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experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000007.fa

@@ -0,0 +1,100 @@
+>ACLBLIBL_01214
+MACRLVGLSRSAYRRPLKGDTVADPDRALRQWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>MOLHKGIG_00157
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>MOLHKGIG_01034
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>MOLHKGIG_01292
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>MOLHKGIG_01384
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETGDSQNVRTE
+>MOLHKGIG_02077
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>MHAAABBN_01011
+MVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIK
+ICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWA
+GTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRH
+SSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>MHAAABBN_01104
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>MHAAABBN_01112
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>MHAAABBN_01114
+MSERIACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEG
+WVVNHKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPI
+KICSIVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADW
+AGTRTGLSYIPPGSPWRNGYVESFNSRIRDECLNINRFYSLLHAQVIIGDWKDEYNHHRR
+HSSLGYLTPAEYARQCTHQMETDDSQNVRTE
+>MHAAABBN_02023
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMEIGDSQNVRTE
+>LFPAFLNI_00588
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVASRGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>LFPAFLNI_00590
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAVVDWAGTR
+TGLWADPVS
+>LFPAFLNI_01250
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE
+>LFPAFLNI_01339
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTH
+>LFPAFLNI_01885
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVAARGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLGHV
+>LFPAFLNI_02205
+MACRLVGLSRSAYRRPLKGDTVADPDRALREWLRAWAKDHPRYGYRRAYHDARAEGWVVN
+HKKIQRLWRDEGLRVPQRRRRKRVGSSTVDAPTADAPNVVWAVDFQFDADEHGRPIKICS
+IVDEHTRECIGGLVERSITADRLTAHLEDLVASRGAPAVLRSDNGPEFISEAMADWAGTR
+TGLSYIPPGSPWRNGYVESFNSRIRDECLNINSFYSLLHAQVIIGDWKDEYNHHRRHSSL
+GYLTPAEYARQCTHQMETDDSQNVRTE

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000008.fa

@@ -0,0 +1,83 @@
+>MOLHKGIG_00711
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>MOLHKGIG_01398
+MEGSLEGSHGDRVRLEDGRGHRGGLHHYPGLNSFTTWDPGASSIPAPTQQSLRTLEWLSR
+RENLVVCGPSGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARI
+LRADLIVIDDIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATAT
+VDRLLHHAHVCQTTGDSVRMTQAMAGKGVMPLN
+>MOLHKGIG_01502
+MAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIGLLPVADDAAEGLYRIVDAA
+YEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQTTGDSVRMTQAMAGKGVMP
+LN
+>MOLHKGIG_02225
+MLWKVRSKAPTVTASVSKMVVATGEGYTTIRDSTPKTLATATVDRLLHHAHVCQTTGDSV
+RMTQAMAGKGVMPLN
+>MOLHKGIG_02227
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTVKSLEVV
+>MHAAABBN_00092
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>MHAAABBN_00343
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>MHAAABBN_01013
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>MHAAABBN_01394
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>MHAAABBN_02284
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>LFPAFLNI_00606
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>LFPAFLNI_01016
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPIADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>LFPAFLNI_01158
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPIADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>LFPAFLNI_01349
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN
+>LFPAFLNI_02164
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAGFPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGPSGT
+GKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVIDDIG
+LLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAHVCQ
+TTGDSVRMTQAMAGKGVMPLN

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000012.fa

@@ -0,0 +1,42 @@
+>ACLBLIBL_00720
+MLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATCSPEDV
+CRYL
+>ACLBLIBL_00722
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGSSPMKWC
+SG
+>MOLHKGIG_00156
+MKGAAQLDFIRRGQAVGLTLAQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQ
+LRTTIADLREDAAAGDPATCSPEDVCRYL
+>MOLHKGIG_00159
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLGPAVG
+>MOLHKGIG_01075
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAVGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATC
+SPEDVCRYL
+>MOLHKGIG_02063
+MRIGEVAAASGVTTKALRFYEERGLLPQADRATNGYRDYPEDTIVRLEFIRRSQVAGLTL
+AEILDILQIRDAGTAPCGHVRDQLAEHLTNLDRHIAELTALRETVAGLHGTAAAGDPAQC
+NAEVICSYL
+>NAFOICDF_02223
+MRIGEVAAASGVTTKALRFYEERGLLPQADRATNGYRDYPEDTIVRLEFIRRSQVAGLTL
+AEILDILQIRDAGTAPCGHVRDQLAEHLTNLDRHIAELTALRETVAGLHGTAAAGDPAQC
+NAEVICSYL
+>MHAAABBN_00297
+MRIGELAERAGTTAKTLRFYEEQGLLPPAERTPSGYRDYAPETAARIDFVHRGQAAGLTL
+AQIRQILDIRDDGAAPCEHVRDLLDARLAEIEQQIAQLAALRDTITELRRDAAQPDPDSC
+SADQVCRYL
+>MHAAABBN_00338
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC
+SPEDVCRYL
+>MHAAABBN_00345
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC
+SPEDVCRYL
+>MHAAABBN_00794
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC
+SPEDVCRYL
+>LFPAFLNI_01024
+MLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATCSPEDV
+CRYL

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000017.fa

@@ -0,0 +1,57 @@
+>ACLBLIBL_01236
+MRVHRRTVPVEHRSVVHGLTVTSPERTWADLCAVRPRWDEADLVAAGDHLVRHPWAGGGR
+LPPRTTVERLAEVLEALAPFHGVGRARAALGRVRVGADSAMETHARLALIDAGLGEPLLQ
+HKVAPDDPALAESDLYFADLRVALEYDGEHHLGRQQQARDARRDRRLLSYGVTPMRITAA
+DHAEGYRSVIAQLQQRRRAHDSPSEETARGES
+>MOLHKGIG_01559
+MPRVVTPLPPDQPAVLLATDLARLGLPPDRARRSDLERVGQGFHRQRARPGTGWADLGLP
+EPGHGFSPDHLAALLRRRPDAVLSHETAAHLHALPMPTRAWRRRDPATGELEADPPVHLT
+VARGTRRVRRAGLMDHRRPLAPEFVTLVHGLRVTTVDRTWLDLCSLTPPWTFEDLVAAGD
+HAVRHPWTPAGRTDPATTIAALRSALHASGRFHGRPAAREALDSVRVGADSPPETRLRLA
+LVAGGLPEPELQAALEPGDPVSPVADLAYRHVRLALQYDGAGHRTREQQARDARRDRYGQ
+ARGWTTLRVTWADGREDFRGVVAVVRRRLGPSAST
+>MOLHKGIG_01658
+MPFAPDLPLVPVFTTRDVLERGLPPSRVRRSDVLRLARGIHRRRDMPLRTWESAGLPPPH
+HGVGLDLLTALLRSRPDAVLSHETAAHLHGLPLPPGGATRRAAVEITLHRGTARARIPGV
+MEHRRPLPAGHVTSVLGLRVTTPERTWLDLCSIGHPWDEASLVSAGDHLVRHPWSPRGRR
+PPITTVTALHEAMRPLGRFVGRPRATAALERVRVGADSPQETRLRLALVEAGLGEPALQH
+VFDPGRRDAPEADLWFEDCRLVLQYDGEVHRSAEQHARDARRDQYYAERGQMTLHVTGRD
+VGEGYARVIEAVLRRRAQVSNGWDA
+>MOLHKGIG_01845
+MPRRPAPLPPALAGRVFTRREALDRLSLSSDRLRSLDLRQVTHGAHRAVVDVPGSWAALG
+YPRPVAALPPEEAAVVVALTRGVASHLTAARLHGLVLPWWAEEDMRVHVSRPHRTGRTGR
+AGVACHGRTVPAEDRVEVHGVPVTSLERTWVDLCSLLRPDQVADAVVAGDALVNRPWVDG
+SRLPPRTTASRLSAALERAGRFKGVRVARAALALIRVGADSPPETRLRLALLDAGLPEPR
+LQAQLVSPAGERTDADMVVERSRVALHYDGGHHRTPEQQRRDARRDRLWQEAGHLSITVM
+GADLAEDFRTVVAAVVRHDRAARATSTISAPAPAAGLSNVKSGEWALSNVG
+>NAFOICDF_01147
+MLERVRVGADSAVVSLARLALVDAGLGEPLLQHRLDPWDPDCPETHMFSPELAVALEYDG
+GGHLTPAQQARDARRDRRLPARGVTPLRNTAEDHAEGYRRLIAQLQDRRRGR
+>MHAAABBN_01269
+MPRVVTPLPPDQPAVLLATDLARLGLPPDRARRSDLERVGQGFHRQRAHPGTGWADLGLP
+EPGHGFSPDHLAALLRRRPDAVLSHETAAHLHGLPMPARAWRRRDPATGELDVDPPVHLT
+VARGTRRVRRAGLMDHRRPLAPEFVTHVHGLRVTTVDRTWLDLCSLTPPWTFEDLVAAGD
+HAVRHPWTPAGRTDPATTIAALRSALHASGRFHGRPAAREALDSVRVGADSPPETRLRLA
+LVAGGLPEPGLQAALEPEDPFSPVADVAYRHVRLALQYDGAGHRTREQQARDARRDRYGQ
+ARGWTTLRVTWADGREDFRGVVAVVRRRLGHSAST
+>MHAAABBN_01363
+MSFAPDLPLVPVFTTRDVLERGLPPSRVRRSDVLRLARGIHRRRDMPLRTWESAGLPPPH
+HGVGLDLLTALLRSRPDAVLSHETAAHLHGLPLPPGGATRRAAVEITLHRGTARARIPGV
+MEHRRPLPAGHVTSVLGLRVTTPERTWLDLCSIGHPWDEASLVSAGDHLVRHPWSPRGRR
+PPITTVTALHEAMRPLGRFVGRPRATAALERVRVGADSPQETRLRLALVEAGLGEPTLQH
+VFDPGRRDAPEADLWFEDCRLVLQYDGEVHRSAEQHARDARRDQYYAERGQMTLHVTSRD
+VGEGYARVIEAVLRRRAQVSNGWDA
+>LFPAFLNI_01486
+MPRVVTPLPPDQPAVLLATDLARLGLPPDRARRSDLERVGQGFHRQRAHPGTGWADLGLP
+EPGHGFSPDHLAALLRRRPDAVLSHETAAHLHGLPMPARAWRRRDPATGELDVDPPVHLT
+VARGTRRVRRAGLMDHRRPLAPEFVTHVHGLRITTVDRTWLDLCSLTPPWTFEDLVAAGD
+HAVRHPWTPAGRTDPATTIAALRWALHASGRFHGRPAAREALDSVRVGADSPPETRLRLA
+LVAGGLPEPELQAALEPGDPFSPVADLAYRHVRLALQYDGAGHRTREQQARDARRDRYGQ
+ARGWTTLRVTWADGREDFRGVVAVVRRRLSPSAST
+>LFPAFLNI_01588
+MSFAPDLPLVPVFTTRDVLERGLPPSRVRRSDVLRLARGIHRRRDMPLRTWESAELPPPH
+HGVGLDLLTALLRSRPDAVLSHETAAHLHGLPLPPGGATRRAAVEITLHRGTARARIPGV
+MEHRRPLPAGHVTSVLGLRVTTPERTWLDLCSIGHPWDEASLVSAGDHLVRHPWSPRGRR
+PPITTVTALHEAMRPLGRFVGRPRATAALERVRVGADSPQETRLRLALVEAGLGEPTLQH
+VFDPGRRDAPEADLWFEDCRLVLQYDGEVHRSAEQHARDARRDQYYAERGQMTLHVTSRD
+VGEGYARVIEAVLRRRAQVSNGWDA

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000020.fa

@@ -0,0 +1,109 @@
+>ACLBLIBL_00405
+MSTPHHHDHPTDQTAEHPDPNPHAGHANHTDHAAHHPADAATHGQAMPQGHAHSALDEDH
+QVHDHGQHAGHSTAMFKNRFWVSLVLSIPVVFFSHMVGQLLGYHVPEFPGSAWIAPVLGT
+VIYLYGGMPFLKGGLTELRARQPGMMLLIAMAITVAFVASWVTTLGIGDLMLDFWWELAL
+LVVIMLLGHWMEMRALGAASSALDALAALLPEEAEKVVDGDTITVPITELAVGDVVLVRA
+GARVPADGTILEGAAEFDEAMITGESKPVLRQAGDTVVAGTVATDNTVRVKVAAVGTDTT
+LAGIQRMVADAQASSSRAQALADRAAALLFWFALVAAIITAIVWTVMGQPTDAVTRTVTV
+LVIACPHALGLAIPLVIALSTEKAAKSGVLIKDRMALERMRTIDVVLFDKTGTLTEGAHV
+VTAVTAMPGVSEAELLAVAAAAEADSEHPVARAIVTAAGQHPQASTLRKRGTDFSAAMGR
+GVRATVDGSEILVGGPNMLRELNLTVPAEITEHTASWTARGAGVLHVLREGSVIGAVALE
+DKVRPESRAAVAALHARGIKVAMITGDARQVAEAVGADLGIDEVFAEVLPQDKDTKVTEL
+QSRGLSVAMVGDGVNDAPALARAEVGIAIGAGTDVAMESAGVVLASNDPRAVLSMIELSQ
+ASYTKMIQNLVWATGYNVLAVPLAAGVLAPIGFVLSPAVGAILMSASTIVVALNAQLLRR
+INLDPGHLAPLGAPRPEAALQPATS
+>MOLHKGIG_00633
+MSTPHHHDHPTDQTAEHPDPNPPAGHANHTDHAAHHPADAAAHGQAMPQGHAHSALDEDH
+QVHDHGQHAGHSTAMFKNRFWVSLVLSIPVVFFSHMVGQLLGYHVPEFPGSAWIAPVLGT
+VIYLYGGMPFLKGGLTELRARQPGMMLLIAMAITVAFVASWVTTLGIGDLMLDFWWELAL
+LVVIMLLGHWMEMRALGAASSALDALAALLPEEAEKVVDGDTITVPITELAVGDVVLVRA
+GARVPADGTILEGAAEFDEAMITGESKPVLRQAGDTVVAGTVATDNTVRVKVAAVGTDTT
+LAGIQRMVADAQESSSRAQALADRAAALLFWFALVAAIITAIVWTAIGQPTDAVTRTVTV
+LVIACPHALGLAIPLVIALSTEKAAKSGVLIKDRMALERMRTIDVVLFDKTGTLTEGAHV
+VTAVTAMPGVSEAELLAVAAAAEADSEHPVARAIVTAAGQHPQASTLRKRGTDFSAAMGR
+GVRATVDGSEILVGGPNMLRELNLTMPAEITEHTASWTARGAGVLHVLREGSVIGAVAVE
+DKVRPESRAAVAALHARGIKVAMITGDARQVAEAVGADLGIDEVFAEVLPQDKDTKVTEL
+QSRGLSVAMVGDGVNDAPALARAEVGIAIGAGTDVAMESAGVVLASNDPRAVLSMIELSQ
+ASYTKMIQNLVWATGYNVLAVPLAAGVLAPIGFVLSPAVGAILMSVSTIVVALNAQLLRR
+IDLDPEHLAPLERPRSQAALQPAAVS
+>MOLHKGIG_01289
+MTDPTTHHHDHAGVATTESGHRDDSRAENEDHTMEHGDHAGHGHHGGGHAGHGDHVGQFR
+RLFWINLIIAIPVVAFSPMFAMLLGYSVPSWAGWVAAVLGSVMYAWGGTPFLTGAVSELK
+SRQPGMMLLIALGITVAFLASWAATVGLVHPELEFWWELALLIVIMLLGHWIEMRSLAQT
+TSALDSLAALLPDEAERIEGDDVVKVDPAELRVGDVVIVRPGGSVPADGTIVDGRADMDE
+SMITGESHPVARGEGENVTAGTVATDSGLRVEITATGDDTALAGINRLVAEAQGSSSRAQ
+RIADRAAALLFWFALGAALITAVVWTLFGLPDDAVVRTITVLVIACPHALGLAIPLVVSI
+ATERAARGGVLIKDRLALESMRQVDAVLFDKTGTLTKGEPTVTGVEPTGGLNAEQLLALA
+ASAEADSEHPLARSIVTAAKEKGLAVEPASGFTSSPAVGVTATVADHEIRVGGPRLLEET
+GQDEIGVADEWRAEGAIILHVLRDGKVIGGLKLADEVRPESRDAVDALHQLGVEVVMITG
+DAEAVANEVGRELGIDRVFAGVRPEDKSAKVDQLQKEGKKVAMVGDGVNDAPALAQADVG
+IAIGAGTDVAIASAGVILASSDPRSVLSVIQLSRAAYRKMRQNLWWAAGYNLLSVPLAAG
+VLAPVGFVMPMSVGAILMSISTVVVALNAQLLRRIDLAPAASTRSVLEHQK
+>NAFOICDF_00711
+MTDPNSQQHHGHETDTPAHGEHHHGSVSAHASADAHGTREGQHTGHQGHAMDHGQHSGHT
+GLDEHGGHDEHAQHGGYGDHSGHGGHGDHVGQFRRLFWINLVIAIPAVALSPMFAMLLGY
+EVPGWAGWVAAALGTVMYVWGGRPFLTGAVSELKSRKPGMMLLIALAITVAFFASWAATL
+GLVHHELEFWWELALLIVIMLLGHWIEMRSLAQTTSALDSLAALLPDEAERVEGENVVKV
+APADLDVGDVVLVRPGGSVPADGTIVDGRAEMDESMITGESRPVSRGEGQTVTAGTVATD
+SGLRVEITATGDDTALAGINRLVAEAQNSSSRAQRIADKAAAWLFWFALGAALVTAVVWT
+LIGMPDEAVVRTITVLVIACPHALGLAIPLVVSIATERAARGGVLVKDRLALESMRQVDA
+VLFDKTGTLTKGEPTVTGVEPTGELDADQVLALAASAEADSEHPLAKAIVTAAKDKGFAL
+QQASGFSSSPAVGVTATVSGQEVRVGGPRLLEETGQHEVGTAEAWRSEGAIILHVLRGGQ
+VVGGLRLADEVRPESRYAVDALHALGVEVVMITGDAEAVANEVGKELGIDRVFAGVRPED
+KSAKVSQLQEEGKRVAMVGDGVNDAPALAQADVGIAIGAGTDVAIASAGVILASSDPRSV
+LSIIQLSRRAYGKMKQNLWWAAGYNLLSVPLAAGILAPVGLVLPMSIGAILMSASTVVVA
+LNAQLLRRIDLTPEASTRSVLERQK
+>NAFOICDF_02196
+MSTPHHHDHPTDQTAEHPDPNPHAGHANHTDHAAHHPADAATHGQAMPQGHAHSALDEDH
+QVHDHGQHAGHSTAMFKNRFWVSLVLSIPVVFFSHMVGQLLGYHVPEFPGSAWIAPVLGT
+VIYLYGGMPFLKGGLTELRARQPGMMLLIAMAITVAFVASWVTTLGIGDLMLDFWWELAL
+LVVIMLLGHWMEMRALGAASSALDALAALLPEEAEKVVDGDTITVPITELAVGDVVLVRA
+GARVPADGTILEGTAEFDEAMITGESKPVLRQAGDTVVAGTVATDNTVRVKVAAVGTDTT
+LAGIQRMVADAQESSSRAQALADRAAALLFWFALVAAIITAIVWTAIGQPTDAVTRTVTV
+LVIACPHALGLAIPLVIALSTEKAAKSGVLIKDRMALERMRTIDVVLFDKTGTLTEGAHV
+VTAVTAMPGVSEAELLAVAAAAEADSEHPVARAIVTAAGQHPQASTLRKRGTDFSAAMGR
+GVRATVDGSEILVGGPNMLRELNLTMPAEITEHTASWTARGAGVLHVLREGSVIGAVAVE
+DKVRPESRAAVAALHARGIKVAMITGDARQVAEAVGADLGIDEVFAEVLPQDKDTKVTEL
+QSRGLSVAMVGDGVNDAPALARAEVGIAIGAGTDVAMESAGVVLASNDPRAVLSMIELSQ
+ASYTKMIQNLVWATGYNVLAVPLAAGVLAPIGFVLSPAVGAILMSASTIVVALNAQLLRR
+INLDPGHLAPLGAPRPEAALQPATS
+>MHAAABBN_01008
+MTDPTTHHHDHAGVATTESGHRDDSRAENEDHTMEHGDHAGHGHHGGGHAGHGDHVGQFR
+RLFWINLIIAIPVVAFSPMFAMLLGYSVPSWAGWVAAVLGSVMYAWGGTPFLTGAVSELK
+SRQPGMMLLIALGITVAFLASWAATVGLVHPELEFWWELALLIVIMLLGHWIEMRSLAQT
+TSALDSLAALLPDEAERIEGDDVVKVDPAELRVGDVVIVRPGGSVPADGTIVDGRADMDE
+SMITGESHPVARGEGENVTAGTVATDSGLRVEITATGDDTALAGINRLVAEAQGSSSRAQ
+RIADRAAALLFWFALGAALITAVVWTLFGLPDDAVVRTITVLVIACPHALGLAIPLVVSI
+ATERAARGGVLIKDRLALESMRQVDAVLFDKTGTLTKGEPTVTGVEPTGGLNAEQLLALA
+ASAEADSEHPLARSIVTAAKEKGLAVEPASGFTSSPAVGVTATVADHEIRVGGPRLLEET
+GQDEIGVADEWRAEGAIILHVLRDGKVIGGLKLADEVRPESRDAVDALHQLGVEVVMITG
+DAEAVANEVGRELGIDRVFAGVRPEDKSAKVDQLQKEGKKVAMVGDGVNDAPALAQADVG
+IAIGAGTDVAIASAGVILASSDPRSVLSVIQLSRAAYRKMRQNLWWAAGYNLLSVPLAAG
+VLAPVGFVMPMSVGAILMSISTVVVALNAQLLRRIDLAPAASTRSVLEHQK
+>LFPAFLNI_00598
+MSTPHHHDHPTDQTAEHPDPNPHAGHANHTDHAAHHPADAATHGQAMPQGHAHSALDEDH
+QVHDHGQHAGHSTAMFKNRFWVSLVLSIPVVFFSHMVGQLLGYHVPEFPGSAWIAPVLGT
+VIYLYGGMPFLKGGLTELRARQPGMMLLIAMAITVAFVASWVTTLGIGDLMLDFWWELAL
+LVVIMLLGHWMEMRALGAASSALDALAALLPEEAEKVVDGDTITVPITELAVGDVVLVRA
+GARVPADGTILEGAAEFDEAMITGESKPVLRQAGDTVVAGTVATDNTVRVKVAAVGTDTT
+LAGIQRMVADAQESSSRAQALADRAAALLFWFALVAAIITAIVWTAIGQPTDAVTRTVTV
+LVIACPHALGLAIPLVIALSTEKAAKSGVLIKDRMALERMRTIDVVLFDKTGTLTEGAHV
+VTAVTAMPGVSEAELLAVAAAAEADSEHPVARAIVTAAGQHPQASTLRKRGTDFSAAMGR
+GVRATVDGSEILVGGPNMLRELNLTMPAEITEHTASWTARGAGVLHVLREGSVIGAVAVE
+DKVRPESRAAVAALHARGIKVAMITGDARQVAEAVGADLGIDEVFAEVLPQDKDTKVTEL
+QSRGLSVAMVGDGVNDAPALARAEVGIAIGAGTDVAMESAGVVLASNDPRAVLSMIELSQ
+ASYTKMIQNLVWATGYNVLAVPLAAGVLAPIGFVLSPAVGAILMSVSTIVVALNAQLLRR
+IDLDPEHLAPLERPRSQAALQPAAVS
+>LFPAFLNI_01247
+MTDPTTHHHDHAGVATTESGHRDDSRAENEDHTMEHGDHAGHGHHGGGHAGHGDHVGQFR
+RLFWINLIIAIPVVAFSPMFAMLLGYSVPSWAGWVAAVLGSVMYAWGGTPFLTGAVSELK
+SRQPGMMLLIALGITVAFLASWAATVGLVHPELEFWWELALLIVIMLLGHWIEMRSLAQT
+TSALDSLAALLPDEAERIEGDDVVKVDPAELRVGDVVIVRPGGSVPADGTIVDGRADMDE
+SMITGESHPVARGEGENVTAGTVATDSGLRVEITATGDDTALAGINRLVAEAQGSSSRAQ
+RIADRAAALLFWFALGAALITAVVWTLFGLPDDAVVRTITVLVIACPHALGLAIPLVVSI
+ATERAARGGVLIKDRLALESMRQVDAVLFDKTGTLTKGEPTVIGVEPTGGLNAEQLLALA
+ASAEADSEHPLARSIVTAAKEKGLAVEPASGFTSSPAVGVTATVADHEIRVGGPRLLEET
+GQDEIGVADEWRAEGAIILHVLRDGKVIGGLKLADEVRPESRDAVDALHQLGVEVVMITG
+DAEAVANEVGRELGIDRVFAGVRPEDKSAKVDQLQKEGKKVAMVGDGVNDAPALAQADVG
+IAIGAGTDVAIASAGVILASSDPRSVLSVIQLSRAAYRKMRQNLWWAAGYNLLSVPLAAG
+VLAPVGFVMPMSVGAILMSISTVVVALNAQLLRRIDLAPDASTRSVLEHQK

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000026.fa

@@ -0,0 +1,42 @@
+>ACLBLIBL_00124
+MSEQTTPDGAESPIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIGAI
+LLSGSPKAFAAGADIKEMATKEFSEMYAADWFAGWDGLTRARTPIVACVTGYALGGGCEL
+AMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGRMIGAEEAER
+IGLVSRVVADEKALEEAQEVAAAIASKSKPAAWMAKETVNAAFETTLAQGIAFERRVFHS
+AFATTDQKEGMDAFANKREAGWQHR
+>MOLHKGIG_00245
+MSEQTTPDGAESPIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIGAI
+LLSGSPKAFAAGADIKEMATKEFSEMYAADWFAGWDGLTRARTPIVACVTGYALGGGCEL
+AMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGRMIGAEEAER
+IGLVSRVVADEKALEEALEVAATIASKSKPASWMAKEAVNAAFETTLAQGIAFERRVFHA
+AFATADQKEGMDAFTAKREAGWQHR
+>NAFOICDF_00093
+MNEQNRTEAAEAEQPVIVGRDGRVGRIQLNRPKALNALNAATMEAVVAAAVEMDADPEVG
+AILLLGSAKAFAAGADIKEMKDKDAADMYAADWFRRWEDLARLRTPIVACVQGYALGGGC
+ELAMMADVLVAGRSAKFGQPEITLGVLPGMGGSQRLTKSVGKAKAMDMVLTGRMVEAEEA
+ERMGLVSRLVEDEDAVATAEEVAATIAGFSKPVAQMNKEVVLNAFETPLTQGLVFERRVF
+HGVFSSEDQAEGMAAFAEKRSPVWKHR
+>MHAAABBN_00096
+MSTGLHIETVDRIGIIRLDRPAELNALTFATVEEIAAQVQRWEVDGETDGVVITGSGQKA
+FAAGADIRELQHKSVQEMTARGMQHAMTALRESSLISVAAVNGLALGGGFELALSCDIRL
+ATPQASFGLPELGLGIIPGAGGTQLLTRYTNASVASYHILTGQPISADRAHQLGLVSELH
+EAEDLMAAAMEVIGTIASKGPLARQLAKRAIHGAAHAGMDSGLEIELLAQAAIFGTQERE
+EGLNAFLERRTPSFIPRPRPRKD
+>MHAAABBN_00100
+MTDRIRTSVEQGVCTITLNRPGALNALENTMIATIVAELERAGADPDVRAILLRGEGKAF
+CAGDDLVDMGTEEHPESPDLVERYSRGYPAIVERMLTLEKPIVASVRRYALGAGLEMALA
+ADLIVAEPQAKLGLPFVLRGIAAGTSLLPKRAPVQLVQRMLYLGEMITAEDAHRMGVVGH
+LAEDEDVDELALATARRLAVGATRAIGLMKTALRTSETLSARDALAVQVGATAASVLTED
+FTEGKVAFTQKRDPEFGGR
+>MHAAABBN_02257
+MSEQTTPDGAESPIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIGAI
+LLSGSPKAFAAGADIKEMATKEFSEMYAADWFAGWDGLTRARTPIVACVTGYALGGGCEL
+AMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGRMIGAEEAER
+IGLVSRVVADEKALEEALEVAATIASKSKPASWMAKEAVNAAFETTLAQGIAFERRVFHS
+AFATADQKEGMDAFTAKREAGWQHR
+>LFPAFLNI_00245
+MSEQTTPDGAESPIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDLEIGAI
+LLSGSPKAFAAGADIKEMATKEFSEMYAADWFAGWDGLTRARTPIVACVTGYALGGGCEL
+AMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGRMIGAEEAER
+IGLVSRVVADEKALEEAKEVAAAIASKSKPAAWMAKETVNAAFETTLAQGIAFERRVFHS
+AFATADQKEGMDAFTAKREAGWRHR

