQSAALTEVLERSAGLIAEHTRVRGLL
+DLVRGGGENLLKMPLTSYVLAGRLEEVAAAATERLLAMTDQRYSIEYSDAVGGRGNKGLE
+LVIRDHYVDETRHPATLSGGETFMASLALALGLADTVQAEAGGIELDTLFVDEGFGSLDA
+DTLDDVLDVVDTLRTGGRTVGLVSHVERMRQEIGVRLEVRKDRRGSSLAVHDGA
+>NAFOICDF_02001
+MRIHRMRLEGIGPYAEPQDLDLDPLNDAGLFLLDGPTGAGKSTVLAALCFALYGSVPGGR
+TPESLVTTLRPPGAVVPQVLVEFTVQGRRFEVLRSPRHARPKKRGGGTTATQASVSLRER
+VDGAWTAPLTRADEVGRQVAEVLRLDAAQFMQVVSLPQGRFAEFLTARSDDRQRLLRRLF
+GTQRFDGVEDRLKECAEALGTRVAADAAEAAGARAQLLEQARLELGEDWHAPDPAPEEGE
+DERLVELTRTRADAALAEARTAQQAADAAEAAARAAQDRLTADTEALRALAAWEGREREH
+RQAADHVAADRSAVALHERASHVLGAATRAEQTRAAHASTAERARAAAEAVAADALAAAW
+LDEAEDADAARRRADRETDALARAVRDRDALTRLEAEGTQADAERERLEDEARSAREKGK
+RRAAQIAELHDTVDAAAARLGAEDEVARRLAEATERAAAAGQAAERAVAQERARAARDER
+RDAQRGAAQARLDLLRSRFEQAAAELAAGLEDGSPCPVCGSAEHPDPAPRADGAVTEADV
+AAADRALEAADAALAEAEQALAAASEEHRAARERAGGQDVAAAEEALSAVRAEHEALAAA
+RTALATDRRALARRESEQRTADEAATARTAALARLSEAQARRTERAAELTAAVAAAQGDA
+ADLDARTAHVRTATRALSALVEAGDAAARAAAVAEDAAQALAGALAEQDFADVAAARAAA
+LPPDDAAARAARVRSWDVEEARLAEAAASEPLVRGRALREAGTSEPTAEEFAAAQETLRE
+ATAARTARAAVVGRREALVASLERQARRLRAVLERSSELLAEHERATGLLALVRGQGENR
+LKMPLASYVLAGRLEEVAAAATERLLAMTDRRYSIEYSDEATGRGNKGLELVIRDHYVDE
+TRHPSTLSGGETFMASLALALGLADTVQAEAGGVELDTLFVDEGFGSLDADTLDDVLDVV
+DGLRAGGRTVGLVSHVERMKQEIPVRLEVTKSRAGSTLAIHDGG
+>MHAAABBN_00552
+MRIHRMRLEGLGPYAQAQDVDFDRLNAAGLFLLDGPTGAGKSTVLAALCFALYGTVPGGR
+SAESLVTTLREPGAVIPEVQVEFTVQGRRFEVVRSPKHERPRRRRSAAGGATVTTQATVS
+LRERVAGEWTAPLTRADEVGQQIAAVLHLDAEQFIQVVLLPQGQFAQFLTAKSDERRVLL
+RRLFGTQRFDGVEEHLRVETARLDTAVAVDADVARTARAQLAEALHEALGPDWHAPEPSP
+DTDDRLLALAAERAGRAHEDARADLATARAAEQRARVTARELETRGRDLAAAEAWASRRR
+DHDAEAETAAARRRAVDAHERAGRVLAAAQRASAAADAAGTASEAVTEALAHVEDEPTAA
+AWLAAARADGAADAPASRQALGEAERAAEAVARAVRDRDRMRELEQEAAAAAERRAEIDR
+DRAALVESRPEREAAVAAHRAVVERGTERLGAREAVDRAVSEAAARRTAAEAAAARAVEV
+ETAARAHREAQERRREAAERHVGLLRARYEQAASELAERLVPGEPCAVCGSPEHPAPAAT
+ADTAVTEADVRDAEQARTAADRAATDAETALRAAEQTLRSAGEAAAGLAPEAAREALERA
+ETERAALDQAAKDLAADRRRLTAAEKTLAGADETAAALAAEDGRLAEAAAHRAARLTELR
+DAVEAARGDAETLDARRDQVTAARRVLAALAAAQDEDARARAVADETGQALTATLAEQRF
+DDVDAARAARLEETEAADRTAAVQEWDAERARLAELEASEPVRRGRALAEAGVEPPTEEQ
+TRAAAEALAAAEAASSSRATAVGRLDSLVATVRRQSAALTEVLERSAGLIAEHTRVRGLL
+DLVRGGGENLLKMPLTSYVLAGRLEEVAAAATERLLAMTDQRYSIEYSDAVGGRGNKGLE
+LVIRDHYVDETRHPATLSGGETFMASLALALGLADTVQAEAGGIELDTLFVDEGFGSLDA
+DTLDDVLDVVDTLRTGGRTVGLVSHVERMRQEIGVRLEVRKDRRGSSLAVHDGA
+>LFPAFLNI_00789
+MRIHRMRLEGLGPYAQAQDVDFDRLNAGGLFLLDGPTGAGKSTVLAALCFALYGTVPGGR
+SAESLVTTLREPGAVIPEVQVEFTVQGRRFEVVRSPKHERPRRRRSAAGGATVTTQATVS
+LRERVDGEWTAPLTRADEVGQQIAAVLHLDAEQFMQVVLLPQGQFAQFLTAKSDERRVLL
+RRLFGTQRFDGVEEHLRVETARLDTAVAVDADVARTARAQLAEALHEALGPDWHAPEPSP
+DTDDRLLGLAAERAGRAHEDARADLATARAAEQRARVTARELETRGRDLAAAEAWASRRR
+DHDAEAETAAARRRAVDAHERAGRVLAAAQRATAAADAAGTASETVTEALAHVEDEPTAA
+AWLAAARADGAADAPASRQALGEAERAAEAVARAVQDRARMGELEQEAAAAAERRAEIGR
+DRAALVESRPEREAAVAAHRAAVERGTERLGAREAVDRAVSEAAARRTAAEAAAARAVEA
+ETAARAHREAQERRREAAERHVGLLRARYEQAASELAERLVPGEPCAVCGSPEHPAPAAT
+ADTTVTEADVRDAEQARTAADRAATDAETALRAAEQTLRTAREAAAGLAPEAAREALERA
+EAERAALDQAAKDLAADRRRLTAAEKTLAGADETAAALAAEDGRLAEAAAHRAARLTELR
+DAVEAARGDAETLDARRDQVTAARRVLAALAAAQDEDARARAVADETDQALTAALAEQHF
+DDVDAARAARLEETEAAARTAAVQEWHAERARLAELEASEPVRRGRALAEAGVEPPTEEQ
+TRAAAEALAAAEAASSSRATAVGRLDSLVATVRRQSAALTEVLERSAGLIAEHTRVRGLL
+DLVRGGGENLLKMPLTSYVLAGRLEEVAAAATERLLAMTDQRYSIEYSDAVGGRGNKGLE
+LVIRDHYVDETRHPATLSGGETFMASLALALGLADTVQAEAGGIELDTLFVDEGFGSLDA
+DTLDDVLDVVDTLRTGGRTVGLVSHVERMRQEIGVRLEVRKDRRGSSLAVHDGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001437.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001437.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ece2e28d2176aa62aaf154aa372f0d0dbf598da
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001437.fa
@@ -0,0 +1,39 @@
+>ACLBLIBL_02113
+MSGVLAPVPGLDFTAIDFETANGFRGSPCALGAVRVRDGVMVERAEWLIRPPVGFDRFDP
+RNVRIHGITEDRVLDAARFADVYDELAGFVGADVLAAHNAGFDVGVIESGLEVSGRDVPR
+LDFVCTLVLARRVYDLASYALPSAAREAGFAPGPHHDALADAEACAAILVDVARRVLGTE
+AGDGAAVAPAGARGLPEPFDVPRLMRAQGLTVNTLAQRAAGEGPESKATRQARRAQGVFD
+ARVPLKDERAMPDFLRWPDEGTNPVPNPDADPGHPLHGQTVVFTGGIGMSRQTAKVRAAR
+LGAQTANRVGAATTMLVVGDGFEAADLDRPAPAPGTREAVTTALAHRKTRDALRRRERGQ
+HISLVSEGEFLQMLDGNWPDAAR
+>MOLHKGIG_00817
+MSGGRVPVPGLDFTAIDFETANGFRGSPCAVGAVRVRDGVMVDRAEWLIRPPVGFDRFDP
+RNVRIHGITEDRVLDAPRFAQVYDELADFVGTDVLAAHNAGFDVGVIESGLEVSGRDVPG
+LEFVCTLVLARRVYDLPSYALPSAAREAGFTPGRHHDALADAEACAAILVDIGRRVLGAP
+PADADVLPGLTDAPAGRGVDRLMRAQGLGVSVLAPRAAGAGAESKATRQARRTEGVFDAR
+VPLRDERAMPDFMRWPDEGVNPLPNPAADPGHPLFGQTVVFTGGIGMSRQRAKTRAAAHG
+AQTANRVGAATTMLVVGDGFEAADLHRPRAEDGAPQAVTTALAHRKTRDALRRRDRG
+>NAFOICDF_02004
+MTAGIAPVRQPGLDFTAIDFETANGFRGSACQLGAVRVRDGLPASRAVWLMRPPAGFDRF
+DPRNVRIHGIHADRVVDAPRFAEVYDAFAAFAGDDVLVAHNAGFDLGVIESGLEVSGRDV
+PAHDYACTLTLARRIYDLPSYSLPSAAREAGFVPGRHHDALADAEACAAILVDLARRVCP
+PGEATVDALLASQGLRRSRLTARAAGTGRESRATRQARTMPGLFDATIPLADDRTLPDLM
+RWPDEGVNPEPAADADPGHPLYGQVVVFTGGIGMSRQEAKNRAAQRGAATANRVNGRTTM
+LVVGDGVDPAELVGAPEVHGVVVDPGATDPAGRGVDPGGAVTHRKTREALQRRAKGQAIA
+LVSEAEFLQMVDGAWPAGAR
+>MHAAABBN_00549
+MSGGRAPVPGLDFTAIDFETANGFRGSPCAVGAVRVRDGVMVDRAEWLIRPPVGFDRFDP
+RNVRIHGITEDRVLDAPRFAQVYDELADFVGTDVLAAHNAGFDVGVIESGLEVSGRDVPG
+LEFVCTLVLARRVYDLPSYALPSAAREAGFTPGRHHDALADAEACAAILVDIGRRVLGAP
+PADAEILPGLTDAPAGRGVDRLMRAQGLGVSVLAPRAAGSGAESKATRQARRTEGVFDAR
+VPLRDERAMPDFMRWPDEGVNPPPNPTADPGHPLFGQTVVFTGGIGMSRQSAKTRAAAHG
+AQTANRVGAATTMLVVGDGFEAADLHRPRAEDGAPQAVTTALAHRKTRDALRRRDRGQAI
+ALVSEGEFLQMLDGNWPDAAR
+>LFPAFLNI_00786
+MSGGRVPVPGLDFTAIDFETANGFRGSPCAVGAVRVRDGVMVDRAEWLIRPPVGFDRFDP
+RNVRIHGITEDRVLDAPRFAQVYDELADFVGTDVLAAHNAGFDVGVIESGLEVSGRDVPG
+LEFVCTLVLARRVYDLPSYALPSAAREAGFTPGRHHDALADAEACAAILVDIGRRVLGAP
+PADAEILPGLTDAPAGRGVDRLMRAQGLSVSVLAPRAAGSGAESKATRQARRTEGVFDAR
+VPLRDERAMPDFMRWPDEGVNPLPNPAADPGHPLFGQTVVFTGGIGMSRQSAKTRAAAHG
+AQTANRVGAATTMLVVGDGFEAADLHRPRAEDGAPQAVTTALAHRKTRDALRRRDRGQAI
+ALVSEGEFLQMLDGNWPDAAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001441.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001441.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f52d42df18fe366605399327e31d00255a50cfab
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001441.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02117
+MSAPPQARPEVSASSPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTAHAPYGPRPIAQ
+VRALALGIMDELVDAGVKALVIACNSASAAVLRDARERYTGRHGIPVVEVIQPAVRRAVA
+ATRSGRIGVIGTQATVGSRAYDDSFSAAPHLQVTSAACPRFVEFVEAGITTGPELLATAQ
+EYTEPLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEH
+PHSAAGSGQDTRHRFAATGDPEHFQALARRFLGPEVGAVRRLDTVRERYPTAALAQLTPD
+LIARLGAEQERET
+>MOLHKGIG_00813
+MSGQRAAVDAAAPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTEHSPYGPRPIAEVRA
+LALAIMDELVARGVKALVIACNSASAAVLRDARERYTGGHGIPVIEVIQPAVRRAVAATR
+TGRIGVIGTEATVGSRAYEDSFSAAPHLEITSVACPRFVEFVEAGITTGPELLETAREYT
+APLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEHPHS
+AAGSGQATRHRFAATGDPDHFQALARRFLGPEVESVRRLETIGAPRPAAAPVPTRSTAFV
+PLGAEQEGVT
+>NAFOICDF_02008
+MSATADTAQTGAGPSSPIGVFDSGVGGLTVARAIMDQLPHEPIIYVGDTAHSPYGPRPIA
+QVRALALGVMDELVEAGVKALVIACNSASAAVLRDARERYTGRLGIPVVEVIQPAVRRAV
+AATRNGRVGVIGTQATVGSRAYEDSFSAAPHLQITSVACPRFVEFVEAGITTGPELLETA
+EEYVAPLKAAGVDTMVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRALVRHGLE
+HPHSAAGSAAAPEHRFAATGDPEHFAALARRFLGPEVGPVRQIQEIRERYPTAALTALTP
+DVLARLRAEMEEDGAR
+>MHAAABBN_00545
+MSGQRAAVDAAAPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTEHSPYGPRPIAEVRA
+LALAIMDELVARGVKALVIACNSASAAVLRDARERYTGGHGIPVIEVIQPAVRRAVAATR
+TGRIGVIGTEATVGSRAYEDSFSAAPHLEITSVACPRFVEFVEAGITTGPELLETAREYT
+APLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEHPHS
+AAGSGQATRHRFAATGDPDHFQALARRFLGPEVESVRRLETIGAPRPAAAPVPTRSAASV
+RPGPEQEGVT
+>LFPAFLNI_00782
+MSGQRAAVDAAAPIGVFDSGVGGLTVARAIMDQLPHESILYVGDTEHSPYGPRPIAEVRA
+LALAIMDELVARGVKALVIACNSASAAVLRDARERYTGGHGIPVIEVIQPAVRRAVAATR
+TGRIGVIGTEATVGSRAYEDSFSAAPHLEITSVACPRFVEFVEAGITTGPELLETAREYT
+APLRAAGVDTLVLGCTHYPLLTGALSLVMGEDVTLVSSAEETAKDLYRELVRLGLEHPHS
+AAGSGQATRHRFAATGDPDHFQALARRFLGPEVESVRRLETIGAPRPAAAPVPTRSAASV
+RPGPEQEGVT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001442.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001442.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fe0e7ff709aa4cbbbceb4200cfe780b74ca6cee1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001442.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_02118
+MAERFRWTRRGYTAQLEKPEVRLLRGLVKDVITLLEGRRRNVLSEADDLPADAPGAPEPS
+ADVAPVPQGPEAGAGPAAGLDEADAAFWELVSGLHLSQDRVPHRAAPADPAVARLLPEAM
+PQADAQERGAHRALTEDALSEGKLADARLALELLRSTRVEVPHHQAPAFGRALNDVRLVL
+AARLGVETEEDAERVHAVDDWRSAEDVESTMALLYNFTTWLLETLMTEMLSELPEGADED
+APGADEAGDDA
+>MOLHKGIG_00812
+MAERFRWTRRGYTAQLELPEVRLLRGLVRDVVALLEGRRADVRPAEADPAEAPAAEDGVD
+TPEDPPAAPPSVSAAQDAGPVAGLDASDAAFWGLVSGLHLSQDPEPQRSAPTDPAVARLL
+PDAMPQAGAAEQGAHRALTEDALSEGKLADARLALELLRSTRVEVPHDQAPAFGRALNDV
+RLVLAARLGVETEEDAARVHAVDDWRSAEDVESTMALLYNFTSWLLETLMTEMLSELPEG
+ADESAPGAGDAEDEQ
+>NAFOICDF_02009
+MAQRFRWTRRGYVAELEDAELRLLRGLVKDVVTLLENRQDEVAPPGSDAGTAEDAPEAGA
+EPVADARPGDAVGPGEETPHDAAFWALVGGLDLVADPVAERSAPEDPAVARLLPDAMPHA
+EPAERARQRALTEDALTAAKLADARRALEALRSVRVTVPHEHAVSFGRALNDVRLVLAAR
+LGIETEQDAARVHAVDDWRDAQDVEATMALLYNFTTWLQETLMAEMLSELPLEGAAGPDE
+EERA
+>MHAAABBN_00544
+MAERFRWTRRGYTAQLELPEVRLLRGLVRDVVALLEGRRADVRPAEADPAEAPAAEDGVD
+TPEDPPAAPPSVSAAQDAGPVAGLDASDAAFWGLVSGLHLSQDPEPQRSAPTDPAVARLL
+PDAMPQAGAAEQGAHRALTEDALSEGKLADARLALELLRSTRVEVPHNQAPAFGRALNDV
+RLVLAARLGVETEEDAARVHAVDDWRSAEDVESTMALLYNFTSWLLETLMTEMLSELPEG
+SDESAPGAGDAEGEQ
+>LFPAFLNI_00781
+MAERFRWTRRGYTAQLELPEVRLLRGLVRDVVALLEGRRADVRPAEADPAEAPAAEDGVD
+TPEDPPAAPPSVSAAQDAGPVAGLDASDAAFWGLVSGLHLSQDPEPQRSAPTDPAVARLL
+PDAMPQAGAAEQGAHRALTEDALSEGKLADARLALELLRSTRVEVPHDQAPAFGRALNDV
+RLVLAARLGVETEEDAARVHAVDDWRSAEDVESTMALLYNFTSWLLETLMTEMLSELPEG
+SDESAPGAGDAEGEQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001444.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001444.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4cfcccab94ddb567d5c9455ef77fcd422bf98fcb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001444.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_02120
+MSQNPVTSAPQTPDDWRIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY
+GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP
+HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA
+VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTSL
+LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTQTGIMVTSDLD
+EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG
+GRKEAARRRDRRGRATAEVVGVNRGAAPDADDRPLLHRFVHAGELAAGWTGPEAVTRAAE
+RHAASLRELPATVGRLQPGDPAIPTIFLED
+>MOLHKGIG_00810
+MSQNPVPSAPRTADDWQIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY
+GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP
+HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA
+VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTTL
+LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTETGIMVTSDLD
+EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG
+GRKEAARRRDPRGRATAEVIGVNRGAAPDADDRPLLHRFVHAGELAEGWTGPEAVTRAAE
+RHAASLRELPASVGRLQPGDPAIPTIFLED
+>NAFOICDF_02011
+MTQNASAPAPSAAPWHVPTSLMTDHYELTMLCAARRAGTAERRSRFELFSRRLPDGRRYG
+VVAGTGRILEGLSRFRFSTAEVDFLADHSVVDDATLQWLADFRFSGDITGYAEGEVYFPH
+SPVLQVESTFAEACILETYLLSILNYDSAVASAASRMASAAQGRPCIEMGARRIHEEAAV
+AAARAAVIAGFAATSNLEAGRRYGVRTVGTAAHSFTLLHDSERAAFEAQVAALGRDTTLL
+VDTYDVEQGVRTAVEVAGRALRNVRLDSGDLVQQAHEVRELLDSLGNTETGIMVTSDLDE
+YAIASLRSAPVASYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASHGG
+RKDAVRRRDARGRAVAELVGVNRAPAADADDRPLLHTFVKDGELQEGWTGPEAVTRAAER
+HAASLAELPRAAARLQPGEALIPTIFQED
+>MHAAABBN_00542
+MSQNPVPSAPRTADDWQIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY
+GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP
+HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA
+VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTTL
+LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTETGIMVTSDLD
+EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG
+GRKEAARRRDPRGRATAEVIGVNRGAAPDADDRPLLHRFVHAGELAEGWTGPEAVTRAAE
+RHAASLRELPASVGRLQPGDPAIPTIFLED
+>LFPAFLNI_00779
+MSQNPVPSAPRTADDWQIPTALMTDHYELTMLQAALKAGTAHRRSRFELFTRRLPSGRRY
+GVVAGVGRALEGLSRFRFDTPELDFLADTTALDDATLAWLADYEFTGDIVGYAEGEAYFP
+HSPLLQVESTFAEACILETYLLSIYNYDSAVASAASRMTAVADGRPCAEMGSRRTHEESA
+VAAARAAAIAGFTATSNLEAGRRYGIPTVGTAAHSFTLLHDSERAAFEAQVAALGADTTL
+LVDTYDVEQGVRTAVEVAGPALRNVRVDSGDLVIQAHRVRELLDELGNTETGIMVTSDLD
+EYAIAALRSAPVSSYGVGTRLVTGSGAPTASMVYKLVARQDDDGTWVDVAKASSGKASRG
+GRKEAARRRDPRGRATAEVIGVNRGAAPDADDRPLLHRFVHAGELAEGWTGPEAVTRAAE
+RHAASLRELPASVGRLQPGDPAIPTIFLED
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001445.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001445.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e5e9d70534677ff8491d2b5f8f568a9aab1d31b6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001445.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02121
+MENLNRALVIVDVQNDFCEGGALGVTGGAAVAAGVSEHLAEHADAYAAVAATRDWHVDPG
+THFAAATGAEPDFRTTWPVHCVAGTAGAELHPDLDIEHLDAEFLKGLHTDAYSGFDGALG
+EPDAVPTGAAGERPSGTVGPYGATAVAAAAVESDAPGLDEWLREQGVDAITVVGIATDHC
+VRATVLDALDAGYEVTVLTDLVAGVDEAASQAALHEMEAAGADLELSEGR
+>MOLHKGIG_00809
+MENLNRALVIVDVQNDFCEGGALGVTGGAAVAAGVSEHLAEHADAYAAVAATRDWHVDPG
+THFAAATGAEPDFRTTWPVHCVAGTAGAELHPDLDAEHLDAEFLKGLHTDAYSGFDGALG
+EPDAVPTGAAGERPSGTVGPYGATAVAAAAVEAGAPGLDEWLREQGVDAITVVGIATDHC
+VRATVLDALDAGYEVTVLTDLVAGVDEAAAQAALHEMEAAGAILATS
+>NAFOICDF_02012
+MSEQNRALVIVDVQNDFCEGGALAVAGGADVAAAIADHVNEAREDYAAVVTTRDWHVDPV
+GHFAAASLEDRDAEPDYVRTWPVHCVAGTPGAELHPGLSAEDLEIDAEFLKGQHSDGYSG
+FDGHAGDPDAVRSGDEARAAAGPYGATQGAAHAADGGLGLDEWLREQDVDALTVVGLATD
+HCVRATVLDGLEAGYEVTVRTDLVAGVDDAAGEAALHEMEAAGALLRAGD
+>MHAAABBN_00541
+MENLNRALVIVDVQNDFCEGGALGVTGGAAVAAGVSEHLAEHADAYASVAATRDWHVDPG
+THFAAATGAEPDFRTTWPVHCVAGTAGAELHPDLDAEHLDAEFLKGLHTDAYSGFDGALG
+EPDAVPTGAAGERPSGTVGPYGATAVAAAAVESGAPGLDEWLREQGVDAITVVGIATDHC
+VRATVLDALDAGYEVTVLTDLVAGVDEAAAQAALHEMEAAGAILATS
+>LFPAFLNI_00778
+MENLNRALVIVDVQNDFCEGGALGVTGGAAVAAGVSEHLAEHADAYASVAATRDWHVDPG
+THFAAATGAEPDFRTTWPVHCVAGTAGAELHPDLDAEHLDAEFLKGLHTDAYSGFDGALG
+EPDAVPTGAAGERPSGTVGPYGATAVAAAAVESGAPGLDEWLREQGVDAITVVGIATDHC
+VRATVLDALDAGYEVTVLTDLVAGVDEAAAQAALHEMEAAGAILATS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001449.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001449.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5783d0b06aa19f546276b4856842a2cd3088e6b6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001449.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_02126
+MSEHPAEPHRTAPSSAEAPHAGPAPAEAPAVVPSAAARRRAVDAPDPDLALVTRGLTKRF
+GDKTALDGLDLDVPAGSFYGVVGPNGAGKTTALSMATGLLRPDLGQAWIHGVDVWAQPLE
+AKRRVGVLADGVRTFDRLTGAQLVTYAGLLHGVDADTVAARTEDLLRVMDLADAGRKLVV
+DYSAGMTKKISLAAAMVHAPDVLVLDEPFEAVDPVSAANIRDILHDYVGRGGTVIVSSHV
+MDLVQRMCSHVAVIAGGTLRAAGTLEEVRAGRDLEDRFVDLVGGRHEQEGLAWL
+>MOLHKGIG_00804
+MTPHASEPAPTHLAAATRRRAVDAPDPDLALVTRGLTQRFGDKLALDALDLDVPAGSFFG
+VVGPNGAGKTTALSMATGLLRPDHGRAWIHGVDVWEQPLEAKRRVGVLADGVRTFDRLTG
+AQLVTYAGLLHGLDADTVAERTADLLRVMDLEDAGRTLVADYSAGMTKKVSLAAAMVHAP
+DLLVLDEPFEAVDPVSAANIRDILHSYVERGGTVIVSSHVMDLVQRMCTHVAVIAAGTLR
+AAGTLEEVRDGRDLEDRFVELVGGRHGSEGLAWL
+>NAFOICDF_02019
+MRAQDAPDPNLALVTRGLAKRFGEKVALAGLDLEVPAGSFFGVVGPNGAGKTTALSMATG
+MLRPDAGRVWIHGVDVWEQPLEAKRRVGVLADGVRTFDRLTGAQLITYAGLLHGLDRDTV
+DVRTADLLRVMDLEEAGRKLVVDYSAGMTKKVNLAAAMVHAPDVLVLDEPFEAVDPVSAA
+NIRDILHDYVGRGGTVIVSSHVMDLVQRMCSHVAVIAGGVLRAAGTLEEVRAGRDLEERF
+VDLVGGRHTGEGLAWL
+>MHAAABBN_00535
+MTPHAPEPAPAHLAAAARRRAADAPDPDLALVTRGLTQRFGDKLALDALDLDVPAGSFFG
+VVGPNGAGKTTALSMATGLLRPDHGRAWIHGVDVWEQPLEAKRRVGVLADGVRTFDRLTG
+TQLVTYAGLLHGLDADTVAERTADLLRVMDLEDAGRKLVADYSAGMTKKVSLAAAMVHAP
+DLLVLDEPFEAVDPVSAANIRDILHSYVERGGTVIVSSHVMDLVQRMCTHVAVIAAGTLR
+AAGTLEEVRDGRDLEDRFVDLVGGRHGSEGLAWL
+>LFPAFLNI_00771
+MTPHAPEPAPAHLAAAARRRAVDAPDPDLAFVTRGLTQRFGDKLALDALDLDVPAGSFFG
+VVGPNGAGKTTALSMATGLLRPDHGRAWIHGVDVWEQPLEAKRRVGVLADGVRTFDRLTG
+AQLVTYAGLLHGLDADTVAERTTDLLRVMDLEDAGRKLVADYSAGMTKKVSLAAAMVHAP
+DLLVLDEPFEAVDPVSAANIRDILHSYVERGGTVIVSSHVMDLVQRMCTHVAVIAAGTLR
+AADTLEEVRDGRDLEDRFVDLVGGRHGSEGLAWL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001453.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001453.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd726340012e63dc12d46b1302ba080425508f3c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001453.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02130
+MRLVIARCSVTYEGRLNAHLPPATRLLMVKADGAVLVHSDGGSYKPLNWMSPPATLHTTA
+PTAEQAEQGVVEVWRVQAAKSDDRLMILIEEILADQSHELGADPGLVKDGVEADLQRLLA
+EQIGLLGDGHTLVRREYMTAIGPVDILARDPEGGTVAVELKRRGDIDGVEQLTRYLELMN
+RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF
+>MOLHKGIG_00800
+MRLVIARCSVTYEGRLNAHLPTATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE
+PSPDQADQGVTQVWRVQAKKSDDRLIVLIEEVLADDSHELGVDPGLVKDGVEADLQRLLA
+EQISLLGDGHTLVRREYMTAIGPVDILARDADGGTVAVELKRRGDIDGVEQLTRYLELMN
+RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF
+>NAFOICDF_02023
+MRLVIARCSVTYEGRLNAHLPSATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE
+PTEEQAAAGVTQVWRVQAKKSDDRLLVLLEEVLADETHELGVDPGLVKDGVEADLQRLLA
+EQIGLLGDGHTLVRREYMTAIGPVDILAKGPGGQTVAVELKRRGDIDGVEQLTRYLDLMN
+RDPLLAPVTGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDADARLF
+>MHAAABBN_00531
+MRLVIARCSVTYEGRLNAHLPTATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE
+PSPDQADQGVTQVWRVQAKKSDDRLIVLIEEVLADDSHELGVDPGLVKDGVEADLQRLLA
+EQISLLGDGHTLVRREYMTAIGPVDILARDADGGTVAVELKRRGDIDGVEQLTRYLELMN
+RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF
+>LFPAFLNI_00767
+MRLVIARCSVTYEGRLNAHLPTATRLLMVKADGSVLVHSDGGSYKPLNWMSPPATLHVEE
+PFPDQADQGVTQVWRVQAKKSDDRLIVLIEEVLADDSHELGVDPGLVKDGVEADLQRLLA
+EQISLLGDGHTLVRREYMTAIGPVDILARDADGGTVAVELKRRGDIDGVEQLTRYLELMN
+RDPLLAPVRGVFAAQQIKPQARTLAEDRGIRCVTLDYDAMRGVDDAESRLF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001457.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001457.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8539dc92f7cffbf50821194ad61fc1a7f7f631b8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001457.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_02134
+MTATITDQGTGTPTGGATGRVSRVIGPVIDAEFPANAMPEIYNALTTEIDLNGQRRTVTF
+EVAQHLGDNMVRAISLQSTDGLVRGTDVVDTGAPISVPVGDAVKGHIFNVLGETLDVETS
+SLNFEERWPIHRAAPNFASLEGSTEMLETGIKVIDLLTPYIKGGKIGLFGGAGVGKTVLI
+QEMITRVARNFGGTSVFAGVGERTREGNDLWVEMDEADVLKDTALVFGQMDEPPGTRLRV
+ALSALTMAEYFRDVQNQDVLLFIDNIFRFSQAGSEVSTLLGRMPSAVGYQPNLADEMGVL
+QERITSTRGHSITSMQAVYVPADDYTDPAPANVFAHLDATTNLTRDLASRGLYPAVDPLA
+STSRILDPQYVGQDHYDTAIRVKQILQKNKELQDIIAILGVDELGEEDKITVARARKIEQ
+FLSQNTYTAKQFTGVEGSTVPIKDTVEGFKAIADGDLDHIAEQAFYNVGGLDDVEREWAK
+IQAEG
+>MOLHKGIG_00797
+MTATITDQGTGTPTGGATGRVSRVIGPVIDAEFPANAMPEIYNALTTEIDLNGQRRTVTF
+EVAQHLGDNMVRAISLQSTDGLVRGTDVVDTGAPISVPVGDAVKGHIFNVLGETLDMPTS
+QLQAEDRWPIHRPAPNFASLEGSTEMLETGIKVIDLLTPYIKGGKIGLFGGAGVGKTVLI
+QEMITRVARNFGGTSVFAGVGERTREGNDLWVEMDEADVLKDTALVFGQMDEPPGTRLRV
+ALSALTMAEYFRDVQNQDVLLFIDNIFRFSQAGSEVSTLLGRMPSAVGYQPNLADEMGVL
+QERITSTRGHSITSMQAVYVPADDYTDPAPANVFAHLDATTNLTRDLASRGLYPAVDPLA
+STSRILDPQYVGQEHYDVAIRVKQILQKNKELQDIIAILGVDELSEEDKITVGRARKIEQ
+FLSQNTYTAKQFTGVEGSTVPVKDTVEGFKAIADGDLDHVAEQAFYNVGGLDDVEREWAK
+IQAEG
+>NAFOICDF_02027
+MTATFTDQGTGTPTAGATGRVARVIGPVIDAEFPANAMPEIYNALTATVELAGQTRVVTF
+EVAQHLGDNMVRAISLQSTDGLVRGADVQDTGAPISVPVGDAVKGHLFNVLGETLDMPIS
+ELDVQERWPIHRPAPSFAALEGSTEMLETGIKVIDLLTPYIKGGKIGLFGGAGVGKTVLI
+QEMITRVARNFGGTSVFAGVGERTREGNDLWVEMDEADVLKDTALVFGQMDEPPGTRLRV
+ALSALTMAEYFRDVQNQDVLLFIDNIFRFSQAGSEVSTLLGRMPSAVGYQPNLADEMGVL
+QERITSTRGHSITSMQAVYVPADDYTDPAPANVFAHLDATTNLTRDLASRGLYPAVDPLA
+STSRILDPQYVGQEHYDVATRVKQILQKNKELQDIIAILGVDELSEEDKITVSRARKMEQ
+FLSQNTYTAKQFTGVEGSTVPIKDTVEGFKAIADGDLDHVAEQAFYNVGGLDDVEREWAK
+IQAEG
+>MHAAABBN_00528
+MTATITDQGTGTPTGGATGRVSRVIGPVIDAEFPANAMPEIYNALTTEIDLNGQRRTVTF
+EVAQHLGDNMVRAISLQSTDGLVRGTDVVDTGAPISVPVGDAVKGHIFNVLGETLDMPAS
+QLQAEDRWPIHRPAPNFASLEGSTEMLETGIKVIDLLTPYIKGGKIGLFGGAGVGKTVLI
+QEMITRVARNFGGTSVFAGVGERTREGNDLWVEMEEADVLKDTALVFGQMDEPPGTRLRV
+ALSALTMAEYFRDVQNQDVLLFIDNIFRFSQAGSEVSTLLGRMPSAVGYQPNLADEMGVL
+QERITSTRGHSITSMQAVYVPADDYTDPAPANVFAHLDATTNLTRDLASRGLYPAVDPLA
+STSRILDPQYVGQDHYDVAIRVKQILQKNKELQDIIAILGVDELSEEDKITVGRARKIEQ
+FLSQNTYTAKQFTGVEGSTVPVKDTVEGFKAIADGDLDHVAEQAFYNVGGLDDVEREWAK
+IQAEG
+>LFPAFLNI_00764
+MTATITDQGTGTPTGGATGRVSRVIGPVIDAEFPANAMPEIYNALTTEIDFNGQRRTVTF
+EVAQHLGDNMVRAISLQSTDGLVRGTDVVDTGAPISVPVGDAVKGHIFNVLGETLDMPTS
+QLQAEDRWPIHRPAPNFASLEGSTEMLETGIKVIDLLTPYIKGGKIGLFGGAGVGKTVLI
+QEMITRVARNFGGTSVFAGVGERTREGNDLWVEMDEADVLKDTALVFGQMDEPPGTRLRV
+ALSALTMAEYFRDVQNQDVLLFIDNIFRFSQAGSEVSTLLGRMPSAVGYQPNLADEMGVL
+QERITSTRGHSITSMQAVYVPADDYTDPAPANVFAHLDATTNLTRDLASRGLYPAVDPLA
+STSRILDPQYVGQDHYDVAIRVKQILQKNKELQDIIAILGVDELSEEDKITVGRARKIEQ
+FLSQNTYTAKQFTGVEGSTVPVKDTVEGFKAIADGDLDHVAEQAFYNVGGLDDVEREWAK
+IQAEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001459.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001459.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f6dcd5b8d79dd1094547647dd23e9a0604595e5c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001459.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_02136
+MAELTINADDVRNALNDFAASYEPSGTDRTEVGRVISAADGIARVEGLPSVMANELLRFE
+NGIQGLAQNLDAREIGVVVLGEFQEIREGMEVQRTGEILSVPVGDGFMGRVVDPLGQPID
+DLGPIQAEGRRALELQAPTVTERKSVHEPLQTGMKAIDAMIPIGRGQRQLIIGDRQTGKT
+AIAVDTILNQKANWESGDVDKQVRCVYVAVGQKASTIAGVRATLEEHGALEYTTIVASPA
+SDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLLRRPPGREAYPG
+DVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISITDGQIFLQSDL
+FNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSMFASDLDPATRR
+QLARGERLMELLKQPQYSPYPVEEQVVSIWAGSKGHLDEVPVEDVLRFEREFIDHLRRRG
+SVLTDIGSTGKLEDGTVSALESEIAEFKKGFQSSEDGGVHAGHEEHRAIEQDQVAQEQIT
+KQKR
+>MOLHKGIG_00795
+MITKHREQGLQMAELTINADDVRNALNEFAASYEPSGTDRTEVGRVISAADGIARVEGLP
+SVMANELLRFENGIQGLAQNLDTREIGVVVLGEFQEIREGMEVQRTGEILSVPVGDAFLG
+RVVDPLGQPIDDLGPIEAEGRRALELQAPTVTERKSVHEPLQTGMKAIDAMIPIGRGQRQ
+LIIGDRQTGKTAIAVDTILNQKANWESGDVEKQVRCVYVAVGQKASTIAGVRATLEEHGA
+LEYTTIVASPASDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLL
+RRPPGREAYPGDVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISI
+TDGQIFLQSDLFNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSM
+FASDLDPATRRQLARGERLMELLKQPQYSPYPVEEQVVSIWAGSKGHLDEVPVQDVLRFE
+REFIDHLRRHTSVLTDIASTGKLEDGTVSALESAVAEFSKGFQSSEEGGVRAGHEEHRAI
+EQDQVAQEQITKQKR
+>NAFOICDF_02029
+MITKHREQGLQMAELTINADDVRNALNDFAASYEPSDTTRTEVGRVISAADGIARVEGLP
+SVMANELLRFSNGILGLAQNLDAREIGVVVLGEFQDIREGMEVQRTGEILSVPVGDGFLG
+RVVDPLGHPLDDLGPIEAEGRRALELQAPTVTQRKSVHEPLQTGMKAIDAMIPIGRGQRQ
+LIIGDRQTGKTAIAVDTILNQKANWQTGDVDKQVRCVYVAVGQKASTIAAVRSTLEEHGA
+LEYTTIVASPASDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLL
+RRPPGREAYPGDVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISI
+TDGQIFLQSDLFNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSM
+FASDLDPATRRQLARGERLMELLKQPQYSPYPVEDQVVAIWAGSKGHLDDVAVEDVLRFE
+REFLDHLRRKDVVLGEIASTGKLEDETVSALEREIDAFKKGFQASGHDGVAAGHEEHAAI
+GQDQVVQEQITKQKR
+>MHAAABBN_00526
+MITKHREQGLQMAELTINADDVRNALNDFAASYEPSGTDRTEVGRVISAADGIARVEGLP
+SVMANELLRFENGIQGLAQNLDTREIGVVVLGEFQEIREGMEVQRTGEILSVPVGDAFLG
+RVVDPLGQPIDDLGPIEAEGRRALELQAPTVTERKSVHEPLQTGMKAIDAMIPIGRGQRQ
+LIIGDRQTGKTAIAVDTILNQKANWESGDVEKQVRCVYVAVGQKASTIAGVRATLEEHGA
+LEYTTIVASPASDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLL
+RRPPGREAYPGDVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISI
+TDGQIFLQSDLFNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSM
+FASDLDPATRRQLARGERLMELLKQPQYSPYPVEEQVVSIWTGSKGHLDEVPVQDVLRFE
+REFIDHLRRHTSVLTDIASTGKLEDGTVSALESAVAEFSKGFQSSEDGGVQAGHEEHRAI
+EQDQVAQEQITKQKR
+>LFPAFLNI_00762
+MITKHREQGLQMAELTINADDVRNALNDFAASYEPSGTDRTEVGRVISAADGIARVEGLP
+SVMANELLRFENGIQGLAQNLDTREIGVVVLGEFQEIREGMEVQRTGEILSVPVGDAFLG
+RVVDPLGQPIDDLGPIEAEGRRALELQAPTVTERKSVHEPLQTGMKAIDAMIPIGRGQRQ
+LIIGDRQTGKTAIAVDTILNQKANWESGDVEKQVRCVYVAVGQKASTIAGVRATLEEHGA
+LEYTTIVASPASDPAGFKYLAPYAGSAIGQHWMYGGKHVLIIFDDLSKQAEAYRAVSLLL
+RRPPGREAYPGDVFYLHSRLLERCAKLSDEMGAGSMTGLPIIETKANDVSAYIPTNVISI
+TDGQIFLQSDLFNANQRPAVDVGISVSRVGGAAQVKAMKKVSGTLKLDLAQYRDQQAFSM
+FASDLDPATRRQLARGERLMELLKQPQYSPYPVEEQVVSIWAGSKGHLDEVPVQDVLRFE
+REFIDHLRRHTSVLTDIASTGKLEDGTVSALESAVAEFSKGFQSSEDGGVQAGHEEHRAI
+EQDQVAQEQITKQKR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001463.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001463.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fdad48e76959cc5e1de878b9ea48d6c1a0e8ebf4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001463.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_02140
+MLTLVLANASFVPPTISDGNLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP
+QLVPGKAQWLAESGYSFVRNGIAKDILGEKNFRQWVPLLFAIFFFVLLNNLFGAIPVLQL
+PSFSHAGAAYGIALIVYAIWIGVGLKRHGIRYLKLAVVPSGVPSWILPLLVPLEIISNFI
+VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVIIGSVALYFLELL
+IMYLQAFVFTLLTAIYIQGAIDANDH
+>MOLHKGIG_00791
+MLTLVLANASFVPPTISDGHLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP
+RLVPGKAQWLAESGYSFVRNDIAKDILGEKNFKQWVPLLFAIFFFVLLNNLFGAIPVLQL
+PTFSHAGAAYGLALIVYAIWIGVGIKRHGVRYLKLAVVPSGVPGWILPLLVPLEIISNFI
+VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVILGSVALYFLELL
+IMYLQAFVFTLLTAIYIQGAIDANDH
+>NAFOICDF_02033
+MLPLVLANAEFVPPSVSDAHLPDLLPWGAEYGTGFGKQMLLVLLSVVLITGFFAWAMRKP
+KLVPGRAQWIAESGYAFVRNGIGRDVMGEKHFKQWVPLLFAIFFFVLLNNLFGAIPLLQM
+PSFSHAGSAYAIALIVYAIWIGVGVKHHGVKYFKLAVVPSGVPGWILPLLVPLEFISNFI
+VRPLTHSLRLMAVMLAGHMIVMLAGAGAAFLITQTGNPLLAGTGVLVILASVALYLLEIL
+LMYLQAFVFTLLTALYIQGAIDANDH
+>MHAAABBN_00522
+MLTLVLANASFVPPTISDGHLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP
+RLVPGKAQWLAESGYSFVRNDIAKDILGEKNFKQWVPLLFAIFFFVLLNNLFGAIPVLQL
+PTFSHAGAAYGLALIVYAIWIGVGIKRHGVRYLKLAVVPSGVPGWILPLLVPLEIISNFI
+VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVILGSVALYFLELL
+IMYLQAFVFTLLTAIYIQGAIDANDH
+>LFPAFLNI_00758
+MLTLVLANASFVPPTISDGHLPEIFPWGAEYGTGFGKQMLLVLLSVVLITAFFAWAMRRP
+RLVPGKAQWLAESGYSFVRNDIAKDILGEKNFKQWVPLLFSIFFFVLLNNLFGAIPVLQL
+PTFSHAGAAYGLALIVYAIWIGVGIKRHGVRYLKLAVVPSGVPGWILPLLVPLEIISNFI
+VRPLTHSLRLMATMLSGHMIVMLAGAGAAYLITQTGSLALQGTGILVILGSVALYFLELL
+IMYLQAFVFTLLTAIYIQGAIDANDH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001471.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001471.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c4e7340e46061cd33ed6525fb8eed741793750a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001471.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_02148
+MPQHTDAPTALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAVRNTGATRDW
+QADPALYTTDAEALVDGADVVIELMGGIEPARTLILRALAAGTSVVTGNKALLAQHGEEL
+YAAAAATGAQLSFEAAVAGAIPILRPLRDSLAGDRVTRVMGIANGTTNYILDKMDSEGAG
+FDEALAEAQRLGYAEADPTADVEGHDAAAKAAILATLAFGAPYTLDQVAVSGITAITAED
+NEAAADAGYVIKLLAIAERARAADSAEGAVLRVHPTLLPREHPLASVRGAFNAVFVEAEN
+AGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVAELPALDPAEAVTSCLV
+VLRVADEPGVLRRVAGVFEEQGVSIETLRQVQSDRDDAPGASLRLITHRARQRDLDATVE
+ALAALDAVHEVASVLRVEGN
+>MOLHKGIG_00782
+MPQHTDAPTALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAVRDTGATRDW
+QADPALYTTDAEALVDGADVVIELMGGIEPARTLILRALAAGTSVVTGNKALLAQHGEEL
+YAAAAATGAQLSFEAAVAGAIPILRPLRDSLGGDRVTRVMGIANGTTNFILDRMDSEGAD
+FDDALAEAQRLGYAEADPTADVEGHDAAAKAAILATIAFGAPYTLDQVAVAGITAITAED
+NAAAAEAGYVIKLLAIAERGRAADGAQGAVLRVHPTLLPREHPLASVRGAFNAVFVEAEN
+AGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVTALPALDPAEAHTSFMV
+VLRAADQPGVLRRVAGVFEEHGVSIETLRQVPSEREDAPGASLRLITHRARQRDLDATVE
+ALAALDVVHEVASVLRVEGN
+>NAFOICDF_02042
+MAEPTASAAQTAPAPARDALRVALLGGGTVGSQAARILTEDAAVLADRVGVRLELTGIAV
+RDTAAVRDWQADPSLYTTDAEALVDGADLVIELMGGIEPARSLIRRALQVGTSVVTGNKA
+LLAEHGEELYRLASETGAQLSFEAAVAGAIPILRPLRDSLSGDTVNRVMGIANGTTNFIL
+DRMDTEGASFADALAEAQRLGYAEADPTADVGGFDAAAKAAILATLAFGSSYTLDQVSVE
+GITEVTAEDNAAAADAGYVIKLLAIAERDTARDGTAGAILRVHPTLIPREHPLGSVRGAY
+NAVFVEAENAGQLMFYGPGAGGAPTASAVMGDAVAIGQRIVRGGPARLRTPVAALPALDV
+SEARTSCMVVLRVADQPGVLRRVAGVFEEHGVSIETLRQVQGADDAAGASLRLITHRARQ
+RDLDDVVAELTTLDAVHEVASVLRVEGN
+>MHAAABBN_00513
+MPQHTDAPTALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAVRDTGATRDW
+QADPALYTTDAEALVDGADVVIELMGGIEPARTLILRALAAGTSVVTGNKALLAQHGEEL
+YAAAAATGAQLSFEAAVAGAIPILRPLRDSLGGDRVTRVMGIANGTTNFILDRMDSEGAD
+FDDALAEAQRLGYAEADPTADVEGHDAAAKAAILATIAFGAPYTLDQVAVAGITAITAED
+NAAAAEAGYVIKLLAIAERGRAADGAQGAVLRVHPTLLPREHPLASVRGAFNAVFVEAEN
+AGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVTALPALDPAEAHTSFMV
+VLRAADQPGVLRRVAGVFEEHGVSIETLRQVPSEREDAPGASLRLITHRARQRDLDATVE
+ALAALDVVHEVASVLRVEGN
+>LFPAFLNI_00749
+MPQHTDAPTALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAVRDTGATRDW
+QADPALYTTDAEALVDGADVVIELMGGVEPARTLILRALAAGTSVVTGNKALLAQHGEEL
+YAAAAATGAQLSFEAAVAGAIPILRPLRDSLGGDRVTRVMGIANGTTNFILDRMDSEGAD
+FDDALAEAQRLGYAEADPTADVEGHDAAAKAAILATIAFGAPYTLDQVAVAGITAITAED
+NAAAAEAGYVIKLLAIAERGRAADGAQGAVLRVHPTLLPREHPLASVRGAFNAVFVEAEN
+AGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVTALPALDPAEAHTSFMV
+VLRAADQPGVLRRVAGVFEEHGVSIETLRQVPSEREDAPGASLRLITHRARQRDLDATVE
+ALAALDVVHEVASVLRVEGN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001475.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001475.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dec84ec6a91c375346124bab32667aa6b45b66a2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001475.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_02152
+MAEHRTPPATPAIPPLRIGGYDLAARLIMGTGGITDLTALEGALVASGTTLTTVALRRWS
+ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP
+DVVETLEATELLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL
+ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG
+FHARRAGRIPRREHALASSPMAGRVTAEEDER
+>MOLHKGIG_00778
+MAEHRTPPAAPAIPPLRIGGYDLASRLIMGTGGITDLTALEGALVASGTTLTTVALRRWS
+ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP
+DVVETLEATERLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL
+ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG
+FHARRAGRIPRREHALASSPMAGRVTAEEDER
+>NAFOICDF_02047
+MAPHDTTERRRAREASTAVPPLRIGGYELSSRLIMGTGGITDLAALEGALVASETTLTTV
+ALRRWSTDARDGLIALLDRLGIDVLPNTAGCRTARDAVLTARLGREALETELVKVEVIAD
+DRTLLPDVVETLDATEQLAAAGFTVLAYTSDDPAMALRLEHAGAAAVMPLGSPIGSGLGI
+LNRTNLELIVSRAGVPVVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACR
+LALEAGYHAHRAGRIPRRLHALASSPMAGRIGGAEERA
+>MHAAABBN_00509
+MAEHRTPPAAPAIPPLRIGGYDLASRLIMGTGGITDLTALEGALVASGTTLTTVALRRWS
+ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP
+DVVETLEATERLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL
+ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG
+FHARRAGRIPRREHALASSPMAGRVTAEEDER
+>LFPAFLNI_00745
+MAEHRTPPAAPAIPPLRIGGYDLASRLIMGTGGITDLTALEGALVASGTTLTTVALRRWS
+ADTRDGLVALLDRLGIDVLPNTAGCYTARDAVLTARLGREALETDLVKVEVIADERTLLP
+DVVETLEATERLAADGFTVLAYTSDDPAMALRLEQAGAAAVMPLGSPIGSGLGILNRAHL
+ELIVSRASVPIVLDAGVGTASDVALAMEAGCDAVLAASAITRAAEPARMAHACRLALEAG
+FHARRAGRIPRREHALASSPMAGRVTAEEDER
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001482.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001482.fa
new file mode 100644
index 0000000000000000000000000000000000000000..246ef23e51cacdf79c8137cd860749b5aac7384e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001482.fa
@@ -0,0 +1,29 @@
+>ACLBLIBL_02160
+MTKEHRTDHDAGDDAGPAAPVRSAAGAAEPPAGVVVGEDGRARAPWADRDPLLRAYYDEE
+WGVPVTDERGLFERLVLEAFQSGLSWRTVLAKRPRFREAFAGFDPDAVAGFGPERVEELL
+QDAGIIRNRAKVEAAIANAQAVVGMRDEPWTPLHPGSPGAGPGWDGPGDRPDRGLAGLVW
+AHQPAATPRPGTVAEVPSASDESRALATALKARGCRFVGPTTCFALMEAAGIVDTHLLSS
+WRRGASGIWE
+>MOLHKGIG_00770
+MSAHHADDGLPAPVSTLAEDPPADGRQAPPSGVVVGEDGRARPPWAARDPLLREYYDTEW
+GLPVTDERGLFERLVLEAFQSGLSWRTVLAKRPRFREVFAGFDPDAVAAFGDAEVEALLA
+DPGIIRNRRKIEAAVANAQAVVGMRGERFAPLHPGAPGAGPAWHGDGDRPARGLPGLVWA
+HQPAATPRPETVAQVPSTSDESRALARALKAHGCRFVGPTTCFALLEAAGIVDTHLLGSW
+RRGASGIWE
+>NAFOICDF_02056
+MDEENSEAAGLVLGADGRARAAWAAADPLLRDYYDAEWGLPVTDERGLFERLTLEAFQSG
+LSWRTVLAKRPRFREVFAGFDPDAVAAFGAVEVEALMADAGIIRNRRKIDAALANARAVV
+GIRDEVFAPLHPGSPGAGPAWDGEGDRPGTGLPGLVWAHQPAQTPTPRTIGEVPSASPES
+TALAKALKARGCRFVGPTTCFALLEAAGVVDTHLVSSWRRGASGIWA
+>MHAAABBN_00501
+MSAHHADDGLPAPVSTLAEDPPADGRQAPPSGVVVGEDGRARPPWAARDPLLREYYDTEW
+GLPVTDERGLFERLVLEAFQSGLSWRTVLAKRPRFREVFAGFDADAVAAFGDAEVEALLA
+DPGIIRNRRKIEAAIANAQAVVGMRGERFTPLHPGSPGAGPAWHGDGDRPARGLAGLVWA
+HQPAATPRPETVAQVPSASEESRALARALKAHGCRFVGPTTCFALMEAAGVVDTHLLGSW
+RRGASGIWE
+>LFPAFLNI_00734
+MSAHHADDGLPAPVSTPAEDPPADGRQAPPSGVVVGEDGRARPPWAARDPLLREYYDTEW
+GLPVTDERGLFERLVLEAFQSGLSWRTVLAKRPRFWEVFAGFDADAVAAFGDAEVEALLS
+DPGIIRNRRKIEAAIANARAVVGMRGERFAPLHPGAPGAGPAWHGDGDRPARGLPGLVWA
+HQPAATPRPETVAQVPSTSDESRALARALKAHGCRFVGPTTCFALLEAAGIVDTHLLGSW
+RRGASGIWE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001484.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001484.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54ec287ec9abbd8c9aa9931c29bac17685e8316c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001484.fa
@@ -0,0 +1,121 @@
+>ACLBLIBL_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
+>MOLHKGIG_00766
+MTQTPPPSTPAAQPSATPHDAVAITFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKT
+TQLPKMCLALGLGEAGSIGHTQPRRIAARSVAERIAQELGEEIGQTVGYQVRFTAQTSKA
+TRVKVMTDGILLAEIPHDPQLRRYSVIIVDEAHERSLNIDFLLGYLRNLLPQRPDLKVII
+TSATIDPERFARHFGRPLAEGEDHADAVEADDGGRVVPAPIIEVSGRTYPVEIRYRPLTD
+EPSPDDPEDDADDAAETRDPLDAIGDAVLELASEPPGDILVFLPGEREIREAADHLTGVV
+AGTTRLAGTEILPLFGRLSMAEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDT
+GTARISRYSHRTKVQRLPIERVSQASANQRSGRSGRTSDGIAIRLYSEEDYLSRPEFTDP
+EILRTSLASVILQMLSLGVARTPGDVKEFPFVQPPDGRQVTDGATTLTELGALEAGGARA
+GTITRVGRRLARLPVDPRLGRMILEAGERGCVREVMVIAAALTIQDPRERPTEQREAADE
+LHRRFADENSDFSAILNLWAYLRERQQELSGSQFRKLCRREHINWLRVQEWQDLVRQLRQ
+LAKDVGLTVEAGPVDPVGRHEAVHKSLLTGLLAQIGAYDERRREYAGARGTRFAVFPGSA
+LFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEVAGHLVKRAYNEPHWSRRAGSVVAR
+EKVTLFGVTLIPDRSVRYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDAL
+ETRLRRRDLRIGDEDLFAFYDARIPANVVSERHFDAWWKKARQEQPDLLDLDVAALLTAD
+AEDLDTDAFPTTFSYPMPGGDVELDLEYTFDPTGAAGTDGVTVAVPILLLNQVSPGPFAW
+LVPGLRVELVTALIKALPKAVRKNLVPAPDVAQQLVADLEAHADPLRDELPEALSAAVRR
+VRGVVVEPGLWAPDAVPLHLRMDYRVVDARGAVMGAGQDLPALQARLAQANRSAIAARLA
+GTDDPASARPGPRGTGRGGRAQADARAGAEGRRRPEGPGRSGATPAFEERHRLTSWSIGT
+VPKTVSTAAGARGPAITGYPSLVPETTPDGGPAAGLTVARSAEDQAAWHRAGVIRLLLAT
+LPSPQRYVLDHLDNREKLTFTQNPHGSVDSLVADCTQAAVDRLVGDELPFDEAAFRALFD
+RVRADLIDTVFAVTSLVEQVLSRAAQVRRRLKGSVSLALAPALSDVKAHLEQLVFPGFVA
+ATGWERLQHLPRYLQGMLTRLDRLDAGGHLQRDGQHMAVVQGLEDEFDAAVAAHRARFAG
+TPVPAELERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALARATRA
+>NAFOICDF_02059
+MTDFPQPPAAAPVITFPAHLPVAERREEIMDAVRENQVVIVAGETGSGKTTQLPKMLLAL
+GLGGAGVVGHTQPRRIAARSVAERIAEELGEDVGRTVGYQVRFTAQTSTRTRVKVMTDGI
+LLAEIPHDPDLRKYSAIIVDEAHERSLNIDFLLGYLKRLLPRRPDLKVIITSATIDPERF
+ARHFGTEDEPAPIIEVSGRTYPVEIRYRPLTEEPSPDDPDDDADDHAETRDPIDAVGDAV
+LELAGEAPGDILVFFPGEREIREAADHLAGVVASTPRLAGTEVLPLYGRLSMAEQHRVFG
+RAGAGVRRRIVLATNVAETSLTVPGIKYVIDTGTARISRYSHRTKVQRLPIERISQASAN
+QRSGRSGRTSDGIAIRLYSEEDFLSRPEFTDPEILRTSLASVILQMLSLGVADTPREVMD
+FPFVQPPDSRQVTDGAATLTELGALHADAPTRGGGRGRGKGAGNRSAAGTITDIGRRLAR
+LPVDPRLGRMILESGRRDCTREVMVLAAALTIQDPRERPVEQRQAADELHARFADDRSDF
+SAYLNLWEYLREQQRELSGSQFRKLCRREHINWLRVHEWQDLVRQLRQLSKDVGVSVHPG
+PVDPVGKHDDVHKSLLTGLLSQIGAYDERRREYQGARNTRFAVFPGSALFKKRHPFVMAA
+ELVETSRLWARAVARIEPEWIEEVAGDLVLRSYAEPHWSRKAGAAVAMEKVTLFGVTIVP
+ERSVRYGRIDPVLSRELFLRHALVEGDWRTRHRFFARNRRLLEEVDELETRLRRRDLRVG
+DEELFAFYDARVPANVVSERHFDAWWKKARQETPDLLDLDLDALLTQDADELDTDAFPTA
+FRYPLPGGDADLALDYTYDPTGASGTDGVTVAVPILLLNEVAPGPFAWLVPGLRGELVTA
+LIKALPKAVRKNLVPAPDVARLLVEDLDAHADPLRDELPAALSSAVRRVRGAVVEPELWR
+LDAVPDHLRMDYRVVDARGAVMGAGQDLPALQARLAKANRSAIAARLAGTDDPRNARPGQ
+GAGRGRGKTEPKGGDGGARGPAADTGRPGPSRTADGAPAFRERHGLTSWTVGEVPRQITT
+APGDRGPAITGYPSLIPETTADGSPAAGLVVARSAQDQAAWHRAGVIALLLATLPSTHRY
+VLDHLDNKEKLTFTQNPHGSVESLVRDATHVAVDRLVGTDLPFTEVGFRALFDRVRADLI
+DTVFAVTALVEQVLSRAAEVRRRLKGGVSLAMAPAKSDVQAHLEQLVFPGFLAATGWQQL
+QHLPRYVQGMLARLDKLDAGGHLQRDGQHMAVVQGLEDEFDAAVTAHRSRFPGTPVPAEL
+ERVRWLLEELRVSYFAQELGTAVSVSEKRVRQALAQARQG
+>MHAAABBN_00496
+MTQTPPPSTPAAQPSATPHDAVAITFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKT
+TQLPKMCLALGLGEAGSIGHTQPRRIAARSVAERIAQELGEEIGQTVGYQVRFTAQTSKA
+TRVKVMTDGILLAEIPHDPQLRRYSVIIVDEAHERSLNIDFLLGYLRNLLPQRPDLKVII
+TSATIDPERFARHFGRPLAAGEDHADAVEADDGGRVVPVPIIEVSGRTYPVEIRYRPLTD
+EPSPDDPEDDADDAAETRDPLDAIGDAVLELAAEPPGDILVFLPGEREIREAADHLTGVV
+AGTTRLAGTEILPLFGRLSMAEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDT
+GTARISRYSHRTKVQRLPIERVSQASANQRAGRSGRTSDGIAIRLYSEEDYLSRPEFTDP
+EILRTSLASVILQMLSLGVARTPGDVKEFPFVQPPDGRQVTDGATTLTELGALEAGGARA
+GTITRVGRRLARLPVDPRLGRMILEAGERGCVREVMVIAAALTIQDPRERPTEQREAADE
+LHRRFADENSDFSAILNLWAYLHERQKELSGSQFRKLCRREHINWLRVQEWQDLVRQLRQ
+LAKDVGLTVEAGPVDPVGRHEAVHKSLLTGLLSQIGAYDERRREYAGARGTRFAVFPGSA
+LFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEVAGHLVKRAYNEPHWSRRAGSVVAR
+EKVTLFGVTLIPDRSVRYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDAL
+ETRLRRRDLRIGDEDLFAFYDARIPGNVVSERHFDAWWKKARQDQPDLLDLDVAALLTAD
+AEDLDTDAFPTTFAYPMPGGDVELDLEYTFDPTGAAGTDGVTVAVPILLLNQVSPGPFAW
+LVPGLRVELVTALIKALPKAVRKNLVPAPDVAQQLVADLEAHADPLRDELPDALSAAVRR
+VRGVVVEPGLWAPDAVPLHLRMDYRVVDARGAVMGAGQDLPALQARLAQANRSAIAARLA
+GTDDPASARPGPRGTGRGGRAPADARAGAEGHRRPEGPGRSGATPVFEERHGLTSWSIGT
+VPKTVSTAAGARGPAITGYPSLVPETTPDGGPAAGLTVARSAEDQAAWHRAGVIRLLLAT
+LPSPQRYVLDHLDNREKLTFTQNPHGSVDSLVADCTQAAVDRLVGDELPFDEAAFRALFD
+RVRADLIDTVFAVTSLVEQVLSRAAQVRRRLKDSVSLALAPALSDVKAHLEQLVFPGFVA
+ATGWERLQHLPRYLQGMLTRLDRLDAGGHLQRDGQHMAVVQGLEDEFDAAVAAHRARFAG
+TPVPAELERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALARATRA
+>LFPAFLNI_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/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001488.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001488.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d0fd293bdcae8946a9ce54886e8f31d18bb99054
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001488.fa
@@ -0,0 +1,31 @@
+>ACLBLIBL_02169
+MDWLIEPFLLGFQQRALVGGLIAAALCAVVGTWLVLRGMSFFGDAFVHGVMPGIALSVVL
+GFDAHLGAALAALVMLAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISLSDSYTGSLT
+AILFGDALGVTWEGIVRQAVIAALVLVLALVLYRPLMALSFSPAKARSLGMRPRLTHALL
+LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRTVPQMMALAVLLGAAGVTIGLVLS
+YHLGTAASATMALVPIAMFFVVLAGRAGLRALRSRRVRADRRRAVVETPSRRSVSP
+>MOLHKGIG_00761
+MDWLLEPFQMGFQQRALVGGLIAVVMCSVVGTWLVLRGMSFFGDAFVHGVLPGIALAVVT
+GGSPHLGAAVAAVVMMAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISKSDSYTGSLT
+SILFGDVLGVSVDGIVTQAVIAVVVIALALLLYRPLLALSFSEVKARSLGMRPGLTHTLL
+LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRSVPQMMLVSVVIGAACVVTGLTLS
+YRLGTAGSATMALMPILLFFVVLAVRAAVLALLGRHVRSRAQRERETPVVALPGAEVAR
+>NAFOICDF_02064
+MDWLIDPFLLGFQQRALLGGLIAALMCSAVGTWLVLRGMSFFGDAFVHGVLPGIALAVLL
+GGSPHLGAALAAVLMMGGISLVHRTTTLKEDTAIGLLFVGMMALGVVIISLSSSYTGSLT
+AILFGDALGVTPENLLVQAAIGVVVVVLALVLYRPLLALSFSEAKSQALGMRPRLTHTLL
+LVLIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRTVPQMMALSAGIGALSVVAGLVLS
+YHWGTAASATMALVPVVLFFVVLLGRSAVQAAAGRRRRTRGAASAPTPAGDDDAESRRET
+EGSPAR
+>MHAAABBN_00491
+MDWLLEPFQMGFQQRALVGGLIAVVMCSVVGTWLVLRGMSFFGDAFVHGVLPGIALAVVT
+GGSPHLGAAVAAVVMMAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISKSDSYTGSLT
+SILFGDVLGVSVDGIVTQAVIAVVVIALALLLYRPLLALSFSEVKARSLGMRPGLTHTLL
+LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRSVPQMMLVSVVIGAACVVTGLTLS
+YRLGTAGSATMALMPILLFFVVLAVRAAVLALLGRHVRSRAQREQEAPVVALPGAEAPR
+>LFPAFLNI_00725
+MDWLLEPFQMGFQQRALVGGLIAVVMCSVVGTWLVLRGMSFFGDAFVHGVLPGIALAVVT
+GGSPHLGAAVAAVVMMAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISKSDSYTGSLT
+SILFGDVLGVSVDGIVTQAVIAVVVIALALLLYRPLLALSFSEVKARSLGMRPGLTHTLL
+LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRSVPQMMLVSVVIGAACVVTGLTLS
+YRLGTAGSATMALMPILLFFVVLAVRAAVLALLGRHVRSRAQREQEAPVVALPGAEAAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001492.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001492.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4acacc27f0f5e96e53620ee2fa3647e2915b39f2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001492.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_02173
+MRFLTSPTVDLTYNDVFLVPSHSEVTSRLDVDIAPDDGTGATIPLVSANMTAVTGRRMVE
+TMARRGGLGILPQDIPVEVIAEVVRRVKSAHPVADTALTVGPQDTVLDLLHLVDRRNHGA
+VCVVDADGGLLGVVRPRDCEDVDRFASAASVMQPASVTLTPAELGEAGGADGGQALRAAF
+DRLNAAGQDMAPVVEPAAGSAAPALRGVVTAAGLLRSSLFTPSLDDAGRLRVGAALGVNG
+AVGDKAAALVEAGVDVLVVDTAHGHQQSMLDALAAVRALDAPVPVVAGNVVSADGVRDLV
+EAGADIVKVGVGPGAMCTTRMQTAVGRPQFSAVLECSAAARDLGARVWADGGVKHPRDVA
+LALAAGASSVMIGSWFAGTLESPGDLVHGPDGRRYKESFGMASARAVQHRTRHEDAFTKA
+RKAMFEEGISSSRMYVDPRRPSVEDLIDTITSGVRSSLTYAGAQDLAQFRERAVVGVQSA
+AGYEEGRPVASSW
+>MOLHKGIG_00757
+MRFLTDPAVDLTYNDVFLVPSHSDVASRMDVDIAPDDGTGATIPLVSANMTAVTGRRMVE
+TMARRGGLGILPQDIPADVIRDVVRRVKAAHPVADTALTVGPQDTVLDLLHLVDRRNHGA
+VCVVDAHGGLLGVVRPQDCEDVDRFTSAASVMHPPAVTLTLAELGGTDGAPDKDALRAAF
+ERLHAAHQEMAPVVDPAVGTAAPVLRGVVTAAGLLRSSLFTPGLDDDGRLRVGAAVGING
+AVGEKAAVLVEAGVDVLVVDTAHGHQQTMLDALAAVRALDPGVPVVAGNVVSGDGVRDLV
+AAGADIVKVGVGPGAMCTTRMQTAVGRPQFSAVLECAAAARELGARVWADGGVKHPRDVA
+LALAAGASSVMIGSWFAGTLESPGDLVHGPDGRRYKESFGMASARAVQHRTRHEDAFTKA
+RKAMFEEGISSSRMYVDPRRPSVEDLLDTITSGVRSSLTYAGAHDLAEFRERAVVGLQSA
+AGYEEGRPVASSW
+>NAFOICDF_02068
+MRLMHEPAVDLTYNDVFLVPSHSEVGSRTAVDIAPDDGTVGSVPLVSANMTAVTGRRMAE
+TLARRGGLGVLPQDVPVDVVAKTVAAVKAAHAVADTALTVDAHATVLDVLHLVDRRAHGA
+VCVVDDDGRLLGVAGAEDCGDVDRFASVVSVMRTPSVLLSPADLEGPDAPRAAFEVLHAA
+GRPLAPVVEDPVADRPVLRGVVTGQGLVRSSLAAPALDASGRLQVGAALGVNGDVGSRAA
+ALLAAGADVLVVDTAHGHQRVMRDALAAVRALDPEVPVVAGNVVTAEGVRDLVAAGADVV
+KVGVGPGAMCTTRMQTAVGRPQFSAVLECAAAAREVGARVWADGGVKHPRDVALALAAGA
+SQVMIGSWFAGTLESPGDLVQGSDGRRYKESFGMASARAVEHRTRDEDAFSRARKAMFEE
+GISSSRMYVDPRRPSVEDLVDGITAGLRSSLTYAGAANLAQFRERAVVGVQSAAGYEEGR
+PVPASW
+>MHAAABBN_00487
+MRFLTDPAVDLTYNDVFLVPSHSDVASRMDVDIAPDDGTGATIPLVSANMTAVTGRRMVE
+TMARRGGLGILPQDIPADVIRDVVRRVKAAHPVADTALTVGPQDTVLDLLHLVDRRNHGA
+VCVVDAHGGLLGVVRPQDCEDVDRFTSAASVMHPPVVTLTLAELGGTDGAPSKDALRAAF
+ERLHAAHQEMAPVVDPAVGTAAPVLRGVVTAAGLLRSSLFTPGLDDDGRLRVGAAVGING
+AVGEKAAVLVEAGVDVLVVDTAHGHQRTMLDALAAVRALDPGVPVVAGNVVSGDGVRDLV
+AAGADIVKVGVGPGAMCTTRMQTAVGRPQFSAVLECAAAARELGARVWADGGVKHPRDVA
+LALAAGASSVMIGSWFAGTLESPGDLVHGPDGRRYKESFGMASARAVQHRTRHEDAFTKA
+RKAMFEEGISSSRMYVDPRRPSVEDLLDTITSGVRSSLTYAGAHDLAEFRERAVVGLQSA
+AGYEEGRPVASSW
+>LFPAFLNI_00721
+MRFLTDPAVDLTYNDVFLVPSHSDVASRMDVDIAPDDGTGATIPLVSANMTAVTGRRMVE
+TMARRGGLGILPQDIPADVIRDVVRRVKAAHPVADTALTVGPQDTVLDLLHLVDRRNHGA
+VCVVDAHGGLLGVVRPQDCVGVDRFASATSVMHPPAVTLTLAELGGTDGAPSKDALRAAF
+ERLHAAHQEMAPVVDPAVGTAAPVLRGVVTAAGLLRSSLFTPGLDDDGRLRVGAAVGING
+AVGEKAAVLVEAGVDVLVVDTAHGHQRTMLDALAAVRALDPGVPVVAGNVVSGDGVRDLV
+AAGADIVKVGVGPGAMCTTRMQTAVGRPQFSAVLECAAAARELGARVWADGGVKHPRDVA
+LALAAGASSVMIGSWFAGTLESPGDLVHGPDGRRYKESFGMASARAVQHRTRHEDAFTKA
+RKAMFEEGISSSRMYVDPRRPSVEDLLDTITSGVRSSLTYAGAHDLAEFRERAVVGLQSA
+AGYEEGRPVASSW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001493.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001493.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9e2d290fb18e025b82a61d82aad30b0627500c1a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001493.fa
@@ -0,0 +1,110 @@
+>ACLBLIBL_02174
+MLRKRRYTVPELTSDRLAQEFPGNERLVAEIYRKYRADSGSVDRQWAQIFARLEASAPAP
+AEKAPAQAAAKAAPKAEPQAEAKVTEPKAKPAPARGAQPKETSTSTGPKVKKTPAAQAVP
+SEPADPSKDAAKEEKQEKATVLKGMAKAVATNMDASLSMPTATTVRDVPAKVLIDNRVVI
+NSHLARTRGGKVSFTHLIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLP
+RPDGSRSLVVPNVKAAETLDFRGFWQAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGT
+VHSVPRLSKGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSG
+EFLKIVHGLLLGEDGFYDEVFHSLRIPYEPVRWAQDLQVNPEEQVGKVARVQQLIHAYRD
+RGHLMANVDPLEYSMPYHPDLDIREHGLTLWDLDRQWPTGGFGGASTLTLRKILGVLRDA
+YCRTIGVEYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIG
+QKRFSLEGGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYGQVFREFE
+GATPGGTSGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRL
+DLGGQRPDSFSVLPILVHGDAAFAGQGVVTEVLQLSQLPGYRTGGTIHVIVNNQVGFTTP
+PTQARSAVYSTDVAKTIQAPILHVNGDEPESVMHVAELAFEYRQRFNKDVVIDLVCYRRR
+GHNEGDDPSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADTALKDYQQQLERVFA
+ETHEGSASSGGEGIRPAEDRDQAPEAPETTAISAETLRAIGQAHIDVPEGFTVHPKLAAL
+LERRAKMAVDGGIDWGFAELAAFGSLLMEGVPVRLAGQDSQRGTFTQRHSVFHDRITGDE
+WAPLKNLSEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFINGAQTIID
+EFISSAEQKWAQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPTTGANHF
+HLLREQAYARPRRPLVVFTPKQLLRLKAAANSVEDFTEGRFQPVIPDAGVDPKKVTRVQL
+VSGRLYYDLLARRNKDGDETTAIVRVEQLYPLPLDELRAALEAYPQAEVVWVQDEPANQG
+PWPFMALNLLPQLDREVRLVSRPASASTSAGTKGRHDQELSTLLDAGFAR
+>MOLHKGIG_00756
+MPELTSDRLAQEFPGNERLVAEIYRKYREDSGSVDRQWAQIFARLEASAPAAEAEPKAAA
+KTEPKTAAKAEPKATAKVTEPKAATAPARGAQPKETSVSTGPKPKKTPAAQAVPSEPADT
+ATTTADEKQEKATVLKGMAKAVATNMDASLSMPTATTVRDLPAKVLIDNRVVINSHLART
+RGGKVSFTHFIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLPRPDGTRA
+LVVPNVKAAETLDFRGFWKAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGTVHSVPRL
+SQGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSGEFLKIVH
+GLLLGEDGFYDEVFHSLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN
+VDPLEYSMAYHPDLDIREHGLTLWDLDRKWPTGGFGGAGSLTLRKILGVLRDAYCRTIGV
+EYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE
+GGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA
+SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRLDLGGQRP
+DSFSVLPILVHGDAAFAGQGVVTEVLQLSQLPGYRTGGTIHVVVNNQVGFTTPPTQARSA
+VYSTDVAKTIQAPIFHVNGDEPESVVHVAQLAFEYRQRFNKDVVIDLVCYRRRGHNEGDD
+PSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADSALKDYQQQLERVFAETHEDAP
+ASGGEGLRPAEDRDAAPEAPASTAISAETLRAIGQAHIDVPEGFTVHPKLAALLERRAKM
+AVDGGIDWGFAELAAFGSLLMERVPVRLAGQDSQRGTFTQRHSVFHDRITGDTWAPLRHL
+SEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFVNGAQTIIDEFISSAD
+QKWSQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSTGANHFHLLREHA
+YARPRRPLIVFTPKQLLRLKAAANSVEDFTEGGFQPVIPDAGVDAKDVTRVLLVSGRLYY
+DLLARRQKSGDTSTAIVRVEQLYPLPLDEIRKALRAYPVADVTWVQDEPANQGPWPFMAL
+NLVPQLDVPVTLVSRPASAATSAGTKGRHDQELSTLLDAAFGR
+>NAFOICDF_02069
+MPELTSDRLSQEFPGNEDLVAQIYRKYREDQGAVDRQWAQIFARLEASQPQPEPAAAAPK
+ATSSATAEPAPAVKPAVKRGAATPADPQAAAKKSGPTDVSAPAQRKRSVSEAVPSEPARD
+AAAGASEKQDKATVLKGMAKAVATNMDASLSMPTATTVRDLPAKLLIDNRTVINSHLART
+RGGKVSFTHLIGYAVVRALKAMPSMNTLYEERDGKPTMVEPAHVNFGLAIDLPKPDGTRA
+LVVPNIKAAETLSFRQFWEAYDDLVKRGRANKLTMDDYAGTTVSLTNPGGIGTVHSVPRL
+SKGQAAIIGVGALTYPAAFQGAAESTLNSLAISKTITLTSTYDHRVIQGAGSGEFLKLIH
+GYLLGEDGFYDDVFHDLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN
+VDPLEYRMPTHPDLDIREHGLTLWDLDREWPTGGFGGADTLTLRRILGVLRDAYCRTVGV
+EYMHIQNPAERAWFQDKLERPYEKPSREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE
+GGESLIPLLDSILGDAADEGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA
+SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVARAKQDRLEAAGESG
+AAFPVLPILVHGDAAFAGQGVVTEVLNLSQLPGYRTGGTIHVVVNNQVGFTTSPAEGRSS
+VYATDVAKTIQAPILHVNGDEPESVLRVARLAYEYRQRFHKDVVIDLVCYRRRGHNEGDD
+PSMTQPRMYTLIEQKRSTRKLYVESLVGRGDITQEEADTALKDYQQQLERVFAETHAAET
+GQAVATTGLEPARDRDAARPAPSTTAISPDTLRRIGDVHLEVPEDFTVHPKLSQLLEKRA
+KMAVDGGIDWGFAELAAFGSLLMEGVPVRLSGQDSQRGTFTQRHSVFHDRVTDETWTPLN
+HLSESEAPFWVYNSLLSEYAVLGFEYGYSVERSDALVLWEAQFGDFINGAQTMIDEFISS
+AEQKWSQNSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSHGANHFHLLRE
+QAYSRPRRPLVVFTPKQLLRLKAAADPVEAFTQGGFRKVIGDASVDAAQVERVILVSGRL
+YYDLLARREKSGDTSTAIVRVEQLYPLPAEEIRAELAKYPGAQVRWVQDEPANQGPWPFM
+ALNLLPQLDREVTLVSRPALAATSAGTKGRHDEELSTLLDTAFGA
+>MHAAABBN_00486
+MPELTSDRLAQEFPGNERLVAEIYRKYREDSGSVDRQWAQIFARLEASAPAAEAEPKAAA
+KTEPKTAAKAEPKATAKVTEPKAATAPARGAQPKETSVSTGPKPKKTPAAQAVPSEPADT
+ATTTADEKQEKATVLKGMAKAVATNMDASLSVPTATTVRDLPAKVLIDNRVVINSHLART
+RGGKVSFTHLIGYAVVRALAAMPSMNVTYEERDGKPTMVEPAHVNFGLAIDLPRPDGTRA
+LVVPNVKAAETLDFRGFWKAYDDLVQRARKNKLTMDDYAGTTVSLTNPGGIGTVHSVPRL
+SQGQAAIIGVGALTYPAAFQGAAESTLHDLAISKTITLTSTYDHRVIQGAGSGEFLKIVH
+GLLLGEDGFYDEVFHSLRIPYEPVRWAQDVQVNPEEQIGKVARIQQLIHAYRDRGHLLAN
+VDPLEYSMAYHPDLDIREHGLTLWDLDRQWPTGGFGGASSLTLRKILGVLRDAYCRTIGV
+EYMHIQDPAERAWFQEKLEQPYAKPTREEQLRILGRLNAAEAFETFLQTKYIGQKRFSLE
+GGESLIPLLDGILGDAADAGLDEVAIGMAHRGRLNVLTNIAGKTYSQVFREFEGATPGGA
+SGSGDVKYHMGTEGTFVSDAGNSTRVYLAANPSHLEAVDPVLEGVVRAKQDRLDLGGQRP
+DSFSVLPILVHGDAAFAGQGVVAEVLQLSQLPGYRTGGTIHVIVNNQVGFTTPPTQARSA
+VYSTDVAKTIQAPILHVNGDEPESVVHVAQLAFEYRQRFNKDVVIDLVCYRRRGHNEGDD
+PSMTQPRMYNLIEQKRSTRKLYVESLVGRGDITQEEADSALKDYQQQLERVFAETHEDAP
+ASGGEGLRPAEDRDAAPEAPASTAISAETLRAIGQAHIDVPEGFTVHPKLAALLERRAKM
+AVDGGIDWGFAELAAFGSLLMEGVPVRLAGQDSQRGTFTQRHSVFHDRITDETWAPLKHL
+SEDQAKFWVYNSLLSEYAALGFEYGYSVERSDALVLWEAQFGDFVNGAQTIIDEFISSAD
+QKWSQTSSVVLLLPHGYEGQGPDHSSARIERFLQMCAEDNMRVVNPSTGANHFHLLREQA
+YARPRRPLVVFTPKQLLRLKAAANSVEDFTEGRFQPVIPDAGVDAKDVTRVLLVSGRLYY
+DLLARREKSGDTSTAIVRVEQLYPLPLEEIRKALRAYPDADVAWVQDEPANQGPWPFMAL
+NLVPQLDVPVTLVSRPASAATSAGTKGRHDQELSTLLDAAFGR
+>LFPAFLNI_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/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001495.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001495.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ff0f43ffaa909f8db22dc430267f96b4c2e21ec7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001495.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_02176
+MTADQHGRECRDAQEDTLERLYQYLDGALTPEEIDQVRAHVEDCEDCRHQQELEQFIRTA
+VRRSCQEKAPEQLRTTILTRITQLSTTRVTWR
+>MOLHKGIG_00754
+MTADQHGHECRVAQDASLERLYQYLDGALTPEDIEQVRAHVAECPDCRHQKELEELIRSA
+VRRCCQEKAPAQLRATIMTRITQISTTTVTWG
+>NAFOICDF_02071
+MSQDGDCRGCNDGEDRLEQLYQYLDGALTPEDIDQVRAHVDQCPDCHHQQELELIIRSAL
+RRSCQEKAPAQLRATIMTRITQVSTTTVRRAG
+>MHAAABBN_00484
+MTVDQHGHECRDAQDASLERLYQYLDGALTPEDIEQVRAHVADCPDCRHQKELEELIRSA
+VRRCCQEKAPAQLRATIMTRITQTPMTTVTWG
+>LFPAFLNI_00718
+MTADQHGHECRDAQDASLERLYQYLDGALTPEDIEQVRAHVADCPDCRHQKELEELIRSA
+VRRCCQEKAPAQLRATIMTRITQTPMTTVTWG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001503.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001503.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf4836e4617abfd5d7439de431f9f856ad4b56b6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001503.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02187
+MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALECAGVAPEDVDMV
+YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLVRLGEADVVV
+AGGQESMTNAPHLLPGARKGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA
+RAEQDEVAAASHQRAARAQSEGVFEGEIAPVEVPQRKGDPLVVSQDEGVRPDTTAESLGA
+LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAYAEEKGLTILATVGALGQTAGPDSSQLH
+SQPSDAINAAMRKQGWDVADLDFIEINEAFGAVAVQSLRDLDYPHEKTNIHGGAIALGHP
+IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR
+>MOLHKGIG_00742
+MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALERAGVAPEDVDMV
+YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLIRLGEADVVV
+AGGQESMTNAPHLLPGARKGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA
+RAEQDEVAAASHQRAARAQSEGVFEGEIAPVEVPQRKGDPLVVSQDEGVRPDTTAESLGA
+LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAFAEEKGLTILATVGAPGQTAGPDSSQLH
+SQPSDAINAAVRKQGWDVADLDFIEINEAFGAVAVQSLRDLDYPHEKTNIHGGAIALGHP
+IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR
+>NAFOICDF_02085
+MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALERAGVAPEDVDMV
+YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLIRLGEADVVV
+AGGQESMTNAPHLLPGARKGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA
+RAEQDEVAAASHQRAARAQSQGVFEGEIAPVEVPQRKGDPLVVSQDEGVRPDTTAESLGS
+LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAFAEEKGLTVLATVGAPGQTAGPDSSQLH
+SQPSDAINAAVRKQGWDVADLDFIEINEAFGAVAVQSLRDLGYPHEKTNIHGGAIALGHP
+IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR
+>MHAAABBN_00473
+MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALERAGVAPEDVDMV
+YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLIRLGEADVVV
+AGGQESMTNAPHLLPGARKGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA
+RAEQDEVAAASHQRAARAQSEGVFEGEIAPVEVPQRKGDPLVVSQDEGVRPDTTAESLGA
+LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAFAEEKGLTILATVGAPGQTAGPDSSQLH
+SQPSDAINAAMRKQGWDVADLDFIEINEAFGAVAVQSLRDLDYPHEKTNIHGGAIALGHP
+IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR
+>LFPAFLNI_00707
+MTAELPQPQPTDAVIVGGARTPFTRLLSQQADLRAVDLGAHAITHALERAGVAPEDVDMV
+YMGQVVQAGAGQNPARQSALAAGIPWNVPAMTINKVCLSGLTAVIDAARLIRLGEADVVV
+AGGQESMTNAPHLLPGARTGFKYGPATMLDAVAWDGLTDSLSHEAMGELTESGNGERNIA
+RAEQDEVAAASHQRAARAQSEGVFEGEIAPVEIPQRKGDPLVVSQDEGVRPDTTAESLGA
+LRPAFAKDGTITAGNSSPLSDGAAALVVTSRAFAEEKGLTILATVGAPGQTAGPDSSQLH
+SQPSDAINAAVRKQGWDVADLDFIEINEAFGAVAVQSLRDLGYPHEKTNIHGGAIALGHP
+IGASGARLALHAALELDRRDGGRAAVSLCGGGGQGEALILFR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001504.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001504.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1dc1dba78863b7e1dfcce2e50bdadb9e6b44b40e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001504.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02188
+MTMRAARWHGKKDIRIEEIASPTAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH
+PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDQDRPDYNLAPDMNF
+IGLGGDGGGLAEQIAVRRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVAVIG
+GAGPIGALTAAVLKGKGLTVYVSELSELRRQKVLEAGVVDEAFDPREVDVPAKIRELHDG
+QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVLKEIDLRGTIAYA
+NDHADTIRMVEDGTVDLAPFITGKIGLDDLVDQGFETLIHHNETAVKILVSPTGQGL
+>MOLHKGIG_00741
+MTMRAARWHGKKDIRIEEIDSPTAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH
+PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDRDRPDYNLAPDMNF
+IGLGGDGGGLAEQIAVQRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVAVIG
+GAGPIGALTAAVLKGKGLTVYVSELSELRRRKVLEAGVVDEAFDPREVDVPAKIRELHDG
+QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVMKEIDLRGTIAYA
+NDHADTIRMVEDGAVDLAPFITGKIGLDDLVDRGFETLIHHNETAVKILVSPTGQGL
+>NAFOICDF_02086
+MTMRAARWHGKKDIRIEEIDSPTAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH
+PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDRDRPDYNLAPDMNF
+IGLGGDGGGLAEQIAVQRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVALIG
+GAGPIGALTAAVLKGKGLTVYVSELSELRRRKVLEAGVVDEAFDPREVDVPAKIRELHDG
+QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVMKEIDLRGTIAYA
+NDHADTIRMVEDGAVDLTPFITGKIGLDDLVDQGFETLIHHNETAVKILVSPTGQGL
+>MHAAABBN_00472
+MTMRAARWHGKKDIRIEEIDSPSAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH
+PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDRDRPDYNLAPDMNF
+IGLGGDGGGLAEQIAVQRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVAVIG
+GAGPIGALTAAVLKGKGLTVYVSELSELRRRKVLEAGVVDEAFDPREVDVPAKIRELHDG
+QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVMKEIDLRGTIAYA
+NDHADTIRMVEDGAVDLAPFITGKIGLDDLVDQGFETLIHHNETAVKILVSPTGQGL
+>LFPAFLNI_00706
+MTMRAARWHGKKDIRIEEIDSPTAGPGQVLVDVAWCGICGTDLHEYLEGPIFIPPAGHPH
+PISGDAAPVTLGHEMSGTVAALGEGVTDLEVGQKVVVEPYIVREEDRDRPDYNLAPDMNF
+IGLGGDGGGLAEQIAVQRRWVHPVADSVPLDQAALIEPLSVAHHAWVRAGSPTSGVAVIG
+GAGPIGALTAAVLKGKGLTVYVSELSELRRQKVLEAGVVDEAFDPREVDVPAKIRELHDG
+QGADVGFECTSVDVVLDMLLDAVRPGGVIVNESIWGHEPAVALHKLVMKEIDLRGTIAYA
+NDHADTIRMVEDGAVDLAPFITGKIGLDDLVDQGFETLIHHNETAVKILVSPTGQGL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001506.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001506.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d1ac950db080b9a1950af210a91b156e3bc15ddb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001506.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02192
+MRALSALRRDDGQTTVLTVGLCALLIGLMLVMLAATTVQLQHRRLQSLADGAALAGAEEL
+GFRLGEDPGVVLDDGDVAASAAAHLDAVDAASSVHGLGGMAAGVADDGATVTVRLDAEVD
+LLAAAGPFAGMLPLSVPIQATGDSRTSLSR
+>MOLHKGIG_00738
+MRRRLTARLGHDDGQTTVLTVGLCAVLVALMLVMLAVTTVQLQHRRLQSLADSAAIAGAE
+ELGFRLGEDPGVVLSDDDVAASASAHLAAVGAQEAVPGLGGMNARVADDGTTVVVTLDAR
+ADLFAMTGPFAGTLPLSVPLEATGSSRTSLAR
+>NAFOICDF_02091
+MTRRHRSRPQRRPDRRHGAHERGEITVLTLGLSAIVVGLLLVVLSATLVLIQARKVQSLA
+DGAALAGAEQLAFQLDADPRVVLEPGSVQASVNEHLDAVGARESVPGLESVSAQVAGDGA
+TVVVRARAKVTLVPSGAGWLADLIPASVPVSAEGSSRTVLTR
+>MHAAABBN_00469
+MSRRLTARLGHDDGQTTVLTVGLCAVLVALMLVMLAVTTVQLQHRRLQSLADSAAIAGAE
+ELGFRLGEDPGVVLSDDDVAASASAHLAAVGAQEAVPGLGGMNARVADDGTTVVVTLDAR
+ADLFAMTGPFAGTLPLSVPLEATGSSRTSLAR
+>LFPAFLNI_00702
+MRRPLTARLGHDDGQTTVLTVGLCAVLVALMLVMLAVTTVQLQHRRLQSLADSAAVAGAE
+ELGFRLGEDPGVVLSDGDVAASASAHLAAVGAREAVPGLGGMSARVAEDGTTVVVTLDAR
+ADLFAMTGPFAGTLPLSVPLEATGSSRTSLAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001507.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001507.fa
new file mode 100644
index 0000000000000000000000000000000000000000..74d94e5f9cc482c5067c8356740582090997445b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001507.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02193
+MPIASDVRDERGSATVEFLGLTLVLLIPVVYLMIYVSQVQAAAFASVAAADQAAKVVVSG
+TEGRSAAQAHAAVRLTLADFGIDYGAYELDLGCSAGDCVSLDPGEVVQARVDVEVPIPLT
+PADWSLAPVTVGSDARQAVPRF
+>MOLHKGIG_00737
+MRSVNDVRDERGAATVEFLGLTLVLLIPVVYLMIYVSQVQAAAFASVAAADQAVKAVVAE
+ADHPSAGAAHATVELTLADYGVGAGQYDLTVGCDQGGCGTLEPGEVVAVRVDVGVPVPLT
+PAAWSLTPVTVGSDARQTVPRF
+>NAFOICDF_02092
+MPSATDARHGPTHAPWRGTDLADDVGSATVEFLGLSLILLIPLAYLMLFVSQVQAAAFGA
+LASADQAARVMVSGEGGNPGQAEGTIPLTLADYGFDAADAEWSVACDVGGCGTLEPGEVV
+DVTVAISLDPPLLPDGWVSVDIATVDSHSRARMPRF
+>MHAAABBN_00468
+MRSVNDVRDERGAATVEFLGLTLVLLIPVVYLMIYVSQVQAAAFASVAAADQAVKAVVAE
+ADHPSAGAAHATVELTLADYGVGAGQYDLTVGCDQGGCGTLEPGEVVAVRVDVGVPVPLT
+PAAWSLTPVTVGSDARQTVPRF
+>LFPAFLNI_00701
+MRSVNDVRDERGAATVEFLGLTLVLLIPVVYLMIYVSQVQAAAFASVAAADQAVKAVVAE
+ADHPSAGAAHATLELTLADYGVGAGQYDLTVGCDQGGCGTLEPGEVVAVRVDVAVPVPLT
+PAAWSMTPVTVGSDARQTVPRF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001509.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001509.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8644d94add7038daaf02fb48600754c62493a8cf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001509.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_02195
+MLHHHVISILTALRGLLHDDVRDDRGDVPGWVMITLMSAVLVAALLTLALPALTDLFDQA
+ISQVTQGE
+>MOLHKGIG_00735
+MLHHHAITVLAALRALIHDDVRDERGDVPGWVMITLMSAVLVAGLLALALPALQGLFNQA
+ISQVSQGG
+>NAFOICDF_02094
+MLTNAYLTVVSALTSLLHDDARDERGDVPGWVMITLMSAALVVALLGLAMPALKAMFDQA
+ITQVNNAAG
+>MHAAABBN_00466
+MLHHHAITVLAALRALIHDDVRDERGDVPGWVMITLMSAVLVAGLLALALPALQGLFNQA
+ISQVSQGG
+>LFPAFLNI_00699
+MLHHHAITVLAALRALIHDDVRDERGDVPGWVMITLMSAVLVAGLLALALPALEGLFNQA
+ISQVSQGG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001514.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001514.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5011bc7484d0c88097b152d6d0c8f8d56a58066
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001514.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02223
+MAQILLFHHALGLTDGVRALAAQIEAGGHTVHTPDLYDGALFTDVEEGIAHVESLGGFDV
+IAERGMRAAAQHPQASVVAGISMGVVAAHKAAQAVPAFRACIDIAGIVPLDAFAPLWQPH
+TALQVHLATRDPWVMDEDLPLARSVAATEEDPDKPAVLFEYDTDAHLFMDSSTDGHDPAL
+TEVLVRRIHELLA
+>MOLHKGIG_00730
+MAQIVLFHHALGLTDGVRALAEQIASGGHTVHTPDLYDGRTFATVDEGVAHAQHLGFEEI
+GRRGMRACAEHQEASVVAGISMGVMPAWRAAQVVPGFRACIAMAGVLALDAYAPLWQPHT
+ALQIHLGTRDPWALEGDLATARSYAATAEHPDRPADLFEYDTDRHLFMNSSTADFDADLT
+AVLVRRIHELLA
+>NAFOICDF_02099
+MAQIILFHHARGLTEGVLALAEQIEQASGHHVHTPDLFGGAVLPTVEDGLAHLQQIGQDE
+VMTRAMHACAEHKEASVVAGISMGVMPAWKAAQTAPGFRACIAMSSALPLDAYARLWQPH
+TSLQIHLAAQDPWVKDEDLPLARTYAATAEHPDRPADLFEYETASHLFMDSSTDQYDARH
+TEVMVERIRELLA
+>MHAAABBN_00461
+MAQIVLFHHALGLTDGVRALAEQIAGGGHTVHTPDLYDGRTFATVDEGVAHAQHIGFEEI
+GRRGMRACAEHQEASVVAGISMGVMPAWRAAQVVPGFRACIAMAGALALDAYAPLWQPHT
+ALQIHLGTRDPWALEGDLETARSYAATAEHPDRPADLFEYDTDRHLFMDSSTADFDADLT
+AVLVRRIHELLA
+>LFPAFLNI_00694
+MAQIVLFHHALGLTDGVRALAEQIASGGHTVHTPDLYDGRTFATVDEGVAHAQHLGFEEI
+GRRGMRACAEHQEASVVAGISMGVMPAWRAAQVVPGFRACIAMAGVLALDAYAPLWQPHT
+ALQIHLGTRDPWALEGDLETARSYAATAEHPDRPADLFEYDTDRHLFMDSSTADFDADLT
+AVLVRRIHELLA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001516.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001516.fa
new file mode 100644
index 0000000000000000000000000000000000000000..81b090ef1032a486335e84ce13e3430725fac90a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001516.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02229
+MNTAFDAGRLGRTDVLTLQQVTSFMSNDMQVTGPDGQTVATVVTTGGGLGRMVLGSRTFD
+VVDGEDGRVLFRLADPATFGRDRYAIVDADGLPLANLVREFALFRTSVSVEVVDGTRFAV
+TGNLWDHDYTMTVGQAPIARATATFGGFMNALAGRSRYELRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRRNN
+>MOLHKGIG_00728
+MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD
+VVDGDDGRVLFRLADPATFGRDRFAILDADGLPFANLVRQIAFLRTSVNVEVVDGTCFAV
+TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRSNG
+>NAFOICDF_02102
+MTTFDAGRLALVNSLALQQVTSFLSNDMQVLGPDGEVVATVQTQGGGLSRMLMGSRRLLV
+CDGDDGRPLFELQDPATFGRDRFQVLDPAGLPLANLRREVAFFRTAVSVEVVDGTVFRVE
+GDLFDHDYRMIAGEVPIARAVSQWSGFGNALLGRSRYRLELDPAMPPVVRCAVLGTAIAL
+DLLRAKDARRND
+>MHAAABBN_00459
+MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD
+VVDGDDGRVLFRLADPATFGRDRFAILDADGLPLAHLVRQFAFLRTSVNVEVVDGTCFAV
+TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRSNG
+>LFPAFLNI_00692
+MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD
+VVDGDDGRVLFRLADPATFGRDRFAILDADGLPFANLVRQIAFLRTSVNVEVVDGTCFAV
+TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRSNG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001519.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001519.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1fdc278e3bb15231e69d5d219aefe238fc8467ca
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001519.fa
@@ -0,0 +1,23 @@
+>ACLBLIBL_02233
+MNSSSTPTPEPSETARHAWRAYFEATQMLSEMLERGLKKDSGMSLADYNLLLLLYEAPEG
+RLRMGELASGMVFSPSRITYQVKTLVARGLIERRAAECDRRGFEAVLTDEGRTAFRRAAA
+GHARQVDELFLSHLEPGEAETLERIFTRLGGRLEGLC
+>MOLHKGIG_00725
+MSSSSTPAPEPAAQDAAPAEPDGGWFGSASEAHRPVDPPKRAWRAYFEATQMLTEVVERR
+LKQDCGMSLADYNLLLLLYESPEGRLRLGELASRMVFSPSRITYQVKTLVARGLIDRRPV
+ACDRRGFEAVLTDEGRSAFRRAAIEHARQVDELFLGDLAPGEAESLTRIFSRLGRRLEGL
+C
+>NAFOICDF_02105
+MTSSSTPAAEPTGPRAARHAWRAYFESTQMLQDQLERGLKAECGITLADYNLLLLLVESD
+GGRLRLGELASRMVFSPSRVTYQVKSLVARGLIERRRVECDRRGFEAVLTDAGRTAFRRA
+AVVHARQVDELFLDLLQPGEAEVLGRVFTRVGTALESRCAGRAAPSEPCGAQASNSADA
+>MHAAABBN_00456
+MSSSSTPAPEPAAQDAAPAEPDGGWFGSASEAHRPVDPPKRAWRAYFEATQMLTEVVERR
+LKQDCGMSLADYNLLLLLYESPEGRLRLGELASRMVFSPSRITYQVKTLVARGLIDRRPV
+ACDRRGFEAVLTDEGRSAFRRAAIEHARQVDELFLGDLAPGEAESLTRIFSRLGRRLEGL
+C
+>LFPAFLNI_00689
+MSSSSTPAPEPAAQDAAPAEPDGGWFGSASEAHRPVDPPKRAWRAYFEATQMLTEVLERR
+LKQDCGMSLADYNLLLLLYESPEDRLRLGELASRMVFSPSRITYQVKTLVARGLIDRRPV
+ACDRRGFEAVLTDEGRSAFRRAAIEHARQVDELFLVDLAPGEAESLTRIFSRLGRRLEGL
+C
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001520.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001520.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d4d489435585c3cade458ffdc0eb0a9b2615fbdb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001520.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02234
+MRTRTLTGVATAALGAVVVAGAGPALAQTVITQGSALSAPAGACSLTIVDDATAYTAAHC
+GAGQWEVGSPVLDAEGVQIGTVSGLPGTSGVDVVRVALAEDVEVVGEWSTRPAASVEVGE
+TVFTHGSSVPLGAPNSLSHTQTFDAATVCDDAYSDQMALDVASTYPGDSGGAVYDAQQRV
+VGVISGVAPVTFDEEGNVVGCDAQSLSSIMVPVESLDAVGQETAAPAAVEPAAAEAPATE
+VTETPAIADVAGPVADEDLPTGGEPAVDESELTEFTPAEEEAIRAELIERAEAEAAAEAP
+AEQPAAEAPVAEAVVAGTEDVVAAPAEGVAYGTQVMAETSQGGFASVTVTAYDADGTVLG
+VDGLDLTGEYRAWMPVPAEVPAGGSVVVTVVDAAGDATDTQVTLGGQLIG
+>MOLHKGIG_00724
+MRTRTLTGVATAALGAVVVAGAGPALAQTTLTQGSAITAPAGACSLTIVDDATAYTAAHC
+GAGQWQIGSTVRDVDGTAIGTVSALPGDSGVDAVRVALADDVDVVGDWSTRPASSIGVGE
+TVYTHGSSVPLGAPNTVSHTQTFEAATVCDDAYADQVALDTASTYAGDSGGAVYDAQQRV
+VGVISGIAPVTFDAEGNVVGCDAQAMSSIMVPVESLDALDASAAPAAETAAAAETAPAAE
+TAPAIADVAGPVADEDLPTGGEPAVDESELTEFTPAEEEAIAAELKARAEAAAEEEAAEA
+APAAEAPVAEAAAPGVTDVVAAPAEGVAYGTQVVAQTDQGGFASVTVTAYDADGTVLGQD
+GLDLTGEYRAWLPVPAEVPAGGSVVVTVVDAAGAATDATVTLGGQLVG
+>NAFOICDF_02106
+MKKTTLTGATTAALGAVVVAGAGSALAATPLTQGAALSVPAGECSITLVSDTTAFTAAHC
+GAGQWTVGSAVHAADGARIGSVSALPGSTGVDVVKIALDEDVDVVGDWSTRPAASVKPGE
+TVYTQGSSVPLGSPNSISDPETYDIAETCGDVYTDQVSLDAATTRPGDSGGAVYDAKQRV
+VGVVSGLAPVSFDEEGRAVGCDAASLSTIMVPAESLKAVAAAPAKATAPAPTVGKHGVIL
+KAPTAPAAKAPAAEKKAPAAKAPAAEKKAAPAPTLGKHGVSAETATAGTTTLKVAPEDGI
+DFRTRVQATTKTGGFSYMAVTAYDAAGKQIGHLHLHSDGQPMTWINTPAQVPAGGHIEVQ
+LKDAAGQPTDATVTLGGVPVN
+>MHAAABBN_00455
+MRTRTLTGVATAALGAVVVAGAGPALAQTTLTQGSAITAPAGACSLTIVDDATAYTAAHC
+GAGQWQIGSTVRDVDGTAIGTVSALPGDSGVDAVRVALADDVDVVGDWSTRPASSIGVGE
+TVYTHGSSVPLGAPNTVSHTQTFEAATVCDDAYADQVALDTASTYAGDSGGAVYDAQQRV
+VGVISGIAPVTFDAEGNVVGCDAQAMSSIMVPVESLDALDASAAPAAETAAAAETAPAAE
+TAPAIADVAGPVADEDLPTGGEPAVDESELTEFTPAEEEAIAAELKARAEAAAEEEAAEA
+APAAEAPVAEAAAPGVTDVVAAPAEGVAYGTQVVAQTDQGGFASVTVTAYDADGTVLGQD
+GLDLTGEYRAWLPVPAEVPAGGSVVVTVVDAAGAATDATVTLGGQLVG
+>LFPAFLNI_00688
+MRTRTLTGVATAALGAVVVAGAGPALAQTTLTQGSAITAPAGACSLTIVDDATAYTAAHC
+GAGQWQIGSTVRDVDGTAIGTVSALPGDSGVDAVRVALADDVDVVGDWSTRPASSIGVGE
+TVYTHGSSVPLGAPNTVSHTQTFEAATVCDDAYADQVALDTASTYAGDSGGAVYDAQQRV
+VGVISGIAPVTFDAEGNVVGCDAQAMSSIMVPVESLDALDASAAPAAETAAAAETAPAAE
+TAPAIADVAGPVADEDLPTGGEPAVDESELTEFTPAEEEAIAAELKARAEAAAEEEAAEA
+APAAEAPVAEAAAPGVTDVVAAPAEGVAYGTQVVAQTDQGGFASVTVTAYDADGTVLGQD
+GLDLTGEYRAWLPVPAEVPAGGSVVVTVVDAAGAATDATVTLGGQLVG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001522.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001522.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1711c1a17fd59513568c449301fc6f81abd57737
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001522.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_02236
+MTPNPAAPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPLTAALDWQRAGAEWIHLVDL
+DAAFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPAWT
+ARVIERFGDKVAVGLDVRGTTLAARGWTQEGGDLWEVLARLEDAGCSRYVVTDVTKDGTL
+KGPNTELLAQVCARTDKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQ
+ALAVAGGATVEQARAEQPGPVAE
+>MOLHKGIG_00722
+MTPNAPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPVTAALDWQRAGAEWIHLVDLDA
+AFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPDWTAR
+VIERFGDRVAVGLDVRGTTLAARGWTKEGGDLWEVLARLEDAGCARYVVTDVTKDGTLKG
+PNTELLAQVCAKTAKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQAL
+AVAGGATVEQARSEQPGPVAP
+>NAFOICDF_02108
+MTETTPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPLTAALDWQDAGAEWIHLVDLDA
+AFGRGDNRDVLRRVVDEIGVKIELSGGIRDDASLENALAMGAARVNLGTAALEDPAWTAR
+AIERFGNRVAVGLDVRGTTLAARGWTQDGGDLWEVLARLEEAGCARYVVTDVTKDGTLRG
+PNRELLARMCAATDKPVVASGGISSLEDIAALAAMVPQGVEGAIMGKALYAGRFSLEQAL
+AVAAGATVERAREQHPFQAAP
+>MHAAABBN_00453
+MTPNAPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPVTAALDWQRAGAEWIHLVDLDA
+AFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPDWTAR
+VIERFADRVAVGLDVRGTTLAARGWTKEGGDLWEVLARLEDAGCARYVVTDVTKDGTLKG
+PNTELLAQVCAKTAKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQAL
+AVAGGATVEQARSEQPGPVAP
+>LFPAFLNI_00686
+MTPNAPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPVTAALDWQRAGAEWIHLVDLDA
+AFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPDWTAR
+VIERFADRVAVGLDVRGTTLAARGWTKEGGDLWEVLARLEDAGCARYVVTDVTKDGTLKG
+PNTELLAQVCAKTAKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQAL
+AVAGGATVEQARSEQPGPVAP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001523.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001523.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f289073b4239fa1d1ce1f6eec64990291892562
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001523.fa
@@ -0,0 +1,10 @@
+>ACLBLIBL_02237
+MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVAR
+>MOLHKGIG_00721
+MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVGA
+>NAFOICDF_02109
+MPYWSVLYLGLGGILLGAAWSMRTQKAPTWAVVIALVLAAMAVAAAFLTV
+>MHAAABBN_00452
+MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVGA
+>LFPAFLNI_00685
+MPYWSVLYLALGGLLLGAAWSMRTQKAPLWAIVIVLVLAGMAIAASFLTVGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001529.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001529.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7f970eda30876f166694d14d0c9239d4d01f1eea
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001529.fa
@@ -0,0 +1,65 @@
+>ACLBLIBL_02243
+MSGAGTEGTTPAGEGAQPRTDHEREALRLLDAAVEATGGQQRAGQREMVLQVARALESRR
+HLLVQAGTGTGKSLAYLIPALQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDEL
+PREPVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGLLGSAADGTGGPSSLLGK
+EVMYLRAWADQTETGDRDDLDVPVTDRAWRQVSVSAIDCLGASRCPMAEECFSERARADA
+ADADVVVTNHAMLAISAFEGLAVLPAYSAVVVDEAHELQDRVTGAVTGQLSGSIVHGAAT
+SLRKHTTVAVEDLMEAGAGLDRAFTDAPSGLLAAGPDEVQEQALNAVLAAARQCLSDLGQ
+DKDKEADADGGRQMARSRVLEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGD
+ESDPPQLFVAPISVAGKLREGLFGKATTVLTSATLTVGAGERRFDSVAGDVGLAGPDAPR
+FEALDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLRASGGGALGLFSSRRAA
+EDAAAEMRRRLGPKATVLCQGDATLSALVRQFAEEPDTSLFGTMSLWQGVDVPGNSLRLV
+AIDRIPFPRPDDPLSQARTRDVARHGGNGFMRISATHAAVRMAQGAGRLVRSVHDRGVVA
+VLDSRLATERYGGYITSALPDFWRTTDRAVVLGVLGRLAETGS
+>MOLHKGIG_00715
+MSGGAEEVGAGGAQPRTEHEREALRLLDAAVQATGGQHRAGQREMVLQVARALESRRHLL
+VQAGTGTGKSLAYLIPAIQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDELPRE
+PVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGMIGSATDGAAGPSSLLGKEVM
+YLRAWADQTETGDRDDLEVPVTDRAWRQVSVSAVDCLGASRCPQAEECFSERARADAADA
+DVVVTNHAMLAISAFEGLAVLPAYSAVVVDEAHELQDRVTGAVTGQLSGSIVHGAATSLR
+RHTTVAVEDLIEAGAALDRAFTDTPSGLIAAGPDEVQEQALTGVLTAARQCLSDLGQDKD
+KEADADGGRQMARSRILEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGDETD
+PPQLYVAPLSVAGKLREGLFGKATTVLTSATLTVGSGERRFDSVAGDVGLAGPDAPKFEA
+LDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLRASRGGALGLFSSRRAAEDA
+AAEMRRRLGPKTTILCQGDATLSALVRQFSEEPDTSLFGTMSLWQGVDVPGNSLRLVVID
+RIPFPRPDDPLSQARTRDVARHGGNGFMRISATHAAVRMAQGAGRLVRSVTDRGVVAVLD
+PRLATERYGGYITSALPDFWRTTDRDVVRGVLARLASGD
+>NAFOICDF_02115
+MTDSTTGPAGAVPTTDREEEALRLLDVVVEATGGQQRAGQREMVLQVARALESRRHLLVQ
+AGTGTGKSLAYLIPALQHAMDQEDPVVVATATLALQAQIMKRDAPRLVQALAGELPREPV
+VALVKGRSNYLCRHKVDGGYPGDEGEETLFEVADDGGLIGSGEDGEPSSPLGKEVMYLRA
+WADVTETGDRDDLEVPVTDRAWRQVSVNAVDCLGATRCPLAEECFSERARADAADADVVV
+TNHAMLAISAFEGLAVLPAYSAVIVDEAHELQDRVTGAVTGQLSGSIVHGAATSLRRHTS
+VAVEDLAQAAAGLDRAFTDTPSGLIQGGPDDVQEQALTAVLSAARQCFSDLGKDKEGEAD
+AGRQMARSRLLEVVEVAERMLAAHPEADFPEVLWATRPGRFEPGSGWQPGDEADPPQLYV
+APISVAGRLREGLFGKATTVLTSATLTVGQGERRFDSVAGDVGLAGPDAPRFTALDVGSP
+FDYPRQGVLYVARHLPKPGRTASPESLDELEALLRASNGGALGLFSSRRAAEDAAEHMRR
+RLGRGHTVLCQGDATLSALVRQFADEPDTSLFGTMSLWQGVDVPGPSLRLVVIDRIPFPR
+PDDPLSQARTRDVARHGGNGFMRVSATHAAVRMAQGAGRLVRSVEDRGVVAVLDSRLATE
+RYGGYITSALPDFWRTTDRAVVRGVLERLAREAH
+>MHAAABBN_00446
+MSEEEQEAGAGGAQPRTEHEREALRLLDAAVQATGGQHRAGQREMVLQVARALESRRHLL
+VQAGTGTGKSLAYLIPAIQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDELPRE
+PVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGVIGSATDGAAGPSSLLGKEVM
+YLRAWADQTETGDRDDLEVPVTDRAWRQVSVSAVDCLGASRCPQAEECFSERARADAADA
+DVVVTNHAMLAISAFEGLAVLPAYSAVIVDEAHELQDRVTGAVTGQLSGSIVHGAATSLR
+RHTTVAVEDLIEAGAALDRAFTDTPSGLIAAGPDEVQEQALTGVLTAARQCLSDLGQDKD
+KEADADGGRQMARSRILEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGDETD
+PPQLYVAPLSVAGKLREGLFGKATTVLTSATLTVGSGERRFDSVAGDVGLAGPDAPKFEA
+LDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLRASRGGALGLFSSRRAAEDA
+AAEMRRRLGPKTTILCQGDATLSALVRQFAEEPDTSLFGTMSLWQGVDVPGNSLRLVVID
+RIPFPRPDDPLSQARTRDVARHGGNGFMRISATHAAVRMAQGAGRLVRSVTDRGVVAVLD
+PRLATERYGGYITSALPDFWRTTDRDVVRGVLARLASGD
+>LFPAFLNI_00679
+MSEEEQEAGAGGAQPRTEHEREALRLLDAAVQATGGQHRAGQREMVLQVARALESRRHLL
+VQAGTGTGKSLAYLIPAIQHAMTQEDPVVVATATLALQAQIMKRDAPRLVEALKDELPRE
+PVVALVKGRSNYLCRHKVDGGYPGDEGEEALFTVADDGGVIGSATDGAAGPSSLLGKEVM
+YLRAWADQTETGDRDDLEVPVTDRAWRQVSVSAVDCLGASRCPQAEECFSERARADAADA
+DVVVTNHAMLAISAFEGLAVLPAYSAVIVDEAHELQDRVTGAVTGQLSGSIVHGAATSLR
+RHTTVAVEDLIEAGAALDRAFTDTPSGLIAAGPDEVQEQALTGVLTAARQCLSDLGQDKD
+KEADADGGRQMARSRILEVLEVVERMLAARPEADFPEVLWATRPGHFEPGVGWQPGDETD
+PPQLYVAPLSVAGKLREGLFGKATTVLTSATLTVGSGERRFDSVAGDVGLAGPDAPKFEA
+LDVGSPFDYPRQGVLYVARHLPRPGRTASPESLDELEALLSASRGGALGLFSSRRAAEDA
+AAEMRRRLGPKTTILCQGDATLSALVRQFAEEPDTSLFGTMSLWQGVDVPGNSLRLVVID
+RIPFPRPDDPLSQARTRDVARNGGNGFMRISATHAAVRMAQGAGRLVRSVTDRGVVAVLD
+PRLATERYGGYITSALPDFWRTTDRDVVRGVLARLASGD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001537.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001537.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc1d7273f58f456b82f40635fb5cf46b054bb10d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001537.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_02253
+MSKTPDREKALEAALAQIDKQFGKGSVMRLGDQTQTPVEVIPTGSVAMDVALGIGGLPRG
+RVVEIYGPESSGKTTLALHAVANAQRNGGIAAFIDAEHALDPVYARKLGVDTDALLVSQP
+DTGEQALEIMDMLVSSGTLDIVVIDSVAALTPRAEIEGEMGDSHVGLQARLMSQALRKIT
+GRLHQTKTTAIFINQLREKIGVFFGSPETTTGGKALKFYASVRIDVRRIETLKEAGNPVG
+NRTRVKIVKNKMAPPFKQAEFDILYGVGISREGGLIDMGVEEGIVKKSGAWFTYDGDQLG
+QGKENARRFLKDNPDLAQEIEERILTKLGIGVDPEAEADEAPALTAVPGDTAAG
+>MOLHKGIG_00704
+MSKVTDREKALEAALAQIDKQFGKGSVMRLGDQTQAPVEVIPTGSVAMDVALGIGGLPRG
+RVVEIYGPESSGKTTLALHAVANAQRNGGIAAFIDAEHALDPVYARQLGVDTDALLVSQP
+DTGEQALEIMDMLVSSGTLDIVVIDSVAALTPRAEIEGEMGDSHVGLQARLMSQALRKVT
+GRLHQTKTTAIFINQLREKIGVFFGSPETTTGGKALKFYASVRIDVRRIETLKEAGNPVG
+NRTRVKIVKNKMAPPFKQAEFDILYGVGISREGGLIDMGVEEGIVKKSGAWFTYDGDQLG
+QGKENARRFLKDNPDLANEIEERILTKLGIGVAPEAEDDEAPALTAVPGDTAAG
+>NAFOICDF_02125
+MSKASATEKVATEREKALEAALAQIDKQFGKGSVMRLGERSQAPVEVIPTGSVAMDVALG
+IGGLPRGRVVEIYGPESSGKTTLALHAVANAQRNGGIAAFIDAEHALDPVYARKLGVDTD
+ALLVSQPDTGEQALEIMDMLVSSGTLDIVVIDSVAALTPRAEIEGEMGDSHVGLQARLMS
+QALRKVTGRLHQTNTTAIFINQLREKIGVFFGSPETTTGGKALKFYASVRIDVRRIETLK
+EAGSPVGNRTRVKIVKNKMAPPFKQAEFDILYGEGISKEGSLIDMGVEEGIVKKSGAWFT
+YDGDQLGQGKENARRFLKDNPDLADEIEHRIFTKLGIGADPQAEDDAEGETPALQAVAGD
+VAAG
+>MHAAABBN_00438
+MSKVTDREKALEAALAQIDKQFGKGSVMRLGDQTQAPVEVIPTGSVAMDVALGIGGLPRG
+RVVEIYGPESSGKTTLALHAVANAQRNGGIAAFIDAEHALDPVYARQLGVDTDALLVSQP
+DTGEQALEIMDMLVSSGTLDIVVIDSVAALTPRAEIEGEMGDSHVGLQARLMSQALRKVT
+GRLHQTKTTAIFINQLREKIGVFFGSPETTTGGKALKFYASVRIDVRRIETLKEAGNPVG
+NRTRVKIVKNKMAPPFKQAEFDILYGVGISREGGLIDMGVEEGIVKKSGAWFTYDGDQLG
+QGKENARRFLKDNPDLANEIEERILTKLGIGVAPEAEDDEAPALTAVPGDTAAG
+>LFPAFLNI_00671
+MSKVTDREKALEAALAQIDKQFGKGSVMRLGDQTQAPVEVIPTGSVAMDVALGIGGLPRG
+RVVEIYGPESSGKTTLALHAVANAQRNGGIAAFIDAEHALDPVYARQLGVDTDALLVSQP
+DTGEQALEIMDMLVSSGTLDIVVIDSVAALTPRAEIEGEMGDSHVGLQARLMSQALRKVT
+GRLHQTKTTAIFINQLREKIGVFFGSPETTTGGKALKFYASVRIDVRRIETLKEAGNPVG
+NRTRVKIVKNKMAPPFKQAEFDILYGVGISREGGLIDMGVEEGIVKKSGAWFTYDGDQLG
+QGKENARRFLRDNPDLANEIEERILTKLGIGVAPEAEDDEAPALTAVPGDTAAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001539.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001539.fa
new file mode 100644
index 0000000000000000000000000000000000000000..99f547415248a6fab5b0b3c1d29412cd556a9815
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001539.fa
@@ -0,0 +1,17 @@
+>ACLBLIBL_02255
+MMRHPVQAHGITRWVDDQPRPRATTPDIKERSMPLLRHEIGDVLRDVRQLQGRTLREVSH
+DARVSLGYLSEVERGQKEASSELLASICQALEIPLSYLLREVSDRLVDQEGIQVPDTLPE
+DLTDAADPSLGTLAGR
+>MOLHKGIG_00699
+MPLLRHEIGDVLRDVRQLQGRTLREVSHDARVSLGYLSEVERGQKEASSELLASICQALD
+IPLSYLLREVSDRLVEQEGMVVPDTLPDDLTDPSLGSLAGR
+>NAFOICDF_02127
+MMRHPVQAHGITRWVDSQPRPSQPTPELKERSMPILRHEIGDVLRDVRQRQGRTLREVSH
+DARVSLGYLSEVERGQKEASSELLASICDALQIPLSFLLREVSDRLAEQEGVVVPDTVPA
+DMAEDGAADVAPLAVR
+>MHAAABBN_00436
+MPLLRHEIGDVLRDVRQLQGRTLREVSHDARVSLGYLSEVERGQKEASSELLASICQALD
+IPLSYLLREVSDRLVEQEGMVVPDTLPDDLTDPSLGSLAGR
+>LFPAFLNI_00669
+MPLLRHEIGDVLRDVRQLQGRTLREVSHDARVSLGYLSEVERGQKEASSELLASICQALD
+IPLSYLLREVSDRLVEQEGMVVPDTLPDDLTDPSLGSLAGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001541.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001541.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b91b5320e6db25366cc603fd4f5a171de36faad
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001541.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02258
+MSTGGEAERVSAWNLPNILTSVRILMVPLFAWALWAGGPWGGDSATARWIAVALFAAAMY
+TDKLDGDIARARGLITDFGKIADPIADKLLTGAALVLFSLLGELWWWVTVVILVREWGIT
+LMRFVVIRYGVMPAGRGGKLKTVLQAVGIGLLLMPLAPVVGGWWPWVGWTVIGAATVLTV
+LTGLEYVKDAWILRRDALAAPRGA
+>MOLHKGIG_00696
+MSAAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWGGDSLVARWVALALFAAAMY
+TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT
+LMRFVVIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPVVGGWWPWAGWVVIGAATVLTV
+LTGLEYVKDAWVLRRDALAAQRGA
+>NAFOICDF_02129
+MNAQPERVSAWNLPNILTTVRILMVPFFVWAVWAGGPWGQDSLTARWIAVALFAAAMYTD
+KLDGDIARSRGLITDFGKIADPIADKLLTGSALVLFALLGELWWWVVIVILVREWGITAM
+RFVVIRYGVMPAGRGGKLKTVLQAVGIGLLLMPLAPVLGGWWPWLGWTVIGAALALTVVT
+GVEYVRDAVRLRADWLASHPEARR
