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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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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