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000027.fa

@@ -0,0 +1,68 @@
+>ACLBLIBL_00171
+MSALRRWSALAVLVLPVLLISIDMSVLGIAVPALSADLDPTSGQLLWIIDLYSFLLAGLL
+IFMGSLGDRIGRRRILLIGAPLFGAASLAAAFASSAEMLIAARALLGVGGATLMPSTLGL
+IRTIFPDRAERRTAIAVWAMAFSGGAALGPVVGGILLERFWWGSVFLMNVPVMAVFLLVA
+PFLLPESRDPSPGPFDPLSSVLSIAGIVGLVYALKTAAKSPDWTALAGLVVGATALAWFI
+ARQRRLAHPMIDVALFRNVAFTSAVSVNVISVFAFMGLMFFLPQFLMLVQGMGPAEAGLW
+MLPLAAAAVVGTLLAPLLARVVAVRTVILTGLALVIAGFAVGTRLDGAAPLVAFVLLSCL
+FGVGVGLAETLTNDVILTAAPPERAGAAAAISETGYEFGGAMGTAVLGTVGMAVYAARVQ
+EAAGLPGLGPADAEAAAQTLAAAHRIGEGLPDGGARLVEVANGAFTAGMDLVAGIGIGVA
+AVTLLLAWRGLRSEARVERPVED
+>ACLBLIBL_00191
+MVILNETIMSVALPRLMAEFTVTAATAQWLTTGFMLTMAVVIPFTGWLLNRMSLRAVFIL
+AMGTFTAGTAIAGLAPTFGLLLTGRVVQAVGTAIMMPLLMTTVLNVVPLSRRGRVMGLIS
+IVISVAPASGPAVGGVILEHLSWRWLFFTVLPIAAIALAAGAAWVRNVTEPRPVRLDVLS
+GVLSAVGFASLIFGLSSIGEAAAGNAAMPPWIPVAVGVLALALFAVRQLRLKDDALLDLR
+TLSRPTFTVALAVMLTSMLALFGTIVLLPIYLQEVLGWTTQQSGLALLPGGMVMALLGYV
+VGHLYDRVGAPPLIVPGAVLGAAGLWGYTFLSEDSSAFMVVGLHVLISTGLSMLFSPLMT
+TALSALPRSLYAHGSALVSTLQQVAGAAGTALFITLLTVGTASSVAGGLGEVASLMDGVH
+LAFLSGALVFTVNVVAVWFVKRPAPNPL
+>ACLBLIBL_02217
+MLSGTSTTSRGTGPAPVRAWLVLCAMSMLQFFIAVDVTVVNIALPSIGADLGVAGHSLTW
+VVVGYTITGGGLLMLGGRIGDLLGRRRTLLVGTSVFGAASLLAGLAPSFPVLVAARLLQG
+AGEAVALPAAMATIVLLFPEGPRRSRALSVWAAVASCGLVLGFALSGIITAHLGWRWVFL
+VSVPFILVVIVTALLLVPADRPASGGRVRLDLPGSLLLTACPLLFVYAAVEAGEPATGLW
+VSGVALLCAVLAAAGFVRVESRSPNPLVPLTFFADRARLRANLTTMLLSGALSTSFLLFT
+FYLQDRLGIGPLGAGLTMLPLAVALIVASVLVPRLLGRWGARACVLVGLGAAAGAMGVVA
+LVAVLGSGATWLLPAMLLIAAGMGFGLVGLQYIAVSGTTEEDAGIASGVQRASDQLGGAA
+GVAVYVGLGFAPALHADAGDPFVVAAVLAVVGLVVGAVVISRSPSTAAGQPQAG
+>ACLBLIBL_02334
+MTVGAGLLLITLDNSILYTALPTLTADLGASGSSTLWIINAYPLVMAGLLLGAGTLGDRI
+GHRRMFVVGLWIFGAASLAAAFSPSPAFLIGARALLAVGAAAMMPATLALIRLAFDDPRE
+RNIAIAIWGSLSIAGAALGPILGGALLERFWWGSVFLINVPVVVIALVATAVIAPHNDPD
+PSKKWDLVSSLYAMVGLVGTVLVIKELAHIPQNWVLIAGALASAVIGFVLFVRRQGRLEE
+PLIEFSIFRNRAFAGGSLAAFFAMFTIAGAQLATTQRFQLVEGFTPLQAGLLVAAIALGA
+LPSGVLGAAILHIVGLRIIISGSLAIAALGLALAVLASANGSLPLLVVSFIVTGFGLGGT
+FAVASAAIMGNAPPRKAGMAASIEEVSYEMGSLSAVALLGSLLTFVYATVVRLPDGTPAA
+AGESIADALGIADGDLDVIAAATSAYDTAYLVTMIVLAVMLASGAALTNRLLRAYGRGSE
+AMEYAENH
+>MOLHKGIG_00169
+MTVGAGLLLITLDNSILYTALPTLTADLGASGSSTLWIINAYPLVMAGLLLGAGTLGDRI
+GHRRMFVVGLWIFGAASLAAALSPNPAFLIGARALLAVGAAAMMPATLALIRLAFNDPRE
+RNIAIAIWGSLSIAGAALGPILGGALLERFWWGSVFLINVPVVVIALVATAIIAPHNDPD
+PSKKWDLVSSLYAMVGLVGTVLVIKELAHIPQNWVLIAGALASAVIGFVLFVRRQGRLEE
+PLIEFSIFRNRAFAGGSLAAFFAMFTIAGAQLATTQRFQLVEGFTPLQAGLLVAASALGA
+LPSGVLGAAILHIVGLRIIISGSLAIAALGLALAVLASANGSLPLLVVSFIVTGFGLGGT
+FAVASAAIMGNAPPRKAGMAASIEEVSYEMGSLSAVALLGSLLTFVYATVVRLPDGTPAA
+AGESIADALGIADGDLDVIAAATSAYDTAYLVTMIVLAVMLASGAALTNRLLRAYGRGSE
+AMEYAENH
+>MHAAABBN_00360
+MTVGAGLLLITLDNSILYTALPTLTADLGASGSSTLWIINAYPLVMAGLLLGAGTLGDRI
+GHRRMFVVGLWIFGAASLAAAFSPNPAFLIGARALLAVGAAAMMPATLALIRLAFDDPRE
+RNIAIAIWGSLSIAGAALGPILGGALLERFWWGSVFLINVPVVAIALVATAIIAPHNHPD
+PSKKWDLVSSLYAMVGLVGTVLVIKELAHIPQNWVLIAGALASAVIGFVLFVRRQGRLEE
+PLIEFSIFRNRAFAGGSLAAFFAMFTIAGAQLATTQRFQLVEGFTPLQAGLLVAAIALGA
+LPSGVLGAAILHIVGLRIIISGSLAIAALGLALAVLASANGSLPLLVVSFIVTGFGLGGT
+FAVASAAIMGNAPPRKAGMAASIEEVSYEMGSLSAVALLGSLLTFVYATVVRLPDGTPAA
+AGESIADALGIADGDLDVIAAATSAYDTAYLVTMIVLAVMLASGAALTNRLLRAYGRGSE
+AMEYAENH
+>LFPAFLNI_02010
+MTVGAGLLLITLDNSILYTALPTLTADLGASGSSTLWIINAYPLVMAGLLLGAGTLGDRI
+GHRRMFVVGLWIFGAASLAAAFSPNPAFLIGARALLAVGAAAMMPATLALIRLAFDDPRE
+RNIAIAIWGSLSIAGAALGPILGGALLERFWWGSVFLINVPVVAIALVATAIIAPHNHPD
+PSKKWDLVSSLYAMVGLVGTVLVIKELAHIPQNWVLIAGALASAVIGFVLFVRRQGRLEE
+PLIEFSIFRNRAFAGGSLAAFFAMFTIAGAQLATTQRFQLVEGFTPLQAGLLVAATALGA
+LPSGVLGAAILHIVGLRIIISGSLAIAALGLALAVLASANGSLPLLVVSFIVTGFGLGGT
+FAVASAAIMGNAPPRKAGMAASIEEVSYEMGSLSAVALLGSLLTFVYATVVRLPDGTPAA
+AGESIADALGIADGDLDVIAAATSAYDTAYLVTMIVLAVMLASGAALTNRLLRAYGRGSE
+AMEYAENH

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000028.fa

@@ -0,0 +1,70 @@
+>ACLBLIBL_00251
+MSTSPSGSRVAEPGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFYGSAGGIQAAGPGV
+ILSFLIAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIV
+ADTAAITAYMAFWFPEVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMI
+FGGVILLFTGASTADGTQAGLANLVDHGGFLPHGILGVLTALTIVTFSFGGIETLGVAAG
+EAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPFVQIFEGLGVPFAP
+HLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMV
+LGAVLITVDPNAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVG
+TYLGLAFVATVVITMATIPDSRQALIIGLVWVAVLTLAWFVTGVRKAAAVHDRTGTLPVA
+SGEEAAASHR
+>MOLHKGIG_00134
+MSTSPSGSRVAETGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFYGSAGGIQAAGPGV
+ILSFLVAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIV
+ADTAAITTYMAFWFPGVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMI
+FGGVILLFTGASTADGTQASLANLVDHGGFLPHGILGVLTALTIVTFSFGGIETLGVAAG
+EAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPFVQIFEGLGVPFAP
+HLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMV
+LGAVLITVDPNAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVG
+TYLGLAFVATVVITMATIPDSRQALIIGLVWVAVLTLAWFVTGTRTSAAAHDRTGTLPVV
+RTRQSHED
+>NAFOICDF_00186
+MNASPSGAHAVDHPRDDAAHAAQSQLHRGLSQRHIMFIALGTAIGTGLFYGSAGGIQTAG
+PGVILSFLIAGFAVYLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAV
+VIVADTAAVTKYMAFWFPGVPAWAWVAATILVIGLVNLTHVGNFGEAEFWLTLIKIGAIV
+AMIFGGLILMFTGASFTDGTPAGLHNLVDHGGFLPHGFGGVLIALTIVTFSFGGIETLGV
+AAGEAKDPETALPKAINTVPVRILLFYVLTMVVIMSLVPWSAVDGKTSPFVQIFEGLGVP
+FAPHILNFVVLTAAISAINACIYASGRLLYAMAHDGQAPRAFTRTTANGVPWLTVAVMLG
+VMVLGAILITVNPDAFGLIAGVASFAVVLTWTMIFLSHRAMRARVKEAGAPPSVYPMPFG
+IVGTVLGLAFVATVVITMATIPESRQALLIGLAWVVALTAAWFVTGVRKTAALHDRTGQL
+PVVHRHH
+>NAFOICDF_00187
+MQSTPAPEAPAQAQLQRGLNPRHITFIALGTAVGTGLFYGSAAGIQAAGPGVVLAFMLAG
+AAVYLVMRALGEMAVREPISGSFVAYASRYLGPFAGFLTGWTYVFELAVVIVADTTAVTV
+YMAFWYPDVPAWVWVAATMVVLGLINVTHVGSFGEAEFWFSLIKVLAIVGMIFGGVILMF
+SGASFQDGVTPGPHNLVEHGGFLPHGLMGVLTALTIVTFSFGGTETLGIAAGEAEDPASA
+LPRAVNTVPVRILFFYIGSMLVIMSLVPWTTVDGETSPFVQIFETLGVPFAPHLLNFVVL
+TAAVSAINACIFTNARLLHHMAHDGHAPRVFTAVTRGGVPWVTVVAMLGVMAAGAVFMSV
+KEDTFGIVAGVATFAVVFTWALILASHLGMRRALARHGQAPGAFPMPGGRVGAWLGLAFV
+AVVAGTMAFDQGGAVLGALGGPDALQTALAQPFVIGVLWLAVLAAAWAVPAVRRSAHRHD
+RHGTPPPLTWDV
+>NAFOICDF_02180
+MTPERRGPGTSPGGRYGVRVNEPPALPEPTGAAPPAPSPAGGATAAPSHGAADARLRRGL
+SMRHIQFIALGSAIGTGLFYGSATAIQLAGPAVILAYLVAGAAVFMVMRALGELAVRHPV
+PGSFGQYADRYLGPFAGFVTGWTFVFEMVVVAIADVTAFGVYMGFWFPDTPRWIWVTAVI
+LFIAAVNTRHVKVFGELEFWLSIVKVSAILAMVIGGVALLVMGVSLDAATPAGVQNLVDH
+GGFAPHGAAGVLAALSVVVFAFGGVETIGITAGEAQDPGRAIPRAVNAVPARILLFYVMT
+MVVIMSLVPWDRITGEASPFVEIFSTLGVPAAPAILNLVVITAAISAINADTFSAGRMLF
+GMAQQGRAPAVFASVSRGGVPWMAAVVMGLALAVGAVLNAVIPEDVFVVVASIATFATVW
+VWLMILLAHIAMRREVARRGLPASAFPVPLWPAASWAAVAFVLLVVGLLGWFSDTRVAMI
+VGLVWLVLLGAAYRLFLHGHGRSRPDLEEGAASSP
+>MHAAABBN_02148
+MSTSPSGSRVAETGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFYGSAGGIQAAGPGV
+ILSFLVAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIV
+ADTAAITTYMAFWFPGVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMI
+FGGVILLFTGASTADGTQASLANLVDHGGFLPHGILGVLTALTIVTFSFGGIETLGVAAG
+EAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPFVQIFEGLGVPFAP
+HLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMV
+LGAVLITVDPNAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVG
+TYLGLAFVATVVITMATIPDSRQALIIGLVWVAVLTLAWFVTGTRTSAAAHDRTGTLPVV
+RTRQSHED
+>LFPAFLNI_00142
+MSTSPFGSRVAETGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFYGSAGGIQAAGPGV
+ILSFLVAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIV
+ADTAAITTYMAFWFPGVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMI
+FGGVILLFTGASTADGTQASLANLVDHGGFLPHGILGVLTALTIVTFSFGGIETLGVAAG
+EAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPFVQIFEGLGVPFAP
+HLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMV
+LGAVLITVDPNAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVG
+TYLGLAFVATVVITMATIPDSRQALIIGLVWVAVLTLAWFVTGTRTSAAAHDRTGTLPVV
+RTRQSHED

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000029.fa

@@ -0,0 +1,21 @@
+>ACLBLIBL_00292
+MNFALDGRNYEIDLSKEHADELREFLKPYMKKGRAVAPPSPKVEAAQIRKWAAENGYEVS
+SRGRLHRDVVEAYRNARRK
+>MOLHKGIG_00099
+MNFALDGRNYEIDLSKEHAAELREFLKPYMKKGRAVAPPSPKVEAAQIRKWAAENGYEVS
+SRGRLHRDVVEAYRNAKRK
+>NAFOICDF_00617
+MATITTIADDFDNSTPAETTYFSVNGKEYAIDLNEEHRRELEDVLEEVAERLSKYTAVAR
+PLGKSSAPARKSSKSPSSRSGASYDAGAVRSWAEENGYKVADRGRISADVLEAYNASKKG
+>NAFOICDF_00670
+MAIISTVADDFDGSTPAEAVRFSVAGRDYEIDLSKEHRAELDAIMAEFQDRLKKFTDVAR
+PAGRAASTGRTPARRSSGSGVDASTVRLWAVENGFDVKDRGRIPVEVMDAYRNRGKKG
+>MHAAABBN_02112
+MNFALDGRNYEIDLSKEHAAELREFLKPYMKKGRAVAPPSPKVEAAQIRKWAAENGYEVS
+SRGRLHRDVVEAYRNAKRK
+>LFPAFLNI_00094
+MNFALDGRNYEIDLSKEHAAELREFLKPYMKKGRAVAPPSPKVEAAQIRKWAAENGYEVS
+SRGRLHRDVVEAYRNAKRK
+>LFPAFLNI_02014
+MAIISTVADDFDGSTPAEAVRFSVAGRDYEIDLSKEHRAELDAIMAEFQDRLKKFTDVAR
+PAGRAASTGRTPARRSSGSGVDASTVRLWAVENGFDVKDRGRIPVEVMDAYRNRGKKG

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000032.fa

@@ -0,0 +1,35 @@
+>ACLBLIBL_00398
+MPIPQPHREGHHRPPGLPPRPGRRQVLAGLAGVASLPLLAACSAEDPLAAQAGKADGKNY
+IAGDGSVLEIGPAERGEPVQFSSAMFSGEPIIAQDLAGDPAVLNFWYAACAPCRVEAPDL
+QALHEQFAPEGVRFLGINVRDTIATAQAFERKFGITYPSVEDRGGQVLLAMTDYVPPQAV
+PTTIVLDHQGRVSARILGIAERSTLRTLITTVLDEQA
+>ACLBLIBL_01066
+MHTPPRPSRRTLLTGLALASLAPALAACSGGDDSLARQAGNADGKNYIAGDGSVLEIAPA
+ERGAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAPHLVSLHEQFAPQGVR
+FLGVNVRDTVTTAQAFERTFEIPYPSIEDTRGDVLLNMADYVPPQAVPSTLVLDVEGRVA
+ARVLGAVEESTLRALLTTVVDEAAA
+>ACLBLIBL_02643
+MNRRRTGAALALPIAALFALAGCSGGDGNLAAEWNEASGKGYVSGDGSSLSIAPDQRTEP
+VEFSGETEDGDIYGSDDTVGSVTVVNFWYAGCAPCRAEAPDLVEAYDEFSPQGVKFVGVN
+TRDQVAQARQFSVRFDIEYPSIMDNAGGRAVQRAFAGQVPLNAVPTTLVLDAEGRVAHRV
+LGQLAGASQLRTLIGETLAEAGGGAAADPASDPAPADEATEQ
+>MOLHKGIG_01808
+MQTPRPSRRTVLTGLSLLGLAPVLAACSGDDSLTRQAGNADGKNYIAGDGSVLEIAPAER
+GAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAPHLVSLHEQFAPQGVRFL
+GVNVRDTVTTAQAFERTFEIPYPSIEDARGEVLLNMTDYVPPQAVPSTLVLDVEGRVAAR
+VLGAVEESTLRALLTTVVDEAAA
+>NAFOICDF_01001
+MPFPPRPSRRAALAGLSAAALAPLLAACSGTDDSLAQQAGNAGGKNYIAGDGSVVEYAAD
+QRGAPVEFSAAGFDGETVSGETLRGEPALLNFWYAACAPCRVEAPHLVKLHGEFEPKGVR
+FLGVNVRDTVTTAQAFERTFGIPYSSVDDTSGSVLLAMSDYVPPQAVPSTLVLDRQGRVA
+ARVLGAVEEGTLRALLDTVVAEA
+>MHAAABBN_01505
+MQTPRPSRRTVLTGLSLLGLAPVLAACSGDDSLTRQAGNADGKNYIAGDGSVLEIAPAER
+GAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAPHLVSLHEQFAPQGVRFL
+GVNVRDTVTTAQAFERTFEIPYPSIEDARGEVLLNMTDYVPPQAVPSTLVLDVEGRVAAR
+VLGAVEESTLRALLTTVVDEAAA
+>LFPAFLNI_01729
+MHTPPRPSRRTLLTGLALASLAPALAACSGGDDSLARQAGNADGKNYIAGDGSVLEIAPA
+ERGAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAPHLVSLHEQFAPQGVR
+FLGVNVRDTVTTAQAFERTFEIPYPSIEDARGDVLLNMTDYVPPQAVPSTLVLDVEGRVA
+ARVLGAVEESTLRALLTTVVDEAAA

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000035.fa

@@ -0,0 +1,40 @@
+>ACLBLIBL_00413
+MAPSSYYAAKTRAPSARAVRDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGRDRA
+ARLMRAAGIEGARRSKRVKTTRPDPASARYPDLVKREFTAPAPNRLWATDLTFVPTWAGV
+AYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIAMARWSRGARHEDLRCHSDAGSQFTSIR
+YGERLAEIGATPSIGTVGDSYDNSLAETVNGYYKAELVRGPARPGPWRTVEDLELATLGW
+VSWHTTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIQ
+>MOLHKGIG_01401
+MAVSGSFPGHLWAAFHGRLHSVRDEELIPQLVELWETNYRVYGVRKLWKTARRAGIDIGR
+DQTGRLMRAAGIKGATRSKRVKTTRPDPTAARHPDLVKREFTAPAPNRLWVTDLAFVTTW
+AGVAYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDLRCHSDAGSQFT
+SIRYGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAELVRGPARPGPWRTVEDLELAT
+LGWVSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLSESNSASLHQTQGASGPTLWSP
+TRSILDRAARPLRKF
+>NAFOICDF_00326
+MAPSSYYAAKTRTPSARAARDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGRDQT
+ARLMRAAGIEGARRSKRVKTTRPDPASARHPDLVKREFTAPAPNRLWVTDLTFVPTWAGV
+AYVCFIIDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDLRCHSDAGSQFTSIR
+YGERLAEIGATPSIGTVGDSYDNALAETVNGYDKAELIRGPARPGPWRTTDDVELATLGW
+VHWHNNQRLHGYLDDLPLTEFEERFYATQQGQYALVEIK
+>NAFOICDF_00649
+MAPSSYYAAKTRAPSARAVRDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGRDQT
+ARLMRAAGIEGARRSKRVKTTRPDPASARHPDLVKREFTAPAPNRLWVTDLTFVPTWAGV
+AYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDLRCHSDAGSQFTSIR
+YGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAELVRGPARPGPWRTVEDLELATLGW
+VSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIK
+>NAFOICDF_02217
+MAPSSYYAAKTRAPSARAVRDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGRDQT
+ARLMRAAGIEGARRSKRVKTTRPDPASARHPDLVKREFTAPAPNRLWVTDLTFVPTWAGV
+AYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDLRCHSDAGSQFTSIR
+YGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAELVRGPARPGPWRTVEDLELATLGW
+VSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIK
+>MHAAABBN_01131
+MAPSSYYAAKTRAPSARAVRDEELIPQLVELWETNYRVYGIRKLWKAAGRAGIMIGRDQA
+ARLMRAAGIEGARRSKRVKTTRPDPASARHPDLVKREFTAPAPNRLWVTDLTFVPTWAGV
+AYVCFIVDAFSRMIVGWRCASHMRTEMVLDAIEMARWSRGARHEDPRCHSDAGSQFTSIR
+YGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAEHVRGPARPGPWRTVEDLELATLGW
+VSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIK
+>LFPAFLNI_01351
+MGSFSWPLTHSDAGSQFTSIRYGERLAEIGATPSIGTVGDSYDNALAETVNGYYKAEHVR
+GPARPGPWRTVEDLELATLGWVSWHNTQRLHGYLGDVPPAEFEDTFYAVEAGREQLVGIK

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000046.fa

@@ -0,0 +1,70 @@
+>ACLBLIBL_00837
+MLFHHHGYVSTDPRVQPAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTR
+IIERRSHRLEIGQADGIQARSVETFQAFGFASQIIDEAYDLTSMAFWNPSSEDADTIVRT
+SLAEDDPEGVSEFPHLIVNQARILDWFAAYMKNSPTRAEPDYGWSFESLEDSAEGEYPVL
+VTLRRTVDAQGEPLADPESGETRQVRAKYVVGADGAGSRVRKAIGHSLAGGASNHAWGVM
+DALAVSDFPDIRTKCAIHSSTGSILHIPREGGHLFRMYVDLGEVPADDNHKVRQTPIEEI
+IRRAQQIIRPYTLEVKDVAWHSVYEVGHRLTSGFDNRERVDHPNVFLLGDACHTHSAKAG
+QGMNVSMQDGWNLGWKLGQVLSGVAPAELVPTYSEERKEIAKNLIDFDKEWSTLMAKPTS
+ELGDPNEVADFYTKTAEFPAGFMTEYKPSILTTDATGQSLAAGFPIGKRFKSALVERSCD
+TNVKHLGHLHRADGRWRVYVFADAASPRSADSKVAAWAKAVEEDPRSFRNRHTPADGPQD
+ARFDVKVVYQQKQTEFAHPDVPAVFRPTSGDLRLLDLNNIFATCQPKHGEDIFEARGISR
+DGAVVVVRPDHYVSGVFGLDEVERLNEFFAGVLLDAS
+>MOLHKGIG_02005
+MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTR
+IIERRPHRLEIGQADGIQARSVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRT
+SLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARPDYGWAFETLEDTNDGEHPVL
+VTLRRTVDAEENALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGVM
+DALADTDFPDIRTKCAIHSSSGSILLIPREGGHLSRMYVDLGEVPADDDHKVRQTPLEEI
+IRRAQQILRPYTLDVKEVAWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAG
+QGMNVSMQDGWNLGWKLGQVLSGLAPVELVPTYAEERKEIAKNLIDFDKEWSTLMATPTS
+ELGDPNEVAEFYTKTAEFPAGFMTEYQPSLLTTDATGQALAQGYPIGKRFKSALVERSCD
+TNVKHLGHLHRADGRWRVYVFADAASPRAEDSKVAAWAKAIEEDPRSFRNRHTPSDGPED
+ARFDIKVVYQQKQTEFAHPDVPSIFRPTTGSLGLHDLNNIFATCRPQHGEDIFEARGISR
+DGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN
+>NAFOICDF_00774
+MLFHHHGYVSTDPRMKPAAGIGLDRPAELPDEMDVLIVGTGPAGMIAAAQLAMFPDVHTR
+IIERRGKRLEIGQADGIQARSVETFQAFGFASQIIDEAYDLTSMAFWNPSPEDEDAIVRT
+SLAEDDPHGVSEFPHLIVNQARILDWFAEFMKNSPTRATPDYGWEFVSLDDSDQDAERPV
+QVTLRRTVDAKGNPLAEGVAGEERVVRAKYVIGADGAGSRVRKAIGHSLSGDAANHAWGV
+MDVLADSNFPDIRTKCAIHSSSGSILHIPREGGHLFRMYVDLGEVPADDNHKVRQTPIEE
+VIRRAQQIIRPYTLDVKDVAWSSVYEVGHRLTSGFDNRERCTHPNVFLLGDACHTHSAKA
+GQGMNVSMQDGWNLAWKLGQVLSGIAPAELVPTYSEERKEIAKNLIDFDKEWSTLMAKPT
+SELGDPNEVAEFYTKTAEFPAGFMTEYRPSMLTTDAAGQELATGFPIGKRFKSAKVERSC
+DTNVKHLGHLHTADGRWRVYVFADAAAPHDADSKVAAWAEAVEEDPQSFRNRHTPAGAPQ
+DERFDLKVVYQQKQTEFAFPDVPAVFRPTTGPLGLHDLNNIFAVCRPEHAEDIFELRGVS
+RDGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN
+>MHAAABBN_01715
+MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTR
+IIERRPHRLEIGQADGIQARSVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRT
+SLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARPDYGWAFETLEDTNDGEHPVL
+VTLRRTVDAQGNALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGVM
+DALADTDFPDIRTKCAIHSSSGSILLIPREGGHLFRMYVDLGEVPADDNHKVRQTPLEEI
+IRRAQQILRPYTLDVKEVAWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAG
+QGMNVSMQDGWNLGWKLGQVLSGMAPVELVPTYSEERKEIAKNLIDFDKEWSTLMAKPTS
+ELGDPNEVAEFYTKTAEFPAGFMTEYQPSLLTTDATGQALAQGYPIGKRFKSGLVERSCD
+TNVKHLGHLHRADGRWRVYVFADTASPRAEDSKVAAWAKAIVEDPRSFRNRHTPSDGPED
+ARFDIKVVYQQKQTEFAHPDVPSIFRPTTGPLGLHDLNNIFATCQPKHGEDIFEARGISR
+DGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN
+>LFPAFLNI_00173
+MFIAGDACHTHSAKAGQGMNVSMQDGWNLAWKLGQVLEGRSDASLLATYSEERQQIAENL
+IEFDKAWEGMMSKRPDELEDPQAVGRFYKDNAEFPNGFATQYPASSVTGEDTHQALAAGV
+PIGKRFESAAVRRVADTSPRQLGHLFEADGRWRLYAFADEDRTAVGELADWLADSPDSPV
+RRFTPESADLNSVFDAKVVYQQPYQEVELADVPALFLPKMGPYQLTDKEVVFAADLADDI
+FEARGIDRGGALIIQRPDMYVAHVLPLSAREEITAFFEQNMVSASV
+>LFPAFLNI_00174
+MRGAADPRRSLSTLPTTAVSEFPFLIVNQARVIDYFAEYAERGPQGQERTVRAKYVVGCD
+GSRSRVRDCTGIEVVRDPSAHAWSVMDVLLETDFPDNRQKCGIQSDKDGTILLIPREGGF
+LARFYVSLGSIDDAPRPRSGGGIRACSSPATPATPTPPRPARA
+>LFPAFLNI_01943
+MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTR
+IIERRPHRLEIGQADGIQARSVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRT
+SLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARPDYGWAFETLEDTNDGEHPVL
+VTLRRTVDAQGNALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGVM
+DALADTDFPDIRTKCAIHSSSGSILLIPREGGHLFRMYVDLGEVPADDNHQVRQTPLEEI
+IRRAQQILRPYTLDVKEVAWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAG
+QGMNVSMQDGWNLGWKLGQVLSGMAPVELVPTYSEERKEIAKNLIDFDKEWSTLMAKPTS
+ELGDPNEVAEFYTKTAEFPAGFMTEYRPSLLTTDATGQALAQGYPIGKRFKSALVERSCD
+TNVKHLGHLHRADGRWRVYVFADAASPRAEDSKVAAWAKAIEEDPRSFRNRHTPSDGPED
+ARFDIKVVYQQKQTEFAHPDVPSVFRPTTGSLGLHDLNNIFATCRPTHGEDIFEARGISR
+DGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000047.fa

@@ -0,0 +1,42 @@
+>ACLBLIBL_00855
+MTLLEVHDVDKTFHSGGEAVPVLRGASLLVPAGEMHAVTGPSGSGKSTLLRILACLDSPD
+SGRVLLGGEPLPEPWSRGGDRYRNQRCGIVLQDFALMEHATALENVMLPLRYGPDRVPRG
+EQRRRAGEALERVGLGTRTGHRARTLSGGEKQRVAVARALINEPPLVLADEPTGALDQER
+TRDVVDLLRGAVGPERAVVVVTHDPRVAAACDRRWHLVDGGLAPQD
+>ACLBLIBL_01010
+MSDGSAPPLLELAGVLKSFKGADRPALDGVDLTVRDGDFVAIVGPSGSGKSTLLNVLGLL
+DRPDGGSYRVSGTDTMSMGERERDRLRSRWFGFVFQSSHALGDEPVAVNAALGLRVQRTP
+PEQRDARAGEALALLGLSHRLDTRAKLLSGGERQRLAIARAIATRPRVILADEPTGNLDS
+VNSRIVIDHLRALHAQGATVLLITHDPEIARQADRQVRIEDGRITELAGHRTAASASADM
+AGTGHGWSAPGAARRHRSPRSSAMLDDLVEAVSSLSTRFLRTVLLMAAFAVGIGGLVASV
+GLTQTATDQVGALLTAAALDEVVVTVPQAEGLLDPGDGRLASWADGLAALPHVTAAGHVA
+QVAPADVVITRHDPSDPEPAVAISLVAASSSYAGLAGLTLPSETSRTLLDSPDARLAWAT
+PAAARALELPVTDTGMLSPGYRVWIQGHAVDVAGIVTLSERTPELDASLVVTPAVMTGVA
+QAHPQLVVRTEAGFPYPVSQAAPLVIAPENPGSVTVRTVADLRNLRAGVSDDLGAFVGVL
+SGVLLVLAVISASTAMYLSVQARTAEIALRRAIGSPRGLIARLFLLEGALIGLAGGAVGA
+AVGSGVILAVSQARGWAAVLPPGAVPLALGLGLVAGVVSALYPGWVASRQRPADALRG
+>NAFOICDF_00792
+MSLLEVHDVDKSFTTAASEVPVLRGVSLSVPAGQMHAVTGPSGSGKSTLLRILACLDSPD
+AGEVLLEGVPLPPPWSRGGDRHRNRRCGIVLQDFALMEHATALDNVLLPLRYGPGGGSRA
+EQRRRAALALDRVGLADRAHHRARTLSGGEKQRVAVARALINDPPLVLADEPTGALDQAR
+TRDVVKLLRSAVGPQRAVVVVTHDPEVAAACDQRWHLEDGRLHSQG
+>NAFOICDF_00870
+MTASAPVLTLDRVQVGYRHPDGGTRVLIESLDLTLAPGEVVGLWGRSGTGKSSLIRHLAG
+LSRPLAGRIAYRSPDGSLNGEVADLSAGDLARYRREHLGYVDQSCELIGELSALDNAAVW
+IHGGRIAGSACDAQETVQGLLERLGLGHRLGAPASRLSGGEAQRVALVRALSKRPHLIVA
+DEPTGHLDGVTAREAIALLREHAEAGAAVLVASHDPLVHAAVDRAVRVGED
+>NAFOICDF_00943
+MNTAPLTPPVLAARGLTKAYGSTHALTGVDLEIRPGESVAVMGPSGSGKTTLLHVLSGII
+APDGGRVTLAGADGTVHEVTALTEEQRARLRRERLGFVFQEGLLLPELTAVENVAMPLML
+NGVDRRAAEQTAARWLGSLGLAGMEDRRPGELSGGQRQRVAIARAQAVEPDVVFADEPTG
+ALDSDTSEAVLDSLIASTVARGRTLVVVTHDPSVAAACSRLIRVRDGRIESDQAQAAAGT
+TREQVR
+>MHAAABBN_01696
+MEHATALENVMLPLRYGPDRVPRGEQRRRAGEALERVGLGMRTGHRARTLSGGEKQRVAV
+ARALINEPPLVLADEPTGALDQARTRDVVDLLRGAVGPERAVVVVTHDPRVAAACDRRWH
+LVDGELAPQD
+>LFPAFLNI_00735
+MSLLTVHDVHRSYRGPAGDVPVLRGVSLQVPGGGVHAIMGPSGSGKSTLLRLLACLDTPD
+AGSIRVAGRSLPAPWSSDGDAYRNRTCGIVLQDHLLIDRATAVDNAALPLLYARPRTSKR
+ERRTMAAELLTRLGLGDRLHHPVGRLSGGERQRVAIARAVIMGPSLLLADEPTGALDEER
+TDEVMGLFRSMSQPERAIVVVTHDPAVAARCDHTWRLRAGRLE