+>MHAAABBN_00433
+MSTAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWGGDSLVARWVALALFAAAMY
+TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT
+LMRFVVIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPLVGGWWPWAGWVVIGAATVLTV
+LTGLEYVKDAWVLRRDALAAQRGA
+>LFPAFLNI_00666
+MSTAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWSGDSLLARWVALALFAAAMY
+TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT
+LMRFVMIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPLVGGWWPWAGWVVIGAATVLTV
+LTGLEYVKDAWVLRRDALAAQRAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001544.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001544.fa
new file mode 100644
index 0000000000000000000000000000000000000000..83af47baad0db70490b173c27182ba0b47edbfec
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001544.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02261
+MSAVRSASAPSELLFGTVVPAMVTPMTDEGAVDLEAAAALAEHLVDGGADGLVVTGTTGE
+TSTLTDEENLAMFRTVVEAVGDRAKVVAGTGTNDTAHTLELSRRAKETGVDGLLLVTPYY
+NKPNQAGIRAHFEAVADGVDLPIMLYDIPGRSVMPIEPETLIALAQHPNIRALKDAKGDL
+QSTTTVLAHSDLDLYSGDDGATLPLMALGAVGVVSVAAHVAPGLYRKLVDAVHAGDLAAA
+REHHFALDPVQRGIMTHVQGAVAAKAVLAAQGVIPSAAVRLPLVQASADELSDIRADLAE
+AGITF
+>MOLHKGIG_00693
+MSAVRSAVIPSELLFGTVVPAMVTPMTDEGAVDLEAAAALAEHLVDRGADGLVVTGTTGE
+TSTLTDDENVAMFRTVVEAVGDRARVVAGTGTNDTAHTLELSRRAAETGVDGLLLVTPYY
+NKPNQAGIRAHFETVADGVDLPIMLYDIPGRSVMPIEPETLIALAQHPNIRALKDAKGDL
+QSTTTVLAHTDLDLYSGDDGATLPLMALGAVGVVSVAAHAAPELYRQLVDAVHAGDLAGA
+RDHHFALDPVQRGIMTHVQGAVAAKAVLAAQGVIPSAAVRLPLVQATRDELSVIRADLAE
+AGITF
+>NAFOICDF_02131
+MTDARRTVNPSELPFGTVVPAMVTPMDQDGAVDLQAAAVLATHLVDQGADALVITGTTGE
+TSTLTDEENLAMFRTVVEAVGERARVIAGTGTNDTHHSLELSRRAAEIGVHGLLLVTPYY
+NKPNQAGIRRHFETIADGVDLPIMLYDIPGRSVMPIQPETLVALAAHPNITALKDAKGDL
+QSTTTVLAHTDLHVYSGDDGATLPLMAMGAVGVVSVAAHVAVPGYRALVDAVHAGDLRAA
+RDAHFALDPVQRGIMSHVQGAVAAKTVLAGQGIIPTAAVRLPLVAADDAELAAIRADLAE
+AGISF
+>MHAAABBN_00430
+MSAVRSAVIPSELLFGTVVPAMVTPMTDEGAVDLEAAAALAEHLVDRGADGLVVTGTTGE
+TSTLTDDENVAMFRTVVEAVGDRARVVAGTGTNDTAHTLELSRRAAETGVDGLLLVTPYY
+NKPNQAGIRAHFETVADGVDLPIMLYDIPGRSVMPIEPETLIALAQHPNIRALKDAKGDL
+QSTTTVLAHTDLDLYSGDDGATLPLMALGAVGVVSVAAHAAPELYRQLVDAVHAGDLAGS
+RDHHFALDPVQRGIMTHVQGAVAAKAVLAAQGVIPSAAVRLPLVQATPDELSVIRADLAE
+AGITF
+>LFPAFLNI_00663
+MSAVRSAVIPSELLFGTVVPAMVTPMTDEGAVDLEAAAVLAEHLVDRGADGLVVTGTTGE
+TSTLTDDENVAMFRTVVEAVGDRARVVAGTGTNDTAHTLELSRRAAETGVDGLLLVTPYY
+NKPNQAGIRAHFEAVADGVDLPIMLYDIPGRSVMPIEPETIIALAQHPNIRALKDAKGDL
+QSTTTVLAHTDLDLYSGDDGATLPLMALGAVGVVSVAAHAAPELYRQLVDAVHAGDLAGA
+RDHHFALDPVQRGIMTHVQGAVAAKAVLAAQGVIPSAAVRLPLVQATPDELSVIRADLAE
+AGITF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001548.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001548.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88bf8e98b841e6d6db49a402777531a26ecb867a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001548.fa
@@ -0,0 +1,70 @@
+>ACLBLIBL_02269
+MEGPEITFAEAVIDNGAYGKRTIRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASVSTQLSGLPFSGPIGGVRMALVDDGAGKRQWVAFPKH
+SQLQDAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGASAPTEEVVAEGLEAAKP
+FIRALCEAQADLVKRAGKDPVDVPVFKDYEDDAFEAVEKLATDRLTEIFSIGDKQTRESA
+SDAYHVEVMDELAGEDKPFAERRGEIAKAYGSVTKQVVRQRILKDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETSKRYLHHYNFPPYST
+GETGRVGSPKRREIGHGALAERAMVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT
+AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGAFVSLTPGKDGLLHVSELRKLNEGKRVDDVEDVLGVGQKVQVEITK
+IDDRGKLSLSPVVAESDADAETADAIESSQTEA
+>MOLHKGIG_00688
+MEGPEITFAEAVIDNGSYGKRTVRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALMDDGSGTRQWVAFPKH
+SQLEGAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGAQAPTEEIVAEGLEAAKP
+FIRALCEAQADLVKRAGKDPVDVPVFQDYQDDAYAAVEKLATDRLTEIFSIGDKQERESA
+SDAYLLEVLEELAGEGKDFAERKGEIAKAYGSLTKQIVRRRILTDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETAKRYMHHYNFPPYST
+GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT
+AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGGFVSLTPGKDGLLHISELRKLNEGKRVDDVEDVLGVGQKVQVEITK
+IDDRGKLSLSPVVAESDALAETADAIESSQIEA
+>NAFOICDF_02136
+MEGPEITFAEAVIDNGRHGTRTVRFETGRLAQQAAGSAMVYIDEETSMLSATTVGKHPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFTKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALLDDGSGQRQWVAFPKH
+SQLEDAVFNMAVAGRVAGDDVAIMMVEAEAGENAWTLVKERGAQAPTEEIVAEGLEAAKP
+FIRALCEAQADLAARAGKAPVEVPVFKDYEQDAYDAVEKIATDRLTEIFSIADKQEREAA
+SDAYHLEVIEELAGEGKDFAERKGEVAKAYGSLTKQIVRRRILKDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETSKRYMHHYNFPPYST
+GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAHVAGIAMGLVSAEVEGQTQYAALTDILGAEDAFGDMDFKVAGTSEFVT
+AIQLDTKLDGIPASVLAGALTQAREARLHILSVLEAAIDQPDELAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGAFVSLTPGKDGLLHISELRKLNEGKRVEDVEDVLGVGQKVQVEITK
+IDDRGKLSLAPVVADEDAAAGESREEDEEA
+>MHAAABBN_00425
+MEGPEITFAEAVIDNGSYGKRTVRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALMDDGSGTRQWVAFPKH
+SQLEGAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGAQAPTEEIVAEGLEAAKP
+FIRALCEAQADLVKRAGKDPVDVPVFQDYQDDAYAAVEKLATDRLTEIFSIGDKQERESA
+SDAYLLEVLEELAGEGKDFAERKGEIAKAYGSLTKQIVRRRILTDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETAKRYMHHYNFPPYST
+GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT
+AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGGSAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGGFVSLTPGKDGLLHISELRKLNEGKRVDDVEDVLGVGQKVQVEITK
+IDDRGKLSLSPVVAESDALAETADAIESSQIEA
+>LFPAFLNI_00658
+MEGPEITFAEAVIDNGSYGKRTVRFETGRLAQQAAGAAMVYIDEETSMLSATTVGKSPRE
+GFDFFPLTVDVEERMYAAGRIPGSFFRREGRPSTDAILTCRLIDRPLRPAFVKGIRNEVQ
+VVVTVTSIAPDEIYDTVAINAASLSTQLSGLPFSGPIGGVRMALMDDGSGTRQWVAFPKH
+SQLEGAVFNMAVAGRVVGDDVAIMMVEAEATPDSWTLVKERGAQAPTEEIVAEGLEAAKP
+FIRALCEAQADLVKRAGKDPVDVPVFQDYQDDAYAAVEKLATDRLTEIFSIGDKQERESA
+SDAYLLEVLEELAGEGKDFAERKGEIAKAYGSLTKQIVRRRILTDQVRIDGRGLTDIRKL
+TAEVEVLPRVHGSAIFERGETQIMGVTTLNMLKMEQQIDSLAPETAKRYMHHYNFPPYST
+GETGRVGSPKRREIGHGALAERALVPVLPAREEFPYAIRQVSEALGSNGSTSMGSVCAST
+LSLLNAGVPLRAPVAGIAMGLVSAEVDGQTQYAALTDILGAEDAFGDMDFKVAGTAEFVT
+AIQLDTKLDGIPASVLAAALTQAREARLHILSVLNAAIDAPDEMAPTAPRIISVRIPVDK
+IGAVIGPKGAMINQIQDDTGADITIEDDGTVLIGATDGASAEAARSAVNAIANPQVPEVG
+ERYLGTVVKLTTFGGFVSLTPGKDGLLHISELRKLNEGKRVDDVEDVLGVGQKVQVEITK
+IDDRGKLSLSPVVAESDALAETADAIESSQIEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001552.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001552.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40802566ee568080cebb30a4483d52c4ca9fa2bf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001552.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02279
+MLVWNSLDEVPTDLPRTVVTLGNFDGVHRGHREVLRRVVELARERDALAVAVTFSPHPRS
+VHRPDEPHVDILGPQQRAVLLSETGLDALLMQRYTLEFADQSPEEFVLSMFVRGLNAAVV
+VVGHDVRFGRGNVGDFAEMVRLGALHGFEVEAVEEHPAEIGDEPERRCSSTWVREALAAG
+DVAQAAAILGRHHTLDGEVVHGFARGRELGFPTANLAPEAEGMIPADGVYAGWVHDVQGE
+AWPAAISIGSNPTFEGVSRVVEAHVIDRPEERVEDFDLYGQHIEVEFVQRLRGMVAYEGV
+EKLVAQMTQDVEQARAILAATPSDR
+>MOLHKGIG_00684
+MRVWNSLDEVPTDLPRTVVTLGNFDGVHRGHREVLRRVVELARARDALAVAVTFTPHPRA
+VHHPEVPHVDIISPEQRVVLLDEAGLDAVLLQRYTLEFADQSPEEFVRGMLVHGLHAAVV
+VVGHDVRFGRGNTGDVAEMVRLGARYGFEVEAVEEFPAEHGAEPERRCSSTWVREALAAG
+DVAQAAAVLGRHHVLAGEVVHGFARGRELGFPTANLETDVQGMIPADGVYAGWVHDAHGG
+VWPAAISIGSNPTFEDVSRVVEAHVIDRHDERVEDFDLYGQHIEVEFVARLRGMVAYEGV
+EKLVAQITQDVDEARAILATTPSDR
+>NAFOICDF_02140
+MLVWNSMAEVPTDLPRTVVALGNFDGVHRGHRAVLERVVEIAHERGQLAVAVTFTPHPRV
+VHQPGLEHVEILSPEQRAVRLDETGIDALFLQHYTLEFAAQTPEEFVTSMFVRGLNAAAV
+VVGRDVRFGRDNAGDFAEMVRLGGVHGFDVVAVEDLPAEDGDGERRCSSTWIRELLAAGD
+VAHAAEVLGRNHVVAGAVVHGFARGRELGFPTANLEADAAGMIPADGVYAGWVHDAHGSV
+WPAAVSIGSNPTFEGVSRVVEAHVIDRPEEPVEDFDLYGQQIEVEFVERLRGMVAYEGVE
+KLVAQMHQDVDQARAVLAAAPQPAGRV
+>MHAAABBN_00421
+MRVWNSLDEVPTDLPRTVVTLGNFDGVHRGHREVLRRVVELARARDALAVAVTFTPHPRA
+VHHPEVPHVDIISPEQRVVLLDEAGLDAVLLQRYTLEFADQSPEEFVRGMLVHGLHAAVV
+VVGHDVRFGRGNTGDVAEMVRLGARYGFEVEAVEEFPAEHGAEPERRCSSTWVREALAAG
+DVAQAAAVLGRHHVLAGEVVHGFARGRELGFPTANLETDVQGMIPADGVYAGWVHDAHGG
+VWPAAISIGSNPTFEDVSRVVEAHVIDRHDERVEDFDLYGQHIEVEFVARLRGMVAYEGV
+EKLVAQITQDVDEARAILATTPSDR
+>LFPAFLNI_00654
+MRVWNSLDEVPTDLPRTVVTLGNFDGVHRGHREVLRRVVELARARDALAVAVTFTPHPRA
+VHQPEVPHVDIISPEQRVVLLEEAGLDAVLLQRYTLEFADQSPEEFVRGMLVHGLHAAVV
+VVGHDVRFGRGNTGDVAEMVRLGARYGFEVEAVEEFPAEHGAEPERRCSSTWVREALAAG
+DVAQAAAVLGRHHVLAGEVVHGFARGRELGFPTANLETDVQGMIPADGVYAGWVHDAHGG
+VWPAAISIGSNPTFEDVSRVVEAHVIDRHDERVEDFDLYGQHIEVEFVARLRGMVAYEGV
+EKLVAQITQDVDEARAILATTPSDR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001554.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001554.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ddf220c85d220259467d9974a31fef31f79d6c8d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001554.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02281
+MILDAWFWAGLVIGAVSLAVCVAMTAIRRHPADSSILSVAAVELFLLVYAVAAAVRQLGG
+EGLNGPGWEFWGYVVTALLVPVIAVAWAVTDKTRWSNLVLAVVGPTVVVMLHRMQVIWFG
+QW
+>MOLHKGIG_00682
+MILDAWFWTGLVIGAVSFVVCVVMTAIRRHPADASILSVAAVELFTLVYAAAAAVRQLGG
+DTLNGPGWEFWGYILTALIVPVIAVGWAVTDKTRWSNLVLAVVGPTIAVMLHRMQVIWFG
+QW
+>NAFOICDF_02142
+MILDAWFWTGAVVGGLSFVVCLAMTALRRHPADSSIVSVAAVELFLLVYGVVGAFRQLGG
+QPLNGPTWEFWGYVLTALLVPVIAVAWAVTDKTRWSNLVMAVAGPTVVVMLHRMQVIWFG
+QW
+>MHAAABBN_00419
+MILDAWFWTGLVIGAVSFVVCVVMTAIRRHPADASILSVAAVELFTLVYAAAAAVRQLGG
+DTLNGPGWEFWGYILTALIVPVIAVGWAVTDKTRWSNLVLAVVGPTIAVMLHRMQVIWFG
+QW
+>LFPAFLNI_00652
+MILDAWFWTGLVIGAVSFVVCVVMTAIRRHPADASILSVAAVELFTLVYAAAAAVRQLGG
+DTLNGPGWEFWGYILTALIVPVIAVGWAVTDKTRWSNLVLAVVGPTIAVMLHRMQVIWFG
+QW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001555.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001555.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4623fb4a3c9c63cf1522c1a0a2071ed9a557c024
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001555.fa
@@ -0,0 +1,31 @@
+>ACLBLIBL_02282
+MDKPQGWTSHDVVGRLRRLAGTRKVGHAGTLDPMATGLLVVGVNKATRLLTAITGTDKTY
+TATIRLGQSTVTDDAEGDVVQTRLANAVTPERVAEQVAALTGPILQAPSAVSAIKVAGRR
+AYDRVRAGEDVALQARPVTVHEFTVHEMRRLDGGRLVDLDVTVRCSSGTYVRALARDLGE
+ALETGGHLTALRRTAVGPFDVADALTLEELAEGFVMTGLSEAAAGLFPVRELTEDEAREL
+AFGRAVAPTGSGEALVAGRAPDGRVVALISDVRRRGADVAKPQLVFAPAEGPGQGGTA
+>MOLHKGIG_00681
+MDKPQGWTSHDVVGRVRRLAGTRKVGHAGTLDPMATGLLVVGVNKATRLLTAITGTDKTY
+TATIRLGQSTVTDDAEGEVVQTRLANAVTPERVAEQVAALTGEILQAPSAVSAVKVAGRR
+AYDRVRAGEDVTLDARPVTVHEFTVHELRRLDGGRLVDLDVTVRCSSGTYIRALARDLGE
+ALETGGHLTALRRTAVGPFDVADALSLEALAERFAMTELSEAAAGLFPVRELTEHEAHEL
+AFGRVVAPTGTGETLVAGRAPDGRVIALVSDVRRRGADVAKPQLVFAPAEGPGQGRTA
+>NAFOICDF_02143
+MNARTAHAPTPDAPGTEASGVVLVDKPAGWTSHDVVGRVRRLAGTRKVGHAGTLDPMATG
+LLVVGVNKATRLLTAITGTDKEYTATIRLGQSTTTDDAEGEVVQTRLANAVTPERVAEQV
+AALTGDILQVPSSVSAVKVAGRRAYDRVRAGEDVQLDARPVTVHAFEVEDFRRLDGGRTV
+DLDVTVRCSSGTYVRALARDLGEALDTGGHLTALRRTAVGPFRVEDAVDLDALAERFVMT
+ELSAAAAGLFPVRELTAHEAAELSFGRAIDPSGELAAAAGASGKAADGLVAGRTPDGTVV
+ALLQDGRRSGRDVARPHLVFAPAEGQGKEEAR
+>MHAAABBN_00418
+MDKPQGWTSHDVVGRVRRLAGTRKVGHAGTLDPMATGLLVVGVNKATRLLTAITGADKTY
+TATIRLGQSTVTDDAEGEVVQTRLANAVTPERVAEQVAALTGEILQAPSAVSAVKVAGRR
+AYDRVRAGEDVTLDARPVTVHEFTVHELRRLDGGRLVDLDVTVRCSSGTYIRALARDLGE
+ALETGGHLTALRRTAVGPFDVADALSLEALAERFAMTELSEAAAGLFPVRELTEHEAHEL
+AFGRVVAPTGTGETLVAGRAPDGRVIALVSDVRRRGADVAKPQLVFAPAEGPGQGRTA
+>LFPAFLNI_00651
+MDKPQGWTSHDVVGRVRRLAGTRKVGHAGTLDPMATGLLVVGVNKATRLLTAITGTDKTY
+TATIRLGQSTVTDDAEGEVVQTRLANAVTPERVAEQVAALTGEILQAPSAVSAVKVAGRR
+AYDRVRAGEDVTLDARPVTVHEFTVHELRRLDGGRLVDLDVTVRCSSGTYIRALARDLGE
+ALETGGHLTALRRTAVGPFDVADALSLEALAERFAMTELSKAAAGLFPVRELTEHEAHEL
+AFGRVVAPTGTGETLVAGRAPDGRVIALVSDVRRRGADVAKPQLVFAPAEGPGQGRTA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001564.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001564.fa
new file mode 100644
index 0000000000000000000000000000000000000000..987ea2966e430c7a9bafc0c93be73ca88308b31f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001564.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_02291
+MSAVEVLWYVLGVVAVALGLAVSIALHEVGHLMPAKLFGVRVTQYMIGFGPTIASWRRGE
+TEYGFKAVPLGGYVAMVGMLPPPRPGQEPRTASTGFVQQLGRMADDARTQAAAELTAADE
+GRQFIQLPVWKRVVIMLGGPFMNLLIALGVTALLVTTVGTSQPSTTAAEVYRCVVTTDEQ
+QARAAEGGGQDCRPGDPVAPAHEAGLRPGDTVTSFDGRPVDDWDALSGLIRERAGQPTAI
+EWERDGEPHSATITPRLTQRPVTDAVGRPERAPDGTALTEEVGFIGMGSQIETVQQSPLA
+AGPVVAQQVRGVVDVVLVLPQRLWDTAVAVVTPAERDPDGPMSVVGVGRIAGEAAALQEA
+ELADKAALLLSLVAGVNVALMVFNLIPLLPLDGGHVAGALWEALRRGWARLRGRPDPGPF
+DLARMLPLTYAVAGLMLVMGVVLIVADIVEPIRLF
+>MOLHKGIG_00671
+MTVVEILWYVAGVLAVALGLAVSIALHEIGHLVPAKLFGVRVTQYMIGFGPTLVSWRRGE
+TEYGFKAVPLGGYVAMIGMLPPPRPGQTPRAASTGFVQQLGRMADDARAQAAEEVRPGDE
+HRRFLALPVWKRVVIMLGGPFMNLLIALGATALLVTTVGTSQPSTTVAEVYRCVVTMQEQ
+QARAASGGTEDCRPGDPAAPAHEAGLRPGDTVLAFDGRPVSDWDALSAAIRDRAGQPTRI
+EWERDGERMSATLTPRLTERPVTDALGRPERAPDGTVATHEVGFIGMGAQLETVRGTPLD
+AGPLVAQQVRGVVDVVLVLPQRLWDTAVAVVTPAERDPDGPMSVVGVGRIAGEAAALEEA
+TLTDKAALLLSLLAGVNVALMVFNLIPLLPLDGGHVAGALWEAVRRGWARITGRPDPGPF
+DLARMLPLTYAVGAAMLLMGVILIVADIVEPVRLF
+>NAFOICDF_02153
+MSAVEALWFVGGVVVVALGLALSIALHEVGHLVPAKLFGVRVTQYMVGFGPTVASWRRGE
+TEYGIKAFPLGGYVAMVGMLPPPKGGTVARTGSTGFRARAGRMADDARAQAAEEITAADE
+GRQFIQLPVWKRVVIMLGGPFVNLLIALALTAVLVSTLGVARPSTTADEVFQCVVSQSEQ
+QSRAADGGAAQDCRPGDPAAPAYEAGLRPGDRVVSFDGRDVGSWAELSTAIRARAGQATA
+IAWERDGTRTESTLTPLLTERPVTDALGVPERGADGGVKTEPVGFIGLASRQETVTLAPW
+EAVPLVGRQAQGVVGVILALPQRLWDTAVAVVTPAPRDPNGPMSVVGVGRIAGEAAALDT
+ASPADKAALLLSLVAGVNVALLVFNLIPLLPLDGGHVAGALWEGLRRGWARLRGRPDPGP
+FDLAVMMPLTYVVGAAMLAMGVLLIVADIVKPVQLF
+>MHAAABBN_00408
+MTVVEILWYVAGVLAVALGLAVSIALHEIGHLVPAKLFGVRVTQYMIGFGPTLVSWRRGE
+TEYGFKAVPLGGYVAMIGMLPPPRPGQTPRAASTGFVQQLGRMADDARAQAAEEVRPGDE
+HRRFLALPVWKRVVIMLGGPFMNLLIALGATALLVTTVGTSQPSTTVAEVYRCVVTMQEQ
+QARAASGGTEDCRPGDPAAPAHEAGLRPGDTVLAFDGRPVSDWDALSAAIRDRAGQPTRI
+EWERDGERMSATLTPRLTERPVTDALGRPERAPDGTVATHEVGFIGMGAQLETVRGTPLD
+AGPLVAQQVRGVVDVVLVLPQRLWDTAVAVVTPAERDPDGPMSVVGVGRIAGEAAALEEA
+TLTDKAALLLSLLAGVNVALMVFNLIPLLPLDGGHVAGALWEAVRRGWARITGRPDPGPF
+DLARMLPLTYAVGAAMLLMGVILIVADIVEPVRLF
+>LFPAFLNI_00641
+MTVVEILWYVAGVLAVALGLAVSIALHEIGHLVPAKLFGVRVTQYMIGFGPTLVSWRRGE
+TEYGFKAVPLGGYVAMIGMLPPPRPGQTPRAASTGFVQQLGRMADDARAQAAEEVRPGDE
+HRRFLALPVWKRVVIMLGGPFMNLLIALGATALLVTTVGTSQPSTTVAEVYRCVVTMQEQ
+QARAASGGTEDCRPGDPAAPAHEAGLRPGDTVLAFDGRPVSDWDALSAAIRDRAGQPTRI
+EWERDGERMSATLTPRLTERPVTDALGRPERAPDGTVATHEVGFIGMGAQLETVRGTPLD
+AGPLVAQQVRGVVDVVLVLPQRLWDTAVAVVTPAERDPDGPMSVVGVGRIAGEAAALEEA
+TLTDKAALLLSLLAGVNVALMVFNLIPLLPLDGGHVAGALWEAVRRGWARITGRPDPGPF
+DLARMLPLTYAVGAAMLLMGVILIVADIVEPVRLF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001566.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001566.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e2ce80b0965053b36d736b6349e8f7e460ab6cb4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001566.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_02293
+MSALTPLLQAAPEAVGSPAVNIGIFLAFVVVTLVIVIRASKTSSSSADYYAGGRGFSGTQ
+NGTAIAGDYLSAASFLGIVGAIALYGYDGFLYSIGFLVAWLVALLLVAELLRNTGKFTMA
+DVLSFRLRQKPVRIAAAFGTMAVCLFYLLAQMAGAGGLVSLLLNINDRAGQALVIAIVGV
+LMIVYVLIGGMKGTTYVQIIKAILLIAGAGVMTVWSLAMFGFDFNAMLGAAVELNPEGEA
+ILEPGLQYGASALTRLDFVSLGIALVLGTAGLPHVLMRFYTVPTAKEARKSVVWAIVLIG
+AFYLFTLVLGYGAGALIGPERIMAAPGGQNSAAPLLAFELGGSILLGVISAVAFATILAV
+VAGLAITAAASFAHDVYGSVIAKHQLTPNEEVRIGKITVVVIGLLAIVGGIAAQGQNVAF
+LVALAFAVAASANLPTILYSLFWRRFTTRGAVWSMYGGLLSAIILIVLSPVMSGAPTSMI
+PGADFAIFPLKNPGIVSIPLAFFLGWLGSVTSSRAEDPDKQAEMEVRSLTGIGAEKPVQH
+>MOLHKGIG_00669
+MSALTPLLQAAPQTVGNPAVNIGIFVAFVVVTLVIVIRASKTNASSADYYAGGRGFSGTQ
+NGTAIAGDYLSAASFLGIVGAIALYGYDGFLYSIGFLVAWLVALLLVAELLRNTGKFTMA
+DVLSFRLQQRPVRIAAAFGTMAVCLFYLLAQMAGAGGLVALLLNINDRAGQALVIVIVGV
+LMIVYVLIGGMKGTTYVQIIKAVLLIAGAGIMTVWTLALFGFDFNALLGAAVEKNPKGEA
+ILEPGLQYGASALTRLDFVSLGLALVLGTAGLPHVLMRFYTVPTAKEARKSVVWAIVLIG
+AFYLFTLVLGYGAGALIGPERILAAPGGQNSAAPLLAFELGGSILLGLISAVAFATILAV
+VAGLAITAAASFAHDVYGSVIAKHPLTPQEEVRIGKITVVVIGVLAIVGGIAAQGQNVAF
+LVALAFAVAASANLPTILYSLFWRRFTTRGAVWSMYGGLLSAIILIVLSPVMSGTPTSMI
+PGADFAVFPLKNPGIVSIPLAFFLGWLGSVTSSRAEDPDKQAEMEVRSLTGIGAEKPVQH
+>NAFOICDF_02155
+MSTFALPLAAAVGDPVVNIGIFVAFVAVTLVIVIRASKKNASAADYYAGGRGFSGTQNGT
+AIAGDYLSAASFLGIVGAIALYGYDGFLYSIGFLVAWLVALLLVAELLRNTGKFTMADVL
+SFRLRQKPVRIAAAFGTMAVCLFYLLAQMAGAGGLVALLLNITDKGGQALVIVIVGVLMI
+VYVLVGGMKGTTYVQIIKAILLITGAGVMTLWSLALFGFDFNAMMGAAVQLNPQGEAILE
+PGLQYGKNFTTRLDFLSLGLALVLGTAGLPHVLMRFYTVPTAKEARTSVVWAIVLIGAFY
+LFTLVLGYGAGALIGPEKILAAPGGVNSAAPLLAFELGGSILLGLISAVAFATILAVVAG
+LALTAAASFAHDVWGSVIAKEPLTPEEEVRIGKITVVVIGVLAIVGGIAAQGQNVAFLVA
+LAFAVAASANLPTILYSLFWRGFTTRGAVWSMYGGLIASIVLIVLSPVMSGAETSMIPTA
+DFAVFPLKNPGIVSIPLAFVLGWLGSVTSKDVEDPDKQAEMEVRSLTGVGAEKPVAH
+>MHAAABBN_00406
+MSALTPLLQAAPQTVGNPAVNIGIFVAFVVVTLVIVIRASKTNASSADYYAGGRGFSGTQ
+NGTAIAGDYLSAASFLGIVGAIALYGYDGFLYSIGFLVAWLVALLLVAELLRNTGKFTMA
+DVLSFRLQQRPVRIAAAFGTMAVCLFYLLAQMAGAGGLVSLLLNINDRAGQALVIVIVGV
+LMIVYVLIGGMKGTTYVQIIKAILLIAGAGIMTVWSLALFGFDFNAMLGAAVEMNPKGEA
+ILEPGLQYGASALTRLDFVSLGIALVLGTAGLPHVLMRFYTVPTAKEARKSVVWAIVLIG
+AFYLFTLVLGYGAGALIGPERILAAPGGQNSAAPLLAFELGGSILLGLISAVAFATILAV
+VAGLAITAAASFAHDVYGSVIAKHPLTPQEEVRIGKITVVVIGVLAIVGGIAAQGQNVAF
+LVALAFAVAASANLPTILYSLFWRRFTTRGAVWSMYGGLLSAIILIVLSPVMSGTPTSMI
+PGADFAVFPLKNPGIVSIPLAFFLGWLGSVTSSRAEDPDKQAEMEVRSLTGIGAEKPVQH
+>LFPAFLNI_00639
+MSALTPLLQAAPQTVGNPAVNIGIFVAFVVVTLVIVIRASKTNTSSADYYAGGRGFSGTQ
+NGTAIAGDYLSAASFLGIVGAIALYGYDGFLYSIGFLVAWLVALLLVAELLRNTGKFTMA
+DVLSFRLQQRPVRIAAAFGTMAVCLFYLLAQMAGAGGLVSLLLNINDRAGQALVIVIVGV
+LMIVYVLIGGMKGTTYVQIIKAILLIAGAGIMTVWSLALFGFDFNAMLGAAVEMNPKGEA
+ILEPGLQYGASALTRLDFVSLGIALVLGTAGLPHVLMRFYTVPTAKEARKSVVWAIVLIG
+AFYLFTLVLGYGAGALIGPERITAAPGGQNSAAPLLAFELGGSILLGLISAVAFATILAV
+VAGLAITAAASFAHDVYGSVIAKHPLTPQEEVRIGKITVVVIGVLAIVGGIAAQGQNVAF
+LVALAFAVAASANLPTILYSLFWRRFTTRGAVWSMYGGLLSAIILIVLSPVMSGTPTSMI
+PGADFAVFPLKNPGIVSIPLAFFLGWLGSVTSSRAEDPDKQAEMEVRSLTGIGAEKPVQH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001567.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001567.fa
new file mode 100644
index 0000000000000000000000000000000000000000..95c45f83b1dd22846a2b3c7f25cfccac7dd47587
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001567.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02294
+MSSSEPTAPAPTAAQFRAAQQSEEFTELRSTYRSFAFPMTVAFFVWYLVFVIAGAFFPEF
+MSIRLGGNITLGLVLGLLQFVTTFLITFAYVRFSNRTLDPRATALRERLEREAAGGAPET
+PEATR
+>MOLHKGIG_00668
+MSSSEPTAPVPTAAQFRAAQQSEEFTELRRTHRSFAFPMTVAFFVWYLVFVIVGAFFPEF
+MAIRLGGNITLGLILGLLQFVTTFLITFAYVRFSNRTLDPRATALRERLEREAAGAHENP
+EATR
+>NAFOICDF_02156
+MSTGPHTPPAPTPAQFRAAQDSPEFRELRRTQRSFAFPMTVTFFVWYLLFVILGAFFPQV
+MAVRLGGNITLGLVLGLLQFVTTFAITFAYVRFSNRVLDPRAAALRERLEREAAGAAPET
+PEVAL
+>MHAAABBN_00405
+MSSSEPTAPVPTAAQFRAAQQSEEFIELRRTHRSFAFPMTVAFFVWYLVFVIVGAFFPEF
+MAIRLGGNITLGLILGLLQFVTTFLITFAYVRFSNRTLDPRATALRERLEREAAGAHENP
+EATR
+>LFPAFLNI_00638
+MSSSEPTAPVPTAAQFRAAQQSEEFIELRRTHRSFAFPMTVAFFVWYLVFVIVGAFFPEF
+MAIRLGGNITLGLILGLLQFVTTFLITFAYVRFSNRTLDPRATALRERLEREAAGAPENP
+EATR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001579.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001579.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3700ae2ed605802d14eaafdf8eb05ea5c950923
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001579.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_02314
+MSVTSSRAASRRAPRTAAASLALALGAGALAGVGSVTAAETAQAVETTYTVRAGDGWWVI
+SQRTGVSMSTLQSLNGMTSATMLHPGMVLKTSGTAAPAPAPAPSASTYTVLAGDGWWIIS
+YRTGVSASVLQSINGMTSSTVLHPGMVLKTSVVASSAPAPAPAPVTNGKQAAVDFVRSTV
+QNPSSYYLWGGNGPYGFDCSGLTQQAMAKAGISIPRRAGDQYNAAKSYVPISQAQPGDLV
+FYANQSTGRIYHVAMYMGGGQLAHALNEDAGLLFTSTTIMKSDMLAVAARY
+>MOLHKGIG_00649
+MSVTSSHAAVRRAPRTAAASVALALGAAALTGVGTVSVAETAQAAETAYTVRSGDGWWII
+AQRTGVSMSRLQSLNGMTAATVLHPGMVLKTSGTATPTPAPAPSTSGSTYTVLAGDGWWI
+ISYRTGVSASILQSINGMSSSTMLHPGMVLKTTSVSTSSAPAVAPAPAPASKQAAVDYVR
+SAVRNPSSYYVWGGNGPSGFDCSGLTQQAMARAGISIPRRAGDQYLAAKSYVPISQAQPG
+DLVFYANQSTGRIYHTAMYMGGGQLAHALNEDAGLVFTSTTIMKSDMLAVAARY
+>NAFOICDF_02171
+MPEALLTPARRPRAAAASLALALGAGAGVTAGAAVIAPQAVAAETYTVQAGDGWWIISQR
+TGVSMATLMQLNGMTSADMLHPGMVLKTSGTVTAAAGTYTVKAGDGWYAISRATGVPVST
+LTSLNGMTITSMLYPGMVLKTTGTPASTAPAPAPAPAPVVRQSSKQAAIDFAVAKVNDPN
+TYYAWGGNGPYGYDCSGLTKAAFAAAGITIPRVSHDQYVNAPAYAPLSQAQPGDLVFWAN
+QSTGRVYHVAVYIGNGKVAHALNTTDDLVITSTDVMTSNRLAVVGRY
+>MHAAABBN_00386
+MSVTSSHAASRRAPRTAAASVALALGAAALTGVGTVSVAETAQAAETTYTVRSGDGWWII
+AQRTGVSMSTLQSLNGMTAATVLHPGMVLETSGTATPAPAPAPSTSGSTYTVLAGDGWWI
+ISYRTGVSASILQSINGMTSSTMLHPGMVLKTTSVSTSSAPALAPASAPASKQAAVDYVR
+AAVRNPSSYYAWGGNGPSGFDCSGLTQQAMAQAGISIPRRAGDQYLAAKSYVPISQAQPG
+DLVFYANQSTGRIYHVAMYMGGGQLAHALNEDAGLVFTSTTIMKSDMLAVAARY
+>LFPAFLNI_00619
+MSVTSPHAAARRAPRTAAASVALALGAAALTGVGTVSVAETAQAAETTYTVRSGDGWWII
+AQRTGVSMSTLQSLNGMTAATVLHPGMVLKTSGTATPAPAPAPSTSGSTYTVLAGDGWWI
+ISYRTGVSASVLQSINGMTSSTMLHPGMVLKTTSVSTSSAPAPAPAPASKQAAVDYVRSA
+VRNPSSYYVWGGNGPSGFDCSGLTQQAMARAGISIPRRAGDQYLAAKSYVPISQAQPGDL
+VFYANQSTGRIYHTAMYMGGGQLAHALNEDAGLVFTSTTIMKSDMLAVAARY
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001582.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001582.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71b1c0221fbcce45ed16a0f70aacb963dc1f393a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001582.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02320
+MTTPEKKDAAAATPVQDSQLAHDDPRTRHPKLDAPEQRQEEPGLDVKTEPVPDIGLDSYR
+GLGRLEGRKALITGGDSGIGAAVAVAYAREGADVAIAYLPEEQPDADRVLAAIEAAGRTA
+VALPGDLMDAGYREGLVEEAATALGGLDILVNNAGKQIISESLEDLTDQQVLETFQVNIL
+SMFTLSRAALTHMGPGSTIINTTSVQAYNPNPMILDYAATKAAINNFTKGLAQQLGERGI
+RVNAVAPGPVWSVLQVSYGQPKEKLPVFGHDTPTGRGGQPVEMAPAYVFLASGESSYVNG
+ETLNANGGTPTP
+>MOLHKGIG_00642
+MTTPEKKDDAPAIPVQDSQLAHDDPRTRHPKLRVDKQRQPEPGLDVKTDPVPDIGLDSYR
+GMGRLTGRKALITGGDSGIGAAVAIAYAREGADVAIAYLPQEQPDADRVLAAIEAAGRTA
+VALPGDLMDADYRASLVDEAAQRLGGLDILVNNAGKQFISDDLTDLTDEQVHETFQINIM
+SMFTLSRAALKHMGPGSTIVNTTSVQAYNPNPRLLDYAATKGAINNFTKGLAEQLGPKGI
+RVNAVAPGPIWTVQHVSYGEPEEKLPEFGHSNPIGRAGQPVEMAPAYVFLASGESSYVNG
+ETLNANGGTPTP
+>NAFOICDF_02183
+MTTPEKKDDAPAIPVQDSQLAHDDPRTRHPKLHITKQRQPEPGLDVKTDPVPDIGLDSYR
+GAGRLTGRKALITGGDSGIGAAVAIAYAREGADVAIAYLPQEQPDADRVLAAIEAAGRTA
+VALPGDLMDVDYRASLVDEAAQRLGGLDILVNNAGKQFISDDLVDLTDEQVHETFQINIM
+SMFTLSRAALKHMGPGSTIVNTTSVQAYNPNPRLLDYAATKGAINNFTKGLAEQLGPKGI
+RVNAVAPGPIWTVQHVSYGEPEEKLPEFGHSTPLGRAGQPVEMAPAYVFLASGESSYVNG
+ETLNANGGTPTP
+>MHAAABBN_00379
+MTTPEKKDDAPAIPVQDSQLAHDDPRTRHPKLRIAKQRQPEPGLDVKTDPVPDIGLDSYR
+GMGRLTGRKALITGGDSGIGAAVAIAYAREGADVAIAYLPQEQPDADRVLAAIEAAGRTA
+VALPGDLMDADYRASLVDEAAQRLGGLDILVNNAGKQFISDDLTDLTDEQVHETFQINIM
+SMFTLSRAALKHMGPGSTIVNTTSVQAYNPNPRLLDYAATKGAINNFTKGLAEQLGPKGI
+RVNAVAPGPIWTVQHVSYGEPEEKLPEFGHSTPIGRAGQPVEMAPAYVFLASGESSYVNG
+ETLNANGGTPTP
+>LFPAFLNI_00612
+MTTPEKKDDAPAIPVQDSQLAHDDPRTRHPKLHITKQRQPEPGLDVKTDPVPDIGLDAYR
+GAGRLTGRKALITGGDSGIGAAVAIAYAREGADVAIAYLPQEQPDADRVLAAIEAAGRTA
+VALPGDLMDADYRAALVDEAAQRLGGLDILVNNAGKQFISDDLTDLTDEQVHETFQINIM
+SMFTLSRAALKHMGPGSTIVNTTSVQAYNPNPRLLDYAATKGAINNFTKGLAEQVGPKGI
+RVNAVAPGPIWTVQHVSYGEPEEKLPEFGHSTPIGRAGQPVEMAPAYVFLASGESSYVNG
+ETLNANGGTPTP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001585.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001585.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0038be75707ed6d828ced4d34f884edddbd35002
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001585.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02343
+MRTPATDTDSPVKTEPLTDLPTERAADPDPSAPAPVPAVARHRPFGLVLLVTGVVGWVAS
+AILVLERLELYEDAGHITSCDINPWVSCGRVMGTWQSELFGFPNPLIGIVAFAVVISTAM
+VVLSGARPGRWYWAGLQAGVTLGMVFVAWLWFQALFVIHILCLYCMIVWAAMIPLFILLT
+VRNLAHGVIPAPPGVVRFATGWAGTLIAVAYVTVTGSVFVQFLPAFTGY
+>MOLHKGIG_00612
+MTTPTIPTDHPIEHRVDTGPASEEAGMPVAARHRPFGVVLLVTGVVGWVASAILVLERLA
+LYENPGHTTSCDINPWVSCGRVMGTWQSELFGFPNPLIGIVAFAVVIATAMVVLSGARPG
+RGYWAGLQAGVTLGMGFVAWLWFQALYEIYILCLYCMIVWAAMIPLFILLTARNLAHGVI
+PAPPGVVRFATGWAGTLIAVAYVAVAGSVFVQFLPAFTGL
+>MHAAABBN_00328
+MSVPDTDTNSPVTIPTTTTDRPAGTGQASDVAGIPTVARHRPFGLVLLITGVVGWVASAI
+LVLERLELYEDAGYITSCDINPWVSCGKVMGTWQSELFGFPNPLIGIVAFAVVITTAMVT
+LSGASPGRWYWAGLQAGVTAGTVFTIWLWSQALFEIHILCLYCMIVWAAMIPLFILLTMR
+NLAHGVIPAHAAVVRFSAGWAGTLVAIAYVAVAASVFWTFFPALTGY
+>MHAAABBN_01772
+MTDRLTEPTAPSAASPVSAAGPAPAPAWFTGRRAFGLVLLVTGAVGWIASATLVLERLAL
+YENPGHTTSCDINPWVSCGRVMGTWQSELFGFPNPLIGIVAFAVVISTAMVVLSGARPGR
+GYWLGLQAGVTLGIGFVAWLWFQALYEIYILCLYCMIVWAAMIPLFLLLTARNLAHGVIP
+APPGVVRFATGWAGTLIAVAYVAVAGSVFVQFLPAFTGF
+>LFPAFLNI_02009
+MSVPDTDTNSPVTIPTTTTDRPAGTGQASDVAGIPTVARHRPFGLVLLITGVVGWVASAI
+LVLERLELYEDAGYITSCDINPWVSCGKVMGTWQSELFGFPNPLIGIVAFAVVITTAMVT
+LSGASPGRWYWAGLQAGVTAGTVFTIWLWSQALFEIHILCLYCMIVWAAMIPLFILLTVR
+NLAHGVIPAHAAVVRFSAGWAGTLVAIAYVAVAASVFWTFFPALTGY
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001586.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001586.fa
new file mode 100644
index 0000000000000000000000000000000000000000..47b4833d80a81809b3f788652d557db93b422ead
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001586.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02350
+MNATSLARKTALTGTGLLAALALAACGTADDDTAANPQETAVQQSPTQAATTAPASASGS
+ASASASGSASASASGSASPAAASGSVERQGDDPAYAAIDAILGLHDDGVIVEMDLDDDDA
+KWEVDVVVGDDVKEYDVTTGGQVSEGVRPQIDDDVRRAGEAQVTAETAISTALQGRTDQT
+VDEVDLDEEGGTLVWKVELDRENGEDGAEVKIDAKTGDVIEVEEG
+>MOLHKGIG_00584
+MTITTLTRKTALTGTGMLAALALAACGTTSDNGDDGSASPEVDASSSLASTPATDDASGS
+ATSSSASSASASSTAAAAGSDSATGQADDPAYAVIDAVLEKYGDGIIVAVDADDDDTTWE
+VDVVVGEEVKELDVTADGDITETDRESDLEDVQKAKDAEVTAQQALDTAREGRDGVTLDE
+MDLDDDNGTLQWEVGFDREDGSDGPEVEIDATSGEVLTVDEH
+>NAFOICDF_02245
+MTITTLTRKTALTGTGVLAALALAACGTTADNGDDGSASLEVDASSAVASTPATEDASTT
+SASASSASSAPASSTAAAAGRDSATGQADDPASAVIDAVLEKYGDGIIVGVDANDDDTTW
+EVDVVVDKEVKELDVTADGDITETDRESDPEDVQKAKDAEVTAQQALDTARKGRDGVTLD
+EMDLDDDNGTLQWEVEFDREDGSDGPEVEIDATSGEVLTVDEH
+>MHAAABBN_00317
+MTITTLTRKTALTGTGVLAALALAACGTTADNGDDGSVSPEVDASSAVASTPATDDASTT
+SASASSSASSTSASSTAAAASSGSGTGQADDPAYAVIDAVLEKHGDGIIVEVDANDDDTT
+WEVDVVVGEEVKELDVTADGDITETDRESDLEDVQKAKDAEVTAQQALDTAREGRDGVTL
+DEMDLEDDNGTLQWEVGFDREDGSDGPEVEIDATSGEVLTVDER
+>LFPAFLNI_00585
+MTITTLTRKTALTGTGMLAALALAACGTTSDNGDDGSASPGVDASSAVASTPTTDDASGS
+ASSSASSASASSTAAAAGSGSATGQADEPAYAVIDAVLEKYADGIIVAVDANDDDTTWEV
+DVVVGEGAKELDVTADGDITETDRESDPEDVQKAKEAEVTAQQALDTAREGRDGVTLDEM
+DLEDDNGTLQWEVRFDREDGSDGPEVEIDATSGEVLTVDER
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001587.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001587.fa
new file mode 100644
index 0000000000000000000000000000000000000000..410dfea75d3aca291f70bf17dcbdc099e33029cc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001587.fa
@@ -0,0 +1,60 @@
+>ACLBLIBL_02351
+MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY
+HCFGCGEHGDVISFLMELEHTTFTETVERLAARVGVELHYEDGGTGPDKAETGRRRRLLE
+ANKVADEFYRRALGSAEAQTGRDFLTQRGFTQEHAEQFGLGYAPQGWSHLLDHLRQKGFR
+DEELRASGLFSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP
+LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKMA
+RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTYVAVEPSGMDPCDLRMQQG
+DEAVRALIASRRPLFEFAIRAGLKDYDLDTVEGRAGALRHAAPIVAGIKDAVLRPGYERE
+LAGWLGLDPNAVHRAVAAAGRGQRRGGGSEPRREPERGPEPDQAPGQGRGPAPEGPSVGP
+QGRHGEAAAPAPQVLVPVDPRDPVARCERESLEVVLQHPTLLSAEQWTALYAARFTIPQY
+AAVHHGVKVAGSSGATPQRWVDAVRYAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIM
+NRLFALQIVHRKEELLGRLQRLGPDGDPAEFTALNSELMELEARRRALRADD
+>MOLHKGIG_00583
+MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY
+HCFGCGAHGDVISFLMELEHTTFTETVERLASRVGVELHYEDGGTGPDKAETGRRRRLFE
+ANKVADEFFRRALGSPEAQAARDFLTQRGFTQEHATQFGLGYAPQGWSHLLDHLRQRGFR
+DEELRASGLVSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP
+LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKVA
+RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTFVAVEPSGMDPCDLRMQKG
+DEAVRALIASRRPLFEFAIRAGLKDYDLDTVEGRAGALRHAVPIVAGIKDAVLRPGYERE
+LAGWLGLDPNAVHRAVAAAGRAPRRGPEPEARPAPADDGQAIGPQGRHGEAAAPAPRIVV
+PVDPRDPVARRERESLEVVLQHPTLLSAEQWTALYAARFTVPQYAAVHQGVKMAGSAGAT
+PQRWVDAVRDAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFALQIVHRKEELL
+GRLQRLGPEGDPAEFTRLNSELMELEARRRALRADD
+>NAFOICDF_02246
+MVRMAGLIVRKDIDLVRERADLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGV
+GTYHCFGCGEHGDVISFLMEMEHTTFTETVERLAARAGVELHYEDGQGPDRAETSRRRRL
+LEANKLADEFYRARLAAPDAQPGRDFLTGRGFTQEHAEQFGLGYAPQGWSALLDHLRQQG
+FRDDELRASGLFSEGQRGLYDRFRGRLLWPIRDMTGNTIGFGARKLFEDDPGPKYLNTPE
+TPLYKKSQVLYGIDLAKRAIAKERQLVLVEGYTDVMAAHLSGVETAVATCGTAFGADHIK
+IARRLISDDGTGGEVIFTFDGDAAGQKAALKAFDEDHRFLAKTFVAVEPNGLDPCDLRMQ
+QGEEAVRALIASRRPLFEFAISAGLKDYDLNTVEGRAGALRHAAPIVAGIKDSVLRPGYE
+RELAGWLGMDPNVVSRAVAQELRGRRRGGPSGGSAERTPAPERAPEGANAGQAPGEEPAA
+PRPALIVPVDPRDPAARRERESLEVVLQHPTLLSAEQWTAFYQARFTIPQYAAVHHAVKV
+AGTAGATPSRWVDAVRDAAPGEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFSLQIV
+HRKEELLGQLQRLGPEGDHDEFMRLNAELMELETRRRALRADD
+>MHAAABBN_00316
+MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY
+HCFGCGAHGDVISFLMELEHTTFTETVERLASRVGVELHYEDGGTGPDKAETGRRRRLFE
+ANKVADEFFRRALGSPEAQAARDFLTQRGFTQEHAVQFGLGYAPQGWSHLLDHLRQRGFR
+DEELRASGLVSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP
+LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKVA
+RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTFVAVEPSGMDPCDLRMQKG
+DEAVRALIASRRPLFEFAIRAGLKDYDLNTVEGRAGALRHAAPIVAGIKDAVLRPGYERE
+LAGWLGLDPNAVHRAVAAAGRAPRRGPEPEARPAPADDGQAIGPTGRHGEAAAPAPKIVV
+PVDPRDPVARRERESLEVVLQHPTLLSAEQWTALYAARFTVPQYAAVHQGVKMAGSAGAT
+PQRWVDAVRDAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFALQIVHRKEELL
+GRLQRLGPEGDPAEFTRLNSELMELEARRRALRADD
+>LFPAFLNI_00584
+MAGLIVRKDIDLVRERTDLKAVVEEFVTLRSAGVGSFKGLCPFHDERTPSFHVRPGVGTY
+HCFGCGAHGDVISFLMELEHTTFMETVERLASRVGVELHYEDGGTGPDKAETGRRRRLFE
+ANKVADEFFRRALGSPEAQAARDFLTQRGFTQEHAVQFGLGYAPQGWSHLLDHLRQRGFR
+DEELRASGLVSEGQRGLYDRFRGRLLWPIRDMTGATIGFGARKLYDDDPGPKYLNTPETP
+LYKKSQVLYGIDLAKRTIAKERQLVLVEGYTDVMAAHLAGVGTAVATCGTAFGADHIKVA
+RRLISDDGTGGEVIFTFDGDEAGQKAALKAFDEDHRFLAKTFVAVEPSGMDPCDLRMQKG
+DEAVRALIASRRPLFEFAIRAGLKDYDLNTVEGRAGALRHAAPIVAGIKDAVLRPGYERE
+LAGWLGLGPNAVHRAVAAAGRAPRRGPEPEARPTPASDGQAVGPTGRHGEAAAPAPRIVV
+PVDPRDPVARRERESLEVVLQHPTLLSAEQWTALYAARFTVPQYAAVHQGVKVAGSAGAT
+PQRWVDAVRDAVPQEVAGVVSELAVRDLPARTPEDVDRYCRDIMNRLFALQIVHRKEELL
+GRLQRLGPEGDPAEFTRLNSELMELEARRRALRADD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001590.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001590.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ded538a8b393396d96bb3520253dbe7f04cfc168
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001590.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_02358
+MAEGWAGPAHQPVLFGPQGRPPYAGRAVQTPGYTPWDRERWLPEPPKSSYRSDFERDRAR
+VLHSAGLRRLGAKTQVVAPDADDFARTRLTHSLEVAQVGRELGRSLGCDPDLVDTACLSH
+DLGHPPFGHNGEKALDALSADVGGFEGNAQTLRLLARLEQKKLFEDGSSAGLNLTRAALD
+AACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFREGVSGSRKSMEAQVMDLADDIS
+YSVHDVEDGVVNAAFQLKWLAIPEHRERVVETTRQWYLPLTDPAEVDEALARLEATDVWV
+SEMDGSRRALAAMKDMTSQLIGRFCTAAFDATRQVFGNEPLTRHGADVVVPAETETEIAV
+MKGIAAAYVMASEQRQPLYARQRELLAELVELLDASGDRYLEPMFAFDWREAADEAARRR
+VVLDQVASLTDSTALEWHHTLVQGAEFTRVWI
+>MOLHKGIG_00575
+MAEPTTPEPAAGAPAAPSSPWTGAAHQPVLFGPEGRPPYAGRAVQTPGYPPWDRERWLPE
+PPKSSYRSDFERDRARVLHSAGLRRLGAKTQVVAPDADDFARTRLTHSLEVAQVGRELGR
+SLGCDPDLVDTACLSHDLGHPPFGHNGEKALDALSEDVGGFEGNAQTLRLLARLEQKKLF
+ADGSSAGLNLTRAALDAACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFRAGVPGT
+RTSMEAQVMDLADDISYSVHDVEDGVVNAVFQLKWLAIPEHRERVVETTRQWYLPHTDPA
+EVDAALARLEATDVWVSEMDGSRRALAAMKDMTSQLIGRFCSAAFDATRQVFGNEPLTRH
+GADVVVPEETETEIAVMKGIAAAYVMTAEQRQPLYARQREVLAELVALLDATGDRYLEPM
+FTFDWAQAPDDAARRRVVIDQIASLTDSTAVEWHHTLVQGAEFRRVWI
+>NAFOICDF_02249
+MAEPQPTLFGPADRPPYAGRPVPTPGYTDWDRRRWLAEPPKSSYRSDFERDRARVLHSAA
+LRRLGAKTQVVAPDLDDFSRTRLTHSLEVAQIGRELGRSLGCDPDLVDTACLSHDLGHPP
+FGHNGEKALDAVAEAAGGFEGNAQTLRLLARLEQKKSFPDGSSAGLNLTRAALDAACKYP
+WVREDAPLRPDGKRSRKFGVYADDLPVFEWFRQGVHGARKSMEAQVMDLADDISYSVHDV
+EDGVVNSAFQLRWITEPGERRARVLETTRDWYLPGGDLEEIDAALTRLESQDVWMGEMDG
+SRRALAGMKDMTSQLIGRFCTAAFDATREVFGNEPLTRHAADVVVPAHTEHEIAVMKGIA
+AAFVMTSEQRQPLYARQRDLLTELVDLLMTTGDRYLDPMFAADFQDAADDAARARVVIDQ
+VASLTDSTAIEWHRTLVRGETFQRVWL
+>MHAAABBN_00307
+MAEPTTPVPAAGTPAAPSSHWTGAAHQPVLFGPEGRPPYAGRAVQTPGYTPWDRERWLPE
+PPKSSYRSDFERDRARVLHSAGLRRLGAKTQVVAPDADDFARTRLTHSLEVAQVGRELGR
+SLGCDPDLVDTACLSHDLGHPPFGHNGEKALDALSEDVGGFEGNAQTLRLLARLEQKKLF
+ADGSSAGLNLTRAALDAACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFRAGVPGT
+RTSMEAQVMDLADDISYSVHDVEDGVVNAVFQLKWLAIPEHRERVVETTRQWYLPHTDPA
+EVDAALARLEATDVWVSEMDGSRRALAAMKDMTSQLIGRFCSAAFDATRQVFGNEPLTRH
+GADVVVPEETETEIAVMKGIAAAYVMTAEQRQPLYARQREVLAELVALLEATGDRYLEPM
+FTFDWAQAPDDAARRRVVIDQIASLTDSTAVEWHHTLVQGAEFRRVWI
+>LFPAFLNI_00576
+MAERTTPAPADGAPAAPSSPWTGAAHQPVLFGPEGRPPYAGRAVQTPGYTPWDRERWLPE
+PPKSSYRSDFERDRARVLHSAGLRRLGDKTQVVAPDADDFARTRLTHSLEVAQVGRELGR
+SLGCDPDLVDTACLSHDLGHPPFGHNGEKALDALSEDVGGFEGNAQTLRLLARLEQKKLF
+ADGSSAGLNLTRAALDAACKYPWTREDAPLRPDGTRSRKFGVYEDDLPVFRWFRAGVPGT
+RTSMEAQVMDLADDISYSVHDVEDGVVNAVFQLKWLAIPEHRERVVETTRQWYLPHTDPA
+EVDAALARLEATDVWVSEMDGSRRALAAMKDMTSQLIGRFCSAAFDATRQVFGNEPLTRH
+GADVVVPEETETEIAVMKGIAAAYVMTAEQRQPLYARQREVLAELVALLDATEDRYLEPM
+FAFDWAQAPDDAARRRVVIDQIASLTDSTAVEWHHTLVQGAEFRRVWI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001593.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001593.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c74507737fc7768181d0338e840e1f95f472f164
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001593.fa
@@ -0,0 +1,33 @@
+>ACLBLIBL_02373
+MNECCNRDIRYENPLYMAEAAATADLLAGGRLELGVSRGSPEAAKDGQAQFGYELADGQT
+WAGVTRKRGRRFLAAVRGEGIATPDLASGWAHSSAPLRIEPHSPGLADRIWWGSGSAGSA
+VEAAKDGYDMLSSTLLLQDDGRPFHVQQADQIAGYLEAYEAAGHAGTGRTAVTRSAFVIQ
+DHEDELYFGRDRNSRESAGMLDGGRARSGPTYAGSAEEVAEKLAADDAVQAADWVLFANP
+NQLGPEYNAKIFAGWAEVWRLLGWDR
+>MOLHKGIG_00572
+MTRKHLGFLNFGHWIHRPGAEPDARQALDDVVAMAVAAEDAGLDGAWLRVHHFQRMFSSP
+FPILAAMAARTERISLGTGVIDLRYENPLYMAEAAATTDLISGGRLELGVSRGSPEAALD
+GQAQFGYALDEGQTWADVTRERGRRFLSAVRGEGIATPDLTSGWAHSSQPLRIEPHSPGL
+ADRIWWGSGSVGSVAGAATDGYNMLSSTLLLQDDGRPFHVQQADQIARYREAFAAAGHAG
+PGRTAVTRSAFVIQDREDELYFGRERASRDSSGMLEGGAARSGPTYAGSAEEVAEKLAAD
+DAVAAADWVLFANPNQLGVEYNAKIFAGWAEVWRLLGWDA
+>NAFOICDF_02253
+MTTKNLGFLNFGHWIHRPRVGRRPVEPDAKQAIDDVVQMAVDAEAAGLDGAWIRIHHFQR
+MFSSPFPILTAMAAHTERIHLGTGVIDLRYENPLYMAEAAATTDLLAGGRLELGVSRGSP
+EAARDGQAQFGYELADGQTWSDVARERGRRLLAGVRGEGIATPDLSSGWAHSSAPLRIEP
+HSPGLADRIWWGSGTVGSAVEAAKDGYGMLSSTLLLQDDGRPFHVQQADQIARYLEAYEA
+GGHTTPARTAVTRSAFVIQDHEDELYFGRDRHSRDSSGHLDGGAARSGPTYAGSAEEVAE
+LLAADDAVQAADWVLFANPNQLGAEYNAKLFAGWAEVWRLLGWDS
+>MHAAABBN_00296
+MRYENPLYMAEAAATTDLISGGRLELGVSRGSPEAALDGQAQFGYALDEGQTWADVTRER
+GRRFLSAVRGEGIATPDLTSGWAHSSQPLRIGPHSPGLADRIWWGSGSTPSAVEAGRDGY
+NMLSSTLLLQDDGRPFHVQQADQIARYREAFAAAGHTGPGRTAVTRSAFVIQDREDELYF
+GRERASRDSSGMLEGGAARSGPTYAGSAEEVAEKLAADDAVAAADWVLFANPNQLGVEYN
+AKIFAGWAEVWRLLGWDA
+>LFPAFLNI_00573
+MTRKHLGFLNFGHWIHRPGTAPDARQALDDVVAMAVAAEDAGLDGAWLRVHHFQRMFSSP
+FPILAAMAARTERISLGTGVIDLRYENPLYMAEAAATTDLLSGGRLELGVSRGSPEAALD
+GQAQFGYALAEGQTWADVTRERGRRFLSAVRGEGIATPDLTSGWAHSSQPLRIEPHSPGL
+ADRIWWGSGSVGSVAGAAADGYNMLSSTLLLQDDGRPFHVQQADQIARYREAFAAAGHAG
+PGRTAVTRSAFVIQDREDELYFGRERASRDSSGMLEGGAARSGPTYAGSAEEVAEKLAAD
+DAVAAADWVLFANPNQLGVEYNAKIFAGWAEVWRLLGWDA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001594.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001594.fa
new file mode 100644
index 0000000000000000000000000000000000000000..63d76dc3c7688a51bd51726782a99886879db956
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001594.fa
@@ -0,0 +1,38 @@
+>ACLBLIBL_02376
+MSGAYDDDAGALFDSAAVSGGEVVLRPWRAGDDLALLQVWGDPANVQQHQDRAMLAEDAE
+RPWRRALVAEDAGVPVAAGVVYASSLHPQRLWLYVETAAPERRRGIGRALVAALRGLAAE
+AHAAGTVPTAALKARFAKDALVPGTAVEEGVDTEAVRAQTAALAAGTEAFLAAEGFTPVQ
+RSRRVAVAPGAIGLPDVRDEDRPDGVVLEEASTGSVELTQAVAAFYDAVHAWDPSTMSVG
+AAQQLLLGPATGASGAVVLRDAPKAEGGRIRAFAVSYTPERQEAPADVLVGWDPELSEED
+ALQSVADLLALLVAQHPVQVEVDEAMAPLERIVDGLIGGNAARTLVDTYVFVDDAA
+>MOLHKGIG_00567
+MDLPAGVTLRPWAEGDDLRLLEVWGDPADVQQHQDRAMLAPDADTPWRHTLVAEDDGVPV
+GAGTVVAQALHPRRLWLYLEVAPTARRRGIGSALLGALRDAVEQAHAAGQVTTTHLKTRF
+AVASRVAVATGRSADAAEATAPAAGEEAGEAHAAQVAGTEAFLVAAAFSPVQRSRRVAVA
+PGSIALPPLRDEDHPEGAVLEDAATGSVELTRAVAAFYDAVHGWDPAQMSVGAAQQLILG
+PATGASGAVVLRDAPREEGGAVQAFAVSYTAERQDAPADVFLGWDPELPLDQAQLAAGQL
+LAMLVAQHPVQVEVDEAMTALEPILDGLIAQRAAATLVDTRIWATDPA
+>NAFOICDF_02260
+MSPRHDDDAPALTAAVSGGEVVLRPWAEGDDLRLLEVWGDPADVQQHQDRAMLAADADSP
+WRRTLVAEEDGVPVGAAVAFAQPLHPGRLWVYGEVARTVRGRGVGRALLEALRGLVAAAH
+EAGAVPTTELKARFAVASRVPVGGGEVVEAAPGEAPEAGAAGAEAHAAQVAATERFLVAA
+GFTPVQRSRRIAVAPGVIALPALRDEEHPEGRVLEEISTGSVELTRAVAAFYDAAHAWDP
+SQMSVGAAQQLILGPQTGAAGAVVLRDAPREEGGTIQAFAVSYTAERQDAPADVLLGWDP
+SLGLEEAQLAVGDLLALLVAQHPVQVEADEAMTALEPILDALLAKRAAGTLVDTRVWATD
+PS
+>MHAAABBN_00292
+MTGAAGAAGHDDGGALFDSAAVAGGEIVLRPWRPGDDLALLEVWGDPANAQQHQDRAMLA
+EDAERPWRRALVAEAAGVPVAAGVVYASSVHPRRLWLYVETAAAERRRGIGRALVAALRG
+LAAEAHAAGAIPTTALKARFAKDALVPGVSGADPQTDAEGPAGQPPVDTEAVRSQTAALA
+AGTEAFLVAEGFTPVQRSRRVAIAPGAIGLPDVRGEEHPDGVVLEEASTGSVELTQAVTA
+FYDAVHAWDPSTLSVGAAQQLLLGPATGAAGAVVLRDAPKAEGGRIRAFAVSYTPERQDA
+PADVLVGWDPELGEEDALQAVADLLALLVAQYPVQIEVDEAMAPLERIVDGLIGGNAART
+LVDTYVFVDDAPGA
+>LFPAFLNI_00570
+MTGAAGAAGHDDGGALFDSAAVGGGEIVLRPWRPGDDLALLEVWGDPANAQQHQDRAMLA
+EDAERPWRRALVAEAAGVPVAAGVVYASSVHPRRLWLYVETAAAERRRGIGRALVAALRG
+LAAEAHAAGAIPTTALKARFAKDALVPGVTGADPQTEADGATGRPPVDTDAVRSQTAALA
+AGTEAFLVAEGFTPVQRSRRVAIAPGAIGLPDVRGEEHPDGVVLEEASTGSVELTQAVTA
+FYDAVHAWDPSTLSVGAAQQLLLGPATGAAGAVVLRDAPKAEGGRIRAFAVSYTPERQDA
+PADVLVGWDPELGEKDALQAVADLLALLVAQYPVQIEVDEAMAPLERIVDGLIGGNAART
+LVDTYVFVDDATGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001597.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001597.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07b675675eaa8f6574a96c976be28be60670eb83
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001597.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02379
+MNNDTANTAPSSETAPFTVRWSRPEGERTEDLLILLHGYGANEDDLFGLVPHLPERFTVA
+AVRAPMTLQPGGYAWFPLSQDPVTGEIGSDAASVRTAIEDLHAWVGAVREGFRTVSLLGF
+SQGMALATSLLRLDPTAYAATVALSGFVVDPTREESGLAGLFDGDDEVARVRPKVFWGRG
+QDDPIISEARVEASHAWLNAHVDLMKIVYAGLPHAINQQELGHVKEYLEHMVR
+>MOLHKGIG_00564
+MPLARLAGVNANPTPAVEPVVRWSRPEGERTEDLLIVLHGYGANEDDLFGLVPHLPEHVT
+VAAVRAPLPLQPGSHAWFPLSQDPVTGELGSTAEPVREAVEALHAWVQAVRGDFRTVSLL
+GFSQGMAMATSLLRLDPEAYACTVALSGFVVDPELDEPRLRELFTRDDDVARVRPKVFWG
+RGQEDPIISEPRVEETHAWLNAHVDLMKIVYAGLGHAINEQELGHVKEYLAHMVPPRG
+>NAFOICDF_02263
+MNDTTPRDPAPFAVRWSRPEGERTEHLLVLLHGYGADEDDLFGLVPQLPEAFTALAVRAP
+MDLPQGGAAWFPLTQDPATGEIGSDAGAVRAAVEDLHAWLPGVSGGFRTVSLLGFSQGMA
+MATSLLRLDPAAYAATVALSGFVVDPLHVEPELEGLFPADETVDAVTPKVFWGRGQEDPI
+ISAQRVEESHGWLTAHTDLTKVVYAGLPHAISPQELGHVREYLTHVVL
+>MHAAABBN_00289
+MNANPTPAVEPVVRWSRPEGERTEDLLIVLHGYGANEDDLFGLVPHLPEHFTVAAVRAPL
+PLQPGSHAWFPLSQDPVTGELGSTAEPVREAVEALHAWVQAVRGDFRTVSLLGFSQGMAM
+ATSLLRLDPEAYACTVALSGFVVDPELTEPRLRELFTRDDDVARVRPKVFWGRGQEDPII
+SEPRVEETHAWLNAHVDLMKIVYAGLGHAINEQELGHVKEYLAHMVPPRG
+>LFPAFLNI_00567
+MPLARLAGVNANPTPAVEPVVRWSRPEGERTEDLLIVLHGYGANEDDLFGLVPHLPEHVT
+VAAVRAPLPLQPGSHAWFPLSQDPVTGELGSTAEPVREAVEALHAWVQAVRGDFRTVSLL
+GFSQGMAMATSLLRLDPEAYACTVALSGFVVDPELAEPQLRELFTRDDDVARVRPKVFWG
+RGQEDPIISEPRVEETHAWLNAHVDLMKIVYAGLGHAINEQELGHVKEYLAHMVPPRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001599.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001599.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b0a3bf2ea270632f83572f67d054e727cc3df00d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001599.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02381
+MTATVSRPPRAALPEGGRHRLRIGELRTETGGVLPDVELAYETWGELDADGSNAVLVLHA
+LTGDSHVAAHAADPTPGWWDALVGPGRAVDTDRWFVVAPNMVGGCHGSTGPSSPAADGRP
+WGSRFPFLTLRDAVAAERRLADHLGVGAWQAVIGGSMGGARALEWAATHPERVAGVGVLA
+ATARSSADQIAWGQAQTAAIRLDPGFLGGDYYEGAGPAAGLGIARRIAHTTYRTAGELER
+RFGRSPQGAEDPFGAVVGVPGGRGRYAVESYLDHQATKLTGRFDANSYLLLTEALLGHDV
+GRGRGGVEAALAGYRGRAFVAAVDSDRLYLPAEAQALAAVLPARPPVHTIVSPIGHDGFL
+TEYGQVADALRDSLAL
+>MOLHKGIG_00562
+MTAVATRPSRTALPRGGRHRLRVGELRTETGGLLPDVELTYETWGTLAADGSNAVLVLHA
+LTGDAHVAAHEEDPTPGWWDALVGPGRAVDTDRWFVVAPAMIGGCHGSTGPSTPAPDGRP
+WGSRFPFLTLRDAVEAERRLADHLGIGAWRAVIGGSMGGARALEWAATHPARVAGVGVLA
+ATAASSADQIAWGQAQTAAIRLDPDFQGGDYYPGPGPVAGLGIARRIAHTTYRTAGELGQ
+RFGREPQGVEDPFGAVVGVPGGRGRYAVESYLDHQAAKLADRFDANSYLVVTEALMGHDV
+GRGRGGVAAALADYRGRAFVAAVDSDRLYLPAESEALAAALPARPPVHTIASPIGHDGFL
+TEYGQVADTLKRTLAL
+>NAFOICDF_02265
+MTAIDPRILPGHAAHRPHQGPQGEAAPSARSAAPHDARPADRLPAGEFRTLSVGPLELEA
+GGRLPGVELAFETWGTLAEDGANAVLVLHALTGDSHVASHRRDESAGWWEELIGPGLAVD
+TDRWFVVAPNMLGGCDGSTGPSSPAPDGAPWGGRFPFVTIRDAVAAERRLLDALGVTALQ
+AVIGGSMGGARAIEWAVSHPDLVRGVAVLASTASSSAEQIAWAQAQTHAIRLDPEWRGGD
+YHPGPGPVTGLGIARRIAHTTYRSAAELQHRFGREPQGAEDPLGTASGERVGRYQVESYL
+DHQASKLVGRFDAGSYVALTEALMSHDVGRGRGGVEAALASYPGRAFVAAVDSDRLYFPA
+ESERLASLLPGEVPVHTIHSPIGHDGFLTEYGQIADELRRTLEL
+>MHAAABBN_00287
+MTAVATRPSRTALPRGGRHRLRVGELRTETGGLLPDVELAYETWGTLAADGANAVLVLHA
+LTGDAHVAAHEEDPTPGWWDALVGPGRAVDTDRWFVVAPAMIGGCHGSTGPSTPAPDGRP
+WGSRFPFLTLRDAVEAERRLADHLGIGAWRAVIGGSMGGARALEWAATHPARVAGVGVLA
+ATAASSADQIAWGQAQTAAIRLDPDFQGGDYYPGPGPVAGLGIARRIAHTTYRTAGELGQ
+RFGREPQGVEDPFGAVVGVPGGRGRYAVESYLDHQAAKLTDRFDANSYLVVTEALMGHDV
+GRGRGGVAAALADYRGRAFVAAVDSDRLYLPAESEALAAALPARPPVHTITSPIGHDGFL
+TEYGQVADTLKRTLAL
+>LFPAFLNI_00565
+MTAVATRPSRTALPRGGRHRLRVGELRTETGGLLPDVELTYETWGTLAADGSNAVLVLHA
+LTGDAHVAAHEEDPTPGWWDALVGPGRAVDTDRWFVVAPAMIGGCHGSTGPSTPAPDGRP
+WGSRFPFLTLRDAVEAERRLADHLGIGAWRAVIGGSMGGARALEWAATHPARVAGVGVLA
+ATAASSADQIAWGQAQTAAIRLDPDFQGGDYYPGPGPVAGLGIARRIAHTTYRTAGELGQ
+RFGREPQGVEDPFGAVVGVPGGRGRYAVESYLDHQAAKLTDRFDANSYLVVTEALMGHDV
+GRGRGGVAAALADYRGRAFVAAVDSDRLYLPAESEALAAALPARPPVHTIASPIGHDGFL
+TEYGQVADTLKRALAL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001601.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001601.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1bb95bb856634bc24e6574605c5c6e5a1d399ec9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001601.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02383
+MDHVSYAAGPEGLDATVARIAEALGVERIKGGIHPRFGTQNALFPMAGGQYLEVVEALDH
+PASLSAPFGQLVRSRSEQGGGWMSWAVSTTDIGRFERRLGREAVPGNRRFPDGRELSWRQ
+IGIKGTIADPQLPFIMRWADGQEDMHPSQAAEAQASIERLSIAGSPDRLAEWLGGEGEDA
+HVEDLNVEYVAPSGTPGIVSVTFRTPRGDVTL
+>MOLHKGIG_00560
+MDHVSYAAGPEGLDATVARIAETLGIERIKGGVHPRFGTQNALFPMAGRQYLEVVEALDH
+PASLSAPFGQLVRARTEQGGGWMSWAVATTDIGRFERRLGREAVPGNRRFPDGRELSWRQ
+IGVKGTLADPQLPFILRWADGQEDMHPSQAAEPQATIERLNIAGSPERLAEWLGDDEDGQ
+VQDVNIEYVAPSGTPGIVSVTFRTPKGEVTL
+>NAFOICDF_02267
+MNTCRMDHVSYAAGPEGLDATVARIAERLGVERVKGGIHPRFGTQNALFPMTGNQYLEVV
+EALDHPASLSAPFGQLVRTRSEQGGGWMSWAVTTNDIGRFERRLGREAVPGNRRFPDGRE
+LSWRQIGVKGTLADPQLPFILRWADGQEDMHPSQAAPAQASIARLSIAGSPDRLREWLGG
+TEDDEVADVSVDYVAPSGTPGIVSVTFSTPKGEVTL
+>MHAAABBN_00285
+MDHVSYAAGPEGLDATVARIAETLGIERIKGGVHPRFGTQNALFPMTEGQYLEVVEALDH
+PASLSAPFGQLVRARTEQGGGWMSWAVATTDIGRFERRLGREAVPGNRRFPDGRELSWRQ
+IGVKGTLADPQLPFILRWADGQEDMHPSQAAEPQATIERLNIAGSPERLAEWLGDDEDGQ
+VQDVNIEYVAPSGTPGIVSVTFRTPKGEVTL
+>LFPAFLNI_00563
+MDHVSYAAGPEGLDATVARIAETLGIERIKGGVHPRFGTQNALFPMTEGQYLEVVEALDH
+PASLSAPFGQLVRARTEQGGGWMSWAVATPDIGRFERRLGREAVPGNRRFPDGRELSWRQ
+IGIKGTLADPQLPYILRWADGQEDMHPSQAAEPQATIEHLNIAGSPERLAEWLGGEDEDG
+QVQDVNIEYVAPSGTPGIVSVTFRTPKGEITL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001603.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001603.fa
new file mode 100644
index 0000000000000000000000000000000000000000..33ba1d3c7433810b1e2025a27947d0fac4b36ee6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001603.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_02385
+MASDPVDSELELVHRALGRLRPHVSPADARALHEADWSAGTVEEGGQFNRVLVCAGAGVL
+RMTRAHEVGAAPAARWSPERDPARQLGRRMALLDGLDAALAEQGVAWTVPVALSDPVPAG
+TGAAVLQRYLPGGPHPPHEGDPAVLRRLLDEIAAVDVADPRIAPHLGRPFSFRGPWTAQR
+AEHVAGIPGRLAPRLGAWPGDDVDARTGADAWADAVARVTRAVTAWTEEPPVPPSLVHGD
+LAGHNMRWRAMPAADDAPGEVRWELAGVLDWDLACAWDPALNVAYLSLWHGEDQVERLAV
+DAGEAARARVWLGAMALETLDDAAARDELVGGLPNGSWRRLLRKALPRVARALTALG
+>MOLHKGIG_00558
+MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL
+RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLASALAERDVSWAVPVALSDPVSAG
+PGAAVLQRFLPGGPYPPHEGDPDVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPAR
+ARHVAALPGAVAARLGAWEGHDVDARLGAEAWPDAVAALTDAVTTWTAAPPVPPSLVHGD
+LAGHNMRWRAVPEDEDPRAPLRWALAGVLDWDLACAWGPALNVAYLALWHGEQKVPDLAR
+DAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLRKTLPRVARALTALDG
+>NAFOICDF_02269
+MASDPARSELDLVAAALQRLRPGLDDGVAARLRGADWSAGRVEEGGQFHRVLVLEDVGVL
+RMTRVHEAGAAPAARWTPERDPAVHLPRRLALLDGLAAVLAEAGVRWSLPTALSAVVEDG
+PGAAVLQRYVPGFPHPPHEGDPAVLRGVLADLAAVDVADPRVAPHLGRPFTFRGPWTPER
+AAHVAGLPARLAPRLGAWPGDALGHAGDETAAGEAAVRLRADAWGESVTALTGVVSAWTR
+EPPVPPALVHGDLAGHNMRWRVVPAAATPDAEVPDAPVRWELAGVLDWDLACAWDPALNV
+AYLGLWHGEDLVEAIAADPAEARRARVWLGAMALETLDDAGARDVLVGGLAESSWRRLLR
+KTLPRVGRALAAAAA
+>MHAAABBN_00283
+MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL
+RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLAAALAERRVPWTVPIALSDPVPAG
+PGAAVLQRFLPGGPHPPHEGDPAVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPER
+ARHVAALPGAVAARLGAWEGHDVDARLGAEAWPDAVAALADAVTTWTAAPPVPPSLVHGD
+LAGHNMRWRAVPEDEDPRAPLRWALAGVLDWDLACAWDPALNVAYLALWHGEEKVPDLAR
+DAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLRKTLPRVARALTALDG
+>LFPAFLNI_00561
+MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL
+RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLAAALAERRVPWTVPIALSDPVPAG
+PGAAVLQRFLPGGPHPPHEGDPAVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPER
+ARHVAALPGAVAARLGAWEGHDVDARLGAEAWPDAVAAVTDAVTAWTAAPPVPPSLVHGD
+LAGHNMRWRAVPEDEDPRAPLRWALAGVLDWDFACAWDPALNVAYLALWHGEEKVPDLAR
+DAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLRKTLPRVARALTALDG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001604.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001604.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab784cfc44580b10a70cbf00335fb2071764d737
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001604.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_02388
+MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG
+TLPVLNREVVEYAVRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD
+VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASNSLVDYNRAGVPLIEIVTKPIV
+GAGARAPELARAYVTAIRDIVKAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN
+VNSTRAVQHAVTHEIQRQAALLAAGGTVTQETRHWHEDTRTTTSGRPKSDADDYRYFPEP
+DLVPVHVDAAWVERVRAEMPELPAVRNKRLKAEWGYTDEEFRDVVNAGVLDEIVATVEAG
+ASPAAARKWWMGEIARLANVRETAVAELGVTPAHVVEVEELIAAKTINDKIAKQVLGLVA
+DGEGTPKEIVEAKGLAVVSDDGALTEAVDAAIAANPDVAEKIRGGKMAAVGALIGPVMKA
+TRGQADAGRVREIVLERLGVS
+>MOLHKGIG_00557
+MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG
+TLPVLNRKVVEYAIRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD
+VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASASLVDYNRAGVPLIEIVTKPIV
+GAGARAPELARAYVTAIRDIVQAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN
+VNSTRAVQHAVTHEIQRQAAVLAAGGTVTQETRHWHEDTRSTTSGRPKSDADDYRYFPEP
+DLVPVHVDAAWVERVRAAMPELPAVRNKRLKAEWGFSDEEFRDVVNAGVLDEIVATVEAG
+ASAAAARKWWMGEIARLANVREVAVAELGITPAHVVEVEELIAAKTINDKIAKQVLGLVA
+DGEGAPKEVVAAKGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMAAVGALIGPVMKA
+TRGQADAGRVREIVLERLGVS
+>NAFOICDF_02271
+MSTAELMDFQEAMDRFDPVLGFEVHVELNTKSKIFSTGANAFGDEPNTNVTPLDLGLPGT
+LPVLNREAVESAIALGLALDAQIAPSCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLDV
+ELEDGTVFRVEIERAHLEDDAGKLTHQGGSGRIQGASASLVDYNRAGVPLIEIVTRPIVG
+AGDRAPEIARAYVTALRDIVKAIGISDARMEHGNVRCDANVSLMEKGASAFGTRTETKNV
+GSTRAVQHAVTHEIQRQAAILAAGGTITQETRHWHEDTRTTTSGRPKSDADDYRYFPEPD
+LLPVVVDEAWIERVRAGMPELPAVRNKRLKGEWGFSDEEFRDVVNAGVADQIAQTVEAGA
+SPAAARKWWMGEIARLANLREVEAAELGVTPAHVVEIEELIAAKTINDKIAKQVLGLVAD
+GEGAPKQIVAAQGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMQAVGALIGPVMKAT
+RGQADAGRVREIVLERLGVA
+>MHAAABBN_00282
+MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG
+TLPVLNRKVVEYAIRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD
+VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASASLVDYNRAGVPLIEIVTKPIV
+GAGARAPELARAYVTAIRDIVQAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN
+VNSTRAVQHAVTHEIQRQAAVLAAGGTVTQETRHWHEDTRSTTSGRPKSDADDYRYFPEP
+DLVPVHVDAAWVERVRAAMPELPAVRNKRLKAEWGFSDEEFRDVVNAGVLDEIVATVEAG
+ASAAAARKWWMGEIARLANVREVAVAELGITPAHVVEIEELIAAKTINDKIAKQVLGLVA
+DGEGAPKEVVTAKGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMAAVGALIGPVMKA
+TRGQADAGRVREIVLERLGVS
+>LFPAFLNI_00560
+MSHAEQTMDFAEAMERFDPVLGFEVHVELNTATKIFSSAPNAFGDEPNTNVTPLDLGLPG
+TLPVLNRKVVEYAIRLGVALDAQVAETCRFARKNYFYPDTPKNFQTSQYDEPIVFDGHLD
+VELEDGEVFRVEIERAHLEDDAGKLTHVGGSGRIQGASASLVDYNRAGVPLIEIVTKPIV
+GAGARAPELARAYVTAIRDIVQAIDISDARMERGNVRCDANVSLMPKGATEFGTRTETKN
+VNSTRAVQHAVTHEIQRQAAVLAAGGTVTQETRHWHEDTRSTTSGRPKSDADDYRYFPEP
+DLVPVHVDAAWVERVRAAMPELPAVRNKRLKAEWGFSDEEFRDVVNAGVLDEIVATVEAG
+ASAAAARKWWMGEIARLANVREVAVAELGITPAHVVEVEELIAAKTINDKIAKQVLGLVA
+DGEGAPKEVVAAKGLAVVSDDGALTEAVDAAIAANPDVAEKIKGGKMAAVGALIGPVMKA
+TRGQADAGRVREIVLERLGVS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001609.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001609.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e97bef658966a470ccd32b9f7c8203719f1f686
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001609.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_02396
+MEPSAETPAAAPRPEAAGATHVGAVRELNEDAWTLVGDPLVLAAVADGMGGHEAGEVASA
+AAIEVLRRRGPEVLAPGVAHTPEELGHLVHEADAAVVAAGGGRSGTTLTVLACIDTAANR
+WAVANVGDSRIYLRPAGAPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGS
+SEPLTVDVAEIPVASGDRLLLCSDGLTGELLDEEIRALIDDADELEDALVKLVEAALWRG
+GRDNVTAVLVRIP
+>MOLHKGIG_00550
+MDPRPETPSAPRPQAAGATHVGAVRDLNEDAWTLVGEPLVLAAVADGMGGHEAGEVASAA
+AIETLRRRAPEVLAPGTAHTPQELGHLIHEADAAVVEAGLGRSGTTLTVLACLDTERGRW
+AVANVGDSRVYLRPVGSPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGSR
+EALTVDVAEVPLASGDLVLLCSDGLTGELLDEEIRALIDDADTLEDALEKLIGAALWRGG
+RDNITAVLVRIP
+>NAFOICDF_02280
+MSEPHAADAAPAEPGAWASVPRPEAVAVTHVGAVRELNEDSWAVVGDPLLLAAVADGMGG
+HEAGEVASAAAVAELHRRAPSVLAPGVAHTPQELGALVHEANAAVLAAGGGRAGTTLTVL
+ACLDTEVGRWAVANVGDSRIYLRPVGAGVLQQVTVDHSAVQLMVDAGELTPAEARVHPRR
+NVITRALGSTQALTVDVMELDVAPGDRFLLCSDGLTGELLDDEILAIMDDAATLDEAAER
+LVEAALWRGGRDNITAVLVRIP
+>MHAAABBN_00275
+MDPRPETPSAPRPQAAGATHVGAVRDLNEDAWTLVGEPLVLAAVADGMGGHEAGEVASAA
+AIETLRRRAPEVLAPGTAHTPQELGHLIHEADAAVVEAGLGRSGTTLTVLACLDTERGRW
+AVANVGDSRVYLRPVGSPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGSR
+EALTVDVAEVPLASGDLVLLCSDGLTGELLDEEIRALIDDADTLEDALEKLIGAALWRGG
+RDNITAVLVRIP
+>LFPAFLNI_00553
+MDPRPETPSAPRPQAAGATHVGAVRDLNEDAWTLVGEPLVLAAVADGMGGHEAGEVASAA
+AIETLRRRAPEVLAPGTAHTPQELGHLIHEADAAVVEAGLGRSGTTLTVLACLDTERGRW
+AVANVGDSRVYLRPVGSPVLQQLTVDHSAVQMLVDAGELTPAEARVHPRRNVITRALGSR
+EALTVDVAEVPLASGDLVLLCSDGLTGELLDEEIRALIDDADTLEDALEKLIGAALWRGG
+RDNITAVLVRIP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001610.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001610.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b59d3f67c4d400c90d6310572a4919cca54662c8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001610.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02397
+MSRAETPETAPLPIIAPDGSGPAEAPRRKDPHDERRADRHEDRRGEAAADRLEEVDAPPP
+GAGWTTAMRTLDAGLVVGPRAYTAREVAQRMGVSTASARKIWRALGYPTSPEGHKAFTEA
+DVEAFESVLELVRSGALNEDAAISLARSIGQMTDRMVVWQIEALVEDKIVSEGLTDPEAR
+RAAVDLLPEIVTPLERAMQIVYRRQLNRAVKRLTVRVEAGLAASEEGRDGSESDSPLPLA
+RAVGFADMVSYTTLSRTMDDRTLARMVQRFETLSAEIISAGGGWLVKTIGDEVMFNAETP
+ETGAAIALALAEAIAADDELPSARVALTWGRVLSRMGDIYGPTVNLAARLTSLADPGTVL
+VDAMTAAALSRDERFVLVPQPPRIVRGVGEVRPSLLLNGSAQTLLAD
+>MOLHKGIG_00549
+MSRPETPDTAPLPIVPPAEDETARDVEERSAEPAGWTSAMRTLDAGLVVGPRAYTSREVA
+QRLGVSMASARKIWRALGYPTSPEGHKAFTEADIEAFESVLTLVRSGTLNEDTAISLARS
+IGQMTDRMVVWQIEALVEDKIASEGLTDPEARRAVVDMLPDMVGPLEKSMRIVYRRQLNR
+AVQRLTVRVEAGLAASAEGRDGSESDAPLPLARAVGFADMVSYTTLSRTMDDRTLARMVL
+RFESLAAETISAGGGWLVKTIGDEVMFNAETPEAGAAIALSLAETIAADEELPSARVALT
+WGRVLSRMGDIYGPTVNLAARLTSLADPGTVLVDAMTAAALSRDERFVLVPQPPRIVRGF
+GEVRPSLLLDGSAQTLLAD
+>NAFOICDF_02281
+MTRDTHHDAVPETAPLPVQAPAGAADPAVGRRESDALHHGWTSAIRTLDAGLLDRPRSYS
+RREAAQRLGISSVSARKIWRALGYPTVKDEEKVFSAEDIDAFEQVLSLVRDGMLNEDTAI
+SLARSVGQMTDRMVVWQIEALVEDQIAAEGKTDPEARRAAVEMLPGLVEPLEKVMRIVYR
+RQLTNAVQRLTVRVEAGLAASERGRDGSEDDAPLPLARAVGFADMVSYTTLSRTMGERTL
+ARTVQRFESKAAEIIAAGGGWLVKTIGDEVLFNAETPEAGATIALALAEAMADDDQLPAA
+RVSLAWGRVLSRLGDIYGPTVNLASRLTSLADPGTVLVDAMTAAALSRDERFVLVPQPPR
+IVRGFGEVRPSLLMNGAAQPLIAD
+>MHAAABBN_00274
+MSRPETPDTAPLPIVPPAEDETARDVEERSAQPAGWTSAMRTLDAGLVVGPRAYTSREVA
+QRLGVSMASARKIWRALGYPTSPEGHKAFTEADIEAFESVLTLVRSGTLNEDTAISLARS
+IGQMTDRMVVWQIEALVEDKIASEDLTDPEARRAVVDMLPDMVGPLEKAMRIVYRRQLNR
+AVQRLTVRVEAGLAASAQGRDGSESDAPLPLARAVGFADMVSYTTLSRTMDDRTLARMVL
+RFESLAAETISAGGGWLVKTIGDEVMFNAETPEAGAAIALSLAETIAADEELPSARVALT
+WGRVLSRMGDIYGPTVNLAARLTSLADPGTVLVDAMTAAALSRDERFVLVPQPPRIVRGF
+GEVRPSLLLDGSAQTLLAD
+>LFPAFLNI_00552
+MSRPETPDTAPLPIVPSAEDETARDVEERSAQPAGWTSAMRTLDAGLVVGPRAYTSREVA
+RRLGVSMGSARKIWRALGYPTSPEGHKAFTEADIEAFESVLTLVRSGTLNEDTAISLARS
+IGQMTDRMVVWQIEALVEDKIASEDLTDPEARRAVVDMLPDMVGPLEKAMRIVYRRQLNR
+AVQRLTVRVEAGLAASAQGRDGSESDAPLPLARAVGFADMVSYTTLSRTMDDRTLARMVL
+RFESLAAETISAGGGWLVKTIGDEVMFNAETPEAGAAIALSLAETIAADEELPSARVALT
+WGRVLSRMGDIYGPTVNLAARLTSLADPGTVLVDAMTAAALSRDERFVLVPQPPRIVRGF
+GEVRPSLLLDGSAQTLLAD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001612.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001612.fa
new file mode 100644
index 0000000000000000000000000000000000000000..915449c2234dce40e217d3162aac452fb506c5ad
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001612.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_02401
+MSDPDLTTTAGRLADLHRRLEATAAPGGEGAVERQHARGKHTARERIDLLLDEGSFVELD
+ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ
+EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA
+YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNSTSGTAHYMASSEE
+DAIAYVQELLELLPSNNLAEAPTFEAADPETTDEDLALDEIVPDSANQPYDMLEVIGAIV
+DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPQQLAGTLDIAASEKAARFVRFCDAF
+NIPILTLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS
+KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATQDAGGDVDARRAEIVADYEAELLN
+PYQAAELGYVDAVVPPHATRGALIRALRATLHKREARPAKKHGNMPL
+>MOLHKGIG_00546
+MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELD
+ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ
+EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA
+YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE
+DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLEVIASIV
+DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAF
+NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS
+KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN
+PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL
+>NAFOICDF_02284
+MSAPELSTTAGRLADLHRRLEATAAPGGEAAVERQHSRGKHTARERIDLLLDEGSFVELD
+ALATHRTTAFGMDAKHPAGDGVVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ
+EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVMASGMIPQISLIMGPSAGGAA
+YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNSTTGTAHYMATSEE
+DAIAYVQDLLEYLPSNNLAEAPVFEAESLEETEQDLALDTIVPDSANQPYDMLEVIAALV
+DDGHLLQLQEMYAPNVITGLARLDGMSVGVVANQPQQLAGTLDIAASEKASRFVRFCDAF
+NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS
+KKLGADLNLAWPSAQIGVMGPQGAVNILYRRELAAAEAAGEDVEARRAQIVADYEAELLN
+PYQAADLGYVDAVVPPRQTRAHLVRALRATFHKREARPAKKHGNMPL
+>MHAAABBN_00271
+MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELD
+ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ
+EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA
+YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE
+DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLAVIASIV
+DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAF
+NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS
+KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN
+PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL
+>LFPAFLNI_00549
+MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELD
+ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ
+EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA
+YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE
+DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLEVIASIV
+DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAF
+NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS
+KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN
+PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001614.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001614.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e4af868b35f4e665c28aa5cf161d74e98c111b6d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001614.fa
@@ -0,0 +1,55 @@
+>ACLBLIBL_02403
+MTQNTPVAADRGARTPSAIDALAERYVADVLALHPDEATTLGFPGHETEYADFSPAGTRA
+DDELNARLLADLEALEPQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAV
+FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVIEQARAHGA
+AGGFFPGLVERAEATDVVDAALAERIRAGADAAAQAYRDFADTLQAELRPHAPEADGVGI
+ELYRLGSRAFLGAEIDLEETYRWGQEELARIIAAQEADAERIKPGATIEEARALLDADPE
+RTLNGTAALQAWMQRLSDEAVQAMKAHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR
+PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG
+EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP
+EKGYAFLEKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRTEHEEREGEGFDLK
+AFHTRALRLGGMGLDTLRAALA
+>MOLHKGIG_00544
+MTQHTSEAAVDGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARA
+DDELNARLLEDLAALELQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAV
+FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVVEQARAHGA
+AGGFFPGLVERAEAADVVDDALAARIRSGADAAAQAYRDFADTLEAELRPHAPEADGVGI
+EYYRLASRDFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPE
+RTLKGTEALRTWMQRLSDDAVEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR
+PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG
+EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP
+EKGYAFLSKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLK
+AFHTRALRLGGMGLDTLREALA
+>NAFOICDF_02286
+MTQTTSAPEGARTPSAVDALAERHVAAYLALRPDEATSLGMPGHETEYPDLSPAGAAALD
+ELNRTTLEELAGLEPADDVDRVTVAAMRERLGLEREIHATGRTELNNIASEAQGIRAIFD
+LMPTDTAEQWGHIAGRLENLPAALRGYAESLLASRDAGHVAAVRQVEIVVEQARAHGAEG
+GFFPGLVERAEAADVVDAALAERIRTGAAGAAAAYAEFADTLEAELRPHAPEADAVGIEH
+YRLASRVFLGAEIDLEETYRWGQEELDRIIAAQEADAERIKPGATIEEARAILDADPART
+LTGTKALQEWMQRLSDEAVEAMKAHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSRPG
+RMWWSVPAGEEEFTTWAETTTVYHEGVPGHHLQIATAMMNRGTLNLWRRNFAWTSGHGEG
+WALYAEKLMEEFGFLDDAGDHLGMLDMQRMRAARVVFDIGYHCGFEMPASEGGGEWTPEK
+GYAFLEKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEAREGADFDLKAF
+HTRALRVGGMGLDTLREALA
+>MHAAABBN_00269
+MTQHTSEAAVDGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARA
+DDELNARLLEDLAALEPQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQSIRAV
+FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVVEQARAHGA
+AGGFFPGLAERAEAADVVDDALAARIRSGADTAAQAYRDFADMLEAELRPHAPEADGVGI
+DYYRLASRVFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPE
+RTLKGTEALRTWMQRLSDDAVEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR
+PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG
+EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP
+EKGYAFLTKHLRISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLK
+AFHTRALRLGGMGLDTLREALA
+>LFPAFLNI_00547
+MTQHTSEAAADGARTPSAIDALAERYVTDLLALHPDTATELGFPGRETEYTDFSPAGARA
+DDELNARLLEDLAALEPQDETDRVTKAAMQERIGLEREIHATGRTELNNIASPAQGIRAV
+FDLMPTDTAEQWGHIAGRLENLPAALRGYTESLLASRDAGHVAAVRQVDIVVEQARAHGG
+AGGFFPGLVERAEAADVVDDALAARIRSGADTAAQAYRDFAATLEAELRPHAPEADGVGI
+DYYRLASRVFLGAEIDLEETYRWGQEELARIIAAQQADAERIRPGATIEEARAILDADPE
+RTLKGTEALRTWMQRLSDDAVEAMKEHFEIPAPMDRLECMIAPTQEGGIYYTGPSDDFSR
+PGRMWWSVPPGEDEFTTWAETTTVYHEGVPGHHLQIATAMMNRENLNLWRRSFCWTSGHG
+EGWALYAEKLMEELGFLDDPGDHLGMLDMQRMRAARVVFDIGYHCGFDAPESEGGGAWTP
+EKGYAFLAKHLMISEGQRRFEFTRYLGWPGQAPAYKVGQRIWEQIRAEHEQAEGADFDLK
+AFHTRALRLGGMGLDTLREALA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001616.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001616.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed9186113327cd1e2b75d1bab684a245b6bdd7b4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001616.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_02408
+MSRTTTPADGTAAGLEAAAEVPRGRVITASLVGTSIEFYDFYVYATAAVSVFPLIFFPGD
+DQTTALLASFAVFGTAFVARPIGSVLFGHFGDIMGRKVTLIGSLLTMGIATFLIGLLPTA
+FQIGLWAPAMLVVLRFCQGLGLGGEWSGAALLATEYAAEGKRARAAMWPQLGAPIGFFLA
+NGLFLALVIGFGHDSTNPDHDGAFLNWVWRLPFLLSIVMVAVGLYVRVKLEETPVFQRAI
+ANDTRVKAPLGEVFKRNWWELILGTFIMYATYVLFYLMTTWILSYAIGKTENGMLGVPYA
+EFLVLQLIGILFFAAFVPASGWLADRFGRKPTLLTVSALMVLFGLSFGLWLSAERMGTGA
+GVNVPLMLAFLAVGMALMGLTFGPMSAVLPELFPTNTRYTGSGISYNVSSILGAALTPFL
+AAWLVKEYGVAYVGYYLAAASVITMIALALAPETRHTDLDGVTSARERRAASV
+>MOLHKGIG_00541
+MSHSTPPVNPGAPTDLTSDAVATAEEVPRSRVIIASLVGTSIEFYDFYIYATAAVSVFPL
+IFFAGGDDNTALLASMATFGAAFIARPLGAVVFGHLGDRVGRKTTLIGSLLTMGIATFLI
+GLLPTYFQIGLWAPAMLTLLRFFQGLGLGGEWSGAALLATEYAKDGKRAQAAMWPQLGAP
+IGFLLANGLFLALVLGFDHDSTNPVLDGPFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP
+VFQRALDRDQRVKAPLSEVFRRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKPANGF
+LGVPYAEFLVLQLVGILFFAAFVPVSGLLADRFGRRPTLIVISVLMVLFGLSFGLWLSPE
+NMGVGAELNGPLMVAFLATGMTLMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA
+ALTPFIAAWLVQKFDVSYVGYYLAAASAITVIALVLSPETRHTDLDTVTSARERRAAR
+>NAFOICDF_02290
+MSHTTARSAEAPSVEDVPKSRVILASLVGTSIEFYDFYVYATAAVSVFPLIFFPGDDPTT
+ALLASFAVFGTAFVARPIGSILFGHFGDRMGRKVTLIGSLLTMGIATFLIGLLPTAFQIG
+LWAPAMLVVLRFCQGLGLGGEWSGAALLATEYADHGKRARAAMWPQLGAPIGFLLANGLF
+LILVRAFGHDSTNPQLEGSFLTWVWRVPFLLSIVMVAVGLYVRVKLEETPVFQRALEDDT
+RVKAPLGEVFKRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKTQNGMLGVKYADFLV
+LQLVGILFFAAFVPVSGWLADRFGRKPTLLVVSGLMVVFGLSFGAWLSPAAMGQGDALNV
+PSMLAFLAVGMALMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGAALTPFLAGWL
+VKEFGVATVGWYLAIASVITMAALALSPETRHADLHEVTSARERRAAAR
+>MHAAABBN_00265
+MSHSTPPVNPGAPTDLTSDAVATAEEVPRSRVIIASLVGTSIEFYDFYIYATAAVSVFPL
+IFFAGGDDNTALLASMATFGAAFIARPLGAVVFGHLGDRVGRKTTLIGSLLTMGIATFLI
+GLLPTYFQIGLWAPAMLTLLRFFQGLGLGGEWSGAALLATEYAKDGKRAQAAMWPQLGAP
+IGFLLANGLFLALVLGFDHDSTNPVLDGPFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP
+VFQRALDRDQRVKAPLGEVFRRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKPANGF
+LGVPYAEFLVLQLVGILFFAAFVPVSGLLADRFGRRPTLIVISVLMVLFGLSFGLWLSPE
+NMGVGAELNVPLMLAFLATGMTLMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA
+ALTPFIAAWLVQKFDVAYVGYYLAAASAITVIALALSPETRHTDLDTVTSARERRAAR
+>LFPAFLNI_00544
+MSHSTPPVNPGAPTDLTSDAVATAEEVPRSRVIIASLVGTSIEFYDFYIYATAAVSVFPL
+IFFAGGDDNTALLASMATFGAAFIARPLGAVVFGHLGDRVGRKTTLIGSLLTMGIATFLI
+GLLPTYFQIGLWAPAMLTLLRFFQGLGLGGEWSGAALLATEYAKDGKRAQAAMWPQLGAP
+IGFLLANGLFLALVLGFDHDSTSPVLDGPFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP
+VFQRALDRDQRVKAPLGEVFRRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKPANGF
+LGVPYAEFLVLQLVGILFFAAFVPVSGLLADRFGRRPTLIVISVLMVLFGLSFGLWLSPE
+NMGVGAELNVPLMLAFLATGMTLMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA
+ALTPFIAAWLVQRFDVSYVGYYLAAASAITVIALALSPETRHADLDTVTSARERRAAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001617.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001617.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a7ec6c8e9d199a5100870aea4c417bafd1fb24e6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001617.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_02409
+MVAAKLGARVTLVERQGVGGAAVLTDVVPSKTLIATADSMRRVGLAEDLGVDLGDAEPRA
+DMRQVDRRILDLAGEQSRDIRAALERRGVRVIDGVARVVGPNEVSVRTLQDADAEPEVIT
+SDAILVAVGASPRELPTAVPDGERIFNWKQLYAMTELPEHLIVVGSGVTGAEFASAYNRL
+GAKVTLVSSRDRVLPGEDADAAELLEKVFQDNGLTVVARSRAEAVERTETGVRVELSGEG
+AADTPYVEGSHALVAVGGIPNTAGLGLEDVGVELTESGHVKVDGVSRTTVPSIYAAGDCT
+GNLALASVAAMQGRIAVAHLLGDALKPLRPHLLASNIFTSPEIATVGVTQAQVDSGQYQA
+DVLRLDFATNPRAKMSGVQEGFVKIFARQGSGTVIGGVVVSPRASELIYALALAVTHKLH
+VDDLADTFTVYPSMSGSIAEAARRLHVRI
+>MOLHKGIG_00540
+MEPVSEENSTFIPSLTIIGGGPGGYEAAMVAAKLGARVTLVERQGLGGAAVLTDVVPSKT
+LIAAADSMRRVGASVDLGVDLGGADVHADMGRVGHRILNLAHEQSSDIRAGLERVGVRVI
+DGVGRVVGPHEVSVRALDDADAGAEPEIITSDAILVAVGASPRELPTAVPDGERIFNWKQ
+VYNLKELPEHLIVVGSGVTGAEFASAYNRLGAKVTLVSSRDRVLPGEDADAAELLEKVFE
+GNGLRVVSRSRAESVERTETGVRVHLSGEGAEDTPSIEGSHALVAVGGVPNTAGLGLDDV
+GVKLTGSGHVLVDGVSRTSVPSIYAAGDCTGKLALASVAAMQGRIAVAHLLGDALKPLRP
+HLLASNIFTSPEIATVGVTQAQVDSGQYQADVLRLDFHTNPRAKMSGAEEGFVKIFARQG
+SGTVIGGVVVSPRASELIYALALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRI
+>NAFOICDF_02291
+MNVTEENTTFLPSLTIIGGGPGGYEAALVAAKLGARVTVVERAGMGGSAVLTDVVPSKTL
+IATADSMRRVMAASGLGVDLGEAQPHADMHAVDRRILELAGQQSSDIHRALEKRGVRVVI
+GDAVVTGPHEVTVRRRGIEEGEEPEVITSDAILVAVGASPRELPTARPDSERIFNWKQVY
+ALQDLPEHLIVVGSGVTGAEFASAYNQLGAAVTLVSSRDRVLPGEDPDAAELLEDVFAQN
+GLDVAGRCRAESVERTETGVRVHLSGEGADGRPYIDGSHCLLAVGGVPNTAGLGLEEVGV
+ELTESGHVKVDGVSRTTVPSIYAAGDCTGQLALASVAAMQGRIAVAHLLGDALKPLRPHL
+LASNIFTSPEIATVGVTQAQVDSGQYQADVIRLDFATNPRAKMQGVSTGFVKIFARQGSG
+TVIGGVVVAPRASDLIYSLALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRV
+>MHAAABBN_00264
+MEPVTEENSTFIPSLTIIGGGPGGYEAAMVAAKLGARVTLVERQGVGGAAVLTDVVPSKT
+LIAAADSMRRVGASVDLGVDLGGAEAHADMGRVGHRILNLAHEQSSDIRAGLERVGVRVI
+DGVGRVVGPHEVSVRALDDADAGAEPEIITSDAILVAVGASPRELPTAVPDGERIFNWKQ
+VYNLKELPEHLIVVGSGVTGAEFASAYNRLGAKVTLVSSRDRVLPGEDADAAELLEKVFE
+GNGLRVVSRSRAESVERTETGVRVHLSGEGAEDTPSIEGSHALVAVGGVPNTAGLGLDDV
+GVKLSGSGHVLVDGVSRTSVPSIYAAGDCTGTLALASVAAMQGRIAVAHLLGDALKPLRP
+HLLASNIFTSPEIATVGVTQAQVDSGQYQADVLRLDFHTNPRAKMSGAEEGFVKIFARQG
+SGTVIGGVVVSPRASELIYALALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRI
+>LFPAFLNI_00543
+MEPVSEENSTFIPSLTIIGGGPGGYEAAMVAAKLGARVTLVERQGLGGAAVLTDVVPSKT
+LIAAADSMRRVGASVDLGVDLGGGDVHADMGRVGHRILNLAHEQSSDIRAGLERVGVRAI
+DGVGRVVGPHEVSVRALDDADAGAEPEIITSDAILVAVGASPRELPTAVPDGERIFNWKQ
+VYNLKELPEHLIVVGSGVTGAEFASAYNRLGAKVTLVSSRDRVLPGEDADAAELLEKVFE
+GNGLRVVSRSRAESVERTETGVRVHLSGEGAEDTPSIEGSHALVAVGGVPNTAGLGLDDV
+GVKLTGSGHVLVDGVSRTSVPSIYAAGDCTGKLALASVAAMQGRIAVAHLLGDALKPLRP
+HLLASNIFTSPEIATVGVTQAQVDSGQYQADVLRLDFHTNPRAKMSGAEEGFVKIFARQG
+SGTVIGGVVVSPRASELIYALALAVTHKLHVDDLADTFTVYPSMSGSIAEAARRLHVRI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001620.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001620.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6d7dd0249fa2ddb1f83fe832124bec4b24a69ca6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001620.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02412
+MTRTLSTAELAQYIDATALKTETSEADVRRLVAEARQAGVKSVCVNPRWVPLVSAELAGS
+DVLTCTVIGFPLGANASEVKTFEARQAIEAGAHEVDMVIDVAAARAGDRARLVEDVRAVA
+EAAHAAGPAGQGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH
+VALMRRTVGEHVGVKASGGVRTREDALAMIEAGATRIGASSALAILGTD
+>MOLHKGIG_00537
+MTVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELAGS
+DVLTCTVIGFPLGANASEVKAFEARQAIDAGADEVDMVLDVAAARAGDRDRLVADVRAVA
+EAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH
+VALMRRTVGERIGVKASGGVRTRADALAMIEAGATRIGASSALAILGSD
+>NAFOICDF_02294
+MSETPQLTTAELAKHIDHTLLKPEASREDILRVVAEAREAGVKSVCVNPRWVREVRAGLE
+GSDVLTCTVIGFPLGASSSAVKAFETTQAIADGADEVDMVIDIAAARAGDRARLEEDVRA
+VVAAAHASGPAGRAGTLVKVIIETALLDDAAKVLACEAAVAAGADFVKTSTGFSTGGATV
+EDVALMRRTVGPEIGVKASGGVRSREDALAMITAGATRIGASSALAILGDD
+>MHAAABBN_00261
+MTVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELADS
+DVLTCTVIGFPLGANTSEVKAFEARQAIDAGADEVDMVLDIAAARAGDRARLVADVRAVA
+EAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH
+VALMRRTVGEDIGVKASGGVRTREDALAMIEAGATRIGASSALAILGSD
+>LFPAFLNI_00540
+MTVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELAGS
+DVLTCTVIGFPLGANASEVKAFEARQAIDAGADEVDMVLDVAAARAGDRDRLVADVRAVA
+EAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH
+VALMRRTVGERIGVKASGGVRTRADALAMIEAGATRIGASSALAILGSD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001621.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001621.fa
new file mode 100644
index 0000000000000000000000000000000000000000..563bd3e180a4b57d4345bd99c2275a85acaa3f9a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001621.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02414
+MDALRLVSIAAVVLGHAYLADLTFSRYLEIWRMPLFFFLTGYFWTRGRPVARDARGRFKA
+LMVPYLVWAVVMSAAALAWFGDDPERLQRLMAAGWYGGADQEPPWWAFWFISVLFFATVL
+RRFLERFPTAVAWGVGLAGLAWAYLVPESAIARTPLGVGLALPCLLFILSGEAFRRRVQP
+RIRRHRTLLGLALVGLGLAAVALGLEPHNIKFGGFGTPLLTPLVGVLMSAGMVLVFGAAV
+ERILREFARRTGSGQALRRVITALVRTGTVVVLLHGWVLMWVMRQGVEDNLLKFVLALGI
+SWLVGLALLATPLSKPLTGARRRWFPLHRLRGEEPPHPPTSALPRVTTASERTHP
+>MOLHKGIG_00535
+MDALRLVSIAAVVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVWGRFRS
+LMVPYLVWAALMSVAAFAWFADDPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFTTVL
+RRFLERFPSAVAWAVGLAGLAWAHLVPDSAIARTPLGVGLALPCLLFVLSGEMFRRRVQP
+HVRRHRTLIGVGLVLLGMVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFGSTV
+ERLLRSFARRTGTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALALAL
+SWLAGLALLATPLSKPFTGARRRWHPVHRLRHVEPPHPVTSALPRVTTASERTHP
+>NAFOICDF_02296
+MDALRLVSISAVVLGHAYLADLTFSPYLEIWRMPLFFFLTGYFWTRGRPWAADALSRFRS
+LMVPYLLWSVLMTLVVLSWSRRSQIDGVTLADLVSAGWYGGADQPPPWWAFWFISVLFFV
+ALLRRALERAPSWAGWAVALAGLAAAELVPESAIARTPLGIGLAAPCLFYVLAGEAFRRR
+VQPRIRRHRTLIGVALVAAGVGAVALGLPPHNIKWGGFGLFPWTPLTGIAMAAGMVLVFG
+AFVERRLRAFARDTGTGRAIRAGITALTRTGTVVVLLHGLVLMEAMRVGIEDNLMKFVVA
+LTVSWAVGLALLATPLARPLTGVPQQWFPFGREAGA
+>MHAAABBN_00259
+MVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVWGRFRSLMVPYLVWAAL
+MSVAAFAWFADDPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFTTVLRRFLERFPSAV
+AWAVGLAGLAWAHLVPDSAIARTPLGVGLALPCLLFVLSGEMFRRRVQPHVRRHRTLIGV
+GLVLLGMVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFGSTVERLLRSFARRT
+GTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALALALSWLAGLALLAT
+PLSKPFTGARRRWHPVHRLRHVEPPHPVTSALPRVTTASERTHP
+>LFPAFLNI_00538
+MDALRLVSIAAVVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVRGRFRS
+LMVPYLVWAALMSVAAFAWFADDPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFTTVL
+RRFLERFPSAVAWAVGLAGLAWAHFVPDSAIARTPLGVGLALPCLLFVLSGETFRRRVQP
+HVRRHRTLIGVGLVLLGLVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFGSTV
+EGLLRSFARRTGTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALALAL
+SWLAGLALLATPLSKPFTGARRRWHPVHRLRRVEPPHPVTSALPRVPTASERTHP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001623.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001623.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cbbc50dd8fa8afc1a8fe6039de6238eca0cd4c16
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001623.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_02419
+MTETGTTDQRAAAQPALDLAVRVRLGHARIAYVMEEAELRGLHVKGYAAEPGVYRGRRSS
+SDVDLLVHPSDAAAAVELLASHGWAPVADFSEGSIFEHAATLWHDHLGYVDVHRLFPGLG
+TDAARTFDALWAERTTRVIAGRPVPVPGPVHQRLVVIVHAARDSHRGALDVRHIRDTSSP
+AEWDALRQEARRLHATAAWHVATGEDADGMDAHDLALFEALQDDESGLDLFRTRWRTAHS
+ARERARLVLHTLPVNRPHLQMRLGHAPTRADLWREQRSRATALARWAWTRGVRRGR
+>MOLHKGIG_00533
+MGERATRQRPAAPPSLDLEVRVRLAHARITHLLDRAGIRGLHLKGYATEPGVYPDHRRSS
+DVDLLVHPADATAVIELLRSHGWEPVATFSEGSIFQHAATLWHDQLGYVDVHRLFPGLGA
+SPEAAFDALWSEHIHLVIAGRSVPVPSPRHQRLVVIVHAARDPFRGGLDVRHIRESLPAE
+SWAALREEAHRLDAGAAWHVATGEAADGVDSRQLTLFAALHESQSGLELFRTRWRSAATA
+RERAVLVARTIPVNRPHLQMRLGRPVTRADLWREQRARLGALAGWAWTKAVRRDR
+>NAFOICDF_02301
+MTAAPAPLETRVRLAHARITHLMAAAGVRSLHIKGYAMGPGVYAGGRTSSDVDLLVHPAD
+LSHALDALTSHGWRRIADFAEGSVFEHAATLWHDQLGYVDVHRRLPGLGRSPVDAFEALW
+GERTTTVVAGHAVPVPSLRHQRLVVLVHGARDAGRGRFDVDHLRHTLDAGQWAELRVQAQ
+ILGAGAAWSIATGETDVAGVDEREALLLSAVRGDESGIRLLATRWHAARGWRERLHLLVR
+TVPVNRAHLQMRLGRPPTTADVLREQASRGAALTRWAAGKAVPRVGR
+>MHAAABBN_00254
+MGEHATGQRPAAPPSLDLEVRVRLAHARITHLLERAGIRGLHLKGYATEPGVYPDHRRSS
+DVDLLVPPADAAAVIALLGSHGWEPVATFSQGSIFQHAATLWHDQLGYVDVHRLFPGLGA
+SPEAAFDALWSEHIHLVIAGRSVPVPSPRHQRLVVIVHAARDPFRGGLDVRHIRESLPAE
+SWAALREEARRLDAGAAWHVATGEAADGVDTRQLTLFAALHESQSGLELFRTRWRSAATV
+RERAALVARTIPVNRPHLQMRLGRPVTRADLWREQRARLGALAGWAWTKAVRRDR
+>LFPAFLNI_00533
+MLAAMGERATGQRPAAPPSLDLEVRVRLAHARITHLLDRAGIRGLHLKGYATEPGVYPDH
+RRSSDVDLLVPPADADAVIALLGSHGWEPVATFSQGSIFQHAATLWHDQLGYVDVHRLFP
+GLGASPEAAFDALWSEHIHLVIAGRSVPVPSPRHQRLVVIVHAARDPFRGGLDVRHIRES
+LPAESWAALREEAHRLDAGAAWHVATGEAADGVDSRQLTLFAALHESQSGLELFRTRWRS
+AATVRERAALVARTIPVNRPHLQMRLGRPVTRADLWREQGARLGALAGWAWTKAVRRDR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001625.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001625.fa
new file mode 100644
index 0000000000000000000000000000000000000000..619fa8fd9aad91b62094b394c604c86c06fc391f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001625.fa
@@ -0,0 +1,110 @@
+>ACLBLIBL_02421
+MPPRPPPVVAPLLPRLRAERAIEAAAASAARPLEARGVELEIGLPDGARAPLLTVLAEAL
+AEGHGERAAVLVVTATTREAEDLVTDLAAWAPAGAAALFPSWETLPHERLSPRSDTVGAR
+LAVLRRLAHPEEHAQGPLRIVVAPVRAVLQPLVAGLGELSPVTLRTGEERDFDGVVAALA
+DAAYSRVDMVSRRGEFAVRGGLIDVFPPTEDHPVRIEFFGDEVEQMRWFSVADQRSLEDT
+TEDGSGHPTELYAPPCRELLITDHVRRRAKELIPAMPAAADMLDRIAEGVAVEGMESLSP
+LLAEAMTSLPRMLPTGSLTVLVEPERLRGRADDLLATNEEFLQAAWAGAAQGAVAPVDIA
+GADQSAAGGFLTVAELRAAALEQDQGFWSVTALAPDDELLPDAATLRSTLGVPRTFAGDM
+EAMVEHTRTRLAEGWHAVILTDGPGSARRLAELHADAGLTASVADGPVPAEPAPGRVTIA
+TAAVGAGFTVPDERLAVITEHDLFGRHRTAGTRAPGARLARKRRNAVDPLALQPGDHVVH
+AQHGIARFVELQRRKVTGGPRTAPGAEESYREYLVLEYAPSKRGAPGDRLFVPTDQLDLV
+SSYVGGEAPSLSKMGGSDWAQTKSKAKRATREIAGELIRLYSARMASRGHAFAPDTPWQS
+ELEEAFPFIETPDQLTTIEDVKKDMEAAVPMDRLVSGDVGFGKTEVAVRAAFKAVQDGKQ
+VAVLVPTTLLARQHHQTFSDRFAGFPVKVAALSRFQTAKESKEVVEGLAHGEVDVVIGTH
+RLLSDQVQFKDLGLVIVDEEQRFGVEHKEALKKMRTNVDVLAMSATPIPRTLEMSLTGIR
+ETSTLATAPEERHPVLTSVGPYSDQQVTAAIRRELMREGQVFYVHNRVTTIDKVARRIAE
+LVPEARIAVAHGKMGEARLEQIMVDFWERRFDVLVSTTIIETGLDIANANTLIVEDAHRY
+GLSQLHQLRGRVGRGRERAYAYFLYDAQKPLGEVALERLKAVATHNELGAGMQLAMKDLE
+IRGAGNLLGGEQSGHIAGVGFDLYLRMVGEAVADFKGEEDTAPAEVKVELPVNAHLPHDY
+VPGERLRLEMYRNLAQAADDAAVDAVVEELKDRYGPLPDPVEALVAVARFRNHARAAGIT
+EVMLLGQNVKFGPAADLPESRQMRLARMYKGSQVKPALNGVLIPRPKTKPVMGQDLVDVP
+LLEWAQQVIDAIFAPEG
+>MOLHKGIG_00531
+MSAPETTPVLAPLLPRLRAERALEAAAASASRPLEARGVELEIGLPDGARAPLLTVLAEA
+LAEGHGERAAVLVVTATTREAEDLVTDLAAWAPAGAAALFPSWETLPHERLSPRSDTVGA
+RLAVLRRLAHPEEHAEGPLRIVVAPVRAVLQPLVAGLGELSPVTLRTGEERDFDGVVAAL
+ADAAYSRVDMVSRRGEFAVRGGLIDVFPPTEDYPVRIEFFGDEVEQMRWFSVADQRSLED
+TTEDGSGHPSELYAPPCRELLITDHVRRRAKELIPAMPAAADMLDRIAEGVAVEGMESLS
+PLLAEAMTSLPRMLPTGSLTVLVEPERLRGRADDLLATNEEFLQAAWAGAAQGAVAPVDV
+AEADQSAAGGFLTVAELRAAALEQDQGFWSVTALVSDAELLPDAATLRATLGVPQTFSGD
+IEAMVAHTRVRLAEGWHAVVLTDGPGSARRLAELNAEAGLTASVVDGPLPADLAPGRVSI
+ATAPVGSGFTIPDAQIALITEHDLFGRHRTAGTRAPGARLARKRRNAVDPLTLQPGGHVV
+HSQHGIARFVELQRRKVTGGPRTAPGAEESYREYLVLEYAPSKRGAPGDRLFVPTDQLDL
+ISTYVGGETPSLSKMGGSDWAQTKSKAKRATREIAGELIRLYSARMASRGHAFAPDTPWQ
+GELEEAFPFIETPDQLTTIEDVKKDMEAAVPMDRLVSGDVGFGKTEVAVRAAFKAVQDGK
+QVAVLVPTTLLARQHHQTFSDRFAGFPVKVAALSRFQTAKESKEVIEGLAHGEVDVVIGT
+HRLLSDQVQFKDLGLVIVDEEQRFGVEHKEALKKMRTNVDVLAMSATPIPRTLEMSLTGI
+RETSTLATAPEERHPVLTSVGPYSDQQVTAAIRRELMREGQVFYVHNRVTTIDKVAKRIA
+ELVPEARIAVAHGKMSEARLEQIMVDFWERKFDVLVSTTIIETGLDIANANTLIVEDAHR
+YGLSQLHQLRGRVGRGRERAYAYFLYDPQKPLGEVALERLKAVATHNELGAGMQLAMKDL
+EIRGAGNLLGGEQSGHIAGVGFDLYLRMVGEAVADFKGEEDTAPAEVKVELPVNAHLPHD
+YVPGERLRLEMYRNLAQAADDAAVDAVVEELKDRYGPLPEPVEALVAVARFRNRARAAGV
+TEVMLLGQNVKFGPAADLPESRQMRLTRMYKGAQVKPALNGVLIPRPKTKPVMGQDLVDV
+PLLEWAQQVVDAIFAPEG
+>NAFOICDF_02303
+MSPADVTAPVPVLAPLLPVLAREPAFEAAAASAARALPARGQELEIGLPDGARAPLFAHL
+ADALAAGHGADAVLLVVTATAREAEDLIGDLAAWADPASVALFPSWETLPHERLSPRSDT
+VGARLDVLRRLAHPGEDGRPPLRVVVAPVRSVIQPLVRGLGELAPVHLRVGQERDFDAVV
+QDLADAAYARVDMVSRRGEFAVRGGLIDVFPPTADHPVRVEFFGDEVEQMRWFSVADQRS
+LQDTSEDGSGHPTELHAPPCRELLVTPSVQERARALMARLPGAADMLERIAEGQAVEGME
+SLSPLLADGMTSLVHLLPEGSLTLLVEPERIRSRADDLLATNEEFLAAAWAGAAQGAQAP
+VDLGADQSAAGGFLTLAELREAVLEERQGHWSTTALSPDAELLPDASALRSSLGVPTTFG
+ADMEAMVRFTRERLADGWSVVLLTDGPGSARRLAELHADAGLTASVLDGPVDPAPAPGRV
+RVATAAVGTGFTDPETKLAVVTEQDLFGRHRTAGTRAAGGKLARRRRNAVDPLALQPGDF
+VVHSQHGIARFVELQRRPVTGGARKRPGEEESYREYLVLEYAPSKRGAPGDRLFVPTDQL
+DLISQYVGGEAPALSKMGGSDWAQTKSKAKRATREIAGELIRLYSARMATRGHSFAPDTP
+WQAELEEAFPYIETPDQLTTIEEVKKDMESPVPMDRLVSGDVGFGKTEVAVRAAFKAVQD
+GKQVAVLVPTTLLARQHHQTFTDRFAGFPVTVAALSRFQTAKESKEVVEGLAAGEVDVVV
+GTHRLLSKEVQFKDLGLVIVDEEQRFGVEHKEALKKMRTNVDVLAMSATPIPRTLEMSLT
+GIRETSTLATAPEERHPVLTSVGPYTDQQVIAAIRRELMREGQVFYVHNRVTTIDKVASR
+LAQLVPEARIAVAHGKMSESRLEQIMVDFWEKRFDVLVSTTIIETGLDIANANTLIVEDA
+HRYGLSQLHQLRGRVGRGRDRAYAYFLYDAQKPLGEVAMERLKAVAQHNELGAGLQLAMK
+DLEIRGAGNLLGGEQSGHIAGVGFDLYLRMVGEAVADFKGEEDTAPAEVKVELPVNAHLP
+HDYVPGERLRLEMYRSLATAVDDAAVDAVVEEMKDRYGPLPEPVQALVAVARFRNRAREA
+GVTEVMLLGQNVKFGPAADLPESRQLRAQRMYKGAQLKPALNALLIPRPKTKPVMGQDLV
+DAPLLEWADQVVQAIFAPEPVSAG
+>MHAAABBN_00252
+MSAPETTPVLAPLLPRLRAERALEAAAASAARPLESRGVELEIGLPDGARAPLLTVLAEA
+LAEGHGERAAVLVVTATTREAEDLVTDLAAWAPAGTAALFPSWETLPHERLSPRSDTVGA
+RLAVLRRLAHPEEHAEGPLRVVVAPVRAVLQPLVAGLGELSPVTLRTGEERDFDGVVAAL