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000053.fa

@@ -0,0 +1,33 @@
+>ACLBLIBL_02181
+MRAPGVRGAVALGGAAGVVAGSTAMELVGVGGLLALAGRDGGVGLGPVAALAFAALPLAV
+VNVLGSFLLGLLLARSRHAGLDRRPALVAGLGTGFLGSFTTIATAAAVFLLTPLEAGWSA
+IAASSGVGGFLSATAGLLLPPLALLALLAALSTAAAVLGLRLGGAPARGADAEARVDGVA
+SDGTAADGAPA
+>MOLHKGIG_00749
+MAARGETTADRRGGRGTDRRPGTAGAVALGGAAGVLCGAGVMNAVTALAGAPNFRGTFGA
+AFGAVDVLVQALPLFVVNVLGSFLLGLLWAASRRRGPDWRPRLVAGLGTGFLGAFTTISS
+AVALVLWPVRLGAAVSGAGGVLAAAVAVLLVLALMAALSTAAAMLGLRAGGAPGSRVVGT
+DRSEEDA
+>NAFOICDF_00685
+MNAALIVVVALGGGAGAAGRFLLDGLINTGREFRLPVGTLTINITGSLLLGIIVGAATHL
+GAVPVAVLGTGVMGGYTTFSTASFETVRLARSGRITAAAINGLGMLVVSVAAATAGILLG
+GTL
+>NAFOICDF_00686
+MTTRTDTPMPDDQLPPDPDVDVSDPATTMRPVHLRWRYVGLVAVGGAGGTALRDVISSVL
+PADGGVSWSIFWINITGALALGVLLEALAHRGPDAGRRRVLRLLLGTGVLGGFTTYSTLA
+ESTAALFLDGHGLAGTGYALLTVLSGAIATACGLVVAGWFRPRTEEA
+>NAFOICDF_02076
+MADARPAAGGAAARRTLPWVALGGAAGALASLGAGALIAQAMGPGDPSISGPLGTASATL
+ASVAAVNVLGSFLLGLLRGASGRPGARWDPRLVAALGTGFLGAFTTFGTVAATLALPVMM
+TAGLAATGDTWWILLAVVVVGLLIAVAVLAALSTAAAALGLHLGGRGAGSGSAGRPDGAA
+A
+>MHAAABBN_00479
+MAARGEPTADRRGGRGTDRRPGTAGAVALGGAAGVLCGAGVMNAVTALAGAPNFRGTFGA
+AFGAVDVLVQALPLFVVNVLGSFLLGLLWAASRRRGPDWRPRLVAGLGTGFLGAFTTISS
+AVALVLWPVRLGAAVSGAGGVLTAAASVLLVLALMAALSTAAAVLGLRAGGAPGSRVVGA
+DRSAEDA
+>LFPAFLNI_00713
+MAARGETTADRRGGRGTDRRPGTAGAVALGGAAGVLCGAGVMNAVTALAGAPNFRGTFGA
+AFGAVDVLVQALPLFVVNVLGSFLLGLLWAASRCRGPDWRPRLVAGLGTGFLGAFTTISS
+AVALVLWPVRLGAAASGAGGVLAAAVAVLLVLALMAALSTAAAVLGLRAGGAPGSRAVGT
+DRSAEDA

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000055.fa

@@ -0,0 +1,35 @@
+>MOLHKGIG_02246
+MDHKEILHQGLRRQRDALFAKLDGLPEREVRLPRTPTGTNLLGLLKHAATCELEYFGEVF
+GRPAGIPLPWDAPGVGEEDGADLFAAEDETLEDVLDYARRCFAHADATIEALVFDARGRV
+PWWPAHLAEVTLAQILSHVALDAARHAGHADILREGIDGQAGLRGPGDNLPGWDAERWAA
+HVRRLEGIARGAGPVR
+>MOLHKGIG_02261
+MDHKQILHDGLRRQRAALLQKLEGLSERDARLPRTPTGTNLLGLVKHAAVVELEYFGETF
+DRPAEVQLPWAAAGQSEEDNVDMFAAEGESLEDVLEFARRCFAHADATITALGADAHGRV
+AWWPDDKAEVTLAQIIAHVALDEARHAGHADILREQIDGQAGLRAPGNNLPVWGADRWAA
+HVDRLTAIAEGSGGPGRN
+>NAFOICDF_00418
+MDHKQILHDGLRRQRAALLHKLEGLSERDARLPRTPTGTNLLGLVKHAAVIELEYFGGTF
+GRPAEVQLPWAAAGQPEEDNVDMFAAEGESLEDVLEFARRCFVHADATITALGADAPGRV
+AWWPDDKAEVTLAQIIAHVALDEARHAGHADILREQIDGQVGLRSPGNNLPPWDADRWAA
+HVDRLTAIAEGSGGVGWN
+>NAFOICDF_00422
+MGFLTPQAHGELAVLTTYALQQLAQMRTTVHGLTDEQAHSVPSASALNLTGLLLHTGEVA
+VYWTAAAASAPGEPVLPEDVNEDHSLDELVADGRPLAQVLERFDRCVEVARQNLAAVADL
+SAPVPVPDAPWFPADLKTWEARWALLHVTAEVARHVGHADLIRESIDGTGSYELNDLADA
+AAQG
+>MHAAABBN_01948
+MDHKEILHQGLRRQRDALFAKLDGLPEREVRLPRTPTGTNLLGLLKHAATCELECFGEVF
+GRPAGIPLPWDAPGVGEEDGADLFAAEDETLEDVLDYARRCFAHADATIEALVLDARGRV
+PWWPAHLAEVTLAQILSHVALDAARHAGHADILREGIDGQAGLRGPGDNLPGWDAERWAA
+HVRRLEGIARGAGPVR
+>LFPAFLNI_02178
+MDHKEILHQGLRRQRDALFAKLDGLPEREVRLPRTPTGTNLLGLLKHAATCELEYFDEVF
+GRPAGIPLPWDAPGVGEEDGADLFAAEDETLEDVLDYARRCFAHADATIEALVFDARGRV
+PWWPAHLAEVTLAQILSHVALDAARHAGHADILREGIDGQAGLRGPGDNLPGWDAERWAA
+HVRRLEGIARGAGPVR
+>LFPAFLNI_02192
+MDHKQILHDGLRRQRAALLQKLEGLSERNARLPRTPTGTNLLGLVKHAAVVELEYFGETF
+GRPAEVQLPWAAAGQPEEDNVDMFAAEGESLEDVLEFARRCFAHADATIAALDADAPGRV
+AWWPDDKAEVTLAQIIAHVALDEARHAGHADILREQIDGQAGLRAPGNNLPPWDADRWAA
+HVDRLTAIAEGSGGPGRN

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000056.fa

@@ -0,0 +1,36 @@
+>ACLBLIBL_00019
+MANTTYTLVLLRHGQSDWNEKNLFTGWVDVPLTEKGRAEASRGGELMKAEGIHPDVLHTS
+LLKRAITTANLALETADRQWIPVKRDWRLNERHYGALQGKDKAQVKEEFGEEQFTVWRRS
+FDTPPPALDDSSEFSQIGDERYAELGDDAPRTEALKNVIDRLIPYWEAEIVPDLKASKTV
+LVAAHGNSLRALVKHLDGISDEDIAGLNIPTGIPLVYELDEDLKPITANGRYLDPEAAAA
+GAAAVAAQGSAH
+>MOLHKGIG_00318
+MANTTYTLVLLRHGQSEWNEKNLFTGWVDVPLTEKGRAEAARGGELLEAEGIRPDVVHTS
+LLKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMVWRRS
+FDTPPPALDDDSEFSQVGDERYADLGKDAPRTEALKQVVDRLLPYWEEQVLPDLKAGKTV
+LIAAHGNSLRALVKHLDGISDEDITGLNIPTGIPLVYELDQNFKPITANGRYLDPEAAAA
+GAAAVAAQGSAH
+>NAFOICDF_00015
+MADTFKLILLRHGQSDWNEKNLFTGWVDVPLTEKGRAEASRGGELLAAEGLLPDVLHTSL
+LKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMTWRRSF
+DVPPPPLDDSSEFSQAGDERYRDIGPDAPRTEALKQVIDRLLPYWTEQIVPDLKAGKTVM
+VAAHGNSLRALVKHLDGISDEEISGLNIPTGIPLFYELDQNLKPVTPHGRYLDPEAAAAG
+AAAVAAQGDKK
+>NAFOICDF_00687
+MLTLLRHGESTANEAGTFTGLLDVPLTHRGERQASAAGQLLRSNHITPDVVVTSTLRRAV
+RTAELVCDALGTQLPTEAVWQLNERNYGALTGMTKTDARRMLGDDEYVRLRRSRTGTPPP
+MSLHLWEELRSSSALRGLPDGALRRTEALSDVIKRVRPVLHDRLLPMVRSGRSVLVVAHG
+NSLRALCACIDDLTDPELEQLNLPTGQPVQYHLAPTGALVPRGGAFLDPVAAQHAAALVA
+AEGGT
+>MHAAABBN_00033
+MANTTYTLVLLRHGQSEWNEKNLFTGWVDVPLTEKGRAEAARGGELLEAEGIRPDVVHTS
+LLKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMVWRRS
+FDTPPPALDDDSEFSQIGDERYADLGKDAPRTEALKQVIDRLLPYWEEQILPDLKAGKTV
+LIAAHGNSLRALVKHLDGISDEDIAGLNIPTGIPLVYELDQNFKPITANGRYLDPEAAAA
+GAAAVAAQGSAH
+>LFPAFLNI_00325
+MANTTYTLVLLRHGQSEWNEKNLFTGWVDVPLTEKGRAEAARGGELLAAEGIRPDVVHTS
+LLKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMVWRRS
+FDTPPPALDDDSEFSQVGDERYADLGKDAPRTEALKQVIDRLLPYWEEQVLPDLKAGKTV
+LIAAHGNSLRALVKHLDGISDEDIAGLNIPTGIPLVYELDQNFKPITANGRYLDPEAAAA
+GAAAVAAQGSAH

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000058.fa

@@ -0,0 +1,52 @@
+>ACLBLIBL_00038
+MSPFDLEELDMTATAPDPLDGAFTAAWLTSQTFAPVEYVVPGLIPEGLTLLVAAPKVGKS
+WMVLDLAHAAATGGKALGSISVDRRPVLYLALEDGPRRLQSRLSMLGVDGGGPDLMFLTA
+LSASPVATVAAYLERHAQDRPLVILDTLGKVRGRDGGNDQYGRDYSQMSALKTLVDAVPG
+SSLIVVHHTNKGGREDFLEAVSGTQGLAGAADSILVIRRDRNQADGTINVTSRDAREGEY
+AVTFDGSRWHTVGADLAEAAAAAESKRATAGVGDDMARVIDAVSRHPGGVGVAQIVAMTE
+LPRATVDKYLSRAVAAERIVRVERGTYAPTPLSEVSDCQIGSDPDPLDF
+>ACLBLIBL_00285
+MATKTAAKRAPGYRCTECGWTTVKWVGRCGECQAWGTVEEVGLTSTTGRTRAATVAEVAP
+RIADVDATLASFRSTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAG
+GGGPRSVLYLTGEESAAQVRSRADRIGAIADTLRLTAETDLGRALGQIERTDPELVIVDS
+VQTLQSTEVDGIAGGVSQVREVAASLIRTAKEKGITTVLVGHVTKDGTIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVAEPVEGT
+CVTVTLEGRRPLVAEVQSLLTPSAGGGPRRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAVASAKLAAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGDVPAGFTVAQVGSIGEALATIPTWTGAGAGA
+>MOLHKGIG_00105
+MATKTAPKRAPGYRCTECGWTTVKWVGRCGECQSWGTVEEIGLTSTTGRTRAATVAEVAP
+RIADVDATLASFRSTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAG
+GGGPRSVLYLTGEESAAQVRSRADRIGAIADTLRLTAETDLGRALGQIERTDPELVIVDS
+VQTLQSTEVDGIAGGVSQVREVAASLIRTAKEKGITTVLVGHVTKDGTIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVSEPVEGT
+CVTVTLEGRRPLVAEVQSLLTPSAGGSPRRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAVASAKLSAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGDVPAGFTVAEVGSIGEALATIPTWTGGGPAAHPEAGPGR
+>NAFOICDF_00231
+MATKSSTKRAPSYRCTECGWTTVKWVGRCGECQAWGTVEEAGGAATAGRTHASTVAQAAP
+RIRDVDATLASFRTTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAA
+GGGPRDVLYLTGEESAAQVRSRADRIGALADTLRLAAETDLGRALGQIEKTDPALVIVDS
+VQTLQSTEVEGVAGGVTQVREVAASLIRTAKEKGITTILVGHVTKDGSIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGTQEPVEGT
+CVTVTLEGRRPLVAEVQALLTPSGGGSARRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAIASAKLGAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGDVPAGFSVAQVGTLSEALGTIPSWTGQRSPGARS
+>MHAAABBN_02118
+MATKTAPKRAPGYRCTECGWTTVKWVGRCGECQSWGTVEEIGLTSTTGRTRAATVAEVAP
+RIADVDATLASFRSTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAG
+GGGPRSVLYLTGEESAAQVRSRADRIGAIADTLRLTAETDLGRALGQIERTDPELVIVDS
+VQTLQSTEVDGIAGGVSQVREVAASLIRTAKEKGITTVLVGHVTKDGTIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVSEPVEGT
+CVTVTLEGRRPLVAEVQSLLTPSAGGSPRRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAVASAKLSAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGDVPAGFTVAEVGSIGEALATIPTWTGGGPAARPEAGPGR
+>LFPAFLNI_00100
+MATKTAPKRAPGYRCTECGWTTVKWVGRCGECQSWGTVEEIGLTSTTGRTRAATVAEVAP
+RIADVDATLASFRSTGVRELDRVLGGGLVPGAVILLAGEPGIGKSTLLLDVAAQTARGAG
+GGGPRSVLYLTGEESAAQVRSRADRIGAIADTLRLTAETDLGRALGQIERTDPELVIVDS
+VQTLQSTEVDGIAGGVSQVREVAASLIRTAKEKGITTVLVGHVTKDGTIAGPRLLEHLVD
+VVCQFEGDRHSRLRLVRAVKNRFGPTDEVGCFDLREDGIESLDDPSGLFLSGVSEPVEGT
+CVTVTLEGRRPLVAEVQSLLTPSAGGSPRRTVSGVDAARVNMLLAVLQRRARFALAQDDC
+YVATVGGVRLSEPASDLAVAVAVASAKLSAPVPQGMIAVGELGLAGEVRPVPGIGRRVRE
+AARLGFTRALVPRSPEPLGEVPAGFTVAEVGSIGEALATIPTWTGGGPAARPEVGPGR

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000061.fa

@@ -0,0 +1,30 @@
+>ACLBLIBL_00071
+MTVLTPAWFAASGGVPTMGAGAAAASGAGAWDPSALLDSLGAWFHPLTALLVALDAPIPP
+VPSEVFVIGSGALAAEGRVGLAAAVLTAWLGCWAGDVGLYALFRHGLADRLDRWAWWRRV
+HRGIRVLLVRVGPAGSLAGLSVLRFVSGGRTASMAAAGIGGIRWPVFLWLSGAGSLAWSG
+WMVGLGWLTGRTTGLPWWASAVVGMVFGTLAGLIIAGVVARRRARKG
+>MOLHKGIG_00282
+MTGGDPAALMDALGAWFHPLTALLVALDAPIPPVPSEVVVIGSGALAAEGRVSPVAAVLA
+AWLGCWAGDVGLYALFRHGLADRLDRWAWWRRIHRGIRSLLVRVGPAGSLAGLSVLRFVS
+GGRTASMAAAGIGGIRWPVFLWLSGAGSLAWSSSMVGLGWITGRATGLPWWASAMVGMVF
+GTLAGLMIAGIMAHRRRGRKG
+>NAFOICDF_00057
+MTDVTALLEGLGPWFHPLTFLLVALDAPVPPTPSEVLVIGSGSLAAAGRLGLATSVLTAW
+LGCWAGDVGLYALFRHRLTSVLDRWGWGRAVHAGIRRLMEKAGPASSLAGLFVLRFVSGG
+RTASMAAAGVAGVRWRPFLWLSGTGSLAWSVYMVGLGWITGSATGLPWWASAVVGVVLGT
+LLGAAVAAVIAWRRRGKEGA
+>NAFOICDF_00450
+MPVLTNILDAASILHSLGPWTLGGIGSMVFIESGVLFPFLPGDSLLVTAAALHVELGIAL
+WAIILVAGLAAILGDQVGFYLGHRYGRRLFKDDARVLKTERLAQAEAFFERRGPLALVLG
+RFVPIVRTYVPVAAGTAGMPYRSFVGWNIGGAVAWVCSMVAVGALLGQIPGITKSIDGIM
+ILIIVISVAPIAIQALRARRKARRDAVMTEGQPVA
+>MHAAABBN_02297
+MTGGDPAALMDALGAWFHPLTALLVALDAPIPPVPSEVVVIGSGALAAEGRVSPVAAVLA
+AWLGCWAGDVGLYALFRHGLADRLDRWAWWRRIHRGIRTLLVRVGPAGSLAGLSVLRFVS
+GGRTASMAAAGIGGIRWPVFLWLSGAGSLAWSGSMVGLGWLTGRATGLPWWASAVVGMVF
+GTLAGLMIAGIMAHRRRGRKG
+>LFPAFLNI_00281
+MTGGDPAALMDALGVWFHPLTALLVALDAPIPPVPSEVVVIGSGALAAEGRVSPVAAVLA
+AWLGCWAGDVGLYALFRHGLADRLDRWAWWRRIHRGIRSLLVRVGPAGSLAGLSVLRFVS
+GGRTASMAAAGIGGIRWPVFLWLSGAGSLAWSGSMVGLGWITGRATGLPWWASAVVGMVF
+GTLAGLMIAGIMAHRRRGRKG

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000062.fa

@@ -0,0 +1,47 @@
+>ACLBLIBL_00074
+MTQTATPQTDAPAVPAIFEPIEINGVRVRNRLILPPMCQYSCEARDGVPHGWQFQHLGAR
+AAGGFGIVVTEATAVTPEGRISPWDTGLWNDEQRDAWAPIAEFIASEGALPAIQLGHAGA
+KASTVPMHPGAPAGQPILEGPDSWETLSPSGVATNSMEIRTHAMRVDEIRETVQAFADAA
+ERADRAGFGAVQLHAAHGYLIHQFLSPLTNTRTDEYGGDFEGRTRFLKEVVAAVREVWPA
+DKVLGIRISGTDWVEGGWSIEETVRLAQELQGQVHWFDLSSAGIGDTYEGPQGPGYQVPL
+ATAVKEGTEGIVVSAVGSLTGAEEVAAVVDEDRADAVCVGRAALANPNWPTAAALALDVP
+SEQVPMARQYFRAKW
+>MOLHKGIG_00279
+MTQTATPQTDAPAVPAIFEPIEINGVRVRNRLILPPMCQYSCEARDGVPHGWHFQHLGAR
+AAGGFGIVVAEATAVTPEGRISAWDTGLWNDEQRDAWAPIAEFIASQGALPAIQLGHAGA
+KASTVPMHPGALAGQPILEGPDSWETLSPSGVATNSMEIRTHAMRVDEIRETVQAFADAA
+ERADRAGFGAVQLHAAHGYLIHQFLSPLTNTRTDEYGGDFEGRTRFLKEVVAAVREVWPA
+DKVLGIRISGSDWVEGGWSIEETVRLAQELQGQVHWFDLSSAGIGDTYEGPQGPGYQVPL
+ATAVKEGTEGIVVSAVGSLTGAEEVAAVVDEDRADAVCVGRAALANPNWPTAAALALDVP
+SEQVPMARQYFRAKW
+>NAFOICDF_02346
+MPDLFDPLPLGGLTLPNRVTMAPLTRQRAGEDGVPGDLHVEYYRQRASAGLIVSEGVFPT
+VDSRAFPGQPGLEDEAQQAGWARVADAVHEAGGRIFVQVMHGGRMCHPDLLRGAEPVAPS
+AIAPGVPVRGFSGKTDGPVPRALETEELPGIAAAFASAARRAVDAGADGVEVHGANGYLL
+HEFTAASSNHRTDAYGGSPENRARLTVEVVRAVAAEIGAERTALRLSPEHDVQGVLEQDR
+ADVLATYGAILDGVADLDLAYLSLLHRDVAGDLVAALRARFGGPVLLNSGFSEVTGAAEA
+RRIVEGGLADAAVVGRALIANPDLVRRWREDRETNAPDPSTFYVGGAHGYTDYPSLEG
+>MHAAABBN_00203
+MPSLFDPLDVGALRLDNRIVMAPLTRQRAGEDGVPTELPAEHYAQRATAGLLVTEGAFPS
+FRSRAFPGQTGLADDAQTDGWRAVAQAVHEAGGHVFVQVMHGGRMCHPDLLRGAEPEAPS
+AIAPGVPVRGFSGKMEGPVPSALDTEELPRVVAEFADAARRAVEAGLDGVEVHGANGYLL
+HEFLAPSSNTREDAYGGSPENRARLTVEVVRAVAQAIGAERTALRISPEHNVQGTIEEDR
+ADVLATYDALLAGLADLDLAYLSVIHQDVAGDLAAHLRESFSGPLVLNSGFGAVTGLEEA
+RRIVEDGLADAVAVGRELIANPDLARRWREGLPLNEPDPTTFYTGGAHGYTDYPFVDGSP
+SS
+>MHAAABBN_02294
+MTQTATPQTDAPAVPAIFEPIEINGVRVRNRLILPPMCQYSCEARDGVPHGWQFQHLGAR
+AAGGFGIVVAEATAVTPEGRISPWDTGLWNDEQRDAWAPIAEFIASEGALPAIQLGHAGA
+KASTVPMHPGAPAGQPILEGPDSWETLSPSGVATNSMEIRTHAMRVDEIRETVQAFADAA
+ERADRAGFGAVQLHAAHGYLIHQFLSPLTNTRTDEYGGDFEGRTRFLKEVVAAVREVWPA
+DKVLGIRISGSDWVEGGWSIEETVRLAQELQGQVHWFDLSSAGIGDTYEGPQGPGYQVPL
+ATAVKEGTEGIVVSAVGSLTGAEEVAAVVDEDRADAVCVGRAALANPNWPTAAALALDVP
+SEQVPMARQYFRAKW
+>LFPAFLNI_00278
+MTQTATPQTDAPAVPAIFEPIEINGVRVRNRLILPPMCQYSCEARDGVPHGWQFQHLGAR
+AAGGFGIVVAEATAVTPEGRISPWDTGLWNDEQRDAWAPIAEYIASEGALPAIQLGHAGA
+KASTVPMHPGAPAGQPILEGPDSWETLSPSGVATNSMEIRTHAMRVDEIRETVQAFADAA
+ERADRAGFGAVQLHAAHGYLIHQFLSPLTNTRTDEYGGDFEGRTRFLKEVVAAVREVWPA
+DKVLGIRISGSDWIEGGWSIEETVRLAQELQGHVHWFDLSSAGIGDTYEGPQGPGYQVPL
+ATAVKEGTEGIVVSAVGSLTGAEEVAAVVDEDRADAVCVGRAALANPNWPTAAALALDVP
+SEQVPMARQYFRAKW

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000066.fa

@@ -0,0 +1,31 @@
+>ACLBLIBL_00111
+MHDAGHTDYSAAHIARTADGTAASGAVSAGPGGRRPGPTTPADAGRSRGSRYADRVSEDL
+RILIADDQPLMSGALRVLVSSAPGMTCVGVVANGAEAVEACAAVEPDVVLMDMQMPLMDG
+VEATSRIKEAHPGIRILAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIHAVHRGE
+SVLSPAVASKLLASIERDHPVVGPAQARPGDPDGSDLTDRERDVLRLLARGQSNPEIAAN
+LHVSESTIKSNLTRIMDKLEVRDRVQVIIRAAQLGLVTLSLD
+>MOLHKGIG_00258
+MSEELRILIADDQPLMSGALRVLVDSAPGMTCVGVVANGVEAVEACAAIEPDVVLMDMQM
+PLMDGMEATRRIKDTHPAIRVLAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIQA
+VHRGESVLSPAVATKLLASIERDRPTVGPTSVQPGSPDGSDLTERELGVLRLLARGQSNP
+EIAANLFVSESTVKANLTRIMAKLEVRDRVQLIIRAAQLGLVTLALD
+>NAFOICDF_00079
+MPDSPEDEIRVLIADDQPLMSGALRVLVDSAPGMRCVGLVADGVEAVEAVEATRVDVVLM
+DMQMPRMDGVEATRRITASRPGTRVLAVTTFSSEDYLVPALRAGAAGYLLKDAEPATVLG
+AVEAVRRGESVLSPAVAAKLIAAVERDHPVVGPAAAEPGDPDGSDLTEREHQVLTLLARG
+RSNPEIAAELQVSESTVKANVGRVIDKLEVRDRVQVVIRAAQLGLVTLSLD
+>NAFOICDF_00526
+MDAITVLIVEDEPLLTQAYTMILEADPGIRVVGTASDGAAGVAEHERLRPDVVLMDLRMP
+VLDGVEATGRIMREHPEAKVLVVTSMTTEDYLSPALANGAAGYLTKDTDAEGLVRAVRAV
+EAGTMALGPSIAREVVDLLLRSGVAPRTDAPASPRDLPEALTPREQDVLELLAEGLTNQE
+MAARLYVSDSTVKSNLARVMHKLGANNRVQALVLGVRAGLVSIPG
+>MHAAABBN_02272
+MSEELRILIADDQPLMSGALRVLVASAPGMTCVGVVANGVEAVEACAAVEPDVVLMDMQM
+PLMDGVEATRRIKEAHPEVRVLAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIQA
+VHRGESVLSPAVATKLLASIERDRPTVGPTSVQPGSPDGSDLTERELGVLRLLARGQSNP
+EIAANLFVSESTVKANLTRIMAKLEVRDRVQLIIRAAQLGLVTLALD
+>LFPAFLNI_00257
+MSEELRILIADDQPLMSGALRVLVDSAPGMTCVGVVANGVEAVEACAAIEPDVVLMDMQM
+PLMDGVEATRRIKDTHPAIRVLAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIQA
+VHRGESVLSPAVATKLLASIERDRPTVGPTSVQPGSPDGSDLTERELGVLRLLARGQSNP
+EIAANLFVSESTVKANLTRIMAKLEVRDRVQLIIRAAQLGLVTLALD