+ADAAYSRVDMVSRRGEFAVRGGLIDVFPPTEDYPVRIEFFGDEVEQMRWFSVADQRSLED
+TTEDGSGHPSELYAPPCRELLITDHVRRRAKELIPAMPAAADMLDRIAEGVAVEGMESLS
+PLLAEAMTSLPRMLPAGSLTVLVEPERLRGRADDLLATNEEFLQAAWAGAAQGAVAPVDV
+AGADQSAAGGFLTVAELRAAALEQDQGFWSVTALVSDDELLPDAATLRATLGVAQTFSGD
+IEAMVAHTRVRLAEGWHAVVLTDGPGSARRLAELTTEAGLTAAVVDGPLPADLAPGRVSI
+ATAPVGSGFTIPDAQIALITEHDLFGRHRTAGTRAPGARLARKRRNAVDPLTLQPGDHVV
+HSQHGIARFVELQRRKVTGGPRTAPGAEESYREYLVLEYAPSKRGAPGDRLFVPTDQLDL
+ISTYVGGETPSLSKMGGSDWAQTKSKAKRATREIAGELIRLYSARMASRGHAFAPDTPWQ
+GELEEAFPFIETPDQLTTIEDVKKDMEAAVPMDRLVSGDVGFGKTEVAVRAAFKAVQDGK
+QVAVLVPTTLLARQHHQTFSDRFAGFPVKVAALSRFQTAKESKEVVEGLAHGEVDVVIGT
+HRLLSDQVQFKDLGLVIVDEEQRFGVEHKEALKKMRTNVDVLAMSATPIPRTLEMSLTGI
+RETSTLATAPEERHPVLTSVGPYSDQQVTAAIRRELMREGQVFYVHNRVTTIDKVAKRIA
+ELVPEARIAVAHGKMSEARLEQIMVDFWERKFDVLVSTTIIETGLDIANANTLIVEDAHR
+YGLSQLHQLRGRVGRGRERAYAYFLYDPQKPLGEVALERLKAVATHNELGAGMQLAMKDL
+EIRGAGNLLGGEQSGHIAGVGFDLYLRMVGEAVADFKGEEDTAPAEVKVELPVNAHLPHD
+YVPGERLRLEMYRNLAQAADDAAVDAVVEELKDRYGPLPEPVEALVAVARFRNRARAAGV
+TEVMLLGQNVKFGPAADLPESRQMRLTRMYKGAQVKPALNGVLIPRPKTKPVMGQDLVDV
+PLLEWAQQVVDAIFAPEG
+>LFPAFLNI_00531
+MSAPVLAPLLPRLRAERAIEAAAASASRPLEARGVELEIGLPDGARAPLLTVLAEALAEG
+HGERAAVLVVTATTREAEDLVTDLAAWAPAGAAALFPSWETLPHERLSPRSDTVGARLAV
+LRRLAHPEEHAEGPLRIVVAPVRAVLQPLVAGLGELSPVTLRTGEERDFDGVVAALADAA
+YSRVDMVSRRGEFAVRGGLIDVFPPTEDYPVRIEFFGDEVEQMRWFSVADQRSLEDTTED
+GSGHPSELYAPPCRELLITDHVRRRAKELIPAMPAAADMLDRIAEGVAVEGMESLSPLLA
+EAMTSLPRMLPTGSLTVLVEPERLRGRADDLLATNEEFLQAAWAGAAQGAVAPVDVAGAD
+QSAAGGFLTVAELRAAALEQDQGFWSVTALVSDAELLPDAATLRATLGVAQTFSGDIEAM
+VAHTRVRLAEGWHAVVLTDGPGSARRLAELNAEAGLTASVVDGPLPADLAPGRVSIATAP
+VGSGFTIPDAQIALITEHDLFGRHRTAGTRAPGARLARKRRNAVDPLTLQPGDHVVHSQH
+GIARFVELQRRKVTGGPRTAPGAEESYREYLVLEYAPSKRGAPGDRLFVPTDQLDLISTY
+VGGETPSLSKMGGSDWAQTKSKAKRATREIAGELIRLYSARMASRGHAFAPDTPWQGELE
+EAFPFIETPDQLTTIEDVKKDMEAAVPMDRLVSGDVGFGKTEVAVRAAFKAVQDGKQVAV
+LVPTTLLARQHHQTFSDRFAGFPVKVAALSRFQTAKESKEVVEGLAHGEVDVVIGTHRLL
+SDQVQFKDLGLVIVDEEQRFGVEHKEALKKMRTNVDVLAMSATPIPRTLEMSLTGIRETS
+TLATAPEERHPVLTSVGPYSDQQVIAAIRRELMREGQVFYVHNRVTTIDKVAKRIAELVP
+EARIAVAHGKMSEARLEQIMVDFWERKFDVLVSTTIIETGLDIANANTLIVEDAHRYGLS
+QLHQLRGRVGRGRERAYAYFLYDPQKPLGEVALERLKAVATHNELGAGMQLAMKDLEIRG
+AGNLLGGEQSGHIAGVGFDLYLRMVGEAVADFKGEEDTAPAEVKVELPVNAHLPHDYVPG
+ERLRLEMYRNLAQAADDAAVDAVVEELKDRYGPLPEPVEALVAVARFRNRARAAGVTEVM
+LLGQNVKFGPAADLPESRQMRLTRMYKGAQVKPALNGVLIPRPKTKPVMGQDLVDVPLLE
+WAQQVVDAIFAPEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001627.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001627.fa
new file mode 100644
index 0000000000000000000000000000000000000000..70ad9d137791ef81188e3782a6b07c4013be075d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001627.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02423
+MAFSAQQSIPHPPAAVAAALASEEFHRSVVEQLGGSLVSFRVEGSPEGPMTVTTVRSAPA
+DRLPEMARKFIGSSLQVEQVERWEAPAADGSRVGTTTITVPAAKATAEGAQRLTAAGEGS
+QYSVDGTVTCKIPLVGSKLAAKAEPMVGKVVNRQARALTSWIGRDGGAAGA
+>MOLHKGIG_00529
+MAFSAQQSIPHPPAAVAAALASEDFHRSVVESFGGSLVSFSVEGSPEGPMTVTAVRSLPA
+DRIPDRVPDMARKLIGSALQVEQVERWDAPAADGSRAGTTTITVPSAKATADGALRLTAA
+GEGSQFSVDGTLVCRIPLVGSKLAAKAEPMVGKVVNRQARALSSWLERDGGAARG
+>NAFOICDF_02305
+MAFSAQQTIPHPPAAVAEALFSEDFHRSVAESLGGGLVSFARQDQADGGVELTIVRSGPT
+DRLPDMVRKVVGENLNIEQVERWSAPAADGSRTGTTTIRVPKAKATAEGTLRLAAAPAGT
+EYGVNGDLQVKIPLVGSKMAQMAEPMVGKVVARAGREVSAWIDRGGRG
+>MHAAABBN_00250
+MAFSAQQSIPHPPAAVAAALASEDFHRSVVESFGGSLVSFSVEGSPEGPMTVTAVRSLPA
+DRIPDRVPDMARKLIGSALQVEQVERWDAPAADGSRAGTTTITVPSAKATADGSLRLTAA
+GEGSQFSVDGTLVCRIPLVGSKLAAKAEPMVGKVVDRQARALSSWLERDGGAARS
+>LFPAFLNI_00529
+MAFSAQQPIPHPPSAVAAALASEDFHRSVVESFGGSLVSFSVEGSPEGPMTVTAVRSLPA
+DRIPDRVPDMARKLIGSALQVEQVERWDAPAADGSRTGTTTITVPSAKATADGSLRLTAA
+GEGSQFSVDGTLVCRIPLVGSKLAAKAEPMVGKVVNRQARALSSWLERDGGAARG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001635.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001635.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9fe7213cf4cb37a7c6c6c7c1d0cf264f85554b3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001635.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02440
+MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAANGFDVVRV
+GGPGRLGYLRALRAWDRDRGNDDVVWCNGLLPATALAGRPRRIVHLHQVPEKPLLRVFSA
+LARPGALAVLAPSRFAADRIRGARVLHNWVPGPTTPPARRARDADEPVTVGFLGRLSEDK
+GIVTLLEAAALLRKTDPGAFVFRVAGESRFVAEDEAERLATALKAAGEDVQVLGWQDTAE
+FLASVDVLAVPSQWAEVFGLVTAEAMAAGVPVVASDAGAVPEVVGNDHPFVFPQRDAAAL
+ADRLQAVRAGDLGAVAHSQRRRWASLFSPEAGRAAVAELLDDLSL
+>MOLHKGIG_00511
+MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAADGFDVVRL
+GGPGRLGYLRALRAWDRGRGKDDVVWCNGLLPATALAGRPRRIVHLHQVPEKPLLRVFSA
+LARPGALAVLAPSRFAADRIRGARVLHNWVPAPTTPQAGRARDADEPLTVGFLGRLSEDK
+GIVTLLEAAALLRKTDPGAFVFRVAGESRFVADDEAERLATALKAAGEDVQVLGWQDTAE
+FLASVDVLAVPSQWAEVFGLVTAEAMAAGVPVVASDAGAVPEVVGSEHPFVFPQRDAAAL
+ADRLQAVRAVDLGAVAHSQQRRWESLFSPEAGRAAVAELLDDLSL
+>NAFOICDF_02323
+MTRRIWIAANQGEVGGGEVMLHHLATALHELGRDIAVVAPAAPSATAARLEADGFTVDRV
+GGPGRAGYMRALRRWHNGHREDVVWCNGLLPATALAGRPRRIVHLHQWLIRPRDRVLGTL
+AMRGALAVIAPSESVAREIPGCRVLHNWVPRPLPLSGAAPARRRPGEGGALRVGYLGRLS
+FDKGFHLLMDVAEELHREQPDEWRFFVAGEPRFTTGDDAREIRERLAASRAVTALGWQAP
+GDFLPTVDVLVVPSLAPESFGLVAAEAMAAGVPVAVSDSGALPEVAGDDHPLLFECDDHE
+ELAAALRRARQIDLAPLVAAQHRRWEALFSPEAGRAGVAALLEELHV
+>MHAAABBN_00231
+MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAADGFDVVRV
+GGPGRLGYMRALRVWDRGRGGDDVVWCNGLLPATALAGRPRRIVHLHQVPEKPLLRVFSA
+LARPGALAVLVPSRFAADRIHGARVLHNWVPGPTTPQAGRARGTDEPVTVGFLGRLSEGK
+GIVTLLEAAALLRRTDPGAFVFRIAGESRFVAEDEAERLATALKAAGEDVQVLGWQDTGE
+FLTSVDVLAVPSQWAESFGLVAAEAMAAGVPVVASDAGAVPEVVGSDHPFVVPQRDAAAL
+ANCLRAVRAVDLGEVAHSQRHRWASLFSPEAGRAAVAELLDDLSL
+>LFPAFLNI_00510
+MTGRIWILANQGEVGGGEVMLHHLATALRELGRDVGVVAPAHPAETADRLAADGFDVVRV
+GGPGRLGYLRALRAWDRGRDGDDVAWCNGLLPATALAGRPRRIVHLHQVPEKPVLRVFSA
+LARPGALAVLVPSRFAANRIRGARVLHNWVPAPTAPQTRPARGADDPVTVGFLGRLSEDK
+GIVTLLEAAALLRKTDPGAFVFRVAGESRFVAEDEADRLATALKAAGEDVQVLGWQDSGE
+FLATVDVLAVPSQWAEVFGLVTAEAMAAGVPVVASDAGAVPEVVGSDHPFVVPQRDAAAL
+ANCLRAVRAIDLGAVAHSQRHRWESLFSPEAGRAAVAELLDDLSL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001639.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001639.fa
new file mode 100644
index 0000000000000000000000000000000000000000..510a5835642dbadb8c6270a68fb0f42078d1d7ad
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001639.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02445
+MSGTGYTVPARGARGTGRAERLFLVSPAFHGYHRSIARAWAAQGFDVTVHCYDAYATVPM
+KLRNKALLELPQKAGVDRTAARVAWDTERAVAALRAARPDRVLVIKGDSLGEAFWSEVVE
+AGLPRLLWLYDDLSRHDYSPEFLRAIGPVLSYARSEAEQLAGEGVDAHYLPNGFDPDMAL
+PSLPRREELVFVGSRYPNRVELLTTLAEAGVPVRAYGRQWSHHPVDRLRTWEVTRPALPA
+ERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYEPGEEV
+LVFENPEHLVELGRRVVAEPSWGERIREAGRSRSHAEHTFAHRAALAQEWWT
+>MOLHKGIG_00505
+MSATGYTVPAPPDARGGRSPERLFLVSPAFHGYHRSIAAAWAAQGFDVTVHCYDAYATLG
+MKLRNKGLLELPQKAGVDRTAARVAWDTGRAVAALREARPDRVLVIKGDSLGEDFWSEIL
+EAGLPRMLWLYDDLARHDYSMEFLRSVGPVLSYARSEAELLAGEGVDAHYMPNGFDPAMA
+LPQVPRRDELVFVGSRYPNRVELLARLAAAGVPVRAYGRQWSHHPVDRLRTWELTRPDLP
+AERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYVPDEE
+VLVFEDADHLIELGRRVVADPAWGARIREAGRRRSHAEHTFAHRAAMAQGWWA
+>NAFOICDF_02329
+MSAGTYTIAARGERPVSGRPERLFLVSPAFHGYHRSIAAAWAAQGFDVTVHCYDAYADLG
+MKLRNKLALELPQKAGLDRTAARVAWDTDRAVAALRAAAPDRVLVIKGDSLGDAFWDEVT
+GRALPRMLWLYDDLSRHDYSMDFLRGIGPVLSYARSEAESLAAQGVDAHYMPNGFDPEMV
+LPAVPRTEELVFVGSRYPNRVELLRALASAGVPVRAYGRQWSHHPVDRLRTWELSRPDLP
+AERDIPLAEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRPDVAEFYVPGEE
+VLVFEDTEHLVELGRRIVAEPAWGDRIRAAGRRRSHAEHTFSHRARMAQEWWA
+>MHAAABBN_00225
+MSATGYTVAAPPEARGGRSPERLFLVSPAFHGYHRSIAAAWAAQGFDVTVHCYDAYATLG
+MKLRNKGLLELPQKAGVDRTAARVAWDTGRAVAALREARPDRVLVIKGDSLGEDFWSEIL
+DAGLPRMLWLYDDLARHDYSMEFLRSVGPVLSYARSEAELLAGEGVDAHYMPNGFDPAMA
+LPEVPRRDELVFVGSRYPNRVELLTRLAAAGVPVRAYGRQWSHHPVDRLRTWELTRPDLP
+AERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYVPDEE
+VLVFEDADHLIELGRRIVADPAWGARIREAGRRRSHVEHTFAHRAAMAQGWWA
+>LFPAFLNI_00504
+MSATGYTVPAPPDARGGRSPERLFLVSPAFHGYHRSIASAWAAQGFDVAVHCYDAYATLG
+MKLRNKGLLELPQKAGVDRTAARVAWDTGRAVAALREARPDRVLVIKGDSLGEDFWSAIL
+DAGLPRMLWLYDDLARHDYSMEFLRSVGPVLSYARSEAELLAGEGVDAHYMPNGFDPAMA
+LPQVPRRDELVFVGSRYPNRVELLSRLTAAGVPVRAYGRQWSHHPVDRLRTWELTRPDLP
+AERDIPLEEAYAVQAAAAGAINIHGLQAGHAMRTFEVPGMGGLQLVDRADVAEFYVPDEE
+VLVFEDADHLIELGRRVVADPAWGARIREAGRRRSHAEHTFAHRAAMAQGWWA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001640.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001640.fa
new file mode 100644
index 0000000000000000000000000000000000000000..83e87d728819e72aac499fa8555599f8f34d6bc7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001640.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02446
+MAAQSTAAAVTVVIPHYGDPAPTLALVDRLLADPGDALAAVVVSDDASPTPYPEAHDPRL
+TVVRRERNGGFGANVNTGLSEVDTDLALVLNSDALITGEQIDALVAAAAPFQPAVVSPQV
+VNEDGSPQWSGRHFPTVLHQGVEWLTPLARFRHLPLLHEAVGHDVAAARSAAPVAVDWVM
+GAVMLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRDRGVASIVVPSVRVEHGMHGSSDPL
+RRRGWLVDSRFRYARKFGRPRALKAVLTAATGVNYAVNRVRQARGTDVDAAAVLRDEHAL
+IWKGTRR
+>MOLHKGIG_00504
+MAAQSTTAAVTVVIPHYGDPAPTLALVDRLLTDPGDALAAVVVSDDASPTPYPEAHDPRL
+TVVRRERNGGFGANVNTGLAAVTTELALVLNSDAEITGAQIDALVVAAAPYQPAVVSPQV
+VNEDGTPQWSGRHFPTVLHQTVEWLTPLARFRHLDVLHEAVGHDVAATRSASPVAVDWVM
+GAVLLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSIVVPAVRVPHGLHGSSDPL
+RRRGWLVDSRYRYARKFGHPRVLKAALTAATGANFAVNALRQARGVDVDARAVLRDEHAL
+VWKGQRR
+>NAFOICDF_02330
+MPASRIAPSVTVVIPHYGDPEPTRALVDALLAAPGRSVAGVVVSDDASPEPYPQPAPGRE
+GLTVVRREANGGFGANVNTGLAEVRTELALVLNSDAEITGEQIDALVEAARPYQPAVVSP
+QVVNEDGSPQWSGRHFPTVTHQTVEWLTPLARFRHLPALHEAVGHDVRAAEADSPVAVDW
+VMGAVMLLPMAEVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSVVVPSVRVVHGLHGSSD
+PLRRRAWLVDSRFRYARKFGRPRLLRGALTAATGVNWAVNRVRQTRGTDVDANAVFRAER
+DLIWKGTRR
+>MHAAABBN_00224
+MAAQSPTAAVTVVIPHYGDPAPTLALVDRLLTDPGDALAAVVVSDDASPTPYPEAHDPRL
+TVVRRERNGGFGANVNTGLAAVTTELALVLNSDAEITGAQIDALVAAAAPYQPAVVSPQV
+VNEDGTPQWSGRHFPTVLHQTVEWLTPLARFRHLDVLHEAVGHDVAATRSASPVAVDWVM
+GAVLLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSIVVPAVRVPHGLHGSSDPL
+RRRGWLVDSRYRYARKFGHPRVLKAALTAATGANFAVNVLRQARGVDVDARAVLRDEHAL
+VWKGKRR
+>LFPAFLNI_00503
+MTAQSPTAAVTVVIPHYGDPAPTLALVDRLLSDPGDALAAVVVSDDASPTPYPEAHDPRL
+TVVRRERNGGFGANVNTGLAAVTTELALVLNSDADITGAQIDALVAAAAPYQPAVVSPQV
+VNEDGSPQWSGRHFPTVLHQTVEWLTPLARFRHLDVLHEAVGHDVAAARSASPVAVDWVM
+GAVLLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSIVVPAVRVPHGLHGSSDPL
+RRRGWLVDSRYRYARKFGHPRVLKAALTAATGANFAVNALRQARGVDVDARAVLRDEHAL
+VWKGRRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001644.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001644.fa
new file mode 100644
index 0000000000000000000000000000000000000000..68f34287a674f25f30d482cc1c761bb3d5457071
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001644.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_02450
+MPQSSVRPSAVIVLAAGQGTRMKSTTPKIMHPIGGRSLVGHALAAAHSLAPEHLVAVVRY
+ERDRVAEHIESVAEGLGIASLAIADQDEVPGTGRAVELGLAALPKDLEGTVVVTYGDVPL
+LTPETLERLVAAHEADGNAVTVLTAALEDATGYGRIVRDGEGLVERIMEHKDALAHAEST
+GDSSFVEIREVNSGIYAFDAALLRRTLPAISTDNVQGEKYLTDVLGMARAEGGRVASVGT
+DDVWEVEGANDRRQLSDLGRRLNDRVLRHWMKEGVTVVDPSSTWVDVTVSLASDVTLKPG
+TQLHGATQVATGAVVGPDTTLTDTRVGERAVVKRTDATEAVIGADATVGPFTYLRPGTVL
+GEEGKIGAFYETKKVTIGRGAKLSHLGYAGDAEIGDYTNIGCGNITANYDGEKKHRTVIG
+AHVRTGSNTVFTAPVTVGDGAYTGAGAVVREDVPAGALALNAVSQRTIEGWVPAKRPGTS
+SAQAAQAADAQGDAPQG
+>MOLHKGIG_00497
+MSQPSARPSAVIVLAAGQGTRMKSTTPKIMHAIGGRSLVGHALAAAWSLSPEHLVAVVRH
+ERARVAEHIETVAAQLGIDALAIADQDDVPGTGRAVELGLAALPADLEGTVVVTYGDVPL
+LTPETLARLVADHEADGNAVTVLTATLEDATGYGRIVRDAEGLVERIMEHKDALAHAEAT
+GDDSFVAIREVNSGIYAFDAALLRRTLPEISTDNVQGEKYLTDVLGMARAEGGRVASVGT
+DDVWEVEGANDRRQLSDLGRQLNDRVLRGWMKEGVTVVDPSSTWVDVTVSLASDVTLKPG
+TQLHGATSVATGAVVGPDSTLTDTQVGEGAVVKRTDATEAVIGAGATVGPFTYLRPGTVL
+GEDGKIGAFYETKNVTVGRGAKLSHLGYAGDAEIGEYTNIGCGNITANYDGVNKHRTVIG
+AHVRTGSNTVFTAPVTVGDGAYTGAGAVVREDVPAGALALNAVSQRTLEGWVPAKRPGTS
+SAEAARAAGAEGSGAQG
+>NAFOICDF_02334
+MPQTAVRPSAVIVLAAGQGTRMKSATPKIMHAIGGRSLVGHALAAAQSLAPEHLVTVVRH
+ERDRVAAHIEEAAADLGVTGLAIADQDEVPGTGRAVELGLAALPEDLEGTVVVTYGDVPL
+LTPETLQRLVAAHEADGNAVTVLTATLADATGYGRIVRDADGLVERIMEHKDALAHAEAT
+GDSSYVEIAEVNSGIYAFDAALLRRTLPQLSTENVQGEKYLTDVLGMARAEGGRVASVGT
+DDVWEVEGANDRRQLSDLGRQLNERVLRRWMKDGVTVVDPSSTWVDVTVELAADVTLKPG
+TQLHGSTTVATGAVVGPDSTLVDTRVGERGTVKRTDATEAVIGDDATVGPFTYLRPGTVL
+GEEGKIGAFYETKKVTIGRGAKLSHLGYAGDAEIGEYTNIGCGNITANYDGVDKHRTVIG
+SHVRTGSNTVFIAPVTVGDGAYTGAAATVRQDVPAGALALNAVDQRNVDGWVVSRRAGTA
+SAEAAQAAGAVGRDQATEAAQD
+>MHAAABBN_00218
+MSQPSARPSAVIVLAAGQGTRMKSTTPKIMHAIGGRSLVGHALAAAWSLAPEHLVAVVRH
+ERARVADHLETVAAQLGIDALAIADQDDVPGTGRAVELGLAALPADLEGTVVVTYGDVPL
+LTPETLARLVADHEADGNAVTVLTATLEDATGYGRIVRDAEGLVERIMEHKDALAHAEST
+GDDSFVAIREVNSGIYAFDAALLRRTLPEISTDNVQGEKYLTDVLGMARAEGGRVASVGT
+DDVWEVEGANDRRQLSDLGRQLNDRVLRGWMKEGVTVVDPSSTWVDVTVSLASDVTLKPG
+TQLHGATSVATGAVVGPDSTLTDTQVGEGAVVKRTDATEAVIGAGATVGPFTYLRPGTVL
+GEDGKIGAFYETKNVTVGRGAKLSHLGYAGDAEIGEYTNIGCGNITANYDGVAKHRTVIG
+AHVRTGSNTVFTAPVSVGDGAYTGAGAVVRDDVPAGALALNAVAQRTIEGWVPAKRPGST
+SAQAARAAGAEGSGAQG
+>LFPAFLNI_00496
+MSQPSARPSAVIVLAAGQGTRMKSTTPKIMHAIGGRSLVGHALAAAWSLAPEHLVAVVRH
+ERARVAEHLETVAAQLGIDALAIADQDDVPGTGRAVELGLAALPADLEGTVVVTYGDVPL
+LTPETLARLVADHEADGNAVTVLTATLEDATGYGRIVRDAEGLVERIMEHKDALAHAEST
+GDDSFVAIREVNSGIYAFDAALLRRTLPEVSTDNVQGEKYLTDVLGMARAEGGRVASVGT
+DDVWEVEGANDRRQLSDLGRQLNDRVLRGWMKEGVTVVDPSSTWVDVTVSLASDVTLKPG
+TQLHGATSVATGAVVGPDSTLTDTQVGEGAVVKRTDATEAVIGAGATVGPFTYLRPGTVL
+GEDGKIGAFYETKNVTVGRGAKLSHLGYAGDAEIGEYTNIGCGNITANYDGVNKHRTVIG
+AHVRTGSNTVFTAPVTVGDGAYTGAGAVVREDVPAGALALNAVSQRTLEGWVPAKRPGTS
+SAEAARAAGAEGSGAQG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001645.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001645.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a2474f1864d2315adc7268d109d909925c1927a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001645.fa
@@ -0,0 +1,60 @@
+>ACLBLIBL_02453
+MAHLLGAENIGIAFGTRTVLEGLSLGVDEGDRIGLVGRNGDGKSTLMRILAGLQEPDTGR
+VTRRGGVRVGVLDQQDRLDPTHTVRQAVVGDVEDHVWASDPKVRDVLGGLLDGLDLEQTV
+EGLSGGQRRRVALARLLAGDDDVLFLDEPTNHLDVEGVAWLARHLKDRWRPTDGGLVVVT
+HDRWFLDEVCTRTWEVHDATVDPFDGGYAAWILARAERARQAAVVEQKRQQLMKKELAWL
+RRGAPARTSKPKFRIEAANAIIADVPEPRDSVSLAKTATARLGKDVLDLEHVGLSLGEKR
+ILDDVTLRLAPGERLGVVGVNGAGKSTLLRLLDGRLEPDSGRVKRGKTVVTATLTQDVKE
+LDEVAHLRVAEVMAREGSAFQVGDKEMSAGQLLEMLGFGTSRQWTQVSELSGGERRRLQL
+LRLLVGEPNVLMLDEPTNDLDTDTLAAVEDVLDGWPGTLVVVSHDRYLLERVTDHQVALL
+GDGKVRGLPGGVDQYLELRAAMDAAGASGGPARGAGAARGRNDVVGTCAGMGGPEEDTGP
+TEAERRLARKEMARLEKQMTRLRDSRSVLEARMAELGQAQDFDALTAASADLKDLDAQLD
+VLEEEWLQAAELTEGD
+>MOLHKGIG_00494
+MAHLLGAENIGIAFGTRTVLEGLSLGVDEGDRIGLVGRNGDGKSTLMRILAGLQEPDTGR
+VTRRGGVRVGVLDQQDRLDPEHTVRQAVVGDVDDHVWASDPKVRDVLGGLLDGFDLEQSV
+RGLSGGQRRRVALARLLAGDDDVLFLDEPTNHLDVEGVAWLARHLKPRWRPTDGGLVVVT
+HDRWFLDEVCTRTWEVHDATVDPFDGGYAAWVLARAERSRQAAVTEQKRQQLVKKELAWL
+RRGAPARTSKPKFRIEAANAIIEDVPAPRDSVSLAKMATARLGKDVLDLEHVSLTLGEKP
+ILDDVTLRLAPGERLGVVGVNGAGKSTLLRLLDGRIAPDSGRVKRGKTVVSATLTQDVKE
+LDDVAHLRVAEVMAREGSSFQVGDREMSSGQLLEMLGFGTSRQWTQVSELSGGERRRLQL
+LRLLVGEPNVLMLDEPTNDLDTDTLAAVEDVLDGWPGTLVVVSHDRYLLERVTDHQVALL
+GDGKVRGLPGGVDQYLELRAAMDEAGGPARGAGPVRGRNDVVGTCAGMGGPEEDTGPTEA
+ERRLARKEMARLEKQMTRLRDRRSGLEARMAALGQAQDFDALTAASADLKDLDAQLDVLE
+EEWLRAAELAEGD
+>NAFOICDF_02337
+MAHLLGAENIGISFGTRTVLDGLSLGVDEGDRIGLVGRNGDGKSTLMRILAGLQEPDTGR
+VTRRGGVHVGVLDQRDVLDPQDTVRRAVVGDVEDHVWASDARIRDVLGGLLAGMDLEQRV
+EGLSGGQRRRVALARLLAGDDDVLFLDEPTNHLDVEGVAWLAGHLNARWRPNDGGLVVVT
+HDRWFLDAVCTRTWEVHDAAVDPFDGGYAAWILARAERARQAQVTEQKRQQLMKKELAWL
+RRGAPARTSKPKFRIEAANAIIADVPEPRDTVSLAKTATARLGKDVIDLEDVTLTLGDRT
+ILDDVTLRLAPGERLGVVGVNGAGKSTLLRLLDGRLQPDSGRMKRGKTVVSATLTQDVKE
+LDEVADLRVAEVMAREGSAFQVGDREMSPGQLLEMLGFGPTRQWTAVSELSGGERRRLQL
+LRLLVGEPNVLMLDEPTNDLDTDTLAAVEDVLDGWPGTLVVVSHDRYLLERVTDHQVALL
+GDGRVRDLPGGVDQYLELRVLMDDAGGAAPAPGSSRGRGDAQGTCAGMVVDIPEVSEAER
+RQARKDMARLERQMQRLRESRGGIEARMAELGQAQKYDELGAATAELTAVDAELEDLEEQ
+WLEAAERDA
+>MHAAABBN_00215
+MAHLLGAENIGIAFGTRTVLEGLSLGVDEGDRIGLVGRNGDGKSTLMRILAGLQEPDTGR
+VTRRGGVRVGVLDQQDRLDPEHTVRQAVVGDVDDHVWASDPKVRDVLGGLLDGFDLEQSV
+RGLSGGQRRRVALARLLAGDDDVLFLDEPTNHLDVEGVAWLARHLKQRWRPTDGGLVVVT
+HDRWFLDEVCTRTWEVHDATVDPFDGGYAAWVLARAERSRQAAVTEQKRQQLVKKELAWL
+RRGAPARTSKPKFRIEAANAIIEDVPAPRDSVSLAKMATARLGKDVLDLEHVSLTLGEKP
+ILDDVTLRLAPGERLGVVGVNGAGKSTLLRLLDGRIAPDSGRVKRGKTVVSATLTQDVKE
+PDDVAHLRVAEVMAREGSSFQVGDREMSSGQLLEMLGFGTSRQWTQVSELSGGERRRLQL
+LRLLVGEPNVLMLDEPTNDLDTDTLAAVEDVLDGWPGTLVVVSHDRYLLERVTDHQVALL
+GDGKVRGLPGGVDQYLELRAAMADAGGPARGAGVARGRNDVVGTCAGMGGPEEDTGPTEA
+ERRLARKEMARLEKQMTRLRDRRSGLEARMAELGQAQDFDALTAASADLKDLDAQLDVLE
+EEWLQAAELAEGD
+>LFPAFLNI_00493
+MAHLLGAENIGIAFGTRTVLEGLSLGVDEGDRIGLVGRNGDGKSTLMRILAGLQEPDTGR
+VTRRGGVRVGVLDQQDRLDPEHTVRQAVVGDVDDHVWASDPKARDVLGGLLDGFDLDQPV
+RGLSGGQRRRVALARLLAGDDDVLFLDEPTNHLDVEGVAWLARHLKQRWRPTDGGLVVVT
+HDRWFLDEVCTRTWEVHDATVDPFDGGYAAWVLARAERSRQAAVTEQKRQQLVKKELAWL
+RRGAPARTSKPKFRIEAANAIIQDVPAPRDSVSLAKMATARLGKDVLDLEHVSLTLGEKP
+ILDDVTLRLAPGERLGVVGVNGAGKSTLLRLLDGRIAPDSGRVKRGKTVVSATLTQDVKE
+LDDVAHLRVAEVMAREGSSFQVGDREMSSGQLLEMLGFGTSRQWTQVSELSGGERRRLQL
+LRLLVGEPNVLMLDEPTNDLDTDTLAAVEDVLDGWPGTLVVVSHDRYLLERVTDHQVALL
+GDGKVRGLPGGVDQYLELRAAMDDAGGPARGAGAARGRNDVVGTCAGMGGPEEDTGPTEA
+ERRLARKEMARLEKQMTRLRDRRSGLEARMAELGQAQDFDALTAASADLKDLDAQLDVLE
+EEWLQAAELAEGD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001648.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001648.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9390f7e3394e47ed383d98a94fb7af0ab3243e28
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001648.fa
@@ -0,0 +1,60 @@
+>ACLBLIBL_02456
+MLTRLLKARLPEGTQYLVDRPMRIRLVFVVLGSVLVAGLEMVALASILPLVSLLTSGELG
+SPALEGLLARFGAVTVPEQTVAFAVVIVLAFLLKAILVLAFRWWTMGFTNQNLIRTSATL
+LRYYLRADYGLHLTRTVGTLVNNVTGTSSMAYTGVVNASVTFLTEAVTLVAVAVVVGVSM
+PLTGLGMALYFLAVAWVIKAVIRRPASRLGWTLVTTGERANTAALQGLENYKDVKIRGND
+SAFMEEYRAARAESAEATRLKMILTMMPRYVLEVAFVAAIAALVAVAFVQGRGGEAFGSL
+ALLAMAGFRVLPSMAALMATTNEIRASWPAFERTTAELADAQPVLDAADRPYERLEFARE
+IEVRGASYTYPGSDEPVLRDIDLTIPFGTSYAFVGGSGAGKTTLIDLLIGFHHAQDGAVL
+VDGVELEANPRGWWDNVAFVPQSVTVVNGSVLHNVVLDLEAAETADRAAVEQVLRDAQLG
+EWLDALPEGLDTVIGEGAVGVSGGQRQRLGIARALFRRPRLLVLDEATSALDNLTERRVT
+EVIESLKGRITVLVVAHRLSTVKHCDQIVLMDQGRIIGQGTFRGLQETSPEFQELVRLGD
+LSA
+>MOLHKGIG_00491
+MLTRLLKARLPEGTQYLVDRPMRIRLVFVVLGSVLVAGLEMVALASILPLVSLLTSGELG
+SPALEGLLARFGAVTVPEQTVAFAVVIVLAFLLKAILVLAFRWWTMGFTNQNLIRTSATL
+LRYYLRADYGLHLTRTVGTLVNNVTGTSSMAYTGVVNASVTFLTEAVTLVAVTVVVGVAM
+PLTGLGMALYFLAVAWVIKTVIRRPASRLGWTLVTAGERANTAALQGLENYKDVKIRGND
+SAFMEEYRAARMESAEATRLKMILTMMPRYVLEVAFVAAIAALVAVAFIQGRGGEAFGSL
+ALLAMAGFRVLPSMAALMATTNEIRTSWPAFERTTAELAAAQPVLHAADRPYERITFEES
+IEVRDASFTYPGKAEPVLRDIDLRIPFGSSYAFVGGSGAGKTTLVDLVIGFHHAQRGGVY
+VDGVELEANPRGWWDNVAFVPQSVTVVNGTVLHNVLLDVEAAQTADRAEVERVLREAQLG
+QWLDELPDGLDTVIGEGAVGVSGGQRQRLGIARALFRRPRLLVLDEATSALDNLTERRVT
+EVIESLRGRITVIVVAHRLSTVKRCDQIVLMDQGRIIGQGTFAGLQETSPEFRELVRLGD
+LST
+>NAFOICDF_02340
+MVTRLLKSRLPEGTQYLVDRPMRIRLGFVVLGSILVALLEMAALASILPLVNLLTTGSPG
+APVITELLASVGAVSVAEQTVAFAGVIVVAYLLKAVLVLSFRWWTMGFTNKNLIQTSAKL
+LRYYLRADYGLHLTRTVGTLVNNVTGTSSMAYTGVVNASVTLLTEAVTLLAVGIVVGVTM
+PLTALGMGAYFLVVTLIIRHVIRKPASQLGWTLVVTGERANTAALQGLENYKDVKVRGND
+SAFMDEYVDARRENAEAIRLKMILTMMPRYVLEVAFVAAIAGLVAVAFASGRGDQAFGSL
+ALLAMAGFRLLPSIASVMATSNEIRASWPAFERTVAELKDAQPVLDAADRPYDRLPFERS
+LEARNASFTYPGKDEPVLKGIDLSIPFGASYAFVGGSGAGKTTLVDLLIGFHHAQQGGVY
+VDGVELQADPRGWWDNVAFVPQSVTVVNGSVLHNVVLDIEAARTADRTEVERVLRDAQMG
+DWLDALPDGLDTVVGEGAVGVSGGQRQRLGIARALYRRPRLLVLDEATSALDNVTERKVT
+DVIESLKGRITVIVVAHRLSTVKHCDQVVLMDEGRILDQGTFAGLQETSPEFQELVRLGD
+LSS
+>MHAAABBN_00212
+MLTRLLKARLPEGTQYLVDRPMRIRLVFVVLGSVLVAGLEMVALASIIPLVSLLTSGELG
+SPALEGLLARFGAVTVPEQTVAFAVVIVVAFLLKAILVLAFRWWTMGFTNQNLIRTSATL
+LRYYLRADYGLHLTRTVGTLVNNVTGTSSMAYTGVVNASVTFLTEAVTLVAVAVVVGVAM
+PLTGLGMALYFLAVAWVIKTVIRRPASRLGWTLVTTGERANTAALQGLENYKDVKIRGND
+SAFMEEYRAARMESAEAMRLKMILTMMPRYVLEVAFVAAIAALVAVAFIQGRGGEAFGSL
+ALLAMAGFRVLPSMAALMATTNEIRTSWPAFERTTAELAAAQPVLHAADRPYERITFEEA
+IEVRDASFTYPGKAEPVLRDIDLRIPFGSSYAFVGGSGAGKTTLVDLVIGFHHAQRGGVY
+VDGVELEANPRGWWDNVAFVPQSVTVVNGTVLHNVLLDVEAAQTADRAEVERVLREAQLG
+QWLDELPDGLDTVIGEGAVGVSGGQRQRLGIARALFRRPRLLVLDEATSALDNLTERRVT
+EVIESLRGRITVIVVAHRLSTVKRCDQIVLMDHGRIIGQGTFAGLQETSPEFRELVRLGD
+LST
+>LFPAFLNI_00490
+MLTRLLKARLPEGTQYLVDRPMRIRLVFVVLGSVLVAGLEMVALASILPLVSLLTSGELD
+SPALEGLLARFGAVTVPEQTVAFAVVIVLAFLLKAILVLAFRWWTMGFTNQNLIRTSATL
+LRYYLRADYGLHLTRTVGTLVNNVTGTSSMAYTGVVNASVTFLTEAVTLVAVAVVVGVAM
+PLTGLGMALYFLAVAWVIKTVIRRPASRLGWTLVTAGERANTAALQGLENYKDVKIRGND
+SAFMEEYRAARMESAEATRLKMILTMMPRYVLEVAFVAAIAALVAVAFIQGRGGEAFGSL
+ALLAMAGFRVLPSMAALMATTNEIRTSWPAFERTTAELAAAQPVLHAADRPYERVTFEEA
+IEVRDASFTYPGKAEPVLRDIDLRIPFGSSYAFVGGSGAGKTTLVDLVIGFHHAQRGGVY
+VDGVELEANPRGWWDNVAFVPQSVTVVNGTVLHNVLLDVEAAQTADRAEVERVLREAQLG
+QWLDELPDGLDTVIGEGAVGVSGGQRQRLGIARALFRRPRLLVLDEATSALDNLTERRVT
+EVIESLRGRITVIVVAHRLSTVKRCDQIVLMDQGRIIGQGTFAGLQETSPEFRELVRLGD
+LST
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001651.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001651.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8dda6564d08821380fca4b39be689beffb8c52c3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001651.fa
@@ -0,0 +1,51 @@
+>ACLBLIBL_02461
+MEPVPATALAPRPAAVAVDGAPFGVAALRARLGVSAAPLTRWHWILPLLVTALAGVLRFT
+NLAHPDQLIFDETYYPKDAYSLLQSGYERRWEEDVNDAFVRGEAEPLESAAYVVHPPLGK
+WLIGLGMLAFGTDNGVGWRFSSAVAGTLSVLLVALVAQHLLRSVSLGAVAGLLLAVEGHH
+LVMSRIGLLDIFLSFFVLAAFAALLADRAHGRQLLARRLAHDVARRGHAALATGPWLGWR
+PWRLLAGVLLGAGCAVKLSGLAFMAAFGLLTVLWDMAARRDAGVRDWARAGVVKDGLLAF
+VAVVGGGLVAYLASWTGWFATEGGYYRMWHRDNPPEGPLAGLVPGPLRSLWHYHVESTTF
+HEGLTSPHDYAASPWTWPFMGRPVSYYYRGGEPGQEVCPADAPSACSAAITDIANPLLWW
+TGLIAVLVCLWLLIRHRDWRAGALLGAYLAGQVVWFLWPERTMFFFYTVAYEPFLILMIV
+LALSLLLRPGRRPGPRWGSALVLAYAAAVVGVSLFFLPVWIGDVIPYDQWRWRMWFNSWI
+>MOLHKGIG_00486
+MEPVPATALAPRPAAVAADDGPFGVAALRARLGVSAAPLTRWHWILPLLVTVIAGVLRFT
+NLAHPDQLIFDETYYPKDAYSLLESGYERRWGEDVNDAFARGEAEPLEGAAYVVHPPLGK
+WLIGLGMLAFGPDNGVGWRFSAAVAGTLSVLLVALATQHLLRSVSLGAVAGLLLAVEGHH
+LVMSRIGLLDIFLSFFVLAAFAALLADRVHGRRLLAERLAHDVARRGRDALASGPWLGWR
+PWRLLAGVLLGAGCAVKLSGLAFMAAFGLLTVLWDMSARRTAGVRRWAWAGVEKDGLYAF
+VAVVGGGLVAYLASWTGWFVTEGGYYRDWHRDNPPEGVLAGLVPGPLRSLWHYHVESTTF
+HQGLTSPHDYAANPWTWPFMGRPVSYYYEGAEPGEGICPADAAGACSAAITDIANPFVWW
+TGLAAVLVCVWLLVRHRDWRAGALLGAYAAGQLVWSLWPERTMFFFYTIAYEPFLVMMIA
+LALSLLLRPGRRPGPRWGSALVLAYVTIAVAVSLFFLPVWIGDVIPYDQWRWRMWFSSWI
+>NAFOICDF_02344
+MACVPASSLTRRPAHALPAPADDAAAHPFGAAALRARLGVQAAVLTRWHWIVPLAVTVLA
+GVIRFTNLAFPDKLIFDETYYPKDAYSLILSGYERRWAPDVDAAFAQGTAQPLDEPAYVV
+HPPLGKWLIALGMLAFGPDNGVGWRFSAAVAGTLSVLLVTLVAQRLFRSVSLGALAGLLL
+AVEGHHIVMSRIGLLDIFLSFFMIAAFAALLADRDHGRRLLASRLAEQVAAHDAGTRRGD
+PLAFGPRLGWRPWRILAGALLGAGCAVKLSGLAFMAVFGILTVLWDMEARRTAGIRHWLR
+AGVVRDGLPAFAAVVGAGLAVWLASWTGWFASEGGYYRRWAQDNPPEGPLSALLPGPLRS
+LIHYQLEAFTFHEGLTSPHDYGSSPWTWPFMGRPVSYFYEGGKPGENGCPSTAADACSSA
+ITDIANPFIWWTGLIAVLVCLAVLVRHRDWRAGALLGAYVAGQVVWFRWPERTMFFFYTV
+AYEPFLILMIVLALSLLLRRGHRPGPRWGAVLVAAYLLVAVGVSLFFLPVWIGERIPYPQ
+WSWRMWFSTWI
+>MHAAABBN_00205
+MEPVPATALAPRPAAVAVDDGPFGVAALRARLGVSAAPLTRWHWILPLLVTVIAGVLRFT
+NLAHPDQLIFDETYYPKDAYSLLESGYERRWDEDVNDAFARGEAEPLEGAAYVVHPPLGK
+WLIGLGMLAFGPDNGVGWRFSAAVAGTLSVLLVALATQHLLRSVSLGAVAGLLLAVEGHH
+LVMSRIGLLDIFLSFFVLAAFAALLADRAHGRRLLAERLAHDVARRGRDALASGPWLGWR
+PWRLLAGVLLGAGCAVKLSGLAFMAAFGLLTVLWDMSARRTAGVRRWAWAGIEKDGLYAF
+VAVVGGGLVAYLASWTGWFVTEGGYYRDWHRDNPPEGLLAGLVPGPLRSLWHYHVESTTF
+HQGLTSPHDYAANPWTWPFMGRPVSYYYEGAEPGEGICPPDAAGACSAAITDIANPFVWW
+TGLAAVLVCVWLLVRHRDWRAGALLGAYAAGQLVWFLWPERTMFFFYTIAYEPFLVMMIA
+LALSLLLRPGRRPGPRWGSALVLAYVTIAVAVSLFFLPVWIGDVIPYDQWRWRMWFSSWI
+>LFPAFLNI_00486
+MEPVPATALASRPAAVAVDDGPFGVAALRARLGVSAAPLTRWHWILPLLVTAIGGVLRFT
+NLAHPDQLIFDETYYPKDAYSLLESGYERRWDEDVNDAFARGEAEPLEGAAYVVHPPLGK
+WLIGLGMLAFGPDNGVGWRFSAAVAGTLSVLLVALATQHLLRSVSLGAAAGLLLAVEGHH
+LVMSRIGLLDIFLSFFVLAAFAALLADRVHGRRLLAERLAHDVARLGRDALASGPWLGWR
+PWRLLAGVLLGAGCAVKLSGLAFMAAFGLLTVLWDMSARRTAGVWHWAWAGVEKDGLYAF
+VAVVGGGLVAYLASWTGWFVTEGGYYRDWHRDNPPEGLLAGLVPGPLRSLWHYHVESTTF
+HQGLTSPHDYAANPWTWPFMGRPVSYYYEGAEPGEGICPADAAGACSSAITDIANPFVWW
+TGLAAVLVCVWLLVRHRDWRAGALLSAYVAGQLVWFLWPERTMFFFYTIAYEPFFVMMIA
+LALSLLLRPGRRPGPRWGSALVLAYVTIAVAVSLFFLPVWIGDVIPYDQWRWRMWFSSWI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001659.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001659.fa
new file mode 100644
index 0000000000000000000000000000000000000000..286f805dddabe2abbb90302cc31c06e2c51e4257
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001659.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02469
+MLSDLWSRLTGLVSMLWREVAKFGTVGAAAFVIDSLVFWWMMTGPLEGSNVKAKIVAGVV
+ATLFSWVANRYWTFREKRSSNKTRELVMFLLMNAIGLGIQAGCVFIAQYLMGVTDPGGLF
+IAGNVVGLFFGTVFRYFAYRFWVFKEELDVEPGFANDIAIITGQMPVLRDEQLHPHGRHE
+ARGRPAERHVRRDDGPARHRAS
+>MOLHKGIG_00478
+MLSDLWGRLTGMASLLWREVAKFGTVGAAAFVVDSLVFWWMMTGPLEGSNVKAKIVGGVV
+ATLFSWVANRYWTFRDKRSSNKTRELVMFLIMNAIGLGIQAGCVAIAQYLMGVTDPTGLF
+IAGNVIGLFFGTVFRYFAYRFWVFKEKLDVEPGFANDLAIITGQMPVLREDQLPPHGRHR
+APDAGV
+>NAFOICDF_02353
+MPTDLWHRFTGLVSMLWREVAKFGTVGAAAFVVDSAVFWWLMHGPLEGSNVKAKICAGVV
+ATIFSWVANRYWTFRDKRQNNVVRELVMFLVMNAVGLGIQAGCVAIAQYGMGVTDPNGLF
+IAGNVIGLFFGTVFRYFAYRFWVFKEELDEEPGFENDIAVITGQLPVLHAHDEHVPGLQH
+RHPRHDVEDGSA
+>MHAAABBN_00196
+MLSDLWGRLTGMASLLWREVAKFGTVGAAAFVVDSLVFWWMMTGPLEGSNVKAKIVGGVV
+ATLFSWVANRYWTFRDKRSSNKTRELVMFLIMNAIGLGIQAGCVAIAQYLLGVTDPTGLF
+IAGNVIGLFFGTVFRYFAYRFWVFKEKLDVEPGFANDLAIITGQMPVLREDQLRPRGRHR
+TPDAGV
+>LFPAFLNI_00478
+MLSDLWGRLTGMASLLWREVAKFGTVGAAAFVVDSLVFWWMMTGPLEGSNVKAKIVGGVV
+ATLFSWVANRYWTFRDKRSSNKTRELVMFLIMNAIGLGIQAGCVAIAQYLMGVTDPTGLF
+IAGNVIGLFFGTVFRYFAYRFWVFKEKLDVEPGFANDLAIITGQMPVLREDQLPPHGRHR
+APDAGV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001660.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001660.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0869fed76b10d2d2e2d9f70fa990c1beb046318a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001660.fa
@@ -0,0 +1,43 @@
+>ACLBLIBL_02470
+MMAGPAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPT
+EHLRVLQEVGVAVRPGPEALQHAQDKLVMRAAVERLGLPNPAWAAVRDLDEVLAFGDEHG
+WPMILKTPRGGYDGKGVLKLDDADDARASASDGTLGTWLGAGIAPLLAEALVPFTRELSA
+QVARTPSGRVAAYPVVDSVQVAGVCDLVVAPARDLDPAVAEAATAAAVRLAEELDVTGML
+AVELFETPGVGPGFQINELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGDTAPRGAG
+VVMKNLLGGAREDLHAGLADALAAHPQAKVHLYGKAVRPGRKVGHVNVVADHGLTLEQAV
+RAAESAAAVLRDGAAPDAVDASPSSPATPHPAGGPPMTATPQNPAQPLQDDAPVVSVVMG
+SDSDWPVMSAAAEALRELDVPVEVGVVSAHRMPHEMVEFGARAHERGIRVIVAGAGGAAH
+LPGMLASVTPLPVIGVPVKLKSLDGLDSLLSIVQMPAGVPVATVSVDGARNAGLLAARIL
+ASADTEEGERLRAALTEHAAELNAQAQAKGARLRERMAADR
+>MOLHKGIG_00477
+MMAGAAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPT
+EHLRALQEAGVAVRPDPEALQHAQDKLVMRAAVERLGLPNPAWAPVDDLEAVLAFGDEHG
+WPMILKTARGGYDGKGVLKLDDADDARASAADGTLAAWLGAGITPLLAEALVPFSRELSA
+QVARTPSGEVAVYPVVDSVQVAGVCDLVVAPAQDLDPAVAAAATAAAVRLAEELDVTGML
+AVELFETPGVGPGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGETAPRGAG
+VVMKNVLGGAREDLHAGSVAALAAHPQAKVHLYGKDVRPGRKVGHVNVVADHGLSLEEAV
+RTAESAAALLRDDAPTTGTETEARP
+>NAFOICDF_02354
+MIGGGQLARMMAGPAAELGVPFRVLAEAPDASAAQVAPHMVGDHASLEDLRAFAATVDVV
+TFDHEHVPTEHLRTLEAAGVAVRPGPDALQYAQDKLLMRGLVERLGLPNPAWAPVSSLEE
+VIAFGDEHGWPMILKTARGGYDGKGVLKVDSADDARSGAADGTLGTWLGAGIAPLLAEAM
+VPFARELSAQVARRPSGEVAAYPVVASLQTQGVCDVVTAPAPDLAPAVAEAASGAAVRIA
+EELDVTGMLAVELFETPGTDAGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDMPL
+GGTAPRGDGTVMKNVLGGAHEDLHSGFSEALAAHPEAKVHVYGKGVRPGRKVGHVNVVAE
+HGLSLADAERIAESTAAVLRDATAPSAPTPKA
+>MHAAABBN_00195
+MMAGAAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPT
+EHLRALQEAGVAVRPDPEALQHAQDKLVMRAAVERLGLPNPAWAPVDDLEAVLAFGDEHG
+WPMILKTARGGYDGKGVLTLDDADDARASAADGTLAAWLGAGIAPLLAEALVPFSRELSA
+QVARTPSGEVAVYPIVDSVQVAGVCDLVVAPAQDLDPAVAAAATAAAVRLAEELDVTGML
+AVELFETPGVGPGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGETAPRGAG
+VVMKNVLGGAREDLHAGSVVALAAHPQAKVHLYGKDVRPGRKVGHVNVVADHGLSLEEAV
+RTAESAAALLRDDAPTTGTETEARP
+>LFPAFLNI_00477
+MMAGAAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPT
+EHLRALQEAGVAVRPDPEALQHAQDKLVMRAAVERLGLPNPAWAPVDDLEAVLAFGDEHG
+WPMILKTARGGYDGKGVLKLDDADDARASAADGTLAAWLGAGITPLLAEALVPFSRELSA
+QVARTPSGEVAVYPVVDSVQVAGVCDLVVAPAQDLDPAVAAAATAAAVRLAEELDVTGML
+AVELFETPGVGPGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGETAPRGAG
+VVMKNVLGGAREDLHAGSVAALAAHPQAKVHLYGKDVRPGRKVGHVNVVADHGLSLEEAV
+RTAESAAALLRDDAPTTGTETEARP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001663.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001663.fa
new file mode 100644
index 0000000000000000000000000000000000000000..14a158b19923f6a7d18b9b6183d37d078ba5558f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001663.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02474
+MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD
+TVSMAGTVVIGEGEKDEAPMLFNGEEVGDGSGAPVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDLRLPVKQNVALVAKALDKPASQVTVCVLDR
+PRHEGLVKEIREAGARVKFILDGDVAAAIAAARPDTGVDMMMGIGGTPEGIVTACAIKAT
+GGVIQGRLAPTDETEKQKALDAGLDLDAVLSTNDLVTSDHCYFAATGITDGDLLRGVRFV
+DGRVVTQSIVMRSWSGTVRTVDAEHDVRKWSKWLEDRGTRTGR
+>MOLHKGIG_00473
+MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD
+TVAMDGTVVIGEGEKDEAPMLFNGEQVGDGSGAAVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR
+PRHEGLVKEIRQAGARVKFILDGDVAGAIAAARPDTGVDMMMGIGGTPEGIVTACAIKAT
+GGIIQGRLAPTDDAEKQKALDAGLDLDAVLTTNELVTSDHCYFAATGITDGDLLRGVRFA
+DGRVHTQSIVMRSSSGTVRTVDAEHDVKKWSKWLGDRDAR
+>NAFOICDF_02358
+MTSASSENTGYENHVPDRNLAMELVRVTEAAAIAASPWVGGGDKNRADGAAVDAMRAFMD
+TVAMDGTVVIGEGEKDEAPMLFNGERVGDGKGASVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR
+PRHEGLVKEIRAAGARVKFILDGDVAGAIAAARPDTGVDMMMGIGGTPEGIVTACAIKAT
+GGVIQGRLAPTDDAEKQKALDAGLDLDAVLTTDELVTSDHCYFAATGITDGDLLRGVRFA
+GGRVHTQSIVMRSKSGTVRTVDAEHHVDKWSQWLKNRG
+>MHAAABBN_00191
+MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD
+TVAMDGTVVIGEGEKDEAPMLFNGEQVGDGSGAAVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR
+PRHEGLVKEIRQAGARVKFILDGDVAGAIAAARPGTGVDMMMGIGGTPEGIVTACAIKAT
+GGIIQGRLAPTDDAEKQKALDAGLDLDAVLTTNELVTSDHCYFAATGITDGDLLRGVRFA
+DGRVHTQSIVMRSSSGTVRTVDAEHDVKKWSKWLGDRDAR
+>LFPAFLNI_00473
+MTSASSEKTGYENHVPDRNLAMELVRVTEAAAIAASPWVGYGDKNKADGAAVDAMRAFMD
+TVAMDGTVVIGEGEKDEAPMLFNGEQVGDGSGAAVDVAVDPIDGTRLTAMGYNNALSVFA
+VAERGTMFDPSAVFYMDKLVVGPEAADFVDMRLPVKQNVNLVAKALDKPVSQVTVCVLDR
+PRHEGLVKEIRQAGARVKFILDGDVAGAIAAARPGTGVDMMMGIGGTPEGIVTACAIKAT
+GGIIQGRLAPTDDAEKQKALDAGLDLDAVLTTNELVTSDHCYFAATGITDGDLLRGVRFA
+DGRVHTQSIVMRSSSGTVRTVDADHDVKKWSKWLEDRDAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001667.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001667.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b67e9f5dedc9221fd02c20ede3ba9087c87a5a1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001667.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02478
+MDGVGWAWAQGLPATAVLWSAGLAWFAVCAAVLVRVDLREHRLPNRWTLRLALGGLAAMA
+GGAALAGRADLVLSSVLGGLGYAAAMLVLHVLSRGSLGMGDVKLAAGLGAYTGVLGGSAV
+VAAGLGAILLGGAVAAVLVAARRASRSTALPFGPPMILAAAAVLAFAPAGG
+>MOLHKGIG_00469
+MSGVGWAWTHGAPATAVLWSLGLVWFAVCAGVLVRTDLREHRLPNRWTLRLALGGLTMMT
+GGALLAGRGDLTLCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV
+LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA
+>NAFOICDF_02362
+MTWWTGAWEAGERLTAMLWAAGLVWFLLCSVVLARTDLREHRLPNRWTGRLALGGVVAMG
+GGAVLGGLWSVVASCLLGGLGYALAMLALHVLTRGGLGLGDVKLAAGLGLYCGVAGLAAV
+LAAAVLAVLLGGVVAVVLVLARRADRHTALPFGPAMVAGALGVLLLA
+>MHAAABBN_00187
+MSGVGWAWTHGAPATAVLWTLGLAWFAVCSGVLVRTDLREHRLSNRWTLRLALGGLAMMT
+GGALLAGRGDLALCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV
+LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA
+>LFPAFLNI_00469
+MSGVGWAWTHGAPATAVLWTLGLAWFAVCSGVLVRTDLREHRLSNRWTLRLALGGLAMMT
+GGALLAGRGDLALCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV
+LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001669.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001669.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f20a3c8b7f8785bd4b92d69e933ac90d342ff795
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001669.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02480
+MSMHRPTPRLPERGAVPAARPAPSLAERVSGRLVAVIAPTLLLVAALWVVQIALVFFGRL
+VIPSLGLIPRSVTGLDGILFSPLLHAGWGHLIGNASALILLGPLAALISGRPLALLAAAW
+LGSGVLTWVIGSPGVHIGASGIVYALVAFLVVYGIAVRRVVPVVVSVLVALTHLGSSLIG
+LLPAPGVSWTGHLAGAVVGVLLGLWWGRGDRRPRHADI
+>MOLHKGIG_00467
+MHRPSPGLPDLPGGPAPAPTLAERAGGRLLGAVAPTAVLIAAMWVAQFVLIFLGRVIIPG
+VGLIPRRLDGLDGVLFSPVLHAGWAHLIGNTTALLVLGPLAALVSRRPVALLVCAWLGSG
+LLTWVIGTPGVHIGASGIVYALIAFLIVYGVAVRRIGAVVVSVLVALTHLGSSLIGLLPA
+PGISWTGHLAGAVVGVLLGLWWGRADRQVPNRR
+>NAFOICDF_02364
+MPLPDRRPADDAVPAPRPSLTQAAAQGLVRTVAPTAVLVAAMWVMFLVSIVGGSTLIGGL
+GLIPRRAAGLDGILFSPLLHGGWRHLVGNTTALLVLGPVAAAVSRRPLALLAAAWLGSGA
+LTWVIGTPGVHVGASGIVYALIAFLLVYGVVARRVLAVVVAVAVAAAHLGSSLLGLLPQP
+GVSWTGHLAGAVVGVGLALLWGRADRPARAPLGP
+>MHAAABBN_00185
+MSMHRPSPGLPDLPGGPAPAPTLAERAGGRLLGAVAPTAVLIAAMWVAQVVLIFLGRVII
+PGVGLIPRRLGGLDGVLFSPVLHAGWAHLIGNTTALLVLGPLAALVSRRPVALLVCAWLG
+SGLLTWVIGTPGVHIGASGIVYALIAFLIVYGIAVRRIGAVVVSVLVALTHLGSSLIGLL
+PAPGISWTGHLAGAVVGVLLGLWWGRADRQVPNRR
+>LFPAFLNI_00467
+MHRPSPGLPDLPGGPAPAPTLAERAGGRLLGAVAPTAVLIAAMWVAQFVLIFLGRVIIPG
+VGLIPRRLDGLDGVLFSPVLHAGWAHLIGNTTALLVLGPLAALVSRRPVALLVCAWLGSG
+LLTWVIGTPGVHIGASGIVYALIAFLIVYGVAVRRIGAVVVSVLVALTHLGSSLIGLLPA
+PGISWTGHLAGAVVGVLLGLWWGRADRQVPNRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001672.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001672.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cbeb39d28b369d2c37ef708eaa3e6b16c7268ded
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001672.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02483
+MSPLSGLPLVLTALAAASPAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMAIIVL
+RVMVRSVRRVQQRSPEAEAMLVDRHQQHLPEDVRELAPEDEERDAQDRLRHLQEKYPGYL
+QEPAPRPQSPDDGRS
+>MOLHKGIG_00464
+MTPLSGLPLVLTALAAASPAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMAIIVL
+RVMVRSVRRVQQRSPQAEAMLVERHQQHLPDEVRAGGEHLDADSEDRLRRLQEKYPGYLQ
+EPAPEPQAPDTGRD
+>NAFOICDF_02367
+MSLAPLALSAVSLAASVSPSAPMPAVPEPTLKPGLDKQDISPGIEGFLFTALMVVMAIIV
+FRLMVRSVRRVQQRSPEAEAMLVDRHQQHLPEEVREGGERLDGDAHDRIERLRRRYPGYL
+QDPTPEPESPDTGREPR
+>MHAAABBN_00182
+MTPLSGLPLVLTALAAASPAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMAIIVL
+RVMVRSVRRVQQRSPEAEAMLVERHQQHLPDEVRAGGEHLDADSEDRLRRLQEKYPGYLQ
+APAPEPQAPDTGRD
+>LFPAFLNI_00464
+MTPLSGLPLVLNALAAASPAPVPAVPEPTLRPGLEEAEVTPGIEGFLFTALMVVMAIIVF
+RVMVRSVRRVQQRSPQAEAMLVERHQQHLPDEVRAGGEHLDADSEDRLRRLQEKYPGYLQ
+EPAPEPQAPDTGRD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001682.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001682.fa
new file mode 100644
index 0000000000000000000000000000000000000000..279bdd3cc839f92a59b991bfd11a5b9ffe6d5fbf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001682.fa
@@ -0,0 +1,27 @@
+>ACLBLIBL_02507
+MAARRRAPLPDPVPARQITGRSLLVVAVLLVAAVLVAPTLRAFLNQQLEIAAAEEEIAAM
+QAQREDYEERIRLWDDPGYVTQQARERLQLVMPGETLYSVTGVPEEAPRDPRPEAPAGEP
+VNTRLPWAEGLWDSAVRAGPRVSPGPRPDPGSGPARP
+>MOLHKGIG_00449
+MSPRRPRVPRVDPTTGAPRRTAVAAPAAPTTASPKADAPTPTPEATTPTPAATGAEVIDL
+HSVQERRQAGHHGHLDGHPDADRADTAPAAPASPSAPPRRTAPARPAGRRTRPAPRRAAS
+AAATAARRRAPLPEPVPARQITGRSLIVVAVLLVAAVLVAPTLRAFLNQQLEISAAREEI
+ATMQAQREDYERRIQLWDDPAYVTQQARERLELVMPGETLYSVTGRPSETETETDTEAED
+TPAARADEVVNTRLPWAEGLWDSAVRAGLE
+>NAFOICDF_02379
+MSARRPRVPRVAVPDTAPERATPAVVEPVVVEPAPVAPAAPEAPAPPAPPGPQVIDLQEA
+AQRRRHEATRPSPRPDAERAAAQRVARLREERRRATVREHAAARRRVPLPEPVPARQLTG
+RSLVVLAVLIIAAVLVAPTARLMLNQQLEISAAQQDIAEQQRRKAEYEEQIRRWDDPGYV
+AQQARQRLELVMPGETLYTVTGLPDESGAVPADSVPQEKVNDRLPWVEGLWDSAVRAATE
+>MHAAABBN_00170
+MSPRRPRVPRVDPTTGAPRRTAVAAPAAPTTAFPEADTPTPTPAAPTPAPAATDAEVIDL
+QSIQERRQAGHPDVDRADTAPAGDTAAPASPSAPPRRTAPARPAGRRPRPAPRGAASAAA
+TAARRRAPLPEPVPARQITGRSLIVVAVLLVAAVLVAPTLRAFLNQQLEISAAREEIATM
+QAQREDYERRIQLWDDPAYVTQQARERLELVMPGETLYSVTGRPSETDTATETEDTPAAG
+ADEVVNTRLPWAEGLWDSAVRAGLE
+>LFPAFLNI_00452
+MSPRRPRVPRVDPTTGAPRRTAVAAPAAPTTAFPEADTPTPTPAAPTPAPAATDAEVIDL
+QSVQERRQAGHPGHLDGHPDADRADTAPAGDTAAPASPSAPPRRTAPARPAGRRPRPAPR
+RAASAAATAARRRAPLPEPVPARQITGRSLIVVAVLLVAAVLVAPTLRAFLNQQLEISAA
+REEIATMQAQREDYERRIQLWDDPAYVTQQARERLELVMPGETLYSVTGRPSETDTATET
+EDTPAAGADEVVNTRLPWAEGLWDSAVRAGLE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001687.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001687.fa
new file mode 100644
index 0000000000000000000000000000000000000000..803bfe7b0949bd7f3a115cc062837a170894dff4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001687.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02514
+MAAEGTTTAPGVDWDRLRRAALAATEHAYVPYSGFRVGAAALTEDGRLVTGCNIENASYG
+LTLCAECALLADLRMGGGGRLAAFVCVDGQGVLTMPCGRCRQLLHEFRAPDMVLLTPAGE
+RTMGQVLPDAFGPEDLERAAAR
+>MOLHKGIG_00443
+MADGQHTTTAPRVDWDRLRAAALAATEHAYVPYSGFRVGAAALTDDGRLVSGCNIENASY
+GLTLCAECALLAELRMGGGGRLAAFVCVDGAGVLTMPCGRCRQLLYEFRAPGLVLLTPAG
+ERGIDAVLPDAFGPADLERADRP
+>NAFOICDF_02385
+MTGTTTPPACAAPVAEADWDRLRAAAADAMERAYAPYSGFRVGAAALTEDGRLVSGCNVE
+NAAYGVALCAECALVGQLHMTGGGRLRAFLCVGGDGRLITPCGRCRQLLWEFRAPGLAVL
+TAAGVTTVEALLPEAFGPDALEA
+>MHAAABBN_00164
+MADGQHTTTAPRVDWDRLRAAALAATEHAYVPYSGFRVGAAALTDDGRLVAGCNIENASY
+GLTLCAECALLADLRMGGGGRLAAFVCVDGAGVLTMPCGRCRQLLYEFRAPGLVLLTPAG
+ERGIDAVLPDAFGPADLERADRP
+>LFPAFLNI_00446
+MADGQHTTTAPRVDWDRLRAAALAATEHAYVPYSGFRVGAAALTDDGRLVSGCNIENASY
+GLTLCAECALLADLRMGGGGRLAAFVCVDGDGVLTMPCGRCRQLLYEFRAPGLVLLTPAG
+ERGIDAVLPDAFGPADLERADRP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001693.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001693.fa
new file mode 100644
index 0000000000000000000000000000000000000000..873c707b2b080582769b347443e8c3ac0320b8df
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001693.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02520
+MSTDPNLTEAGREDAPGSALSRFHVVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR
+ATWDRLAPLAAGMLVVTGAAHRDAVCGQLPDLDTADLVLEPSPKDSAAAIGLAAAILSLR
+DPDTIMGSFAADQVIAPVEVFQDAVRQAVETAATGRIVTIGIEPTHAATGFGYIRRGRRL
+AVPGAPDAHDVAAFVEKPDLKVAQQYVKSGRYLWNAGMFVAPVGLMLAHLEENEPALHAG
+LMEIAHAWETERRDEVMERVWPELTKTAIDYAVAEPAAAVGDVAVIPGAFTWDDVGDFAA
+IARLNPVKDASGITVIGDTPRVYSDDASGVVVTDTRRVIALIGIEDVVVVDTEDALLVTT
+TDHAQEVKKAVEALKAEGVDEVL
+>MOLHKGIG_00437
+MSTDPNLTDAPREAAPGTALSRFHAVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR
+ATWDRLAPLAAGMLVVTGEAHREAVCTQLPALAETDLVLEPSPKDSAAAIGLAAAILSLR
+DPDTIMGSFAADQVISPVEVFQDAVRQAVETAATGRIVTIGIEPTHAATGFGYIRRGRRL
+RVAGAPDAHDVAAFVEKPDLKVAQQYVKSGRYLWNAGMFVAPVGLMLAHLEENEPALHAG
+LMEIARAWETPERDEVMARVWPELTKTAIDYAVAEPAAAVGDVAVIPGSFTWDDVGDFAA
+IARLNPVRDASGITVIGDTPRVYSDDASGVVVTDTKRVIALIGIEDVVVVDTEDALLVTT
+TEHAQEVKKAVEALKAEGVDEVL
+>NAFOICDF_02391
+MSIDPTAAQSAPSQPSASALERFHAVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR
+ATWDRLAPLAGGIMVVTGRAHEDAVCRQLPDVGAADLVLEPEPKDSAAAIGLAAAILWLR
+DSDTIMGSFAADQVIGPVDVFQDAVRQAVETAATGRIVTIGITPTHAATGFGYIRTGRRL
+SVAGAPDAHDVAAFVEKPDQRVAERYVASGRYLWNAGMFVAPVALMLQHLEANEPELHAG
+LTEIARAWETPERDAVMARVWPGLKKTAIDYAVAEPAATAGDVAVIPGAFTWDDVGDFAA
+IARLNPVKDGSGVTVIGDTPRVYSDSATGVVVTDTSRVIALIGVEDVVVVDTGDALLVTT
+TEHAQDVKRTVESLKAQGADDVL
+>MHAAABBN_00158
+MSTDPNLTDAPREAAPGTALSRFHAVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR
+ATWDRLAPLAAGMLVVTGEAHREAVCMQLPALAETDLVLEPSPKDSAAAIGLAATILSLR
+DPDTIMGSFAADQVISPVEVFQDAVRQAVETAATGRIVTIGIEPTHAATGFGYIRRGRRL
+RVAGAPDAHDVAAFVEKPDLKVAQQYVKSGRYLWNAGMFVAPVGLMLAHLEENEPALHAG
+LMEIARAWETPERDEVMARVWPELTKTAIDYAVAEPAAAVGDVAVIPGSFTWDDVGDFAA
+IARLNPVKDASGITVIGDTPRVYSDDASGVVVTDTKRVIALIGIEDVVVVDTEDALLVTT
+TEHAQEVKKAVEALKAEGVDEVL
+>LFPAFLNI_00440
+MSTDPNLTDAPREAAPGTALSRFHAVIPAGGVGTRLWPLSRAAAPKFLHDLTGSGQTLIR
+ATWDRLAPLAAGMLVVTGGAHREAVCMQLPDLAETDLVLEPSPKDSAAAIGLAAAILSLR
+DPDTIMGSFAADQVISPVEVFQDAVRQAVETAATGRIVTIGIEPTHAATGFGYIRRGRRL
+RVAGAPDAHDVAAFVEKPDLKVAQQYVKSGRYLWNAGMFVAPVGLMLAHLEENEPALHAG
+LMQIARAWETPERDEVMARVWPELTKTAIDYAVAEPAAAVGDVAVIPGSFTWDDVGDFAA
+IARLNPVKDASGITVIGDTPRVYSDDASGVVVTDTKRVIALIGIEDVVVVDTEDALLVTT
+TEHAQEVKKAVEALKAEGVDEVL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001697.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001697.fa
new file mode 100644
index 0000000000000000000000000000000000000000..417dab97a92c09bc66859c739dcf36bda4ece9ca
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001697.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_02524
+MSHAATETEAPVAQDQTQAAGGGMGAIESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD
+RVLDALHKVKWDHDGTLSFRRSCAHGICGSDAMRINGRNRLACKTLLKDLDLSKPILVEP
+IKGLPVEKDLIVDMDPFFQSYREVMPFLVAEGHEPSKERYQSQADRARYDDTTKCILCAA
+CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDDAGDMRLEILNDKEGVWRCRTTFNCTDA
+CPRGIQVTKAIAEVKQAILARQF
+>MOLHKGIG_00433
+MSHSATETEAPVAQAQTQSAGGGAGEVESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD
+RVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSKPILVEP
+IKGLPVEKDLIVDMDPFFQSYREIMPFLVAEGHAPTKERYQSQADRAIYDDTTKCILCAA
+CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDEAGDMRLEILNDKEGVWRCRTTFNCTDA
+CPRGIQVTKAISEVKRAILARQF
+>NAFOICDF_02395
+MSHAATETQAPAAPAQQTQGQDGGMGEIESFDITLRVRRFLPESSEESYWDEWRLTMFGT
+DRVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSQPITVE
+PIKGLPVEKDLIVDMEPFFQSYREVMPFLVAKGHEPSKERYQSQADRAIYDDTTKCILCA
+ACTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDDAGDMRLEILNDKEGVWRCRTTFNCTE
+ACPRGIQVTKAIAEVKQAILARSF
+>MHAAABBN_00154
+MSHSATETEAPVAQAQTQSAGGGAGEVESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD
+RVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSKPILVEP
+IKGLPVEKDLIVDMDPFFQSYREIMPFLVAEGHAPTKERYQSQADRAIYDDTTKCILCAA
+CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDEAGDMRLEILNDKEGVWRCRTTFNCTDA
+CPRGIQVTKAISEVKQAILARQF
+>LFPAFLNI_00436
+MSHSATETEAPVAQAQTQSAGGGAGEVESFDIVLKVRRYLPESSEESYWDEWRLTMYGTD
+RVLDALHKVKWDHDGTLSFRRSCAHGVCGSDAMRINGRNRLACKTLLKDLDLSKPILVEP
+IKGLPVEKDLIVDMDPFFQSYREIMPFLVAEGHAPTKERYQSQADRAIYDDTTKCILCAA
+CTSSCPVFWTDGQYFGPAAIVNAHRFIFDSRDEAGDMRLEILNDKEGVWRCRTTFNCTDA
+CPRGIQVTKAISEVKQAILARQF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001702.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001702.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88e348bacd32853b3cad741f6460044fdab1b4d3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001702.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02530
+MKKNSVQDVLAQDVSATAHLAGASDRHRVLSGMQPSADSLHLGNYLGALTNWVRTQDDFE
+AFFFIPDLHAITVPQDPAALAQRTRVAAAQFIAAGIDPERSTLFVQSQVPEHAQLAWVLT
+CMTGMGEAMRMTQFKDKSAKQGAEAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQHVE
+LTRDLAQRFNHRHGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINVMDDPKR
+TAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAMTDVPVAELEGRYVGRMYGHLKVDV
+ADAVVERLAPVKARTEELLADPAELDRILAAGAAKARAVATPVLEDVYAKVGFLPPLR
+>MOLHKGIG_00427
+MTMKKNSVQDVLAQDAAATAHLAGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD
+FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV
+LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH
+VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP
+KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAVSGTPIPQLEEEFVGKMYGHLKV
+AVADAVVERLAPVRERALALLDDPAELDRILAAGAEKARAVATPVLEDVYAKVGFLPPLR
+>NAFOICDF_02400
+MTMKKNSVQDVLAQDAAATAHLAGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD
+FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV
+LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH
+VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP
+KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAVSDRPIPELEAEFEGKMYGHLKV
+AVADAVVERLAPVRERALGLLDDPAELDRILAAGAAKAREVATPVLEDVYARVGFLRPLR
+>MHAAABBN_00148
+MTMKKNSVQDVLAQDAAATAHLPGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD
+FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV
+LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH
+VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP
+KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILAAVSGTPIPQLEEEFVGKMYGHLKV
+AVADAVVERLAPVRERALELLADPAELDRILASGAEKARAVATPVLEDVYAKVGFLPPLR
+>LFPAFLNI_00430
+MTMKKNSVQDVLAQDAAATAHLAGASARHRVLSGMQPSADSLHLGNYLGALVNWERTQAD
+FEAFFFIPDLHAITVPQDPAALAERTRVAAAQFIAGGIDPERSTLFVQSQVPEHAQLAWV
+LTCMTGMGEAMRMTQFKDKSAKQGADAAGVGLLAYPMLMAADILLYQPHGVPVGDDQRQH
+VELTRDLAQRFNHRYGETFVVPTGFYPETGARIYDLQDPTSKMSKSAASPNGLINILEEP
+KKTAKKIKSAVTDDGTEVRFDREAKPGVSNLLTILSAVSGTPIPQLEEEFVGKMYGHLKV
+AVADAVVERLVPVRERALALLADPAELDRILAAGAEKARAVATPVLEDVYAKVGFLPPLR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001703.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001703.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07a46cd977d34ce4f2fef64dafc3c3806b2cbd8a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001703.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02531
+MTVLPEKDPVTGKYPEPAEGEPVVHANAGAPKEDGALRVATVNVNGIRASHRKGMREWFA
+GRGVDVLTLQEVRAPADITAKLVREVVGEDWDEVHLADAEAAAKGRAGVAIASRFPIEAV
+RTGISDADAYFDDAGRWIEADLRLPDGSALTVVSAYVHSGEADTPKQVDKYRFLDEMVRR
+LGELSAGPDHALVTGDLNVGHTELDIKNWKGNQKKAGFLPEERAYFDRFFGELGFTDVHR
+SLAGQVPGPYTWWSMRGKAFDNDAGWRIDYQMATAALAEKASSAVVDRAPSWGTRFSDHA
+PLVVDYRF
+>MOLHKGIG_00426
+MTALPEKDPVTGKYPEPAEGEPVVHANAGAPKADGAVRVATVNVNGIRASHRKGMREWFA
+GRGVDVLTLQEVRAPADVTAQLVREIVGEDWDEVHLADAVAAAKGRAGVAIASRFPLGEV
+RTGIADADGYFDDAGRWIEADLRLPDGSPLTVVSAYVHSGEVDTPKQVDKYRFLDEMVRR
+LSELAAGEGHALVTGDLNVGHTELDIKNWKGNVKKAGFLPEERAYFDRFFGELGFTDVHR
+ALAGPVPGPYTWWSMRGKAFDNDAGWRIDYHMATAGLAERATTAVVDRAPSWGTRFSDHA
+PLVVDYQF
+>NAFOICDF_02401
+MTVPQKDPVTGKHPGPAAGEPVVHANAGAPKPEGALRVATVNVNGIRASHRKGMGGWFAG
+RGVDVLTLQEVRAPQEIAHALVRDVVGDAWDEVHVADVEAASKGRAGVAVASRFPFEDVR
+TGIGGAEDHAADAGRWIEADVRLPDGSLLTVVSAYVHTGGVDTPKQVDKYRLLDEMVRRL
+PELAADGRHVLVTGDLNVGHTERDIKNWRGNVKKAGFLPEERAYFDRFFGELGYVDVHRT
+LAGDVPGPYTWWSMRGQAFDNDAGWRIDYQMATPELAARATSAVVDRAPSWGTRFSDHAP
+LVVDYQF
+>MHAAABBN_00147
+MTALPEKDPVTGKYPEPAEGEPVVHANAGAPKADGAVRVATVNVNGIRASHRKGMREWFA
+GRGVDVLTLQEVRAPADVTAQLVREIVGEDWDEVHLADAVAAAKGRAGVAIASRFPLGEV
+RTGIADADGYFDDAGRWIEADLRLPDGSPLTVVSAYVHSGEVDTPKQEDKYRFLDEMVRR
+LSELAAGEGHALVTGDLNVGHTELDIKNWKGNVKKAGFLPEERAYFDRFFGELGFTDVHR
+ALAGPVPGPYTWWSMRGKAFDNDAGWRIDYHMATAGLAERATTAVVDRAPSWGTRFSDHA
+PLVVDYQF
+>LFPAFLNI_00429
+MTALPEKDPVTGKYPEPAEGEPVVHAHAGAPKADGAVRVATVNVNGIRASHRKGMREWFA
+GRGVDVLTLQEVRAPADVTAQLVREIVGEDWDEVHLADAVAAAKGRAGVAIASRFPLGEV
+RTGIADADGYFDDAGRWIEADLRLPDGSPLTVVSAYVHSGEVDTPKQVDKYRFLDEMVRR
+LSELAAGEGHALVTGDLNVGHTELDIKNWKGNVKKAGFLPEERAYFDRFFGELGFTDVHR
+ALAGPVPGPYTWWSMRGKAFDNDAGWRIDYHMATAGLAERATTAVVDRAPSWGTRFSDHA
+PLVVDYQF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001704.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001704.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5df3137b674f44f1d55cac8247f86b131da5347a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001704.fa
@@ -0,0 +1,25 @@
+>ACLBLIBL_02532
+MSQPLTTGSGETRRGPRAGLRVGSVGFAAMIVILIVAIMFAANQNDVIGWLVVAVAAGWL
+VFALVVFLQMRRGVQAAGRKVDAAMENARADVAALRGQGAAAAPQAAAHAPAGDPMRDTK
+LDHSFKIAQVQVKVVREQLAAGGAMDREMVDRALETIDITAANARDMIKESRGQGGSEGP
+VSGTVIG
+>MOLHKGIG_00425
+MSQSLTPGPDGARRGPRAGLRVGSLGFVAMIVILIVAIIFAANQNDVIGWLVVAVAAGWL
+VFAVVVYLQMRRGVRAAGRKVDTAMQNARADVAALRGREADAAAPAVAPPAPAADPLRDT
+KLDHSFKIAQVQVRVVREQLAAGAGMDREMVDRALETIDITASNARDMIKESRAGGAEGP
+VSGTVIG
+>NAFOICDF_02402
+MPQSIPSGSAGTRPARAGLTVGSTGFAVMVAVLLVAIVFAANANDLIGWLVVAIAAGWLV
+FAVVVFLQMRKGVREAGRKVDTAMQNARADVAALRAPQQPAPAAAVPAAAGDPMRDTKLE
+HSFKICQVQARVITQQLDAEGPLDREMVDRALETITITAQNARDMIKESARDAEGPVSGT
+VVS
+>MHAAABBN_00146
+MSQSLTPGPDGARRGPRAGLRVGSLGFVAMIVILIVAIIFAANQNDVIGWLVVAVAAGWL
+VFAVVVYLQMRRGVRAAGRKVDTAMQNARADVAALRGREADAAAPAVAPPAPAADPLRDT
+KLDHSFKIAQVQVRVVREQLAAGAGMDREMVDRALETIDITASNARDMIKESRAGGAEGP
+VSGTVIG
+>LFPAFLNI_00428
+MSQSLTPGPDGARRGPRAGLRVGSLGFVAMIVILIVAIIFAANQNDVIGWLVVAVAAGWL
+VFAVVVYLQMRRGVQAAGRKVDTAMQNARADVAALRGRDADAAAPAVAPSAPAADPLRDT
+KLDHSFKIAQVQVRVVREQLAAGESMDREMVDRALETIDITASNARDMIKESRAGGAEGP
+VIG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001705.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001705.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e39bdc769da4dc379b1b20319a32285701f08a3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001705.fa
@@ -0,0 +1,49 @@
+>ACLBLIBL_02533
+MGGPVAATARRPANRRAGPVVVRAYPEAVTPRPRSADGDAAPAAFTPEQRRILTALLMPL
+FLALMSVSVVNVALPAIESGLHATSADLQWVLAGYTLTFGTVLVASGRAGDLWGRKSLFL
+VGIGLYVAGALVSGFAADPLMLNAGRLVTGVGAGVFNPQVVGFIQSNFSGRARGRAYGLF
+GTVIGLGVAVGPMLGGLLLGALGPEWGWRSTFLMNAPVGLAAIVMGVLWLPAPTRVHGLP
+AAPGPRGIAALDPVGALLLGLGAVCLMVPFIVPGTAGLLVLAAALVTAWWLWEKRVKARA
+SATGVQPMVDPALFRRLSFTIGALESTIYLATMPAVFAIVAIFLQRGMGFTPLEAGLVGL
+PGAVVVASLSPWVGSMVQRRGPVLVLLGALVGLVSLGVLALAFERSAAGAWSPWIVGVGL
+IVQSASQALLLTSTQVLMMDDVAGHEAGAAGGVAQTAQRLGTALGLSVVTGAFFAALAGA
+AAEGAGPPSAAAYAHAASTAMGMVAVCWALTAVVAALDVVRRRRAVRAA
+>MOLHKGIG_00424
+MTPRPPHPADPASGAFTPDQRRILTALLMPLFLALMSVSVVNVALPAIESGLDATSADLQ
+WVLAGYTLTFGTVLVAAGRAGDLWGRKNLFLAGITLYMLGSLLSGLAGDTLLLNAGRLLT
+GLGAGVFNPQVIGFIQSNFHGRARGRAYGLFGTVVGLGVAVGPLLGGLFLGAFGPEWGWR
+STFLMNVPVGLAAVAMGALWLPPPTRVHGLPPAPGPRGIAALDPVGALLLGAGGVSLMVP
+FIVPGTAWLLVLAAALVTAWWLWEKRVKARASATGVQPMVDPALFRRPSFTIGALESTIY
+LATMPAVFAIVAIFLQRGMGFTPLEAGLVGLPGAVVVASLSPWVGSMVQRRGPVLVLLGA
+LVGLVSLGVLALAFERSAAGAWSPWIVGVGLIVQSASQALLLTSTQVLMMDDVAGHEAGA
+AGGVAQTAQRLGTALGLSVVTGAFFAALAGAAGESAGPPSAAAYAHAASTAMGMVAVCWA
+LTAAVAALDVVRRRRAARAA
+>NAFOICDF_02403
+MTLPSPAAAESGAFTADQRRILTVLLIPLFLALMSVSVVNVALPSIEGGLGASSADLQWV
+LSGYTLTFGMVLVAAGRAGDLWGRRPLFLAGIALYVLGSLLSGLAPDPLWLNAGRLLTGL
+GAGVFNPQTIGFIQSHFTGRARGRAYGLFGMVVGLGVAVGPLLGGLLLGALGPDWGWRST
+FLMNVPVGVLAIVMATAWLSPDTRVKGAAGRSGGPRGIAALDPVGALLLGGASLCLMVPF
+IAPGTWALLAGAAVLGVGWWLWELRVKRRAAATGVEPMVDPALFRRASFSIGAAESTIFL
+SSMPAVFAVTAVFLQQGMGFSPLASGLATLPGAVVQAVASPWAGSKVPSQGARMVFGGGV
+VGLASLAILALAFERSAAGAWSPWIVGAALAVMAVSQALILTTTQVLMMEDVAGHEAGAA
+GGVAQTAQRMGTALGLSVVMGAFYAALAGAAGPGGAPSAAGFAHAASAAVLMVGACWLVT
+TAIAAADLVRRRRTAR
+>MHAAABBN_00145
+MTPRPPHPADPASGAFTPDQRRILTALLMPLFLALMSVSVVNVALPAIESGLDATSADLQ
+WVLAGYTLTFGTVLVAAGRAGDLWGRKNLFLAGITLYMLGSLLSGLAGDTLLLNAGRLLT
+GLGAGVFNPQVIGFIQSNFHGRARGRAYGLFGTVVGLGVAVGPLLGGLFLGAFGPEWGWR
+STFLMNVPVGLAAVAMGALWLPPPTRVHGLPPAPGPRGIAALDPVGALLLGAGGVSLMVP
+FIVPGTAWLLVLAAALVTAWWLWEKRVKARASATGVQPMVDPALFRRPSFTIGALESTIY
+LATMPAVFAIVAIFLQRGMGFTPLEAGLVGLPGAVVVASLSPWVGSMVQRRGPVLVLLGA
+LVGLVSLGVLALAFERSAAGAWSPWIVGVGLIVQSASQALLLTSTQVLMMDDVAGHEAGA
+AGGVAQTAQRLGTALGLSVVTGAFFAALAGAAAESAGPPSAAAYAHAASTAMGMVAVCWA
+LTAVVAALDVVRRRRAVRAA
+>LFPAFLNI_00427
+MPLFLALMSVSVVNVALPAIESGLDATSADLQWVLAGYTLTFGTVLVAAGRAGDLWGRKS
+LFLAGITLYMLGSLLSGLAGDTLLLNAGRLLTGLGAGVFNPQVIGFIQSNFHGRARGRAY
+GLFGTVVGLGVAVGPLLGGLFLGAFGPEWGWRSTFLMNVPVGLAAVAMGALWLPPPTRVH
+GLPPAPGPRGIAALDPVGALLLGAGGVSLMVPFIVPGTAWLLVLAAALVTAWWLWEKRVK
+ARAWATGVQPMVDPALFRRPSFTIGALESTIYLATMPAVFAIVAIFLQRGMGFTPLEAGL
+VGLPGAVVVASLSPWVGSMVQRRGPVLVLLGALVGLVSLGVLALAFERSAAGAWSPWIVG
+VGLIVQSASQALLLTSTQVLMMDDVAGHEAGAAGGVAQTAQRLGTALGLSVVTGAFFAAL
+AGAAAESAGSPSAAAYAHAASTAMGMVAVCWALTAVVAALDVVRRRRAARAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001706.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001706.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3469b5d2f5641b30788e48b47f9ccf2e0c9bc5db
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001706.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02536
+MSHATPASPSPSQSPADAPDAGPAPVIRARGLRKQYGDFHAVKGIDLDVRPGECFGLLGP
+NGAGKSTTMRMLAGTSQRTAGELSILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENI
+LIYGRYFGLPYSYLRPKADELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFL
+LDEPTTGLDPQARHILWDRLYRLKERGTTLLLTTHYMDEAEQLCDRLVVVDGGQIMAAGT
+PAALIREHAAREVLEARFGADRNEAAARTVQARAGDGVVHRVEVLPDRVLVYAAHADDLH
+AVVQGLVDDGALPAPVTTLTRRASLEDVFLILTGRTLVD
+>MOLHKGIG_00422
+MSHTTLHASPGDASVIRARGLRKQYGEFHAVKGIDLDVRPGECFGLLGPNGAGKSTTMRM
+LAGTSQRTAGELTILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENILIYGRYFGLPY
+SYLRPKAEELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEPTTGLDPQ
+ARHILWDRLYRLKERGTTLLLTTHHMDEAEQLCDRLVVVDGGEIMAAGTPAELIREHASR
+EVLEARFGADRNEAAARTVQAHAGDGVVHRVEVLPDRVLVYARRADDLHDVVQRLVDEGA
+LPAPVTTLTRRASLEDVFLILTGRTLVD
+>NAFOICDF_02406
+MTRTTSSPSPAAPAGGGAAPVILARGLRKQYGDFHAVQGIDLDVRPGECFGLLGPNGAGK
+STTMRMLAGTSQRTGGELRILGIDPEEDGPAVRARLGVVPQQDNLDEDLTARENILIYGR
+YFGLPYSYLRPKAEELLAFAQLTDKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEPT
+TGLDPQARHTLWDRLYRLKERGTTLLLTTHYMDEAEQLCDRLVVVDAGRIMAAGTPASLI
+REHASREVLEARFGTDRNATAARLLRESLPGLHRLEVLPDRVLLYTEHADTLQQDLDRLV
+AEGHVTAPVTQLTRRASLEDVFLILTGRTLVD
+>MHAAABBN_00143
+MSHTTLHASPGPASVIRARGLRKQYGEFHAVKGIDLDVRPGECFGLLGPNGAGKSTTMRM
+LAGTSQRTAGELTILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENILIYGRYFGLPY
+SYLRPKAEELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEPTTGLDPQ
+ARHILWDRLYRLKERGTTLLLTTHHMDEAEQLCDRLVVVDGGEIMAAGTPAELIREHASR
+EVLEARFGADRNEAAARTVQAHAGDGVVHRVEVLPDRVLVYARRADDLHDVVQRLVDEGA
+LPAPATTLTRRASLEDVFLILTGRTLVD
+>LFPAFLNI_00425
+MRLCCRLVSPTTLHAPPGPASVIRARGLRKQYGEFHAVKGIDLDVRPGECFGLLGPNGAG
+KSTTMRMLAGTSQRTAGELTILGIDPEEDGPAVRARLGVVPQQDNLDEELTARENILIYG
+RYFGLPYSYLRPKAEELLAFAQLTEKADAKVTDLSGGMKRRLVIARALVNEPALFLLDEP
+TTGLDPQARHILWDRLYRLKERGTTLLLTTHHMDEAEQLCDRLVVVDGGEIMAAGTPAEL
+IREHASREVLEARFGADRNEAAARTVQAHAGDGVVHRVEVLPDRVLVYARRADDLHDVVQ
+RLVDEGALPAPATTLTRRASLEDVFLILTGRTLVD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001710.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001710.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc477ce95649fc2382359b8c4b2c182897830311
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001710.fa
@@ -0,0 +1,50 @@
+>ACLBLIBL_02540
+MTENQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLVETHQHFNRMNIPERR
+PHAKGSGAFGEFEVTEDVSKYTKALVFQPGAKTETLLRFSTVAGELGSPDTWRDVRGFAL
+RFYTDEGNLDVVGNNTPVFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNTPESAH
+QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNFSNEEAEAMA
+GKNADYHRQDLFESIAKGDYPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVG
+TLTLNRNPENHFAQIESAAFNPGNMVPGVGLSPDRMLLGRSFAYHDAQLYRVGAHVNQLP
+VNRPKNEVHNYAFDGQMWYDHTGSRSTYAPNSNGDSWSDETGPVDDGWEADGTLTREAQA
+LRKDDDDFGQAGTLVREVFTDAERDAFVETVAGALDGVREDVQARAFQYWKNVDATIGQR
+IEDEVNKGQGDDIPGAAGGGEARI
+>MOLHKGIG_00419
+MTEYQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERR
+PHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFAL
+RFYSEEGNYDLVGNNTPIFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAH
+QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA
+GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVG
+TLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLP
+VNRPKNAVHNYAFDGQMWYDHTGDRSTYAPNSNGDSWSDETGPVDDGWEADGTLTREAQA
+LRADDDDFGQAGTLVREVFSAQEREDFVETVAGALKGVRQDVQARAFEYWKNVDTAIGQR
+IEDEVKRHEGDGIPGVEAGGEARI
+>NAFOICDF_02409
+MTEYQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERR
+PHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFAL
+RFYSEEGNYDIVGNNTPVFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAH
+QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA
+GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISQKDYPRIKVG
+TLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLP
+VNRPKNAVNNYAFDGQMWYDHTGDRSTYAPNSNGDSWSDETGPVDDGWEADGTLTREAQA
+LRADDDDFGQAGTLVREVFSDQERDDFVETVAGALKGVRQDVQARAFEYWKNVDATIGQR
+IEDEVKRHEGDGIPGVEAGGEARI
+>MHAAABBN_00140
+MTEYQKKTPHATGSTRQNGAPAISDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERR
+PHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFAL
+RFYTEEGNYDIVGNNTPIFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAH
+QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA
+GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVG
+TLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLP
+VNRPKNAVHNYAFEGQMWYDHTGDRSTYVPNSNGDSWSDETGPVDDGWEADGTLTREAQA
+LRADDDDFGQAGTLVREVFSDQERDDFVETVSGALKGVRQDVQARAFEYWKNVDATIGQR
+IEDEVKRHEGDGIPGVEAGGEARI
+>LFPAFLNI_00422
+MTEYQKTTPHATGSTRQNGAPAVSDRQSLTVGSEGPIVLHDTHLLETHQHFNRMNIPERR
+PHAKGSGAFGEFEVTEDVSKYTKALVFQPGTKTETLLRFSTVAGELGSPDTWRDVRGFAL
+RFYSEEGNYDLVGNNTPIFFLRDPMKFTHFIRSQKRLPDSGLRDATMQWDFWTNNPESAH
+QVTYLMGPRGLPRTWREMNGYGSHTYLWVNAQGEKHWVKYHFISQQGVHNLSNDEATKIA
+GENADFHRQDLFESIAKGDHPKWDLYIQAIPYEEGKTYRFNPFDLTKTISKKDYPRIKVG
+TLTLNRNPENHFAQIESAAFSPSNTVPGIGLSPDRMLLGRAFAYHDAQLYRVGAHVNQLP
+VNRPKNAVHNYAFDGQMWYDHTGDRSTYAPNSNGDSWSDETGPVDDGWEADGTLTREAQA
+LRADDDDFGQAGTLVREVFSAQEREDFVETVAGALKGVRQDVQARAFEYWKNVDTAIGQR
+IEDEVKRHEGDGIPGVEAGGEARI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001711.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001711.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed5441bb4263886cfb880341d49260ef8524a781
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001711.fa
@@ -0,0 +1,34 @@
+>ACLBLIBL_02543
+MDTATLSPSPTPASGAEHAHVLTLACTNRMGIVHAVSGALLQVGADITESQQYDSPESGD
+FFMRVEFVTPARREEVAAALEPVREEFGMRMGLWDAGHRMRTLVMCSKDGHTLNDLLFQQ
+RAGTLPIEIPVVVSNHLELQSLASFYGVPFIHVPVSADPESRDSKAAAEDRLRGLIAEYD
+IELVVLARYMQILSDELCRDLAGMAINIHHSFLPSFKGARPYHQAHERGVKLIGATAHYV
+TADLDEGPIIAQSVQPVTHAQTAADFVARGRDVEGSTLVQAVRWHAQHRVLADGRRTVVF
+S
+>MOLHKGIG_00417
+MDTAALSPSPSPASGAEHAHVLTLACTNRKGIVHAVTGALLGVEADITESQQYGSPDTGD
+FFMRVEFMTPAVREDIEQALAPVREEFGMRMGLWDAAHRMRTLVMCSKDGHTLNDLLFQQ
+RAGTLPIEIPVVVSNHLDLQPLASFYGVPFIHVPVSKDPSSRDSKEAAEDRLRDLIAQFD
+IELVVLARYMQILSDELCRDLAGMAINIHHSFLPSFKGARPYHQAHERGVKLIGATAHYV
+TADLDEGPIIAQSVQPVTHAQTAADFVARGRDVEGSTLAQAVRWHAQHRVLTDGRRTVVF
+S
+>NAFOICDF_02411
+MDSTPAAPSEASARHRIVLTLSCPDRPGIVHAVTGALLEADANITESQQYDSPDTGTFFM
+RVAVDAAATREEVEAAVRPVADRFGMHLQVWDADTPLRALVMCSKDGRTLNDLLFQQRTG
+SLPVQIPVVVSNHLDLQPLASFYGVPFIHVPLSTDPASRNSKAAAEDRLRELIREYEIDV
+VVLARYMQILSDELCRDLEGMAINIHHSFLPSFKGARPYHQAHERGVKIIGATAHYVTAD
+LDEGPIIAQSVHPVTHAQTAEDFVERGRDVEGATLVQAVRWHAEHRVLLDGHRTVVFS
+>MHAAABBN_00138
+MDTAALSPSPSPASGAEHARVLTLACTNRKGIVHAVTGALLGVEADITESQQYDSPDTGD
+FFMRVEFVTPATREDIEQALAPVREEFGMRMGLWDAAQRMRTLVMCSKDGHTLNDLLFQQ
+RAGTLPIEIPVVVSNHLDLQPLASFYGVPFIHVPVSKDPSSRDSKEAAEDRLRDLIAQFD
+IELVVLARYMQILSDELCRDLAGMAINIHHSFLPSFKGARPYHQAHERGVKLIGATAHYV
+TADLDEGPIIAQSVQPVTHAQTAADFVARGRDVEGSTLAQAVRWHAQHRVLADGRRTVVF
+S
+>LFPAFLNI_00420
+MDTAALSLSPSPASGAEHAHVLTLACTNRKGIVHAVTGALLGVEADITESQQYGSPDTGD
+FFMRVEFMTPAVREDIEQALAPVREEFGMRMGLWDAAHRMRTLVMCSKDGHTLNDLLFQQ
+RAGTLPIEIPVVVSNHLDLQPLASFYGVPFIHVPVSKDPSSRDSKEAAEDRLRDLIAQFD
+IELVVLARYMQILSDELCRDLAGMAINIHHSFLPSFKGARPYHQAHERGVKLIGATAHYV
+TADLDEGPIIAQSVQPVTHAQTAADFVARGRDVEGSTLAQAVRWHAQHRVLTDGRRTVVF
+S
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001714.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001714.fa
new file mode 100644
index 0000000000000000000000000000000000000000..44dd3f8de348a04c7068712f106c76cfc642ce40
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001714.fa
@@ -0,0 +1,32 @@
+>ACLBLIBL_02546
+MSTAVSAPAPEGRAPEGRGPEGRAPRRRGTGKATALWWILTVVIGVWCLFPLFSIFATSF
+KTPADLANGKLLPTQWSTVNYEEIFVGGSRELFLTALRNSIGITVIATIIAVILATLCAY
+AIARLDFPGKRLVLTVSLMVSMFPVISLVTPLFNMWRTLGLYDTWIGLIIPYLSLTLPIS
+IWTLAAFFRQIPWELDQAAQVDGATPLEAFRKVIVPLAAPGVFTTAIIAFFIAWNDFVFG
+ISLTSTETARTVPAALAFFTGASQFESPTGAISAAAIIVTIPIVILVLAFQRQIVAGLTN
+GAVKG
+>MOLHKGIG_00413
+MSTAASAPAPEGRAPEGRAPHRRGTGKATALWWILTVVIGVWCLFPLFSIFATSFKTPAD
+LANGKLLPTQWSTVNYEEIFVGGSRELFLTALRNSIGITVIATIIAVILATLCAYAIARL
+DFPGKRLVLTVSLMVSMFPVISLVTPLFNMWRTLGLYDTWVGLIIPYLSLTLPISIWTLA
+AFFRQIPWELDQAAQVDGATPLEAFRKVIVPLAAPGVFTTAIIAFFIAWNDFVFGISLTS
+TETARTVPAALAFFTGASQFESPTGAISAAAIIVTIPIVILVLAFQRQIVAGLTNGAVKG
+>NAFOICDF_02414
+MSTGNPIPAPQEPVTTRPDGAAERTEAGTAVGDRGVAPTTTRRTRKGSSSWIWWLLAVLI
+GVWCLFPLFSIFATSFKTPADLSNGKLLPTQWSTVNYEEIFVGGSRELFLTALRNSIGIT
+VIATLIAVVLATLCAYAIARLDFPGKRIVLTVSLMVSMFPVISLVTPLFNVWRTLGLYDT
+WLGLIIPYLSLTLPISIWTLAAFFRQIPWELDQAAQVDGATPLQAFRKVIVPLAAPGVFT
+TAIIAFFIAWNDFVFGISLTSTEAARTVPAALAFFTGASQFESPTGAISAAAIVVTIPIV
+ILVLLFQRQIVAGLTNGAVKG
+>MHAAABBN_00133
+MSTAASAPAPEGRAPEGRAPHRRGTGKATALWWILTVVIGVWCLFPLFSIFATSFKTPAD
+LANGKLLPTQWSTVNYEEIFVGGSRELFLTALRNSIGITVIATIIAVILATLCAYAIARL
+DFPGKRIVLTVSLMVSMFPVISLVTPLFNMWRTLGLYDTWVGLIIPYLSLTLPISIWTLA
+AFFRQIPWELDQAAQVDGATPLEAFRKVIVPLAAPGVFTTAIIAFFIAWNDFVFGISLTS
+TETARTVPAALAFFTGASQFESPTGAISAAAIIVTIPIVILVLAFQRQIVAGLTNGAVKG
+>LFPAFLNI_00416
+MSTAASAPAPEGRAPEGRAPHRRGTGKATALWWILTVVIGVWCLFPLFSIFATSFKTPAD
+LANGKLLPTQWSTVNYEEIFVGGSRELFLTALRNSIGITVIATIIAVILATLCAYAIARL
+DFPGKRIVLTVSLMVSMFPVISLVTPLFNMWRTLGLYDTWVGLIIPYLSLTLPISIWTLA
+AFFRQIPWELDQAAQVDGATPLEAFRKVIVPLAAPGVFTTAIIAFFIAWNDFVFGISLTS
+TETARTVPAALAFFTGASQFESPTGAISAAAIIVTIPIVILVLAFQRQIVAGLTNGAVKG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001717.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001717.fa
new file mode 100644
index 0000000000000000000000000000000000000000..014a64963d5e317506aa50fe5dd7bf7ad2e37011
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001717.fa
@@ -0,0 +1,60 @@
+>ACLBLIBL_02550
+MTTPVQKHLDRLTSAHTGEGDVPDGLGVAMLMVDGHRYVSGSMTSVPLATLASPLFHAQA
+LEDLGAVRVGERVGAAPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA
+RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA
+AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSVMDSCGMDTRDSRWAYDVGQP
+GWASTRGGTVLVVVPGHLGLALQSDTTDENALGAAAMAALRTIVEDFELHPSVVTGSPRA
+ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVLELGGHLGFSQVDAIARVSRGLPEAL
+ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEIRELMAAVEESVEVDL
+PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSQHAPHLLPRDAQEAAVAPLLQ
+HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL
+TPGMTFGEMALGQPGRQPSTVRARGPVTARVLTAQVMVALQEGFPQLALALWEALARDAF
+TALSQLIRETGALQD
+>MOLHKGIG_00406
+MTTPVQEHLDRLTSAHAGEGEVPDGLGVAMLLVDGHRYVSGSMTPVPLATLASPLFHAQA
+LEDLGAVRVGERVGAVPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA
+RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA
+AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSVMDSCGMDTRDSRWAYDVGQP
+GWASTRGGTVLVVVPGHLGLALQSDTTDENGLGAAAMAALRTIVEDFELHPSVVTGSPRA
+ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVMELGGHLGFSQVDAIARVSRGLPEAL
+ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEMKELMSAVEESVEVDL
+PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSRHAPHLLPRDAQEAAVAPLLQ
+HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL
+TPGMTFGEMALGQPGRQPSTVRARGPVTARVLTAQVMVALQEGFPQLALALWEALARDAF
+TALSQLIRETGALQD
+>NAFOICDF_02418
+MKSPVQDRLDRLTAAHTPGTAADADATSDAGTGLALSVATVGGDHYSAGELVAVPLAGLA
+GPVVHALALEDLGVERVGEAVGTVPRPDLRTRLELEPGTGRPLTPLQDAGTMALAALVKG
+RGGRDRAARLLQQLAGLIGRETAPTDAAVRAADRAQHRARAAAWLLRSVGVLEADPDGLL
+ADVATLRAAPVTVADLALLAGTLAAHGVHPVSGERVLAEETVRAVLSALDACGMDTVDGA
+WALDVGQPGWSSARAGTVIAVVPGHMGIAVQGPADPDDADAPSPAALAALRTLVRDFELH
+PSQAAGSPRAAFRTHYRVDQAPSGSVRSAEVLELLSAHGDTAHVLELGGHVGFSQVDALA
+HVARNLPAALETIIVDVRSVSSTSHAAAVLAAQWFAYALHHGLDVVVVDRDTAAVDQVMA
+TAEASGVTLPDPLHDADDADPGHQDLGPAFRFFDSRSRAVQWAEQRLLARHAPHLLPASE
+EEAAMAPLLQHLSSEDARLLESMMDERVYEDGQIIRRAGQPFGGIYVITSGRVELTGQGT
+GGRRVRRTVLTPGMTFGEMALGQPGRQPSTVRARGRVTTRVLTAQVMYALQEGFPSLALT
+LWEALARDAYTALGQLIRETGALQD
+>MHAAABBN_00129
+MTTPVQEHLDRLTSAHAGEGEVPDGLGVAMLMVDGHRYVSGSMTPVPLATLASPLFHAQA
+LEDLGAVRVGERVGAAPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA
+RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA
+AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSVMDSCGMDTRDSRWAYDVGQP
+GWASTRGGTVFVVVPGHLGLALQSDTTDENGLGAAAMAALRTIVEDFELHPSVVTGSPRA
+ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVMELGGHLGFSQVDAIARVSRGLPEAL
+ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEMKELMAAVEESVEVDL
+PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSRHAPHLLPRDAQEAAVAPLLQ
+HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL
+TPGMTFGEMALGQPGRQPSTVRARGPVTTRVLTAQVMVALQEGFPQLALALWEALARDAF
+TALGQLIRETGALQD
+>LFPAFLNI_00412
+MTTPVQEHLDRLTSAHAGEGEVPDGLGVAMLLVDGHRYVSGSMTPVPLATLASPLFHAQA
+LEDLGAVRVGERVGAAPVRDLDHRVEVDAVTGLPHNPLQNAGAVATASLVKGRGGRDRTA
+RMMQLLSALFDREVTVTESAARAENRAQHHTRSAAWLMKSLDTLDADPETLLEDIATVRA
+AAVTVEDLALLAGTLAHGGVHPVTGDRVLSEETVRGVLSAMDSCGMDTRDSRWAYDVGQP
+GWASTRGGTVLVVVPGHLGLALQSNTTDENGLGAAAMTALRTIVEDFELHPSVVTGSPRA
+ALRTHYRIDQAPSGTVRSAVVLEALGRFADTVHVMELGGHLGFSQVDAIARVSRGLPEAL
+ETLVVDMRSVSSISRPARLLVAQWFARALGNGLDVVVVDRDAAEMKELMSAVEESVEVDL
+PEPLQDEAEGVDPAAEGAQFVFFDSRSRAAQWAEQRLLSRHAPHLLPRDAQEAALAPLLQ
+HLSADDARLLESMMDERVYSDGQIIRRAGQPFGGIYVIVSGTVELSGQGTGSRRVRRTLL
+TPGMTFGEMALGQPGRQPSTVRARGPVTARVLTAQVMVALQEGFPQLALALWEALARDAF
+TALGQLIRETGALQD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001725.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001725.fa
new file mode 100644
index 0000000000000000000000000000000000000000..70416d12d804f320e0046f99efda74d54f0faa8f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001725.fa
@@ -0,0 +1,46 @@
+>ACLBLIBL_02560
+MTALLSLLAVMIPTLVVWATGGFQRPTIEGALQVGGTLWLALHAVPVTVATVLPTAEGHV
+LSGTAWLVPWGLTLIPLLLSWRAGRRLARASYRDQAWQAFAGAVVGYALAGLTVAFLPGT
+PELRVSPWAAALLPALLFGIAALAGARREAGTWAHLIGLDLTERIARRSQYERWAGSYAW
+SVVRAAVVALLVLAALSALLVAVRLAVEWPAVVTLAQAIDAGPFGGLLLAVLQIGWLPTL
+TGWAIAWTAGPGFSVGSDSLYSVFGATPAAAPALPALGALPAAWAPWHPLFLAVPIAAGV
+AAGVWLLREGENHLDDWLDARTGHRAVSLALSTLALAVLTGLLAGLLLLVPLALTSGTLG
+VGTLTDIGANVWAVCAAVAGWVALGCAAGYLVALALAGRRFIPPAEAAVAAERPRPRRSR
+D
+>MOLHKGIG_00397
+MSSRPAAPRLLRPVPLPLWLQGVVEALVTAMISLLAVMVPTLAVWATGGFERPTIEGAVQ
+VGGVLWLALHAVPVTVTTAMPTAPDHLITGTAWLVPWGLTLLPLALSWRAGRRLARASYR
+DQAWQAFVGAVGAYALVGLAVAFLPGTDELTAHPAPAALLPALLFGVAALAGARREAGTW
+AHLIGLDLTERISRRSQYERWAGSYAWSVVRAAAVAVLALTGLNALLVAGRLAVEWTAVV
+TVAEAIGGGPLGGLLLALLQIGWLPTFTAWSIAWTAGPGFSVGADSLYSVFGATPATAPA
+LPALGALPGTWSPWQLLLLAVPIGAGAVAGVWLLREGENHLDDWLHTRHGSRAVSLTLST
+LALAVLTGLLTGLLLLVPLALTSGTLGLGALTDLGSHVWAVSAAVAGWVALGCAAGYLTA
+LAVAGHRDGTTTVPRSGDRASGLRDRPSPRRARD
+>NAFOICDF_02431
+MSPRVPSLLRPVPLPLWLQGVVEALVTALTSLALVLVPTLAVWITGGFSSTRIEDVLQTG
+GALWLGLHAVPLAVTTVVAQADTPTVTGTVWLVPWALTALPVWLSWRAGRRLARASYREQ
+AWQALAGAVAAYAVVALACALLPGEGRITVHPLPSVLLPCLLFTTSAVAGARREAGTWAH
+LIGLDLTERIARRSQYERWAGTYAWSVLRGAGVGLAALAGLHALLVTVAVLVRWPRIIEV
+QQMVGAGPVGGLMLALLEIGWLPTFTAWAVAWTAGPGFAVGADGHYSVFGTTPAPVPALP
+LLEALPAPWAPWHPAFLLVPVLAGAVAGWWLLREGENHLDDWIDSRITARWASLTLSTLA
+LALLLGLVSGVAVLVPLALTNGTLGVGSMREIGSNAPLVALAVAGWMALGCALGYLVALA
+VVDRPVRGRRRISLPLPGSAPRAVTGRARRLPPRRLPRGVADAEADEPEVAAPAAAREEI
+PGRETPAQETPSEEPPAAARPAPRRAGAPRVPRVPRPAPRRARD
+>MHAAABBN_00121
+MSSRPAAPRLLRPVPLPLWLQGVVEALVTAMISLLAVMVPTLAVWATGGFERPTIEGAVQ
+VGGVLWLALHAVPVTVATAMPTAPDHLITGTAWLVPWGLTLVPLALSWRAGRRLARASYR
+DQAWQAFVGAVGAYALVGLAVAFLPGTDELTAHPAPAALLPALLFGVAALAGARREAGTW
+AHLIGLDLTERISRRSQYERWAGSYAWSVVRAAAVAVLALTGLNALLVAGRLAVEWTAVV
+TVAQAIGGGPLGGLLVALLQIGWLPTFTAWSIAWTAGPGFSVGADSLYSVFGATPATAPA
+LPALGALPGTWSPWQLLLLAVPISAGVVAGVWLLREGENHLDDWLHTRHGSRAVSLTLST
+LALAVLTGLLAGLLLLVPLALTSGTLGLGTLTDIGPHVWAVCAAVAGWVALGCAAGYLTA
+LAVAGHRDGTTTVPRSGDRASGLRDRPSPRRARD
+>LFPAFLNI_00403
+MSSRPAAPRLLRPVPLPLWLQGVVEALVTAMISLLAVMVPTLAVWATGGFERPTIEGAVQ
+VGGVLWLALHAVPVTVATAMPTAPDHLITGTAWLVPWGLTLVPLALSWRAGRRLARASYR
+DQAWQAFVGAVGAYALVGLAVAFLPGTDELTVHPAPAALLPALLFGVAALAGARREAGTW
+AHLIGLDLTERISRRSQYERWAGSYAWSVVRAAVLAVLALTGLNALLVAGRLAVEWTAVV
+TVAEAIGAGPLGGLLLALLQIGWLPTFTAWSIAWTAGPGFSVGADSLYSVFGATPATAPA
+LPALGALPGTWSPWQLLLLAVPIGAGAVAGVWLLREGENHLDDWLHTRHGSRAVSLTLST
+LALAVLTGLLTGLLLLVPLALTSGTLGLGTLTDIGSHVWAVCAAVAGWVALGCAAGYLTA
+LAVAGHRDGTTTVPRSGDRASGPRDRPSPRRARD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001727.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001727.fa
new file mode 100644
index 0000000000000000000000000000000000000000..390dc981724382bde1332e66bb423c5729b1f25c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001727.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_02562
+MNHALETLRDEVFARNPGEAEFHQAVSEVFEALDPVMERHPQYVEAGVLHRLCEPERQII
+FRVPWIDDNGVVQVNRGFRVEFNSALGPYKGGLRFHPSVYLGIIKFLGFEQIFKNSLTGM
+PIGGGKGGSDFDPAGKSDREIMRFCQSFMTELHRHIGEHTDVPAGDIGVGGREIGYMFGQ
+YKRLTNRFEAGVLTGKGLTWGGSLVRTEATGYGAVMFADSMLKTRGESMDGQQVLISGSG
+NVAIYAAEKAASLGATVLTASDSAGYIVDPDGLDLDLLKQIKEVERARISEYVERKGGRA
+RYVAGGSVWDVEGTVALPCATQNELDESAAKTLLGNGVKAVAEGANMPCTEAATRLFLHA
+KTLFGPGKAANAGGVATSALEMQQNASRDSWNFEYTHDRLEAIMRDIHDRCVETAEEYGT
+PGNYVAGANIAGFIKVADAMIAQGVV
+>MOLHKGIG_00394
+MNESLETLRDEVFARNPGEAEFHQAVSEVFEALGPVVQRHPQYVEAGVMHRLCEPERQII
+FRVPWIDDAGVVQVNRGFRVEFNSALGPYKGGLRFHPSVYLGIVKFLGFEQIFKNSLTGM
+PIGGGKGGSDFDPAGKSDREIMRFCQSFMTELHRHIGEHTDVPAGDIGVGAREIGYMFGQ
+YKRLTNRFEAGALTGKGLTWGGSLVRTEATGYGAVMFVDSMLRTRGESMDGQQVLISGSG
+NVAIYAAEKAAALGATVLTASDSSGYIVDPDGLDLDLLKQIKEVERARISEYAERRGGRS
+RYVTGGSVWDVEGTVALPCATQNELDESAARTLLKNGVKAVAEGANMPCTEAAAHLFVDS
+GTLFGPGKAANAGGVATSALEMQQNASRDSWSFDYTHDRLEQIMRDIHDRCVETAEEYGT
+PGNYVAGANIAGFIKVADAMIAQGVV
+>NAFOICDF_02434
+MHQVLQTLRDEVFARNPGEAEFHQAVSEVFEALDPVVERHPHYVDAGVLHRLCEPERQII
+FRVPWIDDAGVVQVNRGFRVEFNSALGPYKGGLRFHPSVYLGIIKFLGFEQIFKNSLTGM
+PIGGGKGGSDFDPAGKSDREIMRFCQSFMTELHRHIGEHTDVPAGDIGVGGREIGYMFGQ
+YKRLTNRFESGVLTGKGLTWGGSLVRTEATGYGAVMFADSMLRTRGESMDGQKVLISGSG
+NVAIYAAEKAAQLGATVLTASDSAGYIVDPDGVDVELLKQIKEVERARISEYAERKGGKV
+RYVAGGSVWDVEGTVALPCATQNELDESAAKTLLQNGVKAVAEGANMPSTEAATHLFLDA
+GTLFGPGKAANAGGVATSALEMQQNASRDSWDFDYTHDRLERIMRDIHDRCVETAEEYGT
+PGNYVAGANIAGFIKVADAMIAQGVV
+>MHAAABBN_00118
+MNESLETLRDEVFARNPGEAEFHQAVSEVFEALGPVVQRHPQYVEAGVMHRLCEPERQII
+FRVPWIDDAGVVQVNRGFRVEFNSALGPYKGGLRFHPSVYLGIVKFLGFEQIFKNSLTGM
+PIGGGKGGSDFDPAGKSDREIMRFCQSFMTELHRHIGEHTDVPAGDIGVGAREIGYMFGQ
+YKRLTNRFEAGALTGKGLTWGGSLVRTEATGYGAVMFVDSMLRTRGESMDGQQVLISGSG
+NVAIYAAEKAAALGATVLTASDSSGYIVDPDGLDLDLLKQIKEVERARISEYAERRGGRS
+RYVTGGSVWDVEGTVALPCATQNELDESAARTLLKNGVKAVAEGANMPCTEAAAHLFVDS
+GTLFGPGKAANAGGVATSALEMQQNASRDSWSFDYTHDRLEQIMRDIHDRCVETAEEYGT
+PGNYVAGANIAGFIKVADAMIAQGVV
+>LFPAFLNI_00400
+MNESLETLRDEVFARNPGEAEFHQAVSEVFEALGPVVQRHPQYVEAGVMHRLCEPERQII
+FRVPWIDDAGVVQVNRGFRVEFNSALGPYKGGLRFHPSVYLGIVKFLGFEQIFKNSLTGM
+PIGGGKGGSDFDPAGKSDREIMRFCQSFMTELHRHIGEHTDVPAGDIGVGAREIGYMFGQ
+YKRLTNRFEAGALTGKGLTWGGSLVRTEATGYGAVMFVDSMLRTRGESMDGQQVLISGSG
+NVAIYAAEKAAALGATVLTASDSSGYIVDPDGLDLDLLKQIKEVERARISEYAERRGGRS
+RYVTGGSVWDVEGTVALPCATQNELDESAARTLLKNGVKAVAEGANMPCTEAAAHLFVDS
+GTLFGPGKAANAGGVATSALEMQQNASRDSWSFDYTHDRLEQIMRDIHDRCVETAEEYGT
+PGNYVAGANIAGFIKVADAMIAQGVV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001728.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001728.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2fcaae7b1608302f995b554517f4ca3c45bed11c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001728.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02564
+MTGPRAVEVRIPLRWADMDAYGHINNIAVVQLLEEARVAAFGVPANTGAGGGEAPPIDLL
+EGVAPGVRTFISEHTVKYRAQMPYRPVPLRVVVSVEAVKAASVHVGYALHDGVDDTLCAT
+ASSVMVFVDGETGRPVRVTPEQRAALQG
+>MOLHKGIG_00392
+MTASRSVEVRIPLRWADMDAYGHVNNIAVVQLLEEARVAAFGVPANTGAGGGQAPPIDLL
+EGVAPGVRTFISEHTVKYRAQMPYRPVPLRVVVSVDAVKAASVHVGYALHDGVDDTLCAT
+ATSVMVFVDGQTGRPVRISPEQRAALAG
+>NAFOICDF_02435
+MTETTTSSAARDGAGRWVEVSVPLRWADMDAYGHINNIAVVQLLEEARVAVFGVPANTGA
+GGGGAPPVDLLEGVPEGVRTFVSEHTVKYRAQMPYRPVPLRVRVGVAAVKAVSVEVAYEL
+YDGVDGTLCVTARSVMVFVDGASGRPVRLTAEQRAALAG
+>MHAAABBN_00116
+MTASRSVEVRIPLRWADMDAYGHVNNIAVVQLLEEARVAAFGVPANTGAGGGQAPPIDLL
+EGVAPGVRTFISEHTVKYRAQMPYRPVPLRVVVSVDAVKAASVHVGYALHDGVDDTLCAT
+ATSVMVFVDGQTGRPVRISPEQRAALAG
+>LFPAFLNI_00398
+MTASRSVEVRIPLRWADMDAYGHVNNIAVVQLLEEARVAAFGVPANTGAGGGQAPPIDLL
+EGVAPGVRTFISEHTVKYRAQMPYRPVPLRVVVSVDAVKAASVHVGYALHDGVDDTLCAT
+ATSVMVFVDGQTGRPVRISPEQRAALAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001735.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001735.fa
new file mode 100644
index 0000000000000000000000000000000000000000..422fa8a5ea80528f1c9d1e4f774d57b110e5a658
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001735.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02573
+MSPRGRSGSRLTQASLETEGNSFMTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHG
+VILKIVATNICGSDLHIYRGSFPVPEGMVLGHEMTGQVLEVGSDVQFLKEGDLVSVPFNV
+ACGRCRNCRAGRTEVCETANPEQACAAYGFNLGNFQGGQAEYLFVPYADFQLLRFPDQEQ
+AMEKILDLAVLSDILPTAFHGLMAAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVG
+DQDASRLELVRKHGCETIDLSVTENLQDAVNDILGEPMVDCAVDYVGSEAHGLGSESDEM
+QPIAAVNQVLDITRPGGATGIIGIYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQA
+PIMRYNRQLMMSILWDRMPYLTEMVNPRVISLDEAPQAYAEFDQGSVDKFIIDPHGMIAR
+>MOLHKGIG_00382
+MTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHGVILKIVATNICGSDLHIYRGSFP
+APEGMVLGHEMTGQVLEVGSDVQFLQEGDLVSVPFNVACGRCRNCRAGRTEICETANPDQ
+ACAAYGFNLGGFQGGQAEYLFVPYADFQLLRFPDQEQAMEKILDLTVLSDILPTAFHGLV
+EAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVGDQDASRLELVRKHGCETIDLSTT
+ENLQDAVSDILGEPMVDCAVDCVGSEAHGLGSASDEMQPIAAVNQVLDITRPGGATGIIG
+IYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQAPVMRYNRQLMMSILWDRMPYLTE
+MVNPRVISLDEAPQAYAEFDQGSLEKFVIDPHGMIAR
+>NAFOICDF_02445
+MTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHGVILKIVATNICGSDLHIYRGSFP
+VPEGMVLGHEMTGQVLEVGSDVQFLKEGDLVSVPFNVACGRCRNCRAGHTEICETANPEQ
+ACAAYGFNLGNFQGGQAEYLFVPYADFQLLRFPDQEQAMEKILDLAVLSDILPTAFHGLM
+AAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVGDQDASRLELVRKHGCETIDLSVT
+ENLQDAVNDILGEPMVDCAVDYVGSEAHGLGSESDEMQPIAAVNQVLDITRPGGATGIIG
+IYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQAPIMRYNRQLMMSILWDRMPYLTE
+MVNPRVISLDEAPQAYAEFDQGSVDKFIIDPHGMIAR
+>MHAAABBN_00106
+MTTENRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHGVILKIVATNICGSDLHIYRGSFP
+APEGMVLGHEMTGQVLEVGSDVQFLQEGDLVSVPFNVACGRCRNCRAGRTEVCETTNPEQ
+ACAAYGFNLGGFQGGQAEYLFVPYADFQLLRFPDQEQAMEKILDLAVLSDILPTAFHGLM
+EAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVGDQDASRLELVRKHGCETIDLSTT
+ENLQDAVNDILGEPMVDCAVDCVGSEAHGLGSASDEMQPIAAVNQVLDVTRPGGATGIIG
+IYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQAPIMRYNRQLMMSILWDRMPYLTE
+LVNPRVITLDEAPQAYAEFDQGSVEKFVIDPHGMIAR
+>LFPAFLNI_00388
+MTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHGVILKIVATNICGSDLHIYRGSFP
+APEGMVLGHEMTGQVLEVGSDVQFLQEGDLVSVPFNVACGRCRNCRAGRTEICETANPEQ
+ACAAYGFNLGGFQGGQAEYLFVPYADFQLLRFPGQEQAMEKILDLAVLSDILPTAFHGLM
+EAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVGDQDASRLELVRKHGCETIDLSVT
+ENLQDAVNDILGEPMVDCAVDCVGSEAHGLGSASDEMQPIAAVNQVLDITRPGGATGIIG
+IYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQAPIMRYNRQLMMSILWDRMPYLTE
+MVNPRVISLDEAPQAYAEFDQGSLEKFVIDPHGMIAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001736.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001736.fa
new file mode 100644
index 0000000000000000000000000000000000000000..746c8d12b1844363559c03cfd9e44ff73eba35e4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001736.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_02574
+MRLHHDPGLQPERTVMSWGRTVLALGVLSLMFLRWWPAVGAWAFGPAVVAAVGGAAVLAT
+QRRRYVAQSRGIAGEWARPALASVAGMVALVVGLAALGITATLLHAA
+>MOLHKGIG_00381
+MRLHHDPGLQPERTVMSWGRTALALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT
+QRRRYVAHADGIAREQARPALASVACMVALVVGLAALGITATLLHAA
+>NAFOICDF_02446
+MRLHHDPGLQPERTVMSWGRTVLALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT
+QRRRYVAQADGIAREQARPALASVACMVALVVGLAVLGITATLLHAA
+>MHAAABBN_00105
+MRLHHDPGLQPERTVMSWGRTVLALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT
+QRRRYVAHADGIARERARPALASVACMVALVVGLAALGITATLLHAA
+>LFPAFLNI_00387
+MRLHHDPGLQPERTVMSWGRTVLALGVLSLTFLRWWPAVGAWAFGPAVVAAVGGAAVLAT
+QRRRYVAHADGIAREQARPALASVACMVALVVGLAALGITATLLHAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001738.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001738.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6added54de3053c6cc863ba193ac9c8112d2b84a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001738.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02576
+MSPAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER
+RHEQHWRALLGEHAENPPRPSVHRILLRWLARIFGSVFVLALAQRAESDTPYAKDQDAPE
+GMVADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL
+FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELTLVYLARG
+MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA
+SGALIPILPYIFGMSGLWALGLAAAMVGVALLFTGGVVGLLSGSSPLARGLRQLAIGYGA
+AAVTYVLGLLFGANVG
+>MOLHKGIG_00379
+MSPAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER
+RHEQHWRALLGEHAENPPRPSLHRILLRWLARIFGSVFVLALAQRAESDTPYAEDQDAPE
+GMVADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL
+FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELKLVYLARG
+MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA
+SGALIPILPYIFGMSGLWALGLAAAMVGVALLFTGGVVGLLSGSSPLARGLRQLAIGFGA
+AAVTYVLGLLFGANVG
+>NAFOICDF_02448
+MSPAHAATPAALPEPTREQVRRWRRYLADEIAEGQIYRDIAASKDGVERDILIGLAEAEK
+RHEEHWRALLGEHAAHPPRPSVHRILLRALARVFGSVFVLALAQRAESDTPYAKDQDATE
+HMAADEQIHEEVVRGLASRGREQLAGSFRAAVFGMNDGLVSNLALVMGIGATGVASSVVL
+FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAEHLDLDRNELELVYLARG
+MTPEDAKHRALERLGYLSCDCNPQFSARPDGSKGPVDHSESFAEIGSAWGASLSSFCFFA
+SGALIPILPYLFGMTGLGALVVAAVLVGIALLFTGGVVGLLSGSSPLWRGLRQLMIGYGA
+AAVTYLLGLLVGGSIG
+>MHAAABBN_00103
+MSAAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER
+RHEQHWRILLGEHAENPPRPSFRRVLLRWLARIFGSVFVLALAQRAESDTPYEKDQDAPE
+GMAADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL
+FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELKLVYLARG
+MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA
+SGALIPILPYIFGMSGLWALGLAAAMVGAALLFTGGVVGLLSGSSPLARGLRQLAIGYGA
+AAVTYVLGLLFGANVG
+>LFPAFLNI_00385
+MSPAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER
+RHEQHWRALLGEHAENPPRPSLHRILLRWLARIFGSVFVLALAQRAESDTPYAEDQDAPE
+GMVADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL
+FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELKLVYLARG
+MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA
+SGALIPILPYIFGMSGLWALGLAAAMVGVALLFTGGVVGLLSGSSPLARGLRQLAIGFGA
+AAVTYVLGLLFGANVG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001740.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001740.fa
new file mode 100644
index 0000000000000000000000000000000000000000..046ad4537cc6f2c31042bb109b4fd626c8265087
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001740.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_02591
+MDLYEYQARDLFEAHGVPVLAGIVAQTPEEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK
+VAKTADEAYEHAKAILGMDIKGHTVHQVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE
+GGMEIEQLAEERPEALAKVPVSPLTGIDAETAQKIVAEAGFPEELRADVADVIQKLWVVF
+EKEDATLVEVNPLVKTGDGKILALDGKVSLDDNAEFRHEGHAALVDERTEDPLEAKAKAN
+DLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEQHGGVKPANFLDIGGGANAEVMANGLD
+VILGDEQVKSVFVNVFGGITACDAVANGIVKALEILGDAATKPLVVRLDGNAVEEGRRIL
+QEANHPLVTLAATMDEGADKAAELAHSAN
+>MOLHKGIG_00371
+MDLYEYQARDLFEAHGVPVLAGIVAQTPDEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK
+VAKTADEAYEHAKAILGMDIKGHTVHQVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE
+GGMEIEQLAEERPEALAKVPVSALTGIDAETAQKIVTEAGFPEELRADVAEVIQKLWEVF
+EKEDATLVEVNPLVKTGDGTILALDGKVSLDDNAQFRHEDHAALVDERTEDPLEAKAKAN
+GLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEQHGGVKPANFLDIGGGANAEVMANGLD
+VILGDEQVKSVFVNVFGGITACDQVANGIVKALEILGDTATKPLVVRLDGNAVEEGRRIL
+QEANHPLVTLAATMDEGADKAAELAHSAN
+>NAFOICDF_02450
+MDLYEYQARDLFEKHGVPVLQGIVAETPEEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK
+VAKTADEAYEHAKAILGMDIKGHTVNKVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE
+GGMEIEQLAEERPEALAKVPVSALTGLDQATADTIVAEAGFPEELRADVAAVIVKLGEVF
+KNEDATLVEVNPLVKTGDGTILALDGKVSLDDNAEFRQADHAGLVDKTTEDPLEAKAKAN
+DLNYVKLDGQVGIIGNGAGLVMSTLDVVAYAGENHGGVKPANFLDIGGGANAEVMAAGLD
+VILGDEQVKSVFVNVFGGITACDAVANGIVKALEILGDSATKPLVVRLDGNAVEEGRRIL
+QEADHPLVTLAATMDEGADKATELAHSAN
+>MHAAABBN_00087
+MDLYEYQARDLFEAHGVPVLAGIVAQTPDEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK
+VAKTADEAYEHAKAILGMDIKGHTVHQVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE
+GGMEIEQLAEERPEALAKVPVSPLTGIDAETAQKIVTEAGFPEELRADVAEVIQKLWEVF
+EKEDATLVEVNPLVKTGDGTILALDGKVSLDDNAAFRHEGHAALVDERTEDPLEAKAKAN
+GLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEKHGGVKPANFLDIGGGANAEVMANGLD
+VILGDEQVKSVFVNVFGGITACDQVANGIVKALEILGDTATKPLVVRLDGNAVEEGRRIL
+QEANHPLVTLAATMDEGADKAAELAHSAN
+>LFPAFLNI_00378
+MDLYEYQARDLFEAHGVPVLAGIVAQTPDEAKAAAEKIGGVTVVKAQVKVGGRGKAGGVK
+VAKTADEAYEHAKAILGMDIKGHTVHRVMIAQGADIAEEYYFSVLLDRANRTYLAMCSVE
+GGMEIEQLAEERPEALAKVPVSALTGIDAETAQKIVAEAGFPEELRADVAEVIQKLWEVF
+EKEDATLVEVNPLVKTGDGTILALDGKVSLDDNAAFRHEGHAALVDERTEDPLEAKAKAN
+GLNYVKLDGQVGVIGNGAGLVMSTLDVVAYAGEKHGGVKPANFLDIGGGANAEVMANGLD
+VILGDEQVKSVFVNVFGGITACDAVANGIVKALEILGDTATKPLVVRLDGNAVEEGRRIL
+QEANHPLVTLAATMDEGADKAAELAHSAN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001746.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001746.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b8df1fea963ea88e00739da7b1ad1dacb038c1cc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001746.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02599
+MTDREDATPVEQEQAAPAAEEAVVKAPPARRRAPRRDDLLAAAVDEARAGLAGLAAPEEV
+GEHVDVLVDDDRLVTHRFESRLPGYAGWLWYATIARAPRSRLVTVCETGLVAGEGALVAP
+PWVPYAERVSEEERERLRAVAEGRVPGAAAPAGQPAPEGDGKG
+>MOLHKGIG_00362
+MTTHDDAPRVDHRSPDAEPAEERTAVPPARGRAPRRDELLAADVDTARAGLAGLAAPDEV
+GEHVDVLVDDDRLLTHRFACRLPGYAGWLWYVTIARAPRAKQVTVCETGLMAGEGSLVAP
+PWVPYAERVNEEERERLKAVAEGRVPGAPAPDAEGDGTPEAAARG
+>NAFOICDF_02458
+MTEHSDTPGQTDTSGQTHTPEQAPAVAPAGPAADAAPAASARAPRRRAPKRDELLAAAVD
+EARAALTELAEEGQVGPHLGVTVDDDRLMTHRFAAEVPGYTGWVWYSTIARAPRAKKVTV
+CETGLEAGEGAVVAPAWVPYADRVSAEERERLAAVAEGRVPDAG
+>MHAAABBN_00078
+MTTHDDAPRVDHRSPDAEPAPAEERAAVPPARRRAPRRDELLAAAVDAARAGLAGLAAPD
+EVGEHVDVLVDDDRLLTHRFACRMPGYAGWLWYVTIARAPRAKQVTVCETGLMAGEGSLV
+APPWVPYAERVNEEERERLKAVAEGRVPGAPAPEAEGDGTLGAAALG
+>LFPAFLNI_00369
+MTTHDDAPRVDHRSPDAEPAPAEERAAVPPARRRAPRRDELLAAAVDAARAGLAGLAAPD
+EVGEHVDVLVDDDRLLTHRFACRMPGYAGWLWYVTIARAPRAKQVTVCETGLMAGEGALV
+APPWVPYAERVNEEERERLKAVAEGRVPGAPAPETAPDDRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001755.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001755.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4bb6fcdacc8a48d3f47c9f41c2a9df7c846b4b9c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001755.fa
@@ -0,0 +1,59 @@
+>ACLBLIBL_02610
+MLAPADADGALPAPDVLPEPDVTVPDPVVPVGPPEKRGRRRGRKAREVFVENLPTQALVL
+ADRLHSSPYGRRMRSTLQQRREAETHALEARTTLDFALKLGETMFSFGAASLDVETSIIV
+VTQAYGILETEVDLTNQSISLNYAPDSSRGESPYTLQRVVRSSSVNFEGLVAVHRLVEEI
+ADGRLDRAEAQRRLVEIRHQPKPFPPVFEILFAGVFVACFIPFIGGNWTGSLLGMISTWL
+VFWLKIQADRARFPEIFSTMFGAIVATVIALAAFALELPVNPAVVIAGGIMMLLPTARFV
+TAVQDAINGFPVTAAGRFLSALLVFTGVMAGIMVAVALGDLAGLEHLDLAEAGTLQHPPL
+LLLALVTAAGMSDAVVEQSRWPQILACGLVSGAGYGVFLAAQQLGIGDRLVPAAAATAVG
+FLGRLVAQRIAAPALVIVLPSMLFLLPGLMMFRSVYGFTVETGSTLLGLAGLFNAAVIVV
+AIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRG
+>MOLHKGIG_00351
+MEQEGTQEPARFDPLIAEPPAVPTLIPVLRPAGAEDAAAVGDLALDPEDPGLLDLDPAES
+AHPAAVAVEPTEPLPPVVRPAAADPAPAPAPEPEPEESAEPDAETLPEPAADAPLTEPPL
+SEQVPTSVLAPAEADGALPAPDVIPAPDITVPDPVVPVGPPEKRGRRRGRRSREVFVENL
+PTQALVLADRLHSSPYGRRMRSTLQQRRAEAQALEARTTLDFALKLGETMFSFGAASLDV
+ETSIIVATQAYGILETEVDLTNQSISLNYAPDSSRGEAPFTLQRVVRSSSVNFEGLVAVH
+RLVEEIAAGEVDRAEAQRRLVEIRHQPKPFPAVFEVLFSGVFVACFVPFIGGTWTGAALG
+MVSTWLVFWLKIQADKARFPEIFSTMFGAITATVIALMAHALDLPVNPALVIAGGIMMLL
+PTARFVTAVQDAIHGFPVTAAGRFLSALLVFAGVMAGIMIAVGIGDLVGFEQLDLAEAGT
+LSYPPLLLLGLVVAAGMADAVVEQSRWPQILACGLVSGAGFGAYLAAQQVGVSDRLVPAV
+AAAAVGFLGRLVAQRLAAPALVIVLPSMLFLLPGLTMFRSVYGFTVETGATLLGVEGLFN
+AAVIVVAIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRG
+>NAFOICDF_02469
+MGAEPRRGPAQGTGPLGPDRNPRKDPVRSVDPLAPQDGSPEDGGVPQGARRAGTRPDAAG
+SAPAEPAVHVALLPVLRPADARTPAGASDGDAPAGDGVDLAAAPAREPGPEDVLPPVLAP
+VAAPTVPVETLPTPEPAPAPEEEPTPAADAPLTAPPLSEPVPTSVLAPAEGDAPTAQEAA
+AAVPDVVVPDPLKQHGPEEPRGRRRRRRTREDHRAVFEEVLPTQAIVLVDRLQASPYGKR
+MRSTLRQRRDTEAAALEARTTLDFALKLGETMFGFGATSLDVETSIIVVTQAYGIHETEV
+DLTNQAISLNYAPDSSRGEVPYTLQRVVRTYSTNFEGLVAVHRLVEEISDGTLERAEAQR
+RLVEIRRRPKPYPPAVEILLAGVFVACFIPFIGGTWQGSLLGMVSTWFVFWLHTRTSVFL
+PEIYSVMIGAFLATLIALGAYALHVPVNPAIVVAGGIMMLLPTSRFVTAVQDAINGFPVT
+AAGRFISAMLVFIGIMAGIMVAVGLTDMLGIARLDLAATQSTAYPTTLLLALVVAATACD
+AVVERSGWRTLLASCAVTAAAFAAHTVVAGLGVSAQLLPAAAAAMVGFAGRIVALRVGAP
+PIVVVVPAILFLLPGFAVFRGLYEFTVESASTMAGLAGIVNALVIIVGIGAGAVFGDTLA
+RPVTERLSPARSTPGPEGHTR
+>MHAAABBN_00067
+MEQEGTQEPARFDPLIAEPPAVPTLIPVLRPAGAEDAAAVGDLALDPEDPGLLDLDPAES
+AHPAAVAVEPTEPLPPVVRPAAADPAPAPAPEPEPEESAEPDAETLPEPAADAPLTEPPL
+SEQVPTSVLAPAEADGALPAPDVIPAPDITVPDPVVPVGPPEKRGRRRGRRSREVFVENL
+PTQALVLADRLHSSPYGRRMRSTLQQRRAEAQALEARTTLDFALKLGETMFSFGAASLDV
+ETSIIVATQAYGILETEVDLTNQSISLNYAPDSSRGEAPFTLQRVVRSSSVNFEGLVAVH
+RLVEEIAAGEVDRAEAQRRLVEIRHQPKPFPAVFEVLFSGVFVACFVPFIGGTWTGAALG
+MVSTWLVFWLKIQADKARFPEIFSTMFGAITATVIALMAHALDLPVNPALVIAGGIMMLL
+PTARFVTAVQDAIHGFPVTAAGRFLSALLVFAGVMAGIMIAVGIGDLVGFEQLDLAEAGT
+LSYPPLLLLGLVVAAGMADAVVEQSRWPQILACGLVSGVGFGAYLAAQQVGVSDRLVPAV
+AAAAVGFLGRLVAQRLAAPALVIVLPSMLFLLPGLTMFRSVYGFTVETGATLLGVEGLFN
+AAVIVVAIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRR
+>LFPAFLNI_00358
+MEQEGTQEPARFDPRIAEPPAVPTLIPVLRPAGAEDAAAVGDLAIDPEDPGLLDLDPAES
+AHPAAAAVAVEPTEPLPPVVRPAAADPEPEPEEPAEPEAETLPEPAADAPLTEPPLSEQV
+PTSVLAPADADGALPAPDVIPAPDITVPDPVVPVGPPEKRGRRRGRRSREVFVENLPTQA
+LVLADRLHSSPYGRRMRSTLQQRRAEAQALEARTTLDFALKLGETMFSFGAASLDVETSI
+IVATQAYGILETEVDLTNQSISLNYAPDSSRGEAPFTLQRVVRSSSVNFEGLVAVHRLVE
+EIAAGEVDRAEAQRRLVEIRHQPKPFPAVFEVLFSGVFVACFVPFIGGTWTGAALGMVST
+WLVFWLKVQADKARFPEIFSTMFGAITATVIALMAHALDLPVNPALVIAGGIMMLLPTAR
+FVTAVQDAIHGFPVTAAGRFLSALLVFAGVMAGIMIAVGIGDLLGFEQLDLAEAGTLSYP
+PLLLLGLVMAAGMADAVVEQSRWPQILACGLVSGAGFGAYLAAQQVGVSDRLVPAVAAAA
+VGFLGRLVAQRLAAPALVIVLPSMLFLLPGLTMFRSVYGFTVETGATLLGVEGLFNAAVI
+VVAIAAGVAFGNTLAKPITDRMGTLLPTELVMHQRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001758.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001758.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45043598d781de28f3442d9f6e5e65940309f62e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001758.fa
@@ -0,0 +1,45 @@
+>ACLBLIBL_02623
+MSERIVTVDTVETPSPDDRLTVTGAPSGDASEDPATALLALPWSTALEDWPEDVLAALPR
+GISRHVVRFARVGGGVVAVKETTEDLAFREYRLLRRLEGSPAPSVVPVAVVTGRTDGRGE
+PLPAALVTRYLHFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVL
+FRRDAGGFAAHLVDAETGELRERLSTGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPA
+ATPELFVDAYRRLWDELTGPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMML
+AAPVEVHAGYHRRRLTRLTGLQVQENQARRLLVDIEAARRAWDPFLDLEGAAHRWVVEVF
+DPVVRSVPLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRVRRDED
+AVALHPTTTMLRTVPPADED
+>MOLHKGIG_00346
+MDTVETPSPVDRLTITGAPSGDATEDPATSLLALPWALPLETWPREVLAALPRGISRHVV
+RFARMGGGIVAVKETTEELAFHEYRLLRRLERSPAPSVVPVAVVTGRTEDDGTPLPAALV
+TRHLRFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVLFRRDAGG
+FAAHLVDAETGELRERLSNGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPVTTPDLLV
+ASYRRLWDELTGPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMMIARPVEIH
+AGYHRRRLTRLTGLEVQENQARRLLVDIEAARREWDPYMDIEAAAHRWVVEVFDPVVRSV
+PLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRARRDEDAVALHPT
+TTMLRAVPPADAD
+>NAFOICDF_02475
+MDEHEQPRTDPADRLTVTAAPSGDASEDPATSLLALPWERPLEDWPAEVLAALPRGISRH
+VVRFARMGAGVVAVKETTEELAFREYRLLRELEDRPSPSVVPVAVVTGRTREDGTALPAA
+LVTRHLRFSLPYRAVFSERMERRTLVRLMDALALLLVELHLEGFFWGDVSLSNVLFRRDA
+GGFAAHLVDAETGELRERLSTGQREHDLDVARVNIGGELLDLHASGLADPDVDAIATPDL
+FVESYRQLWQQLTEPTVFPRGEPWRMDRRFRRLTELGFEVEEYSLRAADAPGMMVAQPTD
+VNSGYHRRRLERLTGLHVQENQARRLLVDIEAARRSWDPFMDMDHAAHRWVIEVFDPVVR
+SVPLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLDEAVDSYVETVLRARRDEDALALH
+PTTTMLRAVPAPEADPEG
+>MHAAABBN_00062
+MDTAETPSPVDRLTITGAPSGDATEDPATSLLALPWALPLETWPREVLAALPRGISRHVV
+RFARMGGGIVAVKETTEELAFHEYRLLRRLERSPAPSVVPVAVVTGRTEDDGTPLPAALV
+TRHLRFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVLFRRDAGG
+FAAHLVDAETGELRERLSNGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPVTTPDLLV
+ASYRRLWDELTEPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMMIARPVEIH
+AGYHRRRLTRLTGLEVQENQARRLLVDIEAARREWDPYMDIEAAAHRWVVEVFDPVVRSV
+PLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRARRDEDAVALHPT
+TTMLRAVPPADAD
+>LFPAFLNI_00353
+MDTAETPSPVDRLTITGAPSGDATEDPATSLLALPWALPLETWPREVLAALPRGISRHVV
+RFARMGGGIVAVKETTEELAFHEYRLLRRLERSPAPSVVPVAVVTGRTEDDGTPLPAALV
+TRHLRFSLPYRAVFSERLERRTLVRLMDALATLLVELHLEGFFWGDVSLSNVLFRRDAGG
+FAAHLVDAETGELRERLSTGQREHDLDVAAVNVGGELLDLQASGLLDPEVDPVTTPDLLV
+ASYRRLWDELTEPLLFPRAEPWRLDRRVRRLQELGFELAEYSLRAADAPGMMIARPVEIH
+AGYHRRRLTRLTGLEVQENQARRLLVDIEAARREWDPYMDIEAAAHRWVVEVFDPVVRSV
+PLELRAKLEPAEVMHQLLEHRWYLSEARGQAVPLQEAVDSYVDTVLRARRDEDAVALHPT
+TTMLRAVPPADAD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001761.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001761.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d0db1cd875d6bb0b1849f03bfbaaa65bf6202272
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001761.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_02627
+MAWGAAPAPAPAPGEGPALLASAGPEHAEAARERARGALRAGIDAGVDLLDTADIYGAGV
+SEETVGALLHELPYEERSALKVQTKCGIVLDEVDADGRPMVRYDSSPEYVRARLEGSLAR
+LGELRVDTLVIHRPDVLTPVADTVRAFLDAREEGLVGKLGVSNLGVGRTLEFQRELAAQS
+ADGTGLACVQVELGLHHRTLVESVILANHPGAAADADVADLGRVCAAEGIELQAWGSLGQ
+GRFSSGDDGAAGVVGEIARELDTSREAVVLAWLLRLPWGVRPVIGSQDPGRIAACADAAA
+AAEAMDSAQWHRLWTAARGAPLP
+>MOLHKGIG_00342
+MSTAPTHPPLDLDPTPATPIVLGTMAWGSVLPPPPDADPGVGPEGPAGEAQAEAAVERAR
+RALRAGIEAGVDLLDTADIYGAGRSEETVGRLLHELPYEERSALKVQTKCGIVLHETDPA
+GRRLTRYDSSPEHVRASLEGSLARLGEQRVDTLIIHRPDVLTPVADTVRAFLDAREAGLV
+GKLGVSNLGVGRVLEFQRELESQAADGTGLACVQVELGLHHRTLMEAVVLANHPDAPADA
+DAGRLGPVCAAEGIELQAWGPLGQGRFSSGDDGAAGAVGEVAAELGGSREAVVLAWLLRL
+PWDVRPVIGTQDPERVAACAEAAAAAEAMDSAQWHRLWTAARGAGLP
+>NAFOICDF_02479
+MTAQDTAPQTPAASPLILGTMGWGDVERARGALRAGLEAGIGLLDTADIYGAGASEETVG
+ALLAELDPAERTRLRVQTKSGIVLHEPGPDGTPAVRYDNSPAYLHERLALSLERLGLDRV
+DTLVVHRPDVLTPVSDTVRAFLDAREAGRVDALGVSNMGTRRVLEYQHALREVSADGTGL
+ACVQVELGLHHRMLVESVVLANHPAAAPDGGAGDLGEVCAGEGIEIQAWGPLGQGRFTRG
+SDGTVPADPAEQAALAAAGGAPAVVARVARELEVSREAVVLAWLLRLPWGVRPVVGTQDP
+ARIASCAQAADAAARMDGAQWHRLWTAARGETLP
+>MHAAABBN_00058
+MSTAPTHPPLDLDPTPATPIVLGTMAWGSVLPPPPDADPGVGPEGPAGEAQAEAAVERAR
+RALRAGIEAGVDLLDTADIYGAGRSEETVGRLLHELPYEERSALKVQTKCGIVLHEADPA
+GRRLTRYDSSPEHVRASLEGSLARLGEQRVDTLIIHRPDVLTPVADTVRAFLDAREAGLV
+GKLGVSNLGVGRVLEFQRELESQAADGTGLACVQVELGLHHRTLVEAVVLANHPDAPADA
+DAGRLGPVCAAEGIELQAWGPLGQGRFSSGDDGAAGVVGEVAAELGVSREAVVLAWLLRL
+PWGVRPVIGTQDPERVAACAEAASVAEAMDSAQWHRLWTAVRGAGLP
+>LFPAFLNI_00349
+MSTAPTHPPLDLDPTPATPIVLGTMAWGSVPPPPPDADPGAGPEGPAGEAQAEAAVERAR
+RALRAGIEAGVDLLDTADIYGAGRSEETVGRLLHELPYEERSALKVQTKCGIVLHETDPA
+GRRLTRYDSSPEHVRASLEGSLARLGEQRVDTLIIHRPDVLTPVADTVRAFLDAREAGLV
+GKLGLSNLGVGRVLEFQRELESQAADGTGLACVQVELGLHHRTLVEAVVLANHPDAPADA
+DAGRLGPVCAAEGIELQAWGPLGQGRFSSGDDGAAGVVGEVAAELGVSREAVVLAWLLRL
+PWGVRPVIGTQDPERVAACAEAASVAEAMDSAQWHRLWTAARGRPLP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001767.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001767.fa
new file mode 100644
index 0000000000000000000000000000000000000000..87b4c56d50ee0dea83a12bc460ff982423d567a3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001767.fa
@@ -0,0 +1,21 @@
+>ACLBLIBL_02680
+MAWWPFRGPSGAPRDDDASTAGRASLEAAVHSLRALMTAERHRLRPDSRDLAWTITERAA
+EYGPAWDRVSAQRPAEAQELLLLLSHRLEPALRDFLDLPDSQKPRHADELHGRLSELQTE
+AQRLGRRLTRALSSRLRARGEL
+>MOLHKGIG_00335
+MSWWPFPRPSASPSPDDDGAPAAAELEEAVAALRQLLRAERHRLRPDSWALAWEMVEQAA
+EYAPAWTRLQRTRPVETQELVLALTGRLEPLLCDFLALPDSEKPTHADAVHARLREQGTE
+HGRLRRRLTRALTARLRAGEEL
+>NAFOICDF_02492
+MAWWARRRLSSSGPAPLGKPPLVAAEELRRLTDELSEILQRESARIRPDAAAVLRSFLNR
+SRALLPAWDRTAPARSAEALAAYELLRDRVLPGLQDWLCLPDHLKPVHADDLLADAQAWE
+GDLSHHAARLTQVLTARGRAVRELDERQ
+
+>MHAAABBN_00051
+MSWWPFLRSSASPSPDDDGAPAAAELEEAVAALRRLLRAERHRLRPDSWALAWEMVEHAA
+EYGPAWTRLQRTRPVETQELVLALTGRLEPLLRDFLALPDSEKPAHADAVHARLREQSTE
+HGRLRRRLTRALTARLRAGEEL
+>LFPAFLNI_00342
+MSWWPFLHSSASPSPDDDGAPAAAELEEAVAALRRLLRAERHRLRPDSWALAWEMVEHAA
+EYGPAWTRLQRTRPVETQELVLALTGRLEPLLRDFLAIPDSEKPAHADAVHARLREQSTE
+HGRLRRRLTRALTARLRAGEEL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001769.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001769.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9313a34e13bed22c7f05d46b43e4966683d24a60
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001769.fa
@@ -0,0 +1,39 @@
+>MHAAABBN_00329
+MTAPHIVDPERLLREALGEASPDLLRHLLQTIINALLSADADAVCGAEYGTASESRTTQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPDWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMATELDEHIEAFRHRPLSDTGPFVFLAADALTMKVREGGRV
+INAVAMVATGVNADGRREVLGLRVATTESGAAWNEFFADLVARGLTGVKLVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFDRLLD
+YVQDRLPAVTAHLDAAREDILAFTGFPKDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+EAVIRLVGAVLAEQTDEWAEGRRYLGLELLARCSGLDADTTSTTILGTEVMPTLET
+>MHAAABBN_00368
+MTAPHIVDPERLLREALGEASPDLLRHLLQTIINALLSADADAVCGAEYGTASESRTTQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPDWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMATELDEHIEAFRHRPLSDTGPFVFLAADALTMKVREGGRV
+INAVAMVATGVNADGRREVLGLRVATTESGAAWNEFFADLVARGLTGVKLVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFDRLLD
+YVQDRLPAVTAHLDAAREDILAFTGFPKDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+EAVIRLVGAVLAEQTDEWAEGRRYLGLELLARCSGLDADTTSTTILGTEVMPTLET
+>MHAAABBN_01110
+MTAPHILDPAGLLSEALSEASPDMMRHLLQTMINTLLSADADAVVGAEWGKPTPTRSAQR
+NGYRHRDLDTRVGTVDVAIPKLRSGTYFPEWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVKTLGINALSKSQVSRMAADLDEHVESFRHRPLDEAGPLTFVAADALTMKVREGGRV
+VNAVVLLATGVNGDGHREVLGMRVATSETGTAWNEFFADLVARGLAGVRLVTSDAHAGLK
+DAIAANLPGATWQRCRTHYAANLMGITPKSMWPAVKAMLHSVYDQPDATAVNAQFDRLLD
+YVSEKLPAVAEHLGDARADILAFTTFPKDVWTQIWSNNPAERLNREIRCKRP
+>MHAAABBN_01967
+MTAPHIVDPERLLREALGEASPDLLRHLLQTIINALLSADADAVCGAEYGTASESRTTQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPDWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMATELDEHIEAFRHRPLSDTGPFVFLAADALTMKVREGGRV
+INAVAMVATGVNADGRREVLGLRVATTESGAAWNEFFADLVARGLTGVKLVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFDRLLD
+YVQDRLPAVTAHLDAAREDILAFTGFPKDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+EAVIRLVGAVLAEQTDEWAEGRRYLGLELLARCSGLDADTTSTTILGTEVMPTLET
+>MHAAABBN_02017
+MTAPHIVDPERLLREALGEASPDLLRHLLQTIINALLSADADAVCGAEYGTASESRTTQR
+NGYRHRPLDTRAGTIDVAIPKLRAGTYFPDWLLERRKRAESALITVVADCYLAGVSTRRM
+DKLVRQLGIDSLSKSQVSRMATELDEHIEAFRHRPLSDTGPFVFLAADALTMKVREGGRV
+INAVAMVATGVNADGRREVLGLRVATTESGAAWNEFFADLVARGLTGVKLVTSDSHRGLV
+EAVAANLPGAVWQRCRTHYAANLMAVTPKSMWPAVKAMLHSVYDQPDGPAVHAQFDRLLD
+YVQDRLPAVTAHLDAAREDILAFTGFPKDVWSQIWSNNPAERLNREIRRRTDSVGIFPNR
+EAVIRLVGAVLAEQTDEWAEGRRYLGLELLARCSGLDADTTSTTILGTEVMPTLET
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001770.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001770.fa
new file mode 100644
index 0000000000000000000000000000000000000000..81792a1233fbb1e4d9f2b026ccfe9f540f7fa0ec
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001770.fa
@@ -0,0 +1,24 @@
+>ACLBLIBL_00006
+MLEISQVSKTFFPNTVNERRALQGIDLHLAEGDFVTVIGSNGAGKSTILNTIAGKLLPDT
+GTVKVSGKDVTRMADHRRAAWIGRVFQDPTAGTAPNLTIEENMALAWRRGHTRGLARGVS
+RSRRGLFREELTKLELGLEDRLTAKVGLLSGGQRQALSLLMATFSGPKILLLDEHTAALD
+PSRAELVTRLTQQVVAEHRLTTLMVTHNMSQALEVGNRLIMMHDGRIILELDEAQKAGRT
+PADLLAEFAKIKGAVVDDKTMLS
+>MOLHKGIG_00329
+MLEISQVSKTFFPNTVNERRALQGIDLHLAEGDFVTVIGSNGAGKSTILNTIAGKLLPDT
+GTVAVGGKDVTRMPDHRRAASIGRVFQDPTAGTAPNLTIEENMALAWRRGHARGLSRGVS
+RARRAMFRDELTKLELGLENRLTAKVGLLSGGQRQALSLLMATFSGPKILLLDEHTAALD
+PSRAELVTRLTRQVVAEHRLTTLMVTHNMSQALEVGNRLIMMHDGRIILELDEQEKAGRT
+PADLLAEFAKIKGAVVDDKTMLS
+>MHAAABBN_00045
+MLEISQVSKTFFPNTVNERRALQGIDLHLAEGDFVTVIGSNGAGKSTILNTIAGKLLPDT
+GTVAVGGKDVTRMPDHRRAASIGRVFQDPTAGTAPNLTIEENMALAWRRGHARGLSRGVS
+RARRAMFRDELTKLELGLENRLTAKVGLLSGGQRQALSLLMATFSGPKILLLDEHTAALD
+PSRAELVTRLTRQVVAEHRLTTLMVTHNMSQALEVGNRLIMMHDGRIILELDEQEKAGRT
+PADLLAEFGKIKGAVVDDKTMLS
+>LFPAFLNI_00336
+MLEISQVSKTFFPNTVNERRALQGIDLHLAEGDFVTVIGSNGAGKSTILNTIAGKLLPDT
+GTVAVGGKDVTRMPDHRRAASIGRVFQDPTAGTAPNLTIEENMALAWRRGHARGLSRGVS
+RARRAMFRDELTKLELGLENRLTAKVGLLSGGQRQALSLLMATFSGPKILLLDEHTAALD
+PSRAELVTRLTRQVVAEHRLTTLMVTHNMSQALEVGNRLIMMHDGRIILELDEQEKAGRT
+PADLLAEFGKIKGAVVDDKTMLS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001774.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001774.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c341699dad6874930474b3f23057b809bc6db6e3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001774.fa
@@ -0,0 +1,16 @@
+>ACLBLIBL_00068
+MSETTTDPGLPDDVGVDAGADPTGTAPAPAALEESMPHPSDPSVTPFLMFEGDAGAAMDA
+YLSVFVEHLPVTEVRRDLFDGSSPRGAEWAGKVLHGELEVAGQRLRFFDSFTSHGFTFTP
+AISLFVELPDPTAVDAVHDALIAGGGQDYMPPGDYGFSRRFAWVGDRFGVTWQLNAA
+>MOLHKGIG_00286
+MSIDAAPPEDGGTAPTGTSPAPEALEDALPHPSDPSVTPFLLFEGDAGAAMDAYLTAFVE
+YLPVTEVRRDLFDDSSPRGAEWAGKVLHGELEIAGQRLRFFDSFTPHGFTFTPAISLFVE
+LPDATAVDAIHDTLLAGGGRDYMPPDDYGFSRRFAWVGDRFGVTWQLNAA
+>MHAAABBN_02308
+MSIDAAPPEDVGTAPTGTSPAPEALEDSLPHPSDPSVTPFLMFEGDAGAAMDAYLTAFVE
+HLPVTEVRRDLFDDSSPRGAAWAGKVLHGELEIAGQRLRFFDSFTPHGFTFTPAISLFVE
+LPDATAVDAVHDALLAGGGRDYMPPDDDGFSRRFAWVGDRFGVTWQLNAA
+>LFPAFLNI_00292
+MSIDAAPPEDVGTAPTGTSPAPEALEDSLPHPSDPSVTPFLLFEGDAGAAMDAYLTAFVE
+HLPVTEVRRDLFDESSPRGAAWAGKVLHGELEIAGQRLRFFDSFTPHGFTFTPAISLFVE
+LPDATAVDAIHDALLAGGGRDCMPPDDDGFSRRFAWVGDRFGVTWQLNAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001776.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001776.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9535d1e1fecdbbe535840fb419661a9075a9e9b4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001776.fa
@@ -0,0 +1,80 @@
+>ACLBLIBL_00083
+MDRDAVNALAEEYSRGIGQALSMGVAAEPEAQLTVPFAAFLSRFAQEVELGRLDLLREAQ
+LDGVRPDFAAALDGRPCGWIELKAPGHTVVGERWRGREKSQWALLSQLDALLVSNGELLA
+LYVAGAPVETCALPVDGAAGWDPDRLRRVLEQFTLAQPRPITRVSQLADRLAPLARFLRE
+RLAEGLEHSYDSVVEAKAAWDHTMQHTTSPEEFSGDVAQVVAYSMAIAGLSGQADRNADG
+VVSLEEAKHALETAHRNVLAASLGPILGIPALMQHIAPEVGAITRLVAGMDVAAIERSTD
+SRGEPWLWFYEDFLQRYDPEARSRAGVYYTPISVVECQVRVVDALLRERFGQNLGFGAPS
+VVTLDPATGSGTYPLAIIDRAESVAREERGDAGAKQVAMNLTKNLLAFELLPGPYSVAHL
+RIGQRLAEAQGHAFQAEEIGVYLTDTLEDPSAGMPTGLFGDARVLAEAAESARRVKRDQQ
+ITVAIGNPPYDRVTSGTGGWVEQGSGSGDALFDDVIKPAQDSGVIFSAQASLYNLYVYFW
+RWAIWKAFQQDPKDHAVISFITASSWLTGPAFVGLRRLAQATASEIWVMDLGGEGRGARK
+EENVFDIQSPVAIVTLVRTGKASREAKVFYRRFRGSRAEKFTALDRIQRLDAADGWEQIA
+APGGAPFMPASGGEDWTAMPQLADLFPWQQPGIMYNRAWPVASDQNTLRRRWQELLSDDD
+ADARAGKYVTGNSGRTIHTAVAGLPTLASLPADAEPRPIVRVAWRSFDRQWTFDDPRLIN
+LERPALWQALSDRQLFLVSPKTARINGGPAVTVSTAVPDKHHYVGSFGGKDVIPLYRDAA
+AAEPNVTVGLLELLADRLGHDVTPEDLAAYVMAVAAHDGYAQTFDEALETSPVRIPFTAD
+ASLWDAAVALGERLLWLQTYGERFTSADRPRGRVPRVPGLGWSEAVTHIPADTASLSYDA
+ASRELRVGDGVVTGVSPEVRAFSVSGMNIVDKWLGARTAKGIGRAAGKAATPLDRIRPTE
+WADEWNDELLDLLRVLTETVALGDQQAELLAAILAGELITAADLPVPTAAERKVPKTIKR
+GVSPHQEGLL
+>MOLHKGIG_00273
+MIDAPLAQLAETYARDVRLASTSGVSAEPEAQLTVPVSEFLRAFSSVTGIGDLSLLREAQ
+LDGVRPDFAALIDGRPCGWVELKAPGHTVIGEKWRGREKGQWDLLSQLDALLVSNGDEIA
+LYVSGSPVDTAFLPVDGVAGWDADRLRTVLEQFTLAQPRPITRVSQLADRLAPLARFLRE
+RLQEGLSNNYRSVREAKAAWDHTVHHTTTDAQFAGDVAQVVAYSMAIAGLSGQADRNADG
+VVTLEEAKHALETAHRNVLAASLGPIIGIPALMEYIAPEVGAIMRLVSSMDVAAIERSTD
+SRGEPWLWFYEDFLQRYDPAARNRAGVYYTPISVVQCQVRVVDALLRERFGQTLGFGAPS
+VVTLDPATGSGTYPLAVIDRAEAAAREERGPAGVAQVAKNLTKNLLAFELLPGPYSVAHL
+RIGQRLAEAQGHAFQAEEIGVYLTDTLEDPSAGMAEGLFGDARVLAEAAEAARRIKRDRR
+ITVAIGNPPYDRVTSGTGGWVEHGDGEDALFDDVIGPAQEQGVIFSAQASLYNLYVYFWR
+WAIWKAFQQDPGDQAIISFITASSWLTGPAFVGLRDLARRTASEIWVMDLGGEGRGARQE
+ENVFDIQTPVAIVTLVRTGKAAREASVYYRRFRGTRAEKFAALDEVARLDPDDGTWECLP
+GGAGDPLAPASGGEDWAAMPALADLFPWQQPGIKYNRAWPVAPDQDTLQRRWRELLADPS
+ADARAEKYVTGHSGRTIHTAVSGLTPLAALPADAEHRPITRVAWRSFDRQWTFDDPRLIN
+LERPALWQALSDRQLFFVSPKTARISGGPAVTVATAVPDLHYFVGSYGGKDVIPLYRDAE
+AAQPNVTGGLLPLLGERYGREVTPEDLAAYVMGIAGHDAYVQRFDEALEGSPVRVPLTVD
+PALFARAVELGKRLLWLQTYGERFTGVDRPAGRVPRIPGLGWEAPVTALPASPRAVSYDP
+ATQRLKVGDGVVTGVSPEVRAFAVSGMNILDKWLGARTATGIGRAAGKAATPLDRIRPTE
+WADEWNDELLDLLRVLTETVSLGGDQADLLDEILARDLIPANELPEPTPAERKVPKTIKR
+DFSTAQEEMF
+>MHAAABBN_02288
+MIDAPLAQLAETYARDVRLASTSGVSAEPEAQLTVPVSEFLRAFSSVTGIGDLSLLREAQ
+LDGVRPDFAALIDGRPCGWVELKAPGHTVIGEKWRGREKGQWDLLSQLDALLVSNGDEIA
+LYVSGSLVDTAFLPVDGVAGWDADRLRTVLEQFTLAQPRPITRVSQLADRLAPLARFLRE
+RLQEGLSNNYRSVREAKAAWDHTVHHTTTDAQFAGDVAQVVAYSMAIAGLSGQADRNADG
+VVTLEEAKHALETAHRNVLAASLGPIIGIPALMEYIAPEVGAIMRLVSSMDVAAIERSTD
+SRGEPWLWFYEDFLQRYDPAARNRAGVYYTPISVVQCQVRVVDALLRERFGQTLGFGAPS
+VVTLDPATGSGTYPLAVIDRAEAAAREERGPAGVAQVAKNLTKNLLAFELLPGPYSVAHL
+RIGQRLAEAQGHAFQAEEIGVYLTDTLEDPSAGMAEGLFGDARVLAEAAEAARQIKRDRR
+ITVAIGNPPYDRVTSGTGGWVEHGDGEDALFDDVIGPAQEQGVIFSAQASLYNLYVYFWR
+WAIWKAFQQDPGDQAIISFITASSWLTGPAFVGLRDLARRTASEIWVMDLGGEGRGARQE
+ENVFDIQTPVAIVTLVRTGKAAREASVYYRRFRGTRAEKFAALDEVARLDPDDGTWECLP
+GGAGDPLAPASGGEDWAAMPALADLFPWQQPGIKYNRAWPVAPDQDTLQRRWRELLADPS
+ADARAEKYVTGHSGRTIHTAVSGLTPLAALPADAEHRPITRVAWRSFDRQWTFDDPRLIN
+LERPALWQALSDRQLFFVSPKTARISGGPAVTVATAVPDLHYFVGSYGGKDVIPLYRDAE
+AAQPNVTGGLLPLLGERYGREVTPEDLAAYVMGIAGHDAYVQRFDEALEGSPVRVPLTVD
+PALFARAVELGKRLLWLQTYGERFTGVDRPAGRVPRIPGLGWEAPVTALPASPRAVSYDP
+ATQRLKVGDGVVTGVSPEVRAFAVSGMNILDKWLGARTATGIGRAAGKAATPLDRIRPTE
+WADEWNDELLDLLRVLTETVSLGGDQADLLDEILAGDLIPANELPEPTPAERKVPKTIKR
+DFSTAQEEMF
+>LFPAFLNI_00271
+MIDAPLAQLAETYARDVRLASTSGVSAEPEAQLTVPVSEFLRAFSSVTGIGDLSLLREAQ
+LDGVRPDFAALIDGRPCGWVELKAPGHTVIGEKWRGREKGQWDLLSQLDALLVSNGDEIA
+LYVSGSLVDTAFLPVDGVAGWDADRLRTVLEQFTLAQPRPITRVSQLADRLAPLARFLRE
+RLQEGLSNNYRSVREAKAAWDHTVHHTTTDAQFAGDVAQVVAYSMAIAGLSGQADRNADG
+VVTLEEAKHALETAHRNVLAASLGPIIGIPALMEYIAPEVGAIMRLVSSMDVAAIERSTD
+SRGEPWLWFYEDFLQRYDPAARNRAGVYYTPISVVQCQVRVVDALLRERFGQTLGFGAPS
+VVTLDPATGSGTYPLAVIDRAEAAAREERGPAGVAQVAKNLTKNLLAFELLPGPYSVAHL
+RIGQRLAEAQGHAFQAEEIGVYLTDTLEDPSAGMAEGLFGDARVLAEAAEAARQIKRDRR
+ITVAIGNPPYDRVTSGTGGWVEHGDGEDALFDDVIGPAQEQGVIFSAQASLYNLYVYFWR
+WAIWKAFQQDPGDQAIISFITASSWLTGPAFVGLRDLARRTASEIWVMDLGGEGRGARQE
+ENVFDIQTPVAIVTLVRTGKAAREASVYYRRFRGTRAEKFAALDEVARLDPDDGTWECLP
+GGAGDPLAPASGGEDWAAMPALADLFPWQQPGIKYNRAWPVAPDQDTLQRRWRELLADPS
+ADARAEKYVTGHSGRTIHTAVSGLTPLAALPADAEHRPITRVAWRSFDRQWTFDDPRLIN
+LERPALWQALSDRQLFFVSPKTARISGGPAVTVATAVPDLHYFVGSYGGKDVIPLYRDAE
+AAQPNVTGGLLPLLGERYGREVTPEDLAAYVMGIAGHDAYVQRFDEALEGSPVRVPLTVD
+PALFARAVELGKRLLWLQTYGERFTGVDRPAGRVPRIPGLGWEAPVTALPASPRAVSYDP
+ATQRLKVGDGVVTGVSPEVRAFAVSGMNILDKWLGARTATGIGRAAGKAATPLDRIRPTE
+WADEWNDELLDLLRVLTETVSLGGDQADLLDEILAGDLIPANELPEPTPAERKVPKTIKR
+DFSTAQEEMF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001777.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001777.fa
new file mode 100644
index 0000000000000000000000000000000000000000..204f3bdaad96101c6dadca6a291c76d6234ddd61
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001777.fa
@@ -0,0 +1,17 @@
+>ACLBLIBL_00084
+MDALGWTTLAISLLALVAAGWSAFESWRLGRVERQRDQRQEDRERQEQARQVAAWMCVVA
+EREHNLAATVRRRWFLAIENSSQVPVYDGHATITSKYPVPALEAAMFPPGRTYFELGKNE
+WGYGVQSDELAIVPRPLTNAERFRVTSLAFTDAAGTRWTRDEQGRLAEGPAAADTGAMST
+GT
+>MOLHKGIG_00272
+MDAANVIALVVSVLALLAAAWSAVESWRLRQIEKGRDERQDLREKQEQARQVAAWMCVAA
+RINDEFGAPPTRRWFLAVENSSQVPVYGARATVASKYPVPDLTAAMLPPGRTYFELSKNE
+WGYGVQADELDVVPRPLTNAERFRVTAFTFTDAAGDRWSRDHQGRLSATSGKESEATD
+>MHAAABBN_02287
+MDAANVIALVVSVLALLAAAWSAVESWRLRQIEKGRDERQDLREKQEQARQVAAWMCVAA
+RINDEFGAPPTRRWFLAVENSSQVPVYGARATVASKYPVPDLTAAMLPPGRTYFELSKNE
+WGYGVQADELDVVPRPLTNAERFRVTAFTFTDAAGDRWSRDHQGRLSATSGKESEATD
+>LFPAFLNI_00270
+MDAANVIALVVSVLALLAAAWSAVESWRLRQIEKGRDERQDLREKQEQARQVAAWMCVAA
+RINDEFGAPPTRRWFLAVENSSQVPVYGARATVASKYPVPDLTAAMLPPGRTYFELSKNE
+WGYGVQADELDVVPRPLTNAERFRVTAFTFTDAAGDRWSRDHQGRLSATSGKESEATD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001778.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001778.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c2fdcd9e696a434d61a9359b7afeea98cc1872f8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001778.fa
@@ -0,0 +1,16 @@
+>ACLBLIBL_00116
+MYTRSRNDVEKVEWGGGTSERLLTAKDEMGFAVAHTIVRAGSSSKLQYRHHQEACYCIAG
+NGSVVEPDGTVHEITPGVIYVLPDHEPHDLRGGTEDMHLISVFNPAITGDEKHTLSEDGY
+SSY
+>MOLHKGIG_00253
+MYTRSRNDVEKVEWGGGTSERLITAKDEMGFAVAHTIVRAGSSSKLQYRNHKEACYCIAG
+NGSVVEPDGTVHEITPGVIYVLPDHEPHDLRGGTEDMHLISVFNPAITGDEKHTLSEDGY
+SSY
+>MHAAABBN_02265
+MYTRSRNDVEKVEWGGGTSERLITAKDEMGFAVAHTIVRAGSSSKLQYRNHQEACYCIAG
+NGSVVEPDGTVHEITPGVIYVLPDHEPHDLRGGTEDMHLISVFNPAITGDEKHTLSEDGY
+SSY
+>LFPAFLNI_00253
+MYTRSRNDVEKVEWGGGTSERLITAKDEMGFAVAHTIVRAGSSSKLQYRNHQEACYCIAG
+NGSVVEPDGTVHEITPGVIYVLPDHEPHDLRGGTEDMHLISVFNPAITGDEKHTLSEDGY
+SSY
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001783.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001783.fa
new file mode 100644
index 0000000000000000000000000000000000000000..22910775f0ed3b85715e4d48c9bf3299351cc204
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001783.fa
@@ -0,0 +1,18 @@
+>ACLBLIBL_00168
+MNTTADPRSRSASGPERAASTSAAATPAGSAAPSAWGRSARLGGGTGRLVVVSLVFGVLL
+AAMLGVIAYGLAGTADPADPRRPWVLGLVVASGALPVLAGTVWMLLVDRATIKGAVRDPE
+ESIESRWYDAAAGGAFHDLLVVLGLGTFVVSMTGWTAELSLVGAGLVLFMMADVAIRYRV
+QKRRG
+>MOLHKGIG_00217
+MTANHSRHTAAADGQGAAAEHAGTGTATTDPRRDTRSRWGCSSRLGGGTGRLMGVSLAVG
+VVGALGLGSAAWATTVAAGHADSLAWIAAGAMALNGLLFGLLLTWLALVDRHSIRGADTN
+PEESIEGRWYEKATSGAFHDTLVVVGLGAAILSFGGYVISPAAVGAALFVLMGCAAAIRY
+QIQKRRG
+>MHAAABBN_02210
+MATTPHTTTDLARDRRPRWGRSARLGGGSGRLILVSLVAGVVIALLIGAASYGLASSQGD
+AGPRFPAVTGAVMAASALPVGAALAWLFLVDRTTLRGAVRDTEETIEGRWLEKAQSGAFG
+DLLVVLGLGTFVVALAGWQPSLPLVGAGLLLFAGASVAVRYALQKRRG
+>LFPAFLNI_00217
+MATTPHTTTDLARDRRPRWGRSARLGGGSGRLILVSLVAGVVIALLIGAASYGLASSQGD
+AGPRFPAVTGAVMAASALPVGAALAWLFLVDRTTLRGAVRDTEETIEGRWLEKAQSGAFG
+DLLVVLGLGTFVVALAGWQPSLPLVGAGLLLFAGASVAVRYALQKRRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001786.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001786.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08948e544f18297e2e16aefe7c8d3025860e928c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001786.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_00196
+MTASRLIPPAVDPASLPRDLPGLRAHFRPVVEEIARGALERDRARLLPFEAVRALGCAGF
+SVLRVPREAGGPDVDVRTVTALLVDLAAADSNVAHLYRSHLGFLDALRFQPQPVRDRWHA
+LVLAGATVGNASTERGGNALGTLNTRLTAPAGGDDDGAPGAAWTLTGTKYYATGSIFSSH
+TRVSAAVVRADGSLAPGRGFAVVPVDAPGVCLEDDWDGFGQRLTGTGTAVFEDVAVDPRD
+VLERIPGSPEAVHEAAWFQLILLAVLAGIARAARDDAAARVAARVRTFNTGLGVPFREDP
+LIQEAVGRIAAKASAAEAVVLAAADALDASLAAGAATGADRWGFTGPVPPAFAEAELAVE
+HAQITVPELALGAAQELFLTGGASDTSVAKGLDRHWRNAQTVATHNPIAFRARAVGDYWI
+NGTLPEGLNAIGDAPAAPSSSAVDAAQPAPEPAEAGAR
+>NAFOICDF_00148
+MPLTDPTDAPTPLGTVPPLVRPADLPRDLAGLRRHFAPVFARVAEGSRERDRRRILPFAE
+VRALNEAGFATLRVPAEAGGPGVDVRTAVALLIDLAEADANVAHLYRSHLGFLDSLRFQP
+AAVRERWHARILAGATVGNASTEKGGNALGTLNTVLTPPAAGDGPWTLTGTKFYATGSIF
+SSHTRVSAAQTDADGHPAPGRRFAVVPVEAPGVRLDDDWDGFGQRLTGTGTAVFDGVAVP
+PQDVLDRVPGSAEAVYEAAWFQLILLAVLAGIARAARRDAADAVAARVRTFNTGLGLPFR
+EDPLIQEAVGRIAAKAFTAEAAVLSAADALDAALADHDAGRTGSGAPEEVPASFTWAELA
+VEHAQVTVPELALGAAQELFLTGGASATSTAKGLDRHWRNAQTVATHNPIAFRARAIGDY
+WINGTVPEGLNAIGDAPAASAPLGDAPAPGEAAR
+>NAFOICDF_00597
+MTTPVLDRPAPTSAADAPDTAELRARFAPVFARIAANEARRRDAAVPPHAAVRLLAETGF
+TALRLPRERGGSDATLTQLLDLLVDLAAADANLPQALHGHFMFTEQVARDVHPRLTDWWL
+DEVAAGKVFANALVDPPAATGLPGVTARRDPRDPEAFLLTGTKQYSTGTLLADWTLVAAH
+DDAGALQPLVVEVAGPGVEARDDWDGIGQRGTASGTTVYTDAPAPAWRRVDLERPAAAPG
+YPFLWLILAATQAGIAQRALDDFAEILRRRSRSYQHAASASPAHDPVLQHQLGAAAAQVR
+ALRSVVLGAVPALEAAYTAAAGAAPAIGAAATESPDDGAAEAFEAAHTEAWVAAASASSV
+AADLTLRLTSDLFETAGASAVVAGPGLDRHWRNARVLASHTPLPHRRRQIGECLLHGTPA
+PHSADAVETASSTDADPSRDSVSPSPSTPAATKEQ
+>LFPAFLNI_00199
+MPLTDPTDASAPPAATPVPLGAVPPLERPADLPRDLAGLRRHFAPVFARIAEGSRERDRR
+RILPFEEVRALNEAGFATLRVPAEAGGPGVDVRTAVALLIDLAEADANVAHLYRSHLGFL
+DSLRFQPEAVRERWHARILAGATVGNASTEKGGNALGTLNTVLTPAPAGDGPWTLTGTKF
+YATGSIFSSHTRVSAAQTDADGRPAPGRRFAVVPVEAPGVRLDDDWDGFGQRLTGTGTAV
+FDGVAVPPQDVLDRAPGSAEAVYEAAWFQLILLAVLAGIARAARRDAADAVAVRVRTFNT
+GLGLPFREDPLIQEAVGRIAAKAFTAEAAVLSAADALDAALADHEAGRTGSGAPEEVPAS
+FTWAELAVEHAQVTVPELALGAAQELFLTGGASATSTAKGLDRHWRNAQTVATHNPIAFR
+ARAIGDFWINGTVPEGLNAIGDAPAASAPLGADAPASGEAAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001788.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001788.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40733c27808ff770ae74132089214ab9867dfbbe
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001788.fa
@@ -0,0 +1,32 @@
+>ACLBLIBL_00225
+MTAAQDAAVVAPALDPEELVDRIEAGHRLTAAEAVAVLDAPDAETFRLVAAASRLRERHF
+GRTVKVNYLVSLKTGLCPEDCTYCSQRLGTEAQILKYTWLKPDEAVRQAGLGIAGGASRV
+CMVASGTGPTDRDVDRVTEMIGRLKDEHPQVEVCACLGKLKDGQAERLKAAGVDAYNHNL
+NTAESHYESICTSHTYADRVDTVERATAAGLSSCSGLIAGMGETHAQLAEAVLALRELDS
+DSIPVNFLMPFDGTPLAGHVQLTPLECLRILAVVRLACPDKELRIAGGREMHLRSLQAVG
+LQVANSIFLGDYLTSEGQDAEADLSMIADAGFTVLGAAAAPADDDGAPDGGCCGGGGCGE
+GGVEDASTRGGTSPSPSPAPRRRGAGTAEPANA
+>MOLHKGIG_00177
+MTATQDAPAVDPRPAAALDPEALVDRIEAGHRLTADEAVAVLDAPDADTFRIVAAASRLR
+EKHFGRTVKVNYLVSLKTGLCPENCTYCSQRLGTEAEILRYTWLKPEEAVRQAGLGIAGG
+ASRVCMVASGTGPTDRDVDRVAGMVGDLKAQHPDVEVCACLGFLKDGQAEKLKDAGVDAY
+NHNLNTAESHYESICTSHTYEQRVDTVQRAGAAGLSSCSGLIAGMGETHEQLVEAVLALR
+DLDSDSIPVNFLMPFDGTPLQGHQQLTPLECLRILAMVRLACPDKELRIAGGREMHLRSL
+QPVGLQVANSIFLGDYLTSEGQDAEADLQMIADAGFTVLGAEERARRATADDGAPAGGCC
+AGTDDAGPCGSGAAVAAEDVRPDTGAEGAVKPELRRRGAGTAEPANA
+>MHAAABBN_02170
+MTATQDAAAVDPRPAAALDPEALVDRVEAGHRLTAEEAVAVLDAPDADTFRIVAAASRLR
+EKHFGRTVKVNYLVSLKTGLCPENCTYCSQRLGTEAEILRYTWLKPEEAVRQAGLGIAGG
+ASRVCMVASGTGPTDRDVDRVAGMVGDLKAQHPDVEVCACLGFLKDGQAEKLKDAGVDAY
+NHNLNTAESHYESICTSHTYEQRVDTVQRAGAAGLSSCSGLIAGMGETHEQLVEAVLALR
+DLDSDSIPVNFLMPFDGTPLQGHQQLTPLECLRILAMVRLACPDKELRIAGGREMHLRSL
+QPVGLQVANSIFLGDYLTSEGQDAEADLQMIADAGFTVLGAEERARRATADDGAPAGGCC
+AGTDGAGSCGSGAAVASEAGAAEDARPDTGAEGTVKPELRRRGAGTAEPANA
+>LFPAFLNI_00169
+MTATQDAAAVDPRPADALDPEALVDRIEAGHRLTADEAVAVLDAPDADTFRIVAAASRLR
+EKHFGRTVKVNYLVSLKTGLCPENCTYCSQRLGTEAEILRYTWLKPEEAVRQAGLGIAGG
+ASRVCMVASGTGPTDRDVDRVAGMVGDLKAQHPDVEVCACLGFLKDGQAEKLKDAGVDAY
+NHNLNTAESHYESICTSHTYEQRVDTVQRAGAAGLSSCSGLIAGMGETHEQLVEAVLALR
+DLDSDSIPVNFLMPFDGTPLQGHQQLTPLECLRILAMVRLACPDKELRIAGGREMHLRSL
+QPVGLQVANSIFLGDYLTSEGQDAEADLQMIADAGFTVLGAEERAQQAAADDGAPAGCCG
+GGCVGTHDNSKNGAAATPSKPVLRRRGAGTGAAANA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001791.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001791.fa
new file mode 100644
index 0000000000000000000000000000000000000000..74163721e1f4bc0d3b64b48ea27c76b8076c940c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001791.fa
@@ -0,0 +1,12 @@
+>ACLBLIBL_00253
+MTSTPYEDGIDQRELQEDLLAEPDSATDPGPQDGRDGQPVRGSSDDPQHWAGDGRAEDSL
+RNAESEAMHIQQDAEDRTRADEGDVEIL
+>MOLHKGIG_00132
+MTDVPFEDREDERELETDLLADPNAAGDPEPEDGRDGQPVRGGSDDPQHWAGEGRAPDSL
+RNAESAAMHIEEDAQDRTRADEGDVEIL
+>MHAAABBN_02146
+MTDVPFEDREDERELETDLLADPNAAGDPEPEDGRDGQPVRGGSDDPQHRAGEGRAPDSL
+RNAESAAMHIEEDAQDRTRADEGDVEIL
+>LFPAFLNI_00140
+MTDVPFEDREDERELETDLLADPNAAGDPEPEDGRDGQPVRGGSDDPQHRAGEGRAPDSL
+RNAESAAMHIEEDAQDRTRADEGDVEIL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001796.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001796.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca404dd3a3c87b7add35ab5e8c10a6e7f19471b6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001796.fa
@@ -0,0 +1,16 @@
+>ACLBLIBL_00351
+MDDPVDARLAAEVSRDPRATLAQLSERVGLSASAVQARLRKLESTGVITGYQAILDPEAV
+GKPLAAFIEITPLDPRQPDDAPELLEPIAAIEACHSVAGDAAYMLFVRVGSPRELEALVS
+EIRHTASVNTRTTVVLQTFYEHRPMLPLPDAGE
+>MOLHKGIG_00052
+MDDPVDARLAAAVSHDPRATLAQLSERVGLSTSAVQARLRRLESTGVITGYRALLDPEAV
+GRPLSAFIEISPLDPRQPDDAPELLESIAAIEACHSVAGDAAYILFVRVGSPRELEALVT
+EIRQTASVATRTTVVLQTFYEHRPMLELPAED
+>MHAAABBN_02065
+MDDPVDARLAAAVSHDPRATLAQLSERVGLSTSAVQARLRRLESTGVITGYRALLDPEAV
+GRPLSAFIEISPLDPRQPDDAPELLESIAAIEACHSVAGDAAYMLFVRVGSPRELEALVT
+EIRQTASVSTRTTVVLQTFYEHRPMLELPAED
+>LFPAFLNI_00047
+MDDPVDARLAAAVSHDPRATLAQLSERVGLSTSAVQARLRRLESTGVITGYRALLDPEAV
+GRPLSAFIEISPLDPRQPDDAPELLESIAAIEACHSVAGDAAYMLFVRVGSPRELEALVT
+EIRQTASVSTRTTVVLQTFYEHRPMLELPVED
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001802.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001802.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3770596594b1024c6cb9bb90565d2f78fd6e41e6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001802.fa
@@ -0,0 +1,28 @@
+>ACLBLIBL_00407
+MQDKIKVAVNGYGVIGKRVADAVRAQEDMALVGVSDVIADYRIATAAGKGIPVYASTEQA
+LPVMADAGLPVVGGLHDLLENVDVVVDCTPAQVGAGNLELYRAHGVKSVFQGGEKHDLTG
+HSFVAHANYATALGRDSTRVVSCNTTATVRALTALKDVGLLSKARGVLIRRATDPWESDH
+SGIMNTIVPEGRIPSHQGPDAQSVVPDLDVVTMAAKGAHTQNHLHYWTIELTRPAEKQEV
+LEAFRAMPRIAFVRRSDGVVAVNSTVELMEDLGRPRGDMYEVALWEDILTVDGNELYYTY
+TVDNQAIVVPENIDAIRALTGTVDDGGESIRRTDRALGVRQDFVRSSVAAR
+>MOLHKGIG_00635
+MQDKIKVAVNGYGVIGKRVADAVRAQEDMALVGVSDVIADYRIATAAGKGIPVYASTEQA
+LPVMADAGLPVVGGLHDLLENVDVVVDCTPAQVGAGNLELYRAHGVKSVFQGGEKHDLTG
+HSFVAHANYATALGRDSTRVVSCNTTATVRALTALKDVGLLSKARGVLIRRATDPWESDH
+SGIMNTIVPEGRIPSHQGPDAQSVVPDLDVVTMAAKGAHTQNHLHYWTIELTRPAEKQEV
+LETFRAMPRIAFVRRSDGVVAVNSTVELMEDLGRPRGDMYEVALWEDILTVDGNELYYTY
+TVDNQAIVIPENIDAIRALTGTVDDGGESIRCTDRALGVRQDFVRSSVAAR
+>NAFOICDF_02194
+MQDKIKVAVNGYGVIGKRVADAVRAQEDMALVGVSDVIADYRIATAAGKGIPVYASTEQA
+LPVMADAGLPVVGGLHDLLENVDVVVDCTPAQVGAGNLELYRAHGVKSVFQGGEKHDLTG
+HSFVAHANYATALGRDSTRVVSCNTTATVRALTALKDVGLLSKARGVLIRRATDPWESDH
+SGIMNTIVPEGRIPSHQGPDAQSVVPDLDVVTMAAKGAHTQNHLHNWTIELTRPAEKQEV
+LEAFRAMPRIAFVRRSDGVVAVNSTVELMEDLGRPRGDMYEVVLWEDILTVDGNELYYTY
+TVDNQAIVVPENIDAIRALTGTVDDGGESIRRTDRALGVRQDFVRSSVAAR
+>LFPAFLNI_00596
+MQDKIKVAVNGYGVIGKRVADAVRAQEDMALVGVSDVIADYRIATAAGKGIPVYASTEQA
+LPVMADAGLPVVGGLHDLLENVDVVVDCTPAQVGAGNLELYRAHGVKSVFQGGEKHDLTG
+HSFVAHANYATALGRDSTRVVSCNTTATVRALTALKDVGLLSKARGVLIRRATDPWESDH
+SGIMNTIVPEGRIPSHQGPDAQSVVPDLDVVTMAAKGAHTQNHLHYWTIELIRPAEKQEV
+LEAFRAMPRIAFVRRSDGVVAVNSTVELMEDLGRPRGDMYEVALWEDILTVDGNELYYTY
+TVDNQAIVVPENIDAIRALTGTVDDGGESIRRTDRALGVRQDFVRSSVAAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001805.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001805.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b763d2939f25a2d30205112630e3d91652b451d8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001805.fa
@@ -0,0 +1,32 @@
+>ACLBLIBL_00460
+MPAPSLGEEDKRAIPALQPSLSSSNVTAHEHTGHLQAACIDVVARSEVVEVGGPGLMGVN
+GLPGTGKTTMLRDILASNVVERARRLSACENPFDALTERTHEWTGEGRMRRRARELRPEV
+VGFEMVVASANNAAVENLSEEIPQRSAIKDGRHVDADYFACLATAAVGGSGGGRGRPG
+>MOLHKGIG_02272
+MGVNGLPGTGKTTTLRDILASNVVERARRLSACENPFDALTERTHEWTGEGRMRRRAREL
+RPEVAGFEMVVASANNAAGESISEEIPQVESRIVV
+>NAFOICDF_00410
+MGDTRGRTQQDIVRFWQLQELFDPQPLPKLTPRTSPPFGKRVITWRAEDGDVALPWNRLA
+PPPPTTKGAAREWRHTLYLRIYALEDAYQTLHSAFPADADAYDERPGGRSAAAGALVDAD
+GRLIGGTGVLSSALWGIGRLCRGEGFDDSLVDGFEAAGEAFVDAADRAAGVPDDDAFGEQ
+PVLTAGMLVALIRLAQHSAGVEGMPALAGHEVRIASQVVSASSGDETPDIDFLNSFYLSD
+LHRVGEAIARGDVGPALDAYLTPDGDVDTQRRVDVVARPDIVDAGVEPARVPAGRWPAKT
+SYALARSQQFAVNRALNELGAEPGLMGVNGPPGTGKTTMLRDILAANVVERARKLAGFAD
+PSGAFTGRTLAWTGEGRRHRTVHELRPELTGFEMVVASANNAAVENISEEIPHRDAIKDS
+GRADADYFADLATAALGLGVENADEDGAPGACDGPAAEQPAAASSGAWGLVAARLGNKVN
+RARFRDAVLFGGASGGRGARGRGLDTLLKDWAASPSAPAQWTAAREAFHRALHEVDRGLT
+ERRDAAQRTVRTAAAREAVRAAERRLAELSRQRTAKWAGAEAIRRELSAAQAEAGRIRDA
+LDLHRDAKPGFWETITSFGVAGQQWRETYQPLLEAWSTADAGRAALAADTEAAERRLSEL
+EAQIVHLDGECARRRGDLADLEAAVRADEERFGGRHPSAVVDAQTRETTTPWLDEEMEKA
+RTELFLAALELHRAFIAAAARDLRPSFQAAMEVMAGAAPRDLEAEKRRAAWQVFFLLVPL
+VSTTFASFDRMFTGMGRESLGWLFVDEAGQASPQYAAGAIWRANRAVVVGDPLQLEPVVT
+IPVTVSRSLAKAHGVSSTWIAPEASVQRLADRVSRYGTTLPQGEDDVWVSSPLRVHRRCD
+DPMFALSNDLAYGGLMVSGVQRKGPEEDPFERTGDGEIFASSWMDTPARTPGTHLQPNQI
+ERVRRGIEACRRWGIPCTEIIAISPFREVADALRVLSDEFPGLTAGTIHTAQGREADVVF
+FVLGGAPDKPGARNWASSRVNLANVAVSRAKRRLYVIGDREAWSRHNYFRQIAEALPRAA
+EPDAGRER
+>MHAAABBN_01964
+MPAPSLGEEDKRAIPALQPSLSSSNVTAHEHTGHPQAARIDVVARADVVEAGGPGLMGVN
+GLPGTGKTTTLGDILASNVVERARRLSACENPFDALTERTHEWTGEGRMRRRVRELRPEV
+VGFEMVVASANNAAVENLSEEIPQRSAIKDSRNVDADYFAELAAALGGSRGEEDALGEDS
+LTSEQPGTSGLATAPMATAPTPPRSARRRPTRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001814.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001814.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9bc82ce45a0f9fd14ae39b49960c45eb5e493ca9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001814.fa
@@ -0,0 +1,17 @@
+>ACLBLIBL_00553
+MSPADPSPRLLARPPASPAAVAEAFEAAWNAADADALADLFAEDADFVTVLGVWWTRRRQ
+IRLDHARAFRWMFPESRLEMDEVRVRDLGDVAVVHAPWTMTGPGVGGEVGEATGTVGVRE
+AGGDGSGGGDGERTGVLLLVVRRDEAGAWEVVAAQNTDRSPEPRPRPADEDDLLAEVHPH
+PSAWLHPDDDGPASRLSARPRLGWAVHEPVPPLPLPNSPSPPLPLPQGELSCRWPV
+>MOLHKGIG_02193
+MSPADPTADVAAGPAGPAAVAEAFAAAWNAADADALADLFAEDADFVNVVGVWWTRRRQI
+RVNHALGFRWMFPASRLVLGQVRVRELGDVAVVHAPWTMTGQTAPDGDEAGERTGVLLLV
+VRRTEAGAWEAVAGQNTDSVPEAQTHLADDDGLAAVHYHPSAWIDPDDDPDGPEAC
+>MHAAABBN_01906
+MSPADPTADVAARPTGPAAVAEAFAAAWNAADADALAELFAEDADFVNVVGVWWRRRRQI
+RVNHALGFRWMFPHSRLELGRVRVRELGDVAVVHAPWTMTGQTAPDGDEAGERTGVLLLV
+VRRTETGAWEAVAGQNTDSVPGAQTHLADDEGLAAVHYHPSAWFDPDEDPDGPEAC
+>LFPAFLNI_02137
+MPPADPTADVAARPAGPAAVAEAFAAAWNAADADALAELFAEDADFVNVVGVWWTRRRQI
+RVNHALGFRWMFPASRLVLGQVRVRELGDVAVVHAPWTMTGQTAPDGDEAGERTGVLLLV
+VRRTEAGAWEAVAGQNTDSVPEAQTHLADDDGLAAVHYHPSAWIDPDDDPDGPEAC
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001817.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001817.fa
new file mode 100644
index 0000000000000000000000000000000000000000..01a6f4f6adca4b5f47294b10586a17edd925332e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001817.fa
@@ -0,0 +1,44 @@
+>ACLBLIBL_00580
+MSSAPPDPADASSGRGGPRPRRQSSLARRTGAGVVVILLITLTAFALFAGNTTRALTAES
+ASRNTTAAWTRAAEQLASLEAGTAFDAEPTAGDPQVPGTLGQPEGTVVALVSPADLEDHQ
+AGTLRGHRVGKAGESVPLDARQSHDIIHAIRGEPIGAPVDAAVSGEGYRFKALPMTSPGP
+WVGADQLLVVGVPTGALTAVSRRGLLMVVLGLSLTVVVTALAVFLWLRRGLAPLGEVAAM
+AERVAGMDLAHTGIDRRQTRMPKRLLQGPDEVVVVAEAMDRFTGAVEDALEERRRQEQQL
+RSFIADASHELRTPLASVRGYAEMIAMTEDLSETGRRSLDRVLHQAGRMSALVDDMLLLE
+RLESVSRGRAVGLAPSGEVPAADPVDLPEVLLEAVVDARAAWPDHQWVLDLPETLGEEGQ
+GCVTGDPAQLARLVGNLLSNGAKHTPAGTTVTTSLRIGRPLPHQVVVSVHDDGGGIPAEH
+RERLFERFARGASAGGPGREPSTGLGLAIVRSIARSHGGEASVASEAGWTRFDVVLPCAR
+WTARAQAEAAGRGGPEAPEGTGAPRE
+>MOLHKGIG_02172
+MSSGLPETAAVPSGHGSTRRRRPTSLARRIGAGVLLILMATILAYSFYAAGITKALLTES
+ASRDASEAWIRASEQLTAPSPGGGGDGGPGQGDLRVPGTLGQPEGTVVALVPLSGLEEHQ
+QDALIGHRVGDAGESVPLTAREAHDLLHALRDRPGGPMLDAVVGDVSYRVQAQTLTAPGP
+WVAADQVLVVGAPTGAMSDVTRQALLAVAVGLSVTVLTTAILVTLWLRRGLAPLREVAAV
+AERVAQVDMARAGLDPEDSRMPPRLLQGPDEVAVVAQALDRFTGSVEAALEQRRVQEQQM
+RRFMADASHELRTPLASVRGYAEMIAMTEELSATGRRSLDRVLFQADRMAALVDDMLLLE
+RLESVSRGRAMGLEPSEEVALAERVDLSEVVLEGVMDARAAWPDHTWVVDLPEGVEPGTQ
+RSVTGDRSQLARVVGNLLSNAAKHTPVGTTVTASVRQDQPRPGFMLVSVHDDGGGIPADR
+HATLFHRFVRGPGKGRTGPPGTEPSTGLGLAIVRSIARSHGGDVTVASEGGWTRFDVVVP
+CTPGRAGPGAAGSCCGSARAGRP
+>MHAAABBN_01886
+MSSGLPETAAVPSGHGSTRRRRPTSLARRIGAGVLLILMATILAYSFYAAGITKALLTES
+ASRDASEAWIRASEQLTAPSPGGGGDGGPGQGDLRVPGTLGQPEGTVVALVPLSGLEEHQ
+QDALIGHRVGDAGESVPLTAREAHDLLHALRDRPGGPMLDAVVGDVSYRVQAQTLTAPGP
+WVAADQVLVVGAPTGAMSDVTRQALLAVAVGLSVTVLTTAILVTLWLRRGLAPLREVAAV
+AERVAQVDMARAGLDPEDSRMPPRLLQGPDEVAVVAQALERFTGSVEAALEQRRVQEQQM
+RRFMADASHELRTPLASVRGYAEMIAMTEELSAAGRRSLDRVLFQADRMAALVDDMLLLE
+RLESVSRGRAMGLEPSEEVALAERVDLSEVVLEGVMDARAAWPDHTWVVDLPEGVEPGTQ
+RSVTGDRSQLARVVGNLLSNAAKHTPVGTTVTASVRQDQPRPGFMLVSVHDDGGGIPADR
+HATLFHRFVRGPGKGRTGPPGTEPSTGLGLAIVRSIARSHGGDVTVASEGGWTRFDVVVP
+CTPGRAGPGAAGSCCGSARAGRP
+>LFPAFLNI_02117
+MSSGLPETAAVPSGHGSTRRTQPTSLARRIGAGVLLILVATILAYSFFAAGITKALLAES
+ASRDASEAWIRASEQLTAPSPGGGGDARPGEGYLRAPGTLGQPEGTVVALVPLSGLEAHQ
+QDALTGHRVGDTGESVPLTAQEAHDLLHAVRDRPGGPMLDAVVGDVSYRVQAQTLTAPGP
+WVAADQVLVVGAPTGAMSDVARQALLAVAVGLSVTVLTTAILVTLWLRRGLAPLREVAAV
+AERVAQVDMARAGLDPEDSRMPPRLLQGPDEVAVVAQALERFTGSVEAALEQRRVQEQQM
+RRFMADASHELRTPLASVRGYAEMIAMTEELSAAGRRSLDRVLFQADRMAALVDDMLLLE
+RLESVSRGRAMGLEPSEEVALAERVDLSEVVLEGVMDARAAWPDHTWVVDLPEGVEPGTQ
+RSVTGDRSQLARVVGNLLSNAAKHTPVGTTVTASVRQDQPRPGFMLVSVHDDGGGIPADR
+HATLFHRFVRGPGKGRTGPPGTEPSTGLGLAIVRSIARSHGGDVTVASEGGWTRFDVVVP
+CTPGRAGPGAAGSCCGSARAGRP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001818.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001818.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0624441bd03b3224f1b3328248dccd82c7f3895
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001818.fa
@@ -0,0 +1,35 @@
+>ACLBLIBL_00602
+MATVSIGRPDSPVWGPFGARRLSLRIRLIVWISLAVVFGIDVVLAFSGTGVTAAEALPQL
+AGEYLLIGLIAQHAPLGVIAYAIAFTAGARWWDYEALSIVFAGAALMLGLSAQRGLLLLA
+GGLFAAWFVIAGPVLGSFSTAAAVAFAVSAALGVAAGLGLRWLARRFDSALRLAEERQTQ
+LEQAQRDERHRLALELHDVVGHGLTVIALQAGMLPTVTSPVQRTEVEQAIADTARQSLTD
+LRTMLGVLRGSAPGLGPAEDAEPPRPVRELVAEYRDRLTAAGFDVHVRLEAEAEVPDSLR
+HTLRRIVQEASTNVLRHAEPGGRVDVEIRHDGCETSVLVRSPLPARRRQEPAPHSGYGLA
+GMDERVRILGGRITHGPVDGSWVLDVTLPSQERAAQA
+>MOLHKGIG_02155
+MSTAAPAPARPTTATSRPPADSPLDSRLPAILRAEPVSRHMRIVLYVIVGLMVLGEILTL
+VLGPMVAAGLSADPELAAIFEEDGGLTGERREPLLRWVLFLASVLVTLLFGWQPTLAAVF
+VLLGSAFGLAGLVEADHAHLTPQAFSGGVILGAAMVTRYSHRVFVWFALGALILLTVAGE
+ALTDGTWADEDSLKGVMVVTLIVALCVAVPAFMIRRSRHRARDREAALRRAEEAAACAAE
+AERQRIAAELHDVVAHGLTVISMQAAMLPTQRDPEKRAASEKAIEQAARQSLVDLRRMLT
+ALRGSSRNAQTAEGDAVVDLPARLDEFEARLHAAGFAVERSLTELEELPRSLELTVLRVV
+QESVTNILKHAPRRGTVRLTSELEGADRLVLCIASPMDEGEPRRDRVVVAMASGFGLAGM
+RERVAVFGGTLMAGPLGGCWVVRAELPLR
+>MHAAABBN_01868
+MSIAAPAPARTTTATSPPPAESPLGSRLPAILRTEPVSRHTRIVLYVIVGLMVLGEILTL
+MLGPTVAAGLSADPELAGILEEDGGLTGEGREPLLRWVLFLASVLVTLLFGWQPTLAAVF
+VLLGCTFGLVGLVEADHAHLTPQAFSGGVVLGAAMVTRYSHRVFVWFALGALILLTVAGE
+VLTDGTWADEDSLKGVMVITLIVALCVAVPAFMIRRSRHRARDREAALRRAEEAAACAAE
+AERQRIAAELHDVVAHGLTVISMQAAMLPTQRDPDKRAAAEKAIEEAARQSLVDLRRMLT
+ALRGSSRNAQTAEGDAVVDLPARLDEFEAQLHAAGFAVERSLTELDELPRSLELTVLRVV
+QESVTNILKHAPRRGTVRLTSQLEGADRLVLCIASPMDEGEPRRDRVVVAMASGFGLAGM
+RERVAVFGGTLTAGPLGGCWVVRAELPLR
+>LFPAFLNI_02098
+MSIAAPAPARTTTATSPPPAESPLGSRLPAILRTEPVSRHTRIVLYVIVGLMVLGEILTL
+VLGPTVAAGLSADPELAALLEEDGGLTGEGREPLLRWVLFLAGVLVTLLFGWQPTLAAVF
+VLLGSAFGLVGLVEADHAHLTPQAFSGGVVLGAAMVTRYSHRVFVWFALGALILLTVAGE
+VLTDGSWADEDSLKGVMVITLIVALCVAVPAFMIRRSRHRARDREAALRRAEEAAACAAE
+AERQRIAAELHDVVAHGLTVISMQAAMLPTQKDPEKRAAAEKAIEQAARQSLVDLRRMLT
+ALRGSSRNAQTAEGDAVVDLPARLDEFEARLHAAGFAVERSLTELDELPRSLELTVLRVV
+QESVTNILKHAPRRGTVRLTSQLEGADRLVLCIASPMDEGEPRRDRVVVAMASGFGLAGM
+RERVAVFGGTLTAGPLDGCWVVRAELPLR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001820.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001820.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ba7e46c24990007a08fb11051d18f84bb65d07b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001820.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00615
+MTAMTLTPVSPEELLERTEAGTAFVIDVRTPAEFAVEHIAGSYNVPLDTLKEHVRDVAER
+LHGDVVLVCASGARASDAQQRLTGAGFTEAAVLSGGIGSYAQAGGDVVRRGTGWGMERQV
+RMTAGSLVLAGVIASQIGSKRLALLAGGVGGGLVYSALSNTCAMVSVLDRMPWNRQDRER
+PASEVLGALPAGAARKA
+>NAFOICDF_00539
+MTVNVTPITPADLQRELAQHPDTVVIDVRTPGEFEAQHIAGSYNVPLDLIQEHAAEVAAR
+LDGKAVLVCQSGSRAGTALDRLAEAGFTQARVLRGGIGAYAQAGGRVSGTGSRWSMERQV
+RMTAGSLALAGAVASQLGPKRFGLVPAAIGAGLSWSAVSNTCAMASVLSTMPWNRPTEQR
+SADQVLGALPGADADGARG
+>MHAAABBN_01859
+MSVTLSPVAPRDLKAELAARPDAVVLDVRTPGEFETEHIAGSYNVPLDLLQEHADEVAAR
+LDGTAVLVCQSGSRAGTAQDRLAQAGFTSARVLQGGISAYAEAGGEVVRSGNRWSMDRQV
+RMTAGSIALVGAVASQVGSKRFGLIPAAIGAGLSFSAVSNTCAMASVLAKMPWNRPAQER
+SAGDVIGRIPTGAGKRS
+>LFPAFLNI_02089
+MSVTLSPVAPRDLKAELAARPDAVVLDVRTPGEFETEHIAGSYNVPLDLLQEHADEVAAR
+LDGTAVLVCQSGSRAGTAQDRLAQAGFTSARVLQGGISAYAEAGGEVVRSGNRWSMDRQV
+RMTAGSIALVGAVASQVGSKRFGLIPAAIGAGLSFSAVSNTCAMASVLAKMPWNRPAQER
+SAGDVIGRIPTGAGKRS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001823.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001823.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b712c773fa6d7ff5a0b588fe9fa6eb60e87a7bb7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001823.fa
@@ -0,0 +1,24 @@
+>ACLBLIBL_00664
+MPREAHGPVSAAGLAREAAILAGAGAAILLQVAHRPVAAGVAAHSRFTEDPMRRLRHTLG
+YIYAVTLPEAAGARDAVVARVRAAHAPVRGADHEGRPYNAADADAQLWVAATLYWAGEQV
+RRRLWGALDPADADRLYRGFAPLATSLEVPAAAWPADRAAFAAYWDARIAGLEVTDDARA
+VAADLFSGRGVPAPLRAALPLARFVTAGLLPARARAGLGWDWSRRDSIREARLWVLTRTL
+YRPLPAAVRGVVVRGILRGLRRMSEAGGPAS
+>MOLHKGIG_02116
+MRPDRHSAPTSAAALAREAAILAGAGAAILLQVAHRPVGAGVAGHSRFTEDPMRRLRHTL
+AYIYAVTLPEAAPARDAVVDRVRAAHGSVRGVDAGGRPYDAADPDAQLWVAATLYAMGEQ
+VRRRMWGALDAEDADRLYRGYAPLATSLEVPASAWPVDRAAFADYWDDRVARLEVTDDAR
+RVAADLFSGQGVPAPLRAAMPLARFVTAGLLPGRVRAGLGWSWTGRDSVREARLWGLART
+LYRPLPATVRGVVVRWVLRGLPRTRKPRGAVDVEATRREVRPVWENGADV
+>MHAAABBN_01824
+MRPDRHSAPTSAAALAREAVILAGAGAAILLQVAHRPVGAGVAVHSRFTEDPMRRLRHTL
+AYIYAVTLPEAAPLRDAVVDRVRAAHRPVRGLDAGGHPYDAADPDAQLWVAATLYAMGEQ
+VRRRMWGALDAEDADRLYRGYAPLATSLEVPASAWPVDRAAFADYWDDRVARLEVTDDAR
+RVAADLFSGQGVPAPLRAAMPLARFVTAGLLPGRVRAGLGWSWTGRDSVREARLWGLART
+LYRPLPATVRGVVVRWVLRGLPRMPELGDAVAVRATRRDVRSVWENGGDV
+>LFPAFLNI_02054
+MRPDRRSAPTSAAALAREAVILAGAGAAILLQVAHRPVGAGVAVHSRFTEDPMRRLRHTL
+AYIYAVTLPEAASLRDAVVDRVRAAHRPVRGVDAGGHPYDAADPDAQLWVAATLYAMGEQ
+VRRRMWGALDAEDADRLYRGYAPLATSLEVPASAWPVDRAAFADYWDDRVARLEVTDDAR
+RVAADLFSGHGVPAPLRAAMPLARFVTAGLLPGRVRAGLGWSWTGRDSVREARLWGLART
+LYRPLPATVRGVVVRWVLRGLPRTRKPRGAVDVEATRREVRPVWENGADV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001827.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001827.fa
new file mode 100644
index 0000000000000000000000000000000000000000..53a9ea984df37dd7e6d86fee923377b3c5f347a4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001827.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_00682
+MDPQPRLAPGTHHDVAALAPASPVADAAPEDQAAPGDPASPVAPAFAPSARSQVPPFTVM
+TILGRVAELRAAGRDVISLCAGEPGGGAPPTVSAAAAEVHASGSPLTYTPALGLPELRAA
+VAGHYRRWYGIDVRPEQVAITTGSSGAFMLGFLAAFSPGDRVVLPRPGYPAYRNILAALG
+CEVVEVGVDASTRYQPTVAHLEAALAEGPVAGLVLASPSNPTGTMVDADELAALASWCEA
+HGVRLVSDEIYHGIVHPRSGDDDGGPAGGGAAGGAPGASGAEGSRFPHESVGACAWATSR
+TAMVISSFSKYWGMPGWRLGWMLMPEDLAGAIDGLAGSVALCPPAAAQRAAVEAFGEDAY
+AFCEEQAGGFTATRGVVLAALPRLGWADAAPADGAFYLWARLGERQLAEFGDAVAYCTAL
+LEEAGVALTPGADFDGVHGGEFVRMSYAADAGAVAEALERIAAWHAARGLA
+>MOLHKGIG_02097
+MHRPSRSSTAAPAFAPSAPAPTAAPAFAPSVRSQVPPFTVMSILGRVAALRAAGHDVVSL
+CAGEPGGGAPPAVDAAAAAVHASGRALTYTPALGLPELRAAVAGHYRRWYGLDVRPEQVA
+ITTGSSGAFMLGFLAAFSPGDRVLLPRPGYPAYRNILTALGVEVVDVDVDAGTRYQPTVA
+HLEAALAEGPVAGLVLASPANPTGTMVSAAELAELARWCEERGVRLVSDEIYHGIVHTDG
+QGPGACAWRTSRTALVVSSFSKYWGMPGWRLGWMLMPDDLATAVDGLAGSVALCPPAAAQ
+EAAVHAFTEESYAFCAEQAGGFTATRGVVLAALPRLAWADAAPADGAFYLWARLASGMLA
+EFGSAVGYCAALLEEAGVALTPGDDFDAVHGPESVRLSFAAGPDAVHEALERIAAWHAAR
+GLA
+>MHAAABBN_01804
+MRRPSRSSTADPASTAAPAPTATPAFAPSARSQVPPFTVMSILGRVAELRAAGHDVVSLC
+AGEPGGGAPPAVDAAAAAVHASGRAFTYTPALGLPELRTAVAGHYRRWYGLDVRPEQVAI
+TTGSSGAFMLGFLAAFPPGDRVLLPRPGYPAYRNILTALGVEVVDVDVDAGTRYQPTVAH
+LEAALAEGPVAGLVLASPANPTGTMVSADELAELARWCEERGVRLVSDEIYHGIVHTDGE
+GLGACAWRTSRTALVVSSFSKYWGMPGWRLGWMLMPDDLAAAVDGLAGSVALCPPAAAQE
+AAVHAFSEESYAFCAEQAGGFTATRGVVLAALPRLGWADAAPADGAFYLWARLAPGMLAE
+FGSAVGYCAALLEEAGVALTPGDDFDAVHGPESVRLSFAAGPDAVHEALERIAAWHAARG
+LA
+>LFPAFLNI_02037
+MRRPSRSSTADPASTAAPAPTATPAFAPSARSQVPPFTVMSILGRVAELRAAGHDVVSLC
+AGEPGGGAPPAVDAAAAAVHASGRAFTYTPALGLPELRTAVAGHYRRWYGLDVRPEQVAI
+TTGSSGAFMLGFLAAFPPGDRVLLPRPGYPAYRNILTALGVEVVDVDVDAGTRYQPTVAH
+LEAALAEGPVAGLVLASPANPTGTMVSADELAELARWCEERGVRLVSDEIYHGIVHTDGE
+GLGACAWRTSRTALVVSSFSKYWGMPGWRLGWMLMPDDLAAAVDGLAGSVALCPPAAAQE
+AAVHAFSEESYAFCAEQAGGFTATRGVVLAALPRLGWADAAPADGAFYLWARLAPGMLAE
+FGSAVGYCAALLEEAGVALTPGDDFDAVHGPESVRLSFAAGPDAVHEALERIAAWHAGRG
+LA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001829.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001829.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7dc1ee6357a6c281064c798ef6e73664574e8662
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001829.fa
@@ -0,0 +1,16 @@
+>ACLBLIBL_00688
+MITHPALQQPVIDAVDIRSVAEFYRELLGLHYRAGDELADGREPDSADWLVLLDDDGRRV
+LTFQRTEELKPSTWPSPEVPMQLHLDFTVPDRDSLDAAHDHALRLGGRLVQDRSDDEDEP
+LYVFADPAGHPFCVFVG
+>MOLHKGIG_02090
+MVTRPVLQQPVVDAVDIRSVAEFYRELLGLHYRTGDELADGREPDSADWLVLLDDDGRRV
+LTFQRTEELKPSTWPSPEVPMQLHLDFTVPDRESLDAAHDHALRLGGRLVLDRSDDEDEP
+LYVFADPAGHPFCVFVG
+>NAFOICDF_00604
+MVSRPVLQQPVIDAVDIRSVADFYRELLGLHYRTGDELADGREPDSADWLVLLDDDGRRV
+LTFQRTEELKPSTWPSPEVPMQLHLDFTVPDRDSLDAAHDHALRLGGRLVLDRSDDEEEP
+LYVFADPAGHPFCVFVG
+>MHAAABBN_01798
+MVTRPVLQQPVIDAVDIRSVAEFYRELLGLHYRAGDELADGREPDSADWLVLLDDDGRRV
+LTFQRTDELKPSTWPSPEVPMQLHLDFTVPDRDSLDAAHDHALRLGGRLVQDRSDDEDEP
+LYVFADPAGHPFCVFVG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001831.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001831.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26028cff85143970f3587e47ccb062552d677779
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001831.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00702
+MARFSAVLDACVLVPIAQADTLLHLAEAGLYRPVWSGRILDETVRTLEAMHPDMRASGAA
+RHRAGVMDAAFDDARVEGWEQLVPGIDLPDPDDRHVVAAAIQGRADLIVTANLKDFPREV
+VGSFDIEVQSPDEFFMNQLDLDPARVMTALAAQASATRNPPLTVRDVLERLVPCGAPLFA
+EAARAQLWRVDVERP
+>NAFOICDF_00612
+MARFSAVLDACVLVPIAQADTLLHLAEAGLYRPVWSGRILDETVRTLETMHPDMRASGAA
+RHRAEVMDAAFDDARVEGWEQLVLGIDLPDPDDRHVVAAAIQGRADLIVTANLKDFPREV
+VESFDIEVQSPDEFFMNQLDLDPARVMTALAAQAGATRNPPLTVSDVLERLVPCGAPLFA
+EAARAQLWRVDAERP
+>MHAAABBN_01786
+MARFSAVLDACVLVPIAQADTLLHLAEAGLYRPVWSGRILDETVRALEAMHPDMRASGAA
+RHRAGVMDAAFDDARVEGWEQLVPGIDLPDPDDRHVVAAAIQGRADLIVTANLKDFPREV
+VESFDIEVQSPDEFFMNQLDLDPARVMTALAAQAGATRNPPLTVRDVLERLVPCGAPLFA
+EAARAQLWRVDVERP
+>LFPAFLNI_02020
+MARFSAVLDACVLVPIAQADTLLHLAEAGLYRPVWSGRILDETVRALEAMHPDMRASGAA
+RHRAGVMDAAFDDARVEGWEQLVPGIDLPDPDDRHVVAAAIQGRADLIVTANLKDFPREV
+VESFDIEVQSPDEFFMNQLDLDPARVMTALAAQAGATRNPPLTVRDVLERLVPCGAPLFA
+EAARAQLWRVDVERP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001834.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001834.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1bd39ff271a692314bb42b27e8bf0f29ecec325d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001834.fa
@@ -0,0 +1,29 @@
+>ACLBLIBL_00734
+MASKDWARKISDAPEGARRQWRADRALRAPMRSPGRPQPSREVQRQFWRVIATGVTTVEA
+SLSVGVSWPVGARWFRHAGGMTPLPLAEPTGRYLSFAEREEIAILHAQGHGVRQIGRALG
+RDPGTISRELRRNCATRSGGKEYRATVAQWKAQQAARRPKPAKLATNQRLHDYVQARLNG
+VVLGPDGVAVQGPVGPGFKGRKMKPRRADRRWSTAWSPEQISHRLRLEFPDDVSMRISHE
+AIYQSLFVEGRGALKRELVGCLRTGRALREPRARTRNKPQGHVTEDVVFSKRPPEAADRA
+VPGHWEGDLIIGLQRSAIGTLAERKSRATILVHLPRLQGWGEQPPVKNGPSLGGYGAAAM
+SAALTKAMTGLPQQLRQTLTWDRGGELAGHAQFTMATGTRVFFADPHSPWQRPTNENMNG
+LLRQYFPKGTDLSRWSADDLAAVAYTLNNRPRKVLGWKTPAEVFAEQLSSLETSGVATTT
+>ACLBLIBL_00746
+MRISHEAIYQSLFVEGRGALKRELVGCLRTGRALREPRARTRNKPQGHVTEDVVFSKRPP
+EAADRAVPGHWEGDLIIGLQRSAIGTLAERKSRATILVHLPRLQGWGEQPPVKNGPSLGG
+YGAAAMSAALTKAMTGLPQQLRQTLTWDRGGELAGHAQFTMATGTRVFFADPHSPWQRPT
+NENMNGLLRQYFPKGTDLSRWSADDLAAVAYTLNNRPRKVLGWKTPAEVFAEQLSSLETS
+GVATTT
+>ACLBLIBL_00749
+MASKDWARKISDAPEGARRQWRADRALRAPMRSPGRPQPSREVQRQFWRVIATGVTTVEA
+SLSVGVSWPVGARWFRHAGGMTPLPLAEPTGRYLSFAEREEIAILHAQGHGVRQIGRALG
+RDPGTISRELRRNCATRSGGKEYRATVAQWKAQQAARRPKPAKLATNQRLHDYVQARLNG
+VVLGPDGVAVQGPVGPGFKGRKMKPRRAEVKSLEVV
+>MOLHKGIG_00625
+MASKDWARKISDVPEGTRRQWRADRALRAPMRSPGRPQPSREVQRQFWRVIATGVTTVEA
+SLTVGVSWPVGARWFRHAGGMTPLSLAEPTGRYLSFAEREEIAILHAQGQGVRQIARTLG
+RDPGTISRELRRNCATRSGKQEYRATVAQWKAQEAARRPKPAKLATNQRLHDYVQARLNG
+VVLGPDGVAVPGPVGPGFKGRKMKPRRADRRWSTAWSPEQISHRLRLEFPDDVSMRISHE
+AIYQSLFIQGRGALKRELVACLRTGRALREPRARTRNKPQGHVTEDVVFSKRPPEAADRA
+VPGHWEGDLIIGTERSAIGTLAERKSRATILVHLPRLEGWGERPPVKNGPSLGGYGAEAM
+TAALIKAMATVPEQLRQSLTWDRGKELAGHVQFTMATGTKVFFADPHSPWQRPTNENTNG
+VLRQYFPKGTDLSRWSAEDLAAVAYTLNNRPRKVLDWKTPAEVFAEQLRSLSTHGVATTG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001842.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001842.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f4f79bcfca94c9f1e49e10c84e1f714d6976d8f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001842.fa
@@ -0,0 +1,24 @@
+>ACLBLIBL_00845
+MAQPTVTTTLLKAAKSPARVLLVGAGLGTGVHALWSLAAQRMAEDTLVIGYDLPGHGASA
+PHADPYTIAELADAVVAAVARLKDEGAIPADVPLAYAGVSLNGCVALQLALEHADVVSGV
+AVVCSAAKIGEAKAWHERAELVEKAGTPTMVAGSAERWFAPGFIERHPERTTDLLHTLQE
+ADRHSYARLCEALAGFDVRERLGEIRVPVLTVHGAHDAVTPPAAGEEIAAAVPGTTVVAL
+DDAAHQAPLEQPVATAEALAAFLTTVQEAAK
+>NAFOICDF_00778
+MTTPEVAVTLLKPAEAPTRVLVAGAGLGTGVEALWSLAARELPADTLVVGWDLPGHGASA
+PHDAPLTVADLADAVAAAVGRLRAEGTIPADVPVHYAGVSLNGCVALQLALDHADTFASA
+TVICSAAKIGEKDAWLERAELVESAGTPTQVEGSSKRWFAEVFIAEHPERATGLLHTLQQ
+ADRHSYARLCEALAEFDVRGRLGEDTVPLMTIHGVEDQVTAPAAGEEIAAAVPGTVVHAF
+EHTAHQAPLEQPERTAEALAAFLAR
+>MHAAABBN_01707
+MSTPRVTTTLLKPAQDPARVLVVGAGLGTGVQALWSLAAQQLPEDTVVVGYDLPGHGASE
+PHAEPFSMAELADAVVAAVQALQEDGTVPADLPVHFAGVSLNGCVALQLALDHADTVSGV
+AVICSAAKIGEAGSWRERAELVERAGTPTLVEGSAQRWFADGFIAAHPERTTGLLHTLQE
+ADRHSYARLCEALADFDVRGRLGEIAVPVLTIHGVADQVTPPSAGEEIAAAVPGTVTHVF
+DETAHQAPLEQPERTAAALAAFPAR
+>LFPAFLNI_01935
+MSTPRVTTTLLKPAQDPARVLVVGAGLGTGVQALWSLAAQQLPEDTVVVGYDLPGHGASE
+PHAEPFSMAELADAVVAAVQALQEDGTVPADLPVHFAGVSLNGCVALQLALDHADTVSGV
+AVICSAAKIGEAGSWRERAELVERAGTPTLVEGSAQRWFADGFIAAHPERTTGLLHTLQE
+ADRHSYARLCEALADFDVRGRLGEIAVPVLTIHGVADQVTPPSAGEEIAAAVPGTVTHVF
+DETAHQAPLEQPERTAAALAAFPAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001843.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001843.fa
new file mode 100644
index 0000000000000000000000000000000000000000..787c9ff6611f07ae8f43627e8c77fa8dd1b29874
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001843.fa
@@ -0,0 +1,16 @@
+>ACLBLIBL_00846
+MSGGRTEHAGGADAGQTPLGHQMERTSQEILDAGMAVRREVLGDAHVDRAEATKDATTDD
+FQNLISRYAWGTIWTRPGLDRRMRSAVTITAMVSGGYWEECAMHLRAALRNGLSRDEIKE
+ILLQAAIYSSVPAANVAFKLAQEVFAQVDEDLAAGRPL
+>NAFOICDF_00779
+MGEQPIGHDMDRTSREVHDAGMAVRREALEDAHVDRAEANKDAATEDFQNLITRYAWGTV
+WTRPGLDRRMRSAVTITAMVAGGYWDECAMHLRAALRNGLSREEVQEILLQTAVYCSVPA
+ANIAFTLAQRVFAEVDADLAAGRPL
+>MHAAABBN_01706
+MSAEQPIGHDMDRTSQEVLDAGMAVRREVLGDAHVDRAEARKDATTEDFQNLITRYAWGT
+IWTRPGLDRRMRSAVTISAMVAGGYWDECAMHPRAALRNGLTREEIQEILLQTAVYASVP
+AANIAFKLAQEDADLAEGRPL
+>LFPAFLNI_01934
+MSAEQPIGHDMDRTSQEVLDAGRAVRREVLGDAHVDRAEARKDATTEDFQNLITRYAWGT
+IWTRPGLDRRMRSAVTISAMVAGGYWDECAMHPRAALRNGLTREEIQEILLQTAVYASVP
+AANIAFKLAQEDADLAEGRPL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001846.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001846.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af05e9227af6a466dc3f65bdf59d488a49f63998
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001846.fa
@@ -0,0 +1,24 @@
+>ACLBLIBL_00850
+MLEFVDTAAQAVSQVTDGATVLIGGFGNAGQPMELIDALLESGATGLTVVNNNAGQADAG
+LALLIKERRVAKIICSFPRQSDSWHFDEAYRAGEIELELVPQGNLAERLRAGGAGIGGFF
+TPTGYGTQLAEGKEVREIDGRHYVLESPIRGDVALIKAYAADRHGNLVYRKTARNFGPIM
+AAAAEHTVVQVDEVRDEPIDPEHVITPGIYTDVIVRIETESGAKEREEREALAAGKPKPC
+AATKTAAEKAAEGK
+>NAFOICDF_00787
+MLEFVETAAEAVAQVRDGQTVLIGGFGNAGQPMELIDALLESGATGLTVVNNNAGQADAG
+LALLIKERRVAKIICSFPRQSDSWHFDEAYRAGEIELELVPQGNLAERLRAGGAGIGGFF
+TPTGYGTQLAEGKEVREIDGRHYVLESPIKGDVALIKAYAADRHGNLVYRKTARNFGPVM
+AAAAATTIVQVDEISEEPLNPEHVITPSIYVDTVVRIQTESGVKEREALAAGKPKPCLAT
+ETAAGQAAEGK
+>MHAAABBN_01701
+MLEFVDTAAQAVSRITDGATVLIGGFGNAGQPMELIDALLESGATGLTVVNNNAGQADAG
+LALLIKERRVAKIICSFPRHSDSWHFDEAYRAGEIELELVPQGNLAERLRAGGAGIGGFF
+TPTGYGTQLAEGKEVREIDGTHYVLEAPIRGDVALIKAYAADRHGNLVYRKTARNFGPVM
+AAAAATTIVQVDEVREEPIDPEHVVTPGIYTDTVVRIDTESGEKERAERAALAEGRPKPC
+AATTTAAEPAAEGK
+>LFPAFLNI_01929
+MLEFVDTAAQAVSRITDGATVLIGGFGNAGQPMELIDALLESGATGLTVVNNNAGQADAG
+LALLIKERRVAKIICSFPRQSDSWHFDEAYRAGEIELELVPQGNLAERLRAGGAGIGGFF
+TPTGYGTQLAEGKEVREIDGTHYVLEAPIRGDVALIKAYAADRHGNLVYRKTARNFGPVM
+AAAAATTIVQVDEVREEPIDPEHVVTPGIYTDTVVRIDTESGEKERAERAALAEGRPKPC
+AATTTAAEPAAEGK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001849.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001849.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d427aa344b8003faf6f3a83304d1d17484a37df8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001849.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_00854
+MAWSDGLRDTLRFWPLVLVAFVHAVASCSLLGLSFQQASEAQEIGRHLQRWEQLGAASLR
+GFYLAGPGDLEGGGAAPGDSQQEPPEPDFSAGSRADSADDGRRTAALLALLADPHRTAYT
+MDPYGDRFGDDLPGALLVTEDFFAGSGLDETMSPTGQSSHRDAGGTAAPYAVLGSDSSAK
+DPYALTAGGVLPPTTRVQFQDAMIPVTGRLAPGATALDPMMGSVPLDEAVLVVVPPSMLA
+SLYPPDALEALLLRTIVLGQDAVPALDAAGRALETDALLVTAEPLTPQSSALLQSLSASS
+RTLLVLFGAAVLGAVVSLFGVLGVLARALAPTWRIAAMVGAARWQAAVRIIVPVLFAWVL
+PAAVGLTAGASALPGPPSTGLTSTALIAVMAIGAVATLSSWRALAATFGRRPRRRPTKET
+A
+>NAFOICDF_00791
+MSTRALAVALADGLNDAARFWPLILGAFLHAVVSCLLLGLSFQQVSEAGEVSAHLHRWEQ
+QGAASLHGIYLAGVSARPAAEGMTPTLQDGLDETPVLDPEGEAGAASRTAGLLSLLEDPQ
+RLAYTMDPYGDRFGDDLPGAMVVTEDFLRATGVDDSMTPTGAAVPRDSDGAPAPYAVLGS
+ASRAKDPHALLVDGAPPPTTRVQFQGAMIPVVGRLAQGATTLDPMMGSVPLDEAALIVLP
+AASLPGLYPAEELEALLLRTVVLGPDAVPVLDASARPFESERLLVAAQPLTAESSGLLQS
+LTSSSRTLVLLFGSAVLGAVVSLFGALGVLARALAPTWRIAAMVGAARWQAAVRIAVPVL
+LAWVLPAGLGLLAGAAAVPGPSPTALAAVALALVLGVGCWAALSSWRALAATFGPRRRTP
+TRTTTKEAA
+>MHAAABBN_01697
+MAWSEGLRDTLRFWPLVLVAFVHAVASCSLLGLSFQQASEAQEVDRHLQRWEQLGAASLR
+GFYLAAPGHLEGGGAAPGESQQEPPEPDLSADSKAASADDGRRAAALLALLEDPHRTAYT
+MDPYGDRFGDDLPGALLVTEDFFAGSGLAAAMSPTGQSPHRDADGTAAPYAVLGSDSSAK
+DPYALTVGGVLPPPTRVQFQDAMIPVTGRLAPGATALDPMMGSVPLDGAVLVVVPPSALA
+SLYPPDALEAILLRTIVLGQDAVPALDAAGRALETDALVVNAEPLTPQSSALLQSLSASS
+RTLLVLFGAAVLGAVVSLFGVLGVLARALAPTWRIAAMVGAARWQAAVRIIVPVLFAWVL
+PAAVGLTAGASALPGPPPTGLTSTALIAVMAIGAVATLSSWRALAATFGRRPRRHRPTKE
+TARASSKSTTWTRRSSPAGRRCPSSGGPLCWFRPVRCTPSPGLPGPGNPPCCGSSRAWTP
+RTRVASCSGANLSRSRGAGAGTGIGTSGAASSCRTSPSWSTPPHWRT
+>LFPAFLNI_00736
+MMAAMRAVADGLRDLFDTPGLLFLSLLHTTVASVVFGLALGVAGGVTTALEVLEDAESSG
+LVTARILDPAVTTDLHPRAVDTVSRAFAAHVDGVDPRAFLVTDAIGIEDPRLQGAVIATP
+GLAREFGAAAAVSPAEGVYFAPAAITSGGPGGTVYVGSTPHSYAGPLPGDAAAPRADGSL
+WPLGESPVIVTSTTTMAGLIEPAQLAAVYGSVVARQDAASEVRAALDVLEDETGVVAELA
+PIASARSPIAREARGAALMVTAYTAGLASAVVTVVSLLTTVTRRLTPTWLAHLTVGAPRR
+LIRLRIATSVAAVWGIPAVLGSLLGLGIASEAGGLRPAPAVVVVGLAVVLAIAAACTRHP
+LRQLHRAVRTAALVEGTV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001851.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001851.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3544b31cec3e4c2bcfc46e5b9480745f7bdad612
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001851.fa
@@ -0,0 +1,16 @@
+>ACLBLIBL_00870
+MMAWIDGLPLLWSIGFFWMLAILRTLIVFSLGRGLASGVERTRWFARVMEGPVYVRAQRF
+IQRHGVWAIPFCYLTVGIQTAVIGSAGVARMPWRRFLPAAALGTFLWGVVYGTVGMAVVW
+AVIGAALGEGRGVLALVLILAAVAAFVVWRRRRTLRQHGAG
+>MOLHKGIG_01987
+MMAWIDGLPLLWSIGFFWMLAILRTLIVFSLGRGLASGVERTRWFARVMEGPVYVRAQRF
+IQRHGVWAIPFCYLTVGIQTAVIGSAGVARMPWRRFLPAAALGTFLWGVVYGTVGMAVVW
+AVIGAALGEGRGVLALVLILAAVAAFVVWRRRRTLRRHGAG
+>MHAAABBN_01681
+MMAWIDGLPLLWSIGFFWMLAILRTLIVFSLGRGLASGVERTRWFARVMEGPVYVRAQRF
+IQRHGVWAIPFCYLTVGIQTAVIGSAGVARMPWRRFLPAAALGTFLWGVVYGTVGMAVVW
+AVIGAALGEGRGVLALVLILAAVAAFVVWRRRRTLRRHGAG
+>LFPAFLNI_01913
+MMAWIDGLPLLWSIGFFWMLAILRTLIVFSLGRGLASGVERTRWFARVMEGPVYVRAQRF
+IQRHGVWAIPFCYLTVGIQTAVIGSAGVARMPWRRFLPAAALGTFLWGVVYGTVGMAVVW
+AVIGAALGEGRGVLALVLILAAVAAFVVWRRRRTLRRHGAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001853.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001853.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f78acc1cf354c60fb567fa70a1541bfbd9abc16b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001853.fa
@@ -0,0 +1,13 @@
+>ACLBLIBL_00892
+MSELDELDFVAVEIHTAGTDPASVCAVDMALVRGGEIVAAERWPVRPPTGPTSFSRLHTQ
+LHGVDEAAVADAPEWPEVAAQLDLLGEHLPFVASGADRDRGAYEAATRATGGTPQAHEWR
+DALALVGRLRPDVDPPRIATAAQALGVPDGARPAGAGSEAVRTAEVVLALARQSGRGTVR
+RLWSEAAPPTPDEPIIPESLRRRHATEPSVPPAGAHRWAPPAPAPAPASAAPAGRGGGVG
+WKLAGTAMVGIALGAALFFVASVAVIMEYLEDGRGSDATVGMGIAALSAFLAWWFGKTGV
+DWIRRQDG
+>MOLHKGIG_01967
+MSELDELDFAALSAFLAWWFGKTGVDWIRREDG
+>MHAAABBN_01661
+MSELDELDFAALSAFLAWWFGKTGVDWIRREDG
+>LFPAFLNI_01893
+MSELDELDFAALSAFLAWWFGKTGVDWIRREDG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001856.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001856.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24e86548ea5a6ec757b395bb45f972d93d3abda2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001856.fa
@@ -0,0 +1,28 @@
+>ACLBLIBL_00903
+MAHPKTLQVFLMDGVPTGRLKCTLDNWTGLVYVVPRTSLNADGHPEAFEGTGVYLLLGQD
+ADSGDDVVYVGQAVGRANGNGMVGRIREHVRKEAHDFWNRAILLSTLGDTFGPTEVTYLE
+HFFHQAASTTGRFTVDNAVAPSQGNVTEEKKAELEEYADKAKILISALGHRVFESADGSH
+AVVAAGRTTQAPEAVPERTLFTMTVNGVGAQGHPTPDGFVVLRGSGLMEGLRPSAPAGVR
+ASRERFAGHIGADGVLIEDVSFTSSSAAAGFVAGGSMSGPSSWRAPDGRTLGEVEAASAK
+TVPIEDDA
+>NAFOICDF_00842
+MAHPKTLQVFLMDGVPTGRLKCTLDNWTGLVYVVPRTSLNADGHPEAFEGTGVYLLLGQD
+ADSGDDVVYVGQAVGRANGNGMVGRIREHVRKEAHDFWNRAILLSTLGDTFGPTEVTYLE
+HFFHQAASTTGRFTVDNAVAPSQGNVTEEKKAELEEYADKAKILISALGHRVFESADGSH
+AVVAAGRTTQAPEAVPERTLFTMTVNGVGAQGHPTPDGFVVLRGSGLMEGLRPSAPAGVR
+ASRERFAGHIGADGVLIEDVSFTSSSAAAGFVAGGSMSGPSSWRAPDGRTLGEVEAASAK
+TVPIEDDA
+>MHAAABBN_01645
+MAHPKTLQVFLMDGAPTGRLKCTLDNWTGLVYVVPRTSLNADGHPEAFEGTGVYLLLGQD
+ADSGDDVVYVGQAVGRANGNGLVGRIREHVRREAHDFWNRAILLSTLGDTFGPTEVTYLE
+HYFHQAATTAGRFTVDNAVAPSQGNVTQEKRAELEEYADKARLLISALGHRVFESADGSH
+AAAAAGRATQAPEAAPKRTLFTMTVNGVRAQGHPTPDGFVVLRGSGLMEGLRPSAPPGVR
+AGRERFADHIGADGVLTEDVSFTSSSAAAGFVAGGSMSGPSSWRAPDGRTLGEVEAASAA
+PEPMEDDA
+>LFPAFLNI_01875
+MAHPKTLQVFLMDGAPTGRLKCTLDNWTGLVYVVPRTSLNADGHPEAFEGTGVYLLLGQD
+ADSGDDVVYVGQAVGRANGNGLVGRIREHVRREAHDFWNRAILLSTLGDTFGPTEVTYLE
+HYFHQAATTAGRFTVDNAVAPSQGNVTQEKRAELEEYADKAKLLISALGHRVFESADGSH
+AAAAAGRATQAPEAEPKRTLFTMTVNGVRAQGHPTPDGFVVLRGSGLMEGLRPSAPPGVR
+AGRERFADHIGADGVLTEDVSFTSSSAAAGFVAGGSMSGPSSWRAPDGRTLGEVEAASAA
+PEPMEDGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001868.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001868.fa
new file mode 100644
index 0000000000000000000000000000000000000000..356097de6e9dc7ab72992ea5f03b055d4efb5ee1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001868.fa
@@ -0,0 +1,18 @@
+>ACLBLIBL_00982
+MAAKKNDAAFTVPGLALKDGHRVAEILQGRLHALNDLQLTLKHAHWNVVGPGFIGVHEML
+DPQIETVRAMVDVVAERIATLGVSPEGTPGALVAARTWDDYALGRASTLEHLAALDLVYD
+GVVTDHRAAIETVGELDPVSEDMLIGQVAELELFQWFMRSFLTTVDGDLSHAGATREIVA
+AARVSGAQKAPAPKKGAAKKAPAKKK
+>MOLHKGIG_01877
+MAEKNAAEYTVPGLSLSTGRRTAEILQGRLHALNDLQLTLKHAHWNVVGPGFIGVHEMLD
+PQIELVRGMVDVVAERIATLGVSPAGTPGALVAARTWDDYTLGRASTLEHLAALDLVYDG
+VVTDHRAAIDATEDLDPVTQDILIDQVAQLELFQWFMRSFLTTDDGRLSSAGTTTEAAAA
+GRVKGAQSAPAPKAGRTKKSDAKKSKKK
+>NAFOICDF_00920
+MDSRARASTDPGLSVEDGHHVAEVLPVRLHALNDLQLTLKHAHWNVVGPGVIGVHEMPGP
+QIEKVRAMVDAIAELELFPRSMRSFPATDDGELSHADALREAEAAKQK
+>MHAAABBN_01573
+MAEKNAAEYTVPGLSLSTGRRTAEILQGRLHALNDLQLTLKHAHWNVVGPGFIGVHEMLD
+PQIELVRGMVDVLAERIATLGVSPAGTPGALVAARAWDDYTLGRASTLEHLAALDLVYDG
+VVTDHRAAIDATEDLDPVTQDILIDQVAQLELFQWFMRSFLTTDDGRLSSAGTTTEAAAA
+GRVKGAQSAPAPKAGRTKKSDAKKSKKK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001869.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001869.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa3b025f0f1b264013b1515420ac640a0012d493
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001869.fa
@@ -0,0 +1,28 @@
+>ACLBLIBL_01022
+MSHETPASDTTPHSGAAPRGFAGAEALELPGWRHVYSGKVRDLYEPADAAPGESETLLVV
+ASDRISAYDHVLSPPIPDKGAVLTQLTLWWFERLSEGYNGAAGAPVEHHVVSTDVPEAVA
+GRAMVVKRLRMFPVECIARGYLTGSGLAEYRESGTVTGLPLPTGLVDGSRLDPAIFTPSA
+KAEVGEHDENITFEQMSERVGAEAAERLRYLTLDLYSRAEAIARDAGIILADTKVEFGVD
+PATGQVVLGDEVLTPDSSRFWDAEDYEPGRAQASFDKQFVRDWLTSDASGWDRASGAEPP
+ELPADVVEKTRARYVEAYERLTGRPFEA
+>MOLHKGIG_01846
+MSGERVGFTGAEALWLPGWRHVYSGKVRDLYEPADAEPGRSATLLVVASDRISAYDHVLE
+PPIPDKGTILTRLTLWWFEKLAEGYNGAHAEPVEHHVVGTDVPAAVAGRAMVVKRLDMFP
+VECIARGYLTGSGLAEYRASGTVAGLPLPAGLVDGSRVDPPIFTPSAKAEVGEHDENITF
+EQMVERVGTEAAERLRFLTLDLYARAEAIAREAGIILADTKVEFGVDPATGQVVLGDEVL
+TPDSSRFWDAEDYEPGRPQASFDKQFVRDWLTGPDSGWDKTSGEAPPELPADVVAKTRDR
+YVEAYERLTGRPFDA
+>MHAAABBN_01542
+MSGERVGFTGAEALWLPGWRHVYSGKVRDLYEPADAEPGRSATLLVVASDRISAYDHVLE
+PPIPDKGTILTRLTLWWFEKLAEGYNGAHAEPVEHHVVGTDVPAAVAGRAMVVKRLDMFP
+VECIARGYLTGSGLAEYRASGTVAGLPLPAGLVDGSRVDPPIFTPSAKAEVGEHDENITF
+EQMVERVGTEAAERLRFLTLDLYARAEAIAREAGIILADTKVEFGVDPATGQVVLGDEVL
+TPDSSRFWDAEDYEPGRPQASFDKQFVRDWLTGPDSGWDKTSGEAPPALPADVVAKTRDR
+YVEAYERLTGRPFDA
+>LFPAFLNI_01766
+MSGERVGFTGAEALELPGWRHVYSGKVRDLYEPADAEPGRSATLLVVASDRISAYDHVLE
+PPIPDKGTILTRLTLWWFEKLAEGYNGAHAEPVEHHVVGTDVPAAVAGRAMVVKRLDMFP
+VECIARGYLTGSGLAEYRASGTVAGLPLPAGLVDGSRVDPPIFTPSAKAEVGEHDENITF
+EQMVERVGTEAAERLRFLTLDLYARAEAIAREAGIILADTKVEFGVDPATGQVVLGDEVL
+TPDSSRFWDAEDYEPGRAQASFDKQFVRDWLTGPDSGWDKAGGEAPPALPADVVAKTRDR
+YVEAYERLTGRPFDG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001870.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001870.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3fe03bbece75d1c0c0139fcfea7207b0300af078
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001870.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_01032
+MPLSLTWLDAVLLVLLVVLLVQGHRRGLWVVLGNLVGLVGGAAIAFYAMPEVAQLVTAPQ
+WRWAALLATLVLLVAAGQYVGAAIGEAIRLRVNLPALRLVDRILGALAAGVAGALVVWLV
+SFSMSTAGSGAVTREVARSQVIAAIDRVLPDSALAWAARSRSAVADLDMLPELRLPEPVP
+VPDDDGGVRAAPPTSSSPATTPARPAEPEDAAPASGGSATPEERPPAPPTTAPPPFPTPR
+PRRPPRPPPPRPPRPPIPSPRRPTPPNPPPPRPSRTAVPAEAAVVRLTGTAAQCGQVQSG
+SGVAVAPDRVLTNAHVVLGVDAPTVTDAQRGVHDARIVHLDTARDLAVLALDGADLPVMP
+LGAELVGGESALVMGHPDGGPFASTPATVQAVGEVPLGDVVTGAASMVDVYTLAADIRHG
+YSGGPVVDAAGSLAGLVFARAPGADPVGYALSADSIAPAVAAAPGMSATVPSGDCIPGA
+>MOLHKGIG_01836
+MPLGLTWLDVLLIVALAMLLVQGHRRGLWVVLGNLVGLVGGAAIAFYALPEVAEFVTAPQ
+WRWAALIATLVLLVAAGQYVGAAIGEAIRLRVNLPALRLVDRLLGALAAGLAGALVLWLV
+AFSIAASGSTAVTREVNRSQVITALDTVMPDSLLAWAARSRSAVADLDVLPELELPAPVP
+ESDDGVRAAPAPAATPGLPSAASSPSDTATSAPSASATPEEPDDAAAASSSTAAAPSATT
+TAPASSTSTAAPSTPAASSASAAVVRLTGTAAQCNQVQSGSGVAVAPDRVLTNAHVVLGV
+DAPTVTDRARGVHAARIVHLDTAHDLAVLAVDDANLPVMPVGAELTGGASASVLGYPDGG
+PFASTPATVQAVGEVPLGDVLTGAASMVDVYTLAADIRHGYSGGPVVDTAGNLAGLVFAR
+APGSDAVGYALTADTIAPVVAAAPGMTATVPSGDCVPGG
+>MHAAABBN_01533
+MPLGLTWLDVLLIVALAMLLVQGHRRGLWVVLGNLVGLVGGAAIAFYALPEVAKFVTAPQ
+WRWAALIATLVVLVAAGQYVGAAIGEAIRLRVNLPALRLVDRLLGALATGLAGALVLWLV
+AFSIAASGSTAVTREVTRSRVIAALDTVMPDSLLAWAARSRSAVADLDVLPELELPAPVP
+ETDDGVRAAPAPAATPGLPSAASSPSAPPATSAAATPEEPDDAAAASSSTSAAPSATTTA
+PASSTSTAAPSTPAASSASAAVVRLTGTAAQCNQVQSGSGVAVAPDRVLTNAHVVLGVDA
+PTVTDRARGVHAARIVHLDTAHDLAVLAVDDADLPVMPVGAELTGGASASVLGYPDGGPF
+ASTPATVQAVGEVPLGDVLTGAASMVDVYTLAADIRHGYSGGPVVDAAGNLAGLVFARAP
+GSDAVGYALTADTIAPVVAAAPGMTATVPSGDCVPGG
+>LFPAFLNI_01757
+MPLGLTWLDVLLIVALAMLLVQGHRRGLWVVLGNLVGLVGGAAIAFYALPEVAKFVTAPQ
+WRWAALIATLVVLVAAGQYVGAAIGEAIRLRVNLPALRLVDRLLGALATGLAGALVLWLV
+AFSIAASGSTAVTREVTRSRVIAALDTVMPDSLLAWAARSRSAVADLDVLPELELPAPVP
+ETDDGVRAAPAPAATPGLPSAASSPSAPPATSAAATPEEPDDAAAASSSTSAAPSATTTA
+PASSTSTAAPSTPAASSASAAVVRLTGTAAQCNQVQSGSGVAVAPDRVLTNAHVVLGVDA
+PTVTDRARGVHAARIVHLDTAHDLAVLAVDDADLPVMPVGAELTGGASASVLGYPDGGPF
+ASTPATVQAVGEVPLGDVLTGAASMVDVYTLAADIRHGYSGGPVVDAAGNLAGLVFARAP
+GSDAVGYALTADTIAPVVAAAPGMTATVPSGDCVPGG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001871.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001871.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af94b02c9f692bf2d80ed6b31d95835ab81648d0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001871.fa
@@ -0,0 +1,44 @@
+>ACLBLIBL_01111
+MTPSPSVQESYTRGPSDVPMLEQTLAQNLDDAARRSGARPAVVECGPDGDPATDRSWTYE
+QLREESVTVAKALMAAGYEPGDRIGLWSPNVAEWTSLLYGAARAGVILVNLNPAYRAHEL
+TYVVEQCGMRGLVVAPADAHQDRPDIARDVACGGCPELRQLIILPTAGPITAESYAHAVD
+GVLDCRPEPTPVSEGTWSAFLAGADRVSDEELAARESAVSPEDPVNLQYTSGTTGFPKGV
+TLTHRNVLNNGFHIGELLGYSQEDTVVIPVPFFHCFGMVIGVIAAVSHGSLCVIPARGFE
+PVATLRAAAATRATSLYGVPAMFIAMLARPEADELDLSTLRTGVMAGSTCPVEVMRRVID
+RFHMAEVAICYGMTETAPVSTMTRRDDSLEVRTQTVGRTMPHVETKIVDPVSGEVVPRGS
+TGELCTRGYSVMRGYWNDEEKTAEVLDAEGWMHSGDLASMDEGGSVRIEGRIKDLVIRGG
+ENISPREVEEFLYTHPDVQDVQVVGVPDERYGEQLMACLIMKDGTRPLTPEDVRAFCEGK
+IAHFKIPAHVRVLDAFPMTVSGKVRKVELRAEGAKLVEGGDRD
+>MOLHKGIG_01766
+MTESTAPESFTQGPTDVELLEQTLAQNLDDTARRFADRAALLECGPDGDPATGRTWTYGQ
+LREESVTVAKALMAAGYEAGDRIGMWSPNVAEWVSLLYGAARAGVILVNLNPAYRAHELT
+YVVEQCDMRGLVVACADARMDPPATARAVARESAPHLRQLIMLPAGSGEDAYAHVQAGDV
+AGRHAADPVAEGTWADFLAEAARVSDEDLAVREAATGPADPVNLQYTSGTTGFPKGVTLT
+HRNVLNNGFHIGELLGYTEEDTVVIPVPFFHCFGMVIGVIATVSHGSLAVIPARSFEPVS
+ALRAVAATGATSLYGVPAMFIAMLARPEADALDLSTLRTGVMAGSTCPVEVMKKVIDRFH
+MSEVAICYGMTETAPVSTMTRRDDSLEVRTQTVGRTMPHVETKIVDPATGDVVPRGATGE
+LCTRGYSVMLGYWDAPEKTAEVLDADGWMHSGDLASMDEDGSVRIEGRIKDLVIRGGENI
+SPREVEEFLYTHPDIQDVQVVGVPDEKYGEQLMACVIMKDGVEPLTVDAVREFATGRIAH
+FKIPAYVRVLDAFPMTVSGKVRKVELREEGAKVVQAQAHAQGAG
+>MHAAABBN_01473
+MTESTAPESFTQGPTDVELLEQTLAQNLDDTARRFADRAALLECGPDGDPATGRTWTYGQ
+LREESVTVAKALMAAGYEAGDRIGMWSPNVAEWVSLLYGAARAGVILVNLNPAYRAHELT
+YVVEQCDMRGLVVACADARMDPPATARAVARESAPHLRQLIMLPAGSGEDAYAHVQDGDV
+AGRHAADPVAEGTWAAFLAGAARVSDEDLAAREAATRPADPVNLQYTSGTTGFPKGVTLT
+HRNVLNNGFHIGELLGYTEEDTVVIPVPFFHCFGMVIGVIATVSHGSLAVIPARSFEPVS
+ALRAVAATGATSLYGVPAMFIAMLARPEADALDLSTLRTGVMAGSTCPVEVMKKVIDRFH
+MSEVAICYGMTETAPVSTMTRRDDSLQVRTQTVGRTMPHVETKIVDPATGDVVPRGATGE
+LCTRGYSVMLGYWDAPEKTAEVLDADGWMHSGDLASMDEDGSVRIEGRIKDLVIRGGENI
+SPREVEEFLYTHPDIQDVQVVGVPDEKYGEQLMACVIMKDGVEPLTVDAVREFATGRIAH
+FKIPAYVRVLDAFPMTVSGKVRKVELREEGAKVVQAQAHAQGAG
+>LFPAFLNI_01695
+MTESTAPESFTQGPTDVELLEQTLAQNLDDTARRFADRAALLECGPDGDPATGRTWTYGQ
+LREESVTVAKALMAAGYEAGDRIGMWSPNVAEWVSLLYGAARAGVILVNLNPAYRAHELT
+YVVEQCDMRGLVVACADARMDPPATARAVARESAPHLRQLIMLPAGSGEDAYAHVQDGDV
+AGRHAADPVAEGTWAAFLAGAARVSDEDLAAREAATRPADPVNLQYTSGTTGFPKGVTLT
+HRNVLNNGFHIGELLGYTEEDTVVIPVPFFHCFGMVIGVIATVSHGSLAVIPARSFEPVS
+ALRAVAATGATSLYGVPAMFIAMLARPEADELDLTTLRTGVMAGSTCPVEVMKKVIDRFH
+MSEVAICYGMTETAPVSTMTRRDDSLEVRTQTVGRTMPHVETKIVDPATGEVVPRGATGE
+LCTRGYSVMLGYWDAPEKTAEVLDADGWMHSGDLASMDEDGSVRIEGRIKDLVIRGGENI
+SPREVEEFLYTHPDIQDVQVVGVPDEKYGEQLMACVIMKDGVEPLTVDAVREFATGRIAH
+FKIPAYVRVLDAFPMTVSGKVRKVELREEGAKVVQAQAHAQGAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001872.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001872.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee1739b4a0e46db6329ce1b8cdf6f639a4501c92
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001872.fa
@@ -0,0 +1,24 @@
+>ACLBLIBL_01195
+MARRALPAAGLAVLAALAAGCSLSDGQPAPSETTSAPAASSASPSGTATGPAPSSAAPAG
+AHSDPAALDVVVNKARPLSPVDWAPQDLVPVPGSDLPLRAEAARAAGGLIEAAARSGHAL
+STLSAYRSHAYQAQTYGHWVDELGRQEADRVSARPGHSEHQTGLAWDVGDPESPQCHLEA
+CFGDTAAGRWVAEHAAEHGFVVRYPAGAEHVTGYAPEPWHLRFVGREAAAAVEAAGGVLE
+TAWGLPAAPDYPG
+>MOLHKGIG_01683
+MRRTLPLAALAALALLVAGCGTPAAGPSSTPTTPTSGSASAAASSGAASSTAPSSGTHAD
+PATLDVVVNKTRPVAPPDWAPSDLVAVPGSELPLRAEAATAAGDLLDAAAAAGHRLTTLS
+AYRSYDYQVRTYGHWVDELGRAEADRVSARPGYSEHQTGLAWDVGDAATPACDLEACFGD
+TAAGRWVAAHAAEYGFVIRYPVGAEDVTGFAHEPWHLRYVGSAEAARVEAAGGVLETAWG
+LPPAPDYAD
+>MHAAABBN_01387
+MRRTLPLAALAALALLAAGCGTPAAGPSSTPTTPTSGSASAAASSRAASSTAPSSGTHAD
+PATLDVVVNKTRPVAPPDWAPSDLVAVPGSELPLRAEAATAAADLLDAAAAAGHRLTTLS
+AYRSYDYQVRTYGHWVDELGRAEADRVSARPGYSEHQTGLAWDVGDAATPACDLEACFGD
+TAAGRWVAAHAAEYGFVIRYPAGAEDVTGFDHEPWHLRYVGSAEAARVEAAGGVLETAWG
+LPPAPDYAD
+>LFPAFLNI_01612
+MRRTLPLAALAALALLVAGCGTPAAGPSSTPTTPTSGSASAAASSGAASSTAPSSGTHAD
+PAALDVVVNKTRPVAPPDWAPSDLVAVPGSELPLRAEAATAAGDLLDAAAAAGHRLTTLS
+AYRSYDYQVRTYGHWVDELGRAEADRVSARPGYSEHQTGLAWDVGDAATPACDLEACFGD
+TAAGRWVAAHAAEYGFVIRYPAGAEDVTGFDHEPWHLRYVGSAEAARVEAAGGVLETAWG
+LPPARDYAD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001874.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001874.fa
new file mode 100644
index 0000000000000000000000000000000000000000..305f5193d85468efbd4ce5f587bf13a021c6d759
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001874.fa
@@ -0,0 +1,33 @@
+>ACLBLIBL_01224
+MPHDESMCMMNVSAPEPTRPQLPPLARHALLIIWDSVSWILALLAFLVVRYDFGLSPTQW
+DWVLAFTLIAVVGQVAAGLVTQFYLGRHRVGSFSDAGWTAVIVCAIALAIGLALSVAAPA
+FPRGVALTMPPLALVIMLAGRFLVRNVAAGRPRADASAAVPAIVYGAGNAGHQVSQLMRQ
+AEEPPYRIVGFVDDDKGKSRLRIHGLGVRGRGTDLAEVAAELGAEAVIYAISNADAEHVE
+WVSRVCTEEGLDLVVVPPLREMVGGKVTLGSLRHLSVTDLLGRRPISTDISAISDYVSGK
+VVLVTGAGGSIGSELAVQLHHLGPAKLLLLDRDESALHGVQLDIYGNGLLDTDDIILCDI
+RDEQALQAVFEHHRPQVVFHAAALKHLPMLERFPLEGWRTNVLGTRNVLQAAHSVGVQRF
+VNISTDKAAAPTSVLGATKRLAERLTAWHATTYDLPYLSVRFGNVLGSRGSVLISFRNQI
+EKGGPVTVTHPDVTRYFMTIPEACELVLQAGAIGNPGEVLVLDMGQPVKILDVAKRMIAE
+SGQNIDIHFTGLRPGEKMHEVLFSNAEANATSQHPMISEVQVPDLDPVVVAELPSDRESI
+LAMIDDEPPVERADDTQTPGLDQAGARP
+>ACLBLIBL_02437
+MTWVVTGGAGYIGAHVVRAFRERGLPVAVVDDLSTGHREFVPDGVPFFHADVTDTAALTA
+VLRENEAEGVVHVAGYKYAGESVRVPLTAYRANVQGTASVLDAMAAAQVQSVVFSSSAAV
+YGTPAVERVTEDTPPAPESPYGESKLIGEWLLRDQERAVGIRHTSLRYFNVVGSGWADIT
+DLSPHNLFPLVFSALERGERPHIFGDDYPTPDGTCIRDYVHVQDVAEAHVAAARALTSGV
+GLHSVYNLGSGQGTSVHEIMAAVRDVTGVTDPPEVLDRRPGDPARIVADGTLAAQDLGWR
+MRHSVEDMVRSAWDAHRRLGISASGDE
+>MHAAABBN_00238
+MTWVVTGGAGYIGAHVVRALQGAGMDVAVVDDLSTGFADFVPADVPLLRADVGDVGQVAT
+YLTRVGAAGVVHVAGYKFAGESVREPLHTYRVNVRGTLGVLEAMERAGVPAIVFSSSAAV
+YGTPDVERVTEATATAPESPYGESKLIGEWLLADQGRATGLRHTSLRYFNVVGSADPALS
+DTSPHNLFPLVFRALDRGERPRLFGADHPTPDGTCVRDYVHVADVARAHVAAARALAESR
+ALAPVYNLGSGAGTSVRQIMEAVGRVTGRDVDPVVEPRRPGDPARIVADGSLAARDLGWE
+NRHTVEDMVRSAWEARRPPETR
+>LFPAFLNI_00844
+MRLLVTGGAGYIGSHFVSVARQQGRADIVVVDDFSTGLRQRVPADVPVYTIDLASDAAVA
+TLTTLLKEESIDVVVHFAAKKVVADSVVQPEDYFRSNVGATVNVLAAMRAAGAASMIFSS
+SAAVYGEPDSSIVFEDTPTVPINPYGQSKLVSELALANASRAWGLRAVALRYFNVAGAED
+AILADTTTTNLMPAIRDVITRGQRLSVFGDDYPTVDGTCVRDYVHVVDLAEAHLAALPAV
+QGSTDPATRIYNVGTGSGSSVLEVVDAFRRRPGVDLDYDIQPRRPGDPGALTANVSLIEK
+ELGWVARYTRDDIVTSVIDFPPRLVT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001878.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001878.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d74243ca0813d758f098eb56083213729b05fe1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001878.fa
@@ -0,0 +1,40 @@
+>ACLBLIBL_01334
+MTATRSGGAATSRLNAKVVGISVAAALGGFLFGFDTSVINGAVDALAGEFGLGPGLTGFT
+VSSALIGCALGAWFAGPIANRRGRVPVMVIAAILFLVSAIGSGLAFGVVDLIFWRMVGGL
+GVGAASVIAPAYIAEVSPAHVRGRLGSLQQLAIVLGIFAALLSDALFATMAGGAAQPFWL
+GVDAWRWMFLAEAVPAVLYGLFALKLPESPRYLVARGRTDEAAEVLHEFTGVDRVNLMIE
+DIRRSLDSEHRESLADLRGPAAGLQPIVWIGILLSVFQQAVGINVIFYYSTTLWRSVGFG
+ESDALTVTVITSVTNIAVTFIAIALVDRVGRRPMLIAGSAGMAVSLGLMALAFSFAETGG
+AESVSLPQPWSTVALVAANAFVVFFGATWGPLVWVLLGEMFPNRIRAGALAVAAAAQWAA
+NFTVSTTFPWLADIGLTLAYGLYALMAALSLAFVAAFVPETKGKTLEQMSDIVVRSPGQR
+RAGRAEAERDLRG
+>MOLHKGIG_01588
+MTATRSGGAATSRLNAKVVGISVAAALGGFLFGFDTSVINGAVDALAGEFGLGAGLTGFA
+VSSALIGCALGAWFAGPIANRRGRVPVMVIAAILFLVSAIGSGLAFGVVDLIFWRVVGGL
+GVGAASVIAPAYIAEVSPAHVRGRLGSLQQLAIVLGIFAALLTDALFATMAGGAAQPFWL
+GVDAWRWMFLAEAVPAVLYGLFALKLPESPRYLVARGRTDEAAEVLHEFTGVDRVNLMIE
+DIRRSLDSERRESLADLRGPSAGLQPIVWIGILLSVFQQAVGINVIFYYSTTLWRSVGFG
+ESDALTVTVITSVTNIAVTLIAIALVDRVGRRPMLIAGSAGMTVSLGLMALAFSFAQTGG
+AESVSLPQPWSTVALVAANAFVVFFGATWGPLVWVLLGEMFPNRIRAGALAVAAAAQWAA
+NFTVSTTFPWLADIGLTLAYGLYAVMAALSLAFVAAFVPETKGKTLEEMSDVVVRSPGQR
+RAVRAEAERDLRG
+>MHAAABBN_01299
+MTATRSGGAATSRLNAKVVGISVAAALGGFLFGFDTSVINGAVDALAGEFGLGAGLTGFA
+VSSALIGCALGAWFAGPVANRRGRVPVMVIAAILFLVSAIGSGLAFGVVDLIFWRMVGGL
+GVGAASVIAPAYIAEVSPAHVRGRLGSLQQLAIVLGIFAALLTDALFATMAGGAAQPFWL
+GVDAWRWMFLAEAVPAVLYGLFALKLPESPRYLVARGRTDEAAEVLHEFTGVDRVNLMIE
+DIRRSLDSERRESLADLRGPSAGLQPIVWIGILLSVFQQAVGINVIFYYSTTLWRSVGFG
+ESDALTVTVITSVTNIAVTLIAIALVDRVGRRPMLIAGSAGMTVSLGLMALAFSFAQTGG
+AESVSLPQPWSTVALVAANAFVVFFGATWGPLVWVLLGEMFPNRIRAGALAVAAAAQWAA
+NFTVSTTFPWLADIGLTLAYGLYAVMAALSLAFVAAFVPETKGKTLEEMSDVVVRSPGQR
+RAVRAEAERDLRG
+>LFPAFLNI_01515
+MTATRSGGAATSRLNAKVVGISVAAALGGFLFGFDTSVINGAVDALAGEFGLGAGLTGFA
+VSSALIGCALGAWFAGPIANRRGRVPVMVIAAILFLVSAIGSGLAFGVVDLIFWRVVGGL
+GVGAASVIAPAYIAEVSPAHVRGRLGSLQQLAIVLGIFAALLTDALFATMAGGAAQPFWL
+GVDAWRWMFLAEAVPAVLYGLFALKLPESPRYLVARGRTDEAAEVLHEFTGVDRVNLMIE
+DIRRSLDSERRESLADLRGPSAGLQPIVWIGILLSVFQQAVGINVIFYYSTTLWRSVGFG
+ESDALTVTVITSVTNIAVTLIAIALVDRVGRRPMLIAGSAGMTVSLGLMALAFSFAQTGG
+AESVSLPQPWSTVALVAANAFVVFFGATWGPLVWVLLGEMFPNRIRAGALAVAAAAQWAA
+NFTVSTTFPWLADIGLTLAYGLYAVMAALSLAFVAAFVPETKGKTLEEMSDVVVRSPGQR
+RAVRAEAERDLRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001881.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001881.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a10e3a9153fa8ad8d93b3590c28635da2d1ba3ce
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001881.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_01411
+MSNDPRTPGSDDGRDPLEEMLRQLFGGNGPDPDEIRRAMEGMGGPGGMPFDPSQLDPAMM
+QQAMAQFQAMMNPGPGSEGPVNWTLAKQAARQAVAGEDPAVGSFARREVDEALRLAELWL
+DGATQTEPVGSVGVAWSRAEWVEATMDQWRRLTEPVAVSMSRAMSAAIEQQLPGQLPEGM
+DASMLSGIQPMLKNMGGTMFGLQLGGAVGALGKEVLSGTDIGVPIAGHRLAMVPVNVEEF
+GDGLSVPDDQVRIYLALREAARMRLFLHSPWLERDLYAAIEQYAAGIRLDTEGIEQAARS
+VDPMDPESMQAVFDGSSFIAAPDATQRAALAQLELLVALVEGWVDVVVAEAATPLESAAA
+LRETMNRRRASGGPAEQAFAALVGLELRPRRLREAAAFWEHVTAEQGKEYREEIWRHPER
+QPTAEDLEDPAGYAGRRTAADASTDSLDDDLRKLLEGGFGDAPKEG
+>MOLHKGIG_01514
+MSNDARTPGSDDGRDPLEEMLRQLFGGQGPDPDEVRRAMEGLGGPGGVPFDPSQLNPAMM
+QQAMAQFQAMMSSGSGSDGPVNWALAKQAARQAVAGEDPAVGSFARREVDEALRLAELWL
+DGVTQTEPVGSVGVAWSRAEWVEATMDQWRRLTEPVAVSMSRAMSAAIEQQLPGQLPEGM
+DASLLGGLQPMLKNMGGTMFGLQLGGAVGALGKEVLSGTDIGLPVAGHRLALVPVNIEEF
+GDGLSVPDDQIRIYLALREAARMRLFLHSPWLERDLYAAVEQYAAGIRLDTEGIERAAQS
+VDPMDPGSLQAVFDGASFIAAPDATQQAALDQLELLVALVEGWVDVVVAEAARPLESAAA
+LRETMNRRRASGGPAEQAFAALVGLELRPRRLREAAAFWEHVTAEHGTEYREEIWRHPER
+QPTAEDLEDPAGYAGRRSAADASAESLDDELRKLLEGGFGDAPREG
+>MHAAABBN_01223
+MSNDARTPGSDDGRDPLEEMLRQLFGGQGPDPDEVRRAMEGLGGPGGVPFDPSQLNPAMM
+QQAMAQFQAMMSSGSGSDGPVNWALAKQAARQAVAGEDPAVGSFARREVDEALRLAELWL
+DGVTQTEPVGSVGVAWSRAEWVEATMDQWRRLTEPVAVSMSRAMSAAIEQQLPGQLPEGM
+DASLLGGLQPMLKNMGGTMFGLQLGGAVGALGKEVLSGTDIGLPVAGHRLALVPVNIEEF
+GDGLSVPDDQIRIYLALREAARMRLFLHSPWLERDLYAAVEQYAAGIRLDTEGIERAAQS
+VDPMDPGSLQAVFDGASFIAAPDATQQAALDQLELLVALVEGWVDVVVAEAARPLESAAA
+LRETMNRRRASGGPAEQAFAALVGLELRPRRLREAAAFWEHVTAEHGTEYREEIWRHPER
+QPTAEDLEDPAGYAGRRSAADASAESLDDELRKLLEGGFGDAPREG
+>LFPAFLNI_01441
+MSNDARTPGSDDGRDPLEEMLRQLFGGQGPDPDEVRRAMEGLGGPGGVPFDPSQLNPAMM
+QQAMAQFQAMMSSGSGSDGPVNWSLAKQAARQAVAGEDPAVGSFARREVDEALRLAELWL
+DGVTQTEPVGSVGVAWSRAEWVEATMDQWRRLTEPVAISMSRAMSAAIEQQLPGQLPEGM
+DASLLGGLQPMLKNMGGTMFGLQLGGAVGALGKEVLSGTDIGLPVAGHRLALVPVNIEEF
+GDGLSVPDDQIRIYLALREAARMRLFLHSPWLERDLYAAVEQYAAGIRLDTEGIERAAQS
+VDPMDPGSLQAVFDGASFIAAPDATQQAALDQLELLVALVEGWVDVVVAEAARPLESAAA
+LRETMNRRRASGGPAEQAFAALVGLELRPRRLREAAAFWEHVTAEHGTEYREEIWRHPER
+QPTAEDLEDPAGYTGRRSAADASTESLDDELRKLLEGGFGDAPREG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001883.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001883.fa
new file mode 100644
index 0000000000000000000000000000000000000000..91b45a11177e8083376cabfa8f2360668bc15372
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001883.fa
@@ -0,0 +1,28 @@
+>ACLBLIBL_01577
+MSVPVLLLAVVAVALAGPVPVLLGRAAWPARSPVLAALAWQAVALAGGLALLGAPLVWGL
+LPWGEGLVAAAPRLAAHLAGDAAAAPRPTGLPVGLHLMAVGAGAGIAVHLLLTTAVTVVR
+TLRARARHRDAVELVATGPTDAGRWPGGARGARELPVDDPLAYCVPGSPRGGEALTVVSS
+GLLARLSPEELDAVVAHERAHLDQHHGLLRLAFAAWARACAWLPTAETARLAVVQVTEML
+ADDAALRRAPADVLVRALAQAAPGPDAGPAGQTDATGPTSAGLGDRAARLLTRPAPLPAA
+AAALVAAASLALPAATAAALLGLP
+>ACLBLIBL_02666
+MTAGILTMALCTGLVALAVFGPWLLRHAAPALVRVPRLAIVVVAGGIGVWLVTLLAIGPV
+LAWAGAGPALLPERAAEVCQRCLTAANPFSADTTETLIPAVLLLALPVALALALGAGLAR
+QMVRRSSRSRDAARTLLHGARRQLLHGHEVALVDAEHPFALTFPDRHGGIVLSTGAVRAL
+GPGELAAVLAHEHAHLHQRHHLITALVDSIAAYLRWVPLIRAVADALPHYLEIAADDQAR
+RHAGTRALVSALVKLGERTHPAMPQHSCPVALHAAGPERIRHLVHPSAGLAGALPAVAIA
+AYLVGMAALAALVHLPYVSAALTGCTI
+>MOLHKGIG_01315
+MSVPVLLLAVVAVALAGPVPVLLGRAAWPARSPVLAALAWQAVALAGGLALLGAPLVWGL
+LPWGEGLVAAAPRLAAHLAGDAAAAPRPTGLPVGLHLMAVGAGAGIAVHLLLTTAVTAVR
+TLRARARHRDAVELVATGPADAGRWPGGARGARELPVDDPLAYCVPGSPRGGEALTVVSS
+GLLARLSPEELDAVVAHERAHLDQHHGLLRLAFAAWARACAWLPTAETARLAVVQVTEML
+ADDAALRRAPADVLVRALAQAAPGPDAGPAGQTDATGPTSAGLGDRAARLLTRPAPLPAA
+AAALVAAASLALPAATAAALLGLP
+>NAFOICDF_01473
+MSFSVLVLAAVALCLAGPVPVLLGRAAWPSRSPGLAVLAWQAVALAGGLALVGTPLLWGL
+HPWGDGLLDAVPALLADLTSPDSGIARPGSAPAEVHLLAVGAGLTVALHLLLTTAVTALR
+TLRARSRHRAALELIATDPERADDWPGGPRGARELPVDLPLAYCVPGVPGGGTPLTVVSR
+GLLERLSPEELRAVLLHERAHLAQHHGLLRLAFASWARACAWLPSAETARAGVVLVTEML
+ADDAARRTAPAPVLARALALTVRPAEAPGASASGPDAEPDAESGGLGRRVARLLDPPAPV
+PGAVAGAAAAACLALPLAVLAVILGPA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001887.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001887.fa
new file mode 100644
index 0000000000000000000000000000000000000000..db000f1464d1f8d717a260aae9bb9e3fe9a4f04c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001887.fa
@@ -0,0 +1,32 @@
+>ACLBLIBL_01781
+MEINGLTWGLTITLIVGLLAFDYFAHVRKAHTPTIREAAIWSGIYVGLALLFGLVFFAVG
+DTQHAVEYYTGYLLEKALSVDNLFVFLVIMASFRVPREYQQKVLLFGITFALISRTIFIL
+LGAAVIAAWSDVFYLFGLFLLVIAGGQLKGEMAGDADDAKDEADNIMVRMVKRFLPASDR
+FDGDKLFTLENGKRVMTPMLLVMIAIGATDILFAFDSIPAIFGVTTEAYIVFTATAFSLM
+GLRQLYFLIDGLLDRLVYLAYGLSALLAFIGVKLILHALHENNLPFINGGENVPVVTIPT
+TLSLVVVVVILAITVVVSLYSPKGQALRALQNAEKFSYRYSKLDETADPAERSRAAALMD
+EWTAKAEGLDQKWRDELLEHKDTWSGIIRTAHETRLADPRDDDARGVSERIVRQDGPTV
+>MOLHKGIG_01112
+MEINGLTWGLTIALIVGLLAFDYFAHVRKAHTPSIREAAIWSGVYVGLALVFGLVFFAFG
+DTQHAVEYYTGYLLEKALSVDNLFVFLVIMASFRVPREYQQKVLLFGITFALISRTLFIL
+LGAAVIAAWSDVFYLFGLFLLIIAGGQLKGEMSGDAEGAQDEADNVMVRLVKRFLPASEQ
+FDGDRLFTTVDGKRLMTPMLLVMIAIGATDILFAFDSIPAIFGVTQEAYIVFTATAFSLM
+GLRQLYFLIDGLLDRLVYLAYGLSALLAFIGVKLILHALHENNLPFINGGENVPVVEIPT
+TLSLVVVVVILAITVAISLASPKGQALRALQNAEKYSYRYSKLPEDADPAERERAAALMD
+RWTARAEAVDQRWRDQLLEHKDAWSAIIRTAHETRLADPRDDDARGVSEQIVRQDGPTV
+>MHAAABBN_00831
+MEINGLTWGLTIALIVGLLAFDYFAHVRKAHTPSIREAAIWSGIYVGLALLFGLVFFAVG
+DTQHAVEYYTGYLLEKALSVDNLFVFLVIMASFRVPREYQQKVLLFGITFALISRTLFIL
+LGAAVIAAWSDVFYLFGLFLLIIAGGQLKGEMSGDAEGAQDEADNVMVRLVKRFLPASEQ
+FDGDRLFTTVDGKRLMTPMLLVMIAIGATDILFAFDSIPAIFGVTQEAYIVFTATAFSLM
+GLRQLYFLIDGLLDRLVYLAYGLSALLAFIGVKLILHALHENNLPFINGGENVPVVEIPT
+TLSLVVVVVILAITVAISLASPKGQALRALQNAEKYSYRYSKLAEDADPAERERAAALMD
+RWTARAEALDQRWRDQLLEHKDAWSAIIRTAHETRLADPRDDDARGVSEQIVRQDGPTV
+>LFPAFLNI_01062
+MEINGLTWGLTIALIVGLLAFDYFAHVRKAHTPSIREAAIWSGVYVGLALVFGLVFFAFG
+DTQHAVEYYTGYLLEKALSVDNLFVFLVIMASFRVPREYQQKVLLFGITFALISRTLFIL
+LGAAVIATWSDVFYLFGLFLLIIAGGQLKGEMSGDAEGAQDEADNVMVRLVKRFLPASEQ
+FDGDRLFTTVDGKRLMTPMLLVMIAIGATDILFAFDSIPAIFGVTQEAYIVFTATAFSLM
+GLRQLYFLIDGLLDRLVYLAYGLSALLAFIGVKLILHALHENNLPFINGGENVPVVEIPT
+TLSLVVVVVILAITVAISLASPKGQALRALQNAEKYSYRYSKLPEDADPAERERAAALMD
+RWTARAEAVDQRWRDQLLEHKDAWSAIIRTAHETRLADPRDDDARGVSEQIVRQDGPTV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001888.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001888.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e7ad26ee558fc3e428ef5ce81725bf889cd0e219
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001888.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_01872
+MSTPTGYRVQDPSTDQVVETFPTLADGEVDQLLAAAETAQRAWAARPIEERATIVQKVAD
+LFEERKDELAQIIATEMGKRVTEGVEEAEFSSAIFGYFADKGPTLAADRPIETFEGGRAM
+IRHLPLGVLLGVMPWNFPYYQIARFAAPNLMLGNAIVLKHAEICPRSALAVQQIMDDAGV
+PAGVYTNVFATHDQIAEFIADPRVAGVSLTGSERAGSVIGALAGQHLKKAVLELGGSDPY
+IVLDAEDPAEAARTAWATRMYNMGQACNSNKRMIVSADIHDAFVAELVSLAEAMKPGEAA
+DEDPTVFTPLSSRGAAEGLAEQVERARQQGATVHVGGTVTDEAGARFAPAVITGVTSEMD
+AYREELFGPVAVVYKVESADEALALANDSQYGLGGAVFSQDEAQAERVARQLEVGMANVN
+TPAGEGAEIPFGGVKRSGFGRELGPLGMDEFVNKQMYFVQD
+>MOLHKGIG_01016
+MSTPTGYRVQDPSTDQVVETFPALADGEVDQVLAAAETAQRAWAARPIEERATIVQKVAD
+LFEERKDELAQIIATEMGKRVTEGVEEAEFSSAIFGYFADKGPTLAADRPIETYGGGRAM
+IRHLPLGVLLGVMPWNFPYYQIARFAAPNLMLGNAIVLKHAEICPRSALAVQQIMDDAGV
+PAGVYTNVFATHDQIAEFIADPRVAGVSLTGSERAGSVIGALAGQHLKKAVLELGGSDPY
+IVLDAEDPAEAARTAWATRMYNMGQACNSNKRMIVSADIHDAFVAELVSLAEAMKPGEAA
+DEDPTVFTPLSSRGAAEGLAEQVERARQQGATVHVGGTVTDEAGARFAPAVITGVTSEMD
+AYREELFGPVAVVYKVESADEALALANDSQYGLGGAVFSQDEAKAERIARQLEVGMANVN
+TPAGEGAEIPFGGVKRSGFGRELGPLGMDEFVNKQTYFVQD
+>MHAAABBN_00730
+MSTPTGYRVQDPSTDQVVETFPALADGEVDQVLAAAETAQRAWAARPIEERATIVQKVAD
+LFEERKDELAQIIATEMGKRVTEGVEEAEFSSAIFGYFADKGPTLAADRPIETYGGGRAM
+IRHLPLGVLLGVMPWNFPYYQIARFAAPNLMLGNAIVLKHAEICPRSALAVQQIMDDAGV
+PAGVYTNVFATHDQIAEFIADPRVAGVSLTGSERAGSVIGALAGQHLKKAVLELGGSDPY
+IVLDAEDPAEAARTAWATRMYNMGQACNSNKRMIVTADIHDAFVAELVSLAEAMKPGEAA
+DEDPTVFTPLSSRGAAEGLAEQVERARQQGATVHVGGTVTDEAGARFAPAVITGVTSEMD
+AYREELFGPVAVVYKVESADEALALANDSQYGLGGAVFSQDEAQAERIARQLEVGMANVN
+TPAGEGAEIPFGGIKRSGFGRELGPLGMDEFVNKQMYFVQD
+>LFPAFLNI_00960
+MSTPTGYRVQDPSTDQVVETFPALADGEVDQVLAAAETAQRAWAARPIEERATIVQKVAD
+LFEERKDELAQIIATEMGKRVTEGVEEAEFSSAIFGYFADKGPTLAADRPIETYGGGRAM
+IRHLPLGVLLGVMPWNFPYYQIARFAAPNLMLGNAIVLKHAEICPRSALAVQQIMDDAGV
+PAGVYTNVFATHDQIAEFIADPRVAGVSLTGSERAGSVIGALAGQHLKKAVLELGGSDPY
+IVLDAEDPAEAARTAWATRMYNMGQACNSNKRMIVSADIHDAFVAELVSLAEAMKPGEAT
+DEDPTVFTPLSSRGAAEGLAEQVERARQQGATVHVGGTVTDEAGARFAPAVITGVTSEMD
+AYREELFGPVAVVYKVESADEALALANDSQYGLGGAVFSQDEAQAERIARQLEVGMANVN
+TPAGEGAEIPFGGVKRSGFGRELGPLGMDEFVNKQMYFVQD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001895.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001895.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4bf7509c4a175380c453d005e38e4d3b8f98b99
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001895.fa
@@ -0,0 +1,31 @@
+>ACLBLIBL_02247
+MSSLNTVKDTATAAGTAELETDILVIGWGKGGKTLARTLGSQGRKVTLVERDAGMVGGTC
+INVACVPTKALVHRADAVRPGDDPDAAVASAWDFRDALTSKLRDANRAMLEDLDAVTLVQ
+GEARSTGERTVEVRPAEAADGDDDGERLTIRARHVVVNTGTTPLRPEMPGVDLPGVHDSE
+TLQLQMDRSRAPRRRRLRPRPPRSSRHRRSARAA
+>NAFOICDF_00402
+MSEQKTTTPDLDPTGQAIATQAPLAERYDHVIVGGGMAAAKAVESIRELAPEASVAVVSA
+DTAAPVYRPDLSKTLWADADAHVEDSILATPDSEGTAPGERTAYRLGAEVTAIDPQAHTV
+TVDGRTVGYGSLLLATGAEPVAAGIPQSERVHTYRTVADYRRLKEASGPGTTAVVVGGGY
+IGTELAAGLTMAGTDVTLVVPHRPLLARMLPAELSAAVEATFQEKGVRIAEGRLASAAES
+GDAVTARLEDGTELRADLLVLALGVRPRATLAEAAGLALADQGVRVDDRLRTSAPDVYAA
+GDIATFPDALLGERRVEHADAAETQGATAGRNMVGADQAYTHTPFFWADLFDYGYEAIGE
+LDTRHRTVVDLATGEDGRPDPSTAVVYYADEAGHVRGVLLWNVWDSVPQARALIERTAQE
+PVADLGSLKGRIPLG
+>NAFOICDF_00715
+MTPQHVLILGSGAAGAAAARTLASRDDVRVTLVTRTGETPYTRMLIKGIAFGQTPPEMIK
+LPLPQIEVIADTVLKVDTSAKQAQLTSGAQVSYDALIVATGSMPRSLPADVFGGDDAGQG
+RVTALHSVGDALGIRKLLTGLGRPARVAIYGGGIIAAETASSLQADGHMVTLVSRSSVPG
+VGAFGAPVAERLAADHAAKVQARFGRTLQHVDETESGVTITLNDGNPVVADFLLLALGTT
+PAAPSPWTNGIDVDDHLRAAADHVYAAGGVATHHDEALDAWRIDHWEDAAAQGAHAARAA
+LHDLGVSDDPGAYLPRSPYMAMVYGQMISGVGYTAGADAHLEAGEEFIVRHEIDGIVVGV
+TGIDAVGTVYQWGQQLHGVRA
+>NAFOICDF_02120
+MSSLDTVKDTVTTAGTAELETDILVIGWGKGGKTLAKTLGSQGRKVTLVERDAGMVGGTC
+INVACVPTKALVHRADAVRPGDDPDAAVASAWDFRDALTSKLRDANRAMLEDLDAVTLVQ
+GEARFTGERTVEVRPAEAADGDDDGERLTIRARHVVVNTGTTPLRPEMPGVDLPGVHDSE
+TLQLQMDRTRAPRRAVVVGSGPVGLELASMLAGFGAEVTVLVRGEQILPDESDAVRDSLV
+EALQDRGVRLATGASATGFAEADGGLRVDLEEGEPIAADIVVLATGRASTAEALDPAAAG
+IELDEKGFIAVDEHLRTSAPDVWAVGDVNGGPQQTYISLDDHRIVTGQLAGDGAYSRADR
+VAVPTTVFTTPPLGSVGMTAEQAREAGHEVKVASKPVAKIAAMPRPKIEEDAHGVIEVVV
+DAATDLVLGARLHCVEAQELVNLVALAMRADVTASALRDGIWTHPSATEALNEVLGELS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001898.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001898.fa
new file mode 100644
index 0000000000000000000000000000000000000000..820a48f89b2dd73a2c5afeac7c3f36594833d961
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001898.fa
@@ -0,0 +1,24 @@
+>ACLBLIBL_02295
+MSALALGPAVMFTPADRPERYAKALERADAVILDLEDAVTPDARPAARDAVRAAWEGRAA
+GGADGGPLDVARVVVRVNPAGGADYTADLAMLAETGWRTLMLAKAESAAQVDGLVAAMGE
+DVRVVALCETAAGVLAAAELAAHPNVGALMWGAEDLVASMGGSSSRTADGAYRSVVTHAR
+AAVLLAAAAHGAAAWDAVHLDLADEAGLAAEAEDAVALGCAATVCLHPRQVPVVRSAYTP
+AAEAVERAHRVLSEAEGRRGAFELDGAMVDEVVLAQARAVLRRAEAAGAAAG
+>MOLHKGIG_00667
+MSALTLGPAVMFTPADRPERYATALERADAVILDLEDAVIPEARPAARDAVAAAWAGRAT
+GGVDGGPLDEDRVVVRVNPAGTADHDADLAMLAGTGWRTLMLAKAESAAQVDGVVAALGP
+QTRVVALCETAAGILAAAELAAHPHVGALMWGAEDLVASMGGSSSRTPEGAYRSVVQHAR
+ATVLLAAAAHGAAAWDAVHLDLGDEAGLAAEAEDAAALGCTATVCLHPRQVPVVRSAYTP
+APEAVERARRVLAAAEGRHGAFELDGTMVDEVVLAQARAVLRRADAARPAGA
+>MHAAABBN_00404
+MSALTLGPAVMFTPADRPERYATALERADAVILDLEDAVTPDARPTARDAVAAAWAGRAT
+GGVDGGPLDEDRVVVRVNPAGTADHDADLAMLAGTGWRTLMLAKAESAAQVDGVVAALGP
+QTRVVALCETAAGILAAADLAAHPHVGALMWGAEDLVASMGGSSSRTPEGAYRSVVQHAR
+ATVLLAAAAHGAAAWDAVHLDLGDEAGLAAEAEDAVALGCTATVCLHPRQVPVVRSAYTL
+APEAVERARRVLAAAEGRHGAFELDGAMVDEVVLAQARAVLRRADAPRPASA
+>LFPAFLNI_00637
+MSALTLGPAVMFTPADRPERYATALERADAVILDLEDAVTPDARPTARDAVAAAWAGRVT
+GGVDGGPLDEGRVVVRVNPAGTADHDADLAMLAGTGWRTLMLAKAESAAQVDGVVAALGP
+QTRVVALCETAAGILAAADLAAHPHVGALMWGAEDLVASMGGSSSRTPEGAYRSVVQHAR
+ATVLLAAAAHGAAAWDAVHLDLGDEAGLAAEAEDAVALGCTATVCLHPRQVPVVRSAYTP
+APEAVERARRVLAAAEGRHGAFELDGAMVDEVVLAQARAVLRRADAARPASP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001900.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001900.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4f1e889be772f04bf799236efef643f6d061f5b0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001900.fa
@@ -0,0 +1,32 @@
+>ACLBLIBL_02297
+MSTKHRTLPALEEDYQVLSDTVREFADEVVAPVSAELDAKHEFPYEIVAQMGEMGLFGLP
+FPEEFGGMGGDYFALALALEQLGRVNQSVAITLEAGVSLGAMPLLKFGTQEQKEAWLPDL
+VAGRHLAGFGLTEPGAGSDAGGTQTTAVLEDGQWRINGAKEFITNSGTDITSLVTVTAVT
+GTVEGRTGADGKPAKEISTILVPAGTEGFSVAKAYDKVGWNSSDTHALHFSDVRVPEENL
+LGTRGRGFANFLEILDEGRIAIAALATGAAQGCVDESIAYAKQRTSFGQRIGEFQAVSFK
+IARMQARAHAARLAYYEAAQKMLAGKPFKTEAAMAKLIAGEAAMDNARDATQVFGGYGFM
+NETLVARHYRDSKILEVGEGTTEVQLMLIARELGL
+>MOLHKGIG_00665
+MSTKHRTLPALEEDYQVLSDTVREFADEVVAPVSAELDAKHEFPYEIVAQMGEMGLFGLP
+FPEEYGGMGGDYFALALALEQLGRVNQSVAITLEAGVSLGAMPLLKFGTEEQKQRWLPDL
+VAGTHLAGFGLTEPGAGSDAGGTQTTAALEDGQWRINGAKEFITNSGTDITSLVTVTAVT
+GTVEGRTGHDGRPAKEISTILVPAGTEGFSVAKAYDKVGWNSSDTHALHFTDARVPEENL
+LGARGRGFAHFLEILDEGRIAIAALATGAAQGCVDESVAYATQRTSFGQKIGQFQAVSFK
+IARMQARAHAARLAYYEAAQKMLAGKPFKTEAAMAKLIAGEAAMDNARDATQVFGGYGFM
+NETLVARHYRDSKILEIGEGTTEVQLMLIARELGL
+>MHAAABBN_00402
+MSTKHRTLPALEEDYQVLSDTVREFADEVVAPVSAELDAQHEFPYEIVAQMGEMGLFGLP
+FPEEYGGMGGDYFALALALEQLGRVNQSVAITLEAGVSLGAMPLLKFGTEEQKQRWLPDL
+VAGTHLAGFGLTEPGAGSDAGGTQTTAALEDGQWRINGAKEFITNSGTDITSLVTVTAVT
+GTVEGRTGHDGRPAKEISTILVPAGTEGFSVAKAYDKVGWNSSDTHALHFSDVRVPEENL
+LGARGRGFAHFLEILDEGRIAIAALATGAAQGCVDESVAYAKQRTSFGQKIGQFQAVSFK
+IARMQARAHAARLAYYEAAQKMLAGKPFKTEAAMAKLIAGEAAMDNARDATQVFGGYGFM
+NETLVARHYRDSKILEVGEGTTEVQLMLIARELGL
+>LFPAFLNI_00635
+MSTKHRTLPALEEDYQVLSDTVREFADEVVAPVSAELDAQHEFPYEIVAQMGEMGLFGLP
+FPEEYGGMGGDYFALALALEQLGRVNQSVAITLEAGVSLGAMPLLKFGTEEQKQRWLPDL
+VAGTHLAGFGLTEPGAGSDAGGTQTTAALEDGQWRINGAKEFITNSGTDITSLVTVTAVT
+GTVEGRTGHDGRPAKEISTILVPAGTEGFSVAKAYDKVGWNSSDTHALHFSDVRVPEENL
+LGARGRGFAHFLEILDEGRIAIAALATGAAQGCVDESVAYAKQRTSFGQKIGQFQAVSFK
+IARMQARAHAARLAYYEAAQKMLAGKPFKTEAAMAKLIAGEAAMDNARDATQVFGGYGFM
+NETLVARHYRDSKILEVGEGTTEVQLMLIARELGL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001902.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001902.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12ac733bb702a457747aff3d5e6367f1f2fd1da2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001902.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02317
+MRLIDVGLREGHEYRVRDTWLTVPNVITLVRLALVPVFVWLTVTDQFLAAFLTLAFLSST
+DWVDGYIARRFDMISTVGRWLDPVADRLSLVTVALTFVLTGIAPAWLVLSILIPDVVLTL
+VCLRLFGGSPDLKVTVLGKVRTALLLAGTPLLLLARVPGVDQDLWGGLALVLVGAGCVLH
+VLAAVDYLVRAVRKARELRAAGVDPRDRRARPAQGA
+>MOLHKGIG_00646
+MSVIDVGLREGHEYRVRDTWLTVPNLITLARFALVPVFVWLTVDGRHLDAFVILAVLSGT
+DWVDGYVARRFDMISTVGRWLDPVADRLSLLVVAVTFVATGIAPLWLALAIAIPDLVLAA
+VCLWLFGGSPDLPVTVLGKVRTALLLVGTPLLLLARVPGVDGGPWSGVALALVGAGCLLH
+ILAAGDYLVRAVGKARGLRADGQDPREHPSRRG
+>MHAAABBN_00383
+MRVIDVGLREGHEYRVRDTWLTVPNLITLARFALVPVFVWLTVDGRHLDAFVILAVLSGT
+DWVDGYVARRFDMISTVGRWLDPVADRLSLLVVAVTFVATGIAPLWLALAIAIPDLVLAA
+VCLWLFGGSPDLPVTVLGKVRTALLLVGTPLLLLARVPGVDGGPWSGVALALVGAGCLLH
+ILAAGDYLVRAVGKARGLRADGQDPREHPSRRG
+>LFPAFLNI_00616
+MRVIDVGLREGHEYRVRDTWLTVPNLITLARFALVPVFVWLTVDGRHLDAFVILAVLSGT
+DWVDGYVARRFDMISTVGRWLDPVADRLSLLVVAVTFVATGIAPLWLALAIAIPDVVLAA
+VCLWLFGGSPDLPVTVLGKVRTALLLVGTPLLLLARVPGVDGGPWSGVALALVGAGCLLH
+ILAAGDYLVRAVGKARGLRADGQDPREHPSRRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001903.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001903.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a3b57c1d0daa312c580c65771a2ec34209fafd42
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001903.fa
@@ -0,0 +1,28 @@
+>ACLBLIBL_02322
+MTQSPVFVILATIALIALSALFVIMEFSLLAARRHRLEAEAGTSRAARAALRSVDELTIM
+LAGAQLGITLATFALGAITKPAVDAWLGPVLTGWGLPAAVAGTASFFLSLLLVTFLHLVV
+GEMAPKSWAIAHPEFAAKAVAGPARAYVWAVRPLLAFANAVANRLVAASGVTPTDRAAVG
+GHDADSIRQLVEHSASSGALDEQAHGQISGALDLQDATVGDLVSPPRDLVTVPADATAED
+VQAASVASGHLRILVRPADGPDDGVPGVVHVRDTMVLGPREPVAPLVQEALTLPVDTALH
+EASSAMRAAGRQLAVVTSEGRTVGVVTLTDLFRRVLPVSG
+>MOLHKGIG_01076
+MHGPLIVMLVTTALIVLSAIFVIMEFSLLGARRHRLEAEAGRSRAARAALKGVDELTLML
+AAAQLGITLCTFALGAITKPAVDAWLGPVLEDWGIPAAAAGTASFVLSLLAVTFLHLVIG
+EMAPKSWAIAHPETAAKAVAVPARAFVWTVRPLLLLANRLANRLVTLSGVTPVDQAAVGG
+YDAAAIRQLVEHSAAAGTLDRQNHEALAGALDLQTLTLGDLLPQGQHPVKVAPDADVEAV
+QNAAACSGHLRILVQPDHTPESVPGVVHVRDTLTMEPSAPIQPLIQQALTLPSTTPLHEA
+LASMRRNSRQLAAVTQDNRFTGVVTLTDVLRGVLPRAA
+>MHAAABBN_00795
+MHGPLIVMLVTTALIVLSAIFVIMEFSLLGARRHRLEAEAGRSRAARAALKGVDELTLML
+AAAQLGITLCTFALGAITKPAVDAWLGPVLEDWGIPAAAAGTASFVLSLLAVTFLHLVIG
+EMAPKSWAIAHPETAAKAVAVPARAFVWTVRPLLLLANRLANRLVTLSGVTPVDQAAVGG
+YDAAAIRQLVEHSAAAGTLDRQNHEALAGALDLQTLTLGDLLPQGQHPVKVAPDADVEAV
+QNAAACSGHLRILVQPDHTPESVPGVVHVRDTLTMEPSAPIQPLIQQALTLPSTTPLHEA
+LASMRRNSRQLAAVTQDNRFTGVVTLTDVLRGVLPRAA
+>LFPAFLNI_01025
+MHGPLIVMLVTTALIVLSAIFVIMEFSLLGARRHRLEAEAGRSRAARAALKGVDELTLML
+AAAQLGITLCTFALGAITKPAVDAWLGPVLEDWGIPAAAAGTASFVLSLLAVTFLHLVIG
+EMAPKSWAIAHPETAAKAVAVPARAFVWTVRPLLLLANRLANRLVTLSGVTPVDQAAVGG
+YDAAAIRQLVEHSAAAGTLDRQNHEALAGALDLQTLTLGDLLPQGQHPVKVAPDADVEAV
+QNAAACSGHLRILVQPDHTPESVPGVVHVRDTLTMEPSAPIQPLIQQALTLPSTTPLHEA
+LASMRRNSRQLAAVTQDNRFTGVVTLTDVLRGVLPRAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001904.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001904.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ed49442e879977b8fb2b5cfb78bda24699e8863
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001904.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_02323
+MDPILLLILGTVVILVIILANGFFVAQEFAYMSVDRVRLAAAAENGDEAARRALAVTRRT
+SFMLSGAQLGITVTGLLVGYVAEPMVGEALTQLLGGTAIPASVVIAVSTVGVLLVATVVQ
+MIVGELYPKNLAIANPDPLARALARPTQVYLALFGWLIWVFDKSAEALLRLLRIEPVHDV
+DSTATAQDLDRIVEDSRDSGTLPAELSVLLDRILDFPERDAEHAMVPRSQTDEVGPETTV
+AEVRALMAAAHTRYPVISADHQPLGVVHLQDVLALGHAPAPDLLVTDVMRPATVVPTVMP
+LPDVTRALDDADDQLACVIDEHGGFVGVLTLEDLAEELVGDLRDEHDDEAHEEIVPVVVG
+ESWALRGDVHLDELERAIGHPLPEGEAETVSGLLIESLGRLPEEGERVAVDLPEDTRDYG
+GDVLYDRRLEVDVRRVERHVPADVEVHLVETPREDETEEDPR
+>MOLHKGIG_01077
+MDPVLTLILGSLIILAIIAANGFFVAQEFAYMSVDRVRLQTAAKAGDRAAARALQVTRRT
+SFMLSGAQLGITVTGLMVGYVAEPMVGAALTELLGGTALPSEVVIAISTLGVLVVATLVQ
+MIIGELYPKNLAIANPEPLARALARPTQIYLGLFGWLIWVFDKAAEVLLKLLRIEPVHDV
+DSTASAEDLDRIALDSRASGSLPAEVSVLIDRVLDFPDQDVQHAMVPRSRVDEVQPQTSL
+AQVRDLMATGHTRYPVISNEHEPLGVVHLTDLLGETRMAPDTPVSALMRPALVLPTMMSL
+PDAARELDGSGQQMACIVDEFGGFVGVLTVEDLAEELVGELTDEHDLHPQEEITATGLHS
+WVLSAEAHLDELERLVGHPLPVTEAESAAGLTIDALGRLPREGEVITIDLPEDPRDFGAE
+EVYDRHLQVEVLSIQRRVPARLRIHLIEVPRSDTAGSHAAHEAQPDATTDEER
+>MHAAABBN_00796
+MDPVLTLILGSLIILAIIAANGFFVAQEFAYMSVDRVRLQTAAKAGDRAAARALQVTRRT
+SFMLSGAQLGITVTGLMVGYVAEPMVGAALTELLGGTALPSEVVIAISTLGVLVVATLVQ
+MIIGELYPKNLAIANPEPLARALARPTQIYLGLFGWLIWVFDKAAEVLLKLLRIEPVHDV
+DSTASAEDLDRIALDSRASGSLPAEVSVLIDRVLDFPDQDVQHAMVPRSRVDEVQPQTSL
+AQVRDLMATGHTRYPVISNEHEPLGVVHLTDLLGETRMAPDTPVSALMRPALVLPTMMSL
+PDAARELDGSGQQMACIVDEFGGFVGVLTVEDLAEELVGELTDEHDLHPQEEITATGLHS
+WVLSAEAHLDELERLVGHPLPVTEAESAAGLTIDALGRLPREGEVITIDLPEDPRDFGAE
+EVYDRHLQVEVLSIQRRVPARLRIHLIEVPRSDTAGSHAAHEAQPDATTDEER
+>LFPAFLNI_01026
+MDPVLTLILGSLIILAIIAANGFFVAQEFAYMSVDRVRLQTAAKAGDRAAARALQVTRRT
+SFMLSGAQLGITVTGLMVGYVAEPMVGAALTELLGGTALPSEVVIAISTLGVLVVATLVQ
+MIIGELYPKNLAIANPEPLARALARPTQIYLGLFGWLIWVFDKAAEVLLKLLRIEPVHDV
+DSTASAEDLDRIALDSRASGSLPAEVSVLIDRVLDFPDQDVQHAMVPRSRVDEVQPQTSL
+AQVRDLMATGHTRYPVISNEHEPLGVVHLTDLLGETRMAPDTPVSALMRPALVLPTMMSL
+PDAARELDGSGQQMACIVDEFGGFVGVLTVEDLAEELVGELTDEHDLHPQEEITATGLHS
+WVLSAEAHLDELERLVGHPLPVTEAESAAGLTIDALGRLPREGEVITIDLPEDPRDFGAE
+EVYDRHLQVEVLSIQRRVPARLRIHLIEVPRSDTAGSHAAHEAQPDATTDEER
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001912.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001912.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a994706848fc253edce8253a5c6a0fb51ecdfe6d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001912.fa
@@ -0,0 +1,36 @@
+>ACLBLIBL_02416
+MAVRHQTRGPVDTDPRYRALLEARAAQERQAARGTAAWSRDDATGLPREPLRIPELILGA
+LLAMEAFGVRLGPLGVPLNEAAMLLLLFLALCRRSRRDTSALGLSAVLAGAVMVFLAVVS
+VNQGIPDMEWLRRWVRIAALVGLVGCIAGGRLDLRSVLTGLLAAMAANVPLFYAGVVPTP
+YGSFLTGFLADKNVAGLYYAAMPVLALAVVRSRRWKLAILLAAAVCLFLTGSRTSMAGFG
+VALVWLAVTPRLAAGLRVVLLVVLGWAVGFAEENLSRLEVFGDRTGTDWLRGTIQAATEA
+KAATTPWHGRGLTEAYVTIGRDTWLYHDSYAGLFTEGGVVLLVAVLGAYAFFGLRLFSTR
+LRTPSRVAVEAAAAVVFVTATQLGEVFITIPGMLIVAAGVSLWLRERDAPLESEVRERRR
+RQVLAAARRGSTPESSADLAAPGSA
+>NAFOICDF_02298
+MPPHLPSGPALQDPRYQAVLAERGRREAATARGVSVLTAEDAAGPRTSLRVPELLLGFLL
+AMEAYTLPAGGVPVPLNEAAMMVLLGLALCRRAKRRASALGVAALLAVLVGVYLAAVSLA
+MGVPDAVWLRRLVRMAALTALVGCFAARRVDLRSVLTGLLAAMAVNVPLFYAGLVPAPYQ
+GFLTGFLADKNVAGLYYAAVPVLALTFVRRPGVRLLLLSASGLCVFLTGSRTSLAGFACA
+LVWVVLTPRMGPVLRVALLALLAWAVGFAEENLARVGVYSDREGTDWFRSVIQTATGVKV
+EATPWTGQGLAQSFVELDAGRFLFHNSYAALYVEGGVVLTAAMLTAYAVYGLRLGATRLR
+TPSRVAVEAAAVVVLVTATQLGEVFVSIPSMLILAAGATLAITEADAPLDAQARARREER
+TLRQAAARGH
+>MHAAABBN_00257
+MTVGHGAHGPRHSDPRYVALQTEREKHARAAARGTSVWSADQDAAVPREPLRIPELLLGA
+LLAMEAFSVPLGPVALPLNEAGMLLLLALALCRRSRRDVSALGLTAVLAAAVLLFLAIVS
+VSQGIPDLEWLRRWVRMAALVGLVGCIAGGRLSLRSLAVGLGAAMALNVPLFYAGLVPAP
+YGSFLTGILADKNVAGLYYAAMPVLALALVRTRRWKLILLVAAAVCVVLTGSRTSMAGFA
+CAVLWLWLTPRMGAGLRLVLLAVLAWAVAFAEENLARIAFFADRTGTDWLRSNIQAETAV
+RVAETPWYGRGLTTAYVDFGGATWHYHNSYAGLYTEGGVVLLLAVLGAYAFFGLRLFSAR
+LRTPSRVAVEAAAVVVFVSATQLGEVFITIPSMLVVAAGVTLWLDERDAPLESEVLERRR
+RRVLAAARRGQHAPSSGGHAVPDL
+>LFPAFLNI_00536
+MTVGHGAHGPRHSDPRYVALQAEREKHARAAARGTSVWSAGQDAAAPREPLRIPELLLGA
+LLAMEAFSLPLGPVALPLNEAGMLLLLALALCRRSRRDVSALGLTAVLAAAVLLFLAVVS
+VSQGIPDLEWLRRWVRMAALVGLVGCIAGGRLSLRSLAVGLGAAMALNVPLFYAGLVPAP
+YGSFLTGVLADKNVAGLYYAAMPVLALALVRTRRWKLILLVAAAVCVVLTGSRTSMAGFA
+CAVLWLWLTPRMGAGLRLVLLAVLAWAVAFAEENLARIAFFADRTGTDWLRSNIQAETAV
+RVAETPWYGRGLTTAYVDFGGATWHYHNSYAGLYTEGGVVLLLAVLGAYAFFGLRLFSAR
+LRTPSRVAVEAAAVVVFVSATQLGEVFITIPSMLVVAAGVTLWLDERDAPLESEVLERRR
+RRVLAAARRGQHAPSSGGHAVPDL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001913.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001913.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c235c2f226a55c185560486114ba390f1649ba9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001913.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_02418
+MQQNTSSLSRRKVTTGIAWSVPAVVAVAAAPFAAASPSCITSSAGRVVKYPGNSSGYDLK
+QAYGFTVTVTNPTRGKLRVTAKSVSLILDKKVLRGSLLIYTADPCAGGVPVDPNSDLLVL
+EPGESQTLFLVANNTGNSANTSGCIYAKLGVKLVDGSVPVANLCDEHDVVEACFDETSPT
+ATC
+>NAFOICDF_02300
+MQTTPKTVNRRTVSAGIAWSVPAVAAVAAAPFAAASPTGCVNVTSGTAEKFPGGGHPDGI
+KQAYGFTITITNTSPTPVYVNPGTVTVVFGGHTTRNGEARLYTASPCRGGKRLAAMDPEL
+LLQPGQSKTYYYVVNNTGNSAQESGCVKGKLQLALPKGAPEGADLCNGGIVEFKNCFETT
+PPTAGC
+>MHAAABBN_00255
+MQKNTSTLSRRKVTAGIAWSVPAVAAVAAAPFAAASPTGCAAVTTGTAEKFPGGGHPDGI
+KQAYGFTITITNTSPTPVYVDPGTVTVEFKGHPTRSGEALLYTASPCEGGTRLAAMDPEL
+LLQPGESETYYYVVNQTGNSAQESGCVKGKLQLALPKGAPEGADLCNDGVVDFSNCFDTT
+PPTAGC
+>LFPAFLNI_00534
+MQKNTSTLSRRKVTAGIAWSVPAVAAVAAAPFAAASPTGCAAVTTGTAEKFPGGGHPDGI
+KQAYGFTITITNTSPTPVYVDPGTVTVVFGGHTTRNGEARLYTANPCRGGKRLAAMDPAL
+LLQSGQSKTYYYVVNNTGNSANESGCVEGKLQLALPKGAPEGADLCNDGVVEFSNCFETT
+PPTARC
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001921.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001921.fa
new file mode 100644
index 0000000000000000000000000000000000000000..114aa4b3e7c53ae94595cb301c96e908b7e51dc4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001921.fa
@@ -0,0 +1,28 @@
+>MOLHKGIG_00118
+MIAHRGASAAFPEHTRAAMLHALAVGADGLECDVQLTRDREVVCWHDPTVDRTSDGRGAV
+ADHTLDRLRGLDVVSWHARRPGAEPATTTAPPAVYGGAGEQVLTLADLLAIAAAADRPLR
+LAVELKHPSPFGHELEERVLRELLRAGWDPETGRLGQVQVSLMSFHPDALRHVAPLAGTD
+PLCPLMDLMPTELPTRLARGPLSRAAVRAAARQSLAGSEALVWRGRAGMAGPSVAYVREH
+LADVKAWLAAGRRLRVWTVDEREDADSLLAQGVQELTTNRPEDVLRWVRERAAARRERMP
+TGA
+>NAFOICDF_00200
+MTGVLPLVIAHRGASAAFPEHTRAAMLHALAVGADGIECDVQLTRDRQVVLWHDPTVDRT
+SDGRGPLADHTLAQLRALDVVSWHQGMGGDAPGDAAGRVPAVYGRRDEQVLTLADLLRMV
+LAADRPLRLAVELKHPSPFGHELEERVLRELVAAGWDAETGLMGQVRVSLMSLHPGALQY
+LAPLTGPDALCPLIDLVPDEIPSRLARGPLSRAAVRATVRQSLADAETMVWRGRAGLAGP
+SVAYVRSHLADVKAWLASGRRLRVWTVDEREDALFLAAQGVQELTTNRPADVLRWVTQAA
+TSASPGAISGRDMPSPAAR
+>MHAAABBN_02131
+MPALVIAHRGASAAFPEHTRAAMLHALAVGADGLECDVQLTRDREVVCWHDPTVDRTSDG
+RGAVADHTLDRLRGLDVVSWHARRPGAEPATTTAPPAAYGGAGEQVLTLADLLAIATAAD
+RPLRLAVELKHPSPFGHELEERVLRELLRAGWDPETGRVGQVQVSLMSFHPDALRHVAPL
+AGTDPLCPLMDLMPTELPTRLARGPLSRAAVRAAARQSLAGSEALVWRGRAGLAGPSVAY
+VREHLADVKAWLAAGRRLRVWTVDEREDAEFLLAQGVQELTTNRPEDVLRWVRERAAARR
+ERVPTGA
+>LFPAFLNI_00123
+MPALVIAHRGASAAFPEHTRAAMLHALAVGADGLECDVQLTRDREVVCWHDPTVDRTSDG
+RGAVADHTLDRLRGLDVVSWHARRPGAEPATTTAPPAAYGGAGEQVLTLADLLAIATAAD
+RPLRLAVELKHPSPFGHELEERVLRELLRAGWDPETGRVGQVQVSLMSFHPDALRHVAPL
+AGTDPLCPLMDLMPTELPTRLARGPLSRAAVRAAARQSLAGSEALVWRGRAGLAGPSVAY
+VREHLADVKAWLAAGRRLRVWTVDEREDAEFLLAQGVQELTTNRPEDVLRWVRERAAARR
+ERVPTGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001924.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001924.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f49297b40de2a7f63f2a45422806a4b2fbf8121
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001924.fa
@@ -0,0 +1,40 @@
+>MOLHKGIG_00247
+MSEKTAPTETAPVIPHFVHGERREGASGRHSDVYHPATGRVAGRVPLASAEEIDAALASA
+EEGFAAWSTLNPQRRGRILLRWVDLINENMDELATVLAQEHGKTFPDAKGDIQRGIEVVE
+FAAGAPHLLKGEFTADAGTGIDVHSMRQPLGVAVGITPFNFPAMIPLWKAGIALAAGNAF
+VLKPSERDPSVPVRLAELALEAGMPAGALNVVHGDKAAVDALIEDPRVKAVGFVGSTPIA
+QSIYAHAGRMGKRAQCFGGAKNHAVVMPDADLEMTADALVGAAFGSAGERCMAISVAVPV
+GEETADRLIALLRERVKDLRVGPSLEASSDFGPVVSKDAKERIEGYIAAGVEAGADLVED
+GRGVVVEGHEDGFYVGATLFDRVTPEMSIYREEIFGPVLSVVRAKDYEEALTLVNEHEFG
+NGVAIFTRDGDAARDFSTRVDTGMVGVNVPIPVPIAYYTFGGWKASGFGDLNQHGTDGLK
+FYTKTKTVTTRWPSGVREGASFVMPAGS
+>NAFOICDF_00091
+MSQQSQTQQTIPHFVHGARTGTDAARTSDVFDPSTGQVQARVALASPEEVTAAVDSAAEA
+FRTWSAMNPQRRGRVLLTWVDLINANADELAETLSREHGKTFEDAKGDIQRGVEVVEFAA
+GAPHLLKGEFSTSAGTGIDVHSLRQPLGVVAGITPFNFPAMIPLWKAGIALAAGNTFVLK
+PSERDPSVPVRLAELALEAGLPAGALNVVHGDKAAVDALIDDPRVKAVGFVGSTPIAQSI
+YEHAARRGKRAQCFGGAKNHAVIMPDADLEMAADALIGAAFGSAGERCMAISVAVPVGEE
+TADRLVALLRERMASLTVGPSLDPSSDFGPVVSAQAKERIESLIQAGVDEGAELVVDGRG
+VVVEGHEGGFYVGATLFDRVRKGMRIHAEEVFGPVLCVVRAKDYEEALSLPSDHEYGNGV
+AIFTRDGDTARDFSTRVECGMVGVNVPIPVPIAYYTFGGWKASGFGDLNQHGTDGLKFYT
+KTKTVTTRWPSGPRQGGAAASEGASFVMPAGS
+>MHAAABBN_02259
+MSQKTAPTETAPVIPHFVHGERREGASGRHGDVYHPATGGVAGRVPLASAEEIDAALASA
+EEGFAAWSRLNPQRRGRILLRWVDLINENMDELATVLAQEHGKTFPDAKGDIQRGIEVVE
+FAAGAPHLLKGEFTADAGTGIDVHSIRQPLGVAVGITPFNFPAMIPLWKAGIALAAGNAF
+VLKPSERDPSVPVRLAELALEAGMPAGALNVVHGDKAAVDALIEDPRVKAVGFVGSTPIA
+QSIYAHAARMGKRAQCFGGAKNHAVIMPDADLEMAADALVGAAFGSAGERCMAISVAVPV
+GEETADRLIALLRERIKGLTVGPSLEASSDFGPVVSKDAKERIEGYIAAGVEAGAELVED
+GRGVVVEGHEDGFYVGATLFDRVTPEMSIYREEIFGPVLSVVRAKDYEEALTLVNEHEFG
+NGVAIFTRDGDAARDFSTRVDTGMVGVNVPIPVPIAYYTFGGWKASGFGDLNQHGTDGLK
+FYTKTKTVTTRWPSGVREGASFVMPAGS
+>LFPAFLNI_00247
+MSQKTAPTETAPVIPHFVHGEQREGASGRHSDVYHPATGSVAGRVPLASAEEIDAALASA
+EEGFAAWSTLNPQRRGRILLRWVDLINENMDELATVLAQEHGKTVPDAKGDIQRGIEVVE
+FAAGAPHLLKGEFTADAGTGIDVHSIRQPLGVAVGITPFNFPAMIPLWKAGIALAAGNAF
+VLKPSERDPSVPVRLAELALEAGMPAGALNVVHGDKTAVDALIEDPRVKAVGFVGSTPIA
+QSIYAHAARMGKRAQCFGGAKNHAVIMPDADLEMAADALVGAAFGSAGERCMAISVAVPV
+GEETADRLIALLRERVKDLRVGPSLEASSDFGPVVSKDAKERIEGYIAAGVEAGADLVED
+GRGVVVEGHEDGFYVGATLFDRVTPEMSIYREEIFGPVLSVVRAKDYEEALTLVNEHEFG
+NGVAIFTRDGDAARDFSTRVDTGMVGVNVPIPVPIAYYTFGGWKASGFGDLNQHGTDGLK
+FYTKTKTVTTRWPSGVREGASFVMPAGS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001928.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001928.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3ddcf1d6a347efedd32c5d08960d27995225a24
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001928.fa
@@ -0,0 +1,28 @@
+>MOLHKGIG_00463
+MTDQTPQAQPAAGTALPPSTGLRLMAVHAHPDDESSKGAGTMAAYAAAGAEVMVVTCTGG
+EAGTLLNPSFGDTTRADRDIAAVRREEMAEAARILGIRHAWLGFLDSGLPEGDPLPALPA
+NCFAEVPLQDAATPLISLVRRFRPHVLISYDEVGGYPHPDHLQAHAVTMEAYRAAGLADE
+YPEAGPAWEVSKVYYDCGFNPRKFRTMAAVAEADGEDVPFARRLMMFDAMDAMREVLRRR
+EAGEDVPDPEVIPPWVTADHDVTTQVDVTGFLDERDAALRAHRTQIDPDGMFFDAPHDLQ
+RRAWPWEDFALIDSRVPSELPEHDLFAGLR
+>NAFOICDF_02368
+MSEPSIPAPTTASVPDSTGLRLLAVHAHPDDESSKGAATMAAYAAAGAEVLVVTCTGGEA
+GSVLNPSYAHPVRAERDIAGVRHAEMAAAARALGVRHRWLGFLDSGLPEGDPLPALPDHC
+FAEVPLETAAAPLVAVVRRFRPHVILSYDEAGGYPHPDHIRAHEVTRVAWERAGDADAYP
+GTGPAWEPLKLYYDRAFHPAKYQALHEGFLAAGEESPFTDRLEMHARMEAMREVLRRREE
+GEEVPDPEHLPPFVPPVHEVTTQIPVQDFLDERDAALRAHATQVDPEGMFFAAPNELQRS
+TWPWEDYALIESRVRTVPPETDLFAGVR
+>MHAAABBN_00181
+MTDQTPQAQPAAGTALPPSTGLRLMAVHAHPDDESSKGAGTMAAYAAAGAEVMVVTCTGG
+EAGTLLNPSFGDTTRADRDIAAVRREEMAEAAGILGIRHAWLGFLDSGLPEGDPLPALPA
+NCFAEVPLRDAAAPLISLVRRFRPHVLISYDEVGGYPHPDHLQAHAVTMEAYRAAGLADE
+YPEAGPAWEVSKVYYDCGFNPRKFRTMAAVAEADGEDVPFARRLMMFDAMDAMREVLRRR
+EAGEDVPDPEVIPPWVTADHDVTTQVDVTGFLDERDAALRAHRTQIDPDGMFFDAPHDLQ
+RRAWPWEDFALIDSRVPSELPEHDLFAGLR
+>LFPAFLNI_00463
+MTDQTPQAQPAAGTALPPSTGLRLMAVHAHPDDESSKGAGTMAAYAAAGAEVMVVTCTGG
+EAGTLLNPSFGDTTRADRDIAAVRREEMAEAARILGVRHAWLGFLDSGLPEGDPLPALPA
+NCFAEVPLRDAATPLISLVRRFRPHVLISYDEVGGYPHPDHLQAHAVTMEAYRAAGLADE
+YPEAGPAWEVSKVYYDCGFNPRKFRTMAAVAEADGEDVPFARRLMMFDAMDAMREVLRRR
+EAGEDVPDPEVIPPWVTADHDVTTQVDVTGFLDERDAALRAHRTQIDPDGMFFDAPHDLQ
+RRAWPWEDFALIDSRVPSELPEHDLFAGLR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001931.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001931.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a24aee0ab16e1e56798624762d5a20c9d4241b25
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001931.fa
@@ -0,0 +1,20 @@
+>MOLHKGIG_00569
+MDSRVNSGGVVGKVDNLTCLAGLVTTEDPARVRALRGTVLAVALLNGAYLVVEIILALGI
+GSVALVADSVDFFEDFAVNLLIFVALGWTAARQAVIGKVMAGIIVLPAVAALVMAATKIG
+DPDPPAAGVLLGAAVGSLLVNLVCVALLARVRTDGGSLTRAAWLAARNDLVAGAVLIALS
+GITVLTASGWADIIVGVLLVLLNGSAAKEIWEAATEEHLAAQALAGEVDDD
+>NAFOICDF_02259
+MDAMTETSHPRPDPARVRALRGTVLAVSLLNLAYMLVEIGVALGIGSVSLVADSVDFFED
+FAVNMLIVIALGWPLARRARVGKVMAGIIVLPAIAALAMAAVKVGDPEPPATGPLFWTGV
+GSLLVNLVCVGLLARFRADGGSLTRAAWLAARNDLIAGIVLIALAGATALTASGWADIIV
+GVLLVVLNGGAAKEVWQAATEERLAAQALAGEFDDD
+>MHAAABBN_00293
+MNRAAVADRRRTRTLRGTVLAVALLNGAYLVVEIILAVGIGSVALVADSVDFFEDFAVNL
+LIFVALGWTAARQAVIGKVMAGIIVLPAVAALVMAATKIGDPEPPAAGVLLGAAVGSLLV
+NIVCVVLLARVRVDGGSLTRAAWLAARNDLVAGVVLIALSGITVLTASGWADIIVGVLLV
+LLNGSAAKEIWEAATEEHLAAQALAGEVDDD
+>LFPAFLNI_00571
+MNEVPEADRRRTRALRGTVLAVALLNGAYLVVEIILALGIGSVALVADSVDFFEDFAVNL
+LIFVALGWTAARQAVIGKVMAGIIVLPAVAALVMAATKVGDPDPPAAGVLLGVAVGSILV
+NLVCVALLARVRTDGGSLTRAAWLAARNDLVAGVLLIALSGITVLTASGWADIIVGVLLV
+LLNGSAAKEIWEAATEEHLAAQALAGEVDDD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001933.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001933.fa
new file mode 100644
index 0000000000000000000000000000000000000000..74353135b11baaa2cd561b131d79419811d08ee2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001933.fa
@@ -0,0 +1,22 @@
+>MOLHKGIG_00640
+MARPGDPGRECRRGLDVRIGTSGWIYKHGRGTFYPQGLRIADQLDHCTERDRVSRLRALP
+QRGPGPALRRIVLRRRARPWVGRLRELTGADAAGARPAHVSFYNDNHGHAAFNALTLRRM
+AEAEA
+>NAFOICDF_02185
+MDVRIGTSGWTYKHWRGTFYPQGLRIADQLDHYTERFRTVELNGSHYRWPADSTVEAWRE
+RLPAGFEMAVKASRYLTHYRKLNEPQDWVERIVHTLDLLGDHAGPLLLQLPANLHRDDDR
+LAGFLGLLPERVRVAVEVQHESWLDEDVFDLLDRHGAGFVVSVIAGREPVLRATGRLAYV
+RFHNADPDWRYGGSFSDAELAPWVGRLRVLTGADNGGPAGDAAGARPAYVYFNNDNHGHA
+GFNALTLRRMAETGA
+>MHAAABBN_00377
+MISGTLRLPRRVKARPGDPGRGYRRGMDVRIGTSGWTYRHWRGTFYPQGLRIADQLDHYT
+ERFRTVELNGSHYRWPADSTVEAWRERLPAGFEMAVKASRYLTHYRKLNEPQDWVERIVH
+TLDLLGDHAGPLLLQLPAHLHRDDGRLAGFLGLLPERVRVAVEVQHESWLDEDVFDLLDR
+HGAGFVVSVIAGREPVLRATGRLAYVRFHNADPDWRYGGSFSDAELAPWVGRLRELTGAD
+DGGPAGDAAGARPAYVYFNNDNHGHAAFNALTLRRMAETEA
+>LFPAFLNI_00609
+MISGTLRLPRRIKARPGDPGRGYRRGMDVRIGTSGWTYKHWRGTFYPQGLRIADQLDHYT
+ERFGTVELNGSHYRWPADSTVEAWRERLPAGFEMAVKASRYLTHYRKLDEPQDWVQRIVH
+TLDLLGDHAGPLLLQLPAHLHRDDDRLAGFLGLLPERVRVAVEVQHESWLDKDVFDLLDR
+HGAGFVVSVIAGREPVLRATGRLAYVRFHNADPDWRYGGSFSDAELAPWVGRLRELTGAD
+AAGVRPTYVYFNNDNHGHAAFNALTLRRMAEAEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001936.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001936.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9dcf707f9c23582e5de2982493b295c09e0fe97e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001936.fa
@@ -0,0 +1,48 @@
+>MOLHKGIG_00858
+MRARETMAHVPHTDQNAPDLGVDTAVRRVREHLAALELPFETVTAGQDRAERERTLHQID
+DYVLPRLDSLDAPLLAVVGGSTGAGKSTLVNALVGHEVSRSSALRPTTRQPLLLHNPADA
+HWFTGPRVLPDLARVSVHRDAAAGPVEPDQSAMDTVALVAEPALPSGIALVDAPDIDSVA
+DQNRALARQLLEAADLWIFTTTAHRYADAVPWQLLDEAAARDITVAVVLGRVPEGAAEDI
+TPDLRRMLTERGLADARIHVIPETRFDERGLLPQEHVAGLRAWLETLAADAQARGAVARR
+TVDGVLGQLAARVADLARAEEEQRHAADLLARIVGDSTDQAVGRVREATSDGTLLRGEVL
+SRWQDFVGTGEFFRGVETTIGRLRDRLGALVRGRPAPPEEVETALETGLHAVMVEAAAAA
+AEQIERRWASEPAGRALVAGRDLGALAPDTSARAADVVRDWQSDVLALVQEEGAGKRTRA
+RLAATGVNGAAVALMIISFASTGGLAGIEVGIAGGAAVVGQKLLESIFGEDAVRRMARRA
+DELLEHRVRAFLETVLADRFLPLLHLEREPQATEELRALVPVLRRGVAAGVDGPTGPEHV
+PSAAEAGEEPR
+>NAFOICDF_01971
+MESTDLTSPSAAAPIGVDTAVRRVRAHLDALELPFATATVGADRAEAERTRHQIDDYVLP
+RLDSLDAPLLAVVGGSTGAGKSTLVNALVGHEVSRSSALRPTTRQPLLLHHPDDAHWFTG
+SRVLPDLARVTVHRSASAGPVEPDSQAMDTVALVAEPSLPQGIAIVDAPDIDSVADQNRA
+LARQLLEAADLWIFTTTAHRYADAVPWELLDQAAARDITVAVVLGRVPQGAGEAIAPDLR
+RMLVEHGLPEAPIHVIPETRFGEDGLLPAEHVADLRAWLTSLAEDAQARSAVARRTVDGV
+LTQLAVRVEALAEAEHGQQETAARLAGIVADSTELALETVHRATSDGTLLRGEVLARWQD
+FVGTGEFFRGLESAVGRVRDRLGALVRGRPAPPEEVEDALETGLHAVLVEAVASAVEQVE
+RRWRSEPAGRALVEGRDLGSLPAGTSERAATLVREWQGDVLALIQEEGAGRRTRARLAAF
+GVNGAAVALMVISFASTAGLSGIELGIAGGAAAVGQKLLESIFGEDAVRRMARRASELLD
+ERVRVLLEDVVGGRFLPLLRLERDAEDTAALRALVPTLRRGVAAGVDGPQPDAAPDAPRR
+EAADAAIEEDAR
+>MHAAABBN_00580
+MAHVPHTDQNAPDLGVDTAVRRVREHLAALELPFETVTAGQDRAERERTLHQIDDYVLPR
+LDSLDAPLLAVVGGSTGAGKSTLVNALVGHEVSRSSALRPTTRQPLLLHNPADTHWFTGP
+RVLPDLARVSVHRDAAAGPVEPDQSAMDTVALVAEPALPSGIALVDAPDIDSVADQNRAL
+ARQLLEAADLWIFTTTAHRYADAVPWQLLDEAADRDITVAVVLGRVPEGAAEDITPDLRR
+MLTERGLADARIHVIPETRFDERGLLPQEHVAGLRAWLETLAADAQARGAVARRTVDGVL
+GQLAARVADLARAEEEQRHAADLLARIVGDSTDQAVGRVREATSDGTLLRGEVLSRWQDF
+VGTGEFFRGVETTIGRLRDRLGALVRGRPAPPEEVETALETGLHAVMVEAAAAAAEQIER
+RWASEPAGRALVAGRDLGALTPDASARAADVVRDWQSDVLALIQEEGAGKRTRARLAATG
+VNGAAVALMIISFASTGGLAGIEVGIAGGAAVVGQKLLESIFGEDAVRRMARRADELLEL
+RVRAFLETVLADRFLPLLHLEREPQATEELRALVPVLRRGVAAGVDGPTEPEHAPSAAEA
+GEESR
+>LFPAFLNI_00817
+MRARETMAHVPHTDQNAPDLGVDTAVRRVREHLAALELPFETVTAGQDRAERERTLHQID
+DYVLPRLDSLDAPLLAVVGGSTGAGKSTLVNALVGHEVSRSSALRPTTRQPLLLHNPADA
+HWFTGPRVLPDLARVSVHRDAAAGPVEPDQSAMDTVALVAEPALPSGIALVDAPDIDSVA
+DQNRALARQLLEAADLWIFTTTAHRYADAVPWQLLDEAAARDITVAVVLGRVPEGAAEDI
+TPDLRRMLTERGLADARIHVIPETRFDERGLLPQEHVAGLRAWLETLAADAQARGAVARR
+TVDGVLGQLAARVADLARAEEEQRHAADLLARIVGDSTDQAVGRVREATSDGTLLRGEVL
+SRWQDFVGTGEFFRGVETTIGRLRDRLGALVRGRPAPPEEVESALETGLHAVMVEAAAAA
+AEQIERRWASEPAGRALVAGRDLGALTPDTSARAADVVRDWQTDVLALIQEEGAGKRTRA
+RLAATGVNGAAVALMIISFASTGGLAGIEVGIAGGAAVVGQKLLESIFGEDAVRRMARRA
+DELLERRVRAFLETVLADRFLPLLHLEREPQATEELRALVPVLRRGVAAGVDGPTGPEHA
+PSAAEAGEEPR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001943.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001943.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8caf57a35576d83c2eb2f0a03ac7829958474186
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001943.fa
@@ -0,0 +1,20 @@
+>MOLHKGIG_01160
+MNPVTSTARDGRSVRWDRHRAERRLELVRAARSAVHALGAHASMEEIASHAGTSKTVYYR
+YFGDREGLRLAVSERVTAHMERRLLEVADEPVSEPEALRRMVEVYLTVAATSPEVYAFAV
+APSPAAAEAPVLGPFLERVYAMLESGLARGMAARGHAPAPADPLALWPRAAVGLVRAAAE
+TWLRTPAAGRIPVEAMARAIADWLLTGLIGAAPGAALEPAAADAVRARPHSRTGASS
+>NAFOICDF_01627
+MLVRAARAAVHELGPTASMDEIAAHAGTSKSVFYRYFGDRAGLRQAVAERVTASMERRLR
+EAAVDAPDGVSALHRMVAECLSVAASSPAVYAFAVTQGGAADGTGPDLGPFFERIAALLA
+EGLARTLPAADAGPGTTLVLWPRVAVGTVRAAVEAWLATEESVRPDPVRTAHDVAGWLLA
+GLRSADPSASPAADTHTPTQQGEPS
+>MHAAABBN_00879
+MNPVTSTARDGRSVRWDRHRAERRLELVRAARSAVHALGAHASMEEIASHAGTSKTVYYR
+YFGDREGLRLAVSERVTAHMERRLLEVADEPVSEPEALRRMVEVYLTVAATSPEVYAFAV
+APSPAAAEAPVLGPFLERVYAMLESGLARGMAARGHAPAPADPLALWPRAAVGLVRAAAE
+TWLRTPAAGRIPVEAMARAIADWLLTGLIGAAPGAALEPAAADADRARPHSRTGASS
+>LFPAFLNI_01110
+MNPVTSTARDGRSVRWDRHRAERRLELVRAARSAVHALGAHASMEEIASHAGTSKTVYYR
+YFGDREGLRLAVSERVTAHMERRLLEVADEPVSEPEALRRMVEVYLTVAATSPEVYAFAV
+APSPAAAEAPVLGPFLERVYAMLESGLARGMAARGHAPAPADPLALWPRAAVGLVRAAAE
+TWLRTPAAGRIPVEAMARAIADWLLTGLIGAAPGAALEPAAADADRARPHSRTGASS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001944.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001944.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89439dd1cd580b266e6e58c0277cfacd916c4003
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001944.fa
@@ -0,0 +1,24 @@
+>MOLHKGIG_01212
+MSGSGSSRRGARHGGYAANSFRTEAIVLRTHRLGEADRIIEALTPEHGLVRAVAKGVRKT
+SSRLGSVVEPFMHSTLQLARGRGELHIVSQAQLLHPYATMLAADYDAYTVAGALAEAVER
+VPAVDDDGRRAQYRLFHGALAALARGAHDPRLILHSFLLRALAQAGWAPTFDRCARCGAP
+GPHTALHVGLGGAVCPACRPPGAAHPAPETFDLLSALAAGGWATADASGAPARREAAGIV
+AAYLQFHAERRLVSLSVLDQDLGLPAPRVERRP
+>NAFOICDF_01573
+MSGARHGGYSANSFRTEAIVLRTHRLGEADRIVEAITPEHGVLRCVAKGVRKSSSRFGSV
+VEPFMHSTLQVARGRGELHTITQAQLLHPYATAVAADYEAFAVAAALAEGVERIPALDAD
+GRRAQYLLFHGALAALARRAHDPRMILHSFLLRTLTQAGWAPTFDRCARCGAPGPHTAVN
+VALGGAVCAEHRPPGSASPAPETFALLTALTAGDWAVVDTAGPLARREAAGIVSAYLQFH
+AERRLVALSVLDQEIAPPAPRAERSA
+>MHAAABBN_00931
+MSGSGSSRRGARHGGYAANSFRTEAIVLRTHRLGEADRIIEALTPEHGLVRAMAKGVRKT
+SSRLGSVVEPFMHSTLQLARGRGELHTVSQAQLLHPYATMLAADYDAYTVAGALAEAVER
+VPAVDDDGRRAQYRLFHGALAALARGAHNPRLILHSFLLRALAQAGWAPTFDRCARCGAP
+GPHTALHVGLGGAVCPECRPPGAAHPAPETFDLLSALAAGDWATADTSGAPARREAAGIV
+AAYLQFHAERRLVSLSVLDQDLGLPAPRVERRP
+>LFPAFLNI_01169
+MSASGSSRRGARHGGYAANSFRTEAIVLRTHRLGEADRIIEALTPEHGLVRAVAKGVRKT
+SSRLGSVVEPFMHSTLQLARGRGELHTVSQAQLLHPYATMLAADYDAYTVAGALAEAVER
+VPAVDDDGRRAQYRLFHGALAALARGAHDPRLILHSFLLRALAQAGWAPTFDRCARCGAP
+GPHTALHVGLGGAVCPECRPPGAAHPAPETFDLLSALAAGDWATADASGAPARREAAGIV
+AAYLQFHAERRLVSLSVLDQDLGLPAPRVERRP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001946.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001946.fa
new file mode 100644
index 0000000000000000000000000000000000000000..01ccfe0e04d7391c122a54033402ac9681e1e0d0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001946.fa
@@ -0,0 +1,37 @@
+>MOLHKGIG_01306
+MAELRLTGPTEDGDALRLSGPEGEEHTLPLSPYLRRLVIEGAAPEDGRPAEDGPAAWHDM
+TEMDVPGADDEDAEGPVDAATHADDAAAEDERAPEAPSGPARPDEDLALTPRIDPRPVAD
+DSTADGPTPAPLTDQESVKAAATQEAVPLTPREIQQRIRAGASVEQVARESGNAFSRIRT
+YGHPVLAERDWIARQARAVEVWVGGPDLYSDLVQDGGPTTLGELAAHRLAELGVDEASLE
+WDAWREDQAGWTVAARFAVAGARSLPTREEPPALWTFRPAGRHLEPENAWARALSEAEAW
+DLVPRAPAAEPVTDDVDAEDAVTPAGAHSPAADRDADLLEILRVRRGQRVGADLESDDAL
+AHLIAREHQDRSRREAAQAPERLAPVDAEGALTTADDAPVVDAPEPAAETDRAEDTAADV
+ADAGVEDEGAEPAPRERAARPAMPTVTPRPRARSAARRASVPSWDEIVFGRKGD
+>NAFOICDF_01482
+MAELRLTGTTEDGHALRLAAPDGTEHTLERTPFLRRLALDDVARPDAVPAAEPADGAAPA
+SPAQADEPSAEAPAPEVPRPAPSPAQEPAAPVTAVAEQADVRAAATAEAQPLSPRDIQAR
+IRAGASVEQVARESGNAFSRVRTYGYPVLAERGYIAQQARAVQVWVGGPDLYSGTVADGG
+PTTLGALAEHRVRELGTDPASLEWDAWRESGGVAWTVVARFPLPPRGRALTAEEPPARWS
+FRPAGGRLDPENAWARILSDAEAWDVFTAEEPLTREDDAAAPQQGGGEEASGGDAPAAVT
+PLGASPSSVGVDADLLEILRARRGRRVGQDAESDDALAHLIARGVAEREARQDGAEADHT
+EQAETEPAAPGRAARLLRGLPSLREEVAKDGADGRPPVEADSPAAEAAPAVDAAGREDAV
+TPQAPGKTDAGKTVAGPSGADRTETGQAGTMQADAEPSDAPVAAPQEEEPARTARRERPA
+MPTPRPRARSAARRASVPSWDDIVFGKKSD
+>MHAAABBN_01029
+MAELRLTGPTEDGDALRLSGPEGEEHTLPLSPYLRRLVIEGAAPEDGRPAEDGPAAWHDM
+TEMDVPGADDEDAEGPVDAATHADDAAAEDERAPEAPSGPARPDEDLALTPRIDPRPVAD
+DSTADGPTPAPLTDQESVKAAATQEAVPLTPREIQQRIRAGASVEQVARESGNAFSRIRT
+YGHPVLAERDWIARQARAVEVWVGGPDLYSDLVQDGGPTTLGELAAHRLAELGVDEASLE
+WDAWREDQAGWTVAARFAVAGARSLPTREEPPALWTFRPAGRHLEPENAWARALSEAEAW
+DLVPRAPAAEPVTDDVDAEDAVTPAGAHSPAADRDADLLEILRVRRGQRVGADLESDDAL
+AHLIAREHQDRSRREAAQAPERLAPVDAEGALTTADDAPVVDAPEPAAETDRAEDTAADV
+ADAGVEDEGAEPAPRERAARPAMPTVTPRPRARSAARRASVPSWDEIVFGRKGD
+>LFPAFLNI_01264
+MAELRLTGPTEDGDALRLSGPEGEEHTLPLSPYLRRLVIEGAAPEDGRPAEDGPAAWHDM
+TEMDVPRADAEEPVDATTHADDAAEEGERAPDVPSGPARPDEDLALTPRIDPRPVADDST
+ADGPTPAPLTDQESVKAAATQEAVPLTPREIQQRIRAGASVEQVARESGNAFSRIRTYGH
+PVLAERDWIARQARAVEVWVGGPDLYSDLVQDGGPTTLGELAAHRLAELGVDEASLEWDA
+WREDQAGWTVAARFAVAGARSLPTREEPPALWTFRPAGRHLEPENAWARALSEAEAWDLV
+PRAPAAEPVTDDVDAEDAVTPAGAHSPAADRDADLLEILRVRRGQRVGADLESDDALAHL
+IAREHQDRSRREAAQAPERLAPVDAEGALTTADDAPVVDAPEPAAETDRAEDTAADVADA
+GVEDEGAEPAPRERAARPAMPTVTPRPRARSAARRASVPSWDEIVFGRKGD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001948.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001948.fa
new file mode 100644
index 0000000000000000000000000000000000000000..19ab6dcb262d16450c4f5e7cd674f0518c9d62cc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001948.fa
@@ -0,0 +1,17 @@
+>MOLHKGIG_01382
+MSVTSEIARARSLIRVVPDHPSPGVAFQDITPLLADARALRECVEALVAPFEGRFDLVAG
+LEARGFLLAGAAAVLTGTGLVPLRKAGRLPAPAARADYTLEYGTASIEVSEDLRAGSRVL
+LLDDVLATGGTLAAGRRLIEARGAEVVGAACLLELRALGGRAVVPDTHVLFAA
+>NAFOICDF_01893
+MSGVALSAAGRQAADVPGLERAATLFRSVPDFPTDGVVFQDITPVLADPAALRAVVEAMI
+APFEGAYDAVAGLDARGFLLAGFAAALTGTGVIPLRKAGKLPVSVAHVDYALEYGAASLE
+APPELAVPGVRVLILDDVLATGGTLAAARDLAERCGAEVAGSAVVLEVEGLGGRERCPDA
+LTLFSA
+>MHAAABBN_01102
+MSVTSEIARARSLIRVVPDHPSPGVAFQDITPLLADARALRACVEALVAPFEGRFDLVAG
+LEARGFLLAGAAAVLTGTGLVPLRKAGRLPAPAARADYTLEYGNASIEVSEDLRAGSRVL
+LLDDVLATGGTLAAGRRLIEARGAEVVGAACLLELTALGGRAVVPDTHVLFAS
+>LFPAFLNI_01337
+MSVTSEIARARSLIRVVPDHPSPGVAFQDITPLLADARALRECVEALVAPFEGRFDLVAG
+LEARGFLLAGAAAVLTGTGLVPLRKAGRLPAPAARADYTLEYGTASIEVSEDLRAGSRVL
+LLDDVLATGGTLAAGRRLIEARGAEVVGAACLLELRALGGRAVVPDTHVLFAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001954.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001954.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fddfbf0d7cffc4a795b3e25636a33df25b39ed9f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001954.fa
@@ -0,0 +1,16 @@
+>MOLHKGIG_01453
+MARVKRAVNAHKKRRTMLERASGYRGQRSRLYRKAKEQMLHSFTYNYQHRHKRKGDFRRL
+WITRINAAARANGMTYNRFMQGLKLAGVEVDRRMLAEIAVSDAATFAVLVKTAREALPAD
+VNAPAVSR
+>NAFOICDF_01350
+MARVKRAVNAHKKRRTALNRASGYRGQRSRLYRKAKEQLLHSFTYNYQHRHKRKGDFRRL
+WITRINAAARANGMTYNRFMQGLKLAGIEVDRRMLAEIAVSDAATFTALVETARTALPAD
+VNAPAASR
+>MHAAABBN_01185
+MARVKRAVNAHKKRRTMLERASGYRGQRSRLYRKAKEQMLHSFTYNYQHRHKRKGDFRRL
+WITRINAAARANGMTYNRFMQGLKLAGVEVDRRMLAEIAVSDAATFAVLVQTAREALPAD
+VNAPAASR
+>LFPAFLNI_01403
+MARVKRAVNAHKKRRTMLERASGYRGQRSRLYRKAKEQMLHSFTYNYQHRHKRKGDFRRL
+WITRINAAARANGMTYNRFMQGLKLAGVEVDRRMLAEIAVSDAATFAVLVKTAREALPAD
+VNAPAASR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001955.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001955.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aabd0b56c5d095eb88f7efe6f3afbb1c37230084
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001955.fa
@@ -0,0 +1,47 @@
+>MOLHKGIG_01470
+MTVSGPGLSAAPAAEPGAEPVEPAAGRPRSWVPGPAWRALRRRWRRSLRLRTAVLAALLS
+ILAGLVVAAFLTQQITQALFEARYEQVQAEARRGLSQVRETFAQTTATDAQSTDVLVTQT
+LRALEGDSGTTIRRRYHLAPLPGSESAYVGTISSAGLDPAVIPQELQDAVASGPGVYDAS
+VALPDPGGGTRPGLVFGAQVVLPPGATYGLYLVYDLADVQSSLDSVLGVLLVFGVGFLVI
+NVLVSWWVSRRVTLPVQQAARAAESLSSGNLAVRMPVDGEDEMARLGMSFNRMADSIQDQ
+IGQLAQLSQMQQRFVSDVSHELRTPLTTVRMAADVLYGSREDFDPVNRRSTELLYHQVDR
+FQAMLADLLEITRFDAGAATPALEATDMLELARDVVLTSQPLADQSGVPVYVVPMDRDRA
+DGHVAWVDPRRIERILRNLVNNAIEHAEGRPVDVLVAADEEAVTFAVVDHGIGMSPEQVQ
+RVFDRFWRADPSRKRTTGGSGLGLAIATEDTRLHGGRLEAWGELGEGSTFMVTLPRAPRP
+AAQGAEAPEPIGRSVLPIPPRYSTADRRYADDLSRPVPQEADADADAVGRVADVAATAAD
+APPCARQDEQALTAPTRPVRRVPPGDPADGPAAGDRTGEDAAEEAR
+>NAFOICDF_01332
+MTAPAEPPQPAETGDPDETGATSAPASAGPSTSAAPPRAGLRRRLRRRWNGSLQLRTAVL
+AGLLTLLASLMISGLITQQVAQALFDARHQQVEAEARRGLARVQSTFANAAATDQQATDA
+LVSQTMRALELDGGTTIRRRFRLEPLPGGTAASVGTVSSQGLDADVIPQDLRDAVASGPG
+VYDASIALPAADGNTRPGLAYGTQVVLPPGATYALYLVYDLSDVQESLDSVLGVLLMFGS
+GFLLVTVLVSWWAAHSVVRPVQQAATAAESISGGNLAVRMPVRGDDEMARLGTSFNRMAD
+SIQAQITQLAQLSRMQQRFVSDVSHELRTPLTTVRMAADVLYGSREDFDPVNRRSTELLY
+HQVDRFQAMLADLLEITRFDAGAAQLALEDTDLLALARDVVLTAAPLADQAKVPVYLVPL
+PLEEGLDCVAQVDPRRIERILRNLVNNAIEHAEGSPVDVLVAADEGAVSVAVVDEGIGMS
+PEQVQRVFDRFWRADPSRKRTTGGSGLGLAIATEDTRLHGGRLEAWGELGVGSVFMVTLP
+RRNGAESPVRRAVLPMPPSYDRGGRRLAADLHTPVTGPEGTGVHDAAALPERGREQEL
+>MHAAABBN_01202
+MTVSGPDVSAAPAAESGAEPVEPAAARPRSWGPGPAWRALRRRWRRSLRLRTAVLAALLS
+ILAGLVVAAFLTQQITQALFEARYEQVQSEARRGLSQVRETFAQTTATDAQSTDVLVTQT
+LRALEGDSGTTIRRRYHLAPLPDSESAYVGTISSAGLDPAVIPQELQDAVASGPGVYDAS
+VALPNPGGGTRPGLVFGAQVVLPPGATYGLYLVYDLADVQSSLDSVLGVLLVFGVGFLVI
+NVLVSWWVSRHVTLPVQQAARAAESLSSGNLAVRMPVDGEDEMARLGMSFNRMADSIQDQ
+IGQLAQLSQMQQRFVSDVSHELRTPLTTVRMAADVLYGSREDFDPVSRRSTELLYHQVDR
+FQAMLADLLEITRFDAGAATPALEATDMLELARDVVLTSQPLADQIGVPVYMVPMDRDRA
+DGHVAHVDPRRIERILRNLVNNAIEHAEGRPVDVLVAADEEAVTFAVVDHGIGMSPEQVQ
+RVFDRFWRADPSRKRTTGGSGLGLAIATEDTRLHGGRLEAWGELGEGSTFMVTLPRAPRP
+AVQGAEAPEPIGRSVLPIPPRYSTADRRYADDLSRPVPQEADADAVGTVADVATAAPPSA
+RQAEQALTAPTRPVRVVPAEDPAHGSAPGDPTGDDPAEEAR
+>LFPAFLNI_01420
+MTVSGPGLSAAPAAEPGAEPVEPAAGRPRSWVPGPAWRALRRRWRRSLRLRTAVLAALLS
+ILAGLVVAAFLTQQITQALFEARYEQVQAEARRGLSQVRETFAQTTATDAQSTDVLVTQT
+LRALEGDSGTTIRRRYHLAPLPGSESAYVGTISSAGLDPAVIPQELQDAVASGPGVYDAS
+VALPDPGGGTRPGLVFGAQVVLPPGATYGLYLVYDLADVQSSLDSVLGVLLVFGVGFLVI
+NVLVSWWVSRRVTRPVQQAARAAESLSSGNLAVRMPVDGEDEMARLGTSFNRMADSIQDQ
+IGQLAQLSQMQQRFVSDVSHELRTPLTTVRMAADVLYGSREDFDPVNRRSTELLYHQVDR
+FQAMLADLLEITRFDAGAATPALEATDMLELARDVVLTSQPLADQIGVPVYVVPMDRDRA
+DGHVAWVDPRRIERILRNLVNNAIEHAEGRPVDVLVAADEEAVTFAVVDHGIGMSPEQVQ
+RVFDRFWRADPARKRTTGGSGLGLAIATEDTRLHGGRLEAWGELGEGSTFMVTLPRAPRP
+AAQGAEAPEPIGRSVLPIPPRYSTADRRYADDLSRPVPQEADADAVGTVADVTAAAADAP
+PSARQAEQALTAPTRPVRMVPPADGTAAGGWTGDDGAEEAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001963.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001963.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e888706cd071ab6c960a815af7015cfc9a20209e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001963.fa
@@ -0,0 +1,14 @@
+>MOLHKGIG_01893
+MAGRWRAGAALTIRGEFSIVIAGPVLTRYADAFGRSRARAATRRVRAREVAAADPVH
+>NAFOICDF_00903
+MHGTTLALVELGAVLFLLGVLGRLAARIGMSPVPLYLLGGLLIGVGGLLFSGADPSGTLR
+SPVAAIGDFSSLAAEIGVVLLLLTLGLEYSARELMTGLRGSWRSGLLDVALNFTPGAAAG
+WLLGWGPVGAVVLGGITYISSSGIIAKVLNDLGRVGNRETPVMLSVLVFEDLAMAVYLPL
+MTALVAGSAFAAGLRAVGIALVVVAAVLFTALRFGPQISRLVYSPEQETFLLKVLGLALL
+VAGVAGALQVSAGVGAFLLGIAISGAAAKQARSVLEPLRDMFAALFFVLFGMNVDPRTLP
+PVLLGALALAVVTAATKVATGYLAARAAGIGVAGRWRAGATLTIRGEFSIVIAGLATASG
+TLPAEVSAFATAFVLILAVAGPLLTRSADGFGRRRAAAARVREARRARQAPLV
+>MHAAABBN_01589
+MAGRWRAGAALTIRGEFSIVIAGPVLTRYADAFGRSRARAATRRVRAREVAAADPVH
+>LFPAFLNI_01813
+MAGRWRAGAALTIRGKFSIVIAGPVLTRYADAFGRSRARAATRRVQAREVAVADPVH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001967.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001967.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0084fb6c382a68d377dfe8ec3b556cca666109f5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001967.fa
@@ -0,0 +1,44 @@
+>MOLHKGIG_01916
+MSAPHHPAAEPPARPIRWVGTQGFLVECASLEDVMAVHAHLTAHPERGQRQVMAAAATVL
+VTFTSQAAAEHAAPRVSTLTPDAGEVTGGRIVEIPVVYDGEDLAEVGRLTGLGVDGVIRA
+HSEADWFAAFGGFAPGFMYCASEAAPFEAPRRSSPRTAVPAGAVAVAGAFSAVYPRTSPG
+GWQLLGHTTAALWDLGREQPALLQPGDRVRYVPVRPTASVTSGTDAAVDATPPADAAAGL
+PSVAGRRGVTVVDPGLLTLVQDLGRPGLGDLGVVASGAADRDAARQANRLVGNRSREAVL
+ETVLGGLTLAAHGHQVMALAGAEAGGTITAADGAARRVPARSPFVVLDGQTLTVDEPVGG
+LRVYVGLRGGIDVPPVLGSRSTDTLSGLGPAPLTAGDRLARRVGPDARGAAGASAARPTA
+AGAPASEEAGVVMVGDPETSLRPMPAPGQVAVLRVVPGPRDDWFGEAGLERLFTQDWDVS
+QQTDRIGVRLTAPDDGAPLERVREGELKSEGAVRGALQVPPSGEPVLFLSDHPVTGGYPV
+IGVVARADLSLAAQLPPGARVRFVPHPRPGAETVVDSASPSEETPA
+>NAFOICDF_00879
+MSGTQAPGAATPRPIRAVGTQAFLVECASLADVMAVHAHLVAHPERGQRQVLSAARTVLV
+TFTSQAAAQHAAPRVAALDPDAQDRDAGRTVEIPVVYDGEDVAEVGRLTGLSPEAVVRAH
+VETDWFAAFGGFAPGFLYCAAEAPPFDVPRRDSPRTAVPAGAVAVAGQLSAVYPRTSPGG
+WQLLGHTDAVMWDLGRERPALLEPGDRVRYVPVRAEAVRGAAPAAEAPAEDTLVAAHTPD
+AGEASAPGLTVADPGLFTLLQDLGRPGLGDLGVVASGAADRDAARQANRLVGNASGEAVL
+ETVLGGLALTARGDQVLALAGAEATGVVTGPGGVARPVSPRTPFPLLDGETLTVQEPTAG
+LRVYVGVRGGLEAPRTLGSRATDTLSGLGPAPLTAGQALARHADLDAPRAGVVPVGDPEA
+PLRPMPAPGGTAVLRVVPGPRDDWFGPAGLERLTAQEWAVSQQTDRIGVRLTAGEAGPLE
+RIRTGELASEGAVRGALQVPPSGEPVLFLADHPVTGGYPVIGVVARADLGLAAQLPPGAR
+VRFVLHPQPSQEPTA
+>MHAAABBN_01612
+MSAPHHPAAEPPARPIRWVGTQGFLVECASLEDVMAVHAHLTAHPERGQRQVMAAAATVL
+VTFTSQAAAEHAAPRVSTLTPDAGEVTGGRIVEIPVVYDGEDLAEVGRLTGLGVDGVIRA
+HSEADWFAAFGGFAPGFMYCASEAAPFEAPRRSSPRTAVPAGAVAVAGAFSAVYPRTSPG
+GWQLLGHTTAALWDLGREQPALLQPGDRVRYVPVRPTASVTSGTDAAVDATPPADAAAGL
+PSVAGRRGVTVVDPGLLTLVQDLGRPGLGDLGVVASGAADRDAARQANRLVGNRSREAVL
+ETVLGGLTLAAHGHQVMALAGAEAGGTITAADGATRRAPARTPFVVLDGQTLTVDEPVGG
+LRVYVGLRGGIDVPPVLGSRSTDTLSGLGPAPLTAGDRLARRVGPDARGAAGASAARPTA
+AGAPASAEAGVATVGDPETSLRPMPAPGQVAVLRVVPGPRDDWFGEAGLERLFTQDWDVS
+QQTDRIGVRLTAPDDGAPLERVREGELKSEGAVRGALQVPPSGEPVLFLSDHPVTGGYPV
+IGVVARADLSLAAQLPPGARVRFVPHPRPGAETVVDSASPSEETPA
+>LFPAFLNI_01836
+MSAPRHPAATPPARPIRWVGTQGFLVECASLEDVMAVHAHLTAHPARGQRQVMAAAATVL
+VTFTSQAAAEHAAPRVSTLTPDAGELTGGRIVEIPVVYDGEDLAEVGRLTGLGVDGVIRA
+HSEADWFAAFGGFAPGFMYCASEAAPFEAPRRSSPRTAVPAGAVAVAGAFSAVYPRTSPG
+GWQLLGHTTAALWDLGREQPALLQPGDRVRYVPVRPTASLTSGADAAVDATPPADAAAGL
+PSVAGRRGVTVVDPGLLTLVQDLGRPGLGDLGVVASGAADRDAAHQANRLVGNRSREAVL
+ETVLGGLTLTAHGHQVMALAGAEAGGTITAADGATRRVPARTPFVVLDGQTLTVDEPVGG
+LRVYVGLRGGIDVPPVLGSRSTDTLSGLGPAPLTAGDRLARRVGPDARGAAGASAASPTA
+AGAPASAEAGVATVGDPETSLRPMPAPGQVAVLRVVPGPRDDWFGEAGLERLFTQDWDVS
+QQTDRIGVRLTAPDDGAPLERVREGELKSEGAVRGALQVPPSGEPVLFLSDHPVTGGYPV
+IGVVARADLSLAAQLPPGARVRFIPHPRPGAETVVDSASPSEETPA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001970.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001970.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ececfa9399098566469ac85a97b05f0a131b79e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001970.fa
@@ -0,0 +1,28 @@
+>MOLHKGIG_01997
+MPRRPAPLPPSIDPAAFTVDDARRAGVTWSRLQSSDLRRLRHGIYGPAGPAAASVREWTM
+DEVRAYQRRHPGVVVSHETAARLHGLTVPARLLAPGAVHVSVGTSGGRPVQAGLVPHRIE
+VPEGQRMTRGGVLVTTPARTLWDLCAARSALTERDVVAAGDALLCPPWLPGGGRGAPAYT
+PEELVRSLAERGRFRGRGLARAALARMRVGADSPRETRLRLALVDAGLPEPEVQCRLDPS
+DRRAPTVDLGYRQWRLALQYDGEHHRTAEQQARDVLRDRWCADHDWLSIKVMWADARDDY
+ADVVARVRRRAAEFGG
+>NAFOICDF_00796
+MPLRPVALPDSLISGPFTTRELLAAGAPAQRVRSPDLRRVAHGIHRPRSASGSTGDATAA
+ERGWLPEEVRAYQRMVPHAVVSHTTAARLHGLPLPAWAADERDVHLTFTAGAGRTRRRGL
+VAHQAGIPALDVALVAGVRVTTPPRTLWDLCSLHPRLSVEDLVVVADAVMAPGWDDEHGF
+LPGEHSAAALREALGRRGRFRGVRAAREVAERMREDVASPMETRTRLALVDQGLPEPEVQ
+VRLWGEDGAKGPVVDLAFPQWRVVVQYEGARHRTREQQERDVRRDRWCADHGWTVIKVVA
+ADVHAGLGPVAARILRLARQ
+>MHAAABBN_01691
+MPRRPAPLPPSIDPTAFTVDDARRAGVTWSRLQSSDLRRLRHGIYGPAGPAAVSVREWTM
+DEIRAYQRRHPDVVVSHETAARLHGLTVPARLLAPGAVHVSVGTSGGRPVQASLVPHRIE
+VPEGQRMTRGGVLVTTPARTLWDLCAARAALTERDVVVAGDALLCPPWLPGGGRGDPAYT
+PEELVRSLAERGRFRGRGLARAALARMRVGADSPRETRLRLALVDAGLPEPEVQCRLDPS
+DRRAPTVDLGYRPWRLALQYEGEHHRTAEQQARDVLRDRWCADHDWLSIKVMWADARNDY
+ADVVARVRRRAAAFGG
+>LFPAFLNI_01923
+MPRRPAPLPPSIDPAAFTVDDARRAGVTWSRLQSSDLRRLRHGIYGPAGPAAVSVREWTM
+DEVRAYQRRHPDVVVSHETAARLHGLTVPARLLAPRAVHVSVGTSGGRPVQAGLVPHRIE
+VPQGQRMMRGGVLVTTPARTLWDLCAARSALTERDVVVAGDALLCPPWLPGGGRGAPACT
+PEELVRSLAERGRFQGRGLARAALARMRVGADSPRETRLRLALVDAGLPEPEVQCRLDPS
+DRRAPTVDLGYRPWRLALQYEGEHHRTAEQQARDVLRDRWCADRDWLSIKVMWADARDDY
+ADVVARVRRRAAAFGG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001974.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001974.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b7c6f1252080d369911ebebc3eeeb20bc43890a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001974.fa
@@ -0,0 +1,39 @@
+>MOLHKGIG_02062
+MSEHFDVAVLGLGPGGEVAADRLLKAGKNVVVFERELIGGECAYWACIPSKTVLRPPEAR
+TEVQRAAGVSGAELDWAATAKYRDYMIRNLDDQAQVDGYIKEGAVVIKDEARITGPGRIQ
+AGDREITAEHIIIATGSDAVIPPLDGIDQITAWTNRETYTTSTLPERAVIIGGSAVGVET
+ATFLARFGVAITLIHCGERLLDREGPRVGELAHQYLQEAGIDIRLATSAVQARREGADSI
+IELQTRDGDPAGEVAADVVIFGTGRTPRTEGLGFEHAGVTLGDHGEIQIDDHCRAGENTW
+AIGDVTGIMPFTHVAKYQGRIAADAILGRPHPATYDGIPRVVFTDPEIAGAGLTQEQATK
+QGIRTIATELDLADAIARPWTYEQDSRGHLGLLADADRKILIGAWAVGPMAGEWIHHASL
+AIRTQLPIDTLLDQVAQFPTYHEAYQVALEQLDLTP
+>NAFOICDF_02222
+MSEHFDVAVLGLGPGGEVAADRLLKAGKNVVVFERELIGGECAYWACIPSKTVLRPPEAR
+TEVQRAAGVSGAELDWAATAKYRDYMIRNLDDQAQVDGYIKEGAVVIKDEARITGPGRIQ
+AGDREITAENIIIATGSDAVIPPLDGIDQITAWTNRETYTTSTLPERAVIIGGSAVGVET
+ATFLARFGVAITLIHCGERLLDREGPRVGELAHQYLQEAGIDIRLATSAVQARREGADSI
+IKLQTRDGDPAGEVAADVVIFGTGRTPRTEGLGFEHAGVTLGDHGEIQIDDHCRAGENTW
+AIGDVTGIMPFTHVAKYQGRIAADAILGRPHPATYDGIPRVVFTDPEIAGAGLTQEQATK
+QGIRTIATELDLADAIARPWTYEQDPRGHLGLLADADRKILIGAWAVGPMAGEWIHHASL
+AIRTQLPIDTLLDQVAQFPTYHEAYQVALEQLDLTP
+>NAFOICDF_02426
+MTEDLAPTTGPDDATPGAPDEEAVDVVVIGAGPVGENAAQYAHTAGGLEVALVEADLLGG
+ECSYWACMPSKALLRPLEVAGAAAHLGGLTDPDIDLPGLLARRDEWRSHLDDAGQVEWAE
+DAGLRVVRGHGRLAGPRRVEVLGDDGAPARVLRARHAVVVATGSTAVVPGELRGVSPWTS
+RDATGVREVPGRLAIVGGGVVAVEAATWMAALGSDVQLLVRGDRLLSGQEPVASRLVLEG
+LVDAGVRVRFGTSVERAERADVHAESDVGVPHGGPVRLTLAGSGETLEVDELLVAAGRRP
+ALDGLGLEALGLSAEDLQDESGTAVVPASDGAAPWLYAVGDVTGGPALTHWGKHRARLLG
+ERIAALATGRPAPSGEEAGEGVPEAVPQVVFTSPQVARVGVTEAQAREEGGEGELRVVDV
+PLTSAAGAALLRDDAAGRAVLVLRGDRVVGATFVGFEVAELLHAATVAIVGEVPLDRLRH
+AVAAYPTASEVWLRLVEEALGRG
+>NAFOICDF_02440
+MSSVIPDTARPSSGHAGVHRADVVVLGHGLAGLVAACELLEAGRSVVLVDQERAADLGGQ
+AWWSFGGLFLVDSPEQRRLRVRDSVDLAWSDWRETAGFTGGDDALPRAWAEAYVHFAAGE
+KRAWLRERGHRLFPVVGWAERKVPAPGVGGNSVPRFHITWGTGPGIVEPFAAVVEQAAFD
+GRLTYLPRHRVTELVTQNGAVCGVRGDRLADDDGARGTSSSRTVTGAFEVRAQAVLIASG
+GIGADHDAVRAAWPDRLGTPPERMLSGVPAYVDGSGVAAARAVGAHMLHPDRMWHYTEGV
+ANWDPVWPGHGIRILPGPSSLWLDAAGRRLPHPRWPGFDTLGALGEICRPGGARRAEGAD
+HTWFVLNERIIGREFALSGSEQNPDLTGRSLGHVLGRATQGVPAPVRAFLDHGEDFVQAA
+TVEELVDQMNELQDRTGGGGPRVELHAVRQAVAEHEDGAARAGVDPQLDAVRRARQYLGD
+RLIRTAAPHRLTDPAAGPLIAVRLRTLTRKTLGGLHTDLRGRVLDELGGPVPGLYAAGEA
+AGFGGGGMHGFRALEGTFLGGCLFSGRTAGRALAEDVA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001978.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001978.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d42f8bf43ac1be18f46b995ade8d8737cfc2f42e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001978.fa
@@ -0,0 +1,36 @@
+>MOLHKGIG_02222
+MTHRNPEDNALRGAPEPRTLAEACDLVTTPDLDVSADGMFGQYGGAHLPPQLAGPMAEVA
+RAYAEARQDPEFYAEYRRLLRDAVGRPSPLTPLDRLSDELGGARIVLKREDLNHTGAHKI
+NHTIGEALLAKRMGKRSLIAETGAGQHGVALATAAAMVGLDCEIHMGAIDVAKQHPNVVR
+MRLLGTKVVSVEREGRSLKEAVDSAFEVYAADPEKYLFAIGSVVGPHPFPTMIRDFQSVV
+GREARAQFQERFGALPSAVVAAVGGGSNAMGAFTAFLDDADVALVGVEPGGRSATKGEHA
+MTMTQGRDGVLHGMATLVLADDDGTPDPVHSIASGLDYPGVGPQHAHFARLGRVRYVAED
+DAAVLDAFQRLTRLEGVIPALESAHAVAHAIRLAPQMGRDERILVNLSGRGDKDVDYVAE
+KLGLTGEADEVVR
+>NAFOICDF_00461
+MTHRNPEDNALRAADAARPEPRTLAEATDLVHTPDLTAGADGMFGTYGGAVLPPELAGPM
+AEVAEAYEEARHDPEFYAEYRRLLRDVVGRPSPLTPLDRLSDELGGARIVLKREDLNHTG
+AHKINHTIGEALLAKRMGKRSLIAETGAGQHGVALATAAAMVGLDCEIHMGSIDVAKQHP
+NVVRMRLLGATVVSVDREGRSLKEAVDSAFDVYASDPAHYLFAIGSVVGPHPFPTIVRDF
+QAVVGREARAQFLERYGALPSAVVAAVGGGSNAMGAFTAFLDDADVRLIGVEPGGRSATK
+GEHAMSMAQGVDGVLHGMATKVLQDEQGVPDPVHSIASGLDYPGVGPQHARLAQLGRVEY
+VAEDDAAVLEAFQRLTKLEGIIPALESAHAVARAIRMAPGLGTDQRILVNLSGRGDKDVD
+YVAETLGLTGDADEVVR
+>MHAAABBN_01938
+MTHRNPEDNALRGAPEPRTLAEACDLVTTPDLDVSADGMFGQYGGAHLPPQLAGPMAEVA
+RAYAEARQDPEFYAEYRRLLRDAVGRPSPLTPLDRLSDELGGARIVLKREDLNHTGAHKI
+NHTIGEALLAKRMGKRSLIAETGAGQHGVALATAAAMVGLDCEIHMGAIDVAKQHPNVVR
+MRLLGTKVVSVEREGRSLKEAVDSAFEVYAANPEKYLFAIGSVVGPHPFPTMIRDFQSVV
+GREARAQFQERFGALPSAVVAAVGGGSNAIGAFTAFLDDADVALVGVEPGGRSAAKGEHA
+MTMTQGRDGVLHGMATLVLADDDGTPDPVHSIASGLDYPGVGPQHAHFASVGRVRYVAED
+DAAVLDAFQRLTRLEGVIPALESAHAVAHAIRLAPQMGRDARILVNLSGRGDKDVDYVAE
+KLGLTGEADEVVR
+>LFPAFLNI_02161
+MTHRNPEDNALRGAAEPRTLAEACDLVTTPDLDVSADGMFGQYGGAHLPPQLAGPMAEVA
+RAYAEARQDPEFYAEYRRLLRDAVGRPSPLTPLDRLSDELGGARIVLKREDLNHTGAHKI
+NHTIGEALLAKRMGKRSLIAETGAGQHGVALATAAAMVGLDCEIHMGAIDVAKQHPNVVR
+MRLLGTKVVSVEREGRSLKEAVDSAFEVYAADPEKYLFAIGSVVGPHPFPTMIRDFQSVV
+GREARAQFQERFGALPSAVVAAVGGGSNAMGAFTAFLDDADVALVGVEPGGRSATKGEHA
+MTMTQGRDGVLHGMATLVLADDDGTPDPVHSIASGLDYPGVGPQHAHFARVGRVRYVAED
+DAAVLDAFQRLTRLEGVIPALESAHAVAHAIRLAPQMGRDERILVNLSGRGDKDVDYVAE
+KLGLTGEADEVVR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001983.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001983.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e5f605c3721258df7caa3f2c18dc38ca81b9a1a3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001983.fa
@@ -0,0 +1,23 @@
+>NAFOICDF_00423
+MGAMTDPTSRALRLLGLLEARAVWTGAELAERLGVTSRTLRRDVDRLRTLGYVVEADPGP
+GGGYALGRGQVVPPLLLDEDQAVAVTLALTRAAHAGDGVAAESALRALATLDALMPADLR
+HRLEGLRAASTVGAGDGPPVGPELLACADAVRRRVRLTFGYRDRRGARTERRVEPHRLVA
+RARAWLLVAHDLDRDDWRTFRVDRIVDPAVGTWAFTPRPDLAEALARLDEPTPPEAWRHR
+VSVRVHAPLESVRASLPATAGRLTALDARTTAFETGADDPAEAARWLALLGHEFEVLGDE
+PVRAAVAALADRLHRSTVQVLRG
+>NAFOICDF_00644
+MASPCRRFRTPNVRNPRHAGVMADTSARILRLLSLLEARVEWPGGDLAERLGVSARTVRR
+DIDTLRELGYPVEAVPGPGGGYRLGAAGKLPPLVLDDDQAIAIALALQTAPATVTGIDDA
+VARALTTLRQVMPARLRAASEAFEVTALRNYWEFSAPPIDVATLQVVGSAIRTSSCLRFD
+YADPDGRVPGPGDADFRPPHDVEPHHLVVWAGRWYLVARDRNHGTWGTYRVDRIRPKTPA
+GRPFTPTPLDPDDLNRLVVQNPDRGDTPGQWQCVGTATLPLPADVVARWAPGGSAVAPID
+RQSCRLTIGGWSWAGVAGLFITFDTDLTNVEPSGLRDALATIRRRLEPAPLGGLRPTLQQ
+>NAFOICDF_01784
+MPSVKIPPLLLDADEVCSLVTGLLLLEAGGVNEAATVRTKLEQLLPPKLRQQAAATALAT
+QVITPVAAPVDWRLLGVLAEAVAQGQNLRFTYTDQHSKVSERHIRPYRHALRKGAWYLIA
+YDIQRTDWRLFRLDRIQHATPEPTATGIDVPVFPSPSIEEWLTTDFGRLPASAG
+>NAFOICDF_01822
+MLGYDIQSHPGPGGAYVLAPSIKIPPLLLDADEVCALVTGLLILEAGFADDSATTVRAKL
+ERLLPPSLRQRAVAAAAATQVLTATHAFDWPALGMIADTIAVGQHLGFAYTDQHGHASNR
+IVQPYRQVLRHGIWYLVAYDTQREDWRLFRSDRVHEPEPRTPAPGYEAHPFPDESIHRWL
+ITDFGRAAQHVN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001984.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001984.fa
new file mode 100644
index 0000000000000000000000000000000000000000..82c1d7222332aed8bd0937d48193de1dbe060b62
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001984.fa
@@ -0,0 +1,24 @@
+>NAFOICDF_00661
+MDTPVMASLPAGVITLRDARRSQTREVTLEAFEIAVHPVHDQGSGLPWAPFTWFDAVAYC
+NELSRASGLQEAYTWQGRTVDWDTAADGYRLPTEAEWEYACRAGTTSPTYGLVEDIAWTS
+LDDVDSPQPVGSKAPNAWGLHDMLGNVWEWCWDYADPARYGDYRSLRGGGWADEPWSVRA
+SVRRGSAPNAVLEDVGLRLARGPVGSPGQAQGWSHEADRQRAAIRGPLPVGWTPLWEIAR
+>NAFOICDF_00698
+MNQPSMATLSSGKITLRDARRRTTRDVELEPFEMAVHPLHDRSTGRPLTPLTWFETINLC
+NELSKAEELQPAYTRAGGGRSVTWNTSADGYRLPTEAEWEYACRAGTTSPTYGPLEDIAW
+ISLDHLEGPQPVGMKKANPYGLHDMLGNIWEWCWDYADPARYGDYRSLRGGGWADEPWSV
+RASVRRGNAPDAVLEDVGLRLARGPVGSPGQAQGWSHEADRQRAAIRGPLPVGWTPLREI
+FA
+>NAFOICDF_00722
+MNQPSMATLSSGKITLRDARRGTTRDVELEPFEMAVHPLRDRSTGRPLTPLTWFETINLC
+NELSKAEELQPAYTHAGDGRSVTWNTSADGYRLPTEAEWEYACRAGTTSPTYGPLEDIAW
+TSLDHLEGPQPVGMKKANPHGLHDMLGNIWEWCWDYADPARYGDYRSLRGGGWADEPWSV
+RASVRRGNAPDAVLEDVGLRLARGPVGSPGQAQGWSHEADRQRAAICGPLPVGWTPLREI
+FA
+>NAFOICDF_01398
+MQGAIDDDMMLTGAVDEWRFIVQTLADRLDQAAHAAGTPVSTAADVDAGTPAGTVSSDHQ
+AGPDMVVIPAGTYTAGSTDAEHEAWGVPENRRDFELPQREVTIAEPFALGRTEVTVEQFQ
+AFVDDTGYQVCGGSRWWDPEDPSAMTFNPELSYLDPGFEQTPDSPSVALTRQDAQAYVDW
+LSETTGESDRLPTEDEWEWAARGGADTAFFWGDTLDEAARYANTYDTVSQAVNGFPWESL
+SVTDRFAHTAPVGSFEADGFGLYDVTGNARAFMADDWIEDLSGTAGDGSVHDGPVPFPVV
+RGGAWNYQPQNLRLDYRGAYLSAEVATTMFGFRVVRDLG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001985.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001985.fa
new file mode 100644
index 0000000000000000000000000000000000000000..83b04a3e1640e8a103b0f009a49d38f93b9c8b58
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001985.fa
@@ -0,0 +1,12 @@
+>NAFOICDF_00674
+MAYLFLIIAIIFEVAGALSLRMATSGSKKKGLWLLAVLGGYGIAFFGITMALVEGLALGV
+AYGIWAASGVALTAVLSRILFKEPLTKVMAAGIGLIIVGVLMIELGAAH
+>NAFOICDF_00675
+MKWVFLAGAIALEVTGSLSLKAAVDAPGFFALVAVGYIGAFTLLAGALKQGMPLGVGYGI
+WGAAGVALTAILSAVIFGEPLTALMTLGIAVVIGGVLCVELGSQAATKKREGTV
+>NAFOICDF_02225
+MQWLFLAGAVLSEVAATLCLRVAAAGRRGFYAAVAVGYVLAFVFLTLALRAGIGLGVAYG
+IWAAAGVALTAIASHVLFKEPLTRTMILGILLIMAGVLVIEIGSSSH
+>NAFOICDF_02226
+MTKWFLLAGAVGSEVIASLSLKAALTHPALYAVVLLGYVSAFTFLTLVLKRGMALGVAYG
+IWGALGVAATAVLSAVLFDERITAMMGIGIALVIAGVLMVELGSHHTPDTDEQQAGAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001987.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001987.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2bd44c0ad02ced71ad30950c39085ded9afd23f7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001987.fa
@@ -0,0 +1,12 @@
+>ACLBLIBL_00145
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGRIP
+>MHAAABBN_01119
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISAY
+GT
+>MHAAABBN_01966
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGLSRL
+RDLTPGQVPGSGVTVFEAVGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001991.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001991.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c383aeec43668df6d8529d2ca713b6defd680e02
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001991.fa
@@ -0,0 +1,30 @@
+>ACLBLIBL_00211
+MPYAVRVITGDLKTKVDRVWNTFWTGGISNPLEVIEQMTYLLFLRRLDELHTAQEKRAAF
+MNGPIEDPKFTPEQDHLRWSRFRDLDPDTMFLTVSDAVFPFLREYGRQVGGEDSTYSAHM
+KDARFTIPNAGLLATVVDLVDQLPMADRDTNGDLYEYLLSKLASSGVNGQFRTPRHIIDL
+MVRMTAPTPADEICDPACGTAGFLVAASEFIREEHPQVLVDAQQREHFHRSMFHGYDFDS
+TMLRIGSMNMLLHGVESPDIRYRDSLSEGASADAEKYTLILANPPFTGSLDYDSTAADLQ
+RVVKTKKTELLFMALFLRLLKPGGRAAVIVPDGVLFGFTKAHREIRRLLVEEHLLEAVVK
+LPSGVFKPYAGVSTAILFFTKTGTGGTEDVWFYDVRADGFSLDDKRNRVEANDLPDVLER
+WRNRGAEADRARTEQSFLVPRQEIVDNGYDLSLNRYKEIEFEETEHRDPLEIIAELEQLD
+DEIRAGLAELKEMLR
+>MOLHKGIG_00038
+MTVDARRLVDKLWSYVHVLRDDGVGVLDYTEQLTYLLFLKMAHERATRPLKPEQVLPEQY
+SWQRLMDARGQDLEAVYTGMLQGLSREPGVVGTIFRKAQNRIQDPAKLRRIIVDLIGAQQ
+WSQSGTDLNGDAYEAILARSASDGSSGAGQYFTPRALIEAIVDAVDPTVEDTVVDPAAGT
+GGFLLVAHDHASREASSMTPTQREKLRDDFVHGYELVDATARLAAMNLLLHGMGRYDGDS
+LIDVRDSLTSAPSRRWSVVLSNPPFGRKSSMTVVGDDGREVREDREIVRQDFVATTSNKQ
+LNFVQHIMTILDVNGRAAVVLPDNVLFEGGAGEVIRRKLLTDFHLHTLLRLPTGIFYAQG
+VKANVIFFDKKPARPGEVWTDAMAVYDLRTNKHFTLKQSPLRRADLDEFVSGYRRPEAQV
+GERWKTFTYDELIARDKANLDITWLRDETLEDMDNLPSPDVLAREIVEDLTAALAEFEAV
+AVSLEEQLSSADGTQEDR
+>LFPAFLNI_00188
+MHPIAYADPVITGELKTKVDRVWNTFWTGGISNPLEVIEQMTYLLFLRRLDELHTAAQRR
+AEFTGRPIEDAKFAPHQDHLRWSRFKELDPDTMFLTVSDSVFPFLREYGRQVGGEDSTYS
+SHMKDARFTIPNAGLLATVVDLVDQLPMADRDTNGDLYEYLLSKLQSSGVNGQFRTPRHI
+IDLMVRMTAPTPADEICDPACGTAGFLVAASEFVREEHPEALVDATQRRHFHRSMFHGYD
+FDSTMLRIGSMNMLLHGVESPDIRYRDSLSEGASADAEKYTLILANPPFTGSLDYDSTAA
+DLQRVVKTKKTELLFMALFLRLLKPGGRAAVVVPDGVLFGSTKAHREIRRLLVEEHLLEA
+VVKLPSGVFKPYAGVSTAVLFFTKTGTGGTEDVWFYDVQADGFSLDDKRNPVEANDLPDV
+LERWRNREGEAGRARTEQSFLVPKQEIADNAYDLSLNRYKEIEFEEAEHRDPLEIIAKLE
+KLDDEIRAGLAELKEMLK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001997.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001997.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c3d14d5971d1ba996e72830272ddbbc1b0658c74
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001997.fa
@@ -0,0 +1,27 @@
+>ACLBLIBL_00533
+MTSTTPRAALRRPLGLTLTAAFSALALTACGGGGGTAASSSPAAGGSASSSAAGGSDQGA
+ASSSSAGQDLTEAGAATITMWVDQNRQKPLQAVAEDFKEDTGITVELVVKDNSKMKDDFI
+TQTPTGEGPDVIVGAHDWIGSLVQNGTIAPLELGDTADAFSETSVQAVTYDGQTWGVPYS
+VENLAILRNTALAEETPASFDEMIAEGQKAVDAGDADYPFVVGLDPVNGDPYHLYPFQTS
+MGAPVFEQQEDGSYDVSSLAMGGAEGQAFAEKLAEYGESGVLNPNMTADIAKEQFNAGKA
+AYFITGPWNVDEAEEAGVDFAVEEIPSMGDQPAQPFVGVNAFFVSAESENQLAANEFVVN
+YLSSEEAQDALYAEGKRPPALTASFEKAAVDETVKAFGEIGEDGVPMPAAPEMGAVFEFW
+GGAEMSIIKGEGDPAQTWDKMISDIEGRIGQ
+>MOLHKGIG_02211
+MQSTTTGGLFRRPLSLTLTAAFSALALTACGGGSSAPASSSPAGATEQGTATASPSQDLS
+EAGASTITMWVDQNRQEPLQAVAEDFKEDTGITVELVVKDNSTMKDDFITQNPTGEGPDV
+IVGAHDWIGSLVQNGTIEPLELGERAGDFVESSVQAVTYEGQTWGVPYSVENIAILRNTE
+LAESTPASFDEMIAEGRKAVDAGEAEYPFVVGLDAVNGDPYHLYPFQTSMGAPVFKQAED
+GSYDTGSLAMGGPEGEAFAEKLAEYGESGVLNPNMTADIAKEQFNSGNAAYFITGPWNIE
+EAEAAGVDFEVEAIPSMGDQPAQPFVGVNAFFVSSESENQLAANEFVVNYLSTEAAQDAL
+FAEGKRPPALTASFDKAASDETVKAFGEIGENGVPMPAAPEMGAVFEFWGGAEMSIIKGE
+GDPVQTWQKMISDIEGRIGQ
+>MHAAABBN_01924
+MQSTTTGGLLRRPLSLTLTAAFSALALTACGGGSSAPASSSPAGATEQGTAAASPSQDLS
+EAGATTITMWVDQNRQEPLQAVAEDFKEDTGITVELVVKDNSTMKDDFITQNPTGEGPDV
+IVGAHDWIGSLVQNGTIEPLELGDRAGDFVESSVQAVTYEGQTWGVPYSVENIAVLRNTE
+LAESTPASFDEMIAEGQKAVDAGEAEYPFVVGLDPVNGDPYHLYPFQTSMGAPVFKQAED
+GSYDTGSLAMGGAEGEAFAEKLAEYGESGVLNPNMTADIAKEQFNSGNAAYFITGPWNVE
+EAEAAGVDFEVEAIPSMGDQPAQPFVGVNAFFVSSESENQLAANEFVVNYLSTEAAQDAL
+YAEGKRPPALTASFDKAASDETVKAFGEIGENGVPMPAAPEMGAVFEFWGGAEMSIIKGE
+GDPVQTWQKMISDIEGRIGQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001999.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001999.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a5ee0241ec48060fe80210c427f4dc1c4f46fc8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0001999.fa
@@ -0,0 +1,14 @@
+>ACLBLIBL_00551
+MTTTIQDPWAQPTPAGAYDDLLVRALPVTRAQRRWEPADGPMPSLFVSHGAPPTLDDPQW
+LADLFDWAQSMPKPRAIVIVSAHWEDAPVAISSAAAGTPLVYDFGGFHPRYYELQYATPD
+ATDLAARVAGVLGQGRPGSVHQTGRGLDHGAYIPLMAMYPDADVPVVQVSMPSMDPSALL
+DLGVKLRSLREEGVLVIGSGFMTHSFAAMRDPRLFGHVDAFDKWAAEMTHAGDVDSLIGY
+LDKAPGARIAHPTADHYVPLLLTMGAANDPSSARTVFDRFVFSNHIRSFSVD
+>MOLHKGIG_02191
+MGGRPAAGLDPPQTAQSGHADDPSSARTVFDRFVFGNHIRSFSVD
+>NAFOICDF_00474
+MTLADPWAQPTPAGAYDDLLARALPLTRRQKLWEPSDGRMPALFISHGAPPTLDEPQWLN
+DLFEWAQTMPKPRAIVIVSAHWENAPAAISASAAGTPLVYDFGGFHPRYYTLRYDTPDAT
+DLARRLAGVLGAQGQEVHQHTDRGLDHGAYIPLMAMYPDADVPVLQVSMPSQDPADLLRL
+GERLRELRDEGVLVIGSGFMTHSFAAMRDPRLFGHVDAFDTWAAEMAHAGDVDALMGYLD
+RAPGARIAHPTADHYVPLLLTMGAAHDPSTTRTVFNRFVFSNHIRSFTVD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002000.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002000.fa
new file mode 100644
index 0000000000000000000000000000000000000000..115cd1b876a3c89aba2017470864dd205ec80da0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002000.fa
@@ -0,0 +1,13 @@
+>ACLBLIBL_00570
+MPDLQPVPTLADVPELGDGVVTLHPADARHAPALGALLRDADVQVLTGSVHSTAQAAAIA
+RGEAHAGPTPERLAEIYAGWAADEDRAVWTVEAEGAVLGEILLMDLDAGNRACGLRLWLA
+GAGRDRGVGTRALTLVLEHAFTTVGLHRVGLEVYDHNPRARHVYARLGFVHEGTLRQALL
+LDGEWIDCHVVGLLAHEWHARRAAPSSD
+>NAFOICDF_00497
+MTPDPSVDASPQAAPTVAVTADPGRAPADDAGPDERRPSEPTRVQALFYSPPELTDGRIT
+LRPAGADDAAALYPLLQDRETLLLTGSTHSSARADRIVSGEIQPWGSPEKLAEDYDAWSV
+ADDRAVWVIEEDATIVGEMVLMDLDPPNISCALRLWITGATDRGIGTAALTLALDWAFRT
+VELHRVSLDVFEHNPRAIHVYEKLGFVREGTMREALWQDGRWIDSLGMGILRREWLARQD
+G
+>NAFOICDF_00659
+MVDNLRAVQLYLQCGFVVEGLRRTSLIRDGGSVDEYAMAQLVLSSGSESAVVDK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002001.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002001.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26be2338d1396914f375ab2f63e50a8710f95fe0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002001.fa
@@ -0,0 +1,18 @@
+>ACLBLIBL_00591
+MSEHTATPARAGSPAWIDYSATDFAAQQAFYEALFGWTFTDSGEEFGHYRMIAKDGASVG
+GAMDADQMTAMTGEAPAPAAWTVYLRTEDMAATLAAVREHGGTVLVDAMPVGDLGTMAMV
+AGPGGEAVGFWQADTFEGHDLPLTPGTSVWFELLSTRFDEAVEFYQAVAGWQPTLMGDDG
+APEDGHAAADAEDAAQDGPRYATDHPGEGATAGLCDATQWLPANAVGYWRMYIAVEDTDR
+ALEVIREHDGKVLDGPQDSPFGRVTTVQDPAGATFQINEALPGQE
+>ACLBLIBL_01322
+MSITPGQPVWIDLGTTDLERSKAFYRDLFDWNFSDTGGEFGHYHMVDAGVPVGGLGPNVD
+AEGNIDASMPVWWTVYLKVEDVDATLAAVREHGGHVHVEPMQIGDMGRMAIVAAPSGAAF
+GVWEVGSFEGFDTEGRPGTPVWFEALTKDFDADAAFYAAVLGWKNVPMREGSSDEGAAEE
+DGAGMRYVTDAAGDDASAGLFDAAAFLPAEVPSHWRVYFAVPDTDAAVEKVLALGGAVVE
+PAQDSPYGRVAAVADDLGGTFMVIA
+>NAFOICDF_00514
+MSAQHTAIPSGSPIWIDYSAGDFATQQAFYSALFGWTFQDQGEDYGHYTMVRAGDAVIGG
+AMDGELSAQFSGGPVQPAAWTVYLKTEDIARTLGLVAEHGGQVIVEAMPVGELGSMALAM
+TPGGEAVGFWQPGEFSGHDLPLTPGTSVWFEVMSKDFAADAEFYRAVCGWDVVPMGPDGQ
+QDDAAPDEDGMPAYATDHTGEQATAGLCDAAAWLPEAVPSHWRVYFQTTDMDASVKVVEE
+KGGRIVDGPMDSPFGVVASVVDPAGATFQLNQPPARG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002002.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002002.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9f7d446a32a2701403464650567da3a15e58525f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002002.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_00642
+MTRTLEEIWPPYGLVVEAGDLRMTALREADVPEVLDVVAGGIHDPSWTPFLFPWTDAPAE
+EMPANYLRFYASTLTRTVDGDVSLELVVRRNGQVIGMQGMNGPDVAGTRRLETGSWLGLP
+FQGQGLGTRMRRMMCALAFDGLGLDAVTSSAWEDNAASRRVSEKVGYLETGRGQAERRGV
+PTGEVFFELRPEGFVRGDEPVRIMGAEELRRFLGLG
+>MOLHKGIG_00176
+MTRTLEEIWPPYGLVVEAGDLRMTALREADVPEVLDVVAGGIHDPSWTPFLFPWTDAPAE
+EMPANYLRFYASTLTRTVDGDVSLELVVRRNGQVIGMQGMNGPDVAGTRRLETGSWLGLP
+FQGQGLGTRMRRMMCALAFDGLGLDAVTSSAWEDNAASRRVSEKVGYLETGRGQAERRGV
+PTGEVFFELRPEGFVRGDEPVRITGAEELRRFLGLG
+>NAFOICDF_00050
+MTRTLEEIWPPSGLVVEAGDLRMTALREADVPEVLDVVAGGIHDPSWTPFLFPWTDAPAE
+EMPANYLRFYASTLTRTVDGDVSLELVVRRNGQVIGMRGMNGPDVAGTRRLETGSWLGLP
+FQGQGLGTRMRRMMCALAFDGLGLDAVTSSAWEDNAASRRVSEKVGYLETGRGQAERRGV
+PTPEVYFELLPEGFVHGDEPVRITGADELRRFLGLA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002005.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002005.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ef7027bf92553c9201fc3440d16251929a029f5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002005.fa
@@ -0,0 +1,14 @@
+>ACLBLIBL_00731
+MEPEALYEDKASGKSDDRPHLAACLKALRAGDTLLVWKLDRLGRDLRHLVNIVHELTERG
+VGLKVLTGQGAAIDTTTASGKLVFGIFAALAEFERELISERTKAGLASARARGRKGGRPY
+KMTPAKIRLAMASMGNKDTNVGALCKELGITRQTLYRHVSPTGELREAGQKVLAQRR
+>NAFOICDF_00679
+MGHLLGYARVSTTDQDASLQIDALGAAGCYRVFVDTMSGSLQHRPELDKLLDQLRPGDTL
+VVWRLDRLGRSIRHLIDQLHALAERGIGFRSLQETIDTTSPGGRLVFHVFAALAEFERDL
+IKERTNAGLAAARARGRTGGRPSRLSADQVRTARRLYEQQDMTVAQIGDVLGVSRTTIYR
+TLAKHAEPVARRRAKPSPTM
+>MHAAABBN_01775
+MRVSKADGSQATDLQRDALLEAGVEPEALYEDKASGKSDDRPHLAACLKALRAGDTLLVW
+KLDRLGRDLRHLVNIVHELTERGVGLKVLTGQGAAIDTTTASGKLVFGIFAALAEFEREL
+ISERTKAGLASARARGRKGGRPYKMTPAKIRLAMASMGNKDTNVGALCKELGITRQTLYR
+HVSPTGELREAGQKVLAQRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002013.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002013.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2784e8e6bdfd14404df37b0e777367749c7a6575
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002013.fa
@@ -0,0 +1,24 @@
+>ACLBLIBL_00809
+MADRPAVIDHPDYFLLDSDLTDAQRALRDRVRDFGREQVLPIINEWWEKAEFPEPLLPGL
+ADLGIIGTYIEGYGCPGMSRIEAGLVAREMGRIDGSVNTFLGVHSNLCMGSIYILGSDEQ
+RQRWLPAMAKLEKTGAFALTEPKHGSDSVSLETSARRDGDEWVITGHKRWIGNGHAADVV
+VLYARDEADGEVKAFVVEKQEDGSFPAGYNPTVITGKVGKRAILQADIVIENLRVKEENR
+LVNCESFAGVNRVLKATRGGASWEAVGHGMAAFEIAAAYALEREQFGAQIGGYQLVQERL
+ATMLTDLTTMQLMCVRMAELQERDELTLAMASMVKMHTSRKALDMTRTARDIVAGNGLLL
+ERHIGRHLTDMEVVSTYEGTDSMQALIVGRDITGISAFTRSRRKS
+>MHAAABBN_02304
+MSETRSGVLPDHDIYLLDDELTEEQREVRDRVRAFVDAELMPVINDYWERAEFPFELVPK
+LAELNVAGTVIEGYGCPGMSRMAGALVSMELARGDGSFNTFFGVHSGLAMGSINAFGSDE
+QKERWLPRMARMEMIGAFALTEPDHGSDSVALETTARREGDTWVLDGAKRWIGNASYAHV
+IVIYARDVADGQVKAFVLEREPDTEFPAGFEPTVITGKIGKRAILQPDIVISGLRIPEAD
+RLPGCSSFKDVNRVLSTTRGGVAVETLGHAVAAYEAAVAYAGQRVQFGKPIAGHQLVQGQ
+LATMLADVTNIKLTCFRLLELQDQGRLTGPMASLAKMSAARQARRVTSMARDILGGNGLL
+LENHVARHLTDMEVVYTYEGTDSMQSLIVGRAITGVSAFA
+>LFPAFLNI_00288
+MSETRSGVLPDHDIYLLDDELTEEQREVRDRVRAFVDAELMPVINDYWERAEFPFELVPK
+LAELNVAGTVIEGYGCPGMSRMAGALVSMELARGDGSFNTFFGVHSGLAMGSINAFGSDE
+QKERWLPRMARMEMIGAFALTEPDHGSDSVALETTARREGDTWVLDGAKRWIGNASYAHV
+IVIYARDVADGQVKAFVLEREPDTEFPAGFEPTVITGKIGKRAILQPDIVISGLRIPEAD
+RLPGCSSFKDVNRVLSTTRGGVAVETLGHAVAAYEAAVAYAGQRVQFGKPIAGHQLVQGQ
+LATMLADVTNIKLTCFRLLELQDQGRLTGPMASLAKMSAARQARRVTSMARDILGGNGLL
+LENHVARHLTDMEVVYTYEGTDSMQSLIVGRAITGVSAFA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002016.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002016.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c5685b98c603a2ee4e449c9bff8756bf2b8a69d3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002016.fa
@@ -0,0 +1,18 @@
+>ACLBLIBL_00840
+MSGTLDRLIRILSSFDAERPAMTVAALARRADLPLPTAYRWVERLVGAELLQKDDDGLVR
+PGLRLWEMASRSAPSMSLARTAMPFLVDVQSVLRQNTQLAVLDDEGVLVLERLSSQGAVV
+NQAAVAGRLPPFTTSLGLVLLAHSPADVAERFIARHRRQLGVAVEHHPSEAGGAAPAGAR
+VRVTAPTEPHLRALLAGIRREGYAAVDGALDEEARGIAVPVTRADGTVVAALGAVVPCEA
+PYTPGVPPLLMTAARGIARAVGGDSH
+>MHAAABBN_01712
+MDRLIRVRFAFDAERPVLTVAALARRTELPLATAYRWVDRLVRAELLQKDEDGVVRPGLR
+LWEMASRSAPSMSLARTAMPFLLDVQAVLHQHTQLAVLDAEGVLVLARLSSQGAVVNQAD
+VAGRLPPFTTALGLVLLAHAPVETAERFIARHRDRLGAVVDHHPLESGRAVPAGVRARVA
+TPSEPRLRALLADVRREGYAAVDGALDEESRGVAVPVRGADGVAAAALGVVVPREAPYTP
+GVPPLLMTAARGIARGLGGHSH
+>LFPAFLNI_01940
+MDRLIRVRFAFDAERPVLTVAALARRTELPLATAYRWVDRLVRAELLQKDEDGVVRPGLR
+LWEMASRSAPSMSLARTAMPFLVDVQSVLRQHTQLAVLDDDGVLVLARLSSQGAVVNQAD
+VAGRLPPFTTALGLVLLAHAPVETAERFIARHRDRLGAVVDHHPLESGRAVPAGVRARVA
+TPSEPRLRALLADVRREGYAAVDGALDEESRGVAVPVRGADGVAAAALGVVVPREAPYTP
+GVPPLLMTAARGIARGLGGHSH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002017.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002017.fa
new file mode 100644
index 0000000000000000000000000000000000000000..18f99b3dfc860b075305c8dee8f6c340013035ca
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002017.fa
@@ -0,0 +1,24 @@
+>ACLBLIBL_00841
+MTQQPVTRTRVGIVGGGPAGLMLSHLLSKQGIDNVVLESRDHETIANTHRAGILEQPSVD
+MLTGTGVDGRVKTVGDEHRGIFLRFDGESHALDFPELVGATVTLYAQNEVFVDLAAARER
+DGGDVRFETEVVEVLDIDSDTPGVRFRSVAGGEQGPVEELRCDILVGADGSRSTVRKALQ
+AGTEGKDYFTAYPFAWFGILAEAPKSSPELIYARSEHGFGLISQRSETVQRMYFQCDPAT
+RVEDWSDDRIWERLQKIVDGPDGLTLKTGPIIDKTVLGFRSFVRTPMDHRNVFLAGDAGH
+TVPPTGAKGLNLAFADVRVLFEALDSWASTGSRDLLDAYSDTVLARVWKAQNFSSWMTTM
+LHARPEASEFEDMRVRGELLNVVSSRFGQQYLAEQYTGWPHR
+>MHAAABBN_01711
+MTQPPVTRTRVGIVGGGPAGLMLSHLLARQGIDNVVLESRDPETIAHTHRAGILEQPSVE
+MLTDMGVDGRVRTVGDEHRGIILRFDGESHALDFPELVGATVTLYAQNEVFVDLAAARRR
+DGGDVRFETEVLEVLDVDSDTPGVRFRSVAAGEEGPVEELRCDILVGADGSRSTVRKALQ
+RDTEGEDHFHAYPFAWFGILAEAPKSSPELIYARSEHGFGLISQRSETVQRMYFQCDPST
+RVEDWSDDRIWDRLQRIVAGPDGFTLKTGPIIDKTVLGFRSYVRTPLSHRNVFLAGDAGH
+TVPPTGAKGLNLAFADVRVLAEALESWAATGSRDLLDAYSETALTRVWKDQNFSYWMTTM
+LHARPDASEFEDMRVRGELRNVVQSRYGRQFLAEQYTGWPSA
+>LFPAFLNI_01939
+MTQPPVTRTRVGIVGGGPAGLMLSHLLARQGIDNVVLESRDPETIAHTHRAGILEQPSVE
+MLTDMGVDGRVRTVGDEHRGIILRFDGESHALDFPELVGATVTLYAQNEVFVDLAAARRR
+DGGDVRFETEVLEVLDVDSDTPGVRFRSVAAGEEGPVEELRCDILVGADGSRSTVRKALQ
+RDTEGEDHFHAYPFAWFGILAEAPKSSPELIYARSEHGFGLISQRSETVQRMYFQCDPST
+RVEDWSDDRIWDRLQRIVAGPDGFTLKTGPIIDKTVLGFRSYVRTPLSHRNVFLAGDAGH
+TVPPTGAKGLNLAFADVRVLAEALESWAATGSRDLLDAYSETALTRVWKDQNFSYWMTTM
+LHARPDASEFEDMRVRGELRNVVQSRYGRQFLAEQYTGWPSA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002018.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002018.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a2fa26548175235a0493b1344c7d2c0d00417c76
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002018.fa
@@ -0,0 +1,18 @@
+>ACLBLIBL_00842
+MSDPVQKQDDDTFDNARVLDPAATQDSQEQISEEMAAVHGQASGETQPRLDFPPYRSSVF
+RHPTKSMAHADPESIELWSPAFGHRDVHQLESDLTVGQNGEPIGERIKVRGRVLDGQGRP
+VRGQLVEIWQANAAGRYVHKRDQHPAPLDPNFTGVGRTITDDRGFYEFTTIKPAPYPWKN
+HHNAWRPAHIHFSLFGTDFTQRMITQMYFPGDPLFSLDPIYQGITDQKARDRLVATYDHS
+VSEHEWNTGYYWDIVLTGSHRTWTEDEEGDH
+>MHAAABBN_01710
+MSIAAQAKDDDTFDSAHVLDPAATRDSQGQISEEIAAVHAQAQGETQPRLDFPPYRSSVF
+RHPTKSLVHADPETVELWSPAFGHRDVHPLEADLTVGQNGEPIGERIKVRGRVLDDDGRP
+VRHQLVEIWQANAAGRYVHKRDQHPAPLDPNFTGIGRTLTGADGTYEFTTIKPAPYPWKN
+HRNAWRPAHIHFSLFGTDFTQRMITQMYFPGDPLFPLDPIYQGITDQAARDRLVATYDHS
+VTSHEWNTGYWWDIVLTGSHRTWMEDEEGDH
+>LFPAFLNI_01938
+MSIAAQAKDDDTFDSAHVLDPAATRDSQGQISEEIAAVHAQAQGETQPRLDFPPYRSSVF
+RHPTKSLVHADPETVELWSPAFGHRDVHPLEADLTVGQNGEPIGERIKVRGRVLDDDGRP
+VRHQLVEIWQANAAGRYVHKRDQHPAPLDPNFTGIGRTLTGADGTYEFTTIKPAPYPWKN
+HRNAWRPAHIHFSLFGTDFTQRMITQMYFPGDPLFPLDPIYQGITDQAARDRLVATYDHS
+VTSHEWNTGYWWDIVLTGSHRTWMEDEEGDH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002023.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002023.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8fc5cdb568879007953920338a7df304b2319662