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000068.fa

@@ -0,0 +1,54 @@
+>ACLBLIBL_00129
+MAEFSAAPTAHPAESDTHVSPAQRRKAFVGAIAGHLIEWYDYGVYGFLAVYVAANFFKSE
+NPMVGILAAFAVFALSFFVRPLGGLFFGPLADKIGRRKTLMIVLGLMCGATAVIGMLPTY
+ATIGVFAPILLVLMRLVQGFSAGGEVSTISAFVAEYAVKGRRGFATSFLMVTAASGLLLG
+GVVANGLGAIIGTEAMAEWGWRLPFLLAGVLGVVAVFIRMKLEDSPEFRRLHSEGKTSKT
+PLRETLRYQRQLFLMGALITLLGSTFYLVLTYLTTYMRTILELTPGAIFWLVLLTGAAAA
+AFMPVGGAISDRMGDRRPMLAIGAVLVAGAVVWFFLTAPGTDGGLPLVPSLLALGITTGL
+YCGVPYATMTELMPAHVRSTGIALGYNVPVAVFGGSAPFIASWLINETGDVASPMYFFLL
+TAAIALVGVAMLRPTDLLGHEDVPVTGSIDAVGGKVTRTVAPRPKADAL
+>ACLBLIBL_00826
+MSHTTVAHGAEHPARTRDRAEERKVLAGTLVGTTIEWYDFFIYAQAAALVFAPLFFAPMG
+EQGAQIASWASLGISFLVRPLGAIVAGHMGDRFGRKLVLSLTLIGMGAATVLIGLLPTYA
+SIGIWAPILLVVFRLLQGFSAGGEWGGAALLSVEHAPRGKRGLFGSAPQIGVPLGMLLAT
+GVLFAVRASMTNEQFLAWGWRIPFLISVILIFIGYIIRKAVEESPVFKEMQQLKKDESAP
+LGELFRNHTKEVVLAALIFAANNAVGYLVIAWFSKYGQKNLGMAPNDTLIAALVGGFGWF
+IFTLFGGWISDKIGRKTAFVAGYALIIAWAFPMFQMMNTASLPMFAAALFILSIGLGPSY
+GPQSAMYAEMFPARVRFSGVSIGYAIGAIIGGAFAPLIADLLLNDGGWVPVAWYMIIISA
+VSLIAVLFVPKGIQDRNLHDEGVVVAETGTREPVA
+>MOLHKGIG_02014
+MSHTVASPAAPVPARDRREERKVIAGTVVGTTIEWYDFFIFAQATALVFAALFFQPMGEN
+GSQIAAWVTLGISFLVRPLGAIVAGHLGDRFGRKLVLSLTLIGMGLATTLIGLLPTYAQI
+GVWAPILLVALRLLQGLSAGGEWGGAALLSVEHAPHGKRGLFGSAPQIGVPLGMILATGV
+LFIVRSTMSEEQFLTWGWRIPFLISVILIVVGYLIRKAVEESPVFKEMQQLKVDESAPLG
+ELFRHHTKEVILAAVIFAANNGVGYLLIAWFSKYGGPKGLGMTSSEVLIASLVGGVGWFI
+FTLLGGWVSDKIGRKLTFVFGYGFLIVWAFPLFGLLNTASLPLFSLGLFVLTLGLGPSYG
+PQSAMYAEMFPARVRFSGVSIGYALGTIIGGAFAPLLADQLVKTGWENVAWYIIVISAIS
+LIAVLFVPKGIQDRELHDEQVVATRSNPVVPT
+>NAFOICDF_00765
+MSHTVASPAVAAARDPREERKVLAGTLVGTTIEWYDFFIFAQATALVFATLFFQPMGESG
+AQIAAWVTLGISFLVRPLGAIIAGHLGDKFGRKLVLSLTLIGMGAATTLIGLLPTYAQIG
+VWAPILLVLLRLLQGFSAGGEWGGAALLAVEHAPHGKRGLFGSAPQIGVPLGMILATGVL
+FLVRSTMSEEQFLTWGWRIPFLVSVLLIVVGYFIRKAVEESPVFKEMQQLKVDESAPLGE
+LFRHHTKEVILAAVIFAANNGVGYLLIAWFSKYGGPKGLGMTSSEVLIASLVGGVGWFIF
+TLLGGWISDKIGRKTTFVIGYAILIAWAFPMFQLLNTASLLLFSLALFVLTMGLGPSYGP
+QSAMYAEMFPARVRFSGVSIGYAIGTIIGGAFAPLIADELVKSGWPSVAWYIIGISAISL
+IAVLFVPKGIQDRELHDEEVVATRSNPVVPA
+>MHAAABBN_01724
+MSHTVASPAAPAPARDRREERKVIAGTVVGTTIEWYDFFIFAQATALVFAALFFQPMGES
+GSQIAAWATLGISFLIRPLGAIVAGHLGDRFGRKFVLSLTLIGMGLATTLIGLLPTYAQI
+GVWAPILLVALRLLQGLSAGGEWGGAALLSVEHAPHGKRGLFGSAPQIGVPLGMILATGV
+LFIVRSTMSEEQFLTWGWRIPFLISVVLIVVGYLIRKAVEESPVFKEMQQLKVDESAPLG
+ELFRHHTKEVILAAVIFAANNGVGYLLIAWFSKYGGPKGLGMTSSEVLIASLVGGVGWFI
+FTLLGGWVSDKIGRKLTFILGYGFLIIWAFPLFGLLNTASLPLFSLGLFVLTLGLGPSYG
+PQSAMYAEMFPARVRFSGVSIGYALGTIIGGAFAPLLADQLVKTGWENVAWYIIVISAVS
+LIAVLFVPKGIQDRELHDEQVVATRSNPVVPA
+>LFPAFLNI_01952
+MSHTVASPAAPVPARDRREERKVIAGTVVGTTIEWYDFFIFAQATALVFAALFFQPMGES
+GSQIAAWVTLGISFLVRPLGAIIAGHLGDRFGRKLVLSLTLIGMGLATTLIGLLPTYAQI
+GVWAPILLVALRLLQGLSAGGEWGGAALLSVEHAPHGKRGLFGSAPQIGVPLGMILATGV
+LFIVRSTMSEEQFLTWGWRIPFLISVALIVVGYLIRKAVEESPVFKEMQQLKVDESAPLG
+ELFRNHTKEVILAAVIFAANNGVGYLLIAWFSKYGGPKGLGMTSSEVLIASLIGGVGWFI
+FTLLGGWISDKIGRKLTFVLGYGFLIVWAFPLFGLLNTASLPLFSLGLFVLTLGLGPSYG
+PQSAMYAEMFPARVRFSGVSIGYALGTIIGGAFAPLLADQLVKTGWENVAWYIIVISAIS
+LIAVLFVPKGIQDRELHDEQVVATRSNPVVPA

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000072.fa

@@ -0,0 +1,31 @@
+>ACLBLIBL_00163
+MSALAARARAGLAHAVLAVAGARIHASGPDGAEEAEITRERLAALLPRQAVFYANHTSHL
+DFVTLWAVLPPALQRRVRPVAAADYWGSGLRRRVAEGLFHAYLVERGKTRRRGPGAASGS
+GVSPDGGSQLEGMLEILAGGDSLIIFPEGTRGSGEDVARFQRGLHALAAAFPQVPVVPVS
+LVNLGRILPKGEPIPVPHLSTVRFHPPLDPPEPARPPGPGAPASGTAATDAPEPGRGEDE
+AARTAWLERARAVLVQDLSASLRG
+>ACLBLIBL_01775
+MATSEPVRRSAAALLRLTCRPEVTGMDQVPAEGPFIMASNHLSFFDSVILQALAPRPVHF
+FAKEEYFTGAGVRGRAQRWFFESVGSVPVRRGEQAASVAALESLVGLLDSGQGVGIYPEG
+TRSRDGRLYRGRTGAAWLALTTGAPVVPVGLVDTQHLQPPDTNGFRPHRFAVRVGAPLDF
+GHPGRRHTLPQRRDATAAIMDAIGALSGQERLDAYNAAPGARG
+>MOLHKGIG_01118
+MATSEPVRRSAAALLRLTCRPEVVGMEHVPARGPFVMASNHLSFVDSVILQALAPRPVHF
+FAKEEYFTGTGLRGRVRRRFFESVGSVPVRRGEQAASVAALESLVGLLESGQGVGIYPEG
+TRSRDGRLYRGRTGAAWLALATGARVVPVGLVGTQHLQPPDTNGFRPHRFSVRVGAPLDF
+GHPGRRHTLPQRRDATAAIMDAIGALSGQERVDAYNAAPGARG
+>NAFOICDF_01668
+MATSEQLRRAVAGAIRLSCRPHVRGLEHVPPEGPFIVASNHLSFVDSVILQALCPRPVGF
+FAKAEYFEAPGLRGRAQRRFFEAVGSIPVRRGEQAASVAALEDLVALLDGGHGVGIYPEG
+TRSRDGRLYRGRTGAAWLALTTGAPVVPVGLRGTERLQPPGTNGFRPHRFTVEMGEPLDF
+GHPGRRHSLPQRREATATIMAAIAALSGQERVDEYNAAPAARG
+>MHAAABBN_00837
+MATSEPVRRSAAALLRLTCRPEVVGMEHVPARGPFVMASNHLSFVDSVILQALAPRPVHF
+FAKEEYFTGTGLRGRVRRRFFESVGSVPVRRGEQAASVAALESLVGLLESGQGVGIYPEG
+TRSRDGRLYRGRTGAAWLALATGAPVVPVGLVGTQHLQPPDTNGFRPHRFSVRVGAPLDF
+GHPGRRHTLPQRRDATAAIMDAIGALSGQERVDAYNAAPGARG
+>LFPAFLNI_01068
+MATSEPVRRSAAALLRLTCRPEVVGMEHVPARGPFVMASNHLSFVDSVILQALAPRPVHF
+FAKEEYFTGTGLRGRVRRRFFESVGSVPVRRGEQAASVAALESLVGLLESGQGVGIYPEG
+TRSRDGRLYRGRTGAAWLALATGAPVVPVGLVGTQHLQPPDTNGFRPHRFSVRVGAPLDF
+GHPGRRHTLPQRRDATAAIMDAIGALSGQERVDAYNAAPGARG

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000073.fa

@@ -0,0 +1,17 @@
+>ACLBLIBL_00167
+MENSLPAERARLGWSQQRLADELGVSRQTVISLEKGRHDPSLALAFRLAETFGTRIEDLF
+SPDPPA
+>ACLBLIBL_02206
+MSIDRLAEAAAIHRRTIIQIEAGRTAPRVTTLYAIAEATGTPLRDLLAPLDEALERGTR
+>MOLHKGIG_00216
+MENTIPDERARLGWSQQRLADELGVSRQTVISLEKGRYDPSLPLAFRLAAVFGRRIEDLF
+TPDGNAG
+>NAFOICDF_00321
+MARLARAFKVHKANSGMTYDQLAEATGLARQTLLNLAAGRTYGDLRTWLILAKVWGVTLD
+DLTAAAWRGHAGG
+>MHAAABBN_02209
+MENTIPDERARLGWSQQRLADELGVSRQTVISLEKGRYDPSLPLAFRLAAVFGRRIEDLF
+TPDGNAG
+>LFPAFLNI_00216
+MENTIPDERARLGWSQQRLADELGVSRQTVISLEKGRYDPSLPLAFRLAAVFGRRIEDLF
+TPDGNAG

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000078.fa

@@ -0,0 +1,72 @@
+>ACLBLIBL_00193
+MAPARLDPADRTQLRRHPVSLRRIARLFAPHRSTIALVVVLISAASVINLAQPFLVRAVI
+DDALPNQDVPLLIRLTAAMVGVAALTAVIGVVQTWRATAMGQHVMHSLRVRLFTHLQAQP
+LAFFTRTRGGEVQSRLTHDIAGMQSVVTSTATGVASNLTAVVATAAAMVALSPRLSLISL
+VVLPPAVWLSRRVAQLRRAVTDKRQAALAQMHTQVEEGLSVSGARLSKTLGTTGHDAERF
+TGRSHELIGLELRSQLAGRWRMATMSIVFAAIPAVIYLAAGLPPTSGGMTIGTLVAFTAL
+QGQVFRPVMGLLNIGVQWVTALAFFSRIFEYLDLDPAIKPPADPVPVDPARVRGTVRFEG
+VDFAYDDGAPALSGIELTVPAGTTTAVVGSTGSGKSTLASLVPRLHDPTAGRVSIDGIDV
+ARLDPADLAAIVGVVSQETYLIHASVRDNLRLADPEATDERLWAALETASLARTVAALPE
+GLDTLVGARGHRFSGGEQQRLAIARTVLRNPPVLVLDEATSALDNTTEARVQAALDELAE
+HRTTLLVAHRLSTVMGADQVAVLEGGRIVELGAPTELLRAGGPFAALAARGDAVVPGAAP
+AEPALAR
+>ACLBLIBL_02595
+MESAARVSMMRMTHGQNGATQPLAKGTVRRTIAFADRYRARLIVFVLASIVGAVLGVASP
+VLAGDVVNAITGGDDGGLVVRLALLIALVAVLDAALSVFTKWLSSGLGERVIFDLRTQVF
+DHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTLSGVVANVVSVALTLGVMVATSW
+QVTVLSLLLLPLFLIPARAVGSKLAGLSRERAGHNAAMGDQMTERFSAPGATLIKLFGRP
+AAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDAGD
+VVTLALLLTRLYAPLTALANARVEIMSALVSFERVFEVLDLQPLIIEPARPAALPAGPLS
+VRLRDVRFSYPTAQEVSLASLEEVAVLDTRGGEEVLHGIDVAVPAGSTVALVGSSGAGKS
+TIASLVTRLHDVSSGAVELGGVDVRDLSFADLQEAVGMVTQDGHLFHDTVRGNLLLARPD
+ATEEQLWDAVERARLRPVIEALPDRLDTVVGERGYRLSGGERQRMTIARLLLAAPRVVVL
+DEATAALDSTNERAIQEALGEALTGRTAIVIAHRLSTVRSADEILVVEAGRIVERGGHAE
+LLAAGGRYAELYTTQFADAE
+>MOLHKGIG_00366
+MSMESAARMSMMRMTRGQSDAQQSLARGTVRRTIAFAGRYRTRLIVFVAASIVGAVLGVA
+SPVLAGDVVNAITGGADRGLVVRLALLIALVAVLDAALSVFTKWLSSGLGERVIYDLRTA
+VFDHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTLSGVVANVVSVALTLGVMVAT
+SWQVTVLSLVMLPLFLVPARAVGSKLADLSRERAGHNAAMGDQMTERFSAPGATLIKLFG
+RPAAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDA
+GDVVTLALLLTRLYAPLTALANARVEIMSALVSFERVFEVLDLEPLITEPARPAALPEGP
+LSVRLRDVRFAYPTAEQVSLASLEEVAVLDTRGGEEVLHGIDVAVPAGATVALVGSSGAG
+KSTIASLVTRLHDVTSGAVEIGGVDVRDLAFADLQRAVGMVTQDGHLFHETVRANLTLAR
+PDATDEELWDAVERARLRPVVEALPDGLDTVVGERGYRLSGGERQRMTIARLLLAAPRVV
+VLDEATAALDSTNERAIQEALGEALAGRTAIVIAHRLSTVRSADEILVVEAGRIVERGTH
+AALLAADGRYAELYTTQFADAE
+>NAFOICDF_02454
+MSMESVARVSMMRLQRGGTAPQPLAPGTVRRTVAFAAQYRARLIVFVAASVVSAVLGVAS
+PVLAGDVVNAITGGTDRALVVRLALLIAAVALADAALSVFTKWLSSGLGERVIYDLRTRV
+FDHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTLSGVVANAVSLALTLAVMLATS
+WQITLLSLVLLPLFLVPARMVGGRLAALSRERAGHNAAMGDQMTERFSAPGATLIKLFGE
+PGAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDAG
+DVVTMALLLTRLYAPLTSLANARIEIMSALVSFERVFEVLDLEPLITEPAHPVPVPDGPL
+AVTLDDVHFAYPSAQEVSLASLEEVAVLDTRGGEEVLHGVDVDVPAGRTVALVGSSGAGK
+STIASLVTRLYDVTSGAVRLGGVDVRDMAFADLHRAVGMVTQDGHLFHDTVRGNLLLARP
+AATDAEVWDAVDRARLRGVVESLPDGLDTVVGERGYRLSGGERQRMTIARLLLAAPRVVV
+LDEATAALDSTNERAIQEALREALAGRTAVVIAHRLSTVRDADEILVVEGGRIVERGPHA
+ALLAAGGRYAELYTTQFAEGA
+>MHAAABBN_00082
+MSMESAARMSMMRMTRGQSDAQQSLARGTVRRTIAFAGRYRTRLIVFVAASIVGAVLGVA
+SPVLAGDVVNAITGGADRGLVVRLALLIALVAVLDAALSVFTKWLSAGLGEQVIYDLRTA
+VFDHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTLSGVVANVVSVALTLGVMVAT
+SWQVTVLSLVMLPLFLLPARAVGSKLAGLSRERAGHNAAMGDQMTERFSAPGATLIKLFG
+RPAAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDA
+GDVVTLALLLTRLYAPLTALANARVEIMSALVSFERVFEVLDLEPLITEPARPAALPEGP
+LSVRLRDVRFAYPTAEQVSLASLEEVAVLDTRGGEEVLHGIDVAVPAGATVALVGSSGAG
+KSTIASLVTRLHDVTSGAVEIGGVDVRDLAFADLQRAVGMVTQDGHLFHETVRANLTLAR
+PDATDEQLWDAVERARLRPVVEALPDGLDTVVGERGYRLSGGERQRMTIARLLLAAPRVV
+VLDEATAALDSTNERAIQEALGEALAGRTAIVIAHRLSTVRSADEILVVEAGRIVERGTH
+AALLAAGGRYAELYTTQFADAE
+>LFPAFLNI_00373
+MSMESAARMSMMRMTRGQSDAQQSLARGTVRRTIAFAGRYRTRLIVFVAASIVGAVLGVA
+SPVLAGDVVNAITGGADRGLVVRLALLIALVAVLDAALSVFTKWLSAGLGERVIYDLRTA
+VFDHVQRMPVAFFQRTRTGALVSRLNNDVIGAQSAISRTLSGVVANVVSVALTLGVMVAT
+SWQVTVLSLVMLPLFLLPARAVGSKLAGLSRERAGHNAAMGDQMTERFSAPGATLIKLFG
+RPAAESAEFARRADRVRATGVDISVRQAVFTTLLTLVSALALAAVYGVGGLQAIAGTLDA
+GDVVTLALLLTRLYAPLTALANARVEIMSALVSFERVFEVLDLEPLITEPARPAALPEGP
+LSVRLRDVRFAYPTAEQVSLASLEEVAVLDTRGGEEVLHGIDVAVPAGATVALVGSSGAG
+KSTIASLVTRLHDVTSGAVEIGDVDVRDLAFADLQRAVGMVTQDGHLFHETVRANLTLAR
+PDATDEQLWDAVERARLRPVVEALPDGLDTVVGERGYRLSGGERQRMTIARLLLAAPRVV
+VLDEATAALDSTNERAIQEALGEALAGRTAIVIAHRLSTVRSADEILVVEAGRIVERGTH
+AALLAAGGRYAELYTTQFADAE

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000079.fa

@@ -0,0 +1,37 @@
+>ACLBLIBL_00197
+MRLIPLVLLSLLCQQLGASVAGLMFGTTGPAGMVALRLAFSALVLLVLTRPRMRTLAGLS
+RRGWVAVVMLGVTMAGMNLLIYAAFDRIPQGVAVTFEVLGPLALSVLANRRWLSVVWAAL
+AFAGIALLGRDGFSAGMDGAGLDPLGVAFALAAAACWAGFILANRHAGTHLPGVQGLALA
+MVVGSAVAVPVGAADAGPVLLEPWVLAVGLGVALLSSSIPYGIEMQVLRTMPTGLFSLIT
+CLSPVVAALTAWAVRGQRLAVLDLGGMGLVVLACGAAVWAAERAARPSRRAPRTS
+>MOLHKGIG_00198
+MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG
+PRGWAAVVGLGAAMTGMNLAIYEAFARIPQGVAVTFEVLGPLALSVAARPSWRSAAWAAL
+ALAGIGVLGREGFSADGGIGGAGLDPVGVALALAAAACWAGYILLSRRAGTHLPGVQGLA
+LATAAGSLVALPVGVATAGAALLSPVVLGVGLAVALLSTAVPYGIDLQVLRRMPTALFSL
+LTCLSPIAAALTAWAVRGQELTPLDLAGMLLVIAACAAAVWTSRSPGVAGGGRG
+>NAFOICDF_00149
+MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG
+PRGWAAVVGLGAAMTGMNLAIYEAFARIPQGVAVTFEVLGPLALSVAARPSWRSAAWAAL
+ALAGIGVLGREGFSADGGIGGAGLDPVGVALALAAAACWAAYILLSRRAGTHLPGVQGLA
+LATAAGSLVALPVGVATAGAALLSPVVLGVGLAVALLSTAVPYGIDLQVLRRMPTALFSL
+LTCLSPIAAALTAWAVRGQELTPLDLAGMLLVIAACAAAVWTSRSPGVAGGGRG
+>MHAAABBN_02026
+MAVAVYPLAFYTSIHWAGVAIGSVVSLASAPLASGLLERIVEYRRLSRWWMLAAALGGTG
+AALLCLSQLDQEAASSTATLAGVLLGLVAGATYATYSWAAHRLIHDGISRAASMGAVFGA
+GGALLLPVLVLTGAPLIATPQAFAVAAYMALVPMFLGYVLFGYGLTRVPASTATTITLTE
+PAIAAILAVAVVGERLTPVGWTGLGIIAAVLFILALTPTNTTADRHGRTPTSEAIQPALA
+PSPRRHNERTSPRDDAGRGSDVMWVSQTMRCQGATRPSRWEGVRGRFRKPYRLRPVSPDH
+GRATCGERTEIMRPARGLDARSVLAATMET
+>MHAAABBN_02194
+MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG
+PRGWAAVVGLGAAMTGMNLAIYEAFARIPQGVAVTFEVLGPLALSVAARPSWRSAAWAAL
+ALAGIGVLGREGFSADGRIGGAGLDPVGVALALAAAACWAAYILLSQRAGTHLPGVQGLA
+LATAAGSLVALPVGVATAGAALLSPVVLGVGLAVALLSTAVPYGIDLQVLRRMPTALFSL
+LTCLSPIAAALTAWAVRGQQLTPLDLAGMLLVIAACAAAVWTSRSPGVSGGARG
+>LFPAFLNI_00198
+MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG
+PRGWAAVVGLGAAMTGMNLAIYEAFARIPQGVAVTFEVLGPLALSVAARPSWRSAAWAAL
+ALVGIGVLGREGFSADGGIGGAGLDPVGVALALAAAACWAAYILLSRRAGTHLPGVQGLA
+LATAAGSLVALPVGVATAGTALLSPVVLGVGLAVALLSTAVPYGIDLQVLRHMPTALFSL
+LTCLSPIAAALTAWAVRGQELTPLDLAGMLLVIAACAAAVWTGRSPGVAGGGRS

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000085.fa

@@ -0,0 +1,44 @@
+>ACLBLIBL_00354
+MQQIHDPASRGFASDNYSGVHPEVLAAIAEANGGHQTAYGEDAYTGRLAEVVRGHFGEDA
+QVWPMFNGTGANVVALQSMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLTVPTPDGKL
+TPELIDVQAWGWGDEHRAQPLVVAITQSTELGTLYTPEEIRAITEHAHARGMTVFLDGAR
+LANAAAALDLPLRAFTTDVGVDVLSLGGTKNGALGAEAVVALNPAATTGMTYLRKSQMQL
+ASKMRFVSAQLLALFDGDLYLRTARHANAMAQRLQDAVAAGIADGSLPGVALTQRAQVNA
+VFATLPAGVADRLRRSFRFYDWDEANGEVRWVCSFDTAEEDVDAFVAALRAELAPAD
+>ACLBLIBL_01608
+MSAGAPAAGLRAFASDNYAGVHPDVWAALADVDAHHAPAYGADPHTERLQEAVREAFDAP
+DAVALPVFNGTGANVVALQSMLPPWGAVVAADTSHIHHDEGGAPERMGRTKLFTVPTPDG
+RLTPELVDREAHGWGFVHRAQPAVVEIAQVTELGTVYTPEQVRALADHAHGHGMGLYMDG
+ARLFNAAAALELPLSAFTTHAGVHVVSLGGTKAGALGAEAVVVLRPEAVTLASLVPERDL
+PADAGPRERARLAVEYVRKSSMQLASKMRYVSAQLTALLKGDLGIRLAGHANAMARELAG
+RVAGIDGVEVTRTPEANAVFAVLDPQAADRARVRHPFYDWDAARHEVRWMTSWDTTAADV
+DSFAAALGEALSPGRRR
+>MOLHKGIG_00049
+MQRIHDPQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHFGEDA
+TVWPMFNGTGANVVGLQAMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDGKL
+TPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPDEVKAITDYAHEHGMRVYMDGAR
+IANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAADGLVYLRKNQMQL
+ASKMRFVSAQLLALFDGDLYLRSARHANAMAARLRAGIEAGVADGSLAGVEFTQATDANA
+VFAVLPEGVADRLRARFRFYDWDAARREVRWVCGFDTTEEDVDAFTAALRAELVPAA
+>NAFOICDF_01503
+MSAARPAGLRAFASDNYAGVHPDVWAAMADADADHAVSYGEDPTSAALQEKVREVFGERA
+FAVPVFTGTAANVLALQALTPPWGSVVTAASSHLIHDEGGAPERLGRTPLVPVPTPDGRL
+TGELAAAHVRRDGFVHASQPAVVEIAQATELGTVYSAAQVREVADAAHAAGAALYMDGAR
+LSNAAAALDLPLRAFTTDAGVDVVSYGGTKNGGLGAEAVIVLNPEAVVAARMVGPADVPG
+GDAADARDRARAALGYLRKQDMQLASKHRYLAAQLLALLTDDLGIALAAQANRMARVLAD
+AVAGLDDVELARAPEANAVFARLDPDVAAEVRLRHPFYDWDAAAHEVRWMTSWDTTDADV
+ESFVDALAAALRARRPR
+>MHAAABBN_02062
+MQRIHDPQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHFGEDA
+TVWPMFNGTGANVVGLQAMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDGKL
+TPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPEEVKAITDYAHEHGMRVYMDGAR
+IANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAADGLVYLRKNQMQL
+ASKMRFVSAQLLALFDGDLYLRSARHANAMAARLRAGIEAGVADGSLAGVEFTQATDANA
+VFAVLPEGVADRLRTRFRFYDWDAARREVRWVCGFDTTEEDVDAFTAALRAELVPAA
+>LFPAFLNI_00044
+MQRIHDPQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHFGKDA
+TAWPMFNGTGANVVGLQTMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDGKL
+TPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPDEVKAITDYAHEHGMRVYMDGAR
+IANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAADGLVYLRKNQMQL
+ASKMRFISAQLLALFDGDLYLRSARHANAMAARLRAGIEAGVADGSLAGVEFTQATDANA
+VFAVLPEGVADRLRARFRFYDWDAARREVRWVCGFDTTEEDVDAFTAALRAELVPAV

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000086.fa

@@ -0,0 +1,35 @@
+>ACLBLIBL_00370
+MERGPVVGLLDNLERGLERAVRSAFSAGGPRAVKPVEIASALRQAMDDESFALSEGHTVA
+PNSYVVHFSPADFDRARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDTDVRAGD
+LRVVTGLDDGSLPAPAPHDDGASPATAHGPGATATAPDRLVEDLLGGRTP
+>ACLBLIBL_00371
+MGRPVTEPSGPALELDGRMLPLDGDDLILGRSAERADLVIPDSSVSREHLRLLTVGSTVT
+LLDLGSRNGVLVNGRRVDGSVTLRDGDVVTVGQTELLFFSGTGGRA
+>MOLHKGIG_00025
+MERGPVVGLLDNLERGLERAVRSAFSAGGPRAVKPVEIASALRQAMDDESIALSEGHTVA
+PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRGGD
+LRVVTRLDDGSLTAPAPHDDGASPATAHGPGATAPAPDRLVEDPPAAAPREPSPAPRVGP
+RPAPRRAAAPAAPAAPSHADQPTVVMGRPVTEPAGPALELDGRMLPLDGDDLILGRSAER
+ADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRDGDVVTVGQTE
+LLFFGGTGGRA
+>NAFOICDF_00353
+MGLLDNLERGLEKAVRSAFSAGGARAVQPVEIASALRHAMDDESFALSEGHTVAPNDFTV
+HFAPADFDRARTWGSTLAGELCDEVIRHAQSQGYTLPGSVRVAFHEDAQVHAGQVEVDAR
+IDDGSSPVPSPPAATSAPAPAAARTADDRGPRPSRAPRHGATAAPAPRRDPSPAPRPAPT
+PARSESARRAPADEQATVVMPRRTSPAPAVPWLEADGVRHPLTHEDMVLGRSSERADVVV
+PDSSVSRQHARLVRVGRSVTLIDLGSRNGVTVNGRRVDGSTVLREGDRITVGQTDLVFHI
+DPADGRPRA
+>MHAAABBN_02043
+MERGPVVGLLDNLERGLERVVRSAFSAGGPRAVKPVEIASALRQAMDDESLALSEGHTVA
+PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRAGD
+LRVVTRLDDGSLTAPAPHDDGASPATAHGPGASAAAPDRLVEDLPAAAPREPSPAPRVGP
+RPAPRRAAAPAAPAAPAAPAAPAHADQPTVVMGRPVTGPAGPALELDGRMLPLDGDDLIL
+GRSAERADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRDGDVV
+TVGQTELLFFGGTGGRA
+>LFPAFLNI_00025
+MERGPVVGLLDNLERGLERVVRSAFSAGGPRAVKPVEIASALRQAMDDESFALSEGHTVA
+PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRAGD
+LRVVTRLDDGSLTAPAPHDDGASPATAHGPGASAAAPDRLVEDLPAAAPRKPSPAPRVGP
+RPAPRRAAAPTAPAAPAHADQPTVVMGRPVAEPAGPALELDGRMLPLDGDDLILGRSAER
+ADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRDGDVVTVGQTE
+LLFFGGTGGRA

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000088.fa

@@ -0,0 +1,36 @@
+>ACLBLIBL_00399
+MGEYFAQTVQSGALLLAIPLAAIAGIVSFLSPCILPLVPGYLGYVSGLSDPTRPDNRRRV
+MTGVGLFILGFAAVFTLYGAAFGLIGGWLLRWQDLLIRILGVLVILMGLALMGMFTFLQR
+TTTPSFTPRTGLAGAPLLGLGFGLGWTPCMGPTLSAVLALSTTTGGAWRGALLGFVYCLG
+LGIPFVLVARGLGWVSTALGFVRRHMRAFNIAGGTLLVLVGVLMATGIWTVWIYQLQNLA
+GTFTTPV
+>ACLBLIBL_02642
+MDVQQLVADGQLLVASVIALAAGLLSFLSPCVLPLVPGYLAYVSASAGAAPGEKPARGRL
+VLGSLLFVAGFTAVLVALLAAAGTVGVWLLEWEQLITRVMGAVVILMGLVFIGAFGFMQR
+TTKLRIKPRTGLLGAPLLGVVFAIGWTPCLGPTLAAIMTLSVQQGSVARSVVLALAYCIG
+LGLPFVLAAFGFGWMTQTMTFFKRHIRTVNLIGGVLLILIGLLMVTGLWSQMMYALQAVI
+GGYVTPL
+>MOLHKGIG_00610
+MSLGGFFAEMVQSGALLVAMPLAAIAGLVSFLSPCILPLVPGYLGYVSGLADPRRADNRR
+RVMTGVGLFILGFAAVFTFYGAAFGVIGGWLLQWQDALIRALGVFVVLMGLVLIGWLPFL
+QNTRRMSFQPKTGIVGAPLLGVVFGLGWTPCMGPTLSAVLALSTTTGDPWRGALLGFLYC
+LGLGIPFVLVAMGLDWVTRTLGFVRRHIRAFNIIGGILLVLVGVLMVTGIWTLWIYQLQN
+LAGTFTTPV
+>NAFOICDF_02202
+MGEYFAQTVQSGALLLAIPLAAIAGIVSFLSPCILPLVPGYLGYVSGLSDPTRPDNRRRV
+MTGVGLFILGFAAVFTLYGAAFGLIGGWLLRWQDLLIRILGVLVILMGLALMGMLTFLQR
+TTTPSFTPRTGLAGAPLLGLGFGLGWTPCMGPTLSAVLALSTTTGGAWRGALLGFVYCLG
+LGIPFVLVARGLGWVSTALGFVRRHMRAFNIAGGTLLVLVGVLMATGIWTAWIYQLQNLA
+GTFTTPV
+>MHAAABBN_01770
+MSLGGFFAEMVQSGALLVAMPLAVVAGLVSFLSPCILPLVPGYLGYVSGLADPRRADNRR
+RVMTGVGLFIMGFAAVFTLYGAAFGVIGGWLLQWQDALIRALGVFVILMGLVLIGWLPFL
+QNTRRMSFQPRTGIAGAPLLGVVFGLGWTPCMGPTLSAVLALSTTTGDPWRGALLGFLYC
+LGLGIPFVLVAMGLDWVTRTLGFVRRHIRAFNIIGGVLLVLVGVLMVTGIWTLWIYQLQN
+LAGTFTTPV
+>LFPAFLNI_02004
+MSIGNYFAETVNSGALLIAAPLAMIAGIVSFLSPCILPLVPGYLGYVSGLSNPTHPDNRR
+RVLTGVGLFILGFAAVFTLYGAAFGTIGHWLVRWQDPMIRVLGVLVIVMGLVMVGKFSLF
+QRTLKPTLAPRTGLAGAPLLGVVFGLGWTPCMGPTLSAVLALSTTTGDPWRGALLGFLYC
+LGLGIPFLLAAAGINWVTTALSYIRRNIRVFNIIGGCLLVLVGVLMVSGLWMLWMYQLQN
+LAGTFTTPV