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002023.fa
@@ -0,0 +1,26 @@
+>ACLBLIBL_01090
+MPRRSASAARTRQALRGAVQIYAPSTVYAVGLGAMTPALAVAALALGLDAARAAAVVVLV
+GLGSLVANAPASALAARAGERVTIVVSAFLGTAGAALAWATTAGLSSSPGREGVVEPGRL
+ALYLTAVLAMGMAGSGFNLARQAYLAVAVPPSHRARAMSTLGGTIRIGVFLGPFLGAAVQ
+AAMGLDGAFAAATAAMAVGALLCLRIRDLPASGAAAPGADPGAQPVPAHRPRVADVARAR
+REVLLTAGFGVVAVSAARAARNAVIPLWATHLGMDAASASLVFGLAGAVDLLLFYPAGRL
+MDRHGRRAVAVPCLAVLGAGFLAVSLTRDPAAFAAATVLLGIGNGFGAGIVMTLGADYWL
+LGHPVGLGRAG
+>MHAAABBN_01493
+MRPRSASAARTREALRDAVQIYAPSTVYAVGLGAMTPALAVAALALGLDAARAAAVVLLV
+GLGSLVANGPASALAARAGERVTMVVSAGLGTVGAGLAWATTAGVSSGPSAAGVAEPGRL
+ALFLAAVLAVGMAGAGFNLARQAYLAVAVPATHRARAMSTLGGTVRIGTFLGPFLGAAAQ
+APLGLDGAFAAAAAAMAVGALLCLRIRDLPVPASDPAAGEEPGPAGRPRLLDVARARRGA
+LLTAGFGVVAVSAARAARNAVIPLWATHLGLDAATASLVFGLAGAADLLLFYPSGRLMDR
+FGRRAVAVPCLTLLGAGFLAISLTREPTAFAAAAVLLGIGNGFGAGIVMTLGADHSPPNA
+RAPFLGLWRSMSDAGMLAGPLLLSGATAAAGLAVGVGSLAVVCGVGAVVFAAVLPRGPGA
+VADPPPVVVRPR
+>LFPAFLNI_01715
+MRPRSASAARTREALRDAVQIYAPSTVYAVGLGAMTPALAVAALALGLDAARAAAVVLLV
+GLGSLVANGPASALAARAGERVTMVVSAGLGTVGAGLAWATTAGVSSGPSAAGVAEPGRL
+ALFLAAVLAVGMAGAGFNLARQAYLAVAVPATHRARAMSTLGGTVRIGTFLGPFLGAAAQ
+APLGLDGAFAAAAAAMAVGALLCLRIRDLPVPASDPAAGEEPGPAGRPRLRDVARARRGA
+LLTAGFGVVAVSAARAARNAVIPLWATHLGLDAATASLVFGLAGAADLLLFYPSGRLMDR
+FGRRAVAVPCLTLLGAGFLAISLTREPTAFAAAAVLLGIGNGFGAGIVMTLGADHSPPNA
+RAPFLGLWRSMSDAGMLAGPLLLSGATAAAGLAVGVGSLAVVCGVGAVVFAAVLPRGPGA
+VADPPPVVVRSR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002025.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002025.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df6266f7c2dd71bb483108054b735e4ab9490065
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002025.fa
@@ -0,0 +1,24 @@
+>ACLBLIBL_01223
+MTDRIFLSSPDVTQAEEDALVRAFRSNWIAPLGPEVDAFEAELAEYTGRAHAVVLSSGTA
+ALHLGLLNLGVGPGDLVPTSSLTFAATANAIAYTGAEPVFVDADESGNMNPALLEQALAT
+LRGEGHEVKAIVPVDLLGKTADHAAIGRIAAEHGAVVLSDAAESLGATRDGKQSAAYGVA
+AAVSFNGNKIMTTSGGGALLTDDEEMATRTRYLATQARQPVVHYEHTDIGYNYRLSNILA
+ALGRAQLNRLEEMIERRRALRIRYRELFAAVPGVEMFGEPSGADGGPTRDNFWLSSVLVD
+PDAAGFTAEDLRAHLAGQDIEARPLWKPMHLQPVFAGRRAFTDGTGERLFTTGLSLPSGS
+VLDESRISRVLDSITAFLESRA
+>MOLHKGIG_00889
+MAEFIPAAKPLIGDEERAAVDRVLRSGMVAQGPEVAAFEEEFGAAMVDGRACVAVNSGTA
+GLHLGLLASGIGPGDEVIVPAFTFAATGNAVALTGATPVFADVDLDTYTLDPQDVRAKVT
+ERTAAVMPVHLYGHPARMDELEAICREHGLQLFEDAAQAHGARWKGRPVGTFGAWGMFSL
+YPTKNMTSGEGGMVSVGEADVARRLRLLRNQGMEVQYRNELVGFNNRMTDIHAAIGRVQL
+TKVGAWTRRRQEIAARFDAELRGVTVPTVLEGAEHVYHQYTVRLPEELAGTRADVLARLK
+DEFGVGTGVYYPVPTNELPSFGVEADLPNTRVAASTVFSIPVHPSLTDADVTRVVEAVNT
+VVAEAAA
+>MHAAABBN_00611
+MAEFIPAAKPLIGDEERAAVDRVLRSGMVAQGPEVAAFEEEFGAAMVDGRACVAVNSGTA
+GLHLGLLASGIGPGDEVIVPAFTFAATGNAVALTGATPVFADVDLDTYTLDPQDVRAKVT
+ERTAAVMPVHLYGHPARMDELEAICREHGLQLFEDAAQAHGARWKGRPVGTFGAWGMFSL
+YPTKNMTSGEGGMVSVGEADVARRLRLLRNQGMEVQYRNELVGFNNRMTDIHAAIGRVQL
+TKVGAWTRRRQEIAARFDAELRGVTVPTVLEGAEHVYHQYTVRLPEELAGTRADVLARLK
+DEFGVGTGVYYPVPTNELPSFGVEADLPNTRVAASTVFSIPVHPSLTDADVTRVVEAVNT
+VVAEAAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002029.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002029.fa
new file mode 100644
index 0000000000000000000000000000000000000000..263eaeb462cd34f46d91ae5f1ea2dcb8cfcada1b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002029.fa
@@ -0,0 +1,10 @@
+>ACLBLIBL_01309
+MLGALIAGGATFLTGKLADDRARQAERKEHVARVGAEFLREADRVEQYLLDYVHEHAAVP
+GDNEEWGETAELARIAWELRLFAPRPVNDAAAELVDVLEAWESGVDGRGRDVLEIHKRFV
+SVLRVYLHGEDD
+>NAFOICDF_02234
+MARVGAEFLREADRVEQYLLDYVHEHAAVPGDNEEWGETAELARIAWELRLFAPRPVNDA
+AAELVDVLEAWESGVDGRGRDVLEIHKRFVSVLRVYLHGEDD
+>LFPAFLNI_00119
+MDAWIGVVGTLLGAVVGGGVAYLNGTRDRKLEARRDQEKCVTEVAGELLQIVDARERYVH
+GYLEVVGEFPHDGAPDGEEDPARKTLALLELYAPAPVTTAAREYVDLMDKW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002031.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002031.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20416093a8c3f20f0c0bf79e0d6b5ddd4117a7d6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002031.fa
@@ -0,0 +1,9 @@
+>ACLBLIBL_01694
+MTIVTDKRDRPLHATIAILLAILTGGYLAPWAVAATRGKSNVWTVFWVNLLAGWTVIGWA
+IALYMSLTSHRTARVWGARR
+>MHAAABBN_00913
+MTDQRDRPLHATIAVVLAIATAGYLAPWAIAAVRGRSNVWAVFWVNLLTGWTVLGWCIAL
+YMSLTSHRRLRPWGPRGL
+>LFPAFLNI_01144
+MTDQRDRPLHATIAVVLAIATAGYLAPWAIAAVRGRSNVWAVFWVNLLTGWTVLGWCIAL
+YMSLTSHRRLRPWGPRGL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002032.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002032.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09f83a4ef61a69163e370a87b01b72534d324cdc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002032.fa
@@ -0,0 +1,17 @@
+>ACLBLIBL_01938
+MLNHSHTPAEADPVNEPDSLQALAKAVLDKQQASARQIAEYARKAGKRLSYTTLNHMAAG
+TYRSTPTAETLQTLAWLAGVSETVAFHAAGLPVPGPPLADELPPGSDNLSPKSRAAVIQM
+LRVLIDLESNHDEHDHPDQHQDRERGTAERGGARGGDASAEQKTAAAGAPADFDLAAHPD
+FELTRDRQAREWGDAGEESQDHGEGESA
+>ACLBLIBL_02101
+MERIPTSLQELAQLVLDVQGTSARQVALRAEAKGLKLKDTTLNQMKSGSYKFVPREETLR
+ALADLAGVSVETAFHAAGLTAPGPPLADELPPGSDNLSPKSRAAVIQMLRVLIDLESNDD
+HHTTNPTPAHERAQHDDGADAAPDRRRGAGRGDARPGQKTAAAGGTPARSLNPADYDLAA
+HPSFELTRDRQDREWGDVGEENQDPDQEDRRG
+>MOLHKGIG_00948
+MGPRAVPLAIIGDLHLDLTDAQWVNSLYAVLLAALLLSTGNLADRWGRKRLFLTGSALIA
+PYPRRPAAQHPLCCYRFGVHFHATAGVRGRLLPLASHRRLVAMNDMHSLGRLIAPAQERN
+GWSLSDLAARADRAGYDMSHASFARLKSTPVTSIKGENITMLALVLRAPVAHVVTAALES
+IGVELDSALHPSVLDVVQESPDLSTYDQELLAAVLRVMLDRRRTDHHDERDHADQDQDRE
+RGTAERGGARGGDAGAEQKTAAADAPADFDLAAHPDFELTRDRQAREWGDVGEENQDPGD
+EAGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002036.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002036.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4640481a9ac4ac6da613008f034f88ef63b91959
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002036.fa
@@ -0,0 +1,9 @@
+>ACLBLIBL_02272
+MPKKFDPEVKDRAVRMVLDRVEEAGSVTKAVALVSPKVDVGRETLRRWVCQHRVDAGLKD
+GPTSDDLAELKRLRGEVKRLREDNEILRKASIFFAGELDPRNR
+>NAFOICDF_01826
+MPLPFEFERMLFMPKKFDPEVKDRAVRMVLDRVEEAGSVTKAVALVSPKVDVGRETLRRW
+VCQHRVDAGLKDGPTSDDLAELKRLRGEVKRLREDNEILRKASIFFAGELDPRNR
+>MHAAABBN_00324
+MPKKFDPEVKDRAVRMVLDRVEEAGSVTKAVALVSPKVDVGRETLRRWVCQHRVDAGLKD
+GPTSDDLAELKRLRGEVKRLREDNEILRKASIFFAGELDPRNR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002037.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002037.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a73f044a8c8386c44838c19a208b805348ba03b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002037.fa
@@ -0,0 +1,37 @@
+>ACLBLIBL_02329
+MDGFRRSLDGQFVTVDGHDYSEVTRPKLAQADQQERLPDGSERPLPTRTLHLMAAEDGTA
+PVDLNDWERQVLDSEAAEPSLRGWYRNPSRASKQSLAIPFQDGAGQWQALRPDFVFFHAN
+QDGTIRADIVDPHGTHLADALPKLRGLAEYAQAHGMPSVGSRPSLRSRGSCGCWT
+>NAFOICDF_00346
+MRYTLKDYQADAVAEILANIERAQRLRREGHLPTMALTATTGGGKTVIAAAVIEALFFGS
+DTFDFLADPGAVVLWFSDDPTLNAQSRHRLEAAAPDLIGRMTDLNAGYTKPALDPRTVYF
+INTQKFAKTSRMVRGFQPSGTEGQDTFAGLDPRVRPDMVPQTIYDIIAATIQNPDLTLYF
+FLDEAHKGMGTTARAQAEQKTIVKRLIAGQPGVPPMPVVFGISATLQRFTNAMDGIRGRL
+GLDPVQVDPARIQKSGLLKDNILLNIPHPDEVGSFETVLLRSAVRQLLESEAAWDAYVAE
+QRADHPGAEIERVVPLMVLQTPNSVTPSDIAGYLRTIMDVWPEMPAGAVAHVFGEKEAIQ
+AAGLFIPHIDPEKVQDTKRVRILLAKEAVTTGWDCPRAEVLMSFRTVSDLTKITQTLGRM
+VRTPLARRIPGNDELNSVLCLLPNFDEKAARQVVKDLTNDEVPNPIIDPVVDPDPRPEVT
+PPSGGAGASSGGGTEPANPEVPGHGTHATDRVAEPSADGQGTPARPGGLHQGETRGASGG
+GQGGAVGPVVLTDRVKVTPIENGPLWDLFDSLPTETTPSRGLGPVPLLTALGQYLSEDGL
+RPDAGEEAHRHLHGTLDYRAGQFREDVDKAVKDILEVRVRTILADRATGKERIGMFTERA
+DLAVVREAYQRAARAFTADVSRTYVNHIVGPDADEDDLREAYARVAGMASVPDIVADVKE
+EASRLVGRWFQEHRTDIKALADDRQAAYKALMEQSTEPQRGNLAKPVNWQESPVDVDKKP
+LPTRTDHILTAEDGTYPLTLNRVESSVVDQEMRRRGAIAWYRNPSRVKDESLAIAYRDGN
+AWRTMRPDFLFFHEDAQGRVRASIVDPHGHHLSDALPKLRGLARYAEQYGDEFMRIEGLT
+EVNGKMRALDMQDPKVREAVEVATSARALYESDAAVDY
+>NAFOICDF_00693
+MRYTLKDYQAQAVEQVLNRLHRARKNYQDDGVLSQFSLAAATGAGKTVMAAAIIEALFFG
+SDQYTEDIAPDPGATVLWFSDDPDLNDQSRARIHAASSELDGRLRTVENSFAETTFAPGQ
+VYFLNAQKLREGARLVRGAQDPTNAATPVMAAPDMAQRTIYDVIANTVATPGRTLYFILD
+EAHRGMKTTKKNDQERATIVQRLINGTALAPTMPIVLGISATVERFTQAMAHATDRDALS
+PVQVDPALVQASGLLKDDVVLTIPEEAGAFDTTLLREAVARTKASTRAWAAYAAEQGEPN
+PVVPLLVVQVADKPSDEHLSRILDVIHQEWPELRPQDIAHVFGTHTDRHLPGQIVNYIAP
+QRVQETTHIRVLLAMEAISTGWDCPRAEVLMSFRTYKDATYVHQLLGRMVRTPLARRIPG
+NEVLNSIDCFLPHFDKTTSTAIAQTLMRGQSDMDDTTSDPGKQAARRVLFDPVTLTPNPA
+VGEDVWAVFDALPSMNIPQGATKPLKRLDILANALSHDELLPGAVKTAAHTMCKLLDGCR
+VQYSEQIAAARQDVLTLSAQRLTGRLGTTTLSTTSLELLADDRAIEEAAAAAARTLTGWI
+AGAYIDHIVPEDEEDLDLREGDIIIASLARTSEVVADLEAKADKLVQDWLSQYRVQINGL
+TDERQAVYDRVREMARQPERVALTRPKLTQADQQERLPDGSERPLPTRTLHLMAAEDGTM
+PVDLNTWERQVLDSEAAEPSFRGWYRNPSRASKQSLAIPFQDGAGQWQALRPDFLFFHAN
+QDGTIRADIVDPHGTHLADALPKLRGLAEYAQAHGDAFGRIEAVAEIEGQLRVLDMKNDV
+VQAGVHAAQDAESLYKAAPAY
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002039.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002039.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b018def3f9507a735dde69c0ea14ebf06005c2ca
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002039.fa
@@ -0,0 +1,16 @@
+>ACLBLIBL_02429
+MALNAARRAKHQVWTLRKVSAQQARELLDTTAQRLRPLSFNPHRYPLHRFLRFDAPMQET
+LPAPERIFVLWTGLNEMPAIRAANLGRIRTIVGVPVEFVTPATLHEWTVEHHPLHPAYPH
+LSLTHSSDYLRAYLLHHHGGGYMDLKAPAGSWADMFTRLNGDPEAWVLGYPEDSKGRIPP
+YGGHMERDLRIHFARVMGTMAMIARPRSPFTAEWFHEVERRLDYFLPLLRDHPGGVRDEI
+DLYPVGWTQILADIAYPLPLKHHDHIRLEKGFTPPDEAYR
+>NAFOICDF_02313
+MRLMYSARQAKHAAFVANKRTRRVLGAGKWRALTMVTPALSRVWPFRYDAQRYTGPNRGK
+EGHDLSFLQLPPPIDAASSELPRRVFVLWTGNNPLPPNRSRNLAHLRKVIAVPVVLVTPQ
+TLGGWLIPGHPLHPAYEHLSLVHRSDYLRAYLMHHHGGGYIDLKAPVGSWAPAFDRMERD
+PSAWLSGYGEINANASARFPGPMGRDIATHWKSLVGTAAMIVRSHTPFTGEWIREVDRRM
+DALAPRLAASPGLVRLGGPGYPVSWTDLLGKVYQPLQLKYFEHIRVDDDLLVNFTDYQ
+>MHAAABBN_00235
+MHHHGGAFTGIKKHHHAWAPLIEEMQEDVDAWVTGYRVPRSSEAAYFHGPLGRDVRKNFS
+LLLGFSGKIVRPGSPLTSEWLAEVERRLDYYGSLLAQAPGNIYGDNPGYPVPWTRIGSQV
+FEPLTLKYREHIRIDPRLKPQLWGHR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002040.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002040.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20f8904e2cf6d2e65c29599a1763588495c008ac
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002040.fa
@@ -0,0 +1,18 @@
+>ACLBLIBL_02430
+MKFLDKSKSRALKAIRRGDPVSWVPDWMGLGNILYQGLWAFEGDDRQEGRRVLLHPKREA
+AVALFPTLRGRYFVTRDRVPFTARRVMPWREESPEPIPYQPAELPGFIREVLLPGSPVAA
+VPDGLSEDDVVINVRRGDYYSVPQHEAEFGMDQVAYVRAAISRAAAVSGPIGRILVISDG
+LDWCRENLGPVLEPHGPVIYEDGDLFHDLRTIVHARRLVITNSTFSYWGGYIGDELHPGR
+LVIAPALFSHNLNGGRAHQLKPSWTVLEDGCWDRAR
+>MHAAABBN_00242
+MRAVGAVKASILRTVRRGAPVSWAPEWMGLGNLLYQGLWAYEGASLGEPRFVLLPENRVG
+VIELFPRLREKRFLRRSHVPFTAQRVRPWENEERSTGRFAPPLLEDFIRDDLLPGSAVSP
+ATDSYDDAIVVNVRRGDYYSVERHRAQFGMDQEKYLRSALAEAVRTQGPVGRIVVISDGL
+DWCRDHVNDLLSEFAPVEYEDGDIAHDLKAIIHAKRLIITNSTFSYWGGYIGDVLNPGRQ
+VIAPWFFSRTENGGRSHLLAPSWTVIEGDF
+>LFPAFLNI_00514
+MNRLLDMKSNALSAIRRGRPIAWVPEWMGLGNLLYLGHWAYEGSAEDEDRRVLLHADRGA
+AVGIFPRLRERLFVRREDVRFTDRRVMPWSGAATRQRPDHIPAQAHEAFIRDLLLPDSPV
+ATPPHCLKGMLVVNVRRGDYYSVKDHQDDFGMDQVEYIKAALKTSVAAHGSPDGIAVVSD
+GLDWCKEALGGVLEAVAPTTYVDGDLTHDLGTIVHAERLIITNSTFSYWGGYIGDVLSPG
+REVIAPWFFSRSQDGGRATQLRPHWTALEGDFY
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002042.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002042.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ab9dba8922aa0cebdbda4a4539b8414ad569c42
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002042.fa
@@ -0,0 +1,21 @@
+>ACLBLIBL_02436
+MTLDILYVRPRGSGWGPVAELVALAARLFDARVAVVDDHGEVSLFRKTAASLPRGRRRPG
+HHLLVVAPHAGMAAYAARPRLWFPGYDSTAVWVIDSFWTDRTPRLLRGTAHVDRVFITDP
+QLVEEWEQITGTPVSVLPWGADTALYPSAAHHRDIDLLRLGRQPKAWADDDATAADARRR
+GLRFAGRPPMNDDPGQNQHNVREALMGAKLVLAFSNLVSPAPYTHPTRDYLTGRWMDALA
+AGCLVAGTAPAAATSTLWDGATLEISPTSREDAWPVLTAAAEGWSPERAAEQQERARRTL
+DWRWRLRQMSSVMGWPEPPRLTQELERLISSPQQG
+>MOLHKGIG_00515
+MASFDILYIRPAGSGWGPVHELVQLTRRLFDARLIEVDDTGDVNRLQRASALLPRGPRVR
+DRHLLVMGPQPAAIAHVAHPRLWLPGYRSVAVWIIDSFWTDRTPRLLRDRPHVDRLFITD
+PQLVSEWSGQTGLPVGVLPWGSDTTRFTSAQEGTDRPVDVLRVGRQPRAWSDDARTSRDA
+AAHGLHFAGRPPFSDDPARNQMLVREAMGRARVVLAFSNLVSPAPYTHPTRDYLTGRWTD
+ALAAGCLVAGTAPASAASLLWPGATVEISPTSRDDAWPVLAQLASEWTPQAAADRQSEAR
+RRLDWRYRLRDLCMAMDWAVPDRLTAELATL
+>MHAAABBN_00240
+MSVDVLYVRPGGSGWGPVDVLARLAARLLEGRLVEVEDRGAASWAQRASVLLPRGRRARG
+RRLLVLAGNPAALALAARRDLWWPGHESTAAWIVDSFWTDRIAGIARHRPHFDRLFVTDP
+DLVDEWSALTGRPVDALPWGSDTLAVAADDGPRPVDLLRLGRQPEAWDDDARTAREAQDH
+GLVFRGRPPSSPDPLQNQEAVRAALAQARLVLAFSNLVSPAPYTHPTRDYLTGRWTDALA
+AGCRVAGVAPRSAATLLWPEATLEVSPNSRAEAWPVLAEAAAAWTPERAAEQRRRARREL
+DWRLRLQRLCTAMGWPLPPTLDAELAALG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002046.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002046.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2c52dedf92ae6695fba217eabd3f059d853d7bc5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002046.fa
@@ -0,0 +1,9 @@
+>ACLBLIBL_02587
+MKTIRTIAFILFLCATAFGVMLTLHYLPIPEILPSEVTSWVPARDTADATWLIVGMVVAV
+VATAVGFSASHKAVERETQVTS
+>MOLHKGIG_00375
+MKTIRTIAFILFLCATAFGVMLTLHYLPIPEILPSEITSWVPARDTADATWLIVGMVVAV
+VATAVGFSASHKAVERETQVTS
+>LFPAFLNI_00382
+MKTIRTIAFILFLCATAFGVMLTLHYLPIPEILPSEITSWVPARDTADATWLIVGMVVAV
+VATAVGFSASHKAVERETQVTS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002048.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002048.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b5896d189a48f1fea5a3479aa8398983400770f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002048.fa
@@ -0,0 +1,15 @@
+>MOLHKGIG_00013
+MSTTLTLFGHSAVRLEKAGRRLAFDPGAFSDAAVLDGADAVLVTHGHPDHVVPEQLARAV
+AGTEAHVWAPRDLTGPLAEAGLDAGHVHTAVPGETFEAAGFRVEVLGGEHAVIHAEVPRP
+VNVSYLVDGAVLHPGDSFTVPDADVEVLLLPAAAPWLRIADVVDQMRAIAATHTRPIHDG
+ILSEDGKGVVDGVLSGLAEGVTDYRRLAPGEPWTF
+>MHAAABBN_02031
+MSTTLTLFGHSAVRLEKAGRRLAFDPGAFSDAAVLDGADAVLVTHGHPDHVVPEQLARAL
+AGTEAHVWAPRDLTGPLAEAGLAAGRVHTAVPGETFEAAGFRVEVLGGEHAVIHAEVPRP
+VNVSYLVDGAVLHPGDSFTVPDADVEVLLLPAAAPWLRIADVVDQMRAIAATHTRPIHDG
+ILSEDGKGVVDRVLSGLAEGVTDYRRLAPGELWTF
+>LFPAFLNI_00013
+MSTTLTLFGHSAVRLEKAGRRLAFDPGAFSDAAVLDGADAVLVTHGHPDHVVPEQLARAV
+AGTEAHVWAPRDLTGPLAEAGLDAGHVHTAVPGETFEAAGFRVEVLGGEHAVIHAEVPRP
+VNVSYLVDGAVLHPGDSFTVPDADVEVLLLPAAAPWLRIADVVDQMRAIAATHTRPIHDG
+ILSEDGKGVVDGVLSGLAEGVTDYRRLAPGEAWTF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002049.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002049.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9fd22c5f7aad815a33adf8f4d163930129fd800c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002049.fa
@@ -0,0 +1,9 @@
+>MOLHKGIG_00027
+MTIISTGTSTPESAAAWRAALAEAALRGEDVVWFSLDGTEPDEAEAREAGVAVSVAHAQE
+RGRDAVGDLLEHAERVGASRIVVGVKHRSPVGKLLLGSAAQQIILEARVPVVCVKP
+>MHAAABBN_02045
+MTIISTGTSTPESAAAWRAALAEAALRGEDVVWFSLDGTEPDEAEAREAGVVASVAHAQE
+RGRDAVGDLLEHAERVGASRIVVGVKHRSPVGKLLLGSAAQQIILEARVPVVCVKP
+>LFPAFLNI_00027
+MTIISTGTSTPESAAAWRAALAEAALRGEDVVWFSLDGTEPDEAEAREAGVVASVAHAQE
+RGRDAVGDLLEHAERVGASRIVVGVKHRSPVGKLLLGSAAQQIILEARVPVVCVKP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002050.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002050.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8a4bf7b0f2fe2d09b385ce98269dee9d0eb853c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002050.fa
@@ -0,0 +1,21 @@
+>MOLHKGIG_00028
+MSSTSPDGPPRRRTGIGRIVFSVIAVLTVLAASAFSIRSASGGNDIRTNLTLIAPAAAGG
+GWDSFQRELQQTMRVNGLVNNVQVVNIPGAGGTIALGQLTTLEDANNLMVGGTGQIAAHA
+ARGTGPELSQVTAVSRVVEEYSLVVVPADSPYQSMDDLVTAWRADPAHVAWTGGGSFDQL
+VMADIARTADVPVADTTYIPSDGGGEAIQALLNGTAQASAGGFADIYPQVEAGRLRALGV
+VAAEPLAGVEEIPTLRSQGYDVTLTNWRALFAPPGISAEERTELEALIAEAVDTPEWKEA
+VQRNYWNPVPLSGTELEEFIAAEKERIGTLTEEIK
+>MHAAABBN_02046
+MSSTSPDGPPRRRTGIGRIVFSVIAVLTVLAASAFSIRSASGGNDIRTNLTLIAPAAAGG
+GWDSFQRELQQAMRVNGLVNNVQVVNIPGAGGNIALGQLTTLEDANNLMVGGTGQIAAHA
+ARGTGPELSQVTAVSRVVEEYSLVVVPADSPYQTMDDLVTAWRVDPAHVAWTGGGSFDQL
+VMADIARTAGVPVADTTYIPSDGGGEAIQALLNGTAQASAGGFADIYPQVEAGRLRALGV
+VAAEPLAGVEEIPTLRSQGYDVTLTNWRALFAPPGISAEERTELEALIAEAVDTPEWKEA
+VQRNYWNPVPLSGTELEEFIAAEKERIGTLTEEVK
+>LFPAFLNI_00028
+MPSTSPDGPPRRRTGIGRIVFSVIAVLTVLAASAFSIRSASGGNDIRTNLTLIAPAAAGG
+GWDSFQRELQQTMRVNGLVNNVQVVNIPGAGGNIALGQLTTLEDANNLMVGGTGQIAAHA
+ARGTGPELSQVTAVSRVVEEYSLVVVPADSPYQSMDDLVTAWRADPAHVAWTGGGSFDQL
+VMADIARTADVPVADTTYIPSDGGGEAIQALLNGTAQASAGGFADIYPQVEAGRLRALGV
+VAAEPLAGVEEIPTLRSQGYDVTLTNWRALFVPPGVSAEERTELEALIAEAVDTPEWKEA
+VQRNYWNPVPLSGAELEEFIAAEKERIGTLTEEIK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002073.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002073.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cff3e59588ee7bd811d2baf0e1aede3af278b720
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002073.fa
@@ -0,0 +1,14 @@
+>MOLHKGIG_01291
+MPLAIVAPIQSSRSRLRICAALTGLATSAVLLLSGFADAGPSADAGSDHSLVVEHNLDGL
+NAREIIKRLDSTKVTDRSSEFIASIEPDQLVLTDDQNNQTTVPMPEDEFYVSIAPYRSQT
+HECYFHSLTTCTGELANTDVHVTVVEATSGETLLDETLTTYDNGFVGVWLPRGIDATLTV
+SAEGRTAKKAISTRPDDPTCLTGLQLA
+>MHAAABBN_01010
+MVEHNLDGLNAREIIKRLDSTKVTDRSSEFIASIEPDQLVLTDDQNNQTTVPMPEDEFYV
+SIAPYRSQTHECYFHSLTTCTGELANTDVHVTVVEATSGETLLDETLTTYDNGFVGVWLP
+RGIDATLTVSAEGRTAKKAISTRPDDPTCLTGLQLA
+>LFPAFLNI_01249
+MPLAIVAPIQSSRSRLRICAALTGLATSAVLLLSGCADAGPSADAGSDHSLVVEHNLDGL
+NAREIIKRLDSTKVTDRSSEFIASIEPDQLVLTDDQNNQTTLPMPEDEFYVSIAPYRSQT
+HECYFHSLTTCTGELANTDVHVTVVEATSGETLLDETLTTYDNGFVGVWLPRGIDATLTV
+SAEGRTAKKAISTRPDDPTCLTGLQLV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002074.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002074.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e69553c02e8bf64e26eb48e7f5feb5aab8a01aba
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002074.fa
@@ -0,0 +1,20 @@
+>MOLHKGIG_01294
+MGAGAEAGAGPLFIPQCRDRPTLGPDGPRACLTMKPGEGRHPRRHGPGSRCSPTPPQAGR
+AGLSPMPSRWSTPSSTGTGASIPWRDLPEIYGPWLSRVDLARPHGRRGHVGHGAGNTDRR
+SGCRNRDRLVGLGGLHDRPRPSAREEHHPAHRGLDRTTRNPREEPADHGLGRSRSGLSTK
+THQLVDGAGREGVLLAGDRHPSARRWHQGRPPQPADQQGHRRRRGSAGGRPVGLDSEAYT
+GRNVIERQDAHLKQWPGLASRYDEYAIVYWAAVVLNAVLAWSTALSDTPEWRVRTDRRSR
+SSAREARRGSAPAGMSVRTWTERIPRNAHRETE
+>MHAAABBN_01017
+MGAGAEAGAGPLFIPQCRDRPTLGPDGPRACLTMKPGEGRHPRRHGPGSRCSPTPPQAGR
+AGLSPMPSRWSTPSSTGTGASIPWRDLPEIYGPWLSRVDLARPHGRRGHVGHGAGNTDRR
+SGCRNRDRLVGLGGLHDRPRPSAREEHHPAHRGLDRTTRNPREEPADHGLGRSRSGLSTK
+THQLVDGAGREGVLLAGDRHPSARRWHQGRPPQPADQQGHRRRRGSAGGRPVGLDSEAYT
+GRNVIERQDAHLKQWPGLASRYDEYAIVYWAAVVLNAVLAWSTALSDTPEWRVRTDRRSR
+SSAREARRGSAPAGMSVRTWTERIPRNAHRETE
+>LFPAFLNI_01252
+MKPGEGRHPRRHGPGSRCSPTPPQAGRAGLSPMPSRWSTPSSTGTGASIPWRDLPEIYGP
+WLSRVDLARPHGRRGHVGHGAGNTDRRSGCRNRDRLVGLGGLHDRPRPSAREEHHPAHRG
+LDRTTRNPREEPADHGLGRSRSGLSTKTHQLVDGAGREGVLLAGDRHPSARRWHQGRPPQ
+PADQQGHRRRRGSAGGRPVGLDSEAYTGRNVIERQDAHLKQWPGLASRYDEYAIVYWAAV
+VLNAVLAWSTALSDTPEWRVRTDRRSRSSAREARRGSAPAGMSVRTWTERIPRNAHRETE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002075.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002075.fa
new file mode 100644
index 0000000000000000000000000000000000000000..188b2e108a36a123f34c12d1eaa1c216c5ef5fbb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002075.fa
@@ -0,0 +1,21 @@
+>MOLHKGIG_01385
+MGNAVGSNIINVLLILGLSALVVPLAVKRRLIRFDLPLMVVLSVLLLLVSLDGRISAVDG
+LILFFGVVVHTIMSVVISRRDAKTAVNAREGTGDSATVDPADEEGAALGASVSRSLFFVL
+LGVALLVAGATLLVEGAVNIATTLGVSSLVVGLTVVAVGTSLPELATSIIAVRRGERDLA
+VGNVVGSNIFNIGVVLGLTALISLEGIPVSGAAVAFDIPVMLAAAVALLPIAFTGFAVAR
+WEGGLFVVLYAAYTGYLVLAATAHDALEGFTVAMAWFVLPLIALTLISFTAYEIGLRKGR
+RDLDQTTTST
+>MHAAABBN_01113
+MGNAVGSNIINVLLILGLSALVVPLAVKRRLIRFDLPLMVVLSVLLLLVSLDGRISAVDG
+LILFFGVVVHTIMSVVISRRDAKTAVNAREGTGDSATVDPADEEGAALGASVSRSLFFVL
+LGVALLVAGATLLVEGAVNIATTLGVSSLVVGLTVVAVGTSLPELATSIIAVRRGERDLA
+VGNVVGSNIFNIGVVLGLTALISLEGIPVSGAAVAFDIPVMLAAAVALLPIAFTGFAVAR
+WEGGLFVVLYAAYTGYLVLAATAHDALEGFTVAMAWFVLPLIALTLISFTAYEIGLRKGR
+RDLDQTTTST
+>LFPAFLNI_01340
+MGNAVGSNIINVLLILGLSALVVPLAVKRRLIRFDLPLMVVLSVLLLLVSLDGRISAVDG
+LILFFGVVVHTIMSVVISRRDAKTAVNAREGTGDSATVDPADEEGAALGASVSRSLFFVL
+LGVALLVAGATLLVEGAVNIATTLGVSSLVVGLTVVAVGTSLPELATSIIAVRRGERDLA
+VGNVVGSNIFNIGVVLGLTALISLEGIPVSGAAVAFDIPVMLAAAVALLPIAFTGFAVAR
+WEGGLFVVLYAAYTGYLVLAATAHDALEGFTVAMAWFVLPLIALTLISFTAYEIGLRKGR
+RDLDQTTTST
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002078.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002078.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5cf41f5f0c85b03eb4f593337afba5791d94d5ca
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002078.fa
@@ -0,0 +1,9 @@
+>MOLHKGIG_01395
+MAMPETDLLRIGRWCRERVPEHLWDQVRVEAEIADRHVTIIETRPPWDGQGDWTRFPVAR
+LRYTVKTGQWSIYWRDRHMKFHEYTKRRPTKNVQSLLDYIGSHQDPIFWG
+>MHAAABBN_01128
+MAMPETDLLRIGRWCRERVPEHLWDQVRVEAEIADRHVTIIETRPPWDGQGDWTRFPVAR
+LRYTVKTGQWSIYWRDRHMKFHEYTKRRPTKNVQSLLDYIGSHQDPIFWG
+>LFPAFLNI_01345
+MAMPETDLLRIGRWCRERVPEHLWDQVRVEAEIADRHVTIIETRPPWDGQGDWTRFPVAR
+LRYTVKTGQWSIYWRDRHMKFHEYTKRRPTKNVQSLLDYIGSHQDPIFWG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002081.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002081.fa
new file mode 100644
index 0000000000000000000000000000000000000000..77a07cf5b1dfe912ef657962a53ffa8aff4eb3a9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002081.fa
@@ -0,0 +1,24 @@
+>MOLHKGIG_01593
+MTDSPLHLDRPDAPRIIVLGATGYAGSLVVDALVAQGARPVLAGRNRDSLQHAARRHDGL
+EVAVADAGDPASLRALVTEGDVLVSTVGPFERYGRPVARAAAERGAHYVDSTGEVGFVKD
+LKADLDATARRTGATLLPALGFDYAPGMLAGGLALAQAGGRARSLQIGYFADGELDPRVD
+LSHGTRQTMVDALTERTITWRGGRLATTGPASRSAVFRVDGQDRRGVLFGGTESLFLPRM
+QPGLDEVEVFNGWFPARPTQIGAAALGAVGWLPGVARGVQALLRPLAGDPGGPDAADRAR
+TGSRVGAIARDAAGRVVADVHLRGPNAYTLTGDLMAWGARQLAAGRALEAGVVSPIQAFG
+LDDFETACAAVGLVRA
+>MHAAABBN_01305
+MTDSPLHLDHPDAPRIIVLGATGYAGSLVVDALVAQGARPVLAGRNRDSLQHAARRHDGL
+EVAVADAGDPASLRALVTEGDVLVSTVGPFERYGRPVARAAAERGAHYVDSTGEVGFVKD
+LKADLDATARRTGATLLPALGFDYAPGMLAGGLALAEAGGRARSLQIGYFADGELDPRVD
+LSHGTRQTMVGALTERTITWRGGRLATTGPASRSAVFRVDGQDRRGVLFGGTESLFLPRM
+QPGLDEVEVFNGWFPARPTQIGAAALGAVGWLPGVARGVQALLRPLAGDPGGPDAADRAR
+TGSRVGAIARDAAGRIVADVHLSGPNAYTLTGDLMAWGARQLAAGQAREAGVVSPIQAFG
+LDDFETACTAAGLVRA
+>LFPAFLNI_01520
+MTDSPLHLDHPDAPRIIVLGATGYAGSLVVDALVAQGARPVLAGRNRDSLQHAARRHDGL
+EVAVADAGDPASLRALVTEGDVLVSTVGPFERYGRPVARAAAERGAHYVDSTGEIGFVKD
+LKADLDATARRTGATLLPALGFEYAPGMLAGGLALAQAGGRARSLQIGYFADGELDPRVD
+LSHGTRQTMVDALTERTITWRGGRLATTGPASRSAVFRVDGQDRRGVLFGGTESLFLPRM
+QPGLDEVEVFNGWFPARPTQIGAAALGAVGWLPGVARGVQALLRPLAGDPGGPDAADRAR
+TGSRVGAIARDAAGRVVADVHLRGPNAYTLTGDLMAWGARQLVAGRAREAGVVSPIQAFG
+LDDFETACAAVGLVRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002083.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002083.fa
new file mode 100644
index 0000000000000000000000000000000000000000..01eb34caf539bb2a08205fefa2e7ac635a1551ee
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002083.fa
@@ -0,0 +1,8 @@
+>MOLHKGIG_01615
+MRLVWDRSAWEDYTHWQTTDRKVLNRINTLIDAALRDPFEGIGKPEQLKYGAAGAWSRRI
+TEEHRLVYLVDGEDLIILQARYHY
+>NAFOICDF_01188
+MTRKPSGPFGPPLAPASAAAIARRAAGAWSRRITAEHRLVYLVDGEDLIILQARYHY
+>MHAAABBN_01325
+MRLVWDRSAWEDYTHWQTTDRKVLTRVNTLIDAALRDPFEGIGKPEQLKYGAAGAWSRRI
+TEEHRLVYLVDGEDLIILQARYHY
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002086.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002086.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5b72f16e76a489da66ea65a0d6a100d9756c74c4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002086.fa
@@ -0,0 +1,21 @@
+>MOLHKGIG_01897
+MTIRAGIVGYGNLGRSVEKLVKLQPDMELVGIFSRRTGLDTDTPVLPAERAAEHAGEIDV
+LFLCLGSATDIPEQAAGYARHFTTVDTYDNHQLIPRHRAEMDAAAREGGHVAMISTGWDP
+GLFSVNRVLGAALFPQPQQNTFWGKGLSQGHSDAVRRVPGVRRGVQYTIPSEEAIAEARA
+GRGAEITGASAHVRECYVVADEADHAAITEAITTMPDYFAPYETTVHFISEEEFERDHQG
+MPHGGHVVTSGDLGGSRSAVEFVLELESNPDFTAAAQVAYGRAAARLKAQGETGARTVLE
+VAPYLLSPTGLDELIRRDV
+>MHAAABBN_01593
+MTIRAGIVGYGNLGRSVEKLVKLQPDMELVGIFSRRTGLDTDTPVLPAERAAEHAGEIDV
+LFLCLGSATDIPEQAAGYARHFTTVDTYDNHQLIPRHRSEMDAAAREGGHVAMISTGWDP
+GLFSVNRVLGAALFPQPQQNTFWGKGLSQGHSDAVRRVPGVRRGVQYTIPSEEAIAEARA
+GRGAEITGASAHVRECYVVADEADHAAITEAITTMPDYFAPYETTVHFISEEEFERDHQG
+MPHGGHVVTSGDLGGSRSAVEFVLELESNPDFTAAAQVAYGRAAARLKAQGETGARTVLE
+VAPYLLSPTGLDELIRRDV
+>LFPAFLNI_01817
+MTIRAGIVGYGNLGRSVEKLVKLQPDMELVGIFSRRTGLDTDTPVLPAERAAEHAGEIDV
+LFLCLGSATDIPEQAAGYARHFTTVDTYDNHQLIPRHRAEMDAAAREGGHVAMISTGWDP
+GLFSVNRVLGAALFPQPQQNTFWGKGLSQGHSDAVRRVPGVRRGVQYTIPSEEAIAEARA
+GRGAEITGASAHVRECYVVADEADHAAITEAITTMPDYFAPYETTVHFISEEEFERDHQG
+MPHGGHVVTSGDLGGSRSAVEFVLELESNPDFTAAAQVAYGRAAARLKAQGETGARTVLE
+VAPYLLSPTGLDELIRRDV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002088.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002088.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8471bc6bde02b13f9fbe2c7f2fe534397999ceb1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002088.fa
@@ -0,0 +1,18 @@
+>MOLHKGIG_01961
+MAHASTHPAHPLPPVAPRRLLLAQRLLRGEGSVEVTAFRAGETLTTAVHGVSADGRLVVA
+HVPNLLGSLGAFHTPAPLDVRVDVLRDALDLTLPTRLASAHLLGTLRWCRDSAEVAALKL
+RGRVADLVADVGPRVRVGVVETQRILLHDVDGVAVFCRHTLPLTSRGLVDQAELADLADD
+VLGTAPEVLADLADAVALGLLPGESTPLQVDAEPLPEPPAHALDADEAGVTLLRVRDGET
+TAVHVALPGAGRLDHSPRHAWRRLLDAIPARVAHP
+>MHAAABBN_01654
+MAHASTHPAHPLPPVAPRRLLLAQRLLRGEGSVEVTAFRAGETLTTAVHGVSADGRLVVA
+HVPNLLGSLGAFHTLAPLDVRVDVLRDALDLTLPTRLASVHLLGTLRWCRDSAEVAELKL
+RGRVADLVADVGPRVRVGVVETQRILLHDVDGVAVFCCHTLPLTSRGLVDQAELADLADD
+VLGTAPEVLADLADAVALGLLPGESTPLQVDTEPLSESPAHALDVDEAGVTLLRVRDGET
+TAVHVALPGAGRLDHSPRHAWRRLLDAIPARVAHP
+>LFPAFLNI_01887
+MAHASTHPAHPLPPVAPRRLLLAQRLLRGEGSVEVTAFRAGETLMTAVHGVSADGRLVVA
+HAPNLLGSLGAFHTLAPLDVRVDVLRDALDLTVPTRLASVHLLGTLRWCRDSAEVAELGL
+RGRVADLVADVGPRVRVGVIETQRILLHDVDGVAVFCRHTLPLTSRGLIDQAELADLADD
+VLGTAPEVLADLADAVALGLLPGESTPLQVGTGPLPESPAHALDADEAGVTLLRVRDGEA
+TAVHVALPGAGRLDHSPRHAWRRLLDAIPARVAHP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002090.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002090.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2fa8334706fa2a326a83587fb48e46beb85dc4b8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002090.fa
@@ -0,0 +1,18 @@
+>MOLHKGIG_01964
+MSTHRLSSTALGFAAGLGTAAAVTAARKIALMAAVGKGHPLKHRLLDAASGLVQPKYPMG
+AMSTYLNGLHFYADDLGRQVEASHFCIHLRHDLHQCVIFDRNAPDARLIGIEYIISEERF
+RSLPEEERRLWHSHHYEVSSGALTAPGVPELAEHSYFEDLIHTYGKTFHTWQYDRDDFPY
+GIPQLMMGLTGDGQVDEALLRARDERVGVDTAAKRRHRADIPVPDVVPGANSWERGRVVQ
+TTLEERPVRGRDD
+>MHAAABBN_01656
+MSTHRLSSTALGFAAGLGTAAAVTAARRIALMAAVGKGHPLKHRLLDAASGLVQPKYPMG
+AMSTYLNGLHFYADDLGRQVEASHFCIHLRHDLHQCVIFDRNAPDARLIGIEYIISEERF
+RSLPDEERRLWHSHHYEVSSGALTAPGVPELAEHSYFEDLIHTYGKTFHTWQYDRDDFPY
+GIPQLMMGLTGDGQVDEALLRARDERVGVDTAAQRRNRADIPVPDVVPGANSWERGRVVQ
+TTLEERPVRGRDD
+>LFPAFLNI_01890
+MSTHRLSSTALGFAAGLGTAAAVTAARKIALMGAVGKGHPLKHRLLDAASGLVQPKYPMG
+AMSTYLNGLHFYADDLGRQVEASHFCIHLRHDLHQCVIFDRNAPDARLIGIEYIISEERF
+RSLPDEKRRLWHSHHYEVSSGALTAPGVPELAEHSYFEDLIHTYGKTFHTWQYDRDDFPY
+GIPQLMMGLTGDGQVDEALLRARDERVGVDTTAKRRNRADIPVPDVVPGANSWERGRVVQ
+TTLEERPVRGRDD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002092.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002092.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f89ea74c01ad4428d0860d282ddd9c24ac24533
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002092.fa
@@ -0,0 +1,14 @@
+>MOLHKGIG_02096
+MGGASATLRTRGLGRHGRNARVLASHNPLIYRARLLGDRAVNGTPLERHYRLGG
+>NAFOICDF_00596
+MTTTTDRTDTISRPADVGTADSGVPTTAHPADRPQFLAARARLAPVFAWLAETAAERDRE
+RVTDREATDRLAAAGFPGLRVPEDAGGAGLTFPEAARLYVELAEADSNVLQALRVHVVNV
+ETVLGSPDGPRRERWLHRFATGETVANATTEIGNRTGHYETRLTTRPDGSAVVNGRKAYS
+TGTLYADWTIVVVEDEDGAERAATVRSDAPGVTLHDDWDGFGQRLSASGTTEFTDVVVDP
+EELTPVGQSLDDGSSIFASQAIFQFVHLVGLTGIARAVVRDAAAYVAGRTRGFSHGAAPR
+PGDDPQVLQVVGELEAAAFGAQAALDAVVGPLDRALRAEAAGAPLAEAEVDAVYTAVYAA
+QQVIARAALDAATRLFEVGGASATLRTRGLDRHWRNARVLASHNPLIYRARLLGDRAVNG
+TPLERHYRLGG
+>LFPAFLNI_02036
+MRLIHNKDCCGWFAIRRGASARHTGGADGAPPSREPARDALERAATRLFEVGGASATLRT
+RGLDRHGRNARVLASHNPLIYRARLLGDRAVNDTPLERHYRLGG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002093.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002093.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51b0aa4926e3b3971bfd2e874fce6cd6a5cc13ba
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002093.fa
@@ -0,0 +1,15 @@
+>MOLHKGIG_02153
+MDAKPTRLRKKATREEILASLPVQARVRPSRWLLLWLIVVVCIAVFVWVIFRPPEDVSAG
+FGVWRVASFIGLALALAVLPAATMGLFRPRHVTFDERRVWTRDWSVDWADVKEVRAVAPE
+SEHTMKVALKVDERLWNEGGLRKANRWDSGRPLQGGGLTRAQPLVLTQPALAPSALTLLQ
+VFVELKKRNRRAGSPR
+>MHAAABBN_01866
+MDAKPTRLRKKATREEILASLPVQARVRPARWLLLWLIVVVCIAVFVWVIFRPPEDVSAG
+FGVWRVASFIGLALALAVLPAATMGLFRPRHVTFDERRVWTRDWSVDWADVKEVRAVAPE
+SEHTMKVALKVDERLWNEGGLRKANRWDSGRPLQGGGLTRAQPLVLTQPALAPSALTLLQ
+VFVELKKRNRRAGSPR
+>LFPAFLNI_02096
+MDAKPTRLRKKATREEILASLPVQARVRPARWLLLWLIVVVCIAVFVWVIFRPPEDVSAG
+FGVWRVASFIGLALALAVLPAATMGLFRPRHVTFDERRVWTRDWSVDWADVKEVRAVAPE
+SEHTMKVALKVDERLWNEGGLRKANRWDSGRPLQGGGLTRAQPLVLTQPALAPSALTLLQ
+VFVELKKRNRRAGSPR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002097.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002097.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9deb03c3c3d2249862fbd8debe6864d41791261e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002097.fa
@@ -0,0 +1,24 @@
+>MOLHKGIG_02204
+MTEFEDKLAQVARRARDYASSLDTEEATKNALVMPFISQVLGYDVFDPQEVVPEFVADLG
+LKKGEKIDYAIMREGKVNILVEAKKVGSELSLAHASQLVRYFHTSEARIGVLTNGRVWNF
+YTDLDKANILDERPFLVLDLLDIDPVTVPKLEQLAKGSFDLDSVIAAAEELKYVSAIKRE
+ISAEMAAPSDELVKVLAKRVYSGYMNAKAVETFTRLTEEAARQYINDRVNARLKTALGDQ
+VAPVLAAPAEPVATGDQTVLSDEENGQEGQLKPGVVTTEEEIEGFRIIKAILAGIVPMNR
+VYMRDAASYCSVILDDNNRKPIARLHFDGKVKYLVLFDADKNRTRADLENLEDIYESAEA
+LRSVVSSYVGA
+>MHAAABBN_01917
+MTEFEDKLAQVARRARDYASSLDTEEATKNALVMPFISQVLGYDVFDPQEVVPEFVADLG
+LKKGEKIDYAIMREGKVNILVEAKKVGSELSLAHASQLVRYFHTSEARIGVLTNGRVWNF
+YTDLDKANILDERPFLVLDLLDIDPVTVPKLEQLAKGSFDLDSVIAAAEELKYVSAIKRE
+ISAEMAAPSDELVKVLAKRVYSGYMNAKAVETFTRLTEEAARQYINDRVNARLKTALGDQ
+VAPVLAAPAEPVATGDQTVLSDEENGQEGQLKPGVVTTEEEIEGFRIIKAILAGIVPMNR
+VYMRDAASYCSVILDDNNRKPIARLHFDGKVKYLVLFDADKNRTRADLENLEDIYESAEA
+LRSVVSSYVGA
+>LFPAFLNI_02148
+MTEFEDKLAQVARRARDYASSLDTEEATKNALVMPFISQVLGYDVFDPQEVVPEFVADLG
+LKKGEKIDYAIMREGKVNILVEAKKVGSELSLAHASQLVRYFHTSEARIGVLTNGRVWNF
+YTDLDKANILDERPFLVLDLLDIDPVTVPKLEQLAKGSFDLDSVIAAAEELKYVSAIKRE
+ISAEMAAPSDELVKVLAKRVYSGYMNAKAVETFTRLTEEAARQYINDRVNARLKTALGDQ
+VAPVLAAPAEPVATGDQTVLSDEENGQEGQLKPGVVTTEEEIEGFRIIKAILAGIVPMNR
+VYMRDAASYCSVILDDNNRKPIARLHFDGKVKYLVLFDADKNRTRADLENLEDIYESAEA
+LRSVVSSYVGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002100.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002100.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3ead6a2c2ed3ee1f17d9cbeb19115e85060e1f53
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002100.fa
@@ -0,0 +1,12 @@
+>MOLHKGIG_02242
+MIRTPWTRTPAGARRARRPRQFRRVTTTGPAAVDVAWARYADLRLWPRWAPQIRAVEAPR
+RRLRAGLRGVVHAPLGLRVPFVVEEVDDDARTWRWTVRVAGTAVSMTHDLTATPRGTRAG
+LTVHGPAVVALAYRLPARVALRRLCRAHL
+>MHAAABBN_01944
+MIRTPWTRTPAGARRARRPRQFRRVTTTGPAAVDVAWARYADLRLWPRWAPQIRAVEAPR
+RRLRAGLRGVVHAPLGLRVPFVVEEVDDDARTWRWTVRVAGTAVSMTHDLTATPRGTRAG
+LTVHGPAVVALAYRLPARVALRRLCRAHL
+>LFPAFLNI_02174
+MIRTPWTRTPAGARRARRPRQFRRVTTTGPAAVDVAWARYADLRLWPRWAPQIRAVEAPR
+RRLRAGLRGVVHAPLGLRVPFVVEEVDDDARTWRWTVRVAGTAVSMTHDLTATPRGTRAG
+LTVHGPAVVALAYRLPARVALRRLCRAHL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002102.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002102.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09b503657ac1e81e24442e851cbd5b2e9fde1e4b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002102.fa
@@ -0,0 +1,12 @@
+>MOLHKGIG_02262
+MRNGQSGAGPPATAPSPRSTRDVDVGWVPRFDVDVLEAALRPVHERPRWEEWGQIAAPTL
+LITGENGYVPAGELDEMRRRRPDVRHVQVPGAGRDVHLDAPERVAELVRGFAA
+>NAFOICDF_00417
+MSGLGRRSAGPVTREDGTRLHVLDSGGSGPALLLLHGLAGYAREWAQVAERLAAACRVVA
+FDQRGHGSSTRRPADLSRTAHVGDVVAVADALGLQRFTLVGQSMGAHTALLAAAAHPARV
+GRLVLIEGGVGGEGPEATAGVIDWFRAWPIPFATVDDAVAHLGGGPAARVWAEGLEETDA
+GGVPRFDVDVLEAALRPVHERPRWEEWGQIAAPTLLITGENGYVPAGELDEMRRRRPDVR
+HVQMPGAGHDVHLDAPERVAELVRGFAA
+>LFPAFLNI_02193
+MRNGQSGARPPAIAPSPRSTRDVDAGWVPRFDVDVLEAALRPVHERPRWEEWGQIAAPTL
+LITGENGYVPAGELDEMRRRRPEVRHVQVPGAGHDVHLDAPDRVAELVRGFAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002105.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002105.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e6603e8ac2e858d93c6ba246957381ef17c21dcd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002105.fa
@@ -0,0 +1,24 @@
+>MOLHKGIG_02288
+MPSAPPPSDLAGSTAAPRPPLWTRPFILVSATYLFVAMIFYTLMTAMALYAVTSFGASDA
+EAGVVVGAFVLGAVLTRMTTTPATFAWGRRRVLLVALACYVLTTAAYLWADSLAALTAVR
+LLNGMCFGAAGTVLATAVQRIVPPVRRSEGTGWFSTSMTLAGAVGPMVALQLSTTLGYDA
+LFWACIGFTGMALLIALFLRVPEPPLTGRFRLHRADVFSAEVAPAAGVALASGFMYGGIL
+AFMATFAQQQGYPAMVPSLFFLLFAAGTIVGRAVLGVLHDRHGDNAVVYPILAGMAVSYA
+VLALWREPAGMLAAGALLGLTYGPVVSVFQTIAIKVVRPTEIGVATGTFFLLLDLGTGLG
+PMVLGAVAAAVGIPVMYLLSGGVGMALLLYYRLVHGGRAIARRPPPA
+>MHAAABBN_01980
+MPSAPPPSDPAGSTAAPRPPLWTRPFILVSATYLFVAMIFYTLMTAMALYAVTSFGASDA
+EAGVVVGAFVLGAVLTRMTTTPATFAWGRRRVLLVALACYVLTTAAYLWADSLATLTAVR
+LLNGMCFGAAGTVLATAVQRIVPPVRRSEGTGWFSTSMTLAGAVGPMVALQLSTTLGYDA
+LFWACIGFTGMALLIALFLRVPEPPLTGRFRLHRADVFSAEVAPAAGVALASGFMYGGIL
+AFMATFAQQQGYPAMVPSLFFLLFAAGTIVGRAVLGVLHDRHGDNAVVYPILAGMAVSYA
+VLALWREPAGMLAAGALLGLTYGPVVSVFQTIAIKVVRPTEIGVATGTFFLLLDLGTGLG
+PMVLGAVAAAVGIPVMYLLSGGVGMALLLYYRLVHGGRAIARRPPPA
+>LFPAFLNI_02228
+MPSAPPPSDPAGSTAAPRPPLWTRPFILVSATYLFVAMIFYTLMTAMALYAVTSFGASDA
+EAGVVVGAFVLGAVLTRMTTTPATFAWGRRRVLLVALACYVLTTAAYLWADSLATLTAVR
+LLNGMCFGAAGTVLATAVQRIVPPVRRSEGTGWFSTSMTLAGAVGPMVALQLSTALGYDA
+LFRACIGFTGMALLIALFLRVPEPPLTGRFRLHRADVFSAEVAPAAGVALASGFMYGGIL
+AFMATFAQQQGYPAMVPSLFFLLFAAGTIVGRAVLGVLHDRHGDNAVVYPILAGMAVSYA
+VLALWREPAGMLAAGALLGLTYGPVVSVFQTIAIKVVRPTEIGVATGTFFLLLDLGTGLG
+PMVLGAVVAAVGIPVMYLLSGGVGVALLLYYRLVHGGRAIARRLSPA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002110.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002110.fa
new file mode 100644
index 0000000000000000000000000000000000000000..56571d2f9ac994ea0b58f2c5c0d32a8705b247fe
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002110.fa
@@ -0,0 +1,7 @@
+>NAFOICDF_00549
+MGMKQRISKVGADVAVAGLLAVSGAVPGQALTDSGRQDCSAGGGYVGARGEQQRYGDRMS
+FDVGGRTTKVVNRYTYGFDSGLRMSQNWRVSSESLLLSGTYGYCYYPY
+>MHAAABBN_01854
+MGMKQRISKVGAGVAVAGPLAVSGAVPAQALTDSGRQDCSAGLLLSGTYGYCYYPY
+>LFPAFLNI_02084
+MGMKQRISKVGAGVAVAGPLAVSGAVPAQALTDSGRQDCSAGLLLSGTYGYCYYPY
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002111.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002111.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d947571e43d60af4e92573d4ead219977fbb99f1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002111.fa
@@ -0,0 +1,22 @@
+>NAFOICDF_00635
+MDALLWHTQALTPAPAPPEPVLLREFSTLSTQDQDEYWTRMHRWMCASTLDCDRTAAIRR
+GMDRVLQRNEYARSGAKTIIGLSAPNGVGKSTFIKSYAQDRYQRMMHDQPVDKLPSRTDS
+GGSPSHWIPQVYITLRAASEVPDVNAAILSYLGYPIMGRTTKDTTLLVHAVARHGVKLLI
+LDDAHMLRAKQARARDVLDYVKFLNTMMGERDGTLVLVGANMEGGPVYQDPQVAARLHAF
+ALQPYTVQQDTTERVAWQQLLAGAEKKFMPYLDSATEGTLTRELAGQIWARTQGHLGDTH
+QLITTALLDAFDQGDTTLVSEHLQGVRLSARAEAAEADLAREATLTSRREQNRKAKR
+>MHAAABBN_01777
+MVNANEYEPLELSHLHPAAQPVARLPAAERVQRIRADRWIGYPKAVEAVERLETMLGWPA
+KQRMPNLLLVGPTNNGKSMIIERFRRQHPPSSEPDREQVPVVCVQMPSEPSPLRFYTAIL
+SVLGAPLRPRPRLVELERLALSLLREVGARMLVVDELHNVLAGRGDTRREFLNLLRFLGN
+ELRIPLVGVGTREAYLAVRSDDQLENRFEPFVLPLWEADDQARSLLASFAASFPLRKPSV
+IDTEDMARYLLARSEGTIGELAHLLTAAAVAAVESGLEAIDHRTLTMANYTGPTERRRVF
+ERELL
+>LFPAFLNI_02217
+MNSHDWHHQAVTSQPSGLKPITVRKFERLNQQEQNEHWTALNRWMAAQPIDCPRVRQTST
+RMQAEVLRNEYAPRGAKTIIGLSAANGVGKSTLIKRLAHQLYRETVPTTDPGILPTRTVG
+TGATVDWIPQVYITLRAASRIQEVNTALLSFLGYPTIGQTRATTTRVVEAIRTHGVQLLI
+LDDAHMLKTSQADARDVLDYLKFLNTELGELGGTMILVGANLEDSDVYADAQIATRLAPL
+QLQPHAIFPVSERARFQAMLRGVEEKFMCHLDTATTGTLTNELAGEIWQRTQGYLGDIHR
+LITTVILETFDAGEDVITRERLRAVPLSARATAAEASLREAATQRSRRTENRRKKKAGST
+PPAQTPSQDAAGSSSDSPTAAVPETKE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002114.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002114.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7eee4fe7fcc327a98b25cc3fa95291b8eb76b4a9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002114.fa
@@ -0,0 +1,27 @@
+>NAFOICDF_00783
+MTERVALIGAGPSGMALLRALALAEDEGAVVPEVVAFERQADWGGQWNLDWRTAADRFGE
+PVHSAMYRDLWINGPKECMEYPDYSFDAHFGRPVSSYLPQEAMKDYILGRVAHVAERIRP
+LIRFGTVVRWVQPLDDGTFEVTSVDLTTGAARTEAFDRIVVATGHFHAAHTPSWPGVEDF
+PGLVQHAHDYRTPEPFAGRRVLVIGSSYSGQDLALQLHRGGAAHVTTAYRKAPQELDWPA
+GMDERPEVQGFAGSRVAFADGSSAEYDAVLLCTGYRHHYPFLPAELALSGPNLPFVPSLW
+KSVVWQADPRVLYLGATQQWFTLTLLDAQAFFARDVLLGRAPVPSAQERQADIDAWTARM
+AAIDSTPVALAFQADQIRDLTAGTGYPEMDLDGVIATFLQMGEDKRESLTRYRDRTHRSL
+VTGTRAAAHPVPWMHHPDGSLEGYLAHFPG
+>MHAAABBN_01704
+MRERVALIGAGPSGMALLRSLALAEDAGAAVPEVVAFERQDDWGGQWNLDWRTGADRHGE
+PVHSAMYRDLWINGPKECMEYPDYPFDAHFGRAVSSYLPREAMRDYIVGRVAEVAGRIRP
+QIRFATAVRWVQPLDDGGFGVTSEDLVTREAVTERFDRVVVATGHFHTPHLPSWPGVETF
+PGQVQHAHDYRSPEPYTGRRVLVVGSSYSGQDLALQLHRAGAAHVTTAYRARPQDIAWPA
+GMDEAPEVQGFDGAEVTFADGSTAEYDAVLLCTGYRHHYPFLPGELALAGPNLLAPFGLW
+KGVVWHADPRVLYLGATQQLFTLTLLDAQAFFARDVLLGRVPVPGDEERRADMDAWFERM
+TRIDGPPAALAYQGAYIQDLSSHTDCPEVDVEAVARTFLEMRDARIEDVRTFRDRRHRST
+VTGTLAAAHPVPWMDRPDDSLEEYLRRFPA
+>LFPAFLNI_01932
+MRERVALIGAGPSGMALLRSLALAEDAGAAVPEVVAFERQDDWGGQWNLDWRTGADRHGE
+PVHSAMYRDLWINGPKECMEYPDYPFDAHFGRAVSSYLPREAMRDYIVGRVAEVAGRIRP
+QIRFATAVRWVQPLDDGGFGVTSEDLVTREAVTERFDRVVVATGHFHTPHLPSWPGVETF
+PGQVQHAHDYRSPEPYTGRRVLVVGSSYSGQDLALQLHRAGAAHVTTAYRARPQDIAWPA
+GMDEAPEVQGFDGAEVTFADGSTAEYDAVLLCTGYRHHYPFLPGELALAGPNLLAPFGLW
+KGVVWHADPRVLYLGATQQLFTLTLLDAQAFFARDVLLGRVPVPGDEERRADMDAWFERM
+TRIDGPPAALAYQGAYIQDLSSHTDCPEVDVEAVARTFLEMRDARIEDVRTFRDRRHRST
+VTGTLAAAHPVPWMDRPDDSLEEYLRRFPA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002126.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002126.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b69a66ad93386e1881a0e7ed45135470bb2564e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002126.fa
@@ -0,0 +1,16 @@
+>ACLBLIBL_00082
+MTVRVAAAPDVLSWAAERAGWDDALAEKHFPRFHDWLTGTQQPTLKQLEEFAHKTHTPFG
+ALFLPEPPRMDLPIPDLRTVGGAGVSEPSPDLLDVVHECQLRQDWYRDEALRQGEEPVAL
+VGSATVDDDPEAVGARLRHELAIQPVQNKAGAESFRRRLVARLEGLGLLVMISGIVGGNT
+SRALDPQDFRGFALSDPVAPLIFVNGTDAPVAQHFTLLHETAHIVLGHSAVSGSRMRGGT
+GEEAWCNRVASAALVPLDEVRRARRDSAGVPLAELVEDLAARYCVSRSVIYLRLRVAGLV
+SEDVVSRHFEEQDADAPGRTPRRRRESGGDYYRTATVRLGKPLIRAVLRSTREGHTSYRE
+AMRLLGTHKIEVLHEMGRQAGVE
+>LFPAFLNI_01542
+MTVRVSVSPDVLLWALDRSPDPDAVATAFPGVDRWVSGEAEPTVKQLHAFAARTGTAYGY
+FFLQAPPAIELPIEDFREGFEGERYRDPSVNLLAVLHQSLRRQDWYRDYAIENGFADVSV
+VGRGAGMSPLEAAADMRRELNYEVRSRVGNWSDQRKRLLAAFEALGGLTVVTSMVENNTH
+RPLDVDEFRGFSLIDDMAPLVFVNARQTINGQLFTLAHEFAHVWRGVGGISDEDLRYEPR
+NEVEQWCNDVASEFLVPSNDLRERYAGVSSLRLTEQIERLASIYRCGTLVVLQALRRNRL
+YDFEDFQTDYDAEVERLRRFERADSGPGGQFLYNQPYRIGTRLSRALISDAMAGRTRFTD
+AARLMSFKSMKNFDSYASYLGTVRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002129.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002129.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bef82ad0f9e9cf3895c36fca33ed17c0cba5b717
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002129.fa
@@ -0,0 +1,11 @@
+>ACLBLIBL_00104
+MTTALPDALRLTDEARERLHADCRHLHRHPELSMQEHATAAWIEEQLDEIGVERFRCGGT
+GVVGVMRHPGGAEGPVVAFRADTDGLPIEEDTGLEYASTARGTLPDGREVPVMHGCGHDT
+HVVSALAAARLLAAAPDTWGGTIVWVFQPAEETGAGAAAMLEDGLWDRAPRPEVVLGQHV
+MPLAAGKVQLIPGMAMALADSQAITFHGRQAHGSQPQDSIDPILMAAHAVTRLQGVVSRE
+TDPRDPAVVTVGTFHAGLKENIIPDSAEIALNVRTFSAASRDTVLGAIERIVRAEAQASG
+APEPSFRTIARFPRCHNDDEQSARVAAALRAELGEDHVLDGRPLMGSEDVGALADAIDVP
+LVYWFFGGFEGEDPAAFPGNHSPHFGPAMAPALDAGHRAALAGLLAYVGR
+>NAFOICDF_00074
+MAAVAAELGEENVMEIGPLMGSEDVGALTDAIDVPLVSWFVGGFEGEDFGDNPANHTPQF
+GPVMEPTLTTGVHAALAGLLHYVGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002131.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002131.fa
new file mode 100644
index 0000000000000000000000000000000000000000..67bea82dc2997241d6899ae58a24741f4380283d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002131.fa
@@ -0,0 +1,11 @@
+>ACLBLIBL_00115
+MTPTSALSSRAPGLAACLALGLAALGTATAVRPWAPALSPLLLAILAGLAWRNLAPVSER
+LAPGVAFAATSVLRAGIVLLGLQLLLSDVLALGPGVIALVVGVVGVTFAATLALGRVLRL
+PWDLTVLVASGFSICGAAAVAAADSVVRARREMVATAIGLVVLFGTLMIPVMPLLTGALG
+FEEQAAGLWIGAATHEVAQVVAAGGLVGGTALSVAVTAKLARVVMLAPVMTGLAWWQRHR
+DALEPATLDDGAPTAVERPPLVPWFVVGFLLAVLVRATGWLPAGVLDAAALVQQLLLATA
+MAALGLGVHLRSIAAVGPRPLVLGAASTAVVVVVGGFGATLLA
+>NAFOICDF_00083
+MPARLEPGIAVAAKPVLRAGIVLLGLQLLLSDVLALGWGAVGLVVGVVALTFAAALALGR
+ALRLPWDLTALVASGFSICGAAAVAAADGVVRARREMAATAIGLVVLFGTLMIPLLPALT
+GALGLGERAAGLWIGASTHEVAQVVAAGGPRPLVLGAGSTAVALAAGRAGAALLG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002143.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002143.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d763d9d92878b6f76da581bbca0669f1276a3a70
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002143.fa
@@ -0,0 +1,9 @@
+>ACLBLIBL_00345
+MAALTAVVVLGVAGCTGPEGRTGTTTDGPGTSTSPPPVVQQSEAAAHPADNLPLGGEPWA
+VVTLTRGGEALDPGPWRQVRIVTSEPFILAAPELCPQPRFGITAVTESAWEATPDVAQPA
+IGCVSGHEDEAAVAALRELFDGTVQVTPPGGADVEMRLRRADVELVLSEEG
+>NAFOICDF_00283
+MRPSAPPRRPRVTRMAAMTAVVVLGVAGCAGPEGRTGTTTTDGPGTSTSPPPVVQQSEAA
+AHPADNLPLGDEAWAVVSLTRGGEALDPGPWRQVRIDTSEPFILAMPELCPQPRFGITAV
+TESAWEATPDVAQPAIGCVSGHEDEAAVAALRELFDGTVQVTPPGGADVEVRLRRADVEL
+VLSEER
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002144.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002144.fa
new file mode 100644
index 0000000000000000000000000000000000000000..747495810153bed036ef0e0e3a54e51cff56aa0d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002144.fa
@@ -0,0 +1,17 @@
+>ACLBLIBL_00347
+MGDDNARMIRRFRSSSTRRPLHRSLTRRGTRPRRRLHTDDRVSLPPSSVAGLFVVPFLAT
+HLFAWGLFASVYLIAHPGGDSVFTASMWRLTTDVAVNAGLAMEDSLLALTSTGVAVTVAL
+YIPVAAGQLVSPRGGGETQRRLGSLALATSGVFAGITTGAYIASMTHGAHPASMIPELLL
+QGLMIALSLQLGTHLFDDREELRSRLEDDERRLEMQLSDAALNSLSDDIQGKFGGDFTLP
+PMRQWAKAARTLTFRRILRLLIWFFGYLLAGAFLGALTFACTSLTLEREWDARTLALGAL
+IGIYAHFASGMITYHDQSTPALRWLVRAMGATIWLLLLTTGLVLLSASPSQGSASLGTAV
+LGVIHVLWRRRSPGEQGLRLSPFMLSHRINTTLAEEALTSVWSRQLHAGILPRPLLGTTC
+RTSPLRDAAR
+>NAFOICDF_00285
+MVPFLATHLFAWGLFASVYLIAHPGGDSVFTASMWRFTTDVAVNAGLAMEDSLLALTSTG
+VTVTVALYIPVAAGQLVSPRGGGETQRRLGSLALATSGVFAGITTGAYIASMTHGAHPAS
+MIPELLLQGLMIALSLQLGTHLFDDREELRSRLEDDERRLEMQLSDAALNSLSDDIRGKL
+GGDFTLPPTRQWAKAARTLTLRRILRLLIWVFGYLLAGAFLGALTFACTSLTLEREWDAR
+TLALGALIGIYAHFASGMITYHDQSTPALRWLVRAMGATIWLLLLATGLVLLSASPSQGS
+ASLGTAVLGVIHVLWRRRSPGEQGLRLSPFMLSHRINTTLAEEALTSVWSRQLHAGILPR
+PLLGTTCRTSPLRDAAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002145.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002145.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2123b1143c0384b6f351d7324502e08133091d49
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002145.fa
@@ -0,0 +1,8 @@
+>ACLBLIBL_00350
+MAPRPTPIRSVLQVFALDCPDPPALAAFYAGLLGWRVVEDRPDDEWVNVLPPEHEPQTMK
+LAFQLVPDHREPTWPEGDVPQQAHLDFHVPALAEAVPLAEAAGARRHPVQPAEDGSWVVF
+TDPAGHLFCLCQA
+>NAFOICDF_02481
+MDTQNAPVARLAMITLDAPDAAALGTFYQAVLGWPVAYEGDGVVMLAGPGGVNLGIGTVE
+DYTAPRWPDTGRKQYHLDLAAEDVAAAAARCVALGATRPDHQPGETWTVLLDPAGHPFCV
+TDAANWG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002150.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002150.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ef64afe1d54b9937af029f811fec1bfc9a510a35
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002150.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_00395
+MIAFIDEHRDQFGVEAICRTLRATECGFITST
+>NAFOICDF_00664
+MIAFIDEHRERFGVEAICRVLSATECGFITST
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002153.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002153.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c299cd02197cb8d7c62e00c6a9996c0c87a64cf1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002153.fa
@@ -0,0 +1,10 @@
+>ACLBLIBL_00458
+MTAPQLHLPRTVASDQTERAVDLLQLYFKSRKFIGSQWDGFDPSGRRAASANVFTADDVA
+SAALLNTPVPGHAVVHLLITQRERFSELLRIVGPDRDFIDADPDPSGKDMAPVYELYEAL
+KDLPKIGPTIASKLVARKRPRLFPIIDSDLRRTVFHETRKDGHVGRALLHADFSAQERTM
+WQRLESYRCAAALPAEVTTLRVFDVLAWMEAKAY
+>MHAAABBN_01969
+MTAPQLHLPRTVVSDQTDRAVDLLGHYFTPGKFIGGRWDGFDPSGTRAASANVFTSDDVA
+SAALLNTPVPGHAVVHLLITQRVHFAGLLEAVGPDRDFIDVDPDPSGKDMAPVYELYEAL
+KTLPKIGPTIASKLVARKRPRLFPIIDAELRQTVFHETRKDGYVGRALLHAEFSAQERTI
+WQRLASYHSAASLPTEVSVLRVFDVLAWMEAKAYWGPVP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002155.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002155.fa
new file mode 100644
index 0000000000000000000000000000000000000000..68b2b17f1ad90bc7d7dcaa16eda7788b127aa078
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002155.fa
@@ -0,0 +1,12 @@
+>ACLBLIBL_00484
+MVTHTDLMTIGEFSSLSRLSVRMLRHYDAHGVLVPEHVDAHSGYRRYAPAQLRDAADIRN
+LRDVGLGVSAITALLAARGTSTWTDALALQRCTLVEELHAARERLSLIDRMLTPGEIPMT
+IQLNRTAVPAMTVVALRGTVPSYSDEGRLWERLMPALQQQGIRPVGPCGVIEHDDEYREA
+DVDLSVYCPVAPGTRAEGPLVVLQLPERDCLVAHVIGPYTQISQAHDLIVQRMEAEGLAA
+RQDGTLASNVFNRYLVTPDQAAPEDLVTEVCRPLA
+>ACLBLIBL_02684
+MSRRMLRHWEQEGLLSPALVDPVTGYRRFQATQLGRIRAIAELRDLGFSLSEIRQLLDPQ
+IAHSSLERILMQQADRLRDQITEASARLAQVQHRVDTIQKKAQEISMNLSLTPLPELSLQ
+GASTTVLDETDIGSAVARLRDLVPHDQGDLILLFDGTSPDQITVTAATADGATTPGLQPV
+SAPLAPQGATVTFPTPPSSVADAWVLIDAELEKRGLASGGVYRQIISPDGSTTLQAAVHA
+RD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002156.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002156.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ad88505215086e3c5c7a8e57094c9b99dc184af
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002156.fa
@@ -0,0 +1,7 @@
+>ACLBLIBL_00491
+MDEDQGKILATHRQELRRGTLVVACLLACRTPRYGYALLEHLADARLDAEANTLYPLLRR
+LEGQGLLQAEWNTDEPRPRKYYRTTPEGEAIVAELRGDWLRLTDSMTRLGKDPS
+>ACLBLIBL_00765
+MNEPTDRPPSGTAPEAWPSAWVRAALEPAILGSLAGGPLHGYGIAHALADHGFGRLRGGS
+LYPVLGRLEEAGHITARWAPGDAGPGRKDYELTDAGRAAYRDAVANWRRLGDALADLGAT
+PRLTAQEGTAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002157.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002157.fa
new file mode 100644
index 0000000000000000000000000000000000000000..75ffe83bfad420441c30278a3f66036f88387978
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002157.fa
@@ -0,0 +1,18 @@
+>ACLBLIBL_00497
+MRGGVDAAADPNGGPRPRRWWDGPLDVERLAWDAVVAARDAVRELAAARGQDGVAGTTPE
+LVAASFAALDHLRVEGAAVPAWAPMSGFLRAADGWVRTHANYPHHAAALTRALGAVDRPG
+LEAAVARRTAAEVESAVHAAGGIAVAVRSAAAWAAHPHGTATRDEPWASVAPGGPRRRLR
+GGRLPLEGVRVLDLTRVIAGPAAAQLAACLGADVLRVDPPGRPEILAQHLSNGMGRHSAV
+ADLTERAAEVEDLLAGADVVLLGYRPGSLDRFGLDPEALVRRHPHLVVGSVSAWGEAGPW
+AQRAGFDSIVQAACGIADACGRDGEPGALPVQALDHATGHRLFAETVRLLAQGRAGVVRI
+SLLGAARTLLGLSPPPPGPAAELPVPRVEVGSEAGRLDAVPPAIALDGEVLARDVGAYGA
+AALRWL
+>NAFOICDF_00412
+MPRVSAPVPSPRRWWAGPLDVEQLAWGAVEDARDAVQALVDARGQGWRVGTSPELVAASF
+AAIEHLRVVGEPVASWAPMSGFVRAVDGWVRTHANYPHHAAALGRALGATDRASLERAVA
+GRTALDVEEAVHDAGGIAVAVRRATQWAAHPQGVATSGEPWVSVDAGRERAPLSGGALPL
+DGVRVLDLTRVIAGPAGSQLMACLGADVLRIDPPARPEIDAQFLSNGMGKRSATADLAEH
+RTELEALLAGADVVLLGYRPGSLDRFGLGPDALAQRHPHLVVGSLSAWGERGPWARRAGF
+DSIVQAASGVALACSPDDGATPGALPVQALDHATGYALAAGVVRLLVEGRAGVVWASLLG
+AARTLLGFAAPPEERVAELGVPHVTVRSAAGTLNTVPPPLTLDGASVERDVAGYGAASLR
+WA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002160.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002160.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f51cddb6d764845ed624227d4419c75e7cd0c6b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002160.fa
@@ -0,0 +1,7 @@
+>ACLBLIBL_00512
+MSTLSEMHVIDFPGFPTVVVRGPGQSVDGLHHFMDTSFRALGAAMGQGVFAPAGPAFALY
+RGMTGQGLGESMDLEVGHPVDVPPAVPLDVDGVRVEPSSLPAGRLAVAKHTGPYELLPEA
+WEAFLDALRADGHEPGDLCWEAYDTEPGPDVDPETLVTGLAVPVRTVA
+>NAFOICDF_00449
+MRIEPSDLPAGSLGVAKHTGTYELLSEAWPAFLDALRENGHEPGGLCWEAYDTPPTPDTD
+PETLVTGLAVPVRPAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002161.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002161.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f44736cd11b428cc51b260af08798a2ff5f0031
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002161.fa
@@ -0,0 +1,10 @@
+>ACLBLIBL_00517
+MTSVLFVVSAADAWTLKDGTTHPTGFWAEELATPHRLFREAGWDIVFATPGGVPPTVDRA
+SLGEAAGSEEERAALTAHLESIRAELDAPLRLEDVDDREFDVVFYPGGHGPMEDLAADPV
+SGALLSRRVTAGDPVALLCHAPAAALAAKDADGANVFAGRRMTAFSDEEERAGGLAEQAP
+WLLETELKEAGVVYEKADEPMAPKVVVDGAVYTGQNPASSAELAERLIADLG
+>NAFOICDF_00466
+MTKVLFVVSAADQWTLKDGTVHPTGFWAEEFVVPHQTFTEAGWHVDIATPGGRVPTVDQL
+SLGMMAGSPAKREQLRAALDRLRPALERPLVLADVDDSAYDLVFYPGGHGPMEDLAYDPV
+SGALIARRLLDEAPLALLCHAPAAVFAAKRADGTIVAEGRRMTAFSDLEEKLNPFARKAK
+WTLEAQLKHGGVQYEKARFPMQSHVVADGALYTGQNPQSSAALAERLVHDLSARVER
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002165.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002165.fa
new file mode 100644
index 0000000000000000000000000000000000000000..208806f75257d7a6d300c89a9101df84cd87995b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002165.fa
@@ -0,0 +1,8 @@
+>ACLBLIBL_00552
+MPHDSARWLDEEERRAFLALMSVTMRLEPALDAQLRRDADLTHFEYSVMANLSESEGDTR
+RMSELAWLSAGSLPRLSQVVTRLERRGLVKRTPDPTDGRYTLAVLTPEGRAVVEESAPGH
+VEEVRRVVLDPLTRAQVKQLAAIGKRIVGVLDPEDRCLED
+>NAFOICDF_00475
+MSDAARPASDPVADTAPESVVPWLDDEERHAFLALMSVVLRLEPTLDAQLRREAGISHFE
+YTVLASLSEAEGGQRRMSELAYLSSGSLPRLSQVVTRLEKRGWVERRPDPEDGRYTLAVL
+LDEGREVVVAAAPGHVAEVRRAVVDPLTRAQLRQLTAIGRRIMGVIDPEDRCLED
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002170.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002170.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37cb449f777c920bfd7f35fe554dda9256bebacc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002170.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_00618
+MTEQRRHEVTLRFLAAPTDQGHTGTVDAGRVLEWVDKAAFAAATAWAGSYCVTAYVGNIH
+FRQPVLVGQMVEVTGTVLHTGRSSMHINTVVSAGDPKTGELTEAARCLVIFVAVEEGKPV
+PVPEFVPRTLEQELAAEYAVSRIAVRDEIQAAMEGQRYTDAGTADRTVLRFLAAPTDVNW
+GGKVHGGIVMEWIDTAAYLCSTRWAGRETVAVFSGGVRFYRPLHIGDLVEVEARLIYTGE
+KGMHVAVHVRSGDPKTAQLELTTYCLTVMVARDDDGDAVPVPAWEPVSQEDKALWQHARD
+LLEIRGRAPGNRLPNHLLAERGED
+>NAFOICDF_00543
+MTDDAARTPASTDAARPSPGPVPAPASPTEPATPVVERRREVTLRFLAAPTDLGHSGTVD
+AGRVLEWVDKAAFAAATAWAGRYCVTVYVGNIHFRQAVEVGQMVEVTASVLHTGSSSMHI
+STTVRSGDPKTGELTEAARCLVVFVAVGEDGRPVPVPEFVPRSLEQELARDWAISRIAVR
+NEISAAMKTQRHTDAGTAERVVLRFLAAPTDVNWGGKVHGGTVMEWIDTAAYLCSSRWAG
+RDTVAVFSGGIRFLKPLHIGDLVEVEARLIYTGNKGMHVAVDVRSGDPKTDDLQLTTNCL
+TVMVARDEHGDAVPVPAWKPVTDEDRALWAHARTLLEIRAKAPGNRLPDHLLRERGEGPD
+RGEH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002173.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002173.fa
new file mode 100644
index 0000000000000000000000000000000000000000..99e747146cf8a64777e5e4e21562c81c392db1b4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002173.fa
@@ -0,0 +1,7 @@
+>ACLBLIBL_00645
+MTAPHAIPPSGLPSAAEVRRVLSALVQRCFSRETHARLLDADVSEGVLTVVAWQAGPSPV
+VPGRVIGHRTDLGMRLAECEGDLEAVLLDVLQFQEFEPSAPGRAASGAEPAWLLERYPEA
+TWYAQGASGT
+>NAFOICDF_01292
+MPSTEAVLSILRRLERRHFSRDAYARLLDADVTGEVLTVVAWQGGPSPSDPERVIAHRTD
+LRQRLTECRGDLEAVLMDALQFGVYEPSSPGRPPAGDEPARLLEKYPEATWYE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002176.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002176.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb72aab290f0723af51803e6f732e58dbc6a262d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002176.fa
@@ -0,0 +1,10 @@
+>ACLBLIBL_00713
+MTQRRTRWRSAASQDAEYRAHWKAAASADVGTPDALTWAVLGDSAAVGVGAARVEESYVA
+QVAAGVAERTGRPVRVLNLAVSGATAAHVLADQLPLLPADGVDAVTCVVGGNDVAWPVRF
+RVDRFAAPLEKIAQRLPAGATLGTVPVFRIPPYESRVECANAAVRVIAARHGLGVADVHA
+ATRRTSLRHQVSMLSHDLFHPNGAGYRDWARAVLPEVLRQVRGEAPTR
+>LFPAFLNI_02032
+MPSPSGWQAQHDADYRAHWHALAARADPDALTWVVLGDSAAVGIGAESVERTYVAQVAER
+VAAETGRPVRVVNLAVSGAMAKDVLADQLPLMPASGVDAVTCVVGGNDVTWAWRFREAAF
+EEPLEAIARALPAGATLGLVPTFRIPPFEARVRRANTVVRRVAARHGLGVADVHAATWRR
+NLRHQVSRLARDLFHPNGAGYEDWAAAVAPEVLRQVRGQAPAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002178.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002178.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4165108cac927f90694f0f9b22eae8f73cc1f93
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002178.fa
@@ -0,0 +1,10 @@
+>ACLBLIBL_00754
+MSSAKNSDQRRQDRAAVLQAHWAAEAKAARKQKVLWGAGGVTAVALVGALVTVAVVTDPP
+PPTRQDIEIAGLETFEDLDAMHVNSPVDYEQDPPVGGDHASTWLNCGVYTEKVPKENAVH
+SLEHGAVWAAYDPSALSEEEITALQEALPDTHAVVSPYEGLESPITLSAWGAQVAVETPD
+DERIEEFVAKYWQSPEAPEPGAACTGGLDGPGRVA
+>NAFOICDF_02190
+MSTKLMADPEAKAERRRKVLVGAGALTAIAVVGGLVTLAVIQNPPPQAREDIEIAGLQTF
+EGLSANHVSTPVDYEQSPPVGGDHASAWLNCGVYTEPVPNENAVHALEHGAAWVAYDSEA
+LSQEQVDALRTALPAAYVVLAPYEGLDSPIVLSAWQAQVAVDSPEDERIEQFVAEYWQSP
+DAPEPGAACTGGLDAPGRIA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002181.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002181.fa
new file mode 100644
index 0000000000000000000000000000000000000000..47022fbb70f6e4209a6f7231467ae3a51777e78d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002181.fa
@@ -0,0 +1,15 @@
+>ACLBLIBL_00827
+MATPAGAVGKGPNHNPRSTVNTSILATHAELVAQLQKEDARQDAMELTVIGQSVKGRDIH
+LASWISDPENPTILFLTQQHGNEQLTTEGAMAFIKSLGTGKMRSVLDDVNVLVVPMANPD
+GAMGDVDFSLEDYIASGDRNLTRYNANEVDLNRDHVAKTQPETRALHENVLGAYDIDYMI
+DLHHQGTRSAVDGELVSGSILYPTSPNVAPDVVEDSQRLGSVVYDAVEQYGWGNLGRYVG
+GTAETIARNGVAAEYGIATLLFEMRGMSDHEYESYVLGQRSNGYLIKQTVVTLEATTKAI
+ADGSIETADIGLWNTLPEQRTLPLAAE
+>ACLBLIBL_02006
+MSPLTSPSLSRRGALGVLASAVALPLVAAPPAQAAGSMPTPSDTPPLAAIRDLADMLREL
+RKLERTSRGAIRVTTLAEVGTAEAHSEQGRDLYVALVGHGPRHVWLQGRIHGNEPYGLEA
+TLDVLASLGGNGSPAYRRMREEFTVHVIPMYNPDGSEANTRGTTLWDREADAPLLVGRGR
+PRTVDLNRDWGVGRFQARESRAWYEYWTMVKPEFALDIHHQWLKQDWVTGEDVTLSLGVS
+LAPGGPTLPGIRGGEYDRLARQLAGHVWLETLHRGHISTDRYDVGENTVIDIHGGVVSAM
+MMGLDWNGLNPTGHSNVAIFFETSGNTNSLGHKARGKLVQQNVLAVTAALDGMATGAVQR
+VDPAVWDRIPHTPVKYYSTDYAGLIPA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002182.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002182.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2cbfb34e891ca330c16bcf995f430622b573bf6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002182.fa
@@ -0,0 +1,8 @@
+>ACLBLIBL_00847
+MSRLSRAPGLRRPRLLDPWRRPLLPRLPWHVILAASLAGAATIATLSIGQDLTSVPLLVG
+AFGSSCVLVFLVPHGPHSHPANVLVGHVAAAACGIAVSSVLPLAWYSLAAGMGLAMAVMA
+GLRVIHAPAGATALSVMLVEAGWDYLLAPILSGALVLTACALLYRRLMWRVIGPPPPPA
+>MOLHKGIG_02002
+MTRLPGLRPPRFLDPWRRPLAPRLPWHVVLAASIAGALTIATLSLGEDLASVPLLVGAFG
+SSCVLVFLVPHGPHSHPANVLVGHVVSAACGIAVISVLPLAWYSLAAGMGLAMAVMAGLR
+VIHAPAGATALAVMLSNADWHYLVTPVLAGALVLTACALLYRRLMWRVIGPAE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002185.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002185.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a44099ca7738f62d7de2c09e3aaac0c7609efc35
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002185.fa
@@ -0,0 +1,14 @@
+>ACLBLIBL_00883
+MPDSPAPPGAAPSELVPRAFAERIARRPADPLLAAAGGEAVSGEAWLARLPHLVEERLAA
+WNLTLDPDAPGAPWTGHGALVLPVRRHTLRPAVLKLTWPHLEARHEHLALRLWDGAGAVR
+LHAASPPDGALLLERLDADWPLTLEPVLDACVAVGGLLRALDRPATPQFDAVAVKAERWD
+GTLAAPVAAVPRRLQVQARSHLRRLVDSAPEPRLVHEDLHDGNVLAPLPDDGPSGAAPDA
+RRGHVARRGRWLAIDPKPVAGEGAYAVAPIVWNRPEVTAAAHNARIHVRLRADVVAEAAG
+LDEERVRAWTFVRLVLNAVDAAHEGPSADEWRARMIALAGHFAS
+>NAFOICDF_00825
+MPASPPEILVPIPPEFAADIADRPADPLLAAAPDAAAQPLSGEQWLARLPRILAGRLTAW
+DLTLDPDVPGAPWAGTSALVVPVRLPTRRPAVLKVTWPHLEARHEHLALRLWDGAGAVRL
+HAADPRDGALLLERLDAGRPLSAEPILDACEVVGGLLRTLARSATPQFDAVADRGARWLD
+TLAAPVAQVPRRLQVQARSHLRDLLDSAPPPRLLHEDLHDGNVLAAPSPADGGEAARGPW
+LAIDPKLVAGEPAYAVAPIVWSRPEATARAHHARVHVRMRADVVAEAAGLDGERVRAWTF
+VRLVLRAVDAAGRGEAGDEVRARMITLAGHFAS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002188.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002188.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e968ca2f9db09bb7da6efc9296a5f7b61375ffb5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002188.fa
@@ -0,0 +1,8 @@
+>ACLBLIBL_00909
+MDGVRGTWAPGTVRGVLHASGVGAATGYPGVVLATPAATEHPAAQIADVPAQLLVSVDLP
+DHWDRLDAFEGAGYRRVPAVVALDDDAVRPAYLYELVPDAVPPSA
+>LFPAFLNI_01868
+MALTGVPELGGWRVTPSPTPAGTTPPELTITYATDDFATALALANRIGEAAEAADHHPDL
+TVSYGRLTVGMHSHDVRALTSRDVRLARTVARLASEVLAPHALAAYGTLAPGRSNAHVMD
+GVRGTWIPGTLRGTLHASGIGAATGYPGVVLAGTAPAHATTDVPAQVLVSADLPDHWDRL
+DAFEGAGYRRVPGVVALEDDDAVRPAFVYELVPDAVPPSA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002197.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002197.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb9cda62860902365b34a14b08439a96a95efff1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002197.fa
@@ -0,0 +1,12 @@
+>ACLBLIBL_01012
+MKIPAAITGGVAAVLVLGLTSCGASEVRPDHGVTARLDRENGQVVLPIEDYAASQADEAV
+MTQARLAILRSCLQKSGHNGVKPPTSNAERAVEERPYGVWIVDRARAYGFDLPPAAETVE
+PAAPPGGWSDEADPAFNEAYEACSSEVMEQMLAVSSPATSPGTTSVIADVTARARGLAAQ
+DPVWDEARDEWQQCLRDNGLTPVAEEGAVLSAESENLSDTRDAQGQTHSVKAEEIRLATI
+EATCNEQTRLTQRLGDLEAGYQAALIKKHEAALVEEKLVTAEHLEAARAYLARHQ
+>NAFOICDF_00955
+MRPDPRPFRLAVIAGIALSASACAQSGAPDVPPDTSATAHLDREHGQVVLPVDEYSLDHD
+SEQLIGQARHVIMRTCLNSKGVNGLAPTATSSPAEERPYGLWRTASAAQNGYTMPRPAST
+EAPPLGGQWSEESDPAFNTAYDACNEIVRDDLDSVTPPETERTTAIDIRDDAFTLASATP
+EWKEARKQWHDCLTSRGLTPRTDDNAWSSEQGFGILTTADPQNPSPAAKQEEIRIAVIEA
+TCNEQTQLTQRLGDLEAGYQAALFKGKEAQLAQEKADNQKFVDAARAYLASHQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002200.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002200.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b3321711b061d2592ad6729e0044bec0c56f85a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002200.fa
@@ -0,0 +1,16 @@
+>ACLBLIBL_01079
+MILDSYRSPWLTEDAEALLEHCRDFLAREVVPHEERWAEQHGVDRDLWTKAGEAGLLCPS
+LPEEYGGAGGTFALEAAILTEQGRCFDDAWGFSIHSPIVAHYILAYGTEEQKQRWLPGLA
+SGELVGAIAMTEPNTGSDLQAVRTRATRDGDHYVINGSKTFISNATHCGLLLIVARTGDE
+PGGRGLSLIVAETDGLEGFERGRVLKKIGQHGQDTRELSFSDMRVPVSHLLGPDEGQGFV
+QLMAQLPQERLTLAVLAAGVCEAAVRETIRYTKERHAFGEPLMSFQNTQFVLAECVADTL
+ATRTLVDQCIVAHVDGTLTAADASMVKFFASDMQNKVVDRCLQLFGGYGYMEEYPIARAF
+TGARVQKIYGGTNEIMKMLVARAL
+>MOLHKGIG_01797
+MILDSYRSPWLTEDAEALLEHCRDFLAREVVPHEERWAEQHGVDRDLWTKAGEAGLLCPS
+LPEEYGGAGGTFALEAAILTEQGRCFDDAWGFSIHSPIVAHYILAYGTEEQKQRWLPGLA
+SGELVGAIAMTEPNTGSDLQAVRTRATRDGDHYVINGSKTFISNATHCGLLLIVARTGDE
+PGGRGLSLIVAETDGLEGFERGRVLKKIGQHGQDTRELSFSDMRVPVSHLLGPDEGQGFV
+QLMAQLPQERLTLAVLAAGVCEAAVRETIRYTKERHAFGEPLMSFQNTQFVLAECVADTL
+ATRTLVDQCIVAHVDGTLTAADASMVKFFASDMQNKVVDRCLQLFGGYGYMEEYPIARAF
+TGARVQKIYGGTNEIMKMLVARAL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002206.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002206.fa
new file mode 100644
index 0000000000000000000000000000000000000000..adf58beda9b74411d7c432c40350c152796ab787
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002206.fa
@@ -0,0 +1,12 @@
+>ACLBLIBL_01088
+MTGTRVATERHDTALVLTLDGPDRLNAVTPTAMEALHTALGEAGRDPAIRAVILTGRGRA
+FCAGADLRDDLDPEATMRAANRVVETIRAVDVPVIAAVNGPAVGYGAALAAAADLAVAAD
+DAYLLLPFTGIGLVPDGGSSVTIARAVGRALAAEMALTGRRLGAEEARAAGLFSRVVPGP
+DLAGVAHALADAVAERPRRAVALAKAALNAADAEVVGRALEREARDQVELIRSAEFAQRS
+AAFRR
+>MOLHKGIG_01788
+MTGTRVATERHDTALVLTLDGPDRLNAVTPTAMEALHTALGEAGRDPAIRAVILTGRGRA
+FCAGADLRDDLDPEATMRAANRVVETIRAVDVPVIAAVNGPAVGYGAALAAAADLAVAAD
+DAYLLLPFTGIGLVPDGGSSVTIARAVGRALAAEMALTGRRLGAEEARAAGLFSRVVPGP
+DLAGVAHALADAVAERPRRAVALAKAALNAADAEVVGRALEREARDQVELIRSAEFAQRS
+AAFRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002209.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002209.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2741dddb873625211ceedc84a845bb7f7c10ed3e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002209.fa
@@ -0,0 +1,9 @@
+>ACLBLIBL_01264
+MQDARRALEAVGSVPDLAGTAVAVMGVSGSGKTVLALRLAAALGVPFAEADEFHSPEAVA
+KMAGGTPLTDADRLPWLHRIRDWTAVAAAERGAVVTCSALKRSYRDLLRDGPARVVFLHV
+DAPQSEIRDRMARRRHYMPPTLLHSQAATLEPLGVDEPGAVLANDSTVEDLTERALRVLA
+AR
+>NAFOICDF_01173
+MTGQAGPARALLDLAGTAVVVMGVSGSGKTVLAQRLAQALGVPFAEGDEFHSAEAVARMA
+GGTPLTDEDRGPWLRRIRDWMGSGVAARGAVVTCSALKRSYRDVLREAPVRVVFLHVETP
+AEQVLHRMERRRHFMPPALLPGQLATLEPLEADEEGVVLANDSTMEELTERALRALADL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002214.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002214.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07a10972d14b33a49228a57d98438196abe94bce
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002214.fa
@@ -0,0 +1,12 @@
+>ACLBLIBL_01311
+MTVQKFPVFPAGTLEHVCKLIAELYTGNELTRIMSEIPLRDDLGEGNTKWRRLACAVSKN
+QAHTQSGNAVIALVSASMRPERTLDRADAARLTRDQLNQVLSLVGYRVRDDGRVARASRA
+RSTDEAEKRTEHLRGLLERGGAHREVLTYCRPELLRKDYYEAVFEAIKGLGSRLRQLTGV
+DGDGYALVEDAMAGSTPRIRLNALQTRTQRDEQRGVANLTKGLFSAFRNPAAHEPRIEWT
+LSEQDALDVLGTLSMIHRRLDMATVEAL
+>ACLBLIBL_02210
+MQRAGLTPVTIIKNRGSANEERIEVQAQLQNSSLAMFAIEDPLFEGDHVEMPDPRGGQMV
+KVVRKLVQHPMPANMARAFGGSNGYAEVTWGESAAVRQAPVRRLELEGLHPEVVRVSSAL
+FADEQFDSAVTEAMKSLEIRVRRLAASTLSGAPLMQEAFRPKEPKLDVAVEEGRSGEDER
+EGFFHLFRGAMVGIRNPKAHELAHGDNPFEALEALALASMLHRRLDIAAGRLECADDSVT
+VLDQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002216.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002216.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a13d859578fbffa84a469b431acda9fbc745e121
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002216.fa
@@ -0,0 +1,37 @@
+>ACLBLIBL_01502
+MKNSTASGSGFQFDASQPYQLDAIASVVDLFDGQPKDAEKLVTTLRSAAVLPESDQAALD
+IDLTQEVGAVGNSLVLDRDLILANLQRVQDRNGLEVAPALAGDALDFDIEMETGTGKTYV
+YLRTIFDLAVRYNFTKFVILVPSVAIREGVSTSIRLMREHFENLYKPQGVTFDASIYSGK
+SAEEVQSFATSTNVQILIMTIDSIRGNANTRIIHQTRDKLNGLRPIDYLKATHPVVIMDE
+PQNMESQLSQSAVGELDPVFTLRYSATHKKQRNVVYRLDPVDAHDLGLVKQIVVAEVAQQ
+GADATPYIKLVEVRREPSWSARLELSCRKADGSLERRIVSVKQHQELSDARLTNNPIYEG
+WRINEMSIEPAYVDLTLHGFLYEGESIGASAGAIYREMIRETVREHLRKESMLRAKGIKV
+LSLFFVDKVASYLGDGTNNDDANGDFVQWFDEVFVEERAKNARYQELLPQAPSKLRRAYF
+AQIKGKKGAPNAFVDSDERRQGAREDDAYELIMQQKERLLDENEPVRFIFSHSALREGWD
+NPNVFQICTLREMGAETERRQTLGRGLRLPVAKTEDGYTRVADRGVATLTVVANESYTKF
+ADALQREYKEAGVEIGRVRRAEFSKIPLQDENGALTDDQFGYQRSVLVWEHLKDKGFIDK
+DGAVTSKFQPNQLGFDLGLPVDFAWAESIIIELVERANIGKYVKPVSKRQPRMLNKQLYS
+NPEFEEFWETISQKTTYRVRVGRDQLIENAVRAIREAPQIDALRIQVTRAGVKVLRGGAK
+GEELGTRSADLKGSYDLPDIITELQEVTSLTRKTIVDILIGSGRLGEFIGNPNDFIAMTK
+RALQSELAKIVVDGIQYERIAGSVYELRELQRDGAEEKERFLDQMYKVQHTQKTDFDYVV
+FDSDVERQFAELLDSREDIKLFMKLPAKFKIDTPVGPYNPDWAIIKQEDGEDRIYMIRET
+KSTLDDSKLRPTELAKIKSAKRHFEAIGIDDYARAVPGKWNL
+>NAFOICDF_00290
+MKLQFSTKQYQTDAVASVVDVFSGQPRDPGPQYQIDPGRRASTGEDAAVALTGYRNAEIA
+LSLSALLEGIQRVQRAQNLPVSTRLATSAAAPGRPNLDVEMETGTGKTYVYIKTMMEMHR
+RYGWTKFIVVVPSVAIREGVKKTFDITAQHFQQEYGTRPQTFVYDSSRLHEIEAFSSNGG
+VQVMIINIQAFNSSSKDNRRIYDVLDDFQSRRPIDVISANRPIVIIDEPQKIGAAKSLSS
+LANFNALMVLRYSATHEVDHDKVHRLDALDAFNQKLVKRIEVRGLTVRGLSGTTAYLHVS
+DIEVRQGKNPRARVETEMQSAAGTIRRKLAWVTKGTSLHDLSGGLEAYQGLTVVDVDARR
+NVVELSNGDLIESGQLADHDVTEDTKRRIQIREVISAHFHREREMFRRGIKVLSLFFIDE
+VAKYRDYDREDTLGDYARMFEEEYVEARDAVLGELETEDDAAYRDYLRRDEVSAVHEGYF
+SVDNKSRRMVDGKVAGRGDEKGQSTDTDAYDLILRDKERLLSLKEPVRFVFSHSALREGW
+DNPNVFTMGMLKRSDNEVSRRQEIGRGLRLAVDQHGVRMDDPATVHEINRLTVVTDESYT
+DFVTGLQTEIAKSLKGRPRKASVAYLTGKTLTTHEGEILTLNKEMAELLHRHLIRNGYVD
+DDDLLTQQYLNEREAGTLAMPSNEKLLGVVDFCWPLLDALHTGVDIVEPSRAMKRLPVNR
+HNLERQEFQRLWERINRKAVYRVQFDSEELVQKAVTALDEKLRVTGLTYTVETGVQGEDL
+EAEHFRSGQGFTSSAITTQKESATSGSRVRYDLLGEIAERTTLTRRTVSAILRGIRPDTF
+AAFPKNPEQFLTEAGKLINEQKAAMVIEHLAYSPLEDTYDISVFSENQTSQDFTLASEKL
+EKHVYDYVVTDSDVEKRFVTQLDASTEVAVYAKLPGGFTIPTPVGDYNPDWAIAFDEEDT
+HVRHVYFVAETKGTSSSFELRGMEDAKIRCARKFFDALNRKNAGDVRYDVVTDYNGLMDL
+VKGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002217.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002217.fa
new file mode 100644
index 0000000000000000000000000000000000000000..19bec64a14e9de3c51beff97b56ffdd062b15025
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002217.fa
@@ -0,0 +1,18 @@
+>ACLBLIBL_01644
+MSAPHPRPLLLRGARLTTVETADVLVAEGRIAALGAEAAAQAAGLDPAPEEVDCAGLVLL
+PGLVDLHTHLRQPGKEDAETVETGTRAAAMGGFTSVHAMANSTPTADTAGVVEQVWRLGR
+DAGWCDVHPVGAVTVGLAGEALADLGAMADSQARVRMFSDDGMCVHDAVLMRRALEYVKS
+FGGFVAQHAQEPKLTAGAQMNESELSGVLGLAGWPAVAEEAIIARDVLLAQHVDSQLHVC
+HVSTAGSVRLIRWAKEQGVRVTAEVTPHHLLLTEELVRSYDPVFKVNPPLRRESDVMALR
+EALADGTIDTVGTDHAPHTAETKQCEWTVAAMGMTGLETALSVVQHAMVDTGLMDWAGVA
+RVMSVTPASIAGLEDQGQADERGVPRVGAVANLVLVDPEARRTVDPEQHLTKSRNSPYRG
+MELPGAVRHTVYRGARVVADGAPAQPYRHPAVAEAGGRA
+>NAFOICDF_01541
+MSTTVPPALLFRGAALASGRVADVLVSDGRVAAVGEVPAVDAEGASVVEAAGTVLLPGLV
+DLHTHLRQPGKEDAETVETGTRAAARGGFTAVHAMANSTPTADTAGVVEQVWRLGREAGW
+CDVHPVGAVTVGLAGEALADIGAMADSQARVRMFSDDGMCVHDAVLMRRALEYVKSFGGF
+VAQHAQEPRLTAGAQMNESELSGVLGLAGWPAVAEEAIIARDVLLAQHVDSRLHVCHVST
+AGSVELIRWAKAQGVQVTAEVTPHHLLLTEELVRSYDPVFKVNPPLRRESDVHALRAALA
+DGTIDTVGTDHAPHTAESKQCEWTVAAMGMTGLETALSVVQQAMVDTGLMDWSGVARAMS
+TEPARIAGLQDQGQADESGEPLVGAVANLVLWDPAVRRAVDPETHATRSRNSPYRGMELP
+GAVVHTVYRGRRVVADGELTQPVVHADAPEGRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002224.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002224.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0bcbf5a318920a29d9499b7209efffe6c341ace4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002224.fa
@@ -0,0 +1,10 @@
+>ACLBLIBL_02013
+MTTPAPTSRSDWAEYNAAQAGRGRIRPLTARAVDALAADADLGARHAVELGCGAGVEARH
+LLALGLTVSTIDADPSIAPAMAALAAGGALDHRTGRIEDWDPLPAADLVLANAALPFVPR
+HAFDAVWSRIRAALAPGGVLAVDLFGAEDDWSSNAGTYLTRPEVEDLVRGLEVVELTERS
+ERGPAFSGPKHWHVFTVIARARRRPSDRSPV
+>NAFOICDF_01290
+MGDTALMIATPTSSSDWNSYNAARAGTSAVRPLTERALTALRATHQNLSGLRAVELGSGA
+GIEARRLLQEGLTVHTIDVDASVEERMHELTSLGVLEHRTGLIEEWDPLPLADLILANAS
+LPFIPRAHFAPVWERLRQALLPGGILAVDLFGCEDTWASDQGTYLTLQEVERLLDALEVI
+ELNERNEEGRSFDGIKHWHTFTVIARRTA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002228.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002228.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b39f10c939d480b77a022678306eefa9f7fa99d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002228.fa
@@ -0,0 +1,21 @@
+>ACLBLIBL_02200
+MSVRESRPTQADETALKAFTGAEDEVTNFDGVVSYEEEPPAGFLAEPRSGLSPTARPDTE
+EHAEAVLAGLSSLSATDSEILQLATTHFVERMWDGTPGTTRHLLDLCAAVARRLGDRKHD
+GAPRFYAPRALPVSAVAAMLAHLHRYCVVDLGLPASDGVAPLLVRYADDGPLEGTYSRVT
+EASLYVDALALEPESSPKQMEELFARLAARSQVVHRCSDPNLVPVANGIFDYRTKTLREF
+DPELVFLFKAATRYVDAPPMPMIVQPDGTDWNPVDWMASLAPDPEVRHLLWEVTGALLRP
+LNAWDKWLALISPEGRNGKGTLLAMWRALLGPDAHKSATLASFGADFPDIEGLNEKSAIL
+TDENDVGRYLESSATLKSIVTGDVLSAPVKHSKAVPVAFQGLMVQCMNDLPRAKDKSSSF
+YRRLLAVPMEANFTEATENKAIKHDYVQRPEVLEWVLHHVLVEMEAFTSFSEPAACAALK
+DDVRDANDPVRVFVAEFIDQFAWDLVPTTFAHDLYKAWLVRRWPNTHPVNEAEFIRQVSG
+HMAEYGWEHKKNVRVSSRMHSHEPLINEYDLRAWMNPAYNGPDPVKRAAPLLKPSYRGWV
+RIEP
+>MHAAABBN_02228
+MTSPLDIEDVDLSETTRQRPDYFHPDLYAEQPPAERPGEKHRGQLRIAHRLAEAHSGRLM
+YVNGLGWHVWDGQRWAPDETAAAERAVHDVLRSALAESHDGDRNLREDVRRCETAAGIRG
+VLDIAATLEGVRVAVDALDADPHLLNVANGTLDLRTRTLRPHDPADRLTRVCRGAWTAGE
+SDGMWSDFLARVLPDDAERAYFQRVIGQAVFGAVREHLFPVLTGTGANGKGTAYTAIAHA
+LGDYAAIIDPDLLMTSARGPGGPEMMQLFGARLVIGSETEEGKPLDAALMKRLTGGDPIT
+ARHLYQAPVTWEPSHQFLYVTNHLPKVKGNDPAVWRRVRVLPFDVVIPPADRDPALPERL
+REAADAVVTWAVRGWWDYLDAGGMGEPEAVKAATDAYAVQSDAVRRFIADACVIAPGASA
+RTRELHTAWTAWAAADGAEPLAEKKFGAELDRLGYPTTRTRAGSVRQGIGLLADDD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002230.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002230.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb71595ae212b70a5630a6a9cd3fe1b1a136b1fb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002230.fa
@@ -0,0 +1,8 @@
+>ACLBLIBL_02202
+MTASTTKSGRARRQRTIFSKRLELRLTERQFRLASETAKRLSEIRDKKVTVSDYLRMLIE
+DGGKGLIQGLERVSHAPAGILSQADVDRIVAALQEVRDEVRRVGHNVNQMTKVAHQSGQV
+ADDLDGVKQALAGIDAHVLDAAKSFLGYEATDEEEG
+>MOLHKGIG_01494
+MTASTTKSERARRQRTVYSKRLELRLTERQLQLASETAQRLSAIRGKRVTVSDYVRLLID
+DGGRGLVQRLERISQSPAGTLTQADADRVVAALQEVRDEVRRVGHNVNQMTVRAHQAKQV
+VDDLDEVKASLSQIDAHVLDAAKTFLGYEGTDEDEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002233.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002233.fa
new file mode 100644
index 0000000000000000000000000000000000000000..73c71b2601c04d414f425c5d9c9d2646fa53ed78
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002233.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_02209
+MSASTATATFPGVTLFLPDGVMVGDLIYDARTSQLAIVYSDGETEVLSIDLTLEGYLPTP
+GEALIKDWSEHSGVTSALVDAGLVMRTETLVVGPFSSRAYRVLVLTPEVTGR
+>MOLHKGIG_01497
+MSAPATAVTFPGVTLFLPDGVMTGDLTYDARTSQLAITYADGETEVLSIDLTLEGYVAAP
+GEALIKDWSEHSGFTAALVDAGIVMRVETLQIGPFDSRAYRVLVLTEAVTGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002235.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002235.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26605a287a31dde514cc490b8c2ad1113bd6c6fa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002235.fa
@@ -0,0 +1,13 @@
+>ACLBLIBL_02277
+MADAVQVCAFNSTYTASQGPAVPCSSSAREREDALLDALDVDPPGSWWSRAAELARPRTV
+VAGDPPREDWLAVPLRRDGPLATTGDLGRAAAVGLVIREDGPLWDEDLVRTLTPPPICPK
+VLEVRTPADWLRLVEAWPEAASKATAEILARHTGLDGRWLVPRWTAVAEQWDAVHLSIGA
+WARSAGVVQPVGEGSAWTMCAGWDPDATFWLTAQPTVASEQVLPTLTPAEALDGLAG
+>NAFOICDF_01291
+MKASVQDLLPGPRGRRLCLEAARMLSHRVADLVFWLGYELDPDRGISSLVMWPPGGGALE
+AGARPAVSIDQVAQALADLDLSGLTDGVVQAALVGSVMSARYWQEPDGEDVLAGHPDIHA
+ALEAVAAGVLGSAAARHWGSPRAAAQWVIDWRAFEDPAPVPRDARRVLAAWAREERRQEV
+RAAAEHPVDPTANFSGTWWSIPQGAVVSVGQIPTGLDLVEDDIGAEAATVIPVRGAGRTY
+EVRGPGDWIRLCRRFPLEVSASRRHDWYRVTGRSGRWVIPDWEQVASEWDAVHLTTLGYL
+SAATRALPVEAGVATVLAGWDPDTTVWLADAVRESEEPRQCWQRVSGDDGWARCVPVRDV
+GSEGPARGRGASPPVEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002236.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002236.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aaea066b6e6c7530138c41ac24191464fd23daec
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002236.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_02324
+MTAFGIIWLIAVTLVSAVAVRGILRQSTGVHAADRNGSTSFLWFLVALAFLLTNLPSGID
+PFRAVGLHLGAAALLGFLLHVLTRGAPAARD
+>NAFOICDF_02187
+MTVIGIIWLSELTLVSGVAVRGLLLTHLPSGIDPFRAVGLHLGAAALSGFILHVLTRGSA
+SRAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002238.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002238.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28413a59262781bebd859997ab5969dfe667d714
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002238.fa
@@ -0,0 +1,8 @@
+>ACLBLIBL_02345
+MRILGGFCYVAFITDVFTRRIVGWAVSASLHTQGLPLLALEHALLSTGASRGREGLVHHS
+DRGAQYVSLAYSDALIAAGVSASVGTVGDSYDNALAETVNGLYKAELIHSKRVWESVEEV
+ELATMGWVHWWNTARLHEALGYCTPAEVEATYTHDQDSAPVAS
+>NAFOICDF_00308
+MYSRRIVGWAVSGSLHTAGLPLLALEHALVSTGASRGRQGLVHHSDRGSQYVSLAYSDAL
+ITAGVTASVGTVGDSYDNALAESVNGLYKAELIHSKRIWESVQAVELATMGWVHWWNTQR
+LHEALGYRPPAEVEAAYTHDQDPAPVAS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002239.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002239.fa
new file mode 100644
index 0000000000000000000000000000000000000000..61d61c9c27f3ece205f02a5cea1cfced897b14d4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002239.fa
@@ -0,0 +1,8 @@
+>ACLBLIBL_02361
+MDENPSTAWTGTCGFRMLPTDDFAQGPSTARLTEVAGGAALALDYTWVHPEQGEQAGHLV
+LGRPDDGGRVTVAFTDSFHQSPEVRVLEGTAARTEGGGDAGRDRGAGAAPHPIDGDGVAV
+TMEYSGWGWTVAVRRQGGRLAMMMQNVVPAGVEGAEPGPYDVMRAAWTPAGA
+>NAFOICDF_02252
+MSLPSATDWTGTCGFRLYPTDEFSSGPSAARLTPVAGGAALALDYTWVHPDQGEQAGHLV
+IGRPDDAGRVTAALTDSFHQAPEIRVLEGASSSPEGDAHPVEGEGVAVSMEYSGWGWTVA
+VRLQGGTLAMVMQNVIPEGVEGAEPGAYDVMRAAWTRTDA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002240.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002240.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc57198730ab3cd63d8371dc952c087b4ee0cd65
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002240.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_02362
+MTKKHLGFLNFGHWIHRDPVGGRPAEPDATAALDDVVQMAVDAEAAGLDGAWIRIHHFQR
+MFSSPFPILTAMAARTQRIHLGTGVIDLR
+>MHAAABBN_00304
+MTRKHLGFLNFGHWIHRPGAEPDARQALDDVVAMAVAAEDAGLDGAWLRVHHFQRMFSSP
+FPILAAMAARTERISLGTGVIDLR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002245.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002245.fa
new file mode 100644
index 0000000000000000000000000000000000000000..597a3e97708016e897fdd5a5c302f5347de1097c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002245.fa
@@ -0,0 +1,23 @@
+>ACLBLIBL_02386
+MYAFKDQLAAELDELRESGLYKRERAITTPQSAHVKATAAGAEDGEAREVLNFCANNYLG
+LADDSRLIDSAKRALDERGFGMASVRFICGTQDRHLELERRVSRFLGTDDTILFSSCFDA
+NAAVFEPFFGREDAIISDALNHASIIDGVRLSKAHRFRYANRDMADLRAQLEATKELNDG
+AGARRTVIVTDGVFSMDGYLAPLAEICDLADEYGALVMVDDSHAVGFMGDTGAGTPEHAG
+VSDRVDVYTGTFGKALGGASGGYVAARQEIVDVLRQRGRPYLFSNSIAPSIVEATITALD
+LVEDSASLRAQLFENAALFRRRMTEEGFELLEGEHAIIPVMLHDAALAARMADAMLDQGV
+YVTAFSYPVVPKGQARIRVQLSAAHSAEDVEAAVAAFVAAREAVQG
+>MHAAABBN_02172
+MSTAEAGAATSTPADPWSSWLGSRAAVRARRGLERRAEPPEPGAPSSDVVDLAANDYLGL
+AAHPDVRAAAARVATEGPVGARASRVVTGTHPAHADLESAAAALAGADAALAFSSGYTAN
+LGVLGALAGPGTAFLLDEHAHASLRDGTALAATARSGAFAPLPGASVTTVEHNSVPAFRA
+ALGRLRAEGRARRIVLVVESLYSVLGDEADLPALAALAAEHGALLVVDEAHSLGVVPGGS
+RTGALGLWAGQAPVVVTATCSKALGGQGGLALFGGPAARSWRDHVLNTARTFVFDTALAP
+VLAASAAAACRIAATGEPAARLARARETAVDVFTRRTELAGHVEVGAGAVHSIRMPGPEQ
+AVAAAAELRAHGVLVGCFRPPSVPDGIARLRVSVTTAVPEPRLRAALEAVASVAARAWGA
+STGCPFAHGDPRPEAVRGDHLRISDPADLRRVLTDPGTFASDNALTAVVPLSGPARRILA
+AARFRLPPVLASAGGEEHRAVRRVVAPFFSPAKVREARGRILATTRTALTAALADTGRAG
+GAVDLATTVAAAVPARVMSALTGVPNPPEAQLHRWSADSLELFWGWPDEDRQLRLARSAA
+DFHRWLRGAVVEARGDDAQPGNLFAALHEAGVDDERIVSLGYFLVIAGQETTRLLISTAL
+TRALADPARWAALGAGADGGAGADAAEAAAAELVAECLRTSSSVPTWRRLATADVRVGEH
+EVRAGDELLLHLSGEQHDDARLAFGFGLHRCLGAGLAELETALVVREVARLLPDARLTGP
+PATWLRLLSFQAPQHVLVTPGPWHGGEDIRIEQSGVDTCASRS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002252.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002252.fa
new file mode 100644
index 0000000000000000000000000000000000000000..66bf9991cb6c71d4271d265042eb7807c63f20d1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002252.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_02670
+MCRAVTCKTCGKTTWAGCGQHIAEVKRTVPAGQWCPGHDKEKEKAAATSGFFARLFGR
+>NAFOICDF_00542
+MCRPATCDVCGKTTWAGCGQHVDSVKASVPAGQWCDGRHTPAEQAAARKDAPARGGLLAT
+LFGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002258.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002258.fa
new file mode 100644
index 0000000000000000000000000000000000000000..80644a86e40cf17d1e59a670e31e2bb5764af44f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002258.fa
@@ -0,0 +1,18 @@
+>MOLHKGIG_00402
+MTRREVESVEDRIREHLRRDDLNSAVELLRALSPGDALELLDRSEPRMVPVLFRLLDKST
+AVRVFAAMETGQQSDLVRQLQDGQVQDLFAELRVSGQARLLDEMPATVARKMLAGLDAGA
+RGEVGRLLGYPADSVGRRLRMAPVRLREDWTVAVALENLRDHGGREQAAIVSVPVVSPQA
+RLTGVVDVSVLVTQPLDARVSEIMREPVSAVATEDAEEVARLCADRRLWTVPVTDSEGRL
+IGVFTVADALEVLDEESTEDAARAGGVEPLGRPYLATSVLALMRSRITWLLVLAIGATLT
+VQVLGVFEDTLEEMVVLSLFIPLIIGTGGNTGNQAATTVTRALALDDVRPRDAPRVMFRE
+LRVGMALGGCIGLLGLVIAGLVFSWPVGLVIGATLFTVCAFAATVGGLMPLAARTIGADP
+AVFSNPFISTLVDALGLVVYFFIAQAVLGI
+>LFPAFLNI_00408
+MTRREVESVEDRIREHLRRDDLDSAVELLRALSPGDALDLLDRSEPRMAPMLFRLLDKTT
+AVQVFAAMETGQQSDLVRKLQDGQVQDLFAELRVSGQARLLDEMPANVARKMLAGLDAEA
+SGKAGRLLGYPADSVGRRLRMAPVRLREDWTVSTALENLREHGGQEQAAIVSVPVVSPQA
+RLTGVVDVSVLVTQPLDARVSEIMREPVSAVATEDAEEVARLCADRRLWTVPVTDSEGRL
+IGVFTVADALEVLDEGSTEDSARAGGVEPLGRPYLATSVLSLMRSRITWLLVLAIGATLT
+VQVLGVFEDTLEEMVVLSLFIPLIIGTGGNTGNQAATTVTRALALDDVRPRDAPRVMFRE
+LRVGMALGGCIGLLGLVLAGLVFSWPVGLVIGATLFTVCAFAATVGGLMPLAARTIGADP
+AVFSNPFISTLVDALGLVVYFFIAQAVLGI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002259.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002259.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1519f2ee1ecdc32735b93cfa222d3c848e8d24dc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002259.fa
@@ -0,0 +1,11 @@
+>MOLHKGIG_00488
+MVNETRAISRRQVTKGVTWSVPAIAATAAAPAFAVSSVGVVAGATLYANPLMTKYVQAQN
+GTTALYLNATPGVGIPDATACQSVQNKKISIVYTAPAGIVDFRKVLNARKAGTPYNTYTN
+GSVGDSKTFYTLKVGDRFVTGTNPAYWEVTKLASDGSSITLTYSAPITGCYYYAQPSFNP
+YFWAKDVASMVNQVHLTAYIGTQRVAFDTGAASNVTWSADRLEIIGPKTTN
+>MHAAABBN_00208
+MSECLMPVEVPQVLRSATKGIGMVNETRVISRRQVTKGVSWSVPAIAATAAAPAFAVSNP
+GVVAGATLYANPLMTKYVQPQNGTTALYLNATPGVGIPDATACQSVQNKKISIVYTAPAG
+IVDFRKVLNAQKAGTPYNTYTNGSVGDSNFFTLKVGDRFVTGTNPAYWEVTKLASDGSSI
+TLTYSAPITGCYYYAQPSFNPYFWAKDVASMVNQVHLTAYIGTQRVAFEKGAGTNVTWSD
+DRLEIIGPKTTN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002263.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002263.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6635447790658d25af9ed81f15fd82d270572321
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002263.fa
@@ -0,0 +1,20 @@
+>MOLHKGIG_00596
+MATMIQESMDSEYDDVRFPQERTQGLILGLTLEQVIVVLAGVLIGMAFILRGGPAMFVGI
+GLMAVIGAFGATRFRGRSLPGWVWVAAQYLRRGATDQLEYRQGMAPAHVLELVDGEPQAP
+VSEAGPQAQRDAKGRIKPGEPARFRLPGVAGELMVYAMPNGAGFVWDPRAREAVVCAKVM
+TTRGFDLESFDAQEERSLSWGSSLAALSRLPGVVRIQASDQTTLISGAAVEDFYESKQEG
+AGRTGASIDPFLDQAFRELMKEAQSMPVHEQWLTLVVSPSKITSQVKALGGGTPALMEHM
+LKLMTTVESTLPRSGTQVTAWHSPRTLAGLSRSAFDPDASVMVSTMKADGKTAGTAPSSA
+GPMAVEVHAGHMVTDGNYHRTYKVSELPQNLARLGFLDELVFAGDFRHTVSVFLAPVERG
+AAVRSVQRRKTDWHTNSRLMNKLGRIGSLEHDQSLEDVEREEAELRRRHTGVEVVVLVTV
+TGASRSELESAAAEVVASGITAECELRPVWMEQDAAFVAGALPFGRMKL
+>NAFOICDF_01792
+MSSRKKNNSHEPEATGSELVPVKFSRLTRRGILLGLSAAQLVTVGIAIATIITALYAGGG
+MWLAYTAPVWATAVLLTWVPVAGRPVIEWVPVAGWWVYRTTIGQLLYRRRIVTPRPAGTL
+ALPGDQARLREYEDPTTGAGMIHDPHQNTLTVVCEITHPAFVLLDPAEQERRVTAWGRVL
+ATVCRSGRIATLQILERTLPDSGTGLAEWWTTHGQPDDTSWAATTYAELINRAGPAGERH
+ATTLSLSLDMRNAARQIRTAGGGIRGAAAVLRQEMNTLTAALRSADLTPSGWLTPGQIAV
+ILRSAYDPAIAATLERHGEIGHDLATAGPVAVNETWSRIRTDSAHHAVLWISEWPRSMVY
+PGFLSPILLSSGIQRSFSLICTPMRSDQAARDIRKKKVEHISDQAQRAKIGQIEDASQTA
+EYHDVLQQEADLTAGHGILRYTGLITVTATTIEDLDAHVAALEQAAIQANCETRLLAGQQ
+AKAFTAAALPLCRQV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002264.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002264.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a421088b1cfc82fd513b34c959d99f09d62adfb1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002264.fa
@@ -0,0 +1,18 @@
+>MOLHKGIG_00597
+MREEPKVDLFQIIEPGKMSLREARVAQRKMKMAQAQAQRLRNREAREERFPQPQWGKAGP
+RGARQLRGLRTLAPRPVRTTTHTAATAYPFVAGPGLGARGLMIGKDMHGGGAFCFDPWAL
+YEAGIISGMSMMLFGQVGTGKSSLAKSLAVRQVLAGRKLSVASDKKGEWTRVVKGLGGSV
+IQVGPGLDTRLNPLDPGTRPSTDVQGEPMTDRAWASMVRTRRMSILVALVKILTDREMTS
+PEHHVLSAGLDAAVAVADAEGRPPIIPDVIRALDAARTDPDAMKAEAASVTMMTLGRVSS
+GDLAGMFDGETTVVLDEQACATSIDTSALLGASPEAVRVVNACAGAWTEAMVTTRDGGQR
+IVIYEEGWDNISSEADLRRMVEQWKLSRAYGIFNVLVLHKIADLDMAGDQSSKMAAMARS
+LLADADVKVIYRQDRSALKITTSEMELSDRERSLVRSLPKGTGLWRLGDSSFEVQNVLTR
+AELPLFDTDERMDKAKEAVA
+>NAFOICDF_01798
+MAEGGLGSDGVFVGQDLYSGGSFVYDPWVLYARGIITAPNLVLAGIVGSGKSSLAKSLYT
+RSLPFGRRVYVPGDPKGEHTAVAEAVGGKAIVLGHGLHTRLNPLDEGHRPGGLTDQEWAS
+TVASRRRDLIGALAETVLARGLTPLEHTAIDLALTATVAENEVPILPMVVDHILTPSHDP
+GGRLAEDGRLVGHALRRLVAGDLAGLFDGPSTVAFDPDLPMISLDLSRVTENSTLISVLM
+TCSSAWMESALLDPNGGQRWVIYDEAWRLMSHPALLKRMDAHWRLARHYGIANMLIFHKL
+SDLDNVGDEGSAMRSLANSLLANAETRIVYRQESDQLGPTATALGLTGTEQTLLPNLGVG
+QGLWRIKNRSFVIQHQLHPGELELFDTSSRLTAGVK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002266.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002266.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eea1184ddeb810a9a302e68108850c27eda21314
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002266.fa
@@ -0,0 +1,8 @@
+>MOLHKGIG_00599
+MGRFGLHRTGSAEYKRYLRSQAWGYRRVRWFADCRQAGQEPACQVCGITLTRAGTLDLHH
+VSYKGVGQDEEGRWQAREAHNDLMPLCRDHHQRLHQIMDGKKEFFGWDRRRATIVIVARM
+VRQSQA
+>NAFOICDF_02242
+MGRFGLYRTGSAEYKRYLRSQAWGYRRVRWFADCRQAGQEPACQVCGVTLTEAGTLDLHH
+VSYKGVGQDEEGRWQAREAHNDLMPLCRDHHQRLHQIMDGKKEFFGWDRRRATIVIVVRM
+IRQSQA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002267.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002267.fa
new file mode 100644
index 0000000000000000000000000000000000000000..efca1b9d4c75dfe96b495b0aa93974f0a6f2eadc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002267.fa
@@ -0,0 +1,18 @@
+>MOLHKGIG_00601
+MIPVKDLIKAREDWDFEREVALDEQSSVERELASANGHLSRLKEALIERGLASLLWGAQH
+EDVASVPDLVQDTSEAVLAAQMYLADWLVLPDSAVRHLEDIDTAPEAYNWGNKAWRGFRA
+LAAYAQDRASGWDKGGFWEWCASGPVLGWPATSKKLSMTESEGVQTSGKFKGTRDFKVDP
+AVDSSGEITMLAHLKISEGGGNLAPRVYFYDDTNGATKKVHIGLVGPHYLVPNKSTN
+>LFPAFLNI_00187
+MAVGYRAIFAVSPREDALAIARESVHSWLVDKLNRARPEVRQQALELDFNAPFAVQLSDE
+IHVSNTRAHGDNGQLQQLIRLDESSAPGETWRVNITADRNDVGGVRQQTIMVELDPLHLD
+AETAVMRAAPPRFVREMLTQHVLRSGTTVLTATPKALRGSEGGREAYRAVIDPLRQAQAV
+IAAQPPGSDMTIWQAAVASLTRQAMGITTALTLDKDALDQFNRRLPRNLQLQPGEVRTFA
+PHVDLDDPADSLRHRSLGPGTFARHIKPRVKDGVTVPEVDPTFASVHARRARMYALEQPL
+PDSIRSMRQQVRTGELREERDRAAGLVTGFSTVRVRPAAPAPAASPHRPGAGKRPSPTPT
+SGRLGASGAIPVPRPLPPSQEKVAEASSATPVAPAEAPQASAPSSITPVPAWQKTLVQLV
+WSTLGTEEITKEAIELLAEQLAASGRREQVADEQIANAVREAEIAAAQHDDLRARLEDAE
+LAAAAEQEERESLAREVEHLRRKAIEAERYEDLVVPEATDEEAKPSTFDDLIERIQSERF
+TTHEYVVFTGDMKKVNEVEAIDIVGRHLSSCWEFVLTLEGYARAKKDGFNGGVHQYLTSG
+EVDGKRCSPGKHASLESESVKSNAAQRRERLLPVPKNVDRSGAVHMWAHFKCSKDGTKSP
+RMHYYDDTDNTGKIYIGYIGPHLTNRQTSSM
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002272.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002272.fa
new file mode 100644
index 0000000000000000000000000000000000000000..63e6f91c7ef0836d91a4b55a5af9227380d9bd7d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002272.fa
@@ -0,0 +1,26 @@
+>MOLHKGIG_00892
+MSTVLLLTTGTGPAEGLLLQDLRDSGHVVDVLDVASHAWLRRRPGLAPAPLYPWTGTHAL
+RAAGAQIAREMRRVTAAGAYDAILASGLGAAGFAARHVEEEFIPLLRRGDLDFSAARRHA
+EEDFAALTRAVDRLFLADEWEFDKALSKGSRSAHLRHPRVGLAPQTLAPLAAEAETPRVV
+VLHPEHVDADRLAAQMEALQTAVDTVPGASLRSLSASALYRTRDLAAGRAFDAVAATRLG
+GATHVVLVGSSRDHAAVGELLVGTGFAERLVVEDTIGSGAWAAGHPGVRTGRGLRLVTEL
+AAALHGGPETHSAVDTVDGGTTDLLSAYRAAMTGRVDRTFEDLAVLRHDGPLDVFFSTSP
+LEDRTDGARPQRVRNMNDALSEPAAALRLSSVPGVFDRRLRVLDEALAAGRPLGLLYGEN
+STSPIPVDRVTAALADVMARFSAGGGTSVWFVRDLHWLDEIDGYLEDADARRDVQERGLA
+EFDAMAEAAYRLAAPSAESGAGFDALLARHGRGPVDWLPLPPAVSPANTVPADAPAIGEE
+GVTLLYAGGVGGIYGLGQYLTAVGTLDPQVRLDFVVRAGERSVLEDMLAEHGLADRPGLR
+ITTVPLEWYVPATRTVVGVVLLGGKYARFSFPYKTMSLIERGYPVLCFADMGIADFLERN
+RVGLGVARSSEAIRAGIVTLVRDGAPGMAEAQRSQSWAVRVATARAALED
+>MHAAABBN_00614
+MSTVLLLTTGTGPAEGLLLQDLRDSGHVVDVLDVASHAWLRRRPGLAPAPLYPWTGTHAL
+RAAGAQIAREMRRVTAAGAYDAILASGLGAAGFAARHVEEEFIPLLRRGDLDFSAARRHA
+EEDFAALTRAVDRLFLADEWEFDKALSKGSRSAHLRHPRVGLAPQTLAPLAAEAETPRVV
+VLHPEHVDADRLAAQMEALQTAVDTVPGASLRSLSASALYRTRDLAAGRAFDAVAATRLG
+GATHVVLVGSSRDHAAVGELLVGTGFAERLVVEDTIGSGAWAAGHPGVRTGRGLRLVTEL
+AAALHGGPETHSAVDTVDGGTTDLLSAYRAAMTGRVDRTFEDLAVLRHDGPLDVFFSTSP
+LEDRTDGARPQRVRNMNDALSEPAAALRLSSVPGVFDRRLRVLDEALAAGRPLGLLYGEN
+STSPIPVGRVTSALADVMARFSAGGGTSVWFVRDLHWLDEIDGYLEDADARRDVQERGLA
+EFDAMAAAADRLAAPSAESGAGFDALLARHGRGPVDWLPLPPAVSPANTVPADAPAIGEE
+GVTLLYAGGVGGIYGLGQYLTAVGTLDPQVRLDFVVRAGERSVLEDLLAEHGLADRPGLR
+ITTVPLEWYVPATRTVVGVVLLGGEYARFSFPYKTMSLIERGYPVLCFADMGIADFLERN
+RVGLGVARSSEAIRAGIAALVRDGAPGMAEAQRSQSWAARVATARASAED
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002273.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002273.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6291c9953dcc3869f0c6ac1515727f66642ece8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002273.fa
@@ -0,0 +1,32 @@
+>MOLHKGIG_00893
+MAVATPAPRRPRMAMLVGNQVVGDSRVEKAAVSAVRAGYEVVVVGVSHRTTFNLGRYGSV
+PILRVPVTFRRHLAWQTLHGTARPDVTDWSAVLDPEEAAAMTAWDLAHEVGAGLLQAVVR
+GLSPHALPDRARGRLGRAARRLGRLGPARGRRDPAAMRGRRALKNFAAGRTGAWREVWPL
+IADYEDGFLRALIDLAPDLVHVHDRHPLPAAAAYDHYRAARGLPPVPWVYDAHEWLPGQM
+MPGPVDQRIAWKAAEAELIHEADAVVAVTDELAERMREYHALQERPVTVINGPWGTQLPM
+GPAERLPLRTELGLSDDVPLLVYLGKLAAVRGVGTLVDALPLLPGVHIAFVGSPDPDARQ
+GLRDRAAQLDVADRMHIVDYVPSASVTWYVSSATAGVSPLLPTPAHESAVPTKLRECLLA
+GLPLTVSDLREQARFVREQGVGTVFAPGDAADLARAVRDLLARRTELTAAARSPEIAARH
+GWEAAERALHGLWRRLVPTPAAPPPVEIAPDPAREPQPRGLLVVGDPPTVRPLADAWPAG
+AGPVTLRPPRDFPEGRGLVVGGPEAVWGVLQDWVTDDRAHGTVLIGGEGPLWGRAEQSPV
+HELLSLRARGRQVALVAGERILAGVERRLAAVPGHPWGGLDPDARAALDRRIRRQGRPFQ
+AALAAGVPVLSHRRVEALLTPGVLWLPAPIPTPTDRGPGRDGASAPRSVLILPGDRTSAE
+SAAVDELVAELAARGIPVEAPSGPRFRRRPDAFHGDVVVAPLHTEDLEVAALQALAAGSA
+VVAGPPVTPAPDECAPPVTETDDATLLATVLGLLEETSAAAGERRERAREHHARLHAPEA
+VLVRLQALLSPAETTDGPAAV
+>MHAAABBN_00615
+MPVDTPAPRRPRMAMLVGNQVVGDSRVEKAAVSAVRAGYEVVVVGVFHRTTFNLGRYGSV
+PILRVPVTFRRHLAWQTLHGTARPDATDWSAVLDPEEAAAMTAWDLAHETGAGLPQAVVR
+GLSPHALPDGARGRLGRAARRLDRLGPARGRRGPAATRGRRALKNFAAGRTGAWREVWPL
+IADYEDGFLRALIDLAPDIVHVHDLHPLPAAAAYDRYRAARGLPPVPWVYDAHEWLPGQM
+MPGPVDQRIAWKAAEAELIHEADAVVAVTDGLADRMREYHALQERPVTVINGPWGAQVPM
+DPAERLPLRTELGLSDDVPLLVYVGKLAEVRGVRTLVDALPLLPGVHVAYVGSPDPGARQ
+GLRDRAAQLDVADRMHIVDYVPSASVTWYVSSATAGVSPLLPTPAHESAVATKLRECLLA
+GLPLIVSDLREQARFVRDQGVGTVFAPGDAADLARAVRALLARQAELTAAARAPEITARH
+GWEAAERALHGLWRRLVPTPAAPQPVEIAPDPARDPRPRGLLVVGDPPTVRPLLDAWPAD
+AGSATQRPPRDVPEGRGLAVGGPEAVWGVLQDWVTDDRAHGTVLSGGEGPLWGRAEQSPV
+HELLSLRARGRHVALVAGERILAGIDRRLAAVPGHPWGGLDPDARAALDRRIRRQGRPFQ
+AALAAGVPVLSHRRVEALLTPGVLWLPAPIPTPTDRGPGHDGASAPRSVLILPGDRTSAE
+SAAVDELVAELAARGIPVEAPSGPRFRRRPDAFRSDVVVAPLHTGELEIAALQALAAGSA
+VVAGPPVTAAPDGCAPPVIETDDATLLATVLSLLEETSAAARERRERAHEHHARLHAPEA
+VLVRLQALLSPAETTDGPAAV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002276.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002276.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51109438441d42323c2041bfba18b71459507572
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002276.fa
@@ -0,0 +1,6 @@
+>MOLHKGIG_01041
+MTRSEDVIITQDAERSDVFALVESLADGQKPRALNVPAGEDAHTTPDTVETGREVPAGAL
+GALAALGAGLVLMARGRVRRV
+>MHAAABBN_00754
+MTRSEDVIITQDAERSDVFALVESLADGQKPRALNVPAGEDAHTTPDTVETGREVPAGAL
+GALAAVGAGLVFLARGWVRRV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002278.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002278.fa
new file mode 100644
index 0000000000000000000000000000000000000000..137a2c57ffe5600ac021b8b1399b8d8b8a6bc670
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002278.fa
@@ -0,0 +1,13 @@
+>MOLHKGIG_01389
+MIRVEAGMSTARFCQLFDMPERTWRRWQAKARTGTAVKGPWPQPGRQAARELVVKHALAH
+PAWGHRKIWAMVRHDGHVVSEATVLRILRDEGLILPAQYQRERRKLAERRKAAFATEPSG
+PNQVWQLDFSEFETTTGGTWRLAGCRDYWSKYEHPFHVSPTGNQHDAIDAIELALADYEA
+MFGHPLVEACPVDPETGELLPVVTIVTDNGGPFRSFRFESFIAAHPELHHVRTRVKTPGQ
+NGSRERGFGTLKYERLYLDEIDDAIVLAERAEDYRIEYNELRPHEAISWNRPKEVHLGLA
+DPTTPTFKTKEILPTT
+>MHAAABBN_01121
+MVKHALAHPAWGHRKIWAMVRHDGHVVSEATVLRILRDEGLILPAQYQRERRKLAERRKA
+AFATEPSGPNQVWQLDFSEFETTTGGTWRLAGCRDYWSKYEHPFHVSPTGNQHDAIDAIE
+LALADYEAMFGHPLVEACPVDPETGELLPVVTIVTDNGGPFRSFRFESFIAAHPELHHVR
+TRVKTPGQNGSRERGFGTLKYERLYLDEIDDAIVLAERAEDYRIEYNELRPHEAISWNRP
+KEVHLGLADPTTPTFKTKEILPTT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002280.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002280.fa
new file mode 100644
index 0000000000000000000000000000000000000000..543d68f1d4f61753354d7d9b9ed5288793fa9ef4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002280.fa
@@ -0,0 +1,12 @@
+>MOLHKGIG_01605
+MMHDERPTGRLGLALGGGGARGLCHIGVWRVLEELDIRPDVLAGTSMGGLLGALIAAGHD
+AASLEKIERSVDWPRLINWGLTGGILSSERLRAWLRELLPDTFEELQIPLVLTAADVVEG
+QTRYLHTGDLITAIQATTAYPGALEPVTVGDSVLVDGGILNQIPVDGVRFLGAQRVIAVD
+ATTLEPLERPEPGARTRTRRSPATSLRQAMRAIDVMQAQLTTVRLSLYRPDVLISPPIEG
+MTVADFRSSGVAIAAGEEATRARAEKLVELSRGRMA
+>MHAAABBN_01317
+MHDERPTGRLGLALGGGGARGLCHIGVWRVLEELDIRPDVLAGTSMGGLLGALIAAGHDA
+ASLEKIERSVDWPRLINWGLTGGILSSERLRAWLRELLPDTFEELQIPLVLTAADVVEGQ
+TRYLHTGDLITAIQATTAYPGALEPVTVGDSVLVDGGILNQIPVDGVRFLGAQRVIAVDA
+TTLEPLERPEPGARTRTRRSPATSLRQAMRAIDVMQAQLTTVRLSLYRPDVLISPPIEGM
+TVADFRSSGVAIAAGEEATRARAGKLVELSRGRMA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002284.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002284.fa
new file mode 100644
index 0000000000000000000000000000000000000000..48dbe9fa58518065c8080f0fdd663d338c069a34
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002284.fa
@@ -0,0 +1,6 @@
+>MOLHKGIG_01616
+MSISASEARKTLFPLIERVNADRDAVEIVSRKGNAVLMPADEYAAWQETAYLFRSPANAR
+RLLDAYERARAGSVEEHALDRMDGDA
+>MHAAABBN_01326
+MSISASEARKTLFPLIERVNADRDAVEIVSRKGNAVLMPADEYAAWQETAYLFRSPANAR
+RLLDAYERARAGSVEEHALDRLDGDA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002288.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002288.fa
new file mode 100644
index 0000000000000000000000000000000000000000..06c7ca9d3de6b089c3c4ddbf16919d59454cfd56
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002288.fa
@@ -0,0 +1,10 @@
+>MOLHKGIG_02061
+MNNISEVTDRLASNETGMEPWLWMPLLKLLALGDPVDVSDLAAATGRAGEEVRTALKAMG
+DTEYDGSGRIIGQGLTQRPTQHRFEVNGEQLYTWCALDTLIFPTLLGASARIESSHQATG
+TPVRVAVTAMGVTSVEPATAVVSLVNPEDISSVRSSFCNQVHFFASPDDAAPWLETHPGG
+TIMPVKEAYELGSSMAEKMLTHTPGPATDQVSNGVQSCAC
+>NAFOICDF_02221
+MNNISEVTDRLASNETGMEPWLWMPLLKLLALGDPVDVSDLAAATGRAGEEVRTALKAMG
+DTEYDGSGRIIGQGLTQRPTQHRFEVNGEQLYTWCALDTLIFPTLLGASARIESSHQATG
+TPVRVAVTAMGVTSVEPATAVVSLVNPEDISSVRSSFCNQVHFFASPDDAAPWLETHPGG
+TIMPVKEAYELGSSMAEKMLTHTPGPATDQVSNGVQSCAC
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002292.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002292.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37bfec972f6d989e356fd962666895536213b438
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002292.fa
@@ -0,0 +1,20 @@
+>MOLHKGIG_02236
+MGGLVISADFPLGVYTGHGPDGGAERFPDVARLFSALVQAAAAGTLSTGDPEAPFTAESL
+AALDWLEEHPPDALVLPGHTPVAPGVRRFAYRKEGVFLKEVGKTNYKVTGRPVSDGTALG
+GPVQWVWDDGPSGTDTQVCSTLEQLCADVPHLGEASSPVRLTVHEGEGLPAPTHRRDRNA
+SLRAVPGAVRQAMPSPGRRAELDRAHAATTLGRKPSASGDKHTTSAVPHATLPPRDHLRS
+GIFAPVEHHEPDVPWTQVLAVPVIGANSTVPEERYVSVCVALHRALVSRLGPDAPPEITG
+RYAPSVAPPANRVALHLAPGDLPNLPFSDGRDRFLVLVPRGMPGPALGMLASALAGVRRV
+VTSEHQLTVAPEEIEVYDGTEFWKAPTEGAVRTWDAQPAVVVERRLKSKPPIRDVDLAAA
+WSLGNVLRDVEPAFATKDPVARHAAVVESGAQLRGRAFRTLTPTAYVHRTDRRSPIEPFR
+LTLTLSTAVPDRAILALGQSRHLGCGLLVPTDIPGSTQERS
+>LFPAFLNI_02168
+MGGLVISADFPLGVYTGHGSDGGAERFPDVARLFSALVQAAAAGTLSTGDPEAPFTAESL
+AALDWLEEHPPDALVLPGHTPVAPGVRRFAYRKEGVFLKEVGKTNYKVTGRPVSDGTALG
+GPVQWVWDDGPSGTDTQVCSTLEQLCADVPHLGEASSPVRLTVHEGEGLPAPTHRCDRNA
+SLRAVPGAVRQAMPNPGRRAELDRAHAATTLGRKPSASGDKHTTSAVPHAALPPRDHLRS
+GIFASVEQHEPDVPWTQVLAVPVIGANSTVPEERYVSVCVALHRALVSRLGPDAPPEITG
+RYAPSDAPPANRVALHLVPGDLPALPFSDGRDRFLVLVPRGMPGPALGMLASAVAGVRRV
+VTSEHQLTVAPEEIEVYDGAQFWKAPPEGAVRTWDAQPAVVVERRLKSKPPIRDVDLAAA
+WSLGNVLRDLEPAFTTKDPVARHAAVVESGAQLRGRAFRTLTPTAYVHRTDRRSPIEPFR
+LTLTLSTAVPDRAILALGQSRHLGCGLLVPTDIPGSTQERS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002294.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002294.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b0ff5bc17e3ba90019a620399713e6223302e09
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002294.fa
@@ -0,0 +1,14 @@
+>MOLHKGIG_02248
+MAATDHTLNPRAGANPSAAPNRLVRRRAVIGLLTGAPLLAACGGDPLSSDGGGQGSGGSG
+SGGDGGGTVRVGSANFPESEIIGELYAQVLEAKGLTVERKMQIGSREVYLGALKDGSIDL
+IGEYTGNLLAFYDKQAKAKTSEEVFAALQKALPDDLEVLAEAKAENKDAWCAAGDWAKQH
+GISSYADLKDYDGTLRVGGPPEMSQRDYGAGLARVESVYGVPADRMEFTPISDGGGPLTV
+KALKDGDVDLANIFSTTPAIEENGFVMLEDPEGMVTPQNIVPLMAKDRVTDQIREAVESV
+QKVLTTEDLMAMNAENSGEQKKQPREVAGEWLKEKGLV
+>NAFOICDF_00459
+MATSPRPSAPLSSALSRRAPRRAVLGLLAASPLLAACGGDPLAEGSSSPAPGSGGTDAGG
+AVTVGSANFAESEILGELYAQVLEAKGLQVERRMQIGAREVYLDALKDGSIDLIAEYTGN
+LLGYVDKEATATSSADVEAALKAALPDHLTTLAVAQAEDKDSYNVTKAFSEENGITSLAD
+LAAHPGTLRVGGLPELAQRDYGAGLAGLEEVYGVPQDKLEFTPISDGGGPLTVRALVDGD
+VDLANIFSTTPAIKDNGFVTLEDPKGMITAQNVVPLMAKDKVTDRIREAVEAVQAQLTTD
+DLLAMNAANAGEAKRQPRQVAADWLRQKGLV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002298.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002298.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f4be9ed644d768365da7c19e3cb399d84fa9a4ec
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002298.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_00003
+MRSFTRQDQNNNPSEKGRLLSQDPTVCQHQHATTNHMLSNPKAYSHPAGTTTGTIH
+>NAFOICDF_01380
+MRSFTRQDQNNNPSEKGRLLSQDPTVCQHQHVATNHMLSNPKAYSHPAGTTTGTIH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002302.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002302.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a288262007c1627405dc79ff832ed21edd9d3dd0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002302.fa
@@ -0,0 +1,10 @@
+>NAFOICDF_00156
+MNKSEEAYARLTQKIETGELPPGAILSEAALIDAAETGRTPLREAVQRLIRDHWLLVGGG
+RGLQVPPISVDDQLERLEVRRSLEALAVGLACARADEEQLAAVAAHVRHLRTVEDLPAYV
+AAVGRSHELLRTIANNRYLADSLVPLQGLSRRFWLATTKGLPDEVERGRAFYVPALEAVT
+RRDSAGARAGVLALHDFLARSALDYAARRAAHGSAEPPAPWAAGR
+>MHAAABBN_02187
+MNKSEEAYARLTQKIETGELPPGAILSEAALIDAAETGRTPLREAVQRLIRDHWLLAGGG
+RGLQVPAISVDDQLERLEVRRSLEALAVGLACARADEEQLAAVAAHVRHLRTVEDLAAYV
+AAVGRSHELLRTIANNRYLADSLVPLQGLSRRFWLATTKGLPDEVERGRAFYVPALEAVT
+RRDAAGARAGVLALHDFLARSALDYAARRADHGSAEPPAPWAEGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002306.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002306.fa
new file mode 100644
index 0000000000000000000000000000000000000000..27b3e3ccf8cbac1aeb9bfc576746a10de9a3ca02
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002306.fa
@@ -0,0 +1,8 @@
+>NAFOICDF_00324
+MPEYDFETYPTTPDAMAKYLQEREAAGNPMTGEEALAYSDWSRERGRAIQAKIDARKTPE
+EREEFRRFAEEFERQCLEDEKRFAEEAAREAAEDAERAAQGKRPIKRERDIVTPKGFSGI
+GVTPRGW
+>NAFOICDF_00344
+MTKYNFEAYPTEPESMAKYLHEREAAGKPITRAEGEAYIEWSLAKEQEITERKERMSPAE
+RAGHEGFQREEEPMGAIFDLEDARSEVEALVEAAEDAERAAAGKRPLKRERDIVTPEGFS
+GMGVTPRGW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002308.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002308.fa
new file mode 100644
index 0000000000000000000000000000000000000000..437b7f037f9235bb877f948616b30adae0b9bb13
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002308.fa
@@ -0,0 +1,6 @@
+>NAFOICDF_00332
+MGAIDQSTDNDADYDVIEQTWLDAGQTVKELVDRARTLMEENDDIAAGAHQKAGNHMGLV
+HV
+>NAFOICDF_00337
+MTIQYDSAAAAAYEDEVLRIASRIETILGDREQQKRFVADNYQSTDNDADYDVIEQTWLE
+AGQTVKELVDRARTLMEENDEIAAGAHQKAGNHIAGMRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002313.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002313.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba3293cfc1c5d7ca8ddeb3cc851ccae18881bd94
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002313.fa
@@ -0,0 +1,12 @@
+>NAFOICDF_00628
+MAINWRRAQYLLAEDLTDIPVRYIDELFGSNGIALGPENPQDVDTSVRRARMRRYLTTLD
+LDTNRADQQRFADVMAERYRKIALVHQHGNTDETQWKLERWTTLLRAAGFQVDTTALSVT
+WPPGPQMGTLAPDVLAHLNDPSAIEDHLERIHTTIDSDPRLAVATARSLMESTAKIVLTS
+RDKTYTATESLTKLVSRAQASLGMSPKDLGGEQPEVRRLLQSLQGIAAPISTLRNDTNVH
+HGAEVVPQWVRPRHARLVLGAAQLWCQTVLETLSDPTAPWRVTDAAAQR
+>NAFOICDF_00696
+MAINWRRAQYLLAEDLTDFPVRYIDELFDGNGIALGPENPQDVDTSVRRARMRRYLTTLD
+LDINRADQQRFADVLAERYREIALVHQHGNTGETQWNLDRWTTTLQAAGFRVDTTALSVT
+WPPDPQMGTLAPDVLAHLNDPSAIEDHLERIHTTIDSDPRLAVATARSLMESTAKIVLTS
+RGETYTATESLTKLVSRAQTSLGMSPKGLGGEQPEVRQLLQSLQGIAVPISTLRNDTNVH
+HGAEVVPQWVRPRHARLVVGAAQLWCQTVLETLSDPTAPWRVVDAAAQR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002314.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002314.fa
new file mode 100644
index 0000000000000000000000000000000000000000..250bb5da4e2bc62a167a33a16f3340279a66cefe
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002314.fa
@@ -0,0 +1,13 @@
+>NAFOICDF_00633
+MSTLLPIRPRPAPEEALDSYLERVATANGVTTSGFVRQLTTEARAPLRFTNIAPPPPILD
+VLASWTGTDRGLLQDCLLTRYPVIPFIDSQNRHGTRSVVAHGWVLLNRSQACPWCLAETG
+VWKITWRLAWVTACLDHDRLLATDCPGCQKPLRTTHHGALRPAGPGARCGNPRPQGQGKR
+CPFDLSRISPLSAPPPVLQQQRRVERALRGAEVEVAAIALEGTTYLRQLQALTSAAMGLS
+APTTAVQPEYSEGVPAEISTLSGRARPAPRPADIRAAAYVRRDRTIFAPP
+>LFPAFLNI_02215
+MITPLPVRVTPGPNEAMDSYIERVAAANVLAITPFTHHLKRLSGSTLRFLNAAPSPELVA
+TLARLTDTPESALHELTLSRYEVVPEIHNHHRYAARAASAKGWFSLIRTQACPACVGEGQ
+PWASYWRLPWVTACLKHGCLLITRCPGCRVKLRSTRLQGLRAGGFTPLCGNPRATGRVPQ
+CEDDLGTTALTLAGQPVLVQQQVVLAALRGSTVFCHGEPVTGTEYLRRVRSIAVLLFHTV
+AISTATGLPAWAQKLRAEAQARTKERGPRWGVSAPDCPQSRAAVFLIAHQILTGPVGAGR
+GSLDVWLDLVPPSNEGTRAWAEDHTTTPDAISYLIG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002318.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002318.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71c5c389586c392f9043d8c12f45a0f917a8867a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002318.fa
@@ -0,0 +1,29 @@
+>NAFOICDF_00642
+MTSTTHHQEQPVSNRDVIRVRGARTNNLRDVDVDIPKKQLTVVTGVSGSGKSSLAFDTIA
+AESQRLLAATYPAFVQNLMPHLPRPDVDTLEGLSASIVVDQAPLGANPRSTVGTATDAWS
+LLRQLYAGHGTPPVPGPHALSFNAATGMCPACEGTGRTATLDVDLVLDRSLSLNDGAITF
+PNFTVGSLFWKVYARSGAFDNDKPVQSYTPAELEHLLTGTGPNVDTGTYPMAYEGVLTKI
+TRLYLSKDPAALKPRLREALELAATTGPCPGCAGTRLNSAARACTIDNTPITTCHTMPAT
+DLHRWLADLDLPAAAPLIAQLQSLLANLTRVGLGYLALDRPTSTLSGGEGQRIRTVLHLD
+SALTDLTYVFDEPAAGLHAHDTAQVVTLLHALRDKGNTVLVVEHHPDVITAADHVIDLGP
+GAGTDGGTITFQGTPAQLTHTHTPTAAALAARPTLNLTPRTPTGTLRIRDATTHNLHHLD
+VDIPLGVLTCITGVAGAGKTSLLTNLPRRDDLAVIDQRPIRGSRRSTPATYTGVMDWLRD
+AFAKAGSTPGHKLKPAMFSANSAGACPDCTGLGVTYLDAPGSGPVPVTCTTCNGARYTAD
+VLTHTLDGLTIADVLGLPVADAATRYTNTPAGPPLAGLVDVGLGYLTLGQPLSTLSGGER
+QRLRLATRIAQSATVYALDEPTTGLHMSDVDTLTRLLHRLVDTGATVVVADHHLNLIATA
+DHVIDLGPDAGPGGGHITYQGPAADLATTDTHTGRALAARLAL
+>NAFOICDF_01228
+MPTPHASAAPAPHTAHPADGHDVIRVHGARTHNLQDVSLELPKRRLTVFTGVSGSGKSSL
+VFGTLAAESQRLVNETYPSFVQGFMAAMPRPDVDVLEGLTTAIVVGQERMGSNPRSTVGT
+ATDATALLRILFSRLGTPHIGSPQAFSFNVASVSGAGAVSTQKNGRTVKERREFSVTGGM
+CERCEGTGRVSDIDLAALYDEELSLEDGALKIPGYSMDGWCGRIFRGAGLFPVDTPIKKF
+TQRQLDALLHKEATTITVDGINLTYLGLIPQMERSMLSKDVESLQPHIRRFVESAVAFGT
+CPDCHGTRLNERARSVTLGGASIDQVCALQITDAAAWLRGLDAGPAAPLVAGLQELLDAF
+ERIGLGYLSLDRATGTLSGGESQRVKMIRHLGSALTDVTYVFDEPSVGLHPHDLARVNAL
+LTDLRDKGNTVLVVEHKPETIAIADHVVDMGPRAGADGGRVTFEGTVEELAASDTLTGRH
+LKDRAALKGEVRTPTGVVEIRGASEHNLQDVDVDIPLGVLVAVTGVAGSGKSSLVHGSLA
+GREGVVVIDQAPITGSRRSNPATYTGLLEPLRKAFAKANGVKPGLFSPNSDGACPACKGA
+GVIYTDLATLGGVESVCEECQGRRFLPEVLELTLAGRSIADVLEMSVDQAAAYVAEGEAR
+LPAAQKVLGRLQDVGLGYLTVGQPLTTLSGGERQRLKLAVQMGERAEVYVLDEPTTGLHL
+ADVDQLLALLDRLVDGGTSVVVIEHHQAVMAHADWIVDLGPGAGHDGGRIVFEGTPAALV
+ADASTLTGRHLKEYVGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002324.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002324.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac14eb8a4d024c2144895d074c2ee693a1d2b8b7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002324.fa
@@ -0,0 +1,13 @@
+>NAFOICDF_00695
+MSRRSLASLATAAAFVVTAVLGGAGPAAAGTTYSAPLRTAVASLPVAAENNAGYDRAAQF
+GDWKDANRDCQNTRAEVLIAESKTTPKFTTARKCTVATGKWVSSWDLRTHTSASTVQIDH
+MVPVHEAWGSGARYWTKAKRVAFYNDLGDARSLNAQTSALNSAKQARGPEQWLPPKNQCQ
+YIADWTAVKIRWGLKADATEKAFLVKKAASCANTTLKVTRY
+>NAFOICDF_02179
+MLGCSGCLGLVALGLLLLSLLVGGFTGSPSPSAASQAPDGRSAAPSAPDAPGDPAGSAPA
+PAPTPDRAEAPVSDRAEAPAPAPAPASAPAPAPGDAGEAAPSSPAAEAPAADGTALAALQ
+SLPVKGRAPKTGYSREQFGPAWADVDRNGCDTRNDVLRRDLADVVLKAGTNGCVVLSGTL
+HGPYTGEVIAFQRGPGTSTAVQIDHVVSLSDAWQKGAQGLSAGRRAAFGNDPLNLLAVQG
+SVNQSKSDGDAATWLPPLRSARCPMVARQIAVKARYGLWVTPAERDAMARVLRECPGQGL
+PAEGGPVDPSPETAAEPTPQAPAPTVQAPAPAPAAPAGGADPSFSSCRKAKAAGYGPYVQ
+GVDPEYAWYRDGDGDGMNCE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002325.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002325.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7bde10c7da2859b30f0f54602d3a3d373d04521f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002325.fa
@@ -0,0 +1,9 @@
+>NAFOICDF_00736
+MTKSLISSAVVVLLILLVTVLTDASTWLVGLLSGLACLAGAWCAPLFQSGSPYGGTFFGG
+WQSRWDGPKAVQLLAAGAAVAVSVVLNLFGGGVPAVVGIIVALLVGALIPVPGDPAGGGH
+GADPEDARPA
+>NAFOICDF_00738
+MRMTPARVASAAVLAVLTLVCLLLMLDTWSFMGALLVSLIGAVLFVAGAWFAPLARSGDA
+LGGTPLRPWQAGFDGPKTTQVAGGGLVALLVALVTGGAPLVGPILGVVAAVIGGRFLRIP
+SHAQVVAAVGPEVAEASEHLPGEHHDAAPADSVADPDTDPVPVPATEAADSEKPRHEHAA
+DVSPETAPVPVIHPADAEHPHGSHAAMAHPDPVDDVPGDGEPTTR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002329.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002329.fa
new file mode 100644
index 0000000000000000000000000000000000000000..97772e486276e737418404af76e35d7de0b68439
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002329.fa
@@ -0,0 +1,11 @@
+>NAFOICDF_01187
+MDTRDDTELAPSATLGRRERAKAEKRARILAAARALFEERGFERTSMSEVARAADVAEGT
+VFQYAATKVELLMMVVDALWGAHERATTTPSLSAFAAPGAATAGGETADRIAELISPLVT
+AMWRWSELATWVAREILFGADMPHRRRVLDHVDRLEEEIAARLQDGRADASGAIGAARDG
+ATGTAGEEPGAAAAAGARLIVAGVLAELNRSRQRRIDGEDVDVVLRRLIDLVVAGAGAAR
+>NAFOICDF_02289
+MPVTLVSPRARGGEFATNVHMVDARPPLPSRSIDCAVVSHSRLAPESEPEPEPEPEPATP
+TRVPGLRERNKAAQRERILAAVRERLGRQGYRAMTTAQIAQDAGVAAGTVFTYAATKPEM
+LMMATHDRWKDSVPSALAGSLPEDRTEAVRALVDPIVATAVAEPENSAAIARELLFGQPG
+AHHDAVLVLVRRLEEAIARIIADGDPGPRERTAADLVVMGVVLELHRDRTEGGRVEGLEE
+RIERVIGLFID
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002333.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002333.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8df193fce9cde4083c390a60913f33bd1c725a70
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002333.fa
@@ -0,0 +1,16 @@
+>NAFOICDF_01197
+MTEPVTYTPDIEHSVDREEDLTREILAQMGAAQRRTAGEHKHAHRDAHAKSHAVLKATLE
+VHEGLAPELAQGIFARPGTYEAVARLSSAPGDIHTDRTPAPRGWALKVLGVEGKRLLPDL
+DSHNQDFLMVNFPTLAFGTVARYQEMLGLLEKNSQSPELLQRLTTGAARVVRGAVETVGG
+TPSATLEGLGRDNAHVLGETYFTQGALRYGDHVAKISLAPASANVRALTGQDMKVKDFSS
+ISEIVADFFSRESAEYVLRAQLATDAERMPVEDASVLWDEEEAPHQPVATLRIEAQESYS
+HPRRVYGDDALTFNPWNGVVEHQPLGSIMRVRKRAYEQSTRFRHEFNDRPAPEPTSLDEI
+PD
+>LFPAFLNI_01532
+MTEPVKYTPDIEHSVDREEDLTREILAQMGAAQRRAAGEHKHAHRDAHAKSHAVLKATLE
+VHEGLAPELAQGIFARPGTYEAVARLSSAPGDIHTDRTPAPRGWALKVLGVEGKRLLPDL
+DSHNQDFLMVNFPTLAFGTVARYKEMLSLLEKNSQSPELLQRLTTGAARVVRGAVETVGG
+TPSATLEGLGRDNAHVLGETYFTQGALRYGDHVAKISLAPASENVRALTGQDMKVEDFSS
+ISEIVADFFSRESAEYVLRAQLATDPERMPVEDASVLWDEEEAPHQPVATLRIEAQESYS
+HPRRVYGDDALTFNPWNGVVEHQPLGSIMRVRKRAYEQSTRFRHEFNDRPAPEPSSLDDI
+PD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002347.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002347.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bfa55d13faedeb6f2f4dcc82af6d53e3f3d4e9f5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002347.fa
@@ -0,0 +1,8 @@
+>NAFOICDF_02318
+MEIAFASTRHFGQGEVLRHVSADYVLKDFMEMNKVPSAAMFRRSRWAEVGGYLESMRWGM
+EDYEFWVRVLRDGGIARPVPTAYYHYRSRENSRLSTLGTHAARDTHQAIVEANPEHHAIL
+LQAAFLRLEEMHDLHLEYRSYVHKWQDRFRPLIRARDFAKRAVRKMS
+>LFPAFLNI_00519
+MDMNKVPSAAMFRRNRWEAVDGFQEGLDGQEDYAFWVRMLRDGGMARPVPAAQLHYRLRA
+TSRAATAGSEYWEATRKAIISGNADHHEALLRAAFERLDELRADLAEQKRYVQNWQRRAR
+PLIAVRNRIRSLLGG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002352.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002352.fa
new file mode 100644
index 0000000000000000000000000000000000000000..35596376160b7cc63ebb3ccc33c260170b70201e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002352.fa
@@ -0,0 +1,18 @@
+>MHAAABBN_00769
+MSPASTSPRRVLAIGLGPFNLSLAALAHPLPDVEVEVVESRDAFVWHPGMMLPGAQIQVP
+FLADLVTFADPTSPYSFLAYLKAMGRLHRFYIRGSWYPLRREFSDYCAWVAAQLPGIAYA
+TTVTAVRWDDQADEFVVEAASAAGTSTHRADHVVVGTGTVPSLPAPLARVAEESARVGAS
+PVVHTGEYMGRREDIAGAGSVLVVGSGQSAAECALDLLNAGHPDLTWVTRSPRFFGMEVG
+QLTLELTSLDYERHFATLPRARRDEINASHRSLYKGISEYTIEDVYHALYERQVGPLDPA
+RLWPGTSVTDARLVAGPGAPRVEVTLRDEETGVTGGHVVDRVVAGTGYRHPDHPFLEPVR
+HLLRAEDGRTTANADHAIDVSGRRIFVHNTAEQPLGLTGPDLGMAAEHSGRILSTIAGRQ
+VYAQAESIAFQDFGAVAAGVR
+>LFPAFLNI_00997
+MSPASTSPRRVLAIGLGPFDLSLAALAHPLPDVEVEVVESRDAFVWHPGMMLPGAQIQVP
+FLADLVTFADPTSPYSFLAYLKAMGRLHRFYIRGSWYPLRREFSDYCAWVAAQLPGIAYG
+TTVTAVRWDEQADEFVVEAASAAGTSTHRADHVVVGTGTVPSLPAPLARVAEEAVRVGAS
+PVVHTGEYMGRREDIVEAGSVLVVGSGQSAAECALDLLNAGHPDLTWVTRSPRFFGMEVG
+QLTLELTSLDYERHFATLPRARRDEINASHRSLYKGISEHTIEDVYHALYERQVGPLDPA
+RLWPGTSVADARLVAGQGAPRVEVTLRDEETGVTARHVVDRVVAGTGYRHPDHPFLEPVR
+HLLRVEDGRTTANADHAIDVSGRRIFVHNTAEQPLGLTGPDLGMAAEHSGRILSTIAGRE
+VYAQAESIAFQDFGAVAAGVR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002357.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002357.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e31d728cc3e15e0923c68a3179878db9a2e43ef
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002357.fa
@@ -0,0 +1,6 @@
+>MHAAABBN_01745
+MNAKPEKDLRRTVDILFRPARVAVLIDGCYWHGCPQHYIAPKANGGYWSDKVATNRARDL
+ETTRILTERGWLVLRFWEHEDPAVVAERVVAVVNERRPRRTTGAS
+>LFPAFLNI_01973
+MNAKPEKDLRRTVDILFRPARVAVLIDGCYWHGCPQHYIAPKANGGYWSDKVATNRARDL
+ETTRILTERGWLVLRFWEHEDPAVVAERVVAVVNERRPRRTTGAS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002365.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002365.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d2627264d313add1c62454a8ef00f613246e5fd4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002365.fa
@@ -0,0 +1,8 @@
+>MHAAABBN_02301
+MQTFDGLDEFERAVGTHLGHSRWRTVTQEQVDLFADTTDDHQWIHVDPERAARGPFGSTV
+AHGFLTLALLPSMVREIYRVEGMAMVVNYGSDRVRFPHPTPVGARIRAGAELTRLDRGPQ
+GALAMVTTTVEIEGVAKPACVSDSLFLLRPGKDAS
+>LFPAFLNI_00285
+MQTFDGLDEFERAVGTHLGHSRWRTVTQEQVDLFADTTDDHQWIHVDPERAARGPFGSTV
+AHGFLTLALLPSMVREIYRVEGMAMVVNYGSDRVRFPHPTPVGARIRAGAELTRLDRGPQ
+GALAMVTTTVEIEGVAKPACVSDSLFLLRPGKDAS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002367.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002367.fa
new file mode 100644
index 0000000000000000000000000000000000000000..344d2c76616fb3962c9e52d1e66f427e862e12cc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002367.fa
@@ -0,0 +1,16 @@
+>MHAAABBN_02303
+MPEAVIVSAVRSPIGRARKGSLRDLRADDMAAQMVTAALDRVPELDRAEVEDLILGCGAP
+GGEQGGNLGRVVAVLAGLPSVPGTTITRFCSSSLQSTRMAFHAIRAGEGDVFVSAGVESA
+SRLDRGASDEDTRNPAFRSAWERSARRAEGDAPVWTDPAEEGELPDVYIAMGQTAENVAQ
+LRGVSRQAQDEYAVRSQQLTEKSQASGFWDREISPLVLPDGIRVTRDDSPRAGTTLEAVS
+QLNPVFRPDGTVTAGNACPLNDGAAALVVMSDTRAAELGLTPLARIVSTGLSALSPEIMG
+LGPVEASRQALARAGMSIDDVDLVEINEAFAAQVLPSAEDLGIPLDKLNVNGGAIALGHP
+WGMTGARITATLLNSLREHDKHIGLETMCVGGGQGMAMVIERLS
+>LFPAFLNI_00287
+MPEAVIVSAVRSPIGRARKGSLRDLRADDMAAQMVTAALDRVPELDRAEVEDLILGCGAP
+GGEQGGNLGRVVAVLAGLPSVPGTTITRFCSSSLQSTRMAFHAIRAGEGDVFVSAGVESA
+SRLDRGASDEDTRNPAFRSAWERSARRAEGDAPVWTDPAEEGELPDVYIAMGQTAENVAQ
+LRGVSRQAQDEYAVRSQQLTEKSQASGFWDREISPLVLPDGIRVTRDDSPRAGTTLEAVS
+QLNPVFRPDGTVTAGNACPLNDGAAALVVMSDTRAAELGLTPLARIVSTGLSALSPEIMG
+LGPVEASRQALARAGMSIDDVDLVEINEAFAAQVLPSAEDLGIPLDKLNVNGGAIALGHP
+WGMTGARITATLLNSLREHDKHIGLETMCVGGGQGMAMVIERLS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002371.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002371.fa
new file mode 100644
index 0000000000000000000000000000000000000000..59b374b33b35d32e9342f7018f5de5a64545cd82
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002371.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_00036
+MSAAADLQARVTRGNGRGITLFAFQHELSTRDKRGAVDLICETFPRLSRSWAKRHLARIQ
+DMDGARLGEFIAAADPVVYMRRLRTLDPTGDTAARNVDRERREVVA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002374.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002374.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0617ce682de6770295aeb215fdbaa8377fb11ab2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002374.fa
@@ -0,0 +1,7 @@
+>ACLBLIBL_00043
+MTDTMTTPTVHDLAAQLTRERARAVALVNKLENIGVKSSKRLTAAREAQAAHSRLLAEKR
+RDAATVEHEITEAAATANGDALTDALARRQSLAGAVDALNSPAVLERLVQAEVSAAYAAA
+HDARESVAAYFNRAAEEFVDVHREHFSAGPLLAHHVLGTTAAGHWGELVDAAERMSLAAA
+VLDVVDGVEDEAPASRYGRNLLHPAAADHSPIVGGPSMLRADGDLVRVGENITAFAGGWE
+WLGSPEVAPLRPWIDLATADARPGERVAIAYDPDAERADAATFAAMAADHGNVQSSQYDV
+STRAGYAAAWWQKRQG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002375.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002375.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b335573b461e2a88f7ec7a703642b5155ae87f8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002375.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_00045
+MTRERIPEGLRERGTRLWKETTDVLDLEAHEELTLLEACRTADRLDALADALEDAPLTVT
+NARGDEVAQPLMVEARQQSIVLARLIAALRIPDAEDNRPQRRGVRGAYGVQMRSVS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002379.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002379.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5cbd2a2780e62273905c101a59cc1f5a98b4ebae
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002379.fa
@@ -0,0 +1,2 @@
+>ACLBLIBL_00050
+MNQPTRTLPQLLQPVARAATYTAVTVAGFFMLSWPSIFTGAM
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002381.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002381.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c48686f7f8255c933e3a0ca8ef689484386684de
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002381.fa
@@ -0,0 +1,7 @@
+>ACLBLIBL_00085
+MTSTGSAGLDPADVAAFRALLARPETPAEELDDDAVARLAELGLVRRGGDGSLAVMPPHR
+PLLAEAHRAQARADALREAAEVLRGEFRRRPGAGREAIEVVVGGTEIVGAAVQLTRQARR
+IVRGFDRGPYFHAEALPEAAQSRSWERGVHWHVIFEGRSLQSEPPERWELLGSTPGETGR
+ILPRLPFKLLIADDAVALIGLAGVAGQGEGLVVRGSLLVDALVRLFELQWEMAVPIADVA
+GPDDDAAALTEQERRLLAMLSSGMTDEAMARAVGLSHRTVQRRLAELARRVGAEGRFQLG
+VQAARRGWV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002383.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002383.fa
new file mode 100644
index 0000000000000000000000000000000000000000..32946843460d09c1409789012f919ee8ae4adc81
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002383.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_00102
+MPLLTRTVDPRSSDVLSLANSPVLWVFALGVFAVIIVQSALYVRAARRAAPGLGIERAEL
+STAFRSGAVASVGPSLAVVVVAIALLALFGTPAVLVRIGLIGSAAFETGAAKIAAESAGA
+PLGGPGYDQHVFALAFITMSLAGAGWMVATLLFTPLLKRGSARLSDVNPVVLTVIPAAAL
+LGAFAGLTLGEFPKSPVHVITTAVSAAVMLLLLLVARALKADWLKEWALGISIIVGLAAA
+YLAHQALLAPAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002386.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002386.fa
new file mode 100644
index 0000000000000000000000000000000000000000..18595e725637290496b73b44585b7d5d953b4efa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002386.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_00126
+MTPEEFPPIHSQHAVVLDWVGPRWAGHLRYAVHLSEQSLAPGETELRDLWPDGAGLCWLG
+GPAVGPGPWPRNAEGAPLSHVLTLDLRTVAGASDHQGKAVWPAGRLREGLPVSGHLQVFH
+DLQTYGGDPEDGDRAGWAVTWTPEAEDGLRPALVEAPDDDGAPDPVCQLVLPYAGFTLPS
+SLDVAVTDPRDADRLEELDDALREAWTVQRGLDPTWAIPTSHVYGHGWTGDALAGGEILP
+EVLPLEEGDEHRLVLDVESWTTLQGWFGDAGHLEVWMRQSDLERGAFDRAWCLIRTD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002387.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002387.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a1bc4e69d732c14f523ecd8a1e66c264dc11849e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002387.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_00139
+MVPNEFAGDESAAAAGNAATDNFRRAGKTGTAQVDQARVDELAGALIKAANDIVLEKKVT
+YEEYNALKAWLIKVGDDGEWPLFLDVWLEHSVEDVATEHREGNKGSIEGPYYVPDAPVPA
+DGRTIPMREDEGGTAMVFHGQVRSTDGTPLKDAKVELWHADNDGFYSQFAPNLPEWNLRG
+SFPVDAEGNYSINTVQPAPYQIPTDGACGQLIAAAGWHAWRPAHLHLKVSAPGHELLTAQ
+LYFPGDEHNDDDIASAVKPELILDPKPAGEGVDVEYDFVLDPVSEKTPETVRGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002389.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002389.fa
new file mode 100644
index 0000000000000000000000000000000000000000..63d559532d68c9191a0f4cc693bcad45a58aea19
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002389.fa
@@ -0,0 +1,8 @@
+>ACLBLIBL_00141
+MKITRIEAIPYAIPYTRPLKFASGEVQTADHVLVRVHTEDGIVGEADAPPRPYTYGETQV
+SIKNVLEEVFAPHVVGLSVFDRSQIHAVMRRTIHNQVAKGALDIALWDAMGKALKTPVTT
+LLGGWTDSMRVSHMLGFKPAQELLDEARRFGEEHGITTFKLKTGRRPLSLDIEACHVLRE
+GLGDDVDLYLDANRGWTANEAMEVLRRTEGLGLSLLEEPCDAKEAMSRRRLVEKSPIPVV
+GDESVPTAGDASRELLSGGCNAICIKTARSGFTEAQEILGLCTGLGVDVTMGNQIDTQVG
+SLATVTFGAAFEATSRRAGELSNFLDMADDLLAEPLQIRDGRIAVRHVPGVGAAIDEDKL
+TRYRTDR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002394.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002394.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1bee54f71c22d94a1e566d228bf20038d5eb422c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002394.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_00177
+MPDRLSAATRRTTARATAAVALAVGLAAVTTGCTAPGAAISAESAGPSATSRPSDAATAV
+SDEGEVGARDVSGRRPVPVRQATPRPVQAPIPPTRLNYPALGVDMAVESVGMADGGEMQI
+PDDADVAGWYRFGSVPDRGVGSTLLAAHVNTVHQDRGALYHLDEARIGDELQVVDAAGTA
+HPYRVARVEHLQKATLDWLPYVTRQGPEQLVLVTCGGEWIEELGAYDENVVVVARPAD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002402.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002402.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b55cabf4e6188e698705408aacc344bc459c0db
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002402.fa
@@ -0,0 +1,10 @@
+>ACLBLIBL_00274
+MTASSSPASPSRRALGALRGAVPPPRLVRLPRAAREGGAGREGGGVRGHDDGAPGPGAGR
+RTTWSGSASWTPAETARPGSVAEVADVVRRAAAAGRRVKPIGAGHSFSPIAVTDGVQLEL
+DALSGLTGVDRAAGRVRVLAGTPLHRLGPLLGAHGLALANMGDIDRQSLAGALSTSTHGT
+GLGFTGYGGMVTGLRLVTADGAVRWLDVRTEPELFQAARVGLGALGVVVEAEIQAVPAFL
+LRAEERSEPLEDVVASFVERSRAADHLEFYWFPGTSVALTKENTRLPLGSGLDPVPPLRA
+AVMDRILANGLFEATCRLGARVPRLVPALNAAAARGVDRRTYTDVSHRVFVADRAVRFRE
+MEYAPPLERFTEAFTGLRALLADRARGGGPVSFPVEVRTAAADDVWLSTAHGRESVYLAV
+HRYHREDPADCFRAVEELFLGLGGRPHWGKEHTRDAAWAAEAYPRFGDFLAQRDAVDPGR
+VFANDHLDRVLGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002404.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002404.fa
new file mode 100644
index 0000000000000000000000000000000000000000..29886e661f3d182cb98cead5552460059557717d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002404.fa
@@ -0,0 +1,7 @@
+>ACLBLIBL_00310
+MGWSRRSATAASEPRGSAPDRAPTGPFVREMGGSVALTGRTGRRIRDDGTPVFTKARADA
+PAHLFEREAAGLRALAAAGARVPRVLAWSETGLEIEWIDDGGRRTRQTEAAFGRELAGFH
+AGSRPEAGAPDRFGSPDDVAAGWLGACPVDYTPADTWAESWVGRRILPLARRAERAGVVP
+ASARADAERLAELTDGFGADAPADHPGAAVLGSAEPSSLVHGDLWAGNRLVDADGRSWLV
+DPSAHRGHREADLAMMRLFGGFGEEAFAAYREAFPLADGWRERVLPYQAVPLLVHAVLFG
+GGYGEQAAASLRAAVRLAS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002405.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002405.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a0ab8f48a7643716f573d0cab3b36e293b343cd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002405.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_00324
+MSPVSDEHLEQQRTLYGAPLAERFTGVREAYGLSQRALAQTLGLSAPMLSQLASGQRIKI
+GSPAVYARLVMLEERAGEPDPAAVLAEVRDSEPVLTSQSFAASPEADLPARLARLAGPAG
+LRAAESAARAAGAARLADVLGAAAEAGARG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002412.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002412.fa
new file mode 100644
index 0000000000000000000000000000000000000000..160515c20dcfcaa24830647c738f4d3c76396fd0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002412.fa
@@ -0,0 +1,2 @@
+>ACLBLIBL_00367
+MVSRYGLIGEDDDGAPDTVLNPGDAWFEWGARPASLAEAQAAVEESLAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002413.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002413.fa
new file mode 100644
index 0000000000000000000000000000000000000000..89d789199038b900a06e27912e07636aad905e67
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002413.fa
@@ -0,0 +1,7 @@
+>ACLBLIBL_00378
+MALLAALLASTLRGTVEVPATVGLTQEQAEAALEDAGLVPLVSSTHSSEAPAGTVISSDP
+PEGTELDRGTQVGLRVSRGLEGVVLPGSLRGLSEDAVRRELQRLGLTVSSVQYQDDGRLE
+RGMLARTDPALSTSVPPGSSVVLHLSSGTVRVPDVVGMSAEDARRQLALSAPELRVRIQD
+EDGAATETGTVVSQDPGADARVDNRSSLTLTASTWVEATAEPTPPPSPSAEVPPPVRPSA
+PPSSSTPPSSSAPPSEEPEPSEEPEPSASPTPTPSETVDPTPSDSPSPSPSPDPTTPTPS
+PTRTTTPTEDPSPTPTLSDPAPTLTPDPEPSIDPPPSD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002417.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002417.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2abd06227b9bac1feb5ef3092dbbb7c26a7b1d14
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002417.fa
@@ -0,0 +1,7 @@
+>ACLBLIBL_00455
+MVARVGSENIELVDPGTEDSEIRPAKYLPGRRSIGVHLKMREESFARRFVSVQVNRDGGV
+IVIPFLEKWKKVRCVSLNYPLPGHPVVDPTSAVRVGDGSRAKLHYHRSGYTSVQPQDPPG
+EAPRLGVHLAPLDSIHQLPVFTVAARIPSKFPRLERAKRGDLIHATSMLGVRSLLVAGVL
+YDRSQVAPKSIGGYDSATPLTFTSGDPNVMILDLSGYGLNSVLALFFVASPVDLADTSCD
+ATVASYGSAESSGSNGVAIMAGGGYPHTFRIGDIPPLESFHSNTDLDPRVRSFSFEPSLN
+YDEIFYSE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002418.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002418.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1383837cd5badeb168b197e819bcb91448ab3e28
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002418.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_00456
+MHVIIGAGSGIRAAAILQEKWETVVGVDLNDTGLTAGLTQEGCAGAVKDALAATDGRVEA
+VIALR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002420.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002420.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0b9f141de83d3405341ea34f1e2f904a65fdbbce
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002420.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_00465
+MEGFRVRAGKEERAREWIAFLRENPEAFRETLEPERMYVETIFSETVGDALYLWWYTLQG
+EDGAELSDSTHWLDERHAAYWRECIDPDEPSLLLIPEVHMSPERLEDAMRPLGE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002423.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002423.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb8cb1bca8c64aa6e3b9041c82faffa4784b12ce
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002423.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_00471
+MDNLRAMAALFGVSVDHLLDGTGDGAAPAVLRHPVDVASLEPYKPAGRPLGAKSHRAVRE
+AFPDAVIYPLARMRSNNRVQEFLEWGLMLAFDTPYGLFGLSDSLSNRDAYYLVEEKNRHV
+LARVTPKAVEGKELPEPVEGRTFTVGADRFRRTSRPL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002425.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002425.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec3d3c782d006265ce1a7cbe37dbcab9409b8f35
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002425.fa
@@ -0,0 +1,20 @@
+>ACLBLIBL_00479
+MTAPHPAQEQDTFDLGIEFPGRDTADIRQWRLEEVQIANWGTMDGRIHRFPVSRRGHLIT
+GPSGSGKSSILDAIAAVLTPDKWLRFNQAAQGGAERTATRGLVSYVRGAWTRRQDEDEDR
+VVSAYLRPGATWAGVVLTYRDGAGGVVSLCRQFFLRGTAMSRADMKDLCLLERSAVDLAE
+LQTLIDDGIRTRRVQARWPQAVVTTNGGHGPFYARLRSVFGIRDDAALHLLHRTQSAKGL
+DSLDQLFRNHMLERPPTFAMADRAVEEFGALRTAYERVVDLRRQRDHLLEVRTAAQEYET
+AVAEESRLRRLEAAIHPYHQARFLAEIRRALEEVQASLAGLHAARTEADAEQERAEQRRQ
+HALIALASVGGDRVAELGRQIDAAQEQHRERLARRAVLANRLRAADVDAEPSTAVEFGEL
+QAAIAADLEAPPEHPGPSHAQLTELSRLREAVRELEADITALRRRGSTVPRHLASVREDL
+AEHLGVRTDAVPFVAELLDVDARHQEWTGAIERVLAPLSLTLLIPTRLLSAARTWIDRRH
+LGVRLRFEEVRPTRAAIRPASSQDSLVHKVTVKQGVFHDWLQARLSERFDLACVSTAAEL
+ARHERAVTAAGQVKLSATRYEKDDRFRLDDRSRWVLGDPAAKLEVLVEERAARQAAFAVV
+EGEVQRAQERADAERRRRATLRSVLETPWTDVDHAALERRIADLRAQADELSAASGDLQA
+ARRRDEAAQQDLRTARQAADEARLAAAQAERRRAELTQEARELEAESTGREPLPAELTAE
+LDARFRAVRRSATRSALTESADLVRRDVSALAERARSAGAQAGERCTVLTTQFSRQWAVA
+AADASPGVEDRGTYLAILERIVGQGLPEHEDRFHQILHERSSVLFGELHRAISTAPGEIE
+DRVDPINSALRRSPFDEGRFLHLRVRVRRPEAAQQFLRDLSAVAENAWADDSLDDAERRY
+TALAGIMDRLASSDHVDRVWRQQCLDTREHVTFLAQEVDDAGAVHATYDSGAAMSGGQQQ
+KLVVFCLAAALRYQLAAPEDPRPRYGTVILDEAFDKADARYTRMAMDVFVEFGFQMVLAT
+PQKLLQTIAPYVGGITTVENPTRRLTQIAEVMWEDEEK
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002426.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002426.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f98c5a58f982e9fd4a0a1aee3120ea1395cf6285
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002426.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_00480
+MTPDSDDAATPPATDAAHTAGAAPTLWEGDLGTLGEQSRRALLELLQGPYLSGRRRPQLW
+QALIADEAAIRSRLHDLFLDVVIDQHDEFAFTRRVATDEIAVPAALRSKSMTFLDTAMLL
+VLRQHLLTAAGERRVIVGRDEVFEQLAVYQQGDDSGWARRLNSSWTKMLNSFSVLQQLED
+DRAEVSPVLKVMIGPEEARAFTELYREIAAGQNDDDADVTTQEDDR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002428.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002428.fa
new file mode 100644
index 0000000000000000000000000000000000000000..94b03fdcc95356c1badaaf02ec877f267d85b5a4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002428.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_00482
+MTTTLTLLDPAGPDREALTDPTPLFDLRVAERFRGRGLGVEILTALTRHVFETMPDVDRF
+EGQTREDNSPMLRTFQRAGWVKEAHYRRGWPVEGGEPVASVAYAMLRQDWENGTTTPVPW
+E
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002429.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002429.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc20fa31d7c9c419f09d9045bc08c369e0545f75
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002429.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_00483
+MTHAHAPLTPTGEELRQPPQKITARAPGHMVHLDVKKIGKIPDGGGPRAHGRGTEAARAV
+RTAKHGPGAKVGYTSLHSAIDGHTRLAYTEALEDERPAAVNAAIPINECVPCRRPPARTR
+P
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002434.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002434.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa8d786e79996602205cd906d02bd5300d50be81
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002434.fa
@@ -0,0 +1,7 @@
+>ACLBLIBL_00492
+MTTLTHRYIDQVVGRVAADQRHDVAAELEGLLADMVEERTAAGVPEAEAERSALTELGDP
+ARLARRYRGAEEVLIGPELYPGFVLALRWLLPFVAVVALVTSAVDYAASTPVPHLGQAIG
+AVAGPLIQALFGSVGALVLLFWVLDRVLPVESREAVRRDVAPEWTVDALDDDPGSDRGAC
+SEAWASLVFLAVAAVLPVLPTSFLYVGHLNDGAPFVNQALWDFWIPAYYVLLAVGVVQAV
+WVLIRRRQTPGSLVLQAALTLVTAVFFTALVLTQQVIDPAIAAGPVQTGVHPLDWVDGLY
+VAVIWLVALWELWTLSRQWRTRRRSGRRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002442.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002442.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3a16185fe0877a5f30c720920579656cb43be0b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002442.fa
@@ -0,0 +1,7 @@
+>ACLBLIBL_00519
+MSASLAAGAGLVVVGLAARATVQDAGLFLVMTVVALSGMALGNVLIPAWVKLHAGSRTTA
+LMTVYSVFLTLGGSAGALVTAPIAAAARDDGEGWRWALGAWGAVALLPLVVWIVLARRTG
+HDFPAVGAASGDGGSLLRSPTALALTLLFGVQSMNAYVQFAWVPQILRDAGLSAGVAGAA
+VAVTAGLGIAGALLMPTVISRSRTLASWMVLFGAMTALGYVGMLVAPVAGVWLWAVILGV
+GGFAFPTVIALIPARSRDPHVTARLSGFAQPLGYVLAAIGPFAVGLLHEATGGWTAVLVL
+LACSGAVMTAAGLRVAGRVFVDDELLAPR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002451.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002451.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1de227c19b9dc29ff9bcee439050957b72b18eeb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002451.fa
@@ -0,0 +1,2 @@
+>ACLBLIBL_00603
+MKKLVTALALTASLAAAGAAPAAAQATPVEGFPVTAPVSAKGQEDADNIWCLILNRCR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002452.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002452.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de6d6327251aa33dc850e052052dc263eb899d6f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002452.fa
@@ -0,0 +1,2 @@
+>ACLBLIBL_00605
+MLGAAGLRGLEESLRTRVDAYGGECAVRADADRLRLEVLLPRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002453.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002453.fa
new file mode 100644
index 0000000000000000000000000000000000000000..394944e46b885284d49a2810f6461c6fedf42426
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002453.fa
@@ -0,0 +1,10 @@
+>ACLBLIBL_00606
+MNAAPRTGEAAVARPDAWPAPASFSDSPRYVLARWITDLPAMAIGLVGSLTWIAQWPAPW
+GPLVQALMLLWVASLVLGPVVRWRTARFHVSADGVQVDSGLLSRRSESLPWDLVTSVDHR
+QPWAFQLLGITEVTCTQTGEDGSRVRLDGLAPADLAAFQRHADAAAALGRSAPAAPSRVE
+DVAASRVDDDGAPADRASTGQVDAPTGQAAAAPAAVVHRTTLADLLVLSLVYGQVLLLVP
+PVAFGLMELTDVLDLTERLESLLFSGLGSWPTALLIVALAVVVGLVATVVKFHGFTVLAT
+PEGRLRIRYGLVSTHERVITPGAVQGVVWHRNAAEQLLGRARLSVLTLDSAAQLGGNLVL
+PSMPVERARAIVAEHLPEFAGTDRRLSTGLATPAVNLVSLLALAAAFAGTWVLTAQTWGW
+PWPLAAGACLAAAAVVAGIIAVAPARLYADPAAGLFLTRRITVGERVTAVRATRLHGISA
+HHLHHARTPRGRRTAWLPTVFYFAGAPRRAMALVAAPEAVEALQAMVRHSSVPLRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002456.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002456.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eabad1ba9a8233f8b4982e9af67cc37563b4fab4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002456.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_00619
+MTVGEVAALTGVTVRTLHHYDAIGLVRPAARSAAGYRLYGPDDVARLQEVVAYRRLGFGL
+EDIPDASADRRAALVRQRELVAARIDELTRLGRALDAALGRPGDETEEDTMQNEDTRRRP
+GTRPDLDLTDADLRELFGDEYAEEFDGYQAEAEQRWGETDAWAESARRTKRYSKQDWERI
+KADQEAATGLAAAALRAGEPASSVAAMDAAEAARAHITRWFYEVSPGMHRGLGDMYAADP
+RFAKTYDDVEPGLAAYLRDAIHANADRLERDA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002463.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002463.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54cd3afdebf601ae08cccec32b59b5ceea7d9235
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002463.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_00657
+MIRGMSVSLRHPTPDDVPALVDFVVRNRDHFRTGEPARSEAYYTPAGQADLVAAADRARE
+TGTGLLFLVEEDGVLVGRAQLNSVIRGAFDSASVGYGVDRACTGRGIATAALRLLVGVGF
+DVLGLHRLQGETLVDNVASQRVLAACGFKHYGTAPDYLRIDGRWRAHELFQRINPGWRPR
+GA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002466.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002466.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5efb938733fb0bb7ea52d54f21c8bd53bba0f382
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002466.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_00709
+MAGFTLSRGGSTFLRMELFPGNNTYRAGTGKARGWSLHKDTAGHANKAWKLKDRSGSIRA
+SIYADGKFACDRYSQCAV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002471.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002471.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26a7e24ba5c62f8b875d3810e5bd46ea41c26647
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002471.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_00738
+MADTTGADTDGLPVVVIGAGPVGLAAAAHLAERGLTPLVLEAGPVVGAAIREWGHTRLFS
+PWRYNVDAAAARLLETRGWTAPDPEALSTGAELVEQYLQPLAATEALAPGSAPGPGSSRC
+PGPGWTRPAPPAGPRPRFWSESPTRTAPWRTFTPAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002472.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002472.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9a8c1a30add84dc2476174da11dd4116c5d302d1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002472.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_00747
+MKVREGGRVVNAVVLLATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLV
+TSDAHTRDCARRLPRTCPARPGSAAAPTTQRI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002483.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002483.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb631fc7ce76960e8945baf1ed663260bf4830c8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002483.fa
@@ -0,0 +1,7 @@
+>ACLBLIBL_00812
+MTSTPQHITLEQLYSEWTELMTEYPTMNMRLFRAVFDEWHQPTVEPEGVTYREDVVGGVP
+GIWTLPEGADEKQVLVYTHGGGFAVGSASSHRKLAGHLAKALGVVSFVLDYRRAPEHPHP
+AAVEDGVAVIDALIEAGIRPEDITTVGDSAGGNLAVAVPLSRREQGKPLPGQVIAFSPWL
+DMENKGETLATNNDTDKLITPELLEGMIAGVLGGTTEPTAPLANPLYAEYQDFPRTYITA
+GSVESLVDNATRLEERMKAAGVDVTLVVSEGQQHVYPFEAGASDVADREIQSITAWYGQG
+R
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002488.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002488.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e83a912d098124f9a8915566ec89aaccb6caf69b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002488.fa
@@ -0,0 +1,12 @@
+>ACLBLIBL_00819
+MTTETAGDFRLQTPEEIEAVVAVLGDAGMLGENARIAYLGLLDPPRGAERAAVSRDRRFR
+VFVLDVAGGLPVEAVVSATRRELLSSRELDSTVDGEFPVMEEEFAVVEEVLAQDPRWQEA
+MRARGIPVEEVRVAPLSAGVFEYEEERGHRILRGLAFHQQHEADSPWAHPIDGIVGYVDV
+TAKEVTQVIDLGAMPVPQEHGNYTDPELTGDLRTTQKPIEITQPEGPSFTVDGGNHVEWE
+RWSLDIGFDMREGLVLQNIAFDDPHTSRRRTILDRASIAEMVVHYGDPSPIRSWQNYFDT
+GEYLVGQWANSLELGCDCLGDITYLSPWVVNNAGEPRQIKNGICMHEEDWSILSKHTEMW
+TGISYTRRNRRLVISFFTTIGNYDYGFYWYLYLDGTIGFEAKATGIVFTSAVPEGSTDFA
+SEIAPGLGAPFHQHLFSARLDFALDDGTCRVLEEDGVRLPFSEENPRGNAFTRRRTVLAT
+EQQAQRDADMAVGRTWVVESSEHTNRLGAPVGYKLHPEGLPTLMAAEGSSIHRRATFASK
+ALWVSQYHEDERYPTGDFPNQHGGGAGLPEWTAADRNVDGEDLVVWHTFGLTHFPRVEDW
+PIMPVDQVGFRLRPEGFFDRSPVLDVPGPRKGACHSGGAPGAGDGGSDDACGCGH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002494.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002494.fa
new file mode 100644
index 0000000000000000000000000000000000000000..179d40061b655ddd072dc292d7730da30ddcf3e1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002494.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_00886
+MTDAAAVLGAFFVAENARDWETYRSFLHPDVEWVLGDRVIRGIDRYVEAMQAAYGDDVRF
+RCEWSHVSESGSLVAALLVDDAGRRSLDVFEFKDGLVWKEHEFLLGRTASEAEPRSLPTQ
+GEPRSTEATEHQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002496.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002496.fa
new file mode 100644
index 0000000000000000000000000000000000000000..499af04d41c2d618b9adf112710def95250965d6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002496.fa
@@ -0,0 +1,2 @@
+>ACLBLIBL_00917
+MTATMHAHVEDPTDGLATRRINVQVAAEPVVPGIGVVELA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002501.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002501.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1036a4d14126365858c8b1bba40be957f03bd82c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002501.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_01013
+MRRFTAFTSALLMASGMLAAAPVAMAASIYEHRDYSGAAQGGENVNKLGTMNDKTSSIRV
+YGKTVTFYEHAYLSGNALRLWSDASNLREYQYPFAPTLSWNDRISSWYTP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002502.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002502.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1525c86948f7537bb7a4a77c0dd6f9fa7416a7aa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002502.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_01050
+MSAAELVRRWESAAQPAPTVVDVGSVLADHYRARPLDNAVFACGHLQSDDELRPDTDKML
+WTITDPVTLLRCARHAFGSLDAYLSHLESEQQEEDEAIQAEDGIERADVAYWSALEGRIP
+EEDHPYGLALTQHALGQRVTAILEVEDGAVTGFKVEGVLGRMVDEHLEGLVGYPAPGSGY
+DEAVPLMRRGDPGDEMFLQHLRQAARFGLL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002507.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002507.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a457573ba18a446c2412147d45081e4812d07d2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002507.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_01210
+MTRFQWQPGGGDRHALEREGPFKVLFVCTANICRSAYADVTSRARGIQGVEFGSAGTRAL
+VEHPIDPPMAAEVHAAGDPSQHVARQLTRDLLEKADLVLAMGPDHRRWILDAWPQHGRKV
+LLLGQAARIMSDLPADLELDRLVAHLWARRSTDPSDEVQDPYRRGPEAMAIAARQIDAAM
+DVIAPTLEHVAQR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002508.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002508.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b98f6fc657a69953671b323c9eae4e4d892b0e8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002508.fa
@@ -0,0 +1,10 @@
+>ACLBLIBL_01216
+MKSVRKPPATATPGGAGPLVVPVVVTLLVLAAVMLIDPQMRAWSMPVSLWIAAVGFAAAR
+IHDRIMLLALLATYAFFLLGKPIMMGYFGYDGLGWYAEVEDHLILTLSLGLLGIVAGYLL
+YPRAIIALLDRRRRRARSAAREEARRQFSARFASAAELAYWATLPFALAHVITNIRTASQ
+AGYTGLYVSGQSGFASVTAYGNFANTVALCVFLAALASTRRTWVVLITAFTAQALVMVTG
+DRGNFGTFLLMVFAYLVYRARHQDAALIPLRPLMLIGGAAVTALVPVFLLVGANRDGAEG
+SDTLSGFLYGQGSSLNVIEYGLRYESRLPDGHYLMSFASQGILRLILGGDGGLAGNTVAY
+AQSGTSLSHSLSYITLGDLYLTGRGVGSSFLAEGFADYGYGGVLLVAVAYGLLVAWIDAF
+APGSVLANAVRLLSIPAIVFAPRGSASGFLADVLSPVTVAVLLGTWFVALLLKDRRREGA
+PRITPRVVSTTHVGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002512.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002512.fa
new file mode 100644
index 0000000000000000000000000000000000000000..487897f071a8cfe6b69740e1cdf9a702089ba627
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002512.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_01270
+MPYYLRMHADTKISGTPEPFPDHVEMAAEVLRLLSDATRIRLVLALHRDEELPVNALAEA
+VDRKPAAVSQHLAKMRMARMVTTRHEGTRVLYRLTDEHAVTLVLEAIRQAEHSAGPGQPL
+RHTHAPRD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002515.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002515.fa
new file mode 100644
index 0000000000000000000000000000000000000000..01aaff92555455bb3811caf38ac32886494a7722
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002515.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_01283
+MTTPQLFHCLRYTDADRGIDFLQAIGFTTAMIVRDPDDATLVAHAQLAWRDNGGIMLGSV
+RDDDPHYGPGICNLVVASDEDVDSLFAAALAHGATTVTEPNDAPHGGRNACVADFDSHWW
+NLDSYPGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002519.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002519.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b56561d31ce7bc4670df2b40fe42459e580df460
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002519.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_01305
+MESPLTPHPIGATLLPRLPGAVPVLLEFEDVQLGGYAWWRERQAPAILLLHGWGEDASTM
+APVAHQVLERGRHAVSISLRGWHGSTGVDDYGLSASLDISRVLAWIRRQPDVAGIVLVGF
+SMGGLMAALAAADQPAGALDGVVLVNAPAELRSFARDTAFGGARRYLEKTLQPRQWQDSS
+PLNHADRLSHPLLVVVGTEDTMTPPDQGRRLADAAPASALFEVAGMGHHPTHGEWAQILE
+AADTQFDLRRGLPSPAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002523.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002523.fa
new file mode 100644
index 0000000000000000000000000000000000000000..552f4bf8d42c6c46aa56479719d0aa39655a2293
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002523.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_01323
+MAYEQKTTVTDVPVEEYLATVEPARRQEQGFALLRMFREETGAEAVMWGPSMIGFGHVRF
+TYPTGHSGEMFQVGFSPRKSALSLYGLTTYGSHADLLARLGKHKVGKGCLYINKLEDVDE
+AVLREMIRVGWGDDESFVDSHDGTVIERLA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002524.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002524.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5636e62ee23591c179f3cb952465c659db3bc6fa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002524.fa
@@ -0,0 +1,2 @@
+>ACLBLIBL_01325
+MLNWPLRARRLRGDVNAVRSGPRAMGRRAGSRLARRLVSRLFR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002525.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002525.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ebaaaa289e6a642848a8ee469128069e4b75d44
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002525.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_01326
+MALEDIQRHLAWKLQGIPQDGDLLGAAGAPAHLTYWGDLQCPHCRDFVNHDLMELVHQEV
+RAGVVTLRYRPLETATRDRGEFVAQQAAAWAAGRQGRLWEFMETFHLSQQEADSGYVTDR
+FLRAIADEIPELDLERWERDRRTDLTDHLVESERQARAAGVTGSPGLVLEADGRRRGPLR
+PTIHDLLDAVDELLA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002526.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002526.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d19a4ae592277f62d09b9f888dd5a1c617a73104
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002526.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_01328
+MTVTDALPPCPACAEEYAYEDGALLVCPMCGHEWSPESEAADRAEPAAAVVKDAVGNPLA
+DGDDVTIAKDLKVKGGAGIKAGTKVRGIRLLETPVDGHDIAAKVPGAGQMYLKSSVVKKA
+T
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002530.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002530.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7fc32661bbc7ae20dac0b443393679a530eab2d5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002530.fa
@@ -0,0 +1,2 @@
+>ACLBLIBL_01347
+MLDAVVAALSAAWAAGGAARGPAPGRQRELAAAEGWIWLPETDGAGRSR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002535.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002535.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6192aecbb2f7a02d72ba099cdc4d7c693961f6fa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002535.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_01494
+MSENTPTGFSAAYKVLSVRTSEDTRAQLEVLAQLNERSVTEETRIALEHWVEKSKSDPAV
+LKRAEQVRAEIERDAETKRNAINAVLGGKNSKAASARTTKQTQTPQGT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002536.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002536.fa
new file mode 100644
index 0000000000000000000000000000000000000000..22c34586f03e4f3181e44d6647a502864200feb5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002536.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_01495
+MVKGIYVPADDSKALEVRELTKLEDYQTAVDGWIEAVDVPVLGVTIYVNEEGLIRRLPLN
+PRASFLWWYHVPGAHHAMLVGNVILVGAPDENGDGTDVPEEVVDLLTVAREYAVAVRIGG
+SSTPSESDGKLSSVLLPLVHGDPSWCLSLTRHEDYLSAAAWAVVFRERWVAAVDVTVVSS
+VEVPRRMQILMDALPPVA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002539.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002539.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9eb473d8ce4e1dd79e13fde4b4939b5cad541728
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002539.fa
@@ -0,0 +1,10 @@
+>ACLBLIBL_01498
+MRLAPDLTPVGWFLFGAMVLLILTYLYFWWMVIKASAHKHVSREKVTNRKLTASLAHAKR
+KGNTHRFLIQITTKGGALSVVQRGIDNVLAGVARYPVLQKVVWVEIITEDANEVAALQTR
+YRNAVIPVTPYLLPTDYRTPKDTHLKAPALEYMVEQHRASPTESYVVHYDEESVFTPDNL
+ARLVHRLSRHPVGISEGMISYGLDWNETTLLNKTMESNRPFGCHECYSVMTSPPPMHLHG
+SNLVVRQDLENQIGWDIGNLDGSALIAEDLVFGLAAYLKFGKDVFGWHHTEMIEQPPFTL
+KAAYKQRERWVFGAMQALAHIRQQPDWMRLSRKDRWHINVIIRLRVLTYALGFPVSLLAL
+GSNVVILLILAAEAVREGTITVVAPELTVYGIVTSIGLVLWLAGTQLGLFYNLRYTGMTR
+LQRLRDHVLVLLVTPFAGVIDTAGPLVAVLKWLAGIREVAWKPTPKLAVPSRETTPKRVA
+AAEVAAGEKAV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002541.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002541.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3eea1f4213d5d11c4d5a9d3c87bb25ee19dea1ea
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002541.fa
@@ -0,0 +1,9 @@
+>ACLBLIBL_01504
+MHEIKCPHCGKTFTVDEAGYADIVKQVRDSEFEKQLHERLELADQDKQKALELAETKAAS
+ELQKAAAAKDTEIQELKAKLETGDVQQKLAVTEALAAIEKDRDSLATELAQVKQEKQSAV
+ELAEAKALAELQKAAASKDSEIQELKSKLDSIETAKKLELAEAVSAVEKERDALRTGLEK
+AELEKQLAEKSLKDKYETQLKDRDDAIERLKDLKAKLSTKMVGETLEQHCEIEFNKIRAT
+AFPRAYFEKDNDARTGSKGDFIFRDFNDAETEIVSIMFEMKNESDGTATKHKNEDFFKEL
+DKDRNEKGCEYAILVSLLEPENEYYNTGIIDVSHRYPKMYVIRPQFFIQMITLLRNAAIN
+SLKYKTELALVKAQNIDITNFENELDAFKTAFGKNFDLASRRFHTAINEIDKSIDRLQKA
+KEALLGSERNLRLANDKAQDVTIKKLTRRNPTMAAKFAELEGPAHSGSE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002544.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002544.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de30f3267b79f663c501439bf68926ad8d30c0ef
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002544.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_01523
+MTLLLTGVALLLGWTLGSGGLGVGATAVVPELDGLAREAAEERLVAAGLATAVTARHDEL
+RTEGTVVATSPQAGQQVDRGTPVEVTVSAGPAPVPVPDLAGVSVRHAHGVARDARFAVEV
+DARRTDPHVPAGAVLEQRPAAGERATPGTVVRVVLSEGRAVRAVPDVTGLSLAAARTSLQ
+DDGWDVREHRVPVPLPAGDEARVLHQSPAAGTPLLEGTRVELWSR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002545.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002545.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d33c63be0aeb928a5b0f4c02168c702369d16df4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002545.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_01573
+MPSHRNARDAPMTRRAWRLRIVLASTAFGGAAGALALRTQLPPAWLLAAAVVAVVLGVVA
+LPDPALQSPAAAVLAAAVASAVHGVLSLSTTPTPQPVPDVVRPGPSTG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002549.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002549.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c5af1c885fc4abfeb7848a6d8a7874184bd4d54
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002549.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_01725
+MPGAGGDGGRQDVPPGGGLGVLESLGQAGDAVRSDADAERGEDLHEGLVRDGLGRAVLAD
+VVRLHAVRAGESAQQRAGFQGHRVLHAVVSGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002553.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002553.fa
new file mode 100644
index 0000000000000000000000000000000000000000..569ee3cf8eda9e833a0f19b161ec939933e13324
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002553.fa
@@ -0,0 +1,11 @@
+>ACLBLIBL_01802
+MLLTSLLLTLLPVAAAVPISRRLGRDAGWVLALPLLVAAGVLAAAWRGGVEAEHHPWIPA
+IGVDLDLRLNGLALVFSMIVLVIGAAILAYSSRYLGRDPAVHRHGTFYLLMTAFAASMLL
+LVLADNLVVLFVAWEFTSFASFFLIGRSGDHARDPAIRTLLVTVGGGLALLAAVATMVAT
+TGTASLSGVLDSGIWQDPTLSTVLAVLLAVAAFTKSAQFPFQSWLPDSMVAISPVSAYLH
+AAAMVKAGVFLLLVFSPVLAGHAVWSALLLISGLTTAVFGAVAAVRRHDLKGLLAYSTMS
+QLGLLTAVIGIGTPAALTAAIVHTVAHALFKSSLFMLIGVVDHEAGTRDLRVLAGRRVRL
+PVTGAALAVAALSMAGIPPLLGFVSKEGLLAAALGTPGPAWAGPAVTAAIALASVFTVAY
+SGRLVLGALGLWGAEPRRRARALGVRPRRGGPRGAGVVLGDARAGRGGRRRAGPGPARAR
+RPCLRRRPRGRRRGAPRPPGPVARGESGPAGLRRRDRHGGRAGAAAPARRAGRRPSGPAR
+LGPRRGG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002556.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002556.fa
new file mode 100644
index 0000000000000000000000000000000000000000..84e76ff162504a59a22fed22b97f7ffbf0e35c68
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002556.fa
@@ -0,0 +1,11 @@
+>ACLBLIBL_01843
+MIAEDVDRAREAVEQALAAVAAPRWQDVPGGALLPDLLVQAETLSRTVAALQTALAGHLA
+EAYEHEADRQEVLGIPPGKGPHRDAADCLRDTVRIDRRTAQRRLRRAAATRPRRDFVTAP
+LADPALPEVAAVLSEGAADEAACDAVIETLTRARTDLALAAVPQDEADALLAAGESLLAA
+QLHHADLDGMRRLCARWRQHLDAVVLPDSGIPTEAELRAAQGLFHRGRRRGLHRWDLHLT
+DTQHEVLQTVAAAATNPRARGAGPSGQVDAPAGSPDLDPRTRGQRQADTLVSALQAALAL
+ATPGVLPATAGHRPQVLVTIDHETLLRRVRTASGTAAVLSEAEFTGPIDPREIRRIACDA
+EIIPAVLGGEGEILALGRSRRLFTRAQRRAVTARDGGCAAPGCTLPASWCEIHHIGHWED
+GGRTDVDNGVLLCSHHHHAVHAGWWTVAVVAGIPWFTPARHLDPRPDAPGGTGTTGSTAR
+RRPRAPGERHRRRRRRRRNRQGQWNRRTRRDGQDGQVGQVGQGQTEPVRPGPAAPPRPPV
+RRLPPPWTVLSPPWRPPGRRRPRHG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002557.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002557.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f99be5b06d980639878323fafb2d1b871d1b42b6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002557.fa
@@ -0,0 +1,2 @@
+>ACLBLIBL_01855
+MRARLLPALLDLTLTSLVSVPSVTAPARVRAGVIVGEGWIDLSTLWKGDVT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002563.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002563.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0697c65453207cc9ac559682c9fc7113c2e90633
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002563.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_01909
+MGAVFAAAMLAVGGTALATPPPAEAVTTVVITNGNFHNCTSRMNSEMKLFRMEGYTVRIA
+YKCKWFADARRWEGTFYASR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002569.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002569.fa
new file mode 100644
index 0000000000000000000000000000000000000000..74d4bc8b660cdc5d1f224f9f185d77b8ca11eaeb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002569.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_01942
+MTTAAAPFYVENLRRAREARTARAAERTAARLEDLEDLAAARVAREAAARRAGFPSVGAL
+ERFCYRVGRHDLIKSLPLQRSAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002570.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002570.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bf313ccc43520bea550866fa56663427ff794369
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002570.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_01943
+MTAAVAQTVEVPAVLTTSDLAARWQVSEEWVQDAAKAGRIPGFKVGRAWRFRVDAVLAHE
+EAEQAALSPANVFALAPGAVARRARRATA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002571.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002571.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e89ab481aa92f6c748db68d64cf3bcabf2aa813
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002571.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_01944
+MSVHPIRLQIPFADTSLVFGFDADAERDVRLLLRFARARASHGAGGFWLEYGWDTGESQM
+VWIDPAHMPTARFDVTATPVADQGREDDMSRHLARTHHVYLTAKGWQSDTHELAVDN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002581.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002581.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0796af81b04d748c344b18983cb8035b3359266d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002581.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_01955
+MKLFVEIADLRRALQALTPHMDPKDELGVFGRIRGHATDGNLFLMATDRYTAAMAVVSLW
+DKDDLTGSIRDDALEFSAQDVKEVLTLFRAPRRKDEPEGDLLIETSPGSSDPARRLVDVS
+GLFPGKEFRLPGADVDEKFPNLARVMSRRPAPTRTVRSNLTFAGEHLKKFLAASKAYEEP
+ITLQPVAEGSNMMLVAVGESFRGMIAGWRWPEDKTPDFEGWDMQWRLWSEELLGMAPDLR
+RPEGHEEAPADGEERDWSAALEQWAKDLADRLAKEQDDSEDEGDAPEQEG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002584.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002584.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3af1518de8816cae66dd79ff332aafad79cbe0b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002584.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_01958
+MTNWDDADQVNDELLGRMERPDGCTCDLEYTTDYKGRILHIYWSLELTCHHHYPRTAAQL
+ERLNSCPKQEGEA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002585.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002585.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d388d328bde51a3cc3189e4f825182e63c0a62d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002585.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_01959
+MSELMELVDRLTVETRQILHTDAGPAVVRAAPLLEQLQDAVHPSGEGGGGSSGSVGSGAP
+LDVTALALLCQVKDEAIHLSWLARSTPGVLTLRPGLGGFTLAERIRWTASALDGRAAEAE
+MLATVRGWTASIERLFDPPRVVALRGAECPACGIARTPVLNRDLDEFVDVPALTIVQGQT
+PRASCAECGAQWHGPEVVDLAVQLGAPPSVAHLLAG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002587.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002587.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e95ee823b5826843edc430d7ac0f07bf8f3b5639
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002587.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_01961
+MATANRWVRWALRPRGGRLTKVPLTVHGRHASSTRAATWTRRPAAAASRVGAGLGYVLGD
+GVGCYDLDGALDRGRLKDWARDALAAIPEPALFVEVSQSGTGLHVFVVAPPGPGTVTRHA
+GGAVERYTTGRYIAMTGVPFDVPDGLLRWATPLDAALVAARR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002589.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002589.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b06100ad69869f3c2537c110583be504a8509d72
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002589.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_01963
+MADAPAGLGDRGLTIWERYAGVDAGVDALALEAARAADRLDELDNVIQGKGVLKLMQFRL
+RDLPDLDADEPTWRVEVQFQSVLAEARQQQAGFSAMIGRLAAMEAPKGAAAPTAAHAAAV
+QAGGNVTPLQAARSAATR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002593.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002593.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3564bd75780545377a83d54048adaa7b6b94f56
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002593.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_01967
+MRRSFNPLLAGVLRFIEAGAQHGAAATPPPSPATVAAQTTPKSEPATGDADGDQGESPTE
+AGLSEAGKKAIKAERTARRTAEERVRELEAELAAQKNQEPATGSTQRNQEPATGAAPEAA
+TAAGADEDLRAKLRTAEQENWRHRALADHAIPRELVELLAGESEEEVRARAALLSRHVTA
+APLDPVPKSGVQTDASLPGSIAEYRRRIVKPNS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002594.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002594.fa
new file mode 100644
index 0000000000000000000000000000000000000000..719dd2009acfa512538b466ecb4182d9ea45ffa1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002594.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_01968
+MPMLHRQNIGSGRKNWLGSAHGVNHAQTATLDVSTFTAAADHPEGRIPSGTPVNAADRTA
+VVKWDPAAGGGALGFLIDDVDVVDGEAVPCAVLLHGAVVVEELPVEFTVPTAPTAFIFE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002595.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002595.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9422646e1a3cfdcc3d8579615a17889eb0986bf1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002595.fa
@@ -0,0 +1,7 @@
+>ACLBLIBL_01969
+MENLNDLISAVELTAEARMAAEAYEGEGQSFARYLPSVTTDGISIELTQTGSGGLVEEAA
+YRAFSAEPEIAGGELGDIVTLRLPALGQKRPLTEWAQLMDRNAGEEVQRAAFRRTARLAG
+AAIAATAERQRVSVAVTGAATIAGRRFQSTDDFGRAASHTQTAPQLWTDAAVSRTDYLRS
+LVDVYVGTNGVPPGAIVMGSKVYRALLRGSEFTETLANGATRPMGRDAVFAVLDDLDIPV
+IERYDLRTSAGPILPENVVLLMPPAGPTVAEEPTALGAMYWGRTLTSGMEQYGILEAEQP
+GIIVGAFRETGIPHTAWVESDAIALPALANPNLTLAATVL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002597.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002597.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3479b3ffa1daf0ddbd1095c818159827f5ee5477
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002597.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_01971
+MSGFATVQDLEERWPGITTGAVTRAETLIEDAELLIEGDYPAVGEWVASGLLRADVVTFV
+VCRMVKRALGPDADDAPGGQFESMSRTTGPFLTTLNFREPAGDGEELFLRRAERNLLTAH
+LRARARAGRAFTIQPGAGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002603.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002603.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c8b22fcc79037c1cb534f6fa8716b9becfa3422b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002603.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_01977
+MATQKKTDSPKVHASLAKLRKESPAAAEPFQIALEDSHVITFPDPFAMDVDAAERMFALP
+DTQVKAALREWLSEEDFTALFRVKRSLRDLMLISQAAQAHFEATYGPVGEDSASRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002605.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002605.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d4a03f3f701e66fbae714a74c91ee93e690c5d0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002605.fa
@@ -0,0 +1,19 @@
+>ACLBLIBL_01979
+MAVVGVAEVLVRPSFKSFQSEVGKAVDQATPESGPASPGSRMGKRIATGLKVAGGAAITG
+AGVVLGTALTKGFGRLTAIENAQAKLTGLGHDAGTVEGIMRNATAAVKGTAFGLGDAATA
+SAAAVAAGVQPGEELEGVLKLMGDAATIAGTDFTSMATIFNKVKASGKLQGDEILQLSEA
+GIPILQLLAQELGVTASEVSDMASEGEIDFETFRSAMEAGMGGAALKSGETLQGAFANSM
+AAIGRFGANLMSGVYPQVKGFFASFIEWMGPVEAMGKTIGEWLATALGGFVNFLTGTAVP
+GLRSFGETVAAYVGPAFSDFAAFLTGTVLPAASNLATFVSGLLTPVFAALADYITGTVLP
+AVGGLLNWFRESPQWVGLLTTGLAAAIAAVAGIGVALKGWAVATTILTGAKALLTGVLGK
+LWAVMAANPVTIVLGVLAGLAAAAVYAYQNFEQFRVIVDAAWAGIVSAAQAAWTGFLQPT
+FQSIGDWLTNVLAPAFTSFWQNGVVPAWNGIVAAVQGAWTGVILPVLSGMVQWVGTFLAP
+LFVQLWQGHVAPAFLGIASAVQSAWAVIGPALAELARVVGPVLAGAFNFLAPIVARVAQV
+LGTVLGGAVTLAVKFIFMLVGAFVDHLGGAIQGAIRFLQGLVQFISGVFTGNWAAAWEGL
+KSIVVGAFKFIWHTINVVLTVQVLGVVRGALSGLLGLFRGGLSSVTGVFSAAWNGIVSLM
+RGAWSNITGIARSGASGLTSIVNGLVNAVLGFFRSLGSGMGSIVRNAWSVARSTFGGATA
+ALRTMVSQMVQGILGFFRSMRAGITSLSKSTMTNAKNAFIKGIAALEQSVSTGLLRVQAF
+FRDLPGRIMNALGNLGGLLKDSGRALLAGFTDGITNGFSRAKDAVADGLGAIRRLFPFSP
+AKEGPFSGRGYTTYSGRALSRDFADAIADEAGYLRKQAAGFMDAADFSASSRITAGVDLV
+PLSTRDLLLDGAGRLPAALQVAHSVAGPPRSSLERLKLAAPEGRQPLTLVLEDGTAFPAY
+LDRRTDTRLAGHVAGLAQPLRQYAGAMQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002608.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002608.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb6d5df0538e720364fa8a6340bc29444bec9811
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002608.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_01982
+MAGLVQALAGPQEAAKTPGLRVSDGVVVSTNPVRVRQAGADPSTDPLAPLSLVPAADLSV
+GARVLLLHRGTQKILLGRTYPL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002610.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002610.fa
new file mode 100644
index 0000000000000000000000000000000000000000..412504a2eba591cd8ffd3c97fb1578aab7b99932
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002610.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_01984
+MVFLFTLALAAVGAGVVTLARGDAAAAEAGLSRAALVLEGANTIGTSRILGTGAVILLVV
+ALAATTTRRWQRVVCLAVGSGLAATMLATGSRGPLLGVALGIAVVLLVSPSLRGRRVRGL
+LAVALAAAAAYWWSASRSAESVDRALGWITGDRDTSTQARQQLWDIAFDHAKRDPFGVGW
+GGFADLDSVPSDLPYPHNFVLEVLVEGGWLVGGAAVIFVIASLWRLTRQATTPAGAAVLA
+LGIFTVTNAMASGDINDNRLMWTILSSAWVSTRLSQPQSQFASPYPISAVRS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002618.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002618.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92b2e7a70547947180f31d6839cc3e5a05e7e3fd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002618.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_02046
+MTTTGRGSHRAYDSDRDRLLDVIGRAGTPPVDETTFRVDPLALTGHDQTTGPLSGAVVAE
+TVLVVACDALTAEIEQHHRVMHGAPGMTEAQDRRALVDRMVIDFDAFAGGVWSGTDSPHR
+HGVLLDLHTTAVRIRKRGGVVYVVPPADGSADQTRLPGLRVDHDLWLPDTEGAPVSRLLV
+AVRRHAGLMPREDDDQIGELHG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002626.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002626.fa
new file mode 100644
index 0000000000000000000000000000000000000000..058c7e9d036db6be0656aec9c525aead8a009ca1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002626.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_02106
+MPDRERGTGLSVRDHLVLQLWGRRWRHGAARDRAAVELVGLRPTELALRVAVLAEEHAAI
+AAYPVVPRRAREARQTRHRVVGGRAASAAEVVAGGS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002629.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002629.fa
new file mode 100644
index 0000000000000000000000000000000000000000..acef8a50aac34276dba528bed30957c89abb15f5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002629.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_02199
+MTTYSPASARDHYLTLREAVELGYGAYSTLRSWIAQGRLPAVKTGGRVKILRADLDALAR
+PIGPDPAPNDDLDAAIERLVAQAPALSPRQIRELQSILGGVAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002632.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002632.fa
new file mode 100644
index 0000000000000000000000000000000000000000..387b96710dc831aaf2249e77bbf8ac1025050d27
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002632.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_02208
+MTTDTRLVHIITLTGQDYDDAVRVAETEGGSVDAVARHLAQWDHGAEADDAALLWPEDMP
+TRADLGCQPHQLHAARVGGLGYLVQIDHGLRMYALYRPTLTQEAAE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002636.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002636.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a1e37f2b229e1df4605f7b802f69d5bdb8d28cb3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002636.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_02216
+MPVLPGFIADPLWEQFQALLPERNINHPLGCHRPRIPDRVVFDKLLARLVLGGTYQQHAD
+ETCSATTMRARRDEWIRADVFEQLHHLALEAYDQAVGLDLNNLVVDGCIVKAPCGGDNTG
+HSPVDRGKSGLKRSVLVDGGGIPVGWVLAGANRNDSPLLRPTLETLAVLGFRLPEVITVH
+LDAGYDSARTRDLLSELGCTPNITPKGAFLPISHTRRWVVERTNSWHNRGFSALARVTDR
+QGCVQNAWVALASAIIIIRRLVRQSWKRYRWDSRPARCP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002638.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002638.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6659ec0aaed4e2a742bf5617781ae853e681ae66
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002638.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_02224
+MKIRHKLAAATAAFGLAVAAAAPAQASSIPRTYDARTNTYYSYSDSANQVCYQKGTNRTA
+QARLSVQIKINGRWYTRISALYSDTRLHCFTLRSQNGFYEGRSVRLIVSDNRGSSTTRYF
+YR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002640.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002640.fa
new file mode 100644