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000090.fa

@@ -0,0 +1,47 @@
+>ACLBLIBL_00432
+MKTSRRGGLGRGLGALIQSTAEPVDEAPQEADATAEDATAPTAAPAEKKAATSTARRLSK
+ETSEAKTPAPRAASASKSSGGAAKEAPADKKAGSAGRAPAAAKKATPTKKASSSAGEAKA
+NSAAAPAAARKTPDRAAQRPVDVFFSPDPEDAPAARRGTKARPAMPTVKAPTKREAASSS
+GEEAAAGASTAAEGTVSTDIAVLREIPVGDIHPNPRQPREVFDEEHMAELVTSIREVGIL
+QPIVVREVDGPTPYELIMGERRWRATQKAGLDAIPAIVRQTPDQDLLRDALLENLHRSQL
+NALEEAAAYQQLMEDFACTQEELAERIGRSRPQISNTLRLLKLPPLVQRRVAAGTLSAGH
+ARALLGLTDPSDMERLAQRIQAEGLSVRATEEAVAQLQGGLRPGRTPRRTADDARHERLD
+HYATALTSRLDTSVKITLGARKGRIAIDFTTVEDLNRIMDVIQGEKGGRGAAS
+>ACLBLIBL_01948
+MVASVKTQGLLQPLVVAPNPTLEGDYTIIAGHRRLDALKRAGRDDAPVIVRTDLDTEEKQ
+VAAMLQENLHRQDLTAVEEADAFAQLSLFEGWDVKRIARETGVAQTRVRSRIKLTYLSEA
+TLASLHDGQVTLERAQALAEFAGSPEEELLEEHLTATATNWDFYLARAKQTRDRRKALSA
+EQKAHEEAGFEVVPMPESLYTPEREWDRQDFESPTAALEAGAVVAFDPDYDAPVYLVKHA
+EQELEKDAAAAERKAEAAERAARNEALERELATAQETVRLWLVDTVFPKAAAGDERILRV
+AARHLAATACEETHFRRAGLAAIFCPDLGAYAPELRTAVAEVLAGKSAQELAVIIAVATR
+WTSTARVHAWRDATREDSSPAVWLAMRQELGRELAAPEQVAFDAAKAGEL
+>MOLHKGIG_02305
+MPTVKAPSKRATSATSSRKEPGDSSVESAATEGTVSADIAVLREIPVGDIHPNPRQPREV
+FDEDHMAELVTSIREVGILQPIVVREVDGPTPHELIMGERRWRATQKAGLDTIPAIVRQT
+PDQDLLRDALLENLHRSQLNPLEEAAAYQQLMEDFACTQEELSQRIGRSRPQISNTLRLL
+KLPPLVQRRVAAGTLSAGHARALLGLTDPSDMERLAQRIQSEGLSVRSTEEAVAQLQGGL
+RPGRTPRRSTDDARHERLDHYATALTSRLDTAVKITLGARKGRIAIDFTTVEDLNRIMDL
+IQGGQDGKGKGKKS
+>NAFOICDF_00384
+MSTRRGGLGRGLGALIQNTAEIEQPPTREDSSPSAASSNKTTAAPAKRSTRTARTAESSQ
+NGLPASDGATQQDHSSDRAEKTASSGTGSQKTSRSTGSKGAKTPEPTATRSAQEEVPRPA
+DIFFGGGEGTSDEPPESGRHRPTRSARPSMPTVKAPSKPAPKSETEQAAPVRKDEPEGTV
+SADIAVLRELPVGDIHPNPRQPREVFDEDHMAELVASITEVGVLQPIVVREVEGAATPYE
+LIMGERRWRATQRAGLATIPAIVRQTPDQDLLRDALLENLHRSQLNPLEEAAAYQQLMED
+FSCTQEELSQRIGRSRPQISNTLRLLKLPPLVQRRVAAGALTAGHARALLGLTDPAEMER
+LAQRIVSEGLSVRATEDAVAQLQGAVRPAPKSTRSREESTRHERLDYFATALTSRLDTQV
+KITLGARKGKIAIDFASVEDLNRIMDLIQGGGDSTPVKG
+>MHAAABBN_01998
+MPTVKAPSKRATSATSSRKEPGDSSVESAATEGTVSADIAVLREIPVGDIHPNPRQPREV
+FDEDHMAELVTSIREVGILQPIVVREVDGPTPHELIMGERRWRATQKAGLDTIPAIVRQT
+PDQDLLRDALLENLHRSQLNPLEEAAAYQQLMEDFACTQEELSQRIGRSRPQISNTLRLL
+KLPPLVQRRVAAGTLSAGHARALLGLTDPSDMERLAQRIQSEGLSVRSTEEAVAQLQGGL
+RPGRTPRRSTDDARHERLDHYATALTSRLDTAVKITLGARKGRIAIDFTTVEDLNRIMDL
+IQGGQDGKGKGKKS
+>LFPAFLNI_02246
+MPTVKAPSKRATSATSSRKEPGDSSVESAATEGTVSADIAVLREIPVGDIHPNPRQPREV
+FDEDHMAELVTSIREVGILQPIVVREVDGPTPYELIMGERRWRATQKAGLDTIPAIVRQT
+PDQDLLRDALLENLHRSQLNPLEEAAAYQQLMEDFACTQEELSQRIGRSRPQISNTLRLL
+KLPPLVQRRVAAGTLSAGHARALLGLTDPSDMERLAQRIQSEGLSVRSTEEAVAQLQGGL
+RPGRTPRRSTDDARHERLDHYATALTSRLDTAVKITLGARKGRIAIDFTTVEDLNRIMDL
+IQGGQDGKGKGKKS

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000092.fa

@@ -0,0 +1,61 @@
+>ACLBLIBL_00464
+MANTPGSGALIVGVSKTAELIGTALDREWLRFRLYELTGRALTVDVQEVQVQGARLLVLY
+PPAAVEPIRVEGRIRWRVDDHCAEVDASTWFTRQMYRRQYDWSAETSNVPAGEARPAAVD
+IARAFLYDSGDERGEELAEAETPQLLRRLNVVAEGGMLTNAGVLAFVGRPEPALDYTHHE
+VAGADSSIRVHRGGRSLLEELADVLQAFEARNTVRHVQSGLTIGQLRDIPRLAAREALVN
+GLAHREWGDPGATRVEHIGRTLRVTSPGGFFGGVDPSNIITHPSVSRNPALTQLLADLRV
+AERQGIGVDRMVREMVRVGHPQPGIEEVAGPYVRTTLVGETLDEPWMAWLSQVQPRPLTR
+DVSAVLILRHLVDRVWIDEMTAAALTQVSRAESRSMLERLHTATVGGGTILEAVSGVPDA
+VPQAWRLGEAAAQLLAALDQETGIQRTVPDRRALAADYARARGRISTTELASLVGGHASN
+MGAPLRALETEGFLEPSNASRRGRGFFYRWVGDEPA
+>MOLHKGIG_00037
+MLDEVLAQLRSTGSETALIEVKSAAGGCPRSVRETLSAFANARGGVVVLGLDDSTFEPTG
+ADAPALRDALAGMAADDMTPPVRGVISIENAEGGHQVVVMEVPEFAPDQKPCYITAAGRY
+QGSYTRSDEGDRRLTAYEIDRLIEGQGQPQHDREPVHGATADDLRPDLVEALTGRLRTVQ
+PRAFGSLTDQECLRRANVLVDADGVLVPTLAGLLACGEYPQGFFPQLSISVVVLPGTTFG
+DTGPHGERFVDNRTCEGPLVDMIADARDVLVRHMSRASVIDGTGRADRLEYPLEVIRELL
+VNAVMHRDYSAGARGTQVQVELYPDRLVVRSPGGFFGPVDPSSFGEPDVSSSRNSVLARL
+LSDLPGSDGRMIAENRGSGIPTVLKVLEAAGMVPPEFHSTLTRVEVDVAHDSLLTAETHE
+WIQGLGQDGLTQWQIQALALARSGRTVRNQTLQGWGAHQADATRELSDLVRRGLTVKLGD
+RRGARYTLNPDYVPPAAETGAGGLSERQQAILRALADGPMKATEVGDAVGTSYRTAMNAL
+NDLIEAGLVEPTAPPRSRRRRYRLTPQEETA
+>MOLHKGIG_00568
+MDVIQLDQTQLMALLSRAEGHFLDYKRTDVAPGKLTRSLAAFCNSDGGDIYVGIAETDGT
+QSWQGAADPEEFNGHLQAFEEVSPFGADWNAEFITAQNESGYVLRINALKSRQVRSDSSG
+KVYKRVGAQNVPVDSEEGLQTLRRLKGLESFEEETLNVDMEEVTNSTHIIKFLVNDPSPT
+DPELYLKRQQLIRGGKPTVASALLFAELPQAMLPKRCGIKIYRYTSSVAHRDQLYSDPVT
+VEGYLYGQIYEAVDQTIDIINQAQFLDVDGLRQVRYPRETLHEVITNAVLHRDYSIQDDI
+HVRIFENRVEVQSPGRLPGHITLKNILEERLSRNGHLVRNINRFVDPPNKDVGEGLNTAF
+ESMRKFNLKEPIIEELENSVMVTIRHQSLASPEQQIMEYLAEHSQIRNQEARNLVGIESE
+SKMKKILQGLVGTGEIEHVPGTAKRGYAYRARAEAAAQEGNR
+>MOLHKGIG_02274
+MNWSSDDLTATLDALRARRGDTTSVEVKRATGGVPSMPETLCAFANMPDGGTVVCGVDEA
+HGEFRVVGVPDVAVLEAGLVAQAREAVTPSPTLLPQVFRLEGKDVLVAHVVPLRLTDRPA
+TVRGQAYLRQSDGDYVMHAHELRMVEVAKLHADERVDYDVKPVTGMSEEDLVPELVTDYV
+AAVRERDRRLRDRTHQEILRQTNVLTAAGEPTLAGLYALGDYPQGRYPGLTVTAAVQVRG
+GEGQARSRNLTDFTGPVPVLLDEVMAWVRQNLGTEHVYRPDGQLERRPELPLAAVRELLG
+NALVHRDLGPDTLGAGKAIQVRLTDRALFIQSPGGLRGVSLTQLESDEHAQAAVNQRLYQ
+IAKKLTTPDGASVIEGEGGGIHEVFRSARQWGLGRPQLIDTGVQFKALLWRPRPEGARPS
+RREPAVEVARTPPVEEVPDVKADAPSSAVPPSSAPTRHEGRVLGALAAGEAVGIRDLEEA
+TMLTARQIRYALRQPLLDGLVEMTGGQGHKDTRYRLVSARGAGD
+>NAFOICDF_00427
+MDLGPLLAAGETLDVEFKRRLGKDDLYQAVVCMANGIGGRILVGVDDDGTVVGTTADHGG
+AVDADLLAGRIQNGIEPPLSVDVEVVPWEGKDVAVITVPQAKSSFVGTRKGLFVKRVVGP
+DGRPACMPMTPMDVLRAGFDGVGLDYARAEARGAEWGHLDPTEFDRFRRLAGQSAGDSGL
+AELTDAELLRTLDLLTPDGGISLGAVLVFGTSEALRRWAPTAEVLFQDSRPHGVEANEDL
+LLPLLNAFEEIETRLALRNSITPVEVGLVRVDVPLLAESVRRESIANALVHRDYAEAGPI
+QVTLTGSTFSVASPGGFPRDVSPANILNRSAPRSPALANVFKRAGLVERRGKGVQDMFAS
+QLRAGRGAPDYSRSTHRSVIVDIPLGDEDRELLIFLARRQNEGQRALTLTELRVVHEIKH
+GGPAGAAEAAERLRLPVADVRAAATALVEAGVLESRGNGRAQRYMLTARFYELAEDRAAY
+LRLRPVDRIQQRRLIADYIREYGSITRGKAAELCQIAPTAARAVLKGMTEEGLLELRGER
+RAAHYVLPDS
+>LFPAFLNI_02208
+MRRGDTTNVEVKRAAGGVPQLAETLCAFANMPEGGTIILGVDEARGAFNVTGVADVALLE
+AGVAAQAREGVTPSPQIIPQTLQLDERQVLLIHVVPLRTADKPATVQGVAYLRQSDGDYR
+MHEHELRMLEVAKLHADERVDYELKVATGLGEQDLVSSLVDEYVAAVRRKNRRLRDRTSE
+EILRQTSVLTSSGEPTLAGLYALGDFPQGRFPGLTVTAAVQLPGGEGQPRNRNLEDFVGP
+LPDLLRDLMAWVSDNIDTVRRYRRDGHMEEVAELPLTAVRELLANALVHRDLGPSTLGMG
+KGVQVRLTPRNLFIQNPGGLQGLSLTQLQSDDHAQAAVNQRLYQFAKKLTTSDGASLIEG
+EGGGIREVFRAAERQGLPRPQLIDTGVQFKAILWRAADRNARAGVEDAKGASAVETAVPR
+AVPASASPTRHEHAVLAALVRMPDGATLRALTSVTGLTDRQVRYALRLPLDEGIVVMDGG
+QGNRQTAYRLMSDSRRP

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000096.fa

@@ -0,0 +1,66 @@
+>ACLBLIBL_00566
+MDSPASPGAPHPETTRPADVVARLQAALPGRVDVSPPPSRPPARDRSGHRSPAVPLAVVH
+AASVADVQAVCRLAHETRTPLVTRGAGTGLAGGAVAGAGEVVLDVMGMDRILEVSPADRV
+AVVEPGILNGALNAALAEHGLWWAPDPASKDISTVGGNIAMNAGGLLCAKYGVTREAVLG
+LDVVLADGTLMRLGHRTVKGVTGYDLTALMIGSEGTLGVIVGATLSLRPAVRGTQVTLGG
+FFPDVVAGAAAAEAVTGAGHVPALMELMDEVTLAAVRADAGPERGAALPESGAFLLVQAD
+GAGAEEDGAAMADLMRAHGGDVTVTADHAEGEALMALRRTAFPALERLGTPLVEDVAVPR
+SRMAEMFARIRDIEARTGIPIPTTAHAGDGNLHPILLFGAAAQVGGAAEDATSIPADVWE
+AAGELFRAGLELGGTLTGEHGVGLLKRAFLRDELGDAQHALQAKIKAVFDPHGILNPGKV
+FTP
+>MOLHKGIG_02184
+MDFSAPLDPTPAAPPAADAPPADVVARLQAELPGRVDVSAAALEAARADRSGHRSPAAPL
+AVVRARTVEDVQAACRIAHGTRTPLVTRGAGTGLAGGAVAGAGEIVLDMTAMDRILEVSP
+ADRVAVVEPGILNGALNAALAEHGLWWAPDPASKDISTVGGNIAMNAGGLLCAKYGVTRE
+AVLGLDVVLADGTLLRLGHRTVKGVTGYDLVALMIGSEGTLGVIVGATLALRPAVRGVPV
+TLGGFFPDVVAGAAAAEAITGAGHVPALMELMDEATLAAVRAHAGPERGAALPESGAFLL
+VQADGAGAEADGEAMAALMRTHGGDVTVTVDPAEGEALMALRRTAFPALERLGTPLVEDV
+AVPRSRMAEMFARIREIEARTGVAIPTTAHAGDGNLHPILLFGAAAQVGGAAEDAASIPA
+DVWEAAGELFRAGLELGGTLTGEHGVGLLKRAFLRDELGDAQHDLQQRIKAVFDPHGILN
+PGKVFTP
+>NAFOICDF_00491
+MTCIISVSPDDVLHRLRAALGDAVVTDPAALEPLRADRSGHRSPGAPLAAVRARTVEDVQ
+AACRIAHATGTPLVTRGAGTGLAGGAVAGPGQVVLDLSGMDRILEVAPEDRVAVVEPGVL
+NGALNRALEPHGLWWAPDPASKEISTVGGNIAMNAGGLLCAKYGVTREAVLGLAVVLADG
+TLMRLGHRTVKGVTGYDLTALMIGSEGTLGVIVEATLALRPLPEGAVHTLGAFFPDVAVG
+ARAAAAITGAGHVPAIMELMDEATLAAVRAHVSADDAARLPETGAFLLVQADGPGADEQA
+AAMAELIRSAGGEVTVTADPAEADRLVSLRRTAFPALEALGTPLVEDVAVPRSRMPEMFA
+RIREIEAETGLRIPTSAHAGDGNLHPVVLFGEPSRVGGEDGAQEAIPAEVWAAAGMLFRA
+GLELGGTLTGEHGVGLLKRAFLKEELGEAQHGLQERIKAVFDPRGILNPGIVFTP
+>MHAAABBN_01898
+MDFSAPLAPAAPLAPAPAADAPPADVVARLQAELPGRVDVSAAALQAARADRSGHRSPAA
+PRAVVRARTVEDVQAACRIAHGTRTPLVTRGAGTGLAGGAVAGAGEIVLDMTAMDRILEV
+SPADRVAVVEPGILNGALNAALAEHGLWWAPDPASKDISTVGGNIAMNAGGLLCAKYGVT
+REAVLGLDVVLADGTLLRLGHRTVKGVTGYDLVALMIGSEGTLGVIVGATLALRPAVRGV
+PVTLGGFFPDVVAGAAAAEAITGAGHVPALMELMDEATLAAVRAHAGPERGAALPESGAF
+LLVQADGAGAEADGEAMAALMRAHGGDVTVTVDPAEGEALMALRRTAFPALERLGTPLVE
+DVAVPRSRMAEMFARIREIEARTGVAIPTTAHAGDGNLHPILLFGAAAQVGGAAEDAASI
+PADVWEAAGELFRAGLELGGTLTGEHGVGLLKRAFLRDELGDAQHDLQQRIKAVFDPHGI
+LNPGKVFTP
+>LFPAFLNI_00166
+MLRSLEDVLTKPGQVSGRALDRHAAAADASHFLLVPEAVVTPTDAAEVGALMRASAAQGV
+SLTFRSGGTSLSGQAVTDSVLVDVRKNFRDIEVLDEGARVRVRPGATVRQVNARLARHGR
+RLGPDPASEAACTIGGVVANNSSGMNCGITENTYQTLESMTLVLPSGTVIDTAAPDADGI
+LRHHEPHLYRGLAQLADRVRSDSASVATVRRQFSMKNTMGYGLNALLDFDTPAQILAHLA
+IGSEGTLGFVAEAVFRTVVRPTHSATALLVFEELQAANEALPALVDSRAATVELLDATSL
+RVGQRLTGTPPIVRDLRVQDHAALLVEYSATTAEQLEELRQHGEALTGRIGLSQPAGFTT
+DADARAALWHLRKGLYASVAGARPQGTTALLEDIVVPVLALGRTCTALTQLFDRYDYRDS
+VIFGHAKDGNVHFMLTDDFADPARLQRYSDFTEDMVDLVLGEGGSLKAEHGTGRVMAPYV
+RRQYGDELYGVMREIKQLCDPGGVLNPGVLLNDDPQAHLRHIKAEPSVAEEVDRCVSCGY
+CEPVCPSRDLTLTPRQRIVTLRAIRSARLAGDEALAQSLEEDYDYAAVQTCAVDGMCQTA
+CPVEINTGDLVKRLRRQETGAVAQAGWNLAAQHWGTASIVAGRALDLAAKLPAAATITAN
+QLVRRIAGADSVPLYSPELPRGGGRRRRPAPVGEPVAVYFPACVSAMFGPAQPGTGAPGA
+AGVQDSVLALAQRAGVELLVPSDIDALCCGTPWSSKGKHTGQETITGRTIAALRRDSDHG
+RLPIVCDASSCTEGLRHALEVEVPPAGQQPLRILDAVEFTAEHLLPRLPEPRRIPSLTLH
+PTCSSTRMGLNPALARVAEAIAEDVQIPDDWGCCAFAGDRGLLHPELTASATARQAEQVQ
+AIDASAHASCNRTCELGMSRATGYPYSHVLELLNQSTIAGG
+>LFPAFLNI_02129
+MDSSAPLDPTRAAPPAADAPPADVVARLQAELPGRVDVSAAALEAARADRSGHRSPAAPL
+AVVRARTVEDVQAACRIAHGTRTPLVTRGAGTGLAGGAVAGAGEIVLDMTAMDRILEVSP
+ADRVAVVEPGILNGALNAALAEHGLWWAPDPASKDISTVGGNIAMNAGGLLCAKYGVTRE
+AVLGLDVVLADGTLLRLGHRTVKGVTGYDLVALMIGSEGTLGVIVGATLALRPAVRGVPV
+TLGGFFPDVVAGAAAAEAITGAGHVPALMELMDEATLAAVRAHAGPERGAALPESGAFLL
+VQADGAGAEADGEAMAALMRTHGGDVTVTVDPAEGEALMALRRTAFPALERLGTPLVEDV
+AVPRSRMAEMFARIREIEARTGVAIPTTAHAGDGNLHPILLFGAAAQVGGAAEDAASIPA
+DVWEAAGELFRAGLELGGTLTGEHGVGLLKRAFLRDELGDAQHDLQQRIKAVFDPHGILN
+PGKVFTP

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000098.fa

@@ -0,0 +1,25 @@
+>ACLBLIBL_00584
+MSPSPSGSVPSSSSVSAESRGMGAAAPGQAAVPGETGAAAAVETIRVSAVVLARPDRRVL
+TVRKAGTTMFMFPGGKHLPGEDPLDTAVREVAEETGLRLRPDELTRLGAWDTDAANEPGA
+ALHSEVFALWRPVARHETPAPTDEIVELHWMDPAAPAAPAGHQVAPLLVAVLAAVAKNPP
+F
+>MOLHKGIG_02168
+MSPSPSDSARTPTVTAGEVIRVSAVVLARPDRRVLTVRKAGTAMFMFPGGKHLPGEAPVD
+TAVREVAEETGLRLRPDELTRLGAWDTAAANEPGAALHSEVFALWRPVARHEVPEPTDEI
+VALHWMDPAAPAAPGGHGVAPLLHPVLAAVAATPPF
+>NAFOICDF_00510
+MTAPAARSDEPAEIRVSAVVIARPDRRVLTVRKAGTAVFMFPGGKHEPGETPLETAVRET
+REETGLRIRPDELVHLGAWDTPAANEPGMALHSEVFALWRPMARHEVPAADDEIAELHWM
+DPAAPAAPAGAGVAPLLLPVLARVAAQPLF
+>NAFOICDF_01906
+MAAPDFVLSLREHVGHAPLWLSGVKAVALRAGDREVLLVRRADDGRWTLPAGILEPGEEP
+ADAAVREVAEETGVRCAPRRLAGVGTTAGAVYPNGDRARYLDVVLVLDETGGHAHVADDE
+NLEVGWFSVDGLSDLPPLHARALSWALEDGPARFVAGGDVLP
+>MHAAABBN_01882
+MSPSPSDSSRTPTVAAGEVIRVSAVVLARPDRRVLTVRKAGTAMFMFPGGKHVPGEAPVD
+TAVREVAEETGLRLRPDELTRLGAWDTAAANEPGAALHSEVFALWRPVARHEVPEPTDEI
+VELHWMDPAAPAAPGGHGVAPLLHPVLAAVAAAPPF
+>LFPAFLNI_02113
+MSPSPSDSARTPTVAGGEVIRVSAVVLARPDRRVLTVRKAGTAMFMFPGGKHLPGEAAVD
+TAVREVAEETGLRLRPDELTRLGAWDTAAANEPGAALHSEVFALWRPVARHEVPEPTDEI
+VELHWMDPAAPAAPGGHGVAPLLHPVLAAVAAAPPF

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000100.fa

@@ -0,0 +1,25 @@
+>ACLBLIBL_00640
+MERPAPTAEICPVRPEDTDAVVALWERTLPEYGDPTRPQRAPRPSIRRKLDWGDGLFWLA
+VSDEEVVGTVMAGYDGHRGWIYSLAVHPDHRRGGLGTALVAHAEQELARLGCPKVNLQVL
+ATNADGAEFWAATGYQPDPVLGLGKRLGG
+>ACLBLIBL_02391
+MTETAPTVPTPPARPQVRPLRPEDHEAVAALTVASYVDGGHIAPGSRYVKTLRDVAGRAA
+RAEVLVAEVDGQVAGSVVLTPLGSPMAETAAPGEYEFRMLAVHPDHHRRGVARTLMAVIE
+ERARALPGIEAIALTTMPTMTDAHRLYEALGYVRVPERDWYLRDVIPDLDPADETGPFLV
+YRLPLA
+>MOLHKGIG_00554
+MSALVRPLRPEDHEAVAELTLASYVDGGHIAPDDAYVKTLMDVADRAGRAEVLVAEVDGE
+VAGSVVLTPPGSPLAETSGDGEYEFRMLAVHPRFHRRGVGGALLAEIVARARAEEGVDAV
+VLTTMPSMTGAHRMYERAGFVRVPERDWFLADVVPDLDPADETGPFLVYRLALD
+>NAFOICDF_02275
+MSDVTVRALRPEDHEAVAALTLASYTTGGHFEAESDYLETLADVAGRAAVAEVLVAELDG
+QVAGSLVLTPHGSPMAETSVPGEYEFRMLAVDPAVHRRGVATALLAEVVRRARATPGVEA
+IALSTMTSMTDAHRMYERLGFVRVPDRDWRLSDLEPGLDPAEDAGPFLVYRLPLT
+>MHAAABBN_00279
+MSALVRPLRPEDHEAVAELTLASYVDGGHIAPDDAYVKTLMDVADRAGRAEVLVAEVDGE
+VAGSVVLTPPGSPLAETSGDGEYEFRMLAVHPRFHRRGVGGALLAEIVARARAEEGVDAV
+VLTTMPSMTGAHRMYERAGFVRVPERDWFLADVVPDLDPADETGPFLVYRLALD
+>LFPAFLNI_00557
+MSALVRPLRPEDHEAVAELTLASYVDGGHIAPDDAYVKTLMDVADRAGRAEVLVAEVDGE
+VAGSVVLTPPGSPLAETSGDGEYEFRMLAVHPRFHRRGVGGALLAEIVARARAEEGVDAV
+VLTTMPSMTGAHRMYERAGFVRVPERDWFLADVVPDLDPADETGPFLVYRLALD

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000105.fa

@@ -0,0 +1,25 @@
+>ACLBLIBL_00736
+MSEPTTLDTHVLQRSAEHLAECYAGVFSPETVERYVFESYATLSRTAKVRTYLASTASHF
+ADNRLRALAQSEGKIASPVPQVLFVCVHNIGRSQIAAALLTHHAGDKVEVRSAGSLPGSE
+VHPLVVQALAERGIDLSGAYPKPLTDDVVRAADYVITMGCGDACPVYPGKRYLDWEIADP
+AAETPDGVRAIVDAIDTRVKALWDELRSAT
+>ACLBLIBL_00740
+MTAETTPETTKPSVLFVCVHNAGRSQMAAAYLQRLAGGRIEVRSAGSAPADTVNPAAVEA
+MAEEGIDISANQPKVLSEQAVKDSDVVITMGCGDACPFFPGKRYEDWKLDDPAGRGVEGV
+RPIRDEIKTRIQQLITELLPAESTAN
+>ACLBLIBL_00741
+MTTPESASRPSVLFVCAKNGGKSQMAAALMEHHAAGAVQVHSAGTKPGKSINALSAEVIA
+EAGADMSAGHPKPIDPDLLARVDRVVVLGDEARVEPVDGMAGTIVTWHTDEPSTRGIEGI
+ERMRLVRDDIDARVRTLLTELTGSPAS
+>MOLHKGIG_02072
+MTTKRPSVLFVCVKNGGKSQMAAALMRHHAGDAIEVHSAGTRPGTALNAQSTEAIAEVGA
+DMSSAVPQPVTPELLRSVDHVIVIGDEAVIKPVEGMTAPVTTWYTDEPSQRGIEGMERMR
+LVRDDIDIHVRKLLTDLTQPST
+>NAFOICDF_00488
+MTSDRPSVMFVCVHNAGRSQMAAAYAQHLSGGAVEVRSAGSAPADQVNPAVVEAMAEEGI
+DLSAERPKVLTPEAVQASDAVITMGCGDACPLYPGKRYEDWVLEDPAGRGVDAVRPIRDE
+IRGRVAGLLRELGVEPVA
+>LFPAFLNI_02000
+MTTKRPSVLFVCVKNGGKSQMAAALMRHHAGDAIEVHSAGTRPGTALNAQSTEAIAEVGA
+DMSSAVPQPVTPELLRRVDQVIVIGDEAVIKPVEGMTAPVTTWHTDEPSQRGIEGMERMR
+LVRDDIDTHVRKLLTDLTGTAN