index 0000000000000000000000000000000000000000..31599e94d398a6d71c4b79c9d39c02e8530d2ef5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002640.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_02227
+MADPRVLQQPSVRSEVHRRTLCEPVTPWGPARARAPAADWDAVTAALAEPSPEEWYCYDT
+DNRDTPLAGPQVIEDWSVLTAVLRETAELSTADGWVEGFEPPQGGGWTTDQAAATLRLWV
+TRRFRRGDARLTDVPRHPDS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002644.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002644.fa
new file mode 100644
index 0000000000000000000000000000000000000000..024a9f68f0d8e63b34f234fe8990c5e6f014ca93
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002644.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_02267
+MSRTSDPVQPSRPRPVLLLALAVGAVLVYALQGLVPLLMDGEVPRPDELLAPPSPVVLGG
+PIAWAAALAALVLPRGRAHPLATTAVGTLAYVAGLALGAFVEIGPGTGGWNWGWESVVAI
+LLVTGVWVPALVAAAALAWLARPRRTPA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002649.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002649.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5623e7762f8fb9c28239653d91928caf296fccde
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002649.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_02341
+MDSEEPPNVRVACSGDIDEVVRLMHDAAAWMSAKGTPAWDVARIDRTFAETFVLRSELLV
+ASCSDGIVGCCTLSAEDPEFWPDALKGEAAYLHKLAVRRTHAGRGVSSALIEACRHAART
+QGCAKLRLDCHPNLRGLYERLGFTHVDTFNPGWDPTFIAERLELEI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002650.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002650.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2b557b03392c06751817ce5ff58d8f18063c0555
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002650.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_02346
+MPKKYTPELRERAVRMVLERQAAEGGPRSHSIRAIAPQVGVGEETLRMWCNRHGHEVAPV
+PAGESPAEEIRRLKRELAEARRANEILKAASAFFARELDRPTTR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002658.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002658.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bb5ff19646ed179e6febc0bc821985d825e80e4e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002658.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_02494
+MARVRSVKRAEEIIKLYEEIGSEFSPIRIDTGMAESTRRKRREKLFNRESRIVICVNMLG
+EGFDLPSLKIAAIHDPQKSLAVTLQFVGRFTRVGDESLGEASAFVPLQVAGVDEQLRKLY
+GEDADWNEVIRDLTERGVGQEKDRTDFELAFGSVPREVAMRSIHPKMSTVTYQSETSLTW
+NPENIYDVFEDRLLTTRLGINNKGD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002661.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002661.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d716608c08976b46e4598246bd9c279502261429
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002661.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_02501
+MILAFIDEMRAEGYAVESILRVLRQQGLRIAARTYRAWKKPTRIAGRTITDALVEGKIRD
+LVWTIDEVAGRRRMRPEGLYGRRKMLSLIRRQGGARQVW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002665.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002665.fa
new file mode 100644
index 0000000000000000000000000000000000000000..82dd00cd0896af3f172a74ebd2b9142e6d9207a1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002665.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_02582
+MIVTTEIRRRPARRGPDLGDVLMAAPFALWGAATLALQFNRGHRFIRALDPTGLIVPDWR
+FFAPRPASHEYHLLYRDARPDGTMSGWNEIDLGADRRLRHIVWAPHRRLEKGLFDATTEL
+MRVITDVRDPAVVRMSAAYLALLTVVTHSASHQDGAVRTQFMLVRAAAHEPDVIPSIDYI
+SDWHRLEGEH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002667.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002667.fa
new file mode 100644
index 0000000000000000000000000000000000000000..767eb60fb35ad5d112acd7aba4a7a498d4479510
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002667.fa
@@ -0,0 +1,6 @@
+>ACLBLIBL_02584
+MFTLIDAATNTIRPMTAKQPLDREVDGAATAGRLTAVGALVGSLEELSRREDGGDRSLFS
+WPVRQTALRAFRRRSLAPLWSLIEPRRYPILLAGRVLCAGVVLLAPDTSRVRGPALVGLT
+VSGLLKSYRNSYGSDGSDQLSFITFASLATAHLPGLTAGQRAVPLHFVGFQSVLSYTVAG
+VAKLLSTQWRDGSAIEGIFRTRTYGDAGFYRMIKDRPAAARALSWTVIVAETMTPIVLVL
+PPAGRRAVLGLAGLFHLGNARYMGLNRFFWAFTGTYPLVDRSARSIRRVLGLVEGRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002669.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002669.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f8d8a80fd463cdc04a9763a388afb78234038771
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002669.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_02618
+MTEKLLASAQARTRECTRAVLATVKELEASQSAITLKGVAARAGVSRNFIYTTPDVLAAV
+QKAAERQRPKLPSEPAPTAPSSDASLRTRLAAALAHNECLQQEIDRLTATNQALVEEVIE
+LQNPAPKNVTSIRKRRG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002671.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002671.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24b1016181d1090a850a19cc4d13743dd7c8a07f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002671.fa
@@ -0,0 +1,8 @@
+>ACLBLIBL_02620
+MSSGRVSVSREEELKVYVRAGGRCCFCQAYLVEGQIAGAPMKIGEMAHIVGAKISKRSPR
+GEDPLPQQERDKAENLMLVCRGEHKEIDRVGASDWATVDKLRRIKADHEGWIRRVTGLDR
+SRHTTVLRFVGDVRGNAVDITKAAAAGAVLLSGDRYPKFPLSADDFGFEIDIRAFDETSP
+DYWQRAAAHIDRIIDHKLRDEVTAGRVDHVSVFAFALLPLLVHLGSKLDDTFATDVYDNH
+RVTRSWEWPDSEAAARFETSFPADPSSADEAVFVLNVSGSISDAEVPAALADLPQWTLAL
+AGATPGPGPLRSAADLAAFSAASRGLLAEVERRAKHTRRLHVLAALPLSAAIELGRVHDA
+HVHPRLAVYHRADGGYKQALELS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002672.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002672.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3600f66e9537c1f6b502addb5bc324871c2f03ee
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002672.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_02633
+MWEHHRSYVTYTRISPPWHAATAKTTPLVLTPLRIALWDRDRHGHPVQPGELIAHSDAGS
+QYTSLRFAEHLAAEGIAASIGTVADAYDNALMECVIGLYKTECITTTIFHNGPYKTIADV
+EYATAGWVEWYNNRRLHSSLAMTTPAEYETAYYAALNRELAPT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002673.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002673.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dfaf236900e80ebb59b9edfac21758de43128392
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002673.fa
@@ -0,0 +1,2 @@
+>ACLBLIBL_02635
+MMYPLVSELAADGVPVAVSLRVLKLARQPYYRCPSPFLRWSRPTGPTPCTPLT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002677.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002677.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fadebad50a715b89ffe7aafbb61b05e0d1915001
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002677.fa
@@ -0,0 +1,2 @@
+>ACLBLIBL_02654
+MHDPHDRTRPLRVGSLFSGYGGLDLAVEHALDGETIWFSENNEHVSRIFAHH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002680.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002680.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f72d1a7e32a687528142514b827557ccdc3a55e3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002680.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_02657
+MTTIDLTEDAFSAAITDHPIVLVDFWAAWCGPCRSFAPVFEAASTEHPDILFAKVDTEAQ
+ASLAAAAQITSIPTLMGFKDGVLVYSQPGALPAKALHDLIGKIRDLDMDHVRAQMQASDP
+R
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002685.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002685.fa
new file mode 100644
index 0000000000000000000000000000000000000000..25d5891d398b7b13bae24396abb25e0d1cb08ce3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002685.fa
@@ -0,0 +1,5 @@
+>ACLBLIBL_02664
+MGSMTSPTTRSRQGIGESFRLAVQALRGWTGRQVLAAIAASAVVAVVIGVATVLIPNPLF
+GRDIPPVWWNYPVWLVTSVLSGMLVATYIRPYRAAADEQQANAVSEDGAATDAADEAQAR
+RSSRMGMAGGILAWFAVGCPVCNKLALLALGYSGAITWFTPVQPFLALGALILTGVALVW
+RLRGQVACPVRPEPVAAVR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002686.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002686.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9f431c61fd6dd13ed3ce7e1f28d5e7172b18a2da
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002686.fa
@@ -0,0 +1,4 @@
+>ACLBLIBL_02665
+MKAADGRSGDLLRLGALEAQVMDVLWDHGPATVREVIEHLPSDPAYTTIATVLTNLDRKR
+LVTITRQNRSTRYGAKITRHEHAAGLMEQVLEASRDRAASILQFVDSMPENDLDLLRDYL
+ERRDRGDMP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002687.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002687.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d4b709fa8ecdb5ccc940c1a0e7a30b91b7529b81
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002687.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_02667
+MNENTREVILHVADDPADVQRALDAAAGLHAAGLGVRVRVIVNGPALAGLTGTDAVQVPE
+HTEVAACSVGLGRRGIDPGELRPEVGTVPSAVTAIVHAQLADAAYIRI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002690.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002690.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b276218606c3a461cfa2bc9cd5d8ed26b09e3d4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002690.fa
@@ -0,0 +1,3 @@
+>ACLBLIBL_02677
+MAIVVRIDVELARRKMPVGEFAERVGITPANVAVLKNGRAKAVRLSTLERMCEVLGCQPG
+DLLEWVPDAAAAPGPGAAPANDDDGRPGTR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002695.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002695.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b37de278b3ed84f3cb8d99424b10110ac160d4e9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002695.fa
@@ -0,0 +1,2 @@
+>MOLHKGIG_00170
+MVGQTVAYVRVSSAEQNLDRQLEAVGECDRIFEDKISGSSRAKRTGLAELMTYVRAGGTW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002697.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002697.fa
new file mode 100644
index 0000000000000000000000000000000000000000..336b7f56708de94535f1354dd1e7acbff6b024e2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002697.fa
@@ -0,0 +1,3 @@
+>MOLHKGIG_00242
+MSYYHGDDSHTLSPPAVSPPHHPVVDRPRGRPEPQEDEPMFPITDDQKALVDAVRDLAEQ
+RVAPHALDWDAE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002699.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002699.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fbd67ab159ad719bae4e53dd9ec6275050efb976
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002699.fa
@@ -0,0 +1,7 @@
+>MOLHKGIG_00408
+MRKLIFYPNLSKGGVSAVIRGRAQAEPDVQFDAVFLHDRGGSDAFSDMANVHVRLIQESR
+SGPYLTHLAHQFDYESVSVLSHPATANVLSALDHVAVTYEFHSSSIPVIEKELGALELDR
+LAAVVVPSQIMAREIQPLLPRRLRFRLAVEPNLVDVETFGEQGSAQFLADSGFGDGPGTI
+PLLWVGRFDQGKAYAHFLRVIAALPQEYVGHVVVSLEDDPHRAERFFAEAAGLGVLERVR
+LYLNLTPQALGEFYRSVRDADGWLVSTSLKESFGYAVAEATNAGLRVAASDLPVWDLFAG
+TGLVHRVPSGSIADLVRVIREGAPVSAGAATAW
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002706.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002706.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e8ad39f507fd5789b806d83089ec54f2c83a585
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002706.fa
@@ -0,0 +1,7 @@
+>MOLHKGIG_00590
+MSIEAMKWAQKVAETGQLNTGQAFVLLLLGDHADEAWSCHPSQELLARRSAQTVRSVERH
+IARLRDLGLVDTESRYGDGRGRIGLRYYLREEALNDLVQDAETRMNTRPDNLSGKSETRT
+KTRPDNLSGKSETRTKTRPDNLSGKSETRMNTRPDNLSGESTHPTISADSPDNHDFADYK
+DRARTNPQEPSSVRPSVRQSGAVRAETTTDDGRRTDQVIDGGEGVGLVHRGVVLADLVQR
+VPAAADLGDGQLRSIVDVVLARASGPVRKPTAFVARSLASEFEELVTVTRPRPVAVTQAP
+AASGQVRELRTGEPCQDPDVHIPAYGQAVLADCPHCRLERRAMPRALMEAVD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002709.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002709.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1b077c1018ea3b37626c4270e66f6fd7ff2feb5c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002709.fa
@@ -0,0 +1,7 @@
+>MOLHKGIG_00595
+MWEKDFEEFLRGSILGLAKAAAGLIEQAFSVGALTPEWWVTVVGGQVTTTVAGGESTVID
+HPGMLNIIVVAMIPLLVIFVAVQVVLSAVRGSTAGMVRAFLAAVFSIPATYVVVGLVWMA
+MGATQQLTLWILRVGSGGTDGEDEAVAGVLGLFGLTYDAANDKILLDENFAQWEMASENS
+GNGMIVVAVIIALVIFFACFVLMAMMIFRLVLILILASFAPPAIFSLALEPAKALAGRWL
+SMMLGLIMAGPLAAAVVRLGMAMAALSTDWVQTVAGMVLVFVAAAMPIFMLAVTAWLAGG
+AGQAEQAGVMAASRAGRGAMNSMRGVSARAGRMRQRAGAMVMRGGR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002712.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002712.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b09ff7b2c0b8d3c6af456d9a20463a402afceb88
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002712.fa
@@ -0,0 +1,2 @@
+>MOLHKGIG_00615
+MTATTAALALALYLAGLAAAFGARSWIPLRACDLG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002716.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002716.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e54f57670da7f9d64ef7e37b7db52ec67986c863
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002716.fa
@@ -0,0 +1,3 @@
+>MOLHKGIG_00622
+MMSSQKDTATLKVQDVHQLQAIAEAAARIAEQLAGEGAAESVRDAIRAVDDQLGDYAGHW
+DEYAAVNDWSSTIKGGLGNHVKAVPATDLF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002719.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002719.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7494e4dc05eb18aff47a7696901cf314ed5fd448
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002719.fa
@@ -0,0 +1,7 @@
+>MOLHKGIG_00839
+MNRRALLLALLQVAVAAGILGWVVLLFGTGPFVAAVRVLTWPGVVGALVLGSIGVLVQAQ
+RWRLIARRHGIELGWRAAAERCWQAAFINSVLPGGLAGDVVRAAEQRPVGAGRRRDMVKR
+SLGVVAAERLAGTSVVFLAAGFALLAVRPGLGGLGLLVAAVAATAAWPWLRRLGVRDIGL
+VWGLSAVGWCSFAGLFLLACLAVSPDLPPAQIPYLAAVTLAGMSIPLNVAGWGPREGAAA
+LGFMAWGHAAQQGVEVSVAYGILALVSVLPGGLVLLVRTVQGSRRRRLGGGEIELGAHVI
+AQDEAAHGGGEGSGKSVGPVETNPGDPVSHQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002727.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002727.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12a3b7391ed18372a962e63bd78bc4891390311d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002727.fa
@@ -0,0 +1,5 @@
+>MOLHKGIG_00952
+MAKTTKYTAEVSEGRDELLDGKTIARLRTIAVKNQRGETVRELKAADNDEDVRAKLRAAG
+YTLKDWAGGTTPATLERGRNPLVAGCLWPLVAVMALLAWAIFSAFNNASPDEPEEWDAKI
+ACQTLVKEKLRAPSTAKFSRETASGGPKAWTVTGAVEAENALGGTVGHRYSCSVTFTGDD
+EYRGTATITDR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002730.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002730.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e33e1e839354669ca672e39326664c6b6a703c2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002730.fa
@@ -0,0 +1,3 @@
+>MOLHKGIG_01492
+MTVAYTLGDQTFATKKAVLAHASEVLNRASLGEVLRGHDEAFALDLLAQHPEVGRKHGAG
+IAGVAVVVMPEWGTRNFVVLREDGSIDNWSVKKCVANLRPDGTRRSP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002734.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002734.fa
new file mode 100644
index 0000000000000000000000000000000000000000..210d26cca34a4503887b108d4fca8d2e021b01cf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002734.fa
@@ -0,0 +1,2 @@
+>MOLHKGIG_01501
+MSGQKGQLVGYERVSSVDQNLAWQLEALAGADRIFEEKASAKDRERPVLG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002736.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002736.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b4655d1965c3ff603fdd28ef4142f5153e3f2fbd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002736.fa
@@ -0,0 +1,6 @@
+>MOLHKGIG_01510
+MGTLGNPHGTFRLDDPDHWIGSYLRRQDLPEILGVGDDALADLPFVKTEEGEVVDENKVH
+RALGEGRIPGALPPGSRKISLNELVLTAVLRRTFPDCEIQRQVKVKNPRTGRANTVDLRL
+DVPGQEPILIEYDGPSHFIRQYRAEIPHPLARKTELEPSAGMEIVIWPYWMHICSASAQA
+LFDPTVHGVPALWSSNKFFGDFATPDAACVIEEITGRFNAVGEEGYGTVYEAGVDGMHKP
+AHPIIESILDGRAAKETLVPNGAENPNRWLPISVRDS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002738.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002738.fa
new file mode 100644
index 0000000000000000000000000000000000000000..71f95d6e553d19fed4cd5548f808cbe221c4e92b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002738.fa
@@ -0,0 +1,3 @@
+>MOLHKGIG_01619
+MDTDTLDNTPRVWIGCLHCYNSGGLVGEWFDAVDAEEVTLTHVHRGAGGTAPVARSCGAS
+TTRICPCAAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002744.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002744.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f95654d7ae748bccc1cb4185c8e6bbc769174398
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002744.fa
@@ -0,0 +1,3 @@
+>MOLHKGIG_01959
+MNKHDETLAQLREFVAERDWARFHTPASLAKSISIEAAELLEHFQWTEDGADMAEVQDEL
+ADVLTYAFMFADHMGWDVDEIIQAKLVKTRVKHPVPTGGDEEATSS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002748.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002748.fa
new file mode 100644
index 0000000000000000000000000000000000000000..80b42193804b556c8ebdb6fd7071e39af2ae9c0c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002748.fa
@@ -0,0 +1,3 @@
+>MOLHKGIG_02067
+MRRTTYLRILAGLLLMVLLVWFWGRYALFPMEMTTGNARFIGWGLALLAGYGSYRLWMKA
+AELSEDGHDTL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002749.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002749.fa
new file mode 100644
index 0000000000000000000000000000000000000000..944c4f2e173bcb83f1b81a1221fc0d951d583e90
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002749.fa
@@ -0,0 +1,5 @@
+>MOLHKGIG_02142
+MTRTSTYGFREGTLDTVRRSMRTVAVHRDDGELVGRVVRGELAGCERTGTFRWESIGGAA
+TTVGIRRATWRSAVGRLLRPTYAVTHRPEVTAPAEGEPPAPVHDELKEIWGENVLYFAVD
+GTVQGRRVVARADWDGSVEVRAQGEDGGRPRRVARFHSGGMFSLTRVEVDHEAAGTTRDG
+ALFGVLMLLPFVARLHREESSLIEELLG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002750.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002750.fa
new file mode 100644
index 0000000000000000000000000000000000000000..105c9a43ec6672632246657ed46ca9d3ba9fbbee
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002750.fa
@@ -0,0 +1,3 @@
+>MOLHKGIG_02223
+MNLNASLGRVVEWDRDGGWGVIDSEATPGGCWVHFSHLPMLDSVPSSLTVGEEVEFLFEA
+LEAHNDQDGFLYRAIAVHPPHGGLAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002752.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002752.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6c6df35fbdedb25832ec2a60c015316e821ae14f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002752.fa
@@ -0,0 +1,3 @@
+>MOLHKGIG_02281
+MSRFQMLSRAQWELITPRLPTRTGRAGRPFTDARTMVEAIIYRYRYRCFDSLEGPARGLR
+ALADRVDLAPPDGGRGHLGHGADKANRRH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002755.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002755.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5cbed149dc06218faffc034eff45d020b90d5dc4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002755.fa
@@ -0,0 +1,7 @@
+>NAFOICDF_00055
+MDFHRPSLEELRAAAALPSHTAAGLTHEVILTEIAAGRMKPEWSCIATNDDGDVIGRAMW
+WGRDSQEPIALDLWDVAPGTSEPGEVLTGLLTHGGVLVEAPDRRALLPHTLRVPVGWGDQ
+PEVAENVRLKMQVASANGLGRVNERLQFQWDWGETVPPNPARLRFTPASDEVFMRLFADA
+AAGSLDVMTARELEQTTAADLARDEIAYYLSCPGDRSWWRVAQTHDGEIIGLAIPSATPT
+NRNVGYLAVLPQHRGHGYVDEILAYITRFQIEDRARRITATTDAVNTPMVAAFTRAGYTL
+VEVRIDLEQS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002760.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002760.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3134c0fb1edd103fe3eb084e44bda5757adf20b2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002760.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_00142
+MNNLTPAEVVGAYFQNLADGNVEQAMSALDPNIEWHQPGENRFAGVHRGPEAVGALIGGM
+MEVSQGTFAVAPAGPLMTNGDVVAAPVRFTGRRDGEVLDQDGIDLLTVTDGRISQVRLFS
+SDGPAEDRFWGQS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002763.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002763.fa
new file mode 100644
index 0000000000000000000000000000000000000000..36eaf4f6ef624b5fb245ab0b58ac2c6d4529306d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002763.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_00202
+MWAAAVAAPVLFLLTMVVLGSLTQGSVSLGAPLLIAPLVLAVPVIALQVAILQPAGPRPA
+PPTAPAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002766.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002766.fa
new file mode 100644
index 0000000000000000000000000000000000000000..600b11b12c9335c6ec711c76480eafc4697c5fe9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002766.fa
@@ -0,0 +1,2 @@
+>NAFOICDF_00208
+MSTTTAHPAEPTPAALVARVNLAEPDGKDHA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002768.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002768.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f738f68f1854b45731798b2221c1c06bacf37e87
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002768.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_00210
+MVTTATRHHRRTPAGTLRTAAPFFAVLAARHGIPAPDAPTPARTPTTAPRATQDTRPAQD
+HLPNLEGHQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002771.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002771.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e14cf705c1490ec9f9bb830c12aa566bc9400537
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002771.fa
@@ -0,0 +1,2 @@
+>NAFOICDF_00213
+MSAPESHAAAAVAVRRIQAQAWADGYAAGRVDEFHGVTRPNPYALDAGPEDAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002772.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002772.fa
new file mode 100644
index 0000000000000000000000000000000000000000..98ffc2884c9e8a55875a6322abd689c5582d92dc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002772.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_00214
+MSATPTPAAALSLTHLTPQDLAARVGVPVATVYNWRTTGYGPRGFRVGKYLRYRLADVEA
+WEAEQIAAEDAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002777.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002777.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e97d5ce2d2ce997ec6b3b65fae1aac9863d7a6b9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002777.fa
@@ -0,0 +1,9 @@
+>NAFOICDF_00269
+MERLPAWLLETPLLAPWTVPVCVAVGVLLVLGLWVGRTRRRPWWVQALVVGVPAALALAS
+WWWVNVVWAPIPDGVAGPVFAWAALPVVVLAQAAVGPWRPRPLRWGLGGVVAVLAAVLCA
+TLGVNAHYSAYESLAVMTGRNVTWTDWDAVDTAPARQVVPVDRWTAPAGLPEHGTVSRVG
+IPATDARLAPRDAVVYLPPAYFAEERPALPVMILMAGVPGEPPDWFSAGHAAETMDAYAA
+AHHGLAPIVLSVDANGGGALTNRLCWDGPDARVETYLTQDVPAWIGRELQTDRDRTHWAI
+GGLSNGATCALQTVARTPDGFGTVLVFSGELHPSLGTEERTIAEGFGGVRAAYAANDPLS
+LFAAAQRGEGPGADGAYRGVAGVVSVGRSDAYVGMPVPQELVDAGRAAGMDLTLREYPGG
+HTWTVWSRAFADQLPWAAGRMGLG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002788.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002788.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc2468da9f6751c799f53ac6e972f1c18e745764
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002788.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_00328
+MFTHGSGFVKPPAPNGRPESHLFASRKPDSHNSSDTRNEACAECLSACPEYPTCSTCNQS
+TFHAHVDNPSSEIVKCRGNNAPITYTGKQSTINGNPTHINALKIDPTGVVPVESKNNA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002789.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002789.fa
new file mode 100644
index 0000000000000000000000000000000000000000..742a894ccabe638c9109e47e88218fc76b351c0a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002789.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_00331
+MPRPYPPEFRARAIALVREGRQVKQTAQALGIHEVTLHTWLRQDDIDHGRRSGLSSRESA
+ELRAARGRVRQLEQEIAILRRAATWLDEEGGVDPKGRTR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002793.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002793.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eac0d5d3d935e12d3d81f6e520f611e8e5f83b38
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002793.fa
@@ -0,0 +1,9 @@
+>NAFOICDF_00340
+MATKYSRVTLLGERRHADVLLPSDTPVGVLMPQILSLLAEQPGREPAVRALYRDTGAQLA
+PETTLGLAGVLDGETLRVAATTTAPDAPIVYDLHDTVAAQTDARGRWGKRARLTVLGLVA
+VFLGWWAAVQLTVGLPDEASALARLGIGAGLLLASLGVSVWSRRRAVALTLLGAGAVIAL
+NGHWWLMAVRAMPLAPAVLIGLCGGVALLLLAAQVSGQRRPLVLAAGVLAVLTGAWAAGP
+TAAGWLIGERTASVPVTVGALTAVVALLVLSVLAQAAVSHAGLAGLDDQESAGARLLRTD
+VAAAVATAHRSMVLGVLLCAASIAVSFWWISDDIVQPAFSVPFSAVLTIAVWLRAQAFPL
+TLQRAPLLLTAAWGLWCTVRLTSTAFPALAVPLLVALAVIAVLLVALQVVTVPPHVQARA
+RRLSTTLETLAVVALIPLLVGYVGLYAAMLETF
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002794.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002794.fa
new file mode 100644
index 0000000000000000000000000000000000000000..78cb3135b0a2ac9173a683ba9913a43682d78953
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002794.fa
@@ -0,0 +1,8 @@
+>NAFOICDF_00341
+MTRTESFAHDADRRLRGRAARNPAQSAPHAVWHAFHRSTDLRRLEEAAVRLQAPVGTGRR
+IAVTSSRGGTGRTTLTAVLAQTLGRFRLEPIGAVDLDPGHGALRLRLGPLVDGPDAEDGG
+EGGEAAEREGAGPGERGAATADRVAQHIRDHGTGGAADFLAPLEASPHRVYHTAARTTRQ
+VLPQDHVAGLLTGFSRFFPVTLSDCAAGHLPVETAAAVASSHAVLHVVPADALAVDEALH
+FLTATGQHTRRTPEPHVVVAVVQHRSRTNADARDAAAALRRRGFPVHVVPFDRHLDTGVS
+VTPRLMLPRSRAVAAELAADLLERATARSAQSGHTAEDEAVDAAAEAHPAGPPVRSGSTA
+RPRGRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002796.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002796.fa
new file mode 100644
index 0000000000000000000000000000000000000000..280da0907dbf65191b310cd3968a4d0107ced9a4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002796.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_00349
+MGRRARLKPNQVSERWPNTPVDDPIHETLRRYVHNLTEAIGDTSIKAAAERTQVNYSTLY
+AILKGETWPDAITVARTEEGLQARLWEGPASLPED
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002797.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002797.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f01a3219ed79db555d1c560b351310e3e1c26376
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002797.fa
@@ -0,0 +1,7 @@
+>NAFOICDF_00350
+MPCGCYRNNDSLSSHTRSAALDITDYRPATIPAPAWNRIADFTRAVAADTQAHHGNRFNT
+RDLMGAIAHHVHWVTDAACLPLDRSVVFHRDVIEDYIAHGTPTLGPGSRSTRRSFLLRAA
+EAVLPDDERVTRLYPHHKDAPARPYSEFEQRALRSWAVGQTTAQRRLDCHTILALGLGAG
+LGTADMMSLRVEQIDADDKGVVIHVTRPGVERDVPVLAAWEQPLINVLAARGLDDWVVGV
+RRAGVYKNWMTQFLRRALPERGVTVEVARLRNTWLVHHITAGTPLGPLAFAAGLETFRTI
+EKVLRYVPQPSHDEARAHLRHAMAAV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002805.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002805.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2cee2b834e7ce70b4cb224e85c7d29934ebdc828
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002805.fa
@@ -0,0 +1,2 @@
+>NAFOICDF_00426
+MRVRIQEVTRTVVTVAPTVNGAVGEVAKSIDPAASITLSLPTERLCPAS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002806.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002806.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a372964a8a535ab187cca6478479919f6c3d21c1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002806.fa
@@ -0,0 +1,6 @@
+>NAFOICDF_00438
+MSKNPQTVTDVAATGAISRVELTWTPLPWEPLIDHYRVYALPTSGRGGTPDETHLVGKTV
+YPRFVHHGLDPAGEAFRYVVVAVSDAGRRGRPSSAVVGESQRSVTATGRELARIGEFDGK
+SLELRFAPAQYGQIPKAYPKAVIDYVQGVDTPAEAWPYLLPGPGDAWAGRKAYRARWTVT
+LDAAPQREVDLALWFVDTTRLGGRLDVAVNGQSVRSVELAKGATRGSREGDATLPGSTLL
+RSYHEFTLPTGALAAGENVVEFTLAEGGWVAWDALGLYERAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002807.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002807.fa
new file mode 100644
index 0000000000000000000000000000000000000000..353f0294ef8695e5d7da6a77ad36d7a6393e3abe
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002807.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_00445
+MFAGAAAVTLGAGGCAVPETVVWGPDGAAVKSATRDVIAAAQRGGDGLPACPGVSVVTGD
+PAAWRGAGAGEPERPGPDLPAELTRGGEPAWVINVEAGAEAAAPGARVPGSLAFSDLADG
+GLCLSGLDWANVGG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002808.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002808.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c9c651064ba34601ad9ac0537607d1eca004055a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002808.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_00446
+MSTLSETHVIDFPGFPTVVVHSPGQAMGTLPQFMDTAFRALGAAVQRGACAPAGPAFSKY
+RGLTGGSGEAPESADRGRRSIDPAVGLRTRGPGALVPDPEFVAGQLDWPVSKAKTEVDAT
+PGRSGVSRAWACLSQSRS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002810.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002810.fa
new file mode 100644
index 0000000000000000000000000000000000000000..700de6dc62be72dbcb35619cdf303239f29da36b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002810.fa
@@ -0,0 +1,5 @@
+>NAFOICDF_00453
+MATALLPPNSPSHPLRRAPGGRPALAPVRIVAAFLAAVLVVGGGLALIPVTADLPVTRAF
+NDWNTGAVGVLSNALYQALEPAFAVVLALAVASLVALRRGDLALGVRLGLAVALAWLPVG
+AVKLLVHRPRPAAAALPHPTAVPAVDWTFPSGHVAFVAAMAFMLVLASRTSGQRAARAVL
+GVVAVAVMVATVLVLGVHYPTDVLASLAWVLLAGPLMWQLAGLVAGPLRRLTDRRGAHRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002811.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002811.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3082386489a5f1138586a4e1375be7cb3004d99
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002811.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_00460
+MAAAEGAGLIRSRVGGAWAPAPGPHDPRLPLRKAGFRHAGDAARWVRSLTPLGAPVPQGA
+ELTRRILQARPELPVDAAQALTLLAEGAGPGEDAAS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002815.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002815.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5a5eb00ea5b02ef183941b8f04fe45cf28ff2ec0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002815.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_00525
+MTTTTAPRPAARLRSTLVAVAVLPALMIGAPAASAAPAVSPLGHDMRISDPGTASPDFYR
+YICRRVPIIPC
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002825.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002825.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c720d910a1ff6421478774ff45cd7aad37eb6dbf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002825.fa
@@ -0,0 +1,7 @@
+>NAFOICDF_00618
+MTEARRPTSARSPVLRILARILTAALLLALAVLAVAVFTPHSELGQRLTTRLFLAQALAF
+AEPAGAGLTLLGLGVLALHRGAGTRRRTAVGGVAAMLLGLGVGLLAWPDAPPWAAGPATA
+TGNTGRHVRVTVFNSLDTLTAADARRLIDETDPDVLVLPEAAPSRVREALAGTGLAGGVH
+EGADSGFSRGRPAGVAPTTIAMHPRLGAYHQTAPTPTTFGAIRLEPADGADGPVVVGVHT
+GPPLPRLMDDWRGDLDRLSAVDHAAAQGPMVVAGDLNATLRHGPLADRVHLADTALRCPD
+DVGGTWPSDAPGRLRSPIDHVLVTGDVEVLSCTTLRVGASDHLAYAAELRLPGT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002826.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002826.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d9b1bdd82b39b0c8f225f480f4eb5124d638a5f6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002826.fa
@@ -0,0 +1,5 @@
+>NAFOICDF_00622
+MDAGDEVYVRDDHNAYGFVPNLTYSDLMRIASFAKTLGYDTKIRDLGYTLEEVQKRLRED
+GPSAFLRLKRIQEDVSPKAPAKQAIQYVAERLDRLAPQDELLITDPYLFSSSARKDIEAY
+SQSVADLIAPLLANSAKLIAIVDKDASHREVRDAVLDRLAAARDVTDIRVVESKDFHDRF
+WIADRCRGVIMGTSLYKIGRKIFFMDTLSESDIAAVLAEADATLAS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002827.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002827.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a581d6de90bac2da2b307c5b11cae3edfccad0d6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002827.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_00623
+MGDGVEDPESQREAIRAEASRIHESAVFSAQGQFEAAKRWRLVHWGLAVLAAGLSSGTAV
+FTFADGAQAWSAVLAVLAAISTTVLASARPDRLAERAQVAGTGYTTLRNDVRRFHGITVP
+QGDPQDLAGELDALADRAAALDQSADPVPRWAYERARKNIEHDGGQAFEADV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002829.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002829.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b134857c67f51e9ec3106b894caf0de29eb72005
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002829.fa
@@ -0,0 +1,13 @@
+>NAFOICDF_00629
+MAHTTTPPSPRGGKRLTIADVPHMRERYAASNPLPPEEVAAGSNKKFTWSCKAGPDHTWE
+AQANSIRMSKRGGCPFCAGKRPSVTNRLDVLFPDLAAEWDQELNEGPPAVVAGSEKKVWW
+RCRAADHAWQANIRNRTVLRAGCPRCAAEKSSKTRSVPLPGRELTAVAPDVAASWHPTRN
+GTLQPDEVAAFSNVPRWWQCPAGHEWEISPAGRLSKGGAGCPYCSGRLATAETSLEVQRP
+DLTLEWHPTKNAPRTPRDVKPGTSATVWWICSAGHEYESRIANRAYLGRGCPYCSGQKIG
+YGNDLATKAPLVAAEWDHERNGSLTPADVTTGVQRRFWWSCTQGHSWRTTVASRVALGTG
+CPECGAGWRRSRPEIALQFELAHLLPAAVVGDGHVQTADKDFRVDVLCPELKIAVEYDGN
+HWHMDTFERDLAKTQALVEAGWVTVRVRQNPLPLTGRHDVPCENGDPAVYPMTVRLMTSL
+LEEAAAAPTDHPIHAHLDELRLRLETYVDGGTARAVEEAERETRAHHVDRPKRDPFAPPP
+RPKPGRSLAELNPAIAAEWHPSKNGGLTPADVANARNASAWWLCSLCGAEWEAVVGQRTR
+RQTLGCPDCGKARAGAARSRPQPGLSLADLRPDLAAQWHPTRNAPLTPHDVRPGSHKRVW
+WRSPGGQEWESSVYNRTSKRPSSEVHGDAGPDSPDSA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002834.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002834.fa
new file mode 100644
index 0000000000000000000000000000000000000000..35a60603183753a486426fe74008d91325561d2d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002834.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_00653
+MSTRTTQQTVEDFFSAFGAGDLDTVKNLFAPTINFTVHGSPAVPWAGTRHTRDELDTFFP
+AFAALGPATEYTIHQIVVDGDHAVALGHNEFPVLATGKSFSNDFALHFTVQDGQITGYQM
+YEDTYAVDQAFTPTN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002836.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002836.fa
new file mode 100644
index 0000000000000000000000000000000000000000..66fb437a11481f6d397525fc1bbaa00856d7b791
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002836.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_00658
+MAVGDKNALLVQVFDTMVADEHAQRAGATPQSTGDAPDTCVKRLGVLVQPFVAMFTGSPE
+LARSYASILVSGTHSSSLFTELHARLVEEFATAITKQGCTPAADAPAKAQALYAAYVGTL
+FTWSARGLVDPSAITNGLRTSFAAISICKE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002838.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002838.fa
new file mode 100644
index 0000000000000000000000000000000000000000..62b0ff0e6795efc13c726da2436f1a107e850739
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002838.fa
@@ -0,0 +1,5 @@
+>NAFOICDF_00680
+MSTPDELADEVADVRSLNALAEAWRTAPDGSRRFVPNFDPRSGGTSSRVLVLMQSPGPQT
+IAAAHTAICSEDNPGPTAAAFRAARIESGLARNDYLRWNLIPWEILGRVRPVDIDEGRHA
+LETLLKVLPVLDAIVTYGTAALNGVMRHLTLDEHPRLVPVIAAPHPSPANGRHRAEQQRR
+SVQALRLAALTHRL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002846.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002846.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d9ff71950afbfc4e0a748c8b8ad813b81c3bebaa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002846.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_00704
+MPRTISVANTGEWLTRIAVGDAIGITAEATTHNHRAPEVVYLPIEDAPPVTVALTWPGQR
+RSHPQVGVVATCAQDYFTRLIDIGSPPRLLSTGADGQLA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002848.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002848.fa
new file mode 100644
index 0000000000000000000000000000000000000000..add33947e1cf383840599a40659fba16e99d415a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002848.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_00708
+MTMKEVEHAHATYDTPHLNAAVGVFALLANLVSVKMILAIRDIEVSANHLADIVDLPVDQ
+TSHELHRLESAGIVSRQRRESRDFYLLNGVHAGALAEAAIFHAEHQQQERTRAGSPTSNL
+RPN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002849.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002849.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc6143a71a50e1c8b1ee57c23551f7167452810e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002849.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_00713
+MTYVIALPCVDVKDRACIDECPVDCIYEGERSLYIHPDECVDCGACEPVCPVEAIYYEDD
+LPDEWSDYSKANVEFFDELGSPGGAAKTGPTGFDHPLIAALPIQHEQTL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002850.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002850.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9af020681c079450776ebac8b01d9057e39eb16f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002850.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_00716
+MTTTTPTTETHLDTCPAGGDGDASVHGYISDKTKYRNRLRRLEGQIRGIDRMVDEDRYCI
+DILTQISAVTRALENVALGLLDDHLKHCVLDAALAGGPVSEQRLGEASEAIARLVRS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002851.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002851.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b4a5b2a933074033a5f73aec52c6284c611bc639
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002851.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_00717
+MSSCCSTNETNPAVENGGRENLLGGGADDMTTCPVMVGTPVSKKTAEAAGLYRDFEDERY
+YFCCAGCGPAFDSDPAKYAANMA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002859.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002859.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc07cfec39e33070811e3f13caf090ec42102312
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002859.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_00784
+MTGPGLWDDFMVYASREAMKAPSRTEPDGEKNTRCHKTPIKLYRMVNGKPQYVKTRHPRV
+AVSMYNKVVVTSYPTSTPSC
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002863.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002863.fa
new file mode 100644
index 0000000000000000000000000000000000000000..29a509a3a7695ac3b19f88363d6364d24c96678f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002863.fa
@@ -0,0 +1,17 @@
+>NAFOICDF_00869
+MLRLVAGALALAVVLGLFVEAQAARRLRDLVDSSWRGSYDLVVSVPGAASSPASLGAPLD
+TAAWTSAAERLSPADLGRIRAVPGVEVAAPLGDFGVRSVANQDAVMIGYPADGSVQGPRA
+FDVDARVRTDDGLGPRPVLGMDATLIGSFSDGPILDARPLLDDPVVCTPAPPEPGPCTDV
+ELPTVAIGPRGQTPPPAQREIPAGTYWAAPWADPDPQGNRMVVVDAAAEAQLLSLGGHPA
+AADAFRVLAQSSPAGSLPAVVDRLSGATTEEAEALLEAKDRLPAYLQNLADAAGRPVESL
+TAVPLLATNVGSAPLSLEVRATPYREPVTRLDIQQGPVDPRDPTAPRGIVGMPAWALPAG
+GTTGQDEVSTSDISGRFGGLGLGVTVVPLPGLATGQDPVLSYDSPRLSLVEETRTLTRPS
+SADGTLTEAASVETASGTIPGRPDVAVSRALPASTSRESAYYTATDDGRRFGTGDAPLLV
+SVGTLTPEPDTALAGIAPLLTDVELPTTLVADPRGTPQDVRLRPASTGFGLANQMPAAYV
+DAASAEALGLARPFSTVRVRVAGVGEELTPENLATIDAVAQRLEEAGFAATTVAASSLAP
+REMQVVSYRFDSTDGEPRTGPLGTVRQLGPELAASQRVSAAVGTAGTSQAVTVVVLLTVL
+AGLCVAAALRPRRRRAGVLAVQGWTRDATVARHLREDAPTLLVLAVAALAVIGMMSGRLG
+VAVPLVAVGLGTTAGLAAAVVLAAVLAARPAASAVREGGDRAARPARTPAALLTRWTART
+WPRLLTGAAYRAAVAVGSGLLVAVVLQARREAGASLLAGEAVAQDLPFRLALGALSAVVG
+TVLLVQLHRVEGQAVRAEATVLLLAGWTRARLLGRHVPALAVEAITAAVVAGVVPALLTP
+DPDLPLVAGAAGFALLLTLLITLLTRRAQLARAWKGQPA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002865.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002865.fa
new file mode 100644
index 0000000000000000000000000000000000000000..558bdc28b69636af939263f6d510f061f3bd3a8f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002865.fa
@@ -0,0 +1,5 @@
+>NAFOICDF_00885
+MAGQRLRDVRNGMTIPPKISLKTVLDASYRPEWWFDFLTTEPLTFASLSDSAGDLPSIIN
+GMFDPTLDLHDLEWIRSVWLGRLMVKGVLTREDTRRALDTGADGLVVSNHGGRQLDRAPV
+SLQALPEVRDEAGPDVPIILDSGITTGEDIVAALALGADFTLIGRAYLSGLMAGGQEGVR
+RVIELLAQEVRVAMSLMGAATTADLTPASVRAPWLRDGQVVRSGD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002869.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002869.fa
new file mode 100644
index 0000000000000000000000000000000000000000..973d772fc1fa554493aadd487bf2cf7c6e137023
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002869.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_00918
+MASQEELTRIIDNINADVNGFIGASIVDMETGMPLASRSTRADFDLEVASAYNSEMVKSK
+LKTIQVLNIRTTLEDMLLTLGDQLHLIKMLDERTFLYVAADRSATNLALLRSAVNRHTVN
+FR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002871.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002871.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6bd0a961d30516726467402fbb58071239d2528c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002871.fa
@@ -0,0 +1,8 @@
+>NAFOICDF_00934
+MAQDPAGWRRTAVLLSGAWREALRVSAPRVEPEHLFLGVLASGGPAARVSARQGLSLTAA
+RRGAAVRANRQLRAVGEDVARAGRIPRTPLAAVDRGGAATLPLSAASEGMLPARRLAMTE
+AAWALDLLQEPAGAVSALVAAAGVDVDALRHALRAADRDEPRLPGAALDVMPAPCPVPPD
+ALTPPDGIRPSGSRASRAGRLSAIGAEWFVAAPREHVMRLLRDPEPIRAITAQPADAEVD
+DAFGVVTTVRSRGARGGEHRSTSQLFPSETSTPDGAARIRWAEVLDEHRPPHQDSDGTLV
+PDGRDYSGDLAGAYVFTLVDDSGPDPDQPVDYPGHQPLSGAGTRVRLERTRRTVRRRDAL
+ASRATRWPQAWAVAQHLQSLASLAADRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002873.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002873.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e07bb5d372abdcdabad10a7eb795c6fff61c4086
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002873.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_00941
+MTSAQVASPTPLSPGHRFTWANGGTTIRSRVEVVRPGHDLTWTGIALWLVAVHRNVIETL
+PDGQARLTSTESMAGVAAALLMPEEKLQQQLQAFVEAIAAEAERRSR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002874.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002874.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6c8bf613b31c19d5443deb59cb2118f079c42a01
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002874.fa
@@ -0,0 +1,9 @@
+>NAFOICDF_00944
+METRVISLFARRVFRDRTVWVLPVTAFAAASALTLAVAGGVHFFWTLPGEIGGFYKVLSG
+IALALLVLPLAALAGAAARLLARRRDDRLSSLRLLGASTATLTGLAVAEATILAAAGAVL
+GVVGWAALIPVIGLLPFAGGTIGVGAQWIGVPGVLAVLAGLTLIAGLSALTGLRRIAITP
+LGVRTRQNAQSVHWVRLLVFGALVVVGQLLIAVSKGAADVGLAISAVLVALAVPLLALHL
+LGPWVLSLGAKWRLRRARTPESLVAARTVLDAPRLAWQQVGSLAVTTYVGVMAGAGLGLA
+SEGEATLTHPEDLMVMQDLRTGVLLTLLISFLLAACSVALNQSAQVVDRADLHRGLAYGG
+MPVRRIHAMRRASVMLALGTVMTVSIGAAVITGGPLIGASALYAPLSLLVIVASLVGGVL
+LVRGGVDVTAPALRRSVALA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002875.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002875.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4db5b80a542387e58f5e61425968c61f34db4b94
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002875.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_00948
+MNGVPSPSAREMNGVPSPSAREMNGVPSPSARETNGVPSPSAREMNGVPSPSARETDAAW
+HA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002876.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002876.fa
new file mode 100644
index 0000000000000000000000000000000000000000..10f9fb87acd43ca846d49cc82264a70af787a17b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002876.fa
@@ -0,0 +1,5 @@
+>NAFOICDF_00973
+MTTAPTWIDAVLALVLLLALASGLRRGLALTLGSALGLLAGVAAAVLFAVPLGGLVPDPA
+WRPLAVVAAGVLLVVLGQGIGLRIGAAVRRALGRGALSRADGLLGGVAGLAVAAVVIALA
+APVARPLLPADAADEAGRSRVVAAAEHLTPEPVRQAAADLGTQARLFVAEAIAPVLPEPG
+LGGREAVRA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002879.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002879.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8a8f04f2e65d31e4297c300fac36a8c6865aa74
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002879.fa
@@ -0,0 +1,7 @@
+>NAFOICDF_01014
+MSIDQNTADTTTPLATTGVRGRSRRRRTAVGALGAAGALAAVGMASAPAQAATVDASVLQ
+SIQACESGGDYTAVNPASGASGAYQFLDSTWATLAAAQGYASAADAPASVQDAAAQELYA
+QEGTTPWEASQSCWSDAASVAAMSTSTSSTTVSDAAVAQADVATPVETVAQVEPAAGAAD
+EAEADTAAGADAAAEEAAGEETDAGGTAPTAAPDAAASGEQAPAPSEPAPEPAPQGDQTG
+RQPAERPAEQGRGTAEQAEQGRGTADQREQRGQDVEQREGRTGGERQGAAPETGGDAGHQ
+EADAAC
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002887.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002887.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9001c981b5839f3e2edf330886a4977e7076d648
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002887.fa
@@ -0,0 +1,2 @@
+>NAFOICDF_01184
+MSLAPADAFIGWLPQEHERVPGETVAGYIARFTGRLKAELVKNI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002889.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002889.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f633316444fbdc4d337e08f2ec8d0d8d50ea8df6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002889.fa
@@ -0,0 +1,8 @@
+>NAFOICDF_01213
+MTNPFLGRDDQAIDVSDTPRGELEVVHTFTDGPMPTGVSVSHTGRIFVNFPKWGDEVPAT
+VVELVDGAVKPYPSAEANQAKSKADQDAFVSVQSIVIDPADRLWVLDTGSPLFEETQRGG
+PKLVCIDLTTDEITQTILFEPDVALPTTYLNDVRFDLRQGEAGFAYITDSSDQGPNGIIV
+VDLASGAAWRRLHDHPTTKALPPGEMVPVAEGRVFAERSAGEAPQPVKMGADGIAISHDG
+ERLWYCPLISRRWYSVDTAALRDRALSDEDVAATVVDHGDKGGGADGLESDDQGRLYATN
+WEHNAVLRRLPDGEMQTLVHDERLLWPDTMSVARDGHLYVTANQLHRQAKYQDGQDLRVY
+PYHLFRFAIDAGPVLLR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002890.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002890.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2ae44c48b5f384932071cbb2ce2fcc4bf0d762ad
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002890.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_01216
+MLEIADGMVTFTPDSPSAAPGWSVPARQLTLGRAGVRFPGSFVVRGAEAEDIMLEVSTSE
+GARWREAGDARDLPDRSTHREVQQILVGWGARSVRPRPA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002891.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002891.fa
new file mode 100644
index 0000000000000000000000000000000000000000..72d29f5549a83a2edf55e69a2e25036b9f76fb16
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002891.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_01220
+MQPQDLIADAAHRALDLAAPVLDGLSAEAAHTRPGGAGNSIAWLLWHAARQMDVQTVALR
+GGTTVWEAGGWARRLGVERDAQDFGLGDTAEDVSALRVTDVPALGEHLEACVDALVTWTS
+SLTTEDLGEVVDTYEGEPVTRGVRIVSMIDDAAVHVGQAAYARGLVDGWRFAV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002892.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002892.fa
new file mode 100644
index 0000000000000000000000000000000000000000..779e876c6af11d97f689dbcc4319c28ab8fc628a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002892.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_01223
+MRRITTWLLATLAGLVLLFSYHTSTDPNASATASQGTSVHMVSGASFTSAAYEQSLQSAL
+DRAHL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002894.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002894.fa
new file mode 100644
index 0000000000000000000000000000000000000000..11e16c9c47d8ea38bbf0d4181f62709c8c75a705
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002894.fa
@@ -0,0 +1,8 @@
+>NAFOICDF_01232
+MTENQHPDDPRRPEDTGGGAVPGESARHGVEEGAPEAGAAGWPDKPPSAGWPDHTPVTGT
+GHGSSAYTPGGDGAVPGPYEQPSYGQPAYGQDAGTQQAGAHGQPQGAYGADAYGAGAQHP
+GSYEQQGPYGQPTGAYGQQQPGAYGAYGQPLGGYGAYGQQPGVYVTGAGAPRPASNGLAI
+AALVCGVIALLLSFLPFIGLVSVLIGAAAVITGVLGLRRGQSKGMSIAGIVTGALGLLIS
+IAVTALTAAAVSAAVQEGGPALSSIGASLSSEANAPHEVELRATVDQGDATVNYSIGGSS
+SDQDITAEQISVTDSVTGSETLSISVTEDVTDTGSQNVTCEILVDGRSVAKETGTSSAYC
+NAGYGDY
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002895.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002895.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e63540618fe352abdd6745a3a192839dcacfe3b2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002895.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_01293
+MVGQTVAYVRVSSAEQNLDRQLEAVGECDRIFEDKISGSSRAKRTGLAELLGYVREGDLV
+KVASMDRLGRDTRDLYAIVDELTDKGCAVQFVSERITVDKSGTSPVDPTSRTPR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002896.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002896.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c2534ea9de3bd823aca472c63f6b3e2146696d48
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002896.fa
@@ -0,0 +1,5 @@
+>NAFOICDF_01298
+MATVFEGGDRPWLCVLAGRAGTGKTTLAQALAQATGACCLRVDAVETALGRVQDHVGAAG
+YAVVHELAVSNLPLGHDVVVDAVHPVPASRAAWTQTAARAGARLVVLETVLPDGREHRRR
+VETREADIPGHRVPTWEDVQADGWVAWDVERDGPPDRDRHHHPRGRAARRAGGPATPVTR
+TRASEGPGAVPSGTAHP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002897.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002897.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4be375656cbb7310adcfdd7f5609596f90900d5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002897.fa
@@ -0,0 +1,5 @@
+>NAFOICDF_01315
+MLVDAGLIGALLAIGTLARAVFTPLQTLIIPASVIAGILGLALGPNGAGWLPFSDQVGTY
+GSIVIVFVFVCLALTDDFDVRKIGRPVGSFAAYGVLIYASQVAIGALAALLILHPLFHTP
+DSFGLLLFAGWAGGFGSAAAVGAARGQRPRVCRPDLHPRGPAHGRARPGRRVPRDRPPHL
+LRRLRGVPGLPGGHRRHVRRRRLRPG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002899.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002899.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9273bd40897d5c36c9fae8996304dcf73f052cbe
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002899.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_01359
+MAVLAEGERTQAQVATAIAVDPRNVGATIRKLIEARWVQARPNPADARSRLLSLTPEGRQ
+WWNDLQPGLRQGRNAFFHALTPDELTALEALLGKLDASHAADSINVPGQYI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002900.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002900.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b74a02d741decb580c56428597823f9a7a8120f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002900.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_01360
+MPSLTPPTGHNTINPFAIVPDAMGFIRFVESVFDGHEAAHVRTPDRDGSIIHGEVTIGDA
+TIMLCDRKPDWPFTPAFLQVYVPDAQDCLDKAVAAGGRIVTPVSDFYGGYRIARALDPWR
+NLWWIYEPTTQPLHQDERDSDTDWHDRKPSLVYTSLMDAMRSLDRPEPA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002903.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002903.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0607b4887032a409805508eeba86c98b6cfd66b7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002903.fa
@@ -0,0 +1,8 @@
+>NAFOICDF_01588
+MTPHRRTAAATLLAMALLTGCAPTANAPDGAASGTSQDASSSDSASDLRADTPGTSSTMP
+PASPATASGEPRTVTINTSGDLLWNEPLFDAARTGGGFDFRPMLASVRPFVAAADLAVCH
+QEVPLAAPGGPYTGWPRFRAPQQTVAAVVDAGFDVCTTASNHTVDDGWDGMVRTHDALRA
+AGVGVAGTSTTPGEDQAPDLFTTADGVVVGIVSQTFSTNLIPVPEGREWSVDLLDPDRAI
+ADAHAAREAGADVVVFHMHAGDEYVRIPNEDQRWMANQVTASGEVDLVIGQHPHWVQPVE
+KVNGVWVVYSTGNLIASMKGERPGTHDGAIVEVAFREGDDGRFDATGVTWAPTLITDADT
+DPTGRPRVLLIPDELPQAGPELRGRLEESAARTRVAIGSDNTPGLSERTSPGG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002907.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002907.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ce41ab156bd3312cea0e0f58fcaa216d7682beaf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002907.fa
@@ -0,0 +1,8 @@
+>NAFOICDF_01733
+MSETHSTSTAPSRRGVLAGGALAAAGVIAGTAAQAVPAEARGGRHPQGASMPLAFGATRR
+MKIVQFNDTQGGHAADRRTIEFMGKVLDQEKPDFALINGDVIDGSPTTDVQVKQGLNNFV
+SPMESRGVKWAVTFGNHDEDSVEEHGTSMTEDRLLEFVRQYKHNVNPPKMDGVPGHTNAQ
+ILVRGSRGAAPAFAIWLLDSGRYASEADTHGQSTDGLKSYDWIRPAQIRWYEDASAATEA
+RFGRRTPGLMFCHIPTFEHEMMWHASQAAEEASDHAEAVRRHRITGVKHEDVYHGLVNSG
+VYASVKERGEVKGIYCGHDHINTYTGDYYGVELGYAPGTGFDPYGLNDGTWDQHTLRGAR
+VFELDERNASVYAGATRIVWARDLGIDMNPEGQPLATPVPFPPYVKA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002908.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002908.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c68e8b42db17a21ebdc1e6cfc89ab78476fad7ed
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002908.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_01748
+MHDSLRPTRSFVALLRNPRIRRALGALLTGSEVAASDRGALKAAESVGLTRADDDDTPVL
+QEAFLADAVAALDRALGPLAVLDGGRIRVGDLPHGEVDAAVGAVVERVLSPGERVPEATL
+NDRLALFVVDVAFFRRHAYDLGLVDRELDGSAYWRR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002916.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002916.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45f38d4211aa4f1bf86c5e955344199ddcd27cf0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002916.fa
@@ -0,0 +1,7 @@
+>NAFOICDF_01779
+MSPNLYHLARLLAPGSDRSLGRVAGDLASAHVPVFPCVPGQKRPLTARGFHDASTDLAQI
+EHWWARWPEANLGLPTGASGVVVVDVDVREHVDGRESMRCALNAGRVGMPVFTVVSPSGG
+RHGYYPATPDVVQRSWQVARAGVDFRGDGGYILIPPSHTTAGSYRLATVRQGAASGIDSD
+TLRDFLDPRPALKPRAADRGMAQSEPGVVVWRLAAWVAGLGEGERNRGLFWAACRAAEHD
+ITPATAVETLGAAAAEAGLGPREIAATVRSAYRTTHPTTSTARRATEPAAASPVRVPVGA
+GWGLA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002917.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002917.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0c23e7b05244bbfa099925365c5ff268a1576fe
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002917.fa
@@ -0,0 +1,5 @@
+>NAFOICDF_01781
+MSTHEHEHHPVEPPVHDDYGPPDPEELALTTPSPLAENLDQETVSERGDLVPPKAPVEEL
+NEQLAPDIDGPDAGFPELDEGAEGVPEAVKARTARTTSRPVGRQVGRGVEWVRPTDLLAR
+RGATVAGRGIHFQTALSQKTRHGITVSTRRIGDRAAWLAPLSAFGRGRAQSVPGRSAVGM
+S
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002919.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002919.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7cb0ff396c21f7b319c83c441d1b5d500f6c73e1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002919.fa
@@ -0,0 +1,7 @@
+>NAFOICDF_01783
+MSTPGHIELDRAVDSLHVGRRHRADLGDIDALAASIERDGLLQPLTVSPDGVLICGARRL
+AAIKQLGWRTVNVWVRSGISDRLGHLLAEQDDNVLHKPLTALEAAALYRELKSLMAEDAA
+RRKAATQFRSDNQPGTHGPGKFPEPSGATGEAREQAAGMIPGGASYKTLDKIGYLEHAAT
+DETLPEHVRAAAQRGLEQIDAGSPVHPIYETIRNHTANPDAGDEALHQAAADALARVQSA
+GRPKPAPAKKPNSTPESGPVQYPVRAFVVTWTELDQWWTHYDPAVLAVELTDEHVATFLR
+VIEHTIAFADALQAALTNHDDTTTASGTVTESDDGHAGGRPQLRAV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002923.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002923.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5cedde6f78d9e2b25258314c6154d1e2101ace28
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002923.fa
@@ -0,0 +1,6 @@
+>NAFOICDF_01793
+MYNLLIGLTRGEVGADRLLEHTADDVREYLAPEVGQVRIERLLNLPTLLMPETGFDDEPQ
+IARVGHVTNVNKSRYGYTFSFVPNPAIAPIPSPRIEAAAGVLDITDWEFHRTHWAVKDVD
+LYRVLDQELSARVKPKVFQFPTSEPFDPDLVAVMMPFSPAFSAVYESLKEGIEAAGMRCL
+RADDIWERDHILDDVLSLIWRARVVIADLSEKNPNVFYETGIAHTLGRDTILVAQSMSDI
+PFDLQGIRALKYLNNGEGRAALSRGITSRLNTITTS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002925.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002925.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0921c913bbaea2b8b98c78a997d777e6fd7dc3f3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002925.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_01799
+MPKLPALRHRRNDPSEAVPVVLRHVVITVDITGTLTVTVDQQPHLPQAGEVWGRGDFGAI
+LDDLTEQRRIPVRVDVYESDGSHFTDIIHAHRPRRAPEPEPDDPAAADEEAAADTPAPPT
+DDPGRLVGFLPGETVFLGQIVEEVAADENGTITPPDTALGPVVVVGRASGTVIVQETR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002929.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002929.fa
new file mode 100644
index 0000000000000000000000000000000000000000..361b967fd93ab180d804e8e72bf1195a6a1ba34b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002929.fa
@@ -0,0 +1,10 @@
+>NAFOICDF_01804
+MAGQFCFCGDVGRGIDAGVYEDAGGGLLGCVGGVLFVVDGDAGEQGAVEDASFGWVALVV
+ELVEVDEEFGELVQACSGVGVGVGEVVEPSGDLIEAGADAVLFAFEEVEGDRVGVVSLDE
+FEAFGFELVALGGQELAFVLARSFELIEHVVEDLPDVLRLGLGQGIALVGAFDLRFGAFG
+KDRGAGAVGGLAASSGAGEVLVAVPGLVAGAFDHELGSAGAVQRAFEVVVVLLGSFAAGV
+VGVEVGLDAQPGLGVDEGLVGAVVGDAAEGDGALVVGVGQDLVQSGGGDWFGRLRGGGPG
+GQATGCEFLGQARQGPVPGGVGGERETDEVGAFGVDLDLAGLASSGVGGADVEVAQRRFG
+GGATDRGLLGHAFEDFLGQVQRVELGHGGQDAVHQHPRGGLVDVLSDRHQTDVRIPQRGV
+DHGVIEPVAGEAVDLVDDAVPHRMRGRVVEHLLERASLGGLGGLAGLDELLDDDRTELFG
+LALRGFALGRDRQTLFQPVAGGLILGRDPQVADRRHLPLSPGRCGVWAWCGAGEASKA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002937.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002937.fa
new file mode 100644
index 0000000000000000000000000000000000000000..946d8b47b3d515d7e309c6427c05cc02e03332db
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002937.fa
@@ -0,0 +1,6 @@
+>NAFOICDF_01873
+MTEQTPAPGPGVDSVSTGVHREPFSAVGPWKDDPAAAGQVVFTSVHSGHALRPEVAERMV
+LAEADRFREEDPFTDAIGAGVGSGLVMHRSRFEVDLNRPRATSVYTSPEQSWGLDVWRGG
+RLDEDVAERSRQVHDAWYAELGRRLDVLAGRGPYVVFDVHSYNHRRDGAKAAPAPQEQNP
+DVNVGTGSVDREPWAPVVDGFMDSMARPLVAGLGRRLDVRENVKFWGQNEARWAHRRHPD
+QACVLALEFKKEFMDEWTGQPDAAVVRELSAALADAADAVAQALADVKVPTP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002938.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002938.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d95a9950d25f000320c9fca642e4c0a271853f10
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002938.fa
@@ -0,0 +1,9 @@
+>NAFOICDF_01874
+MTGNAGRTATEDTHGTMPAEHAAHDDDGGVTPGVRGTSRVVASRMLSRWSGEHPGGGLSL
+ADRAVDHELGMLASTFRFLLDVTPTNVESARRAFLERDELEPFAYRRLEDDPEVLRQVLY
+DIPVQDVEDPVLGTLLRNKEREIDLQLEMLQARDTSDFMPLSIELYGAITPALRETAEHI
+LDQVPVPEPDADEAVDAPTFLALAREEIERYRDQDADIEAHAEIRRDVSGVMVSGDTLLV
+GPESTVQRRRADALVQHEVGTHLVTHVNGSAQPIACLATGLAGYDETQEGLAVLAEIAAG
+QLTAFRLRQLAARVVTVHRMVAGADFRECHRALVDDGIPASSAFTTVMRAFRSGGMTKDA
+VYLRGLLDLVDHVQRGNELDLFLLGKFSLADLPLLEDLRTRGILRPARIRSRWLTDPVHL
+ARLRALADVTDPAALVNA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002940.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002940.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a0c58b9a7ce254fca22d05c6348cc24906d924e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002940.fa
@@ -0,0 +1,9 @@
+>NAFOICDF_01909
+MPRLHSAHDTADNAPGARALSGVGAARHRALRPAAVLFTAGLLLTGCAGPDGAPAGGSPE
+AGASTTEDAGASSGTAGGSAGGQSGASESRAEGSPPVDPADFPASNTTKLTRVETIKDPG
+LTPKSIVSNQHGLAIANNMMYRHNVMLFDTRSREVVQTLEDTVDTDAMGIDGLSGVVNGS
+PVEAAWTQDGRYAYVSNYQLTGGEGTGVKPDDNCTAGSAISPSLVYRYSVEEKKWDAAYR
+VGRVPKYLALSPDDSRLLVSNWCDATLSVLDAETGELQHTIPLDTMPRGIVVLPDNKTAY
+VVAMWADKLYRVDLDAGTAELVMNTGPQPRHLSLSPDGKTLYMTVAGADRIVKLDAATGK
+VLASASAGDEPRSMDVSRDGTALYVVNYEASTLTKIDAETLEILDTAPAGENTVGVTYDD
+PTGQVWVANYGGTVDVYDDTDGVGPGAAGSAQPTADAPGD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002943.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002943.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e283b3abe948c46eb621197dcdfb09454367548
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002943.fa
@@ -0,0 +1,7 @@
+>NAFOICDF_01978
+MTDSTLLFDAAVTGDRGAVRSSAEALAAVLAADPGDPDAWAALPAAQWAAEQTALTGYAE
+LFNTALPAALALRVAAGSGGRLPEGVAGAWAARLDPTLDAERRAGIDAALADAVAGERER
+RGVPTPEPFEDEPRTVFPRGFMAALTRLRSAALPVPPLYTAALRVVEAPVDEPAEPRPAR
+PLGELLDALVALEDLEWRRPATEKQIATLEQRTGVTLPADYRAFLERANGSKDREFEGAH
+EVARDAKEPPVYSHGTGEFVILDCAPGPEGTAGKVLSYGEGETRVTHPDFRAWLQDHVED
+LED
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002944.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002944.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d570d61cbc00f58c4f24b36fc811b9ab9184934d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002944.fa
@@ -0,0 +1,13 @@
+>NAFOICDF_01979
+MALTIMSRVPDAQPYRDEDLDGRIGAAGLAGATLEHGLLRFHTHESGSEAARLLAFHFPP
+GFTEGWVPFAVDWRGRQYCRVRQDGVDSAVRADPGLFAASSVVDFEVFMDTVLTDPGAAR
+VLGAEDCAAALAARGISDLPFDQCLGYMLPPFAGGEDHSSNILDVPVNPYWAAMADMKNQ
+WQHRQPGAHAIAVAARDGGLTLVFDTDQDPEHSPGAGTRAERLVVTSPHGPAVYNHGLAR
+ELTDEQAREAAEAVREAFGTPDAAAPFLMDWRARCYAVERVDGRDVVVRSCPVTMTRTPV
+AEADGFRDRLAGNPALLDLFGEAEKSLLCARLRLTEIPAGDVLVPPAPPSVAGPEADDPA
+TFRLQSASVAWWLAGNLARLAREAGPERRLQGYVLTPEGRLGLQTAPADGPTPPPRPSED
+TAGLPPVRFAPRFAALAETGVVQTAQDDDAAPDKDAGDAQMAIAWYGLAGRVYNAGLFRF
+LGAEGVAQAAGHLRESFGGQAAEAVPVIVDWLGRYAVREVVEGQSMLVSYDAASGQREEL
+SRFEDGLEQILVTPVARELFDEAGFRRALDTLGLVRIGQGRCVGVKRPLFLGGDESPENW
+EDDSLDVHWSWHGRVFAQARAMPEGARIQRVEPLEDGRPLIHYTLPDGRTGDGLSGLHDG
+GAPGVSEAAAARQDGSGPKQEKGFFGRMFKG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002949.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002949.fa
new file mode 100644
index 0000000000000000000000000000000000000000..14f8ddf3716e341d00604f5dd54aa3782e139926
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002949.fa
@@ -0,0 +1,6 @@
+>NAFOICDF_02045
+MMGPSHAVTGAAGWLALTGPLADLAGVYVGPQVQLVGALTTAGAALISDWDHPRATIATA
+LPPLSTVLARFIRRAAGGHRRGTHSFVGLAAFTAVTWVLTPLTVTVGSVTFSAGQGVVAA
+FLAAVAARILRVAPGPVTGWAVGLAAGALAGTTAPGATWLTVSVALGVGLHIVGDMLTTR
+GVALLWPALPDPPVPTPFWLPGGRFRLPLLGRAGSWREWVVATACTVYVVGAVSAVVRAL
+LAAADPAAWPLPGPFA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002950.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002950.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0aa901d20adfb0ce0b72e5aa53f957360f238abd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002950.fa
@@ -0,0 +1,5 @@
+>NAFOICDF_02078
+MDAAFGPRVRFLGLQGSRARGEASATSDIDAVLVLDALTPRDVDAYRELLDGLPHRELAC
+GFLSGRDELLTWDAADLVQFVHDTTPIRGSLAELLPRLDAAAVARAVTAGAGNVYHGAVH
+TLVHTRSPETIAGLAKAAAFVVQARHLQRTGTHVRRQTDLLDVVDPADRDVLALALAVRG
+GAAVDVDRDGRLLFGWAQRVLVG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002953.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002953.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b95d7247febdaba996d526ce1ac175186bc8ef7b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002953.fa
@@ -0,0 +1,2 @@
+>NAFOICDF_02173
+MSDQQSPEAKNSDAPGDQDEAMQRQAPAQVDCLAEKAEEEAEQDKGGYDH
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002955.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002955.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4807006a080718aeab0d8144641f4ba5d5946aa5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002955.fa
@@ -0,0 +1,5 @@
+>NAFOICDF_02205
+MYVVPVEQLADRGVIRTALDDFGHAWGQRIDRWRADGQTHTEKSFAQQFWSDLLRAFGVI
+PERIDLFERGAARASTGGAGYIDFFWSGVALGEAKSLGANLDVAHAQALDYLAGGSIGQH
+EWPKYVLVTDFARIRVERLGDAGWVAEFGVEDAADHVDQLMFLAVMSREVVEPAGRCGSD
+RGVDSVMIVEVHPPRQRGPAFGL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002957.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002957.fa
new file mode 100644
index 0000000000000000000000000000000000000000..873a6b7ec5a95574ad980f64704f4b2d7db6ae14
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002957.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_02212
+MVEGIVYRYRTGIAWRDLPEVFGPWQTVWTWHYRMASDGTWDRVLAKLTAAADAAGLVDW
+SLSVDSTIARAHQHATNTTRLTGGWIELQESAGRAA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002958.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002958.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1dfd93b56c91851398a16428c7f88f563247f07a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002958.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_02213
+MFLPLMGQLRVGRDRGRPRTRPNAVRADKAYSSRAIRGHLRSRGIKAVIPEPDDQKGHRR
+RRGSRGGRPIGLDAIDYKNRNVIERQYCHLKQWRGLATRYDKHAIVYRAAVVLNAVIAWA
+KTLSDTP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002960.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002960.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1e6df2eb9843392bc38ae8f1360f7390d266fb83
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002960.fa
@@ -0,0 +1,3 @@
+>NAFOICDF_02227
+MDTLTGSRHKNLKELHPGSSGRSEIRILFAFDPRRQAILLVAGDKAGAWKKWYATNIPLA
+EERLDAHLHALRSTPPGA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002964.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002964.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e378b0cafda545e741b67c75d0e4e70b384cc2f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002964.fa
@@ -0,0 +1,7 @@
+>NAFOICDF_02239
+MDESGEVWTYSPSGSTAGSKDGDVQPARIEWLDVRGLPGYLVHPPSNDEGVSPWRRVYPF
+ADALALDVVAIETWTVPVSGDPPGAVNGWRWEEPATGLGEQALEVFDPLMYGRPAATLSQ
+LAGQADGVGRKLMNLREALMGCTTPVDLTVIWDQLDEALRLVVDAERSLTYAHRVIAEDL
+PLRKQLSRGEPPWVSSTGVNRWLTPKQMKRARRRHDVVPEDQLITYREAVVMADDLIPPL
+LAKTLAAMDKQILLDELLDDLLSRQCPGCGAGAGAYCTTASGRIAEVVHAGRRDASPMMR
+GHMELYMEVRQPNEFVPDPECGRVGPAPWDETLPGV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002968.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002968.fa
new file mode 100644
index 0000000000000000000000000000000000000000..243df90505649e360dbf067f6450904216ed5319
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002968.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_02258
+MTDTFPTPLLRRRASRTLALGGTLALAAAMTGCGPDPDYRQTSEDYAQVCRDETTQERVP
+DEDCDDSAGTSHAHAGHRTGWYFIPLAGGRTVPAVGQRAGGGLTTRPGTGTTTKVPSSGG
+EFAKSGTVSRGGFGSKGGGAGS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002969.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002969.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45dcbe4ef5655b381d5c0918b27f84f0ce50d7a2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002969.fa
@@ -0,0 +1,5 @@
+>NAFOICDF_02270
+MRPLTLTVKNTFQGSHIRFGSQFGTENTNLAVQSGIIGGAANPLSLHQSPLSNSATSDSR
+VDANKTVTTFTFDRPVTSLAFSITDIDSTRNDFADAVAVTSAAAFTSSKADSSSSGLQGV
+GTVADPWRPWTTDNPVNNSATNGNVTVRFTSQVTSFQIHYWNQTAASYASVDGDQKIFIS
+NLSLTYNACA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002970.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002970.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1316cbde67585c50844b402e189003afbc64b73c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002970.fa
@@ -0,0 +1,4 @@
+>NAFOICDF_02274
+MDHRTAAAASPLPSEPAVAAPVGGSDTPLTRFLRAGEAGDAAAARGALHPDVRLVSPMAG
+GAVMRGPDDVALLLGEVYAVLRGLEWVEHYADGRVHTVLGRARALGVALTDAMLVTVAED
+GRVLEIRPHLRPWAGLTAFSAALLPRLLRHPGLLARSTRPD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002971.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002971.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2450a11056f1b72714391bf32813348fc5bc8357
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002971.fa
@@ -0,0 +1,15 @@
+>NAFOICDF_02279
+MSTAQTPREPEHGGLEPTPDQVPERDLREQHAELVERIRAARTAYYQDDAPEISDAEYDR
+LYRALEDLEALHPELASNDSPTQEVGGEASEAFAPVRHGSRMYSLEDLFSLEELETWFLR
+AAGSLAEVRPGRAPRWLVEVKIDGLAVALRYRRGRLVQAATRGDGVTGEDVTRNVMTIAD
+VPQTLTGEGWPEEFEVRGEVFMPSRAFAELNERRAEEGQAPFANPRNAAAGALRQKDPAV
+TAQRPLSMFVHGIGTVEAFGADGQEEVYGMLAGWGLPVSPYTRVVEGADEAALTRVVDVI
+EEYGRRRHELVHEIDGIVLKADAFADQRYLGHTSRVPRWAAAYKYPPEEVHTRLLDIAVN
+VGRTGRVTPFAVMEPAQVAGSTVSMATLHNQDVVKAKGVLIGDMVVLRKAGDVIPEVVGP
+VLPVRERLLAQGEDLREFVMPADCPSCGTPLAPAKEGDVDLRCPNARSCPAQVAGRVEHL
+AGRGAFDVEALGEEAARWLVIGHGPDPAEHEGMVLPEGAGPITAEAQLFDLASGTPEEVT
+GPRGEDGLTDLQRSLGDVRVWREGRTKVDGRMVPSGVFSLKPYFFTAGTAKKPAAPTANT
+LRLFDELEKAKTAPLWRVLVGLSIRHVGPAAARSLATAFGSMTALRAAAEAGERDRLAEI
+DGVGPIIADALIEWFAQDWHREIVDRWAAAGVVMEDEQDADTPRTLEGVTVVVTGSLEGF
+SRDSAKEAILVRGGKASGSVSKKTHFLVAGEAAGSKLEKAEQLGVPVLDEAGFVRLLAEG
+PAAFPSEDADAETVDAAAEGESA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002974.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002974.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d9fb1400a896af6842e64d249e0530c80cf8a64
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002974.fa
@@ -0,0 +1,2 @@
+>NAFOICDF_02320
+MWIIRQGKDFQEEVLVFITAKIFIESPHRLCICPPHHLAYLKKALVEELP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002980.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002980.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4ae7bd4b63f2e22eb797edbceb3130b43b3ecf0a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002980.fa
@@ -0,0 +1,3 @@
+>MHAAABBN_00013
+MVTLDTEHTIHLGAVALESPGTSTLTVYGKIVTTEAPGRPRVAWADVRVEDSELSTGGAF
+LPDARQARALADYFLRLADLMDVETGQG
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002983.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002983.fa
new file mode 100644
index 0000000000000000000000000000000000000000..80bbd36a0b5dc36f0ea9bab77088c3e2ff216c3b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002983.fa
@@ -0,0 +1,4 @@
+>MHAAABBN_00017
+MSTPSRQGHFITVVCAHPRHRGERRWIVTRFMGTADGSPVDWIEIPGTSRAWRAERKHPS
+PDRNAAELGWVSDKPGHRFYYQHGQSRPLFELLNEYGEPRDVSAPIENRVILWCERCARA
+GRTPELRCPEPELWRLLDLLLAAGRESVTVRELIQARQQVRPE
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002984.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002984.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09f02e440557c08d54edeeed47184bfb5e2b487f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002984.fa
@@ -0,0 +1,3 @@
+>MHAAABBN_00089
+MRTRGHGTQHPRHDHVDEFMRPVRFSLMAALAGVTSLDFPTVKEQLDVSDSVLSRQASAL
+ESAGHLVVKKGYVGKRPRTWYSLSAEGAQAWKGHLAALRAIASD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002991.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002991.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c3e8eba974faca96e36ff73f303342130cebf88f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002991.fa
@@ -0,0 +1,3 @@
+>MHAAABBN_00354
+MRTGSVSSTSNGGTSRIALNNGKTYNATNGLAVPANGSVGRTDGTCRLGLDRTEACGTTG
+QSPYSVAGSTGASSTAVTAISLYRSITVSGYGTTVVYLNATGVGTNLSVSAAPLI
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002992.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002992.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c5b03016f0d59b5bc230c5311e218d6c2217f1c1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002992.fa
@@ -0,0 +1,3 @@
+>MHAAABBN_00356
+MEISRRSVATGLAWAVPAVAASTAAPAMAASSCAGYTAGKPLPASAFTLTYLRITNETLG
+RLSNKQVALDFDFRLSDEAAACGRVNLSV
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002995.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002995.fa
new file mode 100644
index 0000000000000000000000000000000000000000..860bb3348ed783961c922458d51e6276e23e580f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002995.fa
@@ -0,0 +1,3 @@
+>MHAAABBN_00364
+MVAAAVQGRADLIVTANLKDFPAEVLGRFNLQAQDPDEFFMNQLDLDPAQVMRSVQVQAA
+ATRNPPLTVAAVLASLERCGAGMFAEAARGQTWRL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002998.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002998.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c3288aaf5f6be9585e029d5579f9eb3196932c32
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002998.fa
@@ -0,0 +1,5 @@
+>MHAAABBN_00500
+MTTTSASQGYRTINPATGELLKSFDNATDQQIADALDASQAAYEQWSRKSVAERAAVVKR
+ISELLAERSKDIAALITTEMGKSLGAAVGEVRYSAQIFGYYADEAEELLADQPIKQFSGQ
+EAFVQRLPLGPLLGIMPWNFPVYQVARFVAPNLVLGNTILLKHAEINPQVAQLLEELFTE
+AGLPEGVYQNVFATHD
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002999.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002999.fa
new file mode 100644
index 0000000000000000000000000000000000000000..55145da887566292c5d6215b2de7e5f375d2263e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0002999.fa
@@ -0,0 +1,2 @@
+>MHAAABBN_00667
+MPGGVVPVALAVAALALALFEGLERHREKVRRSAWT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003002.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003002.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7e4661c6b634bbe1c8c7c4e36d3f0f4e1c8690c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003002.fa
@@ -0,0 +1,3 @@
+>MHAAABBN_01142
+MLAGDGALDGQEQVDAVFRVSRERRAEALPKGLTESTLREVVELLGADPETALSAAEVGE
+RLGISRVTARRYLEHLERIRRVRRSARHGGRGRPEQEYRWAGRT
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003006.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003006.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e522c7508652dd28a5152cc094e55ac8752eb493
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003006.fa
@@ -0,0 +1,6 @@
+>MHAAABBN_01650
+MQLTATETCEQLAGNRGGLALDVLDFSVDFYMEDLVMSDRDRRVAGLVEQGDQLRAVAHP
+KYLDTLDRLMAEPEEIQRIVKSGGGRYTMPMQDIVQSVTGAATDCYQPGEELNRFVENMT
+PIINRIPEYAALEVDGASEGASSTPAASSTSTPTAGSAPASEPTPTPEPTPTLSEETEAA
+AEHEAGDVPMEYQSALRKAYSYEENMDMSKMGIYGQLVSEYGEQFSPEAAQYAIDNMTDV
+DWNANALAKAKSYQEMMDMSPSAIYDQLVSEYGEEFTPDQAQYAIDNLSQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003018.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003018.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b300615df9f7860b1c6b220ec407f006b021cd7a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003018.fa
@@ -0,0 +1,5 @@
+>MHAAABBN_02028
+MDTVTTTTPARQRLLDAVARLFYAEGMVATGIDTITAEAGVARKRLYNNFASKQDLMLAY
+IRGRHEEWLELFQDRLDRAGSPRERVLAVFDAYLDHAEAAYAHGFRGCGLLNAAEFRAGS
+AGREAVREHKEQVEAILTDHLTEAGCADPAGTAEHFSFLLEGAMSRAGLEGRSDRLLRAR
+RIAETLLDAR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003019.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003019.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f846c6aa060e28e5d92ecbf6a9aaf8bbca7fbc48
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003019.fa
@@ -0,0 +1,5 @@
+>MHAAABBN_02173
+MRIEVVTGTDTDVGKTWGTAALAARALVAGLRVHVDKPVQTGVAPGEAGDVETVRDLVAA
+AAASGALDAAAPARLTVSEGARVGPAMAPVDAVAHAGEGTPPLPPLGEQLGRWRGLAAGV
+DHLLIEGAGGITVAWTEADEGPVDAVRALRAAGLDAGLTVVARPGLGTQNHARLTVEHAA
+ARGVAPERILVSGVAADPDPVERANLVFLARLAGAHGAVLETVPRGTPPRVMSVR
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003022.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003022.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e209f30f5ea03134d132a8b74887dca96920b744
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003022.fa
@@ -0,0 +1,4 @@
+>MHAAABBN_02216
+MYGDGFAEERSWGINDGPRVGNVGSSWAPDRGFFLEVGPCGIDNLIVGDLTPRQARTLGS
+RLLEVADRIEELQAEDVRDAVRAIASKKGGGTITDLARAADRLGVQVVTMGAAWEAAWAE
+LGGEQ
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003033.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003033.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b25b3d182a7f31601203ee848809a0dcfbb0ac0f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003033.fa
@@ -0,0 +1,2 @@
+>MHAAABBN_02231
+MAPTLYSPREIAEMFGVSTRRINSLIREGALPVYVLGPRTRRIDVQAAREALALERP
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003034.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003034.fa
new file mode 100644
index 0000000000000000000000000000000000000000..50f8bd14fa9880b602ff1188d65853501890bba6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003034.fa
@@ -0,0 +1,3 @@
+>LFPAFLNI_00078
+MRIMTVCLGNICRSPAAEAVLNRKLAEAGLDDVEVTSAGTSDEHVGARPHHLTREVGGEL
+G
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003040.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003040.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8aca0dfc56fc65d59468cfc230f2bd7090c80a34
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003040.fa
@@ -0,0 +1,10 @@
+>LFPAFLNI_00163
+MSTQEISASIDHEDDSAVVIVGSGAGGGTLAHELVEKGIKVVLLEAGPYLKNEDYEQDEW
+AAFNQMAWLDPRTTSGSFRLARDFPNLPAWIVKAVGGTTTHWSGATPRFKAHEFKARSTY
+GRIDGANLLDWPITLSDLEPYYERAEMKMGSTHRQGRPPLPANNNYKVLANGAERLGYRH
+YATGPYATNAEPYDGRPASIQDGFNFQGDKHGSKWSIMVSEIPKSLRTGLLDLRPESQAV
+QITHSPEGRVDGVLYSDAEGNLHRQKARIVAVAGNAIETPRLLLLSASPLFPDGLANSSG
+QLGRNYMRHTTGSVYAQFDEPVNMYRGETMAGLIADESRHDVDRGFAGGYYMETISLGPA
+FLASFADPGAWGPDFTALLDGYRNTAGLWIVGEDMPQETNRVSLNTTVTDRLGLPVPNVH
+FDDHPNDVAMREHGYQQGSLLYEAVGSVSAHHAPPYPSTHNLGTARMSERPEDGVVNQFG
+QAHDVPNLFISDGSQFTTGAAANPTLTIVALAIRQAEYIADQMAASEL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003044.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003044.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e7fd913dcf0fc0c7b0586beca03c02430ec71735
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003044.fa
@@ -0,0 +1,2 @@
+>LFPAFLNI_00186
+MHQRGRMRQEVTREHPGPGSVPLGLSTLGRIGQVLGLSVDGIRAIARLL
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003045.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003045.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bd47c5578b4c68867ad067f6dd4572f602e00a97
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003045.fa
@@ -0,0 +1,7 @@
+>LFPAFLNI_00513
+MTGVESAHSKVPVRSRKSILLANSDMTYRGGTQAWIRQMASTLQSHHDVDVFSLEGAPLE
+FTAFRPEKYYDIALVNHWTTAQALRGARIHTRITTVHGVIPFEEVPVLGSDAYVSVSEAV
+QNHIPYRSMVIRNPIDFAHFSPDPARLMSPVPRRVAFVSNRQGDALPILREACDRAGLEL
+RVVGRETSVEDPREVYLWADVVVGIARVAMEALACGRNVLCFDYQGCHGMATRERLPTLW
+QSNFGGHRPGVWPTADEVARALLEGYDPRRTLRSALLAEHDPERVARSYLRLAETVGSQR
+VARLVRAAPRQVMSPKITRMVAAIRRRPSEVRLAS
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003046.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003046.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4d9ef52770f71355b1981127bbe8b548adc29782
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003046.fa
@@ -0,0 +1,7 @@
+>LFPAFLNI_00775
+MSIVIGSLGGIFLWLIYQAIGTRWPEVYATARDSLDLMPRRSSVKYLLIYRGIPTFSVTV
+LALNLAVESGGDPYWTSAFVFWTYSTLAEIRSTFSPKGALRQLSTVNTVYLSASVVVTTI
+YCSVAVLVYPHFSVLVPSVRELVIALWTALFASVLAISFQRFNTRSGPDVQMEIDYSIKD
+IGQKTWSQIDSICMRENIDPCLIKALAAAEAQQRPRWIRQAERVAGRLFGGGTFGVGQWP
+SSRPIDDLTSIEFRAKQLAPVGLTPHECDIAEVYDFLDIDYFIYSWNSDESFADSARGFY
+SAFRRAKMVEHVAESDA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003049.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003049.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c843ee541683a8bfed9a0ee8c72a4539a3fb30c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003049.fa
@@ -0,0 +1,2 @@
+>LFPAFLNI_01060
+MDVLSPVFEITTLVVLGVILLLDLLYVARRPHEPSM
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003060.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003060.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6e0f6319afbb77146a119c28c6a2a4317c50c1e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003060.fa
@@ -0,0 +1,6 @@
+>LFPAFLNI_02033
+MTPSPPSLRSARHALPATTAALTLALTLAGCSGGGGPATASGTTPSPAASSDTTPSPSST
+SETTTPSAGGPASGTTAPSTPAPASGSATQGSGGGSTAGAGFVPEGADPARNGALPLSEG
+FLAALPEAAVTHRAGSPTEDPLARALEGVELPGTPTTDVNVIASELQGLQTPGEGGAAMG
+GERPEGTLRLMLLCDDPDAGPSSVGILGADGFAAYQPLGWSDRCGGYVVMVPESDAEDLV
+VSAEAPEGTRYRLSVITDHDPVAN
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003061.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003061.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cddfe0f8116cc6a212d32859db768975f953c1d0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003061.fa
@@ -0,0 +1,4 @@
+>LFPAFLNI_02035
+MSHFAPQRRSTRTAAFSATFAAAAIALTACGGDATPSGPTSAPASASGGAESPAGEATAA
+SSVSAEDRVDPTQTTEVSAVTPRILLSHEDGLTLLDAESGEVVKEQDITGFKRLSNAGNG
+KDVLVTTGKGWEVCSPPASRPRPTAITSTTTSPRPA
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003064.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003064.fa
new file mode 100644
index 0000000000000000000000000000000000000000..583ec3d47cca47e869ae4d8f355eba7e33f9bf75
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003064.fa
@@ -0,0 +1,5 @@
+>LFPAFLNI_02207
+MWALENGGGPLTTTGSRMRTITLTTQKPVAFELQRVWVTYTRQDLPEGTAFYDVSDGLGA
+GEREPARFVAALGHEGRATNRFAAKHVSDFDLPQKEAPVPYRLSDATHLDIDLLLSFLTE
+GVYTYSVEVEVAVNGVSRTLKVEKAPIGDQELPLKMVFAREPAMVHEEFTEYPHTRWLPG
+PRPEM
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003066.fa b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003066.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b8e42c4ba6a971e4a90ca33e9302168ab93ace6c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0003066.fa
@@ -0,0 +1,4 @@
+>LFPAFLNI_02210
+MNVPERGEARMRDAIHHAMALPQTALGTHCFVWGEVTTVNHTSAEPPHWFLNVRSGTDRL
+FAFHMSAATAKAVVEAMNHQRGLRWQSLFDAVDAQFMVFGYLKVAKNGVPMVSVKELSHL
+SLRVP