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000108.fa

@@ -0,0 +1,57 @@
+>ACLBLIBL_00786
+MDLPQITPLAVAVGLAVAVVGWLLGRLLGAGVAWLFARRGRSPSSARVFGKLVAAGITVL
+SLGAAVTVVFPSVKPVDLLGGIGVISIAAGIAFQTVLGNMFAGMVILARDRFRVGDQIQV
+GEHAGNVVEMGLSSTAVKTFDGRLVLIPNQMLHSQAVTVQTGFSAVRSSLRVDVETGNDL
+ARTREIAVRAMSELPQVLRDPAPQALLASVGVTTVGMDLRFWSGARQMETKEAMDAVIHA
+VLTAFEKNGVATGDDVRVVDAGPELRRILEGPGAPRGQGGPDYPGGLAGPGEPDRAARPG
+SD
+>ACLBLIBL_00939
+MLLAALSGPASPPVLGSLARLFAGENVPAGVEGNVQDGAAATTAALGVEWGTLLTVLVAF
+AVGATLVYAALQVTRVVLVRRPAFQHGAARLSLPAAVAAGLLASRIWLGVMAEEQTWYRP
+ASFLLLIAVAAAGAWAAWRLVGVIEAGILGRYQETGVEHRRERRIRTQTILIRRILNAVI
+VVVAIAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDAIRVGD
+VVDMEGVFGTVEEITLSNVVLKLWDGRRMVYPSSHFTTQPFENWTRVGTEVSGVVELDVD
+WRVPMPALRERLTQLLDSTDLWDGRESSMQVTDAIGGTVRIRAVVSARNSGDLWDLRCLV
+REDLVTFLRSEHPEAIVVQRVVERHPAHDDAVPASEGSDAGARGGDPTGEPGPDGSGVAA
+REPRPRTAALPRVEGGEPRPDTVTTPLTRVDDHAGLYTGSITAVQRNRELHGPGEDAFAE
+RRAQQAKQAAEAATADEAGRRSGAGSHADGLLDDAVTRRRQDDED
+>MOLHKGIG_01921
+MVLPVLPALATPPLLTALDRLLAGETVPSGVEGDIQDGAAATTRAFGVEWGTLLTVLMAF
+AIGAAVVYLALQVARVVLVRRPAFQHGAARLSLPAAVAAGLLASRIWLGVMAEEQAWYRP
+ASFLLLIAVAAAGAWAAWRLVGVIEAGILGRYQETGVEHRRERRIRTQTILIRRILNAVI
+VVVVVAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDAIRVGD
+VVDMEGVFGTVEEITLSNVVVKLWDGRRVVYPSSHFTTQPFENWTRVGTEVSGVVELDVD
+WRVPMDALRARLAQLLESTDLWDGREHALQVTDATGGVVRIRAVVSARNSGDLWDLRCLV
+REDLVAFLRHEHPEGIVVQRMVVRHPAHDDAAPASEGSDAGARGGDRTGEPGPDGSGVAA
+REPRPRTAPLPRVDGADPRPHTLTTPLTRVGDHSGLYTGSMTAVQRNRELAGPGEEAFAE
+RRAQQAKQAAEAAAADEAGRRSGAGSHADGPLDDAVTRRRQDDED
+>NAFOICDF_00874
+MPVPALLPVLAQTASSDAALSDAVLSAADQVVPGSVEQDVQQGASAASAALGVEWATVAA
+VLGAFLAGGLVVLGVFLVARLALFRRDRLKADAARLTVPVSLFAGFLTARVGLEVMAHGQ
+PWFEAAAFVLLLAVAASAAWAAWRVVDVVESGILARYHQPGVNDRRERKIRTQTMLLRRV
+LNAVIVVVALAVVLLAIPQVRSLGAGLLASAGLISVIAGLAVQSTLTNVIAGFQLAFTDS
+IRVGDVVDMQGVFGTVEEITLSNVVVKLWDGRRMVYPSKHFTSEPFENWTRTGAAVAGVV
+EMDVDWRVPMDPLRARLTELLESTDLWDGRENAMQVIDAVGGMVRIRAVVSAKNSGELWD
+LRCLVREDLVGFLRAEYPEGIYTQRLVERRPSDPAPEAHDDPAPDAHDDAAPAAAPAAPA
+PSDRGSSTRAEPTPQTRPMPTVTGSVPLARAGENASLYTGSIRAVERNQEMDGPGEEAYA
+ERRARAAEREDRAARDAGRGGAHAARS
+>MHAAABBN_01617
+MVLPVLPALATPPLLTALDRLLAGETVPSGVEGDIQDGAAATTRAFGVEWGTLLTVLMAF
+AIGAAVVYLALQVARVVLVRRPAFQQGAARLSLPAAVAAGLLASRIWLGVMAEEQTWYRP
+ASFLMLIAVAAAGAWAAWRLVGVIEKGILGRYQETSVEHRRERRIRTQTILIRRILNAVI
+VVVAVAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDAIRVGD
+VVDMEGVFGTVEEITLSNVVVKLWDGRRMVYPSSHFTTQPFENWTRVGTEVSGVVELDVD
+WRVPMDALRARLAQLLESTDLWDGREHALQVTDATGGVVRIRAVVSARNSGDLWDLRCLV
+REDLVAFLRHEHPEGIVVQRMVVRHPAHDDAAPASEGSDAGARGGDRTGEPGPDGSGVAA
+REPRPRTAPLPRVDGADPRPHTLTTPLTRVGDHSGLYTGSMTAVQRNRELAGPGEEAFAE
+RRAQQAKQAAEAAAADEAGRRSGAGSHADGPLDDAVTRRRQDDED
+>LFPAFLNI_01841
+MVLPVLPALATPPLLTALDRLLAGETVPSGVEGDIQDGAAATTRAFGVEWGTLLTVLMAF
+AIGAAVVYLALQVARVVLVRRPAFQHGAARLSLPAAVAAGLLASRIWLGVMAEEQAWYRP
+ASFLLLIAVAAAGAWAAWRLVGVIEAGILGRYQETGVEHRRERRIRTQTILIRRILNAVI
+VVVVVAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDAIRVGD
+VVDMEGVFGTVEEITLSNVVLKLWDGRRMVYPSSHFTTRPFENWTRVGAEVSGVVELDVD
+WRVPMDALRARLTQLLESTDLWDGREHALQVTDATGGIVRIRAVVSARNSGDLWDLRCLV
+REDLVSFLRHEHPEGIVVQRMVVRHPAHGDASPASEGSDAEARGGDRTGEPGPDGSGVAA
+REPRPRTAPLPRVDGADPRPDTLTTPLTRVGDHSGLYTGSMTAVQRNRELAGPGEEAFAE
+RRAQQAKQAAEAAAADEAGRRSGAGSHTDGLLDDAVTRRRQDDED

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000109.fa

@@ -0,0 +1,97 @@
+>ACLBLIBL_00789
+MFDRAVSAPDEWQEPRANLVFDTVESVGAWERPTPRSNPARTLTVTGRLEPGTEVRPRRN
+SQERFKLNALYEQPPRGAELAPNAVRWQSRSPVDVTEVEEIAPGRFRVSLLQRLSAKYEP
+EPHAEVPMAVFHLNYVRPGGLLERIREQAAEAARRGRLPEGAVFDILARRAPRTTGRTLA
+AIGADVRDGRRDGVGGLVEAVESARGSYVAVQGPPGTGKTYVGSRAVKELLDRGWTVGVT
+AQSHAVVENFLDQLIGVGVDPDRVGKEPKDPDGLHRWTSLGSSEVHAFLAPGRVLGGTAW
+TFANAAAQPVDLLVVDEAGQLSLAHLLGASALAETVLLLGDPQQLPQVSRGEHPQPIGDA
+ALTWIAEGAPVLRADRGFFLDTSWRMHSALTRAVSELSYAGRLGAREEVTDARRLDGVEP
+GLHPWPVSHTGNAVSSPEEAAAVVEIIQSLLGRTWSTGPDDPGRPLEPSDVIVVAPYNAQ
+VATVREALDAAGLEGTAVGTVDKFQGREAAVAILTMAASSPQEVPRGLDFLLNRNRLNVS
+ISRGQWAAYLVHSPALADALPTGPEDLPMIGAFLRLVHR
+>MOLHKGIG_02029
+MVTFAPDRASFMLSPSDITVAATCTYGWLRGTVDPALGRAPRIGVADAFLERVSRLGDEH
+ESRVLARLEAEHGADQVVRLARPERYTPEGVRAARERTAAALAARPAVVFQGMLHDGAFG
+GLADFLVLRTDEEHPEGAYEVVDTKLARHARVTALLQIAAYADLLDGMGVPRARQGSLWL
+GDGSRHVADLDEVIPVYRHQRSRLEALLQDHVAAGEPARWGDDRLSVCGACEVCEEAVAE
+HRDVLLTAGATRLQRTRLREAGITTIEQLAASVAPPEGMARRTWEALREQAAIQLEPAGA
+GGVPPHRIVDPRAVAGLPVPDAGDVFFDFEGDPLWVSADGSMEGLEYLWGWVEAPGGDTA
+RTASADFRFTGLWADTRAAERAVKPLVVV
+>MOLHKGIG_02031
+MAASTSETTCPTTGRYTTMRDSTERAALEEFVAFVEARRAAHPGMRIYHYAAYEVTALKR
+LTVRHGVGERELDDWLRAGLFVDLYSTVRAALRAGVPSYSIKKLEPLYMGAEHRAEDGVT
+TAADSVTEYHRYVAAMEAGDTEVARAIRADIEDYNRYDCVSTARLRDWLLEQVGRTAEHG
+ATAPRPDDDEHLVEPAPALEGEDARLEADLLGLLPTADDADAVLDDEQRGVALLAAGLGF
+YQREDKPVWWAFFDRGISPPDEWQDARANVVADRVDVAEDWHRPKGARTFQRVLRMTGTL
+EPGSSLQPGAEAITVYEDVPADRRDLLQPNAVRWVGAKAVVEDVEDRPDGSSVVLLREKI
+PTQDVEQHSELPMAAFAHTVVNTDKLKERLRERARTAVQAGGLPGSGGDAAAPSTAAFDI
+LARRPPATAGRPLAAISTELREGDSAPAPARQGWEALVEALESARGSYVAVQGPPGTGKT
+HVGSHAVKALLERGWSVGVTAQSHAVVENFLGKLVSIGVPKKQVLKAEKRGKDAPERPWA
+TVSDAKPYIGLPGHVVGGTAWTFAHEDVQEFDLLVIDEAGQFSLAHTLAAAAMARTVLLL
+GDPQQLPQVTKGTHPQPIGEAALSWLAADEPVLRADRGFFLDTSWRMHSALTEAVSTLSY
+AGELGAKEDVTDARRLDGVEPGLHPWPVSHTGNAVSSPEEAAAVVEIVRSLLGRTWSTGP
+DDPGRPLEPSDVIVVAPYNAQVATVREALDAAGLEGTTVGTVDKFQGREAAVAILTMAAS
+SPQEVPRGLDFLLNRNRLNVSISRGQWAAYLVHSPALADALPTRPEDLPMIGAFLRLVHR
+>NAFOICDF_00750
+MASFSPVDPASFLLSPSDITAAATCEYGWLRGAVDPKLGRADGAPEDDAFLARVSALGDA
+HEARTLDALVAEHGAGGVVVLERPSPYTPEGIAAAAERTRQALASGAAVVFQAMLHDGSF
+GGLADFLVREPTAEHPEGAYQVVDTKLARHARVTALLQIAAYADLLDGMGVPRTRHGSLW
+LGDGARHTVDLAEVIPVYRHQRARLERVLRTHVTEGTPVAWGDERHAVCGQCRWCEEAIA
+EHRDVLLTAGATRVQRTRLRAAGVRTVEELAASTAPPEGMSRRTWEALRDQAAAQLEPAG
+ADGVPPHRIVDPAPVRALPAPDAGDLFFDFEGDPLWVSPRGDMEGLEYLWGWVEAAPGRT
+TEGTGFDQFRFTGLWADTRAEEKAALEEFVRFVEARRAVHPGMRIYHYAAYEVTALKRLT
+VRHGVGEAELDDWLRAGLFVDLYATVRASLRAGVPSYSIKKLEPLYMGADHRAEDGVTTA
+ADSVTEYHAYAEQAERAGEGDADAAAEAARLRAGIEDYNRYDCVSTARLRDWLLGQVGGA
+STGVAVDAGEPAEAGEDAPAATDEDAALEQALLDLVPADPADGDDETLGLAMLAAGLGFF
+RREAKPMWWAFFDRGISPVDEWQDPRANVVADRVDVAEDWHRPSSRARTRQRVLRVTGRL
+EAGTQLTPGAEAKTVYEDVPAGRVEGLQPNAVRWVGAAAVVEDVEDHPDGTSTLRLREKV
+ALDAEPHPELPMAAFAHTVIPSATLQERIREDGLRARALGALPRPEEGAAPTAAFDILAR
+RVPETAGRPLAQITADARAGRLEGADALVEALVSARGSYVAVQGPPGTGKTHVGSHAVKE
+LASRGWRIGVTGQSHAVVENFLAKLVAVGVPAGHVGKEKPRGGEDRERPWTVLDDRGDAF
+EHLSQPGHVLGGTAWTFAHPKAPDLDLLVIDEAGQFSLAMTLAAAATARTVLLLGDPQQL
+PQVSQGTHPQPIGDAALGWLMEPGEEVLPPERGFFLDTTWRMHSALTAPVSRLSYDGQLR
+SRSEATDARHLEGIVPGLHPVPVEHTGNAVSSTEEARRVVEIIEDLVGRAWTPGSGEEPR
+PLTPEDVIVVAPYNAQVATVRAALDDAGLQGTTVGTVDRFQGREAAVAILTMAASSAQDV
+PRGLDFLLNRNRLNVSLSRGQWAAYLVHSPALADALPTTPADLPLIGAFLRLLQP
+>MHAAABBN_01738
+MVTFAPDRASFMLSPSDITAAATCTYGWLRGTVDPALGRAPRIGVADAFLERVSRLGDEH
+ESRVLARLEAEHGADQVVRLTRPERYTPEGVQAARERTAAALAARPAVVFQGMLHDGAFG
+GLADFLVLRTDEEHPEGAYEVVDTKLARHARVTALLQIAAYADLLDGMGVPRARQGSLWL
+GDGSRHVADLDEVIPVYRHQRARLEALLQDHVAAGEPTRWGDDRLSVCGACEACEEAVAE
+HRDVLLTAGATRLQRTRLREAGITTIEQLAVSVAPPEGMARRTWEALREQAAIQLEPAGA
+DGLPPHRIVDPRAVTGLPAPDAGDVFFDFEGDPLWVSADGSMEGLEYLWGWVEAPGGDTA
+RTASADFRFTGLWADTRAAERAALEQFVAFVEARRATHPGMRIYHYAAYEVTALKRLTVR
+HGVGERELDDWLRAGLFVDLYSTVRAALRAGVPSYSIKKLEPLYMGAEHRAEDGVTTAAD
+SVTEYHRYVAAMEAGDTEVAKAIRADIEDYNRYDCVSTARLRDWLLEQVGRTAEHGATAP
+RPDDDEHLVEPAPALEGEDARLEADLLGLLPTADDADAVLDDEQRGVALLAAGLGFYQRE
+DKPVWWAFFDRGISPPDEWQDARANVVADRVDVAEDWHRPKGARTFQRVLRMTGTLEPGS
+SLQPGAEAITVYEDVPADRRDLLQPNAVRWVGAKAVVEDVEDRPDGSSVVLLREKIPTQD
+VEQHSELPMAAFAHTVVNTDKLKERLRERARTAVQAGGLPGSGGDAAAPSTAAFDILARR
+PPATAGRPLAAISTELREGDSAPAPARQGWEALVEALESARGSYVAVQGPPGTGKTHVGS
+HAVKALLERGWSVGVTAQSHAVVENFLGKLVSIGVPKKQVLKAEKRGKDAPERPWATVSD
+AKPYIGLPGHVVGGTAWTFAHEDVQEFDLLVIDEAGQFSLAHTLAAAAMARTVLLLGDPQ
+QLPQVTKGTHPQPIGEAALSWLAADEPVLRADRGFFLDTSWRMHSALTEAVSTLSYAGEL
+GAKEDVTDARRLDGVEPGLHPWPVSHTGNAVSSPEEAAAVVEIVRSLLGRTWSTGPDDPG
+RPLEPSDVIVVAPYNAQVATVREALDAAGLEGTTVGTVDKFQGREAAVAILTMAASSPQE
+VPRGLDFLLNRNRLNVSISRGQWAAYLVHSPALADALPTRPEDLPMIGAFLRLVHR
+>LFPAFLNI_01966
+MVTFAPDRASFMLSPSDITAAATCTYGWLRGTVDPALGRAPRIGVADAFLERVSRLGDEH
+ESRVLARLEAEHGADQVVRLARPERYTPEGVRAARERTAAALAARPAVVFQGMLHDGAFG
+GLADFLVLRTDEEHPEGAYEVVDTKLARHARVTALLQIAAYADLLDGMGVPRARQGSLWL
+GDGSRHVADLDEVIPVYRHQRARLEALLQDHVAAGEPARWGDDRLSVCGACEACEEAVAE
+HRDVLLTAGATRLQRTRLREAGIMTIEQLAASVAPPEGMARRTWEALREQAAIQLEPAGA
+DGLPPHRIVDPRAVAGLPVPDAGDVFFDFEGDPLWVSADGSMEGLEYLWGWVEAPGGDTA
+RTASADFRFTGLWADTRAAERAALERFVAFVEARRAAHPGMRIYHYAAYEVTALKRLTVR
+HGVGERELDDWLRAGLFVDLYSTVRAALRAGVPSYSIKKLEPLYMGVEHRAEDGVTTAAD
+SVTEYHRYVAALEAGDTEVARAIRADIEDYNRYDCVSTARLRDWLLAQVEPEEAAVADRP
+VDDAATGNEPLVEAAPSLQEQDAALAASLQALADVERDEAGGTGAPEAELDGGRRGIALL
+AAGLGYFARENKPLWWAMFDRAVSAPDEWQEPRANLVFDTVESVGAWERPTPRSNPARTL
+TVTGRLEPGTEVRPRRNSQERFKLNALYERPPRWAELAPNAVRWQSRSPVDVTEVEEIAP
+GRFRVSLLQRLSTKHEPEPHGEVPMAVFHLNYVRPGGLLERIREQAAEAARRGRLPDGAV
+FDILARRAPRTTGRTLAAIGADVRDGRRDGVGGLVEAVESARGSYVAVQGPPGTGKTYVG
+SRAVKELLDRGWTVGVTAQSHAVVENFLDQLIGVGVDPDRVGKEPKDPDGPHRWTSLGSS
+EVHAFLAPGRVLGGTAWTFANAAAQPVDLLVVDEAGQLSLAHLLGASALAETVLLLGDPQ
+QLPQVSRGEHPQPIGDAALTWIAEGAPVLRPDRGFFLDTSWRMHSALCAPVSELSYAGEL
+GAKEDVTDARRLDGVEPGLHPWPVSHTGNAVSSPEEAAAVVEIVRSLLGRTWSTGPDDPG
+RPLEPSDVIVVAPYNAQVATVREALDAAGLEGTTVGTVDKFQGREAAVAILTMAASSPQE
+VPRGLDFLLNRNRLNVSISRGQWAAYLVHSPALADALPTRPEDLPMIGAFLRLVHR

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000112.fa

@@ -0,0 +1,30 @@
+>ACLBLIBL_00872
+MSALLVGVFALQGDVREHVRVLEGLGARTRPVRRAADLTGLDGIVLPGGESSVMDRLAGL
+MGLKEPLADAIGAGLPAYGTCAGIILLAREIQNPAPGQGSLGVLDVTVRRNAFGAQVDSF
+EADLEVPAVSAEPVHAVFIRAPAVLRAGGEVEVLASVPASRLSAAPPELGLDDAAQVPVA
+VRQGRVLATSFHPEVTGDHSFHREFLRGL
+>MOLHKGIG_01985
+MSPQKTVGVLALQGDVREHVHVLESLGARTRPVRRPADLEGLDGIVLPGGESSVMDRLAR
+IMGMRDPLIAALRDGLPAYGTCAGLIMLAREIRNPAPDQGGLGVLDVAVRRNAFGAQVDS
+FEEDLDIPAVAAEPVHAVFIRAPAVLQAGEGVEVLASVPASRLSVPAADPGLDGDARLPV
+AVRQGHLLATAFHPEVTGDWSFHRAFLAGL
+>NAFOICDF_00808
+MSPQKTVGVFALQGDVREHVHVLESLGARTRPVRRPADLEGLDGIVLPGGESSVMDRLAR
+IMGLKDPLIAALRDGLPAYGTCAGLIMLAREIRNPAPDQGGLGVLDVAVRRNAFGAQVDS
+FEEDLDVPAVAAEPVHAVFIRAPAVVQAGEGVEVLASVPASRLSLPAADPGLDGDARLPV
+AVRQGHLLATAFHPEVTGDWSFHRAFLAGL
+>NAFOICDF_00818
+MRAVQKTVGVFALQGDVREHVHVLEALGARTRPVRRPADLAGLDGIVLPGEESSVMDRLA
+RIMGLRDPLAEAVRAGLPVYGTCAGMILLAAGIENPAPGQGSLGVLDVTVRRNAFGSQAD
+SLEADLQVPAVSADPMHAVLIRAPAVVRVGEGVEVLASVPAARAVAASSSTAETDDGAPA
+ADLPVAVRAGNVSATSFHPEVTGDWSFHRAFLAGL
+>MHAAABBN_01679
+MSPQKTVGVFALQGDVREHVHVLEALGARTRPVRRPADLEGLDGIVLPGGESSVMDRLAR
+IMGLKDPLIAALRDGLPAYGTCAGLIMLAREIRNPAPDQGGLGVLDVAVRRNAFGAQVDS
+FEEDLDIPAVAAEPVHAVFIRAPAVLQAGEGVEVLASVPTSRLSVPAADPGLDGDARLPV
+AVRQGHLLATAFHPEVTGDWSFHRAFLAGLRPPRAPRR
+>LFPAFLNI_01911
+MSPQKTVGVFALQGDVREHVHVLEALGARTRPVRRPADLEGLDGIVLPGGESSVMDRLAR
+IMGLKDPLIAALRDGLPAYGTCAGLIMLAREIRNPAPDQGGLGVLDVAVRRNAFGAQVDS
+FEEDLDVPAVAAEPVHAVFIRAPAVLQAGEGVEVLASVPASRLSVPAADPGLDGDARLPV
+AVRQGHLLATAFHPEVTGDWSFHRAFLAGL

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000115.fa

@@ -0,0 +1,59 @@
+>ACLBLIBL_00920
+MEAITAAVSAFNDKYWYVVMALLFTAGVWFTIRTVGVQVRMLPEMLRSVTAGSQKGFEND
+GVSPFRAFTISAASRVGTGNVAGVAIAIVIGGPGAVFWMWVLAIIGGATAFVESTLAQLY
+KQKGPDGFYGGPAYYIRDGLRSKWLAAVFAVAITVTYGFVFNAVQSNSISESVQANWGVS
+TTTAWIVGVALAVITGLVIFGGVRRLSAVTNVIVPVMAVFYLVLALIVMAVNITEIPGLI
+ALIVGHAFGLQEVTGAAVGMAMVMMGVRRGMFSNEAGMGSAPNAAATAAVSHPAKQGFVQ
+SLGVYFDTLIVCSATAFIILLSNPSYGDGEALGMAVTQGALQQAVGAWAGPALTVIIFFL
+AWSSVLGNTYYGEANIRYLAGKRADAAITVFRVLVLLCVVGGALGSVALVWNLADTFAAL
+MATINLVAIIPLGGLAVKLLRDYERKLKAGEDPGFHVSDLPEARNVALWQDTPETAPLQK
+>MOLHKGIG_01939
+MEATVEQITAAITALNDKYWYVVMALLFVAGVWFTIRTVGVQVRMLPEMLRSVTAKSQTG
+FENDGVSPFRAFTISAASRVGTGNVAGVAIAIVIGGPGAVFWMWLLAIIGGATAFVESTL
+AQLYKQKGSDGYFGGPAYYIRDGLGAKWLAAVFAVAITVTYGFVFNAVQSNSISESVQAN
+WGASSTTAWIVGLGLAALTGLVIFGGVRRLSAVTNVLVPVMATFYIFLALIVMVVNITEV
+PGMIALIVGHAFGLREVAGAAVGMTMVMQGVRRGMFSNEAGMGSAPNAAATAAVSHPAKQ
+GFVQSLGVYFDTLIVCSATAFVILLSNPAYGRGEAIGMQVTQGALQQAVGAWAGPALTVI
+IFFLAWSSVLGNTYYGEANIRYLAGRHAGPAITVFRVLVLVCVVGGALGSVALVWNLADT
+FAALMATINLVAIIPLGGLAVKLLRDYERKLKAGMNPGFHISDLPEARNVALWRDEPKTS
+PLQD
+>NAFOICDF_00854
+MGALADAISAFNSKYWYLVMALLAFAGVWFTVRTVGVQVRMLPEMIRSVAAKSPEGGADD
+GVSPFRAFTISAASRVGTGNVAGVAIAIVLGGPGAVFWMWVMAILGGATAFVESTLAQLY
+KRKDRDGFFGGPAYYIRDGLGLKWLAALFAVAITVTYGFVFNAVQSNSISESVQANWGAS
+TTTAWIVGVALAVITALVIFGGVQRLSSVTNVIVPVMAVAYVLLAVVVMVINITEIPAMF
+ALIVRHALGFEQVAGAAVGMAMVMQGVRRGMFSNEAGMGSAPNAAAAAAVSHPAKQGFVQ
+SLGVYFDTLLVCSATAFIILLSNPEYGNTDALGMVVTQNALQQAVGAWAGPFLTVVIFFL
+AWSSVLGNTYYGEANIRYLAGERAPQWITAFRVLVLLCVVGGALGTVSLVWNLADTFAAL
+MATINLVAIIPLGGLAVKLLQDYERKLKAGEDPHFRLADLPEAKNVPLWGDEDAELMRTE
+QGHGAGAREELHHADRPGRGHGGGSHSA
+>NAFOICDF_02134
+MDAFVTAATDGLGELSGIIWGPFVLIPLLFLTGLYLTIRLGFVQFLRLGAGLHLGLLRRK
+DDGDAEGEISQFQALTTALAATVGTGNIVGVATAIAVGGPGALFWMWVTGVLGMASKYSE
+AFLAVRFRTTDDAGEKSGGPQYYLQRGIKGGLGKGLALFFSVAALLACFGIGNMTQGNSI
+AVNVDSAFGVPTWITGAVLAVMTMVVLVGGIKSIGKVTAGFVPVMIVFYVLGALWILIVN
+ASAIPSAFATIFTEAFTGSAAVGGFTGSAMIVAVQYGMARGIFSNESGMGSAAIAAAAAQ
+TTHPVRQGLVSMTQTFIDTIIVVTCTGLVLITTGTWTEGKATAATMTSDAFATGLPGNWG
+HWIVTIGLVMFAYSTILGWSYYGERQVERLFGTRLIMPFRVLFSLVVFFGCTTELDLAWT
+FSDVMNGLMAIPNLLGLLILSGLIARETRLYLKHDPKLVATEAQIRDFMAEDPGYREWLA
+QEKQLDRAHAEHLHPHATGGSSVR
+>MHAAABBN_01635
+MEATVEQITAAVTAFNDKYWYVVMALLFVAGVWFTIRTVGVQVRMLPEMLRSVTAKSQTG
+FENDGVSPFRAFTISAASRVGTGNVAGVAIAIVIGGPGAVFWMWLLAIIGGATAFVESTL
+AQLYKQKGADGYFGGPAYYIRDGLGAKWLAAVFAVAITVTYGFVFNAVQSNSISESVQAN
+WGASSTTAWIVGLGLAALTGLVIFGGVRRLSAVTNVLVPVMATFYIFLALIVMVVNITEV
+PGMIALIVGHAFGLREVAGAAVGMTMVMQGVRRGMFSNEAGMGSAPNAAATAAVSHPAKQ
+GFVQSLGVYFDTLIVCSATAFVILLSNPAYGRGEALGMQVTQGALQQAVGAWAGPALTVI
+IFFLAWSSVLGNTYYGEANIRYLAGRHAGRAITVFRVLVLVCVVGGALGSVALVWNLADT
+FAALMATINLVAIIPLGGLAVKLLRDYERKLKAGMDPGFHISDLPEARNVALWRDEPKTS
+PLQD
+>LFPAFLNI_01858
+MEATVEQITAAITALNDKYWYVVMALLFVAGVWFTIRTVGVQVRMLPEMLRSVTAKSQTG
+FENDGVSPFRAFTISAASRVGTGNVAGVAIAIVIGGPGAVFWMWLLAIIGGATAFVESTL
+AQLYKQKGSDGYFGGPAYYIRDGLGAKWLAAVFAVAITVTYGFVFNAVQSNSISESVQAN
+WGASSTTAWIVGLGLAALTGLVIFGGVRRLSAVTNVLVPVMATFYIFLALIVMVVNITEV
+PGMIALIVGHAFGLREVAGAAVGMTMVMQGVRRGMFSNEAGMGSAPNAAATAAVSHPAKQ
+GFVQSLGVYFDTLIVCSATAFVILLSNPAYGRGEAIGMQVTQGALQQAVGAWAGPALTVI
+IFFLAWSSVLGNTYYGEANIRYLAGRHAGPAITVFRVLVLVCVVGGALGSVALVWNLADT
+FAALMATINLVAIIPLGGLAVKLLRDYERKLKAGMNPGFHISDLPEARNVALWRDEPKTS
+PLQD

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000116.fa

@@ -0,0 +1,35 @@
+>ACLBLIBL_01016
+MTTTLASQTDLDPMRTPAAAAAHRIAPGTAAPDGSGGTPALSVRDLVLEYPDGERGVLRA
+LDEVSLDLHAGTFTALVGPSGSGKSSLLAVAAGLVPPTSGTVTVAGRELTGLSRTERTGL
+RGREIGVIFQQPNLIPSLTAAEQLELSVHLDRDATRTDRKAARDRAMALLERVDLADQAG
+KRPHQLSGGQRQRVNIVRALMASPALLLVDEPTSALDRERSAAVVDLLGALTRDEGTATL
+MVTHDHEFLAATDRTLTMVDGRLTD
+>ACLBLIBL_01058
+MSTTTPVIQLSSVTKTYQRRDLYTDASVTVIPGRAHAIVGPNGSGKSVMMRLMCGFLLPS
+SGSVTIDPRYLDGRRTFPDKFGVVIDKPGMLPHLTGLENLRRLAEIQKKIGDERIREVMQ
+SFGLDPDARQRVHQYSLGMKQKLNLCQAVMEDPEVLVLDEPFNALDADSADALRGRLASF
+VADGGTLVFTSHDSRDVEQLADSVIRLENGRVTQEDASPRT
+>MOLHKGIG_01852
+MTTLTAPQADLDALRTPAAAAAHRVAGERPAAAADATPALSVRDLVLEYPDGERGVLRAL
+DEVSLDLLPGTFTAMVGPSGSGKSSLLAVAAGLVTPTSGSVSVAGREMAGLSRKERTALR
+GQEIGVIFQQPNLIPSLTAAEQLELTVHLDRDATRADRRAAKARAMELLERVDLADQAGK
+RPHQLSGGQRQRVNIVRALMASPTLLLVDEPTSALDRERSAAVVDLLGTLTREEQVATLM
+VTHDHEFLSVTDRTLTMVDGRLSAE
+>NAFOICDF_00958
+MTISTHTPDLSAYRSPAAARVTAHDAAPAAPDAAPVLSVRDLVLEYPDGEGRTLRALDGV
+SLDLTPGTFTAMIGPSGSGKSSLLAVAAGLIAPTSGSVTVAGTELTGLSRAARTRLRGDR
+IGVVFQQPNLLPSLTAREQLELVVRLDPKSTRADRTAAAARAQELLERVDLGRRADQRPH
+QLSGGQRQRVNIVRALMGTGSGAPALLLVDEPTSALDRERSAAVVELLGELTRQEGVATL
+MVTHDHEFLGATDRVLTMVDGRLAA
+>MHAAABBN_01548
+MTALTAPQADLDALRTPAAAAAHRVAAERPATAADATPALSVRDLVLEYPDGERGVLRAL
+DEVSLDLLPGTFTAMVGPSGSGKSSLLAVAAGLVTPTSGSVSVAGREMAGLSRKERTALR
+GQEIGMIFQQPNLIPSLTAAEQLELTVHLDRDATRADRKAARARALELLERVDLADQARK
+RPHQLSGGQRQRVNIVRALMASPTLLLVDEPTSALDRERSAAVVDLLGTLTREEQVATLM
+VTHDHEFLSATDRTLTMVDGRLHAE
+>LFPAFLNI_01772
+MTTLTAPQADLDALRTPAAAAAHRVAGERPAAAADATPALSVRDLVLEYPDGERGVLRAL
+DEVSLDLLPGTFTAMVGPSGSGKSSLLAVAAGLVTPTSGCVSVAGREMAGLSRKERTALR
+GQEIGMIFQQPNLIPSLTAAEQLELTVHLDRDATRADRRAAKARALELLERVDLADQAGK
+RPHQLSGGQRQRVNIVRALMASPTLLLVDEPTSALDRERSAAVVDLLGTLTREEQVATLM
+VTHDHEFLSATDRTLTMVDGRLSAE

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000117.fa

@@ -0,0 +1,71 @@
+>ACLBLIBL_01024
+MSPRRRTGSTAAPETSTLSVVDPAAARDLRVLGVRAEETLEYTPEERRHVRRRSWALLRQ
+LAGPAKGMLWLTVVLVVVSNAARAAVPLVIAWAIDWGLPQVVEAVRTGADAWGVVVLVGG
+AYALTGVTGGVLLGLYQWLTARASQRMLLALRVRVFRHTQRLSLGFHEKYTSGRVISRQT
+SDLEALRELLDQGVSSLVSGVLFMAFTAVSIVLLDPPSALVLLVAFIPVAVAVRWYQKRS
+EEAYRRSRVSSARAIVHFVETMTGIRAVQAFRRQRANEAKYTRLATDYRDDMVHTLTLFG
+VLQPVLVVTGNLTVAALLVFGGLRVLSGDLEVGVLVALVLAGRRVFQPMEMVAMFYSSFQ
+SAGAALEKVSGLLEEEPAVVEAPEPTPLPGAAAAGEGVASGRIEFRDAVFGYGPEKVVLP
+EFDLTVPAGQTVAVVGQTGAGKSTLVKLIARFYDLTSGSLTLDGVELKELASADLRRNVV
+MVTQEAFLFSGTVAENIALGRPGASEAEIQAAARAVGAHEFILDLPEGYDTDVSKRGGRL
+SAGQRQLVSFARAFLADPAVLILDEATSSLDLPSERLVQDGLERLLGNRTALIIAHRLST
+VEIADRVLVVHDGRVVEDGSPAELVAAGGRFAALHRAWEDSLVPDDA
+>ACLBLIBL_01331
+MPALFVGRRRLLLLGLAGLGLLQAALSVAVAVLTPRLLTAGAGAWGLAAALLVAALLVGG
+ARILERVAAEDLGQDYVRETRRLLVTSALVPEKSLNLGSTIARTTNDLTAVKNWIALGIS
+PIVVGVPLIVGIVIGLFVLLPTLGLVVVVTLGVFFTGLWALSRVFFRRAVAVRRVRGKMA
+GYVADTVTAAGSIRTAGGVQREVGRVDRISGQLQDAAHRRAVVSGTMRGSAASITTVLGV
+LVAITGSAAGSTGAAITTAVFIAGMLGAPVTELGRVGEYRQNYNAACRVLRPIIENARGH
+ARRERRQKRARTRMRHHGNPRGLSRDAVHLADLRDAEGTIPALVAAPGSRVLLTGGSRER
+LERVTREITGDMPASDAWITVAGRHLYAMTAKDRRELIGVAARDVPLQRGTISRIVRYRH
+RGAGETVAQVLDRVGMAERVARLPEGDATRLKRGGEPLSINERALLKIAGAVAGNPPLLV
+LDHVDDQLDARDRPILRRILADYPGCVILRSASPHELLERYEVYNVDELAPTLVVAPSVL
+HSRIQGERPTTYVIGADRDPFGPPVRHSAVELAGTRAASAPRLGESADDLEGVDE
+>MOLHKGIG_01844
+MSAADVSRVRGVGAEEDLDYTRAERRHIRRRSFRLLGELARPVRGTLLVTVVFVLVSNAA
+RAAGPLIIAWAIDAELPRVVEAVRAGESVWPILVPVGGAYVAAALVSGGLLGAYTWLTAR
+ASQAMLLSLRLRVFRHTQRLSLGFHERYTSGRVISRQTSDLEALRELLDQGVSSLVSGLM
+FMSFTAASILLLDPPSFLVLLGAAVPVAIVTRWYQVRSEEAYRRSRVSSARSIVHFVETM
+TGIRAVQAFRRERDNDARYRDLATAYRDDMVATLNLFGILQPVLVATGNLTVAALLVTGG
+LRVLDGDLEVGVLVALLLAGRRVFQPMEMVAMFYSSLQSATAALEKVSGLLEEEPTVVEA
+AEPTPLPGADAPGTGVASGRVEFRDAVFSYGPDRVVLPEFDLVIPAGQTVAVVGQTGAGK
+STLAKLIARFYDVSAGSLTLDGVELRELSQADLRRNVVMVTQEAFLFSGSIAENIALGRP
+DATEAEIQAAARAVGAHDFILGLPEGYATDVAKRGGRLSAGQRQLVSFARAFLADPAVLI
+LDEATSSLDLPSERLVQAGLERLLGNRTALIIAHRLSTVETADRVLVMHDGRIVEDGSPA
+ELVAADGRFAALHRAWEDSLA
+>NAFOICDF_00965
+MSRRADTAPVTSTLTVVDPAEAAGLRVLGVGAEESLDYTPAERRHVRRRSWALLRQLARP
+VRGMLWLTAALVVLSNAARAAMPLVIAWSIDDALPRALEAVRAGTDPTGVVVQTGALYAV
+TGLVGGVLLGLYQWLTAKASQRMLLALRVRVFRHTQRLSLGFHETYTSGRVISRQTSDLE
+ALRELLDQGVSSLVSGVLFTAFTAVSILLLDPPSFLVILVAFVPVAIAVRWYQVRSEEAY
+RRSRVSSARSIVHFVETMTGIRAVQAFRRQRAGERAYARLATDYRDDMMHTLNLFGVLQP
+VLVAVGNLTVAALLLFGGLRVLSGDLAVGVLVALLLAGRRVFQPMEMVAMFYSSLQSATA
+ALEKVSGLLEEEPAVVEPAHPVALPGAERPGEGVASGRIEFRDAVFGYGSDAVVLPGFDL
+TVPAGQTVAVVGQTGAGKSTLVKLIARFYDLTSGSLTLDGVELKDLAGADLRRNVVMVTQ
+EAFLFSGTVGENIALGRPDASEAEIQAAARAVGAHEFILDLPEGYATDVSKRGGRLSAGQ
+RQLVSFARAFLADPAVLILDEATSSLDLPSERLVQDGLERLLGNRTALIIAHRLSTVEIA
+DRVLVVHDGRIVEDGSPTELVAAGGRFAALHRAWEDSLVGEG
+>MHAAABBN_01541
+MSAADVSRVRGVGAEEDLDYTRAERRHIRRRSFRLLGELARPVRGTLLVTVVFVLVSNAA
+RAAGPLIIAWAIDAELPRVVEAVRAGESVWPILVPVGGAYVAAALVSGGLLGAYTWLTAR
+ASQAMLLSLRLRVFRHTQRLSLGFHERYTSGRVISRQTSDLEALRELLDQGVSSLVSGLM
+FMSFTAASILLLDPPSFLVLLGAAVPVAIVTRWYQVRSEEAYRRSRVSSARSIVHFVETM
+TGIRAVQAFRRERDNDARYRDLATAYRDDMVATLNLFGILQPVLVATGNLTVAALLVTGG
+LRVLDGDLEVGVLVALLLAGRRVFQPMEMVAMFYSSLQSATAALEKVSGLLEEEPTVVEA
+AEPTPLPGADAPGTGVASGRVEFRDAVFSYGPDRVVLPEFDLVIPAGQTVAVVGQTGAGK
+STLAKLIARFYDVSAGSLTLDGVELRELSQADLRRNVVMVTQEAFLFSGSIAENIALGRP
+DATEAEIQAAARAVGAHDFILGLPEGYATDVAKRGGRLSAGQRQLVSFARAFLADPAVLI
+LDEATSSLDLPSERLVQAGLERLLGNRTALIIAHRLSTVETADRVLVMHDGRIVEDGSPA
+ELVAADGRFAALHRAWEDSLA
+>LFPAFLNI_01765
+MSAADVSRVRGVGAEEDLDYTRAERRHIRRRSFRLLGELARPVRGTLLLTVVFVLVSNAA
+RAAGPLIIAWAIDAELPRVVEAVRAGESVWPILVPVGGAYVAAALVSGGLLGAYTWLTAR
+ASQAMLLSLRLRVFRHTQRLSLGFHERYTSGRVISRQTSDLEALRELLDQGLSSLVSGLM
+FMSFTAASILLLDPPSFLVLLGAAVPVAIVTRWYQVRSEEAYRRSRVSSARSIVHFVETM
+TGIRAVQAFRRERDNDARYRDLATAYRDDMVATLNLFGILQPVLVATGNLTVAALLVTGG
+LRVLDGDLEVGVLVALLLAGRRVFQPMEMVAMFYSSLQSATAALEKVSGLLEEEPTVVEA
+AEPTPLPGADAPGTGVASGRVEFRDAVFSYGPDRVVLPEFDLVIPAGQTVAVVGQTGAGK
+STLAKLIARFYDVSAGSLTLDGVELRELSQADLRRNVVMVTQEAFLFSGSIAENIALGRP
+DATEAEIQAAARAVGAHDFILGLPEGYATDVAKRGGRLSAGQRQLVSFARAFLADPAVLI
+LDEATSSLDLPSERLVQAGLERLLGNRTALIIAHRLSTVETADRVLVMHDGRIIEDGSPA
+ELVAADGRFAALHRAWEDSLA

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000120.fa

@@ -0,0 +1,30 @@
+>ACLBLIBL_01086
+MDAPASDLTGKARIRHAALRLFAHHGVEGTSMRAIAEEASVTVGLITHHYGSKAGLHREV
+DAAVADDFAAAIASVPAEGTARDVTLRRDAAVAEMLRARPDVLEYVRRHVLLGEPAADSQ
+LVEKLTALAREQVRQLRAAGLISGRRDEVPQVVSMIMRMLGELFFEPLVDRIVDAVDRDA
+ARPAVVVRVQAAEDETARGGRA
+>MOLHKGIG_01790
+MDAPASDLTGKARIRHAALRLFAHHGVEGTSMRAIAEEASVTVGLITHHYGSKAGLHREV
+DAAVADDFAAAIASVPAEGTARDVTLRRDAAVAEMLRARPDVLEYVRRHVLLGEPAADSQ
+LVEKLTALAREQVRQLRAAGLISGRRDEVPQVVSMIMRMLGELFFEPLVDRIVDAVDRDA
+ARPAVVVRVQAAEDETARGGRA
+>MOLHKGIG_02051
+MNTPLPFDQDDLSSPARLRLAALELYAERGVEMASVREIAQRAGVAPGLVRHHFGSKAGL
+TRAVDDDVLRLIAATLDEVPLVGTPQEVSAARDAAFADLLADHPVVGAYVRRSLLEAGGE
+TESLLERLVDLTTEQTERLRRSGFAPRRSMPTSVFGTVIRQMGHLMVDPSADRIWRRIAE
+TQEGAAEQASPRVRLVVDPPR
+>NAFOICDF_00729
+MNTARPLTREDLSSAARLRLSALELYAERGEHAASIRDVGRHAGVAPGLVRHHFGSKDGL
+TRAVDDDIIDLVRATLEAVPLEGTPLEISAARDAAFQELLQERPLIGGYLAQALTASRAS
+GESVLDRLVDLSAEQTRQLIDRGLDPRRGLRTSVFTTVVRQVAVFLVAPVAERAWNRLGH
+TLEGASDVAPMPPVRVVVGPAPEEDRR
+>MHAAABBN_01757
+MNTPLPFDQDDLSSPARLRLAALELYAERGVEMASVREIAQRAGVAPGLVRHHFGSKAGL
+TRAVDDDVLRLIAATLDEVPLVGTPQEVSAARDAAFADLLADHPVVGAYVRRSLLEAGGG
+TESLLERLVDLTTEQTERLRRSGFAPRRSMPTSVFGTVIRQMGHLMVDPSADRIWRRIAE
+TQEAAAEQRSPRVRLVVDPPR
+>LFPAFLNI_01985
+MNTPLPFDQDDLSSPARLRLAALELYAERGVEMASVREIAQRAGVAPGLVRHHFGSKAGL
+TRAVDDDVLRLIAATLDEVPLVGTPQVVSAARDAAFADLLADHPVVGAYVRRSLLEAGGE
+TESLLERLVDLTTEQTERLRRSGFAPRRSMPTSVFGTVIRQMGHLLVDPSADRIWRRIAE
+TQEDAAEQASPRVRLVVDPPR

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000121.fa

@@ -0,0 +1,44 @@
+>ACLBLIBL_01098
+MRVRFRGTDARQALLLRGPAGWAEFSPFPEYGPAESSAWLAAAIEAGWQGWPAPVRDVVP
+VNATVPAVEAEAVESVLARYGEGITAVKVKVAEHRPGGGLVPGSHSADLARVRRVRELLP
+DAHVRIDANAGWTPAEAIAMLTDLADVGLEYAEQPVPGIKKLARVRRELRARGVSTPIAA
+DEAVRKAEDPLAVAAAGAADLIVVKVQPLGGVRRAAAVVAAAGLPAVVSSALDTSVGIAG
+GAALATHLPALPHACGLGTAALFDDDVVTPAWTPRQGVLEAPGERAPEPDPALLARVRAD
+ERTHAWWRDRVAAAHAVLAAGGR
+>MOLHKGIG_01779
+MSTAPALPPLPGAPGGPALPSVEELLADAVAVAVPMRVRFRGTDLRHALLLRGPAGWGEF
+SPFPEYGPHESAAWLAAAIEAGWQGWPAPVRETIPVNATVPAVDADDVEAVLARYGDGIT
+AVKVKVAEHGPEGGLVPGGREADLARVRRVRALLPHAQVRVDANAGWTPAEAVDVLTELA
+DVGLEYAEQPVPGITDLAEVRAELRARGVPTPIAADEAVRKAEDPLAVAAAGAADLIVVK
+VQPLGGVRRAAAIVAAAGLPAVVSSALDTSVGIAGGAALAACLPSLPHACGLGTAALFEH
+DVVAPAWRPRAGALPAPGERAPAPDPELLDRIRADGTRQAWWADRVRAAHAVLAAQG
+>NAFOICDF_01022
+MTVPAAHDDADPRPGSALPPLPGAPGGPALPDVDELLEHAVAVTLPMTVRFRGTTERRAL
+LLRGPAGWAEFSPFPEYGPAEASRWLAAAVEAGWQGWPAPVRSEVPVNATVPAVDAADVE
+SVLARYGDGITAVKVKVAEHRPGGGLVDPTHAADVARVRRVRELLPEAAVRIDANAGWDE
+DRAFAVLGALQDVGLEYAEQPVPGIAGLAALRSRLRAAGIATPIAADEAVRKETDPLAVA
+QAGAADLIVVKVQPLGGVRRAAAIVAAAGLDAVVSSALDTSVGIAGGAALAAHLPSLPFA
+CGLGTASLFAHDVVSPAWRPADGSLPAPGERAPEPDPALLAAARADAAEHAWWAERLRAA
+HAVLAARGR
+>NAFOICDF_01806
+MSPAPGQAPVSVAAVRRHRHRAPLLHPFVTAARRTEAVEYVVVEVELSDGTVGQGSAAET
+VAVTGEDAASIETAVDGVFGPALTGATGGLDGLLARLPAPARGATSARSAVDVAVHDAVA
+RAAGVPLTALLAPAGTAVKQTLENDMTVSLEDPATMAARAAEAVAAGTRILKIKLGRDVA
+EDRRRLHAVLEAAPQARLRLDANQGWSVEDAIAIISGMEDEGLPVDLVEQPVAAADVAGL
+ARVRAAVTTPIMADEALWSSEDARRLIEAGAADLFNVKLAKTGGLADAVAIADLAAEHGI
+GCMVGSMMEPRISIAAAVQLSLAHPAVTMVDLDAPLWFASDAPAGGYTQEGADLRLLPGE
+GLALERLDPGTDPV
+>MHAAABBN_01486
+MSTAPALPPLPGAPGGPALPSVEELLADAVAVALPMRVRFRGTDLRHALLLRGPAGWAEF
+SPFPEYGPHECAAWLAAAIEAGWQGWPGPVRQTVPVNATVPAVAADDVEAVLARYGDGIT
+AVKVKVAEHGPEGGLVPGGREADLARVRRVRALLPHAQVRVDANAGWTPAEAVDVLTALA
+DVGLEYAEQPVPGITALAEVRAELRARGVPTPIAADEAVRKAEDPLAVAAAGAADLIVVK
+VQPLGGVRRAAAIVAAAGLPAVVSSALDTSVGIAGGAALAACLPSLPHACGLGTAALFEH
+DVVAPAWRPRAGALPAPGERAPAPDPELLDRIRADGTRQAWWADRLRAAHAVLAAQG
+>LFPAFLNI_01708
+MSTAPALPPLPGAPGGPALPSIEELLADAVAVALPMRVRFRGTDLRHALLLRGPAGWAEF
+SPFPEYGPHESAAWLAAAIEAGWQGWPAPVRQAVPVNATVPAVDAADVEAVLARYGDGIT
+AVKVKVAEHGPEGELVPGSREADLARVRRVRALLPHAQVRVDANAGWTPTEAVDVLTALA
+DVGLEYAEQPVPGITDLAEVRAELRARGVPTPIAADEAVRKAEDPLAVAAAGAADLIVVK
+VQPLGGVRRAAAIVAAAGLPAVVSSALDTSVGIAGGAALAACLPSLPHACGLGTAALFEH
+DVVAPAWRPRAGALPAPGERASAPDPELLDRVRADGARQAWWADRVRAAHAVLAAQG

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000124.fa

@@ -0,0 +1,48 @@
+>ACLBLIBL_01218
+MTRRLLLFANSFPYGKQEPYLMRECHYLDAFDEVYIFSLSIRKHQRDHRRDLPLERVTVV
+PIPFKSPLFYAAVSPRALVSRAFVTELRQLLRDRRFTVARAVQALSQFSRAEHEASVIGR
+FLRDNITPSPSDETVFYAYRFLYQPYLMSRLAAKFSSSRLIGRAHGIDLFEERQSTDYLP
+GRAINLGALDELHSVSRAGAEYLRARHPEFVEKIKVSYLGTEDHGVRPPRSSSQVLRLVS
+CSEVAPVKRLELLVEALREVSDSIQVEWSHYGEGPDMDRVRAMASTLPGHVSATFHGWTR
+NDEILEAYRSGRHDVFINVSSSEGLPVSIMESSSCGLPTIATDVGGTGEIVSDGVNGRLI
+SANPMPREIAAAVEEFARMAPEAFARRSAAARETWSTHFDSDRNYRQFVAKMLS
+>ACLBLIBL_02441
+MTPEAATTTPAPLTLWVVPVADLGGVARHVLDVAAHGLPGLRLVVLCPEGALAERLREQG
+AAVFTGDVGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFTAFGPGRARRRAGAP
+ALVSTEHGIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGTGAPI
+TVVRNGVDVSAVRAAAAGQRRAPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRL
+TLAGVGPLEGQLRAQAEALGVADAVDLPGFVEPWGAMAEHDVLVQLSAWENLSYTLLDAA
+AAGLPAVATDVGGNGEILPPERLVHETTPAAIADAVMRATVEGPGEVRVGDVETMARATA
+EATLEVLGRRAGKTSG
+>MOLHKGIG_00509
+MIPEAARTTPAPLTLWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQG
+AAVFTGDVGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFAALGPGRARQRAGAP
+ALLSTEHGIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPI
+TVVRNGVDVPAVRAAAAGQRRTPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRL
+TLAGAGPLEGELRAQAEALGVAEAVDLPGFVEPWETMAEHDVLVQLSAWENLSYTLLDAA
+AAGLPAVATDVGGNGEILPPERLVHETTPAAIADAVVRAAADGPGEVRVGDVETMARATA
+EATLEVLGRRVGKVGTR
+>NAFOICDF_02325
+MIPEAATTTPAPLTLWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQG
+AAVFTGDVGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFTALGPGRARRRAGAP
+ALLSTEHGIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPL
+TVVRNGVDVSAVRAAAAGQRRAPGEGLRILSLSRLAPEKGLDRLIAALPALRERDPGTRL
+TLAGSGPLEGQLRAQAEDLGVADAVDLPGFVEPWETMAEHDVLVQLSAWENLSYTLLDAA
+AAGLPAVATDVGGNGEILPPERLVHETTPAAIADAVTRAAAEGPGEVRVDDVEGMAEATA
+RAERDVVETQDARRRKTR
+>MHAAABBN_00229
+MIPEDATTTPAPLTLWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQG
+AAVFTGDVGPDAGLAASVRTLRTAVRTLCPAAVHTHLAYADLAAFTALGAGRALRRAGAP
+ALLSTEHGIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPL
+TVVRNGVDVPAVRAAAAGRRRAPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRV
+TLAGSGPLEGQLRAQAEDLGVADAVHLPGFVEPWGTMAEHDVLVQLSAWENLSYTLLDAA
+AAGLPAVATDVGGNGEILPPERLVRETTPEAIADAVVRAAAEGPGEVRVGDVETMARATA
+EATLEVLGRRVGKGGHR
+>LFPAFLNI_00508
+MIPEAARTALAPLTLWVVPVADLGGVARHVLDVARVGLPGLRLAVLCPEGPLAERLREQG
+AAVFTGDVGPDAGLAASVRTLRTAVRTLRPAAVHTHLAYADLAAFAALGPGRARRRTSAP
+ALLSTEHGIAPDDGLYNRAAAARVKNAAHRARLRGTDLVIAVAQSTADVLRRKWGAGAPI
+TVVRNGVDVPAVRAAAAGQRRTPGEGLRILSLSRLAPEKNLDRLIAALPALLERDPGTRL
+TLAGSGPLEGQLRAQAEALGVAEAVDLPGFVEPWETMAEHDVLAQLSAWENLSYTLLDAA
+AAGLPAVATDVGGNGEILPPERLVRETTPAAIADAVVRAAADGPGEVLVGDVETMARATA
+EATLEVLGRRVGKAGTR

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000127.fa

@@ -0,0 +1,30 @@
+>ACLBLIBL_01252
+MIPVLLIEDEERIAAFVTKGMAAEGIAVTTAGTGAEGVGLAMTGAFELVILDLGLPDADG
+FDVLARIRRQDAHLPVIILTARSSAQDTVEGLTSGADDYMPKPFRFAELLARVRLRLRPG
+APAPEPTDTVMRHGDLELDPASHTARVDGRTVALSAREFALAEEFLRSPGQVLSREQLLD
+GAWGEDFESGSNVVDVYVRYLRAKIGAERILTVRGLGYRLAGEDELSG
+>ACLBLIBL_02602
+MQSQNPEARLLVVDDEPNIRELLSTSLRYAGFEVTAAANGREALDAAEEFQPDLAVLDVM
+LPDMDGFTVTRRLRAAGRHFPVVFLTARDGTEDKITGLTVGGDDYVTKPFSLDEVVARIR
+AVLRRTASLDDDAAVLRVGDLELDDDAHEVRRGGEVVELSPTEFKLLRYLMMNPNRVLSK
+AQILDHVWEYDFNGDASIVESYISYLRRKIDVGGREKMIHTKRGVGYMLRAADKR
+>MOLHKGIG_00359
+MQPQNPEARLLVVDDEPNIRELLSTSLRYAGFEVTAAANGREALDAAEEFQPDLAVLDVM
+LPDMDGFTVTRRLRAAGRHFPVVFLTARDGTEDKITGLTVGGDDYVTKPFSLDEVVARIR
+AVLRRTASLDDDAAVLRVDDLELDDDAHEVRRGGEVVELSPTEFKLLRYLMMNPNRVLSK
+AQILDHVWEYDFNGDASIVESYISYLRRKIDVGGREKMIHTKRGVGYMLRTADKR
+>NAFOICDF_02461
+MQSQTPEARLLVVDDEPNIRELLSTSLRFAGFEVRAAGNGREALEAAEEFQPDLAVLDVM
+LPDMDGFTVTRRLRAAGRLFPVVFLTARDGTEDKVTGLTVGGDDYVTKPFSLDEVVARIR
+AVLRRTAPLDDDSAVLRVDDLELDDDAHEVRRGGEVVDLSPTEFKLLRYLMMNPNRVLSK
+AQILDHVWEYDFNGDASIVESYISYLRRKIDVGGRDKMIHTKRGVGYMFRTADKR
+>MHAAABBN_00075
+MQPQNPEARLLVVDDEPNIRELLSTSLRYAGFEVTAAANGREALDAAEEFQPDLAVLDVM
+LPDMDGFTVTRRLRSAGRHFPVVFLTARDGTEDKITGLTVGGDDYVTKPFSLDEVVARIR
+AVLRRTASLDDDAAVLRVDDLELDDDAHEVRRGGEVVDLSPTEFKLLRYLMMNPNRVLSK
+AQILDHVWEYDFNGDASIVESYISYLRRKIDVGGREKMIHTKRGVGYMLRTADKR
+>LFPAFLNI_00366
+MQPQNPEARLLVVDDEPNIRELLSTSLRYAGFEVTAAANGREALDAAEEFQPDLAVLDVM
+LPDMDGFTVTRRLRSAGRHFPVVFLTARDGTEDKITGLTVGGDDYVTKPFSLDEVVARIR
+AVLRRTASLDDDDAAVLRVDDLELDDDAHEVRRGGEVVELSPTEFKLLRYLMMNPNRVLS
+KAQILDHVWEYDFNGDASIVESYISYLRRKIDVGGREKMIHTKRGVGYMLRTADKR

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000129.fa

@@ -0,0 +1,52 @@
+>ACLBLIBL_01273
+MALTIGFVGLPNVGKSTLFNALTRQTVLAANYPFATIEPNVGVVNLPDERLPQLAEIFGS
+ERILPATVSFVDIAGIVKGASEGEGLGNQFLANIREAHAIAQVVRAFDDGDVVHVDGKVD
+PASDMETINTELIIADMQTVEKAIPRVEKEVKGKKKEPADLEALKAALAVLERGETIFAA
+KDKDKLDMDRLRELSLLTAKPFIYVFNSDEGVLGDEAKQQELRDLVAPADAVFLDAKLES
+DLVELSEEEAAEMLEMAGQNESGLDQLARVGFSTLGLQTYLTAGPKETRAWTIPVGATAP
+EAAGVIHTDFQRGFIKAEIVSFEDLIAAGSMADAKAAGKVRMEGKDYVMKDGDVVEFRFN
+V
+>MOLHKGIG_01624
+MRDASAAAGPPVDCRTVALTIGFVGLPNVGKSTLFNALTRQTVLAANYPFATIEPNVGVV
+NLPDERLPQLAEIFGSERILPATVSFVDIAGIVKGASEGEGLGNQFLANIREAHAIAQVV
+RAFDDGDVVHVDGKVDPASDMETINTELIIADMQTVEKAIPRVEKEVKGKKKEPADLEAL
+KAALAVLERGETIFAAKDKDKLDMDRLRELSLLTAKPFIYVFNSDEGVLGDEAKQQELRD
+LVAPADAVFLDAKLESDLVELSEEEAAEMLEMAGQDESGLDQLARVGFSTLGLQTYLTAG
+PKETRAWTIPVGATAPEAAGVIHTDFQRGFIKAEIVSFDDLIAAGSMADAKAAGKVRMEG
+KDYVMKDGDVVEFRFNV
+>NAFOICDF_00781
+MSHAHHHGGGSSAAVLDSSLTRLGLVGSPNSGKSTLFNALTGLRVKTGNYPGVTVSRAEG
+VMVAEDGTRVVLEDLPGTYSLDPISPDEQVVADLLALDPADADHPQALLLVADATTLRRG
+LTMVAHALAVELPATLVLTFGDELALRGGSVDVTRLSRALGIPVLAATAGDARQREAVRA
+HLATDPAGWAVPPVAPPTDPAGIAAWIDSVLEAARYAVPRPDGRTRRIDDVLLHPVWGTL
+VFLVTMFAFFQVIFTVAAPLQALVEELFGWLGERAAALIPIEWLGRFVAEALIGGVGGVV
+VFLPQILLLFLMISLLESTGYMTRAAFLMDRVMSRFGLEGRSFVALLSSLACAVPGIMAT
+RSLPSARDRLATMMAAPSMTCSARLPVYVLLISLLVPSEVRWGPVGLQGLVMFALYLGGA
+TASMLTAAFWSRVVGRRQAAMPFYMEMPPYRLPKARTVVTSMWASAEGFLRKVTSIILVT
+TALLWVLLNVPVRSEEEMAGAGVAMDDPAAVAQYTIDHSAAAAVGKAVEPAFEPLGFDWR
+IDVGVLASLAAREVFVATLGQMAAAEDPEDPGDALASWTVTDDAGVERPLFTPDVVAALL
+VFFMLALQCMSTLAVMRRETGTWRWPLLAFGYYFTLAWLAAFAVRHVVLALT
+>NAFOICDF_01182
+MALTIGFVGLPNVGKSTLFNALTRQTVLAANYPFATIEPNVGVVNLPDERLPQLAEIFGS
+ERILPATVSFVDIAGIVKGASEGEGLGNQFLANIREAHAIAQVVRAFDDGDVVHVDGKVD
+PASDMETINTELIIADMQTVEKAIPRVEKEVKGKKKEPADLEALKAALAVLERGETIFAA
+KDKDKLDMDRLRELSLLTAKPFIYVFNSDEGVLGDEAKQQELRDLVAPADAVFLDAKLES
+DLVELSEEEAAEMLEMAGQDESGLDQLARVGFSTLGLQTYLTAGPKETRAWTIPVGATAP
+EAAGVIHTDFQRGFIKAEIVSFDDLIAAGSMNDAKAAGKVRMEGKDYVMKDGDVVEFRFN
+V
+>MHAAABBN_01330
+MRDASAAAGPPVDCRTVALTIGFVGLPNVGKSTLFNALTRQTVLAANYPFATIEPNVGVV
+NLPDERLPQLAEIFGSERILPATVSFVDIAGIVKGASEGEGLGNQFLANIREAHAIAQVV
+RAFDDGDVVHVDGKVDPASDMETINTELIIADMQTVEKAIPRVEKEVKGKKKEPADLEAL
+QAALAVLERGETIFAAKDKDKLDMDRLRELSLLTAKPFIYVFNSDEGVLGDEAKQQELRD
+LVAPADAVFLDAKLESDLVELSEEEAAEMLEMAGQDESGLDQLARVGFSTLGLQTYLTAG
+PKETRAWTIPVGATAPEAAGVIHTDFQRGFIKAEIVSFEDLIAAGSMADAKAAGKVRMEG
+KDYVMKDGDVVEFRFNV
+>LFPAFLNI_01551
+MGPPVDCRTVALTIGFVGLPNVGKSTLFNALTRQTVLAANYPFATIEPNVGVVNLPDERL
+PRLAEIFGSERILPATVSFVDIAGIVKGASEGEGLGNQFLANIREAHAIAQVVRVFDDGD
+VVHVDGKVDPASDMETINTELIIADMQTVEKAIPRVEKEVKGKKKEPADLEALQAALAVL
+ERGETIFAAKDKDTLDMDRLRELSLLTAKPFIYVFNSDEGVLGDEAKQQELRDLVAPADA
+VFLDAKLESDLVELSEEEAAEMLEMAGQDESGMDQLARVGFSTLGLQTYLTAGPKETRAW
+TIPVGATAPEAAGVIHTDFQRGFIKAEIVSFDDLIAAGSMNDAKAAGKVRMEGKDYVMKD
+GDVVEFRFNV

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000130.fa

@@ -0,0 +1,59 @@
+>ACLBLIBL_01275
+MPWEPVVRYIGLRAGSAETTAEMDLAATSLAGPDFTNVAANRVSAALARWLATGTTDLEK
+CIRIVLANLGLEMDDIPTGWVALEADVVVDTAGAMIVRFLYVHVVNRCFYASAYDDIRKV
+IARGVAVAGPAHWTGGTAPGLTWAGTSAQN
+>ACLBLIBL_01290
+MTATLVASHLAGGHGHRTLFESLDLTVAPGDVVGVVGANGAGKSTLLRILGGDLAPQAGT
+VSLAPADAFVGWLPQEHERVPGESVAAYIGRRTGCAAATAEMDEAAEALGAPDAGDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLERLERFVQELRGGVVLVSHDREFLARCVTRVLELDLAQHSN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKADLVSRARVQREWSSQGVRNAMKKSPDN
+DKLRRKANAESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGTAPRSSSVVATLNE
+AVFRQGSFTLGPVSLQVNAGERVGITGPNGAGKSTLLRGLLGRQDPDDGAASLGSSVQVG
+EIDQARSLLAGPTPLADAFEALVPEMASGEVRTLLAKFGLRADHVTRPVDELSPGERTRA
+GLALLQARGVNLLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRTDRRW
+QVQDGRVTER
+>MOLHKGIG_01604
+MTATLVASGLAGGHGHRTLFEDLDLTVAPGDVVGVVGANGAGKSTLLRILGGDLAPQAGT
+VSLAPADAFVGWLPQERERVPGETVAGYIARRTGCAEATREMDASASGLADPDVTDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLTRLEAFVQELRGGVVLVSHDREFLARCVTRVLELDLAQRTN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKQDLVSRARIQREWSSQGVRNAMKKSPDN
+DKLRRRANSESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGAAPRSSSVVATLND
+AVFRQGGFTLGPVSLQVNAGERIGITGPNGAGKSTLLRALLGRQAPDEGTAALGSSVQIG
+EIDQARSLLAGTVPLAAAVEALVPEMASGEVRTLLAKFGLKADHVNRPVDELSPGERTRA
+SLALLQARGVNVLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRTDRRW
+QVQDGRVTER
+>NAFOICDF_01198
+MTATLVASGLAGGHGHRTLFDALDLTVAPGDVVGVVGANGAGKSTLLRILGGNLAPQTGT
+VSLAPSDAFVGWLPQEHERVSGETVAGYIARRTGCAEATREMDASAEALAGPDVTDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLTRLEAFVQELRGGVVLVSHDREFLARCVTRVLELDLAQRTN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKQDLVSRARTQREWSSQGVRNAMRKSPDN
+DKLRRKANSESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGAAPRSSSVVATLND
+AVFRQGGFTLGPVSLQVNAGERIGITGPNGAGKSTLLRGLLGRQAPDEGTAALGSSVQIG
+EIDQARSLLAGAVPLAAAFETLAPEMTSGEVRTLLAKFGLKADHVNRPVDELSPGERTRA
+SLALLQARGVNVLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRLDRRW
+HVADGRVTER
+>MHAAABBN_01316
+MTATLVASGLAGGHGHRTLFEDLDLTVAPGDVVGVVGANGAGKSTLLRILGGDLAPQAGT
+VSLAPADAFVGWLPQERERVPGETVAGYIARRTGCAEATREMDASASGLADPDVTDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLTRLEAFVQELRGGVVLVSHDREFLARCVTRVLELDLAQRTN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKQDLVSRARIQREWSSQGVRNAMKKSPDN
+DKLRRRANSESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGAAPRSSSVVATLND
+AVFRQGGFTLGPVSLQVNAGERIGITGPNGAGKSTLLRGLLGRQAPDEGTAALGSSVQIG
+EIDQARSLLAGTVPLAAAVEALVPEMASGEVRTLLAKFGLKADHVNRPVDELSPGERTRA
+SLALLQARGVNVLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRTDRRW
+QVQDGRVTER
+>LFPAFLNI_01531
+MTATLVASGLAGGHGHRTLFEDLDLTVAPGDVVGVVGANGAGKSTLLRILGGDLAPQAGT
+VSLAPADAFVGWLPQEHERVPGETVAGYIARRTGCAEATREMDASASGLADPDVTDAAAD
+RYNTALTRWLASGAADLEERIPAVLADLGLDLSASPEQVLMTSLSGGQAARVGLAALLLS
+RFDVVLLDEPTNDLDLDGLTRLEAFVQELRGGVVLVSHDREFLARCVTRVLELDLAQRTN
+RVYGGGYEAYLEERATLRRQAREKYEEFAEQKQDLVSRARIQREWSSQGVRNAMKKSPDN
+DKLRRRANSESSEKQAQKVRQMESRIARLEEVEEPRKEWRLEFTIGAAPRSSSVVATLND
+AVFRQGGFTLGPVSRQVNAGERIGITGPNGAGKSTLLRGLLGRQAPDEGMAALGSSVQIG
+EIDQARSLLVGTVPLAAAVEALVPEMASGEVRTLLAKFGLKADHVNRPVDELSPGERTRA
+SLALLQARGVNVLVLDEPTNHLDLEAIEQLEQALETYEGALLLVTHDRRMLDTVRTDRRW
+QVQDGRVTER

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000134.fa

@@ -0,0 +1,48 @@
+>ACLBLIBL_01340
+MKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWEFVAGPINAGSFGPNTLDGTFGPRLDF
+EAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRLINAVGRTVYSRTLTAA
+>MOLHKGIG_01582
+MSLACVPHPGPVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVA
+SRLTLPSGVATGDVTSNSAVLWARSSGRSRLHATLRAVDEDGKVLRGRFARGLTLRSGWV
+DGATDHTAKILADTLPSDTRFEVTYAFEDEAGRLGESAVARFTTAPGARFGRKTSAAQSF
+VWTADTAGQGYGINPEIGGMRGYAAMHATKPDFFLHSGDTIYADNPIPETLEVAGEPTWR
+NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYADVPVIAQWDDHETTNNWWPGEVLED
+PRYTQVRDVDTLAARARRAWQEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDM
+RTHKGENTPGLETHETPILGEEQLQWLIRGLRASTATWKVIANDLPLGLVVPDGTGQESL
+SNGDDGAPLGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWE
+FVAGPINAGSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRL
+INAAGRTVYSRTLTAA
+>NAFOICDF_01234
+MSLACVPHPGSVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVA
+SRLTLPSGVATGDVTSNSAVLWARSSGRSRLHATLRAVDEDGKVLRGRFARGLTLRSGWV
+DGATDHTAKILADTLPSGTRFEVTYAFEDEAGRLGESAVARFTTAPGARFGRKTSAAQSF
+VWTADTAGQGYGINPEIGGMRGYAAMHATQPDFFLHSGDTIYADNPIPETLEVAGEPTWR
+NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYADVPVIAQWDDHETTNNWWPGEVLED
+PRYTQVRDVDTLAARARRAWQEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDM
+RTHKGENTPGLETHETPILGEEQLQWLIHGLRASTATWKVIANDLPLGLVVPDGTGQESL
+SNGDDGAPLGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWE
+FVAGPINAGSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRL
+INANGRTVYARTLTAA
+>MHAAABBN_01292
+MRLACVPHPGPVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVA
+SRLTLPSGVATGDVTSNSAVLWARSSGRSRLHATLRAVDEDGKVLRGRFARGLTLRSGWV
+DGATDHTAKILADTLPSDTRFEVTYAFEDEAGRLGESAVARFTTAPGARFGRKTSAAQSF
+VWTADTAGQGYGINPEIGGMRGYAAMHATKPDFFLHSGDTIYADNPIPETLEVAGEPTWR
+NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYADVPVIAQWDDHETTNNW
+>MHAAABBN_01293
+MDTLAARARRAWQEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDMRTHKGENT
+PGLETHETPILGEEQLQWLIRGLRASTATWKVIANDLPLGLVVPDGTGQESLSNGDDGAP
+LGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFESFWEFVAGPINA
+GSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEDGREFRVRLINAVGRTV
+YSRTLTAA
+>LFPAFLNI_01509
+MSLACVPHPGPVKQTTAPLSHSASRRSVLAAASAAVLAPAALAGPAAARPARHTPGGLVA
+SRLTLPSGVATGDVTSNSAVLWARSSGRSRLHATLRAVDEDGKALRGRFSRGLTLRSGWV
+DGATDHTAKILADTLPSGTRFEVTYAFEDEAGRLGESAVARFTTAPGARFGRKTSAAQSF
+VWTADTAGQGYGINPEIGGMRGYAAMHATQPDFFLHSGDTIYADNPIPETLEVAGEPTWR
+NLVTEETSKVAETLNEFRGRHRYNMMDDNLRALYTDVPVIAQWDDHETTNNWWPGEVLED
+PRYTQVRDVDTLAARARRAWQEYMPIADSTALRRGSGFEPARIYRRIPRGATLDVFALDM
+RTHKGENTPGLETHETPILGEEQLQWLIRGLRASTATWKVIANDLPLGLIVPDGTGQESL
+SNGDDGAPLGRELEIARLLKAIKDHGVKNVVFLTGDVHYCAAHHYSPDRAAFTDFEPFWE
+FVAGPINAGSFGPNTLDGTFGPRLDFEAHGPVMGSPRSGEHQYFGHVEIPEGGREFRVRL
+INAAGRTVYSRTLTAA

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000135.fa

@@ -0,0 +1,49 @@
+>ACLBLIBL_01342
+MSAALYLDHAATAPVRRVALEAMWPALTGVYGNPSSAHEAGRAAAALLEDARARVARAIG
+ARAGQVVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGSDLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFAEAEAERAAAADAWSGLRDRFAARALDGVQELVPDARLTGHPARR
+LPRHASFVLPGVNGESVLEEAARRGVLASAGSACSAHSTEPSPALLALGLSEDEARTALR
+CTFGPDADEAMLAAAADAIVDAVRTVSALR
+>MOLHKGIG_01581
+MSTTLDLDHAATAPVRRSALEAMWPALTGVYGNPSSAHEAGRAAAALLEDARARVACAIG
+ARAGQVVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGADLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFEEAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARR
+LPRHASFALPGVNGESVLEEAARRGVLASAGSACSAHDAEPSPALLALGLSEDEARTALR
+CTFGPDADAPLLDAAADAIVDAVRTVSALR
+>NAFOICDF_01235
+MSTILDLDHAATAPVRRSALEAMWPALTGVYGNPSSAHEAGRAAAALLEDARARVARAIG
+ARAGQIVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGADLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFEEAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARR
+LPRHASFVLPGVNGESVLEEAARRGVLASAGSACSAHDAEPSPALLALGLSEDEARTALR
+CTFGPDADAPLLDAAADAIVDAVRTVTALR
+>NAFOICDF_01767
+MALDVAAVRQDFPILRSTLADGRPLVYLDSGATSQRPRQVIEAEVEFLTISNAAVKRGAH
+QLAEAATDRYESARETVAAFVGATDPRELVFTRNATEALNLVAYALGNGDDATPEHLRVR
+AGDEILVTEMEHHANLVPWQELARRTGATLRHIPLGEDFALDLVDLGSLVTERTKVVAFT
+HQSNVTGTVNPVATLGEAARAVGALTVLDACQSVPHMPVDVAALGVDFLAFSGHKMLGPT
+GIGALWGRYELLAELPPFLLGGSMIEVVHLDRSTYAEPPARFEAGTPPISQAVGLAAACD
+YLSALGMDAVAEHEHALTARALEHLAGMDRVRVIGAPAGPERSGAVSFAVEGIHPHDVGQ
+VLDSLGVQVRVGHHCAWPLHRRYGVPGTTRASFSVYSTLDEVDAFADGLAQTLAFFQGFG
+R
+>MHAAABBN_01291
+MSTTLDLDHAATAPVRRSALEAMWPALTGVYGNPSSAHEAGRAAVALLEDARARVARAIG
+ARAGQVVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGADLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFEEAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARR
+LPRHASFVLPGVNGESVLEEAARRGVLASAGSACSAHDAEPSPALLALGLSEDEARTALR
+CTFGPDADAPLLDAAADAIVDAVRTVAALR
+>LFPAFLNI_01508
+MSTTLDLDHAATAPVRRSALEAMWPALTGVYGNPSSAHEAGRAAAALLEDARARVARAIG
+ARAGQVVFTSGGTEADALAVLGTVRARILAGRPAGHVLTTGIEHSAVRQSCDQLARLHGV
+EVEHLALDRDGLTSADDLAARLRPDTALVSVHLAHNEVGTVQPVAELAAVAREAGVPLHV
+DAVQAAGQIPVDVRALGADLVALSGHKVGGPKGVGALWVRPGHALEPLVPGGGQERGRRS
+GTQNVAGAAGFAAAFEEAEAERAAAADAWSGLRDRFAARVLDGVRELVPDARLTGHPARR
+LPRHASFVLPGVNGESVLEEAARRGVLASAGSACSAHDAEPSPALLALGLSEDEARTALR
+CTFGPDADAPLLDAAADAIVDAVRTVAALR

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000143.fa

@@ -0,0 +1,81 @@
+>ACLBLIBL_01524
+MSSTRRDPLVGGIVDGRYEVLARLARGGMSTVYLALDTRLDREVALKVMHPHLAEDPVLV
+GRFEQEAKTAARLSHPHVVAVLDQGHTEDASGEVLAYLVMEHVPGHTLRTVIREQAPLTP
+REALRHLRPLVDGLAAAHRAGLVHRDAKPENVLVRTDGRITVADFGLSRAATAHTSAGQA
+VVGTPAYLAPEHIAGAPADARSDVYAAGIILFELLTGRQPFTAGTALQVAYRHVHERVPV
+PSSLQPGLPEALDDLVLWCTEPDPADRPADAGEVLDRLDAVAAELGPAELDRPPVLVPDA
+VEGRPGPEHDETTTLDALDRLDPKDPLDDADGDETTSLDAGDHHATRVLPSLPADALPTE
+ALAADDVVRRSPARRRRRP
+>MOLHKGIG_01369
+MSSARRDPLVGGIVDGRYRVVERLARGGMSTVYLAVDERLDRQVALKVMHPHLAEDPVLV
+GRFEQEAKTTARLSHPHVVAVLDQGHTEAEDGDVLAYLVMEHVPGRTLRTVIRDRAPLSP
+REALRFLRPLVDGLAAAHGAGLVHRDVKPENVLVRDDGRVTVADFGLSRAATAHTMAGQA
+VVGTPAYLAPEHIAGAPADARSDVYAVGIILFELLTGRQPYTAATALQVAYRHVHERVPV
+PSTLHPGLPEDLDDLVLWCTEPDPADRPAGAGELLHRIEAVAAGLDPDAPDRRPAAQPAE
+GPGADPAPAGPAADGLEDAAPDGNLETRALDAGDHHATRVLPALAESDLDEDMTDVIDTR
+VATHGGDPRPAARPAEPIGPLGLDPAPADRHPGRGSRRRLRRAARRPALDLGQGTGRAAA
+IGAAVTLLLTGVALLLGWTLGSGGLGVGGVAVVPDLDGLAREAAEERLTAAGFTAAVTAR
+HDELRTEGTVVASSPAAGEPAGRGAPVELTVSAGPAPVPVPDLTGVVIRQAHGVARDARF
+TVEVAERRTDPAVPAGAVIEQHPAPGEQATPGTAVRVVLSEGRAVRPVPDMTGQDPETAH
+TTLADEGWDARVHRLPLPLSARGESRVLHQSPAAGTALPEGTAVHVWVG
+>MOLHKGIG_01953
+MSLPDARWHVVSPSPFEHEQQGLDILREVLPDESPFQVWTNFEFPDEDGQWHEVDALVLA
+RTKFILVELKYYSGVLRGTGLRWERPGHSPQRSPLALAKKKAERFRSLLERTIESKMPGA
+GRQRIVPYVDYAVFLHHDRFRNEMAPQDSGRLFGLPHNETASNLPSIEHLVLAPATDRFP
+LIGEPREQVLVALMEHLNLADARQPEVGSWLLEERLGEPTPDGQDWLASHRFQERHFARI
+RFQQPREGAPSSDLARVREAARREFDLTRALHHEGLLTASDRVDNELGVGLVFPYDESLA
+PLPLWLESRAATLSQQNRLDLLRQLAETLEYVHSNGIVHRALSPEALWVKTPKQGEPRIL
+VADWQLAGVADRDKVDHAASLTQLSTQFGTTVRSTEELAPTSGALFRAPEDARRVSSLGR
+YKLDVFSVGALAAYLLTGAPAANTVAELHEHLATHQGLDVSVALPSVPEPVRQAILHATD
+PRPTARTATLNDFLAGLTEAQATAPQPASPALDPLEAAPGQALDSRFTLVRRLGKGSTAV
+GLLVDDAQTGSRQVLKVALDDEAATRLDDEAQVLRLLPLHKRLVRLLDGPFDVGGRRALL
+LTSAGTRTLSEVLRERQRLSLDHLERFGSELLEAAQALDAAGLRHRDVKPANIGVVRTPK
+HGEHLVLFDFSLARARSTDVRAGTPPYLDPFLEQGGRTGYDSAAELYAVAVVLYEMASGQ
+KPFYGDPEANPAAVRDDLTVPDGIFDPSLQAPLSALFERALARDAQARFHTVAELAAAWE
+ALFRNDADPVTAQDAETLAARATLETPLSEAGLSARGLSALEAIKVTAGPGGVAVEPHDV
+RTVRDLVLVDPIKLNSLAGSTTETRAEVRARAKQWRAAFKKELMRQATQVPQGTLPTPLD
+AAELLLRHAGAAHAEGVRAQLRLVLGLDGEVPALSTHAVLADARGVTPGLVPQLFGRAQQ
+AWTDVAETRSLLDSLDGALRAAVAERGGVSTPDELTSALEQTLSPATPAEVRDAEPRRIV
+QGLLWLLLDRERAAARGEADVPALVQRRREGRVVAVAEMPVLLDVAETLGAAAEAAVDGA
+GDPESALVPADLVQTRVAAVLDAVDGLPEALRSWRRAAALAAHVSATTCLSAAGEWHHRL
+LAPATAAHHALQGASGTVQLSRERAAERVGARFPALSPLPRDAALDRVLAEAELGLVFDE
+DLGPQGAYRSRQTLAPTTGFATRAETRLVEHQRPLSELGVEGQRLLDSQRNRSYLALGVP
+AQRLARLESALVRRFHAEPLDLTDLFIRLLKDQAAAHPKMTWDHVTAADAEPDGSRPAQG
+LNVLVRNLLPELEQHLSRTIGDPGRAASPVLLTGAAVLARYGHLGVLARWADLAEYRARP
+VWLVVPQVAGNVGPRLDGVSVPKNTPGQYVPLTPEWIDGLAALMAAQPLTEESRT
+>NAFOICDF_01419
+MSSTRRDPLIGDLVDGRYEVLDRVARGGMSTVYRALDHRLDREVALKVMHPHLAEDPALV
+GRFEREAKTAARISHPHVVAVLDQGHTADEAGDVLAYLVMEHVPGRTLRAVIREEAPVAP
+RRAVALLEPVVEGLAAAHRAGLVHRDVKPENVLVRTDGRITVADFGLSRAATGHTSAGQT
+VFGTPAYLAPELISGTGGDARADVYGVGIMLFELLTGTQPFTAATPLQVAYRHVHERVPV
+PSSVRPGLPEALDDIVLWCTEPRPADRPEDAAALLPELRRVAALLPQTAPADEAPAADDA
+PTVALAVSPTVPTVPVPDAADATARLEPRRPDPRRAEPVPTPATATAASPSSDLSSAVPE
+APRPAPVAPRPASARQRRRTARTPEVVLGAGMGRTVAVGAAVTLLLAGMALLLGWILGSG
+GISGPAGVVVPPLWGLEQQEAAARLAEAGLTSAVVSRHDERFSDGVVLDVSPAAGSTVDA
+GGPVRLTVSDGPAPVPAPDLAGLTVTDAHAVAEDGRVGVVVADRVADRAVPAGAVVSQSP
+EAGAEMTPGDEVAVVLSTGPATHPLPDLGGLTVGEARTRLADLGFVPDVRTLPLPGPSGD
+AARVLRQGTPAGTVLPEGASVQLWTL
+>MHAAABBN_01089
+MSSARRDPLVGGIVDGRYRVVERLARGGMSTVYLAVDERLDRQVALKVMHPHLAEDPVLV
+GRFEQEAKTTARLSHPHVVAVLDQGHTEAEDGDVLAYLVMEHVPGRTLRTVIRDRAPLSP
+REALRFLRPLVDGLAAAHRAGLVHRDVKPENVLVRDDGRVTVADFGLSRAATAHTMAGQA
+VVGTPAYLAPEHIAGAPADARSDVYAVGIILFELLTGRQPYTAATALQVAYRHVHERVPV
+PSTLHPGLPEDLDDLVLWCTEPDPADRPAGAGELLHRIDAVAAGLDPDEPDRHPAEGPGA
+EPAVAAPAADGPEDAAPDGNLQTRALDAGDHHATRVLPALAESDLDADMTDVIDTRAATR
+GADRRPAAHPAEPIGPLGLDPAPADRHPGRESPRRLRRAARRPALDLGQGTGRAAAIGAA
+VTLLLTGVALLLGWTLGSGGLGVGGVAVVPDLDGLAREAAEERLTAAGFTAAVTARHNEL
+RTEGTVVASSPAAGEPAGRGTPVELTVSAGPAPVPVPDLTGVVIRRAHGVARDARFTVEV
+AERRTDPAVPAGAVIEQHPAPGEQATPGTAVRVVLSEGRAVRPVPDVTGQDPETARTTLA
+DDGWDARVHRLPLPLAGRGESRVLHQSPAAGTALPEGTAVHVWVG
+>LFPAFLNI_01324
+MSSARRDPLVGGIVDGRYRVVERLARGGMSTVYLAVDERLDRQVALKVMHPHLAEDPVLV
+GRFEQEAKTTARLSHPHVVAVLDQGHTEAEDGDVLAYLVMEHVPGRTLRTVIRDRAPLSP
+REALRFLRPLVDGLAAAHRAGLVHRDVKPENVLVRDDGRVTVADFGLSRAATAHTMAGQA
+VVGTPAYLAPEHIAGAPADARSDVYAVGIILFELLTGRQPYTAATALQVAYRHVHERVPV
+PSTLHPGLPEDLDDLVLWCTEPDPADRPAGAGELLHRIDAVAAGLDPDEPDRRPAEGPGT
+DPAAAAPAADGLEGAAPDGDLPTRALDAGDHHATRVLPALAESALDDDVTDVIDTRAATH
+GGDPRPAARPAEPVGPLAVDPAPADRHPGRGSRRRLRRAARRPALDLGQGTGRAAAIGAA
+VTLLLTGVALLLGWTLGSGGLGVGGVAVVPDLDGLAREAAEERLTAAGFTAAVTARHDEL
+RTEGTVVDSSPAAGEPAGRGAPVELTVSAGPAPVPVPDLTGVVIRQAHGVARDARFTVEV
+AERRTDPAVPAGAVIEQHPAPGEQATPGTAVRVVLSEGRAVRPVPDMTGQDPETAHTTLA
+DEGWDARVHRLPLPLSARGESRVLHQSPAAGTALPEGTAVHVWVG

experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/Orthogroup_Sequences/OG0000144.fa

@@ -0,0 +1,37 @@
+>ACLBLIBL_01551
+MTTHTTTAQRSSKHPTTIGIDVGGTGMKGGLVRLGSGPKSGTLRGDRFRIPTPQPAMAEP
+VAATLAAITAELDARDKAPAPTAPLGVCFPSIVKDGVCLSANNIDPSWIGTDLKAAFEEH
+LRRPVRVVNDADAAGLAEARYGAGRGVSGLVLVITLGTGIGGAMVHDGVLVPNFEVGSLE
+LDGVMAETRASAKAREREDLSWAEYAQRLQRFFSHVEHVFSPDLFIVGGGISKRPDDYLP
+LLSLRTPIVPAQLRNNAGIVGAALAAHDSLADAR
+>MOLHKGIG_01341
+MTTHTSTAQRSSKYPTTIGIDVGGTGMKGGLVRLGSGPKAGTLRGDRFRIPTPQTAMPEP
+VAATLAAITAELDGREKAPKPSAPLGVCFPSIVKDGVCLSANNIDHSWIGTDLRGTFEEH
+LRRPVTVVNDADAAGLAEARYGAGRGVRGLVHVITLGTGIGGAMIHDGMLVPNFEVGSLE
+LDGVMAESRASAKARERDQLSWAEYAERLQRFFSHVERIFSPDLFIVGGGISKRPDDYLP
+LLRLRTPIVPAQLQNNAGIVGAALAAHGSLADGN
+>NAFOICDF_01415
+MHRSRPAPPSPPAPSAYPRRLLGVDLGGTAAKAGVLELARDGRARILARSRAAHAGADPA
+SAVTRAAADALSRAGVRVPDGAGFACAAWLDPATGRARASPHLPSLVGIRPAALLTPVLE
+AAGAAGHGLVPVALNDADAAALAESRLGAARPAPGDLPGAPTLFVALGTGVGGAVIVDGA
+VLPGARGMHGEAGHICVDPDGPACPCGARGCWELYASASALARTLPGRPIADVLEAAVAG
+PGPERDAVLDAGEWLGRGLAPAVCLLDPVRVVVGGGLMAAGELLLPTARAALRRALPTAA
+ADRPPELVAAALGNDAGWIGAALADGARV
+>NAFOICDF_01447
+MSFPNTGVIPRLPPAPSKHPSVLGVDIGGTGMKGGIVRLGHGPKSGTLRGDRFRLDTPQP
+ASPATMARTLAQIVSELDHREKAPDADSRVGVCFPSIVQHGVCRSANNIDPSWIGVSLQD
+TFEEALQRPVTVVNDADAAGLAEARYGAGAGVPGLVMVITLGTGIGGAMINDGVLVPNFE
+VGSLELDGVMAESRASAKAREREGLDWPEYALRLQRFFSHLERIFSPDLFIVGGGISKRP
+HDYLPLLQLETPIVPAMLQNNAGIVGAALAAHADPADGLLR
+>MHAAABBN_01061
+MTTHTSTAQRSSKYPTTIGIDVGGTGMKGGLVRLGSGPKAGTLRGDRFRIPTPQPAMPEP
+VAATLAAITAELDGREKAPKPSAPLGVCFPSIVKDGVCLSANNIDHSWIGTDLRGRFEEH
+LRRPVTVVNDADAAGLAEARYGAGRGVRGLVHVITLGTGIGGAMIHDGVLVPNFEVGSLE
+LDGVMAESRASAKARERDQLSWAEYAERLQRFFSHVERIFSPDLFIVGGGISKRPDDYLP
+LLRLRTPIVPAQLQNNAGIVGAALAAHGSLADGN
+>LFPAFLNI_01296
+MTTHTSTAQRSSKYPTTIGIDVGGTGMKGGLVRLGSGPKAGTLRGDRFRIPTPQPAMPEP
+VAATLAAITAELDGREKAPKPSAPLGVCFPSIVKDGVCLSANNIDHSWIGTDLRGRFEEH
+LRRPVTVVNDADAAGLAEARYGAGRGVRGLVHVITLGTGIGGAMIHDGVLVPNFEVGSLE
+LDGVMAESRASAKARERDQLSWAEYAERLQRFFSHVERIFSPDLFIVGGGISKRPDDYLP
+LLRLRTPIVPAQLQNNAGIVGAALAAHGSLADGN